# hmmscan :: search sequence(s) against a profile database
# HMMER 3.2.1 (June 2018); http://hmmer.org/
# Copyright (C) 2018 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query sequence file:             /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Crenarchaeota/Thermofilum_pendens_Hrk_5_uid58563/NC_008698.faa
# target HMM database:             /oak/stanford/groups/akundaje/marinovg/genomes/PFam/PFam32.0/Pfam-A.hmm
# output directed to file:         /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Crenarchaeota/Thermofilum_pendens_Hrk_5_uid58563/NC_008698.PFam32-A
# per-seq hits tabular output:     /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Crenarchaeota/Thermofilum_pendens_Hrk_5_uid58563/NC_008698.PFam32-A.tblout
# number of worker threads:        20
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       gi|119718919|ref|YP_919414.1|  [L=283]
Description: phosphoesterase, PA-phosphatase related [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.9e-16   58.7   6.3    4.9e-16   58.7   6.3    3.1  3  PAP2      PAP2 superfamily
    1.2e-05   25.1   4.9    1.2e-05   25.1   4.9    2.6  2  PAP2_3    PAP2 superfamily


Domain annotation for each model (and alignments):
>> PAP2  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.3      0.55     5e+03      73      84 ..      24      43 ..      10      57 .. 0.42
   2 !   58.7   6.3   5.5e-20   4.9e-16       3     133 ..      63     172 ..      61     174 .. 0.91
   3 ?   -0.4   0.5     0.098   8.8e+02       6      76 ..     238     252 ..     226     276 .. 0.53

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.55
                           PAP2 73 lllrrkrkkig........l 84
                                   ++l+ ++  ++         
  gi|119718919|ref|YP_919414.1| 24 AYLTGNWVGFWrlatnlgdE 43
                                   33333333222344444442 PP

  == domain 2  score: 58.7 bits;  conditional E-value: 5.5e-20
                           PAP2   3 lalllalalaalltsvlKdlvgrpRPfflaeetkldtqvstletseskeakesfPSgHsafafalalllalllrrkrkki 82 
                                    +++llal ++a l++v+K++++ pRP          +               +fPSgHs+++++++  l+l  rr+    
  gi|119718919|ref|YP_919414.1|  63 FSVLLALSTTAWLNVVVKNTLRLPRPPRELWLANAEGY--------------GFPSGHSQTSTTFWSSLSLKTRRLGVV- 127
                                    5678889999999*************987777777665..............9*********************99999. PP

                           PAP2  83 glvllalillllavlvalsRlylgvHflsDvlaGlliGialaalayrlvqk 133
                                          ++ +++++ v++sR+ l+vH+++Dv +G+++G+a+ +++y+l+++
  gi|119718919|ref|YP_919414.1| 128 ------VLGVAVVAIVGASRIMLNVHYPWDVAGGIALGLAVSYASYYLFDR 172
                                    ......8999999*********************************99876 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.098
                           PAP2   6 llalalaalltsvlKdlvgrpRPfflaeetkldtqvstletseskeakesfPSgHsafafalalllalllr 76 
                                    ++al++a+llt+v                                                         +
  gi|119718919|ref|YP_919414.1| 238 AVALVVAMLLTTV--------------------------------------------------------AK 252
                                    2222222222222........................................................22 PP

>> PAP2_3  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   4.9   1.3e-09   1.2e-05     125     189 ..     100     164 ..      23     165 .. 0.86
   2 ?    0.7   0.7     0.041   3.7e+02     152     169 ..     235     252 ..     224     272 .. 0.72

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.3e-09
                         PAP2_3 125 aafPSlHvawallvalalwrlrrkrllrvlalllnvlmivatvatgnHYlvDviaGvalalvaia 189
                                    + fPS H   ++ +   l    r+  + vl++++++++ ++ + +  HY  Dv++G+al+l++ +
  gi|119718919|ref|YP_919414.1| 100 YGFPSGHSQTSTTFWSSLSLKTRRLGVVVLGVAVVAIVGASRIMLNVHYPWDVAGGIALGLAVSY 164
                                    55*****99999888886666666689*********************************99876 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.041
                         PAP2_3 152 rvlalllnvlmivatvat 169
                                     ++a++l+v+m+++tva 
  gi|119718919|ref|YP_919414.1| 235 VLAAVALVVAMLLTTVAK 252
                                    455666666677666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       740  (0.0412739); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 1632.49
//
Query:       gi|119718920|ref|YP_919415.1|  [L=365]
Description: cellulase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-98  328.7   0.0    2.8e-98  328.5   0.0    1.0  1  Peptidase_M42  M42 glutamyl aminopeptidase
    3.2e-10   40.1   0.1    8.6e-10   38.7   0.1    1.7  2  Peptidase_M20  Peptidase family M20/M25/M40
    3.2e-05   22.9   0.0       0.04   12.7   0.0    2.3  2  Peptidase_M18  Aminopeptidase I zinc metalloprotease (M18)
  ------ inclusion threshold ------
      0.047   13.4   0.0        0.8    9.4   0.0    2.3  2  Peptidase_M28  Peptidase family M28


Domain annotation for each model (and alignments):
>> Peptidase_M42  M42 glutamyl aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  328.5   0.0  6.3e-102   2.8e-98       1     292 []      51     346 ..      51     346 .. 0.97

  Alignments for each domain:
  == domain 1  score: 328.5 bits;  conditional E-value: 6.3e-102
                                    S-EEEEEESSTTSSEEEEEEE--B-EEEEEEEETTSEEEEEEESS--GGGTTTEEEEEEETTEEEEEEEEE--CGGCHHH CS
                  Peptidase_M42   1 GnliakkkgkekepkvmiaAHmDeiGfmVkeIkedGflrfekvGGvdpkvlegqrvkiltkkgkisGvigskppHllkee 80 
                                    G+li +k+g++++pkv++a+H+De+Gf+V+ I+++Gf++f+++GG+ ++vl +qrv i+tkkg+++Gvi skppHll++e
  gi|119718920|ref|YP_919415.1|  51 GSLILVKRGSSERPKVLVAGHVDEVGFLVTGITPEGFITFTTLGGWFEQVLLAQRVVIRTKKGEVYGVITSKPPHLLTPE 130
                                    89****************************************************************************** PP

                                    HHHCT--GCGEEEEGSGSSHHHHHHTTS-TT-EEEES---EEETTEC.EEETTHHHHHHHHHHHHHHHHHCTSS-S..SE CS
                  Peptidase_M42  81 erkkaleikelfiDigakskeeaeelGisvGdivvfdkefvelangk.ivskalDdragvavllellkelkeeele..at 157
                                    er+k +++++++iD+ga+skee+e+lG+++Gd+v++ ++f+++a +  i++kalDdr+g  +++e+lk+l+ + ++  +t
  gi|119718920|ref|YP_919415.1| 131 ERQKVVQFSQMYIDVGATSKEEVEKLGVRIGDPVAPWSPFTRTAFEDrIMAKALDDRVGAFIAMEVLKHLRLNGIDhpNT 210
                                    *****************************************9997766********************9988777666** PP

                                    EEEEEESTCTTTSHHHHHHHHHH--SEEEEEEEEEE-CSTTSTTTTSS..TTS-CEEEEEETTCCSHHHHHHHHHHHHHH CS
                  Peptidase_M42 158 vylvatvqEEvGlrGaktsaekikpdiaiavDvtaagdtpgskekeak..lgkGpvirvkDasgiyhpklrkkllelAkk 235
                                    +y++atvqEEvGlrGa+t+ +  + d+ai+ +v +agd pg k  ea   lgkGp+i+v+D+s+i +p+++++++e+A++
  gi|119718920|ref|YP_919415.1| 211 LYAAATVQEEVGLRGAETVGWVADHDVAIVTEVDIAGDVPGIKPSEAPakLGKGPSIIVYDRSMIPNPRFKEFVIEVAEE 290
                                    *******************************************9998899****************************** PP

                                    TT--EEEEEESSSSSTHHHHHTSTTTSEEEEEEEEEBSTTSTTEEEEHHHHHHHHHH CS
                  Peptidase_M42 236 nnipyqlevlsgggtDAgaihltgegvptalisiptryiHspvevahlddleatvkL 292
                                    ++ipyql  + +ggtDAg++hl ++g p+++i++ptr+iHs+v++++l+d+e++v+L
  gi|119718920|ref|YP_919415.1| 291 AKIPYQL-SAVSGGTDAGRLHLYKGGRPSIVIGVPTRHIHSHVSIVSLSDVENAVRL 346
                                    *******.78889*****************************************997 PP

>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0         1   4.6e+03      92     106 ..      65      79 ..      40     141 .. 0.64
   2 !   38.7   0.1   1.9e-13   8.6e-10      20     206 ..     169     352 ..     161     353 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1
                                    SEEEEEEEESSSBTC CS
                                    xxxxxxxxxxxxxxx RF
                  Peptidase_M20  92 davfelhieepgile 106
                                    + +++ h+ e g l+
  gi|119718920|ref|YP_919415.1|  65 KVLVAGHVDEVGFLV 79 
                                    444455555444444 PP

  == domain 2  score: 38.7 bits;  conditional E-value: 1.9e-13
                                    TTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTTTHH...HHHHHHHHTTTCESEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxx RF
                  Peptidase_M20  20 pfslteedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggrgGa...kallegleerekvdavfe 96 
                                    pf+ t  ++++ +  a d+  g ++a+e+l++l+ +gi+++ t+  ++++ EE+g +Ga   +++++     ++v  v e
  gi|119718920|ref|YP_919415.1| 169 PFTRTAFEDRIMAK-ALDDRVGAFIAMEVLKHLRLNGIDHPNTLYAAATVQEEVGLRGAetvGWVAD-----HDVAIVTE 242
                                    77777666888888.99************************************87777733333333.....55555556 PP

                                    EEEESSSBTCHSTETEEEE..........EEEEEEEEEESHEEECCHHHHHHHHHHHHHHHTSCEEEEEESSSBHTHHHH CS
                                    xxxxxxxxxxxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M20  97 lhieepgileagklaigvv..........kvevelleggapvtlndsplvkalaeaaeelfgekvelivsgpggtdarff 166
                                    + i  ++++      i+++          +  +     +   +++++++ +++ e+aee+ +  ++l++ + ggtda+ +
  gi|119718920|ref|YP_919415.1| 243 VDIA-GDVPG-----IKPSeapaklgkgpS--I---IVYDRSMIPNPRFKEFVIEVAEEA-KIPYQLSAVS-GGTDAGRL 309
                                    6655.55555.....444455444444332..2...233344555788889999999997.6556677666.9******* PP

                                    ....TTTEEEEEEE.SSGGCTTSTTTEEEHHHHHHHHHHHHHHHH CS
                                    ....xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M20 167 ....agiptvmifg.pgsglaHspnEyvdledlekgikvlarlle 206
                                         g p++ ++g p    +Hs+   v+l+d+e++++++ +l++
  gi|119718920|ref|YP_919415.1| 310 hlykGGRPSI-VIGvPT-RHIHSHVSIVSLSDVENAVRLVLELVK 352
                                    8875555888.578699.***********************9997 PP

>> Peptidase_M18  Aminopeptidase I zinc metalloprotease (M18)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0   0.00025       1.1     228     276 ..     178     225 ..     128     235 .. 0.86
   2 !   12.7   0.0   8.9e-06      0.04     335     427 ..     259     346 ..     253     349 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00025
                                    EEEESSHHHHHHHHHHHHHHCCCCHT-TTTS-SEEEEEEESSCCGTS-S CS
                  Peptidase_M18 228 flfaprlDnkvscfaaleallesaedsleeedkvrivalfDnEEvGSts 276
                                     ++a+ lD++v++f a+e l ++  + +++  ++  +a   +EEvG  +
  gi|119718920|ref|YP_919415.1| 178 RIMAKALDDRVGAFIAMEVLKHLRLNGIDHP-NTLYAAATVQEEVGLRG 225
                                    4899****************99988877665.55556666689999665 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 8.9e-06
                                    --TTSEEEEEEETTSSSTT-HHHHHHHHHHHHHHC-EEEEEEE-TTS----HCHHHHHHHHT-EEEEEE-EEBSTTSSSE CS
                  Peptidase_M18 335 pllnkGvvikvnanqryatnsagaallkevaqkanvklQelvvrndspcGstigpilaaktGirtiDlGaaqlsmHSire 414
                                    ++l+kG+ i v+    +  n +  + + eva++a+++ Q   v     +G+  g +   k G   i +G +   +HS   
  gi|119718920|ref|YP_919415.1| 259 AKLGKGPSIIVYD-RSMIPNPRFKEFVIEVAEEAKIPYQLSAV----SGGTDAGRLHLYKGGRPSIVIGVPTRHIHSHVS 333
                                    5789999999885.457888899999*************9876....58999999************************* PP

                                    EEECCHHHHHHHH CS
                  Peptidase_M18 415 ltgskdveeavkl 427
                                    +++ +dve+av l
  gi|119718920|ref|YP_919415.1| 334 IVSLSDVENAVRL 346
                                    *********9987 PP

>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0     0.052   2.4e+02       8      26 ..      59      77 ..      53      89 .. 0.75
   2 ?    9.4   0.0   0.00018       0.8      31      81 ..     179     229 ..     163     252 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.052
                                   TTCESEEEEEEEE--B-TT CS
                  Peptidase_M28  8 gkatdevlllgAHyDsvgv 26
                                   g+++   +l+++H+D vg+
  gi|119718920|ref|YP_919415.1| 59 GSSERPKVLVAGHVDEVGF 77
                                   5554559*********998 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00018
                                    T---TTTTHHHHHHHHHHHHHCHHGGCCSSEEEEEEEESSCSGSSHHHHHH CS
                  Peptidase_M28  31 ifvGAdDnAsgvaalLelarvlaasgsrpkrgvrflffdaEEagllGSkaf 81 
                                    i+  A D+ +g+ + +e+++ l  +g +  +++  +++  EE gl G++  
  gi|119718920|ref|YP_919415.1| 179 IMAKALDDRVGAFIAMEVLKHLRLNGIDHPNTLYAAATVQEEVGLRGAETV 229
                                    566699******************99999*******************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2379.23
//
Query:       gi|119718921|ref|YP_919416.1|  [L=295]
Description: 2-acetyl-1-alkylglycerophosph ocholine esterase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-18   67.3   0.0      6e-16   58.4   0.0    2.1  2  Hydrolase_4     Serine aminopeptidase, S33
      3e-16   59.8   0.0    5.3e-15   55.8   0.0    2.0  2  Abhydrolase_1   alpha/beta hydrolase fold
    4.8e-14   52.3   0.0    2.3e-13   50.1   0.0    1.9  1  Peptidase_S9    Prolyl oligopeptidase family
    2.5e-12   47.9   0.0    3.6e-12   47.4   0.0    1.4  1  Abhydrolase_6   Alpha/beta hydrolase family
    4.6e-12   46.1   0.0    7.3e-09   35.6   0.0    2.1  2  Peptidase_S15   X-Pro dipeptidyl-peptidase (S15 family)
    4.2e-08   33.0   0.0    6.6e-05   22.6   0.0    2.1  2  DLH             Dienelactone hydrolase family
    1.2e-05   24.1   0.1    3.6e-05   22.6   0.1    1.9  2  AXE1            Acetyl xylan esterase (AXE1)
    0.00022   20.8   0.0    0.00035   20.2   0.0    1.3  1  DUF676          Putative serine esterase (DUF676)
    0.00024   21.1   0.0    0.00032   20.7   0.0    1.2  1  DUF829          Eukaryotic protein of unknown function (DUF82
    0.00058   19.1   0.1       0.11   11.5   0.0    2.1  2  DUF2048         Abhydrolase domain containing 18
    0.00066   19.4   0.0     0.0028   17.3   0.0    1.9  2  FSH1            Serine hydrolase (FSH1)
     0.0085   15.9   0.0      0.016   15.0   0.0    1.4  1  Prok-E2_E       Prokaryotic E2 family E
  ------ inclusion threshold ------
       0.01   15.5   0.0      0.015   14.9   0.0    1.3  1  Esterase        Putative esterase
      0.014   15.3   0.0      0.028   14.3   0.0    1.7  1  BAAT_C          BAAT / Acyl-CoA thioester hydrolase C termina
      0.022   14.3   0.0      0.045   13.3   0.0    1.5  1  Abhydro_lipase  Partial alpha/beta-hydrolase lipase region
      0.073   12.8   0.0       0.17   11.6   0.0    1.6  2  DUF3328         Domain of unknown function (DUF3328)
       0.13   12.0   0.0        3.6    7.3   0.0    2.3  2  Abhydrolase_5   Alpha/beta hydrolase family
        0.2   11.5   0.0       0.37   10.6   0.0    1.4  1  Abhydrolase_3   alpha/beta hydrolase fold
       0.25   11.1   0.0        0.5   10.1   0.0    1.5  1  Abhydrolase_2   Phospholipase/Carboxylesterase


Domain annotation for each model (and alignments):
>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.4   0.0   6.4e-19     6e-16       4     127 ..      70     191 ..      67     224 .. 0.82
   2 !    7.1   0.0    0.0031       2.9     187     218 ..     226     257 ..     221     266 .. 0.87

  Alignments for each domain:
  == domain 1  score: 58.4 bits;  conditional E-value: 6.4e-19
                    Hydrolase_4   4 kavvvlvHGlaehsg..ryae.laeaLaaqGfavyalDhrGhGrsegkrghvpsfddyvdDlaafvekvkeehpelplfl 80 
                                    + +v++vHG++++ +  +y + +++ La+++f+v+a+D r hG+s+g+        + v+D++++++ ++e+   ++l +
  gi|119718921|ref|YP_919416.1|  70 DRTVLVVHGYTSSKWdeWYIKpVIDILARNNFNVVAFDMRAHGESDGRYTT--LGLREVEDISKIIDLLEEKGLASRLGM 147
                                    679********99743367777***********************999884..445669********************* PP

                    Hydrolase_4  81 lGhSmGGliallyllrypdkvaglilsaPalkikaklkappllklll 127
                                    +G SmGG+i+l  ++r+ + v++++  +P ++i+a+   ++++k + 
  gi|119718921|ref|YP_919416.1| 148 IGYSMGGAITLMTAAREDR-VKAAVADSPYIDIRAS--GKRWVKRVG 191
                                    ***********99999999.**************87..455555433 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0031
                    Hydrolase_4 187 aakitlPllllhGeaDkvvdpeasrelyerlg 218
                                    a+ i+ Pll++ G +D +v  e+ + ++++ +
  gi|119718921|ref|YP_919416.1| 226 ASLIRKPLLIIAGRNDDLVALEEIETFFNENK 257
                                    667899*******************9999866 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.8   0.0   5.6e-18   5.3e-15       2     117 ..      72     187 ..      71     195 .. 0.82
   2 ?    2.2   0.0      0.13   1.2e+02     210     234 ..     229     253 ..     207     279 .. 0.68

  Alignments for each domain:
  == domain 1  score: 55.8 bits;  conditional E-value: 5.6e-18
                                    EEEEE-STTT.CGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHH..HHHCTTSSEE.E CS
                  Abhydrolase_1   2 vlvilhGlpg.ssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldri..ldalgddklt.l 77 
                                    +++++hG++   +d w+ + +++ La++ f v+++D+r +g+S+ + ++     g+  v+d+ + i  l+  g+ +   +
  gi|119718921|ref|YP_919416.1|  72 TVLVVHGYTSsKWDEWYIKPVIDILARNNFNVVAFDMRAHGESDGRYTT----LGLREVEDISKIIdlLEEKGLASRLgM 147
                                    69********66677******************************9976....56666666666444477777776666* PP

                                    EEETHHHHHHHHHHHHHGGGEEEEEEESE.CSSCCHHHHHH CS
                  Abhydrolase_1  78 vGhSmGGmialayaaeyperVkalvllga.idpaaslieaq 117
                                    +G+SmGG+i l+ aa+  +rVka v++++ id  as  ++ 
  gi|119718921|ref|YP_919416.1| 148 IGYSMGGAITLMTAAR-EDRVKAAVADSPyIDIRASGKRWV 187
                                    ***************9.9***********776666655555 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.13
                                    HHSEEEEEEETTCSSSCHHHHHHHH CS
                  Abhydrolase_1 210 vlaptlvisgtsDplvppkaledla 234
                                    + +p l+i+g++D lv  +++e + 
  gi|119718921|ref|YP_919416.1| 229 IRKPLLIIAGRNDDLVALEEIETFF 253
                                    334*************887766553 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.1   0.0   2.4e-16   2.3e-13       5     209 ..      91     295 .]      87     295 .] 0.80

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 2.4e-16
                                    HHHHHHHCCT-EEEEE--TTSSTTHCHHHHTTSGGGGHHHHHHHHHHHHHHHHTTS--GGGEEEEEETHHHHHHHHHHHH CS
                   Peptidase_S9   5 selqlladrGyvvvvanirGsggyGeafhdagkrklgqnefdDfiaaaealakegyvdserlaitGgSyGGyltgaalnq 84 
                                     ++ +la +++ vv+ ++r  g+    +       lg +e++D+ ++++ l ++g++  +rl++ G S GG  t+++++ 
  gi|119718921|ref|YP_919416.1|  91 PVIDILARNNFNVVAFDMRAHGESDGRY-----TTLGLREVEDISKIIDLLEEKGLA--SRLGMIGYSMGGAITLMTAA- 162
                                    5678899999999999999988765554.....5599**************999998..9*******************. PP

                                    -GGG-SEEEEESE---CCCHHCSTTS..THH.HCCCC--TTTCHHHHHHHHHH-CGGG--..............---EEE CS
                   Peptidase_S9  85 rpdlFkaavaevpvvdvlrydsdtdl..lte.eymewgnpeeneegykelspyspldnvk..............aypplL 147
                                    r d+ kaava  p +d +++ +       ++ +y            y         +  +              + +plL
  gi|119718921|ref|YP_919416.1| 163 REDRVKAAVADSPYIDIRASGKRWVKrvGAPlRYLLLASY--PLIIY------FTSKTTRtdpsklvmfnyaslIRKPLL 234
                                    *******************999933343222344443333..22222......222222233334566777889****** PP

                                    EEEETT-SSS-THHHHHHHHHHH--S-SEEEEEETTS-SSTTSSHHHHHHHHHHHHHHHHHC CS
                   Peptidase_S9 148 lihGlaDdrvppaealklvaaLqkkgknvlllifpdegHgvgkprakveelarllaFlkeal 209
                                    +i G +Dd v ++e ++++++ +k + n++l + +d++H+++ +++ +e  +r+++F++++l
  gi|119718921|ref|YP_919416.1| 235 IIAGRNDDLVALEEIETFFNENKKVNPNTEL-WVTDSKHVSAIQDYPKEYEKRVVEFFERWL 295
                                    *********************8887777765.779************************996 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.4   0.0   3.8e-15   3.6e-12       1     126 [.      73     201 ..      73     285 .. 0.74

  Alignments for each domain:
  == domain 1  score: 47.4 bits;  conditional E-value: 3.8e-15
                                    EEEE--GC.....G...CHHHHHHHHCCT.CEEEEE--TTSTS-GGCS--HHH..CHHHHHHHCCTT....TTSEEEEEE CS
                  Abhydrolase_6   1 vlllHGagssassW...lvapLaallaag.vhvlapDlpGhGrsdpppldled..ladlaalldelaa..gggpvvlvGH 72 
                                    vl++HG  +++s W   +  p+   la+  + v+a+D + hG+sd++ ++l    ++d++ ++d l +   + +   +G+
  gi|119718921|ref|YP_919416.1|  73 VLVVHG--YTSSKWdewYIKPVIDILARNnFNVVAFDMRAHGESDGRYTTLGLreVEDISKIIDLLEEkgLASRLGMIGY 150
                                    799***..6655554336667755555555888*********88888866655448999999999988766666799*** PP

                                    TCHHHHHHHHHHCC..EEEEES-..----TTTS----TTHHHHHHTT-CCCCHC CS
                  Abhydrolase_6  73 SlGGalalaaaplalvvgvlldppptalpagllaaalelllallallrllawls 126
                                    S+GGa+ l++a+  ++v+ +++    ++ ++ +a   +++++++a+lr l + s
  gi|119718921|ref|YP_919416.1| 151 SMGGAITLMTAAREDRVKAAVAD---SPYIDIRASGKRWVKRVGAPLRYLLLAS 201
                                    *********77777889999999...8888888888888888888666533332 PP

>> Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.0   7.7e-12   7.3e-09      52     139 ..      90     180 ..      25     193 .. 0.83
   2 !    8.6   0.0    0.0014       1.3     223     268 ..     225     273 ..     211     274 .. 0.88

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 7.7e-12
                                    H.....HHHTT-EEEEEE-TTSTTS-S---TTTTTHHHHHHHHHHHHHHCTTEEEEEEEEEECHHHHHHHHHCTT--TTE CS
                  Peptidase_S15  52 v.....fvarGYavVvqdvrGtggSeGeftvgdsdeaedgadvidWlakqpwsnGkVgmtGiSYlGttqllaaatgvpal 126
                                    +     ++++ + vV  d+r +g+S+G +t+ + +e+ed +++id l ++     + gm+G S +G + l+ aa + +++
  gi|119718921|ref|YP_919416.1|  90 KpvidiLARNNFNVVAFDMRAHGESDGRYTTLGLREVEDISKIIDLLEEK-GLASRLGMIGYSMGGAITLMTAA-REDRV 167
                                    0444447888899********************************77666.55669******************.999** PP

                                    EEEEEECE-S-TC CS
                  Peptidase_S15 127 kaivpeaaisdly 139
                                    ka+v+ ++  d  
  gi|119718921|ref|YP_919416.1| 168 KAAVADSPYIDIR 180
                                    *******998876 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0014
                                    HHCT--S-EEEEEECCSSTTC.CHHHHHHHHHCCTT-..EEEEECECTT CS
                  Peptidase_S15 223 dadkvkapvllvgGwnDwnvk.ngaiklyealkapgv..klilgpwtHv 268
                                     a+ ++ p+l++ G nD+ v+ +++  ++++ k+ +   +l+++ ++Hv
  gi|119718921|ref|YP_919416.1| 225 YASLIRKPLLIIAGRNDDLVAlEEIETFFNENKKVNPntELWVTDSKHV 273
                                    4578999**************89999999999999889**********8 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0     7e-08   6.6e-05      79     127 ..     126     172 ..      86     193 .. 0.83
   2 !    8.6   0.0    0.0013       1.3     138     187 ..     224     272 ..     204     293 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 7e-08
                            DLH  79 lddlkaavaylksvpevstkkvgvvGfCmGGalalllaaevpevdaava 127
                                    ++d++  ++ l++++    +++g++G+ mGGa++l  aa++++v+aava
  gi|119718921|ref|YP_919416.1| 126 VEDISKIIDLLEEKG--LASRLGMIGYSMGGAITLMTAAREDRVKAAVA 172
                                    455567788888888..779***************************96 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0013
                            DLH 138 eeaakikapilalfgeeDefipadevekleealkaanvdlelkvYpgagH 187
                                    ++a  i +p+l+++g +D  ++ +e+e++ ++ k+ n++ el v +  +H
  gi|119718921|ref|YP_919416.1| 224 NYASLIRKPLLIIAGRNDDLVALEEIETFFNENKKVNPNTELWVTD-SKH 272
                                    5678899******************************999997755.455 PP

>> AXE1  Acetyl xylan esterase (AXE1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.98   9.2e+02      85      98 ..      72      85 ..      49     127 .. 0.57
   2 !   22.6   0.1   3.8e-08   3.6e-05     174     208 ..     143     177 ..     124     285 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.98
                                   EEEEEE-TT--GGG CS
                           AXE1 85 avvefhGYegsrge 98
                                   +v+  hGY++s+++
  gi|119718921|ref|YP_919416.1| 72 TVLVVHGYTSSKWD 85
                                   45555788887664 PP

  == domain 2  score: 22.6 bits;  conditional E-value: 3.8e-08
                                    EEEEEEEETHHHHHHHHHHHH-SS-SEEEEES-SS CS
                           AXE1 174 eRvavlGasqGGalalavaalekrikavvadyPfL 208
                                    +R++++G s GGa++l +aa e+r+ka+vad P++
  gi|119718921|ref|YP_919416.1| 143 SRLGMIGYSMGGAITLMTAAREDRVKAAVADSPYI 177
                                    79********************************7 PP

>> DUF676  Putative serine esterase (DUF676)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   3.7e-07   0.00035       6      96 ..      71     160 ..      67     181 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 3.7e-07
                         DUF676   6 hLvVlvHGlqgnsaDlelikeqlekikeklpeekieflmsennesktfkgidvlgerlaeevlevvkkkkdk..nkkiSf 83 
                                    + v +vHG  +++ D  +ik  +  +     ++  +++  ++++ ++ +  ++lg r +e + ++++  ++k   +++ +
  gi|119718921|ref|YP_919416.1|  71 RTVLVVHGYTSSKWDEWYIKPVIDIL---ARNNFNVVAFDMRAHGESDGRYTTLGLREVEDISKIIDLLEEKglASRLGM 147
                                    56899*****************9994...4477888888899999999999****************999999999**** PP

                         DUF676  84 vghSlGgliaraa 96 
                                    +g+S+Gg i  + 
  gi|119718921|ref|YP_919416.1| 148 IGYSMGGAITLMT 160
                                    *******997665 PP

>> DUF829  Eukaryotic protein of unknown function (DUF829)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   3.4e-07   0.00032     152     240 ..     203     290 ..     159     291 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 3.4e-07
                         DUF829 152 lvelilglesvasrsrkalndlatkplrcpqlylySkaDeviswrdveshaeeaeqrgvkvtakkfedspHvahmrkhpe 231
                                       + +  + ++++ +k +   +    r p l +  ++D+++  +++e + +e+++   ++t     ds Hv+ ++++p+
  gi|119718921|ref|YP_919416.1| 203 PLIIYFTSKTTRTDPSKLVMFNYASLIRKPLLIIAGRNDDLVALEEIETFFNENKK-VNPNTELWVTDSKHVSAIQDYPK 281
                                    44444444444444444444444445568899**********************99.4458888899************* PP

                         DUF829 232 rYvekvvef 240
                                    +Y + vvef
  gi|119718921|ref|YP_919416.1| 282 EYEKRVVEF 290
                                    *******99 PP

>> DUF2048  Abhydrolase domain containing 18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   0.00012      0.11     160     199 ..     126     166 ..     119     174 .. 0.85
   2 !    5.5   0.0    0.0081       7.6     298     352 .]     235     293 ..     220     293 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00012
                        DUF2048 160 ilEslvllhwlereGyG.plgltGlSmGGhmaslaasnwpk 199
                                    +++ ++++  le++G   +lg+ G SmGG  + ++a+   +
  gi|119718921|ref|YP_919416.1| 126 VEDISKIIDLLEEKGLAsRLGMIGYSMGGAITLMTAAREDR 166
                                    67788999*******9989***************9987766 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0081
                        DUF2048 298 vvaAkdDayvpresva....slqeiwpgsevryldgGHvsayllkkklfrkaivealer 352
                                    ++a ++D  v  e+++    + +++ p++e    d+ Hvsa+    k + k++ve +er
  gi|119718921|ref|YP_919416.1| 235 IIAGRNDDLVALEEIEtffnENKKVNPNTELWVTDSKHVSAIQDYPKEYEKRVVEFFER 293
                                    567788888877666522225689*******99************************98 PP

>> FSH1  Serine hydrolase (FSH1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       1.1   1.1e+03       5      17 ..      71      83 ..      68      84 .. 0.85
   2 !   17.3   0.0     3e-06    0.0028      90     190 ..     129     259 ..     108     274 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.1
                           FSH1  5 kkiLcLhGytqsg 17
                                    ++L++hGyt+s+
  gi|119718921|ref|YP_919416.1| 71 RTVLVVHGYTSSK 83
                                   689*******985 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 3e-06
                           FSH1  90 ldavkdyikengp..fdGiiGFSqGaalaallaslleellkeashpslkfailvsGfkleepk................. 150
                                    ++++ d ++e+g     G iG+S G+a++ + a+  ++ +     +s  + i +sG +  ++                  
  gi|119718921|ref|YP_919416.1| 129 ISKIIDLLEEKGLasRLGMIGYSMGGAITLMTAAREDRVKAAV-ADSPYIDIRASGKRWVKRVgaplrylllasypliiy 207
                                    56677778888764567************99999888877644.455556666666666555555556666666555555 PP

                           FSH1 151 .............yeeyyeedkiqtptLhvlGelDtvvdeerseaLaeafkns 190
                                                 ++  y  + i+ p L + G++D +v+ e+ e++ +  k+ 
  gi|119718921|ref|YP_919416.1| 208 ftskttrtdpsklVMFNY-ASLIRKPLLIIAGRNDDLVALEEIETFFNENKKV 259
                                    555554444443322244.7888****************99999988776654 PP

>> Prok-E2_E  Prokaryotic E2 family E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.7e-05     0.016      12      85 ..      43     110 ..      41     118 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.7e-05
                      Prok-E2_E  12 kglkyeevedggqrglllkefslpegkynvaevdvlilipsgYpdakldmfylepalkradgkeipkaaeaeet 85 
                                    +g++ye++e +++ gl l+++ +p+g       d  +l+ +gY ++k d +y++p++    ++++   a ++++
  gi|119718921|ref|YP_919416.1|  43 MGYTYEKLEVKTSDGLTLRGWLIPRG------SDRTVLVVHGYTSSKWDEWYIKPVIDILARNNFNVVAFDMRA 110
                                    789***********************......666777789*****************9999999876665555 PP

>> Esterase  Putative esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   1.6e-05     0.015     118     198 ..     146     245 ..     129     284 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.6e-05
                                    EEEEETHHHHHHHHHHHCSTTTCCEEEEES--S-CC..HCHHHC....................TTCCHHHCC-CCCCHC CS
                       Esterase 118 avaGqSmGGlgALilalkhpdrFgsvssfSpivnps..namWgq....................eekeawqendpvllak 175
                                      +G SmGG + L++a++  dr + + + Sp+++ +     W +                    ++k++  + dp  l+ 
  gi|119718921|ref|YP_919416.1| 146 GMIGYSMGGAITLMTAAR-EDRVKAAVADSPYIDIRasGKRWVKrvgaplrylllasypliiyfTSKTT--RTDPSKLVM 222
                                    579*************97.59************998763344444444444444444445554444443..667777766 PP

                                    HHCHTTSEEEEEEEECTTBCCCH CS
                       Esterase 176 elsaslkalriyldvGtseddlg 198
                                     ++asl ++  ++ +G ++d ++
  gi|119718921|ref|YP_919416.1| 223 FNYASLIRKPLLIIAGRNDDLVA 245
                                    66777777777777777776554 PP

>> BAAT_C  BAAT / Acyl-CoA thioester hydrolase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0     3e-05     0.028      21      54 ..     142     175 ..     125     255 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3e-05
                                    -SSEEEEEETHHHHHHHHHHHHSSSEEEEEEES- CS
                         BAAT_C  21 kdkigllGiSkGgelalllasflkkisavvling 54 
                                     ++ g++G S Gg ++l+ a++ + ++a+v+ ++
  gi|119718921|ref|YP_919416.1| 142 ASRLGMIGYSMGGAITLMTAAREDRVKAAVADSP 175
                                    3799**************************9776 PP

>> Abhydro_lipase  Partial alpha/beta-hydrolase lipase region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   4.8e-05     0.045       8      35 ..      43      70 ..      41      92 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.8e-05
                 Abhydro_lipase  8 hGypveeheVqTeDGYiLtlhRipaknk 35
                                    Gy  e+ eV+T+DG  L  + ip++ +
  gi|119718921|ref|YP_919416.1| 43 MGYTYEKLEVKTSDGLTLRGWLIPRGSD 70
                                   69*********************99983 PP

>> DUF3328  Domain of unknown function (DUF3328)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00018      0.17      14      65 ..       2      53 ..       1     108 [. 0.83
   2 ?   -1.6   0.0         2   1.9e+03       8      44 ..     184     230 ..     180     282 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00018
                        DUF3328 14 lllvlllllllllllilssllsssekkaakkkspsspspaldaieyelkqfk 65
                                   l l+l++++++++ll++++++s s+k a +++++  +sp +    ye+ ++k
  gi|119718921|ref|YP_919416.1|  2 LTLLLTTVVAVVVLLLVAVAFSASRKLASPPRKVGQWSPGDMGYTYEKLEVK 53
                                   55677778888888888888899999999999***************99887 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2
                        DUF3328   8 sawrrllllvlllllllllllilssllsssekkaak..........k 44 
                                    ++w++++ + l  lll  + li+  ++ ++++ + k           
  gi|119718921|ref|YP_919416.1| 184 KRWVKRVGAPLRYLLLASYPLIIYFTSKTTRTDPSKlvmfnyasliR 230
                                    67888888888888888888888888888877777744444444331 PP

>> Abhydrolase_5  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0038       3.6      56      86 ..     142     172 ..     121     188 .. 0.79
   2 ?    2.2   0.0      0.15   1.4e+02     100     130 ..     230     263 ..     221     281 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0038
                  Abhydrolase_5  56 lekfvvgGhslGGvvasrfaaeeekiegvvf 86 
                                      ++ + G+s+GG+++   aa+e++++++v 
  gi|119718921|ref|YP_919416.1| 142 ASRLGMIGYSMGGAITLMTAAREDRVKAAVA 172
                                    4566778*******************99875 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.15
                  Abhydrolase_5 100 skkvlsivgteDgvlnvksle...kakkflpkdt 130
                                     k++l i g +D+++  +++e   +++k++  +t
  gi|119718921|ref|YP_919416.1| 230 RKPLLIIAGRNDDLVALEEIEtffNENKKVNPNT 263
                                    578999*********9999873333455555555 PP

>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00039      0.37      60     177 ..     137     241 ..     122     270 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00039
                                    HHTHHHHTETTCEEEEEEETHHHHHHHHHHHHHHHTT---EEEEEEESE-SSTSSTTSHHHHHCHHTTTSSSSCHHHHHH CS
                  Abhydrolase_3  60 aeqawelgadpsrivlaGdSaGGnlaaavalrardegepkvagqvliyPvtdlertesesikkaeeladgplltraaldl 139
                                    +e+       +sr+ + G S GG +++ +a  ar++   +v++ v  +P  d  r +++++ k   +  ++ll  a+   
  gi|119718921|ref|YP_919416.1| 137 EEK-----GLASRLGMIGYSMGGAITLMTA--ARED---RVKAAVADSPYIDI-RASGKRWVKRVGAPLRYLL-LASYP- 203
                                    444.....6789**************9999..5665...69999999998888.7767777433222222333.33333. PP

                                    HHHHHSSGGGGGSTTTSGGGC.S-SST---EEEEEETT- CS
                  Abhydrolase_3 140 fwrlylpeadrddplasplla.edlsglpptlvvvaefD 177
                                    ++ +++++ +r+dp   ++++ ++l   +p l++ + +D
  gi|119718921|ref|YP_919416.1| 204 LIIYFTSKTTRTDPSKLVMFNyASLI-RKPLLIIAGRND 241
                                    23333357777777333333322433.356666666665 PP

>> Abhydrolase_2  Phospholipase/Carboxylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00053       0.5      86     126 ..     125     164 ..      99     182 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00053
                                    HHHHHHHHHHHHHHTT--GGGEEEEEETHHHHHHHHHHHT- CS
                  Abhydrolase_2  86 saekleelidaelkkgipssriiigGFSqGaalalylaltl 126
                                     +e ++++id   +kg+ +sr  ++G+S+G+a++l +a  +
  gi|119718921|ref|YP_919416.1| 125 EVEDISKIIDLLEEKGL-ASRLGMIGYSMGGAITLMTAARE 164
                                    56789999998888886.7899*************998654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       778  (0.0433934); expected 358.6 (0.02)
Passed bias filter:                      666  (0.0371465); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.41
# Mc/sec: 2172.58
//
Query:       gi|119718922|ref|YP_919417.1|  [L=428]
Description: major facilitator transporter [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-39  136.3  37.5    1.2e-39  136.3  37.5    1.4  2  MFS_1     Major Facilitator Superfamily
    2.2e-08   33.1  29.5    3.7e-05   22.5  18.8    2.3  2  MFS_2     MFS/sugar transport protein
      1e-07   31.2  23.3    0.00019   20.4   6.8    2.6  2  Sugar_tr  Sugar (and other) transporter
    5.5e-05   21.8   2.3    5.5e-05   21.8   2.3    1.5  2  TRI12     Fungal trichothecene efflux pump (TRI12)
  ------ inclusion threshold ------
      0.019   13.3   0.2      0.019   13.3   0.2    2.8  3  OATP      Organic Anion Transporter Polypeptide (OATP) family


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.3  37.5   3.3e-43   1.2e-39       2     353 .]      16     377 ..      15     377 .. 0.84
   2 ?   -3.2   0.4      0.84     3e+03     263     291 ..     387     415 ..     380     421 .. 0.51

  Alignments for each domain:
  == domain 1  score: 136.3 bits;  conditional E-value: 3.3e-43
                          MFS_1   2 llaaflsalarsilgpalplalaedlgispse......igllltlyalgaavaslplGrlsdrfGrrrvlllglllfalg 75 
                                    +l ++++++++++l+p+l  + ae l   +se      +gl++tl   + +v+s+++G+l+d++Grr+v+++  ++++lg
  gi|119718922|ref|YP_919417.1|  16 ALFVLFYFMGYYMLNPILRTLHAEGLIPGKSEvewrfnAGLIATLLQGTGLVLSFVWGVLADKVGRRPVIFTLGVIMGLG 95 
                                    67788999**********96556666666666333333666999999999****************************** PP

                          MFS_1  76 lllllfa.sslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWrav 153
                                     lll+ + + ++  ll+  +  G+g+ ++ pa++a+i+d  p e rgr+++ +++++ l++ilg +++g+l+    Wr +
  gi|119718922|ref|YP_919417.1|  96 -LLLV-SqARSYaELLAYFIAFGVGYVGVGPAIYAFISDALPSESRGRGYASYYVSSVLAMILGLIVAGVLL---PWRTA 170
                                    .6666.44777779**********************************************************...***** PP

                          MFS_1 154 fyilaivsllafvlfllll.....peepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsgllt 228
                                    ++++++++l++ vl  l++     +  ++e++  + ++        +l++ + +l+k+ vl+ +l++++ +++ + +l++
  gi|119718922|ref|YP_919417.1| 171 YMLAGLLTLVFSVL--LFYssrgiFIGYSEKGAREARRY-------SLRESLPSLRKKSVLL-VLLMIIPWTIPWGMLSI 240
                                    ***********997..77766677666666666655555.......444456799****997.99999999999****** PP

                          MFS_1 229 llplylqevlglsglllaglllallalvgailallagrlsdr.lgr....rrrlllallllllaalglallavt.....s 298
                                    ++  y+ +  g s   +a+l++a++ + +a +++++g lsdr          r+ ++ll++++++++++l+ ++     s
  gi|119718922|ref|YP_919417.1| 241 WSIDYISTKWGVS-TGTASLIIAAATASIALGHIVGGTLSDRlA-GkgdyTGRTKVSLLGVVVGYVSMMLMVTYpypygS 318
                                    *****99999999.567777799999999999**********62.33555668999999999999999999999666663 PP

                          MFS_1 299 savllll...vlvliGf.glgfvfpsllalasdlappeeagtasglfntagslggalgp 353
                                    +++  ll   +l++ G+ +  f++p +++++s+++ pe++gt++++++++++lg+ lgp
  gi|119718922|ref|YP_919417.1| 319 TNFKDLLvpsALAVGGMmFTTFAYPNINTVLSEVVVPEHRGTVFAVYSVLNNLGWTLGP 377
                                    33333336777777888888888***********************************8 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 0.84
                          MFS_1 263 lagrlsdrlgrrrrlllallllllaalgl 291
                                    ++g ++d ++++++   ++++l l+ +++
  gi|119718922|ref|YP_919417.1| 387 FSGVYADQVSAMTAAASTIVSLWLIPALC 415
                                    55555555555444444444444444444 PP

>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   2.8   8.6e-07    0.0031     259     342 ..      52     133 ..      44     138 .. 0.87
   2 !   22.5  18.8     1e-08   3.7e-05     149     415 ..     148     418 ..     137     423 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 8.6e-07
                          MFS_2 259 saasvfllvvtisallgiplwqplakrlgkkntyllgalltivllvlvlllqpsnlllflvllviagfgvgvaallpwsm 338
                                    ++a ++++++   +l+ +++w +la + g++ +++   +++ ++l+lv  +  ++++ +l+ ++++g+g+++ + +++++
  gi|119718922|ref|YP_919417.1|  52 FNAGLIATLLQGTGLVLSFVWGVLADKVGRRPVIFTLGVIMGLGLLLVSQA--RSYAELLAYFIAFGVGYVGVGPAIYAF 129
                                    667777788888899****************99999888888887777766..999999999999*************** PP

                          MFS_2 339 ladv 342
                                    ++d+
  gi|119718922|ref|YP_919417.1| 130 ISDA 133
                                    *997 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 1e-08
                          MFS_2 149 laailafllvlilgg.lkserkgylifaliialLmllgviivvlgtkervemrkkekteqkeklslleqlkevfrnrafl 227
                                    + ++la++l li +g l   r++y++++l+  + ++l+++ +  ++       +++ +++++++sl+e l  ++r++  l
  gi|119718922|ref|YP_919417.1| 148 VSSVLAMILGLIVAGvLLPWRTAYMLAGLLTLVFSVLLFYSSRGIFIGY----SEKGAREARRYSLRESL-PSLRKKSVL 222
                                    4455555555555553334566677766655555555555443333333....33455577777777776.567778899 PP

                          MFS_2 228 illllfllaalalgvlnglllYyltyvlg.ngsaasvfllvvtisallgiplwqplakrlg.......kkntyllgallt 299
                                    ++ll+++  + + g+l  +++ y+   +g +   as++ +++t+s +lg ++   l  rl        + ++ llg ++ 
  gi|119718922|ref|YP_919417.1| 223 LVLLMIIPWTIPWGMLSIWSIDYISTKWGvSTGTASLIIAAATASIALGHIVGGTLSDRLAgkgdytgRTKVSLLGVVVG 302
                                    999999999999***********************************************983333333344445555555 PP

                          MFS_2 300 ivllvlvlll.......qpsnlllflvllviagfgvgvaallpwsmladvvDygelktGkrregvffavlsfisklatgi 372
                                     v ++l   +       + +n   +lv  ++a  g  +++++++  + +v  +  +     ++g++fav+s +++l+ ++
  gi|119718922|ref|YP_919417.1| 303 YVSMML---MvtypypyGSTNFKDLLVPSALAVGG-MMFTTFAYPNINTVLSEVVV---PEHRGTVFAVYSVLNNLGWTL 375
                                    555555...45559988777777777777777666.44555555566666655553...6799***************** PP

                          MFS_2 373 glgvsgllLsaf.gyrakasvqspqvvlalrllyavlpavlllv 415
                                    g  v++llL+af g  a +++   ++ +++ +++ ++pa+++l+
  gi|119718922|ref|YP_919417.1| 376 GPTVYTLLLKAFsGVYADQVSAMTAAASTI-VSLWLIPALCWLL 418
                                    ************998555555555555555.4556789998887 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   6.8   5.4e-08   0.00019     296     434 ..      61     193 ..      51     208 .. 0.74
   2 !   16.3   8.2   9.3e-07    0.0033     312     440 ..     287     414 ..     200     422 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 5.4e-08
                                    HHHHHHHHHHHHHHHHHHS-SHHHHHHHHHHHHHHHHHHH..HHHHTTSS...CHHHHHHHHHHHHHHHTTTTHHHHHHH CS
                       Sugar_tr 296 vgvvnfvatfvaiflvdrfGRRtllllGaagmaicfvilgivalllvakskaasivaivfialfialfalgwgpvpwvlv 375
                                    +  +  v +fv+  l d++GRR++ ++ +++m + +++++      +a+    s++ + ++++ + +  +g+gp ++  +
  gi|119718922|ref|YP_919417.1|  61 LQGTGLVLSFVWGVLADKVGRRPVIFTLGVIMGLGLLLVS------QAR----SYAELLAYFIAFGVGYVGVGPAIYAFI 130
                                    4557789999999**********99999999999999987......333....45555555555556668********** PP

                                    HHHSHTTTHHHHHHHHHHHHHHHH....HHHHHHHHHHHCHHHT-HHHHHHHHHHHHHHHHHH CS
                       Sugar_tr 376 sElfpqsvRskalaiavavnwlan....flisllfpiiteaigggyvflvfaglavlfiifvf 434
                                    s+  p++ R+ ++a  +++++la     ++ ++l p+ t  + +g   lvf +l+  +   +f
  gi|119718922|ref|YP_919417.1| 131 SDALPSESRGRGYASYYVSSVLAMilglIVAGVLLPWRTAYMLAGLLTLVFSVLLFYSSRGIF 193
                                    ************997666655554111156677888888888777777777777666555555 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 9.3e-07
                                    HHS-SHHHHHHHHHHHHHHHHHHH..HHHHTTSS....CHHHHHHHHHHHHHHHTTTTHHHHHHHHHHSHTTTHHHHHHH CS
                       Sugar_tr 312 drfGRRtllllGaagmaicfvilgivalllvaks.kaasivaivfialfialfalgwgpvpwvlvsElfpqsvRskalai 390
                                    d++GR ++ llG++++ + ++++  v+++++ +s + +  ++  ++a+  ++f++   p +  ++sE+  ++ R+++ a+
  gi|119718922|ref|YP_919417.1| 287 DYTGRTKVSLLGVVVGYVSMMLM--VTYPYPYGStNFKDLLVPSALAVGGMMFTTFAYPNINTVLSEVVVPEHRGTVFAV 364
                                    668******************99..5999999997677777777888888888888889999999*************** PP

                                    HHHHHHHHHHHHHHHHHHHHCHHHT-HHHHHHHHHHHHHHHHHHHHS--S CS
                       Sugar_tr 391 avavnwlanflisllfpiiteaigggyvflvfaglavlfiifvfffvpet 440
                                      ++n+l   l  ++++ +++a +g y   v a+ a++++i+ ++ +p+ 
  gi|119718922|ref|YP_919417.1| 365 YSVLNNLGWTLGPTVYTLLLKAFSGVYADQVSAMTAAASTIVSLWLIPAL 414
                                    *******************************************9999975 PP

>> TRI12  Fungal trichothecene efflux pump (TRI12)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   2.3   1.5e-08   5.5e-05      32     157 ..       1     132 [.       1     185 [. 0.79
   2 ?   -3.6   0.3      0.74   2.7e+03      83     126 ..     260     303 ..     251     313 .. 0.61

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.5e-08
                          TRI12  32 lpegyyrsprvvasfaafslnvvatyfvlqasasalpnil.....qdvgqsensslfstlwttgqavsilvmgrltdrfg 106
                                    +peg  r   +vas+a f l     y++l+    +l          +v    n +l++tl      v  +v g l+d++g
  gi|119718922|ref|YP_919417.1|   1 MPEGRPRVKVIVASLALFVLFYFMGYYMLNPILRTLHAEGlipgkSEVEWRFNAGLIATLLQGTGLVLSFVWGVLADKVG 80 
                                    5899999999******************99876666554300111556666699*****998777788899********* PP

                          TRI12 107 rrpfvilthilglvgaivgctatkfntllaamtllgvaagpag.asplfvge 157
                                    rrp++    ++  +g ++   a  +  lla +  +gv     g a   f+ +
  gi|119718922|ref|YP_919417.1|  81 RRPVIFTLGVIMGLGLLLVSQARSYAELLAYFIAFGVGYVGVGpAIYAFISD 132
                                    ***99988877778999999**********9999998643333133445555 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 0.74
                          TRI12  83 fstlwttgqavsilvmgrltdrfgrrpfvilthilglvgaivgc 126
                                    + +  t   a+  +v g l+dr+  +        + l+g +vg 
  gi|119718922|ref|YP_919417.1| 260 IIAAATASIALGHIVGGTLSDRLAGKGDYTGRTKVSLLGVVVGY 303
                                    55555666667777777777777544444444445666777665 PP

>> OATP  Organic Anion Transporter Polypeptide (OATP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   1.9      0.17   5.9e+02     142     192 ..     115     165 ..      99     175 .. 0.80
   2 ?   13.3   0.2   5.2e-06     0.019     299     383 ..     224     312 ..     203     320 .. 0.71
   3 ?   -2.1   0.6      0.25   8.9e+02     155     195 ..     347     387 ..     325     418 .. 0.60

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.17
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           OATP 142 lGiGatpiytlGisYidDnvkkknsplylgilyalrilGpalGfllGslll 192
                                     G+G + + +  +++i D   +++     + +y+ ++l ++lG +++++ll
  gi|119718922|ref|YP_919417.1| 115 FGVGYVGVGPAIYAFISDALPSESRGRGYASYYVSSVLAMILGLIVAGVLL 165
                                    566777777777889999999999999899999999999999999998887 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 5.2e-06
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxx RF
                           OATP 299 vilssvfeillvaGfitFlpkylEtqFslsaseAnlltGvvvipgaalGillgGllvkklklsa.....kklaklvlvvs 373
                                    v+l  +   + +  ++++   y+ t++++s+ +A+l++++++  ++alG ++gG l  +l  +       k+  l +vv+
  gi|119718922|ref|YP_919417.1| 224 VLLMIIPWTIPWGMLSIWSIDYISTKWGVSTGTASLIIAAAT-ASIALGHIVGGTLSDRLAGKGdytgrTKVSLLGVVVG 302
                                    334433333334445678889****************98765.699************9987662211234555666666 PP

                                    xxxxxxxxxx RF
                           OATP 374 llslllllll 383
                                     +s++l++++
  gi|119718922|ref|YP_919417.1| 303 YVSMMLMVTY 312
                                    6666666655 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.25
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           OATP 155 sYidDnvkkknsplylgilyalrilGpalGfllGslllkly 195
                                    + + + v +++  + ++++++l  lG+ lG ++ +lllk +
  gi|119718922|ref|YP_919417.1| 347 TVLSEVVVPEHRGTVFAVYSVLNNLGWTLGPTVYTLLLKAF 387
                                    34455566666666777777777777777766666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       986  (0.0549947); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.67u 0.28s 00:00:00.95 Elapsed: 00:00:00.46
# Mc/sec: 2802.37
//
Query:       gi|119718923|ref|YP_919418.1|  [L=269]
Description: ABC transporter related [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      1e-28  100.6   0.0    1.4e-28  100.1   0.0    1.2  1  ABC_tran     ABC transporter
    1.2e-08   35.2   0.8    7.2e-07   29.3   0.0    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    0.00011   21.9   0.0       0.13   12.0   0.0    2.4  2  IstB_IS21    IstB-like ATP binding protein
  ------ inclusion threshold ------
      0.016   15.5   0.2      0.069   13.4   0.2    2.0  1  AAA_22       AAA domain
      0.019   15.4   0.2      0.034   14.5   0.2    1.7  1  AAA_16       AAA ATPase domain
      0.044   13.9   0.0      0.077   13.2   0.0    1.4  1  AAA_33       AAA domain
      0.053   13.2   0.2       0.23   11.1   0.1    1.9  2  AAA_24       AAA domain
      0.075   12.9   0.0       0.12   12.2   0.0    1.3  1  RsgA_GTPase  RsgA GTPase
       0.12   12.2   0.0       0.22   11.3   0.0    1.4  1  AAA_29       P-loop containing region of AAA domain
       0.14   12.1   0.3       0.28   11.1   0.1    1.6  2  MobB         Molybdopterin guanine dinucleotide synthesis pro
       0.18   11.5   0.0       0.41   10.3   0.0    1.7  1  AAA_30       AAA domain
        0.2   11.4   0.1       0.35   10.6   0.1    1.4  1  PRK          Phosphoribulokinase / Uridine kinase family


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.1   0.0   9.3e-32   1.4e-28       2     136 ..      19     163 ..      18     164 .. 0.84

  Alignments for each domain:
  == domain 1  score: 100.1 bits;  conditional E-value: 9.3e-32
                                    EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSB.HHHH. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx. RF
                       ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpelt.vren. 79 
                                    +++++++k+ge v+++G++GaGK+t++kl  gllkp +G++l+dgkd+++++ ++l +++g++ q+p l   +  + ++ 
  gi|119718923|ref|YP_919418.1|  19 RDLNVEIKRGEFVGVIGHSGAGKTTFAKLAVGLLKPRSGRVLVDGKDTRTTPVSELARKVGYVYQNPDLMIFSPtILDEv 98 
                                    689***************************************************************55543332255556 PP

                                    .........HHHTC.HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    .........xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 .........esdee.iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                               +++  + +l+ l+ ++   ++++ sp+ LS G+k r+a+a +l+++p++l+lDEpt
  gi|119718923|ref|YP_919418.1|  99 gfalrnmgyP-ESKvKDMVLRALESVD-LSKPLDASPHMLSFGEKHRLAIASVLVTEPDVLILDEPT 163
                                    999999**62.3331334455555555.666888889*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1     0.022        33       1      23 [.      30      52 ..      30      75 .. 0.80
   2 !   29.3   0.0   4.8e-10   7.2e-07     233     302 ..     132     198 ..     123     199 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.022
                         AAA_21  1 lnvliGpNgsGKSnLLdaldlla 23
                                   + ++iG  g+GK+++ ++  +l 
  gi|119718923|ref|YP_919418.1| 30 FVGVIGHSGAGKTTFAKLAVGLL 52
                                   5789***********99888775 PP

  == domain 2  score: 29.3 bits;  conditional E-value: 4.8e-10
                         AAA_21 233 parelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSplll 302
                                    +++ lS G k+ la+++ l   +   ++l++DEp +gL++++   l+++l++l ++g  v++ TH+  ll
  gi|119718923|ref|YP_919418.1| 132 SPHMLSFGEKHRLAIASVLVTEP---DVLILDEPTTGLDYARCLQLFRVLEKLYKGGKTVVVITHDLDLL 198
                                    45678*******66666666555...9*************888888888888888***********8876 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0018       2.6      44      68 ..      25      50 ..      12     100 .. 0.87
   2 !   12.0   0.0   8.6e-05      0.13     104     149 ..     149     195 ..     132     203 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0018
                      IstB_IS21 44 iekkenivllGpsGvGKshlai.alg 68
                                   i++ e + ++G+sG+GK+ +a  a+g
  gi|119718923|ref|YP_919418.1| 25 IKRGEFVGVIGHSGAGKTTFAKlAVG 50
                                   67888899**********99842555 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 8.6e-05
                      IstB_IS21 104 krllkvdllilDdlgllpldqaeaellfeviekrye..rrsiiitsnl 149
                                      ++++d+lilD+   + ld a   +lf+v+ek y+  ++ ++it +l
  gi|119718923|ref|YP_919418.1| 149 VLVTEPDVLILDEPT-TGLDYARCLQLFRVLEKLYKggKTVVVITHDL 195
                                    456788*******75.68*****************6336677777665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   4.7e-05     0.069       5      65 ..      28      79 ..      23     198 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.7e-05
                         AAA_22  5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralg 65
                                     ++ v+G+sG+GKTt ++  +  l         +p+  +v + ++ ++++  +el+r++g
  gi|119718923|ref|YP_919418.1| 28 GEFVGVIGHSGAGKTTFAKLAVGLL---------KPRSGRVLVDGKDTRTTPVSELARKVG 79
                                   567779*************999999.........666666666666666666666666555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.2   2.3e-05     0.034      21      75 ..      25      77 ..      17     207 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.3e-05
                         AAA_16 21 sgrpelvllsGesGvGKsslvrellralekdggif.lrgkcdqlesaipysalaqa 75
                                     r+e v ++G+sG GK++ ++ +   l+ + g + + gk ++    +p s la+ 
  gi|119718923|ref|YP_919418.1| 25 IKRGEFVGVIGHSGAGKTTFAKLAVGLLKPRSGRVlVDGKDTRT---TPVSELARK 77
                                   45678999*************99998888886666588888888...777666665 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   5.2e-05     0.077       4      20 ..      33      49 ..      31     105 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.2e-05
                         AAA_33  4 lvGlpGsGKstlaerll 20
                                   ++G++G+GK+t+a+  +
  gi|119718923|ref|YP_919418.1| 33 VIGHSGAGKTTFAKLAV 49
                                   79**********99654 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00016      0.23       6      22 ..      32      48 ..      28      68 .. 0.82
   2 ?   -0.9   0.0      0.75   1.1e+03     113     130 ..     176     193 ..     164     195 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00016
                         AAA_24  6 liyGpsgiGKTtlakel 22
                                    ++G sg+GKTt+ak +
  gi|119718923|ref|YP_919418.1| 32 GVIGHSGAGKTTFAKLA 48
                                   699***********987 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.75
                         AAA_24 113 rllkklqelrknvifiah 130
                                    r+l+kl++ +k+v++i h
  gi|119718923|ref|YP_919418.1| 176 RVLEKLYKGGKTVVVITH 193
                                    678889999999999988 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   8.2e-05      0.12      90     146 ..      18      74 ..       7      91 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.2e-05
                                    HHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S--------------SEEE CS
                    RsgA_GTPase  90 leelkellkd.ktsvlvGqSGvGKStLinallpelelktgevseklgrGkhTTtavel 146
                                    +++l+ ++k  +++ ++G+SG+GK+t+ +  ++ l+ + g v  + g+   TT  +el
  gi|119718923|ref|YP_919418.1|  18 MRDLNVEIKRgEFVGVIGHSGAGKTTFAKLAVGLLKPRSGRVLVD-GKDTRTTPVSEL 74 
                                    566777777668999************999988888888887663.333444444444 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00015      0.22      15      38 ..      21      44 ..      11      58 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00015
                         AAA_29 15 htieidlkgatlltGpsGsGKSTl 38
                                     +ei++ +++ ++G+sG+GK+T+
  gi|119718923|ref|YP_919418.1| 21 LNVEIKRGEFVGVIGHSGAGKTTF 44
                                   456677555999***********7 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00019      0.28       2      30 ..      31      59 ..      30      68 .. 0.90
   2 ?   -3.5   0.0       5.9   8.8e+03      18      36 ..     176     194 ..     174     197 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00019
                           MobB  2 lgivgksgsGKTtLleklipelkarglrv 30
                                   +g++g+sg+GKTt+ +  +  lk r  rv
  gi|119718923|ref|YP_919418.1| 31 VGVIGHSGAGKTTFAKLAVGLLKPRSGRV 59
                                   789****************9999887776 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 5.9
                           MobB  18 klipelkarglrvgtiKha 36 
                                    +++++l + g +v +i h+
  gi|119718923|ref|YP_919418.1| 176 RVLEKLYKGGKTVVVITHD 194
                                    5667777777777777775 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00028      0.41      19      53 ..      29      63 ..      22     194 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00028
                         AAA_30 19 rvavltGpAGtGKttalkalreaweaaggrviglA 53
                                    ++ + G  G+GKtt  k ++ +++ + grv++  
  gi|119718923|ref|YP_919418.1| 29 EFVGVIGHSGAGKTTFAKLAVGLLKPRSGRVLVDG 63
                                   477899***************99999977776544 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00023      0.35       2      23 ..      31      52 ..      30      71 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00023
                            PRK  2 IgvagsSGaGkttvarklekif 23
                                   +gv g SGaGktt+a+  + ++
  gi|119718923|ref|YP_919418.1| 31 VGVIGHSGAGKTTFAKLAVGLL 52
                                   89************98766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.49u 0.32s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1716.85
//
Query:       gi|119718924|ref|YP_919419.1|  [L=273]
Description: ABC transporter related [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-26   93.0   0.0    3.1e-26   92.5   0.0    1.2  1  ABC_tran      ABC transporter
    1.1e-09   38.6   0.4    0.00013   21.9   0.1    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
      1e-07   31.6   0.0    1.6e-05   24.5   0.0    2.1  2  SMC_N         RecF/RecN/SMC N terminal domain
    1.5e-05   25.6   0.8      0.046   14.3   0.2    2.3  2  AAA_18        AAA domain
    0.00022   21.6   0.1     0.0033   17.8   0.1    2.1  1  AAA           ATPase family associated with various cellular 
    0.00031   20.7   0.0    0.00052   20.0   0.0    1.3  1  Rad17         Rad17 P-loop domain
    0.00064   20.2   0.1     0.0011   19.4   0.1    1.7  1  AAA_16        AAA ATPase domain
    0.00085   19.1   0.0     0.0082   15.9   0.0    2.1  1  AAA_30        AAA domain
     0.0014   19.1   0.0     0.0023   18.5   0.0    1.2  1  AAA_23        AAA domain
      0.002   17.6   0.1     0.0087   15.5   0.0    1.9  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
     0.0029   17.6   0.2      0.056   13.4   0.0    2.1  2  NACHT         NACHT domain
     0.0061   16.5   0.0      0.012   15.6   0.0    1.4  1  RsgA_GTPase   RsgA GTPase
      0.009   15.6   0.2      0.032   13.8   0.0    1.9  2  AAA_25        AAA domain
  ------ inclusion threshold ------
      0.013   15.8   0.1      0.045   14.0   0.0    1.8  2  AAA_22        AAA domain
      0.015   15.5   0.3      0.075   13.3   0.1    2.0  2  AAA_28        AAA domain
      0.016   15.0   0.0      0.044   13.5   0.0    1.7  1  AAA_29        P-loop containing region of AAA domain
      0.016   15.4   0.0        0.1   12.8   0.0    2.0  1  SbcCD_C       Putative exonuclease SbcCD, C subunit
      0.016   14.9   0.1       0.46   10.2   0.0    2.1  2  IstB_IS21     IstB-like ATP binding protein
      0.019   14.7   0.0      0.038   13.7   0.0    1.4  1  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
      0.022   14.7   0.1      0.057   13.4   0.1    1.7  1  AAA_5         AAA domain (dynein-related subfamily)
      0.024   14.5   0.0      0.053   13.4   0.0    1.5  1  ATPase_2      ATPase domain predominantly from Archaea
      0.028   14.6   0.2      0.074   13.2   0.1    1.7  2  AAA_33        AAA domain
      0.036   13.5   0.1       0.06   12.8   0.1    1.3  1  SRPRB         Signal recognition particle receptor beta subun
      0.067   13.2   0.1       0.39   10.8   0.1    2.0  2  AAA_14        AAA domain
      0.074   12.6   0.0       0.11   12.1   0.0    1.2  1  AAA_27        AAA domain
      0.079   13.3   0.1          1    9.7   0.0    2.1  2  AAA_19        AAA domain
       0.14   12.0   0.1        3.4    7.6   0.0    2.4  2  MobB          Molybdopterin guanine dinucleotide synthesis pr
       0.17   11.3   0.0         13    5.1   0.0    2.2  2  TniB          Bacterial TniB protein
       0.17   11.2   0.1        6.5    6.0   0.0    2.1  2  ATPase        KaiC
       0.19   12.1   0.0       0.31   11.4   0.0    1.4  1  RNA_helicase  RNA helicase
       0.22   10.7   0.3       0.35   10.0   0.3    1.6  1  NB-ARC        NB-ARC domain
       0.24   10.2   0.0       0.32    9.8   0.0    1.2  1  Adeno_IVa2    Adenovirus IVa2 protein


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.5   0.0   5.5e-29   3.1e-26       1     137 []      16     167 ..      16     167 .. 0.93

  Alignments for each domain:
  == domain 1  score: 92.5 bits;  conditional E-value: 5.5e-29
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--.....SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSB CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp.....teGeilldgkdlkeqeleslrkeigvlpqepqlfpelt 75 
                                    l+ v+++ ++ge+v i+G++G+GK+tL+++lagl         eG+  ++g d+ +   + l   +g + q+p+++  ++
  gi|119718924|ref|YP_919419.1|  16 LRAVDFEANRGELVIIMGPSGCGKTTLFRVLAGLIPSllpgtVEGQAVVEGIDVVSSGYKGLAGVVGLVYQNPEMQVVTR 95 
                                    57899*****************************9889889999999*************************77777766 PP

                                    .HHHH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    .xxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  76 .vren.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                     v e+             e +++i+ +++ l+l+++  +      ++LSgG+kq va+a +l +kpk+lllDEpt+
  gi|119718924|ref|YP_919419.1|  96 sVLEElamgpenlglpreEIRARIDWVVDMLNLHDFLGRDP----QTLSGGEKQLVAIASVLTSKPKVLLLDEPTS 167
                                    688889********999999999999999999999888887....*****************************96 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   2.6e-05     0.015       2      41 ..      29      65 ..      28      85 .. 0.79
   2 !   21.9   0.1   2.3e-07   0.00013     233     295 ..     135     194 ..     112     196 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.6e-05
                         AAA_21  2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsgggg 41
                                    ++ Gp g+GK++L++ l +l   ++++ ++t e +  ++
  gi|119718924|ref|YP_919419.1| 29 VIIMGPSGCGKTTLFRVLAGL---IPSLLPGTVEGQAVVE 65
                                   6899*****************...7777777776665554 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 2.3e-07
                         AAA_21 233 parelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQvilt 295
                                    ++  lS G k+l a+++ l + +   ++ll+DEp + L+++ +r +l+ + el+++g  vi++
  gi|119718924|ref|YP_919419.1| 135 DPQTLSGGEKQLVAIASVLTSKP---KVLLLDEPTSMLDHRGTRLVLDAIAELKKEGLTVIVA 194
                                    56789*******77777777766...9***********************999999**99986 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.021        12      25      41 ..      27      43 ..       8      49 .. 0.82
   2 !   24.5   0.0   2.9e-08   1.6e-05     133     208 ..     135     208 ..      79     215 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.021
                                   SEEEEEESTTSSHHHHH CS
                                   xxxxxxxxxxxxxxxxx RF
                          SMC_N 25 sftaivGpNGSGKsnll 41
                                   ++ +i+Gp G+GK+ l+
  gi|119718924|ref|YP_919419.1| 27 ELVIIMGPSGCGKTTLF 43
                                   46789*********987 PP

  == domain 2  score: 24.5 bits;  conditional E-value: 2.9e-08
                                    STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-.SCE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx.xxx RF
                          SMC_N 133 skelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreemleka.dkl 208
                                    ++++LSgGek+Lva+a ++     kp+   llDe  + LD++ ++ v + + e +k+   +iv  +r e  +++ d++
  gi|119718924|ref|YP_919419.1| 135 DPQTLSGGEKQLVAIASVL---TSKPKV-LLLDEPTSMLDHRGTRLVLDAIAELKKEgLTVIVAEHRVEWAAEVaDRV 208
                                    5669***********9775...567775.589********************99998788999999988765542554 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.2   8.2e-05     0.046       1      21 [.      29      49 ..      29      75 .. 0.80
   2 !    9.7   0.0    0.0021       1.2      60     112 ..     177     231 ..     154     238 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8.2e-05
                         AAA_18  1 IlltGtpGvGKttlakeLskr 21
                                   ++++G++G+GKttl + L+ +
  gi|119718924|ref|YP_919419.1| 29 VIIMGPSGCGKTTLFRVLAGL 49
                                   79**************99755 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0021
                         AAA_18  60 lldaleenssaleegknlvidghlaeleseaakdikk.....vvLtaspeelleRlek 112
                                    +lda+ e      eg ++++  h++e+  e a + +      + L+ +pee + R+e+
  gi|119718924|ref|YP_919419.1| 177 VLDAIAEL---KKEGLTVIVAEHRVEWAAEVADRVVVmgrgtILLEGKPEEVFSRVED 231
                                    45555555...3589999*********99977766669******************97 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   5.9e-06    0.0033       1      74 [.      29     172 ..      29     215 .. 0.61

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 5.9e-06
                                    EEEESSTTSSHHHHHHHHHHHH..........THEEEEEETTTCSSS................................. CS
                            AAA   1 vllyGppGtGKTllakavakel..........gvefleisgsellsk................................. 37 
                                    v+++Gp G+GKT+l + +a  +          +     ++g +++s+                                 
  gi|119718924|ref|YP_919419.1|  29 VIIMGPSGCGKTTLFRVLAGLIpsllpgtvegQ---AVVEGIDVVSSgykglagvvglvyqnpemqvvtrsvleelamgp 105
                                    6899***************99643344333220...22222222222344444445555555555555555555566677 PP

                                    ................................STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH CS
                            AAA  38 ................................yvgesekkirelfkeakekakpsilfiDEidalaksr 74 
                                                                    +++ +ek++ ++ + + +  kp++l++DE  ++  +r
  gi|119718924|ref|YP_919419.1| 106 enlglpreeiraridwvvdmlnlhdflgrdpqTLSGGEKQLVAIASVLTS--KPKVLLLDEPTSMLDHR 172
                                    77777777777777777777777775555555555555555555554433..47888888888888777 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   9.4e-07   0.00052      35      66 ..      16      47 ..       7      59 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 9.4e-07
                          Rad17 35 lkadvLesrkkriLLisGPsGCgkstvvkvLs 66
                                   l+a   e ++ ++++i GPsGCgk+t  +vL+
  gi|119718924|ref|YP_919419.1| 16 LRAVDFEANRGELVIIMGPSGCGKTTLFRVLA 47
                                   566677888888******************98 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1     2e-06    0.0011      21      45 ..      23      47 ..      15     208 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 2e-06
                         AAA_16 21 sgrpelvllsGesGvGKsslvrell 45
                                   ++r+elv++ G+sG+GK++l r l+
  gi|119718924|ref|YP_919419.1| 23 ANRGELVIIMGPSGCGKTTLFRVLA 47
                                   56779***************99887 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.5e-05    0.0082      16      55 ..      24      64 ..      16     197 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.5e-05
                         AAA_30 16 sgdrvavltGpAGtGKttalkalreaweaa.ggrviglApt 55
                                   ++  ++++ Gp G GKtt+ ++l+ ++ +   g+v g A  
  gi|119718924|ref|YP_919419.1| 24 NRGELVIIMGPSGCGKTTLFRVLAGLIPSLlPGTVEGQAVV 64
                                   44569*********************999987777776654 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0     4e-06    0.0023      12      39 ..      13      46 ..       4      49 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 4e-06
                         AAA_23 12 dqe...idF...skgltlItGpNGaGKTTildAi 39
                                   d++   +dF      l++I Gp G+GKTT+++ +
  gi|119718924|ref|YP_919419.1| 13 DWTlraVDFeanRGELVIIMGPSGCGKTTLFRVL 46
                                   555444688664446***************9865 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.6e-05    0.0087      13      51 ..      17      55 ..       9      77 .. 0.80
   2 ?   -0.6   0.0       1.3   7.4e+02     106     124 ..     171     190 ..     137     223 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.6e-05
                   Mg_chelatase 13 raleiaaaGgHnlllvGppGsGKtmlakrlpsllpplse 51
                                   ra++  a  g  ++++Gp+G+GKt l + l++l+p+l  
  gi|119718924|ref|YP_919419.1| 17 RAVDFEANRGELVIIMGPSGCGKTTLFRVLAGLIPSLLP 55
                                   566666666677899*****************9998854 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.3
                   Mg_chelatase 106 hnGv.LfLDElpefkrkvle 124
                                    h+G  L+LD ++e+k++ l 
  gi|119718924|ref|YP_919419.1| 171 HRGTrLVLDAIAELKKEGLT 190
                                    44433455555555554443 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0    0.0001     0.056       2      21 ..      28      47 ..      27      55 .. 0.89
   2 ?    2.2   0.0      0.28   1.6e+02      74      95 ..     151     186 ..     118     200 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.0001
                                   CEEEEC-TTTCHHHHHHHHH CS
                          NACHT  2 lvilqGeaGsGKTtLlqkla 21
                                   lvi+ G++G+GKTtL + la
  gi|119718924|ref|YP_919419.1| 28 LVIIMGPSGCGKTTLFRVLA 47
                                   79*************99887 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.28
                                    HHHCCSCCCEE..............EEEE-STT-SS CS
                          NACHT  74 avllelperlL..............lilDglDelvt 95 
                                    +vl++ p+ lL              l+lD++ el++
  gi|119718924|ref|YP_919419.1| 151 SVLTSKPKVLLldeptsmldhrgtrLVLDAIAELKK 186
                                    4455555555566666666************99986 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   2.1e-05     0.012      98     121 ..      25      48 ..       3      64 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.1e-05
                                    TTSEEEEECSTTSSHHHHHHHHCT CS
                    RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallp 121
                                    ++++++++G+SG GK+tL  +l++
  gi|119718924|ref|YP_919419.1|  25 RGELVIIMGPSGCGKTTLFRVLAG 48 
                                    4599***************99976 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   5.8e-05     0.032      31      53 ..      24      46 ..      19      59 .. 0.90
   2 ?   -1.2   0.1       2.3   1.3e+03     163     175 ..     172     184 ..     111     197 .. 0.49

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.8e-05
                         AAA_25 31 pagelallaGapgtGKttlaldl 53
                                    +gel++++G++g+GKttl   l
  gi|119718924|ref|YP_919419.1| 24 NRGELVIIMGPSGCGKTTLFRVL 46
                                   589***************97655 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.3
                         AAA_25 163 sdvgalvealeri 175
                                    + ++ +++a++++
  gi|119718924|ref|YP_919419.1| 172 RGTRLVLDAIAEL 184
                                    2223333444444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0     8e-05     0.045       6      25 ..      27      46 ..      23      55 .. 0.86
   2 ?   -1.6   0.0       5.4     3e+03      87     102 ..     154     167 ..     123     194 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 8e-05
                         AAA_22  6 gilvvtGesGtGKTtllrrl 25
                                    +++++G+sG+GKTtl r l
  gi|119718924|ref|YP_919419.1| 27 ELVIIMGPSGCGKTTLFRVL 46
                                   6789************9866 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 5.4
                         AAA_22  87 raravielliiDEaqh 102
                                     ++  +++l++DE   
  gi|119718924|ref|YP_919419.1| 154 TSK--PKVLLLDEPTS 167
                                    333..34777777544 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   0.00013     0.075       2      20 ..      29      47 ..      28      65 .. 0.88
   2 ?   -0.1   0.0       1.7   9.6e+02      19      36 ..     193     210 ..     145     234 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00013
                         AAA_28  2 ivitGgestGKTtlleaLa 20
                                   ++i+G++++GKTtl + La
  gi|119718924|ref|YP_919419.1| 29 VIIMGPSGCGKTTLFRVLA 47
                                   89*************9998 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.7
                         AAA_28  19 LaargypvvpEaareile 36 
                                     a++ +++ +E+a +++ 
  gi|119718924|ref|YP_919419.1| 193 VAEHRVEWAAEVADRVVV 210
                                    567778888888887775 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   7.8e-05     0.044      15      39 ..      19      43 ..      11      52 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.8e-05
                         AAA_29 15 htieidlkgatlltGpsGsGKSTll 39
                                    ++e ++ + ++++GpsG GK+Tl+
  gi|119718924|ref|YP_919419.1| 19 VDFEANRGELVIIMGPSGCGKTTLF 43
                                   55667755599************97 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00018       0.1      28      88 ..     134     181 ..     127     183 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00018
                        SbcCD_C  28 rssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllell 88 
                                    r+ +tlSGGekq       + a+a++++s      ++++++LDE  s lD++ ++ +l+++
  gi|119718924|ref|YP_919419.1| 134 RDPQTLSGGEKQ-------LVAIASVLTS------KPKVLLLDEPTSMLDHRGTRLVLDAI 181
                                    666899*****4.......4567788888......589***************99999987 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00081      0.46      38      64 ..      16      43 ..       9      48 .. 0.77
   2 ?    2.5   0.0      0.19   1.1e+02     107     162 ..     155     208 ..     136     212 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00081
                      IstB_IS21 38 Latlsfi.ekkenivllGpsGvGKshla 64
                                   L++ +f  ++ e ++++GpsG GK+ l 
  gi|119718924|ref|YP_919419.1| 16 LRAVDFEaNRGELVIIMGPSGCGKTTLF 43
                                   6666774145688999*********885 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.19
                      IstB_IS21 107 lkvdllilDdlgllpldqaeaellfeviekryerrsiiitsnlpfaewdevlgdat 162
                                     k+++l+lD+  +  ld+  ++l+++ i++  +   ++i ++  + ew + ++d +
  gi|119718924|ref|YP_919419.1| 155 SKPKVLLLDEP-TSMLDHRGTRLVLDAIAELKKEGLTVIVAEHRV-EWAAEVADRV 208
                                    47799****96.5789**************999999999998776.7888888876 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   6.8e-05     0.038       4      23 ..      29      48 ..      27      52 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.8e-05
                      PduV-EutP  4 illiGkvgsGKttLtqalkg 23
                                   ++++G++g+GKttL + l g
  gi|119718924|ref|YP_919419.1| 29 VIIMGPSGCGKTTLFRVLAG 48
                                   89************999976 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1    0.0001     0.057       2      23 ..      29      50 ..      28      62 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.0001
                                   EEEE--SSSSHHHHHHHGGGGB CS
                          AAA_5  2 vlLvGppGtgKselaerlaaal 23
                                   v++ Gp+G+gK++l + la ++
  gi|119718924|ref|YP_919419.1| 29 VIIMGPSGCGKTTLFRVLAGLI 50
                                   899***************9987 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   9.5e-05     0.053      17      40 ..      23      46 ..      18      50 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.5e-05
                       ATPase_2 17 repneiyfiYGpegsGKtaLlkei 40
                                    ++ e + i Gp g+GKt+L++ +
  gi|119718924|ref|YP_919419.1| 23 ANRGELVIIMGPSGCGKTTLFRVL 46
                                   56778999************9976 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   0.00013     0.074       1      20 [.      28      47 ..      28      54 .. 0.90
   2 ?   -2.3   0.0       7.8   4.4e+03      69      92 ..     156     182 ..     136     209 .. 0.54

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00013
                         AAA_33  1 lvllvGlpGsGKstlaerll 20
                                   lv++ G++G+GK+tl + l+
  gi|119718924|ref|YP_919419.1| 28 LVIIMGPSGCGKTTLFRVLA 47
                                   79*************98775 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 7.8
                         AAA_33  69 agrnvildat..nlsr.rerarflkla 92 
                                    + + ++ld +  +l++  +r  ++++a
  gi|119718924|ref|YP_919419.1| 156 KPKVLLLDEPtsMLDHrGTRLVLDAIA 182
                                    333344465533333323333444444 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   0.00011      0.06       4      23 ..      27      46 ..      24      57 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00011
                                   -EEEEE-STTSSHHHHHHHH CS
                          SRPRB  4 pavllvGlsdsGKTslftrL 23
                                   + v+++G+s +GKT+lf  L
  gi|119718924|ref|YP_919419.1| 27 ELVIIMGPSGCGKTTLFRVL 46
                                   579**************987 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00069      0.39       3      22 ..      27      46 ..      25      54 .. 0.86
   2 ?   -0.3   0.0       1.9     1e+03      60      76 ..     153     168 ..     127     195 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00069
                         AAA_14  3 kilvitGaRrvGKTtllkql 22
                                   ++++i+G+  +GKTtl + l
  gi|119718924|ref|YP_919419.1| 27 ELVIIMGPSGCGKTTLFRVL 46
                                   689*************8765 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.9
                         AAA_14  60 lkeekktylflDEiqev 76 
                                    l+ +k ++l+lDE   +
  gi|119718924|ref|YP_919419.1| 153 LT-SKPKVLLLDEPTSM 168
                                    33.47888999997665 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0    0.0002      0.11      15      49 ..      15      49 ..       1      53 [. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0002
                         AAA_27 15 tdrsldfsaeeadlhliyGpNEAGKstalrAisdl 49
                                   t r +df+a++ +l +i+Gp   GK+t++r +  l
  gi|119718924|ref|YP_919419.1| 15 TLRAVDFEANRGELVIIMGPSGCGKTTLFRVLAGL 49
                                   56889***********************9987765 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0    0.0018         1       3      29 ..      17      45 ..      15      58 .. 0.75
   2 ?    1.5   0.0      0.59   3.3e+02      99     129 ..     152     185 ..      97     193 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0018
                         AAA_19  3 eave..alkekvllvtaGpGtGKTrvlkh 29
                                   +av+  a + ++++++++ G+GKT++ + 
  gi|119718924|ref|YP_919419.1| 17 RAVDfeANRGELVIIMGPSGCGKTTLFRV 45
                                   5774435566788888999*****98765 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.59
                         AAA_19  99 klqeee.llivDE.fqdvdelqyrL.lkallgek 129
                                     l+++  +l+ DE ++++d    rL l+a+++ k
  gi|119718924|ref|YP_919419.1| 152 VLTSKPkVLLLDEpTSMLDHRGTRLvLDAIAELK 185
                                    44444459999*9779999555555267776555 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0    0.0061       3.4       2      19 ..      29      46 ..      28      55 .. 0.78
   2 ?    1.9   0.0      0.35     2e+02      13      37 ..     174     198 ..     170     207 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0061
                           MobB  2 lgivgksgsGKTtLlekl 19
                                   + i+g sg+GKTtL   l
  gi|119718924|ref|YP_919419.1| 29 VIIMGPSGCGKTTLFRVL 46
                                   6799*********97654 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.35
                           MobB  13 TtLleklipelkarglrvgtiKhah 37 
                                    T L+   i+elk++gl+v +  h +
  gi|119718924|ref|YP_919419.1| 174 TRLVLDAIAELKKEGLTVIVAEHRV 198
                                    8899999***********9988865 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.023        13      34      53 ..      25      44 ..      18      61 .. 0.87
   2 ?    4.0   0.0     0.052        29     110     152 ..     147     187 ..     132     195 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.023
                           TniB 34 rmpnlllvGdsnnGKtmive 53
                                   r + ++++G+s +GKt++++
  gi|119718924|ref|YP_919419.1| 25 RGELVIIMGPSGCGKTTLFR 44
                                   666789***********986 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.052
                           TniB 110 qvlrllrelkvrvLiiDEihnllagsarkqreflnalksLgne 152
                                     +++   + k++vL++DE  ++l   +r  r +l a+  L+ e
  gi|119718924|ref|YP_919419.1| 147 VAIASVLTSKPKVLLLDEPTSML--DHRGTRLVLDAIAELKKE 187
                                    4556667889************9..677777777777777665 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.012       6.5      18      35 ..      25      42 ..      23      45 .. 0.90
   2 ?    3.1   0.0     0.093        52     142     226 ..     175     256 ..     144     260 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.012
                         ATPase 18 egrvvlitGepGtGKtif 35
                                   +g+ v i+G +G+GKt++
  gi|119718924|ref|YP_919419.1| 25 RGELVIIMGPSGCGKTTL 42
                                   7899************87 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.093
                         ATPase 142 eilrqlvrvlkklgvTailvsekssseeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIte 221
                                    + +   + +lkk g+T i v+e +++  a    +v   +  g+i L+  + ee + R+ +i  +   +   +e+ +e  +
  gi|119718924|ref|YP_919419.1| 175 RLVLDAIAELKKEGLTVI-VAEHRVEWAAEVADRVVV-MGRGTILLE-GKPEEVFSRVEDIQRYGVRPPGVAEVAYELRK 251
                                    346667788999999865.566666666666666666.679999999.66777888888888888888888888888888 PP

                         ATPase 222 egikv 226
                                    +g++v
  gi|119718924|ref|YP_919419.1| 252 RGVNV 256
                                    88876 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00056      0.31       1      19 [.      29      47 ..      29      78 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00056
                   RNA_helicase  1 iwlyGpsgeGKStlakeLa 19
                                   +++ Gpsg+GK+tl + La
  gi|119718924|ref|YP_919419.1| 29 VIIMGPSGCGKTTLFRVLA 47
                                   6899**********99977 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.3   0.00063      0.35      21      38 ..      27      44 ..      17     167 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00063
                                   EEEEEEESTTSSHHHHHH CS
                         NB-ARC 21 lvvalvGmgGvGKttlak 38
                                    +v ++G  G+GKttl++
  gi|119718924|ref|YP_919419.1| 27 ELVIIMGPSGCGKTTLFR 44
                                   4789************87 PP

>> Adeno_IVa2  Adenovirus IVa2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00057      0.32      66     107 ..       3      46 ..       1      59 [. 0.72

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00057
                     Adeno_IVa2  66 kldakll.rddGelsslnyglq.PviGviyGPtGsGksqllrnl 107
                                    +l+ k+l ++d  l +++++ +   + +i GP G+Gk+ l+r l
  gi|119718924|ref|YP_919419.1|   3 NLNVKYLgSKDWTLRAVDFEANrGELVIIMGPSGCGKTTLFRVL 46 
                                    5666666345667777777665245779**************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                       111  (0.00619109); expected 17.9 (0.001)
Passed Fwd filter:                        32  (0.00178482); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              32  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 1910.74
//
Query:       gi|119718925|ref|YP_919420.1|  [L=258]
Description: cobalt transport protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      6e-17   62.0  10.4      8e-17   61.6  10.4    1.2  1  CbiQ      Cobalt transport protein


Domain annotation for each model (and alignments):
>> CbiQ  Cobalt transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.6  10.4   4.5e-21     8e-17       2     207 ..      10     216 ..       9     227 .. 0.83

  Alignments for each domain:
  == domain 1  score: 61.6 bits;  conditional E-value: 4.5e-21
                                    SCCCCS-HHHHHHHHHHHHHHHHHS-H.HHHHHHHHHHHHHHHHTTS---HHHHHHHCCCHCHHHHHHHHHHE....... CS
                           CbiQ   2 ksvlhrldprvkliwlfllllalvlap.nlvtlliiiallllllllvilprvlaqalilpllflllgllillfqlitteg 80 
                                    ks+ h ldprvkl+w  l+l a++  + n +    +++  +++l+l+++   la++li+  l++ll + ++   +++  g
  gi|119718925|ref|YP_919420.1|  10 KSFFHSLDPRVKLLWATLVLAASIATQfNGLKSFPVFVSAIAALTLSGIGAGLAAVLIFNSLVFLLITTLVWAGMYSGHG 89 
                                    7899***********98887777665523444445555556666666666667777777766666655555556899*** PP

                                    EECTTEEE...E-TTHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHHHHCCCSS--HHHHHHHHHHHHHHHHHHHHHHHH CS
                           CbiQ  81 efvfagggqisitseGllrglllalRiltllslllllalTTppeeltsslerlgvPlelalillLayRfiflLleevqri 160
                                      vf+ g  + it+ Gll++   ++ i++ +++ + +++TT+p+ ++ +le++g+P+++++++ +a  ++++++  +++ 
  gi|119718925|ref|YP_919420.1|  90 SPVFVLGF-LRITDVGLLVASGKFFLIMSPVFAFITFFVTTKPYHVAWTLEKMGMPSKVSTAFVIAVSLLPTMVKATRDV 168
                                    ********.*******999999999999999999999******************************************* PP

                                    HHHHHHTTTTS...SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                           CbiQ 161 kqAqklRlgds.klgirrslrslgkliaalflralkraervalAmeaR 207
                                     + qklR++   + ++  +lr +++ i++++ r+l    ++ l +++R
  gi|119718925|ref|YP_919420.1| 169 IDIQKLRGLALdRGSVLDRLRNYIPIIVPVISRLLSDVWDLSLVLASR 216
                                    *********************************998887777777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       758  (0.0422779); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1831.64
//
Query:       gi|119718926|ref|YP_919421.1|  [L=185]
Description: hypothetical protein Tpen_0008 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-09   38.2  16.7    2.1e-09   37.9  16.7    1.1  1  QueT      QueT transporter


Domain annotation for each model (and alignments):
>> QueT  QueT transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9  16.7   1.2e-13   2.1e-09       2     136 ..       2     162 ..       1     168 [. 0.81

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 1.2e-13
                           QueT   2 vraaviaAlYvvltlvla..pisfgaiqvRiseaLtlLpv..ftpaailGltiGcliaNllsplgllDvifGslatliaa 77 
                                    + +a+ aA+Y  l+ ++a  +i  g + +R+ +aL  L    f+   +lG +iG+l+a++ls +  +  + G++ ++++a
  gi|119718926|ref|YP_919421.1|   2 ALVALSAAVYGGLLAATApiTIVPGFTWLRPGNALAPLFGmfFGIPGCLGAAIGNLLADILSGYFGVGSFGGFIGNFLIA 81 
                                    6789**************44466799*********9995323888889***********8886666************** PP

                           QueT  78 lltyllkkkr............llaalppvlvnalivgav.........l.lelpflltvltvglgelivlyvlGlpllk 135
                                    ++ +++ +++            ++ ++++++v a+++ +          l + +++++ +++++++++ v  vl  +l  
  gi|119718926|ref|YP_919421.1|  82 YIPFKFVRDHsfgsassigefyIWGVIVQAFVSAIYICWWldvmqsvvgLpVFVIWAVIATSILINNITVNAVLSPILGV 161
                                    ******88889999999888744666888888888888655665665541567788999999****99999998888765 PP

                           QueT 136 a 136
                                    +
  gi|119718926|ref|YP_919421.1| 162 I 162
                                    5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       648  (0.0361426); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1444.82
//
Query:       gi|119718927|ref|YP_919422.1|  [L=467]
Description: transglutaminase domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-23   82.5   0.2    6.7e-23   81.3   0.2    1.7  1  Transglut_core   Transglutaminase-like superfamily
     0.0053   16.7   0.1      0.016   15.1   0.1    1.8  1  Transglut_core3  Transglutaminase-like superfamily
  ------ inclusion threshold ------
       0.73   10.8   4.2        1.5    9.8   0.2    3.3  4  TPR_14           Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> Transglut_core  Transglutaminase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.3   0.2   1.1e-26   6.7e-23       2     112 .]     284     388 ..     283     388 .. 0.92

  Alignments for each domain:
  == domain 1  score: 81.3 bits;  conditional E-value: 1.1e-26
                 Transglut_core   2 alaeeltagakdplekakaiyewvrknveys.aprrtpgsrdaeavletgkGncedfaslfvallRalGipaRvvtgyls 80 
                                    +++++lt+ga++p+ek+++i  w+ +nv+y+ a+ +   ++ +e+v+++++G+c   a lf++++R +G+paR+ +g+++
  gi|119718927|ref|YP_919422.1| 284 EFVDRLTRGAASPYEKVQRIWGWITENVRYTyAKDYIFYDNIPEYVFREKRGDCGMQALLFITMCRIAGVPARWESGWYM 363
                                    6889***************************76666666666************************************** PP

                 Transglut_core  81 geeekeqsvasedaHawvevylegygWvplDp 112
                                     +        s ++H w+++yle ygW+ +Dp
  gi|119718927|ref|YP_919422.1| 364 HP-------LSPGMHDWAQFYLEPYGWLYADP 388
                                    87.......56678***************998 PP

>> Transglut_core3  Transglutaminase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   2.7e-06     0.016      55      94 ..     334     373 ..     327     377 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.7e-06
                Transglut_core3  55 rskCLpralalalllrrrgipatlviGvrkeddpfaaHAW 94 
                                    r +C  +al+  +++r +g+pa++  G  +++ +   H W
  gi|119718927|ref|YP_919422.1| 334 RGDCGMQALLFITMCRIAGVPARWESGWYMHPLSPGMHDW 373
                                    669************************9998444455666 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.2   0.00026       1.5      11      35 ..      25      49 ..      20      55 .. 0.88
   2 ?   -2.8   0.0       2.9   1.7e+04      18      29 ..      72      83 ..      71      86 .. 0.79
   3 ?   -2.3   0.0         2   1.2e+04      19      33 ..     147     161 ..     147     171 .. 0.75
   4 ?    0.4   0.0      0.28   1.7e+03      29      42 ..     257     270 ..     254     272 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00026
                         TPR_14 11 llalGdpdeAiallrralalaPdda 35
                                   ll++G++++A+  lrr+ ++ P+++
  gi|119718927|ref|YP_919422.1| 25 LLRRGELRKAEGELRRLAETSPQPL 49
                                   89********************965 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.9
                         TPR_14 18 deAiallrrala 29
                                   +eA + lr++++
  gi|119718927|ref|YP_919422.1| 72 EEAFRQLRKRVE 83
                                   689999998876 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2
                         TPR_14  19 eAiallrralalaPd 33 
                                    +A+++l +a +++ +
  gi|119718927|ref|YP_919422.1| 147 RAERVLSAAREKGGG 161
                                    589999999888765 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 0.28
                         TPR_14  29 alaPddaeawllla 42 
                                    + +Pd+++a+++l 
  gi|119718927|ref|YP_919422.1| 257 SVDPDSEVARRYLS 270
                                    569*******9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (467 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 3006.58
//
Query:       gi|119718928|ref|YP_919423.1|  [L=219]
Description: adenylate kinases [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      6e-43  146.5   0.0      7e-43  146.3   0.0    1.0  1  ADK              Adenylate kinase
    1.6e-18   67.5   0.0    2.4e-18   66.8   0.0    1.2  1  AAA_17           AAA domain
    5.9e-14   51.8   5.4    9.5e-14   51.1   5.4    1.3  1  ADK_lid          Adenylate kinase, active site lid
    2.3e-05   24.8   1.7       0.01   16.3   0.1    2.4  2  Zn_ribbon_recom  Recombinase zinc beta ribbon domain
    7.3e-05   23.3   0.0    0.00014   22.4   0.0    1.5  1  AAA_18           AAA domain
    0.00028   21.2   0.0      0.033   14.5   0.1    2.2  2  Hydin_ADK        Hydin Adenylate kinase-like domain
     0.0038   16.6   1.7          2    8.0   0.3    2.4  2  zf-ribbon_3      zinc-ribbon domain
      0.006   16.6   0.0      0.009   16.0   0.0    1.2  1  HypA             Hydrogenase/urease nickel incorporation, met
      0.007   16.1   0.0      0.011   15.5   0.0    1.3  1  Cytidylate_kin   Cytidylate kinase
     0.0071   16.2   1.2        4.9    7.2   0.1    2.7  2  Nudix_N_2        Nudix N-terminal
     0.0072   16.9   0.6      0.012   16.2   0.0    1.7  1  Trm112p          Trm112p-like protein
      0.008   16.2   0.2      0.014   15.4   0.2    1.3  1  DZR              Double zinc ribbon
     0.0086   15.6   1.2      0.019   14.5   1.2    1.6  1  TF_Zn_Ribbon     TFIIB zinc-binding
  ------ inclusion threshold ------
      0.016   15.4   0.8          2    8.7   0.1    2.5  2  Auto_anti-p27    Sjogren's syndrome/scleroderma autoantigen 1
      0.016   15.3   0.6      0.032   14.3   0.6    1.5  1  Zn-ribbon_8      Zinc ribbon domain
      0.018   15.2   0.1      0.055   13.6   0.0    1.9  1  AAA_33           AAA domain
      0.025   14.2   3.4        1.1    9.0   0.3    2.3  2  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
      0.044   14.0   0.0      0.064   13.5   0.0    1.3  1  AAA_28           AAA domain
      0.059   13.2   1.0        1.4    8.8   0.1    2.3  2  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger
       0.14   12.8   1.7        9.4    7.0   0.1    2.3  2  zf-ISL3          zinc-finger of transposase IS204/IS1001/IS10
       0.18   12.2   0.0       0.27   11.7   0.0    1.3  1  AAA              ATPase family associated with various cellul
       0.21   11.5   1.3       0.58   10.1   1.3    1.7  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
       0.22   11.3   4.0       0.94    9.3   0.4    2.2  2  zinc_ribbon_2    zinc-ribbon domain
        5.9    7.0   8.0       0.55   10.2   1.9    2.3  2  DUF1610          Domain of unknown function (DUF1610)


Domain annotation for each model (and alignments):
>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.3   0.0   9.4e-46     7e-43       1     150 [.       8     188 ..       8     189 .. 0.98

  Alignments for each domain:
  == domain 1  score: 146.3 bits;  conditional E-value: 9.4e-46
                                    EEESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHHCT-HHHHHHHHHHHTTSS--HHHHHHHHHHHHHCHGTTTEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            ADK   1 llGaPgaGKGtqaeklvkkyglahlstGdllRaevksgtelGkeakevmdkgelvpdevvvklvkeelekedkkkgfllD 80 
                                    +lG+PgaGKGt a+++++ +g++h+stG+llR+e+++g+elG+++++++ +g lvpd+vv++lv ++l++ d++kgf+lD
  gi|119718928|ref|YP_919423.1|   8 ILGPPGAGKGTYASEVARFFGVPHVSTGELLRQEIRKGSELGRRVATYVSRGLLVPDDVVNELVGSRLSQGDCAKGFVLD 87 
                                    79****************************************************************************** PP

                                    SB-SSHHHHHHHHHHHHHHTSEESEEEEEE--HHHHHHHHHT....................................GS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................................xx RF
                            ADK  81 GfPRtveqaealeelleeekvkldlvleldvpeevlveRltg....................................Dn 124
                                    G+PRt++qa  le+     ++ ld  + l+v+ +v veRl+g                                    D 
  gi|119718928|ref|YP_919423.1|  88 GYPRTLQQALFLEK-----HYPLDKAVLLSVSLKVAVERLSGrlycpncgetyhvswkpprkpgvcdncgsrlvrrrdDD 162
                                    *************9.....8999********************************************************* PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            ADK 125 eetvkkRletykkqtkplidyykkkg 150
                                    +e v++R+++y + t p++d+y++kg
  gi|119718928|ref|YP_919423.1| 163 PEVVEARFREYWRLTLPVVDFYREKG 188
                                    ***********************987 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.8   0.0   3.3e-21   2.4e-18       1     120 [.       9     123 ..       9     126 .. 0.89

  Alignments for each domain:
  == domain 1  score: 66.8 bits;  conditional E-value: 3.3e-21
                                    EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTT.TS.HSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEEEEE CS
                         AAA_17   1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrg.gl.akardemrklpleekkelqkeaaekiaeeakkkgvlvdg 78 
                                    lG+PG+GKgt+++++++ +g++h+s+G+llr+e+++g +l  +   +++++ l++++ + +++  ++ + ++ kg+++dg
  gi|119718928|ref|YP_919423.1|   9 LGPPGAGKGTYASEVARFFGVPHVSTGELLRQEIRKGsELgRRVATYVSRGLLVPDDVVNELVGSRLSQGDCAKGFVLDG 88 
                                    7*********************************999556456678999******************************* PP

                                    -SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHH CS
                         AAA_17  79 hprikeqagfldglpkevleelkpdaiilleadpeeilerrl 120
                                    +pr+ +qa fl+       + +  d+ +ll+++ ++ +er+ 
  gi|119718928|ref|YP_919423.1|  89 YPRTLQQALFLE-------KHYPLDKAVLLSVSLKVAVERLS 123
                                    ****99988765.......34556999999999999988875 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.1   5.4   1.3e-16   9.5e-14       1      36 []     125     160 ..     125     160 .. 0.96

  Alignments for each domain:
  == domain 1  score: 51.1 bits;  conditional E-value: 1.3e-16
                                    EEE-TTT--EEETTTB--SSTTB-TTT--.-B--GG CS
                        ADK_lid   1 RrvCpkCGrsYhvvfnpPkveglCDkCGepLvqRsD 36 
                                    R+ Cp+CG++Yhv  +pP+++g+CD+CG+ Lv+R D
  gi|119718928|ref|YP_919423.1| 125 RLYCPNCGETYHVSWKPPRKPGVCDNCGSRLVRRRD 160
                                    899*********888*******************99 PP

>> Zn_ribbon_recom  Recombinase zinc beta ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   1.4e-05      0.01       2      21 ..     122     141 ..     121     146 .. 0.86
   2 !    7.5   0.2    0.0077       5.8       7      21 ..     147     161 ..     146     177 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.4e-05
                Zn_ribbon_recom   2 LsGllrCgeCGspmtrrkrk 21 
                                    LsG l+C +CG +++++++ 
  gi|119718928|ref|YP_919423.1| 122 LSGRLYCPNCGETYHVSWKP 141
                                    9**************98765 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0077
                Zn_ribbon_recom   7 rCgeCGspmtrrkrk 21 
                                    +C +CGs+++rr+  
  gi|119718928|ref|YP_919423.1| 147 VCDNCGSRLVRRRDD 161
                                    7**********9854 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   1.9e-07   0.00014       3     117 ..       8     129 ..       6     134 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.9e-07
                         AAA_18   3 ltGtpGvGKttlakeLskrlgf.....gvnlrdvakenglllevdpealdeskrldedkldklldaleenssaleegknl 77 
                                    + G+pG+GK t a e+++  g+     g+ lr+ ++++  l  + +  +++ + + +d++++l+     + +    +k  
  gi|119718928|ref|YP_919423.1|   8 ILGPPGAGKGTYASEVARFFGVphvstGELLRQEIRKGSELGRRVATYVSRGLLVPDDVVNELVGSRLSQGD---CAKGF 84 
                                    89**************99778898888888888888866666555557888888888888887766666543...56889 PP

                         AAA_18  78 vidghlaeleseaakdikk.....vvLtaspeelleRlekRgyee 117
                                    v+dg +  l ++ + ++++     v L +s ++  eRl+ R y +
  gi|119718928|ref|YP_919423.1|  85 VLDGYPRTLQQALFLEKHYpldkaVLLSVSLKVAVERLSGRLYCP 129
                                    *****************************************9876 PP

>> Hydin_ADK  Hydin Adenylate kinase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.043        32       4      38 ..       8      42 ..       5      54 .. 0.83
   2 !   14.5   0.1   4.4e-05     0.033     169     197 ..      60      88 ..      56      89 .. 0.94

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.043
                      Hydin_ADK  4 vhGaPlsGKtatavtLakkYeaAlltiDsvvleAi 38
                                   + G+P +GK + a  +a+ ++   ++  +++ + i
  gi|119718928|ref|YP_919423.1|  8 ILGPPGAGKGTYASEVARFFGVPHVSTGELLRQEI 42
                                   67*******************99998877776666 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 4.4e-05
                      Hydin_ADK 169 cvLPedllveIlsERlqlndCyrGvvfDg 197
                                    ++ P+d++ e++  Rl   dC +G v+Dg
  gi|119718928|ref|YP_919423.1|  60 LLVPDDVVNELVGSRLSQGDCAKGFVLDG 88 
                                    578*************************9 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.3    0.0026         2       4      10 ..     127     133 ..     126     135 .. 0.82
   2 !    7.4   0.0     0.004         3       5      15 ..     148     159 ..     147     161 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0026
                    zf-ribbon_3   4 rCPnCGa 10 
                                    +CPnCG+
  gi|119718928|ref|YP_919423.1| 127 YCPNCGE 133
                                    7999986 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.004
                    zf-ribbon_3   5 CPnCGa.plssd 15 
                                    C nCG+ +++ +
  gi|119718928|ref|YP_919423.1| 148 CDNCGSrLVRRR 159
                                    777777666655 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.2e-05     0.009      60      98 ..     115     157 ..      88     167 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.2e-05
                                    -EEEEEEE--EEEETTTS-EEECHHHHH.....S-TTTSSS-EE CS
                           HypA  60 aeLeieevpvkvrCreCgkefeleekal.....rCpkCgsadve 98 
                                     ++++e+ + +++C +Cg++++++ k        C +Cgs+ v+
  gi|119718928|ref|YP_919423.1| 115 LKVAVERLSGRLYCPNCGETYHVSWK-PprkpgVCDNCGSRLVR 157
                                    345599**************997653.1233559*****98665 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.5e-05     0.011       1      35 [.       6      40 ..       6      43 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.5e-05
                                   EEEE-STTSSHHHHHHHHHHHHT-EEEEHHHHHHH CS
                 Cytidylate_kin  1 iaiDGPagsGKssvaralaeklglkyldtgalYRa 35
                                   ++i GP g+GK++ a ++a+ +g+  ++tg+l R+
  gi|119718928|ref|YP_919423.1|  6 VSILGPPGAGKGTYASEVARFFGVPHVSTGELLRQ 40
                                   5788***************************9986 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.1    0.0065       4.9       2       9 ..     127     134 ..     123     143 .. 0.74
   2 !    7.1   0.1    0.0067         5       3      16 ..     148     161 ..     147     165 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0065
                                    B-TTT--B CS
                      Nudix_N_2   2 FCsqCGtp 9  
                                    +C++CG++
  gi|119718928|ref|YP_919423.1| 127 YCPNCGET 134
                                    77777765 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0067
                                    -TTT--B-EEE--T CS
                      Nudix_N_2   3 CsqCGtpvelripd 16 
                                    C +CG+++ +r  d
  gi|119718928|ref|YP_919423.1| 148 CDNCGSRLVRRRDD 161
                                    99*****9999854 PP

>> Trm112p  Trm112p-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.6e-05     0.012      41      65 ..     108     137 ..      79     138 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.6e-05
                                    S.....CHHTTEECCCCEEEETTTTEEEEE CS
                        Trm112p  41 y.....ellleldieegeLvCpncgraYpI 65 
                                    +     +l + +++++g L+Cpncg +Y +
  gi|119718928|ref|YP_919423.1| 108 AvllsvSLKVAVERLSGRLYCPNCGETYHV 137
                                    2555555667789999************87 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.2   1.9e-05     0.014      12      37 ..     125     154 ..     119     160 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.9e-05
                            DZR  12 arfCseCgtk....lkavaa....edrCpsCgek 37 
                                      +C++Cg++         +    + +C++Cg+ 
  gi|119718928|ref|YP_919423.1| 125 RLYCPNCGETyhvsW----KpprkPGVCDNCGSR 154
                                    569999999955443....244459999999987 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   1.2   2.6e-05     0.019       2      27 ..     127     153 ..     126     162 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.6e-05
                                    EETTTTCEE.CHEETSTTCEEESSSSB CS
                   TF_Zn_Ribbon   2 kCPnCgstn.lveDpergelvCtdCGl 27 
                                     CPnCg t+ + + p r   vC +CG+
  gi|119718928|ref|YP_919423.1| 127 YCPNCGETYhVSWKPPRKPGVCDNCGS 153
                                    6********9****************7 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1     0.045        34      32      40 .]     124     132 ..     118     132 .. 0.79
   2 ?    8.7   0.1    0.0026         2      17      30 ..     147     161 ..     146     166 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.045
                  Auto_anti-p27  32 gkvyCvaCd 40 
                                    g++yC++C+
  gi|119718928|ref|YP_919423.1| 124 GRLYCPNCG 132
                                    788999996 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0026
                  Auto_anti-p27  17 tCpvCgvPLmrdr.k 30 
                                    +C++Cg+ L+r r +
  gi|119718928|ref|YP_919423.1| 147 VCDNCGSRLVRRRdD 161
                                    6**********9954 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.6   4.3e-05     0.032       7      38 ..     127     158 ..     125     159 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.3e-05
                    Zn-ribbon_8   7 rCeeCghefevlqsisdaplta.CPeCgs.evrr 38 
                                     C +Cg+++ v  +     ++  C +Cgs  vrr
  gi|119718928|ref|YP_919423.1| 127 YCPNCGETYHVSWKPP--RKPGvCDNCGSrLVRR 158
                                    5*****9999555433..35556******55555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   7.4e-05     0.055       4      70 ..       8      78 ..       6     127 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.4e-05
                         AAA_33  4 lvGlpGsGKstlaerllkklgavllssdtlrr.rlfg...tdqqsktdytrvldrlyqilnelarkalsag 70
                                   + G+pG+GK t+a ++++  g+ ++s+ +l+r  +++    +++  t+ +r l    + +nel+ ++ls+g
  gi|119718928|ref|YP_919423.1|  8 ILGPPGAGKGTYASEVARFFGVPHVSTGELLRqEIRKgseLGRRVATYVSRGLLVPDDVVNELVGSRLSQG 78
                                   57****************99999999988776444445545555566666655556666677777777766 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.2     0.014        11      20      28 ..     124     132 ..     120     135 .. 0.88
   2 ?    9.0   0.3    0.0015       1.1       5      19 ..     146     161 ..     143     161 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.014
                        zf-RRN7  20 GfyyCrrCh 28 
                                    G+ yC +C+
  gi|119718928|ref|YP_919423.1| 124 GRLYCPNCG 132
                                    99******9 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0015
                        zf-RRN7   5 ppCgvCgcrsftl.dd 19 
                                     +C+ Cg+r+++  dd
  gi|119718928|ref|YP_919423.1| 146 GVCDNCGSRLVRRrDD 161
                                    69********999887 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   8.5e-05     0.064       1      59 [.       5      66 ..       5     103 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.5e-05
                         AAA_28  1 kivitGgestGKTtlleaLaar.gypvv..pEaareileeklakgedalpwvedllafaerv 59
                                   ++ i+G++++GK t +++ a+  g+p+v   E  r+ ++++++ g++ + +v + l + + v
  gi|119718928|ref|YP_919423.1|  5 RVSILGPPGAGKGTYASEVARFfGVPHVstGELLRQEIRKGSELGRRVATYVSRGLLVPDDV 66
                                   688******************88***99999****999999999888777776665555555 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1      0.14   1.1e+02       3       9 ..     127     133 ..     126     137 .. 0.84
   2 ?    8.8   0.1    0.0018       1.4       3      15 ..     147     159 ..     145     162 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.14
                                    E-SSS-- CS
                 zf-C4_Topoisom   3 kCPkCgg 9  
                                     CP Cg+
  gi|119718928|ref|YP_919423.1| 127 YCPNCGE 133
                                    5****96 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0018
                                    E-SSS--EEEEEE CS
                 zf-C4_Topoisom   3 kCPkCggdLvlkr 15 
                                     C+ Cg+ Lv++r
  gi|119718928|ref|YP_919423.1| 147 VCDNCGSRLVRRR 159
                                    7**********98 PP

>> zf-ISL3  zinc-finger of transposase IS204/IS1001/IS1096/IS1165
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1     0.054        40       5      11 ..     128     134 ..     125     141 .. 0.82
   2 ?    7.0   0.1     0.013       9.4       2      17 ..     145     160 ..     144     175 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.054
                        zf-ISL3   5 CPnCgsk 11 
                                    CPnCg++
  gi|119718928|ref|YP_919423.1| 128 CPNCGET 134
                                    *****98 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.013
                        zf-ISL3   2 phrCPnCgsktvvkhg 17 
                                    p +C nCgs+ v++++
  gi|119718928|ref|YP_919423.1| 145 PGVCDNCGSRLVRRRD 160
                                    889*******554443 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00036      0.27       3      28 ..       8      33 ..       6      66 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00036
                                   EESSTTSSHHHHHHHHHHHHTHEEEE CS
                            AAA  3 lyGppGtGKTllakavakelgvefle 28
                                   + GppG GK + a+ va+ +gv+ ++
  gi|119718928|ref|YP_919423.1|  8 ILGPPGAGKGTYASEVARFFGVPHVS 33
                                   68****************98876543 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   1.3   0.00078      0.58      30      56 ..     127     155 ..     107     161 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00078
                 OrfB_Zn_ribbon  30 tCseCgsknke..alsgrtfkCpnCgfea 56 
                                     C++Cg++     ++ ++  +C+nCg ++
  gi|119718928|ref|YP_919423.1| 127 YCPNCGETYHVswKPPRKPGVCDNCGSRL 155
                                    599**9998888999999999***99875 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.4    0.0013      0.94       1       7 [.     127     133 ..     125     136 .. 0.75
   2 ?    2.8   0.2      0.14     1e+02      16      22 ..     148     154 ..     144     155 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0013
                  zinc_ribbon_2   1 fCpnCGa 7  
                                    +CpnCG+
  gi|119718928|ref|YP_919423.1| 127 YCPNCGE 133
                                    6777776 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.14
                  zinc_ribbon_2  16 CpyCGtp 22 
                                    C +CG+ 
  gi|119718928|ref|YP_919423.1| 148 CDNCGSR 154
                                    6666654 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.9   0.00074      0.55      18      24 .]     127     133 ..     126     133 .. 0.94
   2 ?   -1.1   0.5       2.5   1.9e+03      19      23 ..     148     152 ..     147     153 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00074
                        DUF1610  18 pCPNCGE 24 
                                    +CPNCGE
  gi|119718928|ref|YP_919423.1| 127 YCPNCGE 133
                                    7*****9 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.5
                        DUF1610  19 CPNCG 23 
                                    C NCG
  gi|119718928|ref|YP_919423.1| 148 CDNCG 152
                                    77**9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                       125  (0.00697194); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1354.63
//
Query:       gi|119718929|ref|YP_919424.1|  [L=166]
Description: hypothetical protein Tpen_0011 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1058.41
//
Query:       gi|119718930|ref|YP_919425.1|  [L=160]
Description: hypothetical protein Tpen_0012 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.7e-23   82.8   0.0    3.6e-23   82.3   0.0    1.2  1  AAA_assoc_C  C-terminal AAA-associated domain


Domain annotation for each model (and alignments):
>> AAA_assoc_C  C-terminal AAA-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.3   0.0     2e-27   3.6e-23       2     119 .]      38     151 ..      37     151 .. 0.97

  Alignments for each domain:
  == domain 1  score: 82.3 bits;  conditional E-value: 2e-27
                    AAA_assoc_C   2 eLaeelelevddLlpiveaaelLglveveegdielTelGrkfveadikerKeifreqllklvplaaairrvLderenkrl 81 
                                    +++++++ +++ L +++++ae Lgl+++++g+++lTelG++++++d k  K+++r+++++++pla++ +++   +e+kr+
  gi|119718930|ref|YP_919425.1|  38 YVGDAVHENIQVLPKAIDVAEALGLIKTHKGNLQLTELGKRVARSDPKSIKKLLRNAISNIEPLAEIASTL---KEKKRM 114
                                    5789999*************************************************************997...99**** PP

                    AAA_assoc_C  82 peerfldeLeeklseeeaertletaieWgrYaelfeyd 119
                                    + e+f  ++ ++++  ++e++ + ++ Wg++ +lf +d
  gi|119718930|ref|YP_919425.1| 115 TVEEFDAIIGKYYP-GNVEEARKNVLIWGAFLHLFVMD 151
                                    *************9.99******************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       742  (0.0413855); expected 358.6 (0.02)
Passed bias filter:                      673  (0.037537); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1206.43
//
Query:       gi|119718931|ref|YP_919426.1|  [L=497]
Description: binding-protein-dependent transport systems inner membrane component [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-25   90.4  44.5    8.1e-15   55.0  13.6    2.8  3  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
       0.23   10.5   4.3       0.66    9.0   4.3    1.8  1  FUSC-like     FUSC-like inner membrane protein yccS


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.4  17.2   8.3e-16   7.4e-12       2     168 ..      27     196 ..      26     203 .. 0.86
   2 ?    1.9   1.6     0.018   1.6e+02     113     180 ..     250     316 ..     244     321 .. 0.63
   3 !   55.0  13.6     9e-19   8.1e-15       2     173 ..     306     479 ..     305     482 .. 0.81

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 8.3e-16
                   BPD_transp_1   2 illGilaalnrnkkldkllrpliivllslPsfvlaillvlvf.vilsilghlilp.viillllsaapyvrlirraalrsl 79 
                                    ++lG+l+a  rnk++  +++p+ ++l+s+P++ +++  +++f + +     ++ + +++l+++s+++ +++ ++a ++sl
  gi|119718931|ref|YP_919426.1|  27 LVLGSLMA--RNKVVESIMLPVLDILQSIPILGFFPAALAMFiA-NLPRALGVEAaAVFLIVTSLVWNMIFGVYASIKSL 103
                                    79******..***************************9999954.44444556665999999999*************** PP

                   BPD_transp_1  80 pkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG......lgtllleailgydysei 153
                                    + +    ar++ ++   +f+++ +P++   +++  +++++g +   +++e ++ +        +g +++e+++  dy++ 
  gi|119718931|ref|YP_919426.1| 104 EPSVFDMARVYSLGAVSRFFYIYVPASRAALLANSLISWAGGWFFLTAAEVITLGEEeykltgIGAFIMESYNRGDYASF 183
                                    ****************************************************97766889999***************77 PP

                   BPD_transp_1 154 snggvlalviavlll 168
                                    +  + +a+++a++  
  gi|119718931|ref|YP_919426.1| 184 Y--IGVAALFATIMA 196
                                    7..333333333332 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.018
                   BPD_transp_1 113 glilafggllggavlleflgswpG.lgtllleailgydyseisnggvlalviavlllnlvadilqrlld 180
                                    g++ +++g+    v+l +lgs+ + l +l +     + ++e    ++la v +vl+++lv+ +l ++l 
  gi|119718931|ref|YP_919426.1| 250 GFVPRVVGATLLVVALFYLGSGVAgLLSLDVVGVAKSFLHELP--LSLARVSIVLVFSLVLSLLIAYLT 316
                                    5555555555555555555544434444444445555555555..899999999999999999998885 PP

  == domain 3  score: 55.0 bits;  conditional E-value: 9e-19
                   BPD_transp_1   2 illGilaa..lnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilp.viillllsaapyvrlir.raalr 77 
                                    ++l++l+a  +++ ++   l+    ++l s+P +++++ll +v      + ++ l  ++++ll ++++y ++++   +l 
  gi|119718931|ref|YP_919426.1| 306 LVLSLLIAylTYSFRRAAMLIGASGELLASVPAIIWWPLLGYV---ALTFSWGPLVvLFTVLLQGSLWYLYFNIlVFGLG 382
                                    678899999999*****************************85...4445555555333344444555555544156899 PP

                   BPD_transp_1  78 slpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis... 154
                                    s+ k+++e+a ++G++ w+ fr + +P+++p+++tg++ ++gg++++++++e+++    lg+++++      + + +   
  gi|119718931|ref|YP_919426.1| 383 SIRKEHEELAAVYGVKGWHFFRSIFFPSVFPSLLTGALSSWGGAWNATIAAEYVT----LGQRTIDLGGVGALLNRYtve 458
                                    *******************************************************....999988876655555555678 PP

                   BPD_transp_1 155 ..nggvlalviavlllnlvad 173
                                      +g ++ +++++ l+++++d
  gi|119718931|ref|YP_919426.1| 459 geAGKTALAALFLSLVIVAVD 479
                                    888888888888888888776 PP

>> FUSC-like  FUSC-like inner membrane protein yccS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   4.3   7.3e-05      0.66      74     109 ..     360     395 ..     292     399 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 7.3e-05
                      FUSC-like  74 qplllllGalwYgllsllwsllfpnrpvqqsLaelf 109
                                      ++ll G+lwY+++++l++ l + r +++ La ++
  gi|119718931|ref|YP_919426.1| 360 LFTVLLQGSLWYLYFNILVFGLGSIRKEHEELAAVY 395
                                    4567999**************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (497 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       785  (0.0437838); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 3167.83
//
Query:       gi|119718932|ref|YP_919427.1|  [L=245]
Description: ABC transporter related [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-28  100.0   0.0    2.3e-28   99.4   0.0    1.3  1  ABC_tran     ABC transporter
    1.5e-07   31.5   0.5    0.00083   19.3   0.1    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    0.00019   21.9   0.0    0.00024   21.5   0.0    1.3  1  AAA_16       AAA ATPase domain
    0.00057   19.8   0.0    0.00099   19.0   0.0    1.4  1  RsgA_GTPase  RsgA GTPase
    0.00072   20.0   0.0     0.0042   17.5   0.0    2.1  1  AAA          ATPase family associated with various cellular a
     0.0012   19.4   0.2     0.0018   18.9   0.2    1.2  1  AAA_23       AAA domain
     0.0025   18.1   0.0     0.0044   17.3   0.0    1.6  1  AAA_22       AAA domain
     0.0035   16.8   0.0       0.33   10.4   0.0    2.1  2  SMC_N        RecF/RecN/SMC N terminal domain
     0.0047   16.9   0.0     0.0083   16.1   0.0    1.4  1  ATPase_2     ATPase domain predominantly from Archaea
     0.0049   16.1   0.1      0.033   13.4   0.0    2.1  2  NB-ARC       NB-ARC domain
      0.008   16.1   0.0      0.017   15.1   0.0    1.5  1  NACHT        NACHT domain
  ------ inclusion threshold ------
      0.014   15.6   0.1      0.033   14.4   0.1    1.6  1  AAA_28       AAA domain
      0.017   15.0   0.0      0.037   14.0   0.0    1.5  1  Rad17        Rad17 P-loop domain
      0.026   14.3   0.0      0.049   13.4   0.0    1.4  1  AAA_29       P-loop containing region of AAA domain
      0.043   13.5   0.0       0.07   12.8   0.0    1.3  1  AAA_30       AAA domain
      0.058   13.4   0.0       0.16   12.0   0.0    1.7  2  AAA_14       AAA domain
      0.059   13.9   0.1       0.14   12.7   0.1    1.6  1  AAA_18       AAA domain
       0.19   11.8   0.0       0.47   10.5   0.0    1.6  1  MMR_HSR1     50S ribosome-binding GTPase
       0.19   12.1   0.1       0.62   10.4   0.0    1.8  2  AAA_19       AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.4   0.0   2.5e-31   2.3e-28       1     136 [.      24     157 ..      24     158 .. 0.94

  Alignments for each domain:
  == domain 1  score: 99.4 bits;  conditional E-value: 2.5e-31
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren. 79 
                                    l+++s+++ e e vai+G++G+GK+tLl+++agl+k ++Gei             + +++ig+++q p+l p ltv en 
  gi|119718932|ref|YP_919427.1|  24 LDHISFDVGE-EFVAILGPSGCGKTTLLRIIAGLEKADSGEIV----------FARGDSRIGFIFQSPTLLPWLTVLENv 92 
                                    5677777764.89*****************************4..........458899********************* PP

                                    ............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    ............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                e++e++ k++s +gl+ +++       ++LSgG+kqrv +aral+ +p lll+DEp+
  gi|119718932|ref|YP_919427.1|  93 alplrangvprrEAEEKARKYISLVGLQAFENFYP----HELSGGMKQRVNIARALAVEPVLLLMDEPF 157
                                    ***********999999************999998....*****************************7 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1   8.8e-07   0.00083       1      31 [.      35      69 ..      35      97 .. 0.69
   2 !   10.5   0.0   0.00041      0.39     231     298 ..     124     192 ..     120     195 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 8.8e-07
                         AAA_21  1 lnvliGpNgsGKSnLLdaldllarl....drdveg 31
                                   + ++ Gp g+GK++LL+++ +l  +    +  ++g
  gi|119718932|ref|YP_919427.1| 35 FVAILGPSGCGKTTLLRIIAGLEKAdsgeIVFARG 69
                                   679****************9996444433333333 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00041
                         AAA_21 231 elparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrll.ell.....kelsrngaQviltTHS 298
                                    ++ ++elS G+k+   ++ al+  +    lll DEp + L+P   ++l  e+l       ++     +i++TH+
  gi|119718932|ref|YP_919427.1| 124 NFYPHELSGGMKQRVNIARALAVEP---VLLLMDEPFSQLDPLTAESLRsEILdmwmwGVTTV--RAIIMVTHN 192
                                    67899*********9*******999...68************877777755555556733333..467888886 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   2.6e-07   0.00024      24      88 ..      33     100 ..      23     200 .. 0.61

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2.6e-07
                         AAA_16  24 pelvllsGesGvGKsslvrellralekd...ggiflrgkcdql..esaipysalaqalareellrqllde 88 
                                    +e v + G+sG+GK++l+r ++  lek+   +++f+rg+ +     ++ ++++++++l++   l   ++ 
  gi|119718932|ref|YP_919427.1|  33 EEFVAILGPSGCGKTTLLRIIA-GLEKAdsgEIVFARGDSRIGfiFQSPTLLPWLTVLEN-VALPLRANG 100
                                    4899****************99.5776656446666665554433222333466666633.444444444 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0     1e-06   0.00099      85     130 ..      19      64 ..       3      72 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1e-06
                                    TTHTTHHHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT-----S-- CS
                    RsgA_GTPase  85 ktkegleelkellkdktsvlvGqSGvGKStLinallpelelktgev 130
                                    kt   l++++  + +++++++G+SG GK+tL+  +++ +++  ge+
  gi|119718932|ref|YP_919427.1|  19 KTLPVLDHISFDVGEEFVAILGPSGCGKTTLLRIIAGLEKADSGEI 64 
                                    55566889999999*********************99888888877 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   4.4e-06    0.0042       3      66 ..      38     155 ..      36     196 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.4e-06
                                    EESSTTSSHHHHHHHHHHHHTHE....................................................EEEEE CS
                            AAA   3 lyGppGtGKTllakavakelgve....................................................fleis 30 
                                    + Gp G+GKT+l + +a   +++                                                    ++++ 
  gi|119718932|ref|YP_919427.1|  38 ILGPSGCGKTTLLRIIAGLEKADsgeivfargdsrigfifqsptllpwltvlenvalplrangvprreaeekarkYISLV 117
                                    78***************985544444444455555555555666666666666666666666666666666666655555 PP

                                    TTTCS.SSSTTHHHHHHHHHHHHHHHTS.TSEEEEEET CS
                            AAA  31 gsell.skyvgesekkirelfkeakeka.kpsilfiDE 66 
                                    g + + + y  e +  +++ ++ a++ a +p+ l++DE
  gi|119718932|ref|YP_919427.1| 118 GLQAFeNFYPHELSGGMKQRVNIARALAvEPVLLLMDE 155
                                    55555344888888888888888888888888888888 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.2   1.9e-06    0.0018      13      39 ..      27      53 ..       5      56 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.9e-06
                         AAA_23 13 qeidFskgltlItGpNGaGKTTildAi 39
                                    ++d +  +++I Gp G+GKTT+l+ i
  gi|119718932|ref|YP_919427.1| 27 ISFDVGEEFVAILGPSGCGKTTLLRII 53
                                   34455999****************987 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   4.6e-06    0.0044       5      64 ..      33      96 ..      30     196 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.6e-06
                         AAA_22  5 agilvvtGesGtGKTtllrrlleqldeeakaee......erpevvfvtlpsst..sskdllrellral 64
                                   + ++++ G+sG+GKTtllr ++   +++           ++++ + +  +s+t   + ++l++++  l
  gi|119718932|ref|YP_919427.1| 33 EEFVAILGPSGCGKTTLLRIIAGLEKAD----SgeivfaRGDSRIGFIFQSPTllPWLTVLENVALPL 96
                                   67899**************998876322....223467766666666666666445555555554444 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0   0.00035      0.33      17      42 ..      26      51 ..      11      58 .. 0.88
   2 ?    4.5   0.0     0.022        20     130     177 ..     123     166 ..     103     210 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00035
                                   EEEEETTSSEEEEEESTTSSHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 17 tvilpfsksftaivGpNGSGKsnlld 42
                                   +++ ++ ++f ai+Gp G+GK+ ll 
  gi|119718932|ref|YP_919427.1| 26 HISFDVGEEFVAILGPSGCGKTTLLR 51
                                   67788999**************9986 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.022
                                    TT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 130 agiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvk 177
                                    +++++++LSgG k+ v +a  +A++ v    l l+De  ++LD    +
  gi|119718932|ref|YP_919427.1| 123 ENFYPHELSGGMKQRVNIARALAVEPV----LLLMDEPFSQLDPLTAE 166
                                    6788999*************9997643....66777777777765544 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   8.8e-06    0.0083      20      53 ..      33      66 ..      19      72 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 8.8e-06
                       ATPase_2 20 neiyfiYGpegsGKtaLlkeiienledkdkyviy 53
                                   +e++ i Gp g+GKt+Ll+ i+   +  + ++++
  gi|119718932|ref|YP_919427.1| 33 EEFVAILGPSGCGKTTLLRIIAGLEKADSGEIVF 66
                                   67899*************9988777666656666 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   3.5e-05     0.033      17      40 ..      30      53 ..      19      61 .. 0.84
   2 ?   -0.0   0.1      0.43     4e+02     133     148 ..     203     218 ..     181     225 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.5e-05
                                   TSCSEEEEEEESTTSSHHHHHHHH CS
                         NB-ARC 17 elqslvvalvGmgGvGKttlakqi 40
                                   +++  +va+ G  G+GKttl++ i
  gi|119718932|ref|YP_919427.1| 30 DVGEEFVAILGPSGCGKTTLLRII 53
                                   67788***************9866 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.43
                                    EEEEEESBCCCCCCS- CS
                         NB-ARC 133 rvllTTRdeevanavs 148
                                     ++lTTR  ++a++v+
  gi|119718932|ref|YP_919427.1| 203 IIVLTTRPAKIAGIVH 218
                                    5899*******99886 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.8e-05     0.017       3      21 ..      36      54 ..      34      66 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.8e-05
                                   EEEEC-TTTCHHHHHHHHH CS
                          NACHT  3 vilqGeaGsGKTtLlqkla 21
                                   v++ G++G+GKTtLl+ +a
  gi|119718932|ref|YP_919427.1| 36 VAILGPSGCGKTTLLRIIA 54
                                   89*************9887 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   3.5e-05     0.033       2      20 ..      36      54 ..      35      68 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.5e-05
                         AAA_28  2 ivitGgestGKTtlleaLa 20
                                   ++i+G++++GKTtll+ +a
  gi|119718932|ref|YP_919427.1| 36 VAILGPSGCGKTTLLRIIA 54
                                   89*************9887 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   3.9e-05     0.037      48      66 ..      36      54 ..      24      63 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.9e-05
                          Rad17 48 LLisGPsGCgkstvvkvLs 66
                                   + i GPsGCgk+t +++++
  gi|119718932|ref|YP_919427.1| 36 VAILGPSGCGKTTLLRIIA 54
                                   5689************987 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   5.2e-05     0.049      17      39 ..      27      50 ..      23      56 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.2e-05
                         AAA_29 17 ieidlkg.atlltGpsGsGKSTll 39
                                   i++d+ + ++ + GpsG GK+Tll
  gi|119718932|ref|YP_919427.1| 27 ISFDVGEeFVAILGPSGCGKTTLL 50
                                   6677777799*************8 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   7.5e-05      0.07      18      50 ..      33      65 ..      28      72 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.5e-05
                         AAA_30 18 drvavltGpAGtGKttalkalreaweaaggrvi 50
                                   + ++++ Gp G GKtt+l+ ++ + +a+ g+++
  gi|119718932|ref|YP_919427.1| 33 EEFVAILGPSGCGKTTLLRIIAGLEKADSGEIV 65
                                   458899***************999998865655 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00016      0.16       3      35 ..      34      66 ..      32      84 .. 0.79
   2 ?   -3.1   0.0       7.8   7.4e+03      32      57 ..     215     240 ..     206     244 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00016
                         AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesily 35
                                   + ++i G+  +GKTtll+ ++  + +++ +i++
  gi|119718932|ref|YP_919427.1| 34 EFVAILGPSGCGKTTLLRIIAGLEKADSGEIVF 66
                                   5789************98877555566666665 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 7.8
                         AAA_14  32 silyinldderdkkladpekllelil 57 
                                     i+ ++l ++rd+++ +++k+++ + 
  gi|119718932|ref|YP_919427.1| 215 GIVHVDLPRPRDRRSPEFQKVEDQVY 240
                                    57778888888877777766655554 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   0.00014      0.14       1      22 [.      36      57 ..      36      79 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00014
                         AAA_18  1 IlltGtpGvGKttlakeLskrl 22
                                   +++ G++G+GKttl + ++ ++
  gi|119718932|ref|YP_919427.1| 36 VAILGPSGCGKTTLLRIIAGLE 57
                                   689************9997554 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0    0.0005      0.47       2      28 ..      36      63 ..      35      76 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0005
                                   EEEEESTTSSHHHHHHHHHTS.TEEESS CS
                       MMR_HSR1  2 vaivGrpNvGKStLinaltge.kaivsd 28
                                   vai+G +  GK+tL++ + g  ka  ++
  gi|119718932|ref|YP_919427.1| 36 VAILGPSGCGKTTLLRIIAGLeKADSGE 63
                                   89**************999843665555 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00066      0.62       7      31 ..      30      54 ..      25      66 .. 0.80
   2 ?   -2.1   0.0       4.6   4.3e+03     102     121 ..     147     168 ..     128     184 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00066
                         AAA_19  7 alkekvllvtaGpGtGKTrvlkhiv 31
                                   ++ e+ ++++++ G+GKT++l+ i 
  gi|119718932|ref|YP_919427.1| 30 DVGEEFVAILGPSGCGKTTLLRIIA 54
                                   5678899************998664 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.6
                         AAA_19 102 eeellivDE.fqdvd.elqyrL 121
                                    e  ll+ DE f+++d  ++ +L
  gi|119718932|ref|YP_919427.1| 147 EPVLLLMDEpFSQLDpLTAESL 168
                                    3348888987888884444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1474.59
//
Query:       gi|119718933|ref|YP_919428.1|  [L=118]
Description: hypothetical protein Tpen_0015 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.1e-05   22.9   0.1    7.6e-05   22.4   0.1    1.3  1  Cupin_2       Cupin domain
  ------ inclusion threshold ------
      0.054   13.6   0.0      0.086   12.9   0.0    1.3  1  cNMP_binding  Cyclic nucleotide-binding domain
      0.066   12.5   0.0      0.078   12.2   0.0    1.1  1  DUF3274       Protein of unknown function (DUF3274)
      0.096   12.3   0.0       0.11   12.2   0.0    1.1  1  3-HAO         3-hydroxyanthranilic acid dioxygenase


Domain annotation for each model (and alignments):
>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.1   1.7e-08   7.6e-05      13      70 ..      41     100 ..      35     101 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.7e-08
                                    EECSSSEEEEEEEEESEEEEEECTE.....EEEEETTEEEEE-TT-EEEEEE-SSS-EEEEEE CS
                        Cupin_2  13 shrHpgedeffyVleGegeltvdge.....eveleaGdsvyfpagtpHrfrNtgdeparllvv 70 
                                     + H++  e+f+ leGe++l v +      ev++e+G +++++   +H+   +g    + lvv
  gi|119718933|ref|YP_919428.1|  41 LEKHDRP-ELFVLLEGEITLVVSEDgselrEVKMEPGKLYVVDE--WHNAYRPGGRRGVALVV 100
                                    5789999.*********9999875555899************98..78877777776666665 PP

>> cNMP_binding  Cyclic nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.9e-05     0.086       9      48 ..      39      76 ..      34      83 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.9e-05
                                   EEE-TTSB-SEEEEEEES-EEEEEEETTS.E.EEEEEE-TT CS
                   cNMP_binding  9 vifrqGdpadslyivlsGevrvyrlsedgke.vvlavlgpG 48
                                   +++++ d++ +l+++l+Ge+ ++ +sedg e + +  + pG
  gi|119718933|ref|YP_919428.1| 39 TVLEKHDRP-ELFVLLEGEITLV-VSEDGSElREV-KMEPG 76
                                   788899998.7***********9.*****883333.35555 PP

>> DUF3274  Protein of unknown function (DUF3274)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.7e-05     0.078       5      42 ..       1      38 [.       1      56 [. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.7e-05
                        DUF3274  5 ltvLeqkrFfqRiwtrrkRdgekvkiG.aaParvplrlk 42
                                   ++vL++ r +   wt+  R+++k ++G   P++  lr+ 
  gi|119718933|ref|YP_919428.1|  1 MKVLDA-RLYGERWTVAYRENDKWQVGiYIPENASLREV 38
                                   789999.99*999**************999*99999974 PP

>> 3-HAO  3-hydroxyanthranilic acid dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.4e-05      0.11      51     116 ..      44     110 ..      28     118 .] 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.4e-05
                                    -SS-EEEEEEES-EEEEEEETTC.CCEEEE-TTEEEEE-TT--EEEEE-..TT-EEEEEEE---TTS-E CS
                          3-HAO  51 eegeeffyqkkGdmvlkvldegk.ardivireGeifllParvphsPqrf..adsvGlvvererleteld 116
                                    ++ +e+f  ++G++ l v ++g+  r++ ++ G+++++     h   r      v lvve    ete  
  gi|119718933|ref|YP_919428.1|  44 HDRPELFVLLEGEITLVVSEDGSeLREVKMEPGKLYVVDEW--HNAYRPggRRGVALVVEAPGVETEYM 110
                                    4679***************9985269**********99765..44455400456888888888777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 809.48
//
Query:       gi|119718934|ref|YP_919429.1|  [L=258]
Description: hypothetical protein Tpen_0016 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       679  (0.0378716); expected 358.6 (0.02)
Passed bias filter:                      599  (0.0334096); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1806.20
//
Query:       gi|119718935|ref|YP_919430.1|  [L=143]
Description: nucleoside 2-deoxyribosyltransferase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-11   43.6   0.0    3.2e-11   43.4   0.0    1.1  1  Nuc_deoxyrib_tr  Nucleoside 2-deoxyribosyltransferase
  ------ inclusion threshold ------
      0.012   15.3   0.1       0.65    9.7   0.0    2.4  2  TFA2_Winged_2    TFA2 Winged helix domain 2
       0.12   12.6   0.2       0.46   10.8   0.0    2.1  2  DUF4129          Domain of unknown function (DUF4129)


Domain annotation for each model (and alignments):
>> Nuc_deoxyrib_tr  Nucleoside 2-deoxyribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.4   0.0   5.3e-15   3.2e-11       1     122 [.       3     115 ..       3     129 .. 0.81

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 5.3e-15
                                    EEEESGGGCSCCCHHHHHHHHHHHHTTTTEEE.-CCTT-TT....--SSHHHHHHHHHHHHHC-SEEEEE--SSSSSS-- CS
                Nuc_deoxyrib_tr   1 iYLAgplvFrpdakalaarlkallaengldgl.aPldneaelelpaeetaraiyeadialirqaDavianldpfrgpeaD 79 
                                    +YLA+p+   ++a a +++l ++l+e g+ +l  ++ +++ l+ ++  t r+++e+di+l+++aD+++a ++      + 
  gi|119718935|ref|YP_919430.1|   3 VYLAAPMRGDRSALANVKKLLQALEERGYVVLtKHVADDV-LDVEKGMTPREVFERDIRLLEEADVLVAEVSY-----PS 76 
                                    8******999******************966625555555.334788999***********************.....99 PP

                                    HHHHHHHHHHHHCT-EEEEE-S-GCGHHHHHTSSB.TTS.B-T CS
                Nuc_deoxyrib_tr  80 sGtafEvGyavalgkpvlayttdarelrervealrdadgllve 122
                                     G+ fE+ y++ +gkpv+a+   +r   e v+     +g++ e
  gi|119718935|ref|YP_919430.1|  77 LGVGFEIAYFLLRGKPVIALALRERL--ESVS--AMIRGITWE 115
                                    *******************9665554..3333..333444444 PP

>> TFA2_Winged_2  TFA2 Winged helix domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00011      0.65      27      59 ..      15      55 ..      13      56 .. 0.84
   2 ?    3.1   0.0     0.013        75      27      39 ..     121     133 ..     119     138 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00011
                  TFA2_Winged_2 27 swpdveealeeLeaegeilvlrt........kkdgqpkiVf 59
                                   +  +v++ l++Le++g + ++++        +k ++p+ Vf
  gi|119718935|ref|YP_919430.1| 15 ALANVKKLLQALEERGYVVLTKHvaddvldvEKGMTPREVF 55
                                   6789*****************99777766666888999888 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.013
                  TFA2_Winged_2  27 swpdveealeeLe 39 
                                    ++ dv+ea+e+L 
  gi|119718935|ref|YP_919430.1| 121 AYSDVDEAIEKLD 133
                                    699********96 PP

>> DUF4129  Domain of unknown function (DUF4129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.22   1.3e+03       5      14 ..      22      31 ..      20      35 .. 0.83
   2 ?   10.8   0.0   7.6e-05      0.46       4      29 ..      33      58 ..      31     103 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.22
                        DUF4129  5 llraLaergl 14
                                   ll+aL+erg+
  gi|119718935|ref|YP_919430.1| 22 LLQALEERGY 31
                                   899*****86 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 7.6e-05
                        DUF4129  4 allraLaergldrrpgeTprEyarrv 29
                                    l+++ a+ +ld   g+TprE+ +r 
  gi|119718935|ref|YP_919430.1| 33 VLTKHVADDVLDVEKGMTPREVFERD 58
                                   577889999*************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1025.02
//
Query:       gi|119718936|ref|YP_919431.1|  [L=170]
Description: AsnC family transcriptional regulator [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.3e-21   74.4   0.2    8.6e-21   73.7   0.2    1.4  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
    3.6e-14   52.1   2.3    5.3e-14   51.5   1.3    1.8  2  HTH_24          Winged helix-turn-helix DNA-binding
      2e-11   43.5   0.4    4.4e-11   42.4   0.4    1.6  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    1.2e-05   25.0   0.1    2.1e-05   24.2   0.1    1.4  1  HTH_IclR        IclR helix-turn-helix domain
     0.0012   18.7   0.1     0.0027   17.6   0.1    1.6  1  HTH_Crp_2       Crp-like helix-turn-helix domain
     0.0025   17.6   0.1     0.0071   16.2   0.1    1.8  1  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0037   17.2   0.1     0.0096   15.8   0.1    1.7  1  MarR            MarR family
     0.0071   16.4   0.1      0.012   15.6   0.1    1.4  1  HTH_20          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.045   14.3   0.1       0.12   12.9   0.1    1.7  1  HTH_27          Winged helix DNA-binding domain
       0.07   13.0   0.1       0.21   11.5   0.1    1.7  1  MarR_2          MarR family


Domain annotation for each model (and alignments):
>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.7   0.2   4.8e-24   8.6e-21       2      74 ..      70     142 ..      69     143 .. 0.94

  Alignments for each domain:
  == domain 1  score: 73.7 bits;  conditional E-value: 4.8e-24
                                    EEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEE CS
                 AsnC_trans_reg   2 lvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivle 74 
                                     +s ++++ ++ +++++++a++peV+e++ +tG++d+l+kv+v ++++l ++++++l++++gv++t ts+vle
  gi|119718936|ref|YP_919431.1|  70 FISFSRDRGLDQRKVAQEIAKIPEVQEVHIITGEWDILAKVRVGSVDELGDLVVNRLRNIEGVEKTYTSVVLE 142
                                    577776668899************************************************************8 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.5   1.3     3e-17   5.3e-14       2      48 .]       4      50 ..       3      50 .. 0.98
   2 ?   -1.9   0.0       1.4   2.5e+03      14      27 ..      75      88 ..      73      89 .. 0.82

  Alignments for each domain:
  == domain 1  score: 51.5 bits;  conditional E-value: 3e-17
                         HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                   de+d +ILelLq+n+r+ ++e+++r+g +++t+++rlkrLe+eG+Ik
  gi|119718936|ref|YP_919431.1|  4 DEKDAAILELLQENARLVIKEISKRIGSPITTTHARLKRLEREGVIK 50
                                   999*******************************************8 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.4
                         HTH_24 14 knprisqreLAerl 27
                                   ++ ++ qr +A+++
  gi|119718936|ref|YP_919431.1| 75 RDRGLDQRKVAQEI 88
                                   68899999999986 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.4   0.4   2.5e-14   4.4e-11       1      42 []       3      44 ..       3      44 .. 0.98

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 2.5e-14
                  HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrLe 42
                                   +De D +ILe+Lqe+aR+  +e+++r+G   +t ++R++rLe
  gi|119718936|ref|YP_919431.1|  3 IDEKDAAILELLQENARLVIKEISKRIGSPITTTHARLKRLE 44
                                   6****************************************8 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.1   1.2e-08   2.1e-05       6      49 ..       8      50 ..       5      51 .. 0.94

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 1.2e-08
                                   HHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                       HTH_IclR  6 laiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                   +aiL++l e ++ l ++e+++r+g p +t+h  L+ L+++G ++
  gi|119718936|ref|YP_919431.1|  8 AAILELLQENAR-LVIKEISKRIGSPITTTHARLKRLEREGVIK 50
                                   79**********.88**************************875 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   1.5e-06    0.0027      25      65 ..      23      61 ..       6      62 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.5e-06
                                   HHHHHHTTSSHHHHHHHHHHHHHTTSEEETEEEEES-HHHH CS
                      HTH_Crp_2 25 eelAsmlGltretvsrilseLkreglisrgrririldleaL 65
                                   +e++ ++G+   t+   l++L+reg+i+  r   ild+++L
  gi|119718936|ref|YP_919431.1| 23 KEISKRIGSPITTTHARLKRLEREGVIKAYR--AILDPKKL 61
                                   79**************************554..599*9998 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1     4e-06    0.0071       8      54 ..       5      51 ..       3      68 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4e-06
                                   HHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEE CS
                           TrmB  8 eyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVer 54
                                   e +a +   L ++ ++ ++ei++++g p ++    L++Le+ G+++ 
  gi|119718936|ref|YP_919431.1|  5 EKDAAILELLQENARLVIKEISKRIGSPITTTHARLKRLEREGVIKA 51
                                   667777777779********************************986 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   5.4e-06    0.0096       7      48 ..       9      50 ..       3      54 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.4e-06
                                   HHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                           MarR  7 viLrilyeqgplsvseLakklgvskstvtrvldrLekkGlie 48
                                    iL++l e+  l ++e+ k++g  ++t+   l+rLe++G i+
  gi|119718936|ref|YP_919431.1|  9 AILELLQENARLVIKEISKRIGSPITTTHARLKRLEREGVIK 50
                                   79*************************************997 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   6.9e-06     0.012      13      55 ..       8      50 ..       2      54 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 6.9e-06
                                   HHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                         HTH_20 13 rrilraLaraegltaselaerldlskntlsyHLrvLeeagLve 55
                                   ++il +L +++ l  +e+ +r++ + +t + +L+ Le+ g ++
  gi|119718936|ref|YP_919431.1|  8 AAILELLQENARLVIKEISKRIGSPITTTHARLKRLEREGVIK 50
                                   689*************************************997 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   6.5e-05      0.12       4      48 ..       6      49 ..       3      54 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.5e-05
                         HTH_27  4 qqalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLv 48
                                    +a++L+l++ +++r  ++++++r     ++++  lk+L++ G++
  gi|119718936|ref|YP_919431.1|  6 KDAAILELLQ-ENARLVIKEISKRIGSPITTTHARLKRLEREGVI 49
                                   6899******.********************************99 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00012      0.21       8      52 ..       8      50 ..       6      57 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00012
                                   HHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                         MarR_2  8 arvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                   a +L  L  + +  l ++e+ +r g +  +++ +lkrL++ G + 
  gi|119718936|ref|YP_919431.1|  8 AAILELLQENAR--LVIKEISKRIGSPITTTHARLKRLEREGVIK 50
                                   567888888887..****************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1136.88
//
Query:       gi|119718937|ref|YP_919432.1|  [L=229]
Description: hypothetical protein Tpen_0019 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1523.74
//
Query:       gi|119718938|ref|YP_919433.1|  [L=75]
Description: hypothetical protein Tpen_0020 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0031   17.6   0.6     0.0049   16.9   0.6    1.5  1  LAB_N     Lipid A Biosynthesis N-terminal domain
  ------ inclusion threshold ------
      0.042   13.7   0.5      0.048   13.5   0.5    1.2  1  Imp-YgjV  Bacterial inner membrane protein


Domain annotation for each model (and alignments):
>> LAB_N  Lipid A Biosynthesis N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.6   5.4e-07    0.0049      37      71 .]      32      66 ..       3      66 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 5.4e-07
                          LAB_N 37 llGslllliYailrkDpvlilgqslglviyirNla 71
                                    +Gs+ll ++++l  Dpv+++ +sl +  ++ Nl+
  gi|119718938|ref|YP_919433.1| 32 AAGSFLLAVHSVLIGDPVFLVLNSLATALALLNLY 66
                                   58*******************************96 PP

>> Imp-YgjV  Bacterial inner membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.5   5.3e-06     0.048     101     157 ..      12      70 ..       1      72 [. 0.74

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.3e-06
                       Imp-YgjV 101 latialfslngikmRll..flvssllWlvynilvgsigglllevlflisnlitiyRlrk 157
                                    +a + +  ++    Rl     ++s+l +v+ +l+g ++ l+l++l     l+++yR ++
  gi|119718938|ref|YP_919433.1|  12 IAAWIASFKDVPSPRLSslYAAGSFLLAVHSVLIGDPVFLVLNSLATALALLNLYRWYR 70 
                                    334444444444446653266889999*****************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.43
# Mc/sec: 523.99
//
Query:       gi|119718939|ref|YP_919434.1|  [L=233]
Description: HAD family hydrolase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-15   57.5   0.0    2.2e-15   57.2   0.0    1.3  1  HAD_2           Haloacid dehalogenase-like hydrolase
    4.3e-12   46.8   0.0    6.6e-11   42.9   0.0    2.0  1  Hydrolase       haloacid dehalogenase-like hydrolase
    4.1e-09   36.4   0.0    7.4e-09   35.5   0.0    1.4  1  Hydrolase_like  HAD-hyrolase-like


Domain annotation for each model (and alignments):
>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.2   0.0   3.7e-19   2.2e-15      63     178 .]      82     198 ..       6     198 .. 0.84

  Alignments for each domain:
  == domain 1  score: 57.2 bits;  conditional E-value: 3.7e-19
                          HAD_2  63 eellrkyneekkkkevkpydgvkelLeeLkeagyklgivTsk.sreaveekleqlgiesyFdvivtsedvekkKPdpevi 141
                                    e++++ + e+  +  +++ ++++ +L   ++ g+++g++T+  s e v++ le+ g+ +y dviv s+ v  kKP+p+++
  gi|119718939|ref|YP_919434.1|  82 EKVYKAVLESYVQ-GFSLDEEAEHALSLSRSLGFTVGLITNVgSYEIVRRRLEEAGLLKYVDVIVASQAVAWKKPSPRIF 160
                                    4444444444444.777778888888877899*********779************************************ PP

                          HAD_2 142 ekaleklklkkeeviyvGDsp.tDieaakkagikviav 178
                                    e a+   ++++ +++ vGD p  D+e+akkag++++ v
  gi|119718939|ref|YP_919434.1| 161 ELACYLAGVEPGNAVHVGDDPrIDVEGAKKAGLRAVQV 198
                                    *********************99**********99865 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   0.0   1.1e-14   6.6e-11     115     210 .]      94     192 ..       2     192 .. 0.67

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 1.1e-14
                                    HTHHBHTTHHHHHHHHHHTTEEEEEEES.SEHHHHHHHHHHTT.GGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGG CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase 115 dplkvkpeaaeavasLkaagievvlltg.dnpetaeraanqlG.ddyfdaviasdietvakpspegkvaaireLqgkpee 192
                                    +  ++ +ea++a+   ++ g+ v+l+t+ ++ e ++r ++++G  +y+d+++as  ++ +kpsp++++ a+   +++p +
  gi|119718939|ref|YP_919434.1|  94 QGFSLDEEAEHALSLSRSLGFTVGLITNvGSYEIVRRRLEEAGlLKYVDVIVASQAVAWKKPSPRIFELACYLAGVEPGN 173
                                    33347789*******************835558888*******99999******************************** PP

                                    EEEEESSHH.HHHHHHHTT CS
                                    xxxxxxxxx.xxxxxxxxx RF
                      Hydrolase 193 vamVGDgvn.DaaalaaAg 210
                                     ++VGD +  D++++++Ag
  gi|119718939|ref|YP_919434.1| 174 AVHVGDDPRiDVEGAKKAG 192
                                    *****************98 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.0   1.2e-12   7.4e-09       2      50 ..     152     200 ..     151     216 .. 0.95

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 1.2e-12
                                    .STTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESS CS
                 Hydrolase_like   2 lgKPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVlt 50 
                                    + KP+p +++ a    g++p++ + +GD+++ D++gA++aG++ v Vl 
  gi|119718939|ref|YP_919434.1| 152 WKKPSPRIFELACYLAGVEPGNAVHVGDDPRIDVEGAKKAGLRAVQVLK 200
                                    68*******************************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1638.21
//
Query:       gi|119718940|ref|YP_919435.1|  [L=203]
Description: hypothetical protein Tpen_0022 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00018   21.4   0.0    0.00042   20.2   0.0    1.6  1  HTH_12    Ribonuclease R winged-helix domain
     0.0011   18.8   0.1      0.002   18.0   0.1    1.4  1  HTH_5     Bacterial regulatory protein, arsR family
  ------ inclusion threshold ------
      0.018   15.3   0.0      0.029   14.6   0.0    1.4  1  DUF4443   Domain of unknown function (DUF4443)
      0.042   14.1   0.1      0.078   13.2   0.1    1.5  1  PaaX      PaaX-like protein
      0.049   13.2   0.1       0.11   12.1   0.0    1.6  2  HTH_24    Winged helix-turn-helix DNA-binding
      0.059   13.4   0.0       0.11   12.6   0.0    1.5  1  HTH_20    Helix-turn-helix domain
       0.11   12.9   0.0       0.17   12.3   0.0    1.3  1  Rrf2      Transcriptional regulator


Domain annotation for each model (and alignments):
>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   1.7e-07   0.00042      30      62 ..      34      65 ..      15      68 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.7e-07
                         HTH_12 30 igeravRyrLrkleergltrrvgyagreltEkG 62
                                   +ge  vR +Lr l+ergl+r v +ag  lt+ G
  gi|119718940|ref|YP_919435.1| 34 LGEGVVRSHLRFLNERGLVRSV-RAGNALTDSG 65
                                   67777**************877.57799**998 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1   7.7e-07     0.002      21      47 .]      28      54 ..      25      54 .. 0.95

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 7.7e-07
                                   HHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                          HTH_5 21 laeelglsqstvShHLkkLreaGLVek 47
                                   l+ elgl ++ v+ HL++L e GLV++
  gi|119718940|ref|YP_919435.1| 28 LSSELGLGEGVVRSHLRFLNERGLVRS 54
                                   899**********************85 PP

>> DUF4443  Domain of unknown function (DUF4443)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.1e-05     0.029      15      60 ..      95     140 ..      90     187 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.1e-05
                        DUF4443  15 ayaivvknppqfksielrdeairffakgamilivkngepvfpeder 60 
                                     y ++   pp  + ++lrdea+r  a ga+i +   g+  +p    
  gi|119718940|ref|YP_919435.1|  95 VYVLLHGYPPAENVVKLRDEAVREGADGAVIAVFDGGKFRLPPGGE 140
                                    577777889************************9999887776555 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1     3e-05     0.078      29      61 ..      28      60 ..      11      65 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3e-05
                           PaaX 29 llaelGiseslvRaalsRlakaGwlvrekegrr 61
                                   l +elG++e++vR+ l  l+++G++++ + g++
  gi|119718940|ref|YP_919435.1| 28 LSSELGLGEGVVRSHLRFLNERGLVRSVRAGNA 60
                                   6789*************************9964 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   4.2e-05      0.11      16      48 .]      21      53 ..      13      53 .. 0.90
   2 ?   -2.5   0.0       1.5   3.9e+03      24      31 ..      78      85 ..      78      86 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.2e-05
                         HTH_24 16 prisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                   +  s + L+ +lgl  + v+ +l+ L e Gl++
  gi|119718940|ref|YP_919435.1| 21 GYVSRKTLSSELGLGEGVVRSHLRFLNERGLVR 53
                                   5578899************************96 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.5
                         HTH_24 24 AerlglSp 31
                                   A+rlgl p
  gi|119718940|ref|YP_919435.1| 78 AKRLGLAP 85
                                   89***987 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   4.3e-05      0.11      19      60 ..      16      58 ..       5      59 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.3e-05
                                   H.STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                         HTH_20 19 L.araegltaselaerldlskntlsyHLrvLeeagLvevvreg 60
                                   L  +++ ++ + l  +l+l    ++ HLr L e gLv++vr g
  gi|119718940|ref|YP_919435.1| 16 LyVSGGYVSRKTLSSELGLGEGVVRSHLRFLNERGLVRSVRAG 58
                                   455778899999****************************976 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   6.5e-05      0.17      12      59 ..      11      56 ..       1      61 [. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.5e-05
                                   HHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                           Rrf2 12 hallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvr 59
                                     ll+L    +   vs ++++++ ++ + +++  l+ L++ glv+svr
  gi|119718940|ref|YP_919435.1| 11 SFLLFLYVSGG--YVSRKTLSSELGLGEGVVRSHLRFLNERGLVRSVR 56
                                   56666666666..4999*****************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 1335.28
//
Query:       gi|119718941|ref|YP_919436.1|  [L=165]
Description: hypothetical protein Tpen_0023 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.6e-10   38.9   1.1    2.1e-09   37.8   1.1    1.6  1  DUF4430   Domain of unknown function (DUF4430)
  ------ inclusion threshold ------
       0.26   11.4   1.4        1.7    8.8   0.4    2.3  2  Imm58     Immunity protein 58


Domain annotation for each model (and alignments):
>> DUF4430  Domain of unknown function (DUF4430)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   1.1   2.3e-13   2.1e-09       1      74 []      83     162 ..      83     162 .. 0.72

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 2.3e-13
                        DUF4430   1 GttvfdvleaaakkkedkteaqsgehyitsIngl.....eqdtakk......syWmye.vNG..epsdvGagsyklkdgd 66 
                                    G++++++l a+ak++ ++++   g+ y+ts+ng+     +     k       + +y+ +    ++ +v+a++y l++gd
  gi|119718941|ref|YP_919436.1|  83 GSSALTALVAVAKVEYKTSQM--GA-YVTSVNGVsekflS-----KnegyswLWYRYDpGKSqlVMGQVAADKYILANGD 154
                                    89999********99999955..44.********853322.....223542344444433333346778*********** PP

                        DUF4430  67 kivfryta 74 
                                    +iv+ry++
  gi|119718941|ref|YP_919436.1| 155 VIVWRYEH 162
                                    ******96 PP

>> Imm58  Immunity protein 58
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.4   0.00019       1.7       5      29 ..      20      44 ..      16      64 .. 0.74
   2 ?    1.2   0.0     0.042   3.8e+02      86      98 ..      68      80 ..      44      90 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00019
                          Imm58  5 tkalllslavaviasilfaylwidr 29
                                    +++l  la a+ias + ayl+++ 
  gi|119718941|ref|YP_919436.1| 20 GLLVLALLAWAIIASGFAAYLYLEN 44
                                   56778899**************975 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.042
                          Imm58 86 kegsiiwfdevrf 98
                                    +g+i+wf+  ++
  gi|119718941|ref|YP_919436.1| 68 GNGTIVWFNSTPL 80
                                   4799****98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1113.21
//
Query:       gi|119718942|ref|YP_919437.1|  [L=179]
Description: hypothetical protein Tpen_0024 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-07   30.7  15.3    5.7e-07   29.7  14.8    1.7  2  ECF-ribofla_trS  ECF-type riboflavin transporter, S component
     0.0018   18.4  21.7     0.0064   16.6  21.7    1.8  1  ECF_trnsprt      ECF transporter, substrate-specific componen


Domain annotation for each model (and alignments):
>> ECF-ribofla_trS  ECF-type riboflavin transporter, S component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7  14.8   6.3e-11   5.7e-07       6     129 ..       5     122 ..       1     149 [. 0.76
   2 ?   -0.2   0.2     0.094   8.4e+02     111     135 ..     129     153 ..     122     168 .. 0.56

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 6.3e-11
                                    HHHHHHHHHHHHHHHHHH---B-S.SS-B--TTHHHHHHHHHHSS--STHHHHHHHHHHHHHHHSS-GGGHHHHHHHHHH CS
                ECF-ribofla_trS   6 kvvatailaAlvvvltlfisIplpantegsinlgdavlalaallfGpvvGflvGaiGsalaDllsgYgiwapftliikgl 85 
                                    +++a+a+++   vv+ +  +  +      ++n+  a+ +++++++G + GflvG+++ +l+D+l g g+w  +  ++ g 
  gi|119718942|ref|YP_919437.1|   5 RIAAVAVFTSTAVVFRVAKNLVTT---VQFVNIPLAMAFVSSAILGYKEGFLVGFLSYVLSDMLIGPGFWTLVNPFLAGA 81 
                                    566666666655555555454443...349***********************************998887777777777 PP

                                    HHHHHHHH--S-S-SSH...HHHHHHHHHHHHHHHHHHHHHHHH CS
                ECF-ribofla_trS  86 iGlivGliakklkknkengvfkilalvlfaivmvigyviaegll 129
                                    +  ++G+  ++    +e++ + + a++   ++ v+  v++++++
  gi|119718942|ref|YP_919437.1|  82 FSAVFGFSYRRG---LEKTYLFVSAFLSCFLFDVTTSVLFYMIF 122
                                    777777766666...77778888899999999999999998887 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.094
                                    HHHHHHHHHHHHHHHHHHH...... CS
                ECF-ribofla_trS 111 lvlfaivmvigyviaegllpildii 135
                                     ++f++++++  v++++l+ ++ ++
  gi|119718942|ref|YP_919437.1| 129 ALVFGLLGLFVPVVGGFLVGVGPLT 153
                                    4555555555555555555444444 PP

>> ECF_trnsprt  ECF transporter, substrate-specific component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6  21.7   7.2e-07    0.0064       1     126 [.       4     125 ..       4     169 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 7.2e-07
                                    HHHHHHHHHHHHHHHHHHHHEEE.STSEEESHHHH...HHHHHHCTTCHHHHHHHHHHHHHHHHCHT-SSTTHHHHHHHH CS
                    ECF_trnsprt   1 kklvitglliAisivlsllgyiplpnikitiihip...vllggllfGpikGailgiitsvlkailtggtgalssfvpiaf 77 
                                    ++++ +++++  ++v++   + + ++  ++++ ip   +++++ ++G + G+++g+++ vl+ +l g++  ++   +++ 
  gi|119718942|ref|YP_919437.1|   4 RRIAAVAVFTSTAVVFR---VAKNLVTTVQFVNIPlamAFVSSAILGYKEGFLVGFLSYVLSDMLIGPG--FWT--LVNP 76 
                                    68999************...666665555555555222568899*********************7666..666..99** PP

                                    HHHHCHHHHHHHHHHCCCHTTHHHHHHHHHHHHCCCCCHHHHHHHCCC..H CS
                    ECF_trnsprt  78 lsriligliagllykkgkkknlkeivvsfilagvlgtivatllvllii..l 126
                                    + ++++  ++g+ y+ g  k   + +vs +l+ +l  ++  +l+++i+   
  gi|119718942|ref|YP_919437.1|  77 FLAGAFSAVFGFSYRRGLEK--TYLFVSAFLSCFLFDVTTSVLFYMIFglK 125
                                    ***********999544444..45688888888888888888888888442 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1201.53
//
Query:       gi|119718943|ref|YP_919438.1|  [L=85]
Description: hypothetical protein Tpen_0025 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.048   13.6   0.9      0.048   13.6   0.9    2.1  2  FixQ             Cbb3-type cytochrome oxidase component FixQ
      0.062   12.5   3.2      0.068   12.4   3.2    1.0  1  7tm_7            7tm Chemosensory receptor
        4.7    7.6   7.0       0.54   10.6   0.8    2.2  2  Defensin_big     Big defensin


Domain annotation for each model (and alignments):
>> FixQ  Cbb3-type cytochrome oxidase component FixQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   4.4       0.5     3e+03       7      18 ..      12      23 ..       6      29 .. 0.45
   2 ?   13.6   0.9     8e-06     0.048       5      31 ..      43      69 ..      39      77 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.5
                           FixQ  7 rgfadswgllfl 18
                                   + f  ++ l +l
  gi|119718943|ref|YP_919438.1| 12 AVFFSFIILAVL 23
                                   333333333333 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 8e-06
                           FixQ  5 alrgfadswgllflvllfygvviyafr 31
                                    +r++a +++l + +++++ vviy+++
  gi|119718943|ref|YP_919438.1| 43 VFRAYAETAVLPLVLAFLAVVVIYVLT 69
                                   689*********************986 PP

>> 7tm_7  7tm Chemosensory receptor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   3.2   1.1e-05     0.068     122     191 ..       8      83 ..       3      85 .] 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.1e-05
                          7tm_7 122 nrllllllvliillllvtll......gylllsqyftlvlllllyllpylvlqlllllyfllllliyellrllnerL 191
                                     +ll++ + +iil++lvtl       g + +s+ + +  +  + +lp ++ +l++  +++l+++  + l++l +r+
  gi|119718943|ref|YP_919438.1|   8 GWLLAVFFSFIILAVLVTLAaaervtGVTPWSSLSVFRAYAETAVLPLVLAFLAVVVIYVLTRYAGKALDFLVQRI 83 
                                    6889999999999999999999*99999999999999999999999999*********************999987 PP

>> Defensin_big  Big defensin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.7      0.15   8.7e+02       9      31 ..       8      32 ..       4      37 .. 0.50
   2 ?   10.6   0.8     9e-05      0.54       6      26 ..      54      74 ..      45      77 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.15
                   Defensin_big  9 lllvaly...gaaavtrigvnvAErv 31
                                    +l+a++    + av +     AErv
  gi|119718943|ref|YP_919438.1|  8 GWLLAVFfsfIILAVLVTLAA-AERV 32
                                   577777622133333322222.4555 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 9e-05
                   Defensin_big  6 slylllvalygaaavtrigvn 26
                                   +l+l+++a+ +++ +tr++ +
  gi|119718943|ref|YP_919438.1| 54 PLVLAFLAVVVIYVLTRYAGK 74
                                   79****************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       982  (0.0547716); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 631.87
//
Query:       gi|119718944|ref|YP_919439.1|  [L=433]
Description: hypothetical protein Tpen_0026 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      4e-06   27.1   0.0    7.1e-06   26.3   0.0    1.3  1  Thioredoxin_4  Thioredoxin
    0.00061   20.2   0.0     0.0041   17.6   0.0    2.3  2  Thioredoxin_2  Thioredoxin-like domain
  ------ inclusion threshold ------
       0.14   10.8   0.0        0.2   10.3   0.0    1.1  1  CBP_GIL        Cellulose biosynthesis GIL


Domain annotation for each model (and alignments):
>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   1.2e-09   7.1e-06      15     145 ..     263     397 ..     258     405 .. 0.80

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 1.2e-09
                                    EEEEEEE-TT-HHHHHHHHHHHHHHHHHHHTTSEEEEEEE-..---STTTHHHHHHHTT--TT...HHHHHHHHHHHHTH CS
                  Thioredoxin_4  15 vtvieyedlrCphCakfeeeveklleeyidtGkvkfiirdfpldkekeslkaamaarcagees...peaflaikallysq 91 
                                     t+++ ed+ Cp Cak+  +++ ++++  ++G++k++  d++ ++e    +   +a+c+++++     +f   ++l+ + 
  gi|119718944|ref|YP_919439.1| 263 LTLYILEDYHCPFCAKLMASLGDTFTRLAKSGSLKVVLVDLIVHPEV--AEMHALAKCVYNKTgdgYLYFNLSRKLYDKL 340
                                    6788889**********************************999986..8999999**9999434467888888888888 PP

                                    HHHTTS-HHHHH.......HHHHHTS-------HHHHHHHHHHH.HHHT--SS-EEE CS
                  Thioredoxin_4  92 qeewaeslkela..aealdkdekfeacleeekldalveaeskea.kkagiestPtfi 145
                                     + ++++l++l   a++   ++ +++cl++  + a+ ++ + +    +g ++tPt+i
  gi|119718944|ref|YP_919439.1| 341 NQGVSTTLEDLSsiASTYTGKALIDECLKQVNAGAEHVRSLSQKlISDGYTGTPTLI 397
                                    88888887777654455555666788888887777665555555499********98 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       2.1   1.3e+04      65      79 ..      60      76 ..      38      98 .. 0.54
   2 !   17.6   0.0   6.8e-07    0.0041       7     100 ..     263     413 ..     258     418 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.1
                  Thioredoxin_2 65 d.ieenvelark.ygvr 79
                                   d i++n++++ + yg++
  gi|119718944|ref|YP_919439.1| 60 DtITSNFKVVLQqYGIN 76
                                   34444444333325433 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 6.8e-07
                  Thioredoxin_2   7 pvlvvftdpdCpyCkklkkelkel.....ddvtvrvllfp..lkpsfepkavaiwcakekkkafkd.............. 65 
                                     +l++ +d +Cp+C+kl++ l +      ++   +v+l++  ++p++ + ++  +c  +k     +              
  gi|119718944|ref|YP_919439.1| 263 LTLYILEDYHCPFCAKLMASLGDTftrlaKSGSLKVVLVDliVHPEVAEMHALAKCVYNKT----Gdgylyfnlsrklyd 338
                                    5899***************999888999999999999999999***999999999999997....234555555667777 PP

                  Thioredoxin_2  66 ....................................ieenvelarky...gvrgtPtivfldgk.eivarlpGyv 100
                                                                         e  + l++k+   g +gtPt++f +++  + +++pG +
  gi|119718944|ref|YP_919439.1| 339 klnqgvsttledlssiastytgkalideclkqvnagAEHVRSLSQKLisdGYTGTPTLIFWNPEkGKGLVVPGCL 413
                                    788888889999********************999877888888888899************9987777778765 PP

>> CBP_GIL  Cellulose biosynthesis GIL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   3.3e-05       0.2     387     419 ..     293     325 ..     275     328 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 3.3e-05
                        CBP_GIL 387 pedlkgvLVaLrllpglahedaLtlckprRaGD 419
                                    +  lk vLV L + p++a + aL+ c  + +GD
  gi|119718944|ref|YP_919439.1| 293 SGSLKVVLVDLIVHPEVAEMHALAKCVYNKTGD 325
                                    45789***************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.36s 00:00:01.00 Elapsed: 00:00:00.56
# Mc/sec: 2322.90
//
Query:       gi|119718945|ref|YP_919440.1|  [L=400]
Description: alanine aminotransferase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-62  210.6   0.0    4.4e-62  210.3   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    1.5e-09   37.7   0.0    2.9e-09   36.7   0.0    1.4  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    2.1e-06   26.9   0.0    1.6e-05   24.1   0.0    2.0  2  Aminotran_5      Aminotransferase class-V
      8e-06   25.3   0.0    1.2e-05   24.8   0.0    1.2  1  Beta_elim_lyase  Beta-eliminating lyase
    0.00036   19.2   0.0    0.00052   18.7   0.0    1.1  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
  ------ inclusion threshold ------
       0.01   16.2   0.5        1.2    9.6   0.0    3.7  4  CBS              CBS domain
      0.027   14.4   0.0       0.22   11.4   0.0    2.5  3  TP_methylase     Tetrapyrrole (Corrin/Porphyrin) Methylases
       0.16   11.4   0.0       0.29   10.6   0.0    1.3  1  ComA             (2R)-phospho-3-sulfolactate synthase (ComA)


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.3   0.0     2e-65   4.4e-62       2     357 ..      33     384 ..      32     389 .. 0.88

  Alignments for each domain:
  == domain 1  score: 210.3 bits;  conditional E-value: 2e-65
                                    EEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHH CS
                  Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagali 81 
                                    +vi L+++++l  +  +++ e ++++ +  +  ++ + y+p++gl+el+ea+a   ++ ++++++++ +v+v++G +++i
  gi|119718945|ref|YP_919440.1|  33 KVIYLNIGDPLKYD-FTPPSELVEEACR--ALREGHHYYSPSEGLKELREAIAFKEKSWNGVQVDPK-NVLVTNGVSEGI 108
                                    79999****99883.3688888999988..889999*****************8888899*******.************ PP

                                    HHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT CS
                  Aminotran_1_2  82 ealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPt 161
                                    +al ++l +n gde+l+pdp+y+ y+n +  + ++ v y++ +ee+++ d +++ +++++      kt++i++++phNPt
  gi|119718945|ref|YP_919440.1| 109 NALYAAL-VNEGDEVLIPDPSYPLYINFADFYNAKKVFYRTLEEEGWRPDPDDIRRKITD------KTRFIVINNPHNPT 181
                                    *******.9***************************************************......************** PP

                                    --B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTT.EEEEEESSSTTSSGGG-EEEEEEEH... CS
                  Aminotran_1_2 162 GtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepn.llivgslsKafGlaGeRvGyilgna... 237
                                    G+v+++++++++ld+a +++l +++De+Y ++vf+  ++ +  a v+ e+n ++ ++++sK f ++G+R+Gyi+      
  gi|119718945|ref|YP_919440.1| 182 GAVYPEKTVKEILDIAAEHGLPVVSDEIYDALVFE-GSFKS-TAAVASEDNvVIGMNGFSKTFLVTGWRLGYIYLRGpee 259
                                    **********************************9.57888.6666666776999*******************955565 PP

                                    ...HHHHHHHHHHHHHTS.SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS.TEEEECCS.CSSEEEEE CS
                  Aminotran_1_2 238 ...avvsqlrklsrpfls.ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLael.glkvlasq.sgmflltd 311
                                       +++ +l  +  + ls  ++lq a+a  + +a++   +le+ ++rl +rr++ + +L+e+ g++  +s+ ++++ + +
  gi|119718945|ref|YP_919440.1| 260 kiaDLRAALLGFLMTRLSaVTPLQVALARFAVKAPK---HLEDLKRRLDERRRYTVRRLNEIpGVSLATSPaGAFYAFPR 336
                                    555555555555555555777777777777777776...9***************************999999******* PP

                                    ETHH.CHHHHHHHHHHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHH CS
                  Aminotran_1_2 312 lsae.takelskkLleevgvyvtpgtsftv..pgrlRitvAglteeele 357
                                    ++   +++e+ k Ll e++v v+ g+ f+     ++R+ +   + ++le
  gi|119718945|ref|YP_919440.1| 337 IDVDmDDEEFTKRLLLEEKVFVVYGSGFGPlgARHVRLVF-LPPVQQLE 384
                                    **9999999999977777**********988877888887.55555555 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.0   1.3e-12   2.9e-09      42     144 ..      98     207 ..      78     209 .. 0.85

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 1.3e-12
                                    EEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-.B-TTTSSB-GGGCGGG--TTEEEEEEB.. CS
                DegT_DnrJ_EryC1  42 iavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvD.vdpdtynidpaaieaaitertkaIlpV.. 118
                                    + v++G +    aL a  v++gdeV++p  ++   +n +   +ak vf    +++ + +dp++i+++it +t+ I++   
  gi|119718945|ref|YP_919440.1|  98 VLVTNGVSEGINALYAALVNEGDEVLIPDPSYPLYINFADFYNAKKVFYRtLEEEGWRPDPDDIRRKITDKTRFIVINnp 177
                                    567778777778899999**************************999985268889********************7622 PP

                                    .-GGGB--...-HHHHHHHHHHCT-EEEEE CS
                DegT_DnrJ_EryC1 119 .hlyGqva...dmdalkaiaakhglkvieD 144
                                     +  G+v     ++++ +iaa+hgl+v++D
  gi|119718945|ref|YP_919440.1| 178 hNPTGAVYpekTVKEILDIAAEHGLPVVSD 207
                                    1567888765679***************99 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0     7e-09   1.6e-05      56     175 ..      91     207 ..      55     211 .. 0.80
   2 ?    0.3   0.0      0.12   2.7e+02     272     338 ..     296     361 ..     285     371 .. 0.72

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 7e-09
                                    HT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBET.TSCBEGGGHHH CS
                    Aminotran_5  56 inaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkviplde.egeldldelek 134
                                    ++++  +++++t G +e+in+   +l   +++gde+++ +  +   ++ +   + +   kv + +l+e +++ d+d+++ 
  gi|119718945|ref|YP_919440.1|  91 VQVDP-KNVLVTNGVSEGINALYAAL---VNEGDEVLIPDPSYPLYINFADFYN-A--KKVFYRTLEEeGWRPDPDDIRR 163
                                    45564.99******************...9**********99998885444444.3..3666767765156999****** PP

                                    H--TTEEEEEEESBETTTTEB--...HHHHHHHHHHTT-EEEEE CS
                    Aminotran_5 135 llnektklvaithvsnvtGtiqp...veeigklakkkgalvlvD 175
                                    ++++kt+ + i+   n tG + p   v+ei ++a ++g  v+ D
  gi|119718945|ref|YP_919440.1| 164 KITDKTRFIVINNPHNPTGAVYPektVKEILDIAAEHGLPVVSD 207
                                    ********************977333667777777777777766 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.12
                                    HHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-CTCBSEEEEEETTCSHHHHHHHHHHTTEEEEEE CS
                    Aminotran_5 272 gleaiekhekelaeyllerlkslpgvrlygpdkaerrasivsfnfkgvhaedvatlLdeegIavrsG 338
                                    +le  +++ +e + y++ rl+++pgv l+  ++a +  +   + ++  + e  ++lL ee++ v  G
  gi|119718945|ref|YP_919440.1| 296 HLEDLKRRLDERRRYTVRRLNEIPGVSLAT-SPAGAFYAFPRIDVDMDDEEFTKRLLLEEKVFVVYG 361
                                    5777888999999**************955.455555555555555555555666666666666655 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   5.3e-09   1.2e-05      19     167 ..      59     207 ..      46     222 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 5.3e-09
                                    HCS----CCCT--HHHHHHHHHHHH........HTT-SEEEEES-H.HHHHHHHHHHH--TTEEEEEETT-HHHHSSTTH CS
                Beta_elim_lyase  19 aaamlGdesYgedktvnrLedavae........lfgkeaalfvpqG.taAnsillkillqrgeevivtepahihfdetga 89 
                                     a+  G+  Y  +++ ++L +a+a          ++  + + v++G   + + l+++l++ g+ev++ +p+         
  gi|119718945|ref|YP_919440.1|  59 RALREGHHYYSPSEGLKELREAIAFkekswngvQVDP-KNVLVTNGvSEGINALYAALVNEGDEVLIPDPSYPLYINFAD 137
                                    5555666666666666666666655455555432222.333444441345556678888888888888888888888888 PP

                                    HHHCC--EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEE CS
                Beta_elim_lyase  90 iaelagvklrdlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlD 167
                                        + v  r+l+ +     d+++++++i++      k+++i++ + +n   G v++ + ++e+ +ia ++g+p++ D
  gi|119718945|ref|YP_919440.1| 138 FYNAKKVFYRTLEEEG-WRPDPDDIRRKITD------KTRFIVINNPHNP-TGAVYPEKTVKEILDIAAEHGLPVVSD 207
                                    8888888888888888.89999999999999......699*********5.9************************99 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   2.3e-07   0.00052      79     178 ..     107     212 ..      85     227 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.3e-07
                                    HHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEEST...TSHHHHHHHCCTTEEEEEEESS-TTTT---. CS
                Cys_Met_Meta_PP  79 AiaaailallkaGdeivvsddlYggtqrllkkvlkklgievkfvdt...sdleelekaikentklvylEtptnpllkvv. 154
                                     i+a   al+++Gde+++ d  Y    ++ + +  k     +  +     d+++++++i+++t+ + +  p np+  v  
  gi|119718945|ref|YP_919440.1| 107 GINALYAALVNEGDEVLIPDPSYPLYINFADFYNAKKVFYRTLEEEgwrPDPDDIRRKITDKTRFIVINNPHNPTGAVYp 186
                                    455557889**************99888887776664443333333455799***********************98863 PP

                                    ..-HHHHHHHHHHTT-EEEEEGTTTH CS
                Cys_Met_Meta_PP 155 ..DiekiaklakkagvlvvvDntfas 178
                                       +++i+++a ++g++vv D  + +
  gi|119718945|ref|YP_919440.1| 187 ekTVKEILDIAAEHGLPVVSDEIYDA 212
                                    336999*************9987765 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.16   3.5e+02      12      32 ..      48      67 ..      41      70 .. 0.81
   2 ?    9.6   0.0   0.00055       1.2      11      37 ..     183     207 ..     161     214 .. 0.86
   3 ?   -1.4   0.0       1.5   3.3e+03      12      32 ..     291     314 ..     280     315 .. 0.69
   4 ?   -1.0   0.0       1.1   2.6e+03       8      27 ..     373     392 ..     369     397 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.16
                                   EETTSBHHHHHHHHHHHTSSE CS
                            CBS 12 vppdttleealelmrekgvsr 32
                                    pp++ +eea + + ++g++ 
  gi|119718945|ref|YP_919440.1| 48 TPPSELVEEACRAL-REGHHY 67
                                   589999********.666654 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00055
                                    EEETTSBHHHHHHHHHHHTSSEEEEE.E CS
                            CBS  11 tvppdttleealelmrekgvsrlPVV.d 37 
                                     v+p+ t++e+l++ +e   ++lPVV d
  gi|119718945|ref|YP_919440.1| 183 AVYPEKTVKEILDIAAE---HGLPVVsD 207
                                    589***********978...8*****33 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 1.5
                                    EETTSBHHHHHHHHHHHT...SSE CS
                            CBS  12 vppdttleealelmrekg...vsr 32 
                                    v+    le++ +++ e++   v+r
  gi|119718945|ref|YP_919440.1| 291 VKAPKHLEDLKRRLDERRrytVRR 314
                                    555667999999995433444555 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 1.1
                                    SCEEEETTSBHHHHHHHHHH CS
                            CBS   8 dvvtvppdttleealelmre 27 
                                    ++v++pp + leea+ +m++
  gi|119718945|ref|YP_919440.1| 373 RLVFLPPVQQLEEAFVRMER 392
                                    67889999999****99943 PP

>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   9.8e-05      0.22      72     105 ..      24      59 ..       8      68 .. 0.79
   2 ?   -1.7   0.0         1   2.3e+03     124     131 ..     196     203 ..     140     243 .. 0.58
   3 ?   -1.4   0.0      0.86   1.9e+03     168     183 ..     292     307 ..     256     328 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9.8e-05
                   TP_methylase  72 laealragkdVvllvsGDPlvy..gtgselvealra 105
                                     + + ++g++V++l +GDPl y  ++ selve++++
  gi|119718945|ref|YP_919440.1|  24 ARSLEEKGEKVIYLNIGDPLKYdfTPPSELVEEACR 59 
                                    46788999**************77777888865444 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1
                   TP_methylase 124 aaarlgip 131
                                    +aa +g+p
  gi|119718945|ref|YP_919440.1| 196 IAAEHGLP 203
                                    23333333 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.86
                   TP_methylase 168 kaprklaelaelLkea 183
                                    kap++l++l+++L e+
  gi|119718945|ref|YP_919440.1| 292 KAPKHLEDLKRRLDER 307
                                    4444455555555444 PP

>> ComA  (2R)-phospho-3-sulfolactate synthase (ComA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00013      0.29      46      87 ..     182     222 ..     179     231 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00013
                                    GGGSTCHHHHHHHHHHHCTT-EEEE-HHHHHHHHHTT-HHHH CS
                           ComA  46 sallpeeilrekielahehgvyvstGgtlfEaalaqgkvdey 87 
                                     a++pe++++e++++a ehg +v+ ++ + +a++ +g+++  
  gi|119718945|ref|YP_919440.1| 182 GAVYPEKTVKEILDIAAEHGLPVVSDE-IYDALVFEGSFKST 222
                                    589************************.99999999998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2669.34
//
Query:       gi|119718946|ref|YP_919441.1|  [L=139]
Description: PilT domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-13   50.7   5.1    2.8e-13   50.5   5.1    1.0  1  PIN       PIN domain
      0.001   19.3   0.4      0.012   15.9   0.0    2.2  2  PIN_9     PIN like domain
  ------ inclusion threshold ------
      0.019   14.4   0.1       0.07   12.5   0.0    1.8  2  PIN_5     PINc domain ribonuclease
       0.02   13.8   0.0      0.034   13.1   0.0    1.3  1  DUF3375   Protein of unknown function (DUF3375)
      0.092   13.2   0.8       0.12   12.9   0.8    1.5  1  PIN_12    PIN domain
       0.15   12.3   0.7        1.3    9.4   0.7    2.0  1  PIN_4     PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.5   5.1   9.2e-17   2.8e-13       1     122 []       7     132 ..       7     132 .. 0.85

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 9.2e-17
                                    EEE-HHHHHHHH.TTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHS.SCHCHHHHHHHHHHHHHHHTSEEEEBCHHHH CS
                            PIN   1 ivlDTsvliall.rgeekaeaarklleeleelvtsalvlaEllyvlar.rkskrekaaelvelllllsalkilpidaeia 78 
                                    iv+DT +l++   +++ek+++a +ll+e++++++ ++v+ E l+ l    k +++  +e +e++   +++ +++ ++e++
  gi|119718946|ref|YP_919441.1|   7 IVVDTDILLHDTfEDSEKHAEASELLDEADRIYLASIVVHEYLWLLLTkFKIDIDSVREKLEEYFSDARFIYISENSEVF 86 
                                    79*******9999*********************************99533333333333344444566666667***** PP

                                    HHHHHHHHHHH...SBHHHHHHHHHHHHHT-EEE.ESSTHHHHHHHC CS
                            PIN  79 eeaaeialkyg...llpnDaliaAtAkehgikliatfDedfrrvakl 122
                                      a++++++ +    ++nD +i+++A++ g++l  t+De++r++ak+
  gi|119718946|ref|YP_919441.1|  87 MGALDLMKEDKadpSMINDYIILVLAQRMGATLA-TYDEELREIAKK 132
                                    *******************************999.*********985 PP

>> PIN_9  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1       0.1     3e+02       1      40 [.       7      47 ..       7      55 .. 0.79
   2 !   15.9   0.0   4.1e-06     0.012      74     110 ..     102     137 ..      60     139 .] 0.82

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.1
                          PIN_9  1 vilDtnaLmipvqfgvdifeelerll.gsvelvvpkavleE 40
                                   +++Dt  L+  +  + +  +e+++ll +++++ + + v++E
  gi|119718946|ref|YP_919441.1|  7 IVVDTDILLHDTFEDSEKHAEASELLdEADRIYLASIVVHE 47
                                   68999999999999999999999999555566666667766 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 4.1e-06
                          PIN_9  74 ekaDdailelakeldaavlvTnDreLkkrllekgipv 110
                                       D +il la++++a+ + T D eL++ +++ g+pv
  gi|119718946|ref|YP_919441.1| 102 MINDYIILVLAQRMGATLA-TYDEELREIAKKLGVPV 137
                                    4568899*******96665.***************99 PP

>> PIN_5  PINc domain ribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.22   6.7e+02       2      28 ..       7      33 ..       6      71 .. 0.68
   2 ?   12.5   0.0   2.3e-05      0.07     159     190 ..     105     136 ..     101     139 .] 0.91

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.22
                          PIN_5  2 fvlDTsaltdpevreklgeeeleeavk 28
                                    v+DT +l   +  ++ ++ e +e ++
  gi|119718946|ref|YP_919441.1|  7 IVVDTDILLHDTFEDSEKHAEASELLD 33
                                   677777777766666555555544433 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 2.3e-05
                          PIN_5 159 DldvllLAkELdaavvssDeGikkwaeklGlr 190
                                    D  +l+LA+ + a++ + De ++++a+klG+ 
  gi|119718946|ref|YP_919441.1| 105 DYIILVLAQRMGATLATYDEELREIAKKLGVP 136
                                    66799*************************96 PP

>> DUF3375  Protein of unknown function (DUF3375)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.1e-05     0.034     211     283 ..      61     133 ..      52     137 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.1e-05
                        DUF3375 211 gskgevLeevlegydalaeSdeGrsFeaFwdlLldpe.rqaeldealdavlarpaareLeaeerreLrrllrrl 283
                                    +s +e Lee++ + + +  S+    F +++dl+ +++   + +++ +  vla+   ++L + + + Lr++ ++l
  gi|119718946|ref|YP_919441.1|  61 DSVREKLEEYFSDARFIYISENSEVFMGALDLMKEDKaDPSMINDYIILVLAQRMGATLATYDEE-LREIAKKL 133
                                    678999***************************86651567889****************88877.***99877 PP

>> PIN_12  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.8     4e-05      0.12       1      53 [.       7      56 ..       7     133 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4e-05
                         PIN_12  1 ifiDTnifldeffrlsee.ealkklleliesgkiklivpdivldEflknrekki 53
                                   i++DT i+l + f++se+ ++ +   el+++  +++++ +iv++E+l  +  k+
  gi|119718946|ref|YP_919441.1|  7 IVVDTDILLHDTFEDSEKhAEAS---ELLDE-ADRIYLASIVVHEYLWLLLTKF 56
                                   89*******98888887734444...44555.599**********975444443 PP

>> PIN_4  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.7   0.00042       1.3       1     126 [.       7     136 ..       7     138 .. 0.53

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00042
                          PIN_4   1 fVlDTnvlLhdpealksf..........keehdvviPitVleE.....LdklKkgsserelarlarqanrlldellekes 65 
                                    +V+DT +lLhd    +            +e  ++++  +V++E     L k+K + +  +++++ ++  +  + +  +e+
  gi|119718946|ref|YP_919441.1|   7 IVVDTDILLHDTF--EDSekhaeasellDEADRIYLASIVVHEylwllLTKFKIDID--SVREKLEEYFSDARFIYISEN 82 
                                    6999999999982..222356788888778888999999999955544444444444..333333322222222222233 PP

                          PIN_4  66 grlkvqtsaeelpeeeseseknDnrIlavalelkeekpdrkvvLvskDinlrikAkalgie 126
                                    +++++  ++ + +      +k+D + ++  + l  ++ +   +L + D +lr  Ak lg++
  gi|119718946|ref|YP_919441.1|  83 SEVFMGALDLMKE------DKADPSMINDYIILVLAQ-RMGATLATYDEELREIAKKLGVP 136
                                    3444433332222......244444444333333333.34556788888888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       670  (0.0373696); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 876.75
//
Query:       gi|119718947|ref|YP_919442.1|  [L=98]
Description: hypothetical protein Tpen_0029 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 670.99
//
Query:       gi|119718948|ref|YP_919443.1|  [L=120]
Description: hypothetical protein Tpen_0030 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 852.98
//
Query:       gi|119718949|ref|YP_919444.1|  [L=308]
Description: NAD-dependent epimerase/dehydratase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-55  188.2   0.1      2e-55  187.9   0.1    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    2.1e-49  168.7   0.0    8.9e-49  166.7   0.0    1.7  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    7.1e-33  113.8   0.0    9.1e-33  113.4   0.0    1.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    1.4e-20   73.6   0.0    1.7e-20   73.3   0.0    1.1  1  RmlD_sub_bind    RmlD substrate binding domain
      9e-18   64.4   0.0    5.4e-17   61.9   0.0    1.9  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    5.8e-12   45.9   0.5    9.4e-12   45.2   0.5    1.3  1  NAD_binding_10   NAD(P)H-binding
    6.5e-12   45.5   0.1    1.2e-07   31.5   0.3    2.1  2  NmrA             NmrA-like family
    6.3e-10   38.7   0.3    6.2e-09   35.4   0.0    2.3  2  NAD_binding_4    Male sterility protein
    1.1e-05   24.9   0.1    2.6e-05   23.8   0.1    1.7  2  adh_short        short chain dehydrogenase
    1.2e-05   25.3   0.1    2.2e-05   24.4   0.1    1.3  1  KR               KR domain
    6.6e-05   22.6   0.1    0.00014   21.5   0.1    1.5  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
     0.0021   18.3   0.1     0.0038   17.5   0.1    1.4  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0029   17.8   0.1     0.0073   16.5   0.1    1.7  1  TrkA_N           TrkA-N domain
     0.0062   16.1   0.0      0.013   15.1   0.0    1.5  2  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
     0.0071   16.0   0.0      0.024   14.2   0.0    1.8  2  DAO              FAD dependent oxidoreductase
     0.0071   16.5   0.1      0.037   14.2   0.1    2.3  2  NAD_binding_8    NAD(P)-binding Rossmann-like domain
  ------ inclusion threshold ------
      0.014   15.3   0.1      0.021   14.7   0.1    1.4  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
      0.032   14.2   0.4      0.079   13.0   0.2    1.8  2  Glyco_transf_4   Glycosyltransferase Family 4
      0.096   12.8   0.0       0.13   12.3   0.0    1.2  1  Ldh_1_N          lactate/malate dehydrogenase, NAD binding do
       0.12   12.6   0.0       0.25   11.5   0.0    1.5  1  UPF0180          Uncharacterised protein family (UPF0180)
        0.2   11.0   0.2       0.68    9.3   0.1    1.9  2  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.9   0.1   2.3e-58     2e-55       3     241 .]       5     233 ..       3     233 .. 0.91

  Alignments for each domain:
  == domain 1  score: 187.9 bits;  conditional E-value: 2.3e-58
                                    EETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.....EEEE--TT-HHHHHHHHHHHT-SEEEE--S---H CS
                      Epimerase   3 VtGatGfiGsalvkallekgyevigldrlssasntarledl.....elveldltdrsalerlfkeeqpdavihlAavggv 77 
                                    +tG++GfiG +++++l+++g +v++ld  s+a     +edl     e++e+d++d++al+r+++  ++davihlAa  +v
  gi|119718949|ref|YP_919444.1|   5 ITGGAGFIGFNTARYLASRGFQVVVLDDFSRATV--GREDLekvgaEVYEGDVRDAEALRRFLS--GVDAVIHLAALVDV 80 
                                    9**************************9954433..333334579*******************..9************* PP

                                    HHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHHHH CS
                      Epimerase  78 aassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklveaya 157
                                    ++s e+p++++  n++gt+ ll +a++agv++++f+sS++vYG+       e++     +p s Y+++K+ ge+l++ + 
  gi|119718949|ref|YP_919444.1|  81 RESEERPEEYWSVNVEGTRALLAEASRAGVRKVVFASSAAVYGDLGGLTAGEEV---DARPKSFYGLTKRVGEELCRFFS 157
                                    ***********************************************5444444...479*****************886 PP

                                    HHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHTT-STTEE CS
                      Epimerase 158 aqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvlehvdagdkgei 237
                                       g+ +++lr+fn+yG++    ++++vi  ++r++l+g  +v+++gdg++ Rdf+yv Dva+a+ +v+++ + g   e+
  gi|119718949|ref|YP_919444.1| 158 GR-GVVCVALRIFNVYGEY----SRRGVIYEFARRVLSGL-PVKVYGDGNQTRDFVYVGDVARAFEAVIAEWSGG--FEV 229
                                    55.59**************....*****************.****************************995554..458 PP

                                    EEES CS
                      Epimerase 238 yniG 241
                                    +n++
  gi|119718949|ref|YP_919444.1| 230 FNVA 233
                                    8875 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.7   0.0     1e-51   8.9e-49       2     331 ..       5     295 ..       5     296 .. 0.89

  Alignments for each domain:
  == domain 1  score: 166.7 bits;  conditional E-value: 1e-51
                                    EETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEEE CS
                  GDP_Man_Dehyd   2 iTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevyn 81 
                                    iTG+aGfiG ++a++L ++g++v+++++ s + ++gr e l+k          ++++gD++D+++l+r l+ v  d+v++
  gi|119718949|ref|YP_919444.1|   5 ITGGAGFIGFNTARYLASRGFQVVVLDDFSRA-TVGR-EDLEKV-------GAEVYEGDVRDAEALRRFLSGV--DAVIH 73 
                                    9**********************999877665.3344.455532.......3479****************99..9**** PP

                                    --S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHHHHHHHHH CS
                  GDP_Man_Dehyd  82 LAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYaaaKlyad 161
                                    LAA   V++s e Pe+++ vnv Gt  LL  + ++g++   ++++aS++ vYG++      E+   +P+s Y+ +K + +
  gi|119718949|ref|YP_919444.1|  74 LAALVDVRESEERPEEYWSVNVEGTRALLAEASRAGVR---KVVFASSAAVYGDLGGLTAGEEVDARPKSFYGLTKRVGE 150
                                    ********************************999996...8999*********************************** PP

                                    HHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHHHHHHHHHC.. CS
                  GDP_Man_Dehyd 162 wivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkDyveamwlmlqq.. 239
                                     +++ +    g+ +v  ++fn ++ +  ++     i +++ r++ g+ +v ++G+++++Rd+ +v D+++a+ +++ +  
  gi|119718949|ref|YP_919444.1| 151 ELCRFF-SGRGVVCVALRIFNVYGEYS-RR---GVIYEFARRVLSGL-PVKVYGDGNQTRDFVYVGDVARAFEAVIAEws 224
                                    ***865.679****************5.33...5699999999***9.77889***********************9844 PP

                                    SS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB--B-THHHHHHH-- CS
                  GDP_Man_Dehyd 240 dkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdlllgdaskakeeLgW 319
                                    +  e +++a+g+ +sv+e+v+l f+++                    g ++v v +++ rp+e ++ ++ ++ka + Lg+
  gi|119718949|ref|YP_919444.1| 225 GGFEVFNVASGRCVSVNELVRL-FEQVT-------------------G-KRVGVLREPARPEEIRRSCASTEKAARMLGF 283
                                    5568899999999999999974.44442...................2.367888999********************** PP

                                    --SS-HHHHHHH CS
                  GDP_Man_Dehyd 320 kpkvsfeelvre 331
                                    ++++s+ee+vr+
  gi|119718949|ref|YP_919444.1| 284 RASTSLEEGVRR 295
                                    **********97 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.4   0.0   1.1e-35   9.1e-33       2     224 ..       5     215 ..       4     222 .. 0.88

  Alignments for each domain:
  == domain 1  score: 113.4 bits;  conditional E-value: 1.1e-35
                      3Beta_HSD   2 vtGgaGFlGralvkeLvrleelkevrvlD.lrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslvdva 80 
                                    +tGgaGF+G +  + L +++   +v vlD     +  +e+l+kv+ + v egDv+d++ l++ l gvd+vihla+lvdv+
  gi|119718949|ref|YP_919444.1|   5 ITGGAGFIGFNTARYLASRG--FQVVVLDdFSRATVGREDLEKVGAE-VYEGDVRDAEALRRFLSGVDAVIHLAALVDVR 81 
                                    8******************9..4666665378888889********9.*******************************9 PP

                      3Beta_HSD  81 g.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKalaEklvlk 159
                                      + + +e+ +vnv+GTr +l+ + +agvr++v+ Ssa v g+  lg  ++ g+E    +  +++ y  +K++ E+l   
  gi|119718949|ref|YP_919444.1|  82 EsEERPEEYWSVNVEGTRALLAEASRAGVRKVVFASSAAVYGD--LG-GLTAGEEV---DARPKSFYGLTKRVGEELCRF 155
                                    978899*************************************..44.45557764...5667889***********987 PP

                      3Beta_HSD 160 aNgrtlknggrlyTcaLRpagiyGegdkllv.pllkqlaklglalfkigdeevlsdrvYvgNvawa 224
                                      g        ++ +aLR   +yGe++++ v   + + + +gl +  +gd +++ d+vYvg va a
  gi|119718949|ref|YP_919444.1| 156 FSG------RGVVCVALRIFNVYGEYSRRGViYEFARRVLSGLPVKVYGDGNQTRDFVYVGDVARA 215
                                    777......34799************99744145566667899*********************87 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.3   0.0     2e-23   1.7e-20       1     264 [.       1     278 [.       1     301 [. 0.84

  Alignments for each domain:
  == domain 1  score: 73.3 bits;  conditional E-value: 2e-23
                                    EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT..................T--TTSHHHHHHHHHHH--SEEEE----- CS
                  RmlD_sub_bind   1 mkilvtGanGqlGseLakqlaeeglevlaltre..................eldltdaeavaellkeakpdvvvnaAAyt 62 
                                    m++ +tG+ G +G + a+ la++g++v+ l+                    e d++daea++++l+    d+v+++AA  
  gi|119718949|ref|YP_919444.1|   1 MNVGITGGAGFIGFNTARYLASRGFQVVVLDDFsratvgredlekvgaevyEGDVRDAEALRRFLSG--VDAVIHLAALV 78 
                                    7888**************************655678******************************9..789******** PP

                                    -HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT-.EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHH... CS
                  RmlD_sub_bind  63 avDkaEseeeaayavnaeavealAeaaaavga.lLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavla... 138
                                    +v + E+ +e+   vn+e+++al ++a+++g+ ++++ S+  V+         e+    P+++YG tK  GE+  +    
  gi|119718949|ref|YP_919444.1|  79 DVRESEERPEEYWSVNVEGTRALLAEASRAGVrKVVFASSAAVYGDLGGLTAGEEVDARPKSFYGLTKRVGEELCRFfsg 158
                                    **********************99999999984699********88888888999999****************998544 PP

                                    H-SSEEEEEE-SEESS.SSS-HHHHHHHHHHH-SEEEEESS..-EE--EEHHHHHHHHHHHHHHCHH.GGG-EEEE---B CS
                  RmlD_sub_bind 139 agkkalivRtswvyge.kgknfvktmlrlakereelkvvaD..qlgsPTsardlAevllqllekaaeekelagvyHlane 215
                                     g  ++ +R+  vyge +++  +  + r++ +  ++kv  D  q++   ++ d+A++  ++++++      ++v+ +a+ 
  gi|119718949|ref|YP_919444.1| 159 RGVVCVALRIFNVYGEySRRGVIYEFARRVLSGLPVKVYGDgnQTRDFVYVGDVARAFEAVIAEWSG---GFEVFNVASG 235
                                    55566779******99556789999*************9987799999***************9996...6899999999 PP

                                    S-EEHHHHHHHHHHHHCHTTSEEEEE-CCCS--SS---SBE-B--HHHH CS
                  RmlD_sub_bind 216 getswlefArailkeagadseevkpistaeyptpAkRPanSvLdtekle 264
                                    + +s  e+ r   + +g+   +v    + + p++ +R   S   tek++
  gi|119718949|ref|YP_919444.1| 236 RCVSVNELVRLFEQVTGK---RVGVLREPARPEEIRRSCAS---TEKAA 278
                                    999998888776555555...67777777777777775544...34444 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.9   0.0   6.4e-20   5.4e-17       2     250 ..       4     254 ..       3     284 .. 0.84

  Alignments for each domain:
  == domain 1  score: 61.9 bits;  conditional E-value: 6.4e-20
                                    EEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T-SEE CS
                Polysacc_synt_2   2 lvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkvdvv 81 
                                     +tG++G iG +  r ++++  + ++l   d+++  ++ +e  e++ + ++ +      gdvrd+e l++ l+  +vd+v
  gi|119718949|ref|YP_919444.1|   4 GITGGAGFIGFNTARYLASRGFQVVVL---DDFSRATVGREDLEKVGA-EV-Y-----EGDVRDAEALRRFLS--GVDAV 71 
                                    59************9999998887776...456666777775455554.23.3.....5**************..***** PP

                                    EE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEGGG..............SS--SHHHHHHHHHHH CS
                Polysacc_synt_2  82 fhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliStDKA..............vnPtnvmGatKrlaek 147
                                    +h AAl  V   ee p e ++ Nv gt+ ++  a +agv+kvv+ S+                 ++P + +G+tKr+ e 
  gi|119718949|ref|YP_919444.1|  72 IHLAALVDVRESEERPEEYWSVNVEGTRALLAEASRAGVRKVVFASSAAVygdlggltageevdARPKSFYGLTKRVGEE 151
                                    ********************************************9985322222222223333379************** PP

                                    HHHHGGG--SSS--EEEEEEE-EETT..GTTSSHHHHHHHHHTTSSEEE.S-TT-EEEEE-HHHHHHHHHHHHHH--SS. CS
                Polysacc_synt_2 148 llqalakeseekktkfvvvRfGNVlg..SrGSviplFkkqikeggpvtv.TdpemtRyfmtieeavqLvlqalalakgg. 223
                                    l+  ++ +        v+ R  NV g  Sr  vi  F +++ +g pv v  d + tR f+ + + ++     +a+ +gg 
  gi|119718949|ref|YP_919444.1| 152 LCRFFSGRG----VVCVALRIFNVYGeySRRGVIYEFARRVLSGLPVKVyGDGNQTRDFVYVGDVARAFEAVIAEWSGGf 227
                                    ***999887....899999*****9877999*****************95589*********999888777777766665 PP

                                    -EEEE--.-EEEHHHHHHHH....... CS
                Polysacc_synt_2 224 eifvldmGepvkivdlakalielsgle 250
                                    e+f +  G  v++ +l++ + +++g++
  gi|119718949|ref|YP_919444.1| 228 EVFNVASGRCVSVNELVRLFEQVTGKR 254
                                    9***************99888888765 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2   0.5   1.1e-14   9.4e-12       1     104 [.       7     124 ..       7     150 .. 0.79

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 1.1e-14
                                    TTTSHHHHHHHHHHHHC-T-EEEEE...ETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES-......--T CS
                 NAD_binding_10   1 GAtGkvGrllvkellargghevtal...vRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsal......ggg 71 
                                    G+ G +G   ++ l++rg ++v++l    R +   ++le + g+ev egdv d+e+l++ l+g+daV+  +         
  gi|119718949|ref|YP_919444.1|   7 GGAGFIGFNTARYLASRG-FQVVVLddfSRATVGREDLE-KVGAEVYEGDVRDAEALRRFLSGVDAVIHLAalvdvrE-- 82 
                                    999**************5.**977522244444446887.79*************************87775666542.. PP

                                    CC..........HHHHHHHHHHHHHHCT--EEEEEEETTTTSG CS
                 NAD_binding_10  72 gk..........deegaknivdaakeagvkRfvlvsaigvgde 104
                                     +          + eg++++++ a +agv+++v+ s++ v+ +
  gi|119718949|ref|YP_919444.1|  83 -SeerpeeywsvNVEGTRALLAEASRAGVRKVVFASSAAVYGD 124
                                    .122234455454455***********************9965 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.3   1.4e-10   1.2e-07       3     102 ..       5     118 ..       3     124 .. 0.91
   2 !   11.9   0.0   0.00014      0.12     167     229 ..     194     255 ..     170     294 .. 0.89

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 1.4e-10
                                    ESSTTSHHHHHHHHHHHHHT-EEEEEES-S.-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-SEEEE---GG...... CS
                           NmrA   3 viGaTGrqGksvvrallkaghkvralvRdt.kselakslkeaGvelvkgdlddkeslvealkgvdvvfsvtgfy...... 75 
                                    ++G++G +G   +r+l+++g++v +l   +  +   + l++ G+e+ +gd+ d e l++ l+gvd+v+   ++       
  gi|119718949|ref|YP_919444.1|   5 ITGGAGFIGFNTARYLASRGFQVVVLDDFSrATVGREDLEKVGAEVYEGDVRDAEALRRFLSGVDAVIHLAALVdvrese 84 
                                    89*********************988544445666799*******************************999889999** PP

                                    .......S-HHHHHHHHHHHHHHHS-SEEEEEE- CS
                           NmrA  76 .......skeiedgkklvdAakeaGvkhfiySsl 102
                                           s ++e   +l + a +aGv++++++s 
  gi|119718949|ref|YP_919444.1|  85 erpeeywSVNVEGTRALLAEASRAGVRKVVFASS 118
                                    ****9999***********************985 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00014
                                    EEEEESS-TTS-EE-HHHHHHHHHHHHHHHHHHHTTEEEEE-SEEE-HHHHHHHHHHHHTS-E CS
                           NmrA 167 vtllgpgnpkavlldaeeDiGafvikilkdprklkgkriklagntlsgneivelfekkigktv 229
                                    v++ g+gn    ++  + D++++  +++ + +    +    +g ++s+ne+v+lfe+++gk+v
  gi|119718949|ref|YP_919444.1| 194 VKVYGDGNQTRDFV-YVGDVARAFEAVIAEWSGGFEVFNVASGRCVSVNELVRLFEQVTGKRV 255
                                    77889999888888.9999999999999998877777777899******************98 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.4      0.22   1.9e+02       1      49 [.       5      54 ..       5      60 .. 0.63
   2 !   35.4   0.0   7.3e-12   6.2e-09      78     217 ..      58     183 ..      48     207 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.22
                                   EE-TTSHHHHHHHHHHHHHS-.TEEEEE...E-SSSHHHHHHHHHHHT-SS- CS
                  NAD_binding_4  1 lTGaTGFLGkvLlekLLrttpevkiyll...vRaksgesaeeRleeelekke 49
                                   +TG+ GF+G    + L ++    ++++l    Ra+ g++ +e++ +e+++ +
  gi|119718949|ref|YP_919444.1|  5 ITGGAGFIGFNTARYLASRGF--QVVVLddfSRATVGREDLEKVGAEVYEGD 54
                                   8********877777766654..45554333566666666666666666555 PP

  == domain 2  score: 35.4 bits;  conditional E-value: 7.3e-12
                                    HHHHHHHHHH--EEEE--SS-S.ST...TSSEEHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H. CS
                  NAD_binding_4  78 eedlqelaeevdviihsaAtvnfde...pykellrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyee 154
                                    +e+l++  + vd++ih aA v++ e   + +e ++vNveGtr +l  a++      +++ S+a+v+g+  g         
  gi|119718949|ref|YP_919444.1|  58 AEALRRFLSGVDAVIHLAALVDVREseeRPEEYWSVNVEGTRALLAEASRAGVR-KVVFASSAAVYGDLGGLT------- 129
                                    67889999*************99874336677****************977666.9**************753....... PP

                                    .....HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE-.-SSST---T CS
                  NAD_binding_4 155 gekeekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitg.esktGwing 217
                                            ++  + ++  +  Y  +K ++E+l+r  + r g+ +v +R+ +++g  s  G+i +
  gi|119718949|ref|YP_919444.1| 130 -------AGE--EVDARPKSFYGLTKRVGEELCRFFSGR-GVVCVALRIFNVYGeYSRRGVIYE 183
                                    .......233..333445567**************9977.9999999*9999995466676654 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.1   3.1e-08   2.6e-05       3      87 ..       3      77 ..       1     123 [. 0.72
   2 ?   -3.3   0.0       5.9     5e+03      31      71 ..     258     300 ..     250     303 .. 0.64

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 3.1e-08
                                   EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEEEE- CS
                      adh_short  3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldvLvnN 84
                                   v +tG+++ IG ++a+ la++G++vvv+d  ++ +    + l++    a ++++Dv+d+e+++++++ +       d++++ 
  gi|119718949|ref|YP_919444.1|  3 VGITGGAGFIGFNTARYLASRGFQVVVLDDFSR-ATVGREDLEK--VGAEVYEGDVRDAEALRRFLSGV-------DAVIHL 74
                                   669************************887754.4345555665..5599************9998876.......555555 PP

                                   --S CS
                      adh_short 85 AGi 87
                                   A++
  gi|119718949|ref|YP_919444.1| 75 AAL 77
                                   555 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 5.9
                                    ESCHHHHHHHHHHHHHT..TSEEEEEE-TTTSHHHHHHHHHHH CS
                      adh_short  31 drseekleevakelkee..gakalaiqvDvtdreevealveka 71 
                                     r++++ ee+  ++ ++  +a++l +++  + +e v+++ve++
  gi|119718949|ref|YP_919444.1| 258 LREPARPEEIRRSCASTekAARMLGFRASTSLEEGVRRVVEWV 300
                                    5666677777777766644556666666666777777777766 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.1   2.6e-08   2.2e-05       5     141 ..       5     122 ..       3     129 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 2.6e-08
                                    EETTTSHHHHHHHHHHHHHHS-EEEE..E-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS-- CS
                             KR   5 itGGlGgLGlelarwlaekgarhlvl..lsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeeppi 82 
                                    itGG+G +G  +ar la++g + +vl  +sR  +         + le+ gae  v++ Dv d++a+++ l+ ++      
  gi|119718949|ref|YP_919444.1|   5 ITGGAGFIGFNTARYLASRGFQVVVLddFSRA-T---V---GREDLEKVGAE--VYEGDVRDAEALRRFLSGVD------ 69 
                                    9*********************9999445555.1...2...23467777765..689*************9987...... PP

                                    -EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTTS--SEEEEEEEHHHHH CS
                             KR  83 kGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelledesldffvlfSSiagll 141
                                      vih A +++ +     ++e+ e+  +  v+G++ L    ++  +  +v+ SS+a ++
  gi|119718949|ref|YP_919444.1|  70 -AVIHLAALVDVRE----SEERPEEYWSVNVEGTRALLAEASRAGVRKVVFASSAA-VY 122
                                    .8******999765....55666666778999**9998888878888887777765.44 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.1   1.7e-07   0.00014       6      86 ..      12      82 ..       7     128 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.7e-07
                                   HHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSEEEE--TTSHHHHHHHHHHHHHHHSSEEEEEE-----EGCSS- CS
                   adh_short_C2  6 IGraiAkalaeeGaevvltdlneeakkrveelaeelgaevlecDVtdeeqvealveevvekfgklDilvnnagiapklkgp 86
                                   IG+ +A+ la++G +vv+ d   +a    +e  e++gaev+e DV+d e+++++ +        +D +++ a+ ++    +
  gi|119718949|ref|YP_919444.1| 12 IGFNTARYLASRGFQVVVLDDFSRA-TVGREDLEKVGAEVYEGDVRDAEALRRFLSG-------VDAVIHLAALVDV--RE 82
                                   9**************9999877776.577888888**************99998764.......6677777777766..44 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   4.5e-06    0.0038       5      77 ..       8      75 ..       3      83 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.5e-06
                                   --SHHHHHHHHHHHCTCCT-GEEEEEE.SSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-S CS
                Sacchrp_dh_NADP  5 GaGsvGqavaellarhfdvdaeitvad.rskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnls 77
                                   GaG++G  +a++la ++ +  +++v d +s++ + ++  ++ +v +e ++ d+ + ea L + l++ d+v++l+
  gi|119718949|ref|YP_919444.1|  8 GAGFIGFNTARYLASRG-F--QVVVLDdFSRATVGRE--DLEKVGAEVYEGDVRDAEA-LRRFLSGVDAVIHLA 75
                                   67*************98.4..5666651666665555..5699***************.*************98 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   8.6e-06    0.0073       5      62 ..       8      70 ..       5      87 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 8.6e-06
                                   S-SHHHHHHHHHHHHTTEEEEEEESSHHH...HHHHHHTTSEEEES-TTSHHHHHHT..TGGG CS
                         TrkA_N  5 GlGrvGrslaeeLseggkdvvvidkdeer...veelreeglevvvgdatdeevLeea..giek 62
                                   G+G +G + a++L ++g +vvv d+  ++    e l++ g+ev+ gd+ d e+L++   g++ 
  gi|119718949|ref|YP_919444.1|  8 GAGFIGFNTARYLASRGFQVVVLDDFSRAtvgREDLEKVGAEVYEGDVRDAEALRRFlsGVDA 70
                                   899************7757999998776666678889999**************997444444 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.5e-05     0.013       7      36 ..       8      38 ..       1      62 [. 0.75
   2 ?   -3.2   0.0         6   5.1e+03      95     113 ..     204     222 ..     196     266 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.5e-05
                                   --STTHHHHHHHHHHCTSEEEEE-.S-HHHH CS
                 UDPG_MGDP_dh_N  7 GlGYvGlvtaavlaeighevigvD.ideekv 36
                                   G+G++G  ta  la++g++v+++D  ++++v
  gi|119718949|ref|YP_919444.1|  8 GAGFIGFNTARYLASRGFQVVVLDdFSRATV 38
                                   79*******************9972455555 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 6
                                    B-THHHHHHHHHHHHHHHC CS
                 UDPG_MGDP_dh_N  95 aDlkyvesaarsiaealkk 113
                                     D  yv ++ar+ + ++ +
  gi|119718949|ref|YP_919444.1| 204 RDFVYVGDVARAFEAVIAE 222
                                    5666777777666666554 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   2.8e-05     0.024       6      31 ..       8      35 ..       8      41 .. 0.90
   2 ?   -1.5   0.0       1.6   1.4e+03     167     167 ..      78      78 ..      40     138 .. 0.51

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.8e-05
                                   CTSHHHHHHHHHHHHTT..EEEEESSSS CS
                            DAO  6 GGGiiGlstAyeLarrg..Vtllekgdi 31
                                   G+G iG  tA++La rg  V++l+  ++
  gi|119718949|ref|YP_919444.1|  8 GAGFIGFNTARYLASRGfqVVVLDDFSR 35
                                   9**********************98755 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.6
                                    E CS
                            DAO 167 t 167
                                     
  gi|119718949|ref|YP_919444.1|  78 V 78 
                                    1 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.1   4.4e-05     0.037       3      27 ..       8      32 ..       7      64 .. 0.93
   2 ?   -1.7   0.0       4.3   3.7e+03      26      51 ..     275     303 ..     267     306 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.4e-05
                                   --SHHHHHHHHHHHCCTEEEEEE-S CS
                  NAD_binding_8  3 GaGlsGlvaAylLakagfdvlllek 27
                                   GaG+ G  +A++La +gf+v++l+ 
  gi|119718949|ref|YP_919444.1|  8 GAGFIGFNTARYLASRGFQVVVLDD 32
                                   9**********************96 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 4.3
                                    -SSSS.SSGGG-EECETT..CEECTS--- CS
                  NAD_binding_8  26 ekrdr.lGGraasyevpg..vrvdygahi 51 
                                    ek+ r lG ra++   +g  ++v++ a++
  gi|119718949|ref|YP_919444.1| 275 EKAARmLGFRASTSLEEGvrRVVEWVARY 303
                                    55555589999998777766777777766 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   2.4e-05     0.021       6      79 ..       8      80 ..       2     120 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.4e-05
                                   --SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEES-HHHHHC- CS
                        3HCDH_N  6 GaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaalarisfttdleeavda 79
                                   GaG +G   a  +as+g++Vv++d  + +++ ++e +ek  +++ e    ++e  ++ l+ + +  +l+++vd+
  gi|119718949|ref|YP_919444.1|  8 GAGFIGFNTARYLASRGFQVVVLDDFS-RATVGREDLEKVGAEVYEGDVRDAEALRRFLSGVDAVIHLAALVDV 80
                                   78*********************9765.5567888888877777776667778888888888888888888776 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2   9.2e-05     0.079       2      44 ..       7      51 ..       6      81 .. 0.61
   2 ?   -2.8   0.0       6.4   5.4e+03       9      29 ..      99     119 ..      97     155 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.2e-05
                 Glyco_transf_4  2 GGverhvleLaraLarrGheVtvv...tpgddgpleeev..elvvrvp 44
                                   GG++   ++ ar+La rG++V+v+   +   +   ++e+  +++ +v 
  gi|119718949|ref|YP_919444.1|  7 GGAGFIGFNTARYLASRGFQVVVLddfS---RATVGREDleKVGAEVY 51
                                   9999999*****************5553...44444442222233322 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 6.4
                 Glyco_transf_4   9 leLaraLarrGheVtvvtpgd 29 
                                    + L  +  r+G++ +v++++ 
  gi|119718949|ref|YP_919444.1|  99 RALLAEASRAGVRKVVFASSA 119
                                    566777778888888886543 PP

>> Ldh_1_N  lactate/malate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00016      0.13       2      78 ..       2      76 ..       1     115 [. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00016
                                   EEEEETTTSHHHHHHHHHHHHTTSSSEEEEE-SSHHHHHHHHHHHHHCHCCSTS.-EEEEESSGGGGTTESEEEE--S CS
                        Ldh_1_N  2 kvavvGaaGgiGqslalllankkladelaLlDiakekleGvaldlshistflsv.kvkvsekeeealkdadvvvitag 78
                                   +v ++G aG+iG ++a  la+++++  ++L D+ + ++ G   dl+ + + ++  +v+  e     l+++d v+  a+
  gi|119718949|ref|YP_919444.1|  2 NVGITGGAGFIGFNTARYLASRGFQV-VVLDDFSR-ATVG-REDLEKVGAEVYEgDVRDAEALRRFLSGVDAVIHLAA 76
                                   799*********************99.99999983.5555.4688887776643145555588999999999997766 PP

>> UPF0180  Uncharacterised protein family (UPF0180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00029      0.25      13      46 ..      17      57 ..      15      78 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00029
                        UPF0180 13 keaLrekGYeVvdlet.......eedaqsvdaiVvtGqdtn 46
                                   +++L+++G++Vv l++        ed ++v a V++G+ ++
  gi|119718949|ref|YP_919444.1| 17 ARYLASRGFQVVVLDDfsratvgREDLEKVGAEVYEGDVRD 57
                                   689*******************9899**********97655 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1   0.00079      0.68      39      73 ..       3      38 ..       1      54 [. 0.77
   2 ?   -2.5   0.0       3.3   2.8e+03     148     161 ..      75      88 ..      48      94 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00079
                                   EEEE.S-SHHHHHHHHHHHHTT-EEEEESSSHHHHH CS
                   2-Hacid_dh_C 39 vGii.GlGrIGqavakrlkafgmkviaydrskkkee 73
                                   vGi  G+G IG ++a++l++ g++v++ d + +++ 
  gi|119718949|ref|YP_919444.1|  3 VGITgGAGFIGFNTARYLASRGFQVVVLDDFSRATV 38
                                   7887369***********************988665 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.3
                                    EEEES--SSSSSGT CS
                   2-Hacid_dh_C 148 gaalDvfeeeplpe 161
                                    +a +Dv e+e+ pe
  gi|119718949|ref|YP_919444.1|  75 AALVDVRESEERPE 88 
                                    45678888887774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 2029.41
//
Query:       gi|119718950|ref|YP_919445.1|  [L=166]
Description: metallopeptidase-like [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1073.54
//
Query:       gi|119718951|ref|YP_919446.1|  [L=124]
Description: hypothetical protein Tpen_0033 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-06   28.1   0.8    1.5e-05   25.4   0.8    1.9  1  Rubrerythrin     Rubrerythrin
     0.0029   16.5   0.0      0.084   11.7   0.0    2.0  2  FA_desaturase_2  Fatty acid desaturase
     0.0038   17.2   0.7     0.0055   16.6   0.7    1.4  1  Ferritin         Ferritin-like domain
  ------ inclusion threshold ------
      0.028   14.5   0.4       0.49   10.5   0.8    2.0  2  Imm30            Immunity protein 30
      0.073   13.4   0.3       0.13   12.6   0.2    1.4  1  DUF4806          Domain of unknown function (DUF4806)


Domain annotation for each model (and alignments):
>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.8   4.1e-09   1.5e-05      32     136 ..       3      93 ..       1      94 [. 0.76

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 4.1e-09
                                    HHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS-------TTGGHHHHHHHHHHHHHHHHHCHHHHHHHHHHHTT CS
                   Rubrerythrin  32 aelFeelAeeEreHakilnklleklepelelevkekvreyaeakpkflttaknLeeaiegayaeeeemyrfyeelaekeg 111
                                    + ++  +A + r+Ha+i   +l+ l++             a ++++f      Le +++  + +eeem++++++  +++ 
  gi|119718951|ref|YP_919446.1|   3 KSILGSIANDSRKHAEIYSGILRILREVGP----------AITEEDF----SRLEGIVKTHIRMEEEMIETLNRFFKEVD 68 
                                    666777888888888887777766443333..........3334444....56777889999999999999999999999 PP

                                    SHHHHHHHHHHHHHHHHHHHHHHHH CS
                   Rubrerythrin 112 neeakklfkklaeaEkkHeerlrkl 136
                                    +++++ lf+++ ++E kH ++l ++
  gi|119718951|ref|YP_919446.1|  69 DKRVEYLFRYILDDEVKHHRLLLNI 93 
                                    999999**************99875 PP

>> FA_desaturase_2  Fatty acid desaturase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   2.3e-05     0.084     184     236 ..       2      57 ..       1      64 [. 0.79
   2 !    3.5   0.0    0.0074        27     174     211 ..      62      99 ..      58     106 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.3e-05
                FA_desaturase_2 184 lakicgaiaadEkrHeaaYtrvvekllevdp...deavlaladmmrkkitmPaall 236
                                    ++ i+g ia+d ++H+  Y+ +++ l ev p   +e    l+ +++++i m  +++
  gi|119718951|ref|YP_919446.1|   2 IKSILGSIANDSRKHAEIYSGILRILREVGPaitEEDFSRLEGIVKTHIRMEEEMI 57 
                                    789********************999999983334556667778888888876665 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.0074
                FA_desaturase_2 174 klakeagdellakicgaiaadEkrHeaaYtrvveklle 211
                                    +  ke +d+ ++ + + i  dE +H+    +++e +++
  gi|119718951|ref|YP_919446.1|  62 RFFKEVDDKRVEYLFRYILDDEVKHHRLLLNILELIVK 99 
                                    677899*******************9998888877765 PP

>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.7   1.5e-06    0.0055      75     139 ..      36      97 ..       4     100 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.5e-06
                                    SSSCSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Ferritin  75 pkefgsveevleaalehekkvteslrelielaeeegDpatadfledfleeqeeheweleallekl 139
                                    +++f+ +e +++  + +e++ +e+l++  + ++   D   + ++  +l+++++h + l ++le +
  gi|119718951|ref|YP_919446.1|  36 EEDFSRLEGIVKTHIRMEEEMIETLNRFFKEVD---DKRVEYLFRYILDDEVKHHRLLLNILELI 97 
                                    23378999***********************99...56999999**************9999976 PP

>> Imm30  Immunity protein 30
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.062   2.2e+02      35      58 ..       8      31 ..       2      57 .. 0.73
   2 ?   10.5   0.8   0.00014      0.49      16      56 ..      58      99 ..      47     112 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.062
                          Imm30 35 kafdDdtedeevmFglvHlledle 58
                                   ++ +D+ ++ e+  g++ +l + +
  gi|119718951|ref|YP_919446.1|  8 SIANDSRKHAEIYSGILRILREVG 31
                                   6779999*****999999988754 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00014
                          Imm30 16 salekllkeqnkdnledlck.afdDdtedeevmFglvHlled 56
                                   ++l+++ ke  ++ +e+l++ ++dD+ +++ ++  ++ l+ +
  gi|119718951|ref|YP_919446.1| 58 ETLNRFFKEVDDKRVEYLFRyILDDEVKHHRLLLNILELIVK 99
                                   6899**************974799********9999988765 PP

>> DUF4806  Domain of unknown function (DUF4806)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   3.5e-05      0.13       8      58 ..      32      84 ..      29      90 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.5e-05
                        DUF4806  8 PvsseeelerLEaavrtdekirqqyvnyLrkikgk..kadlkkvfdklftdea 58
                                   P  +ee+++rLE  v+t   + +++++ L++   +  +++++  f+++++de+
  gi|119718951|ref|YP_919446.1| 32 PAITEEDFSRLEGIVKTHIRMEEEMIETLNRFFKEvdDKRVEYLFRYILDDEV 84
                                   7779***************************99999669999999****9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       886  (0.0494171); expected 358.6 (0.02)
Passed bias filter:                      651  (0.0363099); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 798.03
//
Query:       gi|119718952|ref|YP_919447.1|  [L=138]
Description: hypothetical protein Tpen_0034 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.032   14.5   0.1       0.41   10.9   0.0    2.0  2  GGDEF_2   GGDEF-like domain
       0.12   12.6   0.2        9.4    6.4   0.1    2.2  2  DUF2703   Domain of unknown function (DUF2703)
       0.13   12.8   0.2         22    5.7   0.0    2.3  2  NLE       NLE (NUC135) domain


Domain annotation for each model (and alignments):
>> GGDEF_2  GGDEF-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   6.9e-05      0.41      35     101 ..       8      75 ..       1      78 [. 0.75
   2 ?    3.7   0.0     0.012        72      38      82 ..      67     112 ..      55     132 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 6.9e-05
                        GGDEF_2  35 erllraleealralgpdalvavrgdrlvlllpaedeedaeallerlarrlgg.lsvriGiGspvegla 101
                                    e+++ +++e+l+++g +++v +++ +l++ll +++ ++   l    ++ ++  ++v + ++   e+l+
  gi|119718952|ref|YP_919447.1|   8 EEVVLRVSEELERFGLKNIVSEDSRTLIVLLDVAEGKEVPVLTTFSEESFSIvVPVNASVSELEERLS 75 
                                    5677899***************************9988776655555555556666666666555555 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.012
                        GGDEF_2  38 lraleealralgpdalvavrgd.rlvlllpaedeedaeallerlar 82 
                                    +++lee l+ lg ++ ++  g+    +++ ae+ + ae+l+ +l++
  gi|119718952|ref|YP_919447.1|  67 VSELEERLSGLGGKVHTMDLGEnLAGIVVEAEGLPGAEELAGKLRE 112
                                    4566666666666666666555233444555555555555554443 PP

>> DUF2703  Domain of unknown function (DUF2703)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1    0.0016       9.4      20      45 ..       2      27 ..       1      46 [. 0.89
   2 ?    4.5   0.0    0.0064        38      21      86 ..      66     131 ..      52     136 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0016
                        DUF2703 20 eTgktleeavkelkeaLealgievel 45
                                   eTgk++ee+v +++e+Le++g++  +
  gi|119718952|ref|YP_919447.1|  2 ETGKNVEEVVLRVSEELERFGLKNIV 27
                                   7********************98655 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0064
                        DUF2703  21 TgktleeavkelkeaLealgievelekvelseeelareflesntilingrpleellgvevkeelCe 86 
                                      ++lee ++ l  + +++++  +l  + ++ e l  +     +++  gr le ll  e    +C+
  gi|119718952|ref|YP_919447.1|  66 SVSELEERLSGLGGKVHTMDLGENLAGIVVEAEGLPGAEELAGKLREVGRLLESLLSSEKVGVCCS 131
                                    344455555555555555555555558888888888888888999999999999997777777775 PP

>> NLE  NLE (NUC135) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0    0.0047        28      16      37 ..       7      28 ..       2      48 .. 0.87
   2 ?    5.7   0.0    0.0036        22      16      37 ..      54      75 ..      47      85 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0047
                            NLE 16 vpgtplsvPasltrkqLselvn 37
                                   v++  l+v  +l+r +L ++v 
  gi|119718952|ref|YP_919447.1|  7 VEEVVLRVSEELERFGLKNIVS 28
                                   78999***************96 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0036
                            NLE 16 vpgtplsvPasltrkqLselvn 37
                                    +  ++ vP++ ++++L+e + 
  gi|119718952|ref|YP_919447.1| 54 EESFSIVVPVNASVSELEERLS 75
                                   446799***********99665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.31s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 922.36
//
Query:       gi|119718953|ref|YP_919448.1|  [L=358]
Description: hypothetical protein Tpen_0035 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.8e-05   23.2   0.0    0.00012   21.9   0.0    1.6  1  TrmB          Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.039   13.4   0.2      0.075   12.5   0.2    1.5  1  HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family I


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   1.3e-08   0.00012       4      51 ..      21      66 ..      19      67 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.3e-08
                                   CHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTS CS
                           TrmB  4 lGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGl 51
                                   + L+ +E kv + ++   + t++ ++e++++p+s+v +v+r+L+  Gl
  gi|119718953|ref|YP_919448.1| 21 FRLTPNEWKVLVSVV--NSTTVSRVSEQAKLPYSTVIDVMRRLSGNGL 66
                                   568999*********..789************************9997 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   8.3e-06     0.075      19      51 ..      29      61 ..      27      62 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.3e-06
                   HTH_Tnp_ISL3 19 yilelllesrsvkavArqlgvSwtTVwrildry 51
                                   ++l ++ +s +v+ v++q  +  +TV+++++r+
  gi|119718953|ref|YP_919448.1| 29 KVLVSVVNSTTVSRVSEQAKLPYSTVIDVMRRL 61
                                   78889999**********************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 2257.84
//
Query:       gi|119718954|ref|YP_919449.1|  [L=94]
Description: hypothetical protein Tpen_0036 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 630.32
//
Query:       gi|119718955|ref|YP_919450.1|  [L=141]
Description: hypothetical protein Tpen_0037 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.099   12.5   0.0       0.18   11.6   0.0    1.5  1  ETC_C1_NDUFA5  ETC complex I subunit conserved region


Domain annotation for each model (and alignments):
>> ETC_C1_NDUFA5  ETC complex I subunit conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0     1e-05      0.18      11      42 ..      56      86 ..      48     106 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1e-05
                  ETC_C1_NDUFA5 11 aLialytktLkkLkkiPessvYRqsvEaltkh 42
                                   +L   +++ L k++++P s  YR ++Eal+ +
  gi|119718955|ref|YP_919450.1| 56 TLADALSSFL-KVSSMPLSMEYRGKTEALIEE 86
                                   5555556655.589***************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1060.16
//
Query:       gi|119718956|ref|YP_919451.1|  [L=180]
Description: putative adenylyl cyclase CyaB [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-32  111.7   0.5    4.4e-32  111.5   0.5    1.1  1  CYTH      CYTH domain
     0.0045   16.8   0.0      0.045   13.6   0.0    2.2  2  F-box     F-box domain


Domain annotation for each model (and alignments):
>> CYTH  CYTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.5   0.5   4.9e-36   4.4e-32       2     159 ..       3     154 ..       2     166 .. 0.84

  Alignments for each domain:
  == domain 1  score: 111.5 bits;  conditional E-value: 4.9e-36
                                    EEEEEEEEE-HHHHHHHHHH.HHHCTCEEEEEEEEEEEEEE-TTTHHHHTTEEEEEE...EETTTEEEEEEEEECSSST. CS
                           CYTH   2 iEvEvKflvsaaeyedlelr.laelrakeettveqrdtYydtpdrdlartdeaLRiR...raegdgeeltlKgpgvdge. 76 
                                    +EvEvKf+v   e  d+  r l+e++a+ ++tv q d+Y+++p+rd+a+tdeaLR+R     +g+ +elt+Kgp+ +g  
  gi|119718956|ref|YP_919451.1|   3 REVEVKFRV---EGHDVLRRkLREAGAAYVDTVDQVDIYFQHPCRDFASTDEALRLRvnySGSGSYAELTYKGPKEGGWa 79 
                                    7********...555544456************************************87633366666******966656 PP

                                    ..EEEEEEEECCCEEECCCCHHHHHHHHHHHTT-EEEEEEEEEEEEEEETTEEEEEEEETTTTEEEEEEEEEESSHHHHH CS
                           CYTH  77 ..reevegevsreEyeeplsdaaeaaelldglglepvasvkklRrkyklegvevalDaveflegeevEiElevedeeevk 154
                                      ree+   v+          a++  ++l++lg+ +va+++k R+ y l+g+ev+lD+ve+l g +vEiE +++  e++ 
  gi|119718956|ref|YP_919451.1|  80 knREEIVARVE---------AAEALRKILERLGFSEVATLRKHREFYVLDGTEVSLDYVEGL-GFFVEIEDKGGGVEALR 149
                                    65555555554.........5555569***********************************.************99999 PP

                                    HHHHH CS
                           CYTH 155 eaaek 159
                                    e++  
  gi|119718956|ref|YP_919451.1| 150 EVVSR 154
                                    98765 PP

>> F-box  F-box domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   5.1e-06     0.045       9      28 ..      93     112 ..      83     112 .. 0.94
   2 ?    0.6   0.0     0.063   5.7e+02       9      20 ..     146     157 ..     136     158 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.1e-06
                                    HHHHHHHHTS-HHHHHHHCT CS
                          F-box   9 evlrhILerLplsdllalrr 28 
                                    e lr+ILerL++s++  lr+
  gi|119718956|ref|YP_919451.1|  93 EALRKILERLGFSEVATLRK 112
                                    68***************995 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.063
                                    HHHHHHHHTS-H CS
                          F-box   9 evlrhILerLpl 20 
                                    e lr++ +rL+l
  gi|119718956|ref|YP_919451.1| 146 EALREVVSRLGL 157
                                    789*******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1367.48
//
Query:       gi|119718957|ref|YP_919452.1|  [L=144]
Description: hypothetical protein Tpen_0039 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.62   10.1   9.7      0.061   13.3   4.8    1.7  2  ECF-ribofla_trS  ECF-type riboflavin transporter, S component


Domain annotation for each model (and alignments):
>> ECF-ribofla_trS  ECF-type riboflavin transporter, S component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   4.8   3.4e-06     0.061       4      50 ..      12      56 ..       9      60 .. 0.91
   2 ?   -1.2   0.2     0.098   1.8e+03     100     100 ..     117     117 ..      84     143 .. 0.48

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.4e-06
                                   TTHHHHHHHHHHHHHHHHHH---B-S.SS-B--TTHHHHHHHHHHSS CS
                ECF-ribofla_trS  4 tkkvvatailaAlvvvltlfisIplpantegsinlgdavlalaallf 50
                                   ++ v+a+ai+ Al++ +++ + Ip+p+     +++g++v+a+++++f
  gi|119718957|ref|YP_919452.1| 12 VRGVTALAIVLALMYLFSTSLYIPVPVYK--GVSVGNIVVAVLSIVF 56
                                   67799*********************555..79************99 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.098
                                    S CS
                ECF-ribofla_trS 100 n 100
                                    +
  gi|119718957|ref|YP_919452.1| 117 H 117
                                    2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       633  (0.0353059); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.19s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 1145.10
//
Query:       gi|119718958|ref|YP_919453.1|  [L=340]
Description: glucose-inhibited division protein A [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.3e-38  131.2   1.0    5.5e-38  130.9   1.0    1.1  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    1.2e-13   51.0   0.1      9e-10   38.3   0.0    2.2  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    1.1e-09   38.3   4.9    1.9e-05   24.5   2.1    2.3  2  DAO             FAD dependent oxidoreductase
    3.6e-07   29.6   5.4      3e-06   26.6   3.0    2.6  2  FAD_binding_2   FAD binding domain
    9.7e-07   28.5   1.9    4.9e-06   26.1   0.7    2.2  2  FAD_oxidored    FAD dependent oxidoreductase
    2.9e-06   27.7   0.1     0.0058   17.2   0.0    2.6  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    1.5e-05   24.3   4.5    0.00026   20.2   1.5    2.9  3  GIDA            Glucose inhibited division protein A
      3e-05   22.9   1.5      0.016   13.9   0.8    2.2  2  HI0933_like     HI0933-like protein
    5.7e-05   22.5   0.2    0.00016   21.0   0.2    1.7  1  Thi4            Thi4 family
    0.00013   22.1   2.1    0.00014   22.0   0.2    2.1  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
     0.0016   18.4   1.3       0.11   12.5   0.0    2.3  2  NAD_binding_9   FAD-NAD(P)-binding
  ------ inclusion threshold ------
      0.012   14.7   0.2      0.021   13.9   0.2    1.4  1  Lycopene_cycl   Lycopene cyclase protein
      0.016   14.5   0.6      0.035   13.4   0.6    1.6  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
      0.081   12.2   0.2       0.13   11.5   0.2    1.3  1  FAD_binding_3   FAD binding domain
       0.18   10.6   2.3       0.19   10.5   1.3    1.6  2  Trp_halogenase  Tryptophan halogenase
       0.35    9.6   0.4        1.4    7.6   0.3    1.8  2  MCRA            MCRA family


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.9   1.0   4.9e-41   5.5e-38       1     293 [.       9     294 ..       9     298 .. 0.86

  Alignments for each domain:
  == domain 1  score: 130.9 bits;  conditional E-value: 4.9e-41
                                    CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH........HHHHCHHHHCCCCHC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxx RF
                    Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias........evvkklnqgielllg 72 
                                    +dvv++G+G+AGl+aal++a++++ +++v + +  l+g+ ll++++ +++++ +i          e+ k ++++   + +
  gi|119718958|ref|YP_919453.1|   9 YDVVIVGAGIAGLTAALYAARQKLSTLVV-SAD--LGGQLLLTTEIQNFPGFMSIGGlelirrveEQAKTYGAE--IVFD 83 
                                    69***************************.444..999*************99988897776665554444444..3444 PP

                                    CTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-TSEEEEES-SH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  73 eevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllpkrivvvGgGy 152
                                     evv++++ ++ ++++   + ++ ++a d+l+lA G spr +g+pG+ e  g++v+++  ++a  +  ++  ++ vG G+
  gi|119718958|ref|YP_919453.1|  84 -EVVGVEEREGVFVVK---TASGAEYASDALILAFGKSPREMGVPGEREFKGRGVSYCVICDAPLYRGRR--VALVGWGA 157
                                    .7****9999999994...466889***************************999999999999887776..******** PP

                                    HHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEE.EEETTSCE.....E CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx.....x RF
                    Pyr_redox_2 153 iGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgngekle.vvledgee.....i 226
                                       E  + l++++++v+ v  ++++      e  + l+eal k +ve++  +++ e++g+++ ++ +v  d+++     +
  gi|119718958|ref|YP_919453.1| 158 HNYENIILLRDYASKVYWVFPGEKPI-----EEDELLREALSKGNVELVPFSEPAEVKGDKR-VQaLVVRDKRTselrtL 231
                                    *************************9.....56899999**********************9.4444444444446888* PP

                                    EESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGCTECCSS--HHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 227 dadlvvvavGvrpstelleeklglelderggivvdeflrtnvpgiyaiGDvaggkggpelaqaAvqq 293
                                    ++d v+v +G+  +t +l  +  +el+e+g ivvd+ +rt+ pg++a+GDv+  +   ++a+ A ++
  gi|119718958|ref|YP_919453.1| 232 EVDGVFVEIGYVTKTGFL--RGFVELNEKGEIVVDKACRTSRPGVFAAGDVT--EMPHKQAVIAAAM 294
                                    ***************887..899*****************************..4444455555444 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.3   0.00023      0.26       1      27 [.      12      37 ..      12      55 .. 0.87
   2 !   38.3   0.0     8e-13     9e-10     101     305 .]      82     278 ..      57     278 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00023
                    Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylil 27
                                   +I+GaG aGl+aa+ + + +l+  l++
  gi|119718958|ref|YP_919453.1| 12 VIVGAGIAGLTAALYAARQKLS-TLVV 37
                                   7********************5.5666 PP

  == domain 2  score: 38.3 bits;  conditional E-value: 8e-13
                    Pyr_redox_3 101 feeVesvkkedegfevetske.tyeAkkviiAtGefdkPnklnipGeek...lvkhyskvkefhkyagqkvvViGgknSa 176
                                    f eV  v++ ++ f+v+t ++ +y ++ +i+A G+   P+ +++pGe +     + y  + ++  y+g++v+ +G +   
  gi|119718958|ref|YP_919453.1|  82 FDEVVGVEEREGVFVVKTASGaEYASDALILAFGK--SPREMGVPGEREfkgRGVSYCVICDAPLYRGRRVALVGWGAHN 159
                                    67899*************9987************9..**********975344677777889999*************** PP

                    Pyr_redox_3 177 vDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikv...lfnaevkeikekeeeykvktedgk 253
                                     +  + l ++ ++V +v +g++  +e++             l+e+++++++++    + aevk  k+  +   v+ ++++
  gi|119718958|ref|YP_919453.1| 160 YENIILLRDYASKVYWVFPGEKPIEEDE------------LLREALSKGNVELvpfSEPAEVKGDKRV-QALVVRDKRTS 226
                                    ********************85444332............2333333333333000444444444443.33455555555 PP

                    Pyr_redox_3 254 kvev.kddvvla.tGykpdlsflkkslfeldedgrpvlteeteetnvpglflaG 305
                                    ++++ + d v++ +Gy  ++ fl+   +el+e+g++v++++ + t  pg+f aG
  gi|119718958|ref|YP_919453.1| 227 ELRTlEVDGVFVeIGYVTKTGFLR-GFVELNEKGEIVVDKA-CRTSRPGVFAAG 278
                                    5554455555665**********9.9***********9976.67889****999 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   2.1   1.7e-08   1.9e-05       1      32 [.      10      41 ..      10      45 .. 0.83
   2 !   14.4   0.0   1.9e-05     0.021     148     203 ..      65     117 ..      59     163 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 1.7e-08
                                   EEEEECTSHHHHHHHHHHHHTT..EEEEESSSST CS
                            DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdia 32
                                   dvvi+G+Gi+Gl++A+++ar++  ++++ ++  +
  gi|119718958|ref|YP_919453.1| 10 DVVIVGAGIAGLTAALYAARQKlsTLVVSAD--L 41
                                   9******************999966666555..4 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 1.9e-05
                                    HHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGG CS
                            DAO 148 ltaalaraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGaw 203
                                    l++ + ++a++ G+ei++  ev+g+ee++ +v  v  +t+ g++ a da+++a G  
  gi|119718958|ref|YP_919453.1|  65 LIRRVEEQAKTYGAEIVFD-EVVGVEERE-GVFVV--KTAsGAEYASDALILAFGKS 117
                                    66778899***********.*****7753.44555..7777999666******9944 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   3.0   2.7e-09     3e-06       1      30 [.      10      39 ..      10      45 .. 0.95
   2 ?    2.3   0.0     0.063        71     381     402 ..     258     281 ..     242     294 .. 0.77

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 2.7e-09
                                   SEEEE--SHHHHHHHHHHHHTTT-EEEEES CS
                  FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvek 30
                                   Dv+++G+G+AGL+AAl aa++ l+++vv+ 
  gi|119718958|ref|YP_919453.1| 10 DVVIVGAGIAGLTAALYAARQKLSTLVVSA 39
                                   9***************************96 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.063
                                    TSBE..STTEEESSBTEEE-STCE CS
                  FAD_binding_2 381 ngrv..ldadgqpipGLYAaGeva 402
                                    +g+   ++a  +  pG +AaG v+
  gi|119718958|ref|YP_919453.1| 258 KGEIvvDKACRTSRPGVFAAGDVT 281
                                    5554445556669*********98 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.7   4.4e-09   4.9e-06       1      38 [.      10      45 ..      10      90 .. 0.88
   2 ?    0.9   0.0      0.21   2.3e+02      92     130 ..     188     226 ..     180     233 .. 0.84

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 4.4e-09
                   FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGll 38
                                   Dvv+vG+g+aG++AA+ Aar+  ++l+v+ +  lGG+l
  gi|119718958|ref|YP_919453.1| 10 DVVIVGAGIAGLTAALYAARQKLSTLVVSAD--LGGQL 45
                                   9***************************976..78875 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.21
                   FAD_oxidored  92 vleemlaeagvtvllntrlvevekegkriesvtveske.g 130
                                    +l e l++ +v+++  +++ ev+ ++ r+++++v++k+  
  gi|119718958|ref|YP_919453.1| 188 LLREALSKGNVELVPFSEPAEVKGDK-RVQALVVRDKRtS 226
                                    677889999**************985.9******998743 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.2    0.0043       4.8       2      28 ..      11      37 ..      10      53 .. 0.83
   2 !   17.2   0.0   5.2e-06    0.0058       1      80 [.     149     222 ..     149     225 .. 0.93

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0043
                                   EEEECSSHHHHHHHHHHHHTTSEEEEE CS
                      Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvv 28
                                   vv+vG+G  gl +A ++a+ + ++ vv
  gi|119718958|ref|YP_919453.1| 11 VVIVGAGIAGLTAALYAARQKLSTLVV 37
                                   8*************9998866655555 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 5.2e-06
                                    EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEEEET CS
                      Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedgvesvklkd 80 
                                    +v+ vG G  + E    l+++++kV+ v  ++k+      e  ++l+e l+k ++e++  ++++e++g+++ v++++++d
  gi|119718958|ref|YP_919453.1| 149 RVALVGWGAHNYENIILLRDYASKVYWVFPGEKPI-----EEDELLREALSKGNVELVPFSEPAEVKGDKR-VQALVVRD 222
                                    6899*******************************.....66799**********************9998.99988875 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   1.5   2.3e-07   0.00026       1      29 [.      10      45 ..      10      78 .. 0.77
   2 ?    2.0   0.0     0.078        87     112     150 ..      79     116 ..      64     135 .. 0.79
   3 ?    1.5   0.0      0.11   1.2e+02     354     391 ..     270     309 ..     262     310 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2.3e-07
                                   CEEEE-SSHHHHHHHHHHHHTT--EEEE.......E CS
                           GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi.......t 29
                                   dv+++G+G AG+ AAl aar  +++l +        
  gi|119718958|ref|YP_919453.1| 10 DVVIVGAGIAGLTAALYAARQKLSTLVVsadlggqL 45
                                   79************************9966666653 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.078
                                    EEEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT CS
                           GIDA 112 eiieeeveeliveekkvkgvvtedgetikakavviatGt 150
                                    ei+ +ev  +  e + v +v+t++g+++ ++a ++a G 
  gi|119718958|ref|YP_919453.1|  79 EIVFDEVVGV-EEREGVFVVKTASGAEYASDALILAFGK 116
                                    6777788888.55789999*****************997 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.11
                                    SSBTEEE-CGGGTB..-SHHHHHHHHHHHHHHHHHHHCTS CS
                           GIDA 354 kvkgLflAGqinGt..eGYeEaaaqGllAGinaarkakgk 391
                                    +++g+f+AG+++ +  +  + aaa+G  A++ a +++ +k
  gi|119718958|ref|YP_919453.1| 270 SRPGVFAAGDVTEMphKQAVIAAAMGACAALSAYAYVMEK 309
                                    48999******9994333566899*******999988765 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.8   1.5e-05     0.016       1      30 [.       9      38 ..       9      48 .. 0.90
   2 !    7.8   0.0    0.0011       1.2     110     166 ..      64     117 ..      39     127 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.5e-05
                                   -SEEEE--SHHHHHHHHHHHHTT--EEEE- CS
                    HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVllle 30
                                   +dv+++G+G AGl aA+ aa+++ ++l++ 
  gi|119718958|ref|YP_919453.1|  9 YDVVIVGAGIAGLTAALYAARQKLSTLVVS 38
                                   59*********************9999975 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0011
                                    HHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----SS CS
                    HI0933_like 110 divdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGlS 166
                                    ++++  ++++k  g ++  + ev +ve+ ++g+f vkt s+ e+++d+l+lA G +S
  gi|119718958|ref|YP_919453.1|  64 ELIRRVEEQAKTYGAEIVFD-EVVGVEE-REGVFVVKTASGAEYASDALILAFG-KS 117
                                    67888888889999998876.5778855.7777*******************76.55 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.2   1.4e-07   0.00016      17      51 ..       8      41 ..       3      51 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.4e-07
                                   EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSS CS
                           Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailersv 51
                                   + DvvivGaG +GLtaa y a++ +l ++++ + +
  gi|119718958|ref|YP_919453.1|  8 KYDVVIVGAGIAGLTAALYAARQ-KLSTLVVSADL 41
                                   67********************9.89988887654 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.2   1.3e-07   0.00014       1      35 [.      13      45 ..      13      79 .. 0.87
   2 ?   -1.7   0.1       3.1   3.5e+03       9      22 ..     301     314 ..     294     315 .. 0.67

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.3e-07
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGra 35
                                   IvGaG++Gl+aA ++a+++++ l++  + +lGG++
  gi|119718958|ref|YP_919453.1| 13 IVGAGIAGLTAALYAARQKLSTLVV--SADLGGQL 45
                                   9**********************99..55788886 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.1
                                    HHHHHHHHCCTEEE CS
                  NAD_binding_8   9 lvaAylLakagfdv 22 
                                    +++Ay + k+g++v
  gi|119718958|ref|YP_919453.1| 301 SAYAYVMEKRGRKV 314
                                    56677778889988 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.3     0.025        28       1      19 [.      12      30 ..      12      39 .. 0.83
   2 !   12.5   0.0   9.8e-05      0.11     108     155 ..      70     116 ..      64     117 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.025
                  NAD_binding_9  1 aivGaGprGlavlerLlar 19
                                   +ivGaG++Gl+++   +++
  gi|119718958|ref|YP_919453.1| 12 VIVGAGIAGLTAALYAARQ 30
                                   7**********99877776 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 9.8e-05
                  NAD_binding_9 108 larlpegvtvevhraevvdleeradgqavlladgaslaadaVvLAlGh 155
                                     +++ +    e++ +evv +eer++ + v +a+ga++a da++LA G 
  gi|119718958|ref|YP_919453.1|  70 EEQA-KTYGAEIVFDEVVGVEEREGVFVVKTASGAEYASDALILAFGK 116
                                    4444.3456788899******************************996 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   1.9e-05     0.021       1      39 [.      10      48 ..      10      63 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.9e-05
                  Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieaspsllfp 39
                                   Dvv++GaG Agl  A   +++k    vv+ + + +ll +
  gi|119718958|ref|YP_919453.1| 10 DVVIVGAGIAGLTAALYAARQKLSTLVVSADLGGQLLLT 48
                                   9****************9888888777777777666655 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.6   3.2e-05     0.035      27      51 ..       7      31 ..       1      49 [. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.2e-05
                                   ---EEEEESTSHHHHHHHHHHHHTT CS
                    AlaDh_PNT_C 27 epakvlviGgGvaGlqAiatakglg 51
                                   ++  v+++G+G+aGl A+  a++ +
  gi|119718958|ref|YP_919453.1|  7 KKYDVVIVGAGIAGLTAALYAARQK 31
                                   6778**************9998754 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   0.00011      0.13       2      30 ..       9      37 ..       8      41 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00011
                                   EEEEEE--SHHHHHHHHHHHHTTHHEEEE CS
                  FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlv 30
                                   +dV+IVGaG aGl++al  +++  ++++v
  gi|119718958|ref|YP_919453.1|  9 YDVVIVGAGIAGLTAALYAARQKLSTLVV 37
                                   79**************9888776666665 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.3   0.00017      0.19       1      37 [.      10      42 ..      10      79 .. 0.75
   2 ?   -2.1   0.0       1.1   1.3e+03     161     204 ..      70     111 ..      61     116 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00017
                                   EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS- CS
                 Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlveseeig 37
                                   ++vivG+G+aG +aA + a++       tlv s+++g
  gi|119718958|ref|YP_919453.1| 10 DVVIVGAGIAGLTAALYAARQKLS----TLVVSADLG 42
                                   69****************999844....666666665 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.1
                                    HHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-SEEE CS
                 Trp_halogenase 161 rrvaearGvtrvegkvvevqldedgrveslrledgreveadlfi 204
                                    ++ a+  G ++v ++vv v  +e++ v  +++++g e+  d  i
  gi|119718958|ref|YP_919453.1|  70 EEQAKTYGAEIVFDEVVGV--EEREGVFVVKTASGAEYASDALI 111
                                    5678888999999999665..55666777888889888877665 PP

>> MCRA  MCRA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.3    0.0013       1.4       4      22 ..      11      29 ..       8      36 .. 0.87
   2 ?   -0.8   0.0      0.44   4.9e+02     239     276 ..     210     245 ..     196     249 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0013
                                   EEEE--SHHHHHHHHHHHH CS
                           MCRA  4 aylvGsGiasLaaAvyLir 22
                                   + +vG+Gia+L+aA+y  r
  gi|119718958|ref|YP_919453.1| 11 VVIVGAGIAGLTAALYAAR 29
                                   689*************765 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.44
                                    TTEEEEEEEEEEE.TTEEEEEE--TTEEEEEE---SST CS
                           MCRA 239 edkktvteielekeegeeetieleedDlvfvtnGsite 276
                                    + +k+v+++ +++  +++++++  e D vfv++G +t+
  gi|119718958|ref|YP_919453.1| 210 KGDKRVQALVVRD--KRTSELRTLEVDGVFVEIGYVTK 245
                                    4679999999986..34556888899********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.51
# Mc/sec: 2012.36
//
Query:       gi|119718959|ref|YP_919454.1|  [L=362]
Description: radical SAM domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-24   86.4   0.0    5.8e-24   85.3   0.0    1.6  1  Radical_SAM     Radical SAM superfamily
     0.0016   18.4   0.1     0.0016   18.4   0.1    2.6  3  DZR             Double zinc ribbon
     0.0078   15.8   1.2       0.89    9.3   0.1    2.5  2  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
     0.0087   16.1   2.6        2.4    8.3   0.1    2.9  2  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
     0.0089   15.4   7.7       0.11   11.9   0.1    2.9  2  zf-ribbon_3     zinc-ribbon domain
  ------ inclusion threshold ------
      0.059   13.6   0.0       0.11   12.7   0.0    1.5  1  Fer4_12         4Fe-4S single cluster domain
      0.077   13.0   1.7        4.9    7.2   0.1    2.5  2  Ogr_Delta       Ogr/Delta-like zinc finger
       0.12   12.6   0.2       0.29   11.3   0.2    1.6  1  DiS_P_DiS       Bacterial Peptidase A24 N-terminal domain
       0.12   12.2   0.2       0.12   12.2   0.2    3.1  3  zinc_ribbon_2   zinc-ribbon domain
       0.16   12.0   0.7       0.98    9.4   0.6    2.5  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
        0.5   10.2   2.0       0.76    9.7   0.1    2.1  2  Rad50_zn_hook   Rad50 zinc hook motif
       0.78    9.6   0.0       0.78    9.6   0.0    3.6  3  zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
          1    9.0   3.6        3.8    7.1   0.8    2.6  2  DpnI            Dam-replacing family
        1.1    9.3   6.0        1.2    9.2   0.1    2.8  3  zinc-ribbons_6  zinc-ribbons
        1.2    9.2   3.3        3.5    7.7   0.1    2.7  3  HypA            Hydrogenase/urease nickel incorporation, meta
        3.5    8.4   8.7        6.3    7.6   0.2    2.8  2  zf-ISL3         zinc-finger of transposase IS204/IS1001/IS109
        3.8    7.3   9.2        2.5    7.9   0.1    3.2  3  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
          8    6.5  10.4        2.4    8.2   0.2    3.6  4  Zn_Tnp_IS1595   Transposase zinc-ribbon domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.3   0.0   5.8e-27   5.8e-24       2     166 ..      89     250 ..      88     251 .. 0.91

  Alignments for each domain:
  == domain 1  score: 85.3 bits;  conditional E-value: 5.8e-27
                                    EEESEESS--TTTSCCTT....HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCT CS
                                    xxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM   2 vvtrgCnlrCsfCarpet....vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpg 77 
                                    v t+gCn+ C fC+++e      +r+ +g++ ++e++++e+k+l     ++++  +  ep+  ++f  +++rlak+  +g
  gi|119718959|ref|YP_919454.1|  89 VSTPGCNFFCQFCQNWEIsqsrLERGLYGHYYPPEDVVREAKRLQ----ADGISYTYNEPTIFYEFMLDTARLAKK--EG 162
                                    689*******************999*******************8....99*************************..8* PP

                                    EEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET.EEEEEEEBTTTS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
                    Radical_SAM  78 iritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikr.vvdrivglpGen 156
                                    + +t++tng+   +e l++l+++  d  +++ + + d ++ +++++ ++++ ++++l +++e+gi++ +++ +v + G  
  gi|119718959|ref|YP_919454.1| 163 LFNTMVTNGYIS-PEALDELAPYL-DAATVDFKGGGDPEFYRKFMGVPDPSPIYDTLLRMKEKGIHVeITNLVVPIVGDD 240
                                    ***********8.*********99.********97665455555599*******************77777777777777 PP

                                    HHHHHHHHHH CS
                                    xxxxxxxxxx RF
                    Radical_SAM 157 deeleellel 166
                                    +e+l+ l+++
  gi|119718959|ref|YP_919454.1| 241 EEKLRSLARW 250
                                    7777777776 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.3       1.9   1.9e+03      28      39 ..      26      38 ..      17      47 .. 0.59
   2 ?   -1.1   0.5       2.1   2.1e+03      12      19 ..      95     102 ..      88     108 .. 0.67
   3 !   18.4   0.1   1.6e-06    0.0016       9      40 ..     307     348 ..     304     352 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.9
                            DZR 28 edrCpsCgek.vd 39
                                     +C  C++  v 
  gi|119718959|ref|YP_919454.1| 26 YVKCNLCNRRcVI 38
                                   4567777766444 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.1
                            DZR  12 arfCseCg 19 
                                    + fC+ C+
  gi|119718959|ref|YP_919454.1|  95 NFFCQFCQ 102
                                    44666664 PP

  == domain 3  score: 18.4 bits;  conditional E-value: 1.6e-06
                            DZR   9 ppdarfCseCgtklkavaa..........edrCpsCgekvdp 40 
                                    p ++ +C++Cg+++ +              +rCp Cg+k++ 
  gi|119718959|ref|YP_919454.1| 307 PLENTYCPKCGHRVIERRGffivkwdlteDNRCPVCGAKINI 348
                                    56789*********96666******************99765 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.1   0.00089      0.89       4      14 ..     311     321 ..     309     325 .. 0.78
   2 ?    5.0   0.1      0.02        20       6      16 ..     339     349 ..     337     356 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00089
                  zf-NADH-PPase   4 rFCgrCGapte 14 
                                     +C++CG++++
  gi|119718959|ref|YP_919454.1| 311 TYCPKCGHRVI 321
                                    69*****9976 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.02
                  zf-NADH-PPase   6 CgrCGaptepa 16 
                                    C+ CGa+   +
  gi|119718959|ref|YP_919454.1| 339 CPVCGAKINIK 349
                                    99999987665 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.3    0.0074       7.3       2      10 ..     313     321 ..     312     325 .. 0.83
   2 !    8.3   0.1    0.0024       2.4       1       9 [.     338     346 ..     338     348 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0074
                 DNA_ligase_ZBD   2 CPvCGsavv 10 
                                    CP CG+ v+
  gi|119718959|ref|YP_919454.1| 313 CPKCGHRVI 321
                                    ******998 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0024
                 DNA_ligase_ZBD   1 hCPvCGsav 9  
                                    +CPvCG+++
  gi|119718959|ref|YP_919454.1| 338 RCPVCGAKI 346
                                    5*****985 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.1   0.00011      0.11       2      13 ..     310     322 ..     309     324 .. 0.82
   2 !    7.8   0.2    0.0022       2.2       3      11 ..     337     346 ..     335     351 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                    zf-ribbon_3   2 tvrCPnCGa.pls 13 
                                     ++CP+CG+ +++
  gi|119718959|ref|YP_919454.1| 310 NTYCPKCGHrVIE 322
                                    689******9987 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0022
                    zf-ribbon_3   3 vrCPnCGa.p 11 
                                    +rCP CGa +
  gi|119718959|ref|YP_919454.1| 337 NRCPVCGAkI 346
                                    5899999944 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00012      0.11       8     101 ..      87     179 ..      81     196 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00012
                        Fer4_12   8 lslfvsgCnlsCkgCfnketwsfk.....sgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkee 82 
                                    +s+ + gCn+ C++C n e+ + +     +g+ ++ e   +  ++l   + +g++++  EP     +e +l+ ++  k+e
  gi|119718959|ref|YP_919454.1|  87 FSVSTPGCNFFCQFCQNWEISQSRlerglYGHYYPPEDVVREAKRL---QADGISYTYNEPTI--FYEFMLDTARLAKKE 161
                                    466688*************998877777788888866555544555...89999***99**99..889999999999999 PP

                        Fer4_12  83 kpekdiwlytgytleelsk 101
                                    ++  + ++++gy+  e ++
  gi|119718959|ref|YP_919454.1| 162 GL-FNTMVTNGYISPEALD 179
                                    99.5799999999887764 PP

>> Ogr_Delta  Ogr/Delta-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.2     0.032        32       2      11 ..     313     322 ..     312     325 .. 0.83
   2 ?    7.2   0.1     0.005       4.9       1      13 [.     338     350 ..     338     357 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.032
                      Ogr_Delta   2 CPhCgapaaa 11 
                                    CP+Cg++   
  gi|119718959|ref|YP_919454.1| 313 CPKCGHRVIE 322
                                    ******9765 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.005
                      Ogr_Delta   1 rCPhCgapaaart 13 
                                    rCP Cga++ +  
  gi|119718959|ref|YP_919454.1| 338 RCPVCGAKINIKG 350
                                    7*******98865 PP

>> DiS_P_DiS  Bacterial Peptidase A24 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   0.00029      0.29      27      65 ..     310     349 ..     300     352 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00029
                      DiS_P_DiS  27 rSrCpkCghklkwleliPvlSy.lllrgrCraCkakislr 65 
                                    +  CpkCgh++  ++   ++ + l+   rC  C+aki+++
  gi|119718959|ref|YP_919454.1| 310 NTYCPKCGHRVIERRGFFIVKWdLTEDNRCPVCGAKINIK 349
                                    678*******************777889*********985 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   1.5       7.9   7.8e+03      15      19 ..      97     101 ..      97     103 .. 0.47
   2 ?   12.2   0.2   0.00012      0.12      12      22 ..     309     319 ..     306     320 .. 0.82
   3 ?    7.2   0.2    0.0042       4.2       1       9 [.     338     346 ..     335     349 .. 0.72

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 7.9
                  zinc_ribbon_2  15 FCpyC 19 
                                    FC  C
  gi|119718959|ref|YP_919454.1|  97 FCQFC 101
                                    44444 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00012
                  zinc_ribbon_2  12 nakFCpyCGtp 22 
                                    ++++Cp+CG+ 
  gi|119718959|ref|YP_919454.1| 309 ENTYCPKCGHR 319
                                    6899*****96 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0042
                  zinc_ribbon_2   1 fCpnCGael 9  
                                    +Cp CGa++
  gi|119718959|ref|YP_919454.1| 338 RCPVCGAKI 346
                                    477777776 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.6   0.00098      0.98      29      57 ..     311     347 ..     283     352 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00098
                 OrfB_Zn_ribbon  29 ktCseCgsknke........alsgrtfkCpnCgfead 57 
                                    + C++Cg+++ e         + ++  +Cp Cg++++
  gi|119718959|ref|YP_919454.1| 311 TYCPKCGHRVIErrgffivkWDLTEDNRCPVCGAKIN 347
                                    68********999999988867778889999999875 PP

>> Rad50_zn_hook  Rad50 zinc hook motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.4       1.8   1.8e+03      21      27 ..     312     318 ..     309     319 .. 0.77
   2 ?    9.7   0.1   0.00076      0.76      16      29 ..     334     346 ..     332     349 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.8
                                    E-TTT-- CS
                  Rad50_zn_hook  21 cCPlCgR 27 
                                     CP Cg+
  gi|119718959|ref|YP_919454.1| 312 YCPKCGH 318
                                    6****95 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00076
                                    TT-SEE-TTT--EE CS
                  Rad50_zn_hook  16 keakgcCPlCgRel 29 
                                    +e + +CP+Cg ++
  gi|119718959|ref|YP_919454.1| 334 TEDN-RCPVCGAKI 346
                                    5555.******876 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   1.4       1.2   1.2e+03       2      19 ..      27      44 ..      26      46 .. 0.87
   2 ?    9.6   0.0   0.00078      0.78       3      16 ..     312     325 ..     310     327 .. 0.89
   3 ?    6.9   0.0    0.0054       5.4       2      17 ..     337     352 ..     336     360 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.2
                                   EE-SSS--EEEEEE-SSS CS
                 zf-C4_Topoisom  2 ekCPkCggdLvlkrgkkG 19
                                   +kC  C+   v+  g++G
  gi|119718959|ref|YP_919454.1| 27 VKCNLCNRRCVIAPGRFG 44
                                   69*****99999999988 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00078
                                    E-SSS--EEEEEE- CS
                 zf-C4_Topoisom   3 kCPkCggdLvlkrg 16 
                                     CPkCg  ++++rg
  gi|119718959|ref|YP_919454.1| 312 YCPKCGHRVIERRG 325
                                    7***********98 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0054
                                    EE-SSS--EEEEEE-S CS
                 zf-C4_Topoisom   2 ekCPkCggdLvlkrgk 17 
                                    + CP Cg+++ +k + 
  gi|119718959|ref|YP_919454.1| 337 NRCPVCGAKINIKGSY 352
                                    68********999765 PP

>> DpnI  Dam-replacing family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1      0.27   2.7e+02      46      61 ..      88     103 ..      84     117 .. 0.75
   2 ?    7.1   0.8    0.0038       3.8      30      44 ..     309     323 ..     299     359 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.27
                                    -------EEE-TTT-- CS
                           DpnI  46 ennkpvaDfyCescke 61 
                                    +  +p ++f+C+ c++
  gi|119718959|ref|YP_919454.1|  88 SVSTPGCNFFCQFCQN 103
                                    5667788888888874 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0038
                                    HH---TTT--SS-EE CS
                           DpnI  30 knlyCpkCgskklse 44 
                                    +n+yCpkCg++++++
  gi|119718959|ref|YP_919454.1| 309 ENTYCPKCGHRVIER 323
                                    89********99875 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       3.5   3.5e+03      17      25 ..      27      35 ..      19      40 .. 0.70
   2 ?    2.2   0.2      0.18   1.8e+02      49      58 ..      95     104 ..      87     113 .. 0.66
   3 ?    9.2   0.1    0.0012       1.2       2      27 ..     312     347 ..     309     351 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3.5
                                   EE-TTT--E CS
                 zinc-ribbons_6 17 yhCeaCqed 25
                                   ++C+ C+++
  gi|119718959|ref|YP_919454.1| 27 VKCNLCNRR 35
                                   567777765 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.18
                                    EE--TTTT-- CS
                 zinc-ribbons_6  49 dyfCnkcneL 58 
                                    ++fC+ c++ 
  gi|119718959|ref|YP_919454.1|  95 NFFCQFCQNW 104
                                    7888877664 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0012
                                    --SSS-S--EE-S..........SEEE-TTT--EEE CS
                 zinc-ribbons_6   2 kCpeCqqelekrg..........eqyhCeaCqedlk 27 
                                    +Cp+C + + +r           e  +C  C ++++
  gi|119718959|ref|YP_919454.1| 312 YCPKCGHRVIERRgffivkwdltEDNRCPVCGAKIN 347
                                    799999999976647777777766667777766554 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1      0.73   7.3e+02      66      83 ..      22      39 ..      11      56 .. 0.77
   2 ?   -0.7   0.0       1.4   1.4e+03      60      82 ..      85     106 ..      65     113 .. 0.79
   3 ?    7.7   0.1    0.0036       3.5      71      95 ..     311     345 ..     305     352 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.73
                                   EE--EEEETTTS-EEECH CS
                           HypA 66 evpvkvrCreCgkefele 83
                                    +p  v+C+ C+++  ++
  gi|119718959|ref|YP_919454.1| 22 GKPGYVKCNLCNRRCVIA 39
                                   5688899*9999987765 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.4
                                    -EEEEEEE--EEEETTTS-EEEC CS
                           HypA  60 aeLeieevpvkvrCreCgkefel 82 
                                    a++++++   ++ C+ C+ ++e+
  gi|119718959|ref|YP_919454.1|  85 AVFSVSTPGCNFFCQFCQ-NWEI 106
                                    567778888889999998.5654 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0036
                                    EEETTTS-EEECHHHHH...........S-TTTSSS CS
                           HypA  71 vrCreCgkefeleekal...........rCpkCgsa 95 
                                    ++C +Cg+++ +++  +           rCp Cg++
  gi|119718959|ref|YP_919454.1| 311 TYCPKCGHRVIERRG-FfivkwdltednRCPVCGAK 345
                                    68******9997753.235678889999*****984 PP

>> zf-ISL3  zinc-finger of transposase IS204/IS1001/IS1096/IS1165
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1     0.017        16       5      23 ..     313     331 ..     309     334 .. 0.85
   2 ?    7.6   0.2    0.0063       6.3       4      23 ..     338     357 ..     335     358 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.017
                        zf-ISL3   5 CPnCgsktvvkhgkkerrv 23 
                                    CP+Cg ++  ++g   +++
  gi|119718959|ref|YP_919454.1| 313 CPKCGHRVIERRGFFIVKW 331
                                    *******999999887777 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0063
                        zf-ISL3   4 rCPnCgsk.tvvkhgkkerrv 23 
                                    rCP Cg+k +  k ++++r +
  gi|119718959|ref|YP_919454.1| 338 RCPVCGAKiN-IKGSYRKRSW 357
                                    8*******65.6666788877 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   2.0       3.5   3.4e+03      19      27 ..      28      36 ..      20      49 .. 0.63
   2 ?    7.9   0.1    0.0025       2.5      20      28 ..     313     321 ..     307     322 .. 0.89
   3 ?    3.8   0.1     0.045        45      19      27 ..     338     346 ..     333     350 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 3.5
                                   --SSS---- CS
                 DNA_RNApol_7kD 19 RCkeCGhRi 27
                                   +C  C  R 
  gi|119718959|ref|YP_919454.1| 28 KCNLCNRRC 36
                                   555554443 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0025
                                    -SSS----- CS
                 DNA_RNApol_7kD  20 CkeCGhRil 28 
                                    C +CGhR++
  gi|119718959|ref|YP_919454.1| 313 CPKCGHRVI 321
                                    *******96 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.045
                                    --SSS---- CS
                 DNA_RNApol_7kD  19 RCkeCGhRi 27 
                                    RC  CG +i
  gi|119718959|ref|YP_919454.1| 338 RCPVCGAKI 346
                                    9*****998 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1         2     2e+03      35      45 ..      24      34 ..      13      35 .. 0.78
   2 ?   -1.2   0.3         2     2e+03      19      31 ..      96     110 ..      92     117 .. 0.61
   3 ?    8.2   0.2    0.0024       2.4      14      32 ..     303     321 ..     300     328 .. 0.71
   4 ?    3.0   0.0     0.099        99      20      27 ..     338     345 ..     329     357 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 2
                  Zn_Tnp_IS1595 35 rglfqCkeCrk 45
                                   +g+ +C+ C++
  gi|119718959|ref|YP_919454.1| 24 PGYVKCNLCNR 34
                                   78889999987 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2
                  Zn_Tnp_IS1595  19 fvCPhCgsr..kayr 31 
                                    f C +C++   +  r
  gi|119718959|ref|YP_919454.1|  96 FFCQFCQNWeiSQSR 110
                                    669999976444444 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0024
                  Zn_Tnp_IS1595  14 rWpng...fvCPhCgsrkayri 32 
                                    +W++      CP+Cg+r    i
  gi|119718959|ref|YP_919454.1| 303 VWGHPlenTYCPKCGHR---VI 321
                                    7888888555*****65...33 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.099
                  Zn_Tnp_IS1595  20 vCPhCgsr 27 
                                    +CP Cg +
  gi|119718959|ref|YP_919454.1| 338 RCPVCGAK 345
                                    7*****54 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2466.13
//
Query:       gi|119718960|ref|YP_919455.1|  [L=337]
Description: dual specificity protein phosphatase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.5e-09   36.1   0.1    1.2e-08   35.2   0.1    1.6  1  HD              HD domain
    0.00019   21.3   0.0    0.00028   20.7   0.0    1.2  1  DSPc            Dual specificity phosphatase, catalytic domai
     0.0026   17.3   0.0     0.0047   16.4   0.0    1.5  1  HDOD            HDOD domain
     0.0061   16.6   0.0      0.024   14.6   0.0    1.9  1  Y_phosphatase3  Tyrosine phosphatase family
     0.0076   15.9   0.0      0.013   15.2   0.0    1.3  1  CDKN3           Cyclin-dependent kinase inhibitor 3 (CDKN3)
  ------ inclusion threshold ------
      0.018   14.6   0.1      0.027   14.0   0.1    1.2  1  Y_phosphatase   Protein-tyrosine phosphatase


Domain annotation for each model (and alignments):
>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.1   4.1e-12   1.2e-08      13      99 ..     177     264 ..     165     330 .. 0.75

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 4.1e-12
                                    HHHHHHHHH.....HHHHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHH CS
                             HD  13 rrlaedlge.....eedrellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrlgld.ledvaklir 86 
                                        e+l       + d   ++la+LlHD+G ++ ++            + H++vgae ++++++++g+  +++v+ ++ 
  gi|119718960|ref|YP_919455.1| 177 LDVLESLSGiygfdRRDYVNAYLAGLLHDVGRVLGPE------------ERHHEVGAEWVKRNPLLRGVCdVDIVSFAVY 244
                                    444444444555477777789*************775............68****************888********** PP

                                    TTCCHHHHHHHH.......H CS
                             HD  87 ehheswegkkrp.......r 99 
                                    +h+++ + ++ p       +
  gi|119718960|ref|YP_919455.1| 245 HHRRKTRLTEDPrierlgvK 264
                                    *****998877754444440 PP

>> DSPc  Dual specificity phosphatase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   9.2e-08   0.00028       2      92 ..      12     101 ..      11     120 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 9.2e-08
                                    EEEECCHHC.HHHHHHHTCSEEEEESSSSSECECCTTTTSEEEEECCESSTTSCCGGGHHHHHHHHHHHHHTT-EEEEEE CS
                           DSPc   2 ylgskstas.lallsklgitlvinvtkevpnanalkkseieklripvedehetkiskyleeavefidkakqkgkkvlVHC 80 
                                    y  s ++   l+ l+k g+ lv+++t+e  ++     s+ +++++p+ d++   ++  l +av       ++g+ vlVHC
  gi|119718960|ref|YP_919455.1|  12 YWSSCPDDDlLETLAKRGLGLVVDLTEEECQY--SVPSGVDRVNYPIPDFSFRAFEGVLVKAVLPSLRYLESGRGVLVHC 89 
                                    66677777778899999*********877653..45899**********999999999999988888889********** PP

                                    SSSSSHHHHHHH CS
                           DSPc  81 qaGisRSatlii 92 
                                      Gi RS++ ++
  gi|119718960|ref|YP_919455.1|  90 YGGIGRSGSTVA 101
                                    *******98765 PP

>> HDOD  HDOD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.6e-06    0.0047      77     134 ..     149     210 ..     117     221 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.6e-06
                                    HHHHHHHS--.-SS-HHHHHHHHHHHHHHHHHHHHHT......T-S-HHHHHHHHHTTTHHHHH CS
                           HDOD  77 slkrlfkgkeeegadlkklwehslavAlvarelaeel......gledpeeaflaGLLhdiGklv 134
                                     l+rl+ + e  +    k+ +h+  vA va  + e+l        +d  +a+laGLLhd+G+++
  gi|119718960|ref|YP_919455.1| 149 FLERLLLELE--DEGYWKFLDHASSVAGVALDVLESLsgiygfDRRDYVNAYLAGLLHDVGRVL 210
                                    5555555555..566778999**************99888855444459************986 PP

>> Y_phosphatase3  Tyrosine phosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   8.1e-06     0.024      42     144 ..      22     106 ..      14     111 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 8.1e-06
                 Y_phosphatase3  42 lakLadlgirtviDLRspeEreaeaplegaryvhlpveeaaeeekeeeeaeetlaelYrellesakkayrkvfealadee 121
                                    l++La+ g+  v+DL + eE + + p +g+++v++p+              ++  ++++ +l    ka+   ++ l + +
  gi|119718960|ref|YP_919455.1|  22 LETLAKRGLGLVVDLTE-EECQYSVP-SGVDRVNYPI-------------PDFSFRAFEGVLV---KAVLPSLRYLES-G 82 
                                    67888888888888844.44344355.7888888888.............2344445555555...566677777777.4 PP

                 Y_phosphatase3 122 .pvlfHCtaGKDRTGvlaalllsl 144
                                      vl+HC  G  R G ++a++l+l
  gi|119718960|ref|YP_919455.1|  83 rGVLVHCYGGIGRSGSTVAMILAL 106
                                    59*******************987 PP

>> CDKN3  Cyclin-dependent kinase inhibitor 3 (CDKN3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   4.4e-06     0.013     130     161 ..      79     109 ..      51     115 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.4e-06
                                    HHTT--EEEE-SSSSSHHHHHHHHHHHHH-SS CS
                          CDKN3 130 lknyrktlihcygglgrsclvaaclllylsds 161
                                    l+  r  l+hcygg+grs     +++l l d 
  gi|119718960|ref|YP_919455.1|  79 LESGRGVLVHCYGGIGRSGST-VAMILALRDG 109
                                    6677999***********984.4455666665 PP

>> Y_phosphatase  Protein-tyrosine phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1     9e-06     0.027     171     195 ..      83     107 ..      67     116 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 9e-06
                                    S-EEEECSSSSHHHHHHHHHHHHHH CS
                  Y_phosphatase 171 gpvvVhCsaGvgRtgtfvaldillq 195
                                      v+VhC  G+gR+g+ va+ ++l+
  gi|119718960|ref|YP_919455.1|  83 RGVLVHCYGGIGRSGSTVAMILALR 107
                                    579****************998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2320.73
//
Query:       gi|119718961|ref|YP_919456.1|  [L=463]
Description: peptidase U62, modulator of DNA gyrase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.3e-57  193.5   3.6      1e-56  192.9   3.6    1.3  1  PmbA_TldD  Putative modulator of DNA gyrase
  ------ inclusion threshold ------
      0.017   15.0   0.0      0.034   14.1   0.0    1.4  1  DUF3924    Protein of unknown function (DUF3924)


Domain annotation for each model (and alignments):
>> PmbA_TldD  Putative modulator of DNA gyrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.9   3.6   1.1e-60     1e-56       1     279 []      20     314 ..      20     314 .. 0.82

  Alignments for each domain:
  == domain 1  score: 192.9 bits;  conditional E-value: 1.1e-60
                                    EEEEEEEEEEEEEEEEETTEEEEEEEEEEEEEEEEEEETTEEEEEE...ESSHHHHHHHHHHHHHHCCS---TT-..... CS
                      PmbA_TldD   1 eaevrleesestsvrfengevetnsssedsglgvrvikggrlgfastldtsdealeeaveraveiaklapedpea..... 75 
                                    +aevr+ees+++ +++ ng++ + s+ + +g+gvrv+++g +gfast d+s+++l +a+e+a ++a+  ++ +++     
  gi|119718961|ref|YP_919456.1|  20 FAEVRFEESTREIISYVNGRIASMSNQRLRGVGVRVLYNGNFGFASTFDLSRDGLLSALEEAFKAARALGPGNKRlaeve 99 
                                    69*****************************************************************9999999995555 PP

                                    ...............GGS-HHHHHHHHHHHHHH.CHCSTTEEEEEEEEEE......EEE.EEEEEEETTSEEEEEEEEEE CS
                      PmbA_TldD  76 ...............eevsaeekielleelekalrsadpkienskgarisgvsaslsaskeeklianSeGldveqtrtrv 140
                                                   +  + +ek +l++++           e +k+ ++s++ +++ a ++++ + +SeGl+v+++r  +
  gi|119718961|ref|YP_919456.1| 100 askrrysiegvkrhpARAELAEKLDLVKRAY----------ETLKSGGASSAVVRYGAYYGRVEVYTSEGLEVSSERLVT 169
                                    5554444433332222222222222222222..........2334668899999************************** PP

                                    EEEEEEEE..STCS..ET.EEEEEEEE...SSHHH.S..SSHHHHHHHHHHCTTT-B---SEEEEEEE-HHHHHHHHHGH CS
                      PmbA_TldD 141 slslsvia.ddggs..gd.gmgggsgy...edlee.edleeiaeeaaekalasleakplppgkypVvlspeavgsllhea 212
                                    ++s++++  ++g+   g+   g    +   e + +   +e+iae+a e a+a+l+a+++p+g  +V+  pe +g++ he+
  gi|119718961|ref|YP_919456.1| 170 GVSATAVLrENGRVgdGTeTYGA---SkglEAFTGdRAPEAIAEKALEVARAALNASRPPAGLQTVITRPELTGVFAHES 246
                                    ********555333332222222...244433333588999*************************************** PP

                                    HHHHTBHHHHHTT--TTTT-TTSB-S-TT--EEEETT-......-SB-TTSBB---EEEEETTEE--- CS
                      PmbA_TldD 213 vghaleadavlegrSflkdklGekvaselltivddpts.gglgsypfDdEGvptqrtvlIenGvLkny 279
                                    +gh +e+d v +g+S+l ++lGe +ase +tivd +++  g +    DdEGvpt+rt l+e+GvLk+y
  gi|119718961|ref|YP_919456.1| 247 FGHLTEGDGVFAGSSPLVGRLGEVLASEQVTIVDSGFDeRGGYVLLADDEGVPTERTILVEKGVLKGY 314
                                    *****************77******************8777777888********************9 PP

>> DUF3924  Protein of unknown function (DUF3924)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   3.8e-06     0.034      11      30 ..     118     139 ..     114     143 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.8e-06
                        DUF3924  11 etaekldllkqaye..kktGas 30 
                                    e aekldl+k+aye  k  Gas
  gi|119718961|ref|YP_919456.1| 118 ELAEKLDLVKRAYEtlKSGGAS 139
                                    88************54455665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 3549.87
//
Query:       gi|119718962|ref|YP_919457.1|  [L=442]
Description: peptidase U62, modulator of DNA gyrase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.4e-42  145.7   0.5    3.5e-42  145.2   0.1    1.5  2  PmbA_TldD  Putative modulator of DNA gyrase


Domain annotation for each model (and alignments):
>> PmbA_TldD  Putative modulator of DNA gyrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.2   0.1     2e-46   3.5e-42       1     279 []      23     312 ..      23     312 .. 0.84
   2 ?   -3.6   0.0      0.45     8e+03     136     179 ..     334     361 ..     316     377 .. 0.50

  Alignments for each domain:
  == domain 1  score: 145.2 bits;  conditional E-value: 2e-46
                                    EEEEEEEEEEEEEEEEETTEEEEEEEEEEEEEEEEEEETTEEEEEE...ESSHHHHHHHHHHHHHHCCS---TT-..... CS
                      PmbA_TldD   1 eaevrleesestsvrfengevetnsssedsglgvrvikggrlgfastldtsdealeeaveraveiaklapedpea..... 75 
                                    eae+ ++ ++++sv+ e    + +s+ +   + +rv kg+r++++++++++++ l e +er v++a++a+edp++     
  gi|119718962|ref|YP_919457.1|  23 EAEASFSVYRERSVKSEGAYPKALSRASVD-VWIRVAKGKRVAIVTATSLDRDVLSEILERGVAMARVAEEDPHWgglpd 101
                                    6899999999*****999999998888866.*************665666666**********************99988 PP

                                    ...............GGS-HHHHHHHHHHHHHH.CHCSTTEEEEEEEEEE......EEE.EEEEEEETTSEEEEEEEEEE CS
                      PmbA_TldD  76 ...............eevsaeekielleelekalrsadpkienskgarisgvsaslsaskeeklianSeGldveqtrtrv 140
                                                   +++ a+  i+ ++el++ +r + p        +++ + +  sa  + +++ nS+Gl++e++ t++
  gi|119718962|ref|YP_919457.1| 102 pegpthgwvgfdegvATLGADWLIAAVRELAEEVRGRFP--------DVKVTGSGASAASGYSYVYNSRGLRAEDRGTSM 173
                                    888888877777666444444444444444444333334........5666666777787899***************** PP

                                    EEEEEEEE..STCSETEEEEEEEE...SSHHH..S..SSHHHHHHHHHHCTTT-B---SE.EEEEEE-HHHHHHHHHGHH CS
                      PmbA_TldD 141 slslsvia.ddggsgdgmgggsgy...edlee..edleeiaeeaaekalasleakplppg.kypVvlspeavgsllheav 213
                                    +++ls +a  +gg+    g+g+++   +   +  ++le +ae+a + al++ + ++l +  + +V++ p+ +++ll +++
  gi|119718962|ref|YP_919457.1| 174 GVYLSTKAsHAGGE----GTGFAFihsR---SmvAELEGLAERASRLALDAARGEKLGSSvTGNVLFKPYPLAELLDYLL 246
                                    ********444333....4455555542...24457888**************999999988****************** PP

                                    HHHTBHHHHHTT--TTTT-TTSB-S-TT--EEEETT-......-SB-TTSBB---EEEEETTEE--- CS
                      PmbA_TldD 214 ghaleadavlegrSflkdklGekvaselltivddpts.gglgsypfDdEGvptqrtvlIenGvLkny 279
                                     +al+a +vleg S+l+dk+Gekv+ e +t+ dd+t  gg+ ++ fD+EGvp++rt l+e+GvL++y
  gi|119718962|ref|YP_919457.1| 247 VPALNAMNVLEGLSPLRDKVGEKVLGE-MTLLDDGTLpGGIETSLFDAEGVPRRRTLLVERGVLRGY 312
                                    ****************99*******99.9*******99***************************98 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 0.45
                                    EEEEEEEEEEEEE.STCSETEEEEEEEE.......SSHHHS..SSHHHHHH CS
                      PmbA_TldD 136 trtrvslslsviaddggsgdgmgggsgy.......edleeedleeiaeeaa 179
                                    + ++                               ++  +e+ ee+a++aa
  gi|119718962|ref|YP_919457.1| 334 RGSY-----------------------TvsrsnmvVEGGDESEEELARDAA 361
                                    2222.......................122332232222345555666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (442 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 3005.02
//
Query:       gi|119718963|ref|YP_919458.1|  [L=277]
Description: hypothetical protein Tpen_0045 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-14   54.8   0.0    1.8e-14   54.3   0.0    1.2  1  FdhE             Protein involved in formate dehydrogenase fo
      0.009   15.9   5.5       0.18   11.7   0.4    2.5  2  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
  ------ inclusion threshold ------
      0.012   15.7   1.4        4.8    7.3   0.2    2.3  2  Elf1             Transcription elongation factor Elf1 like
      0.012   15.1  12.0      0.017   14.6   0.6    3.0  2  TF_Zn_Ribbon     TFIIB zinc-binding
      0.024   14.9   2.3      0.024   14.9   2.3    3.4  2  Prim_Zn_Ribbon   Zinc-binding domain of primase-helicase
      0.028   14.3   7.7      0.066   13.1   2.0    2.7  2  Nudix_N_2        Nudix N-terminal
       0.03   14.3   8.3       0.26   11.3   0.3    2.7  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
      0.068   13.2   6.0       0.15   12.1   2.8    2.8  2  HypA             Hydrogenase/urease nickel incorporation, met
       0.12   12.8   9.1        1.1    9.7   1.8    2.5  2  Lar_restr_allev  Restriction alleviation protein Lar
       0.13   11.7   8.2      0.081   12.3   1.1    2.4  2  zf-TFIIB         Transcription factor zinc-finger
       0.16   11.9   4.5        5.2    7.1   0.1    3.1  3  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon
       0.32   11.3   2.6         17    5.8   0.4    2.5  2  zf-Di19          Drought induced 19 protein (Di19), zinc-bind
       0.38   11.1   3.0         12    6.2   0.9    2.5  2  FpoO             F420H2 dehydrogenase subunit FpoO
       0.44   10.0   1.8       0.97    8.8   1.8    1.5  1  NMD3             NMD3 family
       0.71    9.7   2.8         19    5.1   0.4    2.5  2  Cys_rich_KTR     Cysteine-rich KTR
       0.81    9.6   7.2          6    6.8   4.3    2.9  3  zf-C3HC4_3       Zinc finger, C3HC4 type (RING finger)
       0.93    9.4   3.3         10    6.1   0.1    2.9  3  Cys_rich_CPXG    Cysteine-rich CPXCG
          1    9.4   8.4         15    5.7   8.8    2.3  2  DZR              Double zinc ribbon
        1.1    9.1   6.0        2.8    7.9   0.5    2.7  3  Prok-RING_4      Prokaryotic RING finger family 4
        1.4    9.0   7.2        0.6   10.2   1.1    2.7  2  DNA_ligase_ZBD   NAD-dependent DNA ligase C4 zinc finger doma
        3.5    7.6  10.9        1.1    9.2   2.7    2.9  3  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
        9.4    6.7   7.9         63    4.0   7.5    2.3  2  zf-RING_2        Ring finger domain


Domain annotation for each model (and alignments):
>> FdhE  Protein involved in formate dehydrogenase formation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.3   0.0   2.2e-17   1.8e-14      22     249 ..      10     249 ..       5     273 .. 0.69

  Alignments for each domain:
  == domain 1  score: 54.3 bits;  conditional E-value: 2.2e-17
                                    HHHHHTT-T.THHHHHHHHHHHHHHHHHH..CS---..--HHHHHHHHHTT--TT-HHHHH.HH-TTHHHHHHHHHT--S CS
                           FdhE  22 LrqLaeehp.ladYLrflaalaeaqqkvl..aaekplaldaeaieraqehgmpplaakale.rdeawqelLqallealke 97 
                                    L+++ ++ p  ++ L     l+e+q+++    aek   +d e++++  ++g p++    le ++e+++++ +a+   l+e
  gi|119718963|ref|YP_919458.1|  10 LKEIQKDIPiEEGSLATYVGLIEVQEEAKgfYAEKFRDIDVEKVQEGFKEGKPAFLSLPLEiSEEDIEKAYAAVTGYLSE 89 
                                    56666666634456777778888888886323344444889999998899998655544441456667777776666666 PP

                                    -SSHHHHHH...HHHHHH--HHHHHHHHHHHHTT-GGGS-..........GGGHHHHHHHHHHHHHHHHHT--TTSSS-. CS
                           FdhE  98 elpealrea...lerlrkadaeelealadallageleavd..........aakavfvaaAlqvvwtklaaaldakalael 164
                                    +lpe +re    +e+ rk+ +  l++l dal+ag+ e+v+          +    ++a +lq ++++l  a++ +++   
  gi|119718963|ref|YP_919458.1|  90 SLPE-TREPiarIEESRKTGELRLKELSDALFAGDEEHVHgvaervgvdpEILEAVIAWSLQPIFQALSDAVS-SKVDFS 167
                                    6666.34440114555555667778888888877655443111111110033455677788888888888885.555578 PP

                                    -TT-SS-TTT---EEEEEEE-------EEEEEETTT--EEE--TTS-TTT---SS-EEE---.---C-EEEEEETTTTEE CS
                           FdhE 165 aeekglCPvCgsaPvasvvriggeaeglRylhCslCeteWhvvRvkCsnCeetkelaylsle.dekaavkAesCdeChsY 243
                                    ++++g CPvCg++     v  gg    +  l C  C teW +   kC +C+++++ +  ++  +++++ k  +C +C +Y
  gi|119718963|ref|YP_919458.1| 168 TWTSGRCPVCGGPTKLEYVDAGG----HAHLRCQFCGTEWGYPEGKCPYCGNSDRKTVVEIPvKGEDKFKLMVCYKCGGY 243
                                    999****************6665....77899*******************998888888872455789*********** PP

                                    EEEEET CS
                           FdhE 244 lkilyq 249
                                     k++++
  gi|119718963|ref|YP_919458.1| 244 WKVVDE 249
                                    ***976 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.4   0.00022      0.18      26      56 ..     169     203 ..     159     204 .. 0.84
   2 ?    6.1   0.6     0.013        11      30      56 ..     209     244 ..     208     245 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00022
                 OrfB_Zn_ribbon  26 yTSktCseCgsknke....alsgrtfkCpnCgfea 56 
                                    +TS +C++Cg   k     a  +  ++C+ Cg+e+
  gi|119718963|ref|YP_919458.1| 169 WTSGRCPVCGGPTKLeyvdAGGHAHLRCQFCGTEW 203
                                    5*********988877899999999******9986 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.013
                 OrfB_Zn_ribbon  30 tCseCgsknke.........alsgrtfkCpnCgfea 56 
                                    +C+ Cg  +++         +++ ++++C +Cg ++
  gi|119718963|ref|YP_919458.1| 209 KCPYCGNSDRKtvveipvkgEDKFKLMVCYKCGGYW 244
                                    7*******99999999999999999*******9875 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.1    0.0063       5.2      23      54 ..     173     202 ..     161     208 .. 0.86
   2 ?    7.3   0.2    0.0059       4.8      23      55 ..     209     244 ..     207     251 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0063
                           Elf1  23 dCpfCnheksvevkldkkekiaevsCkvCges 54 
                                    +Cp+C+     + +     + a+++C+ Cg++
  gi|119718963|ref|YP_919458.1| 173 RCPVCGGP--TKLEYVDAGGHAHLRCQFCGTE 202
                                    69***999..6777888899*********986 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0059
                           Elf1  23 dCpfCnh...eksvevkldkkekiaevsCkvCgesf 55 
                                    +Cp+C++   +++ve+ ++ ++k   + C +Cg + 
  gi|119718963|ref|YP_919458.1| 209 KCPYCGNsdrKTVVEIPVKGEDKFKLMVCYKCGGYW 244
                                    69999872225579******************9765 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.6   2.1e-05     0.017       2      29 ..     173     203 ..     172     207 .. 0.81
   2 ?    3.4   5.0     0.067        55       2      26 ..     209     241 ..     208     250 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.1e-05
                                    EETTTTCEE.C.HEE.TSTTCEEESSSSBEE CS
                   TF_Zn_Ribbon   2 kCPnCgstn.l.veD.pergelvCtdCGlVl 29 
                                    +CP+Cg+++ l ++D   ++ l+C +CG+ +
  gi|119718963|ref|YP_919458.1| 173 RCPVCGGPTkLeYVDaGGHAHLRCQFCGTEW 203
                                    7******887888885567778******976 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.067
                                    EETTTTCEEC.......HEETSTTCE.EESSSS CS
                   TF_Zn_Ribbon   2 kCPnCgstnl.......veDpergel.vCtdCG 26 
                                    kCP+Cg+++        v  ++   l vC +CG
  gi|119718963|ref|YP_919458.1| 209 KCPYCGNSDRktvveipVKGEDKFKLmVCYKCG 241
                                    9*****976444444443336666666777775 PP

>> Prim_Zn_Ribbon  Zinc-binding domain of primase-helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   2.3   2.9e-05     0.024       5      33 ..     173     200 ..     171     207 .. 0.90
   2 ?    1.7   8.7       0.4   3.3e+02       3      32 ..     207     241 ..     204     249 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.9e-05
                                    --TTTT-TTTEEETT....S-EEETTTTB CS
                 Prim_Zn_Ribbon   5 pCPvCGGrDrFrfddkdgrGtwfCrqCgg 33 
                                     CPvCGG ++  + d+ g  +  C+ C g
  gi|119718963|ref|YP_919458.1| 173 RCPVCGGPTKLEYVDAGGHAHLRCQFC-G 200
                                    6************************99.4 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.4
                                    EE--TTTT-TTTEEETT....S-.....EEETTTT CS
                 Prim_Zn_Ribbon   3 hspCPvCGGrDrFrfddkdgrGt.....wfCrqCg 32 
                                    ++ CP CG +Dr +  + + +G       +C++Cg
  gi|119718963|ref|YP_919458.1| 207 EGKCPYCGNSDRKTVVEIPVKGEdkfklMVCYKCG 241
                                    578*********88777666644333336777775 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   2.0   8.1e-05     0.066       3      30 ..     174     201 ..     174     201 .. 0.98
   2 ?    3.4   0.3     0.092        75       3      29 ..     210     241 ..     210     242 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.1e-05
                                    -TTT--B-EEE--TT-SS-EEEETTTTE CS
                      Nudix_N_2   3 CsqCGtpvelripdgDnreRlvCpaCgt 30 
                                    C+ CG+p++l+  d + +  l+C+ Cgt
  gi|119718963|ref|YP_919458.1| 174 CPVCGGPTKLEYVDAGGHAHLRCQFCGT 201
                                    **************************97 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.092
                                    -TTT--B...-EEE--.TT-SS-E.EEETTTT CS
                      Nudix_N_2   3 CsqCGtp...velrip.dgDnreR.lvCpaCg 29 
                                    C+ CG+    +  +ip +g+++    vC +Cg
  gi|119718963|ref|YP_919458.1| 210 CPYCGNSdrkTVVEIPvKGEDKFKlMVCYKCG 241
                                    89999864335577776555444415888887 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   2.4     0.014        12      15      45 ..     169     201 ..     166     202 .. 0.72
   2 ?   11.3   0.3   0.00032      0.26      15      44 ..     205     241 ..     201     243 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.014
                  Zn_Tnp_IS1595  15 WpngfvCPhCgsr...kayriktrglfqCkeCrk 45 
                                    W +g+ CP Cg+    ++    +   ++C+ C++
  gi|119718963|ref|YP_919458.1| 169 WTSGR-CPVCGGPtklEYVDAGGHAHLRCQFCGT 201
                                    88898.*****87644444444488999999876 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00032
                  Zn_Tnp_IS1595  15 WpngfvCPhCgsr.kayrikt.......rglfqCkeCr 44 
                                    +p+g  CP+Cg++ + + ++         +l  C++C+
  gi|119718963|ref|YP_919458.1| 205 YPEGK-CPYCGNSdRKTVVEIpvkgedkFKLMVCYKCG 241
                                    44554.*******8666665577889999999999997 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   2.8   0.00018      0.15      68      98 ..     191     219 ..     123     227 .. 0.81
   2 ?   -1.5   0.1       3.1   2.5e+03      71      81 ..     235     245 ..     226     251 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00018
                                    --EEEETTTS-EEECHHHHHS-TTTSSS-EE CS
                           HypA  68 pvkvrCreCgkefeleekalrCpkCgsadve 98 
                                    ++++rC+ Cg+e+   e   +Cp Cg++d +
  gi|119718963|ref|YP_919458.1| 191 HAHLRCQFCGTEWGYPE--GKCPYCGNSDRK 219
                                    57899********9764..48*****99765 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.1
                                    EEETTTS-EEE CS
                           HypA  71 vrCreCgkefe 81 
                                    + C +Cg  ++
  gi|119718963|ref|YP_919458.1| 235 MVCYKCGGYWK 245
                                    45666665555 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   1.8    0.0013       1.1       5      36 ..     173     201 ..     170     209 .. 0.84
   2 ?    7.0   0.9    0.0094       7.6       5      36 ..     209     242 ..     207     252 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0013
                Lar_restr_allev   5 pCPfCggravlersqrvvaeigqcvyCadCga 36 
                                     CP Cgg+ +le    +         C+ Cg 
  gi|119718963|ref|YP_919458.1| 173 RCPVCGGPTKLEYVDAGGHA---HLRCQFCGT 201
                                    5***********99887776...999999997 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0094
                Lar_restr_allev   5 pCPfCggravlersqrvvaeigq..cvyCadCga 36 
                                     CP Cg+ + +   + +v++  +   + C +Cg 
  gi|119718963|ref|YP_919458.1| 209 KCPYCGNSDRKTVVEIPVKGEDKfkLMVCYKCGG 242
                                    5*****9888888877777655578999****97 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   1.0     0.086        70       2      25 ..     174     199 ..     173     200 .. 0.62
   2 ?   12.3   1.1   9.9e-05     0.081       1      29 [.     209     244 ..     209     244 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.086
                       zf-TFIIB   2 CPkCqde..leeserggveidyCpqC 25 
                                    CP+C+ +  le ++ gg    +C  C
  gi|119718963|ref|YP_919458.1| 174 CPVCGGPtkLEYVDAGGHAHLRCQFC 199
                                    99998631366777777666666666 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 9.9e-05
                       zf-TFIIB   1 kCPkCqdele....eser.....ggveidyCpqCrGvW 29 
                                    kCP C+++ +    e        +++++ +C +C+G W
  gi|119718963|ref|YP_919458.1| 209 KCPYCGNSDRktvvE--IpvkgeDKFKLMVCYKCGGYW 244
                                    8****9865525442..25577888***********99 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.1    0.0064       5.2       3      29 ..     172     203 ..     168     204 .. 0.92
   2 ?    1.3   0.3      0.42   3.4e+02       3       9 ..     208     214 ..     206     219 .. 0.80
   3 ?    3.6   0.0     0.081        66      19      29 ..     234     244 ..     229     245 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0064
                 PhnA_Zn_Ribbon   3 pkCplCaSeytY.....edgallvCpeCahEw 29 
                                    + Cp C+  + +      ++a l C  C+ Ew
  gi|119718963|ref|YP_919458.1| 172 GRCPVCGGPTKLeyvdaGGHAHLRCQFCGTEW 203
                                    58********999999999************* PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.42
                 PhnA_Zn_Ribbon   3 pkCplCa 9  
                                    +kCp C+
  gi|119718963|ref|YP_919458.1| 208 GKCPYCG 214
                                    6999995 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.081
                 PhnA_Zn_Ribbon  19 llvCpeCahEw 29 
                                    l+vC +C+  w
  gi|119718963|ref|YP_919458.1| 234 LMVCYKCGGYW 244
                                    8******9866 PP

>> zf-Di19  Drought induced 19 protein (Di19), zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1     0.033        27      30      50 ..     170     195 ..     160     201 .. 0.69
   2 ?    5.8   0.4     0.021        17       4      11 ..     209     217 ..     207     242 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.033
                        zf-Di19  30 kevvCPvCa.....ekvtkdlvaHlt 50 
                                    +++ CPvC      e+v++   aHl+
  gi|119718963|ref|YP_919458.1| 170 TSGRCPVCGgptklEYVDAGGHAHLR 195
                                    5678****855444445555555665 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.021
                        zf-Di19   4 tCPyCgk.e 11 
                                    +CPyCg+ +
  gi|119718963|ref|YP_919458.1| 209 KCPYCGNsD 217
                                    7****9743 PP

>> FpoO  F420H2 dehydrogenase subunit FpoO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.066        54      56      76 ..     167     187 ..     149     192 .. 0.76
   2 ?    6.2   0.9     0.015        12      60      97 ..     207     240 ..     199     250 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.066
                           FpoO  56 asgtaGkcdlcgkktrlydve 76 
                                    ++ t+G+c +cg  t+l  v+
  gi|119718963|ref|YP_919458.1| 167 STWTSGRCPVCGGPTKLEYVD 187
                                    45689**********998775 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.015
                           FpoO  60 aGkcdlcgkktrlydvevqvPsfskgsekktaklckrc 97 
                                    +Gkc  cg+  r   ve+ v    kg++k + ++c++c
  gi|119718963|ref|YP_919458.1| 207 EGKCPYCGNSDRKTVVEIPV----KGEDKFKLMVCYKC 240
                                    69*********999999876....89999999999999 PP

>> NMD3  NMD3 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   1.8    0.0012      0.97       1      45 [.     196     244 ..     196     253 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0012
                           NMD3   1 CcrCGkeieelinglCedCllkevdite.....giekievevCkeCgryl 45 
                                    C  CG+e   + +g C+ C  ++ + +      g++k ++ vC +Cg y+
  gi|119718963|ref|YP_919458.1| 196 CQFCGTEWGYP-EGKCPYCGNSDRKTVVeipvkGEDKFKLMVCYKCGGYW 244
                                    889*****967.99*****99987665523333557788********997 PP

>> Cys_rich_KTR  Cysteine-rich KTR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1     0.048        39       6      15 ..     174     183 ..     168     188 .. 0.84
   2 ?    5.1   0.4     0.023        19       6      20 ..     210     224 ..     208     242 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.048
                   Cys_rich_KTR   6 cPvCgnkTRl 15 
                                    cPvCg+ T+l
  gi|119718963|ref|YP_919458.1| 174 CPVCGGPTKL 183
                                    ******9986 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.023
                   Cys_rich_KTR   6 cPvCgnkTRlkired 20 
                                    cP Cgn  R+ + e 
  gi|119718963|ref|YP_919458.1| 210 CPYCGNSDRKTVVEI 224
                                    ******999988764 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1      0.11        90      37      46 ..     171     180 ..     164     183 .. 0.79
   2 ?    6.8   4.3    0.0074         6       4      45 ..     173     215 ..     170     220 .. 0.75
   3 ?    0.7   0.1       0.6   4.9e+02      24      33 ..     235     244 ..     232     250 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.11
                                    T-B-TTT--B CS
                     zf-C3HC4_3  37 kkkCpiCrrp 46 
                                    + +Cp+C  p
  gi|119718963|ref|YP_919458.1| 171 SGRCPVCGGP 180
                                    679****877 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0074
                                    B-TTTSSSBS-EEETTEE..EEEE-HHHHHHHHHTT-B-TTT-- CS
                     zf-C3HC4_3   4 eCviClerprnvvllpCg..HlvlCeeCaekllkrkkkCpiCrr 45 
                                     C++C    +   +   g  Hl  C+ C +++   + kCp+C  
  gi|119718963|ref|YP_919458.1| 173 RCPVCGGPTKLEYVDAGGhaHL-RCQFCGTEWGYPEGKCPYCGN 215
                                    6888887665555555552266.7********99********75 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.6
                                    EE-HHHHHHH CS
                     zf-C3HC4_3  24 vlCeeCaekl 33 
                                    ++C++C   +
  gi|119718963|ref|YP_919458.1| 235 MVCYKCGGYW 244
                                    6899998766 PP

>> Cys_rich_CPXG  Cysteine-rich CPXCG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.2      0.14   1.2e+02      27      37 ..     174     184 ..     173     197 .. 0.63
   2 ?   -1.7   0.1       3.3   2.7e+03       3       8 ..     196     201 ..     194     203 .. 0.74
   3 ?    6.1   0.1     0.013        10       2       9 ..     209     216 ..     209     230 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.14
                  Cys_rich_CPXG  27 CqvCCrPivlq 37 
                                    C+vC  P +l+
  gi|119718963|ref|YP_919458.1| 174 CPVCGGPTKLE 184
                                    56665555554 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.3
                  Cys_rich_CPXG   3 CPyCge 8  
                                    C +Cg 
  gi|119718963|ref|YP_919458.1| 196 CQFCGT 201
                                    888886 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.013
                  Cys_rich_CPXG   2 qCPyCgee 9  
                                    +CPyCg +
  gi|119718963|ref|YP_919458.1| 209 KCPYCGNS 216
                                    6*****86 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   8.8     0.019        15      15      49 .]     174     214 ..     168     241 .. 0.86
   2 ?    0.2   0.2      0.99   8.1e+02      14      19 ..     236     241 ..     226     248 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.019
                            DZR  15 CseCgtk..lkavaa......edrCpsCgekvdpearfCpeCG 49 
                                    C+ Cg +  l+          + rC  Cg++    +  Cp+CG
  gi|119718963|ref|YP_919458.1| 174 CPVCGGPtkLEY--VdagghaHLRCQFCGTEWGYPEGKCPYCG 214
                                    999998833433..24588999999999999999999999998 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.99
                            DZR  14 fCseCg 19 
                                    +C++Cg
  gi|119718963|ref|YP_919458.1| 236 VCYKCG 241
                                    455555 PP

>> Prok-RING_4  Prokaryotic RING finger family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.086        70      25      37 ..     166     178 ..     163     183 .. 0.82
   2 ?    7.9   0.5    0.0034       2.8      17      38 ..     192     215 ..     189     221 .. 0.88
   3 ?   -2.1   0.1       4.6   3.8e+03      19      24 ..     235     240 ..     234     246 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.086
                    Prok-RING_4  25 fdskdlssCPlCq 37 
                                    f+ + + +CP+C 
  gi|119718963|ref|YP_919458.1| 166 FSTWTSGRCPVCG 178
                                    66777889****5 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0034
                    Prok-RING_4  17 gHlvCkeCfdskdls..sCPlCqr 38 
                                    +Hl C+ C  ++ +    CP C +
  gi|119718963|ref|YP_919458.1| 192 AHLRCQFCGTEWGYPegKCPYCGN 215
                                    6***********99889*****85 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 4.6
                    Prok-RING_4  19 lvCkeC 24 
                                    +vC +C
  gi|119718963|ref|YP_919458.1| 235 MVCYKC 240
                                    799999 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.1   0.00073       0.6       1      20 [.     173     196 ..     173     197 .. 0.72
   2 ?    1.3   0.6      0.43   3.5e+02       1       6 [.     209     214 ..     209     216 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00073
                 DNA_ligase_ZBD   1 hCPvCGsavvRee.....geaiyRC 20 
                                    +CPvCG ++   e     g a +RC
  gi|119718963|ref|YP_919458.1| 173 RCPVCGGPTKL-EyvdagGHAHLRC 196
                                    5******9953.3366666777888 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.43
                 DNA_ligase_ZBD   1 hCPvCG 6  
                                    +CP CG
  gi|119718963|ref|YP_919458.1| 209 KCPYCG 214
                                    6****9 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.2      0.13   1.1e+02      27      34 ..     173     180 ..     170     184 .. 0.69
   2 ?    9.2   2.7    0.0014       1.1      13      34 ..     195     216 ..     194     217 .. 0.92
   3 ?   -1.3   0.0       2.6   2.1e+03      27      32 ..     236     241 ..     229     242 .. 0.65

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.13
                        DUF35_N  27 vCphCgsd 34 
                                     Cp Cg+ 
  gi|119718963|ref|YP_919458.1| 173 RCPVCGGP 180
                                    57777765 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0014
                        DUF35_N  13 rCpdCGtvqfPPravCphCgsd 34 
                                    rC  CGt   +P+  Cp+Cg +
  gi|119718963|ref|YP_919458.1| 195 RCQFCGTEWGYPEGKCPYCGNS 216
                                    9******************965 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 2.6
                        DUF35_N  27 vCphCg 32 
                                    vC +Cg
  gi|119718963|ref|YP_919458.1| 236 VCYKCG 241
                                    566666 PP

>> zf-RING_2  Ring finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.6      0.31   2.5e+02      36      43 ..     170     177 ..     166     178 .. 0.76
   2 ?    4.0   7.5     0.078        63       3      43 ..     174     213 ..     172     214 .. 0.68

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.31
                      zf-RING_2  36 ssstCPlC 43 
                                    +s +CP+C
  gi|119718963|ref|YP_919458.1| 170 TSGRCPVC 177
                                    4778***9 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.078
                      zf-RING_2   3 CpICleelssadsvlllpCgH.v.fhreClerwlrssstCPlC 43 
                                    Cp+C  + +  + v +   gH +  ++ C ++w  ++ +CP+C
  gi|119718963|ref|YP_919458.1| 174 CPVCGGPTKL-EYVDAG--GHaHlRCQFCGTEWGYPEGKCPYC 213
                                    8888655532.333333..553225888*************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                        34  (0.00189637); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 1796.75
//
Query:       gi|119718964|ref|YP_919459.1|  [L=297]
Description: hypothetical protein Tpen_0046 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-44  151.2   0.0    3.9e-44  151.0   0.0    1.0  1  DUF89     Protein of unknown function DUF89


Domain annotation for each model (and alignments):
>> DUF89  Protein of unknown function DUF89
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.0   0.0   2.2e-48   3.9e-44       2     352 ..       4     282 ..       3     283 .. 0.94

  Alignments for each domain:
  == domain 1  score: 151.0 bits;  conditional E-value: 2.2e-48
                                    HHTHHHHHH.HHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHCTTCGHHH-HHHHT-BTTBSBHHHHHHHHHHHHHHHH CS
                          DUF89   2 leerlpcil.tqviddlekakdekeeelkkiieelselkeelqtdkpltpledeeekrswfnapwlfaecylyrrllelf 80 
                                    ++e++ ci  t++ + l  + ++  e++ +++++l+ +   l + ++ t +                ++++ +r+++el+
  gi|119718964|ref|YP_919459.1|   4 HPECVLCIYrTRAGEVLASNLSD--EAKVEALGKLTVFYGGLVEPSSSTVV----------------LAWKAFRKVKELL 65 
                                    78999999978888888888888..99999999999999999999999999................************* PP

                                    THSGGGTTS-TTHHHHHHHHHHHHHHHHHHHHHHHHCCSHHHHHHHHHHHHHHHCG--CCCHTSHHCHHHHHHHHHHHHH CS
                          DUF89  81 glskelknyDpFkeqKeesnksalkaveelakrleeledekelfkellkislwGNaiDlsllateediqkdqeeearkal 160
                                    g       +Dp++ +Ke+s ++a+++ve+la+r e+le + e+fk +l +s++ N +D ++          +e+ ++ka+
  gi|119718964|ref|YP_919459.1|  66 G------AEDPYRYFKEQSHAAAMSVVERLAARAEGLEGY-ERFKYFLSLSVAANLVDPGSPM-----GVSPEQLLEKAS 133
                                    *......********************************9.*******************999.....556688889999 PP

                                    HCTESEE-HHHHHHHHCTCHTSEEEEE--BTTHHHHHHHHHHHHHHHCTTTSEEEEEEBSS--TTTB-BHHHHHHHHHHH CS
                          DUF89 161 eknilvddleklweklkkkkakrvdivlDNaGfElvfDlllaeeLlesglatkVvlhvkaiPwfvsDvtpeDfewlleql 240
                                      ++  d++++l+  l   +++rv ++lDN+G E vfD l+++eL++  ++ +  +++k+ P + +Dvt++D+       
  gi|119718964|ref|YP_919459.1| 134 SLRFARDETDRLYLTL--LQSSRVTYLLDNCG-EAVFDGLVLRELRR--MGIQLKIVAKGAP-YQNDVTHDDAL------ 201
                                    9999************..**************.**************..99999999*****.***********...... PP

                                    H-TTTSHHHHCHTTHHHHHHTSEEEEESSCGGSSS--CCGSSSHHHHHHHHHC-SEEEEEHHHHHHHHTTSCTTTTTSEH CS
                          DUF89 241 adsksfelsalgagldellkegklvlrgssfwttglsysempeapelyeelekadLvifKGdlNyrkLtgdrkwppttpf 320
                                               ++g++e   +g++v++gs+   +g++   +  ++e +++le ad+vi+KG++N+++++     pp+t  
  gi|119718964|ref|YP_919459.1| 202 -----------RMGFQE---LGEVVSTGSD--FPGVVPGYV--SEEAVKALEWADVVISKGMANFEAFLM---SPPKTA- 259
                                    ...........******...**********..*********..*************************74...577666. PP

                                    HHHTGTSS--EEEEEE--SHHHHHHH.STTTHE CS
                          DUF89 321 ttalgfspvpvlaLrtvKadvvagll.egegek 352
                                              v++ +++K++++a+   ++ g++
  gi|119718964|ref|YP_919459.1| 260 ----------VFVAFVAKCRPIAQAArVNPGDA 282
                                    ..........*************9988877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 2085.59
//
Query:       gi|119718965|ref|YP_919460.1|  [L=217]
Description: phosphoribosyltransferase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.1e-46  156.1   0.0    9.3e-46  155.9   0.0    1.0  1  UPRTase       Uracil phosphoribosyltransferase
    7.1e-09   35.4   0.0    1.3e-08   34.5   0.0    1.4  1  Pribosyltran  Phosphoribosyl transferase domain
  ------ inclusion threshold ------
        0.1   12.1   0.0       0.18   11.3   0.0    1.4  1  PRTase_2      Phosphoribosyl transferase


Domain annotation for each model (and alignments):
>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.9   0.0   1.6e-49   9.3e-46       2     206 ..      10     217 .]       9     217 .] 0.95

  Alignments for each domain:
  == domain 1  score: 155.9 bits;  conditional E-value: 1.6e-49
                        UPRTase   2 sshpllkakltilRdastsrkdfrelvdriarllaeealsallpveevtvttplgkeysgelldeekialVpilRaGegm 81 
                                    + +p+l+ +l +lR+++t+r++frel+ + + + a+e+ ++ lp+ee+ v+tplg+    ++ +  k+a+V++lRa ++m
  gi|119718965|ref|YP_919460.1|  10 LGNPVLQEILGKLRSRDTPRREFRELLFKAGVFEAYEIAEE-LPTEECSVETPLGRRAPCVRVTG-KLAIVAVLRAALPM 87 
                                    6789************************************9.*****************999997.************** PP

                        UPRTase  82 eealrellpearvghlglqreeet.......lepveyynkLPkkiaertvlllDpviaTGgsaaaaiqlLkergvgeekI 154
                                    + +++e++p+a++g +  +r e++       le +  y  +P +  +++ +++Dp++aTG+++a++i++Lk  g    + 
  gi|119718965|ref|YP_919460.1|  88 AMGMLEVFPDAALGFVAAKRLEADapprdwrLEVSVPYVSMPPD--AENLVIVDPMLATGSTLASVIERLKGGGYSYGRL 165
                                    ********************999967777776767788888887..688999**************************** PP

                        UPRTase 155 lvlsvlaseegvkrlaeefpkvkvvtaavDeeldekgyivpGlGDfGDRlFg 206
                                     v++v++ e+g++r+++  p+ +++t +vD+el++k++ivpGlGD+GDR Fg
  gi|119718965|ref|YP_919460.1| 166 YVATVISTEQGIRRVLSVEPEARIYTLSVDPELNDKAFIVPGLGDAGDRAFG 217
                                    ***************************************************7 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.0   2.2e-12   1.3e-08      31     128 ..      75     175 ..      71     193 .. 0.83

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 2.2e-12
                                    EEEEEEETTTHHHHHHHHHHS.TT-EE-EEEEEE-TTT--EE........EE----TTSEEEEE-SEESSSHHHHHHHHH CS
                   Pribosyltran  31 dvvvgiargGvpfakiladeL.evplayvrkvkyrpdgseeaargssdesrlledpagkkVliVDDildtGgTllaalel 109
                                     ++v+++r ++p+a  +   + ++ l +v +++ ++d  +   r  +  +  +  p+ +  +iVD +l+tG+Tl  ++e+
  gi|119718965|ref|YP_919460.1|  75 LAIVAVLRAALPMAMGMLEVFpDAALGFVAAKRLEADAPPRDWRLEVSVPYVSMPPDAENLVIVDPMLATGSTLASVIER 154
                                    68********************99999999999887776655554444444999999*********************** PP

                                    HHCC-BS..EEEEEEEEE-HH CS
                   Pribosyltran 110 Lkekgpe..evriavlvdkpa 128
                                    Lk  g    ++ +a+++   +
  gi|119718965|ref|YP_919460.1| 155 LKGGGYSygRLYVATVISTEQ 175
                                    **9998877777777775555 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   2.9e-05      0.18     120     161 ..     131     173 ..     125     194 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.9e-05
                       PRTase_2 120 aakelvLvDDEistGktalnliralqeklpr.kryvvvslvdw 161
                                    +a++lv+vD  ++tG+t++ +i++l+    +  r+ v++++  
  gi|119718965|ref|YP_919460.1| 131 DAENLVIVDPMLATGSTLASVIERLKGGGYSyGRLYVATVIST 173
                                    5789*********************998555588888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       235  (0.0131073); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1639.40
//
Query:       gi|119718966|ref|YP_919461.1|  [L=110]
Description: Fis family transcriptional regulator [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 754.24
//
Query:       gi|119718967|ref|YP_919462.1|  [L=77]
Description: hypothetical protein Tpen_0049 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.025   14.5   7.4       0.38   10.7   3.5    3.2  2  RHH_1          Ribbon-helix-helix protein, copG family
      0.028   14.8   2.1      0.097   13.1   2.1    1.8  1  CcdA           Post-segregation antitoxin CcdA
      0.034   13.8   2.1      0.039   13.6   1.8    1.3  1  CoaE           Dephospho-CoA kinase
       0.13   13.0   4.7       0.22   12.3   4.7    1.4  1  PSK_trans_fac  Rv0623-like transcription factor


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   3.5   8.6e-05      0.38      22      38 ..      20      36 ..       3      37 .. 0.69
   2 ?   -0.5   0.1       0.3   1.4e+03      20      27 ..      53      60 ..      48      60 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 8.6e-05
                                   TSSHHHHHHHHHHHHHH CS
                          RHH_1 22 grSrSelIReAlreyle 38
                                   + + Se+IR+A+re ++
  gi|119718967|ref|YP_919462.1| 20 KINWSEFIRRAIREKIA 36
                                   4677**********886 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.3
                                   HHTSSHHH CS
                          RHH_1 20 rrgrSrSe 27
                                    r+rSr+e
  gi|119718967|ref|YP_919462.1| 53 VRKRSRGE 60
                                   45577765 PP

>> CcdA  Post-segregation antitoxin CcdA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   2.1   2.2e-05     0.097       4      42 ..       4      42 ..       3      72 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.2e-05
                           CcdA  4 vnlsldsdllaqAralgiNlSatleeaLaeevkeekaer 42
                                   +++ +d++  +   +++iN S+ + +a++e+++ee+++ 
  gi|119718967|ref|YP_919462.1|  4 ITVRIDEETKRLMESVKINWSEFIRRAIREKIAEERRKN 42
                                   57899****************************999876 PP

>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   1.8   8.7e-06     0.039     127     174 ..       3      51 ..       1      56 [. 0.86

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.7e-06
                                    EEE--HHHHHHHHHHCCTSTHHH.HHHHHHHS--HHHHHHH-SEEEE-. CS
                           CoaE 127 vvdvelelqveRlvardgvseee.vkaiiaaQlseeerlaladvvldNd 174
                                    v++v  +++ +Rl++  +++  e +++ i+  ++ee r++la+ vl N+
  gi|119718967|ref|YP_919462.1|   3 VITVRIDEETKRLMESVKINWSEfIRRAIREKIAEERRKNLAKAVLINE 51 
                                    78888899999******99966637889******************997 PP

>> PSK_trans_fac  Rv0623-like transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   4.7     5e-05      0.22      11      58 ..       9      59 ..       5      76 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5e-05
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XX--HHHHHHHHHHH CS
                  PSK_trans_fac 11 erlareLarltgeskteAvrrAleerlerlrre...raepllerllallrr 58
                                   ++ +++L++  + +  e +rrA++e+++++rr+   +a    er+++  r 
  gi|119718967|ref|YP_919462.1|  9 DEETKRLMESVKINWSEFIRRAIREKIAEERRKnlaKAVLINERVRKRSRG 59
                                   66678899999999****************988877444444555443332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1167  (0.0650901); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 583.65
//
Query:       gi|119718968|ref|YP_919463.1|  [L=140]
Description: hypothetical protein Tpen_0050 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-14   54.7   1.3    1.5e-14   54.5   1.3    1.0  1  PIN       PIN domain
    2.1e-06   28.0   0.0    2.7e-06   27.6   0.0    1.1  1  PIN_2     PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.5   1.3   1.7e-18   1.5e-14       2     118 ..       5     124 ..       4     128 .. 0.93

  Alignments for each domain:
  == domain 1  score: 54.5 bits;  conditional E-value: 1.7e-18
                                    EE-HHHHHHHHTTSHHHHHHHHHHHTS....SEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCHHH CS
                            PIN   2 vlDTsvliallrgeekaeaarklleel....eelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpidaei 77 
                                    v+D+sv+++++ +ee++++a+k  + +     elv ++l ++E+l+ l ++++ +e++ + v++ l++ ++k+ p+  e 
  gi|119718968|ref|YP_919463.1|   5 VVDASVVVKWFVEEEGSDKALKVRDMYvegeVELVAPELLVYEVLNALYYKRLFSEEEMAQVLEALEAYSFKLYPLKGEY 84 
                                    8**********7777777777777766777************************************************** PP

                                    HHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHH CS
                            PIN  78 aeeaaeialkygllpnDaliaAtAkehgikliatfDedfrr 118
                                    a++a+ei+ + +++++Da  +A+A  ++   ++t+De+++r
  gi|119718968|ref|YP_919463.1|  85 ARKALEISYRCDVTVYDASYVALAVLRDT-YVYTADEKLAR 124
                                    *****************************.999*****887 PP

>> PIN_2  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   3.1e-10   2.7e-06       1     116 [.       5     123 ..       5     127 .. 0.86

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 3.1e-10
                          PIN_2   1 VvdaNivvsallk.....srikkrlilvekaleliapeeaveeiekhkealvkksklseeeleellelletkikiveesl 75 
                                    Vvda +vv   ++     +  k r + ve ++el+ape +v e+    +al  k+ +seee++++le+le +  +    l
  gi|119718968|ref|YP_919463.1|   5 VVDASVVVKWFVEeegsdKALKVRDMYVEGEVELVAPELLVYEVL---NALYYKRLFSEEEMAQVLEALEAY-SFKLYPL 80 
                                    9*********99998877778899999****************95...67889**************99865.2223345 PP

                          PIN_2  76 yeskikeAkeriarvDpd..DtpfvAlaLlleapiWTeDkdli 116
                                    + ++ ++A e+  r D    D+ +vAla+l +  + T D++l 
  gi|119718968|ref|YP_919463.1|  81 KGEYARKALEISYRCDVTvyDASYVALAVLRDTYVYTADEKLA 123
                                    55899999999999997444********************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1017.73
//
Query:       gi|119718969|ref|YP_919464.1|  [L=255]
Description: hypothetical protein Tpen_0051 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-44  151.1  44.6    4.4e-44  150.9  44.6    1.0  1  TauE      Sulfite exporter TauE/SafE


Domain annotation for each model (and alignments):
>> TauE  Sulfite exporter TauE/SafE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.9  44.6   2.4e-48   4.4e-44       2     235 ..      11     248 ..       9     249 .. 0.92

  Alignments for each domain:
  == domain 1  score: 150.9 bits;  conditional E-value: 2.4e-48
                           TauE   2 llagllaGfvagllGiGggliavPlLlll..l........ppavavatsllavvatslsgalahrrrgnvdwrlllllll 71 
                                    ++ g+l+Gf  gl+G+Gg+++a+PlLl++  l        + +va++t+ +av++++l+++++h+++gn +++++ +++ 
  gi|119718969|ref|YP_919464.1|  11 AVSGVLVGFALGLVGGGGSILAIPLLLYFagLssvldqdtAVHVAIGTTSVAVGLNALANFAMHLKSGNAELKAGAVFAG 90 
                                    689*************************7454999****999************************************** PP

                           TauE  72 gsliGallGallllllpsellkllfgvlllllallmllrkkrsrakgrerrptaillvligglvGllsGllGiGgGfllv 151
                                     + +++ lGall  +++++ll++l+gv+++ll+++++ +++   a     ++++  l++  +lvG++sG+lGiGgGfl++
  gi|119718969|ref|YP_919464.1|  91 IGTVASTLGALLGRQTKGQLLLALLGVAMVLLSFWVASKRR--YAG---GKTSLKRLAAGSALVGFVSGFLGIGGGFLVA 165
                                    ************************************98776..222...23333333444456***************** PP

                           TauE 152 pllllllglplkkavatslllilvislagalgyalagavdwpllllllpgallGallGarlarrlsertlrrlfallllv 231
                                    p+ll+  gl++kka++tsll++ +++l++ ++ya+ag+ d+ +++++l+g++lG+ lG+++++r +++++ +++ +l+++
  gi|119718969|ref|YP_919464.1| 166 PALLW-AGLDVKKAIGTSLLAVGLFGLSTSAVYASAGYADYAIAAAYLAGGVLGGRLGVHVSTRAPREKVALAYSALIAA 244
                                    ***98.8************************************************************************* PP

                           TauE 232 lgvk 235
                                    +gv+
  gi|119718969|ref|YP_919464.1| 245 VGVY 248
                                    **98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       787  (0.0438954); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1686.21
//
Query:       gi|119718970|ref|YP_919465.1|  [L=133]
Description: hypothetical protein Tpen_0052 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       194  (0.0108205); expected 358.6 (0.02)
Passed bias filter:                      178  (0.00992805); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 912.27
//
Query:       gi|119718971|ref|YP_919466.1|  [L=445]
Description: amino acid permease-associated region [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.2e-34  117.8  40.4    6.4e-34  117.5  40.4    1.1  1  AA_permease_2   Amino acid permease
    3.1e-33  115.1  36.7    4.3e-33  114.6  36.7    1.1  1  AA_permease     Amino acid permease
    5.7e-05   22.1   7.9    0.00013   20.9   7.9    1.5  1  Spore_permease  Spore germination protein


Domain annotation for each model (and alignments):
>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.5  40.4   1.1e-37   6.4e-34       5     392 ..      12     420 ..       8     439 .. 0.84

  Alignments for each domain:
  == domain 1  score: 117.5 bits;  conditional E-value: 1.1e-37
                  AA_permease_2   5 safalvigsvigsgifvkn..laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaaf..gkkvafls 80 
                                     a+++ +g+++g+gi+v    +a+ +g a++ +v ++ +i  +a ++ yaElss + +    y+y+++af    ++af++
  gi|119718971|ref|YP_919466.1|  12 YATLFGVGLILGAGIYVLIgrAAGIVGDAVWASVAFSGVIA-VATAFSYAELSSIFAKAASTYTYVREAFpgAGLLAFFA 90 
                                    588999***********988666669999999999999998.7***************************6558999*** PP

                  AA_permease_2  81 awfnwfayvpvlasilsvaasyllnalgpdlqgntwltyliaiaililvalinirgikesakiqnilgilkillpliili 160
                                    aw+++f+ v+++a+ +  +a+y+  ++g  ++g+   +  + +a+l+++ ++n  gikesa +  + +++   + l++++
  gi|119718971|ref|YP_919466.1|  91 AWMLFFGGVAGAATAALGFAGYFSRLAG-LGEGW--VVP-VTVALLAVLSVLNWWGIKESAFLSAVFTVIEA-GGLVLVV 165
                                    *************************987.34455..444.477*****************************.6889999 PP

                  AA_permease_2 161 ilglitvdgggfsslstetdtffpngwpgv..llgllivlwsfdGfesaanvsee..vkkkdvpkaifigllivlvlyll 236
                                    +lg+++  ++          +f+p++ p +  l+g +++ ++++Gfe+    see  ++++ +pk i+++++++++lyll
  gi|119718971|ref|YP_919466.1| 166 LLGFLFPARSPGY------LSFNPSVDPVMavLVGAAVFYFAYTGFEYQPTLSEEtvDPERVIPKSIVLAVSVTTLLYLL 239
                                    9******998886......48*******953377888899***************98888******************** PP

                  AA_permease_2 237 vniaflgvvpddeianlsnlgsvaalffeavggkvvaiivvilialsllgaintavigssrvlealardgvlPrffakvn 316
                                    v+++++  ++++e+  ++    ++a  + +++ + +++++++++ ++     +++++++sr+++ la++gv  + f +v+
  gi|119718971|ref|YP_919466.1| 240 VSLSVVRLMSWEELGASKA---PMADAASRAW-PPAFHLLMFIALFATTNTSLGFLVSASRLAYGLAEEGVAWSGFGRVD 315
                                    **************98776...5777777777.789999999************************************** PP

                  AA_permease_2 317 .kfgspiraiiltaivslillllfl...............las.saaynfllsvsslgliisyllliigalilrkkrphl 379
                                      + +p +a+ +t +++ +l+  f+               +   +  ++++  ++sl++++ ++++ ++++ lr+++   
  gi|119718971|ref|YP_919466.1| 316 gWRRTPHVAVAFTGVLAALLV--FAtdylpsvtgwrlsfgG-QeYQLIDLVGKTASLAVLLAFFVVNAAVVALRRREGLS 392
                                    99***************5543..545788888888888532.2466677*************************997777 PP

                  AA_permease_2 380 krpgk...............ilvaiiga 392
                                    +r++                il+a + a
  gi|119718971|ref|YP_919466.1| 393 RRFRVplnvgdfpvlpvladILIAVFVA 420
                                    7765555556666444333333333332 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.6  36.7   7.1e-37   4.3e-33       3     433 ..      14     425 ..      12     442 .. 0.81

  Alignments for each domain:
  == domain 1  score: 114.6 bits;  conditional E-value: 7.1e-37
                    AA_permease   3 lvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgp..elGfviGl 80 
                                    +++ +g + G+g++v +g +++ +G  +++ +++++gv+ ++++ s +e+++++ k++++yty+++       l+f+ ++
  gi|119718971|ref|YP_919466.1|  14 TLFGVGLILGAGIYVLIGRAAGIVGD-AVWASVAFSGVIAVATAFSYAELSSIFAKAASTYTYVREAFPGagLLAFFAAW 92 
                                    57788999999999999999988888.88***********************************99875535699***** PP

                    AA_permease  81 nylfswitvlaleltaasiliqfwelvtdlpkawvt..gavflvvlliinlvgvkvygeaefilalikiiaiiafiivgi 158
                                    +++f +++++a +  + + +++ +     l + wv+   + +l+vl+++n  g+k +++ + ++++i    ++ ++++g+
  gi|119718971|ref|YP_919466.1|  93 MLFFGGVAGAATAALGFAGYFSRL---AGLGEGWVVpvTVALLAVLSVLNWWGIKESAFLSAVFTVIEAGGLVLVVLLGF 169
                                    *99999998887766555555555...4444445556555678899999**********999999999999999999996 PP

                    AA_permease 159 illaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiagEvkdPeksiPkailq 238
                                     +    ++++g    +l++n s      ++         ++++++++++++fa+tG+e+ +++++E+ dPe+ iPk+i  
  gi|119718971|ref|YP_919466.1| 170 LFP---ARSPG----YLSFNPS------VDP--------VMAVLVGAAVFYFAYTGFEYQPTLSEETVDPERVIPKSIVL 228
                                    444...44667....7888888......555........8**************************************** PP

                    AA_permease 239 vviritifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplinaviltaalssansslysasRvlysl 318
                                    +v  +t++Y+l++l+++ l+++  lg  +       p+  + + +  +++  l+ ++ l a++++++++l+sasR+ y l
  gi|119718971|ref|YP_919466.1| 229 AVSVTTLLYLLVSLSVVRLMSWEELGASK------APMADAASRAWPPAFHLLMFIA-LFATTNTSLGFLVSASRLAYGL 301
                                    ************************99999......4999999999999997777666.55788999************** PP

                    AA_permease 319 akdglaP.kvlkkvskrgvPlraillsmiisllal...........llaslnlaapivfnfllaisaliglivwlliils 386
                                    a++g+a   ++++ + r+ P++a++++ ++++l++              s+  +  + ++ +   + l+ l+ + +++++
  gi|119718971|ref|YP_919466.1| 302 AEEGVAWsGFGRVDGWRRTPHVAVAFTGVLAALLVfatdylpsvtgWRLSFGGQEYQLIDLVGKTASLAVLLAFFVVNAA 381
                                    ******9788888888999*************999778888877774445555555888888888888888888888888 PP

                    AA_permease 387 ylrfRkalkyqgrsieelgfkaallplgvilvla.aliiillilalya 433
                                     + +R+   +++r    +++ + ++ + v  vla +li+++++l++++
  gi|119718971|ref|YP_919466.1| 382 VVALRRREGLSRR----FRVPLNVGDFPVLPVLAdILIAVFVALSFWD 425
                                    8877777444444....5566665555555554435566666666665 PP

>> Spore_permease  Spore germination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   7.9   2.2e-08   0.00013      13     240 ..      19     254 ..      13     264 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2.2e-08
                 Spore_permease  13 sfqlGvgiltlprsvaeqatpdgWisvllagiiililvllmlkllkkfpe.ktliellkkilg.kwLGsllsilfilyFl 90 
                                      +lG+gi +l + +a   +   W sv + g+i++  +  + +l++ f++  + + ++++ +    L   +  +++l+F 
  gi|119718971|ref|YP_919466.1|  19 GLILGAGIYVLIGRAAGIVGDAVWASVAFSGVIAVATAFSYAELSSIFAKaASTYTYVREAFPgAGL-LAFFAAWMLFFG 97 
                                    679****************999*************************98725788999888861444.4555689***** PP

                 Spore_permease  91 llaafelRefseliqvflledt.plwiiilllllvilYlvvk..Gieslareflfiivi....lliilllillfslklae 163
                                     +a+  +  ++    ++ l  +   w++ +++ l++++ v +  Gi++ a + ++++vi    l++++ll +lf+ ++  
  gi|119718971|ref|YP_919466.1|  98 GVAGAATAALGFAGYFSRLAGLgEGWVVPVTVALLAVLSVLNwwGIKESAFLSAVFTVIeaggLVLVVLLGFLFPARSPG 177
                                    **********9999999998884568888888888888887666**9988633333333222356666666777777777 PP

                 Spore_permease 164 iknlrPvlgngikpvlkslkttslsflgveillllvpflkdkkk.vkkaallgvlistllyllttlivilvlsveqlk 240
                                         P + + ++ vl ++ +++++++g+e    l +   d+++ + k ++l+v ++tllyll+ l v+  +s e+l 
  gi|119718971|ref|YP_919466.1| 178 YLSFNPSV-DPVMAVLVGAAVFYFAYTGFEYQPTLSEETVDPERvIPKSIVLAVSVTTLLYLLVSLSVVRLMSWEELG 254
                                    77778966.568899***************99777776666665167***********************99999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (445 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       703  (0.0392102); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 2857.03
//
Query:       gi|119718972|ref|YP_919467.1|  [L=130]
Description: hypothetical protein Tpen_0054 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 891.51
//
Query:       gi|119718973|ref|YP_919468.1|  [L=158]
Description: hypothetical protein Tpen_0055 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.41   11.6  12.3       0.72   10.8  11.2    2.0  2  Pilin_N   Archaeal Type IV pilin, N-terminal
          1    8.7   3.5        1.3    8.3   3.5    1.2  1  DUF4191   Domain of unknown function (DUF4191)


Domain annotation for each model (and alignments):
>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8  11.2     8e-05      0.72       1      42 [.       8      53 ..       8      91 .. 0.67
   2 ?   -0.3   0.1      0.24   2.1e+03      56      66 ..     116     127 ..      64     147 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 8e-05
                        Pilin_N  1 eAVSpViGviLmvaitvIlaAviaafvlgl....asneekapqasi 42
                                   +++SpVi  +++va+t+ +a  +a  ++g+     ++ ek   +s+
  gi|119718973|ref|YP_919468.1|  8 RGISPVIATVIIVAVTIAIAIAVAFWMTGIvgifTGTVEKLEIVSL 53
                                   69***************99999998888875333444444444444 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.24
                        Pilin_N  56 a.vslehkgGds 66 
                                      ++++  +G+ 
  gi|119718973|ref|YP_919468.1| 116 LtITFTLGNGNE 127
                                    136666655554 PP

>> DUF4191  Domain of unknown function (DUF4191)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   3.5   0.00015       1.3      19      66 ..       4      48 ..       1      59 [. 0.69

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00015
                        DUF4191 19 rkedkkllwlllaaflvvvvvfvvlglllgslilllilgillgllval 66
                                   +++ + + ++++++++v+v +++++ ++    +++ i+gi++g++  l
  gi|119718973|ref|YP_919468.1|  4 AQKRRGISPVIATVIIVAVTIAIAIAVA---FWMTGIVGIFTGTVEKL 48
                                   4444556666666666666666666666...6**********998665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1065  (0.059401); expected 358.6 (0.02)
Passed bias filter:                      583  (0.0325172); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1161.58
//
Query:       gi|119718974|ref|YP_919469.1|  [L=135]
Description: hypothetical protein Tpen_0056 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.072   13.4   0.1       0.13   12.6   0.1    1.5  1  DUF4156         Domain of unknown function (DUF4156)
       0.11   12.8   3.6       0.26   11.6   1.1    2.5  2  DUF11           Domain of unknown function DUF11
        1.9    8.4   6.9    1.2e+02    2.7   6.9    3.0  1  HlyD            HlyD membrane-fusion protein of T1SS


Domain annotation for each model (and alignments):
>> DUF4156  Domain of unknown function (DUF4156)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   2.2e-05      0.13      44      90 ..      46      93 ..      27      93 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.2e-05
                        DUF4156 44 elvrgaandLrneAaalGgntivlvtstatetess.qtdvtmlgqvYk 90
                                   + +  ++ dL+  A++ Gg t+v v   +  t+ +  + v++ gqvY+
  gi|119718974|ref|YP_919469.1| 46 QQMGLEILDLKASASRSGGKTVVTVYAWNRGTKPAtIVAVKVNGQVYE 93
                                   555667889******************988886644789********5 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1      0.63   3.7e+03      66      83 ..      20      37 ..      12      44 .. 0.66
   2 ?   11.6   1.1   4.4e-05      0.26       8      36 ..      58      86 ..      54     128 .. 0.64

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.63
                          DUF11 66 agesatlsftvrvtrtaa 83
                                   +ge   l + v v+++aa
  gi|119718974|ref|YP_919469.1| 20 PGEVVVLVVVVAVAVAAA 37
                                   566666666666666655 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 4.4e-05
                          DUF11  8 sevrpGdtvtytltvtNtgpasangvvvt 36
                                   s+ r+G+++++t+ + N+g+++a+ v v+
  gi|119718974|ref|YP_919469.1| 58 SASRSGGKTVVTVYAWNRGTKPATIVAVK 86
                                   5779*******************555443 PP

>> HlyD  HlyD membrane-fusion protein of T1SS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   6.9      0.02   1.2e+02      20      76 ..      61     102 ..       5     135 .] 0.57

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.02
                                    ECEEEEEEEGCGEEECTTTSEEEEEEECTSBEEEEEEEEEEEETTEEEESSSS-TTE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           HlyD  20 rvgqpvevrfdAfpqtktgkftgvVvgispdrvpvrvvvekaqgpyyplriglkaga 76 
                                    r+g +  v++ A ++                  p+ +v+ k +g++y  r+ + +g+
  gi|119718974|ref|YP_919469.1|  61 RSGGKTVVTVYAWNRG---------------TKPATIVAVKVNGQVYEQRVAVEPGS 102
                                    4444444455555554...............44444444444444444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       877  (0.0489152); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 980.18
//
Query:       gi|119718975|ref|YP_919470.1|  [L=43]
Description: hypothetical protein Tpen_0057 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (43 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.26s 00:00:00.57 Elapsed: 00:00:00.40
# Mc/sec: 323.43
//
Query:       gi|119718976|ref|YP_919471.1|  [L=254]
Description: thioredoxin/glutaredoxin-like [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      3e-05   24.0   0.0    0.00018   21.5   0.0    2.1  2  Thioredoxin_3  Thioredoxin domain
  ------ inclusion threshold ------
       0.18   12.1   0.1        2.1    8.6   0.0    2.1  2  CENP-C_C       Mif2/CENP-C like


Domain annotation for each model (and alignments):
>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0     2e-08   0.00018       4      73 ..       3      72 ..       1      75 [. 0.83
   2 ?   -0.3   0.0      0.13   1.1e+03      61      74 ..     171     184 ..     167     186 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2e-08
                                   EE.ESSSSTTCHHHHHHHHHHCHCC.TCECEEECCTTHHHHHHCT-SSSSEEECTTCEEEESS---CCHHHH CS
                  Thioredoxin_3  4 kv.lgpgCakCpklekavkeaaaek.gikaevekvtdfeeiekygVmsvPalvidgkvvvsGkvpseeeirk 73
                                    v + p Ca  +++++++ +  +++ +i++  ++ + f+ + +ygV svPa  ++g++v +G   + ee+ +
  gi|119718976|ref|YP_919471.1|  3 TVyVHPRCADSYRVYRLLSSRTPQStRITYLDTEKYPFRAL-EYGVFSVPAFSLNGRLVLQG-YFEDEEVVS 72
                                   5778999***********99999995587766666777777.9*******************.777777765 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.13
                                    EESS---CCHHHHH CS
                  Thioredoxin_3  61 vsGkvpseeeirkl 74 
                                     +G+vp++e ++kl
  gi|119718976|ref|YP_919471.1| 171 LTGEVPTRERVEKL 184
                                    58*********997 PP

>> CENP-C_C  Mif2/CENP-C like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0     0.061   5.5e+02      50      67 ..      37      54 ..      31      57 .. 0.84
   2 ?    8.6   0.0   0.00023       2.1      40      68 ..     107     135 ..      93     146 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.061
                                   TEEEEEETT-EEEE-TT- CS
                       CENP-C_C 50 ktsfvigkgsvFqvPagn 67
                                   k  f++ + +vF vPa++
  gi|119718976|ref|YP_919471.1| 37 KYPFRALEYGVFSVPAFS 54
                                   678999999******986 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00023
                                    EESEEEEEETTEEEEEETT-EEEE-TT-E CS
                       CENP-C_C  40 iqGrvevtvsktsfvigkgsvFqvPagne 68 
                                    ++G++ v    +s++++  + F vP g +
  gi|119718976|ref|YP_919471.1| 107 VAGDLSVVAGSKSYLMSASGAFFVPEGEK 135
                                    4799*********************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1825.10
//
Query:       gi|119718977|ref|YP_919472.1|  [L=448]
Description: amidohydrolase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-42  146.7   0.0    1.3e-42  146.4   0.0    1.1  1  Amidohydro_1  Amidohydrolase family
    7.3e-13   48.8   2.9      2e-05   24.3   0.5    3.1  3  Amidohydro_3  Amidohydrolase family


Domain annotation for each model (and alignments):
>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.4   0.0   1.4e-46   1.3e-42       1     344 []      60     402 ..      60     402 .. 0.91

  Alignments for each domain:
  == domain 1  score: 146.4 bits;  conditional E-value: 1.4e-46
                                    EEEE-EEEEEEECETTECSSS..GHHHHH..........STTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHHHHHHHH CS
                   Amidohydro_1   1 ivlPGlIDaHvHleqsllrga..tledwl..........vppetaaealesgiktalksGtttvadmgattstgiealle 68 
                                    +vlPG+ D+H+H+ +  +rg   +  d++          +++e ++  +  g  +alksG+  vad+++     ++++++
  gi|119718977|ref|YP_919472.1|  60 VVLPGFYDLHTHIAMAGFRGLaaDAGDVIyrvfwplerlLSGESVYRFALLGGLEALKSGVVLVADHYF----FMRDVAR 135
                                    69**************999999977777777778888999*****************************....9****** PP

                                    HHHTSSSEEEEEEESSEGGS.GCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHHHHHHHHHHHHTTE CS
                   Amidohydro_1  69 aaeelplglrilggkvsldr.gsaetskasreklkagaaetikgkadgvvkvalapheapafsdeelkealkeakkrdlp 147
                                    a+ el  glr l+g + +dr g +  ++++re+l+      ++ ++++++++ laph++ ++s++ l   +++ ++++l 
  gi|119718977|ref|YP_919472.1| 136 ALVEL--GLRGLLGHTYMDRdGPFTGERELREALDFV----ERWRGHELITPVLAPHAPDTVSRDNLLYFAELSREKNLF 209
                                    ****8..**************6666666666666322....24468899******************************* PP

                                    EEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEEHHHHHHHHHHHHHHCEEHHHHHHHHSEH CS
                   Amidohydro_1 148 vaiHaletkgevedaeaafgetiehgthlevaeslglldeiklilahgvhltpteaellkerlkeagvahcpfsnsilrs 227
                                    v++H++ t  e + ++++ g      t++++a  lgll+  + i+ah  +++ +e +ll++   ++ +++cp++   +++
  gi|119718977|ref|YP_919472.1| 210 VHMHLAQTLREFKTVKEETG-----YTPVRYALRLGLLGG-RSIVAHANYVDENEKALLAHS--GSVIVQCPSTYFMSGT 281
                                    *****99999999*******.....89*************.*****************9999..8888877777777666 PP

                                    HHHHHHHHHHHTSCEEEEEECTTSSCCGGHHHHHHHHHHHHHHCCTTTTHCHCHHHHHHHHHTHHHHHHTT-TTTSSSS- CS
                   Amidohydro_1 228 grealrkaldeGvkvglgtDgaasgnslnlleelrlalklqrgllyedeegglslkealrmaTingAkalglddkvGsie 307
                                       ++ + ++ G +v++gtD    +++++++ee+rl++  qr++l   + g ++++++l+maT   A+ +g+  + G + 
  gi|119718977|ref|YP_919472.1| 282 PF-HAYDYWQLGGNVAIGTDAPCYNDNVDFFEEMRLLVYGQRMKLE--KSGVWRAYDVLEMATRLSARLVGV--RGGFVG 356
                                    65.88899999*********99****************88886666..6999********************..****** PP

                                    TTSB--EEEECC.........CTCGGGTTTCTSEEEEEEEETTEEE CS
                   Amidohydro_1 308 vGkdADlvvvdl.........dilaafvglkkdgnvkkvivkGklv 344
                                    +G  ADlv+v+l         d+ +++v+ +++g v++viv+G++v
  gi|119718977|ref|YP_919472.1| 357 KGALADLVLVNLssvrlrpflDPFSNIVYAASSGDVDTVIVNGRVV 402
                                    ************98877666666********************998 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.5   2.3e-09     2e-05       1      26 [.      52      77 ..      52      87 .. 0.83
   2 ?    2.2   0.0     0.011        97     154     231 ..     158     239 ..     129     268 .. 0.70
   3 !   21.0   0.0   2.2e-08    0.0002     366     472 ..     291     402 ..     285     403 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 2.3e-09
                   Amidohydro_3  1 eviDakGrlvlPGFvDsHtHlagggv 26
                                   eviD +G++vlPGF D HtH+a +g 
  gi|119718977|ref|YP_919472.1| 52 EVIDGRGKVVLPGFYDLHTHIAMAGF 77
                                   79******************998883 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.011
                   Amidohydro_3 154 areaeaaavaaalaalasy.Gitsv.eagggnvsslddleplfeltaeeklplrviikelldaaerlglpls..pgseel 229
                                    ++e e++ +  ++++ +++  it v  ++++ + s+d l  ++el++e++l ++++ ++ l  ++ + + ++  p +++l
  gi|119718977|ref|YP_919472.1| 158 TGERELREALDFVERWRGHeLITPVlAPHAPDTVSRDNLLYFAELSREKNLFVHMHLAQTLREFKTVKEETGytPVRYAL 237
                                    666666666666666666634555588889999999********************888888888887777755555555 PP

                   Amidohydro_3 230 ti 231
                                    ++
  gi|119718977|ref|YP_919472.1| 238 RL 239
                                    44 PP

  == domain 3  score: 21.0 bits;  conditional E-value: 2.2e-08
                   Amidohydro_3 366 agvkvalgsD..apvgpfdpwprigaavmrktrrggevlrpdeelsleealalyTrgpAkalgledrkGtLevGadADlv 443
                                     g +va g+D  +  + +d + +++ +v ++ ++       +     +++l + Tr +A+++g +   G +++Ga ADlv
  gi|119718977|ref|YP_919472.1| 291 LGGNVAIGTDapCYNDNVDFFEEMRLLVYGQRMKL----EKSGVWRAYDVLEMATRLSARLVGVRG--GFVGKGALADLV 364
                                    57789999995444477888888888888888755....59999999*******************..************ PP

                   Amidohydro_3 444 vld.........adpldvdppelaear....vrltvvdGrvv 472
                                    + +               + +++++a     v  ++v+Grvv
  gi|119718977|ref|YP_919472.1| 365 LVNlssvrlrpfL----DPFSNIVYAAssgdVDTVIVNGRVV 402
                                    ***6666532222....22233444437888*********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (448 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 3205.40
//
Query:       gi|119718978|ref|YP_919473.1|  [L=239]
Description: purine phosphorylases family protein 1 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.2e-42  144.9   0.5    2.6e-42  144.7   0.5    1.0  1  PNP_UDP_1  Phosphorylase superfamily


Domain annotation for each model (and alignments):
>> PNP_UDP_1  Phosphorylase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.7   0.5   1.5e-46   2.6e-42       2     228 ..      17     233 ..      16     237 .. 0.89

  Alignments for each domain:
  == domain 1  score: 144.7 bits;  conditional E-value: 1.5e-46
                                    EEEEESSHHHHHHHHHHEEEEEEEEEE.TTEEEEEEEETTEEEEEEE--SSHHHHHHHHHHHHHHHC--SEEEEEEEEEE CS
                      PNP_UDP_1   2 iaiivgspgevellaespleetpfgregrgfkfvtGtlkgkpvvivstGiGkpnaavvaeirllkefgvkaiiriGtaGg 81 
                                    ++i  g+p +v++l++  l++ +  +e+rgf ++tGt+kg+pv+++++ iG+p+aa +   +l++ +g+k i+r+Gt+Gg
  gi|119718978|ref|YP_919473.1|  17 RVIASGDPARVKQLSSY-LDNPRLVNENRGFLVYTGTYKGVPVTVATHMIGAPSAA-IVFEELIM-LGAKLIVRFGTCGG 93 
                                    7999*************.**************************************.66666666.35************ PP

                                    SSTTT-TT-EEEEEEEEESSSCCGCCTHHCCTCCCCTTSSEE--HHHHHHHHHCHHTTTTTEEEEEEEEESESS-CHHHH CS
                      PNP_UDP_1  82 lnpdlkvGDvvipddainfdgrsplygpkeegqyfpdsydapadpelrallkeaaealgikvhrGvvatadgfyaeteae 161
                                    + p+++vGD+vi++ a +  g++  ++      +  +++++ +d + +++l+e+a+++g k+  G+v+++d fy+   ++
  gi|119718978|ref|YP_919473.1|  94 FLPEMRVGDFVIATGASYSGGGTMNTY-----SPGECMAAV-PDYDVLSALVESASRHGLKYFLGPVVSSDNFYSGI-EY 166
                                    ***************888555555444.....667777777.***********************************.88 PP

                                    HHHHHHTC-CEEESSHHHHHHHHHHTT--EEEEEEEEETTTBETTCTCH.HCCCHHHHHHHHHHHHH CS
                      PNP_UDP_1 162 lrllrrlgadaveMEtaavaqlArelgipfaairvvsdlaaggadaeatheeveefaqeaaknaaal 228
                                    l+++ + g  av+ME+a ++++ r++ ++ +a  vvsd+++++  + at ee  e+ ++a++++  +
  gi|119718978|ref|YP_919473.1| 167 LNRWINRGMIAVDMEAATLFVVGRLRRVKTGASFVVSDVIGEAYKKMATAEELREAVDKASRAVLDA 233
                                    888999999********************************98888887777777777777766544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1624.47
//
Query:       gi|119718979|ref|YP_919474.1|  [L=259]
Description: FkbM family methyltransferase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-10   40.9   0.0    2.9e-10   40.4   0.0    1.1  1  Methyltransf_21  Methyltransferase FkbM domain
    4.1e-09   36.5   0.0    9.2e-09   35.3   0.0    1.5  2  Met_10           Met-10+ like-protein
    4.3e-06   26.4   0.0    2.2e-05   24.0   0.0    2.0  2  MTS              Methyltransferase small domain
     0.0042   16.7   0.1     0.0062   16.1   0.1    1.3  1  DUF2381          Protein of unknown function (DUF2381)
  ------ inclusion threshold ------
       0.03   13.6   0.0      0.043   13.1   0.0    1.1  1  V_cholerae_RfbT  Vibrio cholerae RfbT protein
       0.11   12.5   0.1       0.29   11.1   0.1    1.6  1  YEATS            YEATS family
       0.17   12.6   0.0       0.51   11.1   0.0    1.8  2  Methyltransf_25  Methyltransferase domain
        0.2   11.6   0.0       0.31   11.0   0.0    1.2  1  Methyltransf_18  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Methyltransf_21  Methyltransferase FkbM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   0.0   1.3e-13   2.9e-10       1     170 [.      79     236 ..      79     240 .. 0.78

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 1.3e-13
                Methyltransf_21   1 dvGanigvwdsfanltarlcggggevlaiEPvpnslpkfeklranlltlavgndvglyelivegksggkyfpfavgdtng 80 
                                    d Ga++g  ++ + ++   + +g++ +a+E++p     ++ lr+n   l  +  ++++  +  g s+g   +f   d+ +
  gi|119718979|ref|YP_919474.1|  79 DLGAYVG--FFSVKVH--SESPGARLVAVEANPQ---ACRYLRHN---LRMNGVRSEAYCLAVGESDGVGRLFVAEDPVN 148
                                    78*****..7777665..6899************...*****999...88887777777677788787777777777777 PP

                Methyltransf_21  81 fsts...svlggedaryievpvvtldsfleeikksridllkiDvEGaElevLeGaqkglkrcqpnl...ivvEvhkfkef 154
                                    +s     s+++++ ++  +v  + l+s+ ++ + ++  llk+DvEG E  vL+ +++ l+         +vvEvh     
  gi|119718979|ref|YP_919474.1| 149 SSLLeeySSSFSRVSGVARVAQLSLSSLWRRLDVGHASLLKVDVEGVEERVLRASRDVLTP---GCvdrVVVEVHPPY-- 223
                                    7777444334489999************9999********************954444455...33444679**9976.. PP

                Methyltransf_21 155 etelfdeirqflrecg 170
                                      +++++++++l e+g
  gi|119718979|ref|YP_919474.1| 224 --SSPSRVVELL-ERG 236
                                    ..8888888744.555 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.0   4.1e-12   9.2e-09      98     151 ..      71     124 ..      59     141 .. 0.91
   2 ?   -3.1   0.0       2.4   5.5e+03     151     175 ..     194     218 ..     189     221 .. 0.74

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 4.1e-12
                                    --TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TT CS
                         Met_10  98 veegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvek 151
                                    v  g +Vvd+ A +G+f++ +   s + r++a++ nP++ +yl++n+++N v +
  gi|119718979|ref|YP_919474.1|  71 VPRGSTVVDLGAYVGFFSVKVHSESPGARLVAVEANPQACRYLRHNLRMNGVRS 124
                                    67899*********************************************9975 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.4
                                    TCEEEEES-GGG---TT-EEEEEE- CS
                         Met_10 151 kvvkpileDgrevireqladrvvmn 175
                                     v + +l  +r+v+++  +drvv +
  gi|119718979|ref|YP_919474.1| 194 GVEERVLRASRDVLTPGCVDRVVVE 218
                                    5555567788999999999999975 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0     1e-08   2.2e-05      32      84 ..      74     126 ..      51     139 .. 0.90
   2 ?   -0.4   0.0      0.33   7.3e+02     117     150 ..     195     234 ..     188     252 .. 0.73

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1e-08
                                    CSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEE CS
                            MTS  32 sgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevev 84 
                                      +v+DlG+ +G+ ++++ +esp a++++v+++ +A +  ++nl+ n+++ e+
  gi|119718979|ref|YP_919474.1|  74 GSTVVDLGAYVGFFSVKVHSESPGARLVAVEANPQACRYLRHNLRMNGVRSEA 126
                                    568********************************************998554 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.33
                                    HHHHHHHHHHHHEEEEEEEEEEEETTSCHHHH......HH CS
                            MTS 117 vaeeliaeAkeaLkegGeLliVanrklgyesl......le 150
                                    v e+++++++++L++g   ++V++ + +y+s       le
  gi|119718979|ref|YP_919474.1| 195 VEERVLRASRDVLTPGCVDRVVVEVHPPYSSPsrvvelLE 234
                                    6789999999*****9999999999999987544444444 PP

>> DUF2381  Protein of unknown function (DUF2381)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   2.8e-06    0.0062     223     275 ..     182     232 ..     139     238 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.8e-06
                        DUF2381 223 pteArLteksGealralavqmeeaslaPgesgrvvVeveappgaagerftLel 275
                                    +++A+L ++  e ++++ +++ +++l Pg   rvvVev+ p  ++++   +el
  gi|119718979|ref|YP_919474.1| 182 VGHASLLKVDVEGVEERVLRASRDVLTPGCVDRVVVEVHPPYSSPSR--VVEL 232
                                    789999998888999************************88888887..4444 PP

>> V_cholerae_RfbT  Vibrio cholerae RfbT protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.9e-05     0.043      81     208 ..      75     201 ..      66     207 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.9e-05
                V_cholerae_RfbT  81 ttyidiganvgtfcgiaarhitqgkiiaiepltemensirmnvqlnnplvefhhfgcaigenegenifevyefdnrvssl 160
                                    +t +d+ga vg f           +++a+e   +    +r n+++n        +  a+ge +g   + v e d   ssl
  gi|119718979|ref|YP_919474.1|  75 STVVDLGAYVGFFSVKVHSESPGARLVAVEANPQACRYLRHNLRMNGV--RSEAYCLAVGESDGVGRLFVAE-DPVNSSL 151
                                    799**********99999999999*********************985..5557889*******98877776.5555666 PP

                V_cholerae_RfbT 161 yfkkntdiadkvknsqvlvrklssl..disptnsvvikidaegaeieiln 208
                                      +  +  +     ++v    lssl   +    + ++k+d eg e  +l 
  gi|119718979|ref|YP_919474.1| 152 LEEYSSSFSRVSGVARVAQLSLSSLwrRLDVGHASLLKVDVEGVEERVLR 201
                                    6666666655555677777788887333566778899******9988875 PP

>> YEATS  YEATS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00013      0.29      17      51 ..     209     257 ..     188     258 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00013
                          YEATS  17 sefikkVqFkLhetyanptrvvekp..............PFevtetGwG 51 
                                      ++++V+ + h+ y+ p+rvve                PF+v   Gw+
  gi|119718979|ref|YP_919474.1| 209 PGCVDRVVVEVHPPYSSPSRVVELLergfhvatyydyeaPFQVFVYGWA 257
                                    679******************9954555666666666668888888886 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00023      0.51       1      52 [.      77     128 ..      77     137 .. 0.90
   2 ?   -2.6   0.0       4.1   9.2e+03      83      96 ..     197     210 ..     174     210 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00023
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEE CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvq 52 
                                    v+dlG+  G ++ +++ + + a++++v+ +++++++ r++++ +g++ e ++
  gi|119718979|ref|YP_919474.1|  77 VVDLGAYVGFFSVKVHSESPGARLVAVEANPQACRYLRHNLRMNGVRSEAYC 128
                                    89****************956********************99999877665 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4.1
                                    HHHHHHHHHHEEEE CS
                Methyltransf_25  83 ekalkeiarvLkpg 96 
                                    e++l+  ++vL+pg
  gi|119718979|ref|YP_919474.1| 197 ERVLRASRDVLTPG 210
                                    57788888888887 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00014      0.31      12      68 ..      71     127 ..      67     141 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00014
                Methyltransf_18  12 vekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkie 68 
                                    v++gs+v+D G+  g+ ++++ +e+   + +a++ n+++++  ++n++ +g++++  
  gi|119718979|ref|YP_919474.1|  71 VPRGSTVVDLGAYVGFFSVKVHSESPGARLVAVEANPQACRYLRHNLRMNGVRSEAY 127
                                    899**********************************************99977654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1746.87
//
Query:       gi|119718980|ref|YP_919475.1|  [L=237]
Description: purine phosphorylases family protein 1 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.8e-35  120.9   0.4    5.7e-35  120.7   0.4    1.0  1  PNP_UDP_1  Phosphorylase superfamily


Domain annotation for each model (and alignments):
>> PNP_UDP_1  Phosphorylase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.7   0.4   3.2e-39   5.7e-35       2     223 ..      15     227 ..      14     235 .. 0.88

  Alignments for each domain:
  == domain 1  score: 120.7 bits;  conditional E-value: 3.2e-39
                                    EEEEESSHHHHHHHHHHEEEEEEEEEE.TTEEEEEEEETTEEEEEEE--SSHHHHHHHHHHHHHHHC--SEEEEEEEEEE CS
                      PNP_UDP_1   2 iaiivgspgevellaespleetpfgregrgfkfvtGtlkgkpvvivstGiGkpnaavvaeirllkefgvkaiiriGtaGg 81 
                                    ++++vg+pg+++l+a   le+ +  +e+rg  ++ G + g++v+++++G+G   aa +   +ll+ +  ++++r Gt G+
  gi|119718980|ref|YP_919475.1|  15 RVLVVGDPGRARLVAGM-LEDARLVNENRGLLVYNGFWRGVEVSVATHGMGGAGAA-IVFEELLQLG-GRTLVRLGTTGA 91 
                                    689**************.**************************************.9999999966.7*********** PP

                                    SSTTT-TT-EEEEEEEEESSSCCGCCTHHCCTCCCCTTSSEE--HHHHHHHHHCHHTTTTTEEEEEEEEESESS-CHHHH CS
                      PNP_UDP_1  82 lnpdlkvGDvvipddainfdgrsplygpkeegqyfpdsydapadpelrallkeaaealgikvhrGvvatadgfyaeteae 161
                                    ++ +++vGD+v+p++a ++ g+  l ++     + +++++  +d el  ll  +a+  g kv + +v+++d fyaet + 
  gi|119718980|ref|YP_919475.1|  92 IRGEVEVGDFVVPSSAFHHPGGLFLQYF-----GDICVSPS-PDLELAWLLASEARSAGLKVWTAPVVSSDAFYAETGEV 165
                                    ***********************98664.....33444444.99999999999*************************** PP

                                    HHHHHHTC-CEEESSHHHHHHHHHHTT--EEEEEEEEETTTBETTCTCH.HCCCHHHHHHHH CS
                      PNP_UDP_1 162 lrllrrlgadaveMEtaavaqlArelgipfaairvvsdlaaggadaeatheeveefaqeaak 223
                                    +++++++ga  veME+a ++++ r++g++ aai +v   +++ + +  +  e ee + + a+
  gi|119718980|ref|YP_919475.1| 166 ISRWASFGAVSVEMECATLFAVTRLRGARSAAILLVNGSLVQPGKRMVSESELEERLVKGAE 227
                                    ************************************77666655555555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       258  (0.0143901); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1509.83
//
Query:       gi|119718981|ref|YP_919476.1|  [L=143]
Description: hypothetical protein Tpen_0063 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.063   13.1   0.1       0.68    9.8   0.2    2.0  2  DUF659    Protein of unknown function (DUF 659)


Domain annotation for each model (and alignments):
>> DUF659  Protein of unknown function (DUF 659)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0     0.012   2.2e+02     101     135 ..       7      41 ..       1      60 [. 0.80
   2 ?    9.8   0.2   3.8e-05      0.68      77     116 ..      60      99 ..      47     112 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.012
                         DUF659 101 nasnykkagklleekyptifwtpcaahclnlmled 135
                                      ++++ agk + ek++ +++ +c+a+    +l +
  gi|119718981|ref|YP_919476.1|   7 RLTEFNVAGKEIREKRKLLVYGSCLAYEYPELLRE 41 
                                    55678899****************99877666665 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 3.8e-05
                         DUF659  77 ylaelldkvieevgaenVvqvitdnasnykkagklleeky 116
                                     +a +l +++++v++e+Vv    d ++++++ ++++ee  
  gi|119718981|ref|YP_919476.1|  60 VVALKLASMLARVDVEEVVVLTVDGSPHCVQLHHAVEEAK 99 
                                    6778999****************************98764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1018.80
//
Query:       gi|119718982|ref|YP_919477.1|  [L=173]
Description: hypothetical protein Tpen_0064 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-26   92.9  15.5    2.7e-26   92.6  15.5    1.1  1  ECF-ribofla_trS  ECF-type riboflavin transporter, S component
      3e-09   37.2  15.4    4.1e-09   36.8  15.4    1.2  1  ECF_trnsprt      ECF transporter, substrate-specific componen
     0.0043   16.6  11.3     0.0063   16.0  11.3    1.3  1  5TM-5TMR_LYT     5TMR of 5TMR-LYT


Domain annotation for each model (and alignments):
>> ECF-ribofla_trS  ECF-type riboflavin transporter, S component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.6  15.5   4.4e-30   2.7e-26       7     172 .]      11     160 ..       7     160 .. 0.88

  Alignments for each domain:
  == domain 1  score: 92.6 bits;  conditional E-value: 4.4e-30
                                    HHHHHHHHHHHHHHHHH..---B-S.SS-B--TTHHHHHHHHHHSS--STHHHHHHHHHHHHHHHSS-GGGHHHHHHHHH CS
                ECF-ribofla_trS   7 vvatailaAlvvvltlf..isIplpantegsinlgdavlalaallfGpvvGflvGaiGsalaDllsgYgiwapftliikg 84 
                                    +++ +il+Al++vlt+f  +  p+p  t+g+ ++gd++++++allfGp++G++vG++G ++aD+l+gY+ w++  l+++g
  gi|119718982|ref|YP_919477.1|  11 IALASILSALTAVLTYFpgLALPSP--TGGYTHVGDTIIYVSALLFGPWMGLVVGLVGPVIADFLVGYPRWYVT-LVAHG 87 
                                    78899************66666666..999**************************************999988.***** PP

                                    HHHHHHHHH--S-S-SSH...HHHHHHHHHHHHHHHHHHHHHHHH..........S-HHHHHHHHHHHHH.HHHHHHHHH CS
                ECF-ribofla_trS  85 liGlivGliakklkknkengvfkilalvlfaivmvigyviaegllpildiiiysepaekvalqsipanii.qavvgaiia 163
                                    l+G+i+G+ a k+ k++      ++ +v++++vm + y+++++ +           +   al+s+   i+ q++v++++a
  gi|119718982|ref|YP_919477.1|  88 LQGFIAGYGAGKKFKTQ------LVLMVAAGLVMSFTYFVVNVYV----------KGLGPALVSLARDIFgQTLVSIVLA 151
                                    **********9995555......688*******************..........555555555555553399******* PP

                                    HHHHHHHHH CS
                ECF-ribofla_trS 164 lpLlkalak 172
                                     +Llkal+k
  gi|119718982|ref|YP_919477.1| 152 SLLLKALEK 160
                                    ******986 PP

>> ECF_trnsprt  ECF transporter, substrate-specific component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.8  15.4   6.8e-13   4.1e-09       2     125 ..      10     127 ..       9     163 .. 0.76

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 6.8e-13
                                    HHHHHHHHHHHHHHHHH.H.HEEE.STSE.EESHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHCHT-SSTTHHHHHHHHH CS
                    ECF_trnsprt   2 klvitglliAisivlsl.l.gyiplpnik.itiihipvllggllfGpikGailgiitsvlkailtggtgalssfvpiafl 78 
                                    +++++++l+A+ +vl + +   +p p+   +   + ++++++llfGp++G+++g++++v++ +l+ g +  +    +  +
  gi|119718982|ref|YP_919477.1|  10 FIALASILSALTAVLTYfPgLALPSPTGGyTHVGDTIIYVSALLFGPWMGLVVGLVGPVIADFLV-GYP-RW---YVTLV 84 
                                    689*************98878888887765999999999*************************6.443.34...79999 PP

                                    HHHCHHHHHHHHHHCCCHTTHHHHHHHHHHHHCCCCCHHHHHHHCCC CS
                    ECF_trnsprt  79 sriligliagllykkgkkknlkeivvsfilagvlgtivatllvllii 125
                                    + +l g+iag  y  gkk +  + +v +++ag++++++ +++++++ 
  gi|119718982|ref|YP_919477.1|  85 AHGLQGFIAG--YGAGKKFK--TQLVLMVAAGLVMSFTYFVVNVYVK 127
                                    **********..54455554..448****************987765 PP

>> 5TM-5TMR_LYT  5TMR of 5TMR-LYT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0  11.3   1.1e-06    0.0063      30     124 ..      16     117 ..       4     159 .. 0.61

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.1e-06
                   5TM-5TMR_LYT  30 ilgtytgieie..........gaiantRaigvvvaGllgGplvGliagliaglhRyllgG.ftalacgistilagllaGl 98 
                                    il+ +t +             g + ++    + v++ll+Gp++Gl++gl++ +   +l+G   + + +++  l g++aG+
  gi|119718982|ref|YP_919477.1|  16 ILSALTAVLTYfpglalpsptGGYTHVGDTIIYVSALLFGPWMGLVVGLVGPVIADFLVGyPRWYVTLVAHGLQGFIAGY 95 
                                    3333333333222223345657777888889********************88888888846666667777777777777 PP

                   5TM-5TMR_LYT  99 i.hrklkrrrkkltvlvalligllvei 124
                                      ++k+k   ++l ++va+ + +    
  gi|119718982|ref|YP_919477.1|  96 GaGKKFK---TQLVLMVAAGLVM--SF 117
                                    4033333...3444444444333..33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1331.10
//
Query:       gi|119718983|ref|YP_919478.1|  [L=268]
Description: hypothetical protein Tpen_0065 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-05   25.2   0.1    2.6e-05   24.3   0.1    1.4  1  bPH_2     Bacterial PH domain
  ------ inclusion threshold ------
        1.1    9.0   6.3       0.73    9.6   1.8    2.2  2  TMEM40    Transmembrane protein 40 family


Domain annotation for each model (and alignments):
>> bPH_2  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.1   2.9e-09   2.6e-05       2      55 ..     140     193 ..     139     199 .. 0.93

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 2.9e-09
                          bPH_2   2 rattytitdrrvvvrsGillrktldiplerIqavsleqsllqrrlglgtiviet 55 
                                    r+++y +  r+v +++G+l+r++++i  + + +v ++++ll+r+lg+g++v  t
  gi|119718983|ref|YP_919478.1| 140 RTYRYFVGYRKVGITGGLLRRVERYISGDMVSDVIVVKPLLGRLLGFGHVVPVT 193
                                    7899*********************************************98655 PP

>> TMEM40  Transmembrane protein 40 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   1.8   8.1e-05      0.73      54      90 ..      68     104 ..      65     113 .. 0.89
   2 ?    1.3   0.2      0.03   2.7e+02      54     104 ..     113     167 ..     105     171 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 8.1e-05
                         TMEM40  54 lcfaigallvsyhyyadwfmslgvglltfasletvgi 90 
                                    l + +gall       dw++ + vgll+f+ +  vg+
  gi|119718983|ref|YP_919478.1|  68 LLYVLGALLAILVALLDWIINVRVGLLAFSLVAFVGV 104
                                    56889************************99999997 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.03
                         TMEM40  54 lcfaigallvsyh.yyadwfmslgvgllt...fasletvgiyfglvyrihsvlqg 104
                                    l +++ga l     + a w +++ +   t   f     vgi  gl+ r+   + g
  gi|119718983|ref|YP_919478.1| 113 LSLGLGARLALLSlFSAGWVLAVDLRRRTyryFVGYRKVGITGGLLRRVERYISG 167
                                    566777766554415688999888876663336788999***9999999877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1820.31
//
Query:       gi|119718984|ref|YP_919479.1|  [L=238]
Description: cobalt transport protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-12   47.5  13.6    2.8e-12   46.7  13.6    1.4  1  CbiQ      Cobalt transport protein


Domain annotation for each model (and alignments):
>> CbiQ  Cobalt transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.7  13.6   1.6e-16   2.8e-12       2     214 ..       8     207 ..       7     211 .. 0.80

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 1.6e-16
                                    SCCCCS-HHHHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHTTS---..HHHHHHHCCCHCHHHHHHHHHHE...... CS
                           CbiQ   2 ksvlhrldprvkliwlfllllalvlapnlvtlliiiallllllllvilp..rvlaqalilpllflllgllillfqlitte 79 
                                    k +l+ l+p +kl+ ++  ++ + l+  +  +l+   l   ll+lv ++  ++  +a++l  l+  ++++++l   +   
  gi|119718984|ref|YP_919479.1|   8 KDFLSSLNPLTKLALFLVGIFQVALLGDPKYALLHLLLSSTLLALVRPKvgKA-EFAAALSTLVGYTWVNTALY-IY--- 82 
                                    56789999999999999999999999998888544444444445555555333.33444477888888888888.22... PP

                                    .EECTTEEE...E-TTHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHHHHC.CCSS--HHHHHHHHHHHHHHHHHHHHHH CS
                           CbiQ  80 gefvfagggqisitseGllrglllalRiltllslllllalTTppeeltssl.erlgvPlelalillLayRfiflLleevq 158
                                     +        +s ++    ++l l+ R++++++  + +++TT+p  lt +l e+lgvP + a++ ++++R+ +l+   ++
  gi|119718984|ref|YP_919479.1|  83 -NYS------MSPWDAA-RNALQLTARVAIIILYSMTFVATTTPKALTVALtEQLGVPYVYAFMSFVTLRMAPLIRRDLE 154
                                    .222......3455555.99***************************9988579************************** PP

                                    HHHHHHHHTTTTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS-SS... CS
                           CbiQ 159 rikqAqklRlgdsklgirrslrslgkliaalflralkraervalAmeaRGYtgsee 214
                                    ++   +++ +     +++   r ++ ++++l+  a++r+ ++al+m+aRG+    e
  gi|119718984|ref|YP_919479.1| 155 NMIAYRRIKGYF---SWKAPHRYVASYAFPLLFLAVRRSITLALSMQARGFGKYAE 207
                                    **9999887654...599*9*******************************88444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1834.53
//
Query:       gi|119718985|ref|YP_919480.1|  [L=528]
Description: ABC transporter related [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-47  162.0   0.0    2.2e-23   83.3   0.0    2.2  2  ABC_tran         ABC transporter
    2.7e-25   89.8   4.8    7.1e-07   29.3   0.1    4.2  4  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    2.8e-13   49.8   0.0     0.0031   17.0   0.0    4.1  4  SMC_N            RecF/RecN/SMC N terminal domain
    7.3e-13   48.0   0.4    5.5e-06   26.0   0.0    2.4  2  AAA_29           P-loop containing region of AAA domain
    1.4e-09   38.6   2.6    0.00028   21.3   0.1    2.6  2  AAA_16           AAA ATPase domain
    1.7e-09   38.4   0.1    9.6e-05   23.0   0.0    2.2  2  AAA_23           AAA domain
    7.2e-09   36.0   0.2     0.0017   18.6   0.0    2.8  2  AAA_22           AAA domain
    2.8e-07   30.3   1.0      0.017   14.7   0.1    2.9  2  AAA_25           AAA domain
    3.2e-07   29.7   0.3      0.043   12.9   0.1    3.0  3  T2SSE            Type II/IV secretion system protein
    3.6e-07   30.2   0.0    0.00053   19.8   0.0    3.4  4  AAA_15           AAA ATPase domain
    9.2e-07   28.9   0.8       0.02   14.8   0.1    2.5  2  RsgA_GTPase      RsgA GTPase
    2.5e-06   27.3   0.1     0.0027   17.4   0.0    2.7  2  AAA_30           AAA domain
    4.8e-06   26.6   0.1      0.018   14.9   0.0    2.4  2  NACHT            NACHT domain
    3.3e-05   23.9   1.2      0.092   12.7   0.1    2.5  2  AAA_5            AAA domain (dynein-related subfamily)
    3.4e-05   24.3   1.1      0.031   14.7   0.0    2.8  2  AAA              ATPase family associated with various cellul
    4.7e-05   23.2   0.2      0.032   14.0   0.0    2.7  2  IstB_IS21        IstB-like ATP binding protein
    6.9e-05   22.3   0.7       0.18   11.2   0.0    2.7  2  FtsK_SpoIIIE     FtsK/SpoIIIE family
     0.0001   22.5   0.8       0.13   12.4   0.1    2.6  2  AAA_33           AAA domain
    0.00022   21.3   0.3      0.069   13.0   0.0    2.6  2  ATPase_2         ATPase domain predominantly from Archaea
    0.00022   20.9   1.6        0.1   12.2   0.1    2.4  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
    0.00039   19.9   4.8       0.43    9.9   0.0    3.2  3  Mg_chelatase     Magnesium chelatase, subunit ChlI
    0.00044   19.9   0.0     0.0086   15.7   0.0    2.4  2  AAA_27           AAA domain
    0.00048   20.1   0.4       0.77    9.7   0.0    2.3  2  Rad17            Rad17 P-loop domain
    0.00062   19.5   2.0       0.77    9.5   0.1    2.8  3  AAA_24           AAA domain
    0.00066   20.0   0.9       0.18   12.1   0.1    2.8  3  AAA_19           AAA domain
     0.0011   19.2   2.1       0.33   11.2   0.0    2.8  2  AAA_28           AAA domain
     0.0012   18.9   0.3        1.4    8.9   0.1    3.0  3  AAA_14           AAA domain
     0.0016   17.3   0.3      0.028   13.2   0.0    2.6  3  ABC_ATPase       Predicted ATPase of the ABC class
     0.0019   18.8   0.7        1.3    9.6   0.0    2.6  2  AAA_18           AAA domain
     0.0025   17.9   0.6        2.3    8.3   0.0    2.7  2  MMR_HSR1         50S ribosome-binding GTPase
     0.0025   17.4   0.1        1.8    8.0   0.0    2.2  2  AAA_7            P-loop containing dynein motor region
     0.0033   16.7   0.2        1.2    8.3   0.1    2.3  2  TIP49            TIP49 P-loop domain
     0.0042   16.9   0.3       0.81    9.4   0.1    2.5  2  ATP_bind_1       Conserved hypothetical ATP binding protein
     0.0044   17.4   0.2        2.6    8.5   0.0    2.3  2  RNA_helicase     RNA helicase
      0.005   16.5   1.5        0.3   10.7   0.2    2.3  2  SRP54            SRP54-type protein, GTPase domain
     0.0073   16.2   1.6        1.1    9.1   0.2    3.1  3  NTPase_1         NTPase
     0.0074   16.3   0.2        2.8    8.0   0.0    2.5  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
     0.0086   15.8   0.8       0.84    9.4   0.1    2.4  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
  ------ inclusion threshold ------
       0.01   15.0   0.3        3.8    6.6   0.0    2.1  2  G-alpha          G-protein alpha subunit
      0.011   15.5   0.6        2.3    8.0   0.0    3.0  3  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      0.018   14.5   0.1        3.5    7.0   0.0    2.3  2  PhoH             PhoH-like protein
      0.025   13.3   0.0       0.28    9.8   0.0    2.1  2  AAA_13           AAA domain
      0.025   13.7   0.0       0.73    8.9   0.0    2.1  2  PIF1             PIF1-like helicase
      0.031   13.1   0.5        1.3    7.8   0.0    2.1  2  DLIC             Dynein light intermediate chain (DLIC)
      0.032   13.7   0.0         13    5.1   0.0    3.0  3  TniB             Bacterial TniB protein
      0.046   13.5   0.0        2.3    7.9   0.0    2.2  2  AAA_11           AAA domain
      0.051   13.8   0.4         14    6.0   0.0    2.6  2  Roc              Ras of Complex, Roc, domain of DAPkinase
      0.052   12.9   2.9        5.6    6.2   0.0    3.9  4  ATPase           KaiC
      0.083   12.2   0.4        4.2    6.6   0.0    2.3  2  Zeta_toxin       Zeta toxin
      0.098   11.5   1.3        1.2    8.0   0.1    2.5  2  AAA_PrkA         PrkA AAA domain
       0.13   11.9   0.0       0.67    9.6   0.0    1.9  2  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
       0.13   12.0   0.2         14    5.3   0.0    2.3  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
       0.16   11.2   0.5        6.3    5.9   0.1    2.3  2  NB-ARC           NB-ARC domain
        0.2   11.1   0.1         14    5.0   0.0    2.3  2  SRPRB            Signal recognition particle receptor beta su
       0.21   11.7   0.5         13    5.8   0.1    2.3  2  Dynamin_N        Dynamin family
       0.23   11.9   1.4         14    6.1   0.1    2.8  2  AAA_17           AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.7   0.0   7.5e-24   2.4e-21       1     137 []      21     172 ..      21     172 .. 0.84
   2 !   83.3   0.0   6.7e-26   2.2e-23       1     136 [.     288     424 ..     288     425 .. 0.85

  Alignments for each domain:
  == domain 1  score: 76.7 bits;  conditional E-value: 7.5e-24
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--.....SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSB CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp.....teGeilldgkdlkeqeleslrkeigvlpqepqlfpelt 75 
                                    lk vs++l +ge++ ++G++G+GKStLl +lag   +      +Ge+ + gk+  e+ l  +  ++g l+q+p+ +  + 
  gi|119718985|ref|YP_919480.1|  21 LKGVSFQLDRGECLLLLGPTGSGKSTLLLTLAGAIPQvipasVSGELSVGGKNPVEEGLLGMAGKVGLLFQDPEAQVVMP 100
                                    799******************************9888888999*******9999999***************55554443 PP

                                    .HHHH..........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    .xxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  76 .vren..........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                     v e+            ++ ++++ + l+l+   ++ ++s+  +LS G kq++ala +l+ +p+++llDEpta
  gi|119718985|ref|YP_919480.1| 101 tVFEEvafpmenllePPERIVARVGELLDLVS-LKRYARSEVDTLSTGLKQKLALASVLAMDPEVFLLDEPTA 172
                                    37777899998788633333555555555555.566666667*****************************97 PP

  == domain 2  score: 83.3 bits;  conditional E-value: 6.7e-26
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltvren 79 
                                    l++vsl  ++ge++ ++G+nG+GK+tLlk++agl++p +Ge+++ g          + + ++++ q  ++ f e tv e+
  gi|119718985|ref|YP_919480.1| 288 LRDVSLRARRGEVTLVIGPNGSGKTTLLKAIAGLVRPSSGEVRVAGGRP-------SPRLVAFVAQIpDHQFTERTVVEE 360
                                    689***************************************8884333.......334555555554445555555555 PP

                                    ...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                               e+ +++ ++l+  gl +l d+vv    ++LS+G+k+ v+ +++ + +++++llDEpt
  gi|119718985|ref|YP_919480.1| 361 vasvlggsrreERLRRARRVLEARGLGHLSDRVV----YELSQGEKRLVSFVEMYMLDKPVYLLDEPT 424
                                    5999999887788888******************....*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.1   0.00059      0.19       3      22 ..      35      54 ..      33      80 .. 0.82
   2 !   27.2   0.1   9.6e-09   3.1e-06     235     294 ..     142     198 ..     110     201 .. 0.87
   3 !   29.3   0.1   2.2e-09   7.1e-07       1      35 [.     300     328 ..     300     384 .. 0.75
   4 !   21.3   0.0   6.1e-07    0.0002     231     298 ..     391     455 ..     367     459 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00059
                         AAA_21  3 vliGpNgsGKSnLLdaldll 22
                                   +l Gp gsGKS+LL +l ++
  gi|119718985|ref|YP_919480.1| 35 LLLGPTGSGKSTLLLTLAGA 54
                                   699**************887 PP

  == domain 2  score: 27.2 bits;  conditional E-value: 9.6e-09
                         AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQvil 294
                                    + lS G k+ lal++ l+ ++    ++l+DEp ++++P+  ++++ l+k+l+++g  +il
  gi|119718985|ref|YP_919480.1| 142 DTLSTGLKQKLALASVLAMDP---EVFLLDEPTAHIDPRTAKEIYALVKRLKDEGKTFIL 198
                                    568*******99999999999...9***********************999998888876 PP

  == domain 3  score: 29.3 bits;  conditional E-value: 2.2e-09
                         AAA_21   1 lnvliGpNgsGKSnLLdaldllarldrdvegltde 35 
                                    ++++iGpNgsGK++LL+a+ +l      v+++  e
  gi|119718985|ref|YP_919480.1| 300 VTLVIGPNGSGKTTLLKAIAGL------VRPSSGE 328
                                    699****************888......3333333 PP

  == domain 4  score: 21.3 bits;  conditional E-value: 6.1e-07
                         AAA_21 231 elparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHS 298
                                    ++ ++elS+G krl  ++ ++  +    +++l+DEp  gL+ k   ++++ + el++ g  v+++TH+
  gi|119718985|ref|YP_919480.1| 391 DRVVYELSQGEKRLVSFVEMYMLDK---PVYLLDEPTFGLDFKYSLTVARSIAELASSGKAVVVVTHD 455
                                    56789*********99999999888...**************9999999999888888999******8 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0      0.18        58      28      41 ..      35      48 ..      22      54 .. 0.84
   2 !   11.1   0.0   0.00063       0.2     134     203 ..     141     207 ..      93     219 .. 0.83
   3 !   17.0   0.0   9.7e-06    0.0031      25      45 ..     299     319 ..     290     332 .. 0.88
   4 !   13.3   0.0   0.00013     0.041     136     199 ..     396     456 ..     346     472 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.18
                                   EEEESTTSSHHHHH CS
                                   xxxxxxxxxxxxxx RF
                          SMC_N 28 aivGpNGSGKsnll 41
                                    ++Gp GSGKs ll
  gi|119718985|ref|YP_919480.1| 35 LLLGPTGSGKSTLL 48
                                   689********987 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00063
                                    TTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx RF
                          SMC_N 134 kelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreemle 203
                                     ++LS G k+ +ala ++A+   +p+ ++llDe  a++D +  k++  l+k+ +++   fi + +r e ++
  gi|119718985|ref|YP_919480.1| 141 VDTLSTGLKQKLALASVLAM---DPE-VFLLDEPTAHIDPRTAKEIYALVKRLKDEgKTFILVEHRVEYVA 207
                                    56899999999999988886...555.679*********************99888578899999887765 PP

  == domain 3  score: 17.0 bits;  conditional E-value: 9.7e-06
                                    SEEEEEESTTSSHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  25 sftaivGpNGSGKsnlldAil 45 
                                    ++t ++GpNGSGK+ ll Ai 
  gi|119718985|ref|YP_919480.1| 299 EVTLVIGPNGSGKTTLLKAIA 319
                                    6899***************95 PP

  == domain 4  score: 13.3 bits;  conditional E-value: 0.00013
                                    CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                          SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislre 199
                                    +LS Gek Lv+         +  +p+yllDe    LD+k+   va+ + e  ++   ++v+++++
  gi|119718985|ref|YP_919480.1| 396 ELSQGEKRLVSFV----EMYMLDKPVYLLDEPTFGLDFKYSLTVARSIAELASSgKAVVVVTHDS 456
                                    699*****99853....3355678*************************9887746677788876 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.1   1.6e-06   0.00052      13      39 ..      22      48 ..      19      53 .. 0.86
   2 !   26.0   0.0   1.7e-08   5.5e-06      18      50 ..     294     326 ..     287     331 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.6e-06
                         AAA_29 13 dghtieidlkgatlltGpsGsGKSTll 39
                                   +g ++++d+ +  ll Gp+GsGKSTll
  gi|119718985|ref|YP_919480.1| 22 KGVSFQLDRGECLLLLGPTGSGKSTLL 48
                                   567889997779**************8 PP

  == domain 2  score: 26.0 bits;  conditional E-value: 1.7e-08
                         AAA_29  18 eidlkg.atlltGpsGsGKSTllDAiqalLvpak 50 
                                    + + +g +tl++Gp+GsGK+Tll Ai+ l  p++
  gi|119718985|ref|YP_919480.1| 294 RAR-RGeVTLVIGPNGSGKTTLLKAIAGLVRPSS 326
                                    455.445********************9999986 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.5   2.4e-05    0.0076      23      49 ..      30      56 ..      24     199 .. 0.86
   2 !   21.3   0.1   8.8e-07   0.00028      19      80 ..     293     350 ..     286     422 .. 0.60

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.4e-05
                         AAA_16 23 rpelvllsGesGvGKsslvrellrale 49
                                   r+e++ll G+ G+GKs+l+ +l+ a+ 
  gi|119718985|ref|YP_919480.1| 30 RGECLLLLGPTGSGKSTLLLTLAGAIP 56
                                   669****************99886665 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 8.8e-07
                         AAA_16  19 vrsgrpelvllsGesGvGKsslvrellralekd..ggiflrgkcdqlesaipysalaqalaree 80 
                                    +r+ r+e++l++G+ G+GK++l+++++  ++ +  ++ ++ g+         ++a++ ++   +
  gi|119718985|ref|YP_919480.1| 293 LRARRGEVTLVIGPNGSGKTTLLKAIAGLVRPSsgEVRVAGGRPSPR-----LVAFVAQIPD-H 350
                                    4556669********************76666554344555555444.....2335555533.2 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   0.00029     0.093      11      36 ..      22      48 ..      14      71 .. 0.80
   2 !   23.0   0.0     3e-07   9.6e-05      20      40 ..     299     319 ..     288     322 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00029
                         AAA_23 11 rdqeidFsk.gltlItGpNGaGKTTil 36
                                   +++++++++    l+ Gp+G+GK+T+l
  gi|119718985|ref|YP_919480.1| 22 KGVSFQLDRgECLLLLGPTGSGKSTLL 48
                                   666677766247899***********9 PP

  == domain 2  score: 23.0 bits;  conditional E-value: 3e-07
                         AAA_23  20 gltlItGpNGaGKTTildAik 40 
                                     +tl++GpNG+GKTT+l Ai 
  gi|119718985|ref|YP_919480.1| 299 EVTLVIGPNGSGKTTLLKAIA 319
                                    58*****************96 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   9.8e-05     0.031       5      33 ..      31      59 ..      28     200 .. 0.77
   2 !   18.6   0.0   5.4e-06    0.0017       4      71 ..     297     377 ..     294     451 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 9.8e-05
                         AAA_22  5 agilvvtGesGtGKTtllrrlleqldeea 33
                                     +l++ G++G+GK+tll +l+   ++++
  gi|119718985|ref|YP_919480.1| 31 GECLLLLGPTGSGKSTLLLTLAGAIPQVI 59
                                   679***************99998877665 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 5.4e-06
                         AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee.......erpevv..fvtlpsst.sskdllrellralglelka... 70 
                                    +  +++v+G+ G+GKTtll+ ++     +++  e       ++p++v    ++p    + +++ +e+++ lg ++ +   
  gi|119718985|ref|YP_919480.1| 297 RGEVTLVIGPNGSGKTTLLKAIAGLV--RPSSGEvrvaggrPSPRLVafVAQIPDHQfTERTVVEEVASVLGGSRREerl 374
                                    56789*****************9987..5555557899999777777665566666689999999999999976666333 PP

                         AAA_22  71 ..e 71 
                                      +
  gi|119718985|ref|YP_919480.1| 375 rrA 377
                                    220 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   5.4e-05     0.017      30      57 ..      28      55 ..      21      64 .. 0.90
   2 !   13.1   0.0   0.00016     0.051      29      54 ..     294     319 ..     266     346 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.4e-05
                         AAA_25 30 lpagelallaGapgtGKttlaldlalav 57
                                   l +ge  ll G++g+GK+tl+l la a+
  gi|119718985|ref|YP_919480.1| 28 LDRGECLLLLGPTGSGKSTLLLTLAGAI 55
                                   57999*******************9876 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00016
                         AAA_25  29 llpagelallaGapgtGKttlaldla 54 
                                      ++ge++l++G+ g+GKttl+  +a
  gi|119718985|ref|YP_919480.1| 294 RARRGEVTLVIGPNGSGKTTLLKAIA 319
                                    5679*****************86665 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.1   0.00014     0.043     130     155 ..      32      57 ..      15      62 .. 0.85
   2 ?   -0.4   0.0       1.5   4.7e+02     146     171 ..     182     207 ..     178     225 .. 0.84
   3 !   12.8   0.0   0.00014     0.046     128     156 ..     297     325 ..     266     332 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00014
                          T2SSE 130 glilvsGgTgsGKttllyallkeink 155
                                      +l+ G+TgsGK+tll +l   i++
  gi|119718985|ref|YP_919480.1|  32 ECLLLLGPTGSGKSTLLLTLAGAIPQ 57 
                                    568999***********999888775 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.5
                          T2SSE 146 lyallkeinksderivtvEDpvEiql 171
                                    +yal+k ++++ + +++vE  vE+  
  gi|119718985|ref|YP_919480.1| 182 IYALVKRLKDEGKTFILVEHRVEYVA 207
                                    69999*****99********999976 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 0.00014
                          T2SSE 128 erglilvsGgTgsGKttllyallkeinks 156
                                    +  + lv G+ gsGKttll a+   +  s
  gi|119718985|ref|YP_919480.1| 297 RGEVTLVIGPNGSGKTTLLKAIAGLVRPS 325
                                    445679***************99888765 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0         1   3.3e+02      25      41 ..      33      49 ..      21      52 .. 0.77
   2 ?   -1.6   0.0       5.4   1.7e+03     323     356 ..     161     194 ..     149     200 .. 0.86
   3 !   19.8   0.0   1.7e-06   0.00053      23      46 ..     299     321 ..     288     354 .. 0.85
   4 ?    4.7   0.0     0.065        21     298     369 .]     398     459 ..     393     459 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 1
                         AAA_15 25 ltvliGkNnsGKSsile 41
                                     +l G+ +sGKS++l 
  gi|119718985|ref|YP_919480.1| 33 CLLLLGPTGSGKSTLLL 49
                                   77899*********996 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 5.4
                         AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnk 356
                                    ++ ++l++EP ah+ p   k+++ l k+l +++k
  gi|119718985|ref|YP_919480.1| 161 DPEVFLLDEPTAHIDPRTAKEIYALVKRLKDEGK 194
                                    567899*************999999999988886 PP

  == domain 3  score: 19.8 bits;  conditional E-value: 1.7e-06
                         AAA_15  23 eeltvliGkNnsGKSsilealdlF 46 
                                    e +t++iG+N+sGK+++l+a+  +
  gi|119718985|ref|YP_919480.1| 299 E-VTLVIGPNGSGKTTLLKAIAGL 321
                                    3.9*****************9765 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.065
                         AAA_15 298 GsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSphii 369
                                    ++G +rl++++ + +++ k         ++l++EP   L  +    ++++++ela+++k  v++ TH ++i+
  gi|119718985|ref|YP_919480.1| 398 SQGEKRLVSFV-EMYMLDKP--------VYLLDEPTFGLDFKYSLTVARSIAELASSGK-AVVVVTHDSWIL 459
                                    55666655553.44444444........8899999999999999999***********9.9********995 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   6.2e-05      0.02      88     135 ..      19      68 ..       3      85 .. 0.76
   2 !   12.0   0.0   0.00046      0.15      98     132 ..     297     331 ..     272     337 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 6.2e-05
                                    TTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----.S------- CS
                    RsgA_GTPase  88 egleelkellkd.ktsvlvGqSGvGKStLinallpelelkt.gevseklg 135
                                    + l+ ++ +l+  ++ +l+G++G GKStL+ +l++   + + ++vs +l+
  gi|119718985|ref|YP_919480.1|  19 QVLKGVSFQLDRgECLLLLGPTGSGKSTLLLTLAGAIPQVIpASVSGELS 68 
                                    5566677778777999*****************99875544255666665 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00046
                                    TTSEEEEECSTTSSHHHHHHHHCTT-----S---- CS
                    RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallpelelktgevse 132
                                    ++++++++G+ G GK+tL++a+++  + + gev+ 
  gi|119718985|ref|YP_919480.1| 297 RGEVTLVIGPNGSGKTTLLKAIAGLVRPSSGEVRV 331
                                    4699******************9988888888775 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0     0.014       4.5      20      43 ..      33      56 ..      25      67 .. 0.82
   2 !   17.4   0.0   8.6e-06    0.0027      17      51 ..     297     331 ..     291     380 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.014
                         AAA_30 20 vavltGpAGtGKttalkalreawe 43
                                   + +l Gp G+GK+t+l +l+ a+ 
  gi|119718985|ref|YP_919480.1| 33 CLLLLGPTGSGKSTLLLTLAGAIP 56
                                   67899***********99988765 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 8.6e-06
                         AAA_30  17 gdrvavltGpAGtGKttalkalreaweaaggrvig 51 
                                    +  v+++ Gp G+GKtt+lka++ +++ + g+v +
  gi|119718985|ref|YP_919480.1| 297 RGEVTLVIGPNGSGKTTLLKAIAGLVRPSSGEVRV 331
                                    55699*******************99999656554 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0    0.0029      0.94       3      23 ..      34      54 ..      32      62 .. 0.87
   2 !   14.9   0.0   5.7e-05     0.018       2      23 ..     300     321 ..     299     357 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0029
                                   EEEEC-TTTCHHHHHHHHHHH CS
                          NACHT  3 vilqGeaGsGKTtLlqklala 23
                                   ++l G+ GsGK+tLl  la a
  gi|119718985|ref|YP_919480.1| 34 LLLLGPTGSGKSTLLLTLAGA 54
                                   7899***********999865 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 5.7e-05
                                    CEEEEC-TTTCHHHHHHHHHHH CS
                          NACHT   2 lvilqGeaGsGKTtLlqklala 23 
                                    + ++ G++GsGKTtLl+ +a +
  gi|119718985|ref|YP_919480.1| 300 VTLVIGPNGSGKTTLLKAIAGL 321
                                    6799**************9965 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.1   0.00029     0.092       2      25 ..      34      57 ..      33      63 .. 0.90
   2 !    9.6   0.1    0.0027      0.86       3      23 ..     302     322 ..     300     339 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00029
                                   EEEE--SSSSHHHHHHHGGGGBS- CS
                          AAA_5  2 vlLvGppGtgKselaerlaaalnr 25
                                   +lL+Gp+G+gKs+l   la a+ +
  gi|119718985|ref|YP_919480.1| 34 LLLLGPTGSGKSTLLLTLAGAIPQ 57
                                   79*****************99965 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0027
                                    EEE--SSSSHHHHHHHGGGGB CS
                          AAA_5   3 lLvGppGtgKselaerlaaal 23 
                                    l++Gp G+gK++l + +a ++
  gi|119718985|ref|YP_919480.1| 302 LVIGPNGSGKTTLLKAIAGLV 322
                                    78***************9987 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1     0.018       5.7       1      22 [.      34      55 ..      34      98 .. 0.85
   2 !   14.7   0.0   9.7e-05     0.031       2      21 ..     302     321 ..     301     371 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.018
                                   EEEESSTTSSHHHHHHHHHHHH CS
                            AAA  1 vllyGppGtGKTllakavakel 22
                                   +ll Gp G GK++l   +a  +
  gi|119718985|ref|YP_919480.1| 34 LLLLGPTGSGKSTLLLTLAGAI 55
                                   69************99999875 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 9.7e-05
                                    EEESSTTSSHHHHHHHHHHH CS
                            AAA   2 llyGppGtGKTllakavake 21 
                                    l++Gp G GKT+l ka+a  
  gi|119718985|ref|YP_919480.1| 302 LVIGPNGSGKTTLLKAIAGL 321
                                    89***************986 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0    0.0001     0.032      35      68 ..      18      52 ..      11      57 .. 0.84
   2 ?    6.1   0.0     0.026       8.3      46      68 ..     297     319 ..     288     326 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 0.0001
                      IstB_IS21 35 vkeLatlsf.iekkenivllGpsGvGKshlaialg 68
                                   ++ L + sf +++ e+++llGp+G GKs l  +l+
  gi|119718985|ref|YP_919480.1| 18 LQVLKGVSFqLDRGECLLLLGPTGSGKSTLLLTLA 52
                                   5667788886799***************9988776 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.026
                      IstB_IS21  46 kkenivllGpsGvGKshlaialg 68 
                                    + e  +++Gp G GK+ l  a++
  gi|119718985|ref|YP_919480.1| 297 RGEVTLVIGPNGSGKTTLLKAIA 319
                                    5678899***********99986 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.1    0.0024      0.78      38      59 ..      31      51 ..      21      64 .. 0.80
   2 !   11.2   0.0   0.00055      0.18      13      59 ..     273     318 ..     266     459 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0024
                                   S-.SEEEE--TTSSHHHHHHHH CS
                   FtsK_SpoIIIE 38 mashllvaGatgsGKStalntL 59
                                    +  ll++G tgsGKSt l tL
  gi|119718985|ref|YP_919480.1| 31 GE-CLLLLGPTGSGKSTLLLTL 51
                                   55.689*************998 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00055
                                    T---TTEEEEEEETTS-EEEEEGGGS-.SEEEE--TTSSHHHHHHHH CS
                   FtsK_SpoIIIE  13 tessqlpvalgkeisgnplvldlkkmashllvaGatgsGKStalntL 59 
                                    ++ s+l+v  g+e++ + + l ++  +  +lv+G  gsGK+t l+++
  gi|119718985|ref|YP_919480.1| 273 VDVSSLEVRAGPEVILRDVSLRARRGE-VTLVIGPNGSGKTTLLKAI 318
                                    577899999999998888888888888.89**************985 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.1     0.011       3.4       3      20 ..      35      52 ..      34      61 .. 0.83
   2 !   12.4   0.1   0.00041      0.13       1      20 [.     300     319 ..     300     331 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.011
                         AAA_33  3 llvGlpGsGKstlaerll 20
                                   ll G+ GsGKstl+  l+
  gi|119718985|ref|YP_919480.1| 35 LLLGPTGSGKSTLLLTLA 52
                                   688**********98776 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00041
                         AAA_33   1 lvllvGlpGsGKstlaerll 20 
                                    ++l++G++GsGK+tl++ ++
  gi|119718985|ref|YP_919480.1| 300 VTLVIGPNGSGKTTLLKAIA 319
                                    6899***********99765 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.048        16      20      39 ..      31      50 ..      21      54 .. 0.83
   2 !   13.0   0.0   0.00022     0.069      18      41 ..     296     319 ..     288     330 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.048
                       ATPase_2 20 neiyfiYGpegsGKtaLlke 39
                                    e +++ Gp gsGK++Ll  
  gi|119718985|ref|YP_919480.1| 31 GECLLLLGPTGSGKSTLLLT 50
                                   5677899**********976 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00022
                       ATPase_2  18 epneiyfiYGpegsGKtaLlkeii 41 
                                     + e+ ++ Gp gsGKt+Llk i+
  gi|119718985|ref|YP_919480.1| 296 RRGEVTLVIGPNGSGKTTLLKAIA 319
                                    4578999**************997 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.2    0.0071       2.3       3      21 ..      34      52 ..      32      69 .. 0.84
   2 !   12.2   0.1   0.00032       0.1       2      21 ..     300     319 ..     299     332 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0071
                                   EEEEESTTCCHHHHHHHHH CS
                           cobW  3 tvltGflGsGKTtLlnhll 21
                                   ++l G+ GsGK+tLl +l 
  gi|119718985|ref|YP_919480.1| 34 LLLLGPTGSGKSTLLLTLA 52
                                   6789***********9886 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00032
                                    EEEEEESTTCCHHHHHHHHH CS
                           cobW   2 vtvltGflGsGKTtLlnhll 21 
                                    vt++ G+ GsGKTtLl+++ 
  gi|119718985|ref|YP_919480.1| 300 VTLVIGPNGSGKTTLLKAIA 319
                                    7999************9986 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.6    0.0035       1.1      25      49 ..      34      58 ..      30      67 .. 0.81
   2 ?    1.3   0.1      0.61   1.9e+02      85     132 ..      63     112 ..      59     114 .. 0.83
   3 !    9.9   0.0    0.0013      0.43      24      50 ..     300     326 ..     281     332 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0035
                   Mg_chelatase 25 lllvGppGsGKtmlakrlpsllppl 49
                                   lll+Gp GsGK+ l   l++ +p++
  gi|119718985|ref|YP_919480.1| 34 LLLLGPTGSGKSTLLLTLAGAIPQV 58
                                   89**********9988888877765 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.61
                   Mg_chelatase  85 askaalvGggskpkpGeislahn.GvLfLD.ElpefkrkvlevLRePled 132
                                    +s    vGg + ++ G + +a + G+Lf D E+     +v+e +  P+e+
  gi|119718985|ref|YP_919480.1|  63 VSGELSVGGKNPVEEGLLGMAGKvGLLFQDpEAQVVMPTVFEEVAFPMEN 112
                                    5555669************99654*****977777889999999999986 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.0013
                   Mg_chelatase  24 nlllvGppGsGKtmlakrlpsllppls 50 
                                      l++Gp GsGKt l k++++l+ p s
  gi|119718985|ref|YP_919480.1| 300 VTLVIGPNGSGKTTLLKAIAGLVRPSS 326
                                    46899****************997765 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.81   2.6e+02      20      44 ..      25      49 ..      21      54 .. 0.79
   2 !   15.7   0.0   2.7e-05    0.0086      18      49 ..     290     321 ..     285     323 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.81
                         AAA_27 20 dfsaeeadlhliyGpNEAGKstalr 44
                                   +f+ ++ +  l++Gp  +GKst+l 
  gi|119718985|ref|YP_919480.1| 25 SFQLDRGECLLLLGPTGSGKSTLLL 49
                                   566667777899**********985 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 2.7e-05
                         AAA_27  18 sldfsaeeadlhliyGpNEAGKstalrAisdl 49 
                                     ++++a + +++l++GpN +GK+t+l+Ai  l
  gi|119718985|ref|YP_919480.1| 290 DVSLRARRGEVTLVIGPNGSGKTTLLKAIAGL 321
                                    5678888999******************9876 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.1    0.0064       2.1      42      66 ..      28      52 ..      18      63 .. 0.79
   2 !    9.7   0.0    0.0024      0.77      37      66 ..     290     319 ..     284     329 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0064
                          Rad17 42 srkkriLLisGPsGCgkstvvkvLs 66
                                     + + LL+ GP+G gkst +  L+
  gi|119718985|ref|YP_919480.1| 28 LDRGECLLLLGPTGSGKSTLLLTLA 52
                                   4445689************998887 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0024
                          Rad17  37 advLesrkkriLLisGPsGCgkstvvkvLs 66 
                                      +L  r+ ++ L+ GP G gk+t +k ++
  gi|119718985|ref|YP_919480.1| 290 DVSLRARRGEVTLVIGPNGSGKTTLLKAIA 319
                                    5578888888*****************987 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.1     0.005       1.6       4      27 ..      33      57 ..      30      87 .. 0.77
   2 ?   -1.1   0.0         4   1.3e+03     108     131 ..     179     202 ..     177     207 .. 0.88
   3 !    9.5   0.1    0.0024      0.77       5      22 ..     301     318 ..     297     326 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.005
                         AAA_24  4 kiliyGpsgiGKTtlakel.gpkpl 27
                                    +l+ Gp g+GK+tl+++l g  p 
  gi|119718985|ref|YP_919480.1| 33 CLLLLGPTGSGKSTLLLTLaGAIPQ 57
                                   5799*************99654444 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 4
                         AAA_24 108 aeefrrllkklqelrknvifiahe 131
                                    a+e+  l+k+l++ +k++i++ h 
  gi|119718985|ref|YP_919480.1| 179 AKEIYALVKRLKDEGKTFILVEHR 202
                                    789999**************9996 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.0024
                         AAA_24   5 iliyGpsgiGKTtlakel 22 
                                     l++Gp+g+GKTtl+k +
  gi|119718985|ref|YP_919480.1| 301 TLVIGPNGSGKTTLLKAI 318
                                    689***********9976 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.081        26      10      30 ..      31      51 ..      24      62 .. 0.84
   2 ?   -1.6   0.0       9.7   3.1e+03     116     135 ..     180     199 ..     140     202 .. 0.74
   3 !   12.1   0.1   0.00057      0.18       8      33 ..     296     321 ..     290     342 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.081
                         AAA_19 10 ekvllvtaGpGtGKTrvlkhi 30
                                    ++ll++++ G+GK+++l + 
  gi|119718985|ref|YP_919480.1| 31 GECLLLLGPTGSGKSTLLLTL 51
                                   57899***********99765 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 9.7
                         AAA_19 116 elqyrLlkallgekkklllv 135
                                    + +y+L+k+l++e+k+++lv
  gi|119718985|ref|YP_919480.1| 180 KEIYALVKRLKDEGKTFILV 199
                                    45788999999888778776 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 0.00057
                         AAA_19   8 lkekvllvtaGpGtGKTrvlkhival 33 
                                     + +v lv+++ G+GKT++lk+i  l
  gi|119718985|ref|YP_919480.1| 296 RRGEVTLVIGPNGSGKTTLLKAIAGL 321
                                    577899**************998765 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.3     0.022       7.2       3      27 ..      35      59 ..      33      71 .. 0.82
   2 !   11.2   0.0     0.001      0.33       4      21 ..     303     320 ..     300     386 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.022
                         AAA_28  3 vitGgestGKTtlleaLaargypvv 27
                                    ++G+ ++GK+tll  La    +v+
  gi|119718985|ref|YP_919480.1| 35 LLLGPTGSGKSTLLLTLAGAIPQVI 59
                                   689*************997655555 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.001
                         AAA_28   4 itGgestGKTtlleaLaa 21 
                                    ++G+ ++GKTtll+a+a 
  gi|119718985|ref|YP_919480.1| 303 VIGPNGSGKTTLLKAIAG 320
                                    89*************994 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0     0.027       8.8       3      23 ..      32      52 ..      30      64 .. 0.86
   2 ?   -1.2   0.0       6.2     2e+03      64      91 ..     161     194 ..     129     202 .. 0.65
   3 !    8.9   0.1    0.0044       1.4       3      23 ..     299     319 ..     297     328 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.027
                         AAA_14  3 kilvitGaRrvGKTtllkqli 23
                                   + l++ G+  +GK+tll +l+
  gi|119718985|ref|YP_919480.1| 32 ECLLLLGPTGSGKSTLLLTLA 52
                                   57899************9987 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 6.2
                         AAA_14  64 kktylflDEiqev......pewekalkslvdegk 91 
                                    + ++++lDE          +e++  +k+l degk
  gi|119718985|ref|YP_919480.1| 161 DPEVFLLDEPTAHidprtaKEIYALVKRLKDEGK 194
                                    4566777777666666666777777888877773 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0044
                         AAA_14   3 kilvitGaRrvGKTtllkqli 23 
                                    ++ ++ G+  +GKTtllk ++
  gi|119718985|ref|YP_919480.1| 299 EVTLVIGPNGSGKTTLLKAIA 319
                                    6899*************9886 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.79   2.5e+02     246     268 ..      33      55 ..      19      61 .. 0.79
   2 ?   -1.1   0.0         2   6.4e+02     373     413 ..     182     218 ..     165     233 .. 0.78
   3 !   13.2   0.0   8.6e-05     0.028     243     265 ..     296     319 ..     288     324 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.79
                                    EEEEEE-TTSSHHHHHHHHHHCC CS
                     ABC_ATPase 246 vtlIvGggfhGKsTLLeAlekGv 268
                                      l+ G+   GKsTLL  l+  +
  gi|119718985|ref|YP_919480.1|  33 CLLLLGPTGSGKSTLLLTLAGAI 55 
                                    6678899999******9987665 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2
                                    B--HHHCHHHHHHHH--EEEEEESS-GCCTTT-SEEEEEET CS
                     ABC_ATPase 373 itplvdrvrelykklgvstilvvggsgdyldvAdtvilmee 413
                                    i     +v++l k+ g + ilv   ++    +Ad+v+++e+
  gi|119718985|ref|YP_919480.1| 182 I---YALVKRL-KDEGKTFILVEHRVEYVAGIADKVLYLED 218
                                    3...4445555.6779999999999999999******9987 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 8.6e-05
                                    -SS.EEEEEE-TTSSHHHHHHHHH CS
                     ABC_ATPase 243 pkG.vtlIvGggfhGKsTLLeAle 265
                                    ++G vtl++G++  GK+TLL+A++
  gi|119718985|ref|YP_919480.1| 296 RRGeVTLVIGPNGSGKTTLLKAIA 319
                                    6778******************97 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.2     0.029       9.3       2      18 ..      35      51 ..      34      65 .. 0.88
   2 !    9.6   0.0    0.0039       1.3       2      19 ..     302     319 ..     302     358 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.029
                         AAA_18  2 lltGtpGvGKttlakeL 18
                                   ll G+ G+GK+tl   L
  gi|119718985|ref|YP_919480.1| 35 LLLGPTGSGKSTLLLTL 51
                                   689*********98666 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0039
                         AAA_18   2 lltGtpGvGKttlakeLs 19 
                                    l+ G+ G+GKttl k+++
  gi|119718985|ref|YP_919480.1| 302 LVIGPNGSGKTTLLKAIA 319
                                    589************996 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0072       2.3       3      24 ..      35      56 ..      33      66 .. 0.80
   2 ?    7.3   0.1     0.015       4.7       3      22 ..     302     325 ..     300     455 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0072
                                   EEEESTTSSHHHHHHHHHTSTE CS
                       MMR_HSR1  3 aivGrpNvGKStLinaltgeka 24
                                   +++G + +GKStL+ +l g+  
  gi|119718985|ref|YP_919480.1| 35 LLLGPTGSGKSTLLLTLAGAIP 56
                                   689**************99843 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.015
                                    EEEESTTSSHHHHHHHHHT....S CS
                       MMR_HSR1   3 aivGrpNvGKStLinaltg....e 22 
                                    +++G   +GK+tL++a+ g    +
  gi|119718985|ref|YP_919480.1| 302 LVIGPNGSGKTTLLKAIAGlvrpS 325
                                    689**************9844331 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0057       1.8      30      56 ..      28      54 ..      22      65 .. 0.81
   2 ?    7.0   0.0     0.012       3.8      31      53 ..     296     318 ..     290     326 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0057
                          AAA_7 30 lknkkpvllvGptGtGKtviikdllkk 56
                                   l+++  +ll GptG+GK++++ +l  +
  gi|119718985|ref|YP_919480.1| 28 LDRGECLLLLGPTGSGKSTLLLTLAGA 54
                                   5677889************98776655 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.012
                          AAA_7  31 knkkpvllvGptGtGKtviikdl 53 
                                    +++  +l++Gp G+GKt+++k +
  gi|119718985|ref|YP_919480.1| 296 RRGEVTLVIGPNGSGKTTLLKAI 318
                                    567779************99875 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.1    0.0037       1.2      50      79 ..      31      60 ..      23      66 .. 0.89
   2 ?    5.9   0.0     0.019       6.2      31      71 ..     279     319 ..     260     331 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0037
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49 50 GravLlaGpsgtGktalaiaiskelgedvp 79
                                   G ++Ll Gp+g+Gk+ l ++++ ++ + +p
  gi|119718985|ref|YP_919480.1| 31 GECLLLLGPTGSGKSTLLLTLAGAIPQVIP 60
                                   89******************9999988777 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.019
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49  31 kareaagvivelikekklaGravLlaGpsgtGktalaiais 71 
                                    + r    vi++ +  +   G + L+ Gp+g+Gkt l  ai+
  gi|119718985|ref|YP_919480.1| 279 EVRAGPEVILRDVSLRARRGEVTLVIGPNGSGKTTLLKAIA 319
                                    566667777777777777899**************988887 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.053        17       2      18 ..      37      53 ..      36      62 .. 0.82
   2 !    9.4   0.1    0.0025      0.81       1      19 [.     303     321 ..     303     331 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.053
                     ATP_bind_1  2 vGpaGsGKttfvgalse 18
                                   +Gp GsGK+t+  +l+ 
  gi|119718985|ref|YP_919480.1| 37 LGPTGSGKSTLLLTLAG 53
                                   7*********9877765 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0025
                     ATP_bind_1   1 vvGpaGsGKttfvgalsei 19 
                                    v+Gp GsGKtt+ +a++ +
  gi|119718985|ref|YP_919480.1| 303 VIGPNGSGKTTLLKAIAGL 321
                                    89***********998765 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0082       2.6       2      26 ..      35      59 ..      34      92 .. 0.82
   2 ?    6.7   0.0     0.028       9.1       2      19 ..     302     319 ..     301     335 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0082
                   RNA_helicase  2 wlyGpsgeGKStlakeLakallkkl 26
                                   +l Gp+g GKStl  +La a+ + +
  gi|119718985|ref|YP_919480.1| 35 LLLGPTGSGKSTLLLTLAGAIPQVI 59
                                   689***********99999887766 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.028
                   RNA_helicase   2 wlyGpsgeGKStlakeLa 19 
                                    ++ Gp+g GK+tl k +a
  gi|119718985|ref|YP_919480.1| 302 LVIGPNGSGKTTLLKAIA 319
                                    578***********9976 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1     0.067        22       4      23 ..      34      53 ..      32      58 .. 0.86
   2 !   10.7   0.2   0.00093       0.3       3      27 ..     300     324 ..     298     334 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.067
                                   EEEEESTTSSHHHHHHHHHH CS
                          SRP54  4 illvGlqGaGKTttlaKLaa 23
                                   +ll+G++G+GK t l  La 
  gi|119718985|ref|YP_919480.1| 34 LLLLGPTGSGKSTLLLTLAG 53
                                   79***********9988885 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00093
                                    EEEEEESTTSSHHHHHHHHHHHHHH CS
                          SRP54   3 villvGlqGaGKTttlaKLaallkk 27 
                                    v+l++G++G+GKTt l  +a l++ 
  gi|119718985|ref|YP_919480.1| 300 VTLVIGPNGSGKTTLLKAIAGLVRP 324
                                    899************9999877665 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1     0.091        29       3      23 ..      35      55 ..      33      65 .. 0.84
   2 !    9.1   0.2    0.0035       1.1       4      30 ..     303     331 ..     300     335 .. 0.77
   3 ?   -1.1   0.0       4.7   1.5e+03     111     135 ..     432     456 ..     390     464 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.091
                                   EEE--TTSSHHHHHHHHHHHH CS
                       NTPase_1  3 fiTGppGvGKtTlvkkvlell 23
                                   ++ Gp G+GK+Tl+  ++ ++
  gi|119718985|ref|YP_919480.1| 35 LLLGPTGSGKSTLLLTLAGAI 55
                                   678**********99887665 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0035
                                    EE--TTSSHHHHHHHHHHHH.....GGGE CS
                       NTPase_1   4 iTGppGvGKtTlvkkvlellkss..gvkv 30 
                                    + Gp G+GKtTl+k ++ l++ s  +v+v
  gi|119718985|ref|YP_919480.1| 303 VIGPNGSGKTTLLKAIAGLVRPSsgEVRV 331
                                    67**************9999755234555 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 4.7
                                    -HHHHHHHHHHHTTTSEEEEE--SS CS
                       NTPase_1 111 skkfkeaveevLksekpvlavihrr 135
                                    s ++++++ e+ +s+k v++v h +
  gi|119718985|ref|YP_919480.1| 432 SLTVARSIAELASSGKAVVVVTHDS 456
                                    5567889999999999999999976 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1     0.043        14      19      41 ..      31      53 ..      16      63 .. 0.79
   2 !    8.0   0.0    0.0088       2.8      19      41 ..     298     320 ..     285     330 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.043
                                   TEEEEEEESTTSSHHHHHHHHHH CS
                           TsaE 19 gdvilLeGdLGaGKTtlvrglak 41
                                   g+++lL G+ G+GK+tl   la 
  gi|119718985|ref|YP_919480.1| 31 GECLLLLGPTGSGKSTLLLTLAG 53
                                   789*************9877765 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0088
                                    TEEEEEEESTTSSHHHHHHHHHH CS
                           TsaE  19 gdvilLeGdLGaGKTtlvrglak 41 
                                    g+v l  G+ G+GKTtl +++a 
  gi|119718985|ref|YP_919480.1| 298 GEVTLVIGPNGSGKTTLLKAIAG 320
                                    6788999************9985 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1     0.088        28       4      22 ..      34      52 ..      32      56 .. 0.86
   2 !    9.4   0.1    0.0026      0.84       4      23 ..     301     320 ..     299     323 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.088
                      PduV-EutP  4 illiGkvgsGKttLtqalk 22
                                   +ll+G++gsGK tL  +l 
  gi|119718985|ref|YP_919480.1| 34 LLLLGPTGSGKSTLLLTLA 52
                                   689***********87776 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0026
                      PduV-EutP   4 illiGkvgsGKttLtqalkg 23 
                                     l+iG+ gsGKttL +a+ g
  gi|119718985|ref|YP_919480.1| 301 TLVIGPNGSGKTTLLKAIAG 320
                                    589*************9987 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.3     0.016       5.2      26      40 ..      34      48 ..      25      54 .. 0.88
   2 ?    6.6   0.0     0.012       3.8      26      48 ..     301     323 ..     286     332 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.016
                                   EEEEESTTSSHHHHH CS
                        G-alpha 26 llllGqseSGKsTil 40
                                   llllG  +SGKsT+l
  gi|119718985|ref|YP_919480.1| 34 LLLLGPTGSGKSTLL 48
                                   8************98 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.012
                                    EEEEESTTSSHHHHHHHHHHHCS CS
                        G-alpha  26 llllGqseSGKsTilkqlkllyk 48 
                                     l++G ++SGK+T+lk +  l +
  gi|119718985|ref|YP_919480.1| 301 TLVIGPNGSGKTTLLKAIAGLVR 323
                                    5899************9986655 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1       0.2        64      35      57 ..      33      55 ..      19      73 .. 0.82
   2 ?    0.3   0.0       1.6   5.1e+02      46      99 ..     151     206 ..     145     221 .. 0.73
   3 ?    8.0   0.0    0.0071       2.3      20      54 ..     285     319 ..     275     336 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.2
                         RuvB_N 35 hvllyGpPGlGkttlakiiakel 57
                                    +ll Gp G Gk+tl   +a  +
  gi|119718985|ref|YP_919480.1| 33 CLLLLGPTGSGKSTLLLTLAGAI 55
                                   579***********988887655 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.6
                         RuvB_N  46 kttlakiiakelgvklkitsgPvle..kagdlaalltnleekdvlfideihrlsra 99 
                                    k +la+++a + +v l    +  ++   a+++ al+++l+++   fi   hr++ +
  gi|119718985|ref|YP_919480.1| 151 KLALASVLAMDPEVFLLDEPTAHIDprTAKEIYALVKRLKDEGKTFILVEHRVEYV 206
                                    66788888888888877666666653257899*********999999999998754 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0071
                         RuvB_N  20 kifieaakkreealdhvllyGpPGlGkttlakiia 54 
                                    +++++    r +  + +l++Gp G Gkttl k ia
  gi|119718985|ref|YP_919480.1| 285 EVILRDVSLRARRGEVTLVIGPNGSGKTTLLKAIA 319
                                    67777777888888999*************99998 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.045        14      18      40 ..      30      52 ..      22      65 .. 0.73
   2 ?    7.0   0.0     0.011       3.5      18      39 ..     297     318 ..     289     329 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.045
                                   H-SEEEEE--TTSSTTHHHHHHH CS
                           PhoH 18 kndivfaiGpaGtGKtylavala 40
                                   + + +  +Gp+G+GK+ l ++la
  gi|119718985|ref|YP_919480.1| 30 RGECLLLLGPTGSGKSTLLLTLA 52
                                   55677899*******97655443 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.011
                                    H-SEEEEE--TTSSTTHHHHHH CS
                           PhoH  18 kndivfaiGpaGtGKtylaval 39 
                                    + +++ +iGp G+GKt l  a+
  gi|119718985|ref|YP_919480.1| 297 RGEVTLVIGPNGSGKTTLLKAI 318
                                    56799***********886554 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00087      0.28      20      53 ..     302     329 ..     295     376 .. 0.74
   2 ?    0.9   0.0      0.43   1.4e+02     496     512 ..     393     409 ..     386     459 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00087
                         AAA_13  20 liYGwNGaGKTtLSrllrslelgetepkfangsi 53 
                                    l+ G NG+GKTtL ++++ l +       ++g++
  gi|119718985|ref|YP_919480.1| 302 LVIGPNGSGKTTLLKAIAGLVR------PSSGEV 329
                                    788***************9943......234455 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.43
                         AAA_13 496 aaetLSeGEktaIaflY 512
                                      ++LS+GEk ++ f+ 
  gi|119718985|ref|YP_919480.1| 393 VVYELSQGEKRLVSFVE 409
                                    5689*********9973 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.22        70      18      47 ..      27      56 ..      18      64 .. 0.83
   2 ?    8.9   0.0    0.0023      0.73      16      52 ..     292     328 ..     283     333 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.22
                                   ..HCTS-EEEEESTTSSCHHHHHHHHHHCH CS
                           PIF1 18 lnekgklfFvtGsgGtgKtflwkallkklr 47
                                   + ++g+ + + G  G+gK+ l+ +l  ++ 
  gi|119718985|ref|YP_919480.1| 27 QLDRGECLLLLGPTGSGKSTLLLTLAGAIP 56
                                   4478999****************9998876 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0023
                                    ....HCTS-EEEEESTTSSCHHHHHHHHHHCHCTCCC CS
                           PIF1  16 avlnekgklfFvtGsgGtgKtflwkallkklrsegki 52 
                                    ++ +++g++  v G  G+gKt l+ka+   +r++   
  gi|119718985|ref|YP_919480.1| 292 SLRARRGEVTLVIGPNGSGKTTLLKAIAGLVRPSSGE 328
                                    6677899**********************99986544 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1     0.081        26      21      48 ..      27      54 ..      16      58 .. 0.86
   2 ?    7.8   0.0     0.004       1.3      13      52 ..     290     325 ..     285     329 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.081
                           DLIC 21 klPsgksvlvlGedgsGkttliaklqGv 48
                                   +l  g  +l+lG  gsGk+tl+  l G+
  gi|119718985|ref|YP_919480.1| 27 QLDRGECLLLLGPTGSGKSTLLLTLAGA 54
                                   67788999**************999886 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.004
                           DLIC  13 evstrsssklPsgksvlvlGedgsGkttliaklqGveeek 52 
                                    +vs r++     g   lv+G +gsGkttl+  + G+  + 
  gi|119718985|ref|YP_919480.1| 290 DVSLRAR----RGEVTLVIGPNGSGKTTLLKAIAGLVRPS 325
                                    5555554....367789**************999987665 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.041        13      33      52 ..      29      48 ..      21      57 .. 0.89
   2 ?   -0.3   0.0       1.9   6.1e+02     107     153 ..     149     193 ..     134     199 .. 0.79
   3 ?    4.3   0.0     0.074        24      33      56 ..     296     319 ..     288     376 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.041
                           TniB 33 krmpnlllvGdsnnGKtmiv 52
                                   +r ++lll+G++  GK++++
  gi|119718985|ref|YP_919480.1| 29 DRGECLLLLGPTGSGKSTLL 48
                                   6789*************986 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.9
                           TniB 107 leqqvlrllrelkvrvLiiDEihnllagsarkqreflnalksLgnel 153
                                    +++ +l+   +++++v ++DE    +    r+ +e+ +++k+L++e 
  gi|119718985|ref|YP_919480.1| 149 KQKLALASVLAMDPEVFLLDEPTAHI--DPRTAKEIYALVKRLKDEG 193
                                    55566677778999999***987766..7888999999999999875 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.074
                           TniB  33 krmpnlllvGdsnnGKtmivekFa 56 
                                     r +  l++G+   GKt++++  a
  gi|119718985|ref|YP_919480.1| 296 RRGEVTLVIGPNGSGKTTLLKAIA 319
                                    5667889************99766 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0      0.18        57      12      41 ..      26      55 ..      19      77 .. 0.81
   2 ?    7.9   0.0    0.0073       2.3      15      40 ..     296     321 ..     288     408 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.18
                         AAA_11 12 salseseitliqGPPGtgKTktivellsql 41
                                   + l + e  l+ GP G+gK++ ++ l  ++
  gi|119718985|ref|YP_919480.1| 26 FQLDRGECLLLLGPTGSGKSTLLLTLAGAI 55
                                   55677788999*********9999988766 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0073
                         AAA_11  15 seseitliqGPPGtgKTktivellsq 40 
                                    ++ e+tl+ GP G+gKT+ + ++   
  gi|119718985|ref|YP_919480.1| 296 RRGEVTLVIGPNGSGKTTLLKAIAGL 321
                                    56679************655444333 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0      0.08        26       2      19 ..      34      51 ..      33      57 .. 0.88
   2 ?    6.0   0.0     0.042        14       3      19 ..     302     318 ..     301     326 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.08
                                   EEEESSTTSSHHHHHHCH CS
                            Roc  2 vvlvGdsgvGKtsllkrf 19
                                   ++l+G +g+GK++ll  +
  gi|119718985|ref|YP_919480.1| 34 LLLLGPTGSGKSTLLLTL 51
                                   689***********9876 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.042
                                    EEESSTTSSHHHHHHCH CS
                            Roc   3 vlvGdsgvGKtsllkrf 19 
                                    +++G +g+GKt+llk +
  gi|119718985|ref|YP_919480.1| 302 LVIGPNGSGKTTLLKAI 318
                                    689***********976 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.39   1.2e+02      18      35 ..      30      47 ..      23      52 .. 0.87
   2 ?   -0.7   0.0       2.3   7.5e+02     142     166 ..     180     204 ..     171     225 .. 0.82
   3 ?    6.2   0.0     0.017       5.6      17      35 ..     296     314 ..     292     319 .. 0.90
   4 ?    1.0   0.0       0.7   2.2e+02     175     221 ..     357     399 ..     341     405 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.39
                         ATPase 18 egrvvlitGepGtGKtif 35
                                   +g+  l+ G +G+GK+++
  gi|119718985|ref|YP_919480.1| 30 RGECLLLLGPTGSGKSTL 47
                                   78999***********98 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.3
                         ATPase 142 eilrqlvrvlkklgvTailvsekss 166
                                    +++  lv++lk+ g T ilv+ + +
  gi|119718985|ref|YP_919480.1| 180 KEIYALVKRLKDEGKTFILVEHRVE 204
                                    5788999***********9998655 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.017
                         ATPase  17 pegrvvlitGepGtGKtif 35 
                                     +g+v+l+ G  G+GKt++
  gi|119718985|ref|YP_919480.1| 296 RRGEVTLVIGPNGSGKTTL 314
                                    5899*************97 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.7
                         ATPase 175 gveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIte 221
                                     vee     + vL   + ee+l+R  +++  Rg +h ++++++e ++
  gi|119718985|ref|YP_919480.1| 357 VVEE----VASVLGGSRREERLRRARRVLEARGLGHLSDRVVYELSQ 399
                                    4555....233677888999*********************999876 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.1      0.12        39      18      38 ..      33      53 ..      21      59 .. 0.82
   2 ?    6.6   0.0     0.013       4.2      14      49 ..     296     331 ..     285     335 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.12
                     Zeta_toxin 18 lillgGqpGAGKselaellkd 38
                                    +ll G +G+GKs+l+  l+ 
  gi|119718985|ref|YP_919480.1| 33 CLLLLGPTGSGKSTLLLTLAG 53
                                   678999********9987765 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.013
                     Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvvrl 49 
                                    +r  + l+ G  G+GK++l+++++  +++ ++ vr+
  gi|119718985|ref|YP_919480.1| 296 RRGEVTLVIGPNGSGKTTLLKAIAGLVRPSSGEVRV 331
                                    566788999*************99877766666665 PP

>> AAA_PrkA  PrkA AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.1    0.0037       1.2      88     112 ..      31      55 ..      19      82 .. 0.82
   2 ?    1.6   0.0      0.31     1e+02      89     110 ..     299     320 ..     291     332 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0037
                       AAA_PrkA  88 kqilyllGPvggGksslverlkkll 112
                                     + l+llGP g+Gks+l  +l  ++
  gi|119718985|ref|YP_919480.1|  31 GECLLLLGPTGSGKSTLLLTLAGAI 55 
                                    5689************988776555 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.31
                       AAA_PrkA  89 qilyllGPvggGksslverlkk 110
                                    ++ +++GP g+Gk++l +++  
  gi|119718985|ref|YP_919480.1| 299 EVTLVIGPNGSGKTTLLKAIAG 320
                                    68899***********998865 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       2.7   8.7e+02       9      35 ..      26      52 ..      17      64 .. 0.82
   2 ?    9.6   0.0    0.0021      0.67      11      74 ..     295     358 ..     287     373 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 2.7
                                   S-EBTT-EEEEEESTTSSHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    ATP-synt_ab  9 fpivqGqrtlipgafgvGktvisqsls 35
                                   f + +G+ +l++g  g Gk++++ +l+
  gi|119718985|ref|YP_919480.1| 26 FQLDRGECLLLLGPTGSGKSTLLLTLA 52
                                   5567899999***********998776 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0021
                                    EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSSEEEEEEESEEHHHHHHHHHHCHHSSGGGGEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    ATP-synt_ab  11 ivqGqrtlipgafgvGktvisqslskqsnsddaiiyvgiGergnevaevleefpegtimkrtvl 74 
                                      +G+ tl++g +g Gkt+++++++   + ++  + v+ G  +  +  ++ ++p+++  +rtv+
  gi|119718985|ref|YP_919480.1| 295 ARRGEVTLVIGPNGSGKTTLLKAIAGLVRPSSGEVRVAGGRPSPRLVAFVAQIPDHQFTERTVV 358
                                    5699*****************9999887666688999999999999999999999999999987 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1     0.076        24       4      21 ..      37      54 ..      34      66 .. 0.81
   2 ?    5.3   0.0     0.044        14       2      21 ..     302     321 ..     301     362 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.076
                Viral_helicase1  4 hGvpGcGKStlirkllrt 21
                                    G  G+GKStl+ +l+  
  gi|119718985|ref|YP_919480.1| 37 LGPTGSGKSTLLLTLAGA 54
                                   5778********999865 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.044
                Viral_helicase1   2 vvhGvpGcGKStlirkllrt 21 
                                    +v G  G+GK+tl++ ++  
  gi|119718985|ref|YP_919480.1| 302 LVIGPNGSGKTTLLKAIAGL 321
                                    566777*********99977 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1      0.14        46      22      37 ..      33      48 ..      20      59 .. 0.83
   2 ?    5.9   0.1      0.02       6.3      23      40 ..     301     318 ..     293     323 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.14
                                   EEEEEESTTSSHHHHH CS
                         NB-ARC 22 vvalvGmgGvGKttla 37
                                    + l G  G+GK+tl+
  gi|119718985|ref|YP_919480.1| 33 CLLLLGPTGSGKSTLL 48
                                   57799*********97 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.02
                                    EEEEESTTSSHHHHHHHH CS
                         NB-ARC  23 valvGmgGvGKttlakqi 40 
                                      + G  G+GKttl+k i
  gi|119718985|ref|YP_919480.1| 301 TLVIGPNGSGKTTLLKAI 318
                                    4688***********988 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0      0.12        37       5      25 ..      33      53 ..      29      76 .. 0.79
   2 ?    5.0   0.0     0.045        14       6      22 ..     301     317 ..     296     325 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.12
                                   EEEEE-STTSSHHHHHHHHHH CS
                          SRPRB  5 avllvGlsdsGKTslftrLtt 25
                                    +ll+G++ sGK +l+  L  
  gi|119718985|ref|YP_919480.1| 33 CLLLLGPTGSGKSTLLLTLAG 53
                                   689*********999988865 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.045
                                    EEEE-STTSSHHHHHHH CS
                          SRPRB   6 vllvGlsdsGKTslftr 22 
                                     l++G+  sGKT+l++ 
  gi|119718985|ref|YP_919480.1| 301 TLVIGPNGSGKTTLLKA 317
                                    689***********976 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0      0.16        50       2      21 ..      35      54 ..      34      62 .. 0.87
   2 ?    5.8   0.1     0.041        13       2      20 ..     302     320 ..     301     329 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.16
                                   EEEEBTTTTHHHHHHHHHTS CS
                      Dynamin_N  2 avvGsqSsGKSSvlnaLlge 21
                                   +++G + sGKS++l  L g+
  gi|119718985|ref|YP_919480.1| 35 LLLGPTGSGKSTLLLTLAGA 54
                                   5789**********998885 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.041
                                    EEEEBTTTTHHHHHHHHHT CS
                      Dynamin_N   2 avvGsqSsGKSSvlnaLlg 20 
                                    +v+G   sGK+++l a+ g
  gi|119718985|ref|YP_919480.1| 302 LVIGPNGSGKTTLLKAIAG 320
                                    59***************98 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1      0.24        77       1      16 [.      37      52 ..      37      60 .. 0.86
   2 ?    6.1   0.1     0.045        14       1      16 [.     304     319 ..     304     323 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.24
                                   EE-TTSSHHHHHHHHH CS
                         AAA_17  1 lGgPGsGKgtqceklv 16
                                   lG+ GsGK+t++ +l+
  gi|119718985|ref|YP_919480.1| 37 LGPTGSGKSTLLLTLA 52
                                   699*******997665 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.045
                                    EE-TTSSHHHHHHHHH CS
                         AAA_17   1 lGgPGsGKgtqceklv 16 
                                    +G+ GsGK+t+++ ++
  gi|119718985|ref|YP_919480.1| 304 IGPNGSGKTTLLKAIA 319
                                    599*********9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (528 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                       119  (0.00663729); expected 17.9 (0.001)
Passed Fwd filter:                        56  (0.00312343); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              56  [number of targets reported over threshold]
# CPU time: 0.74u 0.29s 00:00:01.03 Elapsed: 00:00:00.47
# Mc/sec: 3355.11
//
Query:       gi|119718986|ref|YP_919481.1|  [L=200]
Description: ABC transporter, permease protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.2e-33  115.0  15.2    2.2e-33  115.0  15.2    1.9  2  ABC_cobalt  ABC-type cobalt transport system, permease compon


Domain annotation for each model (and alignments):
>> ABC_cobalt  ABC-type cobalt transport system, permease component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.0  15.2   1.2e-37   2.2e-33       2     119 ..      10     127 ..       9     129 .. 0.93
   2 ?    0.9   0.2     0.027   4.8e+02      26      57 ..     139     169 ..     125     177 .. 0.63

  Alignments for each domain:
  == domain 1  score: 115.0 bits;  conditional E-value: 1.2e-37
                                    HHHHHHHHHHHHHHHHHHHH.HHHHHHHHHH-GGG.GGGGGGGGGHHHHHHHHHH-STTHHHHHHHHHHHHHHHTT-TTT CS
                     ABC_cobalt   2 diilvavigvvfGviflawg.lvynalsaaltPlgaealllGlWllagvlaaliirkpgaallaellaAlvemllgsqwG 80 
                                    +++l+av+++++G++fl+w+ +v+ a + +++ l ++ +++G+W++ +++ a+i+rkp +all+e+laA++e+++gsq+ 
  gi|119718986|ref|YP_919481.1|  10 ELVLTAVLSAIIGAVFLVWSnVVWGASK-LVLGLTLTPIIYGMWFIGATVPAYIVRKPLVALLGEFLAAVLELFYGSQFA 88 
                                    79******************66676666.6666689******************************************** PP

                                    THHHHHHHHHHHHHHHHHHHTTT---SHHHHHHHHHHHH CS
                     ABC_cobalt  81 astllsglvqGlgaElafaltrYrrftllvlllsgalaa 119
                                     ++ll+g++qGl++El+f++trY+r+++++++l+ga+ a
  gi|119718986|ref|YP_919481.1|  89 STVLLYGFMQGLMSELVFFATRYKRWDWATMALAGAAPA 127
                                    ***********************************9865 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.027
                                    HHHHHH-GGG.GGGGGGGGGHHHHHHHHHH-S CS
                     ABC_cobalt  26 alsaaltPlgaealllGlWllagvlaaliirk 57 
                                     +++ l P g + ++ +l++++g l a ++ k
  gi|119718986|ref|YP_919481.1| 139 GITNPLSP-GQRVVFWSLYFVSGALIAGVLVK 169
                                    44445666.45778888888777655444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       688  (0.0383736); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 1259.53
//
Query:       gi|119718987|ref|YP_919482.1|  [L=320]
Description: phosphomethylpyrimidine kinase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.9e-44  150.6   0.1      4e-44  150.1   0.1    1.2  1  ThiP_synth      Thiamine-phosphate synthase
    2.4e-05   24.3   0.2    5.9e-05   23.0   0.2    1.6  1  HTH_3           Helix-turn-helix
    0.00037   20.4   0.1     0.0008   19.3   0.1    1.5  1  HTH_37          Helix-turn-helix domain
     0.0004   20.3   0.1    0.00081   19.3   0.1    1.4  1  HTH_Crp_2       Crp-like helix-turn-helix domain
     0.0015   18.3   0.2     0.0054   16.5   0.0    2.0  2  LacI            Bacterial regulatory proteins, lacI family
     0.0027   17.5   0.1     0.0072   16.2   0.1    1.6  1  MarR_2          MarR family
     0.0075   16.0   0.1      0.082   12.7   0.1    2.3  2  HTH_23          Homeodomain-like domain
  ------ inclusion threshold ------
      0.042   14.2   0.1      0.085   13.2   0.1    1.5  1  HTH_31          Helix-turn-helix domain
       0.07   13.2   0.1       0.19   11.8   0.1    1.7  1  Cro             Cro
      0.084   12.5   0.1       0.18   11.4   0.1    1.5  1  HTH_24          Winged helix-turn-helix DNA-binding
      0.095   12.6   0.1       0.26   11.2   0.1    1.8  1  HTH_5           Bacterial regulatory protein, arsR family
        0.1   12.5   0.0       0.21   11.4   0.0    1.6  1  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox
       0.14   11.6   0.1       0.27   10.7   0.1    1.5  1  HTH_Tnp_ISL3    Helix-turn-helix domain of transposase family
       0.18   11.7   0.1        0.4   10.7   0.1    1.5  1  MarR            MarR family
       0.63    9.8   2.2       0.73    9.6   0.2    2.0  2  HTH_38          Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> ThiP_synth  Thiamine-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.1   0.1   3.3e-47     4e-44       1     164 [.     139     297 ..     139     298 .. 0.96

  Alignments for each domain:
  == domain 1  score: 150.1 bits;  conditional E-value: 3.3e-47
                                    HHHHHHHHHHCC--.GCC--TT-B-EEEE-ST--SGGGEEEETT-EEE-TSSEEE-S-EEETS-CHHHHHHHHHHCC-TT CS
                     ThiP_synth   1 eleralelleeeeefakliPevgsNiayalpdAksieDvaavpGRIvrvkgrvkvvgepefgasshvarvllaamkfdpe 80 
                                    ++eral  l ++e f  liPev +Nia+a+p+Aksi DvaavpGRI r k++ +  ++pefgas+h++ +ll++   + +
  gi|119718987|ref|YP_919482.1| 139 DMERALIVLWSSEYFGLLIPEVLTNIAMAIPGAKSIYDVAAVPGRISRSKSGEILYRQPEFGASRHLSGILLSI---NGK 215
                                    69***********************************************************************9...899 PP

                                    --EEEEEE--HHHHHHHCCTTSEEEE--CCCS-CCCT-HHHHHHHHHHHCCS-ECEEEE--BCTB--EEEEEESSHHHHH CS
                     ThiP_synth  81 vraainirydekilealeelglkvvefdreeepeevgstmewgvaeaieelevpdviydeGgvGkEpmiyvlgkdaeevv 160
                                    +ra+ini+yde ++eal ++gl++ ef+ e+ p +  +  + ++ae +ee    ++++d Gg ++E ++y++g++a+ev+
  gi|119718987|ref|YP_919482.1| 216 YRAVINIKYDEIVEEALVSMGLRFKEFSSEDYPSA--NPAASAAAELLEECPDCKALVDVGGENVESVTYIFGNRAVEVA 293
                                    ***********************************..8999999999999844689************************ PP

                                    HHHH CS
                     ThiP_synth 161 ekvl 164
                                    + ++
  gi|119718987|ref|YP_919482.1| 294 NIAV 297
                                    9876 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.2   4.9e-08   5.9e-05       3      33 ..      22      51 ..      20      53 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 4.9e-08
                                   HHHHHTTHHHHHHHHHHTSSHHHHHHHHTTS CS
                          HTH_3  3 elRkqlglsqeeLAeklGvsrstisriEnGe 33
                                   elRk l++sq+++A+++Gv+++++s+i + +
  gi|119718987|ref|YP_919482.1| 22 ELRK-LNMSQTDIARLTGVTQAAVSKILREK 51
                                   5566.**********************9865 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1   6.7e-07    0.0008      25      56 ..      21      52 ..      14      55 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 6.7e-07
                                   HHHHHCT--HHHHHHHHT--HHHHHHHHTT-- CS
                         HTH_37 25 eliekrelsqseaaqllgiaqPkvsrllrgkl 56
                                     ++k++ sq+++a+l+g++q+ vs++lr+k+
  gi|119718987|ref|YP_919482.1| 21 SELRKLNMSQTDIARLTGVTQAAVSKILREKQ 52
                                   668899***********************987 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1   6.8e-07   0.00081      18      44 ..      24      50 ..      14      58 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 6.8e-07
                                   EEEEHHHHHHHHHTTSSHHHHHHHHHH CS
                      HTH_Crp_2 18 ielpltqeelAsmlGltretvsrilse 44
                                    +l+++q+++A++ G+t+  vs+il+e
  gi|119718987|ref|YP_919482.1| 24 RKLNMSQTDIARLTGVTQAAVSKILRE 50
                                   469**********************97 PP

>> LacI  Bacterial regulatory proteins, lacI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   4.6e-06    0.0054       4      23 ..      32      51 ..      31      57 .. 0.91
   2 ?   -2.9   0.1         5     6e+03       1       6 [.     173     178 ..     173     180 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.6e-06
                                   HHHHHCTS-HHHHHHHCTTS CS
                           LacI  4 DVArlAGVSkaTVSrvLnnk 23
                                   D+Arl GV+ a+VS++L+ k
  gi|119718987|ref|YP_919482.1| 32 DIARLTGVTQAAVSKILREK 51
                                   9****************987 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5
                                    -HHHHH CS
                           LacI   1 tikDVA 6  
                                    +i+DVA
  gi|119718987|ref|YP_919482.1| 173 SIYDVA 178
                                    59***9 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1     6e-06    0.0072      21      44 ..      27      50 ..      15      53 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 6e-06
                                   EEEHHHHHHHHTSSHHHHHHHHHH CS
                         MarR_2 21 dltvgelarrlglsksavsrilkr 44
                                   +++++++ar +g++++avs+il++
  gi|119718987|ref|YP_919482.1| 27 NMSQTDIARLTGVTQAAVSKILRE 50
                                   379******************985 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.1   6.9e-05     0.082      10      40 ..      19      50 ..      13      58 .. 0.80
   2 ?    0.1   0.0      0.61   7.3e+02       5      23 ..     140     160 ..     138     163 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.9e-05
                         HTH_23 10 illllae.GlsvreIAreLgvsrrTvyrwlkr 40
                                    +  l++  +s+++IAr+ gv++  v+++l+ 
  gi|119718987|ref|YP_919482.1| 19 LVSELRKlNMSQTDIARLTGVTQAAVSKILRE 50
                                   344455569********************986 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.61
                         HTH_23   5 reRlrillllae..GlsvreI 23 
                                    +eR++i+l   e  Gl ++e+
  gi|119718987|ref|YP_919482.1| 140 MERALIVLWSSEyfGLLIPEV 160
                                    79******9999888888776 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   7.1e-05     0.085      12      40 ..      25      53 ..      15      73 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.1e-05
                         HTH_31 12 raGLsqeevAerlgvsestlsrlEqGrrg 40
                                   + ++sq++ A+++gv+++ +s++ + ++g
  gi|119718987|ref|YP_919482.1| 25 KLNMSQTDIARLTGVTQAAVSKILREKQG 53
                                   4579*******************997765 PP

>> Cro  Cro
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00016      0.19      13      36 ..      28      51 ..      16      53 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00016
                                   HHHHHHHHHHTS-HHHHHHHHHCT CS
                            Cro 13 vGQaktAkdlgvkqsaIsKAlkak 36
                                   + Q+  A+  gv+q+a+sK l+ k
  gi|119718987|ref|YP_919482.1| 28 MSQTDIARLTGVTQAAVSKILREK 51
                                   569999*************99876 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00015      0.18      18      40 ..      28      50 ..      25      52 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00015
                         HTH_24 18 isqreLAerlglSpstvnrrlkr 40
                                   +sq+++A+ +g+++++v++ l++
  gi|119718987|ref|YP_919482.1| 28 MSQTDIARLTGVTQAAVSKILRE 50
                                   8******************9996 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00022      0.26       4      34 ..      16      46 ..      15      50 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00022
                                   HHHHHHHHTTSSEEHHHHHHHHTS-HHHHHH CS
                          HTH_5  4 RlkILklLaegelcvcelaeelglsqstvSh 34
                                   R+ +++ L++ +++ +++a+ +g++q++vS 
  gi|119718987|ref|YP_919482.1| 16 RRVLVSELRKLNMSQTDIARLTGVTQAAVSK 46
                                   566788999999******************6 PP

>> YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00018      0.21      10      34 ..      29      53 ..      21      69 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00018
                 YdaS_antitoxin 10 gqkaLAealgvsqqaVsqWlkgkkq 34
                                   +q+  A++ gv+q+aVs+ l+ k++
  gi|119718987|ref|YP_919482.1| 29 SQTDIARLTGVTQAAVSKILREKQG 53
                                   899****************987665 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00022      0.27      19      49 ..      18      49 ..      15      50 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00022
                   HTH_Tnp_ISL3 19 yilellles.rsvkavArqlgvSwtTVwrild 49
                                     + +l++  +s +++Ar++gv+   V  il+
  gi|119718987|ref|YP_919482.1| 18 VLVSELRKLnMSQTDIARLTGVTQAAVSKILR 49
                                   56677888888***********9999988876 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00033       0.4      17      39 ..      27      49 ..      18      50 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00033
                                   TEEHHHHHHHHTS-HHHHHHHHH CS
                           MarR 17 plsvseLakklgvskstvtrvld 39
                                   ++s++++a+  gv++++v+++l+
  gi|119718987|ref|YP_919482.1| 27 NMSQTDIARLTGVTQAAVSKILR 49
                                   799******************98 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.2   0.00061      0.73      11      42 ..      18      49 ..      16      50 .. 0.88
   2 ?   -1.9   0.1       2.5     3e+03      24      30 ..      73      79 ..      72      80 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00061
                         HTH_38 11 eeIerllaeGlslreIArrLgrspsTIsRElk 42
                                   +    l++ ++s+ +IAr+ g+    +s+ l+
  gi|119718987|ref|YP_919482.1| 18 VLVSELRKLNMSQTDIARLTGVTQAAVSKILR 49
                                   556789999***************99999987 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.5
                         HTH_38 24 reIArrL 30
                                   r+IA++L
  gi|119718987|ref|YP_919482.1| 73 RKIAKIL 79
                                   89***98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      615  (0.034302); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2277.22
//
Query:       gi|119718988|ref|YP_919483.1|  [L=354]
Description: transcriptional regulator, TrmB [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      3e-59  200.0   0.2    3.7e-59  199.7   0.2    1.1  1  Regulator_TrmB  Archaeal transcriptional regulator TrmB
      6e-15   54.9   0.1    1.2e-14   53.9   0.1    1.5  1  TrmB            Sugar-specific transcriptional regulator TrmB
    0.00043   20.1   0.0     0.0013   18.6   0.0    1.8  2  MarR_2          MarR family
  ------ inclusion threshold ------
      0.023   14.6   0.0        3.3    7.7   0.0    3.2  3  HTH_11          HTH domain
      0.049   13.6   0.0       0.13   12.2   0.0    1.8  1  HTH_Crp_2       Crp-like helix-turn-helix domain


Domain annotation for each model (and alignments):
>> Regulator_TrmB  Archaeal transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.7   0.2     1e-62   3.7e-59       2     232 ..     124     352 ..     123     353 .. 0.99

  Alignments for each domain:
  == domain 1  score: 199.7 bits;  conditional E-value: 1e-62
                                    EEEESSHHHHHHHHHHHHHH-SSEEEEEE-GGGHHHHHHHHHHHHHTT-EEEEEESS...----GGGSSSSEEEEEE-S- CS
                 Regulator_TrmB   2 vwvvksretvierieelIesAenelivslpselLeelreeliaaaergvtVllliyp...dedleeldleevatevrvrr 78 
                                    vw++++ e +++ri+el++sA+ + +++++ ++L++l+++++aa+ergv+V++l y+   + ++ + +++   +++rv+ 
  gi|119718988|ref|YP_919483.1| 124 VWIIREPEVAKSRIAELLDSATIDALIMGDIKFLHMLSDKIEAAVERGVRVYVLSYSlgeRGAKFIVEDMPFLKKLRVAI 203
                                    9**********************************************************9999999************** PP

                                    --S.EEEEETTTEEEEE-SSS-EEEE--HHHHHHHHHHHHHH........HHH-EEEEEEES-TT-EEES-HHHHHHHHH CS
                 Regulator_TrmB  79 sgapllvivDrkrgvvaprevlrdkeeeyaiifkekelihvlshyFlttlWktseviktdepvekpitfssirlavedik 158
                                    sg+ l+v+vD++rg v +++   + + +++++++e++l+++lsh F+++ W +s+vi  de+ ++p++f+ +r+a+ ++k
  gi|119718988|ref|YP_919483.1| 204 SGD-LVVVVDSERGGVLKAR--PTLPIRHGYLIEERTLTDYLSHDFMNR-WVSSKVIV-DENYDMPLKFTFHRMALYETK 278
                                    ***.***************9..***************************.********.********************* PP

                                    HHT.TTS-EEEEEEEEETTT--EEEEEEEEEEEEEETTTTEEEEEEEETTEEEEEE-TT--SSSEEEEEEEEEE CS
                 Regulator_TrmB 159 kllraglkveaeveGrdtetgeevtieGrvveatlnstpgvaslvvetedgevtVGGlgAvlEDieaeeitler 232
                                    kll +++k++++++G++++tg +v+++Gr+v+a+l+  +g a++ vet++g+++VGGl+A++E+i++e++++++
  gi|119718988|ref|YP_919483.1| 279 KLLLENKKLRLKATGYEIDTGARVEVSGRIVDAVLDLPAGYAHFKVETDSGVIRVGGLDAIVEEIAGEYFEIYE 352
                                    ************************************************************************87 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.9   0.1   3.3e-18   1.2e-14       1      67 [.      22      88 ..      22      89 .. 0.98

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 3.3e-18
                                   HHHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE--H CS
                           TrmB  1 LqklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYravdp 67
                                   L+ lGL+  Ea+ Yl Ll++gp++a ei+  l   r+++  +L +L++kG++e   grpk+Yravdp
  gi|119718988|ref|YP_919483.1| 22 LKLLGLTGLEAELYLLLLEKGPLSAPEISDYLVKHRPQIHVALTRLSSKGYIEELGGRPKKYRAVDP 88
                                   6779**************************************************************9 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   3.5e-07    0.0013       2      53 ..      26      75 ..      25      81 .. 0.88
   2 ?   -3.6   0.0         3   1.1e+04      14      31 ..     126     141 ..     125     142 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 3.5e-07
                                   T--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                         MarR_2  2 gltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53
                                   glt+ +a + + L   ++  l++ e+ ++l   ++ ++ +l rL+++G++e+
  gi|119718988|ref|YP_919483.1| 26 GLTGLEAELYLLLLEKGP--LSAPEISDYLVKHRPQIHVALTRLSSKGYIEE 75
                                   888888887777777777..******************************97 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 3
                                    HHCTTTSEEEHHHHHHHH CS
                         MarR_2  14 Lgrrpgrdltvgelarrl 31 
                                    + r+p+  ++ + +a+ l
  gi|119718988|ref|YP_919483.1| 126 IIREPE--VAKSRIAELL 141
                                    566777..7778888765 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0   0.00093       3.3       5      45 ..      33      72 ..      30      83 .. 0.80
   2 ?    2.9   0.0     0.029     1e+02      34      55 .]     152     173 ..     148     173 .. 0.88
   3 ?   -2.4   0.0       1.3   4.7e+03      38      48 ..     288     298 ..     288     302 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00093
                         HTH_11  5 ilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvp 45
                                    l lLl ++gp+s+ e++++L   r  ++  + +L+++g  
  gi|119718988|ref|YP_919483.1| 33 ELYLLLLEKGPLSAPEISDYLVKHRPQIHVALTRLSSKG-Y 72
                                   5788999**************888888888888888887.3 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.029
                         HTH_11  34 rdIkaLeelgvpIesepgrGYr 55 
                                     dIk L +l ++Ie+   rG r
  gi|119718988|ref|YP_919483.1| 152 GDIKFLHMLSDKIEAAVERGVR 173
                                    69*************9998875 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.3
                         HTH_11  38 aLeelgvpIes 48 
                                    +L+++g++I+ 
  gi|119718988|ref|YP_919483.1| 288 RLKATGYEIDT 298
                                    5999**99985 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   3.7e-05      0.13      21      67 ..      43      93 ..      19      94 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.7e-05
                                   EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ET.E.E.EEES-HHHHHH CS
                      HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglis.rg.r.r.irildleaLra 67
                                   pl+  e++++l  +r ++  +l++L+ +g+i+  g r +  r  d++ L +
  gi|119718988|ref|YP_919483.1| 43 PLSAPEISDYLVKHRPQIHVALTRLSSKGYIEeLGgRpKkYRAVDPQLLLN 93
                                   89999***************************8542323699999988865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2670.97
//
Query:       gi|119718989|ref|YP_919484.1|  [L=551]
Description: radical SAM domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.3e-12   46.7   0.1    2.7e-10   40.9   0.0    2.8  3  Radical_SAM  Radical SAM superfamily
    9.6e-12   45.0   0.0    2.8e-11   43.5   0.0    1.7  2  B12-binding  B12 binding domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.022     2e+02      33      67 ..     103     133 ..      94     167 .. 0.87
   2 !   40.9   0.0     3e-14   2.7e-10       2     161 ..     229     391 ..     228     396 .. 0.92
   3 ?   -1.4   0.0      0.29   2.6e+03     123     143 ..     491     511 ..     444     519 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.022
                                    HHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  33 eileevkelkaekgvkevilgggepllypdfvell 67 
                                    ei+++vkel+    +++v+lgg   ++y++++ + 
  gi|119718989|ref|YP_919484.1| 103 EIARLVKELR----KGHVVLGGFSATYYWREILEK 133
                                    7889999998....********9999998877665 PP

  == domain 2  score: 40.9 bits;  conditional E-value: 3e-14
                                    EEESEESS--TTTSCCTT....HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCT CS
                                    xxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM   2 vvtrgCnlrCsfCarpet....vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpg 77 
                                    ++++gC+++C  C  ++      + +++  ++ +e + ee ke+ ++  +  ++++ +   l + +ve l  l + + +g
  gi|119718989|ref|YP_919484.1| 229 ITYKGCTFNCLACGGSRFtynvIYGRRKLGVKKPETLFEEYKEITERL-KAPIFFVNDLQVLGKSYVERLVSLLRSERAG 307
                                    6889*************9****9999999999************6555.8888888888888899999999999999899 PP

                                    EEEEEEECSSCHGHHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET.EEEEEEEBTTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                    Radical_SAM  78 iritvetngtlpdeeklerllelg.vdrvslgleaaddekvlklmnrghtfeevlealeklreagikr.vvdrivglpGe 155
                                    +++++e   + p +++l+ l+ ++   +++++ e+ d+  ++   +r++t++ +++ l+++ ++g+ r   +++vglpG+
  gi|119718989|ref|YP_919484.1| 308 VEVFFEFFTPPP-RDFLAVLRSAEeRVYLQISPETHDES-IRSTYGRPYTNSSLKAFLRNAEDLGFTRvDLYFMVGLPGQ 385
                                    999999999999.99*********9**************.****************************999********* PP

                                    SHHHHH CS
                                    xxxxxx RF
                    Radical_SAM 156 ndeele 161
                                    + e ++
  gi|119718989|ref|YP_919484.1| 386 TPENVK 391
                                    *99865 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.29
                                    CTSHHHHHHHHHHHHHHTTSE CS
                                    xxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM 123 rghtfeevlealeklreagik 143
                                    + + f ev+e+++++r+ g +
  gi|119718989|ref|YP_919484.1| 491 DEEYFREVMESIQLARRGGRP 511
                                    566788999999988887766 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.5   0.0   3.1e-15   2.8e-11       8     116 ..      36     148 ..      30     149 .. 0.94
   2 ?   -3.5   0.0       1.1     1e+04      45      56 ..     299     311 ..     285     332 .. 0.51

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 3.1e-15
                    B12-binding   8 vggdlhplGlavlaaalrdagfeVqllganven.....edivaairaekpdvvglSalltsqleavkelvellkrirprv 82 
                                      +d++p G+ +la +l+++g++  + ++ +++      d+ + +r++++ v g+ +++  +  ++ e+++l+k+ r++ 
  gi|119718989|ref|YP_919484.1|  36 PVFDMYPAGFFSLASYLEERGVKTGIFNLAAKMvndprFDVPRFLRSLEASVYGIDLHWLVHAHGALEIARLVKELRKG- 114
                                    6689*********************99999999999999*************************************887. PP

                    B12-binding  83 kvvvGGahpsldpeetleaklgiddvvvgegeda 116
                                    +vv+GG  ++++++e+le+ +++d +v+g+ +++
  gi|119718989|ref|YP_919484.1| 115 HVVLGGFSATYYWREILEKFPYVDAIVLGDTTEP 148
                                    *****************866*********98875 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.1
                    B12-binding  45 aairaekpdv.vg 56 
                                    + +r+e++ v v 
  gi|119718989|ref|YP_919484.1| 299 SLLRSERAGVeVF 311
                                    3333333333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (551 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 3651.25
//
Query:       gi|119718990|ref|YP_919485.1|  [L=108]
Description: hypothetical protein Tpen_0072 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       252  (0.0140554); expected 358.6 (0.02)
Passed bias filter:                      192  (0.0107089); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 733.94
//
Query:       gi|119718991|ref|YP_919486.1|  [L=356]
Description: radical SAM domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.9e-14   53.8   0.0    2.9e-14   53.8   0.0    1.8  2  Radical_SAM  Radical SAM superfamily
    2.6e-08   34.2   0.0    5.5e-08   33.2   0.0    1.4  1  Fer4_12      4Fe-4S single cluster domain
    9.7e-07   28.9   0.0    1.9e-06   28.0   0.0    1.4  1  Fer4_14      4Fe-4S single cluster domain
  ------ inclusion threshold ------
          1    9.6   6.1       0.14   12.3   1.5    2.0  2  Prok-RING_2  Prokaryotic RING finger family 2


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.8   0.0   6.5e-18   2.9e-14       3     151 ..       7     144 ..       5     160 .. 0.84
   2 ?   -3.7   0.9         3   1.3e+04       5      13 ..     288     296 ..     286     298 .. 0.88

  Alignments for each domain:
  == domain 1  score: 53.8 bits;  conditional E-value: 6.5e-18
                                    EESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM   3 vtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlaklavpgirit 81 
                                    +t  Cnl+C +C  ++     +r    sv +  +++k+l +e++    v + ggepll++dfv+++++ ++      +++
  gi|119718991|ref|YP_919486.1|   7 TTGQCNLKCDYCGGSF----DPRKVPWSVKYDYHLLKKL-VERDeDSIVAFYGGEPLLNKDFVKWVLENVRA----KHFV 77 
                                    5778***********8....6888888888888889999.666669*************************6....8*** PP

                                    EEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET.EEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
                    Radical_SAM  82 vetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikr.vvdrivg 151
                                    + tngtl+ +   er   +  d v l+++   +  v +++++ + + +v+e+ + lre g+k   + r+++
  gi|119718991|ref|YP_919486.1|  78 IQTNGTLV-KSLPERYWHMF-DAVLLSVDGRES--VTDKHRGSGVYRRVVESARWLREIGFKGdLIARMTV 144
                                    *******9.88888888866.********9999..66666699*******************655555544 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 3
                                    SEESS--TT CS
                                    xxxxxxxxx RF
                    Radical_SAM   5 rgCnlrCsf 13 
                                    ++C +rC +
  gi|119718991|ref|YP_919486.1| 288 EFCGGRCLY 296
                                    79*****98 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   0.0   1.2e-11   5.5e-08       9     124 ..       5     112 ..       2     121 .. 0.80

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 1.2e-11
                        Fer4_12   9 slfvsgCnlsCkgCfnk.etwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekd 87 
                                    ++ ++ Cnl+C++C    + +++  + +++  ll++++e    ++++ + + GGEPll  n++ +  ++++v+++ +   
  gi|119718991|ref|YP_919486.1|   5 VHTTGQCNLKCDYCGGSfDPRKVPWSVKYDYHLLKKLVE---RDEDSIVAFYGGEPLL--NKDFVKWVLENVRAKHF--- 76 
                                    455789********8321344555677778888888875...57999***********..99999999999999999... PP

                        Fer4_12  88 iwlytgytleelskkekeellkeidvlvdGkfeesle 124
                                    ++ ++g+  + l + ++  + + +   vdG+ +   +
  gi|119718991|ref|YP_919486.1|  77 VIQTNGTLVKSLPE-RYWHMFDAVLLSVDGRESVTDK 112
                                    899***99999975.6999999999999999875554 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   4.3e-10   1.9e-06       4     116 ..       7     104 ..       4     106 .. 0.73

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 4.3e-10
                        Fer4_14   4 rlsgCnlsCkgCd.nketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekk 82 
                                     +++Cnl+C  C    +  k  +  +++++ll++ + + +++ i    + + GGePL+        ++vk++ e+++ k+
  gi|119718991|ref|YP_919486.1|   7 TTGQCNLKCDYCGgSFDPRKVPWSVKYDYHLLKKLV-ERDEDSI----VAFYGGEPLLN------KDFVKWVLENVRAKH 75 
                                    5899********96444567799999999***9988.3333333....89*******44......578999999999999 PP

                        Fer4_14  83 iwletngtleielektpdlkeklealskidllvd 116
                                      ++tngtl ++l +  ++    ++ + + l+vd
  gi|119718991|ref|YP_919486.1|  76 FVIQTNGTLVKSLPE-RYW----HMFDAVLLSVD 104
                                    *********977662.333....44444445555 PP

>> Prok-RING_2  Prokaryotic RING finger family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.2       3.8   1.7e+04      10      14 ..      15      19 ..      12      21 .. 0.58
   2 ?   12.3   1.5   3.2e-05      0.14      26      43 ..     173     190 ..     166     197 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 3.8
                    Prok-RING_2 10 cdlca 14
                                   cd c 
  gi|119718991|ref|YP_919486.1| 15 CDYCG 19
                                   66663 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 3.2e-05
                    Prok-RING_2  26 vlcGrWacdacWkdeyyt 43 
                                    v   rW c +cW+d  y+
  gi|119718991|ref|YP_919486.1| 173 VWSDRWKCFSCWRDGNYL 190
                                    6678**********9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2600.74
//
Query:       gi|119718992|ref|YP_919487.1|  [L=240]
Description: hypothetical protein Tpen_0074 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
       0.05   10.9   0.0      0.063   10.6   0.0    1.0  1  TRAPPC9-Trs120  Transport protein Trs120 or TRAPPC9, TRAPP II


Domain annotation for each model (and alignments):
>> TRAPPC9-Trs120  Transport protein Trs120 or TRAPPC9, TRAPP II complex subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   3.5e-06     0.063     693     744 ..      45      98 ..      43     113 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 3.5e-06
                 TRAPPC9-Trs120 693 EkaefkvtLqNPfefeveiesielete.gvefe.alkeslvigpkstqkltltg 744
                                    E  ++++ L NP+++ ++ ++++++++ g +f  a++ +++++p s + l+l +
  gi|119718992|ref|YP_919487.1|  45 ENLTLRIYLSNPYSVPLQFQEVSVKAKcGSSFYgASRGNVTVPPASHSVLQLEV 98 
                                    7889********************9875788889************99999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1684.51
//
Query:       gi|119718993|ref|YP_919488.1|  [L=87]
Description: hypothetical protein Tpen_0075 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.036   14.2   0.1      0.048   13.8   0.1    1.3  1  UPF0180   Uncharacterised protein family (UPF0180)
      0.086   12.8   0.3       0.11   12.5   0.3    1.1  1  PepSY_2   Peptidase propeptide and YPEB domain


Domain annotation for each model (and alignments):
>> UPF0180  Uncharacterised protein family (UPF0180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   5.3e-06     0.048       5      27 ..       3      25 ..       1      47 [. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.3e-06
                        UPF0180  5 VeegLsnvkeaLrekGYeVvdle 27
                                   +ee  + v++ LrekGY+V++  
  gi|119718993|ref|YP_919488.1|  3 IEEAIKTVEKTLREKGYSVTREV 25
                                   799999*************9755 PP

>> PepSY_2  Peptidase propeptide and YPEB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.3   1.3e-05      0.11      33      82 ..       8      54 ..       4      56 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.3e-05
                        PepSY_2 33 eklvakleaqGykvkkievddggcyEvegldkdGkkveikldpatgevvk 82
                                   +++++ l+++Gy+v++ ev+dg   +v ++    +k++++++++ ge ++
  gi|119718993|ref|YP_919488.1|  8 KTVEKTLREKGYSVTR-EVEDGD--QVLVVQLGDRKAKVRFHGEAGELLE 54
                                   68999*******8876.666775..799999***************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 631.27
//
Query:       gi|119718994|ref|YP_919489.1|  [L=286]
Description: 6-phosphogluconate dehydrogenase, NAD-binding [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-33  115.2   0.0    4.9e-33  114.5   0.0    1.2  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
    8.3e-13   48.6   0.0    1.4e-12   47.9   0.0    1.3  1  NAD_binding_11   NAD-binding of NADP-dependent 3-hydroxyisobu
      2e-10   41.1   0.0    6.5e-10   39.5   0.0    1.9  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
      1e-06   28.2   0.0    1.4e-06   27.8   0.0    1.2  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
    3.2e-05   24.0   0.0    0.00012   22.1   0.0    1.9  2  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
    0.00064   19.4   0.0     0.0012   18.5   0.0    1.5  1  ApbA             Ketopantoate reductase PanE/ApbA
     0.0011   19.6   0.0     0.0029   18.3   0.0    1.7  2  NAD_binding_3    Homoserine dehydrogenase, NAD binding domain
     0.0013   18.4   0.0       0.34   10.5   0.0    2.4  2  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
     0.0027   18.5   0.0     0.0049   17.7   0.0    1.4  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
     0.0027   17.9   0.0     0.0058   16.9   0.0    1.6  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0056   17.1   0.2      0.012   16.1   0.2    1.6  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
  ------ inclusion threshold ------
       0.05   13.6   0.0       0.11   12.5   0.0    1.5  1  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
      0.082   12.3   0.1       0.13   11.7   0.1    1.2  1  Bac_luciferase   Luciferase-like monooxygenase
      0.088   12.7   0.0       0.21   11.5   0.0    1.7  2  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
       0.15   12.1   0.2       0.38   10.7   0.1    1.7  2  Glyco_transf_4   Glycosyltransferase Family 4
       0.15   12.3   0.0          2    8.7   0.0    2.3  1  TrkA_N           TrkA-N domain
       0.17   11.8   0.0       0.35   10.7   0.0    1.6  1  SIS              SIS domain


Domain annotation for each model (and alignments):
>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.5   0.0   4.6e-36   4.9e-33       2     154 ..       3     154 ..       2     157 .. 0.96

  Alignments for each domain:
  == domain 1  score: 114.5 bits;  conditional E-value: 4.6e-36
                                    EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSHCCC-- CS
                  NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdeviegllealk 81 
                                    +gfiG+G MG +ma +l++ g+++ v+nrt ek++ l + ga++a+s+ el + ++vv++mv++++a +ev++ +l++ +
  gi|119718994|ref|YP_919489.1|   3 LGFIGTGAMGFPMAARLARTGHELFVWNRTIEKARPLEQYGARVASSLDELSRVAEVVFVMVSDDEASREVLSAVLREGR 82 
                                    8*************************************************************************999875 PP

                                    TT-EEEE-S---HHHHHHHHHHHHHTT-EEEEEEEESHHHHHHHT-EEEEEEE-HHHHHHHHHHHHHHEEEEE CS
                  NAD_binding_2  82 kgdilidgstsspedtrelakelkekglkfldaPVSGGeegAekGtLsimvGGseeafervkpvleaigakvt 154
                                    + +i++++st+sp  tre  +e+k++g+++l +PV GG    e+G+  ++vGG+ee+f++v+p+ +a+ ++ +
  gi|119718994|ref|YP_919489.1|  83 P-RIIVNHSTVSPMYTREAVEEAKRRGVEYLAIPVMGGPSDIERGEGVCIVGGREEVFREVEPLTSAYCKEHV 154
                                    5.8*************************************************************999988655 PP

>> NAD_binding_11  NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.9   0.0   1.3e-15   1.4e-12       3     120 ..     162     278 ..     161     280 .. 0.89

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 1.3e-15
                 NAD_binding_11   3 GqavKlvnnlllainlaaasEalvlaekaGldpekvlevinassgrsnalenklpqrvlsrdfdpgFaldlmlKDlglal 82 
                                    ++++Kl+ n ++   l a++Eal+l e+  ++p++++++ ++     +++ +++ +r+l++++++ F+l l +KDl+ a+
  gi|119718994|ref|YP_919489.1| 162 ASVIKLALNSMYFSALEALAEALLLVEAWNVEPKVFFDAASRLW--LRVVVDRYAKRLLDEKYPTSFQLRLAAKDLHYAV 239
                                    5789**********************************987665..5567788999************************ PP

                 NAD_binding_11  83 elareagaplpllalaeqlyaaaaaegg.gdaDhsaivr 120
                                      +   g plp+l++ ++++ +a+  gg g +D+++i+ 
  gi|119718994|ref|YP_919489.1| 240 FSGYHKGQPLPMLSELAKTFLEASTIGGlGRRDYTRIYY 278
                                    *************99999998887755548999999986 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   0.0   6.2e-13   6.5e-10       1      74 [.       2      69 ..       2      95 .. 0.84
   2 ?   -1.7   0.0       4.4   4.6e+03      26      45 ..     152     170 ..     145     202 .. 0.65

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 6.2e-13
                                   EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHH CS
                  F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedv 74
                                   ++g+iG+G mg+ +a +l+++g   he+ v  +r+ eka+ l e++g++v + +  e+ + a+vv++ v    +
  gi|119718994|ref|YP_919489.1|  2 RLGFIGTGAMGFPMAARLARTG---HELFVW-NRTIEKARPL-EQYGARVAS-SLDELSRVAEVVFVMVSDDEA 69
                                   68********************...****66.**********.788999999.9*************9975443 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 4.4
                                    GCEEEEEESSCCCHHHHHHH CS
                  F420_oxidored  26 heivvansrnpekaeelaee 45 
                                    ++++v+ s+++ ++ +la +
  gi|119718994|ref|YP_919489.1| 152 EHVLVG-SQENASVIKLALN 170
                                    677766.6666666666533 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.0   1.3e-09   1.4e-06      38     111 ..       2      76 ..       1     109 [. 0.93

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 1.3e-09
                                    EEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEEC.SHHHHHHH-SEEEE-S--STTTTTSBSH CS
                   2-Hacid_dh_C  38 tvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelv.sleellaesDivslhlpltpetrhlina 111
                                    ++G iG+G++G  +a rl+  g ++++++r+ +k +  e++g++++ sl+el + +++v++++   ++ r++++a
  gi|119718994|ref|YP_919489.1|   2 RLGFIGTGAMGFPMAARLARTGHELFVWNRTIEKARPLEQYGARVAsSLDELSRVAEVVFVMVSDDEASREVLSA 76 
                                    79*******************************999*******8887****************999999988765 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   1.2e-07   0.00012      16      81 ..       4      65 ..       1      85 [. 0.79
   2 ?   -1.2   0.0       1.8   1.9e+03      80     118 ..      86     124 ..      81     128 .. 0.69

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.2e-07
                                   EEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE CS
                   Shikimate_DH 16 lliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvis 81
                                     iG+G m+  +a  L++ g + ++v NRt+e+a+ l e++++    a +l+el+++ + + v++s
  gi|119718994|ref|YP_919489.1|  4 GFIGTGAMGFPMAARLARTGHE-LFVWNRTIEKARPL-EQYGAR--VASSLDELSRVAEVVFVMVS 65
                                   57***************99998.**************.666555..58888888865544444443 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.8
                                    EE-SSSSS-SB-HHHHHCCHHH.S..EEEEE--SS-SB- CS
                   Shikimate_DH  80 isataseepilekeeveealkkrkkplllvDiavPRdve 118
                                    i+  ++ +p+ ++e+veea+++  + l +  ++ P d+e
  gi|119718994|ref|YP_919489.1|  86 IVNHSTVSPMYTREAVEEAKRRGVEYLAIPVMGGPSDIE 124
                                    555666778899999999986544555555566666665 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.1e-06    0.0012       3      47 ..       5      50 ..       3      75 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.1e-06
                                   EES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEEEETT CS
                           ApbA  3 ilGaGaiGsllaakLakagadvtlilrsr.rlealkknGlrltseg 47
                                    +G+Ga+G  +aa+La++g++  +++r+  ++  l++ G r+ s+ 
  gi|119718994|ref|YP_919489.1|  5 FIGTGAMGFPMAARLARTGHELFVWNRTIeKARPLEQYGARVASSL 50
                                   59***************************88888*******99887 PP

>> NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   2.7e-06    0.0029       1     112 [.       7     109 ..       3     115 .. 0.79
   2 ?   -2.1   0.0       5.6     6e+03     109     109 ..     183     183 ..     157     216 .. 0.59

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.7e-06
                                    --SHHHHHHHHHHHH---SSEEEEEEEEESSEEE-TTHHHHHT--CB---HHHHHHHHS-EEEEE-S--HHHHTTHHHHH CS
                  NAD_binding_3   1 GlGaiGsavleqlkrqqseielelvavadrdsllskdrkallasealtldlddliahldpdvvVEcasseavaelvlkaL 80 
                                    G Ga G  ++++l+r   e      +v++r   ++k+r  +   +++ ++ld+l + ++  v+V +  +ea +e++ ++L
  gi|119718994|ref|YP_919489.1|   7 GTGAMGFPMAARLARTGHE-----LFVWNRT--IEKARPLEQYGARVASSLDELSR-VAEVVFVMVSDDEASREVLSAVL 78 
                                    5555556666666666655.....7999999..77777778889999******888.88999****************** PP

                                    HTTEEEE-S--CGGG-HHHHHHHTSSSTTS-- CS
                  NAD_binding_3  81 kagkdvvtankgaladealyeeLreaaeanga 112
                                    ++g   +++n + ++++ ++e+  ea++  g+
  gi|119718994|ref|YP_919489.1|  79 REGRPRIIVNHSTVSPMYTREAVEEAKR-RGV 109
                                    ***************6666666655555.444 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 5.6
                                    T CS
                  NAD_binding_3 109 a 109
                                    a
  gi|119718994|ref|YP_919489.1| 183 A 183
                                    2 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0   0.00032      0.34       1      28 [.       1      28 [.       1      55 [. 0.88
   2 !    5.9   0.0     0.008       8.4     107     137 ..      74     106 ..      63     164 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00032
                                   SEEEEE--STTHHHHHHHHHHCTSEEEE CS
                 UDPG_MGDP_dh_N  1 mkisviGlGYvGlvtaavlaeighevig 28
                                   m++ +iG+G +G ++aa la+ ghe+ +
  gi|119718994|ref|YP_919489.1|  1 MRLGFIGTGAMGFPMAARLARTGHELFV 28
                                   7899********************9876 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.008
                                    HHHHHHC..EEEEEE-S---TTHHHHCHHHHHH CS
                 UDPG_MGDP_dh_N 107 iaealkk..gkvvvvkSTvpvgtaeelvkkile 137
                                    ++ +l++   +++v+ STv +  ++e+v++  +
  gi|119718994|ref|YP_919489.1|  74 LSAVLREgrPRIIVNHSTVSPMYTREAVEEAKR 106
                                    34455556689*********9999988877655 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   4.7e-06    0.0049       1     111 [.       1     106 [.       1     113 [. 0.79

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4.7e-06
                                    EEEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S-G.GGHHHHH CS
                   GFO_IDH_MocA   1 lrvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysdleelladpeidavivatpn.gtheela 79 
                                    +r ++iG+G +g + ++ l ++  ++e+  ++++  e+a+ + e++g+ + s+l+el++   +++v+v++   +  +e+ 
  gi|119718994|ref|YP_919489.1|   1 MRLGFIGTGAMGFPMAARLART--GHELF-VWNRTIEKARPL-EQYGARVASSLDELSR--VAEVVFVMVSDdEASREVL 74 
                                    689********99998666666..56665.8*********98.****************..99*****9999566999** PP

                                    HHHHHTT-.EEEEES....SS-SSHHHHHHHHHHHHH CS
                   GFO_IDH_MocA  80 kaaleagk.hvllEK....Plattveeakelvelaek 111
                                     a+l+ g   +++ +    P+ t     +e ve a++
  gi|119718994|ref|YP_919489.1|  75 SAVLREGRpRIIVNHstvsPMYT-----REAVEEAKR 106
                                    ****9998899999843334444.....444444444 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   5.5e-06    0.0058       3      98 ..       5     113 ..       3     153 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 5.5e-06
                                    EE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH..............TTTCEEE.EE--TTTHHHHHHHHH CS
                Sacchrp_dh_NADP   3 iiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka..............lgvrfea.ialdaenyeavLaall 67 
                                    +iG G++G ++a  lar+++   e+ v+ r+ ek++ l ++               +  ++ + +  d e  ++vL+a+l
  gi|119718994|ref|YP_919489.1|   5 FIGTGAMGFPMAARLARTGH---ELFVWNRTIEKARPL-EQYgarvassldelsrvA--EVVFvMVSDDEASREVLSAVL 78 
                                    79****************98...59*********7666.4556999*****999533..4443034455566678***** PP

                                    TTS..SEEEE-SSGG..GHHHHHHHHHHHT-EEEE CS
                Sacchrp_dh_NADP  68 keg..dlvvnlsppi..ssldvlkaCietgvhyvd 98 
                                    +eg   ++vn s+    ++++ ++ + ++gv y+ 
  gi|119718994|ref|YP_919489.1|  79 REGrpRIIVNHSTVSpmYTREAVEEAKRRGVEYLA 113
                                    **********9886666999**********99986 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.2   1.1e-05     0.012      10     100 ..      15     112 ..      10     167 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.1e-05
                Glyco_trans_4_4  10 laraLaarGheVtvltpapapgapeleedgvrvhrl.p.vprrps....pladlaalralrrllrqrrerpdvvhahspt 83 
                                    +a++La+ Ghe+ v+ ++   ++p le+ g+rv +  + ++r  +     + d +a+r + +++  r+ rp +++ hs  
  gi|119718994|ref|YP_919489.1|  15 MAARLARTGHELFVWNRTIEKARP-LEQYGARVASSlDeLSRVAEvvfvMVSDDEASREVLSAV-LREGRPRIIVNHSTV 92 
                                    89**************97766666.888899997432224444333333344566778887776.69***********99 PP

                Glyco_trans_4_4  84 aglaarla....rrrrgiplv 100
                                    ++++ r a    + rrg+ ++
  gi|119718994|ref|YP_919489.1|  93 SPMYTREAveeaK-RRGVEYL 112
                                    9999988855423.6666554 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0    0.0001      0.11       3      38 ..       4      39 ..       2      53 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.0001
                                   EEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHH CS
                 NAD_Gly3P_dh_N  3 avlGaGswGtalAkvlaenghevrlwvreeelieei 38
                                   +++G+G+ G  +A+ la++ghe  +w r  e ++ +
  gi|119718994|ref|YP_919489.1|  4 GFIGTGAMGFPMAARLARTGHELFVWNRTIEKARPL 39
                                   689************************998777665 PP

>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00012      0.13     172     305 ..       9     143 ..       6     150 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00012
                 Bac_luciferase 172 aaaspaglelaarhadglllag...eppeeaaelierlragaaeagrdpadirvgisltvivadteeeAraearaliagl 248
                                    +a++  +++  ar+++ l++++   e    ++++ +r+++          ++  ++ + +++  ++e+ r+ + a ++++
  gi|119718994|ref|YP_919489.1|   9 GAMGFPMAARLARTGHELFVWNrtiEKARPLEQYGARVASSLD-------ELSRVAEVVFVMVSDDEASREVLSAVLREG 81 
                                    89999999999***********444444444455555554333.......555577666666667777777777777777 PP

                 Bac_luciferase 249 d.......fyaldsegagreaeaaeiqeeedanlwagaadavpdelvaatalvGtpeqvaerla 305
                                               +   + ++ +ea++++ e+ a   +g  + +  e +++ ++vG  e+v  +++
  gi|119718994|ref|YP_919489.1|  82 RpriivnhSTVSPMYTREAVEEAKRRGVEYLAIPVMGGPSDI--ERGEGVCIVGGREEVFREVE 143
                                    778888443333344444444555777888888888888887..999999****9999988776 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0    0.0002      0.21       3      48 ..       4      52 ..       2      82 .. 0.74
   2 ?   -2.4   0.0       3.5   3.7e+03      45      84 ..     149     188 ..     125     191 .. 0.51

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0002
                                   EEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHH...HHHHHHHHHHHC CS
                        3HCDH_N  3 aviGaGtmGagiaavfasagleVvlvdiseeale...kalekiekslek 48
                                   + iG+G mG  +aa +a++g+e  + +++ e+++   +  +++++sl++
  gi|119718994|ref|YP_919489.1|  4 GFIGTGAMGFPMAARLARTGHELFVWNRTIEKARpleQYGARVASSLDE 52
                                   78*********************99999655554000444444444444 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.5
                                    HHHCCTTTTSS-HHHHCCCHHCEEEES-HHHHHC-SEEEE CS
                        3HCDH_N  45 sleklvekgklkeeeveaalarisfttdleeavdadlviE 84 
                                     +++ v  g+ ++++v +++ +  + + le++++a l +E
  gi|119718994|ref|YP_919489.1| 149 YCKEHVLVGSQENASVIKLALNSMYFSALEALAEALLLVE 188
                                    3334444444444444444444445555555556655555 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00036      0.38      11      88 ..      15      98 ..      12     116 .. 0.75
   2 ?   -2.4   0.0         4   4.2e+03     132     153 ..     202     223 ..     188     244 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00036
                 Glyco_transf_4 11 LaraLarrGheVtvvtpgddgpleeev......elvvrvprvplpllkrllrslaflrrlrrllkrekpDvvHahspaalga 86
                                   +a +Lar Ghe  v  ++ +++ + e+        + ++ rv  + +     + a++  l ++l++++p ++  hs ++ ++
  gi|119718994|ref|YP_919489.1| 15 MAARLARTGHELFVWNRTIEKARPLEQygarvaSSLDELSRVAEVVFVMVSDDEASREVLSAVLREGRPRIIVNHSTVSPMY 96
                                   5899***********888888888885556666444444444445555566666677899999************9999988 PP

                 Glyco_transf_4 87 al 88
                                     
  gi|119718994|ref|YP_919489.1| 97 TR 98
                                   64 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4
                 Glyco_transf_4 132 rradrviavSeatadelreryg 153
                                    +r +  ++v +++++ l e+y+
  gi|119718994|ref|YP_919489.1| 202 SRLWLRVVVDRYAKRLLDEKYP 223
                                    4555556666666666666554 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0    0.0019         2      62     113 ..      56     112 ..       5     115 .. 0.61

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0019
                                    GESEEEE-SSSHHHHHHHHHHH.HHHTSS....SEEEEEESSGGGHHHHHHHTTSEE CS
                         TrkA_N  62 kadaviaatgddeanilavlla.kelnpk....kkiiaraqdpehaellkklgadvv 113
                                     a++v ++++ddea+  ++ ++ +e +p       +++ + ++e +e +k+ g+++ 
  gi|119718994|ref|YP_919489.1|  56 VAEVVFVMVSDDEASREVLSAVlREGRPRiivnHSTVSPMYTREAVEEAKRRGVEYL 112
                                    488999999999888888777768877776555557777777777888888887765 PP

>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00033      0.35      29      86 ..      55     114 ..      51     149 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00033
                                    HHHTSEEEEEEHHHHHHTGG.GG-STTCEEEEEESSSHHHHHHHHHH.HHHHTTSEEEEE CS
                            SIS  29 eiggivvevedaselkhgvl.alideddlvilisfsgetkdlvaaae.lakergakiiaI 86 
                                    +++++v+++++++e   +vl a+++e+ + i++ +s  ++ +++ a  +ak+rg++ +aI
  gi|119718994|ref|YP_919489.1|  55 RVAEVVFVMVSDDEASREVLsAVLREGRPRIIVNHSTVSPMYTREAVeEAKRRGVEYLAI 114
                                    5677788888888877777725689******************99999********9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2072.24
//
Query:       gi|119718995|ref|YP_919490.1|  [L=350]
Description: hypothetical protein Tpen_0077 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2621.57
//
Query:       gi|119718996|ref|YP_919491.1|  [L=277]
Description: hypothetical protein Tpen_0078 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 2126.94
//
Query:       gi|119718997|ref|YP_919492.1|  [L=268]
Description: hypothetical protein Tpen_0079 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.087   13.4   0.1        0.9   10.1   0.0    2.4  2  YjbR      YjbR


Domain annotation for each model (and alignments):
>> YjbR  YjbR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0     0.049   8.9e+02      55      55 ..     109     109 ..      38     158 .. 0.54
   2 ?   10.1   0.0     5e-05       0.9      22      64 ..     183     225 ..     172     241 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.049
                                    E CS
                           YjbR  55 a 55 
                                    +
  gi|119718997|ref|YP_919492.1| 109 T 109
                                    0 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 5e-05
                                    CEEEEEEECCCCGEEEES-HHHHHHHHHSSTT.EEE-TSTTTEE CS
                           YjbR  22 gKmFallgleeeslnlkcdpeeaeaLreqypa.iapgyhkkhWi 64 
                                    + +F l+++ + ++++k+ p ea  Lr   p+ i+  y+    +
  gi|119718997|ref|YP_919492.1| 183 KQVFWLITNAS-NITVKVRPSEAMLLRKYRPSiIFEKYNGGFVN 225
                                    46788887655.6*******************999888643344 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      600  (0.0334653); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1980.65
//
Query:       gi|119718998|ref|YP_919493.1|  [L=171]
Description: small GTP-binding protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.2e-38  131.4   0.0    2.5e-38  131.2   0.0    1.0  1  Ras        Ras family
    6.4e-24   84.5   0.0    7.9e-24   84.2   0.0    1.1  1  Roc        Ras of Complex, Roc, domain of DAPkinase
    2.4e-09   36.9   0.0    2.9e-09   36.6   0.0    1.1  1  Arf        ADP-ribosylation factor family
    2.7e-06   26.9   0.0      4e-06   26.4   0.0    1.3  1  Gtr1_RagA  Gtr1/RagA G protein conserved region
     0.0028   17.7   0.0      0.004   17.2   0.0    1.2  1  MMR_HSR1   50S ribosome-binding GTPase
     0.0059   17.0   0.0     0.0092   16.4   0.0    1.4  1  AAA_16     AAA ATPase domain
  ------ inclusion threshold ------
      0.023   15.1   0.0      0.041   14.3   0.0    1.4  1  AAA        ATPase family associated with various cellular act
      0.024   14.9   0.0      0.051   13.8   0.0    1.6  2  AAA_22     AAA domain
       0.04   13.9   0.0      0.091   12.8   0.0    1.7  1  AAA_5      AAA domain (dynein-related subfamily)
      0.053   13.2   0.0      0.077   12.7   0.0    1.3  1  AAA_24     AAA domain
       0.08   12.1   0.0       0.12   11.5   0.0    1.3  1  NB-ARC     NB-ARC domain
       0.15   12.6   0.1       0.18   12.3   0.1    1.5  1  AAA_18     AAA domain


Domain annotation for each model (and alignments):
>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.2   0.0   1.7e-41   2.5e-38       1     161 [.       6     166 ..       6     167 .. 0.97

  Alignments for each domain:
  == domain 1  score: 131.2 bits;  conditional E-value: 1.7e-41
                                    EEEEEESTTSSHHHHHHHHHHSSCSSSCTTTSSEEEEEEEEEETTEEEEEEEEEETTSGGGHHHHHHHHTTESEEEEEEE CS
                            Ras   1 KlvlvGdsavGKtslllrfvkdkFkeeyesTigvdfytkeievdgkevkleiwDTAGqeefkslrelyyrdaegillvyd 80 
                                    K+ l G ++vGKtsl  +fv+++++ +   T+g++ + ++i++dg+e+++ iwD  G  +f+ l+++++++a+g++ v+d
  gi|119718998|ref|YP_919493.1|   6 KISLCGPGGVGKTSLARKFVEGSYNPQERLTVGIQHFFRKIQLDGRELHVVIWDLGGEHRFRFLAPAFLKGAKGVVYVFD 85 
                                    78899*************************************************************************** PP

                                    TTBHHHHHTHHHHHHHHHHHSTTTSEEEEEEETTTGGGG-SS-HHHHHHHHHHHT.SEEEEEBTTTTCTHHHHHHHHHHH CS
                            Ras  81 itsresfenvkkwveeikrvaeenvpivLvGnKvDleekravsteegeelakelg.lkfletSAktnenveeafeellre 159
                                    +t++e+f ++++w +  ++v   +vp +L+GnK+Dlee r v ++ ++e+a ++g l+++e+SA+t  +veeaf  llr+
  gi|119718998|ref|YP_919493.1|  86 LTREETFLEIDEWRKITESVLG-KVPSILIGNKADLEEYRIVPYNLAREYALSKGfLEYFEVSARTGARVEEAFLFLLRT 164
                                    *************998888888.5*******************************9*********************999 PP

                                    HH CS
                            Ras 160 il 161
                                    i 
  gi|119718998|ref|YP_919493.1| 165 IV 166
                                    86 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.2   0.0   5.3e-27   7.9e-24       1     120 []       6     120 ..       6     120 .. 0.92

  Alignments for each domain:
  == domain 1  score: 84.2 bits;  conditional E-value: 5.3e-27
                                    EEEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SGGCTTTT-HHHHCTS CS
                            Roc   1 KvvlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaGqerfrslhplylrea 80 
                                    K+ l+G +gvGKtsl+++fve++++++e+ t+g++ + +++ +++g       +++++ iWD++G+ rfr l+p +l++a
  gi|119718998|ref|YP_919493.1|   6 KISLCGPGGVGKTSLARKFVEGSYNPQERLTVGIQHFFRKI-QLDG-------RELHVVIWDLGGEHRFRFLAPAFLKGA 77 
                                    899********************************999987.4554.......57899********************** PP

                                    CEEEEEEE...GHHHHCHHHHHHHHHHHCSSS-EEEEEE-TTT CS
                            Roc  81 alailvyd...srssenlkeWlkelkkvagkspvilvgnkiDl 120
                                    + +++v+d   ++++ +++eW k  ++v gk p il+gnk+Dl
  gi|119718998|ref|YP_919493.1|  78 KGVVYVFDltrEETFLEIDEWRKITESVLGKVPSILIGNKADL 120
                                    ********75444566889**********************95 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.0   1.9e-12   2.9e-09      15     169 ..       5     159 ..       2     165 .. 0.73

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 1.9e-12
                                    EEEEEEESTTSSHHHHHHHHHHSSCEE.CSSSSSEE....EEEEEETTEEEEEEEE-SSGGGGGGGGGGCTTESEEEEEE CS
                            Arf  15 lrilllGLDnaGKtTilkklkleelvt.tvPTigfn....veeleiknlkftvwDvGGqeklRplWknYfektdavifvv 89 
                                    ++i l G  + GKt +  k+ +++ +     T+g +      +l  ++l++ +wD+GG+++ R l   +++  ++v++v 
  gi|119718998|ref|YP_919493.1|   5 VKISLCGPGGVGKTSLARKFVEGSYNPqERLTVGIQhffrKIQLDGRELHVVIWDLGGEHRFRFLAPAFLKGAKGVVYVF 84 
                                    67778888899********99988764345566544110034566699999***************************** PP

                                    ETT-CTTHHHHHHHHHHHCTSGCCTTSEEEEEEE-TTSTTS.S-HHHHHHHTTGGGSSSSSSEEEEEEBTTTTBTHHHHH CS
                            Arf  90 DsadreRleeakeeLkalleeeelkevallvlaNKqDlpea.lseeelrellgleelkgkrkleiqkcsavkgeglkegl 168
                                    D + +e + e   e ++ ++e+ l +v+ ++++NK Dl+e  +   +l+++ +l+    k  le +++sa +g  ++e++
  gi|119718998|ref|YP_919493.1|  85 DLTREETFLEID-EWRK-ITESVLGKVPSILIGNKADLEEYrIVPYNLAREYALS----KGFLEYFEVSARTGARVEEAF 158
                                    ******999986.5666.56889***************87413344444433333....444566666666666666666 PP

                                    H CS
                            Arf 169 e 169
                                     
  gi|119718998|ref|YP_919493.1| 159 L 159
                                    5 PP

>> Gtr1_RagA  Gtr1/RagA G protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0   2.7e-09     4e-06       1     110 [.       6     110 ..       6     121 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 2.7e-09
                      Gtr1_RagA   1 kvLLmGksgsGKtsm.rsiiFdnylardtlrlgatidveksevrflgnltlnlwDcgGqeafveeylssqkeeifrnvgv 79 
                                    k+ L+G++g GKts+ r+ +   y +++ l++g+    +k ++   ++l++ +wD+gG ++f        +   ++  + 
  gi|119718998|ref|YP_919493.1|   6 KISLCGPGGVGKTSLaRKFVEGSYNPQERLTVGIQHFFRKIQL-DGRELHVVIWDLGGEHRFR-----FLAPAFLKGAKG 79 
                                    6779**********967899999*****999999999999999.5789**********99875.....45678899999* PP

                      Gtr1_RagA  80 liyVfDvesreleedletlkeilealrqysp 110
                                    ++yVfD + +e   +++++++i e +    p
  gi|119718998|ref|YP_919493.1|  80 VVYVFDLTREETFLEIDEWRKITESVLGKVP 110
                                    ********99999999999999888876655 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.7e-06     0.004       2     113 ..       7     116 ..       6     117 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.7e-06
                                    EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETT..EEEEEEECGGCSSHHHHHHHHHHHHHHHHCTSEE CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkg..keielvDtpGliegaseekglgkaflaleeadli 79 
                                    + + G   vGK++L ++ ++     +++  + ++  +++++l+g   +++++D+ G  e  ++ + l+ afl+   a+ +
  gi|119718998|ref|YP_919493.1|   7 ISLCGPGGVGKTSLARKFVEGSYNPQERLTVGIQHFFRKIQLDGreLHVVIWDLGG--E--HRFRFLAPAFLK--GAKGV 80 
                                    7899****************98888888888888888888877733568999****..5..455579999995..689** PP

                                    EEEEETT.....TTCSHHHHHHHHHHHHH.....TTSEEEEEEE CS
                       MMR_HSR1  80 llvvdas.....eeklkpldeeleellee.....akkplilvln 113
                                    ++v+d++              e+ e+++       k p il+ n
  gi|119718998|ref|YP_919493.1|  81 VYVFDLTreetfL--------EIDEWRKItesvlGKVPSILIGN 116
                                    *****98432221........22222211112323456666655 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   6.2e-06    0.0092      28     107 ..       8     114 ..       6     169 .. 0.61

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6.2e-06
                         AAA_16  28 llsGesGvGKsslvrellr.alekd.....ggiflrgkcdql...esa..............ipy.sa.laqalareell 82 
                                     l G+ GvGK+sl+r++ + +++ +     g   ++  +++    +++              + + ++ +++ ++   ++
  gi|119718998|ref|YP_919493.1|   8 SLCGPGGVGKTSLARKFVEgSYNPQerltvG---IQHFFRKIqldGRElhvviwdlggehrfR-FlAPaFLKGAKGVVYV 83 
                                    578**************98766666444441...44444444222222333333333332212.2455577777777777 PP

                         AAA_16  83 rqlldeaesaeleawrekleeala......a 107
                                     +l +e++  e ++wr+  e++l+      +
  gi|119718998|ref|YP_919493.1|  84 FDLTREETFLEIDEWRKITESVLGkvpsilI 114
                                    7777778888889998888888775544441 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   2.7e-05     0.041       3      23 ..       9      29 ..       7     106 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.7e-05
                                   EESSTTSSHHHHHHHHHHHHT CS
                            AAA  3 lyGppGtGKTllakavakelg 23
                                   l+Gp G+GKT+la+  ++ + 
  gi|119718998|ref|YP_919493.1|  9 LCGPGGVGKTSLARKFVEGSY 29
                                   89************9998863 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.4e-05     0.051       9      28 ..       8      27 ..       6      68 .. 0.87
   2 ?   -2.4   0.0       3.6   5.4e+03     120     134 ..     106     121 ..      81     123 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.4e-05
                         AAA_22  9 vvtGesGtGKTtllrrlleq 28
                                    ++G+ G+GKT l+r+++e 
  gi|119718998|ref|YP_919493.1|  8 SLCGPGGVGKTSLARKFVEG 27
                                   69***************986 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.6
                         AAA_22 120 rkgvqliLvGtp.elr 134
                                      +v+ iL+G   +l+
  gi|119718998|ref|YP_919493.1| 106 LGKVPSILIGNKaDLE 121
                                    3456667777666665 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   6.1e-05     0.091       4      98 ..       9     122 ..       6     146 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.1e-05
                                    EE--SSSSHHHHHHHGGGGB..S--EEEEE--TT--HHHHH--B--.................--------......... CS
                          AAA_5   4 LvGppGtgKselaerlaaal..nreveyvqltrdtteedlkgrreik........ngttslvdsplvraar......... 64 
                                    L Gp G+gK++la+++ +     +e ++v ++ + ++ +l gr            + + ++   ++ + a+         
  gi|119718998|ref|YP_919493.1|   9 LCGPGGVGKTSLARKFVEGSynPQERLTVGIQHFFRKIQLDGREL-HvviwdlggEHRFRFLAPAFLKGAKgvvyvfdlt 87 
                                    89**************99888999999999999999999987632.2235644344444444444444555788888888 PP

                                    .G-SEEEEESGGG--HHHHHHHHHHHHSSEEE..- CS
                          AAA_5  65 .egeilvlDEveraesevlnsLlslleerrlllee 98 
                                     e   l +DE  ++  +vl+++ s+l  ++ +lee
  gi|119718998|ref|YP_919493.1|  88 rEETFLEIDEWRKITESVLGKVPSILIGNKADLEE 122
                                    77777888888888888888887777666666555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   5.1e-05     0.077       3      23 ..       5      28 ..       3      46 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.1e-05
                         AAA_24  3 lkiliyGpsgiGKTtlakel...g 23
                                   +ki + Gp g+GKT+la+++    
  gi|119718998|ref|YP_919493.1|  5 VKISLCGPGGVGKTSLARKFvegS 28
                                   6999***************96542 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   8.3e-05      0.12      23      42 ..       7      26 ..       2      42 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8.3e-05
                                   EEEEESTTSSHHHHHHHHCC CS
                         NB-ARC 23 valvGmgGvGKttlakqiln 42
                                   ++l G gGvGKt la++ ++
  gi|119718998|ref|YP_919493.1|  7 ISLCGPGGVGKTSLARKFVE 26
                                   89*************99876 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00012      0.18       1      21 [.       7      27 ..       7     125 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00012
                         AAA_18  1 IlltGtpGvGKttlakeLskr 21
                                   I l+G+ GvGKt+la+   + 
  gi|119718998|ref|YP_919493.1|  7 ISLCGPGGVGKTSLARKFVEG 27
                                   679*************98554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1242.07
//
Query:       gi|119718999|ref|YP_919494.1|  [L=398]
Description: aminotransferase, class I and II [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.6e-75  252.0   0.0    1.1e-74  251.8   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
      1e-08   34.9   0.0    1.4e-08   34.4   0.0    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    1.7e-06   26.8   0.0    2.7e-06   26.2   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
      5e-06   25.7   0.0      1e-05   24.7   0.0    1.4  1  Aminotran_5      Aminotransferase class-V
  ------ inclusion threshold ------
      0.027   13.2   0.0      0.036   12.8   0.0    1.2  1  OKR_DC_1         Orn/Lys/Arg decarboxylase, major domain


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  251.8   0.0     3e-78   1.1e-74       2     363 .]      37     392 ..      36     392 .. 0.96

  Alignments for each domain:
  == domain 1  score: 251.8 bits;  conditional E-value: 3e-78
                                    EEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHH CS
                  Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagali 81 
                                    dv+ +g++++++     ++p+v+ ++k+  ++ +++n ygp+ g pel+ea+a+f+++++++++k+e +v v+ Ga+++i
  gi|119718999|ref|YP_919494.1|  37 DVVSFGIGQPDFQ----PPPHVISEAKK--AMDEGFNGYGPSLGMPELREAIASFVSEEYGVDVKAE-EVAVTVGAKSAI 109
                                    7999*********....**********9..*************************************.************ PP

                                    HHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT CS
                  Aminotran_1_2  82 ealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPt 161
                                     +++  l l+pgde+++pdp+y+ y+ ++r +g++ v  +l+  +++++++e++e++++       kt++i+++ p NP 
  gi|119718999|ref|YP_919494.1| 110 FMAMISL-LEPGDEVIIPDPSYPLYESVARFAGAKPVFLRLHRGNGYKVTFEEVEKLVTP------KTRMIVLNYPENPV 182
                                    *******.***************************************************9......************** PP

                                    --B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHH CS
                  Aminotran_1_2 162 GtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilgnaavvs 241
                                    Gt ++  ++e+l+d+  k+++++++De+Y +fv++++ + +t+ + + ++++  v+++sK fG++G+R+Gy+++n++++s
  gi|119718999|ref|YP_919494.1| 183 GTTMDQRDVEELVDFSAKRGIVVLSDEIYDHFVYEKKHF-STLQTSSWRDAVYYVNGFSKTFGMTGWRLGYVISNKELIS 261
                                    ***********************************6655.66999999999***************************** PP

                                    HHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS.TEEEECCSCSSEEEEEETHH... CS
                  Aminotran_1_2 242 qlrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLael.glkvlasqsgmflltdlsae... 315
                                     l  ++++++s   +  q a+a+al+  l    +++   + + krr+ ++ e+ ++ g+kv++++++++ + d+++    
  gi|119718999|ref|YP_919494.1| 262 KLSVVANNIYScpVTFEQIAAAKALKEGLS---WFKPILEGYRKRRDLIYREFLSIkGVKVVKPEGAFYIFPDFTEVire 338
                                    ***********9778888888888888885...********************999************************ PP

                                    ....CHHHHHHHHHHTCTEEEEEGGGGTS...TTEEEEECTTS-HHHHHHHHHHH CS
                  Aminotran_1_2 316 ....takelskkLleevgvyvtpgtsftv...pgrlRitvAglteeeleelveal 363
                                        ++ el++ Llee gv+v+pgt f +   +g+lR+++ +++e+++ + + ++
  gi|119718999|ref|YP_919494.1| 339 kglkNERELADRLLEERGVVVLPGTAFPKeggKGHLRFSF-AVSENDIVRGIARI 392
                                    ****************************************.99999988777765 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   0.0     4e-12   1.4e-08      42     144 ..      99     208 ..      61     210 .. 0.83

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 4e-12
                                    EEESSHHH.HHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-T.TTSSB-GGGCGGG--TTEEEEE... CS
                DegT_DnrJ_EryC1  42 iavssGta.AlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvdp.dtynidpaaieaaitertkaIl... 116
                                    +av+ G + A+ +a+    ++pgdeVI+p  ++    ++++ +gakpvf+  ++ + y ++ +++e+++t++t+ I+   
  gi|119718999|ref|YP_919494.1|  99 VAVTVGAKsAIFMAMI-SLLEPGDEVIIPDPSYPLYESVARFAGAKPVFLRLHRgNGYKVTFEEVEKLVTPKTRMIVlny 177
                                    4555555405555544.45789*****************************9863789******************9666 PP

                                    ...EB-GGGB---HHHHHHHHHHCT-EEEEE CS
                DegT_DnrJ_EryC1 117 ...pVhlyGqvadmdalkaiaakhglkvieD 144
                                       pV +  +  d+++l + +ak g++v++D
  gi|119718999|ref|YP_919494.1| 178 penPVGTTMDQRDVEELVDFSAKRGIVVLSD 208
                                    5556777777779999************998 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   7.5e-10   2.7e-06      67     174 ..      96     209 ..      88     217 .. 0.79

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 7.5e-10
                                    -SEEEEESSHHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHH.TTCEEEEEST..TSHHHHHHHCCTTEEEEEE CS
                Cys_Met_Meta_PP  67 geaalavssGmaAiaaailallkaGdeivvsddlYggtqrllkkvlkk.lgievkfvdt..sdleelekaikentklvyl 143
                                    +e++ ++    +Ai++a+++ll+ Gde+++ d  Y   +++ +    k + ++ +  +     +ee+ek ++++t+++ l
  gi|119718999|ref|YP_919494.1|  96 AEEVAVTVGAKSAIFMAMISLLEPGDEVIIPDPSYPLYESVARFAGAKpVFLRLHRGNGykVTFEEVEKLVTPKTRMIVL 175
                                    455556666689******************99888777666666655546666666665336789*************99 PP

                                    ESS-TT...TT----HHHHHHHHHHTT-EEEEEG CS
                Cys_Met_Meta_PP 144 Etptnp...llkvvDiekiaklakkagvlvvvDn 174
                                      p np   +++  D+e+++++  k+g++v+ D 
  gi|119718999|ref|YP_919494.1| 176 NYPENPvgtTMDQRDVEELVDFSAKRGIVVLSDE 209
                                    9998884435777889999999999999999886 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   2.8e-09     1e-05      47     175 ..      77     208 ..      72     211 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 2.8e-09
                                    HHHHHHHHHHT-S.....TGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEB CS
                    Aminotran_5  47 earekvaelinae.....seeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipl 121
                                    e re +a ++  e     ++ee+ +t G+ +ai ++++sl   l+pgde+++ +  +       + +a++ gak ++++l
  gi|119718999|ref|YP_919494.1|  77 ELREAIASFVSEEygvdvKAEEVAVTVGAKSAIFMAMISL---LEPGDEVIIPDPSYP----LYESVARFAGAKPVFLRL 149
                                    5566666665433111123699******************...*********987654....478999**********99 PP

                                    ETTSCBE..GGGHHHH--TTEEEEEEESBETTTTE...B--HHHHHHHHHHTT-EEEEE CS
                    Aminotran_5 122 deegeld..ldelekllnektklvaithvsnvtGt...iqpveeigklakkkgalvlvD 175
                                     ++  ++   +e+ekl+++kt+++ ++  +n  Gt     +vee+++   k+g++vl D
  gi|119718999|ref|YP_919494.1| 150 HRGNGYKvtFEEVEKLVTPKTRMIVLNYPENPVGTtmdQRDVEELVDFSAKRGIVVLSD 208
                                    8776554449*************************544457888998888999999988 PP

>> OKR_DC_1  Orn/Lys/Arg decarboxylase, major domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     1e-05     0.036      85     142 ..      99     157 ..      80     221 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1e-05
                                    EEESSHHHHHHHHHHHHH--TTEEEEEESS--HHHHHHHHHS-EEEEEE--E.B-TTS- CS
                       OKR_DC_1  85 yfvvnGTsssnkvvlnavltpgdlvlvdRNcHKSiehalvlsgatPvylepe.rnalgi 142
                                      v++G  s++ + + ++l+pgd v+++       e    ++ga+Pv+l+ +  n + +
  gi|119718999|ref|YP_919494.1|  99 VAVTVGAKSAIFMAMISLLEPGDEVIIPDPSYPLYESVARFAGAKPVFLRLHrGNGYKV 157
                                    57899***************************9999999**********9984466655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2610.27
//
Query:       gi|119719000|ref|YP_919495.1|  [L=160]
Description: hypothetical protein Tpen_0082 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       904  (0.0504211); expected 358.6 (0.02)
Passed bias filter:                      694  (0.0387082); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1114.59
//
Query:       gi|119719001|ref|YP_919496.1|  [L=122]
Description: hypothetical protein Tpen_0083 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 963.87
//
Query:       gi|119719002|ref|YP_919497.1|  [L=44]
Description: hypothetical protein Tpen_0084 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 318.56
//
Query:       gi|119719003|ref|YP_919498.1|  [L=613]
Description: glucosamine--fructose-6-phosphate aminotransferase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      8e-48  161.6   0.2    4.1e-26   91.4   0.7    2.2  2  SIS       SIS domain
    6.1e-23   81.5   0.0    1.6e-22   80.1   0.0    1.7  1  GATase_6  Glutamine amidotransferase domain
    1.9e-18   66.5   0.0    5.6e-18   65.0   0.0    1.9  1  GATase_7  Glutamine amidotransferase domain
     0.0013   18.7   0.4     0.0046   17.0   0.0    2.1  3  SIS_2     SIS domain
     0.0035   16.3   0.0     0.0066   15.4   0.0    1.4  1  GATase_4  Glutamine amidotransferases class-II


Domain annotation for each model (and alignments):
>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.4   0.7   1.1e-29   4.1e-26       1     126 [.     293     417 ..     293     422 .. 0.96
   2 !   67.7   0.0   2.4e-22   8.5e-19       3     130 ..     468     595 ..     466     596 .. 0.94

  Alignments for each domain:
  == domain 1  score: 91.4 bits;  conditional E-value: 1.1e-29
                                    HHCTSSEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHHTT CS
                            SIS   1 lLakakriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelakerg 80 
                                    lL++a+ iyv+++Gtsy++ +++al  ++i+g+ v    +se   g+++ ++e+d ++++s+sget d+++a +  kerg
  gi|119719003|ref|YP_919498.1| 293 LLSDAEVIYVVASGTSYHASLYFALLTMKIAGKKVIPLISSE-YAGYVSSASERDALLAVSQSGETIDTLMAMRAFKERG 371
                                    5999**************************************.6666********************************* PP

                                    SEEEEEESSTTSHHHHHSSEEEEEEEECHCSSSHCHHHHHHHHHHH CS
                            SIS  81 akiiaITdskgsplareadlalyinaepetlvastksltaqlaald 126
                                    ++++++T+  gs ++re+d+ +y+ a+pe++va+tk++t+ql+al 
  gi|119719003|ref|YP_919498.1| 372 VRTVSLTNVIGSVISRESDHQVYMKAGPEIGVAATKTFTVQLTALT 417
                                    ******************************************9986 PP

  == domain 2  score: 67.7 bits;  conditional E-value: 2.4e-22
                                    CTSSEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHH.HHHHTTS CS
                            SIS   3 akakriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaae.lakerga 81 
                                    +++ + y+l +G   +ia+e+alkl+ei+++++e+++a+e khg++al++++ +v+++s  +e  ++++ +  ++++rga
  gi|119719003|ref|YP_919498.1| 468 SEKSSAYYLSRGLGLPIALEGALKLKEIAYVHAEGYPAGESKHGPIALVERGFPVVFVSVERELEKKLLGNVeEMRARGA 547
                                    566799*****************************************************88888888887777******* PP

                                    EEEEEESSTTSHHHHHSSEEEEEEEECHCSSSHCHHHHHHHHHHHHHHH CS
                            SIS  82 kiiaITdskgsplareadlalyinaepetlvastksltaqlaaldalav 130
                                     +i++   ++s l  + d  + +++++e+ v+++ ++++ql+a++ ++ 
  gi|119719003|ref|YP_919498.1| 548 YTIGVV-PQDSELRGHFDREVVVPSSDEVAVPILATIPLQLVAYYSAVE 595
                                    ******.999**********************************98875 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.1   0.0   4.5e-26   1.6e-22       4     134 .]      66     203 ..      62     203 .. 0.91

  Alignments for each domain:
  == domain 1  score: 80.1 bits;  conditional E-value: 4.5e-26
                       GATase_6   4 sglaslvedevalaHvRlaivglaeeegaqPfpsedgrlllvhNGeiynykelreelpalkglafrsrsDtevllall.. 81 
                                    ++ ++  +++++++H+R+a++g +++e a+P +  +grl++vhNG  +ny+el+  l++ +g+ frs++Dtev ++l+  
  gi|119719003|ref|YP_919498.1|  66 AKCLKCLHGHTGVGHTRWATHGPPTDENAHPHVDCTGRLAVVHNGILENYRELKSWLQE-RGHVFRSNTDTEVFAHLVee 144
                                    55566678889*************88888******************************.****************9977 PP

                       GATase_6  82 ..eelG......eevlerlrGmfafaiwdk.rentlilardrlgvkplyyavdesglafase 134
                                      +e G      ++ l+++rG +a a++++ +++++++ar +   +pl++++ ++++ +as+
  gi|119719003|ref|YP_919498.1| 145 ylKEEGdffkafKKSLKAIRGSYALAVVTSlEPRKIFFARKH---SPLVIGIADGKMFVASD 203
                                    7744457999999999***********************887...9*********9999996 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.0   0.0   1.6e-21   5.6e-18       9     122 ..      90     208 ..      80     209 .. 0.91

  Alignments for each domain:
  == domain 1  score: 65.0 bits;  conditional E-value: 1.6e-21
                       GATase_7   9 seagaQPmvssedgrlvivfnGeiyNykelreeLeakghrfrtksDtevllallea.........ewgeealerlnGmfA 79 
                                    ++++a P v + +grl++v+nG + Ny+el++ L+++gh fr+++Dtev ++l+e+         +  ++ l+ ++G++A
  gi|119719003|ref|YP_919498.1|  90 TDENAHPHV-DCTGRLAVVHNGILENYRELKSWLQERGHVFRSNTDTEVFAHLVEEylkeegdffKAFKKSLKAIRGSYA 168
                                    466788999.689****************************************************99************* PP

                       GATase_7  80 faiwdeeek.rlllaRDrlGikPLyygedkgdallfaSelkall 122
                                    +a++++ e  +++ aR +    PL +g ++g ++++aS + a+l
  gi|119719003|ref|YP_919498.1| 169 LAVVTSLEPrKIFFARKH---SPLVIGIADG-KMFVASDIPAFL 208
                                    ****9765449******5...9*******86.********9987 PP

>> SIS_2  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.98   3.5e+03      32      64 ..     294     326 ..     291     332 .. 0.76
   2 !   17.0   0.0   1.3e-06    0.0046     100     137 ..     341     378 ..     330     379 .. 0.92
   3 ?   -3.9   0.0       3.6   1.3e+04     123     137 ..     539     553 ..     537     553 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.98
                                    HHTT--EEEEESGGGHHHHHHTSSSTT-BTTEE CS
                          SIS_2  32 lenggkvlvfGsGhSaalaeelaaragglaefe 64 
                                    l++ ++++v  sG S  ++ ++a    ++a+ +
  gi|119719003|ref|YP_919498.1| 294 LSDAEVIYVVASGTSYHASLYFALLTMKIAGKK 326
                                    566789999999999998888887777777655 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 1.3e-06
                                    T--TT-EEEEE-SS--SHHHHHHHHHHHHHT-EEEEEE CS
                          SIS_2 100 rlkpgDvLlviSnsGnnavvveaaeaakergmkviAlt 137
                                     ++++D+Ll +S+sG+    + a++a+kerg++++ lt
  gi|119719003|ref|YP_919498.1| 341 SASERDALLAVSQSGETIDTLMAMRAFKERGVRTVSLT 378
                                    57899*******************************99 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 3.6
                                    HHHHHHHT-EEEEEE CS
                          SIS_2 123 aeaakergmkviAlt 137
                                    +e+ ++rg+++i+++
  gi|119719003|ref|YP_919498.1| 539 VEEMRARGAYTIGVV 553
                                    578999******985 PP

>> GATase_4  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.8e-06    0.0066      69     143 ..      72     147 ..      39     169 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.8e-06
                       GATase_4  69 iksknvvaHiRkatqGevklenthpFvRelwgrewifAHnGdlkeykpkl....egrfePvGsTDsElafCelleelas 143
                                    ++ +  v H R at+G  ++en+hp v    gr     HnG l++y++      e  +    +TD+E +f +l+ee  +
  gi|119719003|ref|YP_919498.1|  72 LHGHTGVGHTRWATHGPPTDENAHPHVD-CTGRLA-VVHNGILENYRELKswlqERGHVFRSNTDTE-VFAHLVEEYLK 147
                                    6778889******************995.566654.56*******9886655542233334688888.46777666544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (613 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.48
# Mc/sec: 3856.94
//
Query:       gi|119719004|ref|YP_919499.1|  [L=377]
Description: sugar-phosphate nucleotidyl transferase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-11   42.7   5.0    6.1e-06   25.7   0.5    4.1  5  Hexapep          Bacterial transferase hexapeptide (six repea
    3.2e-06   27.6   0.0      6e-06   26.7   0.0    1.4  1  NTP_transf_3     MobA-like NTP transferase domain
     0.0019   17.8   0.0     0.0026   17.4   0.0    1.1  1  NTP_transferase  Nucleotidyl transferase
  ------ inclusion threshold ------
      0.011   15.5   0.5       0.23   11.2   0.0    3.0  3  Hexapep_2        Hexapeptide repeat of succinyl-transferase
      0.035   13.9   0.0      0.061   13.1   0.0    1.4  1  Glycos_transf_2  Glycosyl transferase family 2
      0.043   13.7   0.0      0.057   13.3   0.0    1.1  1  CTP_transf_3     Cytidylyltransferase


Domain annotation for each model (and alignments):
>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   9.7e-07    0.0029       2      36 .]     218     252 ..     217     252 .. 0.96
   2 !   25.7   0.5   2.1e-09   6.1e-06       3      35 ..     237     269 ..     236     270 .. 0.94
   3 !   15.4   0.0   3.8e-06     0.011       2      35 ..     254     287 ..     253     288 .. 0.94
   4 ?   -2.8   0.0       2.1   6.2e+03       8      17 ..     306     315 ..     305     320 .. 0.55
   5 !    4.5   0.2      0.01        30      22      35 ..     356     369 ..     348     371 .. 0.60

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 9.7e-07
                                    EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEES CS
                        Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvigg 36 
                                    +vI+ ++ + p av+ g V++ ++++I +++v++g
  gi|119719004|ref|YP_919499.1| 218 SVIHPGARVSPLAVLEGCVIVEEGAYIDHYAVVRG 252
                                    79******************************986 PP

  == domain 2  score: 25.7 bits;  conditional E-value: 2.1e-09
                                    EEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                        Hexapep   3 vIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                    +++++++I+++av++g++ IG+nv +g g+ ++
  gi|119719004|ref|YP_919499.1| 237 IVEEGAYIDHYAVVRGPAYIGRNVLVGKGAFVR 269
                                    789**************************9986 PP

  == domain 3  score: 15.4 bits;  conditional E-value: 3.8e-06
                                    EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                        Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                    + IG nvl+g++a +++ + + +++++ga++ ++
  gi|119719004|ref|YP_919499.1| 254 AYIGRNVLVGKGAFVREYTSLEEGSTVGAFSEVK 287
                                    78*****************************997 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 2.1
                                    EEE-TTEEEE CS
                        Hexapep   8 vlIgpfavig 17 
                                    +++gp++v  
  gi|119719004|ref|YP_919499.1| 306 SVLGPYSVAE 315
                                    4556666655 PP

  == domain 5  score: 4.5 bits;  conditional E-value: 0.01
                                    E-TTEEEETTEEEE CS
                        Hexapep  22 IGdnvkIgagvvig 35 
                                    I  ++++g+gv i+
  gi|119719004|ref|YP_919499.1| 356 IAAGSVVGPGVLIH 369
                                    33444444444443 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0     2e-09     6e-06      14     126 ..       8     123 ..       2     220 .. 0.74

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 2e-09
                                    TTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSHCHHHH....HHTTCTS-EEE-T.TSS-SHHHHHHHHHHHH.SSSC CS
                   NTP_transf_3  14 gdKallplggkpllervldalraagvdevvvvggdeevla....alarlgvrvvede.dpgkgplaslaaalraaadada 88 
                                     +K +l++ g p++ + l +l +a  ++v++v+++e   +     l+++++  ve + +pg+    ++++a + + ++++
  gi|119719004|ref|YP_919499.1|   8 YHKFMLKISGNPIFFYPLSSLLQAAGQRVILVVDREMQIDwvkeFLREKNYAHVEVRvQPGESLEDAFLTATKDV-SDEW 86 
                                    389********************9779******998555511114555566555554134778888888888888.9*** PP

                                    EEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESSSE CS
                   NTP_transf_3  89 vlvlacDmPlltpelverllaaaaasgadvvvptyege 126
                                    +l++ +D++  +pe+++ l++ +++s+   + +  + e
  gi|119719004|ref|YP_919499.1|  87 FLLVFGDVVA-PPEALRMLMETYEESQRPSALVIPRAE 123
                                    ********87.9***********977754444333333 PP

>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   8.6e-07    0.0026      14     152 ..       2     131 ..       1     140 [. 0.76

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 8.6e-07
                                    TTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEEEESS--BGGHHHHHT CS
                NTP_transferase  14 wPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlialepegkgtAdAvala 93 
                                    +PL    +k ++ + g+ +++ ++ls l+++  +++i+v+ +e +    +++ +++++  +v++ ++p g+ + dA++ a
  gi|119719004|ref|YP_919499.1|   2 RPLNEGYHKFMLKISGN-PIFFYPLSSLLQAAGQRVILVVDREMQIDWVKEFLREKNYA-HVEVRVQP-GESLEDAFLTA 78 
                                    67777777777777777.************99999999999998888777777777777.78888887.66799999999 PP

                                    HHHHTTSSE..EEEEETTEEEEST.THHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEE CS
                NTP_transferase  94 aelledeksdelvlvLggDhlikd.ayeeavkkaiekaakgtvtfgivpveeateyGvie 152
                                     + + de     +lv+ gD++    a++ +++  +e+++    + ++ p++e + yGv+ 
  gi|119719004|ref|YP_919499.1|  79 TKDVSDEWF---LLVF-GDVVAPPeALRMLMETYEESQR---PSALVIPRAEMSTYGVAY 131
                                    998888884...5555.6677766255555555555555...788888999999***975 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1      0.86   2.6e+03      22      26 ..     233     237 ..     218     245 .. 0.48
   2 ?   11.2   0.0   7.9e-05      0.23       1      28 [.     253     282 ..     253     282 .. 0.91
   3 ?    0.9   0.1      0.13     4e+02      23      32 ..     359     368 ..     355     369 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.86
                                    TT-EE CS
                      Hexapep_2  22 dncvv 26 
                                    ++cv+
  gi|119719004|ref|YP_919499.1| 233 EGCVI 237
                                    44443 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 7.9e-05
                                    .EEE-TT-EE-TT-EE..SEEE-TT-EE-T CS
                      Hexapep_2   1 pviIGdnCliGanagi..GvslGdncvvga 28 
                                    p  IG n+l+G+ a +   +sl+++++vga
  gi|119719004|ref|YP_919499.1| 253 PAYIGRNVLVGKGAFVreYTSLEEGSTVGA 282
                                    678************9756*********98 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.13
                                    T-EE-TT-EE CS
                      Hexapep_2  23 ncvvgaGvvi 32 
                                    ++vvg+Gv i
  gi|119719004|ref|YP_919499.1| 359 GSVVGPGVLI 368
                                    6788888866 PP

>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   2.1e-05     0.061      30     118 ..      35     121 ..      25     166 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.1e-05
                                    EEEEEEES-SSCHHHHHGGGCH..C-TTEEEEEESSS-HHHHHHHHHHHH--SSEEEEEESSEEE-TTHHHHHHHHHHH. CS
                Glycos_transf_2  30 eiivvDDgStDetveileelak..edprvrvirreenvGkagalnaglraatgdyilflDaDdepdpdwleklvealekd 107
                                    ++i+v D +     ++++e+ +  ++ +v v  ++ ++ +  a+ ++ + ++ +++l++  D++ +p+ l+ l+e +e+ 
  gi|119719004|ref|YP_919499.1|  35 RVILVVDRE--MQIDWVKEFLRekNYAHVEVRVQP-GESLEDAFLTATKDVSDEWFLLVFGDVVAPPEALRMLMETYEES 111
                                    445555554..344555555555589999999999.66****************************************96 PP

                                    TTCEEEEEEEE CS
                Glycos_transf_2 108 gadvvlgqrpr 118
                                    ++   +  +pr
  gi|119719004|ref|YP_919499.1| 112 QR-PSALVIPR 121
                                    44.34444444 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.9e-05     0.057      16     121 ..      10     114 ..       8     140 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.9e-05
                                    GGGSEETTEEHHHHHHHHHHHTTTTSEEEEEES-HHHHHHHHHTT.....SEEEE--TTCSSHHHHHHHHHHHHTTT.TT CS
                   CTP_transf_3  16 KnlldlggkpliayvleaalkskafekvivaTDseeiknvakefg.....asvlvtrsslesdterflevvkaflmsene 90 
                                    K +l+++g+p+ +y+l  +l+ +a ++vi+  D e   + +kef      a v v+ ++ es  ++fl + k+++ +   
  gi|119719004|ref|YP_919499.1|  10 KFMLKISGNPIFFYPLSSLLQ-AAGQRVILVVDREMQIDWVKEFLreknyAHVEVRVQPGESLEDAFLTATKDVSDE--- 85 
                                    889******************.777******************9888889899999999999999999999999988... PP

                                    SEEEEE-TT-TT--HHHHHHHHHHHHHSTTS CS
                   CTP_transf_3  91 eiivnlqGdnPllqeevikkaietlkenqed 121
                                       + + Gd    ++e+++ ++et++e+q +
  gi|119719004|ref|YP_919499.1|  86 -WFLLVFGDV-VAPPEALRMLMETYEESQRP 114
                                    .888888775.46777888888888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2455.18
//
Query:       gi|119719005|ref|YP_919500.1|  [L=374]
Description: glycosyl transferase family protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.8e-21   75.0   0.8    2.3e-20   73.5   0.8    1.7  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    1.2e-18   67.5   0.1    1.9e-18   66.8   0.1    1.4  1  Glycos_transf_2  Glycosyl transferase family 2
    2.3e-14   53.7  10.2    9.9e-14   51.7  10.2    1.9  1  Glyco_trans_2_3  Glycosyl transferase family group 2
    3.8e-09   36.3   0.0    5.9e-09   35.6   0.0    1.3  1  Glyco_transf_21  Glycosyl transferase family 21
     0.0029   17.3   0.0     0.0049   16.6   0.0    1.3  1  Glyco_tranf_2_5  Glycosyltransferase like family
  ------ inclusion threshold ------
       0.02   14.4   0.2      0.041   13.4   0.1    1.6  1  Glyco_tranf_2_2  Glycosyltransferase like family 2


Domain annotation for each model (and alignments):
>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.5   0.8   7.8e-24   2.3e-20       3     230 .]       8     224 ..       6     224 .. 0.82

  Alignments for each domain:
  == domain 1  score: 73.5 bits;  conditional E-value: 7.8e-24
                Glyco_tranf_2_3   3 dlavlVptfneedvlgevlesllaqey.prvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralne 81 
                                    +++v+V++++ +++l+++le+l +qe   +vev+vv+de d+e+l  ++e      ++ v+ +v ++   ++gk+ralne
  gi|119719005|ref|YP_919500.1|   8 RVSVIVTVYRHARRLRSLLEALCNQETsFPVEVIVVADEPDEEVLGILRE------KACVKSLVSEN---RRGKVRALNE 78 
                                    59***********************96599*******************9......33466666666...489******* PP

                Glyco_tranf_2_3  82 alravksdlvllvDdDtvvePdt.lkrllqffltpkvgavgtpvfllnrstlvsalgalefaerhlrflaarralgvltl 160
                                    a++  ++d+++++D D+ v+++  ++++  ++  ++ +++  ++ ++ ++     ++++++    ++  +  r ++ + l
  gi|119719005|ref|YP_919500.1|  79 AISLSQGDVLIFLDNDVTVQDRKfVEKIYKWL--QDFDVAEIKKIARVDTFIGKLVYYDYMSFGVASYIFEKRVKRCAGL 156
                                    *******************7665389999**9..5555555555555555555544443322222333333466679*** PP

                Glyco_tranf_2_3 161 nGsgslirrevlkelegldp.lflltdDyelglrlrragfrtayvpgaavrevfpsslkayikqrnRwvyg 230
                                    nG+ ++++r+ lkel   ++ ++++ +D ++g+r   +gfr +y  + +v    pssl +  +qr Rw++g
  gi|119719005|ref|YP_919500.1| 157 NGAAMAFTRKALKEL---GGyRNVVLEDMDIGFRSFFHGFRYKYIWDTEVVVDPPSSLREWLNQRLRWSVG 224
                                    ***************...555679********************************************976 PP

>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.8   0.1   6.5e-22   1.9e-18       1     107 [.      10     113 ..      10     172 .. 0.85

  Alignments for each domain:
  == domain 1  score: 66.8 bits;  conditional E-value: 6.5e-22
                                    EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--S CS
                Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraatg 80 
                                    sv++++y  +  l+ +le+l++q++   +e+ivv D   +e   il+e a    +v+ +  e+++Gk +aln++++ ++g
  gi|119719005|ref|YP_919500.1|  10 SVIVTVYRHARRLRSLLEALCNQETSFPVEVIVVADEPDEEVLGILREKA----CVKSLVSENRRGKVRALNEAISLSQG 85 
                                    8************************************************8....************************** PP

                                    SEEEEEESSEEE-TT.HHHHHHHHHHH. CS
                Glycos_transf_2  81 dyilflDaDdepdpd.wleklvealekd 107
                                    d+++flD D+++++  ++ek++++l++ 
  gi|119719005|ref|YP_919500.1|  86 DVLIFLDNDVTVQDRkFVEKIYKWLQDF 113
                                    **************99********9995 PP

>> Glyco_trans_2_3  Glycosyl transferase family group 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.7  10.2   3.3e-17   9.9e-14       3     192 ..      89     296 ..      87     364 .. 0.71

  Alignments for each domain:
  == domain 1  score: 51.7 bits;  conditional E-value: 3.3e-17
                Glyco_trans_2_3   3 lllDaDtvl.ppdclreiaaelaspevaivqgpvlvmnvanwleelaalffaedhgkdilvrealgrvvpsvGsgaflrr 81 
                                    ++lD D  + ++ ++++i+ +l++   +++ ++ +++ v +++ +l  + +      + ++ ++ +r++ + G+ ++++r
  gi|119719005|ref|YP_919500.1|  89 IFLDNDVTVqDRKFVEKIYKWLQD--FDVAEIKKIAR-VDTFIGKLVYYDYMSFGVASYIFEKRVKRCAGLNGAAMAFTR 165
                                    788999776488999999999976..89999999999.789*********988999999********************* PP

                Glyco_trans_2_3  82 salqevggwdgdessvsEDfdmglrlqrkGyrvrfvpeslvkekspltlraalrQrkRwayGc..el......eklil.. 151
                                    +al+e+gg++     v ED+d+g+r + +G+r  ++ ++ v    p++lr +l+Qr Rw  G+  ++      + +i+  
  gi|119719005|ref|YP_919500.1| 166 KALKELGGYR---NVVLEDMDIGFRSFFHGFRYKYIWDTEVVVDPPSSLREWLNQRLRWSVGAwtWIddyvfhFSKIAsi 242
                                    *********9...89*********************99999*********************855223344443333366 PP

                Glyco_trans_2_3 152 ................................................lvrllgylgsllwsalplhlallllfsllala 183
                                                                                    l                               
  gi|119719005|ref|YP_919500.1| 243 dyalesfaalfamfpggivyasillaeglpllklgllagstvgglfapL------------------------------- 291
                                    6666666665554444444444444444443333333333333333331............................... PP

                Glyco_trans_2_3 184 lvlllllll 192
                                        +++l+
  gi|119719005|ref|YP_919500.1| 292 ----VPVLA 296
                                    ....33333 PP

>> Glyco_transf_21  Glycosyl transferase family 21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.0     2e-12   5.9e-09      13     172 ..      67     222 ..      56     223 .. 0.76

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 2e-12
                Glyco_transf_21  13 vgvnpKvnnllqaleaakydllvisDsdvrvk.pdyLeellaaledpkvglVtslpvgsdakglaaal...eaaflntla 88 
                                    ++ + Kv +l+ a++  + d+l+++D dv+v+ ++++e++ + l+d +v+ +  +   ++ +++ ++l       ++  +
  gi|119719005|ref|YP_919500.1|  67 ENRRGKVRALNEAISLSQGDVLIFLDNDVTVQdRKFVEKIYKWLQDFDVAEIKKI---ARVDTFIGKLvyyDYMSFGVAS 143
                                    445669*9**********************9627888999999999666655555...5666666666200333345556 PP

                Glyco_transf_21  89 gvlqaklsglgfavGksmalrreaLeaiGGfealadeLAeDyalg..kllraaGlkvvlspapiaqtsvprrsslralla 166
                                    +++  ++++    +G++ma++r+aL+++GG++     + eD+ +g    ++   +k +  +++++++     sslr++l+
  gi|119719005|ref|YP_919500.1| 144 YIFEKRVKRCAGLNGAAMAFTRKALKELGGYRN---VVLEDMDIGfrSFFHGFRYKYIWDTEVVVDP----PSSLREWLN 216
                                    666668999999*********************...899******4344555566666666665542....569****** PP

                Glyco_transf_21 167 RqlrWa 172
                                    + lrW+
  gi|119719005|ref|YP_919500.1| 217 QRLRWS 222
                                    *****8 PP

>> Glyco_tranf_2_5  Glycosyltransferase like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.6e-06    0.0049      39      81 ..      70     111 ..      57     116 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.6e-06
                Glyco_tranf_2_5  39 ksiaeaynkalsasdakykvYlhqDvliinkdfikdlleiFkk 81 
                                        +a n+a+s s+  ++++l++Dv +  ++f++++ + + +
  gi|119719005|ref|YP_919500.1|  70 RGKVRALNEAISLSQGDVLIFLDNDVTVQDRKFVEKIYKWL-Q 111
                                    5567899******************************9988.3 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   1.4e-05     0.041       1     114 [.      10     118 ..      10     187 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.4e-05
                Glyco_tranf_2_2   1 svviplraseer.hyieerv.lqkakyydeeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNrGas 78 
                                    sv++ ++ + +r   + e +  q++++    +e+ivv d   e++l  ++     + lv+ +    +  ++ +a N  +s
  gi|119719005|ref|YP_919500.1|  10 SVIVTVYRHARRlRSLLEALcNQETSF---PVEVIVVADEPDEEVLGILREKACVKSLVS-E----NRRGKVRALNEAIS 81 
                                    688888888776234555663566677...89*****99888887777766666666666.3....3469********** PP

                Glyco_tranf_2_2  79 kaesdlvlFlDaDcfissDkf.ekilklitikklren 114
                                     +++d+++FlD D  +   kf eki k ++  ++ e+
  gi|119719005|ref|YP_919500.1|  82 LSQGDVLIFLDNDVTVQDRKFvEKIYKWLQDFDVAEI 118
                                    *************999888775788776665555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2333.89
//
Query:       gi|119719006|ref|YP_919501.1|  [L=164]
Description: hypothetical protein Tpen_0088 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.035   14.1   0.2      0.053   13.5   0.2    1.5  1  Cas6      Cas6 Crispr


Domain annotation for each model (and alignments):
>> Cas6  Cas6 Crispr
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2   2.9e-06     0.053      84     138 ..      95     149 ..      33     161 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.9e-06
                           Cas6  84 ghkl.rlgipklrllepastLkarlVvikgaedeeaFleavqrqLealeikgkkal 138
                                    +++l rl + +l+l+++as ++ r+V+++ a ++++Fle+v+++++ l ++++ ++
  gi|119719006|ref|YP_919501.1|  95 DESLqRLLEEDLKLISTASRIFERVVALTPALEPKEFLEKVNEAIS-LVVEAENVI 149
                                    54442688999******************************99874.555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 1031.19
//
Query:       gi|119719007|ref|YP_919502.1|  [L=54]
Description: hypothetical protein Tpen_0089 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00081   19.4   1.1     0.0011   18.9   1.1    1.2  1  DZR             Double zinc ribbon
     0.0017   18.2   4.0       0.33   10.9   0.5    2.2  2  Zn_ribbon_SprT  SprT-like zinc ribbon domain
     0.0018   18.3   0.5      0.002   18.1   0.5    1.0  1  HypA            Hydrogenase/urease nickel incorporation, meta
     0.0033   18.2   1.1     0.0035   18.0   1.1    1.0  1  zinc_ribbon_15  zinc-ribbon family
      0.007   16.0   3.5       0.28   10.9   0.5    2.2  2  zinc_ribbon_2   zinc-ribbon domain
     0.0081   16.1   2.6       0.03   14.3   0.0    2.0  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
  ------ inclusion threshold ------
       0.02   14.8   2.1          1    9.4   0.2    2.1  2  Nudix_N_2       Nudix N-terminal
       0.02   15.0   1.1      0.085   13.0   1.1    1.8  2  Zn-ribbon_8     Zinc ribbon domain
      0.022   15.0   0.2       0.04   14.2   0.2    1.4  1  zinc_ribbon_9   zinc-ribbon
      0.026   14.8   1.8        3.6    7.9   0.0    2.2  2  zf-LITAF-like   LITAF-like zinc ribbon domain
      0.033   14.4   0.4      0.037   14.2   0.4    1.1  1  PknG_rubred     Protein kinase G rubredoxin domain
      0.039   14.1   0.8        1.7    8.8   0.1    2.1  2  DUF1272         Protein of unknown function (DUF1272)
      0.047   13.7   1.6      0.048   13.7   0.0    1.8  2  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
      0.074   12.7   1.8        4.2    7.0   0.0    2.0  2  TackOD1         Thaumarchaeal output domain 1
      0.098   12.1   3.7       0.38   10.2   0.6    2.1  2  zf-ribbon_3     zinc-ribbon domain
       0.12   12.8   2.8       0.97    9.8   2.8    1.9  1  GFA             Glutathione-dependent formaldehyde-activating
       0.12   12.5   2.9       0.15   12.2   0.2    2.1  2  zf-ACC          Acetyl-coA carboxylase zinc finger domain
       0.15   12.1   2.6        2.3    8.3   2.5    2.0  1  CpXC            CpXC protein
       0.16   12.0   2.0       0.54   10.4   2.0    1.8  1  zf-ANAPC11      Anaphase-promoting complex subunit 11 RING-H2
       0.19   11.9   3.5        2.3    8.4   0.1    2.2  2  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 


Domain annotation for each model (and alignments):
>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   1.1   1.2e-06    0.0011      12      38 ..       7      45 ..       2      47 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.2e-06
                            DZR 12 arfCseCgtklkavaa.............edrCpsCgekv 38
                                     +C +C+++++ +++             + +Cp+Cg+ v
  gi|119719007|ref|YP_919502.1|  7 TAYCVKCRKQVE-MKNpqqvtlkngrlayKGTCPNCGTTV 45
                                   579*******96.444588******************976 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.2    0.0018       1.6       1      14 [.       4      17 ..       4      19 .. 0.83
   2 !   10.9   0.5   0.00037      0.33       3      15 ..      34      46 ..      33      49 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0018
                 Zn_ribbon_SprT  1 kkyvYrCtgCgrey 14
                                   +k +++C+ C++++
  gi|119719007|ref|YP_919502.1|  4 QKITAYCVKCRKQV 17
                                   6889******9775 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00037
                 Zn_ribbon_SprT  3 yvYrCtgCgreyt 15
                                   y+ +C++Cg++++
  gi|119719007|ref|YP_919502.1| 34 YKGTCPNCGTTVY 46
                                   999******9865 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.5   2.2e-06     0.002      66      96 ..       3      45 ..       1      51 [. 0.82

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.2e-06
                                   EE--EEEETTTS-EEECHH.HHH...........S-TTTSSS- CS
                           HypA 66 evpvkvrCreCgkefelee.kal...........rCpkCgsad 96
                                   +++++++C +C+k++e+++ +++           +Cp+Cg++ 
  gi|119719007|ref|YP_919502.1|  3 HQKITAYCVKCRKQVEMKNpQQVtlkngrlaykgTCPNCGTTV 45
                                   68899***********98743336799*************875 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   1.1   3.9e-06    0.0035      33      75 ..       3      45 ..       1      49 [. 0.90

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3.9e-06
                 zinc_ribbon_15 33 kkkpylacskCkslleaskelgkeiekkessekkeCknCgkev 75
                                   ++k  ++c kC++ +e+++ ++ ++++++ + k +C+nCg++v
  gi|119719007|ref|YP_919502.1|  3 HQKITAYCVKCRKQVEMKNPQQVTLKNGRLAYKGTCPNCGTTV 45
                                   568899*************9999999999999********998 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.1     0.011        10       1      10 [.       9      18 ..       7      22 .. 0.81
   2 !   10.9   0.5   0.00031      0.28       2       8 ..      38      44 ..      37      46 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.011
                  zinc_ribbon_2  1 fCpnCGaelq 10
                                   +C +C ++++
  gi|119719007|ref|YP_919502.1|  9 YCVKCRKQVE 18
                                   7999999886 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00031
                  zinc_ribbon_2  2 CpnCGae 8 
                                   CpnCG++
  gi|119719007|ref|YP_919502.1| 38 CPNCGTT 44
                                   7777765 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.9      0.23   2.1e+02      39      46 .]       9      16 ..       2      16 .. 0.83
   2 !   14.3   0.0   3.3e-05      0.03      10      34 ..      27      51 ..      23      54 .] 0.78

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.23
                  Zn_Tnp_IS1595 39 qCkeCrkq 46
                                    C +Crkq
  gi|119719007|ref|YP_919502.1|  9 YCVKCRKQ 16
                                   69999998 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 3.3e-05
                  Zn_Tnp_IS1595 10 LealrWpngfvCPhCgsrkayrikt 34
                                   L++ r + + +CP+Cg + +++i +
  gi|119719007|ref|YP_919502.1| 27 LKNGRLAYKGTCPNCGTTVYRFIGR 51
                                   6777777889******888888866 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1     0.021        19       2      16 ..       9      23 ..       8      26 .. 0.90
   2 ?    9.4   0.2    0.0011         1      25      33 ..      38      46 ..      36      48 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.021
                                   B-TTT--B-EEE--T CS
                      Nudix_N_2  2 FCsqCGtpvelripd 16
                                   +C +C ++ve++ p+
  gi|119719007|ref|YP_919502.1|  9 YCVKCRKQVEMKNPQ 23
                                   9*********99886 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0011
                                   ETTTTEEE- CS
                      Nudix_N_2 25 CpaCgtihY 33
                                   Cp+Cgt+ Y
  gi|119719007|ref|YP_919502.1| 38 CPNCGTTVY 46
                                   888888877 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.2     0.068        61      24      37 ..       4      18 ..       1      20 [. 0.66
   2 ?   13.0   1.1   9.4e-05     0.085       8      39 ..      10      48 ..       8      49 .. 0.68

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.068
                    Zn-ribbon_8 24 aplta.CPeCgsevr 37
                                    + ta C +C ++v+
  gi|119719007|ref|YP_919502.1|  4 QKITAyCVKCRKQVE 18
                                   456777888877664 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 9.4e-05
                    Zn-ribbon_8  8 CeeCghefe.......vlqsisdap.ltaCPeCgsevrrv 39
                                   C +C ++ e        l    + + + +CP+Cg +v r 
  gi|119719007|ref|YP_919502.1| 10 CVKCRKQVEmknpqqvTLK-NGRLAyKGTCPNCGTTVYRF 48
                                   9999999998887653222.223333666*****999885 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.2   4.5e-05      0.04       3      28 ..       8      42 ..       6      45 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.5e-05
                  zinc_ribbon_9  3 yWChqCdrfVsvspdedsd........v.lCPhCg 28
                                    +C  C++ V+   +++          + +CP+Cg
  gi|119719007|ref|YP_919502.1|  8 AYCVKCRKQVEMKNPQQVTlkngrlayKgTCPNCG 42
                                   6999********99988889****988578****8 PP

>> zf-LITAF-like  LITAF-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.4     0.009       8.1      53      68 ..       4      19 ..       1      21 [. 0.78
   2 ?    7.9   0.0    0.0041       3.6      58      67 ..      37      46 ..      22      49 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.009
                  zf-LITAF-like 53 kdvehyCpnCgallgt 68
                                   ++++ yC +C++++ +
  gi|119719007|ref|YP_919502.1|  4 QKITAYCVKCRKQVEM 19
                                   6788899999998876 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0041
                  zf-LITAF-like 58 yCpnCgallg 67
                                   +CpnCg+++ 
  gi|119719007|ref|YP_919502.1| 37 TCPNCGTTVY 46
                                   6888887765 PP

>> PknG_rubred  Protein kinase G rubredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.4   4.2e-05     0.037      94     128 ..       9      50 ..       3      54 .] 0.71

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.2e-05
                                    B-TTT--B-S---SS-......---SEEE-TTT--E.EE-S- CS
                    PknG_rubred  94 fCwrCGrpvGRseker......kgaseGtCpkCgsp.ysFlP 128
                                    +C +C ++v   + ++      + a +GtCp+Cg + y F+ 
  gi|119719007|ref|YP_919502.1|   9 YCVKCRKQVEMKNPQQvtlkngRLAYKGTCPNCGTTvYRFIG 50 
                                    899999999887766645553355668999999974388875 PP

>> DUF1272  Protein of unknown function (DUF1272)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1     0.046        42      30      39 ..       8      17 ..       5      26 .. 0.73
   2 ?    8.8   0.1    0.0019       1.7      40      49 ..      34      43 ..      27      48 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.046
                        DUF1272 30 tFCaeCaeev 39
                                   ++C++C ++v
  gi|119719007|ref|YP_919502.1|  8 AYCVKCRKQV 17
                                   5888888876 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0019
                        DUF1272 40 lenvCPncgG 49
                                   ++++CPncg 
  gi|119719007|ref|YP_919502.1| 34 YKGTCPNCGT 43
                                   4799****96 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.5       4.4     4e+03       5       6 ..      13      14 ..       9      25 .. 0.61
   2 ?   13.7   0.0   5.4e-05     0.048       1      14 [.      37      50 ..      37      54 .] 0.85

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 4.4
                 DNA_ligase_ZBD  5 CG 6 
                                   C 
  gi|119719007|ref|YP_919502.1| 13 CR 14
                                   44 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 5.4e-05
                 DNA_ligase_ZBD  1 hCPvCGsavvReeg 14
                                   +CP CG+ v R  g
  gi|119719007|ref|YP_919502.1| 37 TCPNCGTTVYRFIG 50
                                   7*********9876 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.3     0.005       4.5     157     184 ..       2      29 ..       1      32 [. 0.80
   2 ?    7.0   0.0    0.0047       4.2      81      95 ..      29      43 ..      27      48 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.005
                        TackOD1 157 sepevkarClsCekesesddlkvreiys 184
                                    s +++ a C++C+k++e ++ +  ++ +
  gi|119719007|ref|YP_919502.1|   2 SHQKITAYCVKCRKQVEMKNPQQVTLKN 29 
                                    56788999*******9999888777765 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0047
                        TackOD1 81 sghlnvrevCpkCkS 95
                                    g+l ++ +Cp+C+ 
  gi|119719007|ref|YP_919502.1| 29 NGRLAYKGTCPNCGT 43
                                   5799*********86 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1     0.087        78       2       8 ..       7      13 ..       6      18 .. 0.81
   2 ?   10.2   0.6   0.00043      0.38       5      10 ..      38      43 ..      36      45 .. 0.61

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.087
                    zf-ribbon_3  2 tvrCPnC 8 
                                   t +C +C
  gi|119719007|ref|YP_919502.1|  7 TAYCVKC 13
                                   789**** PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00043
                    zf-ribbon_3  5 CPnCGa 10
                                   CPnCG+
  gi|119719007|ref|YP_919502.1| 38 CPNCGT 43
                                   666665 PP

>> GFA  Glutathione-dependent formaldehyde-activating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   2.8    0.0011      0.97      25      60 ..      15      46 ..       4      53 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0011
                            GFA 25 ealellegelkeykktadsgnkvtrsfCpeCgsply 60
                                   +++e+   ++++++   ++g+ + +  Cp+Cg+++y
  gi|119719007|ref|YP_919502.1| 15 KQVEMK--NPQQVT--LKNGRLAYKGTCPNCGTTVY 46
                                   455532..344444..468889999*********99 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.3      0.81   7.3e+02       4       9 ..      10      15 ..       9      18 .. 0.67
   2 ?   12.2   0.2   0.00017      0.15       4      13 ..      38      47 ..      37      47 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.81
                         zf-ACC  4 CpsCge 9 
                                   C +C  
  gi|119719007|ref|YP_919502.1| 10 CVKCRK 15
                                   777765 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00017
                         zf-ACC  4 CpsCgemlyk 13
                                   Cp Cg+++y+
  gi|119719007|ref|YP_919502.1| 38 CPNCGTTVYR 47
                                   *********8 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   2.5    0.0026       2.3      28      47 ..      25      45 ..       8      48 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0026
                           CpXC 28 eklldgslf.eatCpkCgata 47
                                     l +g+l  + tCp+Cg+t+
  gi|119719007|ref|YP_919502.1| 25 VTLKNGRLAyKGTCPNCGTTV 45
                                   3456888752689*****986 PP

>> zf-ANAPC11  Anaphase-promoting complex subunit 11 RING-H2 finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   2.0    0.0006      0.54      23      39 ..      26      42 ..       4      47 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0006
                                   B-TTT-SBTTS--TTCS CS
                     zf-ANAPC11 23 vcGicrvsfdGtcpsck 39
                                   +    r++++Gtcp+c 
  gi|119719007|ref|YP_919502.1| 26 TLKNGRLAYKGTCPNCG 42
                                   445579**********6 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.7     0.086        77      33      39 ..       7      13 ..       1      14 [. 0.76
   2 ?    8.4   0.1    0.0026       2.3      17      27 ..      37      47 ..      34      53 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.086
                  Auto_anti-p27 33 kvyCvaC 39
                                   + yCv C
  gi|119719007|ref|YP_919502.1|  7 TAYCVKC 13
                                   569**** PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0026
                  Auto_anti-p27 17 tCpvCgvPLmr 27
                                   tCp+Cg+   r
  gi|119719007|ref|YP_919502.1| 37 TCPNCGTTVYR 47
                                   8****997766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       768  (0.0428356); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.33u 0.26s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 424.46
//
Query:       gi|119719008|ref|YP_919503.1|  [L=116]
Description: helix-turn-helix domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-09   37.4   0.6    2.9e-09   36.8   0.6    1.3  1  HTH_3           Helix-turn-helix
    1.2e-07   31.1   0.6    6.1e-07   28.9   0.2    2.2  2  HTH_24          Winged helix-turn-helix DNA-binding
    3.3e-06   26.7   0.3    1.1e-05   25.0   0.1    2.0  2  HTH_23          Homeodomain-like domain
    4.6e-06   26.5   0.0    1.1e-05   25.3   0.0    1.7  2  HTH_37          Helix-turn-helix domain
      6e-06   26.5   0.0    1.5e-05   25.2   0.0    1.6  1  HTH_31          Helix-turn-helix domain
    2.8e-05   23.9   1.4    0.00012   21.9   0.2    2.3  2  HTH_5           Bacterial regulatory protein, arsR family
    4.8e-05   23.0   0.1    0.00064   19.4   0.0    2.3  2  HTH_38          Helix-turn-helix domain
    9.4e-05   22.4   0.2     0.0002   21.3   0.2    1.6  1  HTH_19          Helix-turn-helix domain
     0.0001   21.8   0.4    0.00024   20.5   0.3    1.7  1  Sigma70_r4      Sigma-70, region 4
    0.00022   21.0   0.1     0.0015   18.3   0.0    2.3  1  LacI            Bacterial regulatory proteins, lacI family
    0.00029   20.6   0.0    0.00054   19.8   0.0    1.5  1  MarR_2          MarR family
    0.00035   20.2   0.1    0.00087   18.9   0.1    1.7  1  Sigma70_r4_2    Sigma-70, region 4
    0.00046   20.1   0.0     0.0008   19.3   0.0    1.4  1  MarR            MarR family
    0.00057   19.8   0.1     0.0012   18.8   0.1    1.6  1  HTH_Crp_2       Crp-like helix-turn-helix domain
     0.0011   18.7   0.0     0.0022   17.7   0.0    1.6  1  HTH_Tnp_4       Helix-turn-helix of DDE superfamily endonucle
     0.0012   19.5   0.1     0.0016   19.1   0.1    1.1  1  HNF-1_N         Hepatocyte nuclear factor 1 (HNF-1), N termin
     0.0015   17.6   0.0     0.0017   17.4   0.0    1.1  1  TnsD            Tn7-like transposition protein D
      0.002   17.9   0.0     0.0043   16.8   0.0    1.6  1  HTH_IclR        IclR helix-turn-helix domain
     0.0022   17.7   0.0     0.0032   17.2   0.0    1.3  1  UPF0175         Uncharacterised protein family (UPF0175)
     0.0036   17.4   0.1     0.0063   16.6   0.1    1.4  1  HTH_7           Helix-turn-helix domain of resolvase
     0.0045   17.0   0.0     0.0091   16.0   0.0    1.5  1  HTH_29          Winged helix-turn helix
      0.006   16.4   0.0      0.011   15.6   0.0    1.5  1  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox
  ------ inclusion threshold ------
       0.01   15.9   0.0      0.026   14.6   0.0    1.9  1  HTH_20          Helix-turn-helix domain
      0.019   15.1   0.0       0.11   12.7   0.0    2.1  2  HTH_17          Helix-turn-helix domain
      0.029   14.4   0.0      0.046   13.8   0.0    1.4  1  Cro             Cro
      0.032   13.8   0.0      0.071   12.7   0.0    1.6  1  GerE            Bacterial regulatory proteins, luxR family
      0.037   13.4   0.0      0.046   13.1   0.0    1.2  1  DUF1670         Protein of unknown function (DUF1670)
      0.042   13.7   0.0      0.094   12.5   0.0    1.6  1  HTH_10          HTH DNA binding domain
      0.052   13.5   0.2       0.11   12.4   0.2    1.5  1  HTH_11          HTH domain
      0.073   13.2   0.0       0.13   12.4   0.0    1.6  1  HTH_28          Helix-turn-helix domain
      0.081   12.9   0.0       0.14   12.1   0.0    1.4  1  HTH_1           Bacterial regulatory helix-turn-helix protein
      0.088   12.2   0.0        0.2   11.1   0.0    1.6  1  HTH_Tnp_ISL3    Helix-turn-helix domain of transposase family
      0.097   12.6   0.0       0.16   11.9   0.0    1.4  1  TrmB            Sugar-specific transcriptional regulator TrmB
       0.11   12.7   0.1       0.36   11.0   0.1    1.9  1  HTH_22          HTH domain
       0.12   12.3   0.0       0.16   11.8   0.0    1.2  1  Sigma70_ECF     ECF sigma factor
       0.13   12.7   0.1       0.42   11.1   0.0    1.9  2  HTH_26          Cro/C1-type HTH DNA-binding domain
       0.13   12.4   0.0       0.19   11.9   0.0    1.3  1  DUF739          Protein of unknown function (DUF739)
       0.14   12.1   0.0       0.28   11.2   0.0    1.5  1  HTH_36          Helix-turn-helix domain
       0.16   12.0   0.0       0.27   11.3   0.0    1.4  1  KorB            KorB domain


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.8   0.6   6.3e-12   2.9e-09       2      44 ..      33      75 ..      32      78 .. 0.93

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 6.3e-12
                                   HHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHH CS
                          HTH_3  2 kelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkkl 44
                                   + l +q gl+q ++A++lG+s+s++sr+ n +r  s++ ++++
  gi|119719008|ref|YP_919503.1| 33 RYLYEQEGLTQLQIAKLLGISQSSVSRYLNSQRGLSQRDILEI 75
                                   77889********************************999887 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.2   1.3e-09   6.1e-07       6      39 ..      28      62 ..      26      63 .. 0.93
   2 ?   -0.1   0.0       1.6   7.2e+02      17      25 ..      66      74 ..      62      75 .. 0.69

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 1.3e-09
                         HTH_24  6 rkIL.elLqknprisqreLAerlglSpstvnrrlk 39
                                   r IL ++L+++ +++q ++A+ lg+S+s v+r+l+
  gi|119719008|ref|YP_919503.1| 28 RSILvRYLYEQEGLTQLQIAKLLGISQSSVSRYLN 62
                                   568889***************************97 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.6
                         HTH_24 17 risqreLAe 25
                                   ++sqr++ e
  gi|119719008|ref|YP_919503.1| 66 GLSQRDILE 74
                                   678888755 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       5.3   2.4e+03      17      26 ..      13      22 ..       8      23 .. 0.75
   2 !   25.0   0.1   2.5e-08   1.1e-05      13      46 ..      35      67 ..      26      73 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 5.3
                         HTH_23 17 GlsvreIAre 26
                                   +++++eI+r+
  gi|119719008|ref|YP_919503.1| 13 KAPCEEISRR 22
                                   5789999986 PP

  == domain 2  score: 25.0 bits;  conditional E-value: 2.5e-08
                         HTH_23 13 llae.GlsvreIAreLgvsrrTvyrwlkryreeGl 46
                                   l+ + Gl++ +IA++Lg+s++ v+r+l+   + Gl
  gi|119719008|ref|YP_919503.1| 35 LYEQeGLTQLQIAKLLGISQSSVSRYLNS--QRGL 67
                                   55568*********************997..5665 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   2.4e-08   1.1e-05      12      54 ..      18      63 ..      11      75 .. 0.82
   2 ?    0.2   0.0       1.6   7.5e+02      28      42 ..      63      77 ..      59      80 .. 0.75

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 2.4e-08
                                   HHHHHHHHHHH...HHHHHHHCT--HHHHHHHHT--HHHHHHHHTT CS
                         HTH_37 12 elkaKaqlala...iaeliekrelsqseaaqllgiaqPkvsrllrg 54
                                   e++ ++  a +   +++l e+++l+q ++a+llgi+q++vsr l+ 
  gi|119719008|ref|YP_919503.1| 18 EISRRVLPAVRsilVRYLYEQEGLTQLQIAKLLGISQSSVSRYLNS 63
                                   56666666666666999*************************9984 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.6
                                   HHCT--HHHHHHHHT CS
                         HTH_37 28 ekrelsqseaaqllg 42
                                    +r+lsq+++ ++  
  gi|119719008|ref|YP_919503.1| 63 SQRGLSQRDILEIPS 77
                                   6899****9987755 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   3.4e-08   1.5e-05       8      47 ..      34      72 ..      29      75 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 3.4e-08
                         HTH_31  8 alReraGLsqeevAerlgvsestlsrlEqGrrgrpspavl 47
                                    l e++GL+q + A++lg+s+s +sr+ + +rg  s +++
  gi|119719008|ref|YP_919503.1| 34 YLYEQEGLTQLQIAKLLGISQSSVSRYLNSQRG-LSQRDI 72
                                   566899*************************99.766654 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.2   2.5e-07   0.00012       4      37 ..      28      62 ..      26      64 .. 0.94
   2 ?   -0.1   0.1         2     9e+02      13      27 ..      95     109 ..      93     111 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 2.5e-07
                                   HHHHHHHHTTSS.EEHHHHHHHHTS-HHHHHHHHH CS
                          HTH_5  4 RlkILklLaege.lcvcelaeelglsqstvShHLk 37
                                   R+ ++++L e+e l+  ++a+ lg+sqs vS++L+
  gi|119719008|ref|YP_919503.1| 28 RSILVRYLYEQEgLTQLQIAKLLGISQSSVSRYLN 62
                                   88899*****999********************97 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 2
                                    TSSEEHHHHHHHHTS CS
                          HTH_5  13 egelcvcelaeelgl 27 
                                    +ge   c ++ ++++
  gi|119719008|ref|YP_919503.1|  95 RGEEALCSICQYIRM 109
                                    588899999998876 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   1.4e-06   0.00064      15      40 ..      34      60 ..      30      62 .. 0.89
   2 ?    1.2   0.0      0.71   3.3e+02      18      26 ..      64      72 ..      60      72 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.4e-06
                         HTH_38 15 rll.aeGlslreIArrLgrspsTIsRE 40
                                   +l+ +eGl++ +IA++Lg s s++sR 
  gi|119719008|ref|YP_919503.1| 34 YLYeQEGLTQLQIAKLLGISQSSVSRY 60
                                   6885699*******************5 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.71
                         HTH_38 18 aeGlslreI 26
                                   ++Gls+r+I
  gi|119719008|ref|YP_919503.1| 64 QRGLSQRDI 72
                                   79*****99 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.2   4.3e-07    0.0002       9      50 ..      37      80 ..      31      93 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 4.3e-07
                         HTH_19  9 eelgltqeelaerlgisrskisaiEngkkdvps.aell..lkiae 50
                                   e+ gltq ++a+ lgis+s+ s + n ++  +s ++ l  ++i e
  gi|119719008|ref|YP_919503.1| 37 EQEGLTQLQIAKLLGISQSSVSRYLNSQR-GLSqRDILeiPSIDE 80
                                   789***********************999.777433334455555 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.3   5.2e-07   0.00024      10      39 ..      28      59 ..      22      63 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 5.2e-07
                                   HHHHHHHH..TTT--HHHHHHHHTS-HHHHHH CS
                     Sigma70_r4 10 revlelrf..geglTleEIgerlgiSrerVrq 39
                                   r +l+ +    eglT+ +I++ lgiS++ V++
  gi|119719008|ref|YP_919503.1| 28 RSILVRYLyeQEGLTQLQIAKLLGISQSSVSR 59
                                   566666667899******************98 PP

>> LacI  Bacterial regulatory proteins, lacI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   3.3e-06    0.0015       5      38 ..      46      90 ..      44      92 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.3e-06
                                   HHHHCTS-HHHHHHHCTTS...........SSSTHHHHHHHHHHH CS
                           LacI  5 VArlAGVSkaTVSrvLnnk...........erVseetrerVeaam 38
                                   +A+l G S + VSr+Ln++           +++ e++re V+ ++
  gi|119719008|ref|YP_919503.1| 46 IAKLLGISQSSVSRYLNSQrglsqrdileiPSIDEKLRETVHGIV 90
                                   9******************66666666666666666666666665 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   1.2e-06   0.00054      11      43 ..      32      62 ..      24      67 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.2e-06
                                   HHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHH CS
                         MarR_2 11 LaaLgrrpgrdltvgelarrlglsksavsrilk 43
                                     +L+  +g  lt+ ++a+ lg+s+s+vsr l+
  gi|119719008|ref|YP_919503.1| 32 VRYLYEQEG--LTQLQIAKLLGISQSSVSRYLN 62
                                   568999***..*******************987 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   1.9e-06   0.00087      21      47 ..      35      61 ..      24      63 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.9e-06
                                   HHHTS---HHHHHHHHT--HHHHHHHH CS
                   Sigma70_r4_2 21 lryleglsykEIAellgisegtVksrl 47
                                   l++ egl++ +IA+llgis ++V ++l
  gi|119719008|ref|YP_919503.1| 35 LYEQEGLTQLQIAKLLGISQSSVSRYL 61
                                   77889******************9997 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.7e-06    0.0008       9      38 ..      32      61 ..      29      74 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.7e-06
                                   HHHHHHSTTEEHHHHHHHHTS-HHHHHHHH CS
                           MarR  9 LrilyeqgplsvseLakklgvskstvtrvl 38
                                   +r lyeq++l++ ++ak lg+s+s+v+r l
  gi|119719008|ref|YP_919503.1| 32 VRYLYEQEGLTQLQIAKLLGISQSSVSRYL 61
                                   5679***********************977 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   2.5e-06    0.0012      22      44 ..      41      63 ..      27      80 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.5e-06
                                   HHHHHHHHHTTSSHHHHHHHHHH CS
                      HTH_Crp_2 22 ltqeelAsmlGltretvsrilse 44
                                   ltq ++A +lG+++++vsr l+ 
  gi|119719008|ref|YP_919503.1| 41 LTQLQIAKLLGISQSSVSRYLNS 63
                                   8******************9985 PP

>> HTH_Tnp_4  Helix-turn-helix of DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   4.8e-06    0.0022      14      41 ..      35      62 ..      22      66 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4.8e-06
                      HTH_Tnp_4 14 vyLRlnltyqdLayrFgvsestvsrifh 41
                                    y  ++lt+ ++a + g+s+s+vsr+ +
  gi|119719008|ref|YP_919503.1| 35 LYEQEGLTQLQIAKLLGISQSSVSRYLN 62
                                   566689********************86 PP

>> HNF-1_N  Hepatocyte nuclear factor 1 (HNF-1), N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.1   3.5e-06    0.0016     120     180 ..       6      67 ..       2      72 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 3.5e-06
                        HNF-1_N 120 ieeaaeqrakveellredswrvkeeikafl.qqhrIsQrevvdvTGlsQShlSqwLlkGtpm 180
                                    + e+a+ +a  ee+ r+    v+     +l +q  + Q  +++  G+sQS +S++L++   +
  gi|119719008|ref|YP_919503.1|   6 TSEMAHLKAPCEEISRRVLPAVRSILVRYLyEQEGLTQLQIAKLLGISQSSVSRYLNSQRGL 67 
                                    56888888999999999988898887777746889**********************65544 PP

>> TnsD  Tn7-like transposition protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   3.8e-06    0.0017     192     229 ..      33      70 ..      25      95 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.8e-06
                           TnsD 192 keLveeeglslkeiAkelgvdiktVlryakklgllkek 229
                                    ++L+e+egl++ +iAk lg++ ++V ry++++ +l ++
  gi|119719008|ref|YP_919503.1|  33 RYLYEQEGLTQLQIAKLLGISQSSVSRYLNSQRGLSQR 70 
                                    789***************************99988765 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   9.4e-06    0.0043      17      41 ..      39      63 ..      31      67 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 9.4e-06
                                   SS-BHHHHHHHHTS-HHHHHHHHHH CS
                       HTH_IclR 17 qeltlselArrtglpkStvhRlLqt 41
                                   ++lt  ++A+ +g++ S+v+R+L++
  gi|119719008|ref|YP_919503.1| 39 EGLTQLQIAKLLGISQSSVSRYLNS 63
                                   458999*****************85 PP

>> UPF0175  Uncharacterised protein family (UPF0175)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   6.9e-06    0.0032      19      56 ..      26      63 ..      10      72 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 6.9e-06
                        UPF0175 19 elrialAvklYeegrlSlgkAaelaglsrveflelLar 56
                                    +r  l+ +lYe++ l++ + a+l+g+s+  + ++L++
  gi|119719008|ref|YP_919503.1| 26 AVRSILVRYLYEQEGLTQLQIAKLLGISQSSVSRYLNS 63
                                   56778899*********************999999975 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   1.4e-05    0.0063      17      44 ..      35      63 ..      30      64 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.4e-05
                                   STT.TT--STTTSSSS---SSSS--SS-- CS
                          HTH_7 17 Lle.eGisiskIAkevnisRsTvYRylad 44
                                   L+e eG +  +IAk ++is s+v Ryl+ 
  gi|119719008|ref|YP_919503.1| 35 LYEqEGLTQLQIAKLLGISQSSVSRYLNS 63
                                   6651469999*****************97 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0     2e-05    0.0091      10      35 ..      39      63 ..      32      71 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2e-05
                         HTH_29 10 eGvstvsqiAkllglsrrtvyrwlkr 35
                                   eG+ t  qiAkllg+s ++v r+l+ 
  gi|119719008|ref|YP_919503.1| 39 EGL-TQLQIAKLLGISQSSVSRYLNS 63
                                   666.899*****************97 PP

>> YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   2.4e-05     0.011      11      43 ..      43      75 ..      38      86 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.4e-05
                 YdaS_antitoxin 11 qkaLAealgvsqqaVsqWlkgkkqvpaervpeI 43
                                   q + A++lg+sq+ Vs+ l+ +++++ + ++eI
  gi|119719008|ref|YP_919503.1| 43 QLQIAKLLGISQSSVSRYLNSQRGLSQRDILEI 75
                                   6678****************9999999999998 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   5.6e-05     0.026      12      45 ..      28      61 ..      13      74 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.6e-05
                                   HHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHH CS
                         HTH_20 12 RrrilraLaraegltaselaerldlskntlsyHL 45
                                   R  + r+L + eglt  ++a++l++s++++s+ L
  gi|119719008|ref|YP_919503.1| 28 RSILVRYLYEQEGLTQLQIAKLLGISQSSVSRYL 61
                                   55567999**********************9866 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       2.7   1.2e+03      22      32 ..      19      30 ..       2      39 .. 0.67
   2 ?   12.7   0.0   0.00024      0.11       6      25 ..      45      64 ..      41      72 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 2.7
                         HTH_17 22 irrgelpaak.i 32
                                   i+r  lpa++ i
  gi|119719008|ref|YP_919503.1| 19 ISRRVLPAVRsI 30
                                   457778888742 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00024
                         HTH_17  6 EaAelLgvsrstvyrlirrg 25
                                   ++A+lLg+s+s+v r++++ 
  gi|119719008|ref|YP_919503.1| 45 QIAKLLGISQSSVSRYLNSQ 64
                                   79**************9864 PP

>> Cro  Cro
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0    0.0001     0.046      14      37 ..      42      65 ..      27      70 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.0001
                                   HHHHHHHHHTS-HHHHHHHHHCT- CS
                            Cro 14 GQaktAkdlgvkqsaIsKAlkakR 37
                                    Q + Ak lg+ qs++s+ l+ +R
  gi|119719008|ref|YP_919503.1| 42 TQLQIAKLLGISQSSVSRYLNSQR 65
                                   4999****************9999 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00015     0.071      16      39 ..      39      62 ..      33      65 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00015
                                   TTS-HHHHHHHHTS-HHHHHHHHH CS
                           GerE 16 eGksnkeIAeelniSekTVkvhks 39
                                   eG++  +IA+ l+iS+ +V+ ++ 
  gi|119719008|ref|YP_919503.1| 39 EGLTQLQIAKLLGISQSSVSRYLN 62
                                   79******************9875 PP

>> DUF1670  Protein of unknown function (DUF1670)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0    0.0001     0.046      97     127 ..      33      62 ..       6      74 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.0001
                        DUF1670  97 nEAyeqealltqsDlalllgvstrtvskqvk 127
                                       yeqe+ ltq  +a llg+s+++vs++ +
  gi|119719008|ref|YP_919503.1|  33 RYLYEQEG-LTQLQIAKLLGISQSSVSRYLN 62 
                                    4569***9.59*****************986 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0    0.0002     0.094      27      45 ..      44      62 ..      37      66 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.0002
                         HTH_10 27 keLAkelGIskstlsehLr 45
                                    ++Ak lGIs+s++s +L+
  gi|119719008|ref|YP_919503.1| 44 LQIAKLLGISQSSVSRYLN 62
                                   589**************97 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   0.00024      0.11       5      36 ..      31      61 ..      27      64 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00024
                         HTH_11  5 ilelLleargpisgeeLAeeLnvSrrtvrrdI 36
                                   +++ L+e++g ++  ++A+ L++S + v r++
  gi|119719008|ref|YP_919503.1| 31 LVRYLYEQEG-LTQLQIAKLLGISQSSVSRYL 61
                                   4566888888.*******************98 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00029      0.13      11      34 ..      37      62 ..      28      71 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00029
                         HTH_28 11 aGh..svreaArelgisrrtvyrWik 34
                                   +++  ++ ++A++lgis+++v+r ++
  gi|119719008|ref|YP_919503.1| 37 EQEglTQLQIAKLLGISQSSVSRYLN 62
                                   333259999************99775 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0    0.0003      0.14      20      38 ..      47      65 ..      45      85 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0003
                                   HHHHTS-HHHHHHHHHHHH CS
                          HTH_1 20 AeeLglsqpavsrqikrLE 38
                                   A+ Lg+sq++vsr +++ +
  gi|119719008|ref|YP_919503.1| 47 AKLLGISQSSVSRYLNSQR 65
                                   899**********998765 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00044       0.2      26      49 ..      39      62 ..      31      64 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00044
                   HTH_Tnp_ISL3 26 esrsvkavArqlgvSwtTVwrild 49
                                   e+ +  ++A++lg+S ++V r+l+
  gi|119719008|ref|YP_919503.1| 39 EGLTQLQIAKLLGISQSSVSRYLN 62
                                   6678899**************997 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00035      0.16      17      45 ..      35      63 ..      30      77 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00035
                                   HHHHCCCHHCHHCCCTTSSCHCHHHHHHH CS
                           TrmB 17 LlklgpatadeiaeelgvprskvYevLrs 45
                                   L +++ +t  +ia+ lg+++s+v ++L+s
  gi|119719008|ref|YP_919503.1| 35 LYEQEGLTQLQIAKLLGISQSSVSRYLNS 63
                                   568999*********************97 PP

>> HTH_22  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00077      0.36      46      63 .]      45      62 ..      18      62 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00077
                         HTH_22 46 kvAekLgiSraTvYryLr 63
                                   ++A+ LgiS+ +v ryL+
  gi|119719008|ref|YP_919503.1| 45 QIAKLLGISQSSVSRYLN 62
                                   69**************96 PP

>> Sigma70_ECF  ECF sigma factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00035      0.16     122     176 ..       8      65 ..       2      73 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00035
                    Sigma70_ECF 122 elleLdealerllsldpeqarlvelrkl...eGlsveEiAeklgvskrtverrlalaR 176
                                    e+ +L+  +e++ +      r + +r+l   eGl+   iA+ lg+s+++v r l+  R
  gi|119719008|ref|YP_919503.1|   8 EMAHLKAPCEEISRRVLPAVRSILVRYLyeqEGLTQLQIAKLLGISQSSVSRYLNSQR 65 
                                    56667777777777666667888888876668********************998777 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00092      0.42       8      39 ..      38      68 ..      32      76 .. 0.78
   2 ?   -1.5   0.0       7.8   3.6e+03      26      48 ..      85     105 ..      83     109 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00092
                         HTH_26  8 drgitkseLargtgisaatlsrlvkgkpervs 39
                                   + g+t+ + a+ +gis++++sr+++ + + +s
  gi|119719008|ref|YP_919503.1| 38 QEGLTQLQIAKLLGISQSSVSRYLNSQ-RGLS 68
                                   5677777889**************987.5555 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 7.8
                         HTH_26  26 tlsrlvkgkpervsl.dtLdkiCd 48 
                                    t++++v gk    +  + L  iC+
  gi|119719008|ref|YP_919503.1|  85 TVHGIVEGKL---RGeEALCSICQ 105
                                    6777777662...22244445555 PP

>> DUF739  Protein of unknown function (DUF739)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00041      0.19      17      50 ..      40      74 ..      29      88 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00041
                         DUF739 17 G.tqynfaialgLserslslkLndkvsWkddeilk 50
                                   G tq   a+ lg+s+ s+s  Ln + +  + +il+
  gi|119719008|ref|YP_919503.1| 40 GlTQLQIAKLLGISQSSVSRYLNSQRGLSQRDILE 74
                                   449********************999888888775 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00061      0.28      30      47 ..      45      62 ..      27      64 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00061
                         HTH_36 30 tlakrlglsknTvsraik 47
                                    +ak+lg+s ++vsr+++
  gi|119719008|ref|YP_919503.1| 45 QIAKLLGISQSSVSRYLN 62
                                   79***************8 PP

>> KorB  KorB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00058      0.27       2      25 ..      39      62 ..      38      72 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00058
                           KorB  2 kgvkqadIAkaLGksksfvslylk 25
                                   +g++q +IAk LG s+s vs+yl 
  gi|119719008|ref|YP_919503.1| 39 EGLTQLQIAKLLGISQSSVSRYLN 62
                                   699*******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                       101  (0.00563333); expected 17.9 (0.001)
Passed Fwd filter:                        39  (0.00217525); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              39  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 805.42
//
Query:       gi|119719009|ref|YP_919504.1|  [L=476]
Description: 3-polyprenyl-4-hydroxybenzoate decarboxylase and related decarboxylases-like [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-55  187.2   0.0    5.1e-55  187.0   0.0    1.0  1  UbiD      3-octaprenyl-4-hydroxybenzoate carboxy-lyase


Domain annotation for each model (and alignments):
>> UbiD  3-octaprenyl-4-hydroxybenzoate carboxy-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.0   0.0   2.9e-59   5.1e-55       1     404 [.       7     420 ..       7     422 .. 0.87

  Alignments for each domain:
  == domain 1  score: 187.0 bits;  conditional E-value: 2.9e-59
                                    HHHCCCTTSEEEEESEB-TBTHHHHHHHHHHHHT--EEEEEEBTTB.TT-EEEE-TTS-HCHHHHHHTS-GHHHHHHHHH CS
                           UbiD   1 lealekagelvrikeevdpelEiaeiarrvleeggpallFenvkgkgskfpvltnlfgtrervalalglssleeilekla 80 
                                    l+ le+ ++l ri  e+ p  Ei+ +  ++ +e+ +all+++vkg  ++ +++tnlf    ++ l+l++ s+e+i+e+ a
  gi|119719009|ref|YP_919504.1|   7 LKLLESSDKLMRIGGELAPSIEIPWLSIQLSRETDKALLYDRVKG--GALSLATNLFY--GKLPLVLNAPSVERIIERAA 82 
                                    5789***************************************74..58********7..56788888888888888888 PP

                                    HHHHS...-...................---EE--GCG-GGGSEE.ECCCCC--HHHS---BSSTTSSS-EEECEEEEEE CS
                           UbiD  81 ellepkp.p...................ippkvvesekapcqeev.vlegddvdLskLPvltlwpgDgGpyitlglvitr 139
                                    ++l+    p                   + p+v e   ap    v +l+g dv+L ++P+l++ +++  p++  +++++ 
  gi|119719009|ref|YP_919504.1|  83 RVLHLLStPaaqptdklgllaslawiadYYPTVKE---APGG-AVrILQGYDVNLLEMPFLKHSREEEYPVLVNPIIVAS 158
                                    88884332467778888888888888877787665...4545.333899******************************* PP

                                    -TTTT-EEEEEEEEEEEETTEEEE--TTTHCHHHHHHHHHHCCT--EEEEEEES--HHHHHHCTS--TTT-TCHHHHHHH CS
                           UbiD 140 dpetgkrnlgiyRmqvldknklglhwqihkggaehlrkakkkggeplpvavaiGvdPaltlaAvaplPeglsElefaGal 219
                                    +  tg+r++   R+qv+d+++++lh+++++  ++ ++k  +    +l+v +  G+ Pal+ a+  +  + ++++++aG+l
  gi|119719009|ref|YP_919504.1| 159 SRATGDREIASQRVQVVDEKTMVLHVPRGSPLQFLIEKSSRSR-SSLDVGILAGTVPALYPASLLTWLTPVDKILLAGVL 237
                                    ******************************************9.8*******************888889********** PP

                                    HTS--EEEE-SSSSSEEETT-SEEEEEEEECCEEEECTTTC.-TTSCEEC--CCEEEEEEEEEEE-TT-EEEE-SSSCCS CS
                           UbiD 220 rgepvelvkcetvdlevpadAEivleGeidpgetapEGPfg.dhtGyysevrdefpvfkVtaithRkdpiypttvvgkpp 298
                                    +++++++vk e+ +l +p   E+ + Ge++pg+ +pEG +  +   +y++   ++pv++V++i    +p++++     p 
  gi|119719009|ref|YP_919504.1| 238 SESKISVVKTEE-GLVIPYPTEVAIIGELEPGDERPEGRMLyENGEVYGGS--PMPVVHVKKILLSPSPVFYSS-IIHPE 313
                                    *********987.8*************************986666667544..58*****************66.46666 PP

                                    HHHHCHHHHHHHHHHHHH.HCCSTTEEEEEE-GGGTTTC.EEEEECHHHTCCHHHHHHHHHH.CCTTGGC-SEEEEEEET CS
                           UbiD 299 eedallgkalealflpll.kkqvpevkdvhlpeeggfhl.lavvsikkrypghakkvmealw.alkqqlsltKlvivvDe 375
                                     +d+ + + l a++l ll k+  pe++++++  +  f+  +a v++++r +      +e+l+ ++     + ++vi+v  
  gi|119719009|ref|YP_919504.1| 314 RSDVAQVYSLVASLLVLLmKSLAPEIQELRFLGHDAFRTvIAKVATHRR-ERLLSIGGEILFlSAAV-NPYVDTVILVGP 391
                                    88999888888888888868888***************77777777444.33444466666644433.6799******** PP

                                    TS-TTSHHHHHHHHHHC--CCCCEEEECC CS
                           UbiD 376 dvdvrdlkevlwaiatrvdpdrDlviieg 404
                                    dvdv+d+  +++ ++++vdpdrD++++++
  gi|119719009|ref|YP_919504.1| 392 DVDVEDPTILAKVLLENVDPDRDIIHVDQ 420
                                    **************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (476 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       255  (0.0142228); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 3517.18
//
Query:       gi|119719010|ref|YP_919505.1|  [L=136]
Description: hypothetical protein Tpen_0092 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-52  175.4   1.4    4.4e-52  175.1   1.4    1.0  1  DUF2153   Uncharacterized protein conserved in archaea (DUF21


Domain annotation for each model (and alignments):
>> DUF2153  Uncharacterized protein conserved in archaea (DUF2153)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.1   1.4   2.4e-56   4.4e-52       1     122 [.      11     130 ..      11     131 .. 0.97

  Alignments for each domain:
  == domain 1  score: 175.1 bits;  conditional E-value: 2.4e-56
                        DUF2153   1 nLeeWvkeqkelletlkkvekkveeaDRLdlilasraafqhmmrtlkaFdqWLqdPviishmpremLldvketlreilek 80 
                                    nL++Wv++qk++l+t+++vek++e+aDRL+lil++raaf+hm++t++aFd+WLqdP+i+ hmpremLldv+++++eil+k
  gi|119719010|ref|YP_919505.1|  11 NLTNWVEAQKAFLDTVEAVEKNLENADRLELILTTRAAFSHMVKTIEAFDKWLQDPFIVGHMPREMLLDVQRSVWEILKK 90 
                                    799***************************************************************************** PP

                        DUF2153  81 llelDieHtsevrelleklskegklnpllalekeaeeekeer 122
                                    llelDi+Ht+++r++l kls++gklnp++++ +  +e+k+e+
  gi|119719010|ref|YP_919505.1|  91 LLELDIRHTTAFRDMLLKLSEDGKLNPVFFMPR--GEQKPEE 130
                                    ******************************999..6666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.32s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 909.55
//
Query:       gi|119719011|ref|YP_919506.1|  [L=520]
Description: putative thymidine phosphorylase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-16   58.9   0.0    1.2e-15   57.1   0.0    2.1  2  Glycos_trans_3N  Glycosyl transferase family, helical bundle 
    8.2e-14   51.8   0.5    1.4e-12   47.7   0.2    2.6  2  Glycos_transf_3  Glycosyl transferase family, a/b domain
      3e-13   49.2   0.0    9.5e-13   47.6   0.0    1.9  1  PYNP_C           Pyrimidine nucleoside phosphorylase C-termin
    0.00094   19.3   0.0     0.0025   17.9   0.0    1.7  1  CDC48_N          Cell division protein 48 (CDC48), N-terminal
     0.0024   16.7   0.0     0.0039   16.1   0.0    1.2  1  DUF2254          Predicted membrane protein (DUF2254)
     0.0069   16.6   0.0         10    6.4   0.0    3.2  3  DUF2774          Protein of unknown function (DUF2774)
      0.008   16.1   0.3        1.2    9.1   0.0    3.7  3  MazE_antitoxin   Antidote-toxin recognition MazE, bacterial a
  ------ inclusion threshold ------
      0.035   13.3   0.0        0.3   10.3   0.0    2.3  2  HlyD_D23         Barrel-sandwich domain of CusB or HlyD membr
      0.068   13.2   0.1       0.23   11.6   0.1    1.9  1  DUF1905          Domain of unknown function (DUF1905)
       0.07   13.8   1.4         29    5.4   0.0    3.5  4  HlyD_3           HlyD family secretion protein
      0.079   12.7   0.1       0.28   10.9   0.0    1.9  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      0.083   12.9   0.4       0.55   10.3   0.2    2.1  2  Molydop_binding  Molydopterin dinucleotide binding domain
       0.17   11.8   0.6        5.7    6.9   0.1    3.2  3  PriA_3primeBD    3′ DNA-binding domain (3′BD)


Domain annotation for each model (and alignments):
>> Glycos_trans_3N  Glycosyl transferase family, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       6.2   8.5e+03      41      57 ..      45      61 ..      44      62 .. 0.85
   2 !   57.1   0.0   8.6e-19   1.2e-15       2      63 .]      98     159 ..      97     159 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 6.2
                                   HHHHH---HHHHHHHHH CS
                Glycos_trans_3N 41 AlrlkGetaeEiaalae 57
                                    +r++G t+  ia+ a+
  gi|119719011|ref|YP_919506.1| 45 LVRFNGKTVVAIANIAK 61
                                   68999999999999886 PP

  == domain 2  score: 57.1 bits;  conditional E-value: 8.6e-19
                                    HHHHHHHTT.---HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHH---HHHHHHHHHHHHHHS CS
                Glycos_trans_3N   2 diikklrdgeeLtaeeirfaihgilkgevtdaqiaAfLmAlrlkGetaeEiaalaeAmresg 63 
                                    ++i+k+++g +L  +ei++++++i++g++++ ++aAf +A++++G+t+ Ei  ++  m+e g
  gi|119719011|ref|YP_919506.1|  98 QAIRKKLQGLSLESDEIYQVVKDIVDGKLSELELAAFVTAVHFQGMTPSEIYSFTLSMVETG 159
                                    589********************************************************976 PP

>> Glycos_transf_3  Glycosyl transferase family, a/b domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.19   2.6e+02     166     213 ..      63     110 ..      28     122 .. 0.76
   2 !   47.7   0.2   1.1e-15   1.4e-12       2     252 ..     167     389 ..     166     390 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.19
                                    HHTTEEEEEEEEEGSSTSSSEEESHHHHSSHHHHHHHHTTHHTSCHHH CS
                Glycos_transf_3 166 lkdgeiteytlepedfglkraelealeggepkenaeilkavlegkksa 213
                                      ++++  y+  ++ +g++  +  ++e  +p ++++++++ l+g + +
  gi|119719011|ref|YP_919506.1|  63 FSHEHVGVYVNIAKALGISDGDEVEVEATSPPASLQAIRKKLQGLSLE 110
                                    345566666667788999999999999999999999999999986655 PP

  == domain 2  score: 47.7 bits;  conditional E-value: 1.1e-15
                                    TTBEEEEESS-S.SSTHHHHHHHHHHHHHHTT-BEEEEE-STCTTCS-HHHHHCTST--ST--HHHHHHHHHHHSEEEEE CS
                Glycos_transf_3   2 kdlvDivgTGGd.gantfNiStaaaivvAaaGvkvakhgnrsvssksGsaDvLealgvnleltpeeveklleevgvgflf 80 
                                    k+++D+++ GG+ g++t   S+   +++A++G +++k + r+++s +G+aD +e l   ++l+ +e+e+++e+++ +++ 
  gi|119719011|ref|YP_919506.1| 167 KPILDKHSLGGVpGDKT---SLLVVPIIASLGFTIPKTSSRAITSAAGTADRMEVL-APVNLSIDEIERIVEKTNACLVW 242
                                    679********878999...***********************************9.46778889************996 PP

                                    ..HHSSSSHHHHHHHHHHHHTT.-SSHHHCHHHHHT..SEEEEHHHHHHHHTCHSEEEEEEEESTTSSCCSTSHHHHHHH CS
                Glycos_transf_3  81 ..apeyhkamkhvapvrrelgirTvfnlLGPLinparvkkqllgvyskelaeklaevlkelgveralvvhgdGldevsll 158
                                      a +  +a + ++ v   lgi        P   p        ++++k+la +  +v+ +++++r+  v++  l+e++ +
  gi|119719011|ref|YP_919506.1| 243 ggALNLAPADDIIIRVEYPLGI-------DPFYIP--------SILAKKLAVGSTHVVLDVPTGRGTKVKT--LEEAKRI 305
                                    2144555555666666667777.......588999........****************************..******* PP

                                    HHHHHHHHH.TTEEEEEEEEEGSSTSSSEEESHHHHSSHHHHHHHHTTHHTSCHHHHHHHHHHHHHHHHHHHTTSSSSHH CS
                Glycos_transf_3 159 akttvaelk.dgeiteytlepedfglkraelealeggepkenaeilkavlegkksaakrdlvllnagaalvlagkadslk 237
                                    +++    +   g   +++ + ++ ++++a + ale    +e++ +l+++  ++ +   +d  + +ag +l + g    ++
  gi|119719011|ref|YP_919506.1| 306 SQSFFEIARmFGMNLQAVATYAEEPIGHAIGPALEA---REALIALREL--RPGDL--VDKAASLAGTLLEMVG----VE 374
                                    ***999999889999999999**************9...9********9..77776..699999******9999....99 PP

                                    HHHHHHHHHHHTSHH CS
                Glycos_transf_3 238 egvakaeevidsGkA 252
                                    +g ++a e++++GkA
  gi|119719011|ref|YP_919506.1| 375 NGYETAMEALRTGKA 389
                                    9*************9 PP

>> PYNP_C  Pyrimidine nucleoside phosphorylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.6   0.0   6.9e-16   9.5e-13       1      66 [.     427     485 ..     427     492 .. 0.89

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 6.9e-16
                                    EEEEE-HHHHHHHHHHTTTSBSSTTS---TT-EEEES--TT-EEBTTSEEEEEEESSSCHHHHHHH CS
                         PYNP_C   1 yvseidareiGlaaveLGAGRakkeDpidlavGielhkklGdkVkkGeplatiYankeekleeavk 66 
                                    +v +id+  ++ +   +GA       pid+++G+++h+klG+kV kG+pl+t+Y+++++kl+++  
  gi|119719011|ref|YP_919506.1| 427 FVYYIDNSLLANIGKIAGA-------PIDKGAGVYIHVKLGEKVRKGDPLLTVYSSSSAKLQAVER 485
                                    5788999999999999999.......*********************************8887654 PP

>> CDC48_N  Cell division protein 48 (CDC48), N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.8e-06    0.0025      16      83 ..      25      91 ..      16      93 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.8e-06
                                   EEEE-HHHHHHHTS-TTSEEEEECCCCEEEEEEEBSTTSTTTTEEEE-HHHHHHHT--TTEEEEEEEE CS
                        CDC48_N 16 ivridpedmeelglepgdvveiegkrkTvaivwpaepedegkgiIrmdgvtRknagvsiGdkVtVrka 83
                                    v++d+++ ++l+++p d v ++ + kTv+ + ++++e +  +++ +  ++ k +g+s Gd+V+V+ +
  gi|119719011|ref|YP_919506.1| 25 TVVLDQSVAKKLDVRPSDRVLVRFNGKTVVAIANIAKEFS-HEHVGVYVNIAKALGISDGDEVEVEAT 91
                                   699**************************99999999966.************************976 PP

>> DUF2254  Predicted membrane protein (DUF2254)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   2.8e-06    0.0039     163     246 ..     394     478 ..     367     493 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.8e-06
                        DUF2254 163 rkailearedeeeeeeeeakdeeeseeeeatpiraersGylqaidveaLvklae......ehdlvielevrpGdfvvkge 236
                                    r+ i      e +  + + ++ee +  ++++++++e++G++  id + L ++ +      ++++ ++++v++G+ v kg+
  gi|119719011|ref|YP_919506.1| 394 REII------EAQGGDPDVTPEEIPLGDKTYTLYSEEDGFVYYIDNSLLANIGKiagapiDKGAGVYIHVKLGEKVRKGD 467
                                    3333......33345556677777889999***************999988776333444678899************** PP

                        DUF2254 237 plakvwgee.d 246
                                    pl++v++ +  
  gi|119719011|ref|YP_919506.1| 468 PLLTVYSSSsA 478
                                    ******98842 PP

>> DUF2774  Protein of unknown function (DUF2774)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       0.8   1.1e+03      18      30 ..      31      43 ..      30      53 .. 0.83
   2 ?    5.4   0.0     0.015        21      10      29 ..      65      84 ..      60      99 .. 0.84
   3 !    6.4   0.0    0.0073        10       8      31 ..     298     324 ..     293     329 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.8
                        DUF2774 18 eIAkkldirakdv 30
                                    +Akkld+r+ d 
  gi|119719011|ref|YP_919506.1| 31 SVAKKLDVRPSDR 43
                                   58********985 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.015
                        DUF2774 10 hesgknFveIAkkldirakd 29
                                   he+   +v+IAk+l+i+  d
  gi|119719011|ref|YP_919506.1| 65 HEHVGVYVNIAKALGISDGD 84
                                   899999**********8655 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0073
                        DUF2774   8 flhesg...knFveIAkkldirakdva 31 
                                    +l+e++   ++F eIA++++++ + va
  gi|119719011|ref|YP_919506.1| 298 TLEEAKrisQSFFEIARMFGMNLQAVA 324
                                    66666533379********98877776 PP

>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.13   1.7e+02      15      33 ..      32      50 ..      31      58 .. 0.83
   2 !    9.1   0.0    0.0009       1.2      15      33 ..      74      92 ..      72     105 .. 0.83
   3 ?   -1.6   0.0         2   2.8e+03      16      27 ..     342     357 ..     340     358 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.13
                                   CHHHCCEECTCEEEEEECT CS
                 MazE_antitoxin 15 vrfelgireGdevelevdg 33
                                   v+++l++r+ d+v ++ +g
  gi|119719011|ref|YP_919506.1| 32 VAKKLDVRPSDRVLVRFNG 50
                                   89***********998766 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0009
                                   CHHHCCEECTCEEEEEECT CS
                 MazE_antitoxin 15 vrfelgireGdevelevdg 33
                                   ++++lgi+ Gdeve+e  +
  gi|119719011|ref|YP_919506.1| 74 IAKALGISDGDEVEVEATS 92
                                   799************9766 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 2
                                    HHHC....CEECTCEE CS
                 MazE_antitoxin  16 rfel....gireGdev 27 
                                    r++l    ++r+Gd v
  gi|119719011|ref|YP_919506.1| 342 REALialrELRPGDLV 357
                                    566666678999**88 PP

>> HlyD_D23  Barrel-sandwich domain of CusB or HlyD membrane-fusion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.33   4.6e+02      77     101 ..      88     119 ..      41     126 .. 0.60
   2 ?   10.3   0.0   0.00022       0.3      33      60 ..     455     481 ..     431     491 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.33
                                    ........XXXXXXXXXXXXXXXXXXXXXXXX CS
                       HlyD_D23  77 e.......lleaarerLrllgvseeqiaelek 101
                                             l+a r++L+ l +++++i ++ k
  gi|119719011|ref|YP_919506.1|  88 VeatsppaSLQAIRKKLQGLSLESDEIYQVVK 119
                                    13345667899999999999999999988765 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00022
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       HlyD_D23  33 lyvnatgdkVkkGqpLaelyspelvaaq 60 
                                    ++v+ +g+kV+kG+pL+++ys+  ++ q
  gi|119719011|ref|YP_919506.1| 455 IHVK-LGEKVRKGDPLLTVYSSSSAKLQ 481
                                    5666.9***************9766655 PP

>> DUF1905  Domain of unknown function (DUF1905)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00016      0.23      10      81 ..      21      89 ..      12      90 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00016
                                   T-.S-EEEE--S-HHHHH..-.SS-EEEEEEETT.EEEEEEEESST..T-EEEEE-HHHHHHHT--TTSEEEEE CS
                        DUF1905 10 gkggwtfvevPedvseelktggkgsvkVkatidgttfrtslfpmgk..ggyiLpvkaavrkaigkeaGdtvtve 81
                                   ++   + v+++++v+++l    + s +V ++++g t  + + +  k      ++v  ++ ka+g++ Gd+v+ve
  gi|119719011|ref|YP_919506.1| 21 SA--HYTVVLDQSVAKKL--DVRPSDRVLVRFNGKTVVA-IANIAKefSHEHVGVYVNIAKALGISDGDEVEVE 89
                                   44..68899*********..999***********96543.3333333677778*******************96 PP

>> HlyD_3  HlyD family secretion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       2.1   2.8e+03      30      78 ..      16      61 ..      15      77 .. 0.65
   2 ?    4.5   0.0     0.041        57      30      74 ..      80     127 ..      75     136 .. 0.82
   3 ?   -1.9   0.0       3.9   5.4e+03      73      95 ..     206     228 ..     203     237 .. 0.78
   4 ?    5.4   0.0     0.021        29      12      38 ..     454     480 ..     445     489 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2.1
                         HlyD_3 30 iippdtllveakvpaadlgsik.kkgqkvtlkldqgsdytlkgkierisp 78
                                   i+p +++  ++ +++  +++++  + ++v ++++ g+       i +i+ 
  gi|119719011|ref|YP_919506.1| 16 ILPFESAHYTVVLDQSVAKKLDvRPSDRVLVRFN-GKT---VVAIANIAK 61
                                   6777777777788888888888888888888885.653...234445544 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.041
                         HlyD_3  30 iippdtllveakvpaadlgsikkkgqkvtlkld...qgsdytlkgkie 74 
                                    i + d+++vea+ p+a l+ i+kk q  +l+ d   q  +  ++gk++
  gi|119719011|ref|YP_919506.1|  80 ISDGDEVEVEATSPPASLQAIRKKLQGLSLESDeiyQVVKDIVDGKLS 127
                                    78889*****************99999999888665555556666665 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 3.9
                         HlyD_3  73 ierisptvdaktgaykvevslen 95 
                                    i++ + t+d+++  ++v +s+++
  gi|119719011|ref|YP_919506.1| 206 ITSAAGTADRMEVLAPVNLSIDE 228
                                    67777888888889999988886 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.021
                         HlyD_3  12 elnveegevvqagdelleiippdtllv 38 
                                    +++v+ ge v++gd+ll+++  +++++
  gi|119719011|ref|YP_919506.1| 454 YIHVKLGEKVRKGDPLLTVYSSSSAKL 480
                                    678999*************99776665 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00021      0.28      28     103 ..     165     239 ..     153     247 .. 0.86
   2 ?   -2.3   0.0       2.3   3.2e+03      59      87 ..     329     356 ..     321     370 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00021
                         RuvB_N  28 kreealdhvllyGpPGlGkttlaki.iakelgvklkitsgPvlekagdlaalltnleekdvlfideihrlsraveev 103
                                    kr+  ld   l G PG  kt+l  + i + lg ++  ts+ ++  a+  a  +  l + + l idei r+ ++++  
  gi|119719011|ref|YP_919506.1| 165 KRKPILDKHSLGGVPGD-KTSLLVVpIIASLGFTIPKTSSRAITSAAGTADRMEVLAPVN-LSIDEIERIVEKTNAC 239
                                    6888999999******5.777655448889***********************9999988.78******99887665 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.3
                         RuvB_N  59 vklkitsgPvlekagdlaalltnleekdv 87 
                                      + ++ gP+le    l+al  +l+++d+
  gi|119719011|ref|YP_919506.1| 329 EPIGHAIGPALEAREALIAL-RELRPGDL 356
                                    55667789999999888884.67777775 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1      0.52   7.2e+02      31      70 ..      25      64 ..      15      74 .. 0.80
   2 ?   10.3   0.2    0.0004      0.55      39      54 ..      75      90 ..      51     101 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.52
                                   EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESSB- CS
                Molydop_binding 31 vveinpedAaalGikdGdlVevesrrGsvevrakvtervr 70
                                   +v + +  A++l+++  d+V v+    +v++ a + ++  
  gi|119719011|ref|YP_919506.1| 25 TVVLDQSVAKKLDVRPSDRVLVRFNGKTVVAIANIAKEFS 64
                                   567778889*************988888888888877655 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0004
                                   HHHHT--TT-EEEEEE CS
                Molydop_binding 39 AaalGikdGdlVeves 54
                                   A+alGi+dGd+Veve 
  gi|119719011|ref|YP_919506.1| 75 AKALGISDGDEVEVEA 90
                                   89************85 PP

>> PriA_3primeBD  3′ DNA-binding domain (3′BD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1    0.0042       5.7      13      41 ..      29      57 ..      20     121 .. 0.89
   2 ?   -1.9   0.0       2.2   3.1e+03      51      75 ..     389     413 ..     377     424 .. 0.77
   3 ?    1.1   0.0      0.28   3.8e+02      22      65 ..     449     490 ..     424     498 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0042
                  PriA_3primeBD 13 dYrvpeelevkiGsrVlVpfgkrklvGiV 41
                                   d +v ++l+v++ +rVlV f+++++v+i 
  gi|119719011|ref|YP_919506.1| 29 DQSVAKKLDVRPSDRVLVRFNGKTVVAIA 57
                                   5578899999**************99985 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.2
                  PriA_3primeBD  51 eeeklkpieevldeepllteellel 75 
                                    +e+kl++i+e     p +t+e + l
  gi|119719011|ref|YP_919506.1| 389 AEKKLREIIEAQGGDPDVTPEEIPL 413
                                    5899999999988888888887766 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.28
                  PriA_3primeBD  22 vkiGsrVlVpfgkrklvGiVvalkeeseveeeklkpieevldee 65 
                                    + +G  + V++g++ + G  + +  +s+  ++kl+++e++l+++
  gi|119719011|ref|YP_919506.1| 449 KGAGVYIHVKLGEKVRKGDPLLTVYSSS--SAKLQAVERILEDS 490
                                    3448888888888888886555554544..68999999999864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (520 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); expected 358.6 (0.02)
Passed bias filter:                      613  (0.0341904); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.68u 0.33s 00:00:01.01 Elapsed: 00:00:00.52
# Mc/sec: 3030.19
//
Query:       gi|119719012|ref|YP_919507.1|  [L=614]
Description: aldehyde ferredoxin oxidoreductase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-97  326.1   0.0    3.5e-97  325.8   0.0    1.1  1  AFOR_C    Aldehyde ferredoxin oxidoreductase, domains 2 & 3
    5.2e-71  238.6   0.0    7.3e-71  238.1   0.0    1.2  1  AFOR_N    Aldehyde ferredoxin oxidoreductase, N-terminal doma


Domain annotation for each model (and alignments):
>> AFOR_C  Aldehyde ferredoxin oxidoreductase, domains 2 & 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  325.8   0.0  3.9e-101   3.5e-97       4     382 .]     223     599 ..     220     599 .. 0.96

  Alignments for each domain:
  == domain 1  score: 325.8 bits;  conditional E-value: 3.9e-101
                                    HHHHHHHHHSH.HHHHHHHH-GGGHHHHHHHTT---BTTTTBS--TTGGGGSHHHHHHHTEEEE.E-TT-SS--EEEEE. CS
                         AFOR_C   4 kkiqkeiksspqvtaelrkyGTaelvnianetgalptknfqegtfekaekisgealeekylvknegCfsCpiaCgrevkv 83 
                                    ++++   ks+p +++ +++ GT++++++++e+++lpt nf+eg+f++ + i+g a+e+  +v+++gC +C+  Cg+++  
  gi|119719012|ref|YP_919507.1| 223 AEAYASAKSKP-PYSFWMRQGTMATIQWSQENSVLPTFNFSEGVFDESSGIDGFAMER-LKVSQRGCPNCNSICGNVILD 300
                                    66777788899.778******************************************9.9****99************98 PP

                                    .....ETEE---HHHHHHHTGGGT---HHHHHHHHHHHHHHTB-HHHHHHHHHHHHHHHHTTSS-HHHHTS----TT-TH CS
                         AFOR_C  84 eegkkvkvegpeyetlaalGsnlgiddleailklnelcdelGlDtisaGntiafamelyekGllkkedtdglelefgdae 163
                                    +eg +   +  +ye++a+lGsn+g  dl ++++ln+l+d  G+Dti +G++++fa+e++++Gllk+       +e+gd +
  gi|119719012|ref|YP_919507.1| 301 DEGAE---SELDYENVAMLGSNIGLGDLRKVARLNRLADMWGIDTIGLGSALGFAIEASQRGLLKD------RIEWGDFD 371
                                    88885...667*****************************************************98......78****** PP

                                    HHHHHHHHHHTT-T.THHHHTT-HHHHHHCTT-GGG--EETTEE--SS-GGG-HHHHHHHHH-TTSS-SGGG-THHHHS- CS
                         AFOR_C 164 allellekiAkreg.igdllAeGvkrlaeklgaeelamhvkGlelpaydprgakgmalaYatsnrGacHlraylialeek 242
                                    ++lel ++i  +eg +g +l+eGv+++++ lg ee+a+hvkGl+++ayd+++a+gmal+Y +s+ Ga+H +a++i++e +
  gi|119719012|ref|YP_919507.1| 372 KILELSREISLGEGpVGSVLSEGVEHASKVLGCEECAVHVKGLSVSAYDCHAAPGMALSYGVSSVGAHHKDAWVISWEVA 451
                                    ******************************************************************************** PP

                                    --TT--.HHHHHHHHHHHH.HHHHHHHHT--GGGG-HHH......HHHHHHHHHT----HHHHHHHHHHHHHHHHHHHHH CS
                         AFOR_C 243 vdplet.egkaelvkwfqd.ltalvdslglCkftseaeerldlelyakllsavtGidvteeellkaGeRiynleRlfnlr 320
                                    + ++e+ ++ka+ v   q+ +  +++ l++C++++ +e  l+l++y+kl++ +tG+++t ++ lk+++R ++l R +++r
  gi|119719012|ref|YP_919507.1| 452 HGRFEYsKAKAKRVYELQRiRGGFFENLVACRLPW-VELGLELDWYVKLFNYATGLSWTLDDHLKVADRTITLIRSYWVR 530
                                    ******99***********8889************.8999**************************************** PP

                                    HT--......HHHS---HHHHHS---SSTTTT---...-HHHHHHHHHHHHT--TTS---HHHHHHCT- CS
                         AFOR_C 321 eGlt......rkddtlperlleeplkegpakgkvl.edeleemldeyYelrGWdetGvPtketlkrLgL 382
                                    e+l       r+ d  p +++++p + gp kg+ l  ++++e+l +yYel GWd +GvP ++tl+rLgL
  gi|119719012|ref|YP_919507.1| 531 EYLAegrrwgRQLDYPPLKWFTKPYTRGPLKGARLdPQKYDELLGNYYELVGWDHRGVPRASTLERLGL 599
                                    *887676665666*********************98999*****************************8 PP

>> AFOR_N  Aldehyde ferredoxin oxidoreductase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  238.1   0.0   8.2e-75   7.3e-71       1     197 [.       8     206 ..       8     207 .. 0.98

  Alignments for each domain:
  == domain 1  score: 238.1 bits;  conditional E-value: 8.2e-75
                                    SEEEEEETTTTEEEEEE--HHHHHHH-SCHHHHHHHHHHHS-TTS-TTSTTS-EEEEE-TTTTSSSTTB-EEEEEEE-TT CS
                         AFOR_N   1 gkilrvdLstgkieveelpeelaekylGgrglaakllldevppgvdplspenplvfatGpltgtpapgsgrlvvvaksPl 80 
                                    g++l+vdLs+++++v+el+  ++ +++Ggrgla++ll+d++ pgvdplspen lvf++Gp+t  p p++g+lvv++ksPl
  gi|119719012|ref|YP_919507.1|   8 GRVLWVDLSRKSTKVQELDGGILLSHVGGRGLAVRLLWDYTSPGVDPLSPENLLVFSAGPITALPGPSTGKLVVASKSPL 87 
                                    699****************99*********************************************************** PP

                                    TSSEEEEEEETCHHHHHHHCT-SEEEEES--SS-EEEEEETTEEEEEE-TTTTTS-HHHHHHHHHHHHTS..EEEEE-HH CS
                         AFOR_N  81 tgtlgesnaGgrfgaelkraGydaivieGkaekpvylvieddkveiedaedlwgldtyettealkeelgd..kvaviGpa 158
                                    t+++g+ n G r++ +l++aGyda+v++Gk++kpvy+++e++kve+ da+dlwgldt+ ++++l e++g+   v+ iGp 
  gi|119719012|ref|YP_919507.1|  88 THGYGDGNLGTRAAVMLRWAGYDAVVFKGKSPKPVYVYVENEKVEFLDADDLWGLDTFSAEKRLLERHGKdaGVLLIGPS 167
                                    ******************************************************************999977777***** PP

                                    HHTT-TTB-E.EETTEEE-SSSHHHHHHHTTEEEEEEE- CS
                         AFOR_N 159 GenlvrfAsisvddgraagrgGlGavmgsKnlkaivvrg 197
                                    Ge++v++A+++ ++gr+ gr G+GavmgsKnlka+v+rg
  gi|119719012|ref|YP_919507.1| 168 GERMVKMATVVSQSGRSGGRPGIGAVMGSKNLKAVVFRG 206
                                    **********777*************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (614 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 3987.72
//
Query:       gi|119719013|ref|YP_919508.1|  [L=76]
Description: thiamineS protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-06   27.8   0.1    3.5e-06   27.6   0.1    1.2  1  ThiS      ThiS family


Domain annotation for each model (and alignments):
>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.1     2e-10   3.5e-06      10      77 .]      14      76 .]       5      76 .] 0.76

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 2e-10
                                   HHT..CEEEEESSTSBHHHHHHHHHHHTCHHGTTTTEEEEETTEEEGCCTTTSB--TTCEEEEEESTTC- CS
                           ThiS 10 lag..eeelelaegstvaelleaLgerypelalerrvavavNgeivprlwldtelkdgDevailppVaGG 77
                                   +a+  e ++ ++ ++ ++e+l +         + + ++v+vN+  ++    dt +++gD+v ilp ++GG
  gi|119719013|ref|YP_919508.1| 14 VAKarELTVGVEKPTRLEEILGEGFLAK----SGKDLVVLVNDLPATL---DTYVRPGDVVKILPHIGGG 76
                                   5555555556777888888887643222....34**************...******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       262  (0.0146132); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 519.06
//
Query:       gi|119719014|ref|YP_919509.1|  [L=132]
Description: hypothetical protein Tpen_0096 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 827.13
//
Query:       gi|119719015|ref|YP_919510.1|  [L=140]
Description: hypothetical protein Tpen_0097 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-16   60.9   0.9    1.8e-16   60.6   0.9    1.1  1  CxxCxxCC  Putative zinc- or iron-chelating domain
     0.0055   16.5   2.4      0.031   14.1   2.4    2.2  1  DUF3109   Protein of unknown function (DUF3109)


Domain annotation for each model (and alignments):
>> CxxCxxCC  Putative zinc- or iron-chelating domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.6   0.9     2e-20   1.8e-16       2      85 .]      16     106 ..      15     106 .. 0.92

  Alignments for each domain:
  == domain 1  score: 60.6 bits;  conditional E-value: 2e-20
                       CxxCxxCC   2 CkeCgaCCkelkvklteedlerlkaaevaeeeeeskkiak......adgrCvfldeetklCkiYeeRpkicrlfpas.ek 74 
                                    C+ Cg CC+++++ l eed+er++ +   + e++++++        ++g+Cvf+d e++ C+iY  Rp  c l+p + ++
  gi|119719015|ref|YP_919510.1|  16 CRVCGRCCENTEMILLEEDVERISSYTGLRAEDFAERLGGrfklknVNGKCVFFDAEKGSCTIYPVRPIGCSLYPVVvDE 95 
                                    ***********************99999888888887766899999******************************9777 PP

                       CxxCxxCC  75 eellaraetCa 85 
                                     e l+++e+C+
  gi|119719015|ref|YP_919510.1|  96 YEGLTVDEYCP 106
                                    78899999996 PP

>> DUF3109  Protein of unknown function (DUF3109)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   2.4   3.5e-06     0.031     101     140 ..      74     104 ..      14     118 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.5e-06
                        DUF3109 101 alCaiekayregkikfkKPisChlyPirvkklselealny 140
                                      C+i            +Pi C lyP+ v ++++l+  +y
  gi|119719015|ref|YP_919510.1|  74 GSCTI---------YPVRPIGCSLYPVVVDEYEGLTVDEY 104
                                    22332.........3579****************998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 930.43
//
Query:       gi|119719016|ref|YP_919511.1|  [L=227]
Description: hypothetical protein Tpen_0098 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.4e-35  120.4   0.0    6.2e-35  119.9   0.0    1.2  1  CTP-dep_RFKase  Domain of unknown function DUF120
  ------ inclusion threshold ------
      0.034   14.0   0.0      0.069   13.0   0.0    1.4  1  MarR_2          MarR family
      0.045   14.1   0.0      0.096   13.1   0.0    1.5  1  HARE-HTH        HB1, ASXL, restriction endonuclease HTH domai
       0.14   12.2   0.0       0.47   10.5   0.0    1.8  2  HTH_45          Winged helix-turn-helix
       0.16   12.2   0.0       0.52   10.5   0.0    1.8  2  HTH_34          Winged helix DNA-binding domain
       0.24   11.6   0.0       0.37   11.0   0.0    1.2  1  STN1_2          CST, Suppressor of cdc thirteen homolog, comp


Domain annotation for each model (and alignments):
>> CTP-dep_RFKase  Domain of unknown function DUF120
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.9   0.0   2.1e-38   6.2e-35       1     121 []      99     225 ..      99     225 .. 0.91

  Alignments for each domain:
  == domain 1  score: 119.9 bits;  conditional E-value: 2.1e-38
                                    EE--SSHHHHHHCSHHHHHHHHHHHSS---SS-EEEEESCCGHHHHCHH.HHS--EEE--EE.ETTEEE--EEEEEEEE. CS
                 CTP-dep_RFKase   1 VvsGlgeGkyyvslegykeqfeeklgfepypGTLNvkldeeslelrkal.eklkgieiegfe.deertfgavkvypaki. 77 
                                    Vv GlgeG++y+ ++ y e+f+e lg+epypGTLN+kl +e++ lr+al ek  g++iegf+ de+r+ ++v+vy+a+i 
  gi|119719016|ref|YP_919511.1|  99 VVPGLGEGAIYMGIPRYVEAFKEVLGYEPYPGTLNIKLVDEDVYLRRALrEKRVGFRIEGFRlDEGRESCGVTVYKAMIm 178
                                    899*************************************9776666661566789*****97899*************7 PP

                                    ...CCEEEEEEEESS-SS.TTEEEEE-SS-HHHHTT--TT-EEEEEE CS
                 CTP-dep_RFKase  78 ...ekikaavvvperthyeedvlEiiapekLReklelkdgdevevev 121
                                        ++++a +  ++t++ +++lE+iap++LR++l+lkdgd+vev +
  gi|119719016|ref|YP_919511.1| 179 angVTVSGAALDIDKTKHGDEILELIAPVRLRDELRLKDGDKVEVVI 225
                                    643355999***********************************976 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.3e-05     0.069      19      54 ..      23      58 ..       9      62 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.3e-05
                                   TSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                         MarR_2 19 grdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                   +r+l+  e+ ++lgl++ +  ++++ +++ G++err
  gi|119719016|ref|YP_919511.1| 23 PRRLSRIEILKTLGLTPWRFKKLVEAAEEEGYIERR 58
                                   4578999****************************9 PP

>> HARE-HTH  HB1, ASXL, restriction endonuclease HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   3.2e-05     0.096       8      65 ..      29      97 ..      28     100 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.2e-05
                                   HHHHHHH-.S-EEHHHHHHHHHHHTTS-...........GGHHGCHHH.HHHHHHH...HSTTEEESSSS CS
                       HARE-HTH  8 kqVLeeeg.rpltvkeIwekiqekgliklt.........gktpeatlaaqlytdik..gddslFvkvgpg 65
                                   +++L++ g  p  +k+++e + e+g+i+++          ++  + l  + y d+k   d+s F+++ +g
  gi|119719016|ref|YP_919511.1| 29 IEILKTLGlTPWRFKKLVEAAEEEGYIERRvhgrmvfyvVTERGRALLRRVYDDLKrtIDSSTFLTL-RG 97
                                   589999999********************9********97777777777*******9999999*999.65 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00016      0.47      24      69 ..      30      79 ..      21      87 .. 0.81
   2 ?   -1.6   0.0       0.9   2.7e+03      59      70 ..     194     205 ..     173     209 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00016
                         HTH_45 24 kimykanLsykllnkYLdmLvekgli....kkskekYvlTekGlellekl 69
                                   +i++   L+  +++k ++   e+g+i    + +   Yv+Te+G+ ll+++
  gi|119719016|ref|YP_919511.1| 30 EILKTLGLTPWRFKKLVEAAEEEGYIerrvHGRMVFYVVTERGRALLRRV 79
                                   678888888889999999999999996654557889***********975 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.9
                         HTH_45  59 TekGlelleklk 70 
                                    T+ G e+le + 
  gi|119719016|ref|YP_919511.1| 194 TKHGDEILELIA 205
                                    888999998775 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00017      0.52      18      80 .]      29      87 ..      19      87 .. 0.83
   2 ?   -2.0   0.0       1.4   4.2e+03      17      29 ..     206     218 ..     202     219 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00017
                         HTH_34 18 velkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafkkyvkaLksll 80
                                    e+ ++l++t  +  + +++ e+ gYie++    g+  +  + +T+ Gr+   ++ + Lk+ +
  gi|119719016|ref|YP_919511.1| 29 IEILKTLGLTPWRFKKLVEAAEEEGYIERRV--HGR--MVFYVVTERGRALLRRVYDDLKRTI 87
                                   567788888888999999999******9874..455..99******************99875 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.4
                         HTH_34  17 fvelkealeatdg 29 
                                    +v+l+++l++ dg
  gi|119719016|ref|YP_919511.1| 206 PVRLRDELRLKDG 218
                                    789******9998 PP

>> STN1_2  CST, Suppressor of cdc thirteen homolog, complex subunit STN1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00012      0.37     110     152 ..      42      84 ..      37      89 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00012
                                    HHHHHHHHHHCTSEE-SSSSSTTEEEEGCCSHHHHHHHHHHHH CS
                         STN1_2 110 fkealqllqeeGlvfqkkksqdelyqvteqdkdLlkaildiir 152
                                    fk+ ++  +eeG++ ++++ +   y+vte+ + Ll+ ++d ++
  gi|119719016|ref|YP_919511.1|  42 FKKLVEAAEEEGYIERRVHGRMVFYVVTERGRALLRRVYDDLK 84 
                                    999*********************************9988655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1496.74
//
Query:       gi|119719017|ref|YP_919512.1|  [L=133]
Description: hypothetical protein Tpen_0099 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 988.50
//
Query:       gi|119719018|ref|YP_919513.1|  [L=186]
Description: peptidase, zinc-dependent [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-27   97.2   0.0    1.4e-27   97.0   0.0    1.2  1  Peptidase_M54  Peptidase family M54
     0.0047   15.6   0.1     0.0066   15.1   0.1    1.1  1  Metallopep     Putative peptidase family
     0.0049   17.4   0.0     0.0062   17.1   0.0    1.3  1  Reprolysin_3   Metallo-peptidase family M12B Reprolysin-like
     0.0067   15.4   0.0     0.0096   14.9   0.0    1.2  1  Peptidase_M66  Peptidase M66
     0.0086   15.9   0.0     0.0086   15.9   0.0    1.2  1  Peptidase_M10  Matrixin
  ------ inclusion threshold ------
      0.055   12.7   0.2       0.09   12.0   0.2    1.3  1  DUF4953        Met-zincin
       0.18   11.9   0.0       0.19   11.9   0.0    1.2  1  Reprolysin_5   Metallo-peptidase family M12


Domain annotation for each model (and alignments):
>> Peptidase_M54  Peptidase family M54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.0   0.0   5.5e-31   1.4e-27      96     193 ..      76     176 ..      17     177 .. 0.81

  Alignments for each domain:
  == domain 1  score: 97.0 bits;  conditional E-value: 5.5e-31
                                    ..EEEESS-EE-TT-S-BSEEE-SSSSEEEEE-T..--.......SHHHHHHHHHHHHHHHHHHHTT----S-TSTTS-- CS
                  Peptidase_M54  96 ttlplgsrdqyidiykkvlGievsiGnyavlals..ikefyte..dkeLflervvkevlhelGhlyGLshCkedCvmnfs 171
                                     +l +   d y++++++v+G++ + G   +++ +    efy e   +eLf  r +ke +helGh +GL+hC+++Cvm fs
  gi|119719018|ref|YP_919513.1|  76 RALVVIGADGYVEGLNFVFGVAND-GWGGIVFTErlNPEFYGEqfSEELFRARLLKEAIHELGHSFGLGHCRQNCVMRFS 154
                                    35778889**************99.99999999875568**997889********************************* PP

                                    SSHHHHHHS-SS--HHHHHHHH CS
                  Peptidase_M54 172 ndlkdvDrkapkyCksCleklk 193
                                    n++ dvD k p +Ck+C   + 
  gi|119719018|ref|YP_919513.1| 155 NSVYDVDSKPPFFCKRCSAAIS 176
                                    *****************98876 PP

>> Metallopep  Putative peptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   2.6e-06    0.0066     319     337 ..     133     152 ..     131     159 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.6e-06
                     Metallopep 319 lHEiGHllglpHqed.Gvml 337
                                    +HE+GH +gl+H+ +  vm 
  gi|119719018|ref|YP_919513.1| 133 IHELGHSFGLGHCRQnCVMR 152
                                    8***********98768885 PP

>> Reprolysin_3  Metallo-peptidase family M12B Reprolysin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   2.4e-06    0.0062      77     123 ..      86     144 ..      38     145 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.4e-06
                   Reprolysin_3  77 gvgGlAyvgsvcnsskk...agvnsgssvlgkvga.............dtvaHEiGHnfganH 123
                                     v Gl +v +v n +++   +     ++ + ++               + ++HE+GH+fg+ H
  gi|119719018|ref|YP_919513.1|  86 YVEGLNFVFGVANDGWGgivF----TERLNPEFYGeqfseelfrarllKEAIHELGHSFGLGH 144
                                    566777776666666663221....22222222222344466667777999***********9 PP

>> Peptidase_M66  Peptidase M66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   3.8e-06    0.0096     191     209 ..     127     145 ..     122     162 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.8e-06
                  Peptidase_M66 191 tltgefiHEqGHalGLpHy 209
                                    +l +e iHE+GH++GL+H 
  gi|119719018|ref|YP_919513.1| 127 RLLKEAIHELGHSFGLGHC 145
                                    677899************4 PP

>> Peptidase_M10  Matrixin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   3.3e-06    0.0086     108     133 ..     127     151 ..      39     163 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.3e-06
                                    EHHHHHHHHHHHHTTBESXSSTTSTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M10 108 slflVaaHEiGHalGLeHssdkdalm 133
                                     l+  a+HE+GH+ GL H +++  +m
  gi|119719018|ref|YP_919513.1| 127 RLLKEAIHELGHSFGLGHCRQN-CVM 151
                                    566779************7654.455 PP

>> DUF4953  Met-zincin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   3.5e-05      0.09       2      29 ..     117     144 ..     116     147 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.5e-05
                        DUF4953   2 eefpdelmgallrfvvaHEvGhtLGLrh 29 
                                    e+f++el++a+l   + HE Gh +GL h
  gi|119719018|ref|YP_919513.1| 117 EQFSEELFRARLLKEAIHELGHSFGLGH 144
                                    6899**********************99 PP

>> Reprolysin_5  Metallo-peptidase family M12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   7.3e-05      0.19     147     160 ..     133     146 ..      53     165 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.3e-05
                   Reprolysin_5 147 aHElGHnfGavHDc 160
                                     HElGH+fG  H  
  gi|119719018|ref|YP_919513.1| 133 IHELGHSFGLGHCR 146
                                    6**********944 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1395.61
//
Query:       gi|119719019|ref|YP_919514.1|  [L=243]
Description: 5-formyltetrahydrofolate cyclo-ligase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-25   89.3   0.0    3.6e-25   88.9   0.0    1.1  1  5-FTHF_cyc-lig  5-formyltetrahydrofolate cyclo-ligase family


Domain annotation for each model (and alignments):
>> 5-FTHF_cyc-lig  5-formyltetrahydrofolate cyclo-ligase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.9   0.0     2e-29   3.6e-25       1     186 [.      12     204 ..      12     205 .. 0.84

  Alignments for each domain:
  == domain 1  score: 88.9 bits;  conditional E-value: 2e-29
                                    HHHHHHHHHHHHHTS-HHHHHHHHHHHHHHHHTSHHHHH-.SEE........EE----TTS---HHHHHHHHHTTEEEEE CS
                 5-FTHF_cyc-lig   1 KqelRkqllaalralseeevaaesealsqrieslkesqea.krv........alyvsvkgeidtkelikklleegkevll 71 
                                    K+elR+    ++++l+  eva ++++ +++i+s+++   a +r+        a +v   ++ +t+ l++++l++gk +++
  gi|119719019|ref|YP_919514.1|  12 KAELRRS---VWSKLERMEVAISPRPCYGKIPSFVGIHSAtQRLiktdvyrnARVVYSTPDTSTRLLREETLRRGKTLVV 88 
                                    7899999...9*****************************99999*******999999********************** PP

                                    EEECSSCTEECEEEEEECCCCC.CCCCHCTSSCE--TTECCBCGGG..G-SEEEE--SEEETTS-EE-SSTTHHHHHHHH CS
                 5-FTHF_cyc-lig  72 Prvrlesgslkvvrlttlkeed.slesgkyglkePeeeeerelale..kldlvlvPgvAfdkeGaRlGkGkGyyDrflar 148
                                      + l+     +vr ++l++ d +l+s   ++k  +++  r   le  k+dlv+ ++vA++++GaRlG+G G  D ++a 
  gi|119719019|ref|YP_919514.1|  89 SIPGLKG--YVIVRPDELEPGDvRLAS---SVKGAVTKGDRITLLEglKIDLVVLGSVAVNTDGARLGRGDGMHDLEYAL 163
                                    *999999..334443333333213333...333333333333333456******************************** PP

                                    HTS.T-SS--EEEEE--GGGEES..-----ST----SEEE- CS
                 5-FTHF_cyc-lig 149 lkg.gagdkpltvglaldeqlve..rlPleehDvpvdevvt 186
                                    l++  a +++++v++++++ ++   ++P+  hDvp+d +  
  gi|119719019|ref|YP_919514.1| 164 LREmYAVAESTPVATLVHDLQILeePIPMLMHDVPIDYIAS 204
                                    *******************9987789***********9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1716.82
//
Query:       gi|119719020|ref|YP_919515.1|  [L=82]
Description: CopG family transcriptional regulator [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.2e-09   34.9   0.0    1.7e-08   34.1   0.0    1.4  1  RHH_1          Ribbon-helix-helix protein, copG family
    6.2e-07   29.6   0.1    6.8e-07   29.5   0.1    1.1  1  RHH_8          Ribbon-Helix-Helix transcriptional regulator f
  ------ inclusion threshold ------
      0.052   14.1   0.0      0.065   13.8   0.0    1.1  1  YuiB           Putative membrane protein
      0.069   13.2   0.0       0.14   12.2   0.0    1.5  1  TFIIA_gamma_N  Transcription initiation factor IIA, gamma sub


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.0   3.7e-12   1.7e-08       2      38 ..      26      63 ..      26      64 .. 0.97

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 3.7e-12
                                   EEEEEEHHHHHHHHHHHHHHT.SSHHHHHHHHHHHHHH CS
                          RHH_1  2 vsirldeellerLdelarrrg.rSrSelIReAlreyle 38
                                   vs++l+  l+++Ldel+ ++  ++rS++IReA+r +l+
  gi|119719020|ref|YP_919515.1| 26 VSVKLPVGLIDALDELIQKGYfQNRSDAIREAIRKLLT 63
                                   89********************************9985 PP

>> RHH_8  Ribbon-Helix-Helix transcriptional regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.1   1.5e-10   6.8e-07      12      52 ..      32      72 ..      21      82 .] 0.74

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 1.5e-10
                          RHH_8 12 vvDLgqiDlLveeGfYsnRtDlirtairaqLakhddalkqa 52
                                   v  +  +D L+++G++ nR+D ir+air+ L+++++  ++ 
  gi|119719020|ref|YP_919515.1| 32 VGLIDALDELIQKGYFQNRSDAIREAIRKLLTNYRELDSRK 72
                                   333447899***********************998855444 PP

>> YuiB  Putative membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.4e-05     0.065      27      81 ..      23      78 ..      19      81 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.4e-05
                           YuiB 27 tWilaviypivvllivdkvklleyltepkeafasllek.lvelalvDililvsgli 81
                                   t i+ v +p+ ++  +d+     y+++ ++a+++ ++k l++++  D   ++sgl+
  gi|119719020|ref|YP_919515.1| 23 TKIVSVKLPVGLIDALDELIQKGYFQNRSDAIREAIRKlLTNYRELDSRKISSGLM 78
                                   77999***************************98766626899*****99999985 PP

>> TFIIA_gamma_N  Transcription initiation factor IIA, gamma subunit, helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0     3e-05      0.14      14      28 ..      34      48 ..      30      54 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3e-05
                  TFIIA_gamma_N 14 LtdaLDeliqegkIs 28
                                   L daLDeliq+g ++
  gi|119719020|ref|YP_919515.1| 34 LIDALDELIQKGYFQ 48
                                   99*********9877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       808  (0.0450667); expected 358.6 (0.02)
Passed bias filter:                      745  (0.0415528); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 595.93
//
Query:       gi|119719021|ref|YP_919516.1|  [L=115]
Description: methionyl-tRNA synthetase, beta subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      7e-30  103.0   0.1    8.1e-30  102.8   0.1    1.0  1  tRNA_bind  Putative tRNA binding domain


Domain annotation for each model (and alignments):
>> tRNA_bind  Putative tRNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.8   0.1   4.5e-34   8.1e-30       1      96 []      21     113 ..      21     113 .. 0.98

  Alignments for each domain:
  == domain 1  score: 102.8 bits;  conditional E-value: 4.5e-34
                                    EEEEEEEEEEEETTSSTEEEEEEEESSSSEEEEEESCTTTSTHHHHTTEEEEEETTSESEEETTEEESSEE-EEECCESS CS
                      tRNA_bind   1 lrvGkvleaeehpnadkLlvlkvdvGeeeprqivsgaknvyepeelvakkvvvvanlkpkklrGveSeGMilsaeeldek 80 
                                    +r+G++l+ae+++ +dkLl lkvd+G+e+ rqiv+g++ +y+peelv+k+v+v+anl+pk ++G+ S+GM+l+a   +++
  gi|119719021|ref|YP_919516.1|  21 IRIGRILSAEPIKRSDKLLLLKVDLGTEQ-RQIVAGLAPYYKPEELVGKEVAVLANLQPKTIMGFVSQGMLLAAV--EDG 97 
                                    79***************************.*********************************************..6** PP

                                    CEEEEEESST--TTCE CS
                      tRNA_bind  81 evgilelpadveaGek 96 
                                    +  +l ++++v++G+k
  gi|119719021|ref|YP_919516.1|  98 KPVLLVPEKEVKVGAK 113
                                    *************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       263  (0.014669); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 847.26
//
Query:       gi|119719022|ref|YP_919517.1|  [L=100]
Description: hypothetical protein Tpen_0104 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.6e-07   29.7   0.0    9.4e-07   29.2   0.0    1.2  1  HTH_27    Winged helix DNA-binding domain
    4.9e-05   23.1   0.1    6.4e-05   22.7   0.1    1.1  1  HxlR      HxlR-like helix-turn-helix
    0.00026   20.8   0.0    0.00044   20.1   0.0    1.5  1  TrmB      Sugar-specific transcriptional regulator TrmB
    0.00026   20.9   0.1    0.00036   20.5   0.1    1.2  1  HTH_45    Winged helix-turn-helix
     0.0005   19.9   0.4      0.003   17.4   0.1    2.0  2  HTH_5     Bacterial regulatory protein, arsR family
     0.0011   19.0   0.0      0.015   15.3   0.0    2.1  2  HTH_20    Helix-turn-helix domain
       0.01   16.0   0.0      0.014   15.5   0.0    1.2  1  HTH_34    Winged helix DNA-binding domain
  ------ inclusion threshold ------
      0.011   15.6   0.0      0.019   14.9   0.0    1.4  1  PadR      Transcriptional regulator PadR-like family
      0.018   15.0   0.9      0.038   13.9   0.4    1.8  2  HTH_11    HTH domain
      0.023   14.5   0.0      0.029   14.2   0.0    1.3  1  DUF1495   Winged helix DNA-binding domain (DUF1495)
      0.051   13.4   0.0       0.37   10.6   0.0    2.0  2  HTH_IclR  IclR helix-turn-helix domain
      0.068   13.1   0.0       0.15   12.0   0.0    1.6  1  MarR_2    MarR family


Domain annotation for each model (and alignments):
>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.0   6.3e-10   9.4e-07       7      68 .]      18      76 ..      13      76 .. 0.82

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 6.3e-10
                         HTH_27  7 lvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLv..ertgdeadrrekrvrlTdkG 68
                                   l+L ++   +++kk++dl+++  ++ ++i ++++kL e GL+   r g++   +++ +rlT+kG
  gi|119719022|ref|YP_919517.1| 18 LILLSLL--NGEKKISDLRQAASLSTTSIYNNINKLLEWGLIedDRVGSP---GNRIIRLTEKG 76
                                   4444444..5********************************55555666...67********9 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.1   4.3e-08   6.4e-05       9      81 ..      18      88 ..      16      96 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 4.3e-08
                                   HHHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHHHHHHHHH CS
                           HxlR  9 lilvellkgkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrslepvlqelkk 81
                                   lil +ll+g+k+ s+l++a  ++s+  + +++ +L + glie + + + ++++  +ltekG  ++ +l++l++
  gi|119719022|ref|YP_919517.1| 18 LILLSLLNGEKKISDLRQAA-SLSTTSIYNNINKLLEWGLIEDDRVGSPGNRI-IRLTEKGLRVARILKMLED 88
                                   8***************9998.89999999***************998877765.69*************9976 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   2.9e-07   0.00044      15      56 ..      21      61 ..      13      77 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.9e-07
                                   HHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                           TrmB 15 laLlklgpatadeiaeelgvprskvYevLrsLedkGlVerek 56
                                   l Ll +g+++++++ +++ ++ +++Y+ +++L++ Gl+e  +
  gi|119719022|ref|YP_919517.1| 21 LSLL-NGEKKISDLRQAASLSTTSIYNNINKLLEWGLIEDDR 61
                                   4455.9*********************************877 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.1   2.4e-07   0.00036      11      74 ..      19      88 ..      12      91 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.4e-07
                         HTH_45 11 ILeaisegeakkTkimykanLsykllnkYLdmLvekgli......kkskekYvlTekGlelleklkelee 74
                                   IL ++ +ge+k + +  +a Ls   + + +++L+e gli      +  +   +lTekGl++ + lk le+
  gi|119719022|ref|YP_919517.1| 19 ILLSLLNGEKKISDLRQAASLSTTSIYNNINKLLEWGLIeddrvgSPGNRIIRLTEKGLRVARILKMLED 88
                                   666677*********************************7777755577889********9999998876 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1     2e-06     0.003       7      46 ..      19      58 ..      18      59 .. 0.97
   2 ?    0.5   0.0      0.37   5.6e+02       6      13 ..      81      88 ..      78      96 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2e-06
                                   HHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_5  7 ILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                   IL +L +ge+++++l  +  ls   +    +kL e GL+e
  gi|119719022|ref|YP_919517.1| 19 ILLSLLNGEKKISDLRQAASLSTTSIYNNINKLLEWGLIE 58
                                   9*************************************97 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.37
                                   HHHHHHTT CS
                          HTH_5  6 kILklLae 13
                                   +ILk+L++
  gi|119719022|ref|YP_919517.1| 81 RILKMLED 88
                                   79999987 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0     1e-05     0.015      18      60 ..      23      63 ..      15      64 .. 0.87
   2 ?    1.6   0.0       0.2     3e+02      13      28 ..      80      93 ..      79      96 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1e-05
                                   HHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                         HTH_20 18 aLaraegltaselaerldlskntlsyHLrvLeeagLvevvreg 60
                                   +L  +++   s+l ++ +ls +++++++++L e gL+e  r+g
  gi|119719022|ref|YP_919517.1| 23 LL--NGEKKISDLRQAASLSTTSIYNNINKLLEWGLIEDDRVG 63
                                   45..666677999**************************9997 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.2
                                   HHHHHHHSTCTTB-HH CS
                         HTH_20 13 rrilraLaraegltas 28
                                   +ril++L  +++lt++
  gi|119719022|ref|YP_919517.1| 80 ARILKML--EDELTPK 93
                                   69*****..9999976 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   9.6e-06     0.014      11      67 ..      23      78 ..      17      89 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 9.6e-06
                         HTH_34 11 s.vdeadfvelkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGre 67
                                     + e + ++l++a ++++  ++ +++kL + g ie d   + +  + ++r+T++G+ 
  gi|119719022|ref|YP_919517.1| 23 LlNGEKKISDLRQAASLSTTSIYNNINKLLEWGLIEDDRVGSPG--NRIIRLTEKGLR 78
                                   246677889**************************999887777..899*******85 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   1.3e-05     0.019      18      72 ..      29      79 ..      27      82 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.3e-05
                                   HHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHH CS
                           PadR 18 eleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrre 72
                                   ++++l + +  ls +s+Y + ++L + gl+e  ++ s   p  ++ rlT++G r 
  gi|119719022|ref|YP_919517.1| 29 KISDLRQ-AASLSTTSIYNNINKLLEWGLIEDDRVGS---PGNRIIRLTEKGLRV 79
                                   5556643.47899*******************98865...9999*******9775 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.4   2.5e-05     0.038       9      44 ..      23      56 ..      15      78 .. 0.78
   2 ?   -1.4   0.0       1.6   2.3e+03       1      10 [.      78      87 ..      78      92 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.5e-05
                         HTH_11  9 LleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                   Ll+ ++   +++L +  ++S++ +++ I +L e+g+
  gi|119719022|ref|YP_919517.1| 23 LLNGEK--KISDLRQAASLSTTSIYNNINKLLEWGL 56
                                   334444..6889***********************2 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.6
                         HTH_11  1 RllqilelLl 10
                                   R   il++L 
  gi|119719022|ref|YP_919517.1| 78 RVARILKMLE 87
                                   6678999983 PP

>> DUF1495  Winged helix DNA-binding domain (DUF1495)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0     2e-05     0.029      52      89 ..      44      82 ..      19      83 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2e-05
                        DUF1495 52 rynsessLielGLvee.eeeseglklYklteeGieivev 89
                                    yn+ + L+e GL+e  + +s+g ++ +lte+G +++ +
  gi|119719022|ref|YP_919517.1| 44 IYNNINKLLEWGLIEDdRVGSPGNRIIRLTEKGLRVARI 82
                                   5899999*******862567***************9976 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00025      0.37      15      51 ..      24      60 ..      18      61 .. 0.85
   2 ?    0.6   0.0      0.33     5e+02       4      15 ..      78      89 ..      77      97 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00025
                                   TBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                       HTH_IclR 15 apqeltlselArrtglpkStvhRlLqtLvelGyveqd 51
                                    ++e ++s+l +++ l+ ++ ++ ++ L e+G++e d
  gi|119719022|ref|YP_919517.1| 24 LNGEKKISDLRQAASLSTTSIYNNINKLLEWGLIEDD 60
                                   4556689***************************977 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.33
                                   HHHHHHCT-CTT CS
                       HTH_IclR  4 RalaiLdalaea 15
                                   R ++iL++l+ +
  gi|119719022|ref|YP_919517.1| 78 RVARILKMLEDE 89
                                   788999988765 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0    0.0001      0.15      10      52 ..      19      58 ..      13      68 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0001
                                   HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                         MarR_2 10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                   +L+ L +++     +++l ++  ls  ++ + +++L + GL+e
  gi|119719022|ref|YP_919517.1| 19 ILLSLLNGEK---KISDLRQAASLSTTSIYNNINKLLEWGLIE 58
                                   4555666665...89***************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 764.35
//
Query:       gi|119719023|ref|YP_919518.1|  [L=188]
Description: isochorismatase hydrolase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.3e-48  162.9   0.0    9.4e-48  162.7   0.0    1.0  1  Isochorismatase  Isochorismatase family
  ------ inclusion threshold ------
       0.13   11.8   0.0       0.22   11.1   0.0    1.4  1  AAA_25           AAA domain


Domain annotation for each model (and alignments):
>> Isochorismatase  Isochorismatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.7   0.0     1e-51   9.4e-48       2     171 ..       5     171 ..       4     175 .. 0.96

  Alignments for each domain:
  == domain 1  score: 162.7 bits;  conditional E-value: 1e-51
                Isochorismatase   2 alvviDmqndfveegvkeseeisavveninkllkaarkagipviftrdvheleevkgdlderkaaphfkpgttgaelvpe 81 
                                    a++viDm ++fv +g+ + e+++++v+ i++l++ a++ gipvi+  d+h    +  d++ r + +h ++g+ ++++v+e
  gi|119719023|ref|YP_919518.1|   5 AVLVIDMLEEFV-RGRLRAENAEKIVKPIKRLIDFAHETGIPVIHAVDQHY---PDVDFEFRLWGAHAVRGAAESKIVEE 80 
                                    89**********.**************************************...99************************ PP

                Isochorismatase  82 laplegdvvvdKtrfsafagtdldeiLkelgiktivlaGiatdvCVeatardaldlGyevvvvsDAvaalspelhdaalk 161
                                    lap e+d+vv K+r++af  tdld +L+elg++t++++Gi+t++CV++t++ a+ +Gy v+v+ ++vaa++ + h+ +l+
  gi|119719023|ref|YP_919518.1|  81 LAPSEKDFVVPKRRYDAFMFTDLDMLLRELGVTTLIVTGIHTHICVQQTVLGAFYRGYSVIVPLECVAAFNDTWHKIGLD 160
                                    ******************************************************************************** PP

                Isochorismatase 162 rlkqaf.atvi 171
                                     +k++  at++
  gi|119719023|ref|YP_919518.1| 161 YMKNYAnATLM 171
                                    ***65525554 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   2.5e-05      0.22     141     184 ..       2      47 ..       1      50 [. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.5e-05
                         AAA_25 141 egvrlvviDplsralgg..densnsdvgalvealeriarrtgaavl 184
                                    ++++++viD+l ++++g    ++++++ + +++l ++a++tg+ v+
  gi|119719023|ref|YP_919518.1|   2 PKYAVLVIDMLEEFVRGrlRAENAEKIVKPIKRLIDFAHETGIPVI 47 
                                    5689*************88777777789999***********9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1469.99
//
Query:       gi|119719024|ref|YP_919519.1|  [L=295]
Description: phage integrase family protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.1e-49  166.4   0.5    7.4e-49  165.8   0.5    1.2  1  Phage_integrase  Phage integrase family
    3.7e-10   40.0   3.7    6.1e-10   39.3   0.2    2.9  4  Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain
    2.8e-08   34.1   0.4    2.6e-07   31.0   0.1    2.6  2  Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain
     0.0054   15.7   0.2      0.014   14.4   0.0    1.6  2  DUF3435          Protein of unknown function (DUF3435)
  ------ inclusion threshold ------
      0.042   14.2   0.5       0.18   12.1   0.1    2.1  2  Phage_int_SAM_5  Phage integrase SAM-like domain
      0.044   13.6   0.2        1.3    8.9   0.0    3.2  3  HTH_23           Homeodomain-like domain


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.8   0.5   2.5e-52   7.4e-49       2     170 ..     113     270 ..     112     272 .. 0.99

  Alignments for each domain:
  == domain 1  score: 165.8 bits;  conditional E-value: 2.5e-52
                                    HHHHHHHHHHHHCCGCHHHHHHHHHHHHHHHHT--HHHHTT-BGGGEECTTTEEEEEEEECSSSSEEEEECTHHHHHHHH CS
                Phage_integrase   2 vltedeverllaaleeslkirdklllellyetGlRisEllsLrvkdldlengvilvheregKgskeravplseealellk 81 
                                    +l+++ev r+++a+e+   +rdkl++ ll+ tGlR+sEl+sLrv+d+dle+++++v   +gKgsker v +++ ++ ll+
  gi|119719024|ref|YP_919519.1| 113 YLEAEEVFRMVNAAEN---LRDKLIVLLLFTTGLRVSELVSLRVSDVDLEKRTLRV---RGKGSKERLVYFPDYVADLLR 186
                                    899*************...*************************************...********************* PP

                                    HHHHHHCHCCTTTSBSSBETTSSB--HHHHHHHHHHHHHHCT-SSC--TTHHHHHHHHHHHHHCTSHHHHHHHHT-SSCC CS
                Phage_integrase  82 ellskaleeaeksellfaskrgkplsrqtvrkafkraveeagiekpltpHtlRhsfataLleagvdlrvvqkllGHssis 161
                                     +++       +se+lf+s+ ++++   tv++++kr++e+agiek++tpHtlRhsfat  l ag+d+r++q+llGHs+++
  gi|119719024|ref|YP_919519.1| 187 SYMKGL-----NSEWLFPSETAEHIHYTTVERVLKRLKEKAGIEKKVTPHTLRHSFATLSLAAGLDIREIQELLGHSNLN 261
                                    *****9.....9******************************************************************** PP

                                    HHHHHHCCC CS
                Phage_integrase 162 ttqiYthva 170
                                    ttq+Y+hv+
  gi|119719024|ref|YP_919519.1| 262 TTQVYAHVS 270
                                    *******97 PP

>> Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   0.2   2.1e-13   6.1e-10       1      80 [.      17      92 ..      17      94 .. 0.96
   2 ?   -2.2   0.0       1.8   5.4e+03      19      49 ..     126     156 ..     112     166 .. 0.72
   3 ?   -0.1   0.0       0.4   1.2e+03      40      60 ..     202     222 ..     185     241 .. 0.53
   4 ?   -0.7   0.0      0.63   1.9e+03      13      20 ..     227     234 ..     215     280 .. 0.58

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 2.1e-13
                                   HHHHHHHHHHTT-S-HHHHHHHHHHHHHHHHHHHH.TS--TTT--HHHHHHHHHS----------HHHHHHHHHHHHHHH CS
                Phage_int_SAM_1  1 leqfleyLikerglspnTlraYrrdLrrflkflaergkesleqlttedvraflaeleeeglsatslarrlsalrsFfqfl 80
                                   ++ + ++L  +r++s++T+ +++  L++f++fl +   +++ q+t  dv  fla+l+++g +  s+  +  a+++F+ fl
  gi|119719024|ref|YP_919519.1| 17 IDLYISHLV-ARNRSEKTIKSFKSILEEFVRFLGD---RHVSQVTVYDVDFFLAHLRRKGWKKDSIYTAAVAVKRFLEFL 92
                                   677889998.9************************...****************************************98 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.8
                                    HHHHHHHHHHHHHHHHH.TS--TTT--HHHH CS
                Phage_int_SAM_1  19 lraYrrdLrrflkflaergkesleqlttedv 49 
                                     ++ r++L  +l f +  + + l +l+ +dv
  gi|119719024|ref|YP_919519.1| 126 AENLRDKLIVLLLFTTGLRVSELVSLRVSDV 156
                                    5677888888888877766666666666665 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.4
                                    -TTT--HHHHHHHHHS----- CS
                Phage_int_SAM_1  40 sleqlttedvraflaeleeeg 60 
                                    ++e++    v + l++l+e+ 
  gi|119719024|ref|YP_919519.1| 202 TAEHIHYTTVERVLKRLKEKA 222
                                    566666666666666665544 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 0.63
                                    -S-HHHHH CS
                Phage_int_SAM_1  13 glspnTlr 20 
                                     ++p+Tlr
  gi|119719024|ref|YP_919519.1| 227 KVTPHTLR 234
                                    55555554 PP

>> Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.1   8.7e-11   2.6e-07       5      74 ..      20      88 ..      16      92 .. 0.89
   2 ?   -0.5   0.0      0.58   1.7e+03      16      36 ..     201     221 ..     198     242 .. 0.64

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 8.7e-11
                Phage_int_SAM_4  5 frealrlaglserTiksYlsaikrflrflkkkapeeltkedieaYlnyLanerklsastqknalnalsff 74
                                   ++ +l +++ se+Tiks +s +++f+rfl  ++++++t  d+  +l++L+ ++ +++ ++ +a  a + f
  gi|119719024|ref|YP_919519.1| 20 YISHLVARNRSEKTIKSFKSILEEFVRFLGDRHVSQVTVYDVDFFLAHLR-RKGWKKDSIYTAAVAVKRF 88
                                   567788899*********************9*******************.999****999998777665 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.58
                Phage_int_SAM_4  16 erTiksYlsaikrflrflkkk 36 
                                    e+ ++ ++++++r l+ lk+k
  gi|119719024|ref|YP_919519.1| 201 ETAEHIHYTTVERVLKRLKEK 221
                                    556666777777777777654 PP

>> DUF3435  Protein of unknown function (DUF3435)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.42   1.3e+03      30      55 ..     133     158 ..     122     159 .. 0.87
   2 !   14.4   0.0   4.5e-06     0.014     171     250 ..     204     284 ..     185     292 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.42
                        DUF3435  30 lllllaaftsnRpgalleLryrDlel 55 
                                    l++ll   t+ R + l++Lr  D+ l
  gi|119719024|ref|YP_919519.1| 133 LIVLLLFTTGLRVSELVSLRVSDVDL 158
                                    788889999***********999987 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 4.5e-06
                        DUF3435 171 ealtastlnsrlkrlgeiagfeepitpYklRrgaakalneSgevseaqrnlilqHassrt...FlkhYlsqkvdkdvqav 247
                                    e++ + t++  lkrl e ag+e+++tp+ lR   a            + + +l+H++ +t   + +h  ++++++d ++v
  gi|119719024|ref|YP_919519.1| 204 EHIHYTTVERVLKRLKEKAGIEKKVTPHTLRHSFATLSLA-AGLDIREIQELLGHSNLNTtqvY-AHVSRERLKRDYERV 281
                                    7899***************************998765433.45666667779999876541115.677788899999999 PP

                        DUF3435 248 vlg 250
                                    +  
  gi|119719024|ref|YP_919519.1| 282 WSS 284
                                    875 PP

>> Phage_int_SAM_5  Phage integrase SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   6.2e-05      0.18      10      78 ..      21      87 ..      15      91 .. 0.80
   2 ?   -0.6   0.0      0.56   1.7e+03      58      77 ..     197     219 ..     176     239 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.2e-05
                                   THHHHTTS.-HHHHHHHHHHHHHTTTS-..S---TTT--HHHHHHHHHHHHHTS---HHHHHHHHHHHHH CS
                Phage_int_SAM_5 10 iekkkkkg.skgtlrnykstlkhlkkFlkkkditfeeidkefleeFedYLkkkkglsentiskyfkklka 78
                                   i++   ++ s++t+++ ks l+ + +Fl   d  ++++++  +  F ++L ++kg ++ +i++     k+
  gi|119719024|ref|YP_919519.1| 21 ISHLVARNrSEKTIKSFKSILEEFVRFL--GDRHVSQVTVYDVDFFLAHL-RRKGWKKDSIYTAAVAVKR 87
                                   444433333779****************..99******************.99**999999887666665 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.56
                                    H...HHTS---HHHHHHHHHHHH CS
                Phage_int_SAM_5  58 L...kkkkglsentiskyfkklk 77 
                                    L   ++ ++++ +t+ + +k+lk
  gi|119719024|ref|YP_919519.1| 197 LfpsETAEHIHYTTVERVLKRLK 219
                                    35554555555555555555555 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.5   4.4e+03       5      22 ..     130     147 ..     127     148 .. 0.78
   2 ?    8.9   0.0   0.00044       1.3      28      47 ..     205     225 ..     202     227 .. 0.88
   3 ?    0.3   0.0      0.22   6.7e+02      13      28 ..     240     256 ..     230     258 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.5
                         HTH_23   5 reRlrillllaeGlsvre 22 
                                    r++l +lll+  Gl+v+e
  gi|119719024|ref|YP_919519.1| 130 RDKLIVLLLFTTGLRVSE 147
                                    678888888888998876 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00044
                         HTH_23  28 gvsrrTvyrwlkryre.eGle 47 
                                    ++++ Tv r+lkr +e  G+e
  gi|119719024|ref|YP_919519.1| 205 HIHYTTVERVLKRLKEkAGIE 225
                                    89************9878887 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.22
                         HTH_23  13 llae.GlsvreIAreLg 28 
                                    l +  Gl +reI ++Lg
  gi|119719024|ref|YP_919519.1| 240 LSLAaGLDIREIQELLG 256
                                    33434999******998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2235.79
//
Query:       gi|119719025|ref|YP_919520.1|  [L=155]
Description: hypothetical protein Tpen_0107 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.6e-33  114.0   0.1    4.4e-33  113.7   0.1    1.0  1  DNase-RNase  Bifunctional nuclease


Domain annotation for each model (and alignments):
>> DNase-RNase  Bifunctional nuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.7   0.1   2.5e-37   4.4e-33      10     122 ..      27     145 ..      19     151 .. 0.88

  Alignments for each domain:
  == domain 1  score: 113.7 bits;  conditional E-value: 2.5e-37
                                    TTTEEEEEEEETTS.SEEEEEE--HHHHHHHHHHHCT---SS--HHHHHHHHHHHTTEEEEEEEEEEE.ETTEEEEEEEE CS
                    DNase-RNase  10 ssqspvvlLreeeg.rrvlpIwigaaeaqaialalegeeppRPlthDLlasllealgakvervvItdl.edgtfyAelvl 87 
                                    ++ ++++lL+++e  +++lpI+ig++e  ai+ al g++ +RP+thDL++s+l+alg++ve+v I++l +++++ A+++l
  gi|119719025|ref|YP_919520.1|  27 EQTAYLLLLETAEWkDKALPIIIGENEGLAIQSALMGVKYERPMTHDLIVSILDALGVEVEKVSIDALlNNSVYTATIYL 106
                                    45578888888777888*************************************************973679******** PP

                                    EET.---...EEEEE-HHHHHHHHHHHT--EEEEHHHHH CS
                    DNase-RNase  88 rke.eee...leidaRpSDaiaLAlrtgapIyveeevle 122
                                    +++ +++   +++d+RpSD ia+A+rtg+pIyv+ ++ +
  gi|119719025|ref|YP_919520.1| 107 KRTvNGKveeINVDSRPSDGIAIAVRTGSPIYVAAHLEK 145
                                    *988444678***********************988755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1099.83
//
Query:       gi|119719026|ref|YP_919521.1|  [L=219]
Description: hypothetical protein Tpen_0108 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1389.06
//
Query:       gi|119719027|ref|YP_919522.1|  [L=230]
Description: hypothetical protein Tpen_0109 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.1e-67  226.3   0.0    3.5e-67  226.1   0.0    1.0  1  ATP-grasp_5  ATP-grasp domain


Domain annotation for each model (and alignments):
>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  226.1   0.0   1.9e-71   3.5e-67       1     222 []       9     229 ..       9     229 .. 0.96

  Alignments for each domain:
  == domain 1  score: 226.1 bits;  conditional E-value: 1.9e-71
                    ATP-grasp_5   1 kalaegrtlLteaeakelleaygipvvetrlassaeeaveaaeeigypvvlKivspdilhKtdvgGvrlnlkdaeevraa 80 
                                    kal+e+r+ L+  ea +++e yg+p++  r++   ee+ ea   + ypvv+K++spdi+hKt++gGv+ ++k++ee+ +a
  gi|119719027|ref|YP_919522.1|   9 KALSENRKNLSLGEAFAVCEYYGLPLLGYRFIGVDEEVPEA-LGLSYPVVVKVDSPDIVHKTEYGGVKTGIKSREELVKA 87 
                                    699****************************9877776665.68************************************ PP

                    ATP-grasp_5  81 aeeilervkekspeariegvlVqemakrggrElivgvteDpvFGpvilfGlGGtavevlkdvavalpplnstlarelier 160
                                    +e+i+++vk+k+p+ari+g++Vqe +  +++E+i+g  +D++FGpvi+fGlGG+ ve+l+dva++++p++ ++ar+li r
  gi|119719027|ref|YP_919522.1|  88 IEDIKRSVKAKNPNARINGFIVQEQVS-NAHEVIIGGLKDEQFGPVIAFGLGGVLVEILRDVAFDIAPITPQEARDLITR 166
                                    *************************99.9*************************************************** PP

                    ATP-grasp_5 161 tkaskllkgvrgekkadlaaleellvrlsqLvvdl.peIreldinPllveeegvvalDarirl 222
                                    +k +++l+g+rg +ka+++al+e+l++ s++  d+ ++++e+d+nP++v++e v ++Dar +l
  gi|119719027|ref|YP_919522.1| 167 IKGYQILEGYRGIPKANIDALSEVLSKASRMFADIaKYVKEMDLNPTFVSSEWVKIADARFTL 229
                                    **********************************6266**********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1478.94
//
Query:       gi|119719028|ref|YP_919523.1|  [L=406]
Description: DegT/DnrJ/EryC1/StrS aminotransferase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.2e-115  386.7   0.0   1.9e-115  386.0   0.0    1.3  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    1.1e-05   24.9   0.2    2.3e-05   23.8   0.2    1.6  1  Beta_elim_lyase  Beta-eliminating lyase
    1.4e-05   24.3   0.0    2.1e-05   23.7   0.0    1.2  1  Aminotran_5      Aminotransferase class-V
    0.00014   20.6   0.0    0.00019   20.1   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
     0.0003   20.1   0.0    0.00057   19.2   0.0    1.4  1  Aminotran_1_2    Aminotransferase class I and II
  ------ inclusion threshold ------
       0.19   11.3   0.0        2.1    7.9   0.0    2.1  2  PAS_12           UPF0242 C-terminal PAS-like domain


Domain annotation for each model (and alignments):
>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  386.0   0.0  6.3e-119  1.9e-115       3     360 ..      24     397 ..      22     398 .. 0.96

  Alignments for each domain:
  == domain 1  score: 386.0 bits;  conditional E-value: 6.3e-119
                                    HHHHHHHHHHHHTSS-SSS..SHHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHH CS
                DegT_DnrJ_EryC1   3 keeeleaveevlksgwlts..gpeveeFEkafaaylgvkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanav 80 
                                    +e+e+  v ++l sg l    g++v++FE++fa+y+gv+ha+a+ +GtaAlh a   lg+gpgdeVI+++++Fvata a+
  gi|119719028|ref|YP_919523.1|  24 TEREKSLVLDALSSGRLVYssGSYVKRFEEEFARYVGVRHAVATINGTAALHTAVASLGIGPGDEVITTPFSFVATATAI 103
                                    578899999******554446*********************************************************** PP

                                    HHTT-EEEEE-B-TTTSSB-GGGCGGG--TTEEEEEEB-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT-EETTEECCC CS
                DegT_DnrJ_EryC1  81 lelgakpvfvDvdpdtynidpaaieaaitertkaIlpVhlyGqvadmdalkaiaakhglkvieDaAhAlGatykgkkvGa 160
                                    l+ +a pvf D++ +++n+dp++i  +it+rtkaIl+Vhl+G +a+md++ +ia++hgl+vieD+A+A+G++y+g+kvG 
  gi|119719028|ref|YP_919523.1| 104 LHHNAIPVFGDIELESLNLDPETIVDKITSRTKAILVVHLAGYPAEMDEILKIAREHGLYVIEDCAQAIGSEYRGRKVGG 183
                                    ******************************************************************************** PP

                                    SSSEEEEE-BTTSSS-SSS-EEEEESTHHHHHHHHHHHBTTCECCTCSSCECCSS---B-B-BHHHHHHHHHHHCTHHHH CS
                DegT_DnrJ_EryC1 161 lgdaavfSFyptKnlttGeGGavvtndeelaekarvlrnhGlkrkaekryvgevelGynyrlteiqAAiglaqLerldel 240
                                    +gd+++fSFy+tKn+ttGeGG+v+tn +++   ar++  +G++     +y++++ lG nyr+te+q A+gl qLer+d+l
  gi|119719028|ref|YP_919523.1| 184 IGDVGAFSFYQTKNMTTGEGGMVTTNRDDVYAYARMFVDQGQE----AKYYHSI-LGWNYRMTELQGALGLGQLERVDQL 258
                                    *****************************************88....8******.************************* PP

                                    HHHHHHHHHHHHHHHHTCCCCEESCGGTTSS.SEEESCEEEEEHCCHH.HCHHHHHHHHHHCCEE-B-SGSCHGGGSCC. CS
                DegT_DnrJ_EryC1 241 varRreiaelykeeLaelegtaelttpketk.khawhlyavlveeeae.vkrdelvealkeegigtrvhypnplhrqpv. 317
                                    +++R +ia++y +eL++l+g ++l  + +   kh wh + vl++ e+  v+rd+++eal++e++ + v yp+ +++ p+ 
  gi|119719028|ref|YP_919523.1| 259 NENRARIAKVYLDELQGLDGDLVLLPKVRPYvKHTWHIFQVLLNLEKLrVDRDRVLEALRAENVLALVAYPRVIYENPLf 338
                                    ********************9887777777755***********99999*****************************99 PP

                                    ................HHHHHHCCCHC-HHHHHHHHHEEEEEGGTTGSHHHHHHHHHHH CS
                DegT_DnrJ_EryC1 318 ................yaerkeeasgdlpnaerlaervlsLplypelteedvdrVveal 360
                                                    y  ++++ +g  p ae +a++v++Lp+  +++eed+ + ++al
  gi|119719028|ref|YP_919523.1| 339 qrmigygkgcpwkcpfYGGSVSYRKGLAPKAEMAARSVITLPTLAGMDEEDAIDTAKAL 397
                                    **************************************************998877766 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.2   7.6e-09   2.3e-05      21     216 ..      35     221 ..      24     300 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 7.6e-09
                                    S----CCCT--HHHHHHHHHHHHHTT-SEEEEES-HHHHHHHHHHHH-.-TTEEEEEETT-HHHHSSTTHHHHCC--EEE CS
                Beta_elim_lyase  21 amlGdesYgedktvnrLedavaelfgkeaalfvpqGtaAnsillkill.qrgeevivtepahihfdetgaiaelagvklr 99 
                                    +  G  +Y   + v+r+e+++a+++g  +a+ + +GtaA + +++ l   +g+evi t  + + + ++  +     v + 
  gi|119719028|ref|YP_919523.1|  35 LSSGRLVYSSGSYVKRFEEEFARYVGVRHAVATINGTAALHTAVASLGiGPGDEVITTPFSFVATATAILHHNAIPV-FG 113
                                    56788899999*********************************88877********99999999998777666666.78 PP

                                    EE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHT CS
                Beta_elim_lyase 100 dlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaakslg 179
                                    d++ ++  ++d+e + ++i+       ++k+i++             ++e++e+ +ia+++g+ ++ D A  +     ++
  gi|119719028|ref|YP_919523.1| 114 DIELES-LNLDPETIVDKITS------RTKAILVVHLAG----Y---PAEMDEILKIAREHGLYVIEDCAQAIG----SE 175
                                    888888.89**********99......466776654444....3...67888999*************986544....44 PP

                                    S-CHHHHTTSSE..EEEESSSTT--SS-EEEEE-HH.......... CS
                Beta_elim_lyase 180 eivkemfsyvDs..vtmslkKdllanvGgvlafrddel.......e 216
                                       +++    D+  +++  +K++++  Gg++ +++d+         
  gi|119719028|ref|YP_919523.1| 176 YRGRKVGGIGDVgaFSFYQTKNMTTGEGGMVTTNRDDVyayarmfV 221
                                    5555666666651166667999999999***999996644443331 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0     7e-09   2.1e-05      45     182 ..      48     174 ..      17     180 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 7e-09
                                    HHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETT CS
                    Aminotran_5  45 veearekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldee 124
                                    v+  +e++a+ ++++     + t ++t a+ +++ sl+  + pgde+++t     a+    + l +        i+l e 
  gi|119719028|ref|YP_919523.1|  48 VKRFEEEFARYVGVRH---AVATINGTAALHTAVASLG--IGPGDEVITTPFSFVATA--TAILHHNAIPVFGDIEL-ES 119
                                    6667888888888886...566778888*********5..9***********999998..44444444455556677.78 PP

                                    SCBEGGGHHHH--TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTTT CS
                    Aminotran_5 125 geldldelekllnektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqavgh 182
                                     +ld++++ ++++ +tk++ + h     G   +++ei k+a+++g +v+ D aqa+g+
  gi|119719028|ref|YP_919523.1| 120 LNLDPETIVDKITSRTKAILVVHL---AGYPAEMDEILKIAREHGLYVIEDCAQAIGS 174
                                    899*******************96...7****************************97 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   6.5e-08   0.00019      55     174 ..      49     168 ..      27     219 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 6.5e-08
                                    HHHHHHHHHHHT-SEEEEESSHHHHHHHHHHTT.S-TTEEEEEESTSSHHHHH..HHHHTHHHTT.CEEEEESTTSHHHH CS
                Cys_Met_Meta_PP  55 svleeriaaLeggeaalavssGmaAiaaailal.lkaGdeivvsddlYggtqr..llkkvlkklg.ievkfvdtsdleel 130
                                    + +ee+ a   g+ +a+a+  G+aA+++a+ +l +  Gde++++   +  t    l ++ ++ +g ie +  +  d+e +
  gi|119719028|ref|YP_919523.1|  49 KRFEEEFARYVGVRHAVATINGTAALHTAVASLgIGPGDEVITTPFSFVATATaiLHHNAIPVFGdIELESLNL-DPETI 127
                                    679999************************9996788*******888876654116677778765499999998.89*** PP

                                    HHHCCTTEEEEEEESS-TTTT----HHHHHHHHHHTT-EEEEEG CS
                Cys_Met_Meta_PP 131 ekaikentklvylEtptnpllkvvDiekiaklakkagvlvvvDn 174
                                      +i+++tk++++  ++        + +i+k+a+++g+ v+ D 
  gi|119719028|ref|YP_919523.1| 128 VDKITSRTKAILVVHLAGYPA---EMDEILKIAREHGLYVIEDC 168
                                    ************998887665...56788999999999998775 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.9e-07   0.00057      34     189 ..      36     169 ..      17     175 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.9e-07
                                    HTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHT CS
                  Aminotran_1_2  34 ggtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyknilrls 113
                                    ++++  y+     + +ee+ a+++g           av +++G+ al  a++ l  + pgde++    ++    +++ ++
  gi|119719028|ref|YP_919523.1|  36 SSGRLVYSSGSYVKRFEEEFARYVG--------VRHAVATINGTAALHTAVASLG-IGPGDEVITTPFSFVATATAILHH 106
                                    6678889999999************........666*******************.*******************99999 PP

                                    TSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEET CS
                  Aminotran_1_2 114 ggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDea 189
                                     +  v   ++  e+ +ld e + +++++      +tk ilv    +  G  a  +e+ k+   a++++l+++ D a
  gi|119719028|ref|YP_919523.1| 107 NAIPVFGDIE-LESLNLDPETIVDKITS------RTKAILVV---HLAGYPAEMDEILKI---AREHGLYVIEDCA 169
                                    9999988866.7899*************......99999976...446777777777777...8888888887765 PP

>> PAS_12  UPF0242 C-terminal PAS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.13   3.9e+02      27      62 ..     107     142 ..      95     145 .. 0.84
   2 ?    7.9   0.0   0.00071       2.1      41      84 ..     307     346 ..     299     348 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.13
                         PAS_12  27 neksrfrdlsldnyaldlRrLfDsLrsEnlgailvy 62 
                                    n    f d+ l++  ld  +++D + s +++ ++v+
  gi|119719028|ref|YP_919523.1| 107 NAIPVFGDIELESLNLDPETIVDKITSRTKAILVVH 142
                                    5666799999********************999985 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00071
                         PAS_12  41 aldlRrLfDsLrsEnlgailvysqkenkllfaNaqirallGwss 84 
                                     +d  r+ ++Lr+En  a++ y     ++++ N  +++++G+++
  gi|119719028|ref|YP_919523.1| 307 RVDRDRVLEALRAENVLALVAYP----RVIYENPLFQRMIGYGK 346
                                    57888999**************5....9**************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 2919.69
//
Query:       gi|119719029|ref|YP_919524.1|  [L=267]
Description: metal dependent phosphohydrolase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      5e-05   23.5   0.3    0.00011   22.4   0.1    1.8  2  HD        HD domain


Domain annotation for each model (and alignments):
>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0      0.35   6.3e+03      68      88 ..      14      30 ..       6      42 .. 0.54
   2 !   22.4   0.1   6.2e-09   0.00011      18     121 ..      92     182 ..      60     183 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.35
                                   HHHHHHHHHHHHHHHHHHHTT CS
                             HD 68 revekrlgldledvaklireh 88
                                   ++++k + +    va+l+ + 
  gi|119719029|ref|YP_919524.1| 14 EKWKKADAF----VARLVDYL 30
                                   444444433....44444443 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 6.2e-09
                                    HHHHHHHHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCHHHHHHH CS
                             HD  18 dlgeeedrellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrlgldledvaklirehheswegkkr 97 
                                    +l+  e + +l++a +lHDiG+  +++             +He  g  +++++          v ++ r+ +  +e++ r
  gi|119719029|ref|YP_919524.1|  92 SLD--EVKFILVAASYLHDIGNSIHRE-------------YHEATGSLLAKDI----------VDRALRYTFPEMETRRR 146
                                    444..7778899************886.............7888888777666..........66666666666664444 PP

                                    H........H....HHHCCTSCHHHHHHHHHHHHHH CS
                             HD  98 p........r....glaerqlslearivklaDrlaa 121
                                                  + ++++l+ ea ivklaD l++
  gi|119719029|ref|YP_919524.1| 147 VflrqevlsAifstEMNTKPLTVEASIVKLADGLDM 182
                                    4776655541455789999*************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1955.48
//
Query:       gi|119719030|ref|YP_919525.1|  [L=438]
Description: phosphopyruvate hydratase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   1.7e-124  414.9   0.1   2.2e-124  414.5   0.1    1.1  1  Enolase_C  Enolase, C-terminal TIM barrel domain
    1.5e-55  186.9   0.0    2.7e-55  186.1   0.0    1.4  1  Enolase_N  Enolase, N-terminal domain
    3.4e-13   49.7   0.0    5.4e-13   49.0   0.0    1.3  1  MR_MLE_C   Enolase C-terminal domain-like
  ------ inclusion threshold ------
       0.03   13.5   0.1       0.07   12.3   0.0    1.6  2  MAAL_C     Methylaspartate ammonia-lyase C-terminus


Domain annotation for each model (and alignments):
>> Enolase_C  Enolase, C-terminal TIM barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  414.5   0.1  4.9e-128  2.2e-124       3     294 ..     149     432 ..     147     434 .. 0.98

  Alignments for each domain:
  == domain 1  score: 414.5 bits;  conditional E-value: 4.9e-128
                                    EE-EE-EEEEE-GGGSSSS--SSEEEEE-TT-SSHHHHHHHHHHHHHHHHHHHHHCC.GGGG-B-TTS-B----SSHHHH CS
                      Enolase_C   3 vlPvPalnvinGGshagnklalqefmilPvgassfkealrlGaevyhklksvlkkkygksatnvGdeGGfaPnlqsnkea 82 
                                    +lPvP++n+inGG+hagn+l++qef+i+Pvgassf+eal +G+evyh+l+  lk+kyg sa nvGdeGGfaP ++ ++ea
  gi|119719030|ref|YP_919525.1| 149 TLPVPLMNIINGGKHAGNELKIQEFLIVPVGASSFSEALAIGSEVYHSLRGYLKEKYGVSAINVGDEGGFAPPMSRTREA 228
                                    79****************************************************************************** PP

                                    HHHHHHHHHHCT-TC..TBEEEEE--GGGCEETCTTEEECTTTTTT..GGCEEEHHHHHHHHHHHHHHS-EEEEES-S-T CS
                      Enolase_C  83 ldliveaiekaGykg..kvkialdvassefykekdkkydldfkeeesdkskkltseqladlykelvkkyPivsiedplde 160
                                    ld + +a+++aGy++  +v++ald+a+sefy+ek + y +d+ e        lt e+l ++y++lv++yPivsiedpl e
  gi|119719030|ref|YP_919525.1| 229 LDALIHAVKNAGYEPgrDVVLALDAAASEFYDEKRGVYAIDGAE--------LTREKLIEFYESLVEEYPIVSIEDPLYE 300
                                    **************999************************999........**************************** PP

                                    T-HHHHHHHHHHHTTTSEEEESTTTTT-HHHHHHHHHCT--SEEEE-HHHH-SHHHHHHHHHHHHHTT-EEEEE--SC-- CS
                      Enolase_C 161 ddweawkklteelgdkvqivGddltvtnpkrlkeaiekkaanalllkvnqiGsltesleavklakeagygvvvshrsGet 240
                                    +d+e+++++t +l   +q+vGddl+vtn++rl+++ie +aanalllkvnqiG+lte+l+a+++a e+ y+v+vshrsGet
  gi|119719030|ref|YP_919525.1| 301 EDFEGFAEVTRSLK--IQVVGDDLFVTNVERLRRGIEAGAANALLLKVNQIGTLTEALSAARMALENNYSVIVSHRSGET 378
                                    ***********998..**************************************************************** PP

                                    S--HHHHHHHHCT-SEEE---S-SHHHHHHHHHHHHHHHHHGCC-EE-GGGCTT CS
                      Enolase_C 241 edttiadlavglsaGqiktGaparserlakynqllrieeelgekakyaGkkvrk 294
                                    ed+ti+++av+l+aGqiktGaparser akyn+llriee lg +a+y G k++k
  gi|119719030|ref|YP_919525.1| 379 EDVTISHIAVALNAGQIKTGAPARSERNAKYNELLRIEEYLGGRARYPGIKAFK 432
                                    *************************************************99876 PP

>> Enolase_N  Enolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  186.1   0.0   6.1e-59   2.7e-55       1     131 []      13     142 ..      13     142 .. 0.99

  Alignments for each domain:
  == domain 1  score: 186.1 bits;  conditional E-value: 6.1e-59
                                    EEEEEEEEEE-TTS-EEEEEEEEETTC-EEEEE--B-BSSSSSS-B----SSTTSGGGT--HHHHHHHHHTHHHHHTTSB CS
                      Enolase_N   1 IkkvkareildSrGnpTvevevttedgalgraavpsGaStgekealelrDgdkkrylgkgvekavenvnekiapaligld 80 
                                    I++vkar +ldSrGnpTve+ev t  g +g+a+vpsGaStg++ealelrDg  kr++gkgv+kavenvn++iap+++g d
  gi|119719030|ref|YP_919525.1|  13 ITHVKARWVLDSRGNPTVEAEVRTFAGGYGSAIVPSGASTGTHEALELRDG-GKRFHGKGVSKAVENVNKIIAPEILGED 91 
                                    89**********************9999**********************9.8*************************** PP

                                    TT-HHHHHHHHHHHH-STT-TTT-HHHHHHHHHHHHHHHHHHHTS-HHHHH CS
                      Enolase_N  81 vtdqeeiDkllielDgtenksklGaNailavSlAvakaaAkakelplyryl 131
                                     ++qeeiD+ +i+lDgt+nks+lGaNail+vSlAva+aaA++ +lpl++yl
  gi|119719030|ref|YP_919525.1|  92 SRKQEEIDSKMISLDGTPNKSRLGANAILSVSLAVAHAAADTYGLPLFQYL 142
                                    **************************************************8 PP

>> MR_MLE_C  Enolase C-terminal domain-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.0   0.0   1.2e-16   5.4e-13      34     172 ..     233     389 ..     197     417 .. 0.79

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 1.2e-16
                                    HHHHHHH.HTTTSTSEEEEE-TTT.S...............BHHHHHHHHHHH.GGGTESEEESSSSTTTHHHHHHHHHH CS
                       MR_MLE_C  34 vravrea.vgpgddvdlmvDanqa.w...............dlatAirvarel.eeldllwlEEPvppeddleglaelra 95 
                                    + av++a  +pg dv l++Da ++ +               ++++ i++ + l ee+ +  +E+P+   +d eg ae++ 
  gi|119719030|ref|YP_919525.1| 233 IHAVKNAgYEPGRDVVLALDAAASeFydekrgvyaidgaelTREKLIEFYESLvEEYPIVSIEDPLYE-EDFEGFAEVT- 310
                                    44444442456889999999999962578888888888888************777***********9.57********. PP

                                    HH.SSEEEESTTSSS.HHHHHHHHHHTSESEEEEBHHHHTSHHHHHHHHHHHHHTT-EEEEBSCSSHHHHHHHHHHHHT CS
                       MR_MLE_C  96 ra.sipiaagEslys.radfrelleagavdivqpdvsrvgGitearkvaalaeafgvpvapHsgsgglglaaslhlaaa 172
                                    r+ +i+++++    + ++++r+ +eaga+ ++ ++v+++g +tea+  a++a ++++ v++ + sg  + +   h+a+a
  gi|119719030|ref|YP_919525.1| 311 RSlKIQVVGDDLFVTnVERLRRGIEAGAANALLLKVNQIGTLTEALSAARMALENNYSVIVSHRSGETEDVTISHIAVA 389
                                    8889******987666**************************************9999887763344443333444444 PP

>> MAAL_C  Methylaspartate ammonia-lyase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       0.6   2.7e+03     195     217 ..     105     127 ..     101     131 .. 0.85
   2 ?   12.3   0.0   1.6e-05      0.07     135     221 ..     310     395 ..     265     416 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.6
                         MAAL_C 195 lGGscnetdvsarvsvhvalatr 217
                                    l G+ n    +a+++  v+la+ 
  gi|119719030|ref|YP_919525.1| 105 LDGTPNKSRLGANAILSVSLAVA 127
                                    67999**********99999986 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 1.6e-05
                         MAAL_C 135 ekgikvelvaDe.WcntledirefvdaeaadlvqiktPDlGginntieavlyckekgvgaylGGscnetdvsarvsvhva 213
                                    +++ k+++v D+ +  ++e +r+ ++a+aa+++ +k+  +G++++++ a  ++ e++  + +   + et+    ++ h+a
  gi|119719030|ref|YP_919525.1| 310 TRSLKIQVVGDDlFVTNVERLRRGIEAGAANALLLKVNQIGTLTEALSAARMALENNYSVIVSHRSGETEDV--TISHIA 387
                                    456789999988467789***************************************************976..456777 PP

                         MAAL_C 214 latrpaql 221
                                    +a ++ q+
  gi|119719030|ref|YP_919525.1| 388 VALNAGQI 395
                                    77777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (438 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 3300.56
//
Query:       gi|119719031|ref|YP_919526.1|  [L=254]
Description: nucleotidyl transferase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.7e-26   91.0   0.0    1.1e-25   90.7   0.0    1.0  1  NTP_transferase  Nucleotidyl transferase
    7.2e-11   42.7   0.0    9.6e-11   42.3   0.0    1.2  1  NTP_transf_3     MobA-like NTP transferase domain


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.7   0.0   1.2e-29   1.1e-25       2     240 ..       6     234 ..       5     239 .. 0.87

  Alignments for each domain:
  == domain 1  score: 90.7 bits;  conditional E-value: 1.2e-29
                                    EEEE--S--GGGTTCCTTSSGGGSEETTET.ETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEEEE CS
                NTP_transferase   2 avILaGGsGtRLwPLtrtlakklvpvlgke.rliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevliale 80 
                                    +v+L+GG+G+RL+PLt   +k ++pv++++ +l+++ +  la +g ++ i+ l  ++ + + +++++g+++gv+++++  
  gi|119719031|ref|YP_919526.1|   6 GVVLCGGEGKRLRPLTYYFQKAMIPVGTQQkPLLEYIVRLLAYHGLRR-IILLVGYKGQQIVNYFNSGERYGVNISYVWD 84 
                                    79**********************************************.666666888888889***************9 PP

                                    SS--.BGGHHHHHT..HHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEECTTS CS
                NTP_transferase  81 pegk.gtAdAvala..aelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGvieadeeg 157
                                    +++  g  +A+  a  + ++e     +++lv  gD+l + ++++++ +++  +    +t++++p+ +  + Gv+e d+ +
  gi|119719031|ref|YP_919526.1|  85 DPNYgGNGGALFNAyvRGFFEG---SDNILVYYGDILSDINLSDFLSFHERGQY--AATLALSPNYR-VAVGVAELDG-D 157
                                    9888555555544311344444...557*********************99888..77888877766.578******8.6 PP

                                    BEEEEECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEEXSSHHH CS
                NTP_transferase 158 rverfvEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWsDvGtlds 237
                                    rv ++vEKP   k    +  G+    +++l++l + l e kr+ d ++d+++ +le+g +   +l +    W D+Gt ++
  gi|119719031|ref|YP_919526.1| 158 RVVKLVEKPPLGK---PVTIGVVAIRTKALEYL-RELVEEKREVDIMGDFIRVLLERGLKVGGYLTNS--FWFDLGTTEA 231
                                    **********988...59999999*********.6699999**********************99999..6********* PP

                                    HHH CS
                NTP_transferase 238 lle 240
                                    + +
  gi|119719031|ref|YP_919526.1| 232 YEK 234
                                    976 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   0.0   1.1e-14   9.6e-11       1     150 [.       6     196 ..       6     209 .. 0.75

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 1.1e-14
                                    EEEEEESS-TTTTT.....THHHHCC..CCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHH...TTCT..S-EEE-T CS
                   NTP_transf_3   1 aviLAGGrSsRmgg.....dKallpl..ggkpllervldalraagvdevvvvggd..eevlaal...arlg..vrvvede 66 
                                    +v+L+GG+++R+        Ka++p+  ++kplle++++ l+ +g++++++ +g+  +++ +++   +r+g  +++v+d+
  gi|119719031|ref|YP_919526.1|   6 GVVLCGGEGKRLRPltyyfQKAMIPVgtQQKPLLEYIVRLLAYHGLRRIILLVGYkgQQIVNYFnsgERYGvnISYVWDD 85 
                                    79**********9445678*******88899**********************99545666655333556533778**** PP

                                    TSS-SHHHHHHHHHHH..H.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESSSEE................. CS
                   NTP_transf_3  67 dpgkgplaslaaalra..aadadavlvlacDmPlltpelverllaaaaasgadvvvptyeger................. 127
                                    + + g +++l  a  +   +++d +lv  +D+  l+   +  +l  +++ +++++ + + + r                 
  gi|119719031|ref|YP_919526.1|  86 PNYGGNGGALFNAYVRgfFEGSDNILVYYGDI--LSDINLSDFLSFHERGQYAATLALSPNYRvavgvaeldgdrvvklv 163
                                    *************9988888***********9..5566677777777666666655555555557777777777777777 PP

                                    .....EECC.....EEEGGGHHHHHHHCTHTTH CS
                   NTP_transf_3 128 .....ghpl.....lfrarllsalaallgdqga 150
                                         g+p+     ++r+++l+ l++l +++++
  gi|119719031|ref|YP_919526.1| 164 ekpplGKPVtigvvAIRTKALEYLRELVEEKRE 196
                                    777775555433324466666666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1863.52
//
Query:       gi|119719032|ref|YP_919527.1|  [L=399]
Description: FAD dependent oxidoreductase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.2e-13   49.0   0.0    3.4e-09   36.4   0.0    2.1  2  FAD_binding_3  FAD binding domain
    1.1e-05   24.9   0.0    1.5e-05   24.4   0.0    1.2  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
      0.012   14.7   0.1       0.17   10.9   0.1    2.3  2  Lycopene_cycl  Lycopene cyclase protein
      0.014   14.6   0.6        2.8    7.1   0.0    2.1  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
      0.047   13.7   0.6        9.2    6.2   0.0    2.2  2  NAD_binding_9  FAD-NAD(P)-binding
       0.12   11.8   0.0       0.22   10.9   0.0    1.3  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,


Domain annotation for each model (and alignments):
>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0   9.2e-05      0.27       2      35 ..       8      41 ..       7      45 .. 0.91
   2 !   36.4   0.0   1.1e-12   3.4e-09     143     308 ..     138     300 ..     127     304 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 9.2e-05
                                   EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
                  FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrst 35
                                   ++ +++G GpaG+ + + L+e G++ v +e+ + 
  gi|119719032|ref|YP_919527.1|  8 YEAVVIGLGPAGAAALKRLQELGIKAVGIERKKA 41
                                   5789**************************9875 PP

  == domain 2  score: 36.4 bits;  conditional E-value: 1.1e-12
                                    EECCTTEEEEEEEEEEEE--GTT-HHHHHHTGGEEEEEEEEEEEEEEEEEEC.-SCCCTTC..CEEEEECCTTEEEEEEC CS
                  FAD_binding_3 143 rdketgeeetvrakYlvGaDGgrStvrktlgiefegeetvyeagvldvlfda.dlsdivep..lvlilsaesrgvmviPl 219
                                     + + g+  +++a Y+++aDG+ S++r+ lg++   + ++     ++v+ +    s++++   +++   ++ +   +iP+
  gi|119719032|ref|YP_919527.1| 138 VKTRRGK--EFSASYVIAADGFPSATRRLLGLPAGLQPED---YAVGVNLKMeTPSMPRDTifMYASSFTQGGYAWIIPV 212
                                    4445454..5***********************5555555...78889999945555555577777777777778***** PP

                                    CETEEEEEEEEECCE-GGGSCCCHHHHHHHHHHHHHHTTSSCEEEEEEEEEEEEEEEEESSSEETTEEE-GGGTEEE-ST CS
                  FAD_binding_3 220 entlerfyvqvearaekeersekfteeevkarlreivgektldveieevsawtvaqrvaekyrkgrvflaGDAaHihpPt 299
                                     ++l+++ + +++++ k++ ++    +  ++  r+ + ++  + e  + +  +v+ ++ e+ + g+v+ aGD+  ++ P 
  gi|119719032|ref|YP_919527.1| 213 GDGLSNVGIGLRFNYVKKGANPLKALTSFVELERRGFLDSSRQLEEPRSRMIPVSGFYSEP-STGKVLFAGDSLGAVNPI 291
                                    ********************************************99999********9987.78**************** PP

                                    TSHHHHHHH CS
                  FAD_binding_3 300 gGqGlNtai 308
                                    +G G+ ta+
  gi|119719032|ref|YP_919527.1| 292 NGGGIFTAM 300
                                    *****9998 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   4.9e-09   1.5e-05       3     119 ..      10     171 ..       8     191 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 4.9e-09
                                    EEEE--SHHHHHHHHHHHHHTS-EEEEE....TTHCHHHCSHHH.HCHHHHHHHHHHHHH.................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxx.xxxxxxxxxxxxxxx.................... RF
                    Pyr_redox_2   3 vvviGgGpAGlaaaltlaqagakvtlve....legtclnggcll.skallgvaedaeias.................... 57 
                                     vviG GpAG aa ++l++ g+k + +e     e+  + g  l+ ++a++ +++++++++                    
  gi|119719032|ref|YP_919527.1|  10 AVVIGLGPAGAAALKRLQELGIKAVGIErkkaPEEPAVCGEFLPePSAIEFISRFPSVRKayeyiglarrtnairriils 89 
                                    69*************************988885555555556663667888888888888******************** PP

                                    ...................HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---E...EE-BCT CS
                                    ...................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxx RF
                    Pyr_redox_2  58 ...................evvkklnqgielllgeevvkidpgkkkvklekkkegdeekiaydklvlAtGs...sprdlg 115
                                                       e v+kl +g ++++g+ vv+i +    + + k++   ++++ + +++ A G+   + r+lg
  gi|119719032|ref|YP_919527.1|  90 faggktynleipgftvsrkEMVSKLIEGSDYVTGSDVVGIRRVGDAYLV-KTR--RGKEFSASYVIAADGFpsaTRRLLG 166
                                    *******************99999**********99****766655555.444..3558***********7554455558 PP

                                    CT.TC CS
                                    xx.xx RF
                    Pyr_redox_2 116 ip.Gv 119
                                    +p G+
  gi|119719032|ref|YP_919527.1| 167 LPaGL 171
                                    88555 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   5.8e-05      0.17       3     177 ..      11     198 ..       9     228 .. 0.73
   2 ?   -2.6   0.0      0.72   2.2e+03     241     289 ..     262     309 ..     247     336 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 5.8e-05
                  Lycopene_cycl   3 vviGaGpAglslAarlteakpglkvvlieaspsllfpnny.vWsdefedlga...............leecvehsWsgti 66 
                                    vviG GpAg +  +rl  ++ g+k v ie  + +  p+       e ++++                l++  +   ++ i
  gi|119719032|ref|YP_919527.1|  11 VVIGLGPAGAAALKRL--QELGIKAVGIERKKAPEEPAVCgEFLPEPSAIEFisrfpsvrkayeyigLARRTN-AIRRII 87 
                                    7888888888888888..8888888888755444333333333333333333555666666666554444433.347778 PP

                  Lycopene_cycl  67 vylddgkkillgraYgrvsskrlkeellerlvengvklleakvesveeeeageslvvleggrkirarlvvdarglaslk. 145
                                    + +++gk+  l+ +  +vs+k+    +  +l+e+    + + v  ++ + +   lv +  g++  a+ v+ a g +s++ 
  gi|119719032|ref|YP_919527.1|  88 LSFAGGKTYNLEIPGFTVSRKE----MVSKLIEGSDYVTGSDVVGIRRVGD-AYLVKTRRGKEFSASYVIAADGFPSATr 162
                                    8888888888888888888875....666778778888999*******999.9999******************999987 PP

                  Lycopene_cycl 146 ..karrlglQ...tfyGvevevdnppfdldkmvlMDf 177
                                       ++  glQ    + Gv +++++p   +   ++M +
  gi|119719032|ref|YP_919527.1| 163 rlLGLPAGLQpedYAVGVNLKMETP-SMPRDTIFMYA 198
                                    7766777888544689999999998.55666777755 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.72
                  Lycopene_cycl 241 gviPvtlggslpr.leqkvlaiGaaaglvhPaTGYsvarslaeapllasa 289
                                     +iPv   g+ ++    kvl +G   g+v P  G  +  ++a   l a++
  gi|119719032|ref|YP_919527.1| 262 RMIPV--SGFYSEpSTGKVLFAGDSLGAVNPINGGGIFTAMALGILAAES 309
                                    57888..6666551455689999999999999998888888877666655 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.5    0.0029       8.6       1      31 [.      11      40 ..      11      44 .. 0.85
   2 ?    7.1   0.0   0.00094       2.8     101     134 ..     123     157 ..     107     167 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0029
                    Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgn 31
                                   ++iG GPaG aa   l+++g++  + +E+++
  gi|119719032|ref|YP_919527.1| 11 VVIGLGPAGAAALKRLQELGIK-AVGIERKK 40
                                   79*******************6.55677765 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.00094
                    Pyr_redox_3 101 feeVesvkkedegfevetske.tyeAkkviiAtGe 134
                                     ++V  + + ++ + v+t+++ +++A++vi A G+
  gi|119719032|ref|YP_919527.1| 123 GSDVVGIRRVGDAYLVKTRRGkEFSASYVIAADGF 157
                                    56788899999999999999768999999999997 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.5    0.0053        16       1      18 [.      11      28 ..      11      37 .. 0.89
   2 ?    6.2   0.0    0.0031       9.2     119     154 ..     121     156 ..     107     158 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0053
                  NAD_binding_9  1 aivGaGprGlavlerLla 18
                                   +++G Gp+G+a+l+rL +
  gi|119719032|ref|YP_919527.1| 11 VVIGLGPAGAAALKRLQE 28
                                   69*************976 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0031
                  NAD_binding_9 119 vhraevvdleeradgqavlladgaslaadaVvLAlG 154
                                    v  ++vv +++ +d + v +++g+++ a +V+ A G
  gi|119719032|ref|YP_919527.1| 121 VTGSDVVGIRRVGDAYLVKTRRGKEFSASYVIAADG 156
                                    56789***************************9977 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   7.3e-05      0.22      40      73 ..      11      44 ..       6      54 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 7.3e-05
                                   EEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH CS
                   2-Hacid_dh_C 40 GiiGlGrIGqavakrlkafgmkviaydrskkkee 73
                                    +iGlG  G a+ krl+++g+k ++++r+k +ee
  gi|119719032|ref|YP_919527.1| 11 VVIGLGPAGAAALKRLQELGIKAVGIERKKAPEE 44
                                   79***************************98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2545.85
//
Query:       gi|119719033|ref|YP_919528.1|  [L=118]
Description: PadR-like family transcriptional regulator [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-15   56.8   0.1    2.2e-15   56.4   0.1    1.2  1  PadR          Transcriptional regulator PadR-like family
    0.00029   20.7   0.1    0.00093   19.0   0.1    1.9  1  TrmB          Sugar-specific transcriptional regulator TrmB
     0.0017   18.4   0.0     0.0044   17.1   0.0    1.7  2  CtsR_C        CtsR C-terminal dimerization domain
     0.0031   17.8   0.0     0.0045   17.3   0.0    1.3  1  DUF2513       Hypothetical protein (DUF2513)
     0.0051   16.8   0.0      0.012   15.6   0.0    1.6  2  HTH_45        Winged helix-turn-helix
  ------ inclusion threshold ------
      0.011   14.1   0.1      0.011   14.1   0.1    1.1  1  DUF505        Protein of unknown function (DUF505)
      0.021   14.9   0.0      0.024   14.7   0.0    1.2  1  Replic_Relax  Replication-relaxation
      0.022   14.6   0.0      0.032   14.1   0.0    1.5  1  DUF1495       Winged helix DNA-binding domain (DUF1495)
      0.027   14.3   0.0      0.054   13.3   0.0    1.4  1  DUF3116       Protein of unknown function (DUF3116)
      0.027   14.4   0.0       0.18   11.7   0.0    2.1  1  HTH_5         Bacterial regulatory protein, arsR family
      0.076   13.5   0.0       0.16   12.5   0.0    1.6  1  HTH_27        Winged helix DNA-binding domain
      0.078   12.7   0.0       0.12   12.1   0.0    1.3  1  DUF4364       Domain of unknown function (DUF4364)


Domain annotation for each model (and alignments):
>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.4   0.1   1.5e-18   2.2e-15       2      75 .]      26      94 ..      25      94 .. 0.93

  Alignments for each domain:
  == domain 1  score: 56.4 bits;  conditional E-value: 1.5e-18
                                   HHHHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHHHH CS
                           PadR  2 LalleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrelae 75
                                   L ll+e++ +Gye+++ le+ +e    + ++++Yp L+ Le+ glv+s+++    ++ +k+Y lT++G + l+e
  gi|119719033|ref|YP_919528.1| 26 LILLAEGEKHGYELMRTLEQMIEA--PIGPSQIYPFLRNLENAGLVTSREAG---SRDKKVYSLTPQGYEFLKE 94
                                   6789*****************976..9**********************886...59***********998875 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1   6.2e-07   0.00093      16      65 ..      27      85 ..      17      87 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 6.2e-07
                                   HHHHHCCCHHCHHCCCTT......SSCHCHHHHHHHHHHCTSEEEESST...TTEEEE- CS
                           TrmB 16 aLlklgpatadeiaeelg......vprskvYevLrsLedkGlVerekgr...pklYrav 65
                                    Ll++g++  +e+ + l+      +  s++Y  Lr+Le++GlV+ ++     +k+Y+ +
  gi|119719033|ref|YP_919528.1| 27 ILLAEGEKHGYELMRTLEqmieapIGPSQIYPFLRNLENAGLVTSREAGsrdKKVYSLT 85
                                   3457888887777775543333337789****************999655888899866 PP

>> CtsR_C  CtsR C-terminal dimerization domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0     3e-06    0.0044       4      40 ..      38      74 ..      34      75 .. 0.95
   2 ?   -2.7   0.0       4.5   6.8e+03      38      48 ..      98     108 ..      92     112 .. 0.57

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3e-06
                         CtsR_C  4 elleilinsigdsiseqdaeaiiqrLleegliterEa 40
                                   el++ l+++i+  i  +++  ++++L + gl+t rEa
  gi|119719033|ref|YP_919528.1| 38 ELMRTLEQMIEAPIGPSQIYPFLRNLENAGLVTSREA 74
                                   799*********************************9 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.5
                         CtsR_C  38 rEakLmkaals 48 
                                    +  ++++ a++
  gi|119719033|ref|YP_919528.1|  98 KSLNVIQTAIR 108
                                    34455555555 PP

>> DUF2513  Hypothetical protein (DUF2513)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0     3e-06    0.0045      41      88 ..      55      98 ..      25     105 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3e-06
                        DUF2513 41 eiiyhlkllaeagLieaekkkakssiislvvkrLtweGhdFLdsiRdd 88
                                   +i+  l+ l++agL+ + +  ++++    +v++Lt +G++FL +i ++
  gi|119719033|ref|YP_919528.1| 55 QIYPFLRNLENAGLVTSREAGSRDK----KVYSLTPQGYEFLKEILEK 98
                                   567778899***********99999....*************998766 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0         2     3e+03      61      74 ..      35      48 ..      33      51 .. 0.78
   2 !   15.6   0.0     8e-06     0.012      34      69 ..      54      95 ..      44     102 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2
                         HTH_45 61 kGlelleklkelee 74
                                    G el+++l++++e
  gi|119719033|ref|YP_919528.1| 35 HGYELMRTLEQMIE 48
                                   58888888888765 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 8e-06
                         HTH_45 34 kllnkYLdmLvekgli......kkskekYvlTekGlellekl 69
                                   +++  +L  L + gl+      + +k+ Y+lT +G e+l+++
  gi|119719033|ref|YP_919528.1| 54 SQIYPFLRNLENAGLVtsreagSRDKKVYSLTPQGYEFLKEI 95
                                   5667799************99999***************997 PP

>> DUF505  Protein of unknown function (DUF505)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   7.4e-06     0.011     365     416 ..      55     107 ..       5     113 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.4e-06
                         DUF505 365 dlreaLysLesfeLiesev.eekgkevyvlTeyGekvledqekklrevsaeav 416
                                    ++   L +Le  +L++s++  +  k+vy+lT++G + l++  +k  +v  +a+
  gi|119719033|ref|YP_919528.1|  55 QIYPFLRNLENAGLVTSREaGSRDKKVYSLTPQGYEFLKEILEKSLNVIQTAI 107
                                    5666799*********99866677************99998777666666666 PP

>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.6e-05     0.024      25      71 ..      53      94 ..      31     114 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.6e-05
                   Replic_Relax 25 a.tarrrLarLrelgllsrlrkrvggarggsepyvYaLtpkGarllaa 71
                                     +++  L+ L+  gl+++  +++g      ++ vY Ltp+G+++l++
  gi|119719033|ref|YP_919528.1| 53 PsQIYPFLRNLENAGLVTS--REAG-S---RDKKVYSLTPQGYEFLKE 94
                                   3578999**********99..3322.3...3479***********943 PP

>> DUF1495  Winged helix DNA-binding domain (DUF1495)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.1e-05     0.032      57      88 ..      61      93 ..      10      95 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.1e-05
                        DUF1495 57 ssLielGLveeeee.seglklYklteeGieive 88
                                   + L + GLv+++e  s++ k+Y+lt++G e+ +
  gi|119719033|ref|YP_919528.1| 61 RNLENAGLVTSREAgSRDKKVYSLTPQGYEFLK 93
                                   556688***86554499***********99876 PP

>> DUF3116  Protein of unknown function (DUF3116)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.6e-05     0.054      51      83 ..      63      95 ..      60      97 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.6e-05
                        DUF3116 51 LElkgyilRkeekannkkrYelTekGellykel 83
                                   LE  g +  +e    +kk Y+lT++G +++ke+
  gi|119719033|ref|YP_919528.1| 63 LENAGLVTSREAGSRDKKVYSLTPQGYEFLKEI 95
                                   89999999999999****************998 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00012      0.18      10      47 .]      28      71 ..      21      71 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00012
                                   HHTTSSEEHHHHHHHHT......S-HHHHHHHHHHHHHTTSEEE CS
                          HTH_5 10 lLaegelcvcelaeelg......lsqstvShHLkkLreaGLVek 47
                                   lLaege+   el++ l+      + +s +   L+ L++aGLV++
  gi|119719033|ref|YP_919528.1| 28 LLAEGEKHGYELMRTLEqmieapIGPSQIYPFLRNLENAGLVTS 71
                                   7888888888888887755555578999**************86 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00011      0.16      38      68 .]      59      88 ..      51      88 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                         HTH_27 38 slkkLtekGLvertgdeadrre.krvrlTdkG 68
                                    l+ L+++GLv  t  ea  r+ k ++lT+ G
  gi|119719033|ref|YP_919528.1| 59 FLRNLENAGLV--TSREAGSRDkKVYSLTPQG 88
                                   699********..33344444459******98 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   8.1e-05      0.12      39      74 ..      59      96 ..      54     113 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.1e-05
                        DUF4364 39 alseLvesglieeeek..enktlykiTekGketlelfe 74
                                   +l +L+++gl++++e   ++k++y++T++G e l+++ 
  gi|119719033|ref|YP_919528.1| 59 FLRNLENAGLVTSREAgsRDKKVYSLTPQGYEFLKEIL 96
                                   6899********99655599***********9998754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 713.22
//
Query:       gi|119719034|ref|YP_919529.1|  [L=207]
Description: methyltransferase type 11 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.1e-08   32.8   0.0    1.2e-07   32.3   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
    9.7e-07   28.3   0.0    6.3e-06   25.7   0.0    1.9  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    1.2e-06   29.1   0.0    2.8e-06   28.0   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
    0.00014   21.8   0.0    0.00015   21.6   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    0.00044   19.3   0.0    0.00053   19.0   0.0    1.1  1  Methyltransf_9   Protein of unknown function (DUF1698)
     0.0094   15.5   0.0      0.014   14.9   0.0    1.3  1  MTS              Methyltransferase small domain
  ------ inclusion threshold ------
       0.02   14.7   0.0      0.036   13.8   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
      0.026   14.1   0.0      0.035   13.7   0.0    1.2  1  MetW             Methionine biosynthesis protein MetW
      0.036   14.8   0.0      0.056   14.2   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
      0.086   12.2   0.0        0.1   12.0   0.0    1.2  1  TehB             Tellurite resistance protein TehB


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.0   6.8e-11   1.2e-07       1      90 [.      41     123 ..      41     128 .. 0.85

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 6.8e-11
                                    EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHHHH CS
                Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedpeka 80 
                                    LdvGcG G+++ +l +++ +vv+vD+ ++        ++ + +++ +v+a ae lp++++s+ + ++ +++  + d  + 
  gi|119719034|ref|YP_919529.1|  41 LDVGCGDGYYSLPLLENAQEVVCVDPLARKG------SESD-PRLHVVKAIAEYLPLRSKSVEFSTAMFSFRDFLDKPRG 113
                                    8************************543332......2222.34778********************************* PP

                                    HHHHHHHEEE CS
                Methyltransf_11  81 lkeiaRvLkp 90 
                                    l+e++R  + 
  gi|119719034|ref|YP_919529.1| 114 LSEMKRASRI 123
                                    ******8765 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   3.5e-09   6.3e-06      20     207 ..      13     183 ..       2     197 .. 0.75

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 3.5e-09
                                    HHHHHHHHHTTTHHHHHHHHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSST CS
                Ubie_methyltran  20 yDlmndvlslgihrlWkkfveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkin 99 
                                    y   n  +slg  r+ +  v +l       +vlDv +G g +++ l+++++   +vv +D  +        +   e+  +
  gi|119719034|ref|YP_919529.1|  13 YSPTNFAMSLGLDRKLRGIVYNLAR----GRVLDVGCGDGYYSLPLLENAQ---EVVCVDPLA--------RKGSESDPR 77 
                                    5666777888888877776665543....4699999999999999988776...567777432........333455568 PP

                                    EEEEE--TTT-TTS-T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEEEEE----S..HHHHHHHHHHHH.HHHHH CS
                Ubie_methyltran 100 ieflqanaeeLpfeddsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvvlefskvel..pllsqayelyskevlPvl 177
                                    ++ ++a ae Lp   +s ++ t  f +r++ Dk+++L e+ r  + G   +++e+ ++ +    +  ay l+     P l
  gi|119719034|ref|YP_919529.1|  78 LHVVKAIAEYLPLRSKSVEFSTAMFSFRDFLDKPRGLSEMKRASRIGV--FIVEIFNPSTwfRPFLYAYVLFI---APLL 152
                                    889*******************************************95..55555555540045555555555...5777 PP

                                    HHHHHS.-HHHHHHHHHHHHHS--HHHHHHH CS
                Ubie_methyltran 178 Gkllak.dldsyryLvesirafPdqetlkel 207
                                      l++  + + +r L  +ir  P +  ++ +
  gi|119719034|ref|YP_919529.1| 153 AFLVSRgKGKGWRLLYPTIRIMPRASLFERM 183
                                    7777752457899999999999999888877 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   1.5e-09   2.8e-06       1      92 [.      40     120 ..      40     124 .. 0.84

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 1.5e-09
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHH CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsde 80 
                                    vLd+GcG G ++l l+++   ++v++vD+       ar + +e+++++++v++ ae lp+ ++s+ + ++++++  +   
  gi|119719034|ref|YP_919529.1|  40 VLDVGCGDGYYSLPLLENA--QEVVCVDPL------AR-KGSESDPRLHVVKAIAEYLPLRSKSVEFSTAMFSFRDFL-- 108
                                    9***************996..9******84......34.444667999**********************97766544.. PP

                                    HHHHHHHHHHHH CS
                Methyltransf_25  81 dlekalkeiarv 92 
                                    d ++ l+e++r+
  gi|119719034|ref|YP_919529.1| 109 DKPRGLSEMKRA 120
                                    677899999997 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   8.4e-08   0.00015      19      55 ..      33      69 ..      19     150 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 8.4e-08
                Methyltransf_23 19 klraggrvLdiGcGtGillevlrengfsvtgvDlspe 55
                                   ++ a+grvLd+GcG+G+ +  l en  +v+ vD+  +
  gi|119719034|ref|YP_919529.1| 33 YNLARGRVLDVGCGDGYYSLPLLENAQEVVCVDPLAR 69
                                   57789***********99999999999******9754 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0     3e-07   0.00053     112     147 ..      33      67 ..      11      90 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 3e-07
                                    .--TT-EEEEET-TTSHHHHHHHHCT-SEEEEE--- CS
                 Methyltransf_9 112 sdlkgrtildvGcgnGyhlwrmvgegaklvvGidPs 147
                                     +l   ++ldvGcg+Gy+   ++ e+a+ vv +dP 
  gi|119719034|ref|YP_919529.1|  33 YNLARGRVLDVGCGDGYYSLPLL-ENAQEVVCVDPL 67 
                                    5677789************9987.7899******96 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0     8e-06     0.014      31      62 ..      36      65 ..       9      70 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 8e-06
                                   TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEE CS
                            MTS 31 lsgkvlDlGcGaGvlgaalakespeaevtlvd 62
                                   ++g+vlD+GcG G+ ++ l+++ +e  v++vd
  gi|119719034|ref|YP_919529.1| 36 ARGRVLDVGCGDGYYSLPLLENAQE--VVCVD 65
                                   5689***************998777..77777 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0     2e-05     0.036       6      35 ..      39      65 ..      36      67 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2e-05
                Methyltransf_31  6 rvlDlGCGtGeltfelaeelgpkaevvGiD 35
                                   rvlD+GCG G++++ l e++    evv +D
  gi|119719034|ref|YP_919529.1| 39 RVLDVGCGDGYYSLPLLENA---QEVVCVD 65
                                   89************999643...2366555 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.9e-05     0.035      13      38 ..      36      62 ..      28     107 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.9e-05
                           MetW 13 pgsrvldlGcGdGel.lellkeekqvd 38
                                   ++ rvld+GcGdG   l ll++ ++v 
  gi|119719034|ref|YP_919529.1| 36 ARGRVLDVGCGDGYYsLPLLENAQEVV 62
                                   5789*********75488998888875 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   3.1e-05     0.056       1      28 [.      41      66 ..      41      83 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.1e-05
                Methyltransf_12  1 LeiGcGtGsllralleklpdieytgvDi 28
                                   L++GcG+G ++ +lle+    e+++vD+
  gi|119719034|ref|YP_919529.1| 41 LDVGCGDGYYSLPLLEN--AQEVVCVDP 66
                                   8****************..********8 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   5.8e-05       0.1      29      60 ..      35      66 ..      25     124 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.8e-05
                                   S-S-EEEEES-TTSHHHHHHHHTT-EEEEEES CS
                           TehB 29 vkpgkvldlgcgqgrnslylsllgydvtawdk 60
                                   +  g+vld+gcg+g  sl l  +  +v ++d 
  gi|119719034|ref|YP_919529.1| 35 LARGRVLDVGCGDGYYSLPLLENAQEVVCVDP 66
                                   67799***************999999999884 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1489.26
//
Query:       gi|119719035|ref|YP_919530.1|  [L=302]
Description: polyprenyl synthetase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.8e-35  120.8   0.0    6.7e-35  120.4   0.0    1.1  1  polyprenyl_synt  Polyprenyl synthetase


Domain annotation for each model (and alignments):
>> polyprenyl_synt  Polyprenyl synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.4   0.0   3.8e-39   6.7e-35       8     196 ..      37     213 ..      31     221 .. 0.90

  Alignments for each domain:
  == domain 1  score: 120.4 bits;  conditional E-value: 3.8e-39
                                    HHHHHHSSS--HHHHHHHHHHHHHSCGHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEETTEE-HHHCTCHHHHHHHH CS
                polyprenyl_synt   8 leylveagGKrlRpllvllaaealkeeeeelekaavlawivellhaasLvhDDimDdsetRRGqpcahrlvGnklAindg 87 
                                    ++y +  gGK+lR++l ll+a +++    ++ek++ +a +vel+haasLvhDDi D s tRRG+p+  +++G + Ai + 
  gi|119719035|ref|YP_919530.1|  37 ASYAL-FGGKMLRGTLSLLVASMFT--A-QVEKVLPIALAVELMHAASLVHDDIADASPTRRGRPSFWSKYGLEDAITVP 112
                                    44555.6******************..4.689************************************************ PP

                                    HHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHTTTTTCCC.SHHHHHHHHHHHTHHHCHHHHHHHHHHTT CS
                polyprenyl_synt  88 dfllarafellaklfekslellelfsevllqtveGqlldleeekdddlskfsleeyleivkyKTaylfalpvalaallag 167
                                     +l   a  l+a+     +e+++   ++  + + Gql+d++  +  ++       y++ ++yKTa+ f++++ l +++ g
  gi|119719035|ref|YP_919530.1| 113 HVLMPVAISLVADA---GVEAVKESMNAWRRSALGQLWDTRILRGREV----PVGYEKLIEYKTAAVFEASCTLPLIAIG 185
                                    ************98...679*******************944433333....367************************* PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                polyprenyl_synt 168 asdeelealkdiglelGlaFQiqDDylDl 196
                                      ++ +e+ + +g+ +Gl++Q+ DD+ D 
  gi|119719035|ref|YP_919530.1| 186 R-RDIVESGRVYGRFFGLLYQVLDDFSDA 213
                                    6.7889********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 2230.40
//
Query:       gi|119719036|ref|YP_919531.1|  [L=276]
Description: TatD family hydrolase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-59  201.6   0.0    1.6e-59  201.4   0.0    1.0  1  TatD_DNase    TatD related DNase
    0.00012   22.0   0.0       0.29   10.9   0.1    2.7  2  Amidohydro_2  Amidohydrolase
     0.0052   16.2   0.0     0.0072   15.7   0.0    1.5  1  Amidohydro_1  Amidohydrolase family


Domain annotation for each model (and alignments):
>> TatD_DNase  TatD related DNase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  201.4   0.0   2.7e-63   1.6e-59       1     254 [.       2     257 ..       2     258 .. 0.92

  Alignments for each domain:
  == domain 1  score: 201.4 bits;  conditional E-value: 2.7e-63
                                    EEEEE-TTSCCCTTTHHHHHHHHHHTTEEEEEEE-SSG........GGHHHHHHHHTT.TTTEEEEE---GGGGGCC.CC CS
                     TatD_DNase   1 iDaHcHldskefeedreeileraeeagvaavvvvgtss........kdskavlelakkypnkvyavlGiHPnevdeased 72 
                                    iDaHcHl+ + ++e  e++l++a+ + ++avv+ g+             k++l+l+++y + v+++lG+HP++v e s++
  gi|119719036|ref|YP_919531.1|   2 IDAHCHLTYPGLKERVENVLAEAR-RALKAVVTSGLPYdaekspgfPGAKEALALSERYRGFVFVTLGLHPTQVPEMSDE 80 
                                    8**********9********9999.6789999999988888888765888**************************9666 PP

                                    HH.HHHHHHHHCCCTSEEEEEEEEEET-.CCCCCGHHHHHHHHHHHHHHHHHTTEEEEEEEES-HHHHHHHHHHCGGCCS CS
                     TatD_DNase  73 ll.eelkelanvkhskvvaiGeiGLDyy.sreestkeaqeevFeeqlrlAkelklplviHlrkaeedlleilkeaaeaka 150
                                     + e+++ + + +++++v+iGeiGLD+y  ++e++ ++ +evF   l++A++l++p+viH+rkaee+ +eil+++   + 
  gi|119719036|ref|YP_919531.1|  81 EVaEYINFI-EENRDRIVGIGEIGLDKYwLSSEDDLKRAREVFLSLLEVAEKLGKPVVIHSRKAEEEAVEILSSYSLDG- 158
                                    652666555.889**************745667888***************************************9999. PP

                                    EEEETT--S-HHHHHHHHHTTEEEEE-GGGGTTTTHHHHHHHHHS-GGGEEE---TTSSEECCCTTSE--GGGHHHHHHH CS
                     TatD_DNase 151 kvvlHsfsgsaeeakkflklgyyislsglltfknakelrelvkavpldrlLiETDaPyltpkpyrgkrnepanvayvvek 230
                                    +v lHsf+g++++akk+l++gy++s++  +t   +k +r+++k+ pl+++L+ETD+P+l+    +  +n p +v+ ++e+
  gi|119719036|ref|YP_919531.1| 159 RVLLHSFTGNMTTAKKALDMGYFFSINYKVTN--TKSMRKIAKTFPLESILTETDSPFLSH---EAGVNTPLQVRLILEE 233
                                    ****************************9888..779************************...448************* PP

                                    HHHHHTS-HHHHHHHHHHHHHHHH CS
                     TatD_DNase 231 laelkaltleelaeitaeNakrlf 254
                                    +++l++l +ee+ +it+ Na  +f
  gi|119719036|ref|YP_919531.1| 234 ISRLRGLGFEEVDAITTRNAVSFF 257
                                    *********************999 PP

>> Amidohydro_2  Amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.1   4.9e-05      0.29       2     148 ..       3     139 ..       2     157 .. 0.62
   2 !    7.8   0.0   0.00042       2.5     231     291 .]     192     259 ..     181     259 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 4.9e-05
                                    EEEEEE..SHHHCCCCCCGGCTSCCCHHHHHCHHTSSECCCEHCHHHHHHHHTSHHCHHHHHHHHHHHHHHHHHHHHHHC CS
                   Amidohydro_2   2 DvHaHllppeaairddgepngfdpeerlafmkragvdpqlaspeallvlnaaagiaravivaalcrgannrvlaeaakrp 81 
                                    D+H+Hl+                    ++++k++  ++ +   +al++        +a+++ +++       ++ea++  
  gi|119719036|ref|YP_919531.1|   3 DAHCHLT--------------------YPGLKERVENVLAEARRALKAVVTSGLPYDAEKSPGFP------GAKEALALS 56 
                                    5555542....................22333333333333333333333333344444444444......345555555 PP

                                    TTCBECEEECTSSHCH........HHHHHHHHHHHTTECEEEEESSTTTCCTTTCGGH........HHHHHHHHHHT-EE CS
                   Amidohydro_2  82 drfvggaavvpldped........aaaeleraveelgfkGvrlnphvggddllgdrld........rpifealeelglpv 145
                                     r++g+++v+++ +++         +ae +  +ee + + v ++     +++l+ + d          ++e++e+lg pv
  gi|119719036|ref|YP_919531.1|  57 ERYRGFVFVTLGLHPTqvpemsdeEVAEYINFIEENRDRIVGIGEIGLDKYWLSSEDDlkrarevfLSLLEVAEKLGKPV 136
                                    5555555555444433344445557888888889999999999999999999999999999999999************* PP

                                    EEE CS
                   Amidohydro_2 146 dih 148
                                     ih
  gi|119719036|ref|YP_919531.1| 137 VIH 139
                                    *** PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00042
                                    HHHHHHHHHH-GGGEEEE--BTSTTSTSCTTHHHHCHHHHH.......SSHHHHHHHHTHHHHHHCTB CS
                   Amidohydro_2 231 palarlieavgpdrilfGsDyPhptleaepealalldlval.......lsdeerekilggNAarlygl 291
                                    ++++ + ++++ + il  +D P+ + ea + +  +++l+ +       l  ee+++i   NA+ ++gl
  gi|119719036|ref|YP_919531.1| 192 KSMRKIAKTFPLESILTETDSPFLSHEAGVNTPLQVRLILEeisrlrgLGFEEVDAITTRNAVSFFGL 259
                                    6789999*******************************999************************997 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.2e-06    0.0072       6     162 ..       1     152 [.       1     263 [. 0.77

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.2e-06
                                    EEEEEEECETTECSSSGHHHHHSTTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHHHHHHHHHHHT...SSSEEEEEEE CS
                   Amidohydro_1   6 lIDaHvHleqsllrgatledwlvppetaaealesgiktalksGtttvadmgattstgiealleaaee...lplglrilgg 82 
                                    +IDaH Hl    +             +  e +   +++alk+ +t+ + + a  s+g++  +ea+     +  g+ +++ 
  gi|119719036|ref|YP_919531.1|   1 MIDAHCHLTYP-G-----------LKERVENVLAEARRALKAVVTSGLPYDAEKSPGFPGAKEALALserY-RGFVFVT- 66 
                                    59999999744.3...........45567777788889999999999999999888777777755553222.2333333. PP

                                    SSEGGS..GCCCSHHHHHHHHHHHHHHHHHHCTTTCEE.EEEEECGTCCSHHHHHHHHHH.......HHHHHTTEEEEEE CS
                   Amidohydro_1  83 kvsldr..gsaetskasreklkagaaetikgkadgvvk.valapheapafsdeelkealk.......eakkrdlpvaiHa 152
                                              +++++ s e++++++ ++i ++ d +v   +++    +  s++ lk a +       +a+k ++pv+iH 
  gi|119719036|ref|YP_919531.1|  67 -----LglHPTQVPEMSDEEVAEYI-NFIEENRDRIVGiGEIGLDKYWLSSEDDLKRAREvflslleVAEKLGKPVVIHS 140
                                    .....23366677778888888885.8889999999999999999999999998888888888888799999******** PP

                                    ..TSSCHHHHHH CS
                   Amidohydro_1 153 ..letkgeveda 162
                                      +e+++    +
  gi|119719036|ref|YP_919531.1| 141 rkAEEEAVEILS 152
                                    766655554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1923.05
//
Query:       gi|119719037|ref|YP_919532.1|  [L=492]
Description: carbamoyl-phosphate synthase L chain, ATP-binding [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.4e-70  235.5   0.0    6.3e-70  235.0   0.0    1.1  1  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
    1.3e-43  148.0   0.0    4.8e-43  146.2   0.0    1.9  2  Biotin_carb_N    Biotin carboxylase, N-terminal domain
    5.7e-37  126.1   0.0    1.1e-36  125.3   0.0    1.5  1  Biotin_carb_C    Biotin carboxylase C-terminal domain
    7.5e-13   48.5   0.0    1.2e-12   47.8   0.0    1.3  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
    7.3e-07   28.9   0.0    1.2e-06   28.2   0.0    1.3  1  ATP-grasp        ATP-grasp domain
    2.5e-06   27.2   0.0    4.9e-06   26.3   0.0    1.4  1  RimK             RimK-like ATP-grasp domain
    1.7e-05   25.0   0.0    3.3e-05   24.0   0.0    1.5  1  ATP-grasp_3      ATP-grasp domain
  ------ inclusion threshold ------
      0.012   15.8   0.0        3.2    8.0   0.0    3.4  3  LAL_C2           L-amino acid ligase C-terminal domain 2
      0.025   14.3   0.0      0.045   13.5   0.0    1.4  1  ATPgrasp_Ter     ATP-grasp in the biosynthetic pathway with T
      0.071   12.7   0.0       0.12   11.9   0.0    1.4  1  ATP-grasp_4      ATP-grasp domain
      0.079   12.2   0.0       0.14   11.4   0.0    1.3  1  ATPgrasp_ST      Sugar-transfer associated ATP-grasp
       0.12   11.8   0.0       0.26   10.7   0.0    1.5  1  ATP-grasp_5      ATP-grasp domain


Domain annotation for each model (and alignments):
>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  235.0   0.0   4.2e-73   6.3e-70       1     207 [.     117     322 ..     117     325 .. 0.97

  Alignments for each domain:
  == domain 1  score: 235.0 bits;  conditional E-value: 4.2e-73
                                    SHHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHHST CS
                    CPSase_L_D2   1 DkesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaafgn 80 
                                    Dk  a++  +  ++pvvp++   + + + al+ia+eig+Pvi+k+a g+GG Gm va++ e+l++ ++ka++ a +af++
  gi|119719037|ref|YP_919532.1| 117 DKLGARKFFSSKGIPVVPGAFE-AVDFNSALSIAEEIGFPVIVKPAGGGGGIGMFVAHTPEDLEKNLEKARQLAGSAFAR 195
                                    777888999999*******998.6799***************************************************** PP

                                    S-EEEEE--SSSEEEEEEEEEETTS-EEEEEEEEECCECTCCCCEEEES-SS--HHHHHHHHHHHHHHHHHHT-EEEEEE CS
                    CPSase_L_D2  81 kqvlvekslkgpkeiEvevlrDakgnvitvcerenslqlrtqkvievAPsqtLtdeerqalreaavkvvrevgvvgagtv 160
                                     +v+vek+  + k+iEv++l D++g v++++ere+s+q+r qkv+e+APs+ Lt+eer++l +aavk+++++g+++agt+
  gi|119719037|ref|YP_919532.1| 196 TEVYVEKYFPRAKHIEVQILGDKRGRVVHLFERECSVQRRYQKVVEEAPSPSLTQEEREKLLSAAVKAAEACGYENAGTF 275
                                    ******************************************************************************** PP

                                    EEEEETTTTEEEEEEEESS--CCHHHHHHHHS--HHHHHHHHHTT-- CS
                    CPSase_L_D2 161 eflldpkskeyyviEvNtRlsvesalaekaTGldlvkeaakialgek 207
                                    efl+d +s+++y++EvN+R++ve++++e +TGld+vk ++ +a g +
  gi|119719037|ref|YP_919532.1| 276 EFLFDVESRNFYFLEVNSRIQVEHPVTELVTGLDIVKLQLTVAEGGE 322
                                    *******************************************9976 PP

>> Biotin_carb_N  Biotin carboxylase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.2   0.0   3.2e-46   4.8e-43       2     110 .]       4     112 ..       3     112 .. 0.99
   2 ?   -1.6   0.0       2.7     4e+03      10      29 ..     398     417 ..     396     431 .. 0.85

  Alignments for each domain:
  == domain 1  score: 146.2 bits;  conditional E-value: 3.2e-46
                                    --EEEE---HHHHHHHHHHHHHTT-EEEEEEEGGGTTSHHHHHSSEEEEEESSTTCCGGG-HHHHHHHHHHTT-SEEE-- CS
                  Biotin_carb_N   2 ikkvlianrGeiAvriiravrelgietvavyseedanslhvreadeavelgpasasesYlniekivkaakesgadavhpG 81 
                                    i+k+l+anrGeiAvri+r++r+lgi+tvavys++d+ slh  +ade++ lgp ++++sYln+e+ivk+a ++gadavhpG
  gi|119719037|ref|YP_919532.1|   4 IRKLLVANRGEIAVRIFRTARDLGIKTVAVYSDADKLSLHRLLADESYYLGPPEPAKSYLNAERIVKIAVSAGADAVHPG 83 
                                    89****************************************************************************** PP

                                    SSTTTT-HHHHHHHHHTT-EESSS-HHHH CS
                  Biotin_carb_N  82 yGflsEnaefaeaveeagivfiGPsaeal 110
                                    yGfls n++fa++v e+g++++GP++e++
  gi|119719037|ref|YP_919532.1|  84 YGFLSQNPSFARMVIEEGLIWVGPKPETM 112
                                    **************************998 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.7
                                    -HHHHHHHHHHHHHTT-EEE CS
                  Biotin_carb_N  10 rGeiAvriiravrelgietv 29 
                                    r e+ +r++ra++el+i+ v
  gi|119719037|ref|YP_919532.1| 398 REEARTRLLRALNELRISGV 417
                                    8899999*****99988765 PP

>> Biotin_carb_C  Biotin carboxylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.3   0.0   7.1e-40   1.1e-36       1     107 [.     338     444 ..     338     445 .. 0.99

  Alignments for each domain:
  == domain 1  score: 125.3 bits;  conditional E-value: 7.1e-40
                                    EEEEESEETTTTTEE--CE-SEEE---STTEEEEE---TT-EE-TTS-SEEEEEEEEESSHHHHHHHHHHHHHT-EEESS CS
                  Biotin_carb_C   1 eaRinaEdpeknflpssGkvtelelpegpgvRvdsgveegsevspyyDsllaKlivhgetreealarlrraLaelrieGv 80 
                                    eaR++aEdp+++f ps+G++t+l++p+gp vRvdsgv+eg ev+p+yD+ll+K++ +g++reea +rl raL+elri+Gv
  gi|119719037|ref|YP_919532.1| 338 EARVYAEDPSSGFIPSPGRITYLREPAGPWVRVDSGVYEGFEVPPFYDPLLMKVVSWGQDREEARTRLLRALNELRISGV 417
                                    89****************************************************************************** PP

                                    -BSHHHHHHHHH-HHHHHT---TTTCC CS
                  Biotin_carb_C  81 ktnieflrailedeefakgeldtkfle 107
                                    k+n  ++ ++led++f++++++t++le
  gi|119719037|ref|YP_919532.1| 418 KHNKYLIVRVLEDARFRDASYTTRLLE 444
                                    *************************98 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.8   0.0   7.9e-16   1.2e-12       6     174 ..     129     293 ..     124     294 .. 0.82

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 7.9e-16
                                    T--B--EEEEETTHHCH-H-HHHHHHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHHHTT-......SCEEEEE CS
                Dala_Dala_lig_C   6 GlpvvpyvvlekeeakeekkellekveeelgypvfVKpareGSSvGvskveseeelkeaieeafkyd......ekvlvEe 79 
                                    G+pvvp  ++e  +++++      ++ ee+g+pv+VKpa  G  +G+  +++ e+l++ +e+a +        ++v vE+
  gi|119719037|ref|YP_919532.1| 129 GIPVVPG-AFEAVDFNSA-----LSIAEEIGFPVIVKPAGGGGGIGMFVAHTPEDLEKNLEKARQLAgsafarTEVYVEK 202
                                    5555552.3444444444.....4899************************************9975222222689**** PP

                                    --.ESEEEEEEEEETSSCEEEEEEEEE-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEE CS
                Dala_Dala_lig_C  80 ai.egreievavlgneklevsevgeivvkkgfydyeakysddkaqlevpaklekeveekiqelalkaykaldlrGlaRvD 158
                                    +  +++ iev +lg+ + +v ++ e+  +      + +y+ + ++     +l++e++ek+  +a+ka +a + +  +   
  gi|119719037|ref|YP_919532.1| 203 YFpRAKHIEVQILGDKRGRVVHLFERECSV-----QRRYQ-KVVEEAPSPSLTQEEREKLLSAAVKAAEACGYENAGTFE 276
                                    ********************9999998875.....67785.4455555668999************************** PP

                                    EEE.ETTTEEEEEEEES CS
                Dala_Dala_lig_C 159 ffl.teegeivlnEvNt 174
                                    f+   e+ ++++ EvN 
  gi|119719037|ref|YP_919532.1| 277 FLFdVESRNFYFLEVNS 293
                                    **9557889*******5 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.0   7.8e-10   1.2e-06      11     138 ..     137     269 ..     125     295 .. 0.78

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 7.8e-10
                                    EEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC........GTTCEEEEE----SEEEEEEE CS
                      ATP-grasp  11 flaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal........keekvivEefvpfekElsvlv 82 
                                    f av+  +++ ++aee+g+pv+vK + +g  G G +v + +edle+ le +        ++++v+vE++ p  k + v +
  gi|119719037|ref|YP_919532.1| 137 FEAVD-FNSALSIAEEIGFPVIVK-PAGGGGGIGMFVAHTPEDLEKNLEKArqlagsafARTEVYVEKYFPRAKHIEVQI 214
                                    44444.44666778**********.***********************999999***9999******************* PP

                                    EEETTC-.EEE--EEEEEEETTEEEEEEECEE-SCHHHHHHHHHHHHHHHHHTSSEE CS
                      ATP-grasp  83 vrsaeGe.tafypvvetvqedgilrlsvapaevsekaqkkaeeiakkiveeLggvGv 138
                                      +++G+ ++ ++   +   +  ++ +v  a+ ++  q++ e++++ +v++ + +G 
  gi|119719037|ref|YP_919532.1| 215 LGDKRGRvVHLFER--ECSVQRRYQKVVEEAPSPSLTQEEREKLLSAAVKAAEACGY 269
                                    ******72334444..44455568888888888888888888888888888887775 PP

>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   3.3e-09   4.9e-06      24     173 ..     139     301 ..     116     315 .. 0.72

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 3.3e-09
                                    ESS-S-HHHHHHTT-.-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHH.........GGG--EEEEE--SS-SEEEEEEE CS
                           RimK  24 ardeedaekliekiklrfPvvvKsvegsqGikvvlakkeqklkqvlea.........lkeailvqeyieeaenediRvlv 94 
                                    a d + a ++ e+i  +fPv+vK   g  Gi++++a+++++l++ le           ++++ v +y   a+  ++ +l 
  gi|119719037|ref|YP_919532.1| 139 AVDFNSALSIAEEI--GFPVIVKPAGGGGGIGMFVAHTPEDLEKNLEKarqlagsafARTEVYVEKYFPRAKHIEVQILG 216
                                    44555666667777..7***********************9999998767777777777788999999999999998886 PP

                                    E.TTEEEEEEEEE--SSS----TTTT-EEEE----HHHHH.H...HHHHHHHCT-SEEEEE..EEE.ETTEEEEEEEESS CS
                           RimK  95 v.ddevvaalrrvskeGdFRsnlhrGgvaeklqlseeeke.l...AikaakamelvvaGvD..llr.akrgllvlEvnss 166
                                       + vv  ++r +     R   +    a   +l++ee+e l   A+kaa+a +   aG    l++ + r++++lEvns 
  gi|119719037|ref|YP_919532.1| 217 DkRGRVVHLFERECSV--QRRYQKVVEEAPSPSLTQEEREkLlsaAVKAAEACGYENAGTFefLFDvESRNFYFLEVNSR 294
                                    4146788888887554..3444444455555678887765434559*************86688883469********** PP

                                    --SHHHH CS
                           RimK 167 pglekie 173
                                     ++e+  
  gi|119719037|ref|YP_919532.1| 295 IQVEHPV 301
                                    *999753 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   2.2e-08   3.3e-05       2     159 ..     116     296 ..     115     298 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 2.2e-08
                                    TSHHHHHHHHTTT.S--.-...........-EESS--SSSEEEEESS-------B--SS--TTE................ CS
                    ATP-grasp_3   2 sdKlktykkLkeagvkv.P.......tkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve......... 64 
                                     dKl   k+++ +g++v P        +   + +ee   +++vKp+ G+gg +++v++  e++e+ +e+           
  gi|119719037|ref|YP_919532.1| 116 GDKLGARKFFSSKGIPVvPgafeavdFNSALSIAEEIGFPVIVKPAGGGGGIGMFVAHTPEDLEKNLEKARqlagsafar 195
                                    688888888888887743677766544445556666799*************************999998899******* PP

                                    ....EEEE---SEEEEEEEEE.SSSEEEEEEEEEEEET....TEEEEEEES----H.HHHHHHHHHHHHTTSTT--EEEE CS
                    ATP-grasp_3  65 ....lvqefieGkplSvsllsdgekvlvlavnrqliekaekefvyaGnvtpietel.keevvelaeevvekleglaGyvG 139
                                        + + f + k++ v++l+d+   +v  + r+   +++ + v     +p+ t++ +e++ ++a ++ e+  g      
  gi|119719037|ref|YP_919532.1| 196 tevyVEKYFPRAKHIEVQILGDKRGRVVHLFERECSVQRRYQKVVEEAPSPSLTQEeREKLLSAAVKAAEAC-GYENAGT 274
                                    **99999999***********999888888888887666666777767777766555888888888888888.5555445 PP

                                    EEEE..ESS.SEEEEEEESS-- CS
                    ATP-grasp_3 140 vDlv..lkdeepyviEvNPRlt 159
                                     +++  ++  + y++EvN+R++
  gi|119719037|ref|YP_919532.1| 275 FEFLfdVESRNFYFLEVNSRIQ 296
                                    56664466799*********98 PP

>> LAL_C2  L-amino acid ligase C-terminal domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.056        83      53      71 ..     169     187 ..     159     189 .. 0.88
   2 ?   -2.5   0.0         4     6e+03      25      42 ..     309     326 ..     303     337 .. 0.75
   3 ?    8.0   0.0    0.0022       3.2      52      75 ..     391     414 ..     390     416 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.056
                         LAL_C2  53 iatgdtaeeaeaaaeeaaa 71 
                                    + ++ t+e++e+++e+a++
  gi|119719037|ref|YP_919532.1| 169 MFVAHTPEDLEKNLEKARQ 187
                                    78999************97 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4
                         LAL_C2  25 gvveveltvkpGdevrpp 42 
                                    ++v+++ltv+ G e+   
  gi|119719037|ref|YP_919532.1| 309 DIVKLQLTVAEGGEIPFR 326
                                    578999999999988655 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0022
                         LAL_C2  52 viatgdtaeeaeaaaeeaaaeiri 75 
                                    v+  g+++eea+ ++ +a++e+ri
  gi|119719037|ref|YP_919532.1| 391 VVSWGQDREEARTRLLRALNELRI 414
                                    67789*****************98 PP

>> ATPgrasp_Ter  ATP-grasp in the biosynthetic pathway with Ter operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0     3e-05     0.045      31     111 ..     232     321 ..     203     339 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3e-05
                   ATPgrasp_Ter  31 vpRrKe..kgglq.......elekdeelielaerlaeefgld..glvnvQvrededgpkLLEiNpRasGGlgysal.aGv 98 
                                    v+Rr +      +       + e++e+l+++a + ae+ g +  g + + +  +  + + LE+N+R++    ++ l +G+
  gi|119719037|ref|YP_919532.1| 232 VQRRYQkvV---EeapspslTQEEREKLLSAAVKAAEACGYEnaGTFEFLFDVESRNFYFLEVNSRIQVEHPVTELvTGL 308
                                    455444221...134456556688999**********98886115566666666777***********9999886526** PP

                   ATPgrasp_Ter  99 nlpylalklllgl 111
                                    ++++l l+ + g 
  gi|119719037|ref|YP_919532.1| 309 DIVKLQLTVAEGG 321
                                    ******9999985 PP

>> ATP-grasp_4  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   8.3e-05      0.12       1     130 [.     152     273 ..     152     299 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.3e-05
                    ATP-grasp_4   1 islPvviKPsvgffSlGVykinneeewkaavaaieeeleqakeeykeevveeesflvEeyie.GeEfavdayfdeeGepv 79 
                                    i +Pv++KP+ g + +G+ +++++e++++ +++ ++    a +     +  ++++ vE+y +  + + v ++ d+ G+  
  gi|119719037|ref|YP_919532.1| 152 IGFPVIVKPAGGGGGIGMFVAHTPEDLEKNLEKARQ---LAGS-----AFARTEVYVEKYFPrAKHIEVQILGDKRGR-- 221
                                    579*************************96665553...3333.....334566677777752456677777777765.. PP

                    ATP-grasp_4  80 ilnilkkefaseedvsdrl.yvtsakvieetlealeellkevnallglknfp 130
                                    +++++++e + ++  ++++    s+++++e+ e+l ++  ++++++g +n  
  gi|119719037|ref|YP_919532.1| 222 VVHLFERECSVQRRYQKVVeEAPSPSLTQEEREKLLSAAVKAAEACGYENAG 273
                                    3455666666666666666445566777777777766666666666666654 PP

>> ATPgrasp_ST  Sugar-transfer associated ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   9.3e-05      0.14      14      95 ..     110     188 ..     107     205 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9.3e-05
                    ATPgrasp_ST  14 aefplvddKlkfkelalraglkv.pkllgvikeqaeiseleafvkeleeg..vviKpakgsgGkGilviteredqdylks 90 
                                    + ++lv dKl  +++ + +g++v p  +       +++++ ++ +e+  g  v++Kpa g gG G+ v+   ed +++ +
  gi|119719037|ref|YP_919532.1| 110 ETMKLVGDKLGARKFFSSKGIPVvPGAFEA----VDFNSALSIAEEI--GfpVIVKPAGGGGGIGMFVAHTPEDLEKNLE 183
                                    56799****************972454433....4555566666666..3349***************988777666655 PP

                    ATPgrasp_ST  91 sgksa 95 
                                    +++++
  gi|119719037|ref|YP_919532.1| 184 KARQL 188
                                    55555 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00018      0.26      15      52 ..     121     159 ..     114     163 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00018
                    ATP-grasp_5  15 akelleaygipvvetrl.assaeeaveaaeeigypvvlK 52 
                                    a++ ++  gipvv+  + a + ++a+++aeeig+pv +K
  gi|119719037|ref|YP_919532.1| 121 ARKFFSSKGIPVVPGAFeAVDFNSALSIAEEIGFPVIVK 159
                                    78899999*******99999*****************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (492 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 3367.28
//
Query:       gi|119719038|ref|YP_919533.1|  [L=304]
Description: spermidine synthase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-50  170.3   0.0      6e-50  169.3   0.0    1.5  2  Spermine_synth   Spermine/spermidine synthase domain
    2.6e-08   33.6   0.0    5.3e-08   32.6   0.0    1.6  1  Spermine_synt_N  Spermidine synthase tetramerisation domain
    1.3e-05   25.8   0.0    2.3e-05   25.0   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    2.8e-05   23.5   0.0    4.1e-05   22.9   0.0    1.3  1  DUF43            Branched-chain polyamine synthase A C-termin
    4.1e-05   23.5   0.0    9.5e-05   22.3   0.0    1.6  1  Methyltransf_30  S-adenosyl-L-methionine-dependent methyltran
    0.00023   21.8   0.0    0.00054   20.6   0.0    1.7  2  Methyltransf_12  Methyltransferase domain
  ------ inclusion threshold ------
        0.1   11.8   0.0       0.21   10.7   0.0    1.5  2  TRM              N2,N2-dimethylguanosine tRNA methyltransfera


Domain annotation for each model (and alignments):
>> Spermine_synth  Spermine/spermidine synthase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.3   0.0   2.3e-53     6e-50       1     175 [.      65     239 ..      65     253 .. 0.93
   2 ?   -2.0   0.0      0.76     2e+03     153     171 ..     267     285 ..     243     298 .. 0.69

  Alignments for each domain:
  == domain 1  score: 169.3 bits;  conditional E-value: 2.3e-53
                                    THHHHHHHHHHHHCCSSST-EEEEESSTTSHHHHHHTTSTT-SEEEEEES-HHHHHHHHHHSHHHHTTCGGCTTEEEEES CS
                 Spermine_synth   1 efaykemiahvplmlhknpkevLiiGGgDGgvlrevvkhntvekitlvdiDqkvidfskkflpslaisafndarvklvlg 80 
                                    ef+y+e ++h ++++h++p++vL+iGGg G +lrev+kh++v+++++vdiD++ +++ k+++ + + s+f+d+rv+l+ +
  gi|119719038|ref|YP_919533.1|  65 EFVYHESLVHPAMLTHPHPEKVLVIGGGEGATLREVLKHPSVKRAVMVDIDEELVEIVKRYMWKWHRSSFDDPRVELLFM 144
                                    799***************************************************************************** PP

                                    TCHHHHCTCSS-EEEEEEECCSTTCSSCG..CSSHHHHHHHHHTEEEEEEEEEEEEETTTCHHHHHHHHHHHHTTSSCEE CS
                 Spermine_synth  81 dgfkflkayekkfdvvivdsldpvgpaen..lFskeffdllkkvlkedGviilqaekpelekelvinvdksgkqvfalqv 158
                                    dg kf++++++ fdv+i d++dpv+      l++kef++ ++++l++ Gv+++qa ++ ++ + ++ +++++ +vf+ ++
  gi|119719038|ref|YP_919533.1| 145 DGKKFVEETSERFDVIILDLTDPVSGTPGvhLYTKEFYETIYDKLTPQGVMVTQATSTRYNVKAFSVINNTVASVFP-VA 223
                                    ************************9888778**********************************************.88 PP

                                    EEEEEETTTSCSCEEEE CS
                 Spermine_synth 159 epsavlvPtylsgminf 175
                                    +p+ v v t++s + +f
  gi|119719038|ref|YP_919533.1| 224 RPYKVFVATFYSEW-GF 239
                                    88888888877765.33 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.76
                                    TSSCEEEEEEEETTTSCSC CS
                 Spermine_synth 153 vfalqvepsavlvPtylsg 171
                                    +  l++ ++++ +P+y   
  gi|119719038|ref|YP_919533.1| 267 YLDLETFYYLFHIPKYIRE 285
                                    5567788999999999754 PP

>> Spermine_synt_N  Spermidine synthase tetramerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.0   2.1e-11   5.3e-08       1      53 []      10      62 ..      10      62 .. 0.95

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 2.1e-11
                                   EEEEEEEETTEEEEEEEEEEEEEEEESSSEEEEEEETTTEEEEEETTEEEEET CS
                Spermine_synt_N  1 gWfteisdpglalelkVekvLyeekSeyQdieifesktfGkvLvLDgvvqltE 53
                                   +W+te  +  +a+   ++ ++y+++++yQ + + e+ +fG  L+LDg  q +E
  gi|119719038|ref|YP_919533.1| 10 LWYTEWLSSLEAHVHGIKRIIYDGRTKYQRVTLAETGSFGLTLFLDGYAQSSE 62
                                   599**99999*************************************998776 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   9.1e-09   2.3e-05       1      70 [.      86     162 ..      86     193 .. 0.76

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 9.1e-09
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHH......TTTTEEEEESBCCG.BSSSTTTEEEEEE CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraee......eglnvefvqgdaed.lpfedgsfDlvvs 70 
                                    vL +G G+G ++++++k+ + ++ ++vDi+ee++e++++ + +      ++++ve++ +d ++ +++ +++fD++++
  gi|119719038|ref|YP_919533.1|  86 VLVIGGGEGATLREVLKHPSVKRAVMVDIDEELVEIVKRYMWKwhrssfDDPRVELLFMDGKKfVEETSERFDVIIL 162
                                    899***************658*****************77766554344556*********994567899*****98 PP

>> DUF43  Branched-chain polyamine synthase A C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   1.6e-08   4.1e-05      47     131 ..      85     178 ..      59     216 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.6e-08
                                    EEEEES-TT-HHHHHHHHT.--SEEEEE-S-HHHHHHHHHHHHH...HT--...EEEE---TTS---TTTSS-BSEEE.. CS
                          DUF43  47 eilvlGdDDLtslalaLtg.lpkkvvvvDiDeRlikfiervake...lglk...ieaivyDlrkplpeelkekFdvfi.. 117
                                    ++lv+G  +  +l   L +   k+ v+vDiDe l+++++r   +    +++   +e +  D +k + ee +e+Fdv+i  
  gi|119719038|ref|YP_919533.1|  85 KVLVIGGGEGATLREVLKHpSVKRAVMVDIDEELVEIVKRYMWKwhrSSFDdprVELLFMDGKK-FVEETSERFDVIIld 163
                                    5899998888889888876256999***************875411144544569999999765.8999********766 PP

                                    .E---SSHHHHHHHH CS
                          DUF43 118 .tDPpetvealkaFl 131
                                     tDP+ +  +++++ 
  gi|119719038|ref|YP_919533.1| 164 lTDPVSGTPGVHLYT 178
                                    69********99986 PP

>> Methyltransf_30  S-adenosyl-L-methionine-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   3.7e-08   9.5e-05      11      91 ..     119     200 ..     111     222 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 3.7e-08
                                    HHHTS-S-SEEEEEEETTTTEEEEEEES-HHHHHHHC-T-EEEEEE-SS-TTT.SG..GGCSHHHHHHHHHHEEEEEEEE CS
                Methyltransf_30  11 lkeyllalaglqrlelaaeevtlklligdarealkeldekadawFlDgFsPak.nP..elwseellkelarllkkkgtla 87 
                                    ++ +   + + +r +++  + +++ll++d +++++e +e++d++ lD   P    P   l+++e+++ ++++l ++g+++
  gi|119719038|ref|YP_919533.1| 119 VEIVKRYMWKWHRSSFD--DPRVELLFMDGKKFVEETSERFDVIILDLTDPVSgTPgvHLYTKEFYETIYDKLTPQGVMV 196
                                    45555555677888895..688999*********************9877754233338********************9 PP

                                    ES-- CS
                Methyltransf_30  88 tyss 91 
                                    t + 
  gi|119719038|ref|YP_919533.1| 197 TQAT 200
                                    9654 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   2.1e-07   0.00054       1      98 [.      87     194 ..      87     195 .. 0.81
   2 ?   -3.4   0.0       6.6   1.7e+04      65      84 ..     266     285 ..     247     292 .. 0.56

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.1e-07
                Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg.....ssfDlvv.... 71 
                                    L iG+G G++lr++l++ + ++ + vDi+++ +e  k+ + k+++ +++  ++e l  +  ++      + fD+++    
  gi|119719038|ref|YP_919533.1|  87 LVIGGGEGATLREVLKHPSVKRAVMVDIDEELVEIVKRYMWKWHRSSFDDPRVELLFMD-GKKFveetsERFDVIIldlt 165
                                    569**************999**************************9999999977754.333369*********96633 PP

                Methyltransf_12  72 ..asnvlhhl....kdirevldnirklLkpgGr 98 
                                      +s+    +      ++e+ + i++ L+p G+
  gi|119719038|ref|YP_919533.1| 166 dpVSG----TpgvhLYTKEFYETIYDKLTPQGV 194
                                    33333....344447888888888888888886 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 6.6
                Methyltransf_12  65 ssfDlvvasnvlhhlkdire 84 
                                     + Dl +   ++h  k ire
  gi|119719038|ref|YP_919533.1| 266 RYLDLETFYYLFHIPKYIRE 285
                                    35566666666666666655 PP

>> TRM  N2,N2-dimethylguanosine tRNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   8.3e-05      0.21      65     127 ..      97     163 ..      93     203 .. 0.81
   2 ?   -2.7   0.0      0.95   2.4e+03     301     341 ..     253     293 ..     244     296 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 8.3e-05
                                    HHHHHH-S-EEEEEEE-S-HHHHHHHHHHH.HHTT--..G.GEEEE-S-HHHHHC--SS-EEEEEE- CS
                            TRM  65 iRfalEvpgvkevlaNDisekAvelikeNv.klneve..e.ivvineddAnvllaekkkrfdviDlD 127
                                    +R  l  p+vk++++ Di e+ ve++k+ + k +  +  + +v+   +d + +++e+++rfdvi lD
  gi|119719038|ref|YP_919533.1|  97 LREVLKHPSVKRAVMVDIDEELVEIVKRYMwKWHRSSfdDpRVELLFMDGKKFVEETSERFDVIILD 163
                                    566777899*******************94244433355679*********************9776 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.95
                                    -HHHHHHHHHHHHHHS--SS-EEHHHHHHHHT-SS---HHH CS
                            TRM 301 kkrvkklLklikeElldaplyydlsqlasvlklsvpplkkv 341
                                    k+++ + L+ ++   ld  ++y l ++ + ++ ++++ +++
  gi|119719038|ref|YP_919533.1| 253 KEEISRRLQSLDLRYLDLETFYYLFHIPKYIREEMQKYTQI 293
                                    67788888888888889999999999999999999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2205.37
//
Query:       gi|119719039|ref|YP_919534.1|  [L=300]
Description: periplasmic solute binding protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-14   52.3   0.0    7.4e-14   51.8   0.0    1.2  1  ZnuA      Zinc-uptake complex component A periplasmic


Domain annotation for each model (and alignments):
>> ZnuA  Zinc-uptake complex component A periplasmic
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.8   0.0   4.2e-18   7.4e-14       1     229 [.      40     273 ..      40     292 .. 0.76

  Alignments for each domain:
  == domain 1  score: 51.8 bits;  conditional E-value: 4.2e-18
                                    EEESSHHHHHHHHHHH..GGGCEEEECS-TTSTTTT----HHHHHHHHHSSEEEESS.TTTSGTHHHHHHHHTTCCCEEE CS
                                    xxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                           ZnuA   1 Vvattsplgdlvrqva..GdrvevtvLvppgadpHsyeptprdvrklaeAdllvyng.lelEtwldkllasssqatrvev 77 
                                    +v+t++ l+  ++++   Gd  ev  ++p+g+dpH+y++tp+dv+++ e +l+v++  + +E+ +++l++  + ++r  +
  gi|119719039|ref|YP_919534.1|  40 IVVTFYSLKGDIEYLLcqGD--EVIPVTPQGVDPHEYQLTPSDVARIREGSLIVSTAhAPFEQKIKQLVETGELKSR--L 115
                                    78999999999999984455..9999****************************875489**999999966653344..4 PP

                                    EETTT..TC....CSEBCSSEST.GGGSHHHHHHHHHHHHHHHHHHTGGGHHHHHHHHHHHHHHHHHHHHHHHHHHTTSS CS
                                    xxxxx..xx....xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ZnuA  78 idlse..gv....eeeeeeeDpH.iWlspknaiamveniadaLveadpanadtyeanaaayiekLeeldaeireelaeip 150
                                    i+     g+    ++ + + + H   ++p+n+ia+++ +a  ++++ p+ a+ty  +a  +i++++ +++         p
  gi|119719039|ref|YP_919534.1| 116 IEIPRipGIkllvNPSTGTLNYHwPIYDPNNYIAYINYTAHVMASLRPECASTYLSKASGLIANITSIERSA-------P 188
                                    543322233222255556669995589**************************9999999999998876644.......5 PP

                                    GTEGEEEESSSTTHHHHHHTT-EEEEEESSSSS....HHHHHHHHHHHHHTT-SEEEEET.TS-THHHHHHHH...HHT- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx...xxxx RF
                           ZnuA 151 eekrklvtthdafgylarayglevagiagiste....aaqiaalieeikeagvkaifvep.laspklaetlae...eagv 222
                                    + + + v + ++++y  + +g++v ++   +++    +++ia + +++    ++++++ + l+++++ +tl +   ++g 
  gi|119719039|ref|YP_919534.1| 189 RLNLVAVGSSPVVQYSVEWMGINVSYLLIKEADlpatPQDIATIEDAMARGAINVVVISKgLETTSAGKTLVDlasKYGK 268
                                    556778*******************886444448899*******************998755555554444442115554 PP

                                    EEEEE-S CS
                                    xxxxxxx RF
                           ZnuA 223 kvatlys 229
                                     v  ly 
  gi|119719039|ref|YP_919534.1| 269 PV--LYV 273
                                    44..554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2074.37
//
Query:       gi|119719040|ref|YP_919535.1|  [L=250]
Description: ABC transporter related [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    8.7e-26   91.1   0.0    1.2e-25   90.6   0.0    1.2  1  ABC_tran    ABC transporter
    8.9e-13   48.7   0.5      2e-06   27.8   0.0    2.1  2  AAA_21      AAA domain, putative AbiEii toxin, Type IV TA sys
    6.8e-05   23.4   0.3     0.0001   22.8   0.3    1.2  1  AAA_23      AAA domain
    8.6e-05   22.1   0.1    0.00079   18.9   0.1    2.0  1  SMC_N       RecF/RecN/SMC N terminal domain
     0.0024   17.6   0.3     0.0049   16.6   0.3    1.5  1  AAA_29      P-loop containing region of AAA domain
     0.0052   15.9   0.0     0.0088   15.1   0.0    1.3  1  T2SSE       Type II/IV secretion system protein
     0.0071   16.7   0.1      0.011   16.1   0.1    1.4  1  AAA_16      AAA ATPase domain
     0.0086   16.5   0.2       0.03   14.7   0.2    2.0  1  AAA         ATPase family associated with various cellular ac
  ------ inclusion threshold ------
      0.034   14.4   0.6       0.17   12.2   0.6    2.0  1  AAA_22      AAA domain
      0.041   13.6   0.0      0.092   12.4   0.0    1.5  1  AAA_30      AAA domain
      0.044   14.0   0.0      0.063   13.4   0.0    1.4  1  AAA_33      AAA domain
      0.069   13.1   0.1       0.59   10.1   0.0    2.2  2  AAA_5       AAA domain (dynein-related subfamily)
       0.09   12.7   0.5       0.21   11.5   0.3    1.7  1  NTPase_1    NTPase
       0.12   11.5   0.1       0.24   10.6   0.1    1.4  1  NB-ARC      NB-ARC domain
       0.14   12.1   0.0       0.23   11.3   0.0    1.3  1  ATPase_2    ATPase domain predominantly from Archaea
       0.14   11.4   0.0       0.22   10.8   0.0    1.4  1  Zeta_toxin  Zeta toxin


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.6   0.0   1.1e-28   1.2e-25       3     136 ..      24     168 ..      22     169 .. 0.90

  Alignments for each domain:
  == domain 1  score: 90.6 bits;  conditional E-value: 1.1e-28
                                    EEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                       ABC_tran   3 nvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren... 79 
                                    n +l l+   +v i+G+nG+GK+tL+k+++gllkp +G++ ++g+d++  +  ++ k  + +pq + + ++l +  +   
  gi|119719040|ref|YP_919535.1|  24 NENLFLSGPGLVTILGPNGSGKTTLFKVVLGLLKPSSGSVVINGEDVTG-NPVKAGKYASLVPQLSAIRRDLPLTAHelv 102
                                    5566666667899************************************.777889999999999999988865555679 PP

                                    .............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    .............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 .............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                 e +++  +al+ +g  +++d+++    s++SgGq qrv laral++ +++lllDEp 
  gi|119719040|ref|YP_919535.1| 103 nfvlrtrgrckgrECEAKTMEALEAVGAAGIADKKL----SEMSGGQLQRVLLARALATGADILLLDEPL 168
                                    999********9999999******************....*****************************7 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.2   7.1e-07   0.00079       3      24 ..      36      57 ..      34      87 .. 0.76
   2 !   27.8   0.0   1.8e-09     2e-06     235     302 ..     139     203 ..     136     204 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 7.1e-07
                         AAA_21  3 vliGpNgsGKSnLLdaldllar 24
                                    + GpNgsGK++L++   +l  
  gi|119719040|ref|YP_919535.1| 36 TILGPNGSGKTTLFKVVLGLLK 57
                                   699*************999954 PP

  == domain 2  score: 27.8 bits;  conditional E-value: 1.8e-09
                         AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQv.iltTHSpll.l 302
                                    +e+S G+++   l+ al+  +   ++ll+DEp +g++P+  + +l+ +++ s+   ++ ++tTH+p+l l
  gi|119719040|ref|YP_919535.1| 139 SEMSGGQLQRVLLARALATGA---DILLLDEPLSGIDPSGREYILGEIEKISK--RKLvVMTTHDPVLtL 203
                                    577777777755555555555...************************99999..6776********955 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.3   9.3e-08    0.0001      16      37 ..      28      50 ..      14      67 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 9.3e-08
                         AAA_23 16 dF.skgltlItGpNGaGKTTild 37
                                    + ++gl+ I GpNG+GKTT++ 
  gi|119719040|ref|YP_919535.1| 28 FLsGPGLVTILGPNGSGKTTLFK 50
                                   44689****************96 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1     7e-07   0.00079      24     213 ..      32     213 ..      22     218 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 7e-07
                                    SSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--.BTTCSSTTEEEEEEEE...EETTEESSSSSSCEE. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxx. RF
                          SMC_N  24 ksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk.skekasvkkaeveitf...dnedkklkiekeevs. 98 
                                    +++  i+GpNGSGK+ l+  +   LG      l+ ++ s +i+    +++ vk ++ + ++   +   ++l+ +++e++ 
  gi|119719040|ref|YP_919535.1|  32 PGLVTILGPNGSGKTTLFKVV---LG-----LLKPSSGSVVINGeDVTGNPVKAGKYASLVpqlSAIRRDLPLTAHELVn 103
                                    67889*************987...99.....4899999999998644445555444444432226666667777777441 PP

                                    .EEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHH CS
                                    .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  99 .isrrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvk 177
                                     + r+  r +    + + k+++  e       a+ + +++SgG+ + v la  +A      a + llDe  + +D + ++
  gi|119719040|ref|YP_919535.1| 104 fVLRTRGRCKGR--ECEAKTMEALEAVGAAGIADKKLSEMSGGQLQRVLLARALA----TGADILLLDEPLSGIDPSGRE 177
                                    133333333333..333333333333333333333445799**988666555555....578899*************** PP

                                    HHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 178 kvaellkeksknaQfivislreemlekadklvgvtk 213
                                     +   +++ sk+  +++++++  ++ + +k++ v+ 
  gi|119719040|ref|YP_919535.1| 178 YILGEIEKISKRKLVVMTTHDPVLTLNKSKTIVVFN 213
                                    *******99999888888888887777777776665 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.3   4.4e-06    0.0049      23      50 ..      33      60 ..      22      67 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4.4e-06
                         AAA_29 23 gatlltGpsGsGKSTllDAiqalLvpak 50
                                   g + + Gp+GsGK+Tl+  +  lL p++
  gi|119719040|ref|YP_919535.1| 33 GLVTILGPNGSGKTTLFKVVLGLLKPSS 60
                                   467899***********99999999987 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   7.8e-06    0.0088     130     199 ..      33     109 ..      14     110 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 7.8e-06
                          T2SSE 130 glilvsGgTgsGKttllyallkeinks.derivtvEDpvEiqleganqvqlnak......kakvtfadllraaLRlr 199
                                    gl+ + G+ gsGKttl  ++l  ++ s    ++  ED     +++ ++ +l+++      +  +t+++l+  +LR r
  gi|119719040|ref|YP_919535.1|  33 GLVTILGPNGSGKTTLFKVVLGLLKPSsGSVVINGEDVTGNPVKAGKYASLVPQlsairrDLPLTAHELVNFVLRTR 109
                                    677788******************99934455567999999999999999998888887777788888888888876 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   9.7e-06     0.011      22      63 ..      30      72 ..      24     166 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 9.7e-06
                         AAA_16 22 grpelvllsGesGvGKsslvrellralekd.ggiflrgkcdql 63
                                   ++p+lv + G+ G+GK++l + +l  l+ + g ++++g+ +  
  gi|119719040|ref|YP_919535.1| 30 SGPGLVTILGPNGSGKTTLFKVVLGLLKPSsGSVVINGEDVTG 72
                                   6789********************8888884456655554443 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.2   2.7e-05      0.03       2      37 ..      36      73 ..      35     205 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.7e-05
                                   EEESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSS CS
                            AAA  2 llyGppGtGKTllakavakelg..vefleisgsellsk 37
                                    + Gp G GKT+l k v   l+  +  + i+g +++ +
  gi|119719040|ref|YP_919535.1| 36 TILGPNGSGKTTLFKVVLGLLKpsSGSVVINGEDVTGN 73
                                   578*****************975466789999988854 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.6   0.00015      0.17       4      29 ..      31      56 ..      28     194 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00015
                         AAA_22  4 tagilvvtGesGtGKTtllrrlleql 29
                                   + g++++ G+ G+GKTtl + +l  l
  gi|119719040|ref|YP_919535.1| 31 GPGLVTILGPNGSGKTTLFKVVLGLL 56
                                   568999************99888776 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   8.2e-05     0.092      15      50 ..      29      64 ..      24      73 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.2e-05
                         AAA_30 15 tsgdrvavltGpAGtGKttalkalreaweaaggrvi 50
                                    sg  ++++ Gp G+GKtt+ k++  +++ + g+v+
  gi|119719040|ref|YP_919535.1| 29 LSGPGLVTILGPNGSGKTTLFKVVLGLLKPSSGSVV 64
                                   45566999***************9998888755655 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   5.6e-05     0.063       1      33 [.      34      89 ..      34     202 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.6e-05
                         AAA_33  1 lvllvGlpGsGKstlaerllkklg....avllssdt...................l 33
                                   lv + G++GsGK+tl + +l  l+     v+++  +                   +
  gi|119719040|ref|YP_919535.1| 34 LVTILGPNGSGKTTLFKVVLGLLKpssgSVVINGEDvtgnpvkagkyaslvpqlsA 89
                                   68889***********9987666655676666665545555555555555555550 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00053      0.59       3      37 ..      36      71 ..      34      98 .. 0.82
   2 ?    0.5   0.0      0.49   5.5e+02      65      85 ..     174     194 ..     140     225 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00053
                                   EEE--SSSSHHHHHHHGGGGB.S--EEEEE--TT-- CS
                          AAA_5  3 lLvGppGtgKselaerlaaal.nreveyvqltrdtt 37
                                    ++Gp G+gK++l + ++ +l  ++  +v + +d t
  gi|119719040|ref|YP_919535.1| 36 TILGPNGSGKTTLFKVVLGLLkPSSGSVVINGEDVT 71
                                   689***************999766666666666655 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.49
                                    G-SEEEEESGGG--HHHHHHH CS
                          AAA_5  65 egeilvlDEveraesevlnsL 85 
                                    +g+ ++l+E+e++++  l ++
  gi|119719040|ref|YP_919535.1| 174 SGREYILGEIEKISKRKLVVM 194
                                    777788899998887655544 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.3   0.00019      0.21       2      26 ..      35      59 ..      34      72 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00019
                                   EEEE--TTSSHHHHHHHHHHHH... CS
                       NTPase_1  2 vfiTGppGvGKtTlvkkvlellkss 26
                                   v i Gp G+GKtTl+k vl llk s
  gi|119719040|ref|YP_919535.1| 35 VTILGPNGSGKTTLFKVVLGLLKPS 59
                                   5788****************99865 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00021      0.24      17      40 ..      31      52 ..      24      58 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00021
                                   TSCSEEEEEEESTTSSHHHHHHHH CS
                         NB-ARC 17 elqslvvalvGmgGvGKttlakqi 40
                                   +++  +v++ G  G+GKttl+k +
  gi|119719040|ref|YP_919535.1| 31 GPG--LVTILGPNGSGKTTLFKVV 52
                                   667..89*************9977 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00021      0.23      23      47 ..      35      59 ..      26      70 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00021
                       ATPase_2 23 yfiYGpegsGKtaLlkeiienledk 47
                                   + i Gp gsGKt+L+k ++  l+ +
  gi|119719040|ref|YP_919535.1| 35 VTILGPNGSGKTTLFKVVLGLLKPS 59
                                   5699************998877654 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00019      0.22      16      53 ..      32      69 ..      22     103 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00019
                     Zeta_toxin 16 PklillgGqpGAGKselaellkdelerqgnvvrldpDd 53
                                   P l+ + G  G+GK++l + +   l++ ++ v++++ d
  gi|119719040|ref|YP_919535.1| 32 PGLVTILGPNGSGKTTLFKVVLGLLKPSSGSVVINGED 69
                                   7889999*******************999999999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 1757.85
//
Query:       gi|119719041|ref|YP_919536.1|  [L=266]
Description: ABC-3 protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-27   96.8  26.1    1.6e-27   96.6  26.1    1.0  1  ABC-3     ABC 3 transport family
      3e-06   26.5  22.4    4.1e-06   26.0  22.4    1.2  1  FecCD     FecCD transport family


Domain annotation for each model (and alignments):
>> ABC-3  ABC 3 transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.6  26.1   1.8e-31   1.6e-27      16     256 ..      15     261 ..       2     263 .. 0.90

  Alignments for each domain:
  == domain 1  score: 96.6 bits;  conditional E-value: 1.8e-31
                          ABC-3  16 slacallgsfvvlrrqsllgdalsHaalpGvalayllgvn....lllgailvgliaavalellkrktklkedtaigivls 91 
                                    s+  ++l+  +  rr  +++++l H++l  v l+yll++     ++l ai +++++++ l++l ++  ++ed+a+   +s
  gi|119719041|ref|YP_919536.1|  15 SVSFSVLSPVIHARRLNFFAATLPHSSLLAVSLGYLLSFLlgysPTLWAIPISVALSFLLVVLIHR-GVSEDSATSAFVS 93 
                                    455689999999***********************9998867668888999998888888777665.5788888888888 PP

                          ABC-3  92 vflalglvlvslikk...skvdldsyLfGniltisqedliliaiieavvllllllfwkelllitfdeelAkveglsvkll 168
                                    ++ + +++++ +i +   s+v+l+sy++G+ l ++ ed+ ++++++av  l +ll++ + ++i +d+++++  g++v+l 
  gi|119719041|ref|YP_919536.1|  94 FSVSASVAAMYYILTkfpSEVSLWSYILGDPLLVTWEDVAVTVVVTAVATLSTLLIYMKEVVIGLDRDFSQLLGINVNLH 173
                                    888888877777766678***************************************999******************** PP

                          ABC-3 169 kllllalialavvvalqavGviLvialliiPaatArrltrslesllivAillglvsvvaGlllSyyldlatGavivlvat 248
                                    ++l + ++ l     l++vG +L   +l +Pa +  +l++s ++ l ++ l++ vs ++Gl++S+y+++a++a+   v+ 
  gi|119719041|ref|YP_919536.1| 174 DYLVVFVLTLVSISLLKVVGFVLEHVVLLLPATVSVQLAKSAKEFLGYSLLVSTVSGLLGLFTSIYANVAPSAMYGFVML 253
                                    ****99999999999************************************************************99999 PP

                          ABC-3 249 llfllall 256
                                     l+l++ll
  gi|119719041|ref|YP_919536.1| 254 GLYLAVLL 261
                                    99998876 PP

>> FecCD  FecCD transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0  22.4   4.6e-10   4.1e-06      85     281 ..      43     235 ..      38     262 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 4.6e-10
                          FecCD  85 lgavlalllllgslslfalplaaf.lgallalllvlllarkrkgasplkliLaGiavsallsaltsllllllneealesi 163
                                    l++ l++ll  + l+ ++ +l a+ ++ +l++llv+l+  ++ ++++++   + + vsa ++a+  +l+ +    +  s+
  gi|119719041|ref|YP_919536.1|  43 LAVSLGYLLS-FLLG-YSPTLWAIpISVALSFLLVVLIH-RGVSEDSATSAFVSFSVSASVAAMYYILTKF---PSEVSL 116
                                    5666666663.4444.44555555266666666666666.89999999999**************999988...466788 PP

                          FecCD 164 lfwllGslsgaswskvllllvllllllllllllarkldllalgdetAkslGvnvervrllllllvalltavavalvG.pi 242
                                      ++lG+   ++w++v++ +v++++++l +ll++ k  ++ l+++ ++ lG+nv+   +l++++ +l++ +   +vG ++
  gi|119719041|ref|YP_919536.1| 117 WSYILGDPLLVTWEDVAVTVVVTAVATLSTLLIYMKEVVIGLDRDFSQLLGINVNLHDYLVVFVLTLVSISLLKVVGfVL 196
                                    9999*************************************************************************445 PP

                          FecCD 243 gFvGLivPhiarllvgadhrkllplsallGallllladl 281
                                      v L+ P +++  + ++ +  l +s l++ +  ll  +
  gi|119719041|ref|YP_919536.1| 197 EHVVLLLPATVSVQLAKSAKEFLGYSLLVSTVSGLLGLF 235
                                    8***********999999999999999987765555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       929  (0.0518155); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1587.93
//
Query:       gi|119719042|ref|YP_919537.1|  [L=130]
Description: CopG family transcriptional regulator [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.3e-06   26.1   0.0    1.1e-05   25.5   0.0    1.3  1  NikR_C        NikR C terminal nickel binding domain
  ------ inclusion threshold ------
       0.04   13.9   0.3       0.15   12.0   0.0    2.1  2  RHH_1         Ribbon-helix-helix protein, copG family
       0.13   12.2   0.0       0.18   11.8   0.0    1.2  1  Ribosomal_L2  Ribosomal Proteins L2, RNA binding domain


Domain annotation for each model (and alignments):
>> NikR_C  NikR C terminal nickel binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   1.8e-09   1.1e-05       2      66 ..      56     117 ..      55     123 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 1.8e-09
                                    EEEEEEEETTSTTHHHHHHHHHHHHSSEEEEEEEEEESSSEEEEEEEEEE-HHHHHHHHHHHHTS CS
                         NikR_C   2 GvitivydhhqrelserltdiqheyhdliisslhvhldhdncLevivlkGeaeeikelaeklral 66 
                                    Gv++i yd       +++++   e++ l++s  h h  +  cLe++ lkG++eei  l ++++ l
  gi|119719042|ref|YP_919537.1|  56 GVMIISYDP---ARGQEVAEAIEESKSLVVSRSHFHTGDGCCLEILYLKGDSEEIWLLEKRVSHL 117
                                    677778887...456889999999*******************************9888888766 PP

>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.5e-05      0.15       1      37 [.       6      42 ..       6      44 .. 0.96
   2 ?   -1.0   0.1      0.32   1.9e+03       9      16 ..      69      76 ..      65      85 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.5e-05
                                   EEEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHH CS
                          RHH_1  1 rvsirldeellerLdelarrrgrSrSelIReAlreyl 37
                                   rv ++ld ++ e+L++ a++ +  rS ++  A+reyl
  gi|119719042|ref|YP_919537.1|  6 RVGVSLDGDVFEELERVAKAFNTDRSHIVNMAAREYL 42
                                   899*********************************9 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.32
                                   HHHHHHHH CS
                          RHH_1  9 ellerLde 16
                                   e++e+++e
  gi|119719042|ref|YP_919537.1| 69 EVAEAIEE 76
                                   44444444 PP

>> Ribosomal_L2  Ribosomal Proteins L2, RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0     3e-05      0.18      17      73 ..      37      91 ..      23      94 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3e-05
                                   ----EE-B--S---SS--EEEEEEE--TT-SS-EEEEEETTTEEEEEE--SS--SS- CS
                   Ribosomal_L2 17 hkkkyrlidfkrnkekvkgkVveieyDpgRsApiAlvkyedgekryiiapeglkvGd 73
                                   + + y l +f + k +  + V+ i yDp+R  ++A    e+  k++++     ++Gd
  gi|119719042|ref|YP_919537.1| 37 AAREYLLEKFHYAKPHSCEGVMIISYDPARGQEVAEAIEES--KSLVVSRSHFHTGD 91
                                   56789999999977777788888***********9765555..77777777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 889.90
//
Query:       gi|119719043|ref|YP_919538.1|  [L=202]
Description: hypothetical protein Tpen_0125 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-37  129.6   0.1    1.4e-37  129.1   0.1    1.2  1  TYW3      Methyltransferase TYW3


Domain annotation for each model (and alignments):
>> TYW3  Methyltransferase TYW3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.1   0.1   8.1e-42   1.4e-37       4     211 ..      19     197 ..      16     199 .. 0.91

  Alignments for each domain:
  == domain 1  score: 129.1 bits;  conditional E-value: 8.1e-42
                                    HHHHHHH....HHHHHCCHC-GGGHHHHHHHHC-SSEEEEEEES-EEEEE............EESSTT-STT-EEEEEES CS
                           TYW3   4 akiLeeLsvpdtdkspkGsvDekirelideinsledlvTtSSCsGRvsvflegrksaeaeeeaaksggkkgggkwlfvsH 83 
                                    +k+Le+     +++ ++G+vDe+i++l++++n+ ++++TtSSCsGR+ v             + ++ g kg   ++ ++H
  gi|119719043|ref|YP_919538.1|  19 RKALEQF----ERHLEEGRVDEDIVDLLRLVNNTKNCYTTSSCSGRIQVS------------CGEHPGAKGRLVVVAKWH 82 
                                    5566666....8899***********************************............4444444455579***** PP

                                    S---HHHHHHHHCS--..............SSEEEEEEE--EEEEEESSHHHHHHHHHHHHHCT-TT-EEEEECTTEEEE CS
                           TYW3  84 dpvkeeellaelfgleeeegsaksseseeeerlilfkfePmILHvlcrslesAqkllsaAleaGfreSGivslkkkkviv 163
                                    ++v+ +el++ l +l+              e+ +++++ P+I+Hv +r+l+ A+kll+ A+++Gf++SGi+ l + +v+v
  gi|119719043|ref|YP_919538.1|  83 RTVSLQELVSVLDSLQ--------------EESVWLSVHPPIFHVVARDLSVARKLLAGARNSGFKHSGIQGLGR-RVVV 147
                                    ***************7..............689*****************************************9.**** PP

                                    EEE---EEEEEEE.ST.S---HHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                           TYW3 164 airsglklevpig.ke.llvseeylkllvklanerfeenkkrierfeeal 211
                                    +i+s ++levpi  +   +v++e l +l+++ane + + k+r+  +++ +
  gi|119719043|ref|YP_919538.1| 148 EIMSMERLEVPIRvQGvEVVRRESLPILLETANEFLLRGKSRLGVLRKVF 197
                                    *************94458************************99998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1560.93
//
Query:       gi|119719044|ref|YP_919539.1|  [L=242]
Description: purine phosphorylases family protein 1 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.8e-37  127.4   0.9    5.5e-37  127.3   0.9    1.0  1  PNP_UDP_1  Phosphorylase superfamily


Domain annotation for each model (and alignments):
>> PNP_UDP_1  Phosphorylase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.3   0.9   3.1e-41   5.5e-37       3     204 ..      24     215 ..      22     239 .. 0.85

  Alignments for each domain:
  == domain 1  score: 127.3 bits;  conditional E-value: 3.1e-41
                                    EEEESSHHHHHHHHHHEEEEEEEEEE.TTEEEEEEEETTEEEEEEE--SSHHHHHHHHHHHHHHHC--SEEEEEEEEEES CS
                      PNP_UDP_1   3 aiivgspgevellaespleetpfgregrgfkfvtGtlkgkpvvivstGiGkpnaavvaeirllkefgvkaiiriGtaGgl 82 
                                    ++++g+pg+ve+ ++  l+  ++ +++rg+ +vtG++ g++v+++++GiG+p+aa+v+e  ++   g+k++ir Gt+Ggl
  gi|119719044|ref|YP_919539.1|  24 ILVCGDPGRVEAASSL-LDGATVVNRHRGYLVVTGEYRGERVTLATHGIGAPSAAIVFEELAML--GAKVMIRAGTCGGL 100
                                    79**************.999***********************************666665555..6************* PP

                                    STTT-TT-EEEEEEEEESSSCCGCCTHHCCTCCCCTTSSEE--HHHHHHHHHCHHTTTTTEEEEEEEEESESS-CHHHHH CS
                      PNP_UDP_1  83 npdlkvGDvvipddainfdgrsplygpkeegqyfpdsydapadpelrallkeaaealgikvhrGvvatadgfyaeteael 162
                                     p  + G ++++++a +   ++ + +      + + +++  a pe + +l+ +++++g  ++rG+ ++ d f+    +++
  gi|119719044|ref|YP_919539.1| 101 TPIAESGKIALIEAAAYENSGTLYQY-----FGGVSMPA-YATPEVVLTLESVLREKGLSFVRGIALSHDAFHKVE-ENA 173
                                    **************877444444332.....23344444.59****************************999887.888 PP

                                    HHHHHTC-CEEESSHHHHHHHHHHTT--EEEEEEEEETTTBE CS
                      PNP_UDP_1 163 rllrrlgadaveMEtaavaqlArelgipfaairvvsdlaagg 204
                                    r++++lg+d +eME+a +++l r++g++++a+++v d++  g
  gi|119719044|ref|YP_919539.1| 174 RRWASLGVDFLEMESATLFALGRLRGVKVGAMALVVDNLLSG 215
                                    88*********************************9987763 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1579.70
//
Query:       gi|119719045|ref|YP_919540.1|  [L=220]
Description: hypothetical protein Tpen_0127 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-09   38.8   0.0    4.5e-09   36.7   0.0    1.8  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d


Domain annotation for each model (and alignments):
>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.0   2.5e-13   4.5e-09       3     149 ..       8     189 ..       7     208 .. 0.72

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 2.5e-13
                  Metallophos_2   3 laiiSDlH....snldaleavlealkevgvdaiihaGDl.eeeep.....evleellela...pvlaVrGNnD....eev 65 
                                     ++ SD+H    ++ +ale ++++++++g++ +++aGDl  + ++       +ee+ ++    ++ aV+          +
  gi|119719045|ref|YP_919540.1|   8 ALFASDTHcrrgRKCRALEILASIAEREGAECLFVAGDLfDNFHFkasrrLLIEEFSKIIdveRLPAVFAASLssssH-D 86 
                                    6889*******9999***********************6422222223331444444444444777777666665432.2 PP

                  Metallophos_2  66 ..veedvlreaaelgtdlp.eeaelelagekvlliHgdpl....................gvkdalaellke.aeegsdv 121
                                      +++ + +   + +  +   + e++++g+++ +iHgd l                         l+e+ ++    g++ 
  gi|119719045|ref|YP_919540.1|  87 plLDSPLEEIIDGKRLLFSnGAVEVQVGGRQFIVIHGDRLvgsgvlafllnfvaerlgrkL---YLEEAHRRvLGLGDEW 163
                                    345555555555555555558888889***********88********9999999995532...333333332347777* PP

                  Metallophos_2 122 vvcGHtHvpevekeggvlvvnPGsvgep 149
                                    +v+GHtH+p++++e   ++vn Gs +  
  gi|119719045|ref|YP_919540.1| 164 LVMGHTHIPGIDRE--KRLVNLGSWKTS 189
                                    *************9..699*****8876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       258  (0.0143901); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1398.08
//
Query:       gi|119719046|ref|YP_919541.1|  [L=499]
Description: hypothetical protein Tpen_0128 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-05   25.3   0.7    2.6e-05   23.9   0.7    1.7  1  Peptidase_M1     Peptidase family M1 domain
    0.00088   19.1   0.2     0.0014   18.5   0.2    1.3  1  BSP              Peptidase of plants and bacteria
     0.0083   16.4   0.1       0.02   15.2   0.1    1.6  1  DUF1570          Protein of unknown function (DUF1570)
     0.0092   15.1   0.0      0.015   14.4   0.0    1.4  1  ABC2_membrane_3  ABC-2 family transporter protein
     0.0096   16.3   1.0      0.034   14.5   1.0    1.9  1  Peptidase_M61    M61 glycyl aminopeptidase
  ------ inclusion threshold ------
        0.1   12.6   0.1       0.32   11.0   0.1    1.8  1  Mu-transpos_C    Mu transposase, C-terminal
       0.24   11.4   0.0       0.42   10.6   0.0    1.3  1  DUF45            Protein of unknown function DUF45


Domain annotation for each model (and alignments):
>> Peptidase_M1  Peptidase family M1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.7     1e-08   2.6e-05      68     218 .]     289     431 ..     282     431 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 1e-08
                                    HHHHHHHHHHHHBTTTEEESSGGGGHHHHHHHHHHHHHHHHHHSCCCH.CHHHHHHHCHHHHHHHHTSTTHHHSSGG-GS CS
                   Peptidase_M1  68 aeviaHElaHqWfGnlVtmkwWddlwLnEGfatyleylildklepewe.vseqllleeveealsedaldeshpitqevek 146
                                    +++++HEl+H   G     ++ +  w+ EG+a+y+++l+++kl  + + ++++l   + + a  ++ ++ +  +++    
  gi|119719046|ref|YP_919541.1| 289 ETTVIHELVHVYLGAAGVEANDNTRWFHEGMAQYVSILVAKKLGVNISeYESEL---NESAASYYNYTGGKIGFIE---- 361
                                    689*************9999**********************998666233333...2223333344444434432.... PP

                                    HHHHHHTSSHHHHHHHHHHHHHHHHHCTHHHHHHHHHHHHHHCTTEEE-HHHHHHHHHHCCCSCHHTHHHHH CS
                   Peptidase_M1 147 pseidevFdsiaYeKGasllrmlekllgeevFqkglksYlkefkyknaetedlwdaleealnkdisevmdtw 218
                                    +   d v + +aY  ++ +++ l++  g e+F k + + l+  +   ++t+++++ l++a+++++  ++++w
  gi|119719046|ref|YP_919541.1| 362 NWPSDAVKEGEAYLASYYVVHTLATKYGGENFVKRVFATLQGRH--ITTTREIVNVLSQAAGTNLAPLFREW 431
                                    223455667899999999************99887766665554..466789********99**99999999 PP

>> BSP  Peptidase of plants and bacteria
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.2   5.5e-07    0.0014     101     176 ..     291     370 ..     282     416 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 5.5e-07
                            BSP 101 vLthelvhvyqwea...egrapggliEGiAdyvRlkaglepahwkrpasg..adkwdqgyqvtayFLeyledrvsegfvr 175
                                     ++helvhvy   a   ++++  ++ EG+A yv +   ++  ++ ++ +   +++  + y++t+  + ++e+    ++v+
  gi|119719046|ref|YP_919541.1| 291 TVIHELVHVYLGAAgveANDNTRWFHEGMAQYVSILVAKKLGVNISEYESelNESAASYYNYTGGKIGFIEN-WPSDAVK 369
                                    579********9999999999************998777766666666655677888999999999999999.7778887 PP

                            BSP 176 k 176
                                    +
  gi|119719046|ref|YP_919541.1| 370 E 370
                                    6 PP

>> DUF1570  Protein of unknown function (DUF1570)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   7.9e-06      0.02       3      38 ..     290     323 ..     289     337 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 7.9e-06
                        DUF1570   3 atvaHEavHqlayniGvqsRladtpmWvsEGlaefF 38 
                                    +tv+HE vH  +   Gv    +d+ +W +EG+a++ 
  gi|119719046|ref|YP_919541.1| 290 TTVIHELVHVYLGAAGVEA--NDNTRWFHEGMAQYV 323
                                    59***************85..8899*********95 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0     6e-06     0.015     140     193 ..     442     495 ..     334     497 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 6e-06
                ABC2_membrane_3 140 stsaninvestql.eeelsnvasflvgliliilifitasfiavsiveEkesrike 193
                                    s++++ +++st++ ++++++  +fl+++i++++++++++++++++v E+e ri e
  gi|119719046|ref|YP_919541.1| 442 SNAKTPPSNSTSTpSSSSTGNSRFLIAMIALLAVIFIVTYVVNAVV-ERELRIAE 495
                                    455666666666647777999******************9998777.89999876 PP

>> Peptidase_M61  M61 glycyl aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   1.0   1.3e-05     0.034      32      87 ..     307     361 ..     289     381 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.3e-05
                                    ----STHHHHTHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHHSGGGGT--HH CS
                  Peptidase_M61  32 enytellwvaEGlTsYygdlllarsgliseeeyleelaktlarlentpgrkvqsla 87 
                                    e ++++ w+ EG+ +Y+  l++ + g+ + +ey +el++++a++ n +g k+  ++
  gi|119719046|ref|YP_919541.1| 307 EANDNTRWFHEGMAQYVSILVAKKLGV-NISEYESELNESAASYYNYTGGKIGFIE 361
                                    6778999****************9998.7899************999998776555 PP

>> Mu-transpos_C  Mu transposase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00013      0.32      16      49 ..     158     192 ..     144     197 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00013
                                    TS--EEEEEE-SHHH.HSS-SEEEEEE-GGGTTEE CS
                  Mu-transpos_C  16 GirlngnrYwspeLa.glvgkkVvvryDPrdlsrv 49 
                                    G++ n ++Y+   L  +++g +Vvv yD +  ++v
  gi|119719046|ref|YP_919541.1| 158 GVSGNYRVYVLSPLVeQYIGNRVVVEYDLQSSTPV 192
                                    8888999999988888************9976665 PP

>> DUF45  Protein of unknown function DUF45
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00016      0.42     149     177 ..     271     299 ..     268     301 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00016
                          DUF45 149 kgkirlnwrLvkappevidYVvvHElaHl 177
                                    kg ++ln+ L++  p  ++  v+HEl+H+
  gi|119719046|ref|YP_919541.1| 271 KGPVNLNLALIRYAPGYLETTVIHELVHV 299
                                    57799***********************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (499 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       771  (0.043003); expected 358.6 (0.02)
Passed bias filter:                      593  (0.0330749); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.63u 0.27s 00:00:00.90 Elapsed: 00:00:00.45
# Mc/sec: 3314.53
//
Query:       gi|119719047|ref|YP_919542.1|  [L=83]
Description: 4Fe-4S ferredoxin iron-sulfur binding domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.1e-22   77.4   0.8    1.2e-21   77.0   0.8    1.1  1  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
    2.6e-19   69.7   1.1      3e-19   69.5   1.1    1.1  1  Fer4_15   4Fe-4S single cluster domain
    0.00012   22.0   0.7    0.00012   22.0   0.7    2.3  2  Fer4_6    4Fe-4S binding domain
     0.0004   20.1   7.4    0.00061   19.5   0.7    2.5  3  Fer4      4Fe-4S binding domain
     0.0004   20.4   2.9     0.0052   16.9   3.5    2.0  2  Fer4_10   4Fe-4S dicluster domain
     0.0021   18.1   0.9     0.0036   17.4   0.1    1.7  2  Fer4_19   Divergent 4Fe-4S mono-cluster
  ------ inclusion threshold ------
      0.014   16.0   3.3      0.048   14.2   0.4    2.3  3  Fer4_7    4Fe-4S dicluster domain
       0.15   12.2   0.3       0.56   10.3   0.3    1.8  2  ComFB     Late competence development protein ComFB
        2.4    8.4   5.7       0.72   10.1   1.0    2.3  2  Fer4_2    4Fe-4S binding domain
        7.1    7.8   7.0        5.2    8.2   1.0    2.6  2  Fer4_3    4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.0   0.8   6.5e-25   1.2e-21       1      58 []      12      79 ..      12      79 .. 0.87

  Alignments for each domain:
  == domain 1  score: 77.0 bits;  conditional E-value: 6.5e-25
                        Fer4_13  1 VDrdtCiacgaCvelaPdvFeeddeggasvvaeqpts..........eeekadaeeAadaCPvesIgv 58
                                   +Drd+Ci+++aCv+l+P+vFe+++e+g+s ++++ +            e+++++++Aa+aCPv++I+v
  gi|119719047|ref|YP_919542.1| 12 IDRDQCISDMACVSLCPEVFEMNEEDGKSSIVAKYRVgnnlgeglvpGELEDCVKSAAEACPVSIIHV 79
                                   8***************************9999853322556666776899*****************7 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.5   1.1   1.7e-22     3e-19       1      66 []      10      79 ..      10      79 .. 0.93

  Alignments for each domain:
  == domain 1  score: 69.5 bits;  conditional E-value: 1.7e-22
                        Fer4_15  1 VvvDrdaCigcglCvaeapevfelde.dglasvl....lddgeiaegevpddeeeaaqeAaraCPvdAIrv 66
                                   V++Drd+Ci++ +Cv ++pevfe++e dg++s++    + + +++eg vp ++e++++ Aa+aCPv  I+v
  gi|119719047|ref|YP_919542.1| 10 VTIDRDQCISDMACVSLCPEVFEMNEeDGKSSIVakyrV-GNNLGEGLVPGELEDCVKSAAEACPVSIIHV 79
                                   89**********************9989****9988853.5678999**********************98 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.7   6.7e-08   0.00012       1      21 [.       9      29 ..       9      34 .. 0.94
   2 ?    1.2   1.1      0.25   4.4e+02      17      24 .]      70      77 ..      62      77 .. 0.67

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 6.7e-08
                         Fer4_6  1 vveidpdkCigCgdCvrvCPe 21
                                   +v+id+d Ci+ ++Cv+ CPe
  gi|119719047|ref|YP_919542.1|  9 KVTIDRDQCISDMACVSLCPE 29
                                   79******************7 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.25
                         Fer4_6 17 rvCPegai 24
                                    +CP  +i
  gi|119719047|ref|YP_919542.1| 70 EACPVSII 77
                                   57998876 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.7   3.4e-07   0.00061       1      19 [.      10      28 ..      10      30 .. 0.94
   2 ?   -2.9   0.1       4.1   7.4e+03       6       9 ..      62      65 ..      61      66 .. 0.64
   3 ?    4.7   0.1     0.016        28      15      23 ..      69      77 ..      69      78 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 3.4e-07
                                   EEEETTTSSS-THHHHHST CS
                           Fer4  1 vvideekCigCGaCvevCP 19
                                   v+id + Ci  +aCv+ CP
  gi|119719047|ref|YP_919542.1| 10 VTIDRDQCISDMACVSLCP 28
                                   68***************** PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.1
                                   TTSS CS
                           Fer4  6 ekCi 9 
                                   e+C+
  gi|119719047|ref|YP_919542.1| 62 EDCV 65
                                   5676 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.016
                                   HHHSTTTEE CS
                           Fer4 15 vevCPvgAI 23
                                   +e+CPv  I
  gi|119719047|ref|YP_919542.1| 69 AEACPVSII 77
                                   69****887 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   3.5   2.9e-06    0.0052       1      36 [.       9      51 ..       9      73 .. 0.59
   2 ?    2.7   0.2     0.077   1.4e+02      14      23 ..      63      76 ..      57      83 .] 0.69

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.9e-06
                        Fer4_10  1 kvvidddtCirCgkCvkaCPadl.......tsvgakgeaseee 36
                                   kv id+d+Ci   +Cv+ CP  +       +s+ + +++ +++
  gi|119719047|ref|YP_919542.1|  9 KVTIDRDQCISDMACVSLCPEVFemneedgKSSIVAKYRVGNN 51
                                   589******************7777666663333333333333 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.077
                        Fer4_10 14 kCvk....aCPadl 23
                                   +Cvk    aCP+++
  gi|119719047|ref|YP_919542.1| 63 DCVKsaaeACPVSI 76
                                   56666666899865 PP

>> Fer4_19  Divergent 4Fe-4S mono-cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1     2e-06    0.0036       5      34 ..       7      36 ..       4      46 .. 0.92
   2 ?   -1.2   0.1       1.2   2.2e+03      47      55 ..      65      73 ..      59      75 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2e-06
                        Fer4_19  5 eitiednrelCihsgnCvkglpevFdpkrk 34
                                   +++++ +r+ Ci+   Cv   pevF+++++
  gi|119719047|ref|YP_919542.1|  7 KLKVTIDRDQCISDMACVSLCPEVFEMNEE 36
                                   789***********************9986 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.2
                        Fer4_19 47 iievverCP 55
                                   +++++e CP
  gi|119719047|ref|YP_919542.1| 65 VKSAAEACP 73
                                   456677887 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.4   2.7e-05     0.048      30      49 ..       9      28 ..       2      31 .. 0.88
   2 ?    8.6   4.7    0.0016       2.8       2      50 ..      17      74 ..      16      76 .. 0.60
   3 ?    1.8   0.2      0.21   3.7e+02      10      18 ..      70      78 ..      62      83 .] 0.62

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.7e-05
                         Fer4_7 30 kveidpekClgCgaCvavCP 49
                                   kv+id ++C++  aCv+ CP
  gi|119719047|ref|YP_919542.1|  9 KVTIDRDQCISDMACVSLCP 28
                                   789***************** PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0016
                         Fer4_7  2 CigCgaCvaaCpvkaieldeeenek............gtekveidpekClgCgaCvavCPt 50
                                   Ci   aCv+ Cp +++e++ee+ ++            g   v ++ e+C+   + +++CP+
  gi|119719047|ref|YP_919542.1| 17 CISDMACVSLCP-EVFEMNEEDGKSsivakyrvgnnlGEGLVPGELEDCVK--SAAEACPV 74
                                   88889*******.89999998666644444433333322334555566654..35567776 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.21
                         Fer4_7 10 aaCpvkaie 18
                                   +aCpv+ i 
  gi|119719047|ref|YP_919542.1| 70 EACPVSIIH 78
                                   566666655 PP

>> ComFB  Late competence development protein ComFB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.3   0.00031      0.56      15      38 ..       4      27 ..       1      28 [. 0.81
   2 ?   -0.5   0.0      0.75   1.3e+03       2      23 ..      51      72 ..      50      79 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00031
                                   TGGGTT-S--SHHHHHHHHHHHHT CS
                          ComFB 15 qleelekvckceeclaDvaalaLN 38
                                    +++l+ +++ ++c+ D+a++ L+
  gi|119719047|ref|YP_919542.1|  4 SMAKLKVTIDRDQCISDMACVSLC 27
                                   56676677899**********996 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.75
                                   EHHHHHHHHHHHCTGGGTT-S- CS
                          ComFB  2 NvmEelVleeleeqleelekvc 23
                                   N+ E lV  ele+ +++ ++ c
  gi|119719047|ref|YP_919542.1| 51 NLGEGLVPGELEDCVKSAAEAC 72
                                   7778888888888887765555 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   1.0    0.0004      0.72       2      22 .]       9      29 ..       8      29 .. 0.86
   2 ?    0.2   0.3      0.56     1e+03      18      21 ..      70      73 ..      62      74 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0004
                         Fer4_2  2 pvvvdtdrCigCgaCvsaCPa 22
                                   +v +d+d Ci+  aCvs CP+
  gi|119719047|ref|YP_919542.1|  9 KVTIDRDQCISDMACVSLCPE 29
                                   578999*999868*******5 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.56
                         Fer4_2 18 saCP 21
                                    aCP
  gi|119719047|ref|YP_919542.1| 70 EACP 73
                                   6799 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   1.0    0.0029       5.2       4      12 ..      17      28 ..      15      30 .. 0.73
   2 ?    2.3   0.6      0.23   4.1e+02       9      13 ..      70      74 ..      62      76 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0029
                         Fer4_3  4 C...gaCvevCP 12
                                   C   +aCv  CP
  gi|119719047|ref|YP_919542.1| 17 CisdMACVSLCP 28
                                   54326******* PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.23
                         Fer4_3  9 evCPv 13
                                   e+CPv
  gi|119719047|ref|YP_919542.1| 70 EACPV 74
                                   79997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      187  (0.01043); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 606.96
//
Query:       gi|119719048|ref|YP_919543.1|  [L=1062]
Description: isoleucyl-tRNA synthetase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   3.5e-183  610.1   0.0   4.5e-183  609.8   0.0    1.1  1  tRNA-synt_1      tRNA synthetases class I (I, L, M and V)
    2.2e-32  112.1   0.0    4.2e-32  111.2   0.0    1.4  1  Anticodon_1      Anticodon-binding domain of tRNA
    3.6e-18   65.5   0.0    6.4e-07   28.5   0.0    3.9  3  tRNA-synt_1g     tRNA synthetases class I (M)
    0.00045   19.3   0.0     0.0038   16.2   0.0    2.3  3  tRNA-synt_1f     tRNA synthetases class I (K)
  ------ inclusion threshold ------
      0.041   13.2   0.8        9.9    5.6   0.0    3.1  3  zf-TFIIB         Transcription factor zinc-finger
      0.055   13.0   0.0       0.12   11.8   0.0    1.5  1  tRNA-synt_1_2    Leucyl-tRNA synthetase, Domain 2
      0.072   12.4   0.0       0.18   11.1   0.0    1.7  1  tRNA-synt_1e     tRNA synthetases class I (C) catalytic domai
      0.073   13.6   2.1         65    4.1   0.1    3.8  3  Zn_ribbon_recom  Recombinase zinc beta ribbon domain
       0.79   10.2   3.3        5.1    7.6   0.2    3.6  3  zf-IS66          zinc-finger binding domain of transposase IS
        1.4    8.8   4.9          2    8.3   0.3    3.0  3  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger
        5.2    7.3   7.5        7.5    6.8   3.3    3.1  2  Zn-ribbon_8      Zinc ribbon domain


Domain annotation for each model (and alignments):
>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  609.8   0.0  2.8e-186  4.5e-183       2     602 .]      20     643 ..      19     643 .. 0.96

  Alignments for each domain:
  == domain 1  score: 609.8 bits;  conditional E-value: 2.8e-186
                    tRNA-synt_1   2 lyekWeeedvfkkelekeke.kkefilvdgPPyvtGs.lHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaieak 79 
                                    ++++W+ ++v++k +e+ k+ k+++ + dgPPy   s +H+G  ++k+lkd +ir++r +G++v+ +pG+D++Gl+ie +
  gi|119719048|ref|YP_919543.1|  20 VLKFWDSAKVYDKVRESLKNsKRKYYFLDGPPYPSSSiPHVGTLWNKILKDAIIRFHRASGYSVHDQPGYDCHGLPIEVQ 99 
                                    789*************9999899**********877626***************************************** PP

                    tRNA-synt_1  80 vekklgakekkerkklgreefrekvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkgliyrg 159
                                    +e+klg k kk+ +++g+e+f+e++++++ + +e  ++++k++Gvs+D+d++ylT+ +e+ e+ ++  ++  +kgl+  g
  gi|119719048|ref|YP_919543.1| 100 IERKLGFKSKKDIEEFGVEKFVEECKSFALQNVEGLSRSFKDFGVSMDWDKPYLTMTDEYIESAWWLVKKAEEKGLLDYG 179
                                    ******************************************************************************** PP

                    tRNA-synt_1 160 kklvnwstklktalselEv.eykdkkdalihvafpladkeevklviaTTtPeTllgdtavavnpeldyv...itkeklil 235
                                     k+v+w+++++t+l++ Ev ey+d +d++i+v+fpl+d+ + +l i+TTtP+Tl++++av vnp+l+y+   + +e++++
  gi|119719048|ref|YP_919543.1| 180 LKVVHWCPRCETTLADYEVtEYRDLEDPSIYVKFPLKDNPKKHLLIWTTTPWTLPANVAVMVNPDLEYSwvdVGGEEVLV 259
                                    ********************************************************************999999****** PP

                    tRNA-synt_1 236 aeallkslvkke..sekkiledergkeLegkevelpl..........vnrkipiiaddyvdkeaGtGvVkiaPahdedDy 303
                                    a  ++++++k+   ++++++ ++ g+eLeg+++ +pl          ++ + ++++ +yv + +GtG+V++a +h+e+Dy
  gi|119719048|ref|YP_919543.1| 260 ATERVEAVMKEAgiESYRVTGKVMGRELEGLRYVHPLeeevdvqrklKDAHRVVLSKEYVSAAEGTGLVHMATGHGEEDY 339
                                    *********99986667*************************999988889999999*********************** PP

                    tRNA-synt_1 304 evgkkynlevinildedgtlteeaaefeglkvfdarkkvveelkekglllkaekiehsvpfcerskkpiiyrateqWfvr 383
                                    +vg +y+l+v + +d++g ++ ea++++g++  da+k +v++l+ kg l+++ +i+h +p+c+r k+p++ rat qW++r
  gi|119719048|ref|YP_919543.1| 340 KVGVQYGLPVFSLVDDKGFMEREAGKYAGIYHRDANKLIVDDLRSKGFLFHEGRIKHRYPVCWRCKTPLVLRATRQWYIR 419
                                    ******************************************************************************** PP

                    tRNA-synt_1 384 vkeladaalkavekvqfvpks.kekryaswleniqdWciSRqrwWGhriplfvsketeevvvreelkelvagreeeeaek 462
                                    v++l++  l++  +v +vpk+ + +r+ +wle  +dW iSRqr+WG++ p++v  + +  vv+ +++el++    ++ e 
  gi|119719048|ref|YP_919543.1| 420 VTQLKERFLEEAGNVDWVPKWaGYSRFRNWLEGLRDWIISRQRYWGTPAPIWVCGSCGHRVVVGSKDELER-FAGRKLEL 498
                                    *********************999********************************999999888777766.55566677 PP

                    tRNA-synt_1 463 kalekeakdkl....kkekgelekdedvlDvWFsSgswpfstlgypeedteelkkffpadmlleGlDiirgWvarlills 538
                                    ++l++  +d++     k  ge+++++dvlDvW +Sg  ++++lgyp++ +e++++  p d+++eG D+i gW+ +l+ ++
  gi|119719048|ref|YP_919543.1| 499 RDLHRPWVDQVvlkcPKCGGEMRRVPDVLDVWLDSGVAFYASLGYPKN-EEKFRELMPVDLIIEGHDQIAGWFFSLLRCG 577
                                    77788888877774455569***************************9.99***************************** PP

                    tRNA-synt_1 539 laltgsePfkevlvhglvrdeeGrKmSKslgNvidpldvik.kyga.dalRltlilsdvgrdinls 602
                                    l  ++++P+ +vl+hg+ +de+Gr m KslgN+++p +v++ +yg  d+ R+++++++v +d+++s
  gi|119719048|ref|YP_919543.1| 578 LIAFDRSPYLRVLMHGFALDEQGREMHKSLGNYVEPRQVLEyEYGSrDVFRWFVLKNTVWEDLRFS 643
                                    ****************************************8667644***********99999875 PP

>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.2   0.0   2.6e-35   4.2e-32       1     149 [.     691     840 ..     691     844 .. 0.90

  Alignments for each domain:
  == domain 1  score: 111.2 bits;  conditional E-value: 2.6e-35
                    Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkra.aqevllevletllrllaP 79 
                                    drwils+l kl+++vt +++e++ +kaa+++ +f+++dl+ wy++lv+pr + e++ ++++ a+ +l++vl +ll l +P
  gi|119719048|ref|YP_919543.1| 691 DRWILSRLGKLASTVTSSFKELNVHKAARDIRNFVVEDLSHWYVRLVRPRVWLEEDVEEKKlAYVTLYHVLLNLLVLASP 770
                                    9***************************************************9998888888****************** PP

                    Anticodon_1  80 fmPfitEelwqr...eeeelgkkesimlaewpe.kaeelekeleeeevellkeivkairklrselkikpsselk 149
                                    ++Pf+tE+++++    e   g +esi++ +wp+  + + +++  e+e+++++eiv+++ +lr ++++k +++l 
  gi|119719048|ref|YP_919543.1| 771 ILPFTTEKIYRDafyGE---GLPESIHMYSWPSgLERFIDEKV-ESEMSVAREIVEVALSLRMRKGVKIRQPLP 840
                                    **********6554322...446*********86665557666.89**********************999864 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.0   3.9e-10   6.4e-07       9     135 ..      52     198 ..      48     201 .. 0.75
   2 !   15.9   0.0   2.6e-06    0.0042     167     238 ..     399     469 ..     393     482 .. 0.80
   3 !   16.0   0.0   2.4e-06     0.004     244     374 ..     526     650 ..     512     659 .. 0.80

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 3.9e-10
                                    --S.S---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHH..........TTS-HHHHHHHHH...... CS
                   tRNA-synt_1g   9 Yan.gklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAek..........egvtpeelvekvh...... 71 
                                    Y++ + +H+G l + i  D+++R++r++g+ v+   g D hG pie++ e+          e+  +e++ve+ +      
  gi|119719048|ref|YP_919543.1|  52 YPSsSIPHVGTLWNKILKDAIIRFHRASGYSVHDQPGYDCHGLPIEVQIERklgfkskkdiEEFGVEKFVEECKsfalqn 131
                                    6541579***************************************9876411111111223445666666655111111 PP

                                    .HHHHHHHHHTT---..SEEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG- CS
                   tRNA-synt_1g  72 .eeikelfkklnisf..dkygrttseehkelvqeifkklkekgliyekeieqlycpkderflpdryv 135
                                     e  ++ fk++++s   dk + t ++e  e +  ++kk +ekgl+  +   + +cp++e++l+d +v
  gi|119719048|ref|YP_919543.1| 132 vEGLSRSFKDFGVSMdwDKPYLTMTDEYIESAWWLVKKAEEKGLLDYGLKVVHWCPRCETTLADYEV 198
                                    1456678888888751156778999999999999******************************887 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 2.6e-06
                                    ..........EEE.EEEEEE-GGGGHHHHHHHH.HH-TT..SHHHHHHHH.HHHHT----EE-ESS-SSS-EET CS
                   tRNA-synt_1g 167 pksaisgskpevketehlffklskfekklkewieeeeke..leenvkkivkewlkegLkdlaisrdldwGipvP 238
                                    p++  +++  +++ t++++ ++ +++++  e     + +   +    +  ++wl+  L+d+ isr+  wG p P
  gi|119719048|ref|YP_919543.1| 399 PVCWRCKTPLVLRATRQWYIRVTQLKERFLEEA--GNVDwvPKWAGYSRFRNWLEG-LRDWIISRQRYWGTPAP 469
                                    89999*9999***************99877655..3334224444567789***76.***************99 PP

  == domain 3  score: 16.0 bits;  conditional E-value: 2.4e-06
                                    EE-HHHHHHHHHHHTTTTT-...TTSGGGG.G--S......EEEEEGGGHH.HHHTHHHHHHHHTT----S-EEEE--.E CS
                   tRNA-synt_1g 244 vlYVWldAligYisatkelakkkgeeekwkeyWakdkevelvhfigkdiik.FHtifwPaillgaelklpkkvvahey.l 321
                                    vl VWld  + + +++++      +eek++e        +   + g d i  +   ++ + l++ + +   +v  h++ l
  gi|119719048|ref|YP_919543.1| 526 VLDVWLDSGVAFYASLGYPK----NEEKFRELMPV----D-LIIEGHDQIAgWFFSLLRCGLIAFDRSPYLRVLMHGFaL 596
                                    67799999999999999986....78899999832....2.234477766434555567778888888889999999945 PP

                                    EE--------------HHHHHHH.H-.HHHHHHHHHHHS-TTS-EEE-HHHHHHH CS
                   tRNA-synt_1g 322 tvegkKlSkSrgvvvkakealer.ld.adllRYylaaeapekkDldfswedfver 374
                                      +g+ + kS g+ v ++++le+ +   d++R+++++++   +Dl fsw+ + e+
  gi|119719048|ref|YP_919543.1| 597 DEQGREMHKSLGNYVEPRQVLEYeYGsRDVFRWFVLKNTV-WEDLRFSWRGLEET 650
                                    67899****************9985438******998765.68******988766 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.28   4.6e+02      10      58 ..      32      79 ..      22      84 .. 0.65
   2 ?   -3.5   0.0       2.3   3.8e+03     103     128 ..     123     148 ..     121     155 .. 0.90
   3 !   16.2   0.0   2.3e-06    0.0038     270     338 ..     591     660 ..     582     670 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.28
                   tRNA-synt_1f 10 klieerkkkkaekdevvvesG..ispSGliHiGnlrevltadlvaralrkr 58
                                   k+  e+ k+  +k ++ +  G  +  S  +H+G+l + +  d++ r  r+ 
  gi|119719048|ref|YP_919543.1| 32 KVR-ESLKN--SKRKYYFLDGppYPSSSIPHVGTLWNKILKDAIIRFHRAS 79
                                   232.44333..566666666655778999******9999999888876665 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.3
                   tRNA-synt_1f 103 khesyaehfnaelvesLdelgievef 128
                                    +++s+a ++ + l +s +++g+ +++
  gi|119719048|ref|YP_919543.1| 123 ECKSFALQNVEGLSRSFKDFGVSMDW 148
                                    689*******************9997 PP

  == domain 3  score: 16.2 bits;  conditional E-value: 2.3e-06
                   tRNA-synt_1f 270 vYelillkggekmssSkGnvltledwle..vaepevlrflilrrkPkkakkldldleilrlvdeYdklerk 338
                                    +  + l+++g++m++S Gn++ ++++le  +++++v r+++l++   + ++++ + ++ +++ + + l + 
  gi|119719048|ref|YP_919543.1| 591 MHGFALDEQGREMHKSLGNYVEPRQVLEyeYGSRDVFRWFVLKNTVWEDLRFSWR-GLEETYSDLNILWNV 660
                                    56678899999***************9622689************9999999999.999999987766555 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.013        21       2      15 ..     186     199 ..     185     204 .. 0.87
   2 ?   -2.6   0.1       2.2   3.6e+03      18      26 ..     469     477 ..     468     477 .. 0.88
   3 ?    5.6   0.0    0.0061       9.9       1      10 [.     512     521 ..     512     535 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.013
                       zf-TFIIB   2 CPkCqdeleeserg 15 
                                    CP+C ++l ++e+ 
  gi|119719048|ref|YP_919543.1| 186 CPRCETTLADYEVT 199
                                    ********999875 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.2
                       zf-TFIIB  18 eidyCpqCr 26 
                                    +i++C +C+
  gi|119719048|ref|YP_919543.1| 469 PIWVCGSCG 477
                                    699*****7 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.0061
                       zf-TFIIB   1 kCPkCqdele 10 
                                    kCPkC+ e++
  gi|119719048|ref|YP_919543.1| 512 KCPKCGGEMR 521
                                    7999999997 PP

>> tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   7.6e-05      0.12      11     144 ..     210     357 ..     206     381 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.6e-05
                  tRNA-synt_1_2  11 eiefkvees.eeklevfttrpdtlfGvtfvalapehplvekl..aekkkelaafieevkkksesereletkekeGv.ftg 86 
                                     ++f+++++ +++l ++tt p tl     v++ p+ +        e+    ++ +e v k+  +e+   t +  G   +g
  gi|119719048|ref|YP_919543.1| 210 YVKFPLKDNpKKHLLIWTTTPWTLPANVAVMVNPDLEYSWVDvgGEEVLVATERVEAVMKEAGIESYRVTGKVMGReLEG 289
                                    68999999988899999999999999888888887665433333455555567788889999999999999999997899 PP

                  tRNA-synt_1_2  87 lkaihPitgek..........ipiwvanyvlmeygtgavmavPahdqrDfeFakkynlpikqvikped 144
                                    l  +hP+++e             +   +yv +  gtg v    +h ++D++   +y+lp+   +  ++
  gi|119719048|ref|YP_919543.1| 290 LRYVHPLEEEVdvqrklkdahRVVLSKEYVSAAEGTGLVHMATGHGEEDYKVGVQYGLPVFSLVDDKG 357
                                    *******988778888888765678889********************************99998665 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00011      0.18     232     298 ..     580     649 ..     575     652 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00011
                                    HSS.S--EEEEEEE--EEETTBE--TTTT---BHHHHHTT.S.-HHHHHHHHHSS-TTS-EEE-HHHHHH CS
                   tRNA-synt_1e 232 afd.kqlvkyflhnghlkiegekmsksLknfitikdvlkk.f.dprqlRllllsahyrsqldfkeellee 298
                                    afd +++ +  +h   l  +g+ m ksL+n++  ++vl+  + +  ++R+++l++   + l f+   lee
  gi|119719048|ref|YP_919543.1| 580 AFDrSPYLRVLMHGFALDEQGREMHKSLGNYVEPRQVLEYeYgSRDVFRWFVLKNTVWEDLRFSWRGLEE 649
                                    5666789999****************************8525244578****999999999998777766 PP

>> Zn_ribbon_recom  Recombinase zinc beta ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.092   1.5e+02      22      56 ..     396     430 ..     385     431 .. 0.79
   2 ?    3.3   0.0     0.074   1.2e+02       7      17 ..     472     482 ..     470     497 .. 0.83
   3 ?    4.1   0.1      0.04        65       6      17 ..     511     522 ..     509     526 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.092
                Zn_ribbon_recom  22 gkr.hyYrCstyrrkgkkCsnhsireekleeavlee 56 
                                    +++  ++rC+t    +    +++ir+ +l+e +lee
  gi|119719048|ref|YP_919543.1| 396 HRYpVCWRCKTPLVLR-ATRQWYIRVTQLKERFLEE 430
                                    455689****997777.7777899999999999875 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.074
                Zn_ribbon_recom   7 rCgeCGspmtr 17 
                                    +Cg CG++ ++
  gi|119719048|ref|YP_919543.1| 472 VCGSCGHRVVV 482
                                    8******9876 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.04
                Zn_ribbon_recom   6 lrCgeCGspmtr 17 
                                    l+C +CG+ m+r
  gi|119719048|ref|YP_919543.1| 511 LKCPKCGGEMRR 522
                                    89********98 PP

>> zf-IS66  zinc-finger binding domain of transposase IS66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.63     1e+03       4      10 ..     186     192 ..     183     212 .. 0.56
   2 ?   -1.0   0.0       1.5   2.4e+03       3      15 ..     472     483 ..     470     491 .. 0.72
   3 ?    7.6   0.2    0.0031       5.1       3      16 ..     512     525 ..     511     528 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.63
                        zf-IS66   4 CpcCGgl 10 
                                    Cp C ++
  gi|119719048|ref|YP_919543.1| 186 CPRCETT 192
                                    7777764 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.5
                        zf-IS66   3 tCpcCGgllkpig 15 
                                    +C  CG+  + +g
  gi|119719048|ref|YP_919543.1| 472 VCGSCGHR-VVVG 483
                                    59999986.4555 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0031
                        zf-IS66   3 tCpcCGgllkpige 16 
                                    +Cp+CGg+++++++
  gi|119719048|ref|YP_919543.1| 512 KCPKCGGEMRRVPD 525
                                    6********99976 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       2.5   4.1e+03       4      10 ..     186     192 ..     184     194 .. 0.73
   2 ?    0.9   0.0      0.25   4.1e+02       4      18 ..     401     415 ..     399     417 .. 0.89
   3 ?    8.3   0.3    0.0012         2       3      12 ..     512     521 ..     510     523 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.5
                                    -SSS--E CS
                 zf-C4_Topoisom   4 CPkCggd 10 
                                    CP C   
  gi|119719048|ref|YP_919543.1| 186 CPRCETT 192
                                    9999755 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.25
                                    -SSS--EEEEEE-SS CS
                 zf-C4_Topoisom   4 CPkCggdLvlkrgkk 18 
                                    C  C+ +Lvl+ +++
  gi|119719048|ref|YP_919543.1| 401 CWRCKTPLVLRATRQ 415
                                    778********9996 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0012
                                    E-SSS--EEE CS
                 zf-C4_Topoisom   3 kCPkCggdLv 12 
                                    kCPkCgg++ 
  gi|119719048|ref|YP_919543.1| 512 KCPKCGGEMR 521
                                    9*******96 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1      0.98   1.6e+03      28      35 ..     184     192 ..     181     194 .. 0.74
   2 ?    6.8   3.3    0.0046       7.5      26      39 ..     510     523 ..     470     524 .. 0.67

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.98
                    Zn-ribbon_8  28 a.CPeCgse 35 
                                    + CP+C  +
  gi|119719048|ref|YP_919543.1| 184 HwCPRCETT 192
                                    55****865 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0046
                    Zn-ribbon_8  26 ltaCPeCgsevrrv 39 
                                      +CP+Cg+e+rrv
  gi|119719048|ref|YP_919543.1| 510 VLKCPKCGGEMRRV 523
                                    456**********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1062 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      660  (0.0368119); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.83u 0.30s 00:00:01.12 Elapsed: 00:00:00.51
# Mc/sec: 6215.11
//
Query:       gi|119719049|ref|YP_919544.1|  [L=240]
Description: hypothetical protein Tpen_0131 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-48  166.1   0.3    1.6e-48  165.7   0.3    1.0  1  DUF72     Protein of unknown function DUF72
  ------ inclusion threshold ------
       0.16   11.7   0.0       0.28   10.9   0.0    1.4  1  HeH       HeH/LEM domain


Domain annotation for each model (and alignments):
>> DUF72  Protein of unknown function DUF72
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.7   0.3   1.8e-52   1.6e-48       9     204 ..      17     216 ..      14     226 .. 0.90

  Alignments for each domain:
  == domain 1  score: 165.7 bits;  conditional E-value: 1.8e-52
                                    CHHHHHCCT..-SEEEE-HHCCSSS-HHHHHHHHCTS-TT-EEEEE--CCCCCS...G-SCHHHHHHHHHH.CHHHCT-E CS
                          DUF72   9 erLeyYarh..fntVEinstFYalpspetvakwaaqtpedFrFavKapraither..nedaeealerflesalepLgekl 84 
                                    + L+ Ya++  fn+VE+n +FY++p+++tv+kwa++  e+ r+++K++r+ith r  ne++++ +++f e ++ep+++++
  gi|119719049|ref|YP_919544.1|  17 DGLAWYASQsgFNAVELNMSFYSFPKRTTVEKWAEES-EGLRWSIKVHRSITHVRrlNEKSHATWSKFRE-LFEPIEDRI 94 
                                    689*********************************9.8**************864432699********.6******** PP

                                    EEEEEE--TT--S.HHHHHHHHHHTTTS-SEEEE--BGGGH..HHHHHHHHTT-EEEE.E--SSC----.----SSTEEE CS
                          DUF72  85 gpllfQlppsfkfdeenlerLeaflaalpllavEvRhrswf..ellellrehgvavvl.depkkpklpl.edvttadfvy 160
                                      +lfQlpps++f++e  +r++a+ +  + +avE Rh+swf  e++e+++e+gv +v+ d p  + lp+   v  + +vy
  gi|119719049|ref|YP_919544.1|  95 DFYLFQLPPSMAFTPEAASRVAAYASLAEKIAVEPRHKSWFrkEVYEFFEEKGVFFVTpDSPLFEGLPPdGVVCIRGVVY 174
                                    **************99********775534***********955*********99999898855555553777778**** PP

                                    EEE--SHHTTB----HHHHHHHHHHHHHHHTCSSEEEEEE-SBC CS
                          DUF72 161 vRlhgreeryayrYseeelaewaerikawaaegrevyvffnnda 204
                                    vR+hgr ++y+y+Y +eel+e+ae+i +++   +++yvffnnd+
  gi|119719049|ref|YP_919544.1| 175 VRMHGRLAWYNYGYLDEELREVAEKIISANP--QRAYVFFNNDH 216
                                    *****989******************99887..79*******87 PP

>> HeH  HeH/LEM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   3.1e-05      0.28       8      21 ..     224     237 ..     223     239 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 3.1e-05
                            HeH   8 qLRriLvehgveyP 21 
                                    +L++iL e gv++P
  gi|119719049|ref|YP_919544.1| 224 RLKEILLERGVSFP 237
                                    7************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.33s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1555.45
//
Query:       gi|119719050|ref|YP_919545.1|  [L=577]
Description: membrane protein-like [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.1e-24   84.1   6.6    1.8e-08   34.5   0.1    4.6  4  NPCBM_assoc      NPCBM-associated, NEW3 domain of alpha-galac
    1.4e-10   41.2  10.4    3.9e-10   39.9   0.2    4.8  5  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
    3.2e-09   37.0   0.1       0.21   11.8   0.0    5.4  7  FixG_C           IG-like fold at C-terminal of FixG, putative
     0.0006   20.5   0.4          2    9.1   0.0    4.1  4  fn3_5            Fn3-like domain
     0.0015   18.9   0.0        6.5    7.3   0.0    4.0  4  MG2              MG2 domain
     0.0039   17.0   1.6       0.07   13.0   0.1    3.5  4  PEGA             PEGA domain
  ------ inclusion threshold ------
      0.026   14.8  16.7       0.64   10.4   2.4    4.4  4  DUF11            Domain of unknown function DUF11
      0.047   13.9   3.3       0.92    9.8   0.1    3.8  4  ASH              Abnormal spindle-like microcephaly-assoc'd, 
       0.05   13.9   1.1         12    6.3   0.1    3.6  4  Alpha_adaptinC2  Adaptin C-terminal domain
      0.086   12.6   1.1        1.4    8.7   0.2    3.1  3  fn3_3            Polysaccharide lyase family 4, domain II
       0.11   12.4   0.0       0.26   11.2   0.0    1.6  1  Coatamer_beta_C  Coatomer beta C-terminal region
       0.13   12.4   5.2       0.37   11.0   0.0    3.9  4  fn3_6            Fibronectin type-III domain
       0.14   12.5   0.2        1.6    9.1   0.0    2.9  3  CzcE             Heavy-metal resistance protein CzcE
       0.17   12.3   0.0         15    5.9   0.0    2.9  2  Transglut_N      Transglutaminase family
       0.29   11.4   1.9         20    5.5   0.1    3.6  3  CARDB            CARDB


Domain annotation for each model (and alignments):
>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.0   3.9e-09   4.6e-06       2      74 ..     125     199 ..     124     203 .. 0.90
   2 !   11.8   0.1   0.00018      0.22      24      77 ..     255     312 ..     250     314 .. 0.84
   3 !   11.6   0.1   0.00022      0.26       1      77 [.     344     423 ..     344     425 .. 0.82
   4 !   34.5   0.1   1.5e-11   1.8e-08       3      73 ..     456     525 ..     455     530 .. 0.90

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 3.9e-09
                    NPCBM_assoc   2 epGetvtltltvtndgtaaatnvslslslPeGWtvvevspasaa....slapGetveatvkVtppagaaaGdyevta 74 
                                    ++G+tv++ + v+n++ +++  vs+s+++P+GW++  v p+++      +++G   +  + V +p +a   +  v++
  gi|119719050|ref|YP_919545.1| 125 SQGDTVRIPVKVFNKCLDPVL-VSFSIEVPQGWRAYFVGPNNLVasdfYIEAGSNRSLVFVVEVPLNASE-KESVRV 199
                                    79*****************98.********************9988888*****************9986.345555 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00018
                    NPCBM_assoc  24 vslslslPeGWtvvevspasaa....slapGetveatvkVtppagaaaGdyevtakar 77 
                                    v ls+ +P++  ++ v+ + ++    +++pGe+ + ++ + +p++a  ++y ++++ar
  gi|119719050|ref|YP_919545.1| 255 VTLSVFAPSNFIASLVDENGLTvqsvTVRPGEKRRLQLVIYVPPTARISTYSLRVVAR 312
                                    677777777777777777666666779*****************************98 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.00022
                    NPCBM_assoc   1 vepGetvtltltvtndgtaaatn.vslslslPeGWtvvevspasaa..slapGetveatvkVtppagaaaGdyevtakar 77 
                                    v+ G+tvt++++++n+g+ ++ + ++++ s P     ++vs++ +a   l pGe+    + V + +++  G y v ++a+
  gi|119719050|ref|YP_919545.1| 344 VTSGSTVTFRVALKNEGNMPTVAlLRVQTSSPLLRAYTSVSGEPVAslYLVPGEEKALALIVEVDPSTPSGIYLVSLRAN 423
                                    589**************7665442577777776555557777777766899************************99996 PP

  == domain 4  score: 34.5 bits;  conditional E-value: 1.5e-11
                    NPCBM_assoc   3 pGetvtltltvtndgtaaatnvslslslPeGWtvvevspasaaslapGetveatvkVtppagaaaGdyevt 73 
                                    pG t+t++l ++n g++++ nv +++++P+G   v+v p ++ +l+p+ t+++++ + +p++a  G y++ 
  gi|119719050|ref|YP_919545.1| 456 PGMTTTYKLGLVNAGNTPLNNVMVQVEAPSGGFEVTVHPSTL-ALPPNSTASVDISILIPSNASEGFYNLP 525
                                    89****************************977477777666.6***********************9985 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   0.2   3.3e-13   3.9e-10       4      73 ..      34     100 ..      32     110 .. 0.90
   2 ?    0.6   0.0       0.6   7.2e+02      49      79 ..     250     292 ..     228     294 .. 0.70
   3 ?   -1.4   0.0       2.5     3e+03      65      81 ..     340     356 ..     302     361 .. 0.61
   4 ?    2.5   0.1      0.15   1.8e+02      45      77 ..     411     443 ..     408     451 .. 0.84
   5 ?   -0.1   0.1      0.98   1.2e+03       7      32 ..     467     492 ..     465     497 .. 0.82

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 3.3e-13
                CarboxypepD_reg   4 GrVtdasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatreevtltagq 73 
                                    G+V+d+sgap+  a++tv+ ++++ v+ t+t +dG+f+l  +p g+y+  v ++Gya+   + +++t+++
  gi|119719050|ref|YP_919545.1|  34 GKVVDESGAPVGLAEITVY-KGNSIVTFTRTSPDGSFNLY-VPVGSYTFLVYKKGYAPIYMT-LEVTPEK 100
                                    9******************.69999*************96.*****************9974.7777654 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.6
                CarboxypepD_reg  49 tysvtvsapGyatatr............eevtltagqtttldi 79 
                                    +y+ tv+ + +a++++            ++vt+++g++++l++
  gi|119719050|ref|YP_919545.1| 250 SYEATVTLSVFAPSNFiaslvdengltvQSVTVRPGEKRRLQL 292
                                    5666666666666666666666666666789999999888765 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 2.5
                CarboxypepD_reg  65 eevtltagqtttlditL 81 
                                    +++ +t g t+t +++L
  gi|119719050|ref|YP_919545.1| 340 TSINVTSGSTVTFRVAL 356
                                    34555555555555554 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.15
                CarboxypepD_reg  45 lppgtysvtvsapGyatatreevtltagqtttl 77 
                                     p g y v  +a+G  +++ +++ +++ +t+ +
  gi|119719050|ref|YP_919545.1| 411 TPSGIYLVSLRANGTTSTAEQSFLVRVTGTRKI 443
                                    5779************99999999988777655 PP

  == domain 5  score: -0.1 bits;  conditional E-value: 0.98
                CarboxypepD_reg   7 tdasgapiagatVtvtnadtgtvast 32 
                                    ++a ++p+ ++ V v++ ++g++ ++
  gi|119719050|ref|YP_919545.1| 467 VNAGNTPLNNVMVQVEAPSGGFEVTV 492
                                    567889*********99888887766 PP

>> FixG_C  IG-like fold at C-terminal of FixG, putative oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.7     2e+03      34      76 ..      77     120 ..      77     137 .. 0.72
   2 !    7.8   0.0    0.0031       3.7      37     100 ..     134     202 ..     113     217 .. 0.81
   3 ?   -1.9   0.0       3.1   3.7e+03      49      88 ..     212     250 ..     207     261 .. 0.68
   4 !    6.8   0.1    0.0064       7.7      57      89 ..     273     300 ..     250     320 .. 0.74
   5 ?   -0.8   0.0       1.5   1.7e+03      59      84 ..     333     357 ..     319     362 .. 0.77
   6 ?    2.8   0.0      0.11   1.3e+02      35     101 ..     352     422 ..     342     437 .. 0.66
   7 !   11.8   0.0   0.00017      0.21      34     100 ..     461     529 ..     446     540 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.7
                                    EEEEEEEE-SSS-EEEEEEEES-SS-EE.E...S--EEEE-TT-E CS
                         FixG_C  34 sYtlkilNktekprrytlsveglpglelag..raekeitvapgek 76 
                                    sYt+ +  k   p  +tl+v+ ++g +l g  + +k +tv p+ +
  gi|119719050|ref|YP_919545.1|  77 SYTFLVYKKGYAPIYMTLEVTPEKGGSL-GvlVLKKGVTVVPDVT 120
                                    5899999999999999999997665555.2233457777777765 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0031
                                    EEEEE-SSS-EEEEEEEES-SS-EE.......E.S--EEEE-TT-EEEEEEEEEE-GGG-SSSEEEEEEE CS
                         FixG_C  37 lkilNktekprrytlsveglpglel......agraekeitvapgekrkvpvfvrvpaealkkkstpitfk 100
                                    +k+ Nk  +p  + +s+e  +g +       + + ++ + +++g++r+++++v+vp +a++k+s  ++f+
  gi|119719050|ref|YP_919545.1| 134 VKVFNKCLDPVLVSFSIEVPQGWRAyfvgpnNLV-ASDFYIEAGSNRSLVFVVEVPLNASEKESVRVSFT 202
                                    5788888888888888887666665554442122.68899*******************99988888886 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 3.1
                                    EEEEEES-SS-EE.E.S--EEEE-TT-EEEEEEEEEE-GG CS
                         FixG_C  49 ytlsveglpglelagraekeitvapgekrkvpvfvrvpae 88 
                                    +t++v    + +l + ++++++  pg+++++p+ v++p +
  gi|119719050|ref|YP_919545.1| 212 FTFTVRQ-REWRLLELPTTSVKSFPGGQLSIPINVSTPFS 250
                                    6666663.24444334567777779999999999998865 PP

  == domain 4  score: 6.8 bits;  conditional E-value: 0.0064
                                    SS-EE.E.S--EEEE-TT-EEEEEEEEEE-GGG CS
                         FixG_C  57 pglelagraekeitvapgekrkvpvfvrvpaea 89 
                                    +gl++     +++tv pgekr++ +++ vp+ a
  gi|119719050|ref|YP_919545.1| 273 NGLTV-----QSVTVRPGEKRRLQLVIYVPPTA 300
                                    45555.....68******************987 PP

  == domain 5  score: -0.8 bits;  conditional E-value: 1.5
                                    -EE.E.S--EEEE-TT-EEEEEEEEE CS
                         FixG_C  59 lelagraekeitvapgekrkvpvfvr 84 
                                    l++ ++++++i+v +g++++++v ++
  gi|119719050|ref|YP_919545.1| 333 LKI-SPGATSINVTSGSTVTFRVALK 357
                                    566.5568999999999999999876 PP

  == domain 6  score: 2.8 bits;  conditional E-value: 0.11
                                    EEEEEEE-SSS-EEEEEEEES.-S....S-EE.E.S--EEEE-TT-EEEEEEEEEE-GGG-SSSEE.EEEEEE CS
                         FixG_C  35 YtlkilNktekprrytlsveg.lp....glelagraekeitvapgekrkvpvfvrvpaealkkkst.pitfkv 101
                                    +++ + N  + p    l+v+   p     ++++g++ +++ + pge++ + ++v+v+++  + +++  +++++
  gi|119719050|ref|YP_919545.1| 352 FRVALKNEGNMPTVALLRVQTsSPllraYTSVSGEPVASLYLVPGEEKALALIVEVDPST-P-SGIyLVSLRA 422
                                    56667777777777777777523333333333668889999***************9987.3.3333555555 PP

  == domain 7  score: 11.8 bits;  conditional E-value: 0.00017
                                    EEEEEEEE-SSS-EE.EEEEEES-S.S-EE.E.S--EEEE-TT-EEEEEEEEEE-GGG-SSSEE.EEEEE CS
                         FixG_C  34 sYtlkilNktekprr.ytlsveglp.glelagraekeitvapgekrkvpvfvrvpaealkkkst.pitfk 100
                                    +Y l ++N  ++p + ++++ve    g+e+ +++ ++++++p+++ +v +++ +p++a++   + pi++ 
  gi|119719050|ref|YP_919545.1| 461 TYKLGLVNAGNTPLNnVMVQVEAPSgGFEV-TVHPSTLALPPNSTASVDISILIPSNASEGFYNlPIHVV 529
                                    7************988******74359999.6678*********************99665555555554 PP

>> fn3_5  Fn3-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.82   9.9e+02      63      88 ..     168     193 ..     157     219 .. 0.77
   2 ?    4.5   0.0     0.046        55      57      85 ..     271     299 ..     238     309 .. 0.78
   3 ?    0.0   0.0       1.1   1.3e+03       6      21 ..     345     361 ..     332     392 .. 0.68
   4 !    9.1   0.0    0.0017         2      57      88 ..     488     519 ..     449     537 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.82
                          fn3_5  63 tskvtvpAnssktvtvtldlpsdakk 88 
                                    +s + ++A+s + + + + +p +a++
  gi|119719050|ref|YP_919545.1| 168 ASDFYIEAGSNRSLVFVVEVPLNASE 193
                                    67889999999999999999887777 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.046
                          fn3_5  57 aaltfetskvtvpAnssktvtvtldlpsd 85 
                                      ++++ ++vtv++++++ +++ + +p +
  gi|119719050|ref|YP_919545.1| 271 DENGLTVQSVTVRPGEKRRLQLVIYVPPT 299
                                    56788899*************99999765 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 1.1
                          fn3_5   6 i.gdkfsftltlkNtsn 21 
                                    + g++ +f++ lkN +n
  gi|119719050|ref|YP_919545.1| 345 TsGSTVTFRVALKNEGN 361
                                    33455566666666655 PP

  == domain 4  score: 9.1 bits;  conditional E-value: 0.0017
                          fn3_5  57 aaltfetskvtvpAnssktvtvtldlpsdakk 88 
                                      +t+ +s++++p+ns++ v++ + +ps+a++
  gi|119719050|ref|YP_919545.1| 488 FEVTVHPSTLALPPNSTASVDISILIPSNASE 519
                                    57899*********************997766 PP

>> MG2  MG2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       6.4   7.7e+03      17      57 ..      30      68 ..      26      77 .. 0.60
   2 ?    3.4   0.0     0.086     1e+02      31      82 ..     260     311 ..     248     324 .. 0.85
   3 !    7.3   0.0    0.0054       6.5      13      96 .]     346     435 ..     344     435 .. 0.83
   4 ?    2.9   0.0      0.13   1.5e+02      18      80 ..     461     526 ..     455     540 .. 0.62

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 6.4
                                   EEEEEEEESTTCSB---EEEEEEEE-TTSSEEEEEEEEE-C CS
                            MG2 17 Vslkallrdetlqglaklplkltirdpdgkevkelplatde 57
                                   V + + + de++ ++    +++t+++ ++ ++++ +  + +
  gi|119719050|ref|YP_919545.1| 30 VFFFGKVVDESGAPVGL--AEITVYKGNSIVTFTRTSPDGS 68
                                   55555566666666666..6677777777777776654444 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.086
                                    ---EEEEEEEE-TTSSEEEEEEEEE-CTTEEEEEEE--TT--SEEEEEEEEE CS
                            MG2  31 laklplkltirdpdgkevkelplatdetggaesefalpeaaklGeysvelsa 82 
                                    +a  ++ ++++d++g +v++ +++  e+   +  + +p +a   +ys+++ a
  gi|119719050|ref|YP_919545.1| 260 FAPSNFIASLVDENGLTVQSVTVRPGEKRRLQLVIYVPPTARISTYSLRVVA 311
                                    55566778899***********************************999933 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0054
                                    TT-EEEEEEEEES.TTCSB---......EEEEEEEE-TTSSEEEEEEEEE-CTTEEEEEEE--TT--SEEEEEEEEECST CS
                            MG2  13 PgetVslkallrd.etlqglak......lplkltirdpdgkevkelplatdetggaesefalpeaaklGeysvelsadsa 85 
                                     g tV +++ l++  ++ ++a        pl    ++ +g+ v +l l+  e+      +++  +++ G y v+l   + 
  gi|119719050|ref|YP_919545.1| 346 SGSTVTFRVALKNeGNMPTVALlrvqtsSPLLRAYTSVSGEPVASLYLVPGEEKALALIVEVDPSTPSGIYLVSL-RANG 424
                                    689999999998864444444455566688888899999999*********************************.7777 PP

                                    TT-EEEEEEEE CS
                            MG2  86 eeslssgsfrV 96 
                                    ++s++++sf V
  gi|119719050|ref|YP_919545.1| 425 TTSTAEQSFLV 435
                                    88889999987 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.13
                                    EEEEEEESTTCSB---EEEEEEEE-TTSS...EEEEEEE..EE-CTTEEEEEEE--TT--SEEEEEEE CS
                            MG2  18 slkallrdetlqglaklplkltirdpdgk...evkelpl..atdetggaesefalpeaaklGeysvel 80 
                                     +k  l ++  ++l++  + ++++ p+g+   +v+  +l    ++t +++ ++ +p++a+ G y++ +
  gi|119719050|ref|YP_919545.1| 461 TYKLGLVNAGNTPLNN--VMVQVEAPSGGfevTVHPSTLalPPNSTASVDISILIPSNASEGFYNLPI 526
                                    5555555555555555..55555555555422222233333566777788889999999999999865 PP

>> PEGA  PEGA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.1   5.8e-05      0.07      28      58 ..      70     100 ..      67     108 .. 0.91
   2 ?   -3.1   0.0       6.3   7.5e+03      50      65 ..     278     293 ..     276     294 .. 0.81
   3 ?   -0.8   0.0       1.2   1.5e+03      50      68 ..     340     358 ..     337     360 .. 0.82
   4 ?   -0.5   0.0      0.99   1.2e+03      20      32 ..     467     480 ..     462     493 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.8e-05
                           PEGA  28 tlsleaGnyslrvekeGYedlektvtvtage 58 
                                    +l+++ G+y++ v k GY+++++t +vt+++
  gi|119719050|ref|YP_919545.1|  70 NLYVPVGSYTFLVYKKGYAPIYMTLEVTPEK 100
                                    6789***********************9875 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 6.3
                           PEGA  50 ktvtvtagetvklnlt 65 
                                    + vtv++ge+ +l+l+
  gi|119719050|ref|YP_919545.1| 278 QSVTVRPGEKRRLQLV 293
                                    6799999999998875 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.2
                           PEGA  50 ktvtvtagetvklnltLek 68 
                                    + ++vt+g tv++ + L++
  gi|119719050|ref|YP_919545.1| 340 TSINVTSGSTVTFRVALKN 358
                                    6789999999999999886 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 0.99
                           PEGA  20 kylGkTPvtls.le 32 
                                    ++ G+TP++ + ++
  gi|119719050|ref|YP_919545.1| 467 VNAGNTPLNNVmVQ 480
                                    5789***9987554 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       3.4     4e+03      64      83 ..     173     192 ..     144     201 .. 0.73
   2 ?    1.4   0.1      0.33   3.9e+02      61      83 ..     277     301 ..     244     311 .. 0.76
   3 ?    8.2   3.0    0.0025         3       9      85 ..     343     414 ..     334     442 .. 0.63
   4 ?   10.4   2.4   0.00054      0.64       9      51 ..     453     495 ..     435     525 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 3.4
                          DUF11  64 Leagesatlsftvrvtrtaa 83 
                                    +eag+ + l f v+v+  a+
  gi|119719050|ref|YP_919545.1| 173 IEAGSNRSLVFVVEVPLNAS 192
                                    48889999999988876655 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.33
                          DUF11  61 v..gsLeagesatlsftvrvtrtaa 83 
                                    v   ++ +ge+++l++ + v++ta+
  gi|119719050|ref|YP_919545.1| 277 VqsVTVRPGEKRRLQLVIYVPPTAR 301
                                    2235889999999999999999987 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0025
                          DUF11   9 evrpGdtvtytltvtNtgpasa...ngvvvtDtl..............PaglayvsvsasqgtasaltsvgsLeagesat 71 
                                    +v++G tvt+ + ++N g+ +     +v+ + +l                                      L +ge++ 
  gi|119719050|ref|YP_919545.1| 343 NVTSGSTVTFRVALKNEGNMPTvalLRVQTSSPLlraytsvsgepvasL----------------------YLVPGEEKA 400
                                    799***************9887422444444444444444444444440......................455666666 PP

                          DUF11  72 lsftvrvtrtaasg 85 
                                    l++ v+v +++ sg
  gi|119719050|ref|YP_919545.1| 401 LALIVEVDPSTPSG 414
                                    66666666555544 PP

  == domain 4  score: 10.4 bits;  conditional E-value: 0.00054
                          DUF11   9 evrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsas 51 
                                    + +pG t+ty l + N g++++n+v v+   P+g   v+v  s
  gi|119719050|ref|YP_919545.1| 453 TGAPGMTTTYKLGLVNAGNTPLNNVMVQVEAPSGGFEVTVHPS 495
                                    5689**********************99777765444444433 PP

>> ASH  Abnormal spindle-like microcephaly-assoc'd, ASPM-SPD-2-Hydin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       1.2   1.4e+03      65      79 ..     194     208 ..     178     218 .. 0.66
   2 ?   -0.8   0.0       1.5   1.8e+03      31      71 ..     245     291 ..     238     310 .. 0.66
   3 ?    1.1   0.0      0.39   4.7e+02      56      90 ..     338     372 ..     321     376 .. 0.78
   4 ?    9.8   0.1   0.00077      0.92      22      72 ..     457     509 ..     446     517 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.2
                                    XXXXXXXXXXXXXXX CS
                            ASH  65 gesvtltvtwtPtee 79 
                                    +esv +++tw +++ 
  gi|119719050|ref|YP_919545.1| 194 KESVRVSFTWFNLSG 208
                                    567777777777764 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.5
                                    EESS-SS--EEEEEEEE--XXXXXXXXXX......XXXXXXXXXXXX CS
                            ASH  31 veNpseepaevkvskvpaaekgfsveete......levqpgesvtlt 71 
                                    v+ p  ++a+v++s ++++++  s+  ++      ++v pge+  l+
  gi|119719050|ref|YP_919545.1| 245 VSTPFSYEATVTLSVFAPSNFIASLVDENgltvqsVTVRPGEKRRLQ 291
                                    55555666666666666666666655555544444667777776665 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.39
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                            ASH  56 eetelevqpgesvtltvtwtPteegavrevLqflv 90 
                                     +t+++v+ g++vt++v +++   ++  ++L++ +
  gi|119719050|ref|YP_919545.1| 338 GATSINVTSGSTVTFRVALKNEGNMPTVALLRVQT 372
                                    56779999999999999999998888888887765 PP

  == domain 4  score: 9.8 bits;  conditional E-value: 0.00077
                                    EEEEEEE-EEESS-SS--EEEEEEEE--XXXXXXXXXX..XXXXXXXXXXXXX CS
                            ASH  22 GssaerlLtveNpseepaevkvskvpaaekgfsveete..levqpgesvtltv 72 
                                    G +++ +L ++N +++p++  + +v a++ gf v+ +   l ++p+++ ++++
  gi|119719050|ref|YP_919545.1| 457 GMTTTYKLGLVNAGNTPLNNVMVQVEAPSGGFEVTVHPstLALPPNSTASVDI 509
                                    7788999**********88888888889999988877766999**99998887 PP

>> Alpha_adaptinC2  Adaptin C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.099   1.2e+02      19      96 ..     121     202 ..     104     211 .. 0.67
   2 ?   -0.6   0.0       1.3   1.6e+03      43      84 ..     212     250 ..     173     260 .. 0.61
   3 ?   -0.6   0.0       1.4   1.6e+03      44      94 ..     321     371 ..     309     374 .. 0.82
   4 ?    6.3   0.1      0.01        12      26      79 ..     460     513 ..     447     528 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.099
                                    E..TTSTTEEEEEEEEEE-SSS-EEEEEEEEEEBTTCEEEEEEES-S-B-TT...CEEEEEEEEEEESCTTS-EEEEEEE CS
                Alpha_adaptinC2  19 k..perpgqiritlsftNkssqpisnfsfqaavpkslklqlqppsstvlppn...pggqitqvllienpskkplrmrlri 93 
                                    +  +++++++ri ++ +Nk   p+  +sf++ vp++++     p+  v + +   +g   + v+ +e p + +++  +r+
  gi|119719050|ref|YP_919545.1| 121 SvyTSQGDTVRIPVKVFNKCLDPVL-VSFSIEVPQGWRAYFVGPNNLVASDFyieAGSNRSLVFVVEVPLNASEKESVRV 199
                                    444789999***********99998.999999999997765555544444334544444444555555555555555555 PP

                                    EEE CS
                Alpha_adaptinC2  94 syk 96 
                                    s++
  gi|119719050|ref|YP_919545.1| 200 SFT 202
                                    555 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.3
                                    EEEEEEEBTTCEEEEEEES-S-B-TTCEEEEEEEEEEESCTT CS
                Alpha_adaptinC2  43 fsfqaavpkslklqlqppsstvlppnpggqitqvllienpsk 84 
                                    f+f++   +    +l +  +t++  +pggq +  +++++p +
  gi|119719050|ref|YP_919545.1| 212 FTFTVRQREW---RLLELPTTSVKSFPGGQLSIPINVSTPFS 250
                                    3444333322...23344444444455888888888887554 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.4
                                    EEEEEEBTTCEEEEEEES-S-B-TTCEEEEEEEEEEESCTTS-EEEEEEEE CS
                Alpha_adaptinC2  44 sfqaavpkslklqlqppsstvlppnpggqitqvllienpskkplrmrlris 94 
                                    ++ + v +++ l   +p  t++  ++g ++t  + + n +++p    lr++
  gi|119719050|ref|YP_919545.1| 321 NLDVIVESAYDLLKISPGATSINVTSGSTVTFRVALKNEGNMPTVALLRVQ 371
                                    677888888888888888888888899999999999998888887777775 PP

  == domain 4  score: 6.3 bits;  conditional E-value: 0.01
                                    EEEEEEEEE-SSS-EEEEEEEEEEBTTCEEEEEEES-S-B-TTCEEEEEEEEEE CS
                Alpha_adaptinC2  26 iritlsftNkssqpisnfsfqaavpkslklqlqppsstvlppnpggqitqvlli 79 
                                    ++++l + N  ++p++n++ q+  p+++      ps+  lppn+ +++  ++li
  gi|119719050|ref|YP_919545.1| 460 TTYKLGLVNAGNTPLNNVMVQVEAPSGGFEVTVHPSTLALPPNSTASVDISILI 513
                                    56677778999**************98844455566777778777777777766 PP

>> fn3_3  Polysaccharide lyase family 4, domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.2    0.0012       1.4      29      70 ..      61      99 ..      40     104 .. 0.84
   2 ?   -1.2   0.0       1.5   1.8e+03      61      72 ..     276     287 ..     253     290 .. 0.60
   3 ?    0.3   0.0      0.51   6.1e+02      62      74 ..     339     351 ..     330     352 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0012
                          fn3_3 29 teadssgsftipnVkpGtYrltvYadglfgdykqdsvtVtag 70
                                   t+++ +gsf    V  G+Y+  vY++g++  y   + +Vt+ 
  gi|119719050|ref|YP_919545.1| 61 TRTSPDGSFNL-YVPVGSYTFLVYKKGYAPIY--MTLEVTPE 99
                                   67788888887.799**************999..77777765 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.5
                          fn3_3  61 kqdsvtVtagkt 72 
                                    + +svtV +g++
  gi|119719050|ref|YP_919545.1| 276 TVQSVTVRPGEK 287
                                    357788888876 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.51
                          fn3_3  62 qdsvtVtagkttt 74 
                                     +s++Vt+g+t+t
  gi|119719050|ref|YP_919545.1| 339 ATSINVTSGSTVT 351
                                    479*******987 PP

>> Coatamer_beta_C  Coatomer beta C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00022      0.26      77     126 ..     465     515 ..     458     521 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00022
                Coatamer_beta_C  77 livNqtketLqnltvel.atlgdlklvekpqsvtlaphdfakikatvkvss 126
                                     +vN  ++ L+n++v++ a+ g +++  +p+++ l p+++a++ +++ + s
  gi|119719050|ref|YP_919545.1| 465 GLVNAGNTPLNNVMVQVeAPSGGFEVTVHPSTLALPPNSTASVDISILIPS 515
                                    589*************95689***********************9998776 PP

>> fn3_6  Fibronectin type-III domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.4      0.54   6.5e+02      60      88 ..     178     205 ..      96     217 .. 0.59
   2 ?   -0.6   0.1       1.3   1.5e+03      51      51 ..     284     284 ..     238     373 .. 0.58
   3 ?   -2.1   0.0       3.7   4.5e+03       4      51 ..     362     409 ..     359     447 .. 0.50
   4 ?   11.0   0.0   0.00031      0.37      18      76 ..     459     518 ..     442     531 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.54
                          fn3_6  60 gekksftvtvtakksaesevsfGsltWsd 88 
                                    +++  f v+v  + ++e+e ++ s+tW +
  gi|119719050|ref|YP_919545.1| 178 NRSLVFVVEVPLN-ASEKESVRVSFTWFN 205
                                    3344455555554.445666677777766 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.3
                          fn3_6  51 P 51 
                                    P
  gi|119719050|ref|YP_919545.1| 284 P 284
                                    3 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 3.7
                          fn3_6   4 yPsisvaleeelkgtvtvtRtvtnVgsse..atYkakveap.egvkvtVeP 51 
                                    +P++++    + +++  + R  t+V+ ++  + Y +  e+    + v+V P
  gi|119719050|ref|YP_919545.1| 362 MPTVALL---RVQTSSPLLRAYTSVSGEPvaSLYLVPGEEKaLALIVEVDP 409
                                    5555555...44555555566666655542244444433331234444544 PP

  == domain 4  score: 11.0 bits;  conditional E-value: 0.00031
                          fn3_6  18 tvtvtRtvtnVgsse.atYkakveap.egvkvtVePseLefsekgekksftvtvtakksae 76 
                                    t+t++  + n g+++  +  ++veap  g++vtV+Ps+L++  ++ ++s+ +++   ++a+
  gi|119719050|ref|YP_919545.1| 459 TTTYKLGLVNAGNTPlNNVMVQVEAPsGGFEVTVHPSTLALP-PNSTASVDISILIPSNAS 518
                                    55555555666666435567899999557*************.999999999987776555 PP

>> CzcE  Heavy-metal resistance protein CzcE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       5.5   6.5e+03      51      67 ..     251     267 ..     246     270 .. 0.79
   2 ?    9.1   0.0    0.0013       1.6      16      38 ..     333     355 ..     326     362 .. 0.86
   3 ?   -2.5   0.0       5.6   6.7e+03      51      63 ..     503     515 ..     500     519 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 5.5
                           CzcE  51 gtssvdLsklapevpea 67 
                                    +++ v Ls++ap  + a
  gi|119719050|ref|YP_919545.1| 251 YEATVTLSVFAPSNFIA 267
                                    567899******87765 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0013
                           CzcE  16 vdvspgtkyvnVesGEtvafkvg 38 
                                    + +spg   +nV+sG tv+f+v 
  gi|119719050|ref|YP_919545.1| 333 LKISPGATSINVTSGSTVTFRVA 355
                                    6799****************986 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 5.6
                           CzcE  51 gtssvdLsklape 63 
                                     t+svd+s l+p 
  gi|119719050|ref|YP_919545.1| 503 STASVDISILIPS 515
                                    5789******994 PP

>> Transglut_N  Transglutaminase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.013        15      85     115 ..     279     309 ..     236     312 .. 0.76
   2 ?    3.1   0.0     0.095   1.1e+02      91     117 ..     502     528 ..     457     529 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.013
                    Transglut_N  85 saeveessgnsltvsitspanaivgryklsv 115
                                    s++v   ++++l++ i +p++a ++ y+l v
  gi|119719050|ref|YP_919545.1| 279 SVTVRPGEKRRLQLVIYVPPTARISTYSLRV 309
                                    455554445799*****************98 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.095
                    Transglut_N  91 ssgnsltvsitspanaivgryklsvet 117
                                    +s+ s+ +si +p+na+ g y+l +++
  gi|119719050|ref|YP_919545.1| 502 NSTASVDISILIPSNASEGFYNLPIHV 528
                                    34469*****************99986 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.14   1.7e+02      46      84 ..     179     216 ..     162     219 .. 0.68
   2 ?    5.5   0.1     0.017        20      10      33 ..     339     362 ..     331     411 .. 0.88
   3 ?   -0.4   0.1       1.2   1.4e+03      15      79 ..     454     523 ..     440     532 .. 0.59

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.14
                                    TEEEEEEEESEE-CTEEEEEEEEEE-S-S-CEEEEEEEE CS
                          CARDB  46 gelvgtvtvpsLaagesttvsftwtteategevtltvvv 84 
                                    ++lv  v+v +L+a+e+++v++++t+   +g v++t++v
  gi|119719050|ref|YP_919545.1| 179 RSLVFVVEV-PLNASEKESVRVSFTWFNLSGHVDFTFTV 216
                                    444444444.78888888877777776678888888876 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.017
                                    EC-SEEETTSEEEEEEEEEE-SSS CS
                          CARDB  10 lnpseafvgeentitvtvkNqGta 33 
                                    ++  +++ g+++t++v +kN+G++
  gi|119719050|ref|YP_919545.1| 339 ATSINVTSGSTVTFRVALKNEGNM 362
                                    56678999**************97 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.2
                                    EETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEE....SEE-CTEEEEEEEEEE-S..-S-CEEE CS
                          CARDB  15 afvgeentitvtvkNqGtaasgatkvalyldgelvgtvtv....psLaagesttvsftwtte..ategevt 79 
                                      +g + t ++ + N G+    ++ v++ +      +vtv     +L ++++++v++++ ++  a+eg + 
  gi|119719050|ref|YP_919545.1| 454 GAPGMTTTYKLGLVNAGNTPLNNVMVQVEAPSGGF-EVTVhpstLALPPNSTASVDISILIPsnASEGFYN 523
                                    55666666677777777777777777766543332.23334433456677777777777666555566555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (577 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.63u 0.27s 00:00:00.90 Elapsed: 00:00:00.44
# Mc/sec: 3950.54
//
Query:       gi|119719051|ref|YP_919546.1|  [L=403]
Description: cytochrome c biogenesis protein, transmembrane region [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-15   56.3  19.8      4e-15   56.3  19.8    3.0  3  DsbD      Cytochrome C biogenesis protein transmembrane regio
    2.6e-12   47.1  22.6    2.6e-12   47.1  22.6    2.5  3  DsbD_2    Cytochrome C biogenesis protein transmembrane regio
  ------ inclusion threshold ------
       0.33   11.5   0.2       0.33   11.5   0.2    5.7  7  DUF2523   Protein of unknown function (DUF2523)


Domain annotation for each model (and alignments):
>> DsbD  Cytochrome C biogenesis protein transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.3  19.8   6.7e-19     4e-15       2     209 ..      11     211 ..      10     215 .. 0.76
   2 ?    1.7   1.1     0.033     2e+02      17      92 ..     231     306 ..     229     367 .. 0.75
   3 ?    0.6   0.1     0.072   4.3e+02      78     103 ..     375     400 ..     363     402 .. 0.77

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 6.7e-19
                           DsbD   2 flaGllsflsPCilpliPaylsyisgvsvedvktekkkvkvllkallFvlGlslvfvslglsaaflgqllkdv.....ke 76 
                                    f  Gl + ++PC lp++P++l+ is       ++++k     l +llF+ G++l fv  g+ ++  g +++ +     ++
  gi|119719051|ref|YP_919546.1|  11 FVLGLQTAFTPCYLPVVPVFLAVIS-------RQKAK---RWLASLLFATGVVLSFVVYGILIGLGGGVVRYIfallpQQ 80 
                                    6779*********************.......44333...3467777777777777666665555555554431111266 PP

                           DsbD  77 virrvaglivillGlhflgvfkievleklklllkikkkaelsvlgalllGltFalgwsPCigPvlasvlala..askesl 154
                                     i ++ gli i +G+ +l  ++ ev+    + +  ++k +  +lg++++G++F+l ++PC++ v+ + l  a  +s  + 
  gi|119719051|ref|YP_919546.1|  81 LISTALGLILISIGVALLTPLR-EVFSYIPSAT-PSRKVSG-YLGSFMFGFMFSLAAAPCAAAVMIAALSQAllGSFTDS 157
                                    7778888888888888888777.5555555553.4666666.9***********************99965433888999 PP

                           DsbD 155 akgallllvyvlGlaipfllvglllellkkklkslkkyskaveiaggvllvllGv 209
                                    ++ +l+++vy  G ++pfl +g l + l+ +       ++  e a+g+llv+ G 
  gi|119719051|ref|YP_919546.1| 158 LQPVLYMVVYGAGTGLPFLAIGALGGALR-FRGGAGFLVRRAEEATGLLLVVTGS 211
                                    ************************99665.6666777788899999999999986 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.033
                           DsbD  17 liPaylsyisgvsvedvktekkkv.kvllkallFvlGlslvfvslglsaaflgqllkdvkevirrvaglivillGlh 92 
                                    ++Pa ls+++  +v     +  +    l +    ++G  l+++s +l a+  +  ++++ + +  v+  +v+l  l+
  gi|119719051|ref|YP_919546.1| 231 MYPAVLSFLGLAGVYYSYVS-FRAgAYLESPHPILIGAGLTLLSASLLASWTVPSAGNIATLVGLVGRALVLLGALS 306
                                    67888888876666554444.34413455566678899999999999999999999999999999998888874443 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.072
                           DsbD  78 irrvaglivillGlhflgvfkievle 103
                                      ++ gl +il Gl ++ v+++  l+
  gi|119719051|ref|YP_919546.1| 375 FSVLSGLSIILSGLRTARVLSVLSLY 400
                                    55677888999999999999876665 PP

>> DsbD_2  Cytochrome C biogenesis protein transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.1  22.6   4.3e-16   2.6e-12       2     197 ..      10     210 ..       9     212 .. 0.79
   2 ?   -0.0   3.2      0.12   7.1e+02      75     146 ..     263     332 ..     234     339 .. 0.56
   3 ?   -3.2   0.1       1.2   6.9e+03      71      88 ..     373     390 ..     360     399 .. 0.59

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 4.3e-16
                         DsbD_2   2 afllgLlgsl.hClgmCggivlalslskp.kralalllynlGRilsYallGalvgllgsvlqlageleglrallgvllgl 79 
                                    +f+lgL +++ +C++   ++ la+ ++++ kr+la+ll+ +G +ls+++ G+l+gl g v+  + +l   ++l++ +lgl
  gi|119719051|ref|YP_919546.1|  10 LFVLGLQTAFtPCYLPVVPVFLAVISRQKaKRWLASLLFATGVVLSFVVYGILIGLGGGVVRYIFALL-PQQLISTALGL 88 
                                    79**********************8888736677***************************8887764.5899999999* PP

                         DsbD_2  80 lllllglklllkkkllklerlgkllsrllkklakklkslasalllGllnGll..pCgl.vysalllalasgsa...leGa 153
                                    +l+ +g++ll     + l+++ + + +++ + +  + ++ +++++G++++l+  pC+  v+ a+l  ++ gs+   l+ +
  gi|119719051|ref|YP_919546.1|  89 ILISIGVALL-----TPLREVFSYIPSATPSRK--VSGYLGSFMFGFMFSLAaaPCAAaVMIAALSQALLGSFtdsLQPV 161
                                    *9*99*9997.....456666666655555544..4799**********996669*66566666666666665222789* PP

                         DsbD_2 154 lvmlaFgLGTlpalllfglllgllskklr.....kkllrlagvllillg 197
                                    l+m+++g GT +++l++g+l g l+ +       ++  +++g+ll++ g
  gi|119719051|ref|YP_919546.1| 162 LYMVVYGAGTGLPFLAIGALGGALRFRGGagflvRRAEEATGLLLVVTG 210
                                    **********************996533323333666667777777766 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.12
                         DsbD_2  75 vllgllllllglklllkkkllklerlgkllsrllkklakklkslasalllGllnGllpCglvysalllalas 146
                                    +l+g+ l ll ++ll + ++ + +++  l+  + ++l     +  s+ l G+l Gl+p ++ + a+l al++
  gi|119719051|ref|YP_919546.1| 263 ILIGAGLTLLSASLLASWTVPSAGNIATLVGLVGRALVL--LGALSITLKGVLAGLIPVPPYLQAALDALLA 332
                                    444444444444444444444444444433333333332..5777888888888888888777777766665 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 1.2
                         DsbD_2  71 allgvllgllllllglkl 88 
                                     +++vl gl ++l+gl+ 
  gi|119719051|ref|YP_919546.1| 373 VVFSVLSGLSIILSGLRT 390
                                    344555555555555544 PP

>> DUF2523  Protein of unknown function (DUF2523)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1       2.3   1.4e+04      54      65 ..       8      19 ..       7      20 .. 0.80
   2 ?    4.9   0.9    0.0068        40       4      29 ..      30      56 ..      29      64 .. 0.88
   3 ?   -1.1   0.6      0.49   2.9e+03      20      36 ..      86     100 ..      65     148 .. 0.59
   4 ?   -1.5   0.1      0.64   3.8e+03      32      55 ..     141     164 ..     126     174 .. 0.70
   5 ?    3.0   0.1     0.025   1.5e+02      18      61 ..     200     244 ..     191     251 .. 0.68
   6 ?   11.5   0.2   5.6e-05      0.33       9      49 ..     291     331 ..     285     345 .. 0.88
   7 ?    2.1   0.0      0.05     3e+02      48      78 ..     364     394 ..     359     396 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.3
                        DUF2523 54 qllgllgfgeAl 65
                                   +ll++lg+ +A+
  gi|119719051|ref|YP_919546.1|  8 ALLFVLGLQTAF 19
                                   689999999997 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0068
                        DUF2523  4 flawllkslvgrvLva.Lglgfvtyag 29
                                   fla + ++ ++r+L++ L++++v+  +
  gi|119719051|ref|YP_919546.1| 30 FLAVISRQKAKRWLASlLFATGVVLSF 56
                                   899*************99999998655 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.49
                        DUF2523  20 Lglgfvtyagidalidg 36 
                                    Lgl++++ ++  al+++
  gi|119719051|ref|YP_919546.1|  86 LGLILISIGV--ALLTP 100
                                    3333333332..34444 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 0.64
                        DUF2523  32 alidglisllqsalnglpssvlql 55 
                                     +i+ l+++l + ++   + vl++
  gi|119719051|ref|YP_919546.1| 141 VMIAALSQALLGSFTDSLQPVLYM 164
                                    567777777777777666666655 PP

  == domain 5  score: 3.0 bits;  conditional E-value: 0.025
                        DUF2523  18 vaLglgfvtyagidal.idglisllqsalnglpssvlqllgllgf 61 
                                     a gl++v+++ + +l i+++   +   ++ + ++vl++lgl+g+
  gi|119719051|ref|YP_919546.1| 200 EATGLLLVVTGSASILtIEHFEVVVFEVAKEMYPAVLSFLGLAGV 244
                                    566777666666666545666777777777788888888888876 PP

  == domain 6  score: 11.5 bits;  conditional E-value: 5.6e-05
                        DUF2523   9 lkslvgrvLvaLglgfvtyagidalidglisllqsalnglp 49 
                                    l  lvgr Lv Lg++ +t +g+ a + ++  +lq+al++l 
  gi|119719051|ref|YP_919546.1| 291 LVGLVGRALVLLGALSITLKGVLAGLIPVPPYLQAALDALL 331
                                    6789******************************9999876 PP

  == domain 7  score: 2.1 bits;  conditional E-value: 0.05
                        DUF2523  48 lpssvlqllgllgfgeAlniilsAvvtrlal 78 
                                    lp +   ++ ++ +  +l+iils++ t  +l
  gi|119719051|ref|YP_919546.1| 364 LPWDLSPFFVVFSVLSGLSIILSGLRTARVL 394
                                    5556677889999999*******99876666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       776  (0.0432818); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2601.86
//
Query:       gi|119719052|ref|YP_919547.1|  [L=95]
Description: hypothetical protein Tpen_0134 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0017   18.2   0.1     0.0028   17.5   0.1    1.4  1  TrmB      Sugar-specific transcriptional regulator TrmB


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   1.6e-07    0.0028      37      63 ..      51      77 ..      19      80 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.6e-07
                                   HCHHHHHHHHHHCTSEEEESSTTTEEE CS
                           TrmB 37 skvYevLrsLedkGlVerekgrpklYr 63
                                   s v +vL++++++G+ e+++++p+lYr
  gi|119719052|ref|YP_919547.1| 51 SHVARVLERMVSMGVLEIVDENPRLYR 77
                                   5799**********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 648.53
//
Query:       gi|119719053|ref|YP_919548.1|  [L=518]
Description: Alpha-amylase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.4e-66  223.3   0.1    7.4e-66  222.6   0.1    1.3  1  Glyco_hydro_57   Glycosyl hydrolase family 57
     0.0064   16.4   0.0      0.014   15.3   0.0    1.6  1  Polysacc_deac_1  Polysaccharide deacetylase


Domain annotation for each model (and alignments):
>> Glyco_hydro_57  Glycosyl hydrolase family 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  222.6   0.1   8.2e-70   7.4e-66       1     325 []       5     307 ..       5     307 .. 0.95

  Alignments for each domain:
  == domain 1  score: 222.6 bits;  conditional E-value: 8.2e-70
                                    EEEEEE-----TTS-.......SSSSSHHHHHHHHHHTHHHHHHHHHHHHHTT----EEEEE-HHHHHHHT-HHHHHHHH CS
                 Glyco_hydro_57   1 afvfhqHqplykkpg.......kgeytlpwvrehaaedYiklalilekfpkvhvtfeLsgsLiaqLeeylngekksylpa 73 
                                    +f+f++Hqp++ +++           + + + e   + Y++++l+  +f++v+                    k++ylpa
  gi|119719053|ref|YP_919548.1|   5 VFMFEVHQPYRLSRNirgtlseLTARKGKITAEDLERVYFDDELNRRIFERVS--------------------KRCYLPA 64 
                                    599*********99997775542233346788899999***************....................******* PP

                                    HHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHT.TT-HHHHHHHHHHCTSEEEEEE-TT-B-GGG-S-HHHH CS
                 Glyco_hydro_57  74 teellelieeglerctelkldlavlfnlaisgplleqiqkwlnkevlelfrelqesgqvElltspyyHpllpllpdsedi 153
                                    ++++ +  e + ++++ +k      +++++sg lleq++kw  +ev+e+fr+l+++g vE+l ++yyH+l+ l+ + e++
  gi|119719053|ref|YP_919548.1|  65 NNVIRDMVEFFKDSGKPFK------VSYSLSGVLLEQAEKW-YPEVIESFRSLAKTGMVEFLDQTYYHSLAFLFAE-EEL 136
                                    ********9999*******......****************.**********************************.*** PP

                                    HHHHHHHHHHHHHHHSS--SBEE-GGG-B--SHHHHHHHTT--EEEE-C------------TTS-EE-TTS.-EEEE--C CS
                 Glyco_hydro_57 154 eaqvkkarelyeeyfgqePrgfwlpElavspeileilaelGfeylftdelaeiledkskespyrpyllknggiavffRdr 233
                                     +qv+++re +++++g+eP+ + ++E+++++ ++ ++ +lG+++++t++++++l ++   sp++ y++k  +i v++R++
  gi|119719053|ref|YP_919548.1| 137 LEQVREHREALRKHLGVEPTAVENTEFTYNNYLACLFDKLGYKVILTEGVERVLGWR---SPNYLYKAKGCNIRVLMRNY 213
                                    *********************************************************...******************** PP

                                    HH-TTTSGGG-................TTSB..........-TT---TTT-..-BB-TT-S---HHHHHHHHHHHHHHHH CS
                 Glyco_hydro_57 234 eLsddigFrys....eqypleavddfinwlkkvkkaksevvtialdgEnwg..hypetgkkeFleklyeeleenglielv 307
                                    +LsddigFr++    + ypl ++d++  wl+ +   ++ev+++a+d+E++g    +etg++eFl++l+ e+ + g + + 
  gi|119719053|ref|YP_919548.1| 214 RLSDDIGFRFGarwwSEYPL-TADKYSAWLSAT---PGEVILVAIDYETFGehFPAETGIFEFLRWLPGEILKWGNLVTS 289
                                    **************999***.**********98...***************966779*********************** PP

                                    HHHHHHHHHSS-EEEEEE CS
                 Glyco_hydro_57 308 tpsefikklkpkgliklp 325
                                    tpse++++l+p++ +++p
  gi|119719053|ref|YP_919548.1| 290 TPSEVAERLTPRDEVDVP 307
                                    ************998876 PP

>> Polysacc_deac_1  Polysaccharide deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.6e-06     0.014      49     122 ..     105     179 ..      64     181 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.6e-06
                                    HHHHHHHHTT.EEEEE--SS--EGGGSHHHHHHHHHHHHHHHHHHHHS----EEE-GGGEE-HHHHHHHHHTT.E CS
                Polysacc_deac_1  49 devremaasG.veignHtinhsnlkrlseeevrreierakdalrkalgreprlfryPygsasatvlevarelgfa 122
                                    +  r +a+ G ve+   t+ hs  +   eee+ +++ + ++alrk+lg ep+ +      +++       +lg++
  gi|119719053|ref|YP_919548.1| 105 ESFRSLAKTGmVEFLDQTYYHSLAFLFAEEELLEQVREHREALRKHLGVEPTAVENTEFTYNNYLACLFDKLGYK 179
                                    668999**********************************************99998888888888888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (518 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 3483.72
//
Query:       gi|119719054|ref|YP_919549.1|  [L=177]
Description: inorganic diphosphatase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.3e-56  188.1   0.1    1.1e-55  187.9   0.1    1.0  1  Pyrophosphatase  Inorganic pyrophosphatase


Domain annotation for each model (and alignments):
>> Pyrophosphatase  Inorganic pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.9   0.1   5.9e-60   1.1e-55       1     160 []      17     172 ..      17     172 .. 0.98

  Alignments for each domain:
  == domain 1  score: 187.9 bits;  conditional E-value: 5.9e-60
                                    EEEEE-TTCSEEEEEETTTTEEEEEEE-SSSB-BSSEEEEETT--BTCCBEETSSSEEEEEESSS---TTEEEEEEEEEE CS
                Pyrophosphatase   1 vvvEiprgsnaKyeidkeegklrldrvlftskgypanYGfipqTledtelkGDgDPlDvlvlgeeplspgevvevkvlGv 80 
                                    vv+Eip+gsn+Kyeidke+g++++drvlfts+ +p+nYGfip Tle+     DgDP+Dv+ l+++p++pg+vv+++++++
  gi|119719054|ref|YP_919549.1|  17 VVIEIPMGSNVKYEIDKESGMVFVDRVLFTSMVFPFNYGFIPGTLEE-----DGDPVDVVLLSHDPFVPGSVVRARPVAL 91 
                                    79*********************************************.....**************************** PP

                                    EEEEETTEEEEEEEEEETT..SGGGTT-SSGGGSTHHHHHHHHHHHHHTTTTSCCT-SEEEEEEEEHHHHHHHHHHHHHH CS
                Pyrophosphatase  81 lamiDegetDdKiiavpvk..dprlkkindiedlpgllleeiehfFetykdlegkkknvkveewkdkeeAekvieeaher 158
                                    l+m+De++ D K++avp++  d+r++ ++d++d+ + ++++i+hfFe+yk+le k+k+vkv+ewk++ +Ae+ i++a+er
  gi|119719054|ref|YP_919549.1|  92 LEMEDENGPDSKVVAVPHEkiDNRFSGVKDVDDIDDAVKDRIKHFFEHYKELE-KGKWVKVKEWKGRFAAEESIRRAVER 170
                                    *******************999999****************************.789********************999 PP

                                    HH CS
                Pyrophosphatase 159 yk 160
                                    +k
  gi|119719054|ref|YP_919549.1| 171 FK 172
                                    75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1217.01
//
Query:       gi|119719055|ref|YP_919550.1|  [L=524]
Description: elongation factor Tu domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      4e-20   72.2   0.0    7.4e-20   71.3   0.0    1.4  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    2.6e-08   34.1   0.3    4.1e-07   30.3   0.1    2.6  2  GTP_EFTU_D2  Elongation factor Tu domain 2
     0.0002   21.6   0.0    0.00045   20.5   0.0    1.6  1  GTP_EFTU_D3  Elongation factor Tu C-terminal domain
  ------ inclusion threshold ------
      0.015   15.4   0.0      0.034   14.2   0.0    1.6  1  MMR_HSR1     50S ribosome-binding GTPase
       0.19   11.5   0.3        1.5    8.5   0.0    2.0  2  ATP_bind_1   Conserved hypothetical ATP binding protein


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.3   0.0   2.1e-23   7.4e-20       4     192 ..     113     331 ..     111     334 .. 0.81

  Alignments for each domain:
  == domain 1  score: 71.3 bits;  conditional E-value: 2.1e-23
                                    EEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEE................... CS
                       GTP_EFTU   4 rnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisle................... 64 
                                    ++i+++g vD+GK+T++++L +   ++ +      + r + + ++E   g T ++ +  l                    
  gi|119719055|ref|YP_919550.1| 113 VTIAVMGNVDAGKSTTVGTLCTGELDDGR--G--RGMRRVARYSHEIITGRTSSVVVRLLGfdmegkpvnwnlpnpldea 188
                                    5799*****************55555444..2..2346677888888777777766666658899*************99 PP

                                    ..TTCSSEEEEEEEESSSGGGHHHHHHH..HHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGST.HHHH CS
                       GTP_EFTU  65 ..ketkkylinliDtPGHvdFskevirg..lrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrl.kael 139
                                         +k+ + ++D  GH+ + ++  rg   r  D+++lvv+a++G ++  +e+l + l++++p++ +++K+D + k+ l
  gi|119719055|ref|YP_919550.1| 189 qiYLASKKIVYFVDVGGHERYLRTALRGvmSRLPDYVMLVVAANSGLQVMGREHLGVSLALRIPVFAVVTKVDLVdKSVL 268
                                    7658999999******************9889*******************************************76667 PP

                                    HHHHHHHHHHHHHH............HHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHHS CS
                       GTP_EFTU 140 keiveevkqklsrk............eeklekygekgekevpvvfgSalkgegvktllealvell 192
                                    + +  +  ++l+r+             +++ + + +g + vpv+ +S  +geg++ ll  + +ll
  gi|119719055|ref|YP_919550.1| 269 EATLIDTVETLRRVdrkpvlvkslseVYRIVELMPSG-RVVPVFLVSNTTGEGLE-LLTEFLNLL 331
                                    7777888888866677788877766644444444444.69**************9.555555555 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.19   6.7e+02      18      41 ..     114     135 ..     113     141 .. 0.86
   2 !   30.3   0.1   1.2e-10   4.1e-07       1      73 [.     359     429 ..     359     430 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.19
                                    EEEEEC.TCTTSEEEEEEEEEEEEE CS
                    GTP_EFTU_D2  18 evrilg.ndtskkeivtrissletf 41 
                                    ++ ++g +d +k+   t+++ l t 
  gi|119719055|ref|YP_919550.1| 114 TIAVMGnVDAGKS---TTVGTLCTG 135
                                    7899**9999999...***999875 PP

  == domain 2  score: 30.3 bits;  conditional E-value: 1.2e-10
                                    EEEEEEEEEESEEETTEEEEEEC.TCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEE CS
                    GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilg.ndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtl 73 
                                    G v+ +++++G++++G+ v++++  d s +  ++r++s++ ++     a+ag+ a + +a+++ ++ +++G ++
  gi|119719055|ref|YP_919550.1| 359 GPVVAVSIERGVIREGEDVYLGPlRDASWR--RVRVKSIHINRVVASSARAGEEATLALAGVDFDE-LEKGLVV 429
                                    67999******************8887666..9*********************************.9***876 PP

>> GTP_EFTU_D3  Elongation factor Tu C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   1.2e-07   0.00045       4     108 ..     436     518 ..     433     521 .. 0.70

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.2e-07
                                    EECCEEEEEEESSS..SS-BSTT-EEEEESSS-EEEEEEEEEEECCSSTTSB-BSS-SSCCSTT-CEEEEEE.ECCEEEE CS
                    GTP_EFTU_D3   4 phtkfeAqvyilekerhtpitagYrpvlyirtadvtgkvveLlskldkktekvsekkpefvkpGdnviveve.likpial 82 
                                    ++ ++ A++++l++  +t i +gY+ vl++++    +k++ + ++               +++Gd+ +v+++ l++p  +
  gi|119719055|ref|YP_919550.1| 436 AVWEVAAHIVVLRH--PTTIRTGYQTVLHAHSIRSPVKFTYMSRE--------------PMRTGDSGSVRLRfLNHPWYI 499
                                    566789********..*********************99999222..............234455555555534555666 PP

                                    --TTTHCCCCEEEEECTTCEEEEEEE CS
                    GTP_EFTU_D3  83 ekgseypqlGrFaiReggrTvaaGvv 108
                                    e g+      r  +R+  rT a+G+v
  gi|119719055|ref|YP_919550.1| 500 EPGT------RIILRDS-RTRAIGTV 518
                                    6666......6666553.45555555 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   9.4e-06     0.034       2     113 ..     115     258 ..     114     259 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 9.4e-06
                                    EEEEESTTSSHHHHHHHHHT............STEEESSST..TSSSSEEEEEEE..ETTEE.................. CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltg............ekaivsdkp..gtTrdinegrvk..lkgke.................. 47 
                                    +a++G+  +GKSt + +l+             ++a+ s++   g T  ++ + +   +   e                  
  gi|119719055|ref|YP_919550.1| 115 IAVMGNVDAGKSTTVGTLCTgelddgrgrgmrRVARYSHEIitGRTSSVVVRLLGfdM---Egkpvnwnlpnpldeaqiy 191
                                    89****************9445555544444234455444322555555555444332...1233566666677777777 PP

                                    ......EEEEECGGCSSHHHHHHHHHHHHHHHHC..TSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEE CS
                       MMR_HSR1  48 ......ielvDtpGliegaseekglgkaflalee..adlillvvdaseeklkpldeeleelleeakkplilvln 113
                                          +++vD+ G  +    e+ l+ a++ + +   d ++lvv a+ ++l+ + +e   +    ++p++ v++
  gi|119719055|ref|YP_919550.1| 192 laskkiVYFVDVGG--H----ERYLRTALRGVMSrlPDYVMLVVAAN-SGLQVMGREHLGVSLALRIPVFAVVT 258
                                    7777779*******..4....35566666665444349999999876.44666656655555555666666665 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1      0.11   3.9e+02       1      16 [.     117     132 ..     117     141 .. 0.90
   2 ?    8.5   0.0   0.00042       1.5     151     232 ..     245     325 ..     237     330 .. 0.68

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.11
                     ATP_bind_1   1 vvGpaGsGKttfvgal 16 
                                    v+G + +GK+t vg+l
  gi|119719055|ref|YP_919550.1| 117 VMGNVDAGKSTTVGTL 132
                                    89***********987 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00042
                     ATP_bind_1 151 amlrlelPhvvvlnkfDllkeklekeleffedvealslllekee....ekykklaeaiaelleefalvlrflplssekee 226
                                    + l l++P   v++k+Dl++++    +   + ++++++l   ++     k  +  + i+el+     v  ++ +s+ ++e
  gi|119719055|ref|YP_919550.1| 245 VSLALRIPVFAVVTKVDLVDKS----VLEATLIDTVETLRRVDRkpvlVKSLSEVYRIVELMPSGRVV-PVFLVSNTTGE 319
                                    678999************9933....333333455555555444534655566667777777766666.77788889999 PP

                     ATP_bind_1 227 siedll 232
                                    ++e l+
  gi|119719055|ref|YP_919550.1| 320 GLELLT 325
                                    988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (524 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 3843.15
//
Query:       gi|119719056|ref|YP_919551.1|  [L=387]
Description: hypothetical protein Tpen_0138 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-56  192.5   0.2    2.1e-56  191.5   0.1    1.4  2  DUF72     Protein of unknown function DUF72
  ------ inclusion threshold ------
      0.069   12.6   0.0       0.11   11.9   0.0    1.2  1  SNAP      Soluble NSF attachment protein, SNAP


Domain annotation for each model (and alignments):
>> DUF72  Protein of unknown function DUF72
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.5   0.1   2.3e-60   2.1e-56       9     215 ..      27     240 ..      23     242 .. 0.92
   2 ?   -3.6   0.0       1.1   9.9e+03     171     189 ..     361     379 ..     344     381 .. 0.69

  Alignments for each domain:
  == domain 1  score: 191.5 bits;  conditional E-value: 2.3e-60
                                    C.HHHHHCCT-SEEEE-HHCCSSS-HHHHHHHHCTS-TT-EEEEE--CCCCCS...G..-SCHHHHHHHHHH.CHHH..C CS
                          DUF72   9 e.rLeyYarhfntVEinstFYalpspetvakwaaqtpedFrFavKapraither..n..edaeealerflesalepL..g 81 
                                    + +++yYar fntVEins+FY+l+ ++ ++  a+++pe+F+F++K+++ ith+r  n    +e++l+ fl+s +epL  +
  gi|119719056|ref|YP_919551.1|  27 RgMFTYYARFFNTVEINSSFYSLLGEKFYKGLAEAAPEGFVFSLKMYQGITHKRllNprL-VEKELDFFLKS-IEPLraA 104
                                    4499************************************************97764334.9*********9.****766 PP

                                    T-EEEEEEE--TT--S.HHHHHHHHHHTTTS-...SEEEE--BGGGH.H.HHHHHHHTT-E.EEEE--SSC--------S CS
                          DUF72  82 eklgpllfQlppsfkfdeenlerLeaflaalp...llavEvRhrswf.e.llellrehgva.vvldepkkpklpledvtt 155
                                    +klg++l+Q+pp+    ++++  + +fl+ lp   ++avE+R++sw+ e +++ l+++++a  v+d   +p lp+  + t
  gi|119719056|ref|YP_919551.1| 105 GKLGAVLIQMPPRS---RREIPWFNEFLDMLPsnvRFAVEFRDESWLsEdIFKRLADRNIAyTVVD---EPLLPPVVRIT 178
                                    *************8...66899***********955**********9955***********66669...67999999999 PP

                                    STEEEEEE--S..HHTTB----HHHHHHHHHHHHHHHTCSSEEEEEE-SBCCCHHHHHHHHH CS
                          DUF72 156 adfvyvRlhgr..eeryayrYseeelaewaerikawaaegrevyvffnndaegqaplnaraL 215
                                    adf y+R+hgr  + +y y+Ys eel+ wa++i ++  e + +  +fnn+++g ap+na ++
  gi|119719056|ref|YP_919551.1| 179 ADFGYFRWHGRgeRPWYYYHYSLEELKGWASKISEVIGEVKMLLGYFNNHFRGFAPHNALQM 240
                                    ***********95489*******************************************987 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1.1
                                    B----HHHHHHHHHHHHHH CS
                          DUF72 171 ayrYseeelaewaerikaw 189
                                      +Ys   l+++ae +++w
  gi|119719056|ref|YP_919551.1| 361 PREYSLNVLRDFAENMDEW 379
                                    4578888888888888777 PP

>> SNAP  Soluble NSF attachment protein, SNAP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   1.3e-05      0.11     127     200 ..     251     324 ..     237     326 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.3e-05
                                    TT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTTSS-TTTGGGHHHHHH CS
                           SNAP 127 elgdlekAieaYekAaelyeqeeakalankcllkvAelsaelekyekAieiyekvakkslennllkysvkeyfl 200
                                    + ++le+  ++++ A   ye e ++al++  l k+  l a ++++e+A+ i ++  k +l+  +l+  vk+yf+
  gi|119719056|ref|YP_919551.1| 251 QREKLEEMEKYFASAPRKYERELQEALSSGDLDKALRLLAGERRFERATGISDSEVKYTLQGGVLRGTVKQYFV 324
                                    44678888899**************************************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 2775.44
//
Query:       gi|119719057|ref|YP_919552.1|  [L=192]
Description: hypothetical protein Tpen_0139 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.5e-11   41.9   0.0    2.6e-10   40.5   0.0    1.6  1  DUF429    Protein of unknown function (DUF429)


Domain annotation for each model (and alignments):
>> DUF429  Protein of unknown function (DUF429)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.5   0.0   1.4e-14   2.6e-10       1     201 [.       6     169 ..       6     176 .. 0.79

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 1.4e-14
                         DUF429   1 GvDla..gcrtgwaavaledgrlrlvdv.eaeeivaalaallaaaeeaavvaiDaPiglperetggRaaDraarkllarr 77 
                                    GvDl+   +r+   a+++ed ++++  + +++e+va  +++     +++vv+iDaP++ p ++ + R +D+a+     r 
  gi|119719057|ref|YP_919552.1|   6 GVDLSasRRRKSAYALLYEDLSCKAGFFsGDDELVALAEEY-----SPRVVGIDAPLSFP-KGGRLRGCDKAL----LRL 75 
                                    9****988888888888888788885555555999999999.....9*************.9***********....688 PP

                         DUF429  78 gasvfpvpar.aalaagkglserafgllpklrevdelldarpelrgrvvEvhPeaafvalnggaplakkkktaegraeRr 156
                                    g  vf++    +   +      r+++l ++l+e++            v+Ev+P  +   l g  + +  k   +g+ e  
  gi|119719057|ref|YP_919552.1|  76 GVKVFSPVFSgMLELTS-----RGIKLKEALEERG----------FEVIEVYPGGSQDLL-GIPRKSRNK---KGLLEGL 136
                                    *****999995555555.....**********776..........5799********999.555555555...3655544 PP

                         DUF429 157 ellaraiaellleseakkeklvaadDvlDAvacaltArraarGra 201
                                    + l   +          k +   + D+lDA+ +a t ++ a G+ 
  gi|119719057|ref|YP_919552.1| 137 RSLG--V----------KFEETLQGDILDAITAAFTSYAYAVGEY 169
                                    4444..2..........223344569**********999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1442.63
//
Query:       gi|119719058|ref|YP_919553.1|  [L=171]
Description: deoxycytidine triphosphate deaminase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-15   56.7   0.0    2.9e-15   56.1   0.0    1.2  1  dUTPase   dUTPase
      1e-07   31.1   0.0    2.5e-07   29.8   0.0    1.6  1  DCD       2'-deoxycytidine 5'-triphosphate deaminase (DCD)


Domain annotation for each model (and alignments):
>> dUTPase  dUTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.1   0.0   3.2e-19   2.9e-15      16     119 ..      63     164 ..      55     168 .. 0.88

  Alignments for each domain:
  == domain 1  score: 56.1 bits;  conditional E-value: 3.2e-19
                                    EEEE-SSSEEEETTEEEEEEEEEEEE--TTEEEEEEE-HHHHHHHEEEEEEEEETTBTSEEEEEEEE-SSS.-EEE-TT- CS
                        dUTPase  16 yDlsaakdltvkpgetvlvptdisiklpdglaalilpRSglaakglivvpgvidsdyrGevkvvlfnltkk.dvkikkgd 94 
                                    y + +++ ++++p  +vlv+t  +ik+p ++aa+i  RS +a++g+ ++p++id+ ++G  ++++  ++++ ++ + kg+
  gi|119719058|ref|YP_919553.1|  63 YRVFKTDSFVLQPYMKVLVTTLEYIKMPVDVAAIIGVRSTFARLGVSIPPTLIDAGFEG--QITIEIHGGAfPIVLRKGQ 140
                                    566778999**************************************************..999999***99******** PP

                                    EEEEEEEEEBECGEEEEESSTTTES CS
                        dUTPase  95 RiAqLifariltaeleevetlkate 119
                                    R+A++ f r++  e+ +++   +++
  gi|119719058|ref|YP_919553.1| 141 RFAHVAFYRLEG-EPVPYKGKYQRQ 164
                                    *******99888.666666544444 PP

>> DCD  2'-deoxycytidine 5'-triphosphate deaminase (DCD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.0   2.8e-11   2.5e-07       5     162 ..       2     149 ..       1     164 [. 0.86

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 2.8e-11
                            DCD   5 lpdqeiealieegaikaeepleeeqiqPaslDLrLgkkayrvrasFlpgkgekvaekleelkl...heldLtegavlekg 81 
                                    l+  ei++li+eg++   ep+++e +  + +DLr+g++     a  l +++    e+l+e++l   +++  t++ vl+  
  gi|119719058|ref|YP_919553.1|   2 LSGAEIRRLINEGKL-VIEPFSDEIVRENGVDLRIGEEV----AVLLNNPEPLDPERLREVDLsqyYRVFKTDSFVLQPY 76 
                                    77889*********9.5679*****************96....667777777777888776551115688899******* PP

                            DCD  82 cvYivplleslaLpadlsaaanpksstGRlDvftRvitdkgeefdeveagYkGplyleisprsFsilvrkGsrLsqirfr 161
                                    +  +v  le +++p d++a+   +s+  Rl v +            ++ag++G++ +ei   +F+i++rkG+r + + f 
  gi|119719058|ref|YP_919553.1|  77 MKVLVTTLEYIKMPVDVAAIIGVRSTFARLGVSI--------PPTLIDAGFEGQITIEIHGGAFPIVLRKGQRFAHVAFY 148
                                    *9****************************9854........345699***************************99997 PP

                            DCD 162 r 162
                                    r
  gi|119719058|ref|YP_919553.1| 149 R 149
                                    5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       253  (0.0141112); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1196.79
//
Query:       gi|119719059|ref|YP_919554.1|  [L=236]
Description: HhH-GPD family protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-15   57.5   0.0      2e-15   57.2   0.0    1.2  1  HhH-GPD        HhH-GPD superfamily base excision DNA repair p
    9.1e-06   25.9   6.5    1.7e-05   25.0   6.5    1.5  1  EndIII_4Fe-2S  Iron-sulfur binding domain of endonuclease III


Domain annotation for each model (and alignments):
>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.2   0.0   2.2e-19     2e-15       1     102 [.      48     185 ..      48     191 .. 0.94

  Alignments for each domain:
  == domain 1  score: 57.2 bits;  conditional E-value: 2.2e-19
                                    HHHHHHTTS-HHHHHHHHHHHHHHHSHCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH.............. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............. RF
                        HhH-GPD   1 vsailsqqtsderanriierlferfgfptpedladadeekLrelirelGfyrrKakyikelArilv.............. 66 
                                    v++i+sq+t+ +++ +++++l er+g ++ e++ +a  ++L+e+ir++G+ ++Kak ik++A  l               
  gi|119719059|ref|YP_919554.1|  48 VATIISQNTNENNTLKAFASLEERVG-VECEKIRKAGLSELAEAIRPAGLQEQKAKAIKQVASLLYekygcdigkllsrg 126
                                    789**********************7.9**************************************************** PP

                                    ..........................S-SSS--TTSHHHHHHHHHHTTSSSSTTHHHHHHHH CS
                                    ..........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        HhH-GPD  67 ..........................gkpdvlivvDvhvrrilkrlrsikekktkkkvekkl 102
                                                              g+  ++ + D+hvrr+  rl+++++  +++ ++k l
  gi|119719059|ref|YP_919554.1| 127 veevirelkqiegigdktidvllanyGY--PVLPIDTHVRRVSVRLGLARPG-SYRAMQKSL 185
                                    ***********************97776..55666**************995.888888776 PP

>> EndIII_4Fe-2S  Iron-sulfur binding domain of endonuclease III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   6.5   1.9e-09   1.7e-05       1      17 []     209     225 ..     209     225 .. 0.99

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.9e-09
                  EndIII_4Fe-2S   1 CTARkPkCeaCPLaDlC 17 
                                    C A++P C++CPL+DlC
  gi|119719059|ref|YP_919554.1| 209 CRAKNPLCDECPLSDLC 225
                                    ***************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1707.29
//
Query:       gi|119719060|ref|YP_919555.1|  [L=251]
Description: stationary-phase survival protein SurE [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-35  121.9   0.0    3.5e-35  121.5   0.0    1.1  1  SurE      Survival protein SurE


Domain annotation for each model (and alignments):
>> SurE  Survival protein SurE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.5   0.0     2e-39   3.5e-35       1     181 [.       3     177 ..       3     185 .. 0.85

  Alignments for each domain:
  == domain 1  score: 121.5 bits;  conditional E-value: 2e-39
                                    EEEE-SS-TT-HHHHHHHHHHTTTTSEEEEEEESSS-TTCTTS--SSSEEEEEEEECSTTTCEEEESS-HHHHHHHHHHT CS
                           SurE   1 iLltNDDGieapgiralvealaaaghevvvvaPdserSgigkaltleeplrveseeeeeeeeeyavsGtPadcvklalee 80 
                                    iL++NDDG+  +g+ al++  ++ gh v ++  + +rSg++k+++++ + +     + ++ e ++++++Pa++v la++ 
  gi|119719060|ref|YP_919555.1|   3 ILVVNDDGV-GDGLLALARVAERLGHSVFLATTHDQRSGYSKSVSFKATYTPA---KIGGYEGIVTNSSPASAVLLAFKV 78 
                                    8********.79********************************877776533...2378999999************77 PP

                                    TTTTS.SSEEEEEEEES---GG.GGGG-HHHHHHHHHHHTTSEEEEEEEESSS..SS-SSS---HHHHHHHHHHHHTTET CS
                           SurE  81 llkekkpdlVvSGiNhGaNlgt.dvlySGTvgAaleaalegipaiAvSlaskk..eeekkeedtfeaaakvaaklvekli 157
                                    + ke   d+V+SG+N G+Nlg  d+l+SGTvgA+leaal+g+p+ AvSl   +  e ++ + +++e+aa++a++l+e+l 
  gi|119719060|ref|YP_919555.1|  79 FGKE--FDFVLSGVNMGPNLGLwDILSSGTVGAVLEAALHGVPGAAVSLVAGSheEYSSLTYEDYERAARLAVDLLERL- 155
                                    7754..6**************7366************************987655444455666888888888888877. PP

                                    TS-...SS-EEEEEEESS.GCG-S CS
                           SurE 158 eklllekvellnvNvPeleeeeik 181
                                       + +  e+ln+NvP  ++ ++k
  gi|119719060|ref|YP_919555.1| 156 --EWRPPCEVLNINVPLRTNGSVK 177
                                    ..6799**********77777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 1584.68
//
Query:       gi|119719061|ref|YP_919556.1|  [L=452]
Description: FAD-dependent pyridine nucleotide-disulphide oxidoreductase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.1e-64  216.1   0.9    7.6e-64  215.8   0.9    1.1  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    5.1e-24   84.6   2.0    5.1e-18   65.4   0.5    3.4  3  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    2.2e-16   60.1   0.0    9.8e-16   58.0   0.0    2.1  1  Pyr_redox_dim   Pyridine nucleotide-disulphide oxidoreductase
    8.6e-15   54.8   0.1    2.8e-11   43.2   0.0    2.2  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    1.6e-10   41.1   8.5      0.043   13.4   0.7    4.2  4  DAO             FAD dependent oxidoreductase
    3.1e-10   39.3   2.1    0.00043   19.1   0.1    4.1  4  HI0933_like     HI0933-like protein
    1.4e-09   38.0   1.6    0.00038   20.6   0.0    3.0  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    2.4e-08   33.5   0.2      9e-07   28.4   0.0    2.3  2  Thi4            Thi4 family
    1.8e-07   30.7   0.0    8.3e-05   21.9   0.0    2.6  3  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
    1.4e-06   28.4   2.3      0.018   15.0   0.0    3.7  4  NAD_binding_9   FAD-NAD(P)-binding
    5.4e-06   25.7   0.7     0.0014   17.8   0.0    2.4  2  Lycopene_cycl   Lycopene cyclase protein
    8.1e-06   25.2   6.1    0.00091   18.4   0.0    3.6  4  FAD_binding_2   FAD binding domain
    8.7e-06   25.1   0.5      0.049   12.7   0.1    2.5  2  GIDA            Glucose inhibited division protein A
    3.2e-05   23.3   1.1       0.09   12.0   0.0    2.4  2  FAD_binding_3   FAD binding domain
    8.1e-05   22.0   1.1       0.21   10.9   0.1    2.4  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
    0.00092   18.7   3.6        0.1   11.9   0.1    3.0  3  FAD_oxidored    FAD dependent oxidoreductase
     0.0016   18.8   0.5       0.15   12.5   0.2    2.4  2  NAD_binding_7   Putative NAD(P)-binding
     0.0055   16.6   0.5      0.017   15.0   0.1    1.9  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
  ------ inclusion threshold ------
       0.01   14.7   0.9       0.13   11.1   0.0    2.5  3  Trp_halogenase  Tryptophan halogenase
      0.024   13.2   0.0      0.035   12.6   0.0    1.2  1  Mqo             Malate:quinone oxidoreductase (Mqo)
       0.03   13.7   0.1      0.078   12.3   0.1    1.6  2  ThiF            ThiF family
      0.032   14.5   0.4        1.1    9.5   0.3    2.5  2  TrkA_N          TrkA-N domain
      0.048   13.2   0.1      0.087   12.4   0.1    1.5  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
      0.073   13.2   0.0       0.51   10.4   0.0    2.3  2  tRNA_edit       Aminoacyl-tRNA editing domain
      0.095   13.5   0.3       0.84   10.5   0.1    2.5  2  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  215.8   0.9   1.1e-66   7.6e-64       2     294 .]      10     309 ..       9     309 .. 0.93

  Alignments for each domain:
  == domain 1  score: 215.8 bits;  conditional E-value: 1.1e-66
                                    SEEEE--SHHHHHHHHHHHH..HTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH....HHHHCHHHHCCCCHCCTC CS
                                    xxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2   2 dvvviGgGpAGlaaaltlaq..agakvtlvelegtclnggcllskallgvaedaeias....evvkklnqgielllgeev 75 
                                    dv+viGgGpAG++aa ++++   +++v+++e+ g++ +  c l++ l g  +  e +     + v   + gie+++++ev
  gi|119719061|ref|YP_919556.1|  10 DVAVIGGGPAGMTAASRIKRlkPELRVAVFERSGYVSYAPCGLPYYLGGLVDSLEHLVhypvR-VFTEERGIEVYTRTEV 88 
                                    8*******************755******************************9988899953.5667889********* PP

                                    EEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-T.SEEEEES-SHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
                    Pyr_redox_2  76 vkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllp.krivvvGgGyiG 154
                                    v++  g   +  ++   + e++++ +kl++AtG++p+ ++++Gv  ++++ +r l++ e+ ++ l +  r++vvGgGyiG
  gi|119719061|ref|YP_919556.1|  89 VEVGDGY--LRARD--ASGERTYEWGKLLIATGARPKVPPVEGVDLEGVFTLRVLEDGEKARRYLEKaTRVAVVGGGYIG 164
                                    ***5444..55543..45679***********************77777888*********99999889*********** PP

                                    HHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 155 vElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgngeklevvledgeeidadlvvva 234
                                    +E+A  l ++gk v l e +d++ +a+d++++  +e++l ++Gve++lg+  k i g+++ +e  ++++ e+++d v++a
  gi|119719061|ref|YP_919556.1| 165 LEVAENLVRAGKTVLLFEVLDHVFPAVDPDMALLVEKELARNGVELHLGEGLKGIHGRDR-VESLETTKGEYKVDAVFIA 243
                                    ***********************************************************8.99888888889******** PP

                                    S-EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGC.......TECCSS--HHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 235 vGvrpstelleeklglelderggivvdeflrtnvpgiyaiGDva.......ggkggpelaqaAvqqG 294
                                    +Gv p+t+l+ eklg++  ++g++ vd+++rtnv+++ya+GDva       g+ + + la++A ++G
  gi|119719061|ref|YP_919556.1| 244 TGVAPETRLA-EKLGVKKGSTGALSVDKSMRTNVDDVYAAGDVAealnlvtGKNDWFPLAPVANKMG 309
                                    **********.****************************************999*********9987 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   0.00032      0.23       2      33 ..      11      44 ..      10      49 .. 0.90
   2 ?    4.6   0.0     0.067        48      51      67 ..      76      92 ..      70      98 .. 0.88
   3 !   65.4   0.5   7.1e-21   5.1e-18       1      79 [.     154     231 ..     154     234 .. 0.96

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00032
                                   EEEECSSHHHHHHHHHHHHTT..SEEEEEESSSS CS
                      Pyr_redox  2 vvvvGgGyiglElAgalaelg..kkVtvversdk 33
                                   v+v+GgG  g+ +A+ +++l+   +V v+ers  
  gi|119719061|ref|YP_919556.1| 11 VAVIGGGPAGMTAASRIKRLKpeLRVAVFERSGY 44
                                   89******************98789999999865 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.067
                                   HHTTEEEECSEEEEEEE CS
                      Pyr_redox 51 ekngievllntkveeie 67
                                   e++giev++ t+v+e+ 
  gi|119719061|ref|YP_919556.1| 76 EERGIEVYTRTEVVEVG 92
                                   789***********985 PP

  == domain 3  score: 65.4 bits;  conditional E-value: 7.1e-21
                                    EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEEEE CS
                      Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedgvesvklk 79 
                                    +v+vvGgGyiglE+A++l + gk V ++e  d++ ++ D++++ +++++l +ng+e++l++ ++ i+g ++ ves++++
  gi|119719061|ref|YP_919556.1| 154 RVAVVGGGYIGLEVAENLVRAGKTVLLFEVLDHVFPAVDPDMALLVEKELARNGVELHLGEGLKGIHGRDR-VESLETT 231
                                    79*******************************************************************99.9988875 PP

>> Pyr_redox_dim  Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.0   0.0   1.4e-18   9.8e-16       4     104 ..     332     433 ..     329     437 .. 0.93

  Alignments for each domain:
  == domain 1  score: 58.0 bits;  conditional E-value: 1.4e-18
                                    EEESSSEEEEEES-HHHHHHHHSGEEEEEEEEECGHHHCHTTH.TEEEEEEEEETTTTBEEEEEEEC.TTHHHHHHHHHH CS
                  Pyr_redox_dim   4 vvftdpevasvGlteeeAkaagieikvgkfpfkangralayae.tkgfvKlvadaktgkvlGahivG.pgageliqelav 81 
                                    ++++ +ev+  Glt + A+++g  ++ +++ ++an++a +y+  + + vKl+ad++tg++lG +i+G +g+  +++ lav
  gi|119719061|ref|YP_919556.1| 332 TKVFGLEVGRAGLTTARAQQEG--FDPVSVMINANSKASYYPGsSAMSVKLIADRRTGQLLGGQIIGgDGVLARLNSLAV 409
                                    678899****************..99999**************99999******************9788889******* PP

                                    HHHTTSBHHH.HHTSBSSSSSTGG CS
                  Pyr_redox_dim  82 aikagltved.ladtihihPtlse 104
                                    ++++++ ved + ++++++P++s 
  gi|119719061|ref|YP_919556.1| 410 LLSFRARVEDaFFSDLGYAPPFSP 433
                                    *********55***********94 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0   0.00071      0.51       2      29 ..      13      41 ..      12      47 .. 0.77
   2 !   43.2   0.0   3.9e-14   2.8e-11      88     305 .]      72     283 ..      62     283 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00071
                    Pyr_redox_3  2 IiGaGPaGlaaaielkkagl.edylilEk 29
                                   +iG+GPaG++aa  +k+++   ++ + E+
  gi|119719061|ref|YP_919556.1| 13 VIGGGPAGMTAASRIKRLKPeLRVAVFER 41
                                   8*************998865235556665 PP

  == domain 2  score: 43.2 bits;  conditional E-value: 3.9e-14
                    Pyr_redox_3  88 revaksfelpiklfeeVesvkkedegfevetsketyeAkkviiAtGefdkPnklnipGeeklvkhyskv....kefhky. 162
                                    r  +++  +++ + +eV +v       +  + ++tye  k++iAtG   +P+++ ++G +   + +  v    ++++ y 
  gi|119719061|ref|YP_919556.1|  72 RVFTEERGIEVYTRTEVVEVGDGYLRARDASGERTYEWGKLLIATGA--RPKVPPVEGVDLEGVFTLRVledgEKARRYl 149
                                    4456677888999999998888888888778888************9..**********964443333222224555552 PP

                    Pyr_redox_3 163 .agqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfnaevkeikek 241
                                     + ++v+V+Gg+  + ++A +lvr+g++V ++   ++       +   + pd+   +e+ ++++ ++++  + +k i+ +
  gi|119719061|ref|YP_919556.1| 150 eKATRVAVVGGGYIGLEVAENLVRAGKTVLLFEVLDH-------VFPAVDPDMALLVEKELARNGVELHLGEGLKGIHGR 222
                                    2489***************************998874.......445678888877777777777**************9 PP

                    Pyr_redox_3 242 eeeykvktedgkkvevkddvvlatGykpdlsflkkslfeldedgrpvlteeteetnvpglflaG 305
                                    ++   ++t++g + +v d v++atG  p++++ +k ++++ ++g   +++  + tnv++++ aG
  gi|119719061|ref|YP_919556.1| 223 DRVESLETTKG-EYKV-DAVFIATGVAPETRLAEKLGVKKGSTGALSVDK-SMRTNVDDVYAAG 283
                                    99889999997.5565.888999************999998999888875.799********99 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.1     8e-05     0.058       1      29 [.      10      42 ..      10      52 .. 0.87
   2 ?    4.1   0.0      0.04        29     156     203 ..      75     119 ..      48     135 .. 0.71
   3 !   13.4   0.7     6e-05     0.043       1      27 [.     154     182 ..     154     185 .. 0.93
   4 !   13.0   0.0     8e-05     0.057     152     204 ..     199     248 ..     190     273 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8e-05
                                   EEEEECTSHHHHHHHHHHHHTT....EEEEESS CS
                            DAO  1 dvviiGGGiiGlstAyeLarrg....Vtllekg 29
                                   dv++iGGG +G+++A    r +    V+++e++
  gi|119719061|ref|YP_919556.1| 10 DVAVIGGGPAGMTAASRIKRLKpelrVAVFERS 42
                                   8*****************65444899*****97 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.04
                                    HHHTT-EEEESECEEEEEEEETCEEEEE..EECTEEE.EEEEEEEE--GGG CS
                            DAO 156 aealGveilegtevtgleeedgkvwgve..rttpgen.daadavVnaaGaw 203
                                     e++G+e++++tev+++      + g    r+++ge+  +  ++ +a+Ga 
  gi|119719061|ref|YP_919556.1|  75 TEERGIEVYTRTEVVEV------GDGYLraRDASGERtYEWGKLLIATGAR 119
                                    4899************9......3444445555566534545599999986 PP

  == domain 3  score: 13.4 bits;  conditional E-value: 6e-05
                                    EEEEECTSHHHHHHHHHHHHTT..EEEEE CS
                            DAO   1 dvviiGGGiiGlstAyeLarrg..Vtlle 27 
                                    +v+++GGG+iGl +A  L r+g  V+l+e
  gi|119719061|ref|YP_919556.1| 154 RVAVVGGGYIGLEVAENLVRAGktVLLFE 182
                                    59*******************99999987 PP

  == domain 4  score: 13.0 bits;  conditional E-value: 8e-05
                                    HHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEEEEEEEEEE--GGGH CS
                            DAO 152 laraaealGveilegtevtgleeedgkvwgverttpgendaadavVnaaGaws 204
                                    + ++++++Gve+++g+  +g+ + +++v  + +tt+ge  ++dav +a+G+  
  gi|119719061|ref|YP_919556.1| 199 VEKELARNGVELHLGEGLKGI-HGRDRVESL-ETTKGEY-KVDAVFIATGVAP 248
                                    457799**************9.333466777.6666775.68********764 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.1   5.9e-07   0.00043       2      32 ..      10      42 ..       9      46 .. 0.88
   2 ?    2.2   0.0     0.082        59     120     164 ..      76     118 ..      71     127 .. 0.85
   3 !    7.7   0.2    0.0017       1.2       2      31 ..     154     183 ..     153     187 .. 0.92
   4 !    6.9   0.0     0.003       2.2     114     164 ..     198     246 ..     182     259 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 5.9e-07
                                   SEEEE--SHHHHHHHHHH..HHTT--EEEE-SS CS
                    HI0933_like  2 dviviGgGaAGlmaAisa..akrgkrVllleka 32
                                   dv+viGgG+AG+ aA ++   k + rV+++e+ 
  gi|119719061|ref|YP_919556.1| 10 DVAVIGGGPAGMTAASRIkrLKPELRVAVFERS 42
                                   89*************9996568999*****986 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.082
                                    HHHT-EEE-S--EEEEECETTE.EEEEE..TTEEEEESEEEE---- CS
                    HI0933_like 120 keagvklrletevksvekeedgkfrvkt.kseeeleadklvlAtGG 164
                                    +e+g++++++tev +v    dg +r +  ++e+++e  kl++AtG 
  gi|119719061|ref|YP_919556.1|  76 EERGIEVYTRTEVVEV---GDGYLRARDaSGERTYEWGKLLIATGA 118
                                    689*************...55556666657999***********97 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0017
                                    SEEEE--SHHHHHHHHHHHHTT--EEEE-S CS
                    HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllek 31 
                                    +v+v+GgG  Gl  A+++ ++gk Vll+e 
  gi|119719061|ref|YP_919556.1| 154 RVAVVGGGYIGLEVAENLVRAGKTVLLFEV 183
                                    69*************************995 PP

  == domain 4  score: 6.9 bits;  conditional E-value: 0.003
                                    HHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE---- CS
                    HI0933_like 114 allkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGG 164
                                    + +kel ++gv+l+l + +k++ + +d++ +++t +++e++ d++ +AtG 
  gi|119719061|ref|YP_919556.1| 198 LVEKELARNGVELHLGEGLKGI-HGRDRVESLET-TKGEYKVDAVFIATGV 246
                                    56899*****************.55777799999.9*************95 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   5.3e-07   0.00038       1      30 [.      13      44 ..      13      52 .. 0.90
   2 !   15.3   0.2   2.4e-05     0.017       1      30 [.     157     186 ..     157     188 .. 0.94

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 5.3e-07
                                   EE--SHHHHHHHHHHHCC..TEEEEEE-SSSS CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLaka..gfdvlllekrdr 30
                                   ++G+G +G++aA+++++    ++v ++e++ +
  gi|119719061|ref|YP_919556.1| 13 VIGGGPAGMTAASRIKRLkpELRVAVFERSGY 44
                                   8***************966799******9765 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 2.4e-05
                                    EE--SHHHHHHHHHHHCCTEEEEEE-SSSS CS
                  NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdr 30 
                                    +vG+G  Gl  A  L +ag+ vll+e  d+
  gi|119719061|ref|YP_919556.1| 157 VVGGGYIGLEVAENLVRAGKTVLLFEVLDH 186
                                    8*************************8887 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0   1.3e-09     9e-07      17      95 ..       8      93 ..       2     100 .. 0.80
   2 ?    2.7   0.0     0.088        63      18      48 ..     153     182 ..     142     186 .. 0.82

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 1.3e-09
                                   EEEEEEE--SHHHHHHHHHHHHC.TTS-EEEEESS....SS--T.TTTTTSTTBS.EEEEETTTHHHHHHTT---EEESSEE CS
                           Thi4 17 esDvvivGaGssGLtaayylakk.pdlkvailers....vspGG.GawlGGqlfs.aivvrkpakelLdelgikyedegdyv 91
                                   + Dv+++G+G++G+taa  + +  p+l+va++ers     +p G   +lGG + s + +v+ p + + +e gi+   + + v
  gi|119719061|ref|YP_919556.1|  8 KVDVAVIGGGPAGMTAASRIKRLkPELRVAVFERSgyvsYAPCGlPYYLGGLVDSlEHLVHYPVRVFTEERGIEVYTRTEVV 89
                                   57******************9988*********9755223444425789998866356889999999999999988888888 PP

                                   EESE CS
                           Thi4 92 vvkd 95
                                    v d
  gi|119719061|ref|YP_919556.1| 90 EVGD 93
                                   7766 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.088
                                    EEEEEE--SHHHHHHHHHHHHCTTS-EEEEE CS
                           Thi4  18 sDvvivGaGssGLtaayylakkpdlkvaile 48 
                                    + v++vG+G  GL  a  l ++ +  v+++e
  gi|119719061|ref|YP_919556.1| 153 TRVAVVGGGYIGLEVAENLVRA-GKTVLLFE 182
                                    5699***************998.76777766 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.0    0.0083         6       2      36 ..       8      42 ..       7      49 .. 0.91
   2 !   21.9   0.0   1.2e-07   8.3e-05     137     216 ..      98     177 ..      60     190 .. 0.79
   3 ?   -2.2   0.0       2.5   1.8e+03     325     339 ..     231     245 ..     224     247 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0083
                    K_oxygenase  2 ilDligiGiGpsnLsLailleevkkelkalflerq 36
                                    +D++ iG Gp+ ++ a +++  k el++ ++er+
  gi|119719061|ref|YP_919556.1|  8 KVDVAVIGGGPAGMTAASRIKRLKPELRVAVFERS 42
                                   589******************************86 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 1.2e-07
                    K_oxygenase 137 skdaegeeeelearnlvlgvGtepkiPevleklegkervvHsseylerkee....llakkriaVvGsGqSaaeifedllr 212
                                     +da+g e+++e  +l++++G +pk+P+v   ++  e v+   ++le+ e+    l+++ r+aVvG+G  + e++e+l+r
  gi|119719061|ref|YP_919556.1|  98 ARDASG-ERTYEWGKLLIATGARPKVPPVEG-VDL-EGVFT-LRVLEDGEKarryLEKATRVAVVGGGYIGLEVAENLVR 173
                                    455677.5899999*************9854.442.44443.344444333355699*********************99 PP

                    K_oxygenase 213 rqkk 216
                                      k+
  gi|119719061|ref|YP_919556.1| 174 AGKT 177
                                    8664 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 2.5
                    K_oxygenase 325 eeetlevdavvlATG 339
                                    ++ + +vdav++ATG
  gi|119719061|ref|YP_919556.1| 231 TKGEYKVDAVFIATG 245
                                    5567899*******9 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   2.6e-05     0.018       1      37 [.      12      45 ..      12      56 .. 0.91
   2 ?   -1.8   0.0       3.9   2.8e+03     125     154 ..      86     117 ..      63     118 .. 0.72
   3 !    6.7   0.2    0.0093       6.6       1      23 [.     156     176 ..     156     191 .. 0.81
   4 ?    4.1   0.0     0.058        41     130     155 ..     221     246 ..     197     247 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.6e-05
                  NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsepg 37
                                   a++G+Gp+G++++ r+ +    k +l++ +f++s++ 
  gi|119719061|ref|YP_919556.1| 12 AVIGGGPAGMTAASRIKRL---KPELRVAVFERSGYV 45
                                   89**************999...6**********9875 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.9
                  NAD_binding_9 125 vdleeradgq.avlladg.aslaadaVvLAlG 154
                                    +++ e +dg+ + + a+g ++++  ++ +A+G
  gi|119719061|ref|YP_919556.1|  86 TEVVEVGDGYlRARDASGeRTYEWGKLLIATG 117
                                    34455567765677777745679999999998 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0093
                  NAD_binding_9   1 aivGaGprGlavlerLlarakkk 23 
                                    a+vG+G  Gl v+e+L++    k
  gi|119719061|ref|YP_919556.1| 156 AVVGGGYIGLEVAENLVRAG--K 176
                                    89***************985..4 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.058
                  NAD_binding_9 130 radgqavlladgaslaadaVvLAlGh 155
                                     +d+++ l++++ ++++daV++A+G 
  gi|119719061|ref|YP_919556.1| 221 GRDRVESLETTKGEYKVDAVFIATGV 246
                                    4566788899999***********95 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.9e-06    0.0014       1      36 [.      10      45 ..      10      67 .. 0.92
   2 !    6.0   0.1    0.0073       5.3       2      31 ..     155     182 ..     154     191 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.9e-06
                  Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieaspsl 36
                                   Dv+viG+GpAg+  A r+ + kp+l+v + e s  +
  gi|119719061|ref|YP_919556.1| 10 DVAVIGGGPAGMTAASRIKRLKPELRVAVFERSGYV 45
                                   9***************************99987655 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0073
                  Lycopene_cycl   2 vvviGaGpAglslAarlteakpglkvvlie 31 
                                    v+v+G+G  gl +A++l   ++g  v+l e
  gi|119719061|ref|YP_919556.1| 155 VAVVGGGYIGLEVAENL--VRAGKTVLLFE 182
                                    89***************..55555566555 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.3e-06   0.00091       1      34 [.      10      45 ..      10      50 .. 0.87
   2 ?    4.0   0.4     0.029        21       2      29 ..     155     182 ..     154     187 .. 0.93
   3 ?    4.0   0.0      0.03        22     372     402 ..     262     286 ..     210     297 .. 0.84
   4 ?   -3.3   0.0         5   3.6e+03     245     274 ..     324     353 ..     306     369 .. 0.58

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.3e-06
                                   SEEEE--SHHHHHHHHHHHH..TTT-EEEEESSSGG CS
                  FAD_binding_2  1 DviViGsGlAGLaAAleaae..aGlkvavvekeqef 34
                                   Dv ViG+G AG++AA ++++    l+vav e  +++
  gi|119719061|ref|YP_919556.1| 10 DVAVIGGGPAGMTAASRIKRlkPELRVAVFERSGYV 45
                                   9*****************9974566****9998775 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.029
                                    EEEE--SHHHHHHHHHHHHTTT-EEEEE CS
                  FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavve 29 
                                    v V+G+G  GL  A ++ +aG++v++ e
  gi|119719061|ref|YP_919556.1| 155 VAVVGGGYIGLEVAENLVRAGKTVLLFE 182
                                    89**********************9987 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.03
                                    ES-EEEBETTSBESTTEEESSBTEEE-STCE CS
                  FAD_binding_2 372 tmgGvetdengrvldadgqpipGLYAaGeva 402
                                    + g + +d ++r+      ++++ YAaG va
  gi|119719061|ref|YP_919556.1| 262 STGALSVDKSMRT------NVDDVYAAGDVA 286
                                    5556788999999......***********9 PP

  == domain 4  score: -3.3 bits;  conditional E-value: 5
                                    TT-EEEEEEEET....TTTBB--THHHHTT CS
                  FAD_binding_2 245 meevqfhPtslvpirdgsgiLitealrgeG 274
                                    + +v + +t +++++ g ++L t ++++eG
  gi|119719061|ref|YP_919556.1| 324 PGAVGTSITKVFGLEVGRAGLTTARAQQEG 353
                                    445556666666666666666666666666 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.1   6.9e-05     0.049       1      22 [.      10      31 ..      10      51 .. 0.80
   2 !   10.1   0.1   0.00041       0.3       2      30 ..     155     182 ..     154     200 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.9e-05
                                   CEEEE-SSHHHHHHHHHHHHTT CS
                           GIDA  1 dviViGgGhAGceAAlaaarlG 22
                                   dv ViGgG AG+ AA  ++rl 
  gi|119719061|ref|YP_919556.1| 10 DVAVIGGGPAGMTAASRIKRLK 31
                                   79***************99975 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00041
                                    EEEE-SSHHHHHHHHHHHHTT--EEEEES CS
                           GIDA   2 viViGgGhAGceAAlaaarlGakvlLith 30 
                                    v V+GgG  G+e A ++ r+G  vlL+ +
  gi|119719061|ref|YP_919556.1| 155 VAVVGGGYIGLEVAENLVRAGKTVLLF-E 182
                                    89*******************999998.3 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   0.00013      0.09       1      18 [.       8      25 ..       8      41 .. 0.90
   2 !    9.8   0.3   0.00059      0.42       2      31 ..     153     182 ..     152     190 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00013
                                   EEEEEEE--SHHHHHHHH CS
                  FAD_binding_3  1 etdVlIVGaGpaGlmlal 18
                                   ++dV+++G+GpaG+++a+
  gi|119719061|ref|YP_919556.1|  8 KVDVAVIGGGPAGMTAAS 25
                                   589*************97 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00059
                                    EEEEEE--SHHHHHHHHHHHHTTHHEEEEE CS
                  FAD_binding_3   2 tdVlIVGaGpaGlmlallLseaGvrvvlve 31 
                                    t V++VG+G  Gl  a  L +aG  v+l e
  gi|119719061|ref|YP_919556.1| 153 TRVAVVGGGYIGLEVAENLVRAGKTVLLFE 182
                                    78**********************999876 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.1   0.00029      0.21      26      54 ..       6      34 ..       2      43 .. 0.83
   2 !    9.4   0.1   0.00081      0.58      28      62 ..     152     186 ..     148     213 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00029
                                   B---EEEEESTSHHHHHHHHHHHHTT-EE CS
                    AlaDh_PNT_C 26 vepakvlviGgGvaGlqAiatakglgakV 54
                                   ve+  v viGgG aG+ A++  k+l+ + 
  gi|119719061|ref|YP_919556.1|  6 VEKVDVAVIGGGPAGMTAASRIKRLKPEL 34
                                   56889****************99998654 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00081
                                    --EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHH CS
                    AlaDh_PNT_C  28 pakvlviGgGvaGlqAiatakglgakVtvlDvrpa 62 
                                    + +v v+GgG  Gl+ +++ ++ g +V +++v  +
  gi|119719061|ref|YP_919556.1| 152 ATRVAVVGGGYIGLEVAENLVRAGKTVLLFEVLDH 186
                                    689************************99998655 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.1   0.00015       0.1       1      21 [.      10      30 ..      10      45 .. 0.74
   2 ?    5.0   0.5     0.018        13       2      31 ..     155     184 ..     154     187 .. 0.91
   3 ?    1.1   0.0      0.28     2e+02      84     136 ..     191     239 ..     184     258 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00015
                   FAD_oxidored  1 DvvVvGGgpaGvaAAiaAara 21
                                   Dv V+GGgpaG++AA   +r 
  gi|119719061|ref|YP_919556.1| 10 DVAVIGGGPAGMTAASRIKRL 30
                                   9**************877765 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.018
                   FAD_oxidored   2 vvVvGGgpaGvaAAiaAaraGakvlLveer 31 
                                    v VvGGg  G+  A    raG++vlL e  
  gi|119719061|ref|YP_919556.1| 155 VAVVGGGYIGLEVAENLVRAGKTVLLFEVL 184
                                    89************************9865 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.28
                   FAD_oxidored  84 fepevakavleemlaeagvtvllntrlvevekegkriesvtveskegrktirA 136
                                    ++p++a  v +e+ ++ gv++ l++ l++++ ++ r+es+++   +g++++ A
  gi|119719061|ref|YP_919556.1| 191 VDPDMALLVEKELARN-GVELHLGEGLKGIHGRD-RVESLETT--KGEYKVDA 239
                                    7888888888888777.**************997.9***9995..35666665 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.077        56       6      35 ..       7      38 ..       4      69 .. 0.76
   2 !   12.5   0.2   0.00021      0.15       8      41 ..     153     196 ..     150     264 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.077
                  NAD_binding_7  6 kgkkvlvvGgGevAa...rkvrklleagakvtv 35
                                   ++  v v+GgG+ ++   +++++l ++  +v v
  gi|119719061|ref|YP_919556.1|  7 EKVDVAVIGGGPAGMtaaSRIKRLKPE-LRVAV 38
                                   566799****99765111666666665.55555 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00021
                  NAD_binding_7   8 kkvlvvGgGevAarkvrklleagakvtv..........vapevk 41 
                                     +v vvGgG ++++ +++l++ag++v +          v+p+++
  gi|119719061|ref|YP_919556.1| 153 TRVAVVGGGYIGLEVAENLVRAGKTVLLfevldhvfpaVDPDMA 196
                                    689***********************997766665555555543 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       1.9   1.3e+03       2      19 ..      11      28 ..      10      43 .. 0.72
   2 !   15.0   0.1   2.4e-05     0.017       2      33 ..     155     186 ..     154     233 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.9
                                   EEEE--SCCHHHHHHHHH CS
                        3HCDH_N  2 vaviGaGtmGagiaavfa 19
                                   vaviG G  G   a+ + 
  gi|119719061|ref|YP_919556.1| 11 VAVIGGGPAGMTAASRIK 28
                                   9******99998887654 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 2.4e-05
                                    EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HH CS
                        3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdisee 33 
                                    vav+G G +G ++a+ +++ag +V l+++ ++
  gi|119719061|ref|YP_919556.1| 155 VAVVGGGYIGLEVAENLVRAGKTVLLFEVLDH 186
                                    9*************************998555 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00017      0.13       1      32 [.      10      40 ..      10      47 .. 0.86
   2 ?    1.2   0.1      0.18   1.3e+02       1      29 [.     154     179 ..     154     191 .. 0.83
   3 ?   -1.8   0.0       1.5   1.1e+03     181     209 ..     219     246 ..     195     312 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00017
                                   EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE CS
                 Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlve 32
                                   ++ ++GGG+aG +aA+ +++   + l+v + e
  gi|119719061|ref|YP_919556.1| 10 DVAVIGGGPAGMTAASRIKRLKPE-LRVAVFE 40
                                   589***************999854.8888877 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.18
                                    EEEEE--SHHHHHHHHHHHHHTTTSSEEE CS
                 Trp_halogenase   1 kivivGGGtaGwlaAaalakalkgklevt 29 
                                    ++ +vGGG  G  +A  l +a+k    v+
  gi|119719061|ref|YP_919556.1| 154 RVAVVGGGYIGLEVAENLVRAGKT---VL 179
                                    689*****************9954...44 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1.5
                                    E-TTS-EEEEEETTS-EEE-SEEEE-SGG CS
                 Trp_halogenase 181 ldedgrveslrledgreveadlfiDcsGf 209
                                    ++ ++rvesl++++g+ +++d +  ++G 
  gi|119719061|ref|YP_919556.1| 219 IHGRDRVESLETTKGE-YKVDAVFIATGV 246
                                    6778999999998887.555554445554 PP

>> Mqo  Malate:quinone oxidoreductase (Mqo)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   4.9e-05     0.035       2      37 ..       8      43 ..       7      48 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.9e-05
                            Mqo  2 kvdvvliGaGimsatlgvllkelepelsievlerld 37
                                   kvdv +iG+G    t ++ +k+l+pel+++v+er  
  gi|119719061|ref|YP_919556.1|  8 KVDVAVIGGGPAGMTAASRIKRLKPELRVAVFERSG 43
                                   79*******************************975 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       4.3   3.1e+03      75      94 ..      21      40 ..      10      42 .. 0.82
   2 ?   12.3   0.1   0.00011     0.078      18      42 ..     151     176 ..     135     186 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 4.3
                                   HHHHHHHHHT-TTSEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxx RF
                           ThiF 75 evaaealqeinpdveveavt 94
                                   ++aa +++++ p++ v  ++
  gi|119719061|ref|YP_919556.1| 21 MTAASRIKRLKPELRVAVFE 40
                                   58999999999999987765 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00011
                                    T.SEEEEE--SHHHHHHHHHHHHHTT CS
                                    x.xxxxxxxxxxxxxxxxxxxxxxxx RF
                           ThiF  18 d.skvllvGaGglGsellknLalsGv 42 
                                    + ++v++vG G +G e+++nL+++G 
  gi|119719061|ref|YP_919556.1| 151 KaTRVAVVGGGYIGLEVAENLVRAGK 176
                                    349*********************95 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.23   1.6e+02       1      26 [.      11      38 ..      11      54 .. 0.80
   2 ?    9.5   0.3    0.0015       1.1       1      28 [.     155     182 ..     155     253 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.23
                                   EEEES-SHHHHHHHHHHHH.TT..EEEEE CS
                         TrkA_N  1 iiiiGlGrvGrslaeeLse.gg..kdvvv 26
                                   +++iG G  G++ a ++++ +   + v v
  gi|119719061|ref|YP_919556.1| 11 VAVIGGGPAGMTAASRIKRlKPelR-VAV 38
                                   68*************9998443433.555 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0015
                                    EEEES-SHHHHHHHHHHHHTTEEEEEEE CS
                         TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvid 28 
                                    ++++G G +G ++ae+L ++gk v++ +
  gi|119719061|ref|YP_919556.1| 155 VAVVGGGYIGLEVAENLVRAGKTVLLFE 182
                                    68*****************664577665 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00012     0.087       2      51 ..     154     203 ..     153     247 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00012
                                    EEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS--TTH CS
                 UDPG_MGDP_dh_N   2 kisviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipiyepgL 51 
                                    +++v+G GY+Gl  a  l ++g++v++  + ++   ++  +   ++e++L
  gi|119719061|ref|YP_919556.1| 154 RVAVVGGGYIGLEVAENLVRAGKTVLLFEVLDHVFPAVDPDMALLVEKEL 203
                                    89***********************9988777766666666666666666 PP

>> tRNA_edit  Aminoacyl-tRNA editing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00071      0.51      61      94 ..     246     278 ..     243     295 .. 0.92
   2 ?   -0.9   0.0       2.3   1.7e+03      65      83 ..     415     433 ..     402     444 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00071
                      tRNA_edit  61 laseeelrellgvepGgvgPlglkaagvpvllDe 94 
                                    +a e +l+e lgv++G+ g l++ ++++++ +D+
  gi|119719061|ref|YP_919556.1| 246 VAPETRLAEKLGVKKGSTGALSV-DKSMRTNVDD 278
                                    5899*******************.9***999996 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.3
                      tRNA_edit  65 eelrellgvepGgvgPlgl 83 
                                    +++++++ +  G+ +P++ 
  gi|119719061|ref|YP_919556.1| 415 ARVEDAFFSDLGYAPPFSP 433
                                    6889999999*******85 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       2.9   2.1e+03       2      29 ..      10      37 ..       9      43 .. 0.76
   2 ?   10.5   0.1    0.0012      0.84       2     110 ..     154     287 ..     153     294 .. 0.63

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 2.9
                                   EEEEETTSHHHHHHHHHHHHTTTTEEEE CS
                   GFO_IDH_MocA  2 rvaiiGaGkigskhlrplnesqrleevv 29
                                    va+iG+G +g   +  +++ +++++v+
  gi|119719061|ref|YP_919556.1| 10 DVAVIGGGPAGMTAASRIKRLKPELRVA 37
                                   599******9999988888876665554 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0012
                                    EEEEETTSHHHHHHHHHHHHTTTTE.......EEEEEECSSHHHHHHH...HHHTTHEEESS.................. CS
                   GFO_IDH_MocA   2 rvaiiGaGkigskhlrplnesqrle.......evvalldpdaeraeav...aesfgveaysd.................. 53 
                                    rva++G+G+ig + +++l ++ ++        +v  ++dpd +    v    ++       +                  
  gi|119719061|ref|YP_919556.1| 154 RVAVVGGGYIGLEVAENLVRAGKTVllfevldHVFPAVDPDMAL--LVekeLAR-------Ngvelhlgeglkgihgrdr 224
                                    89*******************99995555555444444444322..12112222.......2333344456777777777 PP

                                    ...HHHHHTCTTESEEEE-S-GGGHHHHHHHH.HHTT-..EEEEESSS-SSHHHHHHHHHHHH CS
                   GFO_IDH_MocA  54 ...leelladpeidavivatpngtheelakaa.leagk..hvllEKPlattveeakelvelae 110
                                       le  + + ++dav++at      +la+++ +++g   ++ ++K + t+v+++ +  + ae
  gi|119719061|ref|YP_919556.1| 225 vesLETTKGEYKVDAVFIATGVAPETRLAEKLgVKKGStgALSVDKSMRTNVDDVYAAGDVAE 287
                                    443444444449999999999988888777753566657777777777777777666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (452 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.45
# Mc/sec: 2994.18
//
Query:       gi|119719062|ref|YP_919557.1|  [L=185]
Description: hypothetical protein Tpen_0144 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.017   15.2   1.3      0.025   14.7   0.1    1.8  2  Phage_holin_3_5  Bacteriophage holin Hol, superfamily III


Domain annotation for each model (and alignments):
>> Phage_holin_3_5  Bacteriophage holin Hol, superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.2      0.16   2.8e+03      62      82 ..      12      32 ..       8      35 .. 0.81
   2 ?   14.7   0.1   1.4e-06     0.025      36     108 ..     103     182 ..      87     185 .] 0.76

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.16
                Phage_holin_3_5 62 llllaagaallsaaalgslta 82
                                   l+lla+g + l a  l sl a
  gi|119719062|ref|YP_919557.1| 12 LFLLAVGFSALLAGFLASLYA 32
                                   678899999999999988877 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 1.4e-06
                Phage_holin_3_5  36 glsgwallr....rlllrsgasvvcglavilllla..agaallsaaalgsltaaag.aevavglykrwvakrlgvcelte 108
                                      sgw++l+    r+ l s +s+     +++ll++  + + +   ++lg+l + +g a ++ gly+   ak l   e + 
  gi|119719062|ref|YP_919557.1| 103 NSSGWVVLQgqpyRVTLESTCSLCRSNVTLILLYSrfSRTEVDILSTLGALLSITGmASLSAGLYQYLFAKYLSRTEQSA 182
                                    5689*999755558999998888777788888888333456778899**9877666489************998777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1177.83
//
Query:       gi|119719063|ref|YP_919558.1|  [L=331]
Description: oligopeptide/dipeptide ABC transporter, ATPase subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-29  103.5   0.0    1.8e-29  103.0   0.0    1.2  1  ABC_tran     ABC transporter
    1.5e-21   76.7   1.3    2.3e-21   76.0   1.3    1.3  1  oligo_HPY    Oligopeptide/dipeptide transporter, C-terminal r
    1.2e-05   25.3   0.0      0.034   14.0   0.0    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
     0.0002   20.2   0.1      0.002   16.9   0.0    2.0  2  AAA_13       AAA domain
    0.00029   21.2   0.1     0.0007   20.0   0.1    1.8  2  AAA_16       AAA ATPase domain
    0.00046   20.5   1.4     0.0074   16.6   1.4    2.1  1  AAA_22       AAA domain
     0.0041   16.6   0.0       0.31   10.4   0.0    2.1  2  SMC_N        RecF/RecN/SMC N terminal domain
     0.0069   16.1   0.1      0.012   15.3   0.1    1.3  1  AAA_29       P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.081   12.1   0.0       0.15   11.2   0.0    1.3  1  NB-ARC       NB-ARC domain
        0.1   11.8   0.0       0.11   11.7   0.0    1.1  1  G-alpha      G-protein alpha subunit
       0.12   12.4   0.1       0.21   11.6   0.1    1.4  1  TsaE         Threonylcarbamoyl adenosine biosynthesis protein
       0.12   12.4   0.0       0.23   11.4   0.0    1.5  1  AAA_5        AAA domain (dynein-related subfamily)
       0.15   12.0   0.0       0.33   10.8   0.0    1.6  1  NACHT        NACHT domain
       0.16   11.7   0.4       0.74    9.5   0.1    1.9  2  AAA_30       AAA domain
        0.2   11.6   0.0        0.3   11.0   0.0    1.3  1  RsgA_GTPase  RsgA GTPase
       0.35   11.3   0.9        2.1    8.8   0.2    2.2  2  AAA          ATPase family associated with various cellular a


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.0   0.0   1.6e-32   1.8e-29       1     136 [.      33     186 ..      33     187 .. 0.87

  Alignments for each domain:
  == domain 1  score: 103.0 bits;  conditional E-value: 1.6e-32
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG...B-HHHCCHCEEEE-SS.....--S-T CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxx.....xxxxx RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke...qeleslrkeigvlpqe.....pqlfp 72 
                                    l+ vs++l++ge v +vGe+G+GK+tL k++++l++pt G++ ++g+d+++   +el ++++e g ++q+     p++ +
  gi|119719063|ref|YP_919558.1|  33 LDGVSFELRAGEAVSLVGESGSGKTTLGKTILRLYEPTDGKLVFKGRDITHtpeKELMWYKRETGLVQQDpygamPSFMN 112
                                    789************************************************9999999************8766555555 PP

                                    TSBHHHH...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    xxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  73 eltvren...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                     +++ e+           e+ e + kal++++l+ + ++ +++ p+ LSgGq qrva+aral+ kp+l+++DEp 
  gi|119719063|ref|YP_919558.1| 113 IYRILEEpliihkvgskeERAEMVFKALEEVRLTPV-EDFAYKYPHMLSGGQLQRVAIARALILKPSLVVADEPV 186
                                    55555559******9654444447788888888885.55556999*****************************7 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.0   1.3   2.1e-24   2.3e-21       1      65 []     238     304 ..     238     304 .. 0.97

  Alignments for each domain:
  == domain 1  score: 76.0 bits;  conditional E-value: 2.1e-24
                      oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekd..klekikgeapslerldeGCpFapRCpfaleeC 65 
                                    vEr+p+++l+++plHPYT+aLl+++p++d+e++    e  +ge+psl + + GC+FapRCpfa++ C
  gi|119719063|ref|YP_919558.1| 238 VERAPTKTLLRNPLHPYTRALLSAIPDPDPENRkrYREVPPGEPPSLVNPPPGCRFAPRCPFATSRC 304
                                    8********************************87788899*************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0   0.00072       0.8       4      23 ..      48      67 ..      46     107 .. 0.81
   2 !   14.0   0.0     3e-05     0.034     235     300 ..     157     220 ..     110     222 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00072
                         AAA_21  4 liGpNgsGKSnLLdaldlla 23
                                   l+G  gsGK++L +++  l 
  gi|119719063|ref|YP_919558.1| 48 LVGESGSGKTTLGKTILRLY 67
                                   8***************8874 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 3e-05
                         AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSpl 300
                                    + lS G+++  a++ al+  +   sl++ DEp + L+ ++  ++l+l+++l++ +++ +i  TH+ +
  gi|119719063|ref|YP_919558.1| 157 HMLSGGQLQRVAIARALILKP---SLVVADEPVSMLDASVRVEILTLMRDLQEkRNISFIYITHDLS 220
                                    556778777767777777655...************************888888**********975 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1       0.1   1.1e+02      23      39 ..      50      66 ..      48      89 .. 0.83
   2 !   16.9   0.0   1.8e-06     0.002     523     581 ..     173     229 ..     164     248 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.1
                         AAA_13 23 GwNGaGKTtLSrllrsl 39
                                   G  G+GKTtL + +  l
  gi|119719063|ref|YP_919558.1| 50 GESGSGKTTLGKTILRL 66
                                   778*******9988665 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 1.8e-06
                         AAA_13 523 eigkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleffkevkknt 581
                                     i k   vv D PvS LD+ +   + +l+++   +k +++ ++i TH l+  +++++++
  gi|119719063|ref|YP_919558.1| 173 LILKPSLVVADEPVSMLDASVRVEILTLMRDLQ-EKRNISFIYI-THDLSTTRYFSEWI 229
                                    567999**************************7.9999998887.*********99986 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.1   6.3e-07    0.0007       3      59 ..      24      79 ..      22     213 .. 0.78
   2 ?   -1.1   0.0       1.9   2.2e+03      44     109 ..     200     263 ..     194     277 .. 0.59

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 6.3e-07
                         AAA_16  3 vGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekdg.giflrgk 59
                                   +G   e+++L  +   +r+g  e+v l+GesG+GK++l +++lr +e ++  ++++g+
  gi|119719063|ref|YP_919558.1| 24 FGGTVEVKALDGVSFELRAG--EAVSLVGESGSGKTTLGKTILRLYEPTDgKLVFKGR 79
                                   66677777777776678888..79*******************988877513334444 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.9
                         AAA_16  44 llralekdg.giflrgkcdqlesaipy.salaqalareellrqlldeaesaeleawrekleealaavp 109
                                    l+r l++++ + f++ + d +   ++y s ++ +  + ++++   ++  + ++++ +   ++ l+a+p
  gi|119719063|ref|YP_919558.1| 200 LMRDLQEKRnISFIYITHDLS--TTRYfSEWIFIMYAGHIVERAPTK--TLLRNPLHPYTRALLSAIP 263
                                    455555554488899988888..566645577777776777776666..3344444444444444444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   1.4   6.6e-06    0.0074       8     128 ..      46     215 ..      41     225 .. 0.62

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 6.6e-06
                         AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee.......................................erpevvfvtlp 48 
                                    + ++GesG+GKTtl +++l+ ++    +++                                       +          
  gi|119719063|ref|YP_919558.1|  46 VSLVGESGSGKTTLGKTILRLYE----PTDgklvfkgrdithtpekelmwykretglvqqdpygampsfM---------- 111
                                    679******************94....3334678888888888888888877444444444444333331.......... PP

                         AAA_22  49 sstsskdllre..llralglelka........................erlsseell.ealeqalrarav...ielliiD 98 
                                       +   +l+e  + +++     +                        + +  + l   +l++ + ara    ++l++ D
  gi|119719063|ref|YP_919558.1| 112 ---NIYRILEEplIIHKV-----GskeeraemvfkaleevrltpvedfAYKYPHMLSgGQLQRVAIARALilkPSLVVAD 183
                                    ...222222221111111.....122233444444444444446667766666666667777777777778888888888 PP

                         AAA_22  99 Eaqh.lr...seealeeLrsllnlsrkgvqliLv 128
                                    E    l+   + e+l+  r+l++  + ++++i++
  gi|119719063|ref|YP_919558.1| 184 EPVSmLDasvRVEILTLMRDLQE--KRNISFIYI 215
                                    87775657444888888888888..888888877 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0      0.02        22      26      44 ..      45      63 ..      29      74 .. 0.83
   2 !   10.4   0.0   0.00028      0.31     135     204 ..     148     224 ..      76     237 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.02
                                   EEEEEESTTSSHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxx RF
                          SMC_N 26 ftaivGpNGSGKsnlldAi 44
                                     ++vG+ GSGK+ l   i
  gi|119719063|ref|YP_919558.1| 45 AVSLVGESGSGKTTLGKTI 63
                                   5679*********998887 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00028
                                    T.........CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHH..HHCTTSEEEEE-SSHHHCC CS
                                    x.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxx RF
                          SMC_N 135 e.........lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellk..eksknaQfivislreemle 203
                                              +LSgG+ + va+a  + +    + +l++ De  + LD++ + ++ +l++  +++ n  fi i+++  +++
  gi|119719063|ref|YP_919558.1| 148 VedfaykyphMLSGGQLQRVAIARALIL----KPSLVVADEPVSMLDASVRVEILTLMRdlQEKRNISFIYITHDLSTTR 223
                                    35555555559*****998888765433....45799*************999999999554555799*****9877766 PP

                                    C CS
                                    x RF
                          SMC_N 204 k 204
                                     
  gi|119719063|ref|YP_919558.1| 224 Y 224
                                    5 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   1.1e-05     0.012      12      38 ..      33      59 ..      28      74 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.1e-05
                         AAA_29 12 fdghtieidlkgatlltGpsGsGKSTl 38
                                   +dg ++e++  +a+ l+G+sGsGK+Tl
  gi|119719063|ref|YP_919558.1| 33 LDGVSFELRAGEAVSLVGESGSGKTTL 59
                                   577889998666**************9 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00013      0.15      22      43 ..      45      66 ..      33      77 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00013
                                   EEEEEESTTSSHHHHHHHHCCS CS
                         NB-ARC 22 vvalvGmgGvGKttlakqilnk 43
                                    v+lvG  G+GKttl k il+ 
  gi|119719063|ref|YP_919558.1| 45 AVSLVGESGSGKTTLGKTILRL 66
                                   699**************99986 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   9.5e-05      0.11      27      52 ..      47      77 ..      39     214 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.5e-05
                                   EEEESTTSSHHHHHHHHHHHCS--.....-- CS
                        G-alpha 27 lllGqseSGKsTilkqlkllykkg.....fs 52
                                    l+G+s+SGK+T+ k + +ly+++     f+
  gi|119719063|ref|YP_919558.1| 47 SLVGESGSGKTTLGKTILRLYEPTdgklvFK 77
                                   699******************9987677744 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00019      0.21      18      42 ..      42      66 ..      27      73 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00019
                                   HTEEEEEEESTTSSHHHHHHHHHHH CS
                           TsaE 18 lgdvilLeGdLGaGKTtlvrglaka 42
                                   +g+++ L G+ G+GKTtl + +++ 
  gi|119719063|ref|YP_919558.1| 42 AGEAVSLVGESGSGKTTLGKTILRL 66
                                   2788****************99985 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00021      0.23       2      24 ..      46      69 ..      45      92 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00021
                                   EEEE--SSSSHHHHHHHGGGGB.S CS
                          AAA_5  2 vlLvGppGtgKselaerlaaal.n 24
                                   v LvG++G+gK++l + +++++  
  gi|119719063|ref|YP_919558.1| 46 VSLVGESGSGKTTLGKTILRLYeP 69
                                   669****************99862 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0    0.0003      0.33       3      22 ..      46      65 ..      44      76 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0003
                                   EEEEC-TTTCHHHHHHHHHH CS
                          NACHT  3 vilqGeaGsGKTtLlqklal 22
                                   v l Ge+GsGKTtL + + +
  gi|119719063|ref|YP_919558.1| 46 VSLVGESGSGKTTLGKTILR 65
                                   6799**********998876 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1   0.00066      0.74      20      48 ..      45      73 ..      39      84 .. 0.83
   2 ?   -0.1   0.0      0.59   6.6e+02      83     114 ..     171     203 ..     126     210 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00066
                         AAA_30 20 vavltGpAGtGKttalkalreaweaaggr 48
                                    + l+G  G+GKtt+ k++ +++e   g+
  gi|119719063|ref|YP_919558.1| 45 AVSLVGESGSGKTTLGKTILRLYEPTDGK 73
                                   56799**************9999988444 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.59
                         AAA_30  83 rarlepgtllivDE.agmvdtkqlaallkaaek 114
                                    ra + + +l++ DE ++m+d++   ++l+ +++
  gi|119719063|ref|YP_919558.1| 171 RALILKPSLVVADEpVSMLDASVRVEILTLMRD 203
                                    344455589999997799999998888888776 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00027       0.3      89     120 ..      32      64 ..      13     100 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00027
                                    THHHHHHHCTT.SEEEEECSTTSSHHHHHHHHC CS
                    RsgA_GTPase  89 gleelkellkd.ktsvlvGqSGvGKStLinall 120
                                    +l+ ++ +l+  + + lvG+SG GK+tL +++l
  gi|119719063|ref|YP_919558.1|  32 ALDGVSFELRAgEAVSLVGESGSGKTTLGKTIL 64 
                                    5667777787779999************88775 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.2    0.0019       2.1       2      23 ..      47      68 ..      46     149 .. 0.53
   2 ?    0.4   0.0      0.72     8e+02      74     112 ..     192     219 ..     160     223 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0019
                                   EEESSTTSSHHHHHHHHHHHHT CS
                            AAA  2 llyGppGtGKTllakavakelg 23
                                    l+G  G GKT+l k + +  +
  gi|119719063|ref|YP_919558.1| 47 SLVGESGSGKTTLGKTILRLYE 68
                                   599*************998753 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.72
                                    HTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSG CS
                            AAA  74 rsgseseeeervvnqLlteldgvkkkeskvivigatnrp 112
                                    +          v  ++lt + ++++k +++ +i +t++ 
  gi|119719063|ref|YP_919558.1| 192 S----------VRVEILTLMRDLQEK-RNISFIYITHDL 219
                                    3..........666889999999996.559999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                       104  (0.00580066); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 2382.26
//
Query:       gi|119719064|ref|YP_919559.1|  [L=322]
Description: oligopeptide/dipeptide ABC transporter, ATPase subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.8e-29  101.1   0.0    9.3e-29  100.7   0.0    1.2  1  ABC_tran         ABC transporter
    1.4e-18   67.1   0.7    2.8e-18   66.2   0.7    1.5  1  oligo_HPY        Oligopeptide/dipeptide transporter, C-termin
    8.1e-10   39.0   0.2    2.8e-06   27.4   0.1    2.1  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
      1e-06   28.3   0.0    2.2e-05   24.0   0.0    2.1  1  SMC_N            RecF/RecN/SMC N terminal domain
    8.7e-06   26.0   0.0     0.0031   17.8   0.0    2.3  2  AAA_22           AAA domain
    6.2e-05   22.5   0.0      0.036   13.5   0.0    2.6  3  TniB             Bacterial TniB protein
    6.8e-05   23.3   0.0    9.9e-05   22.8   0.0    1.3  1  AAA_16           AAA ATPase domain
    0.00037   20.5   0.0     0.0021   18.1   0.0    2.1  2  AAA_5            AAA domain (dynein-related subfamily)
    0.00041   20.3   0.0    0.00088   19.2   0.0    1.5  1  RsgA_GTPase      RsgA GTPase
     0.0017   18.1   0.1      0.043   13.5   0.0    2.1  2  IstB_IS21        IstB-like ATP binding protein
      0.002   18.7   0.0     0.0029   18.1   0.0    1.3  1  AAA_23           AAA domain
     0.0022   17.7   0.0     0.0042   16.8   0.0    1.4  1  AAA_29           P-loop containing region of AAA domain
     0.0043   17.5   0.0      0.051   14.0   0.0    2.2  2  AAA              ATPase family associated with various cellul
     0.0052   16.5   0.6     0.0065   16.2   0.0    1.4  1  AAA_15           AAA ATPase domain
     0.0068   16.8   0.0      0.015   15.6   0.0    1.6  1  RNA_helicase     RNA helicase
  ------ inclusion threshold ------
      0.012   15.5   0.0       0.02   14.8   0.0    1.3  1  NACHT            NACHT domain
      0.016   14.9   0.0      0.027   14.2   0.0    1.3  1  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
      0.016   15.1   0.0       0.03   14.3   0.0    1.3  1  DUF2612          Protein of unknown function (DUF2612)
      0.018   14.8   0.0      0.033   13.9   0.0    1.4  1  Sigma54_activat  Sigma-54 interaction domain
      0.021   14.0   0.0      0.062   12.5   0.0    1.8  1  NB-ARC           NB-ARC domain
      0.028   13.8   0.0      0.056   12.8   0.0    1.5  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.028   14.5   0.0      0.053   13.6   0.0    1.5  1  MMR_HSR1         50S ribosome-binding GTPase
      0.029   14.5   0.1      0.062   13.4   0.0    1.5  1  DUF87            Helicase HerA, central domain
      0.075   12.6   0.0       0.17   11.4   0.0    1.7  1  AAA_25           AAA domain
      0.082   12.6   0.0       0.14   11.9   0.0    1.4  1  PRK              Phosphoribulokinase / Uridine kinase family
      0.093   12.1   0.0       0.19   11.1   0.0    1.4  1  FtsK_SpoIIIE     FtsK/SpoIIIE family
      0.098   12.2   0.0       0.15   11.5   0.0    1.3  1  AAA_7            P-loop containing dynein motor region
       0.15   11.2   0.0       0.23   10.6   0.0    1.3  1  DUF815           Protein of unknown function (DUF815)
       0.17   12.5   0.0       0.39   11.3   0.0    1.6  1  AAA_18           AAA domain
       0.19   10.5   0.8        2.6    6.7   0.2    2.4  2  ABC_ATPase       Predicted ATPase of the ABC class
        0.2   10.9   0.0       0.31   10.3   0.0    1.3  1  DUF2813          Protein of unknown function (DUF2813)


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.7   0.0   1.6e-31   9.3e-29       1     137 []      24     182 ..      24     182 .. 0.87

  Alignments for each domain:
  == domain 1  score: 100.7 bits;  conditional E-value: 1.6e-31
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--....SEEEEEETTCEGGG.....B-HHHCCHCEEEE-SS..-- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxx..xx RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp....teGeilldgkdlke.....qeleslrkeigvlpqe..pq 69 
                                    ++nvs++lk+ge++aivGe+G+GKS+L+++l++ll        Gei ++g+d+ +      ++ +  ++i++++q   ++
  gi|119719064|ref|YP_919559.1|  24 VDNVSFDLKKGETLAIVGESGCGKSSLARALIRLLPRnvhtFTGEIYINGNDVMKlsdemFRRLIRWRKISMVFQGaqNS 103
                                    58***************************99999877666689*********9998777644444456899999997778 PP

                                    S-TTSBHHHH...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    xxxxxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  70 lfpeltvren...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                    l+p l+v+ +             +e +++a + l+l++++++ +++ p +LSgG+kqr ++a+al+++p++++lDEpt+
  gi|119719064|ref|YP_919559.1| 104 LNPVLKVGFQvaeplmihnnmSPEEALAEAKKYLRLVGIHESFADRYPFELSGGMKQRAVIAMALITHPDIIILDEPTS 182
                                    88888877778999***998766666888889999999999************************************96 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.2   0.7   4.9e-21   2.8e-18       1      65 []     233     296 ..     233     296 .. 0.99

  Alignments for each domain:
  == domain 1  score: 66.2 bits;  conditional E-value: 4.9e-21
                      oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekdklekikgeapslerldeGCpFapRCpfaleeC 65 
                                    vE+++++++ ++p+HPY+++L++svp l+  k+ le i+g +psl + + GC+F+pRCp+a e C
  gi|119719064|ref|YP_919559.1| 233 VEIADADEFYTNPRHPYSEKLMASVPTLRTDKK-LEFIPGAPPSLINPPPGCRFHPRCPYAYERC 296
                                    8***************************99999.*****************************99 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0   0.00092      0.53       3      36 ..      38      69 ..      37      98 .. 0.73
   2 !   27.4   0.1   4.9e-09   2.8e-06     225     300 ..     142     215 ..      84     218 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00092
                         AAA_21  3 vliGpNgsGKSnLLdaldllarldrdvegltdel 36
                                   +++G  g+GKS+L +al  l    r+v+  t e 
  gi|119719064|ref|YP_919559.1| 38 AIVGESGCGKSSLARALIRLL--PRNVHTFTGEI 69
                                   79***************8886..34444444443 PP

  == domain 2  score: 27.4 bits;  conditional E-value: 4.9e-09
                         AAA_21 225 engdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSpl 300
                                     +++  ++ ++elS G+k+  a++++ l +++  +++++DEp + L+   ++ ++ llk+ ++  g   i+ TH+  
  gi|119719064|ref|YP_919559.1| 142 IHESFADRYPFELSGGMKQR-AVIAMALITHP--DIIILDEPTSALDVITQANIINLLKRIKNeMGLSYIFITHDIA 215
                                    5566677899**********.**********9..9*************99999999994444446799******965 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   3.7e-08   2.2e-05      26     210 ..      36     225 ..      21     233 .. 0.71

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 3.7e-08
                                    EEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCC...CCCC--..BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  26 ftaivGpNGSGKsnlldAilFvLGersakklrsekl...sdlihk..skekasvkkaeveitfdnedkklkiekeevsis 100
                                      aivG+ G+GKs+l  A+  +L  r+ +++  e +   +d+++   +  ++ +   +++++f+  +++    ++ +++ 
  gi|119719064|ref|YP_919559.1|  36 TLAIVGESGCGKSSLARALIRLLP-RNVHTFTGEIYingNDVMKLsdEMFRRLIRWRKISMVFQGAQNS---LNPVLKVG 111
                                    458****************99998.677788877543337787774334456677889*****999988...45555565 PP

                                    EEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT.......CS-HH..HHHHHHHHHHHHHHCCS--SEEEECTTTTTS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 101 rrvkrkgeseykingkevtkkevsellesagiske.......lLSgG..ektLvalaLlfAiqkvkpaplyllDeidaaL 171
                                     +v +    +  +  +e   +e ++ l+ +gi+++       +LSgG  +++++a+aL+          + +lDe  +aL
  gi|119719064|ref|YP_919559.1| 112 FQVAEPLMIHNNMSPEE-ALAEAKKYLRLVGIHESfadrypfELSGGmkQRAVIAMALI------THPDIIILDEPTSAL 184
                                    55555444333333332.348889999999999999999999*****555567777777......334589********* PP

                                    -HHHHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC-SCEEE CS
                                    xxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 172 Deknvkkvaellkekskn..aQfivislreemlekadklvg 210
                                    D    +++ +llk+ +++    +i i+++  ++++    v 
  gi|119719064|ref|YP_919559.1| 185 DVITQANIINLLKRIKNEmgLSYIFITHDIAVTSELADRVA 225
                                    ************98777744678999998777665533333 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   5.3e-06    0.0031       6      39 ..      35      61 ..      30     106 .. 0.82
   2 ?    6.1   0.0     0.022        13      91     128 ..     168     210 ..     130     216 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 5.3e-06
                         AAA_22  6 gilvvtGesGtGKTtllrrlleqldeeakaeeer 39
                                     l+++GesG+GK+ l+r l + l++       +
  gi|119719064|ref|YP_919559.1| 35 ETLAIVGESGCGKSSLARALIRLLPR-------N 61
                                   5689*****************99974.......3 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.022
                         AAA_22  91 v...ielliiDEaqh.lr...seealeeLrsllnlsrkgvqliLv 128
                                        + ++i+DE    l+   ++++++ L+++ n  + g++ i++
  gi|119719064|ref|YP_919559.1| 168 LithPDIIILDEPTSaLDvitQANIINLLKRIKN--EMGLSYIFI 210
                                    355668******9999988877************..*****9998 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.012       7.1      36      61 ..      35      60 ..      27      71 .. 0.82
   2 ?   -2.3   0.0       4.3   2.5e+03     145     167 ..      83     105 ..      80     109 .. 0.83
   3 !   13.5   0.0   6.2e-05     0.036     106     161 ..     158     211 ..     139     223 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.012
                           TniB 36 pnlllvGdsnnGKtmivekFarlhpp 61
                                   + l +vG+s +GK+++++   rl p+
  gi|119719064|ref|YP_919559.1| 35 ETLAIVGESGCGKSSLARALIRLLPR 60
                                   5799************9987776665 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4.3
                           TniB 145 alksLgnelkipivlvGteealr 167
                                    + ++L +  ki++v  G ++ l+
  gi|119719064|ref|YP_919559.1|  83 MFRRLIRWRKISMVFQGAQNSLN 105
                                    5688999999****999998765 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 6.2e-05
                           TniB 106 kleqqvlrllrelkvrvLiiDEihnllagsarkqreflnalksLgnelkipivlvG 161
                                     ++++v+++   +++ ++i+DE  ++l   + +q +++n+lk+++ne+ ++ + + 
  gi|119719064|ref|YP_919559.1| 158 MKQRAVIAMALITHPDIIILDEPTSAL--DVITQANIINLLKRIKNEMGLSYIFIT 211
                                    5666777777778899**********9..899******************999875 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   1.7e-07   9.9e-05      22      63 ..      34      72 ..      17     148 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.7e-07
                         AAA_16 22 grpelvllsGesGvGKsslvrellralekdggiflrgkcdql 63
                                   g  e + ++GesG+GKssl+r+l r l ++ +++++g+   +
  gi|119719064|ref|YP_919559.1| 34 G--ETLAIVGESGCGKSSLARALIRLLPRN-VHTFTGEIYIN 72
                                   3..7899*****************777766.88877765555 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   3.6e-06    0.0021       3      40 ..      38      75 ..      36      96 .. 0.86
   2 ?   -0.6   0.0       2.1   1.2e+03      59      81 ..     165     187 ..     146     203 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3.6e-06
                                   EEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHH CS
                          AAA_5  3 lLvGppGtgKselaerlaaalnreveyvqltrdtteed 40
                                    +vG++G+gKs+la+ l ++l r+v++  +  +++ +d
  gi|119719064|ref|YP_919559.1| 38 AIVGESGCGKSSLARALIRLLPRNVHTFTGEIYINGND 75
                                   589*********************99988776666555 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2.1
                                    ------G-SEEEEESGGG--HHH CS
                          AAA_5  59 lvraaregeilvlDEveraesev 81 
                                    ++  +++++i++lDE + a + +
  gi|119719064|ref|YP_919559.1| 165 AMALITHPDIIILDEPTSALDVI 187
                                    44444599999999988776443 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.5e-06   0.00088      87     121 ..      21      56 ..       6      73 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.5e-06
                                    HTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                    RsgA_GTPase  87 kegleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                     +++++++  lk+ +t ++vG+SG GKS+L  al+ 
  gi|119719064|ref|YP_919559.1|  21 VKAVDNVSFDLKKgETLAIVGESGCGKSSLARALIR 56 
                                    47788999999998****************999875 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   7.5e-05     0.043      35      67 ..      21      54 ..      11      65 .. 0.82
   2 ?    2.3   0.1      0.21   1.2e+02     102     151 ..     165     216 ..     156     224 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.5e-05
                      IstB_IS21 35 vkeLatlsf.iekkenivllGpsGvGKshlaial 67
                                   vk++ + sf ++k e ++++G sG GKs la al
  gi|119719064|ref|YP_919559.1| 21 VKAVDNVSFdLKKGETLAIVGESGCGKSSLARAL 54
                                   55666666657899******************98 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.21
                      IstB_IS21 102 alkrllkvdllilDd..lgllpldqaeaellfeviekryerrsiiitsnlpf 151
                                    a++ ++++d++ilD+   +l  + qa+  +l++ i++  + + i it ++ +
  gi|119719064|ref|YP_919559.1| 165 AMALITHPDIIILDEptSALDVITQANIINLLKRIKNEMGLSYIFITHDIAV 216
                                    56778999******94446778889999999999999999988888877655 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0     5e-06    0.0029       3      43 ..       6      58 ..       5     115 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 5e-06
                         AAA_23  3 kienfrsf...........rdqeidFskglt.lItGpNGaGKTTildAiklaL 43
                                   +++n+r +           +++++d++kg t +I+G+ G+GK+++ +A+   L
  gi|119719064|ref|YP_919559.1|  6 TVRNLRLYfstrkgvvkavDNVSFDLKKGETlAIVGESGCGKSSLARALIRLL 58
                                   566666666666666666688999**9976637***************97655 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   7.2e-06    0.0042      13      46 ..      25      58 ..      22      66 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 7.2e-06
                         AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDAiqalL 46
                                   d+ +++++  ++  ++G+sG GKS+l  A++ lL
  gi|119719064|ref|YP_919559.1| 25 DNVSFDLKKGETLAIVGESGCGKSSLARALIRLL 58
                                   56677888555999************99999987 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   8.8e-05     0.051       3      37 ..      39      78 ..      37     110 .. 0.61
   2 ?    1.1   0.0      0.83   4.8e+02      45      72 ..     159     185 ..     129     228 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 8.8e-05
                                   EESSTTSSHHHHHHHHHHHHTHE......EEEEETTTCSSS CS
                            AAA  3 lyGppGtGKTllakavakelgve......fleisgsellsk 37
                                   ++G  G+GK++la+a+++ l ++       + i+g +++ k
  gi|119719064|ref|YP_919559.1| 39 IVGESGCGKSSLARALIRLLPRNvhtftgEIYINGNDVM-K 78
                                   79****************995441122223445555544.3 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.83
                                    HHHHHHHHHHHTSTSEEEEEETGGGHHH CS
                            AAA  45 kirelfkeakekakpsilfiDEidalak 72 
                                    k r++++ a     p i+++DE  +   
  gi|119719064|ref|YP_919559.1| 159 KQRAVIAMALITH-PDIIILDEPTSALD 185
                                    5566666655554.89999999555544 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.1e-05    0.0065      13      60 ..      23      79 ..      22     115 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.1e-05
                         AAA_15 13 slkdveidlsee.ltvliGkNnsGKSsilealdlFlnnkekkn........kkviki 60
                                   + ++v+ dl++  +  ++G+ ++GKSs+++al  +l ++   +        ++v+k+
  gi|119719064|ref|YP_919559.1| 23 AVDNVSFDLKKGeTLAIVGESGCGKSSLARALIRLLPRNVHTFtgeiyingNDVMKL 79
                                   5677888999986779****************9999977555545455555444444 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   2.6e-05     0.015       2      38 ..      38      73 ..      37      83 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.6e-05
                   RNA_helicase  2 wlyGpsgeGKStlakeLakallkklklkkkdsvysrn 38
                                    ++G+sg+GKS+la+ L++ l +++  + ++++y+++
  gi|119719064|ref|YP_919559.1| 38 AIVGESGCGKSSLARALIRLLPRNV-HTFTGEIYING 73
                                   589****************999888.66668888854 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   3.4e-05      0.02       2      24 ..      36      58 ..      35      65 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.4e-05
                                   CEEEEC-TTTCHHHHHHHHHHHH CS
                          NACHT  2 lvilqGeaGsGKTtLlqklalaw 24
                                   ++++ Ge+G+GK+ L++ l++++
  gi|119719064|ref|YP_919559.1| 36 TLAIVGESGCGKSSLARALIRLL 58
                                   789****************9987 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   4.6e-05     0.027       8      49 ..      28      66 ..      21     124 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.6e-05
                                   HS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSSEEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    ATP-synt_ab  8 lfpivqGqrtlipgafgvGktvisqslskqsnsddaiiyvgi 49
                                    f + +G++++i+g++g+Gk+ ++++l++    +   +    
  gi|119719064|ref|YP_919559.1| 28 SFDLKKGETLAIVGESGCGKSSLARALIRLLPRN---VHTFT 66
                                   477899********************99985433...44444 PP

>> DUF2612  Protein of unknown function (DUF2612)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   5.1e-05      0.03      94     142 ..      74     122 ..      64     128 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.1e-05
                        DUF2612  94 tgltsLddetyRklirakilaniwdgtvpninailrslfadggrvfvlD 142
                                    +++++L+de++R lir++ ++ + +g  +++n +l+  f+  +  ++ +
  gi|119719064|ref|YP_919559.1|  74 NDVMKLSDEMFRRLIRWRKISMVFQGAQNSLNPVLKVGFQVAEPLMIHN 122
                                    5778*******************************99887665555555 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   5.7e-05     0.033      12      53 ..      24      65 ..      14      86 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.7e-05
                                   HHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-E CS
                Sigma54_activat 12 leqikkvaktdlsvlitGesGtGKellaraiheaskrkekpf 53
                                   +++++   k+  ++ i+GesG+GK+ lara+ +  +r+ + f
  gi|119719064|ref|YP_919559.1| 24 VDNVSFDLKKGETLAIVGESGCGKSSLARALIRLLPRNVHTF 65
                                   444555556667889****************99999888777 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00011     0.062      22     150 ..      36     223 ..      20     252 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                                    EEEEEESTTSSHHHHHHHHCCSHCCCCCCBTEEEEE............................................ CS
                         NB-ARC  22 vvalvGmgGvGKttlakqilnksdevegrFdsvawv............................................ 57 
                                     +a+vG  G+GK+ la+  ++ +    ++F + +++                                            
  gi|119719064|ref|YP_919559.1|  36 TLAIVGESGCGKSSLARALIRLLPRNVHTFTGEIYIngndvmklsdemfrrlirwrkismvfqgaqnslnpvlkvgfqva 115
                                    589******************99999999999999877777766666666666666666666666666666665555555 PP

                                    ...EEESXXHHHHHHHXXHHHHHCCCTTSSSS-STTS........HHHHHHHHCCCTTEEEEEE......EE-SHHHH.. CS
                         NB-ARC  58 ...vvsktdkseeiletilkeLslseddleekeeves........lkrklvrlLltkrfllvlD......DVweeedwdk 120
                                       ++ ++++ ee l +  k L l     e+++++++            +  +L+t+  +++lD      DV ++ +  +
  gi|119719064|ref|YP_919559.1| 116 eplMIHNNMSPEEALAEAKKYLRLV-GIHESFADRYPfelsggmkQRAVIAMALITHPDIIILDeptsalDVITQANIIN 194
                                    5543433333333333333333333.333444444445555555344445556666666666665555555555555434 PP

                                    ...HHHHCHTTSEEEEEESBCCCCCCS-S- CS
                         NB-ARC 121 igvvlparenrlrvllTTRdeevanavsat 150
                                    +   ++ +e +l+ ++ T d +v+++ +++
  gi|119719064|ref|YP_919559.1| 195 LLKRIK-NEMGLSYIFITHDIAVTSELADR 223
                                    444444.55566666666666666655555 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   9.7e-05     0.056      24      51 ..      36      63 ..      18      92 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.7e-05
                   Mg_chelatase 24 nlllvGppGsGKtmlakrlpsllpplse 51
                                    l +vG +G+GK+ la++l  llp+  +
  gi|119719064|ref|YP_919559.1| 36 TLAIVGESGCGKSSLARALIRLLPRNVH 63
                                   6789********************8655 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   9.2e-05     0.053       2      21 ..      37      56 ..      36      76 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.2e-05
                                   EEEEESTTSSHHHHHHHHHT CS
                       MMR_HSR1  2 vaivGrpNvGKStLinaltg 21
                                    aivG +  GKS+L +al++
  gi|119719064|ref|YP_919559.1| 37 LAIVGESGCGKSSLARALIR 56
                                   69****************97 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   0.00011     0.062      14      47 ..      27      58 ..      19      65 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00011
                          DUF87 14 vyldlnklvtrHlAilgsTGsGKSntvavLleel 47
                                   v++dl+k   + lAi+g++G GKS +++ L++ l
  gi|119719064|ref|YP_919559.1| 27 VSFDLKKG--ETLAIVGESGCGKSSLARALIRLL 58
                                   67777665..789******************976 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00029      0.17      30      97 ..      31     100 ..      23     213 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00029
                         AAA_25  30 lpagelallaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVlyvsaEdsedelrrRlra.vgeal 97 
                                    l +ge+ +++G +g+GK+ la  l   +    + ++g++      V+ +s E+ +  +r+R    v++ +
  gi|119719064|ref|YP_919559.1|  31 LKKGETLAIVGESGCGKSSLARALIRLLPrNVHTFTGEIYINGNDVMKLSDEMFRRLIRWRKISmVFQGA 100
                                    5799*****************9998888844555555666677888888888888777755433144444 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00025      0.14       3      29 ..      38      63 ..      36      86 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00025
                            PRK  3 gvagsSGaGkttvarklekifgrekvk 29
                                   ++ g+SG+Gk+++ar+l  ++   +v+
  gi|119719064|ref|YP_919559.1| 38 AIVGESGCGKSSLARALIRLLP-RNVH 63
                                   899**************99998.4455 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00032      0.19      29      60 ..      25      55 ..      12      58 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00032
                                   -EEEEEGGGS-.SEEEE--TTSSHHHHHHHHH CS
                   FtsK_SpoIIIE 29 nplvldlkkmashllvaGatgsGKStalntLi 60
                                   +++ +dlkk +  l ++G +g GKS   ++Li
  gi|119719064|ref|YP_919559.1| 25 DNVSFDLKKGE-TLAIVGESGCGKSSLARALI 55
                                   56899******.*******************9 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00027      0.15      30      62 ..      31      63 ..      20     100 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00027
                          AAA_7 30 lknkkpvllvGptGtGKtviikdllkkldkeky 62
                                   lk++  + +vG++G+GK+++++ l++ l+++ +
  gi|119719064|ref|YP_919559.1| 31 LKKGETLAIVGESGCGKSSLARALIRLLPRNVH 63
                                   67888999*****************99995444 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00039      0.23      52      77 ..      33      58 ..       3      97 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00039
                         DUF815 52 pannvLLwGarGtGKSslvkallney 77
                                   + + + ++G+ G+GKSsl +al++ +
  gi|119719064|ref|YP_919559.1| 33 KGETLAIVGESGCGKSSLARALIRLL 58
                                   44556689*************98755 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00067      0.39       3      33 ..      39      78 ..      37     105 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00067
                         AAA_18  3 ltGtpGvGKttlakeLskrl.gf........gvnlrdvak 33
                                   + G +G+GK++la++L ++l  +         +n +dv k
  gi|119719064|ref|YP_919559.1| 39 IVGESGCGKSSLARALIRLLpRNvhtftgeiYINGNDVMK 78
                                   8899************999865566666666444444444 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.23   1.3e+02     242     264 ..      31      54 ..      27      78 .. 0.91
   2 ?    6.7   0.2    0.0045       2.6     324     413 ..     155     229 ..     151     261 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.23
                                    E-SS.EEEEEE-TTSSHHHHHHHH CS
                     ABC_ATPase 242 ipkG.vtlIvGggfhGKsTLLeAl 264
                                    ++kG   +IvG    GKs L +Al
  gi|119719064|ref|YP_919559.1|  31 LKKGeTLAIVGESGCGKSSLARAL 54 
                                    67886678***************9 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0045
                                    -HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HHHHHHS-GGG--B--HHHCHHHHHHHH--EEEEEESS-GCCTT CS
                     ABC_ATPase 324 SGStsqAanimealeagakllLiDEDtsAtNlmirDermqelvskekepitplvdrvrelykklgvstilvvggsgdyld 403
                                    SG + q a i+ al    +++++DE tsA   + +              i   +++++++ +++g+s i ++  +    +
  gi|119719064|ref|YP_919559.1| 155 SGGMKQRAVIAMALITHPDIIILDEPTSALDVITQA------------NI---INLLKRIKNEMGLSYIFITHDIAVTSE 219
                                    99999999********************99887722............22...334444445577777777777777777 PP

                                    T-SEEEEEET CS
                     ABC_ATPase 404 vAdtvilmee 413
                                    +Ad+v +m +
  gi|119719064|ref|YP_919559.1| 220 LADRVAVMYA 229
                                    7777777765 PP

>> DUF2813  Protein of unknown function (DUF2813)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00053      0.31      18      52 ..      28      64 ..      21      93 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00053
                        DUF2813 18 Slslee..ntvLiGENaWGKSSLldALslilnvekel 52
                                   S  l++  + +++GE   GKSSL +AL  +l+ + + 
  gi|119719064|ref|YP_919559.1| 28 SFDLKKgeTLAIVGESGCGKSSLARALIRLLPRNVHT 64
                                   5566541145679*****************9976544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       647  (0.0360868); expected 358.6 (0.02)
Passed bias filter:                      624  (0.0348039); expected 358.6 (0.02)
Passed Vit filter:                       117  (0.00652574); expected 17.9 (0.001)
Passed Fwd filter:                        31  (0.00172904); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              31  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.49
# Mc/sec: 1988.34
//
Query:       gi|119719065|ref|YP_919560.1|  [L=474]
Description: binding-protein-dependent transport systems inner membrane component [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-21   76.2  15.1    2.6e-21   76.2  15.1    1.9  2  BPD_transp_1     Binding-protein-dependent transport system i
    0.00057   19.8   0.1    0.00057   19.8   0.1    3.1  3  OppC_N           N-terminal TM domain of oligopeptide transpo
  ------ inclusion threshold ------
      0.094   12.3   0.1       0.26   10.9   0.1    1.7  1  2-oxogl_dehyd_N  2-oxoglutarate dehydrogenase N-terminus


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1      0.23   1.4e+03      51      71 ..      21      42 ..      12      50 .. 0.56
   2 !   76.2  15.1   4.3e-25   2.6e-21       4     184 ..     289     472 ..     283     473 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.23
                   BPD_transp_1 51 hlilp.viillllsaapyvrli 71
                                   +++l+ +i+++l+ + +y++++
  gi|119719065|ref|YP_919560.1| 21 SGVLGlAILAFLVAFSIYAVVT 42
                                   4555544444444444444443 PP

  == domain 2  score: 76.2 bits;  conditional E-value: 4.3e-25
                   BPD_transp_1   4 lGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalrslpkdl 83 
                                    ++ + a  +++++d +++++++v + lP++ ++i++ +   +  ++  +++  ++++l  +++ +  +r+ +l++ +  +
  gi|119719065|ref|YP_919560.1| 289 IATIGA-WYGGVVDSVIQRITEVYMILPFLPFLIIIAA---FY-KVDIWVILTVVIVLSIFGAGIKSTRALVLSIKEYPY 363
                                    444445.9***********************9999994...33.344344444444555555557899************ PP

                   BPD_transp_1  84 veaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis......... 154
                                    +eaa+a+Gas+w+i++ +++P ++ppi++gli a++g +   ++l+flg    lg+++  +++g+ ++ ++         
  gi|119719065|ref|YP_919560.1| 364 IEAAKAYGASDWRIIFLYIIPKIIPPIVPGLIGAVPGYVFLEAALSFLG----LGDPF-LPTWGKVLNDAYnggalyrgy 438
                                    *************************************************....**887.589****999999******** PP

                   BPD_transp_1 155 ....nggvlalviavlllnlvadilqrlldprvr 184
                                          +++ l +  +++ ++ ++l r+++pr+r
  gi|119719065|ref|YP_919560.1| 439 yywvLEPSILLMLTAFAFAFLGFALDRIVNPRLR 472
                                    ********************************98 PP

>> OppC_N  N-terminal TM domain of oligopeptide transport permease C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.1   9.6e-08   0.00057      14      42 ..      20      55 ..      10      68 .. 0.80
   2 ?   -4.4   1.0         3   1.8e+04      25      32 ..     319     326 ..     316     327 .. 0.51
   3 ?    1.8   0.3      0.04   2.4e+02      21      36 ..     333     348 ..     331     365 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 9.6e-08
                         OppC_N 14 klAvvglvilllllliaifaPliaPydp.......q 42
                                   k  v+gl+il++l++++i+a + +Pyd+       +
  gi|119719065|ref|YP_919560.1| 20 KSGVLGLAILAFLVAFSIYAVVTIPYDQaiklwrgS 55
                                   7789**********************9866555442 PP

  == domain 2  score: -4.4 bits;  conditional E-value: 3
                         OppC_N  25 lllliaif 32 
                                    +l++ia+f
  gi|119719065|ref|YP_919560.1| 319 FLIIIAAF 326
                                    44444443 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.04
                         OppC_N  21 villlllliaifaPli 36 
                                    vil ++++++if+  i
  gi|119719065|ref|YP_919560.1| 333 VILTVVIVLSIFGAGI 348
                                    688889999***9777 PP

>> 2-oxogl_dehyd_N  2-oxoglutarate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   4.3e-05      0.26      19      34 ..      59      74 ..      57      77 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 4.3e-05
                2-oxogl_dehyd_N 19 yleDPsSVdesWrayF 34
                                   + e+P  V+++W ++F
  gi|119719065|ref|YP_919560.1| 59 WIENPRAVPPEWWEIF 74
                                   99************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (474 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       688  (0.0383736); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 3137.71
//
Query:       gi|119719066|ref|YP_919561.1|  [L=354]
Description: binding-protein-dependent transport systems inner membrane component [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.9e-30  103.8  12.4    8.9e-30  103.8  12.4    2.2  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.2      0.02   3.6e+02      96     122 ..       5      31 ..       2      44 .. 0.69
   2 !  103.8  12.4     5e-34   8.9e-30       2     184 ..     147     350 ..     146     351 .. 0.98

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.02
                   BPD_transp_1  96 qifrkvvlPnalppiitglilafggll 122
                                    +++++++l+++++++   +++ +++++
  gi|119719066|ref|YP_919561.1|   5 KLVKHIALRAIVIYLTVVVAVYLTIIV 31 
                                    556777777777777776666666655 PP

  == domain 2  score: 103.8 bits;  conditional E-value: 5e-34
                   BPD_transp_1   2 illGilaalnrnkkldkllrpliivllslPsfvlaillvlvf.......................vilsilghlilpvii 58 
                                    ++lG+++ +++++++dkl+  l+  +++lP    +i+l+l+f                       + ls+l+h+ilp++ 
  gi|119719066|ref|YP_919561.1| 147 LFLGLYLSRHYGSFFDKLVVALSP-TSTLPGWFYGIFLILIFytwlhvlppggmvdvppppdpisYALSVLKHMILPMAS 225
                                    689*******************99.99******99999999999************************************ PP

                   BPD_transp_1  59 llllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlg 138
                                     ++ +++  v+ +r  +l    +d+veaa+a+G++++ i  +++l+ +lppi+t ++l+++g++gga+++e+++ wpGlg
  gi|119719066|ref|YP_919561.1| 226 WIISGFFLGVYGTRTFFLIFSTEDYVEAAKAKGLPPRLIETRYILRPSLPPIVTNFALSLIGSWGGAIITETVFEWPGLG 305
                                    ******************************************************************************** PP

                   BPD_transp_1 139 tllleailgydyseisnggvlalviavlllnlvadilqrlldprvr 184
                                    +++++ai+++d++    g++++++ ++++ +l++d++++l+dpr++
  gi|119719066|ref|YP_919561.1| 306 LVTWRAIQSFDTPVLV-GITVIYAYLLAATVLILDFVYALIDPRIK 350
                                    ****************.***************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 2251.41
//
Query:       gi|119719067|ref|YP_919562.1|  [L=895]
Description: solute binding protein-like protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.5e-22   77.8   1.7    3.7e-19   68.9   0.3    2.3  2  SBP_bac_5  Bacterial extracellular solute-binding proteins, f
  ------ inclusion threshold ------
       0.01   16.2   0.0       0.03   14.7   0.0    1.7  2  FlaC_arch  Flagella accessory protein C (FlaC)


Domain annotation for each model (and alignments):
>> SBP_bac_5  Bacterial extracellular solute-binding proteins, family 5 Middle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.9   0.3   4.1e-23   3.7e-19     150     367 ..      32     273 ..      25     280 .. 0.82
   2 !    7.5   0.1   0.00019       1.7      28     147 ..     496     695 ..     495     720 .. 0.77

  Alignments for each domain:
  == domain 1  score: 68.9 bits;  conditional E-value: 4.1e-23
                                    SSSSEEEEEE-.SHHHHHHHHHTTSSSEE...ESTTCCTHCHHHHHTTEEEEEEEEEEEEEEEEETTT.........STG CS
                      SBP_bac_5 150 pkldriefkvipdsdaraaalqsGeiddv...aepppsdieqlkeakglkvlyespgggvtylafNtk.........kpp 217
                                    p +d++ f    d++  +++  +G+++++   + + ++ +++lk+++++++  + + g ++ l+fN            +p
  gi|119719067|ref|YP_919562.1|  32 PWVDEVSFLKEGDPAKVMDMIAKGDVQVYfsdVRVDAAIAQRLKTDPNINY--KYAFGLYFELTFNPVgpefpktgkLNP 109
                                    668899998888999999999*****9998666666777777777777777..66666666677777799999999977* PP

                                    GGSHHHHHHHHHHS-HHHHHHHCTTTSSEEESSSSTTTSTTCCSCHCCCSHH.....SHHHHHHHH....HHHTT-BCSS CS
                      SBP_bac_5 218 fddkrvRqAlsyAiDreeivkavlegyatpansllppsspgadeeykpayka.....ydpekAkkl....LkeaGykdgd 288
                                    f+ +r+R+A++y +Dr+ iv++++ g a+p   +l +++p + +  ++ +       y+ ek k++    +++ G + +d
  gi|119719067|ref|YP_919562.1| 110 FSVPRIREAMNYIVDRNYIVNEIMLGFAVPKWLPLISQFPEYAKLADTVKLLeaqysYNFEKGKEIifeeMAKLGATYKD 189
                                    *******************************************999998544************9843335788888888 PP

                                    TSCEETCEEEEEEEEETTSHHHHHHHHHHHHHHHHTTEEEEEEEECHH....HHHHHHHHCTTESEEEEEEECT.TSTTH CS
                      SBP_bac_5 289 ggglrekklkltlllasgspaekaiaeliqqqlkkiGikvevktvdwa....atylervkdgdfdmillgwgad.ypdpd 363
                                    g+++ + +++++ +l  +   +++i +++++ql+k+G++ve  +  +      +      dg++ ++ +gw ++  + +d
  gi|119719067|ref|YP_919562.1| 190 GKWYYKGEPVVIKFLIRTEDQRRRIGDYVADQLEKLGFTVERMYKTAReaspIWIRGNPADGQWHIYTGGWITTaVSRDD 269
                                    88888888888888888889999*****************98777544577844444588***********999444444 PP

                                    HHHH CS
                      SBP_bac_5 364 nfln 367
                                    ++++
  gi|119719067|ref|YP_919562.1| 270 SSVW 273
                                    4444 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00019
                                    -B-TTSSB-SHHHHHHHHHHHHTGGGHCTTHHHHHCTCTEEEEEEEETTEEEEEESSETTTTTTHCHHHHHHHGC..... CS
                      SBP_bac_5  28 vkFsDGtpltAeDvvfsferlldpdtasgyaslleedqdikkveavddytvrftlkkpnalfltllaavpasiak..... 102
                                    +k++DGt +  +D+v  +  +    ++s++ ++ +    + +++a   y +  ++ ++ +l +++  ++ ++ ++     
  gi|119719067|ref|YP_919562.1| 496 IKYHDGTTMSLADWVIGWPLTFARVDPSSPLYDES---AVPSFQAWRSYFIAWRFVSTSPLVIEYYVNYTSPDVElivsg 572
                                    78999999999999998888777777777777775...788888888888888888888877777777777666677778 PP

                                    ...............................................................................C CS
                      SBP_bac_5 103 ...............................................................................k 103
                                                                                                                   +
  gi|119719067|ref|YP_919562.1| 573 fagwpnfpwhalaigiraeekgllafsadkadkmkvewmnyiggpsldilskmldealaegyipfkdfmskyvsvdeakA 652
                                    88888888888888999999999999999999999999999999999999999999999999999999999999997741 PP

                                    HTCTCTTT.TTGTTTSE-BSSSEEEEEEETTT.EEEEEE-TTSTTT CS
                      SBP_bac_5 104 aaekeddk.dkdtnekpvgtGPYklkefkpgq.kivlernpdYwgg 147
                                     + ++ ++  +  +   vg GPY l+  + +   +vl++n +Y  +
  gi|119719067|ref|YP_919562.1| 653 -RYNALKSwYAAHKHFWVGDGPYYLDTADYNAhVAVLKANRNY--P 695
                                    .333333203444455799********777664888*******..3 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0         2   1.8e+04      21      33 ..     220     232 ..     217     236 .. 0.63
   2 ?   14.7   0.0   3.4e-06      0.03       4      43 ..     829     868 ..     828     869 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 2
                      FlaC_arch  21 keneelsksveel 33 
                                    +++e+l  +ve++
  gi|119719067|ref|YP_919562.1| 220 DQLEKLGFTVERM 232
                                    5666666666666 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 3.4e-06
                      FlaC_arch   4 elEnklsklsteletvkkeneelsksveelkenVkdllsL 43 
                                    +lE+++  ++t ++ v+ +++++ +sv  l+ +V+ +l+L
  gi|119719067|ref|YP_919562.1| 829 QLESRIAGVETGVSEVRGKISDIANSVSSLQGTVNTVLAL 868
                                    79***********************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (895 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.70u 0.31s 00:00:01.01 Elapsed: 00:00:00.47
# Mc/sec: 5683.87
//
Query:       gi|119719068|ref|YP_919563.1|  [L=167]
Description: AsnC family transcriptional regulator [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      3e-13   49.4   0.9    5.2e-13   48.6   0.9    1.4  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
      3e-12   46.3   0.0    5.5e-12   45.5   0.0    1.5  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
    3.4e-12   45.7   0.8    5.9e-12   45.0   0.8    1.4  1  HTH_24          Winged helix-turn-helix DNA-binding
    1.5e-06   28.1   0.4    2.7e-06   27.2   0.4    1.4  1  HTH_11          HTH domain
    8.5e-06   25.6   0.1    2.3e-05   24.2   0.1    1.7  2  MarR            MarR family
    1.3e-05   25.0   0.0    2.2e-05   24.2   0.0    1.4  1  HxlR            HxlR-like helix-turn-helix
    1.4e-05   25.1   0.2    2.1e-05   24.5   0.2    1.3  1  HTH_20          Helix-turn-helix domain
    6.9e-05   22.6   0.1    0.00013   21.8   0.1    1.4  1  MarR_2          MarR family
    0.00022   21.6   0.2    0.00049   20.5   0.1    1.6  1  HTH_27          Winged helix DNA-binding domain
    0.00059   19.8   0.0    0.00097   19.1   0.0    1.4  1  HTH_Mga         M protein trans-acting positive regulator (MG
     0.0047   16.9   0.1     0.0075   16.2   0.1    1.4  1  HTH_Crp_2       Crp-like helix-turn-helix domain
     0.0047   17.1   0.0     0.0084   16.3   0.0    1.4  1  HTH_34          Winged helix DNA-binding domain
     0.0049   16.4   0.7      0.011   15.3   0.1    1.9  2  HTH_CodY        CodY helix-turn-helix domain
     0.0064   16.5   0.0      0.013   15.5   0.0    1.5  1  FeoC            FeoC like transcriptional regulator
     0.0082   15.9   0.1      0.015   15.1   0.1    1.4  1  LexA_DNA_bind   LexA DNA binding domain
     0.0084   15.9   0.1      0.018   14.9   0.1    1.5  1  HTH_10          HTH DNA binding domain
  ------ inclusion threshold ------
      0.013   15.4   0.2      0.024   14.5   0.2    1.5  1  TrmB            Sugar-specific transcriptional regulator TrmB
      0.017   14.8   0.0      0.023   14.4   0.0    1.2  1  DUF4423         Domain of unknown function (DUF4423)
      0.019   14.8   0.1      0.033   14.0   0.1    1.5  1  HTH_5           Bacterial regulatory protein, arsR family
      0.024   15.0   0.1      0.067   13.6   0.1    1.7  1  Rrf2            Transcriptional regulator
      0.025   14.3   0.2      0.043   13.6   0.2    1.4  1  HTH_DeoR        DeoR-like helix-turn-helix domain
      0.026   14.9   0.1      0.045   14.1   0.1    1.4  1  HTH_WhiA        WhiA C-terminal HTH domain
      0.031   14.2   2.2       0.81    9.7   0.2    2.5  2  HTH_12          Ribonuclease R winged-helix domain
      0.049   14.0   0.0          1    9.8   0.0    2.2  2  FaeA            FaeA-like protein
      0.082   12.8   0.0        1.1    9.2   0.0    2.0  2  Tail_tube       Phage tail tube protein


Domain annotation for each model (and alignments):
>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.6   0.9   7.3e-16   5.2e-13       1      42 []      29      70 ..      29      70 .. 0.99

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 7.3e-16
                  HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrLe 42
                                   +De D++++++L e++R+s +eL++++G++  +v +R+r+Le
  gi|119719068|ref|YP_919563.1| 29 MDEKDLALIRELTENGRASLTELGRKLGITDVAVKKRLRKLE 70
                                   9****************************************8 PP

>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.5   0.0   7.6e-15   5.5e-12       1      74 [.      95     164 ..      95     165 .. 0.97

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 7.6e-15
                                    EEEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEE CS
                 AsnC_trans_reg   1 vlvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivle 74 
                                    +++ +ep++   + +++ ++a  +  v +y +tGd+ +++++++rd+++l +++ e ++s +gv+r+   ivle
  gi|119719068|ref|YP_919563.1|  95 IGIDVEPEK---ILDVASKIASKDFAVKVYLTTGDHMIMVEAWARDNKHLTQIIGE-IGSTEGVKRVCPAIVLE 164
                                    689999999...********************************************.****************8 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.0   0.8   8.2e-15   5.9e-12       1      48 []      29      76 ..      29      76 .. 0.99

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 8.2e-15
                         HTH_24  1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                   +de+d++++++L +n+r s +eL ++lg++  +v++rl++Le++G+Ik
  gi|119719068|ref|YP_919563.1| 29 MDEKDLALIRELTENGRASLTELGRKLGITDVAVKKRLRKLERAGVIK 76
                                   8**********************************************8 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.4   3.7e-09   2.7e-06       4      55 .]      35      90 ..      32      90 .. 0.92

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 3.7e-09
                         HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg....vpIesepgr.GYr 55
                                   ++++ L  ++g  s  eL ++L+++  +v +++++Le +g    + +e +p++ GY+
  gi|119719068|ref|YP_919563.1| 35 ALIREL-TENGRASLTELGRKLGITDVAVKKRLRKLERAGvikkYTVEVDPSKlGYK 90
                                   578888.666679*******************************************6 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.1   3.2e-08   2.3e-05       6      51 ..      34      79 ..      30      83 .. 0.92
   2 ?   -2.5   0.0       7.2   5.2e+03       2      23 ..     123     144 ..     122     153 .. 0.69

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 3.2e-08
                                   HHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                           MarR  6 fviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRsk 51
                                   + ++r l e+g +s++eL++klg++  +v + l++Le++G i+++ 
  gi|119719068|ref|YP_919563.1| 34 LALIRELTENGRASLTELGRKLGITDVAVKKRLRKLERAGVIKKYT 79
                                   678999************************************9986 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 7.2
                                    -HHHHHHHHHHHHSTTEEHHHH CS
                           MarR   2 tltqfviLrilyeqgplsvseL 23 
                                    t   ++i++  + +++  ++++
  gi|119719068|ref|YP_919563.1| 123 TTGDHMIMVEAWARDNKHLTQI 144
                                    6666778888888888777766 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   3.1e-08   2.2e-05       9      66 ..      35      92 ..      29     115 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 3.1e-08
                                   HHHHHHTT.S-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE- CS
                           HxlR  9 lilvellk.gkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYslt 66
                                    +++el++ g+   +el r+l +i+     +rLr+Le+ g+i++ +++  P k  Y+  
  gi|119719068|ref|YP_919563.1| 35 ALIRELTEnGRASLTELGRKL-GITDVAVKKRLRKLERAGVIKKYTVEVDPSKLGYKSV 92
                                   5678888779999********.9*********************************753 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.2     3e-08   2.1e-05      13      57 ..      34      78 ..      23      81 .. 0.92

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 3e-08
                                   HHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                         HTH_20 13 rrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevv 57
                                   +++ r+L++++ ++++el + l++++  + ++Lr+Le+ag ++  
  gi|119719068|ref|YP_919563.1| 34 LALIRELTENGRASLTELGRKLGITDVAVKKRLRKLERAGVIKKY 78
                                   67899************************************9865 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.1   1.8e-07   0.00013       9      54 ..      35      78 ..      29      83 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.8e-07
                                   HHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                         MarR_2  9 rvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                    ++ +L  +++   + +el r+lg++  av ++l++L++aG + + 
  gi|119719068|ref|YP_919563.1| 35 ALIRELTENGR--ASLTELGRKLGITDVAVKKRLRKLERAGVIKKY 78
                                   57788888987..9****************************9875 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.1   6.8e-07   0.00049       7      50 ..      35      77 ..      29      84 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 6.8e-07
                         HTH_27  7 lvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLver 50
                                   ++++ +  +++r++l++l ++l ++d ++ + l+kL+++G++++
  gi|119719068|ref|YP_919563.1| 35 ALIRELT-ENGRASLTELGRKLGITDVAVKKRLRKLERAGVIKK 77
                                   4556666.99*******************************965 PP

>> HTH_Mga  M protein trans-acting positive regulator (MGA) HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   1.4e-06   0.00097       6      55 ..      32      81 ..      29      86 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.4e-06
                        HTH_Mga  6 rklkLlelLteneksltldelakeLglseltlqsdiseLnel.Fpeelsiv 55
                                    +l L+  Lte +++ +l+el  +Lg++ +++++++++L  + ++++++++
  gi|119719068|ref|YP_919563.1| 32 KDLALIRELTE-NGRASLTELGRKLGITDVAVKKRLRKLERAgVIKKYTVE 81
                                   67889999***.***************************998888888776 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   1.1e-05    0.0075      21      59 ..      45      82 ..      14      88 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.1e-05
                                   EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETEEEEE CS
                      HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglisrgrriri 59
                                   + + +el++ lG+t + v + l++L+r+g+i++ + +++
  gi|119719068|ref|YP_919563.1| 45 RASLTELGRKLGITDVAVKKRLRKLERAGVIKKYT-VEV 82
                                   567789*************************9765.554 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.2e-05    0.0084       3      45 ..      34      76 ..      33      86 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.2e-05
                         HTH_34  3 lavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYie 45
                                   la++  L ++ +a+ +el  +l++td +  + l+kLe ag i+
  gi|119719068|ref|YP_919563.1| 34 LALIRELTENGRASLTELGRKLGITDVAVKKRLRKLERAGVIK 76
                                   789999**********************************987 PP

>> HTH_CodY  CodY helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   1.5e-05     0.011       3      35 ..      44      76 ..      42      83 .. 0.85
   2 ?   -3.0   0.1         8   5.7e+03       6      12 ..     107     113 ..     104     114 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.5e-05
                       HTH_CodY  3 GrLtaskiaDriGitrsvivnaLrkLesaGiie 35
                                   Gr    ++  ++Git   +   LrkLe aG+i 
  gi|119719068|ref|YP_919563.1| 44 GRASLTELGRKLGITDVAVKKRLRKLERAGVIK 76
                                   666667778899*******************97 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 8
                       HTH_CodY   6 taskiaD 12 
                                    +askia 
  gi|119719068|ref|YP_919563.1| 107 VASKIAS 113
                                    7999996 PP

>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.8e-05     0.013       7      50 ..      39      81 ..      34      86 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.8e-05
                           FeoC  7 eyleergrvslkeLsrhfkaspealeamLeqwvrkGrvekvaat 50
                                   e+  e+gr+sl eL r++ ++  a+++ L  ++r G ++k + +
  gi|119719068|ref|YP_919563.1| 39 EL-TENGRASLTELGRKLGITDVAVKKRLRKLERAGVIKKYTVE 81
                                   54.89**********************************98876 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   2.1e-05     0.015      19      57 ..      40      76 ..      33      81 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.1e-05
                                   HHHHSS---HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE CS
                  LexA_DNA_bind 19 ieetgypPsireiaralglkSpsaveehLkaLerKGyie 57
                                   ++e+g + s  e++r+lg++   av+++L++Ler G+i+
  gi|119719068|ref|YP_919563.1| 40 LTENGRA-SLTELGRKLGIT-DVAVKKRLRKLERAGVIK 76
                                   5566655.899*********.99**************97 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   2.4e-05     0.018      23      49 ..      45      71 ..      42      72 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.4e-05
                         HTH_10 23 rvtlkeLAkelGIskstlsehLrkaes 49
                                   r++l eL  +lGI++ +++++Lrk e+
  gi|119719068|ref|YP_919563.1| 45 RASLTELGRKLGITDVAVKKRLRKLER 71
                                   799*********************886 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.2   3.4e-05     0.024      17      57 ..      40      80 ..      30      93 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.4e-05
                                   HHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESS CS
                           TrmB 17 LlklgpatadeiaeelgvprskvYevLrsLedkGlVerekg 57
                                   L ++g+a+ +e+ ++lg+    v + Lr+Le++G++++   
  gi|119719068|ref|YP_919563.1| 40 LTENGRASLTELGRKLGITDVAVKKRLRKLERAGVIKKYTV 80
                                   6699********************************98665 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   3.2e-05     0.023      26      71 ..      37      78 ..      29     107 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.2e-05
                        DUF4423 26 irellplkdfkadpeelakrlrpkisaeevekalefLlklgllkkd 71
                                   irel +  +++a+  el ++l+  i+   v+k l+ L+++g++kk 
  gi|119719068|ref|YP_919563.1| 37 IRELTE--NGRASLTELGRKLG--ITDVAVKKRLRKLERAGVIKKY 78
                                   566554..45679*********..********************95 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   4.7e-05     0.033       5      47 .]      34      77 ..      30      77 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.7e-05
                                   HHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                          HTH_5  5 lkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                   l +++ L e g ++ +el ++lg++  +v   L+kL+ aG+++k
  gi|119719068|ref|YP_919563.1| 34 LALIRELTEnGRASLTELGRKLGITDVAVKKRLRKLERAGVIKK 77
                                   66777888889999***************************986 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   9.3e-05     0.067      17      56 ..      37      76 ..      31      79 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.3e-05
                                   HHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                           Rrf2 17 LakeeeeepvsseeiaerqnispsylekilakLrkaglvk 56
                                   + +  e++ +s++e+ ++ +i ++ ++k l+kL++ag++k
  gi|119719068|ref|YP_919563.1| 37 IRELTENGRASLTELGRKLGITDVAVKKRLRKLERAGVIK 76
                                   5556667779****************************98 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2     6e-05     0.043       5      46 ..      36      77 ..      33      79 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6e-05
                       HTH_DeoR  5 ilellkqqgklsveelvellgvSeaTiRRDLneLeeqglltR 46
                                   ++  l + g  s++el   lg+++  + + L++Le +g++++
  gi|119719068|ref|YP_919563.1| 36 LIRELTENGRASLTELGRKLGITDVAVKKRLRKLERAGVIKK 77
                                   78899**********************************987 PP

>> HTH_WhiA  WhiA C-terminal HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   6.2e-05     0.045      40      82 ..      29      71 ..      14      72 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.2e-05
                                   HHHHHHHHHH..HH-TTS-HHHHHHTT..T--HHHHHHHHHHHHH CS
                       HTH_WhiA 40 eklkevaelR..lenpdaSLkeLgelleppisKSgvnhrlrklke 82
                                    + k++a +R   en  aSL+eLg+ l   i+  +v++rlrkl++
  gi|119719068|ref|YP_919563.1| 29 MDEKDLALIRelTENGRASLTELGRKL--GITDVAVKKRLRKLER 71
                                   4445555555226999***********..9*************85 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.2     0.075        53      42      64 ..      29      54 ..      21      56 .. 0.81
   2 ?    9.7   0.2    0.0011      0.81      31      51 ..      58      78 ..      54      82 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.075
                         HTH_12 42 leerg..ltrrvgyagr.eltEkGle 64
                                   ++e++  l+r    +gr  ltE G +
  gi|119719068|ref|YP_919563.1| 29 MDEKDlaLIRELTENGRaSLTELGRK 54
                                   89998889999998876379*99976 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0011
                         HTH_12 31 geravRyrLrkleergltrrv 51
                                    + av  rLrkle+ g +++ 
  gi|119719068|ref|YP_919563.1| 58 TDVAVKKRLRKLERAGVIKKY 78
                                   5669**************995 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0    0.0014         1       9      49 ..      37      79 ..      29      82 .. 0.76
   2 ?    1.9   0.0       0.4   2.9e+02      15      45 ..     101     131 ..      94     135 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0014
                                   HHH...S----HHHHHHHHTS-HHHHHHHHHHHHHHSSEEEE- CS
                           FaeA  9 lnsi..kapckTreiAdalglsaYQaRyYLeqLekegkikrsp 49
                                   + ++  ++ +  +e+   lg+++  ++  L +Le++g ik+  
  gi|119719068|ref|YP_919563.1| 37 IRELteNGRASLTELGRKLGITDVAVKKRLRKLERAGVIKKYT 79
                                   55552244444579999***********************976 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.4
                                    ---HHHHHHHHTS-HHHHHHHHHHHHHHSSE CS
                           FaeA  15 pckTreiAdalglsaYQaRyYLeqLekegki 45 
                                    p k  ++A  ++  ++ ++ YL + ++  ++
  gi|119719068|ref|YP_919563.1| 101 PEKILDVASKIASKDFAVKVYLTTGDHMIMV 131
                                    667789****************998877776 PP

>> Tail_tube  Phage tail tube protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.36   2.5e+02      38      71 ..       3      37 ..       1      41 [. 0.59
   2 ?    9.2   0.0    0.0015       1.1      43     106 ..      88     148 ..      65     152 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.36
                      Tail_tube 38 gdgVvgysekpkapsiea..tiadeedldleelkal 71
                                   g +V gy+e    ++i++   +a+e ++d ++l  +
  gi|119719068|ref|YP_919563.1|  3 GFKVDGYNEA-FLAEITVstVVAREVRMDEKDLALI 37
                                   5789999999.5555655115555555666666555 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0015
                      Tail_tube  43 gysekpkapsieatiadeedldleelkaltnatvtfeldnGktyvlsgAwlvdepelkskdGti 106
                                    gy+++   + i + +  e+ ld++   a ++  v + l +G   ++ +Aw  d+  l++  G+i
  gi|119719068|ref|YP_919563.1|  88 GYKSV---ALIGIDVEPEKILDVASKIASKDFAVKVYLTTGDHMIMVEAWARDNKHLTQIIGEI 148
                                    55554...8888999999999999999***************************9998765665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       741  (0.0413297); expected 358.6 (0.02)
Passed bias filter:                      616  (0.0343577); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1228.26
//
Query:       gi|119719069|ref|YP_919564.1|  [L=472]
Description: hypothetical protein Tpen_0151 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0061   16.8  11.9       0.65   10.3   0.0    4.0  4  DUF5122   Domain of unknown function (DUF5122) beta-propeller


Domain annotation for each model (and alignments):
>> DUF5122  Domain of unknown function (DUF5122) beta-propeller
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.4       0.9   1.6e+04       8      19 ..      76      86 ..      75      88 .. 0.56
   2 !    7.0   0.1   0.00041       7.4       2      26 ..     131     157 ..     130     159 .. 0.86
   3 !   10.3   0.0   3.6e-05      0.65       4      28 ..     185     210 ..     185     214 .. 0.89
   4 !    5.7   0.7     0.001        18       3      26 ..     236     259 ..     234     264 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 0.9
                        DUF5122  8 VaGsftsyngss 19
                                   V Gs+   ngs+
  gi|119719069|ref|YP_919564.1| 76 VTGSYA-TNGSG 86
                                   556655.56665 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.00041
                        DUF5122   2 pDGKIlVaGsftsy..ngssdfalvRL 26 
                                    ++G ++VaG+ +      ssd  +vRL
  gi|119719069|ref|YP_919564.1| 131 GNGTLFVAGYVYAEatTRSSDVVVVRL 157
                                    5899********447999999999998 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 3.6e-05
                        DUF5122   4 GKIlVaGsftsy.ngssdfalvRLna 28 
                                    G ++V+G+++ y  +++d  ++RL++
  gi|119719069|ref|YP_919564.1| 185 GYLVVVGETWAYnVSQGDVFVARLTP 210
                                    679*******555***********98 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.001
                        DUF5122   3 DGKIlVaGsftsyngssdfalvRL 26 
                                    DG++l++Gs+   +g  d  ++R 
  gi|119719069|ref|YP_919564.1| 236 DGSLLLVGSTVGGDGTHDGFVARV 259
                                    ***********7799999999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (472 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 3096.16
//
Query:       gi|119719070|ref|YP_919565.1|  [L=203]
Description: hypothetical protein Tpen_0152 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.2e-05   23.8   2.2    3.4e-05   23.7   0.4    1.9  2  HTH_1         Bacterial regulatory helix-turn-helix protein, 
  ------ inclusion threshold ------
      0.011   15.6   0.0      0.042   13.7   0.0    2.0  2  MarR_2        MarR family
      0.013   15.6   0.1       0.23   11.6   0.0    2.5  2  HTH_28        Helix-turn-helix domain
      0.025   14.6   0.7       0.24   11.5   0.7    2.6  1  HTH_20        Helix-turn-helix domain
      0.074   13.0   0.4       0.75    9.8   0.0    2.4  2  HTH_Crp_2     Crp-like helix-turn-helix domain
      0.075   13.0   0.0        0.2   11.7   0.0    1.8  1  Hjc           Archaeal holliday junction resolvase (hjc)
      0.096   12.1   1.0       0.32   10.4   0.0    2.4  3  HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family I
       0.12   12.2   0.3       0.64    9.9   0.0    2.4  3  HTH_23        Homeodomain-like domain


Domain annotation for each model (and alignments):
>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1       3.9   8.8e+03      18      25 ..      92      99 ..      90     100 .. 0.78
   2 !   23.7   0.4   1.5e-08   3.4e-05       5      40 ..     145     180 ..     143     186 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 3.9
                                   HHHHHHTS CS
                          HTH_1 18 rAAeeLgl 25
                                   + AeeLg+
  gi|119719070|ref|YP_919565.1| 92 ATAEELGV 99
                                   68999987 PP

  == domain 2  score: 23.7 bits;  conditional E-value: 1.5e-08
                                    HHHHHHHHHSSHHHHHHHHTS-HHHHHHHHHHHHHH CS
                          HTH_1   5 rlfvavaeegsftrAAeeLglsqpavsrqikrLEee 40 
                                    ++ +a+a + sf +AA++Lg+s  a+ +++ +L+e 
  gi|119719070|ref|YP_919565.1| 145 EVVKAIASSSSFEEAARRLGVSTDALGKAVEALREK 180
                                    7889*****************************986 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.7   3.8e+03       2      12 ..      33      43 ..      32      44 .. 0.88
   2 ?   13.7   0.0   1.9e-05     0.042       3      52 ..     139     184 ..     137     188 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.7
                                   T--HHHHHHHH CS
                         MarR_2  2 gltpaqarvLa 12
                                   g+++a+ ++La
  gi|119719070|ref|YP_919565.1| 33 GVSLAEVDILA 43
                                   8999****997 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 1.9e-05
                                    --HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                         MarR_2   3 ltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52 
                                    l+p +  v  a++ +     +  e arrlg+s  a+ ++++ L ++G ++
  gi|119719070|ref|YP_919565.1| 139 LSPPEVEVVKAIASSS----SFEEAARRLGVSTDALGKAVEALREKGAIT 184
                                    7788888888888886....99*************************886 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.22     5e+02      13      24 ..      88      99 ..      79     101 .. 0.75
   2 ?   11.6   0.0    0.0001      0.23       4      42 ..     145     183 ..     144     188 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.22
                         HTH_28 13 hsvreaArelgi 24
                                   ++++++A+elg+
  gi|119719070|ref|YP_919565.1| 88 EAAKATAEELGV 99
                                   58999*****98 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.0001
                         HTH_28   4 eiikllaaGhsvreaArelgisrrtvyrWikryeegGia 42 
                                    e++k++a+  s  eaAr+lg+s + + + + +++e G  
  gi|119719070|ref|YP_919565.1| 145 EVVKAIASSSSFEEAARRLGVSTDALGKAVEALREKGAI 183
                                    7999999999*******************9999999965 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.7   0.00011      0.24      16      59 ..     147     188 ..     114     190 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00011
                                    HHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
                         HTH_20  16 lraLaraegltaselaerldlskntlsyHLrvLeeagLvevvre 59 
                                     +a+  a   +++e a+rl++s   l + +++L+e g++++  +
  gi|119719070|ref|YP_919565.1| 147 VKAI--ASSSSFEEAARRLGVSTDALGKAVEALREKGAITLHSP 188
                                    4444..88889****************************98766 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1      0.19   4.3e+02       1      13 [.       8      20 ..       8      41 .. 0.63
   2 ?    9.8   0.0   0.00033      0.75      23      61 ..     155     193 ..     116     196 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.19
                                   HHHHHHHHHHHCT CS
                      HTH_Crp_2  1 qRlArfLlrlaer 13
                                   + lAr++l+l+  
  gi|119719070|ref|YP_919565.1|  8 EALARLILELEGF 20
                                   579*****99432 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00033
                                    HHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ETEEEEES- CS
                      HTH_Crp_2  23 tqeelAsmlGltretvsrilseLkreglis.rgrririld 61 
                                    + ee A++lG++   + ++  +L+++g i+  +  +r+l 
  gi|119719070|ref|YP_919565.1| 155 SFEEAARRLGVSTDALGKAVEALREKGAITlHSP-FRLLR 193
                                    56899************************94445.66665 PP

>> Hjc  Archaeal holliday junction resolvase (hjc)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   8.9e-05       0.2      29      79 ..      37      82 ..      12      94 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8.9e-05
                                   SS-SEEEEETTEEEEEEEEEESSSEEEEEHHHHHHHHHHHHHHTCEEEEEE CS
                            Hjc 29 plpDviAirgdvvlviEvKsskkeriylkkeqvekllefarkaggelllav 79
                                     +D++A ++++ +++EvKs +     ++  +v+++   a   g+++ll +
  gi|119719070|ref|YP_919565.1| 37 AEVDILARKNGEAYAVEVKSGR-----VSVTDVRQVYANAALLGAKPLLIA 82
                                   569*****************98.....666777777777777777776655 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.83   1.9e+03      24      35 ..      54      66 ..      48      68 .. 0.69
   2 ?   -3.3   0.0       2.9   6.4e+03      31      39 ..      91      99 ..      89      99 .. 0.85
   3 ?   10.4   0.0   0.00014      0.32      22      44 ..     148     170 ..     143     177 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.83
                   HTH_Tnp_ISL3 24 lles.rsvkavAr 35
                                   ++++  sv++v +
  gi|119719070|ref|YP_919565.1| 54 VKSGrVSVTDVRQ 66
                                   4555589999975 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.9
                   HTH_Tnp_ISL3 31 kavArqlgv 39
                                   ka A++lgv
  gi|119719070|ref|YP_919565.1| 91 KATAEELGV 99
                                   789999997 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00014
                   HTH_Tnp_ISL3  22 elllesrsvkavArqlgvSwtTV 44 
                                    ++  +s s+ ++Ar+lgvS++ +
  gi|119719070|ref|YP_919565.1| 148 KAIASSSSFEEAARRLGVSTDAL 170
                                    5555667*************976 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       3.5   7.8e+03      10      22 ..      13      24 ..      10      25 .. 0.60
   2 ?   -2.3   0.0       1.9   4.3e+03      21      29 ..      91      99 ..      89     100 .. 0.84
   3 ?    9.9   0.0   0.00028      0.64      10      46 ..     146     182 ..     144     185 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3.5
                         HTH_23 10 illllaeGlsvre 22
                                    +l l  G sv++
  gi|119719070|ref|YP_919565.1| 13 LILELE-GFSVEQ 24
                                   344444.999887 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.9
                         HTH_23 21 reIAreLgv 29
                                   ++ A+eLgv
  gi|119719070|ref|YP_919565.1| 91 KATAEELGV 99
                                   5789***98 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.00028
                         HTH_23  10 illllaeGlsvreIAreLgvsrrTvyrwlkryreeGl 46 
                                    ++++ a   s +e+Ar+Lgvs   + + +++ re+G+
  gi|119719070|ref|YP_919565.1| 146 VVKAIASSSSFEEAARRLGVSTDALGKAVEALREKGA 182
                                    566667677889*****************99999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1543.38
//
Query:       gi|119719071|ref|YP_919566.1|  [L=353]
Description: phosphoadenosine phosphosulfate reductase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.5e-07   29.6   0.0      1e-06   28.9   0.0    1.4  1  PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
      0.002   17.9   0.0     0.0036   17.1   0.0    1.4  1  ATP_bind_3   PP-loop family


Domain annotation for each model (and alignments):
>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0   1.1e-10     1e-06       5     117 ..      94     210 ..      90     266 .. 0.80

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 1.1e-10
                                    E--SSCTCHHHHHHHHHHCTTH....EEEEEE-ST.B-HHHHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHHH-S-THHH CS
                    PAPS_reduct   5 svsgGkdslVllhLalkafkpv....pvvfvdtgh.efpetiefvdeleeryglrlkvyepeeevaekinaekhgsslye 79 
                                      sgGkds++ l L++k ++ v    + v+v + + e  e i+f +++++r+g++l ++ep++++ e +   + g  +  
  gi|119719071|ref|YP_919566.1|  94 DLSGGKDSTANLYLLTKLQEIVgfkvTAVYVHMPYlEPVENIAFAEKVASRLGVDLRIVEPDRRKLE-FYLLREGLPKRG 172
                                    58***************9998566779999998772667****************999999988444.444444444445 PP

                                    CHHHHHHTHHHHHHHHHCTTECEEE----CCCTTTTTT CS
                    PAPS_reduct  80 eaaeriaKveplkkaLekldedalltGaRrdesksrak 117
                                    +++++  K+++l++a +++++++     R+ e  +r +
  gi|119719071|ref|YP_919566.1| 173 DRWCTYLKTRALREAKKEIGAEVEAKAERALEAGKRYE 210
                                    578************99999999888888888887754 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0     4e-07    0.0036       2      65 ..      91     153 ..      90     165 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4e-07
                                    EEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE CS
                     ATP_bind_3   2 vlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckklnikleiek 65 
                                    v++ +SgG DS+a l+ll kl++  g+k++a++v+     e  e+ ++ ++++++l+++l+i +
  gi|119719071|ref|YP_919566.1|  91 VMADLSGGKDSTANLYLLTKLQEIVGFKVTAVYVHMP-YLEPVENIAFAEKVASRLGVDLRIVE 153
                                    56679****************************9655.45667788899999999999888866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2356.39
//
Query:       gi|119719072|ref|YP_919567.1|  [L=214]
Description: hypothetical protein Tpen_0154 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.8e-32  111.4   0.3    6.6e-32  110.7   0.3    1.4  1  Lactamase_B_3  Beta-lactamase superfamily domain
    1.8e-19   70.1   0.1    2.4e-19   69.7   0.1    1.2  1  Lactamase_B_2  Beta-lactamase superfamily domain
    0.00051   20.1   1.3     0.0082   16.2   1.3    2.1  1  Lactamase_B    Metallo-beta-lactamase superfamily


Domain annotation for each model (and alignments):
>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.7   0.3   1.1e-35   6.6e-32       2     163 .]      11     187 ..      10     187 .. 0.87

  Alignments for each domain:
  == domain 1  score: 110.7 bits;  conditional E-value: 1.1e-35
                  Lactamase_B_3   2 ltwlghnsflletagarilvDPfkanlgyeppaeeaDlvlisqaledHahletlkqlaenvkvlee.............. 67 
                                    +t lgh++f+++++ +++++DPf+    +  ++++aD+v+ ++++ dH+ ++ ++++a++++v+                
  gi|119719072|ref|YP_919567.1|  11 ITRLGHAAFRITDGKVVVYIDPFQ----VPSSPRDADIVVCTHDHYDHCSPDDIRKVAKQTTVVVAsvncaakvkglgye 86 
                                    899********************9....8999*************************66666666666666666666666 PP

                  Lactamase_B_3  68 ......geslevggleiravatshdavggs.ergenngflleqdgltiyhlGhlahelsseelkelgrvDvvltPvggpl 140
                                          g+ ++v+g+ei+av++++ ++  + +  +++g l++ +++ +yh G+++  +++++l   g+v v l+Pv g++
  gi|119719072|ref|YP_919567.1|  87 ykllnpGDRVAVKGVEIEAVPAYNVGKRFHpKDYKGIGVLVRLGDVVVYHAGDTDFIPEMASL--KGKVSVALLPVSGTY 164
                                    666665999***************888655255679*******************96555555..678************ PP

                  Lactamase_B_3 141 tlgqeealelakrLkpklvlPmh 163
                                    +++++ea+++a+ ++p+l +Pmh
  gi|119719072|ref|YP_919567.1| 165 VMDADEAVKAAETISPELAIPMH 187
                                    **********************9 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.7   0.1     4e-23   2.4e-19      21     201 .]      32     188 ..      19     188 .. 0.88

  Alignments for each domain:
  == domain 1  score: 69.7 bits;  conditional E-value: 4e-23
                                    --SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTTTTEEEEEE-TTSEEEECS CS
                  Lactamase_B_2  21 PvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleeepavnvheldwgesfelgd 100
                                    P +  +++++ d V+ th+HyDH+   +++r+ +++   ++a+  ++a+++            + + + l++g++++++ 
  gi|119719072|ref|YP_919567.1|  32 PFQVPSSPRDADIVVCTHDHYDHC-SPDDIRKVAKQTTVVVASVNCAAKVKGL----------GYEYKLLNPGDRVAVK- 99 
                                    5566678999**************.579****665533355888888888888..........45678899*******9. PP

                                    TTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---HHHHHHHCT-SEEEEE-S-SSTTHHHHHHT--- CS
                  Lactamase_B_2 101 ggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyipeeigerlggadllllditayeddemirhmgHlt 180
                                     g+ei+a+pa   ++r + ++  + +G++++ g+  vy++gDt +ipe++  + g++ ++ll++          + + ++
  gi|119719072|ref|YP_919567.1| 100 -GVEIEAVPAYNVGKR-FHPKDYKGIGVLVRLGDVVVYHAGDTDFIPEMAS-LKGKVSVALLPVS---------GTYVMD 167
                                    .899********9999.99****************************8844.7777*******98.........8899** PP

                                    STSHHHHCTTSSSSEEEEESB CS
                  Lactamase_B_2 181 peeaveaaadlgakrlvliHi 201
                                     +eav+aa+ ++++ ++++H+
  gi|119719072|ref|YP_919567.1| 168 ADEAVKAAETISPELAIPMHY 188
                                    ********************7 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   1.3   1.4e-06    0.0082      36     175 ..      33     171 ..      15     187 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.4e-06
                                    HHHTSGGGGEEEEE-SBSSHHHHT..TGGGCTTHHCCEETCCEHHHHCCHCHHHHHHHHHCCHHTTCHCGCCEEEEETTT CS
                    Lactamase_B  36 aalglkpkdvdavilTHlHlDHiG..glgglveatdvpvgavaeeapalfmeeaddaasrkglllagvsadkpdvdeeel 113
                                    +++   p+d d v+ TH H+DH++  + ++++++t v+v+ v  +a++    ++++            ++ + ++++ ++
  gi|119719072|ref|YP_919567.1|  33 FQVPSSPRDADIVVCTHDHYDHCSpdDIRKVAKQTTVVVASVNCAAKVKGLGYEYKL----------LNPGDRVAVKGVE 102
                                    5666789****************9778888888888888888777777777777443..........4445556666666 PP

                                    EECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCCCCC........TTCEEE-SHCHH CS
                    Lactamase_B 114 dgnaggrralyvtggpghghghgvveygggkvlftGDallagetgridl.......tlrgaevrdpsda 175
                                     + ++    ++ ++     ++++ v++g+  v  +GD+ +++e +++         +  g +v+d+++a
  gi|119719072|ref|YP_919567.1| 103 IEAVPAYNVGKRFHPKDYKGIGVLVRLGDVVVYHAGDTDFIPEMASLKGkvsvallPVSGTYVMDADEA 171
                                    666666666666666666778888888888888888888888888877765555555555555554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1496.29
//
Query:       gi|119719073|ref|YP_919568.1|  [L=106]
Description: biotin/lipoyl attachment domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-17   61.9   2.7    3.9e-17   61.9   2.7    1.6  2  Biotin_lipoyl    Biotin-requiring enzyme
    1.4e-16   60.0   0.3    1.9e-08   34.0   0.0    2.3  2  Biotin_lipoyl_2  Biotin-lipoyl like
    5.2e-11   43.2   1.3    0.00023   21.8   0.2    2.3  2  HlyD_3           HlyD family secretion protein
    4.7e-09   35.8   2.5    0.00036   19.8   0.2    2.1  2  HlyD_D23         Barrel-sandwich domain of CusB or HlyD membr
    5.1e-07   29.8   1.3     0.0012   19.1   0.2    2.6  2  Peptidase_M23    Peptidase family M23
    1.2e-06   28.4   2.8    6.1e-06   26.1   0.8    2.1  2  RnfC_N           RnfC Barrel sandwich hybrid domain
    6.6e-05   22.9   0.5       0.16   12.1   0.1    2.7  3  QRPTase_N        Quinolinate phosphoribosyl transferase, N-te
    0.00012   21.8   0.7     0.0072   16.1   0.7    3.0  1  PTS_EIIA_1       phosphoenolpyruvate-dependent sugar phosphot
     0.0017   18.3   1.2     0.0027   17.6   1.0    1.6  1  GCV_H            Glycine cleavage H-protein
      0.002   18.1   1.6      0.016   15.2   1.4    2.1  1  DUF2118          Uncharacterized protein conserved in archaea
  ------ inclusion threshold ------
      0.014   14.5   0.1      0.014   14.5   0.1    1.1  1  SatRNA_48        Satellite RNA 48 kDa protein
      0.026   14.2   0.3        3.6    7.3   0.1    2.3  2  PYNP_C           Pyrimidine nucleoside phosphorylase C-termin
        0.1   12.5   2.6       0.84    9.5   0.8    2.2  2  PASTA            PASTA domain


Domain annotation for each model (and alignments):
>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       2.5   3.5e+03      44      62 ..       4       9 ..       1      22 [. 0.45
   2 !   61.9   2.7   2.8e-20   3.9e-17       8      73 .]      42     102 ..      31     102 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.5
                                   EEEBSSSEEEEEESSTTTE CS
                  Biotin_lipoyl 44 eieapkaGvvkeilvkeGd 62
                                   e+             +eG+
  gi|119719073|ref|YP_919568.1|  4 EV-------------PEGE 9 
                                   33.............3332 PP

  == domain 2  score: 61.9 bits;  conditional E-value: 2.8e-20
                                    SEEEEEE.ECSESSSTTCEE-TTSEEEEEECTTEEEEEEBSSSEEEEEESSTTTEEE-TTCEEEEE CS
                  Biotin_lipoyl   8 iGesveegvvevlvkvGdkVkagqvlaeveamKmemeieapkaGvvkeilvkeGdtvevgdllaki 73 
                                     G      v ++lvk+G+ V++g ++a++eamK  +e+++ ++Gvvke+lv eG+ v++g ++a+i
  gi|119719073|ref|YP_919568.1|  42 TGR-----VSRILVKEGQRVEKGTTIATMEAMKTLIEVKSSMNGVVKEVLVAEGEVVKQGAPIARI 102
                                    344.....566*****************************************************97 PP

>> Biotin_lipoyl_2  Biotin-lipoyl like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   0.0   1.4e-11   1.9e-08       7      42 ..      39      74 ..      37      76 .. 0.90
   2 !   25.5   0.1   6.1e-09   8.4e-06       4      36 ..      73     105 ..      70     106 .] 0.93

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 1.4e-11
                Biotin_lipoyl_2  7 apvsGrVaqlnVkdGqrVkaGdvLaelDsralqlal 42
                                   ap+ GrV++++Vk+GqrV++G ++a+ +  +++ ++
  gi|119719073|ref|YP_919568.1| 39 APITGRVSRILVKEGQRVEKGTTIATMEAMKTLIEV 74
                                   8999***********************999988776 PP

  == domain 2  score: 25.5 bits;  conditional E-value: 6.1e-09
                Biotin_lipoyl_2   4 sIaapvsGrVaqlnVkdGqrVkaGdvLaelDsr 36 
                                    +++++ +G+V++++V +G +Vk+G  +a++ +r
  gi|119719073|ref|YP_919568.1|  73 EVKSSMNGVVKEVLVAEGEVVKQGAPIARIAPR 105
                                    7999*************************9887 PP

>> HlyD_3  HlyD family secretion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.1   4.8e-07   0.00066       2      36 ..      37      71 ..      36      73 .. 0.92
   2 !   21.8   0.2   1.7e-07   0.00023       2      32 ..      74     104 ..      73     106 .] 0.94

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 4.8e-07
                         HlyD_3  2 lrApvdGvvvelnveegevvqagdelleiippdtl 36
                                   + Ap++G+v+ + v+eg+ v++g+++++    +tl
  gi|119719073|ref|YP_919568.1| 37 VVAPITGRVSRILVKEGQRVEKGTTIATMEAMKTL 71
                                   78**************************9887776 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 1.7e-07
                         HlyD_3   2 lrApvdGvvvelnveegevvqagdelleiip 32 
                                    ++++  Gvv+e+ v egevv +g+++++i+p
  gi|119719073|ref|YP_919568.1|  74 VKSSMNGVVKEVLVAEGEVVKQGAPIARIAP 104
                                    899***************************9 PP

>> HlyD_D23  Barrel-sandwich domain of CusB or HlyD membrane-fusion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.2     1e-06    0.0014      11     142 ..      26      68 ..      16      71 .. 0.54
   2 !   19.8   0.2   2.6e-07   0.00036     104     140 ..      67     103 ..      63     106 .] 0.91

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1e-06
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXX CS
                       HlyD_D23  11 tvayderrlarvsarveGwveklyvnatgdkVkkGqpLaelyspelvaaqeeyllalkakkklkkkelleaarerLrllg 90 
                                    +v+++ ++                                                                        
  gi|119719073|ref|YP_919568.1|  26 KVEAQPQSKEY--------------------------------------------------------------------- 36 
                                    44444444444..................................................................... PP

                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       HlyD_D23  91 vseeqiaelektgkvqktvtvkapisGvVteknvreGqyvqpgdtlftiadl 142
                                                        v api+G V +  v eGq+v++g+t++t+  +
  gi|119719073|ref|YP_919568.1|  37 --------------------VVAPITGRVSRILVKEGQRVEKGTTIATMEAM 68 
                                    ....................55666666666666666666666666555544 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 2.6e-07
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       HlyD_D23 104 kvqktvtvkapisGvVteknvreGqyvqpgdtlftia 140
                                     +++ ++vk++++GvV e  v+eG++v++g ++++ia
  gi|119719073|ref|YP_919568.1|  67 AMKTLIEVKSSMNGVVKEVLVAEGEVVKQGAPIARIA 103
                                    577889*****************************98 PP

>> Peptidase_M23  Peptidase family M23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.2   8.4e-07    0.0012      50      74 ..      43      67 ..      13      76 .. 0.85
   2 !    9.4   0.1   0.00086       1.2      52      73 ..      82     103 ..      73     106 .] 0.85

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 8.4e-07
                                   EEESEESS-TTEEE-TTCEEEEEBS CS
                  Peptidase_M23 50 ahlskisvkegqkVkaGqvIGtvgs 74
                                   + +s+i vkegq+V++G++I+t+ +
  gi|119719073|ref|YP_919568.1| 43 GRVSRILVKEGQRVEKGTTIATMEA 67
                                   56899******************85 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00086
                                    ESEESS-TTEEE-TTCEEEEEB CS
                  Peptidase_M23  52 lskisvkegqkVkaGqvIGtvg 73 
                                    ++++ v eg+ Vk+G++I+++ 
  gi|119719073|ref|YP_919568.1|  82 VKEVLVAEGEVVKQGAPIARIA 103
                                    67899**************975 PP

>> RnfC_N  RnfC Barrel sandwich hybrid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.8   4.4e-09   6.1e-06      18      80 ..      24      85 ..      16      86 .. 0.82
   2 ?    3.9   0.1     0.037        51      43      60 ..      84     101 ..      83     104 .. 0.90

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 4.4e-09
                         RnfC_N 18 ekpieklplpkelvlplsqhiGapakplvkvgdkVlkGqkiaeaeg.fvsapvhasvsGtVkai 80
                                    k++e++p+ ke+v+      G   ++lvk+g++V+kG  ia+ e+  +  +v +s+ G Vk++
  gi|119719073|ref|YP_919568.1| 24 VKKVEAQPQSKEYVVA--PITGRVSRILVKEGQRVEKGTTIATMEAmKTLIEVKSSMNGVVKEV 85
                                   5677777777776654..346999********************99556789*********997 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.037
                         RnfC_N  43 kplvkvgdkVlkGqkiae 60 
                                    ++lv++g+ V++G  ia+
  gi|119719073|ref|YP_919568.1|  84 EVLVAEGEVVKQGAPIAR 101
                                    689*************96 PP

>> QRPTase_N  Quinolinate phosphoribosyl transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.075     1e+02      51      78 ..      25      52 ..      14      52 .. 0.80
   2 !   12.1   0.1   0.00011      0.16      49      69 ..      47      67 ..      35      72 .. 0.85
   3 !    8.7   0.1    0.0013       1.8      44      67 ..      79     102 ..      66     105 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.075
                                   SS-TT-EEETTEEEEEEEEEHHHHHHHH CS
                      QRPTase_N 51 lvkDGervekgdvlleieGnarallsaE 78
                                   ++ + +  +k+ v++ i+G+++++l  E
  gi|119719073|ref|YP_919568.1| 25 KKVEAQPQSKEYVVAPITGRVSRILVKE 52
                                   456778888999************9765 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00011
                                   EESS-TT-EEETTEEEEEEEE CS
                      QRPTase_N 49 ellvkDGervekgdvlleieG 69
                                    +lvk+G+rvekg++++++e+
  gi|119719073|ref|YP_919568.1| 47 RILVKEGQRVEKGTTIATMEA 67
                                   5899**************987 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.0013
                                    TTTEEEESS-TT-EEETTEEEEEE CS
                      QRPTase_N  44 pglevellvkDGervekgdvllei 67 
                                    +g+  e+lv++Ge v++g+ +++i
  gi|119719073|ref|YP_919568.1|  79 NGVVKEVLVAEGEVVKQGAPIARI 102
                                    6788889***************98 PP

>> PTS_EIIA_1  phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.7   5.2e-06    0.0072      34     103 ..      30     102 ..      18     106 .] 0.76

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 5.2e-06
                                    EE-.SSEEEES--EEEEE--.....SSSSEEEEESSSS-EEEEE-SSSTTTTTTTTEEES----SEE-SEEEEEEE CS
                     PTS_EIIA_1  34 eps.egkvvapvdGkvekvf.....ptkHaigiktddgvevlihiGidtvklkgegFellvkegdkVkagdklvev 103
                                    +p+ ++ vvap++G+v+ +        +   +i t + ++ li +   + +++g + e+lv+eg+ Vk+g +++++
  gi|119719073|ref|YP_919568.1|  30 QPQsKEYVVAPITGRVSRILvkegqRVEKGTTIATMEAMKTLIEV---KSSMNGVVKEVLVAEGEVVKQGAPIARI 102
                                    5663567*********99873221123345567777888888887...6899********************9986 PP

>> GCV_H  Glycine cleavage H-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   1.0     2e-06    0.0027      33      74 ..      45      85 ..      35     101 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2e-06
                                   EEEEE---TT-EE-TT-EEEEEEESS-EEEEE-SSSEEEEEE CS
                          GCV_H 33 vvfvelpevgtkvkkgeslaavEsvKaasevyapvsGevvev 74
                                   v  + l ++g++v+kg ++a++E+ K+  ev + ++G v ev
  gi|119719073|ref|YP_919568.1| 45 VSRI-LVKEGQRVEKGTTIATMEAMKTLIEVKSSMNGVVKEV 85
                                   4444.4467******************************997 PP

>> DUF2118  Uncharacterized protein conserved in archaea (DUF2118)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   1.4   1.2e-05     0.016      86     131 ..      39      83 ..      18     104 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.2e-05
                        DUF2118  86 ipvegvkvtlivdvGdrveegdtlaavttrkgevrylrapvegvVv 131
                                     p+ g +  + v++G+rve+g t+a + + k  +  +++  +gvV 
  gi|119719073|ref|YP_919568.1|  39 APITGRVSRILVKEGQRVEKGTTIATMEAMKTLI-EVKSSMNGVVK 83 
                                    5888999999********************9877.68999999994 PP

>> SatRNA_48  Satellite RNA 48 kDa protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1     1e-05     0.014      59     121 ..       7      69 ..       1     102 [. 0.80

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1e-05
                      SatRNA_48  59 eestpfvvndkraqhlfckkverkvgrreilvcpitneeshidlkrgikarivdsmasvvhte 121
                                    e  tp+++  +  q  ++kkve +   +e +v pit+  s i +k+g + +   ++a++   +
  gi|119719073|ref|YP_919568.1|   7 EGETPLGTVLSVLQTSLVKKVEAQPQSKEYVVAPITGRVSRILVKEGQRVEKGTTIATMEAMK 69 
                                    567899999999999********************************9988766666555444 PP

>> PYNP_C  Pyrimidine nucleoside phosphorylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.1    0.0026       3.6      37      53 ..      49      65 ..      47      83 .. 0.89
   2 ?    5.0   0.0     0.014        19      38      53 ..      87     102 ..      79     103 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0026
                                   S--TT-EEBTTSEEEEE CS
                         PYNP_C 37 hkklGdkVkkGeplati 53
                                    +k G++V+kG+++at 
  gi|119719073|ref|YP_919568.1| 49 LVKEGQRVEKGTTIATM 65
                                   6899***********95 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.014
                                    --TT-EEBTTSEEEEE CS
                         PYNP_C  38 kklGdkVkkGeplati 53 
                                    +  G+ Vk+G p+a+i
  gi|119719073|ref|YP_919568.1|  87 VAEGEVVKQGAPIARI 102
                                    6679**********98 PP

>> PASTA  PASTA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.8   0.00061      0.84      13      57 ..      14      62 ..       3      63 .. 0.74
   2 ?    2.7   0.0      0.08   1.1e+02      31      43 ..      83      95 ..      65      99 .. 0.54

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00061
                                   HHHHHHHHTT-.-CCCEEE...ECTCCGTTBEEEECS-TTSEECTTS-E CS
                          PASTA 13 eAkatLkalGl.kiktvee...tsddvpeGtVisQsPeaGtevskgskv 57
                                   ++ + L+ + + k+  +++   +++   +G+V +  +++G++v+kg+++
  gi|119719073|ref|YP_919568.1| 14 TVLSVLQTSLVkKVEAQPQskeYVVAPITGRVSRILVKEGQRVEKGTTI 62
                                   5666666655542333333555999999*******************98 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.08
                                   ECTCCGTTBEEEE CS
                          PASTA 31 tsddvpeGtVisQ 43
                                   + + v+eG V++Q
  gi|119719073|ref|YP_919568.1| 83 KEVLVAEGEVVKQ 95
                                   3355666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 704.79
//
Query:       gi|119719074|ref|YP_919569.1|  [L=513]
Description: carboxyl transferase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   1.7e-188  627.3   0.0   1.9e-188  627.1   0.0    1.0  1  Carboxyl_trans  Carboxyl transferase domain
    6.6e-05   22.5   0.2    0.00032   20.2   0.0    2.0  2  MdcE            Malonate decarboxylase gamma subunit (MdcE)


Domain annotation for each model (and alignments):
>> Carboxyl_trans  Carboxyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  627.1   0.0  2.1e-192  1.9e-188       3     492 ..      26     509 ..      24     511 .. 0.98

  Alignments for each domain:
  == domain 1  score: 627.1 bits;  conditional E-value: 2.1e-192
                                    CTTCEEEEEEEEHTTSGGGEBEHHHHHHHHHHHHHHH.HHT..EEEEEEEESBETTEEHHHHTTEEEEESSTTSGGGCEE CS
                 Carboxyl_trans   3 hprGkltareridllldpgsFgeledlffhrvtelgr.kkklprdgvvtgsGaviGravevvaqdktvlggslgpakgek 81 
                                    h++G+lta er++ lld+gsF++++++++hr+t +g+  +k+ +dgvv+g+G ++Gr+v+v+aqd+ ++ggs+g++++ k
  gi|119719074|ref|YP_919569.1|  26 HEQGRLTAHERLERLLDKGSFVPIARFIQHRATGFGMeSRKVFGDGVVAGLGSIDGRRVAVYAQDFSFMGGSVGEMHAYK 105
                                    89***********************************9899*************************************** PP

                                    ECHHHHHHHHHTEEEEEEEEE-ESSSGHHSSHHHHHHHHHHHHHHHHHHHCS-EEEEESSEEETHHHHHHHHTSEEEEET CS
                 Carboxyl_trans  82 llkaqeeaikagepligindsgGaegriqegveslrgsGkifgenskasgeIpqislvtgrcaGggaYlpalgdrvimve 161
                                    + ++ e+a+k g p+ig+ndsgGa  riqegv+sl+g+G+if++n+ asg+Ipqi+ ++g++aGg++Y+pal+d+++m++
  gi|119719074|ref|YP_919569.1| 106 IARTIETALKLGIPVIGLNDSGGA--RIQEGVDSLKGYGEIFYRNVMASGVIPQIVAIMGPAAGGAVYSPALADFIVMTK 183
                                    ************************..****************************************************** PP

                                    TEEEEESSTHHHHHHHHSSCC-SSCHHHHSHHHHTTTTSSSEEESSHHHHHHHHHHHHTTS-SSTTSGGSS----ECSSG CS
                 Carboxyl_trans 162 etskifltGpdvikkvlgreevtseelgGatqhmtksGvahltaeddeealelirkllsylPkkasnnresaPivetade 241
                                    + s++f+tGp+v+k+ +g e+vt eelgGa++h+tksGvah++aedd++a+++i+ llsylP   snn+e++P +et d+
  gi|119719074|ref|YP_919569.1| 184 K-SYMFITGPKVVKASIG-EDVTFEELGGAEIHATKSGVAHFLAEDDDHAIRIIKALLSYLP---SNNTEDPPYAETGDD 258
                                    *.****************.*******************************************...99999********** PP

                                    SSSH.....HCS-CTTTS---HHHHHHCEECTTC-EEESTTSSTTEEEEEEEETTEEEEEEEE--SEEETTEE-HHHHHH CS
                 Carboxyl_trans 242 pdrd...lieivPdnakkpyDvreviarlvdegeFlEikegyAktvVvGfArlgGipvGvvAnetrveaGqvlfidsavK 318
                                    p r+   l+ +vP+++ kpyDv+evi+r++d+g+FlE+++++A++ VvGfArlgG pv vvAn+++v aG +l+ids++K
  gi|119719074|ref|YP_919569.1| 259 PFREdseLDGLVPEDPVKPYDVKEVINRVFDKGSFLEVHAHFATNAVVGFARLGGFPVCVVANQPAVSAG-CLDIDSSDK 337
                                    ***999999*************************************************************.********* PP

                                    HHHHHHHHHHTT--EEEEE-BSEE--SHHHHHTTHHHHHHHHHHHHHT--S-EEEEE-TEEEHHHHHTTTGGGSTTTTEE CS
                 Carboxyl_trans 319 aarfirlcdaenlPlviladvrGflvGqrqeyggilkhGaklvdalaeakvPkitvilrkayGGayvvmdskingadlva 398
                                     arf+++cd +n P+++++dv+Gfl+G+ qe+gg+++hGak+++a+a+a++PkitvilrkayGGay++m+sk++gad+v+
  gi|119719074|ref|YP_919569.1| 338 IARFVTFCDSFNFPIITFVDVPGFLPGTYQEHGGVIRHGAKIIYAYADATTPKITVILRKAYGGAYIAMGSKHLGADYVL 417
                                    ******************************************************************************** PP

                                    ETTT-EEESS-HHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSHHHHHHTTSSSEEE CS
                 Carboxyl_trans 399 awptariaVlgpegaveilfrkekaaaemerkdlaaerkkklkeyeeellnpyvaaargfaDavidpsetraklvialel 478
                                    awpta+iaV+gp  a+ei++++e+++a+    ++++ +k+ +++y++e+++py aa+rg++D+++ p+etr ++ +al +
  gi|119719074|ref|YP_919569.1| 418 AWPTAEIAVMGPREAIEIIYKRELEKAA----NPEELAKEFEEKYRKEITTPYFAASRGYVDDIVFPRETRSYIYKALMF 493
                                    *************************999....89999******************************************* PP

                                    HGGGHH..HHHHHHHH CS
                 Carboxyl_trans 479 ewkkar..klparkrr 492
                                    + +k++   +p+rk++
  gi|119719074|ref|YP_919569.1| 494 LRDKREkhPRPPRKHG 509
                                    **99994345666766 PP

>> MdcE  Malonate decarboxylase gamma subunit (MdcE)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1     0.068   6.1e+02      26      77 ..      78     130 ..      64     176 .. 0.76
   2 !   20.2   0.0   3.6e-08   0.00032      65     150 ..     350     435 ..     294     453 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.068
                                    TEEEEEEEE---TT...SS-B-HHHHHHHHHHHHHHHTSSS--EEEEEEEE--B- CS
                           MdcE  26 lesvrfvaVigdan...kgevGvdealaLaaaVleaieraekrpilvlvDvasQr 77 
                                      ++r vaV ++     +g vG  +a+++a +++ a+  +   p++ l D+ + r
  gi|119719074|ref|YP_919569.1|  78 SIDGRRVAVYAQDFsfmGGSVGEMHAYKIARTIETAL--KLGIPVIGLNDSGGAR 130
                                    4477888887765567789999999999999999888..4556666666666655 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 3.6e-08
                                    -EEEEEEEE--B--SHHHHHHTHHHHHHHHHHHHHHHHHHT--EEEEEEEEEEHHHHHHTT...TT-SEEEEEET-EEES CS
                           MdcE  65 rpilvlvDvasQrlgrrdEllGihealahlakalarArlaGhpvigllvGkavsGaflahg...lqanrlialpgvqvav 141
                                     pi+  vDv++   g  +E  G+    a ++ a+a A     p i+++  ka  Ga++a+g   l a+ ++a p +++av
  gi|119719074|ref|YP_919569.1| 350 FPIITFVDVPGFLPGTYQEHGGVIRHGAKIIYAYADAT---TPKITVILRKAYGGAYIAMGskhLGADYVLAWPTAEIAV 426
                                    69*********************999999999998886...69****************9966567************** PP

                                    S-HHHHHHH CS
                           MdcE 142 mdkasaArv 150
                                    m+ + a  +
  gi|119719074|ref|YP_919569.1| 427 MGPREAIEI 435
                                    **8766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (513 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 3286.69
//
Query:       gi|119719075|ref|YP_919570.1|  [L=188]
Description: hypothetical protein Tpen_0157 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-05   25.3   0.1      2e-05   24.3   0.1    1.4  1  CT_A_B    Carboxyltransferase domain, subdomain A and B


Domain annotation for each model (and alignments):
>> CT_A_B  Carboxyltransferase domain, subdomain A and B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.1   1.1e-09     2e-05       9      74 ..      21      85 ..      19     106 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 1.1e-09
                                   SSHHHHHHHHHHTTS-TTS-EEEEESC-EEEEESS-EEEEEEESCEEEEETTEEE-SSCEEEE-TT CS
                         CT_A_B  9 mDrlalrlANrlvgNeegaaaLEitlggpelrfeedavvavtGadleatldgepvplwepvevkaG 74
                                   +D++ +++AN++  N+  a+a E+  g +el+++e+++ avtG d+++  dge++++w++  +++ 
  gi|119719075|ref|YP_919570.1| 21 IDKYLHAAANIISFNPLIAPAFEVRGGALELQLHERVTYAVTG-DATVLADGEQAETWRAGVAQRS 85
                                   699****************************************.888999********97665543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1247.62
//
Query:       gi|119719076|ref|YP_919571.1|  [L=386]
Description: glycosyl transferase family protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.5e-29  101.1   0.0    1.1e-28  100.6   0.0    1.1  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    6.9e-24   84.6   0.2    1.1e-23   83.9   0.2    1.4  1  Glycos_transf_2  Glycosyl transferase family 2
      4e-18   66.0  10.8    2.4e-17   63.5  10.8    2.1  1  Glyco_trans_2_3  Glycosyl transferase family group 2
    1.3e-12   47.6   0.0      2e-12   46.9   0.0    1.4  1  Glyco_transf_21  Glycosyl transferase family 21
    1.4e-07   31.2   0.1    5.6e-07   29.3   0.1    1.9  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
    0.00066   19.4   0.0     0.0017   18.1   0.0    1.6  2  Glyco_tranf_2_5  Glycosyltransferase like family
  ------ inclusion threshold ------
       0.22   11.9   1.0         12    6.3   0.0    2.8  3  PG_binding_2     Putative peptidoglycan binding domain


Domain annotation for each model (and alignments):
>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.6   0.0   4.5e-32   1.1e-28       3     229 ..      20     235 ..      18     236 .. 0.91

  Alignments for each domain:
  == domain 1  score: 100.6 bits;  conditional E-value: 4.5e-32
                Glyco_tranf_2_3   3 dlavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnea 82 
                                    +++v++p+++ +++l++++  +++ +y + evvvvvde  +e++e+++      +  +v+++ +++   ++gk+ alnea
  gi|119719076|ref|YP_919571.1|  20 KVSVIIPSYRGSERLVRLVKRVASLPYEDKEVVVVVDEPLREVAEELRR----IG--GVKLILRPK---RGGKVSALNEA 90 
                                    59**********************************9999999998886....44..578998877...4689******* PP

                Glyco_tranf_2_3  83 lravksdlvllvDdDtvv.ePdtlkrllqffltpkvgavgtpvfllnrstlvsalgalefaerhlrflaarralg.vltl 160
                                    lr  ++++v+++DdD+ v ++++++++l ++  ++++++  ++        +s l ++e+a  ++   +++ra + ++++
  gi|119719076|ref|YP_919571.1|  91 LRESSGEVVIFLDDDVYVeDDRFIEKVLKAM--EGYDIADIKKVIVDTGGILSKLVYIEYASYNFASKLMARAARrTVAV 168
                                    ******************77888*******9..*******888888888888889999999999988777777765899* PP

                Glyco_tranf_2_3 161 nGsgslirrevlkelegldplflltdDyelglrlrragfrtayvpgaavrevfpsslkayikqrnRwvy 229
                                    nG+ +++rr+ l+e++ ++p  ++ +D++++lr  +a++   y +   v  + ps++ + +kqr Rw+ 
  gi|119719076|ref|YP_919571.1| 169 NGAAFAVRRKALDEIGYFRP--SISEDFDIALRSFKAKHNFTYIENTYVLNYPPSDFRKWFKQRKRWAI 235
                                    ***************99999..*********************************************86 PP

>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.9   0.2   4.4e-27   1.1e-23       1     169 [.      22     183 ..      22     184 .. 0.80

  Alignments for each domain:
  == domain 1  score: 83.9 bits;  conditional E-value: 4.4e-27
                                    EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--S CS
                Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraatg 80 
                                    sv+ip+y  ++ l ++++++++  py+d+e++vv D     ++e++eel+ + ++v++i r+++ Gk +aln++lr+++g
  gi|119719076|ref|YP_919571.1|  22 SVIIPSYRGSERLVRLVKRVASL-PYEDKEVVVVVDEP---LREVAEELR-RIGGVKLILRPKRGGKVSALNEALRESSG 96 
                                    8**********************.**************...555555554.359************************** PP

                                    SEEEEEESSEEE-TT.HHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTTCSTCCC CS
                Glycos_transf_2  81 dyilflDaDdepdpd.wleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsfeigsaa 159
                                    ++++flD+D+++++d ++ek+++a+e   +d++  + +  + +    +  +  +  +++  k   r   ++++++   +a
  gi|119719076|ref|YP_919571.1|  97 EVVIFLDDDVYVEDDrFIEKVLKAMEG--YDIADIKKVIVDTGGILSKLVYIEYASYNFASKLMARAARRTVAVNGAAFA 174
                                    *************************99..544555555444444444444444566666666666666666666666666 PP

                                    EEEEHHHHHC CS
                Glycos_transf_2 160 llrrealeel 169
                                    + rr+al+e+
  gi|119719076|ref|YP_919571.1| 175 V-RRKALDEI 183
                                    6.77777776 PP

>> Glyco_trans_2_3  Glycosyl transferase family group 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.5  10.8   9.4e-21   2.4e-17       1     181 [.      98     317 ..      98     371 .. 0.74

  Alignments for each domain:
  == domain 1  score: 63.5 bits;  conditional E-value: 9.4e-21
                Glyco_trans_2_3   1 iilllDaDtvlppdclreiaa.elaspevaivqgpvlvmnvanwleelaalffaedhgkdilvrealgrvvpsvGsgafl 79 
                                    ++++lD+D  +  d + e +   +    ++i+ ++ +++  + +l++l  +++a     + l++ a  r+v + G+ +++
  gi|119719076|ref|YP_919571.1|  98 VVIFLDDDVYVEDDRFIEKVLkAM--EGYDIADIKKVIVDTGGILSKLVYIEYASYNFASKLMARAARRTVAVNGAAFAV 175
                                    5899*******9997765544266..57*******9988899***********99999999******************* PP

                Glyco_trans_2_3  80 rrsalqevggwdgdessvsEDfdmglrlqrkGyrvrfvpeslvkekspltlraalrQrkRwayGc..eleklil...... 151
                                    rr+al+e+g+++    s+sEDfd++lr +++  ++ +++ + v  + p+++r +++QrkRwa G   +     l      
  gi|119719076|ref|YP_919571.1| 176 RRKALDEIGYFR---PSISEDFDIALRSFKAKHNFTYIENTYVLNYPPSDFRKWFKQRKRWAIGLaaW-----Leenfad 247
                                    ***********9...99***********************************************7662.....1333334 PP

                Glyco_trans_2_3 152 .........................................lvrll..gylgsllwsalplhlallllfslla 181
                                                                             +   l    l sl++ alp++ +lll   l++
  gi|119719076|ref|YP_919571.1| 248 alktllrmphavipglllalpslssalitfvlsnhvyektaY---LfmLTLSSLVAQALPFASILLLNIQLIY 317
                                    445544455555555555555555555555544444443210...1112234444444555554444444444 PP

>> Glyco_transf_21  Glycosyl transferase family 21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.9   0.0   7.8e-16     2e-12      15     172 ..      80     234 ..      52     235 .. 0.84

  Alignments for each domain:
  == domain 1  score: 46.9 bits;  conditional E-value: 7.8e-16
                Glyco_transf_21  15 vnpKvnnllqaleaakydllvisDsdvrvkpd.yLeellaaledpkvglVtslpvgsdakglaaaleaafl...ntlagv 90 
                                       Kv++l+ al++   ++++++D+dv v+ d ++e++l+a+e     +     v +d+ g+ ++l+       n+ +++
  gi|119719076|ref|YP_919571.1|  80 RGGKVSALNEALRESSGEVVIFLDDDVYVEDDrFIEKVLKAMEG--YDIADIKKVIVDTGGILSKLVYIEYasyNFASKL 157
                                    456**************************9874799*******7..5566666667788888888866665554788888 PP

                Glyco_transf_21  91 lqaklsglgfavGksmalrreaLeaiGGfealadeLAeDyalg.kllraaGlkvvlspapiaqtsvprrsslrallaRql 169
                                    +++++ ++  ++G++ a+rr+aL++iG f++    + eD+ ++ + ++a++  +++ ++ +++   p  s +r+++++  
  gi|119719076|ref|YP_919571.1| 158 MARAARRTVAVNGAAFAVRRKALDEIGYFRP---SISEDFDIAlRSFKAKHNFTYIENTYVLN--YP-PSDFRKWFKQRK 231
                                    888888999**********************...*********66677777777777877776..45.56899******* PP

                Glyco_transf_21 170 rWa 172
                                    rWa
  gi|119719076|ref|YP_919571.1| 232 RWA 234
                                    **8 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.1   2.2e-10   5.6e-07       1     236 [.      22     231 ..      22     251 .. 0.74

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 2.2e-10
                Glyco_tranf_2_2   1 svviplraseerhyieervlqkakyydeeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNrGaska 80 
                                    sv+ip + + er  +   v++ a+   e+ e++vv d    +++ee++ i   +l    k       ++  a N    ++
  gi|119719076|ref|YP_919571.1|  22 SVIIPSYRGSER--LVRLVKRVASLPYEDKEVVVVVDEPLREVAEELRRIGGVKLILRPKRG-----GKVSALNEALRES 94 
                                    799999999999..55556666665557778888888888888*******999988874444.....99999******** PP

                Glyco_tranf_2_2  81 esdlvlFlDaDcfissDkf.ekilklitikklrenidaavvlpvvdlnkedsevlkdvedl.tassrvledllaakstlv 158
                                     +++v+FlD D ++  D+f ek+lk ++  ++ ++ +      +v    +   +l +  ++ +as ++  +l+a   +  
  gi|119719076|ref|YP_919571.1|  95 SGEVVIFLDDDVYVEDDRFiEKVLKAMEGYDIADIKK-----VIV----DTGGILSKLVYIeYASYNFASKLMA--RAAR 163
                                    *****************98689999555555444332.....222....2333333333321456678888998..5666 PP

                Glyco_tranf_2_2 159 kffapssssilinrraflevGGyDErfrGhgaEDfdlllRlakaikslekmpvellykarakslsnykGfrrfleala 236
                                    + +a ++  + ++r+a+ e+G +  ++    +EDfd+ lR  ka  ++     e +y ++     + + fr+++++  
  gi|119719076|ref|YP_919571.1| 164 RTVAVNGAAFAVRRKALDEIGYFRPSI----SEDFDIALRSFKAKHNF--TYIENTYVLNY----PPSDFRKWFKQRK 231
                                    799******************998888....*********99999999..33333443333....3456889887655 PP

>> Glyco_tranf_2_5  Glycosyltransferase like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   6.7e-07    0.0017      43      79 ..      85     121 ..      79     126 .. 0.93
   2 ?   -2.7   0.0       1.5     4e+03     126     160 ..     156     195 ..     143     207 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 6.7e-07
                Glyco_tranf_2_5  43 eaynkalsasdakykvYlhqDvliinkdfikdlleiF 79 
                                    +a n+al++s+ +++++l++Dv++   +fi+++l+ +
  gi|119719076|ref|YP_919571.1|  85 SALNEALRESSGEVVIFLDDDVYVEDDRFIEKVLKAM 121
                                    799*******************************987 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.5
                Glyco_tranf_2_5 126 eeeeseyeeVeaidGllmatqydv.....pwredlftgfh 160
                                    + ++++ +   a++G  +a+++        +r  + ++f+
  gi|119719076|ref|YP_919571.1| 156 KLMARAARRTVAVNGAAFAVRRKAldeigYFRPSISEDFD 195
                                    5556677778899999999987655555666666666665 PP

>> PG_binding_2  Putative peptidoglycan binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0      0.04     1e+02       6      29 ..      47      70 ..      44      93 .. 0.88
   2 ?    6.3   0.0    0.0045        12      22      56 ..     177     207 ..     157     214 .. 0.87
   3 ?   -2.8   0.0       3.3   8.4e+03      39      50 ..     241     252 ..     235     255 .. 0.67

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.04
                   PG_binding_2  6 kpeeervlaedvaeevqaaLsrLG 29
                                   +++e +v +++  +ev++ L+r G
  gi|119719076|ref|YP_919571.1| 47 EDKEVVVVVDEPLREVAEELRRIG 70
                                   799*******************99 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0045
                   PG_binding_2  22 qaaLsrLGyydgeaggafrealrdALrafiaveNF 56 
                                    ++aL + Gy    +  +++e +  ALr+f a  NF
  gi|119719076|ref|YP_919571.1| 177 RKALDEIGY----FRPSISEDFDIALRSFKAKHNF 207
                                    689******....888899*************999 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 3.3
                   PG_binding_2  39 frealrdALraf 50 
                                    ++e+++dAL+++
  gi|119719076|ref|YP_919571.1| 241 LEENFADALKTL 252
                                    456677777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       831  (0.0463495); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 2642.72
//
Query:       gi|119719077|ref|YP_919572.1|  [L=86]
Description: hypothetical protein Tpen_0159 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0042   16.9   0.0       0.06   13.3   0.0    2.3  2  UBA       UBA/TS-N domain
  ------ inclusion threshold ------
      0.067   13.0   0.0       0.12   12.2   0.0    1.4  1  UBA_3     Fungal ubiquitin-associated domain


Domain annotation for each model (and alignments):
>> UBA  UBA/TS-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0     0.038   3.4e+02      21      33 ..      25      37 ..      22      38 .. 0.88
   2 !   13.3   0.0   6.7e-06      0.06       6      25 ..      39      58 ..      39      63 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.038
                                   HHHHHTTTSHHHH CS
                            UBA 21 eALratgnNeErA 33
                                    ALr  +n++ rA
  gi|119719077|ref|YP_919572.1| 25 SALRDQFNGVGRA 37
                                   69********999 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 6.7e-06
                                   HHHHHHTTS-HHHHHHHHHH CS
                            UBA  6 iqrLveMGFdreevveALra 25
                                   i+ L+e GF+r+ev eA ra
  gi|119719077|ref|YP_919572.1| 39 ISSLLEQGFTRDEVSEAVRA 58
                                   689**************997 PP

>> UBA_3  Fungal ubiquitin-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.3e-05      0.12       6      33 ..      32      59 ..      28      64 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.3e-05
                                   ---SHHHHHHHHHHT--HHHHHHHHHHS CS
                          UBA_3  6 yGidrdlVdefvsqGFekdkvievLkrL 33
                                    G+ r  +  +  qGF +d v e+ + L
  gi|119719077|ref|YP_919572.1| 32 NGVGRAFISSLLEQGFTRDEVSEAVRAL 59
                                   6999999******************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 603.82
//
Query:       gi|119719078|ref|YP_919573.1|  [L=150]
Description: methylated-DNA--protein-cysteine methyltransferase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-25   88.1   0.0    5.2e-25   87.4   0.0    1.3  1  DNA_binding_1  6-O-methylguanine DNA methyltransferase, DNA b
  ------ inclusion threshold ------
       0.12   12.2   0.7        0.4   10.5   0.0    2.0  2  HTH_AsnC-type  AsnC-type helix-turn-helix domain
       0.15   11.7   0.0       0.32   10.6   0.0    1.6  1  HTH_24         Winged helix-turn-helix DNA-binding


Domain annotation for each model (and alignments):
>> DNA_binding_1  6-O-methylguanine DNA methyltransferase, DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.4   0.0   8.7e-29   5.2e-25       3      80 ..      73     147 ..      71     148 .. 0.97

  Alignments for each domain:
  == domain 1  score: 87.4 bits;  conditional E-value: 8.7e-29
                                    HHHHHHHHTTS-TT-BEEHHHHHHHTT.TSCHHHHHHHHHTSSBTTTSGGGGEEBTTSBCCTTTTCHHHHHHHHHHTT CS
                  DNA_binding_1   3 qqrVwellrqIpyGkvttYgeiAkllgkpkaaraVgqalaanplailvPcHRVvgadgklggyagglerkralLeaEg 80 
                                    +++V e + +IpyG+++tYge+A+++g  +++raVg++l +n++ +++PcHRVv+++g +ggya g+e+k++lL+ E 
  gi|119719078|ref|YP_919573.1|  73 RKKVFEEVLRIPYGSTITYGELAARVG--SSPRAVGRVLSENRILLVIPCHRVVASKG-VGGYAFGVEAKKYLLRLEA 147
                                    799************************..*****************************.9***************995 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1      0.26   1.5e+03      28      40 ..      36      48 ..      35      48 .. 0.89
   2 ?   10.5   0.0   6.7e-05       0.4      17      36 ..      88     107 ..      85     107 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.26
                  HTH_AsnC-type 28 GlSestvlrRvrr 40
                                   G+++ + ++R+rr
  gi|119719078|ref|YP_919573.1| 36 GVTRGEFAERLRR 48
                                   89999999**998 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 6.7e-05
                  HTH_AsnC-type  17 RisyaeLAervGlSestvlr 36 
                                     i+y eLA+rvG S+ +v r
  gi|119719078|ref|YP_919573.1|  88 TITYGELAARVGSSPRAVGR 107
                                    689**************976 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   5.3e-05      0.32      17      36 ..      88     107 ..      73     111 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 5.3e-05
                         HTH_24  17 risqreLAerlglSpstvnr 36 
                                     i++ eLA r+g Sp +v r
  gi|119719078|ref|YP_919573.1|  88 TITYGELAARVGSSPRAVGR 107
                                    59*************99966 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 1004.76
//
Query:       gi|119719079|ref|YP_919574.1|  [L=300]
Description: anion-transporting ATPase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-31  110.1   0.0    1.5e-31  109.8   0.0    1.2  1  ArsA_ATPase  Anion-transporting ATPase
    4.7e-10   39.6   0.0    1.2e-09   38.3   0.0    1.6  2  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    4.9e-07   29.4   0.0      7e-07   28.9   0.0    1.2  1  ParA         NUBPL iron-transfer P-loop NTPase
    9.9e-06   25.6   0.0    1.6e-05   24.9   0.0    1.3  1  AAA_31       AAA domain
     0.0055   16.6   0.0      0.017   15.1   0.0    1.7  2  APS_kinase   Adenylylsulphate kinase
     0.0082   15.4   0.1      0.032   13.4   0.1    1.8  2  NB-ARC       NB-ARC domain
     0.0095   15.4   0.0      0.022   14.2   0.1    1.7  2  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
  ------ inclusion threshold ------
      0.054   13.1   0.0       0.11   12.2   0.0    1.4  1  SRP54        SRP54-type protein, GTPase domain
      0.057   14.0   0.0       0.11   13.1   0.0    1.5  1  AAA_18       AAA domain
       0.12   11.9   0.2       0.27   10.8   0.2    1.5  1  AAA_25       AAA domain
       0.18   11.2   0.0       0.29   10.5   0.0    1.4  1  PhoH         PhoH-like protein
       0.19   11.0   0.1       0.37   10.0   0.1    1.4  1  MipZ         ATPase MipZ
        0.2   12.1   0.0       0.31   11.4   0.0    1.4  1  AAA          ATPase family associated with various cellular a


Domain annotation for each model (and alignments):
>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.8   0.0   1.1e-34   1.5e-31       2     249 ..       7     247 ..       6     284 .. 0.85

  Alignments for each domain:
  == domain 1  score: 109.8 bits;  conditional E-value: 1.1e-34
                                    EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STTTHHHHHHTS--BSS-EEETSSEEEEE--HH....HHHHHHH CS
                    ArsA_ATPase   2 kvilvgGKGGVGKttvsaatavklsekgkkvllistDPAhslsDsfdqklgkeptkvkeNLsavEidpe....veleeak 77 
                                    k++ + GKGGVGKtt+s+a+av ls++g+++ l+s D  +sl D++  +l++ep  ++eNL++  +  e    +  e+  
  gi|119719079|ref|YP_919574.1|   7 KLVSFWGKGGVGKTTLSSAVAVSLSKMGYRTYLLSSDFVPSLQDVLGVELSREPLELSENLVVDQLFEEkvieMWKERFG 86 
                                    678899********************************************************999876633222223333 PP

                                    CCHHGGGSCCHHHHHHHHHHHHHHTSSTTHHHHHHHHHHHHHHHCSSSSEEEEESBSCCHTCGGGGHHHHHHHHHHHHHH CS
                    ArsA_ATPase  78 qevqkeeeallgleeledvlaeelaslPGideilsfeellkyvkeeeydvvvlDtaPTGhtlrllslpevleklleklvk 157
                                    +ev++ + +   +   +++++  + + PGi e +++ ++ +++++e++dv+v Dt  TG  lr+l++ + +   l ++vk
  gi|119719079|ref|YP_919574.1|  87 EEVYRVASS--IFPVGREIIDYVAGA-PGIVEEFTLYYIYELYRNEDFDVLVWDTMATGGGLRMLRIEKEFYDHLGEAVK 163
                                    333333333..445789999999999.*************************************************9999 PP

                                    HHHHHHHHHHHHCCCSHCHHHHHHHHHHHHHHHHHHHHHHHHHHTSTTTEEEEEEEESSHHHHHHHHHHHHHHHHTT-EE CS
                    ArsA_ATPase 158 lkeklsplakqlvkllglggvsieealeeleetkeeikkveeiltdpertsfrlVvipEklslkEteRaikeLkkygikv 237
                                    l   ++ ++  +        +  e+ l+ +e+  e  +kv + l   +     lV+ +  +  +   R  +eL ++gi v
  gi|119719079|ref|YP_919574.1| 164 LYLRVKGVIDRI-------RTGSEDPLKLIESWRELAQKVLDFLRGSHH-VASLVSRSLPVDYYVATRVYRELLEFGIPV 235
                                    999888888877.......344455677777777777888899998877.6689999999999***************** PP

                                    EEEEEEEE-TTC CS
                    ArsA_ATPase 238 davivNkllpee 249
                                    +++ vN +    
  gi|119719079|ref|YP_919574.1| 236 KMLFVNMVSGSA 247
                                    ******875554 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.3   0.0   8.5e-13   1.2e-09       6     128 .]      13     216 ..       9     216 .. 0.92
   2 ?   -2.3   0.0       3.2   4.4e+03      74      96 ..     233     255 ..     222     274 .. 0.72

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 8.5e-13
                                    SSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH............................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................... RF
                           CbiA   6 tkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep............................... 54 
                                    +kGGvGKTtl+ + a++l++ g+r+ l+  D   ++   + g+e  +ep                               
  gi|119719079|ref|YP_919574.1|  13 GKGGVGKTTLSSAVAVSLSKMGYRTYLLSSDFVPSLQD-VLGVELSREPlelsenlvvdqlfeekviemwkerfgeevyr 91 
                                    8********************************88877.8888888888888**************************** PP

                                    ......................................................CCHCCCHHH.HHHCHCHHHH..EEEE CS
                                    ......................................................xxxxxxxxx.xxxxxxxxxxxxxxxx RF
                           CbiA  55 ......................................................dlkrllell.ealgkkkalllkiagv 79 
                                                                                           + r+++ +  +lg+ ++l l+++gv
  gi|119719079|ref|YP_919574.1|  92 vassifpvgreiidyvagapgiveeftlyyiyelyrnedfdvlvwdtmatggglRMLRIEKEFyDHLGEAVKLYLRVKGV 171
                                    ***************************************************87766666655557788776666****** PP

                                    EEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHHTS-H CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           CbiA  80 vlnrvdgeneetllkealeelkqrygvpvlgviprdeavaeapargepv 128
                                    ++    g++   +l+e+ +el    + +vl++++ + +va +++r +pv
  gi|119719079|ref|YP_919574.1| 172 IDRIRTGSEDPLKLIESWREL----AQKVLDFLRGSHHVASLVSRSLPV 216
                                    **9888888999999999998....89***************9998876 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.2
                                    ..EEEEEEEEESS...-TTCHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxx RF
                           CbiA  74 lkiagvvlnrvdgeneetllkea 96 
                                    + ++++ +n+v g++ee+l  + 
  gi|119719079|ref|YP_919574.1| 233 IPVKMLFVNMVSGSAEENLYFKK 255
                                    66778889999998887776655 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0   5.1e-10     7e-07       5      56 ..       7      57 ..       3      79 .. 0.85

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 5.1e-10
                           ParA  5 viavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveee 56
                                   +++   gKGGVGK+t+++ +A++L+k+g+++ ll  D + ps+ ++lgve +
  gi|119719079|ref|YP_919574.1|  7 KLVSFWGKGGVGKTTLSSAVAVSLSKMGYRTYLLSSDFV-PSLQDVLGVELS 57
                                   556667*******************************87.999999999864 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   1.2e-08   1.6e-05       9      54 ..      13      58 ..       6     104 .. 0.74

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.2e-08
                         AAA_31  9 qKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgiekne 54
                                    KGGvGKTT s ++a++l+k+g+++ l   D   ++   lg+e ++
  gi|119719079|ref|YP_919574.1| 13 GKGGVGKTTLSSAVAVSLSKMGYRTYLLSSDFVPSLQDVLGVELSR 58
                                   5************************999998777777766665544 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.2e-05     0.017       5      41 ..       9      45 ..       6      66 .. 0.88
   2 ?   -2.0   0.0       2.2     3e+03      18      52 ..     220     254 ..     218     256 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.2e-05
                                   EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHH CS
                     APS_kinase  5 vwltGlsgsGKstianalekkLvekgisvylLdGdnv 41
                                   v + G  g GK+t++ a++ +L ++g+++ylL  d v
  gi|119719079|ref|YP_919574.1|  9 VSFWGKGGVGKTTLSSAVAVSLSKMGYRTYLLSSDFV 45
                                   5678999*************************99977 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.2
                                    HHHHHHHHHHHTT--EEEEEHHHHTTTTTTT--SS CS
                     APS_kinase  18 ianalekkLvekgisvylLdGdnvRhgLnkdLgfs 52 
                                    +a+++ ++L e gi v++L  + v    +++L f+
  gi|119719079|ref|YP_919574.1| 220 VATRVYRELLEFGIPVKMLFVNMVSGSAEENLYFK 254
                                    78999999999999999998888877777777776 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.1   2.3e-05     0.032      21      46 ..       7      32 ..       2      41 .. 0.83
   2 ?   -1.5   0.0      0.83   1.1e+03     157     201 ..      70     114 ..      54     119 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.3e-05
                                   EEEEEEESTTSSHHHHHHHHCCSHCC CS
                         NB-ARC 21 lvvalvGmgGvGKttlakqilnksde 46
                                    +v++ G+gGvGKttl++ +  ++++
  gi|119719079|ref|YP_919574.1|  7 KLVSFWGKGGVGKTTLSSAVAVSLSK 32
                                   5799*************999776555 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.83
                                    SS--HHHHHHHHHHCCTS-GGCHH..CHHHHHHHHHHCTT-HHHH CS
                         NB-ARC 157 elLekdeawellenkvfekkleekesleevakeivekckGlPlal 201
                                      L +++  e+ ++   e+     +s+  v++ei+    G P  +
  gi|119719079|ref|YP_919574.1|  70 DQLFEEKVIEMWKERFGEEVYRVASSIFPVGREIIDYVAGAPGIV 114
                                    445555555555555555555555558889999999999888665 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.1   1.6e-05     0.022       3      37 ..       9      43 ..       7     143 .. 0.86
   2 ?   -3.1   0.0         3   4.2e+03     230     246 ..     182     198 ..     166     203 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.6e-05
                      Fer4_NifH  3 iaiyGkGGiGksttsqnlsaalaemgkkvlivGCD 37
                                   ++++GkGG+Gk+t s+ ++ +l++mg +  ++  D
  gi|119719079|ref|YP_919574.1|  9 VSFWGKGGVGKTTLSSAVAVSLSKMGYRTYLLSSD 43
                                   789***********************998776665 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3
                      Fer4_NifH 230 eseqakeyrelarkile 246
                                      +  + +rela+k+l+
  gi|119719079|ref|YP_919574.1| 182 PLKLIESWRELAQKVLD 198
                                    45567889999999876 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   7.7e-05      0.11       4      39 ..       9      44 ..       6      46 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.7e-05
                                   EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEEST CS
                          SRP54  4 illvGlqGaGKTttlaKLaallkkegkkvllvaaDt 39
                                   + + G  G+GKTt  + +a  l+k+g+++ l + D 
  gi|119719079|ref|YP_919574.1|  9 VSFWGKGGVGKTTLSSAVAVSLSKMGYRTYLLSSDF 44
                                   668899**************************9995 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   7.7e-05      0.11       5      67 ..      13      84 ..       9     128 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.7e-05
                         AAA_18  5 GtpGvGKttlakeLskrl.gf........gvnlrdvakenglllevdpealdeskrldedkldklldaleen 67
                                   G+ GvGKttl+ +++ +l ++        ++ + ++    g +l+++p +l+e++++d+ + +k+++ ++e 
  gi|119719079|ref|YP_919574.1| 13 GKGGVGKTTLSSAVAVSLsKMgyrtyllsSDFVPSLQDVLGVELSREPLELSENLVVDQLFEEKVIEMWKER 84
                                   888**********97666555669988877777777777777777777799999999999999999888875 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2    0.0002      0.27      33      58 ..       6      31 ..       2      42 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0002
                         AAA_25 33 gelallaGapgtGKttlaldlalava 58
                                   ++l+ ++G +g+GKttl + +a++++
  gi|119719079|ref|YP_919574.1|  6 KKLVSFWGKGGVGKTTLSSAVAVSLS 31
                                   678899****************9976 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00021      0.29      19      47 ..       6      34 ..       1      93 [. 0.84

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00021
                                   -SEEEEE--TTSSTTHHHHHHHHHHHHTT CS
                           PhoH 19 ndivfaiGpaGtGKtylavalavealkkk 47
                                   +++v   G+ G GKt l+ a+av++ k +
  gi|119719079|ref|YP_919574.1|  6 KKLVSFWGKGGVGKTTLSSAVAVSLSKMG 34
                                   689999*****************987654 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00027      0.37       8      32 ..      13      37 ..       7      44 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00027
                                   SSTTSSHHHHHHHHHHHHHTTT--E CS
                           MipZ  8 ekGGsGksttavhvavaLlkkGarv 32
                                    kGG Gk+t +  vav+L+k+G r 
  gi|119719079|ref|YP_919574.1| 13 GKGGVGKTTLSSAVAVSLSKMGYRT 37
                                   59********************985 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00023      0.31       2      23 ..      10      31 ..       9      81 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00023
                                   EEESSTTSSHHHHHHHHHHHHT CS
                            AAA  2 llyGppGtGKTllakavakelg 23
                                    ++G  G+GKT+l +ava +l+
  gi|119719079|ref|YP_919574.1| 10 SFWGKGGVGKTTLSSAVAVSLS 31
                                   589***************9974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2054.02
//
Query:       gi|119719080|ref|YP_919575.1|  [L=299]
Description: hypothetical protein Tpen_0162 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-10   41.0   0.1    3.7e-10   39.9   0.1    1.6  1  DUF4129   Domain of unknown function (DUF4129)


Domain annotation for each model (and alignments):
>> DUF4129  Domain of unknown function (DUF4129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   0.1   2.1e-14   3.7e-10       1      69 []     218     288 ..     218     288 .. 0.92

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 2.1e-14
                        DUF4129   1 ayrallraLaergldrrpgeTprEyarrv.riaps.paaalaalaelfeearYGgrpasaeeyrrlvealr 69 
                                    +y  l+ a  e+g +   ++T+rE+ r +    p  pa++l+ l+elfe a+Y++rp+++ +++ +v+ lr
  gi|119719080|ref|YP_919575.1| 218 LYNSLCNAVNEKGARLEKSWTAREIMRFLsDTMPFiPARPLEKLTELFELALYSRRPLTERDRENAVRSLR 288
                                    588899***********************6444448*******************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       724  (0.0403815); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2152.20
//
Query:       gi|119719081|ref|YP_919576.1|  [L=75]
Description: hypothetical protein Tpen_0163 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 559.89
//
Query:       gi|119719082|ref|YP_919577.1|  [L=319]
Description: ATPase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-66  221.7   0.1    3.4e-66  221.0   0.1    1.3  1  AAA_3            ATPase family associated with various cellul
    4.4e-21   74.5   1.1    8.8e-21   73.5   1.1    1.5  1  AAA_lid_2        AAA lid domain
    1.9e-14   53.8   0.0    1.1e-13   51.4   0.0    2.2  2  AAA_5            AAA domain (dynein-related subfamily)
    0.00067   20.1   0.0     0.0015   18.9   0.0    1.7  1  AAA              ATPase family associated with various cellul
    0.00079   18.6   0.1     0.0037   16.4   0.0    2.1  2  MCM              MCM P-loop domain
     0.0026   17.5   0.0     0.0071   16.1   0.0    1.7  1  Sigma54_activat  Sigma-54 interaction domain
     0.0029   17.4   0.0      0.074   12.8   0.0    2.7  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
     0.0072   15.7   0.2        1.1    8.6   0.0    2.3  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
  ------ inclusion threshold ------
      0.025   15.0   0.2      0.051   14.0   0.2    1.6  1  MCM_lid          MCM AAA-lid domain
      0.048   12.1   0.0      0.065   11.7   0.0    1.1  1  NUT              NUT protein


Domain annotation for each model (and alignments):
>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  221.0   0.1   1.9e-69   3.4e-66       1     131 []      39     169 ..      39     169 .. 1.00

  Alignments for each domain:
  == domain 1  score: 221.0 bits;  conditional E-value: 1.9e-69
                          AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvfanllladeinrappktqs 80 
                                    hvl+e+ PG+aktll++++akaldlefkr+qftpdllPsdi+G++v+++++++f+f++Gp+f+n+lladeinrappktqs
  gi|119719082|ref|YP_919577.1|  39 HVLIEDFPGMAKTLLASSFAKALDLEFKRVQFTPDLLPSDITGSHVYDMHSSTFRFRRGPIFTNILLADEINRAPPKTQS 118
                                    9******************************************************************************* PP

                          AAA_3  81 alleameerqvtvegethklpepflvlatqnPieqeGtyplpeaqldrfll 131
                                    alleam+erqvtv+g t++l+epf+v+at nPie eGtyplpeaq+drf+l
  gi|119719082|ref|YP_919577.1| 119 ALLEAMQERQVTVDGVTFALEEPFMVIATLNPIEFEGTYPLPEAQMDRFML 169
                                    *************************************************97 PP

>> AAA_lid_2  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.5   1.1   4.9e-24   8.8e-21       1      72 [.     232     304 ..     232     305 .. 0.89

  Alignments for each domain:
  == domain 1  score: 73.5 bits;  conditional E-value: 4.9e-24
                      AAA_lid_2   1 latrahlaielgvsgrRadlallraArAlAalegrdyVtpeDvkeaaplVLaHRlr..repeaegetteeivee 72 
                                    +atr+ + +e+gvs+r ++ al++a+rAlA+++grd+V+p+Dvke+a  VLaHR++   e    g++ e+iv++
  gi|119719082|ref|YP_919577.1| 232 RATRSVRDVEVGVSPR-GTEALMKASRALAFIRGRDFVLPDDVKEVAVEVLAHRIVlrTESLVRGVSPEDIVRR 304
                                    589999**********.***************************************954555555888888875 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.96   1.7e+03      10      24 ..      21      37 ..      21      45 .. 0.76
   2 !   51.4   0.0     6e-17   1.1e-13       8     138 .]      46     167 ..      39     167 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.96
                                   SSHHHHHHHGGGGB..S CS
                          AAA_5 10 tgKselaerlaaal..n 24
                                   +gK++++erl+ al  +
  gi|119719082|ref|YP_919577.1| 21 VGKRRVVERLLVALlsG 37
                                   69999999999887543 PP

  == domain 2  score: 51.4 bits;  conditional E-value: 6e-17
                                    SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--...........--------G-SEEEEESGGG--HHHHHHH CS
                          AAA_5   8 pGtgKselaerlaaalnreveyvqltrdtteedlkgrreik..ngttslvdsplvraaregeilvlDEveraesevlnsL 85 
                                    pG +K+ la ++a+al  e+  vq+t d+ ++d++g+  ++  ++t +++ +p+        il+ DE++ra+++++++L
  gi|119719082|ref|YP_919577.1|  46 PGMAKTLLASSFAKALDLEFKRVQFTPDLLPSDITGSHVYDmhSSTFRFRRGPIF-----TNILLADEINRAPPKTQSAL 120
                                    9************************************9999999***********.....78****************** PP

                                    HHHHHSSEEE..-SSSEEE---......-EEEEEESS--..-TT-TTHHHHTT- CS
                          AAA_5  86 lslleerrllleeggelvkaknddllerfrviatanpld.rslnelspalrsRf 138
                                    l  + er++   +g +   +++      f+viat np +  +  +l +a  +Rf
  gi|119719082|ref|YP_919577.1| 121 LEAMQERQVT-VDGVTFALEEP------FMVIATLNPIEfEGTYPLPEAQMDRF 167
                                    **********.66666666777......***********777777888888887 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   8.4e-07    0.0015       7     111 ..      46     150 ..      40     175 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 8.4e-07
                                    TTSSHHHHHHHHHHHHTHEEEEEET.TTCS.SSSTTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHH CS
                            AAA   7 pGtGKTllakavakelgvefleisg.sell.skyvgesekkirelfkeakeka.kpsilfiDEidalaksrsgseseeee 83 
                                    pG+ KTlla++ ak l+ ef +++  ++ll s++ g    +++    + ++    + il+ DEi +  ++          
  gi|119719082|ref|YP_919577.1|  46 PGMAKTLLASSFAKALDLEFKRVQFtPDLLpSDITGSHVYDMHSSTFRFRRGPiFTNILLADEINRAPPKT--------- 116
                                    9*******************9999537888888988888888877667677666559**********9999......... PP

                                    HHHHHHHHHHHHTTTS........SSTEEEEEEESS CS
                            AAA  84 rvvnqLlteldgvkkk........eskvivigatnr 111
                                      +++Ll+++++ +          e++++vi++ n 
  gi|119719082|ref|YP_919577.1| 117 --QSALLEAMQERQVTvdgvtfalEEPFMVIATLNP 150
                                    ..************9999999999888999999886 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   2.1e-06    0.0037      94     176 ..      76     155 ..       3     171 .. 0.73
   2 ?   -2.6   0.1       1.3   2.4e+03     193     220 ..     200     227 ..     198     230 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.1e-06
                                    SSHSSSEEEEESSSSSEEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEESSSCEEEEE--EEEEEEE-- CS
                            MCM  94 aagLtaavvrdeetgefvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisiaKaGivatLnartsvlaAanp 173
                                     +++t + v d +++ f +  G + +    +++ De+++   +++sal+Eam + ++++   G++  L+    v+a  np
  gi|119719082|ref|YP_919577.1|  76 PSDITGSHVYDMHSSTFRFRRGPIFT---NILLADEINRAPPKTQSALLEAMQERQVTVD--GVTFALEEPFMVIATLNP 150
                                    45666677777777777777776664...48999********************999996..9***************** PP

                                    S..SS CS
                            MCM 174 k..ag 176
                                    +  +g
  gi|119719082|ref|YP_919577.1| 151 IefEG 155
                                    94445 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.3
                                    HHHHHSSEEEEE-SSTTHHHHHHHHHHH CS
                            MCM 193 alLsrFDlifvllDkvdeekDeelaehi 220
                                    ++Ls+ D++ +++   +   D ++ ++i
  gi|119719082|ref|YP_919577.1| 200 KVLSKSDVLSMIRKVEEVYVDDAVLSYI 227
                                    6788888888888888888887777776 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0     4e-06    0.0071      95     139 ..     102     146 ..      22     152 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4e-06
                                    SEEEEETGGGS-HHHHHHHHHHHHHSEEESBTSSSEEE--EEEEE CS
                Sigma54_activat  95 GtlfLDeigelplelQekLlrvlqegevervGsskeikvdvriia 139
                                     +l+ Dei++ p+++Q+ Ll+++qe++v+  G +   +  +++ia
  gi|119719082|ref|YP_919577.1| 102 NILLADEINRAPPKTQSALLEAMQERQVTVDGVTFALEEPFMVIA 146
                                    58999**********************998887777766666665 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   4.2e-05     0.074      34     114 ..      38     130 ..      21     135 .. 0.75
   2 ?   -0.7   0.0       0.6   1.1e+03      64      92 ..     193     221 ..     184     241 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.2e-05
                         RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvklkits.gPvl.......ekagdlaalltnlee....kdvlfideihrlsrave 101
                                     hvl+   PG+ kt la+  ak l+ ++k    +P l       ++  d+ +   ++++    +++l+ dei r  ++++
  gi|119719082|ref|YP_919577.1|  38 GHVLIEDFPGMAKTLLASSFAKALDLEFKRVQfTPDLlpsditgSHVYDMHSSTFRFRRgpifTNILLADEINRAPPKTQ 117
                                    5************************9997653266552221122344556555556655233347899999999999999 PP

                         RuvB_N 102 evlysamedfrld 114
                                      l  am++ ++ 
  gi|119719082|ref|YP_919577.1| 118 SALLEAMQERQVT 130
                                    9999999988775 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.6
                         RuvB_N  64 tsgPvlekagdlaalltnleekdvlfide 92 
                                    t  P +ek    + +l+ +++ + +++d+
  gi|119719082|ref|YP_919577.1| 193 TDKPSIEKVLSKSDVLSMIRKVEEVYVDD 221
                                    66677777655555555555554444443 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0   0.00062       1.1       4      44 ..      19      59 ..      17      67 .. 0.89
   2 !    4.9   0.1    0.0083        15     109     159 ..     103     151 ..      99     181 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00062
                   Mg_chelatase  4 dvkGqeeakraleiaaaGgHnlllvGppGsGKtmlakrlps 44
                                    v+G+++  + l +a   g ++l+   pG  Kt+la+ +++
  gi|119719082|ref|YP_919577.1| 19 AVVGKRRVVERLLVALLSGGHVLIEDFPGMAKTLLASSFAK 59
                                   69999999999****98888899*************98876 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0083
                   Mg_chelatase 109 vLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpc 159
                                    +L+ DE+     k+  +L e +++++vt+   +  +e p  f+++a++Np 
  gi|119719082|ref|YP_919577.1| 103 ILLADEINRAPPKTQSALLEAMQERQVTVDGVTFALEEP--FMVIATLNPI 151
                                    7999*************************9988877766..9*******96 PP

>> MCM_lid  MCM AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.2   2.8e-05     0.051      41      79 ..     238     276 ..     208     285 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.8e-05
                                    TSSSST--HHHHHHHHHHHHHHHHHHTSSSE-HHHHHHH CS
                        MCM_lid  41 krksipitvRqLesliRLseAlAklrlsevvteedveea 79 
                                    ++ ++ +++R  e+l++ s+AlA +r +++v ++dv+e+
  gi|119719082|ref|YP_919577.1| 238 RDVEVGVSPRGTEALMKASRALAFIRGRDFVLPDDVKEV 276
                                    3557899*****************************985 PP

>> NUT  NUT protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   3.6e-05     0.065     411     453 ..     214     256 ..     197     262 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.6e-05
                            NUT 411 eeglypDpglLsYidkLCsqedFvtkvEAvihPrFleellSpe 453
                                     e++y D  +LsYi ++C   + v  vE  + Pr  e l+ + 
  gi|119719082|ref|YP_919577.1| 214 VEEVYVDDAVLSYIAEICRATRSVRDVEVGVSPRGTEALMKAS 256
                                    5789******************************999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 2365.81
//
Query:       gi|119719083|ref|YP_919578.1|  [L=410]
Description: hypothetical protein Tpen_0165 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-15   55.9   0.0      1e-14   54.5   0.0    1.8  1  DUF58            Protein of unknown function DUF58
  ------ inclusion threshold ------
      0.016   15.5   0.0      0.036   14.4   0.0    1.5  1  DUF11            Domain of unknown function DUF11
      0.056   13.6   0.2        3.6    7.8   0.0    2.3  2  bMG10            Bacterial Alpha-2-macroglobulin MG10 domain
       0.17   10.7   0.0       0.24   10.1   0.0    1.1  1  BatD             Oxygen tolerance
        0.2   10.4   0.0       0.36    9.6   0.0    1.3  1  Monooxygenase_B  Monooxygenase subunit B protein


Domain annotation for each model (and alignments):
>> DUF58  Protein of unknown function DUF58
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.5   0.0   2.9e-18     1e-14       2      86 .]     191     275 ..     190     275 .. 0.93

  Alignments for each domain:
  == domain 1  score: 54.5 bits;  conditional E-value: 2.9e-18
                          DUF58   2 ldfaglReYvpgDplrrIdWkatARtgelyvrefeaerartvllvldlspemslgstg.dekletavsaaaslarqllde 80 
                                     +f ++ e ++g  lrrI+WkatA+tg+++v+ + +er+++ l+vld  ++  lg +  +  ++++v+ + sla++l ++
  gi|119719083|ref|YP_919578.1| 191 FEFMEVGE-ARGSGLRRINWKATAKTGRPMVNVYLGERSAECLIVLDVPSSRLLGRALtEVLVDKMVEYTGSLAYYLTRR 269
                                    56777777.7999***************************************99999889999***************** PP

                          DUF58  81 gdrvgl 86 
                                    g+rv+l
  gi|119719083|ref|YP_919578.1| 270 GNRVSL 275
                                    ****86 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   9.9e-06     0.036       5      82 ..      58     126 ..      54     132 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 9.9e-06
                          DUF11   5 vdksevrpGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsvgsLeagesatlsftvrvtrta 82 
                                    v +s++ +Gdtv++ + v+N +++s   + v+  l +gl++v + +             L++ +++++++ v++ r++
  gi|119719083|ref|YP_919578.1|  58 VPRSNFVAGDTVRVEISVRNVSNRSV-VLEVREKLGEGLRLVGGDTV------ML--SVLKPHQEKRFTYYVTADRRG 126
                                    6678899*******************.***************99888......22..348888888888888887776 PP

>> bMG10  Bacterial Alpha-2-macroglobulin MG10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1     0.021        74      19      42 ..      61      82 ..      44      99 .. 0.74
   2 ?    7.8   0.0   0.00099       3.6      99     125 ..     111     137 ..     100     138 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.021
                          bMG10 19 sdaklkvGdkvrvrltvttprdle 42
                                   s  ++ +Gd+vrv+++v+  + ++
  gi|119719083|ref|YP_919578.1| 61 S--NFVAGDTVRVEISVRNVSNRS 82
                                   2..899***********9766655 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00099
                          bMG10  99 kgtytfeylvravtpGtfsvppakaee 125
                                     ++ +f+y v+a+++G + ++p ++++
  gi|119719083|ref|YP_919578.1| 111 HQEKRFTYYVTADRRGHYDLGPLEVYS 137
                                    56789*****************99986 PP

>> BatD  Oxygen tolerance
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   6.8e-05      0.24      16      96 ..      58     135 ..      49     145 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 6.8e-05
                           BatD  16 vdknevevgetfrLtftvngas...gepdfsapslekdfevlsgsqssstqiinGkssssssktwtytLapkkeGtltIp 92 
                                    v +++  +g+t+r++++v + s    + +++ ++l +++++++g + +   +   k  ++++  +ty + + + G + ++
  gi|119719083|ref|YP_919578.1|  58 VPRSNFVAGDTVRVEISVRNVSnrsVVLEVR-EKLGEGLRLVGGDTVMLS-V--LKPHQEKR--FTYYVTADRRGHYDLG 131
                                    6789999*************98744356666.58999*******643332.3..46666668..**************** PP

                           BatD  93 aati 96 
                                    ++++
  gi|119719083|ref|YP_919578.1| 132 PLEV 135
                                    *998 PP

>> Monooxygenase_B  Monooxygenase subunit B protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0    0.0001      0.36     209     282 ..      16      86 ..       3     104 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0001
                                    HHHHHHHHHHHHHCCSS---------B---------.--SEEEEEEEEEEESS-SEEEEEEEEEE-SSS-EEEE CS
                Monooxygenase_B 209 lvllivlvgyavtekkypitvPlQaglkkieplplelkatvkvevekatykvpgralelklevtNkgdepvrlg 282
                                    l +++ +    v+    p  +Pl a+l  ++p + +   +v+ +v+  +  v+g++++++++v N +++ v l+
  gi|119719083|ref|YP_919578.1|  16 LLVAVLAQRWFVALFSVPLLLPLFASLLYVHPSEKH---IVAERVVPRSNFVAGDTVRVEISVRNVSNRSVVLE 86 
                                    2233334456788889999*****999999998877...999999999999******************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2889.10
//
Query:       gi|119719084|ref|YP_919579.1|  [L=162]
Description: hypothetical protein Tpen_0166 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.11   12.9   3.7       0.24   11.7   0.3    2.2  2  SepA      Multidrug Resistance efflux pump


Domain annotation for each model (and alignments):
>> SepA  Multidrug Resistance efflux pump
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.2     0.017     3e+02       3      31 ..      34      62 ..      30      82 .. 0.82
   2 ?   11.7   0.3   1.4e-05      0.24       8      81 ..      92     161 ..      83     162 .] 0.73

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.017
                           SepA  3 allfvlsvvlisgtafilmvffgmyglsr 31
                                   al +v+s  l++g a  + v+  +y +s 
  gi|119719084|ref|YP_919579.1| 34 ALAMVFSASLLTGNASAVNVVASIYCVSL 62
                                   67889999999999999999999998774 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 1.4e-05
                           SepA   8 lsvvlisgtafilmvffgmyglsrlliyfhlaeftynesvmdnsfyygsyliigyvllfiieyimdelkrilpe 81 
                                    l+    +gta++l v++ +y l+ + +y+ l       s    sf        g+v l+++  +  +lkr + e
  gi|119719084|ref|YP_919579.1|  92 LAYGERAGTAYLLKVYLPLYSLAAIAVYVWLQVRKST-SA-FASFQL--VAASGFVALLVLYKVAGDLKRAVKE 161
                                    5555568*********************999654332.22.234443..3346889999888888999987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       942  (0.0525406); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1282.93
//
Query:       gi|119719085|ref|YP_919580.1|  [L=228]
Description: adenylate kinases [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-47  161.3   0.0    2.2e-47  161.0   0.0    1.1  1  ADK              Adenylate kinase
    4.2e-23   82.3   0.0    7.2e-23   81.5   0.0    1.3  1  AAA_17           AAA domain
    5.5e-18   64.6   3.1      1e-17   63.8   3.1    1.5  1  ADK_lid          Adenylate kinase, active site lid
    1.1e-05   25.9   0.0    1.8e-05   25.3   0.0    1.3  1  AAA_18           AAA domain
    0.00044   20.6   0.9     0.0058   16.9   0.6    2.3  2  Hydin_ADK        Hydin Adenylate kinase-like domain
    0.00098   19.3   0.0     0.0069   16.5   0.0    2.2  1  AAA_33           AAA domain
     0.0014   19.1   0.0     0.0021   18.5   0.0    1.3  1  AAA              ATPase family associated with various cellul
     0.0023   17.6   0.3     0.0044   16.7   0.3    1.4  1  DUF3039          Protein of unknown function (DUF3039)
     0.0025   18.1   0.0     0.0033   17.7   0.0    1.2  1  AAA_28           AAA domain
     0.0046   16.7   0.0     0.0073   16.1   0.0    1.2  1  Cytidylate_kin   Cytidylate kinase
     0.0051   17.3   0.6       0.79   10.3   0.2    2.4  2  Zn_ribbon_recom  Recombinase zinc beta ribbon domain
  ------ inclusion threshold ------
      0.026   14.7   0.4        1.2    9.3   0.1    2.5  2  Auto_anti-p27    Sjogren's syndrome/scleroderma autoantigen 1
       0.03   14.1   0.6      0.068   13.0   0.1    1.8  2  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger
      0.078   12.2   0.0       0.11   11.7   0.0    1.2  1  TIP49            TIP49 P-loop domain
      0.095   13.1   3.6        2.6    8.5   0.1    3.7  4  zf-IS66          zinc-finger binding domain of transposase IS
       0.12   12.0   0.1        4.7    6.8   0.0    2.4  3  Thymidylate_kin  Thymidylate kinase
       0.14   11.3   0.0       0.19   10.9   0.0    1.1  1  DUF815           Protein of unknown function (DUF815)
       0.17   11.6   0.0       0.29   10.9   0.0    1.4  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
       0.55    9.9   3.6        9.3    5.9   0.6    2.3  2  zf_C2H2_13       Zinc finger domain
       0.73    9.8   5.9        5.7    7.0   0.2    2.5  2  Nudix_N_2        Nudix N-terminal


Domain annotation for each model (and alignments):
>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.0   0.0   2.4e-50   2.2e-47       2     150 ..      20     199 ..      19     200 .. 0.98

  Alignments for each domain:
  == domain 1  score: 161.0 bits;  conditional E-value: 2.4e-50
                                    EESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHHCT-HHHHHHHHHHHTTSS--HHHHHHHHHHHHHCHGTTTEEEEES CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            ADK   2 lGaPgaGKGtqaeklvkkyglahlstGdllRaevksgtelGkeakevmdkgelvpdevvvklvkeelekedkkkgfllDG 81 
                                    +G+Pg GKGt a+ + +++g++h+stGd++R+evk+gtelGk++ke++d+g lvpd++v+++v+++l +ed+++g++lDG
  gi|119719085|ref|YP_919580.1|  20 IGPPGVGKGTYAKAVSETFGIPHISTGDIFREEVKKGTELGKRVKEYLDRGLLVPDDLVIEVVRHRLLQEDCRRGYILDG 99 
                                    8******************************************************************************* PP

                                    B-SSHHHHHHHHHHHHHHTSEESEEEEEE--HHHHHHHHHT....................................GSH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................................xxx RF
                            ADK  82 fPRtveqaealeelleeekvkldlvleldvpeevlveRltg....................................Dne 125
                                    fPRt+ qaeale+         d  l ++++++v++eRl+g                                    D++
  gi|119719085|ref|YP_919580.1| 100 FPRTIVQAEALER-----FSPPDWALLFHAEDSVILERLSGrricarcgaiyhvkymppkipgicdkcggplvqrrdDTP 174
                                    *************.....899*********************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHHHHHTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxx RF
                            ADK 126 etvkkRletykkqtkplidyykkkg 150
                                    e +++Rl++y++q +p+i yy+ +g
  gi|119719085|ref|YP_919580.1| 175 EVISERLKVYREQFTPIIAYYEGRG 199
                                    *********************9765 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.5   0.0     8e-26   7.2e-23       1     123 [.      20     137 ..      20     141 .. 0.92

  Alignments for each domain:
  == domain 1  score: 81.5 bits;  conditional E-value: 8e-26
                                    EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTT.TS.HSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEEEEE CS
                         AAA_17   1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrg.gl.akardemrklpleekkelqkeaaekiaeeakkkgvlvdg 78 
                                    +G+PG+GKgt+++ + e +g++h+s+Gd++ree+k+g +l ++ +++++++ l++++ + + +  ++ +e++++g+++dg
  gi|119719085|ref|YP_919580.1|  20 IGPPGVGKGTYAKAVSETFGIPHISTGDIFREEVKKGtELgKRVKEYLDRGLLVPDDLVIEVVRHRLLQEDCRRGYILDG 99 
                                    69**********************************966756678999999***************************** PP

                                    -SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHHT CS
                         AAA_17  79 hprikeqagfldglpkevleelkpdaiilleadpeeilerrlkdr 123
                                    +pr+  qa++l+++         pd  +l++a++ +iler+  +r
  gi|119719085|ref|YP_919580.1| 100 FPRTIVQAEALERFS-------PPDWALLFHAEDSVILERLSGRR 137
                                    ******999988776.......5899**************98775 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.8   3.1   1.2e-20     1e-17       1      36 []     136     171 ..     136     171 .. 0.99

  Alignments for each domain:
  == domain 1  score: 63.8 bits;  conditional E-value: 1.2e-20
                                    EEE-TTT--EEETTTB--SSTTB-TTT--.-B--GG CS
                        ADK_lid   1 RrvCpkCGrsYhvvfnpPkveglCDkCGepLvqRsD 36 
                                    Rr+C  CG++Yhv+++pPk +g+CDkCG+pLvqR D
  gi|119719085|ref|YP_919580.1| 136 RRICARCGAIYHVKYMPPKIPGICDKCGGPLVQRRD 171
                                    9***********999*******************99 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0     2e-08   1.8e-05       3     114 ..      19     137 ..      17     141 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 2e-08
                         AAA_18   3 ltGtpGvGKttlakeLskrlgf.....gvnlrdvakenglllevdpealdeskrldedkldklld..aleenssaleegk 75 
                                      G+pGvGK t ak++s+  g+     g++ r+ +k++  l  + +e ld+ + + +d + ++++  +l+e ++      
  gi|119719085|ref|YP_919580.1|  19 FIGPPGVGKGTYAKAVSETFGIphistGDIFREEVKKGTELGKRVKEYLDRGLLVPDDLVIEVVRhrLLQEDCR-----R 93 
                                    67****************9999*999999999999998888888888899999999998888765114555554.....7 PP

                         AAA_18  76 nlvidghlaeleseaakdikk.....vvLtaspeelleRlekRg 114
                                     +++dg++   ++++a ++          +a++++ leRl+ R+
  gi|119719085|ref|YP_919580.1|  94 GYILDGFPRTIVQAEALERFSppdwaLLFHAEDSVILERLSGRR 137
                                    88***************9999****9999************996 PP

>> Hydin_ADK  Hydin Adenylate kinase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.33     3e+02       3      40 ..      18      55 ..      16      69 .. 0.82
   2 !   16.9   0.6   6.5e-06    0.0058     170     197 ..      72      99 ..      66     100 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.33
                      Hydin_ADK  3 ivhGaPlsGKtatavtLakkYeaAlltiDsvvleAisd 40
                                   +  G+P  GK + a +++ ++++  ++  ++  e + +
  gi|119719085|ref|YP_919580.1| 18 VFIGPPGVGKGTYAKAVSETFGIPHISTGDIFREEVKK 55
                                   5569*******************999998888887654 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 6.5e-06
                      Hydin_ADK 170 vLPedllveIlsERlqlndCyrGvvfDg 197
                                    + P+dl++e++  Rl  +dC rG ++Dg
  gi|119719085|ref|YP_919580.1|  72 LVPDDLVIEVVRHRLLQEDCRRGYILDG 99 
                                    78*************************9 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   7.7e-06    0.0069       3      40 ..      18      59 ..      17     139 .. 0.63

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 7.7e-06
                         AAA_33  3 llvGlpGsGKstlaerllkklgavllssdtlrr.rlfg...t 40
                                   +++G+pG+GK t+a+ + +  g  ++s+ +++r  +++    
  gi|119719085|ref|YP_919580.1| 18 VFIGPPGVGKGTYAKAVSETFGIPHISTGDIFReEVKKgteL 59
                                   89*****************99999999877666366555532 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   2.4e-06    0.0021       2      28 ..      18      44 ..      17      73 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.4e-06
                                   EEESSTTSSHHHHHHHHHHHHTHEEEE CS
                            AAA  2 llyGppGtGKTllakavakelgvefle 28
                                   +++GppG+GK + akav +++g++ ++
  gi|119719085|ref|YP_919580.1| 18 VFIGPPGVGKGTYAKAVSETFGIPHIS 44
                                   799*****************9876443 PP

>> DUF3039  Protein of unknown function (DUF3039)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.3   4.9e-06    0.0044      14      49 ..     126     162 ..     122     164 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.9e-06
                        DUF3039  14 dkiaesavtGtpVvALCGkvwvptrdpkkfP.vCpeC 49 
                                    d ++  +++G+++ A CG+++ ++  p k P +C +C
  gi|119719085|ref|YP_919580.1| 126 DSVILERLSGRRICARCGAIYHVKYMPPKIPgICDKC 162
                                    55666789***********************9***** PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   3.7e-06    0.0033       2      79 ..      17      98 ..      16     125 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.7e-06
                         AAA_28  2 ivitGgestGKTtlleaLaar.gypvv..pEaareileeklakgedalpwvedllafa.ervleeqleeeaaaaankvlfcD 79
                                    v++G+++ GK t ++a +++ g+p++   +++re ++++++ g++  ++ ++ l +  ++v+e  ++++ + + ++ +++D
  gi|119719085|ref|YP_919580.1| 17 LVFIGPPGVGKGTYAKAVSETfGIPHIstGDIFREEVKKGTELGKRVKEYLDRGLLVPdDLVIEVVRHRLLQEDCRRGYILD 98
                                   79*******************9***99999*********9999998666655555444256666666666666667777766 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   8.1e-06    0.0073       5      34 ..      21      50 ..      18      54 .. 0.96

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 8.1e-06
                                   -STTSSHHHHHHHHHHHHT-EEEEHHHHHH CS
                 Cytidylate_kin  5 GPagsGKssvaralaeklglkyldtgalYR 34
                                   GP g GK++ a+a++e++g+  ++tg ++R
  gi|119719085|ref|YP_919580.1| 21 GPPGVGKGTYAKAVSETFGIPHISTGDIFR 50
                                   9****************************9 PP

>> Zn_ribbon_recom  Recombinase zinc beta ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.2   0.00088      0.79       2      19 ..     133     150 ..     132     155 .. 0.91
   2 ?    5.1   0.0     0.036        32       7      20 ..     158     171 ..     157     200 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00088
                Zn_ribbon_recom   2 LsGllrCgeCGspmtrrk 19 
                                    LsG  +C++CG+ +++++
  gi|119719085|ref|YP_919580.1| 133 LSGRRICARCGAIYHVKY 150
                                    89999**********997 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.036
                Zn_ribbon_recom   7 rCgeCGspmtrrkr 20 
                                    +C +CG+p+++r+ 
  gi|119719085|ref|YP_919580.1| 158 ICDKCGGPLVQRRD 171
                                    6********99874 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.14   1.3e+02      23      40 .]     128     143 ..     123     143 .. 0.75
   2 ?    9.3   0.1    0.0014       1.2      18      30 ..     159     172 ..     157     177 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.14
                  Auto_anti-p27  23 vPLmrdrkggkvyCvaCd 40 
                                    v+L r   +g+ +C++C+
  gi|119719085|ref|YP_919580.1| 128 VILERL--SGRRICARCG 143
                                    666665..4788*****6 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0014
                  Auto_anti-p27  18 CpvCgvPLmrdr.k 30 
                                    C++Cg PL++ r +
  gi|119719085|ref|YP_919580.1| 159 CDKCGGPLVQRRdD 172
                                    **********9843 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       3.3   2.9e+03       2      10 ..     137     145 ..     136     150 .. 0.72
   2 ?   13.0   0.1   7.6e-05     0.068       2      15 ..     157     170 ..     156     173 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3.3
                                    EE-SSS--E CS
                 zf-C4_Topoisom   2 ekCPkCggd 10 
                                    + C  Cg+ 
  gi|119719085|ref|YP_919580.1| 137 RICARCGAI 145
                                    57999*975 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 7.6e-05
                                    EE-SSS--EEEEEE CS
                 zf-C4_Topoisom   2 ekCPkCggdLvlkr 15 
                                    + C+kCgg+Lv++r
  gi|119719085|ref|YP_919580.1| 157 GICDKCGGPLVQRR 170
                                    57***********8 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00012      0.11      47      99 ..      11      59 ..       6      73 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00012
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49 47 klaGravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkktevl 99
                                    l G  +++ Gp+g Gk   a a+s+ +g  +p  ++s++++++ evkk   l
  gi|119719085|ref|YP_919580.1| 11 SLRGMKLVFIGPPGVGKGTYAKAVSETFG--IP--HISTGDIFREEVKKGTEL 59
                                   567888999****************9999..65..7899**********7655 PP

>> zf-IS66  zinc-finger binding domain of transposase IS66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.32   2.8e+02      29      43 ..      78      92 ..      58      94 .. 0.84
   2 ?    0.7   0.0      0.82   7.3e+02       2       9 ..     137     144 ..     136     151 .. 0.79
   3 ?    8.5   0.1    0.0029       2.6       1      25 [.     156     183 ..     156     189 .. 0.75
   4 ?   -1.9   0.0       5.3   4.7e+03      15      30 ..     205     217 ..     197     219 .. 0.62

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.32
                        zf-IS66 29 kfrViehirpkyaCp 43
                                    ++V++h+  +  C+
  gi|119719085|ref|YP_919580.1| 78 VIEVVRHRLLQEDCR 92
                                   578999998887777 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.82
                        zf-IS66   2 rtCpcCGg 9  
                                    r+C+ CG+
  gi|119719085|ref|YP_919580.1| 137 RICARCGA 144
                                    67999996 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0029
                        zf-IS66   1 prtCpcCGg.l...lkpigedrvreeldi 25 
                                    p +C++CGg l    +  +e+ ++e+l++
  gi|119719085|ref|YP_919580.1| 156 PGICDKCGGpLvqrRDDTPEV-ISERLKV 183
                                    679******667776677777.7777765 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 5.3
                        zf-IS66  15 gedrvreeldipPakf 30 
                                    +     e+ d++ +++
  gi|119719085|ref|YP_919580.1| 205 E---ANEQADVVVPRV 217
                                    3...348999886665 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0    0.0052       4.7       3      47 ..      21      68 ..      19      80 .. 0.84
   2 ?    2.4   0.0      0.12   1.1e+02     117     140 ..     115     138 ..      96     143 .. 0.83
   3 ?   -2.5   0.0       3.8   3.4e+03     144     180 ..     176     212 ..     167     216 .. 0.58

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0052
                                   ESTTSSHHHHHHHHHHHHHHTTE...EEEESS.STTSHHHHHHHHHHH CS
                Thymidylate_kin  3 GlDGaGKttqaellkerlkeegik..vvltre.pggteiGekirelll 47
                                   G  G+GK t a+++ e++   +i+   +++ e ++gte+G+ ++e+l 
  gi|119719085|ref|YP_919580.1| 21 GPPGVGKGTYAKAVSETFGIPHIStgDIFREEvKKGTELGKRVKEYLD 68
                                   6669**************999998875555552689**********97 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.12
                                    E-SEEEEEESSHHHHHTSCCTTSS CS
                Thymidylate_kin 117 kPdltflldvdpevalkRlakrde 140
                                     Pd+ +l+  + +v l+Rl+ r+ 
  gi|119719085|ref|YP_919580.1| 115 PPDWALLFHAEDSVILERLSGRRI 138
                                    6******************99975 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 3.8
                                    SHHHHHHHHHHHHHHHHHHHHTTSTEEEEETTS-HHH CS
                Thymidylate_kin 144 eeeeqldflrkvrerylelakederiliidasksiee 180
                                     + e+l+++r+  +   + ++ +++++ i+a+++ + 
  gi|119719085|ref|YP_919580.1| 176 VISERLKVYREQFTPIIAYYEGRGKLVRIEANEQADV 212
                                    4555556555555555566666666777777766655 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00021      0.19      54     119 ..      15      80 ..       3      86 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00021
                         DUF815  54 nnvLLwGarGtGKSslvkallneyaeegLrlievekedlkelpklvellrerperfilfvDDLsFe 119
                                     +++++G  G+GK +  ka+ +++   ++   ++ +e++k+  +l + ++e   r +l+ DDL  e
  gi|119719085|ref|YP_919580.1|  15 MKLVFIGPPGVGKGTYAKAVSETFGIPHISTGDIFREEVKKGTELGKRVKEYLDRGLLVPDDLVIE 80 
                                    567889*********************************************************876 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00032      0.29      36      60 ..      17      41 ..       5      66 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00032
                         RuvB_N 36 vllyGpPGlGkttlakiiakelgvk 60
                                   ++++GpPG+Gk t ak +++ +g+ 
  gi|119719085|ref|YP_919580.1| 17 LVFIGPPGVGKGTYAKAVSETFGIP 41
                                   6899**************9988865 PP

>> zf_C2H2_13  Zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1     0.032        28      15      24 ..     134     143 ..     125     145 .. 0.77
   2 ?    5.9   0.6      0.01       9.3      19      27 ..     158     166 ..     157     169 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.032
                     zf_C2H2_13  15 lnYRvCnkCG 24 
                                    +  R+C  CG
  gi|119719085|ref|YP_919580.1| 134 SGRRICARCG 143
                                    566******* PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.01
                     zf_C2H2_13  19 vCnkCGkPi 27 
                                    +C+kCG P+
  gi|119719085|ref|YP_919580.1| 158 ICDKCGGPL 166
                                    8*******8 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   1.2     0.034        30      22      31 ..     136     145 ..     134     147 .. 0.90
   2 ?    7.0   0.2    0.0063       5.7       3      15 ..     159     171 ..     159     175 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.034
                                    EEEETTTTEE CS
                      Nudix_N_2  22 RlvCpaCgti 31 
                                    R +C++Cg+i
  gi|119719085|ref|YP_919580.1| 136 RRICARCGAI 145
                                    99******99 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0063
                                    -TTT--B-EEE-- CS
                      Nudix_N_2   3 CsqCGtpvelrip 15 
                                    C +CG+p+ +r  
  gi|119719085|ref|YP_919580.1| 159 CDKCGGPLVQRRD 171
                                    9******999874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1439.76
//
Query:       gi|119719086|ref|YP_919581.1|  [L=481]
Description: peptidase U62, modulator of DNA gyrase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      8e-50  170.2   0.4    1.7e-49  169.2   0.1    1.6  2  PmbA_TldD  Putative modulator of DNA gyrase


Domain annotation for each model (and alignments):
>> PmbA_TldD  Putative modulator of DNA gyrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.2   0.1   9.3e-54   1.7e-49       1     279 []      23     332 ..      23     332 .. 0.79
   2 ?   -1.7   0.0      0.11     2e+03     269     278 ..     411     420 ..     409     420 .. 0.88

  Alignments for each domain:
  == domain 1  score: 169.2 bits;  conditional E-value: 9.3e-54
                                    EEEEEEEEEEEEEEEEETTEEEEEEEEEEEEEEEEEEETTEEEEEE...ESSHHHHHHHHHHHHHHCCS---TT-..... CS
                      PmbA_TldD   1 eaevrleesestsvrfengevetnsssedsglgvrvikggrlgfastldtsdealeeaveraveiaklapedpea..... 75 
                                    ++e+r++   +  ++ +ngev  ++ s ++g+++rvi++g+lgfast+ ++ e++  ave+a++ ak  ++ +++     
  gi|119719086|ref|YP_919581.1|  23 YVEARYHLIARSGLSSRNGEVIGVEKSFSQGIAIRVIVDGSLGFASTSVLTPEGVTGAVEKAYKKAKAHAKLQKRpiefs 102
                                    6889999999999*******************************996666668999999999999987777776665556 PP

                                    .................GGS-HHHHHHHHHHHHHH.CHCST...........TEEEEE..EEEEE......EEE.EEEEE CS
                      PmbA_TldD  76 .................eevsaeekielleelekalrsadp...........kiensk..garisgvsaslsaskeekli 125
                                                     ++v+                               k+++ +  +ar++  ++++ +s+eek++
  gi|119719086|ref|YP_919581.1| 103 derlgrvtyeavekkspRDVD-------------------FqektryhqelwKLVSGAisTARVATLTSFYGESVEEKIV 163
                                    666655544444444444444...................04444444444422222246779***************** PP

                                    EETTSEEEEEEEEEEEEEEEEEE...STCS....ETEEEEEEEESSHHH.S..SSHHHHHHHHHHCTTT-B---SEE.EE CS
                      PmbA_TldD 126 anSeGldveqtrtrvslslsvia.d.dggs....gdgmgggsgyedlee.edleeiaeeaaekalasleakplppgk.yp 197
                                    +nS+G++v+++ +rvsl+++v++   + g+      ++   +gye +++ +  e + e+++   + +leak++p  +  +
  gi|119719086|ref|YP_919581.1| 164 VNSDGAYVKSRVPRVSLGYNVVVtLpSKGTiqrfF-SHAASGGYELVDAwKVHEYLPEDVKTFEKILLEAKSPPVDRpVD 242
                                    ***********************655544466452.333444444444433355666666666666667788777745** PP

                                    EEE-HHHHHHHHHGHHHHHTBHHHHH......TT--TTTT.-TTSB-S-TT--EEEETT-......-SB-TTSBB---EE CS
                      PmbA_TldD 198 Vvlspeavgsllheavghaleadavl......egrSflkd.klGekvaselltivddpts.gglgsypfDdEGvptqrtv 269
                                    V+ ++e vg+++he++gh+ ead++       +g+Sf k+ +lGe+++se  t++ddpt+ g+ g+y +DdEGvp+++++
  gi|119719086|ref|YP_919581.1| 243 VIVGSEIVGLMVHESCGHPSEADRIMgreaaqAGKSFIKPnMLGERIGSEYATVIDDPTIpGSNGFYLYDDEGVPARPRY 322
                                    ****************************99999*****9978************************************** PP

                                    EEETTEE--- CS
                      PmbA_TldD 270 lIenGvLkny 279
                                    l +nGv + +
  gi|119719086|ref|YP_919581.1| 323 LYKNGVINEF 332
                                    ******9876 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.11
                                    EEEETTEE-- CS
                      PmbA_TldD 269 vlIenGvLkn 278
                                    +lIenG Lk+
  gi|119719086|ref|YP_919581.1| 411 YLIENGELKG 420
                                    8*******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (481 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 3215.20
//
Query:       gi|119719087|ref|YP_919582.1|  [L=445]
Description: peptidase U62, modulator of DNA gyrase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.6e-43  147.4   0.0    9.6e-43  147.0   0.0    1.1  1  PmbA_TldD  Putative modulator of DNA gyrase


Domain annotation for each model (and alignments):
>> PmbA_TldD  Putative modulator of DNA gyrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.0   0.0   5.4e-47   9.6e-43       2     278 ..      24     306 ..      23     306 .. 0.83

  Alignments for each domain:
  == domain 1  score: 147.0 bits;  conditional E-value: 5.4e-47
                                    EEEEEEEEEEEEEEEETTEEEEEEEEEEEEEEEEEEETTEEEEEE...ESSHHHHHHHHHHHHHHCCS---TT-GGS-HH CS
                      PmbA_TldD   2 aevrleesestsvrfengevetnsssedsglgvrvikggrlgfastldtsdealeeaveraveiaklapedpeaeevsae 81 
                                    + v l ++es  v+f+nge + +++++d+ + + + kgg++  +s+++ s e++ ++++   ++ +  p+   ++++++ 
  gi|119719087|ref|YP_919582.1|  24 VAVLLYRRESVMVKFANGEPSVTQNWTDHAADIYLAKGGKILGTSAPTHSLEEIYRVIDSLHQMQERLPPSMLYAPLPEP 103
                                    67999**********************************9888887777778*******988888777777777555555 PP

                                    HHHH....H.HHHHHHH.CHCST....TEEEEEEEEEE......EEE.EEEEEEETTSEEEEEEEEEEEEEEEEEE..ST CS
                      PmbA_TldD  82 ekie....l.leelekalrsadp....kienskgarisgvsaslsaskeeklianSeGldveqtrtrvslslsvia.ddg 151
                                    ek e    l  +++ +a++++       +e +++ +++++ ++l+ ++e k+++nS+G++ ++ +t+v  ++   a +  
  gi|119719087|ref|YP_919582.1| 104 EKHEplpgLvDKRIVEAIEDPAHvseaVVEAANRYKVDSFAGMLQLTYEVKALVNSKGASFSEDSTYVKTYIRSFAgE-- 181
                                    555433332344444444444443332222233559****************************************33.. PP

                                    CSETEEEEEEEE...SSHHHS..SSHHHHHHHHHHCTTT-B---SEEEEEEE-HHHHHHHHHGHHHHHTBHHHHHTT--T CS
                      PmbA_TldD 152 gsgdgmgggsgy...edleeedleeiaeeaaekalasleakplppgkypVvlspeavgsllheavghaleadavlegrSf 228
                                          g+g ++   ++l   d+e++ae a   a +s ++++ ppg+++V+lsp+++g++l ++v  ++ a+++  g S+
  gi|119719087|ref|YP_919582.1| 182 ------GSGQWSlgsRRLSISDVEKVAETASHLAYQSRRQEDYPPGRTNVLLSPMVAGNFLNYIV-EMATASSIMMGFSI 254
                                    ......3344434443344477999*************************************888.8************* PP

                                    TTT.-TTSB-S-TT--EEEETT-......-SB-TTSBB---EEEEETTEE-- CS
                      PmbA_TldD 229 lkd.klGekvaselltivddpts.gglgsypfDdEGvptqrtvlIenGvLkn 278
                                    + + k Gekv sellt+ d p+  + +gs++fDdEG+ t  +++Ie+GvL+n
  gi|119719087|ref|YP_919582.1| 255 FMNrKPGEKVSSELLTVEDAPRLaELPGSTSFDDEGIRTYTKPVIEKGVLRN 306
                                    *9988*****************99**************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (445 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.24s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2936.21
//
Query:       gi|119719088|ref|YP_919583.1|  [L=363]
Description: hypothetical protein Tpen_0170 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.23s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2541.86
//
Query:       gi|119719089|ref|YP_919584.1|  [L=340]
Description: transglutaminase domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-21   77.3   0.1    2.4e-21   76.3   0.1    1.6  1  Transglut_core  Transglutaminase-like superfamily
  ------ inclusion threshold ------
       0.13   12.4   0.0       0.25   11.5   0.0    1.5  1  Big_8           Bacterial Ig domain


Domain annotation for each model (and alignments):
>> Transglut_core  Transglutaminase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.3   0.1   2.7e-25   2.4e-21       3     112 .]     163     288 ..     161     288 .. 0.84

  Alignments for each domain:
  == domain 1  score: 76.3 bits;  conditional E-value: 2.7e-25
                 Transglut_core   3 laeeltagakdplekakaiyewvr..knveysaprrtpgsrdaeavletgk......GncedfaslfvallRalGipaRv 74 
                                    la+e+ a a++pl  +k++++wv+  ++ +y+    + g++  +++++ g       G+c ++a +fv+++R lG+paR 
  gi|119719089|ref|YP_919584.1| 163 LAREV-AFAQTPLSTVKKLASWVEqaNRGNYR---VSFGRAGSDHAVTYGYrgyaitGDCVEVADVFVTMARILGVPART 238
                                    88998.9*****************88677777...4444444444444333334577*********************** PP

                 Transglut_core  75 vtgylsgeeekeq............svasedaHawvevylegygWvplDp 112
                                    ++g+l +++e+++            + ++++ H+w++vy+e ygW+ +D+
  gi|119719089|ref|YP_919584.1| 239 AFGILLTDSERMWlnfstieaegenILTHWGGHMWPQVYVEPYGWIDVDM 288
                                    ******9887777**********99***********************95 PP

>> Big_8  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   2.8e-05      0.25      14      64 ..      54     108 ..      43     136 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.8e-05
                          Big_8  14 fsvgksvkeGDyftitlpdnlkfngistsektfd....ikdsngnviakakvdpg 64 
                                    ++++++v   Dy+ + lp+n +f+++   + +++    + d++gn++a   v ++
  gi|119719089|ref|YP_919584.1|  54 LKNENNVSVNDYVYVALPQNTTFQKSYVVSINPKplrfVVDEDGNTYAVVLVRAE 108
                                    567899*****************99765555554323356889999999877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2480.42
//
Query:       gi|119719090|ref|YP_919585.1|  [L=307]
Description: carbamate kinase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.7e-28   99.8   0.0    4.1e-28   98.6   0.0    1.6  1  AA_kinase  Amino acid kinase family


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.6   0.0   2.3e-32   4.1e-28       2     239 ..       5     286 ..       4     288 .. 0.83

  Alignments for each domain:
  == domain 1  score: 98.6 bits;  conditional E-value: 2.3e-32
                                    EEEEEE-TTCCC.CTCC.......HHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHH...TCCCCCHHHC....E.. CS
                      AA_kinase   2 rvVvKlGGsslt.dkee.......aslrrlaeqiaalkesgnklvvVhGggsftdgllal...ksglssgelaaglrstl 70 
                                    +vV++lGG++l  ++e+        +l+r+   ia+l  s +klv+ hG+g+++ +l+ +    ++++  +l        
  gi|119719090|ref|YP_919585.1|   5 LVVLALGGNALLrTGERgtfeeqvRNLQRVSGHIARL-ASRYKLVITHGNGPQVGNLYLQqeaFKEVPGMPL-------- 75 
                                    79*******77758888********************.*****************99999775555555555........ PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE................................... CS
                      AA_kinase  71 eeagevatrdalaslgerlvaallaaglpavglsaaaldateagr................................... 115
                                             +a++++ ++l  +++++++++v  s +   +t+                                      
  gi|119719090|ref|YP_919585.1|  76 ---------HACVAMTQSLIGYMVQQAVSSVDPSLKVAVLTTRVEvdaedpafkspskpigpyyqesevprllekgwtlv 146
                                    .........67888888888888888887777666655555554467777777777777777777789999********* PP

                                    ...........HHHTTTCEEECCHHHHHH.HTT-EEEEESEE...EEETTTE...EEEE-HHHHHHHHHHHCTSSEEEEE CS
                      AA_kinase 116 .........degsdgnvesvdaeaieell.eagvvpvltgfi...gldeege...lgrgssDtiaallAealgAdkliil 179
                                              ++s+++ + v+ e +++l  e ++v+ ++g++   + + +g     +++++D +++llA++l+A+k +il
  gi|119719090|ref|YP_919585.1| 147 nvpgkgwrrVVPSPRPKRIVELEVVKRLAgEVDIVVAVGGGGipvVRSGKGYegvDAVIDKDLASSLLAQELNAEKFVIL 226
                                    *****************************7777666666644455444444488888*********************** PP

                                    ESSSSCESSTTTTCCTTCECCEEEHHHCHH..CSSS.TTTHHHHCHHHHHHHHHCTT-EEEE CS
                      AA_kinase 180 tdVdGVydadpkkvpdarllpeisvdeaee..saselatgGmkvkhpaalaaarrggipvvI 239
                                    tdV+GVy + +      rl++e+ ++ea+e  +++ + +g+m +k++aa+  a + g  +vI
  gi|119719090|ref|YP_919585.1| 227 TDVEGVYLDYGTPS--QRLVEELCAREALElvNKGVFPRGSMGPKVEAAALYAAKTGKVAVI 286
                                    *******9998666..8*********************************999997555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2031.96
//
Query:       gi|119719091|ref|YP_919586.1|  [L=109]
Description: ModE family transcriptional regulator [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-15   56.6   0.3    2.9e-15   55.9   0.3    1.2  1  HTH_1     Bacterial regulatory helix-turn-helix protein, lysR
     0.0062   16.3   0.3      0.017   14.9   0.0    1.8  2  HTH_23    Homeodomain-like domain
     0.0078   16.2   0.3      0.012   15.7   0.3    1.3  1  HTH_29    Winged helix-turn helix


Domain annotation for each model (and alignments):
>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.9   0.3   4.9e-19   2.9e-15       5      60 .]      26      86 ..      25      86 .. 0.89

  Alignments for each domain:
  == domain 1  score: 55.9 bits;  conditional E-value: 4.9e-19
                                   HHHHHHHHHSSHHHHHHHHTS-HHHHHHHHHHHHHHHTS-SEEESSSE.....EEE-HHHH CS
                          HTH_1  5 rlfvavaeegsftrAAeeLglsqpavsrqikrLEeelgvpLfeRtgrg.....lrLTeaGe 60
                                   +l++a+ e gs+ +AAe+Lg+s++ ++  +k+LEe+ gv+L+eR  +g     ++LTe+++
  gi|119719091|ref|YP_919586.1| 26 ELLKAIEEKGSLHAAAEALGYSYSFAWSYLKKLEERAGVTLIERRRGGqrhggMVLTEEAR 86
                                   689****************************************8443345567*****986 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   2.8e-06     0.017       9      45 ..      26      63 ..      25      66 .. 0.87
   2 ?   -1.5   0.1      0.41   2.4e+03       6      17 ..      86     100 ..      82     108 .. 0.49

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.8e-06
                         HTH_23  9 rillllaeGlsvreIAreLgvsrrTvyrwlkryre.eG 45
                                   + l++  e+ s +++A++Lg s++  + +lk+ +e  G
  gi|119719091|ref|YP_919586.1| 26 ELLKAIEEKGSLHAAAEALGYSYSFAWSYLKKLEErAG 63
                                   6789999999**********************976555 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.41
                         HTH_23   6 eRlrillllae...G 17 
                                    ++l+ l+l ae   G
  gi|119719091|ref|YP_919586.1|  86 RKLLKLYLEAErvvG 100
                                    444444444434444 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.3   1.9e-06     0.012       3      62 ..      26      86 ..      25      87 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.9e-06
                         HTH_29  3 qallllaeGvstvsqiAkllglsrrtvyrwlkrfeegGlaalld.rrrsgrprn.rlseeqe 62
                                   + l +++e +s    +A++lg+s++    +lk  ee     l++ rr++ r+   +l+ee +
  gi|119719091|ref|YP_919586.1| 26 ELLKAIEEKGS-LHAAAEALGYSYSFAWSYLKKLEERAGVTLIErRRGGQRHGGmVLTEEAR 86
                                   56788889987.*********************66655444888788899999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.36u 0.28s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 774.68
//
Query:       gi|119719092|ref|YP_919587.1|  [L=111]
Description: MoaD family protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-11   44.9   0.0    2.2e-11   44.2   0.0    1.4  1  ThiS      ThiS family
  ------ inclusion threshold ------
       0.02   14.7   0.3       0.15   12.0   0.0    2.1  2  Ub-Mut7C  Mut7-C ubiquitin


Domain annotation for each model (and alignments):
>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   0.0   2.4e-15   2.2e-11       2      77 .]      28     111 .]      27     111 .] 0.89

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 2.4e-15
                                    EETTCCHHHHTCEEEEESSTSBHHHHHHHHHHHTCHHG.........TTTTEEEEETTEEEGCCTTTSB--TTCEEEEEE CS
                           ThiS   2 llfaelrelageeelelaegstvaelleaLgerypela.........lerrvavavNgeivprlwldtelkdgDevailp 72 
                                    llfa+lr++ g  e+ ++++ +++  +e+ +   ++ +          +r  +++vNg+++++  ++t+lkdgD+va++p
  gi|119719092|ref|YP_919587.1|  28 LLFATLRDKYGVPEVSVDCDGSLRGCVEEAARILGRDFveevfegddYRRDRIILVNGRHIQF-VQSTQLKDGDVVAVFP 106
                                    69*********777778888889999999988887777888899999889999**********.88************** PP

                                    STTC- CS
                           ThiS  73 pVaGG 77 
                                    p+aGG
  gi|119719092|ref|YP_919587.1| 107 PIAGG 111
                                    ****9 PP

>> Ub-Mut7C  Mut7-C ubiquitin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1     0.057   5.1e+02      14      49 ..      10      44 ..       1      48 [. 0.56
   2 ?   12.0   0.0   1.6e-05      0.15      51      75 ..      80     106 ..      79     109 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.057
                       Ub-Mut7C 14 dflprarre..ralavafdeaatvkhviEalGVPhtEV 49
                                   +fl+ +r +    ++v+f  +at+++     GVP + V
  gi|119719092|ref|YP_919587.1| 10 KFLNLRRNSlhVRVHVKFLLFATLRDK---YGVPEVSV 44
                                   555554444103445566667777764...57776665 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 1.6e-05
                       Ub-Mut7C  51 lilvnGesvgf..shiledGdrvavyp 75 
                                    +ilvnG++ +f  s  l+dGd vav p
  gi|119719092|ref|YP_919587.1|  80 IILVNGRHIQFvqSTQLKDGDVVAVFP 106
                                    69********95567899*******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 801.19
//
Query:       gi|119719093|ref|YP_919588.1|  [L=455]
Description: 4Fe-4S ferredoxin iron-sulfur binding domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.4e-15   55.3  44.2    8.8e-09   35.8  12.7    5.0  5  Fer4_7          4Fe-4S dicluster domain
    1.3e-14   53.3  41.8    3.5e-05   23.4   5.3    6.2  5  Fer4            4Fe-4S binding domain
    1.9e-14   53.5  31.0    6.6e-09   35.8  10.3    4.2  4  Fer4_9          4Fe-4S dicluster domain
    1.4e-11   44.0  51.7    0.00012   22.0   2.4    6.1  6  Fer4_6          4Fe-4S binding domain
      1e-09   37.9  49.8    0.00044   20.2   4.5    7.1  7  Fer4_2          4Fe-4S binding domain
    1.8e-09   37.6  34.4    2.3e-08   34.0   7.3    4.2  4  Fer4_21         4Fe-4S dicluster domain
    1.9e-09   37.5  43.2    1.6e-08   34.5  10.4    4.9  6  Fer4_10         4Fe-4S dicluster domain
    5.9e-09   36.3  30.5     0.0014   19.0   0.9    5.5  5  Fer4_8          4Fe-4S dicluster domain
    6.1e-09   36.7  35.6      0.013   16.4   1.6    5.3  4  Fer4_16         4Fe-4S double cluster binding domain
    1.6e-05   25.4  42.2      0.003   18.1   2.1    5.6  4  Fer4_17         4Fe-4S dicluster domain
    2.8e-05   24.3  57.4    0.00091   19.6   3.7    7.0  7  Fer4_4          4Fe-4S binding domain
     0.0025   18.6   4.1     0.0025   18.6   4.1    6.7  6  Fer4_3          4Fe-4S binding domain
  ------ inclusion threshold ------
      0.043   13.8   0.1      0.043   13.8   0.1    5.0  6  zf-dskA_traR    Prokaryotic dksA/traR C4-type zinc finger
       0.25   12.1  19.7       0.28   11.9   4.7    4.0  3  zinc_ribbon_15  zinc-ribbon family
       0.27   12.1  25.5        2.1    9.2   0.0    5.4  6  Fer4_22         4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.6    0.0002      0.23      30      52 .]     122     147 ..      94     147 .. 0.80
   2 !   20.1  10.3   6.1e-07   0.00073       4      51 ..     135     173 ..     129     174 .. 0.91
   3 !    9.2   7.9    0.0015       1.8       1      20 [.     159     178 ..     159     262 .. 0.85
   4 !   35.8  12.7   7.4e-12   8.8e-09       1      52 []     323     371 ..     323     371 .. 0.94
   5 !   27.3   5.2   3.5e-09   4.2e-06       1      42 [.     356     403 ..     356     407 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0002
                         Fer4_7  30 kveidpekCl...gCgaCvavCPtga 52 
                                     +++d+++Cl   +C++C + CP++a
  gi|119719093|ref|YP_919588.1| 122 IPAVDSSRCLtlrNCDVCLSSCPYDA 147
                                    4578999**95556*********987 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 6.1e-07
                         Fer4_7   4 gCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtg 51 
                                    +C  C + Cp++a++ ++          + d+++C+ Cg C + CP+g
  gi|119719093|ref|YP_919588.1| 135 NCDVCLSSCPYDAMSGKPP---------KPDADRCVECGLCTSSCPSG 173
                                    8***************996.........5699**************98 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0015
                         Fer4_7   1 rCigCgaCvaaCpvkaield 20 
                                    rC++Cg C++ Cp++ + ++
  gi|119719093|ref|YP_919588.1| 159 RCVECGLCTSSCPSGLMFTP 178
                                    79**********99988765 PP

  == domain 4  score: 35.8 bits;  conditional E-value: 7.4e-12
                         Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                    +C+ CgaC+++Cp ka++   +   +g+ ++++ p++C+gC++Cv+vCP +a
  gi|119719093|ref|YP_919588.1| 323 SCTLCGACAKNCPEKALNAVAS---SGRVELRFYPWRCIGCRECVEVCPEDA 371
                                    5******************998...68889*******************986 PP

  == domain 5  score: 27.3 bits;  conditional E-value: 3.5e-09
                         Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgt...ekv...eidpekClgCg 42 
                                    rCigC+ Cv++Cp +a+e+d ++n++ +   e++     ++ +C+ Cg
  gi|119719093|ref|YP_919588.1| 356 RCIGCRECVEVCPEDAVEIDRAANPALMsrhEHIvlsSSEMARCSKCG 403
                                    8********************999995533344434444577899998 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.2   0.00063      0.75      10      23 ..     135     148 ..     134     149 .. 0.91
   2 !   21.4   2.0   1.2e-07   0.00015       2      21 ..     154     173 ..     153     175 .. 0.91
   3 !   21.7   2.2     1e-07   0.00012       5      23 ..     321     339 ..     318     340 .. 0.91
   4 !   23.4   5.3   2.9e-08   3.5e-05       7      23 ..     356     372 ..     356     373 .. 0.93
   5 ?   -0.1   0.3       0.8   9.5e+02       7      13 ..     398     404 ..     395     404 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00063
                                    S-THHHHHSTTTEE CS
                           Fer4  10 gCGaCvevCPvgAI 23 
                                    +C  C + CP++A 
  gi|119719093|ref|YP_919588.1| 135 NCDVCLSSCPYDAM 148
                                    6***********96 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 1.2e-07
                                    EEETTTSSS-THHHHHSTTT CS
                           Fer4   2 videekCigCGaCvevCPvg 21 
                                    + d ++C+ CG+C + CP g
  gi|119719093|ref|YP_919588.1| 154 KPDADRCVECGLCTSSCPSG 173
                                    5699**************86 PP

  == domain 3  score: 21.7 bits;  conditional E-value: 1e-07
                                    TTTSSS-THHHHHSTTTEE CS
                           Fer4   5 eekCigCGaCvevCPvgAI 23 
                                    ++ C+ CGaC++ CP  A+
  gi|119719093|ref|YP_919588.1| 321 KDSCTLCGACAKNCPEKAL 339
                                    699************9997 PP

  == domain 4  score: 23.4 bits;  conditional E-value: 2.9e-08
                                    TSSS-THHHHHSTTTEE CS
                           Fer4   7 kCigCGaCvevCPvgAI 23 
                                    +CigC +CvevCP +A 
  gi|119719093|ref|YP_919588.1| 356 RCIGCRECVEVCPEDAV 372
                                    7**************97 PP

  == domain 5  score: -0.1 bits;  conditional E-value: 0.8
                                    TSSS-TH CS
                           Fer4   7 kCigCGa 13 
                                    +C +CG+
  gi|119719093|ref|YP_919588.1| 398 RCSKCGR 404
                                    8****95 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   6.0     7e-09   8.4e-06       4      49 ..     135     173 ..     133     175 .. 0.94
   2 !   14.8   2.7     2e-05     0.024      34      50 ..     322     338 ..     298     339 .. 0.74
   3 !   35.8  10.3   5.6e-12   6.6e-09       2      50 ..     324     371 ..     323     372 .. 0.93
   4 !   17.9  10.0   2.2e-06    0.0026       1      40 [.     356     403 ..     356     440 .. 0.95

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 7e-09
                         Fer4_9   4 gCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkg 49 
                                    +C+ C ++Cp+++++++  +  a         C++Cg C+  Cp+g
  gi|119719093|ref|YP_919588.1| 135 NCDVCLSSCPYDAMSGKPPKPDADR-------CVECGLCTSSCPSG 173
                                    8********************9995.......************98 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 2e-05
                         Fer4_9  34 eaCigCgaCveaCpkga 50 
                                    ++C+ CgaC++ Cp++a
  gi|119719093|ref|YP_919588.1| 322 DSCTLCGACAKNCPEKA 338
                                    57************986 PP

  == domain 3  score: 35.8 bits;  conditional E-value: 5.6e-12
                         Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50 
                                    Ct CgaC + Cp ++ +  a+ + ++lr + + +CigC++Cve+Cp++a
  gi|119719093|ref|YP_919588.1| 324 CTLCGACAKNCPEKALNAVASSGRVELRFYPW-RCIGCRECVEVCPEDA 371
                                    **************************988765.*************997 PP

  == domain 4  score: 17.9 bits;  conditional E-value: 2.2e-06
                         Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase........eaCigCg 40 
                                    +C+gC++Cve+Cp ++v+ d+a++ a + + +          +C +Cg
  gi|119719093|ref|YP_919588.1| 356 RCIGCRECVEVCPEDAVEIDRAANPALMSRHEHivlsssemARCSKCG 403
                                    6**************************988877*******999*9998 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   1.3   9.3e-06     0.011       1      23 [.     122     147 ..     122     148 .. 0.93
   2 !   16.6   2.4   4.9e-06    0.0059       5      22 ..     156     173 ..     156     175 .. 0.93
   3 !   22.0   2.4   9.7e-08   0.00012       6      24 .]     321     339 ..     318     339 .. 0.93
   4 !   20.5   5.6     3e-07   0.00036       8      23 ..     356     371 ..     356     372 .. 0.94
   5 ?   -0.9   0.3       1.7   2.1e+03       7      14 ..     397     404 ..     395     404 .. 0.81
   6 ?   -3.1   0.7       8.6     1e+04       9      13 ..     435     439 ..     434     440 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 9.3e-06
                         Fer4_6   1 vveidpdkCi...gCgdCvrvCPega 23 
                                    ++++d ++C+    C+ C + CP++a
  gi|119719093|ref|YP_919588.1| 122 IPAVDSSRCLtlrNCDVCLSSCPYDA 147
                                    689******99999**********98 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 4.9e-06
                         Fer4_6   5 dpdkCigCgdCvrvCPeg 22 
                                    d+d+C+ Cg C++ CP g
  gi|119719093|ref|YP_919588.1| 156 DADRCVECGLCTSSCPSG 173
                                    89**************87 PP

  == domain 3  score: 22.0 bits;  conditional E-value: 9.7e-08
                         Fer4_6   6 pdkCigCgdCvrvCPegai 24 
                                    +d+C+ Cg+C+++CPe+a+
  gi|119719093|ref|YP_919588.1| 321 KDSCTLCGACAKNCPEKAL 339
                                    69**************996 PP

  == domain 4  score: 20.5 bits;  conditional E-value: 3e-07
                         Fer4_6   8 kCigCgdCvrvCPega 23 
                                    +CigC++Cv vCPe+a
  gi|119719093|ref|YP_919588.1| 356 RCIGCRECVEVCPEDA 371
                                    7*************98 PP

  == domain 5  score: -0.9 bits;  conditional E-value: 1.7
                         Fer4_6   7 dkCigCgd 14 
                                     +C  Cg+
  gi|119719093|ref|YP_919588.1| 397 ARCSKCGR 404
                                    58999996 PP

  == domain 6  score: -3.1 bits;  conditional E-value: 8.6
                         Fer4_6   9 CigCg 13 
                                    C+ C 
  gi|119719093|ref|YP_919588.1| 435 CDECK 439
                                    66664 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   1.9   0.00045      0.53       3      22 .]     123     145 ..     121     145 .. 0.89
   2 !   20.2   4.5   3.7e-07   0.00044       3      21 ..     153     171 ..     151     172 .. 0.88
   3 ?    0.1   0.1      0.89   1.1e+03       5      13 ..     252     260 ..     249     262 .. 0.77
   4 !   14.6   3.8   2.2e-05     0.026       7      22 .]     321     336 ..     317     336 .. 0.91
   5 !   18.7   1.8   1.1e-06    0.0013       7      22 .]     354     369 ..     349     369 .. 0.88
   6 ?   -1.0   0.5         2   2.4e+03       8      14 ..     397     403 ..     395     404 .. 0.70
   7 ?   -1.4   0.1       2.8   3.3e+03       8      14 ..     433     439 ..     428     440 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00045
                         Fer4_2   3 vvvdtdrCig...CgaCvsaCPa 22 
                                    ++vd+ rC+    C  C+s+CP+
  gi|119719093|ref|YP_919588.1| 123 PAVDSSRCLTlrnCDVCLSSCPY 145
                                    7899****87799*********5 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 3.7e-07
                         Fer4_2   3 vvvdtdrCigCgaCvsaCP 21 
                                    ++ d+drC++Cg C+s+CP
  gi|119719093|ref|YP_919588.1| 153 PKPDADRCVECGLCTSSCP 171
                                    66699************** PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.89
                         Fer4_2   5 vdtdrCigC 13 
                                    + ++ C gC
  gi|119719093|ref|YP_919588.1| 252 APSNVCSGC 260
                                    567889999 PP

  == domain 4  score: 14.6 bits;  conditional E-value: 2.2e-05
                         Fer4_2   7 tdrCigCgaCvsaCPa 22 
                                     d+C+ CgaC ++CP+
  gi|119719093|ref|YP_919588.1| 321 KDSCTLCGACAKNCPE 336
                                    699************5 PP

  == domain 5  score: 18.7 bits;  conditional E-value: 1.1e-06
                         Fer4_2   7 tdrCigCgaCvsaCPa 22 
                                    + rCigC+ Cv +CP+
  gi|119719093|ref|YP_919588.1| 354 PWRCIGCRECVEVCPE 369
                                    679************5 PP

  == domain 6  score: -1.0 bits;  conditional E-value: 2
                         Fer4_2   8 drCigCg 14 
                                    +rC  Cg
  gi|119719093|ref|YP_919588.1| 397 ARCSKCG 403
                                    5787777 PP

  == domain 7  score: -1.4 bits;  conditional E-value: 2.8
                         Fer4_2   8 drCigCg 14 
                                    ++C +C+
  gi|119719093|ref|YP_919588.1| 433 RICDECK 439
                                    5799996 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.1       9.5   1.1e+04      14      20 ..       4      10 ..       3      28 .. 0.70
   2 !   15.9   8.2     9e-06     0.011       3      52 ..     125     171 ..     123     176 .. 0.85
   3 !   15.4   3.0   1.2e-05     0.015       4      52 ..     156     205 ..     153     210 .. 0.82
   4 !   34.0   7.3     2e-11   2.3e-08       5      58 ..     321     373 ..     318     374 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 9.5
                        Fer4_21 14 CliaCed 20
                                   C++ C+d
  gi|119719093|ref|YP_919588.1|  4 CVVRCRD 10
                                   8888877 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 9e-06
                        Fer4_21   3 idedkCi...gCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCP 52 
                                    +d+++C+   +C  Cl +C+   ++a+++++ +     +d+Cv C lC+s CP
  gi|119719093|ref|YP_919588.1| 125 VDSSRCLtlrNCDVCLSSCP---YDAMSGKPPKP---DADRCVECGLCTSSCP 171
                                    78888886667*********...8**99987665...89************** PP

  == domain 3  score: 15.4 bits;  conditional E-value: 1.2e-05
                        Fer4_21   4 dedkCigCgkCliaCedtshqaieidaktvlkvv.edeCvGCnlCssvCP 52 
                                    d d+C++Cg+C+ +C+ + +   +i +++  +++   +  GC+  + vCP
  gi|119719093|ref|YP_919588.1| 156 DADRCVECGLCTSSCPSGLMFTPHIPPEKLRTLIkGARRGGCEALLVVCP 205
                                    6799************8777777888888888773567889999999999 PP

  == domain 4  score: 34.0 bits;  conditional E-value: 2e-11
                        Fer4_21   5 edkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedcie 58 
                                    +d+C  Cg C++ C++++ +a+  +++  l+    +C+GC  C++vCP ed++e
  gi|119719093|ref|YP_919588.1| 321 KDSCTLCGACAKNCPEKALNAVASSGRVELRFYPWRCIGCRECVEVCP-EDAVE 373
                                    589*********************************************.79886 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6  12.0   1.1e-05     0.013       4      56 .]     125     171 ..     122     171 .. 0.90
   2 !   15.3   4.8   1.4e-05     0.016       5      23 ..     156     174 ..     152     205 .. 0.80
   3 ?   -2.6   0.1       5.4   6.5e+03       5      13 ..     253     261 ..     250     263 .. 0.69
   4 !   34.5  10.4   1.4e-11   1.6e-08       5      56 .]     320     368 ..     317     368 .. 0.93
   5 ?   -1.4   0.2       2.3   2.7e+03       7      13 ..     397     403 ..     390     406 .. 0.67
   6 ?   -2.8   0.1         6   7.2e+03       6      13 ..     432     439 ..     427     440 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.1e-05
                        Fer4_10   4 idddtC...irCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                    +d+++C    +C  C ++CP+          a+ +++ + + ++C +cg C+++CP
  gi|119719093|ref|YP_919588.1| 125 VDSSRCltlRNCDVCLSSCPY---------DAMSGKPPKPDADRCVECGLCTSSCP 171
                                    68889966669**********.........9999999999***************9 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 1.4e-05
                        Fer4_10   5 dddtCirCgkCvkaCPadl 23 
                                    d+d+C++Cg C+++CP+ l
  gi|119719093|ref|YP_919588.1| 156 DADRCVECGLCTSSCPSGL 174
                                    89**************955 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 5.4
                        Fer4_10   5 dddtCirCg 13 
                                    +++ C +C 
  gi|119719093|ref|YP_919588.1| 253 PSNVCSGCP 261
                                    567788885 PP

  == domain 4  score: 34.5 bits;  conditional E-value: 1.4e-11
                        Fer4_10   5 dddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                     +d+C+ Cg+C k CP    +  +  + s+  + r  +++C+gc +Cve+CP
  gi|119719093|ref|YP_919588.1| 320 VKDSCTLCGACAKNCPE---KALNAVASSGRVELRFYPWRCIGCRECVEVCP 368
                                    579**************...9999999999999999***************9 PP

  == domain 5  score: -1.4 bits;  conditional E-value: 2.3
                        Fer4_10   7 dtCirCg 13 
                                     +C +Cg
  gi|119719093|ref|YP_919588.1| 397 ARCSKCG 403
                                    5566665 PP

  == domain 6  score: -2.8 bits;  conditional E-value: 6
                        Fer4_10   6 ddtCirCg 13 
                                       C +C+
  gi|119719093|ref|YP_919588.1| 432 LRICDECK 439
                                    56677775 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   1.0      0.22   2.6e+02       7      17 ..     135     145 ..     126     155 .. 0.76
   2 !   19.0   0.9   1.2e-06    0.0014       2      24 ..     157     179 ..     156     216 .. 0.82
   3 !   18.1   0.4   2.3e-06    0.0027      34      64 ..     286     337 ..     254     338 .. 0.57
   4 !   15.3   1.9   1.8e-05     0.021      47      64 ..     353     370 ..     339     371 .. 0.83
   5 !    7.9   8.0    0.0036       4.2      49      64 ..     355     370 ..     355     404 .. 0.59

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.22
                         Fer4_8   7 eCgaCqsaCpv 17 
                                    +C  C s+Cp 
  gi|119719093|ref|YP_919588.1| 135 NCDVCLSSCPY 145
                                    58889999984 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 1.2e-06
                         Fer4_8   2 lekCieCgaCqsaCpvlrrtkkh 24 
                                    +++C+eCg+C+s+Cp+   +  h
  gi|119719093|ref|YP_919588.1| 157 ADRCVECGLCTSSCPSGLMFTPH 179
                                    789************87665544 PP

  == domain 3  score: 18.1 bits;  conditional E-value: 2.3e-06
                         Fer4_8  34 e...........dvqeeqvlee..........eealwsCttcgaCtevCpvg 64 
                                    e            v +e+v++               +sCt cgaC+++Cp++
  gi|119719093|ref|YP_919588.1| 286 EptpgplpavfsHVSREDVNQWlsleflpifrVSVKDSCTLCGACAKNCPEK 337
                                    14444444444433333332226666677777777899************97 PP

  == domain 4  score: 15.3 bits;  conditional E-value: 1.8e-05
                         Fer4_8  47 alwsCttcgaCtevCpvg 64 
                                    + w+C +c++C+evCp++
  gi|119719093|ref|YP_919588.1| 353 YPWRCIGCRECVEVCPED 370
                                    67**************85 PP

  == domain 5  score: 7.9 bits;  conditional E-value: 0.0036
                         Fer4_8  49 wsCttcgaCtevCpvg 64 
                                    w+C +c++C+evCp++
  gi|119719093|ref|YP_919588.1| 355 WRCIGCRECVEVCPED 370
                                    5566666666666653 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   1.3   0.00022      0.26       4      30 ..     135     160 ..     132     161 .. 0.88
   2 !   13.9   1.3   6.5e-05     0.078       1      20 [.     159     178 ..     159     195 .. 0.85
   3 !   16.4   1.6   1.1e-05     0.013       2      20 ..     324     342 ..     323     351 .. 0.87
   4 !   12.1   8.7   0.00024      0.29       1      22 [.     356     377 ..     356     440 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00022
                        Fer4_16   4 tCgkCaevCPtnaikekkekeiearec 30 
                                    +C  C+++CP +a+++k  ++ +a++c
  gi|119719093|ref|YP_919588.1| 135 NCDVCLSSCPYDAMSGK-PPKPDADRC 160
                                    7**************99.688888877 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 6.5e-05
                        Fer4_16   1 rCgtCgkCaevCPtnaikek 20 
                                    rC++Cg C+++CP++ + ++
  gi|119719093|ref|YP_919588.1| 159 RCVECGLCTSSCPSGLMFTP 178
                                    6************9987655 PP

  == domain 3  score: 16.4 bits;  conditional E-value: 1.1e-05
                        Fer4_16   2 CgtCgkCaevCPtnaikek 20 
                                    C+ Cg+Ca+ CP++a+++ 
  gi|119719093|ref|YP_919588.1| 324 CTLCGACAKNCPEKALNAV 342
                                    ***************9876 PP

  == domain 4  score: 12.1 bits;  conditional E-value: 0.00024
                        Fer4_16   1 rCgtCgkCaevCPtnaikekke 22 
                                    rC++C++C+evCP++a++ +++
  gi|119719093|ref|YP_919588.1| 356 RCIGCRECVEVCPEDAVEIDRA 377
                                    6***************987732 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   2.0      0.14   1.7e+02      48      59 ..     135     146 ..     125     148 .. 0.67
   2 !   18.1   2.1   2.5e-06     0.003      41      60 ..     155     174 ..     146     175 .. 0.85
   3 !   10.4   5.0   0.00064      0.77      41      58 ..     319     336 ..     253     339 .. 0.63
   4 !   12.8   6.5   0.00011      0.13       1      50 [.     356     403 ..     356     404 .. 0.69

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.14
                        Fer4_17  48 eCgeCerkCPqg 59 
                                    +C  C ++CP++
  gi|119719093|ref|YP_919588.1| 135 NCDVCLSSCPYD 146
                                    355556666664 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 2.5e-06
                        Fer4_17  41 ekaslCieCgeCerkCPqgl 60 
                                    + a++C+eCg+C+++CP+gl
  gi|119719093|ref|YP_919588.1| 155 PDADRCVECGLCTSSCPSGL 174
                                    5799*************998 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00064
                        Fer4_17  41 ekaslCieCgeCerkCPq 58 
                                    ++ ++C+ Cg C++ CP+
  gi|119719093|ref|YP_919588.1| 319 SVKDSCTLCGACAKNCPE 336
                                    57789***********98 PP

  == domain 4  score: 12.8 bits;  conditional E-value: 0.00011
                        Fer4_17   1 rCiqCgyClpeCpsyeaydnepkkllraaklglleea.ekeekaslCieCg 50 
                                    rCi+C+ C+++Cp  +   ++ ++++    ++++e +   ++++ +C++Cg
  gi|119719093|ref|YP_919588.1| 356 RCIGCRECVEVCPEDAVEIDRAANPAL---MSRHEHIvLSSSEMARCSKCG 403
                                    7************98775554444333...344555425568999999998 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   1.9    0.0002      0.24       2      16 ..     128     145 ..     127     146 .. 0.83
   2 !   19.6   3.7   7.6e-07   0.00091       2      17 .]     158     173 ..     157     173 .. 0.92
   3 ?   -2.5   0.1       8.7     1e+04       6      15 ..     196     205 ..     196     208 .. 0.69
   4 ?    0.2   0.2       1.2   1.4e+03       2       8 ..     255     261 ..     254     262 .. 0.79
   5 !   12.3   1.9   0.00016      0.19       1      16 [.     321     336 ..     321     343 .. 0.92
   6 !   15.9   2.5   1.1e-05     0.014       3      16 ..     356     369 ..     355     376 .. 0.93
   7 ?   -1.2   0.6       3.3   3.9e+03       3       8 ..     398     403 ..     396     404 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0002
                         Fer4_4   2 erCi...gCgsCvaaCPq 16 
                                    +rC+   +C++C ++CP+
  gi|119719093|ref|YP_919588.1| 128 SRCLtlrNCDVCLSSCPY 145
                                    6896666**********8 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 7.6e-07
                         Fer4_4   2 erCigCgsCvaaCPqg 17 
                                    +rC++Cg C+++CP+g
  gi|119719093|ref|YP_919588.1| 158 DRCVECGLCTSSCPSG 173
                                    9*************86 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 8.7
                         Fer4_4   6 gCgsCvaaCP 15 
                                    gC +   +CP
  gi|119719093|ref|YP_919588.1| 196 GCEALLVVCP 205
                                    5666667788 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 1.2
                         Fer4_4   2 erCigCg 8  
                                    + C gC+
  gi|119719093|ref|YP_919588.1| 255 NVCSGCP 261
                                    67****8 PP

  == domain 5  score: 12.3 bits;  conditional E-value: 0.00016
                         Fer4_4   1 qerCigCgsCvaaCPq 16 
                                    +++C+ Cg+C   CP 
  gi|119719093|ref|YP_919588.1| 321 KDSCTLCGACAKNCPE 336
                                    699************5 PP

  == domain 6  score: 15.9 bits;  conditional E-value: 1.1e-05
                         Fer4_4   3 rCigCgsCvaaCPq 16 
                                    rCigC+ Cv +CP 
  gi|119719093|ref|YP_919588.1| 356 RCIGCRECVEVCPE 369
                                    8************4 PP

  == domain 7  score: -1.2 bits;  conditional E-value: 3.3
                         Fer4_4   3 rCigCg 8  
                                    rC  Cg
  gi|119719093|ref|YP_919588.1| 398 RCSKCG 403
                                    899998 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.7       7.9   9.4e+03       7      12 ..       4       9 ..       2      10 .. 0.83
   2 !    7.9   1.6    0.0054       6.5       3      15 .]     135     147 ..     130     147 .. 0.83
   3 !   10.7   5.2   0.00073      0.87       1      14 [.     160     173 ..     160     173 .. 0.96
   4 ?   -0.9   0.1       3.5   4.2e+03       9      13 ..     202     206 ..     201     207 .. 0.82
   5 !   12.1   5.6   0.00026      0.31       1      15 []     324     338 ..     324     338 .. 0.97
   6 !   18.6   4.1   2.1e-06    0.0025       1      15 []     357     371 ..     357     371 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 7.9
                         Fer4_3  7 CvevCP 12
                                   Cv+ C+
  gi|119719093|ref|YP_919588.1|  4 CVVRCR 9 
                                   999995 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0054
                         Fer4_3   3 gCgaCvevCPvgA 15 
                                    +C  C+ +CP++A
  gi|119719093|ref|YP_919588.1| 135 NCDVCLSSCPYDA 147
                                    6999*******98 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00073
                         Fer4_3   1 CtgCgaCvevCPvg 14 
                                    C+ Cg+C  +CP+g
  gi|119719093|ref|YP_919588.1| 160 CVECGLCTSSCPSG 173
                                    ************97 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 3.5
                         Fer4_3   9 evCPv 13 
                                    +vCP+
  gi|119719093|ref|YP_919588.1| 202 VVCPK 206
                                    69**7 PP

  == domain 5  score: 12.1 bits;  conditional E-value: 0.00026
                         Fer4_3   1 CtgCgaCvevCPvgA 15 
                                    Ct CgaC + CP++A
  gi|119719093|ref|YP_919588.1| 324 CTLCGACAKNCPEKA 338
                                    ************998 PP

  == domain 6  score: 18.6 bits;  conditional E-value: 2.1e-06
                         Fer4_3   1 CtgCgaCvevCPvgA 15 
                                    C+gC+ CvevCP++A
  gi|119719093|ref|YP_919588.1| 357 CIGCRECVEVCPEDA 371
                                    ************998 PP

>> zf-dskA_traR  Prokaryotic dksA/traR C4-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.4     0.097   1.2e+02      22      30 ..     155     163 ..     154     164 .. 0.85
   2 ?   -3.6   0.1       9.6   1.1e+04      13      21 ..     180     188 ..     180     194 .. 0.71
   3 ?   -2.2   0.6       3.4   4.1e+03      22      31 ..     322     331 ..     317     332 .. 0.74
   4 ?   -2.6   1.1       4.6   5.5e+03      27      31 ..     357     361 ..     353     363 .. 0.58
   5 ?   13.8   0.1   3.6e-05     0.043       6      26 ..     399     419 ..     392     422 .. 0.84
   6 ?    0.0   0.1      0.72   8.6e+02       3       9 ..     432     438 ..     430     441 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.097
                   zf-dskA_traR  22 PgarlCveC 30 
                                    P+a +CveC
  gi|119719093|ref|YP_919588.1| 155 PDADRCVEC 163
                                    88999***9 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 9.6
                   zf-dskA_traR  13 IpeaRlral 21 
                                    Ip+++lr l
  gi|119719093|ref|YP_919588.1| 180 IPPEKLRTL 188
                                    899999976 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 3.4
                   zf-dskA_traR  22 PgarlCveCq 31 
                                    + ++lC +C+
  gi|119719093|ref|YP_919588.1| 322 DSCTLCGACA 331
                                    6689998887 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 4.6
                   zf-dskA_traR  27 CveCq 31 
                                    C+ C 
  gi|119719093|ref|YP_919588.1| 357 CIGCR 361
                                    55553 PP

  == domain 5  score: 13.8 bits;  conditional E-value: 3.6e-05
                   zf-dskA_traR   6 CeeCGEpIpeaRlralPgarl 26 
                                    C++CG +I++++l+a   a++
  gi|119719093|ref|YP_919588.1| 399 CSKCGREIAPEKLVASLEAKM 419
                                    **************9876665 PP

  == domain 6  score: 0.0 bits;  conditional E-value: 0.72
                   zf-dskA_traR   3 ygsCeeC 9  
                                    +++C+eC
  gi|119719093|ref|YP_919588.1| 432 LRICDEC 438
                                    6889999 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   1.2      0.18   2.2e+02      25      74 ..     121     169 ..     115     179 .. 0.63
   2 ?   11.9   4.7   0.00024      0.28      17      76 ..     304     407 ..     296     412 .. 0.75
   3 ?    6.6   1.1     0.011        13      35      74 ..     394     441 ..     388     448 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.18
                 zinc_ribbon_15  25 fipvfkwkkkkpylacskCkslleaskelgkeiekkessekkeCknCgke 74 
                                     ip ++ ++  ++  c+ C s ++ +  +gk  +   + +  eC  C+++
  gi|119719093|ref|YP_919588.1| 121 SIPAVDSSRCLTLRNCDVCLSSCPYDAMSGKPPKPD-ADRCVECGLCTSS 169
                                    577777777777788999999999998666655433.2234445555544 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00024
                 zinc_ribbon_15  17 kkkvlklffipvfkwkkkkpylacskCkslleaskelgkeiekkesse................................ 64 
                                     +++l+l f+p+f+++ k+    c  C ++++++    +++ ++ ++e                                
  gi|119719093|ref|YP_919588.1| 304 VNQWLSLEFLPIFRVSVKDSCTLCGACAKNCPEKA--LNAVASSGRVElrfypwrcigcrecvevcpedaveidraanpa 381
                                    578999**************************998..4455555555567999997777777777777777777777777 PP

                 zinc_ribbon_15  65 ..............kkeCknCgkeve 76 
                                                  + +C++Cg+e+ 
  gi|119719093|ref|YP_919588.1| 382 lmsrhehivlssseMARCSKCGREIA 407
                                    77777777777777777777777766 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.011
                 zinc_ribbon_15  35 kpylacskCkslleaskelgkeiekkesse.........kkeCknCgke 74 
                                    + ++ cskC+  ++ +k l  ++e+k +++          ++C++C+++
  gi|119719093|ref|YP_919588.1| 394 SEMARCSKCGREIAPEK-LVASLEAKMTRKglprevvssLRICDECKRK 441
                                    67899*****9999998.666666666666789999999999****986 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   1.3       8.2   9.8e+03       4      13 ..     135     144 ..     129     154 .. 0.64
   2 ?    6.3   4.1     0.015        18       1      16 [.     159     174 ..     159     180 .. 0.83
   3 ?   -0.4   0.0       1.8   2.2e+03      79      89 ..     254     264 ..     233     283 .. 0.80
   4 ?    9.2   0.0    0.0018       2.1      58      95 ..     300     337 ..     292     338 .. 0.81
   5 ?    7.8   1.0     0.005       5.9      81      94 ..     356     369 ..     345     371 .. 0.76
   6 ?   -1.2   0.0       3.1   3.7e+03      74      87 ..     391     404 ..     376     410 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 8.2
                        Fer4_22   4 sCgaCtlvCp 13 
                                    +C  C   Cp
  gi|119719093|ref|YP_919588.1| 135 NCDVCLSSCP 144
                                    3555555555 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.015
                        Fer4_22   1 rClsCgaCtlvCptCs 16 
                                    rC++Cg Ct  Cp+  
  gi|119719093|ref|YP_919588.1| 159 RCVECGLCTSSCPSGL 174
                                    7999999999999865 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.8
                        Fer4_22  79 esgCvGCgRCi 89 
                                    +++C GC R +
  gi|119719093|ref|YP_919588.1| 254 SNVCSGCPRVS 264
                                    57899998865 PP

  == domain 4  score: 9.2 bits;  conditional E-value: 0.0018
                        Fer4_22  58 kkerlrqrllhklsefkekfgesgCvGCgRCieacpvk 95 
                                    ++e ++q+l   +  + +   + +C+ Cg C ++cp+k
  gi|119719093|ref|YP_919588.1| 300 SREDVNQWLSLEFLPIFRVSVKDSCTLCGACAKNCPEK 337
                                    566778888888888888888999***********986 PP

  == domain 5  score: 7.8 bits;  conditional E-value: 0.005
                        Fer4_22  81 gCvGCgRCieacpv 94 
                                     C+GC  C+e+cp+
  gi|119719093|ref|YP_919588.1| 356 RCIGCRECVEVCPE 369
                                    68888888888876 PP

  == domain 6  score: -1.2 bits;  conditional E-value: 3.1
                        Fer4_22  74 kekfgesgCvGCgR 87 
                                     ++ ++  C  CgR
  gi|119719093|ref|YP_919588.1| 391 LSSSEMARCSKCGR 404
                                    45567888999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (455 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.64u 0.26s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 2875.62
//
Query:       gi|119719094|ref|YP_919589.1|  [L=618]
Description: aldehyde ferredoxin oxidoreductase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   3.8e-148  493.6   0.0   4.6e-148  493.3   0.0    1.1  1  AFOR_C    Aldehyde ferredoxin oxidoreductase, domains 2 & 3
    6.6e-77  257.9   0.2    1.2e-76  257.0   0.2    1.5  1  AFOR_N    Aldehyde ferredoxin oxidoreductase, N-terminal doma


Domain annotation for each model (and alignments):
>> AFOR_C  Aldehyde ferredoxin oxidoreductase, domains 2 & 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  493.3   0.0  5.2e-152  4.6e-148       2     382 .]     235     616 ..     234     616 .. 0.98

  Alignments for each domain:
  == domain 1  score: 493.3 bits;  conditional E-value: 5.2e-152
                                    HHHHHHHHHHHSH.HHHHHHHH-GGGHHHHHHHTT---BTTTTBS--TTGGGGSHHHHHHHTEEEE.E-TT-SS--EEEE CS
                         AFOR_C   2 lgkkiqkeiksspqvtaelrkyGTaelvnianetgalptknfqegtfekaekisgealeekylvknegCfsCpiaCgrev 81 
                                    l k + ++i+++p++ ++l+kyGTa+lvni+n++g+lp kn+q g+ ++a+kisge+le++yl++++ C++C+i Cgr+v
  gi|119719094|ref|YP_919589.1| 235 LSKSLIERIRKNPVTGGGLPKYGTAVLVNIINQAGMLPYKNWQFGYNPEADKISGETLEKTYLISRRPCWGCQIGCGRVV 314
                                    6788899******7777*************************************************99************ PP

                                    E.......ET.EE---HHHHHHHTGGGT---HHHHHHHHHHHHHHTB-HHHHHHHHHHHHHHHHTTSS-HHHHTS----T CS
                         AFOR_C  82 kveegkk.vk.vegpeyetlaalGsnlgiddleailklnelcdelGlDtisaGntiafamelyekGllkkedtdglelef 159
                                    kv++g+  +  +egpeye+++alG+++g+ dl+ai+k+n++cde GlDtis+G+tia amelyekG++ +ed++gl+l+f
  gi|119719094|ref|YP_919589.1| 315 KVPSGPFqILySEGPEYESIWALGNATGVMDLAAIIKANHYCDEFGLDTISMGSTIAAAMELYEKGYIPQEDLQGLDLRF 394
                                    *****986559********************************************************************* PP

                                    T-THHHHHHHHHHHTT-TTHHHHTT-HHHHHHCTT-GGG--EETTEE--SS-GGG-HHHHHHHHH-TTSS-SGGG-THHH CS
                         AFOR_C 160 gdaeallellekiAkregigdllAeGvkrlaeklgaeelamhvkGlelpaydprgakgmalaYatsnrGacHlraylial 239
                                    g+a+al+e++ ++A+++g+g+ lA G++rlae +ga+el+m+vkGle+paydprgakg++l+Yat+nrG+cH+ +y+i++
  gi|119719094|ref|YP_919589.1| 395 GNAAALVEAVWRTAYKSGFGAKLALGSRRLAEMYGAPELSMSVKGLEMPAYDPRGAKGIGLEYATANRGGCHVTGYTISP 474
                                    ******************************************************************************** PP

                                    H.....S---TT--HHHHHHHHHHHHHHHHHHHHT--GGGG-HHH......HHHHHHHHHT----HHHHHHHHHHHHHHH CS
                         AFOR_C 240 e.....ekvdpletegkaelvkwfqdltalvdslglCkftseaeerldlelyakllsavtGidvteeellkaGeRiynle 314
                                    e     +k dpl++egka++vk+fqdlt++v+s++ C+ft+     +  ++ya+l++ + G+++te+++l++GeRiynle
  gi|119719094|ref|YP_919589.1| 475 EilgipQKIDPLTPEGKAQWVKVFQDLTSVVNSAVNCLFTT---FEIGAKDYADLFNTIAGFNFTEKDVLTIGERIYNLE 551
                                    ************99***************************...5678899***************************** PP

                                    HHHHHHHT--HHHS---HHHHHS---SSTTTT---..-HHHHHHHHHHHHT--TTS---HHHHHHCT- CS
                         AFOR_C 315 RlfnlreGltrkddtlperlleeplkegpakgkvledeleemldeyYelrGWdetGvPtketlkrLgL 382
                                    R++    G+++kddtlp+rll+ep++egpakg+v+  el++ml+eyY++rGW  +GvPtke+lk+Lg+
  gi|119719094|ref|YP_919589.1| 552 RYMMSLYGFSAKDDTLPPRLLKEPMPEGPAKGQVV--ELDKMLEEYYKIRGWV-NGVPTKEKLKELGI 616
                                    **********************************9..9***************.*************7 PP

>> AFOR_N  Aldehyde ferredoxin oxidoreductase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  257.0   0.2   1.4e-80   1.2e-76       2     197 ..      10     220 ..       9     221 .. 0.95

  Alignments for each domain:
  == domain 1  score: 257.0 bits;  conditional E-value: 1.4e-80
                                    EEEEEETTTTEEEEEE--HHHHHHH-SCHHHHHHHHHHHS..........-TTS-TTSTTS-EEEEE-TTTTSS.STTB- CS
                         AFOR_N   2 kilrvdLstgkieveelpeelaekylGgrglaakllldev..........ppgvdplspenplvfatGpltgtp.apgsg 70 
                                    kil+v+L++++i++ ++++ +aeky+Gg+g+a+++++ ++          p+++dpl+pen+l+f+tGp+tg++ +p+ g
  gi|119719094|ref|YP_919589.1|  10 KILTVNLTDKTIREDPIDPAVAEKYIGGKGYALYVFYYKYlkeymakgiaPKDIDPLGPENVLAFTTGPITGIAgVPSPG 89 
                                    9***********************************9955566677888799**********************9***** PP

                                    EEEEEE.E-TTTSSEEEEEEETCHHHHHHHCT-SEEEEES--SS-EEEEEETTEEEEEE-TTTTTS-HHHHHHHHHHHHT CS
                         AFOR_N  71 rlvvva.ksPltgtlgesnaGgrfgaelkraGydaivieGkaekpvylvieddkveiedaedlwgldtyettealkeelg 149
                                    r +v+a +sPltg+++++n+Gg+fga+lk+aGyd+i+ieG++ekpvy++i d++vei+da+dlwg+++++tt+ lk++++
  gi|119719094|ref|YP_919589.1|  90 RHHVMAlRSPLTGSIASANSGGEFGAYLKFAGYDMIFIEGASEKPVYIEIVDGHVEIKDASDLWGKNVFDTTRVLKSRVK 169
                                    *****999*********************************************************************777 PP

                                    S...EEEEE-HHHHTT-TTB-E.EETTEEE-SSSHHHHHHHTTEEEEEEE- CS
                         AFOR_N 150 d...kvaviGpaGenlvrfAsisvddgraagrgGlGavmgsKnlkaivvrg 197
                                        +va+iGpaGenlv fA+i+ dd+raagr+G+GavmgsK+lkaivv+g
  gi|119719094|ref|YP_919589.1| 170 GknvSVACIGPAGENLVLFANIMNDDHRAAGRTGVGAVMGSKKLKAIVVSG 220
                                    7778999***************666************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (618 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.51
# Mc/sec: 3679.66
//
Query:       gi|119719095|ref|YP_919590.1|  [L=339]
Description: cellulase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-87  292.6   0.0    2.8e-87  292.4   0.0    1.0  1  Peptidase_M42  M42 glutamyl aminopeptidase
    1.5e-09   37.9   0.1    4.5e-09   36.3   0.1    1.8  2  Peptidase_M20  Peptidase family M20/M25/M40
    4.2e-08   33.1   0.0    6.3e-07   29.3   0.0    2.0  2  Peptidase_M28  Peptidase family M28
     0.0026   16.6   0.0       0.12   11.1   0.0    2.1  2  Peptidase_M18  Aminopeptidase I zinc metalloprotease (M18)


Domain annotation for each model (and alignments):
>> Peptidase_M42  M42 glutamyl aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  292.4   0.0   6.3e-91   2.8e-87       1     292 []      44     329 ..      44     329 .. 0.97

  Alignments for each domain:
  == domain 1  score: 292.4 bits;  conditional E-value: 6.3e-91
                                    S-EEEEEESSTTSSEEEEEEE--B-EEEEEEEETTSEEEEEEESS--GGGTTTEEEEEEETTEEEEEEEEE--CGGCHHH CS
                  Peptidase_M42   1 GnliakkkgkekepkvmiaAHmDeiGfmVkeIkedGflrfekvGGvdpkvlegqrvkiltkkgkisGvigskppHllkee 80 
                                    Gnl++++ +   +p++++aAHmDe+Gf+V++++edGflr++++GGv ++ l+gq+v +lt++g ++Gvig++ppHl+   
  gi|119719095|ref|YP_919590.1|  44 GNLYVVLGE--GRPSLVLAAHMDEVGFIVTHVTEDGFLRVAPLGGVVAEGLPGQEVVVLTDEGLVEGVIGATPPHLRG-- 119
                                    899999888..99***************************************************************99.. PP

                                    HHHCT--GCGEEEEGSGSSHHHHHHTTS-TT-EEEES---EEETTECEEETTHHHHHHHHHHHHHHHHHCTSS-SSEEEE CS
                  Peptidase_M42  81 erkkaleikelfiDigakskeeaeelGisvGdivvfdkefvelangkivskalDdragvavllellkelkeeeleatvyl 160
                                     ++k+l+++e+fiDig+ s+eea++ G++vG +v+f  +f+e ++  ++skalDdr+g+++lle+l++ ++ + +  v++
  gi|119719095|ref|YP_919590.1| 120 ATQKELTVEEIFIDIGVLSREEARSKGVDVGSPVTFAGNFKERGDA-VISKALDDRVGCYALLEALRSGATPK-KGSVVV 197
                                    5788899*************************************99.**********************9998.9***** PP

                                    EEESTCTTTSHHHHHHHHHH--SEEEEEEEEEE-CSTTSTTTTSS..TTS-CEEEEEETTCCSHHHHHHHHHHHHHHTT- CS
                  Peptidase_M42 161 vatvqEEvGlrGaktsaekikpdiaiavDvtaagdtpgskekeak..lgkGpvirvkDasgiyhpklrkkllelAkknni 238
                                    ++tvqEEvGlrG++++a+ ++p++a+av+ t+a+dtpg++ ++    lg Gp++r++D+s+i++ +l k++++lA++++i
  gi|119719095|ref|YP_919590.1| 198 AFTVQEEVGLRGSSALAKALEPNFAVAVEGTIANDTPGTPPEKVVtrLGRGPAVRLMDKSMIASMELYKHIKALAESKSI 277
                                    ******************************************98899********************************* PP

                                    -EEEEEESSSSSTHHHHHTSTTTSEEEEEEEEEBSTTSTTEEEEHHHHHHHHHH CS
                  Peptidase_M42 239 pyqlevlsgggtDAgaihltgegvptalisiptryiHspvevahlddleatvkL 292
                                    pyq+++ ++ gtDAg++ +   g  + ++s+p+ryiHsp+++a ++d++atv+L
  gi|119719095|ref|YP_919590.1| 278 PYQVQISPYSGTDAGSFAVH--GAAVSAVSVPVRYIHSPASLALKKDVDATVEL 329
                                    *****************998..888899***********************997 PP

>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.62   2.8e+03     127     153 ..      14      40 ..       7      51 .. 0.73
   2 !   36.3   0.1     1e-12   4.5e-09      35     206 ..     170     335 ..     154     336 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.62
                                    HEEEC.CHHHHHHHHHHHHHHHTSCEEE CS
                                    xxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M20 127 pvtln.dsplvkalaeaaeelfgekvel 153
                                    p+++  ++++++++ae +eel g+++ +
  gi|119719095|ref|YP_919590.1|  14 PAPSGfENRVREIIAEELEEL-GYEPVT 40 
                                    444445699999999999998.988544 PP

  == domain 2  score: 36.3 bits;  conditional E-value: 1e-12
                                    TTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTTTHHHHHHHHHHTTTCESEEEEEEEESSSBTCHSTETEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M20  35 addmkggvlaalealralkdegikpkgtivllfqpdEEggrgGakallegleerekvdavfelhieepgileagklaigv 114
                                    a d+  g+ a+lealr+ +  +   kg++v++f++ EE+g +G+ al++    + ++ +  ++ +e ++i + ++    +
  gi|119719095|ref|YP_919590.1| 170 ALDDRVGCYALLEALRSGATPK---KGSVVVAFTVQEEVGLRGSSALAK----ALEPNF--AVAVE-GTIAN-DT----P 234
                                    568999999******9977766...99***********988********....445555..44555.88888.55....3 PP

                                    E...EEEEEEEEEESHEEEC......CHHHHHHHHHHHHHHHTSCEEEEEESSSBHTHHHH..TTTEEEEEEE.SSGGCT CS
                                    x...xxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxx.xxxxxx RF
                  Peptidase_M20 115 v...kvevelleggapvtln......dsplvkalaeaaeelfgekvelivsgpggtdarff..agiptvmifg.pgsgla 182
                                    +   +  v++l++g++v+l       + +l+k++++ ae+     +++ +s+  gtda+ f  +g  +v  +  p    +
  gi|119719095|ref|YP_919590.1| 235 GtppEKVVTRLGRGPAVRLMdksmiaSMELYKHIKALAESK-SIPYQVQISPYSGTDAGSFavHGA-AVSAVSvPV-RYI 311
                                    33334455557888877777555555778888888888874.333555566678999999945444.553344377.9** PP

                                    TSTTTEEEHHHHHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M20 183 HspnEyvdledlekgikvlarlle 206
                                    Hsp      +d+ + +++l++l+e
  gi|119719095|ref|YP_919590.1| 312 HSPASLALKKDVDATVELLKALIE 335
                                    ********************9997 PP

>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.04   1.8e+02      13      26 ..      55      68 ..      45      79 .. 0.78
   2 !   29.3   0.0   1.4e-10   6.3e-07      31     163 ..     166     304 ..     153     333 .. 0.71

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.04
                                   EEEEEEEE--B-TT CS
                  Peptidase_M28 13 evlllgAHyDsvgv 26
                                     l+l+AH+D vg+
  gi|119719095|ref|YP_919590.1| 55 PSLVLAAHMDEVGF 68
                                   479********997 PP

  == domain 2  score: 29.3 bits;  conditional E-value: 1.4e-10
                                    T---TTTTHHHHHHHHHHHHHCHHGGCCSSEEEEEEEESSCSGSSHHHHHHHH.HHC.CCTTEEEEEEECS-SSSS--EE CS
                  Peptidase_M28  31 ifvGAdDnAsgvaalLelarvlaasgsrpkrgvrflffdaEEagllGSkafak.akp.elkkiaavlnlDmvgsggkell 108
                                    ++  A D+ +g+ alLe +r  a+     k +v+++f+  EE gl GS+a+ak  +p  + +++  +  D  g++ ++++
  gi|119719095|ref|YP_919590.1| 166 VISKALDDRVGCYALLEALRSGAT---PKKGSVVVAFTVQEEVGLRGSSALAKaLEPnFAVAVEGTIANDTPGTPPEKVV 242
                                    566699**************9997...449**********************97445599999***************99 PP

                                    E.......HHHHHHCHHHHHHHHHHHHHTT-TTSCCEEEEES.STT-STTHHHHTTT--EEEE CS
                  Peptidase_M28 109 f.......esgdkssselekelkalakpvgraaaedpfders.grgrsDhspflkagvpvldl 163
                                    +       ++  ++s   + el + +k++++++ + p + +   ++ +D+ +f+ +g  v  +
  gi|119719095|ref|YP_919590.1| 243 TrlgrgpaVRLMDKSMIASMELYKHIKALAESK-SIPYQVQIsPYSGTDAGSFAVHGAAVSAV 304
                                    977777662223333333333334444444432.23333333266679999999877555544 PP

>> Peptidase_M18  Aminopeptidase I zinc metalloprotease (M18)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   2.7e-05      0.12     229     278 ..     166     211 ..     157     230 .. 0.81
   2 !    3.4   0.0    0.0058        26     336     430 ..     244     332 ..     238     334 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.7e-05
                                    EEESSHHHHHHHHHHHHHHCCCCHT-TTTS-SEEEEEEESSCCGTS-STT CS
                  Peptidase_M18 229 lfaprlDnkvscfaaleallesaedsleeedkvrivalfDnEEvGStsaq 278
                                    + ++ lD++v+c+a leal + a+    +++   +va+  +EEvG  ++ 
  gi|119719095|ref|YP_919590.1| 166 VISKALDDRVGCYALLEALRSGAT----PKKGSVVVAFTVQEEVGLRGSS 211
                                    7899**************988754....4656777788889***977665 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.0058
                                    -TTSEEEEEEETTSSSTT-HHHHHHHHHHHHHHC-EEEEEEE-TTS----HCHHHHHHHHT-EEEEEE-EEBSTTSSSEE CS
                  Peptidase_M18 336 llnkGvvikvnanqryatnsagaallkevaqkanvklQelvvrndspcGstigpilaaktGirtiDlGaaqlsmHSirel 415
                                     l+ G+ +++  +  + ++    + +k +a+   ++ Q+ +      +G+  g    a  G+ +  +  ++  +HS+  l
  gi|119719095|ref|YP_919590.1| 244 RLGRGPAVRLMDK-SMIASMELYKHIKALAESKSIPYQVQI---SPYSGTDAGSF--AVHGAAVSAVSVPVRYIHSPASL 317
                                    5677777777544.455666667888999999999988654...45677777754..667888888899*********** PP

                                    EECCHHHHHHHHHHH CS
                  Peptidase_M18 416 tgskdveeavklfka 430
                                    + +kdv  +v l+ka
  gi|119719095|ref|YP_919590.1| 318 ALKKDVDATVELLKA 332
                                    ***********9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 2154.82
//
Query:       gi|119719096|ref|YP_919591.1|  [L=208]
Description: molybdopterin-guanine dinucleotide biosynthesis protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.2e-23   81.5   2.2      1e-22   81.2   2.2    1.1  1  NTP_transf_3     MobA-like NTP transferase domain
  ------ inclusion threshold ------
      0.061   12.9   0.0      0.076   12.6   0.0    1.1  1  NTP_transferase  Nucleotidyl transferase


Domain annotation for each model (and alignments):
>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.2   2.2   1.1e-26     1e-22       2     154 ..       6     165 ..       5     172 .. 0.80

  Alignments for each domain:
  == domain 1  score: 81.2 bits;  conditional E-value: 1.1e-26
                                    EEEEESS-TTTTT.THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH....CHHHHHHTTC....TS-EEE-TTSS-SH CS
                   NTP_transf_3   2 viLAGGrSsRmgg.dKallplggkpllervldalraagvdevvvvggd....eevlaalarl....gvrvvededpgkgp 72 
                                    +iLAGG ++R+gg  K+ ++++gkp +  ++++l +a ++ +++v+ d    + +++ lar+    ++rv+ de p + p
  gi|119719096|ref|YP_919591.1|   6 AILAGGSGKRLGGvYKPVVEVCGKPAVVLLAENLGEA-ASSLILVVHDsvqkRVLEDVLARYpvatRYRVLLDEVPVRAP 84 
                                    69***********************************.6666666666354333444455554444799*********** PP

                                    HHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESSSEEEECCEEEGGGHHHHHHH...CTHTT CS
                   NTP_transf_3  73 laslaaalraaadadavlvlacDmPlltpelverllaaaaasgadvvvptyegerghpllfrarllsalaal...lgdqg 149
                                    la+l++alr++ +++ + v+++D+P+l+ + + +l+  a+  g+d +vp++ +++ +pl++++r+ + l a+   l+ +g
  gi|119719096|ref|YP_919591.1|  85 LAGLYTALRNS-RSEFLGVAPADTPFLRGSSLLKLRSLAE--GYDGAVPVWPNGYVEPLIAVYRVPRVLTAVasaLS-SG 160
                                    *********98.9************************986..999**************997777555554421043.45 PP

                                    HHHCH CS
                   NTP_transf_3 150 arrll 154
                                      r++
  gi|119719096|ref|YP_919591.1| 161 RLRVM 165
                                    55555 PP

>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   8.5e-06     0.076       4      65 ..       7      63 ..       5     105 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.5e-06
                                   EE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHH CS
                NTP_transferase  4 ILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeql 65
                                   ILaGGsG+RL      ++k+ v v gk + +   +++l ++    i+vv  + ++  +e+ l
  gi|119719096|ref|YP_919591.1|  7 ILAGGSGKRLG----GVYKPVVEVCGK-PAVVLLAENLGEAASSLILVVHDSVQKRVLEDVL 63
                                   9*********7....57**********.9999999999987777766665555555554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1350.29
//
Query:       gi|119719097|ref|YP_919592.1|  [L=119]
Description: hypothetical protein Tpen_0179 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 786.22
//
Query:       gi|119719098|ref|YP_919593.1|  [L=457]
Description: hydrogenase 4 subunit D [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.4e-58  196.8  23.0    4.4e-58  196.8  23.0    1.7  2  Proton_antipo_M  Proton-conducting membrane transporter
    6.1e-05   22.5   2.3    6.1e-05   22.5   2.3    2.2  2  NADHdeh_related  NADH dehydrogenase I, subunit N related prot
    0.00081   19.4   0.5     0.0037   17.3   0.0    2.4  2  Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), 


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.2       0.4   2.4e+03     116     128 ..      58      69 ..      11      86 .. 0.55
   2 !  196.8  23.0   7.4e-62   4.4e-58       1     288 [.     115     396 ..     115     400 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.4
                Proton_antipo_M 116 vsallAatlvkag 128
                                     s+l+ +++v++ 
  gi|119719098|ref|YP_919593.1|  58 LSVLV-SLMVALN 69 
                                    23344.4444444 PP

  == domain 2  score: 196.8 bits;  conditional E-value: 7.4e-62
                Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskalelglnsle 80 
                                    ++ Ll+++ ++El++l++y Li ++ ++p+s +++l +f++t ++ l L l+  l y+ tg++e+ +l+ +      +  
  gi|119719098|ref|YP_919593.1| 115 SSTLLSMVAFFELTSLCSYALISYY-EDPESRRSGLQAFIVTHIAALGLYLAAGLTYASTGSVEVVALKGM-----PEEL 188
                                    5789*******************99.778***************************************999.....8889 PP

                Proton_antipo_M  81 lllllllllvgllvKsaqvplhlWlpdayveaPtpvsall.Aatlvkagvlllirlllllavssneisqlllilaiisml 159
                                     ++++llllv+++ Ksaq+p+h+Wlpda + aPtpvsa l Aa +vk+g++l++r+l+    ++ +++   l+++++sm 
  gi|119719098|ref|YP_919593.1| 189 KTIAELLLLVAAAGKSAQIPFHRWLPDA-MVAPTPVSAYLhAAAMVKLGAYLMLRVLVDAG-YTHTVALACLAVGVVSMA 266
                                    99**************************.*************************9888887.****************** PP

                Proton_antipo_M 160 lgslvalaqtdiKrllAySsishlGymlialav...atqygveaaiihllthalfkallFllagsviyerektrdirayg 236
                                    +g  +   q d+KrllAyS+i +l y+++++++   ++++++++a +h++th++ k l Fl+ag ++ +   tr +++++
  gi|119719098|ref|YP_919593.1| 267 YGCAMYFPQLDMKRLLAYSTITQLSYIFMGAGLaslGSAMALKGAELHIFTHGFAKELFFLVAGLISFS-AGTRMLDKIS 345
                                    ******************************99866778999**********************888555.59******** PP

                Proton_antipo_M 237 gLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslillvlavv 288
                                    gL+   ++ a+ ++v++ls++G+Pp+  F+sk+l++ + +++++i+++++ +
  gi|119719098|ref|YP_919593.1| 346 GLRA-ARTAAVGFTVAALSVTGVPPFGLFWSKILLILGGYSAGSIVAAIIAT 396
                                    **97.57899***********************************9999844 PP

>> NADHdeh_related  NADH dehydrogenase I, subunit N related protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   2.3     1e-08   6.1e-05      81     185 ..     108     212 ..      80     250 .. 0.86
   2 ?   -2.5   0.5      0.45   2.7e+03     136     182 ..     326     370 ..     304     384 .. 0.70

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1e-08
                NADHdeh_related  81 atlgavvtgdvfnftlflaliGianiGivaavkkefvleaafnyGlvaliatlplfggaalilastGtlsifelaklagd 160
                                    ++lg v +  ++    f  l  +    +++ +++ +   +  +  +v+ ia+l l+ +a+l  astG + +  l ++  +
  gi|119719098|ref|YP_919593.1| 108 SALGFVYSSTLLSMVAFFELTSLCSYALISYYEDPESRRSGLQAFIVTHIAALGLYLAAGLTYASTGSVEVVALKGMPEE 187
                                    56788888899999999999999999****************************************************** PP

                NADHdeh_related 161 vlliaklllvlGvvGetGvaPfyaa 185
                                    + +ia+lll++  +G +   Pf+  
  gi|119719098|ref|YP_919593.1| 188 LKTIAELLLLVAAAGKSAQIPFHRW 212
                                    *****************99999754 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.45
                NADHdeh_related 136 fggaalilastGtlsifelaklagdvlliaklllvlGvvGetGvaPf 182
                                    f  a+li  s+Gt  +  +++l  +    a++ +++  +  tGv Pf
  gi|119719098|ref|YP_919593.1| 326 FLVAGLISFSAGTRMLDKISGLRAA--RTAAVGFTVAALSVTGVPPF 370
                                    5567777777777766666666553..44555566666666677776 PP

>> Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   6.2e-07    0.0037      13      56 ..      50     101 ..      45     103 .. 0.77
   2 ?   -2.0   0.1      0.68   4.1e+03      17      37 ..     340     360 ..     326     365 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 6.2e-07
                Proton_antipo_N  13 eigfllDklsalmllvvtfvsllvhlYSigYMa.dd.......egyqRFfay 56 
                                     +gf  D+ls+l+ l+v + +l  +++S  YM+ +        e+ +R++  
  gi|119719098|ref|YP_919593.1|  50 ALGFVNDSLSVLVSLMVALNGLATIVFSKHYMSpSNrehpvslEETPRYYGW 101
                                    579*****************************63222222333367777765 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.68
                Proton_antipo_N  17 llDklsalmllvvtfvsllvh 37 
                                    +lDk+s l ++    v++ v 
  gi|119719098|ref|YP_919593.1| 340 MLDKISGLRAARTAAVGFTVA 360
                                    578888888777777777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (457 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 3203.78
//
Query:       gi|119719099|ref|YP_919594.1|  [L=245]
Description: NADH ubiquinone oxidoreductase, 20 kDa subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.4e-26   91.6   1.7    5.5e-26   90.9   1.7    1.3  1  Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit


Domain annotation for each model (and alignments):
>> Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.9   1.7   3.1e-30   5.5e-26       1     128 [.      27     135 ..      27     138 .. 0.95

  Alignments for each domain:
  == domain 1  score: 90.9 bits;  conditional E-value: 3.1e-30
                                    -SHHHHHHT-TTTTHHHHHHTEEEEEETTT-S--HHHHHHTHTTTSEEEEEESBE...EEEHHHHHHHHGGGSSEEEEES CS
                    Oxidored_q6   1 CtGcsisllaleedlldllelielryhetlladskeeeieakekeadvlvveGavtrkpkealellkelaekakaviavG 80 
                                    C+Gc+i++ ++ ++++d+     +r++ +l+ +++          adv++v+G+vtr+  + l+ ++e+a+k+ +v+a+G
  gi|119719099|ref|YP_919594.1|  27 CNGCDIEVFDALTPYFDV-----ERLGVKLVLSPR---------MADVILVTGPVTRQFLPVLKATYEAAPKPCVVVACG 92 
                                    ******************.....************.........8*********************************** PP

                                    HHHHH-TGGGSTT-TEE-HHHHHHHC.S-E.EEE-SSS--HHHHHHHH CS
                    Oxidored_q6  81 tCAafGGipaaannpsvgeevgellevvpvdinipGCPphpeailetl 128
                                    +CA+ GGi+  ++  ++g  +g++++v+pvd++ipGCPp+p+ail+++
  gi|119719099|ref|YP_919594.1|  93 ACACGGGIW--YD--TYG-TAGGVDKVIPVDVYIPGCPPRPHAILHGV 135
                                    *********..77..667.459**********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1753.42
//
Query:       gi|119719100|ref|YP_919595.1|  [L=194]
Description: 4Fe-4S ferredoxin iron-sulfur binding domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.1e-17   61.7  34.9    4.5e-10   40.0  12.2    2.6  4  Fer4_7     4Fe-4S dicluster domain
    1.1e-14   53.5  20.6    4.5e-08   32.6   6.6    3.1  3  Fer4       4Fe-4S binding domain
    1.6e-11   44.2  32.4    7.1e-07   29.3  11.7    2.9  4  Fer4_9     4Fe-4S dicluster domain
    1.1e-09   38.2  26.3    4.3e-07   30.0  14.6    3.0  3  Fer4_10    4Fe-4S dicluster domain
    1.5e-07   31.8  12.4    8.1e-05   23.0   2.7    2.7  3  Fer4_8     4Fe-4S dicluster domain
    3.3e-07   30.4  19.3    2.3e-06   27.6   9.8    2.4  3  Fer4_21    4Fe-4S dicluster domain
    6.6e-07   29.1  14.8    6.7e-06   26.0   5.8    3.0  3  Fer4_6     4Fe-4S binding domain
    1.5e-06   29.0  20.1      0.005   17.7   8.7    2.9  2  Fer4_16    4Fe-4S double cluster binding domain
    3.8e-06   26.7  21.8    1.6e-05   24.7   4.0    3.7  4  Fer4_2     4Fe-4S binding domain
     0.0048   17.8  19.2      0.024   15.5   3.2    3.2  3  Fer4_3     4Fe-4S binding domain
  ------ inclusion threshold ------
      0.013   15.5   0.5      0.013   15.5   0.5    2.1  1  HypA       Hydrogenase/urease nickel incorporation, metalloch
      0.013   15.1   0.7      0.013   15.1   0.7    1.9  2  DUF2321    Uncharacterized protein conserved in bacteria (DUF
      0.019   15.5  21.2       0.17   12.5   5.7    3.3  4  Fer4_17    4Fe-4S dicluster domain
      0.059   13.9  27.3      0.081   13.5   1.9    4.1  4  Fer4_4     4Fe-4S binding domain
       0.49   10.0   0.1       0.49   10.0   0.1    3.4  3  zf_UBZ     Ubiquitin-Binding Zinc Finger
        1.1   10.1  15.1       0.22   12.3   2.2    2.9  2  Fer4_15    4Fe-4S single cluster domain
        2.3    8.4  11.1        3.7    7.8   8.8    2.4  2  Fer4_18    4Fe-4S dicluster domain
        5.8    7.5  19.3        1.3    9.6   4.3    3.1  3  Fer4_13    4Fe-4S single cluster domain of Ferredoxin I


Domain annotation for each model (and alignments):
>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   2.4     5e-08   4.9e-05      28      52 .]      31      56 ..      15      56 .. 0.75
   2 !   40.0  12.2   4.5e-13   4.5e-10       2      51 ..      42      90 ..      41      91 .. 0.94
   3 !   23.1   4.6   8.4e-08   8.3e-05       1      43 [.      76     124 ..      76     128 .. 0.68
   4 ?   -2.7   0.0       9.8   9.8e+03      41      44 ..     160     163 ..     141     165 .. 0.72

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 5e-08
                         Fer4_7 28 t.ekveidpekClgCgaCvavCPtga 52
                                   +  k+eidp+ C+gCgaC++vCP +a
  gi|119719100|ref|YP_919595.1| 31 FrGKPEIDPSICMGCGACANVCPPDA 56
                                   13789******************776 PP

  == domain 2  score: 40.0 bits;  conditional E-value: 4.5e-13
                         Fer4_7  2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtg 51
                                   C+gCgaC+++Cp +ai+  ++  e+g ++++i + +C++Cg+C+++CP  
  gi|119719100|ref|YP_919595.1| 42 CMGCGACANVCPPDAITCVDD-LERGLRTWKIFYGRCIFCGRCEEACPLS 90
                                   *****************9997.67899*********************65 PP

  == domain 3  score: 23.1 bits;  conditional E-value: 8.4e-08
                         Fer4_7   1 rCigCgaCvaaCpvkaieldeeenek..gt....ekveidpekClgCga 43 
                                    rCi Cg+C++aCp +ai+  +e + +  ++      ve    +C++Cg+
  gi|119719100|ref|YP_919595.1|  76 RCIFCGRCEEACPLSAIRQSKEYELAskTRedleVVVETPLARCSTCGK 124
                                    8****************99864222211222221444555679****85 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 9.8
                         Fer4_7  41 CgaC 44 
                                    C +C
  gi|119719100|ref|YP_919595.1| 160 CPEC 163
                                    3333 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   6.6   4.5e-11   4.5e-08       1      24 []      35      58 ..      35      58 .. 0.95
   2 !   30.3   1.1   2.4e-10   2.4e-07       2      24 .]      71      93 ..      70      93 .. 0.91
   3 ?   -1.3   0.3       2.2   2.2e+03       7      12 ..     118     123 ..     116     124 .. 0.77

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 4.5e-11
                                   EEEETTTSSS-THHHHHSTTTEEE CS
                           Fer4  1 vvideekCigCGaCvevCPvgAIt 24
                                   ++id++ C+gCGaC++vCP +AIt
  gi|119719100|ref|YP_919595.1| 35 PEIDPSICMGCGACANVCPPDAIT 58
                                   68*********************7 PP

  == domain 2  score: 30.3 bits;  conditional E-value: 2.4e-10
                                   EEETTTSSS-THHHHHSTTTEEE CS
                           Fer4  2 videekCigCGaCvevCPvgAIt 24
                                   +i + +Ci+CG+C+e+CP  AI+
  gi|119719100|ref|YP_919595.1| 71 KIFYGRCIFCGRCEEACPLSAIR 93
                                   57899*************99995 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 2.2
                                    TSSS-T CS
                           Fer4   7 kCigCG 12 
                                    +C  CG
  gi|119719100|ref|YP_919595.1| 118 RCSTCG 123
                                    788898 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   1.8   2.6e-06    0.0026      34      51 .]      40      57 ..      18      57 .. 0.72
   2 !   29.3  11.7   7.2e-10   7.1e-07       2      51 .]      42      92 ..      41      92 .. 0.81
   3 !   21.9   3.4   1.5e-07   0.00015       1      41 [.      76     124 ..      76     124 .. 0.89
   4 ?   -0.6   0.0       1.5   1.5e+03      35      39 ..     159     163 ..     127     166 .. 0.64

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.6e-06
                         Fer4_9 34 eaCigCgaCveaCpkgai 51
                                   + C+gCgaC+++Cp +ai
  gi|119719100|ref|YP_919595.1| 40 SICMGCGACANVCPPDAI 57
                                   56************9987 PP

  == domain 2  score: 29.3 bits;  conditional E-value: 7.2e-10
                         Fer4_9  2 CtgCgaCveaCpagvv.vedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                   C+gCgaC ++Cp +++   d+ er  r  +  + +Ci+Cg+C+eaCp  ai
  gi|119719100|ref|YP_919595.1| 42 CMGCGACANVCPPDAItCVDDLERGLRTWKIFYGRCIFCGRCEEACPLSAI 92
                                   ***********999985456666666665555589************9876 PP

  == domain 3  score: 21.9 bits;  conditional E-value: 1.5e-07
                         Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase........eaCigCga 41 
                                    +C+ Cg+C+eaCp  ++++++  + a+ ++++          +C +Cg+
  gi|119719100|ref|YP_919595.1|  76 RCIFCGRCEEACPLSAIRQSKEYELASKTREDLevvvetplARCSTCGK 124
                                    5****************99999999997666559*******99****95 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 1.5
                         Fer4_9  35 aCigC 39 
                                    +C +C
  gi|119719100|ref|YP_919595.1| 159 ECPEC 163
                                    44444 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0  14.6   4.3e-10   4.3e-07       2      56 .]      35      88 ..      34      88 .. 0.79
   2 !   20.9   3.8   2.8e-07   0.00028       6      49 ..      74     123 ..      69     127 .. 0.70
   3 ?   -2.2   0.3       4.7   4.7e+03      11      16 ..     159     164 ..     156     166 .. 0.58

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 4.3e-10
                        Fer4_10  2 vvidddtCirCgkCvkaCPadl.tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                   ++id++ C++Cg+C ++CP d+ t+v+  +   +  + ++ +++C++cg C eaCP
  gi|119719100|ref|YP_919595.1| 35 PEIDPSICMGCGACANVCPPDAiTCVDDLE--RGLRTWKIFYGRCIFCGRCEEACP 88
                                   689*****************7744444444..4445555678*************9 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 2.8e-07
                        Fer4_10   6 ddtCirCgkCvkaCPadl......tsvgakgeaseeeavrkkvekCtgcg 49 
                                      +Ci Cg+C +aCP ++       +   k  ++ e +v++ + +C +cg
  gi|119719100|ref|YP_919595.1|  74 YGRCIFCGRCEEACPLSAirqskeYELASKTREDLEVVVETPLARCSTCG 123
                                    568*************9988776333333334444445555888899998 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 4.7
                        Fer4_10  11 rCgkCv 16 
                                    +C +C+
  gi|119719100|ref|YP_919595.1| 159 ECPECK 164
                                    344443 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   1.2   4.5e-05     0.045       5      16 ..      42      53 ..      29      69 .. 0.81
   2 !   23.0   2.7   8.1e-08   8.1e-05       4      56 ..      76     124 ..      74     124 .. 0.70
   3 ?   -1.6   0.0         4     4e+03      15      18 ..     160     163 ..     135     176 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.5e-05
                         Fer4_8  5 CieCgaCqsaCp 16
                                   C++CgaC + Cp
  gi|119719100|ref|YP_919595.1| 42 CMGCGACANVCP 53
                                   777777777776 PP

  == domain 2  score: 23.0 bits;  conditional E-value: 8.1e-08
                         Fer4_8   4 kCieCgaCqsaCpvlrrtk.khlldargeaae.dvqeeqvleeeealwsCttcga 56 
                                    +Ci Cg+C++aCp+   ++ k+   a + +++ +v+ e      + l +C+tcg+
  gi|119719100|ref|YP_919595.1|  76 RCIFCGRCEEACPLSAIRQsKEYELASKTREDlEVVVE------TPLARCSTCGK 124
                                    7************6666655666666666555233333......459******85 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 4
                         Fer4_8  15 Cpvl 18 
                                    Cp +
  gi|119719100|ref|YP_919595.1| 160 CPEC 163
                                    3322 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   9.8   2.3e-09   2.3e-06       2      57 ..      36      92 ..      35      95 .. 0.86
   2 !   15.0   2.0     2e-05      0.02       7      54 ..      76     129 ..      71     134 .. 0.63
   3 ?    1.4   0.2      0.35   3.5e+02       7      32 ..     118     143 ..     113     169 .. 0.61

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 2.3e-09
                        Fer4_21  2 ridedkCigCgkCliaCedtshqaie..idaktvlkvvedeCvGCnlCssvCPvedci 57
                                    id++ C+gCg C+ +C+  ++++++    + +++k+   +C+ C  C + CP+  +i
  gi|119719100|ref|YP_919595.1| 36 EIDPSICMGCGACANVCPPDAITCVDdlERGLRTWKIFYGRCIFCGRCEEACPL-SAI 92
                                   69***********************6213355788999***************7.665 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 2e-05
                        Fer4_21   7 kCigCgkCliaCedtshqai......eidaktvl.........kvvedeCvGCnlCssvCPve 54 
                                    +Ci Cg+C  aC+     ai      e      l          vve     C  C +  Pv+
  gi|119719100|ref|YP_919595.1|  76 RCIFCGRCEEACP---LSAIrqskeyE------LasktredleVVVETPLARCSTCGKYFPVT 129
                                    7************...56663334442......112222233244566667788888877775 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.35
                        Fer4_21   7 kCigCgkCliaCedtshqaieidakt 32 
                                    +C  Cgk + + e +  qa +i a++
  gi|119719100|ref|YP_919595.1| 118 RCSTCGKYFPVTEREVAQAAQILAEA 143
                                    68888888888888888877654443 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   5.8   6.7e-09   6.7e-06       1      24 []      34      57 ..      34      57 .. 0.95
   2 !   15.3   1.6   1.5e-05     0.015       6      20 ..      74      88 ..      71      92 .. 0.83
   3 ?   -2.4   0.4       6.1   6.1e+03       8      13 ..     118     123 ..     117     124 .. 0.70

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 6.7e-09
                         Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                                   ++eidp+ C gCg+C++vCP +ai
  gi|119719100|ref|YP_919595.1| 34 KPEIDPSICMGCGACANVCPPDAI 57
                                   69******************9887 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 1.5e-05
                         Fer4_6  6 pdkCigCgdCvrvCP 20
                                   + +Ci Cg+C+ +CP
  gi|119719100|ref|YP_919595.1| 74 YGRCIFCGRCEEACP 88
                                   669************ PP

  == domain 3  score: -2.4 bits;  conditional E-value: 6.1
                         Fer4_6   8 kCigCg 13 
                                    +C  Cg
  gi|119719100|ref|YP_919595.1| 118 RCSTCG 123
                                    688887 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   3.5   1.4e-05     0.014       2      19 ..      42      59 ..      41      68 .. 0.89
   2 !   17.7   8.7     5e-06     0.005       1      32 [.      76     107 ..      76     165 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.4e-05
                        Fer4_16  2 CgtCgkCaevCPtnaike 19
                                   C +Cg+Ca+vCP +ai+ 
  gi|119719100|ref|YP_919595.1| 42 CMGCGACANVCPPDAITC 59
                                   9**************985 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 5e-06
                        Fer4_16   1 rCgtCgkCaevCPtnaikekkekeiearecis 32 
                                    rC+ Cg+C e+CP +ai++ ke+e+++++ ++
  gi|119719100|ref|YP_919595.1|  76 RCIFCGRCEEACPLSAIRQSKEYELASKTRED 107
                                    6*******************999998877544 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   4.0   1.6e-08   1.6e-05       2      21 ..      34      53 ..      33      54 .. 0.94
   2 !   12.1   1.0   0.00016      0.16       9      21 ..      76      88 ..      70      89 .. 0.87
   3 ?    1.9   0.1      0.29   2.9e+02       8      14 ..     117     123 ..     109     124 .. 0.72
   4 ?   -2.7   0.3       8.2   8.1e+03      10      13 ..     160     163 ..     158     165 .. 0.61

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.6e-08
                         Fer4_2  2 pvvvdtdrCigCgaCvsaCP 21
                                   ++++d+ +C+gCgaC ++CP
  gi|119719100|ref|YP_919595.1| 34 KPEIDPSICMGCGACANVCP 53
                                   689****************9 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00016
                         Fer4_2  9 rCigCgaCvsaCP 21
                                   rCi Cg C  aCP
  gi|119719100|ref|YP_919595.1| 76 RCIFCGRCEEACP 88
                                   8999********9 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.29
                         Fer4_2   8 drCigCg 14 
                                    +rC  Cg
  gi|119719100|ref|YP_919595.1| 117 ARCSTCG 123
                                    5899998 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 8.2
                         Fer4_2  10 CigC 13 
                                    C +C
  gi|119719100|ref|YP_919595.1| 160 CPEC 163
                                    5555 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   8.2   4.2e-05     0.042       1      15 []      42      56 ..      42      56 .. 0.97
   2 !   15.5   3.2   2.5e-05     0.024       1      13 [.      77      89 ..      77      91 .. 0.91
   3 ?   -1.7   0.4       7.7   7.6e+03       4       7 ..     119     122 ..     118     124 .. 0.57

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.2e-05
                         Fer4_3  1 CtgCgaCvevCPvgA 15
                                   C+gCgaC +vCP++A
  gi|119719100|ref|YP_919595.1| 42 CMGCGACANVCPPDA 56
                                   *************98 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 2.5e-05
                         Fer4_3  1 CtgCgaCvevCPv 13
                                   C+ Cg+C+e+CP 
  gi|119719100|ref|YP_919595.1| 77 CIFCGRCEEACPL 89
                                   ************5 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 7.7
                         Fer4_3   4 CgaC 7  
                                    C++C
  gi|119719100|ref|YP_919595.1| 119 CSTC 122
                                    5555 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.5   1.3e-05     0.013      60      97 ..     106     168 ..      92     177 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.3e-05
                                    -EEEEEEE--EEEETTTS-EEECHHHHH.........................S-TTTSSS-E CS
                           HypA  60 aeLeieevpvkvrCreCgkefeleekal.........................rCpkCgsadv 97 
                                     +Le+  +   +rC++Cgk f ++e+++                         +Cp+C+++++
  gi|119719100|ref|YP_919595.1| 106 EDLEVVVETPLARCSTCGKYFPVTEREVaqaaqilaeaktlprsvlellengvECPECKRRRT 168
                                    5799999999************877533457899************************99865 PP

>> DUF2321  Uncharacterized protein conserved in bacteria (DUF2321)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.9       1.2   1.2e+03      67      91 ..      78     102 ..      33     115 .. 0.71
   2 ?   15.1   0.7   1.3e-05     0.013      67     107 ..     117     157 ..      76     177 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.2
                        DUF2321  67 syCkkCgkpyPWtkakleaakelie 91 
                                     +C +C ++ P ++ +     el++
  gi|119719100|ref|YP_919595.1|  78 IFCGRCEEACPLSAIRQSKEYELAS 102
                                    5788888887777766666666655 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 1.3e-05
                        DUF2321  67 syCkkCgkpyPWtkakleaakelieeleelsddekeklkas 107
                                    + C++Cgk +P t+++++ a++++ e++ l+++  e l++ 
  gi|119719100|ref|YP_919595.1| 117 ARCSTCGKYFPVTEREVAQAAQILAEAKTLPRSVLELLENG 157
                                    46**************************9999877777665 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   3.1   0.00058      0.57      44      57 ..      40      53 ..      16      57 .. 0.79
   2 ?    8.8  14.0    0.0023       2.3       2      57 ..      42      88 ..      41      91 .. 0.73
   3 ?   12.5   5.7   0.00017      0.17       1      51 [.      76     124 ..      76     125 .. 0.79
   4 ?   -0.8   2.2       2.3   2.3e+03      24      53 ..     132     164 ..     117     168 .. 0.38

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00058
                        Fer4_17 44 slCieCgeCerkCP 57
                                   s C++Cg C+ +CP
  gi|119719100|ref|YP_919595.1| 40 SICMGCGACANVCP 53
                                   56888888888888 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0023
                        Fer4_17  2 CiqCgyClpeCpsyeaydn.epkkllraaklglleeaekeekaslCieCgeCerkCP 57
                                   C++Cg+C+++Cp  +++   + ++ lr +          +   ++Ci Cg+Ce++CP
  gi|119719100|ref|YP_919595.1| 42 CMGCGACANVCPPDAITCVdDLERGLRTW----------KIFYGRCIFCGRCEEACP 88
                                   ************87774430233444443..........34678************* PP

  == domain 3  score: 12.5 bits;  conditional E-value: 0.00017
                        Fer4_17   1 rCiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCge 51 
                                    rCi Cg C+++Cp  +++++++ +l+ +++  +le    e+   +C++Cg+
  gi|119719100|ref|YP_919595.1|  76 RCIFCGRCEEACPLSAIRQSKEYELASKTRE-DLEV-VVETPLARCSTCGK 124
                                    79***************99999999999554.3333.34567889999985 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 2.3
                        Fer4_17  24 kllraakl.glleeaeke..ekaslCieCgeCe 53 
                                    ++++aa++ ++ ++  ++  e  ++ +eC eC+
  gi|119719100|ref|YP_919595.1| 132 EVAQAAQIlAEAKTLPRSvlELLENGVECPECK 164
                                    333333332222222222334444555555555 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   5.4   0.00025      0.25       4      15 ..      42      53 ..      39      62 .. 0.90
   2 ?   13.5   1.9   8.2e-05     0.081       3      15 ..      76      88 ..      74      99 .. 0.89
   3 ?    0.9   0.3      0.88   8.8e+02       3       9 ..     118     124 ..     116     124 .. 0.81
   4 ?    0.9   0.5      0.84   8.4e+02       5      11 ..     158     164 ..     158     165 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00025
                         Fer4_4  4 CigCgsCvaaCP 15
                                   C gCg+C ++CP
  gi|119719100|ref|YP_919595.1| 42 CMGCGACANVCP 53
                                   ************ PP

  == domain 2  score: 13.5 bits;  conditional E-value: 8.2e-05
                         Fer4_4  3 rCigCgsCvaaCP 15
                                   rCi Cg+C+ aCP
  gi|119719100|ref|YP_919595.1| 76 RCIFCGRCEEACP 88
                                   9************ PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.88
                         Fer4_4   3 rCigCgs 9  
                                    rC  Cg+
  gi|119719100|ref|YP_919595.1| 118 RCSTCGK 124
                                    9*99*95 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 0.84
                         Fer4_4   5 igCgsCv 11 
                                    ++C+ C 
  gi|119719100|ref|YP_919595.1| 158 VECPECK 164
                                    58**997 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   1.9      0.35   3.5e+02       3      15 ..      78      90 ..      76      94 .. 0.78
   2 ?   10.0   0.1   0.00049      0.49       5      17 ..     119     131 ..     117     132 .. 0.91
   3 ?    2.8   0.4     0.089        89       3      10 ..     158     165 ..     156     167 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.35
                         zf_UBZ  3 ylCerCgkeipes 15
                                   ++C rC +  p s
  gi|119719100|ref|YP_919595.1| 78 IFCGRCEEACPLS 90
                                   79****9877765 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00049
                         zf_UBZ   5 CerCgkeipesel 17 
                                    C+ Cgk++p++e+
  gi|119719100|ref|YP_919595.1| 119 CSTCGKYFPVTER 131
                                    **********998 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.089
                         zf_UBZ   3 ylCerCgk 10 
                                    + C++C++
  gi|119719100|ref|YP_919595.1| 158 VECPECKR 165
                                    68****97 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   2.2   0.00022      0.22       3      19 ..      37      53 ..      36      68 .. 0.84
   2 ?    2.4   5.3      0.27   2.7e+02       7      19 ..      76      88 ..      74     149 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00022
                        Fer4_15  3 vDrdaCigcglCvaeap 19
                                   +D + C+gcg+C+ ++p
  gi|119719100|ref|YP_919595.1| 37 IDPSICMGCGACANVCP 53
                                   9***************5 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.27
                        Fer4_15  7 aCigcglCvaeap 19
                                   +Ci cg+C +++p
  gi|119719100|ref|YP_919595.1| 76 RCIFCGRCEEACP 88
                                   8**********96 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   8.8    0.0037       3.7      60      96 ..      41      88 ..      23     100 .. 0.76
   2 ?   -1.1   0.0       2.1   2.1e+03      46      72 ..     101     127 ..      90     139 .. 0.54

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0037
                        Fer4_18 60 dcidcescvkvcP....tgi.dirkGlql......eciscllcidacd 96
                                    c+ c++c +vcP    t + d+  Gl+        ci c++c +ac 
  gi|119719100|ref|YP_919595.1| 41 ICMGCGACANVCPpdaiTCVdDLERGLRTwkifygRCIFCGRCEEACP 88
                                   5***********954443345688898754444558***********5 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.1
                        Fer4_18  46 alkekeerkekgagdcidcescvkvcP 72 
                                    a k++e+ +   ++    c++c k  P
  gi|119719100|ref|YP_919595.1| 101 ASKTREDLEVVVETPLARCSTCGKYFP 127
                                    444444444444444445555544444 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   4.3    0.0013       1.3       1      17 [.      37      53 ..      37      54 .. 0.93
   2 ?    2.5   7.1      0.23   2.2e+02       5      17 ..      76      88 ..      75     138 .. 0.85
   3 ?   -1.8   0.1       4.9   4.9e+03       9      15 ..     119     125 ..     117     145 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0013
                        Fer4_13  1 VDrdtCiacgaCvelaP 17
                                   +D + C++cgaC++++P
  gi|119719100|ref|YP_919595.1| 37 IDPSICMGCGACANVCP 53
                                   78899***********9 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.23
                        Fer4_13  5 tCiacgaCvelaP 17
                                   +Ci cg C e++P
  gi|119719100|ref|YP_919595.1| 76 RCIFCGRCEEACP 88
                                   7************ PP

  == domain 3  score: -1.8 bits;  conditional E-value: 4.9
                        Fer4_13   9 cgaCvel 15 
                                    c +C++ 
  gi|119719100|ref|YP_919595.1| 119 CSTCGKY 125
                                    5555443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       767  (0.0427799); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1385.19
//
Query:       gi|119719101|ref|YP_919596.1|  [L=567]
Description: NADH dehydrogenase (ubiquinone), 30 kDa subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.8e-60  203.7   0.1    1.2e-44  152.4   0.2    2.1  2  Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd s
    4.7e-25   88.6   0.0    1.1e-24   87.4   0.0    1.6  1  Complex1_30kDa  Respiratory-chain NADH dehydrogenase, 30 Kd s
    1.2e-18   67.3   4.4    7.4e-16   58.1   0.3    3.2  4  NiFeSe_Hases    Nickel-dependent hydrogenase
  ------ inclusion threshold ------
        0.2   12.2   0.1       0.45   11.0   0.1    1.5  1  BMFP            Membrane fusogenic activity


Domain annotation for each model (and alignments):
>> Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.4   0.2   2.7e-48   1.2e-44       7     172 ..     299     464 ..     294     471 .. 0.97
   2 !   49.5   0.0   6.4e-17   2.9e-13     207     271 .]     472     536 ..     464     536 .. 0.95

  Alignments for each domain:
  == domain 1  score: 152.4 bits;  conditional E-value: 2.7e-48
                                    HHHHHHHHHHHHHHHHHHHHSSSSS-TTBESSBBSS---TTHHHHHHHHHHHHHHHHHHHHHHHHSSSSHHHHHSSSS-B CS
                 Complex1_49kDa   7 vflyafreRekildlleevtGaRltasyiriGGvarDlpegllekikeflkelekkldeleklltknrifkkRtkgvgvl 86 
                                     f+  f+ Rek++ + e +tG R t+ +  +GGv+rD++e+  +k  e+lke+ek+ + + + + + +++++R k+vgvl
  gi|119719101|ref|YP_919596.1| 299 GFMAFFKAREKVMYMAELLTGGRKTYGMNVVGGVRRDITEDRAKKALEILKEVEKEYKAVLDAVLSTSTLVSRAKDVGVL 378
                                    6999**************************************************************************** PP

                                    SHHHHHHHTT-SSSSGGGT-TTTHHHHSS-SSGGGS-------SSBSHHHHHHHHHHHHHHHHHHHHHHHHT--.S-SB- CS
                 Complex1_49kDa  87 skeealelgltGpvlRasGvkyDlRkaepYeaYdeldfdvpvgeegDvydRylvrveEmrqSlkIieqaleklpegpvla 166
                                     ++ a +++++Gpv+R+s +k D Rk++pY+aY+e+df+vpv++egDv++R+ vr eE  + ++Ii+q+le++p gp++a
  gi|119719101|ref|YP_919596.1| 379 PRDVARKVSVVGPVARGSSIKRDTRKDHPYAAYSEVDFKVPVHSEGDVLARLSVRAEETFETISIIRQVLENMPGGPIQA 458
                                    ******************************************************************************99 PP

                                    --TTTS CS
                 Complex1_49kDa 167 edkkva 172
                                    e k++ 
  gi|119719101|ref|YP_919596.1| 459 EVKEYR 464
                                    988765 PP

  == domain 2  score: 49.5 bits;  conditional E-value: 6.4e-17
                                    EEEETTEEEEEEEEEESSSS-SEEEEE-HHHHTTTTHHHHTTTS-SGGGTHHHHTT---HHHHH- CS
                 Complex1_49kDa 207 avEapkGelgvylvsdgsskpyrlkirapsfvnlqaleellkgellaDvvailgsldivlgevDR 271
                                     vEap+Ge ++++++  +sk yr+++ra++++n  a++++++g++laD++ i+gs+d++ ++++R
  gi|119719101|ref|YP_919596.1| 472 YVEAPRGEDVHFVITGPHSKVYRWRVRASTYNNWPAIPYMCRGYTLADLPLIIGSIDPCYSCTER 536
                                    69*********************************************************999877 PP

>> Complex1_30kDa  Respiratory-chain NADH dehydrogenase, 30 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.4   0.0   2.4e-28   1.1e-24       1     120 [.      33     158 ..      33     160 .. 0.85

  Alignments for each domain:
  == domain 1  score: 87.4 bits;  conditional E-value: 2.4e-28
                                    EE--HHHHHHHHHHHHH...TT--EEEEEEEEETT..SSSEEEEEEEE--S-.......-EEEEEE....-S-BEE--TT CS
                 Complex1_30kDa   1 lvvepedllevakflkdeeelgfdvlsdltavDek..eerfevvyhllslekn......erirvkvevdeeepevpSvtd 72 
                                    l+ve+ +l+ev+++++ e  lg  +ls++ + De+  ++ ++++y+++ +e+         ++v ++++ +++++ Svt+
  gi|119719101|ref|YP_919596.1|  33 LYVERTKLPEVCSYVYYE--LG-GFLSTMAGSDERslHGAYRLYYVFS-IEEGyedgkkPWVVVVTNIPPHDTKFSSVTP 108
                                    5899************94..55.7*********988778888888887.5333445555667777778999999****** PP

                                    T-STHHHHHHHHHHHSHHBCTTSSTSS-SSSSTTS..SS-TTSTTS---- CS
                 Complex1_30kDa  73 lfpgadwyEREayDmfGivfeghpdlrrillpedf..eghPLRkdfplsg 120
                                     +p+a+wyERE++D++G+v e+hpd+rr++lp+d+    hPLRk+f  ++
  gi|119719101|ref|YP_919596.1| 109 KIPAASWYEREVRDLLGLVPENHPDPRRLVLPDDWpeGVHPLRKEFTYTE 158
                                    ***********************************96668******9876 PP

>> NiFeSe_Hases  Nickel-dependent hydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.1   0.3   1.6e-19   7.4e-16       1      78 [.     217     298 ..     217     308 .. 0.92
   2 ?   -0.5   0.0     0.099   4.4e+02     157     209 ..     304     353 ..     299     370 .. 0.63
   3 !    8.6   0.0   0.00017      0.78     333     449 ..     389     495 ..     379     510 .. 0.60
   4 ?   -1.6   0.1      0.21   9.6e+02     492     503 ..     523     534 ..     520     535 .. 0.88

  Alignments for each domain:
  == domain 1  score: 58.1 bits;  conditional E-value: 1.6e-19
                                    --HHHHTTTS.-GGGHHHHHHTT-SSSTTHHHHHHHHHHHHHHT----HHHHHHHHHHHHHHHHHHHHHHH...HHTTGG CS
                   NiFeSe_Hases   1 RGlElilkgr.dprdawalvqRiCGVCttvHalasvravedAlgikipknarlirnliaaalllhdhivhF...YhLhal 76 
                                    RG+E++ + r + +++ ++++RiCG+C ++H+ a  +ave+Algi++p+ a +ir+l+  ++ lh+h++ +    hL+++
  gi|119719101|ref|YP_919596.1| 217 RGIEKLAESRlTYNQVPFIAERICGICGYAHSCAYCQAVEQALGIEVPERALYIRTLMLEVERLHSHLLNLglaCHLAGF 296
                                    9******999556789999*************************************************987444699999 PP

                                    GT CS
                   NiFeSe_Hases  77 Dw 78 
                                    Dw
  gi|119719101|ref|YP_919596.1| 297 DW 298
                                    98 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.099
                                    HHHHHHHTHHHHHH.HSSSSS--.EBTTBESSGBGSBSHHHHHHHHHHHHHHHH CS
                   NiFeSe_Hases 157 Lelqrkaakivaif.ggknPhpqslvvGGvtcaidllnaerlaevkslikevke 209
                                    +++++k++ +  ++ gg++   +  vvGGv      ++++r ++  +++kev++
  gi|119719101|ref|YP_919596.1| 304 FKAREKVMYMAELLtGGRKTYGM-NVVGGVRRD---ITEDRAKKALEILKEVEK 353
                                    56667777777665266666666.89****999...455555555555555543 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.00017
                                    ESHHHHHHHHHHTT-HHHHHHHHHHHHHHT-HGGGGSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTB---B--TT CS
                   NiFeSe_Hases 333 vGplarvlvayakgkeevkelvdkllkklglkvealfstlGRtaaRaleakliaellkewldelvenikkgdtetaneek 412
                                    vGp+ar        +++ + ++     +++++v++   +l+R   Ra e+  +++     ++++ en+  g  ++     
  gi|119719101|ref|YP_919596.1| 389 VGPVARGSSIKRD-TRKDHPYAAYSEVDFKVPVHSEGDVLARLSVRAEETFETISI----IRQVLENMPGGPIQA----- 458
                                    6777766444333.233333444444556677777777888888888777655544....555666677762222..... PP

                                    -SGGGS-SEEEEEEEEEETTEEEEEEEEE.ETTEEEEE CS
                   NiFeSe_Hases 413 ldkkevpkeakGvglveapRGaLsHwiki.kdgkienY 449
                                     + ke+   a+G+g+veapRG   H++     +k+ ++
  gi|119719101|ref|YP_919596.1| 459 -EVKEYRPYARGLGYVEAPRGEDVHFVITgPHSKVYRW 495
                                    .223333449***************9865234455554 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 0.21
                                    HHHHT--BHHHH CS
                   NiFeSe_Hases 492 tihSfDPClACa 503
                                    +i S DPC +C+
  gi|119719101|ref|YP_919596.1| 523 IIGSIDPCYSCT 534
                                    588********5 PP

>> BMFP  Membrane fusogenic activity
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1    0.0001      0.45      16      48 ..     339     371 ..     334     373 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0001
                           BMFP  16 dalpaaagvreeieknvravlqealsklDLVtR 48 
                                    d +++a ++ +e+ek  +avl+++ls+  LV+R
  gi|119719101|ref|YP_919596.1| 339 DRAKKALEILKEVEKEYKAVLDAVLSTSTLVSR 371
                                    5667778899**********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (567 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.48
# Mc/sec: 3523.31
//
Query:       gi|119719102|ref|YP_919597.1|  [L=487]
Description: NADH dehydrogenase (quinone) [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-46  158.6  22.9    1.9e-46  158.6  22.9    1.9  2  Proton_antipo_M  Proton-conducting membrane transporter
    0.00016   21.7   2.2    0.00016   21.7   2.2    2.6  2  Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), 


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   1.0      0.55   4.9e+03     128     154 ..      13      39 ..       7      56 .. 0.51
   2 !  158.6  22.9   2.2e-50   1.9e-46       2     277 ..     135     408 ..     134     424 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 0.55
                Proton_antipo_M 128 gvlllirlllllavssneisqlllila 154
                                    +++l +++l ll+ s++++++++ + +
  gi|119719102|ref|YP_919597.1|  13 AAYLAAAVLALLFDSKPKLANVVSMAS 39 
                                    555555555555556666665554432 PP

  == domain 2  score: 158.6 bits;  conditional E-value: 2.2e-50
                Proton_antipo_M   2 ndLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskalelglnslel 81 
                                    +++l + +++El+  ++y+L+ +  + p+  + +  +f+l  +g   + ++++l    +g+ ++ ++      +++    
  gi|119719102|ref|YP_919597.1| 135 DNVLWFLFFWELMTASSYFLVIYE-DTPDVRRIGYLYFILMHVGFACIAVSLVLTVLTSGSWSLLKVDPH---TIEPGVK 210
                                    68999****************999.7779999****************************9988877777...8888888 PP

                Proton_antipo_M  82 llllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirlllllavssneisqlllilaiismllg 161
                                    +++l l l+g+ +K+++vplh+Wlp+a+ +aP  vsall+++++ +g+++l+r++l l+   +++++ ++ila++s+ +g
  gi|119719102|ref|YP_919597.1| 211 TAILALALIGFGMKLGLVPLHVWLPEAHPAAPSNVSALLSGVMLSMGLYGLTRISLALQANMEWWYSAIAILAVLSVAVG 290
                                    888889999**************************************************99******************* PP

                Proton_antipo_M 162 slvalaqtdiKrllAySsishlGymlialav...atqygveaaiihllthalfkallFllagsviyerektrdirayggL 238
                                     l   aq+d KrllAySsi  +G+  + l+    ++q g++a+++h++  a+ k +lF+l+g +   +  t+ + +++gL
  gi|119719102|ref|YP_919597.1| 291 VLCMPAQMDFKRLLAYSSIVEMGLASLSLSYylaGSQLGLKAMLMHVVNQAYAKGALFALSGLL-LYCAGTKRLSDIRGL 369
                                    ***********************998887766668999***********************887.55669********** PP

                Proton_antipo_M 239 akkmPilalvllvlllslaGlPptagFlskfliLeaava 277
                                    + ++P++a+vll ++l ++GlPp+ +F+sk++i  + ++
  gi|119719102|ref|YP_919597.1| 370 WDANPLVAAVLLAAALDIMGLPPFGCFFSKAYIVLSGFN 408
                                    *********************************988776 PP

>> Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   2.2   1.7e-08   0.00016      12      46 ..      73     107 ..      68     125 .. 0.86
   2 ?   -1.8   1.2      0.37   3.3e+03      24      41 ..     465     482 ..     462     483 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.7e-08
                Proton_antipo_N  12 ieigfllDklsalmllvvtfvsllvhlYSigYMad 46 
                                     ++++++D+lsa +++ v ++++ + ++S+gY++ 
  gi|119719102|ref|YP_919597.1|  73 APLTVYIDSLSASFVFAVATLTFAISIFSVGYLKM 107
                                    56889***************************984 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.37
                Proton_antipo_N  24 lmllvvtfvsllvhlYSi 41 
                                    l+l++ ++vs +v lY i
  gi|119719102|ref|YP_919597.1| 465 LVLVLLCVVSGFVSLYLI 482
                                    678889999999999955 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (487 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       925  (0.0515924); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.24s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 3508.61
//
Query:       gi|119719103|ref|YP_919598.1|  [L=491]
Description: NADH dehydrogenase (quinone) [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-45  154.6  27.6    3.1e-45  154.6  27.6    2.7  4  Proton_antipo_M  Proton-conducting membrane transporter
    6.7e-08   32.5   2.8    6.7e-08   32.5   2.8    3.6  4  Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), 


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   1.7      0.13   1.2e+03      45      94 ..      34      83 ..      12      87 .. 0.81
   2 ?   -3.5   0.1      0.51   4.6e+03     205     220 ..     106     121 ..      97     124 .. 0.74
   3 !  154.6  27.6   3.4e-49   3.1e-45       2     290 ..     126     421 ..     125     425 .. 0.92
   4 !    4.3   0.4    0.0022        20     111     160 ..     410     460 ..     405     468 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.13
                Proton_antipo_M 45 gsliLLlgilllynltgtlefeelskalelglnslelllllllllvgllv 94
                                    s +LL +++ l+ ++ ++  + l++  e+ ++sl+ l+l ++ +v+l+v
  gi|119719103|ref|YP_919598.1| 34 VSTLLLSAVSCLLMVETSTGRKFLLLGDEFIVDSLTSLMLVVISFVSLMV 83
                                   46678888888888888888888888888999999999999988888887 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 0.51
                Proton_antipo_M 205 llthalfkallFllag 220
                                    +l+++l++a +F +++
  gi|119719103|ref|YP_919598.1| 106 VLFYVLLNAFIFTMIL 121
                                    5778888888887774 PP

  == domain 3  score: 154.6 bits;  conditional E-value: 3.4e-49
                Proton_antipo_M   2 ndLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltg.........tlefeelskal 72 
                                    n+++ ++++lE++ +++  L++ +++  +++eAs k+++l + g  + L+g++ ly  +          ++++ + +k+ 
  gi|119719103|ref|YP_919598.1| 126 NNIAIMWVALEATTIATAHLVATYRTA-EAIEASWKYIILCSTGIAFGLYGVVTLYYTAYlagipapllWTSLVDHAKM- 203
                                    78999******************9776.**************************9987653447776666666666666. PP

                Proton_antipo_M  73 elglnslelllllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirllllla..vssneisqll 150
                                     l ++s ++ +++ l lvg+ +K++++p+h+Wlpd y eaP  vsallA++l   +++ l+r+ ++     ++ +++ +l
  gi|119719103|ref|YP_919598.1| 204 -LEAHSTMVKIAFTLALVGFGTKAGLAPFHTWLPDTYSEAPPYVSALLASILEGCAIYTLVRFYSVSVlaGVGAFAQTVL 282
                                    .77888999999999************************************************887766699******** PP

                Proton_antipo_M 151 lilaiismllgslvalaqtdiKrllAySsishlGymlialavatqygveaaiihllthalfkallFllagsviyerektr 230
                                    l+++i+s+++ sl  la td+ rl A Ss+ h+G++  al+ +++ g  aa++h++ hal+k++lFl +g v  +   tr
  gi|119719103|ref|YP_919598.1| 283 LVVGIASLFISSLHMLAVTDVNRLFALSSVEHMGIIACALGFGGYLGALAAVFHVVNHALVKSALFLSSGLVTLSY-GTR 361
                                    *********************************************************************9997766.9** PP

                Proton_antipo_M 231 dirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslillvlavvas 290
                                    +i+ ++g++ + P l +++l ++ ++ G Pp+  F s++l ++a v+ +  +++++++a+
  gi|119719103|ref|YP_919598.1| 362 KIEGIRGMMRSYPALGALVLAGAYAIIGGPPFGTFQSELLAIMAGVKSGNPFALVLFLAA 421
                                    ****************************************99999999998888885444 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.0022
                Proton_antipo_M 111 eaPtpvsallAatlvkagvlllirllllla.vssneisqlllilaiismll 160
                                    + P +  ++lAa++v+ ++ll+  +++++   +s + ++  ++ a i++ll
  gi|119719103|ref|YP_919598.1| 410 GNPFALVLFLAAIVVAFAALLVSCTNMVFGePASSTEKYPHILKAPITILL 460
                                    7899999**************999998887766666666666666666655 PP

>> Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   2.8   7.5e-12   6.7e-08      16      48 ..      63      95 ..      60     113 .. 0.81
   2 ?   -0.5   0.6      0.15   1.4e+03      16      33 ..     110     127 ..     100     132 .. 0.76
   3 ?   -2.6   0.3      0.67     6e+03      26      36 ..     282     292 ..     277     315 .. 0.64
   4 ?   -4.1   0.7       1.9   1.7e+04      25      36 ..     420     431 ..     415     432 .. 0.65

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 7.5e-12
                Proton_antipo_N 16 fllDklsalmllvvtfvsllvhlYSigYMadde 48
                                   f +D+l+ lml+v++fvsl+v lYS +Y+a + 
  gi|119719103|ref|YP_919598.1| 63 FIVDSLTSLMLVVISFVSLMVSLYSPKYLAYEV 95
                                   89***************************9873 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.15
                Proton_antipo_N  16 fllDklsalmllvvtfvs 33 
                                    +ll+ +  +m+lvvt+  
  gi|119719103|ref|YP_919598.1| 110 VLLNAFIFTMILVVTTNN 127
                                    566777789999999855 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 0.67
                Proton_antipo_N  26 llvvtfvsllv 36 
                                    llvv + sl++
  gi|119719103|ref|YP_919598.1| 282 LLVVGIASLFI 292
                                    55555555544 PP

  == domain 4  score: -4.1 bits;  conditional E-value: 1.9
                Proton_antipo_N  25 mllvvtfvsllv 36 
                                     ++vv f +llv
  gi|119719103|ref|YP_919598.1| 420 AAIVVAFAALLV 431
                                    566777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (491 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       986  (0.0549947); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.46
# Mc/sec: 3179.13
//
Query:       gi|119719104|ref|YP_919599.1|  [L=212]
Description: NADH-ubiquinone oxidoreductase, chain 4L [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.1e-06   27.3   1.2    2.1e-06   27.3   1.2    3.0  3  Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase cha
  ------ inclusion threshold ------
        4.7    7.5  10.2        4.7    7.5   0.1    2.7  3  YesK         YesK-like protein


Domain annotation for each model (and alignments):
>> Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase chain 4L
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1      0.17   1.5e+03      76      90 ..       8      22 ..       7      32 .. 0.72
   2 ?   -1.0   1.9      0.15   1.3e+03      15      46 ..      46      77 ..      32     117 .. 0.44
   3 !   27.3   1.2   2.3e-10   2.1e-06       5      48 ..     126     169 ..     122     204 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.17
                                   HHHHHHHHHHHHHHH CS
                    Oxidored_q2 76 igaaetavgLallvr 90
                                   iga+ + ++L+  + 
  gi|119719104|ref|YP_919599.1|  8 IGACAALMVLTASYI 22
                                   788888877776654 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.15
                                   HHHHHSSCCHHHHHHHHHHHHHHHHHHHHHHH CS
                    Oxidored_q2 15 ygvllrrnllkvliglelisnavnlllvlagv 46
                                   + +l +   +  l gl  i++ + l+   + +
  gi|119719104|ref|YP_919599.1| 46 FFMLSTVEWYFALWGLTAILTKAVLVPYFILR 77
                                   44444444444444444443333333333333 PP

  == domain 3  score: 27.3 bits;  conditional E-value: 2.3e-10
                                    HHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHHHHHHHHC CS
                    Oxidored_q2   5 liallfliGlygvllrrnllkvliglelisnavnlllvlagvft 48 
                                    ++++lfliGl ++++rr++lk+++g++  +n+ +l+l++++   
  gi|119719104|ref|YP_919599.1| 126 VSVALFLIGLHLMVTRRDALKQILGICHFENGSHLTLAVMAPGL 169
                                    789**********************************9997655 PP

>> YesK  YesK-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.1   0.00052       4.7       4      47 ..       8      50 ..       7      54 .. 0.83
   2 ?    4.0   3.0    0.0065        58      31      71 ..      99     136 ..      92     143 .. 0.81
   3 ?   -2.7   0.0      0.76   6.8e+03      61      77 ..     177     193 ..     175     197 .. 0.56

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00052
                           YesK  4 igiitaillfavsyllkkrfpkkkygiilllilillslivvlys 47
                                   ig+  a++++ +sy+ ++r+  +      + +l l s++ ++ s
  gi|119719104|ref|YP_919599.1|  8 IGACAALMVLTASYINEERNLRRATYAYCVQTLLLASIF-FMLS 50
                                   688899*************99999888888888888888.4444 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.0065
                           YesK  31 illlilillslivvlysllvvGGweGmglgilgvsvligtl 71 
                                    ill +li ++ +   +   +v Gwe + l+++ +  lig  
  gi|119719104|ref|YP_919599.1|  99 ILLGALIAIGFA---IGTRIVSGWESVPLSVSVALFLIGLH 136
                                    666677777766...88999***********9999999965 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 0.76
                           YesK  61 ilgvsvligtllgliie 77 
                                    +l+ +vl+  + +l+ e
  gi|119719104|ref|YP_919599.1| 177 VLTDAVLLVLVCCLLAE 193
                                    55556666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       808  (0.0450667); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1368.00
//
Query:       gi|119719105|ref|YP_919600.1|  [L=312]
Description: respiratory-chain NADH dehydrogenase, subunit 1 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-46  157.9  20.7    4.1e-46  157.6  20.7    1.0  1  NADHdh    NADH dehydrogenase


Domain annotation for each model (and alignments):
>> NADHdh  NADH dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.6  20.7   2.3e-50   4.1e-46       8     296 ..      13     307 ..       6     310 .. 0.90

  Alignments for each domain:
  == domain 1  score: 157.6 bits;  conditional E-value: 2.3e-50
                                    HHHHHHHH.HHHHHHHHHHHHHTTS--S-SSTTTTTTHHHHHHHHHCCS-----TTS-HHHHHHHHHHHHHHHHCTTTTS CS
                         NADHdh   8 vvlllvva.lltlleRkvlAriqdRlGPnrvGplGllqplaDalKlllKediipkkadkllfllapvlalilallafavi 86 
                                     v+l+++a l+ +++Rk++Ar+q R+GP      +++qp+ D+lKl  K+++   ++++++++++p+l l++++++ + i
  gi|119719105|ref|YP_919600.1|  13 GVCLVLLApLAYGIQRKIIARLQLRKGP------PVIQPYRDLLKLWSKDKLSVPEVSSWIYMATPLLYLAITVVIAMSI 86 
                                    4556666679******************......9********************************************* PP

                                    -SSSSSS--TT...HHHHHHHHHHHCHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-SS-HHHHH CS
                         NADHdh  87 Pfgevladlnv...glllilalsslgvygillaGwasnskYallGalRsaaqmisyEvalglsllavvllagslslseiv 163
                                    P+    +++ +   +++l+++ ++l+ +++ +a+++++s+ a  Ga R+ a  + +Ev++++++l ++l  gs sl  +v
  gi|119719105|ref|YP_919600.1|  87 PVF---VNMGIplaDIFLLIYSLALARFVLSIASLDTGSPLAAAGAWRENAAAVVIEVPMLFAALLPALEGGSSSLYAVV 163
                                    *66...44433336*****************************************************************9 PP

                                    HCCCTT-C....CCCHHHHHHHHHHHHHHCCTCTTBTTTTSTTSSSSCCCTT-HCHHHHHHHHHHHHHHHHHHHHHHHHC CS
                         NADHdh 164 eaqeeiwf....illqllafiifliallaetnraPFDlpeaesELvaGfhtEYsgmkfalfflaeyanmvlvsalavllF 239
                                    ++    w      +  ++a+++f++++lae++  PFD++eae+E+ +G+  EYsg ++al+ l+ +++  ++ +l+v +F
  gi|119719105|ref|YP_919600.1| 164 SHTCLRWEtfiaRPSYIVAALAFFVCMLAEAGVLPFDVAEAEQEIQEGLLQEYSGRQLALMQLSMMVKRAVLFTLFVDIF 243
                                    98866674457867779*************************************************************** PP

                                    T..SS-HCCS........HHHHHHHHHHHHHHHHHHHHHC----TCHHHHHHHCCTCHHHHHHHHH CS
                         NADHdh 240 lg.Gwllpfs........gllwfllKvllllflfiwiratlpRlRydqlmklgwkvllplalanll 296
                                    l  G++l           g+  +l+K+l+l+ +++++ a  +R+++ +l k    v++ + +a ++
  gi|119719105|ref|YP_919600.1| 244 LPyGVAL--TleplgilvGVASYLIKLLALVTIAALVIAGNARYKVVELHKNLSLVFVLVVCATIF 307
                                    *423433..2458889999999***************************99988888888877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       841  (0.0469072); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2212.65
//
Query:       gi|119719106|ref|YP_919601.1|  [L=737]
Description: NADH dehydrogenase (quinone) [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-59  200.3  18.4    3.8e-59  200.3  18.4    2.8  3  Proton_antipo_M  Proton-conducting membrane transporter
     0.0018   18.3   6.7     0.0018   18.3   6.7    3.3  4  Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), 
  ------ inclusion threshold ------
          2    8.5   5.0       0.74    9.9   0.6    2.6  2  DUF4235          Protein of unknown function (DUF4235)


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.5      0.15   9.2e+02      12     251 ..      11      53 ..       4      69 .. 0.45
   2 ?   -3.9   2.1       1.1   6.3e+03      57     185 ..     104     112 ..      74     140 .. 0.45
   3 !  200.3  18.4   6.4e-63   3.8e-59       1     278 [.     142     430 ..     142     466 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.15
                Proton_antipo_M  12 ElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskalelglnslelllllllllvg 91 
                                    +                                                                               
  gi|119719106|ref|YP_919601.1|  11 GS------------------------------------------------------------------------------ 12 
                                    32.............................................................................. PP

                Proton_antipo_M  92 llvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirlllllavssneisqlllilaiismllgslvalaqtdi 171
                                                                                                                    
  gi|119719106|ref|YP_919601.1|   - --------------------------------------------------------------------------------   -
                                    ................................................................................ PP

                Proton_antipo_M 172 KrllAySsishlGymlialavatqygveaaiihllthalfkallFllagsviyerektrdirayggLakkmPilalvllv 251
                                                                           + + ++ +++s+i + +  ++ir + +L     +l ++  +
  gi|119719106|ref|YP_919601.1|  13 ---------------------------------------IALYVVSIVLSLILRSKPKENIRLTYALTALASLLLMLYSL 53 
                                    .......................................23333334444444444444444444444444444444333 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 1.1
                Proton_antipo_M  57 ynltgtlefeelskalelglnslelllllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirll 136
                                    y                                                                               
  gi|119719106|ref|YP_919601.1| 104 Y------------------------------------------------------------------------------- 104
                                    2............................................................................... PP

                Proton_antipo_M 137 lllavssneisqlllilaiismllgslvalaqtdiKrllAySsishlGy 185
                                                                             Ssi  +Gy
  gi|119719106|ref|YP_919601.1| 105 -----------------------------------------SSIFSIGY 112
                                    .........................................22222222 PP

  == domain 3  score: 200.3 bits;  conditional E-value: 6.4e-63
                Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskalelglnsle 80 
                                    and l++yl++El+ l++y+L+g+  ++++s  A+  +f++  +g   +Ll+ +lly ++g+l+f++  +    g+    
  gi|119719106|ref|YP_919601.1| 142 ANDALSFYLSWELMTLSSYMLVGYEHRSEESRDAAKTYFIIAHAGGACILLSYALLYFIKGSLSFDAFREG---GVPPGI 218
                                    7999******************************************************************9...999999 PP

                Proton_antipo_M  81 lllllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirllllla....vssneisqlllilaii 156
                                    ++l++ll lvg+  K++ vplh Wlp+a+ +aP  vsall+++++k++v++lir+++ +     v ++ +   ++i+a+ 
  gi|119719106|ref|YP_919601.1| 219 ASLIFLLALVGFGSKAGIVPLHAWLPQAHPAAPSNVSALLSGVMLKVAVYGLIRVVFDFLkpsgVEGGLWGCAVMIIAAF 298
                                    9********************************************************999877777889*********** PP

                Proton_antipo_M 157 smllgslvalaqtdiKrllAySsishlGymlialav...........atqygveaaiihllthalfkallFllagsviye 225
                                    s ++g   a++q d+KrllAy si  +G++l+++++             + +++aa+ hll ha+fk+llFl +gsv ++
  gi|119719106|ref|YP_919601.1| 299 STIIGVQFAVVQHDLKRLLAYHSIENIGIILLGVGAslilyseglkdVAALALTAALYHLLNHAVFKSLLFLGSGSVLKS 378
                                    *********************************9885444442222113457899**********************777 PP

                Proton_antipo_M 226 rektrdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavav 278
                                    + +tr+++ +ggL+k+ P +++++l++++++aG+Pp+ gF s++l+ ++++av
  gi|119719106|ref|YP_919601.1| 379 C-RTRNFELLGGLSKYLPWTSVTFLIAAMAIAGVPPLNGFASEWLTYQSLLAV 430
                                    7.9******************************************98888765 PP

>> Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.2   0.9         3   1.8e+04      24      36 ..      13      25 ..      10      26 .. 0.80
   2 ?   -3.2   0.1       1.6   9.7e+03      30      41 ..      42      53 ..      38      54 .. 0.78
   3 !   18.3   6.7     3e-07    0.0018      13      43 ..      82     112 ..      76     132 .. 0.82
   4 ?   -5.2   1.9         3   1.8e+04      26      36 ..     721     731 ..     714     734 .. 0.59

  Alignments for each domain:
  == domain 1  score: -4.2 bits;  conditional E-value: 3
                Proton_antipo_N 24 lmllvvtfvsllv 36
                                   + l vv++v +l+
  gi|119719106|ref|YP_919601.1| 13 IALYVVSIVLSLI 25
                                   7889999999988 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.6
                Proton_antipo_N 30 tfvsllvhlYSi 41
                                    + sll +lYS+
  gi|119719106|ref|YP_919601.1| 42 ALASLLLMLYSL 53
                                   567999999996 PP

  == domain 3  score: 18.3 bits;  conditional E-value: 3e-07
                Proton_antipo_N  13 eigfllDklsalmllvvtfvsllvhlYSigY 43 
                                     +++++Dklsa  llv++fv+l   ++SigY
  gi|119719106|ref|YP_919601.1|  82 FFALYVDKLSAFLLLVISFVALYSSIFSIGY 112
                                    5899*************************** PP

  == domain 4  score: -5.2 bits;  conditional E-value: 3
                Proton_antipo_N  26 llvvtfvsllv 36 
                                     ++v +v llv
  gi|119719106|ref|YP_919601.1| 721 YILVMVVLLLV 731
                                    45555555554 PP

>> DUF4235  Protein of unknown function (DUF4235)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.3      0.48   2.9e+03      47      66 ..     296     315 ..     291     318 .. 0.77
   2 ?    9.9   0.6   0.00012      0.74       9      71 ..     452     520 ..     445     523 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.48
                        DUF4235  47 llfAaisGavlavvrvaadR 66 
                                     +f +i G+ +avv+   +R
  gi|119719106|ref|YP_919601.1| 296 AAFSTIIGVQFAVVQHDLKR 315
                                    57899999999999876666 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00012
                        DUF4235   9 glvaGavagkafaavWkkvt....gedaPkdpkdedvslrevllfAa..isGavlavvrvaadRgtarg 71 
                                      +aGa+a   f++v++ ++    g+  Pk  ++ ++++++++ +Aa  + G+ +  v v++d++++++
  gi|119719106|ref|YP_919601.1| 452 LGLAGALAVLCFTKVYGVTFlgplGRVKPKGGESLTMKIGMAIPAAAciVLGVAMPYVAVFVDKASRQI 520
                                    5589**************994444457789*************99984468999999999999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (737 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       799  (0.0445647); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.47
# Mc/sec: 4691.51
//
Query:       gi|119719107|ref|YP_919602.1|  [L=180]
Description: 4Fe-4S ferredoxin iron-sulfur binding domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.7e-25   87.6  13.8    4.7e-25   87.6  13.8    1.8  2  Fer4_11        4Fe-4S dicluster domain
    1.5e-10   41.0  50.0    9.9e-06   25.6   8.7    3.4  4  Fer4_9         4Fe-4S dicluster domain
    1.9e-10   40.4  42.5    1.2e-05   25.2   1.6    5.3  4  Fer4_6         4Fe-4S binding domain
    4.5e-10   40.0  36.3    3.6e-05   24.3  13.3    4.0  4  Fer4_7         4Fe-4S dicluster domain
    1.8e-09   37.0  47.6    6.2e-07   29.0   2.0    5.7  6  Fer4           4Fe-4S binding domain
    6.3e-09   36.2  41.2     0.0015   19.3   3.1    4.5  4  Fer4_3         4Fe-4S binding domain
    8.8e-09   35.2  34.6    0.00077   19.8   1.8    4.8  4  Fer4_4         4Fe-4S binding domain
    2.2e-08   34.1  34.4    9.8e-06   25.6   9.1    3.6  4  Fer4_10        4Fe-4S dicluster domain
    4.4e-08   32.7  41.6      2e-05   24.4   1.5    4.6  4  Fer4_2         4Fe-4S binding domain
    9.4e-06   26.5  32.7       0.14   13.1   3.6    4.9  5  Fer4_16        4Fe-4S double cluster binding domain
    0.00017   21.6  34.4    0.00088   19.4  13.6    3.6  4  Fer4_21        4Fe-4S dicluster domain
     0.0018   18.8  28.9      0.058   13.9   0.8    4.4  5  Fer4_17        4Fe-4S dicluster domain
  ------ inclusion threshold ------
       0.12   12.9   1.4       0.12   12.9   1.4    4.6  3  Fer4_13        4Fe-4S single cluster domain of Ferredoxin I
       0.27    9.7   0.0       0.35    9.3   0.0    1.0  1  Peptidase_S64  Peptidase family S64
       0.37   11.3  33.7         17    6.0  10.0    4.3  2  Fer4_8         4Fe-4S dicluster domain
        1.2    8.9  29.0        2.5    7.9   0.5    4.1  4  Fer4_20        Dihydroprymidine dehydrogenase domain II, 4Fe-


Domain annotation for each model (and alignments):
>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   1.7       5.2   5.9e+03       5      20 ..      22      35 ..      19      45 .. 0.62
   2 !   87.6  13.8   4.2e-28   4.7e-25       5      96 ..      58     147 ..      55     151 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 5.2
                        Fer4_11  5 flpeqCrhCleppCva 20
                                   + pe C  C   +C  
  gi|119719107|ref|YP_919602.1| 22 IYPERCIGCR--ACEV 35
                                   5577776664..3333 PP

  == domain 2  score: 87.6 bits;  conditional E-value: 4.2e-28
                        Fer4_11   5 flpeqCrhCleppCvasapseaivkdeetGaVlldektkkeevrevveacPykivrkneetgkvekCdmcldrveaGllp 84 
                                     +p +CrhC+e+pC+a++p++ai +d  +GaV++d+ ++  ++r +v acP+ i+ +++e + + kCdmc++r   Gl+p
  gi|119719107|ref|YP_919602.1|  58 CVPLNCRHCEEAPCMAVCPVKAIKRDA-EGAVIVDSLRCI-GCRLCVLACPFGIPTVDKELKIMVKCDMCAERRARGLEP 135
                                    6899****************9987776.9**********7.*************************************** PP

                        Fer4_11  85 acvescptgaln 96 
                                    acv +cp+ al 
  gi|119719107|ref|YP_919602.1| 136 ACVATCPADALV 147
                                    *******99876 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0  14.5   8.8e-06    0.0099       1      51 []      26      80 ..      26      80 .. 0.68
   2 !   24.7  10.8   1.8e-08     2e-05       1      49 [.      62     108 ..      62     109 .. 0.90
   3 !   25.6   8.7   8.9e-09   9.9e-06       1      50 [.      94     145 ..      94     146 .. 0.95
   4 !    9.2   2.8    0.0012       1.3       1      29 [.     121     158 ..     121     163 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 8.8e-06
                         Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraase...eaCigCga..CveaCpkgai 51
                                   +C+gC+aC+ aC+ ++  ++    +   ++a++    +C +C++  C+++Cp +ai
  gi|119719107|ref|YP_919602.1| 26 RCIGCRACEVACEIEHGGKSFIDVYLI-EEARMcvpLNCRHCEEapCMAVCPVKAI 80
                                   6***********655433333222222.2222335568**************9987 PP

  == domain 2  score: 24.7 bits;  conditional E-value: 1.8e-08
                         Fer4_9   1 kCtgCga..CveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkg 49 
                                    +C  C +  C+++Cp +++++da +  +        +CigC+ Cv aCp g
  gi|119719107|ref|YP_919602.1|  62 NCRHCEEapCMAVCPVKAIKRDAEGAVIVDSL----RCIGCRLCVLACPFG 108
                                    5999*8667****************9999877....5************77 PP

  == domain 3  score: 25.6 bits;  conditional E-value: 8.9e-09
                         Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCga.........CveaCpkga 50 
                                    +C+gC+ Cv aCp+g+ + d+  +++        +C +C +         Cv+ Cp +a
  gi|119719107|ref|YP_919602.1|  94 RCIGCRLCVLACPFGIPTVDKELKIMV-------KCDMCAErrarglepaCVATCPADA 145
                                    6********************999999.......5*********************987 PP

  == domain 4  score: 9.2 bits;  conditional E-value: 0.0012
                         Fer4_9   1 kCtgCga.........CveaCpagvvvedaaerkarlr 29 
                                    kC  C +         Cv+ Cpa++ v++++e++ r +
  gi|119719107|ref|YP_919602.1| 121 KCDMCAErrarglepaCVATCPADALVYESVEEYQRAK 158
                                    57777333344444559999999999999999888765 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   3.2   1.4e-06    0.0015       6      20 ..      24      38 ..      22      42 .. 0.92
   2 !   10.1   7.2    0.0006      0.67       8      24 .]      62      80 ..      57      80 .. 0.91
   3 !   25.2   1.6     1e-08   1.2e-05       2      23 ..      88     109 ..      87     115 .. 0.91
   4 ?    2.8   7.3      0.13   1.4e+02       9      24 .]     122     146 ..     119     146 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.4e-06
                         Fer4_6  6 pdkCigCgdCvrvCP 20
                                   p++CigC++C+++C 
  gi|119719107|ref|YP_919602.1| 24 PERCIGCRACEVACE 38
                                   79************6 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0006
                         Fer4_6  8 kCigCgd..CvrvCPegai 24
                                   +C +C++  C++vCP +ai
  gi|119719107|ref|YP_919602.1| 62 NCRHCEEapCMAVCPVKAI 80
                                   799**999********998 PP

  == domain 3  score: 25.2 bits;  conditional E-value: 1e-08
                         Fer4_6   2 veidpdkCigCgdCvrvCPega 23 
                                    v +d  +CigC+ Cv +CP+g+
  gi|119719107|ref|YP_919602.1|  88 VIVDSLRCIGCRLCVLACPFGI 109
                                    568999*************996 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.13
                         Fer4_6   9 CigCgd.........CvrvCPegai 24 
                                    C+ C +         Cv+ CP++a+
  gi|119719107|ref|YP_919602.1| 122 CDMCAErrarglepaCVATCPADAL 146
                                    666644466666666*******997 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5  18.3   2.1e-06    0.0023       1      52 []      26      79 ..      26      79 .. 0.73
   2 !   24.3  13.3   3.2e-08   3.6e-05       2      52 .]      63     109 ..      62     109 .. 0.90
   3 !   20.3  10.9   5.5e-07   0.00062       1      52 []      94     145 ..      94     145 .. 0.77
   4 !   10.4   2.1   0.00068      0.76       1      29 [.     121     158 ..     120     168 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.1e-06
                         Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekvei.dpekClgCga..CvavCPtga 52
                                   rCigC+aC++aC  +        +   +e++++ +p +C +C++  C+avCP++a
  gi|119719107|ref|YP_919602.1| 26 RCIGCRACEVACEIEHGGKSFI-DVYLIEEARMcVPLNCRHCEEapCMAVCPVKA 79
                                   8***********9443333322.223445555538********99*******987 PP

  == domain 2  score: 24.3 bits;  conditional E-value: 3.2e-08
                         Fer4_7   2 CigCg..aCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                    C +C+   C+a+Cpvkai+ d e        v +d+ +C+gC+ Cv +CP+g+
  gi|119719107|ref|YP_919602.1|  63 CRHCEeaPCMAVCPVKAIKRDAE------GAVIVDSLRCIGCRLCVLACPFGI 109
                                    ****7669************887......478899****************96 PP

  == domain 3  score: 20.3 bits;  conditional E-value: 5.5e-07
                         Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCg......aCvavCPtga 52 
                                    rCigC+ Cv aCp +  ++d+e       k+ ++ ++C   +      aCva+CP++a
  gi|119719107|ref|YP_919602.1|  94 RCIGCRLCVLACPFGIPTVDKE------LKIMVKCDMCAERRarglepACVATCPADA 145
                                    8******************997......356667777776443333336******987 PP

  == domain 4  score: 10.4 bits;  conditional E-value: 0.00068
                         Fer4_7   1 rCigCg.........aCvaaCpvkaieldeeenekgte 29 
                                    +C  C          aCva+Cp++a+ ++ +e+ ++ +
  gi|119719107|ref|YP_919602.1| 121 KCDMCAerrarglepACVATCPADALVYESVEEYQRAK 158
                                    5777755555556669**********999776555443 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   9.0     1e-05     0.011       3      18 ..      22      37 ..      20      40 .. 0.90
   2 ?   -1.3   0.1       2.1   2.3e+03      10      17 ..      62      69 ..      61      69 .. 0.72
   3 !    9.9   1.8    0.0006      0.68      14      24 .]      71      81 ..      70      81 .. 0.95
   4 !   29.0   2.0   5.5e-10   6.2e-07       1      23 [.      88     110 ..      88     111 .. 0.91
   5 ?    0.3   0.3      0.63     7e+02      10      16 ..     121     127 ..     120     128 .. 0.75
   6 !    7.2   1.8    0.0042       4.7      13      23 ..     136     146 ..     136     147 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1e-05
                                   EETTTSSS-THHHHHS CS
                           Fer4  3 ideekCigCGaCvevC 18
                                   i +e+CigC aC+ +C
  gi|119719107|ref|YP_919602.1| 22 IYPERCIGCRACEVAC 37
                                   89************** PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.1
                                   S-THHHHH CS
                           Fer4 10 gCGaCvev 17
                                   +C  C+e+
  gi|119719107|ref|YP_919602.1| 62 NCRHCEEA 69
                                   58888876 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.0006
                                   HHHHSTTTEEE CS
                           Fer4 14 CvevCPvgAIt 24
                                   C+ vCPv AI+
  gi|119719107|ref|YP_919602.1| 71 CMAVCPVKAIK 81
                                   **********6 PP

  == domain 4  score: 29.0 bits;  conditional E-value: 5.5e-10
                                    EEEETTTSSS-THHHHHSTTTEE CS
                           Fer4   1 vvideekCigCGaCvevCPvgAI 23 
                                    v++d  +CigC +Cv +CP+g  
  gi|119719107|ref|YP_919602.1|  88 VIVDSLRCIGCRLCVLACPFGIP 110
                                    58999***************975 PP

  == domain 5  score: 0.3 bits;  conditional E-value: 0.63
                                    S-THHHH CS
                           Fer4  10 gCGaCve 16 
                                    +C  C+e
  gi|119719107|ref|YP_919602.1| 121 KCDMCAE 127
                                    7888886 PP

  == domain 6  score: 7.2 bits;  conditional E-value: 0.0042
                                    HHHHHSTTTEE CS
                           Fer4  13 aCvevCPvgAI 23 
                                    aCv  CP +A+
  gi|119719107|ref|YP_919602.1| 136 ACVATCPADAL 146
                                    7*********8 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   4.9     0.002       2.2       1      11 [.      27      37 ..      27      39 .. 0.98
   2 !   13.3   6.6   0.00011      0.13       1      15 []      63      79 ..      63      79 .. 0.91
   3 !   19.3   3.1   1.4e-06    0.0015       1      14 [.      95     108 ..      95     109 .. 0.94
   4 !   12.3   3.0   0.00024      0.27       1      15 []     122     145 ..     122     145 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.002
                         Fer4_3  1 CtgCgaCvevC 11
                                   C+gC+aC+++C
  gi|119719107|ref|YP_919602.1| 27 CIGCRACEVAC 37
                                   *********** PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.00011
                         Fer4_3  1 CtgCg..aCvevCPvgA 15
                                   C +C+  +C+ vCPv+A
  gi|119719107|ref|YP_919602.1| 63 CRHCEeaPCMAVCPVKA 79
                                   99**8778*******98 PP

  == domain 3  score: 19.3 bits;  conditional E-value: 1.4e-06
                         Fer4_3   1 CtgCgaCvevCPvg 14 
                                    C+gC++Cv +CP g
  gi|119719107|ref|YP_919602.1|  95 CIGCRLCVLACPFG 108
                                    ************98 PP

  == domain 4  score: 12.3 bits;  conditional E-value: 0.00024
                         Fer4_3   1 CtgCg.........aCvevCPvgA 15 
                                    C++C          aCv  CP +A
  gi|119719107|ref|YP_919602.1| 122 CDMCAerrarglepACVATCPADA 145
                                    ****88999999999******887 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   1.9   7.3e-07   0.00082       1      15 [.      24      38 ..      24      48 .. 0.94
   2 !    8.6   3.3    0.0026       2.9       3      16 ..      62      77 ..      60      78 .. 0.91
   3 !   19.8   1.8   6.9e-07   0.00077       3      17 .]      94     108 ..      92     108 .. 0.93
   4 ?    3.7   4.8     0.097   1.1e+02       8      16 ..     135     143 ..     120     155 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 7.3e-07
                         Fer4_4  1 qerCigCgsCvaaCP 15
                                   +erCigC++C+ aC+
  gi|119719107|ref|YP_919602.1| 24 PERCIGCRACEVACE 38
                                   69************7 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0026
                         Fer4_4  3 rCigCgs..CvaaCPq 16
                                   +C +C    C+a+CP+
  gi|119719107|ref|YP_919602.1| 62 NCRHCEEapCMAVCPV 77
                                   7*****99*******7 PP

  == domain 3  score: 19.8 bits;  conditional E-value: 6.9e-07
                         Fer4_4   3 rCigCgsCvaaCPqg 17 
                                    rCigC+ Cv aCP+g
  gi|119719107|ref|YP_919602.1|  94 RCIGCRLCVLACPFG 108
                                    8************86 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.097
                         Fer4_4   8 gsCvaaCPq 16 
                                    ++Cva+CP 
  gi|119719107|ref|YP_919602.1| 135 PACVATCPA 143
                                    68******5 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7  18.3   0.00078      0.88       4      56 .]      22      76 ..      19      76 .. 0.74
   2 !   10.0   5.0   0.00063      0.71       8      24 ..      62      80 ..      56      89 .. 0.75
   3 !   25.6   9.1   8.7e-09   9.8e-06       2      56 .]      88     142 ..      87     142 .. 0.79
   4 !    7.5   0.2    0.0039       4.3      14      35 ..     136     160 ..     132     169 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00078
                        Fer4_10  4 idddtCirCgkCvkaCPadl..tsvgakgeaseeeavrkkvekCtgcg..aCveaCP 56
                                   i +++Ci+C++C  aC   +   +++ ++ + +eea   ++ +C +c+   C+++CP
  gi|119719107|ref|YP_919602.1| 22 IYPERCIGCRACEVAC--EIehGGKSFIDVYLIEEARMCVPLNCRHCEeaPCMAVCP 76
                                   6789************..662233334444555555556********7779*****9 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00063
                        Fer4_10  8 tCirCg..kCvkaCPadlt 24
                                    C +C+   C+++CP+++ 
  gi|119719107|ref|YP_919602.1| 62 NCRHCEeaPCMAVCPVKAI 80
                                   6****9889*******442 PP

  == domain 3  score: 25.6 bits;  conditional E-value: 8.7e-09
                        Fer4_10   2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgc......g...aCveaCP 56 
                                    v++d+ +Ci+C+ Cv aCP+          +   +++ k + kC++c      g   aCv+ CP
  gi|119719107|ref|YP_919602.1|  88 VIVDSLRCIGCRLCVLACPF---------GIPTVDKELKIMVKCDMCaerrarGlepACVATCP 142
                                    688999**************.........6666666667788888885555552678******9 PP

  == domain 4  score: 7.5 bits;  conditional E-value: 0.0039
                        Fer4_10  14 kCvkaCPadl...tsvgakgeasee 35 
                                    +Cv+ CPad+   +sv+ ++ a++ 
  gi|119719107|ref|YP_919602.1| 136 ACVATCPADAlvyESVEEYQRAKRA 160
                                    6*******88887555555555544 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   5.9   1.5e-05     0.017       3      20 ..      20      37 ..      17      38 .. 0.89
   2 !    7.1   7.0    0.0059       6.6       7      21 ..      60      76 ..      54      77 .. 0.86
   3 !   24.4   1.5   1.8e-08     2e-05       3      21 ..      88     106 ..      86     107 .. 0.91
   4 ?    3.8   3.9     0.063        71       9      22 .]     121     143 ..     109     143 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.5e-05
                         Fer4_2  3 vvvdtdrCigCgaCvsaC 20
                                   v + ++rCigC+aC  aC
  gi|119719107|ref|YP_919602.1| 20 VCIYPERCIGCRACEVAC 37
                                   66889************* PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0059
                         Fer4_2  7 tdrCigCg..aCvsaCP 21
                                   + +C +C+  +C  +CP
  gi|119719107|ref|YP_919602.1| 60 PLNCRHCEeaPCMAVCP 76
                                   567****889******* PP

  == domain 3  score: 24.4 bits;  conditional E-value: 1.8e-08
                         Fer4_2   3 vvvdtdrCigCgaCvsaCP 21 
                                    v vd+ rCigC+ Cv aCP
  gi|119719107|ref|YP_919602.1|  88 VIVDSLRCIGCRLCVLACP 106
                                    789**************** PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.063
                         Fer4_2   9 rCigC..g.......aCvsaCPa 22 
                                    +C  C  +       aCv  CPa
  gi|119719107|ref|YP_919602.1| 121 KCDMCaeRrarglepACVATCPA 143
                                    677775514556889*******8 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   2.0    0.0012       1.3      37      64 ..      10      37 ..       4      40 .. 0.84
   2 !   13.1   3.6   0.00013      0.14       1      22 [.      62      85 ..      62      93 .. 0.87
   3 !   11.4   1.9   0.00044      0.49      53      66 ..      94     107 ..      84     108 .. 0.68
   4 ?    0.7   0.3      0.93     1e+03      53      62 ..     118     127 ..     109     128 .. 0.72
   5 !    9.1   0.1    0.0023       2.6       7      29 ..     136     158 ..     135     176 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0012
                        Fer4_16 37 ekkdlaedeekckkqeaitgCdiCqdvC 64
                                   e+kd a+++  c   e+++gC++C+ +C
  gi|119719107|ref|YP_919602.1| 10 EEKDPAIEKLVCIYPERCIGCRACEVAC 37
                                   6788888999999889999999999999 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00013
                        Fer4_16  1 rCgtCgk..CaevCPtnaikekke 22
                                   +C  C++  C+ vCP++aik ++e
  gi|119719107|ref|YP_919602.1| 62 NCRHCEEapCMAVCPVKAIKRDAE 85
                                   599**9999***********9955 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.00044
                        Fer4_16  53 aitgCdiCqdvCPa 66 
                                    +++gC+ C+ +CP+
  gi|119719107|ref|YP_919602.1|  94 RCIGCRLCVLACPF 107
                                    45566666666665 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.93
                        Fer4_16  53 aitgCdiCqd 62 
                                     +  Cd+C++
  gi|119719107|ref|YP_919602.1| 118 IMVKCDMCAE 127
                                    4578999976 PP

  == domain 5  score: 9.1 bits;  conditional E-value: 0.0023
                        Fer4_16   7 kCaevCPtnaikekkekeieare 29 
                                    +C+ +CP++a+  ++ +e++  +
  gi|119719107|ref|YP_919602.1| 136 ACVATCPADALVYESVEEYQRAK 158
                                    6***********99544444333 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1  15.1   3.3e-05     0.037       3      57 ..      22      80 ..      20      82 .. 0.75
   2 !   19.4  13.6   7.8e-07   0.00088       7      53 ..      62     107 ..      51     112 .. 0.89
   3 !    8.0  11.7    0.0027         3       3      52 ..      90     142 ..      89     148 .. 0.51
   4 ?   -0.8   2.6       1.5   1.7e+03      47      53 ..     137     143 ..     117     158 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.3e-05
                        Fer4_21  3 idedkCigCgkCliaCe..dtshqaieidaktvlkv.vedeCvGCnl..CssvCPvedci 57
                                   i +++CigC  C +aCe   ++   i++   + +++ v  +C  C+   C++vCPv ++i
  gi|119719107|ref|YP_919602.1| 22 IYPERCIGCRACEVACEieHGGKSFIDVYLIEEARMcVPLNCRHCEEapCMAVCPV-KAI 80
                                   7789************7435678888766444444427889****8555******9.776 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 7.8e-07
                        Fer4_21   7 kCigCgk..CliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPv 53 
                                    +C +C++  C+ +C+   ++ai+ da+  + v + +C+GC lC+  CP 
  gi|119719107|ref|YP_919602.1|  62 NCRHCEEapCMAVCP---VKAIKRDAEGAVIVDSLRCIGCRLCVLACPF 107
                                    6888875559999*9...8**********999****************5 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0027
                        Fer4_21   3 idedkCigCgkCliaCedtshqaieidaktvlkvv...edeCvGCn.lCssvCP 52 
                                    +d+ +CigC +C++aC+  ++  ++++ k ++k     e +  G +  C++ CP
  gi|119719107|ref|YP_919602.1|  90 VDSLRCIGCRLCVLACP-FGIPTVDKELKIMVKCDmcaERRARGLEpACVATCP 142
                                    56667888888888888.344444443333332211113333344334666666 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 1.5
                        Fer4_21  47 CssvCPv 53 
                                    C++ CP 
  gi|119719107|ref|YP_919602.1| 137 CVATCPA 143
                                    7777774 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   2.3   0.00052      0.59      43      57 ..      24      38 ..       5      41 .. 0.79
   2 !    8.0   2.3    0.0037       4.1       1      20 [.      62      83 ..      62      92 .. 0.81
   3 !   13.9   0.8   5.2e-05     0.058      45      60 ..      94     109 ..      87     110 .. 0.83
   4 !    7.8   9.0    0.0044       4.9       1      31 [.      94     124 ..      94     145 .. 0.75
   5 ?    1.0   2.0      0.57   6.4e+02       7      15 ..     136     144 ..     120     176 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00052
                        Fer4_17 43 aslCieCgeCerkCP 57
                                    ++Ci+C+ Ce +C 
  gi|119719107|ref|YP_919602.1| 24 PERCIGCRACEVACE 38
                                   589999999999995 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0037
                        Fer4_17  1 rCiqCgy..ClpeCpsyeaydn 20
                                   +C++C+   C+++Cp  ++ ++
  gi|119719107|ref|YP_919602.1| 62 NCRHCEEapCMAVCPVKAIKRD 83
                                   6*****889******9877665 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 5.2e-05
                        Fer4_17  45 lCieCgeCerkCPqgl 60 
                                    +Ci+C++C+ +CP g+
  gi|119719107|ref|YP_919602.1|  94 RCIGCRLCVLACPFGI 109
                                    7999999999999876 PP

  == domain 4  score: 7.8 bits;  conditional E-value: 0.0044
                        Fer4_17   1 rCiqCgyClpeCpsyeaydnepkkllraakl 31 
                                    rCi+C+ C+ +Cp+++ + +++ k++ +  +
  gi|119719107|ref|YP_919602.1|  94 RCIGCRLCVLACPFGIPTVDKELKIMVKCDM 124
                                    6999999999999888888888888877666 PP

  == domain 5  score: 1.0 bits;  conditional E-value: 0.57
                        Fer4_17   7 yClpeCpsy 15 
                                    +C++ Cp  
  gi|119719107|ref|YP_919602.1| 136 ACVATCPAD 144
                                    355577753 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.4   0.00011      0.12       1      17 [.      90     106 ..      90     121 .. 0.93
   2 ?   -2.5   0.1       7.1     8e+03       8      14 ..     121     127 ..     112     130 .. 0.81
   3 ?    0.5   1.1      0.81   9.1e+02      11      18 ..     136     143 ..     134     162 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
                        Fer4_13   1 VDrdtCiacgaCvelaP 17 
                                    VD  +Ci+c +Cv ++P
  gi|119719107|ref|YP_919602.1|  90 VDSLRCIGCRLCVLACP 106
                                    89999***********9 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 7.1
                        Fer4_13   8 acgaCve 14 
                                     c+ C+e
  gi|119719107|ref|YP_919602.1| 121 KCDMCAE 127
                                    6888875 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.81
                        Fer4_13  11 aCvelaPd 18 
                                    aCv+++P 
  gi|119719107|ref|YP_919602.1| 136 ACVATCPA 143
                                    68888885 PP

>> Peptidase_S64  Peptidase family S64
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00031      0.35     315     357 ..      79     121 ..      72     124 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00031
                  Peptidase_S64 315 ssikdqeGsfiApilRGlskklsiLtlyFGlPdpqqehyelik 357
                                    ++ +d eG+ i   lR +  +l +L+  FG+P++ +e + ++k
  gi|119719107|ref|YP_919602.1|  79 AIKRDAEGAVIVDSLRCIGCRLCVLACPFGIPTVDKELKIMVK 121
                                    56689*****************************999888876 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4  15.8     0.094   1.1e+02       3      64 ..      25      78 ..      23      79 .. 0.75
   2 ?    6.0  10.0     0.015        17       3      22 ..      93     112 ..      91     175 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.094
                         Fer4_8  3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcga..CtevCpvg 64
                                   e+Ci+C aC+ aC + +   k   d +   ++   + +v        +C +c++  C  vCpv+
  gi|119719107|ref|YP_919602.1| 25 ERCIGCRACEVACEIEHGG-KSFIDVYLIEEA---RMCV------PLNCRHCEEapCMAVCPVK 78
                                   68***********755555.554555555333...5566......678****9999******97 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.015
                         Fer4_8   3 ekCieCgaCqsaCpvlrrtk 22 
                                     +Ci+C +C  aCp+   t 
  gi|119719107|ref|YP_919602.1|  93 LRCIGCRLCVLACPFGIPTV 112
                                    68***********9654443 PP

>> Fer4_20  Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   2.0     0.015        17      22      47 ..      25      48 ..       8      57 .. 0.83
   2 ?    6.4   5.6    0.0063       7.1      23      39 ..      62      78 ..      48      82 .. 0.77
   3 ?    7.9   0.5    0.0022       2.5      16      40 ..      87     109 ..      80     118 .. 0.84
   4 ?    5.3   0.5     0.015        16      21      55 ..     126     160 ..     113     177 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.015
                                   TT----TT-HHHHCSTT---HHHHHH CS
                        Fer4_20 22 sRClqCkkapcvkgCPveidipefik 47
                                   +RC+ C  + c+ +C +e   ++fi+
  gi|119719107|ref|YP_919602.1| 25 ERCIGC--RACEVACEIEHGGKSFID 48
                                   89****..889999*99999999986 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0063
                                   T----TT-HHHHCSTT- CS
                        Fer4_20 23 RClqCkkapcvkgCPve 39
                                    C +C++apc++ CPv+
  gi|119719107|ref|YP_919602.1| 62 NCRHCEEAPCMAVCPVK 78
                                   3777***********97 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0022
                                    HHHHHHTT----TT-HHHHCSTT-- CS
                        Fer4_20  16 ealeeAsRClqCkkapcvkgCPvei 40 
                                    +++ ++ RC+ C  + cv +CP  i
  gi|119719107|ref|YP_919602.1|  87 AVIVDSLRCIGC--RLCVLACPFGI 109
                                    5678899*****..89******987 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.015
                                    HTT----TT-HHHHCSTT---HHHHHHHHHTT-HH CS
                        Fer4_20  21 AsRClqCkkapcvkgCPveidipefikkiaegnle 55 
                                    A+R  +  ++ cv++CP++  + e +++ ++ + +
  gi|119719107|ref|YP_919602.1| 126 AERRARGLEPACVATCPADALVYESVEEYQRAKRA 160
                                    55555566899********9999999887765433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1231.22
//
Query:       gi|119719108|ref|YP_919603.1|  [L=685]
Description: formate dehydrogenase, alpha subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   2.4e-102  343.1   0.0   2.8e-102  342.9   0.0    1.1  1  Molybdopterin    Molybdopterin oxidoreductase
    5.5e-27   94.0   0.1    1.3e-26   92.8   0.1    1.6  1  Molydop_binding  Molydopterin dinucleotide binding domain
    1.5e-15   56.9   0.4    3.8e-15   55.6   0.4    1.7  1  Molybdop_Fe4S4   Molybdopterin oxidoreductase Fe4S4 domain


Domain annotation for each model (and alignments):
>> Molybdopterin  Molybdopterin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  342.9   0.0  4.7e-106  2.8e-102       1     432 []      60     485 ..      60     485 .. 0.95

  Alignments for each domain:
  == domain 1  score: 342.9 bits;  conditional E-value: 4.7e-106
                                    B--S-EEECTTTTTSEEEE--HHHHHHHHHHHHHHHHHHCSGGGEEEEEBTSSCSHHHHHHHHHHHHHTT-EEE-BEECC CS
                  Molybdopterin   1 RlkyPmvRkqargeGkFvrvsWdeAleliaaslkytikkygpdrvagfssgplmsmeslaslkkllsllggknlsfydwy 80 
                                    Rl++P++R    + G+F+++sW +A  ++a++l++++k+ygp++v + +s + + +e+ ++++kl++ +g    +++d++
  gi|119719108|ref|YP_919603.1|  60 RLTKPLKR---TESGEFKEISWSDAIREVAENLNNVRKEYGPQAVGFLASARVF-NEENYAMQKLARVFGT---NNIDHC 132
                                    9*******...779********************************98888999.999999*****99999...8***** PP

                                    GGGTTHHHH....CHHCCCCCTTTS-SS-CCGGGG-SEEEEESS-HHHHSHHHHHHHHHHHHTTC-EEEEECSSB-HCGG CS
                  Molybdopterin  81 adlppasaq....qtigsdsrsnyessnpledlensdliilwGsNvreerpilnarirkaalkkkakvivigpryaellk 156
                                    a+l++a              + + +++ p+ed++ s +i++wG N++e++pil ++ + +a++k+ak++v+++r + ++ 
  gi|119719108|ref|YP_919603.1| 133 ARLCHAPSLaglsA-----TVGAGAMTAPFEDIAASNFILIWGYNPAETHPILMGQYILKAKEKGAKIAVVDTRCTRTAW 207
                                    *****987544433.....455668999*************************877777788888************999 PP

                                    GCSEEEEEHTTTHHHHHHHHHHHHHHCCCCTCHHHHHHEECHHHCCCCCCCEECCSHHHHHHCCHHHHHHHHHHHHHHTS CS
                  Molybdopterin 157 fadewlaikpgtdaalalamghvilqelkvdkeflrkytygkeetdmpllvtleeetgkkkevvariarelarnaaktag 236
                                    +ad  ++ikpgtd+a++ am +vi+qe ++d++f++ +   ++ ++  ++++++e ++  ++++a  +r++ar++ak+ +
  gi|119719108|ref|YP_919603.1| 208 HADYFIPIKPGTDLAVIYAMINVIIQEKLYDEKFVKERVERFDDLARFVSKYTPEYAESVSGAPAHLIRQVAREFAKAGK 287
                                    **************************************************************************999877 PP

                                    SEEEEECHHHHTSTTHHHHHHHHHHHHHHCTHCSSTTCEEEEESSCTTHHHCHHHHTCCTTCCCCCCCTT....HHHHHC CS
                  Molybdopterin 237 ksmiivGaglnhrqdgdaiyravinLallvgnvgqpgGgwahlnGqlilagaaekvgalpvllsvkslke....ekikfa 312
                                     + i + +g++++++g++++ ++++La+++g +g++g+ +a ++Gq++++g a+++galpv l+ +  +     +k+ + 
  gi|119719108|ref|YP_919603.1| 288 -ASICWCMGITQHTKGTNNVIGLATLAAICGYYGKEGCAVAPVRGQNNVQG-ACDMGALPVFLPGYARVIdaekRKKVAS 365
                                    .99999*********************************************.********99888877767987777788 PP

                                    CCTTTCSTSS--ECGGCHHHHHHTTSSSEEEEESH.HHHHSTTSCCCHCHHHCSSEEEEEESCSSHHHHTSSEEEEBE-C CS
                  Molybdopterin 313 aeqpgnlgnfprnlfversnllkssgkkvlyllgnnpevdhadenevekalekldlvvvldgrltstalyaDiiLPaatw 392
                                    a++ ++l+  p+++++e+s +++++++k++y++g+np +++a++n+v kale ld++vv d++lt+ta+ aDi+LP+a+w
  gi|119719108|ref|YP_919603.1| 366 AWGLDDLPAEPGYTVIEMSYAAEQGKLKAMYIMGENPLISDANANHVRKALEHLDFLVVQDIFLTETAQLADIVLPSACW 445
                                    99****************************************************************************** PP

                                    CGSEEEEE-TTSEEEEEEESSS-STT-BEHHHHHHHHHHH CS
                  Molybdopterin 393 yEkedlytndegrfqhlkqavsppgeaksdwkIlkaLakk 432
                                     Eke+ +tn+e+r+q   +av+ppgeak+dw I+ ++ak+
  gi|119719108|ref|YP_919603.1| 446 AEKEGSFTNTERRVQWSFKAVEPPGEAKPDWVIITEIAKA 485
                                    **************************************95 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.8   0.1   2.1e-30   1.3e-26       1     111 []     573     676 ..     573     676 .. 0.97

  Alignments for each domain:
  == domain 1  score: 92.8 bits;  conditional E-value: 2.1e-30
                                    EEEEEE-BTTBSTTTTTCGCCHHHHCSSS.-EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESSB-TTEEEEESS CS
                Molydop_binding   1 lrLitgrsldqlhsqtrtrpvlrlakpep.evveinpedAaalGikdGdlVevesrrGsvevrakvtervrpGvvfmpfg 79 
                                    l+L+t r+++q+h+ t+t ++  l+k+ p +v+ei+pe+A+++G++dG l+++ +rrG+ ++r+kvt+ ++++vv++p +
  gi|119719108|ref|YP_919603.1| 573 LILTTFRYVGQYHTATMTHRSVHLRKRWPePVAEIHPETARKYGVRDGGLIKIITRRGEYTCRVKVTNLIAKDVVAVPWH 652
                                    79*******************9999999999************************************************* PP

                                    HCC.....S-GHCTS--SCSTTT--CSTT-EE CS
                Molydop_binding  80 wweagekggnaNaltddatdplsgtpefksva 111
                                    +++        N+lt+da+dp++++pe k++a
  gi|119719108|ref|YP_919603.1| 653 FGA--------NVLTNDALDPVAKIPETKVCA 676
                                    *88........******************996 PP

>> Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.6   0.4   6.3e-19   3.8e-15       3      52 ..       4      54 ..       3      57 .. 0.93

  Alignments for each domain:
  == domain 1  score: 55.6 bits;  conditional E-value: 6.3e-19
                                   EEEEE-SSBTT--EEEEEE.ETTEEEEEEE-TTSTTTTT---HHHHTCHHC CS
                 Molybdop_Fe4S4  3 vvktaCpyCgvgCglevhv.kdgkivkvegdpdhpvnegrlCvKGrtller 52
                                   +vk +CpyCgvgCg+ ++v  +g+ v +e  p+hpvn+g+lC+KGr++l+ 
  gi|119719108|ref|YP_919603.1|  4 KVKVICPYCGVGCGFYISVdDYGNPVGIEHMPEHPVNRGKLCPKGRSALDV 54
                                   6889***************878999**********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (685 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.46
# Mc/sec: 4484.29
//
Query:       gi|119719109|ref|YP_919604.1|  [L=382]
Description: formate/nitrite transporter [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-72  243.9  22.8    2.4e-72  243.1  22.8    1.4  1  Form_Nir_trans  Formate/nitrite transporter


Domain annotation for each model (and alignments):
>> Form_Nir_trans  Formate/nitrite transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  243.1  22.8   1.4e-76   2.4e-72       1     236 []      15     291 ..      15     291 .. 0.96

  Alignments for each domain:
  == domain 1  score: 243.1 bits;  conditional E-value: 1.4e-76
                                    HHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHCCT........................TCHHHHH CS
                 Form_Nir_trans   1 eivekvvaagvkkaklsldklfllgilAGafigfgvllalvvaaalaes........................npglakl 56 
                                    e+v+++++a+v ka ++  +lfl+gi+AG+fig+g++la++v++a+ ++                        + +++k+
  gi|119719109|ref|YP_919604.1|  15 ETVDAAASAAVVKAFQPPGRLFLMGIMAGIFIGIGFWLAVTVSSAFWTTkvtgfdaathklvtepfnvawplnPSAMMKF 94 
                                    68999*****************************************999***********************9899**** PP

                                    HHHHCCCHHHHHHHHHT---CCCCCCHHHHHHCTTSSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTG.....GHHHH CS
                 Form_Nir_trans  57 lgglvFpvGlilvvllgaeLfTgntllltlavlkkkvslkkllknwlvvllgNliGsllvalllvvlsgl.....laekl 131
                                    l+g+vFpvGli v+++gaeL+Tg   +++l++++kk++lk+l+ nw++ + gN++Gs+++a+l ++ s+l     ++++l
  gi|119719109|ref|YP_919604.1|  95 LLGAVFPVGLIAVCIGGAELWTGCANVIPLGYMQKKLKLKALIYNWVTAYGGNWVGSVFLAFLATYGSTLllaspFRDEL 174
                                    *************************************************************888888888655555**** PP

                                    HHHHHCCCSS-HHHHHHHHHHHHHHHHHHHHHHCC-S..SHHHHHHHHHHHHHHHHHCT---HHHHHHHHHHHHHH.... CS
                 Form_Nir_trans 132 lsiaeaklslsfleaflrGilCNwlVclavwlalaak..dvigkilaiflpifafvasgfeHsvanmfliplglll.... 205
                                    +s++ ak++ls +eaf+rG++CN+lV+la+wl l++k  d +g+ ++i++pif+fv++gfeHs+anmflip+++++    
  gi|119719109|ref|YP_919604.1| 175 ISVVWAKVNLSPWEAFWRGVGCNFLVNLAIWLWLRSKkgDFMGQAFLIWFPIFTFVTIGFEHSIANMFLIPAAIFAspla 254
                                    ************************************96677*********************************888888 PP

                                    ......SHHHHHHHCHHHHHHHHHHHHHCCHHHHHHH CS
                 Form_Nir_trans 206 ......tvadfilknlipvtlGNivGGallvgllyly 236
                                          t +df+++nl+pvt GN+vGG+++++l+y+y
  gi|119719109|ref|YP_919604.1| 255 lkqyiiTYYDFFFNNLLPVTYGNLVGGFVFIALVYWY 291
                                    88888899****************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 2278.27
//
Query:       gi|119719110|ref|YP_919605.1|  [L=528]
Description: Fis family transcriptional regulator [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.11   13.0   0.0       0.25   11.8   0.0    1.6  1  Fer4_23   4Fe-4S iron-sulfur cluster binding domain


Domain annotation for each model (and alignments):
>> Fer4_23  4Fe-4S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   1.4e-05      0.25      35      71 ..     136     171 ..     131     176 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.4e-05
                        Fer4_23  35 vealCadsvClkrrlWavekgeklevegaagelPCaE 71 
                                     +++C d+ Clk+ l+ v+k  +l +      lPC+E
  gi|119719110|ref|YP_919605.1| 136 LGTVCDDEECLKNSLYMVDKAYRLGIPFY-VLLPCEE 171
                                    679*******************9999887.7899998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (528 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 3378.82
//
Query:       gi|119719111|ref|YP_919606.1|  [L=141]
Description: hypothetical protein Tpen_0193 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.5e-08   32.8  10.5    6.5e-08   32.8  10.5    2.0  2  PsiE          Phosphate-starvation-inducible E
  ------ inclusion threshold ------
       0.19   11.4   9.3       0.24   11.1   9.3    1.1  1  CTP_transf_1  Cytidylyltransferase family
       0.64    9.3   7.3        1.3    8.3   7.3    1.5  1  Far-17a_AIG1  FAR-17a/AIG1-like protein


Domain annotation for each model (and alignments):
>> PsiE  Phosphate-starvation-inducible E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.5      0.39   2.3e+03      58      68 .]      12      22 ..       6      30 .. 0.63
   2 !   32.8  10.5   1.1e-11   6.5e-08       1      66 [.      57     122 ..      57     124 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.39
                           PsiE 58 glaaailaLgl 68
                                   ++++++la+++
  gi|119719111|ref|YP_919606.1| 12 FITVLELAIAI 22
                                   45555555443 PP

  == domain 2  score: 32.8 bits;  conditional E-value: 1.1e-11
                           PsiE   1 lgdiLllLillEllrtivaylkehriavrlvieaaiiavaRklIildlkdggyltllglaaailaL 66 
                                    l++ Ll+++ ++l+rt+v ++ e+ri+v +v+eaa+i+++R++I+++lk  +  +ll++ ++  aL
  gi|119719111|ref|YP_919606.1|  57 LDESLLMIVSIDLMRTLVGGIVEKRISVIIVLEAALIFIVREIITMELKAVSETRLLLYVVVFAAL 122
                                    57789************************************************9999999887777 PP

>> CTP_transf_1  Cytidylyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   9.3     4e-05      0.24      14     123 ..      13     125 ..       2     138 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4e-05
                                    HHHTTTSH.HHHHHHHHHHHHHHHHHHHHTT--SHHHHHHHHH.......HHHHHHHHHHTTTSSSHHHHHHHHHHHHHH CS
                   CTP_transf_1  14 vliilllgglvflllvavvvilalkElirlvrlkkrekrllll....llslvlllllllflylesliallklvlllvlvl 89 
                                    ++++ l+  +++ ++v++  + +++E ++++ ++  +++++++     l +++ + l+ +l++ ++ + ++++++l + l
  gi|119719111|ref|YP_919606.1|  13 ITVLELAIAIILGVAVLLSLYKLASEAVKIAVTATFDRQHFVTfldeSLLMIVSIDLMRTLVGGIVEKRISVIIVLEAAL 92 
                                    22333334477888899999999************99999999777667777777788899999**************** PP

                                    HHHH---...HHHHHHHHHHHHHHHHHTHHHH.T CS
                   CTP_transf_1  90 lllvlkvlkskskklervilallallyvvlllqs 123
                                    +++v+++++ + k+++++ l+l ++++++l++ s
  gi|119719111|ref|YP_919606.1|  93 IFIVREIITMELKAVSETRLLLYVVVFAALFI-S 125
                                    *******9888888888887777777777776.3 PP

>> Far-17a_AIG1  FAR-17a/AIG1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   7.3   0.00022       1.3      37     160 ..      11     131 ..       3     137 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00022
                   Far-17a_AIG1  37 kyLtfiglvlqalfftlallaDeltlsallklrdnllavlafPvevlvsvlFWgLyliDrelvypklldelipd..Wlnh 114
                                     ++t+++l+++++  ++a+l     l +l + +  +  +++f  +++v++l  +L +i    +++ l+  ++++   +++
  gi|119719111|ref|YP_919606.1|  11 LFITVLELAIAIIL-GVAVLLS---LYKLASEAVKIAVTATFDRQHFVTFLDESLLMIVSIDLMRTLVGGIVEKriSVII 86 
                                    57777777776554.4444433...3333333333446667777788888877777766666667788888877656777 PP

                   Far-17a_AIG1 115 smHtvvlvailleifllkhkypsrlaalalsaafallYliwierva 160
                                    ++ + +l++i+ ei++++ k+ s ++ l ++++fa+l++ wi   +
  gi|119719111|ref|YP_919606.1|  87 VLEA-ALIFIVREIITMELKAVSETRLLLYVVVFAALFISWIFAGR 131
                                    7777.9************************************8655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       903  (0.0503653); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 942.37
//
Query:       gi|119719112|ref|YP_919607.1|  [L=189]
Description: hypothetical protein Tpen_0194 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-36  123.8   0.0    6.6e-36  122.9   0.0    1.5  1  Macro     Macro domain


Domain annotation for each model (and alignments):
>> Macro  Macro domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.9   0.0   3.7e-40   6.6e-36       1     118 []      29     143 ..      29     143 .. 0.99

  Alignments for each domain:
  == domain 1  score: 122.9 bits;  conditional E-value: 3.7e-40
                                    EEEEETTSS-CSHHHHHHHHHHHHHHHHHHHHHHHHHHS--TTSEEEEE-TTSSSSEEEEEESE-TTTSTSTTHHHHHHH CS
                          Macro   1 VnAaNsrllggggvagaihraagkalkeeckelekkqggcllGeavvtpaynlpakyvihtvgplftsskskeeeellak 80 
                                    VnAaNs+l++gggva ai r++g  +++e++e  k++g+++ Ge++vt a++l+akyvih+vgp +   ++   +e+la+
  gi|119719112|ref|YP_919607.1|  29 VNAANSYLKHGGGVALAIVRKGGDVIQRESDEWVKRYGPVPEGEVAVTGAGKLKAKYVIHAVGPKY---GDPLGDEKLAR 105
                                    9*****************************************************************...79********* PP

                                    HHHHHHHHHHHTT-SEEEEE-TTSSTTSBTHHHHHHHH CS
                          Macro  81 ayknalelaeekgiksvafPaistGifgvpweeaarva 118
                                    a+ n+l +aee g+ks+a+PaistG+fg+p +++a+++
  gi|119719112|ref|YP_919607.1| 106 AISNSLLKAEELGLKSIALPAISTGVFGYPYRRCAEIM 143
                                    ***********************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1382.17
//
Query:       gi|119719113|ref|YP_919608.1|  [L=421]
Description: GTPase or GTP-binding protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-38  133.0   0.0    1.6e-38  132.4   0.0    1.3  1  CLP1_P    mRNA cleavage and polyadenylation factor CLP1 P-loo
     0.0029   17.8   0.0     0.0066   16.6   0.0    1.6  1  CLP1_N    N-terminal beta-sandwich domain of polyadenylation 
     0.0032   16.9   0.2     0.0086   15.6   0.3    1.5  2  ParA      NUBPL iron-transfer P-loop NTPase
      0.004   17.2   0.0     0.0088   16.1   0.0    1.7  1  CbiA      CobQ/CobB/MinD/ParA nucleotide binding domain
  ------ inclusion threshold ------
      0.028   13.5   0.1      0.081   12.0   0.1    1.7  2  LpxK      Tetraacyldisaccharide-1-P 4'-kinase
      0.068   12.8   0.1       0.22   11.2   0.0    1.8  2  SRP54     SRP54-type protein, GTPase domain
      0.084   12.2   0.0       0.14   11.5   0.0    1.3  1  ATPase    KaiC
      0.088   11.4   0.0       0.14   10.7   0.0    1.2  1  MutL      MutL protein
       0.12   12.3   0.0        0.2   11.6   0.0    1.3  1  MobB      Molybdopterin guanine dinucleotide synthesis protei
        1.4    7.8   7.1        2.6    7.0   7.1    1.4  1  MeaB      Methylmalonyl Co-A mutase-associated GTPase MeaB


Domain annotation for each model (and alignments):
>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.4   0.0   9.1e-42   1.6e-38       1     188 []      96     275 ..      96     275 .. 0.93

  Alignments for each domain:
  == domain 1  score: 132.4 bits;  conditional E-value: 9.1e-42
                         CLP1_P   1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvGqseispPgtislalverpi..dveegfsldaplvyffGdtspsdnps 78 
                                    G++dsGK++++++L+N++ ++g+++ +vD+D+Gq++i+pP+ti+l +v +p+   +e++f       +f+G+ +ps+ ++
  gi|119719113|ref|YP_919608.1|  96 GGVDSGKTSFVTFLANRLSQAGERVGIVDADLGQKSIGPPATIGLGVVASPLvsLGEAEF----VDGFFVGSVTPSGLLH 171
                                    899*************************************************44333333....336899********** PP

                         CLP1_P  79 lylalvkelareveekleenkkakasgliIntpGwvkgl.gaellleliealepdvvvvldqeellnelkrdlplskvkv 157
                                    + +  v+ +++++e+      +++  +++++t+Gwv+++ g+el+l ++ alepdvvvv+++ +++ ++ + l  + ++v
  gi|119719113|ref|YP_919608.1| 172 RHVVGVRLMVEVAET------RMGVRRVVVDTTGWVSEQgGRELKLFKAMALEPDVVVVVSRGDECLHIVNTLG-RLFEV 244
                                    **************4......67779***********99458********************99999******9.***** PP

                         CLP1_P 158 vklpkspgvvqrsreerrelreerireYFyg 188
                                    v+++  ++v+ r r +rre+r+ ++r++F+g
  gi|119719113|ref|YP_919608.1| 245 VQVEAPKAVRLRGRIDRREYRKVMYRKFFEG 275
                                    *****************************96 PP

>> CLP1_N  N-terminal beta-sandwich domain of polyadenylation factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   3.7e-06    0.0066      18      73 ..      18      72 ..       3      91 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3.7e-06
                                   EEEEEEEE--EETTEE--TT-EEEE-TT-EEEEEESS-EEEEEES-EEEEEEES-- CS
                         CLP1_N 18 lkikllsGtaEifGtELaknkeytfskgtkfaiftwegcklevkgeaeseyvseet 73
                                    ++++l+G +  fG+ L ++key++ +   + +++ +++++ev++ +  +yv+ +t
  gi|119719113|ref|YP_919608.1| 18 AAFRVLNGEVVTFGATLESGKEYKVDPFRAIPLYALRDSEVEVESGK-FSYVKGNT 72
                                   5789**************************************95544.45666544 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.3   4.8e-06    0.0086      13      47 ..      96     132 ..      91     142 .. 0.89
   2 ?   -3.7   0.0       3.5   6.3e+03     124     148 ..     228     253 ..     227     256 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.8e-06
                           ParA  13 GGV..GKStvavnlAlaLakkglkvgllDaDiyGpsi 47 
                                    GGV  GK+++ + lA  L++ g +vg++DaD+   si
  gi|119719113|ref|YP_919608.1|  96 GGVdsGKTSFVTFLANRLSQAGERVGIVDADLGQKSI 132
                                    77777**************************977666 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 3.5
                           ParA 124 gDeqltvaqkl.plagaviVttpqev 148
                                    gDe l ++++l +l ++v V  p+ v
  gi|119719113|ref|YP_919608.1| 228 GDECLHIVNTLgRLFEVVQVEAPKAV 253
                                    89999999999888899999999887 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   4.9e-06    0.0088       9      55 ..      99     234 ..      92     305 .. 0.61

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.9e-06
                                    TSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH.................................. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................................. RF
                           CbiA   9 GvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep.................................. 54 
                                    ++GKT++++ La  l+++g rV  vDaD   ++           ++                                  
  gi|119719113|ref|YP_919608.1|  99 DSGKTSFVTFLANRLSQAGERVGIVDADLGQKSIG-------PPATiglgvvasplvslgeaefvdgffvgsvtpsgllh 171
                                    68**************************9844422.......22223334444456666666677777777777777777 PP

                                    ..............................................................C CS
                                    ..............................................................x RF
                           CbiA  55 ..............................................................d 55 
                                                                                                   
  gi|119719113|ref|YP_919608.1| 172 rhvvgvrlmvevaetrmgvrrvvvdttgwvseqggrelklfkamalepdvvvvvsrgdeclhI 234
                                    777755555555555555555555555555555555555555555555555555555544443 PP

>> LpxK  Tetraacyldisaccharide-1-P 4'-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   4.5e-05     0.081      37      71 ..      92     123 ..      83     138 .. 0.84
   2 ?   -2.5   0.0       1.2   2.2e+03      89     102 ..     390     403 ..     374     406 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.5e-05
                                    EEEEEESBSS-HSHHHHHHHHHHHTTTS..-EEEE CS
                           LpxK  37 VivVGNitvGGtGKTPlvialvkllqarglkvgvl 71 
                                    V+vVG +    +GKT++v  l+++l+++g +vg++
  gi|119719113|ref|YP_919608.1|  92 VMVVGGVD---SGKTSFVTFLANRLSQAGERVGIV 123
                                    55555554...79*********************8 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.2
                                    TT-HHHH-HHHHHH CS
                           LpxK  89 essaaevGDEplll 102
                                     s+aa  GDE+l+l
  gi|119719113|ref|YP_919608.1| 390 LSTAAPSGDETLML 403
                                    4689999*****98 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00012      0.22       4      39 ..      92     127 ..      89     130 .. 0.93
   2 ?   -1.5   0.0      0.92   1.7e+03      84     112 ..     190     216 ..     180     245 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00012
                                    EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEEST CS
                          SRP54   4 illvGlqGaGKTttlaKLaallkkegkkvllvaaDt 39 
                                    +++vG   +GKT+ ++ La++l++ g++v +v aD 
  gi|119719113|ref|YP_919608.1|  92 VMVVGGVDSGKTSFVTFLANRLSQAGERVGIVDADL 127
                                    899*****************************9995 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.92
                                    SSEEEEEE--SSTTHHHHHHHHHHHHHHH CS
                          SRP54  84 idvvlvDTaGrlqndkelmeelkkikkvv 112
                                    +  v+vDT+G   ++    +elk +k ++
  gi|119719113|ref|YP_919608.1| 190 VRRVVVDTTGWVSEQG--GRELKLFKAMA 216
                                    5568999999876654..45666666665 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   7.8e-05      0.14      19     129 ..      89     199 ..      82     211 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.8e-05
                         ATPase  19 grvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenak.slGwdlekleeegklaiidasesaeesae 97 
                                    +r v ++G+ ++GKt f+ +Fl + +++ ge++ +v  +  ++++   a+  lG+    l + g+  ++d +  ++ +++
  gi|119719113|ref|YP_919608.1|  89 ARRVMVVGGVDSGKTSFV-TFLANRLSQAGERVGIVDADLGQKSIGPPATiGLGVVASPLVSLGEAEFVDGFFVGSVTPS 167
                                    577899***********7.7***************999999999988887788998888888888888888888877666 PP

                         ATPase  98 ekdkedleelieelaeaikeikakrvviDsit 129
                                       +  +  +   ++ a  +++++rvv+D+ +
  gi|119719113|ref|YP_919608.1| 168 GLLHRHVVGVRLMVEVAETRMGVRRVVVDTTG 199
                                    55555555554455555556666888888765 PP

>> MutL  MutL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   7.7e-05      0.14     111     156 ..      79     124 ..      60     131 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 7.7e-05
                           MutL 111 edleelrelrpdiiLLaGGtDgGnkevllenAellaeaklklpviy 156
                                    +  e++  l +  ++ +GG+D G+++ ++ +A++l++a+ ++ ++ 
  gi|119719113|ref|YP_919608.1|  79 AAAERIGSLGARRVMVVGGVDSGKTSFVTFLANRLSQAGERVGIVD 124
                                    4678899999999*************************99998885 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00011       0.2       2      34 ..      92     124 ..      91     134 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00011
                           MobB   2 lgivgksgsGKTtLleklipelkarglrvgtiK 34 
                                    + +vg  +sGKT++++ l + l++ g rvg++ 
  gi|119719113|ref|YP_919608.1|  92 VMVVGGVDSGKTSFVTFLANRLSQAGERVGIVD 124
                                    578999************************985 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   7.1    0.0014       2.6      29     131 ..      89     199 ..      67     268 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0014
                                    SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE--------.......----------HCCCTSTTEEEEEE---- CS
                           MeaB  29 aqvvGltGvPGaGkstlvealglelrrrGkrvavlavDPsspftG.......GsilGDklRleelavdegvfiRslpsrG 101
                                    a++v + G   +Gk  +v  l+ +l ++G+rv+++  D + +  G       G +    + l e +  +g f+ s++ +G
  gi|119719113|ref|YP_919608.1|  89 ARRVMVVGGVDSGKTSFVTFLANRLSQAGERVGIVDADLGQKSIGppatiglGVVASPLVSLGEAEFVDGFFVGSVTPSG 168
                                    67888888889************************888665554422222226666677788888899999999999999 PP

                                    -HHHHHHHHHHHHHHHHH.TT-SEEEEEEES CS
                           MeaB 102 alGGlaaktrevvlllea.aGfDvvlietvG 131
                                     l       r +v++ e+ +G   v+++t G
  gi|119719113|ref|YP_919608.1| 169 LLHRHVVGVRLMVEVAETrMGVRRVVVDTTG 199
                                    9999999999999999865899999999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 3037.24
//
Query:       gi|119719114|ref|YP_919609.1|  [L=368]
Description: hypothetical protein Tpen_0196 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   2.5e-186  619.1   0.0   2.8e-186  618.9   0.0    1.0  1  FBPase_3  Fructose-1,6-bisphosphatase


Domain annotation for each model (and alignments):
>> FBPase_3  Fructose-1,6-bisphosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  618.9   0.0  1.6e-190  2.8e-186       1     360 [.       2     362 ..       2     363 .. 0.99

  Alignments for each domain:
  == domain 1  score: 618.9 bits;  conditional E-value: 1.6e-190
                       FBPase_3   1 kvtlsvikaDvGslaGhtkvheellekveevleeakkkgllidfyvtkvGDDielimthtkgvdneevhklawdafkeat 80 
                                    ++t+s+ikaDvG+laGh+ vh++l e ++++leea+++gllidfyv++vGDD++l+mthtkg++n e+hklawd+f e+t
  gi|119719114|ref|YP_919609.1|   2 RITVSLIKADVGGLAGHVVVHPKLEELARKRLEEARETGLLIDFYVYHVGDDLQLLMTHTKGENNAEIHKLAWDIFVEVT 81 
                                    69****************************************************************************** PP

                       FBPase_3  81 .evakelklygaGqDlLkdafsGnvkGlGPgvaelefeeRksepvvvfaaDktepgafnlplykifadpfntaGlvidpk 159
                                     +v+k lklygaGqDlLkd+fsGn+kG+GPg+ae+efeeR+sep++vf aDktepga+n++ly+ifadpfntaGl+idp+
  gi|119719114|ref|YP_919609.1|  82 eKVSKPLKLYGAGQDLLKDTFSGNIKGMGPGCAEMEFEERRSEPILVFSADKTEPGAWNYKLYRIFADPFNTAGLIIDPA 161
                                    789***************************************************************************** PP

                       FBPase_3 160 lheGfkfevlDvieekkillsapeelydllallgakeryvikrvyskkdeeiaavvsterlsliaGkYvGkDDPvaivRa 239
                                    +h+Gf fev+Dv+e+k+++ls+pee+ydllal+g+++ryv+krvy+k+d+eiaav+s++rlsliaG+YvGkDDPv+i+Ra
  gi|119719114|ref|YP_919609.1| 162 MHSGFIFEVVDVYEHKSVKLSTPEESYDLLALIGTPGRYVVKRVYRKSDGEIAAVSSATRLSLIAGRYVGKDDPVLIIRA 241
                                    ******************************************************************************** PP

                       FBPase_3 240 qsglPavgevlepfalphlvaGwmrGshngplmPvslkdakptrfdgpprvvalgfqlkegklvgpvDlfddpafdeaRe 319
                                    q+g+Pa+gevle+fa+phlvaGwmrGsh+gplmPv+l+ a++trfdgpprvv+lgfql++g+l+gpvDlfddpaf+ +R+
  gi|119719114|ref|YP_919609.1| 242 QHGFPATGEVLEAFAFPHLVAGWMRGSHTGPLMPVPLRYAQCTRFDGPPRVVGLGFQLHDGRLEGPVDLFDDPAFEMTRR 321
                                    ******************************************************************************** PP

                       FBPase_3 320 kaaeiadelRrqGpfephrlpeeeleYttlpevleklkerf 360
                                    +a+e+ad++Rr+Gpf+phrl +ee+eYttlp+vleklk rf
  gi|119719114|ref|YP_919609.1| 322 MAEEVADYMRRHGPFMPHRLGPEEMEYTTLPSVLEKLKARF 362
                                    ****************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2875.22
//
Query:       gi|119719115|ref|YP_919610.1|  [L=888]
Description: ATPase, P-type (transporting), HAD superfamily, subfamily IC [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-54  184.6   3.2    1.2e-54  184.6   3.2    2.8  4  E1-E2_ATPase     E1-E2 ATPase
      8e-38  130.0   3.0      8e-38  130.0   3.0    2.4  2  Cation_ATPase_C  Cation transporting ATPase, C-terminus
    3.6e-26   92.7   5.3    1.6e-25   90.6   5.3    2.1  1  Hydrolase        haloacid dehalogenase-like hydrolase
    1.1e-21   76.3   0.5    6.1e-21   73.9   0.0    2.6  3  Cation_ATPase_N  Cation transporter/ATPase, N-terminus
    4.7e-15   55.4   0.0    9.9e-15   54.4   0.0    1.5  1  Cation_ATPase    Cation transport ATPase (P-type)
    5.8e-07   30.1   0.2    2.6e-06   28.0   0.1    2.2  2  HAD              haloacid dehalogenase-like hydrolase
    1.3e-06   28.4   0.1    0.00028   20.7   0.2    2.4  2  Hydrolase_3      haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
       0.11   12.7   0.9       0.54   10.5   0.1    2.5  2  DUF3784          Domain of unknown function (DUF3784)


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1      0.17   3.9e+02     103     137 ..      41      75 ..      36      94 .. 0.62
   2 !  184.6   3.2   5.3e-58   1.2e-54       2     181 .]     111     304 ..     110     304 .. 0.97
   3 ?   -3.1   0.1       2.2   4.9e+03     122     148 ..     766     796 ..     759     810 .. 0.49
   4 ?   -2.9   0.3       1.9   4.3e+03     103     155 ..     816     871 ..     798     876 .. 0.57

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.17
                                    -------HHHHHHHHHHHHHHHHHHHHHHHHHHS- CS
                   E1-E2_ATPase 103 eakskktplqkkldklgkvlvpvvlliallvflia 137
                                    e+++k  pl+ +l+++ + l+++ +++++l +++ 
  gi|119719115|ref|YP_919610.1|  41 EEEKKVHPLEIFLRQFKSPLILLLIFASILSYAVG 75 
                                    45577888888888888888888888877777765 PP

  == domain 2  score: 184.6 bits;  conditional E-value: 5.3e-58
                                    SS--EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-S.EEE-TTTS---S-EE-............G-TT CS
                   E1-E2_ATPase   2 llpptakvirdgteeeidakelvpGDivllkagdrvpaDgrivegsa.evdesaLTGEslpvek............ekgd 68 
                                    + +p+a+v+r+g+ + ++a+e+vpGD++ll agdrv+aD+rive+ + +v+e+ LTGEs+pvek            ++ +
  gi|119719115|ref|YP_919610.1| 111 MVAPQATVLRGGEKVVVNASEVVPGDVLLLSAGDRVVADARIVESVNlRVNEAPLTGESTPVEKmvdpipedtplpDRAN 190
                                    7899**************************************************************************** PP

                                    EE-TT-EEEE-EEEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTT.HH CS
                   E1-E2_ATPase  69 mvfsGtvvvsgeakavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgksla.ea 147
                                    mv++Gtvvv g+ kavV+atg++telgki + +e+ ++++tpl+++l++l++++ +++l++a++v l+ ++++k    + 
  gi|119719115|ref|YP_919610.1| 191 MVYAGTVVVYGRGKAVVVATGKNTELGKISATLEAVEERETPLERELSRLSRWILVFMLVVAVVVSLVGFFVKKYSPiDL 270
                                    ***********************************************************************999777466 PP

                                    HHHHHHHHHHHS-TTHHHHHHHHHHHHHHHHHHT CS
                   E1-E2_ATPase 148 llralallvaaiPcaLplavplalalgarrlakk 181
                                    ll +++l+vaa+P+aLp++v+ +lalg+ r+akk
  gi|119719115|ref|YP_919610.1| 271 LLWIVSLAVAAVPEALPVVVTSSLALGVYRMAKK 304
                                    777*****************************97 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 2.2
                                    HHHHHHHHHHHHHHS-STTTSSTT....HHH CS
                   E1-E2_ATPase 122 lvpvvlliallvflialllgksla....eal 148
                                     vp+v++++l+ ++  ll  +++     +a+
  gi|119719115|ref|YP_919610.1| 766 AVPLVFTVLLTYAFSSLLSLGEPEaearTAI 796
                                    4445555544444444444443334433333 PP

  == domain 4  score: -2.9 bits;  conditional E-value: 1.9
                                    -------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTT...HHHHHHHHHH CS
                   E1-E2_ATPase 103 eakskktplqkkldklgkvlvpvvlliallvflialllgksla...eallralall 155
                                    +++ + +pl +k   ++ +l+++  l++++   ++ +l+  ++   ++++ al+++
  gi|119719115|ref|YP_919610.1| 816 KPSLTLSPLDNKPLVVSIILSVTLQLAFFASPYVMHVLEIHPVtinDIIYAALVTA 871
                                    55555555555555566665555555555555555554444445655555555554 PP

>> Cation_ATPase_C  Cation transporting ATPase, C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   1.4     0.016        36     131     172 ..     244     283 ..     234     289 .. 0.73
   2 !  130.0   3.0   3.6e-41     8e-38       1     182 []     710     883 ..     710     883 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.016
                Cation_ATPase_C 131 aillslllqvlivyvpglnavfgtaplsleewlialllalvv 172
                                    +++++l+++v++++v  +  v + +p++l  w+++l++a+v+
  gi|119719115|ref|YP_919610.1| 244 ILVFMLVVAVVVSLV--GFFVKKYSPIDLLLWIVSLAVAAVP 283
                                    333344444444444..55677999**************986 PP

  == domain 2  score: 130.0 bits;  conditional E-value: 3.6e-41
                Cation_ATPase_C   1 plplsaiqiLwinLvtDllpalaLaleppekdimkrpPrkkkepliskkmlrriliqgllqalvtllvffltlllfgise 80 
                                    plp++a+qiLw+nLvtD+ pa+aL+le+ ekd++ r Prk+ ep++skk ++ +l+   l++ v l++ f  ll+ g  e
  gi|119719115|ref|YP_919610.1| 710 PLPFTATQILWVNLVTDGPPAIALSLEKGEKDLIYRNPRKPGEPIFSKKEILLFLVAVPLVFTVLLTYAFSSLLSLGEPE 789
                                    89***************************************************977777777777777777777566666 PP

                Cation_ATPase_C  81 kenklssnyaqtmaFitlvlsqifnalnlrsrreslfkfsglfsnkllllaillslllqvlivyvpglnavfgtaplsle 160
                                     e       a+t++F++lv+++++ a+++rs+r++ ++  +   nk l+++i+ls++lq+++   p++ +v++++p++++
  gi|119719115|ref|YP_919610.1| 790 AE-------ARTAIFTSLVVAELAMAYAWRSLRKPSLT-LSPLDNKPLVVSIILSVTLQLAFFASPYVMHVLEIHPVTIN 861
                                    55.......*****************************.77789************************************ PP

                Cation_ATPase_C 161 ewlialllalvvllvdelvKll 182
                                    + ++a+l+ +++++ +e++K+l
  gi|119719115|ref|YP_919610.1| 862 DIIYAALVTAAMFVSVEAFKYL 883
                                    ********************96 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.6   5.3   7.2e-29   1.6e-25       4     210 .]     323     640 ..     320     640 .. 0.71

  Alignments for each domain:
  == domain 1  score: 90.6 bits;  conditional E-value: 7.2e-29
                                    EEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHH...........HHHHHHHHHETTTE..... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxxxx..... RF
                      Hydrolase   4 vvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakar...........sgaltgfatfigrg..... 67 
                                    ++ Dk+GT+t+ge+  ++v+ +   a  +++ tg   p gk lv   +                 + f     +      
  gi|119719115|ref|YP_919610.1| 323 ICSDKTGTITKGEMTAVKVWMKD--ATIEVTGTG-YEPTGKLLVGSKEVDpngyeglrlllL---AAFNN---NDsevry 393
                                    889*****************999..333333333.444444443333333334433332220...11111...1111122 PP

                                    ................HHHHTHHHHHHHH......HCHHHHHHHHHHHHHHCHHHHHH...................... CS
                                    ................xxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxx...................... RF
                      Hydrolase  68 ................ayaigkpewltal......dippdlgaaigsaqsqgrtvall...................... 103
                                                    +++  k    ++l      +++++ +   + ++  gr v++                       
  gi|119719115|ref|YP_919610.1| 394 qdgrwvtsgdgteialKVLALKAGVNAELprlgevPFSSERKRMSTLHELGGRRVVFTkgapevvvplcryissmdgrve 473
                                    22222333333444443333333333333333555666666666666666666666667777777777777777777777 PP

                                    .............................................TTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEE CS
                                    .............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase 104 .............................................qaralavftiadplkvkpeaaeavasLkaagievv 138
                                                                                 +  +l+++ + dp  ++pe+++a+++ k+agi+v+
  gi|119719115|ref|YP_919610.1| 474 elseeakrlvlavndelagqglrniaiayrylddgrstitesdekDLVLLGIVSMIDP--PRPEVKDALETCKKAGIRVA 551
                                    77777777777789****************************99999***********..******************** PP

                                    EEESSEHHHHHHHHHHTT.............GGGE.SEEEEHHCES...STTTSHHHHHHHHHHHTSTGGGEEEEESSHH CS
                                    xxxxxxxxxxxxxxxxxx.............xxxx.xxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase 139 lltgdnpetaeraanqlG.............ddyf.daviasdiet...vakpspegkvaaireLqgkpeevamVGDgvn 201
                                    ++tgd++ ta ++a++lG              d + da++   +e+    a +spe+k+++++ L+ +++ vam GDgvn
  gi|119719115|ref|YP_919610.1| 552 MITGDHKLTAVAVARELGmlgeddivvtgkeLDSMsDAELYEKVEKirvYARVSPEHKLRIVEALKKRGHVVAMTGDGVN 631
                                    *********************98888877663333366666666669999999*************************** PP

                                    HHHHHHHTT CS
                                    xxxxxxxxx RF
                      Hydrolase 202 DaaalaaAg 210
                                    Da+al+aA+
  gi|119719115|ref|YP_919610.1| 632 DAPALKAAD 640
                                    ********8 PP

>> Cation_ATPase_N  Cation transporter/ATPase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.9   0.0   2.7e-24   6.1e-21       1      69 []       4      71 ..       4      71 .. 0.99
   2 ?   -1.6   0.0         1   2.3e+03      57      68 ..     244     255 ..     225     256 .. 0.53
   3 ?   -3.4   0.0       3.6   8.1e+03      45      62 ..     674     691 ..     671     693 .. 0.82

  Alignments for each domain:
  == domain 1  score: 73.9 bits;  conditional E-value: 2.7e-24
                Cation_ATPase_N  1 ehalsleevlekLetdlenGLtqaeaaerlkkyGpNelkekkkkslwvkllkqftnplvilLlvaalvs 69
                                   +ha+ +e+vl++L+ ++ +GL  +ea++rl++yGpN+++e+kk+  ++++l+qf++pl++lL++a+++s
  gi|119719115|ref|YP_919610.1|  4 WHAMKVEDVLRELG-TSLQGLPVEEARRRLQVYGPNVIEEEKKVHPLEIFLRQFKSPLILLLIFASILS 71
                                   9************9.89**************************************************98 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1
                Cation_ATPase_N  57 plvilLlvaalv 68 
                                     lv +L+va++v
  gi|119719115|ref|YP_919610.1| 244 ILVFMLVVAVVV 255
                                    345566666666 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 3.6
                Cation_ATPase_N  45 slwvkllkqftnplvilL 62 
                                     l + ++++++ +lv+lL
  gi|119719115|ref|YP_919610.1| 674 KLGREIFENIKKFLVYLL 691
                                    567789999999****99 PP

>> Cation_ATPase  Cation transport ATPase (P-type)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.4   0.0   4.4e-18   9.9e-15       4      91 .]     387     465 ..     382     465 .. 0.91

  Alignments for each domain:
  == domain 1  score: 54.4 bits;  conditional E-value: 4.4e-18
                  Cation_ATPase   4 NsaafsensekdevkllGnktEsALlvlaeklgldteelreetkkvqeipFnssrKrmsvvlklepekkvrlyvKGApei 83 
                                    N++++  + +++++ ++G+ tE+AL vla k+      +++e +++ e+pF+s+rKrms++++l   ++ ++++KGApe+
  gi|119719115|ref|YP_919610.1| 387 NDSEV--RYQDGRWVTSGDGTEIALKVLALKA-----GVNAELPRLGEVPFSSERKRMSTLHELG--GRRVVFTKGAPEV 457
                                    35555..788899*******************.....899***********************86..************* PP

                  Cation_ATPase  84 ilkrCthv 91 
                                    ++  C ++
  gi|119719115|ref|YP_919610.1| 458 VVPLCRYI 465
                                    *****986 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.1   1.2e-09   2.6e-06      44     188 .]     488     637 ..     467     637 .. 0.59
   2 ?   -3.2   0.0       4.2   9.5e+03     102     130 ..     686     716 ..     684     738 .. 0.74

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 1.2e-09
                            HAD  44 rellrldraglaelleallaglseelaaelerfv....aevirpklldpgalellaahraaGdrvvvvSgglrplvepll 119
                                    +el+ +  + +a ++++l  g s   + + +++v     ++i p   +p+++++l+ +++aG+rv++++g ++  + +++
  gi|119719115|ref|YP_919610.1| 488 DELAGQGLRNIAIAYRYLDDGRSTITESDEKDLVllgiVSMIDPP--RPEVKDALETCKKAGIRVAMITGDHKLTAVAVA 565
                                    556666666666666666666665555555555545554444443..48******************************* PP

                            HAD 120 aelg...adevlatelevddrltge..lg.legkpvrgegkvaalre.....wlaaegegidlee.......vvay.GDs 180
                                    +elg    d++         ++tg+      +  +  + +k+++ ++     +l          e       vva  GD+
  gi|119719115|ref|YP_919610.1| 566 RELGmlgEDDI---------VVTGKelDSmSDAELYEKVEKIRVYARvspehKLRIV-------EalkkrghVVAMtGDG 629
                                    ****5554444.........4444411110222222223333333333333322222.......1223333388888*** PP

                            HAD 181 psDlpllr 188
                                    ++D p+l+
  gi|119719115|ref|YP_919610.1| 630 VNDAPALK 637
                                    ******96 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 4.2
                            HAD 102 drvvvvSgglrplvepll.aelg.adevlat 130
                                    + v+++S++  +l+ pl    lg +  + at
  gi|119719115|ref|YP_919610.1| 686 FLVYLLSANVTELMLPLVsSVLGlPLPFTAT 716
                                    56899****9999999986677765555555 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.1   0.0     0.007        16      18      54 ..     534     570 ..     530     599 .. 0.87
   2 !   20.7   0.2   1.2e-07   0.00028     196     252 ..     613     670 ..     606     673 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.007
                                    HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCC CS
                    Hydrolase_3  18 ektkeaikklkekgikvviATGRslravlpvleelgl 54 
                                    ++ k+a++ +k++gi v+  TG +  ++  v++elg+
  gi|119719115|ref|YP_919610.1| 534 PEVKDALETCKKAGIRVAMITGDHKLTAVAVARELGM 570
                                    6899*******************99999999999984 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 1.2e-07
                                    HHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETT.S-HHHHHHSSEEE--GGGTHHH CS
                    Hydrolase_3 196 akelnisleeviafGDgeNDieMLeaaglgvAmgn.aseevkkaAdyvtksnnedGVa 252
                                    ++ l+     v+  GDg ND + L+aa++gvAmg  ++e +k+a+d v ++ n   ++
  gi|119719115|ref|YP_919610.1| 613 VEALKKRGHVVAMTGDGVNDAPALKAADVGVAMGRtGTEVAKEASDLVLADDNFATIV 670
                                    56666666778889*******************9626777788888888877766655 PP

>> DUF3784  Domain of unknown function (DUF3784)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1       1.5   3.3e+03      52      77 ..      64      87 ..      41      97 .. 0.52
   2 ?   10.5   0.1   0.00024      0.54      32      86 ..     227     280 ..     217     283 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.5
                        DUF3784 52 ligilflllgllsaiesealliiali 77
                                   li  + +l++++ +   ++++i+al+
  gi|119719115|ref|YP_919610.1| 64 LIF-ASILSYAV-GEAFDSIVILALV 87
                                   222.34444444.2222222222222 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00024
                        DUF3784  32 eekekydekklsrfmgivllligilflllgllsaiesealliialiviiiiviyl 86 
                                    ee+e   e+ lsr ++++l+++ ++ ++ +l+ +++ ++++ i l+++i+++ ++
  gi|119719115|ref|YP_919610.1| 227 EERETPLERELSRLSRWILVFMLVVAVVVSLV-GFFVKKYSPIDLLLWIVSLAVA 280
                                    78888888888888888888888888888888.7778899999999998887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (888 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       903  (0.0503653); expected 358.6 (0.02)
Passed bias filter:                      575  (0.0320709); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.80u 0.27s 00:00:01.07 Elapsed: 00:00:00.45
# Mc/sec: 5918.18
//
Query:       gi|119719116|ref|YP_919611.1|  [L=257]
Description: hypothetical protein Tpen_0198 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.3e-43  149.5   0.1    1.5e-43  149.3   0.1    1.0  1  PAC2       PAC2 family
  ------ inclusion threshold ------
      0.099   12.4   0.5       0.16   11.7   0.5    1.2  1  T6SS_VipA  Type VI secretion system, VipA, VC_A0107 or Hcp2
       0.21   10.0   0.1       0.28    9.6   0.1    1.1  1  FHIPEP     FHIPEP family


Domain annotation for each model (and alignments):
>> PAC2  PAC2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.3   0.1   2.6e-47   1.5e-43       1     212 [.      24     237 ..      24     238 .. 0.90

  Alignments for each domain:
  == domain 1  score: 149.3 bits;  conditional E-value: 2.6e-47
                                    EEEESSCGGGHHHHHHHHHHHHTTEEEEEEEEHCCHSBCCCC.SEEEEETT..EEE-SEEEEEETTT.SEEEEEEE...E CS
                           PAC2   1 LilGfpgiGnVgqlavdlLiesleaekvgeidsdyllpfvgprpvvlveeg..relepprlyakdsgsrdllvlqg...r 75 
                                    L++G+pgiG+Vg++avd+++++l+++kv+e+  ++++  vg+   v+v+++   +++++++y+ + gsrd+l++++   +
  gi|119719116|ref|YP_919611.1|  24 LVQGLPGIGLVGKIAVDYIVSTLNLRKVAELIGPGIILPVGNV-GVYVTNEgaLQIPSYKFYLLNGGSRDILFVTSeaqP 102
                                    799********************************88878885.35666663677777777988989*********6666 PP

                                    -HSCHHHHHHHHHHHHHHHTTESEEEEEEEEEESS-ES..TTS-.EEEEEESSHHHHHHHH.....CT-CEEEEHHHHHH CS
                           PAC2  76 epilqyeefakalldwaeelgvkevvvLggldageradvphtrpekvtgaatdeelleele.....eseyggivgitglL 150
                                    + ++qye +a+++ld++ ++g +ev+   g+ a+e+      ++++v++a+ +e+++++le     +s++g+i+g++glL
  gi|119719116|ref|YP_919611.1| 103 ALWAQYE-VAEKVLDFFVSIGGREVIGACGTTAEES------EHVGVYYAYASEDCAKKLEalgakRSTGGTITGACGLL 175
                                    6666666.***********************97754......899***************75765444************ PP

                                    HHHHHHTT-EEEEEEEEEECCC--HHHHHHHHHHHHHHHT---HCHHHHHHHHHHHHHHHHH CS
                           PAC2 151 lsaakergipavgllaevphylpdPkaaaalleflskllglevdtedLeedaeeleeqleel 212
                                      +a+ rg++a++l+++++   p+  aa++l+++lskll++ev++edLe+  e+++++ ee+
  gi|119719116|ref|YP_919611.1| 176 PALAALRGLKAYVLMGSTQTPEPNFVAARELIRVLSKLLEFEVSLEDLEKTIEQIRRREEEM 237
                                    ********************************************************987776 PP

>> T6SS_VipA  Type VI secretion system, VipA, VC_A0107 or Hcp2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.5   2.7e-05      0.16     107     147 ..     207     247 ..     192     251 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.7e-05
                                    -HHHHHHHHHHHHHHHHHTTTTTXTTHHHHHHHHHHXXHHH CS
                      T6SS_VipA 107 vpeLkkLlelReaLadLkskldnkekleklleevlkdeell 147
                                    +  L+kLle   +L+dL++++++ ++ e+++e+vl+  +++
  gi|119719116|ref|YP_919611.1| 207 IRVLSKLLEFEVSLEDLEKTIEQIRRREEEMEKVLETARQK 247
                                    7889*******************************988765 PP

>> FHIPEP  FHIPEP family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1   4.6e-05      0.28     499     551 ..     198     247 ..     192     256 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 4.6e-05
                                    .HHS-HHHHHHHHHHHHCTTXXXXXHHHHHHHHHHHTTTXXSHHHHHHHHHHH CS
                         FHIPEP 499 pkllslgelqkvLqnLlkErvsirdlrtIletlaeaakktkdvellteavRqa 551
                                    p+ +   el +vL +Ll+ +vs+ dl++ +e++      ++++e + e++Rq+
  gi|119719116|ref|YP_919611.1| 198 PNFVAARELIRVLSKLLEFEVSLEDLEKTIEQIRRR---EEEMEKVLETARQK 247
                                    67788999*******************999988765...57788888888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1304  (0.0727313); expected 358.6 (0.02)
Passed bias filter:                     1088  (0.0606838); expected 358.6 (0.02)
Passed Vit filter:                       133  (0.00741815); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.34s 00:00:00.97 Elapsed: 00:00:00.51
# Mc/sec: 1516.31
//
Query:       gi|119719117|ref|YP_919612.1|  [L=242]
Description: TatD-related deoxyribonuclease [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      4e-44  150.9   0.0    4.8e-44  150.7   0.0    1.0  1  TatD_DNase  TatD related DNase
  ------ inclusion threshold ------
       0.14   11.9   0.0       0.21   11.3   0.0    1.2  1  DUF1415     Protein of unknown function (DUF1415)


Domain annotation for each model (and alignments):
>> TatD_DNase  TatD related DNase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.7   0.0   5.3e-48   4.8e-44       1     254 [.       4     240 ..       4     241 .. 0.90

  Alignments for each domain:
  == domain 1  score: 150.7 bits;  conditional E-value: 5.3e-48
                                    EEEEE-TTSCCCTTTHHHHHHHHHHTTEEEEEEE-SSGGGHHHHHHHHTT.TTTEEEEE---GGGGGCC.CCHHHHHHHH CS
                     TatD_DNase   1 iDaHcHldskefeedreeileraeeagvaavvvvgtsskdskavlelakkypnkvyavlGiHPnevdeasedlleelkel 80 
                                    +D H+Hl +  f     e +e++  +g   +v v  + ++s +vlel  +yp++v a++GiHP+++++  ed  +el+ +
  gi|119719117|ref|YP_919612.1|   4 VDVHIHLAE--F---TREKIEEFVSRGYI-LVGVAEDYETSLKVLELRDSYPENVKACVGIHPWSLRN-LEDYTRELELV 76 
                                    79******9..7...77777888765554.446777788999************************95.68888888777 PP

                                    HHCCCTSEEEEEEEEEET-CCCCCGHHHHHHHHHHHHHHHHHTTEEEEEEEES-HHHHHHHHHHCGGCCSEEEETT--S- CS
                     TatD_DNase  81 anvkhskvvaiGeiGLDyysreestkeaqeevFeeqlrlAkelklplviHlrkaeedlleilkeaaeakakvvlHsfsgs 160
                                     +   +++ ++Ge+GLD+ +  ++t ++q +vF+e    A e + pl +H+  a++++le+l e+++ k kvvlH+++g 
  gi|119719117|ref|YP_919612.1|  77 -SQLLPDADCVGEVGLDK-KFVPETFHQQLAVFRELAGRAVERGVPLNVHSAGAWREVLEVLGELGA-K-KVVLHWWTGP 152
                                    .334566667********.55569****************************************965.5.7********* PP

                                    HHHHHHHHHTTEEEEE-GGGGTTTTHHHHHHHHHS-GGGEEE---TTSSEECCCTTSE--GGGHHHHHHHHHHHHTS-HH CS
                     TatD_DNase 161 aeeakkflklgyyislsglltfknakelrelvkavpldrlLiETDaPyltpkpyrgkrnepanvayvveklaelkaltle 240
                                     + + +++ +gy++s++++l    +++ r ++++ pld lL+E+D Py       g +  p  +++ ++ +a++k+l+++
  gi|119719117|ref|YP_919612.1| 153 LNLLLELSRRGYFVSVNAALKV--QEKSRVIAREAPLDALLTESDGPYEYR----GLSLSPSLIPEALQIIAQIKGLAVD 226
                                    ******************9999..77999999***************9877....9************************ PP

                                    HHHHHHHHHHHHHH CS
                     TatD_DNase 241 elaeitaeNakrlf 254
                                    el+++++ N+ r+f
  gi|119719117|ref|YP_919612.1| 227 ELERAIYRNFTRVF 240
                                    ************99 PP

>> DUF1415  Protein of unknown function (DUF1415)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   2.3e-05      0.21      27     102 ..      13      90 ..      10     105 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.3e-05
                        DUF1415  27 vekkqiryvvseaekeeklleelleelell..eeekeeeieTtLlilpevledfedyldlldlaealleelelegvlq 102
                                    +++++i+  vs+      ++e++++ l++l  +++ +e+++  + i+p  l+++edy++ l+l+ +ll + ++ g++ 
  gi|119719117|ref|YP_919612.1|  13 FTREKIEEFVSRGYILVGVAEDYETSLKVLelRDSYPENVKACVGIHPWSLRNLEDYTRELELVSQLLPDADCVGEVG 90 
                                    5677888888888888999999999999882245667999****************************9999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1758.82
//
Query:       gi|119719118|ref|YP_919613.1|  [L=290]
Description: inositol-phosphate phosphatase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.6e-34  118.5   0.0    4.2e-34  118.3   0.0    1.0  1  Inositol_P  Inositol monophosphatase family
    0.00028   20.4   0.0    0.00047   19.7   0.0    1.3  1  FBPase      Fructose-1-6-bisphosphatase, N-terminal domain


Domain annotation for each model (and alignments):
>> Inositol_P  Inositol monophosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.3   0.0   4.7e-38   4.2e-34       3     268 ..       3     272 ..       1     275 [. 0.79

  Alignments for each domain:
  == domain 1  score: 118.3 bits;  conditional E-value: 4.7e-38
                                    HHHHHHHHHHHHHHHHHHHHHTTTSEEEESTTTCCHHHHHHHHHHHHHHHHHHHHHHHHSTTSEEEHHCHHHHCCCT.SS CS
                     Inositol_P   3 eevtkaavelaakagevlreefsenelvieekskegeedlvtaadeaveelilealaekfpshkilgeetlakgekselt 82 
                                    +e++++  ++ + a+e+  ++++ + + ++e++  +  d+  + d  +e+  +e l++++ + ++++ee ++k     ++
  gi|119719118|ref|YP_919613.1|   3 REILDVVRQASKVAAEAAIKALE-EGVGAREEGRGSGGDISLRGDILAERSAIEYLEKRIGDFSVVSEEIGEKTY---GK 78 
                                    56777778888888888888887.66666666667999**********************************999...77 PP

                                    SSSEEEEEEEEETHHHHHHT-SG-EEEEEEEE...TTEEEEEEEEETTTTEEECEETTTEEEETCEEEEECTTSEGGGTE CS
                     Inositol_P  83 edgltwivDPiDGTknFvrgipqvaVsigllv...egkpvlGviaqPllgqlysaakgkGaflngeklplsrappiseal 159
                                      g+ +i+DPiDG +n+ rg+p +aVs++ ++    + +++G++++Pllg  + a +g Gaflng++l++  ++  ++a+
  gi|119719118|ref|YP_919613.1|  79 GGGYRFIIDPIDGSRNYKRGTPFFAVSVAAAEgetLEDVIAGAVYAPLLGMEFYALAGGGAFLNGRRLRVPPGG-DTGAV 157
                                    77899***************************76667799*************************999999999.23333 PP

                                    EEEEESSSSSSHHHHCHHHHHHHCCCCCH....EEEBESSHHHHHHHHHHTSTSEEEEEC..EBHHHHHHHHHHHHHTTE CS
                     Inositol_P 160 lvtlfavssrkdtseasllekvesavsae....gvrsvgssalklaavaeGkadaylefg.rekkWDhAAGeaileeaGG 234
                                      +   v + ++t++ +++  + +a++       vr++gs+ l++ +va+G +day++++ ++   D+AA+ ++ +eaG+
  gi|119719118|ref|YP_919613.1| 158 EGK---VVAISSTPK-AFFLPYVFALNLSlrgaVVRMLGSASLEVSMVASGGVDAYIDAWgTMRVVDVAAATLVAREAGA 233
                                    323...333334444.3333344444444455579************************99******************8 PP

                                    EEEESSSC....SSSTTSS..EEEEESCHHHHHHHHHHHC CS
                     Inositol_P 235 vvtdakge....grlllar..giiaanqkelaellaaave 268
                                     v+    +    +r  l+    i++a++k lae +aa  e
  gi|119719118|ref|YP_919613.1| 234 YVVLGG-RlgtpPRISLDErlYILVASSKILAEHVAAIYE 272
                                    776433.335775555443225666667777777776655 PP

>> FBPase  Fructose-1-6-bisphosphatase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   5.2e-08   0.00047      24     116 ..       5      94 ..       2     105 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 5.2e-08
                         FBPase  24 llsalklalkiisskvrkaelvnllGlagaeNvtGdeqkklDvladeiliealkaseevkvlvSEEeeelivlerekegk 103
                                    +l  +++a k+ +++  ka    +      + + Gd   + D+la+   ie l+++     +vSEE  e +     k g+
  gi|119719118|ref|YP_919613.1|   5 ILDVVRQASKVAAEAAIKALEEGVGAREEGRGSGGDISLRGDILAERSAIEYLEKRIGDFSVVSEEIGEKTYG---KGGG 81 
                                    67777888888888877775444444556788999*********************9999*******998776...99** PP

                         FBPase 104 yvvafDPlDGSSn 116
                                    y  ++DP+DGS n
  gi|119719118|ref|YP_919613.1|  82 YRFIIDPIDGSRN 94 
                                    ***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2051.25
//
Query:       gi|119719119|ref|YP_919614.1|  [L=168]
Description: phosphodiesterase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      5e-30  104.9   0.1    5.9e-30  104.6   0.1    1.0  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    2.6e-08   34.6   0.1    6.5e-05   23.5   0.0    2.4  2  Metallophos    Calcineurin-like phosphoesterase
    8.9e-08   31.8   0.3    1.9e-05   24.1   0.0    2.1  2  Metallophos_3  Metallophosphoesterase, calcineurin superfamil


Domain annotation for each model (and alignments):
>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.6   0.1   9.8e-34   5.9e-30       2     163 ..       3     159 ..       2     161 .. 0.85

  Alignments for each domain:
  == domain 1  score: 104.6 bits;  conditional E-value: 9.8e-34
                  Metallophos_2   2 klaiiSDlHsnldaleavlealkevgvdaiihaGDleeeepevleellelapvlaVrGNnDeevveedvlreaaelgtdl 81 
                                    ++a++SD+H++l+a++ +++ lk+++v+a+ihaGD+  ++p +l+ +   ++++aV+GNnD    e+ +l++ a+  +++
  gi|119719119|ref|YP_919614.1|   3 RVAVVSDSHDSLEAIRLFVNSLKNENVEAVIHAGDI--ISPFALRMFSG-YRLYAVFGNND---GEKLLLKKTADEIGAV 76 
                                    699*********************************..***77777766.7**********...5666666666666666 PP

                  Metallophos_2  82 peeaelel..agekvlliHgdpl.gvkdalaellkeaeegsd.vvvcGHtHvpevekeggvlvvnPGsvgeprdgdpety 157
                                     +e+ + +  + ++++++Hg +   v+ +la++l +  +g++ +vv+GHtH+  ve++g+ lvvnPG +++   +++ t+
  gi|119719119|ref|YP_919614.1|  77 LSEQPMLVrvGSFDIAVLHGVDGlDVSRRLARALAK--SGEFrLVVYGHTHRVDVERIGDALVVNPGTLSGYLAEKR-TF 153
                                    55555554349999******9768999999999999..88888****************************966655.** PP

                  Metallophos_2 158 aildtd 163
                                    ai+d++
  gi|119719119|ref|YP_919614.1| 154 AIVDLE 159
                                    ****97 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   1.1e-08   6.5e-05       2      75 ..       3      60 ..       2      82 .. 0.77
   2 !    8.6   0.0    0.0004       2.4     179     203 ..     102     126 ..      67     127 .. 0.72

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.1e-08
                                   EEEEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHHTSEEEEEC-TTS CS
                    Metallophos  2 rilvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvkypipvylllGNHe 75
                                   r++v++D H      +l++++ +++ l++e ++ +v++aGD++         l++++       ++y++ GN +
  gi|119719119|ref|YP_919614.1|  3 RVAVVSDSH-----DSLEAIRLFVNSLKNE-NVEAVIHAGDIISPF-----ALRMFSGY-----RLYAVFGNND 60
                                   8********.....************9888.**********77765.....44442222.....4477777777 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0004
                                    CCHHHHHHHHHHTTESEEEEESSSS CS
                    Metallophos 179 fgdealedllkkygvdlvisGHtHv 203
                                     +++ ++ l k ++  lv++GHtH+
  gi|119719119|ref|YP_919614.1| 102 VSRRLARALAKSGEFRLVVYGHTHR 126
                                    45556667799999**********6 PP

>> Metallophos_3  Metallophosphoesterase, calcineurin superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   0.0     0.001       6.1       7      47 ..       3      43 ..       1      51 [. 0.91
   2 !   24.1   0.0   3.2e-09   1.9e-05     204     253 ..     109     164 ..      83     168 .] 0.81

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.001
                                   EEEEEE--TT-GGGHHHHHHHHHHH--SEEEEES-----HH CS
                  Metallophos_3  7 kvlaisdlkgevellerlveviedkdpDllvlvGdlvkaea 47
                                   +v  +sd +++ e +   v+ +++ ++++++  Gd++++ a
  gi|119719119|ref|YP_919614.1|  3 RVAVVSDSHDSLEAIRLFVNSLKNENVEAVIHAGDIISPFA 43
                                   78889999****************************99866 PP

  == domain 2  score: 24.1 bits;  conditional E-value: 3.2e-09
                                    HHHHHH--SEEEE-SS--EE.EEETTEEEEE--BG.....GGTEEEEEETTTTEEE CS
                  Metallophos_3 204 elvktlnPevvvvghavkeh.eelgktlvvnPGal.....eeGdfavvdleekkve 253
                                     l k+ + ++vv gh+++   e +g++lvvnPG l     e+  fa+vdle+ + e
  gi|119719119|ref|YP_919614.1| 109 ALAKSGEFRLVVYGHTHRVDvERIGDALVVNPGTLsgylaEKRTFAIVDLEKLEAE 164
                                    57899999*********9999************98333333567******987766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1130.10
//
Query:       gi|119719120|ref|YP_919615.1|  [L=125]
Description: zinc finger SWIM domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00072   19.2   0.3     0.0014   18.2   0.3    1.4  1  SWIM      SWIM zinc finger


Domain annotation for each model (and alignments):
>> SWIM  SWIM zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.3   7.9e-08    0.0014      17      36 ..      76      94 ..      76      97 .. 0.95

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 7.9e-08
                           SWIM 17 CsCpefqkngipCkHalAvl 36
                                   C+C+ f+  +  C H++Av+
  gi|119719120|ref|YP_919615.1| 76 CTCKGFE-EKGVCSHVIAVA 94
                                   *******.***********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       684  (0.0381505); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 950.30
//
Query:       gi|119719121|ref|YP_919616.1|  [L=363]
Description: hypothetical protein Tpen_0203 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-41  142.9  36.9    1.8e-41  142.6  36.9    1.1  1  LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region
  ------ inclusion threshold ------
        2.9    8.0   4.6        6.2    6.9   0.1    2.9  3  LRR19-TM         Leucine-rich repeat family 19 TM domain


Domain annotation for each model (and alignments):
>> LPG_synthase_TM  Lysylphosphatidylglycerol synthase TM region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.6  36.9   2.1e-45   1.8e-41       1     300 [.      10     318 ..      10     319 .. 0.91

  Alignments for each domain:
  == domain 1  score: 142.6 bits;  conditional E-value: 2.1e-45
                LPG_synthase_TM   1 illglalsalllalllrgvdlaalaaalrsldpwwlllalllallsvllralrWrlllrslgarislrrllrayliglfv 80 
                                    ill +++++l+++++l+g+d+ ++++alr++d w +l+++++ l +++ +a++++ll+r+ ++ is++ +l  ++++++v
  gi|119719121|ref|YP_919616.1|  10 ILLEVLVVLLVFVYTLYGFDVVSFIEALRNVDAWDILPIVVFELAYYFSHAAAFWLLCRK-RFSISMWEALGGSMLAWLV 88 
                                    689999999999999**************************9999999999999999998.******************* PP

                LPG_synthase_TM  81 nnvtPgalg.Gevvrayllkrkegvslskalasvvverlldllalvllgllallllggllaegaa.......vllllala 152
                                     +++Pga++ G+++ra++lk k++ + + +  +++ ++l+++ ++v++++ +ll++  l  ++         v+++l+++
  gi|119719121|ref|YP_919616.1|  89 DILLPGAFVeGDIARAIFLKTKSDWPSAVS-YTIFFRFLINVTMVVFIVFTSLLAINLLKFYEEYlvlylgiVVATLLAS 167
                                    *************************99885.7788899999999999999999999999998888755444333333333 PP

                LPG_synthase_TM 153 llllavla.............lllllllrrrlarlarvlkrlarllarfarklasakrklvlasprrlllafllslliwl 219
                                    l      +             ++++l+++++ +rl ++ k l  +l+ +a+ ++ +++ + ++    l+ a+++ +l+w+
  gi|119719121|ref|YP_919616.1| 168 L------LlvlvltkpllvknVAVFLARKAKVKRLEKFEKDLENFLSLVAEASRDFNF-RNIH----LWGAVAFLFLQWV 236
                                    3......24555669999********************************99998875.8888....************* PP

                LPG_synthase_TM 220 lealtlylllralgvdvslalll.lillaltlvgalpplPgGlGvrEaalalllallGvsaaealaaallyrlitlylll 298
                                    + +lt ++ lra+g++v+lal+   +++++++ +a   +P  +G+++aal +l+ llGv+ + alaa+++ r +t++++l
  gi|119719121|ref|YP_919616.1| 237 SGILTPFFSLRAVGANVNLALIGpGYTILTLYSLASIGIPFMVGSIDAALLSLYLLLGVPREKALAATIIGRSVTILTSL 316
                                    ***********************99999999999999***************************************9988 PP

                LPG_synthase_TM 299 ll 300
                                    l+
  gi|119719121|ref|YP_919616.1| 317 LV 318
                                    86 PP

>> LRR19-TM  Leucine-rich repeat family 19 TM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.3      0.17   1.5e+03      19      33 ..     129     143 ..     114     153 .. 0.64
   2 ?    6.9   0.1   0.00069       6.2      18      65 ..     156     203 ..     147     216 .. 0.84
   3 ?    1.3   0.0     0.039   3.5e+02      24      63 ..     310     350 ..     300     362 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.17
                       LRR19-TM  19 vgvvvlalvtsllil 33 
                                    v++vv +++tsll +
  gi|119719121|ref|YP_919616.1| 129 VTMVVFIVFTSLLAI 143
                                    455666666777644 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.00069
                       LRR19-TM  18 lvgvvvlalvtsllillaikckllykfllsYrHrrLeeseaetyeegl 65 
                                     +g+vv  l+ sll++l++  +ll k+++ +  r+ + ++ e+ e++l
  gi|119719121|ref|YP_919616.1| 156 YLGIVVATLLASLLLVLVLTKPLLVKNVAVFLARKAKVKRLEKFEKDL 203
                                    5799***********************999988888888877777765 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.039
                       LRR19-TM  24 lalvtsllillaikckllykfllsYrHrrLeese.aetyee 63 
                                    + ++tsll++  i   + +k++ s +   L+es     +e 
  gi|119719121|ref|YP_919616.1| 310 VTILTSLLVIYPIGMFFAKKVFSSRNISVLKESIkRAAAEY 350
                                    56899********9999999999999999999763333344 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1042  (0.0581181); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2302.99
//
Query:       gi|119719122|ref|YP_919617.1|  [L=435]
Description: amine oxidase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.2e-14   51.7   0.3    3.4e-12   46.4   0.3    2.1  1  Amino_oxidase  Flavin containing amine oxidoreductase
    2.4e-13   50.1   0.1    5.6e-13   48.9   0.1    1.6  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    1.5e-06   27.6   0.5    2.3e-06   27.0   0.5    1.2  1  FAD_binding_2  FAD binding domain
      2e-06   27.6   1.8    4.4e-06   26.5   1.0    2.2  2  DAO            FAD dependent oxidoreductase
    2.5e-06   26.9   0.0    9.9e-06   25.0   0.0    1.9  2  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    8.2e-06   25.4   0.0    1.1e-05   25.0   0.0    1.2  1  FAD_oxidored   FAD dependent oxidoreductase
    1.2e-05   25.8   1.6    4.4e-05   24.0   0.4    2.4  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
     0.0014   17.8   0.3     0.0023   17.1   0.3    1.3  1  GIDA           Glucose inhibited division protein A
     0.0016   17.2   0.0     0.0021   16.9   0.0    1.1  1  HI0933_like    HI0933-like protein
     0.0022   17.3   0.0     0.0035   16.7   0.0    1.3  1  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
  ------ inclusion threshold ------
      0.019   14.0   0.2      0.054   12.5   0.1    1.7  2  Lycopene_cycl  Lycopene cyclase protein
      0.021   14.1   0.1      0.035   13.3   0.1    1.3  1  FAD_binding_3  FAD binding domain
       0.11   11.8   0.1       0.19   10.9   0.1    1.3  1  Thi4           Thi4 family
       0.16   11.2   0.1       0.39    9.9   0.0    1.5  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
        0.2   11.5   0.1       0.31   10.9   0.1    1.2  1  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d


Domain annotation for each model (and alignments):
>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.4   0.3   2.9e-15   3.4e-12       1     370 [.      13     357 ..      13     409 .. 0.66

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 2.9e-15
                                    HHHHHHHHHHHHTTEEEEEEESSSSSBTTS-EEEETTEEEES.S--EEETTTHHHHHHHHHTTCCCCEEEESCCGCEEEE CS
                  Amino_oxidase   1 laGLaaArqLlsaGfdVtvlEardrvGGRirtvrsdGyliel.Gamwftgagnpllellkelgledslslpdpgapkrvl 79 
                                    laGL+ A++ ++ G++Vt++E +  +GG +r+++ +Gy++++ G+++++ ++++  ++l +  + +  ++++    ++ +
  gi|119719122|ref|YP_919617.1|  13 LAGLSFAYEATRLGHSVTLVEKEAEAGGLLRSEEVNGYVFDTgGSHVIFSKYPERVKFLTR--ILNGNIVRNRR--DARI 88 
                                    79****************************************6678899999999999999..44444434433..4445 PP

                                    ETTEECCTTEECHH.HHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCHHHHHHHHHHHHHHHH CS
                  Amino_oxidase  80 skggrefpgdlspv.paewealleqgalsaellsleeklrlgleallqktldeldldskslaesleelgrrepgdvevwd 158
                                    +++g+ ++ +++   +a++++               + l+  le+ + + +    +  ++++e+l ++++         +
  gi|119719122|ref|YP_919617.1|  89 FYNGTLVKYPFENGlYALPAEKRY------------KALKDILERYI-EYRCGGSRSVENFEEWLYATFGETIAS----E 151
                                    556666644444443333222222............34444444444.333334444444455544444444444....3 PP

                                    HHHHHHHHHHHHHHHHCHTSTTTTCBHHHHTCCCCHHHHHTSCCCEE...................TTHTHHHHHHHHH. CS
                  Amino_oxidase 159 rliepelfaklefasglfagdpselsaklalpllwelegfggslllp...................rgGlsqlpealae. 218
                                    +l+         ++ +l+ +  ++ + +l++  ++  +   +++++                     gG+++l++a+ + 
  gi|119719122|ref|YP_919617.1| 152 YLVP--------YNRKLWKR--DLKQISLDWVGNRVPQPPLDDVIRSavgiptegylhqlffyyprSGGIQSLADAFKAr 221
                                    3333........55555555..3355666666666666666666666666666666666666666669***********8 PP

                                    ..TTTTEEEETSEEEEEEEEETTCEEEEETTSTEEEESEEEE-S-HHHHHSSEEESCCSHHHHHHHHHSEEEEEEEEEEE CS
                  Amino_oxidase 219 ..elrgldirlntrVkeikregdgvtvtledgevveaDaVvvTvplgvlkailfsPplpdekaeairnlgfgsvnkvile 296
                                       ++  ++ l+++  +++  +++v +  +dg+ v++D++v+T+pl+ l            +     nl++ s+++v + 
  gi|119719122|ref|YP_919617.1| 222 veGSPLSSLVLGKEAVKVDPYEGEVVL--SDGSAVRGDRIVSTIPLPELY----------RALGLRLNLDYNSLVVVGVG 289
                                    8888888************96666666..6*******************9..........55555557888888888888 PP

                                    ESSGGSGCSTSECECECCCEEETTTEEEEECC.ECCCSTTTEEEEEEEEECHHHHHHHTTS-HHHHHHHHHHHHH CS
                  Amino_oxidase 297 fdrkfwednalgqgvlvseltttlgeafissd.fpsrappgkglvllvyvggdaaneleslsdeelvqavlrdLr 370
                                    ++ +  +   +     +++   + ++ +i s+  p+ +p g+   l++ +  + ++ +   ++e +v+a+l+ L+
  gi|119719122|ref|YP_919617.1| 290 VKDARLPRVHW---IYFPNEDIVFHRLAILSNySPYMSPKGSAT-LVAEITLRPGETF---DEEKVVNATLDGLE 357
                                    88776444333...345555555555555555244444444444.7777775555555...77777777777666 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.9   0.1   4.6e-16   5.6e-13       1      64 [.       8      70 ..       8      74 .. 0.85

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 4.6e-16
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECETTCEECTS.---EEETTHHHHCHHH CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasyevpgvrvdyg.ahifhgsgyypnvrrl 64
                                   ++GaGl+Gl++Ay++++ g++v+l+ek    GG ++s+ev+g+++d+g  h++++  +yp+  ++
  gi|119719122|ref|YP_919617.1|  8 VLGAGLAGLSFAYEATRLGHSVTLVEKEAEAGGLLRSEEVNGYVFDTGgSHVIFS--KYPERVKF 70
                                   89********************************************872455555..46665555 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.5   1.9e-09   2.3e-06       2      36 ..       6      40 ..       5      45 .. 0.94

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 1.9e-09
                                   EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS CS
                  FAD_binding_2  2 viViGsGlAGLaAAleaaeaGlkvavvekeqefgg 36
                                   ++V G+GlAGL+ A+ea++ G++v++veke e gg
  gi|119719122|ref|YP_919617.1|  6 IVVLGAGLAGLSFAYEATRLGHSVTLVEKEAEAGG 40
                                   79*****************************9887 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   1.0   3.7e-09   4.4e-06       2      33 ..       6      39 ..       5     199 .. 0.93
   2 ?   -2.5   0.0       2.5     3e+03     187     227 ..     339     378 ..     325     395 .. 0.61

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 3.7e-09
                                   EEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                            DAO  2 vviiGGGiiGlstAyeLarrg..Vtllekgdiag 33
                                   +v+ G+G +Gls Aye++r g  Vtl+ek+ +ag
  gi|119719122|ref|YP_919617.1|  6 IVVLGAGLAGLSFAYEATRLGhsVTLVEKEAEAG 39
                                   9****************99999********9888 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.5
                                    TEEE.EEEEEEEE--..GGGHH.HHHTTCTTTSEEEEEEEEEEEE CS
                            DAO 187 pgen.daadavVnaa..Gawsd.llgllkeldlpispvrgqvlvl 227
                                    pge+ d+ ++vVna+  G+ +  ll    + +  ++ vr+ ++++
  gi|119719122|ref|YP_919617.1| 339 PGETfDE-EKVVNATldGLEAAgLL----RGRGSVEVVRAWYWRY 378
                                    4666566.77999886666554333....1123455566655555 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   8.3e-09   9.9e-06       2      72 ..       5      73 ..       4     126 .. 0.78
   2 ?   -1.0   0.0      0.66   7.9e+02     203     233 ..     233     261 ..     227     290 .. 0.60

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 8.3e-09
                                   SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHHHHHHCHHHHCCCCHC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeiasevvkklnqgielllg 72
                                   ++vv+G+G AGl++a ++ + g+ vtlv  e++   gg l s+++ g+  d+   +  ++k+ + +++l++
  gi|119719122|ref|YP_919617.1|  5 SIVVLGAGLAGLSFAYEATRLGHSVTLV--EKEAEAGGLLRSEEVNGYVFDTGGSHVIFSKYPERVKFLTR 73
                                   69**************************..56666788888888888888888777555566666666555 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.66
                                    SCEEEEEEETTEEEEEEETTSCEEEESEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 203 gtsvkeidgngeklevvledgeeidadlvvv 233
                                    g++++++d+ +   evvl+dg+ +  d +v 
  gi|119719122|ref|YP_919617.1| 233 GKEAVKVDPYEG--EVVLSDGSAVRGDRIVS 261
                                    444444554444..55666666655555554 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   9.1e-09   1.1e-05       2      43 ..       6      47 ..       5      88 .. 0.90

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 9.1e-09
                   FAD_oxidored  2 vvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglv 43
                                   +vV G+g+aG+  A+ A r G +v Lve++   GGll s+ v
  gi|119719122|ref|YP_919617.1|  6 IVVLGAGLAGLSFAYEATRLGHSVTLVEKEAEAGGLLRSEEV 47
                                   8***********************************987765 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.4   3.7e-08   4.4e-05       1      33 [.       5      37 ..       5      49 .. 0.91
   2 ?   -0.4   0.0       1.4   1.7e+03      11      29 ..     355     372 ..     353     409 .. 0.58

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 3.7e-08
                                   EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSS CS
                      Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversdk 33
                                   ++vv+G+G+ gl +A ++++lg++Vt+ve + +
  gi|119719122|ref|YP_919617.1|  5 SIVVLGAGLAGLSFAYEATRLGHSVTLVEKEAE 37
                                   69***************************9876 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.4
                                    HHHHHHHHHHTTSEEEEEE CS
                      Pyr_redox  11 glElAgalaelgkkVtvve 29 
                                    glE+Ag l+  g +V vv 
  gi|119719122|ref|YP_919617.1| 355 GLEAAGLLRGRG-SVEVVR 372
                                    778888888877.555554 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.3   1.9e-06    0.0023       2      31 ..       6      35 ..       5      49 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.9e-06
                                   EEEE-SSHHHHHHHHHHHHTT--EEEEES- CS
                           GIDA  2 viViGgGhAGceAAlaaarlGakvlLithk 31
                                   ++V+G+G+AG+  A++a rlG++v+L+ ++
  gi|119719122|ref|YP_919617.1|  6 IVVLGAGLAGLSFAYEATRLGHSVTLVEKE 35
                                   89************************9554 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.7e-06    0.0021       2      36 ..       5      39 ..       4      76 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.7e-06
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                    HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklg 36
                                   +++v+G+G AGl  A +a + g++V+l+ek+ ++g
  gi|119719122|ref|YP_919617.1|  5 SIVVLGAGLAGLSFAYEATRLGHSVTLVEKEAEAG 39
                                   689***************************99988 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   2.9e-06    0.0035      30      64 ..       5      39 ..       1      81 [. 0.86

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.9e-06
                                   EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHH CS
                    AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrparl 64
                                    ++v+G+G aGl+ +  a++lg +Vt++++++++ 
  gi|119719122|ref|YP_919617.1|  5 SIVVLGAGLAGLSFAYEATRLGHSVTLVEKEAEAG 39
                                   69**************************9998765 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   4.5e-05     0.054       2      33 ..       6      35 ..       5      45 .. 0.91
   2 ?   -1.9   0.0       1.1   1.3e+03     112     148 ..     237     272 ..     233     286 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.5e-05
                  Lycopene_cycl  2 vvviGaGpAglslAarlteakpglkvvlieas 33
                                   +vv GaG+Agls A +    + g +v+l+e  
  gi|119719122|ref|YP_919617.1|  6 IVVLGAGLAGLSFAYEA--TRLGHSVTLVEKE 35
                                   89***************..99********865 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.1
                  Lycopene_cycl 112 veeeeageslvvleggrkirarlvvdarglaslkkar 148
                                    v+ ++  e  vvl++g  +r+  +v   +l++l +a+
  gi|119719122|ref|YP_919617.1| 237 VKVDPY-EGEVVLSDGSAVRGDRIVSTIPLPELYRAL 272
                                    555555.7789**********9999999998877654 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1     3e-05     0.035       4      43 ..       6      45 ..       3      54 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3e-05
                                   EEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS-- CS
                  FAD_binding_3  4 VlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlprad 43
                                   +++ GaG+aGl+ a + ++ G +v+lvek +++  l r++
  gi|119719122|ref|YP_919617.1|  6 IVVLGAGLAGLSFAYEATRLGHSVTLVEKEAEAGGLLRSE 45
                                   6799**************************9987777766 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00016      0.19      19      55 ..       5      40 ..       2      52 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00016
                                   EEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--T CS
                           Thi4 19 DvvivGaGssGLtaayylakkpdlkvailersvspGG 55
                                    +v+ GaG +GL+ ay  ++  +  v+++e++   GG
  gi|119719122|ref|YP_919617.1|  5 SIVVLGAGLAGLSFAYEATRL-GHSVTLVEKEAEAGG 40
                                   599**************9988.99*******998888 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00033      0.39       1      31 [.       7      36 ..       6      46 .. 0.87
   2 ?   -2.2   0.0       1.6   1.9e+03      26      49 ..      51      74 ..      38      81 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00033
                    Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgn 31
                                   ++ GaG aGl++a+e+ ++g  +++ +Ek++
  gi|119719122|ref|YP_919617.1|  7 VVLGAGLAGLSFAYEATRLGH-SVTLVEKEA 36
                                   688*****************9.799***983 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.6
                    Pyr_redox_3 26 ilEkgnignsiyrypkemtfisps 49
                                   + + g     +++yp++ +f++  
  gi|119719122|ref|YP_919617.1| 51 VFDTGGSHVIFSKYPERVKFLTRI 74
                                   666666666899********9965 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00026      0.31       2      34 ..       6      38 ..       5      46 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00026
                                   EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHH CS
                        3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseea 34
                                   + v+GaG+ G + a+ + + g++V+lv+ ++ea
  gi|119719122|ref|YP_919617.1|  6 IVVLGAGLAGLSFAYEATRLGHSVTLVEKEAEA 38
                                   78*************************998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (435 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 2990.74
//
Query:       gi|119719123|ref|YP_919618.1|  [L=339]
Description: glycosyl transferase family protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.8e-22   78.6   0.0    3.3e-21   75.8   0.0    2.2  2  Glycos_transf_2  Glycosyl transferase family 2
    1.1e-16   61.4   0.0    1.5e-16   61.0   0.0    1.1  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    1.1e-05   25.1   0.8    2.6e-05   23.8   0.8    1.6  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
    0.00029   20.8   0.3    0.00052   20.0   0.3    1.4  1  Glyco_trans_2_3  Glycosyl transferase family group 2
     0.0045   16.5   0.0     0.0093   15.5   0.0    1.6  1  Glyco_transf_21  Glycosyl transferase family 21
  ------ inclusion threshold ------
      0.023   15.2   0.1          3    8.4   0.0    2.3  2  Glyco_tranf_2_4  Glycosyl transferase family 2
      0.024   14.3   0.0      0.056   13.1   0.0    1.6  2  Glyco_tranf_2_5  Glycosyltransferase like family
      0.041   13.8   0.5      0.078   12.9   0.5    1.4  1  DUF3487          Protein of unknown function (DUF3487)
       0.12   12.1   0.0       0.19   11.4   0.0    1.3  1  AAA_24           AAA domain


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.8   0.0   1.7e-24   3.3e-21       1     164 [.       6     174 ..       6     180 .. 0.87
   2 ?   -0.1   0.0      0.36   7.1e+02      99     165 ..     268     336 ..     264     339 .] 0.77

  Alignments for each domain:
  == domain 1  score: 75.8 bits;  conditional E-value: 1.7e-24
                                    EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--S CS
                Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraatg 80 
                                    s+vi+ +   + l+++l+s+ +  +ypd+e+ivvD    D+ ++ l++   +++++++i+ + n G +g+ n g+ a++ 
  gi|119719123|ref|YP_919618.1|   6 SIVIVNFKGTEALKKCLRSVFET-EYPDYEVIVVDSLT-DNVEKALRDEFGSKENLKIIHFDSNIGASGSHNVGAMASDP 83 
                                    89********************9.**********9777.***************************************99 PP

                                    S..EEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SS.....EEEECCHCCCCHCCCCCCSTT CS
                Glycos_transf_2  81 d..yilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrv.....generlyfkerkrslkgnlsf 153
                                    +  y++flD D+e+++dwl++lve +e+ ++ + +++ + ++++++++ ++        ++ + + f+e+ ++++++l++
  gi|119719123|ref|YP_919618.1|  84 NskYLVFLDNDVEVEKDWLKRLVETAEESPRIGCVQAKVISKSNEGRMDHAGLAldltaTWLSTYGFREEIFQRPIELFV 163
                                    999*************************99988888888888888888888777****6666666666666666666666 PP

                                    CSTCCCEEEEH CS
                Glycos_transf_2 154 eigsaallrre 164
                                     ++ a l  re
  gi|119719123|ref|YP_919618.1| 164 ASSAALLTPRE 174
                                    66666665555 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.36
                                    HHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SS...EEEECCHCCCCHCCCCCCSTTCSTCCCEEEEHH CS
                Glycos_transf_2  99 klvealekdgadvvlgqrprifgetdeiernkrv...generlyfkerkrslkgnlsfeigsaallrrea 165
                                     l++++ +  a+ +l ++ + f+ ++ ++++k v   ++ +  yf+++ + +k+ l  ++ + all r++
  gi|119719123|ref|YP_919618.1| 268 ALAGRIRE-TAAYFLSSTSVVFSLPRLMWKRKLVslkRRVPDSYFEKKGFLRKDLLGTIYMTRALLIRSV 336
                                    56777777.7778999999999999999999999997777778888888877777777777777777765 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.0   0.0   7.6e-20   1.5e-16       1     215 [.       3     220 ..       3     238 .. 0.84

  Alignments for each domain:
  == domain 1  score: 61.0 bits;  conditional E-value: 7.6e-20
                Glyco_tranf_2_3   1 prdlavlVptfneedvlgevlesllaqeyprvevvvvv..desdaetlevaeelaaalp.dvrvrvvvnarnlgstgksr 77 
                                    p  +++++++f+ ++ l ++l+s+   eyp++ev+vv+  + + +++l+  +e    ++ ++ +++++ + n g  + s+
  gi|119719123|ref|YP_919618.1|   3 PK-VSIVIVNFKGTEALKKCLRSVFETEYPDYEVIVVDslTDNVEKALR--DE----FGsKENLKIIHFDSNIGA-SGSH 74 
                                    55.9*********************************988555555544..34....3335689*****999995.8889 PP

                Glyco_tranf_2_3  78 alnealravksdlvllvDdDtvvePdtlkrllqff.ltpkvgavgtpvfll.nrstl.....vsalgalefaerhlrfla 150
                                    ++  + +  +s++++++D D+ ve+d lkrl+ ++ ++p++g+v+++v ++ n+ ++        l+a+ +    +r+  
  gi|119719123|ref|YP_919618.1|  75 NVGAMASDPNSKYLVFLDNDVEVEKDWLKRLVETAeESPRIGCVQAKVISKsNEGRMdhaglALDLTATWLSTYGFREEI 154
                                    9999999999**************************************99757777766655333466677777888899 PP

                Glyco_tranf_2_3 151 arralgvltlnGsgslirrevlkelegldp.lflltdDyelglrlrragfrtayvpgaavrevfps 215
                                    ++r +     + + +l +re++   +g+d   f+  dD +++ r+r +g+ +    +a v++++  
  gi|119719123|ref|YP_919618.1| 155 FQRPIELFVASSAALLTPRELYFKVGGFDSsYFIYDDDTDYTWRVRLQGYISLLETRARVYHEDKI 220
                                    99999965557899************************************9999999999998664 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.8   1.3e-08   2.6e-05      23     244 ..      28     249 ..       5     258 .. 0.71

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1.3e-08
                Glyco_tranf_2_2  23 akyydeeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNrGa..skaesdlvlFlDaDcfissDkfe 100
                                    + y  ++ e+ivvd   ++++ + ++     + +  + +  d   + + ++N Ga  s  +s +++FlD D  +  D ++
  gi|119719123|ref|YP_919618.1|  28 TEY--PDYEVIVVDSL-TDNVEKALRDEFGSKENLKIIHF-DSNIGASGSHNVGAmaSDPNSKYLVFLDNDVEVEKDWLK 103
                                    444..88899999876.55556666665555555544566.6678999******733667899***************** PP

                Glyco_tranf_2_2 101 kilklitikklrenidaavvlpvvd.lnkedsevlkdvedltassrvledllaakstlvkffapssssilinrraflevG 179
                                    ++++ ++       ++a v+    +   + +   l  +        + e+++      ++ f+ ss  +l  r+ + +vG
  gi|119719123|ref|YP_919618.1| 104 RLVETAEESPRIGCVQAKVISKSNEgRMDHAGLALDLTATWLSTYGFREEIFQ---RPIELFVASSAALLTPRELYFKVG 180
                                    ****8887766677888776554441455555555555555556678888777...556788889999************ PP

                Glyco_tranf_2_2 180 GyDEr.frGhgaEDfdlllRlakaikslekmpvellykaraks.ls...nykGfrrflealakeaaalgl 244
                                    G+D + f+     D+   +Rl  +i  le  +  + ++++  s l+    y G+r+ l+++ k+  a  +
  gi|119719123|ref|YP_919618.1| 181 GFDSSyFIYDDDTDYTWRVRLQGYISLLETRA-RVYHEDKISSrLRfdkLYFGYRNRLQNIVKNMDAKNM 249
                                    ***98468888999***********9996554.4444554443144777789999999999887554444 PP

>> Glyco_trans_2_3  Glycosyl transferase family group 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.3   2.6e-07   0.00052       1     168 [.      87     268 ..      87     296 .. 0.63

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.6e-07
                Glyco_trans_2_3   1 iilllDaDtvlppdclreiaaela.spevaivqgpvlvm.nvanwleelaalf.faedhgkdilvrealgrvvpsv...G 74 
                                    + ++lD D  +  d l+++++  + sp+++ vq +v+   n +++ +   al  +a +    ++  e + r++ ++    
  gi|119719123|ref|YP_919618.1|  87 YLVFLDNDVEVEKDWLKRLVETAEeSPRIGCVQAKVISKsNEGRMDHAGLALDlTATWLSTYGFREEIFQRPIELFvasS 166
                                    5799*******************967***********9855544444444444255566666666668888766333335 PP

                Glyco_trans_2_3  75 sgaflrrsalqevggwdgdessvsEDfdmglrlqrkGyrvrfvpeslvkekspltlraalrQrkRwayGc.....elekl 149
                                    +  +++r++  +vgg+d++ +   +D+d   r + +Gy+  + + +  + ++++ +  +l +  + ++G+     +    
  gi|119719123|ref|YP_919618.1| 167 AALLTPRELYFKVGGFDSSYFIYDDDTDYTWRVRLQGYISLLETRA--RVYHEDKISSRL-RFDKLYFGYrnrlqN---- 239
                                    55566888889****************************9999877..666666666444.577888885322220.... PP

                Glyco_trans_2_3 150 il........lvrll..gylgsllwsalp 168
                                    i          v+ll   ylg l+++ l 
  gi|119719123|ref|YP_919618.1| 240 IVknmdaknmVVSLLvtLYLGYLVTVLLA 268
                                    11222222221211122222222222222 PP

>> Glyco_transf_21  Glycosyl transferase family 21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   4.7e-06    0.0093      29      75 ..      83     130 ..      73     223 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.7e-06
                Glyco_transf_21  29 akydllvisDsdvrvkpdyLeellaaled.pkvglVtslpvgsdakgl 75 
                                     + ++lv++D dv v++d L++l+++ e+ p++g+V++ ++    +g 
  gi|119719123|ref|YP_919618.1|  83 PNSKYLVFLDNDVEVEKDWLKRLVETAEEsPRIGCVQAKVISKSNEGR 130
                                    5789*********************99888******997775555543 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0    0.0015         3       7      81 ..      18      94 ..      15     101 .. 0.81
   2 ?    4.4   0.0     0.026        52      18      65 ..     181     237 ..     168     251 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0015
                Glyco_tranf_2_4  7 Lpeflahhlalgf.drilvydndstDgtrailke....lpevkllhvdksyederrqvellkallaryaeadwvlvvDaD 81
                                   L+++l+   +  + d+ +++ +  tD++ + l+      +++k++h+d+++   + + +   a++ +  ++++++++D D
  gi|119719123|ref|YP_919618.1| 18 LKKCLRSVFETEYpDYEVIVVDSLTDNVEKALRDefgsKENLKIIHFDSNIG--ASGSHNVGAMASD-PNSKYLVFLDND 94
                                   6666666666666577899999**********886665699*********97..5677777777766.6999*****998 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.026
                Glyco_tranf_2_4  18 gfdrilvydndstDgtrailke......lpevkllhvdksyederrq...vellkal 65 
                                    gfd  +++ +d+tD t+++  +        +++++h dk  ++ r+    + ++++l
  gi|119719123|ref|YP_919618.1| 181 GFDSSYFIYDDDTDYTWRVRLQgyisllETRARVYHEDKISSRLRFDklyFGYRNRL 237
                                    699999999999999988755546666446677888777665555442223455554 PP

>> Glyco_tranf_2_5  Glycosyltransferase like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0         3   6.1e+03       3      36 ..       9      39 ..       8      50 .. 0.68
   2 ?   13.1   0.0   2.8e-05     0.056      46      88 ..      75     118 ..      54     121 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3
                Glyco_tranf_2_5  3 ivcvnneelyeeclsylenlevpegyeveiiair 36
                                   iv  + +e +++cl+ + + e p+   +e+i ++
  gi|119719123|ref|YP_919618.1|  9 IVNFKGTEALKKCLRSVFETEYPD---YEVIVVD 39
                                   666777778888877777766665...6666654 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 2.8e-05
                Glyco_tranf_2_5  46 nkalsasd..akykvYlhqDvliinkdfikdlleiFkkdkkiGmi 88 
                                    n ++ asd   ky+v+l++Dv  ++kd++k+l+e  ++ ++iG +
  gi|119719123|ref|YP_919618.1|  75 NVGAMASDpnSKYLVFLDNDVE-VEKDWLKRLVETAEESPRIGCV 118
                                    444444432289*********9.699****************976 PP

>> DUF3487  Protein of unknown function (DUF3487)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.5   3.9e-05     0.078      14      88 ..     238     315 ..     234     337 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.9e-05
                        DUF3487  14 PvVfrGltadEllvlaglglvvglvlglllall...vgslaliptialllvllvvlvggkllarlKRgkPdtylyrrl 88 
                                      +++ + a+ ++v +++ l +g ++ +llal+    ++ a ++  + ++  l  l+ ++ l +lKR+ Pd+y++++ 
  gi|119719123|ref|YP_919618.1| 238 QNIVKNMDAKNMVVSLLVTLYLGYLVTVLLALAgriRETAAYFLSSTSVVFSLPRLMWKRKLVSLKRRVPDSYFEKKG 315
                                    56889999999***************99997764423334444555555556666788999*************9874 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   9.6e-05      0.19      53      82 ..      19      49 ..       4      66 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9.6e-05
                         AAA_24 53 ldevvel.aaeladyktlviDtideleelcl 82
                                   ++ + ++ ++e++dy+++v+D++++ +e +l
  gi|119719123|ref|YP_919618.1| 19 KKCLRSVfETEYPDYEVIVVDSLTDNVEKAL 49
                                   444444369**************99877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       786  (0.0438396); expected 358.6 (0.02)
Passed bias filter:                      665  (0.0370907); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 2341.14
//
Query:       gi|119719124|ref|YP_919619.1|  [L=142]
Description: single-stranded DNA-binding protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0013   18.6   0.1     0.0022   17.9   0.1    1.3  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
     0.0045   16.9   0.0       0.01   15.8   0.0    1.5  1  REPA_OB_2        Replication protein A OB domain


Domain annotation for each model (and alignments):
>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.1   2.5e-07    0.0022       7      67 ..      38      96 ..      36     116 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.5e-07
                                   EEEEEEEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEEEEEEECTTSSEE CS
                tRNA_anti-codon  7 vtsisdrsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvtGrvkrrpggele 67
                                   +ts++d+s+ +v+++ + D+tg   +++++ +  + + n   ++v  v G+v+ ++g+ l 
  gi|119719124|ref|YP_919619.1| 38 ITSRRDGSEHRVADVLVGDETGVALLTAWD-NEIDEFRNMVGETVSLVNGYVSLYQGK-LR 96
                                   89999*************************.999999999999************998.54 PP

>> REPA_OB_2  Replication protein A OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.1e-06      0.01      19      85 ..      29      94 ..      19     100 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.1e-06
                      REPA_OB_2 19 vksveevseitskstekelkkreltlvDesgasvevtlWgkeaekfesseepvvalkgvkvsdFggr 85
                                   v +v++ ++its+ ++ e +  ++ + De+g+++ +t W++e ++f++   + v l ++ vs ++g+
  gi|119719124|ref|YP_919619.1| 29 VLNVGDEKQITSRRDGSEHRVADVLVGDETGVAL-LTAWDNEIDEFRNMVGETVSLVNGYVSLYQGK 94
                                   5689999*********99999**********986.9*****************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 963.24
//
Query:       gi|119719125|ref|YP_919620.1|  [L=459]
Description: hydroxypyruvate reductase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-73  246.5   1.4    3.6e-73  245.9   1.4    1.3  1  DUF4147          Domain of unknown function (DUF4147)
    1.4e-38  131.5   1.5    2.6e-38  130.6   1.5    1.5  1  MOFRL            MOFRL family


Domain annotation for each model (and alignments):
>> DUF4147  Domain of unknown function (DUF4147)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  245.9   1.4     4e-77   3.6e-73       5     229 .]      21     258 ..      17     258 .. 0.92

  Alignments for each domain:
  == domain 1  score: 245.9 bits;  conditional E-value: 4e-77
                                    HHHHHHHTTSHHHHHHTTHHHH--.............-SEEEEEESTTHHHHHHHHH....HHHGEEEEEEETT---... CS
                        DUF4147   5 ifeaaveavdpeklvkralslkee......eldlskkkrvvvvgaGKAaaamaaalee...ealksgvvvvkkghae... 72 
                                    +  ++v+ +dp+k+v++ ++l+ +       +++  ++rv+vvgaGKA+ +ma  +e+   +++++gv++v+++  e   
  gi|119719125|ref|YP_919620.1|  21 LALEGVAVADPAKAVENYVRLEGDelvlrdGTRVGLRGRVIVVGAGKATGGMAVGIEKvlgDRISGGVISVPEDLVEsvs 100
                                    66789**************995554444444555577********************98888899******844443344 PP

                                    .--TT-EEEEE-SSS--HHHHHHHHHHHHHHSS--TT-EEEEEE-TTHHHHS--B-TT--HHHHHHHHHHHHHCT--HHH CS
                        DUF4147  73 .ekerievleaahplPdeesveaarkilelaeklkeddlvlvliSGGgSAllaaPaegitledkqaltkaLlasGasIqe 151
                                     + +ri+v+ a+hp  +++svea ++i++++++l+e+d+v++l SGGgSAl ++Paeg+ +e++ +l+ +L+++Ga+I e
  gi|119719125|ref|YP_919620.1| 101 kQLSRIQVVGATHPRASRKSVEAGERIVSTVRGLREEDTVIALFSGGGSALAELPAEGVDIEELGELSVKLMKAGADIVE 180
                                    48889*************************************************************************** PP

                                    HHHHHHTTBSSTTTHHHHHHTTSEEEEEEE--STT--TTTGGG-TTS-----HHHHHHHHHHTT---..-HHHHHHH. CS
                        DUF4147 152 lNtVRkhlsaikGGrLaraaaparvvsLilSDVvgddldvIASGPtvpdsstfadalailekykleeklpesvrelLe 229
                                    lNtVRkhls++kGG La++a+pa vv+L++SDVvgd++d+IASGPtvpd++t++da+a+++ky+le++lp+s+r++Le
  gi|119719125|ref|YP_919620.1| 181 LNTVRKHLSRFKGGWLAKHAYPAAVVALLISDVVGDRMDTIASGPTVPDPTTYQDAVAVIRKYRLEDSLPQSIRRILE 258
                                    ***************************************************************************996 PP

>> MOFRL  MOFRL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.6   1.5   2.9e-42   2.6e-38       2     109 .]     342     446 ..     341     446 .. 0.97

  Alignments for each domain:
  == domain 1  score: 130.6 bits;  conditional E-value: 2.9e-42
                                    EEEEEE--B----S-----HHHHHHHHHHH...HTTT-TTEEEEEEETTS--SSSS--EEEEETTHHHHHHHTT--HHHH CS
                          MOFRL   2 vllsgGEttvtvkgkGkGGrnqelalalalelkelegaeevvllsagtDGiDGptdaaGaivdaetleraeaagldakea 81 
                                    v+l+gGEttvtvkgkG GGrnqelal++a++lk   g ++v+l+s+g+DG DGptd+aGa+vd+ t++ra a+g++++e+
  gi|119719125|ref|YP_919620.1| 342 VILAGGETTVTVKGKGLGGRNQELALSAAIALK---GVDRVALVSIGSDGRDGPTDVAGAVVDGYTYQRALAKGVRPEEY 418
                                    89****************************555...559***************************************** PP

                                    HHTT-HHHHHHHTT-EE-----S----E CS
                          MOFRL  82 LanndsyeffeklgallktgpTgtNVnD 109
                                    L+nndsy+ff+ +g  +ktg TgtNVnD
  gi|119719125|ref|YP_919620.1| 419 LENNDSYNFFRVVGGHVKTGYTGTNVND 446
                                    ***************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 3366.39
//
Query:       gi|119719126|ref|YP_919621.1|  [L=345]
Description: ornithine cyclodeaminase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-95  318.6   0.1    4.1e-95  318.4   0.1    1.0  1  OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin famil
  ------ inclusion threshold ------
      0.085   13.4   0.0       0.17   12.5   0.0    1.5  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent


Domain annotation for each model (and alignments):
>> OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  318.4   0.1   4.6e-99   4.1e-95       8     314 ..      15     312 ..       8     316 .. 0.97

  Alignments for each domain:
  == domain 1  score: 318.4 bits;  conditional E-value: 4.6e-99
                                    HHHHHCCH-HCCCHHHHHHHHHHHHCC-CE----EEEEECCGTEEEEEEEEEETTTTEEEEEEEEEETTTCCCTSSSEEE CS
                OCD_Mu_crystall   8 aveveeelllddlakaveeafrrlasgkvkkpprvalevkdsrgelevmpaylagrellgvKlvnshpenkksglptvta 87 
                                      ev+ +++ld l++ +ee frr+ +  +k  prv  +     g++e+mpa++a    ++vK+vn+hp+n+ +gl+tv a
  gi|119719126|ref|YP_919621.1|  15 IREVGLNTFLDGLINRLEEVFRRWRE--LKVVPRVSFHYAS--GVMEAMPASDAR--WYSVKIVNGHPGNPLRGLQTVVA 88 
                                    5689999*******************..***********99..************..*********************** PP

                                    EEEEE-TTT--EEEEEE-HHHHHHHHHHHHHHHHHHHS-TT--EEEEE--SHHHHHHHHHHCCCS-.-SEEEEE-SSHHH CS
                OCD_Mu_crystall  88 lvvLndpetGvplalmdatlltalRTaAvsavaakyLarkdasvlaiiGaGvqaetqlealkavld.ikevriydrdeea 166
                                    ++vL+d+etG+p+++ datlltalRT+A+sa+a+kyLar+ ++ l+iiG G+q+e+ +  +++v++ +++v  yd+d++a
  gi|119719126|ref|YP_919621.1|  89 VGVLADVETGYPVMIADATLLTALRTGATSALATKYLARRGSENLGIIGTGAQSEFLVYSISRVANsVEKVFFYDIDPKA 168
                                    ****************************************************************999************* PP

                                    HHHHHHHCCS.CTT-EEECSCHHHHTTSSEEEE----SS..-SB-GGGS-TT-EEEE-S--STT--SB-HHHHHCCEEEE CS
                OCD_Mu_crystall 167 aekfaenlqefefevsackseeeavegadivvtvTaaka..pilkaewvkpGahinavgadapgkteLdddilkradifv 244
                                    +ekf +n+++ +fe + ++s++e++ + d++vt+T++k    ++ +ewv pG+hinavg+dapgkteLd++il+r++++v
  gi|119719126|ref|YP_919621.1| 169 MEKFEKNISRLGFELVRAGSPREVALNSDVLVTATTSKGkdRVVLNEWVRPGTHINAVGGDAPGKTELDPAILLRSKLVV 248
                                    *************************************98889************************************** PP

                                    SHHHHHHHCCCCHCHHHTTSSTCGGEEEEHHHHHCTSS-..-STTSEEEEE----HHHHHHHHHHHHHHH CS
                OCD_Mu_crystall 245 dseaqareeGeiqvaiekgvlaedakvaelgeviaGkkpGRtsdeeitlfdsvGlaveDvaaaklvyera 314
                                    + ++qa  eGe q       + +da+ ael+ev++G k+GR s+ee+t+fdsvG+aveD+a++++ y  a
  gi|119719126|ref|YP_919621.1| 249 ELLEQAIVEGETQS------VGRDAVYAELWEVVSGLKHGRSSEEEVTVFDSVGIAVEDLATLTYLYGLA 312
                                    **************......9********************************************99765 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.9e-05      0.17       2      69 ..     133     203 ..     132     215 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.9e-05
                                    EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC....-EEECECHHHHHHH-SEEEE-S CS
                  F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg....vkvtavdneeaaeeadvvvlav 69 
                                    +giiG+G + e l+  +++   + +++ +  + +p+ +e+++++++      v a++  e+a ++dv+v a 
  gi|119719126|ref|YP_919621.1| 133 LGIIGTGAQSEFLVYSISRVANSVEKVFFY-DIDPKAMEKFEKNISrlgfELVRAGSPREVALNSDVLVTAT 203
                                    79*************999997799****66.***************999978888889999999***99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 2376.33
//
Query:       gi|119719127|ref|YP_919622.1|  [L=176]
Description: hypothetical protein Tpen_0209 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-28   99.5  15.7    2.1e-28   99.3  15.7    1.0  1  SpoIIM    Stage II sporulation protein M
  ------ inclusion threshold ------
      0.018   14.2   2.5      0.026   13.7   2.5    1.2  1  EIID-AGA  PTS system mannose/fructose/sorbose family IID comp
       0.56   10.5   5.1         11    6.4   0.1    2.5  2  DUF5379   Family of unknown function (DUF5379)


Domain annotation for each model (and alignments):
>> SpoIIM  Stage II sporulation protein M
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.3  15.7   3.6e-32   2.1e-28       2     156 .]       2     165 ..       1     165 [. 0.88

  Alignments for each domain:
  == domain 1  score: 99.3 bits;  conditional E-value: 3.6e-32
                         SpoIIM   2 lllflvgillgallaa..........snfaeqis..seskensalslflaifanNlrvalllfllGllllgiptilvlli 69 
                                    +++f  gil+ga+l+                       ++  s+++l+l if+nN++v+ll++l+ l+++g p+i  +++
  gi|119719127|ref|YP_919622.1|   2 VFFFSSGILVGAFLVYpvagksalgyL------GstPFDVRISPAALALLIFTNNVKVVLLIVLSALAVIGPPLI--VFL 73 
                                    68999***********77654444330......255567889999****************99999866665555..567 PP

                         SpoIIM  70 nGfvlGavaalvaefgglllflllilPhgilelpaiiiagaaglrlgkal.....rsrrkalkeakrellklllllvpll 144
                                    nG+++Gav+++ +e +++ ++ll++ Phg++e+pai++ +a ++ +g+++     ++ r +++  + el++ ll++++ll
  gi|119719127|ref|YP_919622.1|  74 NGVIVGAVSMYAVERTSIVTLLLSLTPHGVIEVPAILYVSARSYAFGISVwkeilHKSRGNTHTHALELVRALLVTIVLL 153
                                    ********999999999*********************************99999778888888999************* PP

                         SpoIIM 145 liAaliEafvtp 156
                                    +iAa+iEafvtp
  gi|119719127|ref|YP_919622.1| 154 FIAAVIEAFVTP 165
                                    ***********8 PP

>> EIID-AGA  PTS system mannose/fructose/sorbose family IID component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   2.5   4.3e-06     0.026     100     187 ..      59     146 ..      46     167 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.3e-06
                       EIID-AGA 100 mGPlAGiGDslfwgtlrpilaaiaaslAlqgnilGpilflvvfnvvrlalryyllelGYklGtkaieklsesgllqkltk 179
                                       lA iG +l++++  +i++a+ +      +i+  +l l    v+++   +y+   +Y  G ++ +++ +++  ++ t+
  gi|119719127|ref|YP_919622.1|  59 LSALAVIGPPLIVFLNGVIVGAVSMYAVERTSIVTLLLSLTPHGVIEVPAILYVSARSYAFGISVWKEILHKSRGNTHTH 138
                                    5789*****************************************************************99988888888 PP

                       EIID-AGA 180 aasilGlf 187
                                    a++++   
  gi|119719127|ref|YP_919622.1| 139 ALELVRAL 146
                                    87766444 PP

>> DUF5379  Family of unknown function (DUF5379)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   1.2     0.004        24      19      62 ..      45      91 ..      36      96 .. 0.80
   2 ?    6.4   0.1    0.0018        11      36      59 ..     147     170 ..     134     175 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.004
                        DUF5379 19 gylanyvytlglgllsglatl...lflfiglvilghlsakvlgeesl 62
                                     ++n v ++ l +ls la +   l++f+  vi+g +s   + + s+
  gi|119719127|ref|YP_919622.1| 45 LIFTNNVKVVLLIVLSALAVIgppLIVFLNGVIVGAVSMYAVERTSI 91
                                   457888888888888888876666999**********9998888876 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0018
                        DUF5379  36 latllflfiglvilghlsakvlge 59 
                                    l t+++lfi++vi   ++ ++ g 
  gi|119719127|ref|YP_919622.1| 147 LVTIVLLFIAAVIEAFVTPRIAGI 170
                                    6899**************999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       737  (0.0411066); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1216.43
//
Query:       gi|119719128|ref|YP_919623.1|  [L=609]
Description: glycoside hydrolase family protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.2e-28   98.9   1.9      7e-27   94.5   1.9    2.2  1  Glyco_hydro_57  Glycosyl hydrolase family 57
  ------ inclusion threshold ------
       0.17   11.7   0.0       0.36   10.7   0.0    1.5  1  DUF824          Salmonella repeat of unknown function (DUF824


Domain annotation for each model (and alignments):
>> Glyco_hydro_57  Glycosyl hydrolase family 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.5   1.9   7.9e-31     7e-27     117     322 ..     194     420 ..     109     424 .. 0.86

  Alignments for each domain:
  == domain 1  score: 94.5 bits;  conditional E-value: 7.9e-31
                                    T-HHHHHHHHHHCTSEEEEEE-TT-B-GGG-.........S-..HHHHHHHHHHHHHHHHHHHSS--SBEE-GGG-B--S CS
                 Glyco_hydro_57 117 kevlelfrelqesgqvElltspyyHpllpll.........pd..sedieaqvkkarelyeeyfgqePrgfwlpElavspe 185
                                    + +l+ +re + +g vE l+s y+H +l l+          +  ++ ie +++++ +++ee +g++P+g+w pE+ +  +
  gi|119719128|ref|YP_919623.1| 194 EGLLSFLREKIREGIVEPLGSVYAHTVLGLVlkkakqrglDEiaKKLIEWELREGLKIVEEALGRRPSGLWTPEMFWHMD 273
                                    66788899999*******************98877666551166799********************************* PP

                                    HHHHHHHTT--EEEE-C------------TTS-EE-TTS.....-EEEE--CHH-TTTSGGG-...............TT CS
                 Glyco_hydro_57 186 ileilaelGfeylftdelaeiledkskespyrpyllkngg....iavffRdreLsddigFryseqyplea...vddfinw 258
                                    ++ ++  lG +y++  e +++ ++  ke+ y py+++++     + vffRd +Ls+ i+F+ +  +p+ea   +++f+ +
  gi|119719128|ref|YP_919623.1| 274 LVDLYGSLGVRYTVLCEQHFTRAGGDKENIYEPYVVEDPIsgrsVVVFFRDLKLSNWISFKVDFKNPEEAdneARRFVIE 353
                                    *************************************9988899*******************55555321116777777 PP

                                    SB...........-TT---TTT-...-BB-TT-S---HHHHHHHHHHHHHHHHHHHHHHHHHSS-EEE CS
                 Glyco_hydro_57 259 lkkvkka.ksevvtialdgEnwg...hypetgkkeFleklyeeleenglielvtpsefikklkpkgli 322
                                    l k  +  ++ +vtialdgEnw+    y++   + Flek  e++ e ++i+l t+s+++++ +pk+++
  gi|119719128|ref|YP_919623.1| 354 LAKRREVaPGGIVTIALDGENWMimpAYRKYA-PYFLEKVLEYILESQVIRLTTLSKYLDQNPPKRVL 420
                                    77654448***************885444444.45***99999999999****************985 PP

>> DUF824  Salmonella repeat of unknown function (DUF824)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0     4e-05      0.36      11      34 ..      15      38 ..      10      45 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 4e-05
                         DUF824 11 kGEsipltitvkDasGnPvpnapf 34
                                    G  + l+ tv ++ G+Pv+ +pf
  gi|119719128|ref|YP_919623.1| 15 QGSKVSLNFTVENDEGTPVKGTPF 38
                                   6999*******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (609 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.27s 00:00:00.90 Elapsed: 00:00:00.45
# Mc/sec: 4102.93
//
Query:       gi|119719129|ref|YP_919624.1|  [L=91]
Description: DNA-binding protein Alba [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-16   59.0   0.1    4.4e-16   58.4   0.1    1.3  1  Alba      Alba
  ------ inclusion threshold ------
      0.029   14.3   0.4       0.11   12.5   0.1    1.9  2  Rpp20     Rpp20 subunit of nuclear RNase MRP and P


Domain annotation for each model (and alignments):
>> Alba  Alba
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.4   0.1   4.9e-20   4.4e-16       2      66 ..       6      67 ..       5      68 .. 0.93

  Alignments for each domain:
  == domain 1  score: 58.4 bits;  conditional E-value: 4.9e-20
                                   EEEE-STS-HHHHHHHHHHHHTHTTESEEEEEEETTHHHHHHHHHHHHHHHTCTT.EEEEEEEEE CS
                           Alba  2 eiyVsskspimsyvkralklLsnkkeeeVvlkatGraIskAvsvaeilkrrfgkglyqvnvltss 66
                                   +++V++ +p++syv++a++++  ++ + Vvlka+GraIs+Av+ ae ++r +  g++ + +++++
  gi|119719129|ref|YP_919624.1|  6 TVFVGN-KPVSSYVLAAVTQF-TSGSKRVVLKARGRAISRAVDAAELVRRFL-GGKVDYGNIKIG 67
                                   689999.**************.***************************977.599**9999876 PP

>> Rpp20  Rpp20 subunit of nuclear RNase MRP and P
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   1.2e-05      0.11      59      82 ..      27      50 ..      19      71 .. 0.79
   2 ?    0.3   0.0     0.069   6.2e+02     127     136 ..      76      85 ..      66      86 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.2e-05
                          Rpp20 59 lkkeeVfvkatGrAiekalsvgrw 82
                                     ++ V++ka GrAi +a+  ++ 
  gi|119719129|ref|YP_919624.1| 27 SGSKRVVLKARGRAISRAVDAAEL 50
                                   67899*************987654 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.069
                          Rpp20 127 rtRwvsmvev 136
                                    ++R+vs++e+
  gi|119719129|ref|YP_919624.1|  76 KERTVSTIEI 85 
                                    89******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.29s 00:00:00.68 Elapsed: 00:00:00.46
# Mc/sec: 600.72
//
Query:       gi|119719130|ref|YP_919625.1|  [L=601]
Description: putative ATPase RIL [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-40  138.6   0.0    6.3e-20   72.1   0.0    2.5  2  ABC_tran      ABC transporter
    4.2e-12   45.7   1.4      9e-12   44.6   1.4    1.6  1  RLI           Possible Fer4-like domain in RNase L inhibitor,
      3e-11   43.7   6.1     0.0097   15.7   0.1    4.3  4  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    1.9e-09   37.3   1.7       0.02   14.3   0.0    4.0  4  SMC_N         RecF/RecN/SMC N terminal domain
    6.7e-08   32.0   2.3    6.7e-08   32.0   2.3    2.7  2  Fer4          4Fe-4S binding domain
    2.5e-07   30.5  11.9    1.4e-05   25.0   2.0    2.4  2  Fer4_6        4Fe-4S binding domain
    5.8e-05   23.1   0.0       0.22   11.4   0.0    2.3  2  Rad17         Rad17 P-loop domain
    0.00011   22.6   0.1       0.19   12.1   0.0    2.4  2  AAA_16        AAA ATPase domain
    0.00012   22.2  10.7    0.00018   21.5  10.7    1.3  1  Fer4_21       4Fe-4S dicluster domain
    0.00012   21.9   0.3       0.13   12.0   0.1    2.4  2  AAA_24        AAA domain
    0.00019   21.5  12.2     0.0014   18.7   1.2    2.1  2  Fer4_10       4Fe-4S dicluster domain
    0.00074   20.0   0.5       0.32   11.4   0.0    3.5  3  AAA           ATPase family associated with various cellular 
    0.00085   19.0   0.7        1.7    8.5   0.1    2.4  2  AAA_29        P-loop containing region of AAA domain
    0.00087   19.6   0.5       0.78   10.0   0.0    3.3  2  AAA_22        AAA domain
     0.0019   18.7   9.6     0.0039   17.8   9.6    1.6  1  Fer4_7        4Fe-4S dicluster domain
     0.0021   18.1   1.4     0.0021   18.1   1.4    2.5  2  Fer4_2        4Fe-4S binding domain
     0.0029   18.2   1.3       0.29   11.6   0.3    2.3  2  AAA_23        AAA domain
     0.0039   17.3  12.2     0.0073   16.5  12.2    1.4  1  Fer4_9        4Fe-4S dicluster domain
     0.0085   16.5   0.1        2.7    8.4   0.0    3.0  2  RNA_helicase  RNA helicase
     0.0096   16.5   0.4          4    8.0   0.0    2.7  2  AAA_18        AAA domain
  ------ inclusion threshold ------
       0.01   15.9   0.7        1.2    9.1   0.1    2.4  2  DUF87         Helicase HerA, central domain
      0.013   15.4   1.0        3.6    7.5   0.0    2.5  2  RsgA_GTPase   RsgA GTPase
      0.017   15.4   1.0          5    7.3   0.0    3.3  3  AAA_28        AAA domain
      0.033   13.8   0.4          2    8.0   0.0    2.3  2  SRP54         SRP54-type protein, GTPase domain
      0.033   13.9   0.2        3.1    7.4   0.1    2.5  2  AAA_15        AAA ATPase domain
      0.037   13.9   0.9       0.82    9.6   0.0    2.4  2  NACHT         NACHT domain
      0.045   13.8   0.1        9.7    6.2   0.1    3.4  3  AAA_14        AAA domain
      0.052   13.3   1.1        6.5    6.4   0.0    2.9  2  AAA_30        AAA domain
      0.053   12.5   0.5        3.8    6.4   0.0    2.2  2  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
       0.13   12.5   0.2         24    5.3   0.0    3.4  2  SbcCD_C       Putative exonuclease SbcCD, C subunit
       0.26   11.3   1.3        7.6    6.5   0.1    3.2  3  AAA_5         AAA domain (dynein-related subfamily)
       0.48   11.4  11.9       0.07   14.1   2.2    2.4  2  Fer4_16       4Fe-4S double cluster binding domain
       0.82   10.0   2.2         12    6.3   0.2    3.0  2  AAA_19        AAA domain
        1.2    9.0   3.8        3.3    7.6   0.1    3.0  2  NTPase_1      NTPase
        1.7    9.3  13.5       0.18   12.4   2.4    2.3  2  Fer4_4        4Fe-4S binding domain
        2.2    8.4   3.5        8.9    6.5   0.0    3.1  3  AAA_33        AAA domain
        6.7    7.9  16.0        2.5    9.2   4.8    2.4  2  Fer4_3        4Fe-4S binding domain
        9.8    6.8  11.5         60    4.3  11.5    2.1  1  Fer4_17       4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.1   0.0   1.3e-22   6.3e-20       9     136 ..      96     238 ..      95     239 .. 0.86
   2 !   63.8   0.0   4.7e-20   2.2e-17       7     137 .]     361     485 ..     355     485 .. 0.71

  Alignments for each domain:
  == domain 1  score: 72.1 bits;  conditional E-value: 1.3e-22
                                    ETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEE...........EETTCEGGG..B-HHHCCHCEEEE-SS..--S-TT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxx..xxxxxxxxxxxxxxxx..xxxxxx RF
                       ABC_tran   9 kegekvaivGenGaGKStLlkllagllkpteGei...........lldgkdlke..qeleslrkeigvlpqe..pqlfpe 73 
                                    keg+ ++i+G+nG GKSt lk+lag ++p+ G+             ++g +l++  ++l++ + ++++ pq   +  + +
  gi|119719130|ref|YP_919625.1|  96 KEGRSLGILGSNGVGKSTSLKILAGITRPNLGNFesppswdevidFFKGSELQTyfEKLSQGKLRVAYKPQAvdALAKVT 175
                                    68999****************************99999999988888899999888888888888999999953333344 PP

                                    SBHHHH....HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    xxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  74 ltvren....esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                    l+v+e     +++  + +++++lgl +l d++v    + LSgG+ q+va+a++++k+++++l+DEp+
  gi|119719130|ref|YP_919625.1| 176 LSVGEAlkkvDEKGVAREVAEELGLLHLWDRPV----KALSGGEMQKVAIAATIVKDANVFLIDEPS 238
                                    448888875444444******************....*****************************7 PP

  == domain 2  score: 63.8 bits;  conditional E-value: 4.7e-20
                                    EEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHHHH....HH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx....xx RF
                       ABC_tran   7 klkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltvren....es 81 
                                    ++++ge+++i+G+nG GK+t++k+lag l+p++G ++           ++   ++++ pq   +++   tvre       
  gi|119719130|ref|YP_919625.1| 361 EIHKGEVIGILGPNGIGKTTFVKILAGILEPDAGWVQ-----------RIGALKLSYKPQFlGEVKVAGTVREFlresGV 429
                                    799*********************************3...........34444555555554334444445555432222 PP

                                    HTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  82 deeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                    d   + + s+l  +   +t  +s +++LSgG+ qrv +++al ++++l+llDEp+a
  gi|119719130|ref|YP_919625.1| 430 DTASSFVQSELIKPLRVHTLFDSYMEELSGGELQRVLIVAALGREADLYLLDEPMA 485
                                    2223333333333334556666666*****************************85 PP

>> RLI  Possible Fer4-like domain in RNase L inhibitor, RLI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.6   1.4   1.9e-14     9e-12       1      35 []       1      32 [.       1      32 [. 0.97

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 1.9e-14
                                   --EEEES---------TTHHHHHTTSEEEESS--S CS
                            RLI  1 mrlAivdadqCdPKKCtgkkcarfcpvrlvrtgkk 35
                                   mr+A++d+  C P+KC++ +c++fcp+  +r+g k
  gi|119719130|ref|YP_919625.1|  1 MRVAVIDRSLCRPSKCNQ-ECVKFCPI--NRSGSK 32
                                   9*****************.********..***975 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   1.2    0.0022       1.1       3      24 ..     102     123 ..     100     156 .. 0.71
   2 !   10.2   0.0     0.001      0.49     232     298 ..     206     269 ..     136     274 .. 0.66
   3 !   15.7   0.1   2.1e-05    0.0097       2      53 ..     368     413 ..     367     442 .. 0.76
   4 !    8.6   0.0     0.003       1.4     234     290 ..     454     508 ..     448     521 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0022
                         AAA_21   3 vliGpNgsGKSnLLdaldllar 24 
                                    ++ G Ng+GKS+ L++l ++ r
  gi|119719130|ref|YP_919625.1| 102 GILGSNGVGKSTSLKILAGITR 123
                                    699**************99965 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.001
                         AAA_21 232 lparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHS 298
                                    +p+  lS G  +  a+++ +  ++    ++liDEp + L+ k   r+++ +++l+r g+ ++++ H+
  gi|119719130|ref|YP_919625.1| 206 RPVKALSGGEMQKVAIAATIVKDA---NVFLIDEPSSYLDVKERLRVADAIRRLARPGVYLVVVEHD 269
                                    455566999999999999999999...89************88888888888888767666666555 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 2.1e-05
                         AAA_21   2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlyd 53 
                                     ++ GpNg GK+++ ++l ++      +e++    +++g ++   + ++l++
  gi|119719130|ref|YP_919625.1| 368 IGILGPNGIGKTTFVKILAGI------LEPDAGWVQRIGALKLSYKPQFLGE 413
                                    689***************665......5777777777777766666666655 PP

  == domain 4  score: 8.6 bits;  conditional E-value: 0.003
                         AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.nga 290
                                    + elS G ++   +++al r +   +l+l+DEp + L+ +    + +++++l++ +g+
  gi|119719130|ref|YP_919625.1| 454 MEELSGGELQRVLIVAALGREA---DLYLLDEPMAYLDVEQRYAVSRVIRRLTAeKGV 508
                                    5678999999989999999999...9*************9999999999777664555 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1      0.26   1.2e+02      27      39 ..     101     113 ..      86     122 .. 0.83
   2 !   14.3   0.0   4.2e-05      0.02     135     212 ..     209     283 ..     133     290 .. 0.76
   3 ?    4.7   0.1     0.038        18      25      42 ..     366     383 ..     353     391 .. 0.80
   4 !   12.6   0.0   0.00015     0.069     134     195 ..     454     513 ..     412     535 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.26
                                    EEEEESTTSSHHH CS
                                    xxxxxxxxxxxxx RF
                          SMC_N  27 taivGpNGSGKsn 39 
                                      i+G+NG GKs 
  gi|119719130|ref|YP_919625.1| 101 LGILGSNGVGKST 113
                                    569********96 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 4.2e-05
                                    TCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-SCEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 135 elLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreemlekadklvgvt 212
                                    ++LSgGe + va+a       vk a ++l+De  + LD k++ +va+ +++     + ++v+ ++  +l  ++ lv + 
  gi|119719130|ref|YP_919625.1| 209 KALSGGEMQKVAIA----ATIVKDANVFLIDEPSSYLDVKERLRVADAIRRLARPgVYLVVVEHDLAVLDYVSDLVSII 283
                                    48*****9888876....457999**************************98876466666777777777666666665 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.038
                                    SEEEEEESTTSSHHHHHH CS
                                    xxxxxxxxxxxxxxxxxx RF
                          SMC_N  25 sftaivGpNGSGKsnlld 42 
                                    ++  i+GpNG GK+ ++ 
  gi|119719130|ref|YP_919625.1| 366 EVIGILGPNGIGKTTFVK 383
                                    46789*********9876 PP

  == domain 4  score: 12.6 bits;  conditional E-value: 0.00015
                                    TTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxx RF
                          SMC_N 134 kelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQfivi 195
                                    +e+LSgGe + v   L++A    + a lyllDe  a LD +++ +v++++++ + +  +  +v+
  gi|119719130|ref|YP_919625.1| 454 MEELSGGELQRV---LIVAAL-GREADLYLLDEPMAYLDVEQRYAVSRVIRRLTAEkgVATFVV 513
                                    4589***96533...555544.46788************************7765522444554 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.3      0.25   1.2e+02      13      21 ..      19      27 ..      18      27 .. 0.87
   2 !   32.0   2.3   1.4e-10   6.7e-08       2      24 .]      44      66 ..      43      66 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.25
                                   HHHHHSTTT CS
                           Fer4 13 aCvevCPvg 21
                                   +Cv+ CP +
  gi|119719130|ref|YP_919625.1| 19 ECVKFCPIN 27
                                   6******76 PP

  == domain 2  score: 32.0 bits;  conditional E-value: 1.4e-10
                                   EEETTTSSS-THHHHHSTTTEEE CS
                           Fer4  2 videekCigCGaCvevCPvgAIt 24
                                    i ee+C+gCG+Cv+ CP+ AI+
  gi|119719130|ref|YP_919625.1| 44 RISEELCVGCGICVKKCPFSAIS 66
                                   689******************95 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   2.6    0.0011      0.51       1      20 [.       3      25 ..       3      29 .. 0.88
   2 !   25.0   2.0   2.9e-08   1.4e-05       1      24 []      42      65 ..      42      65 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0011
                         Fer4_6  1 vveidpdkCi..gCgd.CvrvCP 20
                                   v++id+++C    C+  Cv+ CP
  gi|119719130|ref|YP_919625.1|  3 VAVIDRSLCRpsKCNQeCVKFCP 25
                                   689******9888*888****** PP

  == domain 2  score: 25.0 bits;  conditional E-value: 2.9e-08
                         Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                                   +++i +++C+gCg Cv+ CP+ ai
  gi|119719130|ref|YP_919625.1| 42 KARISEELCVGCGICVKKCPFSAI 65
                                   58899****************998 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0    0.0023       1.1      47     100 ..     100     155 ..      92     178 .. 0.81
   2 !   11.4   0.0   0.00047      0.22      43      71 ..     363     391 ..     342     419 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0023
                          Rad17  47 iLLisGPsGCgkstvvkvLskelgiklrewlnpvslkep.dn.qksdfkgltekes 100
                                     L i G  G gkst +k+L+ +  ++l ++  p s  e  d+ + s++++ +ek s
  gi|119719130|ref|YP_919625.1| 100 SLGILGSNGVGKSTSLKILAGITRPNLGNFESPPSWDEViDFfKGSELQTYFEKLS 155
                                    57799******************999999988888776423357777777777665 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00047
                          Rad17  43 rkkriLLisGPsGCgkstvvkvLskelgi 71 
                                    +k +++ i GP G gk+t vk+L+ +l +
  gi|119719130|ref|YP_919625.1| 363 HKGEVIGILGPNGIGKTTFVKILAGILEP 391
                                    444588899***************98866 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0063         3      22      52 ..      96     143 ..      88     274 .. 0.53
   2 !   12.1   0.0   0.00041      0.19      23      63 ..     364     404 ..     349     506 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0063
                         AAA_16  22 grpelvllsGesGvGKsslvrellralekd..................g 52 
                                     +++++ + G  GvGKs+ ++ l+  +++                   +
  gi|119719130|ref|YP_919625.1|  96 KEGRSLGILGSNGVGKSTSLKILA-GITRPnlgnfesppswdevidffK 143
                                    45589999************8888.677772333333333333332221 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00041
                         AAA_16  23 rpelvllsGesGvGKsslvrellralekdggiflrgkcdql 63 
                                     +e++ + G+ G+GK++ v+ l+  le d g++ r  + +l
  gi|119719130|ref|YP_919625.1| 364 KGEVIGILGPNGIGKTTFVKILAGILEPDAGWVQRIGALKL 404
                                    338899****************9999999777766555555 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5  10.7   3.9e-07   0.00018       1      57 [.       4      65 ..       4      67 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 3.9e-07
                        Fer4_21  1 AridedkC..igCgk.CliaCe..dtshqaieidak.tvlkvvedeCvGCnlCssvCPvedci 57
                                   A+id++ C   +C++ C++ C+   ++ +++ id+  +++++ e+ CvGC +C++ CP   +i
  gi|119719130|ref|YP_919625.1|  4 AVIDRSLCrpSKCNQeCVKFCPinRSGSKCVWIDEVeNKARISEELCVGCGICVKKCPF-SAI 65
                                   7899999944489855*****7336799***9997615667789**************7.666 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0056       2.6       3      57 ..      99     143 ..      97     193 .. 0.77
   2 !   12.0   0.1   0.00027      0.13       4      22 ..     367     385 ..     364     395 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0056
                         AAA_24   3 lkiliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdieswedfldevv 57 
                                    +++ i G++g+GK+t++k l          +G  + +  +f++++sw++++d+++
  gi|119719130|ref|YP_919625.1|  99 RSLGILGSNGVGKSTSLKIL----------AGITRPNLGNFESPPSWDEVIDFFK 143
                                    67889*************99..........6666666666666666666666665 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00027
                         AAA_24   4 kiliyGpsgiGKTtlakel 22 
                                     i i Gp+giGKTt++k l
  gi|119719130|ref|YP_919625.1| 367 VIGILGPNGIGKTTFVKIL 385
                                    689*************977 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2  14.1   1.7e-05    0.0081       2      56 .]       4      61 ..       3      61 .. 0.91
   2 !   18.7   1.2   2.9e-06    0.0014       2      30 ..      43      71 ..      42      86 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.7e-05
                        Fer4_10  2 vvidddtC..irCg.kCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                   +vid++ C   +C+ +Cvk+CP + ++++   +++ e++ r+  e C gcg Cv++CP
  gi|119719130|ref|YP_919625.1|  4 AVIDRSLCrpSKCNqECVKFCPINRSGSKCVWIDEVENKARISEELCVGCGICVKKCP 61
                                   589999**6669999********999999999999999999999*************9 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 2.9e-06
                        Fer4_10  2 vvidddtCirCgkCvkaCPadltsvgakg 30
                                   ++i ++ C++Cg Cvk CP+++ s ++ +
  gi|119719130|ref|YP_919625.1| 43 ARISEELCVGCGICVKKCPFSAISIVNLP 71
                                   68999***************775544444 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       3.5   1.6e+03      59      72 ..      31      44 ..      19      49 .. 0.77
   2 ?    4.4   0.1     0.097        46       3      27 ..     103     127 ..     101     239 .. 0.80
   3 !   11.4   0.0   0.00068      0.32       3      23 ..     370     390 ..     368     445 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 3.5
                                   SEEEEEETGGGHHH CS
                            AAA 59 psilfiDEidalak 72
                                    ++++iDE+++ a+
  gi|119719130|ref|YP_919625.1| 31 SKCVWIDEVENKAR 44
                                   489******98766 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.097
                                    EESSTTSSHHHHHHHHHHHHTHEEE CS
                            AAA   3 lyGppGtGKTllakavakelgvefl 27 
                                    + G  G+GK++  k +a  +  ++ 
  gi|119719130|ref|YP_919625.1| 103 ILGSNGVGKSTSLKILAGITRPNLG 127
                                    5799************998754443 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.00068
                                    EESSTTSSHHHHHHHHHHHHT CS
                            AAA   3 lyGppGtGKTllakavakelg 23 
                                    + Gp G+GKT+++k +a  l+
  gi|119719130|ref|YP_919625.1| 370 ILGPNGIGKTTFVKILAGILE 390
                                    57***************9874 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.1    0.0035       1.7      18      38 ..      93     114 ..      85     123 .. 0.81
   2 !    8.5   0.0    0.0035       1.7      19      49 ..     362     392 ..     354     397 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0035
                         AAA_29  18 eidlkg.atlltGpsGsGKSTl 38 
                                    ++  +g +  + G +G+GKST 
  gi|119719130|ref|YP_919625.1|  93 PVPKEGrSLGILGSNGVGKSTS 114
                                    56666767789**********5 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0035
                         AAA_29  19 idlkgatlltGpsGsGKSTllDAiqalLvpa 49 
                                    i+  +++ + Gp+G GK+T++  ++ +L p+
  gi|119719130|ref|YP_919625.1| 362 IHKGEVIGILGPNGIGKTTFVKILAGILEPD 392
                                    553447889***********97666666665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.4     0.038        18       6      26 ..      99     119 ..      95     266 .. 0.84
   2 !   10.0   0.0    0.0017      0.78       7      97 ..     367     468 ..     362     482 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.038
                         AAA_22   6 gilvvtGesGtGKTtllrrll 26 
                                    ++l + G  G+GK+t+l+ l+
  gi|119719130|ref|YP_919625.1|  99 RSLGILGSNGVGKSTSLKILA 119
                                    667789**********99776 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0017
                         AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaee.erpevv..fvtlpsst..sskdllrellralglelka........erl 73 
                                    ++ + G+ G+GKTt ++ l+  l+  ++a + +r + +  +++++ ++  + +   re+lr+ g+++ +        ++l
  gi|119719130|ref|YP_919625.1| 367 VIGILGPNGIGKTTFVKILAGILE--PDAGWvQRIGALklSYKPQFLGevKVAGTVREFLRESGVDTASsfvqseliKPL 444
                                    56689****************994..556668666666556666666677777777777888887777788889999899 PP

                         AAA_22  74 sseell.ealeqalraraviellii 97 
                                    + + l+ +++e+ +      ++li+
  gi|119719130|ref|YP_919625.1| 445 RVHTLFdSYMEELSGGELQ-RVLIV 468
                                    9999997777777666666.66665 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   9.6   8.2e-06    0.0039       4      52 .]      15      64 ..      10      68 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 8.2e-06
                         Fer4_7  4 gCg.aCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                   +C+  Cv+ Cp +    + +  ++   k++i++e C+gCg Cv+ CP+ a
  gi|119719130|ref|YP_919625.1| 15 KCNqECVKFCPINRSGSKCVWIDEVENKARISEELCVGCGICVKKCPFSA 64
                                   67658******6666655443333456789*****************976 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   2.6      0.54   2.5e+02       3      21 ..       4      25 ..       2      25 .. 0.76
   2 !   18.1   1.4   4.4e-06    0.0021       5      21 ..      45      61 ..      42      62 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.54
                         Fer4_2  3 vvvdtdrCi.g.Cg.aCvsaCP 21
                                   +v+d+  C  + C+  Cv+ CP
  gi|119719130|ref|YP_919625.1|  4 AVIDRSLCRpSkCNqECVKFCP 25
                                   6788888854569669*****9 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 4.4e-06
                         Fer4_2  5 vdtdrCigCgaCvsaCP 21
                                   + ++ C+gCg+Cv+ CP
  gi|119719130|ref|YP_919625.1| 45 ISEELCVGCGICVKKCP 61
                                   56899************ PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0      0.06        28      24      38 ..     103     117 ..      94     153 .. 0.90
   2 !   11.6   0.3   0.00062      0.29      20      40 ..     366     386 ..     348     394 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.06
                         AAA_23  24 ItGpNGaGKTTildA 38 
                                    I G NG GK+T l  
  gi|119719130|ref|YP_919625.1| 103 ILGSNGVGKSTSLKI 117
                                    99*********7765 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00062
                         AAA_23  20 gltlItGpNGaGKTTildAik 40 
                                     +  I GpNG GKTT++  + 
  gi|119719130|ref|YP_919625.1| 366 EVIGILGPNGIGKTTFVKILA 386
                                    4788***********998776 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5  12.2   1.5e-05    0.0073       4      51 .]      15      65 ..      11      65 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.5e-05
                         Fer4_9  4 gCga.CveaCpagvvvedaaerkarlraase..eaCigCgaCveaCpkgai 51
                                   +C++ Cv+ Cp +    +++      ++a+   e C+gCg Cv++Cp  ai
  gi|119719130|ref|YP_919625.1| 15 KCNQeCVKFCPINRSGSKCVWIDEVENKARIseELCVGCGICVKKCPFSAI 65
                                   68644*****9888888877555444443334589************8876 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.083        39       3      19 ..     103     119 ..     101     158 .. 0.76
   2 !    8.4   0.0    0.0057       2.7       3      22 ..     370     389 ..     368     406 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.083
                   RNA_helicase   3 lyGpsgeGKStlakeLa 19 
                                    + G++g+GKSt  k La
  gi|119719130|ref|YP_919625.1| 103 ILGSNGVGKSTSLKILA 119
                                    68**********99965 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0057
                   RNA_helicase   3 lyGpsgeGKStlakeLakal 22 
                                    + Gp+g+GK+t++k La  l
  gi|119719130|ref|YP_919625.1| 370 ILGPNGIGKTTFVKILAGIL 389
                                    78************988655 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0086         4       3      44 ..     103     154 ..     101     219 .. 0.82
   2 ?    6.1   0.2     0.033        15       1      19 [.     368     386 ..     368     404 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0086
                         AAA_18   3 ltGtpGvGKttlakeL....skrl.gf.....gvnlrdvakenglllevdpe 44 
                                    + G  GvGK+t  k L    +  l +f     +++++d +k ++l +++++ 
  gi|119719130|ref|YP_919625.1| 103 ILGSNGVGKSTSLKILagitRPNLgNFesppsWDEVIDFFKGSELQTYFEKL 154
                                    88999***********666655564449999999999999999999888877 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.033
                         AAA_18   1 IlltGtpGvGKttlakeLs 19 
                                    I++ G+ G GKtt+ k L+
  gi|119719130|ref|YP_919625.1| 368 IGILGPNGIGKTTFVKILA 386
                                    89**************996 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1    0.0026       1.2      24      43 ..      99     118 ..      95     124 .. 0.92
   2 ?    4.5   0.0     0.067        31      26      43 ..     368     385 ..     366     395 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0026
                          DUF87  24 rHlAilgsTGsGKSntvavL 43 
                                    r+l+ilgs G+GKS+  ++L
  gi|119719130|ref|YP_919625.1|  99 RSLGILGSNGVGKSTSLKIL 118
                                    899************99987 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.067
                          DUF87  26 lAilgsTGsGKSntvavL 43 
                                    ++ilg  G GK+++v++L
  gi|119719130|ref|YP_919625.1| 368 IGILGPNGIGKTTFVKIL 385
                                    69*************987 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.2     0.022        10     101     121 ..     100     120 ..      92     131 .. 0.82
   2 ?    7.5   0.0    0.0076       3.6      98     122 ..     364     388 ..     354     401 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.022
                                    EEEEECSTTSSHHHHHHHHCT CS
                    RsgA_GTPase 101 tsvlvGqSGvGKStLinallp 121
                                       ++G+ GvGKSt ++ l++
  gi|119719130|ref|YP_919625.1| 100 SLGILGSNGVGKSTSLKILAG 120
                                    55689*********9998876 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0076
                                    TTSEEEEECSTTSSHHHHHHHHCTT CS
                    RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallpe 122
                                    k++++ ++G+ G+GK+t+++ l++ 
  gi|119719130|ref|YP_919625.1| 364 KGEVIGILGPNGIGKTTFVKILAGI 388
                                    5688999*************99875 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1     0.089        42       4      20 ..     103     119 ..     101     135 .. 0.88
   2 ?    7.3   0.0     0.011         5       2      21 ..     368     387 ..     367     413 .. 0.77
   3 ?   -0.4   0.0       2.5   1.2e+03      88     128 ..     453     493 ..     449     522 .. 0.64

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.089
                         AAA_28   4 itGgestGKTtlleaLa 20 
                                    i+G  + GK+t l+ La
  gi|119719130|ref|YP_919625.1| 103 ILGSNGVGKSTSLKILA 119
                                    89*************99 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.011
                         AAA_28   2 ivitGgestGKTtlleaLaa 21 
                                    i i+G+ + GKTt ++ La 
  gi|119719130|ref|YP_919625.1| 368 IGILGPNGIGKTTFVKILAG 387
                                    5699**************94 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 2.5
                         AAA_28  88 Yaraygge.aeaeleaaarekrydlvfllppapeidddgeRr 128
                                    Y++ + g   ++ l  aa  ++ dl++l +p++++ d ++R 
  gi|119719130|ref|YP_919625.1| 453 YMEELSGGeLQRVLIVAALGREADLYLLDEPMAYL-DVEQRY 493
                                    77655444255556666667779999999999999.544443 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1     0.084        40       6      24 ..     103     121 ..      99     128 .. 0.85
   2 ?    8.0   0.0    0.0043         2       3      26 ..     367     390 ..     365     399 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.084
                                    EEESTTSSHHHHHHHHHHH CS
                          SRP54   6 lvGlqGaGKTttlaKLaal 24 
                                    ++G +G+GK t+l  La +
  gi|119719130|ref|YP_919625.1| 103 ILGSNGVGKSTSLKILAGI 121
                                    68***********999866 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0043
                                    EEEEEESTTSSHHHHHHHHHHHHH CS
                          SRP54   3 villvGlqGaGKTttlaKLaallk 26 
                                    vi ++G++G+GKTt +  La +l+
  gi|119719130|ref|YP_919625.1| 367 VIGILGPNGIGKTTFVKILAGILE 390
                                    77899***********99998765 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.076        36      28      44 ..     103     119 ..     100     178 .. 0.83
   2 ?    7.4   0.1    0.0065       3.1      25      44 ..     367     386 ..     348     397 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.076
                         AAA_15  28 liGkNnsGKSsileald 44 
                                    + G N++GKS+ l++l 
  gi|119719130|ref|YP_919625.1| 103 ILGSNGVGKSTSLKILA 119
                                    569***********995 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0065
                         AAA_15  25 ltvliGkNnsGKSsileald 44 
                                    +  + G+N++GK++++++l 
  gi|119719130|ref|YP_919625.1| 367 VIGILGPNGIGKTTFVKILA 386
                                    66789************996 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1      0.27   1.3e+02       5      20 ..     103     118 ..      99     124 .. 0.84
   2 ?    9.6   0.0    0.0017      0.82       2      21 ..     367     386 ..     366     393 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.27
                                    EEC-TTTCHHHHHHHH CS
                          NACHT   5 lqGeaGsGKTtLlqkl 20 
                                    + G +G+GK+t l+ l
  gi|119719130|ref|YP_919625.1| 103 ILGSNGVGKSTSLKIL 118
                                    89*********98866 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0017
                                    CEEEEC-TTTCHHHHHHHHH CS
                          NACHT   2 lvilqGeaGsGKTtLlqkla 21 
                                    ++ + G++G+GKTt+++ la
  gi|119719130|ref|YP_919625.1| 367 VIGILGPNGIGKTTFVKILA 386
                                    56799***********9877 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       2.4   1.1e+03      60      78 ..      26      44 ..       7      49 .. 0.70
   2 ?    2.6   0.0      0.27   1.3e+02       4      23 ..     100     119 ..      97     156 .. 0.87
   3 ?    6.2   0.1     0.021       9.7       2      23 ..     365     386 ..     364     399 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 2.4
                         AAA_14 60 lkeekktylflDEiqevpe 78
                                   +++++ +++ +DE+ +  +
  gi|119719130|ref|YP_919625.1| 26 INRSGSKCVWIDEVENKAR 44
                                   3347899*******98655 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.27
                         AAA_14   4 ilvitGaRrvGKTtllkqli 23 
                                     l i G   vGK+t lk l+
  gi|119719130|ref|YP_919625.1| 100 SLGILGSNGVGKSTSLKILA 119
                                    67899**********98765 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.021
                         AAA_14   2 rkilvitGaRrvGKTtllkqli 23 
                                    ++++ i G+  +GKTt++k l+
  gi|119719130|ref|YP_919625.1| 365 GEVIGILGPNGIGKTTFVKILA 386
                                    57899************98765 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.6      0.08        38      22      46 ..     102     127 ..      94     266 .. 0.62
   2 ?    6.4   0.0     0.014       6.5      19      46 ..     366     394 ..     359     506 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.08
                         AAA_30  22 vltGpAGtGKttalkalreaweaa.g 46 
                                     + G  G GK+t+lk l+ + + + g
  gi|119719130|ref|YP_919625.1| 102 GILGSNGVGKSTSLKILAGITRPNlG 127
                                    5789999******9999887765544 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.014
                         AAA_30  19 rvavltGpAGtGKttalkalreaweaa.g 46 
                                     v  + Gp G GKtt +k l+ ++e + g
  gi|119719130|ref|YP_919625.1| 366 EVIGILGPNGIGKTTFVKILAGILEPDaG 394
                                    378899**************999987744 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0    0.0081       3.8      11      49 ..      82     118 ..      74     123 .. 0.78
   2 ?    4.0   0.1     0.044        21      28      51 ..     364     387 ..     354     401 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0081
                                    -SHHHHHHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHH CS
                           MeaB  11 erpeakellerllakaGraqvvGltGvPGaGkstlveal 49 
                                      p+  el++  ++k Gr+  +G+ G+ G+Gkst ++ l
  gi|119719130|ref|YP_919625.1|  82 YGPNGFELFRLPVPKEGRS--LGILGSNGVGKSTSLKIL 118
                                    5566677777778888886..8************98765 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.044
                                    -SEEEEEEE-TTSSHHHHHHHHHH CS
                           MeaB  28 raqvvGltGvPGaGkstlvealgl 51 
                                    + +v+G+ G  G Gk t+v+ l+ 
  gi|119719130|ref|YP_919625.1| 364 KGEVIGILGPNGIGKTTFVKILAG 387
                                    5689***************98865 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.051        24      26      45 ..     204     223 ..     189     254 .. 0.86
   2 ?    2.8   0.0       0.3   1.4e+02      30      46 ..     454     470 ..     444     501 .. 0.60

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.051
                        SbcCD_C  26 lsrssgtlSGGekqflayla 45 
                                    ++r +++lSGGe q++a  a
  gi|119719130|ref|YP_919625.1| 204 WDRPVKALSGGEMQKVAIAA 223
                                    67999********9877554 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.3
                        SbcCD_C  30 sgtlSGGekqflaylal 46 
                                    +++lSGGe q ++ +a 
  gi|119719130|ref|YP_919625.1| 454 MEELSGGELQRVLIVAA 470
                                    66788888766655543 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1      0.77   3.6e+02       4      23 ..     103     122 ..     100     130 .. 0.84
   2 ?    6.5   0.1     0.016       7.6       4      23 ..     370     389 ..     368     482 .. 0.89
   3 ?   -0.2   0.0       1.9   8.8e+02      20      54 ..     468     502 ..     460     521 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.77
                                    EE--SSSSHHHHHHHGGGGB CS
                          AAA_5   4 LvGppGtgKselaerlaaal 23 
                                    ++G  G+gKs+  + la  +
  gi|119719130|ref|YP_919625.1| 103 ILGSNGVGKSTSLKILAGIT 122
                                    68*********999998776 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.016
                                    EE--SSSSHHHHHHHGGGGB CS
                          AAA_5   4 LvGppGtgKselaerlaaal 23 
                                    ++Gp G+gK+++++ la  l
  gi|119719130|ref|YP_919625.1| 370 ILGPNGIGKTTFVKILAGIL 389
                                    68**************9988 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 1.9
                                    GGGBS--EEEEE--TT--HHHHH--B--....... CS
                          AAA_5  20 aaalnreveyvqltrdtteedlkgrreikngttsl 54 
                                     aal+re   ++l + + + d+ +r+ ++   ++l
  gi|119719130|ref|YP_919625.1| 468 VAALGREADLYLLDEPMAYLDVEQRYAVSRVIRRL 502
                                    57889999999***************997444443 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7  12.5      0.52   2.5e+02      46      66 ..      40      62 ..      11      63 .. 0.60
   2 ?   14.1   2.2   0.00015      0.07       2      18 ..      50      66 ..      49      77 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.52
                        Fer4_16 46 ekck..kqeaitgCdiCqdvCPa 66
                                   e++   ++e + gC+iC++ CP+
  gi|119719130|ref|YP_919625.1| 40 ENKAriSEELCVGCGICVKKCPF 62
                                   222212346689*********98 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 0.00015
                        Fer4_16  2 CgtCgkCaevCPtnaik 18
                                   C++Cg C++ CP +ai+
  gi|119719130|ref|YP_919625.1| 50 CVGCGICVKKCPFSAIS 66
                                   ***************97 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.2      0.56   2.6e+02      13      68 ..     101     181 ..      95     266 .. 0.49
   2 ?    6.3   0.2     0.025        12       7      34 ..     362     389 ..     357     405 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.56
                         AAA_19  13 llvtaGpGtGKTrvlkhivallvelggvkp.........................eeillvaftgrAakelrerlaalga 67 
                                    l +++  G GK++ lk    +   + g                            +  l va+  +A++ l++ + ++g+
  gi|119719130|ref|YP_919625.1| 101 LGILGSNGVGKSTSLKILAGITRPNLGNFEsppswdevidffkgselqtyfeklsQGKLRVAYKPQAVDALAKVTLSVGE 180
                                    56777777777777765544443332221122344444444444444444444444445555555666666655555555 PP

                         AAA_19  68 e 68 
                                    +
  gi|119719130|ref|YP_919625.1| 181 A 181
                                    5 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.025
                         AAA_19   7 alkekvllvtaGpGtGKTrvlkhivall 34 
                                     +k +v+ ++++ G GKT+ +k    +l
  gi|119719130|ref|YP_919625.1| 362 IHKGEVIGILGPNGIGKTTFVKILAGIL 389
                                    5788999************998776665 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1      0.67   3.2e+02       3      18 ..     102     117 ..     100     125 .. 0.80
   2 ?    7.6   0.1    0.0069       3.3       2      23 ..     368     389 ..     367     397 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.67
                                    EEE--TTSSHHHHHHH CS
                       NTPase_1   3 fiTGppGvGKtTlvkk 18 
                                     i G+ GvGK+T +k 
  gi|119719130|ref|YP_919625.1| 102 GILGSNGVGKSTSLKI 117
                                    57799*******8865 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0069
                                    EEEE--TTSSHHHHHHHHHHHH CS
                       NTPase_1   2 vfiTGppGvGKtTlvkkvlell 23 
                                    + i Gp G+GKtT+vk ++  l
  gi|119719130|ref|YP_919625.1| 368 IGILGPNGIGKTTFVKILAGIL 389
                                    6688***********9888777 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   3.5      0.88   4.1e+02       6      15 ..      15      25 ..       9      37 .. 0.83
   2 ?   12.4   2.4   0.00038      0.18       2      16 ..      48      62 ..      47      66 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.88
                         Fer4_4  6 gCgs.CvaaCP 15
                                    C + Cv +CP
  gi|119719130|ref|YP_919625.1| 15 KCNQeCVKFCP 25
                                   57767*****9 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00038
                         Fer4_4  2 erCigCgsCvaaCPq 16
                                   e C+gCg Cv  CP+
  gi|119719130|ref|YP_919625.1| 48 ELCVGCGICVKKCPF 62
                                   67************6 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1       1.3   5.9e+02       6      17 ..     105     116 ..     103     122 .. 0.83
   2 ?   -1.5   0.0       5.3   2.5e+03      66     110 ..     225     272 ..     215     274 .. 0.70
   3 ?    6.5   0.0     0.019       8.9       4      20 ..     370     386 ..     367     400 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 1.3
                         AAA_33   6 GlpGsGKstlae 17 
                                    G +G+GKst ++
  gi|119719130|ref|YP_919625.1| 105 GSNGVGKSTSLK 116
                                    99*******876 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 5.3
                         AAA_33  66 alsagrnvildat..nlsrrerarflklarrlgvp.vrivvvetdeet 110
                                      + ++ +++d +  +l+ +er r+  + rrl  p v +vvve d ++
  gi|119719130|ref|YP_919625.1| 225 IVKDANVFLIDEPssYLDVKERLRVADAIRRLARPgVYLVVVEHDLAV 272
                                    455556677777766788999998888888888775566777776665 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.019
                         AAA_33   4 lvGlpGsGKstlaerll 20 
                                    + G++G GK+t+++ l+
  gi|119719130|ref|YP_919625.1| 370 ILGPNGIGKTTFVKILA 386
                                    67**********99775 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   3.4      0.25   1.2e+02       4      13 ..      16      26 ..      11      28 .. 0.79
   2 ?    9.2   4.8    0.0053       2.5       1      15 []      50      64 ..      50      64 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.25
                         Fer4_3  4 Cg.aCvevCPv 13
                                   C+  Cv+ CP 
  gi|119719130|ref|YP_919625.1| 16 CNqECVKFCPI 26
                                   8646******6 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0053
                         Fer4_3  1 CtgCgaCvevCPvgA 15
                                   C+gCg Cv+ CP  A
  gi|119719130|ref|YP_919625.1| 50 CVGCGICVKKCPFSA 64
                                   ************765 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3  11.5      0.13        60      26      58 ..      36      62 ..      10      65 .. 0.58

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.13
                        Fer4_17 26 lraaklglleeaekeekaslCieCgeCerkCPq 58
                                   + +++++      ++   +lC++Cg C++kCP 
  gi|119719130|ref|YP_919625.1| 36 IDEVENK------ARISEELCVGCGICVKKCPF 62
                                   3332221......2235589***********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (601 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); expected 17.9 (0.001)
Passed Fwd filter:                        38  (0.00211947); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              38  [number of targets reported over threshold]
# CPU time: 0.69u 0.28s 00:00:00.97 Elapsed: 00:00:00.43
# Mc/sec: 4195.37
//
Query:       gi|119719131|ref|YP_919626.1|  [L=93]
Description: DNA-directed RNA polymerase, M/15 kDa subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-09   36.3   1.2    9.7e-09   35.0   1.2    1.7  1  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
    0.00057   19.6   2.7     0.0008   19.1   2.7    1.3  1  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger
     0.0017   17.9   1.5     0.0071   15.8   1.5    2.0  1  TF_Zn_Ribbon     TFIIB zinc-binding
     0.0049   16.4   2.5     0.0056   16.2   2.5    1.1  1  Baculo_PP31      Baculovirus 33KDa late protein (PP31)
     0.0076   15.9   2.2       0.58   10.0   0.1    2.2  2  A2L_zn_ribbon    A2L zinc ribbon domain
     0.0079   16.2   0.8      0.014   15.3   0.8    1.4  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
     0.0082   16.2   1.0      0.016   15.2   1.0    1.6  1  DZR              Double zinc ribbon
  ------ inclusion threshold ------
      0.012   15.9   1.8       0.03   14.7   1.8    1.9  1  Lar_restr_allev  Restriction alleviation protein Lar
       0.02   14.5   4.3       0.48   10.1   4.3    2.5  1  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
      0.026   15.3   0.9      0.046   14.5   0.9    1.4  1  Tnp_zf-ribbon_2  DDE_Tnp_1-like zinc-ribbon
      0.032   13.6   1.9        0.6    9.6   0.2    2.2  2  zf-ribbon_3      zinc-ribbon domain
      0.044   13.9   2.1        5.5    7.1   0.1    2.3  2  zf-ACC           Acetyl-coA carboxylase zinc finger domain
      0.072   13.0   0.9       0.11   12.4   0.9    1.2  1  C1_1             Phorbol esters/diacylglycerol binding domain
       0.11   12.3   4.8        3.2    7.6   2.4    2.3  2  zinc_ribbon_2    zinc-ribbon domain
       0.12   12.3   4.9       0.98    9.4   4.9    2.2  1  Nudix_N_2        Nudix N-terminal
       0.35   11.7   6.2       0.55   11.0   0.6    2.4  2  zinc_ribbon_15   zinc-ribbon family
       0.79   10.2   4.5        1.1    9.7   0.3    2.6  3  zf-IS66          zinc-finger binding domain of transposase IS
       0.89    9.8   5.3        1.4    9.2   0.5    2.4  2  NOB1_Zn_bind     Nin one binding (NOB1) Zn-ribbon like


Domain annotation for each model (and alignments):
>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   1.2   9.8e-12   9.7e-09       1      29 [.       1      29 [.       1      34 [. 0.96

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 9.8e-12
                                   EEBESTTTSBEEEEECSCCCEEEESSSS- CS
                 RNA_POL_M_15KD  1 lkFCpkCgNlLlpkedkegknfeCrqCgY 29
                                   ++FCpkCg l+lpk+ k  +++ C +CgY
  gi|119719131|ref|YP_919626.1|  1 MEFCPKCGGLMLPKKIKRSTYLVCQSCGY 29
                                   99*************************** PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   2.7     8e-07    0.0008       3      38 ..       3      35 ..       1      36 [. 0.91

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 8e-07
                                   E-SSS--EEEEEE-SSSEEEEESST.T----EEB-G CS
                 zf-C4_Topoisom  3 kCPkCggdLvlkrgkkGkFvGCsnYPeCkftkklkk 38
                                    CPkCgg ++ k+ k+ +++ C++   C + +k kk
  gi|119719131|ref|YP_919626.1|  3 FCPKCGGLMLPKKIKRSTYLVCQS---CGYMVKAKK 35
                                   5**********************9...999998886 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   1.5   7.1e-06    0.0071       3      30 ..       4      32 ..       2      38 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 7.1e-06
                                   ETTTTCEECHEETSTTCE.EESSSSBEEE CS
                   TF_Zn_Ribbon  3 CPnCgstnlveDpergel.vCtdCGlVle 30
                                   CP+Cg+ +l    +r ++ vC +CG+++ 
  gi|119719131|ref|YP_919626.1|  4 CPKCGGLMLPKKIKRSTYlVCQSCGYMVK 32
                                   ******8777777888777*******996 PP

>> Baculo_PP31  Baculovirus 33KDa late protein (PP31)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   2.5   5.6e-06    0.0056     114     170 ..      31      89 ..      17      92 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5.6e-06
                    Baculo_PP31 114 ievkksssse..tesnkkkkknskkvelnveeikesnekRsklYnEFyrvltetfkngs 170
                                    +++kk++++    +++ +++k++k + ++v+ + + +e+R++  +E+y+v  et+++++
  gi|119719131|ref|YP_919626.1|  31 VKAKKAETAGysMRESISEDKRTKVSVFDVKSVTQAEEERAQAKEEYYEVFLETYAEEE 89 
                                    555555544455566667777777888****************************9876 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.4     0.012        12      22      28 ..       2       8 ..       1      10 [. 0.92
   2 !   10.0   0.1   0.00058      0.58      19      29 ..      19      29 ..      14      31 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.012
                  A2L_zn_ribbon 22 lvCieCg 28
                                   ++C++Cg
  gi|119719131|ref|YP_919626.1|  2 EFCPKCG 8 
                                   8*****9 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00058
                  A2L_zn_ribbon 19 qgylvCieCga 29
                                   + ylvC+ Cg+
  gi|119719131|ref|YP_919626.1| 19 STYLVCQSCGY 29
                                   569*******8 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.8   1.5e-05     0.014      21      45 ..       4      29 ..       2      30 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.5e-05
                  Zn_Tnp_IS1595 21 CPhCgsr.kayriktrglfqCkeCrk 45
                                   CP+Cg+   + +ik+  ++ C++C++
  gi|119719131|ref|YP_919626.1|  4 CPKCGGLmLPKKIKRSTYLVCQSCGY 29
                                   ************************97 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   1.0   1.6e-05     0.016      13      42 ..       2      35 ..       1      41 [. 0.77

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.6e-05
                            DZR 13 rfCseCgtk.lkavaa.....edrCpsCgekvdpea 42
                                   +fC++Cg   l++  +       +C sCg++v++++
  gi|119719131|ref|YP_919626.1|  2 EFCPKCGGLmLPK--KikrstYLVCQSCGYMVKAKK 35
                                   69****9883332..23578899********99875 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   1.8   3.1e-05      0.03       6      47 ..       4      39 ..       1      81 [. 0.79

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.1e-05
                Lar_restr_allev  6 CPfCggravlersqrvvaeigqcvyCadCgastpwfkiaede 47
                                   CP Cgg    ++ +r +     +  C+ Cg+   ++k ae  
  gi|119719131|ref|YP_919626.1|  4 CPKCGGLMLPKKIKRST-----YLVCQSCGY-MVKAKKAETA 39
                                   ******99999999998.....89*******.2333333333 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   4.3   0.00048      0.48       5      31 ..       3      31 ..       1      32 [. 0.79

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00048
                  zf-NADH-PPase  5 FCgrCGaptepaeggwa..rvCpaCgleh 31
                                   FC++CG+ + p++  ++  +vC +Cg+++
  gi|119719131|ref|YP_919626.1|  3 FCPKCGGLMLPKKIKRStyLVCQSCGYMV 31
                                   *********99876554448999999875 PP

>> Tnp_zf-ribbon_2  DDE_Tnp_1-like zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.9   4.6e-05     0.046       6      23 ..       4      28 ..       2      34 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.6e-05
                Tnp_zf-ribbon_2  6 Clk.......kkikkeTriiCqeCd 23
                                   C+k       kkik+ T   Cq+C+
  gi|119719131|ref|YP_919626.1|  4 CPKcgglmlpKKIKRSTYLVCQSCG 28
                                   6666668999**************7 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.2   0.00061       0.6      17      24 ..       2       9 ..       1      11 [. 0.64
   2 ?    3.5   0.1      0.05        50      18      24 ..      23      29 ..      18      30 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00061
                    zf-ribbon_3 17 nvCpyCGt 24
                                    +Cp+CG+
  gi|119719131|ref|YP_919626.1|  2 EFCPKCGG 9 
                                   46777775 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.05
                    zf-ribbon_3 18 vCpyCGt 24
                                   vC +CG+
  gi|119719131|ref|YP_919626.1| 23 VCQSCGY 29
                                   799**97 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.1    0.0056       5.5       4      18 ..       4      18 ..       4      21 .. 0.79
   2 ?    6.2   0.4     0.011        11       4      14 ..      24      34 ..      23      37 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0056
                         zf-ACC  4 CpsCgemlykkeLer 18
                                   Cp+Cg +++ k + r
  gi|119719131|ref|YP_919626.1|  4 CPKCGGLMLPKKIKR 18
                                   9****9998776665 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.011
                         zf-ACC  4 CpsCgemlykk 14
                                   C sCg m+ +k
  gi|119719131|ref|YP_919626.1| 24 CQSCGYMVKAK 34
                                   ********988 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.9   0.00011      0.11      12      38 ..       2      31 ..       1      35 [. 0.91

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00011
                                   -B-TTT-SB-..-S.SSS-EEEETTT--EE CS
                           C1_1 12 tfCkhCgefl..wg.kekqglkCswCkllv 38
                                    fC +Cg ++  ++ k+++ l C+ C++ v
  gi|119719131|ref|YP_919626.1|  2 EFCPKCGGLMlpKKiKRSTYLVCQSCGYMV 31
                                   69********99888************987 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   2.4    0.0033       3.2      15      20 ..       3       8 ..       2       9 .. 0.73
   2 ?    4.9   0.0     0.023        23       2       8 ..      24      30 ..      18      36 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0033
                  zinc_ribbon_2 15 FCpyCG 20
                                   FCp+CG
  gi|119719131|ref|YP_919626.1|  3 FCPKCG 8 
                                   777776 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.023
                  zinc_ribbon_2  2 CpnCGae 8 
                                   C +CG+ 
  gi|119719131|ref|YP_919626.1| 24 CQSCGYM 30
                                   8888865 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   4.9   0.00098      0.98       2      30 ..       3      29 ..       2      31 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00098
                                   B-TTT--B.-EEE--TT-SS-EEEETTTTE CS
                      Nudix_N_2  2 FCsqCGtp.velripdgDnreRlvCpaCgt 30
                                   FC++CG+  +  +i      + lvC++Cg+
  gi|119719131|ref|YP_919626.1|  3 FCPKCGGLmLPKKI---KRSTYLVCQSCGY 29
                                   9******9555777...588889*****98 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.6      0.11   1.1e+02      80      86 .]       2       8 ..       1       8 [. 0.88
   2 ?   11.0   0.6   0.00055      0.55      31      63 ..      16      47 ..      11      80 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.11
                 zinc_ribbon_15 80 kyCpkCg 86
                                   ++CpkCg
  gi|119719131|ref|YP_919626.1|  2 EFCPKCG 8 
                                   8*****9 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00055
                 zinc_ribbon_15 31 wkkkkpylacskCkslleaskelgkeiekkess 63
                                   +k+ ++yl+c++C+++++a+k ++   + +es+
  gi|119719131|ref|YP_919626.1| 16 IKR-STYLVCQSCGYMVKAKKAETAGYSMRESI 47
                                   555.89************999777666666555 PP

>> zf-IS66  zinc-finger binding domain of transposase IS66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.3    0.0011       1.1       3      13 ..       3      13 ..       2      22 .. 0.74
   2 ?    1.5   0.2      0.41     4e+02       3      14 ..      23      33 ..      21      39 .. 0.68
   3 ?   -2.6   0.0       7.7   7.7e+03      13      23 ..      46      55 ..      40      61 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0011
                        zf-IS66  3 tCpcCGgllkp 13
                                    Cp+CGgl+ p
  gi|119719131|ref|YP_919626.1|  3 FCPKCGGLMLP 13
                                   6******8655 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.41
                        zf-IS66  3 tCpcCGgllkpi 14
                                   +C  CG  ++++
  gi|119719131|ref|YP_919626.1| 23 VCQSCGY-MVKA 33
                                   6888884.5555 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 7.7
                        zf-IS66 13 pigedrvreel 23
                                    i ed  r ++
  gi|119719131|ref|YP_919626.1| 46 SISED-KRTKV 55
                                   56677.55544 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.5    0.0014       1.4      24      36 ..       2      14 ..       1      20 [. 0.83
   2 ?    3.4   0.7     0.089        89       6      19 ..      19      32 ..      14      78 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0014
                   NOB1_Zn_bind 24 kFCpkCGnktLkr 36
                                   +FCpkCG  +L +
  gi|119719131|ref|YP_919626.1|  2 EFCPKCGGLMLPK 14
                                   6******988855 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.089
                   NOB1_Zn_bind  6 swvlrChaCfkvtk 19
                                   s  l C++C  ++k
  gi|119719131|ref|YP_919626.1| 19 STYLVCQSCGYMVK 32
                                   44556666655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1500  (0.0836633); expected 358.6 (0.02)
Passed bias filter:                      640  (0.0356964); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.57u 0.34s 00:00:00.90 Elapsed: 00:00:00.55
# Mc/sec: 511.82
//
Query:       gi|119719132|ref|YP_919627.1|  [L=190]
Description: THUMP domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-16   59.8   1.1    4.2e-16   59.4   1.1    1.2  1  THUMP     THUMP domain


Domain annotation for each model (and alignments):
>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.4   1.1   2.3e-20   4.2e-16      35     143 ..      60     161 ..      45     162 .. 0.92

  Alignments for each domain:
  == domain 1  score: 59.4 bits;  conditional E-value: 2.3e-20
                                    ETHHHHHHHHHTSTTECEEEEEEEEEESSHHHHHHHHHHHHHHHHHHCT-EEEEEEEESSSTSSSHHHHHHHHHHHHHHC CS
                          THUMP  35 edeellkealekargiqrvipvcevceadledileaakeivkkkfeeeketFaVrvkrrgkhfeftsreinrevGkaive 114
                                    +++e+++e   + r+i ++ p+  ++ ad+++i eaa  + + ++ +++ tF+V++  r +  e  + +i re++ +i +
  gi|119719132|ref|YP_919627.1|  60 KAREKIEENPWYFRYILKITPIQVTVDADIQQIVEAALRLSSSRLNPGE-TFKVEAHIRLS--ELRREDIIREIASRITN 136
                                    46788888888888*******************************9886.***********..8**************99 PP

                                    CTT-EE-SSS-SEEEEEEEETTEEEEEEE CS
                          THUMP 115 ktglkVdlenPdivvrveiikdkayisid 143
                                        kV+l+nPd++v+ve+i+d+a++s+ 
  gi|119719132|ref|YP_919627.1| 137 ----KVNLDNPDKIVLVEVIGDRAGVSVI 161
                                    ....9*********************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.34s 00:00:00.92 Elapsed: 00:00:00.55
# Mc/sec: 1036.27
//
Query:       gi|119719133|ref|YP_919628.1|  [L=178]
Description: hypothetical protein Tpen_0215 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00015   21.9   0.0    0.00018   21.6   0.0    1.2  1  CGI-121   Kinase binding protein CGI-121


Domain annotation for each model (and alignments):
>> CGI-121  Kinase binding protein CGI-121
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0     1e-08   0.00018      28      99 ..      53     122 ..      30     141 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1e-08
                                    GGG---HHHHHHHHHHHHHHHHHS---SSSHHHHHHHHHSSSS-HHHHHHHHB--TT-S-EEEEEEESSS-- CS
                        CGI-121  28 aslilskehllsAvlrallaaargklktktlhsEilfsLspnnnIgealkrfgisdkttsllvvkvsssead 99 
                                     ++i   e ++sAv  ++    +gk  ++ ++ ++l++ ++++nIgealk f  s + +s  vv +s    +
  gi|119719133|ref|YP_919628.1|  53 CRKIPPLEVVVSAVGYTVRGIMEGKTISRDPSLDVLLYVNGSRNIGEALKAFFSSCT-ESFGVVAFSLG-RE 122
                                    566777788999999*************************************87765.44888888776.22 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       246  (0.0137208); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1186.82
//
Query:       gi|119719134|ref|YP_919629.1|  [L=263]
Description: hypothetical protein Tpen_0216 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-77  260.8   0.0    1.1e-77  260.6   0.0    1.0  1  SAM_adeno_trans  S-adenosyl-l-methionine hydroxide adenosyltr


Domain annotation for each model (and alignments):
>> SAM_adeno_trans  S-adenosyl-l-methionine hydroxide adenosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  260.6   0.0   6.4e-82   1.1e-77       1     234 [.       7     259 ..       7     260 .. 0.88

  Alignments for each domain:
  == domain 1  score: 260.6 bits;  conditional E-value: 6.4e-82
                                    EEEEESSTSSSSHHHHHHHHHHHH-TTSEEEEEES-S-TT-HHHHHHHHHHHHGGS-TTEEEEEE--TTTTSS--EEEEE CS
                SAM_adeno_trans   1 itLlTDFGlkdpyvgamkgvilsiapdarivDitHdippfdvreaaflLaaalpyfpkgtvhlavVDpgvgterralvve 80 
                                    i++l+DFG++d+yvga+k+v++s++p+ ++vD+tH+++p +v++a ++L+ ++  fp+ tv+l+vVDpgvgt+r+a+++e
  gi|119719134|ref|YP_919629.1|   7 IAFLSDFGTRDYYVGAVKAVVHSLCPQSTVVDVTHEVEPWSVEDACYILRCCYDDFPSRTVFLVVVDPGVGTSRKAIILE 86 
                                    89****************************************************************************** PP

                                    ETTSEEEEESSSTTHHHH..SEEEEEEGSSCC.....--TS-HHHHTHHHHHHHHHCT--GGGCSEEESGGGS-SSS... CS
                SAM_adeno_trans  81 akggyfvgPDNGlltlal..lleeaveieeee.....ssatFhgrDvFapvaarlaagvsleelgeeldpeelvrle... 150
                                     kg++fvgPDNGll +a+  +  +a+ei +       +s+tFhgrDvFapvaa l+ g  +ee+g+e+++  l+++e   
  gi|119719134|ref|YP_919629.1|  87 HKGYLFVGPDNGLLPCAVgnKEFKAWEILRVPgarrkTSHTFHGRDVFAPVAAFLSCGGRPEEIGREYADPVLMDIEeti 166
                                    ***************999763366788874445667789*****************************999999988765 PP

                                    .ECSCEEEEEEEE-TTS-EEEEEE...EHHHHHTTC...EE........EEEEESSGGGSTTTSEEEEE-TTSEEEEEET CS
                SAM_adeno_trans 151 .ederlegevlyvDrFGNvitniskelleelekerk...va........klkkvetyaevaegellalvnssglleiavn 218
                                     e++ ++++v++vDrFGNv ++++ e   ++ +e++   ++         + +v+t++++++g+l+alvns g+le+avn
  gi|119719134|ref|YP_919629.1| 167 lEEGWVKARVIHVDRFGNVALGVRPE---KFFREYGptrIRvafddhevDVPFVRTFGDAPRGSLVALVNSCGYLELAVN 243
                                    4477889****************944...3334433444124567787755677************************** PP

                                    TC-HHHHHT--TT-EE CS
                SAM_adeno_trans 219 kgsaaellglkvgdev 234
                                    +g+a+e+lglk+g  v
  gi|119719134|ref|YP_919629.1| 244 MGNASEVLGLKPGRIV 259
                                    ************9866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1765.52
//
Query:       gi|119719135|ref|YP_919630.1|  [L=349]
Description: RNA-3'-phosphate cyclase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.8e-75  252.9   0.0    2.1e-75  252.8   0.0    1.0  1  RTC         RNA 3'-terminal phosphate cyclase
    2.9e-17   63.0   0.1    5.9e-17   62.1   0.1    1.5  1  RTC_insert  RNA 3'-terminal phosphate cyclase (RTC), insert d


Domain annotation for each model (and alignments):
>> RTC  RNA 3'-terminal phosphate cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  252.8   0.0   2.3e-79   2.1e-75       1     222 []       8     331 ..       8     331 .. 0.98

  Alignments for each domain:
  == domain 1  score: 252.8 bits;  conditional E-value: 2.3e-79
                                    STTTSTHHHHHHHHHHHHH---EEEESTTTTSSS-S--HHHHHHHHHHHHHHT-EEE--STT-SEEEEE-----..-SEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxx RF
                            RTC   1 lgegGgqiLRtalaLsaltgkpvrIenIRanRkkPGLraqhltavrllakitnaevegaeigsteleFkPgeik..agey 78 
                                    +gegGgq+LR ++aLsa+++ p+rI+nIRa+R+ PGLr+qhlta++ +a++ ++e+eg ++gste++F P+  +  +g+y
  gi|119719135|ref|YP_919630.1|   8 MGEGGGQLLRYSIALSAIMNVPLRIYNIRAKRDPPGLRPQHLTALKFIAELVKGEAEGLRVGSTEVKFVPRLRRpaPGKY 87 
                                    58********************************************************************95443369** PP

                                    EEEEESSEBHHHHHHHHHHHHTTSSS-EEEEEEEBSBBTTS--HHHHHHTHHHHHHHHT.-EEEEEEEE--BTTTB-EEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            RTC  79 evdigtAGsitlllqtllplllfakkpseltlkGgTnvsaapsvdylktvllpllkrfgvlelelelkkrGfypkGgGev 158
                                     +digtAGs+tlllq++lp+ll a++++ l+++GgT v+++p++ y+++vl+pl+++fg ++++ +l ++Gfyp+GgG v
  gi|119719135|ref|YP_919630.1|  88 VADIGTAGSVTLLLQASLPVLLAAEGKVGLEVRGGTSVRWSPPYRYFENVLIPLISKFG-AKISSKLLREGFYPEGGGAV 166
                                    ***********************************************************.8******************* PP

                                    EEEEE-.-S---EB.................................................................. CS
                                    xxxxxxxxxxxxxx.................................................................. RF
                            RTC 159 elevepskklkpie.................................................................. 172
                                     +e++p   l+pi+                                                                  
  gi|119719135|ref|YP_919630.1| 167 YVETTPGYPLEPINltakstpgpvegasyvgnlpchiaerqarsareriesagfnvgkvnvvcnqpatgrgsgivlwarv 246
                                    *****9767*********************************************************************** PP

                                    ...................................BSS-HHHHHHHHHHHHHHT.-EEEEESS--HHHHHHHHHHHHHSS CS
                                    ...................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            RTC 173 ...................................acvDehlqdqlilfmaLakgksrirvaeltlhtetairvieqflg 217
                                                                       a+vD+h  d+l+++m La+g+s i ++elt+h+eta+++++q++g
  gi|119719135|ref|YP_919630.1| 247 gegvvgsdalgergkpaedvgreaaerllpilkagAPVDPHASDNLVIYMSLARGESAILTTELTSHAETALELCRQITG 326
                                    ******************************************************************************** PP

                                    -EEEE CS
                                    xxxxx RF
                            RTC 218 vkfkv 222
                                    ++++v
  gi|119719135|ref|YP_919630.1| 327 ATYTV 331
                                    *9976 PP

>> RTC_insert  RNA 3'-terminal phosphate cyclase (RTC), insert domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.1   0.1   6.6e-21   5.9e-17       9      99 ..     190     275 ..     187     279 .. 0.89

  Alignments for each domain:
  == domain 1  score: 62.1 bits;  conditional E-value: 6.6e-21
                                    EEEEEEEESS-THHHHHHHHHHHHHHTTTSSEEEEEEE.EE-CGGC-SS-EEEEEEEEE-T.TS-EEEEEEEE-TT--HH CS
                     RTC_insert   9 irGvafaarvspsvanrmveaargvLnkllpdvyiytdvvkegkesgkspGfgisLvaetttegvllgaealgekgvppe 88 
                                    ++G +++ +++ ++a+r++++ar+++++++ +v  ++ vv++  + + ++G+gi+L+a    +++++g++alge+g+p+e
  gi|119719135|ref|YP_919630.1| 190 VEGASYVGNLPCHIAERQARSARERIESAGFNVG-KVNVVCN--QPATGRGSGIVLWARV--GEGVVGSDALGERGKPAE 264
                                    7899*************************88777.4443444..45689***********..5799************** PP

                                    HHHHHHHHHHH CS
                     RTC_insert  89 dvGeeaaeeLl 99 
                                    dvG+eaae+Ll
  gi|119719135|ref|YP_919630.1| 265 DVGREAAERLL 275
                                    **********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       192  (0.0107089); expected 358.6 (0.02)
Passed bias filter:                      179  (0.00998383); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 2187.22
//
Query:       gi|119719136|ref|YP_919631.1|  [L=199]
Description: CDP-alcohol phosphatidyltransferase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-13   51.5   1.1    1.3e-13   51.5   1.1    2.5  2  CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
  ------ inclusion threshold ------
      0.054   12.8   0.1      0.071   12.4   0.1    1.1  1  TMEM164          TMEM164 family


Domain annotation for each model (and alignments):
>> CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.5   1.1   1.4e-17   1.3e-13       3      66 .]      27      90 ..      25      90 .. 0.93
   2 ?    0.2   1.6      0.15   1.4e+03      26      27 ..     121     154 ..      93     182 .. 0.42

  Alignments for each domain:
  == domain 1  score: 51.5 bits;  conditional E-value: 1.4e-17
                                   HHHHHHHHHHHHHHHHHGGGS-H..HHHHHHHHHHHHHTTHHHHHHHHTT---HHHHHHHHHHH CS
                CDP-OH_P_transf  3 PnaiTllrlllsvlailllltyyplvlailllliasltDalDGklARrlnqvstlGkllDslaD 66
                                   Pn iT+l+++l  +++ ll+++  l   ++++ +asl+D lDG++AR+++ vs +G++lDs +D
  gi|119719136|ref|YP_919631.1| 27 PNHITVLGFALNASSVALLAWTGSLPSFLAVFTLASLMDVLDGYVARKTGRVSAFGAFLDSTLD 90
                                   9***************99988888888888888****************************998 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.15
                                    .................................. CS
                CDP-OH_P_transf  26 p................................l 27 
                                                                     +
  gi|119719136|ref|YP_919631.1| 121 LvsytraraeslgvkmagigiaeraerlllkfsV 154
                                    0444444444444444444444444444333330 PP

>> TMEM164  TMEM164 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   7.9e-06     0.071      25     110 ..      87     183 ..      69     196 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.9e-06
                        TMEM164  25 slkqrlletvlvvvlsileilvalkkl.........rkklpkkeeekevkkkessg...........krllLvllslvfG 84 
                                    s+  r+ +t++  +l+++ +  a++++         +          + ++ es g            + lL+ +s+ f+
  gi|119719136|ref|YP_919631.1|  87 STLDRVSDTLTSFALMLVGVASAYETIflvlgeylvS---------YTRARAESLGvkmagigiaerAERLLLKFSVFFA 157
                                    4567999*******************95555544332.........2222233333344455566657889999****** PP

                        TMEM164  85 iEigfKlatktviylLnpCHvvtvlq 110
                                    i ig  ++ + v+++L     +tvlq
  gi|119719136|ref|YP_919631.1| 158 ILIGASIVARAVLWVLILVTYITVLQ 183
                                    ****************9988888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       714  (0.0398237); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1440.18
//
Query:       gi|119719137|ref|YP_919632.1|  [L=118]
Description: ubiquitin-associated domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-12   46.4   0.3      5e-12   45.6   0.3    1.4  1  NAC       NAC domain
     0.0059   16.6   0.0     0.0075   16.3   0.0    1.3  1  HOIP-UBA  HOIP UBA domain pair
  ------ inclusion threshold ------
        0.1   12.4   0.0        0.3   10.9   0.0    1.7  2  UBA_4     UBA-like domain


Domain annotation for each model (and alignments):
>> NAC  NAC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   0.3   8.4e-16     5e-12       3      56 ..       7      64 ..       5      65 .. 0.91

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 8.4e-16
                            NAC  3 Klrkalkklgl..keipgieeVtirksdgkvlvfdnPkVq...kspgsntyvvfGeaee 56
                                   + r++l ++gl  k+i+g++eV i+ ++ k +++  P+Vq   +  g ++y+v+G  ee
  gi|119719137|ref|YP_919632.1|  7 EQRRMLERMGLvfKPIEGVQEVQIKLAG-KTIIIRSPEVQvleIKGGGKIYYVTGVEEE 64
                                   679*************************.*************5555589******8876 PP

>> HOIP-UBA  HOIP UBA domain pair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.3e-06    0.0075      73      99 ..      90     115 ..      67     118 .] 0.84

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.3e-06
                       HOIP-UBA  73 lsraEakealleagGdvekAvkqclre 99 
                                     s +Eak+al+e+gGd+ kA+ ++ ++
  gi|119719137|ref|YP_919632.1|  90 ASPEEAKRALIESGGDIAKAILSL-SQ 115
                                    589*****************9654.34 PP

>> UBA_4  UBA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.58   3.5e+03      10      17 ..      58      65 ..      58      65 .. 0.86
   2 ?   10.9   0.0     5e-05       0.3      11      33 ..      88     110 ..      88     112 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.58
                          UBA_4 10 iTGadeek 17
                                   +TG++ee+
  gi|119719137|ref|YP_919632.1| 58 VTGVEEEV 65
                                   7***9986 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 5e-05
                          UBA_4  11 TGadeekArqlLeannWdLerAi 33 
                                    TGa++e+A++ L  +++d+  Ai
  gi|119719137|ref|YP_919632.1|  88 TGASPEEAKRALIESGGDIAKAI 110
                                    9******************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 936.95
//
Query:       gi|119719138|ref|YP_919633.1|  [L=244]
Description: hypothetical protein Tpen_0220 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-30  106.9   0.0    1.3e-30  106.6   0.0    1.1  1  DUF5616   Domain of unknown function (DUF5616)
    1.9e-20   72.3   0.7    1.9e-20   72.3   0.7    1.7  2  DUF434    Protein of unknown function (DUF434)


Domain annotation for each model (and alignments):
>> DUF5616  Domain of unknown function (DUF5616)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.6   0.0   1.4e-34   1.3e-30       3     139 ..      80     221 ..      78     222 .. 0.96

  Alignments for each domain:
  == domain 1  score: 106.6 bits;  conditional E-value: 1.4e-34
                        DUF5616   3 elkgkelliDGfNvlitlesalsgevlllcdDgviRDlagvrgkyklveeteealelilellkelkvkkvifllDkpvSn 82 
                                    +l    l++D+fN + t++sal g+vl++++Dg++RDla+ +++++ ++ + +al ++l++l++l+v++++f++D++vS 
  gi|119719138|ref|YP_919633.1|  80 SLGTGLLVVDAFNQVGTVSSALLGDVLVVGNDGIVRDLAAGYRRISFSPLYVSALYVLLSYLSRLGVERAVFVFDSQVSF 159
                                    5666789************************************************************************* PP

                        DUF5616  83 SgelaklireileeaglegevelvknvDkeLkesee....ivatsDsvildkvks.vldlaa 139
                                    S+++a++++++++  g e+   +++n+D+++++++e    +vatsDsvil+k+k+ v+d+a+
  gi|119719138|ref|YP_919633.1| 160 SARFAGILKSFASLLGHECWSIISPNADNTVIQLSEwegaAVATSDSVILEKTKApVVDVAK 221
                                    ********************************99999999*************997888876 PP

>> DUF434  Protein of unknown function (DUF434)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.3   0.7   2.1e-24   1.9e-20       2      56 .]      20      74 ..      19      74 .. 0.97
   2 ?   -3.1   0.0      0.72   6.5e+03      32      45 ..     138     151 ..     133     156 .. 0.80

  Alignments for each domain:
  == domain 1  score: 72.3 bits;  conditional E-value: 2.1e-24
                         DUF434  2 LkeAaeDlryLLnRGYpkksalelVgnhYqLskrqRlaLaRcvssdeeiearksK 56
                                   ++eAa+D+ yL nRGY++k++lelV+++Y+Lsk ++laL+R+++++e +++r+++
  gi|119719138|ref|YP_919633.1| 20 ICEAAKDFFYLVNRGYSRKQSLELVTARYGLSKVEKLALYRSIFPREVAASRRKR 74
                                   689*************************************************985 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.72
                         DUF434  32 LskrqRlaLaRcvs 45 
                                    Ls   Rl + R+v+
  gi|119719138|ref|YP_919633.1| 138 LSYLSRLGVERAVF 151
                                    77788888899887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1680.58
//
Query:       gi|119719139|ref|YP_919634.1|  [L=907]
Description: alanyl-tRNA synthetase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   4.6e-121  405.0   0.0   7.4e-121  404.3   0.0    1.3  1  tRNA-synt_2c  tRNA synthetases class II (A)
    6.3e-14   51.8   0.4    1.4e-13   50.7   0.4    1.6  1  tRNA_SAD      Threonyl and Alanyl tRNA synthetase second addi
    3.4e-09   37.2   0.2    1.1e-08   35.6   0.2    1.9  1  DHHA1         DHHA1 domain
    0.00044   19.6   0.5    0.00086   18.6   0.5    1.4  1  tRNA-synt_2e  Glycyl-tRNA synthetase alpha subunit
  ------ inclusion threshold ------
      0.012   16.0   3.4      0.056   13.8   0.1    2.8  3  CCDC-167      Coiled-coil domain-containing protein 167
      0.078   13.1   1.7       0.22   11.6   1.7    1.8  1  bZIP_2        Basic region leucine zipper
      0.092   11.8   0.4        0.2   10.7   0.1    1.6  2  FH2           Formin Homology 2 Domain
      0.093   13.1   0.1      0.093   13.1   0.1    2.8  3  CLZ           C-terminal leucine zipper domain of cyclic nucl
       0.12   12.3   0.0       0.33   10.9   0.0    1.7  1  Pyr_excise    Pyrimidine dimer DNA glycosylase
       0.13   12.4   0.8       0.42   10.7   0.8    1.9  1  DUF5595       Domain of unknown function (DUF5595)
       0.13   12.0   1.3       0.47   10.3   1.3    1.9  1  DivIC         Septum formation initiator
       0.14   12.2   0.0       0.28   11.3   0.0    1.4  1  ADIP          Afadin- and alpha -actinin-Binding
       0.15   12.4   4.2       0.41   10.9   0.3    2.9  2  ABC_tran_CTD  ABC transporter C-terminal domain
       0.19   11.9   3.4       0.51   10.6   3.4    1.7  1  HALZ          Homeobox associated leucine zipper
       0.25   11.2   3.1          5    7.0   0.1    2.3  2  DASH_Spc19    Spc19
       0.32   11.0   9.4      0.053   13.5   3.8    2.4  2  Prefoldin_2   Prefoldin subunit
        0.5   10.5   5.8        1.2    9.3   5.8    1.6  1  bZIP_1        bZIP transcription factor
        2.2    8.5   5.3       0.46   10.7   1.0    2.2  1  JIP_LZII      JNK-interacting protein  leucine zipper II


Domain annotation for each model (and alignments):
>> tRNA-synt_2c  tRNA synthetases class II (A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  404.3   0.0  7.5e-124  7.4e-121       3     552 .]      65     594 ..      63     594 .. 0.93

  Alignments for each domain:
  == domain 1  score: 404.3 bits;  conditional E-value: 7.5e-124
                                    HHHHHHHHHCTT-EEE----SS-SSSTTCSS--SGGGGGHHHHTTSSCGGSSSEEEEEEEEE-EETTEEGGGGTTTSSS- CS
                   tRNA-synt_2c   3 rekFldfFekkgHtvvksssvvpendptllfvnAgmaqfkpiflgkeakpklkravnsQkciRagGkhnDlenVGktarH 82 
                                    r++F+dfFek++Ht+vk+++vv+++++++++v A++++f+p+++ +   p+++++v+sQ++iR++    Dl+nVGkt+rH
  gi|119719139|ref|YP_919634.1|  65 RKMFIDFFEKRNHTPVKRYPVVARWREDVYLVGASIYDFQPWVTEGLVPPPANPLVISQPSIRLT----DLDNVGKTGRH 140
                                    99***************************************************************....*********** PP

                                    -SEEEEEEEEESS.....SS-HHHHHHHHHHHHHTTTT--GGGEEEEEETTEH..HHHHHHHHTTTTEGGGEEEE-HHHH CS
                   tRNA-synt_2c  83 hTfFeMlGnfsfg.....dYfkeeaiefawelltkelgldkerlyvtvfeedd..eaveiweklvgvpeerilrfgekdn 155
                                    +T FeM+++++f+      Y+ +e++e+a+e+ltk++g+++e+++++   + +  +a+e +e +v++ e ++l+f   + 
  gi|119719139|ref|YP_919634.1| 141 LTGFEMMAHHAFNirdqrVYWANETVEYAFEVLTKVYGVKPEEITFIFDMWSGggNAGEDYEVIVRGLEVATLVF---MH 217
                                    *****************99******************************999999********************...99 PP

                                    EEESSSS.EEEEEEEEEEEECETTSHHCHCCCCTTCTCCHEEEEEEEEEEEEEESTTSHEEEEEEEEEEEE.EEHHHHHH CS
                   tRNA-synt_2c 156 fwemgdt.gpcgpcseiyydrgeeigkrkaaseveadddrvleiwnlvfmqfnreedgtlkpLpkksidtG.mglerlva 233
                                    ++++ d     +++ ++++++g e+  +  +++ +++++ +  +++ + +  ++e+      + + +   G + +++  +
  gi|119719139|ref|YP_919634.1| 218 YKTAEDGsLIPIENRIVDTGYGLERIYWLLTGHYNVYEAVFSGVIDRLRKLSGVEK-PPDDLMYRLALKSGrLDFKKPLE 296
                                    999988534567889***************************************96.33344444555556255667777 PP

                                    HHTTHSSGGGSCCTHHHHHHHHHHHT--TCSTCCHHHHHHHHHHHHHHHHHHHHTT--SSSSHHHHHHHHHHHHHHHHHH CS
                   tRNA-synt_2c 234 vLqevrsnydtdlfvpvieaieeisgatyedkdetdealrviaDHvralafaladGvvpsnegrgYvlRrllRravrhak 313
                                     L+ +r n+  +++++ +e+++ + +         +eal+++aDH+r++a +l+dGvvpsn+g+gY++R+l+Rr++r+++
  gi|119719139|ref|YP_919634.1| 297 ALETLR-NVSREVGISFEELQRVLEP---------NEALYALADHTRTIAWMLGDGVVPSNSGAGYLARLLIRRSLRLLR 366
                                    777765.7999*********999999.........89******************************************* PP

                                    HTT-SSTHHHHHHHHHHHHHTTTGCCHHCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCC..CSEEXHHHHHHHH CS
                   tRNA-synt_2c 314 kLglkekflaklvavvvevlgdvypelkekeekveeiieeEeerFakTlerGlklleelikklkk..kkelsgedafkLy 391
                                    +L+l+ + l+++v  +++   + +pe  e ++++++i+++EeerF++ ++rG+k+l  l+ +lk+   ++++ e++ kLy
  gi|119719139|ref|YP_919634.1| 367 RLQLELP-LSEIVLWQIQYWRNDFPEYLELQDEIRDIVDTEEERFEESVKRGEKVLGALLGELKSkgLRVVPAEEIVKLY 445
                                    *******.******************************************************99977799********** PP

                                    HCHXXXHHHHHHHHHCTTXEEXHHHHHHHHHHHHHHHCCHHSXSSXXXXXXXXTTSHCHHCCTSTTTXXXXXXTSXXXXX CS
                   tRNA-synt_2c 392 dtyGfPvdltkeiaeekglkvdiegfekameeqrerskkekkekklikkdvealkelkkteeflgyeeleaeakvlallk 471
                                    +++G+P++l+ke ae++gl+ di+gf   ++e r+r++ ++ke  ++  d + lke++ t+  l+ye+           k
  gi|119719139|ref|YP_919634.1| 446 ESHGVPPELVKEKAESEGLEADITGFYSRLAEMRSRAQVQQKEALQLPLDPSRLKEFRPTRL-LYYEN----------EK 514
                                    *************************************988888889************9999.99999..........23 PP

                                    XSEEEEEEEE.EETTEEEESEEXXXXSSSSCSXXXEEEEESSEEEEESEEEEETTEEEEEXSS.XSXXXTTSEEEEEEXH CS
                   tRNA-synt_2c 472 dkefveevee.geevgvvLdrTpfYaesGGqigDeGliekegaefrvkdvqkakgvvlhkgkleegklkvgdkvkaevde 550
                                      ef++ v    + ++vvLd+T+fY+e+GGq +D+G++  eg+e rvk + k++ +v+h+++ +     vg +vk++vd 
  gi|119719139|ref|YP_919634.1| 515 LAEFEATVLGvLDGKYVVLDSTAFYPEGGGQLSDTGVLVYEGGECRVKYAFKVGDIVVHECEGN--APPVGARVKGVVDM 592
                                    3466666665246679*********************************************995..999*********98 PP

                                    HH CS
                   tRNA-synt_2c 551 er 552
                                    er
  gi|119719139|ref|YP_919634.1| 593 ER 594
                                    75 PP

>> tRNA_SAD  Threonyl and Alanyl tRNA synthetase second additional domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.7   0.4   1.4e-16   1.4e-13       1      44 []     693     736 ..     693     736 .. 0.96

  Alignments for each domain:
  == domain 1  score: 50.7 bits;  conditional E-value: 1.4e-16
                                    EEEEEETT.EEEEESS---SBGGGC-SEEEECCECCCTCEEEEE CS
                       tRNA_SAD   1 vrvvsiGdisvelCgGtHvpnTgeIgafkilseesiakglrRIy 44 
                                    +rvv+i  ++ e+CgGtH+++TgeIg++kil  e+i++g+ R++
  gi|119719139|ref|YP_919634.1| 693 LRVVEIPGWDAEACGGTHCDRTGEIGLIKILGFEKIQDGVVRVV 736
                                    69****66**********************************96 PP

>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.2   1.1e-11   1.1e-08       2     131 ..     773     896 ..     772     904 .. 0.85

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 1.1e-11
                                    HHHCHHHHHHHHHHHCHHHHHHHHHHHHHHHTCEEECTCEEEEEECHCCHHHHHHHHHHHHHHTHGBTTCEEEEEEEECT CS
                          DHHA1   2 eslneerkelekeleelkealaklkaeellekaeevkgvkvlvaevgeewdagalgiaadklksklkkpvivfvakeegd 81 
                                    +sl+ ++++leke+++l+e+l  lk +  ++ + +v+gv+v+v ++ +e++++  + a+++ ++     +++++++    
  gi|119719139|ref|YP_919634.1| 773 KSLKSRIEALEKEVKKLREEL--LKGGVSVSPVATVQGVQVYVYFS-DEYEPREAALAISRTRT----SSVILAYNS--- 842
                                    6899999*******6666666..67778889999999*********.*****999999999999....999999987... PP

                                    EEEEEEEESSH...SS-HHHHHHHHHHHTTCCEEEE.TCEEEEEEEHCHHHHHH CS
                          DHHA1  82 kvkvsarskkd...gvdagelakeaaaklgggGGGH.dlAaGagipaekleeal 131
                                    k ++ +++++d   ++da+e+ + +++ l g+GGG  dl +G   +  ++++++
  gi|119719139|ref|YP_919634.1| 843 KGNFALKVTDDlldRLDAREIGRSVCESLRGKGGGVrDLYQGRIDETKSVDKVI 896
                                    55888888888889*********************88*****888877766654 PP

>> tRNA-synt_2e  Glycyl-tRNA synthetase alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.5   8.7e-07   0.00086     102     179 ..     180     260 ..     161     269 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 8.7e-07
                                    CCS-EEEEEEEEEEGGGTEEEEEEEEEETTCEEEEEEEEEEETTEE-SS-.....-EEEEEEHHHHHHHHCT-SSGGG-E CS
                   tRNA-synt_2e 102 kehdirfveDdWesptlGawGlGwevwldGmeitqftYfqqvgglelkpv.....sveityGleRlamylqevdnvydle 176
                                    k ++i f+ D W     G  G  +ev + G+e++ + ++   ++ + + +      v+  yGleR+   l +  nvy+ +
  gi|119719139|ref|YP_919634.1| 180 KPEEITFIFDMWS--GGGNAGEDYEVIVRGLEVATLVFMHYKTAEDGSLIpienrIVDTGYGLERIYWLLTGHYNVYEAV 257
                                    456899******7..5699***************98888766555544440011145578*****************998 PP

                                    CCT CS
                   tRNA-synt_2e 177 wne 179
                                    ++ 
  gi|119719139|ref|YP_919634.1| 258 FSG 260
                                    875 PP

>> CCDC-167  Coiled-coil domain-containing protein 167
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1      0.34   3.4e+02      31      64 ..     394     427 ..     391     437 .. 0.88
   2 ?   -2.9   0.0       9.2   9.1e+03       7      31 ..     462     486 ..     459     492 .. 0.79
   3 ?   13.8   0.1   5.6e-05     0.056      30      78 ..     758     806 ..     747     814 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.34
                       CCDC-167  31 elseeeResleeEeaslkeqleenekeLksLrke 64 
                                    el++e R+ + +Ee+  +e +++ ek L  L +e
  gi|119719139|ref|YP_919634.1| 394 ELQDEIRDIVDTEEERFEESVKRGEKVLGALLGE 427
                                    788999********************99988766 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 9.2
                       CCDC-167   7 dkleeklascrerLeaverrlrkee 31 
                                    ++le  ++ ++ rL ++ +r + ++
  gi|119719139|ref|YP_919634.1| 462 EGLEADITGFYSRLAEMRSRAQVQQ 486
                                    7899999999999999988876555 PP

  == domain 3  score: 13.8 bits;  conditional E-value: 5.6e-05
                       CCDC-167  30 eelseeeResleeEeaslkeqleenekeLksLrkeNrksmllsvalllv 78 
                                    +e+ +   e+lee  +slk+++e  eke k+Lr+e  k  + + ++ +v
  gi|119719139|ref|YP_919634.1| 758 QEILDASYEGLEEKAKSLKSRIEALEKEVKKLREELLKGGVSVSPVATV 806
                                    5666777899************************988866655555544 PP

>> bZIP_2  Basic region leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.7   0.00022      0.22      27      54 .]     765     792 ..     763     792 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00022
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         bZIP_2  27 eeeleervkeLeeeNaqLrqkveqLeke 54 
                                    +e+lee++k+L++++++L+++v++L+ e
  gi|119719139|ref|YP_919634.1| 765 YEGLEEKAKSLKSRIEALEKEVKKLREE 792
                                    689**********************876 PP

>> FH2  Formin Homology 2 Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       4.7   4.7e+03     251     275 ..     383     407 ..     382     443 .. 0.71
   2 ?   10.7   0.1    0.0002       0.2     257     304 ..     744     791 ..     726     801 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 4.7
                                    HHHHTTSGGGGGHHHHTTTHHHCCT CS
                            FH2 251 kiireklpevldfsseLknvkkaak 275
                                    ++ r+ +pe l++++e++++ ++ +
  gi|119719139|ref|YP_919634.1| 383 QYWRNDFPEYLELQDEIRDIVDTEE 407
                                    6778899999999999998877544 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0002
                                    SGGGGGHHHHTTTHHHCCTS-HHHHHHHHHHHHHHHHHHHHHHHHCCT CS
                            FH2 257 lpevldfsseLknvkkaakvnleslekevkklekglkklekelessek 304
                                    l+ v+++ ++Lkn++++   ++e le++ k l++++++leke+++ ++
  gi|119719139|ref|YP_919634.1| 744 LEYVQGMGDKLKNLQEILDASYEGLEEKAKSLKSRIEALEKEVKKLRE 791
                                    66788999***********************************98766 PP

>> CLZ  C-terminal leucine zipper domain of cyclic nucleotide-gated channels
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       7.8   7.7e+03      24      43 ..     405     424 ..     396     431 .. 0.64
   2 ?   -0.1   0.1       1.3   1.3e+03      21      47 ..     456     482 ..     452     490 .. 0.85
   3 ?   13.1   0.1   9.4e-05     0.093      31      71 .]     745     785 ..     738     785 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 7.8
                            CLZ  24 aeqkeleekverLessLeaL 43 
                                    +e++ +ee v+r e+ L aL
  gi|119719139|ref|YP_919634.1| 405 TEEERFEESVKRGEKVLGAL 424
                                    56666777777666665554 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.3
                            CLZ  21 kagaeqkeleekverLessLeaLqtrl 47 
                                    k++ae + le  ++ ++s+L  +  r 
  gi|119719139|ref|YP_919634.1| 456 KEKAESEGLEADITGFYSRLAEMRSRA 482
                                    67799999************9999886 PP

  == domain 3  score: 13.1 bits;  conditional E-value: 9.4e-05
                            CLZ  31 ekverLessLeaLqtrlarLlaeyessqrkLkqRitkLEkk 71 
                                    e v+ +  +L++Lq  l    + +e+ ++ Lk+Ri++LEk+
  gi|119719139|ref|YP_919634.1| 745 EYVQGMGDKLKNLQEILDASYEGLEEKAKSLKSRIEALEKE 785
                                    789999*********************************86 PP

>> Pyr_excise  Pyrimidine dimer DNA glycosylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00033      0.33      56     121 ..     777     842 ..     773     849 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00033
                                    TBHHHHHHHHHHHHHHHHHTT---S--S----TTS-GGGB------HHHHHHHHHHHHHHHTTSGG CS
                     Pyr_excise  56 nkleyLrkrylllieEmlkRgynvneeekddisevekeyrgdwtpteeaialnleriaekipikpe 121
                                    +++e L k  ++l eE+lk g++v++ ++ +  +v   +  +++p+e+a+a++++r +  i  +++
  gi|119719139|ref|YP_919634.1| 777 SRIEALEKEVKKLREELLKGGVSVSPVATVQGVQVYVYFSDEYEPREAALAISRTRTSSVILAYNS 842
                                    5678999999********************9999999999****************9988877765 PP

>> DUF5595  Domain of unknown function (DUF5595)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.8   0.00043      0.42      39      73 .]     751     785 ..     745     785 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00043
                        DUF5595  39 eskLkelynvdeaqlesleeeekrLeeEierleke 73 
                                      kLk+l ++ +a  e lee+ k L+  ie+leke
  gi|119719139|ref|YP_919634.1| 751 GDKLKNLQEILDASYEGLEEKAKSLKSRIEALEKE 785
                                    569*******************************8 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.3   0.00047      0.47      22      51 ..     761     790 ..     746     795 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00047
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHCC-X CS
                          DivIC  22 lkqeiaalqaelaklkaeneeLeaevkdLk 51 
                                    l++ ++ l+++ ++lk ++e+Le+evk+L+
  gi|119719139|ref|YP_919634.1| 761 LDASYEGLEEKAKSLKSRIEALEKEVKKLR 790
                                    67788999*********************6 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00028      0.28      77     125 ..     752     800 ..     747     811 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00028
                           ADIP  77 erlktqleqlerelalvqakerqlekklktleqklknekeelqrlknal 125
                                    ++lk+  e l+   + +++k ++l+ ++++le+ +k+++eel +    +
  gi|119719139|ref|YP_919634.1| 752 DKLKNLQEILDASYEGLEEKAKSLKSRIEALEKEVKKLREELLKGGVSV 800
                                    588999999999999***************************9976555 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.2      0.44   4.4e+02       5      28 ..     456     479 ..     455     490 .. 0.84
   2 ?   10.9   0.3   0.00041      0.41      10      38 ..     772     800 ..     762     810 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.44
                   ABC_tran_CTD   5 keqreleeleaeIeaLEeeiaele 28 
                                    ke+ e e lea+I     ++ae+ 
  gi|119719139|ref|YP_919634.1| 456 KEKAESEGLEADITGFYSRLAEMR 479
                                    9************98877777765 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00041
                   ABC_tran_CTD  10 leeleaeIeaLEeeiaeleaeladpelys 38 
                                     + l ++IeaLE+e ++l +el + ++  
  gi|119719139|ref|YP_919634.1| 772 AKSLKSRIEALEKEVKKLREELLKGGVSV 800
                                    56799*****************9887764 PP

>> HALZ  Homeobox associated leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   3.4   0.00051      0.51       8      42 ..     759     793 ..     759     794 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00051
                           HALZ   8 dvLKasYdaLksdydsLkkenekLkaelqeLkekl 42 
                                    ++L asY+ L  +  sLk   e+L++e+++L+e l
  gi|119719139|ref|YP_919634.1| 759 EILDASYEGLEEKAKSLKSRIEALEKEVKKLREEL 793
                                    57889999999999999999999999999999976 PP

>> DASH_Spc19  Spc19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1     0.005         5      56     151 ..     394     491 ..     392     495 .. 0.84
   2 ?    4.3   0.4     0.033        33      63     101 ..     752     790 ..     744     801 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.005
                                    HHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH......HHHHT-XXXXXXXXXXXX....XXXX.... CS
                     DASH_Spc19  56 slaeeiePqieellekaekeleklerreetLkaklelqegrlsnaesskkeeeeseeskeeeeeeenkeeekskkk.... 131
                                    +l++ei+  +++  e+ e+++++ e+   +L  +l+ + +r+  ae+  k  e+     e  +e++++e  ++  +    
  gi|119719139|ref|YP_919634.1| 394 ELQDEIRDIVDTEEERFEESVKRGEKVLGALLGELKSKGLRVVPAEEIVKLYESHGVPPELVKEKAESEGLEA--Ditgf 471
                                    699*****************************************99999888888877776666555443332..14578 PP

                                    XXXXXXXXXXXXXXXXXXXX CS
                     DASH_Spc19 132 ltkeelerlkkLkqkKerLk 151
                                    +++  + r ++  q+Ke+L+
  gi|119719139|ref|YP_919634.1| 472 YSRLAEMRSRAQVQQKEALQ 491
                                    9999999***********98 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.033
                                    THHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.. CS
                     DASH_Spc19  63 PqieellekaekeleklerreetLkaklelqegrlsnae 101
                                     ++++l e ++++ e le++ ++Lk+++e +e+ +++ +
  gi|119719139|ref|YP_919634.1| 752 DKLKNLQEILDASYEGLEEKAKSLKSRIEALEKEVKKLR 790
                                    567788888888888888888888888888888887754 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.3       1.5   1.5e+03      60      86 ..     396     422 ..     393     430 .. 0.81
   2 ?   13.5   3.8   5.3e-05     0.053      60      99 ..     754     793 ..     751     796 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.5
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    Prefoldin_2  60 keevkeeLeerketlekeiktlekqle 86 
                                    ++e+++ +++++e+ e+ +k+ ek l 
  gi|119719139|ref|YP_919634.1| 396 QDEIRDIVDTEEERFEESVKRGEKVLG 422
                                    688999999999999999999998765 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 5.3e-05
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    Prefoldin_2  60 keevkeeLeerketlekeiktlekqleklekeleelkeel 99 
                                    +++++e L+++ e le++ k+l++++e leke+++l+eel
  gi|119719139|ref|YP_919634.1| 754 LKNLQEILDASYEGLEEKAKSLKSRIEALEKEVKKLREEL 793
                                    7889999******************************998 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   5.8    0.0012       1.2      28      63 ..     758     793 ..     753     794 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0012
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         bZIP_1  28 ieeLerrvkaLekeNksLkseleelkkevekLkskv 63 
                                    +e L    + Le++ ksLks++e l+kev+kL++++
  gi|119719139|ref|YP_919634.1| 758 QEILDASYEGLEEKAKSLKSRIEALEKEVKKLREEL 793
                                    566777788999999***************999875 PP

>> JIP_LZII  JNK-interacting protein  leucine zipper II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.0   0.00046      0.46      36      71 .]     752     787 ..     751     787 .. 0.97

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00046
                       JIP_LZII  36 deLtsereiLreEleslqkakerlesrikelEeelk 71 
                                    d+L++ +eiL    e l++  ++l+sri++lE+e+k
  gi|119719139|ref|YP_919634.1| 752 DKLKNLQEILDASYEGLEEKAKSLKSRIEALEKEVK 787
                                    789999****************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (907 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1063  (0.0592894); expected 358.6 (0.02)
Passed bias filter:                     1010  (0.0563333); expected 358.6 (0.02)
Passed Vit filter:                       232  (0.0129399); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.94u 0.31s 00:00:01.25 Elapsed: 00:00:00.47
# Mc/sec: 5811.84
//
Query:       gi|119719140|ref|YP_919635.1|  [L=294]
Description: acidic ribosomal protein P0 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.1e-24   84.4   0.0    1.4e-23   82.6   0.0    2.0  2  RL10P_insert   Insertion domain in 60S ribosomal protein L10P
    1.3e-22   79.8   0.1    2.7e-22   78.8   0.1    1.6  1  Ribosomal_L10  Ribosomal protein L10


Domain annotation for each model (and alignments):
>> RL10P_insert  Insertion domain in 60S ribosomal protein L10P
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.6   0.0   1.6e-27   1.4e-23       1      70 [.     116     185 ..     116     186 .. 0.99
   2 ?   -2.9   0.0      0.81   7.2e+03      31      48 ..     192     209 ..     191     213 .. 0.63

  Alignments for each domain:
  == domain 1  score: 82.6 bits;  conditional E-value: 1.6e-27
                   RL10P_insert   1 AraGtiAtedviipagplelaPgsiepeLrklglptklkkGkivleedylvckkGetltseqaqlLklLg 70 
                                    AraG+iAt+++++pag+++  Pg++++ ++klg+pt++++G i++ +d++v+k G+++++e a+lL++Lg
  gi|119719140|ref|YP_919635.1| 116 ARAGDIATSEIVLPAGNTGIPPGPMISNFNKLGIPTRVQEGSIWIAKDTVVAKPGDVISPELAELLSKLG 185
                                    9********************************************************************8 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.81
                   RL10P_insert  31 klglptklkkGkivleed 48 
                                    kl+++t   +Gk+v  +d
  gi|119719140|ref|YP_919635.1| 192 KLQIKTIYLDGKVVSPKD 209
                                    566777666777776555 PP

>> Ribosomal_L10  Ribosomal protein L10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.8   0.1     3e-26   2.7e-22       2      97 ..      13     109 ..      12     111 .. 0.94

  Alignments for each domain:
  == domain 1  score: 78.8 bits;  conditional E-value: 3e-26
                                    SCCCHCCCCCCCCCCCTTSSEEEEEE-TTS-HHHHHHCCCHHHHHGCEEEEESCCCCCCCCHCCTSS.S.SCGCCSSSEE CS
                  Ribosomal_L10   2 tkekKeelvkelkellkkyksvvvvdyegltvaqlqelRkklrengaelkvvKntlmrrAleetgeeek.lkellkgpva 80 
                                    ++++K++l++el+  lk+y++ +v++++gl+++ +++ R  lr++g+ +kvvKnt++ +Al++tg+  + ++e+l+g++a
  gi|119719140|ref|YP_919635.1|  13 ARARKAKLLEELSGYLKQYRYYMVASITGLPASVVKTSRSLLRSDGSLMKVVKNTIFLLALKNTGKYVEgIEEHLRGQNA 92 
                                    589***************************************************************7535********** PP

                                    EEEESS-TCHHHHCCCC CS
                  Ribosomal_L10  81 lvftnedpvalakvlee 97 
                                    ++ftn++p+++   l++
  gi|119719140|ref|YP_919635.1|  93 VIFTNKNPFEILFFLDK 109
                                    **********9877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 1725.08
//
Query:       gi|119719141|ref|YP_919636.1|  [L=225]
Description: 50S ribosomal protein L1P [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.4e-40  138.5   0.1    2.9e-40  138.2   0.1    1.0  1  Ribosomal_L1  Ribosomal protein L1p/L10e family
  ------ inclusion threshold ------
       0.18   11.7   1.6       0.78    9.7   0.0    2.3  3  NOG1_N        NOG1 N-terminal helical domain


Domain annotation for each model (and alignments):
>> Ribosomal_L1  Ribosomal protein L1p/L10e family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.2   0.1   3.2e-44   2.9e-40       5     203 ..      25     213 ..      16     214 .. 0.94

  Alignments for each domain:
  == domain 1  score: 138.2 bits;  conditional E-value: 3.2e-44
                                    S-SSS--EEEEEEEESSS-TTSGGG--EEEEE-STS.TSSCS-EEEEE-HHHHH...HHHHTT..-SEEETCHHHHHHT- CS
                   Ribosomal_L1   5 akkkfdesveialnlttkkpkkadqrkpgkipLphp.lgkevkiclitkdpqaeyakeakeagriakviglkklkkkyks 83 
                                    +k++f++sve++++l+++++kk+++r +  + Lphp  gk +k+++i+ +++a    +akeag  + v++ ++l+k   +
  gi|119719141|ref|YP_919636.1|  25 KKRRFTQSVEMIVTLRDVDVKKPENRLNTVVALPHPaPGKLAKVAVIASGDTAL---KAKEAG-ADIVVDKDELQKIGND 100
                                    3778********************************99999*************...9*****.6667899999999999 PP

                                    HHHHHHTCCH-SEEEEEGGGHHHHHHHCHHHHGGGT-S-ECC..CT.BTS-HHHHHHHHCTTEEEEE-TTTSEEEEEEEE CS
                   Ribosomal_L1  84 feakrkllkefdlfladdrimpllpklLGkvfgkrkkmPipvltkgtvkedvkkevekalkstvvvrldkgtclsvkvGk 163
                                    ++a +kl+k +d+fla++++mpl++++LGk +g+r+kmP p+    +v   + + +e++ + +v +r++++  +++++G 
  gi|119719141|ref|YP_919636.1| 101 KKAAKKLAKRYDFFLAQPDLMPLVGRVLGKYLGPRGKMPQPI--PPNV--ALDALIERFRR-SVRIRMKDEPQIACRIGV 175
                                    ******************************************..5334..59*********.****************** PP

                                    TTSSHHHHHHHHHHHHHHHHHTSTTTSGSEEEEEEEETTS CS
                   Ribosomal_L1 164 lsftaeelaeNieavvkalvekvpkkwkniksiylkttms 203
                                      ++ e+laeN+ av+ ++ +k p    ni  iy k tm+
  gi|119719141|ref|YP_919636.1| 176 ETQPVEHLAENARAVLAEILKKFP--PPNIDRIYFKLTMG 213
                                    **********************77..57**********98 PP

>> NOG1_N  NOG1 N-terminal helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0      0.89     8e+03      12      43 ..      14      44 ..      11      54 .. 0.53
   2 ?    0.7   0.0      0.05   4.5e+02      78     106 ..      85     109 ..      81     116 .. 0.64
   3 ?    9.7   0.0   8.7e-05      0.78       3      66 ..     137     200 ..     136     211 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 0.89
                         NOG1_N 12 elidkalrrakraakttkkkkneikrlrnlea 43
                                   e i++al  + ++ + t+   ++i  lr++  
  gi|119719141|ref|YP_919636.1| 14 EAIKEALVSSPKKRRFTQS-VEMIVTLRDVDV 44
                                   5555555544444444433.355556665555 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.05
                         NOG1_N  78 ldvlvdkdelkksLaqvkwarklirkigk 106
                                    +d++vdkdel+k      + +k ++k++k
  gi|119719141|ref|YP_919636.1|  85 ADIVVDKDELQKI----GNDKKAAKKLAK 109
                                    7899999987654....444444444444 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 8.7e-05
                         NOG1_N   3 kiptvptseelidkalrrakraakttkkkkneik.rlrnlearkvrtasntlsdkLeeivkkfPn 66 
                                    k+p + +++  +d+ ++r  r  +   k++ +i+ r+  +e++ v+ ++++ ++ L+ei+kkfP 
  gi|119719141|ref|YP_919636.1| 137 KMPQPIPPNVALDALIERFRRSVRIRMKDEPQIAcRI-GVETQPVEHLAENARAVLAEILKKFPP 200
                                    7888888888888888888887766666666665155.9************************83 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1683.15
//
Query:       gi|119719142|ref|YP_919637.1|  [L=168]
Description: ribosomal protein L11 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-24   86.1   4.4    2.6e-24   85.5   4.4    1.3  1  Ribosomal_L11    Ribosomal protein L11, RNA binding domain
    3.5e-24   84.4   0.6    7.3e-24   83.4   0.6    1.6  1  Ribosomal_L11_N  Ribosomal protein L11, N-terminal domain


Domain annotation for each model (and alignments):
>> Ribosomal_L11  Ribosomal protein L11, RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.5   4.4   2.9e-28   2.6e-24       2      70 .]      72     139 ..      71     139 .. 0.98

  Alignments for each domain:
  == domain 1  score: 85.5 bits;  conditional E-value: 2.9e-28
                                    --SHHHHHHHHHTXSSXXSSTTTSXXEEEEHHHHHHHHHHHGGGHTXS.SHHHHHHHHHHHHCTTTEEE CS
                  Ribosomal_L11   2 tPptsylLkkaagiekgsgkpgketvGtvslkqvyeIAkiKksdlnaalsleaavksilgtArsmGikV 70 
                                    tP+t++l++k++++ekg+ +p++e vG+++l+qv++IAkiKk+d+ a+ +l+aavk+++gtA+smG+++
  gi|119719142|ref|YP_919637.1|  72 TPTTAALIIKELKVEKGAHQPSRENVGNLTLQQVIKIAKIKKKDMGAS-TLKAAVKTVAGTAQSMGVTI 139
                                    9*********************************************99.******************97 PP

>> Ribosomal_L11_N  Ribosomal protein L11, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.4   0.6   8.2e-28   7.3e-24       6      63 ..       6      64 ..       2      81 .. 0.93

  Alignments for each domain:
  == domain 1  score: 83.4 bits;  conditional E-value: 8.2e-28
                Ribosomal_L11_N  6 kvvklrvpaGkAtpaPplGpaLGplGlnikkfckefnkaTkdkkglripVkitv.yqdr 63
                                   k++   v++GkAt++Pp+GpaLGplGln+++++k +n+ T+d++g+r+pVk+tv  + +
  gi|119719142|ref|YP_919637.1|  6 KTFTFLVEGGKATAGPPIGPALGPLGLNVMQVVKRINELTADYAGMRVPVKVTVdVEKK 64
                                   788999************************************************54555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       799  (0.0445647); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 1084.31
//
Query:       gi|119719143|ref|YP_919638.1|  [L=141]
Description: 30S ribosomal protein S19P [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-32  110.7   0.6    3.4e-32  110.2   0.6    1.3  1  Ribosomal_S19  Ribosomal protein S19


Domain annotation for each model (and alignments):
>> Ribosomal_S19  Ribosomal protein S19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.2   0.6   1.9e-36   3.4e-32       2      81 .]      40     124 ..      39     124 .. 0.91

  Alignments for each domain:
  == domain 1  score: 110.2 bits;  conditional E-value: 1.9e-36
                                    HHHSS.TTCCCHHHHHHHHHH....TS-----EEES-TT-B--GGGTT-EEEEE-SSSEEEEE--CCCTTSBCGGGT-SS CS
                  Ribosomal_S19   2 slkkg.pfvqesllkkvrkak....aekkkevikthsRdstIlPemvgltvgVynGktfvpveikeemvGhkLgEFspTr 76 
                                     +k+g + ++ +ll+k+r+a     + kk+ vikth+Rd +IlPemvglt++V+nGk+fvpvei++e +Gh+LgEF++T 
  gi|119719143|ref|YP_919638.1|  40 VFKQGtSEEHLKLLEKIRRAAklasEGKKQPVIKTHLRDFIILPEMVGLTIHVHNGKEFVPVEITPEKIGHYLGEFALTT 119
                                    57888788999******955548655569999************************************************ PP

                                    ----S CS
                  Ribosomal_S19  77 kpvkh 81 
                                    k v+h
  gi|119719143|ref|YP_919638.1| 120 KKVEH 124
                                    ***99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 937.14
//
Query:       gi|119719144|ref|YP_919639.1|  [L=391]
Description: FAD-dependent pyridine nucleotide-disulphide oxidoreductase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-46  158.1   0.2    3.3e-46  157.8   0.2    1.1  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    2.7e-11   43.9   6.3    3.4e-09   37.1   0.8    2.8  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    2.8e-09   37.0   6.2      0.012   15.2   0.0    4.1  4  DAO             FAD dependent oxidoreductase
    3.2e-06   27.2   1.6        3.3    7.7   0.0    4.1  4  NAD_binding_9   FAD-NAD(P)-binding
     0.0029   16.9   0.6       0.72    9.0   0.1    2.2  2  FAD_binding_3   FAD binding domain
      0.004   16.5   0.1        1.5    8.0   0.0    2.4  2  Amino_oxidase   Flavin containing amine oxidoreductase
     0.0042   17.3   0.7       0.38   11.0   0.1    2.7  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
     0.0074   15.2   4.4        1.5    7.6   0.7    3.8  4  Trp_halogenase  Tryptophan halogenase
     0.0086   16.3   1.3        1.4    9.2   0.2    2.9  2  TrkA_N          TrkA-N domain
  ------ inclusion threshold ------
      0.049   12.8   0.1       0.28   10.3   0.0    2.1  2  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
      0.086   11.5   2.6        9.8    4.7   0.0    3.4  4  HI0933_like     HI0933-like protein
       0.11   11.8   0.3        5.6    6.2   0.0    2.5  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
       0.21   10.6   1.3        3.8    6.5   0.2    2.2  2  FAD_binding_2   FAD binding domain


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.8   0.2   2.4e-49   3.3e-46       2     294 .]       5     300 ..       4     300 .. 0.88

  Alignments for each domain:
  == domain 1  score: 157.8 bits;  conditional E-value: 2.4e-49
                                    SEEEE--SHHHHHHHHHHHH....HTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH...HHHHCHHHHCCCCHCCT CS
                                    xxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2   2 dvvviGgGpAGlaaaltlaq....agakvtlvelegtclnggcllskallgvaedaeias...evvkklnqgielllgee 74 
                                     +vv+GgG++G+ a +tl+        +v+lv++ + +++  ++l++ + g +  ++  +   e  k+l  g e+llg e
  gi|119719144|ref|YP_919639.1|   5 TIVVVGGGFGGFYALKTLSGlgltERNRVVLVDKSRRFVYL-PSLPYLISGKKTVEDLTEpleEIAKRL--GAEFLLG-E 80 
                                    69******************8887799*****999999999.888888888888887666775444444..5679999.9 PP

                                    CEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-T....SEEEEES- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxx RF
                    Pyr_redox_2  75 vvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllp....krivvvGg 150
                                    v+++  ++k+++l     +++ek+ yd+lvlA G+++   gipG+  ++      l++ e++ ++l +     r+++ Gg
  gi|119719144|ref|YP_919639.1|  81 VTRVSLQEKTIEL-----SNGEKLRYDYLVLAAGATTEYYGIPGA-HQALPA-WRLEDYERIVRELGKcgsgCRVCIAGG 153
                                    *************.....7899***********************.333333.689***********9************ PP

                                    SHHHHHHHHH.HHHH.T-.EEEEEESSSSSSTTS-.HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEE CS
                                    xxxxxxxxxx.xxxx.xx.xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 151 GyiGvElAaa.lakl.gk.evtlveardrllrald.kelsaaleealekeGvevklgtsvkeidgngeklevvledgeei 226
                                    G++GvE+A++ + k+ gk ev++ve ++ l+++l+ +++s+++ee l  +Gv++  g+ v  + +++    + ledg++i
  gi|119719144|ref|YP_919639.1| 154 GLTGVEVAGEvAEKYeGKsEVVVVEKMQMLMPTLNsQRASKIIEEFLSSKGVRIIKGNGVSSVSEKN----LNLEDGTSI 229
                                    **********5566686636***********8887589**********************9999666....8******** PP

                                    EESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBE.SSTTEEE-GGGC....TECCSS--HHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx....xxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 227 dadlvvvavGvrpstelleeklglelderggivvdeflrt.nvpgiyaiGDva....ggkggpelaqaAvqqG 294
                                    ++d vv+ vGvrp + ++  ++ ++++ rg+i v+++l++ + +++yaiGD+     + ++ ++ a +A+ qG
  gi|119719144|ref|YP_919639.1| 230 QCDIVVWTVGVRPPD-IR-FDVDVPVKGRGWICVKPTLQVmSRDDVYAIGDINhfavDSDYAMKMAEEAILQG 300
                                    **************7.55.89******************945**********999988888888888888776 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.5    0.0017       2.3       2      35 ..       6      43 ..       5      95 .. 0.89
   2 !   37.1   0.8   2.5e-12   3.4e-09       1      70 [.     147     220 ..     147     227 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0017
                                   EEEECSSHHHHHHHHHHHHTT....SEEEEEESSSSSS CS
                      Pyr_redox  2 vvvvGgGyiglElAgalaelg....kkVtvversdkll 35
                                   +vvvGgG+ g  + ++l+ lg    ++V +v+ s ++ 
  gi|119719144|ref|YP_919639.1|  6 IVVVGGGFGGFYALKTLSGLGlterNRVVLVDKSRRFV 43
                                   8********************88888999999998886 PP

  == domain 2  score: 37.1 bits;  conditional E-value: 2.5e-12
                                    EEEEECSSHHHHHHHHHHHH.TT..SEEEEEESSSSSSTTSS.HHHHHHHHHHHHHTTEEEECSEEEEEEEEET CS
                      Pyr_redox   1 kvvvvGgGyiglElAgalae.lg..kkVtvversdkllrllD.eeaskilqeklekngievllntkveeiegse 70 
                                    +v + GgG++g+E+Ag+ ae +   ++V vve + +l++ l+ + aski++e l+ +g++++ ++ v ++ +++
  gi|119719144|ref|YP_919639.1| 147 RVCIAGGGLTGVEVAGEVAEkYEgkSEVVVVEKMQMLMPTLNsQRASKIIEEFLSSKGVRIIKGNGVSSVSEKN 220
                                    6889**************87444678************6665267999*********************98654 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.2     0.014        19       2      31 ..       6      41 ..       5      43 .. 0.80
   2 !   15.2   0.0     9e-06     0.012     148     205 ..      61     113 ..      58     131 .. 0.77
   3 !    8.6   0.4   0.00087       1.2       1      30 [.     147     181 ..     147     199 .. 0.79
   4 !    9.6   0.0   0.00044       0.6     152     269 ..     196     303 ..     182     322 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.014
                                   EEEECTSHHHHHHHHHHHHTT......EEEEESSSS CS
                            DAO  2 vviiGGGiiGlstAyeLarrg......Vtllekgdi 31
                                   +v++GGG  G  +   L+  g      V+l++k+++
  gi|119719144|ref|YP_919639.1|  6 IVVVGGGFGGFYALKTLSGLGlternrVVLVDKSRR 41
                                   9*********99999995544555559*****9865 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 9e-06
                                    HHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEE..EECTEEE.EEEEEEEE--GGGHH CS
                            DAO 148 ltaalaraaealGveilegtevtgleeedgkvwgve..rttpgen.daadavVnaaGawsd 205
                                    lt  l + a++lG+e+l+g evt+++ +    +++e  +   ge+ + +d++V+aaGa + 
  gi|119719144|ref|YP_919639.1|  61 LTEPLEEIAKRLGAEFLLG-EVTRVSLQ---EKTIElsN---GEKlR-YDYLVLAAGATTE 113
                                    566677889**********.*****886...45673323...88844.599******9875 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.00087
                                    EEEEECTSHHHHHHHHHHHHT..T...EEEEESSS CS
                            DAO   1 dvviiGGGiiGlstAyeLarr..g...Vtllekgd 30 
                                    +v+i GGG +G+ +A e a++  g   V+++ek  
  gi|119719144|ref|YP_919639.1| 147 RVCIAGGGLTGVEVAGEVAEKyeGkseVVVVEKMQ 181
                                    59*****************9877689******974 PP

  == domain 4  score: 9.6 bits;  conditional E-value: 0.00044
                                    HHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEEEEEEEEEE--GGGHHHHHTTCTTTSEE.EEEEEEEEEEEEC CS
                            DAO 152 laraaealGveilegtevtgleeedgkvwgverttpgendaadavVnaaGawsdllgllkeldlpi.spvrgqvlvlkpl 230
                                    + + + ++Gv+i++g  v +++e+     ++   ++g+  ++d vV + G+         +++  + +pv+g  +   ++
  gi|119719144|ref|YP_919639.1| 196 IEEFLSSKGVRIIKGNGVSSVSEK---NLNL---EDGTSIQCDIVVWTVGVRPP------DIRFDVdVPVKGRGWICVKP 263
                                    45557899************9765...3334...3355434688******9954......33333449999999888666 PP

                                    CTHSTGSGCSEEEEE.EEETTTTEEEEEETTSEEEEEESS CS
                            DAO 231 seklvspaailpvpe.tdddgrgvyvtprkdgrvlvGgta 269
                                    +++  s++ ++++ + ++   ++ y++ +++  +l G ta
  gi|119719144|ref|YP_919639.1| 264 TLQVMSRDDVYAIGDiNHFAVDSDYAMKMAEEAILQGKTA 303
                                    7766677789998888888888888888876655557765 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0024       3.3       1      35 [.       7      40 ..       7      48 .. 0.89
   2 !    7.6   0.0    0.0025       3.4     113     155 ..      70     110 ..      58     111 .. 0.77
   3 ?    5.1   0.1     0.015        20       2      36 ..     150     182 ..     149     196 .. 0.85
   4 ?    3.3   0.0     0.053        73     134     154 ..     219     239 ..     188     241 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0024
                  NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpse 35
                                   ++vG+G+ G ++l+ L      +++ ++ l+d+s 
  gi|119719144|ref|YP_919639.1|  7 VVVGGGFGGFYALKTLSGLG-LTERNRVVLVDKSR 40
                                   69***************997.89999999999965 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0025
                  NAD_binding_9 113 egvtvevhraevvdleeradgqavlladgaslaadaVvLAlGh 155
                                    +++  e++ +ev++++ ++++  + l++g++l++d++vLA G 
  gi|119719144|ref|YP_919639.1|  70 KRLGAEFLLGEVTRVSLQEKT--IELSNGEKLRYDYLVLAAGA 110
                                    445567888999999988775..899**************995 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.015
                  NAD_binding_9   2 ivGaGprGlavlerLlarakkkspleitlfdpsep 36 
                                    i G+G +G+ v+ +++++   + + e+ ++++ ++
  gi|119719144|ref|YP_919639.1| 150 IAGGGLTGVEVAGEVAEKY--EGKSEVVVVEKMQM 182
                                    89****************8..999*******9766 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.053
                  NAD_binding_9 134 qavlladgaslaadaVvLAlG 154
                                      + l+dg+s+++d Vv ++G
  gi|119719144|ref|YP_919639.1| 219 KNLNLEDGTSIQCDIVVWTVG 239
                                    34679**************99 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.0    0.0032       4.4       4      40 ..       6      46 ..       4      63 .. 0.90
   2 !    9.0   0.1   0.00053      0.72       2      42 ..     146     189 ..     145     270 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0032
                                   EEEE--SHHHHHHHHHHHHTTHH....EEEEESSSSSCCSS CS
                  FAD_binding_3  4 VlIVGaGpaGlmlallLseaGvr....vvlvekrsttvvlp 40
                                   +++VG+G  G+ + + Ls  G      vvlv+k ++ v+lp
  gi|119719144|ref|YP_919639.1|  6 IVVVGGGFGGFYALKTLSGLGLTernrVVLVDKSRRFVYLP 46
                                   68*******************988888*******9999876 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00053
                                    EEEEEE--SHHHHHHHHHHHHT..THH.EEEEESSSSSCCSSS- CS
                  FAD_binding_3   2 tdVlIVGaGpaGlmlallLsea..Gvr.vvlvekrsttvvlpra 42 
                                    + V+I G+G++G+  a + +e+  G + vv+vek++  +++  +
  gi|119719144|ref|YP_919639.1| 146 CRVCIAGGGLTGVEVAGEVAEKyeGKSeVVVVEKMQMLMPTLNS 189
                                    78**************999986336658999***9987776533 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0011       1.5     211     262 ..      63     110 ..      19     150 .. 0.83
   2 !    6.3   0.1    0.0035       4.8     218     263 ..     201     241 ..     158     254 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0011
                                    HHHHHHHHTTTTEEEETSEEEEEEEEETTCEEEEETTSTEEEESEEEE-S-H CS
                  Amino_oxidase 211 qlpealaeelrgldirlntrVkeikregdgvtvtledgevveaDaVvvTvpl 262
                                    ++ e +a+ ++g +++l+ +V++++ +  + t++l++ge++++D+ v+++  
  gi|119719144|ref|YP_919639.1|  63 EPLEEIAK-RLGAEFLLG-EVTRVSLQ--EKTIELSNGEKLRYDYLVLAAGA 110
                                    45566666.*********.9******4..4566668************9876 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0035
                                    HTTTTEEEETSEEEEEEEEETTCEEEEETTSTEEEESEEEE-S-HH CS
                  Amino_oxidase 218 eelrgldirlntrVkeikregdgvtvtledgevveaDaVvvTvplg 263
                                    + ++g++i  ++ V++++      +++ledg+++++D Vv Tv ++
  gi|119719144|ref|YP_919639.1| 201 S-SKGVRIIKGNGVSSVSE----KNLNLEDGTSIQCDIVVWTVGVR 241
                                    3.67888888888888888....9******************9876 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.1   0.00027      0.38       1      30 [.       8      41 ..       8      42 .. 0.82
   2 ?    3.9   0.0     0.046        63       1      27 [.     150     179 ..     150     212 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00027
                                   EE--SHHHHHHHHHHHC....CTEEEEEE-SSSS CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLak....agfdvlllekrdr 30
                                   +vG+G++G +a  +L+     ++ +v+l++k++r
  gi|119719144|ref|YP_919639.1|  8 VVGGGFGGFYALKTLSGlgltERNRVVLVDKSRR 41
                                   8***************722224669*****9987 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.046
                                    EE--SHHHHHHHHHHHCC..TE.EEEEE-S CS
                  NAD_binding_8   1 IvGaGlsGlvaAylLaka..gf.dvlllek 27 
                                    I G+Gl+G   A + a++  g+ +v+++ek
  gi|119719144|ref|YP_919639.1| 150 IAGGGLTGVEVAGEVAEKyeGKsEVVVVEK 179
                                    67*******999888875586548***998 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.013        19       2      34 ..       6      39 ..       5      44 .. 0.86
   2 ?    0.3   0.0      0.17   2.4e+02     158     209 ..      63     110 ..      58     116 .. 0.86
   3 !    7.6   0.7    0.0011       1.5       1      36 [.     147     182 ..     147     187 .. 0.93
   4 ?    1.1   0.0       0.1   1.4e+02     152     210 ..     188     241 ..     186     246 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.013
                                   EEEE--SHHHHHHHHHHHHHTTTS.SEEEEEE-S CS
                 Trp_halogenase  2 ivivGGGtaGwlaAaalakalkgk.levtlvese 34
                                   iv+vGGG  G+ a  +l+  +  +  +v lv+++
  gi|119719144|ref|YP_919639.1|  6 IVVVGGGFGGFYALKTLSGLGLTErNRVVLVDKS 39
                                   9****************99876666999999876 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.17
                                    HHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-SEEEE-SGG CS
                 Trp_halogenase 158 kfLrrvaearGvtrvegkvvevqldedgrveslrledgreveadlfiDcsGf 209
                                    + L+++a++ G + + g+v+ v l+e+     ++l++g+++ +d  + + G 
  gi|119719144|ref|YP_919639.1|  63 EPLEEIAKRLGAEFLLGEVTRVSLQEK----TIELSNGEKLRYDYLVLAAGA 110
                                    568999******************994....689999999999999988886 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0011
                                    EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS CS
                 Trp_halogenase   1 kivivGGGtaGwlaAaalakalkgklevtlveseei 36 
                                    ++ i+GGG  G  +A  +a+  +gk ev +ve+ ++
  gi|119719144|ref|YP_919639.1| 147 RVCIAGGGLTGVEVAGEVAEKYEGKSEVVVVEKMQM 182
                                    699*****************************9875 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.1
                                    -HHHHHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-SEEEE-SGGG CS
                 Trp_halogenase 152 daalyakfLrrvaearGvtrvegkvvevqldedgrveslrledgreveadlfiDcsGfr 210
                                    + ++  k+++++  ++Gv++++g+ v+ + ++     +l+ledg++++ d+++   G r
  gi|119719144|ref|YP_919639.1| 188 NSQRASKIIEEFLSSKGVRIIKGNGVSSVSEK-----NLNLEDGTSIQCDIVVWTVGVR 241
                                    6677788999999999*****99998877774.....799***********99887776 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0      0.02        28       1      34 [.       6      43 ..       6      63 .. 0.87
   2 !    9.2   0.2     0.001       1.4       1      40 [.     148     190 ..     148     226 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.02
                                   EEEES-SHHHHHHHHHHHH.TT...EEEEEEESSHHHH CS
                         TrkA_N  1 iiiiGlGrvGrslaeeLse.gg...kdvvvidkdeerv 34
                                   i+++G G  G   +++Ls  g    ++vv++dk+++ v
  gi|119719144|ref|YP_919639.1|  6 IVVVGGGFGGFYALKTLSGlGLterNRVVLVDKSRRFV 43
                                   79***************9955499988******98765 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.001
                                    EEEES-SHHHHHHHHHHHHTT...EEEEEEESSHHHHHHHHHT CS
                         TrkA_N   1 iiiiGlGrvGrslaeeLsegg...kdvvvidkdeerveelree 40 
                                    + i+G G +G ++a e+ e++   ++vvv++k +  + +l  +
  gi|119719144|ref|YP_919639.1| 148 VCIAGGGLTGVEVAGEVAEKYegkSEVVVVEKMQMLMPTLNSQ 190
                                    579****************6669967*****988776666554 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       0.5   6.8e+02     191     203 ..       3      15 ..       1      45 [. 0.75
   2 ?   10.3   0.0   0.00021      0.28     147     236 ..      99     191 ..      78     211 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.5
                    K_oxygenase 191 kkriaVvGsGqSa 203
                                    +k+i+VvG+G  +
  gi|119719144|ref|YP_919639.1|   3 GKTIVVVGGGFGG 15 
                                    789*******766 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00021
                    K_oxygenase 147 learnlvlgvGtepk...iPevleklegkervvHsseylerkeellakkriaVvGsGqSaaeifedllrr.qkkvelklv 222
                                    l+   lvl+ G + +   iP + ++l    r+   +++ ++  +  ++ r+ + G+G ++ e++ +++++ + k+e+ +v
  gi|119719144|ref|YP_919639.1|  99 LRYDYLVLAAGATTEyygIPGAHQALP-AWRLEDYERIVRELGKCGSGCRVCIAGGGLTGVEVAGEVAEKyEGKSEVVVV 177
                                    555567777774432234788888887.477778888888888899999*********************5457999999 PP

                    K_oxygenase 223 trsealeplddspf 236
                                     + + l p  +s+ 
  gi|119719144|ref|YP_919639.1| 178 EKMQMLMPTLNSQR 191
                                    88888877655543 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0    0.0071       9.8       2      34 ..       5      41 ..       4      44 .. 0.83
   2 ?    1.3   0.0     0.079   1.1e+02     131     165 ..      80     111 ..      53     117 .. 0.69
   3 ?    0.3   0.2      0.16   2.2e+02       2      34 ..     147     182 ..     146     185 .. 0.78
   4 ?    3.0   0.1     0.024        33      97     163 ..     178     239 ..     165     242 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0071
                                   SEEEE--SHHHHHHHHHH....HHTT--EEEE-SSSS CS
                    HI0933_like  2 dviviGgGaAGlmaAisa....akrgkrVlllekakk 34
                                   +++v+GgG  G++a  ++     ++ +rV+l++k ++
  gi|119719144|ref|YP_919639.1|  5 TIVVVGGGFGGFYALKTLsglgLTERNRVVLVDKSRR 41
                                   69************99995555577789999999876 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.079
                                    -EEEEECETTE.EEEEE.TTEEEEESEEEE----S CS
                    HI0933_like 131 evksvekeedgkfrvktkseeeleadklvlAtGGl 165
                                    ev++v+    ++ +++++++e+l+ d+lvlA G +
  gi|119719144|ref|YP_919639.1|  80 EVTRVSL---QEKTIELSNGEKLRYDYLVLAAGAT 111
                                    4555533...445789999************9975 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.16
                                    SEEEE--SHHHHHHHHHH...HHTT--EEEE-SSSS CS
                    HI0933_like   2 dviviGgGaAGlmaAisa...akrgkrVlllekakk 34 
                                    +v + GgG  G+  A ++    + +++V+++ek++ 
  gi|119719144|ref|YP_919639.1| 147 RVCIAGGGLTGVEVAGEVaekYEGKSEVVVVEKMQM 182
                                    68999*******999887333345679*****9975 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.024
                                    STTEEEETT.-CHHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE--- CS
                    HI0933_like  97 dsgrlFpvsdkaedivdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtG 163
                                    ++ ++   + ++++  +++++ l+++gv++   + v+sv++  +   ++++++++++++d +v ++G
  gi|119719144|ref|YP_919639.1| 178 EKMQMLMPTLNSQRASKIIEEFLSSKGVRIIKGNGVSSVSE--K---NLNLEDGTSIQCDIVVWTVG 239
                                    4555555555888888888899999**************33..3...4677789********99988 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.004       5.6      30      52 ..       5      27 ..       2      72 .. 0.87
   2 ?    3.0   0.2     0.038        53      27      99 ..     144     238 ..     135     242 .. 0.59

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.004
                                   EEEEESTSHHHHHHHHHHHHTT- CS
                    AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglga 52
                                   +++v+GgG  G  A++t +glg 
  gi|119719144|ref|YP_919639.1|  5 TIVVVGGGFGGFYALKTLSGLGL 27
                                   589*****************995 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.038
                                    ---EEEEESTSHHHHHHH.HHHHHT..T-EEEEEESSHHHHHHHHH.TTTCECEE.................HCHHHHHH CS
                    AlaDh_PNT_C  27 epakvlviGgGvaGlqAi.atakgl..gakVtvlDvrparleqles.lgakfvev.................lksqeell 85 
                                    + ++v + GgG  G++ + ++a +   + +V+v+++ +  +  l+s   +k++e                  +++++ +l
  gi|119719144|ref|YP_919639.1| 144 SGCRVCIAGGGLTGVEVAgEVAEKYegKSEVVVVEKMQMLMPTLNSqRASKIIEEflsskgvriikgngvssVSEKNLNL 223
                                    56899*********986624666552245677777777777777775444444445555666666666665522233333 PP

                                    H.HHHHH-SEEEE-- CS
                    AlaDh_PNT_C  86 a.eavkeadvvigtv 99 
                                    +  +  ++d+v+ tv
  gi|119719144|ref|YP_919639.1| 224 EdGTSIQCDIVVWTV 238
                                    303444666666665 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1     0.033        45       2      22 ..       6      26 ..       5      42 .. 0.65
   2 ?    6.5   0.2    0.0028       3.8       2      32 ..     148     181 ..     147     192 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.033
                                   EEEE--SHHHHHHHHHHHHTT CS
                  FAD_binding_2  2 viViGsGlAGLaAAleaaeaG 22
                                   ++V+G+G++G  A  +++  G
  gi|119719144|ref|YP_919639.1|  6 IVVVGGGFGGFYALKTLSGLG 26
                                   79********99855555444 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0028
                                    EEEE--SHHHHHHHHHHHH..TTT.-EEEEESSS CS
                  FAD_binding_2   2 viViGsGlAGLaAAleaae..aGl.kvavvekeq 32 
                                    v + G+Gl G   A e ae  +G+ +v+vvek+q
  gi|119719144|ref|YP_919639.1| 148 VCIAGGGLTGVEVAGEVAEkyEGKsEVVVVEKMQ 181
                                    6799**************9889**9*******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.42
# Mc/sec: 2790.99
//
Query:       gi|119719145|ref|YP_919640.1|  [L=248]
Description: 50S ribosomal protein L2P [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-37  128.8   1.9      2e-37  128.2   1.9    1.3  1  Ribosomal_L2_C  Ribosomal Proteins L2, C-terminal domain
    7.4e-17   61.1   0.1    3.6e-16   58.9   0.0    2.2  3  Ribosomal_L2    Ribosomal Proteins L2, RNA binding domain


Domain annotation for each model (and alignments):
>> Ribosomal_L2_C  Ribosomal Proteins L2, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.2   1.9   2.2e-41     2e-37       3     121 ..      96     223 ..      94     229 .. 0.93

  Alignments for each domain:
  == domain 1  score: 128.2 bits;  conditional E-value: 2.2e-41
                                    SS-EBSSSS-TTB-BBSE-SSTTS--SSS-SSSB-EEBB-B.SSEEEEEETTS-EEEEETTSBEBES-BS-TTCTT---- CS
                 Ribosomal_L2_C   3 GnvlplknipeGtivhnielkpgkggklarsaGtyaqvvakegkkvtvklpSgevrkvssecrAtiGvvsngehkekklg 82 
                                    G++++++n+peGtiv nie++pg+ggklars+G+ya v+a+++ k+ ++lpS++v++vsse+rAtiG+v+ g++ ek+++
  gi|119719145|ref|YP_919640.1|  96 GSIVEIGNVPEGTIVSNIEIRPGDGGKLARSSGAYALVLAHSNGKTLIQLPSKKVKEVSSEARATIGMVAAGGRIEKPML 175
                                    8999*************************************99************************************* PP

                                    STTHHHHT.....TBS----SSSS-TTTSSS--SS...SS--S.SSST CS
                 Ribosomal_L2_C  83 kAgrkrwl.....grrpkvrGvamnpvdHphGGGe...Gktks.rkap 121
                                    kAg+  +       ++p+vrG am ++ Hp GGG+   G t++ r+ap
  gi|119719145|ref|YP_919640.1| 176 KAGKMWHWsraksFKYPTVRGKAMSAYAHPAGGGHhpkGLTPApRNAP 223
                                    ***8887788888889******************98777777766665 PP

>> Ribosomal_L2  Ribosomal Proteins L2, RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.9   0.0     4e-20   3.6e-16       1      76 [.      11      86 ..      11      87 .. 0.97
   2 ?   -1.8   0.0      0.35   3.1e+03      51      67 ..     131     147 ..     125     150 .. 0.82
   3 ?   -3.2   0.2      0.96   8.6e+03       6      19 ..     199     212 ..     195     213 .. 0.70

  Alignments for each domain:
  == domain 1  score: 58.9 bits;  conditional E-value: 4e-20
                                   TB-TT.--BSSTT--------EE-B--S-.--SS--EEEEEEE--TT-SS-EEEEEETTTEEEEEE--SS--SS-EE- CS
                   Ribosomal_L2  1 Grnns.gritvrhrggGhkkkyrlidfkr.nkekvkgkVveieyDpgRsApiAlvkyedgekryiiapeglkvGdtvv 76
                                   Gr+ s +r + ++r g   ++y+ ++ ++ +++ + g+V+++ + pgR Ap+Alv++edg+k y+i pegl vG++++
  gi|119719145|ref|YP_919640.1| 11 GRGGSvFRNPGWKRLG--PARYPPYNPEEfKNKVLVGVVKDLLHEPGRGAPLALVEFEDGTKMYMIPPEGLAVGQKIY 86
                                   9***************..***********8888899****************************************98 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.35
                                    EEEEETTTEEEEEE--S CS
                   Ribosomal_L2  51 Alvkyedgekryiiape 67 
                                    Alv   ++ k++i +p 
  gi|119719145|ref|YP_919640.1| 131 ALVLAHSNGKTLIQLPS 147
                                    89999999999999886 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 0.96
                                    --BSSTT------- CS
                   Ribosomal_L2   6 gritvrhrggGhkk 19 
                                      + ++  ggGh +
  gi|119719145|ref|YP_919640.1| 199 MSAYAHPAGGGHHP 212
                                    56678899999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1788.70
//
Query:       gi|119719146|ref|YP_919641.1|  [L=90]
Description: ribosomal protein L25/L23 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.4e-21   74.8   4.1    5.8e-20   71.5   4.1    1.9  1  Ribosomal_L23   Ribosomal protein L23
  ------ inclusion threshold ------
      0.019   14.8   0.1      0.024   14.5   0.1    1.3  1  TusA            Sulfurtransferase TusA
      0.034   13.8   0.0      0.039   13.6   0.0    1.2  1  DNA_mis_repair  DNA mismatch repair protein, C-terminal domai


Domain annotation for each model (and alignments):
>> Ribosomal_L23  Ribosomal protein L23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.5   4.1   9.7e-24   5.8e-20       1      82 [.       9      78 ..       9      82 .. 0.90

  Alignments for each domain:
  == domain 1  score: 71.5 bits;  conditional E-value: 9.7e-24
                                   SSEEEE--SHHHHHHHTT.E.EEEEE-SS-THHHHHHHHHHHHT--EEEEEEEEE--EBESSSSSEEBE--EEEEEEEESSS CS
                  Ribosomal_L23  1 dvilkPvitEkstklaek.nkyvFeVakdanKleikkaveklFgVkVekVntlnvkgkkkrvgrkvgrrksyKkaiVtLkeg 81
                                   ++i+kP++tEk+ +l+e+ n++vF V+++a+K+eik+ave+l++VkV+kVntl+ ++              +Kka+V+L+++
  gi|119719146|ref|YP_919641.1|  9 KIIVKPYLTEKTLRLMEEtNTLVFIVDRRASKPEIKRAVEALYNVKVAKVNTLITPE-------------GFKKAYVKLSKE 77
                                   69***************9889**********************************99.............566777777655 PP

                                   - CS
                  Ribosomal_L23 82 e 82
                                   +
  gi|119719146|ref|YP_919641.1| 78 Y 78
                                   4 PP

>> TusA  Sulfurtransferase TusA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1     4e-06     0.024      17      52 ..      17      52 ..      15      78 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4e-06
                                   HHHHHCCCGCT-EEEEEESSCHHHHHHHHHHHHHTE CS
                           TusA 17 lkkalekleegevlevladdpaatediprfakklgh 52
                                   + k+l+ +ee ++l +++d +a++  i+r ++ l +
  gi|119719146|ref|YP_919641.1| 17 TEKTLRLMEETNTLVFIVDRRASKPEIKRAVEALYN 52
                                   899**************************9998765 PP

>> DNA_mis_repair  DNA mismatch repair protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   6.5e-06     0.039      22      70 ..       9      57 ..       2      84 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.5e-06
                                   TEEEEEEEE-CCG-BTTGGEEEEEETTEEE--HHHHHHHHHHHHCCSSS CS
                 DNA_mis_repair 22 qlkieGfiskpelsrskrdkqflfvNgRlvkskelkkaireaYkellpk 70
                                   ++ ++ ++++++l   ++++ ++f+  R  +++e+k+a+++ Y+ +++k
  gi|119719146|ref|YP_919641.1|  9 KIIVKPYLTEKTLRLMEETNTLVFIVDRRASKPEIKRAVEALYNVKVAK 57
                                   5778889999999999999999*********************954443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 688.47
//
Query:       gi|119719147|ref|YP_919642.1|  [L=267]
Description: 50S ribosomal protein L4P [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.5e-42  143.2   0.6    9.1e-42  142.9   0.6    1.1  1  Ribosomal_L4  Ribosomal protein L4/L1 family


Domain annotation for each model (and alignments):
>> Ribosomal_L4  Ribosomal protein L4/L1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.9   0.6   5.1e-46   9.1e-42       1     192 []      24     259 ..      24     259 .. 0.95

  Alignments for each domain:
  == domain 1  score: 142.9 bits;  conditional E-value: 5.1e-46
                                    EEE-HHHHSS---HHHHHHHHHHHHHSS-EE-----.-TTTSS---S-SS-SSSSSS---S-TT.......STTSTT--- CS
                   Ribosomal_L4   1 veLspkvFaapirrdlihravvaylanrrqgtastk.arsevsgsgrklwkQKGtGrARvgsir.......spiargGgv 72 
                                    ++L p++F++p+r+dli+r++ a  ++r q+++ ++ a+ ++++  ++l+   G+G ARv +i+       + +a++G++
  gi|119719147|ref|YP_919642.1|  24 IKL-PSFFKSPVRPDLIRRVYIALFTSRLQPKGTDPlAGLRTTA--ESLGV--GHGIARVARIKgglraarVVQAVKGRR 98 
                                    578.9***************************************..6****..*************************** PP

                                    SS---S.EEHHHHHHHHHHHHHHHHHHHHHHHTT-EEEES---..-S...........S--HHHHHHHHHHTT-...... CS
                   Ribosomal_L4  73 ahgpkperdystklnkKvrrlAlrsaLsakakqglllvvdnle.ple...........esktkelvellkklgl...... 134
                                    ah+p++e+ +++++n+K++r+Al saL+a a+ + +l ++++  +++           +sk+++l+++l+klgl      
  gi|119719147|ref|YP_919642.1|  99 AHPPRVEKIIREEVNRKEKRKALLSALAAVASRDFVLKRGHVVpDIPlpvvvaddlesISKARDLRAFLEKLGLwkdver 178
                                    ****************************************774445566889999999*************999999999 PP

                                    ....................TTSSEEEEESSSSCHHHHHHTT-TTEEEEESTT--CHHHHHSSE....EEEEHHHHHHHH CS
                   Ribosomal_L4 135 ....................ksksvLivvsekdenlvlaarnlpgvevieveslnvydllkadk....vvitksavekle 190
                                                        k+ks+Livv+e  +++ laarn+pgv+v++ ++l+v++l+++ +    +v+tksav+ le
  gi|119719147|ref|YP_919642.1| 179 aqtntrvragkgkmrgrrykKPKSLLIVVGE-ARGIELAARNMPGVDVVTYKELSVLHLAPGGNpgrlTVFTKSAVKGLE 257
                                    9999999999999999999999********7.99*********************************************9 PP

                                    HH CS
                   Ribosomal_L4 191 ek 192
                                    e+
  gi|119719147|ref|YP_919642.1| 258 ER 259
                                    96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 1722.45
//
Query:       gi|119719148|ref|YP_919643.1|  [L=334]
Description: 50S ribosomal protein L3P [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.7e-75  252.0   0.1    1.6e-74  251.1   0.1    1.4  1  Ribosomal_L3  Ribosomal protein L3


Domain annotation for each model (and alignments):
>> Ribosomal_L3  Ribosomal protein L3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  251.1   0.1   8.9e-79   1.6e-74       5     346 ..       3     312 ..       1     328 [. 0.92

  Alignments for each domain:
  == domain 1  score: 251.1 bits;  conditional E-value: 8.9e-79
                                    .SXXXXSSXCCCTTXSBXSXSSXXXSX.XXSBTTTTTXBSEEEEEEEEEEEEEEECHHTTSCCCCCEEEEEEEEEEC--E CS
                   Ribosomal_L3   5 kfeaprhgslGflprkRaerergkvksfPkddtskpvkltaflGyKaGmthiVrevdkpgskldkkevveavtvvetppm 84 
                                    k ++pr+gs  + prkRa + +++v+ +P++++     + +f+GyK Gm h++ +    +s++ ++e   a tv+e pp+
  gi|119719148|ref|YP_919643.1|   3 KGHRPRRGSRAYYPRKRARSIVARVRRWPQNREG----FLGFAGYKVGMLHVIGVEMNKNSPFYGQERFYAATVIEVPPL 78 
                                    5579****************************98....89**************************************** PP

                                    EEEEEEEEEEETTEEEEEEEEESSS.SHHHHCCCSTSTTTSSSSSSHCCCCHCSSCCCCCCHHHHHHHHHHSCSCEEEEE CS
                   Ribosomal_L3  85 vivgvvgyvetprGlrslktvwaehlseevkrrlyknwykskkkaftkyskkyeskdvkklieadleeikkeasvvrvia 164
                                    ++v+v+ y++tp+G+++l +vwa++l ++++r +                 + ++   +++++ +lee+k + s vrv+a
  gi|119719148|ref|YP_919643.1|  79 KVVAVRVYEKTPYGKKTLCEVWAKDLPKDLERVF---------------PLPKDQSYHEEQLK-KLEEVKSRVSEVRVLA 142
                                    *********************************9...............22333333344443.699************* PP

                                    EEECCCSS-SCCSSHHEEEEECHCSCHHHHHHHHHHCCTCEEECCCCS-TTSEEEEEEEE---EEE-HHHHCT----ST. CS
                   Ribosomal_L3 165 htvirktkslaqKkahllEiqvngGtiaekldfarealektvavaavFrqgeliDvigvtkGkGfeGvvkRWgvkklpr. 243
                                     t+ r   +l +Kk++l+Ei v gG   + l +a e+l k  ++++vF++g++iDvi+vtkGkGf+G vkR+gv++ pr 
  gi|119719148|ref|YP_919643.1| 143 ATQPRLS-GLGKKKPELIEIAV-GGPPEKALSLALEKLGKDLTISDVFKEGDYIDVIAVTKGKGFQGSVKRFGVEEMPRw 220
                                    ****966.5***********99.678899*************************************************95 PP

                                    .TTSSSSSS-S-SS-SSSSS--TTS--SEEESCCEEEEEEEEEEEEETTTSSTTTSSTTT.SS..SS.TTTCTTCB..TS CS
                   Ribosomal_L3 244 .kthrglRkvaaigawdparVsstvaraGqkGyhhRtelnkkiyrigkgedaknastefdltekeitPmGGfvhyGevkn 322
                                     k+ +g+ +++++g+ +pa +++ ++ +Gq G+h+Rte+nk+i ++g+             + kei+P GG++hyG v+ 
  gi|119719148|ref|YP_919643.1| 221 hKHRKGHSRIGSVGPQKPA-IMFYTPFPGQLGFHQRTEYNKRILKVGD-----------AESLKEINPPGGWPHYGLVRS 288
                                    456677************9.67778***********************...........45789**************** PP

                                    CEEEEES--SSSTTEEEEEEE-SS CS
                   Ribosomal_L3 323 dfilvkGsvpGpkkrlvklrksll 346
                                    +fi+v+GsvpG  krlv+lr++++
  gi|119719148|ref|YP_919643.1| 289 QFIIVEGSVPGAVKRLVRLRHAIR 312
                                    *********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2336.54
//
Query:       gi|119719149|ref|YP_919644.1|  [L=273]
Description: hypothetical protein Tpen_0231 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-52  179.3   0.0    1.3e-52  179.1   0.0    1.0  1  Methyltrn_RNA_3  Putative RNA methyltransferase
     0.0031   17.7   0.0      0.013   15.7   0.0    1.8  2  SpoU_methylase   SpoU rRNA Methylase family


Domain annotation for each model (and alignments):
>> Methyltrn_RNA_3  Putative RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.1   0.0   1.4e-56   1.3e-52       3     286 .]      12     268 ..      10     268 .. 0.93

  Alignments for each domain:
  == domain 1  score: 179.1 bits;  conditional E-value: 1.4e-56
                Methyltrn_RNA_3   3 siaiPssiisnaqsleqktylagqIARaaaiFnVdeivvfddseseeekkekpseflarlLqYletPpYLrkelFplhke 82 
                                     +a+Pss  sn +++  +t+ ++ +ARa++iF+V+e+ ++++s        +p+  l r+L  le+P+YLrk l p  +e
  gi|119719149|ref|YP_919644.1|  12 AVAVPSSTFSNLSEP-ARTFHVALLARAVTIFRVEEVAIYQESG-------HPCAELKRILDALEVPQYLRKYLVPRSRE 83 
                                    69*******999776.5799999*****************9888.......3899************************* PP

                Methyltrn_RNA_3  83 lkyaglLppldaphhlrsseegeyreGvvvekskekkskkklVniGlkkevklelkqevpegtRVtVklsseesveakvV 162
                                    ++y gl ppl++p hl + ee+eyreG vv+++ + k    lV++Gl ++v+ e     ++g RVt++    e    + V
  gi|119719149|ref|YP_919644.1|  84 YRYLGLVPPLRSPSHLLRGEESEYREGYVVSRRGT-KA---LVDVGLGNPVEAEV--PTDAGRRVTLRR---EGAGWRYV 154
                                    ****************999*************774.34...9*********8888..889********9...67999*** PP

                Methyltrn_RNA_3 163 spsepreeaglywGYsVrlakslsavftespfeggydlsigtsergekveeklaelekkk.efkhllivfGg.vrgleaa 240
                                    sp+e     ++ywGY+ ++ +sl++++++    ++  l +gts++ ++v+ +l+e++++   ++ + + fG   +gl+++
  gi|119719149|ref|YP_919644.1| 155 SPEEV----KVYWGYRTKCYSSLREALEHY--RSRGFLLVGTSRKAAPVSLVLEEIKREAtAKNGVAVFFGTwNKGLQEI 228
                                    ***99....6******************96..66888999****************999877999*******889***** PP

                Methyltrn_RNA_3 241 leadeelklegekaeelFdlwlntvpnqgsrtirtEEavliaLalL 286
                                     e++      g + e+++d ++nt p qg +tirtEEav i+La L
  gi|119719149|ref|YP_919644.1| 229 SEEE------GFELESFLDFIVNTAPIQGVKTIRTEEAVYISLAIL 268
                                    *877......999******************************976 PP

>> SpoU_methylase  SpoU rRNA Methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       0.2   1.8e+03      17      37 ..      34      54 ..      23      69 .. 0.78
   2 !   15.7   0.0   1.5e-06     0.013      59     110 ..     168     227 ..     161     232 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.2
                                   HHHHHHHHTT-SEEEEESGSS CS
                 SpoU_methylase 17 aiaRtakafgaselvlvkprs 37
                                    +aR++ +f ++e+ + ++ +
  gi|119719149|ref|YP_919644.1| 34 LLARAVTIFRVEEVAIYQESG 54
                                   579999999999999987655 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1.5e-06
                                    EEESSHHHHHHHHCCCTEEEEEESTT-SEGC........CSHHHTTEEEEEEBTTTBS-H CS
                 SpoU_methylase  59 kvvdsleealkelkeegfalvatslkgksls........eidlkekvalvfGnEdkGlsn 110
                                    k ++sl+eal++ + +gf lv+ts+k+ ++s        e++ k+ va++fG+ +kGl++
  gi|119719149|ref|YP_919644.1| 168 KCYSSLREALEHYRSRGFLLVGTSRKAAPVSlvleeikrEATAKNGVAVFFGTWNKGLQE 227
                                    5689************************9998787444444667*************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1991.98
//
Query:       gi|119719150|ref|YP_919645.1|  [L=73]
Description: putative transcriptional regulator [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.7e-05   24.0   0.1    4.6e-05   23.7   0.1    1.1  1  FaeA           FaeA-like protein
    0.00048   20.2   0.1    0.00058   19.9   0.1    1.2  1  HTH_9          RNA polymerase III subunit RPC82 helix-turn-he
     0.0048   16.8   0.3      0.006   16.5   0.3    1.1  1  TrmB           Sugar-specific transcriptional regulator TrmB
     0.0077   15.8   0.0     0.0093   15.5   0.0    1.2  1  HTH_24         Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.019   15.1   0.0      0.024   14.8   0.0    1.2  1  DUF2582        Winged helix-turn-helix domain (DUF2582)
      0.042   13.2   0.1      0.046   13.1   0.1    1.0  1  RNA_pol_Rpc34  RNA polymerase Rpc34 subunit
      0.045   13.5   0.1      0.082   12.7   0.0    1.5  2  HTH_DeoR       DeoR-like helix-turn-helix domain
      0.063   13.2   0.0      0.076   12.9   0.0    1.2  1  MarR_2         MarR family
       0.12   12.2   0.0       0.15   11.9   0.0    1.2  1  HTH_IclR       IclR helix-turn-helix domain
       0.13   12.1   0.0       0.21   11.3   0.0    1.5  1  PheRS_DBD1     PheRS DNA binding domain 1


Domain annotation for each model (and alignments):
>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.1   2.6e-08   4.6e-05       2      59 ..      13      67 ..      12      70 .. 0.93

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 2.6e-08
                                   HHHHHHHHHH.S----HHHHHHHHTS-HHHHHHHHHHHHHHSSEEEE--SSSSS-EEE CS
                           FaeA  2 keeIleylnsikapckTreiAdalglsaYQaRyYLeqLekegkikrspvrrGvstlWe 59
                                   k  I eyl++ ++p  T e+   l ls  Q+ y L  L +e+k+k    rrG  ++W 
  gi|119719150|ref|YP_919645.1| 13 KKLIYEYLKK-HGPMPTVELVRDLKLSHSQVFYILRLLLREKKVKE--ERRGKMAYWI 67
                                   67799*****.*********************************96..599*999*95 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.1   3.2e-07   0.00058      18      53 ..      16      51 ..       7      56 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 3.2e-07
                                   HHHHHHHHSSBEHHHHHHHHSSTHHHHHHHHHHHHH CS
                          HTH_9 18 VvetLlrkgrltlrelvkktkLsldqVkksLvvLiq 53
                                   ++e+L ++g  +  elv+++kLs++qV  +L +L++
  gi|119719150|ref|YP_919645.1| 16 IYEYLKKHGPMPTVELVRDLKLSHSQVFYILRLLLR 51
                                   89*************************999999987 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.3   3.3e-06     0.006      13      62 ..      16      65 ..       9      68 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.3e-06
                                   HCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEE CS
                           TrmB 13 vYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklY 62
                                   +Y +L k+gp+ + e+ ++l++++s+v  +Lr L++   V+ e++ ++ Y
  gi|119719150|ref|YP_919645.1| 16 IYEYLKKHGPMPTVELVRDLKLSHSQVFYILRLLLREKKVKEERRGKMAY 65
                                   7999*********************************9999999888777 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   5.2e-06    0.0093       4      46 ..      12      54 ..       9      56 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 5.2e-06
                         HTH_24  4 tdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGl 46
                                    ++ I+e+L+k++ ++  eL + l lS s v + l+ L +e  
  gi|119719150|ref|YP_919645.1| 12 RKKLIYEYLKKHGPMPTVELVRDLKLSHSQVFYILRLLLREKK 54
                                   5678********************************9988765 PP

>> DUF2582  Winged helix-turn-helix domain (DUF2582)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   1.3e-05     0.024      13      62 ..      16      65 ..      11      68 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.3e-05
                                   HHHHHCCSSSEEHHHHHHHCT-SCHHHHHHHHHHHCTTSEEEEEETTEEE CS
                        DUF2582 13 vwhlLnengeislkelkrktglsdkelalAiGWLaREdKivierkekelf 62
                                   +++ L+++g + + el r  +ls+++++  +  L RE K++ er+ k  +
  gi|119719150|ref|YP_919645.1| 16 IYEYLKKHGPMPTVELVRDLKLSHSQVFYILRLLLREKKVKEERRGKMAY 65
                                   9****************************************999988765 PP

>> RNA_pol_Rpc34  RNA polymerase Rpc34 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   2.6e-05     0.046       7      73 ..       8      68 ..       3      73 .] 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.6e-05
                                   -HHHHHHHHHHHHHCSSSSSHCCHHHHHHHSTTSHHHHHHHHHHHHHHCTSEECCC.STTSCECEE- CS
                  RNA_pol_Rpc34  7 klqelkkrlleelrkaseqklfsqqdLqddipslslklllsavqeLldkkllvllknsndeLvyrav 73
                                   k+ e kk ++e l+k+    ++   +L +d ++ls++++  +++ Ll +k+++  +   ++++y + 
  gi|119719150|ref|YP_919645.1|  8 KILERKKLIYEYLKKH---GPMPTVELVRD-LKLSHSQVFYILRLLLREKKVKEER--RGKMAYWIA 68
                                   6778899999999999...899999*****.9*********************999..666676554 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.6e-05     0.082       1      28 [.      12      39 ..      12      42 .. 0.93
   2 ?   -3.4   0.1       4.7   8.5e+03       5      15 ..      45      55 ..      45      56 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.6e-05
                       HTH_DeoR  1 RieqilellkqqgklsveelvellgvSe 28
                                   R + i e+lk++g + + elv  l+ S 
  gi|119719150|ref|YP_919645.1| 12 RKKLIYEYLKKHGPMPTVELVRDLKLSH 39
                                   8999********************9996 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 4.7
                       HTH_DeoR  5 ilellkqqgkl 15
                                   il ll ++ k+
  gi|119719150|ref|YP_919645.1| 45 ILRLLLREKKV 55
                                   67788777776 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   4.2e-05     0.076      13      53 ..      19      57 ..      10      62 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.2e-05
                                   HHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                         MarR_2 13 aLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53
                                   +L  +++  +   el+r l+ls+s v +il+ L +   v +
  gi|119719150|ref|YP_919645.1| 19 YLKKHGP--MPTVELVRDLKLSHSQVFYILRLLLREKKVKE 57
                                   5778888..9999******************9988776654 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   8.1e-05      0.15      13      49 ..      21      56 ..      15      59 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.1e-05
                                   CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                       HTH_IclR 13 aeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                    ++++ +   el r + l+ S v+ +L+ L +++ v+
  gi|119719150|ref|YP_919645.1| 21 KKHGP-MPTVELVRDLKLSHSQVFYILRLLLREKKVK 56
                                   55555.999*********************9998776 PP

>> PheRS_DBD1  PheRS DNA binding domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00012      0.21       7      35 ..      14      42 ..       1      43 [. 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00012
                     PheRS_DBD1  7 eqlLqrLekkgevdslelAaelgvdHqkv 35
                                   +++ ++L+k+g+  + el + l+++H +v
  gi|119719150|ref|YP_919645.1| 14 KLIYEYLKKHGPMPTVELVRDLKLSHSQV 42
                                   567789********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 532.56
//
Query:       gi|119719151|ref|YP_919646.1|  [L=476]
Description: preprotein translocase subunit SecY [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-61  207.6  17.7      3e-61  207.4  17.7    1.1  1  SecY             SecY translocase
    2.3e-12   46.5   0.1    1.2e-11   44.2   0.1    2.3  2  Plug_translocon  Plug domain of Sec61p
  ------ inclusion threshold ------
       0.26   11.6   0.0       0.43   10.9   0.0    1.2  1  Trigger_N        Bacterial trigger factor protein (TF)


Domain annotation for each model (and alignments):
>> SecY  SecY translocase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  207.4  17.7     5e-65     3e-61       1     306 []      75     455 ..      75     455 .. 0.82

  Alignments for each domain:
  == domain 1  score: 207.4 bits;  conditional E-value: 5e-65
                                    BTTSSTCHHHHHHHHHHHHH.HHHSSSSSSTS-SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC.......HH.HHHH CS
                           SecY   1 sifaLGImPyitasIilqLl.tvvipkleelkkegeegrkkinqitryltvvlalvqalgialslg.......lallliv 72 
                                    ++++LGI+P++t++I+++Ll ++   ++ +l+ + +egr++++++++++++++a+++a++++l+ g        + ++++
  gi|119719151|ref|YP_919646.1|  75 TLIELGIGPIVTSGIVWELLvGS---RIVNLDLTTPEGRRTFAGLQKLTAFLFAALEAAAYILG-GvygaltqQQQIIVF 150
                                    899*****************888...6666665689************************8854.46789999889**** PP

                                    HHHHHHHHHHHHHHHHHHH.HSSTTHHHHHHHHHHHHHHC.CHSS..................-HHHH.......SS... CS
                           SecY  73 lqltagtvllmwLgEqite.kGiGnGisllifagivarlp.kals..................gliel.......ale.. 123
                                    +ql++++++++++ +++++ +GiG+ +sl+i+ag++++++ + +s                  +                
  gi|119719151|ref|YP_919646.1| 151 VQLFVASTFVILMNDMLEKgWGIGSAVSLFIAAGVAQQIFwELFSpigplgdglyyglfpslfS---AlvsgnstL-Lmh 226
                                    ****************************************777778888888777765554440...134444330.033 PP

                                    ......THHHHHHHHHHHHHHHHHCHHHHBEEEECBBBSTT....S.S-EEEEETTCCCSCHHHHHHHHHH......... CS
                           SecY 124 .....gilallllllvtllvillvvyveeaerripvqyakrgrkggqssylPlklnyagviPiIfasslla......... 189
                                         +  + l+ ++ +++++ll+ y+e++++ ipv++ +    gg+++++Plk++y +v+P+I++ +l a         
  gi|119719151|ref|YP_919646.1| 227 vvvrpSGYPDLVGFVGMVVMLLLLTYMESMKITIPVSSVRF---GGAKTRIPLKFLYVSVMPVILVGALYAnvvmftqal 303
                                    44567558*****************************9977...99*************************777777766 PP

                                    ..................................H....HHCCCCS.TCCCS..THHHHHHHHHHHHHHHHHHHHTCT.T CS
                           SecY 190 ..................................l....pstiaqfllalls..psvlyvvlyvlliifFayfyteit.f 228
                                                                           p+++a+ l+   +  + v+y +ly+ + ++F + ++ ++ +
  gi|119719151|ref|YP_919646.1| 304 wprvnpgnqnpwlnviakynyteygpvplpgsfvYyispPRSLASALA---DpvHLVVYSLLYIGFAVLFGVAWILTSgM 380
                                    666666666666666666555555555533332202223444433332...233335677777777777*********** PP

                                    HHHHHHHCCHHTBSSSCTTT.TCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS.TT.TTHHHHHHHHHHHHHHH CS
                           SecY 229 npkevaenlkksggfipgir.pgketakyLekvlsritliGalflaliavlpdllgasligafggtslLivVgvaletv 306
                                    +p+  ae+l k + +ipg+r ++k +a +L++++  +t+++++++++iav++d+++   +g  ggt++L++Vg++++++
  gi|119719151|ref|YP_919646.1| 381 DPETQAEQLAKAQLQIPGFRkSEKVIASMLKRYIWGLTILSSIIIGVIAVVSDIFRV--MG--GGTGILLLVGIIVQYY 455
                                    ********************999**********************************..77..*************986 PP

>> Plug_translocon  Plug domain of Sec61p
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   0.1   2.1e-15   1.2e-11       1      35 []      38      74 ..      38      74 .. 0.94
   2 ?   -2.3   0.0      0.71   4.2e+03      28      34 ..     456     462 ..     452     462 .. 0.85

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 2.1e-15
                                   HHHHHHCCSB-TT--..SSS-TCCHTTTCCCCTSSTT CS
                Plug_translocon  1 llYlvlsqiPLyGis..sssssDpfywlRaifAsnrG 35
                                   + Y+v++q+PLyGi+  ++++   +++lR+++As rG
  gi|119719151|ref|YP_919646.1| 38 VAYFVMGQTPLYGIPrqTQGTLGALEFLRVVMASKRG 74
                                   68*************9666*****************9 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.71
                                    CCCTSST CS
                Plug_translocon  28 aifAsnr 34 
                                    +i+As+r
  gi|119719151|ref|YP_919646.1| 456 SILASER 462
                                    79***97 PP

>> Trigger_N  Bacterial trigger factor protein (TF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   7.1e-05      0.43      31      58 ..     385     414 ..     382     428 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 7.1e-05
                                    HHHHHHT.TS-BTTC-TT.---CCCHHHHC CS
                      Trigger_N  31 alkklak.kvkipGFRkG.kvPrsiiekry 58 
                                    + ++lak +++ipGFRk  kv +s++++++
  gi|119719151|ref|YP_919646.1| 385 QAEQLAKaQLQIPGFRKSeKVIASMLKRYI 414
                                    456666669********7699999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (476 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 3118.73
//
Query:       gi|119719152|ref|YP_919647.1|  [L=151]
Description: 50S ribosomal protein L15P [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-20   74.7   0.5    1.3e-20   74.3   0.1    1.4  2  Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27


Domain annotation for each model (and alignments):
>> Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.18   3.3e+03       4      17 ..      15      28 ..      13      29 .. 0.85
   2 !   74.3   0.1   7.4e-25   1.3e-20       2     127 ..      28     142 ..      27     143 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.18
                                   GTSSTTTTTTTTT- CS
                 Ribosomal_L27A  4 tgGrGhkGqkkrsg 17
                                   t+G G+ Gq+ +sg
  gi|119719152|ref|YP_919647.1| 15 THGWGRVGQHRKSG 28
                                   8999*****99886 PP

  == domain 2  score: 74.3 bits;  conditional E-value: 7.4e-25
                                    GGGTSSTTTTTTTTT-..S--........S--.........---.GGG..---EEEEHHHHHHTTTTGTTS.--...--- CS
                 Ribosomal_L27A   2 GktgGrGhkGqkkrsg..vkk.kpg.feGGqmplyrrlpkrGfk.nskfkkeykvvnlkdLdelideerle.la...dea 72 
                                    G++gGrG  G +k+++  + k +p+ +  G++         Gf+ +     ey+++n+++Ld  ++e  ++ la   ++a
  gi|119719152|ref|YP_919647.1|  28 GSRGGRGLVGYHKHKWswTVKyAPDwY--GKH---------GFTrHPSLVVEYRTINVGQLDAEVEEFFRKgLAsreGDA 96 
                                    99**************98444566669..***.........***8666789***********99999888877799899* PP

                                    -EEEGGGTTTTSSS....SE.EEE--S---.--EEEESEE-HHHHHHHHHTT-EEE CS
                 Ribosomal_L27A  73 eeidleelaeaglikkkdgv.KvlgkgeltkklkvkaskfSkkAkekIeaaGGkve 127
                                    +++dl++l          g+ K+ g+g++++k++vk+  ++k+A++kIea GG+ve
  gi|119719152|ref|YP_919647.1|  97 YVVDLTQL----------GFnKLTGSGQVRNKIIVKVPVATKRAISKIEAQGGRVE 142
                                    ********..........************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1154.45
//
Query:       gi|119719153|ref|YP_919648.1|  [L=156]
Description: 50S ribosomal protein L30P [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-11   44.5   0.0    4.9e-11   42.3   0.0    2.0  2  Ribosomal_L30  Ribosomal protein L30p/L7e


Domain annotation for each model (and alignments):
>> Ribosomal_L30  Ribosomal protein L30p/L7e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   0.0   2.7e-15   4.9e-11       1      45 [.       4      48 ..       4      50 .. 0.91
   2 ?   -1.0   0.0     0.095   1.7e+03      25      42 ..      86     104 ..      85     107 .. 0.80

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 2.7e-15
                                   EEEEE-S-STTS-HHHHHHHHHTT-SSTTEEEE--SSHHHHHHHH CS
                  Ribosomal_L30  1 lfVtrirsiigvppkvrktLqlLgLrkingtvvklntpsirGmLk 45
                                   ++V+r r+  ++ p + k L+lL+L+k+ + v +++ psi+GmL 
  gi|119719153|ref|YP_919648.1|  4 YLVIRLRGQPDRRPEEEKALELLRLHKVYHAVLVKDDPSIKGMLE 48
                                   58***************************77777777******96 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.095
                                    -SSTT.EEEE--SSHHHHH CS
                  Ribosomal_L30  25 Lrkin.gtvvklntpsirG 42 
                                    L+ki+  +++ l ++ i G
  gi|119719153|ref|YP_919648.1|  86 LKKIGfNSFEELAEALISG 104
                                    899*999999887776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 1067.88
//
Query:       gi|119719154|ref|YP_919649.1|  [L=202]
Description: 30S ribosomal protein S5P [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.5e-25   87.2   0.0    5.9e-25   86.5   0.0    1.4  1  Ribosomal_S5_C  Ribosomal protein S5, C-terminal domain
    1.4e-21   76.2   0.9    1.4e-21   76.2   0.9    1.6  2  Ribosomal_S5    Ribosomal protein S5, N-terminal domain


Domain annotation for each model (and alignments):
>> Ribosomal_S5_C  Ribosomal protein S5, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.5   0.0   6.6e-29   5.9e-25       1      66 [.     131     197 ..     131     202 .] 0.95

  Alignments for each domain:
  == domain 1  score: 86.5 bits;  conditional E-value: 6.6e-29
                                    EEEETTEEEEEEE--TT--EES-HHHHHHHHHHT--SEE---BS.-SSHHHHHHHHHHHHHHTTTT- CS
                 Ribosomal_S5_C   1 tgkfgavkvllkpaprGtGiiaggavravlelaGikDvlakslg.srnpinvvkAtfeALkklrspe 66 
                                    +gk g+vk+ l+pap+G G++a++++++vl+laGikDv+++s+g +r+++n++kA++eALkk++++ 
  gi|119719154|ref|YP_919649.1| 131 EGKAGSVKIELIPAPKGVGLVASDVAKTVLRLAGIKDVWSRSYGeTRTTHNMAKAVYEALKKTYQFY 197
                                    59*************************************************************9875 PP

>> Ribosomal_S5  Ribosomal protein S5, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.2   0.9   1.6e-25   1.4e-21       1      65 []      46     110 ..      46     110 .. 0.98
   2 ?   -3.2   0.0         1     9e+03      43      59 ..     183     191 ..     179     194 .. 0.47

  Alignments for each domain:
  == domain 1  score: 76.2 bits;  conditional E-value: 1.6e-25
                                    XEEEEEEEEEEEEEETTEEEEEEEEEEEEEETTTEEEEEEEEESSHHHHHHHHHHHHHHTEEE-- CS
                   Ribosomal_S5   1 lkekvlkikrvqkvtkgGrrtsfsalvvvGdgnGlvGlGvgkakevatAirkAiekAkknlvpvp 65 
                                    lk++vl++  vq++t++G + +++++v+vG+++G+vG+G+gk++++  Ai+kA+++Ak+n+vpv+
  gi|119719154|ref|YP_919649.1|  46 LKSEVLSVGFVQRQTDSGEVSQYQVTVAVGNEDGYVGVGMGKSRQIGIAIEKATRRAKLNIVPVR 110
                                    799************************************************************96 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1
                                    ESSHHHHHHHHHHHHHH CS
                   Ribosomal_S5  43 akevatAirkAiekAkk 59 
                                    a        kA+  A k
  gi|119719154|ref|YP_919649.1| 183 A--------KAVYEALK 191
                                    3........33333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.40s 00:00:01.00 Elapsed: 00:00:00.58
# Mc/sec: 1045.74
//
Query:       gi|119719155|ref|YP_919650.1|  [L=196]
Description: 50S ribosomal protein L18P [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-32  111.9   2.7    9.9e-23   80.9   1.1    2.3  2  Ribosomal_L5e    Ribosomal large subunit proteins 60S L5, and
    9.5e-10   39.3   0.1    2.3e-09   38.1   0.0    1.6  2  Ribosomal_L18_c  Ribosomal L18 C-terminal region
    0.00036   20.9   0.3    0.00051   20.4   0.3    1.2  1  Ribosomal_L18p   Ribosomal L18 of archaea, bacteria, mitoch. 


Domain annotation for each model (and alignments):
>> Ribosomal_L5e  Ribosomal large subunit proteins 60S L5, and 50S L18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.9   1.1   1.7e-26   9.9e-23       2      99 ..       6      96 ..       5      99 .. 0.96
   2 !   31.1   0.0   3.6e-11   2.1e-07     128     161 ..      98     131 ..      95     133 .. 0.92

  Alignments for each domain:
  == domain 1  score: 80.9 bits;  conditional E-value: 1.7e-26
                  Ribosomal_L5e  2 rfqvkfrrrregktdYyarkrliiqdknkyntpkyRlvVrvtnkdiicqiayakiegdkvlaaayskelpkygvkvgltnya 83
                                   r++v ++rrregkt+Yy+r++lii         k RlvVrv  ++ i+qia+a+ +gd+v+a+a+s+el+kyg k    n  
  gi|119719155|ref|YP_919650.1|  6 RYRVPLKRRREGKTNYYKRRKLIISG-------KPRLVVRVLSRTAIVQIAKATPKGDVVIASAHSNELKKYGWKGYRRNTP 80
                                   9***********************76.......67****************************************9999*** PP

                  Ribosomal_L5e 84 aaYatglllarrllkk 99
                                   a Y+ g+l a+++lk+
  gi|119719155|ref|YP_919650.1| 81 ALYLLGFLAAKKALKQ 96
                                   ************9986 PP

  == domain 2  score: 31.1 bits;  conditional E-value: 3.6e-11
                  Ribosomal_L5e 128 afkaiLdvGLartttgakvfgalkgavdgglsip 161
                                      +ai+d+GL+r  + ++vf+a+kga+d+gl+ip
  gi|119719155|ref|YP_919650.1|  98 VTEAIVDIGLHRPVKASRVFAAVKGALDAGLKIP 131
                                    5789*****************************9 PP

>> Ribosomal_L18_c  Ribosomal L18 C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0         3   1.8e+04      73      83 ..      17      27 ..      10      31 .. 0.54
   2 !   38.1   0.0   3.8e-13   2.3e-09       6      58 ..     141     193 ..     139     195 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 3
                Ribosomal_L18_c 73 keskkykkkkl 83
                                    ++++yk++kl
  gi|119719155|ref|YP_919650.1| 17 GKTNYYKRRKL 27
                                   33445555554 PP

  == domain 2  score: 38.1 bits;  conditional E-value: 3.8e-13
                Ribosomal_L18_c   6 krIfgkhvaeYmeeLkeedeekykkqFskyikkgieaddleelykkahaaIre 58 
                                    +r+ g+h+a+Y ++Lke ++e +k +Fs y+++g+++++l e + ++ ++I e
  gi|119719155|ref|YP_919650.1| 141 DRVRGEHIANYAKMLKESNPELFKLRFSGYLSAGLDPESLPEHFDSVKQKIEE 193
                                    7899***********************************************86 PP

>> Ribosomal_L18p  Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.3   8.5e-08   0.00051      21     114 ..      29     128 ..      11     130 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 8.5e-08
                                    TSSS-EEEEEE-SS-EEEEEE-TTT--EEEEECS-SCCCT....S-SSSCHHHHHHHHHHHHHHHCHHCHTC-EE--TTS CS
                 Ribosomal_L18p  21 taerprlvvfrsnrhiyaQviddvkgktlasastlekelk....lkstknkeaakkvgeliAerakekgiekvvfDrggy 96 
                                     + +prlvv    r   +Q+   + +  ++ as+  +elk    + ++ n+ a   +g l A++a+++g+++++ D g +
  gi|119719155|ref|YP_919650.1|  29 ISGKPRLVVRVLSRTAIVQIAKATPKGDVVIASAHSNELKkygwKGYRRNTPALYLLGFLAAKKALKQGVTEAIVDIGLH 108
                                    23479****************999888888888888888877877889999999*********************98866 PP

                                    S..S-CHHHHHHHHHHCTSS CS
                 Ribosomal_L18p  97 k..YhGrvaalAdaaReaGl 114
                                    +   + rv a  ++a +aGl
  gi|119719155|ref|YP_919650.1| 109 RpvKASRVFAAVKGALDAGL 128
                                    52234555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1392.79
//
Query:       gi|119719156|ref|YP_919651.1|  [L=155]
Description: 50S ribosomal protein L19e [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-50  170.8   1.5    1.9e-50  170.7   1.5    1.0  1  Ribosomal_L19e  Ribosomal protein L19e
  ------ inclusion threshold ------
      0.013   15.7   2.1       0.27   11.5   0.5    3.2  3  HTH_17          Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> Ribosomal_L19e  Ribosomal protein L19e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.7   1.5   2.1e-54   1.9e-50       2     144 .]       3     142 ..       2     142 .. 0.98

  Alignments for each domain:
  == domain 1  score: 170.7 bits;  conditional E-value: 2.1e-54
                                    THHHHHHHHHHTTS-GGGEEE-GGGHHHHHH--SHHHHHHHHHTTSEEE-------THHHHHHHHHHHTT-S-SGGG--S CS
                 Ribosomal_L19e   2 lklqkrlaasvlkvGknrvwldpeeleeiaeAitredirklikdglIikkpkkgnsrararerkekkrkgrrrgsGkrkG 81 
                                    ++l +rla++vl+vG++r+w+dp++l+e+++Ai+r+d+r+likdg+I + p ++ sr+r+rer+ k++kgr rg+G++kG
  gi|119719156|ref|YP_919651.1|   3 VSLARRLASEVLGVGESRIWIDPDKLDEVSAAISRSDVRRLIKDGVIRVLPPSTPSRGRVRERRLKRKKGRGRGPGSKKG 82 
                                    6789***************************************************************************9 PP

                                    -HHHHS-HHHHHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHTT--SSHHHHHHHHT-XX CS
                 Ribosomal_L19e  82 tkeaRlpekelWikriRalRrlLkelrekkkidkktYrelYrkakGgefknkavLkeyiekkk 144
                                        R++ek++Wi+r+Ra+Rr+Lk l+ek++id+kt+r lYr +kGg+f++ ++Lk yi+++k
  gi|119719156|ref|YP_919651.1|  83 ---PRVDEKRAWINRVRAQRRYLKFLKEKGQIDTKTFRYLYRLVKGGMFRSLSHLKLYISEHK 142
                                    ...89******************************************************9875 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.27   2.5e+03       7      18 ..      10      21 ..      10      22 .. 0.83
   2 ?   11.5   0.5     3e-05      0.27      13      34 ..      35      61 ..      34      75 .. 0.76
   3 ?    1.4   0.1     0.041   3.7e+02      17      41 ..     118     141 ..     117     149 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.27
                         HTH_17  7 aAelLgvsrstv 18
                                   a+e Lgv++s +
  gi|119719156|ref|YP_919651.1| 10 ASEVLGVGESRI 21
                                   6899***99876 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 3e-05
                         HTH_17 13 vsrstvyrlirrgelpaa.....kiGr 34
                                   +srs v+rli++g ++++      +Gr
  gi|119719156|ref|YP_919651.1| 35 ISRSDVRRLIKDGVIRVLppstpSRGR 61
                                   8************99988665541444 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.041
                         HTH_17  17 tvyrlirrgelpaakiGrrwriprs 41 
                                     +yrl++ g ++ + +  +++i++ 
  gi|119719156|ref|YP_919651.1| 118 YLYRLVKGGMFRSLSH-LKLYISEH 141
                                    58****9999999864.34777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 996.41
//
Query:       gi|119719157|ref|YP_919652.1|  [L=159]
Description: ribosomal protein L32e [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      3e-35  120.9   0.0      4e-35  120.5   0.0    1.2  1  Ribosomal_L32e  Ribosomal protein L32


Domain annotation for each model (and alignments):
>> Ribosomal_L32e  Ribosomal protein L32
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.5   0.0   2.2e-39     4e-35       2     108 .]      51     156 ..      50     156 .. 0.98

  Alignments for each domain:
  == domain 1  score: 120.5 bits;  conditional E-value: 2.2e-39
                                    -----TTTTT-TTS-SS------.TT-TTTTT-TTS-----GGG---TTTTT--TTS-EEEEESSGGGGTT--TTTE..E CS
                 Ribosomal_L32e   2 kkFirhqsdryvklkeswrkprG.idnrvrrrfkgqilmpkiGYgspkktrgllpsGfkkvlVhnvkeLevllmenksya 80 
                                    ++F+r++ +++++l++ wr pr  +dn++r + kg ++m+k+GY+ p+++rgl+psGf++vlV++vk+L  l+++++  a
  gi|119719157|ref|YP_919652.1|  51 PHFTRMNIWQFKRLEDVWRSPRHfLDNKIRLQRKGFPPMVKVGYRGPRAVRGLHPSGFEEVLVSSVKDLLGLDPAKH--A 128
                                    79********************978**************************************************99..* PP

                                    EEE-TTS-HHHHHHHHHHHHHTT-EBSS CS
                 Ribosomal_L32e  81 aeiahsVsskkrkeiverAaelgikVtN 108
                                    ++i+++V++kkr ei+++A+elg++++N
  gi|119719157|ref|YP_919652.1| 129 IRISAKVGKKKRGEIIKKAEELGFRILN 156
                                    **************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 1083.25
//
Query:       gi|119719158|ref|YP_919653.1|  [L=129]
Description: 30S ribosomal protein S8P [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-25   89.8   0.0    1.6e-25   89.5   0.0    1.1  1  Ribosomal_S8  Ribosomal protein S8


Domain annotation for each model (and alignments):
>> Ribosomal_S8  Ribosomal protein S8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.5   0.0   9.1e-30   1.6e-25       1     127 []       4     129 .]       4     129 .] 0.86

  Alignments for each domain:
  == domain 1  score: 89.5 bits;  conditional E-value: 9.1e-30
                                    -HHHHHHHHHHHHHHTT-SEEEE.E--HHHHHHHHHHHHCTSEEEEEEE.CCCCCC..EEEEE-BSSS-SBSSSEEEE-S CS
                   Ribosomal_S8   1 DpiadmltrirNaekakkeevev.pasklkeeilkvLkeeGyikdfeve.eekkkk..ikielkynkkkksvikklkrvs 76 
                                    D++a++l++i N+e ++k+++ + p+skl+ ++l+ Lk+ Gyi dfe   + +  k  +++ +++nk   +vik    v+
  gi|119719158|ref|YP_919653.1|   4 DTLANALSTIMNNEVRGKKQCVIyPSSKLIVAVLDTLKRSGYIGDFELIdDGRGGKivVNLLGRINK--IGVIKPRYPVK 81 
                                    89********************99************************8544444434777777777..99***999999 PP

                                    BTTC--EE-CCC---CGGGTSEEEEEETTEEEEHHHHHHCT--EEEEEEEE CS
                   Ribosomal_S8  77 kpgrrvYakvkelpkvlnglGiaivsTskGvmtdkeArkkkvGGevlayvw 127
                                    k   + + + + lp   + +G++ivsT+kGvmt++eA++k++GG +layv+
  gi|119719158|ref|YP_919653.1|  82 KNEFEAW-EREYLP--SRDVGLLIVSTPKGVMTHREAKEKGLGGVLLAYVY 129
                                    8777733.344555..4789******************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 922.95
//
Query:       gi|119719159|ref|YP_919654.1|  [L=54]
Description: 30S ribosomal protein S14P [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-14   52.4   3.3    3.8e-14   52.2   3.3    1.0  1  Ribosomal_S14  Ribosomal protein S14p/S29e
  ------ inclusion threshold ------
       0.15   12.0   5.1        0.3   11.0   5.1    1.5  1  zf-FPG_IleRS   Zinc finger found in FPG and IleRS


Domain annotation for each model (and alignments):
>> Ribosomal_S14  Ribosomal protein S14p/S29e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.2   3.3   4.2e-18   3.8e-14       6      54 .]       7      54 .]       4      54 .] 0.95

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 4.2e-18
                                   --SS..CTTT---SSS--SSSEE-GGG-..EHHHHHHHTTT...TT-EE-- CS
                  Ribosomal_S14  6 prnssptrirnrCrvtGrprGvirkfgL..sRicfRelAlkgelpGvkKaS 54
                                   p++ + +++++rC+ +G + ++ir +gL  +R cfRe A++   +G+kK+S
  gi|119719159|ref|YP_919654.1|  7 PKKRKYGKGSRRCIRCGTHEAIIRVYGLnlCRRCFREVAEE---IGFKKYS 54
                                   778888***********************************...******8 PP

>> zf-FPG_IleRS  Zinc finger found in FPG and IleRS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   5.1   3.3e-05       0.3       3      27 ..      18      40 ..      18      42 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.3e-05
                                   B-TTT--BBEEEECTTEEEEE-TTT CS
                   zf-FPG_IleRS  3 pCpRCwryiervgqagrstyfCprC 27
                                   +C RC+++ + +++  ++ ++C rC
  gi|119719159|ref|YP_919654.1| 18 RCIRCGTHEAIIRV--YGLNLCRRC 40
                                   5*************..********* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.44
# Mc/sec: 370.51
//
Query:       gi|119719160|ref|YP_919655.1|  [L=182]
Description: 50S ribosomal protein L5P [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.2e-24   84.2   0.1    8.6e-24   83.5   0.1    1.4  1  Ribosomal_L5_C  ribosomal L5P family C-terminus
      6e-18   64.9   0.2    3.3e-17   62.6   0.1    2.2  2  Ribosomal_L5    Ribosomal protein L5
  ------ inclusion threshold ------
       0.16   12.2   0.1       0.29   11.4   0.1    1.4  1  DUF5511         Family of unknown function (DUF5511)


Domain annotation for each model (and alignments):
>> Ribosomal_L5_C  ribosomal L5P family C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.5   0.1   1.4e-27   8.6e-24       1      94 []      69     168 ..      69     175 .. 0.92

  Alignments for each domain:
  == domain 1  score: 83.5 bits;  conditional E-value: 1.4e-27
                 Ribosomal_L5_C   1 piGvkvtLrgekmyefldkllevvlprlrdFkGiskssfdgrGnvsfGikeqiifpeieydkdkgifGmditivttak.. 78 
                                    +iGv+vtLrgek+ +fl+k+l +v ++++      ++s+d++Gnv+fG+ke+i +p+++yd++ gifG+d++i ++++  
  gi|119719160|ref|YP_919655.1|  69 NIGVMVTLRGEKAINFLKKALAAVDYKIH------EKSIDRHGNVAFGVKEHILIPGVKYDPEVGIFGFDVIIAMERPgy 142
                                    59***************************......*******************************************87 PP

                 Ribosomal_L5_C  79 .tde..........earallkelgipf 94 
                                     +++          ++r ++ke++i f
  gi|119719160|ref|YP_919655.1| 143 rVARrrrkkskvpaRHR-VTKEETITF 168
                                    73335677888887888.999998877 PP

>> Ribosomal_L5  Ribosomal protein L5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.6   0.1   5.5e-21   3.3e-17       2      57 .]      13      65 ..      12      65 .. 0.97
   2 ?   -0.4   0.0      0.25   1.5e+03      29      45 ..     164     180 ..     148     182 .] 0.77

  Alignments for each domain:
  == domain 1  score: 62.6 bits;  conditional E-value: 5.5e-21
                                   CTTS-EEEEEEEEEE-SSSSSCHHHHHCCHHHHCCCHSS--EECC--TTCTTTCSC CS
                   Ribosomal_L5  2 vMqvPrleKivinmgvGeagedkkllekaakeLaeItGQkPvvtkakksianFkiR 57
                                   +M+ + + K+v+n+gvGe ge+   l kaak L+e+tGQkP ++ akk++++F+++
  gi|119719160|ref|YP_919655.1| 13 PMRRVFIGKVVVNIGVGEGGER---LMKAAKLLEELTGQKPSLRPAKKTVREFGVK 65
                                   8*********************...****************************995 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.25
                                    CCHHHHCCCHSS--EEC CS
                   Ribosomal_L5  29 kaakeLaeItGQkPvvt 45 
                                    + + +L++I G + ++ 
  gi|119719160|ref|YP_919655.1| 164 ETITFLEKILGVQVIRG 180
                                    55677999999987765 PP

>> DUF5511  Family of unknown function (DUF5511)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   4.9e-05      0.29      32      66 ..      94     128 ..      81     130 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.9e-05
                        DUF5511  32 vkvsekeaaayaefmnGavehdsipfvkydeerGl 66 
                                     k+ ek    + +   G  eh  ip vkyd e G+
  gi|119719160|ref|YP_919655.1|  94 YKIHEKSIDRHGNVAFGVKEHILIPGVKYDPEVGI 128
                                    6899999999999999****************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1368.03
//
Query:       gi|119719161|ref|YP_919656.1|  [L=251]
Description: 30S ribosomal protein S4e [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      5e-21   74.4   0.1    9.8e-21   73.5   0.1    1.5  1  Ribosomal_S4e  Ribosomal family S4e
    5.1e-16   58.5   3.7    7.9e-16   57.9   3.7    1.3  1  RS4NT          RS4NT (NUC023) domain
    6.9e-08   32.1   0.0    1.6e-07   30.9   0.0    1.6  1  S4             S4 domain
  ------ inclusion threshold ------
        0.4   10.7   0.2        0.4   10.7   0.2    2.1  2  KOW            KOW motif


Domain annotation for each model (and alignments):
>> Ribosomal_S4e  Ribosomal family S4e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.5   0.1   2.2e-24   9.8e-21       2      75 .]      99     180 ..      98     180 .. 0.96

  Alignments for each domain:
  == domain 1  score: 73.5 bits;  conditional E-value: 2.2e-24
                                    TEEEEEEE-TTSSEEEEEE-TTCCCEEEEEECEEEEECCCEEEEEETTS-EEEES........STT-STTEEEEEETTTT CS
                  Ribosomal_S4e   2 genyrllydtkgrfalhkItseeakyKLcKikkkttvkkgipqlvthdGrtiryp........dpdikvnDtvkidleen 73 
                                    +++yr+++d+ +++++++I++eea yKL +i++k tvk+g +q ++hdGr+++++          ++k+ D ++i+++ +
  gi|119719161|ref|YP_919656.1|  99 EKYYRVVPDPARKLRFVEIKPEEAGYKLAQIRRKMTVKNGDLQFTLHDGRNVLIRkgseaystAISYKTYDALLITIPRQ 178
                                    689*************************************************99999999999667*************9 PP

                                    EE CS
                  Ribosomal_S4e  74 kI 75 
                                    +I
  gi|119719161|ref|YP_919656.1| 179 SI 180
                                    88 PP

>> RS4NT  RS4NT (NUC023) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.9   3.7   1.8e-19   7.9e-16       1      36 [.       6      41 ..       6      42 .. 0.96

  Alignments for each domain:
  == domain 1  score: 57.9 bits;  conditional E-value: 1.8e-19
                                   -S----EETTTS-TTS---SSSSSEE----SSSS-T CS
                          RS4NT  1 rGpkkHLKrlaAPkhWpldkkegvfavkPspGPHkl 36
                                   +G+ +HL+r +AP +Wp+++ke+v++vkPspGPH+l
  gi|119719161|ref|YP_919656.1|  6 KGSLRHLRRSVAPPFWPIKRKEYVWTVKPSPGPHSL 41
                                   6999******************************97 PP

>> S4  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.0   3.7e-11   1.6e-07      11      48 .]      56      93 ..      54      93 .. 0.97

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 3.7e-11
                                   TSSSSHHHHHHHHHTTTEEETTEEE--TT-EE-TTCEE CS
                             S4 11 glassrreArqlIehGrVlVNGkvvkdpsyrVkpgDvi 48
                                   g+a++ +eAr++   + + V+G+vv+d++++V+ +Dv+
  gi|119719161|ref|YP_919656.1| 56 GYAKTMKEARRILASRVIEVDGRVVTDYKFPVGLMDVL 93
                                   89**********************************85 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.3       1.3   5.7e+03      19      27 ..      72      80 ..      71      81 .. 0.72
   2 ?   10.7   0.2   8.9e-05       0.4       1      24 [.     188     211 ..     188     221 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.3
                                   EEEEETTTT CS
                            KOW 19 Vvkvdqhkv 27
                                   V +vd  +v
  gi|119719161|ref|YP_919656.1| 72 VIEVDGRVV 80
                                   889998774 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 8.9e-05
                                    TTSEEEESSSTTTTCEEEEEEEET CS
                            KOW   1 pGdhVkVvsGphkGktGkVvkvdq 24 
                                    +G   +Vv+G++ G+ G++  + q
  gi|119719161|ref|YP_919656.1| 188 VGTLAIVVDGRNVGFMGRINAIQQ 211
                                    578899************977665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1575.75
//
Query:       gi|119719162|ref|YP_919657.1|  [L=131]
Description: 50S ribosomal protein L24P [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-27   95.0   0.5    3.5e-27   94.7   0.5    1.1  1  Ribosomal_L26  Ribosomal proteins L26 eukaryotic, L24P archae
    7.7e-08   32.0   5.1    7.7e-08   32.0   5.1    2.0  2  KOW            KOW motif
  ------ inclusion threshold ------
      0.012   15.4   0.6      0.035   13.9   0.6    1.9  1  eIF-1a         Translation initiation factor 1A / IF-1


Domain annotation for each model (and alignments):
>> Ribosomal_L26  Ribosomal proteins L26 eukaryotic, L24P archaeal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.7   0.5   5.8e-31   3.5e-27       1      82 []       6     121 ..       6     121 .. 0.98

  Alignments for each domain:
  == domain 1  score: 94.7 bits;  conditional E-value: 5.8e-31
                                    xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................xxxx RF
                  Ribosomal_L26   1 sssrrkqrKa.hfnapshirrklmsapLskeLrekygvrslpir................................gvtr 47 
                                    ss++ k rK+  ++ap+hir+k + apLs eL++k g++++++r                                g+t 
  gi|119719162|ref|YP_919657.1|   6 SSKPGKVRKReVYDAPLHIRSKKIVAPLSAELQQKLGIKRIRVRkgdrvlivrgsfkghegkvtsvdvkkgrihveGATL 85 
                                    899******83589****************************************************************** PP

                                    xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                  Ribosomal_L26  48 ekangttvpvgihpSkvvItklkl.DkdrkkiLerk 82 
                                    +ka+gt+vp++ihpSkvv+t+l+l D +rk+++erk
  gi|119719162|ref|YP_919657.1|  86 RKADGTEVPFPIHPSKVVVTELDLsDPRRKELVERK 121
                                    ***********************************8 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   5.1   1.3e-11   7.7e-08       1      32 []      50      81 ..      50      81 .. 0.98
   2 ?   -2.4   0.1      0.87   5.2e+03      23      31 ..     119     126 ..     118     128 .. 0.45

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 1.3e-11
                                   TTSEEEESSSTTTTCEEEEEEEETTTTEEEEE CS
                            KOW  1 pGdhVkVvsGphkGktGkVvkvdqhkvrVfvd 32
                                   +Gd V +v+G +kG +GkV++vd +k r++v+
  gi|119719162|ref|YP_919657.1| 50 KGDRVLIVRGSFKGHEGKVTSVDVKKGRIHVE 81
                                   7*****************************97 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.87
                                    ETTTTEEEE CS
                            KOW  23 dqhkvrVfv 31 
                                    +++k  V+v
  gi|119719162|ref|YP_919657.1| 119 ERKK-QVVV 126
                                    5555.2322 PP

>> eIF-1a  Translation initiation factor 1A / IF-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.6   5.8e-06     0.035      28      54 ..      34      61 ..      25      79 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.8e-06
                                   EEEE-HHHH.CT----TT-EEEEEE-TT CS
                         eIF-1a 28 laeipgkfR.nkiwikrGdyVlVelspy 54
                                    ae+++k+  ++i++++Gd+Vl+    +
  gi|119719162|ref|YP_919657.1| 34 SAELQQKLGiKRIRVRKGDRVLIVRGSF 61
                                   58999*****************977444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 886.83
//
Query:       gi|119719163|ref|YP_919658.1|  [L=135]
Description: hypothetical protein Tpen_0245 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 938.11
//
Query:       gi|119719164|ref|YP_919659.1|  [L=345]
Description: eIF-2B alpha/beta/delta-related uncharacterized proteins [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.4e-80  269.3   0.1      4e-80  269.1   0.1    1.0  1  IF-2B           Initiation factor 2 subunit family
  ------ inclusion threshold ------
      0.069   13.4   0.1       0.25   11.5   0.0    1.9  2  DUF5130         Domain of unknown function (DUF5130)
       0.15   11.8   0.1       0.23   11.2   0.1    1.2  1  ADP_ribosyl_GH  ADP-ribosylglycohydrolase


Domain annotation for each model (and alignments):
>> IF-2B  Initiation factor 2 subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  269.1   0.1   6.6e-84     4e-80       1     282 []      46     334 ..      46     334 .. 0.98

  Alignments for each domain:
  == domain 1  score: 269.1 bits;  conditional E-value: 6.6e-84
                                    SS-SHHHHHHHHHHHHHHHHHHCCCSTHHHHHHHHHHHHHHHHTSSTS-HHHHHHHHHHHHHHHCCTTTSSHHHHHHHHH CS
                          IF-2B   1 kvrGspaiaiaalevllevikdaktskvaeLkeelrkaidlLkkarPtavslgnairrllkeiselksssdvkeakksli 80 
                                    ++rG+pai++aa+++++ ++ +   ++ + +++el++ + + k+arPtav+l++a++r+ +        ++v+ea+k ++
  gi|119719164|ref|YP_919659.1|  46 EIRGAPAIGVAAAYAVALFAVNFPGENLEAFMKELERVAGVVKSARPTAVNLSWAVNRVVR---VAMTATSVEEARKVIL 122
                                    58***********************************************************...4578999********* PP

                                    HHHHHHHHHHHHHHHHHHHHHHTTC-TTEEEEEES--SH........HHHHHHHHHHTTEEEEEEEEEXTTTTHH.HTHH CS
                          IF-2B  81 ekikelikeieeadekigdiaaelikdgdtilTicnskt........vlevlraaakekkkfkVivvEsrPrlqG.rlta 151
                                    e++ ++++e+eea++ ig+ +++li+dgdti+T+cn+++        +++ +  a++++k+f+Vi++E+rP+lqG rlta
  gi|119719164|ref|YP_919659.1| 123 EEAVKIHREDEEANRRIGELGEQLISDGDTIITVCNAGSlatsywgtATAPMYVAKEKGKNFRVIALETRPYLQGaRLTA 202
                                    ******************************************************************************** PP

                                    HHHHHTTXEEEEEEGGGHHHH.HHCTESEEEEEXSEEETTSEEEEETTHHHHHHHHHHTTXEEEEEXXGGGBESTSSSGG CS
                          IF-2B 152 keLvqagipvtlitdsavayv.mseevdkvivGAdrilenGaiankiGTsslAvlAkefnipvlvvaeslkfservqlde 230
                                    +eL+ agi+v ++td++++++ m+e++d +i GAdri++ G +ank GT+ lA++A+ +nip++v+a+s+ f+ +++  e
  gi|119719164|ref|YP_919659.1| 203 WELKMAGIDVVIATDNSIGILaMKEKIDLAITGADRITAQGYVANKLGTYPLALVARVHNIPFYVAAPSSSFDLNARGPE 282
                                    *******************863777******************************************************* PP

                                    GSSXXBEXTHHHHEETTEESSTTTEEEEEBSEEEEEGGGXSEEEETTEEEXC CS
                          IF-2B 231 difieerdpeellnitgeriaeeelkvvnpafDvtPpelItliITevGvlpp 282
                                    di ie r p+e+++i+g+ri++e +  + +afD+tPp+l+t+iITe+G++ p
  gi|119719164|ref|YP_919659.1| 283 DIEIEVRSPDEVVYIAGQRITPEGVSAIYYAFDITPPQLVTGIITEKGIIYP 334
                                    *************************************************976 PP

>> DUF5130  Domain of unknown function (DUF5130)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       0.7   4.2e+03      34      70 ..     120     154 ..     101     160 .. 0.64
   2 ?   11.5   0.0   4.2e-05      0.25      81     129 ..     276     326 ..     228     331 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.7
                        DUF5130  34 valDdaLkeasrkakvrfavyiGdlgedtaaaareil 70 
                                    v l++a+k   ++ ++     iG+lge+   + + i+
  gi|119719164|ref|YP_919659.1| 120 VILEEAVKIHREDEEAN--RRIGELGEQLISDGDTII 154
                                    55555555554444443..347888888777777665 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 4.2e-05
                        DUF5130  81 LiavsPnqraievvsGaevadrvadrvaqlGvtaavssfr..eGdLidglv 129
                                    L a  P++ +iev+s  ev   + +r+++ Gv+a   +f+    +L+ g++
  gi|119719164|ref|YP_919659.1| 276 LNARGPEDIEIEVRSPDEVVYIAGQRITPEGVSAIYYAFDitPPQLVTGII 326
                                    66889******************************9999722468888887 PP

>> ADP_ribosyl_GH  ADP-ribosylglycohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   3.8e-05      0.23     122     229 ..      52     159 ..      21     194 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.8e-05
                                    --BTTTGGG-HHHHHHTSS.-HHHHHHHHHHHH.HTTB--HHHHHHHHHHHHHHHHHHTT--STHHHHHH...HHHHTTT CS
                 ADP_ribosyl_GH 122 sagngalmRaaplgllyag.dpeeaaelaeeaa.rlTHnhpeavagaaayaaliaaalrgksleealdaa.eeelavapa 198
                                    + g  a+  +a +++ ++g ++e+ ++  e++a  +  + p+av+ + a++++++ a++ +s+eea +   ee+ + + +
  gi|119719164|ref|YP_919659.1|  52 AIGVAAAYAVALFAVNFPGeNLEAFMKELERVAgVVKSARPTAVNLSWAVNRVVRVAMTATSVEEARKVIlEEAVKIHRE 131
                                    5667788888999999999999999999999984666778*************************999997778888888 PP

                                    -HHHHHHHGGGGG---HHH........HHHH CS
                 ADP_ribosyl_GH 199 eeelaaalrkalaladsdkdvdvdaeeavde 229
                                    +ee  +++ ++ ++  sd+d   +   ++++
  gi|119719164|ref|YP_919659.1| 132 DEEANRRIGELGEQLISDGD---TIITVCNA 159
                                    99999999999998888884...33333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2278.87
//
Query:       gi|119719165|ref|YP_919660.1|  [L=199]
Description: hypothetical protein Tpen_0247 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-62  210.6   0.1    1.3e-62  210.5   0.1    1.0  1  DUF99     Protein of unknown function DUF99


Domain annotation for each model (and alignments):
>> DUF99  Protein of unknown function DUF99
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.5   0.1   7.3e-67   1.3e-62       2     182 ..       7     183 ..       6     184 .. 0.96

  Alignments for each domain:
  == domain 1  score: 210.5 bits;  conditional E-value: 7.3e-67
                                    GSEEEEEEEEE.....-SS-EEEEEEEEETT.EEEEEEEEEE-TT-S-HHHHHHHHHCC-TTTTEEEEEESSSEETTTEE CS
                          DUF99   2 eirvlGiddsfferkkkdgksvlvGvvmradrvvdgvafgrvtvdGtDateaiielvkrleredirvvlldGitiagFNv 81 
                                    ++rvlG++++f  rk+ ++ksv++Gvv+r+d +vdgv+++ ++v+G+Dat+ai++++ r+ r+di+v++l+G++i++FN+
  gi|119719165|ref|YP_919660.1|   7 AFRVLGVAECF--RKR-ARKSVIAGVVWRRDGFVDGVYLSFASVGGMDATDAIVDMYLRSSRRDINVIMLNGCIISWFNI 83 
                                    68*********..444.9************************************************************** PP

                                    --HHHHHHHH---EEEEESS---HHHHHHCCT.TSTTHHHHHHHHHHC.---EEETT.....EEEEEESS-HHHHHHHHH CS
                          DUF99  82 vDlerlheetglPviavtreepdlgklekaLrkhfpdeeeRlelieklgerieevek.tgeelyvravGieleeaaklvr 160
                                    +D+e+++e+tg+Pvi++++ee++ g lek+++k+fp++ +R++++++lg+r+ +++k ++  +yvra Gi ++e++++++
  gi|119719165|ref|YP_919660.1|  84 ADPEKIYERTGIPVICLSYEESE-G-LEKYIEKYFPGDVHRMRAYQSLGSRRLVYVKpARTYVYVRASGIAMDEVSRILN 161
                                    ***********************.8.***********************9999999934556****************** PP

                                    HC-SSSSS-HHHHHHHHHHHHH CS
                          DUF99 161 kltlegriPEPlRvAhliAsal 182
                                     +t+ g++PEPlRvA+ +A+a+
  gi|119719165|ref|YP_919660.1| 162 VTTKSGKVPEPLRVARQVARAV 183
                                    ********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.37s 00:00:00.99 Elapsed: 00:00:00.58
# Mc/sec: 1040.55
//
Query:       gi|119719166|ref|YP_919661.1|  [L=366]
Description: peptidase M24 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-65  221.4   0.1    1.3e-65  221.0   0.1    1.2  1  Peptidase_M24  Metallopeptidase family M24
    2.2e-08   34.8   0.1    4.1e-08   34.0   0.1    1.4  1  Creatinase_N   Creatinase/Prolidase N-terminal domain


Domain annotation for each model (and alignments):
>> Peptidase_M24  Metallopeptidase family M24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  221.0   0.1   1.5e-69   1.3e-65       1     208 [.     149     350 ..     149     351 .. 0.96

  Alignments for each domain:
  == domain 1  score: 221.0 bits;  conditional E-value: 1.5e-69
                                    HHHHHHHHHHHHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHTTTCEESSSSEEEEGGGGGSTTTBCSSSB--TTEEEEEE CS
                  Peptidase_M24   1 elirkaariasaaleavleaikpgvterelaaeieattlkrhgarglafppivasgenaavlhytpndrvlkegdlvlid 80 
                                    e+i +aar+a+ a++++l+ ++pgvte e+a ei +   +   + +++fppiva+ge+aa +h+ p+ r+l +gd+v+id
  gi|119719166|ref|YP_919661.1| 149 EAINRAARLAELAMRKALDTLEPGVTESEVASEILKV--IVSSGAYPSFPPIVAFGEHAAHPHAKPSLRRLIKGDFVKID 226
                                    5799*******************************88..4445789********************************** PP

                                    EEEEETTEEEEEEEEEECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHHHHTTBCCGBSSCSEEEESSS CS
                  Peptidase_M24  81 agaeydgyasDitrTvlvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarevlesaglakffphglGHgvGle 160
                                    +ga++dgy+sD+trT+++G+++++qr+++eav +aqe a++ +k+Gv ++e++a+a + l++agl ++f hglGHgvG +
  gi|119719166|ref|YP_919661.1| 227 LGAKVDGYCSDMTRTLVFGEPSEKQRRIFEAVVKAQESALASIKAGVQAREVHAIALRALKEAGLSQYFNHGLGHGVGVD 306
                                    ******************************************************************************** PP

                                    SSEEEEEESSSTTCSSB--TTBEEEEEEEEEEETTTEEEEEBEEEEEE CS
                  Peptidase_M24 161 vhdegpsvsresndgrkleeGmvftiEpgiyfapgeggvriedtvlvt 208
                                    +h+e p+++   +++ +l eG+v+t+Epg+y  pg ggvried+v+v 
  gi|119719166|ref|YP_919661.1| 307 IHEE-PYLN--LQSEAVLLEGDVVTVEPGVY-LPGYGGVRIEDMVYVE 350
                                    ***9.**99..678*****************.9************996 PP

>> Creatinase_N  Creatinase/Prolidase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   0.1   4.5e-12   4.1e-08       9     131 ..      16     141 ..      10     142 .. 0.82

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 4.5e-12
                                    HHHTT-SEEEEECCHHHHHHHSS...-SSSEEEEEEESSCE.EEEEECTTHHHHHHHH..........TTSEEEEEST.H CS
                   Creatinase_N   9 meekgldallvtspenlrYltGfatetgsrglalvvtadga.lllvdalryteaaees.........atveevveydd.p 77 
                                    +  ++l  l+v+s +n++Yl+G       ++ alvv+++g+ + l  +l+y++a  e+          + e+v ey++ +
  gi|119719166|ref|YP_919661.1|  16 LVPNDLNYLVVMSASNIFYLSGS-----DAPSALVVSKEGEvSALASRLEYFRAVSETsglrvvafaREGEDVSEYEEvV 90 
                                    55678999***************.....9999**************************6665555555555555555599 PP

                                    SSHHHHHHHHHHHHT-EEEE-TTSSBHHHHHHHHHHCTTSEEEETHHHHHHHHS CS
                   Creatinase_N  78 vealadllkellesekrvgveldaltvafyealkealpdaelvdaselieelRv 131
                                      +++++l+  +++++r+gv   +  ++  e+l e+  +++l d s  +  +R 
  gi|119719166|ref|YP_919661.1|  91 RGDFYEALSRMVSGSERIGVVGAS--CEAKEKLAEKT-GKQLYDYSKEFSLIRR 141
                                    999999999999999****99986..55556888887.7899999998888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2612.44
//
Query:       gi|119719167|ref|YP_919662.1|  [L=457]
Description: hypothetical protein Tpen_0249 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (457 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       609  (0.0339673); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 3226.99
//
Query:       gi|119719168|ref|YP_919663.1|  [L=397]
Description: galactose-1-phosphate uridylyltransferase-like [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00012   22.5   0.0    0.00058   20.3   0.0    2.1  2  DcpS_C         Scavenger mRNA decapping enzyme C-term binding
    0.00013   22.6   0.0    0.00076   20.2   0.0    2.3  2  HIT            HIT domain
  ------ inclusion threshold ------
      0.091   12.5   0.1       0.29   10.8   0.1    1.8  1  GalP_UDP_tr_C  Galactose-1-phosphate uridyl transferase, C-te


Domain annotation for each model (and alignments):
>> DcpS_C  Scavenger mRNA decapping enzyme C-term binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.64   3.8e+03      51      83 ..     180     212 ..     167     218 .. 0.73
   2 !   20.3   0.0   9.7e-08   0.00058       5      95 ..     266     357 ..     264     371 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.64
                                    --TTTTTHHHHHHHHHHHHHHHTT-T-EEEEE- CS
                         DcpS_C  51 Ltkehlpllkemrekakkvieekynevdaeelr 83 
                                    L++  l++l +m   +k++i +  +e +++ +r
  gi|119719168|ref|YP_919663.1| 180 LSDVPLEILVSMLSSMKSAIIRAVEESRSKGFR 212
                                    555567788888888888887777666666655 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 9.7e-08
                                    HHHHTTSS-B-EEEE-SSEEEEE-SS-SSSEEEEEEESS---SGGG--TTTTTHHHHHHHHHHHHHHHTT-T-EEEEE-- CS
                         DcpS_C   5 nilakgkepervvyedekfvvlkDikpkaklhllvipkrdikslrdLtkehlpllkemrekakkvieekynevdaeelrv 84 
                                    ++l   + ++r+vye+e+++      p+ ++h+ + pkr+++  +dL++++l  l+++ + +  ++++  ++  + + +v
  gi|119719168|ref|YP_919663.1| 266 CHLCTSRHEDRIVYENETWISWATSSPRRNYHVRAAPKRHVARYTDLSSSELLGLADVLRRVSRAMDRLGIT--R-DRNV 342
                                    5566677899******************************************99999999999999888755..2.2334 PP

                                    SCCCT-....-S-S- CS
                         DcpS_C  85 gvhyqP....svyhl 95 
                                     +  +P    s++h+
  gi|119719168|ref|YP_919663.1| 343 LFYSNPygydSFFHM 357
                                    444444344444444 PP

>> HIT  HIT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.52   3.1e+03      36      73 ..     176     213 ..     168     237 .. 0.67
   2 !   20.2   0.0   1.3e-07   0.00076       5      89 ..     274     358 ..     270     367 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.52
                                    TGCSGGGCCHHHHHH.HHHHHHHHHHHHHTCTTCCCEEE CS
                            HIT  36 hlselhdlteeelak.llsavkkvakalqkkfknkglrv 73 
                                     +++l+d++ e+l   l s+   + +a+++  + kg+r+
  gi|119719168|ref|YP_919663.1| 176 YYETLSDVPLEILVSmLSSMKSAIIRAVEE-SRSKGFRL 213
                                    677888888555544044555567777776.45566665 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 1.3e-07
                                    -CCEEEE-SSEEEEE-SS-SSSSEEEEEESSTGCSGGGCCHHHHHHHHHHHHHHHHHHHTCTTCCCEEEEEEESGGGT-S CS
                            HIT   5 pstvvyeddlvlafldidpkapghlLvipkkhlselhdlteeelakllsavkkvakalqkkfknkglrvvinngahagqs 84 
                                    ++++vye++  +   +++p+   h+   pk+h+++++dl+ +el  l  + ++v +a+ +   ++  +v+   ++ +  s
  gi|119719168|ref|YP_919663.1| 274 EDRIVYENETWISWATSSPRRNYHVRAAPKRHVARYTDLSSSELLGLADVLRRVSRAMDRLGITRDRNVLFYSNPYGYDS 353
                                    789***************************************************99998865555555555555555555 PP

                                    SSS-E CS
                            HIT  85 vahlH 89 
                                     +h+ 
  gi|119719168|ref|YP_919663.1| 354 FFHMF 358
                                    55555 PP

>> GalP_UDP_tr_C  Galactose-1-phosphate uridyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   4.8e-05      0.29      26     158 ..     271     393 ..     253     397 .] 0.79

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 4.8e-05
                                    HHH-TTEEEE-SSEEEE--TT--STT-EEEEESS--SSGGG--HHHHHHHHHHHHHHHHHHHHHCTS---EEEEEE---S CS
                  GalP_UDP_tr_C  26 laekervvelkdsflavvpylakWPfevlllrkaevkslaeladeekedlaailkklarkydnlfetsfeysmGlhqapl 105
                                     ++++r+v +++ ++  +       ++v   +k++v++ ++l+  e  +la +l+ + r  d l  t     +       
  gi|119719168|ref|YP_919663.1| 271 SRHEDRIVYENETWISWATSSPRRNYHVRAAPKRHVARYTDLSSSELLGLADVLRRVSRAMDRLGITRDRNVLFY----S 346
                                    57899******************************************************9999987776666555....4 PP

                                    CCCTTTT--EEEEE--BCSSTTEB----THHHHT-.EEESS-HHHHHHHHH.CS CS
                  GalP_UDP_tr_C 106 naeednswlHaHfevpllrsatvrkieVGlelLpe.rlrdllaEqaaerlrnal 158
                                    n+   +s++H+ +++  +  + v+    G e+L   r   +++E aae+lr ++
  gi|119719168|ref|YP_919663.1| 347 NPYGYDSFFHMFIDI--IPFEHVG----GIEMLDSvRVARVTPEEAAEQLR-SM 393
                                    555557778877764..4445554....66777542566777788888877.44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2530.78
//
Query:       gi|119719169|ref|YP_919664.1|  [L=263]
Description: hypothetical protein Tpen_0251 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
       0.11   12.9   0.8        1.8    9.1   0.4    2.2  2  NPV_P10       Nucleopolyhedrovirus P10 protein
       0.22   11.8   2.0       0.83    9.9   1.8    1.9  2  ABC_tran_CTD  ABC transporter C-terminal domain
        1.4    8.9   5.5         12    5.9   0.4    3.1  3  Shugoshin_N   Shugoshin N-terminal coiled-coil region


Domain annotation for each model (and alignments):
>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1     0.025   1.5e+02      39      61 ..      59      81 ..      51      88 .. 0.84
   2 ?    9.1   0.4    0.0003       1.8      34      66 ..      90     122 ..      71     132 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.025
                        NPV_P10 39 elnekLdaqsaqLaeletkvenI 61
                                   +  ++L++++ +L+ele+kve  
  gi|119719169|ref|YP_919664.1| 59 NFAKELESLALTLKELEKKVELL 81
                                   56789**************9865 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0003
                        NPV_P10  34 lpdvtelnekLdaqsaqLaeletkvenIqdiLn 66 
                                    ++d+ +l e L+ +sa++++letk+   ++  +
  gi|119719169|ref|YP_919664.1|  90 SEDIRKLVEGLETLSAKVNTLETKLVVLEKRIS 122
                                    589999*****************9876666555 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   1.8   0.00014      0.83       8      63 ..      62     113 ..      59     120 .. 0.72
   2 ?    5.7   0.0     0.003        18      10      33 ..     100     123 ..      93     128 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00014
                   ABC_tran_CTD   8 releeleaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeLeelyer 63 
                                    +ele l  ++ +LE++ + le    +p+  s +  + +l + le+l a+ ++l+ +
  gi|119719169|ref|YP_919664.1|  62 KELESLALTLKELEKKVELLESGAGKPG--SED--IRKLVEGLETLSAKVNTLETK 113
                                    8**************************9..444..555555555555555555443 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.003
                   ABC_tran_CTD  10 leeleaeIeaLEeeiaeleaelad 33 
                                    le+l a+ + LE+++  le++++ 
  gi|119719169|ref|YP_919664.1| 100 LETLSAKVNTLETKLVVLEKRISR 123
                                    899****************99985 PP

>> Shugoshin_N  Shugoshin N-terminal coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.4     0.002        12      13      35 ..      61      83 ..      58      83 .. 0.83
   2 ?    4.0   0.1    0.0077        46      18      31 ..     102     115 ..      93     123 .. 0.73
   3 ?   -0.7   0.0      0.22   1.3e+03       4      14 ..     196     206 ..     195     207 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.002
                    Shugoshin_N 13 AKsNsalslkirelekevseLls 35
                                   AK   +l l+++elek+v+ L s
  gi|119719169|ref|YP_919664.1| 61 AKELESLALTLKELEKKVELLES 83
                                   55567899***********9975 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.0077
                    Shugoshin_N  18 alslkirelekevs 31 
                                    +ls+k+++le+++ 
  gi|119719169|ref|YP_919664.1| 102 TLSAKVNTLETKLV 115
                                    67778888777754 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.22
                    Shugoshin_N   4 kylrqNreLAK 14 
                                     y++qN +L +
  gi|119719169|ref|YP_919664.1| 196 LYNSQNVSLTR 206
                                    6999**99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       883  (0.0492498); expected 358.6 (0.02)
Passed bias filter:                      779  (0.0434492); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 1889.37
//
Query:       gi|119719170|ref|YP_919665.1|  [L=138]
Description: hypothetical protein Tpen_0252 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      4e-05   23.3   0.0    6.3e-05   22.7   0.0    1.3  1  Robl_LC7    Roadblock/LC7 domain
  ------ inclusion threshold ------
      0.073   12.9   0.0       0.16   11.8   0.0    1.7  1  MAPKK1_Int  Mitogen-activated protein kinase kinase 1 interac
       0.15   11.3   0.0       0.21   10.8   0.0    1.1  1  DUF3271     Protein of unknown function (DUF3271)


Domain annotation for each model (and alignments):
>> Robl_LC7  Roadblock/LC7 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   1.1e-08   6.3e-05      22      89 ..      31      97 ..      18      99 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.1e-08
                                   ETTS-EEEECCSSSS-HHHHHHHHHHHHHHHHHHHHHCTSSSECEEEEEETTEEEEEEECTTTEEEEE CS
                       Robl_LC7 22 skdGlviatstldnddadqlAalasgllsaakaaarelgegelkelliegkkgelyltpagegalLvv 89
                                    +dG+++a+ ++d+++a+ lA + +++l+   a+++ ++  ++k + +e+++ge ++++  +g+++++
  gi|119719170|ref|YP_919665.1| 31 WRDGIPVAYVAPDQPQAEFLAVASAAALGSLDALGDIFN-SKVKRVDVEFENGEHIVISSLDGSFIAL 97
                                   58***************************9999998888.9*****************9999988876 PP

>> MAPKK1_Int  Mitogen-activated protein kinase kinase 1 interacting
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   2.7e-05      0.16       2      40 ..       8      47 ..       7     114 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.7e-05
                     MAPKK1_Int  2 dvkrfl.kkllsevdgllaiivtDrDGvvllkvgddssad 40
                                   +v+  l k++ ++ d + +i+ + rDG++++ v+ d+ + 
  gi|119719170|ref|YP_919665.1|  8 QVRGVLaKIIKETHDAIVSIVFAWRDGIPVAYVAPDQPQA 47
                                   57777834455667889****************9887644 PP

>> DUF3271  Protein of unknown function (DUF3271)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   3.5e-05      0.21      30      85 ..      36      91 ..      32     100 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3.5e-05
                        DUF3271 30 siayasvaqPtvtfekd.ekkhtkyLdiinnilrdesenikyayeggnyHwvitdfd 85
                                   ++ay++ +qP + f    +      Ld++ +i++ + + +  ++e g+ H+vi+ +d
  gi|119719170|ref|YP_919665.1| 36 PVAYVAPDQPQAEFLAVaSAAALGSLDALGDIFNSKVKRVDVEFENGE-HIVISSLD 91
                                   799*********997761566789*********************886.89998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 918.52
//
Query:       gi|119719171|ref|YP_919666.1|  [L=182]
Description: protein of unknown function, ATP binding [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.2e-11   43.1   0.0    4.3e-07   30.0   0.0    2.2  2  ATP_bind_1  Conserved hypothetical ATP binding protein
      1e-07   31.6   0.0    5.5e-07   29.2   0.0    1.9  1  Arf         ADP-ribosylation factor family
     0.0016   18.4   0.1     0.0023   18.0   0.1    1.2  1  TsaE        Threonylcarbamoyl adenosine biosynthesis protein 
     0.0019   18.4   0.0     0.0027   17.9   0.0    1.2  1  Roc         Ras of Complex, Roc, domain of DAPkinase
     0.0061   15.7   0.0      0.012   14.7   0.0    1.4  1  T2SSE       Type II/IV secretion system protein
  ------ inclusion threshold ------
      0.013   15.6   0.0      0.021   14.9   0.0    1.3  1  MMR_HSR1    50S ribosome-binding GTPase
      0.014   15.3   0.1      0.034   14.1   0.1    1.7  2  NTPase_1    NTPase
      0.025   15.0   0.0      0.025   15.0   0.0    1.3  1  AAA_16      AAA ATPase domain
      0.039   14.4   0.0       0.28   11.6   0.0    2.0  2  AAA         ATPase family associated with various cellular ac
      0.052   12.8   0.0      0.076   12.3   0.0    1.2  1  Septin      Septin
       0.15   12.3   0.1       0.19   12.0   0.1    1.4  1  AAA_28      AAA domain
       0.15   11.8   0.0       0.35   10.6   0.0    1.6  2  AAA_24      AAA domain
       0.16   12.1   0.0       0.26   11.4   0.0    1.3  1  AAA_33      AAA domain


Domain annotation for each model (and alignments):
>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   0.00016      0.22       1      23 [.      12      34 ..      12      41 .. 0.84
   2 !   30.0   0.0   3.1e-10   4.3e-07      68     170 ..      50     132 ..      42     177 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00016
                     ATP_bind_1  1 vvGpaGsGKttfvgalseilelr 23
                                   v Gp  sGKttfv++++e + ++
  gi|119719171|ref|YP_919666.1| 12 VSGPYASGKTTFVRTVAENVLST 34
                                   78**************9976655 PP

  == domain 2  score: 30.0 bits;  conditional E-value: 3.1e-10
                     ATP_bind_1  68 lvvaleflresldwldeelekeeddyllfDtPGQielfthseslakiveeLesefalvvvyLvDsqrltdptkfisglls 147
                                    ++va+++++  l    + +       +lf+tPGQ +l +++ +la        ++  + ++LvD   l ++     g  +
  gi|119719171|ref|YP_919666.1|  50 TTVAFDYGKLYL----DGI-----PIYLFGTPGQTRLQFMWRVLA--------QGMHGYLFLVDGSSLLEVYR-ARG--I 109
                                    778888888877....344.....589******************........8999*******999998332.233..2 PP

                     ATP_bind_1 148 alsamlrlelPhvvvlnkfDllk 170
                                       +    + Ph++++nk D+  
  gi|119719171|ref|YP_919666.1| 110 YTYMKSLGNYPHIIAVNKQDVKG 132
                                    2223334689**********944 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.0     4e-10   5.5e-07      14     142 ..       7     145 ..       1     169 [. 0.83

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 4e-10
                                    EEEEEEEESTTSSHHHHHHHHHHSSCEECSSSSSEEEEEEEE.............TTEEEEEEEE-SSGGGGGGGGGGCT CS
                            Arf  14 elrilllGLDnaGKtTilkklkleelvttvPTigfnveelei.............knlkftvwDvGGqeklRplWknYfe 80 
                                     l+il+ G  ++GKtT +  + ++ l+t vP + +  ++++               ++ + ++   Gq++l  +W+   +
  gi|119719171|ref|YP_919666.1|   7 YLKILVSGPYASGKTTFVRTVAENVLSTEVPVTTPGEQKVKEyttvafdygklylDGIPIYLFGTPGQTRLQFMWRVLAQ 86 
                                    579*******************999999888666655555544555666666666999999******************* PP

                                    TESEEEEEEETT-CTTHHHHHHHHHHHCTSGCCTTSEEEEEEE-TTSTTSS-HHHHHHHTTG CS
                            Arf  81 ktdavifvvDsadreRleeakeeLkalleeeelkevallvlaNKqDlpealseeelrellgl 142
                                     +++ +f+vD +    +  a+   +    ++ l + + ++  NKqD+++++  + ++++ ++
  gi|119719171|ref|YP_919666.1|  87 GMHGYLFLVDGSSLLEVYRARGIYTY---MKSLGNYPHIIAVNKQDVKGSVPPSRVASIFNV 145
                                    ***********998888888766554...478999****************99999887765 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1   1.6e-06    0.0023      22      61 ..      10      51 ..       1      62 [. 0.84

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.6e-06
                                   EEEEESTTSSHHHHHHHHHHHTT--..----TTTTSEEEEEE CS
                           TsaE 22 ilLeGdLGaGKTtlvrglakalgve..evkSPTFtlveeYel 61
                                   il +G+  +GKTt+vr +a+++  +  +v+ P  + v+eY++
  gi|119719171|ref|YP_919666.1| 10 ILVSGPYASGKTTFVRTVAENVLSTevPVTTPGEQKVKEYTT 51
                                   899*****************98665599****9999999965 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0     2e-06    0.0027       1     119 [.       9     129 ..       9     130 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2e-06
                                    EEEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SGGCTTTT-HHHHCTS CS
                            Roc   1 KvvlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaGqerfrslhplylrea 80 
                                    K+++ G  ++GKt++++ + e+  s++   t+  + + ke+t++     +  ++ + + ++ t Gq+r + + ++  ++ 
  gi|119719171|ref|YP_919666.1|   9 KILVSGPYASGKTTFVRTVAENVLSTEVPVTTPGEQKVKEYTTVAFDYGKLYLDGIPIYLFGTPGQTRLQFMWRVLAQGM 88 
                                    89999********************99998888888888888776544455677899*********************** PP

                                    CEEEEEEEGHHHHCH..HHHHHHHHHHCSSS-EEEEEE-TT CS
                            Roc  81 alailvydsrssenl..keWlkelkkvagkspvilvgnkiD 119
                                    + +++++d +s  ++   + +    k  g+ p i+ +nk D
  gi|119719171|ref|YP_919666.1|  89 HGYLFLVDGSSLLEVyrARGIYTYMKSLGNYPHIIAVNKQD 129
                                    ********776544311445555666677888888899988 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   8.5e-06     0.012     129     156 ..       7      34 ..       2      49 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 8.5e-06
                          T2SSE 129 rglilvsGgTgsGKttllyallkeinks 156
                                    +  ilvsG+  sGKtt++ ++ + + ++
  gi|119719171|ref|YP_919666.1|   7 YLKILVSGPYASGKTTFVRTVAENVLST 34 
                                    678***************9888777655 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   1.5e-05     0.021       2      87 ..      10     101 ..       9     127 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.5e-05
                                    EEEEESTTSSHHHHHHHHHT..........STEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHH CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltg..........ekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgkafl 71 
                                    +++ G   +GK+t++++  +          +  + + k  tT    +g++ l+g +i+l  tpG       + ++  ++l
  gi|119719171|ref|YP_919666.1|  10 ILVSGPYASGKTTFVRTVAEnvlstevpvtTPGEQKVKEYTTVAFDYGKLYLDGIPIYLFGTPG-QT----RLQFMWRVL 84 
                                    78899999**********985554444332233555566788888888888999**********.33....333444444 PP

                                    HHHC.TSEEEEEEETT..T CS
                       MMR_HSR1  72 alee.adlillvvdas..e 87 
                                       + ++  l++vd s   
  gi|119719171|ref|YP_919666.1|  85 --AQgMHGYLFLVDGSslL 101
                                    ..34478888888855442 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   2.4e-05     0.034       1      31 [.       9      39 ..       9      59 .. 0.89
   2 ?   -2.2   0.0       2.5   3.5e+03      42      68 ..      74     100 ..      69     118 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.4e-05
                                   EEEEE--TTSSHHHHHHHHHHHH...GGGEE CS
                       NTPase_1  1 kvfiTGppGvGKtTlvkkvlellkssgvkvg 31
                                   k++++Gp  +GKtT+v+ v+e++ s +v+v+
  gi|119719171|ref|YP_919666.1|  9 KILVSGPYASGKTTFVRTVAENVLSTEVPVT 39
                                   689********************99999986 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.5
                                    ----EEEEEET.T--EEEEEETT---S CS
                       NTPase_1  42 grrigFkivdlasgeegiLarveakre 68 
                                    ++r  F    la+g +g+L  v++++ 
  gi|119719171|ref|YP_919666.1|  74 QTRLQFMWRVLAQGMHGYLFLVDGSSL 100
                                    567778888888888888877775544 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   1.8e-05     0.025      27      53 ..      10      36 ..       2     180 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.8e-05
                         AAA_16 27 vllsGesGvGKsslvrellralekdgg 53
                                   +l+sG+ ++GK++ vr++++ +  +++
  gi|119719171|ref|YP_919666.1| 10 ILVSGPYASGKTTFVRTVAENVLSTEV 36
                                   89*****************98887753 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0    0.0002      0.28       1      22 [.      10      31 ..      10      56 .. 0.77
   2 ?    0.5   0.0      0.53   7.4e+02       2      38 ..      67     104 ..      66     131 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0002
                                   EEEESSTTSSHHHHHHHHHHHH CS
                            AAA  1 vllyGppGtGKTllakavakel 22
                                   +l++Gp   GKT++++ va+++
  gi|119719171|ref|YP_919666.1| 10 ILVSGPYASGKTTFVRTVAENV 31
                                   699****************995 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.53
                                    EEESSTTSSH.HHHHHHHHHHHTHEEEEEETTTCSSSS CS
                            AAA   2 llyGppGtGK.Tllakavakelgvefleisgsellsky 38 
                                    +l+G+pG  +   + + +a+ ++ +++ ++gs+ll+ y
  gi|119719171|ref|YP_919666.1|  67 YLFGTPGQTRlQFMWRVLAQGMHGYLFLVDGSSLLEVY 104
                                    67777776552356788899999999999999999554 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   5.5e-05     0.076       5      45 ..       8      48 ..       5      68 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.5e-05
                                   EEEEEEEBTTSSCCCCCCTTSSSS----------------- CS
                         Septin  5 ftlmvvGesglGkttlintlfetdlieeekleeasekkkkt 45
                                   + ++v G  + Gktt+++t+ e+ l +e  ++++ e+k k+
  gi|119719171|ref|YP_919666.1|  8 LKILVSGPYASGKTTFVRTVAENVLSTEVPVTTPGEQKVKE 48
                                   689**********************9997666666644433 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00014      0.19       1      23 [.       9      35 ..       9     103 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00014
                         AAA_28  1 kivitGgestGKTtlleaLaar....g 23
                                   ki ++G++ +GKTt ++  a++    +
  gi|119719171|ref|YP_919666.1|  9 KILVSGPYASGKTTFVRTVAENvlstE 35
                                   799*****************8766443 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00026      0.35       3      27 ..       8      32 ..       7      56 .. 0.91
   2 ?   -3.6   0.0       5.4   7.4e+03     114     132 ..     109     129 ..     106     138 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00026
                         AAA_24  3 lkiliyGpsgiGKTtlakelgpkpl 27
                                   lkil+ Gp  +GKTt++++  +++l
  gi|119719171|ref|YP_919666.1|  8 LKILVSGPYASGKTTFVRTVAENVL 32
                                   69*****************977766 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 5.4
                         AAA_24 114 llkklqelrk..nvifiahek 132
                                    +++++++l++  ++i++ +++
  gi|119719171|ref|YP_919666.1| 109 IYTYMKSLGNypHIIAVNKQD 129
                                    567788888888888887665 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00019      0.26       2      22 ..      10      30 ..      10      53 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00019
                         AAA_33  2 vllvGlpGsGKstlaerllkk 22
                                   +l+ G+ +sGK+t+++ ++++
  gi|119719171|ref|YP_919666.1| 10 ILVSGPYASGKTTFVRTVAEN 30
                                   5789************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1162.75
//
Query:       gi|119719172|ref|YP_919667.1|  [L=125]
Description: roadblock/LC7 family protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-11   43.9   0.0      2e-11   43.5   0.0    1.2  1  Robl_LC7     Roadblock/LC7 domain
  ------ inclusion threshold ------
       0.07   13.8   0.5       0.11   13.2   0.5    1.2  1  ACC_epsilon  Acyl-CoA carboxylase epsilon subunit


Domain annotation for each model (and alignments):
>> Robl_LC7  Roadblock/LC7 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.5   0.0   2.2e-15     2e-11       5      91 .]      11      98 ..       8      98 .. 0.89

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 2.2e-15
                                   HHHHCCHHCTECEEEEEETTS-EEEECCSSSS-HHHHHHHHHHHHHHHHHHHHHCTSSSECEEEEEETTEE.EEEEECTTTE CS
                       Robl_LC7  5 lleelqsvpgvrgalvvskdGlviatstldnddadqlAalasgllsaakaaarelgegelkelliegkkge.lyltpagega 85
                                   +++ +++v+gv+g+++ s+dGl++ +s  d+d  +++Aal++ l + +++a++elg+ge + +++   +g+ ++ t  ge  
  gi|119719172|ref|YP_919667.1| 11 IIDPVTRVAGVEGFVISSSDGLPLFSSLTDKDLEEKVAALTAVLSEVGNRASTELGKGEAEWITVNAPDGSgIIYTKLGEIG 92
                                   567899***********************************************************99877615556778888 PP

                                   EEEEEE CS
                       Robl_LC7 86 lLvvla 91
                                   +++vl+
  gi|119719172|ref|YP_919667.1| 93 YMAVLF 98
                                   888875 PP

>> ACC_epsilon  Acyl-CoA carboxylase epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.5   1.2e-05      0.11      12      35 ..      44      67 ..      43      77 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.2e-05
                    ACC_epsilon 12 deELAALtaVLaaraaaaaaaaae 35
                                   +e +AALtaVL+ + ++a  +  +
  gi|119719172|ref|YP_919667.1| 44 EEKVAALTAVLSEVGNRASTELGK 67
                                   5789************99876555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 958.17
//
Query:       gi|119719173|ref|YP_919668.1|  [L=411]
Description: aminotransferase, class I and II [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-51  175.7   0.0    1.7e-51  175.5   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    5.9e-09   35.4   0.0    8.6e-09   34.8   0.0    1.1  1  Aminotran_5      Aminotransferase class-V
    1.5e-07   31.0   0.0    2.3e-07   30.4   0.0    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    2.8e-05   22.9   0.0    4.1e-05   22.3   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    0.00019   20.4   0.0    0.00026   19.9   0.0    1.2  1  Aminotran_MocR   Alanine-glyoxylate amino-transferase
  ------ inclusion threshold ------
      0.017   15.5   0.1      0.035   14.4   0.1    1.5  1  Trigger_N        Bacterial trigger factor protein (TF)
      0.034   13.4   0.0      0.051   12.9   0.0    1.2  1  Beta_elim_lyase  Beta-eliminating lyase


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.5   0.0   6.5e-55   1.7e-51       2     361 ..      41     401 ..      40     403 .. 0.93

  Alignments for each domain:
  == domain 1  score: 175.5 bits;  conditional E-value: 6.5e-55
                                    EEEESSSSSTTSTTSSHHHHHHHHHHHH.HHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHH CS
                  Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaeke.galaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagal 80 
                                    d+i +g ++++      +++ev+    +   +  ++   yg ++g  el+e +a+ l++  +++++++++++  +G +++
  gi|119719173|ref|YP_919668.1|  41 DIISFGGGAPSLP----PPQEVVDFLVDfLKNNPQKSVAYGSTRGMIELRELIAQDLKKYWGVDYDPKDEIIIVNGGTEG 116
                                    5677888888887....9999999999988888888899***************88887778****************** PP

                                    HHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TT CS
                  Aminotran_1_2  81 iealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNP 160
                                    i ++  ++ l+pgde++v dpty  y++ ++l gg v+++p++ e++++  +e++++ ++        tk +++ sp NP
  gi|119719173|ref|YP_919668.1| 117 IYLALSAI-LEPGDEVIVLDPTYLGYHEPVKLLGGRVRTVPVTVENGYQPRIEDVKKVISP------LTKAFILLSPDNP 189
                                    ********.***************************************************9......89*********** PP

                                    T--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHH CS
                  Aminotran_1_2 161 tGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilgnaavv 240
                                    tG v t+e ++ l+dla ++ +++++D +Y +  +g + ++   ++ ++e  +++ +s+sK  +++G+R+Gy+++  +vv
  gi|119719173|ref|YP_919668.1| 190 TGRVVTEEFVRGLVDLAVEHDFWIVFDAVYKHISYGRPTPWVDSFKGARER-TITINSFSKEASIPGFRLGYVTAPREVV 268
                                    ************************************887766555555544.6*************************** PP

                                    HHHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHS..TEEEECCSCSSEEEEEETHH CS
                  Aminotran_1_2 241 sqlrklsrpfls..ssllqaavaaalsdallkqseleemrq.rlqkrrkelrdeLael..glkvlasqsgmflltdlsae 315
                                    + ++k+++ +    ++++q a  + l+   +  ++l+e +  ++ krr+++++ ++e   + k   ++++++ ++ ++++
  gi|119719173|ref|YP_919668.1| 269 EVMEKIKQYVSLapDTPGQIAMIKFLESGIKD-RYLQEVVIpTYRKRRDFMYKCIQEYlpEAKTSLPEGAFYFFVNIEEY 347
                                    ********9999****************9975.59999987589999********99999999999************** PP

                                    ......CHHHHHHHHHHTCTEEEEEGGGGTS..TTEEEEECTTS-HHHHHHHHH CS
                  Aminotran_1_2 316 ......takelskkLleevgvyvtpgtsftv..pgrlRitvAglteeeleelve 361
                                          +++e++  Ll ++ v+v+pg++f+   ++++R+t+ + +ee +ee ++
  gi|119719173|ref|YP_919668.1| 348 lkamgrDDEEFANRLLYRKSVVVIPGRYFGEmgKNHIRMTFVSEPEERIEEGIK 401
                                    *****************************************7777777777666 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   0.0   3.4e-12   8.6e-09      11     177 ..      54     218 ..      45     224 .. 0.80

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 3.4e-12
                                    --HHHHHHHHHHHHCTCCSSSSSS.SHHHHHHHHHHHHHHHHHHHHHT-ST..GGGEEEESSHHHHHHHHHHHCCCC-TT CS
                    Aminotran_5  11 kpqeVldalqeyytdynanvhrsv.hhlgkeatkaveearekvaelinaes..eeeiiftsGtteainlvalslarslkp 87 
                                     pqeV+d l ++++   +n+++sv +  +  +++  e + +++++  +++   ++eii + G+te+i l++ ++   l+p
  gi|119719173|ref|YP_919668.1|  54 PPQEVVDFLVDFLK---NNPQKSVaYGSTRGMIELRELIAQDLKKYWGVDYdpKDEIIIVNGGTEGIYLALSAI---LEP 127
                                    47889999999955...55544330333344466666677777888777652269*******************...*** PP

                                    TSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTE...B--HHHHHHH CS
                    Aminotran_5  88 gdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvtGt...iqpveeigkl 164
                                    gde++v +  + + + p + l  r  ++ + ++++++ + ++++++k +++ tk+ ++    n tG     + v  +++l
  gi|119719173|ref|YP_919668.1| 128 GDEVIVLDPTYLGYHEPVKLLGGR--VRTVPVTVENGYQPRIEDVKKVISPLTKAFILLSPDNPTGRvvtEEFVRGLVDL 205
                                    ***************999999844..777778888888888*************************632257899***** PP

                                    HHHTT-EEEEE-T CS
                    Aminotran_5 165 akkkgalvlvDaa 177
                                    a +++ +++ Da+
  gi|119719173|ref|YP_919668.1| 206 AVEHDFWIVFDAV 218
                                    ***********98 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.0   9.1e-11   2.3e-07      38     145 ..     104     217 ..      86     224 .. 0.78

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 9.1e-11
                                    -SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-.TTTSSB-GGGCGGG--TTEEEEE CS
                DegT_DnrJ_EryC1  38 vkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvd.pdtynidpaaieaaitertkaIl 116
                                    ++  i v+ Gt+++ laL+a+ ++pgdeVIv   t+++  ++v  lg ++  v v+ ++ y++  ++++++i + tka +
  gi|119719173|ref|YP_919668.1| 104 KDEIIIVNGGTEGIYLALSAI-LEPGDEVIVLDPTYLGYHEPVKLLGGRVRTVPVTvENGYQPRIEDVKKVISPLTKAFI 182
                                    456799**************7.6789*********************8876666552378*****************987 PP

                                    EB...-GGGB--..-.HHHHHHHHHHCT-EEEEE- CS
                DegT_DnrJ_EryC1 117 pV...hlyGqva..d.mdalkaiaakhglkvieDa 145
                                    +    +  G+v+  + +  l ++a +h+ +++ Da
  gi|119719173|ref|YP_919668.1| 183 LLspdNPTGRVVteEfVRGLVDLAVEHDFWIVFDA 217
                                    54222567777643235667777888888888777 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   1.6e-08   4.1e-05      70     175 ..     107     218 ..      98     227 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.6e-08
                                    EEEESSHHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTT...CEEEEESTTSHHHHHHHCCTTEEEEEEESS CS
                Cys_Met_Meta_PP  70 alavssGmaAiaaailallkaGdeivvsddlYggtqrllkkvlkklg...ievkfvdtsdleelekaikentklvylEtp 146
                                     ++v+ G+  i +a+ a+l+ Gde++v d  Y g ++ +k +  ++    ++v+   +  +e+++k+i++ tk++ l +p
  gi|119719173|ref|YP_919668.1| 107 IIIVNGGTEGIYLALSAILEPGDEVIVLDPTYLGYHEPVKLLGGRVRtvpVTVENGYQPRIEDVKKVISPLTKAFILLSP 186
                                    5788999***************************999888887775410044444445789******************* PP

                                    -TTTT----...HHHHHHHHHHTT-EEEEEGT CS
                Cys_Met_Meta_PP 147 tnpllkvvD...iekiaklakkagvlvvvDnt 175
                                     np+ +vv    ++ +++la +++  +v D++
  gi|119719173|ref|YP_919668.1| 187 DNPTGRVVTeefVRGLVDLAVEHDFWIVFDAV 218
                                    ****9998533355667777777777777765 PP

>> Aminotran_MocR  Alanine-glyoxylate amino-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0     1e-07   0.00026     158     324 ..     165     318 ..     124     347 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1e-07
                                    E-HHHHHHHHHC-TTEEE.EEE-SSS-TTT-----HHHHHHHHT---SSTT-EEEEE-TTSS-BS.SSSS----HHHHHH CS
                 Aminotran_MocR 158 pdvdaveklvaedasvkG.ilavpkysnptGetiseevarrlaalkaaapdfrifaddayavhdlvaeedkdanivalar 236
                                    p ++ v+k+++     k  il  p   nptG +++ee +r l+ l     df i +d  y+ h  ++        v   +
  gi|119719173|ref|YP_919668.1| 165 PRIEDVKKVISP--LTKAfILLSP--DNPTGRVVTEEFVRGLVDLA-VEHDFWIVFDAVYK-HISYGRPTP---WVDSFK 235
                                    555555555542..2232133334..6*****************95.678*******9998.555555444...444443 PP

                                    HHT-TTSEEEEEESTT.TS-TTSS-EEEEE-HHHHHHHHHHHHHC-S---HHHHHHHHHHHHHSTHHHHHHHHHHHHHHH CS
                 Aminotran_MocR 237 daGhpdrafvlastsk.itfaGaGvafvassedniawlkkylGlqsiGpdkveqlrhvkflkdyeGlealmrdhaeliap 315
                                      G  +r++ + s sk  +  G  +++v++  + +  ++k     s+ pd   q+  +kfl+   G++   r  +e++ p
  gi|119719173|ref|YP_919668.1| 236 --GARERTITINSFSKeASIPGFRLGYVTAPREVVEVMEKIKQYVSLAPDTPGQIAMIKFLES--GIKD--RYLQEVVIP 309
                                    ..6678*********945789***************************************985..5554..334556666 PP

                                    HHHHHHHHH CS
                 Aminotran_MocR 316 kfeavlevl 324
                                     +++  + +
  gi|119719173|ref|YP_919668.1| 310 TYRKRRDFM 318
                                    666555555 PP

>> Trigger_N  Bacterial trigger factor protein (TF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   1.4e-05     0.035      31      64 ..     243     276 ..     235     339 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.4e-05
                                    HHHHHHTTS-BTTC-TT..---CCCHHHHCTCCCHH CS
                      Trigger_N  31 alkklakkvkipGFRkG..kvPrsiiekrygkevle 64 
                                    ++++++k+++ipGFR G   +Pr+++e +  +++++
  gi|119719173|ref|YP_919668.1| 243 TINSFSKEASIPGFRLGyvTAPREVVEVM--EKIKQ 276
                                    6899*************6669*****998..33333 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0     2e-05     0.051      28     168 ..      76     217 ..      71     218 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2e-05
                                    CT--HHHHHHHHHHHH.........HTT-SEEEEES-HHHHHHHHHHHH--TTEEEEEETT-HHHHSSTTHHHHC.C--E CS
                Beta_elim_lyase  28 YgedktvnrLedavae.........lfgkeaalfvpqGtaAnsillkillqrgeevivtepahihfdetgaiael.agvk 97 
                                    Yg  +++ +L + +a+         +  k+ ++ v  Gt +  ++l+++l++g+eviv +p     +e   ++ l + v+
  gi|119719173|ref|YP_919668.1|  76 YGSTRGMIELRELIAQdlkkywgvdYDPKDEIIIVNGGTEGIYLALSAILEPGDEVIVLDPTYLGYHEP--VKLLgGRVR 153
                                    5666666666666555555555444445677888999************************99888886..444646677 PP

                                    EEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEE CS
                Beta_elim_lyase  98 lrdlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDg 168
                                     ++++ ++  +  +e+++++i +  +     ++i+l   n t  G+vv+ e +r + ++a +++  +++D+
  gi|119719173|ref|YP_919668.1| 154 TVPVTVENGYQPRIEDVKKVISPLTK-----AFILLSPDNPT--GRVVTEEFVRGLVDLAVEHDFWIVFDA 217
                                    788888887799***********555.....9*****99999..*************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 3054.81
//
Query:       gi|119719174|ref|YP_919669.1|  [L=275]
Description: hypothetical protein Tpen_0256 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       705  (0.0393218); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2098.99
//
Query:       gi|119719175|ref|YP_919670.1|  [L=156]
Description: 30S ribosomal protein S11P [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.4e-42  142.6   0.7    7.4e-42  142.2   0.7    1.2  1  Ribosomal_S11  Ribosomal protein S11


Domain annotation for each model (and alignments):
>> Ribosomal_S11  Ribosomal protein S11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.2   0.7   4.1e-46   7.4e-42       1     110 []      34     152 ..      34     152 .. 0.99

  Alignments for each domain:
  == domain 1  score: 142.2 bits;  conditional E-value: 4.1e-46
                  Ribosomal_S11   1 GvahiqasfnntiititdlkGaevlvksaGglgvkasr.kssPyaaqlaaekaaekvldkGikavevkvkg........p 71 
                                    G+a i+as+nntii+itdl+Gae+++ ++Gg++ ka+r k+sP+aa++aa +aa+ +ldkGi+ v+vk+k+        p
  gi|119719175|ref|YP_919670.1|  34 GIAWIYASYNNTIIHITDLSGAETIAFASGGMVAKADRdKPSPWAAMQAAARAAKIALDKGIRVVHVKIKApggygpktP 113
                                    89****************************************************************************** PP

                  Ribosomal_S11  72 GpGreaalralaraGlkigriedvtPiPhdgirrpkkrr 110
                                    GpG+ +a+ral raGl + riedvtP+P+d+ir+p++rr
  gi|119719175|ref|YP_919670.1| 114 GPGAGPAIRALVRAGLMVDRIEDVTPLPTDSIRKPGGRR 152
                                    *************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       812  (0.0452898); expected 358.6 (0.02)
Passed bias filter:                      592  (0.0330191); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 983.18
//
Query:       gi|119719176|ref|YP_919671.1|  [L=172]
Description: 30S ribosomal protein S4P [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.3e-16   58.4   0.2    4.3e-16   58.4   0.2    2.0  3  S4            S4 domain
    2.7e-05   25.0   0.3    5.1e-05   24.1   0.1    1.6  2  Ribosomal_S4  Ribosomal protein S4/S9 N-terminal domain
  ------ inclusion threshold ------
       0.17   12.7   0.0       0.23   12.2   0.0    1.3  1  DIOX_N        non-haem dioxygenase in morphine synthesis N-te


Domain annotation for each model (and alignments):
>> S4  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1      0.78   4.6e+03      16      22 ..      52      58 ..      42      59 .. 0.68
   2 ?   -3.3   0.0       1.3   7.8e+03       4      15 ..      74      85 ..      72      85 .. 0.70
   3 !   58.4   0.2   7.2e-20   4.3e-16       1      46 [.     104     149 ..     104     151 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.78
                                   HHHHHHH CS
                             S4 16 rreArql 22
                                   r +Ar+l
  gi|119719176|ref|YP_919671.1| 52 RAKARKL 58
                                   8899998 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.3
                                   HHHHHHTTSSSS CS
                             S4  4 dkvlarlglass 15
                                      l+++gl +s
  gi|119719176|ref|YP_919671.1| 74 VSRLYKMGLLPS 85
                                   556899998775 PP

  == domain 3  score: 58.4 bits;  conditional E-value: 7.2e-20
                                    EEHHHHHHHTTSSSSHHHHHHHHHTTTEEETTEEE--TT-EE-TTC CS
                             S4   1 rRLdkvlarlglassrreArqlIehGrVlVNGkvvkdpsyrVkpgD 46 
                                    rRL+++++r+gla ++r+ArqlI hG++ VN ++v++p+y V+  +
  gi|119719176|ref|YP_919671.1| 104 RRLQTIVYRKGLATTIRHARQLITHGHIAVNSRRVRSPGYLVSRDE 149
                                    8*****************************************9876 PP

>> Ribosomal_S4  Ribosomal protein S4/S9 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.1   8.6e-09   5.1e-05      34      81 ..      13      61 ..       2     103 .. 0.87
   2 ?   -1.6   0.0       0.9   5.4e+03      11      22 ..     104     123 ..      99     157 .. 0.53

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 8.6e-09
                                   ----CHCH.HHHHHHHHHHHHT-S.HHHHHHHHHHHHHCCSHHHHHHHHH CS
                   Ribosomal_S4 34 kklseYgk.qlrekqklkrrYgll.ekqfrryfkearrirGktgenLlql 81
                                       +++k  l e+++l ++Ygl+ +++++ + +++r+ir   +++Ll+l
  gi|119719176|ref|YP_919671.1| 13 GPSHPWRKeTLLEEMQLVGEYGLRnKRELWIAKSLLREIR-AKARKLLAL 61
                                   45579***9*******************************.******984 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.9
                                    CHCTS-STSSS........S CS
                   Ribosomal_S4  11 Rrvgfklflkg........r 22 
                                    Rr+++ ++ kg        r
  gi|119719176|ref|YP_919671.1| 104 RRLQTIVYRKGlattirhaR 123
                                    56666666555555444441 PP

>> DIOX_N  non-haem dioxygenase in morphine synthesis N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   3.8e-05      0.23      39      75 ..      43      79 ..      21     105 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.8e-05
                         DIOX_N 39 vpeelidelfeaareFFalPeeeKeklakspsfrGys 75
                                   + ++l++e+++ ar++ alP ee+ kl+k+   r y+
  gi|119719176|ref|YP_919671.1| 43 IAKSLLREIRAKARKLLALPAEERIKLEKPLVSRLYK 79
                                   7899***********************9986555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1221.58
//
Query:       gi|119719177|ref|YP_919672.1|  [L=157]
Description: 30S ribosomal protein S13P [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-38  131.8   0.0    2.2e-38  131.5   0.0    1.1  1  Ribosomal_S13  Ribosomal protein S13/S18
  ------ inclusion threshold ------
      0.061   13.3   0.0       0.11   12.5   0.0    1.5  1  HHH_4          Helix-hairpin-helix containing domain
      0.066   13.1   0.2       0.17   11.8   0.2    1.7  1  HHH            Helix-hairpin-helix motif
      0.082   11.7   0.0       0.11   11.3   0.0    1.1  1  FbpA           Fibronectin-binding protein A N-terminus (FbpA
       0.17   11.5   0.1       0.52   10.0   0.0    1.8  2  DUF5053        Domain of unknown function (DUF5053)


Domain annotation for each model (and alignments):
>> Ribosomal_S13  Ribosomal protein S13/S18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.5   0.0   6.1e-42   2.2e-38       1     128 []      10     138 ..      10     138 .. 0.98

  Alignments for each domain:
  == domain 1  score: 131.5 bits;  conditional E-value: 6.1e-42
                  Ribosomal_S13   1 RilgtdidgkkkveialtaikGiGrrkakiilkkadvdedkrigelteeeiekieeivenkaqykipnwi.nrqkdikdG 79 
                                    R++g+d++g+k +++al+ ikGiG  +a++++kk+++d    +g l+eee+ek+   + +  +   p w+ nr+kd + G
  gi|119719177|ref|YP_919672.1|  10 RVAGVDLPGDKALVYALADIKGIGVSTAQAVAKKLGLDPYRLLGTLSEEEVEKLSAALREIEKLGLPPWMlNRRKDPFLG 89 
                                    99**********************************************************99999888888********* PP

                  Ribosomal_S13  80 kdshvvendlrrklredieRlkkirsyrGlRHkrGlkvRGQrTkttgRt 128
                                     d h++++dl  ++r+die +kki+sy+G+RH+ GlkvRGQrT+ttgRt
  gi|119719177|ref|YP_919672.1|  90 VDRHLITSDLLITVRNDIEFMKKIKSYKGVRHMLGLKVRGQRTRTTGRT 138
                                    ************************************************8 PP

>> HHH_4  Helix-hairpin-helix containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   3.1e-05      0.11      41      67 ..      23      48 ..      20      69 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.1e-05
                          HHH_4 41 PYrliedvegigFktaDkiakklgiee 67
                                    Y l+ d++gig +ta+++akklg+++
  gi|119719177|ref|YP_919672.1| 23 VYALA-DIKGIGVSTAQAVAKKLGLDP 48
                                   58776.6****************9765 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   4.7e-05      0.17      13      28 ..      26      41 ..      25      43 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.7e-05
                                   HHTSTT-SHHHHHHHH CS
                            HHH 13 LlalPGVGpktAeaIl 28
                                   L++++G+G +tA+a++
  gi|119719177|ref|YP_919672.1| 26 LADIKGIGVSTAQAVA 41
                                   899***********97 PP

>> FbpA  Fibronectin-binding protein A N-terminus (FbpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0     3e-05      0.11     187     238 ..      20      70 ..      10      80 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3e-05
                                    XXXHHHHHHHBTTXXHHHHHHHHTTXSSSH...............HHHHHHH CS
                           FbpA 187 kdlvkaLvkafqGlspllaeelleragldketsakelseedlerlyealqel 238
                                    k lv aL++  +G++  +a+ +++++gld+   + +lsee++e+l +al+e+
  gi|119719177|ref|YP_919672.1|  20 KALVYALADI-KGIGVSTAQAVAKKLGLDPYRLLGTLSEEEVEKLSAALREI 70 
                                    5566666665.7*************************************986 PP

>> DUF5053  Domain of unknown function (DUF5053)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       2.3   8.3e+03      48      56 ..      22      30 ..      20      30 .. 0.77
   2 ?   10.0   0.0   0.00014      0.52      38      57 ..      53      72 ..      48      73 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2.3
                        DUF5053 48 LkeALqdls 56
                                   L  AL d++
  gi|119719177|ref|YP_919672.1| 22 LVYALADIK 30
                                   778999995 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00014
                        DUF5053 38 atFteeeletLkeALqdlsk 57
                                   +t++eee+e+L+ AL+++ k
  gi|119719177|ref|YP_919672.1| 53 GTLSEEEVEKLSAALREIEK 72
                                   589**************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 955.71
//
Query:       gi|119719178|ref|YP_919673.1|  [L=493]
Description: hypothetical protein Tpen_0260 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (493 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 3680.96
//
Query:       gi|119719179|ref|YP_919674.1|  [L=79]
Description: hypothetical protein Tpen_0261 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       177  (0.00987227); expected 358.6 (0.02)
Passed bias filter:                      149  (0.00831056); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.28s 00:00:00.63 Elapsed: 00:00:00.43
# Mc/sec: 552.18
//
Query:       gi|119719180|ref|YP_919675.1|  [L=76]
Description: hypothetical protein Tpen_0262 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.031   14.3   0.4      0.044   13.8   0.4    1.1  1  Mis12     Mis12 protein


Domain annotation for each model (and alignments):
>> Mis12  Mis12 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.4   2.4e-06     0.044      26      67 ..      33      73 ..      28      74 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.4e-06
                                   HHHHHHHHHHH........TTSTHHHH-HHHHHHHHHHHHHH CS
                          Mis12 26 yravdavekvLdkkleedeeeekaaeesteeieeGtakletl 67
                                    +a+da+e++L +  +  +++ +++ee ++e+eeG+++l++l
  gi|119719180|ref|YP_919675.1| 33 VEALDAIEEFL-ASVRGATTQVEEDEELARELEEGIEELREL 73
                                   689********.57777788899999*************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       937  (0.0522617); expected 358.6 (0.02)
Passed bias filter:                      666  (0.0371465); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 576.20
//
Query:       gi|119719181|ref|YP_919676.1|  [L=370]
Description: mandelate racemase/muconate lactonizing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.2e-37  126.7   0.0    1.3e-36  126.2   0.0    1.1  1  MR_MLE_C         Enolase C-terminal domain-like
    2.2e-16   60.1   0.0    4.1e-16   59.3   0.0    1.4  1  MR_MLE_N         Mandelate racemase / muconate lactonizing en
      0.002   18.4   0.7        1.7    9.1   0.2    2.5  2  DinI             DinI-like family
  ------ inclusion threshold ------
      0.054   13.4   0.2       0.23   11.3   0.0    2.1  3  HU-CCDC81_bac_2  CCDC81-like prokaryotic HU domain 2


Domain annotation for each model (and alignments):
>> MR_MLE_C  Enolase C-terminal domain-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.2   0.0   2.9e-40   1.3e-36       2     219 ..     146     356 ..     145     357 .. 0.89

  Alignments for each domain:
  == domain 1  score: 126.2 bits;  conditional E-value: 2.9e-40
                                    HHHHHHHHHHHHT-SEEEEETSSSHHHHHHHHHHHHHHHHTTTSTSEEEEE-TTTSBHHHHHHHHHHHGGGTESEEESSS CS
                       MR_MLE_C   2 laeearelvaeqgfravKlkvggddvaedvervravreavgpgddvdlmvDanqawdlatAirvareleeldllwlEEPv 81 
                                    l +e+r++++e g++++K+k+ +     dve+v+ +re++  gd ++l vDan+a++l+  i v rel+ ++ll+lE+P+
  gi|119719181|ref|YP_919676.1| 146 LLREVRRRLEE-GYQRIKVKIKP---GYDVEVVKRIREEF--GD-IRLQVDANGAYSLR-DIGVFRELDRFNLLMLEQPL 217
                                    67899998887.********655...6*************..64.8***********97.59******88********** PP

                                    STTTHHHHHHHHHHHH.SSEEEESTTSSSHHHHHHHHHHTSESEEEEBHHHHTSHHHHHHHHHHHHHTT-EEEEBSCS.S CS
                       MR_MLE_C  82 ppeddleglaelrara.sipiaagEslysradfrelleagavdivqpdvsrvgGitearkvaalaeafgvpvapHsgs.g 159
                                       ddl ++  l+ r+ s+p++++Es++s++d+  +   g + +v+++++rvgG+ +a+ ++++a++ g+  +++++  +
  gi|119719181|ref|YP_919676.1| 218 AY-DDLYEHSVLS-RKiSTPVCLDESIRSLHDLVVASILGSAEVVNVKPARVGGVLKAKSILEVAAKLGWGAWVGGMLeT 295
                                    *9.67999*****.7779**********************************************************9559 PP

                                    HHHHHHHHHHHHTTTTBEEEEEEGGGGH.TSGCSBSSSSEEE.TTEEECTSSSBTSSEB-HH CS
                       MR_MLE_C 160 glglaaslhlaaaipnllileyfldael.leeelleepleve.dGrvtvpdgpGlGveldee 219
                                    g+g+a  +  +a++p +++  +   +++ ++e+++e+p e+   G+++vp + GlGve+++e
  gi|119719181|ref|YP_919676.1| 296 GIGRAFLVA-LASLPFVNYPNDISASNRyWDEDIVEPPWEITpRGTIAVPRRRGLGVEVKRE 356
                                    ****87555.56777777777777666679999999999886489**************965 PP

>> MR_MLE_N  Mandelate racemase / muconate lactonizing enzyme, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.3   0.0   9.1e-20   4.1e-16      14     117 .]      16     125 ..       5     125 .. 0.91

  Alignments for each domain:
  == domain 1  score: 59.3 bits;  conditional E-value: 9.1e-20
                                    C.EEEETTEEEEEEEEEEEEEEECTTEEEEEEEE-STT......GHHHHHHHHHHHHHHHHTTSBTTHHHHHHHHHHHHC CS
                       MR_MLE_N  14 r.PvqlavttvqkqslvlvkietseGvvGigeatsvgg......raetikaelddhlapllvgkdaanisdlaqllkrav 86 
                                    +  +++++++v++ ++vlv++e ++G +G+ge+++  g      + et+   +++ +ap lvg+d ++++d  +l++  +
  gi|119719181|ref|YP_919676.1|  16 KeEFRTSFGSVSTRPVVLVRVEEKGGEEGWGELVADRGpwysyeTYETSSLVIRKFIAPSLVGRDIEEVEDFHRLVA-SI 94 
                                    44789*****************************99888**999999999*********************998886.67 PP

                                    SSCHHHHHHHHHHHHHHHHHHTTSBHHHHTT CS
                       MR_MLE_N  87 lgnmsAkaaidmAlwDlkakalnlpladLlG 117
                                     g  +Ak a++ Al+Dl+a+  + ++++ lG
  gi|119719181|ref|YP_919676.1|  95 RGYPMAKTAVEEALLDLEARMEGRSVSEVLG 125
                                    8899*************************99 PP

>> DinI  DinI-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.2   0.00037       1.7       5      30 ..     143     168 ..     140     171 .. 0.91
   2 !    7.7   0.0     0.001       4.5       9      36 ..     170     197 ..     168     210 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00037
                                    HHHHHHHHHHHHHHH-SS-EEEEEEE CS
                           DinI   5 iealeaELskRiqevfPdaevrvrka 30 
                                    +e l  E+ +R++e +  ++v+++++
  gi|119719181|ref|YP_919676.1| 143 VEELLREVRRRLEEGYQRIKVKIKPG 168
                                    7999********************97 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.001
                                    HHHHHHHHHHH-SS-EEEEEEESS-EEE CS
                           DinI   9 eaELskRiqevfPdaevrvrkasangls 36 
                                      E+ kRi+e f d++++v   +a +l+
  gi|119719181|ref|YP_919676.1| 170 DVEVVKRIREEFGDIRLQVDANGAYSLR 197
                                    6799***************999887776 PP

>> HU-CCDC81_bac_2  CCDC81-like prokaryotic HU domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.1     5e+03      15      33 ..      97     115 ..      96     119 .. 0.79
   2 ?   -3.3   0.0         2   8.9e+03      22      35 ..     143     156 ..     140     162 .. 0.54
   3 ?   11.3   0.0   5.2e-05      0.23      17      48 ..     172     203 ..     170     210 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.1
                HU-CCDC81_bac_2  15 yeeAlqkiekeveelkqeL 33 
                                    y+ A +++e++  +l+ ++
  gi|119719181|ref|YP_919676.1|  97 YPMAKTAVEEALLDLEARM 115
                                    8889999999988887665 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2
                HU-CCDC81_bac_2  22 iekeveelkqeLee 35 
                                    +e+  +e++++Lee
  gi|119719181|ref|YP_919676.1| 143 VEELLREVRRRLEE 156
                                    44445555555554 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 5.2e-05
                HU-CCDC81_bac_2  17 eAlqkiekeveelkqeLeeegrveleniGeLs 48 
                                    e++++i++e  +++ + + +g ++l +iG+++
  gi|119719181|ref|YP_919676.1| 172 EVVKRIREEFGDIRLQVDANGAYSLRDIGVFR 203
                                    6789**************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2649.65
//
Query:       gi|119719182|ref|YP_919677.1|  [L=169]
Description: hypothetical protein Tpen_0264 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1224.15
//
Query:       gi|119719183|ref|YP_919678.1|  [L=437]
Description: cell division control protein 6 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-12   47.5   0.0    2.5e-12   46.6   0.0    1.5  1  Cdc6_C           CDC6, C terminal winged helix domain
    4.5e-08   33.5   0.0      1e-07   32.3   0.0    1.6  1  AAA_22           AAA domain
    5.1e-06   27.0   0.9      3e-05   24.5   0.1    2.5  3  AAA_16           AAA ATPase domain
    6.5e-05   22.9   0.0    0.00016   21.7   0.0    1.6  1  NACHT            NACHT domain
    0.00012   22.5   0.1    0.00034   21.1   0.1    1.8  1  AAA              ATPase family associated with various cellul
    0.00092   18.5   0.1      0.002   17.4   0.1    1.5  1  TIP49            TIP49 P-loop domain
     0.0044   16.9   0.1        1.9    8.2   0.0    2.2  2  Bac_DnaA         Bacterial dnaA  protein
  ------ inclusion threshold ------
      0.022   14.5   0.0       0.04   13.6   0.0    1.4  1  AAA_30           AAA domain
      0.025   14.3   0.1      0.049   13.4   0.1    1.4  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      0.031   13.7   0.3       0.39   10.2   0.1    2.3  2  PhoH             PhoH-like protein
      0.082   12.6   0.0       0.17   11.6   0.0    1.5  1  Sigma54_activat  Sigma-54 interaction domain
      0.089   12.6   0.1        6.6    6.5   0.0    2.3  2  DEAD             DEAD/DEAH box helicase
       0.11   11.7   0.1       0.22   10.7   0.1    1.4  1  DUF2075          Uncharacterized conserved protein (DUF2075)
       0.17   11.9   0.0       0.31   11.0   0.0    1.4  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro


Domain annotation for each model (and alignments):
>> Cdc6_C  CDC6, C terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.6   0.0     2e-15   2.5e-12       1      74 [.     320     393 ..     320     400 .. 0.90

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 2e-15
                                    HHHHHHHHC.HCSSS-EEHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEE CS
                         Cdc6_C   1 Lcalvlllr.ksgkeevttgevyevYkslCesegvdpltqrevsdllseLemlgileleksskGrregrtrkisL 74 
                                    L+a+++ll  +++k +v +gev  +Y+++C++ g +pl  +++++ ++ L+++g+++++++ +G+ +grt+ i++
  gi|119719183|ref|YP_919678.1| 320 LLAITELLLlEREKAYVNMGEVVIQYEDVCNKFGEKPLRYTRIWEKVQFLKKMGLVDTRTG-RGETRGRTTMITF 393
                                    566666655559**********************************************987.99999****9987 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.0   8.1e-11     1e-07      11     107 ..      61     158 ..      55     191 .. 0.80

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 8.1e-11
                         AAA_22  11 tGesGtGKTtllrrlleqldeeakaee..erpevvfvtlpsstsskdllrellralglelkaerlsseellealeqalra 88 
                                     G++GtGKT ++r++ ++ + +++a+   ++  v +v++++  +  +++r++ ++ gl+  +++ ss+el e++   +++
  gi|119719183|ref|YP_919678.1|  61 AGQAGTGKTAVARTIGREVK-DKAAKGkiPPILVSYVNAQEYRTKFQVFRKIGSDCGLDIPRRGFSSQELAEYVFGFISR 139
                                    69***************985.44444454555555****************************************99999 PP

                         AAA_22  89 ravielliiDEaqhlr.see 107
                                    r   +l+i+DEa+ l  + +
  gi|119719183|ref|YP_919678.1| 140 RENNALIILDEADILAkQ-K 158
                                    9999*********99742.2 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.1   2.3e-08     3e-05       1      88 [.      29     114 ..      29     186 .. 0.62
   2 ?   -1.9   0.0       2.9   3.7e+03      53      88 ..     200     234 ..     185     287 .. 0.56
   3 ?   -3.5   0.0       8.9   1.1e+04      80     103 ..     410     433 ..     402     436 .. 0.65

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 2.3e-08
                         AAA_16   1 rlvGReeeleqLlsalervrsgrp...elvllsGesGvGKsslvrellralekd..............ggiflrgkcdql 63 
                                    +l+ R e++++ l+++++v +g+    + ++  G++G+GK++++r++ r+++++              +           
  gi|119719183|ref|YP_919678.1|  29 KLPHRAEQIAETLRVMQDVIRGQKdvlRTIIYAGQAGTGKTAVARTIGREVKDKaakgkippilvsyvN----------- 97 
                                    5889*********************************************99999666666544433331........... PP

                         AAA_16  64 esaipysalaqalareellrqllde 88 
                                              ++ ++ +++r+++++
  gi|119719183|ref|YP_919678.1|  98 --------AQEYRTKFQVFRKIGSD 114
                                    ........22223333444444444 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.9
                         AAA_16  53 gif..lrgkcdqlesaipy.salaqalareellrqllde 88 
                                    +++  l+g+ +++    py s+ +q + +   +r++++ 
  gi|119719183|ref|YP_919678.1| 200 AVVssLSGRVVRF---NPYtSQQLQDILW-ARIRDEGAI 234
                                    3444577777777...6774223333323.333333332 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 8.9
                         AAA_16  80 ellrqlldeaesaeleawreklee 103
                                    +ll+++l+++ ++el+   e+  e
  gi|119719183|ref|YP_919678.1| 410 DLLEKILRDSIEKELSSRGEERGE 433
                                    677777777777777666665555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   1.2e-07   0.00016       1      98 [.      56     159 ..      56     179 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.2e-07
                                    SCEEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-...-HCHHHCCCC.TS--SSS-C.......C CS
                          NACHT   1 rlvilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgnarsladllfsql.pepaapvse.......v 72 
                                    r++i  G+aG GKT+ ++ + ++ +++  +++  + +++  + + + ++++  + + + s++ +++ ++          v
  gi|119719183|ref|YP_919678.1|  56 RTIIYAGQAGTGKTAVARTIGREVKDKAAKGKI-PPILVSYVNAQEYRTKF-QVFRKIGSDCgLDIPRRGFSsqelaeyV 133
                                    78999***************9999999988864.44444444444444444.333333333213322221113347777* PP

                                    HHHHCCSCCCEEEEEE-STT-SS-TC CS
                          NACHT  73 wavllelperlLlilDglDelvtdlg 98 
                                    + ++ ++++ +L+ilD +D l+++ +
  gi|119719183|ref|YP_919678.1| 134 FGFISRRENNALIILDEADILAKQKD 159
                                    *******************9998765 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.1   2.6e-07   0.00034       3      77 ..      60     161 ..      58     178 .. 0.70

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2.6e-07
                                    EESSTTSSHHHHHHHHHHHHTHE..........EEEEETTTCSSS....................STTHHHHHHHHHHHH CS
                            AAA   3 lyGppGtGKTllakavakelgve..........fleisgsellsk....................yvgesekkirelfke 52 
                                      G  GtGKT++a+ + +e++ +          +  +++ e + k                      +e ++ + +++++
  gi|119719183|ref|YP_919678.1|  60 YAGQAGTGKTAVARTIGREVKDKaakgkippilVSYVNAQEYRTKfqvfrkigsdcgldiprrgfSSQELAEYVFGFISR 139
                                    6799***************9744233444444456666666666688999999999999996554444444444444444 PP

                                    HHHTSTSEEEEEETGGGHHHHHTTC CS
                            AAA  53 akekakpsilfiDEidalaksrsgs 77 
                                     +e+     +++DE+d lak+++g+
  gi|119719183|ref|YP_919678.1| 140 -REN--NALIILDEADILAKQKDGN 161
                                    .444..38**********9999444 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   1.5e-06     0.002      34      77 ..      39      82 ..      34     110 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.5e-06
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49 34 eaagvivelikekklaGravLlaGpsgtGktalaiaiskelged 77
                                   e   v+ ++i+ +k   r+++ aG++gtGkta+a +i +e+ ++
  gi|119719183|ref|YP_919678.1| 39 ETLRVMQDVIRGQKDVLRTIIYAGQAGTGKTAVARTIGREVKDK 82
                                   566789999**999999***********************9865 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.0    0.0058       7.4      39      79 ..      59     105 ..      40     111 .. 0.80
   2 !    8.2   0.0    0.0015       1.9      96     199 ..     140     252 ..     134     259 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0058
                                    EE.-SSSSSHHHHHHHHHHHHHHHSSSS-.....EEEEEHHHHHHHH CS
                       Bac_DnaA  39 iy.gevGlGktHLlkaignevlenapelr.....vvYltaeeFlnel 79 
                                    iy g+ G Gkt + ++ig ev+++a + +     v+Y++a+e+ +++
  gi|119719183|ref|YP_919678.1|  59 IYaGQAGTGKTAVARTIGREVKDKAAKGKippilVSYVNAQEYRTKF 105
                                    553789***************99988777334336899999887766 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0015
                                    TT-SEEEEE-GGGGTT-HHHHHHHHHHHHHHHTT......T-EEEEEESS-TTT-SS--HHHHHHHHSSEEEE-----HH CS
                       Bac_DnaA  96 rkvDvLliDDiqflagkektqeelfhtfnallee......gkqvvlssDrsPkeleeledrlrsrfeaGlvvdieppdle 169
                                    r++++L+i D  ++  k+k  +elf +f  + e       g  +++   +  ++l+ l++ + s ++ G vv  +p   +
  gi|119719183|ref|YP_919678.1| 140 RENNALIILDEADILAKQKDGNELFYVFSRVREVlpevqlGLGLIVIFRQLDESLAYLDKAVVSSLS-GRVVRFNPYTSQ 218
                                    78899999999999999***********99877522111133457777888999**********996.88999***9999 PP

                                    HHHHHHHHHHHHTT--....--TTHHHHHHHH-- CS
                       Bac_DnaA 170 trlailkkkieaekle....vpeevlefiaervt 199
                                       +il  +i+ e+      v ee++e+ia++v 
  gi|119719183|ref|YP_919678.1| 219 QLQDILWARIRDEGAIreeaVSEEIIEMIADTVG 252
                                    9999*99999976553456799*******99875 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   3.1e-05      0.04      20     101 ..      57     155 ..      42     172 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.1e-05
                         AAA_30  20 vavltGpAGtGKttalkal.reaweaa.ggrviglAptgkaAkvLae.................elgieastiakllkrl 80 
                                    + +  G AGtGKt + +++ re+ ++a +g++  +  +   A++ ++                   g+ ++ +a+++   
  gi|119719183|ref|YP_919678.1|  57 TIIYAGQAGTGKTAVARTIgREVKDKAaKGKIPPILVSYVNAQEYRTkfqvfrkigsdcgldipRRGFSSQELAEYVFGF 136
                                    45778**************9999988878888888888888888774333333344433333334455777777777444 PP

                         AAA_30  81 kgrarlepgtllivDEagmvd 101
                                     +  r e++ l+i DEa  ++
  gi|119719183|ref|YP_919678.1| 137 IS--RRENNALIILDEADILA 155
                                    33..45666999999987763 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   3.8e-05     0.049      13      63 ..      35      85 ..      29      97 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.8e-05
                         RuvB_N 13 ekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakelgvklki 63
                                   e++ e+l+++ +  + +++ l  ++ +G  G Gkt++a+ i +e++ k   
  gi|119719183|ref|YP_919678.1| 35 EQIAETLRVMQDVIRGQKDVLRTIIYAGQAGTGKTAVARTIGREVKDKAAK 85
                                   68999***************************************9876654 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1    0.0003      0.39      21      43 ..      57      79 ..      35      93 .. 0.75
   2 ?    0.8   0.0      0.22   2.8e+02     119     130 ..     142     153 ..     138     160 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0003
                                   EEEEE--TTSSTTHHHHHHHHHH CS
                           PhoH 21 ivfaiGpaGtGKtylavalavea 43
                                    ++ +G+aGtGKt +a +++ e+
  gi|119719183|ref|YP_919678.1| 57 TIIYAGQAGTGKTAVARTIGREV 79
                                   56789***********9988654 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.22
                                    -SEEEEE-SGGG CS
                           PhoH 119 ndafvilDEAQn 130
                                    n+a++ilDEA  
  gi|119719183|ref|YP_919678.1| 142 NNALIILDEADI 153
                                    79*******965 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00013      0.17       6      49 ..      35      82 ..      30      98 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00013
                                   HHHHHHHHHHHHHCTSS....S-EEEECSTTSSHHHHHHHHHHHSTTT CS
                Sigma54_activat  6 ealkelleqikkvaktd....lsvlitGesGtGKellaraiheaskrk 49
                                   e+++e+l+ ++ v++ +     +++  G+ GtGK+ +ar+i ++ k k
  gi|119719183|ref|YP_919678.1| 35 EQIAETLRVMQDVIRGQkdvlRTIIYAGQAGTGKTAVARTIGREVKDK 82
                                   566667777777776663443566678*************98866654 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.034        44      13      31 ..      50      72 ..      35      93 .. 0.78
   2 ?    6.5   0.0    0.0052       6.6     122     153 ..     143     174 ..     127     186 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.034
                                   TTCEEE....EEESTTSSHHHHH CS
                                   xxxxxx....xxxxxxxxxxxxx RF
                           DEAD 13 gggdvl....vaaeTGsGKTlaf 31
                                   g++dvl     a++ G+GKT+++
  gi|119719183|ref|YP_919678.1| 50 GQKDVLrtiiYAGQAGTGKTAVA 72
                                   444555555599********996 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0052
                                    EEEEEEETHHHHHHTTTHHHHHHHHHHSHHHC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD 122 vrflVlDEadrlldqgfsdfinrilnqlpqit 153
                                      +++lDEad l +q+ ++++  +++++++  
  gi|119719183|ref|YP_919678.1| 143 NALIILDEADILAKQKDGNELFYVFSRVREVL 174
                                    5689***********99999999999887665 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00017      0.22       5     106 ..      59     160 ..      56     184 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00017
                        DUF2075   5 lVtGvaGtGKtvvllnllaeleddeeertav...ylsvNhplvl...vlrealakke..ekkkkkeafeklssfinnlse 76 
                                    +  G+aGtGKt v+ ++  e++d++ + +     + +vN ++ +    + +++ ++      +++ + ++l++++  +  
  gi|119719183|ref|YP_919678.1|  59 IYAGQAGTGKTAVARTIGREVKDKAAKGKIPpilVSYVNAQEYRtkfQVFRKIGSDCglDIPRRGFSSQELAEYVFGFI- 137
                                    557*****************95555444433111233444444321111122222223322222222222222222222. PP

                        DUF2075  77 fkkaeekkeepkedvvivDEAhrlltksdq 106
                                            ++++  ++i DEA  l +++d 
  gi|119719183|ref|YP_919678.1| 138 -------SRRENNALIILDEADILAKQKDG 160
                                    .......44556667777888777776665 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00024      0.31       6      45 ..      39      81 ..      30     108 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00024
                                   HHHHHHHHHHHCHTEE...EEEEESTTSSHHHHHHHHHHHTT- CS
                           TsaE  6 etealgkklakalgdv...ilLeGdLGaGKTtlvrglakalgv 45
                                   et ++ +++ +  +dv   i+  G+ G+GKT+ +r + ++++ 
  gi|119719183|ref|YP_919678.1| 39 ETLRVMQDVIRGQKDVlrtIIYAGQAGTGKTAVARTIGREVKD 81
                                   2333333333322332666******************999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (437 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2815.97
//
Query:       gi|119719184|ref|YP_919679.1|  [L=413]
Description: replication factor C large subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.7e-14   53.0   0.0    1.2e-13   51.7   0.0    1.7  1  AAA             ATPase family associated with various cellula
    1.1e-07   31.3   0.0    5.5e-07   29.0   0.0    2.1  3  DUF815          Protein of unknown function (DUF815)
    9.3e-07   28.9   0.0    2.2e-06   27.7   0.0    1.6  1  Rad17           Rad17 P-loop domain
    1.6e-06   28.0   0.0    3.1e-06   27.0   0.0    1.5  1  RuvB_N          Holliday junction DNA helicase RuvB P-loop do
    1.1e-05   25.4   0.1      3e-05   24.1   0.0    1.7  1  AAA_5           AAA domain (dynein-related subfamily)
    5.2e-05   23.5   0.0    0.00011   22.4   0.0    1.5  1  RFC1            Replication factor RFC1 C terminal domain
    5.2e-05   23.1   0.0    8.4e-05   22.4   0.0    1.3  1  DNA_pol3_delta  DNA polymerase III, delta subunit
    5.7e-05   23.6   0.1     0.0002   21.8   0.1    1.9  1  AAA_16          AAA ATPase domain
    0.00017   20.9   0.0    0.00029   20.2   0.0    1.3  1  TIP49           TIP49 P-loop domain
    0.00037   20.1   0.0     0.0014   18.2   0.0    1.8  2  AAA_7           P-loop containing dynein motor region
    0.00051   20.3   0.3      0.079   13.2   0.1    2.9  3  AAA_22          AAA domain
    0.00067   19.7   0.0     0.0013   18.8   0.0    1.5  1  AAA_14          AAA domain
     0.0011   19.3   0.1     0.0036   17.6   0.1    1.9  1  AAA_assoc_2     AAA C-terminal domain
     0.0014   18.8   0.0     0.0025   18.0   0.0    1.3  1  AAA_2           AAA domain (Cdc48 subfamily)
     0.0024   17.2   0.0     0.0048   16.2   0.0    1.4  1  Zeta_toxin      Zeta toxin
  ------ inclusion threshold ------
      0.021   15.0   0.0       0.14   12.3   0.0    2.4  2  AAA_33          AAA domain
      0.033   14.5   0.1       0.13   12.6   0.0    1.9  2  AAA_19          AAA domain
      0.037   13.9   0.0       0.14   12.0   0.0    2.0  1  Bac_DnaA        Bacterial dnaA  protein
      0.048   13.2   0.0       0.12   11.9   0.0    1.6  1  AAA_25          AAA domain
      0.054   12.3   0.0      0.091   11.6   0.0    1.3  1  PPV_E1_C        Papillomavirus helicase
      0.061   13.1   0.0       0.18   11.6   0.0    1.7  1  AAA_29          P-loop containing region of AAA domain
      0.082   12.8   0.1         12    5.8   0.0    2.7  3  NACHT           NACHT domain
       0.11   12.3   0.0       0.22   11.3   0.0    1.4  1  AAA_11          AAA domain
       0.14   12.7   0.0       0.39   11.2   0.0    1.8  1  ABC_tran        ABC transporter
       0.17   12.3   0.0       0.42   11.0   0.0    1.8  1  RNA_helicase    RNA helicase
       0.18   10.8   0.0        1.2    8.1   0.0    2.1  2  AAA_6           Hydrolytic ATP binding site of dynein motor r


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.7   0.0   1.7e-16   1.2e-13       2     114 ..      51     150 ..      50     166 .. 0.73

  Alignments for each domain:
  == domain 1  score: 51.7 bits;  conditional E-value: 1.7e-16
                                    EEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS....TSEEEEEETGGGHHHHHTTC CS
                            AAA   2 llyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakeka....kpsilfiDEidalaksrsgs 77 
                                    llyGppG GKT++++a ake++ e++e+++s+++  + ++ ++++ + +++    +    + +i+++DE+d + +++   
  gi|119719184|ref|YP_919679.1|  51 LLYGPPGSGKTSIVHATAKEFSWELIELNASDVR--TREALQQRLLGALNTR---SvlgySGKIILLDEVDGISTKE--- 122
                                    9*********************************..5555566666666554...3446767***********9998... PP

                                    CCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGG CS
                            AAA  78 eseeeervvnqLlteldgvkkkeskvivigatnrpdk 114
                                        +   ++++++ +++      +  +++++n+p++
  gi|119719184|ref|YP_919679.1| 123 ----DAGGLQAIVELIEKS-----NWPIVLTANDPWD 150
                                    ....333344444444332.....3566777776655 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.0     8e-10   5.5e-07      20     102 ..      13      93 ..       3     105 .. 0.85
   2 ?   -2.3   0.0       2.8   1.9e+03     190     222 ..     163     195 ..     162     201 .. 0.84
   3 ?   -2.4   0.0       3.2   2.2e+03     178     215 ..     219     253 ..     189     284 .. 0.64

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 8e-10
                         DUF815  20 eevdevklddLvgidkqkealventeqfleglpann.vLLwGarGtGKSslvkallneyaeegLrlievekedlkelpkl 98 
                                    e++++ +++d+vg ++ k++ v+ ++ +++g+p+++ +LL+G  G+GK s+v+a+ +e++     lie++ +d+++ ++l
  gi|119719184|ref|YP_919679.1|  13 EKYRPARIADVVGNEEAKKKYVAWINSWVKGKPSKKaALLYGPPGSGKTSIVHATAKEFSW---ELIELNASDVRTREAL 89 
                                    56778899*************************98637******************99986...5889999988888877 PP

                         DUF815  99 vell 102
                                    ++ l
  gi|119719184|ref|YP_919679.1|  90 QQRL 93 
                                    7655 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.8
                         DUF815 190 lgFykldqeeYleiveklakklglelekeelee 222
                                    + F+k+ +++ ++++e++++k+g+e+++e l++
  gi|119719184|ref|YP_919679.1| 163 IEFKKIGKRDIMKVLENICSKEGVECSREVLSA 195
                                    679999999999999999999999999877665 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 3.2
                         DUF815 178 eklsLsdRFGlwlgFykldqeeYleiveklakklglel 215
                                     ++sL+d   l++   +++qe+ ++iv+++++    e 
  gi|119719184|ref|YP_919679.1| 219 KTISLAD---LQILGDRAEQETIFDIVRSVLTAKYPEQ 253
                                    5566666...6666677888888888888876554443 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.0   3.2e-09   2.2e-06       8     100 ..      10     101 ..       5     122 .. 0.83

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 3.2e-09
                          Rad17   8 lWfekykPekaeelavhkkkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskelgiklrewlnpvslkepdn 87 
                                    +W eky+P   +++    +  ++   w+++ v  +  k+  L+ GP+G gk+ +v+  +ke++ +l+e ln+  ++  + 
  gi|119719184|ref|YP_919679.1|  10 PWTEKYRPARIADVVGNEEAKKKYVAWINSWVKGKPSKKAALLYGPPGSGKTSIVHATAKEFSWELIE-LNASDVRTREA 88 
                                    7*************987776677777888888888888889*************************98.57777777777 PP

                          Rad17  88 qksdfkgltekes 100
                                     ++ ++g +++ s
  gi|119719184|ref|YP_919679.1|  89 LQQRLLGALNTRS 101
                                    6666666666665 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0   4.4e-09   3.1e-06       2      88 ..      16     103 ..      15     123 .. 0.81

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 4.4e-09
                         RuvB_N   2 rPksleeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakelgvklkitsgPvlekagdl.aallt 80 
                                    rP ++++ +g e+ k+k    i++  k + +    llyGpPG Gkt++ +  ake+  +l    +  +     l   ll 
  gi|119719184|ref|YP_919679.1|  16 RPARIADVVGNEEAKKKYVAWINSWVKGKPSKKAALLYGPPGSGKTSIVHATAKEFSWELIELNASDVRTREALqQRLLG 95 
                                    9*******************************************************998765555555444444145666 PP

                         RuvB_N  81 nleekdvl 88 
                                     l+++ vl
  gi|119719184|ref|YP_919679.1|  96 ALNTRSVL 103
                                    77766655 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   4.3e-08     3e-05       3      79 ..      51     121 ..      49     139 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 4.3e-08
                                    EEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------...G-SEEEEESGGG--. CS
                          AAA_5   3 lLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar...egeilvlDEverae. 78 
                                    lL GppG+gK++++   a+ + +e+ + + ++  t+e l++r+           ++l +      +g+i++lDEv+ ++ 
  gi|119719184|ref|YP_919679.1|  51 LLYGPPGSGKTSIVHATAKEFSWELIELNASDVRTREALQQRLL----------GALNTRSVlgySGKIILLDEVDGISt 120
                                    8*****************************99999999999999..........33332222344**********98874 PP

                                    H CS
                          AAA_5  79 s 79 
                                    +
  gi|119719184|ref|YP_919679.1| 121 K 121
                                    4 PP

>> RFC1  Replication factor RFC1 C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   1.6e-07   0.00011       2      89 ..     295     384 ..     294     392 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.6e-07
                                    HHHHHHHHHHTTSS-GGGHHHHHHHHTHHHHHTT-EE-SS......-----...SHHHHHHHHHHHHHHHHHHHTTTTT- CS
                           RFC1   2 sdgDlvdkkirseqnWsLlpthavlssvlPaslvrgsleg......risFp...swLGknSktnKnkRllqelqshlrlk 72 
                                    s +D++ +++++eq+W Ll +   l +   as+ +    +      ++sFp   ++L++  +++K++++++ ++  +++k
  gi|119719184|ref|YP_919679.1| 295 SWADIMLTRMKREQQWALLSYALELMTAGVASARE----RppfkfvKYSFPeklRILAR--SKEKREKFVRAVR-GAAAK 367
                                    889*****************965555444333333....123457899***77777777..7788889999998.5567* PP

                                    -----HHHHHTTTHHHH CS
                           RFC1  73 tsaskselrldylpllk 89 
                                    ++ s+s++r+d+lp+l+
  gi|119719184|ref|YP_919679.1| 368 IHVSTSKFRTDVLPYLR 384
                                    ***************97 PP

>> DNA_pol3_delta  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   1.2e-07   8.4e-05      29     173 ..      77     215 ..      60     216 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.2e-07
                                    EEEEEE-STTS-HHH.HTTTSTTTT.SSSSEEEEEEE--.....TT-S-TTHHHHHHHHTTT--SSEEEEEEES.S--HH CS
                 DNA_pol3_delta  29 dlnyikfdlnedwiddvleecetlp.ffsdkrivvlknpklltkesklnekllkeLeeylsnlpedtlLiliapkklder 107
                                    +ln +++ + e+  + +l ++ t + ++ + +i++l+    +  ++k+++  l+++ e++++   +  ++l+a++  d +
  gi|119719184|ref|YP_919679.1|  77 ELNASDVRTREALQQRLLGALNTRSvLGYSGKIILLDEVDGI--STKEDAGGLQAIVELIEK--SNWPIVLTANDPWDPK 152
                                    5666666666655666777777765367799********888..888889999999999998..7888999999999999 PP

                                    HHHHHHHTTTEEEEEE----TTTHHHHHHHHHHHTT-EE-HHHHHHHHHHHTT-HHHHHHHHHHHH CS
                 DNA_pol3_delta 108 kklvklLkkkatvveaktlkeeelkkwiqkraqelglkiekealelLlelvennlsaikqelekLa 173
                                     + +  L +   ++e+k+  + ++ k ++++++++g++ ++e+l+ ++++  ++l+a+ + l+ La
  gi|119719184|ref|YP_919679.1| 153 LRPLRDLCE---LIEFKKIGKRDIMKVLENICSKEGVECSREVLSAIADNAKGDLRAAINDLQSLA 215
                                    997777775...9**************************************************997 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.1   2.9e-07    0.0002      19      88 ..      40     100 ..      24     147 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 2.9e-07
                         AAA_16  19 vrsgrp..elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqllde 88 
                                    + +g p   + ll+G++G+GK+s+v + +++++ +   +++ ++ +           +al + +ll +l+++
  gi|119719184|ref|YP_919679.1|  40 WVKGKPskKAALLYGPPGSGKTSIVHATAKEFSWE---LIELNASDV-------RTREAL-QQRLLGALNTR 100
                                    5667777799*****************99988855...566666666.......345666.33777777666 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   4.2e-07   0.00029      25      93 ..      22      88 ..      12     109 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 4.2e-07
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49 25 glvGqkkareaagvivelikekklaGravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslev 93
                                    +vG ++a++     ++   ++k + +a Ll Gp+g+Gkt++  a +ke++     + l++s+v + e 
  gi|119719184|ref|YP_919679.1| 22 DVVGNEEAKKKYVAWINSWVKGKPSKKAALLYGPPGSGKTSIVHATAKEFS--WELIELNASDVRTREA 88
                                   589*****998777666666677799************************9..5678899998877665 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0     2e-06    0.0014      32      90 ..      46     101 ..      31     136 .. 0.85
   2 ?   -1.3   0.1         2   1.4e+03     124     148 ..     266     289 ..     263     293 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2e-06
                          AAA_7  32 nkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdiiesklekrr 90 
                                    +kk  ll+Gp G+GKt+i++ + k+++   +  + +n s   + + lq+ +   l+ r+
  gi|119719184|ref|YP_919679.1|  46 SKKAALLYGPPGSGKTSIVHATAKEFS---WELIELNASDVRTREALQQRLLGALNTRS 101
                                    57999*******************999...*********************99999887 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2
                          AAA_7 124 ellRqlldyggwYdrkklefkeikd 148
                                    e+l q+l+++ +Y+ +  +++ i d
  gi|119719184|ref|YP_919679.1| 266 EMLMQWLSENIVYQYEP-SLQAIAD 289
                                    8999*********9875.6666665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.1   0.00011     0.079       5      64 ..      47      97 ..      44      99 .. 0.81
   2 ?    5.9   0.0     0.021        15      74     127 ..      85     143 ..      73     149 .. 0.66
   3 ?   -2.0   0.0       5.7     4e+03      57      88 ..     177     202 ..     161     238 .. 0.53

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00011
                         AAA_22  5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellral 64
                                   ++  +++G++G+GKT  +   ++++         + e+++ +++   +++ l ++ll al
  gi|119719184|ref|YP_919679.1| 47 KKAALLYGPPGSGKTSIVHATAKEF---------SWELIELNASDVRTREALQQRLLGAL 97
                                   67899***************99999.........77777777777777777777777766 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.021
                         AAA_22  74 sseellealeqalrarav....ielliiDEaqhlrs....eealeeLrsllnlsrkgvqliL 127
                                    ++e+l ++l  al++r+v     +++++DE++ + s    +  l+ +++l +  +++ +++L
  gi|119719184|ref|YP_919679.1|  85 TREALQQRLLGALNTRSVlgysGKIILLDEVDGI-StkedAGGLQAIVELIE--KSNWPIVL 143
                                    44555566666666666666666***********.44345666666666666..77777777 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 5.7
                         AAA_22  57 lrellralglelkaerlsseellealeqalra 88 
                                    l++++++ g+e+++      e+l+a++++++ 
  gi|119719184|ref|YP_919679.1| 177 LENICSKEGVECSR------EVLSAIADNAKG 202
                                    44444444444444......333333332222 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.9e-06    0.0013       2      81 ..      47     123 ..      46     146 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.9e-06
                         AAA_14   2 rkilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelilek.lkeekktylflDEiqevpewe 80 
                                    +k+ ++ G+  +GKT +++  +ke      + +++n  d r++++ ++ +ll ++  + + +   ++++lDE+  +++ e
  gi|119719184|ref|YP_919679.1|  47 KKAALLYGPPGSGKTSIVHATAKEFS---WELIELNASDVRTREALQQ-RLLGALNTRsVLGYSGKIILLDEVDGISTKE 122
                                    68899*****************9988...99***********987765.577777776654557899******9886555 PP

                         AAA_14  81 k 81 
                                    +
  gi|119719184|ref|YP_919679.1| 123 D 123
                                    4 PP

>> AAA_assoc_2  AAA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   5.2e-06    0.0036       3      39 ..     184     220 ..     182     252 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 5.2e-06
                                    X.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                    AAA_assoc_2   3 kklkleddalealaeladGDaRkaLnlLElaaeaaea 39 
                                    + +++++++l+a+a+ a+GD R+a+n L+ +a  +++
  gi|119719184|ref|YP_919679.1| 184 EGVECSREVLSAIADNAKGDLRAAINDLQSLAMGKKT 220
                                    56899************************77665543 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   3.6e-06    0.0025       6      84 ..      50     122 ..      46     138 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3.6e-06
                                    EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS.EEEEETGGG----- CS
                          AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG.ivllDEidKihpke 84 
                                     ll gp g+Gkt +  a+a+  +     +li ++as++ +    e l +rl+ga +       +G i+llDE+d i+ ke
  gi|119719184|ref|YP_919679.1|  50 ALLYGPPGSGKTSIVHATAKEFSW----ELIELNASDVRT---REALQQRLLGALNTRSVLGYSGkIILLDEVDGISTKE 122
                                    6789******************97....************...56666789999999999999999**********9952 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0     7e-06    0.0048      14      56 ..      45      85 ..      35      88 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7e-06
                     Zeta_toxin 14 erPklillgGqpGAGKselaellkdelerqgnvvrldpDdlRe 56
                                    ++k+ ll G pG+GK+++ +++++e+    + ++l++ d+R+
  gi|119719184|ref|YP_919679.1| 45 PSKKAALLYGPPGSGKTSIVHATAKEF--SWELIELNASDVRT 85
                                   67899*********************9..8999***9999997 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00021      0.14       3      32 ..      51      80 ..      50     145 .. 0.81
   2 ?   -0.5   0.0       1.8   1.3e+03     107     107 ..     376     376 ..     342     412 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00021
                         AAA_33  3 llvGlpGsGKstlaerllkklgavllssdt 32
                                   ll G+pGsGK+  ++  +k+  ++l++ ++
  gi|119719184|ref|YP_919679.1| 51 LLYGPPGSGKTSIVHATAKEFSWELIELNA 80
                                   578****************99999987766 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.8
                         AAA_33 107 d 107
                                     
  gi|119719184|ref|YP_919679.1| 376 R 376
                                    0 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00019      0.13       9      37 ..      46      74 ..      39     101 .. 0.84
   2 ?   -1.8   0.0       5.3   3.6e+03      38      70 ..     184     216 ..     168     309 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00019
                         AAA_19  9 kekvllvtaGpGtGKTrvlkhivallvel 37
                                   ++k  l+ ++pG+GKT ++++  +++ ++
  gi|119719184|ref|YP_919679.1| 46 SKKAALLYGPPGSGKTSIVHATAKEFSWE 74
                                   578899*************9999887765 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 5.3
                         AAA_19  38 ggvkpeeillvaftgrAakelrerlaalgaeat 70 
                                    +gv+  + +l a +  A   lr +++ l+  a+
  gi|119719184|ref|YP_919679.1| 184 EGVECSREVLSAIADNAKGDLRAAINDLQSLAM 216
                                    445556666666666666666666655444433 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0    0.0002      0.14      35     207 ..      48     209 ..      23     220 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0002
                                    --EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEH.HHHHHHHHHHHHTT-HHHHHHHHTT-SEEEEE-GGGGTT-H CS
                       Bac_DnaA  35 nPlfiygevGlGktHLlkaignevlenapelrvvYlta.eeFlnelvkalrdkkaeefkeklrkvDvLliDDiqflagke 113
                                       ++yg+ G Gkt +++a ++e   +  el  + + + e   ++l+ al+++++  +  k     ++l+D++  +++ke
  gi|119719184|ref|YP_919679.1|  48 KAALLYGPPGSGKTSIVHATAKEFSWELIELNASDVRTrEALQQRLLGALNTRSVLGYSGK-----IILLDEVDGISTKE 122
                                    4579********************9999999999986626677889999999999988765.....6899********** PP

                                    HHHHHHHHHHHHHHTTT-EEEEEESS-TTT-SS--HHHHHHHHSSEEEE-----HHHHHHHHHHHHHHTT----TTHHHH CS
                       Bac_DnaA 114 ktqeelfhtfnalleegkqvvlssDrsPkeleeledrlrsrfeaGlvvdieppdletrlailkkkieaeklevpeevlef 193
                                    +    l  +++ + +++  +vl+++  P+     + +lr   +    ++ ++  +   +++l+   ++e++e  +evl+ 
  gi|119719184|ref|YP_919679.1| 123 DA-GGLQAIVELIEKSNWPIVLTAN-DPW-----DPKLRPLRDLCELIEFKKIGKRDIMKVLENICSKEGVECSREVLSA 195
                                    54.5667777766677778888886.455.....567777777777899999999999999999999************* PP

                                    HHHH--S-HHHHHH CS
                       Bac_DnaA 194 iaervtdnvReleg 207
                                    ia++ + ++R    
  gi|119719184|ref|YP_919679.1| 196 IADNAKGDLRAAIN 209
                                    **999998875444 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00017      0.12      23      50 ..      38      64 ..      15      71 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00017
                         AAA_25 23 rwlvkgllpagelallaGapgtGKttla 50
                                   + +vkg  p ++ all+G+pg+GKt ++
  gi|119719184|ref|YP_919679.1| 38 NSWVKGK-PSKKAALLYGPPGSGKTSIV 64
                                   5578898.99***************987 PP

>> PPV_E1_C  Papillomavirus helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00013     0.091     248     280 ..      33      65 ..      26      81 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00013
                       PPV_E1_C 248 fltalkefLkgvPkknclvllGppntGkslfam 280
                                    +++ +++++kg+P k++ +l+Gpp +Gk+    
  gi|119719184|ref|YP_919679.1|  33 YVAWINSWVKGKPSKKAALLYGPPGSGKTSIVH 65 
                                    778899**********************87665 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00026      0.18      23      42 ..      47      67 ..      39      71 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00026
                         AAA_29 23 g.atlltGpsGsGKSTllDAi 42
                                     a ll Gp GsGK++++ A 
  gi|119719184|ref|YP_919679.1| 47 KkAALLYGPPGSGKTSIVHAT 67
                                   3379*************9886 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.017        12       4      21 ..      51      68 ..      48      74 .. 0.83
   2 ?    4.2   0.0     0.052        36      76     127 ..      86     145 ..      73     184 .. 0.78
   3 ?   -3.0   0.0       8.5   5.8e+03      63      93 ..     251     294 ..     233     312 .. 0.51

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.017
                                   EEEC-TTTCHHHHHHHHH CS
                          NACHT  4 ilqGeaGsGKTtLlqkla 21
                                   +l G++GsGKT  ++  a
  gi|119719184|ref|YP_919679.1| 51 LLYGPPGSGKTSIVHATA 68
                                   799********9998655 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.052
                                    HCCSCCCEE...............EEEE-STT-SS-TCH.........HHHHHCTTTTT--EEEEEE CS
                          NACHT  76 llelperlL...............lilDglDelvtdlgqkekqpvrtlLselirkkllpeasllltv 127
                                    + +l++rlL               ++lD +D ++t+ +    +   + + eli+k   ++ +++lt+
  gi|119719184|ref|YP_919679.1|  86 REALQQRLLgalntrsvlgysgkiILLDEVDGISTKED----AGGLQAIVELIEK---SNWPIVLTA 145
                                    667888888899999999*****9***********555....5999999999999...666666665 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 8.5
                                    TS--SSS-C............CHHHHCCSCCCEE.EEEE-STT- CS
                          NACHT  63 pepaapvse............vwavllelperlL.lilDglDel 93 
                                    pe a +v++              ++++ + e  L  i D++D l
  gi|119719184|ref|YP_919679.1| 251 PEQALAVTRlpsldyemlmqwLSENIVYQYEPSLqAIADAYDAL 294
                                    44444444433333333333322222222222223455555555 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00031      0.22      17      41 ..      47      71 ..      34     100 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00031
                         AAA_11 17 seitliqGPPGtgKTktivellsql 41
                                   ++ +l+ GPPG+gKT+ + +  ++ 
  gi|119719184|ref|YP_919679.1| 47 KKAALLYGPPGSGKTSIVHATAKEF 71
                                   3369***********9998887776 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00056      0.39      13      51 ..      49      85 ..      40     114 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00056
                                   EEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran 13 kvaivGenGaGKStLlkllagllkpteGeilldgkdlke 51
                                      + G+ G+GK++++ + a++ ++  + i+l+  d+++
  gi|119719184|ref|YP_919679.1| 49 AALLYGPPGSGKTSIVHATAKEFSW--ELIELNASDVRT 85
                                   44578*****************998..455556555555 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00061      0.42       2      37 ..      51      86 ..      50     140 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00061
                   RNA_helicase  2 wlyGpsgeGKStlakeLakallkklklkkkdsvysr 37
                                   +lyGp+g GK+++++  ak+++ +l + ++++v +r
  gi|119719184|ref|YP_919679.1| 51 LLYGPPGSGKTSIVHATAKEFSWELIELNASDVRTR 86
                                   69**************99999877745555555554 PP

>> AAA_6  Hydrolytic ATP binding site of dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0    0.0017       1.2      34      82 ..      49      97 ..      40     117 .. 0.90
   2 ?   -0.4   0.0      0.63   4.3e+02      96     131 ..     188     223 ..     157     227 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0017
                          AAA_6 34 ggapaGpagtGKtEtvkdLakalakqvvvfncsdqldykslgkifkGla 82
                                    + ++Gp g GKt  v   ak+++  ++ +n sd  + ++l++ + G  
  gi|119719184|ref|YP_919679.1| 49 AALLYGPPGSGKTSIVHATAKEFSWELIELNASDVRTREALQQRLLGAL 97
                                   56789*****************************999999998887765 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.63
                          AAA_6  96 ielevLSvvaqqiktiqqalkekkkkfvfegkeikl 131
                                     + evLS++a + k  ++a  ++++++ + +k+i+l
  gi|119719184|ref|YP_919679.1| 188 CSREVLSAIADNAKGDLRAAINDLQSLAMGKKTISL 223
                                    567899999999999888888888888888888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       748  (0.0417201); expected 358.6 (0.02)
Passed bias filter:                      663  (0.0369792); expected 358.6 (0.02)
Passed Vit filter:                       111  (0.00619109); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.69u 0.32s 00:00:01.01 Elapsed: 00:00:00.53
# Mc/sec: 2359.83
//
Query:       gi|119719185|ref|YP_919680.1|  [L=325]
Description: replication factor C small subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.7e-19   68.3   0.4    1.5e-18   67.0   0.1    1.9  1  Rep_fac_C        Replication factor C C-terminal domain
    5.9e-17   61.9   0.0    1.9e-11   44.0   0.0    2.2  2  DNA_pol3_delta2  DNA polymerase III, delta subunit
    8.4e-15   55.4   0.0    2.2e-14   54.0   0.0    1.7  1  AAA              ATPase family associated with various cellul
    1.6e-07   31.2   0.0    4.9e-07   29.6   0.0    1.8  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    1.9e-07   31.4   0.3      0.029   14.7   0.0    3.2  3  AAA_22           AAA domain
    4.1e-07   30.1   0.0    2.4e-06   27.6   0.0    2.1  2  Rad17            Rad17 P-loop domain
      1e-05   25.6   0.0    0.00026   21.0   0.0    2.3  2  AAA_14           AAA domain
    1.8e-05   24.8   0.0    0.00014   22.0   0.0    2.0  1  ResIII           Type III restriction enzyme, res subunit
    3.7e-05   24.0   2.0    4.2e-05   23.8   0.1    2.1  1  AAA_assoc_2      AAA C-terminal domain
    5.7e-05   22.8   0.0    0.00011   21.8   0.0    1.5  1  AAA_25           AAA domain
    8.6e-05   23.0   0.0      0.013   15.9   0.0    2.6  2  AAA_16           AAA ATPase domain
    0.00036   20.1   0.0      0.088   12.2   0.0    2.4  2  PhoH             PhoH-like protein
    0.00044   20.1   0.0    0.00074   19.4   0.0    1.3  1  AAA_3            ATPase family associated with various cellul
    0.00066   19.5   0.0     0.0024   17.7   0.0    1.8  2  AAA_11           AAA domain
    0.00099   18.9   0.0      0.012   15.4   0.0    2.5  3  DNA_pol3_delta   DNA polymerase III, delta subunit
     0.0014   19.2   0.0     0.0065   17.0   0.0    2.2  2  AAA_18           AAA domain
     0.0022   17.3   0.0      0.004   16.4   0.0    1.4  1  TIP49            TIP49 P-loop domain
     0.0022   17.7   0.0      0.028   14.2   0.0    2.1  2  AAA_24           AAA domain
     0.0028   17.4   0.1      0.011   15.4   0.0    2.1  2  IstB_IS21        IstB-like ATP binding protein
     0.0029   17.1   0.0      0.097   12.1   0.0    2.3  2  TniB             Bacterial TniB protein
     0.0033   16.8   0.0      0.036   13.4   0.0    2.3  3  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0069   16.6   0.0      0.016   15.3   0.0    1.6  1  AAA_33           AAA domain
     0.0073   16.1   0.1        1.6    8.5   0.0    2.3  2  DEAD             DEAD/DEAH box helicase
  ------ inclusion threshold ------
       0.01   15.3   0.0      0.017   14.6   0.0    1.3  1  AAA_7            P-loop containing dynein motor region
      0.011   15.7   0.0       0.05   13.6   0.0    2.2  1  AAA_5            AAA domain (dynein-related subfamily)
      0.014   14.4   0.0      0.032   13.3   0.0    1.5  1  T2SSE            Type II/IV secretion system protein
      0.024   14.4   0.2      0.093   12.4   0.0    2.1  2  AAA_30           AAA domain
      0.032   13.6   0.0      0.073   12.4   0.0    1.6  1  FtsK_SpoIIIE     FtsK/SpoIIIE family
      0.034   14.4   0.0      0.072   13.3   0.0    1.7  1  AAA_28           AAA domain
      0.035   14.5   0.0       0.12   12.8   0.0    1.9  1  RNA_helicase     RNA helicase
      0.039   13.1   0.0      0.066   12.4   0.0    1.4  1  DUF815           Protein of unknown function (DUF815)
      0.058   13.7   0.0       0.63   10.4   0.0    2.2  2  AAA_19           AAA domain
        0.1   11.8   0.0       0.52    9.5   0.0    1.9  2  DUF2075          Uncharacterized conserved protein (DUF2075)
       0.16   11.7   0.0       0.28   10.9   0.0    1.4  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
       0.22   12.5   1.2        1.1   10.3   0.0    2.8  2  TPR_14           Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> Rep_fac_C  Replication factor C C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.0   0.1   2.9e-21   1.5e-18       1      88 []     225     314 ..     225     314 .. 0.95

  Alignments for each domain:
  == domain 1  score: 67.0 bits;  conditional E-value: 2.9e-21
                                    --HHHHHHHHHHHHHT-HHHHHHHHHHHHHHC---HHHHHHHHHHHGCCS....S-HHHHHHHHHHHHHHHHHHHCTH-H CS
                      Rep_fac_C   1 phpteieeileaclngdfeeaykklrellvekGysaediltqlhrvvkeq..eelpeaqkleilellgeiekrlveGase 78 
                                    ++p+e++e++e++l+g++ ea++klr ll+++G+s+ di++ +hr v +q   +l++a+ +e+l l+ge+ +r+veG+++
  gi|119719185|ref|YP_919680.1| 225 VKPKEVREMIESALKGNLLEARDKLRLLLYNYGLSGVDIIRFIHREVLSQksVRLDDATLAELLVLVGETNYRIVEGSDD 304
                                    589**********************************************9655599********99************** PP

                                    HHHHHHHHHH CS
                      Rep_fac_C  79 hlqlsallar 88 
                                    ++ql all++
  gi|119719185|ref|YP_919680.1| 305 EIQLMALLSK 314
                                    *******985 PP

>> DNA_pol3_delta2  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.6e-05    0.0081       2      50 ..      21      68 ..      20      79 .. 0.89
   2 !   44.0   0.0   3.8e-14   1.9e-11      84     162 ..      80     160 ..      72     161 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.6e-05
                DNA_pol3_delta2  2 qeealkilskalksgrlahayLfeGdegigkkelalnlakallceekne 50
                                   qee++k l++ +k++++ h +Lf+G+ g+gk ++al+la+ l  e+ ++
  gi|119719185|ref|YP_919680.1| 21 QEEIVKRLKEFVKNKNMPH-LLFAGPPGTGKTTAALALAHDLYGESWRD 68
                                   8999************999.8********************99887655 PP

  == domain 2  score: 44.0 bits;  conditional E-value: 3.8e-14
                DNA_pol3_delta2  84 kldqirelieelsrkpre..skkkiiiiedaekmtksAaNalLktlEEPsenaifiLitsdtnklLktirSRcqelkfsp 161
                                     +d ir+ i++  r+  +     k++i+++a++mt  A+ al +t+E  s+n+ fiLi++  +k++++i+SRc +++f+p
  gi|119719185|ref|YP_919680.1|  80 GIDVIRSRIKDYARTLPIgdVPFKLVILDEADNMTGDAQQALRRTMELFSRNTRFILIANYASKIIEPIQSRCAVFRFQP 159
                                    57888876666666655513467********************************************************9 PP

                DNA_pol3_delta2 162 l 162
                                    l
  gi|119719185|ref|YP_919680.1| 160 L 160
                                    7 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.0   0.0   4.4e-17   2.2e-14       1     129 [.      40     157 ..      40     160 .. 0.88

  Alignments for each domain:
  == domain 1  score: 54.0 bits;  conditional E-value: 4.4e-17
                                    EEEESSTTSSHHHHHHHHHHHHT.....HEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTS.EEEEEETGGGHHHHH CS
                            AAA   1 vllyGppGtGKTllakavakelg.....vefleisgsellskyvgesekkirelfkeakekakp.silfiDEidalaksr 74 
                                    +l+ GppGtGKT++a a+a++l       + le+++s+ +   +    ++i+++ +++     p + +++DE+d+++++ 
  gi|119719185|ref|YP_919680.1|  40 LLFAGPPGTGKTTAALALAHDLYgeswrDNTLELNASDER--GIDVIRSRIKDYARTLPIGDVPfKLVILDEADNMTGDA 117
                                    699******************9434444889*********..88888888888888876666778***********9999 PP

                                    TTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSSEEEE CS
                            AAA  75 sgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfdrkie 129
                                               +++L + ++ +++   ++ +i+++n+ +k+ +++  +R+ +  +
  gi|119719185|ref|YP_919680.1| 118 -----------QQALRRTMELFSR---NTRFILIANYASKIIEPIQ-SRCAVFRF 157
                                    ...........*************...699****************.9**98765 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0   9.6e-10   4.9e-07       2      58 ..      11      62 ..      10      75 .. 0.92

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 9.6e-10
                         RuvB_N  2 rPksleeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakelg 58
                                   rP+sl+e + qe++ ++lk f++     ++++ h+l++GpPG Gktt a  +a++l 
  gi|119719185|ref|YP_919680.1| 11 RPRSLDEIVDQEEIVKRLKEFVK-----NKNMPHLLFAGPPGTGKTTAALALAHDLY 62
                                   9******************9996.....67899********************9985 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0    0.0003      0.15       7      29 ..      39      61 ..      32      88 .. 0.78
   2 !   14.7   0.0   5.6e-05     0.029      76     129 ..      82     138 ..      66     142 .. 0.81
   3 ?    1.2   0.0      0.81   4.1e+02      45      71 ..     218     256 ..     194     299 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0003
                         AAA_22  7 ilvvtGesGtGKTtllrrlleql 29
                                   +l+  G++GtGKTt +  l++ l
  gi|119719185|ref|YP_919680.1| 39 HLLFAGPPGTGKTTAALALAHDL 61
                                   78999***********9999877 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 5.6e-05
                         AAA_22  76 eellealeqalrarav....ielliiDEaqhlrseealeeLrsllnlsrkgvqliLvG 129
                                    + +++++ +++r+        +l+i+DEa+++ + +a + Lr+ ++l + ++++iL+ 
  gi|119719185|ref|YP_919680.1|  82 DVIRSRIKDYARTLPIgdvpFKLVILDEADNM-TGDAQQALRRTMELFSRNTRFILIA 138
                                    4455777777777777888889**********.999999**99999999*******96 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.81
                         AAA_22  45 vtlpsst.sskdllrellralglelka...........e 71 
                                    v+++ +  ++k++++++ +al+ +l +           +
  gi|119719185|ref|YP_919680.1| 218 VYAALGRvKPKEVREMIESALKGNLLEardklrlllynY 256
                                    233333358999999999999988888444444444433 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   4.6e-09   2.4e-06       6      77 ..       3      70 ..       1     140 [. 0.78
   2 ?   -0.2   0.0       1.6   8.4e+02      29      49 ..     232     253 ..     224     276 .. 0.74

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 4.6e-09
                          Rad17  6 nelWfekykPekaeelavhkkkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskel.giklrewl 77
                                    elW+eky+P  ++e+    + ++ +ke++k + +++     LL +GP+G gk+t+   L+  l g + r++ 
  gi|119719185|ref|YP_919680.1|  3 EELWVEKYRPRSLDEIVDQEEIVKRLKEFVKNKNMPH-----LLFAGPPGTGKTTAALALAHDLyGESWRDNT 70
                                   689*************988888999999988887775.....6*************99999875255555544 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.6
                          Rad17  29 eevkewlkadvLesrkkr.iLL 49 
                                    e ++ +lk + Le r k  +LL
  gi|119719185|ref|YP_919680.1| 232 EMIESALKGNLLEARDKLrLLL 253
                                    558999*******997753444 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1      0.17        86      69      92 ..      14      37 ..       3      44 .. 0.80
   2 !   21.0   0.0   5.2e-07   0.00026       5      99 ..      40     138 ..      36     160 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.17
                         AAA_14 69 flDEiqevpewekalkslvdegkn 92
                                    lDEi   +e+ k lk++v++++ 
  gi|119719185|ref|YP_919680.1| 14 SLDEIVDQEEIVKRLKEFVKNKNM 37
                                   59******************9944 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 5.2e-07
                         AAA_14   5 lvitGaRrvGKTtllkqlikell..vkkesilyinldderdkkladpekllelilek.lkeekktylflDEiqevpe.we 80 
                                    l+  G+  +GKTt +  l+++l+    ++++l++n  der  +   + ++ ++ + + + +   ++++lDE+ ++++ ++
  gi|119719185|ref|YP_919680.1|  40 LLFAGPPGTGKTTAALALAHDLYgeSWRDNTLELNASDERGIDVIRS-RIKDYARTLpIGDVPFKLVILDEADNMTGdAQ 118
                                    56789999***************99889**********999775544.477888887665556789******9986449* PP

                         AAA_14  81 kalkslvdeg.knldvivtG 99 
                                    +al++ ++   +n ++i+  
  gi|119719185|ref|YP_919680.1| 119 QALRRTMELFsRNTRFILIA 138
                                    ********665788888765 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   2.6e-07   0.00014       8      58 ..      21      71 ..      16     142 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 2.6e-07
                                   HHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EE CS
                         ResIII  8 QeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekfl 58
                                   Qee++++l+e +k+k+  ++l++ + GtGKT  a++l+  l+ + +++++l
  gi|119719185|ref|YP_919680.1| 21 QEEIVKRLKEFVKNKNMPHLLFAGPPGTGKTTAALALAHDLYGESWRDNTL 71
                                   9************99999************************999999887 PP

>> AAA_assoc_2  AAA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.1   8.2e-08   4.2e-05       3      51 ..     176     230 ..     174     247 .. 0.74

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 8.2e-08
                                    X.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.......XXXXXXXXXXX CS
                    AAA_assoc_2   3 kklkleddalealaeladGDaRkaLnlLElaaeaaeak......egkieitledl 51 
                                    + ++++d alea+ e ++GD Rka+n+L++a + +++       +   +++ +++
  gi|119719185|ref|YP_919680.1| 176 EGITVDDGALEAIWEESQGDLRKAINTLQAASAISRNVteevvyAALGRVKPKEV 230
                                    6799*************************99888775444444433333444444 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   2.2e-07   0.00011      37     111 ..      41     112 ..      26     137 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 2.2e-07
                         AAA_25  37 llaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEds..edelrrRlravgeal...rddarllvldlagv 111
                                    l+aG+pgtGKtt+al la+++  G++w +       ++l ++a d    d +r R++   ++l   + + +l +ld a+ 
  gi|119719185|ref|YP_919680.1|  41 LFAGPPGTGKTTAALALAHDLY-GESWRD-------NTLELNASDErgIDVIRSRIKDYARTLpigDVPFKLVILDEADN 112
                                    789******************9.999988.......66666665551267999999999988888888888888886553 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   2.5e-05     0.013       6      50 ..      22      63 ..      17      73 .. 0.78
   2 ?    4.2   0.0       0.1        52     120     169 ..      85     136 ..      63     137 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.5e-05
                         AAA_16  6 eeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralek 50
                                   ee +++L++ +++ +    + +l+ G++G+GK++ + +l++ l +
  gi|119719185|ref|YP_919680.1| 22 EEIVKRLKEFVKNKN---MPHLLFAGPPGTGKTTAALALAHDLYG 63
                                   667777777777444...379**************9999987765 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.1
                         AAA_16 120 lellkrllallsrderp.lvlvlDdlqwadeaslqllaaLlrllesk.pllv 169
                                    +  +k+ ++ l+ ++ p  +++lD+++    + +q+l+ +++l +++ ++++
  gi|119719185|ref|YP_919680.1|  85 RSRIKDYARTLPIGDVPfKLVILDEADNMTGDAQQALRRTMELFSRNtRFIL 136
                                    3444444444444555656899****************99999877546555 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   0.00017     0.088       8      44 ..      20      62 ..      17      70 .. 0.77
   2 ?    5.2   0.0     0.024        13     122     138 ..     104     120 ..     100     153 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00017
                                   HHHHHHHHHH....H-S...EEEEE--TTSSTTHHHHHHHHHHH CS
                           PhoH  8 eQkeylealk....knd...ivfaiGpaGtGKtylavalaveal 44
                                    Q+e+++ lk    + +    +  +Gp GtGKt  a+ala +++
  gi|119719185|ref|YP_919680.1| 20 DQEEIVKRLKefvkN-KnmpHLLFAGPPGTGKTTAALALAHDLY 62
                                   577788887777642.334457789**************98876 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.024
                                    EEEE-SGGG--HHHHHH CS
                           PhoH 122 fvilDEAQnttkeqmkm 138
                                    +vilDEA n+t    + 
  gi|119719185|ref|YP_919680.1| 104 LVILDEADNMTGDAQQA 120
                                    79********9755443 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   1.4e-06   0.00074       1      87 [.      39     126 ..      39     136 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.4e-06
                          AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekef..efkkGpvfanllladeinrappkt 78 
                                    h+l+ g PG++kt+++ ala+ l  e  r   t +l  sd  G++v++++ k++  ++  G v  +l++ de +  +  +
  gi|119719185|ref|YP_919680.1|  39 HLLFAGPPGTGKTTAALALAHDLYGESWR-DNTLELNASDERGIDVIRSRIKDYarTLPIGDVPFKLVILDEADNMTGDA 117
                                    99*********************999999.6799**************999877224678******************** PP

                          AAA_3  79 qsalleame 87 
                                    q al  +me
  gi|119719185|ref|YP_919680.1| 118 QQALRRTME 126
                                    ****99997 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   4.7e-06    0.0024      13      74 ..      31      88 ..      20      96 .. 0.68
   2 ?   -1.8   0.0       4.1   2.1e+03     217     226 ..     101     110 ..      91     117 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4.7e-06
                         AAA_11 13 alsese..itliqGPPGtgKTktivellsqllsrrkseeeksakpriLvCapSNaAvDellerl 74
                                   ++++++    l+ GPPGtgKT++ ++l + l+       e  +++ + + a+ +  +D++ +r+
  gi|119719185|ref|YP_919680.1| 31 FVKNKNmpHLLFAGPPGTGKTTAALALAHDLY------GESWRDNTLELNASDERGIDVIRSRI 88
                                   444444455799*******************3......34455555555555555555555555 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.1
                         AAA_11 217 kfdvviIDEA 226
                                     f++vi DEA
  gi|119719185|ref|YP_919680.1| 101 PFKLVILDEA 110
                                    79*******9 PP

>> DNA_pol3_delta  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       6.4   3.3e+03      75      93 ..      20      37 ..      13      51 .. 0.71
   2 !   15.4   0.0   2.3e-05     0.012      59     170 ..     103     204 ..      84     205 .. 0.91
   3 ?   -0.3   0.0       1.5   7.9e+02      29      57 ..     293     320 ..     264     322 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 6.4
                                   S-TTHHHHHHHHTTT--SS CS
                 DNA_pol3_delta 75 lnekllkeLeeylsnlped 93
                                   ++e+ +k+L+e+++n +  
  gi|119719185|ref|YP_919680.1| 20 DQEEIVKRLKEFVKNKN-M 37
                                   56778889999888833.3 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 2.3e-05
                                    EEEEEE--.....TT-S-TTHHHHHHHHTTT--SSEEEEEEES.S--HHHHHHHHHTTTEEEEEE----TTTHHHHHHHH CS
                 DNA_pol3_delta  59 rivvlknpklltkesklnekllkeLeeylsnlpedtlLiliapkklderkklvklLkkkatvveaktlkeeelkkwiqkr 138
                                    ++v+l+ +      ++ + + +++L ++++  + +t +ilia+     + k++  ++++  v+++++l + +  + +  +
  gi|119719185|ref|YP_919680.1| 103 KLVILDEA------DNMTGDAQQALRRTMELFSRNTRFILIAN----YASKIIEPIQSRCAVFRFQPLPKGDAFQRLRWI 172
                                    67777777......66889999*********************....6789*****************999999999*** PP

                                    HHHTT-EE-HHHHHHHHHHHTT-HHHHHHHHH CS
                 DNA_pol3_delta 139 aqelglkiekealelLlelvennlsaikqele 170
                                    aq++g+  ++ ale + e + ++l+ + + l+
  gi|119719185|ref|YP_919680.1| 173 AQQEGITVDDGALEAIWEESQGDLRKAINTLQ 204
                                    *************************9999887 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1.5
                                    EEEEEE-STTS-HHH.HTTTSTTTTSSSS CS
                 DNA_pol3_delta  29 dlnyikfdlnedwiddvleecetlpffsd 57 
                                    ++ny  +++++d+i+ ++  +  l + s+
  gi|119719185|ref|YP_919680.1| 293 ETNYRIVEGSDDEIQ-LMALLSKLALVSK 320
                                    789999999999999.7777777777776 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   1.3e-05    0.0065       3      32 ..      42      92 ..      40     143 .. 0.63
   2 ?   -0.6   0.0       3.7   1.9e+03      70      70 ..     223     223 ..     142     306 .. 0.60

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.3e-05
                         AAA_18  3 ltGtpGvGKttlakeLskrlgf......................gvnlrdva 32
                                    +G+pG+GKtt a +L+  l +                        +++d+a
  gi|119719185|ref|YP_919680.1| 42 FAGPPGTGKTTAALALAHDL-YgeswrdntlelnasdergidviRSRIKDYA 92
                                   79**************8776.4223444444444444444444444444444 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 3.7
                         AAA_18  70 a 70 
                                     
  gi|119719185|ref|YP_919680.1| 223 G 223
                                    0 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   7.8e-06     0.004      40      74 ..      29      61 ..      17      77 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 7.8e-06
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49 40 velikekklaGravLlaGpsgtGktalaiaiskel 74
                                    e++k+k++    +L+aGp+gtGkt  a+a++++l
  gi|119719185|ref|YP_919680.1| 29 KEFVKNKNMP--HLLFAGPPGTGKTTAALALAHDL 61
                                   68899***99..9*******************998 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   5.4e-05     0.028       5      88 ..      40     124 ..      37     144 .. 0.80
   2 ?    1.0   0.0      0.57   2.9e+02      84     123 ..     171     208 ..     164     222 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.4e-05
                         AAA_24   5 iliyGpsgiGKTtlakel.........gpkplfidtekGlksldadkfpdieswedfldevvelaaeladyktlviDtid 75 
                                    +l  Gp+g+GKTt a+ l          +++l ++  +  + +d+++         ++d++ +l+  + ++k +++D +d
  gi|119719185|ref|YP_919680.1|  40 LLFAGPPGTGKTTAALALahdlygeswRDNTLELNASD-ERGIDVIRS-------RIKDYARTLPIGDVPFKLVILDEAD 111
                                    5678**************99999999999999998755.345556553.......3578888999999999999999999 PP

                         AAA_24  76 eleelclaevirq 88 
                                     +   + + ++r 
  gi|119719185|ref|YP_919680.1| 112 NMTGDAQQALRRT 124
                                    9988877777665 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.57
                         AAA_24  84 evirqnekaeskedkgdgkG.ygelaeefrrllkklqelrk 123
                                    ++ +q ++     d+g++ + + e + ++r+++++lq++  
  gi|119719185|ref|YP_919680.1| 171 WIAQQEGI---TVDDGALEAiWEESQGDLRKAINTLQAASA 208
                                    66666666...3578999******************98765 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   2.2e-05     0.011      41      76 ..      29      66 ..      13     132 .. 0.72
   2 ?   -2.0   0.0       5.1   2.6e+03       6       6 ..     201     201 ..     164     237 .. 0.55

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.2e-05
                      IstB_IS21 41 lsfiekke..nivllGpsGvGKshlaialgveavragl 76
                                    +f+++k+   +++ Gp+G+GK+  a al+++   + +
  gi|119719185|ref|YP_919680.1| 29 KEFVKNKNmpHLLFAGPPGTGKTTAALALAHDLYGESW 66
                                   467776652258999***************98766555 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 5.1
                      IstB_IS21   6 t 6  
                                    +
  gi|119719185|ref|YP_919680.1| 201 N 201
                                    2 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   0.00019     0.097      23      52 ..      25      54 ..      13      70 .. 0.84
   2 ?    2.6   0.0      0.15        77     117     140 ..      99     122 ..      82     138 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00019
                           TniB 23 LeeLleypkrkrmpnlllvGdsnnGKtmiv 52
                                    ++L e+ k+k mp+ll++G++ +GKt+ +
  gi|119719185|ref|YP_919680.1| 25 VKRLKEFVKNKNMPHLLFAGPPGTGKTTAA 54
                                   35566778899****************975 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.15
                           TniB 117 elkvrvLiiDEihnllagsarkqr 140
                                    ++  +++i+DE +n+    +++ r
  gi|119719185|ref|YP_919680.1|  99 DVPFKLVILDEADNMTGDAQQALR 122
                                    56789*********9843333334 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0     7e-05     0.036      21      44 ..      36      59 ..      14      81 .. 0.66
   2 ?    0.1   0.0      0.84   4.3e+02     110     131 ..     105     126 ..     103     133 .. 0.90
   3 ?   -2.7   0.0       6.1   3.1e+03     178     193 ..     137     152 ..     129     157 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7e-05
                   Mg_chelatase 21 GgHnlllvGppGsGKtmlakrlps 44
                                      +ll++GppG+GKt  a +l+ 
  gi|119719185|ref|YP_919680.1| 36 NMPHLLFAGPPGTGKTTAALALAH 59
                                   4569*************9988864 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.84
                   Mg_chelatase 110 LfLDElpefkrkvlevLRePle 131
                                    ++LDE+ +++ ++ ++LR+ +e
  gi|119719185|ref|YP_919680.1| 105 VILDEADNMTGDAQQALRRTME 126
                                    68*****************998 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 6.1
                   Mg_chelatase 178 ierYlsklsgplldRi 193
                                    i++Y sk+ +p+  R 
  gi|119719185|ref|YP_919680.1| 137 IANYASKIIEPIQSRC 152
                                    67999******99996 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   3.2e-05     0.016       3      96 ..      41     177 ..      40     198 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.2e-05
                         AAA_33   3 llvGlpGsGKstlaerllkklgavllssdt......................................lrrrlfgtdqqs 44 
                                    l+ G+pG+GK+t a  l+  l ++  + +t                                      + ++++g+ qq 
  gi|119719185|ref|YP_919680.1|  41 LFAGPPGTGKTTAALALAHDLYGESWRDNTlelnasdergidvirsrikdyartlpigdvpfklvildEADNMTGDAQQA 120
                                    799**************998887776666666666777888888888888777777777777777777777777777776 PP

                         AAA_33  45 ktdytrvldr......lyqilnelarkalsagrnvildatnlsrrerarflklarrlg 96 
                                    +++  ++ +r      + +  ++++ +  +++++v   +++ + ++++r++++a++ g
  gi|119719185|ref|YP_919680.1| 121 LRRTMELFSRntrfilIANYASKII-EPIQSRCAVFRFQPLPKGDAFQRLRWIAQQEG 177
                                    6666665444333333233333333.33455555555666666666666666666666 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.031        16      16      35 ..      39      58 ..      19      77 .. 0.75
   2 !    8.5   0.0    0.0031       1.6     123     150 ..     103     129 ..      79     138 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.031
                                   EEEEEESTTSSHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxx RF
                           DEAD 16 dvlvaaeTGsGKTlaflipv 35
                                   ++l a++ G+GKT+a+l  +
  gi|119719185|ref|YP_919680.1| 39 HLLFAGPPGTGKTTAALALA 58
                                   67899**********88655 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0031
                                    EEEEEETHHHHHHTTTHHHHHHHHHHSH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD 123 rflVlDEadrlldqgfsdfinrilnqlp 150
                                    ++++lDEad++  +  ++ ++r ++ ++
  gi|119719185|ref|YP_919680.1| 103 KLVILDEADNMTGD-AQQALRRTMELFS 129
                                    78**********98.7777777777664 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   3.4e-05     0.017      31      72 ..      35      76 ..      17      90 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.4e-05
                          AAA_7 31 knkkpvllvGptGtGKtviikdllkkldkekylsltinfsaq 72
                                   kn  ++l+ Gp GtGKt+ +  l + l  e++  +t++++a+
  gi|119719185|ref|YP_919680.1| 35 KNMPHLLFAGPPGTGKTTAALALAHDLYGESWRDNTLELNAS 76
                                   334589*********************999999999999875 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   9.7e-05      0.05       1      24 [.      39      65 ..      39     133 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.7e-05
                                   EEEEE--SSSSHHHHHHHGGGGB...S CS
                          AAA_5  1 dvlLvGppGtgKselaerlaaal...n 24
                                   ++l  GppGtgK++ a  la+ l    
  gi|119719185|ref|YP_919680.1| 39 HLLFAGPPGTGKTTAALALAHDLygeS 65
                                   6899****************9886442 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   6.2e-05     0.032     104     153 ..      14      61 ..       7      87 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.2e-05
                          T2SSE 104 tlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkei 153
                                    +ld+++ +e+  ++++e++++   +   +l++G+ g+GKtt + al + +
  gi|119719185|ref|YP_919680.1|  14 SLDEIVDQEEIVKRLKEFVKNK--NMPHLLFAGPPGTGKTTAALALAHDL 61 
                                    6899999999999999999999..8889*************998887665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00018     0.093      21     100 ..      40     113 ..      20     141 .. 0.65
   2 ?   -2.0   0.0       4.8   2.5e+03      40      63 ..     187     210 ..     162     237 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00018
                         AAA_30  21 avltGpAGtGKttalkal.reaweaa..ggrviglAptgkaAkvLaeelgieastiakllkrlkgrarlepgtllivDEa 97 
                                     +  Gp+GtGKtta  al  +++ ++    ++ + A+ ++  +v++  +   a+t+              p +l+i DEa
  gi|119719185|ref|YP_919680.1|  40 LLFAGPPGTGKTTAALALaHDLYGESwrDNTLELNASDERGIDVIRSRIKDYARTLPIGD----V-----PFKLVILDEA 110
                                    4668********986666366776665347777888888888888877776666654221....2.....3467777777 PP

                         AAA_30  98 gmv 100
                                      +
  gi|119719185|ref|YP_919680.1| 111 DNM 113
                                    655 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.8
                         AAA_30  40 eaweaaggrviglAptgkaAkvLa 63 
                                    ++we+++g++  +  t +aA +++
  gi|119719185|ref|YP_919680.1| 187 AIWEESQGDLRKAINTLQAASAIS 210
                                    444444333333333333333333 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00014     0.073      25      58 ..      23      56 ..       2      61 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00014
                                   ET.TS-EEEEEGGGS-.SEEEE--TTSSHHHHHHH CS
                   FtsK_SpoIIIE 25 ei.sgnplvldlkkmashllvaGatgsGKStalnt 58
                                   ei  + ++ +  k+m+ hll aG +g+GK+ta  +
  gi|119719185|ref|YP_919680.1| 23 EIvKRLKEFVKNKNMP-HLLFAGPPGTGKTTAALA 56
                                   3437778888999999.**************8655 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   0.00014     0.072       4      25 ..      42      65 ..      39     128 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00014
                         AAA_28  4 itGgestGKTtlleaLaar..gyp 25
                                   + G+++tGKTt + aLa +  g +
  gi|119719185|ref|YP_919680.1| 42 FAGPPGTGKTTAALALAHDlyGES 65
                                   78***************7645443 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00023      0.12       2      34 ..      41      70 ..      40      82 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00023
                   RNA_helicase  2 wlyGpsgeGKStlakeLakallkklklkkkdsv 34
                                   ++ Gp+g+GK+t+a  La++l +++   ++d++
  gi|119719185|ref|YP_919680.1| 41 LFAGPPGTGKTTAALALAHDLYGES---WRDNT 70
                                   689******************9655...44444 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00013     0.066      37      82 ..      21      66 ..       6     107 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                         DUF815 37 kealventeqfleglpannvLLwGarGtGKSslvkallneyaeegL 82
                                   +e++v+  ++f+++++  ++L+ G  GtGK +   al +++  e+ 
  gi|119719185|ref|YP_919680.1| 21 QEEIVKRLKEFVKNKNMPHLLFAGPPGTGKTTAALALAHDLYGESW 66
                                   56788999*************************9999999887774 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0    0.0012      0.63       8      35 ..      35      62 ..      28      95 .. 0.61
   2 ?   -0.0   0.0         2     1e+03     105     125 ..     104     125 ..      87     138 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0012
                         AAA_19  8 lkekvllvtaGpGtGKTrvlkhivallv 35
                                    + ++ll  ++pGtGKT+   +  + l 
  gi|119719185|ref|YP_919680.1| 35 KNMPHLLFAGPPGTGKTTAALALAHDLY 62
                                   455667778889*****98766655554 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 2
                         AAA_19 105 llivDEfqdvd.elqyrLlkal 125
                                    l+i DE+ +++ + q++L +++
  gi|119719185|ref|YP_919680.1| 104 LVILDEADNMTgDAQQALRRTM 125
                                    8999999999978888876665 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0     0.001      0.52       7      49 ..      43      86 ..      39      99 .. 0.71
   2 ?   -0.1   0.0      0.85   4.4e+02      88     108 ..     101     121 ..      82     139 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.001
                        DUF2075  7 tGvaGtGKtvvllnllael.eddeeertavylsvNhplvlvlre 49
                                    G +GtGKt  +l+l+++l  ++ +++t  +    ++ ++v+r+
  gi|119719185|ref|YP_919680.1| 43 AGPPGTGKTTAALALAHDLyGESWRDNTLELNASDERGIDVIRS 86
                                   699***************96444455555555555555555555 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.85
                        DUF2075  88 kedvvivDEAhrlltksdqae 108
                                    ++++vi DEA  ++  ++qa 
  gi|119719185|ref|YP_919680.1| 101 PFKLVILDEADNMTGDAQQAL 121
                                    6889******99998555544 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00055      0.28       3      71 ..      42     110 ..      40     122 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00055
                Viral_helicase1   3 vhGvpGcGKStlirkllrtsliltvnrptaelltegkpklpnlsvrtvdsflmalvks.tkgkililDEy 71 
                                     +G pG GK+t+   l+++ l   + r ++  l+++ ++  +   ++++++  +l  +   +k++ilDE+
  gi|119719185|ref|YP_919680.1|  42 FAGPPGTGKTTAALALAHD-LYGESWRDNTLELNASDERGIDVIRSRIKDYARTLPIGdVPFKLVILDEA 110
                                    5799*************99.666667776666777666666666677777777776666779*******7 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0    0.0021       1.1       9      43 ..     188     224 ..     184     225 .. 0.82
   2 ?    0.6   0.0       2.7   1.4e+03      10      30 ..     218     240 ..     215     253 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0021
                         TPR_14   9 eallalGdpdeAiallrra..lalaPddaeawlllaq 43 
                                      ++ +Gd+++Ai+ l++a  ++++ ++++++ +l++
  gi|119719185|ref|YP_919680.1| 188 IWEESQGDLRKAINTLQAAsaISRNVTEEVVYAALGR 224
                                    56789*************7335588999999999987 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 2.7
                         TPR_14  10 allalGd..pdeAiallrralal 30 
                                    +++alG+  p+e +++ + al+ 
  gi|119719185|ref|YP_919680.1| 218 VYAALGRvkPKEVREMIESALKG 240
                                    68888976699999999999983 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       879  (0.0490267); expected 358.6 (0.02)
Passed bias filter:                      756  (0.0421663); expected 358.6 (0.02)
Passed Vit filter:                       131  (0.0073066); expected 17.9 (0.001)
Passed Fwd filter:                        35  (0.00195214); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              35  [number of targets reported over threshold]
# CPU time: 0.67u 0.29s 00:00:00.96 Elapsed: 00:00:00.46
# Mc/sec: 2108.09
//
Query:       gi|119719186|ref|YP_919681.1|  [L=200]
Description: 30S ribosomal protein S7P [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      3e-42  143.8   0.4    3.7e-42  143.5   0.4    1.1  1  Ribosomal_S7  Ribosomal protein S7p/S5e


Domain annotation for each model (and alignments):
>> Ribosomal_S7  Ribosomal protein S7p/S5e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.5   0.4     2e-46   3.7e-42      16     149 .]      58     200 .]      47     200 .] 0.95

  Alignments for each domain:
  == domain 1  score: 143.5 bits;  conditional E-value: 2e-46
                                    SSTTSBHHHHHHHHHSB....TTBHHHHHHHHHHHHHHHHHHHSS-HHHHHHHHHHHCS-SEEEEEEBSSSSBEEEEEEE CS
                   Ribosomal_S7  16 pkynselveklinklmk....dGkkslAekivygaldiieektkkdplevleeAlenvkPrvevksrrvGGatyqvpvev 91 
                                    +k++ ++ve+l n+lm+     Gkk lA +iv++a++iie kt+k+p++vl+ A+en++Pr+e++++ +GG+ y+v+v+v
  gi|119719186|ref|YP_919681.1|  58 AKARVSIVERLANNLMRpgrnAGKKMLALNIVKRAFEIIELKTGKNPIQVLVWAIENASPREETTRVIYGGILYHVSVDV 137
                                    458889**************9*********************************************************** PP

                                    -HHHHHHHHHHHHHHHH...STSSSS-HHHHHHHHHHHHHTT-..SHHHHHHHHHHHHHHHTG CS
                   Ribosomal_S7  92 rpkRrqalAlrwiieaa...rkrkeksmaekLaeElidAaege..gaavkkreethrmAeanr 149
                                    +p+Rr++lAlr+i+e+a   ++++ k+++e+La+E+++Aa g+  ++a +k+ee++r+A a+r
  gi|119719186|ref|YP_919681.1| 138 SPQRRVDLALRFITEGAracAFNNPKPIEECLADEIVAAAYGDpnSYALRKKEEVERVALAAR 200
                                    *****************88899********************999**************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 1380.71
//
Query:       gi|119719187|ref|YP_919682.1|  [L=482]
Description: hypothetical protein Tpen_0269 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   2.9e-169  563.6   0.0   3.4e-169  563.4   0.0    1.0  1  RtcB          tRNA-splicing ligase RtcB
  ------ inclusion threshold ------
      0.012   15.7   0.2      0.029   14.4   0.0    1.8  2  Complex1_LYR  Complex 1 protein (LYR family)


Domain annotation for each model (and alignments):
>> RtcB  tRNA-splicing ligase RtcB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  563.4   0.0  3.8e-173  3.4e-169       1     412 []      47     482 .]      47     482 .] 0.99

  Alignments for each domain:
  == domain 1  score: 563.4 bits;  conditional E-value: 3.8e-173
                                    HHHHHTTSTTB-S-EEEEEEEE--SSS-EEEEEEE-...-EE-HHHC-SST.-EEEEEEEEEEHHHHGGGHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           RtcB   1 qlknvaslpgivkhvaamPDvHlGkgapiGsViatk...gviiPaaVGvDI.CGvrllktnltaeeleeklkelvkelek 76 
                                    q++nva+lpgi+k+++++PD H+G+g+piG+V+a++   gv +P++VG+DI CGvr+l+tnlt++e+++kl+el+++l++
  gi|119719187|ref|YP_919682.1|  47 QVANVAMLPGIYKYSIVLPDGHQGYGFPIGGVAAFDaekGVLSPGGVGYDInCGVRVLSTNLTEQEVRPKLRELAETLFR 126
                                    89****************************************************************************** PP

                                    HS-------------HHHHHHHHHHTHHHHHHTTSS-GGGGGGBGGGG--TT--GGGS-HHHHHHHGGGTT---STT-EE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           RtcB  77 avpvglgskkkvklskkeleevleegakwaveeglgeeedlekieeegalkeadlekvskkakerarkqlGtlGsGNHFi 156
                                    ++p+glgs++ ++ls++el++vleeg++wa+e+g+g+ ed+e+iee+g++++ad+++vs++ak+r+ +qlGtlGsGNHF+
  gi|119719187|ref|YP_919682.1| 127 KIPSGLGSTSGLRLSHAELDRVLEEGVEWAIERGYGWREDMEHIEEKGRMEGADADAVSNEAKQRGSNQLGTLGSGNHFL 206
                                    ******************************************************************************** PP

                                    EEEEEEEES-HHHHHHHT-.-TTEEEEEEEE--HHHHHHHHHHHHHHHHCCHHHCT---SSGGG--EETTSHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           RtcB 157 Evqlveeildeeaakalgl.eegqvvvmlHsGSRglGhqiaedylkiakkalkkkgiklpdrdLaylpagseegqaYlka 235
                                    Evq v++i+d e+ak +g+ +egqv+vm+H+GSRglGhq+a+dylki+++ ++k+++ lpdr+L+ +pa+s+e+++Y++a
  gi|119719187|ref|YP_919682.1| 207 EVQRVDKIYDPEVAKVFGIeREGQVTVMIHTGSRGLGHQVASDYLKIMERVVRKYNMPLPDRELVSVPATSPEAERYFAA 286
                                    *******************889********************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHT.T--HHHH--EEEEEEESEEEEEEEE..T...EEEEEEEES-EE-......... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x...xxxxxxxxxxxxx......... RF
                           RtcB 236 mqaaanyAkaNRqvitervreilekvlkkekedlelelvvdvaHNiakkEehe.d...ekvlVhRKGAtrA......... 302
                                    m+aaan+A++NRqvit++vre+++ v+k++ ++l+l++++dvaHNiak Eeh  d    kv+VhRKGAtrA         
  gi|119719187|ref|YP_919682.1| 287 MKAAANFAWTNRQVITHWVRESFRAVFKTDPDKLGLNVIYDVAHNIAKLEEHVvDgkrVKVYVHRKGATRAfppghpeip 366
                                    *****************************999*********************966899********************* PP

                                    ....TT--EEEE--STTS-EEEEE--HHHH..SSSEE---S-----------------TTTTTCCCT-EEEE-------- CS
                                    ....xxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           RtcB 303 ....kvgqpviipGsmgtkSyivkGkgnae..sfgStsHGAGRlmsRakakkkfkleevkkdleeqgigvearkkegvle 376
                                        ++gqpv+ipGsmgt+Syi++G+++a+  +fgS+ HGAGR+ sRa+a+++++++e+k++le++gi+v+a++ ++v+e
  gi|119719187|ref|YP_919682.1| 367 adykSIGQPVLIPGSMGTASYILVGTQKAMdlTFGSSPHGAGRMQSRAEARRSVRGQEIKSELESRGIVVRAASLAVVAE 446
                                    ******************************************************************************** PP

                                    ----------HHHHHHHHCTS-EEEEEEEEEEEEE- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           RtcB 377 EapeaYKdideVveaqaeaglvevvarlkpvlvvkg 412
                                    Eap+aYKd+d+Vv ++++ g++++++r++p++vvkg
  gi|119719187|ref|YP_919682.1| 447 EAPDAYKDVDRVVMVADAVGIARKIVRMTPIAVVKG 482
                                    ***********************************8 PP

>> Complex1_LYR  Complex 1 protein (LYR family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   3.2e-06     0.029      10      46 ..     286     320 ..     283     343 .. 0.89
   2 ?   -3.3   0.1       1.1     1e+04      23      32 ..     413     422 ..     410     423 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.2e-06
                   Complex1_LYR  10 lLRearkfpdyntreyfrrriRdeFrknkhvtDpeki 46 
                                     +++a+ f ++n r+ + +++R++Fr+  + tDp+k+
  gi|119719187|ref|YP_919682.1| 286 AMKAAANFAWTN-RQVITHWVRESFRAVFK-TDPDKL 320
                                    6799********.**************776.788887 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.1
                   Complex1_LYR  23 reyfrrriRd 32 
                                    r+++rr +R 
  gi|119719187|ref|YP_919682.1| 413 RAEARRSVRG 422
                                    8999999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (482 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 3247.58
//
Query:       gi|119719188|ref|YP_919683.1|  [L=127]
Description: hypothetical protein Tpen_0270 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.6e-06   26.9   0.2    6.1e-06   26.2   0.2    1.4  1  HTH_20          Helix-turn-helix domain
    4.1e-05   23.3   0.0    6.7e-05   22.6   0.0    1.3  1  HTH_IclR        IclR helix-turn-helix domain
    0.00036   20.4   0.5    0.00069   19.4   0.2    1.6  2  MarR_2          MarR family
    0.00045   19.9   1.5       0.27   11.1   0.0    2.8  3  HTH_23          Homeodomain-like domain
    0.00047   19.7   0.9     0.0012   18.4   0.6    2.0  2  HTH_24          Winged helix-turn-helix DNA-binding
    0.00053   19.7   0.1     0.0015   18.3   0.1    1.9  1  HTH_38          Helix-turn-helix domain
    0.00057   19.8   0.6     0.0013   18.6   0.6    1.7  1  HTH_11          HTH domain
    0.00085   19.1   0.1     0.0027   17.5   0.1    1.9  2  HTH_5           Bacterial regulatory protein, arsR family
     0.0037   17.2   0.1      0.013   15.4   0.0    1.9  2  MarR            MarR family
     0.0038   17.4   0.2          4    7.7   0.0    2.4  2  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
     0.0065   16.5   0.1      0.023   14.7   0.1    2.0  2  HTH_29          Winged helix-turn helix
     0.0087   16.2   0.7       0.68   10.1   0.0    3.0  3  HTH_28          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.021   15.0   0.1      0.039   14.2   0.1    1.4  1  DUF3253         Protein of unknown function (DUF3253)
      0.035   14.2   0.3        0.3   11.2   0.1    2.6  2  HTH_7           Helix-turn-helix domain of resolvase
       0.17   12.0   0.0        0.3   11.2   0.0    1.4  1  FeoC            FeoC like transcriptional regulator


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.2   5.1e-09   6.1e-06      14      61 .]      64     111 ..      51     111 .. 0.92

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 5.1e-09
                                    HHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTEE CS
                         HTH_20  14 rilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvregr 61 
                                    ++l+a+++++g++ sela+ l+ s++++++ L++L++  ++++++ gr
  gi|119719188|ref|YP_919683.1|  64 ELLSAIKENKGASISELARILRRSPSNVYRDLAELARWRIIKLREDGR 111
                                    679999***********************************9999886 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   5.6e-08   6.7e-05       4      50 ..      61     106 ..      60     108 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 5.6e-08
                                    HHHHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                       HTH_IclR   4 RalaiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50 
                                    R +++L a+ e  ++ ++selAr +  ++S+v+R L+ L ++++++ 
  gi|119719188|ref|YP_919683.1|  61 RVIELLSAIKENKGA-SISELARILRRSPSNVYRDLAELARWRIIKL 106
                                    8999**********8.**************************99886 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       3.6   4.3e+03      11      19 ..      30      38 ..      20      54 .. 0.57
   2 !   19.4   0.2   5.8e-07   0.00069       8      61 ..      63     111 ..      58     113 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.6
                                   HHHHHCTTT CS
                         MarR_2 11 LaaLgrrpg 19
                                   L+ L+ ++g
  gi|119719188|ref|YP_919683.1| 30 LYSLYEEEG 38
                                   445555555 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 5.8e-07
                                    HHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSSS CS
                         MarR_2   8 arvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeDkR 61 
                                      +L a+  + g   +++elar l+ s+s+v r l++L +   +  r+   D+R
  gi|119719188|ref|YP_919683.1|  63 IELLSAIKENKG--ASISELARILRRSPSNVYRDLAELARWRIIKLRE---DGR 111
                                    56899*******..9*****************************9996...444 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.6   1.9e+03      34      46 ..      27      39 ..      24      43 .. 0.72
   2 !   11.1   0.0   0.00022      0.27      11      36 ..      66      93 ..      59      93 .. 0.77
   3 !    6.8   0.3    0.0049       5.8       3      23 ..      96     117 ..      94     120 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.6
                         HTH_23 34 vyrwlkryreeGl 46
                                   +++  + y+eeG 
  gi|119719188|ref|YP_919683.1| 27 LRQLYSLYEEEGE 39
                                   5667788999995 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00022
                         HTH_23 11 llllae..GlsvreIAreLgvsrrTvyr 36
                                   l + +e  G+s++e Ar+L +s++ vyr
  gi|119719188|ref|YP_919683.1| 66 LSAIKEnkGASISELARILRRSPSNVYR 93
                                   44444466***************98887 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0049
                         HTH_23   3 sereRlrillllae.GlsvreI 23 
                                     e+ R+ri++l  + ++ v+eI
  gi|119719188|ref|YP_919683.1|  96 AELARWRIIKLREDgRKKVPEI 117
                                    6789**********99999988 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.6   9.9e-07    0.0012       6      36 ..      63      93 ..      58     105 .. 0.89
   2 ?   -1.9   0.0       2.2   2.6e+03      35      45 ..     100     110 ..      96     111 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 9.9e-07
                         HTH_24  6 rkILelLqknprisqreLAerlglSpstvnr 36
                                   +++L+++++n + s++eLA+ l  Sps+v r
  gi|119719188|ref|YP_919683.1| 63 IELLSAIKENKGASISELARILRRSPSNVYR 93
                                   689*************************987 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.2
                         HTH_24  35 nrrlkrLeeeG 45 
                                    ++r+ +L e+G
  gi|119719188|ref|YP_919683.1| 100 RWRIIKLREDG 110
                                    57777888887 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   1.2e-06    0.0015      18      40 ..      72      94 ..      59      98 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.2e-06
                         HTH_38 18 aeGlslreIArrLgrspsTIsRE 40
                                   ++G s++e Ar+L rsps ++R 
  gi|119719188|ref|YP_919683.1| 72 NKGASISELARILRRSPSNVYRD 94
                                   699***************99995 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.6   1.1e-06    0.0013       1      43 [.      61     102 ..      61     112 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.1e-06
                         HTH_11   1 RllqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg 43 
                                    R   +l  ++e++g  s++eLA+ L +S + v+rd+++L  + 
  gi|119719188|ref|YP_919683.1|  61 RVIELLSAIKENKG-ASISELARILRRSPSNVYRDLAELARWR 102
                                    56678889989998.8***********************8885 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   2.3e-06    0.0027       5      40 ..      63      99 ..      59     105 .. 0.87
   2 ?   -1.4   0.0       1.8   2.2e+03       4      22 ..     100     118 ..      99     120 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.3e-06
                                   HHHHHHHTTSS.EEHHHHHHHHTS-HHHHHHHHHHHH CS
                          HTH_5  5 lkILklLaege.lcvcelaeelglsqstvShHLkkLr 40
                                   +++L++  e++ ++++ela++l+ s+s+v + L+ L 
  gi|119719188|ref|YP_919683.1| 63 IELLSAIKENKgASISELARILRRSPSNVYRDLAELA 99
                                   799******888*******************999885 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.8
                                    HHHHHHHHTTSSEEHHHHH CS
                          HTH_5   4 RlkILklLaegelcvcela 22 
                                    R +I+kl ++g ++v e+ 
  gi|119719188|ref|YP_919683.1| 100 RWRIIKLREDGRKKVPEII 118
                                    6677777667888888876 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       2.4   2.8e+03       5      11 ..      26      32 ..      19      38 .. 0.50
   2 !   15.4   0.0   1.1e-05     0.013       4      41 ..      61      98 ..      58     101 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2.4
                                   HHHHHHH CS
                           MarR  5 qfviLri 11
                                    ++ L++
  gi|119719188|ref|YP_919683.1| 26 ALRQLYS 32
                                   3333444 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1.1e-05
                                   HHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHH CS
                           MarR  4 tqfviLrilyeqgplsvseLakklgvskstvtrvldrL 41
                                     +++L  ++e+ ++s+seLa+ l  s+s+v r l +L
  gi|119719188|ref|YP_919683.1| 61 RVIELLSAIKENKGASISELARILRRSPSNVYRDLAEL 98
                                   55789*************************98877666 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.0    0.0039       4.7      10      37 ..      27      54 ..      24      55 .. 0.94
   2 !    7.7   0.0    0.0033         4      15      48 ..      67     100 ..      61     111 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0039
                                   HHHHHHHHHHHSSB-HHHHHHHHTS-HH CS
                 Fe_dep_repress 10 LetIYtlseekkvvktkdlaerLnvsps 37
                                   L+++Y+l ee++ v +k + e L v+++
  gi|119719188|ref|YP_919683.1| 27 LRQLYSLYEEEGEVAPKIIRENLSVEAA 54
                                   9**********************99876 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0033
                                    HHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHH CS
                 Fe_dep_repress  15 tlseekkvvktkdlaerLnvspssVsemlkkLek 48 
                                    ++ +e+k ++ ++la++L  sps V   l +L++
  gi|119719188|ref|YP_919683.1|  67 SAIKENKGASISELARILRRSPSNVYRDLAELAR 100
                                    67789999*****************999998876 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       2.1   2.5e+03      35      43 ..      33      41 ..      25      50 .. 0.79
   2 !   14.7   0.1   1.9e-05     0.023       9      48 ..      72     111 ..      62     119 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 2.1
                         HTH_29 35 rfeegGlaa 43
                                   ++ee+G+ a
  gi|119719188|ref|YP_919683.1| 33 LYEEEGEVA 41
                                   799999766 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 1.9e-05
                         HTH_29   9 aeGvstvsqiAkllglsrrtvyrwlkrfeegGlaalld.rr 48 
                                    ++G s +s++A++l+ s++ vyr l     +++ +l++ +r
  gi|119719188|ref|YP_919683.1|  72 NKGAS-ISELARILRRSPSNVYRDLAELARWRIIKLREdGR 111
                                    56665.*****************999999999888865443 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.15   1.8e+02      28      41 ..      26      39 ..      23      46 .. 0.84
   2 !   10.1   0.0   0.00057      0.68      11      31 ..      73      93 ..      61      96 .. 0.78
   3 ?    0.3   0.0      0.66   7.9e+02       4      19 ..     102     119 ..      99     124 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.15
                         HTH_28 28 tvyrWikryeegGi 41
                                    ++++ + yee+G+
  gi|119719188|ref|YP_919683.1| 26 ALRQLYSLYEEEGE 39
                                   689999******97 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00057
                         HTH_28 11 aGhsvreaArelgisrrtvyr 31
                                   +G s++e+Ar+l  s++ vyr
  gi|119719188|ref|YP_919683.1| 73 KGASISELARILRRSPSNVYR 93
                                   366*****************8 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.66
                         HTH_28   4 eiikllaaGh.svre.aA 19 
                                    +iikl  +G+  v+e +A
  gi|119719188|ref|YP_919683.1| 102 RIIKLREDGRkKVPEiIA 119
                                    799999999999999444 PP

>> DUF3253  Protein of unknown function (DUF3253)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   3.3e-05     0.039       4      58 ..      58     112 ..      55     116 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.3e-05
                                    HHHHHHHHHHHS-TT--B-HHHHHHHH...-TTS-GGGHHHHHHHHHHHHHTTSE CS
                        DUF3253   4 leaailallaerepgkticPsevAralsaeegeeWrelmekvRevavrlaaaGev 58 
                                    l +++++ll++ +++k  + se Ar l ++  + +r+l e +R   ++l+++G+ 
  gi|119719188|ref|YP_919683.1|  58 LSNRVIELLSAIKENKGASISELARILRRSPSNVYRDLAELARWRIIKLREDGRK 112
                                    778999*********************9998899******************985 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00025       0.3      12      43 ..      60      96 ..      32      98 .. 0.81
   2 ?   -0.1   0.0      0.83   9.9e+02      13      23 ..     102     113 ..     101     121 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00025
                                   GGGGSST.....TTT--STTTSSSS---SSSS--SS- CS
                          HTH_7 12 nrvvkLl.....eeGisiskIAkevnisRsTvYRyla 43
                                   nrv++Ll     ++G sis++A+++  s+s vYR la
  gi|119719188|ref|YP_919683.1| 60 NRVIELLsaikeNKGASISELARILRRSPSNVYRDLA 96
                                   566666633332479*******************766 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.83
                                    GGGSSTTTT.-- CS
                          HTH_7  13 rvvkLleeG.is 23 
                                    r++kL+e+G  +
  gi|119719188|ref|YP_919683.1| 102 RIIKLREDGrKK 113
                                    789999999544 PP

>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00025       0.3       4      32 ..      64      92 ..      62     108 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00025
                           FeoC  4 elkeyleergrvslkeLsrhfkaspeale 32
                                   el ++++e++ +s++eL+r ++ sp+ + 
  gi|119719188|ref|YP_919683.1| 64 ELLSAIKENKGASISELARILRRSPSNVY 92
                                   677899*******************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       740  (0.0412739); expected 358.6 (0.02)
Passed bias filter:                      589  (0.0328518); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.42u 0.30s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 862.85
//
Query:       gi|119719189|ref|YP_919684.1|  [L=165]
Description: hypothetical protein Tpen_0271 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-41  142.4   0.0    1.2e-41  142.2   0.0    1.0  1  Archease  Archease protein family (MTH1598/TM1083)


Domain annotation for each model (and alignments):
>> Archease  Archease protein family (MTH1598/TM1083)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.2   0.0   6.7e-46   1.2e-41       1     138 []      27     165 .]      27     165 .] 0.96

  Alignments for each domain:
  == domain 1  score: 142.2 bits;  conditional E-value: 6.7e-46
                                    EEE---SSEEEEEEE-SSSHHHHHHHHHHHHHHHS--TT---S-EEEEEEEESSSHHHHHHHHHHHHHHHHHT--S---- CS
                       Archease   1 yeyldhtADviieawGksleeafesaalalfeymtdlskvepkeekeieveaedledlLfdfLdellylfdteyfvfkev 80 
                                    +e+l+htAD++++a+G+s+eeaf++aa +++e+mt ++++ep e++e+ +e+ dle+lL++fL++ll+l+dte f++++v
  gi|119719189|ref|YP_919684.1|  27 FELLPHTADIMVRAKGRSIEEAFSNAAVGMYEVMTSVASIEPLEDREVVAEGFDLENLLYNFLENLLVLLDTEGFLVSRV 106
                                    89****************************************************************************** PP

                                    EEEE..E-SSSEEEEEEEE----.-TT--------B--S---EEEEETTEEEEEEEEE- CS
                       Archease  81 kvde.eeeeeeleleaeargekfdkekhevqtevKAvTyhelrieeeddgweayvvvDi 138
                                    k  + +++ee+++l+a++ ge+f+++khe +  vKA+Tyhe+ri +ed+ + ++ v Di
  gi|119719189|ref|YP_919684.1| 107 KSLRiSKTEEGYRLTAVVSGERFSPDKHESRVLVKAITYHEMRIYREDNCYVVEYVPDI 165
                                    7733248899*******************99**********************999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1122.93
//
Query:       gi|119719190|ref|YP_919685.1|  [L=361]
Description: isopentenyl pyrophosphate isomerase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.2e-22   77.7   6.3    7.7e-15   54.8   3.3    2.2  2  FMN_dh        FMN-dependent dehydrogenase
     0.0012   18.1   3.9     0.0021   17.3   0.2    2.4  2  Glu_synthase  Conserved region in glutamate synthase
     0.0024   17.1   0.1     0.0057   15.9   0.0    1.6  2  DHO_dh        Dihydroorotate dehydrogenase
  ------ inclusion threshold ------
      0.017   14.1   5.6      0.029   13.4   0.0    3.4  5  IMPDH         IMP dehydrogenase / GMP reductase domain


Domain annotation for each model (and alignments):
>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   4.9e-09   2.2e-05      28     106 ..      29     108 ..      11     137 .. 0.76
   2 !   54.8   3.3   1.7e-18   7.7e-15     207     344 ..     179     342 ..     144     346 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 4.9e-09
                                    HGGGGEEE---SS..SS-SS-B--EEETTEEESSSEEE--BSTGGGTSTTHHHHHHHHHHHHTS-EEEETT-SS-HHHHH CS
                         FMN_dh  28 aaferirlrprvl..rdvskvdlsttllGqklslPvliaPvglaklahpdgelalaraaakagipfvlstvastsleeva 105
                                    + +e +r++++++  ++ s+vd+st++lG+++++P++i+ +   + +  + + +la+ a+++++p++++++ +++l++ a
  gi|119719190|ref|YP_919685.1|  29 TLLECVRFVHQTVleANFSDVDVSTKFLGYEVAAPIVISGMTGGTPMGGKVNAMLAEVAQRLKVPIGVGSQ-RAALKDRA 107
                                    556667777666522467899********************99999999*******************998.66666655 PP

                                    H CS
                         FMN_dh 106 a 106
                                    a
  gi|119719190|ref|YP_919685.1| 108 A 108
                                    5 PP

  == domain 2  score: 54.8 bits;  conditional E-value: 1.7e-18
                                    HHHHHHHHHSSEEEEEEE...-SHHHHHHHHHTTESEEEE--GGG........................TSSTT---HHH CS
                         FMN_dh 207 dikwlreqtklplvvKGv...ltaedakraveaGvdgivvSNHGG........................Rqldgapatid 259
                                    +++++ + +k+p+++K      + e a ++++ Gv+g+ v   GG                              ++t  
  gi|119719190|ref|YP_919685.1| 179 NLREIVKSVKVPVILKQTgegFSRESALKIADTGVKGVDVGGAGGtsfavieglraryagldlheeiafEFAGWGIPTAA 258
                                    689999**********998889*****************************88888888888887766533334455555 PP

                                    CHHHHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-SBHH CS
                         FMN_dh 260 vLpeiveavggrievlvDgGirrGsDvlkAlalGAdavllGRpflyglaagGeeGvervleilraelertmallGvksva 339
                                       e++ a++ +i +++ gGir+G D++k + lGAd+ +l+ p+l  + + G eG  r le + +el+ +  l+G +++a
  gi|119719190|ref|YP_919685.1| 259 SVLEVRSALP-DILLIATGGIRSGLDAAKVIRLGADFAGLALPVLKEVYYRGVEGGYRFLEKVIRELKIAVFLTGGRTLA 337
                                    5568888888.9******************************************************************** PP

                                    HHHCG CS
                         FMN_dh 340 eldrs 344
                                    +l+++
  gi|119719190|ref|YP_919685.1| 338 DLKNA 342
                                    *9875 PP

>> Glu_synthase  Conserved region in glutamate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.5     0.027   1.2e+02     226     241 ..      59      74 ..      14     139 .. 0.78
   2 !   17.3   0.2   4.7e-07    0.0021     192     303 ..     175     298 ..     165     303 .. 0.68

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.027
                                    TT-SEEEEE-TT---S CS
                   Glu_synthase 226 anadiilidGleGGTG 241
                                      a  i+i+G+ GGT 
  gi|119719190|ref|YP_919685.1|  59 EVAAPIVISGMTGGTP 74 
                                    4566789999999983 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 4.7e-07
                                    HHHHHHHHH-..TTSEEEEEEE-STTHHHHHHHHHHTT-SEEEEE-TT---SSEEHHH.HHHB---HH.........HHH CS
                   Glu_synthase 192 qliedLkevn..keakvsvKlvaeagvetiaagvakanadiilidGleGGTGAspkss.ikhaGlPle.........lal 259
                                    +++ +L+e+    +++v  K + e      a+ +a+ ++  + + G  G   A+ + + + +aGl l           ++
  gi|119719190|ref|YP_919685.1| 175 NFLGNLREIVksVKVPVILKQTGEGFSRESALKIADTGVKGVDVGGAGGTSFAVIEGLrARYAGLDLHeeiafefagWGI 254
                                    56667777762334445555555555666666677777777777776555555555441456776653222222222478 PP

                                    HHHHHHHHHTT-GGG-EEEEESS--SHHHHHHHHHHT-SEEE-S CS
                   Glu_synthase 260 aevdqtlkeeglrdrvsliadGglktgadvvkalalGAdavgig 303
                                    + +  +l        + lia+Gg+++g d +k + lGAd+ g++
  gi|119719190|ref|YP_919685.1| 255 PTAASVLEVRSALPDILLIATGGIRSGLDAAKVIRLGADFAGLA 298
                                    899999999999999************************99887 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0      0.69   3.1e+03     224     250 ..     101     127 ..      79     135 .. 0.63
   2 !   15.9   0.0   1.3e-06    0.0057     234     271 ..     260     296 ..     255     327 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.69
                                    GGGHHHH.HHHHHHHHHHTTT.S-EEEE CS
                         DHO_dh 224 kalkdia.lkvirelykrlkkeipiIgv 250
                                    +alkd+a +++ r +++   +++p+I+ 
  gi|119719190|ref|YP_919685.1| 101 AALKDRAaVETFRVVRE-KAPDVPVIAN 127
                                    45666651444444444.4447777775 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.3e-06
                                    HHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEE CS
                         DHO_dh 234 irelykrlkkeipiIgvGGiesgeDalekieaGAslvq 271
                                    + e+++ l  +i +I++GGi sg Da   i+ GA +  
  gi|119719190|ref|YP_919685.1| 260 VLEVRSALP-DILLIATGGIRSGLDAAKVIRLGADFAG 296
                                    556666665.9***********************8654 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1     0.087   3.9e+02     285     315 ..      65      95 ..      44     119 .. 0.71
   2 ?   -2.3   0.0      0.37   1.7e+03     132     153 ..     108     128 ..     100     156 .. 0.63
   3 ?    0.4   0.2     0.056   2.5e+02     135     177 ..     179     223 ..     169     229 .. 0.75
   4 ?   13.4   0.0   6.4e-06     0.029     185     232 ..     249     294 ..     245     304 .. 0.90
   5 ?   -3.1   0.0      0.67     3e+03     302     327 ..     316     341 ..     311     346 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.087
                                    S-SBEEEEEE--B-HHHHHHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH 285 vpeGvegrvpykgsvkevveqlvgglrsgmg 315
                                    v  G+ g +p+ g+v++++ ++++ l+  +g
  gi|119719190|ref|YP_919685.1|  65 VISGMTGGTPMGGKVNAMLAEVAQRLKVPIG 95 
                                    5566666667777777776666666665443 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.37
                                    HHHHHHHHHHHTTTSEEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH 132 vleavkeikkkveeveviaGnv 153
                                     +e+ + +++k+++v via n+
  gi|119719190|ref|YP_919685.1| 108 AVETFRVVREKAPDVPVIA-NI 128
                                    5566666666666666665.33 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.056
                                    HHHHHHHHTTTSEEE...EEEE-SHHHHHHHHHTT-SEEEE-SS-S CS
                                    xxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH 135 avkeikkkveevevi...aGnvataegakaLieagadavkvGiGpG 177
                                     ++ei k+v +v vi   +G+  ++e a +++++g+++v vG   G
  gi|119719190|ref|YP_919685.1| 179 NLREIVKSV-KVPVIlkqTGEGFSRESALKIADTGVKGVDVGGAGG 223
                                    556666666.466665567888999****************94433 PP

  == domain 4  score: 13.4 bits;  conditional E-value: 6.4e-06
                                    HCSB---HHHHHHHHHHHHCTCT-EEEEES---SHHHHHHHHHTT-SE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH 185 vagvGvpqltAvaevaeaakkagvpviaDGGikysgdivkAlaaGada 232
                                     ag G+p + +v+ev +a    ++ +ia GGi++  d +k + +Gad+
  gi|119719190|ref|YP_919685.1| 249 FAGWGIPTAASVLEVRSALP--DILLIATGGIRSGLDAAKVIRLGADF 294
                                    689************98875..79**********************97 PP

  == domain 5  score: -3.1 bits;  conditional E-value: 0.67
                                    HHHHHHHHHHHHHHHHT-SSHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH 302 vveqlvgglrsgmgylGaktieelke 327
                                    ++e+++ +l+ ++  +G +t+++lk+
  gi|119719190|ref|YP_919685.1| 316 FLEKVIRELKIAVFLTGGRTLADLKN 341
                                    67888899999999999999999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 2675.71
//
Query:       gi|119719191|ref|YP_919686.1|  [L=287]
Description: hypothetical protein Tpen_0273 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-78  263.9   0.0    1.5e-78  263.7   0.0    1.0  1  Memo      Memo-like protein
    4.1e-07   29.4   0.1    5.7e-07   28.9   0.1    1.2  1  LigB      Catalytic LigB subunit of aromatic ring-opening dio


Domain annotation for each model (and alignments):
>> Memo  Memo-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  263.7   0.0   1.7e-82   1.5e-78       2     270 ..       8     282 ..       7     283 .. 0.96

  Alignments for each domain:
  == domain 1  score: 263.7 bits;  conditional E-value: 1.7e-82
                           Memo   2 aavAGsfYpedeeelkkqleeflekntgkkei......arviis........PHagyvysgevaakayaeles.skverv 66 
                                    a +AG fYp++++el + l++ +++++g+++       +    +        PHagy+ysg+vaa+ay +l++  k++ v
  gi|119719191|ref|YP_919686.1|   8 AVHAGYFYPAEKRELIEALKNAFLHELGPGKLpekpgsY----TgnligvvaPHAGYIYSGHVAAHAYLALAEgGKPDVV 83 
                                    78****************************996666552....044446778**************************** PP

                           Memo  67 vilGpsHtilgskvsvlaaseleTPlGdlkvDeelveeLvkkeeiadldetaalaEHSlEvqlpfLkellkekkfkivPi 146
                                    +ilGp+H+ lg ++++ + + +eTPlGd++vD  + +eL   e+i+ +d +a+ +EHS+Evq+pfL+ ++ e  f+ivPi
  gi|119719191|ref|YP_919686.1|  84 FILGPNHHALGAPIALDENEVWETPLGDVEVDFRVSKELASREQIIRFDFQAHAYEHSIEVQVPFLQFVFGE-GFTIVPI 162
                                    ************************************************************************.6****** PP

                           Memo 147 lvsaqseetakevgealakvikdes..nlviiSsDlsHygrrFgspqeiaesieDrevikaleelneeelkeylektnnt 224
                                     ++ q++e a+ vgea+a  i ++   + v++SsD+sHy      +  ia ++ D+ +i+++  l+ e+l++++ + +++
  gi|119719191|ref|YP_919686.1| 163 SMMLQTPEAARRVGEAIAGLIMEKGlrAYVVASSDMSHYV-----ESRIAAEK-DKVAIERVLFLDAEGLYNAVIEEDIS 236
                                    *********************999988*************.....999****9.************************** PP

                           Memo 225 icGekpiavilkalkklgakkakllkYaqssdvtsdtdsvVsyasl 270
                                    +cG +p++++++++kklg ++++llkYa s+dvt+d++svV+yasl
  gi|119719191|ref|YP_919686.1| 237 MCGPGPVMALIYIAKKLGYANVRLLKYADSGDVTGDKSSVVAYASL 282
                                    ********************************************96 PP

>> LigB  Catalytic LigB subunit of aromatic ring-opening dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.1   6.3e-11   5.7e-07      37     194 ..      73     212 ..      52     234 .. 0.82

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 6.3e-11
                           LigB  37 riaek.sPdtiivvsphhltdvnpvfvlgvaeefeaiddfgkflprleyelkgnpeLaekiaealkksgidlavesnsmk 115
                                    ++ae  +Pd++++  p h     p+      +e+e +++    l ++e ++++++eLa++  e+++  ++++ ++ +s +
  gi|119719191|ref|YP_919686.1|  73 ALAEGgKPDVVFILGPNHHALGAPI---AL-DENEVWET-P--LGDVEVDFRVSKELASR--EQIIRFDFQAHAYEHSIE 143
                                    4556679*****9998777756555...44.55889998.3..789************95..999999999877555555 PP

                           LigB 116 lDHGtlvP.LelmlpdeakvpvikvslntvaypllsferlykLGeAlrkaveeldknvlilgsGglsHqlegdeaakada 194
                                        + vP L++++++    + +++s++       ++e  +++GeA++ ++ e   +  +++s ++sH+ e   aa++d 
  gi|119719191|ref|YP_919686.1| 144 ----VQVPfLQFVFGE--GFTIVPISMML-----QTPEAARRVGEAIAGLIMEKGLRAYVVASSDMSHYVESRIAAEKDK 212
                                    ....5799679****6..67889999998.....799**************999****************9988886665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       284  (0.0158403); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 1647.39
//
Query:       gi|119719192|ref|YP_919687.1|  [L=214]
Description: 30S ribosomal protein S2 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.8e-21   75.0   0.0    5.6e-14   51.9   0.1    2.0  2  Ribosomal_S2  Ribosomal protein S2


Domain annotation for each model (and alignments):
>> Ribosomal_S2  Ribosomal protein S2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   6.7e-09   0.00012       2      95 ..      21     111 ..      20     119 .. 0.90
   2 !   51.9   0.1   3.1e-18   5.6e-14     150     212 ..     121     183 ..     114     185 .. 0.95

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 6.7e-09
                   Ribosomal_S2   2 LeagvhfGhqtrrwnpkmkpyIyger.ngihiidlektlaalrraykvvkevaakggkilfvgtkkqakeavkeaakran 80 
                                    L+ag+ +G  t+   + m+p+Iy +r +g +++d++kt + +r a+k++ +   + +k++ v+ ++  ++ v++ +  ++
  gi|119719192|ref|YP_919687.1|  21 LAAGIRIG--TKMKSKFMEPFIYSARpDGLYLLDVKKTDERIRIAAKMIAR--YDPSKFVVVSGRQYGHRPVRKFCGLVG 96 
                                    67888888..5556899******999679********************86..577899********************* PP

                   Ribosomal_S2  81 gyyvnerWlgGtLTN 95 
                                       +  r l+Gt+TN
  gi|119719192|ref|YP_919687.1|  97 CKPMLGRVLPGTFTN 111
                                    *************** PP

  == domain 2  score: 51.9 bits;  conditional E-value: 3.1e-18
                   Ribosomal_S2 150 dlvvvldpkkekiavkEakklgipviaivDtnvdpdlvdypIpaNddsirsiklilgvladai 212
                                    dl++v+dp+ ++ av Ea ++gipvia++Dt++  ++vd +Ip N+   +++ li+ +la+ +
  gi|119719192|ref|YP_919687.1| 121 DLMMVTDPRVDEQAVVEAGTMGIPVIALCDTDSPISNVDLIIPTNNRGRKALALIFWLLAREV 183
                                    89*********************************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       201  (0.0112109); expected 358.6 (0.02)
Passed bias filter:                      200  (0.0111551); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1432.34
//
Query:       gi|119719193|ref|YP_919688.1|  [L=243]
Description: hypothetical protein Tpen_0275 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1664.94
//
Query:       gi|119719194|ref|YP_919689.1|  [L=90]
Description: DNA-directed RNA polymerase subunit N [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.8e-30  103.1   0.2    8.9e-30  102.8   0.2    1.2  1  RNA_pol_N       RNA polymerases N / 8 kDa subunit
  ------ inclusion threshold ------
      0.086   13.1   0.2       0.16   12.2   0.2    1.5  1  Chordopox_RPO7  Chordopoxvirus DNA-directed RNA polymerase 7 
      0.095   11.9   0.2       0.11   11.7   0.2    1.0  1  Baculo_ME53     Baculoviridae ME53
       0.11   12.1   0.3       0.13   11.8   0.3    1.1  1  DUF572          Family of unknown function (DUF572)


Domain annotation for each model (and alignments):
>> RNA_pol_N  RNA polymerases N / 8 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.8   0.2     2e-33   8.9e-30       1      59 []      15      73 ..      15      73 .. 0.99

  Alignments for each domain:
  == domain 1  score: 102.8 bits;  conditional E-value: 2e-33
                                   ----SS-TTT--B-STHHHHHHHHHHTT--HHHHHHHHT--SHHHHHHHHTB--THHHH CS
                      RNA_pol_N  1 MiiPVrCFtCGkvigekweeylellekgeepkdaLdaLglkryCCrrmllthvdliekl 59
                                   M++P+rCFtCG +ig+kw+ey +++ +ge+p+++Ld+Lg++ryCCrrm+l+h++ i+k+
  gi|119719194|ref|YP_919689.1| 15 MMFPIRCFTCGALIGDKWNEYSTRVANGEDPNKVLDDLGITRYCCRRMFLSHTEAIDKI 73
                                   9*******************************************************986 PP

>> Chordopox_RPO7  Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide (RPO7)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   3.6e-05      0.16       1      41 [.      15      60 ..      15      71 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.6e-05
                 Chordopox_RPO7  1 mvfplvCstCGrDlsee..ryrLlv.kkkkLkdvlat..vkrkCCr 41
                                   m+fp+ C tCG  + ++   y   v + ++ ++vl+   ++r CCr
  gi|119719194|ref|YP_919689.1| 15 MMFPIRCFTCGALIGDKwnEYSTRVaNGEDPNKVLDDlgITRYCCR 60
                                   99*********99887522565544156778999987335899998 PP

>> Baculo_ME53  Baculoviridae ME53
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   2.4e-05      0.11      49     117 ..      11      79 ..       2      82 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.4e-05
                    Baculo_ME53  49 ykktmehlddsrctacnykfkdikrenflyvvv..kiekplddddrldicclkcylysrvvkdiielyPsl 117
                                    y+     +   rc++c     d  +e+   v      +k ldd +   +cc++ +l +  + d i  y s+
  gi|119719194|ref|YP_919689.1|  11 YRTR--MMFPIRCFTCGALIGDKWNEYSTRVANgeDPNKVLDDLGITRYCCRRMFLSHTEAIDKIIKYGSI 79 
                                    4433..366789******999999998766553112345567888889**********9999999889887 PP

>> DUF572  Family of unknown function (DUF572)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.3     3e-05      0.13      19      59 ..       5      40 ..       2      43 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3e-05
                         DUF572 19 arlknrqlvvRlmaPfnmrCktCgeyIykGvkFNarKekVg 59
                                   ++   r +  R+m P  +rC tCg+ I+   k+N   ++V 
  gi|119719194|ref|YP_919689.1|  5 LN-ATRKYRTRMMFP--IRCFTCGALIGD--KWNEYSTRVA 40
                                   44.678899999976..9*********75..7776666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 667.60
//
Query:       gi|119719195|ref|YP_919690.1|  [L=132]
Description: 30S ribosomal protein S9P [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.1e-32  110.1   0.4      1e-31  110.0   0.4    1.0  1  Ribosomal_S9     Ribosomal protein S9/S16
  ------ inclusion threshold ------
      0.092   12.9   1.9       0.22   11.7   1.9    1.6  1  PBCV_basic_adap  PBCV-specific basic adaptor domain


Domain annotation for each model (and alignments):
>> Ribosomal_S9  Ribosomal protein S9/S16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.0   0.4   1.1e-35     1e-31       2     121 .]       9     132 .]       8     132 .] 0.93

  Alignments for each domain:
  == domain 1  score: 110.0 bits;  conditional E-value: 1.1e-35
                                    ECTTEEEEEEEEESSSEEEETTEECCHHSTTSCHHHHHCHHHHHTTTSSS.EEEEEEEESS-HHHHHHHHHHHHHHHHHH CS
                   Ribosomal_S9   2 rrKesvArvwikegkgkilvngksleeYfkeeaarekvleplkltgllgk.fdvfvkvkgGGlsgqaeAirlgiaraLva 80 
                                    rrK+++Arv +++g+g++ vng++le  ++ e  r k++epl+l+g+l + +d++++ +gGG+++qa Air++iaraLv+
  gi|119719195|ref|YP_919690.1|   9 RRKTARARVILRDGRGRVFVNGTPLEI-LEPEVIRLKIMEPLRLAGSLAEkVDIYAEAEGGGIVSQASAIRTAIARALVE 87 
                                    9**************************.988***************99855***************************** PP

                                    HHHHHHHHHC......TCCCTS-B--------TTSSCTTB----S-- CS
                   Ribosomal_S9  81 lekeekkeLk......kaglltrDpRvvErkKtgkkkARkkyqwskR 121
                                    ++    +eLk      ++ ll++DpR+ E+kK+  + AR+k q+s+R
  gi|119719195|ref|YP_919690.1|  88 WSG--SEELKklylayDRRLLVEDPRQAEPKKPRGRSARAKRQKSYR 132
                                    *88..456664557788****************************99 PP

>> PBCV_basic_adap  PBCV-specific basic adaptor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.9   2.4e-05      0.22       2      22 ..      10      30 ..       9      31 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.4e-05
                PBCV_basic_adap  2 rvDaKGRivfkgprGgkyVkd 22
                                   r+ a+ R ++++ rG+ +V +
  gi|119719195|ref|YP_919690.1| 10 RKTARARVILRDGRGRVFVNG 30
                                   78899**************76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 926.91
//
Query:       gi|119719196|ref|YP_919691.1|  [L=154]
Description: ribosomal protein L13 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.9e-13   50.1   0.7    3.5e-11   43.5   0.7    2.3  1  Ribosomal_L13  Ribosomal protein L13


Domain annotation for each model (and alignments):
>> Ribosomal_L13  Ribosomal protein L13
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.5   0.7   1.9e-15   3.5e-11       4     115 ..       9     111 ..       7     120 .. 0.77

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 1.9e-15
                                    EEEETTSBHHHHHHHHHHHHHTTTSTT--TTS--S-EEEEEEGGCBB-SS......THHTT-EEEEE-SSTTSEEEEEHH CS
                  Ribosomal_L13   4 viDAegqvlgrlaskiakvLrGkhkptytphvdcGdyvvvinaekvaltg......kkleqkvyyrhtgypgglkevtak 77 
                                    viD +g++ grlas +ak+L              Gd vvv+naek+++tg      +k  ++   ++t y  +l+  ++ 
  gi|119719196|ref|YP_919691.1|   9 VIDGTGHIAGRLASVVAKRLL------------KGDRVVVVNAEKIVITGkpkrvvEKYLKRWVEWKTYYNPELRGPKY- 75 
                                    789999999999999998884............6****************66444445555555555555555555444. PP

                                    HHHCCSHHHHHHHHHHCCS-S.SHHHHHHGCTEEEESSS CS
                  Ribosomal_L13  78 ellekkpeeilekaVkgmLpk.nklgrrrlkrLkvyage 115
                                        k p+++++++V+gmLp  +++gr+ lkrL vy g 
  gi|119719196|ref|YP_919691.1|  76 ---PKTPDRLFKRMVRGMLPMeKTIGRDSLKRLTVYVGL 111
                                    ...6789*************73669***********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1101.03
//
Query:       gi|119719197|ref|YP_919692.1|  [L=120]
Description: 50S ribosomal protein L18e [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-06   27.4   0.0      2e-06   27.3   0.0    1.0  1  Ribosomal_L18   Ribosomal protein 60S L18 and 50S L18e
     0.0039   17.8   0.0      0.016   15.9   0.0    1.9  1  Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27
  ------ inclusion threshold ------
      0.078   13.2   0.3       0.25   11.6   0.0    1.8  2  DUF3006         Protein of unknown function (DUF3006)


Domain annotation for each model (and alignments):
>> Ribosomal_L18  Ribosomal protein 60S L18 and 50S L18e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   3.4e-10     2e-06      20     137 ..       7     118 ..       1     120 [] 0.90

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 3.4e-10
                  Ribosomal_L18  20 envylklLvklyrfLarRtdskFnkvvlkrLfmsrinrpplslsrlvkkvkkkeeekkiavvvgtvtdDvrllevPklsv 99 
                                    +n+ l+lL++  r  +r  ++   + v   L   r++r  + lsr+ +++k+    + ++vv g+v+    +++  ++ +
  gi|119719197|ref|YP_919692.1|   7 TNIHLRLLIHKLRKYSRLYKAPVWRDVAEYLERPRRKRVEVNLSRIDRHIKE----GDVVVVPGKVLGGGSITK-SNVVI 81 
                                    79999**999999999**********************************95....69***********99988.5799* PP

                  Ribosomal_L18 100 aALrftetararilkaGGeiltlDqLalraPtGkntvL 137
                                    aA rf+++a +r+     + +++++L  ++P+Gkn+ +
  gi|119719197|ref|YP_919692.1|  82 AAWRFSRSALERLD-GRVKAISIEELLEQNPEGKNVKI 118
                                    ************85.55799***************866 PP

>> Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   2.6e-06     0.016      66     118 ..      42      93 ..      15      97 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.6e-06
                                    TS------EEEGGGTTTTSSS........SEEEE--S---.-.-EEEESEE-HHHHHH CS
                 Ribosomal_L27A  66 leladeaeeidleelaeaglikk....kdgvKvlgkgeltkk.lkvkaskfSkkAkek 118
                                    +    ++ e++l+++   + ik+        Kvlg g++tk  + + a +fS++A e+
  gi|119719197|ref|YP_919692.1|  42 R----KRVEVNLSRI--DRHIKEgdvvVVPGKVLGGGSITKSnVVIAAWRFSRSALER 93 
                                    3....4557888888..45555546544445**********77************986 PP

>> DUF3006  Protein of unknown function (DUF3006)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   4.2e-05      0.25      14      40 ..      38      64 ..      36      76 .. 0.85
   2 ?   -0.9   0.1      0.34     2e+03      14      39 ..      92     117 ..      90     119 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.2e-05
                        DUF3006 14 eledgetidiprsdLpegakeGdvLei 40
                                   e  +++ +++++s++   +keGdv+ +
  gi|119719197|ref|YP_919692.1| 38 ERPRRKRVEVNLSRIDRHIKEGDVVVV 64
                                   44446669****************987 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.34
                        DUF3006  14 eledgetidiprsdLpegakeGdvLe 39 
                                    e  dg++  i++++L e   eG  ++
  gi|119719197|ref|YP_919692.1|  92 ERLDGRVKAISIEELLEQNPEGKNVK 117
                                    45567788899999888777776555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 886.15
//
Query:       gi|119719198|ref|YP_919693.1|  [L=283]
Description: RNA polymerase, insert [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-21   76.3   0.0    3.6e-21   75.6   0.0    1.3  1  RNA_pol_A_bac  RNA polymerase Rpb3/RpoA insert domain
    1.1e-16   60.0   0.0    1.3e-16   59.7   0.0    1.1  1  RNA_pol_L      RNA polymerase Rpb3/Rpb11 dimerisation domain


Domain annotation for each model (and alignments):
>> RNA_pol_A_bac  RNA polymerase Rpb3/RpoA insert domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.6   0.0     4e-25   3.6e-21       3     112 .]      42     158 ..      40     158 .. 0.91

  Alignments for each domain:
  == domain 1  score: 75.6 bits;  conditional E-value: 4e-25
                                    EEECTSSS.HHHHHCHHHCSTCBSSCHHHHHHHHCTT-ETSSSSTTCSEEEEEEEEESSEC...EEGGGCBES....... CS
                  RNA_pol_A_bac   3 ieentsvlqDEvvaHrlgliplvsedvleillnlkelveeeeegeeeksvelkLnvkgpge...vtagdlkle....... 72 
                                    + ents+l DE++aHrl+l+pl+ ++++     l++l    e+g++ + v+++L+ +  ++   v +g+l +e       
  gi|119719198|ref|YP_919693.1|  42 VTENTSALWDEMIAHRLALVPLKIDPETY--DALRDL-Y--EQGKDPQ-VIFSLEEEAGERprtVLSGHLRFEgiegapl 115
                                    789********************999888..9*****.3..4566665.8****9987666677**************** PP

                                    ...SSSCEESSTTSEEEEEETT-EEEEEEEEEEESSEECTTT- CS
                  RNA_pol_A_bac  73 ...dadveivnpdilIakLrkgqeleleakvkkGiGkehakfs 112
                                       +a +e+v+++i+I+kL kgq+++l+a+++ G+G++hak++
  gi|119719198|ref|YP_919693.1| 116 ppeSAGIEPVSKNIPILKLGKGQKISLTAIARMGTGRQHAKWQ 158
                                    ******************************************6 PP

>> RNA_pol_L  RNA polymerase Rpb3/Rpb11 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.7   0.0   1.5e-20   1.3e-16       2      69 .]      11     260 ..      10     260 .. 0.86

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 1.5e-20
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................................... RF
                      RNA_pol_L   2 fllrgvdhtlgNaLRrillsevpgvaiea................................................... 30 
                                    f lr+++++++NaLRr l+sevp +ai++                                                   
  gi|119719198|ref|YP_919693.1|  11 FMLRNTTPAFANALRRALISEVPILAIDEvivtentsalwdemiahrlalvplkidpetydalrdlyeqgkdpqvifsle 90 
                                    889******************************************************************99999999999 PP

                                    .......................................................................xx....... RF
                      RNA_pol_L  31 .......................................................................pv....... 32 
                                                                                                           pv       
  gi|119719198|ref|YP_919693.1|  91 eeagerprtvlsghlrfegiegaplppesagiepvsknipilklgkgqkisltaiarmgtgrqhakwqpvgPVgykykpv 170
                                    99999999999999999999999999999999988888877777777777777777777777777777666115566666 PP

                                    .....................................................xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      RNA_pol_L  33 .....................................................vkvntdkdklilevetdgslkPeealk 59 
                                                                                         v+v  d++++il+ve+ g l+Pe++l+
  gi|119719198|ref|YP_919693.1| 171 vrilredlpedealkiistcprrvfgyvdgkltvinemqcslcreceekfpgiVEVDGDPSNIILTVESIGCLPPEKLLA 250
                                    777777777777777777777777888888888888888888888888888889************************** PP

                                    xxxxxxxxxx RF
                      RNA_pol_L  60 eAlkiLkekl 69 
                                     A+++L +kl
  gi|119719198|ref|YP_919693.1| 251 VAADVLSKKL 260
                                    *******997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1956.52
//
Query:       gi|119719199|ref|YP_919694.1|  [L=147]
Description: 30S ribosomal protein S12P [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-47  158.9   0.4      4e-47  158.5   0.4    1.1  1  Ribosom_S12_S23  Ribosomal protein S12/S23


Domain annotation for each model (and alignments):
>> Ribosom_S12_S23  Ribosomal protein S12/S23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.5   0.4   2.2e-51     4e-47       1     113 [.      32     145 ..      32     146 .. 0.98

  Alignments for each domain:
  == domain 1  score: 158.5 bits;  conditional E-value: 2.2e-51
                                    --------S-TSSTTSSEEEEEEEEEEEE---TT--S-EEEEEEEET.TSEEEEEEE-SSS..----TT-EEEEEE--.. CS
                Ribosom_S12_S23   1 rkelrkktksdalegapqkrGvvlekvtveakkPnsAlRkvvrvrLikngkevtafipgegalnfldEhdevlvrGirrk 80 
                                    r+ l++k+k+d+legapq+rG+v+ekv++e+++PnsA+Rk+vrv+L kngk vtaf+pg+gal f++Ehdev+++Gi+++
  gi|119719199|ref|YP_919694.1|  32 RRILQLKKKVDPLEGAPQARGIVVEKVGIESRQPNSAVRKCVRVQLLKNGKVVTAFLPGDGALLFVNEHDEVVIEGIGGP 111
                                    567889*************************************************************************9 PP

                                    ....BTTSTTEEEEBETS---TSSSTTTTT---- CS
                Ribosom_S12_S23  81 .gkavkDlpGvrykvvkvagvslkalskykkekp 113
                                     g+a +DlpGvr+kv+kv+gvslk+  +++k+kp
  gi|119719199|ref|YP_919694.1| 112 eGRAYGDLPGVRWKVIKVNGVSLKEILRGRKQKP 145
                                    9*******************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 941.44
//
Query:       gi|119719200|ref|YP_919695.1|  [L=149]
Description: NusA family protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.5e-16   59.9   0.4    1.8e-10   40.5   0.0    2.1  2  KH_2        KH domain
    2.2e-10   40.5   1.5      8e-08   32.3   0.1    2.2  2  KH_5        NusA-like KH domain
      2e-06   27.6   0.1      5e-06   26.3   0.0    1.6  2  KH_4        KH domain
    3.4e-05   23.6   0.4       0.22   11.4   0.1    2.5  2  KH_1        KH domain
  ------ inclusion threshold ------
       0.14   12.5   0.0       0.67   10.3   0.0    1.9  2  PP-binding  Phosphopantetheine attachment site


Domain annotation for each model (and alignments):
>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.5   0.0   5.1e-14   1.8e-10       6      69 ..      19      97 ..      15     103 .. 0.87
   2 !   19.5   0.2   1.8e-07   0.00064      17      57 ..      95     137 ..      79     146 .. 0.78

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 5.1e-14
                                   HHHHTECETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTC...............EEEE CS
                           KH_2  6 laveikkagvskveIertanrviiviresqpgivIGkgGsnikkigkelrkdieklegkk...............Vkln 69
                                   l++ei+k   ++++ ++t +r i+ + ++   +++Gk+Gs+i++i++ lrkd+e++e++                V+++
  gi|119719200|ref|YP_919695.1| 19 LFEEITKVPPKDIVYDDTFQRYIFLVDKGFAPLAVGKNGSKIRMIKELLRKDVEVVEDGSsledfvksvffparvVEVK 97
                                   899**************99**************************************9988888877777775554444 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 1.8e-07
                                    EEEEEC..CSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHH CS
                           KH_2  17 kveIer..tanrviiviresqpgivIGkgGsnikkigkelrkd 57 
                                    +v++++  +++ vi v+   q g++IG++G+n+++ +  l++ 
  gi|119719200|ref|YP_919695.1|  95 EVKVREenNRKVVIAVVPPDQLGLAIGRNGRNVQRAKILLKRY 137
                                    455544325588999********************99988765 PP

>> KH_5  NusA-like KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.1   2.2e-11     8e-08      22      69 .]      52      98 ..      39      98 .. 0.96
   2 !    7.5   0.1    0.0012       4.4       4      32 ..     105     129 ..     102     136 .. 0.82

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 2.2e-11
                           KH_5 22 ivgkkGsrikavsseLkgekidvvewseDlaefianalsPaevlsVki 69
                                   +vgk+Gs+i+ +++ L  + ++vve  + l+ f++++++Pa+v +Vk+
  gi|119719200|ref|YP_919695.1| 52 AVGKNGSKIRMIKELL-RKDVEVVEDGSSLEDFVKSVFFPARVVEVKV 98
                                   69**************.9****************************86 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0012
                           KH_5   4 rtkvaVkshnpnvdpvGaivgkkGsrika 32 
                                    ++++aV   +    ++G ++g++G++++ 
  gi|119719200|ref|YP_919695.1| 105 KVVIAVVPPD----QLGLAIGRNGRNVQR 129
                                    6778888777....9************96 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.97   3.5e+03      44      56 ..      53      65 ..      31      71 .. 0.70
   2 !   26.3   0.0   1.4e-09     5e-06       4      69 ..      80     145 ..      78     148 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.97
                           KH_4 44 IGkrGrtldAlqy 56
                                   +Gk+G  ++ ++ 
  gi|119719200|ref|YP_919695.1| 53 VGKNGSKIRMIKE 65
                                   5777776665555 PP

  == domain 2  score: 26.3 bits;  conditional E-value: 1.4e-09
                           KH_4   4 vedilkalvddpeevevteeeeeeeveielnvegedlGrvIGkrGrtldAlqylvsaaankegkrv 69 
                                    +ed++k+++  +  vev+++ee++++++   v +++lG+ IG++Gr+++  + l++++   ++ rv
  gi|119719200|ref|YP_919695.1|  80 LEDFVKSVFFPARVVEVKVREENNRKVVIAVVPPDQLGLAIGRNGRNVQRAKILLKRYYGADEVRV 145
                                    899****99655699****97777777777778888***********9988888888877777666 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.1     6e-05      0.22       3      27 ..      41      65 ..      39     109 .. 0.79
   2 !   10.4   0.1   0.00012      0.45       4      24 ..     108     129 ..     105     130 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6e-05
                                   EEEEGGGHHHHHHTGGGHHHHHHHH CS
                           KH_1  3 rilvPsslvgriIGkgGsnIkeIre 27
                                    +lv++ ++++ +Gk+Gs+I+ I+e
  gi|119719200|ref|YP_919695.1| 41 IFLVDKGFAPLAVGKNGSKIRMIKE 65
                                   47999******************99 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00012
                                    E.EEGGGHHHHHHTGGGHHHHH CS
                           KH_1   4 i.lvPsslvgriIGkgGsnIke 24 
                                    i  vP ++ g+ IG++G+n+++
  gi|119719200|ref|YP_919695.1| 108 IaVVPPDQLGLAIGRNGRNVQR 129
                                    5579***************986 PP

>> PP-binding  Phosphopantetheine attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00019      0.67       2      25 ..      15      38 ..      14      40 .. 0.91
   2 ?   -0.5   0.0      0.47   1.7e+03       6      26 ..      62      82 ..      60      83 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00019
                     PP-binding  2 klrelvaevlgvpleeidpdtdlf 25
                                   ++ +l++e+++vp+++i  d+++ 
  gi|119719200|ref|YP_919695.1| 15 QIMNLFEEITKVPPKDIVYDDTFQ 38
                                   6899******************96 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.47
                     PP-binding  6 lvaevlgvpleeidpdtdlfd 26
                                   +++e+l+ ++e +++ ++l d
  gi|119719200|ref|YP_919695.1| 62 MIKELLRKDVEVVEDGSSLED 82
                                   789999999999888888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 983.56
//
Query:       gi|119719201|ref|YP_919696.1|  [L=104]
Description: ribosomal protein L7Ae/L30e/S12e/Gadd45 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.4e-20   71.2   0.1    4.7e-20   71.1   0.1    1.0  1  Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 famil


Domain annotation for each model (and alignments):
>> Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.1   0.1   2.6e-24   4.7e-20       6      93 ..       8      95 ..       3      97 .. 0.95

  Alignments for each domain:
  == domain 1  score: 71.1 bits;  conditional E-value: 2.6e-24
                                   HHHHHHHHTEEEESHHHHHHHHHTTTESEEEEETTSSSGGHHHHHHHHHH..HTTEEEEEESCHHHHHHHTTSSSECSEEEE CS
                 Ribosomal_L7Ae  6 vlkkakkagklvlGlkevtkalergeaklvilAedvepeekkkllealck..ekevpyvkvkskkeLGelvgkkrpvsalai 85
                                   +l++a k+gk+vlG ++++k+l  g+ak+vilA++++ +  ++ +++ ++   ++v++++++s k+LG++++k++ vsa+a+
  gi|119719201|ref|YP_919696.1|  8 ELQTAIKTGKVVLGSRKTIKLLSTGKAKMVILAQNAPTIIAEE-IKYKARlaGIPVYVFEGTS-KDLGAACNKPFFVSAIAV 87
                                   7899***************************************.******99999999*****.****************** PP

                                   EESTTTHH CS
                 Ribosomal_L7Ae 86 kdegdskd 93
                                    d+g+s+ 
  gi|119719201|ref|YP_919696.1| 88 LDPGESNL 95
                                   ****9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 765.58
//
Query:       gi|119719202|ref|YP_919697.1|  [L=403]
Description: DNA-directed RNA polymerase, subunit A'' [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.6e-56  189.7   0.0    8.1e-56  189.4   0.0    1.1  1  RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
  ------ inclusion threshold ------
      0.041   14.1   0.1       0.76   10.0   0.0    2.5  2  FliG_M          FliG middle domain
      0.053   13.8   0.2       0.32   11.3   0.1    2.4  2  PHA_gran_rgn    Putative polyhydroxyalkanoic acid system prot
       0.12   12.5   0.0       0.94    9.7   0.0    2.5  2  DUF2087         Uncharacterized protein conserved in bacteria


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.4   0.0   1.8e-59   8.1e-56      67     263 ..      58     337 ..       6     341 .. 0.93

  Alignments for each domain:
  == domain 1  score: 189.4 bits;  conditional E-value: 1.8e-59
                                    B--TT-BHHHHHHHHHHHHHHCCCSSTTSSTCSSTSSSSSSHHHHHHHHTT-SS-SS-EEEEEB-SSSSSCHHHCHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_5  67 lvepGeavGiiaaQSiGePgTQltlnTFHfaGvasknvtlGvprlkeilnvskniksksltvllvdeeakelekakkvkk 146
                                    lv+pGeavG++aaQSiGeP+TQ+tl+TFHfaGv + nvtlG+prl ei++  ++ +++ ++v+l +e+ak+l+ a k+++
  gi|119719202|ref|YP_919697.1|  58 LVSPGEAVGMVAAQSIGEPATQMTLRTFHFAGVRELNVTLGLPRLIEIVDLRREPSTPIMEVYLEPEHAKDLDFALKIAR 137
                                    89*****************************************************************************9 PP

                                    HHSE............................................................................ CS
                                    xxxx............................................................................ RF
                 RNA_pol_Rpb1_5 147 aiek............................................................................ 150
                                    +ie                                                                             
  gi|119719202|ref|YP_919697.1| 138 EIELttmenlcssitidyfefaivmeldpdmmenrgvtmddvinaleklkgkkgkievngntvvlytgledvtklrrmyd 217
                                    99999*************************************************************************** PP

                                    ........CBTTEEEEEEEEEEEEEEETEEEEEEECS--HHHHTTSTTTBETTTEEESSHHHHHHHHCHHHHHHHHHHHH CS
                                    ........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_5 151 ........gikkikrilvkeaekgkeeekelvletegvnlsevlkveevvdageilsndiaeileilgieaarkallkei 222
                                            g+k+i++++vk  +++k e  e+v+ teg nl++vl +e+ vd +++++n+i ei+e+lgieaar+a++kei
  gi|119719202|ref|YP_919697.1| 218 rvlnlrikGLKGIRHAIVKPVRDEKGELVEYVILTEGSNLKAVLGIEG-VDPRRTTTNNILEIYEVLGIEAARAAIIKEI 296
                                    *******************88877777789******************.******************************* PP

                                    HHHHHHTTS---HHHHHHHHHHHTTTSS---SSTTCHCCSS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_5 223 qevykvqgvsvndrHlelivdqmtkkgeivavnrsGinkae 263
                                    ++v+ ++g++v+ rH+++++d mt  g++ +v+r+G+  ++
  gi|119719202|ref|YP_919697.1| 297 KKVLDEHGLDVDWRHIMMVADAMTYSGKVRQVGRHGVAGEK 337
                                    ************************************97665 PP

>> FliG_M  FliG middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00017      0.76      34      73 ..      20      59 ..      17      61 .. 0.94
   2 ?    0.8   0.1      0.13   5.7e+02      45      67 ..     280     302 ..     278     307 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00017
                                   TS-HHHHHHHHHHHHTCCTCSHHHHHHHHHHHHHHCHHHH CS
                         FliG_M 34 eLpeelraevirriatlekvspevlkeveevLekklssvg 73
                                    Lp  lr+e+  +i++ +   +e+l+ ++e+L+++lss++
  gi|119719202|ref|YP_919697.1| 20 LLPASLRRELYDKILKAGLSRSEALSVINEALRRYLSSLV 59
                                   69***********************************986 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.13
                                    HHHHTCCTCSHHHHHHHHHHHHH CS
                         FliG_M  45 rriatlekvspevlkeveevLek 67 
                                    + ++ +e    +++ke+++vL +
  gi|119719202|ref|YP_919697.1| 280 YEVLGIEAARAAIIKEIKKVLDE 302
                                    667778889999********987 PP

>> PHA_gran_rgn  Putative polyhydroxyalkanoic acid system protein (PHA_gran_rgn)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.99   4.4e+03      45      60 ..     187     202 ..     177     207 .. 0.79
   2 ?   11.3   0.1     7e-05      0.32       9      49 ..     283     335 ..     278     373 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.99
                   PHA_gran_rgn  45 sgvdGqlevepdkvrl 60 
                                    +g +G++ev+ ++v l
  gi|119719202|ref|YP_919697.1| 187 KGKKGKIEVNGNTVVL 202
                                    5779999999999877 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 7e-05
                   PHA_gran_rgn   9 LgleeAreraeelaekleeefglelewe.....gdtlkfkrs.......gvdG 49 
                                    Lg+e+Ar+++ + ++k+ +e+gl++ w+      d ++++++       gv G
  gi|119719202|ref|YP_919697.1| 283 LGIEAARAAIIKEIKKVLDEHGLDVDWRhimmvADAMTYSGKvrqvgrhGVAG 335
                                    89**************************9999988888888877776665555 PP

>> DUF2087  Uncharacterized protein conserved in bacteria (DUF2087)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00021      0.94      28      55 ..       4      32 ..       1      42 [. 0.91
   2 ?   -1.2   0.0      0.52   2.3e+03      33      51 ..     194     215 ..     166     216 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00021
                        DUF2087 28 eysEkevneiLkevhd.DhatlRReLvda 55
                                     sE+e+   ++++h+  +a lRReL d+
  gi|119719202|ref|YP_919697.1|  4 PISEEELWNEIEKYHElLPASLRRELYDK 32
                                   679***********************996 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.52
                        DUF2087  33 evneiLkevhd...DhatlRRe 51 
                                    evn +   +++   D+  lRR+
  gi|119719202|ref|YP_919697.1| 194 EVNGNTVVLYTgleDVTKLRRM 215
                                    6664444444445599999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      624  (0.0348039); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 2961.35
//
Query:       gi|119719203|ref|YP_919698.1|  [L=888]
Description: DNA-directed RNA polymerase subunit A' [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.9e-95  318.8   0.0    5.8e-95  318.2   0.0    1.3  1  RNA_pol_Rpb1_1  RNA polymerase Rpb1, domain 1
    6.2e-77  257.5   0.0    9.4e-77  256.9   0.0    1.3  1  RNA_pol_Rpb1_2  RNA polymerase Rpb1, domain 2
    1.1e-37  129.4   0.0    1.7e-37  128.8   0.0    1.3  1  RNA_pol_Rpb1_3  RNA polymerase Rpb1, domain 3
    2.9e-30  104.4   0.0    6.7e-30  103.2   0.0    1.6  1  RNA_pol_Rpb1_4  RNA polymerase Rpb1, domain 4
    3.2e-25   89.1   0.0    7.8e-25   87.8   0.0    1.6  2  RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
  ------ inclusion threshold ------
      0.017   15.2   1.3          3    8.0   0.1    2.8  2  Zn-ribbon_8     Zinc ribbon domain
      0.089   12.8   2.2        6.3    6.9   0.3    2.4  2  DZR             Double zinc ribbon
       0.68    9.4   6.4       0.35   10.3   0.2    2.9  3  zf-ribbon_3     zinc-ribbon domain
        1.1    9.3   4.4        1.7    8.7   0.0    2.7  3  CpXC            CpXC protein


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb1_1  RNA polymerase Rpb1, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  318.2   0.0   2.9e-98   5.8e-95       2     312 .]       8     317 ..       7     317 .. 0.93

  Alignments for each domain:
  == domain 1  score: 318.2 bits;  conditional E-value: 2.9e-98
                                    E---EEEEEE--HHHHHHH-SBB--STTSTCSTSSSSBBSSSSSSSSS-SSSSSTSTTTSSTTTT-----EEEEEECEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_1   2 kkikeiqfgiaspeeirkwSvvevtkaetieekslkPeegGllDerlgtidkdleCetCgkkkkeCeghfGhieLakPvf 81 
                                    k +  i+fgi+spe irk++v +++++e+++e+  +P +gGl+D r+g+i+    C+tCg+ +++C+ghfG+ieLa+Pv+
  gi|119719203|ref|YP_919698.1|   8 KIVAGIKFGILSPEMIRKIAVLRIETSELYDEEG-FPIPGGLMDRRMGSIEPGAVCQTCGNRFTNCPGHFGYIELARPVI 86 
                                    67899**************************995.********************************************* PP

                                    -HHHHHHHHHHCTTCETTTTEBSS-TTSH....HHHHHHCSSSCC......CCHHHHHHHHCCS-BE-SSSSB-EEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_1  82 higffklilkilecvckecskllldeekkkllsklkkrekleelk......krlkaieelckkinlcekCgavqpkleee 155
                                    h  f  +i  +l+ +c++c++l l eek    +k kkr ++ + k      k ++ + +   k ++c +Cg  +p+++  
  gi|119719203|ref|YP_919698.1|  87 HPSFAPYIAILLKATCNRCGRLKLPEEKI---NKAKKRMEVYSAKwpslktKYANTLLKEAAKATVCPHCG--APQYKIR 161
                                    *************************9987...333333333333355555667777888888889999***..8999999 PP

                                    TTEEEEEESSSSTSCEEEE-HHHHHHHHHCSTHHHHHHTTSBTTTB-GGGCCECCEEE--GGGS-BEESSSSSEEBECCC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_1 156 geklkaalkkskeeekeklsaekvkkllkriededvevlgfkssgsrPewliltvlPVpPpeiRPsvqldggrrsedDlt 235
                                      k ++  ++++e    kl++ ++ + l+ri++ d++v g++++++rPew++l+v+PV+Pp++RPs++l++g rsedDlt
  gi|119719203|ref|YP_919698.1| 162 LDKPYTFYEEREE-GLVKLTPLEIWERLSRIPEGDLRVVGIDPKEARPEWMVLRVIPVVPPSVRPSITLESGDRSEDDLT 240
                                    9999998888887.99**************************************************************** PP

                                    CHHHHHHHHHHHHHHHHHSSSSSTCHHHHHHHHHHHHHHCC-TTSSSSSEEBSTTSSS--THHHHHTSSSSCCCCCT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_1 236 eklrdiikrNnrLkkaeeegapeliieeekelLQehvatlfdneisglkpatqkskrplkslsqrLkGKeGrfRgnL 312
                                    +kl+dii+ N+rLk+++++g p+l+ie+ ++lLQ+hvat+fdne +g++pa+++s+rpl++l qrLkGKeGrfRg+L
  gi|119719203|ref|YP_919698.1| 241 HKLVDIIRVNQRLKENIDAGSPSLVIEDLWNLLQFHVATYFDNELPGIPPARHRSGRPLRTLAQRLKGKEGRFRGSL 317
                                    ***************************************************************************98 PP

>> RNA_pol_Rpb1_2  RNA polymerase Rpb1, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  256.9   0.0   4.7e-80   9.4e-77       1     166 []     319     486 ..     319     486 .. 0.98

  Alignments for each domain:
  == domain 1  score: 256.9 bits;  conditional E-value: 4.7e-80
                                    SEEESSEEEEEEEEESSS-TTEEEEEHHHHTTSEEEEE-STTTHHHHHHHHHHTTTSSSSEEEEESTTSSEEETTTT-S. CS
                 RNA_pol_Rpb1_2   1 GkrvdysaRsvispdpnlkldevgvPisvakkltvpeivtelnikklrklvengpevyPgasyvkredgsekklkakkr. 79 
                                    Gkrvd+s+R+vispdpnl+++evgvPi vak+ltvpe+vt++ni+klrklv+ngp+v+Pga+y+++ dgs+ +l++ k+ 
  gi|119719203|ref|YP_919698.1| 319 GKRVDFSSRTVISPDPNLSINEVGVPIDVAKVLTVPEKVTPWNIEKLRKLVINGPDVWPGANYIIKPDGSRIDLRYVKHr 398
                                    9***************************************************************************9884 PP

                                    .CHHCCTTTTSEEEEE--TTSEEEEE-SSTTSGGGEEEEEEEEESSSSEEEEGGGHCCCT--SSS-EEEEE--SSHHHHH CS
                 RNA_pol_Rpb1_2  80 .klakelekgdiverhvkdgdvvllNRqPsLhklsimahrvkvlekktlrlnlsvttayNaDFDGDemnlhlpqseeara 158
                                     +++++l+ g+iverh++dgdvvl+NRqPsLh++simah vkvl++kt+rlnl+vt +yNaDFDGDemnlh+pqseeara
  gi|119719203|ref|YP_919698.1| 399 eEISQTLKPGYIVERHLMDGDVVLFNRQPSLHRISIMAHIVKVLPYKTFRLNLLVTIPYNADFDGDEMNLHVPQSEEARA 478
                                    3499**************************************************************************** PP

                                    HHHHCSBT CS
                 RNA_pol_Rpb1_2 159 Eaeelllv 166
                                    Ea+el+lv
  gi|119719203|ref|YP_919698.1| 479 EARELMLV 486
                                    ******86 PP

>> RNA_pol_Rpb1_3  RNA polymerase Rpb1, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.8   0.0   8.5e-41   1.7e-37       1     155 [.     489     653 ..     489     655 .. 0.93

  Alignments for each domain:
  == domain 1  score: 128.8 bits;  conditional E-value: 8.5e-41
                                    CSEETTTTEESSS--THHHHHHHHHSSTTEEEEHHHHHHHHHHSSSCCSSSSSSSSSBESSSEBEEHHHHHHCCCHCCCC CS
                 RNA_pol_Rpb1_3   1 nilspqsgkPvigivQDsllGvyllTkedvfidreeaqqllykgvgsdsktvtlrpailkpkelwtgkqtfsrilpnein 80 
                                    +i++p+ g P+ig  +D ++G+yllT++d+++d++ a++lly g+       +++pai+kp + wtgkq++s++lp+ +n
  gi|119719203|ref|YP_919698.1| 489 HIMTPRYGAPIIGGLHDYISGSYLLTRKDALLDKKSALRLLYIGNNC---DPLVEPAIIKPGPYWTGKQIVSMFLPKGLN 565
                                    79******************************************444...458************************999 PP

                                    EEEE...SSSS............STSEEECSSEEEES--SHHHHSSSSTTSHHHHHHHHCHHHHHHHHHHHHHHHHHHHH CS
                 RNA_pol_Rpb1_3  81 yerk...neek............dgkvlikngelikGvidkkvvgkksqgslihvlakeygiketvrfldslqrlgfkyl 145
                                    y +                    dg+vlik+g l+ Gv dk+++g++++g ++h++++e+g++++++++d + +++++yl
  gi|119719203|ref|YP_919698.1| 566 YVGRasvA--PasgkcdeeycenDGYVLIKDGKLLLGVFDKQAIGAEKHGTVLHEIVREFGVEKAKELMDGMFKVFIAYL 643
                                    99976541..1556677799999********************************************************* PP

                                    HHHCEB-TGG CS
                 RNA_pol_Rpb1_3 146 lqsgftigig 155
                                     ++gft+g++
  gi|119719203|ref|YP_919698.1| 644 DMHGFTMGVD 653
                                    ********98 PP

>> RNA_pol_Rpb1_4  RNA polymerase Rpb1, domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.2   0.0   3.3e-33   6.7e-30       2     108 .]     681     786 ..     680     786 .. 0.97

  Alignments for each domain:
  == domain 1  score: 103.2 bits;  conditional E-value: 3.3e-33
                                    HHHCTHTCCHHHTTHCHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTTSHHHHHHHCTSSS-HHHHHHHHTB-EEEEBTTB CS
                 RNA_pol_Rpb1_4   2 eeaerygkledlpgksleelfeakinkilnkardkagkiaskslaasNsiliMvksGaKGsiinisqiagclGqqnvegk 81 
                                     ++e+ g+l+++pgk+ +e++e++i+++l +ar +ag++ sk+l   N+ +iM+k+Ga+Gs++n++q+a+++Gqq+v+gk
  gi|119719203|ref|YP_919698.1| 681 RQYES-GELQPMPGKTRKETLEDLIMNVLAEARTRAGEVTSKHLGLLNHAVIMAKTGARGSMLNLTQMAAVVGQQSVRGK 759
                                    56788.9**************************************55********************************* PP

                                    SS--SSTSCSSTTSSSSESSTTTSSEE CS
                 RNA_pol_Rpb1_4  82 ripkgfsgrtlphfkkidespesrGFv 108
                                    ri +g++gr+lphf k d sp ++GFv
  gi|119719203|ref|YP_919698.1| 760 RIERGYTGRALPHFVKGDLSPLAKGFV 786
                                    **************************8 PP

>> RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0       3.8   7.6e+03     200     217 ..     614     631 ..     574     634 .. 0.67
   2 !   87.8   0.0   3.9e-28   7.8e-25       1      66 [.     793     858 ..     793     880 .. 0.95

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 3.8
                                    SSHHHHHHHHCHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_5 200 ndiaeileilgieaarka 217
                                      ++ei++ +g+e+a++ 
  gi|119719203|ref|YP_919698.1| 614 TVLHEIVREFGVEKAKEL 631
                                    368999999999999876 PP

  == domain 2  score: 87.8 bits;  conditional E-value: 3.9e-28
                                    B--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTEEEETTSEEEETTS-EEESSGGGTS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb1_5   1 GLkvkefffhtmggReGLiDtAvkTaesGYlqRrlvkaledvvvkyddtvrnsggeivqflygedg 66 
                                    GL++ efffh+  gReGL+DtAv+Ta+sGY+ Rrl  a++d  v+yd+tvrns+g i+qf yged+
  gi|119719203|ref|YP_919698.1| 793 GLSPVEFFFHAISGREGLVDTAVRTAQSGYMYRRLQSAMQDFYVSYDGTVRNSEGMIIQFRYGEDS 858
                                    9***************************************************************97 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1     0.015        29       8      34 ..      62     107 ..      60     112 .. 0.68
   2 ?    8.0   0.1    0.0015         3      23      34 ..     143     155 ..     138     160 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.015
                    Zn-ribbon_8   8 CeeCghefe..............vlqsisdap.....lta.CPeCgs 34 
                                    C+ Cg++f+              v+++++  p     l+a C +Cg 
  gi|119719203|ref|YP_919698.1|  62 CQTCGNRFTncpghfgyielarpVIHPSFA-PyiailLKAtCNRCGR 107
                                    9*******9888877777666655554443.2477775555888886 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0015
                    Zn-ribbon_8  23 daplta.CPeCgs 34 
                                    +a++ + CP+Cg+
  gi|119719203|ref|YP_919698.1| 143 EAAKATvCPHCGA 155
                                    4455555*****9 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.3    0.0032       6.3      14      38 ..      61     109 ..      56     118 .. 0.87
   2 ?    5.0   0.1     0.012        25      22      37 ..     141     156 ..     133     161 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0032
                            DZR  14 fCseCgtklkavaa........................edrCpsCgekv 38 
                                    +C++Cg++  + +                         + +C +Cg+  
  gi|119719203|ref|YP_919698.1|  61 VCQTCGNRFTNCPGhfgyielarpvihpsfapyiaillKATCNRCGRLK 109
                                    7*******988777899****************************9974 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.012
                            DZR  22 lkavaaedrCpsCgek 37 
                                    lk++a++++Cp+Cg++
  gi|119719203|ref|YP_919698.1| 141 LKEAAKATVCPHCGAP 156
                                    5555556777777665 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.2       1.2   2.3e+03      18      25 ..      61      68 ..      60      69 .. 0.69
   2 ?    1.3   0.1      0.12   2.4e+02       3      12 ..     100     110 ..      99     116 .. 0.73
   3 ?   10.3   0.2   0.00018      0.35      16      25 ..     147     156 ..     144     157 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.2
                    zf-ribbon_3 18 vCpyCGtk 25
                                   vC  CG +
  gi|119719203|ref|YP_919698.1| 61 VCQTCGNR 68
                                   67778865 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.12
                    zf-ribbon_3   3 vrCPnCGa.pl 12 
                                     +C++CG  +l
  gi|119719203|ref|YP_919698.1| 100 ATCNRCGRlKL 110
                                    58*****7555 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00018
                    zf-ribbon_3  16 dnvCpyCGtk 25 
                                    ++vCp+CG++
  gi|119719203|ref|YP_919698.1| 147 ATVCPHCGAP 156
                                    7999999987 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.2         4     8e+03      39      47 ..      61      69 ..      60      71 .. 0.60
   2 ?    1.6   0.1      0.14   2.7e+02      35      53 ..      97     115 ..      95     126 .. 0.79
   3 ?    8.7   0.0   0.00083       1.7      15      68 ..     125     181 ..     117     199 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 4
                           CpXC 39 tCpkCgata 47
                                   +C+ Cg+++
  gi|119719203|ref|YP_919698.1| 61 VCQTCGNRF 69
                                   566676655 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.14
                           CpXC  35 lfeatCpkCgatakleapl 53 
                                    l++atC +Cg+   +e ++
  gi|119719203|ref|YP_919698.1|  97 LLKATCNRCGRLKLPEEKI 115
                                    6799******998877665 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.00083
                           CpXC  15 wtsidadedpelkeklldgslfeatCpkCga...takleapllyhdpekellillvp 68 
                                    +    ++ + ++++ ll++    ++Cp+Cga   +++l+ p  + ++++e l+ l+p
  gi|119719203|ref|YP_919698.1| 125 YSAKWPSLKTKYANTLLKEAAKATVCPHCGApqyKIRLDKPYTFYEEREEGLVKLTP 181
                                    555556677889999**************9633367888888877777777766666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (888 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.74u 0.30s 00:00:01.04 Elapsed: 00:00:00.47
# Mc/sec: 5695.07
//
Query:       gi|119719204|ref|YP_919699.1|  [L=1130]
Description: DNA-directed RNA polymerase subunit B [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   2.2e-121  405.6   0.0     3e-121  405.2   0.0    1.2  1  RNA_pol_Rpb2_6   RNA polymerase Rpb2, domain 6
    1.4e-53  181.5   0.0      2e-53  181.0   0.0    1.2  1  RNA_pol_Rpb2_1   RNA polymerase beta subunit
    7.3e-33  113.8   0.0    1.2e-32  113.1   0.0    1.3  1  RNA_pol_Rpb2_2   RNA polymerase Rpb2, domain 2
    3.3e-30  104.3   0.0    7.4e-30  103.2   0.0    1.6  1  RNA_pol_Rpb2_7   RNA polymerase Rpb2, domain 7
      4e-29  100.6   0.1    1.7e-28   98.6   0.1    2.1  2  RNA_pol_Rpb2_3   RNA polymerase Rpb2, domain 3
    3.1e-23   81.8   0.9    7.1e-23   80.7   0.9    1.7  1  RNA_pol_Rpb2_4   RNA polymerase Rpb2, domain 4
    7.2e-11   42.5   0.8    2.2e-10   40.9   0.8    1.8  1  RNA_pol_Rpb2_5   RNA polymerase Rpb2, domain 5
  ------ inclusion threshold ------
      0.086   13.1   0.4       0.51   10.6   0.2    2.4  2  RNA_pol_Rpb2_45  RNA polymerase beta subunit external 1 domai
       0.19   11.5   1.3       0.37   10.6   1.3    1.4  1  YdjO             Cold-inducible protein YdjO


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb2_6  RNA polymerase Rpb2, domain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  405.2   0.0  1.5e-124    3e-121       2     390 .]     658    1031 ..     657    1031 .. 0.96

  Alignments for each domain:
  == domain 1  score: 405.2 bits;  conditional E-value: 1.5e-124
                                     HHT-SS-TTB-HHHHHHHHHHGGGB-S---TTTTT---SSEEEESS----SSB-S.TTTTTS........GGGS-SEE CS
                 RNA_pol_Rpb2_6    2 aklapvvehvqspriiiqaamekqalgiyslnkfkrsnqktyllcinqkPlvktgdkveagqvldgpatekgelalGq 79  
                                     a  +p++e++qspr+ +qaam+kq+lgi ++n   r++ ++++++++qkPlvkt+   +++          ++l+ G+
  gi|119719204|ref|YP_919699.1|  658 AMTIPFIEYNQSPRNSYQAAMAKQSLGIPHYNFKLRMDPRMHVMYYPQKPLVKTR-IFDLLP--------LDNLPYGT 726 
                                     7889***************************************************.999999........******** PP

                                     EEEBBBS--TTTTTTT-EEEBCHHHHTTTT-EEEEEE..EEE--SSSS---.-S--..-.......-SS-GGGS-T.T CS
                 RNA_pol_Rpb2_6   80 navVAvmsyeGYniEDaiilnerlvdrdvftsihikeyeveardtklgeeeitrdipnv.......seealkkLde.d 149 
                                     n+vVAv++  GYni Da+++n+++++r++ +s+++++ye e r++++g e+ +++++ +         +a++ +d  d
  gi|119719204|ref|YP_919699.1|  727 NMVVAVLTGGGYNIQDAVVINKAAIERGMSRSVFFRTYEAEERRYPGGLEDRFEKPSLEkdlldvkPPQAYEAIDPvD 804 
                                     *************************************************99999998778999999999*****9548 PP

                                     SB--SS-EEETT-EEE---..B-----...-----------..-B---EE--TT-EEEEEEEEE.......EE-TT-- CS
                 RNA_pol_Rpb2_6  150 GivrvgaevkegdilvgkvtkgeteltpeekllraifgekarevkdtslrvksgeegvVdkvkvfsrekgdelkagvn 227 
                                     Gi +v+ae+  g+ +v+++  ++ ++      +++ + +  ++ kdtsl +++ge+g++d+v +        +++g++
  gi|119719204|ref|YP_919699.1|  805 GIAYVEAELYGGQAVVSRT--SPPRFY-----TSTLEPRVMTKRKDTSLLLRHGEKGIIDRVFI-------MESPGGI 868 
                                     ******************8..666665.....4455556666679*******************.......799**** PP

                                     EEEEEEEEEEE---TT-BEEETTS---BBEEEB-TTTSEEETTS---SEEE-GGGCHHH-BTTHHHHHHHHHCCCSSS CS
                 RNA_pol_Rpb2_6  228 klvkvyvaqkRklqvGDKfasrhGqKGvvslilpqeDmPfledGivvDivlNPlgvPSRmtigqllEtllgkaaaleg 305 
                                     kl+kv+v++ R  ++GDKfasrhGqKGvv++++pqeDmPf+e+Gi++D+++NP+++PSRmt+gqllE + gkaaal g
  gi|119719204|ref|YP_919699.1|  869 KLAKVRVRDLRPTELGDKFASRHGQKGVVGMLVPQEDMPFTEEGITPDLIINPHAIPSRMTVGQLLEAITGKAAALAG 946 
                                     ****************************************************************************** PP

                                     S--B--TT-...-HHHHHHHHHTTS-TT-EE-EEETTTS-B-SS-EEB-EEEEEEBS--CCCS----SS--B-TTT-- CS
                 RNA_pol_Rpb2_6  306 kkvdatvFdgakeeeikelLeeagleasGkevlydGrtGekleaeifvGviYylkLkhlvedKihaRstGpyslltqQ 383 
                                     +++dat+F+  + +ei+e L++ g++++GkevlydG+tGekleaeif+Gv+Yy kL+hlv+dK+haR++G+++ lt+Q
  gi|119719204|ref|YP_919699.1|  947 RRIDATAFEPPSLDEIREILRSYGFRSDGKEVLYDGVTGEKLEAEIFIGVVYYEKLHHLVADKMHARARGRVQILTRQ 1024
                                     *********8889***************************************************************** PP

                                     B-SCGGG CS
                 RNA_pol_Rpb2_6  384 PlgGkaq 390 
                                     P++G+a+
  gi|119719204|ref|YP_919699.1| 1025 PTEGRAR 1031
                                     *****96 PP

>> RNA_pol_Rpb2_1  RNA polymerase beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.0   0.0   9.9e-57     2e-53       1     202 [.      27     398 ..      27     399 .. 0.98

  Alignments for each domain:
  == domain 1  score: 181.0 bits;  conditional E-value: 9.9e-57
                                    CTTHHHHHHHHHHHHTHHHHHCTTSSECCHCSSSHCSSSCEEEEEEEEEEESCSSECTTSCEEES.HHHHHHCTSBXEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb2_1   1 gLvsqqldSFnkfveqdlekiikeeaaieseeeiqssgeelelkfvsirlgkPvvdesdasereiyPkearlrnltYsap 80 
                                    gLv+q+ldSFn+f+e  l++i++e   i++e++       +e+kf++i +g+P+++e+d+s+ +++P+ arlrn+tY ap
  gi|119719204|ref|YP_919699.1|  27 GLVRQHLDSFNAFLERGLQEIVDEVGGIKVESQG------VEIKFGKIEVGQPTFREADGSDLALTPMIARLRNITYAAP 100
                                    69****************************9997......8*************************************** PP

                                    EEEEEEEEECCCCTCCEEEEEEEEEEEEEXBTTSTTSSSTTS..HHHHHHTTS.TTS..SSEEETTCEEEEXEEEE.... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.... RF
                 RNA_pol_Rpb2_1  81 lyvklklvvyekdnkeeikeeevyiGelPlMlrskacvlsea.seeelvelkEcpldqGGyFiinGtekvivaqek.... 155
                                    ly+ ++l v    ++ee + e vyiG lP+M++sk+cvl+++ se+e+v+ +E+p+d+GGyFi+nG+e+viv+qe+    
  gi|119719204|ref|YP_919699.1| 101 LYLTMTLYV----DGEERRTESVYIGSLPIMVKSKKCVLYGLkSEDEIVKYGEDPYDPGGYFIVNGSERVIVMQEDlsvn 176
                                    *********....8*************************99626889********************************* PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                 RNA_pol_Rpb2_1 156 ................................................................................ 155
                                                                                                                    
  gi|119719204|ref|YP_919699.1| 177 rvlvdyggasgsvthtakvfsvaagqrspltvertkdgmiyasfpacpskipvvvlmralglktdqeiayaigndpiiqq 256
                                    ******************************************************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                 RNA_pol_Rpb2_1 156 ................................................................................ 155
                                                                                                                    
  gi|119719204|ref|YP_919699.1| 257 eflpvlmeqskiaatpeealdyigsrvspgqprnvrieraqavldenllphigrgpaariskaffvgqmvsrllelklgm 336
                                    ******************************************************************************** PP

                                    ...............XHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSSSSSHHHHSCSHHHH CS
                                    ...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                 RNA_pol_Rpb2_1 156 ...............laGeLlaslfrvllkklerdvkerlqksleklddlmlqllvnakpit 202
                                                    aGeL+a++fr+++++l++++  +++++  k +d++l  +v+ + it
  gi|119719204|ref|YP_919699.1| 337 rgpddkdhlankrirQAGELIAQVFRSAFRQLVKEMTYSIERHTSKTRDINLVSIVRPDIIT 398
                                    ********************************************************999998 PP

>> RNA_pol_Rpb2_2  RNA polymerase Rpb2, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.1   0.0     6e-36   1.2e-32      17     190 .]     192     351 ..     163     351 .. 0.89

  Alignments for each domain:
  == domain 1  score: 113.1 bits;  conditional E-value: 6e-36
                                    SSSCCEECCCEEEEECCCCSTSCEEEEECTTSSSEEEHHHHHHHTT--STTHHHHHHTSSSTTHHHHHHHHHHHHHHCTS CS
                 RNA_pol_Rpb2_2  17 satvtsslisqrgsvlklekdgktliwtriskkrkipivivlkAlglvsdreIlericydsedsqlleelleeleekeei 96 
                                     a+v s+ + qr+ +++++++++ ++++ +   +kip+v++++Algl +d+eI ++i    +d+ +++e+l+ l e+++i
  gi|119719204|ref|YP_919699.1| 192 TAKVFSVAAGQRSPLTVERTKDGMIYASFPACPSKIPVVVLMRALGLKTDQEIAYAIG---NDPIIQQEFLPVLMEQSKI 268
                                    5789999999**********************************************99...8************999998 PP

                                    S.SCHHHHHHHHHCSSTTSSSCCCCCHHHHHHHCHHHHHHHTTTTSSTTTTTSSSTCHH...HHHHHHHHHHHHHHHHTT CS
                 RNA_pol_Rpb2_2  97 q.tqeealdyigkvvalrrgeearlqsareilqkrydlgeigreklnkhlglseslenkr.lkaqdilymidrLlslklg 174
                                    + t eealdyig++v  ++++++r+++a+ +l+          e+l++h+g        r  ka++++ m+ rLl+lklg
  gi|119719204|ref|YP_919699.1| 269 AaTPEEALDYIGSRVSPGQPRNVRIERAQAVLD----------ENLLPHIGRGPA---ARiSKAFFVGQMVSRLLELKLG 335
                                    5389***************************94..........67777*******...4558****************** PP

                                    SSSS--TTSGGGEEEE CS
                 RNA_pol_Rpb2_2 175 rrevDDiDhlgnkRvr 190
                                    +r +DD+Dhl+nkR+r
  gi|119719204|ref|YP_919699.1| 336 MRGPDDKDHLANKRIR 351
                                    **************97 PP

>> RNA_pol_Rpb2_7  RNA polymerase Rpb2, domain 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.2   0.0   3.7e-33   7.4e-30       1      86 [.    1033    1124 ..    1033    1125 .. 0.98

  Alignments for each domain:
  == domain 1  score: 103.2 bits;  conditional E-value: 3.7e-33
                                     BBEEEEHHHHHHHHHHTBHHHHHHHHTTTTTEEEEEEESSSSSCCCEE......EBTTTTCSSSEEEEEEEHHHHHHH CS
                 RNA_pol_Rpb2_7    1 GGlrfGEMErdaliayGaaalLkerltikSDavevdvcgrckllaaan......eCkivkseekiekveipeafklLl 72  
                                     GGlrfGEME+d+l+++Ga++lL+erl+++SD+++++vc++c+ + + +       C+++ ++ ++++ve+++afklLl
  gi|119719204|ref|YP_919699.1| 1033 GGLRFGEMEKDCLVGHGASMLLRERLLESSDKTTIWVCENCGYMGWFDarkntpVCPVCGDKGRLSPVEVSYAFKLLL 1110
                                     9*********************************************999***************************** PP

                                     HHHHHTTBEEEEES CS
                 RNA_pol_Rpb2_7   73 qeLqslgialklll 86  
                                     qeL++lg++++l+l
  gi|119719204|ref|YP_919699.1| 1111 QELTGLGLSVRLIL 1124
                                     **********9976 PP

>> RNA_pol_Rpb2_3  RNA polymerase Rpb2, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.6   0.1   8.5e-32   1.7e-28       1      67 [.     419     482 ..     419     483 .. 0.98
   2 ?   -1.8   0.0       1.9   3.7e+03      30      43 ..     871     884 ..     862     885 .. 0.83

  Alignments for each domain:
  == domain 1  score: 98.6 bits;  conditional E-value: 8.5e-32
                 RNA_pol_Rpb2_3   1 qvldrlnplselshlrrvsslrgglskerkttevRdlhpshwGriCpveTPEGencGlvksLallar 67 
                                    q+ldr+n+ls++shlrrv s+   ls+++ ++e+R+lhp++wGr+Cpve+PEG+ncGlvk+Lalla 
  gi|119719204|ref|YP_919699.1| 419 QILDRTNYLSTISHLRRVVSP---LSRTQPHFEARELHPTQWGRLCPVESPEGQNCGLVKHLALLAT 482
                                    89*******************...****************************************985 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.9
                 RNA_pol_Rpb2_3  30 kttevRdlhpshwG 43 
                                    ++ +vRdl+p+  G
  gi|119719204|ref|YP_919699.1| 871 AKVRVRDLRPTELG 884
                                    6789******9987 PP

>> RNA_pol_Rpb2_4  RNA polymerase Rpb2, domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.7   0.9   3.6e-26   7.1e-23       1      62 []     518     589 ..     518     589 .. 0.99

  Alignments for each domain:
  == domain 1  score: 80.7 bits;  conditional E-value: 3.6e-26
                                    EECTT-BEEE-S-HCCHHHHHHHHCCTTSS-TT-EEEE-TT..........T--EEEE-SSEEB-EEEEE-S CS
                 RNA_pol_Rpb2_4   1 VfvNGrllGvtrdpkklvetlRelRRkgkiseevsivlnek..........qkevkiatDgGRvcRPliiVe 62 
                                    V++NGrl+G+++d+k l+etlR+lRR+g+is+ev+++++++           +ev++++D+GR++RPli+Ve
  gi|119719204|ref|YP_919699.1| 518 VYLNGRLIGYVEDGKGLAETLRKLRREGRISHEVNVAFYSHeytvggvkgrIEEVYVNCDAGRIRRPLIVVE 589
                                    9**********************************************************************7 PP

>> RNA_pol_Rpb2_5  RNA polymerase Rpb2, domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   0.8   1.1e-13   2.2e-10       1      56 [.     610     648 ..     610     650 .. 0.88

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 1.1e-13
                                    HHHHHHTTSEEEEEHHHHTT--EESSTTTCSST-SSTTTSS--TTSSSST-SEEES CS
                 RNA_pol_Rpb2_5   1 wddLlregvvEylDaeEEetamIamtpedleksreekealeekenskshtyTHcEI 56 
                                    w+dL+++g+vEylDaeEEe+a+Ia ++++l+ +                 +TH+EI
  gi|119719204|ref|YP_919699.1| 610 WSDLIENGIVEYLDAEEEENAYIATDVSELTPQ-----------------HTHLEI 648
                                    ******************************876.................455555 PP

>> RNA_pol_Rpb2_45  RNA polymerase beta subunit external 1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.2   0.00026      0.51      12      32 ..     619     639 ..     611     649 .. 0.83
   2 ?   -2.1   0.0       2.5     5e+03      36      56 ..    1003    1023 ..     999    1025 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00026
                                    EEEEEHHHHTTSEEE-SSS-B CS
                RNA_pol_Rpb2_45  12 vvYLtAdeEekyviAqAnapl 32 
                                    v+YL A+eEe+ +iA   ++l
  gi|119719204|ref|YP_919699.1| 619 VEYLDAEEEENAYIATDVSEL 639
                                    89*************866666 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.5
                                     SCBSSSEEEEECSSCEEEEEG CS
                RNA_pol_Rpb2_45   36 grfveerVlaRrkgevelvep 56  
                                      ++v ++ +aR +g v++ ++
  gi|119719204|ref|YP_919699.1| 1003 HHLVADKMHARARGRVQILTR 1023
                                     57899******9999988775 PP

>> YdjO  Cold-inducible protein YdjO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.3   0.00018      0.37      14      47 ..    1063    1093 ..    1055    1096 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00018
                           YdjO   14 eetkvWeCtsedCngWmRdnFsfeeePtCplCks 47  
                                      +t++W C++ +  gW     + +++P+Cp+C+ 
  gi|119719204|ref|YP_919699.1| 1063 DKTTIWVCENCGYMGWFD---ARKNTPVCPVCGD 1093
                                     58*******999999974...46789******85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.79u 0.28s 00:00:01.07 Elapsed: 00:00:00.48
# Mc/sec: 7059.87
//
Query:       gi|119719205|ref|YP_919700.1|  [L=80]
Description: DNA-directed RNA polymerase subunit H [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-30  104.5   0.0    2.1e-30  104.4   0.0    1.0  1  RNA_pol_Rpb5_C  RNA polymerase Rpb5, C-terminal domain
     0.0025   17.6   0.2      0.014   15.2   0.2    1.9  1  PASTA           PASTA domain


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb5_C  RNA polymerase Rpb5, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.4   0.0   2.3e-34   2.1e-30       1      73 []       5      77 ..       5      77 .. 0.99

  Alignments for each domain:
  == domain 1  score: 104.4 bits;  conditional E-value: 2.3e-34
                                   ..-TSSSS--EEEEE-HHHHHHHHHHTT--TTCSS-EETTSHHHHCCT--TTSEEEEEEEETTTEEEEEEEEE CS
                 RNA_pol_Rpb5_C  1 vnitkHelvPkhevlseeekkellkklkikeeqLPkisksDpvarylglkkGdvvkItrksetageavtYRlV 73
                                   +++++HelvPkh++ls+ee+++llk +++k+++LP+i+++Dpvar+l++k+Gdv+ I+r+s+tage+v++RlV
  gi|119719205|ref|YP_919700.1|  5 FDVLEHELVPKHVLLSKEEANRLLKAMGLKKSELPWIYSTDPVARALKAKPGDVIMIIRQSPTAGESVAFRLV 77
                                   69**********************************************************************9 PP

>> PASTA  PASTA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.2   1.6e-06     0.014       9      51 ..      19      72 ..      13      74 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.6e-06
                                   SBHHHHHHHHHHTT-.......-CCCEEE..ECTCCGTTB..EEEECS-TTSEE CS
                          PASTA  9 msvdeAkatLkalGl.......kiktvee..tsddvpeGt..VisQsPeaGtev 51
                                   +s++eA ++Lka Gl        ++t+++    + +p +   +i+QsP aG++v
  gi|119719205|ref|YP_919700.1| 19 LSKEEANRLLKAMGLkkselpwIYSTDPVarALKAKPGDVimIIRQSPTAGESV 72
                                   699************999888877777778555555555589**********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 581.42
//
Query:       gi|119719206|ref|YP_919701.1|  [L=497]
Description: glycyl-tRNA synthetase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.9e-19   68.3   0.1      1e-18   67.3   0.1    1.5  1  HGTP_anticodon  Anticodon binding domain
    1.1e-09   38.5   0.0    4.1e-09   36.7   0.0    1.9  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
     0.0091   16.1   0.2      0.024   14.8   0.2    1.7  1  DUF678          Protein of unknown function (DUF678)
  ------ inclusion threshold ------
      0.014   15.1   1.1        2.9    7.8   0.1    2.5  2  zinc_ribbon_2   zinc-ribbon domain
      0.017   15.0   0.6        2.2    8.3   0.0    2.6  2  zinc_ribbon_4   zinc-ribbon domain
      0.091   12.6   0.0       0.34   10.8   0.0    1.9  1  Rad50_zn_hook   Rad50 zinc hook motif
      0.092   12.9   1.3        1.2    9.3   1.3    2.3  1  Zn-ribbon_8     Zinc ribbon domain
       0.25   11.3   1.2        8.7    6.4   0.1    2.4  2  Prok-RING_1     Prokaryotic RING finger family 1
       0.69    9.4   3.0        3.5    7.2   0.3    2.4  2  zf-ribbon_3     zinc-ribbon domain


Domain annotation for each model (and alignments):
>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.3   0.1     5e-22     1e-18       1      93 [.     403     492 ..     403     493 .. 0.94

  Alignments for each domain:
  == domain 1  score: 67.3 bits;  conditional E-value: 5e-22
                                    SEEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTCEEE CS
                 HGTP_anticodon   1 qvvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtreqe 80 
                                    +++v pl + ++ l   a++++++L+++ +r+ +d +++sig+++++ad++g+pf ++++ ++l+++tvt+r rdt+eq+
  gi|119719206|ref|YP_919701.1| 403 KCAVFPLVK-RDGLDVKAREIYNQLKKH-FRCYYD-EDGSIGRRYAKADEIGVPFSITIDGQTLRDDTVTIRFRDTKEQI 479
                                    79******9.777*************99.877775.8******************************************* PP

                                    EEETTHHHHHHHH CS
                 HGTP_anticodon  81 rvsldelveklke 93 
                                    r  +++l++ l+e
  gi|119719206|ref|YP_919701.1| 480 RERVENLKARLSE 492
                                    *******999887 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.0     2e-12   4.1e-09      10     176 ..     162     380 ..     154     383 .. 0.75

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 2e-12
                                    EEEE-SSSHHHHHHHHHHHEEEB.GGSSEEEEEEEEEEBTTTSTBC.TTTB-SEEEEEEEEEEESGGGHHHH..HHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxx RF
                   tRNA-synt_2b  10 eyiLkPtneetfvelirdevlrs.krLPlklyqiqtkyRdEksdsr.GLlRvreFhqkdgyvfhaeasldds..lrdlik 85 
                                      +L+P+  + +   +++ v      LP+ ++qi+  +R+E s  r  L+R+reF+q + + f+ +++l++   ++++++
  gi|119719206|ref|YP_919701.1| 162 TAYLRPETAQLIFTNFKNVVFTMgATLPFGIAQIGKAFRNEIS-PRnFLFRLREFTQMEIEYFVNPEKLNECpyFKEVEE 240
                                    5699************9998877677****************9.5559******************99998532566666 PP

                                    HHHHHHHHTT.SCEEEEEEGTTSC...............................................BTTSEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxx...............................................xxxxxxxxx RF
                   tRNA-synt_2b  86 aisriferlglefraiielmsaks...............................................adykdkkef 118
                                    +  +++++   ++r + e  s+ +                                                 + ++ ++
  gi|119719206|ref|YP_919701.1| 241 LRVNFLSAEE-QERGVSEAKSI-KlgeavetgviknawhaywigeslrwlwslglrperlrvrehvktelaHYAVQTFDI 318
                                    6666666664.33444444443.135566677888899999999999999999999999999999999996556677788 PP

                                    EEEETTTSEEEEEEEEEEEET.HHHHHTTE....EEECTTSSEEEEEEEEEEEEHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxx.xxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2b 119 eavsesltkgieigtiqklgt.rlserlga....tvldennreksvimicaaigveRllsail 176
                                    e  ++ ++   ei  i ++ +  l +  +       +  n++   +++i  ++g+eR+l+a+l
  gi|119719206|ref|YP_919701.1| 319 EYFFPYMG-WKEIEGIANRSDyDLKRHQEYsgeaLHIVDNGKTVIPYVIEPSFGLERILLAVL 380
                                    88888444.5568888888663343333323333334568899999999999*****999987 PP

>> DUF678  Protein of unknown function (DUF678)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.2   1.2e-05     0.024      23      73 ..      90     146 ..      75     148 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.2e-05
                         DUF678  23 ddctTCSlCqS.....kLvkvs..dvskvslsklkvavgkgntlrCaACgSsLtlLrd 73 
                                    d  +TC +C       +L+      +  +sl+++k    ++n++rC ACg +L   r 
  gi|119719206|ref|YP_919701.1|  90 DYIVTCTSCGAeyradHLLEEVgvKIPEYSLETIKSL-IENNNVRCPACGGKLSEPRK 146
                                    66688888865222224555431146799******99.9************9987665 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1    0.0069        14       2       9 ..      95     102 ..      94     105 .. 0.82
   2 ?    7.8   0.1    0.0014       2.9       9      22 ..     127     140 ..     125     141 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0069
                  zinc_ribbon_2   2 CpnCGael 9  
                                    C++CGae 
  gi|119719206|ref|YP_919701.1|  95 CTSCGAEY 102
                                    99999996 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0014
                  zinc_ribbon_2   9 lqdnakFCpyCGtp 22 
                                    +++n++ Cp CG +
  gi|119719206|ref|YP_919701.1| 127 IENNNVRCPACGGK 140
                                    7899*******966 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0011       2.2       2      15 ..      92     105 ..      92     115 .. 0.78
   2 ?    4.3   0.1     0.019        38      25      32 ..     131     138 ..     127     140 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0011
                  zinc_ribbon_4   2 kitCpsCkakyeid 15 
                                    ++tC sC+a+y+ d
  gi|119719206|ref|YP_919701.1|  92 IVTCTSCGAEYRAD 105
                                    69*********955 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.019
                  zinc_ribbon_4  25 kvrCskCg 32 
                                    +vrC++Cg
  gi|119719206|ref|YP_919701.1| 131 NVRCPACG 138
                                    58888887 PP

>> Rad50_zn_hook  Rad50 zinc hook motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00017      0.34      12      37 ..     123     149 ..     120     154 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00017
                                    HHHHTT-SE.E-TTT--EE-HHHHHHH CS
                  Rad50_zn_hook  12 ieelkeakg.cCPlCgReldeehrseL 37 
                                    i+ l e+++ +CP Cg +l+e ++ +L
  gi|119719206|ref|YP_919701.1| 123 IKSLIENNNvRCPACGGKLSEPRKFNL 149
                                    5667788999**********9887655 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   1.3   0.00062       1.2       6      36 ..      93     141 ..      90     143 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00062
                    Zn-ribbon_8   6 YrCeeCghefe..................vlqsisdapltaCPeCgsev 36 
                                      C++Cg e+                    + s  +++++ CP+Cg+++
  gi|119719206|ref|YP_919701.1|  93 VTCTSCGAEYRadhlleevgvkipeysleTIKSLIENNNVRCPACGGKL 141
                                    56888888887778777777777777665666666777888*****976 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1    0.0043       8.7      19      30 ..      91     102 ..      85     106 .. 0.87
   2 ?    3.2   0.1     0.044        87       3      15 ..     130     142 ..     128     145 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0043
                    Prok-RING_1  19 DiVvCpeCgtpy 30 
                                     iV+C+ Cg+ y
  gi|119719206|ref|YP_919701.1|  91 YIVTCTSCGAEY 102
                                    59********98 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.044
                    Prok-RING_1   3 tgkkCpvCgkelk 15 
                                    ++ +Cp+Cg +l+
  gi|119719206|ref|YP_919701.1| 130 NNVRCPACGGKLS 142
                                    5677888887776 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.2     0.074   1.5e+02      18      24 ..      94     100 ..      93     101 .. 0.76
   2 ?    7.2   0.3    0.0018       3.5       3      10 ..     132     139 ..     130     143 .. 0.71

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.074
                    zf-ribbon_3  18 vCpyCGt 24 
                                    +C++CG+
  gi|119719206|ref|YP_919701.1|  94 TCTSCGA 100
                                    6999996 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0018
                    zf-ribbon_3   3 vrCPnCGa 10 
                                    vrCP+CG 
  gi|119719206|ref|YP_919701.1| 132 VRCPACGG 139
                                    78999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (497 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       749  (0.0417759); expected 358.6 (0.02)
Passed bias filter:                      697  (0.0388756); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 3201.50
//
Query:       gi|119719207|ref|YP_919702.1|  [L=112]
Description: hypothetical protein Tpen_0289 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.9e-44  148.2   1.8    8.9e-44  148.1   1.8    1.0  1  Arcadin_1  Arcadin 1


Domain annotation for each model (and alignments):
>> Arcadin_1  Arcadin 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.1   1.8     5e-48   8.9e-44       2     111 .]       4     111 ..       3     111 .. 0.98

  Alignments for each domain:
  == domain 1  score: 148.1 bits;  conditional E-value: 5e-48
                                    EEEEEEEEEEEEE-TT--EEEEEEEEEEE------------------------------------.--EEEEEEEEEE-H CS
                      Arcadin_1   2 lvrvkvssitlvkdPegekgvkielvEerelpgpvlvasdeedaeiaRevapivqqivrslpllslnkvkvpritLvlte 81 
                                    ++r+kv++i+l+++P+gek+vk+el+Eerelpgpv+v++d  ++ei+Re+api++q++r++p+l++n+v++pr+tLvlte
  gi|119719207|ref|YP_919702.1|   4 SFRAKVTNISLMDAPFGEKLVKLELTEERELPGPVIVQKD--ESEIGREIAPIIAQVMRMMPGLAPNTVRIPRVTLVLTE 81 
                                    89*************************************9..9************************************* PP

                                    HHHHHH-.---TT-EEEEEEETTEEEEEE- CS
                      Arcadin_1  82 eEleklevklevgdvyeieisegkisikre 111
                                    +E+e++ vk+++gd++ ie+s ++++i+re
  gi|119719207|ref|YP_919702.1|  82 DEWERFPVKPSIGDFFVIEVSGENVKIRRE 111
                                    ****************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       217  (0.0121033); expected 358.6 (0.02)
Passed bias filter:                      203  (0.0113224); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 783.18
//
Query:       gi|119719208|ref|YP_919703.1|  [L=81]
Description: RNA polymerase Rpb6 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.2e-15   54.6   0.0    9.7e-15   54.2   0.0    1.2  1  RNA_pol_Rpb6  RNA polymerase Rpb6


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb6  RNA polymerase Rpb6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.2   0.0   5.4e-19   9.7e-15       3      49 .]       4      56 ..       2      56 .. 0.86

  Alignments for each domain:
  == domain 1  score: 54.2 bits;  conditional E-value: 5.4e-19
                                   TTSS--HHHHHHHHHHHHHHH....HT..........SS-SSSSTTCHHHHTT-S-- CS
                   RNA_pol_Rpb6  3 tskvltrYelvriaakRArQieegesl..........etqkpvviAlrEiaegkipi 49
                                    +++ltr+e +ri++ RA+Qi    sl          e ++p++iA++E++ g++pi
  gi|119719208|ref|YP_919703.1|  4 GPPWLTRFERARIIGIRALQI----SLgapvliqvseELSDPITIAEKELELGLLPI 56
                                   5799*****************....777777787774256***************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       230  (0.0128284); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.30s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 552.38
//
Query:       gi|119719209|ref|YP_919704.1|  [L=545]
Description: thermosome [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   9.9e-188  624.7  15.4   1.1e-187  624.5  15.4    1.0  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  624.5  15.4  6.3e-192  1.1e-187       1     490 [.      34     524 ..      34     525 .. 0.99

  Alignments for each domain:
  == domain 1  score: 624.5 bits;  conditional E-value: 6.3e-192
                                    HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHHHHH CS
                     Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleeaekl 80 
                                    +a++++++lGP+GmdK+lv+++g+ ++T DGatilke+e++hPaak+lve+a++qd+evGDGTttvv+Lag+Ll ++e+l
  gi|119719209|ref|YP_919704.1|  34 IAEAMASSLGPRGMDKLLVDSFGNATITGDGATILKEMEVQHPAAKMLVEVAKAQDDEVGDGTTTVVVLAGQLLAASEEL 113
                                    799***************************************************************************** PP

                                    HHCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHH.HCHCCCS.. CS
                     Cpn60_TCP1  81 iaagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAv.klieene.. 157
                                    +++++hptti+eg+ekal +a ++++ei  +  ++  dr+ L +va+t+lssk++++ +++l+klvvdA  +++e+++  
  gi|119719209|ref|YP_919704.1| 114 LDEDIHPTTIVEGFEKALVEATRIIDEI--SETVDPLDRTVLENVAKTALSSKVVADYKDFLAKLVVDAAlTVVEKKDgk 191
                                    ****************************..6666688*********************************8999888899 PP

                                    EECSCCCEECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCCSCCHHHHHHHHH CS
                     Cpn60_TCP1 158 keldlgrikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvlsdaeeleklekae 237
                                    ++l l+ ikv+k+ g+s++++ lv+G+vldk+v++p mpk+++nak++lld +Leiek+e +++++++++e+l+ ++++e
  gi|119719209|ref|YP_919704.1| 192 YNLSLDDIKVEKKRGESITETMLVKGIVLDKEVVHPGMPKRVTNAKIALLDAPLEIEKPEWTAKINVTTPEQLKMFLDQE 271
                                    9999999************************************************************************* PP

                                    HHHHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGGGGGCGC-EEEEEEEE CS
                     Cpn60_TCP1 238 ekqleellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssledltpeelGtakkvee 317
                                     ++l++++eki++sg+nvv+cqkgidd+a+ +lak+gila+rrvkk+d+e+la+atGa++++++ed+tpe+lG a+ vee
  gi|119719209|ref|YP_919704.1| 272 AEILRKKVEKIKESGANVVFCQKGIDDVAQYYLAKAGILAVRRVKKSDMEKLARATGARILTRVEDITPEALGRAELVEE 351
                                    ******************************************************************************** PP

                                    CCETTCCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHHHHHHHHHCCCCTSXCC CS
                     Cpn60_TCP1 318 ekigsekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatelelakklkeyaksvsge 397
                                    +k+ +ek++++e+++++k++til+rg  d+v+de+erai+dAl+vv+n+i+++k+v+GGGa+e+ela +l+++a++++++
  gi|119719209|ref|YP_919704.1| 352 RKVADEKMVFVEGCPNPKSVTILVRGGADHVVDEAERAIHDALSVVRNVIREPKIVAGGGAVEIELAMRLRDFARTLPSR 431
                                    ******************************************************************************** PP

                                    HHHHHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTXTTEEEETTTTCEEECCCCTXEEEHHHHHHHHHHHHHHH CS
                     Cpn60_TCP1 398 eqlaieafakALevipktLaeNaGldpievlaklraahnkgekelgidvesgeiidlveagvvDplkvkrqalksAteaa 477
                                    eqla++++a+ALe+i+ +La+NaG++pi+vla+l+ +h+kgek++g+++ + +++d+++agv++p+ vk+q+lksAteaa
  gi|119719209|ref|YP_919704.1| 432 EQLAVQKYAEALESIVGILAQNAGMEPIDVLAELKTRHAKGEKWAGVNAYTAKVEDMKKAGVLEPALVKKQVLKSATEAA 511
                                    ******************************************************************************** PP

                                    HHHHCEEEEEXXX CS
                     Cpn60_TCP1 478 stiLrideiikak 490
                                     +iLrid+ii a+
  gi|119719209|ref|YP_919704.1| 512 VMILRIDDIIAAQ 524
                                    **********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (545 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       663  (0.0369792); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.26s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 3478.71
//
Query:       gi|119719210|ref|YP_919705.1|  [L=129]
Description: putative phage repressor [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-08   34.5   0.2      2e-08   34.1   0.2    1.2  1  Peptidase_S24  Peptidase S24-like
  ------ inclusion threshold ------
       0.03   14.0   0.3      0.047   13.4   0.3    1.3  1  DUF2512        Protein of unknown function (DUF2512)


Domain annotation for each model (and alignments):
>> Peptidase_S24  Peptidase S24-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.2   2.2e-12     2e-08       2      60 ..      38      94 ..      37     105 .. 0.86

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 2.2e-12
                                   XXSSTTCCTXXTTXEEEEECTS---TTSEEEEEETTCE-EEEEEEEEETTEEEEE.SST CS
                  Peptidase_S24  2 vpGdSMeptlldGdlilVdkfsepkrGdivvfrlpgeeeayiKrviglpgdrvllasnn 60
                                   v + SMep l+ Gd+++V  ++++  Gdiv+    ge  ++++r++   ++++ ++ + 
  gi|119719210|ref|YP_919705.1| 38 VSSWSMEPVLHVGDVVVVAGGNSYTLGDIVIYERGGE--LIVHRIVLSVNGKYVTKGDA 94
                                   899*****************************99999..9******8888888877665 PP

>> DUF2512  Protein of unknown function (DUF2512)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.3   5.2e-06     0.047       6      61 ..      22      77 ..      18      84 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.2e-06
                        DUF2512  6 aLliKfiatlvvlllvlglflgvsfsevllisllltlvsYlvgDlliLprtgnliA 61
                                   +L ++f+++++v l+v++  +  ++ +v  + ++ +  sY +gD++i+ r g+li+
  gi|119719210|ref|YP_919705.1| 22 LLSLRFVLSTPVPLAVVSSWSMEPVLHVGDVVVVAGGNSYTLGDIVIYERGGELIV 77
                                   688999999999999999999999999999********************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 906.18
//
Query:       gi|119719211|ref|YP_919706.1|  [L=142]
Description: TATA-box binding [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-48  162.3   1.3    2.7e-33  113.7   0.1    2.0  2  TBP              Transcription factor TFIID (or TATA-binding 
    3.8e-06   26.9   0.0     0.0015   18.6   0.0    2.2  2  DUF3378          Domain of unknown function (DUF3378)
  ------ inclusion threshold ------
      0.014   15.2   2.0        1.9    8.5   0.1    2.4  2  Thiamine_BP      Thiamine-binding protein
      0.015   15.4   0.6        4.5    7.3   0.0    2.1  2  CagE_TrbE_VirB   CagE, TrbE, VirB family, component of type I
      0.022   14.6   0.4       0.64    9.9   0.1    2.1  2  RTT107_BRCT_5    Regulator of Ty1 transposition protein 107 B
      0.044   14.0   0.2        2.9    8.2   0.0    2.2  2  Ribosomal_S10    Ribosomal protein S10p/S20e
      0.071   13.2   0.2          8    6.5   0.0    2.4  2  DUF155           Uncharacterised ACR, YagE family COG1723
      0.071   13.9   1.9        3.8    8.4   0.1    2.2  2  Histone_HNS      H-NS histone family
       0.12   13.0   0.1        6.1    7.6   0.0    2.7  2  Methyltransf_11  Methyltransferase domain


Domain annotation for each model (and alignments):
>> TBP  Transcription factor TFIID (or TATA-binding protein, TBP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.1   0.1   4.2e-16   8.4e-13      43      83 ..       2      42 ..       1      44 [. 0.96
   2 !  113.7   0.1   1.4e-36   2.7e-33       2      84 ..      54     134 ..      53     135 .. 0.98

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 4.2e-16
                                   EEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHHHHHHH CS
                            TBP 43 yrlrepkvtaliFssGkvvitGakseeelreaakkiapilk 83
                                   +rl +pk++ liFssGk+v+tGakse e+++a+k i+++lk
  gi|119719211|ref|YP_919706.1|  2 LRLTRPKTATLIFSSGKMVCTGAKSEAEVQKAVKSIIKLLK 42
                                   799************************************98 PP

  == domain 2  score: 113.7 bits;  conditional E-value: 1.4e-36
                                    EEEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHHHHH CS
                            TBP   2 fkiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakkiapi 81 
                                    +++qN+vasanl+ ++dLe+ a+ +  +n+ Yepe+fpgl+yr+++pkv++liFssGkvv+tGak+eee+++a++ki++i
  gi|119719211|ref|YP_919706.1|  54 IEVQNIVASANLKASVDLERAAFLL--ENSMYEPEQFPGLIYRMQDPKVVLLIFSSGKVVCTGAKKEEEVKRAVEKIYNI 131
                                    69*******************9998..***************************************************** PP

                                    HHH CS
                            TBP  82 lkk 84 
                                    lk+
  gi|119719211|ref|YP_919706.1| 132 LKE 134
                                    *96 PP

>> DUF3378  Domain of unknown function (DUF3378)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.0     0.005       9.9      37      62 ..       7      32 ..       2      42 .. 0.88
   2 !   18.6   0.0   7.6e-07    0.0015      23      61 ..      84     122 ..      78     134 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.005
                        DUF3378 37 ndttItaYtSgKVlFQGknaeaeAsk 62
                                   ++t   ++ SgK +  G++ eae +k
  gi|119719211|ref|YP_919706.1|  7 PKTATLIFSSGKMVCTGAKSEAEVQK 32
                                   56777899**************9987 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 7.6e-07
                        DUF3378  23 rskkppyavfaakkndttItaYtSgKVlFQGknaeaeAs 61 
                                    + ++ p+ +++ ++++++  ++ SgKV+  G++ e+e +
  gi|119719211|ref|YP_919706.1|  84 EPEQFPGLIYRMQDPKVVLLIFSSGKVVCTGAKKEEEVK 122
                                    56789******************************9986 PP

>> Thiamine_BP  Thiamine-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.1   0.00094       1.9      10      37 ..      25      52 ..      18      57 .. 0.84
   2 ?    6.1   0.2     0.005        10      10      31 ..     116     137 ..     109     141 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00094
                                   SSSSGHHHHHHHHHHHHHTTSSEEEEET CS
                    Thiamine_BP 10 tegesvskyVakvvevlkesglkyeltp 37
                                   +++++v+k+V+ ++++lk++g+  + +p
  gi|119719211|ref|YP_919706.1| 25 KSEAEVQKAVKSIIKLLKAHGIDIKNEP 52
                                   4589*****************9887665 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.005
                                    SSSSGHHHHHHHHHHHHHTTSS CS
                    Thiamine_BP  10 tegesvskyVakvvevlkesgl 31 
                                    +++e+v+++V+k+ ++lke+g+
  gi|119719211|ref|YP_919706.1| 116 KKEEEVKRAVEKIYNILKEQGV 137
                                    5699***************998 PP

>> CagE_TrbE_VirB  CagE, TrbE, VirB family, component of type IV transporter system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0023       4.5     154     181 ..      20      47 ..       8      54 .. 0.84
   2 ?    6.6   0.1    0.0036       7.3     152     185 ..     109     142 .]     101     142 .] 0.89

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0023
                 CagE_TrbE_VirB 154 lvlfaedkekLdkavseatkllnakGiv 181
                                    ++  a+++++++kav+ + kll+a Gi 
  gi|119719211|ref|YP_919706.1|  20 VCTGAKSEAEVQKAVKSIIKLLKAHGID 47 
                                    7888**********************95 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0036
                 CagE_TrbE_VirB 152 lslvlfaedkekLdkavseatkllnakGivavke 185
                                     +++  a+++e+++ av+++ ++l+++G+++  e
  gi|119719211|ref|YP_919706.1| 109 KVVCTGAKKEEEVKRAVEKIYNILKEQGVLVEEE 142
                                    679999**********************998765 PP

>> RTT107_BRCT_5  Regulator of Ty1 transposition protein 107 BRCT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   0.00032      0.64      19      61 ..      18      64 ..       5      68 .. 0.81
   2 ?    3.1   0.0     0.044        87      19      46 ..     109     139 ..     105     142 .] 0.73

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00032
                                   EEEESSS.TT.....SSHHHHHHHHHTTEEE-SGCCT.-SEEE-SS- CS
                  RTT107_BRCT_5 19 ravlTgceeevn...kedsdkkkLrklGikivqeakk.cntliApki 61
                                   ++v+Tg ++e +     +s +k L+  Gi i +e+   ++ ++A+  
  gi|119719211|ref|YP_919706.1| 18 KMVCTGAKSEAEvqkAVKSIIKLLKAHGIDIKNEPVIeVQNIVASAN 64
                                   79********99876667778899999*****988766888888765 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.044
                                    EEEESSS.TT.....SSHHHHHHHHHTTEEE CS
                  RTT107_BRCT_5  19 ravlTgceeevn...kedsdkkkLrklGiki 46 
                                    ++v+Tg ++e +     ++  ++L++ G+ +
  gi|119719211|ref|YP_919706.1| 109 KVVCTGAKKEEEvkrAVEKIYNILKEQGVLV 139
                                    79******99877555555667787777765 PP

>> Ribosomal_S10  Ribosomal protein S10p/S20e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0    0.0014       2.9       9      32 ..      27      50 ..      19      72 .. 0.87
   2 ?    4.1   0.0     0.028        55       8      31 ..     117     140 ..     111     142 .] 0.87

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0014
                                   HHHHHHHHHHHHHHTTSSS-EE-- CS
                  Ribosomal_S10  9 sklLekavkkivraakelgikvkg 32
                                    + ++kavk i++++k +gi++k+
  gi|119719211|ref|YP_919706.1| 27 EAEVQKAVKSIIKLLKAHGIDIKN 50
                                   5789*****************996 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.028
                                    SHHHHHHHHHHHHHHTTSSS-EE- CS
                  Ribosomal_S10   8 dsklLekavkkivraakelgikvk 31 
                                    + + +++av+ki++++ke+g+ v+
  gi|119719211|ref|YP_919706.1| 117 KEEEVKRAVEKIYNILKEQGVLVE 140
                                    56789***************9986 PP

>> DUF155  Uncharacterised ACR, YagE family COG1723
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.014        29       3      35 ..      13      50 ..      11      98 .. 0.61
   2 ?    6.5   0.0     0.004         8       2      31 ..     103     133 ..     102     142 .] 0.67

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.014
                         DUF155  3 iFknGsvVfwglde.eeeknflnkllkflnees....e 35
                                   iF++G +V+ g +  +e+++ +++++k l+ +     +
  gi|119719211|ref|YP_919706.1| 13 IFSSGKMVCTGAKSeAEVQKAVKSIIKLLKAHGidikN 50
                                   89999999999665555555555555554444344331 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.004
                         DUF155   2 fiFknGsvVfwglde.eeeknflnkllkfln 31 
                                     iF++G vV+ g ++ ee+k+ ++k+ + l+
  gi|119719211|ref|YP_919706.1| 103 LIFSSGKVVCTGAKKeEEVKRAVEKIYNILK 133
                                    79**********6654555555666555544 PP

>> Histone_HNS  H-NS histone family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.1    0.0019       3.8      16      40 ..      25      49 ..      22      72 .. 0.89
   2 ?    5.1   0.3      0.02        40      16      41 ..     116     141 ..     113     142 .] 0.89

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0019
                                   XXXXXXXXXXXXXXXXXXXXX---- CS
                    Histone_HNS 16 leaeerkealaeirelaaeyGltle 40
                                   + ++e ++a++ i +l++++G++++
  gi|119719211|ref|YP_919706.1| 25 KSEAEVQKAVKSIIKLLKAHGIDIK 49
                                   56899****************9986 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.02
                                    XXXXXXXXXXXXXXXXXXXXX----S CS
                    Histone_HNS  16 leaeerkealaeirelaaeyGltlee 41 
                                    +++ee k+a+++i ++++e+G+ +ee
  gi|119719211|ref|YP_919706.1| 116 KKEEEVKRAVEKIYNILKEQGVLVEE 141
                                    6899*****************98776 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.13   2.5e+02      74      93 ..      24      46 ..       6      48 .. 0.74
   2 ?    7.6   0.0    0.0031       6.1      74      95 ..     114     139 ..      48     139 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.13
                                   -...CCHHHHHHHHHHHEEEEEE CS
                Methyltransf_11 74 v...edpekalkeiaRvLkpgGl 93
                                       ++++ka+k i ++Lk  G+
  gi|119719211|ref|YP_919706.1| 24 AkseAEVQKAVKSIIKLLKAHGI 46
                                   1444699************9996 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0031
                                    -....CCHHHHHHHHHHHEEEEEEEE CS
                Methyltransf_11  74 v....edpekalkeiaRvLkpgGllv 95 
                                         e++++a+++i+ +Lk  G+lv
  gi|119719211|ref|YP_919706.1| 114 GakkeEEVKRAVEKIYNILKEQGVLV 139
                                    24444799***************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       939  (0.0523733); expected 358.6 (0.02)
Passed bias filter:                      629  (0.0350828); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1014.54
//
Query:       gi|119719212|ref|YP_919707.1|  [L=150]
Description: ribosomal-protein-alanine acetyltransferase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      8e-21   74.5   0.5    9.5e-21   74.2   0.5    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    1.6e-13   50.8   0.7    2.8e-13   50.1   0.5    1.5  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
      6e-13   48.8   0.2    1.4e-12   47.6   0.2    1.4  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    3.1e-08   33.5   0.0    4.8e-08   32.9   0.0    1.3  1  FR47             FR47-like protein
      1e-06   29.0   0.3    1.8e-06   28.1   0.3    1.4  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
    2.2e-05   24.2   0.0    3.4e-05   23.6   0.0    1.3  1  Acetyltransf_8   Acetyltransferase (GNAT) domain
    4.1e-05   24.3   0.1      5e-05   24.0   0.1    1.1  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
     0.0026   17.8   0.4     0.0042   17.2   0.4    1.4  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
     0.0033   16.9   1.8     0.0044   16.5   1.8    1.2  1  Acetyltransf_15  Putative acetyl-transferase


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.2   0.5   4.8e-24   9.5e-21      21     117 .]      19     127 ..       3     127 .. 0.83

  Alignments for each domain:
  == domain 1  score: 74.2 bits;  conditional E-value: 4.8e-24
                                    HHH...HHHHHHSTTC.EEEEEEETTEEEEEEEEEEEET.......TSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHH CS
                 Acetyltransf_1  21 eee...feesfsleae.gllvaeedgeliGfisllkipd.......ekggvayieslaVspeyrgkGlGsaLlealeera 89 
                                    e +   ++e + ++ +  +lvae  g+++G+i+++  +d         g++++++slaV +e+r+kG+G  L+ +++e +
  gi|119719212|ref|YP_919707.1|  19 ENYpafYFELHYRNFGkAFLVAEVKGKIVGYIMCRVEYDnlytnpqKVGRRGHVISLAVLEEWRRKGIGYNLMVKAMEAM 98 
                                    333333233333344448899************************98899****************************** PP

                                    HHT.TESEEEEEEETTEHHHHHHHHHTTE CS
                 Acetyltransf_1  90 ree.gikkivlaveedndaairlYeklGF 117
                                    +   g+++ +l+v+++n++airlY+klGF
  gi|119719212|ref|YP_919707.1|  99 KTYyGAEEYYLEVRVSNEPAIRLYKKLGF 127
                                    ******999***************88**9 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.1   0.5   1.4e-16   2.8e-13       4      75 ..      36     128 ..      32     129 .. 0.74

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 1.4e-16
                                    EEEEEEETTEEEEEEEEEEES.............TCTEEEEE-GGGTTSSHHHHHHH.H.TT....SEEE.EE.EEEETH CS
                 Acetyltransf_7   4 evfVaeddgkivGfialslld.............aeitrlaVdpeyrgkGiGraLle.a.ae....kgii.le.qlelna 62 
                                     ++Vae +gkivG+i + ++              ++ + laV++e+r+kGiG  L+  a ++     g +  + ++++++
  gi|119719212|ref|YP_919707.1|  36 AFLVAEVKGKIVGYIMCRVEYdnlytnpqkvgrrGHVISLAVLEEWRRKGIGYNLMVkAmEAmktyYGAEeYYlEVRVSN 115
                                    699************999999999999987765555555****************9634422444544222123344455 PP

                                    HHHHHHHHHTTEE CS
                 Acetyltransf_7  63 ekaikfYeklGFe 75 
                                    e+ai++Y+klGF 
  gi|119719212|ref|YP_919707.1| 116 EPAIRLYKKLGFN 128
                                    69**********6 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.6   0.2   7.2e-16   1.4e-12      31     110 ..      35     131 ..      27     135 .. 0.87

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 7.2e-16
                Acetyltransf_10  31 alllvaeeggkivGvi..el.rdgs............hisllfVdpeyrgqGigkaLleaveeeaekdgikl..eltvna 93 
                                    + +lvae++gkivG+i  ++ +d +            h+  l+V +e+r++Gig +L+ ++ e++++  +++   l+v+ 
  gi|119719212|ref|YP_919707.1|  35 KAFLVAEVKGKIVGYImcRVeYD-NlytnpqkvgrrgHVISLAVLEEWRRKGIGYNLMVKAMEAMKTYYGAEeyYLEVRV 113
                                    5699************7755333.2588889999999*********************9999998877777779****** PP

                Acetyltransf_10  94 sp.yavpfYeklGFkavg 110
                                    s+  a+++Y+klGF +v+
  gi|119719212|ref|YP_919707.1| 114 SNePAIRLYKKLGFNVVK 131
                                    **************9986 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.0   2.4e-11   4.8e-08      22      80 ..      70     130 ..      52     137 .. 0.83

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 2.4e-11
                                    SSEEEEEE-GGG-SSSHHHHHHHHHHHHHHH..S-S-EEEEEETT-HHHHHHHHHHT-EEE CS
                           FR47  22 gelgalqvlpehrrrGlgsrlvkalakeiae..rgktvllvvvasNtpsirlyeklGfeki 80 
                                    g + +l vl+e rr+G g  l  +  +++ +    ++  l v+ sN+p+irly+klGf++ 
  gi|119719212|ref|YP_919707.1|  70 GHVISLAVLEEWRRKGIGYNLMVKAMEAMKTyyGAEEYYLEVRVSNEPAIRLYKKLGFNVV 130
                                    77889*************9875555555555545678999******************875 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.3   9.2e-10   1.8e-06      52     148 ..      37     141 ..      28     147 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 9.2e-10
                 Acetyltransf_4  52 flvae.sdrivGyay........lgqfkkrakdwkaelsvylaerdnnkeglgrelidaleqvl.keqnienllaeiasp 121
                                    flvae +++ivGy          + +++k++++++++    l     + +g+g +l+   ++ +   ++ e+ + e+ ++
  gi|119719212|ref|YP_919707.1|  37 FLVAEvKGKIVGYIMcrveydnlYTNPQKVGRRGHVISLAVLE--EWRRKGIGYNLMVKAMEAMkTYYGAEEYYLEVRVS 114
                                    9999*9******9862222222245678889999999888884..5899999988555555555499************* PP

                 Acetyltransf_4 122 nensiqfhkalGFelvgifkkcikkng 148
                                    ne++i ++k+lGF++v+i+++++ ++ 
  gi|119719212|ref|YP_919707.1| 115 NEPAIRLYKKLGFNVVKILQGYYLDGE 141
                                    *******************99987665 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   1.7e-08   3.4e-05      47     142 ..      38     132 ..      16     134 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 1.7e-08
                                    EEEEETTEEEEEEEEEEGGGCGGGGCS..---TT-EEEEEEES.SHHHCTTTCHHHHHHHHHHHHHCCTT--EEEE--BT CS
                 Acetyltransf_8  47 liglldgepvgyfeiYwakedelaeyy..daepgdrGiHllig.eaeargkglttallralvhylfadprtrrvvvEPdv 123
                                    l+++++g+ vgy+ + +++ d+l   y  + + g rG  + ++  +e r+kg++  l+ + ++ + +  +++   +E +v
  gi|119719212|ref|YP_919707.1|  38 LVAEVKGKIVGYIMC-RVEYDNL---YtnPQKVGRRGHVISLAvLEEWRRKGIGYNLMVKAMEAMKTYYGAEEYYLEVRV 113
                                    567899999999976.8999965...434667777777777775566789****************************** PP

                                    T-HHHHHHHHHTT-EEEEE CS
                 Acetyltransf_8 124 rNerairllekaGfekeke 142
                                    +Ne airl++k+Gf+ +k 
  gi|119719212|ref|YP_919707.1| 114 SNEPAIRLYKKLGFNVVKI 132
                                    **************99875 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.1   2.5e-08     5e-05      54     138 .]      33     128 ..       6     128 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 2.5e-08
                 Acetyltransf_3  54 yg..waivlkdtgviGsvglrdleeedee.........aelgymlapsfwgkGyateavralleyafeelglerlvavid 122
                                    +g  +++ + +++++G++++r   ++  +           +++ + +++++kG++   +  ++e++ +  g+e+ + ++ 
  gi|119719212|ref|YP_919707.1|  33 FGkaFLVAEVKGKIVGYIMCRVEYDNLYTnpqkvgrrgHVISLAVLEEWRRKGIGYNLMVKAMEAMKTYYGAEEYYLEVR 112
                                    33337887745548****99955555555677788887778888889999****************9999********** PP

                 Acetyltransf_3 123 keNeaSirvleklGfe 138
                                     +Ne  ir+++klGf+
  gi|119719212|ref|YP_919707.1| 113 VSNEPAIRLYKKLGFN 128
                                    ***************6 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.4   2.1e-06    0.0042       6     127 ..       2     129 ..       1     130 [. 0.74

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.1e-06
                                    -GGGHHHHHHHHHHHTT----H..HHHHHHHHHHTT..SEEEEEEETTEEEEEEEE.EEEE.EEE.TTEEEEEEEEEEEE CS
                 Acetyltransf_9   6 teedldevlellkyaFqdeespleeireyfrkllee..srvlgaedngelvgqlal.lple.lnv.pGktlkaagvtgVa 80 
                                    +ee+l +v+++ k++  ++ ++++     f+  + +  + +l+ae +g++vg +++ + ++ l++ p k  + + v + a
  gi|119719212|ref|YP_919707.1|   2 REEELGDVMRINKKVLPENYPAFY-----FELHYRNfgKAFLVAEVKGKIVGYIMCrVEYDnLYTnPQKVGRRGHVISLA 76 
                                    788999999999999999999863.....33333332257999999******9887434431333255777889****** PP

                                    E-CCGTTS-HHHHHHHHHHHHHHHT.T--EEEE--.....SSHHHHHTTT-EE CS
                 Acetyltransf_9  81 vapehrgrgvlskLlaraleemree.gqplsllfP.....ssipiYrrfGyei 127
                                    v  e r++g+   L+ +a+e m+   g++  +l        +i++Y+++G+++
  gi|119719212|ref|YP_919707.1|  77 VLEEWRRKGIGYNLMVKAMEAMKTYyGAEEYYLEVrvsnePAIRLYKKLGFNV 129
                                    **********9999999999999877777777766554333368899999876 PP

>> Acetyltransf_15  Putative acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   1.8   2.2e-06    0.0044      45     138 ..      43     129 ..      12     136 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.2e-06
                Acetyltransf_15  45 keeLvasvfivkkkyyslvssilieknvleiYtlyvsekyrgkGlakklLeeslkelkknYkvdnelllaLHlnpkDksM 124
                                    k+++v+ ++  +  y +l++++ +      + +l v e++r+kG+ ++l+ ++++++k  Y   +e +l   ++ +    
  gi|119719212|ref|YP_919707.1|  43 KGKIVGYIM-CRVEYDNLYTNPQKVGRRGHVISLAVLEEWRRKGIGYNLMVKAMEAMK-TYYGAEEYYLEVRVSNE---- 116
                                    555565554.45677777777777777778899********************88885.55555599999999874.... PP

                Acetyltransf_15 125 nisfalYyslgFrk 138
                                      + +lY +lgF+ 
  gi|119719212|ref|YP_919707.1| 117 -PAIRLYKKLGFNV 129
                                    .6889999999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1088.03
//
Query:       gi|119719213|ref|YP_919708.1|  [L=425]
Description: extracellular ligand-binding receptor [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.1e-45  154.8   0.0    3.7e-45  154.6   0.0    1.1  1  ANF_receptor  Receptor family ligand binding region
    2.5e-42  145.8   2.4      3e-42  145.5   2.4    1.0  1  Peripla_BP_6  Periplasmic binding protein
    1.6e-08   33.8   0.1    2.2e-08   33.4   0.1    1.3  1  LppC          LppC putative lipoprotein
  ------ inclusion threshold ------
      0.014   14.4   0.0        1.9    7.4   0.0    2.1  2  Peripla_BP_5  Periplasmic binding protein domain
       0.14   12.5   0.0        0.3   11.4   0.0    1.5  1  Peripla_BP_3  Periplasmic binding protein-like domain


Domain annotation for each model (and alignments):
>> ANF_receptor  Receptor family ligand binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.6   0.0     1e-48   3.7e-45       3     351 ..      73     399 ..      71     402 .. 0.89

  Alignments for each domain:
  == domain 1  score: 154.6 bits;  conditional E-value: 1e-48
                                    HHHHHHHHHHHHT-TTSSTTE.EEEEEEEE-TT-HHHHHHHHHHHCCCCEEEEEE-SSHHHHHHHHHHHCCTT-EEEESS CS
                   ANF_receptor   3 leAmklAveeinsdpnllpgi.klgyeiidtccdfslaleaaldflkgkvvaviGpssssvsdavaslanlfkiPvisyg 81 
                                    ++Am+ A+e++n+  + +++  ++ + ++d+  ++++al    ++ ++ v aviG   ss+++av+++a+++++ v+s+g
  gi|119719213|ref|YP_919708.1|  73 ELAMQIAIEDVNNFAEKIGSPyRFKLLVEDSGTSPEQALSRIKTLAAQGVRAVIGLEASSEVAAVKQFADTNHVVVLSVG 152
                                    78***********877776666*************************88******************************* PP

                                    ---GGGG-TTTTTTEEESS--CHHHHHHHHHHHHHTT--EEEEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEESTCHH CS
                   ANF_receptor  82 stspelsdknryptflrtvpsdtsqaqAivdilkhfgWkkvaliysdddygesglqaleeeleergicvalkekipessn 161
                                    st+ +l       ++lr+vp+d+ q++A+++++  +g++ va+iy +d++g ++ + ++ +++e g +va +++ p +++
  gi|119719213|ref|YP_919708.1| 153 STALSLAIPGD--YILRVVPPDSVQSKALARLIYSLGYRNVAVIYRNDAWGVGLFEGFSARFKELGGNVAGVAYDPAAKD 230
                                    *9999999888..77************************************************************99777 PP

                                    HCHHHHHHHHHHTT..T--EEEEEE-HHHHHHHHHHHHHTTS-STTEEEEETCHCCCECTTS-CC..HHHHHTT-EEEEE CS
                   ANF_receptor 162 ddevvrkllkeiks..karvivlfcssedarellkaarrlgltgeeyvwiasdawtsslvldkpeltgleaaegvlgfrl 239
                                     +  v++l   ++s  +  +++  + ++d  +++k a r  + ++   w+++d++++s +l+++  ++l a++g+     
  gi|119719213|ref|YP_919708.1| 231 LSGEVNRLADIAASmgSNTAVLAITFEDDGIQIVKLAARNPVLSK-LKWFGTDGVAQSTKLASEAGEELIALGGFPCTIF 309
                                    777777776555556644799999999****************96.****************998556666777777777 PP

                                    --B-HHHHHHHHHST--CCCSSSTCCGSTTCCHHHHH...HHHHHHHHHHHHHHHCHHSSSHCCB-HHHHCCHHHHHHHH CS
                   ANF_receptor 240 kdpnspkfsefldkreklsdekqnyenegkeqisyqaalmYdaVyllaeAlnkllrkkkpgralscntlkpweggqkllr 319
                                    ++++++++ +f+         + + +  g+e + + a+  YdaV+l+a  +  ++                 ++g+kll+
  gi|119719213|ref|YP_919708.1| 310 QPSENQRLADFV---------NRFRSRSGGEDPHAYAMNAYDAVWLVALSVMLTG----------------SYSGDKLLS 364
                                    99**********.........5566666777767777777********9999999................799*****9 PP

                                    HHHT-..EEEETTSCEEB-TTSBBE.-EEEEEEEE CS
                   ANF_receptor 320 ylrnv..nfeGltGdvkfdengdrv.ptydilnlq 351
                                    ++  v  nf+G+tG +++d+ngdr+ ++y i+ + 
  gi|119719213|ref|YP_919708.1| 365 TIPLVaqNFNGITGPLTLDANGDRAsGDYAIWRVV 399
                                    98765449************************876 PP

>> Peripla_BP_6  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.5   2.4   8.4e-46     3e-42       1     339 [.      52     399 ..      52     404 .. 0.91

  Alignments for each domain:
  == domain 1  score: 145.5 bits;  conditional E-value: 8.4e-46
                                    EEEEEEEE-SSSTTHHHHHHHHHHHHHHHHHHHH.TTEET.TEEEEEEEEE-TTSHHHHHHHHHHHHHCT--SEEEE-BS CS
                   Peripla_BP_6   1 pikiGlltplsGpyassgksllagaqaafeeiNa.aGGin.GrkielverDdaydpdraaeaarrlvdqdgvdalvgpls 78 
                                    +i iG+l+ lsG+++s+gk  + ++q a+e++N  a +i+  ++++l+++D + +p++a++  + l   +gv+a++g   
  gi|119719213|ref|YP_919708.1|  52 TIPIGALVELSGDLSSYGKRDELAMQIAIEDVNNfAEKIGsPYRFKLLVEDSGTSPEQALSRIKTLAA-QGVRAVIGLEA 130
                                    799*************************************556*************************.*********** PP

                                    HHHHHHHHHHHHHHT-EEEESS..-HHCCTTSTTEEESS--HHHHHHHHHHHHHHHTTSCEEEEEEESSHHHHHHHHHHH CS
                   Peripla_BP_6  79 savaaavaevlakdgvpvigpa..gltgekcspyvfslgpsysaqasalveylakelggkkvalvyadyafgregiaalk 156
                                    s+ +aav +++++++v+v++++  +l+     +y+ ++ p +s q +al++ + + lg ++va++y ++a+g  + +++ 
  gi|119719213|ref|YP_919708.1| 131 SSEVAAVKQFADTNHVVVLSVGstALSLAIPGDYILRVVPPDSVQSKALARLIYS-LGYRNVAVIYRNDAWGVGLFEGFS 209
                                    ********************652366689**********************7666.************************ PP

                                    HHHHCCTEEEEEEEEE-TTHHHHHHHHHHHHTTT-S.....EEEEESSHHHHHHHHHHHHHTT-SSSCEEEECCC-CHHH CS
                   Peripla_BP_6 157 aaakaaGgevvgeepvplgttdfsaqvlqikaagad.....avllagtgadlaallkaaaeaGldakrillvswsgseed 231
                                    a +k++Gg+v   + +++++ d+s  v+++++  a      avl++++ +d ++++k aa++ +  k ++ ++++g +++
  gi|119719213|ref|YP_919708.1| 210 ARFKELGGNVA-GVAYDPAAKDLSGEVNRLADIAASmgsntAVLAITFEDDGIQIVKLAARNPVLSK-LKWFGTDGVAQS 287
                                    *********97.69******************9999555555*********************9986.999999999988 PP

                                    HHHHHHHHHTTEEEEESCSTC....CCSHHHHHHHHHHHHHHTTGGC--HHHHHHHHHHHHHHHHHHCCTHCCHHHHHHH CS
                   Peripla_BP_6 232 lkalggeaaegvlavtpyfpd....ldnpavrafvaayeaayggapppsqfaaggyiaadlllealkaagsltreavraa 307
                                     k + + a e ++a  +++       +n++  +fv++++++ gg+ +p+++a+++y+a++l++  +  +gs +++++ ++
  gi|119719213|ref|YP_919708.1| 288 TKLASE-AGEELIALGGFPCTifqpSENQRLADFVNRFRSRSGGE-DPHAYAMNAYDAVWLVALSVMLTGSYSGDKLLST 365
                                    887776.7887777766554444446899***************8.8********************************* PP

                                    HHHS-..BECCCTCCBEECTTSBEE--EEEEEE- CS
                   Peripla_BP_6 308 leslg..fdgllgplkftaedhqasrpvyvvqvd 339
                                    +  +   f+g++gpl+ +a+  +as+++++ +v 
  gi|119719213|ref|YP_919708.1| 366 IPLVAqnFNGITGPLTLDANGDRASGDYAIWRVV 399
                                    9875547*********************999876 PP

>> LppC  LppC putative lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.1   6.1e-12   2.2e-08     241     416 ..      82     278 ..      37     346 .. 0.82

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 6.1e-12
                                    HHHHHHH...TT--S-EEEEE..TTTS-HHHHHHHHHHTT--EEE---SHHHHHHHHHSGG.GTTSEEEES---TT---B CS
                           LppC 241 dGFlaakdaetqsnaqvkvfD..taaeslediyaqakaagidlvVGPLlkqnvdkllaqeqlvqsidvLaLNssdnsrai 318
                                    d  ++a++  + ++ ++ v D  t+ e + + ++ + a+g++ v+G     +v ++ +++    ++ vL+  s+  s ai
  gi|119719213|ref|YP_919708.1|  82 DVNNFAEKIGSPYRFKLLVEDsgTSPEQALSRIKTLAAQGVRAVIGLEASSEVAAVKQFADT-NHVVVLSVGSTALSLAI 160
                                    5555555556666677777774455556666678899*********999*********9999.99*************** PP

                                    TTEEE----HHHHHHH..HHHHHHHTT-SSEEEEEESSHHHHHHHHHHHHHHHHHHSS--EEEEESSGGGHHHHHH.... CS
                           LppC 319 aqlcyfgLspEdeaes..aAsklwadgvRnplvlvpqndlGrRvveAFnerwqqlagtdaaielvdqpadlaqqlk.... 392
                                    ++   +   p d ++s   A  +++ g+Rn+ v+  ++++G    e F+ r+++l+g++a + +    +dl+ +++    
  gi|119719213|ref|YP_919708.1| 161 PGDYILRVVPPDSVQSkaLARLIYSLGYRNVAVIYRNDAWGVGLFEGFSARFKELGGNVAGVAYDPAAKDLSGEVNrlad 240
                                    ************987621567899*************************************************9999999 PP

                                    ................HH-.TTTEEEEE---HHHHHHHHH CS
                           LppC 393 ................dasrqdidavyivanskelaeikp 416
                                                    +   + i+ v ++a+++ l ++k 
  gi|119719213|ref|YP_919708.1| 241 iaasmgsntavlaitfE--DDGIQIVKLAARNPVLSKLKW 278
                                    98877777777777543..345777777777777777765 PP

>> Peripla_BP_5  Periplasmic binding protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0   0.00054       1.9       1      87 [.      53     140 ..      53     149 .. 0.82
   2 ?    4.9   0.0    0.0029        11     249     324 ..     309     385 ..     301     402 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00054
                   Peripla_BP_5   1 ikvGvLhSlsGtmaisekslkdaallaieeinaagGvlg..rkieavvvdpasdwelfaekaeklieedkvevvfGcwtS 78 
                                    i +G L  lsG ++   k    a+++aie++n+ +   g   + +  v+d+   +e+  ++ + l + ++v++v+G   S
  gi|119719213|ref|YP_919708.1|  53 IPIGALVELSGDLSSYGKRDELAMQIAIEDVNNFAEKIGspYRFKLLVEDSGTSPEQALSRIKTLAA-QGVRAVIGLEAS 131
                                    679*****************************97765552367889999999888888777777766.89******9988 PP

                   Peripla_BP_5  79 asRkavlpv 87 
                                    +   av++ 
  gi|119719213|ref|YP_919708.1| 132 SEVAAVKQF 140
                                    877777664 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0029
                   Peripla_BP_5 249 fqsvdtpenkafvakfkarvgedrvtndpmeaayiqvklwaqAvekagstdvekvreal..lgqelkapeGevkidpe 324
                                    fq  ++++  +fv++f++r g +   +  m  ay +v l+a +v   gs + +k+ +++  + q+++  +G++++d +
  gi|119719213|ref|YP_919708.1| 309 FQPSENQRLADFVNRFRSRSGGEDPHAYAM-NAYDAVWLVALSVMLTGSYSGDKLLSTIplVAQNFNGITGPLTLDAN 385
                                    67777888889*********9988876665.68**********************99864389999999999999875 PP

>> Peripla_BP_3  Periplasmic binding protein-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   8.3e-05       0.3       4      80 ..     183     253 ..     180     270 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.3e-05
                                    HHHCS--EEEEEE--TTSS-HHHHHHHHHHHHHHTTSSS-EEEEE-S-SS-SSHHHHH.....HHHHHCC-SEEEEE CS
                   Peripla_BP_3   4 LvelGhrriafiggegdrgasasderergfrqaleelglplnetvvaaddpaaaaaaraalllqalklaalPtAvia 80 
                                     ++lG+r++a+i+    r++ +   +++gf    +elg +++ + ++++ +++ +++++   + a+ + +  tAv+a
  gi|119719213|ref|YP_919708.1| 183 IYSLGYRNVAVIY----RNDAWGVGLFEGFSARFKELGGNVAGVAYDPAAKDLSGEVNRLADIAASMGSN--TAVLA 253
                                    489**********....7899********************************99999976443333333..66655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      634  (0.0353617); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 2861.38
//
Query:       gi|119719214|ref|YP_919709.1|  [L=51]
Description: 50S ribosomal protein L40e [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.2e-06   26.9   7.4    3.4e-06   26.8   7.4    1.1  1  Ribosomal_L40e  Ribosomal L40e family
     0.0037   17.0   0.8     0.0039   16.9   0.8    1.0  1  TackOD1         Thaumarchaeal output domain 1
     0.0067   16.4   0.6     0.0072   16.3   0.6    1.0  1  HypA            Hydrogenase/urease nickel incorporation, meta
  ------ inclusion threshold ------
      0.045   13.7   5.8        1.6    8.7   0.7    2.2  2  Zn_ribbon_SprT  SprT-like zinc ribbon domain


Domain annotation for each model (and alignments):
>> Ribosomal_L40e  Ribosomal L40e family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   7.4   7.6e-10   3.4e-06       3      48 ..       6      48 ..       4      51 .] 0.89

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 7.6e-10
                 Ribosomal_L40e  3 psLrqLAqKyncdKmiCrkCYArlpprAtnCrkkkCghsnnlrpKK 48
                                   p   qLA  + ++ +iCr+C Ar p  A  Cr  +C +s +lrpK+
  gi|119719214|ref|YP_919709.1|  6 PEKLQLALEHHFKVKICRRCNARNPWNAERCR--RC-KSRDLRPKR 48
                                   55679***************************..78.699999995 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.8   8.8e-07    0.0039      67     101 ..      13      47 ..       4      50 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 8.8e-07
                        TackOD1  67 eelvdrirlCpsCksghlnvrevCpkCkSidieeq 101
                                     e++ ++++C++C+  +    e C+ CkS d++ +
  gi|119719214|ref|YP_919709.1|  13 LEHHFKVKICRRCNARNPWNAERCRRCKSRDLRPK 47 
                                    56677999***********************9876 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.6   1.6e-06    0.0072      59      98 ..       8      45 ..       4      50 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.6e-06
                                   T-EEEEEEE--EEEETTTS-EEECHHHHHS-TTTSSS-EE CS
                           HypA 59 gaeLeieevpvkvrCreCgkefeleekalrCpkCgsadve 98
                                   + +L++e+   +  Cr+C+++   +  a+rC +C+s+d++
  gi|119719214|ref|YP_919709.1|  8 KLQLALEHHFKVKICRRCNARNPWN--AERCRRCKSRDLR 45
                                   56888999999999*****999977..459******9986 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.4   0.00057       2.6      15      31 ..      14      26 ..      10      29 .. 0.85
   2 ?    8.7   0.7   0.00036       1.6      26      35 ..      35      45 ..      31      48 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00057
                 Zn_ribbon_SprT 15 thhlsirrhnYrCrrCk 31
                                   +hh++++     CrrC 
  gi|119719214|ref|YP_919709.1| 14 EHHFKVKI----CRRCN 26
                                   79999999....****7 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00036
                 Zn_ribbon_SprT 26 rCrrCk.gtLr 35
                                   rCrrCk   Lr
  gi|119719214|ref|YP_919709.1| 35 RCRRCKsRDLR 45
                                   8*****55555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.43
# Mc/sec: 360.17
//
Query:       gi|119719215|ref|YP_919710.1|  [L=71]
Description: hypothetical protein Tpen_0297 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 516.68
//
Query:       gi|119719216|ref|YP_919711.1|  [L=835]
Description: DNA polymerase I [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      3e-56  191.1   0.8    5.9e-56  190.1   0.8    1.4  1  DNA_pol_B       DNA polymerase family B
    2.7e-33  115.5   0.0    7.1e-33  114.2   0.0    1.6  1  DNA_pol_B_exo1  DNA polymerase family B, exonuclease domain
    3.9e-06   27.0   0.0      1e-05   25.6   0.0    1.8  1  RNase_H_2       RNase_H superfamily
    4.7e-06   26.4   0.0    1.1e-05   25.2   0.0    1.6  1  DNA_pol_B_exo2  Predicted 3'-5' exonuclease related to the ex
     0.0022   17.0   0.1        1.8    7.3   0.0    2.3  2  DNA_pol_B_2     DNA polymerase type B, organellar and viral


Domain annotation for each model (and alignments):
>> DNA_pol_B  DNA polymerase family B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.1   0.8   1.6e-59   5.9e-56      14     431 ..     411     801 ..     399     829 .. 0.85

  Alignments for each domain:
  == domain 1  score: 190.1 bits;  conditional E-value: 1.6e-59
                                    HHHHHHHHHHHHTTBE-B-...........----.--SS.-S----BE----EEESS-EEEEEETTHHHHHHHHTT-STT CS
                      DNA_pol_B  14 rveslLlrlakeegfilpd...........rtekkgkeeegYqGatVlePkkglydkpvlvlDFaSLYPsiiqahNlcyt 82 
                                     +  +L+ +++++g  +p+           +t++  k + +Y Ga V++Pk g+y + v+v+DFaSLYPs+i   Nl+y+
  gi|119719216|ref|YP_919711.1| 411 WIRNMLYYEHRQRGWLIPNledilrlkgqtSTKAIIKGK-KYLGAIVINPKPGVYFN-VVVVDFASLYPSVIKTWNLSYE 488
                                    57789999***********99988887744333323333.6**************85.7789****************** PP

                                    TCE-HCCHCCT--BTT...TEEE-TCC-EEE-TTS---HHHHHHHHHHHHHHH.HHHHHHCS--HHHHHHHHHHHHHHHH CS
                      DNA_pol_B  83 tlvaseeeakeleaedeyleveveprlvefvkksvregllpklLkdllakRka.ikkelkeekdefekalldkqQlalKv 161
                                    t+ ++++e  e +               + +  ++r+gl+++++  l + R   +kk  k++k+e+e++++d  Q alKv
  gi|119719216|ref|YP_919711.1| 489 TVRCQHKECMENRV-------PG----TNHWVCKKRRGLMSEIIGILRDLRVYvYKKGAKSSKNEEERQQYDVIQSALKV 557
                                    ****9998665443.......22....345667899***************862699999******************** PP

                                    HHHHHHHHHTSTTSTT--HHHHHHHHHHHHHHHHHHHHHHHHT...SSGGGT-SS.....T-EEEEEBSSEEEEE-S-SS CS
                      DNA_pol_B 162 taNsvYGftGvansrlpclalAasvTtiGRemLektkelvekkaellskllalpeeaeeeklkviYGDTDSvfielkvkd 241
                                    + N+ YG+ G +  +l+c ++A+s T+ GR+ ++kt +   ++                 ++ v YGDTDS+f+    ++
  gi|119719216|ref|YP_919711.1| 558 FLNASYGVFGSEAFPLYCPPVAESTTALGRYSILKTMQKAVEM-----------------GIPVLYGDTDSLFLWNPPQE 620
                                    ******************************9988887666657.................89***********9776643 PP

                                    HHHHHHHHHHHHHHHHT.TSTTT--EEEEEEEEEEEEEE.TTEEEEEEEEESSTTSEEEEESSGGGSTTS-HHHHHHHHH CS
                      DNA_pol_B 242 veellkigkelaeevseklfkkplklefekvykkllLis.KKkYaglkvektskanklliKGvdlvRrdncklvkevikk 320
                                             +l+e +++ l + ++ l ++k y  +++ + KK Y gl  e     +k++iKG+   +r+  +++k++ ++
  gi|119719216|ref|YP_919711.1| 621 ---------KLEELLQNILNELQIDLSIDKEYLWVVFSKrKKNYLGLLKE-----RKVDIKGLTGKKRNTPDYIKNLFNE 686
                                    .........3444444444446799***********9863777*****99.....99*********************** PP

                                    HHHHHSSS....S-HHHHHHHHHHHHHHHHHHHHTT-S-GGGG-EEEEESS.CCCSSGCCSHHHHHHHHHHHHCSS-... CS
                      DNA_pol_B 321 vlelllkdeteersleeglealksilkdvleeleenkvplekfvlskelskepenyksknlphlevakrlkkrneea... 397
                                    ++e l ++  + ++ e+ ++++++++ ++ ++l++++vpl+++ +  +l+k+ ++y++++  h+++a++l + + +    
  gi|119719216|ref|YP_919711.1| 687 IVEDLSEA-DNVSEFEKSVDKIRDLVFTAIQRLKKHEVPLDQLAFKVALTKPLKEYTKTTPQHVKAARQLLEYRSKLgis 765
                                    *****999.78899*******************************************************99998777889 PP

                                    ..--TTCEEEEEEBETSS.....SS-GGGTEEEHHH CS
                      DNA_pol_B 398 ..pevgdrisYvivekkkevkkknllaseraedpey 431
                                      +evg+ i+Yv + +k+ vk  ++ + + + + +y
  gi|119719216|ref|YP_919711.1| 766 gnVEVGEIIAYVKTRNKDGVKAVQVARIDEVDNDKY 801
                                    99*************999886666555444444444 PP

>> DNA_pol_B_exo1  DNA polymerase family B, exonuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.2   0.0     2e-36   7.1e-33      19     327 ..      44     320 ..      20     325 .. 0.79

  Alignments for each domain:
  == domain 1  score: 114.2 bits;  conditional E-value: 2e-36
                                    EEEEESSCGGHHHHHHHHHHHCCTTCCCEEEEEEEECCCCEECCTSSCCHHCEEEEEESSTCHHHHHHHHHHHCCCCCCC CS
                 DNA_pol_B_exo1  19 fYceapdgkeleevkeelkelyeelskkvtkivkvelvlkkslygyekkpvpylkvsvsnpnelkkirkelspleeivdv 98 
                                    ++++ +    +ee++++  +++  +  +       +l + +++ +++++   ++kv+  +p  +  ++k ++ +    + 
  gi|119719216|ref|YP_919711.1|  44 LLTDLK----PEELIAQYPDVFTHKGFN-------RLEVVEKYDALNDRWFLMTKVEALDPLSIGGTQKSIR-EILRGHA 111
                                    444444....445555555555444322.......2234445555555544599999999999999999996.66789** PP

                                    CSSS--HHHHHHHHCTS-TTCEEEEETEEEEGCC--C-.SEEEEEETTTSCEETTT...........CC..S-EEEEEEE CS
                 DNA_pol_B_exo1  99 yeydvdylerflidnkivgfgwysvkkylvraegkisncdveidcdvddliakpke...........se..pplrvlsFD 165
                                    +e++++y+  +++d ++ ++  y+++  + +++   ++ + ei++  +dl++++ +           +   p+lr  ++D
  gi|119719216|ref|YP_919711.1| 112 WEAKIKYHHCYIYDANLIPGMPYTLE--NGKPKLVDTKVPEEIEKLIRDLVKEKRDlaeylswaqilNApiPRLRRVAID 189
                                    **************************..4444444555555999999999999988999998876653389********* PP

                                    EEETEETTSEETTTT..--EEEEEEEECCTC.SS.SEEEEEEECCCTSS----EE--SSTCSTTEEEEEESSHHHHHHHH CS
                 DNA_pol_B_exo1 166 IeckskkgkfpdaensedpiiqIscvldglgekepearklftlrecaseeeedfeltpkpeypgvkvlefdsEkelLqaf 245
                                    Ie++s +g  p++e+ ++ +i++s+ +d+ +        ++ l+  +          pk e+++ ++  f++EkelLqa 
  gi|119719216|ref|YP_919711.1| 190 IEVDSPPGIVPNPEKADRAVIAVSYYSDDRK-------GVLLLKRSN--------DIPKLEQNDAEITVFENEKELLQAA 254
                                    ***************************7777.......677777777........5778888999*************** PP

                                    HHHHHHH--SEEEESSTTTTHHHHHHHHHHHCCTCCHCG.SCCSCTCEECCCCESEEEEEECEEEETTSEEEEHHHHHHH CS
                 DNA_pol_B_exo1 246 lefikqydPdvitgYNidnFDlpYilnRakelykvklsklgrlnkggrskvseigfskqarekvkisgrihlDlyrvvkr 325
                                    ++++ +y   v++++N+dnFDlpY+lnRa               k g+ + + +   + +++  +i+g ih+Dly+++++
  gi|119719216|ref|YP_919711.1| 255 FKIMTSY--PVVLTFNGDNFDLPYLLNRAL--------------KLGLREEEIPIEWSPRSDYAEIKGSIHIDLYKFFTN 318
                                    *******..*********************..............44555544444444555699***************9 PP

                                    HS CS
                 DNA_pol_B_exo1 326 kl 327
                                    k+
  gi|119719216|ref|YP_919711.1| 319 KS 320
                                    97 PP

>> RNase_H_2  RNase_H superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   2.9e-09     1e-05      42     162 ..     245     392 ..     221     396 .. 0.73

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 2.9e-09
                      RNase_H_2  42 eeekailelflellekkkalvtfngksFDvpflkrlf.....kkyklde................eefrhiDLlkelrkk 100
                                    e ek++l+++ ++++ ++ ++tfng +FD+p+l +++     +     e                +   hiDL+k +++k
  gi|119719216|ref|YP_919711.1| 245 ENEKELLQAAFKIMTSYPVVLTFNGDNFDLPYLLNRAlklglR-----EeeipiewsprsdyaeiKGSIHIDLYKFFTNK 319
                                    55666666667*********************99999566552.....44444466988888777777*******99988 PP

                      RNase_H_2 101 kl..........esysLksveke.lgier.reedlsGsqavklyqeylrtgdeellekilaYNedDvralatly 162
                                     +          e+  L +v  + lgi   + e++  +++++   ey   +d el  k+ ++N d v++l+ l+
  gi|119719216|ref|YP_919711.1| 320 SMrvyafgnkyrEGRTLDEVSMAlLGIGKvKHEEAISEMTPERLVEYS-LRDAELTYKLTSFNNDLVMKLIILM 392
                                    887778888788666888888776666665556677777788888886.4677777788888887777777776 PP

>> DNA_pol_B_exo2  Predicted 3'-5' exonuclease related to the exonuclease domain of PolB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   3.1e-09   1.1e-05      35     111 ..     245     315 ..     207     330 .. 0.73

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 3.1e-09
                 DNA_pol_B_exo2  35 ssekelikkffegvekkkpqlVsfngrgfDlpvleyralkhgvsapkyfdegdedrekkwnnylsrystrhlDLmdl 111
                                    ++ekel++  f+++ ++ p + +fng +fDlp l  ralk g++ ++   e +     +  +y +   + h+DL+  
  gi|119719216|ref|YP_919711.1| 245 ENEKELLQAAFKIMTSY-PVVLTFNGDNFDLPYLLNRALKLGLREEEIPIEWS-----PRSDYAEIKGSIHIDLYKF 315
                                    35*********998876.899*********************98776533322.....3345666666666666655 PP

>> DNA_pol_B_2  DNA polymerase type B, organellar and viral
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0   0.00051       1.8     211     253 ..     449     490 ..     436     503 .. 0.83
   2 !    7.2   0.0   0.00055         2     358     387 ..     539     568 ..     528     572 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00051
                    DNA_pol_B_2 211 kayrGGrc.ypsvlgiyeeniyvyDvnSlYPsamthypmPygkp 253
                                    k y G ++ +p+  g+y  n++v D+ SlYPs+ +   ++y++ 
  gi|119719216|ref|YP_919711.1| 449 KKYLGAIViNPK-PGVY-FNVVVVDFASLYPSVIKTWNLSYETV 490
                                    579999997777.7888.8***************9988888764 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00055
                    DNA_pol_B_2 358 aKekakkeknevkrsiaKlllNsLYGrFat 387
                                     K++ ++++ +v++s  K  lN+ YG F+ 
  gi|119719216|ref|YP_919711.1| 539 SKNEEERQQYDVIQSALKVFLNASYGVFGS 568
                                    56777777778999999***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (835 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       889  (0.0495845); expected 358.6 (0.02)
Passed bias filter:                      673  (0.037537); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.75u 0.32s 00:00:01.07 Elapsed: 00:00:00.47
# Mc/sec: 5383.32
//
Query:       gi|119719217|ref|YP_919712.1|  [L=101]
Description: hypothetical protein Tpen_0299 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 714.53
//
Query:       gi|119719218|ref|YP_919713.1|  [L=127]
Description: hypothetical protein Tpen_0300 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       724  (0.0403815); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 937.55
//
Query:       gi|119719219|ref|YP_919714.1|  [L=122]
Description: hypothetical protein Tpen_0301 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-21   76.7   0.0      2e-21   76.3   0.0    1.1  1  DUF371       Domain of unknown function (DUF371)
  ------ inclusion threshold ------
      0.093   13.0   0.1       0.33   11.2   0.1    1.8  1  THF_DHG_CYH  Tetrahydrofolate dehydrogenase/cyclohydrolase, c


Domain annotation for each model (and alignments):
>> DUF371  Domain of unknown function (DUF371)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.3   0.0   2.2e-25     2e-21      36     126 ..       2      94 ..       1      99 [. 0.87

  Alignments for each domain:
  == domain 1  score: 76.3 bits;  conditional E-value: 2.2e-25
                                    S-S--GGGS-HHHHHHHS----EEE.EEEE-SS-EEEEEEE--TT-----SSEEEEESSS---TTEEEBS-S--GGGS-H CS
                         DUF371  36 eadkaaadlseelkealkeeeatit.vtlevgeledeitgrGspkltlenerdlvvRkSdyvddrTllvkadkaaadldr 114
                                    +a+kaa+dl  e ke l++ + ++  ++l  ++l d+  +rG+p+lt+++ +++vvRkS+y+d+rT++v+++kaa ++dr
  gi|119719219|ref|YP_919714.1|   2 KANKAARDLRPEAKEYLRSGQRVLLaLVLPGQGLYDTFYARGHPDLTFTDRTSIVVRKSSYIDGRTIAVNSQKAAYEIDR 81 
                                    799****************99554414445577*********************************************** PP

                                    HHHHHHHT.T-EE CS
                         DUF371 115 elveaLkk.gael 126
                                    +++e++k+ +a l
  gi|119719219|ref|YP_919714.1|  82 RIIEEIKNpDAVL 94 
                                    *******955544 PP

>> THF_DHG_CYH  Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   3.7e-05      0.33       6     116 .]       5     119 ..       1     119 [. 0.53

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.7e-05
                                    HHHHHHHHHHHHHHHHHHHHT---EEEEEEES--HHHHHHHHHHHH..HHHH........TT-EEEEEEE-TT--HHHHH CS
                    THF_DHG_CYH   6 alakeireelkeeveklkekgvkpkLavilvgddpasevYvrnkkk..acee........vGieseliklpedvseeell 75 
                                    + a+++r e+ke++++    g +  La +l g+    + Y+r   +    ++          i+ ++i+++++    e+ 
  gi|119719219|ref|YP_919714.1|   5 KAARDLRPEAKEYLRS----GQRVLLALVLPGQGLYDTFYARGHPDltFTDRtsivvrksSYIDGRTIAVNSQKAAYEID 80 
                                    4455555555555543....335567777777755555555543320022220000000023333334444434444444 PP

                                    HHHHHHHH-TT--EEEE-SS-STTS-HHHHHCCS-GGGBTT CS
                    THF_DHG_CYH  76 klieelneddsvdGilvqlPlpkhidekaileaispeKDVD 116
                                    + i e  e ++ d++l+ + lp + +++++leai  + DVD
  gi|119719219|ref|YP_919714.1|  81 RRIIE--EIKNPDAVLLLYILPGEASQSEVLEAIREDLDVD 119
                                    44443..4567789999999999999**************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.33s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 784.52
//
Query:       gi|119719220|ref|YP_919715.1|  [L=346]
Description: flap endonuclease-1 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-26   91.6   0.0    5.7e-26   90.7   0.0    1.5  1  XPG_I            XPG I-region
    7.4e-23   80.9   0.0    1.5e-22   79.9   0.0    1.6  1  XPG_N            XPG N-terminal domain
  ------ inclusion threshold ------
      0.024   15.2   1.1      0.067   13.8   0.0    2.4  3  5_3_exonuc       5'-3' exonuclease, C-terminal SAM fold
      0.056   13.8   3.3       0.27   11.6   0.1    2.8  3  AMP-binding_C_2  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> XPG_I  XPG I-region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.7   0.0   1.3e-29   5.7e-26       2      94 .]     143     238 ..     142     238 .. 0.94

  Alignments for each domain:
  == domain 1  score: 90.7 bits;  conditional E-value: 1.3e-29
                                    HHT--EEE-SS-HHHHHHHHHHTTSSSEEE-SSSHHHHTT-SEEEESTT..ECECTT....EEECEEEEEEHHHHHHHHT CS
                          XPG_I   2 lmgipyvvApgEAEAqcayLqkkglvdaviseDsDlllFGapkvlrnls.kkkskkk..kekekkkvevidlekvlkelg 78 
                                     mg+pyv+Ap+E+EAq+ay++kkg+++a  s+D D+llFG+p+++rnl  ++k+k    + ++++k+e+++le++l+ +g
  gi|119719220|ref|YP_919715.1| 143 YMGVPYVEAPSEGEAQAAYMVKKGDAWASGSQDFDSLLFGSPRLVRNLAiTGKRKLPrkDVYVEVKPEIVELEELLRVHG 222
                                    79**********************************************965555544779999***************** PP

                                    --HHHHHHHHHHHCET CS
                          XPG_I  79 ltreqlidlaillgcD 94 
                                    +t++ql+ + il+g+D
  gi|119719220|ref|YP_919715.1| 223 ITHQQLVVIGILVGTD 238
                                    **************99 PP

>> XPG_N  XPG N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.9   0.0   3.4e-26   1.5e-22       6     100 ..       5     102 ..       1     103 [. 0.93

  Alignments for each domain:
  == domain 1  score: 79.9 bits;  conditional E-value: 3.4e-26
                                    HHHHHHHH-GEEEEEGGGGTTEEEEEEHHHHHHHHHHHSE.ETTEE-BS.....-HHHHHHHHHHHHHHHTTEEEEEEE- CS
                          XPG_N   6 LlkllkevaairsvsiealegkklaiDaslwlyrfliavreqlgnalen.....tshlmglfsrllrlldfgikPifVFd 80 
                                    + +l+++va  ++v++ ++++k++aiDa+ +ly+fl ++r+++g+ l       tshl glf+r++  +++gikP++VFd
  gi|119719220|ref|YP_919715.1|   5 IKELVEPVA--KEVELGFFSKKVIAIDAYNSLYQFLATIRQKDGTPLLDaqgnvTSHLNGLFYRTINYIELGIKPVYVFD 82 
                                    6789999**..*********************************988777888*************************** PP

                                    -S--GGGHHHHHHHHHHHHH CS
                          XPG_N  81 gkapdlkkeelekrserrqe 100
                                    g +p+lk++ele+r +++ e
  gi|119719220|ref|YP_919715.1|  83 GRPPELKQKELERRYQIKVE 102
                                    **************999876 PP

>> 5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0         2     9e+03      59      77 ..      24      42 ..       5      51 .. 0.58
   2 ?   -2.5   0.1       1.9   8.4e+03      52      69 ..     103     121 ..      90     140 .. 0.56
   3 ?   13.8   0.0   1.5e-05     0.067      21      50 ..     242     272 ..     226     341 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2
                     5_3_exonuc 59 kLeenkeearlskkLatik 77
                                   k+ +   +  l++ Lati+
  gi|119719220|ref|YP_919715.1| 24 KVIAIDAYNSLYQFLATIR 42
                                   4444444445555566655 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.9
                     5_3_exonuc  52 kekklkekLeenk.eearl 69 
                                    +ekk++e++e++  eear+
  gi|119719220|ref|YP_919715.1| 103 AEKKYREAIERGDlEEARI 121
                                    3356777766643355544 PP

  == domain 3  score: 13.8 bits;  conditional E-value: 1.5e-05
                     5_3_exonuc  21 pGvpgiGektAakLlkeygsleeilenld.e 50 
                                    +G +giG k+A kL+ke ++ e+i+++++ +
  gi|119719220|ref|YP_919715.1| 242 EGARGIGVKKALKLVKELKDPEKIFRSVEwS 272
                                    5899*********************988641 PP

>> AMP-binding_C_2  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1     0.094   4.2e+02      17      32 ..      91     106 ..      88     139 .. 0.67
   2 ?   -1.3   0.0      0.63   2.8e+03      67      85 ..     202     220 ..     188     230 .. 0.65
   3 ?   11.6   0.1     6e-05      0.27      16      67 ..     286     338 ..     275     341 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.094
                                    TTEEEEEEEEEEEETT CS
                AMP-binding_C_2  17 eevepeYqivvtrege 32 
                                    +e+e  Yqi v+ e++
  gi|119719220|ref|YP_919715.1|  91 KELERRYQIKVEAEKK 106
                                    5666667777766654 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.63
                                    HHSS--EEEEE-TT-S--- CS
                AMP-binding_C_2  67 klgvsvkvelvepgtlprs 85 
                                     + v+vk e+ve ++l r 
  gi|119719220|ref|YP_919715.1| 202 DVYVEVKPEIVELEELLRV 220
                                    3566667777776666665 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 6e-05
                                    -TTEEEEEEEEEEEETTEEEEEEEEEE-T.T----HHHHHHHHHHHHHHHHHH CS
                AMP-binding_C_2  16 ieevepeYqivvtregelDelevkvEvke.gfsdelkelealekkiakklksk 67 
                                     +ev++ Y+++ +++++  ++e+ vE+++ ++ + +++l++lek++++++k++
  gi|119719220|ref|YP_919715.1| 286 HPEVTDSYELTWKEPDKEKVIELLVERHQfSMERVTNALDRLEKAVKTHFKQQ 338
                                    489**************************7887888999********999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       694  (0.0387082); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.23s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2445.77
//
Query:       gi|119719221|ref|YP_919716.1|  [L=87]
Description: hypothetical protein Tpen_0303 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.30s 00:00:00.69 Elapsed: 00:00:00.46
# Mc/sec: 573.80
//
Query:       gi|119719222|ref|YP_919717.1|  [L=732]
Description: AAA family ATPase, CDC48 subfamily protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.9e-100  332.5   0.0    2.6e-49  167.0   0.0    2.4  2  AAA              ATPase family associated with various cellul
    5.3e-37  125.4   3.9    1.8e-17   62.8   0.3    2.9  2  AAA_lid_3        AAA+ lid domain
    8.6e-36  122.0   1.8      7e-35  119.1   1.1    2.9  2  CDC48_N          Cell division protein 48 (CDC48), N-terminal
    1.4e-16   60.6   0.0    9.7e-08   31.9   0.0    2.6  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    3.7e-16   58.7   2.6      8e-16   57.6   1.8    2.1  1  CDC48_2          Cell division protein 48 (CDC48), domain 2
    4.5e-15   56.5   0.0    1.9e-06   28.4   0.0    3.3  2  AAA_16           AAA ATPase domain
      4e-14   53.1   0.0    6.2e-08   32.9   0.0    2.6  2  AAA_2            AAA domain (Cdc48 subfamily)
    1.1e-12   47.9   2.0    1.8e-06   27.4   0.0    3.4  3  TIP49            TIP49 P-loop domain
    1.9e-12   47.6   1.3     0.0028   17.9   0.0    4.5  4  AAA_22           AAA domain
      2e-11   44.1   0.7    0.00035   20.6   0.1    3.8  2  AAA_5            AAA domain (dynein-related subfamily)
    6.6e-10   39.3   0.0    0.00032   20.9   0.0    2.7  2  AAA_33           AAA domain
      8e-10   38.9   0.0     0.0002   21.4   0.0    2.5  2  AAA_14           AAA domain
    4.1e-08   33.8   0.1      0.011   16.3   0.0    3.1  2  AAA_18           AAA domain
    4.9e-08   32.6   0.1    8.9e-07   28.5   0.0    2.2  2  UFD1             Ubiquitin fusion degradation protein UFD1
      8e-08   32.6   0.0      0.007   16.8   0.0    2.8  2  RNA_helicase     RNA helicase
    9.9e-08   31.9   0.0      0.017   14.8   0.0    2.4  2  IstB_IS21        IstB-like ATP binding protein
    1.6e-07   31.2   0.0      0.014   15.1   0.0    2.7  2  AAA_24           AAA domain
    2.3e-07   30.6   2.0       0.97    9.0   0.0    4.4  4  AAA_25           AAA domain
    4.5e-07   30.3   0.0      0.045   14.0   0.0    2.5  2  AAA_28           AAA domain
    5.4e-07   29.2   0.5      0.034   13.5   0.1    2.5  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    8.6e-07   28.4   0.3       0.12   11.6   0.0    3.5  3  Zeta_toxin       Zeta toxin
    1.1e-06   28.4   0.1      0.083   12.6   0.0    3.6  2  Sigma54_activat  Sigma-54 interaction domain
    1.3e-05   24.8   0.0       0.15   11.5   0.0    2.6  2  AAA_7            P-loop containing dynein motor region
    1.6e-05   24.2   0.0       0.11   11.6   0.0    2.5  2  DUF815           Protein of unknown function (DUF815)
    2.3e-05   24.4   0.3       0.12   12.3   0.0    3.4  3  ATPase_2         ATPase domain predominantly from Archaea
    2.7e-05   23.4   0.1       0.11   11.5   0.0    2.2  2  Parvo_NS1        Parvovirus non-structural protein NS1
    2.9e-05   24.1   0.0        0.4   10.7   0.0    2.6  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    2.9e-05   24.0   0.3      0.033   14.2   0.0    2.9  2  Vps4_C           Vps4 C terminal oligomerisation domain
    4.7e-05   23.3   0.0        0.4   10.5   0.0    2.6  2  AAA_3            ATPase family associated with various cellul
    6.5e-05   23.5   0.0       0.56   10.7   0.0    2.5  2  ABC_tran         ABC transporter
    0.00011   21.7   0.1       0.42   10.0   0.0    2.5  2  PhoH             PhoH-like protein
    0.00024   20.5   4.3        0.4   10.0   0.0    3.7  3  ATPase           KaiC
    0.00035   19.9   0.0       0.58    9.3   0.0    2.3  2  DUF2075          Uncharacterized conserved protein (DUF2075)
    0.00039   20.3   0.0          1    9.1   0.0    3.2  3  Bac_DnaA         Bacterial dnaA  protein
    0.00044   20.2   0.2        1.4    8.8   0.0    2.8  2  NACHT            NACHT domain
     0.0005   20.0   8.7          4    7.3   0.0    6.1  6  NTPase_1         NTPase
    0.00065   19.0   0.0       0.87    8.7   0.0    2.6  2  NB-ARC           NB-ARC domain
    0.00095   19.5   0.5        3.3    8.0   0.0    3.2  3  AAA_19           AAA domain
     0.0012   18.6   0.0        2.1    8.0   0.0    2.7  2  AAA_30           AAA domain
     0.0022   17.8   0.0        2.8    7.6   0.0    2.4  2  AAA_11           AAA domain
     0.0023   18.4   0.0          4    7.9   0.0    3.2  2  AAA_17           AAA domain
     0.0048   16.9   0.6       0.03   14.4   0.2    2.3  2  Molydop_binding  Molydopterin dinucleotide binding domain
     0.0059   16.7   0.0        5.6    7.1   0.0    2.8  2  Sigma54_activ_2  Sigma-54 interaction domain
     0.0087   15.5   0.2          5    6.4   0.0    2.6  2  IPT              Isopentenyl transferase
  ------ inclusion threshold ------
      0.031   14.0   0.1         41    3.8   0.0    3.6  4  Guanylate_kin    Guanylate kinase
      0.031   13.3   0.0        7.4    5.5   0.0    2.5  2  T2SSE            Type II/IV secretion system protein
      0.036   13.8   0.0          1    9.0   0.0    2.3  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.048   12.6   0.0        5.3    5.8   0.0    2.4  2  AFG1_ATPase      AFG1-like ATPase
      0.049   13.5   0.0        9.1    6.1   0.0    2.7  2  CPT              Chloramphenicol phosphotransferase-like prot
      0.057   13.1   0.1         13    5.5   0.0    2.5  2  Cytidylate_kin   Cytidylate kinase
      0.079   12.7   0.0         17    5.2   0.0    2.4  2  AAA_29           P-loop containing region of AAA domain
      0.087   12.6   0.0         10    5.9   0.0    2.5  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
       0.11   11.6   0.0          8    5.5   0.0    2.3  2  DAP3             Mitochondrial ribosomal death-associated pro
       0.12   12.0   0.1         10    5.6   0.0    2.6  2  cobW             CobW/HypB/UreG, nucleotide-binding domain


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.0   0.0   7.8e-52   2.6e-49       1     131 [.     220     349 ..     220     350 .. 0.98
   2 !  163.3   0.0   1.1e-50   3.8e-48       1     131 [.     493     624 ..     493     625 .. 0.98

  Alignments for each domain:
  == domain 1  score: 167.0 bits;  conditional E-value: 7.8e-52
                                    EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCH CS
                            AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgsese 80 
                                    +llyGppGtGKTllakava+e++++f+ i+g+e++sk+ gese+++re+f+eake+a p i+fiDEida+a++r++ + e
  gi|119719222|ref|YP_919717.1| 220 ILLYGPPGTGKTLLAKAVANETDAYFIAINGPEIMSKFYGESEQRLREIFEEAKEHA-PAIIFIDEIDAIAPKREEVTGE 298
                                    69******************************************************9.********************** PP

                                    HHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                            AAA  81 eeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                    +e+rvv+qLl+ +dg++ + ++vivigatnrp+ ldpal+r gRfdr+iei+
  gi|119719222|ref|YP_919717.1| 299 VEKRVVAQLLALMDGLEAR-GDVIVIGATNRPNALDPALRRpGRFDREIEIG 349
                                    ******************7.66***************************986 PP

  == domain 2  score: 163.3 bits;  conditional E-value: 1.1e-50
                                    EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH..TTCC CS
                            AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr..sgse 78 
                                    +llyGppGtGKTllakava+e++++f++i+g+e+ sk+vgese+ irelf++a++ a psi+fiDEidala+ r   +s+
  gi|119719222|ref|YP_919717.1| 493 ILLYGPPGTGKTLLAKAVATESEANFVSIKGPEVYSKWVGESERAIRELFRKARQVA-PSIIFIDEIDALAPMRglVTSD 571
                                    69******************************************************9.****************999999 PP

                                    CHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                            AAA  79 seeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                    s+++ervv+qLlte+dg+++ e+ v+vi+atnrpd +dpallr gRfdr i+++
  gi|119719222|ref|YP_919717.1| 572 SGVTERVVSQLLTEMDGLERLEG-VVVIAATNRPDIIDPALLRpGRFDRLIYVP 624
                                    ********************877.***************************997 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.8   0.3   5.8e-20   1.9e-17       1      34 [.     372     415 ..     372     433 .. 0.73
   2 !   62.8   0.3   5.4e-20   1.8e-17       1      45 []     647     693 ..     647     693 .. 0.95

  Alignments for each domain:
  == domain 1  score: 62.8 bits;  conditional E-value: 5.8e-20
                      AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrr..........g 34 
                                    dvdl++LAe T+G++GAD+aalcreAa+ Alrr           
  gi|119719222|ref|YP_919717.1| 372 DVDLEKLAEITHGFVGADIAALCREAAMKALRRvlpkidlekdE 415
                                    9********************************44444444440 PP

  == domain 2  score: 62.8 bits;  conditional E-value: 5.4e-20
                      AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgik..eitmedfee 45 
                                    dvdl+e+A++TeGy+GAD++ l+reA+llAlr++i   ++  ++fee
  gi|119719222|ref|YP_919717.1| 647 DVDLAEIARKTEGYTGADIEVLVREAGLLALRENISidKVYRRHFEE 693
                                    9********************************988546******97 PP

>> CDC48_N  Cell division protein 48 (CDC48), N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.1   1.1   2.1e-37     7e-35       1      85 []      11      95 ..      11      95 .. 0.98
   2 ?   -1.5   0.1       8.8   2.9e+03      15      39 ..     116     139 ..     111     162 .. 0.72

  Alignments for each domain:
  == domain 1  score: 119.1 bits;  conditional E-value: 2.1e-37
                                   CEEEECCSS-CSSTTEEEE-HHHHHHHTS-TTSEEEEECCCCEEEEEEEBSTTSTTTTEEEE-HHHHHHHT--TTEEEEEEE CS
                        CDC48_N  1 rLrVaeapqedvgrgivridpedmeelglepgdvveiegkrkTvaivwpaepedegkgiIrmdgvtRknagvsiGdkVtVrk 82
                                   +L+V e +q+++grg+vrid+++me+lg++ gdvveiegkrkTvai+wp++ ed+gkgiIrmdg tRknagvsiGdkV+Vrk
  gi|119719222|ref|YP_919717.1| 11 ELKVLEVRQHEAGRGRVRIDEDAMEALGISAGDVVEIEGKRKTVAIAWPGYAEDKGKGIIRMDGWTRKNAGVSIGDKVKVRK 92
                                   599******************************************************************************* PP

                                   E-- CS
                        CDC48_N 83 aev 85
                                   aev
  gi|119719222|ref|YP_919717.1| 93 AEV 95
                                   985 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 8.8
                                    TEEEE-HHHHHHHTS-TTSEEEEEC CS
                        CDC48_N  15 givridpedmeelglepgdvveieg 39 
                                     ++++++  +++  + +gdv++i+ 
  gi|119719222|ref|YP_919717.1| 116 FVAYVKKRLVDR-PIIEGDVIQIPV 139
                                    567787788887.999999999976 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.0   2.9e-10   9.7e-08      35     105 ..     219     297 ..     193     345 .. 0.78
   2 !   25.8   0.0   2.2e-08   7.4e-06      34      98 ..     491     563 ..     455     568 .. 0.78

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 2.9e-10
                         RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrlsraveevly 105
                                     +llyGpPG Gkt lak +a+e ++ + +  gP +      e ++ l  ++ + +e+   ++fidei  ++++ eev  
  gi|119719222|ref|YP_919717.1| 219 GILLYGPPGTGKTLLAKAVANETDAYFIAINGPEImskfygESEQRLREIFEEAKEHapAIIFIDEIDAIAPKREEVTG 297
                                    69*******************************994444334567799999998876336***************9864 PP

  == domain 2  score: 25.8 bits;  conditional E-value: 2.2e-08
                         RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrlsr 98 
                                      +llyGpPG Gkt lak +a+e ++++ +  gP +      e ++ +  l+ + ++    ++fidei  l++
  gi|119719222|ref|YP_919717.1| 491 KGILLYGPPGTGKTLLAKAVATESEANFVSIKGPEVyskwvgESERAIRELFRKARQVapSIIFIDEIDALAP 563
                                    569*******************************883322223445566666655543237999**9998865 PP

>> CDC48_2  Cell division protein 48 (CDC48), domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.6   1.8   2.4e-18     8e-16       2      63 ..     112     173 ..     111     174 .. 0.97

  Alignments for each domain:
  == domain 1  score: 57.6 bits;  conditional E-value: 2.4e-18
                                    .SCCCCHHHHCCCTTEEE-TTEEEEECCTCCCEEEEEEEECCCCSCEEECTSCCEEESTTCC CS
                        CDC48_2   2 idgdemaylkrqFlgrpvtkGdlvvfefkgqeiklvVvstePkgpvgitetTeielgtkpve 63 
                                    +d++++ay+k+++ +rp+ +Gd+++++++gq i + Vv+++Pkg+v++t++T+ ++ ++pv+
  gi|119719222|ref|YP_919717.1| 112 VDENFVAYVKKRLVDRPIIEGDVIQIPVLGQVIHFNVVNIKPKGVVVVTDKTQLKILERPVD 173
                                    799*********************************************************96 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0   5.6e-09   1.9e-06      16     139 ..     209     322 ..     206     324 .. 0.72
   2 !   23.5   0.1   1.8e-07   6.1e-05      24     132 ..     490     591 ..     480     598 .. 0.68

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 5.6e-09
                         AAA_16  16 lervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqllde.aesael 94 
                                    ++r+  + p  +ll+G++G+GK+ l++++++   +++++f++ +  +      +s +      e+ lr++ +e +e a +
  gi|119719222|ref|YP_919717.1| 209 FKRLGIDPPKGILLYGPPGTGKTLLAKAVAN---ETDAYFIAINGPEI-----MSKFYGES--EQRLREIFEEaKEHAPA 278
                                    66666666799*******************6...5559*********9.....33433333..35555555551444555 PP

                         AAA_16  95 eawrekleealaavpelagaeasrllellkrllallsrderplvl 139
                                      + +++++ +    e++g+ ++r+ ++l +l++ l+ +++ +++
  gi|119719222|ref|YP_919717.1| 279 IIFIDEIDAIAPKREEVTGEVEKRVVAQLLALMDGLEARGD-VIV 322
                                    5555666666668888888888***********99998777.443 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 1.8e-07
                         AAA_16  24 pelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawreklee 103
                                    p  +ll+G++G+GK+ l+++++++ e++   f++ k  +      ys ++    + + +r+l ++a++ +++       +
  gi|119719222|ref|YP_919717.1| 490 PKGILLYGPPGTGKTLLAKAVATESEAN---FVSIKGPEV-----YSKWVGES-E-RAIRELFRKARQVAPSIIFIDEID 559
                                    589*******************988888...999999998.....77777666.3.677777777666566655555555 PP

                         AAA_16 104 alaavpelagaea...srllellkrllallsr 132
                                    ala+ + l  +++   +r+  +l   ++ l+r
  gi|119719222|ref|YP_919717.1| 560 ALAPMRGLVTSDSgvtERVVSQLLTEMDGLER 591
                                    55555555555555555555555555555555 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.0   1.9e-10   6.2e-08       6     105 ..     220     313 ..     215     320 .. 0.90
   2 !   17.4   0.0   1.1e-05    0.0038       6     100 ..     493     583 ..     488     590 .. 0.69

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 1.9e-10
                                    EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG---- CS
                          AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKihpk 83 
                                    ill gp g+Gkt+laka+a+  ++     +i ++  e++     + + ++++  ++   +a+e+   i+++DEid i+pk
  gi|119719222|ref|YP_919717.1| 220 ILLYGPPGTGKTLLAKAVANETDA----YFIAINGPEIMS----KFYGESEQRLREIFEEAKEHApaIIFIDEIDAIAPK 291
                                    8999******************96....************....9999****************999************9 PP

                                    .---------HHHHHHHHHHHH- CS
                          AAA_2  84 .essgadvSregVqrdLLqileg 105
                                     e+ + +v +  V+  LL +++g
  gi|119719222|ref|YP_919717.1| 292 rEEVTGEVEK-RVVAQLLALMDG 313
                                    7777777766.577789999998 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 1.1e-05
                                    EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG---- CS
                          AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKihpk 83 
                                    ill gp g+Gkt+laka+a   ++    +++ +   e+      + + +++   ++   +a +    i+++DEid  +p 
  gi|119719222|ref|YP_919717.1| 493 ILLYGPPGTGKTLLAKAVATESEA----NFVSIKGPEVYS----KWVGESERAIRELFRKARQVApsIIFIDEIDALAPM 564
                                    8999***************99985....888888888888....44444444555555555555577************7 PP

                                    .--------.-HHHHHHHH CS
                          AAA_2  84 .essgadvS.regVqrdLL 100
                                     +  ++d    e V+  LL
  gi|119719222|ref|YP_919717.1| 565 rGLVTSDSGvTERVVSQLL 583
                                    6333333321344444444 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.3       3.6   1.2e+03     115     175 ..     127     184 ..     107     199 .. 0.61
   2 !   17.9   0.0   4.1e-06    0.0014      51      96 ..     218     261 ..     210     288 .. 0.88
   3 !   27.4   0.0   5.4e-09   1.8e-06      51     108 ..     491     547 ..     488     559 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 3.6
                                    S-EEEEEEEEEEE...-SSS-..TTS--EEEEEE-SS-EEEEEE-HHHHHHHHHHT--TT- CS
                          TIP49 115 kevleGevveleveeaenplskekkikevkitlktakeekklklgskiaeellkekvkegD 175
                                    + ++eG+v+++ v  +  +++   +ik   +++ t k  ++lk+ ++ +++ +  +v+ +D
  gi|119719222|ref|YP_919717.1| 127 RPIIEGDVIQIPVLGQVIHFN-VVNIKPKGVVVVTDK--TQLKILERPVDTGKIPRVTYDD 184
                                    458899999998876666666.444444444444443..3445555555555555555555 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 4.1e-06
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkt 96 
                                    +++Ll Gp+gtGkt la a+++e   d  f+a++g e+ s     +
  gi|119719222|ref|YP_919717.1| 218 KGILLYGPPGTGKTLLAKAVANET--DAYFIAINGPEIMSKFYGES 261
                                    89********************96..699*********99755555 PP

  == domain 3  score: 27.4 bits;  conditional E-value: 5.4e-09
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXX CS
                          TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte.vltqalrksig 108
                                    +++Ll Gp+gtGkt la a++ e  ++  fv+++g evys  v  +e ++ + +rk+ +
  gi|119719222|ref|YP_919717.1| 491 KGILLYGPPGTGKTLLAKAVATE--SEANFVSIKGPEVYSKWVGESErAIRELFRKARQ 547
                                    89*******************98..5689**************99985788999*9865 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   8.5e-06    0.0028       8      33 ..     220     245 ..     215     258 .. 0.83
   2 ?    6.1   0.0     0.039        13      73     130 ..     260     325 ..     252     332 .. 0.67
   3 !   15.7   0.0     4e-05     0.013       8      30 ..     493     515 ..     488     536 .. 0.81
   4 ?    2.9   0.0      0.37   1.2e+02      81     104 ..     537     562 ..     531     592 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 8.5e-06
                         AAA_22   8 lvvtGesGtGKTtllrrlleqldeea 33 
                                    ++++G++GtGKT+l++ ++++ d++ 
  gi|119719222|ref|YP_919717.1| 220 ILLYGPPGTGKTLLAKAVANETDAYF 245
                                    89******************997654 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.039
                         AAA_22  73 lsseellealeqalraravielliiDEaqhlr..s........eealeeLrsllnlsrkgvqliLvGt 130
                                     s+++l+e +e+a +++ +  ++ iDE++ +   +        ++++ +L  l++  +    +i++G 
  gi|119719222|ref|YP_919717.1| 260 ESEQRLREIFEEAKEHAPA--IIFIDEIDAIApkReevtgeveKRVVAQLLALMDGLEARGDVIVIGA 325
                                    5667777777777666666..*********98762445556667777777777776555555566665 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 4e-05
                         AAA_22   8 lvvtGesGtGKTtllrrlleqld 30 
                                    ++++G++GtGKT+l++ ++ + +
  gi|119719222|ref|YP_919717.1| 493 ILLYGPPGTGKTLLAKAVATESE 515
                                    89***************999863 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.37
                         AAA_22  81 aleqalrarav..ielliiDEaqhlr 104
                                    a+++ +r+++   ++++ iDE++ l 
  gi|119719222|ref|YP_919717.1| 537 AIRELFRKARQvaPSIIFIDEIDALA 562
                                    455555555556779*********95 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   3.8e-06    0.0012       2     135 ..     220     337 ..     219     339 .. 0.66
   2 !   20.6   0.1   1.1e-06   0.00035       2     134 ..     493     611 ..     492     615 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 3.8e-06
                                    EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGGG--H CS
                          AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEveraes 79 
                                    +lL GppGtgK+ la+ +a  + + +  +++++ +++  + g+ e        +  ++ ++a+   ++i+++DE++ + +
  gi|119719222|ref|YP_919717.1| 220 ILLYGPPGTGKTLLAKAVANETDAYFIAINGPEIMSK--FYGESE-------QRLREIFEEAKehAPAIIFIDEIDAIAP 290
                                    89***************************99998875..444444.......3446667777777889999999998875 PP

                                    ...HHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHH CS
                          AAA_5  80 ...evlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalr 135
                                       ev++++ +    + l l++g e  +         + vi+++n+++     l+palr
  gi|119719222|ref|YP_919717.1| 291 kreEVTGEVEKRVVAQLLALMDGLEARGD--------VIVIGATNRPN----ALDPALR 337
                                    11134444433333333333333333322........77777777776....6666666 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 1.1e-06
                                    EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGGG--. CS
                          AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEverae. 78 
                                    +lL GppGtgK+ la+ +a   +++++ + +++ +++     +         +   +l r+ar   ++i+++DE++ +  
  gi|119719222|ref|YP_919717.1| 493 ILLYGPPGTGKTLLAKAVATESEANFVSIKGPEVYSKWVGESE---------RAIRELFRKARqvAPSIIFIDEIDALAp 563
                                    89******************99***999999996555444444.........55599999**9999**********7764 PP

                                    HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHH CS
                          AAA_5  79 sevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspal 134
                                       l +  s   er ++  ++ ++++  +  +le + via++n++d     ++pal
  gi|119719222|ref|YP_919717.1| 564 MRGLVTSDSGVTERVVS--QLLTEMDGLE--RLEGVVVIAATNRPD----IIDPAL 611
                                    45555555666666665..5555555544..456688888888888....555555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   9.6e-07   0.00032       2      79 ..     220     327 ..     220     349 .. 0.72
   2 !   15.5   0.0   4.3e-05     0.014       2      48 ..     493     541 ..     493     603 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 9.6e-07
                         AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt............................dytrv 51 
                                    +ll G+pG+GK+ la+ ++++++  ++ ++ ++++++ +g+ +q+++                               +v
  gi|119719222|ref|YP_919717.1| 220 ILLYGPPGTGKTLLAKAVANETDayFIAINGPEIMSKFYGESEQRLReifeeakehapaiifideidaiapkreeVTGEV 299
                                    6789***************999998888***********99888888667666777777777777777766555433346 PP

                         AAA_33  52 ldrlyqilnelarkalsagrnvildatn 79 
                                    ++r+ ++l +l +   ++g  +++ atn
  gi|119719222|ref|YP_919717.1| 300 EKRVVAQLLALMDGLEARGDVIVIGATN 327
                                    6666666666664333333334445555 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 4.3e-05
                         AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqsktdy 48 
                                    +ll G+pG+GK+ la+ ++ +    +v +  ++++++ +g+ ++ ++++
  gi|119719222|ref|YP_919717.1| 493 ILLYGPPGTGKTLLAKAVATESEanFVSIKGPEVYSKWVGESERAIREL 541
                                    6789***************999988888889998888887666655544 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   5.9e-07    0.0002       5     101 ..     220     326 ..     217     344 .. 0.80
   2 !   14.7   0.0   7.2e-05     0.024       5      76 ..     493     561 ..     490     581 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 5.9e-07
                         AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev........ 76 
                                    +++ G+  +GKT l+k +++e       ++ in  +   k + ++e+ l++i+e++ke+   ++f+DEi  +        
  gi|119719222|ref|YP_919717.1| 220 ILLYGPPGTGKTLLAKAVANETD---AYFIAINGPEIMSKFYGESEQRLREIFEEAKEHAPAIIFIDEIDAIapkreevt 296
                                    7899**************98888...889999988887776666665666666666677999**********88888888 PP

                         AAA_14  77 ....pewekalkslvd..egknldvivtGSn 101
                                        +++   l  l+d  e  ++dviv G  
  gi|119719222|ref|YP_919717.1| 297 geveKRVVAQLLALMDglE-ARGDVIVIGAT 326
                                    8888888888888888532.57788888865 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 7.2e-05
                         AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev 76 
                                    +++ G+  +GKT l+k ++ e+     +++ i+  +   k   ++e+ ++++++k+++   +++f+DEi  +
  gi|119719222|ref|YP_919717.1| 493 ILLYGPPGTGKTLLAKAVATESE---ANFVSIKGPEVYSKWVGESERAIRELFRKARQVAPSIIFIDEIDAL 561
                                    7899***************8888...8888888888888777766655555555544457899******876 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   3.2e-05     0.011       1      42 [.     220     269 ..     220     328 .. 0.63
   2 !   14.1   0.0   0.00016     0.052       1      25 [.     493     528 ..     493     601 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.2e-05
                         AAA_18   1 IlltGtpGvGKttlakeLskrl.gf....................gvnlrdvakenglllevd 42 
                                    Ill G+pG+GKt lak++++++ ++                                   e +
  gi|119719222|ref|YP_919717.1| 220 ILLYGPPGTGKTLLAKAVANETdAYfiaingpeimskfygeseqrL-------------REIF 269
                                    99******************99777888887744444444443332.............3333 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 0.00016
                         AAA_18   1 IlltGtpGvGKttlakeLskrl..gf.........g 25 
                                    Ill G+pG+GKt lak+++ +   +f         +
  gi|119719222|ref|YP_919717.1| 493 ILLYGPPGTGKTLLAKAVATESeaNFvsikgpevyS 528
                                    99****************655322335555554440 PP

>> UFD1  Ubiquitin fusion degradation protein UFD1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.56   1.9e+02      61      93 ..      17      49 ..       9      56 .. 0.85
   2 !   28.5   0.0   2.7e-09   8.9e-07      68     163 ..      67     161 ..      62     170 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.56
                           UFD1 61 VleFtaeegtvylPewmmenlgleegdlveies 93
                                   V +  a  g+v + e  me+lg++ gd+veie 
  gi|119719222|ref|YP_919717.1| 17 VRQHEAGRGRVRIDEDAMEALGISAGDVVEIEG 49
                                   55567888999********************86 PP

  == domain 2  score: 28.5 bits;  conditional E-value: 2.7e-09
                           UFD1  68 egtvylPewmmenlgleegdlveiesvslpkgkfvklqpqsedfldisdpkavLekaLrnfatLtkgdvieikyndkvye 147
                                    +g + +  w  +n g++ gd v++++++++ ++f++l p s+++   ++  a  +k+L +  +  +gdvi+i +  +v +
  gi|119719222|ref|YP_919717.1|  67 KGIIRMDGWTRKNAGVSIGDKVKVRKAEVKPAQFIRLAPVSMTLAVDENFVAYVKKRLVDRPI-IEGDVIQIPVLGQVIH 145
                                    58899999*************************************99************9776.59************** PP

                           UFD1 148 lkvlevkpesavsiie 163
                                    ++v+++kp+  v + +
  gi|119719222|ref|YP_919717.1| 146 FNVVNIKPKGVVVVTD 161
                                    *********9877765 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   0.00035      0.12       1      23 [.     220     242 ..     220     291 .. 0.83
   2 !   16.8   0.0   2.1e-05     0.007       1      37 [.     493     529 ..     493     535 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00035
                   RNA_helicase   1 iwlyGpsgeGKStlakeLakall 23 
                                    i+lyGp+g+GK++lak +a++  
  gi|119719222|ref|YP_919717.1| 220 ILLYGPPGTGKTLLAKAVANETD 242
                                    789**************988765 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 2.1e-05
                   RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysr 37 
                                    i+lyGp+g+GK++lak +a++ + ++ ++k ++vys+
  gi|119719222|ref|YP_919717.1| 493 ILLYGPPGTGKTLLAKAVATESEANFVSIKGPEVYSK 529
                                    789********************99999999999986 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   6.5e-05     0.022      45      70 ..     215     240 ..     190     282 .. 0.92
   2 !   14.8   0.0   5.2e-05     0.017      47      71 ..     490     514 ..     485     558 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.5e-05
                      IstB_IS21  45 ekkenivllGpsGvGKshlaialgve 70 
                                    +  ++i+l Gp+G+GK+ la a++ e
  gi|119719222|ref|YP_919717.1| 215 DPPKGILLYGPPGTGKTLLAKAVANE 240
                                    556789****************9976 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 5.2e-05
                      IstB_IS21  47 kenivllGpsGvGKshlaialgvea 71 
                                     ++i+l Gp+G+GK+ la a+++e 
  gi|119719222|ref|YP_919717.1| 490 PKGILLYGPPGTGKTLLAKAVATES 514
                                    5789****************99876 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   4.3e-05     0.014       5      76 ..     220     287 ..     217     301 .. 0.65
   2 !   13.1   0.0   0.00017     0.057       5      22 ..     493     510 ..     490     566 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.3e-05
                         AAA_24   5 iliyGpsgiGKTtlakel..gpkplfidtekGlksldadkfpdieswedfldevvelaaeladyktlviDtide 76 
                                    il+yGp+g+GKT lak    + ++ fi +++    +    ++   s + +++ ++e +++ +   +++iD id 
  gi|119719222|ref|YP_919717.1| 220 ILLYGPPGTGKTLLAKAVanETDAYFIAING-PEIMSKFYGE---SEQRLREIFEEAKEHAP--AIIFIDEIDA 287
                                    89**************997666666666555.2222222222...55566666655554444..6677777765 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00017
                         AAA_24   5 iliyGpsgiGKTtlakel 22 
                                    il+yGp+g+GKT lak  
  gi|119719222|ref|YP_919717.1| 493 ILLYGPPGTGKTLLAKAV 510
                                    89*************987 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0    0.0038       1.3      36      53 ..     220     237 ..     214     241 .. 0.87
   2 ?    6.6   0.0     0.015       5.1     128     177 ..     263     312 ..     249     326 .. 0.84
   3 !    9.0   0.0    0.0029      0.97      36      54 ..     493     511 ..     487     515 .. 0.87
   4 ?    2.1   0.0      0.36   1.2e+02     127     172 ..     535     582 ..     519     600 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0038
                         AAA_25  36 allaGapgtGKttlaldl 53 
                                    +ll+G+pgtGKt la  +
  gi|119719222|ref|YP_919717.1| 220 ILLYGPPGTGKTLLAKAV 237
                                    69***********99655 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.015
                         AAA_25 128 advdaleaaieevegvrlvviDplsralggdensnsdv.galvealeriar 177
                                    + ++++ ++++e + ++ + iD ++++ +  e+   +v +++v++l  + +
  gi|119719222|ref|YP_919717.1| 263 QRLREIFEEAKE-HAPAIIFIDEIDAIAPKREEVTGEVeKRVVAQLLALMD 312
                                    567889999***.77***************999999988999999987765 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0029
                         AAA_25  36 allaGapgtGKttlaldla 54 
                                    +ll+G+pgtGKt la  +a
  gi|119719222|ref|YP_919717.1| 493 ILLYGPPGTGKTLLAKAVA 511
                                    69************97666 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.36
                         AAA_25 127 tadvdaleaaieevegvrlvviDplsralgg..densnsdv.galveal 172
                                    ++++++l +++++v+ +  + iD ++++ +     +s+s v +++v++l
  gi|119719222|ref|YP_919717.1| 535 ERAIRELFRKARQVA-PSIIFIDEIDALAPMrgLVTSDSGVtERVVSQL 582
                                    57899********87.**********98766558888888777777765 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   0.00014     0.047       2      48 ..     220     271 ..     219     308 .. 0.71
   2 !   14.0   0.0   0.00014     0.045       2      39 ..     493     535 ..     492     633 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00014
                         AAA_28   2 ivitGgestGKTtlleaLaar....gypvv..pEaareileeklakgedalpw 48 
                                    i + G+++tGKT l++a a++     +  +  pE++ +++ e  ++ +++ ++
  gi|119719222|ref|YP_919717.1| 220 ILLYGPPGTGKTLLAKAVANEtdayFI-AIngPEIMSKFYGESEQRLREIFEE 271
                                    7899***************76554222.3347777777776666555555544 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 0.00014
                         AAA_28   2 ivitGgestGKTtlleaLaar...gypvv..pEaareileekl 39 
                                    i + G+++tGKT l++a a +   +++ +  pE++ + + e  
  gi|119719222|ref|YP_919717.1| 493 ILLYGPPGTGKTLLAKAVATEseaNFVSIkgPEVYSKWVGESE 535
                                    7899***************554455555567777766664433 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.1   0.00012      0.04      25      42 ..     220     237 ..     217     241 .. 0.90
   2 !   13.5   0.1    0.0001     0.034      25      43 ..     493     511 ..     490     515 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00012
                   Mg_chelatase  25 lllvGppGsGKtmlakrl 42 
                                    +ll+GppG+GKt+lak++
  gi|119719222|ref|YP_919717.1| 220 ILLYGPPGTGKTLLAKAV 237
                                    89*************987 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.0001
                   Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                    +ll+GppG+GKt+lak+++
  gi|119719222|ref|YP_919717.1| 493 ILLYGPPGTGKTLLAKAVA 511
                                    89*************9875 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0    0.0013      0.42      15      49 ..     216     248 ..     207     263 .. 0.85
   2 !   11.6   0.0   0.00037      0.12      16      51 ..     490     523 ..     483     527 .. 0.91
   3 ?    2.5   0.0      0.22        75     128     178 ..     674     725 ..     660     730 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0013
                     Zeta_toxin  15 rPklillgGqpGAGKselaellkdelerqgnvvrl 49 
                                     Pk ill G pG GK+ la+++++e+  +  ++ +
  gi|119719222|ref|YP_919717.1| 216 PPKGILLYGPPGTGKTLLAKAVANET--DAYFIAI 248
                                    5999*********************8..4555555 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00037
                     Zeta_toxin  16 PklillgGqpGAGKselaellkdelerqgnvvrldp 51 
                                    Pk ill G pG GK+ la+++++e   + n+v +++
  gi|119719222|ref|YP_919717.1| 490 PKGILLYGPPGTGKTLLAKAVATES--EANFVSIKG 523
                                    999*********************8..899999875 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.22
                     Zeta_toxin 128 vvavkkelSrlgvldRyeee.vaegRlvpkeehdeafeglresvealeeekq 178
                                    ++a ++++S+ +v+ R+ ee +++ R     e+++ +e   e ++++ ++++
  gi|119719222|ref|YP_919717.1| 674 LLALRENISIDKVYRRHFEEaLKKVRPSLTPEIIKFYESWNERARKVSKQQL 725
                                    78999***************55556999999999999999999999998874 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   0.00025     0.083      24      62 ..     219     254 ..     210     331 .. 0.76
   2 !   11.0   0.0   0.00079      0.26      23      55 ..     491     520 ..     481     604 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00025
                                    -EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS- CS
                Sigma54_activat  24 svlitGesGtGKellaraiheaskrkekpfvavncaaip 62 
                                     +l+ G  GtGK+lla+a+ +++   ++ f+a+n  +i 
  gi|119719222|ref|YP_919717.1| 219 GILLYGPPGTGKTLLAKAVANET---DAYFIAINGPEIM 254
                                    69****************97655...5889999977654 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00079
                                    S-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEE CS
                Sigma54_activat  23 lsvlitGesGtGKellaraiheaskrkekpfva 55 
                                      +l+ G  GtGK+lla+a+ ++s+   ++fv+
  gi|119719222|ref|YP_919717.1| 491 KGILLYGPPGTGKTLLAKAVATESE---ANFVS 520
                                    569****************998876...44555 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   0.00046      0.15      34      58 ..     218     242 ..     207     295 .. 0.84
   2 !   10.4   0.0     0.001      0.34      33      60 ..     490     516 ..     480     524 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00046
                          AAA_7  34 kpvllvGptGtGKtviikdllkkld 58 
                                    k +ll+Gp GtGKt+++k + ++ d
  gi|119719222|ref|YP_919717.1| 218 KGILLYGPPGTGKTLLAKAVANETD 242
                                    779****************999988 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.001
                          AAA_7  33 kkpvllvGptGtGKtviikdllkkldke 60 
                                     k +ll+Gp GtGKt+++k + ++ +  
  gi|119719222|ref|YP_919717.1| 490 PKGILLYGPPGTGKTLLAKAVATESE-A 516
                                    5789**************99877766.4 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0     0.001      0.35      52      84 ..     216     248 ..     170     330 .. 0.71
   2 !   11.6   0.0   0.00034      0.11      22     114 ..     450     556 ..     431     559 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.001
                         DUF815  52 pannvLLwGarGtGKSslvkallneyaeegLrl 84 
                                    p + +LL+G  GtGK  l ka+ ne+ +  +++
  gi|119719222|ref|YP_919717.1| 216 PPKGILLYGPPGTGKTLLAKAVANETDAYFIAI 248
                                    56789*******************998877554 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00034
                         DUF815  22 vdevklddLvgidkqkealvente.......qfle..glpannvLLwGarGtGKSslvkallneyaeeg..Lrlieveke 90 
                                    v +v++dd+ g+++ k++l e +e        f +    p + +LL+G  GtGK  l ka+ +e +++   ++  ev  +
  gi|119719222|ref|YP_919717.1| 450 VPAVHWDDIGGLEDVKQQLREAVEwplkypeSFSRlgIDPPKGILLYGPPGTGKTLLAKAVATESEANFvsIKGPEVYSK 529
                                    5567888888888888888877752221111332221357899*******************999888733444577777 PP

                         DUF815  91 dlkelpklvellrerperf...ilfvD 114
                                     + e ++ +++l ++++++   i+f+D
  gi|119719222|ref|YP_919717.1| 530 WVGESERAIRELFRKARQVapsIIFID 556
                                    666666555555433333222266666 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   0.00036      0.12      19     116 ..     216     317 ..     207     325 .. 0.54
   2 ?    7.5   0.0      0.01       3.5      21      45 ..     491     515 ..     483     522 .. 0.83
   3 ?   -0.9   0.0       3.9   1.3e+03     108     131 ..     536     562 ..     516     602 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00036
                       ATPase_2  19 pneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekal..........giavpk 88 
                                    p + +++YGp g GKt L k ++++ +       y+ia+++ +i ++     e++ ++ +e+a+           i+   
  gi|119719222|ref|YP_919717.1| 216 PPKGILLYGPPGTGKTLLAKAVANETD------AYFIAINGPEIMSKFYGESEQRLREIFEEAKehapaiifidEIDAIA 289
                                    6666899**********9999999984......45666665555555555222222222222224444444445333333 PP

                       ATPase_2  89 aeleeilkeksklvfkaielllekikkk 116
                                     + ee+  e  k v +++ +l++ ++ +
  gi|119719222|ref|YP_919717.1| 290 PKREEVTGEVEKRVVAQLLALMDGLEAR 317
                                    3333444455555555555555555555 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.01
                       ATPase_2  21 eiyfiYGpegsGKtaLlkeiienle 45 
                                    + +++YGp g GKt L k +++++e
  gi|119719222|ref|YP_919717.1| 491 KGILLYGPPGTGKTLLAKAVATESE 515
                                    55799************99988774 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 3.9
                       ATPase_2 108 lllekikkkgkk...iiiiiDelqkli 131
                                    ++++++ +k+++    ii+iDe+  l 
  gi|119719222|ref|YP_919717.1| 536 RAIRELFRKARQvapSIIFIDEIDALA 562
                                    455666666666666799999987765 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   0.00034      0.11     117     141 ..     220     244 ..     215     250 .. 0.90
   2 !    9.4   0.0    0.0015      0.49     117     136 ..     493     512 ..     488     517 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00034
                      Parvo_NS1 117 vwfyGpantGktnlaeaIakavply 141
                                    +++yGp+ tGkt la+a a+ ++ y
  gi|119719222|ref|YP_919717.1| 220 ILLYGPPGTGKTLLAKAVANETDAY 244
                                    89*****************988876 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0015
                      Parvo_NS1 117 vwfyGpantGktnlaeaIak 136
                                    +++yGp+ tGkt la+a a+
  gi|119719222|ref|YP_919717.1| 493 ILLYGPPGTGKTLLAKAVAT 512
                                    89***************997 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0    0.0012       0.4      19      45 ..     217     243 ..     187     263 .. 0.75
   2 !   10.5   0.0    0.0014      0.46      20      49 ..     491     522 ..     460     527 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0012
                                    TEEEEEEESTTSSHHHHHHHHHHHTT- CS
                           TsaE  19 gdvilLeGdLGaGKTtlvrglakalgv 45 
                                     + ilL+G+ G+GKT l++++a++ + 
  gi|119719222|ref|YP_919717.1| 217 PKGILLYGPPGTGKTLLAKAVANETDA 243
                                    3449*****************998765 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0014
                                    EEEEEEESTTSSHHHHHHHHHHHTT--..--- CS
                           TsaE  20 dvilLeGdLGaGKTtlvrglakalgve..evk 49 
                                    + ilL+G+ G+GKT l++++a + + +  ++k
  gi|119719222|ref|YP_919717.1| 491 KGILLYGPPGTGKTLLAKAVATESEANfvSIK 522
                                    349******************99877655555 PP

>> Vps4_C  Vps4 C terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1     0.021         7      17      44 ..     414     441 ..     407     445 .. 0.82
   2 !   14.2   0.0    0.0001     0.033      28      58 ..     685     715 ..     678     717 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.021
                         Vps4_C  17 mdipsdkllePpvtlkDflkalkkarpt 44 
                                     +ip + l   +vt++Df++a ++  p+
  gi|119719222|ref|YP_919717.1| 414 DEIPVEVLETIEVTMDDFMNAFREITPS 441
                                    56776777777***********999887 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 0.0001
                         Vps4_C  28 pvtlkDflkalkkarptVskeDLekheeFTk 58 
                                    +v +++f++alkk+rp+ ++e ++ +e + +
  gi|119719222|ref|YP_919717.1| 685 KVYRRHFEEALKKVRPSLTPEIIKFYESWNE 715
                                    68899************************65 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0    0.0017      0.55       2      30 ..     220     248 ..     219     301 .. 0.83
   2 !   10.5   0.0    0.0012       0.4       2      31 ..     493     522 ..     492     610 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0017
                          AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                                    +ll g PG++ktll+ka+a+  d+ f  i
  gi|119719222|ref|YP_919717.1| 220 ILLYGPPGTGKTLLAKAVANETDAYFIAI 248
                                    7999*****************99998766 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0012
                          AAA_3   2 vllegvPGlaktllvkalakaldlefkriq 31 
                                    +ll g PG++ktll+ka+a+  +++f  i+
  gi|119719222|ref|YP_919717.1| 493 ILLYGPPGTGKTLLAKAVATESEANFVSIK 522
                                    7999*****************999998876 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0    0.0027      0.88       8      67 ..     214     271 ..     211     321 .. 0.73
   2 !   10.7   0.0    0.0017      0.56       8      72 ..     487     550 ..     483     597 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0027
                                    EETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe 67 
                                    + + + + + G+ G+GK+ L+k++a++++     i ++g ++ ++   +++++++ +++e
  gi|119719222|ref|YP_919717.1| 214 IDPPKGILLYGPPGTGKTLLAKAVANETDA--YFIAINGPEIMSKFYGESEQRLREIFEE 271
                                    556667889*****************9975..4455566666665555555555555555 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0017
                                    EETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-T CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx RF
                       ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfp 72 
                                    + + + + + G+ G+GK+ L+k++a +++  +  + ++g ++ ++   ++++ i+ l+ +  q+ p
  gi|119719222|ref|YP_919717.1| 487 IDPPKGILLYGPPGTGKTLLAKAVATESE--ANFVSIKGPEVYSKWVGESERAIRELFRKaRQVAP 550
                                    566677889****************9986..56666688777777777777777766666455555 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0    0.0027      0.89      23      40 ..     221     238 ..     214     243 .. 0.87
   2 !   10.0   0.0    0.0013      0.42      23      42 ..     494     513 ..     487     520 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0027
                                    EEE--TTSSTTHHHHHHH CS
                           PhoH  23 faiGpaGtGKtylavala 40 
                                       Gp GtGKt+la a+a
  gi|119719222|ref|YP_919717.1| 221 LLYGPPGTGKTLLAKAVA 238
                                    578***********9998 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0013
                                    EEE--TTSSTTHHHHHHHHH CS
                           PhoH  23 faiGpaGtGKtylavalave 42 
                                       Gp GtGKt+la a+a e
  gi|119719222|ref|YP_919717.1| 494 LLYGPPGTGKTLLAKAVATE 513
                                    578************99976 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0    0.0019      0.64      15      37 ..     213     235 ..     206     249 .. 0.85
   2 ?   -0.7   0.0       2.2   7.4e+02     109     151 ..     263     311 ..     254     318 .. 0.58
   3 !   10.0   0.0    0.0012       0.4      15      41 ..     486     512 ..     477     526 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0019
                         ATPase  15 GipegrvvlitGepGtGKtifal 37 
                                    Gi   + +l++G pGtGKt++a+
  gi|119719222|ref|YP_919717.1| 213 GIDPPKGILLYGPPGTGKTLLAK 235
                                    66667789*************97 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.2
                         ATPase 109 eelaeaikeika...krvviDsitgl...ayeekeavaReilrqlvrvl 151
                                    ++l+e+ +e k+     + iD i+++    +e + +v ++ + ql+  +
  gi|119719222|ref|YP_919717.1| 263 QRLREIFEEAKEhapAIIFIDEIDAIapkREEVTGEVEKRVVAQLLALM 311
                                    4555555555553337788999999932112222333455566666665 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.0012
                         ATPase  15 GipegrvvlitGepGtGKtifalqFli 41 
                                    Gi   + +l++G pGtGKt++a+  + 
  gi|119719222|ref|YP_919717.1| 486 GIDPPKGILLYGPPGTGKTLLAKAVAT 512
                                    66666779*************987655 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0    0.0018      0.58       4      42 ..     220     251 ..     217     300 .. 0.71
   2 !    8.4   0.0    0.0033       1.1       4      25 ..     493     514 ..     490     549 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0018
                        DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertavylsvNhp 42 
                                    +l  G +GtGKt+++ ++++e         a ++  N+p
  gi|119719222|ref|YP_919717.1| 220 ILLYGPPGTGKTLLAKAVANET-------DAYFIAINGP 251
                                    6789*************99998.......3344444444 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0033
                        DUF2075   4 vlVtGvaGtGKtvvllnllael 25 
                                    +l  G +GtGKt+++ ++++e 
  gi|119719222|ref|YP_919717.1| 493 ILLYGPPGTGKTLLAKAVATES 514
                                    6789***********9999997 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0    0.0031         1      37     146 ..     220     334 ..     217     405 .. 0.64
   2 ?   -2.3   0.0       9.8   3.2e+03     178     200 ..     408     430 ..     380     448 .. 0.64
   3 ?    7.4   0.0      0.01       3.4      37      66 ..     493     522 ..     488     658 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0031
                                    EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHT.T-SEEEEE-GGGGTT-HH. CS
                       Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkeklr.kvDvLliDDiqflagkek. 114
                                    +++yg+ G Gkt L ka++ne+ +       + +++ e ++++    +++  e f e    +  ++ iD+i  +a k + 
  gi|119719222|ref|YP_919717.1| 220 ILLYGPPGTGKTLLAKAVANETDA-----YFIAINGPEIMSKFYGESEQRLREIFEEAKEhAPAIIFIDEIDAIAPKREe 294
                                    79***************9987654.....455677777777777777777777776665524456678888888876431 PP

                                    ........HHHHHHHHHHHHHTTT-EEEEEESS-TTT-SS CS
                       Bac_DnaA 115 ........tqeelfhtfnalleegkqvvlssDrsPkelee 146
                                            +  +l+ +++ l   g  +v+ +   P++l+ 
  gi|119719222|ref|YP_919717.1| 295 vtgevekrVVAQLLALMDGLEARGDVIVIGATNRPNALDP 334
                                    1111000122234444455555566677777777766654 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 9.8
                                    HHHHTT----TTHHHHHHHH--S CS
                       Bac_DnaA 178 kieaeklevpeevlefiaervtd 200
                                    ki+ ek e+p evle i  +++d
  gi|119719222|ref|YP_919717.1| 408 KIDLEKDEIPVEVLETIEVTMDD 430
                                    56677777999998888655544 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.01
                                    EEEE-SSSSSHHHHHHHHHHHHHHHSSSS- CS
                       Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelr 66 
                                    +++yg+ G Gkt L ka++ e ++n+ + +
  gi|119719222|ref|YP_919717.1| 493 ILLYGPPGTGKTLLAKAVATESEANFVSIK 522
                                    79****************999888776554 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0059         2       3      23 ..     220     240 ..     218     244 .. 0.89
   2 !    8.8   0.0    0.0042       1.4       3      23 ..     493     513 ..     491     518 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0059
                                    EEEEC-TTTCHHHHHHHHHHH CS
                          NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                    ++l G++G GKT L++ +a +
  gi|119719222|ref|YP_919717.1| 220 ILLYGPPGTGKTLLAKAVANE 240
                                    7899************99875 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0042
                                    EEEEC-TTTCHHHHHHHHHHH CS
                          NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                    ++l G++G GKT L++ +a++
  gi|119719222|ref|YP_919717.1| 493 ILLYGPPGTGKTLLAKAVATE 513
                                    7899************99986 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.44   1.5e+02     101     122 ..     182     203 ..     151     208 .. 0.80
   2 ?    5.3   0.0     0.049        16       2      23 ..     220     241 ..     219     253 .. 0.84
   3 ?    0.8   0.1       1.2   4.1e+02      81     115 ..     261     296 ..     254     311 .. 0.72
   4 ?    2.6   0.1      0.33   1.1e+02      79     123 ..     433     477 ..     415     482 .. 0.79
   5 ?    7.3   0.0     0.012         4       2      32 ..     493     523 ..     492     539 .. 0.84
   6 ?    0.4   0.0       1.6   5.3e+02      78     104 ..     531     558 ..     524     562 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.44
                                    E---STTGGG-HHHHHHHHHHH CS
                       NTPase_1 101 iDEiGkmElkskkfkeaveevL 122
                                     D iG +E   +k++e+ve  L
  gi|119719222|ref|YP_919717.1| 182 YDDIGDLEEAKQKIREMVELPL 203
                                    69***************98655 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.049
                                    EEEE--TTSSHHHHHHHHHHHH CS
                       NTPase_1   2 vfiTGppGvGKtTlvkkvlell 23 
                                    +++ GppG+GKt l k v+++ 
  gi|119719222|ref|YP_919717.1| 220 ILLYGPPGTGKTLLAKAVANET 241
                                    6788***********9999876 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 1.2
                                    HHHHHHHHHHHHHHHH-.EEEE---STTGGG-HHHH CS
                       NTPase_1  81 feelalealrkalsead.viviDEiGkmElkskkfk 115
                                     e+   e++++a ++a  +i iDEi  +  k +++ 
  gi|119719222|ref|YP_919717.1| 261 SEQRLREIFEEAKEHAPaIIFIDEIDAIAPKREEVT 296
                                    577778888888855545*******77665555555 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.33
                                    HHHHHHHHHHHHHHHHHH-EEEE---STTGGG-HHHHHHHHHHHT CS
                       NTPase_1  79 esfeelalealrkalseadviviDEiGkmElkskkfkeaveevLk 123
                                    ++f e++ +alr+   e   +  D iG +E   ++++eave  Lk
  gi|119719222|ref|YP_919717.1| 433 NAFREITPSALREIEVEVPAVHWDDIGGLEDVKQQLREAVEWPLK 477
                                    45667777777776666677888*****************97665 PP

  == domain 5  score: 7.3 bits;  conditional E-value: 0.012
                                    EEEE--TTSSHHHHHHHHHHHH...GGGEEE CS
                       NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgG 32 
                                    +++ GppG+GKt l k v+ + + + v+++G
  gi|119719222|ref|YP_919717.1| 493 ILLYGPPGTGKTLLAKAVATESEANFVSIKG 523
                                    6788***************999999899988 PP

  == domain 6  score: 0.4 bits;  conditional E-value: 1.6
                                    HHHHHHHHHHHHHHHH.HHH-EEEE--- CS
                       NTPase_1  78 vesfeelalealrkal.seadviviDEi 104
                                    v + e+ + e +rka    + +i iDEi
  gi|119719222|ref|YP_919717.1| 531 VGESERAIRELFRKARqVAPSIIFIDEI 558
                                    556788888889999856667******9 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0    0.0026      0.87      23      45 ..     220     242 ..     207     245 .. 0.85
   2 !    7.3   0.0    0.0073       2.4      23      44 ..     493     514 ..     486     522 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0026
                                    EEEEESTTSSHHHHHHHHCCSHC CS
                         NB-ARC  23 valvGmgGvGKttlakqilnksd 45 
                                    + l+G +G GKt lak + n+ d
  gi|119719222|ref|YP_919717.1| 220 ILLYGPPGTGKTLLAKAVANETD 242
                                    779***************99865 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0073
                                    EEEEESTTSSHHHHHHHHCCSH CS
                         NB-ARC  23 valvGmgGvGKttlakqilnks 44 
                                    + l+G +G GKt lak +  +s
  gi|119719222|ref|YP_919717.1| 493 ILLYGPPGTGKTLLAKAVATES 514
                                    679*************998874 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.2     0.013       4.4      12      32 ..     219     239 ..     215     279 .. 0.81
   2 ?   -1.0   0.0         6     2e+03      97     129 ..     271     303 ..     254     313 .. 0.66
   3 ?    8.0   0.0      0.01       3.3      12      32 ..     492     512 ..     488     565 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.013
                         AAA_19  12 vllvtaGpGtGKTrvlkhiva 32 
                                     +l+ ++pGtGKT + k++ +
  gi|119719222|ref|YP_919717.1| 219 GILLYGPPGTGKTLLAKAVAN 239
                                    5899*********98877665 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 6
                         AAA_19  97 ekklqeeellivDEfqdvdelqyrLlkallgek 129
                                    e k ++ +++++DE+  + +   ++  ++ ++ 
  gi|119719222|ref|YP_919717.1| 271 EAKEHAPAIIFIDEIDAIAPKREEVTGEVEKRV 303
                                    3333345699****9999987777776666555 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.01
                         AAA_19  12 vllvtaGpGtGKTrvlkhiva 32 
                                     +l+ ++pGtGKT + k++ +
  gi|119719222|ref|YP_919717.1| 492 GILLYGPPGTGKTLLAKAVAT 512
                                    5899*********87766554 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0085       2.8      22      40 ..     221     239 ..     209     250 .. 0.86
   2 !    8.0   0.0    0.0064       2.1      22      44 ..     494     516 ..     488     554 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0085
                         AAA_30  22 vltGpAGtGKttalkalre 40 
                                    +l Gp+GtGKt + ka+++
  gi|119719222|ref|YP_919717.1| 221 LLYGPPGTGKTLLAKAVAN 239
                                    688**********999976 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0064
                         AAA_30  22 vltGpAGtGKttalkalreawea 44 
                                    +l Gp+GtGKt + ka++   ea
  gi|119719222|ref|YP_919717.1| 494 LLYGPPGTGKTLLAKAVATESEA 516
                                    678***********999876555 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0087       2.9      20      39 ..     220     239 ..     199     276 .. 0.83
   2 !    7.6   0.0    0.0085       2.8      20      38 ..     493     511 ..     468     557 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0087
                         AAA_11  20 tliqGPPGtgKTktivells 39 
                                     l+ GPPGtgKT    ++ +
  gi|119719222|ref|YP_919717.1| 220 ILLYGPPGTGKTLLAKAVAN 239
                                    5899********76655555 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0085
                         AAA_11  20 tliqGPPGtgKTktivell 38 
                                     l+ GPPGtgKT    ++ 
  gi|119719222|ref|YP_919717.1| 493 ILLYGPPGTGKTLLAKAVA 511
                                    5899********6555544 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0     0.023       7.7       1      21 [.     223     243 ..     223     301 .. 0.80
   2 ?    7.9   0.0     0.012         4       1      26 [.     496     521 ..     496     584 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.023
                                    EE-TTSSHHHHHHHHHHHHTE CS
                         AAA_17   1 lGgPGsGKgtqceklvekygf 21 
                                    +G+PG GK+ +++ ++ + + 
  gi|119719222|ref|YP_919717.1| 223 YGPPGTGKTLLAKAVANETDA 243
                                    7***********999988743 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.012
                                    EE-TTSSHHHHHHHHHHHHTEEEEEH CS
                         AAA_17   1 lGgPGsGKgtqceklvekygfthlsa 26 
                                    +G+PG GK+ +++ ++ + +  ++s 
  gi|119719222|ref|YP_919717.1| 496 YGPPGTGKTLLAKAVATESEANFVSI 521
                                    7***********99998876666554 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.2   8.9e-05      0.03      24      59 ..      17      54 ..      10      58 .. 0.80
   2 ?   -1.1   0.0       5.5   1.8e+03      26      53 ..      63      91 ..      55      97 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 8.9e-05
                                   HHCSSS..-EEEEEHHHHHHHT--TT-EEEEEETTEEE CS
                Molydop_binding 24 lakpep..evveinpedAaalGikdGdlVevesrrGsv 59
                                    +++e    +v+i ++ ++alGi+ Gd Ve+e +r +v
  gi|119719222|ref|YP_919717.1| 17 VRQHEAgrGRVRIDEDAMEALGISAGDVVEIEGKRKTV 54
                                   3444444459**********************999876 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 5.5
                                   CSSS.-EEEEEHHHHHHHT--TT-EEEEE CS
                Molydop_binding 26 kpep.evveinpedAaalGikdGdlVeve 53
                                   ++++   +++   + +  G++ Gd+V+v+
  gi|119719222|ref|YP_919717.1| 63 EDKGkGIIRMDGWTRKNAGVSIGDKVKVR 91
                                   444455888888899999*********97 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0     0.028       9.3      24      80 ..     220     287 ..     216     294 .. 0.58
   2 ?    7.1   0.0     0.017       5.6      24      82 ..     493     562 ..     489     567 .. 0.59

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.028
                                    EEEEEETT--HHHHHHCC--TTS-E.E--SSTTHHHH-H.........HHHHHHT...TTSEEEEEE-TT CS
                Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgpw.leifvverlaklp.........ldlleqa...kggtLylkdiad 80 
                                    ++l G++G+gk+l A++ +++     ++i   e  +             +++e+a    ++++++ +i+ 
  gi|119719222|ref|YP_919717.1| 220 ILLYGPPGTGKTLLAKAVANETDAYfIAINGPEIMS--KfygeseqrlREIFEEAkehAPAIIFIDEIDA 287
                                    799*************99987544212222211111..02222233336666665333456666666665 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.017
                                    EEEEEETT--HHHHHHCC--TTS-E.E--SSTTHHHH-H........HHHHHH...TTTSEEEEEE-TT-- CS
                Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgpw.leifvverlaklp........ldlleq...akggtLylkdiadls 82 
                                    ++l G++G+gk+l A++ + +s+ + ++i+  e  +k           +l+ +   + + ++++ +i+ l 
  gi|119719222|ref|YP_919717.1| 493 ILLYGPPGTGKTLLAKAVATESEANfVSIKGPEVYSK-WvgeseraiRELFRKarqVAPSIIFIDEIDALA 562
                                    799***************9988764123322222221.012223333444444222466777777777665 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0      0.02       6.6       5      32 ..     221     248 ..     218     251 .. 0.90
   2 ?    6.4   0.0     0.015         5       5      56 ..     494     545 ..     491     551 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.02
                            IPT   5 lifGatttGKtaeaiklaketgapvivl 32 
                                    l++G+ +tGKt  a ++a+et a  i++
  gi|119719222|ref|YP_919717.1| 221 LLYGPPGTGKTLLAKAVANETDAYFIAI 248
                                    89******************99887775 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.015
                            IPT   5 lifGatttGKtaeaiklaketgapvivlDRvqcyselavgsGrpleeelegt 56 
                                    l++G+ +tGKt  a ++a e  a  +++     ys+    s r++ e +++ 
  gi|119719222|ref|YP_919717.1| 494 LLYGPPGTGKTLLAKAVATESEANFVSIKGPEVYSKWVGESERAIRELFRKA 545
                                    89*******************9999999887777777777777776666655 PP

>> Guanylate_kin  Guanylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.22        74       4      30 ..     219     245 ..     217     253 .. 0.86
   2 ?    2.5   0.0      0.31     1e+02      75     101 ..     254     283 ..     246     297 .. 0.78
   3 ?    3.8   0.0      0.12        41       4      31 ..     492     519 ..     490     529 .. 0.87
   4 ?   -2.2   0.0       8.8   2.9e+03      77      96 ..     529     548 ..     519     565 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.22
                                    EEEEESTTTSSHHHHHHHHHHHSTTTE CS
                  Guanylate_kin   4 pvvlvgpsgaGksslkkaLlselpekf 30 
                                     + l gp g+Gk  l ka+ +e   +f
  gi|119719222|ref|YP_919717.1| 219 GILLYGPPGTGKTLLAKAVANETDAYF 245
                                    6899***************99988887 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.31
                                    TTEEEEEEHHHHHHHHHTTSE...EEEE-- CS
                  Guanylate_kin  75 sgnlygtsveaieevlekgki...viLDvd 101
                                     ++ yg+s +  +e++e++k+   +i+ +d
  gi|119719222|ref|YP_919717.1| 254 MSKFYGESEQRLREIFEEAKEhapAIIFID 283
                                    6789**************998666454444 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.12
                                    EEEEESTTTSSHHHHHHHHHHHSTTTEE CS
                  Guanylate_kin   4 pvvlvgpsgaGksslkkaLlselpekfg 31 
                                     + l gp g+Gk  l ka+ +e + +f 
  gi|119719222|ref|YP_919717.1| 492 GILLYGPPGTGKTLLAKAVATESEANFV 519
                                    6899***************999999885 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 8.8
                                    EEEEEEHHHHHHHHHTTSEE CS
                  Guanylate_kin  77 nlygtsveaieevlekgkiv 96 
                                    +  g+s  ai+e + k+++v
  gi|119719222|ref|YP_919717.1| 529 KWVGESERAIRELFRKARQV 548
                                    56688888888888888875 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.022       7.4     130     155 ..     218     243 ..     174     251 .. 0.79
   2 ?    5.0   0.0     0.033        11     130     154 ..     491     515 ..     436     525 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.022
                          T2SSE 130 glilvsGgTgsGKttllyallkeink 155
                                    + il+ G+ g+GKt l+ a+ +e ++
  gi|119719222|ref|YP_919717.1| 218 KGILLYGPPGTGKTLLAKAVANETDA 243
                                    569**************999988765 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.033
                          T2SSE 130 glilvsGgTgsGKttllyallkein 154
                                    + il+ G+ g+GKt l+ a+ +e +
  gi|119719222|ref|YP_919717.1| 491 KGILLYGPPGTGKTLLAKAVATESE 515
                                    679*************999877654 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.33   1.1e+02       4      71 ..     223     285 ..     220     290 .. 0.60
   2 ?    9.0   0.0    0.0031         1       4      74 ..     496     561 ..     493     575 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.33
                Viral_helicase1   4 hGvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                     G pG GK+ l + ++++    + +++   e+ ++   +++++  + ++++ +++       i+++DE+
  gi|119719222|ref|YP_919717.1| 223 YGPPGTGKTLLAKAVANETdAYFIAING-PEIMSKFYGESEQRLREIFEEAKEHA-----PAIIFIDEI 285
                                    588*************996633333333.34444443444444444444444444.....347788876 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0031
                Viral_helicase1   4 hGvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEylll 74 
                                     G pG GK+ l + ++ +s  ++++++   e++++++ ++++   + ++++ + +  +    i+++DE+ +l
  gi|119719222|ref|YP_919717.1| 496 YGPPGTGKTLLAKAVATESeANFVSIKG-PEVYSKWVGESERAIRELFRKARQVA--P---SIIFIDEIDAL 561
                                    588*************999*99999999.9*******888888888888766633..3...59****99666 PP

>> AFG1_ATPase  AFG1-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.016       5.3      56      79 ..     211     234 ..     181     266 .. 0.84
   2 ?    4.1   0.0     0.055        18      60      79 ..     488     507 ..     464     515 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.016
                    AFG1_ATPase  56 rksvepvrglYlwGgvGrGKtylm 79 
                                    r    p++g+ l+G+ G GKt l 
  gi|119719222|ref|YP_919717.1| 211 RLGIDPPKGILLYGPPGTGKTLLA 234
                                    34678****************986 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.055
                    AFG1_ATPase  60 epvrglYlwGgvGrGKtylm 79 
                                     p++g+ l+G+ G GKt l 
  gi|119719222|ref|YP_919717.1| 488 DPPKGILLYGPPGTGKTLLA 507
                                    69***************985 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.027       9.1       4      40 ..     220     256 ..     218     317 .. 0.84
   2 ?    4.2   0.0      0.11        35       4      32 ..     493     521 ..     491     537 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.027
                                    EEEEE-TTSSHHHHHHHHHHHSSS-EEEEEHHHHHHH CS
                            CPT   4 ilLnGgsssGKsslaralqevldepwlhlgvDafvea 40 
                                    ilL G + +GK+ la+a+ + +d+ +++++  + + +
  gi|119719222|ref|YP_919717.1| 220 ILLYGPPGTGKTLLAKAVANETDAYFIAINGPEIMSK 256
                                    89************************99976666655 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.11
                                    EEEEE-TTSSHHHHHHHHHHHSSS-EEEE CS
                            CPT   4 ilLnGgsssGKsslaralqevldepwlhl 32 
                                    ilL G + +GK+ la+a+ + +++ ++ +
  gi|119719222|ref|YP_919717.1| 493 ILLYGPPGTGKTLLAKAVATESEANFVSI 521
                                    89******************999999876 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0      0.05        17       3      27 ..     222     246 ..     220     250 .. 0.87
   2 ?    5.5   0.0     0.039        13       3      28 ..     495     520 ..     493     528 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.05
                                    EE-STTSSHHHHHHHHHHHHT-EEE CS
                 Cytidylate_kin   3 iDGPagsGKssvaralaeklglkyl 27 
                                    + GP g+GK  +a+a+a++ ++ ++
  gi|119719222|ref|YP_919717.1| 222 LYGPPGTGKTLLAKAVANETDAYFI 246
                                    67****************9988776 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.039
                                    EE-STTSSHHHHHHHHHHHHT-EEEE CS
                 Cytidylate_kin   3 iDGPagsGKssvaralaeklglkyld 28 
                                    + GP g+GK  +a+a+a++ ++++++
  gi|119719222|ref|YP_919717.1| 495 LYGPPGTGKTLLAKAVATESEANFVS 520
                                    67****************99998875 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.072        24      21      39 ..     217     234 ..     208     239 .. 0.75
   2 ?    5.2   0.0     0.052        17      21      42 ..     490     510 ..     480     513 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.072
                         AAA_29  21 lkgatlltGpsGsGKSTll 39 
                                    +kg +ll Gp G+GK+ l 
  gi|119719222|ref|YP_919717.1| 217 PKG-ILLYGPPGTGKTLLA 234
                                    355.9**********8765 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.052
                         AAA_29  21 lkgatlltGpsGsGKSTllDAi 42 
                                    +kg +ll Gp G+GK+ l  A+
  gi|119719222|ref|YP_919717.1| 490 PKG-ILLYGPPGTGKTLLAKAV 510
                                    355.9**********8776665 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0      0.03        10       2      27 ..     218     243 ..     217     247 .. 0.88
   2 ?    4.1   0.0      0.11        36       2      24 ..     491     513 ..     490     521 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.03
                      PduV-EutP   2 kkilliGkvgsGKttLtqalkgeelk 27 
                                    k ill G+ g+GKt L++a+ +e+  
  gi|119719222|ref|YP_919717.1| 218 KGILLYGPPGTGKTLLAKAVANETDA 243
                                    6699****************998755 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.11
                      PduV-EutP   2 kkilliGkvgsGKttLtqalkge 24 
                                    k ill G+ g+GKt L++a+  e
  gi|119719222|ref|YP_919717.1| 491 KGILLYGPPGTGKTLLAKAVATE 513
                                    6699**************98765 PP

>> DAP3  Mitochondrial ribosomal death-associated protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0       0.1        34      24      50 ..     218     243 ..     207     261 .. 0.75
   2 ?    5.5   0.0     0.024         8      26      60 ..     493     526 ..     486     543 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.1
                                    -EEEEE-SSSSSTTTTHHHHHHHGGGS CS
                           DAP3  24 krlvltGekgsGKSvlLlqalayAlek 50 
                                    k ++l+G +g+GK++ L++a+a  +++
  gi|119719222|ref|YP_919717.1| 218 KGILLYGPPGTGKTL-LAKAVANETDA 243
                                    5679*********86.66666655555 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.024
                                    EEEE-SSSSSTTTTHHHHHHHGGGS--EEEEES-G CS
                           DAP3  26 lvltGekgsGKSvlLlqalayAlekgwvvlhvpea 60 
                                    ++l+G +g+GK+ lL++a+a   e+++v ++ pe+
  gi|119719222|ref|YP_919717.1| 493 ILLYGPPGTGKT-LLAKAVATESEANFVSIKGPEV 526
                                    78*********8.5899999888889988887776 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.031        10       4      31 ..     221     248 ..     219     274 .. 0.86
   2 ?    3.3   0.1      0.16        54       4      24 ..     494     514 ..     492     523 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.031
                                    EEEESTTCCHHHHHHHHHCT--SS-EEE CS
                           cobW   4 vltGflGsGKTtLlnhllenraglklav 31 
                                    +l G++G+GKT L +++ ++++ + +a+
  gi|119719222|ref|YP_919717.1| 221 LLYGPPGTGKTLLAKAVANETDAYFIAI 248
                                    689********99999998888888876 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.16
                                    EEEESTTCCHHHHHHHHHCT- CS
                           cobW   4 vltGflGsGKTtLlnhllenr 24 
                                    +l G++G+GKT L +++ +++
  gi|119719222|ref|YP_919717.1| 494 LLYGPPGTGKTLLAKAVATES 514
                                    689********9988877554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (732 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); expected 17.9 (0.001)
Passed Fwd filter:                        54  (0.00301188); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              54  [number of targets reported over threshold]
# CPU time: 0.87u 0.32s 00:00:01.19 Elapsed: 00:00:00.52
# Mc/sec: 4244.70
//
Query:       gi|119719223|ref|YP_919718.1|  [L=263]
Description: peptidylprolyl isomerase, FKBP-type [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-08   33.5   0.2      1e-07   32.1   0.2    2.0  1  FKBP_C    FKBP-type peptidyl-prolyl cis-trans isomerase
    4.5e-07   29.9   0.1    1.2e-06   28.5   0.1    1.8  2  FKBP26_C  FKBP26_C-terminal


Domain annotation for each model (and alignments):
>> FKBP_C  FKBP-type peptidyl-prolyl cis-trans isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.2   1.2e-11     1e-07       6      82 ..       4      97 ..       2     193 .. 0.87

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 1.2e-11
                                   -TTCEEEEEEEEEE..T.TSSEEEEH..........CC...HTSEEEEETTSSSSCHHHHHHHTTSBTT-EEEEEEEGGGTT CS
                         FKBP_C  6 kegdtVtvhykgkl..e.dgkvfdss..........rs...rakplefkvGsgqvikGfeealegmkvGekrtltippelaY 71
                                   ++gd+V v+y+  +  e +++v+d++          r+     +p  ++vG+g ++k  ee l++m+ Gekr++  +p++a+
  gi|119719223|ref|YP_919718.1|  4 QKGDFVLVNYTISVleEsGERVIDTTikeeaekagfRTenvAFEPELVVVGEGFLLKPVEEKLVEMNEGEKREIVLEPSQAF 85
                                   79***********965445888888866666666652233455666789********************************* PP

                                   TTTTBCTTT.B. CS
                         FKBP_C 72 gekglaggv.ip 82
                                   ge++ ++   ip
  gi|119719223|ref|YP_919718.1| 86 GERDPKNIRvIP 97
                                   **9886533444 PP

>> FKBP26_C  FKBP26_C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0      0.84   7.5e+03      23      33 ..     124     134 ..     114     140 .. 0.78
   2 !   28.5   0.1   1.3e-10   1.2e-06       1      71 [.     157     227 ..     157     228 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.84
                                    EEEETTEEEEE CS
                       FKBP26_C  23 ieiedktvtIe 33 
                                    i+i  + vtI 
  gi|119719223|ref|YP_919718.1| 124 IKIGAGRVTID 134
                                    78888888886 PP

  == domain 2  score: 28.5 bits;  conditional E-value: 1.3e-10
                                    HHHHHHHHHHHH-TT--..--EEEEETTEEEEE--TTGGGSTTHHHHHHHHHHHHHHH-TTEEEEEEEEEE CS
                       FKBP26_C   1 dkekikelIkryiPnidlekfkieiedktvtIelpeeakFieniqlaklrIAkdilkrieevekVkFvdef 71 
                                    ++ekik l  r    i ++k++++  d++v+Ie+p + ++ en      + ++d+ k++ ++  +++v+ +
  gi|119719223|ref|YP_919718.1| 157 EEEKIKVLFRRWFRGIPQDKVNVTKGDGAVRIEVPPSIFLFENSFNLLSGFVRDVEKYFGDIASIELVEKI 227
                                    59*******************************************9***********************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       818  (0.0456244); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1758.13
//
Query:       gi|119719224|ref|YP_919719.1|  [L=200]
Description: proteasome endopeptidase complex [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.2e-55  187.9   0.1    1.4e-55  187.8   0.1    1.0  1  Proteasome  Proteasome subunit


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.8   0.1   7.7e-60   1.4e-55       3     190 .]      11     190 ..       9     190 .. 0.94

  Alignments for each domain:
  == domain 1  score: 187.8 bits;  conditional E-value: 7.7e-60
                                    HS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSGTCHH CS
                     Proteasome   3 kGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrpipve 82 
                                    kGtt+vG+ gkd+vvlaad+ratag  +++k+t  Ki +id hi++++aG+++Da++lv+r+r+ea+ y+  +g+ +pv+
  gi|119719224|ref|YP_919719.1|  11 KGTTTVGLVGKDFVVLAADRRATAGYFIANKQT-WKIVEIDSHIAATIAGTVGDAQQLVDRLRVEARYYKTITGDSMPVK 89 
                                    8***************************88885.********************************************** PP

                                    HHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHHSTTBSHHH CS
                     Proteasome  83 rlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekeykedltlee 162
                                          +a+l++ ++ ++r  + v++li+gvd +g p+L+++d  G++++ek ++a+Gsgs +a ++le ey+edl+lee
  gi|119719224|ref|YP_919719.1|  90 -----SVATLASLILFQYRPILSVQMLIGGVDSDG-PSLFSVDWLGTVTREK-YTATGSGSPYAVSLLEHEYREDLSLEE 162
                                    .....555556666666677778*********888.***************8.*************************** PP

                                    HHHHHHHHHHHHHHHBTTSCSSEEEEEE CS
                     Proteasome 163 avelavkalkealerdklsgknievavi 190
                                    av lavka++ al rd  sg+++++a+i
  gi|119719224|ref|YP_919719.1| 163 AVNLAVKAVNIALARDPGSGEGVDIATI 190
                                    *************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1442.67
//
Query:       gi|119719225|ref|YP_919720.1|  [L=90]
Description: hypothetical protein Tpen_0308 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
        0.1   12.8   0.2       0.19   12.0   0.1    1.5  2  Spindle_Spc25  Chromosome segregation protein Spc25


Domain annotation for each model (and alignments):
>> Spindle_Spc25  Chromosome segregation protein Spc25
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   1.1e-05      0.19      20      70 ..       9      57 ..       2      58 .. 0.87
   2 ?   -2.5   0.0      0.33     6e+03      36      44 ..      72      80 ..      62      86 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.1e-05
                  Spindle_Spc25 20 erefsftLdvsedtyevlecsPkLedeeleelleeLnetndlgkFlkevRk 70
                                   e+++ +++dv+e +y +  ++  L    l++ + eL  t+dl  ++ +vR+
  gi|119719225|ref|YP_919720.1|  9 EEQVDLDVDVDEPEYLLDASDKALRG--LSRAVIELAITRDLAVLIDAVRR 57
                                   55667778888888*99999999998..*********************97 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.33
                  Spindle_Spc25 36 vlecsPkLe 44
                                   v + sP L+
  gi|119719225|ref|YP_919720.1| 72 VEQASPDLD 80
                                   555566655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 674.14
//
Query:       gi|119719226|ref|YP_919721.1|  [L=639]
Description: beta-lactamase domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.8e-23   80.6   2.7    2.6e-22   78.5   1.6    2.5  2  KH_7           KH domain
    7.8e-20   71.2   0.0      2e-19   69.9   0.0    1.8  1  Beta-Casp      Beta-Casp domain
    1.9e-16   59.7   0.0    8.2e-16   57.7   0.0    2.2  1  RMMBL          Zn-dependent metallo-hydrolase RNA specificity
    4.9e-15   55.5   0.0    8.1e-15   54.8   0.0    1.3  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain
    1.6e-13   51.1   0.4    8.6e-13   48.7   0.4    2.0  1  Lactamase_B    Metallo-beta-lactamase superfamily
    2.8e-10   40.0   0.0    5.3e-10   39.2   0.0    1.4  1  Lactamase_B_2  Beta-lactamase superfamily domain
     0.0035   17.2   0.0      0.012   15.5   0.0    2.0  1  Lactamase_B_3  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.024   14.5   2.1      0.032   14.1   0.4    2.1  2  KH_2           KH domain


Domain annotation for each model (and alignments):
>> KH_7  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.5   1.6   1.2e-25   2.6e-22       4      67 ..       8      72 ..       6      73 .. 0.94
   2 ?   -0.4   0.0      0.52   1.2e+03       8      26 ..      80      98 ..      76      99 .. 0.88

  Alignments for each domain:
  == domain 1  score: 78.5 bits;  conditional E-value: 1.2e-25
                           KH_7  4 leelkekieeklPkevkitdveFEGPelViYtknpklfa.engdlirklAkelrkRiviRpDpsv 67
                                     e++e+i +++Pke++it+v+FEGP+++iYtk p+ f+ ++g+l++++Ak+++kR+++R Dp+ 
  gi|119719226|ref|YP_919721.1|  8 AREIRETIASNVPKEAEITKVDFEGPKVAIYTKRPQVFLeNDGELVKRIAKTIKKRVIVRGDPES 72
                                   579************************************6678********************86 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.52
                           KH_7  8 kekieeklPkevkitdveF 26
                                   +e i++ +P+e+ +++v F
  gi|119719226|ref|YP_919721.1| 80 EEFIKKAVPPEAGLKNVYF 98
                                   57799***********988 PP

>> Beta-Casp  Beta-Casp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.9   0.0     9e-23     2e-19       1     110 []     419     541 ..     419     541 .. 0.83

  Alignments for each domain:
  == domain 1  score: 69.9 bits;  conditional E-value: 9e-23
                                    HHHHHHHH..HCTT..TTS-S-EEEEE-HHHHHHHHHGGGGGG................E-SHH....HHHH...HHHS- CS
                      Beta-Casp   1 aqellylLeelwkekkledlklpiyldsplaskatevYkeyae................veakslewmeskke.elnssk 63 
                                    aqe+l+ L +l+k+++   +++pi++ + ++ ++ +v+ +++e                 ++++++ +  +++ ++ ++k
  gi|119719226|ref|YP_919721.1| 419 AQEVLLALLDLMKKGA--VPRVPIFIEG-MIDEVSAVHMTFPEylsatiremiyrdenpFTSENIHVIRGEAReDI-TEK 494
                                    69**********9966..5679******.*************9988888888777777522222444444433233.668 PP

                                    SSEEEEES-TTSSSSHHHHHHHHHTTSTTSEEEESS---TTSHHHHH CS
                      Beta-Casp  64 gpkvilassgmlegGrsrellkklledprntvilvgyqaegTlgrkl 110
                                    +p++ila+sgml+gG++ ++l+ l++d+++++++v+yq+egTlgrk+
  gi|119719226|ref|YP_919721.1| 495 KPSIILATSGMLTGGPVLDYLRILADDENSSLVFVSYQVEGTLGRKI 541
                                    9********************************************97 PP

>> RMMBL  Zn-dependent metallo-hydrolase RNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.7   0.0   3.6e-19   8.2e-16       3      56 ..     561     622 ..     559     630 .. 0.85

  Alignments for each domain:
  == domain 1  score: 57.7 bits;  conditional E-value: 3.6e-19
                          RMMBL   3 pvkarieeid.fSgHadknellelirklkprn..vilvHGeeeatsalarll.....keeeg 56 
                                    ++k+r++ ++ fSgH+d+++l  +ir+++p +  vil+HGe  ++++++r+l     k+++g
  gi|119719226|ref|YP_919721.1| 561 DLKMRVYRVEgFSGHSDRRQLEAFIRRMEPSPrtVILNHGEAGKIEEFRRYLssewfKKKTG 622
                                    68**************************************************4444435555 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.8   0.0   3.6e-18   8.1e-15       2     172 ..     198     361 ..     197     372 .. 0.86

  Alignments for each domain:
  == domain 1  score: 54.8 bits;  conditional E-value: 3.6e-18
                  Lactamase_B_6   2 LeldnvkiLlDvGwdeskvslesalkelekv.iptvdliLLshatlehlGayallyakfksklllnipvyatlpvvkLGr 80 
                                    ++  +++iLlD G + +   +e  l +l +  ++++d+++++ha l+h+Ga+++l++     ++ + pvy t p+ +L +
  gi|119719226|ref|YP_919721.1| 198 VQTPEANILLDAGLKPTGNGDELPLFDLPEFdLESLDAVVITHAHLDHVGALPVLFK-----YGYKGPVYMTEPTLHLSK 272
                                    5666899********98666666666666655*******************998875.....57799************* PP

                  Lactamase_B_6  81 vslldlyaskgllgpedseeleledideafdkiktlkYsQklelkskldgltitaynaGhtlGGtiWki..skesekivY 158
                                    ++  d+++ ++ +g+ +    ++ d++    +  tl Y   +++     ++ +t y+aGh lG ++ ++   +++ +ivY
  gi|119719226|ref|YP_919721.1| 273 LLFEDYIKVAQREGKNELY--SMRDVNSLLLNTYTLSYGEVTDIAP---EIRLTFYRAGHILGSAMVHLhiGEGLINIVY 347
                                    ********99998877655..67*****************999985...8***************98762257788**** PP

                  Lactamase_B_6 159 avdwnhakeshLng 172
                                      d+  a+  +L+ 
  gi|119719226|ref|YP_919721.1| 348 TGDMKYARTMLLDP 361
                                    **999999888876 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.7   0.4   3.8e-16   8.6e-13       5     162 ..     192     362 ..     189     398 .. 0.81

  Alignments for each domain:
  == domain 1  score: 48.7 bits;  conditional E-value: 3.8e-16
                                    SSEEEEEEETTCEEEES--SCHHHHHHHH.HHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCH CS
                    Lactamase_B   5 pvnsyliegdggviLiDtGtsteaaraal.elaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalf 83 
                                    + +++l+++++ +iL D+G+ +  +   l +  + +++++ +dav++TH+HlDH+G+l+ l +     +++  e + +l 
  gi|119719226|ref|YP_919721.1| 192 GRSAVLVQTPEANILLDAGLKPTGNGDELpLFDLPEFDLESLDAVVITHAHLDHVGALPVLFKYGYKGPVYMTEPTLHLS 271
                                    6789*******************999999999999********************************************* PP

                                    CHHHHHHHHHCCHH..............TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEEC CS
                    Lactamase_B  84 meeaddaasrkgll..............lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftG 149
                                    +   +d+    + +              l   +  + ++++++ +++++   ++ + ++ g+  +h++++ g  ++++tG
  gi|119719226|ref|YP_919721.1| 272 KLLFEDYIKVAQREgknelysmrdvnslLLNTYTLSYGEVTDIAPEIRL--TFYRAGHILGSAMVHLHIGEGLINIVYTG 349
                                    ****99999999889**9*999977665444444444444444444333..345555666666677777777889***** PP

                                    TTTSSHHCCCCCC CS
                    Lactamase_B 150 Dallagetgridl 162
                                    D+ +a+  ++++ 
  gi|119719226|ref|YP_919721.1| 350 DMKYARTMLLDPA 362
                                    **99988777665 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   0.0   2.4e-13   5.3e-10       2     166 ..     204     378 ..     203     391 .. 0.78

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 2.4e-13
                                    EEEES--TTHHHH..HTCGG.S--SSS--..SEEEEE-SS--HHHHGGGGCCCC.C--EEEEEEEEHHHHH......... CS
                  Lactamase_B_2   2 riLiDagpdlrqq..alral.qPvelrdelppidaVllthaHyDHlaglltlre.lrpkklplyapkgvla......... 68 
                                    +iL+Dag+   ++  +l++      +  +l+++daV++thaH DH+  l+ l + ++  k p+y ++ +l          
  gi|119719226|ref|YP_919721.1| 204 NILLDAGLKPTGNgdELPLFdL---PEFDLESLDAVVITHAHLDHVGALPVLFKyGY--KGPVYMTEPTLHlskllfedy 278
                                    89*******7777666777633...466899***************99****99433..479**9988887666655555 PP

                                    .HCCTTCGHHHCHTT.............TTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTT CS
                  Lactamase_B_2  69 .vleanfvylaleee.............pavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlrieggg 134
                                     +++++        e               +n+ +l  ge +++++ ++++t+  a h  g         ++ l i++g 
  gi|119719226|ref|YP_919721.1| 279 iKVAQR--------EgknelysmrdvnsLLLNTYTLSYGEVTDIAP-EIRLTFYRAGHILGS-------AMVHLHIGEGL 342
                                    522222........02344444566668889999999*******95.789999999998888.......8999******* PP

                                    EEEEEESS-S---....HHHHHHHCT-SEEEEE-S- CS
                  Lactamase_B_2 135 krvyyigDtgyip....eeigerlggadlllldita 166
                                     +++y+gD++y      + + +++  a++l+++ t+
  gi|119719226|ref|YP_919721.1| 343 INIVYTGDMKYARtmllDPAYNKFPRAEVLIIESTY 378
                                    ***********9965555566899999999999886 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   5.4e-06     0.012       6      51 ..     192     247 ..     189     375 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 5.4e-06
                  Lactamase_B_3   6 ghnsflletagarilvDPfka..nlgyeppa........eeaDlvlisqaledHah 51 
                                    g +++l++t++a+il+D + +  + g e p         e+ D+v+i++a+ dH  
  gi|119719226|ref|YP_919721.1| 192 GRSAVLVQTPEANILLDAGLKptGNGDELPLfdlpefdlESLDAVVITHAHLDHVG 247
                                    8899*************9975333344444488999999***************75 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.4   1.4e-05     0.032       1      59 [.      10      65 ..      10     109 .. 0.89
   2 ?   -2.0   0.1       1.4   3.2e+03      45      63 ..     478     494 ..     477     500 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.4e-05
                                   HHHHHHHHHT.ECETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHH CS
                           KH_2  1 eipeslavei.kkagvskveIertanrviiviresqpgivIGkgGsnikkigkelrkdie 59
                                   ei+e +a ++ k+a++ kv+     ++ ++ i++ +p++ +   G+ +k+i k+++k++ 
  gi|119719226|ref|YP_919721.1| 10 EIRETIASNVpKEAEITKVDF----EGPKVAIYTKRPQVFLENDGELVKRIAKTIKKRVI 65
                                   89*******************....8889*****************************94 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.4
                                    HHHHHHHHHHHHHHHHHHT CS
                           KH_2  45 snikkigkelrkdiekleg 63 
                                    +ni  i+ e+r+di   e+
  gi|119719226|ref|YP_919721.1| 478 ENIHVIRGEAREDIT--EK 494
                                    689999999999994..44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (639 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.45
# Mc/sec: 4309.15
//
Query:       gi|119719227|ref|YP_919722.1|  [L=151]
Description: PUA domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-19   70.1   0.4    1.8e-19   69.5   0.4    1.3  1  PUA       PUA domain
    0.00014   22.1   0.1    0.00025   21.2   0.1    1.4  1  UPF0113   UPF0113 PUA domain
     0.0011   19.2   0.0     0.0031   17.8   0.0    1.7  2  DUF1947   Domain of unknown function (DUF1947)
     0.0017   19.0   0.0     0.0031   18.2   0.0    1.4  1  Pre-PUA   Pre-PUA-like domain


Domain annotation for each model (and alignments):
>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.5   0.4   3.9e-23   1.8e-19       2      74 .]      67     140 ..      66     140 .. 0.96

  Alignments for each domain:
  == domain 1  score: 69.5 bits;  conditional E-value: 3.9e-23
                                    EEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETT.SCEEEEEEESS-HHHHHHHCTSEEEEEEEEE CS
                            PUA   2 rvvvddgAvkallsgasLlapGvvevegdfeegdvVaivded.gelvavGlanysseelakikggksveiervl 74 
                                     v vd gAv  +l+ga++++pG+ +++g+f++gd V +   + ++++a+G+a + s+e++ +++gk+v+++++l
  gi|119719227|ref|YP_919722.1|  67 NVYVDSGAVPRILNGADVMVPGIKKIDGEFKPGDRVLVREIEkNRVIALGIAIMGSDEIRGAQKGKAVRNIHYL 140
                                    699***********************************98755*****************************97 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.1   5.6e-08   0.00025       2      68 ..      68     138 ..      67     142 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 5.6e-08
                        UPF0113   2 vvvkekaeklFLYGrdvlkesilkitesvkenqvvvV.lnengeplGiGkirkdt...kaspgkivvknla 68 
                                    v+v+  a  ++L G dv+  +i+ki++++k +++v+V   e+++++++G+++  +   +  ++++ v+n+ 
  gi|119719227|ref|YP_919722.1|  68 VYVDSGAVPRILNGADVMVPGIKKIDGEFKPGDRVLVrEIEKNRVIALGIAIMGSdeiRGAQKGKAVRNIH 138
                                    7889999999***************************6335556666666666556565788888888886 PP

>> DUF1947  Domain of unknown function (DUF1947)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0     7e-07    0.0031      28      65 ..      15      58 ..       3      59 .. 0.79
   2 ?   -2.4   0.0       1.3     6e+03      42      61 ..      69      90 ..      67      93 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 7e-07
                                   -...-EEEE-S...S-EEEEETTEEEEEE..SSSEEE-HHHHHH CS
                        DUF1947 28 sdk.iEieeek...keklYlingvpilfe..eekliPtLklLlk 65
                                   + + iE++  k    e +Y+++gv+ +++  +  l+PtL +++k
  gi|119719227|ref|YP_919722.1| 15 KASrIEVASVKheeIEEMYYVDGVLTVVKtrSAGLVPTLFFIYK 58
                                   444588877772114578***********98899********98 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.3
                                   EEETT.EEEEEE.SSSEEE-HH CS
                        DUF1947 42 Yling.vpilfe.eekliPtLk 61
                                   Y+++g vp +++ ++ ++P +k
  gi|119719227|ref|YP_919722.1| 69 YVDSGaVPRILNgADVMVPGIK 90
                                   5554437888888888888877 PP

>> Pre-PUA  Pre-PUA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   6.8e-07    0.0031      35      85 ..       7      58 ..       2      59 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 6.8e-07
                        Pre-PUA 35 eqleellpkkeevkvvklq.gehvelyvvdgeplffqdregellPtlytlwk 85
                                   e++ + + k + ++v++++ +e  e+y+vdg ++++++r+  l+Ptl++++k
  gi|119719227|ref|YP_919722.1|  7 EVFATYFEKASRIEVASVKhEEIEEMYYVDGVLTVVKTRSAGLVPTLFFIYK 58
                                   5667778887777777777446778***********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 992.00
//
Query:       gi|119719228|ref|YP_919723.1|  [L=193]
Description: tRNA intron endonuclease domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-17   61.7   0.4    6.5e-17   61.0   0.4    1.4  1  tRNA_int_endo_N  tRNA intron endonuclease, N-terminal domain
    2.8e-12   46.5   0.0    6.4e-12   45.4   0.0    1.6  2  tRNA_int_endo    tRNA intron endonuclease, catalytic C-termin
  ------ inclusion threshold ------
      0.011   16.0   0.0      0.017   15.4   0.0    1.3  1  Sen15            Sen15 protein


Domain annotation for each model (and alignments):
>> tRNA_int_endo_N  tRNA intron endonuclease, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.0   0.4   1.1e-20   6.5e-17       2      66 ..      13      76 ..      12      77 .. 0.96

  Alignments for each domain:
  == domain 1  score: 61.0 bits;  conditional E-value: 1.1e-20
                                   EEEEETTEEEESSHHHHHHHHHTTT-SEECCTSSEEEEHHHHHHHHHTTSEEEE.TTSEEE-HHHH CS
                tRNA_int_endo_N  2 egeLsgdrvlvedeeaakrlyekgfYGkplidepLqLslvEAlYLlekGklevv.kggeplsfeel 66
                                   eg++ g+ v v d+e+a++ly++g YG  l +e L+L+lvEA+YL+++++l+v+ ++g++lsf e+
  gi|119719228|ref|YP_919723.1| 13 EGVFDGRIVRVLDKEFAEQLYQRG-YGM-LSGEILELTLVEAAYLVYREMLKVKdDQGRTLSFPEI 76
                                   799*******************98.***.*********************************9875 PP

>> tRNA_int_endo  tRNA intron endonuclease, catalytic C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.3   7.6e+03      27      32 ..      53      58 ..      51      79 .. 0.65
   2 !   45.4   0.0   1.1e-15   6.4e-12       1      85 []      87     169 ..      87     169 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.3
                                   SEEEET CS
                  tRNA_int_endo 27 dFrvYq 32
                                    ++vY+
  gi|119719228|ref|YP_919723.1| 53 AYLVYR 58
                                   455551 PP

  == domain 2  score: 45.4 bits;  conditional E-value: 1.1e-15
                                    HHHHHHHHHHHHHTT-EEEECGGGTSSEEEETSCTTTSSCSEEEEEEETTSEEEHHHHHHHHHHHHHTTSEEEEEEETTT CS
                  tRNA_int_endo   1 falkyavyrdLrekGyvvrsGlkFGadFrvYqrrpslehseylVvvvsedeeldwpdlsaavrlahsvkKklilaivdae 80 
                                    f+ k++vy+dLr++ +  ++G++ + +F+v +++++ +  ++lV++++e++++++p++ +  r a + +++l++aivd+e
  gi|119719228|ref|YP_919723.1|  87 FWVKLNVYTDLRNRALPAKPGVN-PYEFLV-DWKKKGKPRRLLVRILREGTRVSFPEFEDMFRRALESDRELVIAIVDKE 164
                                    99*********************.******.7************************************************ PP

                                    SCEEE CS
                  tRNA_int_endo  81 gdvty 85 
                                    g vty
  gi|119719228|ref|YP_919723.1| 165 GVVTY 169
                                    *9998 PP

>> Sen15  Sen15 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.0   2.9e-06     0.017      49      94 ..     135     176 ..     114     179 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.9e-06
                          Sen15  49 eklslekldkvfkelkeekserkkrivLaivddDsTvvYYkvtdGl 94 
                                    + +s+ +++++f++  e+     +++v+aivd+++ v YY+v+ G 
  gi|119719228|ref|YP_919723.1| 135 TRVSFPEFEDMFRRALES----DRELVIAIVDKEGVVTYYTVEGGS 176
                                    567888888888885544....689****************99885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1231.69
//
Query:       gi|119719229|ref|YP_919724.1|  [L=182]
Description: molybdenum cofactor synthesis domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.5e-30  103.9   0.0    6.4e-30  103.7   0.0    1.0  1  MoCF_biosynth  Probable molybdopterin binding domain
  ------ inclusion threshold ------
      0.084   12.4   0.1       0.12   11.9   0.1    1.2  1  Uma2           Putative restriction endonuclease
        0.1   12.8   0.1        2.4    8.5   0.1    2.4  1  GGDEF_2        GGDEF-like domain
       0.16   11.9   0.0       0.28   11.1   0.0    1.3  1  DUF3487        Protein of unknown function (DUF3487)


Domain annotation for each model (and alignments):
>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.7   0.0   1.4e-33   6.4e-30       2     141 ..      24     170 ..      23     173 .. 0.91

  Alignments for each domain:
  == domain 1  score: 103.7 bits;  conditional E-value: 1.4e-33
                                    EEEE-HHHH.....TTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHH..HHHHHTS..SEEEEESS-SSSTT- CS
                  MoCF_biosynth   2 vitvGdell.....sgkieDtngpllaellkelgvevskytvvpDdeeeikeal..laaleea..dviittGGtGptpdD 72 
                                     +tv+++++      ++i D +  +  el++++g ++  y +vpD++  i eal  l  le++  dv++++GGtGp+p D
  gi|119719229|ref|YP_919724.1|  24 FVTVSTSRFdaelrGERIPDVSVEVARELIERHGDKLVSYILVPDNPRLILEALvnL--LERNdvDVVVFSGGTGPAPSD 101
                                    578999999888877889************************************653..444445*************** PP

                                    -HHHHHHHHHSEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EE.....TTEEEEE-SSHHHHHHHHHHHHHGG CS
                  MoCF_biosynth  73 vtpealaklfekelegfeeafrrvslkpgkpvgvapgailsrav.....gktiigLPGspkavkealeeillpa 141
                                    vt+e++++l+ek+l gf+ +fr++s+++     v+  a ls+a+     gk ++ LPGsp av+ea+e+++lp+
  gi|119719229|ref|YP_919724.1| 102 VTVETVEPLLEKRLAGFGDVFRGLSYQE-----VGSSAFLSNAIagvvhGKLVFLLPGSPDAVREAFEKLILPE 170
                                    ***************************9.....999999***99****7777******************9886 PP

>> Uma2  Putative restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   2.8e-05      0.12      41     101 ..      11      75 ..       3      87 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.8e-05
                                    HHHHHHHHHH-SEEEEETT--EE-TTS-EE--SEEEEEHH..HHTS-HH..HHSS-SS--SEEEE CS
                           Uma2  41 allgnwlrerklgrvfaselgvrlpeeserePDvavvrge..weresrr..iweelpaaPdlvvE 101
                                    +  +++lr+ +  +v++s+ ++  + ++er PDv+v  ++   er++++   +  +p +P l++E
  gi|119719229|ref|YP_919724.1|  11 EHKRKALRDLRYAFVTVSTSRFDAELRGERIPDVSVEVARelIERHGDKlvSYILVPDNPRLILE 75 
                                    4445556665556777778888888***********88776888888888866689999999999 PP

>> GGDEF_2  GGDEF-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.1   0.00053       2.4      49      91 ..     136     177 ..      45     181 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00053
                        GGDEF_2  49 gpdalvavrgdrlvlllpaedeedaeallerlarrlgglsvri 91 
                                      +a+++v +++lv+llp+++++ +ea+ + ++ + g+  ++i
  gi|119719229|ref|YP_919724.1| 136 LSNAIAGVVHGKLVFLLPGSPDAVREAFEKLILPESGH-VLSI 177
                                    5788999**************99888888877777777.5555 PP

>> DUF3487  Protein of unknown function (DUF3487)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   6.2e-05      0.28       5      47 ..     110     153 ..     106     161 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 6.2e-05
                        DUF3487   5 flpdrLnrePvVfrGltadEllvlaglg.lvvglvlglllallv 47 
                                    +l +rL     VfrGl+ +E++  a l+ +++g+v g l++ll 
  gi|119719229|ref|YP_919724.1| 110 LLEKRLAGFGDVFRGLSYQEVGSSAFLSnAIAGVVHGKLVFLLP 153
                                    67789999999***********9997662678999998887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1273.26
//
Query:       gi|119719230|ref|YP_919725.1|  [L=150]
Description: molybdenum cofactor biosynthesis protein C [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-52  176.0   2.2    4.6e-52  175.7   2.2    1.0  1  MoaC      MoaC family
  ------ inclusion threshold ------
      0.013   14.9   0.4      0.023   14.1   0.4    1.4  1  DUF5321   Family of unknown function (DUF5321)


Domain annotation for each model (and alignments):
>> MoaC  MoaC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.7   2.2   5.1e-56   4.6e-52       1     134 [.       8     146 ..       8     147 .. 0.98

  Alignments for each domain:
  == domain 1  score: 175.7 bits;  conditional E-value: 5.1e-56
                                    E---TTS--EEEEEEEEEEEEE-HHHHHHHHTTSSTTB-HHHHHHHHHHHHHHHHHHHSTT-----EEEEEEEEEEETTT CS
                           MoaC   1 mvdvsekeetkrtAvAegrvklseetlelikekklkkGdvlavariagimaaKktseliplcHplpltkveveleleeee 80 
                                    mvd++ k+e++r AvAeg+++l++et+e+i++++++kGdvlava+ a+ima+Kkt+e+iplcHp+p+t v+v++++   e
  gi|119719230|ref|YP_919725.1|   8 MVDITGKAESERLAVAEGKIRLRRETIEKIRRGEVPKGDVLAVAKTAAIMAVKKTWEIIPLCHPIPITFVDVNFDVM--E 85 
                                    9*************************************************************************987..7 PP

                                    TEEEEEEEEEEEESS--HHHHHHHHHHHHHHHHHHHTTTHTT.......-EEEEEEEEEEE CS
                           MoaC  81 esveieatvktegktGvemEALtavsvaaltvyDmvKavdke.......mvieevrlveKs 134
                                    e+++++++vkt++ktGvemEALt++sva+ltv+DmvK+++k+       ++i+++r+veK 
  gi|119719230|ref|YP_919725.1|  86 EELRVRVEVKTTAKTGVEMEALTGASVALLTVWDMVKSLEKDqegqypyTEINSIRVVEKV 146
                                    99***************************************99****************96 PP

>> DUF5321  Family of unknown function (DUF5321)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.4   2.6e-06     0.023      58      95 ..       3      41 ..       1      56 [. 0.79

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.6e-06
                        DUF5321 58 Sqairmialknefa.aytrkadakielLreviekvqrGE 95
                                   S  +rm+ +  + + +    a+ ki+l re iek++rGE
  gi|119719230|ref|YP_919725.1|  3 SVNVRMVDITGKAEsERLAVAEGKIRLRRETIEKIRRGE 41
                                   5567888876555414566799****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1143.60
//
Query:       gi|119719231|ref|YP_919726.1|  [L=125]
Description: molybdopterin biosynthesis MoaE [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.9e-21   75.1   0.3    5.7e-21   74.9   0.3    1.0  1  MoaE      MoaE protein


Domain annotation for each model (and alignments):
>> MoaE  MoaE protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.9   0.3   3.2e-25   5.7e-21      20     113 .]       1      94 [.       1      94 [. 0.98

  Alignments for each domain:
  == domain 1  score: 74.9 bits;  conditional E-value: 3.2e-25
                                    --EEEEEEEE------TS-EEEEEECC-HHHHHHHHHHHHHHHHCCCTTSEEEEEEE-EEEETTSEEEEEEEEESSHHHH CS
                           MoaE  20 aGAvvlFvGtvRdsfdgkkvteLeyeayepmaektleeiaeearerwelervavvHrlGelevgeasvvvavssahRkea 99 
                                    +GAv++F+G v+ + +g++v++L ye  ep+  ++le+ia+e  e+ +l +v ++H+ G   +ge+++++av+s+ R+ea
  gi|119719231|ref|YP_919726.1|   1 MGAVAVFIGRVKGRIEGRRVESLMYEVVEPSSSQSLERIAREELEKNNLLAVSIHHKKGVAVPGEPVLFIAVASKSREEA 80 
                                    6***********9999**************************************************************** PP

                                    HHHHHHHHHHHHHH CS
                           MoaE 100 feaceylidelKkr 113
                                    ++  +  ++++K++
  gi|119719231|ref|YP_919726.1|  81 VSGLRSTLERVKHE 94 
                                    ************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.27s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 985.99
//
Query:       gi|119719232|ref|YP_919727.1|  [L=83]
Description: MoaD family protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.8e-10   40.3   0.1    4.3e-10   40.1   0.1    1.1  1  ThiS       ThiS family
  ------ inclusion threshold ------
      0.027   14.3   0.0      0.043   13.7   0.0    1.3  1  Ub-Mut7C   Mut7-C ubiquitin
      0.074   13.2   0.0      0.087   12.9   0.0    1.1  1  ddrB-ParB  ddrB-like ParB superfamily domain


Domain annotation for each model (and alignments):
>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.1   0.1   7.3e-14   4.3e-10       1      77 []       5      83 .]       5      83 .] 0.90

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 7.3e-14
                                   EEETTCCHHHHT...CEEEEESSTSBHHHHHHHHHHHTCHHG..TTTTEEEEETTEEEGCCTTTSB--TTCEEEEEESTTC- CS
                           ThiS  1 vllfaelrelag...eeelelaegstvaelleaLgerypela..lerrvavavNgeivprlwldtelkdgDevailppVaGG 77
                                   v++    ++++g   ee +++ae+ t+++ll+ L+e+y+      e+ + v+vNg+       +++l+dg +v+i ppV+GG
  gi|119719232|ref|YP_919727.1|  5 VRYVSLMKDKTGkeqEEIELDAEEPTLEDLLRILEEKYGVPMlsGEEEMLVLVNGRRSGL---KEKLSDGSQVVIAPPVSGG 83
                                   566667788889988899999*****************66559978**********9999...******************9 PP

>> Ub-Mut7C  Mut7-C ubiquitin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   7.2e-06     0.043      40      75 ..      40      78 ..      26      81 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.2e-06
                       Ub-Mut7C 40 EalGVPh...tEVelilvnGesvgfshiledGdrvavyp 75
                                   E  GVP     E  l+lvnG+ +g+++ l+dG +v ++p
  gi|119719232|ref|YP_919727.1| 40 EKYGVPMlsgEEEMLVLVNGRRSGLKEKLSDGSQVVIAP 78
                                   5668886332356689*******************9988 PP

>> ddrB-ParB  ddrB-like ParB superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.5e-05     0.087      33      88 ..      15      71 ..       5      74 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.5e-05
                      ddrB-ParB 33 raaseaqieeiAanldperlgdsreaasGaPivg.kdgvvesGNgRtaalkaayeeg 88
                                   + +++++ie  A+++  e l +  e + G+P+++ ++++    NgR  +lk+   +g
  gi|119719232|ref|YP_919727.1| 15 TGKEQEEIELDAEEPTLEDLLRILEEKYGVPMLSgEEEMLVLVNGRRSGLKEKLSDG 71
                                   67889999999**********************956669***********9876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 597.77
//
Query:       gi|119719233|ref|YP_919728.1|  [L=402]
Description: succinyl-diaminopimelate desuccinylase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-29  103.2   0.1    2.1e-29  102.7   0.1    1.1  1  Peptidase_M20  Peptidase family M20/M25/M40
    1.4e-19   70.0   0.0    1.5e-18   66.7   0.0    2.1  2  M20_dimer      Peptidase dimerisation domain
    0.00014   21.6   0.0     0.0018   18.0   0.0    2.1  2  Peptidase_M28  Peptidase family M28
  ------ inclusion threshold ------
      0.019   14.8   0.0      0.045   13.5   0.0    1.6  1  EKR            Domain of unknown function


Domain annotation for each model (and alignments):
>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.7   0.1   4.7e-33   2.1e-29       2     205 ..      79     400 ..      78     401 .. 0.91

  Alignments for each domain:
  == domain 1  score: 102.7 bits;  conditional E-value: 4.7e-33
                                    EEEES-BSS.TTCG..GGSSS.TTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTTTH CS
                                    xxxxxxxxx.xxxx..xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M20   2 lgsHlDvVp.eeet..dgwtt.pfslteedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggrgG 77 
                                    +  H+DvVp +++   +g t  p+s+ + dGk+yGrGa+d+k g++a ++ l  ++++gi+p+++ v+++++dEE+g+ G
  gi|119719233|ref|YP_919728.1|  79 FVTHYDVVPaKGPWvvEGRTMdPYSPLVLDGKVYGRGAADDKSGIVATIAGLVDIREAGIEPRYNPVVVVTGDEEVGGTG 158
                                    568******877766677788******************************************************988** PP

                                    HHHHHHHHHTTTCESEEEEEEEESSSBTCHSTETEEEE.......................................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......................................... RF
                  Peptidase_M20  78 akallegleerekvdavfelhieepgileagklaigvv.......................................... 115
                                    ++ lle   +++++d+v+  ++  ++  +    a gvv                                          
  gi|119719233|ref|YP_919728.1| 159 IRRLLE---KGYRWDYVI--IVDSGSEYV-SVGASGVVhgwikvkgksghagyphvarnavedlvrvlgelmelktvrga 232
                                    ******...699999966..555555555.4446777799**************************************** PP

                                    ............................................................................EEEE CS
                                    ............................................................................xxxx RF
                  Peptidase_M20 116 ............................................................................kvev 119
                                                                                                                + ev
  gi|119719233|ref|YP_919728.1| 233 rlskypsppgspvpyvwgrltfnilrlpptepekhnripgeawcgfdmrllpeedveeavrelyaklssiamklgvSLEV 312
                                    ***************************************************************************88999 PP

                                    EEEEEESHEEECCHHHHHHHHHHHHHHHTSCEEEEEES.SSBHTHHHH..TTTEEEEEEE.SSG.GCTTSTTTEEEHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx..xxxxxxxxxx.xxx.xxxxxxxxxxxxxxx RF
                  Peptidase_M20 120 elleggapvtlndsplvkalaeaaeelfgekvelivsg.pggtdarff..agiptvmifg.pgs.glaHspnEyvdledl 194
                                    e ++ ++ + ++++++v+ +  aa +  g+  e++v +  gg d  ff   g+  v+ fg   +  ++Hs+ E+v +ed+
  gi|119719233|ref|YP_919728.1| 313 EIIGKQKGWYSKNEAFVREVLTAAGRSKGR--EVPVAAeLGGNDGTFFdeYGM-DVVAFGtIREgTNIHSEGEHVYVEDI 389
                                    999*************99999999996574..44555567********87777.77779955546*************** PP

                                    HHHHHHHHHHH CS
                                    xxxxxxxxxxx RF
                  Peptidase_M20 195 ekgikvlarll 205
                                    e+  k+++++l
  gi|119719233|ref|YP_919728.1| 390 EAFRKFMYEFL 400
                                    ********998 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0       0.1   4.7e+02      32      89 ..      34      84 ..      32      89 .. 0.80
   2 !   66.7   0.0   3.3e-22   1.5e-18       2     105 ..     185     303 ..     184     306 .. 0.95

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.1
                                   HHHHHHHCSCTTEEC.....TCCTCCCCCEECCE-C...CCCEESSEEEEEEEEEHHHHHH CS
                      M20_dimer 32 klarllaeledeegdiaeerslprttlnvtgiegGs...aknvipdeaeakidiRllpged 89
                                   ++a+++a+l ++          ++  ++   +egG     + ++p++a+ k ++ ++ + d
  gi|119719233|ref|YP_919728.1| 34 EAAEAVARLAET----------HGLRVEKVDLEGGEiptVIASLPGKASGKPSVAFVTHYD 84
                                   788899999888..........458888888899997778888999999888888888777 PP

  == domain 2  score: 66.7 bits;  conditional E-value: 3.3e-22
                                    EB-EEEEEEEEEE-B-EEGG-TTTTB-HHHHHHHHHHCSCTTEEC..................TCCTCCCCCEECCE-C. CS
                      M20_dimer   2 ghkGlaggkitvkgkagHsgapgagaNAieklarllaeledeegdia.............eerslprttlnvtgiegGs. 67 
                                    g  G++ g+i+vkgk+gH+g+p+ ++NA+e l+r+l el +++   +              ++ ++r t+n+  +     
  gi|119719233|ref|YP_919728.1| 185 GASGVVHGWIKVKGKSGHAGYPHVARNAVEDLVRVLGELMELKTVRGarlskypsppgspVPYVWGRLTFNILRLPPTEp 264
                                    778***************************************87777****************************99889 PP

                                    .CCCEESSEEEEEEEEEHHHHHHHHHHHHHHHHHHTSCC CS
                      M20_dimer  68 .aknvipdeaeakidiRllpgedpeevleeieeilekea 105
                                     + n ip+ea + +d+Rllp+ed+ee+  e+ + l++ a
  gi|119719233|ref|YP_919728.1| 265 eKHNRIPGEAWCGFDMRLLPEEDVEEAVRELYAKLSSIA 303
                                    9*****************************999988765 PP

>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   3.9e-07    0.0018       2      82 ..      63     163 ..      62     184 .. 0.88
   2 ?    1.3   0.0     0.052   2.3e+02     120     179 ..     326     384 ..     306     400 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3.9e-07
                                    EEEEESTTCE.SEEEEEEEE--B-TTT..................TCC.T---TTTTHHHHHHHHHHHHHCHHGGCCSSE CS
                  Peptidase_M28   2 viatlegkat.devlllgAHyDsvgvg..................rgp.ifvGAdDnAsgvaalLelarvlaasgsrpkr 61 
                                    via+l+gka+ +  +++  HyD v+ +                  +g+    GA D+ sg++a +  +  + + g +p++
  gi|119719233|ref|YP_919728.1|  63 VIASLPGKASgKPSVAFVTHYDVVPAKgpwvvegrtmdpysplvlDGKvYGRGAADDKSGIVATIAGLVDIREAGIEPRY 142
                                    9*********888************99*********9998888886666678*************99999999999**** PP

                                    EEEEEEESSCSGSSHHHHHHH CS
                  Peptidase_M28  62 gvrflffdaEEagllGSkafa 82 
                                    + ++++++ EE g  G +++ 
  gi|119719233|ref|YP_919728.1| 143 NPVVVVTGDEEVGGTGIRRLL 163
                                    *99*********999988877 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.052
                                    HHHHHHHHHHTT-TTSCCEEEEESSTT-STTHHHHTTT--EEEECTSSS-TTTTSTTSSG CS
                  Peptidase_M28 120 ekelkalakpvgraaaedpfdersgrgrsDhspflkagvpvldlaetgfpevyHtprDtl 179
                                    e+ ++++  ++gr++  ++ + +   g +D + f ++g+ v+ + +   ++++H++  ++
  gi|119719233|ref|YP_919728.1| 326 EAFVREVLTAAGRSKGREV-PVAAELGGNDGTFFDEYGMDVVAFGTIREGTNIHSEGEHV 384
                                    5556666666666655544.34456899****************8888888888876555 PP

>> EKR  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0     1e-05     0.045      12      44 ..     325     357 ..     317     359 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1e-05
                                    --HHHHHTHHHHHTT-GGGS-GGGS-..TT-EE CS
                            EKR  12 apefVkevlapinaqeGDeLpVSafpgmeDGtf 44 
                                      +fV+evl    + +G e+pV a  g +DGtf
  gi|119719233|ref|YP_919728.1| 325 NEAFVREVLTAAGRSKGREVPVAAELGGNDGTF 357
                                    567*********************999*****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2837.81
//
Query:       gi|119719234|ref|YP_919729.1|  [L=276]
Description: ribose-phosphate pyrophosphokinase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.6e-22   77.4   0.1    1.8e-18   66.6   0.0    2.2  2  Pribosyltran_N  N-terminal domain of ribose phosphate pyropho
    1.1e-13   51.1   1.5    1.7e-13   50.4   1.1    1.5  2  Pribosyltran    Phosphoribosyl transferase domain
    5.3e-10   39.6   1.7    3.2e-09   37.1   0.7    2.1  2  Pribosyl_synth  Phosphoribosyl synthetase-associated domain
  ------ inclusion threshold ------
      0.012   15.1   0.1       0.02   14.4   0.1    1.3  1  PRTase_2        Phosphoribosyl transferase
      0.088   12.2   0.1       0.15   11.5   0.1    1.4  1  UPRTase         Uracil phosphoribosyltransferase


Domain annotation for each model (and alignments):
>> Pribosyltran_N  N-terminal domain of ribose phosphate pyrophosphokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.6   0.0     5e-22   1.8e-18      24     116 .]       5      97 ..       1      97 [. 0.92
   2 !    8.8   0.1   0.00042       1.5      28      86 ..     169     224 ..     148     229 .. 0.69

  Alignments for each domain:
  == domain 1  score: 66.6 bits;  conditional E-value: 5e-22
                 Pribosyltran_N  24 lgkakvsrfadgEikveieesvrgkdvfiiqslskpvndnlmelllmidalrrasakritaViPylgysrqdrk.ksrep 102
                                    l+ ++ + f+dgEi+v++ ++  g  + ++ s+++p + +l+elll+++al+     +++aV+Pyl+y+rqd++  + ep
  gi|119719234|ref|YP_919729.1|   5 LVFVEKKVFPDGEIYVRVPSKPSGVAI-VVSSTHPPQERRLLELLLTVEALSSYAQGSVIAVVPYLAYARQDKRfLEGEP 83 
                                    56677889***********99988765.689999999***************9999************************ PP

                 Pribosyltran_N 103 isaklvaklLeaaG 116
                                    is k+v+k LeaaG
  gi|119719234|ref|YP_919729.1|  84 ISIKVVLKALEAAG 97 
                                    ************99 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00042
                 Pribosyltran_N  28 kvsrfadgEikveiee.svrgkdvfiiqslskpvndnlmelllmidalrrasakritaVi 86 
                                    k +   +gE++v+ ++ +v g+dv+i+ ++ +   +  +  l   +al  + a+++taV 
  gi|119719234|ref|YP_919729.1| 169 KERDRVTGEVRVQPKSlEVNGRDVVIVDDIISTGKT--I-ALAAKSAL-AQGASSVTAVC 224
                                    4555678********99***********99876322..2.23333444.46677777775 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       1.9   6.7e+03     106     125 ..      50      72 ..      47      80 .. 0.63
   2 !   50.4   1.1   4.8e-17   1.7e-13      28     134 ..     137     236 ..     121     256 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.9
                                    HHHHHHCC-BSEEEEEEEE...E CS
                   Pribosyltran 106 alelLkekgpeevriavlv...d 125
                                    ++e+L ++   +v+++v++   +
  gi|119719234|ref|YP_919729.1|  50 TVEALSSYAQGSVIAVVPYlayA 72 
                                    66777777777788888774433 PP

  == domain 2  score: 50.4 bits;  conditional E-value: 4.8e-17
                                    GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE----TTSEEEEE-SEESSSHHHHHHH CS
                   Pribosyltran  28 gkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdesrlledpagkkVliVDDildtGgTllaal 107
                                     k+ vv++++ g++ +a ++a  +++ ++y+ k++ r  g   +++       ++ ++ g+ V+iVDDi++tG+T+  a+
  gi|119719234|ref|YP_919729.1| 137 VKNAVVLAPDMGALERARRVAELIGADFDYLVKERDRVTGEVRVQP-------KSLEVNGRDVVIVDDIISTGKTIALAA 209
                                    4669**************************9999999888888876.......899************************ PP

                                    HHHHCC-BSEEEEEEEEE-HHHHHHHH CS
                   Pribosyltran 108 elLkekgpeevriavlvdkpateeevd 134
                                    +   ++g+ +v +++ ++ + +   + 
  gi|119719234|ref|YP_919729.1| 210 KSALAQGASSVTAVCTHAVMVQGALDL 236
                                    *9999**********998776666555 PP

>> Pribosyl_synth  Phosphoribosyl synthetase-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.09   3.2e+02       2      23 ..     137     158 ..     136     171 .. 0.91
   2 !   37.1   0.7     9e-13   3.2e-09      80     152 ..     186     258 ..     180     265 .. 0.95

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.09
                                    GGGEEEEESSGGGHHHHHHHHH CS
                 Pribosyl_synth   2 yrnavivakspgsakkatsyae 23 
                                    ++nav++a + g+ ++a+  ae
  gi|119719234|ref|YP_919729.1| 137 VKNAVVLAPDMGALERARRVAE 158
                                    69***************99988 PP

  == domain 2  score: 37.1 bits;  conditional E-value: 9e-13
                                    --TTSEEEEEEEEE-S-HHHHHHHHHHHHTT--EEEEEEEEE---TTHHHHHHHSS--EEEEESSS--HHHHH CS
                 Pribosyl_synth  80 dvgGriaiivddliddvesfvaaaevlkerGaykiyvlathGllssdaprlleesaidevvvtntipheiqkl 152
                                    +v+Gr  +ivdd+i   +++  aa+   ++Ga  + +++th ++ + a  ll  s + evv t+t+p  + k+
  gi|119719234|ref|YP_919729.1| 186 EVNGRDVVIVDDIISTGKTIALAAKSALAQGASSVTAVCTHAVMVQGALDLLYYSGVREVVATDTVPSPVSKI 258
                                    699****************************************************************999876 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   5.4e-06      0.02     119     149 ..     187     217 ..     174     233 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.4e-06
                       PRTase_2 119 aaakelvLvDDEistGktalnliralqeklp 149
                                     + + +v+vDD istGkt++  +++  ++  
  gi|119719234|ref|YP_919729.1| 187 VNGRDVVIVDDIISTGKTIALAAKSALAQGA 217
                                    36689*************9887777665544 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   4.2e-05      0.15     116     152 ..     182     220 ..     159     249 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.2e-05
                        UPRTase 116 Pkki..aertvlllDpviaTGgsaaaaiqlLkergvgee 152
                                    Pk++  + r v+++D +i+TG+++a a +  + +g+ + 
  gi|119719234|ref|YP_919729.1| 182 PKSLevNGRDVVIVDDIISTGKTIALAAKSALAQGASSV 220
                                    4444447789**************999988777666433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1875.52
//
Query:       gi|119719235|ref|YP_919730.1|  [L=755]
Description: (NiFe) hydrogenase maturation protein HypF [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.9e-49  165.6   0.0    1.2e-48  165.0   0.0    1.3  1  Sua5_yciO_yrdC   Telomere recombination
    6.2e-32  109.1   9.5    1.4e-16   59.9   1.5    2.5  2  zf-HYPF          HypF finger
    4.5e-24   85.1   0.1    7.7e-24   84.3   0.1    1.3  1  HypF_C           HypF Kae1-like domain
    2.5e-22   79.0   0.0    4.7e-22   78.2   0.0    1.5  1  Acylphosphatase  Acylphosphatase
  ------ inclusion threshold ------
       0.02   14.6   0.0          4    7.1   0.1    2.3  2  Peptidase_M22    Glycoprotease family
      0.086   13.6   0.3          6    7.6   0.1    2.4  2  TniQ             TniQ
       0.33   10.4   0.7         18    4.7   0.8    2.2  2  NMD3             NMD3 family
        1.7    8.8   3.7        9.1    6.5   1.2    2.5  2  Zn-ribbon_8      Zinc ribbon domain


Domain annotation for each model (and alignments):
>> Sua5_yciO_yrdC  Telomere recombination
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.0   0.0   5.3e-52   1.2e-48       2     178 ..     210     383 ..     209     384 .. 0.95

  Alignments for each domain:
  == domain 1  score: 165.0 bits;  conditional E-value: 5.3e-52
                                    HHHTTSEEEEE-SSSEEEEEETTSHHHHHHHHHHHTSHCCC--EEEESSCCCCCCCC-.TC--HHHHHHHHCT-SSSCEE CS
                 Sua5_yciO_yrdC   2 alrkGgivaiptetvYgLacdatneeaverlreiKgrpsdkplavlvasledlkklae.seveeealkllerfwPGpitl 80 
                                    ++++G iva++++++++Lac at++++ +rlr++K+rp +kp+av++ +l+ ++++a  +e+ + +l +++r    pi +
  gi|119719235|ref|YP_919730.1| 210 LIDEGSIVAVKGIGGFHLACLATDDDVLRRLRDRKKRP-RKPFAVMALDLKVAERIAVlDENAKSILSSPAR----PILI 284
                                    689***********************************.*******************99************....9988 PP

                                    EEE..E-TS-HHHHTTTTEEEEEE-SSHHHHHHHHHCT.S-EEEEES-STTS-S-SSHHHHHHHC-TTSECB-SS-.--S CS
                 Sua5_yciO_yrdC  81 llkrskeklpkevapglktvGvrlPdtplarlLlealg.eplvaTSanlsgepsitdaeeveeelgeivdlildgg.eia 158
                                    l +    +l++ vapgl+tvGv+l++++l++lLl+a++ + lv+TS+n sgep+i+d+ee+ ++l++i+d++l ++ +i 
  gi|119719235|ref|YP_919730.1| 285 LPRV-PGSLSELVAPGLRTVGVMLAYSALHYLLLSATRdKYLVMTSGNESGEPIIKDNEEALRKLSGIADYFLMHNrRIV 363
                                    8776.666****************************95256***********************************9*** PP

                                    SS---EEEETTSSTSSECEX CS
                 Sua5_yciO_yrdC 159 vgvdstVvdltegkpkilRr 178
                                    ++vd++Vv++t+g+  ++Rr
  gi|119719235|ref|YP_919730.1| 364 NRVDDSVVRFTDGETVLIRR 383
                                    *******************8 PP

>> zf-HYPF  HypF finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.4   1.4   6.9e-18   1.5e-14       1      34 []     107     140 ..     107     140 .. 0.97
   2 !   59.9   1.5   6.2e-20   1.4e-16       1      34 []     157     191 ..     157     191 .. 0.97

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 6.9e-18
                                    --HHHHHHHC-TTSTTTT-TT---TTTS--EEEE CS
                        zf-HYPF   1 lCedClrEykdpldRRfhaqfisCtnCGPrlsli 34 
                                    +C+dClrE+ dp++R+++++f sC +CGPr+s+i
  gi|119719235|ref|YP_919730.1| 107 ICDDCLREVLDPSSRWYRYPFHSCAWCGPRFSVI 140
                                    7******************************986 PP

  == domain 2  score: 59.9 bits;  conditional E-value: 6.2e-20
                                    --HHHHHHHC-TTS.TTTT-TT---TTTS--EEEE CS
                        zf-HYPF   1 lCedClrEykdpld.RRfhaqfisCtnCGPrlsli 34 
                                    lC+dCl+Ey dp++ RRfh+q+isC+nCGP+++l+
  gi|119719235|ref|YP_919730.1| 157 LCPDCLEEYGDPGNiRRFHIQGISCPNCGPQVYLV 191
                                    7******************************9985 PP

>> HypF_C  HypF Kae1-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.3   0.1   3.4e-27   7.7e-24       5     102 .]     401     500 ..     398     500 .. 0.96

  Alignments for each domain:
  == domain 1  score: 84.3 bits;  conditional E-value: 3.4e-27
                         HypF_C   5 evLAlGaelkntfalakggqallsqhlGdlenletleayeealeeleklleik..pevivcDlhpdylstklaeelaeke 82 
                                    ++L++Ga l nt ++a ++ ++ +qh+Gdlenlet++++ eale l+++++++   +v ++D+hp yls+++aeel++k 
  gi|119719235|ref|YP_919730.1| 401 PALSTGAFLMNTGSIAVEKYVITTQHIGDLENLETYNFLIEALEFLKRTYGVSdcDAVPIVDKHPYYLSRRVAEELSAKC 480
                                    689*************************************************85467899******************** PP

                         HypF_C  83 klelievqHHhAHllavlae 102
                                    + el+evqHH AH++a++ e
  gi|119719235|ref|YP_919730.1| 481 SRELVEVQHHVAHVAAAMLE 500
                                    ******************87 PP

>> Acylphosphatase  Acylphosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.2   0.0   2.1e-25   4.7e-22       2      85 .]       5      88 ..       4      88 .. 0.97

  Alignments for each domain:
  == domain 1  score: 78.2 bits;  conditional E-value: 2.1e-25
                Acylphosphatase  2 rllvtGrVQgvgFRkfvrrlAkelglkGyvrNlsdgsVeivaegeeekvekfleelksgppk.arvdeveveeleeeeefkd 82
                                   r++vtG VQgvgFR++v+rlAk+ gl+Gyv+Nl   +Vei +egee  +++fle+lk + p+ a+ dev vee+e  +  +d
  gi|119719235|ref|YP_919730.1|  5 RIRVTGVVQGVGFRPHVYRLAKKYGLRGYVQNLGGSEVEIWVEGEETLLRSFLEDLKLKTPRsAELDEVVVEEVEPSGF-SD 85
                                   89********************************************************99999***********99999.99 PP

                Acylphosphatase 83 Fei 85
                                   F+i
  gi|119719235|ref|YP_919730.1| 86 FAI 88
                                   987 PP

>> Peptidase_M22  Glycoprotease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.1    0.0018         4      72     113 ..     472     513 ..     469     514 .. 0.84
   2 ?    5.1   0.0     0.007        16     195     258 ..     671     732 ..     585     743 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0018
                                    HHHHHHHHCT--EEEEEHHHHHHHCCHCTSECSSCEEEEESS CS
                  Peptidase_M22  72 fAkglalalnkPlvgVnhleahalaarleekeefPvvllvsG 113
                                    +A+ l+ ++  +lv V+h  ah++aa+le+ ee+ v ++++G
  gi|119719235|ref|YP_919730.1| 472 VAEELSAKCSRELVEVQHHVAHVAAAMLEAWEEDAVGIAIDG 513
                                    799************************994333337777777 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.007
                                    T....HHHHHHHHHHHHHHHHHHHHHHHHHHCTBSEEEEESGGGGXHHHHHCHCCHHHHTTSEEEXXX CS
                  Peptidase_M22 195 e....vedlaasfqeavvdhlvekteralklpkakelvilGGvaankrLrealeeeaeelglkliiPp 258
                                    e     +dla+ +q    + l+e++     + +a++++++GG a n  + ++++++    g +++iP+
  gi|119719235|ref|YP_919730.1| 671 EvkghPRDLAYTVQFLLGRRLAEIAL----ESGARKVYVAGGSAVNTVIIKGIKSVLG--GENVYIPR 732
                                    1345689********76666666655....78****************9999986544..34677776 PP

>> TniQ  TniQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.041        93      87     118 ..      89     122 ..      23     139 .. 0.84
   2 ?    7.6   0.1    0.0027         6      94     119 ..     146     172 ..     133     182 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.041
                           TniQ  87 kllgeaisrrglrrsgrryCplClaedgepy..w 118
                                     ++g +i+++++ ++ + +C  Cl+e   p   w
  gi|119719235|ref|YP_919730.1|  89 LRSGTNITKVSMIPPDFGICDDCLREVLDPSsrW 122
                                    5778899999****************99988331 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0027
                           TniQ  94 srrglrrsgrryCplClaedgepy.wr 119
                                     r+ ++ +++ +Cp Cl+e g p   r
  gi|119719235|ref|YP_919730.1| 146 DRENTSMRHFPLCPDCLEEYGDPGnIR 172
                                    56668899***********99988533 PP

>> NMD3  NMD3 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1    0.0083        19      13      43 ..     105     135 ..      92     143 .. 0.84
   2 ?    4.7   0.8    0.0082        18       1      42 [.     130     185 ..     130     194 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0083
                           NMD3  13 nglCedCllkevditegiekievevCkeCgr 43 
                                     g+C+dCl++  d ++   ++ ++ C+ Cg 
  gi|119719235|ref|YP_919730.1| 105 FGICDDCLREVLDPSSRWYRYPFHSCAWCGP 135
                                    359**************************95 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0082
                           NMD3   1 CcrCGkei...........eeling......lCedCllkevditegiek.ievevCkeCg 42 
                                    C  CG +            +    +      lC+dCl +  d  ++    i+   C++Cg
  gi|119719235|ref|YP_919730.1| 130 CAWCGPRFsvieripydreN----TsmrhfpLCPDCLEEYGDPGNIRRFhIQGISCPNCG 185
                                    66677776555555543321....2455677***********999999899********9 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   1.2     0.004       9.1       7      32 ..     128     161 ..     123     165 .. 0.82
   2 ?    1.7   0.1      0.13   2.8e+02      27      33 ..     179     185 ..     170     189 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.004
                    Zn-ribbon_8   7 r.CeeCghefevlqsis.dap......ltaCPeC 32 
                                    + C  Cg +f v+ +i  d++       + CP+C
  gi|119719235|ref|YP_919730.1| 128 HsCAWCGPRFSVIERIPyDREntsmrhFPLCPDC 161
                                    36*************9998888899977779999 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.13
                    Zn-ribbon_8  27 taCPeCg 33 
                                    + CP+Cg
  gi|119719235|ref|YP_919730.1| 179 ISCPNCG 185
                                    4599998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (755 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.64u 0.26s 00:00:00.90 Elapsed: 00:00:00.44
# Mc/sec: 5206.37
//
Query:       gi|119719236|ref|YP_919731.1|  [L=416]
Description: peptidase M28 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-33  116.8   0.0    1.3e-33  116.3   0.0    1.2  1  Peptidase_M28  Peptidase family M28
    2.6e-07   30.5   0.3    1.1e-06   28.5   0.3    1.9  1  Peptidase_M20  Peptidase family M20/M25/M40
     0.0087   15.1   0.0      0.043   12.8   0.0    1.9  2  Peptidase_M42  M42 glutamyl aminopeptidase


Domain annotation for each model (and alignments):
>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.3   0.0   2.2e-37   1.3e-33       1     197 [.     194     380 ..     194     381 .. 0.85

  Alignments for each domain:
  == domain 1  score: 116.3 bits;  conditional E-value: 2.2e-37
                                    EEEEEESTTCE.SEEEEEEEE--B-TTTTCCT---TTTTHHHHHHHHHHHHHCHHGGCCSSEEEEEEEESSCSGSSHHHH CS
                  Peptidase_M28   1 Nviatlegkat.devlllgAHyDsvgvgrgpifvGAdDnAsgvaalLelarvlaasgsrpkrgvrflffdaEEagllGSk 79 
                                    N+ia+++g +  de + l+AHyDsv     p   GA+DnA g+a+lL la++la    +pkr+vrf+ff aEE gl GS 
  gi|119719236|ref|YP_919731.1| 194 NIIAEVKGYKYpDEIVYLTAHYDSVMG--VP---GATDNAGGTALLLALAKALAG--FKPKRTVRFAFFAAEELGLRGSL 266
                                    9*******999999************9..99...********************6..59********************* PP

                                    HHHH..HHCCCTTEEEEEEECS-SSSS--EEEHHHHHHCHHHHHHHHHHHHHTT-TTSCCEEEEESSTT-STTHHHHTTT CS
                  Peptidase_M28  80 afak..akpelkkiaavlnlDmvgsggkellfesgdkssselekelkalakpvgraaaedpfdersgrgrsDhspflkag 157
                                    + +   +++e+kki++v+nlD  g        +   ++ ++l+  ++  ak++g++     + e    + sD ++f+k+g
  gi|119719236|ref|YP_919731.1| 267 FHVGslNEEEKKKIKVVVNLDVHGGALGSSAAV--ISGPKSLRYFAEIHAKKLGVN---LSISE--DIMSSDGTSFVKHG 339
                                    ***987677************987654444433..444445555555556667765...33333..4589********** PP

                                    --EEEE.CTSSS-TTTTSTTSSGGGB-HHHHHHHHHHHHHH CS
                  Peptidase_M28 158 vpvldl.aetgfpevyHtprDtldnidkdtlariaelvlel 197
                                    +p+++l  + g + ++Ht++D ++++++ +++ i++ +l+l
  gi|119719236|ref|YP_919731.1| 340 IPAVNLyRSSGSGADIHTESDSPEHLHPLAFKVIGHYALHL 380
                                    ******888999****************9999999888876 PP

>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.3   1.8e-10   1.1e-06      33     105 ..     222     294 ..     210     379 .. 0.74

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 1.8e-10
                                    TTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTTTHHHHHHHHHH..TTTCESEEEEEEEESSSBT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M20  33 rGaddmkggvlaalealralkdegikpkgtivllfqpdEEggrgGakallegle..erekvdavfelhieepgil 105
                                    +Ga+d+ gg + +l++++al+  g+kpk+t++++f+++EE g +G+   +++l   e++k++ v+ l + ++ + 
  gi|119719236|ref|YP_919731.1| 222 PGATDNAGGTALLLALAKALA--GFKPKRTVRFAFFAAEELGLRGSLFHVGSLNeeEKKKIKVVVNLDVHGGALG 294
                                    79***************9986..5679*************77799988888444325778888887776655444 PP

>> Peptidase_M42  M42 glutamyl aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.11   6.7e+02       2      25 ..     194     218 ..     194     222 .. 0.86
   2 !   12.8   0.0   7.3e-06     0.043     132     178 ..     224     270 ..     219     295 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.11
                                    -EEEEEES.STTSSEEEEEEE--B- CS
                  Peptidase_M42   2 nliakkkg.kekepkvmiaAHmDei 25 
                                    n+ia+ kg k  +  v+++AH D +
  gi|119719236|ref|YP_919731.1| 194 NIIAEVKGyKYPDEIVYLTAHYDSV 218
                                    79999999777778899******87 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 7.3e-06
                                    THHHHHHHHHHHHHHHHHCTSS-SSEEEEEEESTCTTTSHHHHHHHH CS
                  Peptidase_M42 132 alDdragvavllellkelkeeeleatvylvatvqEEvGlrGaktsae 178
                                    a D+  g a+ll+l+k+l+  + + tv +++   EE GlrG+ + + 
  gi|119719236|ref|YP_919731.1| 224 ATDNAGGTALLLALAKALAGFKPKRTVRFAFFAAEELGLRGSLFHVG 270
                                    679*******************99*****************987654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 3091.65
//
Query:       gi|119719237|ref|YP_919732.1|  [L=484]
Description: thiamine biosynthesis protein ThiI [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-59  200.4   0.0    3.4e-59  199.8   0.0    1.2  1  ThiI             Thiamine biosynthesis protein (ThiI)
    6.7e-21   74.9   0.0    1.6e-20   73.6   0.0    1.7  2  THUMP            THUMP domain
    1.2e-16   61.2   0.0    7.6e-16   58.6   0.0    2.2  2  Rhodanese        Rhodanese-like domain
    7.7e-07   28.8   0.0     0.0038   16.8   0.0    2.2  2  QueC             Queuosine biosynthesis protein QueC
     0.0033   17.0   0.1     0.0063   16.0   0.1    1.5  1  Diphthami_syn_2  Diphthamide synthase
     0.0066   15.3   0.1      0.011   14.5   0.1    1.3  1  tRNA_Me_trans    tRNA methyl transferase
  ------ inclusion threshold ------
       0.14   12.3   1.7       0.61   10.2   0.0    2.3  2  OCC1             OCC1 family
       0.23   11.2   0.1        3.4    7.4   0.0    2.2  2  ATP_bind_3       PP-loop family


Domain annotation for each model (and alignments):
>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.8   0.0   1.5e-62   3.4e-59       1     195 [.     172     364 ..     172     365 .. 0.94

  Alignments for each domain:
  == domain 1  score: 199.8 bits;  conditional E-value: 1.5e-62
                           ThiI   1 gtqgkvlaLlSgGiDSpVaaylllkRGcrvvlvhlknepgtseeaiekveklaellae.yqtslevklvvvdfkevlkei 79 
                                    g++gkvlaL+SgG DS Vaa+ +lkRG +v++++ +   + ++ ++  v ++a++la+ ++ + + +l+v df ++l+e+
  gi|119719237|ref|YP_919732.1| 172 GSEGKVLALISGGYDSAVAAWYMLKRGAEVHYLYCN---MAGDLTKSLVLSVAKKLADsWSYGYKPRLYVADFSPLLREL 248
                                    789*******************************95...66777777777777777753556789*************** PP

                           ThiI  80 lekvkekltivllkrkmlriAekvaeeegakalvtGesLgqVaSqtleNlrvisavvnllilrPLigldKeeiiklAkei 159
                                    + kv ++l  v+lkr m+r+Ae +a + ga  +vtGesLgqV+SqtleNl v s+++ ++i rPLig+dKeeii   kei
  gi|119719237|ref|YP_919732.1| 249 RAKVAPELFGVVLKRYMYRVAEAIAGRIGAIGIVTGESLGQVSSQTLENLYVASQATSMPIYRPLIGFDKEEIISKSKEI 328
                                    ******************************************************************************** PP

                           ThiI 160 gtyeisiekedkCsvlakhPttkakleevekaeekl 195
                                    gtye s + ++ C+v++ hP+t+++leeve++e+kl
  gi|119719237|ref|YP_919732.1| 329 GTYEESSKVKEVCGVFSVHPKTRSRLEEVEREESKL 364
                                    *********************************997 PP

>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.6   0.0   7.3e-24   1.6e-20       2     143 ..      33     161 ..      32     162 .. 0.90
   2 ?   -3.4   0.1       4.3   9.6e+03      14      43 ..     331     360 ..     320     376 .. 0.58

  Alignments for each domain:
  == domain 1  score: 73.6 bits;  conditional E-value: 7.3e-24
                                    HHHHHHHHTT.H-SEEEEETTEEEEECTEEEEEETHHHHHHHHHTSTTECEEEEEEEEEESSHHHHHHHHHHHHHHHHHH CS
                          THUMP   2 eieellkegkvnverveagkgrivvelkgekpeedeellkealekargiqrvipvcevceadledileaakeivkkkfee 81 
                                    +i+ +l   +v  e++++ +gri+v+                l +++gi ++++++e  +++l+di   ++++  +k+++
  gi|119719237|ref|YP_919732.1|  33 NIRDALSSSGVSGEVRRE-YGRIYVYAP--------SSFAGVLRRVFGITSFSMALEYEFKALDDIASTVYNLYCDKLKG 103
                                    788888888988886666.689999965........5566779999*********************************9 PP

                                    CT-EEEEEEEESSSTSSSHHHHHHHHHHHHHHCCTT-EE-SSS-SEEEEEEEETTEEEEEEE CS
                          THUMP  82 eketFaVrvkrrgkhfeftsreinrevGkaivektglkVdlenPdivvrveiikdkayisid 143
                                    +  tFaVr++r g+h  fts++++r+vG+ +    +  Vdl+nP++ v++e+++++ay ++d
  gi|119719237|ref|YP_919732.1| 104 K--TFAVRARRTGDH-PFTSMDVARKVGEKLYPCSS-GVDLSNPEVQVFIEVRGSRAYFYTD 161
                                    9..************.*************9999666.*********************9876 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 4.3
                                    -SEEEEETTEEEEECTEEEEEETHHHHHHH CS
                          THUMP  14 verveagkgrivvelkgekpeedeellkea 43 
                                    +e+  ++k+++ v++  +k   + e++++ 
  gi|119719237|ref|YP_919732.1| 331 YEESSKVKEVCGVFSVHPKTRSRLEEVERE 360
                                    455555555555555555444455555444 PP

>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       0.9     2e+03      80      97 ..     189     204 ..     170     240 .. 0.58
   2 !   58.6   0.0   3.4e-19   7.6e-16      15     105 ..     402     476 ..     392     478 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.9
                      Rhodanese  80 aaaaallkklGyknvsvl 97 
                                     aa+++lk  G  +v++l
  gi|119719237|ref|YP_919732.1| 189 VAAWYMLK-RG-AEVHYL 204
                                    44455555.34.333333 PP

  == domain 2  score: 58.6 bits;  conditional E-value: 3.4e-19
                      Rhodanese  15 allDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellelgidnkktvvvycdgggraaaaaallkklGyknv 94 
                                    +++DvRp+e+Ye+ghIpg++++             ++ elp  l++l  d+ kt v++cd+gg +++aa++l+k+G  n 
  gi|119719237|ref|YP_919732.1| 402 IIVDVRPKEKYEEGHIPGSLHI-------------EFTELPLFLERL--DKSKTYVFVCDEGGLSREAAYMLRKAG-FNA 465
                                    4*********************.............9******99999..***************************.7** PP

                      Rhodanese  95 svldGGfkawk 105
                                    + l+GG++ ++
  gi|119719237|ref|YP_919732.1| 466 WSLKGGLRRFS 476
                                    *******9987 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.7e-06    0.0038       1      48 [.     176     225 ..     176     237 .. 0.79
   2 !    9.9   0.0   0.00022      0.49     139     178 ..     294     333 ..     268     340 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.7e-06
                                    EEEEE--SSHHHHHHHHHHHHH-SEEEEEEEESS-T..TSHHHHHHHHHH CS
                           QueC   1 kavvllSGGlDSttvlalakkegkevealtfdYgqr..hkkeleaakkia 48 
                                    k++ l+SGG DS++++++++k+g+ev+ l  +      ++  l++akk+a
  gi|119719237|ref|YP_919732.1| 176 KVLALISGGYDSAVAAWYMLKRGAEVHYLYCNMAGDltKSLVLSVAKKLA 225
                                    5789***********************99877654433445555666655 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00022
                                    HHHHHHHHHHTS--EEE-TTTT--HHHHHHHHHHTTHHHH CS
                           QueC 139 alnkalnlgedkkieieaPlidlsKaeivklgkelgvple 178
                                    +l++++ +++++++ i  Pli ++K+ei+  +ke+g   e
  gi|119719237|ref|YP_919732.1| 294 TLENLYVASQATSMPIYRPLIGFDKEEIISKSKEIGTYEE 333
                                    566677777999***********************97544 PP

>> Diphthami_syn_2  Diphthamide synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   2.8e-06    0.0063       1      34 [.     175     209 ..     175     225 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.8e-06
                Diphthami_syn_2   1 mkvavlysGGkDsilaLykalke.sevesLvsvis 34 
                                    +kv +l+sGG Ds++a +  lk+  ev++L + + 
  gi|119719237|ref|YP_919732.1| 175 GKVLALISGGYDSAVAAWYMLKRgAEVHYLYCNMA 209
                                    599*******************99******98664 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   5.1e-06     0.011       2      37 ..     176     211 ..     175     227 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.1e-06
                  tRNA_Me_trans   2 kvvvalSgGVDSsvaaallkeqgyevigvflklwee 37 
                                    kv++++SgG DS+vaa  + ++g ev  ++ ++  +
  gi|119719237|ref|YP_919732.1| 176 KVLALISGGYDSAVAAWYMLKRGAEVHYLYCNMAGD 211
                                    799***********************9999877655 PP

>> OCC1  OCC1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00027      0.61      20      49 ..      34      63 ..      31      67 .. 0.87
   2 ?    0.3   0.3      0.35   7.8e+02      34      54 ..     163     183 ..     159     189 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00027
                           OCC1 20 akDvaeesvsdddkRRnYGGvYvGlPsdav 49
                                    +D+   s    + RR YG +Yv  Ps  +
  gi|119719237|ref|YP_919732.1| 34 IRDALSSSGVSGEVRREYGRIYVYAPSSFA 63
                                   578889999999**************9765 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.35
                           OCC1  34 RRnYGGvYvGlPsdavnmvsg 54 
                                     R YGG  vG    + + +sg
  gi|119719237|ref|YP_919732.1| 163 VRGYGGLPVGSEGKVLALISG 183
                                    599*******88888888887 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.11   2.4e+02       2      24 ..     177     199 ..     176     217 .. 0.78
   2 ?    7.4   0.0    0.0015       3.4     129     160 ..     298     327 ..     285     339 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.11
                                    EEEE--SCHHHHHHHHHHHHHCT CS
                     ATP_bind_3   2 vlvAvSgGlDSmaLllllaklkk 24 
                                    vl+ +SgG DS +  + + k   
  gi|119719237|ref|YP_919732.1| 177 VLALISGGYDSAVAAWYMLKRGA 199
                                    56668******998888777654 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0015
                                    S-SEEEETTCCEE-CCCT--HHHHHHHHHHTT CS
                     ATP_bind_3 129 ikeaseiasirlvRPlLkvskeeleeylkekk 160
                                    +  as+ +s+ ++RPl+ + kee+ +  k k+
  gi|119719237|ref|YP_919732.1| 298 LYVASQATSMPIYRPLIGFDKEEIIS--KSKE 327
                                    445667789**************987..4444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (484 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.40
# Mc/sec: 3661.86
//
Query:       gi|119719238|ref|YP_919733.1|  [L=85]
Description: 50S ribosomal protein L35Ae [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-15   56.0   0.4    4.3e-15   55.6   0.4    1.2  1  Ribosomal_L35Ae  Ribosomal protein L35Ae
     0.0031   17.7   0.1        0.5   10.6   0.1    2.1  2  RimM             RimM N-terminal domain


Domain annotation for each model (and alignments):
>> Ribosomal_L35Ae  Ribosomal protein L35Ae
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.6   0.4   4.8e-19   4.3e-15       4      94 ..       2      84 ..       1      85 [] 0.91

  Alignments for each domain:
  == domain 1  score: 55.6 bits;  conditional E-value: 4.8e-19
                                   EEEEEEEE--SSSSS-EEEEEEESS--SHHHHHCCTT-EE..EEE-......TTT-EEEEEEEEECTTTTEEEEEETT--SS CS
                Ribosomal_L35Ae  4 kavflgykrgkrnqrentaLlkiegvkskeeaefylGkrvayvykakkkkkgskvrviwGkvtrahGnsgvvrakFkknLpp 85
                                   ++ +++++rg ++ ++++ +l ++gv+ k +a +++G++v +v          + +   Gk++r+hG++g v a Fk++Lp+
  gi|119719238|ref|YP_919733.1|  2 EGWIVSFRRGMNKYYPRQVILSLDGVTYK-DAVKVIGRKVLWVHPE-------TGEKFVGKIVRMHGRRGHVLAYFKRHLPG 75
                                   6899**********************986.567899*****99887.......455679*********************** PP

                                   S-TT-EEEE CS
                Ribosomal_L35Ae 86 kaigarvrv 94
                                   +a+g++v++
  gi|119719238|ref|YP_919733.1| 76 QAVGTKVKI 84
                                   *******98 PP

>> RimM  RimM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.4   0.0    0.0024        21      52      83 ..      15      46 ..       3      47 .. 0.80
   2 !   10.6   0.1   5.5e-05       0.5       2      16 ..      52      66 ..      51      77 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0024
                                   EETTEEEEEETT--SHHHHHTTTT-EEEEETT CS
                           RimM 52 vhkkgvivklegvddrdaAealkgaelfvprs 83
                                   +  + vi++l+gv+  da++ +    l+v+++
  gi|119719238|ref|YP_919733.1| 15 YYPRQVILSLDGVTYKDAVKVIGRKVLWVHPE 46
                                   44899************999998888888765 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 5.5e-05
                                   EEEEEEEETTTTEEE CS
                           RimM  2 vGkIvgahGlkGevk 16
                                   vGkIv+ hG +G+v 
  gi|119719238|ref|YP_919733.1| 52 VGKIVRMHGRRGHVL 66
                                   9***********995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.28s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 612.53
//
Query:       gi|119719239|ref|YP_919734.1|  [L=485]
Description: hypothetical protein Tpen_0322 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (485 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.23s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 3487.82
//
Query:       gi|119719240|ref|YP_919735.1|  [L=76]
Description: hypothetical protein Tpen_0323 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.064   13.7   0.2      0.082   13.3   0.2    1.3  1  SCP2_2    Sterol carrier protein domain


Domain annotation for each model (and alignments):
>> SCP2_2  Sterol carrier protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   4.6e-06     0.082      54      89 ..       4      39 ..       2      65 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.6e-06
                                   E..EEEEHHHHHHHHTTSS-HHHHHHTTSSBSSHHHH CS
                         SCP2_2 54 a.dltldiqtLaqlllGyrsaseLarlgriegaeeal 89
                                   + d++ +i++L++ll+ + + +eL+++  +e+ + a+
  gi|119719240|ref|YP_919735.1|  4 PrDIVRTIGALSRLLASTLKGDELYEARLVEALD-AI 39
                                   348999************************9433.33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       753  (0.041999); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 559.82
//
Query:       gi|119719241|ref|YP_919736.1|  [L=202]
Description: hypothetical protein Tpen_0324 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      1e-15   58.2   0.0    1.9e-15   57.4   0.0    1.3  1  ASCH       ASCH domain
  ------ inclusion threshold ------
      0.039   13.8   0.0       0.29   11.0   0.0    2.2  3  pP_pnuc_1  Predicted pPIWI-associating nuclease
       0.14   11.8   2.1       0.32   10.6   0.0    2.7  4  HTH_50     Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> ASCH  ASCH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.4   0.0   3.1e-19   1.9e-15       3     107 .]       8     105 ..       6     105 .. 0.94

  Alignments for each domain:
  == domain 1  score: 57.4 bits;  conditional E-value: 3.1e-19
                                    E-TTHHHHHHTTS--EEEESSTTTGGGT-CEEEEEECCCCTSEEEEEEEEEEEEEEHHHHHHHHHCHCC--.-HCHHHHH CS
                           ASCH   3 fhqelaslivsGkKtaeirvwdeelpkvrgdllilaalkptgralgivevtkvevkpfeevteehalkege.sleewrev 81 
                                    f   ++++++s +Kt++irv++++l++   ++++l   +  gr lg +++t +++k+++++t ++a  +g+ slee+++ 
  gi|119719241|ref|YP_919736.1|   8 FSRQYLEKLLSNEKTTTIRVKRPRLKP---GDEVL--VHCGGRVLGRAKITYIYKKKLRDLTLDEAVRDGFgSLEELIRN 82 
                                    66789*******************666...77888..89***************************************** PP

                                    HHCCHHHHHCCEEEEEEEEEEEEEEE CS
                           ASCH  82 heefyeeeseeyedelvvveefelve 107
                                    ++++y+++s+   d +v+v+ f +ve
  gi|119719241|ref|YP_919736.1|  83 LKRHYPRLSA---DSYVYVINFSWVE 105
                                    *********9...*********9986 PP

>> pP_pnuc_1  Predicted pPIWI-associating nuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   4.8e-05      0.29      71     109 ..      49      85 ..      39      95 .. 0.89
   2 ?   -1.2   0.0      0.29   1.8e+03      33      47 ..     121     135 ..     119     148 .. 0.79
   3 ?   -1.7   0.0      0.41   2.4e+03      73      99 ..     156     183 ..     153     190 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4.8e-05
                      pP_pnuc_1  71 kqrikYalqkglsddflekflevdddikevlelfdkLnk 109
                                    +++i Y+ +k+l d +l+++  v d    + el+++L +
  gi|119719241|ref|YP_919736.1|  49 RAKITYIYKKKLRDLTLDEA--VRDGFGSLEELIRNLKR 85 
                                    89*****************9..99999999999999876 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.29
                      pP_pnuc_1  33 avslRElltqiLhkl 47 
                                    a+s+RE+ ++ L++l
  gi|119719241|ref|YP_919736.1| 121 AASFREVAEKALNTL 135
                                    678888888888765 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.41
                      pP_pnuc_1  73 rikYalqkglsddflekf.le.vdddike 99 
                                    ++ Yal +gl++ f+    l  v + ++e
  gi|119719241|ref|YP_919736.1| 156 KAAYAL-GGLNQRFIVRDvLRrVAQRLEE 183
                                    677777.7777777776645556655555 PP

>> HTH_50  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       1.1   6.3e+03       3      12 ..      75      84 ..      74      88 .. 0.51
   2 ?   -2.2   0.0      0.53   3.2e+03      25      32 ..     123     130 ..     122     132 .. 0.84
   3 ?   10.6   0.0   5.4e-05      0.32       8      34 ..     137     162 ..     133     171 .. 0.89
   4 ?   -2.5   0.1      0.66   3.9e+03      27      33 ..     175     181 ..     173     182 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.1
                         HTH_50  3 sLkeyveefE 12
                                   sL+e++ +  
  gi|119719241|ref|YP_919736.1| 75 SLEELIRNLK 84
                                   5666554443 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.53
                         HTH_50  25 StRklAkr 32 
                                    S+R +A++
  gi|119719241|ref|YP_919736.1| 123 SFREVAEK 130
                                    99999986 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 5.4e-05
                         HTH_50   8 veefErelikkayekYpStRklAkrLG 34 
                                    ++efEr+++k ++++ +S+Rk+A +LG
  gi|119719241|ref|YP_919736.1| 137 LDEFERNVLKLVVSE-GSIRKAAYALG 162
                                    689*****9887777.9*********8 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 0.66
                         HTH_50  27 RklAkrL 33 
                                    R +A+rL
  gi|119719241|ref|YP_919736.1| 175 RRVAQRL 181
                                    8999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      605  (0.0337442); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1485.45
//
Query:       gi|119719242|ref|YP_919737.1|  [L=809]
Description: valyl-tRNA synthetase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   5.1e-149  497.3   0.0   1.2e-147  492.8   0.0    2.1  1  tRNA-synt_1      tRNA synthetases class I (I, L, M and V)
    8.2e-34  116.8   0.1    1.6e-33  115.9   0.1    1.4  1  Anticodon_1      Anticodon-binding domain of tRNA
    8.7e-21   74.1   0.3    4.4e-14   52.0   0.0    3.4  4  tRNA-synt_1g     tRNA synthetases class I (M)
    1.2e-09   37.9   0.1      3e-08   33.4   0.1    2.4  2  tRNA-synt_1_2    Leucyl-tRNA synthetase, Domain 2
    1.5e-05   24.5   0.0      0.013   14.9   0.0    2.3  2  tRNA-synt_1e     tRNA synthetases class I (C) catalytic domai
    0.00037   20.4   1.5      0.018   15.1   0.2    3.0  3  DZR              Double zinc ribbon
  ------ inclusion threshold ------
      0.011   14.7   0.0        3.1    6.6   0.0    2.4  2  tRNA-synt_1f     tRNA synthetases class I (K)
      0.013   15.8   0.1         18    5.8   0.1    3.4  3  Lar_restr_allev  Restriction alleviation protein Lar
      0.017   15.2   1.2      0.017   15.2   1.2    2.8  3  Zn-ribbon_8      Zinc ribbon domain
      0.019   14.9   0.1       0.48   10.5   0.0    2.9  2  HypA             Hydrogenase/urease nickel incorporation, met
       0.26   10.8   5.9        0.8    9.3   0.3    3.2  3  TF_Zn_Ribbon     TFIIB zinc-binding
       0.85    9.0   3.9         57    3.1   0.2    3.4  3  zf-TFIIB         Transcription factor zinc-finger
        1.2    9.8   3.5         15    6.3   0.0    3.5  3  zf-ISL3          zinc-finger of transposase IS204/IS1001/IS10
          3    7.7  11.7        3.9    7.3   0.9    3.7  4  zinc_ribbon_2    zinc-ribbon domain


Domain annotation for each model (and alignments):
>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  492.8   0.0  9.5e-151  1.2e-147       1     602 []      19     574 ..      19     574 .. 0.95

  Alignments for each domain:
  == domain 1  score: 492.8 bits;  conditional E-value: 9.5e-151
                    tRNA-synt_1   1 klyekWeeedvfkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaieakv 80 
                                    k++ +Wee+++++   +k+++++ +++  +PPy  G lH+G+al+ +  d+v rykrm+G++vl+  GwD++Gl++e  v
  gi|119719242|ref|YP_919737.1|  19 KWQRFWEEKGIYRFD-RKDRSRPVYVIDTPPPYPSGDLHVGNALNFSYIDFVARYKRMRGYNVLFPQGWDCHGLPTEVRV 97 
                                    5889*********99.777789********************************************************** PP

                    tRNA-synt_1  81 ekklgakekkerkklgreefrekvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkgliyrgk 160
                                    ek +g+++     ++  +ef   +re+  + +e+++ ++k lG s+D++ ey+T+d+++   ++  fv +++kgliyrg+
  gi|119719242|ref|YP_919737.1|  98 EKAVGKRKS----EMDPNEFLRLCREYTLKWIESMKAALKGLGLSIDWSTEYKTMDPDYWRRTQLSFVLMYNKGLIYRGE 173
                                    ****88886....9****************************************************************** PP

                    tRNA-synt_1 161 klvnwstklktalselEveykdkkdalihvafpladkeevklviaTTtPeTllgdtavavnpeldyvitkeklilaeall 240
                                    ++v w+++++ta++e+Evey++ + +l++++f +++  e +lv+a T+Pe l + +avavnp                  
  gi|119719242|ref|YP_919737.1| 174 HPVIWCPRCETAIAEAEVEYEERDRPLYYFKFGVEGTGE-ELVVASTRPELLASCVAVAVNPS----------------- 235
                                    ************************************999.***********************................. PP

                    tRNA-synt_1 241 kslvkkesekkiledergkeLegkevelplvnrkipiiaddyvdkeaGtGvVkiaPahdedDyevgkkynlevinilded 320
                                                  der+k+L+gk++  p+ +rk+piiad+ vdk++GtG+V +  + d+ D +  kkynl+vi  ++e+
  gi|119719242|ref|YP_919737.1| 236 --------------DERYKHLVGKNAVVPIYGRKVPIIADEAVDKDFGTGAVMVCTYGDKTDVKWQKKYNLPVIISITEQ 301
                                    ..............9***************************************************************** PP

                    tRNA-synt_1 321 gtlteeaaefeglkvfdarkkvveelkekglllkaekiehsvpfcerskkpiiyrateqWfvrvkeladaalkavekvqf 400
                                    gt++++a+  +glkv+darkk+ve lke+gll+k+e+i+ +v++c+r ++p++   ++qWfvr ++l++++l++ +kv++
  gi|119719242|ref|YP_919737.1| 302 GTMNDNAGPLKGLKVEDARKKIVEMLKENGLLVKVESIRSTVGTCWRCHTPVEIIPKKQWFVRSTALNEKVLEEGRKVNW 381
                                    ******************************************************************************** PP

                    tRNA-synt_1 401 vpkskekryaswleniq.dWciSRqrwWGhriplfvsketeevvvreelkelvagreeeeaekkalekeakdkl.kkekg 478
                                    vp    kr ++w+     dW+iSRqr   ++ip+++ k+ + + v+           e+   +  ++    +k  k++ +
  gi|119719242|ref|YP_919737.1| 382 VPSYMYKRLENWVLSLDwDWVISRQRLFATPIPVYYCKDCGAELVVP---------PEKLPIDPRFDPPPFEKCpKCGSK 452
                                    ************988755*********************98666622.........233333344444444455578999 PP

                    tRNA-synt_1 479 elekdedvlDvWFsSgswpfstlgypeedteelkkffpadmlleGlDiirgWvarlillslaltgsePfkevlvhglvrd 558
                                    ++  + dv+D+W +S+ +     g+p++  +  ++ fpad+  +G+Diir W + lil ++al+g++ fk+ l++g+vr 
  gi|119719242|ref|YP_919737.1| 453 NIVPERDVMDTWMDSSITAAVHAGWPDN-FD--ERLFPADLQPNGYDIIRTWDYYLILRGVALFGRSQFKTALINGMVRG 529
                                    999************************9.33..347******************************************** PP

                    tRNA-synt_1 559 eeGrKmSKslgNvidpldvikkygadalRltli.lsdvgrdinls 602
                                     +Gr m Ks gN+++ ++v++kygad+ Rl+++  + +g+d+++s
  gi|119719242|ref|YP_919737.1| 530 TDGRMMHKSYGNYVAVQEVLEKYGADSFRLWVAlAAATGQDVRFS 574
                                    *********************************899999**9986 PP

>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.9   0.1   1.2e-36   1.6e-33       1     150 [.     614     757 ..     614     759 .. 0.89

  Alignments for each domain:
  == domain 1  score: 115.9 bits;  conditional E-value: 1.2e-36
                    Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkraaqevllevletllrllaPf 80 
                                    d wil+el+++v +vt+a+e+y+f++a +al +f+w++l+d+y+e+vk+rl+ ++++    a+++l+ vl + l++l+ f
  gi|119719242|ref|YP_919737.1| 614 DHWILRELASTVTRVTQALENYNFQEASQALVDFTWHKLADHYVEAVKHRLSRSDEA----AKYTLYVVLIKTLQMLSVF 689
                                    89*************************************************776654....56***************** PP

                    Anticodon_1  81 mPfitEelwqreeeelgkkesimlaewpekaeel.ekeleeeevellkeivkairklrselkikpsselkv 150
                                    +P+i+Ee++ +  ++ g+ esi +++wpe +++  ek    +  ++l++++   r+++ +  i+ ++e+++
  gi|119719242|ref|YP_919737.1| 690 APHISEEIYVDVLKKAGGWESITVSPWPEPPAYDeEK---ARVGDILIAVLAEGRRAKHDARIPLNKEVSA 757
                                    *********7644456788*********855444233...46**********************9999876 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.5         3   3.8e+03     268     284 ..      16      29 ..      10      36 .. 0.66
   2 !   52.0   0.0   3.5e-17   4.4e-14       2     136 ..      43     192 ..      42     195 .. 0.81
   3 ?    0.8   0.0      0.13   1.7e+02     169     238 ..     346     414 ..     325     422 .. 0.78
   4 !   16.7   0.0   1.9e-06    0.0024     323     370 ..     530     577 ..     507     583 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 3
                                    TSGGGG.G--S...... CS
                   tRNA-synt_1g 268 eeekwkeyWakdkevel 284
                                     e kw+++W+   e  +
  gi|119719242|ref|YP_919737.1|  16 VEGKWQRFWE---EKGI 29 
                                    4669*****3...3444 PP

  == domain 2  score: 52.0 bits;  conditional E-value: 3.5e-17
                                    EEEE--B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHH......HTTS-HHHH...HHHHH. CS
                   tRNA-synt_1g   2 lvttalpYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAe......kegvtpeel...vekvh. 71 
                                    ++ t+ pY++g+lH+G++l+    D +aRykr+rg++vlf  g D hG p+e++ e      k++++p+e+   +++++ 
  gi|119719242|ref|YP_919737.1|  43 VIDTPPPYPSGDLHVGNALNFSYIDFVARYKRMRGYNVLFPQGWDCHGLPTEVRVEkavgkrKSEMDPNEFlrlCREYTl 122
                                    78999**************99999***************************99876111222568999986222455542 PP

                                    ...HHHHHHHHHTT---S..EEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG-E CS
                   tRNA-synt_1g  72 ...eeikelfkklnisfd..kygrttseehkelvqeifkklkekgliyekeieqlycpkderflpdryve 136
                                       e++k+ +k l++s d  + ++t + +  + +q  f  +++kgliy++e  +++cp++e+ +++ +ve
  gi|119719242|ref|YP_919737.1| 123 kwiESMKAALKGLGLSIDwsTEYKTMDPDYWRRTQLSFVLMYNKGLIYRGEHPVIWCPRCETAIAEAEVE 192
                                    2225677778887776662255689999999*********************************999987 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.13
                                    ........EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS-SSS-EET CS
                   tRNA-synt_1g 169 saisgskpevketehlffklskfekklkewieeeekeleenvkkivkewlkegLkdlaisrdldwGipvP 238
                                    +  + +  e+  ++++f +  ++++k+ e   ++ +  ++ + k +++w+ +   d+ isr+  ++ p+P
  gi|119719242|ref|YP_919737.1| 346 CWRCHTPVEIIPKKQWFVRSTALNEKVLEEG-RKVNWVPSYMYKRLENWVLSLDWDWVISRQRLFATPIP 414
                                    6666777777778889999999988887766.44445788888999999988666999999999999998 PP

  == domain 4  score: 16.7 bits;  conditional E-value: 1.9e-06
                                    E--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-HHH CS
                   tRNA-synt_1g 323 vegkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfswed 370
                                    ++g+ + kS g+ v ++e+le++ ad +R ++a +a + +D+ fsw+ 
  gi|119719242|ref|YP_919737.1| 530 TDGRMMHKSYGNYVAVQEVLEKYGADSFRLWVALAAATGQDVRFSWDG 577
                                    689999****************************************86 PP

>> tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.081     1e+02      12      49 ..     203     240 ..     201     247 .. 0.83
   2 !   33.4   0.1   2.4e-11     3e-08      86     146 ..     244     304 ..     235     328 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.081
                  tRNA-synt_1_2  12 iefkveeseeklevfttrpdtlfGvtfvalapehplve 49 
                                    ++f ve++ e+l v  trp+ l +   va+ p+ +  +
  gi|119719242|ref|YP_919737.1| 203 FKFGVEGTGEELVVASTRPELLASCVAVAVNPSDERYK 240
                                    7899****99************9999999888776555 PP

  == domain 2  score: 33.4 bits;  conditional E-value: 2.4e-11
                  tRNA-synt_1_2  86 glkaihPitgekipiwvanyvlmeygtgavmavPahdqrDfeFakkynlpikqvikpedee 146
                                    g +a+ Pi g+k+pi   + v  ++gtgavm +   d+ D ++ kkynlp++  i+++++ 
  gi|119719242|ref|YP_919737.1| 244 GKNAVVPIYGRKVPIIADEAVDKDFGTGAVMVCTYGDKTDVKWQKKYNLPVIISITEQGTM 304
                                    7889**********************************************99888866543 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.0    0.0022       2.8      22      52 ..      54      84 ..      49     135 .. 0.94
   2 !   14.9   0.0     1e-05     0.013     230     282 ..     510     563 ..     489     579 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0022
                                   --BHHHHHHHHHHHHHHHHHHHTT-EEEEEE CS
                   tRNA-synt_1e 22 ashlGhaRslvafDilrrilqalgYdvqfvq 52
                                   + h+G+a ++  +D ++r+ +++gY+v f q
  gi|119719242|ref|YP_919737.1| 54 DLHVGNALNFSYIDFVARYKRMRGYNVLFPQ 84
                                   68*************************9965 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 1e-05
                                    HHHSSS--EEEEEEE--EE.ETTBE--TTTT---BHHHHHTTS-HHHHHHHHHS CS
                   tRNA-synt_1e 230 eaafdkqlvkyflhnghlk.iegekmsksLknfitikdvlkkfdprqlRlllls 282
                                     a+f+++  k  l ng+++  +g+ m ks +n++ +++vl+k+ +  +Rl ++ 
  gi|119719242|ref|YP_919737.1| 510 VALFGRSQFKTALINGMVRgTDGRMMHKSYGNYVAVQEVLEKYGADSFRLWVAL 563
                                    67888888888999999985789999***********************98765 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.38   4.9e+02      15      22 ..     179     186 ..     169     195 .. 0.66
   2 ?    1.2   0.0      0.31     4e+02      28      38 ..     343     353 ..     321     360 .. 0.77
   3 !   15.1   0.2   1.4e-05     0.018      13      39 ..     416     454 ..     410     459 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.38
                            DZR  15 CseCgtkl 22 
                                    C++C t++
  gi|119719242|ref|YP_919737.1| 179 CPRCETAI 186
                                    44444443 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.31
                            DZR  28 edrCpsCgekv 38 
                                      +C++C+++v
  gi|119719242|ref|YP_919737.1| 343 VGTCWRCHTPV 353
                                    45788887775 PP

  == domain 3  score: 15.1 bits;  conditional E-value: 1.4e-05
                            DZR  13 rfCseCgtklkavaa............edrCpsCgekvd 39 
                                     +C++Cg++l  +++             ++Cp+Cg+k+ 
  gi|119719242|ref|YP_919737.1| 416 YYCKDCGAELVVPPEklpidprfdpppFEKCPKCGSKNI 454
                                    59*******9988889***********9*******9965 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0    0.0055       7.1      21     128 ..      38     141 ..      19     159 .. 0.65
   2 ?    6.6   0.0    0.0024       3.1     277     310 ..     530     563 ..     517     582 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0055
                   tRNA-synt_1f  21 ekdevvvesGi.spSGliHiGnlrevltadlvaralrkrgeevrlilisDdmDglRkvpenlpek.llekylgkpltsi. 97 
                                    +++ +v+++    pSG +H+Gn+ +    d+var  r rg +v +   +D         + lp +  +ek +gk  ++  
  gi|119719242|ref|YP_919737.1|  38 SRPVYVIDTPPpYPSGDLHVGNALNFSYIDFVARYKRMRGYNVLFPQGWDC--------HGLPTEvRVEKAVGKRKSEMd 109
                                    55666666653159********************99999988765555552........233333344555555555443 PP

                   tRNA-synt_1f  98 Pdpkgk.hesyaehfnaelvesLdelgievef 128
                                    P+ + + + +y  ++ + ++++L+ lg  +++
  gi|119719242|ref|YP_919737.1| 110 PNEFLRlCREYTLKWIESMKAALKGLGLSIDW 141
                                    44454445666666666666666666655555 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0024
                   tRNA-synt_1f 277 kggekmssSkGnvltledwlevaepevlrflilr 310
                                      g+ m++S Gn+++++++le +  ++ r+ ++ 
  gi|119719242|ref|YP_919737.1| 530 TDGRMMHKSYGNYVAVQEVLEKYGADSFRLWVAL 563
                                    45669****************9999999987765 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.45   5.7e+02      27      38 ..     171     188 ..     139     198 .. 0.68
   2 ?    4.2   0.0     0.044        57      28      36 ..     415     423 ..     370     437 .. 0.75
   3 ?    5.8   0.1     0.014        18       5      18 ..     445     458 ..     443     465 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.45
                Lar_restr_allev  27 q....cvyCadCga..st 38 
                                         +++C  C+   ++
  gi|119719242|ref|YP_919737.1| 171 RgehpVIWCPRCETaiAE 188
                                    03345999*99*993322 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.044
                Lar_restr_allev  28 cvyCadCga 36 
                                    + yC+dCga
  gi|119719242|ref|YP_919737.1| 415 VYYCKDCGA 423
                                    78******9 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.014
                Lar_restr_allev   5 pCPfCggravlers 18 
                                     CP Cg+++++ ++
  gi|119719242|ref|YP_919737.1| 445 KCPKCGSKNIVPER 458
                                    7*******999876 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.38   4.9e+02      24      34 ..     174     184 ..     169     188 .. 0.73
   2 ?   -3.0   0.0       6.4   8.2e+03      29      37 ..     346     354 ..     338     356 .. 0.69
   3 ?   15.2   1.2   1.3e-05     0.017       5      35 ..     415     453 ..     412     455 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.38
                    Zn-ribbon_8  24 apltaCPeCgs 34 
                                     p + CP+C  
  gi|119719242|ref|YP_919737.1| 174 HPVIWCPRCET 184
                                    55566****76 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 6.4
                    Zn-ribbon_8  29 CPeCgsevr 37 
                                    C +C+ +v+
  gi|119719242|ref|YP_919737.1| 346 CWRCHTPVE 354
                                    777776664 PP

  == domain 3  score: 15.2 bits;  conditional E-value: 1.3e-05
                    Zn-ribbon_8   5 eYrCeeCghefe......vlqsisdaplta.CPeCgs.e 35 
                                     Y C++Cg e        ++ + +d+p+ + CP+Cgs +
  gi|119719242|ref|YP_919737.1| 415 VYYCKDCGAELVvppeklPIDPRFDPPPFEkCPKCGSkN 453
                                    69******9999***9999999998887667*****955 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.44   5.6e+02      62      83 ..     168     189 ..     153     200 .. 0.76
   2 ?   10.5   0.0   0.00037      0.48      69      97 ..     414     454 ..     321     460 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.44
                                    EEEEEE--EEEETTTS-EEECH CS
                           HypA  62 LeieevpvkvrCreCgkefele 83 
                                    L ++ ++ +++C +C++ + ++
  gi|119719242|ref|YP_919737.1| 168 LIYRGEHPVIWCPRCETAIAEA 189
                                    5566677889999999887755 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00037
                                    -EEEETTTS-EEECHHHHH............S-TTTSSS-E CS
                           HypA  69 vkvrCreCgkefeleekal............rCpkCgsadv 97 
                                     +++C++Cg+e  +  ++l            +CpkCgs+++
  gi|119719242|ref|YP_919737.1| 414 PVYYCKDCGAELVVPPEKLpidprfdpppfeKCPKCGSKNI 454
                                    4679******999665444678899*************986 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1       1.2   1.6e+03       3       8 ..     179     184 ..     177     194 .. 0.63
   2 ?    2.8   0.1     0.063        81      20      27 ..     416     423 ..     416     432 .. 0.56
   3 ?    9.3   0.3   0.00062       0.8       2      14 ..     445     459 ..     444     463 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.2
                                    ETTTTC CS
                   TF_Zn_Ribbon   3 CPnCgs 8  
                                    CP C +
  gi|119719242|ref|YP_919737.1| 179 CPRCET 184
                                    555543 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.063
                                    EEESSSSB CS
                   TF_Zn_Ribbon  20 lvCtdCGl 27 
                                    ++C+dCG+
  gi|119719242|ref|YP_919737.1| 416 YYCKDCGA 423
                                    44555554 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.00062
                                    EETTTTCEEC..HEE CS
                   TF_Zn_Ribbon   2 kCPnCgstnl..veD 14 
                                    kCP+Cgs+n+  ++D
  gi|119719242|ref|YP_919737.1| 445 KCPKCGSKNIvpERD 459
                                    8********845555 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.11   1.5e+02       2      14 ..     179     191 ..     178     198 .. 0.82
   2 ?    2.8   0.1     0.058        75      16      26 ..     412     422 ..     405     422 .. 0.85
   3 ?    3.1   0.2     0.045        57       1       7 [.     445     451 ..     443     459 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.11
                       zf-TFIIB   2 CPkCqdeleeser 14 
                                    CP+C ++  e+e+
  gi|119719242|ref|YP_919737.1| 179 CPRCETAIAEAEV 191
                                    ****998877765 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.058
                       zf-TFIIB  16 gveidyCpqCr 26 
                                     ++++yC +C+
  gi|119719242|ref|YP_919737.1| 412 PIPVYYCKDCG 422
                                    589*******7 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.045
                       zf-TFIIB   1 kCPkCqd 7  
                                    kCPkC++
  gi|119719242|ref|YP_919737.1| 445 KCPKCGS 451
                                    7999987 PP

>> zf-ISL3  zinc-finger of transposase IS204/IS1001/IS1096/IS1165
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1      0.36   4.6e+02       2       9 ..     176     183 ..     175     192 .. 0.86
   2 ?   -0.4   0.2       1.5     2e+03      38      47 .]     412     421 ..     404     421 .. 0.87
   3 ?    6.3   0.0     0.012        15       4      15 ..     445     456 ..     443     469 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.36
                        zf-ISL3   2 phrCPnCg 9  
                                    +++CP+C 
  gi|119719242|ref|YP_919737.1| 176 VIWCPRCE 183
                                    689****7 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.5
                        zf-ISL3  38 rkrRyrCkeC 47 
                                    + + y+Ck+C
  gi|119719242|ref|YP_919737.1| 412 PIPVYYCKDC 421
                                    5788****** PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.012
                        zf-ISL3   4 rCPnCgsktvvk 15 
                                    +CP+Cgsk+ v 
  gi|119719242|ref|YP_919737.1| 445 KCPKCGSKNIVP 456
                                    6*******9875 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1       1.3   1.7e+03       2       7 ..     179     184 ..     179     190 .. 0.73
   2 ?   -0.8   0.1       1.1   1.4e+03       2       9 ..     346     353 ..     345     354 .. 0.84
   3 ?    5.5   0.1     0.011        14       1       9 [.     417     425 ..     417     428 .. 0.90
   4 ?    7.3   0.9     0.003       3.9       1       9 [.     445     453 ..     445     456 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.3
                  zinc_ribbon_2   2 CpnCGa 7  
                                    Cp+C +
  gi|119719242|ref|YP_919737.1| 179 CPRCET 184
                                    888866 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.1
                  zinc_ribbon_2   2 CpnCGael 9  
                                    C++C++++
  gi|119719242|ref|YP_919737.1| 346 CWRCHTPV 353
                                    ****9987 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.011
                  zinc_ribbon_2   1 fCpnCGael 9  
                                    +C+ CGael
  gi|119719242|ref|YP_919737.1| 417 YCKDCGAEL 425
                                    8******98 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.003
                  zinc_ribbon_2   1 fCpnCGael 9  
                                    +Cp+CG ++
  gi|119719242|ref|YP_919737.1| 445 KCPKCGSKN 453
                                    799999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (809 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       780  (0.0435049); expected 358.6 (0.02)
Passed bias filter:                      716  (0.0399353); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.78u 0.27s 00:00:01.05 Elapsed: 00:00:00.48
# Mc/sec: 5044.42
//
Query:       gi|119719243|ref|YP_919738.1|  [L=255]
Description: glutaredoxin-like domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.8e-26   89.8   0.0    3.4e-18   65.4   0.0    2.5  3  Thioredoxin_3   Thioredoxin domain
    9.6e-08   32.1   0.1    0.00024   21.2   0.0    3.0  3  Glutaredoxin    Glutaredoxin
    5.2e-05   23.2   0.0     0.0088   16.0   0.0    2.3  2  Thioredoxin     Thioredoxin
    0.00061   19.6   0.0     0.0013   18.5   0.0    1.5  1  Thioredoxin_9   Thioredoxin
     0.0071   16.8   2.3         17    5.9   0.0    3.3  2  Thioredoxin_2   Thioredoxin-like domain
  ------ inclusion threshold ------
      0.014   14.9   0.0       0.34   10.3   0.0    2.3  2  ABC_transp_aux  ABC-type uncharacterized transport system
      0.024   14.4   0.0        2.1    8.1   0.0    2.4  2  TraF            F plasmid transfer operon protein


Domain annotation for each model (and alignments):
>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   5.1e-08   0.00013       7      75 ..      33     105 ..      24     106 .. 0.83
   2 ?   -3.6   0.0       4.7   1.2e+04      61      75 ..     112     126 ..     111     126 .. 0.82
   3 !   65.4   0.0   1.3e-21   3.4e-18       2      76 .]     135     216 ..     134     216 .. 0.97

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 5.1e-08
                                    SSSSTTCHHHHHHHHHHCHCCTCECEEECC.TTHHHHHHCT-SSSSEEECTTC....EEEESS---CCHHHHHH CS
                  Thioredoxin_3   7 gpgCakCpklekavkeaaaekgikaevekv.tdfeeiekygVmsvPalvidgk....vvvsGkvpseeeirkll 75 
                                    g+ C +C+++e++++ + + +g k+ v++  ++ +e +ky + + Pa++i g+    v++ G +p ++e+ +++
  gi|119719243|ref|YP_919738.1|  33 GSECVYCDDTEQILNLVQQVSGGKVRVTRYtSKDPEAKKYSIDMFPAILIHGVdewnVRFFG-IPAGYEFGAFV 105
                                    788***************************5566666*************974333488899.99988887765 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 4.7
                                    EESS---CCHHHHHH CS
                  Thioredoxin_3  61 vsGkvpseeeirkll 75 
                                    ++G+v    eir++l
  gi|119719243|ref|YP_919738.1| 112 STGRVNISPEIREIL 126
                                    689999999999986 PP

  == domain 3  score: 65.4 bits;  conditional E-value: 1.3e-21
                                    EEEE.ESSSSTTCH.HHHHHHHHHCHCCTCECEEECCTTHHHH.HHCT-SSSSEEECT....TCEEEESS---CCHHHHH CS
                  Thioredoxin_3   2 eikv.lgpgCakCp.klekavkeaaaekgikaevekvtdfeei.ekygVmsvPalvid....gkvvvsGkvpseeeirkl 74 
                                    +i++ ++p+C++Cp ++++a++ a+ +k+i+ +++++ +f+++ ++ygV++vP+ vi+    +k +++G++p++++++k+
  gi|119719243|ref|YP_919738.1| 135 RIMIfVTPTCPYCPiAVRAAHRFAMVNKNIYGDMIEALEFSDLaDRYGVYAVPKNVIQvngeDKNEFEGAAPDPYFVAKI 214
                                    799*99***************************************************99999*****************9 PP

                                    HH CS
                  Thioredoxin_3  75 le 76 
                                    le
  gi|119719243|ref|YP_919738.1| 215 LE 216
                                    96 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0017       4.2       7      57 ..      34      84 ..      25      86 .. 0.83
   2 ?   -2.7   0.0       2.9   7.4e+03      32      48 ..     117     133 ..     114     134 .. 0.67
   3 !   21.2   0.0   9.4e-08   0.00024       1      51 [.     136     187 ..     136     196 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0017
                                   TSSHHHHHHHHHHHHTT.GGEEEEEGCCSHHHHHHHHHHHTSSSSSEEEETT CS
                   Glutaredoxin  7 ptCpyCkkakrlLkelg.vkfeeidvdkdeeireelkelsgvrtvPqvfidg 57
                                   + C+yC  + ++L+    v+   + v+   +   e k++  +  +P + i g
  gi|119719243|ref|YP_919738.1| 34 SECVYCDDTEQILNLVQqVSGGKVRVTRYTSKDPEAKKY-SIDMFPAILIHG 84
                                   57***********65555999999999999999999888.678899998887 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.9
                                    CCSHHHHHHHHHHHTSS CS
                   Glutaredoxin  32 dkdeeireelkelsgvr 48 
                                    +  +eire l +++  +
  gi|119719243|ref|YP_919738.1| 117 NISPEIREILLKYVTKP 133
                                    55678888887776555 PP

  == domain 3  score: 21.2 bits;  conditional E-value: 9.4e-08
                                    EEEEESTSSHHHHHHHHHHHHTTGG....E.EEEEGCCSHHHHHHHHHHHTSSSSS CS
                   Glutaredoxin   1 vvlftkptCpyCkkakrlLkelgvk....f.eeidvdkdeeireelkelsgvrtvP 51 
                                    +++f++ptCpyC+ a+r+++++ +     + ++i+ ++ +++ +    + gv +vP
  gi|119719243|ref|YP_919738.1| 136 IMIFVTPTCPYCPIAVRAAHRFAMVnkniYgDMIEALEFSDLAD----RYGVYAVP 187
                                    79******************999652444335555555544433....33666666 PP

>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.1   0.0    0.0088        22      50      79 ..      56      83 ..      18      95 .. 0.74
   2 !   16.0   0.0   3.4e-06    0.0088      20      99 ..     134     212 ..     121     216 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0088
                                   TSEEEEEETTTSHHHHHHTT-SSSSEEEEE CS
                    Thioredoxin 50 kvklakvdvdenedlakkyevegiPtlklf 79
                                   kv++ +   ++++  akky+++++P++++ 
  gi|119719243|ref|YP_919738.1| 56 KVRVTR--YTSKDPEAKKYSIDMFPAILIH 83
                                   444443..4677889***********9875 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 3.4e-06
                                    EEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEETTEEEEEEESS-HHHHHHH CS
                    Thioredoxin  20 lvlveFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklfkngkevkkyegarekeklaa 99 
                                    + ++ F  p C+ C  +a + ++    +++++    +++ e +dla++y+v ++P+ ++  ng+  +++ega++   ++a
  gi|119719243|ref|YP_919738.1| 134 TRIMIFVTPTCPYCP-IAVRAAHRFAMVNKNIYGDMIEALEFSDLADRYGVYAVPKNVIQVNGEDKNEFEGAAPDPYFVA 212
                                    45667999******6.555555555566669*****************************************98666555 PP

>> Thioredoxin_9  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   5.1e-07    0.0013      25     124 ..     115     214 ..     108     219 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 5.1e-07
                                    HHHHH---HH.HHHT--S-EEEEEE--TT-HHHHHHHHHHHHHHHH-TTEEEEEE-HHHHHHHTTTTTT-SS--SSEEEE CS
                  Thioredoxin_9  25 kvelseetee.kiksiekklkilvltedwCgDaavnvPvlakiaelnpnievkillrdenlelmdqyltngaraiPtlii 103
                                    +v++s+e +e  +k ++k+ +i+++ ++ C+ + + v + +++a  n+ni  +++   e  +l d+y   g  a+P+ +i
  gi|119719243|ref|YP_919738.1| 115 RVNISPEIREiLLKYVTKPTRIMIFVTPTCPYCPIAVRAAHRFAMVNKNIYGDMIEALEFSDLADRY---GVYAVPKNVI 191
                                    688999999978888****************************************999999999999...8899999776 PP

                                    E-TT..--EEEEEESS-HHHHH. CS
                  Thioredoxin_9 104 ldee..geelgvwgerPaevqel 124
                                      ++   +e++   + P +v ++
  gi|119719243|ref|YP_919738.1| 192 QVNGedKNEFEGAAPDPYFVAKI 214
                                    54332577776666666666665 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.0    0.0067        17      15      53 ..      34      76 ..      23      92 .. 0.80
   2 ?    5.0   1.3     0.012        32      10      20 ..     137     147 ..     131     214 .. 0.58

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0067
                  Thioredoxin_2 15 pdCpyCkklkkelkel...ddvtvrvllfp.lkpsfepkavai 53
                                   ++C yC+  ++ l  +   ++ +vrv  +   +p+++++++++
  gi|119719243|ref|YP_919738.1| 34 SECVYCDDTEQILNLVqqvSGGKVRVTRYTsKDPEAKKYSIDM 76
                                   5799*99999965555557888888888888888888888765 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.012
                  Thioredoxin_2  10 vvftdpdCpyC 20 
                                    ++f +p+CpyC
  gi|119719243|ref|YP_919738.1| 137 MIFVTPTCPYC 147
                                    56666777776 PP

>> ABC_transp_aux  ABC-type uncharacterized transport system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00013      0.34      18      82 ..      15      69 ..       9      94 .. 0.83
   2 ?    2.1   0.0     0.042   1.1e+02      23     101 ..     130     200 ..     112     238 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00013
                 ABC_transp_aux 18 ellknleepvtikvylsenla.lppelkalekevkdlLeeyaaysggkisvefidpspneeeeeea 82
                                   ++ + le+pv+ik+++++  + +      + ++++++L+  ++ sggk++v+ +  ++ e     a
  gi|119719243|ref|YP_919738.1| 15 QMFQALENPVSIKWFVDPGSEcV------YCDDTEQILNLVQQVSGGKVRVTRYTSKDPE-----A 69
                                   788999*************8655......79********************998776444.....3 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.042
                 ABC_transp_aux  23 leepvtikvylsenlalppelkalekevkdlLeeyaaysggkisvefidpspneeeeeeaeaygitpvq...isveekde 99 
                                    +++p +i +++++       +      +    +++a  ++ +i  ++i++ +++   ++a +yg+++v+   i+v+++d+
  gi|119719243|ref|YP_919738.1| 130 VTKPTRIMIFVTPTCP----Y---CPIAVRAAHRFAMVNK-NIYGDMIEALEFS---DLADRYGVYAVPknvIQVNGEDK 198
                                    4666666666666632....1...2223344456677655.7777888888777...66666666665544466655554 PP

                 ABC_transp_aux 100 lk 101
                                     +
  gi|119719243|ref|YP_919738.1| 199 NE 200
                                    33 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.014        35     126     170 ..      19      65 ..       4      90 .. 0.70
   2 ?    8.1   0.0   0.00081       2.1     121     155 ..     124     158 ..     115     193 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.014
                           TraF 126 klakeygLlfFyr..gkcpyceaqapilqafadkyglevraVsvdgr 170
                                    +l++ + +  F++  ++c yc+   +il+ +++  g +vr+     +
  gi|119719243|ref|YP_919738.1|  19 ALENPVSIKWFVDpgSECVYCDDTEQILNLVQQVSGGKVRVTRYTSK 65 
                                    555556666677744669***********999999998887555444 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00081
                           TraF 121 eaalkklakeygLlfFyrgkcpyceaqapilqafa 155
                                    e  lk + k   +++F+ ++cpyc  ++    +fa
  gi|119719243|ref|YP_919738.1| 124 EILLKYVTKPTRIMIFVTPTCPYCPIAVRAAHRFA 158
                                    5567778888889************9999988886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 1544.61
//
Query:       gi|119719244|ref|YP_919739.1|  [L=223]
Description: ribose 5-phosphate isomerase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-45  154.7   0.0    2.1e-45  154.4   0.0    1.1  1  Rib_5-P_isom_A  Ribose 5-phosphate isomerase A (phosphoribois
    8.2e-06   25.8   0.1    5.1e-05   23.3   0.0    2.0  2  DeoRC           DeoR C terminal sensor domain
  ------ inclusion threshold ------
      0.038   13.1   0.1      0.086   11.9   0.0    1.5  2  Sugar-bind      Putative sugar-binding domain


Domain annotation for each model (and alignments):
>> Rib_5-P_isom_A  Ribose 5-phosphate isomerase A (phosphoriboisomerase A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.4   0.0   3.5e-49   2.1e-45       2     170 ..      47     216 ..      46     219 .. 0.93

  Alignments for each domain:
  == domain 1  score: 154.4 bits;  conditional E-value: 3.5e-49
                                    EEESSHHHHHHHHHTT--BE-GGCCSSEEEEEE--SEEETTS-EE--TTS-HHHHHHHHHTEEEEEEEEEGGGBESSTTS CS
                 Rib_5-P_isom_A   2 gvptSeqteelaeelgipllsldeveeidlaiDGaDevdedlnliKGgGgallrEKivaaaakkfiviadesKlveklgk 81 
                                    +v++S +t+  a+  g+  + l+e+ + ++ +DGaD v +d +liKGgGg+llrEKiv++ +k+++vi+d +K+ e+  +
  gi|119719244|ref|YP_919739.1|  47 FVSSSIDTSLYAAGKGLLEVPLHEY-TPEVSFDGADTVLPDRSLIKGGGGCLLREKIVDYYSKEYVVIVDATKVAETPRN 125
                                    79********************999.89***********************************************99989 PP

                                    S-EEEEE-GGGHHHHHHHHHHTTT.-EEEE-TE.TTTTEE-B-TTS-EEEEEESSSBSSSHHHHHHHHHTSTTEEEESEE CS
                 Rib_5-P_isom_A  82 fpvPveVlpfaleavarelekllg.gkpelRea.kgkdgpvvTdngnlilDvkfeekiedpeelekelksipGVvetGlF 159
                                     +vPveV p a+++v++el+k  g ++++lR+  kgk gpv+Tdngn+ilD+ f+ +++dp +le +lks+pG +etG+F
  gi|119719244|ref|YP_919739.1| 126 LNVPVEVHPQAFKKVMEELRKSYGaVNVTLRTYeKGKLGPVLTDNGNFILDALFD-ELKDPLRLELSLKSVPGLIETGIF 204
                                    ********************876636779**987889*****************5.677********************* PP

                                    -.S--SEEEEEE CS
                 Rib_5-P_isom_A 160 l.gladkvlvgk 170
                                      +  +k++vg+
  gi|119719244|ref|YP_919739.1| 205 SvKKPSKIIVGY 216
                                    846999999986 PP

>> DeoRC  DeoR C terminal sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   8.5e-09   5.1e-05       6      47 ..       2      46 ..       1      68 [. 0.83
   2 ?    1.4   0.0     0.046   2.8e+02      83     141 ..      63     121 ..      38     126 .. 0.65

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 8.5e-09
                          DeoRC  6 KrrIAkaAaeliedgdtifldaGtTtlelaraLaekk...nltvv 47
                                   K + A++Aa++++dg+++ l++GtT+  +++ Lae+    nlt++
  gi|119719244|ref|YP_919739.1|  2 KLNAAREAARHVRDGMVVGLGSGTTVKIFIDVLAERVrqeNLTIF 46
                                   7789*****************************998666678775 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.046
                          DeoRC  83 laeealrqfnvdkaflgangidaegglttsdeeeaevkralieaarrvillaDssKfgk 141
                                    l e  l++++ ++ f ga+ + ++++l++        ++ +   +++ ++++D +K+ +
  gi|119719244|ref|YP_919739.1|  63 LLEVPLHEYTPEVSFDGADTVLPDRSLIKGGGGCLLREKIVDYYSKEYVVIVDATKVAE 121
                                    555556666666666666666666666666666666666666679999999***99875 PP

>> Sugar-bind  Putative sugar-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   1.4e-05     0.086      43      80 ..       6      44 ..       3      58 .. 0.77
   2 ?   -2.6   0.0      0.39   2.3e+03     104     131 ..     116     143 ..     101     152 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.4e-05
                                   HHHHHHH--TTEEEEE-SSHHHHHHHHHTHH.CCHTCEE CS
                     Sugar-bind 43 aqllesllkdgdvvgvgwGrtlsavaealtp.kslrdvk 80
                                   a    ++++dg+vvg+g+G+t++ +++ l +  + ++++
  gi|119719244|ref|YP_919739.1|  6 AREAARHVRDGMVVGLGSGTTVKIFIDVLAErVRQENLT 44
                                   5666799****************9999888754444444 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.39
                                    HHHCTSEEE--SSBSB-SSHHHHHHHHT CS
                     Sugar-bind 104 AqklggeyellpaPavlssaelrealla 131
                                    A k+  + + l++P+ +  ++ ++++ +
  gi|119719244|ref|YP_919739.1| 116 ATKVAETPRNLNVPVEVHPQAFKKVMEE 143
                                    6677777788888888888888887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1590.45
//
Query:       gi|119719245|ref|YP_919740.1|  [L=102]
Description: hypothetical protein Tpen_0328 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 778.82
//
Query:       gi|119719246|ref|YP_919741.1|  [L=221]
Description: hypothetical protein Tpen_0329 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      1e-33  116.6   0.0    1.2e-33  116.4   0.0    1.0  1  RNA_Me_trans  Predicted SAM-dependent RNA methyltransferase
  ------ inclusion threshold ------
      0.052   13.8   0.0      0.092   13.0   0.0    1.3  1  PaaX_C        PaaX-like protein C-terminal domain


Domain annotation for each model (and alignments):
>> RNA_Me_trans  Predicted SAM-dependent RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.4   0.0   1.3e-37   1.2e-33       4     188 ..      16     195 ..      13     207 .. 0.87

  Alignments for each domain:
  == domain 1  score: 116.4 bits;  conditional E-value: 1.3e-37
                   RNA_Me_trans   4 iEhleeelseWvllEYrhiakevgaenliltslskasleslpeelkslaklelekesveellkelkevkkekvclLDpka 83 
                                    iE le+ +s+W+ +E +hia+ ++++ ++  +++++ +e + + lk++   e+ +esv+e l+     + + v++LDp+a
  gi|119719246|ref|YP_919741.1|  16 IEVLEPFISKWMFIELKHIATVLEPKCIHVFNVKRD-CE-I-DVLKKV-FGEVRHESVTEELRLA--ETYDTVIILDPSA 89 
                                    9*********************************95.44.3.445543.3456677888888775..3689********* PP

                   RNA_Me_trans  84 ekelspedaeefdvflfGGIlGddpprdRTselrkkg...fegRrLGpvqmttDtAvrvtklvvedkvkleeieyvdepe 160
                                    ++ lsped ++  ++++GGI+G +ppr RT+e  +++    ++R++G+ q+t+D+A +v+  v + + +l+ei++     
  gi|119719246|ref|YP_919741.1|  90 PTPLSPEDFRGKTAVVIGGIMGSHPPRRRTREELTSKmriGAARNIGDGQFTIDGAAYVALEVSR-GRRLDEIPVQRGLS 168
                                    ******************************9887777577789********************99.9************* PP

                   RNA_Me_trans 161 lkfnkkesvempfrYvkdeegkpllpeg 188
                                    l++++  +v +p+ Y+    g p+++++
  gi|119719246|ref|YP_919741.1| 169 LSLKEGIEVVLPYVYPL-VGGVPFISKE 195
                                    ****************9.7888888876 PP

>> PaaX_C  PaaX-like protein C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0     1e-05     0.092      42      78 ..      67     103 ..      55     106 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1e-05
                         PaaX_C  42 eaFlvrtlllheyrkllfrDPgLPeellpedWpGaaa 78 
                                    e+  ++++l + y  ++  DP  P++l ped+ G++a
  gi|119719246|ref|YP_919741.1|  67 ESVTEELRLAETYDTVIILDPSAPTPLSPEDFRGKTA 103
                                    566778899999**********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1566.91
//
Query:       gi|119719247|ref|YP_919742.1|  [L=464]
Description: pyruvate kinase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.9e-88  296.1   0.0    3.8e-88  295.7   0.0    1.1  1  PK          Pyruvate kinase, barrel domain
    1.5e-21   76.8   0.0    3.7e-21   75.5   0.0    1.7  1  PK_C        Pyruvate kinase, alpha/beta domain
    0.00027   20.1   0.1     0.0008   18.6   0.0    1.7  2  HpcH_HpaI   HpcH/HpaI aldolase/citrate lyase family
  ------ inclusion threshold ------
      0.035   14.0   0.0       0.11   12.4   0.0    1.9  1  DNA_meth_N  DNA methylase N-terminal domain


Domain annotation for each model (and alignments):
>> PK  Pyruvate kinase, barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  295.7   0.0   8.5e-92   3.8e-88       2     341 ..       2     333 ..       1     339 [. 0.96

  Alignments for each domain:
  == domain 1  score: 295.7 bits;  conditional E-value: 8.5e-92
                                    --SEEEEEESCCCTSHHHHHHHHHHTEEEEEEETTSS-HHHHHHHHHHHHHHHHTTTTS-EEEEE---S-EBB--BTTCS CS
                             PK   2 rrtkivctlGPasesvekleklieaGlnvvrlnfshGsheehqerienvreaekklgkkvaillDtkGpeirtgllkdgk 81 
                                     ++k+v+tlGP+s s e++++++++G+n +rlnfsh ++   +e  ++vr+ e  l + ++++ D++Gp ir g ++   
  gi|119719247|ref|YP_919742.1|   2 AKVKLVATLGPSSWSEETMKRMVAEGVNAFRLNFSHVDYARFEELAKQVRRLETPL-RPLTLIADLQGPVIRLGEFAP-- 78 
                                    589***********************************************998765.4589999***********998.. PP

                                    SSEEE-TTSEEEEE-SCTCTTTBBTTEEEBS-TTHHHHS-TTEEEEETTTTEEEEEEEEETTEEEEEEESS-EEE-SS-B CS
                             PK  82 kdielkegdklkvsldeklkeegdeelialdyknivkdvevGktilvdDGllslkvlevdeekeleveventgvlgskkg 161
                                      ++++ gd+++++l++k++e+     + +     ++ v+ G+ +lv+ G+l++++ +  +ek  + e+  +g+++ +k 
  gi|119719247|ref|YP_919742.1|  79 --FQVRPGDRVTFTLSSKTEEK---YAVPVPNGVFFEIVREGDEVLVEGGRLAFRIVDAGPEK-AVGEALLEGEVKPRKT 152
                                    ..99***********9988754...66777777799*************************99.7889************ PP

                                    EE-TTS---S-SS-HHHHHHHHHHHHCT-SEEEETTE-SHHHHHHHHHHHTCCC.TTSEEEEEE-SCHHHHTHHHHHHHS CS
                             PK 162 vnlpgtkvdlpalsekDkadlrfgvkqgvdliaasfvrkasDvkevrevleeeg.keikiiakienqegvenldeileas 240
                                    v + g +++lp+++ekD +d++f+vk g d ia+sfvr++sDv+++r++l + g +++kiiakie + +ve+ld il++s
  gi|119719247|ref|YP_919742.1| 153 VTVRGKDIPLPTITEKDLRDIEFSVKAGFDAIALSFVRSSSDVQRLRDILFDYGaEDVKIIAKIETKSAVEDLDSILQKS 232
                                    **************************************************999989************************ PP

                                    SEEEEEHHHHHHHSTCCCHHHHHHHHHHHHHHHT--EEEESSTTGGGGTSSS--HHHHHHHHHHHHHT-SEEEESHHHHT CS
                             PK 241 DgimvarGDlGieipaekvllvqkklikkcnlagkpvitatqmlesmiknPrptraevsDvanavlDGtDavmLsgetak 320
                                    D+ +varGDl    + e+++ +q+ +i+++++ gkp i+atq+lesmi+nP ptr+ev Dv  av  G+Da++L+geta+
  gi|119719247|ref|YP_919742.1| 233 DAALVARGDLANFYGLEEIYSIQRYIISRARRFGKPSIVATQLLESMISNPLPTRSEVVDVITAVRMGADALLLAGETAA 312
                                    ******************************************************************************** PP

                                    SS-HHHHHHHHHHHHHHHHHT CS
                             PK 321 GkyPveavkamaevaleaeka 341
                                    GkyPve+v  + ++  eae++
  gi|119719247|ref|YP_919742.1| 313 GKYPVESVYWLRRIVEEAERE 333
                                    *****************9975 PP

>> PK_C  Pyruvate kinase, alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.5   0.0   8.2e-25   3.7e-21       1     116 [.     349     458 ..     349     459 .. 0.91

  Alignments for each domain:
  == domain 1  score: 75.5 bits;  conditional E-value: 8.2e-25
                                    HHHHHHHHHHHHHHT-SEEEEE-SSSHHHHHHHHT-TSSEEEEEESHHHHHHHHHHCTTEEHHH.HHHHH...TTS.HHH CS
                           PK_C   1 eaiakaaveaaeelgakaIvvltesGetArliskyrpkvpiiavtpneltarqlalyrGvypvlvekaktaestde.llr 79 
                                    e+iak +v++ae +   +I++++e+G+tAr+isk+rpk+ +i++t+++ tar +++  Gv+ v+ + +   +++d+ l+ 
  gi|119719247|ref|YP_919742.1| 349 ESIAKGVVSLAEVI-SGKIIAFSEKGNTARRISKFRPKAGLIVFTNDPATARYVNMIYGVRVVY-DPS--LSKADQnLFS 424
                                    789********966.777*********************************************6.655..5677776899 PP

                                    HHHHHHHHTTSS-STSEEEEEE-SSSS..SS--EEEE CS
                           PK_C  80 eavkvakeaglvkkgdevvvtaGtpkgesgttNtlrV 116
                                    +++  a+e++lv+ gd+vv t+G ++g   +t+++ V
  gi|119719247|ref|YP_919742.1| 425 KMLSKALEHNLVNLGDLVVFTSGRRRG---STDLVSV 458
                                    ***********************9877...8998876 PP

>> HpcH_HpaI  HpcH/HpaI aldolase/citrate lyase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.8e-07    0.0008      76     155 ..     171     243 ..     149     272 .. 0.83
   2 ?   -2.1   0.0      0.37   1.7e+03      17      33 ..     296     312 ..     291     314 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.8e-07
                                    HHGG.HHHTTSSEEEESS--SHHHHHHHHHHTSHTTTS---HCCC-EEEEEE-SHHHHHTHHHHHTSTTEEEEEE-HHHH CS
                      HpcH_HpaI  76 qdle.vldlgaqvvlvPkvetaeealevvsalrepekgirganketrllaqiEsaegvknaeeIaavegldgvflGaeDl 154
                                    +d+e  +++g++++ + +v +  +++ +  +l+         ++ ++++a iE++ +v+++++I++    d++ ++  Dl
  gi|119719247|ref|YP_919742.1| 171 RDIEfSVKAGFDAIALSFVRSSSDVQRLRDILFDYG------AEDVKIIAKIETKSAVEDLDSILQK--SDAALVARGDL 242
                                    346699***************************999......89********************954..45555555566 PP

                                    H CS
                      HpcH_HpaI 155 s 155
                                    +
  gi|119719247|ref|YP_919742.1| 243 A 243
                                    5 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.37
                                    HCTC--SEEEEESSTSS CS
                      HpcH_HpaI  17 aaiagaDsvliDlEdav 33 
                                    a  +gaD++l+ +E a 
  gi|119719247|ref|YP_919742.1| 296 AVRMGADALLLAGETAA 312
                                    67899*****9999875 PP

>> DNA_meth_N  DNA methylase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   2.6e-05      0.11      20      46 ..       8      34 ..       4      46 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.6e-05
                     DNA_meth_N 20 rkvgeseWsretLnRwvkgksaarrLt 46
                                    ++g+s+Ws et++R+v++  +a rL+
  gi|119719247|ref|YP_919742.1|  8 ATLGPSSWSEETMKRMVAEGVNAFRLN 34
                                   5689***************99998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (464 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.73u 0.34s 00:00:01.07 Elapsed: 00:00:00.57
# Mc/sec: 2435.30
//
Query:       gi|119719248|ref|YP_919743.1|  [L=1052]
Description: DEAD/DEAH box helicase domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.5e-19   69.2   0.1    1.1e-18   67.6   0.0    1.8  2  DEAD        DEAD/DEAH box helicase
    8.1e-13   48.7   0.0    2.5e-12   47.1   0.0    1.8  1  Helicase_C  Helicase conserved C-terminal domain
  ------ inclusion threshold ------
      0.013   15.5   0.3      0.028   14.4   0.0    1.6  2  ResIII      Type III restriction enzyme, res subunit
      0.019   14.7   0.0      0.038   13.7   0.0    1.5  1  AAA_30      AAA domain
        0.1   12.9   0.0        0.2   12.0   0.0    1.5  1  AAA_19      AAA domain


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.6   0.0   3.1e-22   1.1e-18       2     170 ..      55     227 ..      54     232 .. 0.74
   2 ?   -2.0   0.0      0.73   2.6e+03      51     109 ..     339     401 ..     328     411 .. 0.70

  Alignments for each domain:
  == domain 1  score: 67.6 bits;  conditional E-value: 3.1e-22
                                    HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD   2 diQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlli 81 
                                    + Q ea++++ +g++v+++a TGsGKT+a+++ v+        k++++al v Pt +La ++l +lk + + +++rv+ i
  gi|119719248|ref|YP_919743.1|  55 KHQVEAFKALSEGKNVVLKAGTGSGKTEAWFLYVV--------KSKKRALAVYPTLALASDQLARLKDYSQSLGVRVSQI 126
                                    689********************************........78889***********************999888866 PP

                                    ET.........TSSHHHHHHHHHTTCSEEEEEHHHHHHHH.......HCTSSH....CTTEEEEEEETHHHHHHT..TTH CS
                                    xx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxx....xxxxxxxxxxxxxxxxxx..xxx RF
                           DEAD  82 ig.........gvaardqlskldngvdivvgtpgrlddll.......stgkln....lsqvrflVlDEadrlldq..gfs 139
                                               g + +  +s+l ++ divv++p  l+  l       st   +    ++q+ +lVlDE+d ++       
  gi|119719248|ref|YP_919743.1| 127 DAtsksemfekGLKSSGIRSAL-SESDIVVTNPAFLLMDLkrlatkpSTC--TlfsfFQQLDLLVLDEIDFYSPRelALL 203
                                    3311222222234444444444.77********98887555876655333..14479*************9998833344 PP

                                    HHHHHHHHHSHHHCTTST.TTSEEEEEESSBS CS
                                    xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx RF
                           DEAD 140 dfinrilnqlpqitcdgk.lqrqvivlSATlp 170
                                      i +il++l       + lq  + vl+A l+
  gi|119719248|ref|YP_919743.1| 204 VSIMKILSEL------RPtLQ--FAVLTAGLS 227
                                    4444444444......34344..888888775 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.73
                                    EEEESSHHHHHHHHHHHHHHTTT.ST..SEEE.EEETTSSHHHHHHHHHTTCSEEEEEHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxx.xx..xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  51 livePtreLaeqtlnnlkkfkky.id..lrvl.liiggvaardqlskldngvdivvgtpgrld 109
                                    ++ + +   ae+++++l+ +  + +   + v+  ++ ++++r+  +k+++g+  vv  p  l 
  gi|119719248|ref|YP_919743.1| 339 IVFTGSINKAEEVYRKLRHRVGEeLAgrVAVHhHLVAKSKRREVEEKIREGAVRVVLSPRTLS 401
                                    566666677888888888877754443444443446678888888999888777777777765 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.1   0.0   6.9e-16   2.5e-12       6     109 ..     328     433 ..     323     434 .. 0.87

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 6.9e-16
                                    HHHHHHHTTTTSEEEEEESSHHHHHH.HHHHHHHT....TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSS CS
                     Helicase_C   6 llellkleeeggkilifvntidrlek.vklllekk....gikvavlhgelpqnereeileqfnkgesdvLiatdvaerGi 80 
                                    l ++l    ++g +++f+ +i+++e+  + l+++     + +vav+h    +++r+e+ e+ ++g ++v+++ + +++Gi
  gi|119719248|ref|YP_919743.1| 328 LENYL---YDDGVTIVFTGSINKAEEvYRKLRHRVgeelAGRVAVHHHLVAKSKRREVEEKIREGAVRVVLSPRTLSQGI 404
                                    55555...678899********9986656663333565689*************************************** PP

                                    TSTTESEEEESSSSSSHHHHHHHHTTSSS CS
                     Helicase_C  81 dipkvnlVinfdlprnvtsyiqriGRtgR 109
                                    di +v  V++++lp++v+++ q  GR gR
  gi|119719248|ref|YP_919743.1| 405 DIGNVVRVVHLGLPEEVREFYQKEGRKGR 433
                                    ***************************99 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   7.8e-06     0.028       3     111 ..      52     158 ..      51     192 .. 0.66
   2 ?   -3.6   0.1       2.7   9.6e+03     142     159 ..     371     388 ..     370     395 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 7.8e-06
                                    EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG.. CS
                         ResIII   3 elreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseay 82 
                                    +l+++Q ea ++l       + k++++k+ TG+GKT   +  + + +k     ++l + p+++l +  l ++k+++++  
  gi|119719248|ref|YP_919743.1|  52 KLYKHQVEAFKALS------EGKNVVLKAGTGSGKTEAWFLYVVKSKK-----RALAVYPTLALASDQLARLKDYSQSLG 120
                                    57888999998885......6789************988776665555.....9************99977777766543 PP

                                    ..........GEEEESSS-B--.................-SEEEEEH CS
                         ResIII  83 ke........igkkvsgdkkka..........kekdstnkkilvtti 111
                                     +        +       +  +           +++ ++++i+vt+ 
  gi|119719248|ref|YP_919743.1| 121 VRvsqidatsK-------S--EmfekglkssgIRSALSESDIVVTNP 158
                                    33222222211.......1..11123333344555566666666665 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2.7
                                    GGTTS.TTTHHHHHT--- CS
                         ResIII 142 Hrlgakkswreilekfke 159
                                    H+l ak++ re+ ek++e
  gi|119719248|ref|YP_919743.1| 371 HHLVAKSKRREVEEKIRE 388
                                    9****8899999999976 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.1e-05     0.038       2     111 ..      53     206 ..      52     211 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.1e-05
                         AAA_30   2 lnaeQaaavealltsgdrvavltGpAGtGKttalkalreaweaaggrvi.glAptgkaAkvLa...eelgieastiakll 77 
                                    l + Q +a++al ++++  +vl+++ G+GKt a   ++   +++   v   lA  + + ++L+   ++lg++ s i+   
  gi|119719248|ref|YP_919743.1|  53 LYKHQVEAFKALSEGKN--VVLKAGTGSGKTEAWFLYVVKSKKRALAVYpTLALASDQLARLKdysQSLGVRVSQIDATS 130
                                    7789*****98877775..9************987776555555533333444444444455533357777666666555 PP

                         AAA_30  78 krlk.........................................grarlepg.tllivDEagmvdtkqlaallka 111
                                    k+                                              ++ ++ +ll+ DE+   + ++la l+++
  gi|119719248|ref|YP_919743.1| 131 KSEMfekglkssgirsalsesdivvtnpafllmdlkrlatkpstcTLFSFFQQlDLLVLDEIDFYSPRELALLVSI 206
                                    4444555555666666666666888888888888888888888884444555558888888888888888777765 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   5.6e-05       0.2       1     125 [.      57     206 ..      57     213 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.6e-05
                         AAA_19   1 qreave.alkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgaeatTiHrlal.. 77 
                                    q ea +  ++ k++++ aG G+GKT+     v   +++    ++ +  +a+++    +l++  ++lg++ + i + +   
  gi|119719248|ref|YP_919743.1|  57 QVEAFKaLSEGKNVVLKAGTGSGKTEAWFLYVVKSKKRA---LAVYPTLALASDQLARLKDYSQSLGVRVSQIDATSKse 133
                                    567887678999*************87654443333333...33344445555556688888888888866666665566 PP

                         AAA_19  78 .............................ldfddlltealelleeaeeekklqeeellivDEfqdvdelqyrLlkal 125
                                                                 +d+++l t++ +     +  +++q+ +ll+ DE+   ++ + +Ll  +
  gi|119719248|ref|YP_919743.1| 134 mfekglkssgirsalsesdivvtnpafllMDLKRLATKPSTC----TLFSFFQQLDLLVLDEIDFYSPRELALLVSI 206
                                    677777777777777777777777777667777777666655....2334554556888888888778777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1052 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.80u 0.26s 00:00:01.06 Elapsed: 00:00:00.45
# Mc/sec: 7012.75
//
Query:       gi|119719249|ref|YP_919744.1|  [L=222]
Description: hypothetical protein Tpen_0332 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.6e-12   46.2   8.2    5.6e-12   46.2   8.2    2.4  3  SNARE_assoc  SNARE associated Golgi protein
  ------ inclusion threshold ------
      0.056   12.9   0.0      0.091   12.2   0.0    1.2  1  adh_short    short chain dehydrogenase


Domain annotation for each model (and alignments):
>> SNARE_assoc  SNARE associated Golgi protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   1.7      0.13   1.2e+03      69      86 ..      23      40 ..       7      49 .. 0.70
   2 !   46.2   8.2   6.2e-16   5.6e-12      10     119 ..      41     154 ..      31     155 .. 0.86
   3 ?   -1.5   0.0      0.39   3.5e+03      26      41 ..     169     184 ..     163     218 .. 0.56

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.13
                    SNARE_assoc 69 lallllrllpivPrdlvn 86
                                   ++ +l+ l+p++P++++ 
  gi|119719249|ref|YP_919744.1| 23 VISILGNLIPFIPIPYLV 40
                                   445677788888777665 PP

  == domain 2  score: 46.2 bits;  conditional E-value: 6.2e-16
                    SNARE_assoc  10 aGvlf.......glllgtlvtslgallGaslayllgrylgrkalrrkllsekrvkalerlverygflallllrllpivPr 82 
                                    a++l+       +++l+ +v+ +ga +G++l+yl++r  +r  l     s++r++++ +++ +yg++a++l+ ++p  P+
  gi|119719249|ref|YP_919744.1|  41 AVYLYaayvpgsNPFLVGVVSGVGAGVGKLLVYLFSRGGAR--LFMSQESRERFEKIGKMLGNYGAIAVFLFAVTPS-PD 117
                                    3333333456678999********************98884..4444589999999********************7.8* PP

                    SNARE_assoc  83 dlvnyvaGltrvsfkrFflatfiGsipwalvyaylGs 119
                                    d++ +++G++++++ +Ff+a  +G+i+ ++ +a++G+
  gi|119719249|ref|YP_919744.1| 118 DAIIIPLGMMGYHPLKFFAAVTAGKIIISIATAFAGK 154
                                    **********************************996 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.39
                    SNARE_assoc  26 gallGaslayllgryl 41 
                                    +++++ +++ +l  yl
  gi|119719249|ref|YP_919744.1| 169 ATSIALFVVVMLLIYL 184
                                    3333333333333333 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0     1e-05     0.091       4      53 ..      59     108 ..      57     119 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1e-05
                                    EEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEE CS
                      adh_short   4 lvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakala 53 
                                    +v G ++G+G+ +++ + + Ga++++ ++s e+ e++ k l++ ga a++
  gi|119719249|ref|YP_919744.1|  59 VVSGVGAGVGKLLVYLFSRGGARLFMSQESRERFEKIGKMLGNYGAIAVF 108
                                    789**************************************998544443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1420.18
//
Query:       gi|119719250|ref|YP_919745.1|  [L=82]
Description: hypothetical protein Tpen_0333 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1130  (0.0630264); expected 358.6 (0.02)
Passed bias filter:                      749  (0.0417759); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 608.29
//
Query:       gi|119719251|ref|YP_919746.1|  [L=281]
Description: bis(5'nucleosyl)-tetraphosphatase, ApaH [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.6e-27   95.8   0.0    5.8e-27   95.5   0.0    1.1  1  Metallophos    Calcineurin-like phosphoesterase
      0.003   17.8   0.0     0.0051   17.0   0.0    1.3  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
  ------ inclusion threshold ------
      0.059   13.8   0.1       0.13   12.7   0.1    1.6  1  STPPase_N      Serine-threonine protein phosphatase N-termina
      0.067   13.0   0.0       0.17   11.7   0.0    1.6  1  Peptidase_S26  Signal peptidase, peptidase S26


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.5   0.0   1.3e-30   5.8e-27       2     203 ..      47     236 ..      46     237 .. 0.84

  Alignments for each domain:
  == domain 1  score: 95.5 bits;  conditional E-value: 1.3e-30
                                    EEEEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSS..HHHHHHHHHHHHHHHHTSEEEEEC-TTS.... CS
                    Metallophos   2 rilvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrg..dlekellellaalvkypipvylllGNHe.... 75 
                                    r+l++gD+H     g+ ++++++++++    +++++l  GD+vdrg  +le+ ++ ll+ + +++ +++ll+GNHe    
  gi|119719251|ref|YP_919746.1|  47 RVLFVGDTH-----GDVESTINAFREA---ADVYVFL--GDYVDRGryQLEN-IVLLLQVKRDNRERIVLLRGNHEtrsm 115
                                    89*******.....**********666...5668888..*******888888.6666888888899**********6555 PP

                                    ....CHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESECEEETHHHHHHHHHHHSCHHHHCC..HH CS
                    Metallophos  76 ....gfeeellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGgspellvsldklgslnleleapepg..de 149
                                        gf   +  +yg      + +  + evf+ +   +l++   +vl +hGg p  l  ++++ sl++e+e+++p+  ++
  gi|119719251|ref|YP_919746.1| 116 nmvyGFLRVVITRYG-----ERMYDLFEEVFSQMSYGALVNR--EVLAVHGGIPKGLSRVEEIQSLKKEQEPSDPRtfQL 188
                                    555554444455544.....5566666***************..********55559*********************** PP

                                    HHHHHHHHTTCSEEEEEESSESS.CSSSCSCCHHHHHHHHHHTTESEEEEESSSS CS
                    Metallophos 150 wlkdlekrekadwvivlgHsply.rgsgylfgdealedllkkygvdlvisGHtHv 203
                                    +++d       +   + g  p +   + ylfg+++++++l+++g++l ++GH+ v
  gi|119719251|ref|YP_919746.1| 189 LWND-------PDEGITGFEPSPrGEGIYLFGEDVARRFLDENGLKLLVRGHEPV 236
                                    ****.......6666666666666699*************************975 PP

>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   1.1e-06    0.0051       2     101 ..      47     161 ..      47     186 .. 0.60

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.1e-06
                  Metallophos_2   2 klaiiSDlHsnldaleavlealkevgvdaiihaGDl...eeeepevleellela.....pvlaVrGNnD...eev...ve 67 
                                    +++++ D+H+ ++ + ++   ++e+ +d  +++GD+   +  ++e +  ll+++     +++  rGN++   +++   + 
  gi|119719251|ref|YP_919746.1|  47 RVLFVGDTHGDVESTINA---FREA-ADVYVFLGDYvdrGRYQLENIVLLLQVKrdnreRIVLLRGNHEtrsMNMvygFL 122
                                    6899*****655555555...5555.5779*****875433333433334444466699**********88733334644 PP

                  Metallophos_2  68 edvlreaaelgtdlpeeaelel.....agekvlliHgdp 101
                                    + v  +  e + dl ee + ++      +++vl +Hg  
  gi|119719251|ref|YP_919746.1| 123 RVVITRYGERMYDLFEEVFSQMsygalVNREVLAVHGGI 161
                                    444444444444443444444344545566688888863 PP

>> STPPase_N  Serine-threonine protein phosphatase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   2.9e-05      0.13      19      47 ..      15      43 ..       7      44 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.9e-05
                      STPPase_N 19 kvqLseaEIrqlCakareiFLsQPtLLeL 47
                                   k+ L+ +E++ l+ ++++++ s P L e+
  gi|119719251|ref|YP_919746.1| 15 KLSLTPEELKRLLEESKKVLSSDPPLVEV 43
                                   789***********************996 PP

>> Peptidase_S26  Signal peptidase, peptidase S26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   3.7e-05      0.17      78     127 ..     216     263 ..     199     268 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.7e-05
                  Peptidase_S26  78 vsealerDrkgrplpslqgcrvlaegelfllskevadSfDsRYfGpvpas 127
                                    v++ +  D++g +l + +g + ++eg  fl++++va+ f  RY+G+ p++
  gi|119719251|ref|YP_919746.1| 216 VAR-RFLDENGLKLLV-RGHEPVQEGVKFLFGERVATVFSCRYYGITPTA 263
                                    555.556888888875.45899************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2035.93
//
Query:       gi|119719252|ref|YP_919747.1|  [L=639]
Description: anaerobic ribonucleoside triphosphate reductase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     8e-150  500.3   0.0   9.4e-150  500.1   0.0    1.0  1  NRDD          Anaerobic ribonucleoside-triphosphate reductase
     0.0087   15.7   0.0      0.017   14.8   0.0    1.4  1  TackOD1       Thaumarchaeal output domain 1
  ------ inclusion threshold ------
      0.019   15.0   0.1      0.038   14.0   0.1    1.4  1  HypA          Hydrogenase/urease nickel incorporation, metall
       0.28   10.9   3.3       0.57   10.0   3.3    1.5  1  Rubredoxin_2  Rubredoxin metal binding domain
        0.6   10.0   5.6        2.1    8.3   5.6    2.0  1  DUF35_N       Rubredoxin-like zinc ribbon domain (DUF35_N)
        2.2    8.5   4.0         60    3.9   4.8    2.5  2  Zn-ribbon_8   Zinc ribbon domain


Domain annotation for each model (and alignments):
>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  500.1   0.0  3.2e-153  9.4e-150       1     561 []      29     639 .]      29     639 .] 0.92

  Alignments for each domain:
  == domain 1  score: 500.1 bits;  conditional E-value: 3.2e-153
                                    .XHTTHHHHHHHHHHHHHHHHHHH.H-H..HHHHHHHHHHHTTSEEETTGGGTTT.S--EEE--SHHHHHH-CTT-SSS- CS
                           NRDD   1 enanvdskslsglrlklasevske.yalkkllpkevaeaheegdiHiHDldylallttyClgidlkdlleeGlktgngvs 79 
                                    enan  + s+s +r++l ++++k+  +l++ lp+  +e+h +gdiHiH+l   +l ++yC+g++ k++l+ Glkt   +s
  gi|119719252|ref|YP_919747.1|  29 ENANH-NVSYSNFRNYLFEKLVKSkEVLSEYLPPLAIEQHYRGDIHIHKLPD-SLWIPYCAGWSYKKILQLGLKTPTIIS 106
                                    8****.99**********998775268899********************88.688*******************9999* PP

                                    B---SHHHHHHHHHHHHHHHHTSSSS-EEETTHHHHHHHHHHHHHHTTSS-GHHHHHHHHHHHHHHHTTS-S..SSSS-- CS
                           NRDD  80 rppkhietalalavnilqtlqneqaGgqaissfdtylapfvrkdyekklkkltkkeikqamqefvynlntlpsrrGaQvp 159
                                    +p++h++ta+a++vn++++ ++e++G+qa+s+fd ++apf++ d      +l+k++ikq +q+++++ln +p+r+G+Q+p
  gi|119719252|ref|YP_919747.1| 107 APARHFDTAVAHLVNFFFMGAQEWTGAQAVSAFDLFVAPFAEGD------GLSKERIKQTLQGMLFELN-YPARAGYQSP 179
                                    ********************************************......*******************.********** PP

                                    -EEEEEE.-HH...............................HHHHHTTTTS-HCH----SEEEEEEEEETETTH..... CS
                           NRDD 160 Ftninlgldtp................tegrfee..kliikallevmleGdgnkgtpftFPilifklkedfnleeedpny 221
                                    Ftni+l +dt+                + g++ e    + +al+e + eGd+  g+pftFPi++++l+++f+++   ++ 
  gi|119719252|ref|YP_919747.1| 180 FTNITLVMDTSkdmlegeaivagkkagSLGDYIEkaLAVDEALFELYAEGDAA-GQPFTFPIPTIMLTKNFDWNG-RRWG 257
                                    ***************************888888877788999***********.********************9.88** PP

                                    HHHHHHHHHHTTT--EEE.......EEES--GGGTT-------......-.............................. CS
                           NRDD 222 dlfklalevtakrgfpyffnlledlepedekevasmgCRlrld......ege............................ 267
                                    +l++++++  +++g++y  n +     ++ + + +m+CRl++d      +                              
  gi|119719252|ref|YP_919747.1| 258 ELTDKIFTALSRKGSAYLLNGY----ASNVEALYAMCCRLTIDvnhvmgK-Sgngspsfslklsradeedafekfmksre 332
                                    ******************9996....45666799*********8655441.13344555566666666666666666665 PP

                                    ..S---.......EEEEEEEEEEHHHHHH..HH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT.-HHH.HTTSS-G CS
                           NRDD 268 ..rlgg.......rgslgvvtiNlprlaleakgdeekffelLdellelakealeerrkilekllakg.lpflmgkgylks 337
                                      r++g       +gs+gvvt+Nlprla ++kg+   f elLd+ll+ a+++l++ rk+ ek+la+g +p+  +k yl  
  gi|119719252|ref|YP_919747.1| 333 nsRTYGiwalpdaTGSIGVVTLNLPRLAALSKGEWPLFEELLDSLLKNARDVLLTWRKRYEKTLAAGlMPL--TKTYLG- 409
                                    555555*****************************************************************..9****7. PP

                                    E.............EEEEEEE-HHHHHHHT.......TEEEE..-HHHHHHHHHHHHHHHHHHHHHHHHHSS-EEEEE-- CS
                           NRDD 338 rkkkdeveevlkngtltiGfiGlaEalkal.......tgkkigeseeakefalkvlkhmrekadelkeetglnfsleatP 410
                                              ++++++tiG+iGl Ea++++        + ++ge +ea e+ +k+++ +re+a+el+e++g+ +++e++P
  gi|119719252|ref|YP_919747.1| 410 ---------HFNHHFNTIGVIGLPEAAANFmrnpkvwFEGGVGELQEAVEIEKKMVSLIRERASELEERDGYLYNVEEIP 480
                                    .........59**************************777999************************************* PP

                                    -TTHHHHHHHHH..HH.....................HHG-SSSS-TTSSB-HHHHHHHHHHHTGGGTT-S-EEEEBSS- CS
                           NRDD 411 aEslsgrfakldkkkfgeipgv.dke..........pyYtNsfhvpvdekislfekikleaefqklttGGailyieldee 479
                                    +Es+++++a  d + f   ++   ++          p+Y+Ns+ vp+++++ ++++  +e+ +q+ +tGG++++++l+e+
  gi|119719252|ref|YP_919747.1| 481 GESTGYKLALADLQLF---KEEhARGevlipsdgkaPFYSNSV-VPYYADVPMYQRAIWEGYVQQEFTGGVMMHLFLHEQ 556
                                    ****************...44434447899999999*****97.788889***************************766 PP

                                    -SSHHHHHHHHH.HHHHTT--EEEEE--EEEETT.--..EESSSB-TTT--BE.EEEEEESSSSEEEHHHHHHHHHHHSG CS
                           NRDD 480 kknpealeklvk.iakktgigYfsinpkidvCnecgy..kgeiekCpkCgseeevevirRitGYlrpvsswnkgkkaElk 556
                                     ++p+al++lv  ia++t+++Yfsi+p+i+vC++cg+  +g+ + Cp+Cgs+e ve+++Ri+GY+rpvs+wn+gkkaE+k
  gi|119719252|ref|YP_919747.1| 557 -PDPKALRNLVYrIATNTKVVYFSITPTITVCRKCGRstTGYLDGCPHCGSSE-VEHWSRIVGYYRPVSNWNPGKKAEFK 634
                                    .***********9************************999999*******777.************************** PP

                                    G---B CS
                           NRDD 557 dRvkh 561
                                     Rv++
  gi|119719252|ref|YP_919747.1| 635 LRVTY 639
                                    ***98 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   5.7e-06     0.017      63     100 ..     574     611 ..     533     618 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.7e-06
                        TackOD1  63 glleeelvdrirlCpsCksghlnvrevCpkCkSidiee 100
                                    +++  ++  +i +C++C  +   + + Cp+C+S+++e+
  gi|119719252|ref|YP_919747.1| 574 KVVYFSITPTITVCRKCGRSTTGYLDGCPHCGSSEVEH 611
                                    445567788999**********************9987 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   1.3e-05     0.038      61      98 ..     575     610 ..     556     613 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.3e-05
                                    EEEEEEE--EEEETTTS-EEECHHHHHS-TTTSSS-EE CS
                           HypA  61 eLeieevpvkvrCreCgkefeleekalrCpkCgsadve 98 
                                    ++ ++ +p  + Cr+Cg++++   +   Cp+Cgs++ve
  gi|119719252|ref|YP_919747.1| 575 VVYFSITPTITVCRKCGRSTTGYLD--GCPHCGSSEVE 610
                                    45577889999******88874434..7******9987 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   3.3   0.00019      0.57       2      23 ..     586     607 ..     586     608 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00019
                   Rubredoxin_2   2 vCsqCGfesakwfGrCpsCgsW 23 
                                    vC++CG ++  ++  Cp+Cgs 
  gi|119719252|ref|YP_919747.1| 586 VCRKCGRSTTGYLDGCPHCGSS 607
                                    7*******************85 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   5.6   0.00069       2.1      11      37 .]     584     610 ..     583     610 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00069
                        DUF35_N  11 gqrCpdCGtvqfPPravCphCgsddle 37 
                                    ++ C++CG+        CphCgs+++e
  gi|119719252|ref|YP_919747.1| 584 ITVCRKCGRSTTGYLDGCPHCGSSEVE 610
                                    689********************9987 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.2     0.045   1.3e+02      23      34 ..     581     592 ..     572     596 .. 0.64
   2 ?    3.9   4.8      0.02        60       8      37 ..     587     610 ..     586     611 .. 0.68

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.045
                    Zn-ribbon_8  23 dapltaCPeCgs 34 
                                     +  t+C +Cg 
  gi|119719252|ref|YP_919747.1| 581 TPTITVCRKCGR 592
                                    344455999997 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.02
                    Zn-ribbon_8   8 CeeCghefevlqsisdapltaCPeCgs.evr 37 
                                    C++Cg+  +         l  CP+Cgs ev+
  gi|119719252|ref|YP_919747.1| 587 CRKCGRSTTG-------YLDGCPHCGSsEVE 610
                                    7778844442.......2445******8886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (639 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 4049.01
//
Query:       gi|119719253|ref|YP_919748.1|  [L=508]
Description: CoA-binding domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.9e-59  198.8   2.1    7.9e-57  190.9   0.3    2.7  3  Succ_CoA_lig   Succinyl-CoA ligase like flavodoxin domain
    3.1e-25   88.9   0.1    1.1e-24   87.2   0.2    1.9  2  CoA_binding_2  CoA binding domain
    3.3e-11   43.7   0.2    7.4e-11   42.6   0.2    1.7  1  CoA_binding    CoA binding domain


Domain annotation for each model (and alignments):
>> Succ_CoA_lig  Succinyl-CoA ligase like flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.9   0.3   1.3e-60   7.9e-57       2     138 .]     172     308 ..     171     308 .. 0.99
   2 ?   -3.3   0.0       1.2     7e+03       3      26 ..     318     341 ..     317     343 .. 0.78
   3 !    6.6   0.0    0.0011       6.5      56      94 ..     399     442 ..     368     450 .. 0.71

  Alignments for each domain:
  == domain 1  score: 190.9 bits;  conditional E-value: 1.3e-60
                   Succ_CoA_lig   2 GkialisqSGalalalldwaasrglgfskvvslGneadvdvadlleylaedpetkvillylEsirdgrkflsaarraark 81 
                                    G +alisqSGa+++a ld++  +g+g+s++vs+Gn+advd+ +l+eyl+ d++t+villylE+i++gr+f+++a +++ k
  gi|119719253|ref|YP_919748.1| 172 GFVALISQSGAVGTAALDYMYGEGIGLSHFVSIGNKADVDEVELVEYLGGDDRTRVILLYLENIKRGREFIEVAGKVTLK 251
                                    789***************************************************************************** PP

                   Succ_CoA_lig  82 kpvvvlksGrseagaraaashtgalagsdavvdaafrqaGvlrvdsleelfdaaell 138
                                    kpvvvlk+Gr++ag+raaasht+alag d+v+daafr++Gv+r++++eelfd+a++l
  gi|119719253|ref|YP_919748.1| 252 KPVVVLKAGRTSAGRRAAASHTAALAGVDEVYDAAFRRSGVIRANDIEELFDYAKAL 308
                                    ******************************************************986 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.2
                   Succ_CoA_lig   3 kialisqSGalalalldwaasrgl 26 
                                    +i++i+  G+ +++  d a+  gl
  gi|119719253|ref|YP_919748.1| 318 RIGIITDGGGAGVMATDIAEMLGL 341
                                    689999999999999888876655 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.0011
                   Succ_CoA_lig  56 kvilly...lEsirdgrkflsaarraark..kpvvvlksGrsea 94 
                                     v++l    + +i d+ k+++ + r+a+   kpvv++  G sea
  gi|119719253|ref|YP_919748.1| 399 AVVVLAlhqVPGIPDPVKLAREISRLAAGyaKPVVAVDTGWSEA 442
                                    333333112567899*****99999998778*********9987 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.2   0.2   1.8e-28   1.1e-24       3     114 ..      15     140 ..      13     142 .. 0.95
   2 ?   -3.5   0.0       2.4   1.4e+04      79     102 ..     172     195 ..     149     197 .. 0.68

  Alignments for each domain:
  == domain 1  score: 87.2 bits;  conditional E-value: 1.8e-28
                                    EEEET--S-TTSHHHHHHHHHHH......HT--EEEESSS-SEETTEES----T....T--EEEE-S-HHHHGGGHHHHH CS
                  CoA_binding_2   3 iaVvGasdnpgkfgykvlrylle......hglpvvpVnpkeeeilgekvyaslaedpepvdlvdvftppeatpeivkeal 76 
                                    ++VvGas +++k+g+ ++r lle       + pv+ Vnpk++ ilgekv++s+++ p++vdl+++++p+e++   +++++
  gi|119719253|ref|YP_919748.1|  15 VVVVGASREEEKPGHVIFRVLLEnrkkglLKAPVYGVNPKADYILGEKVFPSVKDIPGEVDLAVIVIPAEHVKRAIEDLG 94 
                                    89************************888456**********************868*********************** PP

                                    HH--SEEEE-TT........---HHHHHHHHHTT-EEE.ES-HHHH CS
                  CoA_binding_2  77 algakavwlqpg........sedeeaaelaeeagirvvgdrCilve 114
                                     +g+ka+++ ++          ++e+ae a+++gir++g++Ci+v 
  gi|119719253|ref|YP_919748.1|  95 VKGIKAAIIISAgfseigrsDLEREVAETAKKHGIRIIGPNCIGVY 140
                                    **********999*******9***********************96 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.4
                                    --SEEEE-TT---HHHHHHHHHTT CS
                  CoA_binding_2  79 gakavwlqpgsedeeaaelaeeag 102
                                    g  a++ q+g++  +a++++  +g
  gi|119719253|ref|YP_919748.1| 172 GFVALISQSGAVGTAALDYMYGEG 195
                                    666778888888888887766655 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.6   0.2   1.2e-14   7.4e-11       5      96 .]      14     107 ..      10     107 .. 0.85

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 1.2e-14
                                    EEEEETTTSHHHHHH.HHHHHHHHEC....EE.EEEEC-TTTTTCEETTEEEESCHHHHHHHCTTTEEEEES-HHHHHHH CS
                    CoA_binding   5 kviviGagglgiagl.yhfkeklkyg....ik.avfgvnprkvgtevlglpvyksvdeleektevdvavitvPaesaqea 78 
                                     v+v+Ga++++ + + + f+  l+ +    +k  v+gvnp+  ++ +lg +v++sv++++ +  vd avi++Pae+++ a
  gi|119719253|ref|YP_919748.1|  14 GVVVVGASREEEKPGhVIFRVLLENRkkglLKaPVYGVNPK--ADYILGEKVFPSVKDIPGE--VDLAVIVIPAEHVKRA 89 
                                    69999999999988877776544444111144569******..*******************..**************** PP

                                    HHHHHHTT-SEEEEESST CS
                    CoA_binding  79 vdelveagikgiviiteg 96 
                                    +++l  +gik ++ii++g
  gi|119719253|ref|YP_919748.1|  90 IEDLGVKGIKAAIIISAG 107
                                    ***************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (508 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 3260.35
//
Query:       gi|119719254|ref|YP_919749.1|  [L=943]
Description: V-type ATPase, 116 kDa subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.6e-21   76.0   5.6    1.1e-13   50.1   0.0    3.3  4  V_ATPase_I  V-type ATPase 116kDa subunit family


Domain annotation for each model (and alignments):
>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0     0.062   1.1e+03     103     297 ..     216     262 ..     190     283 .. 0.50
   2 !   50.1   0.0   6.3e-18   1.1e-13     259     454 ..     524     715 ..     497     722 .. 0.76
   3 ?   -4.2   0.3      0.16   2.9e+03     518     544 ..     743     769 ..     740     779 .. 0.83
   4 !   26.7   0.7   7.5e-11   1.3e-06     699     812 ..     835     932 ..     828     933 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.062
                     V_ATPase_I 103 velkavlekakefleeeeeeeeeeeseeeeeekeeeeeeeseeeeeeelleeeeelsfvaGvikrekveaferilwralr 182
                                    +e ++vl+                                                                        
  gi|119719254|ref|YP_919749.1| 216 IEVSSVLRD----------------------------------------------------------------------- 224
                                    222222222....................................................................... PP

                     V_ATPase_I 183 gnlflrqaeieepledpetgekveksvfiiffqgeqlkekikkicesfgaklyelpeseeereeklkeveeriedlekvl 262
                                                                                                                  ++
  gi|119719254|ref|YP_919749.1| 225 ------------------------------------------------------------------------------AF 226
                                    ..............................................................................23 PP

                     V_ATPase_I 263 eqteealkevleeiakeleewklkvkk.ekaiyhtL 297
                                    e  + ++ e+++++ + +e+ + +v k ek  y+tL
  gi|119719254|ref|YP_919749.1| 227 EFEHATRLEIVSNALRAIENSEKQVDKlEKIFYDTL 262
                                    333444555555556666666666666233345555 PP

  == domain 2  score: 50.1 bits;  conditional E-value: 6.3e-18
                     V_ATPase_I 259 ekvleqteealkevleeiakeleewklkvkkekaiyh...tLnlfnldvtkkvliaegWvpkeeleeiqkalkeateess 335
                                    +++l  + ++l++ l +++++l+e+  +   + a+y     L  +++ +++++++ eg+vp++ +  ++++l+ +  +  
  gi|119719254|ref|YP_919749.1| 524 SEALADSIRKLETSLVSVSRRLAEILSYKAVTEAMYRahpLLSEVRIFRSRRIVVVEGYVPVKYVGLLEDSLRGKVPR-- 601
                                    46667777778888888877777666555555555551116888889999***********************97733.. PP

                     V_ATPase_I 336 ssvpsilneietketpPTyfrtnkfteafQeivdaYGiarYrEvNpalftiitFPFlFavMFGDiGHGlllllfalllvl 415
                                           +e+  +   PTy++   + +   ++    G++ Y E+ p+l+   +F  ++++MFGDiG Gl+l +f+++l+ 
  gi|119719254|ref|YP_919749.1| 602 -LLYFKYSEVPRSAGAPTYIERRGLKKYLYSLTSMRGTPAYWEIDPTLIFTAMFVVMYGMMFGDIGQGLVLSAFGAWLLK 680
                                    .455556666778999***************************************************************9 PP

                     V_ATPase_I 416 kekklkkkkkdeilemlfsgRYiillmGlfsiYtGliYN 454
                                    ++ +l   + +e    + +   + l+ G+ s+  G +Y 
  gi|119719254|ref|YP_919749.1| 681 TKYRLLGIT-SE---GAATLGALSLMAGISSMVFGAVYG 715
                                    998887753.33...333333455677777777777775 PP

  == domain 3  score: -4.2 bits;  conditional E-value: 0.16
                     V_ATPase_I 518 ilGviqMlfgvllslvNalyfkkkldi 544
                                     +Gv+q+++++ l++vN   + +++  
  gi|119719254|ref|YP_919749.1| 743 WFGVAQLVVAMALNMVNLWRMGDNIGA 769
                                    69***************9988877665 PP

  == domain 4  score: 26.7 bits;  conditional E-value: 7.5e-11
                     V_ATPase_I 699 gevfihqvIhtIEfvLgciSnTASYLRLWALSLAHaqLseVlwemvlkkallksksvlgvillvilfavfavltvavLll 778
                                    +e ++h v + IE ++    n  SY+RL A  +AH+         +l++ l+           v  +a +av+ + vL  
  gi|119719254|ref|YP_919749.1| 835 KEKIMHAVSEVIEMIIALPANSLSYIRLAAFAMAHEAFG------ILAENLT---P------SVGEIASYAVANLLVL-G 898
                                    57789******************************9865......2333121...1......2234578888888876.7 PP

                     V_ATPase_I 779 meglsafLHaLRLhWVEfqsKFykgdGykFepfs 812
                                    +egl   + a+RL   Ef +KF+kg G++F+p s
  gi|119719254|ref|YP_919749.1| 899 IEGLAVGIQAMRLTYYEFSTKFFKGVGVEFKPIS 932
                                    8*******************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (943 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       887  (0.0494729); expected 358.6 (0.02)
Passed bias filter:                      571  (0.0318478); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.79u 0.31s 00:00:01.10 Elapsed: 00:00:00.48
# Mc/sec: 5921.19
//
Query:       gi|119719255|ref|YP_919750.1|  [L=118]
Description: H+-transporting two-sector ATPase, C subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-09   37.8  12.9    1.8e-09   37.8  12.9    2.1  2  ATP-synt_C     ATP synthase subunit C
  ------ inclusion threshold ------
      0.083   12.4   3.5      0.098   12.2   3.5    1.1  1  Lipoprotein_2  Borrelia lipoprotein


Domain annotation for each model (and alignments):
>> ATP-synt_C  ATP synthase subunit C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.2     0.044   3.9e+02      16      31 ..      20      35 ..       6      45 .. 0.72
   2 !   37.8  12.9     2e-13   1.8e-09       1      60 []      55     114 ..      55     114 .. 0.97

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.044
                                   HHHHHHHHHHHHHHHH CS
                     ATP-synt_C 16 igiGkagsagiravar 31
                                   +++ + +sa+ ra+a 
  gi|119719255|ref|YP_919750.1| 20 LATTVMASAISRATAY 35
                                   6777777777777775 PP

  == domain 2  score: 37.8 bits;  conditional E-value: 2e-13
                                    HHHHHHH.GGGHHHHHHHHHHHHHHHHHHHHSGHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     ATP-synt_C   1 lgaglavGlsalgsGigiGkagsagiravarnpklftksliilafaeaialygLivalil 60 
                                    l+ ++av+ s ++sGi+   +++ag  ava++p+l+t +li+ ++ae ia+ygL+ a+++
  gi|119719255|ref|YP_919750.1|  55 LAGAIAVVGSTIASGIALRSVATAGFAAVAEKPELTTWMLIMGGLAEGIAVYGLLLAILI 114
                                    67899*****************************************************98 PP

>> Lipoprotein_2  Borrelia lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   3.5   1.1e-05     0.098     192     253 ..      27      84 ..      16      91 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.1e-05
                  Lipoprotein_2 192 aaIvkskedaaaikaakdaaklalggaskaelakaaakkdaaiAgGIALRalaKdGKlaaka 253
                                    +aI+ ++  a +++ ++ a+kl l  ++ a la a a   ++iA GIALR+ a +G +aa a
  gi|119719255|ref|YP_919750.1|  27 SAISRAT--AYNVQGQEAAKKLEL-PDAIALLAGAIAVVGSTIASGIALRSVATAG-FAAVA 84 
                                    4563333..344999999999999.5578999999999***************999.66555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       938  (0.0523175); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 783.35
//
Query:       gi|119719256|ref|YP_919751.1|  [L=296]
Description: hypothetical protein Tpen_0339 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-06   27.2   1.5     0.0092   15.5   2.4    2.5  2  vATP-synt_AC39  ATP synthase (C/AC39) subunit


Domain annotation for each model (and alignments):
>> vATP-synt_AC39  ATP synthase (C/AC39) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   2.4   5.1e-07    0.0092       4     104 ..       8      97 ..       5     189 .. 0.71
   2 !    8.5   0.0   7.2e-05       1.3     273     333 ..     224     286 ..     194     289 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 5.1e-07
                                    HHHHHGGGS--HHHHHHHTTS.-HHHHHHHHHTSGGGGG--.....SSSHHHHHHHHHHH...HHHHTTTGGGGS-H..H CS
                 vATP-synt_AC39   4 rvramrsglLteedyenLlqcesledvkryLketdYgnfladelseplsrsdiekalrek...larefnklreqapgp.s 79 
                                    r ++++s+lL++edye+++  e + d+ +y    +Y+   ++e+      +++e++l++    +++ +   ++q++ + +
  gi|119719256|ref|YP_919751.1|   8 RAHGLKSRLLSREDYEQIV--EETRDISSY---HEYSI--INEK------DTLEEKLDKIyrvYVSRITI-LAQSSSElA 73 
                                    789***************4..558888883...34555..3443......45666665541114444444.445555525 PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHH CS
                 vATP-synt_AC39  80 refldyllyrydidNvklllrgkls 104
                                      f+ +ll r +++Nvk+ lr++l 
  gi|119719256|ref|YP_919751.1|  74 -PFFYALLDRLEFENVKIQLRSILG 97 
                                    .********************9875 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 7.2e-05
                                    S..HHHHHHHHHHHHHHHHHT.TTSSSTSTHHHHHHHHHHHHHHHHHHHHHHHHHHT--SHHH CS
                 vATP-synt_AC39 273 gs.lksledaldealvkllkk.afrqqfsvgvfyaYlklkeqEirnlrwIaegiaqglpkekI 333
                                    gs ++ l +al+e   ++ k   ++ + s+  +ya+ +    E  nl  I+ g++ glpke I
  gi|119719256|ref|YP_919751.1| 224 GStTDLLRQALEEVTRRVVKPlEKKFPVSLPYAYAFNHYARLEASNLEKILLGKSIGLPKEVI 286
                                    44477889999999999999999999999999*****************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1928.18
//
Query:       gi|119719257|ref|YP_919752.1|  [L=200]
Description: V-type ATPase, D subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.5e-31  107.9   5.1    6.6e-31  107.7   5.1    1.0  1  ATP-synt_D       ATP synthase subunit D
  ------ inclusion threshold ------
      0.026   14.6   0.5        2.2    8.3   0.1    2.0  2  DUF87            Helicase HerA, central domain
      0.078   12.3   0.0        0.1   12.0   0.0    1.2  1  Guanylate_cyc_2  Guanylylate cyclase


Domain annotation for each model (and alignments):
>> ATP-synt_D  ATP synthase subunit D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.7   5.1   1.1e-34   6.6e-31       2     193 ..      16     196 ..      15     198 .. 0.92

  Alignments for each domain:
  == domain 1  score: 107.7 bits;  conditional E-value: 1.1e-34
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSTSTTSTSHHHHHHHSSS.SS-..TSS CS
                     ATP-synt_D   2 LirlkkrlklaqrghslLkkKrdaLilefreilkelkelreeleeelkeayfslaeafaaggeediesavlesvklakvv 81 
                                    L+ l+++l l++rg+++L+++rd+L++e+ +i++elk+ r e e+++ ea+ + a+++++ ge++++s++       k  
  gi|119719257|ref|YP_919752.1|  16 LQYLRRKLDLVKRGKNVLQMRRDQLAKELLAIMDELKK-RPEAEKQFIEAARTAALMRMSRGEYEFRSMSSLV----KPP 90 
                                    899*********************************99.89999***********99**********999844....458 PP

                                    -SEEEEEEBTTSEEEEEEE-..S.SSTSSSSSSSSTCHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     ATP-synt_D  82 kvelktenvaGVkvpvfeleeeksdstelygllrtgaqldeavealrellellvelasletslelLdeeikktnrRvNaL 161
                                    k++    +  GV vp+ +++ee +       l    + ++++ve+l +++++++++a++e ++e++++++  +nr vN L
  gi|119719257|ref|YP_919752.1|  91 KITHVLVSYQGVPVPQARVQEEPDW----SKL--LDPDYRRVVETLWNAVKTMIDVANKEVAVEKISDQLLYINRVVNSL 164
                                    9*****************9775333....333..467999**************************************** PP

                                    HTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     ATP-synt_D 162 ekvvIPrleetikyIkseLdEqereeffrlkk 193
                                    ek vIP+le+++++++++  ++e e+f+r+k 
  gi|119719257|ref|YP_919752.1| 165 EKNVIPQLESALRRVEERVVDEELEDFVRVKL 196
                                    ******************************96 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0    0.0042        25     117     182 ..      15      80 ..       3     103 .. 0.70
   2 ?    8.3   0.1   0.00037       2.2     118     182 ..     124     182 ..     112     196 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0042
                          DUF87 117 qrsvleealdqakakeekeklssdepveklleelkkekeelrklknqaiarlldkledllrkggsf 182
                                      ++l+++ld +k+++++ ++  d++ ++ll  + + k+  + +k+ ++a+  ++l ++ r +++f
  gi|119719257|ref|YP_919752.1|  15 TLQYLRRKLDLVKRGKNVLQMRRDQLAKELLAIMDELKKRPEAEKQFIEAARTAALMRMSRGEYEF 80 
                                    56899**************************99993333333333334444444455555444444 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00037
                          DUF87 118 rsvleealdqakakeekeklssdepveklleelkkekeelrklknqaiarlldkledllrkggsf 182
                                    r+v+e +++ +k  + +  ++ +  vek+ ++l     ++++  n+++++++ +le+ lr+ +++
  gi|119719257|ref|YP_919752.1| 124 RRVVETLWNAVK--TMIDVANKEVAVEKISDQLL----YINRVVNSLEKNVIPQLESALRRVEER 182
                                    899********9..********************....666666666666666665555555544 PP

>> Guanylate_cyc_2  Guanylylate cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.7e-05       0.1      80     128 ..     113     161 ..      85     187 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.7e-05
                Guanylate_cyc_2  80 sfykktldkdekRvnklfkkakeagievekrsvsveelvehlasgkvai 128
                                      ++k ld d +Rv + + +a ++ i+v +++v ve++++ l   + ++
  gi|119719257|ref|YP_919752.1| 113 PDWSKLLDPDYRRVVETLWNAVKTMIDVANKEVAVEKISDQLLYINRVV 161
                                    556788999******************************9998776555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1109  (0.0618551); expected 358.6 (0.02)
Passed bias filter:                      680  (0.0379274); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1438.54
//
Query:       gi|119719258|ref|YP_919753.1|  [L=472]
Description: V-type ATP synthase subunit B [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-66  223.8   0.0    3.3e-66  223.0   0.0    1.4  1  ATP-synt_ab    ATP synthase alpha/beta family, nucleotide-bin
    2.2e-05   24.9   0.8    5.5e-05   23.6   0.8    1.8  1  ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel do


Domain annotation for each model (and alignments):
>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  223.0   0.0   3.7e-70   3.3e-66       1     213 []     144     362 ..     144     362 .. 0.98

  Alignments for each domain:
  == domain 1  score: 223.0 bits;  conditional E-value: 3.7e-70
                                    SSHHHHHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTS....S.EEEEEEESEEHHHHHHHHHHCHHSSGGGGEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    ATP-synt_ab   1 GirvlDalfpivqGqrtlipgafgvGktvisqslskqsnsd....d.aiiyvgiGergnevaevleefpegtimkrtvlv 75 
                                    G++++D lf++v+Gq++ i++ +g++++ +++++++q++ +    + a++++giG r+ e++ +le+f+e+++++r v v
  gi|119719258|ref|YP_919753.1| 144 GVSAIDGLFSMVRGQKLPIFSVSGLPHNLLAAQVARQATVRgegeQfAVVFAGIGLRKTEAEFFLEQFRETGAIERLVAV 223
                                    899**********************************9888999878********************************* PP

                                    EEETTS-HHHHHHHHHHHHHHHHHHHH.TTSEEEEEEETHHHHHHHHHHHHHHTTTSBEGGGSBTTHHHHHHHHHTTSEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    ATP-synt_ab  76 antsnepvaareasiytgitlAEyfrd.qgknvlliadslsrwaeAlreislrlgempadqgypaylgaklaslyERagk 154
                                    +n +++p+++r++++++++t+AEy++   +++vl+i+ ++++++eAlre+s + ge+p++ gyp+y++++la++yERag 
  gi|119719258|ref|YP_919753.1| 224 LNMADDPAVERLMTPRIALTVAEYLAFdLDMHVLVIMSDMTNYCEALREVSSARGEIPGRLGYPGYMYSDLATIYERAGV 303
                                    *************************9879*************************************************** PP

                                    ETSSEEEEEEEEEEE-GGCSTTSHHHHHHHHHSSEEEEB-HHHHHTTBSSSBCTTTEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    ATP-synt_ab 155 apdrtGsvtivaavspaggDfsdpvttatlgitdgfivLdkklaqrkhfPainvlvSvS 213
                                    ++ ++Gs+t +++++++ggD+ +p+++ t +it+g+i+L++++ +++++P+in+l S+S
  gi|119719258|ref|YP_919753.1| 304 IKGKKGSITLFPILTMPGGDLRHPIPDLTGYITEGQIFLSQEMYAQGIYPPINILPSLS 362
                                    *********************************************************98 PP

>> ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.8   6.1e-09   5.5e-05       2      69 .]      23      87 ..      22      87 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 6.1e-09
                                   EEEETTEEEEESST.SCETCTTEEEEECCETCSTEEEEEEEEEETTEEEEEESS-STTBBTTSEEEEES CS
                  ATP-synt_ab_N  2 vqviGpvvdvefgi.grlpgiynalevelvefgtlllgvalnlgedkVrvivmgstdGlsrGteVkrTG 69
                                    ++ G +++v +gi +   ++++++++ +++ ++ + g +l+ + ++++v+v+g+ +Gl+  t  k+TG
  gi|119719258|ref|YP_919753.1| 23 KEIRGSLLIV-DGIeE--AAYDEVVKIYGKD-SRERFGRVLETSIGQAVVQVLGDREGLETDTLLKFTG 87
                                   6899******.66626..6677777777669.**********************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (472 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 3210.98
//
Query:       gi|119719259|ref|YP_919754.1|  [L=601]
Description: V-type ATP synthase subunit A [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-84  283.3   0.0    1.6e-84  282.8   0.0    1.2  1  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
    1.3e-47  160.6   0.2    6.8e-47  158.3   0.3    2.1  2  ATP-synt_ab_Xtn  ATPsynthase alpha/beta subunit N-term extens
    4.2e-13   49.6   5.2    9.6e-12   45.3   1.6    2.7  2  ATP-synt_ab_N    ATP synthase alpha/beta family, beta-barrel 
    0.00063   19.7   1.3     0.0012   18.8   0.2    2.0  2  RnfC_N           RnfC Barrel sandwich hybrid domain
     0.0064   16.7   0.3        1.4    9.2   0.0    2.7  2  Peptidase_M23    Peptidase family M23
  ------ inclusion threshold ------
        0.2   11.5   3.8       0.76    9.7   3.5    2.3  1  Biotin_lipoyl    Biotin-requiring enzyme


Domain annotation for each model (and alignments):
>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  282.8   0.0   5.3e-88   1.6e-84       1     213 []     215     438 ..     215     438 .. 0.98

  Alignments for each domain:
  == domain 1  score: 282.8 bits;  conditional E-value: 5.3e-88
                                    SSHHHHHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSSEEEEEEESEEHHHHHHHHHHCHH......SS.GGGGEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xx.xxxxxx RF
                    ATP-synt_ab   1 GirvlDalfpivqGqrtlipgafgvGktvisqslskqsnsddaiiyvgiGergnevaevleefpe......gt.imkrtv 73 
                                    G+r++D++fpi++G+  +ipg+fg+Gktv ++++s +s+s+ +++y+g+Gergne+ae+l+efp       g+ i++r++
  gi|119719259|ref|YP_919754.1| 215 GQRIIDTFFPIAKGGAGAIPGGFGTGKTVTLHKVSMYSDSQ-IVVYIGCGERGNEIAEMLKEFPVlvdpksGRpIIERSI 293
                                    9************************************9999.***********************999875337****** PP

                                    EEEEETTS-HHHHHHHHHHHHHHHHHHHHTTSEEEEEEETHHHHHHHHHHHHHHTTTSBEGGGSBTTHHHHHHHHHTTSE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    ATP-synt_ab  74 lvantsnepvaareasiytgitlAEyfrdqgknvlliadslsrwaeAlreislrlgempadqgypaylgaklaslyERag 153
                                    ++antsn+pv areasiy+g+t+AEy+rdqg++v liads+srwaeAlrei++rlge p ++gypayl  k+a++yER g
  gi|119719259|ref|YP_919754.1| 294 IIANTSNMPVSAREASIYMGVTIAEYYRDQGYDVTLIADSTSRWAEALREIAGRLGELPVERGYPAYLPDKIAEFYERGG 373
                                    ******************************************************************************** PP

                                    EE.....TSSEEEEEEEEEEE-GGCSTTSHHHHHHHHHSSEEEEB-HHHHHTTBSSSBCTTTEEE CS
                                    xx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    ATP-synt_ab 154 ka.....pdrtGsvtivaavspaggDfsdpvttatlgitdgfivLdkklaqrkhfPainvlvSvS 213
                                    ++     p+r+Gsvt++ avsp+ggD+++pvt +tl+++ + + Ld++la r+hfPain+l+S+S
  gi|119719259|ref|YP_919754.1| 374 RVkalgsPERSGSVTVLGAVSPPGGDYNEPVTIHTLRFVGTMWALDTDLAYRRHFPAINWLKSFS 438
                                    **99***99******************************************************98 PP

>> ATP-synt_ab_Xtn  ATPsynthase alpha/beta subunit N-term extension
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.3   0.3   2.3e-50   6.8e-47       1     121 []      87     206 ..      87     206 .. 0.98
   2 ?   -1.3   0.0      0.61   1.8e+03      73     112 ..     240     279 ..     236     291 .. 0.77

  Alignments for each domain:
  == domain 1  score: 158.3 bits;  conditional E-value: 2.3e-50
                                    EETTS-BHHHHHHHHTSBE-TT----SS-SSS-EEEEESS-TT-EEETT-EEEEEECTTCEEEEEE--TT-EEEEEEE-- CS
                ATP-synt_ab_Xtn   1 yDGiqrpLekiaeksgsfierGvkvpaldrekkwefkpkvkvgdkvsggdilGtvqeteliehkimvppkvegkvkeiae 80 
                                    +DG+qrpL++i+e  g f++rGvkv++l r+ kw+fkp+vkvgdkvs+gdi+G+vqet lieh++mvp +v+gkvke+++
  gi|119719259|ref|YP_919754.1|  87 FDGVQRPLKSIEELVGPFVKRGVKVNPLPRNVKWHFKPSVKVGDKVSSGDIIGVVQETPLIEHRVMVPIGVSGKVKEVVP 166
                                    9******************************************************************************* PP

                                    EEEE-TTSECEEECETT.ECEEEESSEEEETTS---ESEEE CS
                ATP-synt_ab_Xtn  81 egeytvedtiaeveteegkekeltllqkwPvrkprpvkekl 121
                                    eg+ytved ++ +e+++ + +elt+ q+wPvr+prp+ke+l
  gi|119719259|ref|YP_919754.1| 167 EGDYTVEDPVVILESDG-RVVELTMKQEWPVRQPRPYKERL 206
                                    **************877.7********************96 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.61
                                    EEEEEE--EEEE-TTSECEEECETT.ECEEEESSEEEETT CS
                ATP-synt_ab_Xtn  73 gkvkeiaeegeytvedtiaeveteegkekeltllqkwPvr 112
                                    gk +++++ + y+ +++++ +  +e+ ++  ++l+++Pv 
  gi|119719259|ref|YP_919754.1| 240 GKTVTLHKVSMYSDSQIVVYIGCGERGNEIAEMLKEFPVL 279
                                    55566666778888999999999998889999******94 PP

>> ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   1.6   3.2e-15   9.6e-12       1      69 []       9      71 ..       9      71 .. 0.97
   2 ?    5.2   0.1      0.01        31      14      39 ..     547     570 ..     543     600 .. 0.91

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 3.2e-15
                                   EEEEETTEEEEESSTSCETCTTEEEEECCETCSTEEEEEEEEEETTEEEEEESS-STTBBTTSEEEEES CS
                  ATP-synt_ab_N  1 ivqviGpvvdvefgigrlpgiynalevelvefgtlllgvalnlgedkVrvivmgstdGlsrGteVkrTG 69
                                   i +v+Gpvv++++ ++  +++ +++ v+  +  ++llg+++++++d+  v+v+++t+Gl++ ++V+ TG
  gi|119719259|ref|YP_919754.1|  9 IAKVSGPVVIAKGISD--IKMGEVVYVG--N--EGLLGEVVRVSQDSFAVQVYEDTSGLRPKEPVTATG 71
                                   678********9999*..**********..9..9**********************************9 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.01
                                    STSCETCTTEEEEECCETCSTEEEEE CS
                  ATP-synt_ab_N  14 gigrlpgiynalevelvefgtlllgv 39 
                                    +i r+p+iy++++v+  e++++l++v
  gi|119719259|ref|YP_919754.1| 547 EILRMPEIYEMMRVK--EDERGLQAV 570
                                    6789***********..879998876 PP

>> RnfC_N  RnfC Barrel sandwich hybrid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1         1   3.1e+03      45      75 ..      30      60 ..      26      61 .. 0.86
   2 !   18.8   0.2   3.9e-07    0.0012      32     100 ..     112     183 ..     100     184 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1
                         RnfC_N 45 lvkvgdkVlkGqkiaeaegfvsapvhasvsG 75
                                   +v vg++ l G+++  ++  ++++v+  +sG
  gi|119719259|ref|YP_919754.1| 30 VVYVGNEGLLGEVVRVSQDSFAVQVYEDTSG 60
                                   7889999999999999988669999999998 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 3.9e-07
                         RnfC_N  32 lplsqhiGapakplvkvgdkVlkGqkiaeaeg..fvsapvhas..vsGtVkaiekrlvahgsgveavvienDg 100
                                     pl + +  + kp vkvgdkV  G++i+  ++  ++   v  +  vsG+Vk++ +    + +  + v++e+Dg
  gi|119719259|ref|YP_919754.1| 112 NPLPRNVKWHFKPSVKVGDKVSSGDIIGVVQEtpLIEHRVMVPigVSGKVKEVVPEGDYTVE-DPVVILESDG 183
                                    58888888999*****************987767899888887557******9886554443.4566666665 PP

>> Peptidase_M23  Peptidase family M23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1     0.013        39      20      54 ..      26      60 ..      17      75 .. 0.82
   2 !    9.2   0.0   0.00046       1.4      56      75 ..     125     144 ..     118     156 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.013
                                   SSEEEEEEEEETTTEEEEEEEECTCEEEEEEEESE CS
                  Peptidase_M23 20 adGtVvfagkkegyGnvviidhgdgystlyahlsk 54
                                   + G+Vv++g+++ +G+vv++ +++  +++y   s 
  gi|119719259|ref|YP_919754.1| 26 KMGEVVYVGNEGLLGEVVRVSQDSFAVQVYEDTSG 60
                                   579*******9667******999888888876665 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00046
                                    SS-TTEEE-TTCEEEEEBST CS
                  Peptidase_M23  56 svkegqkVkaGqvIGtvgst 75 
                                    svk+g+kV+ G++IG v +t
  gi|119719259|ref|YP_919754.1| 125 SVKVGDKVSSGDIIGVVQET 144
                                    7**************99877 PP

>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   3.5   0.00025      0.76      18      66 ..     123     174 ..     116     180 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00025
                                    SESSSTTCEE-TTSEEEEEECTTE...EEEEEBSSSEEEEEESSTTTEEE-T CS
                  Biotin_lipoyl  18 evlvkvGdkVkagqvlaeveamKm...emeieapkaGvvkeilvkeGdtvev 66 
                                    +  vkvGdkV+ g+++ +v+   +    + ++  ++G+vke++ + + tve 
  gi|119719259|ref|YP_919754.1| 123 KPSVKVGDKVSSGDIIGVVQETPLiehRVMVPIGVSGKVKEVVPEGDYTVED 174
                                    568*************9998665421145677889******98885555664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (601 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.58u 0.24s 00:00:00.82 Elapsed: 00:00:00.40
# Mc/sec: 4553.84
//
Query:       gi|119719260|ref|YP_919755.1|  [L=358]
Description: hypothetical protein Tpen_0343 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-07   32.0   0.0    2.1e-07   31.4   0.0    1.3  1  Transglut_core  Transglutaminase-like superfamily
    0.00035   20.1   0.0    0.00096   18.7   0.0    1.7  2  DUF553          Transglutaminase-like domain


Domain annotation for each model (and alignments):
>> Transglut_core  Transglutaminase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.0   2.3e-11   2.1e-07       2      84 ..     154     234 ..     153     265 .. 0.85

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 2.3e-11
                 Transglut_core   2 alaeeltagakdplekakaiyewvrknveysaprrtpgsrdaeavletgkGncedfaslfvallRalGipaRvvtgylsg 81 
                                    +++++l a+a+ p + a ++++w  ++ +y+  +++ g   ++a+l+++kG c df++  +all+  G+ a +v+ ++++
  gi|119719260|ref|YP_919755.1| 154 SISNRLAANASGPVDFAYKVARWALSEAKYE--ESYGGISCPSAFLKEKKGACGDFSAFIAALLKIQGLNAYLVYSLVED 231
                                    78899**************************..77777777*********************************999987 PP

                 Transglut_core  82 eee 84 
                                    + +
  gi|119719260|ref|YP_919755.1| 232 QGA 234
                                    654 PP

>> DUF553  Transglutaminase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0     0.078     7e+02       2      34 ..     151     185 ..     150     192 .. 0.84
   2 !   18.7   0.0   1.1e-07   0.00096      59     106 ..     185     231 ..     161     268 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.078
                         DUF553   2 klkklaekl..kkensketiinvlewvdenikYdy 34 
                                    +l++++++l  + +   + + +v++w  ++ kY+ 
  gi|119719260|ref|YP_919755.1| 151 DLRSISNRLaaNASGPVDFAYKVARWALSEAKYEE 185
                                    6788999997777778999********99999986 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 1.1e-07
                         DUF553  59 kilklietpkeilktkkgiCrDYaiLTaalLlnlniskvylvsvtfen 106
                                    + +  i  p+ +lk+kkg C D++ + aalL  +++ ++ylv+  +e+
  gi|119719260|ref|YP_919755.1| 185 ESYGGISCPSAFLKEKKGACGDFSAFIAALLKIQGL-NAYLVYSLVED 231
                                    44556779*********************6665555.55999887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2705.50
//
Query:       gi|119719261|ref|YP_919756.1|  [L=184]
Description: hypothetical protein Tpen_0344 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0006   19.1   2.3     0.0012   18.1   2.3    1.6  1  zf-ribbon_3    zinc-ribbon domain
     0.0039   17.1   0.2     0.0058   16.5   0.2    1.2  1  Prok-RING_1    Prokaryotic RING finger family 1
     0.0085   15.6   0.7      0.015   14.8   0.7    1.4  1  TF_Zn_Ribbon   TFIIB zinc-binding
  ------ inclusion threshold ------
      0.014   15.4   0.3      0.023   14.7   0.3    1.3  1  DZR            Double zinc ribbon
      0.029   14.1   0.5      0.053   13.3   0.5    1.4  1  YacG           DNA gyrase inhibitor YacG
       0.03   14.1   4.6       0.29   10.9   0.3    2.2  2  zinc_ribbon_2  zinc-ribbon domain
      0.031   14.2   7.4       0.68    9.9   1.8    2.3  2  zf-C2HC_2      zinc-finger of a C2HC-type
      0.031   14.1   4.0       0.08   12.8   0.3    2.2  2  Rad50_zn_hook  Rad50 zinc hook motif
       0.04   14.0   1.1       0.78    9.8   0.2    2.2  2  zf-CHCC        Zinc-finger domain
      0.042   14.0   2.7        2.4    8.4   0.4    2.4  2  zf-RING_7      C4-type zinc ribbon domain
       0.07   13.3   1.6        1.1    9.4   0.1    2.3  2  DUF2256        Uncharacterized protein conserved in bacteria 
       0.18   11.9   5.0        2.1    8.5   5.0    2.2  1  UPF0547        Uncharacterised protein family UPF0547
       0.61   10.0   3.1         18    5.3   0.6    2.2  2  Cys_rich_CPXG  Cysteine-rich CPXCG
        1.1    9.6   4.9        8.7    6.7   0.5    2.2  2  zf-Di19        Drought induced 19 protein (Di19), zinc-bindin
        1.8    8.3   5.6       0.77    9.4   0.5    2.1  2  DUF3149        Protein of unknown function (DUF3149)
        6.3    6.9   6.5         15    5.7   0.8    2.3  2  Zn_Tnp_IS1595  Transposase zinc-ribbon domain


Domain annotation for each model (and alignments):
>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   2.3   1.1e-06    0.0012       1      23 [.     156     180 ..     156     183 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.1e-06
                    zf-ribbon_3   1 stvrCPnCGa.p.lssddnvCpyCG 23 
                                    +t+rCP+CG  +   +  ++Cp CG
  gi|119719261|ref|YP_919756.1| 156 ETKRCPYCGReLpYGDLHIICPFCG 180
                                    699******998799999******9 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.2   5.1e-06    0.0058       3      27 ..     156     180 ..     154     182 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.1e-06
                    Prok-RING_1   3 tgkkCpvCgkelkeedDiVvCpeCg 27 
                                    + k+Cp Cg+el  +d  ++Cp Cg
  gi|119719261|ref|YP_919756.1| 156 ETKRCPYCGRELPYGDLHIICPFCG 180
                                    6789***********999******9 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.7   1.3e-05     0.015       2      27 ..     159     181 ..     158     183 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.3e-05
                                    EETTTTCEECHEETSTTCEEESSSSB CS
                   TF_Zn_Ribbon   2 kCPnCgstnlveDpergelvCtdCGl 27 
                                    +CP+Cg    ++++    ++C++CG 
  gi|119719261|ref|YP_919756.1| 159 RCPYCGR---ELPYGDLHIICPFCGR 181
                                    6*****8...69*************5 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.3     2e-05     0.023      10      37 ..     155     182 ..     148     184 .] 0.75

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2e-05
                            DZR  10 pdarfCseCgtklkavaa.edrCpsCgek 37 
                                    ++ + C++Cg +l+ + + ++ Cp Cg++
  gi|119719261|ref|YP_919756.1| 155 AETKRCPYCGRELP-YGDlHIICPFCGRA 182
                                    45678999999996.55569999999876 PP

>> YacG  DNA gyrase inhibitor YacG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.5   4.7e-05     0.053       2      23 ..     159     180 ..     158     182 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.7e-05
                           YacG   2 kCPtCkkevewseenpfrPFCS 23 
                                    +CP C++e  + + +   PFC 
  gi|119719261|ref|YP_919756.1| 159 RCPYCGRELPYGDLHIICPFCG 180
                                    7********************7 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.3   0.00026      0.29      14      23 .]     156     167 ..     150     167 .. 0.67
   2 ?   10.3   4.7   0.00041      0.46       1      22 [.     159     182 ..     159     183 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00026
                  zinc_ribbon_2  14 kF..CpyCGtpl 23 
                                        CpyCG +l
  gi|119719261|ref|YP_919756.1| 156 ETkrCPYCGREL 167
                                    444499999876 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00041
                  zinc_ribbon_2   1 fCpnCGaelqdnakF..CpyCGtp 22 
                                    +Cp CG+el+ ++    Cp CG  
  gi|119719261|ref|YP_919756.1| 159 RCPYCGRELPYGDLHiiCPFCGRA 182
                                    6*********9999999****975 PP

>> zf-C2HC_2  zinc-finger of a C2HC-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   1.8   0.00061      0.68       1      10 [.     156     165 ..     156     166 .. 0.90
   2 ?    7.5   0.3    0.0033       3.7       3      10 ..     174     181 ..     174     182 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00061
                      zf-C2HC_2   1 elvpCpkCgR 10 
                                    e+  Cp+CgR
  gi|119719261|ref|YP_919756.1| 156 ETKRCPYCGR 165
                                    7899****** PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0033
                      zf-C2HC_2   3 vpCpkCgR 10 
                                    + Cp+CgR
  gi|119719261|ref|YP_919756.1| 174 IICPFCGR 181
                                    57****** PP

>> Rad50_zn_hook  Rad50 zinc hook motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.3   7.1e-05      0.08      14      30 ..     153     168 ..     150     171 .. 0.83
   2 ?    2.3   0.4      0.13   1.5e+02      22      29 ..     176     183 ..     175     184 .] 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.1e-05
                                    HHTT-SEE-TTT--EE- CS
                  Rad50_zn_hook  14 elkeakgcCPlCgReld 30 
                                    e +e+k +CP CgRel+
  gi|119719261|ref|YP_919756.1| 153 ENAETK-RCPYCGRELP 168
                                    557777.********97 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.13
                                    -TTT--EE CS
                  Rad50_zn_hook  22 CPlCgRel 29 
                                    CP CgR l
  gi|119719261|ref|YP_919756.1| 176 CPFCGRAL 183
                                    ******87 PP

>> zf-CHCC  Zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.2    0.0007      0.78      26      35 ..     156     165 ..     151     166 .. 0.83
   2 ?    2.6   0.0      0.13   1.5e+02      29      35 ..     175     181 ..     171     182 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0007
                                    SEEEETTTTE CS
                        zf-CHCC  26 gpvdCgYCgl 35 
                                    ++ +C+YCg+
  gi|119719261|ref|YP_919756.1| 156 ETKRCPYCGR 165
                                    6789*****8 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.13
                                    EETTTTE CS
                        zf-CHCC  29 dCgYCgl 35 
                                     C++Cg+
  gi|119719261|ref|YP_919756.1| 175 ICPFCGR 181
                                    6*****8 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.4    0.0021       2.4      25      31 ..     159     165 ..     151     165 .. 0.87
   2 ?    5.4   0.1     0.019        21      24      31 ..     174     181 ..     170     183 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0021
                                    E-TTT-- CS
                      zf-RING_7  25 tCpeCGR 31 
                                    +Cp+CGR
  gi|119719261|ref|YP_919756.1| 159 RCPYCGR 165
                                    9*****9 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.019
                                    EE-TTT-- CS
                      zf-RING_7  24 vtCpeCGR 31 
                                    + Cp CGR
  gi|119719261|ref|YP_919756.1| 174 IICPFCGR 181
                                    68*****9 PP

>> DUF2256  Uncharacterized protein conserved in bacteria (DUF2256)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.1   0.00098       1.1       4      17 ..     154     167 ..     152     169 .. 0.84
   2 ?    2.9   0.2      0.11   1.2e+02       9      17 ..     175     183 ..     173     184 .] 0.86

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00098
                        DUF2256   4 elpsKiCavCgrpf 17 
                                    +  +K C++Cgr++
  gi|119719261|ref|YP_919756.1| 154 NAETKRCPYCGREL 167
                                    6789********86 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.11
                        DUF2256   9 iCavCgrpf 17 
                                    iC+ Cgr +
  gi|119719261|ref|YP_919756.1| 175 ICPFCGRAL 183
                                    8******75 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   5.0    0.0018       2.1       1      21 [.     158     180 ..     158     180 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0018
                        UPF0547   1 KvCPeCeakvPva..aqfCphCG 21 
                                    K+CP C +++P      +Cp+CG
  gi|119719261|ref|YP_919756.1| 158 KRCPYCGRELPYGdlHIICPFCG 180
                                    99*********9744689****9 PP

>> Cys_rich_CPXG  Cysteine-rich CPXCG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.6     0.016        18       3       9 ..     160     166 ..     159     168 .. 0.84
   2 ?    5.0   0.1     0.021        24       1       9 [.     174     182 ..     174     184 .] 0.83

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.016
                  Cys_rich_CPXG   3 CPyCgee 9  
                                    CPyCg e
  gi|119719261|ref|YP_919756.1| 160 CPYCGRE 166
                                    *****86 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.021
                  Cys_rich_CPXG   1 iqCPyCgee 9  
                                    i+CP+Cg  
  gi|119719261|ref|YP_919756.1| 174 IICPFCGRA 182
                                    78****975 PP

>> zf-Di19  Drought induced 19 protein (Di19), zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.5    0.0078       8.7       4      12 ..     159     167 ..     156     174 .. 0.80
   2 ?    5.2   0.3     0.023        26       4      11 ..     175     182 ..     172     184 .] 0.78

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0078
                        zf-Di19   4 tCPyCgkel 12 
                                     CPyCg+el
  gi|119719261|ref|YP_919756.1| 159 RCPYCGREL 167
                                    7*****976 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.023
                        zf-Di19   4 tCPyCgke 11 
                                     CP+Cg++
  gi|119719261|ref|YP_919756.1| 175 ICPFCGRA 182
                                    6****986 PP

>> DUF3149  Protein of unknown function (DUF3149)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.6      0.23   2.5e+02      19      33 ..      28      42 ..      26      43 .. 0.81
   2 ?    9.4   0.5   0.00069      0.77       6      28 ..      43      65 ..      43      66 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.23
                        DUF3149 19 ftigmgaffiryFir 33
                                   ++ g++af + +F++
  gi|119719261|ref|YP_919756.1| 28 PAAGLIAFLVAFFVG 42
                                   566999999999985 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00069
                        DUF3149  6 ssdvGLlSliVIvftigmgaffi 28
                                   ++  G+l l+V v+tig+g++f+
  gi|119719261|ref|YP_919756.1| 43 GNSWGILALGVEVATIGVGLYFT 65
                                   6888*****************96 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.8     0.013        15      19      30 ..     158     169 ..     154     173 .. 0.78
   2 ?    4.3   0.5     0.035        39      19      26 ..     174     181 ..     169     184 .] 0.78

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.013
                  Zn_Tnp_IS1595  19 fvCPhCgsrkay 30 
                                     +CP+Cg + +y
  gi|119719261|ref|YP_919756.1| 158 KRCPYCGRELPY 169
                                    57*****87655 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.035
                  Zn_Tnp_IS1595  19 fvCPhCgs 26 
                                     +CP+Cg 
  gi|119719261|ref|YP_919756.1| 174 IICPFCGR 181
                                    57****95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       731  (0.0407719); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 1162.10
//
Query:       gi|119719262|ref|YP_919757.1|  [L=106]
Description: hypothetical protein Tpen_0345 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       885  (0.0493614); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 787.12
//
Query:       gi|119719263|ref|YP_919758.1|  [L=438]
Description: peptidase M48, Ste24p [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.9e-09   37.0   0.0    5.7e-09   36.0   0.0    1.5  1  Peptidase_M48  Peptidase family M48
    0.00012   21.4   0.0     0.0002   20.6   0.0    1.4  1  Peptidase_M56  BlaR1 peptidase M56
  ------ inclusion threshold ------
       0.09   12.6   0.1       0.16   11.9   0.1    1.3  1  SprT-like      SprT-like family
        0.1   12.7   0.0       0.41   10.7   0.0    2.0  2  HicA_toxin     HicA toxin of bacterial toxin-antitoxin,


Domain annotation for each model (and alignments):
>> Peptidase_M48  Peptidase family M48
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.0   1.3e-12   5.7e-09      13     149 ..     242     363 ..     234     408 .. 0.72

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 1.3e-12
                                    HHHHHTT-..-EEEEEEE-GGGT-EEEEESSS-EEEEEEHHHH-SSB-HHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M48  13 elakeaglpkpltkvyvvnspkrNAFalgggknkrivltdgLlkqllseeelaaVlGHElGHikhrhsvvslivsllasi 92 
                                    +++++++l  +++ ++ +++++r A  lg      i+lt +Ll   lseeela Vl HE +Hi hr++++ l+  +    
  gi|119719263|ref|YP_919758.1| 242 SIFEKLKL-RKPPSIFLLDDKRRTALSLGLP--PAIALTPALL-VDLSEEELASVLVHEAAHIRHRDALRALLLITSGLA 317
                                    56777888.88899999****99**999999..79********.************************999444333333 PP

                                    HHHHHHHHHTT-SHHHHHTT--S---HHHHHHHHHHTTHHHHHHHHHHHHHHHHTTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M48  93 llllglallisraeedaagafldalavliglliillflalSRkrEyqADeagvellk 149
                                    l  l +++ +s + ++  + +      +i      l   l ++ E +AD  ++e+  
  gi|119719263|ref|YP_919758.1| 318 LGALIYLFSYSIELLALYAVAS-----YI------LTSMLLKSLEIRADLEAAEAFP 363
                                    3333333344443333322221.....11......1112335667777777777766 PP

>> Peptidase_M56  BlaR1 peptidase M56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   4.5e-08    0.0002     171     219 ..     265     312 ..     234     369 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 4.5e-08
                  Peptidase_M56 171 PavlgllkprIvlPadflkklsdeeleyillHElaHlkrkDllvnllva 219
                                      +lgl  p I l  ++l  ls+eel+ +l+HE aH++++D+l  ll++
  gi|119719263|ref|YP_919758.1| 265 ALSLGLP-PAIALTPALLVDLSEEELASVLVHEAAHIRHRDALRALLLI 312
                                    4455655.55666556788***********************9888875 PP

>> SprT-like  SprT-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   3.5e-05      0.16      49      75 ..     274     300 ..     269     303 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.5e-05
                      SprT-like  49 IeLseklldsrsedrllntLaHElcHl 75 
                                    I L + ll + se++l ++L+HE +H+
  gi|119719263|ref|YP_919758.1| 274 IALTPALLVDLSEEELASVLVHEAAHI 300
                                    899999********************7 PP

>> HicA_toxin  HicA toxin of bacterial toxin-antitoxin,
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0     9e-05      0.41       6      38 ..      28      60 ..      25      67 .. 0.87
   2 ?   -2.6   0.0       1.3     6e+03      43      57 ..     234     248 ..     233     249 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 9e-05
                                   HHHHHTT-EEEEEETTEEEEE-TTSS-EEEEE. CS
                     HicA_toxin  6 klLeklGfevvrqkGSHvrfkhpdkrgivtvpp 38
                                     +ek+Gf +++ +GS v+f+  +k+ +vt ++
  gi|119719263|ref|YP_919758.1| 28 GFFEKNGFSKEPISGSVVVFRSSTKDVVVTCKF 60
                                   579*******************99998888876 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.3
                                    S--CCCHHHHHHHCC CS
                     HicA_toxin  43 elkpgtlksIlkqaG 57 
                                    elk++  +sI ++++
  gi|119719263|ref|YP_919758.1| 234 ELKTYDFRSIFEKLK 248
                                    8999999***88765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (438 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 3370.70
//
Query:       gi|119719264|ref|YP_919759.1|  [L=642]
Description: hypothetical protein Tpen_0347 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-15   56.2  12.0    6.7e-11   42.3   1.8    4.4  4  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
    7.1e-06   25.9   8.6     0.0006   19.8   1.2    3.4  3  Big_1            Bacterial Ig-like domain (group 1)
    1.2e-05   25.4   0.8     0.0021   18.1   0.1    3.3  3  MG4              Macroglobulin domain MG4
    0.00013   22.2   5.6       0.25   11.7   0.6    3.3  4  Invasin_D3       Invasin, domain 3
    0.00021   21.2   9.2     0.0013   18.6   1.0    3.6  4  CarbopepD_reg_2  CarboxypepD_reg-like domain
    0.00024   21.4   0.8          1    9.7   0.1    2.8  2  SpaA             Prealbumin-like fold domain
     0.0026   18.0   4.1     0.0065   16.7   0.6    2.6  3  SdrD_B           SdrD B-like domain
  ------ inclusion threshold ------
      0.024   14.3   0.6      0.055   13.1   0.2    1.7  2  DUF4249          Domain of unknown function (DUF4249)
      0.049   13.7   0.0       0.13   12.3   0.0    1.7  1  bMG3             Bacterial alpha-2-macroglobulin MG3 domain
      0.053   13.4   0.3       0.15   11.9   0.3    1.7  1  DUF4493          Domain of unknown function (DUF4493)


Domain annotation for each model (and alignments):
>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.43   7.6e+02      42      70 ..     150     178 ..     108     189 .. 0.72
   2 ?   -1.3   0.0       1.5   2.6e+03      47      77 ..     201     228 ..     198     234 .. 0.75
   3 !   16.3   0.7   4.9e-06    0.0088       7      58 ..     447     495 ..     442     503 .. 0.90
   4 !   42.3   1.8   3.8e-14   6.7e-11       2      78 ..     520     593 ..     519     597 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.43
                CarboxypepD_reg  42 lrglppgtysvtvsapGyatatreevtlt 70 
                                    ++gl   + +++v+ ++ya++++ +v   
  gi|119719264|ref|YP_919759.1| 150 FTGLNLPSVRLKVTLDNYAPYSVAGVLGP 178
                                    44555556788888899998888655443 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.5
                CarboxypepD_reg  47 pgtysvtvsapGyatatreevtltagqtttl 77 
                                    p   +v vs+ G+  +t++   l+ g+++ l
  gi|119719264|ref|YP_919759.1| 201 PKHVEVDVSKVGFGVYTVK---LAQGEENKL 228
                                    5667899999999999965...777776655 PP

  == domain 3  score: 16.3 bits;  conditional E-value: 4.9e-06
                CarboxypepD_reg   7 tdasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapG 58 
                                    +d+ g pi+g++ t++   ++++as++++adG  +l+  +pg y++t  ++G
  gi|119719264|ref|YP_919759.1| 447 VDSKGYPISGVEATLK---GSVSASAVSGADGVATLNVYAPGVYTLTGVYKG 495
                                    79**************...7999*************99999*****977777 PP

  == domain 4  score: 42.3 bits;  conditional E-value: 3.8e-14
                CarboxypepD_reg   2 isGrVtdasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatreevtltagqtttld 78 
                                    ++ +V++a gapi+gatVtv+n ++g+++s+ tda+G+  +++lp  +y+++v ++   t +  ++tlt +q+ t++
  gi|119719264|ref|YP_919759.1| 520 LNVKVVNALGAPITGATVTVSN-NGGFTQSMETDASGKALFQQLPGAQYTIEVNYKRISTKS--TLTLTQDQDITIN 593
                                    5679*****************6.999***************************999998888..599*999998887 PP

>> Big_1  Bacterial Ig-like domain (group 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1       1.6   2.9e+03      11      33 ..     128     151 ..     119     158 .. 0.68
   2 !    9.1   0.1    0.0007       1.2       9      52 ..     442     481 ..     441     490 .. 0.85
   3 !   19.8   1.2   3.3e-07    0.0006       9      50 ..     520     559 ..     518     561 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.6
                          Big_1  11 atvkDangnpvagatVtfsvsg.g 33 
                                       +  + +p++g ++t+ +s  +
  gi|119719264|ref|YP_919759.1| 128 TYFRKTSWKPIKGNNITVDTSEfT 151
                                    555666678999999999998753 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0007
                          Big_1   9 ltatvkDangnpvagatVtfsvsggalsassgtTdanGkatvtl 52 
                                    l++  +D++g p++g++ t++   g++ ++s++++a+G+at ++
  gi|119719264|ref|YP_919759.1| 442 LRVKFVDSKGYPISGVEATLK---GSV-SASAVSGADGVATLNV 481
                                    678999*********999988...444.889**********987 PP

  == domain 3  score: 19.8 bits;  conditional E-value: 3.3e-07
                          Big_1   9 ltatvkDangnpvagatVtfsvsggalsassgtTdanGkatv 50 
                                    l++ v++a g p+ gatVt+s +gg   ++s  Tda+Gka +
  gi|119719264|ref|YP_919759.1| 520 LNVKVVNALGAPITGATVTVSNNGG-F-TQSMETDASGKALF 559
                                    789****************995554.3.69*********976 PP

>> MG4  Macroglobulin domain MG4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       2.1   3.8e+03      19      63 ..      73     116 ..      69     136 .. 0.69
   2 ?    3.8   0.0     0.037        66      18      65 ..     442     484 ..     441     491 .. 0.83
   3 !   18.1   0.1   1.2e-06    0.0021      16      62 ..     518     561 ..     505     586 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.1
                            MG4  19 kVlvkdpdgspaknvpVkiealkseteekeslttdedGtakfsin 63 
                                    +V v+ + g p + +pVk   ++ e+    +  ++++G + +  n
  gi|119719264|ref|YP_919759.1|  73 RVVVVFQGGAPSGLIPVKYDSIS-ESMGRITSISSRSGEVVVASN 116
                                    57788888999999999998855.333344445557776666555 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.037
                            MG4  18 ikVlvkdpdgspaknvpVkiealkseteekeslttdedGtakfsintp 65 
                                    ++V+ +d++g p+++v  +++  +       s  + +dG+a +++  p
  gi|119719264|ref|YP_919759.1| 442 LRVKFVDSKGYPISGVEATLKG-S----VSASAVSGADGVATLNVYAP 484
                                    689*************999999.3....34667889999999987665 PP

  == domain 3  score: 18.1 bits;  conditional E-value: 1.2e-06
                            MG4  16 fsikVlvkdpdgspaknvpVkiealkseteekeslttdedGtakfsi 62 
                                    +++ V+v++++g p+ + +V+++    +  + +s +td++G a f  
  gi|119719264|ref|YP_919759.1| 518 YNLNVKVVNALGAPITGATVTVSN---NGGFTQSMETDASGKALFQQ 561
                                    99**********************...589*************9974 PP

>> Invasin_D3  Invasin, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       8.6   1.5e+04      34      46 ..     136     148 ..     131     158 .. 0.75
   2 ?   -3.0   0.0       5.1   9.2e+03      54      67 ..     208     221 ..     195     227 .. 0.74
   3 !   11.5   0.1   0.00015      0.28      24      84 ..     442     497 ..     414     503 .. 0.77
   4 !   11.7   0.6   0.00014      0.25      24      61 ..     520     556 ..     518     587 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 8.6
                     Invasin_D3  34 npvsgltvtfstt 46 
                                    +p++g+++t+ t+
  gi|119719264|ref|YP_919759.1| 136 KPIKGNNITVDTS 148
                                    6888888888876 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 5.1
                     Invasin_D3  54 vtdngdGtytatLt 67 
                                    v++ g G+yt++L 
  gi|119719264|ref|YP_919759.1| 208 VSKVGFGVYTVKLA 221
                                    55668899999985 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.00015
                     Invasin_D3  24 ltvtlkDangnpvsgltvtfsttsagtlsavtdngdGtytatLtattagtatitptvnGva 84 
                                    l v+  D +g p+sg + t++ +  ++ sav + +dG+ t  +   + g++t+t  ++G+ 
  gi|119719264|ref|YP_919759.1| 442 LRVKFVDSKGYPISGVEATLKGS--VSASAV-SGADGVATLNV--YAPGVYTLTGVYKGSN 497
                                    68999**********99999955..555666.7888*988888..5679999999999944 PP

  == domain 4  score: 11.7 bits;  conditional E-value: 0.00014
                     Invasin_D3  24 ltvtlkDangnpvsgltvtfsttsagtlsavtdngdGt 61 
                                    l v++ +a g p++g+tvt+s +  g +++++++++G 
  gi|119719264|ref|YP_919759.1| 520 LNVKVVNALGAPITGATVTVSNN-GGFTQSMETDASGK 556
                                    789******************77.77446677777675 PP

>> CarbopepD_reg_2  CarboxypepD_reg-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1      0.51   9.2e+02      44      74 ..     202     232 ..     196     244 .. 0.59
   2 ?   -4.1   0.0       9.2   1.7e+04      57      75 ..     321     339 ..     318     341 .. 0.70
   3 ?    5.1   0.1     0.013        23       9      52 ..     449     493 ..     445     506 .. 0.86
   4 !   18.6   1.0   7.5e-07    0.0013       5      73 ..     524     593 ..     523     598 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.51
                CarbopepD_reg_2  44 gkytLvvsyvGyktqekkvtvskektldvni 74 
                                    + +++ vs vG+   ++k+   +e++l   +
  gi|119719264|ref|YP_919759.1| 202 KHVEVDVSKVGFGVYTVKLAQGEENKLPNAM 232
                                    5567777777777777666666655554333 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 9.2
                CarbopepD_reg_2  57 tqekkvtvskektldvnil 75 
                                       + v+v ++++ d+++l
  gi|119719264|ref|YP_919759.1| 321 AFGQAVKVVNNENRDIQVL 339
                                    5557788888888888776 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.013
                CarbopepD_reg_2   9 etkeplpgatVyvkgt.kkgtvTdenGnFelknlpagkytLvvsy 52 
                                    +++ p+ g+  ++kg+ ++ +v+ ++G  +l+   +g ytL+  y
  gi|119719264|ref|YP_919759.1| 449 SKGYPISGVEATLKGSvSASAVSGADGVATLNVYAPGVYTLTGVY 493
                                    4578***********86799************9999*****8666 PP

  == domain 4  score: 18.6 bits;  conditional E-value: 7.5e-07
                CarbopepD_reg_2   5 VvdketkeplpgatVyvkgt...kkgtvTdenGnFelknlpagkytLvvsyvGyktqekkvtvskektldvn 73 
                                    Vv++  + p+ gatV+v ++   ++ + Td++G+  +++lp  +yt+ v+y    t+  ++t+++++ +++n
  gi|119719264|ref|YP_919759.1| 524 VVNAL-GAPITGATVTVSNNggfTQSMETDASGKALFQQLPGAQYTIEVNYKRISTK-STLTLTQDQDITIN 593
                                    66554.58*********99844458888***********************999996.58999888887776 PP

>> SpaA  Prealbumin-like fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.1   0.00091       1.6      28      59 ..     456     490 ..     413     492 .. 0.78
   2 !    9.7   0.1   0.00057         1       8      58 ..     534     569 ..     517     572 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00091
                                    T....TTCCEESEEE-BTTSEEEEEEEESEEEEEE CS
                           SpaA  28 a...kktgtevttlttdenGkatfegLplGtYllv 59 
                                    +   + +g+++++++++++G at +  ++G Y+l+
  gi|119719264|ref|YP_919759.1| 456 GveaTLKGSVSASAVSGADGVATLNVYAPGVYTLT 490
                                    14446778889**********************96 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00057
                                    S-EEEEEETTTSCCCHCHHTT.TTCCEESEEE-BTTSEEEEEEEESEEEEE CS
                           SpaA   8 GaeFtlykvdtttdgkdaleakktgtevttlttdenGkatfegLplGtYll 58 
                                    Ga+ t+                ++g  +++++td+ Gka f  Lp  +Y++
  gi|119719264|ref|YP_919759.1| 534 GATVTV---------------SNNGGFTQSMETDASGKALFQQLPGAQYTI 569
                                    333333...............44567889****************99**98 PP

>> SdrD_B  SdrD B-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       8.2   1.5e+04      55      64 ..     428     437 ..     426     442 .. 0.79
   2 ?    1.3   0.2      0.22     4e+02      18      63 ..     448     490 ..     444     504 .. 0.78
   3 !   16.7   0.6   3.6e-06    0.0065      22      78 ..     530     585 ..     524     599 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 8.2
                         SdrD_B  55 ltpGeYkVef 64 
                                    +++G+YkV++
  gi|119719264|ref|YP_919759.1| 428 VEDGTYKVNI 437
                                    78999*9987 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.22
                         SdrD_B  18 dagekgisgvtVtLkdakgevvatttTdasGkYkFtnltpGeYkVe 63 
                                    d++   isgv+ tL   kg+v a+ ++ a+G  + +  +pG Y+++
  gi|119719264|ref|YP_919759.1| 448 DSKGYPISGVEATL---KGSVSASAVSGADGVATLNVYAPGVYTLT 490
                                    66667899999999...77777888888888888888888888765 PP

  == domain 3  score: 16.7 bits;  conditional E-value: 3.6e-06
                         SdrD_B  22 kgisgvtVtLkdakgevvatttTdasGkYkFtnltpGeYkVeftapagytvtakkaG 78 
                                    + i+g tVt+ +++g  +++  TdasGk  F++l   +Y++e+ +    t ++ + +
  gi|119719264|ref|YP_919759.1| 530 APITGATVTV-SNNGGFTQSMETDASGKALFQQLPGAQYTIEVNYKRISTKSTLTLT 585
                                    5799*****9.77888999***********************987655544444444 PP

>> DUF4249  Domain of unknown function (DUF4249)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.3   2.4e+03     122     149 ..     122     149 ..     104     173 .. 0.66
   2 ?   13.1   0.2   3.1e-05     0.055      62     107 ..     531     575 ..     517     595 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.3
                        DUF4249 122 ppeidtvsaeestedne.egyeitvdlkD 149
                                    +p +  +++ ++t++++ +g +itvd++ 
  gi|119719264|ref|YP_919759.1| 122 VP-VRVITYFRKTSWKPiKGNNITVDTSE 149
                                    33.56666666666666767777776543 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 3.1e-05
                        DUF4249  62 avtdAtVtlyvnegqeyelsetkagyyss......frlkpgdtyrLeittpd 107
                                    ++t+AtVt++ n g    +++++++   +      f+  pg++y++e++++ 
  gi|119719264|ref|YP_919759.1| 531 PITGATVTVSNN-G---GFTQSMET---DasgkalFQQLPGAQYTIEVNYKR 575
                                    689*********.7...56655552...1223467**************963 PP

>> bMG3  Bacterial alpha-2-macroglobulin MG3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   7.3e-05      0.13      25      60 ..     529     563 ..     509     593 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.3e-05
                           bMG3  25 gkPvagaeVrlldkkgevlaegtTDaqGvarfaall 60 
                                    g P++ga+V++++ +g   ++ +TDa+G a f++l 
  gi|119719264|ref|YP_919759.1| 529 GAPITGATVTVSN-NGGFTQSMETDASGKALFQQLP 563
                                    89********987.566779*************983 PP

>> DUF4493  Domain of unknown function (DUF4493)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.3   8.1e-05      0.15      96     177 ..     508     586 ..     487     600 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.1e-05
                        DUF4493  96 ttevevtCklaNvkvsvefdeefkeyfsdykvtvstgaggsltfdktetrkagYfkageesstltvtlkgtkkngktvtk 175
                                     t++e++C + N  v+v+  +++ +  + ++vtvs++ g +  ++ ++++ka + ++++++ t++v+ k  ++ + t t 
  gi|119719264|ref|YP_919759.1| 508 DTDLEIKCPVYNLNVKVV--NALGAPITGATVTVSNNGGFTQSMETDASGKALFQQLPGAQYTIEVNYKRIST-KSTLTL 584
                                    58899*******888776..99***********************************************9555.445544 PP

                        DUF4493 176 et 177
                                    ++
  gi|119719264|ref|YP_919759.1| 585 TQ 586
                                    22 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (642 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.67u 0.28s 00:00:00.95 Elapsed: 00:00:00.48
# Mc/sec: 3984.71
//
Query:       gi|119719265|ref|YP_919760.1|  [L=86]
Description: transcription factor CBF/NF-Y histone [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.3e-16   58.4   0.1    7.5e-16   58.2   0.1    1.1  1  CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) a
    7.9e-10   39.2   0.3      1e-09   38.8   0.3    1.1  1  Histone        Core histone H2A/H2B/H3/H4
    1.1e-05   25.6   0.1    1.4e-05   25.2   0.1    1.1  1  TAF            TATA box binding protein associated factor (TA
    8.6e-05   22.6   0.0    8.8e-05   22.6   0.0    1.1  1  TFIID-31kDa    Transcription initiation factor IID, 31kD subu
     0.0014   18.9   0.3     0.0017   18.6   0.3    1.2  1  CENP-X         CENP-S associating Centromere protein X
     0.0019   18.5   0.1     0.0024   18.2   0.1    1.2  1  CENP-S         CENP-S protein
     0.0051   16.9   0.1     0.0058   16.7   0.1    1.1  1  CENP-T_C       Centromere kinetochore component CENP-T histon
     0.0067   16.4   0.1     0.0085   16.1   0.1    1.2  1  TFIID-18kDa    Transcription initiation factor IID, 18kD subu
  ------ inclusion threshold ------
      0.059   13.4   0.0      0.077   13.0   0.0    1.1  1  Bromo_TP       Bromodomain associated
      0.069   12.4   0.0      0.075   12.3   0.0    1.1  1  EAP30          EAP30/Vps36 family


Domain annotation for each model (and alignments):
>> CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) and archaeal histone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.2   0.1   4.2e-19   7.5e-16       2      65 .]      12      74 ..      11      74 .. 0.98

  Alignments for each domain:
  == domain 1  score: 58.2 bits;  conditional E-value: 4.2e-19
                                   XXXHHHHHHHHHCCTTXS-B-HHHHHHHHHHHHHHHHHHHHHHHHHHCCTTSSCE-HHHHHHHH CS
                  CBFD_NFYB_HMF  2 eLPiarvkkImksdpdarkiakdAkeliaecveefieelaseAaeickkekrKtikaehiklAv 65
                                   e+P+a+ ++I++s+ +a++i++dA +++ e +e  ++e+a eA e   +++r+t++ e++k A+
  gi|119719265|ref|YP_919760.1| 12 EIPLAPLRRIFRSQ-GAERISDDAVVFLREYLEKLAREIALEAIEASRHANRRTVTDEDVKFAI 74
                                   79************.**********************************************996 PP

>> Histone  Core histone H2A/H2B/H3/H4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.3   5.8e-13     1e-09      56     128 ..       7      74 ..       2      77 .. 0.84

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 5.8e-13
                                    HXXSXXSXHHHHHHHHHHHH.TTSSSXEEXHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTXSEEXHHHHHHHH CS
                        Histone  56 kstdlliqklpfaRvvreivksekedlrisaeavlalqealEallvelfeeAnllakhaKRvTitpkDiqlAr 128
                                    +  +++i+ +p +R+ r     ++   ris +av++l e lE l  e++ eA  +++ha+R+T+t +D+++A+
  gi|119719265|ref|YP_919760.1|   7 RTRQHEIPLAPLRRIFR-----SQGAERISDDAVVFLREYLEKLAREIALEAIEASRHANRRTVTDEDVKFAI 74 
                                    45566666666666554.....56789********************************************98 PP

>> TAF  TATA box binding protein associated factor (TAF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.1   7.7e-09   1.4e-05      10      65 ..      19      74 ..      11      75 .. 0.91

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 7.7e-09
                                   HHHHHHTT---B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH CS
                            TAF 10 kviAeslGitnLsdeaaalLaedveyrlkeivqeaakfmrhskRqkLtvaDvdsAL 65
                                   + i  s G + +sd+a   L e +e   +ei+ ea+   rh+ R++ t +Dv  A+
  gi|119719265|ref|YP_919760.1| 19 RRIFRSQGAERISDDAVVFLREYLEKLAREIALEAIEASRHANRRTVTDEDVKFAI 74
                                   66778999********************************************9886 PP

>> TFIID-31kDa  Transcription initiation factor IID, 31kD subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   4.9e-08   8.8e-05      11      71 ..      18      78 ..       4      86 .] 0.90

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 4.9e-08
                    TFIID-31kDa 11 ihliLaslgvteyeerVvlqLldfayrytssvLedAkvlaehakkkevslddvrlAiqsrl 71
                                   ++ i++s+g + ++++ v  L +   +   ++  +A   ++ha++++v+ +dv++Ai+   
  gi|119719265|ref|YP_919760.1| 18 LRRIFRSQGAERISDDAVVFLREYLEKLAREIALEAIEASRHANRRTVTDEDVKFAISRLQ 78
                                   5789*****************************************************8644 PP

>> CENP-X  CENP-S associating Centromere protein X
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.3   9.5e-07    0.0017      15      55 ..      26      66 ..      17      83 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 9.5e-07
                                   TT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SE.. CS
                         CENP-X 15 ektkItkdalelvaeylklFvrEavaRaaeeaeeegkeese 55
                                      +I++da+  + eyl+ + rE ++ a+e  +  + ++ +
  gi|119719265|ref|YP_919760.1| 26 GAERISDDAVVFLREYLEKLAREIALEAIEASRHANRRTVT 66
                                   4569**************************77766655533 PP

>> CENP-S  CENP-S protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   1.4e-06    0.0024      25      70 ..      29      74 ..      19      79 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.4e-06
                         CENP-S 25 eatkqfiaaltelvykqlenlakDLeaFakHAkRstittdDvlLla 70
                                   +++ +++  l e   k ++++a      ++HA+R t+t +Dv+   
  gi|119719265|ref|YP_919760.1| 29 RISDDAVVFLREYLEKLAREIALEAIEASRHANRRTVTDEDVKFAI 74
                                   57778888888888888888888888889*************9865 PP

>> CENP-T_C  Centromere kinetochore component CENP-T histone fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   3.2e-06    0.0058      26      83 ..      26      84 ..       8      86 .] 0.77

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.2e-06
                       CENP-T_C 26 skaklekealkalekasdkffeqvgeDLeayakHagRKtidesDvilLmkr.qrkvtsk 83
                                     ++++ +a+  l + ++k  + ++ +    ++Ha R+t+ ++Dv   + r qr  +s+
  gi|119719265|ref|YP_919760.1| 26 GAERISDDAVVFLREYLEKLAREIALEAIEASRHANRRTVTDEDVKFAISRlQRAHSSQ 84
                                   5678999999999999999999999888888**************98777635554444 PP

>> TFIID-18kDa  Transcription initiation factor IID, 18kD subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   4.8e-06    0.0085      22      66 ..      32      76 ..      19      82 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.8e-06
                                   HHHHHHHHHHHHHHHHHHHHHHHC-XXXX...XXXXXXXXXXXXX CS
                    TFIID-18kDa 22 qetvqlledlvrgyliellqqaakvaklrgsrkitlEDllfliRk 66
                                   +++v  l + +++   e+  +a++ +++ ++r +t ED++f+i +
  gi|119719265|ref|YP_919760.1| 32 DDAVVFLREYLEKLAREIALEAIEASRHANRRTVTDEDVKFAISR 76
                                   5677888888899999**************************965 PP

>> Bromo_TP  Bromodomain associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   4.3e-05     0.077      18      71 ..      24      77 ..      20      81 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.3e-05
                                   HHT-SEE-HHHHHHHHHHHHHHHHHHHHHHHHHHTTSS-SS--HHHHHHHHHHT CS
                       Bromo_TP 18 eaGfdsaeesaLEtLteiaqkYirelgeqaksfaehagRseptlkDvvltLqel 71
                                   + G +++ + a+  L+e ++k  re++ +a + + ha+R ++t +Dv +++ +l
  gi|119719265|ref|YP_919760.1| 24 SQGAERISDDAVVFLREYLEKLAREIALEAIEASRHANRRTVTDEDVKFAISRL 77
                                   5677888888999999999999999999999999***************99887 PP

>> EAP30  EAP30/Vps36 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   4.2e-05     0.075      72     130 ..      15      78 ..       3      85 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.2e-05
                          EAP30  72 vdplssk.kseslgfl...ellglgdfyyeLavqiv.evclatraengglisleelyalvnrar 130
                                    ++pl +  +s++ + +    ++ l +++++La++i+ e++ a+r++n   ++ e++  ++ r +
  gi|119719265|ref|YP_919760.1|  15 LAPLRRIfRSQGAERIsddAVVFLREYLEKLAREIAlEAIEASRHANRRTVTDEDVKFAISRLQ 78 
                                    556622242233334456556679***********86999999************999988844 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 611.83
//
Query:       gi|119719266|ref|YP_919761.1|  [L=95]
Description: ribosomal protein S17e [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-20   73.5   0.8    1.5e-20   73.4   0.8    1.1  1  Ribosomal_S17e  Ribosomal S17


Domain annotation for each model (and alignments):
>> Ribosomal_S17e  Ribosomal S17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.4   0.8   8.1e-25   1.5e-20       1      82 [.       1      86 [.       1      95 [] 0.81

  Alignments for each domain:
  == domain 1  score: 73.4 bits;  conditional E-value: 8.1e-25
                                   XX----HHHHHHHHHHHHS-TTT--S-HHHHHHHHHHHS----SHHHHHHHHHHHHHHHH...TTSS--SS---HHH.HHHH CS
                 Ribosomal_S17e  1 mgrvrtktvKkaarviiekyyskltndFhtnkkvceevaiipskklrnkiaGyvthlmkr...iqkgpvrgislklq.eeer 78
                                   mg+vr+k vK++a++++e+y   +t dF+ nkk ++e+a ips++lrn+iaGy+t+l++r   i++       + +  eee 
  gi|119719266|ref|YP_919761.1|  1 MGNVRSKLVKRTAKMLVEQYPDAFTVDFELNKKKLMEIADIPSRQLRNQIAGYITRLVRRkklIEQRLSMRQEITMTdEEEY 82
                                   9*********************************************************996655444433334444336666 PP

                                   HHHH CS
                 Ribosomal_S17e 79 errd 82
                                    rr 
  gi|119719266|ref|YP_919761.1| 83 IRRI 86
                                   6665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       741  (0.0413297); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 592.93
//
Query:       gi|119719267|ref|YP_919762.1|  [L=143]
Description: hypothetical protein Tpen_0350 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      7e-05   23.0   0.0    9.5e-05   22.6   0.0    1.1  1  RNA_pol_Rpb8  RNA polymerase Rpb8
  ------ inclusion threshold ------
      0.098   12.7   0.0       0.12   12.5   0.0    1.2  1  RNA_pol_RpbG  DNA-directed RNA polymerase, subunit G


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb8  RNA polymerase Rpb8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   1.1e-08   9.5e-05      75     135 ..      84     138 ..      63     140 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.1e-08
                                    GGS-CGGGSSEEEBEEEEEEEE-ST..T-EEEEEEBTTBEEEEEBSHHTTTSGSSS.EEBE CS
                   RNA_pol_Rpb8  75 geksladkydYvmyGkvYkieeeeskeekvkvyvSfGGLlmaLegdakklsklevdkrvYl 135
                                    +e+   d++  vm G+vY  +e es     +vy+S GGL + ++++ k  ++++v+++vY 
  gi|119719267|ref|YP_919762.1|  84 REAGSIDEWSVVMQGEVYLKKEGES-----AVYASLGGLQLVVKSP-KIYNEFNVGDKVYF 138
                                    677889************9988886.....8**********99975.67899***999995 PP

>> RNA_pol_RpbG  DNA-directed RNA polymerase, subunit G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.3e-05      0.12      44     117 ..      74     141 ..      51     143 .] 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.3e-05
                   RNA_pol_RpbG  44 eedkveviisrekPeyldgkdFcghGylvtekeeenkiitliSlfGllvkisskkdllnelglkvmdkvYlcvr 117
                                    e+ +v +++ re  +  +    + +G +  +ke   + + + Sl Gl + ++s k +    +++v dkvY++++
  gi|119719267|ref|YP_919762.1|  74 EGVEVVFEVAREAGSIDE-WSVVMQGEVYLKKEG--ESAVYASLGGLQLVVKSPKIY---NEFNVGDKVYFKLA 141
                                    556777788888877777.899999999999885..556788****98886676444...79**********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.31s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 928.92
//
Query:       gi|119719268|ref|YP_919763.1|  [L=91]
Description: hypothetical protein Tpen_0351 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 656.04
//
Query:       gi|119719269|ref|YP_919764.1|  [L=110]
Description: RNA polymerase Rpb4 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.4e-13   49.6   1.0    5.8e-13   49.2   1.0    1.2  1  RNA_pol_Rpb4   RNA polymerase Rpb4
  ------ inclusion threshold ------
       0.15   12.3   0.0       0.26   11.5   0.0    1.4  1  DOPA_dioxygen  Dopa 4,5-dioxygenase family


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb4  RNA polymerase Rpb4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.2   1.0   6.5e-17   5.8e-13      31     120 ..      18     107 ..       4     110 .] 0.91

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 6.5e-17
                                    CHHSHCHTCHHCHHHHHHHHHHHCTHHTTSSHHHHHHHHHHHT.TSTSTHHHHHHHHHCSTSSHHHHHHHSTTGTTTSTS CS
                   RNA_pol_Rpb4  31 isekeevkgnlnkilkktleyltnkfsrlkneekfnelvellk.sfeLtkaEklqlvnlkPesavelktlieeleerfed 109
                                    i  kee  ++l+ i + tleyl++ fs+ ++++++++lve+l  +f++ +  ++q+vn kP +  e+k  +  l++ f+d
  gi|119719269|ref|YP_919764.1|  18 ILLKEESSRELTSIERYTLEYLRK-FSKVRDAQTARSLVERLMkEFDIPEDVAVQIVNVKPADPQEAKIFVSHLNKVFTD 96 
                                    567889999**************9.************9998875999********************************* PP

                                    HHHHHHHHHHH CS
                   RNA_pol_Rpb4 110 eqleeiLdelk 120
                                    ++  +i+++l+
  gi|119719269|ref|YP_919764.1|  97 KDFARIIEILS 107
                                    *********98 PP

>> DOPA_dioxygen  Dopa 4,5-dioxygenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   2.9e-05      0.26      13      66 ..      46     104 ..      38     109 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.9e-05
                                    GGHHHHHHHHHHHHHHT..TTT..E---BSS--TT-SSEEEEEE...E.-HHHHHHHHH CS
                  DOPA_dioxygen  13 aekkeAkeLrekirref..eeelrvgklaekpiGPhpvamfevd...vftpeqfgkvvs 66 
                                    +++++A++L e++++ef  +e+++v+ ++ kp+ P + + f  +   vft + f+++++
  gi|119719269|ref|YP_919764.1|  46 RDAQTARSLVERLMKEFdiPEDVAVQIVNVKPADPQEAKIFVSHlnkVFTDKDFARIIE 104
                                    57899************5556699999*********99999776111456666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       762  (0.042501); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 798.21
//
Query:       gi|119719270|ref|YP_919765.1|  [L=209]
Description: putative nucleotide binding protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-48  164.7   0.3    2.4e-48  164.5   0.3    1.0  1  DUF655    Protein of unknown function (DUF655)
    0.00016   21.8   0.1    0.00067   19.9   0.0    1.9  2  HHH_6     Helix-hairpin-helix motif
  ------ inclusion threshold ------
        4.1    8.1   4.8        8.8    7.0   0.1    3.0  3  HHH_5     Helix-hairpin-helix domain


Domain annotation for each model (and alignments):
>> DUF655  Protein of unknown function (DUF655)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.5   0.3   4.1e-52   2.4e-48       2     180 ..      15     188 ..      14     189 .. 0.94

  Alignments for each domain:
  == domain 1  score: 164.5 bits;  conditional E-value: 4.1e-52
                                    --EEEEEEEETT--TT--S-GGG---EEEEEETTT--EEEEEE-..TT----TT-EEE-SSS--SSEEEEEEE--GGGS- CS
                         DUF655   2 eeeaivLDylpeGypddkhrehrdkpvvqalgereltLlelvpl..kevdilkldevaigkgksdkivkikreisyedLt 79 
                                    +e+ +vLD lp+G +        + p+vq++ge++++L+el     +   ++ ld++  +   + ++ +  r + y++L+
  gi|119719270|ref|YP_919765.1|  15 DENLVVLDMLPYGDAVRGI----KYPLVQTIGEYRFLLVELKSTtpQAPSLKPLDRISSEYLREARLLSFARYLTYDELS 90 
                                    67789********999886....88***************9877435567899*************************** PP

                                    HHHHHHHHHHHHHHHHTTHHHHHHHH-----B-SSSBGGGGSTT--HHHHHHHHHHHHHS---SHHHHHHHSTT---HHH CS
                         DUF655  80 dvaraeLpdvvekivkekEdrfveffneaepitiRlHaLelLpgvgkklarkileeRerrrFesFedvkkrvkglkdpae 159
                                    ++a+a+L ++v+ ivk +E+rfv+ffn+a+p++ + H+LelL+g+gk++++kil+eR+r++FesFed+k r +  +dp+e
  gi|119719270|ref|YP_919765.1|  91 ATAKANLVEAVTAIVKVQEKRFVDFFNNAQPLSKKAHTLELLKGIGKRTLWKILDERRRKPFESFEDIKARAD--IDPVE 168
                                    *************************************************************************..***** PP

                                    HHHHHHHHHHH-TTSS--SS- CS
                         DUF655 160 ilverileEiedktekYylFv 180
                                    ++verileE++++++  y+Fv
  gi|119719270|ref|YP_919765.1| 169 LIVERILEELKEPQT-IYIFV 188
                                    *************55.55665 PP

>> HHH_6  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.32   1.9e+03      39      69 ..     100     125 ..      97     132 .. 0.58
   2 !   19.9   0.0   1.1e-07   0.00067      29      67 ..     129     165 ..     126     180 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.32
                          HHH_6  39 aaerivaeRekegpfksledlarrvdslnkr 69 
                                    a+ +iv+  e     k + d+++ +++l+k+
  gi|119719270|ref|YP_919765.1| 100 AVTAIVKVQE-----KRFVDFFNNAQPLSKK 125
                                    6777777665.....3455555555554443 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 1.1e-07
                          HHH_6  29 LaaikglgeaaaerivaeRekegpfksledlarrvdsln 67 
                                    L+ +kg+g++++ +i++eR+ ++pf+s+ed+  r+d  +
  gi|119719270|ref|YP_919765.1| 129 LELLKGIGKRTLWKILDERR-RKPFESFEDIKARADI-D 165
                                    7889***************9.8*************94.3 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       0.9   5.4e+03      23      38 ..      83      98 ..      74     112 .. 0.60
   2 ?    7.0   0.1    0.0015       8.8      34      56 ..     126     148 ..     119     150 .. 0.86
   3 ?    4.8   2.5    0.0072        43      39      56 ..     131     148 ..     126     180 .. 0.56

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.9
                                   --SHHHHHHS-HHHHH CS
                          HHH_5 23 iesvedlaaadveeLa 38
                                   + ++++l a +++ L 
  gi|119719270|ref|YP_919765.1| 83 YLTYDELSATAKANLV 98
                                   4677777665444333 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0015
                                    HHHHHTSTTS-HHHHHHHHHHHH CS
                          HHH_5  34 veeLakipGiGkktAeriilelk 56 
                                    +++L  ++GiGk+t  +i++e +
  gi|119719270|ref|YP_919765.1| 126 AHTLELLKGIGKRTLWKILDERR 148
                                    5789999**********999987 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.0072
                                    TSTTS-HHHHHHHHHHHH CS
                          HHH_5  39 kipGiGkktAeriilelk 56 
                                     ++GiGk+t  +i++e +
  gi|119719270|ref|YP_919765.1| 131 LLKGIGKRTLWKILDERR 148
                                    445555555555555443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1546.76
//
Query:       gi|119719271|ref|YP_919766.1|  [L=444]
Description: pseudouridylate synthase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.3e-07   29.2   0.1    8.3e-07   29.2   0.1    2.1  3  THUMP     THUMP domain
  ------ inclusion threshold ------
      0.077   13.5   0.1       0.14   12.6   0.1    1.4  1  DUF3614   Protein of unknown function (DUF3614)


Domain annotation for each model (and alignments):
>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.1   9.3e-11   8.3e-07       2     137 ..      38     200 ..      37     204 .. 0.87
   2 ?   -1.6   0.1      0.28   2.5e+03      15      56 ..     296     335 ..     281     358 .. 0.60
   3 ?   -3.3   0.0         1     9e+03      16      51 ..     372     407 ..     368     420 .. 0.70

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 9.3e-11
                                    HHHHHHHHTT.H-SEEEEETTEEEEECTEEEEEETHHHHHHHHHTST......TECEEEEE......EEEEESSHHHHHH CS
                          THUMP   2 eieellkegkvnverveagkgrivvelkgekpeedeellkealekar......giqrvipv......cevceadledile 69 
                                    +++ l + g  n er++a k  ++++    +p  ++ +l + l +        ++++++ +      c++ce    + +e
  gi|119719271|ref|YP_919766.1|  38 RLFGLRGYGLSNTERGRALKTLLIMKAFQASPRQADLELLRVLARTGfepareLLKKLSGEdvevkaCSICEGLTGRYYE 117
                                    6777778888888999999999999988888888888887777776677777766677666888889************* PP

                                    HHHHHHHHHHHHCT-EEEEEEEESSSTS...............SSHHHHHHHHHHHHHHCCTT-EE-SSS-SEEEEEEEE CS
                          THUMP  70 aakeivkkkfeeeketFaVrvkrrgkhf...............eftsreinrevGkaivektglkVdlenPdivvrveii 134
                                    +a  +v++ +  e +tF V+v+   + +               e +++e  revGk+i ++tg++ + +n +++++v++ 
  gi|119719271|ref|YP_919766.1| 118 LALRAVEEAKSYEFNTFEVGVRIDAEVIrreeelwrryglesaESIRNEASREVGKIISKLTGKEYSRNNSELLIIVDLS 197
                                    **********************98888899999********************************************997 PP

                                    TTE CS
                          THUMP 135 kdk 137
                                      +
  gi|119719271|ref|YP_919766.1| 198 AGA 200
                                    665 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.28
                                    SEEEEETTEEEEECTEEEEEETHHHHHHHHHTSTTECEEEEE CS
                          THUMP  15 erveagkgrivvelkgekpeedeellkealekargiqrvipv 56 
                                    e++ +g g+++ +l     ++d++++k++ + a  +++ +++
  gi|119719271|ref|YP_919766.1| 296 EKINSGAGGLIEVLDLA--YTDRKTIKKLKSLASIAKKAYVA 335
                                    55555555555555433..66666666666666644444444 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 1
                                    EEEEETTEEEEECTEEEEEETHHHHHHHHHTSTTEC CS
                          THUMP  16 rveagkgrivvelkgekpeedeellkealekargiq 51 
                                    rv + +++iv +l  +k+  de + +  ++  ++++
  gi|119719271|ref|YP_919766.1| 372 RVDKLRKKIVYRLEARKISQDEVEFYLETQGGFYVK 407
                                    556667788888888777777777766666555555 PP

>> DUF3614  Protein of unknown function (DUF3614)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   1.6e-05      0.14     131     162 ..     347     378 ..     328     380 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.6e-05
                        DUF3614 131 kimrfsrFpsstVynvrvdervyknrVlkLRd 162
                                    k  ++s+ +s  V n r+ +rv+ +rV kLR 
  gi|119719271|ref|YP_919766.1| 347 KLAEISKVFSNAVINQRTPTRVLHRRVDKLRK 378
                                    56789*************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (444 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 3286.67
//
Query:       gi|119719272|ref|YP_919767.1|  [L=102]
Description: 50S ribosomal protein L21e [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-30  105.1   2.6    1.5e-30  105.0   2.6    1.0  1  Ribosomal_L21e  Ribosomal protein L21e


Domain annotation for each model (and alignments):
>> Ribosomal_L21e  Ribosomal protein L21e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.0   2.6   8.6e-35   1.5e-30       1      99 [.       1      95 [.       1      97 [. 0.98

  Alignments for each domain:
  == domain 1  score: 105.0 bits;  conditional E-value: 8.6e-35
                                   X--S-STTTT-TTTTS--GGG-SS--SHHHH----TT-EEEE---TT--SS---GGGTT-EEEE..EEEETTEEEEEEEETT CS
                 Ribosomal_L21e  1 mknskglrrgtrklfskkfrkkgvpplstylreykkGdkVdikidpsvqkgmphkryhGktgrvynvtkravgvivnkkvgg 82
                                   m++s+g+r++ rkl++k++r++g   ls+++ ey+ Gd+V i+idp++ ++ ph+ry+G++grv  v+kr++++++++ +g+
  gi|119719272|ref|YP_919767.1|  1 MRHSHGYRNRGRKLLRKHPRRRGYGGLSRLMYEYNPGDRVVIDIDPTFIETAPHRRYQGRVGRV--VEKRGRAYVIEVVLGS 80
                                   89**************************************************************..**************** PP

                                   E..EEEEEE-GGGEEE- CS
                 Ribosomal_L21e 83 kileKriivriehlkks 99
                                   k   K+ii++ eh+k++
  gi|119719272|ref|YP_919767.1| 81 K--VKKIITTKEHIKPL 95
                                   *..************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 754.35
//
Query:       gi|119719273|ref|YP_919768.1|  [L=543]
Description: tRNA-guanine transglycosylases, various specificities [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-76  256.3   0.0    5.9e-76  255.9   0.0    1.1  1  TGT       Queuine tRNA-ribosyltransferase
    6.3e-10   39.1   0.0    1.3e-09   38.1   0.0    1.5  1  DUF5591   Domain of unknown function (DUF5591)


Domain annotation for each model (and alignments):
>> TGT  Queuine tRNA-ribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  255.9   0.0   6.6e-80   5.9e-76       3     349 ..      16     337 ..      13     338 .. 0.94

  Alignments for each domain:
  == domain 1  score: 255.9 bits;  conditional E-value: 6.6e-80
                                    EEEEEEEETTEEEEESEEEEBETTSSBTTB-HHHHH.HTTES-EEEEHHHHHHTTTHHHHHHTTHHHHHHT--S-EEEE- CS
                            TGT   3 aRlGklelphgtietPafmpvgtqgtvkgltpdelkeelgaqiilsntyhlelrpgeelvakagglhkflgwdkpiltds 82 
                                    +R+G++++++g++etP++ pv  +++ + l+p+e+ +++g ++i++n+y+++ r+  +l ak+  +h++lg+d p++tds
  gi|119719273|ref|YP_919768.1|  16 GRIGSISTRRGNVETPTLTPV-INPSKPVLEPREI-QQMGFNLIMTNSYIIK-RQYGDL-AKEVKVHQLLGVDTPVMTDS 91 
                                    7********************.999**********.599**********999.555556.67788*************** PP

                                    SHHHHHHHEEEESSEEEEE-TTTS-EEEE-HHHHHHHHHHHT-SEEE-------SS--HHHHHHHHHHHHHHHHHHHHHH CS
                            TGT  83 ggfqvfslkkiteegvsfqsridGskvlltpeesieiqeklgsDiimalddvvpspaskkrveksverTlrwldrcleah 162
                                    g++q++               + G+ v+++p e++++q ++gsDi ++ld ++++   + +v  +ve+Tlr+++ +l+  
  gi|119719273|ref|YP_919768.1|  92 GAYQLMV--------------Y-GR-VEVDPLEIVRFQVEIGSDIGVILDIPTKKGVPRGQVLAEVEETLRRAEASLAVE 155
                                    ****664..............4.99.***************************************************777 PP

                                    ..SE.EEEEE--TT-HHHHHHHHHHHHHH--SEEEE-S.SSSSS..HHHHHHHHHHHHGGGS-TTS-EEETTB-SHHHHH CS
                            TGT 163 ..qa.lfgivqGglyedlreesaeelakrdfdgyaigG.lsvge..ekeellevveavtellpedkprylmGvgtPedll 236
                                      ++ l+g+vqGgly+d  + +a++l ++ fd+ya+gG  +++e  + +el+++v +++ +lp + p +l+G+g+P +l 
  gi|119719273|ref|YP_919768.1| 156 rdGMlLVGPVQGGLYTDIVATAARRLGEMPFDVYAVGGpTQLMEeyDFSELVKLVMTARLNLPWEAPLHLFGAGHPVMLP 235
                                    88777*********************************88899978889******************************* PP

                                    HHHHTT--EEEESHHHHHHHTTEEEETTEEEETTSGGGTT--SBSSSS--SHHHHH-BHHHHHHHHHTT-HHHHHHHHHH CS
                            TGT 237 eavalGvDmfdcvyptrtarngraltsegelnlknakyaedfspldegCsCytCknytraylhhllktkemlgaiLltiH 316
                                     ava+GvD fd++ + ++ar++r++ts+g+l+l   +++e   p    C+C++C++y+  +l++l k+++    +Ll+ H
  gi|119719273|ref|YP_919768.1| 236 LAVAMGVDTFDSASYVLYARDDRVFTSRGTLRLG--EVEEL--P----CNCPVCSKYSARELRELPKQER---VVLLARH 304
                                    *****************************99997..66655..9....******99***********999...******* PP

                                    HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHT CS
                            TGT 317 NlhyylelfkriReaIkegtfeefveefarkye 349
                                    Nl+++++++k+iReaI+eg+++e+ ee+ ++++
  gi|119719273|ref|YP_919768.1| 305 NLYVIQKELKEIREAIHEGRLWELLEERSMTHP 337
                                    ***************************999886 PP

>> DUF5591  Domain of unknown function (DUF5591)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.0   1.4e-13   1.3e-09       1     130 [.     380     505 ..     380     524 .. 0.87

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 1.4e-13
                                    X-HHHHHHHHH---S..SSEEEEEE--SSSSGGGSHHHHHHHHHS---...SEEEEE-SS-.EEEGGGTT---------- CS
                        DUF5591   1 vkrfrervlerYeppeekkvlvLlPcsakkPyseskshrkfaeaikkrkakvheviltsPlGvvPreleevYPaaqYdia 80 
                                    v+r+ +r+ +rY+    +++lv++ ++ +kP+++    +++  a      +v++ +l+  + v+P el+ +YP++qY++ 
  gi|119719273|ref|YP_919768.1| 380 VVRHVNRLAQRYKRA--RDTLVVFEETPQKPFTRAGLVKEILGADPMLPVDVDVAVLSGAFSVIPLELDGFYPLSQYEA- 456
                                    89**********999..699***************999999999888888***************************97. PP

                                    ------HHHHHHHHHHHHHHHHHHT-SEEEE---THHHHHHHHHHTT-SS CS
                        DUF5591  81 vtgewseeeiefvaellakylektkyekviahleeeyreiveevaeelgl 130
                                     +ge  +e ++ v   la ++ ++ y++v+++ ++  + ++++ +e+l+l
  gi|119719273|ref|YP_919768.1| 457 -SGEVFREAVDEVLADLAWFVLSKGYRRVVLVYHSLPKVFLDKLKERLSL 505
                                    .5778899999999999999999*****9998887767777777666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (543 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 3674.84
//
Query:       gi|119719274|ref|YP_919769.1|  [L=247]
Description: hypothetical protein Tpen_0357 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-33  116.5   0.1    1.9e-33  116.3   0.1    1.0  1  PAC2           PAC2 family
      0.009   16.4   0.9      0.028   14.8   0.2    1.9  2  GPS2_interact  G-protein pathway suppressor 2-interacting dom


Domain annotation for each model (and alignments):
>> PAC2  PAC2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.3   0.1   2.2e-37   1.9e-33       1     212 [.      23     229 ..      23     230 .. 0.84

  Alignments for each domain:
  == domain 1  score: 116.3 bits;  conditional E-value: 2.2e-37
                                    EEEESSCGGGHHHHHHHHHHHHTTEEEEEEEEHCCHSBCCCC.SEEEEETTEEE-SEEEEEETTT.SEEEEEEEE-HSCH CS
                           PAC2   1 LilGfpgiGnVgqlavdlLiesleaekvgeidsdyllpfvgprpvvlveegrelepprlyakdsgsrdllvlqgrepilq 80 
                                    +++Gf g+G+Vg +av++++e+lea++vg++ ++y +p     p v v++g  ++p++ly ++     +l++    p+ +
  gi|119719274|ref|YP_919769.1|  23 FLAGFHGVGHVGWIAVKHVVEKLEAQRVGYLFTQY-MP-----PFVNVRSG-IRTPYELYFSQ----GMLIFLPNVPVSP 91 
                                    589********************************.77.....77777777.56999999985....4777777777777 PP

                                    HH..HHHHHHHHHHHHTTESEEEEEEEEEESS-ES..TTS-.EE..EEEE..SSHHHHHHHHCT......-CEEEEHHHH CS
                           PAC2  81 ye..efakalldwaeelgvkevvvLggldageradvphtrpekv..tgaa..tdeelleelees......eyggivgitg 148
                                     +  ++ +al+++   lgvk  v++gglda  ++  p+ +p ++  t a+  + e+l++   e+      e+ givg+ +
  gi|119719274|ref|YP_919769.1|  92 KDfiSVPEALAELSITLGVKLSVLFGGLDASYKE--PDAKP-RIapTRAFllSKEDLIK---EKgypvleEHLGIVGPLA 165
                                    7777799**********************88775..45555.44221121334444442...225667789********* PP

                                    HHHHHHHHTT-EEEEEEEEEECCC--HHHHHHHHHHHHHHHT---HCHHHHHHHHHHHHHHHHH CS
                           PAC2 149 lLlsaakergipavgllaevphylpdPkaaaalleflskllglevdtedLeedaeeleeqleel 212
                                    +Lls ++++++pav++l+++    pdP+aaa++++++++++g+ +++e+L e+ e+le++++e+
  gi|119719274|ref|YP_919769.1| 166 ILLSVFEANNVPAVAILPYAAADRPDPRAAAEAIKVFQEITGVRISVEELLEQGERLEKEVAEV 229
                                    ************************************************************9985 PP

>> GPS2_interact  G-protein pathway suppressor 2-interacting domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       0.2   1.8e+03      25      34 ..     138     147 ..     124     149 .. 0.78
   2 !   14.8   0.2   3.1e-06     0.028      20      52 ..     203     235 ..     190     242 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.2
                  GPS2_interact  25 srlsKdeLlq 34 
                                    + lsK++L++
  gi|119719274|ref|YP_919769.1| 138 FLLSKEDLIK 147
                                    568*****98 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 3.1e-06
                  GPS2_interact  20 qelvpsrlsKdeLlqnidkvDREiakveqqisk 52 
                                    qe +  r+s +eLl++ ++  +E+a ve++i++
  gi|119719274|ref|YP_919769.1| 203 QEITGVRISVEELLEQGERLEKEVAEVEKKIKE 235
                                    567789*************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       978  (0.0545485); expected 358.6 (0.02)
Passed bias filter:                      873  (0.0486921); expected 358.6 (0.02)
Passed Vit filter:                       112  (0.00624686); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 1775.78
//
Query:       gi|119719275|ref|YP_919770.1|  [L=128]
Description: 30S ribosomal protein S8e [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.6e-27   94.0   2.7    9.9e-27   93.8   2.7    1.1  1  Ribosomal_S8e  Ribosomal protein S8e
  ------ inclusion threshold ------
        0.1   12.6   0.0       0.14   12.2   0.0    1.2  1  RNA_pol_RpbG   DNA-directed RNA polymerase, subunit G


Domain annotation for each model (and alignments):
>> Ribosomal_S8e  Ribosomal protein S8e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.8   2.7   1.1e-30   9.9e-27       5     137 .]       4     127 ..       1     127 [. 0.92

  Alignments for each domain:
  == domain 1  score: 93.8 bits;  conditional E-value: 1.1e-30
                                    XXCCCSEESSTE.EXXXSSXXXCCSBXXXXXXXEES.SHEEEEEEETTCEEEEEEESESEEEEEETTTTEEEEEEEEEEE CS
                  Ribosomal_S8e   5 rdskhkrkltGg.kakllrkkrkielgrkekatklg.aervkvvrvrgGkrkkralrlkkanvthpeekvtkklkIlgVk 82 
                                     ++++ rk+tGg k ++++ krk+  gr +  t  g a+ vkvv++rg+ +k +   +++ nv+ p+e++t++++I++V 
  gi|119719275|ref|YP_919770.1|   4 YHGNDLRKITGGiKGRHVKTKRKYLSGRYPILTVPGqATEVKVVKARGNTYKLKVKVASEVNVYIPKEGKTVRAQIIKVL 83 
                                    56788899998725556666***************8899***************************************** PP

                                    CSSSTCHHHHTTC--TTEEEEEESHHHHHHHHTTEEEEEEESEHHHHSSEEEEEE CS
                  Ribosomal_S8e  83 knpsnneyvrlgvltKgaiievdvseLgevtqsgkvvAqvtsrPgqdGcvnavlL 137
                                    +npsn++++r+g+++Kgai++++v++            +vtsrPgqdG+vn+vl+
  gi|119719275|ref|YP_919770.1|  84 DNPSNKDFARRGIISKGAILQTSVGK-----------VKVTSRPGQDGVVNGVLV 127
                                    **************************...........89**************95 PP

>> RNA_pol_RpbG  DNA-directed RNA polymerase, subunit G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.6e-05      0.14      14      72 ..      39      98 ..      36     110 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.6e-05
                   RNA_pol_RpbG 14 sklkdlkivkikcqneeielDiiselnif..keedkveviisrekPeyldgkdFcghGylv 72
                                   ++  ++k+vk++++ +++++ ++se+n+   ke+  v+  i +   + ++ kdF  +G + 
  gi|119719275|ref|YP_919770.1| 39 GQATEVKVVKARGNTYKLKVKVASEVNVYipKEGKTVRAQIIKVLDNPSN-KDFARRGIIS 98
                                   566899****************9998765348999999999998877777.99*9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 809.88
//
Query:       gi|119719276|ref|YP_919771.1|  [L=101]
Description: ribonucleoprotein complex SRP, Srp19 component [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.9e-20   71.6   0.5    1.1e-19   71.1   0.5    1.2  1  SRP19     SRP19 protein
  ------ inclusion threshold ------
      0.045   14.1   0.0        0.1   13.0   0.0    1.6  1  Nif11     Nif11 domain


Domain annotation for each model (and alignments):
>> SRP19  SRP19 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.1   0.5   1.2e-23   1.1e-19       1      93 [.       8      90 ..       8      91 .. 0.93

  Alignments for each domain:
  == domain 1  score: 71.1 bits;  conditional E-value: 1.2e-23
                                   EEECCCCBTTS-CCCT--S-CCCSBSS--HHHHHHHHHHCTSCEEEEEEECTTSSTTCC.EEEEEC-..........SS-CH CS
                          SRP19  1 viYPvYldskktrkeGRrvpkelavenPtaqeiaealkalglevvvepeksyPrdwanp.GrVrvklkedgkevnekiknkk 81
                                   +++PvY+ds+k rk  Rrvp++lave+Pt++ei+ea+k+ g++++ve++ ++P  w++  GrV v+ +           +k+
  gi|119719276|ref|YP_919771.1|  8 IVWPVYFDSTKPRKW-RRVPRKLAVEKPTLSEIVEAVKREGFSFTVEENAKHPAYWYEVqGRVIVQAN----------VKKS 78
                                   79**********998.***************************************99655******84..........6899 PP

                                   HHHHHHHHHHHH CS
                          SRP19 82 ellkkiaellke 93
                                    llkkiae+l++
  gi|119719276|ref|YP_919771.1| 79 VLLKKIAENLQK 90
                                   999999999986 PP

>> Nif11  Nif11 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.1e-05       0.1      28      47 ..      35      54 ..      27      54 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.1e-05
                          Nif11 28 dheevvalAkeaGyefteee 47
                                   +  e+v+ +k++G++ft+ee
  gi|119719276|ref|YP_919771.1| 35 TLSEIVEAVKREGFSFTVEE 54
                                   7789**************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1050  (0.0585643); expected 358.6 (0.02)
Passed bias filter:                      567  (0.0316247); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 742.49
//
Query:       gi|119719277|ref|YP_919772.1|  [L=632]
Description: glutamyl-tRNA(Gln) amidotransferase subunit E [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.8e-70  236.1   0.0    7.3e-70  235.5   0.0    1.3  1  GatB_N     GatB/GatE catalytic domain
    4.9e-26   91.4   1.8    8.5e-26   90.6   0.8    1.9  2  GatB_Yqey  GatB domain
      2e-17   63.2   0.1    6.6e-17   61.5   0.0    2.0  2  GAD        GAD domain
      2e-07   31.2   1.0    3.9e-07   30.2   1.0    1.5  1  YqeY       Yqey-like protein
  ------ inclusion threshold ------
       0.16   12.6   0.3       0.47   11.1   0.3    1.7  1  MDMPI_N    Mycothiol maleylpyruvate isomerase N-terminal doma


Domain annotation for each model (and alignments):
>> GatB_N  GatB/GatE catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  235.5   0.0     2e-73   7.3e-70       2     273 .]       6     445 ..       5     445 .. 0.96

  Alignments for each domain:
  == domain 1  score: 235.5 bits;  conditional E-value: 2e-73
                                    EEEEEEEEEB--SB-SSSSSBSS..SSCE..........S.TTSS--TTTTTS........................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxx..xxxx..........x.xxxxxxxxxxxx........................... RF
                         GatB_N   2 viGlEiHaqlktksKlFssaste..eege..........e.pnsevsevdlal........................... 41 
                                     +GlEiH+ l+t++KlF+s++t   +  +          + ++sev+e+d a+                           
  gi|119719277|ref|YP_919772.1|   6 RCGLEIHQMLDTEKKLFCSCPTYlrK--DdphftfrrrlRlAKSEVGEIDPAAlfeyekglsylyegyrenvclvemdee 83 
                                    69*******************87531..23567777888569**********9************************999 PP

                                    TT..--.EEHHHHHHHHHHHHHTTEEE-SEE-EEEEE-TCTTCTTSEEEEESSS.SEEEEEEEE.TEEEEEEEEEEEE-- CS
                                    xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
                         GatB_N  42 PGtlPv.lnkeavelaikaalalnceiaeeskfdRKnyfypdlpkgyQitqkeeplakeGslel.ekkvrierihlEeDa 119
                                    P   P+ ln+ea+ela+k+al++++++ +e++++RK+++++++ +g+Q+t+    +a +Gs+e+  k+v+i++i+lEeDa
  gi|119719277|ref|YP_919772.1|  84 P---PHeLNREALELALKFALMVGASVVDEVHVMRKIVIDGSNVTGFQRTA---LIAIGGSVEVnGKRVGIQTICLEEDA 157
                                    8...999********************************************...7889*****97789************ PP

                                    -EEEEE..ETTEEEEETTSTT-EEEEEEE-STB-SHHHHHHHHHHHHHHHHHHTSB--SGGGTTEEEEEEEEECTSETTS CS
                                    xxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         GatB_N 120 aksvhe..ekeeslvdlnRaGvpLiEivtepdlrspeearavveklrellralgvsdgnmeeGslRcDvNvSvreeekge 197
                                    a+++ e  e++   ++l+R+G+pLiE++t+pd++speear+v+ +++ llr+lg++++++  G++R+D+NvSv+      
  gi|119719277|ref|YP_919772.1| 158 ARKTGEviEENALRYRLDRMGIPLIEVATAPDITSPEEAREVALRIGLLLRSLGKVKREL--GAIRQDLNVSVEG----- 230
                                    ****955577799***********************************************..************4..... PP

                                    SS.--EEEEEE-SHHHHHHHHHHHHHHHHHHH................................................ CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................................ RF
                         GatB_N 198 eegtrvEiKnlnslksiekaieyeierqiell................................................ 229
                                      g++vEiK+++ l+ i k++e e++rq++ll                                                
  gi|119719277|ref|YP_919772.1| 231 --GAKVEIKGVQYLDLIPKVVELEVKRQLALLeirdelkrrgvtrddlvfkpvdvteifrntkskvarkaleaggralal 308
                                    ..59**************************************************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                         GatB_N 230 ................................................................................ 229
                                                                                                                    
  gi|119719277|ref|YP_919772.1| 309 rlkgfagllgrevqpgrrlgtelsdrakywgrvgglfhsdelpaygisqeeveavkqalgveqgdafilifdepekalrg 388
                                    ******************************************************************************** PP

                                    ................-EEEEEETTTTEEEEECC--.--...-EEE-TTS--EE--HHHHH CS
                                    ................xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
                         GatB_N 230 ................qeTrkfdedkgetvslRske.eaedYryfpepdlppleiseelie 273
                                                     eTr++++d g+t+ +R+++ +a   r++pe+d+ p+++++e++e
  gi|119719277|ref|YP_919772.1| 389 lraayeralealegvpPETRAANPD-GTTRFMRPRPgSA---RMYPETDIRPIRVTREYLE 445
                                    *************************.**********555...***************9985 PP

>> GatB_Yqey  GatB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.72   2.6e+03      22      50 ..     260     288 ..     251     295 .. 0.85
   2 !   90.6   0.8   2.4e-29   8.5e-26       2     148 .]     484     625 ..     483     625 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.72
                                    TCHHHHHHHHTXXTTCSSTTHHHHHHHHH CS
                      GatB_Yqey  22 nellgelnkegleieelkltpeqlaellk 50 
                                     e+  el+++g++ ++l ++p +++e+++
  gi|119719277|ref|YP_919772.1| 260 LEIRDELKRRGVTRDDLVFKPVDVTEIFR 288
                                    588899***********9**999999875 PP

  == domain 2  score: 90.6 bits;  conditional E-value: 2.4e-29
                                    HHHHHHHHSS.HHHHHHHHHTCHHHHHHHHTXXTTCSSTTHHHHHHHHHHHHTTSSGHHHHHHHHHHHHHH.TXXHHHHH CS
                      GatB_Yqey   2 ffeevvkegadaklaanwllnellgelnkegleieelkltpeqlaellkliaegkIskkiakevleellee.gkspeeii 80 
                                    ffee+vk++  ++++++ +l+++l +l++e++++e+  l++e+l e+++++aeg I+k+++ +vl+el+ + +++ e+++
  gi|119719277|ref|YP_919772.1| 484 FFEEAVKKTGASPQVVATTLVNTLVSLRRENVPVEN--LSEERLLEVFRMVAEGSIAKEAIPDVLRELALNpEEQLENVL 561
                                    8********99999**********************..9******************************999******** PP

                                    HHCTXXXXXXSSXHHHHHHHHHHTXHHHHHHHTTXXTTSTHHHHHHHHHTTSSXSXHHHHHHHHHHHS CS
                      GatB_Yqey  81 eekgLkqisdeeeleklveeviaenpkavedyksgkekalkflvGqvMkktkGkadpklvnellkekL 148
                                    ++ g++ i   + l++++ eviaen    + + ++ eka++ l+G vM k++G++d+ +v ++lke+L
  gi|119719277|ref|YP_919772.1| 562 RRIGIERID-VDRLRAMIREVIAEN---KDYVLQKREKAFGKLMGVVMDKVRGRIDGSVVAKVLKEEL 625
                                    ********6.59*************...444566778*****************************98 PP

>> GAD  GAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.5   0.0   1.8e-20   6.6e-17       3      93 ..     297     387 ..     295     389 .. 0.96
   2 ?   -2.6   0.0       1.8   6.5e+03      67      82 ..     575     590 ..     558     626 .. 0.62

  Alignments for each domain:
  == domain 1  score: 61.5 bits;  conditional E-value: 1.8e-20
                                    HHHHSTEEEEEEEETTG-TTTSHHHHHHHHHHHHHTTHSHCEEEEESSGGEETTTCCC.S-HHHHHHHHHHCT--TTEEE CS
                            GAD   3 ealksggsvkalrvpggaaklsrkeideleefakelgakglawikvegegltgpiakf.lteeevkklleavgaeegDil 81 
                                    +al+ gg+  alr++g +a+l ++e+++++++++el++++++w +v+g +++++++++ +++eev+ +++a+g+e+gD++
  gi|119719277|ref|YP_919772.1| 297 KALEAGGRALALRLKG-FAGLLGREVQPGRRLGTELSDRAKYWGRVGGLFHSDELPAYgISQEEVEAVKQALGVEQGDAF 375
                                    7899************.8************************************************************** PP

                                    EEEEEEHHHHHH CS
                            GAD  82 lfvAdkkktvnk 93 
                                    +++ d+ +++ +
  gi|119719277|ref|YP_919772.1| 376 ILIFDEPEKALR 387
                                    ***999888765 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.8
                                    HHHHHHCT--TTEEEE CS
                            GAD  67 kklleavgaeegDill 82 
                                    + +++ v ae+ D +l
  gi|119719277|ref|YP_919772.1| 575 RAMIREVIAENKDYVL 590
                                    3344444444444333 PP

>> YqeY  Yqey-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   1.0   1.1e-10   3.9e-07      69     143 .]     547     625 ..     488     625 .. 0.76

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 1.1e-10
                                    -HHHHHHHHHHHHHHGGGS-----HHHHHHHHHHHHHHT....T--BGGGHHHHHHHHHHHHTTTS-HHHHHHHHHHH- CS
                           YqeY  69 RedlaekekaEievleeYlPeqlseeeiealvkeaiaev....gaesmkdmGkvmkalkpkvkGkaDgkkvsalvkekL 143
                                    Re   + e++  +vl++   e+++ ++++a+++e+iae      ++  k++Gk+m+++++kv+G++Dg+ v +++ke+L
  gi|119719277|ref|YP_919772.1| 547 RELALNPEEQLENVLRRIGIERIDVDRLRAMIREVIAENkdyvLQKREKAFGKLMGVVMDKVRGRIDGSVVAKVLKEEL 625
                                    5555566666667888888899999************98332245699****************************987 PP

>> MDMPI_N  Mycothiol maleylpyruvate isomerase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.3   0.00013      0.47      82     115 ..     381     415 ..     378     429 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00013
                        MDMPI_N  82 apeallaafraavtrlaaalaalppdaiadrl.gi 115
                                    +pe  l  +raa++r+++al+ +pp+ +a++  g+
  gi|119719277|ref|YP_919772.1| 381 EPEKALRGLRAAYERALEALEGVPPETRAANPdGT 415
                                    79999************************998443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (632 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       632  (0.0352502); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.49
# Mc/sec: 3854.49
//
Query:       gi|119719278|ref|YP_919773.1|  [L=451]
Description: glutamyl-tRNA(Gln) amidotransferase subunit D [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.7e-58  195.6   0.1    9.4e-58  194.9   0.1    1.3  1  Asparaginase    Asparaginase, N-terminal
      7e-37  126.1   0.1    8.5e-36  122.6   0.0    2.6  3  Asparaginase_C  Glutaminase/Asparaginase C-terminal domain
      4e-19   67.7   0.0    8.1e-19   66.7   0.0    1.6  1  GatD_N          GatD N-terminal domain


Domain annotation for each model (and alignments):
>> Asparaginase  Asparaginase, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  194.9   0.1   1.6e-61   9.4e-58       1     179 [.     100     287 ..     100     299 .. 0.96

  Alignments for each domain:
  == domain 1  score: 194.9 bits;  conditional E-value: 1.6e-61
                                    EEEEEEEESGGGEEECTTS--CCEES-HHHHHCCTTTCCCCSEEEEEEEEEE-GGG--HHHHHHHHHHHHHHC.CT..-S CS
                   Asparaginase   1 kvlvlatGGTiasekdesggalapalsaeellealpelekiaeleseqlanidSsnmtpadwlklaeaieeal.ee..yd 77 
                                    +v++++tGGTias++d+ +ga+ p ++aeel++++pel+++a+++se l++i S++mtp++w++la++i e + +e  ++
  gi|119719278|ref|YP_919773.1| 100 RVFFVGTGGTIASRVDYVTGAVYPYFTAEELYSMIPELKRLARISSETLFSIFSEDMTPSHWQQLASKIGEIFrREsdVK 179
                                    6999*******************************************************************9984458** PP

                                    EEEEE--STTHHHHHHHHHHHEES.SSEEEEE--SS-TTSTT-SHHHHHHHHHHHHHCGGTTSECEEEETTE.......E CS
                   Asparaginase  78 gfVvlhGTDTlaytAsaLslmlknldkpvvltGsqrplselrsDgpeNlldAllvaasseriagvlvvfngk.......l 150
                                    g+Vv+hGTDTl+y+A+a+++++++++ p+v++G+qr++++++sD++ N+++A +va +  ++a+ +++++g+       +
  gi|119719278|ref|YP_919773.1| 180 GVVVAHGTDTLHYSAAAMAFAVQEAPGPIVFVGAQRSSDRPSSDAALNVIGATVVAVHA-PFAESVIAMHGSvnddtilV 258
                                    ***********************************************************.******************** PP

                                    EETTTEEE-BSSSSS-EEETTT--SEEEE CS
                   Asparaginase 151 lranrvtKvhtssldaFespnlgplaeve 179
                                    +r+ r++K+hts++daF s+n +p+aev+
  gi|119719278|ref|YP_919773.1| 259 HRGVRARKMHTSRRDAFMSINSKPIAEVD 287
                                    **************************994 PP

>> Asparaginase_C  Glutaminase/Asparaginase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       0.7   4.2e+03      16      31 ..      21      36 ..      12      37 .. 0.76
   2 ?    0.1   0.0      0.15   9.1e+02      21      54 ..     175     208 ..     117     270 .. 0.65
   3 !  122.6   0.0   1.4e-39   8.5e-36       1     114 []     316     429 ..     316     429 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.7
                                   HHHHHHTT--EEEEEE CS
                 Asparaginase_C 16 lkallkkgakGvvleg 31
                                   ++ +  k+a+G+vleg
  gi|119719278|ref|YP_919773.1| 21 FDRVKIKLADGLVLEG 36
                                   555555799*****98 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.15
                                    HTT--EEEEEEBTTTB--HHHHHHHHHHHTTT-E CS
                 Asparaginase_C  21 kkgakGvvlegtGvGnlpsallealkeakargiv 54 
                                    ++ +kGvv++ +  +   sa   a+++  a g +
  gi|119719278|ref|YP_919773.1| 175 ESDVKGVVVAHGTDTLHYSAAAMAFAVQEAPGPI 208
                                    5677788877766665555555555444444444 PP

  == domain 3  score: 122.6 bits;  conditional E-value: 1.4e-39
                                    -EEEEE--TT--HHHHHHHHHTT--EEEEEEBTTTB--HHHHHHHHHHHTTT-EEEEEESSSBS-----H.....HHHHH CS
                 Asparaginase_C   1 rVvvlklhpgmdtkvlkallkkgakGvvlegtGvGnlpsallealkeakargivvvatsqcpsgsvsnseyeagkelerl 80 
                                    +V+++k++pgm++++++ +l+kg kG+v+egtG G++++al++ +++++++g+ v ++sqc++g+v++++y +g el ++
  gi|119719278|ref|YP_919773.1| 316 KVALVKFYPGMSPDIFDFYLEKGFKGLVIEGTGLGHVSTALIDSVRRLVREGVFVAMASQCIFGRVNMNVYRTGVELIKA 395
                                    7******************************************************************************* PP

                                    TEEE-TT--HHHHHHHHHHHCTT---HHHHHHHH CS
                 Asparaginase_C  81 gvisaddmtpeaarikLmlllgkgldpaevrklf 114
                                    gv+ a+dm pe+a++kL ++lg+++dp+e+++lf
  gi|119719278|ref|YP_919773.1| 396 GVVPAGDMIPETAYVKLSWILGQTEDPEEIQRLF 429
                                    *********************************9 PP

>> GatD_N  GatD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.7   0.0   1.4e-22   8.1e-19       2      55 .]      19      73 ..      18      73 .. 0.96

  Alignments for each domain:
  == domain 1  score: 66.7 bits;  conditional E-value: 1.4e-22
                                   -TT-EEEEE-SS.-EEEEEE----TTS-SSEEEEEETTS-EEEEE-TT-.---EE CS
                         GatD_N  2 evGDlikvekkg.reyeGilmPrselsdddiivlKLdnGYNiGikieeiekiell 55
                                   + +D++k++  +  ++eG+lmPr+ ++d+d++vlKLdnGYNiGi+ ++i ++ell
  gi|119719278|ref|YP_919773.1| 19 AFFDRVKIKLADgLVLEGLLMPRPAFGDPDVVVLKLDNGYNIGISLQRIVSVELL 73
                                   679*******999****************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 3120.30
//
Query:       gi|119719279|ref|YP_919774.1|  [L=49]
Description: 30S ribosomal protein S30e [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-10   40.7   1.2    2.2e-10   40.5   1.2    1.0  1  Ribosomal_S30  Ribosomal protein S30


Domain annotation for each model (and alignments):
>> Ribosomal_S30  Ribosomal protein S30
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.5   1.2   1.2e-14   2.2e-10       3      44 ..       4      44 ..       3      49 .] 0.88

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 1.2e-14
                                   BX-STTTTHHHHHS-------------THHHHHHHHHHHTTS CS
                  Ribosomal_S30  3 hGsLarAGKVrnqTPKveKqekkKkptGRakkRlqYnrRfvn 44
                                   hGsL++AGKVrn TPK+  +  kK+   R +    Y rR   
  gi|119719279|ref|YP_919774.1|  4 HGSLTKAGKVRNATPKIPPK-PKKNLIPRRRNYRNYRRRILY 44
                                   ******************99.88989889888889***9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      184  (0.0102627); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 373.61
//
Query:       gi|119719280|ref|YP_919775.1|  [L=124]
Description: hypothetical protein Tpen_0363 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.5e-48  161.9   0.2    8.9e-48  161.6   0.2    1.1  1  Ribonucleas_3_2  Ribonuclease III


Domain annotation for each model (and alignments):
>> Ribonucleas_3_2  Ribonuclease III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.6   0.2     5e-52   8.9e-48       1     119 []      16     123 ..      16     123 .. 0.99

  Alignments for each domain:
  == domain 1  score: 161.6 bits;  conditional E-value: 5e-52
                                    HHHHHHHHHHHHHHHHHHHHHHHTS-------HHHHHHHHHHTTGGGCS-.CGGCCGHHHHHHHHHHHHHHTTSS-HHHH CS
                Ribonucleas_3_2   1 kglaklGdslinllvslaltellGkPtGervPnaslaialelaglskllkprvdkhakGdiaeallayaWlkgkisieea 80 
                                    k+la+lGdsl+n+lvs+alt l+G+PtG++vP+++la+a+ +++lskl+kpr  ++a+G+++ea+layaWlkg++s+ee+
  gi|119719280|ref|YP_919775.1|  16 KELARLGDSLVNFLVSAALT-LIGRPTGVKVPGETLARAFLSSRLSKLGKPR--GIAPGEAMEAFLAYAWLKGSLSCEES 92 
                                    89******************.*******************************..************************** PP

                                    HHHHHCT--GGGG-TTTHHHHHHHHHHHHHHHHHHHHHT CS
                Ribonucleas_3_2  81 veilkknlddevldfsrkkeaigkalaklleeiserlea 119
                                    ve+l+++l        r+++++++alakl+++++e++ea
  gi|119719280|ref|YP_919775.1|  93 VEMLYTGL--------REGYDVAQALAKLADYLLEKIEA 123
                                    ********........********************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 883.47
//
Query:       gi|119719281|ref|YP_919776.1|  [L=101]
Description: Fis family transcriptional regulator [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.4e-17   62.5   0.1    3.7e-17   61.9   0.0    1.3  2  RNA_pol_L_2  RNA polymerase Rpb3/Rpb11 dimerisation domain
    5.8e-07   28.8   0.0      3e-06   26.6   0.0    2.0  2  RNA_pol_L    RNA polymerase Rpb3/Rpb11 dimerisation domain


Domain annotation for each model (and alignments):
>> RNA_pol_L_2  RNA polymerase Rpb3/Rpb11 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0      0.74   6.6e+03      23      33 ..      10      20 ..       7      22 .. 0.61
   2 !   61.9   0.0   4.1e-21   3.7e-17       2      73 ..      24      94 ..      23      96 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.74
                                   TSTTEEEEEEE CS
                    RNA_pol_L_2 23 knpsVefagYk 33
                                   ++  Ve+++Y+
  gi|119719281|ref|YP_919776.1| 10 EDTVVEVVRYA 20
                                   45556777775 PP

  == domain 2  score: 61.9 bits;  conditional E-value: 4.1e-21
                                   EEEEEES--HHHHHHHHHHHTTSTTEEEEEEECSSTTTSEEEEEEEESTSS-HHHHHHHHHHHHHHHHHHHH CS
                    RNA_pol_L_2  2 ltfeingEDhTLgnlLrhlllknpsVefagYkipHPlepkmnlriqtkssnnpleaLkkalkdlldicdele 73
                                   l++ i gE hTL+nlL ++l++ p+Ve+ +Y+++HPl +  +l + tk+s++plea+++a+++l+++++ + 
  gi|119719281|ref|YP_919776.1| 24 LELRIRGEGHTLLNLLVDELNRIPDVEA-TYRVDHPLLNVAHLLVRTKGSKQPLEAIREAVESLRAKLKVVA 94
                                   6899***********************7.5**********************************99988765 PP

>> RNA_pol_L  RNA polymerase Rpb3/Rpb11 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0     0.054   4.9e+02      47      66 ..       2      25 ..       1      27 [. 0.77
   2 !   26.6   0.0   3.3e-10     3e-06       2      69 .]      26      90 ..      25      90 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.054
                                   xxxxxx....xxxxxxxxxxxxxx RF
                      RNA_pol_L 47 etdgsl....kPeealkeAlkiLk 66
                                   +++g +    ++ e++++A ++L+
  gi|119719281|ref|YP_919776.1|  2 QSTGGVaredTVVEVVRYATNVLE 25
                                   566666677788999999999985 PP

  == domain 2  score: 26.6 bits;  conditional E-value: 3.3e-10
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      RNA_pol_L  2 fllrgvdhtlgNaLRrillsevpgvaiea.......pvvkvntdkdklilevetdgslkPeealkeAlkiLkekl 69
                                     +rg++htl N L   l   +p+v+ +         v          +l v t+gs +P ea++eA++ L++kl
  gi|119719281|ref|YP_919776.1| 26 LRIRGEGHTLLNLLVDELN-RIPDVEATYrvdhpllNV---------AHLLVRTKGSKQPLEAIREAVESLRAKL 90
                                   579****************.*********777755555.........89999999*****************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       609  (0.0339673); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 689.09
//
Query:       gi|119719282|ref|YP_919777.1|  [L=161]
Description: putative RNA methylase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-09   37.1   0.0    5.4e-09   36.6   0.0    1.1  1  Methyltransf_25  Methyltransferase domain
    3.7e-08   33.3   0.0    4.4e-08   33.0   0.0    1.1  1  Methyltransf_31  Methyltransferase domain
    4.5e-06   26.2   0.0    5.2e-06   25.9   0.0    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
    1.1e-05   25.1   0.1    0.00019   21.0   0.1    2.3  1  DOT1             Histone methylation protein DOT1
    1.7e-05   25.4   0.0    2.3e-05   25.0   0.0    1.2  1  Methyltransf_11  Methyltransferase domain
    6.6e-05   22.8   0.0    9.1e-05   22.3   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
     0.0001   21.9   0.0    0.00015   21.3   0.0    1.3  1  Methyltransf_4   Putative methyltransferase
     0.0002   20.9   0.0    0.00025   20.5   0.0    1.0  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    0.00049   19.5   0.0    0.00061   19.2   0.0    1.1  1  Methyltransf_2   O-methyltransferase domain
     0.0018   17.9   0.0     0.0039   16.8   0.0    1.5  2  Methyltransf_15  RNA cap guanine-N2 methyltransferase
     0.0037   17.0   0.2       0.37   10.4   0.2    2.2  1  UPF0020          Putative RNA methylase family UPF0020
     0.0044   16.9   0.0     0.0051   16.7   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
     0.0058   16.4   0.0     0.0081   15.9   0.0    1.1  1  N6_N4_Mtase      DNA methylase
  ------ inclusion threshold ------
      0.015   14.9   0.0      0.018   14.6   0.0    1.2  1  MetW             Methionine biosynthesis protein MetW
      0.076   12.3   0.0      0.088   12.1   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.0   4.5e-12   5.4e-09       2      90 ..      31     117 ..      30     121 .. 0.93

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 4.5e-12
                                    EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEEESTGGGSSH CS
                Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvssgalhhlsd 79 
                                    Ld GcG Gr +  ++k++g ak +g++i  ++le+a +++ e+g+  nv +v+g++ +++f++   D+v++ + l  +++
  gi|119719282|ref|YP_919777.1|  31 LDPGCGDGRSLVIASKEFG-AKAVGIEIRRDLLEQAMKNVIEAGVsgNVVLVNGSFFEVKFPK--ADVVFL-YLLTSVNE 106
                                    99****************8.*************************999*************97..9*****.78899999 PP

                                    HHHHHHHHHHH CS
                Methyltransf_25  80 edlekalkeia 90 
                                    +  +k+l+e++
  gi|119719282|ref|YP_919777.1| 107 KLKPKLLSELK 117
                                    99999999986 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.0   3.7e-11   4.4e-08       3     119 ..      26     134 ..      24     157 .. 0.78

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 3.7e-11
                Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieeleklledekfDlilsn 81 
                                    +g  +lD+GCG G+ +  + +e   +a+ vGi+i  + +e+A +n  + g++ nv +  g+++e +  +   k D+++  
  gi|119719282|ref|YP_919777.1|  26 SGELFLDPGCGDGRSLVIASKEF--GAKAVGIEIRRDLLEQAMKNVIEAGVSgNVVLVNGSFFEVK--FP--KADVVFL- 98 
                                    66778*********999888775..5899***********************************99..77..6***999. PP

                Methyltransf_31  82 evlnaladpdkile.eiervlkpggilliedprllaelp 119
                                       ++l++ ++ l+ ++ + lkp +++++ d+ +  + p
  gi|119719282|ref|YP_919777.1|  99 ---YLLTSVNEKLKpKLLSELKPSTRIVSHDFEITGWRP 134
                                    ...444444444444778889999999999988544444 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   4.4e-09   5.2e-06      51     121 ..      15      85 ..      11     120 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 4.4e-09
                                    HHHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-G CS
                           CMAS  51 ldlileklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldy 121
                                    ++ +le ++lk G+  Ld GcG G  ++ a +++++k vg+ + ++  ++a k+v e++++ +v +    +
  gi|119719282|ref|YP_919777.1|  15 IRKALEIAGLKSGELFLDPGCGDGRSLVIASKEFGAKAVGIEIRRDLLEQAMKNVIEAGVSGNVVLVNGSF 85 
                                    678999***********************************************999999887766555555 PP

>> DOT1  Histone methylation protein DOT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.1   1.6e-07   0.00019      29     157 ..      13     125 ..       7     157 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.6e-07
                                    HHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHH--SEEEEEE--HHHHHHHHHHHHHHHHHHHHTTB----EEEESS CS
                           DOT1  29 eflsevldkvnlkkedvFvDLGSGvGnvvlqaalevgcklsvGvEimdnaselaekqkeelkkrlklfGkklakiefirk 108
                                    e++ + l+   lk+ ++F+D G G G+  + a+ e+g k +vG+Ei  +  e a k+  e  +     G+  +++ ++++
  gi|119719282|ref|YP_919777.1|  13 EVIRKALEIAGLKSGELFLDPGCGDGRSLVIASKEFGAK-AVGIEIRRDLLEQAMKNVIE--A-----GV-SGNVVLVNG 83 
                                    66777888899***************************9.9*****99886655544433..3.....44.467889999 PP

                                    -STT-HHHHHHGGG-SEEEE--TT--HHHHHHH.HHHHTT--TT-EEEES CS
                           DOT1 109 sFvenekveeiieeadvilvNNfaFdaelnkql.kellqdlkegtkiisl 157
                                    sF e +      ++adv++       +++n++l  +ll +lk  t+i+s 
  gi|119719282|ref|YP_919777.1|  84 SFFEVK-----FPKADVVFL---YLLTSVNEKLkPKLLSELKPSTRIVSH 125
                                    998765.....488999997...344678999955899999999999985 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   1.9e-08   2.3e-05       1      70 [.      31     101 ..      31     121 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.9e-08
                                    EEET-TTSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEEEEES- CS
                Methyltransf_11   1 LdvGcGtGrlaealakrg.arvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlvvssev 70 
                                    Ld GcG Gr +    k + a+ vg+++   +l++a +++ e+g+  +v +v +++ +++f++   D+v+++  
  gi|119719282|ref|YP_919777.1|  31 LDPGCGDGRSLVIASKEFgAKAVGIEIRRDLLEQAMKNVIEAGVsgNVVLVNGSFFEVKFPK--ADVVFLYLL 101
                                    8**************6666************************9**9**************9..999998863 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   7.6e-08   9.1e-05      61     131 ..      14      83 ..       2      98 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 7.6e-08
                                    HHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTC.SEEEEES CS
                           PCMT  61 mvalalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldle.nvivvvg 131
                                    ++ +ale   lk g+  L+ G+G G   ++ ++ +g+k+  v+ie  ++l e+a +n+ + +++ nv++v g
  gi|119719282|ref|YP_919777.1|  14 VIRKALEIAGLKSGELFLDPGCGDGRSLVIASKEFGAKA--VGIEIRRDLLEQAMKNVIEAGVSgNVVLVNG 83 
                                    4567899999**************************999..*****************99999888887765 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   1.2e-07   0.00015       3      59 ..      28      84 ..      26     101 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.2e-07
                                   EEEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTS.SEEEEES- CS
                 Methyltransf_4  3 pvvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelk.Nlrilrgd 59
                                    ++l+ GcG G++lv  +k++   + +GiEir++++++++k++ + +++ N+ +++g 
  gi|119719282|ref|YP_919777.1| 28 ELFLDPGCGDGRSLVIASKEFG-AKAVGIEIRRDLLEQAMKNVIEAGVSgNVVLVNGS 84
                                   579999********97666665.6689***************9999775477776654 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   2.1e-07   0.00025     159     257 ..      24     123 ..      15     125 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.1e-07
                           PrmA 159 vkegeevlDvGtGSG.iLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellk..eekadvivaNIL 235
                                    +k+ge +lD G+G G  L ia++ +gak +v++ i    ++ a +N+   +v+ ++ v ++++ ++    kadv++   L
  gi|119719282|ref|YP_919777.1|  24 LKSGELFLDPGCGDGrSLVIASKEFGAK-AVGIEIRRDLLEQAMKNVIEAGVSGNV-VLVNGSFFEvkFPKADVVFLYLL 101
                                    6889999*******956*********97.67***********************99.556666664336789******** PP

                           PrmA 236 aevlielaedikklvkegglli 257
                                     +v  +l +++ + +k++++++
  gi|119719282|ref|YP_919777.1| 102 TSVNEKLKPKLLSELKPSTRIV 123
                                    *****************99876 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   5.1e-07   0.00061      52     134 ..      16      99 ..      12     121 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 5.1e-07
                                    HHHHHSS-GGG-SEEEEET-TTSHHHHHHHHH-TT-EEEEEE-HHHHHHHHHHS.-----TTEEEEES-TTTS-----SE CS
                 Methyltransf_2  52 kkvleafdleglkslvDvGGGtGalakaivsayPtikvivfDlpeVveaAkehl.sageeervefvgGdffkdslPeaDa 130
                                    +k+le   l++ + ++D G G G  +  +++ +    v +    +  e+A + + +ag + +v  v+G+ff+ + P+aD+
  gi|119719282|ref|YP_919777.1|  16 RKALEIAGLKSGELFLDPGCGDGRSLVIASKEFGAKAVGIEIRRDLLEQAMKNViEAGVSGNVVLVNGSFFEVKFPKADV 95 
                                    6777777788888899999999999998888886655544444578888877777************************* PP

                                    EEEE CS
                 Methyltransf_2 131 illk 134
                                    ++l 
  gi|119719282|ref|YP_919777.1|  96 VFLY 99 
                                    9985 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   3.3e-06    0.0039       3      76 ..      29      97 ..      27     125 .. 0.79
   2 ?   -1.6   0.0       1.5   1.8e+03     144     162 ..     135     153 ..     105     155 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.3e-06
                Methyltransf_15  3 vilDlfsGaGGn.viqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklklekikvdlvf 76
                                   + lD+ +G G   vi+ ++ + k ++iei ++ l++a +N    gvs ++ lv g++fe+    k+ k+  d+vf
  gi|119719282|ref|YP_919777.1| 29 LFLDPGCGDGRSlVIASKEFGAKAVGIEIRRDLLEQAMKNVIEAGVSGNVVLVNGSFFEV----KFPKA--DVVF 97
                                   67999999997724555555789***********************************82....33333..3333 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.5
                Methyltransf_15 144 vkvveikenglvkallayl 162
                                    v+v +++e g+++ +++y+
  gi|119719282|ref|YP_919777.1| 135 VEVYNLEEGGRSHRIYYYV 153
                                    6688888889988888886 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.2   0.00031      0.37      21     102 ..      19      75 ..      16      97 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00031
                                    HHHTT--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--EEEEES-HHHHHHHHHHHHHTT CS
                        UPF0020  21 vrlagwkpgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelklygsDldrrvvqgareNaekag 100
                                    +++ag+k ge +lDP CG G  l+ a       a                         +g+++ r ++++a +N  +ag
  gi|119719282|ref|YP_919777.1|  19 LEIAGLKSGELFLDPGCGDGRSLVIASKEFGAKA-------------------------VGIEIRRDLLEQAMKNVIEAG 73 
                                    5688999999999999998865554443332222.........................344444444444444444444 PP

                                    -G CS
                        UPF0020 101 vg 102
                                    v+
  gi|119719282|ref|YP_919777.1|  74 VS 75 
                                    44 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   4.2e-06    0.0051       8      60 ..      13      65 ..       7     132 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.2e-06
                Methyltransf_23  8 elsdklerllpklraggrvLdiGcGtGillevl.rengfsvtgvDlspeaveia 60
                                   e+ +k +++++ l++g   Ld GcG+G+ l ++ +e+g++ +g+++++ + e a
  gi|119719282|ref|YP_919777.1| 13 EVIRKALEIAG-LKSGELFLDPGCGDGRSLVIAsKEFGAKAVGIEIRRDLLEQA 65
                                   55556666776.8999999********888888577799*******98776655 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   6.8e-06    0.0081     176     230 ..      10      66 ..       8      67 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 6.8e-06
                                    --HHHHHHHHH.HHS-TT-EEEETT-TTTHH.HHHHHHTT-EEEEEESSHHHHHHHH CS
                    N6_N4_Mtase 176 kPvallerlIk.lstkkgdivlDpFaGSGtT.avaakelgrkfiGieieeeyvelae 230
                                     P + ++++++ + +k g++ lDp +G G   ++a ke g k++Giei +  +e+a+
  gi|119719282|ref|YP_919777.1|  10 SPYEVIRKALEiAGLKSGELFLDPGCGDGRSlVIASKEFGAKAVGIEIRRDLLEQAM 66 
                                    58888999996246778************7615667889***********9999886 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.5e-05     0.018      12      57 ..      25      70 ..      15      99 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.5e-05
                           MetW 12 kpgsrvldlGcGdGellellkeekqvdgrGleldeegvaecvakGl 57
                                   k+g   ld GcGdG  l +  +e + ++ G+e+ ++ + ++++  +
  gi|119719282|ref|YP_919777.1| 25 KSGELFLDPGCGDGRSLVIASKEFGAKAVGIEIRRDLLEQAMKNVI 70
                                   5566789***************************999998887644 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   7.4e-05     0.088      40     114 ..      19      92 ..      13     123 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.4e-05
                                    HHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSS.TEEEEE--TTT-TTS- CS
                Ubie_methyltran  40 eklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegki.nieflqanaeeLpfed 114
                                     ++ + k+g+ +lD  +G g   +  s++ g+  k v+++i  ++L+++ k + e g++ n+ +++++  e++f +
  gi|119719282|ref|YP_919777.1|  19 LEIAGLKSGELFLDPGCGDGRSLVIASKEFGA--KAVGIEIRRDLLEQAMKNVIEAGVSgNVVLVNGSFFEVKFPK 92 
                                    57888999*******99999877776776665..679*********************99*******999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1009.26
//
Query:       gi|119719283|ref|YP_919778.1|  [L=154]
Description: AsnC family transcriptional regulator [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.1e-08   32.5   0.2    9.9e-08   31.8   0.2    1.4  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
    6.5e-08   32.4   0.0    2.9e-07   30.3   0.0    1.8  2  MarR_2          MarR family
    1.1e-06   28.1   0.2    2.4e-06   27.0   0.2    1.6  1  HTH_24          Winged helix-turn-helix DNA-binding
    2.3e-05   24.3   0.1      4e-05   23.5   0.1    1.4  1  HTH_Crp_2       Crp-like helix-turn-helix domain
    0.00039   20.2   0.5    0.00073   19.4   0.1    1.7  2  HTH_5           Bacterial regulatory protein, arsR family
      0.001   19.1   0.0     0.0017   18.4   0.0    1.4  1  HTH_20          Helix-turn-helix domain
     0.0017   18.3   0.3     0.0063   16.4   0.3    2.1  2  HTH_11          HTH domain
     0.0026   17.6   0.1        0.2   11.6   0.0    3.0  3  TrmB            Sugar-specific transcriptional regulator TrmB
      0.007   16.5   0.5       0.02   15.1   0.1    2.0  2  HTH_34          Winged helix DNA-binding domain
     0.0099   16.2   0.0      0.037   14.4   0.0    1.8  2  Rrf2            Transcriptional regulator
  ------ inclusion threshold ------
      0.016   15.0   0.8       0.41   10.5   0.1    2.4  2  HTH_10          HTH DNA binding domain
      0.038   13.9   0.1      0.082   12.9   0.0    1.5  2  AbiEii          Nucleotidyl transferase AbiEii toxin, Type IV
      0.072   12.9   0.6       0.29   11.0   0.6    1.9  1  LexA_DNA_bind   LexA DNA binding domain
       0.15   12.0   0.0       0.23   11.5   0.0    1.4  1  HTH_36          Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.2   7.7e-11   9.9e-08       2      74 ..      87     151 ..      86     152 .. 0.90

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 7.7e-11
                                    EEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEE CS
                 AsnC_trans_reg   2 lvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivle 74 
                                     v+l p +     ++ e +++lp V  +yrvtGd d++++   ++ + l+++l++ ++s++gv++t+t++++e
  gi|119719283|ref|YP_919778.1|  87 FVKLHPTK---RLQAYEIIKTLP-VDRVYRVTGDIDLIIQ---ASQAMLDEILDK-INSIEGVKETKTYVIIE 151
                                    57777777...778888999999.****************...8999*****999.**************998 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.0   2.3e-10   2.9e-07       2      55 ..       5      64 ..       4      68 .. 0.93
   2 ?   -0.6   0.0         1   1.3e+03      13      35 ..      87     109 ..      82     115 .. 0.78

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 2.3e-10
                                   T--HHHHHHHHHHHCTTTS.......EEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                         MarR_2  2 gltpaqarvLaaLgrrpgr.......dltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                   glt  q  ++ +L rr  +       d t++ +  +lg+s++a++ +lk+L +aG++++ +
  gi|119719283|ref|YP_919778.1|  5 GLTEKQVELIRHLFRRSKPlrvftvtD-TQQKISLELGISRQALNIHLKKLKEAGYIRTGR 64
                                   89999999*********99*9998877.******************************976 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1
                                    HHHCTTTSEEEHHHHHHHHTSSH CS
                         MarR_2  13 aLgrrpgrdltvgelarrlglsk 35 
                                    ++  +p ++l + e+ ++l +++
  gi|119719283|ref|YP_919778.1|  87 FVKLHPTKRLQAYEIIKTLPVDR 109
                                    56678888999999999999887 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.2   1.9e-09   2.4e-06      19      48 .]      32      61 ..      32      61 .. 0.97

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 1.9e-09
                         HTH_24 19 sqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                   +q+ ++ +lg+S++++n +lk+L+e+G+I+
  gi|119719283|ref|YP_919778.1| 32 TQQKISLELGISRQALNIHLKKLKEAGYIR 61
                                   89***************************7 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.1   3.1e-08     4e-05      16      56 ..      23      65 ..      11      71 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 3.1e-08
                                   C..EEEEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETEE CS
                      HTH_Crp_2 16 g..eielpltqeelAsmlGltretvsrilseLkreglisrgrr 56
                                       +++  tq+ ++  lG++r+ ++  l++Lk++g+i++gr+
  gi|119719283|ref|YP_919778.1| 23 PlrVFTVTDTQQKISLELGISRQALNIHLKKLKEAGYIRTGRG 65
                                   244678888******************************8864 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       4.2   5.4e+03       2      14 ..       8      20 ..       7      26 .. 0.66
   2 !   19.4   0.1   5.7e-07   0.00073      21      46 ..      36      61 ..      32      62 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 4.2
                                   HHHHHHHHHHTTS CS
                          HTH_5  2 ptRlkILklLaeg 14
                                   ++++++++ L ++
  gi|119719283|ref|YP_919778.1|  8 EKQVELIRHLFRR 20
                                   5777888777773 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 5.7e-07
                                   HHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_5 21 laeelglsqstvShHLkkLreaGLVe 46
                                   ++ elg+s+ ++  HLkkL+eaG+++
  gi|119719283|ref|YP_919778.1| 36 ISLELGISRQALNIHLKKLKEAGYIR 61
                                   899*********************97 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.3e-06    0.0017      31      58 ..      33      64 ..       8      66 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.3e-06
                                   HHHH....TS-HHHHHHHHHHHHHCTTEEEEC CS
                         HTH_20 31 aerl....dlskntlsyHLrvLeeagLvevvr 58
                                    + +    ++s++ l+ HL++L eag++++ r
  gi|119719283|ref|YP_919778.1| 33 QQKIslelGISRQALNIHLKKLKEAGYIRTGR 64
                                   555533348*******************9866 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.3   4.9e-06    0.0063      17      44 ..      32      59 ..      30      82 .. 0.85
   2 ?   -3.2   0.0       6.8   8.7e+03      16      27 ..      96     107 ..      89     110 .. 0.62

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 4.9e-06
                         HTH_11 17 sgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                   + ++++ eL++Sr++   ++k+L+e+g+
  gi|119719283|ref|YP_919778.1| 32 TQQKISLELGISRQALNIHLKKLKEAGY 59
                                   6789999********************4 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 6.8
                         HTH_11  16 isgeeLAeeLnv 27 
                                    + + e+ + L v
  gi|119719283|ref|YP_919778.1|  96 LQAYEIIKTLPV 107
                                    666666666655 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   0.00015       0.2      24      54 ..      32      62 ..      26      71 .. 0.91
   2 ?    1.6   0.0       0.2   2.6e+02      14      41 ..      87     112 ..      81     116 .. 0.75
   3 ?    0.1   0.0      0.57   7.3e+02      26      46 ..     133     153 ..     130     154 .] 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00015
                                   HHCHHCCCTTSSCHCHHHHHHHHHHCTSEEE CS
                           TrmB 24 tadeiaeelgvprskvYevLrsLedkGlVer 54
                                   t ++i+ elg++r+  +  L++L+++G++++
  gi|119719283|ref|YP_919778.1| 32 TQQKISLELGISRQALNIHLKKLKEAGYIRT 62
                                   7789************************986 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.2
                                    CHHHHHHCCCHHCHHCCCTTSSCHCHHH CS
                           TrmB  14 YlaLlklgpatadeiaeelgvprskvYe 41 
                                    +++L   ++++a+ei + l v+r  vY+
  gi|119719283|ref|YP_919778.1|  87 FVKLHPTKRLQAYEIIKTLPVDR--VYR 112
                                    55666677889999999998876..565 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.57
                                    CHHCCCTTSSCHCHHHHHHHH CS
                           TrmB  26 deiaeelgvprskvYevLrsL 46 
                                    d+i ++ gv ++k Y +++ L
  gi|119719283|ref|YP_919778.1| 133 DKINSIEGVKETKTYVIIEAL 153
                                    567888899999999999988 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   1.6e-05      0.02      18      50 ..      34      66 ..      27      75 .. 0.87
   2 ?   -2.5   0.0       4.6   5.8e+03      24      46 ..     121     143 ..     116     148 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.6e-05
                         HTH_34 18 velkealeatdgnLsvhlkkLekagYievdkef 50
                                   ++++ +l+++  +L +hlkkL++agYi    +f
  gi|119719283|ref|YP_919778.1| 34 QKISLELGISRQALNIHLKKLKEAGYIRTGRGF 66
                                   67888999*******************987766 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.6
                         HTH_34  24 leatdgnLsvhlkkLekagYiev 46 
                                    ++a+++ L   l+k+++ + ++ 
  gi|119719283|ref|YP_919778.1| 121 IQASQAMLDEILDKINSIEGVKE 143
                                    56666666666666666555555 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   2.9e-05     0.037      29      60 ..      34      65 ..      28      66 .. 0.93
   2 ?   -2.0   0.0       3.8   4.8e+03      14      41 ..      85     111 ..      78     112 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.9e-05
                                   HHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT CS
                           Rrf2 29 eeiaerqnispsylekilakLrkaglvksvrG 60
                                   ++i+ + +is++ l   l+kL++ag++++ rG
  gi|119719283|ref|YP_919778.1| 34 QKISLELGISRQALNIHLKKLKEAGYIRTGRG 65
                                   78999************************999 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.8
                                    HHHHHHSSTCC-B-HHHHHHHHTS-HHH CS
                           Rrf2  14 llyLakeeeeepvsseeiaerqnispsy 41 
                                     ++ +++++++ +++ ei +   + ++y
  gi|119719283|ref|YP_919778.1|  85 FIFVKLHPTKR-LQAYEIIKTLPVDRVY 111
                                    56677777777.8888887777776665 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.083   1.1e+02       1      11 [.       6      16 ..       6      19 .. 0.90
   2 ?   10.5   0.1   0.00032      0.41      27      47 ..      34      54 ..      30      57 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.083
                         HTH_10  1 LTdkqlevlkl 11
                                   LT+kq+e +++
  gi|119719283|ref|YP_919778.1|  6 LTEKQVELIRH 16
                                   9******9986 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00032
                         HTH_10 27 keLAkelGIskstlsehLrka 47
                                   ++++ elGIs+++l  hL+k 
  gi|119719283|ref|YP_919778.1| 34 QKISLELGISRQALNIHLKKL 54
                                   78999*************985 PP

>> AbiEii  Nucleotidyl transferase AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       3.7   4.7e+03      95     108 ..      29      42 ..       4      54 .. 0.62
   2 ?   12.9   0.0   6.4e-05     0.082      29      68 ..     109     146 ..     105     153 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3.7
                         AbiEii  95 ggyarqkikieigf 108
                                        +qki +e+g+
  gi|119719283|ref|YP_919778.1|  29 VTDTQQKISLELGI 42 
                                    34556666666654 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 6.4e-05
                         AbiEii  29 lipRfSeDIDlsllrgdrkellealkealeeiaaalaeeg 68 
                                    + +R + DIDl +  + ++++l+++ + ++ i +  + + 
  gi|119719283|ref|YP_919778.1| 109 RVYRVTGDIDLII--QASQAMLDEILDKINSIEGVKETKT 146
                                    579**********..***************9999887765 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.6   0.00022      0.29       2      58 ..       4      62 ..       3      65 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00022
                                   X---HHHHHHHHHH.HHH..HHHHSS---HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE- CS
                  LexA_DNA_bind  2 kkLTerQrevldli.kas..ieetgypPsireiaralglkSpsaveehLkaLerKGyier 58
                                   ++LTe+Q e+++ + ++s  +       +   i+ +lg++  +a + hLk+L+  Gyi+ 
  gi|119719283|ref|YP_919778.1|  4 EGLTEKQVELIRHLfRRSkpLRVFTVTDTQQKISLELGIS-RQALNIHLKKLKEAGYIRT 62
                                   5688888888876623331244445566788899999996.9****************96 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00018      0.23      27      55 .]      32      60 ..       6      60 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00018
                         HTH_36 27 sqetlakrlglsknTvsraikeLeqlGyi 55
                                   +q+ ++  lg+s++    ++k+L ++Gyi
  gi|119719283|ref|YP_919778.1| 32 TQQKISLELGISRQALNIHLKKLKEAGYI 60
                                   6899************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 1055.88
//
Query:       gi|119719284|ref|YP_919779.1|  [L=236]
Description: putative serine/threonine protein kinase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-07   31.2   0.0    1.9e-07   30.7   0.0    1.2  1  Pkinase   Protein kinase domain
    1.5e-06   27.9   0.0    2.3e-06   27.4   0.0    1.3  1  RIO1      RIO1 family
  ------ inclusion threshold ------
      0.011   15.7   0.2        2.4    8.0   0.1    2.1  2  APH       Phosphotransferase enzyme family


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.0   3.2e-11   1.9e-07       4     159 ..      32     179 ..      29     182 .. 0.90

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 3.2e-11
                                    EEEEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHHHHHHHHHHHHHHHSCTTB--EEEEEEESSEEEEEEE--TTE CS
                        Pkinase   4 leklGeGsfGkVykaveketgkivAvKkikkekakkkkekkvlrEikilkklkhpnivrlyevfeekdelylvleyvegg 83 
                                    l+ +G+G+++ V+k++  +++  vAvK+ +++ ++     ++lrE +il+++k   +   +++ +   + +lv ++++g 
  gi|119719284|ref|YP_919779.1|  32 LRVIGKGTTSLVVKGL--ARSGVVAVKIRRTDANRV----SLLREARILESVKELGVGPRIRCAS---RNFLVWDFINGV 102
                                    689*************..7999*****988887665....579**********999888877766...6789******** PP

                                    BHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-.SGGG.EEEE.TTTEEEE-SGTTSEESSSSCSBCTTTS CS
                        Pkinase  84 eladllerkgslseeeakkiakqilegleylHskgiiHrDl.KpeN.iLid.ekgelKitDFGlakelessskltsfvg 159
                                    ++a+++e  ++ s ee++ +++++l+ l  l ++gi+H  l  p+N iL+d e+ e  ++DF  a+  +++s+lt+f+g
  gi|119719284|ref|YP_919779.1| 103 DFAEWVE--KVASREELETVLEKLLTKLFLLDQHGIVHAELsQPSNhILVDlERLEPVLVDFESASLDSQKSNLTQFMG 179
                                    ******8..599*****************************658887999999999**********9999999999876 PP

>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   3.8e-10   2.3e-06      45     149 ..      57     162 ..      43     179 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 3.8e-10
                                    S-HHHHHHHHHHHHHHHHHHHHHTT--S--EEEEETTEEEEE--EETTEEGGB.HHHCG-HHHHHHHHHHHHHHHHHHHH CS
                           RIO1  45 tnprklvklwaekEfrnLkrleeagvpvPkpielkrhvlvmefigedgvaapk.lkdveeeeeaeelyeevleemrklyk 123
                                    + + +  +++  +E r+L+ ++e gv  P+     r+ lv +fi+  gv  ++ +++v ++ee+e+++e++l +   l+ 
  gi|119719284|ref|YP_919779.1|  57 IRRTDANRVSLLREARILESVKELGV-GPRIRCASRNFLVWDFIN--GVDFAEwVEKVASREELETVLEKLLTK-LFLLD 132
                                    555666778889************96.5*****************..777666155555899***********7.56777 PP

                                    TSTEEESS-ST..TSEEEETT..EEEE--G CS
                           RIO1 124 eaglvHaDLSe..yNvlvded..kvviIDv 149
                                    ++g+vHa LS+    +lvd +  ++v++D+
  gi|119719284|ref|YP_919779.1| 133 QHGIVHAELSQpsNHILVDLErlEPVLVDF 162
                                    **********74234777766677888887 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0    0.0014       8.6       2      68 ..      32      95 ..      31     110 .. 0.78
   2 ?    8.0   0.1    0.0004       2.4     144     198 ..     113     167 ..     100     169 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0014
                                   EEEE--.SSCEEEEEEETT--EEEEEE-TTS-HHHHHHHHHHHHHHHHTT-B--B-CTTBS-EEETT CS
                            APH  2 vrelsggasnrtylvttpagryvlrrnpparaaeeirrevallrlLakagvpvPevlagdtddeeig 68
                                   +r+++ g+ + +++    +g +++++ ++  +  ++ re+++l  + ++gv  P++     +++++ 
  gi|119719284|ref|YP_919779.1| 32 LRVIGKGTTSLVVKGLARSGVVAVKIRRTDANRVSLLREARILESVKELGV-GPRIRC--ASRNFLV 95
                                   578888888888888888899*****************************9.777766..3444433 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0004
                                    HHHHHHHHHHHHHHHH--SSS-EEEE-SS-S..GGGEEEC...TTEEEEE---TT-EE CS
                            APH 144 lleeleeqvlaalaallpgelptvllHgDlh..pgNllvd.pddgrvtGviDfedagl 198
                                     +eele  vl++l+  l   ++++++H  l+  ++++lvd ++  +v  ++Dfe a+l
  gi|119719284|ref|YP_919779.1| 113 SREELET-VLEKLLTKLFLLDQHGIVHAELSqpSNHILVDlERLEPV--LVDFESASL 167
                                    4778888.88888888888**********995457999999999999..*****9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1633.36
//
Query:       gi|119719285|ref|YP_919780.1|  [L=467]
Description: tRNA CCA-pyrophosphorylase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-35  120.8   0.0    6.8e-35  119.7   0.0    1.5  1  tRNA_NucTransf2  tRNA nucleotidyltransferase, second domain
    3.9e-10   39.9   0.1    1.3e-09   38.2   0.0    1.9  2  NTP_transf_2     Nucleotidyltransferase domain
     0.0011   19.2   0.0     0.0022   18.2   0.0    1.4  1  SMODS            Second Messenger Oligonucleotide or Dinucleo
  ------ inclusion threshold ------
       0.04   14.0   0.0      0.084   13.0   0.0    1.5  1  Polbeta          Polymerase beta, Nucleotidyltransferase


Domain annotation for each model (and alignments):
>> tRNA_NucTransf2  tRNA nucleotidyltransferase, second domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.7   0.0   1.5e-38   6.8e-35       1     108 [.     169     276 ..     169     279 .. 0.91

  Alignments for each domain:
  == domain 1  score: 119.7 bits;  conditional E-value: 1.5e-38
                                    HHHHHHHHHHHHTT-BSSSTTT-SB-HHHHHHHHHHHSSHHHHHHHHTT--TTEEEE......EEE...-SS-EEEETTE CS
                tRNA_NucTransf2   1 devrllKkflkgigvYGselkvkGfsGYlaEllvleygsfeevleaaakwkpkvvidleekeallkkf.deplvviDPvD 79 
                                    de+rllK++lk++g+YG+e + kGfsGYlaE+lv++y+++e++l++aa+w+p+ v  ++ k+ ll++f  +plvv+DPvD
  gi|119719285|ref|YP_919780.1| 169 DEIRLLKRLLKNLGIYGAEQSLKGFSGYLAEILVVYYDGLEKLLREAARWRPGKVAVPDGKD-LLERFkGQPLVVLDPVD 247
                                    89**************************************************6655344554.57888689********* PP

                                    EEEETTTTS-HHHHHHHHHHHHHHHHS-- CS
                tRNA_NucTransf2  80 pkRNvaaalsleklaefilaareflkkps 108
                                    ++RN+aa++sl++l++filaa++f ++++
  gi|119719285|ref|YP_919780.1| 248 SRRNAAASVSLDSLSKFILAAKMFSEDEN 276
                                    ************************99875 PP

>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2   0.0   2.8e-13   1.3e-09       5      93 ..      44     151 ..      40     154 .. 0.84
   2 ?   -2.6   0.0       1.5   6.8e+03      57      79 ..     425     447 ..     408     457 .. 0.59

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 2.8e-13
                                    HHHHHHHTT.TSEEEEEHHHHCTTSCTT.SSEEEEEEESTTCHHH................HHHEHHHHHHHHCCCEEEC CS
                   NTP_transf_2   5 leelkelep.vakvvlfGSyarGtalkg.SDiDllvvlpeevsre................kkeegleklaeiikfleel 66 
                                    lee  ++ +  ++v l+GSy+ +t+lkg  DiDl++++p+  s e                   + +e++a +++ +  +
  gi|119719285|ref|YP_919780.1|  44 LEEANTRAGgEVSVELHGSYRHDTWLKGeADIDLFLLFPKKYSLEemkevarrvsegssarLGARVEERYASHPYYTLVF 123
                                    67777777789******************************9999****************4445569999999999888 PP

                                    T.TEEEEEECEEECCCCTEEEEEECEEE CS
                   NTP_transf_2  67 l.glevdlvtrekledpllvksileerp 93 
                                    +  +evd+v+ + + +p+ + + +++++
  gi|119719285|ref|YP_919780.1| 124 PnSVEVDVVPAYRVFSPSEIVTPVDRTQ 151
                                    5379*****9988776666666666655 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.5
                                    HHHCCCEEECTTEEEEEECEEEC CS
                   NTP_transf_2  57 aeiikfleellglevdlvtrekl 79 
                                    a +  +++ l+ +  dl+ +ek+
  gi|119719285|ref|YP_919780.1| 425 AGFSWEVKDLRNILRDLSAEEKK 447
                                    55555555555555555533333 PP

>> SMODS  Second Messenger Oligonucleotide or Dinucleotide Synthetase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   4.8e-07    0.0022       7     132 ..      15     136 ..      10     146 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 4.8e-07
                          SMODS   7 FkeflsnielsqttkdsissrvkaitkrLnkdfrelkskiaesllvGSyardTaikpvsdkdmlfeldvdl.lvvvneve 85 
                                    ++e l+++++s+++k  ++   +++ + + ++ ++     ++  l+GSy++dT +k+ +d d+   ++  + l +++ev+
  gi|119719285|ref|YP_919780.1|  15 LEEVLKKVKPSAEDKRALDLFAERLMAVVLEEANTRAGGEVSVELHGSYRHDTWLKGEADIDLFLLFPKKYsLEEMKEVA 94 
                                    67889999**********999999999887777444446667779************99999999999876245677777 PP

                          SMODS  86 gdepsdlleklkkalkktyksseirqdrqvvvvel.neikidvvPave 132
                                    +   +    +l + ++++y+s      ++  ++ + n +++dvvPa +
  gi|119719285|ref|YP_919780.1|  95 RRVSEGSSARLGARVEERYAS------HPYYTLVFpNSVEVDVVPAYR 136
                                    777777777777777777777......7777777779********975 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.9e-05     0.084      17      56 ..      58      98 ..      54     109 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.9e-05
                                   TEEEEEE-S----.--EEEEEEEESS---HHHHHHHHHHHH CS
                        Polbeta 17 ylFGSrakgkare.eSDiDlavllkekldleeelelaaele 56
                                    l+GS+ +++  + e DiDl++l+ +k +lee  e+a  ++
  gi|119719285|ref|YP_919780.1| 58 ELHGSYRHDTWLKgEADIDLFLLFPKKYSLEEMKEVARRVS 98
                                   59****97776544*************99999888887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (467 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 3362.16
//
Query:       gi|119719286|ref|YP_919781.1|  [L=187]
Description: 2'-5' RNA ligase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-32  110.4   0.1    1.2e-18   67.1   0.1    2.0  2  LigT_PEase       LigT like Phosphoesterase
    7.8e-15   55.1   0.0    9.8e-15   54.8   0.0    1.1  1  2_5_RNA_ligase2  2'-5' RNA ligase superfamily
    1.4e-11   44.7   0.0    5.9e-11   42.6   0.0    1.9  1  AKAP7_NLS        AKAP7 2'5' RNA ligase-like domain
     0.0026   17.3   0.0     0.0047   16.4   0.0    1.3  1  HVSL             Uncharacterised conserved protein


Domain annotation for each model (and alignments):
>> LigT_PEase  LigT like Phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.1   0.1   2.6e-22   1.2e-18       4      87 .]      15      94 ..      11      94 .. 0.94
   2 !   41.7   0.0   2.2e-14   9.9e-11       2      87 .]      96     178 ..      95     178 .. 0.92

  Alignments for each domain:
  == domain 1  score: 67.1 bits;  conditional E-value: 2.6e-22
                                   CHHHHHHHHHHHHHHHHHHCCTTEEETSGGGSEEEEEEEEEESHHHHHHHHHHHHHHHHTSBEEEEEEEEEEEEEECCSCCE CS
                     LigT_PEase  4 peeiaeelarlaaeleralaklglkpvrpfnpHiTLaflgevdeekvpellealaeiasgaepfelkvdgvglfpsrlrprv 85
                                   ++++ +++++l+++l+   a+l +k+v+++n+HiTL+flge+++++++e+ ++la++    ++f++ ++gvg fps  rprv
  gi|119719286|ref|YP_919781.1| 15 SPSVLQRVEALQSDLR--DAGLSAKFVEKENLHITLRFLGEIPPHTLEEVRNRLAKL--SYHRFKIVLKGVGGFPSLDRPRV 92
                                   6778899*********..999************************************..6779*************99**** PP

                                   EE CS
                     LigT_PEase 86 iy 87
                                   ++
  gi|119719286|ref|YP_919781.1| 93 LW 94
                                   *9 PP

  == domain 2  score: 41.7 bits;  conditional E-value: 2.2e-14
                                    E-CHHHHHHHHHHHHHHHHHHCCTTEEET.SGGGSEEEEEEEEEESHHHHHHHHHHHHHHHHTSBEEEEEEEEEEEEEEC CS
                     LigT_PEase   2 gppeeiaeelarlaaeleralaklglkpv.rpfnpHiTLaflgevdeekvpellealaeiasgaepfelkvdgvglfpsr 80 
                                    g ++e ++el++la+ ++  l++ +l+   ++f+pH+T+a+l+      + ++++  a+  +g      +v+ ++l++s+
  gi|119719286|ref|YP_919781.1|  96 G-VDEGSRELSELAELVRTSLKGVKLPEPdEEFHPHLTIARLKGPLSAGARRIIAGSADTVFGE----QEVTSFSLYKST 170
                                    5.567799**********999999988778******************************9996....78********** PP

                                    C.SCCEEE CS
                     LigT_PEase  81 l.rprviy 87 
                                    l + ++iy
  gi|119719286|ref|YP_919781.1| 171 LtPRGPIY 178
                                    *******9 PP

>> 2_5_RNA_ligase2  2'-5' RNA ligase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.8   0.0   2.2e-18   9.8e-15       5     122 ..      18     142 ..      14     170 .. 0.80

  Alignments for each domain:
  == domain 1  score: 54.8 bits;  conditional E-value: 2.2e-18
                2_5_RNA_ligase2   5 laapiealr.....rslydkayprwppHitLlypfvededl.adlaellsrlaketepfevrldgfgvFeh..kksvvyl 76 
                                    + +++eal+     + l  k +++  +HitL ++++++++  ++++++l++l  ++  f++ l+g+g F++  + +v+++
  gi|119719286|ref|YP_919781.1|  18 VLQRVEALQsdlrdAGLSAKFVEKENLHITLRFLGEIPPHTlEEVRNRLAKL--SYHRFKIVLKGVGGFPSldRPRVLWI 95 
                                    5566777775555555666669****************97555555555555..6889**************5555**** PP

                2_5_RNA_ligase2  77 sv.sdsealqalraallealpeagdkedsgeftPHlTiaqsadstsa 122
                                     v ++s +l++l + +++ l+  ++ e ++ef+PHlTia+ + + sa
  gi|119719286|ref|YP_919781.1|  96 GVdEGSRELSELAELVRTSLKGVKLPEPDEEFHPHLTIARLKGPLSA 142
                                    ***************************99**********99866665 PP

>> AKAP7_NLS  AKAP7 2'5' RNA ligase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.6   0.0   1.3e-14   5.9e-11       4     190 ..       8     170 ..       7     186 .. 0.84

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 1.3e-14
                                    EEEEE---HHHHHHHHHHHHHHHHH-GGGGGGB.--TT--EEEEEEE---SHHHHHHHHHHHHHHHHHHHHHHTTS--EE CS
                      AKAP7_NLS   4 FlsiplnsnklrkklekfqesvlsklpgldeslfikpeklHlTllvlkLknkeeiaaakevLkevkeeikdaldnkplsl 83 
                                    F++++++s+++ +++e++q ++ +++   +++  +++e+lH+Tl  l      ei      L+ev++++ ++ + +++++
  gi|119719286|ref|YP_919781.1|   8 FVAVKVSSPSVLQRVEALQSDLRDAGL--SAKF-VEKENLHITLRFLG-----EIPPH--TLEEVRNRLAKL-SYHRFKI 76 
                                    9*********************99665..5555.**********9996.....45555..799999999999.479**** PP

                                    EEEEEEEE.....TTTEEEEEE--SHHHHHHHHHHHHHHHHHHTTT--B--SS-.---EEEEEEGGG-THHHHTT--S-- CS
                      AKAP7_NLS  84 rlkGletfnddpakarVlYakveeesneekLqeladriikafeeaglvlekdkkkvklHaTlmnsrkrkkkqakskesfd 163
                                     lkG++ f  +  + rVl+++v+e   + +L ela+ +++ +  +g++l + ++++++H+T++  +   +  +     + 
  gi|119719286|ref|YP_919781.1|  77 VLKGVGGF-PSLDRPRVLWIGVDEG--SRELSELAELVRTSL--KGVKLPEPDEEFHPHLTIARLK---GPLS-----AG 143
                                    ********.78899********965..69*************..788888888899******9876...3332.....34 PP

                                    GG.GGGGGTT-EEEEEE--EEEEEESS CS
                      AKAP7_NLS 164 areilkqfkdfefgeekineihLsqle 190
                                    ar i+    d+ fge+++++++L + +
  gi|119719286|ref|YP_919781.1| 144 ARRIIAGSADTVFGEQEVTSFSLYKST 170
                                    788999999999999999999997765 PP

>> HVSL  Uncharacterised conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0     1e-06    0.0047      82     197 ..      37     146 ..      15     170 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1e-06
                           HVSL  82 dlgaplplHiSLSrplvlrthqkdsfldslkkelkssakrrFevsfsglkwvsndektRsFlvlrvkspendeLkkllea 161
                                    ++ ++++lHi+L     +  h  +    +++++l++   +rF++ ++g+  +++ ++ R+ ++  v +  + eL++l e 
  gi|119719286|ref|YP_919781.1|  37 KFVEKENLHITLRFLGEIPPHTLE----EVRNRLAKLSYHRFKIVLKGVGGFPSLDRPRVLWIG-VDEG-SRELSELAEL 110
                                    455666788877666666666555....5555555555679******************96665.6665.5********* PP

                           HVSL 162 vnkvleefglpplykdeaFHiSiawslgepseeeke 197
                                    v ++l+ ++lp+  ++ ++H+ ia   g  s+ +++
  gi|119719286|ref|YP_919781.1| 111 VRTSLKGVKLPEPDEEFHPHLTIARLKGPLSAGARR 146
                                    ************************877755554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1360.07
//
Query:       gi|119719287|ref|YP_919782.1|  [L=137]
Description: hypothetical protein Tpen_0370 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-10   40.6   0.3    3.1e-10   40.1   0.3    1.2  1  B-block_TFIIIC  B-block binding subunit of TFIIIC
    4.9e-07   29.4   2.0    8.6e-06   25.4   0.4    2.0  2  RNA_pol_Rpc34   RNA polymerase Rpc34 subunit
     0.0003   21.2   0.2    0.00042   20.8   0.2    1.3  1  HTH_27          Winged helix DNA-binding domain
    0.00051   19.9   0.2    0.00074   19.4   0.2    1.3  1  MarR_2          MarR family
     0.0045   16.9   0.1     0.0079   16.1   0.1    1.3  1  MarR            MarR family
  ------ inclusion threshold ------
      0.021   14.8   0.3      0.042   13.9   0.3    1.5  1  z-alpha         Adenosine deaminase z-alpha domain
      0.022   14.4   0.1      0.026   14.1   0.1    1.1  1  RED_N           RED-like protein N-terminal region
      0.022   14.7   0.5      0.041   13.8   0.5    1.5  1  TrmB            Sugar-specific transcriptional regulator TrmB
      0.044   13.3   0.8      0.082   12.5   0.8    1.4  1  HTH_24          Winged helix-turn-helix DNA-binding
      0.045   12.6   0.1       0.05   12.4   0.1    1.1  1  HTH_micro       HTH-like
      0.056   13.4   0.7          2    8.4   0.1    2.2  2  Cdc6_C          CDC6, C terminal winged helix domain
      0.063   13.9   0.0      0.085   13.5   0.0    1.2  1  RPA_C           Replication protein A C terminal


Domain annotation for each model (and alignments):
>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.1   0.3   2.1e-13   3.1e-10       3      71 ..      27      91 ..      25      92 .. 0.95

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 2.1e-13
                 B-block_TFIIIC  3 dqfklLelIassRysGitqsdLakeskqdprslfyrlksLekkgLIvkqsiidsatkksistsllvlkk 71
                                   +++++Lel+  ++++G++q++L+k ++ d+r+  ++l++Le++gLI k ++     +k+ +t++l l k
  gi|119719287|ref|YP_919782.1| 27 LERRVLELLREAGEKGVLQRELWKKLDVDSRKGLKILRKLESQGLIAKEQV----VYKGRKTYVLKLAK 91
                                   67899**********************************************....*********99865 PP

>> RNA_pol_Rpc34  RNA polymerase Rpc34 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.4   5.8e-09   8.6e-06      85     148 ..      25      87 ..       7      97 .. 0.86
   2 ?    4.3   0.1     0.015        22     303     336 .]     102     134 ..      88     134 .. 0.82

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 5.8e-09
                                    XHHHHHHHHHHHHHXSSXEEHHHHHHTTGXXHHHHHHHHHHHHHTTXXEEEEXSSSSSXEEEES CS
                  RNA_pol_Rpc34  85 sedeslVysiIeesGneGIwsrtiksklnLhksvvkkcLksLeskkyiksvksvkaptkkiYll 148
                                    ++ e  V++  +e+G +G+ +r++ +kl        k+L+ Les+++i++ + v ++ +k Y+l
  gi|119719287|ref|YP_919782.1|  25 QALERRVLELLREAGEKGVLQRELWKKLDVDSRKGLKILRKLESQGLIAKEQ-VVYKGRKTYVL 87 
                                    4556779*****************************************9865.66888999987 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.015
                                    TTXXSSXSSSSSXXTSSSSSSSSSSTTSSSSXXX CS
                  RNA_pol_Rpc34 303 lveapcgecpvfdlceeggavspkncvYlkeWle 336
                                    l e pc  cp +++c + g+    +c+ l+eWl+
  gi|119719287|ref|YP_919782.1| 102 LEEIPCFFCPFLHKCAS-GERDIYSCAILQEWLN 134
                                    5689***********75.6778899*******85 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.2   2.8e-07   0.00042       4      51 ..      27      75 ..      24      89 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.8e-07
                         HTH_27  4 qqalvLhlirhrrrrkkl.adlcgrlnvedshisyslkkLtekGLvert 51
                                   +++ vL+l+r+ +++  l ++l ++l+v++  + ++l+kL+ +GL+ ++
  gi|119719287|ref|YP_919782.1| 27 LERRVLELLREAGEKGVLqRELWKKLDVDSRKGLKILRKLESQGLIAKE 75
                                   57779999**999999999***************************444 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.2     5e-07   0.00074       4      55 ..      25      76 ..      22      83 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 5e-07
                                   -HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                         MarR_2  4 tpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                      ++rvL  L+ ++++ + ++el ++l+++     +il++L+++GL+ ++ 
  gi|119719287|ref|YP_919782.1| 25 QALERRVLELLREAGEKGVLQRELWKKLDVDSRKGLKILRKLESQGLIAKEQ 76
                                   5679********************************************9875 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   5.3e-06    0.0079       7      51 ..      30      76 ..      25      79 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 5.3e-06
                                   HHHHHHHHSTTEEHH..HHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                           MarR  7 viLrilyeqgplsvs..eLakklgvskstvtrvldrLekkGlieRsk 51
                                   ++L++l+e g+  v   eL+kkl v++    ++l++Le +Gli +++
  gi|119719287|ref|YP_919782.1| 30 RVLELLREAGEKGVLqrELWKKLDVDSRKGLKILRKLESQGLIAKEQ 76
                                   78999999999776556**************************9986 PP

>> z-alpha  Adenosine deaminase z-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.3   2.8e-05     0.042       5      54 ..      27      75 ..      23      77 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.8e-05
                                   HHHHHHHHHHHC-TTCECCHHHHHHHHCC-HHHHHHHHHHHHHTTSEEEE CS
                        z-alpha  5 qaekilelLeelgekkaatalalergLstpkreiNrvLydlerkgkvyre 54
                                    + ++lelL+e g +k++++ +l  +L  + r   ++L +le +g + +e
  gi|119719287|ref|YP_919782.1| 27 LERRVLELLREAG-EKGVLQRELWKKLDVDSRKGLKILRKLESQGLIAKE 75
                                   6889*********.9***************************99988876 PP

>> RED_N  RED-like protein N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   1.8e-05     0.026     107     187 ..      11     100 ..       4     104 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.8e-05
                                    XXXXXXXXXXXXXXXXXXXX..........HHHHHCS--.....SSHHHHHHHH.HHTTXXXXXXXXXXXXXXXXXXXXX CS
                          RED_N 107 eeeeeeeeekelekkaeeek..........ekekekeeeeeikfktklaksifktvlkkqkkvernelFlpgRmaYvvdL 176
                                    ee+ ee ee++++ +a e++          +   ++e  ++++++++ + +i +  l++q  + ++++  +gR +Yv+ L
  gi|119719287|ref|YP_919782.1|  11 EEDIEELEESSVQFQALERRvlellreageKGVLQRELWKKLDVDSRKGLKILR-KLESQGLIAKEQVVYKGRKTYVLKL 89 
                                    445455555555555555445555554432334455555999************.9999********************* PP

                                    XXX..XXXXXX CS
                          RED_N 177 edesvdsdiPt 187
                                     +e  + +iP 
  gi|119719287|ref|YP_919782.1|  90 AKEAEEVQIPG 100
                                    *********96 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.5   2.7e-05     0.041       7      58 ..      25      78 ..      19      90 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.7e-05
                                   HHHCCCHCHHHHHHCCCHH..CHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                           TrmB  7 seyEakvYlaLlklgpata..deiaeelgvprskvYevLrsLedkGlVerekgr 58
                                   +  E +v   L + g++ +  +e+ ++l+v+  k  ++Lr+Le+ Gl+ +e+  
  gi|119719287|ref|YP_919782.1| 25 QALERRVLELLREAGEKGVlqRELWKKLDVDSRKGLKILRKLESQGLIAKEQVV 78
                                   55666666666666666554489***************************9976 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.8   5.5e-05     0.082       4      47 ..      27      72 ..      25      73 .. 0.96

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.5e-05
                         HTH_24  4 tdrkILelLqk..nprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                   ++r++LelL++  + +  qreL ++l++ +   ++ l++Le++GlI
  gi|119719287|ref|YP_919782.1| 27 LERRVLELLREagEKGVLQRELWKKLDVDSRKGLKILRKLESQGLI 72
                                   589********99999*****************************9 PP

>> HTH_micro  HTH-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   3.4e-05      0.05     103     152 ..      38      91 ..      15     101 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.4e-05
                      HTH_micro 103 ak.dyvkaaelraklnidpKklfYvikkLakkglieqktk..eeak.ivikink 152
                                    a  + v + el +kl++d++k   +++kL+++gli ++++  ++ k +v+k+ k
  gi|119719287|ref|YP_919782.1|  38 AGeKGVLQRELWKKLDVDSRKGLKILRKLESQGLIAKEQVvyKGRKtYVLKLAK 91 
                                    443445566666666666666666666666666665333211222235555555 PP

>> Cdc6_C  CDC6, C terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.061        91      39      58 ..      28      47 ..      18      51 .. 0.86
   2 ?    8.4   0.1    0.0014         2      39      81 ..      56      96 ..      50      97 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.061
                                   HHHHHHHHHHHHHTTSEEEE CS
                         Cdc6_C 39 qrevsdllseLemlgilele 58
                                   +r+v++ll+e   +g+l++e
  gi|119719287|ref|YP_919782.1| 28 ERRVLELLREAGEKGVLQRE 47
                                   58999999999999999987 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0014
                                   HHHHHHHHHHHHHTTSEEEEEE.E-CC.C-EEEEEEESSSCHHH CS
                         Cdc6_C 39 qrevsdllseLemlgileleks.skGrregrtrkisLnvdpddv 81
                                   +r  +++l++Le++g++  e++  kGr   +t+  +L  + ++v
  gi|119719287|ref|YP_919782.1| 56 SRKGLKILRKLESQGLIAKEQVvYKGR---KTYVLKLAKEAEEV 96
                                   5666899************96504555...57777777777766 PP

>> RPA_C  Replication protein A C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   5.7e-05     0.085      38      97 ..      17      72 ..       4      74 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.7e-05
                                   XXXXXXX.XSXHHHHHHHHHHHH.SXSTTTEEHHHHHHHSTSXHHHHHHHHHHHHHTTSE CS
                          RPA_C 38 nqaklankgltalaqqvlnlikqspeseeGvhvdeiaqklrlsvndvkqavdeLsneGii 97
                                    ++++++   +al+++vl+l+++  ++e+Gv  +e+ +kl ++ ++  +++++L+++G+i
  gi|119719287|ref|YP_919782.1| 17 LEESSVQ--FQALERRVLELLRE--AGEKGVLQRELWKKLDVDSRKGLKILRKLESQGLI 72
                                   5556666..8899**********..9********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1000.12
//
Query:       gi|119719288|ref|YP_919783.1|  [L=262]
Description: GTPase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-62  211.5   0.1    1.7e-62  211.4   0.1    1.0  1  ATP_bind_1       Conserved hypothetical ATP binding protein
    2.6e-06   27.1   0.0    0.00012   21.6   0.0    2.4  2  GTP_EFTU         Elongation factor Tu GTP binding domain
    4.8e-05   23.3   0.8       0.52   10.2   0.1    3.4  3  RsgA_GTPase      RsgA GTPase
    6.4e-05   23.1   0.0       0.15   12.2   0.0    2.2  2  Sigma54_activ_2  Sigma-54 interaction domain
     0.0016   18.5   0.0     0.0046   17.0   0.0    1.8  1  MMR_HSR1         50S ribosome-binding GTPase
     0.0021   18.3   0.0     0.0051   17.1   0.0    1.7  1  AAA_22           AAA domain
     0.0036   16.9   0.0       0.44   10.1   0.0    2.2  2  Ras              Ras family
     0.0051   16.6   0.0     0.0071   16.1   0.0    1.3  1  AAA_24           AAA domain
     0.0059   17.0   0.0      0.072   13.5   0.0    2.3  2  RNA_helicase     RNA helicase
     0.0073   16.1   0.0      0.024   14.4   0.0    1.9  1  NOG1             Nucleolar GTP-binding protein 1 (NOG1)
     0.0074   16.4   0.1       0.45   10.6   0.0    2.4  2  Dynamin_N        Dynamin family
       0.01   16.0   0.0      0.047   13.8   0.0    1.8  2  DUF87            Helicase HerA, central domain
  ------ inclusion threshold ------
       0.01   16.0   0.0      0.018   15.2   0.0    1.6  1  AAA_33           AAA domain
      0.016   14.6   0.0       0.28   10.6   0.0    2.1  2  SRPRB            Signal recognition particle receptor beta su
       0.02   15.4   0.0       0.03   14.8   0.0    1.5  1  AAA_23           AAA domain
      0.035   13.8   0.0      0.078   12.7   0.0    1.5  1  AAA_29           P-loop containing region of AAA domain
      0.057   13.3   0.0       0.12   12.3   0.0    1.5  1  NACHT            NACHT domain
      0.061   13.7   0.0      0.071   13.5   0.0    1.5  1  AAA_16           AAA ATPase domain
      0.073   12.8   0.0       0.11   12.2   0.0    1.3  1  PRK              Phosphoribulokinase / Uridine kinase family
      0.078   12.8   0.0       0.77    9.5   0.0    2.2  2  CLP1_P           mRNA cleavage and polyadenylation factor CLP
      0.087   12.0   0.0       0.18   10.9   0.0    1.5  1  NB-ARC           NB-ARC domain
      0.087   12.3   0.0       0.15   11.5   0.0    1.4  1  PhoH             PhoH-like protein
       0.11   12.2   0.0       0.23   11.1   0.0    1.5  1  AAA_30           AAA domain
       0.12   12.9   0.0       0.26   11.8   0.0    1.5  1  ABC_tran         ABC transporter
       0.12   11.8   0.0       0.21   11.0   0.0    1.3  1  SMC_N            RecF/RecN/SMC N terminal domain
       0.13   12.8   0.1       0.27   11.8   0.0    1.8  2  AAA_18           AAA domain
       0.23   11.0   0.1         14    5.2   0.1    2.2  2  cobW             CobW/HypB/UreG, nucleotide-binding domain


Domain annotation for each model (and alignments):
>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  211.4   0.1   2.6e-65   1.7e-62       1     239 [.       9     249 ..       9     251 .. 0.96

  Alignments for each domain:
  == domain 1  score: 211.4 bits;  conditional E-value: 2.6e-65
                     ATP_bind_1   1 vvGpaGsGKttfvgalseilelrgrsvavvNLDPAaeelpYeaavdirelitledvmedlglgpngalvvaleflresld 80 
                                    +vGpaGsGK+tf++++ ++l ++ ++  ++NLDPA+e l Y++++dire++ ++dv e+++lgpnga++ ++++ +e+ld
  gi|119719288|ref|YP_919783.1|   9 IVGPAGSGKSTFTSSFKDWLLSQSTPASTINLDPAVEYLDYDPDIDIREYVFVRDVIEKYNLGPNGAIIASVDLAVEHLD 88 
                                    79****************************************************************************** PP

                     ATP_bind_1  81 wldeelekeeddyllfDtPGQielfthseslakiveeLesefalv.vvyLvDsqrltdptkfisgllsalsamlrlelPh 159
                                    +++ ++e+  + y+l+DtPGQ+e+f +++s+  iv eL s+ +l+ +v++vD+ ++t+p +f+s+l+++ s+ +rl+lP 
  gi|119719288|ref|YP_919783.1|  89 KVQAAMEDLPEGYVLVDTPGQMEIFAYRQSGTYIVSELCSSSSLCaAVFMVDASIATQPYNFLSQLFLSASMYYRLRLPL 168
                                    ******999*******************************666663699******************************* PP

                     ATP_bind_1 160 vvvlnkfDllkek.lekeleffedvealslllekeeekykklaeaiaelleefalvlrflplssekeesiedllslidea 238
                                     v++nk+D+l++  +++ l++++dve++++ le  ++  +  ++ + +ll++f +v  f+p+s++++e +e+++ +++++
  gi|119719288|ref|YP_919783.1| 169 TVAVNKIDVLEDMeKNRLLNWLSDVESMENELEFASNVDRVFTKRVLRLLSDFMEVVPFVPVSAKTKENFEQVYFYLQQI 248
                                    **********988888999******************************************************9888887 PP

                     ATP_bind_1 239 l 239
                                    +
  gi|119719288|ref|YP_919783.1| 249 Y 249
                                    5 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0      0.12        76       5      22 ..       6      23 ..       3      52 .. 0.86
   2 !   21.6   0.0   1.9e-07   0.00012      72     185 ..     101     242 ..      85     250 .. 0.64

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.12
                                   EEEEEESTTSSHHHHHHH CS
                       GTP_EFTU  5 nigiighvDhGKtTLtdr 22
                                    + i+g   +GK+T+t +
  gi|119719288|ref|YP_919783.1|  6 VVFIVGPAGSGKSTFTSS 23
                                   6889***********976 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 1.9e-07
                                    EEEEEESSSGG.GHHHHHHH........HHT-SEEEEEEETTTB.....STHHHHHHHHHHHHTTTEEEEEEESCGST.. CS
                       GTP_EFTU  72 inliDtPGHvd.Fskevirg........lrvlDgavlvvdaveG.....vepqteevlrlalkegvpiivfiNKmDrl.. 135
                                    + l+DtPG ++ F    + +         + l  av++vda+         +q    + +  ++++p+ v++NK+D l  
  gi|119719288|ref|YP_919783.1| 101 YVLVDTPGQMEiFAYRQSGTyivselcsSSSLCAAVFMVDASIAtqpynFLSQLFLSASMYYRLRLPLTVAVNKIDVLed 180
                                    6788888888765444333322223333445557888888884423322555666666677788899***********98 PP

                                    .....HHHHHHHHHHHHHHHHHHHHHHHHHHHTTT.............TTEEEEEEBTTTTBTHHHHH CS
                       GTP_EFTU 136 .....kaelkeiveevkqklsrkeeklekygekge.............kevpvvfgSalkgegvktll 185
                                           +    ve ++++l +  ++++                    + vp+v++Sa+++e+++++ 
  gi|119719288|ref|YP_919783.1| 181 meknrLLNWLSDVESMENEL-EFASNVDR-----VftkrvlrllsdfmEVVPFVPVSAKTKENFEQVY 242
                                    88444333334444444444.22333333.....1333457888888899*************99765 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.1    0.0097       6.4     101     119 ..       6      24 ..       1      37 [. 0.82
   2 ?    3.3   0.0       0.1        66     145     162 ..      93     110 ..      89     114 .. 0.81
   3 !   10.2   0.1   0.00078      0.52      43      99 ..     162     220 ..     134     247 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0097
                                    EEEEECSTTSSHHHHHHHH CS
                    RsgA_GTPase 101 tsvlvGqSGvGKStLinal 119
                                    ++++vG+ G GKSt+  ++
  gi|119719288|ref|YP_919783.1|   6 VVFIVGPAGSGKSTFTSSF 24 
                                    6789**********98766 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.1
                                    EEEEETTTEEEESS-SSS CS
                    RsgA_GTPase 145 ellelaegglliDtPGfr 162
                                     + +l+eg +l+DtPG  
  gi|119719288|ref|YP_919783.1|  93 AMEDLPEGYVLVDTPGQM 110
                                    567899999*******65 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.00078
                                    HHTT-EEEEEEE-GGG--HHH..HHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTT CS
                    RsgA_GTPase  43 eekgiepvivlnKiDlleeee..eleelkeelealgyevllvsaktkegleelkellkd 99 
                                     + ++++++++nKiD+le++e  +l ++ +++e+++ e+ + s+ ++  ++++ +ll+d
  gi|119719288|ref|YP_919783.1| 162 YRLRLPLTVAVNKIDVLEDMEknRLLNWLSDVESMENELEFASNVDRVFTKRVLRLLSD 220
                                    34567999***********9988889999999999999999999888777777777776 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0    0.0029       1.9      22      41 ..       5      24 ..       2      44 .. 0.78
   2 !   12.2   0.0   0.00022      0.15      14     100 ..     110     197 ..     105     208 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0029
                                   S-EEEEEETT--HHHHHHCC CS
                Sigma54_activ_2 22 lpvfltGekGsgkelvArlL 41
                                   l+vf++G++Gsgk+++   +
  gi|119719288|ref|YP_919783.1|  5 LVVFIVGPAGSGKSTFTSSF 24
                                   78***********9987655 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00022
                                    HHHHHT-SS-EEEEEETT--HHHHHHCC--TTS-EE--SSTTHHHH-HHHHHHHT.TTSEEEEEE-TT--HHHHHHHHHH CS
                Sigma54_activ_2  14 LeqaaqsklpvfltGekGsgkelvArlLhknsgpwleifvverlaklpldlleqa.kggtLylkdiadlskaeqkeLlel 92 
                                    +e  a++++  ++++e  s  +l+A ++   ++   ++ ++ ++  l +++  ++  + t  ++ i+ l+ +e  +Ll++
  gi|119719288|ref|YP_919783.1| 110 MEIFAYRQSGTYIVSELCSSSSLCAAVFMVDASIATQPYNFLSQLFLSASMYYRLrLPLTVAVNKIDVLEDMEKNRLLNW 189
                                    67778899999****************************9988888888988886589********************** PP

                                    HHHHTTTT CS
                Sigma54_activ_2  93 lakaekss 100
                                    l   e  +
  gi|119719288|ref|YP_919783.1| 190 LSDVESME 197
                                    *9987554 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   6.9e-06    0.0046       2      88 ..       7     146 ..       6     174 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6.9e-06
                                    EEEEESTTSSHHHHHHHHHTS.TEEESSSTTSSSSEEEEEEEETTEE................................. CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltge.kaivsdkpgtTrdinegrvklkgke................................. 47 
                                    v ivG   +GKSt+ ++  +   ++ +      +d+  + ++++  +                                 
  gi|119719288|ref|YP_919783.1|   7 VFIVGPAGSGKSTFTSSFKDWlLSQSTPASTINLDPAVEYLDYD--Pdidireyvfvrdviekynlgpngaiiasvdlav 84 
                                    78*************99977544555555555556666666633..2466778888888999999999999999999999 PP

                                    ................EEEEECGGCSS...HHHHHHHHHHHHHHHHCTSEEEEEEETT..TT CS
                       MMR_HSR1  48 ................ielvDtpGlie...gaseekglgkaflaleeadlillvvdas..ee 88 
                                                    ++lvDtpG +e     +++  +  ++++  +  +++++vdas  ++
  gi|119719288|ref|YP_919783.1|  85 ehldkvqaamedlpegYVLVDTPGQMEifaYRQSGTYIVSELCSSSSLCAAVFMVDASiaTQ 146
                                    9999999999999999********65544344556678888888888899999999885422 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   7.7e-06    0.0051       7      38 ..       6      40 ..       3     105 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 7.7e-06
                         AAA_22  7 ilvvtGesGtGKTtllrrlleqldeeakaee...e 38
                                   +++++G++G+GK+t    ++++l  ++ ++     
  gi|119719288|ref|YP_919783.1|  6 VVFIVGPAGSGKSTFTSSFKDWLLSQSTPAStinL 40
                                   578********************887766555541 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.031        20       3      37 ..       8      43 ..       6      57 .. 0.75
   2 !   10.1   0.0   0.00066      0.44      84     156 ..     145     245 ..     100     250 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.031
                                   EEEESTTSSHHHHHHHHHHSSCSSSC.TTTSSEEEE CS
                            Ras  3 vlvGdsavGKtslllrfvkdkFkeey.esTigvdfy 37
                                    +vG  + GK++++ +f +   +++   sTi  d  
  gi|119719288|ref|YP_919783.1|  8 FIVGPAGSGKSTFTSSFKDWLLSQSTpASTINLDPA 43
                                   69***************9877665542567766655 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00066
                                    HHHHHTHHHHHHHHHHHSTTTSEEEEEEETTTGGG...........................G-SS-HHHHHHHHHHHT. CS
                            Ras  84 resfenvkkwveeikrvaeenvpivLvGnKvDlee...........................kravsteegeelakelg. 135
                                    ++ ++ +++++   +++ + ++p+ +  nK+D+ e                           +r+ +++  + l++ ++ 
  gi|119719288|ref|YP_919783.1| 145 TQPYNFLSQLFLSASMYYRLRLPLTVAVNKIDVLEdmeknrllnwlsdvesmenelefasnvDRVFTKRVLRLLSDFMEv 224
                                    34566666666666666667789999999999888899999999999999999999999995555555555556666669 PP

                                    SEEEEEBTTTTCTHHHHHHHH CS
                            Ras 136 lkfletSAktnenveeafeel 156
                                    ++f+ +SAkt+en+e+++  l
  gi|119719288|ref|YP_919783.1| 225 VPFVPVSAKTKENFEQVYFYL 245
                                    9***************98765 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.1e-05    0.0071       3      57 ..       5      66 ..       3     117 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.1e-05
                         AAA_24  3 lkiliyGpsgiGKTtlakel.......gpkplfidtekGlksldadkfpdieswedfldevv 57
                                   l ++i+Gp+g+GK+t+ +++          +  i+++  +  ld d   di+ +  ++d ++
  gi|119719288|ref|YP_919783.1|  5 LVVFIVGPAGSGKSTFTSSFkdwllsqSTPASTINLDPAVEYLDYDPDIDIREYVFVRDVIE 66
                                   5799****************555555333334457777777777777777775544444444 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   0.00011     0.072       1      43 [.       7      46 ..       7      64 .. 0.79
   2 ?    0.8   0.0      0.97   6.4e+02      23      83 ..      91     149 ..      82     158 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00011
                   RNA_helicase  1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddf 43
                                   ++++Gp+g GKSt++ ++ + ll+++   +  s++   p+ ++
  gi|119719288|ref|YP_919783.1|  7 VFIVGPAGSGKSTFTSSFKDWLLSQS---TPASTINLDPAVEY 46
                                   689**************888888655...44455555555555 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.97
                   RNA_helicase  23 lkklklkkkdsvysrnpeddfwdgYtgqevvvidDfgqvkdeenpsdlaelirlvsstpyp 83 
                                    + ++++  ++ v + +p +     Y++    ++ +++++++      ++++   + ++py+
  gi|119719288|ref|YP_919783.1|  91 QAAMEDLPEGYVLVDTPGQMEIFAYRQSGTYIVSELCSSSSL--CAAVFMVDASIATQPYN 149
                                    555566666777778888888899999999999999999877..66888888888888886 PP

>> NOG1  Nucleolar GTP-binding protein 1 (NOG1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   3.7e-05     0.024      16      58 .]     134     176 ..     132     176 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.7e-05
                           NOG1  16 avlFllDpseecg.ysleeQlsLleeikelfankpvivvlnKiD 58 
                                    a +F++D+s     y++ +Ql L  +++ +++  p+ v++nKiD
  gi|119719288|ref|YP_919783.1| 134 AAVFMVDASIATQpYNFLSQLFLSASMYYRLR-LPLTVAVNKID 176
                                    569******87766*****************9.9*********9 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.2      0.12        78       1      14 [.       7      20 ..       7      31 .. 0.90
   2 !   10.6   0.0   0.00067      0.45     100     155 ..      98     156 ..      88     176 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.12
                                   EEEEEBTTTTHHHH CS
                      Dynamin_N  1 iavvGsqSsGKSSv 14
                                   + +vG   sGKS++
  gi|119719288|ref|YP_919783.1|  7 VFIVGPAGSGKSTF 20
                                   679**********9 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00067
                                    S-SEEEEE---B-SSSGTTS...HHHHHHHSTTEEEEEEEETTS-CCC-CHHHHHHHHS CS
                      Dynamin_N 100 vkgltlvDlPGldsvnkrdq...elvkeyikkadiilavtsanhdlsnsealflarevd 155
                                     +g++lvD+PG  ++ + +q    +v e++ ++++  av   + +++++   fl+++  
  gi|119719288|ref|YP_919783.1|  98 PEGYVLVDTPGQMEIFAYRQsgtYIVSELCSSSSLCAAVFMVDASIATQPYNFLSQLFL 156
                                    57899******9998888777879999999*******************9999998765 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   7.1e-05     0.047      28      69 ..       9      58 ..       7     105 .. 0.80
   2 ?   -0.0   0.0       1.2   7.7e+02     131     182 ..     181     228 ..     146     248 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.1e-05
                          DUF87 28 ilgsTGsGKSntvavLleelle.kkgatililDpHGEYgkal.......e 69
                                   i+g +GsGKS+++++  + ll+ +  a+++ lDp  EY +++       +
  gi|119719288|ref|YP_919783.1|  9 IVGPAGSGKSTFTSSFKDWLLSqSTPASTINLDPAVEYLDYDpdidireY 58
                                   8999*****************877788************99966665442 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1.2
                          DUF87 131 keekeklssdepveklleelkkekeelrklknqaiarlldkledllrkggsf 182
                                     e++  l+  + ve++++el+     +++ ++   +r+l+ l+d+++   + 
  gi|119719288|ref|YP_919783.1| 181 MEKNRLLNWLSDVESMENELE----FASNVDRVFTKRVLRLLSDFMEVVPFV 228
                                    466777777778888888888....788888888888888888888776666 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   2.6e-05     0.018       1      19 [.       6      24 ..       6     109 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.6e-05
                         AAA_33  1 lvllvGlpGsGKstlaerl 19
                                   +v++vG++GsGKst+  + 
  gi|119719288|ref|YP_919783.1|  6 VVFIVGPAGSGKSTFTSSF 24
                                   89*************9775 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.21   1.4e+02       6      20 ..       7      21 ..       3      48 .. 0.71
   2 ?   10.6   0.0   0.00042      0.28      51     124 ..     101     177 ..      84     201 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.21
                                   EEEE-STTSSHHHHH CS
                          SRPRB  6 vllvGlsdsGKTslf 20
                                   v +vG+  sGK ++ 
  gi|119719288|ref|YP_919783.1|  7 VFIVGPAGSGKSTFT 21
                                   889********7643 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00042
                                    -SEEEETT-GCC...SHH...HHHHHHHHGGEEEEEEEEETTS-HHHHHHHHHHHHHH.HHHHHHHTT---EEEEEE-TT CS
                          SRPRB  51 ltliDfPGhekl...rqk...lleklkaksslkglvfvvDStidpkevkevAEllyei.lliteklkdavdiliACnKqe 123
                                      l+D PG+ ++   rq    ++ +l  +ssl + vf+vD++i  +  +    +l ++ l+ ++  +  +++ +A nK +
  gi|119719288|ref|YP_919783.1| 101 YVLVDTPGQMEIfayRQSgtyIVSELCSSSSLCAAVFMVDASIATQPYN----FLSQLfLSASMYYRLRLPLTVAVNKID 176
                                    5699999987643223323338888999999************877655....555542455666678888888888877 PP

                                    S CS
                          SRPRB 124 l 124
                                    +
  gi|119719288|ref|YP_919783.1| 177 V 177
                                    6 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   4.5e-05      0.03      22      85 ..       7      90 ..       5     248 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.5e-05
                         AAA_23 22 tlItGpNGaGKTTildAiklaLygetprlsrks................grgfeksdveiese.......gkvkayveltfe 80
                                   + I+Gp G+GK+T+   +k  L  ++++ s+ +                ++  + +dv    e       g   a+v+l +e
  gi|119719288|ref|YP_919783.1|  7 VFIVGPAGSGKSTFTSSFKDWLLSQSTPASTINldpaveyldydpdidiREYVFVRDVI---EkynlgpnGAIIASVDLAVE 85
                                   68*****************9998888888888888888777776666653233322222...02224444777777777777 PP

                         AAA_23 81 nkdgr 85
                                   + d+ 
  gi|119719288|ref|YP_919783.1| 86 HLDKV 90
                                   77664 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00012     0.078      25      39 ..       7      21 ..       2      35 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00012
                         AAA_29 25 tlltGpsGsGKSTll 39
                                   ++++Gp GsGKST+ 
  gi|119719288|ref|YP_919783.1|  7 VFIVGPAGSGKSTFT 21
                                   689**********85 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00018      0.12       2      23 ..       6      27 ..       5      40 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00018
                                   CEEEEC-TTTCHHHHHHHHHHH CS
                          NACHT  2 lvilqGeaGsGKTtLlqklala 23
                                   +v++ G+aGsGK+t+  ++ + 
  gi|119719288|ref|YP_919783.1|  6 VVFIVGPAGSGKSTFTSSFKDW 27
                                   799************9888765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   0.00011     0.071      26      49 ..       6      29 ..       3     221 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00011
                         AAA_16 26 lvllsGesGvGKsslvrellrale 49
                                   +v+++G++G+GKs+   ++++ l 
  gi|119719288|ref|YP_919783.1|  6 VVFIVGPAGSGKSTFTSSFKDWLL 29
                                   699************999987444 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00017      0.11       2      46 ..       7      51 ..       6      63 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00017
                            PRK  2 IgvagsSGaGkttvarklekifgrekvkaaeiegdsflrldraek 46
                                   + + g+ G+Gk+t++  +++ +  ++ +a +i++d  +++   + 
  gi|119719288|ref|YP_919783.1|  7 VFIVGPAGSGKSTFTSSFKDWLLSQSTPASTINLDPAVEYLDYDP 51
                                   5689*************************9999998877766555 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0    0.0012      0.77       1      32 [.      11      42 ..      11      47 .. 0.91
   2 ?    0.8   0.0      0.54   3.6e+02      87     119 ..      83     115 ..      71     163 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0012
                         CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDv 32
                                   Gp  sGKST++    +++l+++     ++lD+
  gi|119719288|ref|YP_919783.1| 11 GPAGSGKSTFTSSFKDWLLSQSTPASTINLDP 42
                                   899***************99998777999998 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.54
                         CLP1_P  87 lareveekleenkkakasgliIntpGwvkglga 119
                                     ++++++  ++ ++  ++ ++++tpG ++ +++
  gi|119719288|ref|YP_919783.1|  83 AVEHLDKVQAAMEDLPEGYVLVDTPGQMEIFAY 115
                                    344444444455557899999****98875554 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00027      0.18      20      38 ..       4      22 ..       1      29 [. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00027
                                   SEEEEEEESTTSSHHHHHH CS
                         NB-ARC 20 slvvalvGmgGvGKttlak 38
                                    lvv++vG +G+GK+t  +
  gi|119719288|ref|YP_919783.1|  4 YLVVFIVGPAGSGKSTFTS 22
                                   689*************876 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00022      0.15      18      60 ..       3      45 ..       1      56 [. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00022
                                   H-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S-- CS
                           PhoH 18 kndivfaiGpaGtGKtylavalavealkkkkvkriiltrpave 60
                                   k+ +vf++GpaG+GK+ ++ +    +l++++    i + pave
  gi|119719288|ref|YP_919783.1|  3 KYLVVFIVGPAGSGKSTFTSSFKDWLLSQSTPASTINLDPAVE 45
                                   5679************999888777777777777777777766 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00035      0.23      19      39 ..       5      25 ..       2      38 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00035
                         AAA_30 19 rvavltGpAGtGKttalkalr 39
                                   +v++++GpAG+GK+t  ++ +
  gi|119719288|ref|YP_919783.1|  5 LVVFIVGPAGSGKSTFTSSFK 25
                                   6899***********877665 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00039      0.26      13      30 ..       6      23 ..       3      43 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00039
                                   EEEEEESTTSSHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxx RF
                       ABC_tran 13 kvaivGenGaGKStLlkl 30
                                   +v ivG+ G+GKSt+ + 
  gi|119719288|ref|YP_919783.1|  6 VVFIVGPAGSGKSTFTSS 23
                                   689***********9765 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00032      0.21      26      50 ..       6      31 ..       2      38 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00032
                                   EEEEEESTTSSHHHHHHHHH.HHCTT CS
                                   xxxxxxxxxxxxxxxxxxxx.xxxxx RF
                          SMC_N 26 ftaivGpNGSGKsnlldAil.FvLGe 50
                                   + +ivGp GSGKs ++ + + ++L++
  gi|119719288|ref|YP_919783.1|  6 VVFIVGPAGSGKSTFTSSFKdWLLSQ 31
                                   579************99985477764 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00041      0.27       1      19 [.       7      25 ..       7     144 .. 0.72
   2 ?   -2.2   0.0       8.4   5.6e+03      52      62 ..     181     191 ..     149     222 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00041
                         AAA_18  1 IlltGtpGvGKttlakeLs 19
                                   +++ G++G+GK+t++   +
  gi|119719288|ref|YP_919783.1|  7 VFIVGPAGSGKSTFTSSFK 25
                                   79************98764 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 8.4
                         AAA_18  52 ldedkldklld 62 
                                    +++++l ++l+
  gi|119719288|ref|YP_919783.1| 181 MEKNRLLNWLS 191
                                    22222222222 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1     0.021        14       2      16 ..       6      20 ..       5      31 .. 0.89
   2 ?    3.8   0.0     0.058        39     103     170 ..     123     194 ..      74     202 .. 0.65

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.021
                                   EEEEEESTTCCHHHH CS
                           cobW  2 vtvltGflGsGKTtL 16
                                   v+ ++G+ GsGK+t+
  gi|119719288|ref|YP_919783.1|  6 VVFIVGPAGSGKSTF 20
                                   789**********97 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.058
                                    SHHHHHCCCECEEEEEEETTTH......CCHCCHHHHHHHHHHTSSEEEEE-HHHHCHC..HHHHHHHHHHHH CS
                           cobW 103 eeelksdltldavvavvDaknl.....eaeeekieekaedqlaaadllvlnKtDlldeeallekleerlrqln 170
                                     +el+s+  l a v++vDa+ +       ++   +  +   l    ++ +nK+D+l++ ++ ++l ++l++++
  gi|119719288|ref|YP_919783.1| 123 VSELCSSSSLCAAVFMVDASIAtqpynFLSQLFLSASMYYRLRLPLTVAVNKIDVLEDMEK-NRLLNWLSDVE 194
                                    56666666777777777775445555533444555566666777778899*******9977.67766666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       708  (0.0394891); expected 358.6 (0.02)
Passed bias filter:                      612  (0.0341346); expected 358.6 (0.02)
Passed Vit filter:                       106  (0.00591221); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              27  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 1846.85
//
Query:       gi|119719289|ref|YP_919784.1|  [L=231]
Description: orotidine 5'-phosphate decarboxylase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.8e-11   44.1   0.3    2.2e-10   40.5   0.3    2.2  1  OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS famil


Domain annotation for each model (and alignments):
>> OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.5   0.3   1.2e-14   2.2e-10       3     224 ..       7     229 ..       5     230 .. 0.72

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 1.2e-14
                                    EEEEE-SSSHHHHHHHHHHHG........G.GSSEEEEEHHHHHHHTHH.HHTHHHHHHHHHT..SEEEEEEEE-S-HHH CS
                      OMPdecase   3 LclalDvatarelleladkvg........p.sivvlKthydlvegwgfegtgaklaalarkhg..flifeDrKfaDIGnt 71 
                                    +++alDv +++++l++a  +g        p   +v++ +++l+++ g     ++++ +++       + +D+K+aD+G+ 
  gi|119719289|ref|YP_919784.1|   7 VQVALDVVDEERALRVAGAMGegcrqgafPcDRLVVEAGTPLIKAVG-----VRVLPKLKLASggLTLYADLKTADVGEL 81 
                                    79**************998773333222255579*************.....55555444332249999*********** PP

                                    HHHHHHSTCHHHHTTESEEEEEGTGHHHHHHHHHHHHHHTTS.EEEEEESTSSGGHHHHHHHSHHHHHHHHHHHHHHHTT CS
                      OMPdecase  72 vekqatagsarikewadivtvhavaGkasvkalaeaaekwgnrgllilaqmsskgnlmlqekgytqacveaarehkaedf 151
                                    ++  a       + +adi  v a a  +++ka++ea  k g   l++++ +  +  +         +++  are      
  gi|119719289|ref|YP_919784.1|  82 EASLA------YDFGADIASVLARAPMGTLKAFLEAGLKRG--RLVAVDTIGIEAREVPFL---VREIIRVAREIG--FP 148
                                    ***99......59************************9998..888888888777644444...677777777777..22 PP

                                    ESEEECCCHTH.....HHHHH........TTCSCEEEHHHTTEEEEECTTCCGGGHHHHHHHTTCSEEEESHHHHTSSSH CS
                      OMPdecase 152 vmGfvaqetln.....ateed........addfihltpgigleqggdgkgqqyntpekligiagadiiivGRgIlkagdp 218
                                    +  +v+  +       a++++         +++  l p ++    ++++g+ +  ++ l+++ + di +vGR I+++++ 
  gi|119719289|ref|YP_919784.1| 149 LEKLVVELH-RgideeASRQKyfeelgvaVNQIRELSPEVK---IAVAGGITPA-VKSLVEKLEPDIYVVGRYITQSPNV 223
                                    222333322.2354433333352223344555555555555...5*******99.666666677***************9 PP

                                    HHHHHH CS
                      OMPdecase 219 veeaer 224
                                    ve +++
  gi|119719289|ref|YP_919784.1| 224 VERIKE 229
                                    998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1624.20
//
Query:       gi|119719290|ref|YP_919785.1|  [L=318]
Description: hypothetical protein Tpen_0373 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-08   34.1  28.5    3.8e-05   23.7   8.2    3.7  3  Laminin_II       Laminin Domain II
    1.4e-07   31.7  11.2    1.4e-07   31.7  11.2    4.7  4  TMF_TATA_bd      TATA element modulatory factor 1 TATA bindin
      6e-07   28.6  45.5     0.0045   15.9  13.5    4.0  4  Spc7             Spc7 kinetochore protein
    2.9e-06   27.8  34.2     0.0017   18.9   4.8    4.2  4  HIP1_clath_bdg   Clathrin-binding domain of Huntingtin-intera
    5.8e-06   26.2  23.0    0.00094   19.1   4.0    4.0  4  Sec34            Sec34-like family
    1.1e-05   25.7  11.7    1.1e-05   25.7  11.7    3.2  2  UPF0242          Uncharacterised protein family (UPF0242) N-t
    2.2e-05   23.9  10.9    2.2e-05   23.9  10.9    3.1  3  DUF4763          Domain of unknown function (DUF4763)
    4.1e-05   23.0  48.3      0.026   13.9  11.7    3.9  4  GAS              Growth-arrest specific micro-tubule binding
    4.7e-05   23.4  48.2     0.0018   18.3   8.8    4.7  4  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
    4.9e-05   23.3  23.1    4.9e-05   23.3  23.1    2.7  1  KASH_CCD         Coiled-coil region of CCDC155 or KASH
    6.2e-05   23.3  40.9    0.00013   22.3  13.8    3.2  2  ATG16            Autophagy protein 16 (ATG16)
    9.8e-05   22.7  17.9        0.1   13.1   4.6    4.7  3  NPV_P10          Nucleopolyhedrovirus P10 protein
    0.00011   22.7  47.6     0.0066   17.0  21.3    3.6  3  APG6_N           Apg6 coiled-coil region
    0.00011   22.2  12.8      0.026   14.6   0.7    3.2  3  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
    0.00019   20.8  37.0     0.0046   16.3   6.7    3.4  3  DUF3450          Protein of unknown function (DUF3450)
    0.00021   21.8  39.6      0.012   16.1  15.3    2.3  2  Fez1             Fez1
    0.00024   20.8  32.6     0.0015   18.3  10.9    4.9  3  SKA2             Spindle and kinetochore-associated protein 2
    0.00029   20.6  42.4      0.092   12.5   7.2    4.2  4  DUF4201          Domain of unknown function (DUF4201)
    0.00061   19.7  10.1    0.00061   19.7  10.1    3.6  3  NleF_casp_inhib  NleF caspase inhibitor
    0.00062   18.8  36.6      0.031   13.2  14.4    2.7  2  IFT57            Intra-flagellar transport protein 57
     0.0007   19.5  36.6     0.0096   15.9   6.9    4.6  6  FlxA             FlxA-like protein
    0.00074   19.3  34.0     0.0036   17.1  11.5    3.3  3  Laminin_I        Laminin Domain I
    0.00075   19.5  47.6      0.029   14.4   8.9    4.2  4  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
    0.00093   19.5  19.0       0.12   12.7   0.1    5.6  5  LPP              Lipoprotein leucine-zipper
    0.00093   19.6  37.9     0.0095   16.3   9.4    4.2  3  Uso1_p115_C      Uso1 / p115 like vesicle tethering protein, 
    0.00095   19.4  13.4       0.36   11.1   2.7    4.4  4  DUF948           Bacterial protein of unknown function (DUF94
    0.00097   19.2  26.9       0.14   12.2   4.2    4.7  4  DUF1664          Protein of unknown function (DUF1664)
     0.0012   18.5  42.2     0.0031   17.1  20.8    2.6  2  MscS_porin       Mechanosensitive ion channel porin domain
     0.0013   18.0  18.2      0.042   13.0   3.9    2.3  2  FH2              Formin Homology 2 Domain
     0.0013   18.6  34.6     0.0078   16.1  10.8    2.8  3  DUF724           Protein of unknown function (DUF724)
     0.0024   16.6  39.0      0.096   11.3  14.4    3.1  3  FapA             Flagellar Assembly Protein A
     0.0029   18.0   9.1     0.0029   18.0   9.1    4.2  4  CENP-H           Centromere protein H (CENP-H)
      0.003   17.7   8.7      0.003   17.7   8.7    4.2  2  Mod_r            Modifier of rudimentary (Mod(r)) protein
     0.0033   17.1  30.1      0.042   13.5  15.9    2.6  2  DUF2968          Protein of unknown function (DUF2968)
     0.0035   17.2  34.3       0.14   12.0  12.9    2.7  2  TACC_C           Transforming acidic coiled-coil-containing p
     0.0036   15.6  24.8      0.081   11.1   5.9    3.7  4  COG6             Conserved oligomeric complex COG6
     0.0037   15.5  41.7      0.096   10.8   6.2    3.5  2  HOOK             HOOK protein
     0.0039   17.8  37.7        1.6    9.4   6.0    4.9  3  YabA             Initiation control protein YabA
     0.0047   17.0   9.2     0.0047   17.0   9.2    3.8  4  BRE1             BRE1 E3 ubiquitin ligase
     0.0051   15.4   8.2       0.02   13.5   6.7    2.0  1  FUSC             Fusaric acid resistance protein family
     0.0051   14.4  35.6     0.0067   14.0  35.6    1.2  1  DUF3584          Protein of unknown function (DUF3584)
     0.0057   16.9  40.8       0.02   15.1   7.2    4.5  4  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
     0.0064   16.1  37.6      0.053   13.1  15.0    3.4  2  PI3K_P85_iSH2    Phosphatidylinositol 3-kinase regulatory sub
     0.0065   16.9   8.4     0.0065   16.9   8.4    5.0  2  DUF4200          Domain of unknown function (DUF4200)
     0.0078   15.8  42.2      0.026   14.1  17.0    3.2  2  Filament         Intermediate filament protein
     0.0084   16.4   5.7     0.0084   16.4   5.7    4.6  3  DUF349           Domain of Unknown Function (DUF349)
     0.0085   16.2  10.4     0.0085   16.2  10.4    4.7  5  ADIP             Afadin- and alpha -actinin-Binding
  ------ inclusion threshold ------
       0.01   16.3  10.4       0.01   16.3  10.4    6.0  4  ZapB             Cell division protein ZapB
      0.012   15.7   3.0      0.012   15.7   3.0    6.8  5  TolA_bind_tri    TolA binding protein trimerisation
      0.013   15.2  49.4       0.21   11.4   5.9    6.1  6  DivIC            Septum formation initiator
      0.013   15.9   5.2      0.013   15.9   5.2    5.1  3  KELK             KELK-motif containing domain of MRCK Ser/Thr
      0.015   14.8  18.2      0.036   13.6   4.7    2.9  3  Allexi_40kDa     Allexivirus 40kDa protein
      0.016   13.4  42.1      0.014   13.6   6.6    3.6  2  EzrA             Septation ring formation regulator, EzrA
      0.017   15.2  20.1      0.027   14.6   1.3    4.3  5  DUF2730          Protein of unknown function (DUF2730)
      0.021   14.9  29.3       0.27   11.3   6.4    4.3  4  COG2             COG (conserved oligomeric Golgi) complex com
      0.022   15.0  37.7      0.027   14.7   8.1    4.2  4  DUF5082          Domain of unknown function (DUF5082)
      0.027   14.2  24.1        0.1   12.3   5.5    2.9  3  LXG              LXG domain of WXG superfamily
       0.03   14.7  30.2      0.032   14.6   2.6    6.4  6  FlaC_arch        Flagella accessory protein C (FlaC)
      0.037   12.7  26.4      0.043   12.5   4.5    3.8  4  Dor1             Dor1-like family
      0.043   14.7   3.7        1.2   10.0   0.1    3.2  3  Cytochrom_C_2    Cytochrome C'
      0.045   14.2  29.3       0.25   11.8   9.8    3.6  3  DUF16            Protein of unknown function DUF16
      0.055   12.9  32.7       0.34   10.3   8.7    3.0  2  Flagellar_rod    Paraflagellar rod protein
      0.067   12.5  39.4       0.25   10.7  12.7    3.0  2  DUF2353          Uncharacterized coiled-coil protein (DUF2353
      0.073   12.1  45.0      0.013   14.6  20.0    2.7  2  Atg14            Vacuolar sorting 38 and autophagy-related su
      0.077   13.0  19.6       0.24   11.4   3.3    3.9  4  PilJ             Type IV pili methyl-accepting chemotaxis tra
      0.083   12.1  40.5        0.1   11.8   6.2    3.5  3  HAP1_N           HAP1 N-terminal conserved region
      0.084   12.2  27.9       0.24   10.7  13.0    2.4  2  DUF4407          Domain of unknown function (DUF4407)
      0.086   12.3  43.7      0.045   13.2  16.7    2.3  2  Golgin_A5        Golgin subfamily A member 5
      0.089   12.6  11.9       0.23   11.3   2.7    2.4  2  MCPsignal        Methyl-accepting chemotaxis protein (MCP) si
      0.094   13.2  40.7       0.83   10.1   1.5    6.0  5  DUF4140          N-terminal domain of unknown function (DUF41
      0.097   12.6  40.1        0.5   10.2  15.8    3.9  3  FTA4             Kinetochore complex Fta4 of Sim4 subunit, or
        0.1   12.7  39.8        1.5    8.9  14.8    3.4  2  Nup54            Nucleoporin complex subunit 54
       0.11   12.7  35.9        1.7    8.7   5.1    5.8  5  Swi5             Swi5
       0.12   12.2   4.3        1.6    8.5   0.2    3.6  3  DUF4051          Protein of unknown function (DUF4051)
       0.14   11.2  38.8       0.26   10.4  14.3    2.8  2  CCDC144C         CCDC144C protein coiled-coil region
       0.16   12.2  18.1         12    6.3   0.8    5.7  4  WXG100           Proteins of 100 residues with WXG
       0.17   12.0  14.7        0.4   10.8   2.8    3.1  2  Cob_adeno_trans  Cobalamin adenosyltransferase
       0.23   11.6   9.5       0.26   11.5   0.7    3.4  4  PI_PP_I          Phosphoinositide phosphatase insertion domai
       0.28   10.8  35.2       0.32   10.7  15.3    3.7  3  SHE3             SWI5-dependent HO expression protein 3
        0.3    9.7  34.6      0.021   13.5  21.1    2.6  2  AAA_13           AAA domain
       0.36   11.1   5.9        2.6    8.4   0.1    3.2  3  Cyclase_polyket  Polyketide synthesis cyclase
       0.38   11.0  36.2       0.14   12.4  11.9    2.2  2  zf-C4H2          Zinc finger-containing protein
        0.4    9.5  43.6      0.069   12.0  16.6    2.8  2  CALCOCO1         Calcium binding and coiled-coil domain (CALC
       0.45    9.4   8.1       0.15   10.9   1.9    2.2  2  DUF1729          Domain of unknown function (DUF1729)
       0.46   11.3  33.6       0.33   11.7   6.4    4.5  5  Occludin_ELL     Occludin homology domain
       0.48   10.2  26.1       0.28   11.0   6.0    3.5  3  SKA1             Spindle and kinetochore-associated protein 1
       0.52    9.5  32.7       0.23   10.6   5.6    3.6  4  TMPIT            TMPIT-like protein
       0.56   10.9  20.1        1.3    9.8   0.6    3.8  3  Cytochrom_B562   Cytochrome b562
       0.61   10.7   5.6       0.41   11.2   2.0    2.6  1  HD_assoc         Phosphohydrolase-associated domain
       0.66   10.2  45.7       0.62   10.3  16.4    3.9  3  FliJ             Flagellar FliJ protein
       0.89    7.4  20.5       0.59    8.0   4.8    2.1  2  Prominin         Prominin
       0.89   10.0  15.8        4.6    7.7   1.7    2.9  3  T3SSipB          Type III cell invasion protein SipB
       0.91    9.2  10.0       0.23   11.2   1.3    2.4  2  DUF932           Domain of unknown function (DUF932)
       0.91    9.5  40.1       0.21   11.6  17.1    2.6  2  Rootletin        Ciliary rootlet component, centrosome cohesi
          1   10.1  36.8       0.67   10.7   5.6    4.4  4  DUF4472          Domain of unknown function (DUF4472)
        1.1    7.3  40.4       0.49    8.5  13.6    2.6  2  FPP              Filament-like plant protein, long coiled-coi
        1.2    8.8  13.6        0.9    9.1   3.2    2.7  2  CDPS             Cyclodipeptide synthase
        1.3    8.3  25.8       0.64    9.3   8.4    2.6  2  CorA             CorA-like Mg2+ transporter protein
        1.3    8.3  36.6      0.066   12.6  13.0    3.0  3  Rab5-bind        Rabaptin-like protein
        1.3    9.3  37.1        3.2    8.1   1.1    5.9  2  Spc24            Spc24 subunit of Ndc80
        1.5    9.2  47.7        1.3    9.3   2.5    4.1  4  OmpH             Outer membrane protein (OmpH-like)
        1.6    8.4  27.6       0.37   10.5  10.2    2.6  3  DUF745           Protein of unknown function (DUF745)
        1.7    6.8  19.4       0.17   10.2   9.7    2.1  2  SpecificRecomb   Site-specific recombinase
        1.8    8.6  17.7       0.42   10.6   2.8    3.4  3  LOH1CR12         Tumour suppressor protein
        1.8    8.0  36.1       0.13   11.7  12.9    2.7  3  Leu_zip          Leucine zipper
        1.9    7.5  30.6        2.3    7.2   3.3    2.9  2  APG17            Autophagy protein Apg17
        1.9    8.2  16.4       0.24   11.1   2.0    3.1  2  DUF2937          Protein of unknown function (DUF2937)
        1.9    8.3   7.5         40    4.1   0.1    5.1  5  DASH_Dam1        DASH complex subunit Dam1
        2.2    9.0  25.5        4.6    7.9   1.6    4.0  1  AATF-Che1        Apoptosis antagonizing transcription factor
        2.3    9.0  30.6         32    5.3  10.3    4.2  3  DUF2203          Uncharacterized conserved protein (DUF2203)
        2.3    7.8  18.8        2.4    7.7   4.2    2.7  2  Phage_GPO        Phage capsid scaffolding protein (GPO) serin
        2.4    8.4  48.3       0.97    9.6  14.6    3.7  4  Jnk-SapK_ap_N    JNK_SAPK-associated protein-1
        2.4    8.2  50.8       0.66   10.0   8.2    5.0  5  DHR10            Designed helical repeat protein 10 domain
        2.6    7.4  37.5       0.78    9.1   2.7    5.0  4  DUF4618          Domain of unknown function (DUF4618)
        2.8    7.7  28.9      0.021   14.6   8.7    3.1  3  Mer2             Mer2
        2.8    7.3  29.1       0.78    9.1   1.3    3.8  4  HBM              Helical bimodular sensor domain
        3.1    8.4  28.9        9.8    6.8   6.0    4.4  4  Syntaxin-6_N     Syntaxin 6, N-terminal
        3.5    7.7  23.7        0.3   11.1   0.5    5.0  5  DUF4298          Domain of unknown function (DUF4298)
        3.6    7.9  46.1        3.4    8.0   9.6    5.1  5  THOC7            Tho complex subunit 7
          4    7.5  23.3         13    5.8   7.9    3.6  3  GldM_N           GldM N-terminal domain
        4.1    6.5  44.1        2.9    7.0  12.8    3.4  2  Taxilin          Myosin-like coiled-coil protein
        4.5    6.4  15.6        3.7    6.6   5.0    3.0  4  Med3             Mediator complex subunit 3 fungal
        5.1    6.7  51.2       0.94    9.1  27.3    3.7  1  Lebercilin       Ciliary protein causing Leber congenital ama
        5.2    6.6  44.5        2.9    7.4   1.5    4.4  3  PspA_IM30        PspA/IM30 family
        5.5    7.4   9.9        8.6    6.8   1.0    3.3  3  DUF3037          Protein of unknown function (DUF3037)
        5.8    5.7  46.1       0.16   10.9   6.1    3.4  3  DUF812           Protein of unknown function (DUF812)
        5.9    6.9  13.6       0.77    9.8   1.9    3.5  2  COX5A            Cytochrome c oxidase subunit Va
        6.5    4.5  28.7        2.3    6.1  12.5    2.1  2  V_ATPase_I       V-type ATPase 116kDa subunit family
        6.8    4.9  45.8       0.66    8.3  29.7    2.3  1  MAD              Mitotic checkpoint protein
        7.5    6.1  36.6       0.14   11.8  17.7    3.7  3  DUF4795          Domain of unknown function (DUF4795)
          8    7.0  25.4        7.2    7.1   2.4    5.6  5  DASH_Dad2        DASH complex subunit Dad2
        8.4    7.1  23.7        2.5    8.8   0.7    4.0  3  DUF4665          Domain of unknown function (DUF4665)
        8.9    6.1  31.8        4.1    7.2   4.1    3.8  3  She9_MDM33       She9 / Mdm33 family
          9    7.3  46.0         10    7.1   1.8    4.8  4  PRKG1_interact   cGMP-dependent protein kinase interacting do
        9.3    6.5  39.8       0.57   10.4  11.1    5.5  5  JIP_LZII         JNK-interacting protein  leucine zipper II


Domain annotation for each model (and alignments):
>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   6.1   4.9e-05    0.0065      18      97 ..       7      83 ..       2      85 .. 0.76
   2 ?    5.6   0.2      0.11        15      12      65 ..      78     131 ..      75     160 .. 0.64
   3 !   23.7   8.2   2.9e-07   3.8e-05       4      84 ..     150     229 ..     148     240 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.9e-05
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH...HHHHHHHHHH CS
                     Laminin_II 18 qlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeassslsdniseike 97
                                    ++ l q+l + ++kl+ei ++++e   k ++an  ++  + +++ L ++ + L +++  + ++++    l ++is+++e
  gi|119719290|ref|YP_919785.1|  7 SIESLRQQLIEYRQKLQEISAKIQEARSKRDSANGEVKRISAEIRSLREQYQALRQQIAAVAEQKKT---LYEKISKLRE 83
                                   4567778888888888888888888888888888888888888888888888888888888777777...9999999887 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.11
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX- CS
                     Laminin_II  12 akevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLe 65 
                                    +++  e ++++ ++l++++++l+++n++ ++    + ++    ++ r+ + +Le
  gi|119719290|ref|YP_919785.1|  78 ISKLREEKKGILEQLNKLRDELKRLNAEYNNLRGFLGSKRYDEDELRNRIEQLE 131
                                    455556666666666666666666666666555556666666666666666655 PP

  == domain 3  score: 23.7 bits;  conditional E-value: 2.9e-07
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHH CS
                     Laminin_II   4 laaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqlee 83 
                                    ++++ +++ ++v + l+++ +++e++++++ e++++v+ +ne++k        ++++++ L+++ ++L+++l elkq ++
  gi|119719290|ref|YP_919785.1| 150 KIRSLESIYVNV-KHLNEVRAKIEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQRDELVKRLVELKQERD 228
                                    567777777777.5689************************************************************998 PP

                                    H CS
                     Laminin_II  84 a 84 
                                     
  gi|119719290|ref|YP_919785.1| 229 R 229
                                    6 PP

>> TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   1.1       2.1   2.8e+02      54      82 ..       3      31 ..       1      39 [. 0.66
   2 !   31.7  11.2   1.1e-09   1.4e-07      12     109 ..      41     135 ..      30     138 .. 0.91
   3 ?    4.5   0.4      0.29        38      58      83 ..     163     188 ..     142     196 .. 0.54
   4 ?    4.8  16.7      0.24        32      15      88 ..     186     263 ..     184     291 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 2.1
                    TMF_TATA_bd 54 keneelkelkkeleelekeleelqeryet 82
                                   +e+e+ ++l ++l e +++l+e++ + ++
  gi|119719290|ref|YP_919785.1|  3 AETESIESLRQQLIEYRQKLQEISAKIQE 31
                                   46666677777777777777777666655 PP

  == domain 2  score: 31.7 bits;  conditional E-value: 1.1e-09
                    TMF_TATA_bd  12 qlverlsseirrlEgElaslkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqeryetlLellGeks 91 
                                      v+r+s+eir+l  ++++l+++++ ++++++++ e i kl    ee+k   ++l++l+ el+ l+ +y++l   lG k 
  gi|119719290|ref|YP_919785.1|  41 GEVKRISAEIRSLREQYQALRQQIAAVAEQKKTLYEKISKLR---EEKKGILEQLNKLRDELKRLNAEYNNLRGFLGSKR 117
                                    5589**********************************9997...899999***************************** PP

                    TMF_TATA_bd  92 EeveELraDvaDlKemyk 109
                                       +ELr+ ++ l   y+
  gi|119719290|ref|YP_919785.1| 118 YDEDELRNRIEQLEWQYQ 135
                                    **********99876665 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.29
                    TMF_TATA_bd  58 elkelkkeleelekeleelqeryetl 83 
                                     l+e  +++ee+++++ el+++ +++
  gi|119719290|ref|YP_919785.1| 163 HLNEVRAKIEEIRAQIPELKKKVQAI 188
                                    34444444444444444444444443 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.24
                    TMF_TATA_bd  15 erlsseirrlEgElaslkeelerleaerdeareeivklmkeneelkelkkeleelek....eleelqeryetlLellG 88 
                                    + ++ e++   +E+ ++ke+++ l+++rde+ + +v+l +e ++ +e+++++ ++      e ++l+e++e +  ll+
  gi|119719290|ref|YP_919785.1| 186 QAINEELKTVVSEYLKVKEQMQALKQQRDELVKRLVELKQERDRIRETANNYHQIYIsllsEEKSLREELERISILLK 263
                                    56778899999*********************************9999998887654333355555555555555554 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9  13.5   3.4e-05    0.0045     162     245 ..       5      87 ..       1      91 [. 0.47
   2 !   11.6   4.7   0.00069     0.091     174     247 ..      69     138 ..      67     156 .. 0.85
   3 !   11.3   7.8   0.00086      0.11     182     247 ..     150     217 ..     142     222 .. 0.48
   4 ?    5.5   9.5      0.05       6.6     134     208 ..     206     278 ..     205     291 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.4e-05
                           Spc7 162 eeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelke 241
                                     e +++l ++l e++++l+e  +k+qea+ +  ++ + e++ +  e+++l ++++++++++a + eq+++l eki++l+e
  gi|119719290|ref|YP_919785.1|   5 TESIESLRQQLIEYRQKLQEISAKIQEARSK-RDSANGEVKRISAEIRSLREQYQALRQQIAAVAEQKKTLYEKISKLRE 83 
                                    4445555555555555555555555553332.444555555555555555555555555555555555555555555555 PP

                           Spc7 242 qkse 245
                                    +k+ 
  gi|119719290|ref|YP_919785.1|  84 EKKG 87 
                                    5544 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00069
                           Spc7 174 eekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqksele 247
                                    e+k++l e++ kl+e+++       e+L++lr+el++l+ae+++++  l +++ + +el+++ie+l+ q++++ 
  gi|119719290|ref|YP_919785.1|  69 EQKKTLYEKISKLREEKKG----ILEQLNKLRDELKRLNAEYNNLRGFLGSKRYDEDELRNRIEQLEWQYQTMT 138
                                    6788888999999996665....5789*************************************9999998875 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.00086
                           Spc7 182 eleklqeaaeelesid..keeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqksele 247
                                    ++++l++ + +++ ++  ++++ee+r ++ elk+++++ ++el+++ ++  +++e++++lk+q++el 
  gi|119719290|ref|YP_919785.1| 150 KIRSLESIYVNVKHLNevRAKIEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQRDELV 217
                                    44444444444444333344555555555555555555555555555555555555555555555544 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.05
                           Spc7 134 mqllegLkegleenlegleedkelLekqeeeldellpeleeekaeleeeleklqe..aaeelesidkeeLeelreel 208
                                    mq l++ +++l ++l +l+++++++ +  ++ ++++ +l +e+++l+eele++    +a+el    ++ Lee +++l
  gi|119719290|ref|YP_919785.1| 206 MQALKQQRDELVKRLVELKQERDRIRETANNYHQIYISLLSEEKSLREELERISIllKAKEL----SQHLEERKRQL 278
                                    78888889999999999999999999999999999999999999999999988763222222....33455555554 PP

>> HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interacting protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   2.1     0.026       3.5      50      97 ..       4      51 ..       1      53 [. 0.90
   2 !   18.9   4.8   1.3e-05    0.0017      14      93 ..      56     131 ..      52     136 .. 0.93
   3 !   15.3   5.9   0.00017     0.022      36      98 ..     167     229 ..     149     230 .. 0.88
   4 ?    1.0   0.4       4.8   6.4e+02      28      55 ..     247     272 ..     234     291 .. 0.49

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.026
                 HIP1_clath_bdg 50 qkeelekLkreleakraelarlkssLesseqsgeqlssqlaaLqaEke 97
                                    +e +e+L+++l + r++l+++ + +++   + +  + +++ + aE  
  gi|119719290|ref|YP_919785.1|  4 ETESIESLRQQLIEYRQKLQEISAKIQEARSKRDSANGEVKRISAEIR 51
                                   67899*******************************999999999855 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 1.3e-05
                 HIP1_clath_bdg  14 qlsvarqaqeeverekkeleeelerlkeeaerkleeqkeelekLkreleakraelarlkssLesseqsgeqlssqlaaLq 93 
                                    q ++ rq+   v+ +kk+l e++ +l+ee++  l    e+l+kL+ el++ +ae ++l++ L s+   +++l +++++L+
  gi|119719290|ref|YP_919785.1|  56 QYQALRQQIAAVAEQKKTLYEKISKLREEKKGIL----EQLNKLRDELKRLNAEYNNLRGFLGSKRYDEDELRNRIEQLE 131
                                    78899999********************998776....5799************************************98 PP

  == domain 3  score: 15.3 bits;  conditional E-value: 0.00017
                 HIP1_clath_bdg  36 lerlkeeaerkleeqkeelekLkreleakraelarlkssLesseqsgeqlssqlaaLqaEkes 98 
                                    +++  ee + ++ e k++++++++el++   e  ++k+ ++  +q+ ++l ++l +L++E+++
  gi|119719290|ref|YP_919785.1| 167 VRAKIEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQRDELVKRLVELKQERDR 229
                                    44444666778889999********************************************97 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 4.8
                 HIP1_clath_bdg  28 ekkeleeelerlkeeaerkleeqkeele 55 
                                    e k l eeler++   + k+    ++le
  gi|119719290|ref|YP_919785.1| 247 EEKSLREELERISILLKAKELS--QHLE 272
                                    3444444444444332222222..2222 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.4      0.54        72      38      66 ..       3      31 ..       1      35 [. 0.78
   2 !   10.7   6.9    0.0028      0.37       9      69 ..      33      93 ..      11     108 .. 0.56
   3 !   19.1   4.0   7.1e-06   0.00094       4      73 ..     170     239 ..     153     243 .. 0.94
   4 !   11.2   3.2     0.002      0.26       8      68 ..     202     262 ..     196     284 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.54
                          Sec34 38 ektsslheaceqlleeqkrleelaeeiee 66
                                   ++t+s+++  +ql+e +++l+e++ +i+e
  gi|119719290|ref|YP_919785.1|  3 AETESIESLRQQLIEYRQKLQEISAKIQE 31
                                   57888888888888888888888888876 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0028
                          Sec34  9 eeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLk 69
                                   +++ d+   +++++  ++++l+e++++  ++  ++ e+ ++l+e+ ++l+e ++ i e+L+
  gi|119719290|ref|YP_919785.1| 33 RSKRDSANGEVKRISAEIRSLREQYQALRQQIAAVAEQKKTLYEKISKLREEKKGILEQLN 93
                                   4444444445555555555555555555555555555555555555555555555555543 PP

  == domain 3  score: 19.1 bits;  conditional E-value: 7.1e-06
                          Sec34   4 qLeskeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLkyFee 73 
                                    ++e+ ++++ el +++++++e+L+++ +++ +v+e++++l+++ ++l++   +l++  + i+e  + + +
  gi|119719290|ref|YP_919785.1| 170 KIEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQRDELVKRLVELKQERDRIRETANNYHQ 239
                                    6778889999*****************************************************9998876 PP

  == domain 4  score: 11.2 bits;  conditional E-value: 0.002
                          Sec34   8 keeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekL 68 
                                     +e++++l +q de+ + L el+++ +++ e  ++ h+   +ll+e+k+l+e  e i+  L
  gi|119719290|ref|YP_919785.1| 202 VKEQMQALKQQRDELVKRLVELKQERDRIRETANNYHQIYISLLSEEKSLREELERISILL 262
                                    57899**********************************************9999997655 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   6.5     0.029       3.8      66     133 ..       4      71 ..       1      75 [. 0.78
   2 !   25.7  11.7   8.1e-08   1.1e-05      66     190 ..      70     196 ..      67     198 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.029
                        UPF0242  66 ekskleekeaklteldeglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedf 133
                                    e++ +e+  ++l e +++l+++  +++e++++ +  + e++  + e++ l+e+ q L+++  a+ae+ 
  gi|119719290|ref|YP_919785.1|   4 ETESIESLRQQLIEYRQKLQEISAKIQEARSKRDSANGEVKRISAEIRSLREQYQALRQQIAAVAEQK 71 
                                    55666777777788888888888899999999999999999999999999999999998888877765 PP

  == domain 2  score: 25.7 bits;  conditional E-value: 8.1e-08
                        UPF0242  66 ekskleekeaklteldeglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelkl..eleeq 143
                                    +k++l ek++kl e++   k + e+l++l++e ++L+ e+++    l   + ++ +L+ + e+   +++ + l  e+e+ 
  gi|119719290|ref|YP_919785.1|  70 QKKTLYEKISKLREEK---KGILEQLNKLRDELKRLNAEYNNLRGFLGSKRYDEDELRNRIEQLEWQYQTMTLppEVEKV 146
                                    6777888889998888...999******************************************99999887655999** PP

                        UPF0242 144 Laekqellqey...qetieeqrsvlekrqdqieqLeskVrDlnyEiktLl 190
                                    L +k   l+      + ++e r+ +e+  +qi +L  kV+ +n E+kt +
  gi|119719290|ref|YP_919785.1| 147 LVNKIRSLESIyvnVKHLNEVRAKIEEIRAQIPELKKKVQAINEELKTVV 196
                                    *9998877765122577899****************************86 PP

>> DUF4763  Domain of unknown function (DUF4763)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9  10.9   1.6e-07   2.2e-05      58     155 ..       8     103 ..       2     109 .. 0.85
   2 ?    6.5   8.2     0.035       4.6      98     155 ..     160     217 ..     115     229 .. 0.76
   3 ?    4.0  11.0       0.2        26     102     155 ..     164     217 ..     150     289 .. 0.58

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 1.6e-07
                        DUF4763  58 lekiKqrvlelrskLalnvpecPei.decvdedlelelltseqpeileLqrnnhkLrqqlaelqqhlkasrkslkelres 136
                                    +e ++q++ e+r+kL  ++    +i +   ++d  + +++  + ei+ L+ + + Lrqq+a +++++k+  +++++lre+
  gi|119719290|ref|YP_919785.1|   8 IESLRQQLIEYRQKLQ-EIS--AKIqEARSKRDSANGEVKRISAEIRSLREQYQALRQQIAAVAEQKKTLYEKISKLREE 84 
                                    5667777777777777.333..2332777788888889999*************************************** PP

                        DUF4763 137 lcqekkrlrklqkrlneld 155
                                        +++l+kl+ +l++l+
  gi|119719290|ref|YP_919785.1|  85 KKGILEQLNKLRDELKRLN 103
                                    ***************9987 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.035
                        DUF4763  98 eqpeileLqrnnhkLrqqlaelqqhlkasrkslkelreslcqekkrlrklqkrlneld 155
                                    +  +++e++ +   +r q+ el+++ +a +++lk + +++ + k+++++l+++ +el 
  gi|119719290|ref|YP_919785.1| 160 NVKHLNEVRAKIEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQRDELV 217
                                    4467888999999999999999999999999999999999999999999998888774 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.2
                        DUF4763 102 ileLqrnnhkLrqqlaelqqhlkasrkslkelreslcqekkrlrklqkrlneld 155
                                    ++e++ +   +r q+ el+++ +a +++lk + +++ + k+++++l+++ +el 
  gi|119719290|ref|YP_919785.1| 164 LNEVRAKIEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQRDELV 217
                                    444444444444444444444444444444444444444444444444444432 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9  11.7    0.0002     0.026      56     131 ..       8      80 ..       1      86 [. 0.69
   2 ?    7.8   3.2     0.014       1.9      54     110 ..      83     136 ..      77     146 .. 0.53
   3 !   12.8  11.2   0.00042     0.055      63     131 ..     154     222 ..     144     226 .. 0.80
   4 !    9.0  20.6     0.006       0.8      27     109 ..     170     249 ..     164     291 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.0002
                            GAS  56 nkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrfekvekerdelykkfea 131
                                     ++l+++L + +++++e  ++++   + +++ ++++ ++k+   e+++l+++++ l+q++++v +++++ly+k  +
  gi|119719290|ref|YP_919785.1|   8 IESLRQQLIEYRQKLQEISAKIQ---EARSKRDSANGEVKRISAEIRSLREQYQALRQQIAAVAEQKKTLYEKISK 80 
                                    33344444444444444444443...44445557788999999****************************99766 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.014
                            GAS  54 qenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehev 110
                                    +e+k     L+++++ ++eL++  ++y++ +  l + +    el + +++l+w+++ 
  gi|119719290|ref|YP_919785.1|  83 EEKK---GILEQLNKLRDELKRLNAEYNNLRGFLGSKRYDEDELRNRIEQLEWQYQT 136
                                    3333...33344444444444444555555566666666666666666666666655 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 0.00042
                            GAS  63 LkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrfekvekerdelykkfea 131
                                    L+    +v++L++  ++ e+ ++++ +lk++++  ++elk++  e+  +++++++++++rdel k+  +
  gi|119719290|ref|YP_919785.1| 154 LESIYVNVKHLNEVRAKIEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQRDELVKRLVE 222
                                    566666788888888888888889999999999999999999999999999999999999998887665 PP

  == domain 4  score: 9.0 bits;  conditional E-value: 0.006
                            GAS  27 lIkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkw 106
                                    +I++ + +i elkkk ++ + el+ + +e  + ke++++++++++eL k+l + ++++ +++++ +++++    l +   
  gi|119719290|ref|YP_919785.1| 170 KIEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQRDELVKRLVELKQERDRIRETANNYHQIYISLLSE-- 247
                                    688899999999999999999999999999999999999999999999999988888887777766665543322222.. PP

                            GAS 107 ehe 109
                                      +
  gi|119719290|ref|YP_919785.1| 248 -EK 249
                                    .22 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5  12.3   0.00021     0.027      53     127 ..       2      79 ..       1      81 [. 0.86
   2 !   11.6  11.0    0.0017      0.23       3     102 ..      36     135 ..      34     138 .. 0.85
   3 !   18.3   8.8   1.4e-05    0.0018      56     118 ..     161     226 ..     159     232 .. 0.89
   4 ?   -0.1   3.2       6.8     9e+02      69     108 ..     244     285 ..     227     290 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 0.00021
                     TPR_MLP1_2  53 aedvkelqalreelnelkaeiaelkaeaesakaeleeseeswe...eqkeelekelselekriedlneqNklLhdQlE 127
                                    a++++++++lr++l e++++++e+ a+ ++a+++ + +  + +    +  +l+++ + l+++i  + eq k+L++++ 
  gi|119719290|ref|YP_919785.1|   2 AAETESIESLRQQLIEYRQKLQEISAKIQEARSKRDSANGEVKrisAEIRSLREQYQALRQQIAAVAEQKKTLYEKIS 79 
                                    7889999************************9999998866541116788999*********************9985 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.0017
                     TPR_MLP1_2   3 lksleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaes 82 
                                     +s++ e+k++++e+ +++++ q+l++++ + ae+ k+  +k ++   +++  +++l++lr+el++l+ae+++l+  + s
  gi|119719290|ref|YP_919785.1|  36 RDSANGEVKRISAEIRSLREQYQALRQQIAAVAEQKKTLYEKISKLREEKKGILEQLNKLRDELKRLNAEYNNLRGFLGS 115
                                    67888899999999999999999999999999999999999999999999999999999999999999999999988888 PP

                     TPR_MLP1_2  83 akaeleeseesweeqkeele 102
                                     + + +e ++ +e+ + +++
  gi|119719290|ref|YP_919785.1| 116 KRYDEDELRNRIEQLEWQYQ 135
                                    88777777777777666665 PP

  == domain 3  score: 18.3 bits;  conditional E-value: 1.4e-05
                     TPR_MLP1_2  56 vkelqalreelnelkaeiaelkaeaesakaeleesee...sweeqkeelekelselekriedlneq 118
                                    vk l+++r++++e++a+i elk+++++ ++el++  +   + +eq ++l+++ +el kr+ +l++ 
  gi|119719290|ref|YP_919785.1| 161 VKHLNEVRAKIEEIRAQIPELKKKVQAINEELKTVVSeylKVKEQMQALKQQRDELVKRLVELKQE 226
                                    899*****************************9987722357999999**************9975 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 6.8
                     TPR_MLP1_2  69 lkaeiaelkaeaesakaeleese..esweeqkeelekelsel 108
                                    l +e ++l++e+e+ +  l+++e  +++ee+k +l  +  e+
  gi|119719290|ref|YP_919785.1| 244 LLSEEKSLREELERISILLKAKElsQHLEERKRQLYGKAMEA 285
                                    445556666666666666665543255666666665555554 PP

>> KASH_CCD  Coiled-coil region of CCDC155 or KASH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3  23.1   3.7e-07   4.9e-05      16     189 ..      18     193 ..       4     195 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 3.7e-07
                       KASH_CCD  16 nNkkLaeenskLkkavetaeetn...akLteeieeLkkklkstQqalqkaklleeEleelkalvkeleEkrarlkaqnkq 92 
                                      +kL+e  +k+++a  + + +n   +++++ei  L+++ +    + q+  +++e    l + +++l E+++ +  q ++
  gi|119719290|ref|YP_919785.1|  18 YRQKLQEISAKIQEARSKRDSANgevKRISAEIRSLREQYQ---ALRQQIAAVAEQKKTLYEKISKLREEKKGILEQLNK 94 
                                    369**********99888887774447899********975...55667889**************************** PP

                       KASH_CCD  93 lekenqsLiakiesLqeenikllaekdelkkklkeLlkekaeLkkqlheleellaekeallee...ktkqieeLkltieE 169
                                    l  e + L+a+ ++L   +   + ++del++++++L  + +++     e+e++l++k ++le      k+ +e+++ ieE
  gi|119719290|ref|YP_919785.1|  95 LRDELKRLNAEYNNLRGFLGSKRYDEDELRNRIEQLEWQYQTMTLPP-EVEKVLVNKIRSLESiyvNVKHLNEVRAKIEE 173
                                    *************************************9999999988.99999999988776522267888899999*** PP

                       KASH_CCD 170 yssiieeLraeksrLeeqlq 189
                                    +++ i eL++ ++ ++e+l+
  gi|119719290|ref|YP_919785.1| 174 IRAQIPELKKKVQAINEELK 193
                                    ************99999886 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3  13.8   9.5e-07   0.00013      73     169 ..      12     108 ..       2     113 .. 0.88
   2 !   12.1  11.1    0.0012      0.17     125     194 ..     157     226 ..     117     229 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 9.5e-07
                          ATG16  73 sakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekekl 152
                                    ++++ +  qkl+++ +  +e+  +r   +  +++ ++e++ l+e+ ++ ++++a++ +++++l +k+++++ee ++  + 
  gi|119719290|ref|YP_919785.1|  12 RQQLIEYRQKLQEISAKIQEARSKRDSANGEVKRISAEIRSLREQYQALRQQIAAVAEQKKTLYEKISKLREEKKGILEQ 91 
                                    445666677777777888888888889999************************************************** PP

                          ATG16 153 vqdlqDElsaLqlqlnq 169
                                    +++l+DEl  L+ ++n 
  gi|119719290|ref|YP_919785.1|  92 LNKLRDELKRLNAEYNN 108
                                    **************996 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.0012
                          ATG16 125 laeleaeraaletklkdreeelrekeklvqdlqDElsaLqlqlnqaEeklrklekENkeLveRWmkrkaq 194
                                    +    ++ ++++ k+++ ++++ e++k vq++ +El +   ++ ++ e+ + l++   eLv+R+++ k++
  gi|119719290|ref|YP_919785.1| 157 IYVNVKHLNEVRAKIEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQRDELVKRLVELKQE 226
                                    44555677888999*****************************************************997 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.2       1.1   1.4e+02      36      60 ..       7      31 ..       1      52 [. 0.60
   2 !   11.2   5.3     0.003       0.4      26      66 ..     153     193 ..      43     201 .. 0.88
   3 !   13.1   4.6   0.00077       0.1       8      52 ..     173     217 ..     171     269 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 1.1
                        NPV_P10 36 dvtelnekLdaqsaqLaeletkven 60
                                    ++ l ++L +  ++L+e+++k+++
  gi|119719290|ref|YP_919785.1|  7 SIESLRQQLIEYRQKLQEISAKIQE 31
                                   4445555555555555555555443 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.003
                        NPV_P10  26 qvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiLn 66 
                                    +++++  n++ ++e+ +k++++ aq+ el++kv++I++ L 
  gi|119719290|ref|YP_919785.1| 153 SLESIYVNVKHLNEVRAKIEEIRAQIPELKKKVQAINEELK 193
                                    45667778899999999999999999999999999998775 PP

  == domain 3  score: 13.1 bits;  conditional E-value: 0.00077
                        NPV_P10   8 vIradikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLa 52 
                                     Ira i ++++kV+a++++++ v ++  +v+e  + L +q ++L 
  gi|119719290|ref|YP_919785.1| 173 EIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQRDELV 217
                                    69*********************9999988766666655555442 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0  21.3     5e-05    0.0066      24     122 ..      11     109 ..       1     139 [. 0.48
   2 ?    7.0   0.5     0.061       8.2      67     105 ..     161     199 ..     149     201 .. 0.85
   3 !   10.6  16.4    0.0046      0.61      33     121 ..     172     257 ..     160     271 .. 0.59

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 5e-05
                         APG6_N  24 erdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwr 103
                                     r+++ e+ +kl++ + + ++ ++++++++ e++++++e ++l e+ ++l ++ ++++++ ++l e+ ++l ee++  ++
  gi|119719290|ref|YP_919785.1|  11 LRQQLIEYRQKLQEISAKIQEARSKRDSANGEVKRISAEIRSLREQYQALRQQIAAVAEQKKTLYEKISKLREEKKGILE 90 
                                    45555555555554444444444455555555555555555555555555555555555555555555555555555555 PP

                         APG6_N 104 eynelqlelleleeeldsl 122
                                    + n+l+ el++l+ e + l
  gi|119719290|ref|YP_919785.1|  91 QLNKLRDELKRLNAEYNNL 109
                                    5555555555555444433 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.061
                         APG6_N  67 leeLkelekereeleaelaaleeelealeeeeerfwrey 105
                                    ++ L+e+ ++ ee++a++ +l+++ +a++ee +  ++ey
  gi|119719290|ref|YP_919785.1| 161 VKHLNEVRAKIEEIRAQIPELKKKVQAINEELKTVVSEY 199
                                    578899999999999999999999999999988877776 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.0046
                         APG6_N  33 kklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynelqlel 112
                                    ++++++ +e    ++++++++eel+++ +e  +  e++++l+++r+el + l +l++e +++ e  +++ + y +l  e 
  gi|119719290|ref|YP_919785.1| 172 EEIRAQIPE---LKKKVQAINEELKTVVSEYLKVKEQMQALKQQRDELVKRLVELKQERDRIRETANNYHQIYISLLSEE 248
                                    233333333...34566666666666666666666666666666666666666666666666666666666666666666 PP

                         APG6_N 113 leleeelds 121
                                    ++l eel+ 
  gi|119719290|ref|YP_919785.1| 249 KSLREELER 257
                                    666666554 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   4.1     0.011       1.4      18      80 ..      43     103 ..       2     109 .. 0.39
   2 !   14.6   0.7    0.0002     0.026      25      98 ..      50     138 ..      38     162 .. 0.60
   3 !   11.6   2.8    0.0016      0.22      18      99 ..     164     246 ..     148     264 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.011
                   Baculo_PEP_C  18 LtnvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq 80 
                                    +  + + ir++  q   +l ++++a+++q ++l e++++l +  ++ + ++l++L d l++l+
  gi|119719290|ref|YP_919785.1|  43 VKRISAEIRSLREQY-QALRQQIAAVAEQKKTLYEKISKLRE-EKKGILEQLNKLRDELKRLN 103
                                    222223333333333.33333333333333333333333222.22222223333333333333 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 0.0002
                   Baculo_PEP_C  25 irlqnvqilaqlatlldaietqLnalsedlksllaeldt......rldtlltnLtdalnalq..........dtlrneLt 88 
                                    ir++  q   +l ++++a+++q ++l e++++l +e +       +l + l++L++  n+l           d+lrn+++
  gi|119719290|ref|YP_919785.1|  50 IRSLREQY-QALRQQIAAVAEQKKTLYEKISKLREEKKGileqlnKLRDELKRLNAEYNNLRgflgskrydeDELRNRIE 128
                                    55555555.55555555555555555555555444333333322266666666777777776888888888888888888 PP

                   Baculo_PEP_C  89 nlnsiltnLl 98 
                                     l+ +  +++
  gi|119719290|ref|YP_919785.1| 129 QLEWQYQTMT 138
                                    8887666655 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.0016
                   Baculo_PEP_C  18 LtnvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq...dtlrneLtnlnsil 94 
                                    L++v + i    +qi  +l++ ++ai+++L+++ ++  + ++e+ ++l+++ ++L + l +l+   d +r+  +n  +i 
  gi|119719290|ref|YP_919785.1| 164 LNEVRAKIEEIRAQI-PELKKKVQAINEELKTVVSEYLK-VKEQMQALKQQRDELVKRLVELKqerDRIRETANNYHQIY 241
                                    444444555555555.55666667777777777766666.5666668999999999999999888888888888877777 PP

                   Baculo_PEP_C  95 tnLls 99 
                                     +Lls
  gi|119719290|ref|YP_919785.1| 242 ISLLS 246
                                    77666 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   9.4       0.3        39      42      93 ..      18      69 ..       1      75 [. 0.39
   2 !   16.3   6.7   3.5e-05    0.0046      16      93 ..      55     132 ..      52     140 .. 0.91
   3 !   12.0  11.5   0.00072     0.096      16      94 ..     162     240 ..     153     279 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.3
                        DUF3450 42 lddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeiee 93
                                   + ++ qe++a++++++++ +s++ + ++ ++ ++s++++ + l++qi+ + e
  gi|119719290|ref|YP_919785.1| 18 YRQKLQEISAKIQEARSKRDSANGEVKRISAEIRSLREQYQALRQQIAAVAE 69
                                   2333333333333334444444444444444444444444444444333333 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 3.5e-05
                        DUF3450  16 atldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeiee 93 
                                    ++ ++++++ ++  ++++   +ki+kl +ek+ +l+++++l++el++l+++ ++l+  + s + + ++l+++ie++e 
  gi|119719290|ref|YP_919785.1|  55 EQYQALRQQIAAVAEQKKTLYEKISKLREEKKGILEQLNKLRDELKRLNAEYNNLRGFLGSKRYDEDELRNRIEQLEW 132
                                    56778888888999999999******************************************************9985 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 0.00072
                        DUF3450  16 atldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieei 94 
                                    + l++++++ e++ a+  +  kk++++++e +++++ey ++ke+ ++l+ ++++l + + +++qe+++++e  ++  +i
  gi|119719290|ref|YP_919785.1| 162 KHLNEVRAKIEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQRDELVKRLVELKQERDRIRETANNYHQI 240
                                    678999999999999999999***********************************************99999988776 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1  15.3   9.2e-05     0.012      32     165 ..       7     132 ..       1     161 [. 0.80
   2 !   12.0  16.1    0.0016      0.21      35     151 ..     166     278 ..     157     292 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 9.2e-05
                           Fez1  32 eivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelselsleee 111
                                     i +l+ ql e r+kl+e  ++i+e+++++++ + e++++ +e++  +++ + lr+++ ++ e+ k l e++s+l +e++
  gi|119719290|ref|YP_919785.1|   7 SIESLRQQLIEYRQKLQEISAKIQEARSKRDSANGEVKRISAEIRSLREQYQALRQQIAAVAEQKKTLYEKISKLREEKK 86 
                                    56689****************************************************************99999765544 PP

                           Fez1 112 eaalesdeakaqrqeaeeleelkreverlraeLkeerqkkeeqassFeqERrtW 165
                                      +le+ +     + ++el++l++e ++lr+ L  +r  ++e ++    E   W
  gi|119719290|ref|YP_919785.1|  87 G-ILEQLN-----KLRDELKRLNAEYNNLRGFLGSKRYDEDELRNR--IEQLEW 132
                                    4.433333.....223568888889999998888888776666544..344444 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.0016
                           Fez1  35 alkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelselsleeeeaa 114
                                    +++a++ e+ra++ e  ++++ ++e+l++   e  ++++++q  k++ + l +++ +l++e  ++re++++ ++      
  gi|119719290|ref|YP_919785.1| 166 EVRAKIEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQRDELVKRLVELKQERDRIRETANNYHQIYI--- 242
                                    57889999999999999999999999999999999999999999999999999999999999999997776433222... PP

                           Fez1 115 lesdeakaqrqeaeeleelkreverlraeLkeerqkk 151
                                    +  +e k  r+e e+++ l +  ++l ++L+e +++ 
  gi|119719290|ref|YP_919785.1| 243 SLLSEEKSLREELERISILLK-AKELSQHLEERKRQL 278
                                    233333555666444444433.455666666555443 PP

>> SKA2  Spindle and kinetochore-associated protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3  10.9   1.1e-05    0.0015       2      95 ..       6      99 ..       5     110 .. 0.90
   2 ?    0.5   0.2       3.9   5.2e+02      44      63 ..     161     180 ..     118     183 .. 0.59
   3 ?    6.5   8.8     0.053         7      28      75 ..     173     220 ..     162     248 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.1e-05
                           SKA2  2 savdklealFqkaesdLdyvqhrLekefqqsypdnaeNpvkLlerlkkvkeelqaLkeqceellaekkelidkirttlvanr 83
                                   +++++l++++ +  ++L+ ++ + ++  ++  + n+ ++ ++ ++++ ++e++qaL++q+ +++++kk l +ki++   + +
  gi|119719290|ref|YP_919785.1|  6 ESIESLRQQLIEYRQKLQEISAKIQEARSKRDSANG-EVKRISAEIRSLREQYQALRQQIAAVAEQKKTLYEKISKLREEKK 86
                                   5899*********************99999999998.**************************************9999999 PP

                           SKA2 84 ellqqLqasa.el 95
                                    +l+qL++   el
  gi|119719290|ref|YP_919785.1| 87 GILEQLNKLRdEL 99
                                   9999998755555 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 3.9
                           SKA2  44 lerlkkvkeelqaLkeqcee 63 
                                    ++ l++v+++++++++q+ e
  gi|119719290|ref|YP_919785.1| 161 VKHLNEVRAKIEEIRAQIPE 180
                                    34455555555555555544 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.053
                           SKA2  28 efqqsypdnaeNpvkLlerlkkvkeelqaLkeqceellaekkelidki 75 
                                    e++++ p+ ++ +  + e+lk v +e+ ++keq+++l +++ el++++
  gi|119719290|ref|YP_919785.1| 173 EIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQRDELVKRL 220
                                    566666666667777788888888888888888888888888887765 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5  17.3    0.0007     0.092      56     174 ..       6     133 ..       2     135 .. 0.66
   2 ?    7.7   8.7     0.021       2.7      79     172 ..      78     175 ..      76     187 .. 0.70
   3 !   12.5   7.2   0.00069     0.092      72     136 ..     157     221 ..     148     224 .. 0.91
   4 ?   -0.1   7.3       5.1   6.8e+02     105     132 ..     211     238 ..     209     284 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.0007
                        DUF4201  56 kkIeernkeLkrlkkkttktvhalthlkeklh..............mleselselkkelkekeerlaklrkelykvkler 121
                                    + Ie+  ++L + ++k +  + ++++ + k++               l++++++l++++    e+++ l ++++k+++e+
  gi|119719290|ref|YP_919785.1|   6 ESIESLRQQLIEYRQKLQEISAKIQEARSKRDsangevkrisaeirSLREQYQALRQQIAAVAEQKKTLYEKISKLREEK 85 
                                    66777777777777777777777777777777444444444444436666666666666666666666666666666666 PP

                        DUF4201 122 dklrkqneklkqqggllrvPaLlkDYdktkekveekrksvkkLrrkvkilemr 174
                                    + + +q +kl++++       L  +Y +   ++ +kr+  ++Lr ++++le +
  gi|119719290|ref|YP_919785.1|  86 KGILEQLNKLRDELKR-----LNAEYNNLRGFLGSKRYDEDELRNRIEQLEWQ 133
                                    6666666666666666.....66778888888888888888888888888866 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.021
                        DUF4201  79 lthlkeklhmleselselkkelkekeerlaklrkelykvklerdklrkqneklkqqggllrvP.aLlkDYdktkekveek 157
                                    ++ l+e  + + ++l++l++elk+++++ + lr  l + + + d lr++ e+l+ q + +  P ++ k  +++   +e+ 
  gi|119719290|ref|YP_919785.1|  78 ISKLREEKKGILEQLNKLRDELKRLNAEYNNLRGFLGSKRYDEDELRNRIEQLEWQYQTMTLPpEVEKVLVNKIRSLESI 157
                                    67889999999999999999999999999999999999999999999999999988888875424555444444444444 PP

                        DUF4201 158 rksvkkLrr...kvkile 172
                                       vk+L +   k++++ 
  gi|119719290|ref|YP_919785.1| 158 YVNVKHLNEvraKIEEIR 175
                                    444444433222555555 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 0.00069
                        DUF4201  72 ttktvhalthlkeklhmleselselkkelkekeerlaklrkelykvklerdklrkqneklkqqgg 136
                                    +  +v+ l++++ k  +++++  elkk+ + ++e+l+ +  e  kvk++ + l++q+++l +++ 
  gi|119719290|ref|YP_919785.1| 157 IYVNVKHLNEVRAKIEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQRDELVKRLV 221
                                    5668999*****************************************************99875 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 5.1
                        DUF4201 105 erlaklrkelykvklerdklrkqneklk 132
                                    +++++l k+l ++k+erd++r+  ++ +
  gi|119719290|ref|YP_919785.1| 211 QQRDELVKRLVELKQERDRIRETANNYH 238
                                    5555666666666666666665554443 PP

>> NleF_casp_inhib  NleF caspase inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   3.3      0.45        60       8      75 ..      17      82 ..      13     103 .. 0.53
   2 !   19.7  10.1   4.6e-06   0.00061       8     107 ..     142     237 ..     138     249 .. 0.85
   3 ?    5.5   1.0      0.11        15      35      98 ..     228     291 ..     226     301 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.45
                NleF_casp_inhib  8 etektlkdIkdklklifereiastTaeekikE....lsdkltkl...knsvlseredlYevedykleggqkveLk 75
                                   e  + l++I +k++++  +  +     + i      l+++ ++l   +  v ++++ lYe + +         L+
  gi|119719290|ref|YP_919785.1| 17 EYRQKLQEISAKIQEARSKRDSANGEVKRISAeirsLREQYQALrqqIAAVAEQKKTLYEKISK---------LR 82
                                   5567889999999888854444333333333223334444333300033344555555555443.........33 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 4.6e-06
                NleF_casp_inhib   8 etektlkdIkdklklifereiastTaeekikElsdkltklknsvlseredlYev.edykleggqkveLkegitaedRdny 86 
                                    e ek l +   +l+ i+ +   +  ++ ki+E++ ++ +lk++v+   e+l  v  +y   + q+  Lk     ++Rd++
  gi|119719290|ref|YP_919785.1| 142 EVEKVLVNKIRSLESIYVNVKHLNEVRAKIEEIRAQIPELKKKVQAINEELKTVvSEYLKVKEQMQALK-----QQRDEL 216
                                    567777777789999**999999****************************999777777777888887.....68**** PP

                NleF_casp_inhib  87 lkdlvalyqiknavkekidna 107
                                    +k lv l+q ++ ++e+ +n 
  gi|119719290|ref|YP_919785.1| 217 VKRLVELKQERDRIRETANNY 237
                                    ****************98664 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.11
                NleF_casp_inhib  35 ekikElsdkltklknsvlseredlYevedykleggqkveLkegitaedRdnylkdlvalyqikn 98 
                                      i+E +++  +++ s+lse + l e ++      +  eL+++ ++ +R+ y k + a+ + ++
  gi|119719290|ref|YP_919785.1| 228 DRIRETANNYHQIYISLLSEEKSLREELERISILLKAKELSQHLEERKRQLYGKAMEAYERFRR 291
                                    679999*********************88888888899**************999999988876 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2  14.4   0.00024     0.031     234     329 ..       9     107 ..       3     133 .. 0.89
   2 !    9.0  16.1    0.0045       0.6     225     318 ..     163     238 ..     115     278 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00024
                          IFT57 234 ksieeslpetksqlkklhedisktlekiesrE...kylnsqleellqeyreaqeelsevkekykqlsegvseltrelaei 310
                                    +s++++l e++++l++++ +i+++ +k  s     k++  ++++l ++y+++++++++v e+ k+l e++s+l++e + i
  gi|119719290|ref|YP_919785.1|   9 ESLRQQLIEYRQKLQEISAKIQEARSKRDSANgevKRISAEIRSLREQYQALRQQIAAVAEQKKTLYEKISKLREEKKGI 88 
                                    57899999***************999877654335999****************************************** PP

                          IFT57 311 seelekvkqemeergssmt 329
                                     e+l+k+  e++  +++ +
  gi|119719290|ref|YP_919785.1|  89 LEQLNKLRDELKRLNAEYN 107
                                    **********998877665 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0045
                          IFT57 225 hleqmkkhkksieeslpetksqlkklhedisktlekiesrEkylnsqleellqeyreaqeelsevkekykqlsegvselt 304
                                    hl++++   ++i++++pe+k                  ++ + +n++l++ ++ey +++e+++++k++ ++l +++ el+
  gi|119719290|ref|YP_919785.1| 163 HLNEVRAKIEEIRAQIPELK------------------KKVQAINEELKTVVSEYLKVKEQMQALKQQRDELVKRLVELK 224
                                    33333333333333333333..................444455666666666666666666666666666666666666 PP

                          IFT57 305 relaeiseelekvk 318
                                    +e ++i e  ++  
  gi|119719290|ref|YP_919785.1| 225 QERDRIRETANNYH 238
                                    66666666655543 PP

>> FlxA  FlxA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   2.6     0.033       4.4      16      44 ..       5      35 ..       2      42 .. 0.81
   2 !   15.9   6.9   7.2e-05    0.0096      13      71 ..      44     105 ..      36     110 .. 0.85
   3 ?    0.1   0.0       5.8   7.7e+02      12      29 ..     120     137 ..     112     140 .. 0.66
   4 ?    7.7   0.4     0.026       3.5      44      71 ..     164     191 ..     145     198 .. 0.60
   5 ?    8.0   8.4     0.021       2.9      15      75 ..     167     230 ..     156     243 .. 0.81
   6 ?    1.4   4.6       2.4   3.2e+02      16      40 ..     203     228 ..     199     282 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.033
                           FlxA 16 asqiasLqkQiknlqkqLkelses..deltk 44
                                   ++ i+sL++Q+ ++ ++L+e+s++  ++ +k
  gi|119719290|ref|YP_919785.1|  5 TESIESLRQQLIEYRQKLQEISAKiqEARSK 35
                                   5789******************996544444 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 7.2e-05
                           FlxA  13 sgsasqiasLqkQiknlqkqLkelsesdeltkeekk....kqqqliqaQIqqlqaQIaqlqqq 71 
                                    + ++++i+sL++Q++ l +q+  ++e+ ++t  ek     + ++ i +Q+++l+ ++++l ++
  gi|119719290|ref|YP_919785.1|  44 KRISAEIRSLREQYQALRQQIAAVAEQ-KKTLYEKIsklrEEKKGILEQLNKLRDELKRLNAE 105
                                    668899*********************.77777776567789999*************99887 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 5.8
                           FlxA  12 ssgsasqiasLqkQiknl 29 
                                    +++  ++i++L+ Q++++
  gi|119719290|ref|YP_919785.1| 120 EDELRNRIEQLEWQYQTM 137
                                    455566777777777765 PP

  == domain 4  score: 7.7 bits;  conditional E-value: 0.026
                           FlxA  44 keekkkqqqliqaQIqqlqaQIaqlqqq 71 
                                     +e ++++++i aQI  l++ ++ + ++
  gi|119719290|ref|YP_919785.1| 164 LNEVRAKIEEIRAQIPELKKKVQAINEE 191
                                    4555566666666666666655555544 PP

  == domain 5  score: 8.0 bits;  conditional E-value: 0.021
                           FlxA  15 sasqiasLqkQiknlqkqLkelses.deltkeekk..kqqqliqaQIqqlqaQIaqlqqqqaek 75 
                                      ++i++++ Qi +l+k+++ + e+ ++   e  k  +q q +++Q + l + +  l+q+ ++ 
  gi|119719290|ref|YP_919785.1| 167 VRAKIEEIRAQIPELKKKVQAINEElKTVVSEYLKvkEQMQALKQQRDELVKRLVELKQERDRI 230
                                    5689999999999999999999999877777766566999999999999999999888887665 PP

  == domain 6  score: 1.4 bits;  conditional E-value: 2.4
                           FlxA  16 asqiasLqkQiknlqkqLkelses.d 40 
                                    ++q+++L++Q ++l k L el+++ d
  gi|119719290|ref|YP_919785.1| 203 KEQMQALKQQRDELVKRLVELKQErD 228
                                    57889999999999999999999842 PP

>> Laminin_I  Laminin Domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1  11.5   2.7e-05    0.0036      20     110 ..       7      97 ..       2     103 .. 0.74
   2 !   13.5   3.0   0.00033     0.043      14     120 ..      99     200 ..      96     205 .. 0.91
   3 ?   -0.5   7.1       6.1   8.1e+02      39     100 ..     203     257 ..     191     288 .. 0.50

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.7e-05
                      Laminin_I  20 nledltkeLqeklskesakkskieilekelesLaqeteeLqkkatqvlakaqkvnaesertlnnakeLaekikkladnik 99 
                                    ++e l+++L e+++k ++ + ki+ +  +  s + e+++   +    +++ q +++++ +  ++ k+L+eki kl+++ k
  gi|119719290|ref|YP_919785.1|   7 SIESLRQQLIEYRQKLQEISAKIQEARSKRDSANGEVKRISAEIRSLREQYQALRQQIAAVAEQKKTLYEKISKLREEKK 86 
                                    57778888888888888888888888778888888888888888888888888888888888888888888888888888 PP

                      Laminin_I 100 eilekvatlne 110
                                     ile+  +l  
  gi|119719290|ref|YP_919785.1|  87 GILEQLNKLRD 97 
                                    88877776655 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00033
                      Laminin_I  14 pykinanledltkeLqeklskesakkskieilekelesLaqeteeLqkkatqvlakaqkvnaesertlnnakeLaekikk 93 
                                    ++++na++++l+  L +k+  e++   +ie l     + + +t +L  ++++vl +     + +   +++ +e  +ki++
  gi|119719290|ref|YP_919785.1|  99 LKRLNAEYNNLRGFLGSKRYDEDELRNRIEQL-----EWQYQTMTLPPEVEKVLVNKIRSLESIYVNVKHLNEVRAKIEE 173
                                    6899***************************9.....5667889999********9999999****************** PP

                      Laminin_I  94 ladnikeilekvatlneneealpsskl 120
                                    ++++i e+ +kv+++ne+ + + s+ l
  gi|119719290|ref|YP_919785.1| 174 IRAQIPELKKKVQAINEELKTVVSEYL 200
                                    *****************9888777665 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 6.1
                      Laminin_I  39 kskieilekelesLaqeteeLqkkatqvlakaqkvnaesertlnnakeLaekikkladnike 100
                                    k       ++++ L+q+ +eL+k++++  ++   +++ +++  +   +L  + k l+++++ 
  gi|119719290|ref|YP_919785.1| 203 K-------EQMQALKQQRDELVKRLVELKQERDRIRETANNYHQIYISLLSEEKSLREELER 257
                                    2.......344444444444444444444444444444444444444444444444433332 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   3.1     0.007      0.93      52      99 ..       6      53 ..       1      56 [. 0.90
   2 !   14.4   8.9   0.00022     0.029      46     137 ..      49     136 ..      39     139 .. 0.79
   3 !   13.3  13.9   0.00047     0.062      16     125 ..     117     235 ..     110     238 .. 0.78
   4 ?    5.6  22.2      0.12        15      11     129 ..     163     287 ..     143     292 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.007
                 CENP-F_leu_zip 52 aevetlkeeieelaeelreleldLvalrsekeeLekelqkkqervseL 99
                                   + +e+l++++ e +++l+e+++++++ rs +++ + e++    ++ +L
  gi|119719290|ref|YP_919785.1|  6 ESIESLRQQLIEYRQKLQEISAKIQEARSKRDSANGEVKRISAEIRSL 53
                                   67999****************************999999999999888 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 0.00022
                 CENP-F_leu_zip  46 eaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelqkkqervseLeslnsslenlleekEqekvqmkeesk 125
                                    e  + +++ ++l+++i   ae+ + l  ++++lr+ek+ + ++l+k +++ + L++    l+ +l  k    +  ++e  
  gi|119719290|ref|YP_919785.1|  49 EIRSLREQYQALRQQIAAVAEQKKTLYEKISKLREEKKGILEQLNKLRDELKRLNAEYNNLRGFLGSK----RYDEDELR 124
                                    55566888999999999999999999999999999999999999999999999988888888888765....44567777 PP

                 CENP-F_leu_zip 126 aaveeLqtqlke 137
                                    +++e+L+ q + 
  gi|119719290|ref|YP_919785.1| 125 NRIEQLEWQYQT 136
                                    778888777765 PP

  == domain 3  score: 13.3 bits;  conditional E-value: 0.00047
                 CENP-F_leu_zip  16 erkadsLkdkvenLerelemse..enqekvileaEtskaevet.......lkeeieelaeelreleldLvalrsekeeLe 86 
                                    + ++d L++++e+Le + +++    + ekv +++  s + +         ++++iee++++  el+ +++a+ +e +++ 
  gi|119719290|ref|YP_919785.1| 117 RYDEDELRNRIEQLEWQYQTMTlpPEVEKVLVNKIRSLESIYVnvkhlneVRAKIEEIRAQIPELKKKVQAINEELKTVV 196
                                    557899999999999999875422566666665555544332222223338999************************** PP

                 CENP-F_leu_zip  87 kelqkkqervseLeslnsslenlleekEqekvqmkeesk 125
                                     e  k +e+++ L++ + +l + l e+ qe+ +++e ++
  gi|119719290|ref|YP_919785.1| 197 SEYLKVKEQMQALKQQRDELVKRLVELKQERDRIRETAN 235
                                    ********************9999999999999999876 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.12
                 CENP-F_leu_zip  11 kLKeserkadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLek... 87 
                                     L e++ k + ++ ++ +L++ ++ ++e++  v+ e  + k+++++lk++ +el ++l el+++ + +r+  ++ ++   
  gi|119719290|ref|YP_919785.1| 163 HLNEVRAKIEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQRDELVKRLVELKQERDRIRETANNYHQiyi 242
                                    68889999999999999999999999999999999999999999999999999999999999999999977777665322 PP

                 CENP-F_leu_zip  88 .elqkkqervseLesln..sslenlleekEqekvqmkeeskaave 129
                                      l ++++  +eLe++   ++ ++l +++E+ k+q++ ++ +a e
  gi|119719290|ref|YP_919785.1| 243 sLLSEEKSLREELERISilLKAKELSQHLEERKRQLYGKAMEAYE 287
                                    246677777778887651145567777888888888887777766 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.7      0.25        33       2      39 ..       8      45 ..       7      46 .. 0.86
   2 ?    7.5   0.1     0.041       5.4       2      32 ..      43      73 ..      42      76 .. 0.82
   3 ?    6.6   0.4     0.076        10       5      42 ..      67     104 ..      63     110 .. 0.84
   4 !   12.7   0.1   0.00093      0.12       1      35 [.     170     204 ..     170     205 .. 0.88
   5 ?    1.9   0.4       2.2     3e+02       6      37 ..     203     234 ..     199     237 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.25
                            LPP  2 ldeLssqVsqLkskvdqlssdvnsakaaaqaakeEAaR 39
                                   ++ L +q+ +  +k +++s+++++a++  ++a  E +R
  gi|119719290|ref|YP_919785.1|  8 IESLRQQLIEYRQKLQEISAKIQEARSKRDSANGEVKR 45
                                   56778888888999999999999999999999999887 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.041
                            LPP  2 ldeLssqVsqLkskvdqlssdvnsakaaaqa 32
                                   ++ +s+++ +L ++ ++l +++++++++ ++
  gi|119719290|ref|YP_919785.1| 43 VKRISAEIRSLREQYQALRQQIAAVAEQKKT 73
                                   6789999999999999999999988877665 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.076
                            LPP   5 LssqVsqLkskvdqlssdvnsakaaaqaakeEAaRANq 42 
                                    +++q ++L +k+++l ++ + + +++++ ++E +R N 
  gi|119719290|ref|YP_919785.1|  67 VAEQKKTLYEKISKLREEKKGILEQLNKLRDELKRLNA 104
                                    567778999**********************9999886 PP

  == domain 4  score: 12.7 bits;  conditional E-value: 0.00093
                            LPP   1 kldeLssqVsqLkskvdqlssdvnsakaaaqaake 35 
                                    k++e+ +q+ +Lk+kv++++++++ + ++  ++ke
  gi|119719290|ref|YP_919785.1| 170 KIEEIRAQIPELKKKVQAINEELKTVVSEYLKVKE 204
                                    899*******************9998877776665 PP

  == domain 5  score: 1.9 bits;  conditional E-value: 2.2
                            LPP   6 ssqVsqLkskvdqlssdvnsakaaaqaakeEA 37 
                                     +q ++Lk++ d+l + + ++k++ + ++e A
  gi|119719290|ref|YP_919785.1| 203 KEQMQALKQQRDELVKRLVELKQERDRIRETA 234
                                    57999999999999888888777777777666 PP

>> Uso1_p115_C  Uso1 / p115 like vesicle tethering protein, C terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   9.4   7.1e-05    0.0095       8      76 ..       6      72 ..       1      77 [. 0.92
   2 ?    5.7   5.5      0.14        18       2      76 ..      77     186 ..      76     199 .. 0.72
   3 ?    3.9   9.5      0.48        64       8      70 ..     197     257 ..     190     278 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 7.1e-05
                    Uso1_p115_C  8 seaaslkdeneklkaelqslskalesleqkeakkaaesqakeleaenkklekeleklraelkeekekek 76
                                   ++ +sl+++  ++ ++lq+ s +++++++k    +a+ + k+++ae+ +l+++ ++lr+++++ +e++k
  gi|119719290|ref|YP_919785.1|  6 ESIESLRQQLIEYRQKLQEISAKIQEARSK--RDSANGEVKRISAEIRSLREQYQALRQQIAAVAEQKK 72
                                   56889*************************..999***************************9999886 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.14
                    Uso1_p115_C   2 kaseleseaaslkdeneklkaelqslskalesleqkeakkaaesqakeleaenkklek...................... 59 
                                    k s+l +e++ + ++ +kl +el+ l+ ++++l+    + + ++ ++el++++++le                       
  gi|119719290|ref|YP_919785.1|  77 KISKLREEKKGILEQLNKLRDELKRLNAEYNNLRGF--LGSKRYDEDELRNRIEQLEWqyqtmtlppevekvlvnkirsl 154
                                    668899999999999******************999..777777777777777777765555666666666666666666 PP

                    Uso1_p115_C  60 ...............eleklraelkeekekek 76 
                                                   ++e++ra++ e k+k +
  gi|119719290|ref|YP_919785.1| 155 esiyvnvkhlnevraKIEEIRAQIPELKKKVQ 186
                                    66777777666666666666666666666655 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.48
                    Uso1_p115_C   8 seaaslkdeneklkaelqslskalesleqkeakkaaesqakeleaenkklekeleklraelke 70 
                                    se  ++k++ ++lk++ ++l k+l +l+q+     +++ a+++ +  ++l +e + lr+el+ 
  gi|119719290|ref|YP_919785.1| 197 SEYLKVKEQMQALKQQRDELVKRLVELKQE--RDRIRETANNYHQIYISLLSEEKSLREELER 257
                                    555667888888888888888888888888..8888888888888888888888888888765 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   1.0    0.0097       1.3      23      82 ..      45     104 ..      11     110 .. 0.69
   2 !    9.5   0.1    0.0089       1.2      29      87 ..     121     181 ..     119     183 .. 0.87
   3 !   11.1   2.7    0.0027      0.36      18      75 ..     161     218 ..     157     226 .. 0.79
   4 ?    3.8   0.4      0.53        70      22      58 ..     200     236 ..     196     274 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0097
                         DUF948  23 klkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlge 82 
                                    +++  +++++++ + l++q+ ++ ++ ++l +k+ +l e+ ++ le++++l ++++ l +
  gi|119719290|ref|YP_919785.1|  45 RISAEIRSLREQYQALRQQIAAVAEQKKTLYEKISKLREEKKGILEQLNKLRDELKRLNA 104
                                    455556666666666666666666666666666666666666666666666666666555 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0089
                         DUF948  29 deaaatieelekqvdpil..kevedllakvnelledvneklekvdplteavadlgesvsel 87 
                                    de++++ie+le q + ++   eve++l +  + le +   +++++++ ++++++ +++ el
  gi|119719290|ref|YP_919785.1| 121 DELRNRIEQLEWQYQTMTlpPEVEKVLVNKIRSLESIYVNVKHLNEVRAKIEEIRAQIPEL 181
                                    7999******96655554338*********************************9999887 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.0027
                         DUF948  18 ivvllklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplte 75 
                                    ++ l++++  ++e++a+i el+k+v++i +e+++++++  ++ e+++   ++ d+l++
  gi|119719290|ref|YP_919785.1| 161 VKHLNEVRAKIEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQRDELVK 218
                                    5678889999999999999999999999999999999999977777776666666665 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.53
                         DUF948  22 lklkktldeaaatieelekqvdpilkevedllakvne 58 
                                    lk+k+ +++++++ +el k++ ++ +e +++ +++n+
  gi|119719290|ref|YP_919785.1| 200 LKVKEQMQALKQQRDELVKRLVELKQERDRIRETANN 236
                                    6889999999999999999999999999999888887 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   4.2     0.001      0.14      50     120 ..       8      81 ..       3      83 .. 0.73
   2 !   10.6   1.4    0.0033      0.44      49     121 ..      59     131 ..      56     138 .. 0.80
   3 ?    7.0   7.8     0.043       5.8      67     116 ..     163     212 ..     116     225 .. 0.62
   4 ?    3.2   3.6      0.65        86      53     108 ..     205     260 ..     201     276 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.001
                        DUF1664  50 leqvseslaatkrhL...ssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleri 120
                                    +e++ ++l + +++L   s++i++  +k d+ +   k i++e+ ++re+ +++++++ +v e  ++l +k++++
  gi|119719290|ref|YP_919785.1|   8 IESLRQQLIEYRQKLqeiSAKIQEARSKRDSANGEVKRISAEIRSLREQYQALRQQIAAVAEQKKTLYEKISKL 81 
                                    55555555554444311167888888899999988999999999999999999999999999999999998877 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0033
                        DUF1664  49 qleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                     l q  +++a++k+ L ++i ++ ++ +   e  +++++e+++++ + ++++  + s +    +l +++e++e
  gi|119719290|ref|YP_919785.1|  59 ALRQQIAAVAEQKKTLYEKISKLREEKKGILEQLNKLRDELKRLNAEYNNLRGFLGSKRYDEDELRNRIEQLE 131
                                    5778889999999999999999999999999999999999999999999988766666655556666665555 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.043
                        DUF1664  67 ridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesk 116
                                    ++++v +k++e  + + e+k++v++++e+l+++ ++  +vke ++ l+++
  gi|119719290|ref|YP_919785.1| 163 HLNEVRAKIEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQ 212
                                    34444444444444444444444444444444444444444444444443 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.65
                        DUF1664  53 vseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvke 108
                                     +++l++++++L +r+ ++ ++ d   e++++ ++   ++ ++ ++++e++e ++ 
  gi|119719290|ref|YP_919785.1| 205 QMQALKQQRDELVKRLVELKQERDRIRETANNYHQIYISLLSEEKSLREELERISI 260
                                    56789999999999999999999999999999988888888888888888887765 PP

>> MscS_porin  Mechanosensitive ion channel porin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1  20.8   2.3e-05    0.0031      76     202 ..       4     136 ..       2     138 .. 0.93
   2 ?    6.5  13.4      0.04       5.4      80     168 ..     164     252 ..     162     285 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.3e-05
                     MscS_porin  76 aklsleeLeqrllqtssqlqelqeqlaqlnsqlvelqtrperaqqqltearqrlqeirnrLnstaaage....alsqaqr 151
                                    ++ s+e L q+l++  ++lqe +++++++ s+  +++    r+ +++ + r++ q++r+++++ a++++    ++s+ + 
  gi|119719290|ref|YP_919785.1|   4 ETESIESLRQQLIEYRQKLQEISAKIQEARSKRDSANGEVKRISAEIRSLREQYQALRQQIAAVAEQKKtlyeKISKLRE 83 
                                    5679*********************************************************888777777999******* PP

                     MscS_porin 152 talqaelaaleaqieeleqellsnnnrqeLlklqrdl..lklriqqleqelqa 202
                                     +  + +++ +++ e+ ++ ++ nn r  L+ ++ d+  l+ ri+qle + q+
  gi|119719290|ref|YP_919785.1|  84 EKKGILEQLNKLRDELKRLNAEYNNLRGFLGSKRYDEdeLRNRIEQLEWQYQT 136
                                    **********************************9885577889999888776 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.04
                     MscS_porin  80 leeLeqrllqtssqlqelqeqlaqlnsqlvelqtrperaqqqltearqrlqeirnrLnstaaagealsqaqrtalqaela 159
                                    l+e   ++++  +q  el+++ + +n++l +  +   ++ +q+ + +q+ +e+ +rL +++++  +++++  +  q+  +
  gi|119719290|ref|YP_919785.1| 164 LNEVRAKIEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQRDELVKRLVELKQERDRIRETANNYHQIYIS 243
                                    56667777777788888888888888888888888888888888888888888888877766777888888888777777 PP

                     MscS_porin 160 aleaqieel 168
                                    +l+ + +++
  gi|119719290|ref|YP_919785.1| 244 LLSEEKSLR 252
                                    777664443 PP

>> FH2  Formin Homology 2 Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   3.9   0.00032     0.042     252     352 ..      17     117 ..       9     130 .. 0.84
   2 !   10.9   6.5    0.0013      0.17     241     348 ..     135     241 ..     125     266 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00032
                                    HHHTTSGGGGGHHHHTTTHHHCCTS-HHHHHHHHHHHHHHHHHHHHHHHHCCTTSSTT-THHHHHHHHHHHHHHHHHHHH CS
                            FH2 252 iireklpevldfsseLknvkkaakvnleslekevkklekglkklekelessekkeepsdkflevlkeflkeaeeklkkle 331
                                    ++r+kl+e++   +e ++ +++a+ +++ +++e++ l+++ ++l++++ + +++++   + +++l+e  k   e+l+kl+
  gi|119719290|ref|YP_919785.1|  17 EYRQKLQEISAKIQEARSKRDSANGEVKRISAEIRSLREQYQALRQQIAAVAEQKKTLYEKISKLREEKKGILEQLNKLR 96 
                                    5678888888888888888999999****************************666666666677777777779****** PP

                                    HHHHHHHHHHHHHHHHTT--T CS
                            FH2 332 eelkeakelvkelveYfgedk 352
                                    +elk++++++++l  ++g+++
  gi|119719290|ref|YP_919785.1|  97 DELKRLNAEYNNLRGFLGSKR 117
                                    **************9998754 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0013
                                    TTSBHHHHHHHHHHTTSGGGGGHHHHTTTHHHCCTS-HHHHHHHHHHHHHHHHHHHHHHHHCCTTSSTT-THHHHHHHHH CS
                            FH2 241 nkttLLHylvkiireklpevldfsseLknvkkaakvnleslekevkklekglkklekelessekkeepsdkflevlkefl 320
                                    +++tL   ++k++ +k  +++  +   k++++  + ++e++++++ +l+k+++++++el++  ++  + ++ +++lk+  
  gi|119719290|ref|YP_919785.1| 135 QTMTLPPEVEKVLVNKIRSLESIYVNVKHLNE-VRAKIEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQR 213
                                    678888899***********************.899****************************5555666666666666 PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                            FH2 321 keaeeklkkleeelkeakelvkelveYf 348
                                    +e  ++l +l++e ++++e++++  + +
  gi|119719290|ref|YP_919785.1| 214 DELVKRLVELKQERDRIRETANNYHQIY 241
                                    6666677777888888888888777766 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1  10.8   5.9e-05    0.0078      99     185 ..      10     103 ..       3     106 .. 0.86
   2 ?    5.4   1.9      0.11        14     144     183 ..     162     201 ..     115     203 .. 0.61
   3 ?    8.3  14.9     0.014       1.9      82     176 ..     166     257 ..     141     283 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 5.9e-05
                         DUF724  99 slkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallk.......ekkeaadkeiarlkseaekle 171
                                    sl+++  +++++++++  ki+e++s++ +++ e++ ++ +i+ l++q ++l+       e+k++  ++i++l+ e++ + 
  gi|119719290|ref|YP_919785.1|  10 SLRQQLIEYRQKLQEISAKIQEARSKRDSANGEVKRISAEIRSLREQYQALRqqiaavaEQKKTLYEKISKLREEKKGIL 89 
                                    56777777788888888999999999999999999999999999999999999999999********************* PP

                         DUF724 172 eeledveqeFeava 185
                                    e+l++ ++e +++ 
  gi|119719290|ref|YP_919785.1|  90 EQLNKLRDELKRLN 103
                                    *******9998875 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.11
                         DUF724 144 rqlallkekkeaadkeiarlkseaekleeeledveqeFea 183
                                    ++l  +++k e+  ++i +lk+++++++eel+ v +e+ +
  gi|119719290|ref|YP_919785.1| 162 KHLNEVRAKIEEIRAQIPELKKKVQAINEELKTVVSEYLK 201
                                    2333344788888888888888888888888888777655 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.014
                         DUF724  82 khGFdVkalqsrl....nkLlslkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaad 157
                                    +        ++++     ++ +lk++ + + ee+k + ++  + +++++ l+++ del k+ +el++++++++e  ++  
  gi|119719290|ref|YP_919785.1| 166 EV-------RAKIeeirAQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQRDELVKRLVELKQERDRIRETANNYH 238
                                    22.......33341112334468999999999999999999999999999999999*****************8888888 PP

                         DUF724 158 keiarlkseaekleeeled 176
                                    +   +l se+++l+eele+
  gi|119719290|ref|YP_919785.1| 239 QIYISLLSEEKSLREELER 257
                                    8888888999988888876 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8  11.1     0.001      0.13     336     415 ..       5      85 ..       2      88 .. 0.86
   2 !   10.2   9.8    0.0015       0.2     329     400 ..      47     119 ..      42     162 .. 0.63
   3 !   11.3  14.4   0.00072     0.096     321     411 ..     166     258 ..     144     276 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.001
                           FapA 336 keklkeleeeleeleeeleklkkkikklpklka.ekqlesekkeqlkklletkeklkeeleeleeelkelkeeleskkee 414
                                     e+++ l+++l e++++l+++ +ki++ ++++   +   ++++ ++ +l+e++++l+++++++ e++k+l e++ + +ee
  gi|119719290|ref|YP_919785.1|   5 TESIESLRQQLIEYRQKLQEISAKIQEARSKRDsANGEVKRISAEIRSLREQYQALRQQIAAVAEQKKTLYEKISKLREE 84 
                                    68899*********************99997775555567778899999************************9999655 PP

                           FapA 415 a 415
                                    +
  gi|119719290|ref|YP_919785.1|  85 K 85 
                                    5 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0015
                           FapA 329 gldepelkeklkeleeeleeleeeleklkkkikklpklka.ekqlesekkeqlkklletkeklkeeleeleee 400
                                    + +  +l+e++++l++++ ++ e+ ++l +ki+kl+++k+   ++  + +++lk+l  ++++l+  l + + +
  gi|119719290|ref|YP_919785.1|  47 SAEIRSLREQYQALRQQIAAVAEQKKTLYEKISKLREEKKgILEQLNKLRDELKRLNAEYNNLRGFLGSKRYD 119
                                    3444578888888888888888888888888888888544333333344444444444444444444444444 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.00072
                           FapA 321 gtkteiev.gldepelkeklkeleeeleeleeeleklkkkikklpklka.ekqlesekkeqlkklletkeklkeeleele 398
                                    +++ +ie    + pelk+k+++++eel+ + +e  k+k++++ l++ +    +   e k++ ++++et +++ +++ +l 
  gi|119719290|ref|YP_919785.1| 166 EVRAKIEEiRAQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQRDeLVKRLVELKQERDRIRETANNYHQIYISLL 245
                                    44444444466667777777777777777777777777777777775555566666777777777777777777777777 PP

                           FapA 399 eelkelkeelesk 411
                                     e k+l eele+ 
  gi|119719290|ref|YP_919785.1| 246 SEEKSLREELERI 258
                                    7777777777765 PP

>> CENP-H  Centromere protein H (CENP-H)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   1.1      0.48        63      27      58 ..       6      37 ..       1      44 [. 0.63
   2 !   18.0   9.1   2.2e-05    0.0029       4      77 ..      32     108 ..      29     111 .. 0.88
   3 !   10.2  10.4     0.006      0.79       6      66 ..     176     239 ..     164     260 .. 0.79
   4 ?    5.1   8.1      0.21        28       3      68 ..     208     275 ..     206     291 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.48
                         CENP-H 27 eeltevekenlrlkrknrelaaellelakeke 58
                                   e++++++++ ++ ++k +e+ a+++e +++ +
  gi|119719290|ref|YP_919785.1|  6 ESIESLRQQLIEYRQKLQEISAKIQEARSKRD 37
                                   56667777777777777777777755555544 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 2.2e-05
                         CENP-H   4 lieqrdelssellklsqelrelqeeltevekenlrlkrknrelaaellelakekesek...eklkeelekleaelkk 77 
                                       +rd ++ e++++s+e+r+l+e+ + +++++ ++ +++++l +++ +l++ek+      +kl++el++l ae+++
  gi|119719290|ref|YP_919785.1|  32 ARSKRDSANGEVKRISAEIRSLREQYQALRQQIAAVAEQKKTLYEKISKLREEKKGILeqlNKLRDELKRLNAEYNN 108
                                    5578*******************************************8887777766667899999***99999876 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.006
                         CENP-H   6 eqrdelssellklsqelrelqeeltevekenlrlkrknrelaaellelakekesek...eklke 66 
                                     q+ el ++++++++el+++ +e  +v+++  +lk++  el+++l el++e ++ +   +++ +
  gi|119719290|ref|YP_919785.1| 176 AQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQRDELVKRLVELKQERDRIRetaNNYHQ 239
                                    56789999*************************************9999999998866522333 PP

  == domain 4  score: 5.1 bits;  conditional E-value: 0.21
                         CENP-H   3 plieqrdelssellklsqelrelqeeltevekenlrlkrknrelaaellelakekesek..eklkeel 68 
                                    +l +qrdel+++l +l+qe   ++e  ++  +  ++l  ++++l +el++ +   ++++  ++l+e+ 
  gi|119719290|ref|YP_919785.1| 208 ALKQQRDELVKRLVELKQERDRIRETANNYHQIYISLLSEEKSLREELERISILLKAKElsQHLEERK 275
                                    56689******************************************965554444443323333333 PP

>> Mod_r  Modifier of rudimentary (Mod(r)) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   2.0      0.22        29      54      87 ..       6      39 ..       1      49 [. 0.74
   2 !   17.7   8.7   2.2e-05     0.003      21     102 ..      42     129 ..      29     131 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.22
                          Mod_r 54 peleelrselqekleelkelekefeekeqeldel 87
                                   +++e lr++l+e +++l+e++++ +e  ++ d++
  gi|119719290|ref|YP_919785.1|  6 ESIESLRQQLIEYRQKLQEISAKIQEARSKRDSA 39
                                   5778888888888888888888888888777765 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 2.2e-05
                          Mod_r  21 lvktl.pevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqeldell.....qkfspd 94 
                                     vk +  e+++l+e+ + l++++ ++ae++  l +++ +lr+e +  le+l++l++e++++++e+++l      +++++d
  gi|119719290|ref|YP_919785.1|  42 EVKRIsAEIRSLREQYQALRQQIAAVAEQKKTLYEKISKLREEKKGILEQLNKLRDELKRLNAEYNNLRgflgsKRYDED 121
                                    556665789***********************************************************999999****** PP

                          Mod_r  95 allarLqt 102
                                     l++r ++
  gi|119719290|ref|YP_919785.1| 122 ELRNRIEQ 129
                                    *9999765 PP

>> DUF2968  Protein of unknown function (DUF2968)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5  15.9   0.00032     0.042      80     179 ..       8     107 ..       2     108 .. 0.90
   2 !    8.9   6.2    0.0082       1.1      99     166 ..     169     236 ..     151     250 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00032
                        DUF2968  80 AeaiYadfarqtaelaeveirrikleaqkaqlerqiaasearaerLqadlavarqQeqavaerQkqarkeaaaLeaqrea 159
                                     e++ +++ +  ++l e+  +  +  +++++++ ++++ +a++++L+++ +  rqQ +avae+ k++ ++ ++L+++++ 
  gi|119719290|ref|YP_919785.1|   8 IESLRQQLIEYRQKLQEISAKIQEARSKRDSANGEVKRISAEIRSLREQYQALRQQIAAVAEQKKTLYEKISKLREEKKG 87 
                                    5666677777778888888888889999999999********************************************** PP

                        DUF2968 160 aqaqlralqrqirqLqaqqe 179
                                    + +ql++l+ ++++L+a+ +
  gi|119719290|ref|YP_919785.1|  88 ILEQLNKLRDELKRLNAEYN 107
                                    ****************9976 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0082
                        DUF2968  99 irrikleaqkaqlerqiaasearaerLqadlavarqQeqavaerQkqarkeaaaLeaqreaaqaqlra 166
                                     +  ++ aq   l+++++a +++++++ ++    ++Q qa++++ +++ k    L+++r+++++  ++
  gi|119719290|ref|YP_919785.1| 169 AKIEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQRDELVKRLVELKQERDRIRETANN 236
                                    33344555666666666666666666666666666666666666666666666666666666665555 PP

>> TACC_C  Transforming acidic coiled-coil-containing protein (TACC), C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3  13.4    0.0034      0.45      13     122 ..      18     130 ..       4     138 .. 0.68
   2 !   12.0  12.9     0.001      0.14      10     107 ..     164     257 ..     158     289 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0034
                         TACC_C  13 vkeeveekeeeiqelkkkveelkkenq....emkkivaefektiaqlieekqkqkelakkeiqkvleekeqlladlnsve 88 
                                     +++ +e   +iqe ++k +  + e++    e++ + +++     q i+   +qk+   ++i+k+ eek+ +l++ln++ 
  gi|119719290|ref|YP_919785.1|  18 YRQKLQEISAKIQEARSKRDSANGEVKrisaEIRSLREQYQAL-RQQIAAVAEQKKTLYEKISKLREEKKGILEQLNKLR 96 
                                    3444444444555544444433333332222666666777665.55555555666777889******************* PP

                         TACC_C  89 ksfsdlfkryekqkevlegykkneeslkkcaeey 122
                                     +++ l   y++++  l   +  e+ l++ +e++
  gi|119719290|ref|YP_919785.1|  97 DELKRLNAEYNNLRGFLGSKRYDEDELRNRIEQL 130
                                    ***************9999999999999998876 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.001
                         TACC_C  10 lekvkeeveekeeeiqelkkkveelkkenqemkkivaefektiaqlieekqkqkelakkeiqkvleekeqlladlnsvek 89 
                                    l++v++++ee   +i elkkkv+     n+e+k +v+e+ k+ +q+ + kq++  +  k + ++++e++ + +  n+  +
  gi|119719290|ref|YP_919785.1| 164 LNEVRAKIEEIRAQIPELKKKVQA---INEELKTVVSEYLKVKEQMQALKQQRD-ELVKRLVELKQERDRIRETANNYHQ 239
                                    556777888888888888888765...4679**********8777777776555.55667888999****9999999999 PP

                         TACC_C  90 sfsdlfkryekqkevleg 107
                                     +  l++  + ++e le 
  gi|119719290|ref|YP_919785.1| 240 IYISLLSEEKSLREELER 257
                                    999999988888887664 PP

>> COG6  Conserved oligomeric complex COG6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   7.1    0.0017      0.22      42      97 ..      39      94 ..       9     101 .. 0.79
   2 ?    5.0   0.2     0.045       5.9      41      91 ..      87     137 ..      83     144 .. 0.89
   3 !   11.1   5.9   0.00061     0.081      36      92 ..     161     217 ..     138     229 .. 0.61
   4 ?    0.7   0.2      0.85   1.1e+02      49      92 ..     216     259 ..     214     273 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0017
                           COG6 42 vaeqLkriesdveklnelcdemkkklssakeetsdlleeaeeLkeekkklelkqkl 97
                                   ++ ++kri++++ +l e ++ +++++ +  e+ ++l e++++L+eekk + ++ + 
  gi|119719290|ref|YP_919785.1| 39 ANGEVKRISAEIRSLREQYQALRQQIAAVAEQKKTLYEKISKLREEKKGILEQLNK 94
                                   44499*******************************************99887665 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.045
                           COG6  41 pvaeqLkriesdveklnelcdemkkklssakeetsdlleeaeeLkeekkkl 91 
                                     + eqL++++++++ ln+ +++++  l s++ + ++l + +e+L+ + + +
  gi|119719290|ref|YP_919785.1|  87 GILEQLNKLRDELKRLNAEYNNLRGFLGSKRYDEDELRNRIEQLEWQYQTM 137
                                    5789**************************************999887765 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00061
                           COG6  36 leefqpvaeqLkriesdveklnelcdemkkklssakeetsdlleeaeeLkeekkkle 92 
                                    ++ +++v+ ++++i++++ +l++ ++ ++++l++  +e  ++ e++++Lk+++++l 
  gi|119719290|ref|YP_919785.1| 161 VKHLNEVRAKIEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQRDELV 217
                                    455566666666666666666666666666666666666666666666666666554 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.85
                           COG6  49 iesdveklnelcdemkkklssakeetsdlleeaeeLkeekkkle 92 
                                    + +++ +l++  d++++  ++ ++   +ll+e ++L+ee+++++
  gi|119719290|ref|YP_919785.1| 216 LVKRLVELKQERDRIRETANNYHQIYISLLSEEKSLREELERIS 259
                                    567788999999**************************999886 PP

>> HOOK  HOOK protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   6.2   0.00072     0.096     351     413 ..       7      69 ..       1      76 [. 0.57
   2 !    9.8  18.2    0.0015      0.19     348     429 ..     160     241 ..     142     289 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00072
                           HOOK 351 kanalrsqlelykkqvqelhkklseeskkadklefelkkleeklealqkekerllaerdaLke 413
                                      ++lr+ql  y++++qe+ +k +e  +k d ++ e+k+  + + +l  + + l ++  a  e
  gi|119719290|ref|YP_919785.1|   7 SIESLRQQLIEYRQKLQEISAKIQEARSKRDSANGEVKRISAEIRSLREQYQALRQQIAAVAE 69 
                                    455666666666666666666666666666666666666666666655555555554444433 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0015
                           HOOK 348 elkkanalrsqlelykkqvqelhkklseeskkadklefelkkleeklealqkekerllaerdaLketneELkcaqlqqke 427
                                    ++k  n++r+++e ++ q+ el+kk+++ ++  +++  e+ k++e+++al+++++ l++    Lk+  + ++ +  + ++
  gi|119719290|ref|YP_919785.1| 160 NVKHLNEVRAKIEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQRDELVKRLVELKQERDRIRETANNYHQ 239
                                    68999**************************************************9999999999988888876655555 PP

                           HOOK 428 ls 429
                                    ++
  gi|119719290|ref|YP_919785.1| 240 IY 241
                                    43 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   5.4     0.013       1.7       6      77 ..      11      82 ..       3      84 .. 0.66
   2 ?    9.4   6.0     0.012       1.6       3      52 ..      71     127 ..      58     163 .. 0.52
   3 ?    3.2  16.7       1.1   1.4e+02      11      77 ..     165     241 ..     154     291 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.013
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXXXXXXXXXXXX CS
                           YabA  6 lfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkkelsegkenLarlY 77
                                   l ++l e  ++l+e++++++e +++  +   e +++++e ++lre+ +  +++ ++  +++++ +e++++l 
  gi|119719290|ref|YP_919785.1| 11 LRQQLIEYRQKLQEISAKIQEARSKRDSANGEVKRISAEIRSLREQYQALRQQIAAVAEQKKTLYEKISKLR 82
                                   556677777777777777777777777777777777777777777776666666666666666666666654 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.012
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHH CS
                           YabA   3 kkelfdkleeleeqleelleeleelkeelaelleenaeLele.......neklrerl 52 
                                    kk l++k+++l e+ + +le+l++l++el++l  e ++L+          ++lr+r+
  gi|119719290|ref|YP_919785.1|  71 KKTLYEKISKLREEKKGILEQLNKLRDELKRLNAEYNNLRGFlgskrydEDELRNRI 127
                                    344444444444444444444444444444444444444322222222233333333 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 1.1
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH..........XXXXXXXXXXXXXXXXXXXXXXXXX CS
                           YabA  11 eeleeqleelleeleelkeelaelleenaeLeleneklrerl..........eeeekkekekkkelsegkenLarlY 77 
                                    +e+  ++ee+ +++ elk++++++ ee +++  e  k++e++           ++  + k+++ +++e+ +n +++Y
  gi|119719290|ref|YP_919785.1| 165 NEVRAKIEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMqalkqqrdelVKRLVELKQERDRIRETANNYHQIY 241
                                    45555555555555555555555555555555555555555533322223333344445555555666666666666 PP

>> BRE1  BRE1 E3 ubiquitin ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   1.8      0.76     1e+02      16      47 ..       5      36 ..       1      40 [. 0.84
   2 !   17.0   9.2   3.5e-05    0.0047       2      93 ..      40     131 ..      39     133 .. 0.93
   3 ?    8.2  13.5     0.019       2.5       5      90 ..     164     256 ..     161     259 .. 0.91
   4 ?    4.5  10.2      0.28        37       8      86 ..     202     279 ..     201     287 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.76
                           BRE1 16 seqlskkvkeltileekklrleaekakadqky 47
                                    e+++++ ++l    +k++ ++a++++a+ k 
  gi|119719290|ref|YP_919785.1|  5 TESIESLRQQLIEYRQKLQEISAKIQEARSKR 36
                                   57788999999999999999999999999885 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 3.5e-05
                           BRE1   2 qkELvklekafeelseqlskkvkeltileekklrleaekakadqkyfaamrskdalenelkkLnkllsKsselieqLkel 81 
                                    + E+++++++++ l+eq +++ +++++  e+k+ l  +++k +++ + +  + ++l+ elk+Ln+ ++  +         
  gi|119719290|ref|YP_919785.1|  40 NGEVKRISAEIRSLREQYQALRQQIAAVAEQKKTLYEKISKLREEKKGILEQLNKLRDELKRLNAEYNNLRGFLGSKRYD 119
                                    689***************************************************************99988888888888 PP

                           BRE1  82 ekefvrklkele 93 
                                    e e+++++++le
  gi|119719290|ref|YP_919785.1| 120 EDELRNRIEQLE 131
                                    888888888887 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.019
                           BRE1   5 LvklekafeelseqlskkvkeltileekklrleaekakadqkyfaamrskdalenelkkLnkllsKsselieqLke.... 80 
                                    L ++ + +ee ++q+ +++k++++  e+++ + +e  k +++  a++ ++d l + l+ L++  ++ +e+ ++ ++    
  gi|119719290|ref|YP_919785.1| 164 LNEVRAKIEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQRDELVKRLVELKQERDRIRETANNYHQiyis 243
                                    7889999*********************************************************************8888 PP

                           BRE1  81 ...lekefvrklk 90 
                                        ek+++++l+
  gi|119719290|ref|YP_919785.1| 244 llsEEKSLREELE 256
                                    7777777776665 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.28
                           BRE1   8 lekafeelseqlskkvkeltileekklrleaekakadqkyfaamrskdalenelkkLnkllsKsselieqLkelekefv 86 
                                    +++++++l++q +++vk l  l+++  r+    +  +q y ++  + ++l+ el +++ ll K +el++ L+e+ +++ 
  gi|119719290|ref|YP_919785.1| 202 VKEQMQALKQQRDELVKRLVELKQERDRIRETANNYHQIYISLLSEEKSLREELERISILL-KAKELSQHLEERKRQLY 279
                                    678899***************************************************9877.89999999999887765 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   6.7   0.00015      0.02     187     343 ..      19     229 ..       2     246 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00015
                           FUSC 187 eaararlaadilalealrsqaayesprirararalr....rllsrmlallallsslarllarlraeeaaavpelaallae 262
                                    +++++++ a+i +  + r+ a  e  ri+a++r lr    +l+++++a+  +   l++    lr+e+++  ++l +l +e
  gi|119719290|ref|YP_919785.1|  19 RQKLQEISAKIQEARSKRDSANGEVKRISAEIRSLReqyqALRQQIAAVAEQKKTLYEKISKLREEKKGILEQLNKLRDE 98 
                                    57899999999999999999999999998888876522226888888888899999999999999999998889999999 PP

                           FUSC 263 laal.................................................eaaaaaealeaalaalrarlralrral 293
                                    l++l                                                 ++ ++     ++l+++ra+++++r++ 
  gi|119719290|ref|YP_919785.1|  99 LKRLnaeynnlrgflgskrydedelrnrieqlewqyqtmtlppevekvlvnkiRSLESIYVNVKHLNEVRAKIEEIRAQI 178
                                    9999*****99999999999999999999999999999999999999999766444555555666677788888888888 PP

                           FUSC 294 eadadtaalllarlaellaelaqllaslraleaaiaa........arraerlarhrdh 343
                                    ++     +++ ++l+++++e++ + ++++al++++ +        +         rd+
  gi|119719290|ref|YP_919785.1| 179 PELKKKVQAINEELKTVVSEYLKVKEQMQALKQQRDElvkrlvelK-------QERDR 229
                                    8999999999999999999999999999999999998855544442.......43333 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0  35.6   5.1e-05    0.0067     613     871 ..       6     263 ..       1     291 [. 0.72

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.1e-05
                        DUF3584 613 ealqsaeakqkqaeeelkqlnaeleeakravaeaatalknardtlerlqnekesekdklekaiaerkqqaeeqlqkldaq 692
                                    e ++s +++  +  ++l++++a+++ea+ +   a+ ++k    +++ l+++ +++++++ +a+ae+k++  e++ kl ++
  gi|119719290|ref|YP_919785.1|   6 ESIESLRQQLIEYRQKLQEISAKIQEARSKRDSANGEVKRISAEIRSLREQYQALRQQI-AAVAEQKKTLYEKISKLREE 84 
                                    44555555555666677777777777777777777777777777777777777777666.46677777777788888888 PP

                        DUF3584 693 lkqleeqqkaaleelkedlseerlekkakwqevvgeldeqlaelkkaieaartqaka.....rlkeleeaykreLkskdv 767
                                    +k ++eq +++  elk+   e       +++   g++   ++el + ie+ + q +      +++++  +  r+L+s  v
  gi|119719290|ref|YP_919785.1|  85 KKGILEQLNKLRDELKRLNAEYN-----NLRGFLGSKRYDEDELRNRIEQLEWQYQTmtlppEVEKVLVNKIRSLESIYV 159
                                    88888877777777766555544.....4555555555555555555555544443311122788999999999****** PP

                        DUF3584 768 DpetvkelkrkieeLekkieriekrreevreYraflqetwlkvdslaeerpalkeqveelesaaeeleqeltrliedtkl 847
                                    + + ++e+++kiee+ ++i + +k+ ++++e  + + +++lk   ++e+ +alk+q  el + + el+qe  r+ e +++
  gi|119719290|ref|YP_919785.1| 160 NVKHLNEVRAKIEEIRAQIPELKKKVQAINEELKTVVSEYLK---VKEQMQALKQQRDELVKRLVELKQERDRIRETANN 236
                                    ******************************************...999**********************9998777666 PP

                        DUF3584 848 erk...klekerkalekqldqldenlr 871
                                      +    l +e k+l++ l++++ +l+
  gi|119719290|ref|YP_919785.1| 237 YHQiyiSLLSEEKSLREELERISILLK 263
                                    544222556666777777776665555 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   8.6   0.00055     0.074      27      99 ..      11      80 ..       2      82 .. 0.84
   2 !   15.1   7.2   0.00015      0.02      37     100 ..      42     109 ..      38     114 .. 0.85
   3 ?    8.0  10.9     0.024       3.2      38      97 ..     158     220 ..     119     237 .. 0.54
   4 ?    2.4   7.8       1.3   1.8e+02      30      88 ..     205     267 ..     201     284 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00055
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH CS
                   Seryl_tRNA_N 27 dvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaelek 99
                                   + ++l+e  +k +e+ ++++e++++r +++ e++++++   ++ +l+++ ++l ++++a+ ++ k+l +++ k
  gi|119719290|ref|YP_919785.1| 11 LRQQLIEYRQKLQEISAKIQEARSKRDSANGEVKRISA---EIRSLREQYQALRQQIAAVAEQKKTLYEKISK 80
                                   55789999999999999999999999999999999997...58889999999999999999998888888876 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 0.00015
                                    HHHHHHHHHHHHHHHHHHHHHHCCCCCCTT....S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                   Seryl_tRNA_N  37 krrelqveleelqaerNelskeIgkakkkk....edaeeliaevkelkeelkaleaelkeleaelekl 100
                                    + +++ +e+ +l+++  +l ++I+   ++k    e++++l++e k + e+l++l +elk l+ae ++l
  gi|119719290|ref|YP_919785.1|  42 EVKRISAEIRSLREQYQALRQQIAAVAEQKktlyEKISKLREEKKGILEQLNKLRDELKRLNAEYNNL 109
                                    66778888888888888888888888888888889999999999999999999999999999998875 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.024
                                    HHHHHHHHHHHHHHHHHHHHHCCCCCCTT....S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHH CS
                   Seryl_tRNA_N  38 rrelqveleelqaerNelskeIgkakkkk....edaeeliaevkelkeelkaleaelkeleael 97 
                                      +++ +l+e++a+  e+ ++I ++kkk     e+ + ++ e  ++ke+++al+++ +el ++l
  gi|119719290|ref|YP_919785.1| 158 YVNVK-HLNEVRAKIEEIRAQIPELKKKVqainEELKTVVSEYLKVKEQMQALKQQRDELVKRL 220
                                    44433.3555555555555555555554333333333333333333333333333333332222 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 1.3
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT....S-TCCCCCCCHHHHHHHHHHHH CS
                   Seryl_tRNA_N  30 elleldekrrelqveleelqaerNelskeIgkakkkk....edaeeliaevkelkeelkalea 88 
                                    ++ +l ++r el ++l el++er ++ ++  +  +       + ++l++e + ++  lka+e 
  gi|119719290|ref|YP_919785.1| 205 QMQALKQQRDELVKRLVELKQERDRIRETANNYHQIYisllSEEKSLREELERISILLKAKEL 267
                                    566777888888888888888888777777766666666677777788888888776666553 PP

>> PI3K_P85_iSH2  Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1  15.0    0.0004     0.053      16     133 ..      19     135 ..       2     140 .. 0.72
   2 !   11.4  10.0    0.0014      0.18      80     138 ..     161     219 ..     127     235 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.0004
                  PI3K_P85_iSH2  16 seklrevskqlqekskeydqlkeeynkiseeiqlkrqaleaFneaikmFeeqikl.qekfskeaqehEieklqenleqlk 94 
                                     +kl+e+s ++qe   ++d+   e ++is ei   r + +a +  i    eq k+  ek+sk   ++E++ + e+l++l+
  gi|119719290|ref|YP_919785.1|  19 RQKLQEISAKIQEARSKRDSANGEVKRISAEIRSLREQYQALRQQIAAVAEQKKTlYEKISK--LREEKKGILEQLNKLR 96 
                                    45666666666666677777777777777777777777777777776666666651344333..5899************ PP

                  PI3K_P85_iSH2  95 srlkelhsskekLeedlkqqkeeereleReinalkpell 133
                                    + lk l+++ ++L   l ++  +e el  +i +l  + +
  gi|119719290|ref|YP_919785.1|  97 DELKRLNAEYNNLRGFLGSKRYDEDELRNRIEQLEWQYQ 135
                                    **************9999999999999888887766555 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.0014
                  PI3K_P85_iSH2  80 ehEieklqenleqlksrlkelhsskekLeedlkqqkeeereleReinalkpellqLqkr 138
                                     +  +++   +e++++++ el+++ + ++e+lk+ ++e++++  +++alk +  +L kr
  gi|119719290|ref|YP_919785.1| 161 VKHLNEVRAKIEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQRDELVKR 219
                                    45566677788888888888888888888888888888888888888877766666554 PP

>> DUF4200  Domain of unknown function (DUF4200)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   8.4   4.9e-05    0.0065      41     102 ..       9      70 ..       3      75 .. 0.93
   2 ?    1.9  12.4       2.1   2.8e+02      37     105 ..     168     236 ..     163     245 .. 0.49

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.9e-05
                        DUF4200  41 qeleedllkfdkflkendakraralkkaeeerklkkekeaeikklkaeietlkseiekleek 102
                                    + l+++l+++ + l+e+ ak ++a+ k ++ + + k+  aei+ l+++ ++l+++i+  +e+
  gi|119719290|ref|YP_919785.1|   9 ESLRQQLIEYRQKLQEISAKIQEARSKRDSANGEVKRISAEIRSLREQYQALRQQIAAVAEQ 70 
                                    6799****************************************************998876 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 2.1
                        DUF4200  37 ekkeqeleedllkfdkflkendakraralkkaeeerklkkekeaeikklkaeietlkseiekleeklee 105
                                    ++k +e++ ++ +++k ++ ++++ +    ++ + +++ +  +++  +l + +++lk+e+++  e+ ++
  gi|119719290|ref|YP_919785.1| 168 RAKIEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQRDELVKRLVELKQERDRIRETANN 236
                                    444444444444444444444444444444444444444444444444444445555555555554444 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1  17.0    0.0002     0.026     193     288 ..      11     109 ..       2     111 .. 0.79
   2 ?    6.5  15.9     0.041       5.4     167     291 ..     123     247 ..     115     268 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 0.0002
                                    XXXXXXXXXXXXXXXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHH CS
                       Filament 193 ykskleelqeaaeknsealrsakeeitelrrqiqsleieleslkkqkasleaql...aeleerleaeleklqeklselee 269
                                     +++l e +++ ++ s+++++a++    ++ ++++ ++e+ sl++q ++l++q+   ae +++l ++++kl+e+ + + e
  gi|119719290|ref|YP_919785.1|  11 LRQQLIEYRQKLQEISAKIQEARSKRDSANGEVKRISAEIRSLREQYQALRQQIaavAEQKKTLYEKISKLREEKKGILE 90 
                                    46677777888888888888888888888888889999999999999988887622257778888888999999999999 PP

                                    HHHHHHHHHHHHHHHHHHH CS
                       Filament 270 elaeireemarqlreYqeL 288
                                    +l+++r+e++r + eY++L
  gi|119719290|ref|YP_919785.1|  91 QLNKLRDELKRLNAEYNNL 109
                                    9999999999999999987 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.041
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.. CS
                       Filament 167 Lteilkeiraqyeelaeknreeaeewykskleelqeaaeknsealrsakeeitelrrqiqsleieleslkkqkaslea.. 244
                                    L + ++++  qy ++      e+e++  +k+  l+ ++  n ++l++++  i+e+r qi +l+ +++++ ++ +++ +  
  gi|119719290|ref|YP_919785.1| 123 LRNRIEQLEWQYQTMT--LPPEVEKVLVNKIRSLE-SIYVNVKHLNEVRAKIEEIRAQIPELKKKVQAINEELKTVVSey 199
                                    4444555555554443..34688888889998885.67889999999999999999999999999999988887776512 PP

                                    .HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Filament 245 .qlaeleerleaeleklqeklseleeelaeireemarqlreYqeLLdv 291
                                     +++e  + l++++++l + l el +e  +ire+ +   + Y +LL+ 
  gi|119719290|ref|YP_919785.1| 200 lKVKEQMQALKQQRDELVKRLVELKQERDRIRETANNYHQIYISLLSE 247
                                    256666666777777777777777777777777777777777777765 PP

>> DUF349  Domain of Unknown Function (DUF349)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   3.6      0.47        63      19      68 ..       6      59 ..       2      60 .. 0.78
   2 !   16.4   5.7   6.4e-05    0.0084      17      69 ..      53     109 ..      50     114 .. 0.92
   3 ?    0.8   8.8       4.7   6.3e+02       2      67 ..     181     238 ..     147     241 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.47
                         DUF349 19 ahfeeqdaereenlekKealieeaealakstt....dwksatkrlkelqeeWke 68
                                   + +e+++++  e  +k +++ +++++   + +    ++k  ++++++l+e++++
  gi|119719290|ref|YP_919785.1|  6 ESIESLRQQLIEYRQKLQEISAKIQEARSKRDsangEVKRISAEIRSLREQYQA 59
                                   678899999999999999999999999555434566667779999999999876 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 6.4e-05
                         DUF349  17 rkahfeeqdaereenlekKealieeaealakstt....dwksatkrlkelqeeWkei 69 
                                    +++++++++++ ++  e+K+ l e++++l ++++    ++++ +++lk l +e++++
  gi|119719290|ref|YP_919785.1|  53 LREQYQALRQQIAAVAEQKKTLYEKISKLREEKKgileQLNKLRDELKRLNAEYNNL 109
                                    689**************************99876899999999***********997 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 4.7
                         DUF349   2 LwkrFraacdafferrkahfeeqdaereenlekKealieeaealaksttdwksatkrlkelqeeWk 67 
                                    L+k+ +a+ ++ +    ++ +  ++++++  +++ +l++++ +l+++       ++r++e  + ++
  gi|119719290|ref|YP_919785.1| 181 LKKKVQAINEELKTVVSEYLK-VKEQMQALKQQRDELVKRLVELKQE-------RDRIRETANNYH 238
                                    555556666666666666554.4566788899999999999999555.......444444444444 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   1.5       1.2   1.5e+02      74     117 ..       6      42 ..       1      46 [. 0.46
   2 !   16.2  10.4   6.4e-05    0.0085      64     134 ..      38     108 ..      30     111 .. 0.77
   3 ?    2.3   0.2       1.2   1.6e+02      64      85 ..     115     136 ..     107     156 .. 0.80
   4 ?    6.1  10.2     0.083        11      49     127 ..     158     236 ..     144     243 .. 0.87
   5 ?    0.7   0.4       3.8     5e+02     110     141 ..     247     278 ..     241     284 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 1.2
                           ADIP  74 skierlktqleqlerelalvqakerqlekklktleqklknekee 117
                                     +ie+l +ql +++++l+   ak ++++       +k  +   e
  gi|119719290|ref|YP_919785.1|   6 ESIESLRQQLIEYRQKLQEISAKIQEAR-------SKRDSANGE 42 
                                    4455555555555555555555544444.......444444444 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 6.4e-05
                           ADIP  64 kleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrlknalqqiktqyah 134
                                    + + e +r +++i++l +q+++l++++a+v +++++l  k+ +l +  k+  e+l++l+  l+++ + y++
  gi|119719290|ref|YP_919785.1|  38 SANGEVKRISAEIRSLREQYQALRQQIAAVAEQKKTLYEKISKLREEKKGILEQLNKLRDELKRLNAEYNN 108
                                    44557777888888888888888888888888888888888888888888888888888888888888775 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 1.2
                           ADIP  64 kleaeierlqskierlktqleq 85 
                                    +++++ + l+++ie+l+ q++ 
  gi|119719290|ref|YP_919785.1| 115 SKRYDEDELRNRIEQLEWQYQT 136
                                    6899************988764 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.083
                           ADIP  49 drdleqreslnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrlknalqq 127
                                      + ++ +++ ++i++++a i  l++k++   ++l+   +e   v+++ + l+++  +l + l ++k+e  r + ++ +
  gi|119719290|ref|YP_919785.1| 158 YVNVKHLNEVRAKIEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQRDELVKRLVELKQERDRIRETANN 236
                                    5688999999********************************9999999999999999999999999999998888766 PP

  == domain 5  score: 0.7 bits;  conditional E-value: 3.8
                           ADIP 110 klknekeelqrlknalqqiktqyahelkkkdr 141
                                      k+++eel+r    l++ + ++  e +k+++
  gi|119719290|ref|YP_919785.1| 247 EEKSLREELERISILLKAKELSQHLEERKRQL 278
                                    56899999999999999999999999999876 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   2.5      0.57        76      27      57 ..       8      38 ..       4      47 .. 0.63
   2 ?   16.3  10.4   7.7e-05      0.01      19      69 ..      49      99 ..      42     103 .. 0.91
   3 ?    2.2   3.4       1.9   2.6e+02      17      38 ..      89     110 ..      86     146 .. 0.68
   4 ?   10.2   8.4    0.0058      0.77      19      63 ..     170     221 ..     155     223 .. 0.64

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.57
                           ZapB 27 ieeLkeeneelkeenreleeeneqlkeerea 57
                                   ie L+++  e+ ++ +e+++++++ +  r +
  gi|119719290|ref|YP_919785.1|  8 IESLRQQLIEYRQKLQEISAKIQEARSKRDS 38
                                   6666666666666666666666666665554 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 7.7e-05
                           ZapB 19 titlLqmeieeLkeeneelkeenreleeeneqlkeereawqerlkkLLgkl 69
                                   +i++L++++++L+++ ++ +e+++ l e++++l+ee++ + e l+kL ++l
  gi|119719290|ref|YP_919785.1| 49 EIRSLREQYQALRQQIAAVAEQKKTLYEKISKLREEKKGILEQLNKLRDEL 99
                                   79********************************************96655 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 1.9
                           ZapB  17 idtitlLqmeieeLkeeneelk 38 
                                    ++++ +L+ e+++L +e ++l 
  gi|119719290|ref|YP_919785.1|  89 LEQLNKLRDELKRLNAEYNNLR 110
                                    5666777777777777776654 PP

  == domain 4  score: 10.2 bits;  conditional E-value: 0.0058
                           ZapB  19 titlLqmeieeLkeeneelkeenrele.......eeneqlkeereawqerlk 63 
                                    +i++ + +i eLk+++++ +ee + +        e+ ++lk++r ++ +rl 
  gi|119719290|ref|YP_919785.1| 170 KIEEIRAQIPELKKKVQAINEELKTVVseylkvkEQMQALKQQRDELVKRLV 221
                                    4566666666666666666666665554444444888888888888777775 PP

>> TolA_bind_tri  TolA binding protein trimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   1.4       4.4   5.9e+02      20      44 ..       8      32 ..       1      40 [. 0.53
   2 ?   15.7   3.0   8.7e-05     0.012      27      68 ..      43      84 ..      40      91 .. 0.90
   3 ?    4.7   3.1      0.24        32      19      55 ..      91     127 ..      78     139 .. 0.81
   4 ?    3.9   2.9      0.43        57      18      51 ..     162     195 ..     147     214 .. 0.54
   5 ?    1.1   1.4       3.3   4.3e+02      49      61 ..     269     281 ..     234     294 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 4.4
                  TolA_bind_tri 20 llelqqqlealqqelreLRGqiEel 44
                                   +  l qql + +q l+e+  +i+e 
  gi|119719290|ref|YP_919785.1|  8 IESLRQQLIEYRQKLQEISAKIQEA 32
                                   3344455555555555544444443 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 8.7e-05
                  TolA_bind_tri 27 lealqqelreLRGqiEelqyqleqleerQrdlYldlDerlrk 68
                                   +++ ++e+r+LR q + l+ q+  + e+ + lY+++ ++ ++
  gi|119719290|ref|YP_919785.1| 43 VKRISAEIRSLREQYQALRQQIAAVAEQKKTLYEKISKLREE 84
                                   678899*****************************9988765 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.24
                  TolA_bind_tri  19 lllelqqqlealqqelreLRGqiEelqyqleqleerQ 55 
                                     l +l  +l++l++e + LRG +   +y+ ++l++r 
  gi|119719290|ref|YP_919785.1|  91 QLNKLRDELKRLNAEYNNLRGFLGSKRYDEDELRNRI 127
                                    5677888999999999999999999888888888775 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.43
                  TolA_bind_tri  18 qlllelqqqlealqqelreLRGqiEelqyqleql 51 
                                    + l e+  ++e+ ++++ eL+ +++  + +l+++
  gi|119719290|ref|YP_919785.1| 162 KHLNEVRAKIEEIRAQIPELKKKVQAINEELKTV 195
                                    4455555555555555555555555555555443 PP

  == domain 5  score: 1.1 bits;  conditional E-value: 3.3
                  TolA_bind_tri  49 eqleerQrdlYld 61 
                                    + leer r+lY +
  gi|119719290|ref|YP_919785.1| 269 QHLEERKRQLYGK 281
                                    5588899998866 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   3.3     0.058       7.7      20      58 ..       9      47 ..       4      52 .. 0.52
   2 ?    9.5   6.5    0.0062      0.83      18      60 ..      49      91 ..      43      91 .. 0.89
   3 ?    6.8   5.0     0.042       5.6      16      52 ..      75     111 ..      72     127 .. 0.84
   4 ?    0.2   0.1       4.8   6.4e+02      32      48 ..     119     135 ..     113     146 .. 0.73
   5 ?    7.6   1.4     0.024       3.2      18      48 ..     163     193 ..     153     200 .. 0.75
   6 ?   11.4   5.9    0.0016      0.21      25      61 ..     198     234 ..     192     243 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.058
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXXX CS
                          DivIC 20 kqlkqeiaalqaelaklkaeneeLeaevkdLksdedyie 58
                                    +l+q++ +  ++l++++a+++e  ++ +  + +  +i 
  gi|119719290|ref|YP_919785.1|  9 ESLRQQLIEYRQKLQEISAKIQEARSKRDSANGEVKRIS 47
                                   455555555555555555555555555555544444444 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0062
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXXXXX CS
                          DivIC 18 aykqlkqeiaalqaelaklkaeneeLeaevkdLksdedyieer 60
                                    +++l+++++al +++a++ ++++ L +++++L+ ++  i e+
  gi|119719290|ref|YP_919785.1| 49 EIRSLREQYQALRQQIAAVAEQKKTLYEKISKLREEKKGILEQ 91
                                   5789*****************************9888777765 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.042
                                    XXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XX CS
                          DivIC  16 llaykqlkqeiaalqaelaklkaeneeLeaevkdLks 52 
                                    + ++++l++e + + ++l+kl++e ++L+ae ++L+ 
  gi|119719290|ref|YP_919785.1|  75 YEKISKLREEKKGILEQLNKLRDELKRLNAEYNNLRG 111
                                    668899*****************************74 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 4.8
                                    HHHHHHHHHHHHHHHHC CS
                          DivIC  32 elaklkaeneeLeaevk 48 
                                    + ++l++++e+Le + +
  gi|119719290|ref|YP_919785.1| 119 DEDELRNRIEQLEWQYQ 135
                                    56788888888886665 PP

  == domain 5  score: 7.6 bits;  conditional E-value: 0.024
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                          DivIC  18 aykqlkqeiaalqaelaklkaeneeLeaevk 48 
                                     + +++++i+++ a++ +lk++ ++ ++e+k
  gi|119719290|ref|YP_919785.1| 163 HLNEVRAKIEEIRAQIPELKKKVQAINEELK 193
                                    4667788888888888888888888777776 PP

  == domain 6  score: 11.4 bits;  conditional E-value: 0.0016
                                    HHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXXXXXX CS
                          DivIC  25 eiaalqaelaklkaeneeLeaevkdLksdedyieerA 61 
                                    e+ + ++++++lk++++eL +++ +Lk+++d+i+e A
  gi|119719290|ref|YP_919785.1| 198 EYLKVKEQMQALKQQRDELVKRLVELKQERDRIRETA 234
                                    5566777778888888888888888877888887776 PP

>> KELK  KELK-motif containing domain of MRCK Ser/Thr protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.9   5.2    0.0001     0.013      17      71 ..       9      63 ..       2      66 .. 0.93
   2 ?    4.4   3.2      0.39        52       3      36 ..      72     105 ..      70     136 .. 0.88
   3 ?    5.8   0.5      0.14        19      49      79 ..     162     192 ..     158     193 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 0.0001
                           KELK 17 eelqkelaeaqErlksqkkeLkdaisqrklamqefsevneklselrsqkqklsRq 71
                                   e+l ++l e + +l++ +  +++a s+r+ a  e + ++  + +lr+q q l  q
  gi|119719290|ref|YP_919785.1|  9 ESLRQQLIEYRQKLQEISAKIQEARSKRDSANGEVKRISAEIRSLREQYQALRQQ 63
                                   7889*********************************************998766 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.39
                           KELK   3 keLekqlrllkqEkeelqkelaeaqErlksqkke 36 
                                    k+L +++  l++Ek+ +  +l+ +++ lk  + e
  gi|119719290|ref|YP_919785.1|  72 KTLYEKISKLREEKKGILEQLNKLRDELKRLNAE 105
                                    899999****************999999988776 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.14
                           KELK  49 qefsevneklselrsqkqklsRqlrdkeeEl 79 
                                    + ++ev  k++e+r+q  +l  +++  +eEl
  gi|119719290|ref|YP_919785.1| 162 KHLNEVRAKIEEIRAQIPELKKKVQAINEEL 192
                                    67899*******************9999997 PP

>> Allexi_40kDa  Allexivirus 40kDa protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   5.0     0.046       6.1      75     150 ..       3      80 ..       1     124 [. 0.72
   2 ?    0.8   0.1       2.2   2.9e+02      78     108 ..      90     120 ..      75     140 .. 0.63
   3 ?   13.6   4.7   0.00027     0.036      60     147 ..     142     233 ..     127     256 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.046
                   Allexi_40kDa  75 sqttlLselrdalrtltklldklksvekklelsaetas..dskllkklesietsleelhakldelsssetsesegPss 150
                                    ++t ++  lr++l + +++l++++++ ++ + + ++a+   +++  ++ s+ ++ ++l +++  ++++++   e+ s+
  gi|119719290|ref|YP_919785.1|   3 AETESIESLRQQLIEYRQKLQEISAKIQEARSKRDSANgeVKRISAEIRSLREQYQALRQQIAAVAEQKKTLYEKISK 80 
                                    678888999999999999999999988888777666541145677889999999999999998887776665555444 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 2.2
                   Allexi_40kDa  78 tlLselrdalrtltklldklksvekklelsa 108
                                     +L++lrd+l++l+ + ++l+    +++ ++
  gi|119719290|ref|YP_919785.1|  90 EQLNKLRDELKRLNAEYNNLRGFLGSKRYDE 120
                                    4577777777777777777766555544443 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 0.00027
                   Allexi_40kDa  60 dvdsi.inklnpvslls.qttlLselrdalrtltklldklksvekklelsaetasds..kllkklesietsleelhakld 135
                                    +v+++ +nk+ +++++  + ++L+e+r+++++++ ++ +lk++ + ++++ +t  ++  k+ +++++++++ +el ++l 
  gi|119719290|ref|YP_919785.1| 142 EVEKVlVNKIRSLESIYvNVKHLNEVRAKIEEIRAQIPELKKKVQAINEELKTVVSEylKVKEQMQALKQQRDELVKRLV 221
                                    5555514566666554437789****************************99988763366789999**99999999999 PP

                   Allexi_40kDa 136 elsssetseseg 147
                                    el ++ ++  e+
  gi|119719290|ref|YP_919785.1| 222 ELKQERDRIRET 233
                                    998877665554 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1  21.5      0.02       2.7     307     474 ..       7     178 ..       2     182 .. 0.64
   2 ?   13.6   6.6    0.0001     0.014      91     152 ..     159     220 ..     150     222 .. 0.93

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.02
                                    TSSSSSHHHHT--HHHHTTGGG-TTTS-GGGSSTTTSTTHHHHHHHHHHHHHHHHHHHHHH....S-SS---...STTGG CS
                           EzrA 307 nlkelkeklehlekqnkelkeeldrlkqsYeLseeeleklrelekelkelekdyeeleekl....eekkvaY...Selqe 379
                                    ++++l+++l + +++++e+++++++ + +    ++   +++ +++e+ +l+++y+ l++++    e+kk+ Y   S+l+e
  gi|119719290|ref|YP_919785.1|   7 SIESLRQQLIEYRQKLQEISAKIQEARSK---RDSANGEVKRISAEIRSLREQYQALRQQIaavaEQKKTLYekiSKLRE 83 
                                    55666667777777777777777777666...444555555566666666666666655552222345555555566777 PP

                                    GTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSS-SS-S-TTTHHHHSTTTSTTTHHHHHH CS
                           EzrA 380 eleeleekleeieekqeeileslkslrkdEkrAreqldeikkelkeikrkieksnLPgiPesyleelkeasdeieelake 459
                                    e + + e+l+++ +++++++ + ++lr      r   de+++++++++ + ++  LP   e++l++   + ++i   +k 
  gi|119719290|ref|YP_919785.1|  84 EKKGILEQLNKLRDELKRLNAEYNNLRGFLGSKRYDEDELRNRIEQLEWQYQTMTLPPEVEKVLVNKIRSLESIYVNVKH 163
                                    77777777777777777777777777777777777777777777777777777777777777777777777777777777 PP

                                    HT-TT--HHHHHHHH CS
                           EzrA 460 Lekkpinikevnkrl 474
                                    L++++ +i+e+ +++
  gi|119719290|ref|YP_919785.1| 164 LNEVRAKIEEIRAQI 178
                                    777777777776664 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 0.0001
                                    S-SHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHHHHHHHHHHT- CS
                           EzrA  91 ldkykfkkakkklaeleeeldeveekikkileelkelteseeknreeieklkekYrelrkkl 152
                                    ++ ++++++++k++e+++++ e+++k+++i+eelk +++   k +e++++lk++ +el k+l
  gi|119719290|ref|YP_919785.1| 159 VNVKHLNEVRAKIEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQRDELVKRL 220
                                    5678999**********************************************999998876 PP

>> DUF2730  Protein of unknown function (DUF2730)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   1.3    0.0002     0.027      33      99 ..       6      77 ..       3      82 .. 0.85
   2 ?    1.2   0.1       2.9   3.9e+02      62      78 ..      96     112 ..      73     139 .. 0.58
   3 ?    6.7   1.3     0.057       7.6      63      92 ..     162     191 ..     115     201 .. 0.73
   4 ?    6.0   5.7     0.094        12      25      89 ..     154     216 ..     138     227 .. 0.71
   5 ?    2.2   2.7       1.5     2e+02      26      72 ..     196     244 ..     192     267 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 0.0002
                        DUF2730 33 edleklaekveendkrlteletkvenLPtakd.....lekLkllladlrgelkaleaevrqlshqvdLLLen 99
                                   e +e+l +++ e++++l+e+ +k+++  +++d     +++++ +++ lr + +al++++++++ q + L e+
  gi|119719290|ref|YP_919785.1|  6 ESIESLRQQLIEYRQKLQEISAKIQEARSKRDsangeVKRISAEIRSLREQYQALRQQIAAVAEQKKTLYEK 77
                                   67899999999*************9998776433333999***********************999988875 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 2.9
                        DUF2730  62 akdlekLkllladlrge 78 
                                    +++l++L+ + ++lrg 
  gi|119719290|ref|YP_919785.1|  96 RDELKRLNAEYNNLRGF 112
                                    44555555555555554 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.057
                        DUF2730  63 kdlekLkllladlrgelkaleaevrqlshq 92 
                                    k l++++ +++++r+++ +l+++v++++  
  gi|119719290|ref|YP_919785.1| 162 KHLNEVRAKIEEIRAQIPELKKKVQAINEE 191
                                    455566666666666666666666666655 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.094
                        DUF2730  25 ldskYakredleklaekveendkrlteletkvenLPtakdlekLkllladlrgelkaleaevrql 89 
                                    l+s Y+  + l+++  k+ee++ ++ el+ kv+ +  +++l+++  +  +++ +++al+++ ++l
  gi|119719290|ref|YP_919785.1| 154 LESIYVNVKHLNEVRAKIEEIRAQIPELKKKVQAI--NEELKTVVSEYLKVKEQMQALKQQRDEL 216
                                    67777888888888777777777777777777776..5667777777777777777777666655 PP

  == domain 5  score: 2.2 bits;  conditional E-value: 1.5
                        DUF2730  26 dskYak.redleklaekveendkrlteletkvenLP.takdlekLklll 72 
                                     s Y k +e+++ l+++ +e  krl el+++ + +  ta++ +++ + l
  gi|119719290|ref|YP_919785.1| 196 VSEYLKvKEQMQALKQQRDELVKRLVELKQERDRIReTANNYHQIYISL 244
                                    5778876888999*999999*****999999888743667777776655 PP

>> COG2  COG (conserved oligomeric Golgi) complex component, COG2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   8.8     0.052       6.9      62     117 ..      13      69 ..       3     113 .. 0.54
   2 ?    1.1   0.4         3     4e+02      76     116 ..      90     130 ..      80     157 .. 0.52
   3 ?   11.3   6.4     0.002      0.27      56     124 ..     156     225 ..     141     233 .. 0.79
   4 ?    4.6   5.5      0.25        33      16     130 ..     197     272 ..     195     288 .. 0.55

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.052
                           COG2  62 ghLvglqeeleevesplaaarkkvesvreklsereeeveskleeakeleekr.ellk 117
                                    ++L+ ++++l+e++ ++++ar+k +s++ ++++ ++e++s  e+ ++l+++  ++ +
  gi|119719290|ref|YP_919785.1|  13 QQLIEYRQKLQEISAKIQEARSKRDSANGEVKRISAEIRSLREQYQALRQQIaAVAE 69 
                                    455555555555555555555555555555555555555555555555554431111 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 3
                           COG2  76 splaaarkkvesvreklsereeeveskleeakeleekrell 116
                                     +l+++r++++ ++++ ++ +  + sk  +  el++  e l
  gi|119719290|ref|YP_919785.1|  90 EQLNKLRDELKRLNAEYNNLRGFLGSKRYDEDELRNRIEQL 130
                                    44444444444444444444444444444444444444333 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.002
                           COG2  56 d.FvslSghLvglqeeleevesplaaarkkvesvreklsereeeveskleeakeleekr.ellklllklde 124
                                      +v++ +hL  +++++ee++ ++ +++kkv++++e+l+   +e  +  e+ ++l+++r el+k+l++l++
  gi|119719290|ref|YP_919785.1| 156 SiYVNV-KHLNEVRAKIEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQRdELVKRLVELKQ 225
                                    557777.79*****************************999887666666666666666688888887765 PP

  == domain 4  score: 4.6 bits;  conditional E-value: 0.25
                           COG2  16 dqFvselrhgvpLeslrrdLeaylklleke..llelvnedyad.FvslSghLvglqeeleevesplaaarkkvesvrekl 92 
                                     ++++  ++ + L++ r++L + l +l++e   ++   ++y+  ++sl ++ ++l+eele+++                 
  gi|119719290|ref|YP_919785.1| 197 SEYLKVKEQMQALKQQRDELVKRLVELKQErdRIRETANNYHQiYISLLSEEKSLREELERISI---------------- 260
                                    4555556666666666666666666665431134444456666666666666666666666654................ PP

                           COG2  93 sereeeveskleeakeleekrellklllkldevvekle 130
                                                              llk +e+ + le
  gi|119719290|ref|YP_919785.1| 261 --------------------------LLKAKELSQHLE 272
                                    ..........................444444444443 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   6.0       0.2        27       3      53 ..       6      56 ..       5      58 .. 0.91
   2 ?   14.7   8.1    0.0002     0.027       3     102 ..      55     156 ..      53     181 .. 0.83
   3 ?    2.1   9.9       1.7   2.3e+02       2      58 ..     182     238 ..     153     259 .. 0.67
   4 ?    4.2   8.7      0.38        50       2      88 ..     182     273 ..     181     288 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.2
                        DUF5082  3 tkisklqaqiaelrseiaaleekIerLkeaktklsdekeslkqkkkklekp 53
                                   ++i++l++q  e+r++++ ++ kI++ ++ +++  +e +++++++++l+++
  gi|119719290|ref|YP_919785.1|  6 ESIESLRQQLIEYRQKLQEISAKIQEARSKRDSANGEVKRISAEIRSLREQ 56
                                   689**********************99999999999999999999998875 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 0.0002
                        DUF5082   3 tkisklqaqiaelrseiaaleekIerLkeaktklsdekeslkqkkkklekplnssesWkGkeennydgirs...nlessy 79 
                                    ++ ++l++qia   ++ ++l ekI++L+e k+ + ++ ++l ++ k l+   n+     G+++ ++d+ r    +le +y
  gi|119719290|ref|YP_919785.1|  55 EQYQALRQQIAAVAEQKKTLYEKISKLREEKKGILEQLNKLRDELKRLNAEYNNLRGFLGSKRYDEDELRNrieQLEWQY 134
                                    566899********************************************999999999999999999988777777788 PP

                        DUF5082  80 qtyvdkldelidaieeEIerLen 102
                                    qt+     e+++ + ++I+ Le+
  gi|119719290|ref|YP_919785.1| 135 QTMTL-PPEVEKVLVNKIRSLES 156
                                    87643.24566666666766665 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 1.7
                        DUF5082   2 ktkisklqaqiaelrseiaaleekIerLkeaktklsdekeslkqkkkklekplnsse 58 
                                    k+k ++ +++     se  ++ e+ + Lk+ +++l++   +lkq++  +++++n+++
  gi|119719290|ref|YP_919785.1| 182 KKKVQAINEELKTVVSEYLKVKEQMQALKQQRDELVKRLVELKQERDRIRETANNYH 238
                                    445555555566666666666666666666666666666666666666666666655 PP

  == domain 4  score: 4.2 bits;  conditional E-value: 0.38
                        DUF5082   2 ktkisklqaqiaelrseiaaleekIerLkeaktklsdekeslkqkkkklekplnsse....sWkGkeennydgirs.nle 76 
                                    k+k ++ +++     se  ++ e+ + Lk+ +++l++   +lkq++  +++++n+++    s+  +e++  ++ ++ ++ 
  gi|119719290|ref|YP_919785.1| 182 KKKVQAINEELKTVVSEYLKVKEQMQALKQQRDELVKRLVELKQERDRIRETANNYHqiyiSLLSEEKSLREELERiSIL 261
                                    6777888888999999999999********************************99976666655544333333334666 PP

                        DUF5082  77 ssyqtyvdklde 88 
                                     + ++  ++l+e
  gi|119719290|ref|YP_919785.1| 262 LKAKELSQHLEE 273
                                    666666666665 PP

>> LXG  LXG domain of WXG superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   7.2    0.0043      0.57      83     185 ..       4     102 ..       1     117 [. 0.82
   2 ?   12.3   5.5   0.00078       0.1      84     177 ..     151     236 ..     142     247 .. 0.83
   3 ?   -0.7   0.1       7.1   9.5e+02       7      30 ..     236     259 ..     234     289 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0043
                            LXG  83 alesvepssngfid.edfLeqelenglkkakevteelkdeinkilasvsdivslpelddsevkdslqkakkkvqetiekl 161
                                    ++es+e+  +  i+ +++L+ e++ ++++a+++  +   e+++i a+++ +    + ++++++++++ + ++ ++  ek+
  gi|119719290|ref|YP_919785.1|   4 ETESIESLRQQLIEyRQKLQ-EISAKIQEARSKRDSANGEVKRISAEIRSL----REQYQALRQQIAAVAEQKKTLYEKI 78 
                                    56666666677776245566.999********9999999****99999999....************************* PP

                            LXG 162 edfdqeqksalanlesdlkalkty 185
                                     ++ +e k  l++l+   ++lk++
  gi|119719290|ref|YP_919785.1|  79 SKLREEKKGILEQLNKLRDELKRL 102
                                    *********999988776666654 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00078
                            LXG  84 lesvepssngfidedfLeqelenglkkakevteelkdeinkilasvsdivslpelddsevkdslqkakkkvqetiekled 163
                                    + s+e   + +++ ++L+ e+  ++++ ++++ elk+++++i ++ +++v     ++ +vk+++q  k++++e ++ l +
  gi|119719290|ref|YP_919785.1| 151 IRSLE---SIYVNVKHLN-EVRAKIEEIRAQIPELKKKVQAINEELKTVV----SEYLKVKEQMQALKQQRDELVKRLVE 222
                                    44444...6799999***.**********************777777775....58999********************* PP

                            LXG 164 fdqeqksalanles 177
                                    + qe ++  +++++
  gi|119719290|ref|YP_919785.1| 223 LKQERDRIRETANN 236
                                    *9999887777666 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 7.1
                            LXG   7 elieaieqlkseleelkeqleqlk 30 
                                    ++++ + +l se ++l+e+le+++
  gi|119719290|ref|YP_919785.1| 236 NYHQIYISLLSEEKSLREELERIS 259
                                    567777778888888888888775 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.3      0.73        97      15      38 ..       7      30 ..       2      34 .. 0.74
   2 ?    9.2   0.2     0.012       1.6       7      39 ..      41      73 ..      35      80 .. 0.83
   3 ?    3.1   0.5      0.94   1.2e+02      15      40 ..      77     102 ..      70     109 .. 0.65
   4 ?    1.4   0.1       3.2   4.2e+02       4      34 ..     101     131 ..      91     137 .. 0.68
   5 ?   14.6   2.6   0.00024     0.032       8      44 ..     163     199 ..     147     206 .. 0.86
   6 ?    1.6   0.7       2.7   3.6e+02      12      35 ..     202     225 ..     198     230 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.73
                      FlaC_arch 15 eletvkkeneelsksveelkenVk 38
                                   ++e++++++ e +++++e+  +++
  gi|119719290|ref|YP_919785.1|  7 SIESLRQQLIEYRQKLQEISAKIQ 30
                                   677888888888888888877776 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.012
                      FlaC_arch  7 nklsklsteletvkkeneelsksveelkenVkd 39
                                    +++++s e+ +++++ + l++++  + e+ k 
  gi|119719290|ref|YP_919785.1| 41 GEVKRISAEIRSLREQYQALRQQIAAVAEQKKT 73
                                   5899********************999887664 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.94
                      FlaC_arch  15 eletvkkeneelsksveelkenVkdl 40 
                                    +++ +++e + + +++++l ++ k+l
  gi|119719290|ref|YP_919785.1|  77 KISKLREEKKGILEQLNKLRDELKRL 102
                                    56666666666666666666666655 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 3.2
                      FlaC_arch   4 elEnklsklsteletvkkeneelsksveelk 34 
                                     l  + ++l   l++ + + +el++ +e+l+
  gi|119719290|ref|YP_919785.1| 101 RLNAEYNNLRGFLGSKRYDEDELRNRIEQLE 131
                                    4555666666667777777777777777776 PP

  == domain 5  score: 14.6 bits;  conditional E-value: 0.00024
                      FlaC_arch   8 klsklsteletvkkeneelsksveelkenVkdllsLY 44 
                                     l+++  ++e +++++ el+k+v+ ++e+ k ++s Y
  gi|119719290|ref|YP_919785.1| 163 HLNEVRAKIEEIRAQIPELKKKVQAINEELKTVVSEY 199
                                    578888899***********************99877 PP

  == domain 6  score: 1.6 bits;  conditional E-value: 2.7
                      FlaC_arch  12 lsteletvkkeneelsksveelke 35 
                                    ++ +++ +k++ +el k + elk+
  gi|119719290|ref|YP_919785.1| 202 VKEQMQALKQQRDELVKRLVELKQ 225
                                    556788899999999999988887 PP

>> Dor1  Dor1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   1.4      0.33        43      44      89 ..       4      49 ..       1      62 [. 0.69
   2 ?    9.9   5.0    0.0021      0.27      15      86 ..      42     109 ..      26     111 .. 0.82
   3 ?   12.5   4.5   0.00032     0.043      18     103 ..     122     216 ..     113     226 .. 0.72
   4 ?    1.5   3.4      0.71        94      53      87 ..     204     238 ..     197     288 .. 0.55

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.33
                           Dor1 44 aaealeairqelediraqledLvlklpkLteectrfskkaeeisek 89
                                    +e +e++rq+l + r++l++++ k+ +  ++    + + ++is +
  gi|119719290|ref|YP_919785.1|  4 ETESIESLRQQLIEYRQKLQEISAKIQEARSKRDSANGEVKRISAE 49
                                   5677888888888888888888888877777777777777766665 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0021
                           Dor1  15 epelLaeeaeeilaqiqdLarknyktlidaaealeairqelediraqledLvlklpkLteectrfskkaeei 86 
                                    e +++ +e++ + +q q+L    +++++  ae+ ++++++++++r++ + ++++l+kL  e +r +++++++
  gi|119719290|ref|YP_919785.1|  42 EVKRISAEIRSLREQYQAL----RQQIAAVAEQKKTLYEKISKLREEKKGILEQLNKLRDELKRLNAEYNNL 109
                                    4456667777777777776....5678899************************************999876 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 0.00032
                           Dor1  18 lLaeeaeeilaqiq..dLarknyktlidaaealeair...qelediraqledLvlklpkLteectrfskkaeeisek... 89 
                                    +L++ +e++  q q   L  +  k+l+++ + le+i+   + l+++ra++e+++ ++p+L+++++ ++++++ ++++   
  gi|119719290|ref|YP_919785.1| 122 ELRNRIEQLEWQYQtmTLPPEVEKVLVNKIRSLESIYvnvKHLNEVRAKIEEIRAQIPELKKKVQAINEELKTVVSEylk 201
                                    5666666655554411455678888888888888876333677899****************************999666 PP

                           Dor1  90 .rkenkllldkheql 103
                                     +++ ++l+++  +l
  gi|119719290|ref|YP_919785.1| 202 vKEQMQALKQQRDEL 216
                                    655555555555554 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.71
                           Dor1  53 qelediraqledLvlklpkLteectrfskkaeeis 87 
                                    ++++++++q ++Lv++l +L++e  r+++ a++  
  gi|119719290|ref|YP_919785.1| 204 EQMQALKQQRDELVKRLVELKQERDRIRETANNYH 238
                                    44555555555566666555555555555554433 PP

>> Cytochrom_C_2  Cytochrome C'
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   1.3     0.052       6.9      32     109 ..      54     130 ..       6     133 .. 0.76
   2 ?   10.0   0.1    0.0094       1.2      10      98 ..      99     191 ..      90     212 .. 0.69
   3 ?    1.6   0.3       3.7   4.9e+02      66      86 ..     192     212 ..     162     241 .. 0.47

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.052
                                    HHHHHHHHHHHHHHHCSGGGGC-TTGSSSSS--B-THHHHTHHHHHHHHHHHHHHHHHHH..HHHHCTSHHHHHHHHHHH CS
                  Cytochrom_C_2  32 aeavaaaaealaalakklpalFpegsdkgektkakpeiWedkekfkakaaaleeaaaeLa..aaakagdlaalkaafgkv 109
                                    +e+ +a  +++aa+a++ ++l+++ s+ +   + k+ i e+ +k +++ + l+++ ++L     +k  d+++l++ ++++
  gi|119719290|ref|YP_919785.1|  54 REQYQALRQQIAAVAEQKKTLYEKISKLR---EEKKGILEQLNKLRDELKRLNAEYNNLRgfLGSKRYDEDELRNRIEQL 130
                                    57788888899999999999999988886...788899999999999999999999999843344447888888887776 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0094
                                    HHHHHHHHHHHHHHHTTSST--HHHHHHHHHHHHHHHCSGGGGC-TTGSS.SSS--B-THHHHTHHHHH...HHHHHHHH CS
                  Cytochrom_C_2  10 fksigknmgklgamlkgeapydaeavaaaaealaalakklpalFpegsdk.gektkakpeiWedkekfk...akaaalee 85 
                                    +k +++++++l + l g++ yd++++++++e+l+   ++ ++l pe ++   +k +++++i+ + ++ +   ak++++++
  gi|119719290|ref|YP_919785.1|  99 LKRLNAEYNNLRGFL-GSKRYDEDELRNRIEQLEWQYQT-MTLPPEVEKVlVNKIRSLESIYVNVKHLNevrAKIEEIRA 176
                                    677888899999999.7888*************987776.566666666696699*******988766511155566666 PP

                                    HHHHHHHHHHC..TS CS
                  Cytochrom_C_2  86 aaaeLaaaaka..gd 98 
                                    ++ eL++  +a  ++
  gi|119719290|ref|YP_919785.1| 177 QIPELKKKVQAinEE 191
                                    666777555553223 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 3.7
                                    -THHHHTHHHHHHHHHHHHHH CS
                  Cytochrom_C_2  66 kpeiWedkekfkakaaaleea 86 
                                    ++ + ++  k+k++++al+++
  gi|119719290|ref|YP_919785.1| 192 LKTVVSEYLKVKEQMQALKQQ 212
                                    222233333333333333333 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   9.8    0.0019      0.25      29      92 ..      36      99 ..       9     130 .. 0.54
   2 ?    6.6  10.4     0.079        11      32      97 ..     160     225 ..     122     233 .. 0.73
   3 ?    6.2  10.6      0.11        14      32      98 ..     160     226 ..     151     269 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0019
                                   -..BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHH CS
                          DUF16 29 kdsnkqrLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetleliletL 92
                                   +ds + ++k+i a++++l eq ++l q++ +  e+ k l +++ + +ee + + e l+ + + L
  gi|119719290|ref|YP_919785.1| 36 RDSANGEVKRISAEIRSLREQYQALRQQIAAVAEQKKTLYEKISKLREEKKGILEQLNKLRDEL 99
                                   2234445555555555555555555555555555444444444444444444444444444444 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.079
                                    BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHHHHH CS
                          DUF16  32 nkqrLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetleliletLqkink 97 
                                    n ++L+++ ak++    qi +l++kv++ +e++k    e  + +e+++++++  + +++ L ++++
  gi|119719290|ref|YP_919785.1| 160 NVKHLNEVRAKIEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQRDELVKRLVELKQ 225
                                    456677777777777777777777777777777777777777777777666666666666665555 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.11
                                    BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHHHHHH CS
                          DUF16  32 nkqrLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetleliletLqkinkR 98 
                                    n ++L+++ ak++    qi +l++kv++ +e++k    e  + +e+++++++  + +++ L ++++ 
  gi|119719290|ref|YP_919785.1| 160 NVKHLNEVRAKIEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQRDELVKRLVELKQE 226
                                    4456777777777777777777777777777777777777777777776666666666666555554 PP

>> Flagellar_rod  Paraflagellar rod protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   8.7    0.0026      0.34       1      80 [.      23     105 ..      23     110 .. 0.86
   2 ?   10.1  12.7     0.003       0.4      39     105 ..     171     237 ..     154     274 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0026
                  Flagellar_rod   1 keisavidakkrlkeaveeDlekikekreeeaaade...kqrkrykaqreesdkflqeneeqqeklvreieelereLqkl 77 
                                    +eisa i + +++++  +  +++i+++++  +++ +   +q ++ ++q+++  + +++ +e+++ +++++++l  eL++l
  gi|119719290|ref|YP_919785.1|  23 QEISAKIQEARSKRDSANGEVKRISAEIRSLREQYQalrQQIAAVAEQKKTLYEKISKLREEKKGILEQLNKLRDELKRL 102
                                    68999********************9987766554411167788899999****************************** PP

                  Flagellar_rod  78 aee 80 
                                     +e
  gi|119719290|ref|YP_919785.1| 103 NAE 105
                                    987 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.003
                  Flagellar_rod  39 rkrykaqreesdkflqeneeqqeklvreieelereLqklaeerrelvedrieaeerEekR.etdyeeF 105
                                     ++  aq  e +k +q+++e+ + +v e  + ++++q l+++r elv++ +e ++ E+ R +++++++
  gi|119719290|ref|YP_919785.1| 171 IEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQRDELVKRLVELKQ-ERDRiRETANNY 237
                                    46677888899*************************************9999765.444414444444 PP

>> DUF2353  Uncharacterized coiled-coil protein (DUF2353)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7  12.7    0.0018      0.25     135     228 ..       8     101 ..       3     111 .. 0.48
   2 ?    4.2  18.7      0.18        23      18     174 ..     113     259 ..     108     290 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0018
                        DUF2353 135 lEklkekiqqlerdlkavldekeelvterdaykeKaerLnqeLnviLkgdekrivDiDaLilENrYlkerlkqleeEkel 214
                                    +E+l+++  +++++l+++  + +e    rd+    ++r++ e+  + +  +     i a+    + l e++++l eEk+ 
  gi|119719290|ref|YP_919785.1|   8 IESLRQQLIEYRQKLQEISAKIQEARSKRDSANGEVKRISAEIRSLREQYQALRQQIAAVAEQKKTLYEKISKLREEKKG 87 
                                    45555555555555555555555555555555555555555554433322222235555555555555555555555555 PP

                        DUF2353 215 akqtlskYksllek 228
                                    + ++l+k++  l++
  gi|119719290|ref|YP_919785.1|  88 ILEQLNKLRDELKR 101
                                    55555555544332 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.18
                        DUF2353  18 LekcrqerdqyklmaeqLqerlsalkkqleeekakaadlkeekekekklsqlleesreenkalkleveeLrqklkeaqgD 97 
                                    L + r + d++++++eqL+ ++++++   e ek+  ++++ + e+    ++ l+e+r + ++++ ++ eL++k++ +++ 
  gi|119719290|ref|YP_919785.1| 113 LGSKRYDEDELRNRIEQLEWQYQTMTLPPEVEKVLVNKIR-SLESIYVNVKHLNEVRAKIEEIRAQIPELKKKVQAINEE 191
                                    6677888999999999999999999999888888888765.455555566778888888888888888888888888888 PP

                        DUF2353  98 iklLReqlarqrlglkdedlletrhssaeereelvkqlEklkekiqqlerdlkavldekeelvterdaykeKaerLn 174
                                     k++  +  + + +++      +    +++r elvk+l +lk+    ++   ++ +     l  e  + +e  er++
  gi|119719290|ref|YP_919785.1| 192 LKTVVSEYLKVKEQMQ------A---LKQQRDELVKRLVELKQERDRIRETANNYHQIYISLLSEEKSLREELERIS 259
                                    8877633332222211......1...234445555555444444444444444444444444444444444444432 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6  20.0   9.8e-05     0.013      22     115 ..       6     117 ..       2     140 .. 0.84
   2 ?    3.4  16.3      0.24        32      37     150 ..     119     240 ..     113     270 .. 0.56

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 9.8e-05
                          Atg14  22 erlyelrerlaklksekeslkkkiekalegke....eaeqledkiknkkakleelksliadlrerlqelkdklsqlkkei 97 
                                    e++++lr++l+  + + +++  ki++a ++++    e+++ +++i++++++ + l+++ia   e++++l +k+s+l++e 
  gi|119719290|ref|YP_919785.1|   6 ESIESLRQQLIEYRQKLQEISAKIQEARSKRDsangEVKRISAEIRSLREQYQALRQQIAAVAEQKKTLYEKISKLREEK 85 
                                    7999*********************99999999999999***************************************** PP

                          Atg14  98 eekkkklaklsdklk..............kRr 115
                                    +   ++l kl+d+lk               +r
  gi|119719290|ref|YP_919785.1|  86 KGILEQLNKLRDELKrlnaeynnlrgflgSKR 117
                                    ***************55555555555555333 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.24
                          Atg14  37 ekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklk.... 112
                                    + ++l+++ie+++ + +  +   + +k + +k+++l s i    ++l+e+++k+++ +++i e kkk+++ +++lk    
  gi|119719290|ref|YP_919785.1| 119 DEDELRNRIEQLEWQYQTMTLPPEVEKVLVNKIRSLES-IYVNVKHLNEVRAKIEEIRAQIPELKKKVQAINEELKtvvs 197
                                    56777888887766666333333333334444444433.23344679999999999999999999999999999997776 PP

                          Atg14 113 .............kRrsdleslqneleerrkkqiaklqdaik......rieqklssl 150
                                                 +               r +++++l++  +      +++++++++
  gi|119719290|ref|YP_919785.1| 198 eylkvkeqmqalkQ--------------QRDELVKRLVELKQerdrirETANNYHQI 240
                                    65544433333333..............44444444443333333222333333333 PP

>> PilJ  Type IV pili methyl-accepting chemotaxis transducer N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   3.3    0.0018      0.24      41     107 ..       5      75 ..       1      81 [. 0.82
   2 ?   -0.3   0.0       7.8     1e+03      50      69 ..      91     111 ..      77     150 .. 0.52
   3 ?    5.2   0.6      0.16        21      52     104 ..     165     214 ..     148     222 .. 0.57
   4 ?    6.1   2.3     0.081        11      30      95 ..     205     278 ..     199     289 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0018
                           PilJ  41 aearaqlretiaqfdrtlaalrlg.dpapgllvpae....avraqleaveqlWqelkkpaeaalaqqddaay 107
                                    +e+ ++lr+++ ++++ l++ + + ++a++  + a+     ++a++ +++++ q+l+++++a++ q+++  y
  gi|119719290|ref|YP_919785.1|   5 TESIESLRQQLIEYRQKLQEISAKiQEARSKRDSANgevkRISAEIRSLREQYQALRQQIAAVAEQKKT-LY 75 
                                    567789***************99967777777777799**********************666655554.44 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 7.8
                           PilJ  50 tiaqfdrtlaalrlg.dpapg 69 
                                    +++ +++ l++l+   ++ +g
  gi|119719290|ref|YP_919785.1|  91 QLNKLRDELKRLNAEyNNLRG 111
                                    333333333333322233322 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.16
                           PilJ  52 aqfdrtlaalrlgdpapgllvpaeavraqleaveqlWqelkkpaeaalaqqdd 104
                                    ++ ++ +++ r + p+   +v   a+ ++l+ v ++  + k+++ +al+qq d
  gi|119719290|ref|YP_919785.1| 165 NEVRAKIEEIRAQIPELKKKVQ--AINEELKTVVSEYLKVKEQM-QALKQQRD 214
                                    3344444444444444333333..66666666666666666666.45555544 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.081
                           PilJ  30 allaaaga........ydaaearaqlretiaqfdrtlaalrlgdpapgllvpaeavraqleaveqlWqelkkpa 95 
                                     ++a+ ++        ++  ++r+++ret++ + +   +l + +++ +    + ++  + +++ q+ +e+k+++
  gi|119719290|ref|YP_919785.1| 205 QMQALKQQrdelvkrlVELKQERDRIRETANNYHQIYISLLSEEKSLREELERISILLKAKELSQHLEERKRQL 278
                                    555555555666666688999*******************9999997666665599999999999999999998 PP

>> HAP1_N  HAP1 N-terminal conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   7.0     0.015         2     236     304 ..       5      73 ..       1      74 [. 0.82
   2 ?   11.8   6.2   0.00077       0.1     215     290 ..      61     136 ..      58     139 .. 0.95
   3 ?    6.5  15.2     0.031       4.1     181     288 ..     122     227 ..     119     240 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.015
                         HAP1_N 236 qeeissLlaqivdlqqklkelgveneelkqhLaaskeaqrqLtaELqdlqekyaevegmLheaqeevke 304
                                     e i+sL+ q+++ +qkl+e+++  +e +++  ++    +++ aE++ l+e+y+   + +    e+ k+
  gi|119719290|ref|YP_919785.1|   5 TESIESLRQQLIEYRQKLQEISAKIQEARSKRDSANGEVKRISAEIRSLREQYQALRQQIAAVAEQKKT 73 
                                    578899999999999999999999999999999988888899999999999999888888777777776 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00077
                         HAP1_N 215 nqqiaelseelarkleelerqqeeissLlaqivdlqqklkelgveneelkqhLaaskeaqrqLtaELqdlqekyae 290
                                    +qqia ++e+ +   e++++ +ee + +l q+ +l+  lk+l++e ++l+  L +++  + +L++ +++l+ +y+ 
  gi|119719290|ref|YP_919785.1|  61 RQQIAAVAEQKKTLYEKISKLREEKKGILEQLNKLRDELKRLNAEYNNLRGFLGSKRYDEDELRNRIEQLEWQYQT 136
                                    69******************************************************************99998875 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.031
                         HAP1_N 181 kLreeasqLk..tetdtlEekEqqLvldcveqlseanqqiaelseelarkleelerqqeeissLlaqivdlqqklkelgv 258
                                    +Lr++ +qL+   +t+tl  + ++ + + ++ l++   ++++l+e+   k ee+   + +i +L+ +++ +++ lk++++
  gi|119719290|ref|YP_919785.1| 122 ELRNRIEQLEwqYQTMTLPPEVEKVLVNKIRSLESIYVNVKHLNEV-RAKIEEI---RAQIPELKKKVQAINEELKTVVS 197
                                    67777777751156777766555555556789999999***99876.5567776...678999***************** PP

                         HAP1_N 259 eneelkqhLaaskeaqrqLtaELqdlqeky 288
                                    e  ++k++++a k+ + +L + L +l++  
  gi|119719290|ref|YP_919785.1| 198 EYLKVKEQMQALKQQRDELVKRLVELKQER 227
                                    ********************9999997644 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7  13.0    0.0018      0.24     126     240 ..      10     120 ..       1     138 [. 0.43
   2 ?    5.4   9.0     0.077        10     130     237 ..     164     255 ..     120     303 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0018
                        DUF4407 126 qlaaa...ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaqldaaqaelael 202
                                    +l+++   ++++l+e+ a+i++++++ d+a+ ++++  ae ++  ++  ++    ++   ++a++kk+ ++++++  +e 
  gi|119719290|ref|YP_919785.1|  10 SLRQQlieYRQKLQEISAKIQEARSKRDSANGEVKRISAEIRSLREQ-YQAL---RQQIAAVAEQKKTLYEKISKLREE- 84 
                                    33433444555555555555544444444444444444444433332.1111...333344444444444444443333. PP

                        DUF4407 203 kakldatarlaalraelaeleaerakeraasqaaaaad 240
                                    k+     ++l++lr+el++l+ae+++ r    +++ + 
  gi|119719290|ref|YP_919785.1|  85 KKG--ILEQLNKLRDELKRLNAEYNNLRGFLGSKRYDE 120
                                    222..355555555555555555554444333333333 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.077
                        DUF4407 130 a..ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaqldaaqaelaelkakld 207
                                        +a+++e++aqi +l+++++a +++l++   e+ k  +                +++ k+q d++ ++l elk+++d
  gi|119719290|ref|YP_919785.1| 164 LneVRAKIEEIRAQIPELKKKVQAINEELKTVVSEYLKVKE---------------QMQALKQQRDELVKRLVELKQERD 228
                                    13356666666666666666666666666655555554433...............345566666666666666666633 PP

                        DUF4407 208 ..................atarlaalraelaeleaerakeraasqaaa 237
                                                      +                     +++ +++ 
  gi|119719290|ref|YP_919785.1| 229 riretannyhqiyisllsE---------------------EKSLREEL 255
                                    3333333333333343330.....................33222222 PP

>> Golgin_A5  Golgin subfamily A member 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2  16.7   0.00034     0.045      27     170 ..       8     149 ..       2     160 .. 0.61
   2 ?    4.9  19.2      0.12        15      61     175 ..     162     278 ..     146     287 .. 0.53

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00034
                      Golgin_A5  27 iasLkegsgeeglesstalsaeldelkqerdllreelqklnqqieqlrtelqdleaqqqaeaeslreqlqeleeqleeer 106
                                    i+sL+++   e  +  ++ sa+++e++++rd ++ e+++ + +i++lr + q l +q       + eq + l e++++ r
  gi|119719290|ref|YP_919785.1|   8 IESLRQQL-IEYRQKLQEISAKIQEARSKRDSANGEVKRISAEIRSLREQYQALRQQI----AAVAEQKKTLYEKISKLR 82 
                                    66666443.4444444667777777777777777777777777777777777766665....445556666777777777 PP

                      Golgin_A5 107 kakeeveaelerlkeelryleeelvrskatlqsrikdrek...eieklrnqlttkslsssseseles 170
                                    ++k+ + ++l++l++el++l+ e  + +  l s+  d ++    ie+l+ q +t +l    e+ l +
  gi|119719290|ref|YP_919785.1|  83 EEKKGILEQLNKLRDELKRLNAEYNNLRGFLGSKRYDEDElrnRIEQLEWQYQTMTLPPEVEKVLVN 149
                                    7777777777777777777777777777766666555443111455555555555555445555555 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.12
                      Golgin_A5  61 eelqklnqqieqlrtelqdleaqqqa...eaeslreqlqeleeqleeerkakeeveaelerlkeelrylee...elvrsk 134
                                    + l++++ +ie++r+++ +l++++qa   e +++  +  +++eq+++ ++++ e+ + l +lk+e ++++e   + ++  
  gi|119719290|ref|YP_919785.1| 162 KHLNEVRAKIEEIRAQIPELKKKVQAineELKTVVSEYLKVKEQMQALKQQRDELVKRLVELKQERDRIREtanNYHQIY 241
                                    34555666666666666666655543111444444444455666666666666666655555555555554111334444 PP

                      Golgin_A5 135 atlqsrikdrekeieklrnqlttkslsssseselesRlkqL 175
                                     +l s+ k   +e+e++   l+ k+ls+     le+R +qL
  gi|119719290|ref|YP_919785.1| 242 ISLLSEEKSLREELERISILLKAKELSQ----HLEERKRQL 278
                                    4445555555556666655555555553....666666666 PP

>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   1.8     0.049       6.5      95     157 ..       8      73 ..       1     108 [. 0.66
   2 ?   11.3   2.7    0.0017      0.23      98     168 ..     160     230 ..     142     234 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.049
                                    H..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHH...HHHHHHHHH CS
                      MCPsignal  95 iieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeia...aaseeqsas 157
                                    i+ + ++  +  + l+e   +++e+ ++ ++++ ++k+i++++ ++ ++ q +    aa++eq ++
  gi|119719290|ref|YP_919785.1|   8 IESLRQQLIEYRQKLQEISAKIQEARSKRDSANGEVKRISAEIRSLREQYQALRqqiAAVAEQKKT 73 
                                    556667777777777888888888888888888888888887777766554443111233333333 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.0017
                                    ............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      MCPsignal  98 iqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasieevnqaveev 168
                                     +k+ n++ + +ee r ++ e  ++v+  +e+lk++v++  +v++++q +++  +e+ + + e  q  +++
  gi|119719290|ref|YP_919785.1| 160 NVKHLNEVRAKIEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQRDELVKRLVELKQERDRI 230
                                    358899**********************************************9999988888777766655 PP

>> DUF4140  N-terminal domain of unknown function (DUF4140)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   2.6      0.11        15      64      95 ..       5      36 ..       1      39 [. 0.83
   2 ?    9.6   5.3    0.0092       1.2      58      98 .]      34      74 ..      27      78 .. 0.72
   3 ?    5.6   0.6      0.16        21      67      96 ..      78     107 ..      73     111 .. 0.76
   4 ?   10.1   1.5    0.0063      0.83      65      96 ..     145     193 ..     115     198 .. 0.66
   5 ?    4.3   2.9      0.43        56      66      92 ..     205     231 ..     192     240 .. 0.54

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.11
                        DUF4140 64 eeelkalraeleeledelaaledelaaaearl 95
                                   +e++++lr++l e +++l++++++++ a++++
  gi|119719290|ref|YP_919785.1|  5 TESIESLRQQLIEYRQKLQEISAKIQEARSKR 36
                                   334999*******************9999865 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0092
                        DUF4140 58 pnreaeeeelkalraeleeledelaaledelaaaearlafl 98
                                     r++++ e+k++ ae+++l+++ +al++++aa+ ++++ l
  gi|119719290|ref|YP_919785.1| 34 SKRDSANGEVKRISAEIRSLREQYQALRQQIAAVAEQKKTL 74
                                   33444444788888999999999999999888888888765 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.16
                        DUF4140  67 lkalraeleeledelaaledelaaaearla 96 
                                    +++lr+e + + ++l++l+del++++a+ +
  gi|119719290|ref|YP_919785.1|  78 ISKLREEKKGILEQLNKLRDELKRLNAEYN 107
                                    678888888888888888888888887754 PP

  == domain 4  score: 10.1 bits;  conditional E-value: 0.0063
                        DUF4140  65 e.................elkalraeleeledelaaledelaaaearla 96 
                                    +                  l+++ra++ee+++++ +l+++ +a++++l+
  gi|119719290|ref|YP_919785.1| 145 KvlvnkirslesiyvnvkHLNEVRAKIEEIRAQIPELKKKVQAINEELK 193
                                    2666666666666777744777777777777777777777777777766 PP

  == domain 5  score: 4.3 bits;  conditional E-value: 0.43
                        DUF4140  66 elkalraeleeledelaaledelaaae 92 
                                    +++al+++ +el ++l +l++e+++++
  gi|119719290|ref|YP_919785.1| 205 QMQALKQQRDELVKRLVELKQERDRIR 231
                                    245555555555555555555555544 PP

>> FTA4  Kinetochore complex Fta4 of Sim4 subunit, or CENP-50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   1.4       0.2        26     127     155 ..       6      34 ..       1      42 [. 0.58
   2 ?    5.7   9.8     0.091        12     121     166 ..      49      95 ..      37     139 .. 0.78
   3 ?   10.2  15.8    0.0038       0.5      74     196 ..     148     263 ..     123     266 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.2
                           FTA4 127 erYaelrarLielserrqqlqarlarlrk 155
                                    e+ + lr++Lie ++++q+  a++++ r+
  gi|119719290|ref|YP_919785.1|   6 ESIESLRQQLIEYRQKLQEISAKIQEARS 34 
                                    44455666666666666666666665554 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.091
                           FTA4 121 pleallerYaelrarLielserrqqlqarlarlrklka.llepflgs 166
                                    ++ +l+e+Y+ lr+++++++e++++l++++++lr+ k+  le++ + 
  gi|119719290|ref|YP_919785.1|  49 EIRSLREQYQALRQQIAAVAEQKKTLYEKISKLREEKKgILEQLNKL 95 
                                    4567889**************************98765145555444 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.0038
                           FTA4  74 aeQidklYleaedekleievnedltk.................eelIkeLPesweveekeaeeepleallerYaelrarL 136
                                    +++i +                                     ee+ +++Pe +++   +a +e+l++   +Y ++++++
  gi|119719290|ref|YP_919785.1| 148 VNKIRS-------------------LesiyvnvkhlnevrakiEEIRAQIPELKKKV--QAINEELKTVVSEYLKVKEQM 206
                                    222222...................02233333333344444444446799999954..44444567778********** PP

                           FTA4 137 ielserrqqlqarlarlrklkallepflgsedpqesvqenlvtrdgeleaElermRvLla 196
                                    ++l+++r++l +rl +l++ +  + ++    ++  ++   l+ +++ l++Eler+ +Ll+
  gi|119719290|ref|YP_919785.1| 207 QALKQQRDELVKRLVELKQERDRIRET---ANNYHQIYISLLSEEKSLREELERISILLK 263
                                    ***************************...889999*********************985 PP

>> Nup54  Nucleoporin complex subunit 54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2  19.6      0.64        85      43     126 ..      13     102 ..       6     178 .. 0.82
   2 ?    8.9  14.8     0.011       1.5      32     132 ..     165     270 ..     155     282 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.64
                                    HHHHHHHHHHHHHHHHHHHHH......HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SS---SSHHHHHHHH CS
                          Nup54  43 kevaqhrerlkeisdrleele......qkhqletsvrlekakkrhvelshRllrllrkleilrsrgyaldaeEeelrarl 116
                                    +++ ++r++l+eis +++e +      + +  ++s++++ ++ + ++l +++  ++ + + l  + + l++e + + ++l
  gi|119719290|ref|YP_919785.1|  13 QQLIEYRQKLQEISAKIQEARskrdsaNGEVKRISAEIRSLREQYQALRQQIAAVAEQKKTLYEKISKLREEKKGILEQL 92 
                                    677788999999999999998333333344568999*********************99999899999999888888888 PP

                                    HHHHHHHS-H CS
                          Nup54 117 etleaqlndp 126
                                    ++l ++l++ 
  gi|119719290|ref|YP_919785.1|  93 NKLRDELKRL 102
                                    8888888752 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.011
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SS.......- CS
                          Nup54  32 edLakRvkaQqkevaqhrerlkeisdrleeleqkhqletsvrlekakkrhvelshRllrllrkleilrsrgy.......a 104
                                    ++++ + +  ++++ ++++++++i+++l+ +  ++ l++ ++++ +k++  el +Rl++l +  + +r  +        +
  gi|119719290|ref|YP_919785.1| 165 NEVRAKIEEIRAQIPELKKKVQAINEELKTVV-SEYLKVKEQMQALKQQRDELVKRLVELKQERDRIRETANnyhqiyiS 243
                                    6677788888899999****************.****************************9999665554445667889 PP

                                    --SSHHHHHHHHHHHHHHHS-HHH.HHH CS
                          Nup54 105 ldaeEeelrarletleaqlndpaqlkgr 132
                                    l  eE++lr++le ++  l++++ l++ 
  gi|119719290|ref|YP_919785.1| 244 LLSEEKSLREELERISILLKAKE-LSQH 270
                                    999**********9999888643.3444 PP

>> Swi5  Swi5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   2.0     0.056       7.4       2      43 ..      12      53 ..       5      55 .. 0.56
   2 ?    8.7   5.1     0.013       1.7       1      50 [.      60     110 ..      39     112 .. 0.71
   3 ?    5.5   0.3      0.13        18       3      43 ..      90     130 ..      88     156 .. 0.91
   4 ?    6.5   0.9     0.064       8.5       2      28 ..     168     194 ..     162     204 .. 0.74
   5 ?    7.0   2.4     0.045         6       2      45 ..     203     247 ..     202     253 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.056
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHH CS
                           Swi5  2 eaeikeleeqleelekelaelkeelkekkdpeetvkrhIklL 43
                                   ++++ e +++l+e+ ++++e++++ ++ +   + ++  I+ L
  gi|119719290|ref|YP_919785.1| 12 RQQLIEYRQKLQEISAKIQEARSKRDSANGEVKRISAEIRSL 53
                                   455555556666666666666666665555555555566666 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.013
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHH.HHHHHH CS
                           Swi5   1 leaeikeleeqleelekelaelkeelkekkdpeetvkrhIklLh.eYNEiK 50 
                                    l+++i+++ eq ++l +++++l+ee k   +  + +++ +k+L+ eYN ++
  gi|119719290|ref|YP_919785.1|  60 LRQQIAAVAEQKKTLYEKISKLREEKKGILEQLNKLRDELKRLNaEYNNLR 110
                                    356677777777777777777777766666788888888888865788776 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.13
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHH CS
                           Swi5   3 aeikeleeqleelekelaelkeelkekkdpeetvkrhIklL 43 
                                    +++++l+++l++l++e+++l+  l++k   e+++++ I++L
  gi|119719290|ref|YP_919785.1|  90 EQLNKLRDELKRLNAEYNNLRGFLGSKRYDEDELRNRIEQL 130
                                    67899999999********9999999999999999999988 PP

  == domain 4  score: 6.5 bits;  conditional E-value: 0.064
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           Swi5   2 eaeikeleeqleelekelaelkeelke 28 
                                    +a+i+e+++q+ el+k++++++eelk 
  gi|119719290|ref|YP_919785.1| 168 RAKIEEIRAQIPELKKKVQAINEELKT 194
                                    467888888888888888888888773 PP

  == domain 5  score: 7.0 bits;  conditional E-value: 0.045
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHH..HHHHHHHHHHHHHH CS
                           Swi5   2 eaeikeleeqleelekelaelkeelkekk.dpeetvkrhIklLhe 45 
                                    ++++++l++q +el k l elk+e +    ++++  + +I+lL e
  gi|119719290|ref|YP_919785.1| 203 KEQMQALKQQRDELVKRLVELKQERDRIReTANNYHQIYISLLSE 247
                                    6799*****************99987544599999999**99976 PP

>> DUF4051  Protein of unknown function (DUF4051)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.2     0.012       1.6      19      48 ..      50      79 ..      46      85 .. 0.87
   2 ?    2.2   0.5       1.1   1.5e+02      15      37 ..     195     217 ..     194     231 .. 0.81
   3 ?   -0.2   0.2       6.4   8.5e+02      30      43 ..     224     237 ..     217     240 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.012
                        DUF4051 19 ichlkRycrAfRqdRDAllEarnklyrraq 48
                                   i  l+ +++A Rq+  A+ E ++ ly + +
  gi|119719290|ref|YP_919785.1| 50 IRSLREQYQALRQQIAAVAEQKKTLYEKIS 79
                                   6789*****************999998865 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 1.1
                        DUF4051  15 vvgyichlkRycrAfRqdRDAll 37 
                                    vv+ +  +k + +A +q+RD l 
  gi|119719290|ref|YP_919785.1| 195 VVSEYLKVKEQMQALKQQRDELV 217
                                    56667889999*********875 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 6.4
                        DUF4051  30 RqdRDAllEarnkl 43 
                                    +q+RD + E  n  
  gi|119719290|ref|YP_919785.1| 224 KQERDRIRETANNY 237
                                    79*****9996654 PP

>> CCDC144C  CCDC144C protein coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4  14.3    0.0019      0.26      73     211 ..       9     150 ..       2     158 .. 0.85
   2 ?    5.6  16.5     0.056       7.4      31     107 ..     169     248 ..     159     287 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0019
                       CCDC144C  73 tmlnskLekekqnkerleaevesyrsrLaaAiqdheqsqtskrdlelalqrerdewlrl...qdklnfdvsnlkdknevL 149
                                    + l+++L + +q+ + + a+++  rs+  +A  ++++  +  r l  ++q  r++   +   ++ l   +s+l+++ + +
  gi|119719290|ref|YP_919785.1|   9 ESLRQQLIEYRQKLQEISAKIQEARSKRDSANGEVKRISAEIRSLREQYQALRQQIAAVaeqKKTLYEKISKLREEKKGI 88 
                                    67999999*****************************99999999998888888765542215556778*********** PP

                       CCDC144C 150 sqqLskaeskansLenelhetrdaLrektlllesvqrdlsqaqcqikeleqmyqneeekvnk 211
                                     +qL k   ++++L+ e +++r  L  k    +++ +  +q + q + +    + e+  vnk
  gi|119719290|ref|YP_919785.1|  89 LEQLNKLRDELKRLNAEYNNLRGFLGSKRYDEDELRNRIEQLEWQYQTMTLPPEVEKVLVNK 150
                                    *************************9999999999999999988888887777777766666 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.056
                       CCDC144C  31 edieilkeknddlqkslKlneetltktvfqy...ngqLnvlkaentmlnskLekekqnkerleaevesyrsrLaaAiqdh 107
                                      ie ++ ++ +l+k+++  +e l++ v++y   ++q+++lk +  +l  +L + kq+++r+ +  + y+    + +++ 
  gi|119719290|ref|YP_919785.1| 169 AKIEEIRAQIPELKKKVQAINEELKTVVSEYlkvKEQMQALKQQRDELVKRLVELKQERDRIRETANNYHQIYISLLSEE 248
                                    46788889999999999999999999998875446799999999999999999999999999999998888777766663 PP

>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.3      0.14        18      52      79 ..       7      34 ..       2      40 .. 0.85
   2 ?    6.3   0.8     0.087        12       5      34 ..      56      85 ..      52      91 .. 0.87
   3 ?    3.1   0.0      0.86   1.1e+02      16      38 ..      88     110 ..      79     113 .. 0.67
   4 ?    4.8   1.3      0.25        33       4      40 ..     169     205 ..     163     240 .. 0.52

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.14
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         WXG100 52 efeewkqaaqklvdaLeeisealkqaan 79
                                    +e ++q++ ++ ++L+eis ++++a +
  gi|119719290|ref|YP_919785.1|  7 SIESLRQQLIEYRQKLQEISAKIQEARS 34
                                   5678999999***********9999865 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.087
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         WXG100  5 dpeelrqaaarfqkqaeeledelqrlkaev 34
                                   ++++lrq +a++++q+++l + +++l+ e 
  gi|119719290|ref|YP_919785.1| 56 QYQALRQQIAAVAEQKKTLYEKISKLREEK 85
                                   89*********************9999876 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.86
                                    HHHHHHHHHHHHHHHHHHHHHCG CS
                         WXG100  16 fqkqaeeledelqrlkaevdalq 38 
                                    + +q ++l+del+rl+ae+++l+
  gi|119719290|ref|YP_919785.1|  88 ILEQLNKLRDELKRLNAEYNNLR 110
                                    55566678888888888888875 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.25
                                    SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCGCG CS
                         WXG100   4 vdpeelrqaaarfqkqaeeledelqrlkaevdalqsg 40 
                                    +  ee+r+ + +++k+ + + +el+++ +e+ +++++
  gi|119719290|ref|YP_919785.1| 169 AKIEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQ 205
                                    4444555555555555555555555555444444433 PP

>> Cob_adeno_trans  Cobalamin adenosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   2.8     0.003       0.4      25     109 ..      36     113 ..      12     161 .. 0.74
   2 ?    5.3   3.6      0.15        20      33     103 ..     165     235 ..     155     273 .. 0.51

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.003
                                    HHHHHHHHHHHHHHHHHHHHHCTTTTHHHHHHHHHHHHHHHHHHHHHHT.-BTCCG-S--HHHHHHHHHHHHHHHHHS-- CS
                Cob_adeno_trans  25 rveayGtvDelnsaiglarallaeeeeelkeaLeeiqneLfdlgaelatpekkkekkkiteeeveelekeideleaelpp 104
                                    r +a G+v  +++ i  +r++     ++l+++++ + ++  +l ++++  + ++ekk i e+ +++l +e+++l+ae+++
  gi|119719290|ref|YP_919785.1|  36 RDSANGEVKRISAEIRSLREQ----YQALRQQIAAVAEQKKTLYEKIS--KLREEKKGILEQ-LNKLRDELKRLNAEYNN 108
                                    334555555666666555533....34566666666666666666665..445566666666.99999999999999999 PP

                                    EESEE CS
                Cob_adeno_trans 105 lksfi 109
                                    l+ f+
  gi|119719290|ref|YP_919785.1| 109 LRGFL 113
                                    99986 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.15
                                    HHHHHHHHHHHHHCTTT...THHHHHHHHHHHHHHHHHHHHHHT.-BTCCG-S--HHHHHHHHHHHHHHHHHS- CS
                Cob_adeno_trans  33 Delnsaiglarallaee...eeelkeaLeeiqneLfdlgaelatpekkkekkkiteeeveelekeideleaelp 103
                                    +e+ + i  +ra+++e     ++++e+L+ + +e +++ +++ +   k+++ ++ ++ + el +e d+++++ +
  gi|119719290|ref|YP_919785.1| 165 NEVRAKIEEIRAQIPELkkkVQAINEELKTVVSEYLKVKEQMQA--LKQQRDELVKR-LVELKQERDRIRETAN 235
                                    55556666666554322222234444444444444444444432..12222223322.3344444444444444 PP

>> PI_PP_I  Phosphoinositide phosphatase insertion domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1       4.7   6.2e+02      23      73 ..      12      62 ..       4      74 .. 0.66
   2 ?    3.1   0.3      0.79     1e+02       6      63 ..      51     108 ..      49     124 .. 0.74
   3 ?   11.5   0.7     0.002      0.26      19      92 ..     157     230 ..     137     235 .. 0.89
   4 ?    0.7   0.0       4.6   6.1e+02      27      58 ..     228     259 ..     224     278 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 4.7
                                   --SHHHHHHHHHHHHHHHHHHHHH-SSHHHHHHHHHCT-SS--HHHHTS-H CS
                        PI_PP_I 23 easlkklkqdlnqfllkWeeikktslsLeedLnkiannktplPsWfnelsk 73
                                   +++l + +q+l+++  k +e +++  s + + ++i+++  +l + +++l +
  gi|119719290|ref|YP_919785.1| 12 RQQLIEYRQKLQEISAKIQEARSKRDSANGEVKRISAEIRSLREQYQALRQ 62
                                   455555666667777777777766667777777777777777666666654 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.79
                                    HCS-HHHHHHHHC--TT--SHHHHHHHHHHHHHHHHHHHHH-SSHHHHHHHHHCT-SS CS
                        PI_PP_I   6 rkLeeyqqaYflnleskeaslkklkqdlnqfllkWeeikktslsLeedLnkiannktp 63 
                                    r+L+e  qa   ++   +++ k+l  ++ ++  + + i ++  +L  +L++++++ ++
  gi|119719290|ref|YP_919785.1|  51 RSLREQYQALRQQIAAVAEQKKTLYEKISKLREEKKGILEQLNKLRDELKRLNAEYNN 108
                                    6677777777777777777777777888888888888887777888888877776555 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.002
                                    --TT--SHHHHHHHHHHHHHHHHHHHHH-SSHHHHHHHHHCT-SS--HHHHTS-HHHHHHHHHHT.T..SCCCH CS
                        PI_PP_I  19 leskeaslkklkqdlnqfllkWeeikktslsLeedLnkiannktplPsWfnelskaqqellrvlaeaklsveei 92 
                                    +  + ++l++++ ++ ++  +  e+kk+   ++e+L+++ ++     +  ++l++++ el++ l+e k +  +i
  gi|119719290|ref|YP_919785.1| 157 IYVNVKHLNEVRAKIEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQRDELVKRLVELKQERDRI 230
                                    566788999********************************************************887766655 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 4.6
                                    HHHHHHHHHHHHHHHHHHHH-SSHHHHHHHHH CS
                        PI_PP_I  27 kklkqdlnqfllkWeeikktslsLeedLnkia 58 
                                     +++   n++ + + ++ ++  sL e+L++i+
  gi|119719290|ref|YP_919785.1| 228 DRIRETANNYHQIYISLLSEEKSLREELERIS 259
                                    56777788888888888888889999998886 PP

>> SHE3  SWI5-dependent HO expression protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7  15.3    0.0024      0.32      15     163 ..      46     198 ..      40     207 .. 0.47
   2 ?    6.8   5.6     0.037       4.9      66     122 ..     162     218 ..     149     225 .. 0.89
   3 ?    5.7   7.0     0.081        11       6      66 ..     207     267 ..     205     288 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0024
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           SHE3  15 LtktnlqLtqqsqeLleklelaqkkeskflenlaslkhENdnLsslLkRKerrlkdlekelselkesveelklekkqlkk 94 
                                    ++ ++ +L++q q L ++   ++++++ + e++++l++E   +   L++    lk l+ e+++l+    + + ++++l++
  gi|119719290|ref|YP_919785.1|  46 ISAEIRSLREQYQALRQQIAAVAEQKKTLYEKISKLREEKKGILEQLNKLRDELKRLNAEYNNLRGFLGSKRYDEDELRN 125
                                    45555556666666666666666666666666666666666655556655556666666666666666666666666666 PP

                                    HHHHCC..CHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHSSSXXXXXXXXXX CS
                           SHE3  95 rlenss..aseteleeelerlkvqYdalvdsqk...eYkehYqqeieeLkesleklklenekqleelqerissn 163
                                    r+e+++   + ++l  e+e++ v+    ++s     +  +  + +iee++ ++ +lk+  +  +eel+ +++s+
  gi|119719290|ref|YP_919785.1| 126 RIEQLEwqYQTMTLPPEVEKVLVNKIRSLESIYvnvKHLNEVRAKIEEIRAQIPELKKKVQAINEELK-TVVSE 198
                                    66655311333444455555444433333332200022333344555555555555555553333333.33333 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.037
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH CS
                           SHE3  66 rrlkdlekelselkesveelklekkqlkkrlenssaseteleeelerlkvqYdalvd 122
                                    ++l ++  +++e + ++ elk++ ++++++l++  ++  +++e+++ lk q d lv+
  gi|119719290|ref|YP_919785.1| 162 KHLNEVRAKIEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQRDELVK 218
                                    56788889999999999999999999*************************999997 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.081
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           SHE3   6 esLHeqiDaLtktnlqLtqqsqeLleklelaqkkeskflenlaslkhENdnLsslLkRKer 66 
                                    ++L +q D+L k +++L+q+ + + e  ++ ++   ++l +  sl++E + +s lLk Ke 
  gi|119719290|ref|YP_919785.1| 207 QALKQQRDELVKRLVELKQERDRIRETANNYHQIYISLLSEEKSLREELERISILLKAKEL 267
                                    6899****************************************************99984 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5  21.1   0.00016     0.021     283     470 ..       6     195 ..       2     199 .. 0.65
   2 ?   -0.3   6.1       2.4   3.2e+02     285     353 ..     199     269 ..     193     284 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00016
                         AAA_13 283 ekqerLekliekveskkselleklkavsdeasensafeedkeelkaeaealeeqLkglqr...aleaKrkepfksve.l. 357
                                    e++e+L + + ++ +k +e+++k++++     ++  ++ +++ ++ae++ l+eq ++l++   a+ + +k + ++++ l 
  gi|119719290|ref|YP_919785.1|   6 ESIESLRQQLIEYRQKLQEISAKIQEARS---KRDSANGEVKRISAEIRSLREQYQALRQqiaAVAEQKKTLYEKISkLr 82 
                                    44555555555555555555555544433...334455668888888888888866655511145566667777776454 PP

                         AAA_13 358 esvkakiesikklvaeineliakhNek...vanleeekeeakkklelhlveeleseldeyk...kkykklekaiekleke 431
                                    e+ k+ +e+++kl +e+++l a++N+      +   ++ e+++ +e+ + +     +++++   +  k l ++i +le +
  gi|119719290|ref|YP_919785.1|  83 EEKKGILEQLNKLRDELKRLNAEYNNLrgfLGSKRYDEDELRNRIEQLEWQ-----YQTMTlppEVEKVLVNKIRSLE-S 156
                                    555555589999999999999999875111334444455555555554444.....4433333366677899*****9.9 PP

                         AAA_13 432 lkeeeaelkkleeeikeLekqlrdekpaaeeinkeLkaf 470
                                    +  + + l++++++i+e+++q+ + k+ ++ in+eLk +
  gi|119719290|ref|YP_919785.1| 157 IYVNVKHLNEVRAKIEEIRAQIPELKKKVQAINEELKTV 195
                                    99999*******************************975 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 2.4
                         AAA_13 285 qerLekliekveskkselleklkavsdeasensafeedkeelka....eaealeeqLkglqraleaKrkepfk 353
                                    + + ++ ++ ++++++el+++l ++ +e ++ ++++++++++      e + l+e+L+ ++  l+aK  e+++
  gi|119719290|ref|YP_919785.1| 199 YLKVKEQMQALKQQRDELVKRLVELKQERDRIRETANNYHQIYIsllsEEKSLREELERISILLKAK--ELSQ 269
                                    5567788888888888888888888887777777777766665512214444444454444444444..3544 PP

>> Cyclase_polyket  Polyketide synthesis cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.2       3.3   4.4e+02      50      98 ..      22      69 ..       9      76 .. 0.72
   2 ?    8.4   0.1     0.019       2.6      35      86 ..     146     201 ..     120     216 .. 0.76
   3 ?    3.1   0.1      0.86   1.1e+02      41      79 ..     235     273 ..     221     283 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 3.3
                Cyclase_polyket 50 lieadeeaeea.laearekpefkkvserlseyvspydpetWrspkdavae 98
                                   l+e +++ +ea  ++ + + e k++s+++++  ++y++   r+   avae
  gi|119719290|ref|YP_919785.1| 22 LQEISAKIQEArSKRDSANGEVKRISAEIRSLREQYQAL--RQQIAAVAE 69
                                   667777744440444555889999999999999999776..666666665 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.019
                Cyclase_polyket  35 vrrRslfsfedlyl...Hlieadeeaeealaeare.kpefkkvserlseyvspydp 86 
                                    v   ++ s+e +y+   Hl e++++ ee  a++ e k++ ++++e+l++ vs+y +
  gi|119719290|ref|YP_919785.1| 146 VLVNKIRSLESIYVnvkHLNEVRAKIEEIRAQIPElKKKVQAINEELKTVVSEYLK 201
                                    555666777888876668888888877766666665899***************76 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.86
                Cyclase_polyket  41 fsfedlylHlieadeeaeealaearekpefkkvserlse 79 
                                     +++++y+ l+  +++ +e+l++++   + k++s++l+e
  gi|119719290|ref|YP_919785.1| 235 NNYHQIYISLLSEEKSLREELERISILLKAKELSQHLEE 273
                                    579*******************99999999999998875 PP

>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4  11.9    0.0011      0.14       8     133 ..       4     127 ..       1     157 [. 0.75
   2 ?    4.4  16.6      0.32        42       5     112 ..     157     265 ..     153     291 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0011
                        zf-C4H2   8 ktleleklknklakevealekeekcleeykkelelLeqEkmaHveeLrlIhaDinalEsvikeaeeekekslekakklye 87 
                                    +t+++e+l+++l++  + l++ +  ++e +++ +  + E +  + e+r +++  +al + i    e+k+   ek++kl e
  gi|119719290|ref|YP_919785.1|   4 ETESIESLRQQLIEYRQKLQEISAKIQEARSKRDSANGEVKRISAEIRSLREQYQALRQQIAAVAEQKKTLYEKISKLRE 83 
                                    57788999999999999999999999999999999999999999999999999999999999999999999999999999 PP

                        zf-C4H2  88 eykklkeevnelrselglekledleeeeeellkeeifekqklkaaa 133
                                    e k ++e++n+lr el  ++l+   ++ +  l +++ ++ +l+++ 
  gi|119719290|ref|YP_919785.1|  84 EKKGILEQLNKLRDEL--KRLNAEYNNLRGFLGSKRYDEDELRNRI 127
                                    9999999999999884..4445544554445555554555544444 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.32
                        zf-C4H2   5 irektleleklknklakevealekeekcleeykkelelLeqEkmaHveeLrlIhaDinalEsvikeaeeekekslekakk 84 
                                    i  ++++l+++++k+ +   ++ + +k ++ +++el+++ +E ++  e+++ +++  ++l + + e ++e+++  e+a++
  gi|119719290|ref|YP_919785.1| 157 IYVNVKHLNEVRAKIEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQRDELVKRLVELKQERDRIRETANN 236
                                    556788999******9999999********************************************************** PP

                        zf-C4H2  85 lyeeykklkeevnelrse.lglekledle 112
                                     ++ y  l++e  +lr+e   ++ l + +
  gi|119719290|ref|YP_919785.1| 237 YHQIYISLLSEEKSLREElERISILLKAK 265
                                    *********99999999944444443333 PP

>> CALCOCO1  Calcium binding and coiled-coil domain (CALCOCO1) like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0  16.6   0.00052     0.069      92     225 ..       4     137 ..       1     163 [. 0.83
   2 ?    2.2  19.2      0.48        64      72     174 ..     168     276 ..     159     292 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00052
                       CALCOCO1  92 srekveeleekqkelerlseelaeeksalleakeesearirELEeDiktltqralekEteLeRlkerakkalaqrkeeea 171
                                     +e +e+l+++  e ++  +e++++ +   ++++  +  ++ +  +i++l ++ +    ++  + e+ k + ++    ++
  gi|119719290|ref|YP_919785.1|   4 ETESIESLRQQLIEYRQKLQEISAKIQEARSKRDSANGEVKRISAEIRSLREQYQALRQQIAAVAEQKKTLYEKISKLRE 83 
                                    56778888888888888888888887777777777788888888899999999999999999*******99999999999 PP

                       CALCOCO1 172 erkqlqakleqseeelrslskelqelrnslaerdtqvlqLqdtittltqkLttA 225
                                    e+k +  +l++ ++el++l++e+++lr+ l  +  +  +L++ i +l+ + +t 
  gi|119719290|ref|YP_919785.1|  84 EKKGILEQLNKLRDELKRLNAEYNNLRGFLGSKRYDEDELRNRIEQLEWQYQTM 137
                                    9999999***************************************99877665 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.48
                       CALCOCO1  72 drerkelesrveelkeelkesrekveeleekqkelerlseelaeeksallea...keesearirELEeDiktltqralek 148
                                      + +e++ ++ elk++++  +e+ +++ +++ ++++  ++l+++++ l++     ++++ rirE  ++ + +    l  
  gi|119719290|ref|YP_919785.1| 168 RAKIEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQRDELVKRlveLKQERDRIRETANNYHQIYISLLSE 247
                                    45667888999999999999999999999999999999999999998887751114556779999988877665555555 PP

                       CALCOCO1 149 Et....eLeRlkerak.kalaqrkeeeaerk 174
                                    E     eLeR+    k k l q+ e  + ++
  gi|119719290|ref|YP_919785.1| 248 EKslreELERISILLKaKELSQHLE--ERKR 276
                                    5411114555544444333333332..2333 PP

>> DUF1729  Domain of unknown function (DUF1729)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.5      0.49        65     134     175 ..      66     107 ..       6     137 .. 0.66
   2 ?   10.9   1.9    0.0012      0.15     117     204 ..     167     222 ..     143     288 .. 0.69

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.49
                        DUF1729 134 raaklwkeldetifsleavekr.kaalekkrdeiierlnkdya 175
                                     +a+  k+l e+i +l++++k     l+k rde+ +rln++y+
  gi|119719290|ref|YP_919785.1|  66 AVAEQKKTLYEKISKLREEKKGiLEQLNKLRDEL-KRLNAEYN 107
                                    2344556777777777544443134566777775.77887775 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0012
                        DUF1729 117 vvsvrSelgepihkianraaklwkeldetifsleavekrkaalekkrdeiierlnkdyakpwfavdeegelveleemtYs 196
                                    v +   e++++i +++ ++ ++ +el  ++ +  +v+++ +al+++rde+++rl                          
  gi|119719290|ref|YP_919785.1| 167 VRAKIEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQRDELVKRLV------------------------- 221
                                    3344456666666666666666666666666666666666667777777666664......................... PP

                        DUF1729 197 evvrRlve 204
                                           e
  gi|119719290|ref|YP_919785.1| 222 -------E 222
                                    .......3 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   6.0      0.17        22      26      91 ..      17      80 ..       3      84 .. 0.56
   2 ?    8.1   3.9     0.034       4.5      22      74 ..      55     105 ..      51     130 .. 0.84
   3 ?    2.3   0.9         2   2.7e+02      25      69 ..      93     137 ..      80     167 .. 0.67
   4 ?   11.7   6.4    0.0025      0.33      29      94 ..     162     225 ..     157     232 .. 0.92
   5 ?    2.1   1.7       2.4   3.1e+02      17      70 ..     234     290 ..     225     301 .. 0.47

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.17
                   Occludin_ELL 26 elhaeleevskkfseLerelkelkegskeykkieeeilqeykklkkdpeyqekkkrceyLkekLsh 91
                                   e  ++l+e+s+k++e +++ ++++ + k+++  ++++ ++y+ l+++ +  +++k  + L+ek s 
  gi|119719290|ref|YP_919785.1| 17 EYRQKLQEISAKIQEARSKRDSANGEVKRISAEIRSLREQYQALRQQIAAVAEQK--KTLYEKISK 80
                                   3345556666666666666666666555555555666667777766544444443..445555554 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.034
                   Occludin_ELL  22 keYkelhaeleevskkfseLerelkelkegskeykkieeeilqeykklkkdpe 74 
                                    ++Y++l +++++v+++ + L +++++l+e++k + +  +++ +e+k+l+   e
  gi|119719290|ref|YP_919785.1|  55 EQYQALRQQIAAVAEQKKTLYEKISKLREEKKGILEQLNKLRDELKRLNA--E 105
                                    58******************************887777888888887743..3 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 2
                   Occludin_ELL  25 kelhaeleevskkfseLerelkelkegskeykkieeeilqeykkl 69 
                                    ++l +el+ ++++ ++L+  l + + +++e ++++e++  +y+ +
  gi|119719290|ref|YP_919785.1|  93 NKLRDELKRLNAEYNNLRGFLGSKRYDEDELRNRIEQLEWQYQTM 137
                                    445555555555555555555555555556666666666666655 PP

  == domain 4  score: 11.7 bits;  conditional E-value: 0.0025
                   Occludin_ELL  29 aeleevskkfseLerelkelkegskeykkieeeilqeykklkkdpeyqekkkrceyLkekLshiKk 94 
                                    ++l+ev++k++e+++++ elk++ + +++  + +++ey k+  +++ q+ k++ ++L ++L  +K+
  gi|119719290|ref|YP_919785.1| 162 KHLNEVRAKIEEIRAQIPELKKKVQAINEELKTVVSEYLKV--KEQMQALKQQRDELVKRLVELKQ 225
                                    67999**********************************99..67889999999********9998 PP

  == domain 5  score: 2.1 bits;  conditional E-value: 2.4
                   Occludin_ELL  17 FnkeYkeYkelhaeleevskkfseLerelkelkegsk....eykkieeeilqeykklk 70 
                                     n+ ++ Y +l +e +++++++++++  lk+  e s+    + +++  + ++ y++++
  gi|119719290|ref|YP_919785.1| 234 ANNYHQIYISLLSEEKSLREELERISILLKAK-ELSQhleeRKRQLYGKAMEAYERFR 290
                                    44555666666666666666666665333322.2222011122222223334454444 PP

>> SKA1  Spindle and kinetochore-associated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   6.0    0.0021      0.28      11      77 ..      29      95 ..      19     111 .. 0.79
   2 ?    3.5   0.1      0.42        55      23      70 ..      90     136 ..      84     159 .. 0.81
   3 ?    3.8  10.5      0.33        44      18      83 ..     164     222 ..     147     279 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0021
                                   .............XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX......XXXXXXXX CS
                           SKA1 11 lrainqdpallkedlskieaevsaleellnklkkelqeeeeaikklkkeieaslkqqek.lqhlkenl 77
                                   +++  +++++++  ++ i+ae+++l+e+ ++l+++++  +e++k+l ++i + +++++  l++l+ +l
  gi|119719290|ref|YP_919785.1| 29 IQEARSKRDSANGEVKRISAEIRSLREQYQALRQQIAAVAEQKKTLYEKISKLREEKKGiLEQLN-KL 95
                                   3445567777799****************************************999988555554.44 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.42
                                    .XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.....X CS
                           SKA1  23 edlskieaevsaleellnklkkelqeeeeaikklkkeieaslkqqekl 70 
                                    e l+k+++e++ l+   n+l+ +l +++   ++l++ ie+   q + +
  gi|119719290|ref|YP_919785.1|  90 EQLNKLRDELKRLNAEYNNLRGFLGSKRYDEDELRNRIEQLEWQYQ-T 136
                                    6799*******************************99998764433.3 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.33
                                    ......XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.....XXXXXXXXXXXXXX CS
                           SKA1  18 pallkedlskieaevsaleellnklkkelqeeeeaikklkkeieaslkqqeklqhlkenlpshlpk 83 
                                     +  + ++++i+a++ +l+++++++ +el++  +   k+k++++a  +q  +       l ++l +
  gi|119719290|ref|YP_919785.1| 164 LNEVRAKIEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQRDE-------LVKRLVE 222
                                    2222444555555555555555555555555555555555555544444444.......3333333 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   8.6    0.0031      0.41      12      91 ..       9     101 ..       2     115 .. 0.50
   2 ?   10.6   5.6    0.0018      0.23       3      83 ..      49     135 ..      42     165 .. 0.49
   3 ?    6.1   6.4     0.043       5.7      11      85 ..     151     223 ..     142     226 .. 0.69
   4 ?    3.2  11.5      0.33        44       5      90 ..     179     263 ..     172     291 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0031
                          TMPIT  12 keleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk.............eeeeeeveelkeelker 78 
                                    ++l+++  ey+qkl+e+s+ +++ +++ ++ + ++k++++++++l+++ +             +   e++++l+ee k +
  gi|119719290|ref|YP_919785.1|   9 ESLRQQLIEYRQKLQEISAKIQEARSKRDSANGEVKRISAEIRSLREQYQalrqqiaavaeqkKTLYEKISKLREEKKGI 88 
                                    55555555666666666666666666666666666666666666665544333333344311123333444455555555 PP

                          TMPIT  79 kkvlkevesllpk 91 
                                     ++l+++ + l +
  gi|119719290|ref|YP_919785.1|  89 LEQLNKLRDELKR 101
                                    5555555555555 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0018
                          TMPIT   3 eweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk......eeeeeeveelkeelk 76 
                                    e+++l++++++l+++   + ++ ++l + +sk+++e k   ++l++l+++lk+l+++ +       +++   +el+++++
  gi|119719290|ref|YP_919785.1|  49 EIRSLREQYQALRQQIAAVAEQKKTLYEKISKLREEKKGILEQLNKLRDELKRLNAEYNnlrgflGSKRYDEDELRNRIE 128
                                    34444444444444444444444444444444444444444445555555555554433666666444444455555555 PP

                          TMPIT  77 erkkvlk 83 
                                    + + + +
  gi|119719290|ref|YP_919785.1| 129 QLEWQYQ 135
                                    4444444 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.043
                          TMPIT  11 fkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlkev 85 
                                    +++le+      ++l+e+ + +++++ +i + kk++++++++lk++ ++   + +e+++ lk++ +e  k l e+
  gi|119719290|ref|YP_919785.1| 151 IRSLESIY-VNVKHLNEVRAKIEEIRAQIPELKKKVQAINEELKTVVSEY-LKVKEQMQALKQQRDELVKRLVEL 223
                                    45555554.34567888888888888888888888888888888888774.567777777777766665555554 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.33
                          TMPIT   5 eelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlke 84 
                                     el+k++++++e+ k++ ++  +++++ ++++++ ++  krl elk++ ++++++++ ++++++ +l +e k+ ++ l++
  gi|119719290|ref|YP_919785.1| 179 PELKKKVQAINEELKTVVSEYLKVKEQMQALKQQRDELVKRLVELKQERDRIRETAN-NYHQIYISLLSEEKSLREELER 257
                                    567777777777777777777777777777777777777777777777777776654.3333333333333333334444 PP

                          TMPIT  85 vesllp 90 
                                    ++ ll 
  gi|119719290|ref|YP_919785.1| 258 ISILLK 263
                                    443333 PP

>> Cytochrom_B562  Cytochrome b562
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.6    0.0095       1.3      45      97 ..       6      57 ..       1      61 [. 0.83
   2 ?    6.6   0.9     0.089        12      28      74 ..      59     105 ..      57     109 .. 0.89
   3 ?    5.7   3.2      0.18        23      24      99 ..     159     239 ..     145     241 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0095
                 Cytochrom_B562 45 sklekdseeqkdYqeGldklidqldkaealakagkleeakaalkelkdlrkey 97
                                   +++e  +++  +Y++ l+++ +++++a+++ ++  + e+k + +e+++lr++y
  gi|119719290|ref|YP_919785.1|  6 ESIESLRQQLIEYRQKLQEISAKIQEARSKRDS-ANGEVKRISAEIRSLREQY 57
                                   455666778889*****************9885.5689999999999999998 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.089
                 Cytochrom_B562  28 alkelraaaedakeatpsklekdseeqkdYqeGldklidqldkaeal 74 
                                    al + +aa+++ k++ ++k+ k +ee k+  e l+kl d+l++++a+
  gi|119719290|ref|YP_919785.1|  59 ALRQQIAAVAEQKKTLYEKISKLREEKKGILEQLNKLRDELKRLNAE 105
                                    667778899999******************************99876 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.18
                 Cytochrom_B562  24 elkkalkelraaaedakeatpsklek........dseeqkdYqeGldklidqldkaealakagkleeakaalkelkdlrk 95 
                                     + k+l+e ra  e+ +++ p +l+k         +  +++Y +  +++++  ++ ++l+k   l e k++ ++++++ +
  gi|119719290|ref|YP_919785.1| 159 VNVKHLNEVRAKIEEIRAQIP-ELKKkvqaineeLKTVVSEYLKVKEQMQALKQQRDELVK--RLVELKQERDRIRETAN 235
                                    455666666666666666666.444445442222444445555444444444444444444..78899999999999999 PP

                 Cytochrom_B562  96 eyHk 99 
                                    +yH+
  gi|119719290|ref|YP_919785.1| 236 NYHQ 239
                                    9997 PP

>> HD_assoc  Phosphohydrolase-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   2.0    0.0031      0.41       4      50 ..     182     228 ..     180     254 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0031
                       HD_assoc   4 seevaaeiaeLkkflfenvyrhpevqreeekarriireLfealledp 50 
                                    +++v+a  +eLk+++ e++  ++++q+++++  +++++L+e+  e++
  gi|119719290|ref|YP_919785.1| 182 KKKVQAINEELKTVVSEYLKVKEQMQALKQQRDELVKRLVELKQERD 228
                                    67899999********************************9876654 PP

>> FliJ  Flagellar FliJ protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5  15.0     0.072       9.5       6      90 ..       7      86 ..       2      87 .. 0.83
   2 ?   10.3  16.4    0.0047      0.62       3     113 ..      25     130 ..      23     132 .. 0.96
   3 ?    6.3  15.3      0.08        11       6      81 ..     163     233 ..     160     278 .. 0.93

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.072
                           FliJ  6 eLaeaqrelqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqvekareewqearq 87
                                     ++ +++l ++++kl+e+   +qe +++  ++       e + ++a i++l+e+ + ++q++a   +q ++  e+  + r 
  gi|119719290|ref|YP_919785.1|  7 SIESLRQQLIEYRQKLQEISAKIQEARSKRDSAN-----GEVKRISAEIRSLREQYQALRQQIAAVAEQKKTLYEKISKLRE 83
                                   5667899999999999999999999988888888.....8999999999999999999999999999998888888888777 PP

                           FliJ 88 erk 90
                                   e+k
  gi|119719290|ref|YP_919785.1| 84 EKK 86
                                   776 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0047
                           FliJ   3 aareLaeaqrelqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqvekareew 82 
                                    +  + +ea+ ++++a+ ++ ++  +++++++q ++       +++ ++ +++++l e+i+++++e +   +q++k r+e+
  gi|119719290|ref|YP_919785.1|  25 ISAKIQEARSKRDSANGEVKRISAEIRSLREQYQALR-----QQIAAVAEQKKTLYEKISKLREEKKGILEQLNKLRDEL 99 
                                    566789******************************9.....************************************** PP

                           FliJ  83 qearqerkklekLkerekkeeqkeenrrEqk 113
                                    +  + e++ l+     ++ +e +  nr Eq 
  gi|119719290|ref|YP_919785.1| 100 KRLNAEYNNLRGFLGSKRYDEDELRNRIEQL 130
                                    *****************************96 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.08
                           FliJ   6 eLaeaqrelqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqvekaree 81 
                                     L+e+++++++ ++++ el++  q   ++l+        +e+ +++++++al+++ +++ + l  +++++++ re 
  gi|119719290|ref|YP_919785.1| 163 HLNEVRAKIEEIRAQIPELKKKVQAINEELKTVV-----SEYLKVKEQMQALKQQRDELVKRLVELKQERDRIRET 233
                                    799******************************9.....********************************99986 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   4.8    0.0044      0.59     239     329 ..      20     111 ..       6     131 .. 0.48
   2 ?    4.2   8.8     0.063       8.3     238     327 ..     151     240 ..     120     288 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0044
                       Prominin 239 aelerllenlkeakeqLeqvnklekeLrksgsqLrdglrgvkrdlnqalsnlCqs.eeCskilssleiekldtskcl.dq 316
                                    ++l+++  +++ea+ +  + n   k++  + + Lr+  ++ ++++  +++++ +  e+ sk++++++  +l++ ++l d+
  gi|119719290|ref|YP_919785.1|  20 QKLQEISAKIQEARSKRDSANGEVKRISAEIRSLREQYQALRQQIAAVAEQKKTLyEKISKLREEKKG-ILEQLNKLrDE 98 
                                    44445555555555555555555555555555555555555555555444433322444444444433.44444444455 PP

                       Prominin 317 lpnvdevlealee 329
                                    l+ ++ + ++l++
  gi|119719290|ref|YP_919785.1|  99 LKRLNAEYNNLRG 111
                                    5555544444443 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.063
                       Prominin 238 LaelerllenlkeakeqLeqvnklekeLrksgsqLrdglrgvkrdlnqalsnlCq...s.eeCskilssleiekldtskc 313
                                    +      le++    ++L++v++  +e+r +  +L++ ++++ ++l++++s+  +   + +  ++ +++l +  ++++++
  gi|119719290|ref|YP_919785.1| 151 IR----SLESIYVNVKHLNEVRAKIEEIRAQIPELKKKVQAINEELKTVVSEYLKvkeQmQALKQQRDELVKRLVELKQE 226
                                    33....33455555678888888888888888888888888888888888886552221122222222222333333333 PP

                       Prominin 314 ldqlpnvdevleal 327
                                     d + ++ +  +++
  gi|119719290|ref|YP_919785.1| 227 RDRIRETANNYHQI 240
                                    34444444444433 PP

>> T3SSipB  Type III cell invasion protein SipB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   6.5     0.081        11      20      93 ..      22      95 ..       4     110 .. 0.70
   2 ?    7.1   1.3     0.053         7      21      73 ..      58     110 ..      50     137 .. 0.64
   3 ?    7.7   1.7     0.035       4.6      25      99 ..     169     229 ..     153     288 .. 0.57

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.081
                                   HHHHHHHHHHHHHHHHHTTTTT----STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT- CS
                        T3SSipB 20 LsqLenrlaawkamskaqqeaasklSdelqtalseakgatddleaaiekadqaksaadaatkkvdeaqkrlkeL 93
                                   L++++ +++  +++  +++ + +++S e++ + ++ +++ +++ a +e+ +++  ++ ++ +  + ++++l++L
  gi|119719290|ref|YP_919785.1| 22 LQEISAKIQEARSKRDSANGEVKRISAEIRSLREQYQALRQQIAAVAEQKKTLYEKISKLREEKKGILEQLNKL 95
                                   67777777777777777777777777777777777777777777777777777777777777777777777777 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.053
                                    HHHHHHHHHHHHHHHHTTTTT----STHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        T3SSipB  21 sqLenrlaawkamskaqqeaasklSdelqtalseakgatddleaaiekadqak 73 
                                    ++L++++aa   ++k   e+ skl +e +  l++ +++ d+l+   ++++++ 
  gi|119719290|ref|YP_919785.1|  58 QALRQQIAAVAEQKKTLYEKISKLREEKKGILEQLNKLRDELKRLNAEYNNLR 110
                                    55666666666666666666666666666666666666666666666665554 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.035
                                    HHHHHHHHHHHHTTTTT----STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT------- CS
                        T3SSipB  25 nrlaawkamskaqqeaasklSdelqtalseakgatddleaaiekadqaksaadaatkkvdeaqkrlkeLaPdePe 99 
                                     +++  +a+              + ++ ++ +++ ++l+  + ++ ++k +++a++++ de  krl eL+ +   
  gi|119719290|ref|YP_919785.1| 169 AKIEEIRAQ--------------IPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQRDELVKRLVELKQERDR 229
                                    444444444..............4444555555555555555555555555555555555555555555333222 PP

>> DUF932  Domain of unknown function (DUF932)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   1.9      0.74        98     116     180 ..      23     107 ..       5     137 .. 0.52
   2 ?   11.2   1.3    0.0018      0.23     103     180 ..     159     238 ..     152     302 .. 0.65

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.74
                         DUF932 116 ieakkaLglvveefeefeeeaealaavklteaeaeafaeavlpepkeaaeerkk....................ralaal 175
                                    +e++ ++++++++ + ++ e+++ +a   + +e+ + +++ ++   e++++  +                     +l++l
  gi|119719290|ref|YP_919785.1|  23 QEISAKIQEARSKRDSANGEVKRISAEIRSLREQYQALRQQIAAVAEQKKTLYEkisklreekkgileqlnklrDELKRL 102
                                    44444444444444444444444444444444444444433332222222222233333334444444444455555555 PP

                         DUF932 176 alrfe 180
                                    ++ ++
  gi|119719290|ref|YP_919785.1| 103 NAEYN 107
                                    55555 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.0018
                         DUF932 103 vkvrHtgnvdakvieakkaLglvveefeefeeeaealaavklteaeaeafaeavlpepkeaaeerkk.....ralaalal 177
                                    v v+H ++v+ak++e++ ++ +  +++++++ee ++  +  l+ +e+ + +++   e  +      +      + ++ a+
  gi|119719290|ref|YP_919785.1| 159 VNVKHLNEVRAKIEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQRDELVKRLV---ElkqerDRIRETAN 235
                                    789999999999999999999999999999999999999999999998888833222222222...24435555566666 PP

                         DUF932 178 rfe 180
                                    +++
  gi|119719290|ref|YP_919785.1| 236 NYH 238
                                    666 PP

>> Rootletin  Ciliary rootlet component, centrosome cohesion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6  17.1    0.0016      0.21      18     143 ..       8     134 ..       3     139 .. 0.74
   2 ?    0.2  19.1       4.9   6.5e+02      68     166 ..     163     257 ..     120     290 .. 0.49

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0016
                      Rootletin  18 vskLqaKvlqYkkrcseleqrllektselektkltlllssareleeeesadleealakLeeErqrseklaqvnslLreql 97 
                                    +++L++++++Y+++ +e+ ++++e  s+ ++ +++ +    ++  ++  ++++ ++++     ++ ++l +  s Lre+ 
  gi|119719290|ref|YP_919785.1|   8 IESLRQQLIEYRQKLQEISAKIQEARSKRDSANGEVKR--ISAEIRSLREQYQALRQQIAAVAEQKKTLYEKISKLREEK 85 
                                    689*********************66666665554332..2233333444455667777777777788889999999999 PP

                      Rootletin  98 eearqaneaLtedlqkltkdwerlreeleqk...ekewreeeeafneyl 143
                                    +   ++ ++L+++l++l+++ ++lr  l +k   e+e+r++ e+++ ++
  gi|119719290|ref|YP_919785.1|  86 KGILEQLNKLRDELKRLNAEYNNLRGFLGSKrydEDELRNRIEQLEWQY 134
                                    9999999999999999999999999876555333777777777666555 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 4.9
                      Rootletin  68 dleealakLeeErqrseklaqvnslLreqleearqaneaLtedlqkltkdwerlreeleqkekewreeeeafneylsseh 147
                                     l+e++ak ee r +  +l++  +   e+l+   ++  + +e +q     +++ r+el ++  e+++e+ +++e  ++ h
  gi|119719290|ref|YP_919785.1| 163 HLNEVRAKIEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMQA----LKQQRDELVKRLVELKQERDRIRETANNYH 238
                                    3444444444444444444444444444444444444444444444....233345555555555555555555555555 PP

                      Rootletin 148 srllsLWrevvavrrqfse 166
                                    +  +sL  e +++r +++ 
  gi|119719290|ref|YP_919785.1| 239 QIYISLLSEEKSLREELER 257
                                    5555555555555544433 PP

>> DUF4472  Domain of unknown function (DUF4472)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   5.6    0.0051      0.67      39     102 ..      10      73 ..       3      77 .. 0.86
   2 ?    4.6   1.4      0.39        52      51     103 ..      71     123 ..      66     138 .. 0.71
   3 ?    9.0   5.2     0.017       2.2      35     104 ..     149     217 ..     143     220 .. 0.84
   4 ?    2.6   5.0       1.7   2.2e+02       9      67 ..     217     273 ..     215     289 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0051
                        DUF4472  39 alenrvlelelerekaaeeiqslrerlaeleeekkeleeeyvvlkknyqalekefekekkkqqe 102
                                    +l ++++e   + ++   +iq++r++ + ++ e k++++e  +l+++yqal+++  + +++++ 
  gi|119719290|ref|YP_919785.1|  10 SLRQQLIEYRQKLQEISAKIQEARSKRDSANGEVKRISAEIRSLREQYQALRQQIAAVAEQKKT 73 
                                    6778999999999999999999999999999999999999999999999999998887777665 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.39
                        DUF4472  51 rekaaeeiqslrerlaeleeekkeleeeyvvlkknyqalekefekekkkqqel 103
                                    ++++ e+i++lre+ +++ e+ ++l++e++ l+ +y +l+  + +++  ++el
  gi|119719290|ref|YP_919785.1|  71 KKTLYEKISKLREEKKGILEQLNKLRDELKRLNAEYNNLRGFLGSKRYDEDEL 123
                                    45566777778888888888888888888888887777766655555555555 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.017
                        DUF4472  35 nkvlalenrvlelelerekaaeeiqslrerlaeleeekkeleeeyvvlkknyqalekefekekkkqqels 104
                                    nk+ +le+  ++++ + ++ + +i+++r++  el+++ ++++ee++++ ++y+++++++++ k++ +el 
  gi|119719290|ref|YP_919785.1| 149 NKIRSLESIYVNVK-HLNEVRAKIEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQRDELV 217
                                    67777777666665.567788999999999999**************************99999999985 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 1.7
                        DUF4472   9 sKeLVdlqietnklreqheaekfelknkvlalenrvlelelerekaaeeiqslrerlae 67 
                                     K LV+l+ e++++re +++   +    +l+ e+++   eler     ++++l+++l+e
  gi|119719290|ref|YP_919785.1| 217 VKRLVELKQERDRIRETANN-YHQIYISLLSEEKSLR-EELERISILLKAKELSQHLEE 273
                                    57777777777777776543.3455555555554333.345555544444444444333 PP

>> FPP  Filament-like plant protein, long coiled-coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5  13.6    0.0037      0.49     713     813 ..       3     103 ..       1     110 [. 0.87
   2 ?    3.3  17.5      0.14        19     687     793 ..     168     276 ..     140     288 .. 0.60

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0037
                            FPP 713 satenleslkaqlqesEqllaelkseLeslkeskslaetqlkcmkesyesletrateleaelnelkqkieaLeveLeeek 792
                                     +te++esl  ql e  q+l+e+ +++++++  +  a+ ++k  +   +sl  + + l++++  + ++ ++L +++++ +
  gi|119719290|ref|YP_919785.1|   3 AETESIESLRQQLIEYRQKLQEISAKIQEARSKRDSANGEVKRISAEIRSLREQYQALRQQIAAVAEQKKTLYEKISKLR 82 
                                    67999***********************************************************99999***98887777 PP

                            FPP 793 ksheeleakckelqeqlerve 813
                                    +  +  + + ++l+  l+r +
  gi|119719290|ref|YP_919785.1|  83 EEKKGILEQLNKLRDELKRLN 103
                                    777777777777777777765 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.14
                            FPP 687 keenkllkeeleelksekenlevelksatenleslkaqlqesEqllaelkseLeslkeskslaetqlkcmkesyesletr 766
                                    +++ +  + ++ elk + + ++ elk+  ++  ++k q+q   q+ +el + L +lk+ +  + +  ++ +++y sl + 
  gi|119719290|ref|YP_919785.1| 168 RAKIEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQRDELVKRLVELKQERDRIRETANNYHQIYISLLSE 247
                                    33444455566666666666677777777777777777777777777777777777766666666677777777777777 PP

                            FPP 767 ateleaelnelk..qkieaLeveLeeekk 793
                                    ++ l++el+++    k+++L++ Lee+k+
  gi|119719290|ref|YP_919785.1| 248 EKSLREELERISilLKAKELSQHLEERKR 276
                                    77777777654311466667777776665 PP

>> CDPS  Cyclodipeptide synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   3.2    0.0068       0.9      79     140 ..      20      81 ..      14     101 .. 0.85
   2 ?    5.3   1.7       0.1        13      79     138 ..     162     221 ..     158     243 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0068
                                    HHHHHHHHHHHHHHHHHTTTTTCEEEEECCCCCC-HHHHHHHHHHHHHHHH-HHHHHHHHHH CS
                           CDPS  79 relravrarieraleeagpepervrvrrlseflanpaYrelraeveralaedeelreacdem 140
                                    ++l+++ a+i++a ++ + ++++v+ +  +  +  ++Y++lr+++ ++ ++++ l+e++ ++
  gi|119719290|ref|YP_919785.1|  20 QKLQEISAKIQEARSKRDSANGEVKRISAEIRSLREQYQALRQQIAAVAEQKKTLYEKISKL 81 
                                    56788889999999999888888777777777889********************9998765 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.1
                                    HHHHHHHHHHHHHHHHHTTTTTCEEEEECCCCCC-HHHHHHHHHHHHHHHH-HHHHHHHH CS
                           CDPS  79 relravrarieraleeagpepervrvrrlseflanpaYrelraeveralaedeelreacd 138
                                    ++l++vra+ie++  ++   +++v+ ++ +  +  ++Y ++++++++  ++++el +   
  gi|119719290|ref|YP_919785.1| 162 KHLNEVRAKIEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQRDELVKRLV 221
                                    789999*****9999997666665555555556679999999999999999999876654 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   8.4    0.0048      0.64     120     225 ..       8     109 ..       5     113 .. 0.68
   2 ?    4.5   8.7      0.14        18     119     229 ..     184     248 ..     164     286 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0048
                           CorA 120 vdrlfellekleeeldeledel..edstkkeilrelaqlrrrlvklrralapnrevlkrllakaddkllddedkeylrdl 197
                                    +++l+++l +  ++l+e++  +   +s++++  +e+ ++  ++  lr++  ++r+ + + +a + +k+l ++    ++ l
  gi|119719290|ref|YP_919785.1|   8 IESLRQQLIEYRQKLQEISAKIqeARSKRDSANGEVKRISAEIRSLREQYQALRQQI-AAVA-EQKKTLYEK----ISKL 81 
                                    667777777777888888888865333334444444444446666677777777777.4445.455555555....7999 PP

                           CorA 198 ldelerllemlealrerleslqdtyssl 225
                                    ++e + +le+l+ lr+ l +l+ +y++l
  gi|119719290|ref|YP_919785.1|  82 REEKKGILEQLNKLRDELKRLNAEYNNL 109
                                    9999999999999999999999999987 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.14
                           CorA 119 ivdrlfellekleeeldeledel..edstkkeilrelaqlrrrlvklrralapnrevlkrllakaddkllddedkeylrd 196
                                     v+ ++e+l+++ +e  ++ +++   +++++e++++l++l+++  ++r+ +++  +++ +ll+                 
  gi|119719290|ref|YP_919785.1| 184 KVQAINEELKTVVSEYLKVKEQMqaLKQQRDELVKRLVELKQERDRIRETANNYHQIYISLLS----------------- 246
                                    344555555555555555555557777777777777777777777777777777777766666................. PP

                           CorA 197 lldelerllemlealrerleslqdtyssllser 229
                                                                   e+
  gi|119719290|ref|YP_919785.1| 247 -------------------------------EE 248
                                    ...............................22 PP

>> Rab5-bind  Rabaptin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6  13.0   0.00049     0.066     137     255 ..      14     138 ..       3     153 .. 0.86
   2 ?    5.1   8.2     0.093        12     209     277 ..     154     218 ..     135     229 .. 0.61
   3 ?    0.9   1.4       1.8   2.4e+02       5      47 ..     235     275 ..     231     288 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00049
                      Rab5-bind 137 dlPddveeLqelvlklrEeliesRtakdHlEekLkaEillLkeqiqaEkal...kEnlEetlqleierlkee....lasi 209
                                    +l +  ++Lqe+  k +E   + R +++   +++ aEi  L+eq qa +++     ++ +tl   i++l+ee    l+++
  gi|119719290|ref|YP_919785.1|  14 QLIEYRQKLQEISAKIQEAR-SKRDSANGEVKRISAEIRSLREQYQALRQQiaaVAEQKKTLYEKISKLREEkkgiLEQL 92 
                                    455667999****9999874.778888888899*************98876222578999***********977778899 PP

                      Rab5-bind 210 sslkveleeikvekeslekslaektrqldklqtikselEeqlkele 255
                                    + l+ el+++ +e ++l+  l  k    d+l++++++lE q + ++
  gi|119719290|ref|YP_919785.1|  93 NKLRDELKRLNAEYNNLRGFLGSKRYDEDELRNRIEQLEWQYQTMT 138
                                    ****************************************998765 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.093
                      Rab5-bind 209 isslkveleeikvekeslekslaektrqldklqtikselEeqlkelekekaaveqlvleeknkaqrLqt 277
                                    ++s  v+++++     ++++  +e  +q+ +l++ ++ ++e+lk + +e ++v+++++  k++   L +
  gi|119719290|ref|YP_919785.1| 154 LESIYVNVKHLN----EVRAKIEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQRDELVK 218
                                    333333333322....22344567777888888888888888888888888888888877777666654 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 1.8
                      Rab5-bind   5 snYEkqLqaiqeqEaelrdqvkklqellrraneqLekerkdkk 47 
                                    +nY +   ++  +E+ lr+++ ++  ll+   ++L+++++++k
  gi|119719290|ref|YP_919785.1| 235 NNYHQIYISLLSEEKSLREELERISILLKA--KELSQHLEERK 275
                                    688888888889999999999999888874..46666666655 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   1.1     0.024       3.2      18      49 ..       6      37 ..       2      47 .. 0.77
   2 ?    2.1   8.6       1.7   2.2e+02       4      43 ..      69     108 ..      33     155 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.024
                          Spc24 18 selesleselaelkeeleeleeeseekeserv 49
                                   +++esl+++l e +++l+e++ + +e +s+r 
  gi|119719290|ref|YP_919785.1|  6 ESIESLRQQLIEYRQKLQEISAKIQEARSKRD 37
                                   6899*********************9555552 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 1.7
                          Spc24   4 nekfriakelsdleselesleselaelkeeleeleeesee 43 
                                    ++k ++ +++s+l +e + + ++l++l++el+ l+ e ++
  gi|119719290|ref|YP_919785.1|  69 EQKKTLYEKISKLREEKKGILEQLNKLRDELKRLNAEYNN 108
                                    3444555555555555555556666666666666666555 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0  11.8      0.11        14      40     110 ..       6      72 ..       1      75 [. 0.66
   2 ?    9.3   2.5      0.01       1.3      22      77 ..      79     135 ..      72     154 .. 0.77
   3 ?    6.5  10.1     0.075       9.9      14      76 ..     164     227 ..     151     235 .. 0.55
   4 ?    4.9  12.4      0.23        30       9      97 ..     194     285 ..     191     291 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.11
                                    HHHHHHHHHHHHHTTTS.-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH..HHHHHHHHHHHHHHHHTT CS
                           OmpH  40 kelqklqeelqkkakklekeekeqelqkkeqelqqkqqqkaqelqkkqqellk..pildkinkaikevakekg 110
                                    +++++l+++l       e ++k qe+ +k qe + k++ +++e+++ ++e++   + ++ +++ i++va++k+
  gi|119719290|ref|YP_919785.1|   6 ESIESLRQQLI------EYRQKLQEISAKIQEARSKRDSANGEVKRISAEIRSlrEQYQALRQQIAAVAEQKK 72 
                                    44444444442......47788888888888888877777788777777765555567888888888888876 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.01
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS......-HHHHHHHHHHHHHHHHHHH CS
                           OmpH  22 eqlekkfkklqaeleakekelqklqeelqkkakkle.....keekeqelqkkeqelqqkqq 77 
                                    ++l +++k + ++l+++++el++l +e++    +l      k+ +e el+++ ++l+ ++q
  gi|119719290|ref|YP_919785.1|  79 SKLREEKKGILEQLNKLRDELKRLNAEYN----NLRgflgsKRYDEDELRNRIEQLEWQYQ 135
                                    47899999999*****************6....3324677666666678877777776444 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.075
                                    SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS..-HHHHHHHHHHHHHHHHHH CS
                           OmpH  14 spegkaaqeqlekkfkklqaeleakekelqklqeelqkkakkl.ekeekeqelqkkeqelqqkq 76 
                                     +e +a  e++ +++ +l+++++a ++el++ + e+ k ++++ + ++++ el k+  el+q++
  gi|119719290|ref|YP_919785.1| 164 LNEVRAKIEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMqALKQQRDELVKRLVELKQER 227
                                    3333344445555556777777777777777777776655555445555555555555555533 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.23
                                    HHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS.....-HHHHHHHHHHHHHHHHHHHHHH..HH CS
                           OmpH   9 kileespegkaaqeqlekkfkklqaeleakekelqklqeelqkkakkle....keekeqelqkkeqelqqkqqqka..qe 82 
                                    ++++e+ + k+ ++ l++++ +l + l ++++e ++ +e+ +++    +       +e+ l+++ +++  ++++k+  q 
  gi|119719290|ref|YP_919785.1| 194 TVVSEYLKVKEQMQALKQQRDELVKRLVELKQERDRIRETANNYH---QiyisLLSEEKSLREELERISILLKAKElsQH 270
                                    577777888888888877776666666655555555555554333...35565666666699999999998888888888 PP

                                    HHHHHHHHHHHHHHH CS
                           OmpH  83 lqkkqqellkpildk 97 
                                    l++++++l+ + ++ 
  gi|119719290|ref|YP_919785.1| 271 LEERKRQLYGKAMEA 285
                                    999998888876554 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5  10.2    0.0028      0.37      63     160 ..       7     104 ..       1     111 [. 0.70
   2 ?    5.3   7.1      0.11        14      74     170 ..     143     235 ..     127     239 .. 0.62
   3 ?    2.4   8.4      0.82   1.1e+02      64     132 ..     171     239 ..     164     288 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0028
                         DUF745  63 lveqleqelreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeq....vaagaqqelaekt 138
                                     +e+l q+l e  + +qe+++++q++ ++ ++a+  +k + +++ +l++ ++a +++++ + +    + ++ ++  +ek+
  gi|119719290|ref|YP_919785.1|   7 SIESLRQQLIEYRQKLQEISAKIQEARSKRDSANGEVKRISAEIRSLREQYQALRQQIAAVAEqkktLYEKISKLREEKK 86 
                                    5899***************************************9999999888887766554400003344444445566 PP

                         DUF745 139 qlleaAkkRveeLkkqlkeark 160
                                     +le+ +k    L+ +lk   +
  gi|119719290|ref|YP_919785.1|  87 GILEQLNK----LRDELKRLNA 104
                                    66655433....4444444444 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.11
                         DUF745  74 aeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaektqlleaAkkRveeLkk 153
                                     e+v+ +  +sl+s   n+k  +++++++++  +++ +l k++++  e++++    +++ l+ k+q+ +a k++ +eL k
  gi|119719290|ref|YP_919785.1| 143 VEKVLVNKIRSLESIYVNVKHLNEVRAKIEEIRAQIPELKKKVQAINEELKT---VVSEYLKVKEQM-QALKQQRDELVK 218
                                    5555555666666555555555555555444444444444444444444433...344556667776.667777788899 PP

                         DUF745 154 qlkearkdlektkkaAy 170
                                    +l e +++ +++++ A+
  gi|119719290|ref|YP_919785.1| 219 RLVELKQERDRIRETAN 235
                                    99999999999998886 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.82
                         DUF745  64 veqleqelreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqq 132
                                    +e++ +++ e ++ vq ++++l++  +    +++ ++  +qq + l + l + k++ ++++++a++  q
  gi|119719290|ref|YP_919785.1| 171 IEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQRDELVKRLVELKQERDRIRETANNYHQ 239
                                    455666666666666666666666666666666666666666666666666666666666666665554 PP

>> SpecificRecomb  Site-specific recombinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   2.1      0.37        49     165     227 ..      42     104 ..       3     112 .. 0.65
   2 ?   10.2   9.7    0.0013      0.17     149     271 ..     153     275 ..     116     291 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.37
                 SpecificRecomb 165 elrrrlpeleeeespFlalqrelealleayeaaledeeeaeedlkhlrvlldqcreavdrvrk 227
                                    e+ r + e+++ ++ + al+++++a++e+ ++  e+ ++ +e++k +   l++ r+ ++r+ +
  gi|119719290|ref|YP_919785.1|  42 EVKRISAEIRSLREQYQALRQQIAAVAEQKKTLYEKISKLREEKKGILEQLNKLRDELKRLNA 104
                                    455555666666666777777777777777776666667777777777777777766666655 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0013
                 SpecificRecomb 149 alevlsvqiaal.glepelrrrlpeleeeespFlalqrelealleayeaaledeeeaeedlkhlrvlldqcreavdrvrk 227
                                    +le + v+++ l ++  ++ +   ++ e ++ + a+++el++++++y + +e+ ++ +++ ++l   l + ++  dr+r+
  gi|119719290|ref|YP_919785.1| 153 SLESIYVNVKHLnEVRAKIEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQRDELVKRLVELKQERDRIRE 232
                                    44444444443215566666777789999999************************************************ PP

                 SpecificRecomb 228 hleen.GvsvslvfllerlrqrleRleeLldlll.eeeeeeraral 271
                                     ++++  + +sl  + + lr++leR++ Ll++ + +   ++ +++ 
  gi|119719290|ref|YP_919785.1| 233 TANNYhQIYISLLSEEKSLREELERISILLKAKElS---QHLEERK 275
                                    *9998689***********************98732...2222233 PP

>> LOH1CR12  Tumour suppressor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   2.8    0.0032      0.42      56     124 ..      34     103 ..      12     107 .. 0.85
   2 ?    3.2   3.6      0.61        81      47     100 ..     167     220 ..     151     236 .. 0.71
   3 ?    2.0   0.5       1.5     2e+02      75     104 ..     234     263 ..     211     273 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0032
                       LOH1CR12  56 erikevdakiitllaelrekqkqyasyaealskvnelsdqls.riqiiledivpllEtlnelLdedeRLe 124
                                     +  + + +++++ ae+r  ++qy+   ++++ v e ++ l  +i ++ e++  +lE+ln+l de  RL+
  gi|119719290|ref|YP_919785.1|  34 SKRDSANGEVKRISAEIRSLREQYQALRQQIAAVAEQKKTLYeKISKLREEKKGILEQLNKLRDELKRLN 103
                                    445567789999***********************999998537999999999***********999996 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.61
                       LOH1CR12  47 vAadqaklverikevdakiitllaelrekqkqyasyaealskvnelsdqlsriq 100
                                    v a  +++ ++i e+++k++ + +el+    +y +  e+++ +++  d+l +  
  gi|119719290|ref|YP_919785.1| 167 VRAKIEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQRDELVKRL 220
                                    555566777777788888888888888888888888888888887777776544 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 1.5
                       LOH1CR12  75 kqkqyasyaealskvnelsdqlsriqiile 104
                                     ++ ++ y+  ls+ ++l ++l ri i+l+
  gi|119719290|ref|YP_919785.1| 234 ANNYHQIYISLLSEEKSLREELERISILLK 263
                                    234577899999*************99986 PP

>> Leu_zip  Leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7  12.9     0.001      0.13     149     275 ..       5     128 ..       1     129 [. 0.80
   2 ?    5.6   4.8     0.075       9.9     194     242 ..     161     212 ..     138     222 .. 0.58
   3 ?    1.8   4.0       1.1   1.4e+02     133     188 ..     218     273 ..     213     291 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.001
                        Leu_zip 149 lkelEkqatsaleeksklekalkelqkelgekkdekenskeiskleeklaelkldlektleektasaksleedlastkhe 228
                                    ++++E+  ++++e ++kl++  +++q++ +++++++ + k+is   ++l e  + l ++  + ++++k+l e + + ++e
  gi|119719290|ref|YP_919785.1|   5 TESIESLRQQLIEYRQKLQEISAKIQEARSKRDSANGEVKRISAEIRSLREQYQALRQQIAAVAEQKKTLYEKISKLREE 84 
                                    5678888888899999988777777666665555555666666666666666666777888889999************* PP

                        Leu_zip 229 lLkvqeqLelaekeLekkfqqtaayknlkemltkkneqikelRkrLs 275
                                       + eqL+  + eL++     a+y+nl+  l +k     elR+r++
  gi|119719290|ref|YP_919785.1|  85 KKGILEQLNKLRDELKRL---NAEYNNLRGFLGSKRYDEDELRNRIE 128
                                    ***************764...589********************986 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.075
                        Leu_zip 194 eeklaelkldlek...tleektasaksleedlastkhelLkvqeqLelaeke 242
                                     ++l+e+++++e+   +  e +++ ++++e+l +   e+Lkv+eq++  +++
  gi|119719290|ref|YP_919785.1| 161 VKHLNEVRAKIEEiraQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQ 212
                                    3334444444433222444556777788888999999999999986654432 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 1.1
                        Leu_zip 133 keierLkeenekLkerlkelEkqatsaleeksklekalkelqkelgekkdekensk 188
                                    k + +Lk+e ++++e  +++ +  +s+l+e++ l+++l+++   l++k+ +++ ++
  gi|119719290|ref|YP_919785.1| 218 KRLVELKQERDRIRETANNYHQIYISLLSEEKSLREELERISILLKAKELSQHLEE 273
                                    567789**********************************9988888887766433 PP

>> APG17  Autophagy protein Apg17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   3.3     0.017       2.3     245     320 ..      58     130 ..      40     138 .. 0.53
   2 ?    5.8  13.6     0.047       6.2     241     360 ..     144     266 ..     140     290 .. 0.57

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.017
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHHHHHH...HHHHHHHHHHHH CS
                          APG17 245 kelqerleemekakkllsekkeeiekllsalkkaleeleevgkklpeylaifkaeeeflerweeekekieekleel 320
                                    + l+++++++ ++kk+l ek +++++  + + ++l++l++   +l++  a  ++ + fl  +  +++++ +++e+l
  gi|119719290|ref|YP_919785.1|  58 QALRQQIAAVAEQKKTLYEKISKLREEKKGILEQLNKLRD---ELKRLNAEYNNLRGFLGSKRYDEDELRNRIEQL 130
                                    3445555555555555555555555555555555555554...333333333355555555555555555555554 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.047
                                    HHHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.....HHHHHHHHHHHHHHHHHH...HHHHHHHH CS
                          APG17 241 edVvkelqerleem...ekakkllsekkeeiekllsalkkaleeleev.gkklpeylaifkaeeeflerweeekekieek 316
                                    e+V+     +le++    k  +++++k eei++++ +lkk ++ ++e  ++ ++eyl++ ++ +++ ++ +e  +++ e 
  gi|119719290|ref|YP_919785.1| 144 EKVLVNKIRSLESIyvnVKHLNEVRAKIEEIRAQIPELKKKVQAINEElKTVVSEYLKVKEQMQALKQQRDELVKRLVEL 223
                                    55544444445555333333334444444444444444444444443334567777774445555555546666667777 PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHH CS
                          APG17 317 leeleeLrefYegFlsaYdklllEveR.Rraveekmekilkkare 360
                                     +e +  re  +++ ++Y +ll E +  R++ e    +il ka+e
  gi|119719290|ref|YP_919785.1| 224 KQERDRIRETANNYHQIYISLLSEEKSlREELERI--SILLKAKE 266
                                    77888899999999999999977754314444433..55555555 PP

>> DUF2937  Protein of unknown function (DUF2937)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   4.3      0.48        63      38     105 ..      11      78 ..       7      91 .. 0.58
   2 ?   11.1   2.0    0.0018      0.24      31     118 ..     167     253 ..     163     256 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.48
                        DUF2937  38 lkrqlagfqatAkrffkgdlealiahyrqsedpvvradaesiqalverlerLeqelqalqqa..sllerl 105
                                    l++ql +++++ ++     ++++ +  r s+   v++  ++i++l e++++L+q+ +a +++  +l+e++
  gi|119719290|ref|YP_919785.1|  11 LRQQLIEYRQKLQEISA-KIQEA-RSKRDSANGEVKRISAEIRSLREQYQALRQQIAAVAEQkkTLYEKI 78 
                                    55555555555555555.55554.3334555556777777777777777777777777765433455544 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0018
                        DUF2937  31 LeghldelkrqlagfqatAkrffkgdlealiahyrqsedpvvradaesiqalverlerLeqelqalqqa.sllerlvvll 109
                                    + ++++e + q+ +++++ ++ ++ +l+ +++ y++ ++  ++a  ++ ++lv+rl +L+qe +++++  + ++++++ l
  gi|119719290|ref|YP_919785.1| 167 VRAKIEEIRAQIPELKKKVQAINE-ELKTVVSEYLKVKE-QMQALKQQRDELVKRLVELKQERDRIRETaNNYHQIYISL 244
                                    7899********************.*************8.789999*****************99987558888888777 PP

                        DUF2937 110 raadaeile 118
                                     + +++++e
  gi|119719290|ref|YP_919785.1| 245 LSEEKSLRE 253
                                    776666665 PP

>> DASH_Dam1  DASH complex subunit Dam1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.2       1.1   1.5e+02      19      33 ..      89     103 ..      60     105 .. 0.71
   2 ?    4.1   0.1       0.3        40       2      22 ..      89     109 ..      88     112 .. 0.75
   3 ?    1.6   0.0       1.9   2.5e+02      11      31 ..     153     173 ..     149     177 .. 0.81
   4 ?    0.5   0.0       4.2   5.6e+02       4      24 ..     170     190 ..     167     199 .. 0.72
   5 ?    0.7   0.1       3.4   4.5e+02       3      30 ..     204     231 ..     202     237 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 1.1
                      DASH_Dam1  19 ledLqqihesLsdfN 33 
                                    le+L++++++L+++N
  gi|119719290|ref|YP_919785.1|  89 LEQLNKLRDELKRLN 103
                                    456666666666666 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.3
                      DASH_Dam1   2 epafaeLaDsletLdknledL 22 
                                     +++++L D+l+ L++ +++L
  gi|119719290|ref|YP_919785.1|  89 LEQLNKLRDELKRLNAEYNNL 109
                                    567888888888888888777 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 1.9
                      DASH_Dam1  11 sletLdknledLqqihesLsd 31 
                                    sle +  n+++L++++ ++++
  gi|119719290|ref|YP_919785.1| 153 SLESIYVNVKHLNEVRAKIEE 173
                                    567778899999999988875 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 4.2
                      DASH_Dam1   4 afaeLaDsletLdknledLqq 24 
                                    +++e+  ++ +L+k+++ +++
  gi|119719290|ref|YP_919785.1| 170 KIEEIRAQIPELKKKVQAINE 190
                                    677888888888888877764 PP

  == domain 5  score: 0.7 bits;  conditional E-value: 3.4
                      DASH_Dam1   3 pafaeLaDsletLdknledLqqihesLs 30 
                                    ++++ L+ + ++L k+l +L+q ++++ 
  gi|119719290|ref|YP_919785.1| 204 EQMQALKQQRDELVKRLVELKQERDRIR 231
                                    7888888888999998888888777665 PP

>> AATF-Che1  Apoptosis antagonizing transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   1.6     0.035       4.6      67     132 ..       6      64 ..       2      66 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.035
                      AATF-Che1  67 eslleLreelleqne.ikklaeskeeeekkkskrkrkkkkkeetsleelwkeleklekalkpfrnat 132
                                    es+ +Lr++l+e  + ++        e ++k ++ r k+++++ +++ ++ e+++l +++++ r+++
  gi|119719290|ref|YP_919785.1|   6 ESIESLRQQLIEYRQkLQ--------EISAKIQEARSKRDSANGEVKRISAEIRSLREQYQALRQQI 64 
                                    456666666644444223........33444455555567778899999999999999999999875 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3  10.3      0.24        32      14      76 ..      42     106 ..       2     123 .. 0.61
   2 ?    1.7  10.3       3.2   4.2e+02      12      69 ..     164     220 ..      72     223 .. 0.74
   3 ?    3.7   9.7      0.76     1e+02       5      72 ..     171     240 ..     170     306 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.24
                        DUF2203  14 llkelleelralrkeleeleeeleeakaeaekse..aaeleaeleeleaeieelveeieelGvev 76 
                                    ++k++ +e+r+lr++++ l++++++  +++++     ++l++e + + +++++l +e+++l +e+
  gi|119719290|ref|YP_919785.1|  42 EVKRISAEIRSLREQYQALRQQIAAVAEQKKTLYekISKLREEKKGILEQLNKLRDELKRLNAEY 106
                                    34555555555555555555555554444322222355555555556666666666666655555 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 3.2
                        DUF2203  12 Lpllkelleelralrkeleeleeeleeakaeaekse..aaeleaeleeleaeieelveei 69 
                                    L +++ ++ee+ra+  el++++++++e+ ++       + + ++++++l+++ +elv+++
  gi|119719290|ref|YP_919785.1| 164 LNEVRAKIEEIRAQIPELKKKVQAINEELKTV---VseYLKVKEQMQALKQQRDELVKRL 220
                                    44444444444433333333333333333332...1337777777777777777777766 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.76
                        DUF2203   5 leeAnalLpllkelleelr....alrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieel 72 
                                    +ee +a +p+lk+++++++    ++ +e+ +++e++++ k++++  e  ++  el++ +++i+e+ ++ +++
  gi|119719290|ref|YP_919785.1| 171 IEEIRAQIPELKKKVQAINeelkTVVSEYLKVKEQMQALKQQRD--ELVKRLVELKQERDRIRETANNYHQI 240
                                    57778888888888877773333444444444555555555533..25555556666666666665555544 PP

>> Phage_GPO  Phage capsid scaffolding protein (GPO) serine peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   5.9     0.064       8.4     176     256 ..      24     107 ..       1     127 [. 0.43
   2 ?    7.7   4.2     0.018       2.4     192     253 ..     167     235 ..     127     249 .. 0.61

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.064
                      Phage_GPO 176 slferikallskkkksddarfadveeavelvAeevkelsekveall....aleaelaalkkeveklkaeleaLkekLskt 251
                                    ++ ++i++  sk + s + +++ ++  +  + e+ ++l+++++a++    +l +++++l++e +   ++l++L+++L++ 
  gi|119719290|ref|YP_919785.1|  24 EISAKIQEARSK-RDSANGEVKRISAEIRSLREQYQALRQQIAAVAeqkkTLYEKISKLREEKKGILEQLNKLRDELKRL 102
                                    333333333222.2222333333444444444444444444443331111222223333333333333555555555544 PP

                      Phage_GPO 252 dakek 256
                                    +a+++
  gi|119719290|ref|YP_919785.1| 103 NAEYN 107
                                    44433 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.018
                      Phage_GPO 192 ddarfadveeavelvAeevkelsekveall....aleaelaalkkeveklkaeleaLkek...Lsktda 253
                                      a++ +++  + ++ ++v++++e++++++    + +++++alk++ ++l ++l +Lk++   + +t +
  gi|119719290|ref|YP_919785.1| 167 VRAKIEEIRAQIPELKKKVQAINEELKTVVseylKVKEQMQALKQQRDELVKRLVELKQErdrIRETAN 235
                                    235555666666666666655555555443444477777777777777777777777776333444444 PP

>> Jnk-SapK_ap_N  JNK_SAPK-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1  14.9     0.045       5.9      57     148 ..       6     100 ..       1     107 [. 0.57
   2 ?    7.8  14.4     0.026       3.5      43     140 ..      34     134 ..      30     139 .. 0.74
   3 ?    9.6  14.6    0.0073      0.97      51     151 ..     119     224 ..     114     228 .. 0.84
   4 ?    6.4  20.5     0.071       9.4      31     155 ..     150     290 ..     140     291 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.045
                  Jnk-SapK_ap_N  57 eeleqLeteyerekelrkrae...eeleeiedqweeerkelqekveqleeenrelelkaknaadqlsrleekeaelkkey 133
                                    e +e+L++++ + +++ ++     +e   + d+ ++e k +++++ +l+e+ + l +++ ++a+q ++l ek ++l++e+
  gi|119719290|ref|YP_919785.1|   6 ESIESLRQQLIEYRQKLQEISakiQEARSKRDSANGEVKRISAEIRSLREQYQALRQQIAAVAEQKKTLYEKISKLREEK 85 
                                    44555555555444443333333355555666666677777777777777777777666666666666666666666666 PP

                  Jnk-SapK_ap_N 134 sklheretellkklk 148
                                    +   e+ ++l  +lk
  gi|119719290|ref|YP_919785.1|  86 KGILEQLNKLRDELK 100
                                    666666666555555 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.026
                  Jnk-SapK_ap_N  43 srneeeeaeleelreeleqLeteyerekelrkrae...eeleeiedqweeerkelqekveqleeenrelelkaknaadql 119
                                    s++++ + e+++ ++e+ +L+++y+  +++  +     ++l e+  +++ee+k + e++++l++e ++l++  +n+   l
  gi|119719290|ref|YP_919785.1|  34 SKRDSANGEVKRISAEIRSLREQYQALRQQIAAVAeqkKTLYEKISKLREEKKGILEQLNKLRDELKRLNAEYNNLRGFL 113
                                    566777888888888888888888876665443222236777777899**********************8888888777 PP

                  Jnk-SapK_ap_N 120 srleekeaelkkeysklhere 140
                                     +    e+el+++ ++l+ ++
  gi|119719290|ref|YP_919785.1| 114 GSKRYDEDELRNRIEQLEWQY 134
                                    777777777776666665555 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.0073
                  Jnk-SapK_ap_N  51 eleelreeleqLeteyerekelrkrae...eeleeiedqwe..eerkelqekveqleeenrelelkaknaadqlsrleek 125
                                    +++elr+ +eqLe +y+  +   + ++   +++  +e  +   +  +e+++k+e+ + ++ el++k+++++++l+++ ++
  gi|119719290|ref|YP_919785.1| 119 DEDELRNRIEQLEWQYQTMTLPPEVEKvlvNKIRSLESIYVnvKHLNEVRAKIEEIRAQIPELKKKVQAINEELKTVVSE 198
                                    6799*************99977777668885555555544311345799******************************* PP

                  Jnk-SapK_ap_N 126 eaelkkeysklheretellkklkelv 151
                                      ++k++ ++l+++  el+k+l+el 
  gi|119719290|ref|YP_919785.1| 199 YLKVKEQMQALKQQRDELVKRLVELK 224
                                    ***********************975 PP

  == domain 4  score: 6.4 bits;  conditional E-value: 0.071
                  Jnk-SapK_ap_N  31 vVkvLElLeslasrneeeeaeleelreeleqLeteyerekelrkraeeeleeiedqw...eeerkelqekveqleeenre 107
                                     ++ LE++   +++ +e  a++ee r+++ +L+++ +  +e+ k    e++++ +q+   +++r el +++ +l++e+++
  gi|119719290|ref|YP_919785.1| 150 KIRSLESIYVNVKHLNEVRAKIEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMqalKQQRDELVKRLVELKQERDR 229
                                    4788999999999999************************999999999999998862225788899999999999**** PP

                  Jnk-SapK_ap_N 108 lelkaknaadqlsrleekeaelkkeysklhe.............retellkklkelverqr 155
                                    +   a+n+++   +l ++e++l++e ++ +              r+++l  k +e  er r
  gi|119719290|ref|YP_919785.1| 230 IRETANNYHQIYISLLSEEKSLREELERISIllkakelsqhleeRKRQLYGKAMEAYERFR 290
                                    *99*******************999999887887777888888888888888888877766 PP

>> DHR10  Designed helical repeat protein 10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7  12.4     0.026       3.5      36     100 ..      20      84 ..       2      88 .. 0.77
   2 ?    6.6   1.1     0.057       7.6      42      90 ..      89     137 ..      85     139 .. 0.75
   3 ?   10.0   8.2     0.005      0.66      31     102 ..     143     214 ..     142     215 .. 0.89
   4 ?    9.2   8.0    0.0093       1.2      31      80 ..     181     230 ..     178     241 .. 0.88
   5 ?   -0.4   1.9       8.4   1.1e+03      72      87 ..     263     278 ..     243     293 .. 0.48

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.026
                          DHR10  36 rsciklleeieaelakleeakkklkelrdaleekeielrelerkeerlqrqlenaeeklerlreq 100
                                    +++ ++  +i++   k ++a+ ++k+ ++++ +++++ + l ++++ +  q +   ek+++lre+
  gi|119719290|ref|YP_919785.1|  20 QKLQEISAKIQEARSKRDSANGEVKRISAEIRSLREQYQALRQQIAAVAEQKKTLYEKISKLREE 84 
                                    46667777778888888999999999999999999999999999999999999999999999986 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.057
                          DHR10  42 leeieaelakleeakkklkelrdaleekeielrelerkeerlqrqlena 90 
                                    le++++   +l+  +++ ++lr  l +k+ +  el +++e+l+ q + +
  gi|119719290|ref|YP_919785.1|  89 LEQLNKLRDELKRLNAEYNNLRGFLGSKRYDEDELRNRIEQLEWQYQTM 137
                                    444444445555556677889999999***************9998875 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.005
                          DHR10  31 vekdlrsciklleeieaelakleeakkklkelrdaleekeielrelerkeerlqrqlenaeeklerlreqae 102
                                    vek l + i+ le i ++++ l+e+++k++e r+++ e++++++ ++ + + +     + +e+++ l++q++
  gi|119719290|ref|YP_919785.1| 143 VEKVLVNKIRSLESIYVNVKHLNEVRAKIEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQRD 214
                                    677777889999999999999999999999999999999999999999999999999999999999999987 PP

  == domain 4  score: 9.2 bits;  conditional E-value: 0.0093
                          DHR10  31 vekdlrsciklleeieaelakleeakkklkelrdaleekeielrelerke 80 
                                    ++k ++++ + l+++ +e  k++e+++ lk++rd+l ++  el++   ++
  gi|119719290|ref|YP_919785.1| 181 LKKKVQAINEELKTVVSEYLKVKEQMQALKQQRDELVKRLVELKQERDRI 230
                                    7899**********************************999888765555 PP

  == domain 5  score: -0.4 bits;  conditional E-value: 8.4
                          DHR10  72 elrelerkeerlqrql 87 
                                    +++el+++ e  +rql
  gi|119719290|ref|YP_919785.1| 263 KAKELSQHLEERKRQL 278
                                    2344444444444444 PP

>> DUF4618  Domain of unknown function (DUF4618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   4.4      0.02       2.7     172     230 ..       6      64 ..       1      71 [. 0.86
   2 ?    7.6   1.6     0.017       2.3     187     227 ..      70     110 ..      63     114 .. 0.76
   3 ?    9.1   2.7    0.0059      0.78     180     224 ..     146     193 ..     120     199 .. 0.71
   4 ?    1.9   5.4      0.94   1.2e+02     178     231 ..     189     241 ..     186     249 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.02
                        DUF4618 172 ktlkatqeaLlqktlenqvlkkeiekfrefieeleeeipeLkaeveqLqaqaeeprevi 230
                                    +++++ ++ L +  ++ q+++ +i++ r + +  + e++++ ae+  L++q +  r++i
  gi|119719290|ref|YP_919785.1|   6 ESIESLRQQLIEYRQKLQEISAKIQEARSKRDSANGEVKRISAEIRSLREQYQALRQQI 64 
                                    56677788888999999999999999999999999999999999999999999999988 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.017
                        DUF4618 187 enqvlkkeiekfrefieeleeeipeLkaeveqLqaqaeepr 227
                                    ++++l ++i k re+ + + e++++L+ e+++L+a+ ++ r
  gi|119719290|ref|YP_919785.1|  70 QKKTLYEKISKLREEKKGILEQLNKLRDELKRLNAEYNNLR 110
                                    56677788888888888888888888888888888887776 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0059
                        DUF4618 180 aLlqktlenqvlk...keiekfrefieeleeeipeLkaeveqLqaqae 224
                                    +L++k+++ +++    k+++++r +iee++ +ipeLk++v++++++ +
  gi|119719290|ref|YP_919785.1| 146 VLVNKIRSLESIYvnvKHLNEVRAKIEEIRAQIPELKKKVQAINEELK 193
                                    455555444443222388889999999999999999999999887765 PP

  == domain 4  score: 1.9 bits;  conditional E-value: 0.94
                        DUF4618 178 qeaLlqktlenqvlkkeiekfrefieeleeeipeLkaeveqLqaqaeepreviF 231
                                    +e L+  + e  ++k++++  +++ +el +++ eLk+e +++++ a++   +i+
  gi|119719290|ref|YP_919785.1| 189 NEELKTVVSEYLKVKEQMQALKQQRDELVKRLVELKQERDRIRETANNYH-QIY 241
                                    56666666777778888888888888888888888888888887776544.455 PP

>> Mer2  Mer2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   7.5       1.6   2.1e+02      47     144 ..       9     100 ..       4     132 .. 0.54
   2 ?   14.6   8.7   0.00016     0.021      55     145 ..     142     235 ..     122     252 .. 0.81
   3 ?   -0.3   0.2         6     8e+02      36      62 ..     254     280 ..     251     290 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 1.6
                           Mer2  47 skLinvlkenskeLlkvisklnellidlkeeesdnskekeikdlikdLsvkienqlskvskavldklkvkkhksntdtks 126
                                    ++L + l e  ++L ++++k++e     k  +s n + k i   i+ L  + +   +++  +  +k +  ++ s++ +++
  gi|119719290|ref|YP_919785.1|   9 ESLRQQLIEYRQKLQEISAKIQEAR--SK-RDSANGEVKRISAEIRSLREQYQALRQQIAAVAEQKKTLYEKISKLREEK 85 
                                    5666666666777777777776666..23.35666666777777777766655544444444444444333333332222 PP

                           Mer2 127 nLtellekkeakileeid 144
                                       + + ++ +k+++e++
  gi|119719290|ref|YP_919785.1|  86 ---KGILEQLNKLRDELK 100
                                    ...222233333333333 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 0.00016
                           Mer2  55 enskeLlkvisklnellidlkeeesdnskekeikdlikdLsvkienqlskvskavldklkvkkhksntdt.ksnLte... 130
                                    e  k L+++i +l+ + +++k+ +  ++k++ei  +i +L+ k++   ++++++v++ lkvk++ + +++ + +L++   
  gi|119719290|ref|YP_919785.1| 142 EVEKVLVNKIRSLESIYVNVKHLNEVRAKIEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQqRDELVKrlv 221
                                    56799********************************************************9999987651568998322 PP

                           Mer2 131 llekkeakileeidk 145
                                    +l+++  +i+ e  +
  gi|119719290|ref|YP_919785.1| 222 ELKQERDRIR-ETAN 235
                                    2333333333.3334 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 6
                           Mer2  36 ELEsvdLrEksskLinvlkenskeLlk 62 
                                    ELE + +  k+++L++ l+e  ++L  
  gi|119719290|ref|YP_919785.1| 254 ELERISILLKAKELSQHLEERKRQLYG 280
                                    888888888999999999999888864 PP

>> HBM  Helical bimodular sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   8.9     0.038         5      71     143 ..       6      82 ..       1      86 [. 0.69
   2 ?    3.3   3.6      0.35        47      44     121 ..      58     133 ..      55     157 .. 0.81
   3 ?    9.1   1.3    0.0059      0.78      69     121 ..     160     212 ..     145     213 .. 0.87
   4 ?    2.8   8.3       0.5        66      42     150 ..     170     275 ..     164     290 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.038
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCS-S-H....HHHHHHHHHHHHHH CS
                            HBM  71 rlLqeqlalvqeyrksfnelraayesrnaaRqeldsaaeraleaideleaevlqtpead....serlaqlqaiaelk 143
                                      +++ ++++ eyr++++e+ a +++++  R + + + +r+++ i +l+++  ++ ++     +++ + +++i++l+
  gi|119719290|ref|YP_919785.1|   6 ESIESLRQQLIEYRQKLQEISAKIQEARSKRDSANGEVKRISAEIRSLREQYQALRQQIaavaEQKKTLYEKISKLR 82 
                                    56777788888888888888888888888888888888888888888888876655443444455555555555555 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.35
                                    HHHHHHHHHHHHHHHHHHHH--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            HBM  44 aavqkkldelkaqlqklkakfkspenvrlLqeqlalvqeyrksfnelraayesrnaaRqeldsaaeraleaideleae 121
                                    +a+ ++++ +++q ++l++k ++  + +  +++l++++++r++++ l+a y++ +    + +  ++++ ++i++le +
  gi|119719290|ref|YP_919785.1|  58 QALRQQIAAVAEQKKTLYEKISKLREEK--KGILEQLNKLRDELKRLNAEYNNLRGFLGSKRYDEDELRNRIEQLEWQ 133
                                    5588999999999999999998877666..589999999999999999999999999999999999999999999855 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0059
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            HBM  69 nvrlLqeqlalvqeyrksfnelraayesrnaaRqeldsaaeraleaideleae 121
                                    nv++L+e +a+++e+r +  el++ +++ n+  + ++s+  +++e +++l+++
  gi|119719290|ref|YP_919785.1| 160 NVKHLNEVRAKIEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQ 212
                                    89**************************9998888888888888888887765 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.5
                                    HHHHHHHHHHHHHHHHHHHHHH--SHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            HBM  42 taaavqkkldelkaqlqklkakfkspen.vrlLqeqlalvqeyrksfnelraayesrnaaRqeldsaaeraleaidelea 120
                                    + +++ +++ elk+++q++++++k+  +   +++eq+++   ++++ +el +   + ++ R +++++a++  +   +l +
  gi|119719290|ref|YP_919785.1| 170 KIEEIRAQIPELKKKVQAINEELKTVVSeYLKVKEQMQA---LKQQRDELVKRLVELKQERDRIRETANNYHQIYISLLS 246
                                    445577777777777777777777654314445555554...55555666777777777888888888888887666555 PP

                                    HHHCS-S-HHHHHHHHHHHHHHHHHHHHHH CS
                            HBM 121 evlqtpeadserlaqlqaiaelkrqvqlar 150
                                    e   + e + er+ +l +++el++++++ +
  gi|119719290|ref|YP_919785.1| 247 EEKSLRE-ELERISILLKAKELSQHLEERK 275
                                    5544333.4688888888888888887655 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   4.8     0.088        12      13      73 ..       7      73 ..       3      91 .. 0.63
   2 ?    5.6   1.5      0.18        24      10      58 ..      88     135 ..      72     139 .. 0.64
   3 ?    6.8   6.0     0.074       9.8      14      83 ..     151     218 ..     141     240 .. 0.44
   4 ?    0.6   2.8       6.6   8.7e+02      11      64 ..     207     234 ..     199     279 .. 0.44

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.088
                   Syntaxin-6_N 13 slnkaeslyrrw.erlledtss.s....tseeldetrteLrkalrsiewdledLeetvriveknpsk 73
                                   s++++++ + ++ ++l+e + + +    ++++ +   + + +++rs++++ + L++ +++v ++++ 
  gi|119719290|ref|YP_919785.1|  7 SIESLRQQLIEYrQKLQEISAKiQearsKRDSANGEVKRISAEIRSLREQYQALRQQIAAVAEQKKT 73
                                   45555555555522333333333133346777777888899999**************988776544 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.18
                   Syntaxin-6_N  10 Vqkslnkaeslyrrwe.rlledtssstseeldetrteLrkalrsiewdle 58 
                                    + ++lnk++  ++r + +  ++     s+ +d  ++eLr+ ++++ew+ +
  gi|119719290|ref|YP_919785.1|  88 ILEQLNKLRDELKRLNaEYNNLRGFLGSKRYD--EDELRNRIEQLEWQYQ 135
                                    55666666666666652333332222445554..4899999999999976 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.074
                   Syntaxin-6_N  14 lnkaeslyrrwerlledtssstseeldetrteLrkalrsiewdledLeetvriveknpskfkidekelsr 83 
                                    ++++es+y + ++l e+  +   ee++ +  eL+k+++ i+++l+        v+++ +  k + +el +
  gi|119719290|ref|YP_919785.1| 151 IRSLESIYVNVKHLNEVRAK--IEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQRDELVK 218
                                    44455555555444444332..444444444444444444444444333333333333333333333333 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 6.6
                   Syntaxin-6_N  11 qkslnkaeslyrrwerlledtssstseeldetrteLrkalrsiewdledLeetv 64 
                                    q   ++  +l++r                            +++++ + ++et 
  gi|119719290|ref|YP_919785.1| 207 QALKQQRDELVKRL--------------------------VELKQERDRIRETA 234
                                    33333333333333..........................33333333332222 PP

>> DUF4298  Domain of unknown function (DUF4298)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.4       1.1   1.4e+02       8      34 ..       5      31 ..       1      38 [. 0.71
   2 ?    2.9   3.2       0.8   1.1e+02       4      54 ..      22      72 ..      20      84 .. 0.54
   3 ?   11.1   0.5    0.0023       0.3       4      47 ..      78     121 ..      75     138 .. 0.85
   4 ?    3.9   2.9      0.38        51       9      53 ..     169     214 ..     151     226 .. 0.59
   5 ?    0.7   0.8       3.9   5.2e+02       9      34 ..     207     232 ..     196     261 .. 0.54

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 1.1
                                   HHHHHHHHHHHHHHHHHHHHTHHHHHH CS
                        DUF4298  8 ldeisallqqLeealeqwkklqkklak 34
                                   +++i++l qqL e  ++++++++k+++
  gi|119719290|ref|YP_919785.1|  5 TESIESLRQQLIEYRQKLQEISAKIQE 31
                                   567777777777777777777777765 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.8
                                   HHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHTSHHHHHHHTS--SS CS
                        DUF4298  4 mekildeisallqqLeealeqwkklqkklakLdeYYqseqwredleasnkg 54
                                   +++i ++i+++  + + a  + k+++++++ L+e Yq   ++  + a +k+
  gi|119719290|ref|YP_919785.1| 22 LQEISAKIQEARSKRDSANGEVKRISAEIRSLREQYQALRQQIAAVAEQKK 72
                                   666666666666666666666666666666666666655444333333333 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.0023
                                    HHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHTSHHHHHH CS
                        DUF4298   4 mekildeisallqqLeealeqwkklqkklakLdeYYqseqwred 47 
                                    + k+ +e + +l+qL+++ +++k+l +++++L+ + +s+ + ed
  gi|119719290|ref|YP_919785.1|  78 ISKLREEKKGILEQLNKLRDELKRLNAEYNNLRGFLGSKRYDED 121
                                    66777888889****************************99877 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.38
                                    HHHHHHHHHHHHHHHHHHHTHHHHHH.HHHHHTSHHHHHHHTS--S CS
                        DUF4298   9 deisallqqLeealeqwkklqkklak.LdeYYqseqwredleasnk 53 
                                    ++i+++ +q+ e+ ++ +++ ++l++ ++eY + +++++ l++ ++
  gi|119719290|ref|YP_919785.1| 169 AKIEEIRAQIPELKKKVQAINEELKTvVSEYLKVKEQMQALKQQRD 214
                                    3344444444444444444444443314677777777777776655 PP

  == domain 5  score: 0.7 bits;  conditional E-value: 3.9
                                    HHHHHHHHHHHHHHHHHHHTHHHHHH CS
                        DUF4298   9 deisallqqLeealeqwkklqkklak 34 
                                    + +++  ++L + l ++k+  + +++
  gi|119719290|ref|YP_919785.1| 207 QALKQQRDELVKRLVELKQERDRIRE 232
                                    22223333333333344444444444 PP

>> THOC7  Tho complex subunit 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   9.6     0.025       3.4      64     122 ..       9      68 ..       5      75 .. 0.87
   2 ?    3.9   8.9      0.45        59      63     122 ..      57     117 ..      49     139 .. 0.69
   3 ?    5.9   0.8      0.11        15      69      99 ..     163     193 ..     152     201 .. 0.57
   4 ?    6.5  11.7     0.073       9.7      48     110 ..     170     232 ..     166     241 .. 0.84
   5 ?    0.4   0.8       5.6   7.4e+02      12      40 ..     247     277 ..     236     290 .. 0.51

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.025
                          THOC7  64 kanerereryeaekeeieseieavreeieelkaqLeeara.tranrkeydelaekItsnp 122
                                    ++ +++  +y ++ +ei ++i+++r++ ++ + + ++  a +r  r++y +l ++I +  
  gi|119719290|ref|YP_919785.1|   9 ESLRQQLIEYRQKLQEISAKIQEARSKRDSANGEVKRISAeIRSLREQYQALRQQIAAVA 68 
                                    67789999*****************************87527999**********98765 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.45
                          THOC7  63 akanerereryeaekeeieseieavreeieelkaqLeearatran.rkeydelaekItsnp 122
                                     +a +++++ ++++k+++ ++i+++ree +   +qL + r ++++   ey++l   + s++
  gi|119719290|ref|YP_919785.1|  57 YQALRQQIAAVAEQKKTLYEKISKLREEKKGILEQLNKLRDELKRlNAEYNNLRGFLGSKR 117
                                    4566666666666666666888888888888888888888776652567777766555555 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.11
                          THOC7  69 ereryeaekeeieseieavreeieelkaqLe 99 
                                      +++ a+ eei ++i++++++ ++ +++L+
  gi|119719290|ref|YP_919785.1| 163 HLNEVRAKIEEIRAQIPELKKKVQAINEELK 193
                                    4444444555555555555555555555444 PP

  == domain 4  score: 6.5 bits;  conditional E-value: 0.073
                          THOC7  48 dfaafelsierlqllakanerereryeaekeeieseieavreeieelkaqLeearatranrke 110
                                    ++++ + +i  l+   +a  +e + +  e+ +++++++a++++ +el ++L e +++r++ +e
  gi|119719290|ref|YP_919785.1| 170 KIEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQRDELVKRLVELKQERDRIRE 232
                                    6667777777777778888999999999999****************************9887 PP

  == domain 5  score: 0.4 bits;  conditional E-value: 5.6
                          THOC7  12 eerplkrltkrllklltsla..esteeeleq 40 
                                    ee+ l+  ++r++ ll++++  ++ ee+ +q
  gi|119719290|ref|YP_919785.1| 247 EEKSLREELERISILLKAKElsQHLEERKRQ 277
                                    5555555555554444443333333333333 PP

>> GldM_N  GldM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.5       0.2        26      28      63 ..       8      43 ..       2      56 .. 0.68
   2 ?    5.8   7.9     0.096        13      25     140 ..      54     194 ..      43     198 .. 0.74
   3 ?    3.6   6.4      0.46        62      26     117 ..     183     275 ..     167     288 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.2
                         GldM_N 28 yasleakaeenpekakewlekAkevkkksdelynyi 63
                                   ++sl++++ e ++k +e+ +k +e++ k d+    +
  gi|119719290|ref|YP_919785.1|  8 IESLRQQLIEYRQKLQEISAKIQEARSKRDSANGEV 43
                                   567777777777777777777777777766655554 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.096
                         GldM_N  25 aalyasleakaeenpekakewlekAkevkkksdelynyiealKeeivkeaggk.....................dedvge 83 
                                     + y++l+++++   e+ k ++ek  +++++ + + +++++l++e+ +   ++                     ++ + +
  gi|119719290|ref|YP_919785.1|  54 REQYQALRQQIAAVAEQKKTLYEKISKLREEKKGILEQLNKLRDELKRLNAEYnnlrgflgskrydedelrnriEQLEWQ 133
                                    567999****************************************8876666788999999988766666655444778 PP

                         GldM_N  84 ikakdnldaaselmlaeg.ksgkGkeLkkkineyreellklvnd...lakdaklieselst 140
                                    ++++    +++++++++  + +  +   k +ne r ++ ++ ++   l+k+++ i++el+t
  gi|119719290|ref|YP_919785.1| 134 YQTMTLPPEVEKVLVNKIrSLESIYVNVKHLNEVRAKIEEIRAQipeLKKKVQAINEELKT 194
                                    8888888888888885554223333334566666666666655555566667778888887 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.46
                         GldM_N  26 alyasleakaeenpekakewlekAkevkkksdelynyiealKeeivkeaggkded.....vgeikakdnldaaselmlae 100
                                    + ++++++++++   ++ +++e+ +++k++ del++ + +lK+e  +  ++ ++          ++k+  ++++++ +  
  gi|119719290|ref|YP_919785.1| 183 KKVQAINEELKTVVSEYLKVKEQMQALKQQRDELVKRLVELKQERDRIRETANNYhqiyiSLLSEEKSLREELERISI-- 260
                                    4566777777777777888999999***********999999997666666655522232122222222333333333.. PP

                         GldM_N 101 gksgkGkeLkkkineyr 117
                                        k+keL + ++e +
  gi|119719290|ref|YP_919785.1| 261 --LLKAKELSQHLEERK 275
                                    ..336666666666655 PP

>> Taxilin  Myosin-like coiled-coil protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5  23.0         1   1.3e+02      57     223 ..       7     190 ..       2     195 .. 0.58
   2 ?    7.0  12.8     0.022       2.9       4      87 ..     197     279 ..     194     288 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 1
                        Taxilin  57 qlqaelskaalaksKLekLcRelqkqnkklkeeskqrareeeekrkelaekfqakLkdiqaqieeksernek...lreen 133
                                    ++++ +++ +  ++KL++++  +q+++ k    + ++ r   e r +l e++qa  ++i a+ e+k++  ek   lree+
  gi|119719290|ref|YP_919785.1|   7 SIESLRQQLIEYRQKLQEISAKIQEARSKRDSANGEVKRISAEIR-SLREQYQALRQQIAAVAEQKKTLYEKiskLREEK 85 
                                    445555555666666666666666655555555555544444444.4566666666666666666655433322144444 PP

                        Taxilin 134 aelteKlkslieqyelreehf...............ekllktkelelqlaeaKlqqadallkeeqekkkrekeyllkeak 198
                                    + + e l++l ++ +  + ++               e  ++  +le q+++  l  + +++  ++ ++ +   + +k+++
  gi|119719290|ref|YP_919785.1|  86 KGILEQLNKLRDELKRLNAEYnnlrgflgskrydedELRNRIEQLEWQYQTMTLPPEVEKVLVNKIRSLESIYVNVKHLN 165
                                    44444444444444433333355555556555565577778888888888888877777777777777777777778888 PP

                        Taxilin 199 eltkkvkalketekelkeqlnlYae 223
                                    e ++k++++  +  elk++++  +e
  gi|119719290|ref|YP_919785.1| 166 EVRAKIEEIRAQIPELKKKVQAINE 190
                                    8888888888888888888876555 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.022
                        Taxilin   4 eqlkeslsklespeekleaLvkkyaelleerkrlqkqlkklkkkleqlqkekeqlqaelskaalaksKLekLcRelqkqn 83 
                                    +++ +  ++++  +++ ++Lvk++ el +er r  ++++ + + +  l  e+++l++el++ ++   K  +L++ l +++
  gi|119719290|ref|YP_919785.1| 197 SEYLKVKEQMQALKQQRDELVKRLVELKQERDRIRETANNYHQIYISLLSEEKSLREELER-ISILLKAKELSQHLEERK 275
                                    56667777888888899********************************************.677778889999999999 PP

                        Taxilin  84 kklk 87 
                                    ++l 
  gi|119719290|ref|YP_919785.1| 276 RQLY 279
                                    9886 PP

>> Med3  Mediator complex subunit 3 fungal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.2      0.35        47      69      93 ..       7      31 ..       2      34 .. 0.86
   2 ?    6.6   5.0     0.028       3.7       7      95 ..      20     110 ..      14     132 .. 0.69
   3 ?    5.0   1.3     0.088        12      65     110 ..     166     211 ..     145     237 .. 0.73
   4 ?    0.8   1.3       1.6   2.1e+02      20      81 ..     188     248 ..     177     274 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.35
                           Med3 69 kflsirdkvLdLnerlqelssdlee 93
                                      s+r+++++  ++lqe+s++++e
  gi|119719290|ref|YP_919785.1|  7 SIESLRQQLIEYRQKLQEISAKIQE 31
                                   56789****************9987 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.028
                           Med3   7 lkLdeLevklakeedskakdvvakrikeaedeiLPLrLqfnefiqimaslDeertkekskqekfls....irdkvLdLne 82 
                                     kL+e+  k+ +      +d    ++k+   ei  Lr q+  + q +a++ e++ +  +k  k       i +++ +L +
  gi|119719290|ref|YP_919785.1|  20 QKLQEISAKIQEARS--KRDSANGEVKRISAEIRSLREQYQALRQQIAAVAEQKKTLYEKISKLREekkgILEQLNKLRD 97 
                                    566777777655554..7999999**************************997666555555554411113344444555 PP

                           Med3  83 rlqelssdleeLq 95 
                                     l+ l +++++L+
  gi|119719290|ref|YP_919785.1|  98 ELKRLNAEYNNLR 110
                                    5555555555554 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.088
                           Med3  65 skqekflsirdkvLdLnerlqelssdleeLqPLfatveeysktakn 110
                                    + ++k   ir ++ +L++++q + ++l+++   +  v+e +++ k 
  gi|119719290|ref|YP_919785.1| 166 EVRAKIEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQ 211
                                    4567788899999999999999999998887777777777765554 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 1.6
                           Med3  20 edskakdvvakrikeaedeiLPLrLqfnefiqimaslDeertkekskqekflsirdkvLdLn 81 
                                    ++ + k vv++ + + ++++  L+ q +e+++ + +l +er +  +  + + +i  ++L  +
  gi|119719290|ref|YP_919785.1| 188 INEELKTVVSEYL-KVKEQMQALKQQRDELVKRLVELKQERDRIRETANNYHQIYISLLSEE 248
                                    4545666666555.566778888888888888888888888888888888888877777533 PP

>> Lebercilin  Ciliary protein causing Leber congenital amaurosis disease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1  27.3    0.0071      0.94      12     185 ..      14     191 ..       1     193 [. 0.74

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0071
                     Lebercilin  12 kikeLqnelaelqskleelrkEnklLkrlqkrqekaLskyedteaeLpqllarhneEvrvlrerlRksqekerelekklk 91 
                                    ++ e +++l+e+  k++e r      +   kr +++++ + ++ + L q +a   e  ++l e++ k++e+ +   ++l+
  gi|119719290|ref|YP_919785.1|  14 QLIEYRQKLQEISAKIQEARSKRDSANGEVKRISAEIRSLREQYQALRQQIAAVAEQKKTLYEKISKLREEKKGILEQLN 93 
                                    3345667777777777777777777888899************************************************* PP

                     Lebercilin  92 ekeaellrlkdklkklkkLsedknLaereeLqkkLeeleakleeke...ekikeLerkleleeksfr..rqlaaekkktk 166
                                    +  +el+rl+ ++++l+     k   + +eL +++e+le ++++ +   e  k L +k++ +e+ +   ++l+  + k+ 
  gi|119719290|ref|YP_919785.1|  94 KLRDELKRLNAEYNNLRGFLGSKRY-DEDELRNRIEQLEWQYQTMTlppEVEKVLVNKIRSLESIYVnvKHLNEVRAKIE 172
                                    ******************9988887.789**********99887652224445555555555554321134444555555 PP

                     Lebercilin 167 eaqeevkalqeeierlkqk 185
                                    e+++++ +l+++++ ++++
  gi|119719290|ref|YP_919785.1| 173 EIRAQIPELKKKVQAINEE 191
                                    5555555555555555554 PP

>> PspA_IM30  PspA/IM30 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4  19.5     0.088        12      26     132 ..       9     110 ..       1     148 [. 0.86
   2 ?    7.4   1.5     0.022       2.9     105     139 ..     162     196 ..     143     201 .. 0.83
   3 ?    2.7   8.6      0.59        78      35     107 ..     202     278 ..     200     291 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.088
                      PspA_IM30  26 kileqairdmqselakarqalaqviarqkqlerkleeqkeqakklekkAkaALtkgeeeLArealaeikslekqaealet 105
                                      l+q + + +++l++   ++ ++  ++ ++  ++++ ++++++l ++  +AL+++    ++++++++k+l +++ +l++
  gi|119719290|ref|YP_919785.1|   9 ESLRQQLIEYRQKLQEISAKIQEARSKRDSANGEVKRISAEIRSLREQY-QALRQQ----IAAVAEQKKTLYEKISKLRE 83 
                                    5577888888888888888888888888888888888888888888874.567665....789***************** PP

                      PspA_IM30 106 qlaqqrsaveqlrkqlealetkieelk 132
                                    + +   ++  +lr +l++l + ++ l+
  gi|119719290|ref|YP_919785.1|  84 EKKGILEQLNKLRDELKRLNAEYNNLR 110
                                    ********************9999876 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.022
                      PspA_IM30 105 tqlaqqrsaveqlrkqlealetkieelkakkellk 139
                                    + l+++r+ +e++r+q+ +l++k++++ ++ +++ 
  gi|119719290|ref|YP_919785.1| 162 KHLNEVRAKIEEIRAQIPELKKKVQAINEELKTVV 196
                                    5678999999**************99999999875 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.59
                      PspA_IM30  35 mqselakarqalaqviarqkqlerkleeqkeqakklekkAkaALtkg...eeeLAr.ealaeikslekqaealetql 107
                                    +++++++++q++ ++++r ++l+++ ++ +e a+++ +   ++L++    +eeL r  +l ++k+l +++e+ + ql
  gi|119719290|ref|YP_919785.1| 202 VKEQMQALKQQRDELVKRLVELKQERDRIRETANNYHQIYISLLSEEkslREELERiSILLKAKELSQHLEERKRQL 278
                                    5799*****************************************99999999988567888888888888776654 PP

>> DUF3037  Protein of unknown function (DUF3037)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   1.1      0.56        74      29      93 ..      24      89 ..      10     109 .. 0.53
   2 ?    3.0   0.1      0.99   1.3e+02      39     105 ..      76     150 ..      60     160 .. 0.70
   3 ?    6.8   1.0     0.064       8.6      30      89 ..     167     227 ..     146     259 .. 0.56

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.56
                        DUF3037 29 flkvrleldeaRlralfpeldlealeeelkaleeicegeka...agpiakldlaerfrwltaprstvi 93
                                   ++++++++  aR ++ + + +++ +++e+++l+e+ +  ++   a +++k++l e + +l +++++++
  gi|119719290|ref|YP_919785.1| 24 EISAKIQE--ARSKRDSANGEVKRISAEIRSLREQYQALRQqiaAVAEQKKTLYEKISKLREEKKGIL 89
                                   33333333..3333333333445555555555555433322110333444677777777777777766 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.99
                        DUF3037  39 aRlralfpel.....dlealeeelkaleeicegeka.agpiak..ldlaerfrwltaprstviqtsevhtglted 105
                                    +++++l +e      +l+ l++elk+l++  ++ +   g +    ++l++r+++l+ + +t+  + ev+ +l ++
  gi|119719290|ref|YP_919785.1|  76 EKISKLREEKkgileQLNKLRDELKRLNAEYNNLRGfLGSKRYdeDELRNRIEQLEWQYQTMTLPPEVEKVLVNK 150
                                    666667666667777889999999999999866665433332245999999999999988888887777777655 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.064
                        DUF3037  30 lkvrleldeaRlralfpeldlealeeelkaleeic...egekaagpiakldlaerfrwltapr 89 
                                    +++++e+ +a + +l +  +++a++eelk++       +++ +a ++++++l +r+ +l+++r
  gi|119719290|ref|YP_919785.1| 167 VRAKIEEIRAQIPELKK--KVQAINEELKTVVSEYlkvKEQMQALKQQRDELVKRLVELKQER 227
                                    22222222222222222..44555555554444432222222233333355555555555555 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   8.5     0.019       2.5     323     380 ..      14      70 ..       1      73 [. 0.51
   2 ?   10.9   6.1    0.0012      0.16     426     482 ..      53     109 ..      51     114 .. 0.94
   3 ?    1.4  21.8      0.85   1.1e+02     330     455 ..     169     262 ..     114     292 .. 0.48

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.019
                         DUF812 323 elkkkreeeleelqeqieeleskieeleeeikklessikqveeeleeekeeneeleke 380
                                    +l +   ++l+e++ +i+e++sk ++ + e+k+++++i+ + e++++++++ +  +++
  gi|119719290|ref|YP_919785.1|  14 QLIEY-RQKLQEISAKIQEARSKRDSANGEVKRISAEIRSLREQYQALRQQIAAVAEQ 70 
                                    22222.2355666666666666666666666666666666666666666665555555 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0012
                         DUF812 426 lieeyrelkesksekekeaerkleeikklrekmkevaeelrqkeellkqLvaelekl 482
                                    l e+y++l+++++  +++ +   e+i klre+ k + e+l +  ++lk+L+ae+++l
  gi|119719290|ref|YP_919785.1|  53 LREQYQALRQQIAAVAEQKKTLYEKISKLREEKKGILEQLNKLRDELKRLNAEYNNL 109
                                    5689**************************************************997 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.85
                         DUF812 330 eeleelqeqieeleskieeleeeikklessikqveeeleeekeeneelekevklkkktlellpdaeeniekLqalveasa 409
                                    +++ee++ qi el++k+++++ee+k++ s+  +                                +e++++L++  ++  
  gi|119719290|ref|YP_919785.1| 169 AKIEEIRAQIPELKKKVQAINEELKTVVSEYLK-------------------------------VKEQMQALKQQRDELV 217
                                    233344444444444444444444444444444...............................4444555555555555 PP

                         DUF812 410 qrlvelakqWekhRvplieeyrelkesksekekeaerkleeikklr 455
                                    +rlvel+++ ++ R++  ++y +   s  + ek+ ++ le+i  l 
  gi|119719290|ref|YP_919785.1| 218 KRLVELKQERDRIRET-ANNYHQIYISLLSEEKSLREELERISILL 262
                                    5555555444444443.24444444444444444444444444443 PP

>> COX5A  Cytochrome c oxidase subunit Va
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   1.9    0.0058      0.77      15     101 ..     112     200 ..      97     202 .. 0.80
   2 ?    4.3   0.3      0.29        39      67      94 ..     229     256 ..     203     265 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0058
                          COX5A  15 fferediDlfelrrglnnlf.ayDlvPe.pkvieaalracrrvndfalavRilEavkekvenkkqiYeyllqelkpvlee 92 
                                    f+ +++ D+ elr+ +++l  +y  +   p+v +  ++  r ++ + + v+ l  v++k+e+ +   + l ++++ + ee
  gi|119719290|ref|YP_919785.1| 112 FLGSKRYDEDELRNRIEQLEwQYQTMTLpPEVEKVLVNKIRSLESIYVNVKHLNEVRAKIEEIRAQIPELKKKVQAINEE 191
                                    5667777899999999988435666655055555566889**********************99999************* PP

                          COX5A  93 Lgistkeel 101
                                    L+  + e l
  gi|119719290|ref|YP_919785.1| 192 LKTVVSEYL 200
                                    *99888876 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.29
                          COX5A  67 avkekvenkkqiYeyllqelkpvleeLg 94 
                                     ++e ++n +qiY  ll+e k+++eeL+
  gi|119719290|ref|YP_919785.1| 229 RIRETANNYHQIYISLLSEEKSLREELE 256
                                    5899999*******************96 PP

>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   8.6     0.057       7.6      34     121 ..      17     101 ..       3     139 .. 0.56
   2 ?    6.1  12.5     0.017       2.3      22     127 ..     144     249 ..     133     291 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.057
                     V_ATPase_I  34 emerklrfleeeieklekavikeeeaeesleapeekeldeleeelekleeelkelnenleklkkelnelvelka.vleka 112
                                    e  +kl+ ++++i++++++    +++++ + ++ ++e+ +l e+ + l +++  + e++++l ++ ++l e+k+ +le+ 
  gi|119719290|ref|YP_919785.1|  17 EYRQKLQEISAKIQEARSK----RDSANGEVKRISAEIRSLREQYQALRQQIAAVAEQKKTLYEKISKLREEKKgILEQL 92 
                                    3444444444444442211....112345555666677777777777777777777777777777777765543255555 PP

                     V_ATPase_I 113 kefleeeee 121
                                    +++ +e ++
  gi|119719290|ref|YP_919785.1|  93 NKLRDELKR 101
                                    555543333 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.017
                     V_ATPase_I  22 qrkfvkevrrcdemerklrfleeeieklekavikeeeaeesleapeekeldeleeelekleeelkelnenleklkkelne 101
                                    ++  v+++r ++ +  +++ l+e  +k e++ ++  e  +++ ++ ++el+++ +e  k++e+++ l+++ ++l k+l e
  gi|119719290|ref|YP_919785.1| 144 EKVLVNKIRSLESIYVNVKHLNEVRAKIEEIRAQIPE-LKKKVQAINEELKTVVSEYLKVKEQMQALKQQRDELVKRLVE 222
                                    5667888999999999999998888887777766665.677777778888888899999999999999999999999999 PP

                     V_ATPase_I 102 lvelkavlekakefleee.eeeeeeee 127
                                    l++++  ++++++ +++   +  +ee+
  gi|119719290|ref|YP_919785.1| 223 LKQERDRIRETANNYHQIyISLLSEEK 249
                                    988888888887777654332222222 PP

>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3  29.7     0.005      0.66      37     234 ..       9     210 ..       1     211 [. 0.70

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.005
                            MAD  37 salkrqleeesdrnqelqkrikllekre.eekeealreqiElarlkkknlealnkkekekesklaearevisalknelae 115
                                    ++l++ql e +++ qe+ ++i++ + +  +++ e  r  +E+  +++ + +al ++     ++++++ e is+l++e + 
  gi|119719290|ref|YP_919785.1|   9 ESLRQQLIEYRQKLQEISAKIQEARSKRdSANGEVKRISAEIR-SLREQYQALRQQIAAVAEQKKTLYEKISKLREEKKG 87 
                                    6788999999************999887355555555566655.566666777888888888888888888888888888 PP

                            MAD 116 lkrqiekqelelsekeseleelqerldllkkklseleqliqqlekkqkelaeaeqrikeLefeiqsqeddslivknskse 195
                                      +q++k   el++ + e ++l+  l  ++    el ++i+qle + ++++   +  k L  +i s e+  + vk+ ++ 
  gi|119719290|ref|YP_919785.1|  88 ILEQLNKLRDELKRLNAEYNNLRGFLGSKRYDEDELRNRIEQLEWQYQTMTLPPEVEKVLVNKIRSLESIYVNVKHLNEV 167
                                    88888888888888888888888888888888888888888888888888777777777777777755555555555554 PP

                            MAD 196 l.......aripelekelerlreenkklnelkenkelLkEevedlk 234
                                            a+ipel+k+++   + n++l+++  + + +kE+++ lk
  gi|119719290|ref|YP_919785.1| 168 RakieeirAQIPELKKKVQ---AINEELKTVVSEYLKVKEQMQALK 210
                                    4000000355555555444...456777777888888888888776 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   1.2       0.2        27     129     164 ..       6      41 ..       2      47 .. 0.70
   2 ?   11.8  17.7     0.001      0.14      15     168 ..      42     212 ..      37     212 .. 0.78
   3 ?    0.5  19.8         3     4e+02      10     148 ..     121     282 ..      86     293 .. 0.69

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.2
                        DUF4795 129 lelepLkeqle...erlkelqkelqeamekedkedeaag 164
                                     ++e+L++ql    ++l+e++ ++qea +k+d   +a g
  gi|119719290|ref|YP_919785.1|   6 ESIESLRQQLIeyrQKLQEISAKIQEARSKRD---SANG 41 
                                    68999*99998577777777777777766664...4544 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.001
                        DUF4795  15 aieklqeelekleekvkelekrledkekklealkkqieelekvk....adkeeveeel.aekadkeaLatkvsrdq.... 85 
                                    +++ +++e+ +l e+ + l +++++  ++ ++l+++i++l+++k    +  +++ +el ++ a  + L+     +     
  gi|119719290|ref|YP_919785.1|  42 EVKRISAEIRSLREQYQALRQQIAAVAEQKKTLYEKISKLREEKkgilEQLNKLRDELkRLNAEYNNLRGFLGSKRyded 121
                                    68899**************************************9888866677777775688999999987766554444 PP

                        DUF4795  86 .fDeakkeLekmleellekle......eqeealkkaldtLq..eelkekld..rlelepLkeqleerlkelqkelqeame 154
                                     + +++++Le + + +    e      ++ ++l++++ +++  +e+  k++  r ++ +Lk++++  ++el++ + e+++
  gi|119719290|ref|YP_919785.1| 122 eLRNRIEQLEWQYQTMTLPPEvekvlvNKIRSLESIYVNVKhlNEVRAKIEeiRAQIPELKKKVQAINEELKTVVSEYLK 201
                                    47777777777776655542222333366666666666666999999999999999999999999999999999999888 PP

                        DUF4795 155 kedkedeaaglrkk 168
                                     ++   ++ +l+++
  gi|119719290|ref|YP_919785.1| 202 VKE---QMQALKQQ 212
                                    875...59999875 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 3
                        DUF4795  10 kklqeaieklqeelekleekvkelekrledkekklealkkqieelekvkadkeeveeel.....aekadkeaLatkvsrd 84 
                                    ++l++ ie+l+ ++ +      e+ek l +k ++le+++  +++l++v a+ ee+  ++     ++ a  e L+t+vs+ 
  gi|119719290|ref|YP_919785.1| 121 DELRNRIEQLEWQY-QTMTLPPEVEKVLVNKIRSLESIYVNVKHLNEVRAKIEEIRAQIpelkkKVQAINEELKTVVSEY 199
                                    45668888888888.34555567788888888999999999*******99999998887656555667788999999997 PP

                        DUF4795  85 q.fDeakkeLekmleellekleeqeealkkaldtLq.............eelkekldrlel....epLkeqleerlkelq 146
                                      + e +++L+++  el+++l e  ++ +++ +t +             ++l e l+r+++    ++L+++leer ++l 
  gi|119719290|ref|YP_919785.1| 200 LkVKEQMQALKQQRDELVKRLVELKQERDRIRETANnyhqiyisllseeKSLREELERISIllkaKELSQHLEERKRQLY 279
                                    77999999999999999999874444444444444444455554445555555555533332222556666665555555 PP

                        DUF4795 147 .ke 148
                                     k+
  gi|119719290|ref|YP_919785.1| 280 gKA 282
                                    333 PP

>> DASH_Dad2  DASH complex subunit Dad2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   2.0       4.9   6.4e+02      13      32 ..      49      68 ..       2      75 .. 0.56
   2 ?    7.1   2.4     0.054       7.2       5      40 ..      69     104 ..      65     110 .. 0.91
   3 ?    0.7   0.0       5.5   7.3e+02      22      39 ..     121     138 ..     104     157 .. 0.83
   4 ?    4.8   0.1      0.28        38      12      45 ..     162     195 ..     154     202 .. 0.76
   5 ?    5.7   1.7      0.15        20      16      65 ..     201     250 ..     196     284 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 4.9
                      DASH_Dad2 13 aLkqlrdlsdslakqleeLe 32
                                   +++ lr++ ++l++q+ +++
  gi|119719290|ref|YP_919785.1| 49 EIRSLREQYQALRQQIAAVA 68
                                   33344444444444444444 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.054
                      DASH_Dad2   5 aeKraELeaLkqlrdlsdslakqleeLeeklstlad 40 
                                    ++K+  +e++ +lr+  + + +ql++L ++l+ l+ 
  gi|119719290|ref|YP_919785.1|  69 EQKKTLYEKISKLREEKKGILEQLNKLRDELKRLNA 104
                                    789999**************************9986 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 5.5
                      DASH_Dad2  22 dslakqleeLeeklstla 39 
                                    d+l++++e+Le +++t++
  gi|119719290|ref|YP_919785.1| 121 DELRNRIEQLEWQYQTMT 138
                                    78999**********997 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.28
                      DASH_Dad2  12 eaLkqlrdlsdslakqleeLeeklstladgteav 45 
                                    ++L+++r+  ++++ q+ eL++k++ +++  ++v
  gi|119719290|ref|YP_919785.1| 162 KHLNEVRAKIEEIRAQIPELKKKVQAINEELKTV 195
                                    6677888888888888888888888888776665 PP

  == domain 5  score: 5.7 bits;  conditional E-value: 0.15
                      DASH_Dad2  16 qlrdlsdslakqleeLeeklstladgteavasVlanWqnvlraismaslk 65 
                                    +++++ ++l++q +eL ++l +l++  + + +  +n++++  +    + +
  gi|119719290|ref|YP_919785.1| 201 KVKEQMQALKQQRDELVKRLVELKQERDRIRETANNYHQIYISLLSEEKS 250
                                    67888899999999999999999999999999999999998554444444 PP

>> DUF4665  Domain of unknown function (DUF4665)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.7     0.019       2.5      43      89 ..       4      50 ..       1      60 [. 0.82
   2 ?    3.8   1.4      0.65        86      44      96 ..      47      99 ..      39     102 .. 0.66
   3 ?    7.3   5.5     0.053         7      32      88 ..     157     212 ..     144     223 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.019
                        DUF4665 43 kkekvenldkalvdiqkdlkslskklkletkkkekvkkkkekekvnv 89
                                   + e +e+l ++l++ +++l+++s k++    k+  ++ + +  ++++
  gi|119719290|ref|YP_919785.1|  4 ETESIESLRQQLIEYRQKLQEISAKIQEARSKRDSANGEVKRISAEI 50
                                   6789***********************99999999887666666655 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.65
                        DUF4665 44 kekvenldkalvdiqkdlkslskklkletkkkekvkkkkekekvnvdeaaell 96
                                   +  +++l ++++ ++++++++++++k+  +k +k++++k+   +++++  ++l
  gi|119719290|ref|YP_919785.1| 47 SAEIRSLREQYQALRQQIAAVAEQKKTLYEKISKLREEKKGILEQLNKLRDEL 99
                                   44577777777777777777777777777777777777776666666666655 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.053
                        DUF4665  32 VttnLKkinavkkekvenldkalvdiqkdlkslskklkletkkkekvkkkkekekvn 88 
                                    +  n K++n v + k+e++  ++ +++k+++++ ++lk+   +  kvk++ +  k++
  gi|119719290|ref|YP_919785.1| 157 IYVNVKHLNEV-RAKIEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQ 212
                                    56799***776.689********************9999999988888766655554 PP

>> She9_MDM33  She9 / Mdm33 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   2.1      0.24        32      30      74 ..       6      50 ..       3      55 .. 0.75
   2 ?    7.2   4.1     0.031       4.1       5      63 ..      53     109 ..      43     137 .. 0.79
   3 ?    4.5  11.7       0.2        26      15      81 ..     156     220 ..     143     288 .. 0.60

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.24
                     She9_MDM33 30 seieklkksieeleeeleeakeevreakeayeeaiekrsksqrev 74
                                   ++ie+l+++  e  ++l+e  ++++ea+++ ++a+ + ++   e+
  gi|119719290|ref|YP_919785.1|  6 ESIESLRQQLIEYRQKLQEISAKIQEARSKRDSANGEVKRISAEI 50
                                   578888888888888888888888888888888877666655555 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.031
                     She9_MDM33   5 leelldslqetlltaskalndvtGYseieklkksieeleeeleeakeevreakeayeea 63 
                                    l+e ++ l++++  +++   + t Y++i kl+++ + + e+l++ ++e++++ ++y++ 
  gi|119719290|ref|YP_919785.1|  53 LREQYQALRQQIAAVAE--QKKTLYEKISKLREEKKGILEQLNKLRDELKRLNAEYNNL 109
                                    44455555555555544..46788********************************975 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.2
                     She9_MDM33  15 tlltaskalndvtGYseieklkksieeleeeleeakeevreakeayeeaiekrsksqrevneLLqRk 81 
                                    ++ +  k+ln+v    +ie+++++i el++++++ +ee++++ ++y ++ e+ ++ +++ +eL++R 
  gi|119719290|ref|YP_919785.1| 156 SIYVNVKHLNEVR--AKIEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQRDELVKRL 220
                                    5566667777775..5788888888888888888888888888777777777766666666666653 PP

>> PRKG1_interact  cGMP-dependent protein kinase interacting domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3  17.0      0.56        75       9      89 ..       4     105 ..       2     110 .. 0.56
   2 ?    1.1   6.4       5.5   7.3e+02       9      89 ..     116     191 ..      87     196 .. 0.38
   3 ?    6.1   8.2      0.16        21      19      88 ..     163     232 ..     156     235 .. 0.75
   4 ?    7.1   1.8     0.076        10       1      40 [.     236     277 ..     236     293 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.56
                 PRKG1_interact   9 ekeenerLkreLeelekelselkseleklkqqrqe.................svskrssllelekrerrslerkiselee 71 
                                    e e  e L+++L e +++l+e+ +++++++++r +                 + ++  + + +  +++++l +kis+l e
  gi|119719290|ref|YP_919785.1|   4 ETESIESLRQQLIEYRQKLQEISAKIQEARSKRDSangevkrisaeirslreQYQALRQQIAAVAEQKKTLYEKISKLRE 83 
                                    56677899999999999999999999998866544445444444444444332222222222333333333444444433 PP

                 PRKG1_interact  72 el....keleeLraenqrLkdE 89 
                                    e     ++l++Lr e +rL +E
  gi|119719290|ref|YP_919785.1|  84 EKkgilEQLNKLRDELKRLNAE 105
                                    3333446667777777777766 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 5.5
                 PRKG1_interact   9 ekeenerLkreLeelekelselkseleklkqqrqe..........svskrssllelekrerrslerkiseleeelkelee 78 
                                    ++ ++++L++++e+le + +              +           v+k  sl ++  + ++ +e ++ ++ee   ++ e
  gi|119719290|ref|YP_919785.1| 116 KRYDEDELRNRIEQLEWQYQ--------------TmtlppevekvLVNKIRSLESIYVNVKHLNEVRA-KIEEIRAQIPE 180
                                    22233333333333322222..............1222222211112222233333333332222222.24555555555 PP

                 PRKG1_interact  79 LraenqrLkdE 89 
                                    L+++ q + +E
  gi|119719290|ref|YP_919785.1| 181 LKKKVQAINEE 191
                                    55555555555 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.16
                 PRKG1_interact  19 eLeelekelselkseleklkqqrqesvskrssllelekrerrslerkiseleeelkeleeLraenqrLkd 88 
                                    +L+e++ +++e+++++ +lk++ q  +++ +++++   + +++++   ++ +e +k l eL++e +r+++
  gi|119719290|ref|YP_919785.1| 163 HLNEVRAKIEEIRAQIPELKKKVQAINEELKTVVSEYLKVKEQMQALKQQRDELVKRLVELKQERDRIRE 232
                                    5778888888888888888866555555556666666667777777777888888999999999999876 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.076
                 PRKG1_interact   1 dYkkLYeeekeenerLkreLeelekel..selkseleklkqq 40 
                                    +Y ++Y + ++e++ L++eLe+++  l  +el ++le+ k+q
  gi|119719290|ref|YP_919785.1| 236 NYHQIYISLLSEEKSLREELERISILLkaKELSQHLEERKRQ 277
                                    79*******************998655115566666665543 PP

>> JIP_LZII  JNK-interacting protein  leucine zipper II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.5       5.4   7.2e+02      43      63 ..       9      29 ..       1      44 [. 0.56
   2 ?    6.2   8.0      0.09        12       5      65 ..      48     108 ..      44     135 .. 0.90
   3 ?    1.9   0.5       1.9   2.6e+02      46      71 .]     168     193 ..     143     193 .. 0.81
   4 ?   10.4  11.1    0.0043      0.57       3      70 ..     188     255 ..     186     256 .. 0.94
   5 ?    2.5   1.1       1.3   1.7e+02      38      56 ..     244     262 ..     242     278 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 5.4
                       JIP_LZII 43 eiLreEleslqkakerlesri 63
                                   e+Lr+ l + ++ ++++  +i
  gi|119719290|ref|YP_919785.1|  9 ESLRQQLIEYRQKLQEISAKI 29
                                   334444444444444444444 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.09
                       JIP_LZII   5 kevenLikENteLletknaLnvvkddLIarvdeLtsereiLreEleslqkakerlesrike 65 
                                     e+ +L ++++ L++   a+  +k+ L +++ +L +e++ + e l++l+++++rl+ + ++
  gi|119719290|ref|YP_919785.1|  48 AEIRSLREQYQALRQQIAAVAEQKKTLYEKISKLREEKKGILEQLNKLRDELKRLNAEYNN 108
                                    6888899999999999999999999999999999999999999999999999999987765 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 1.9
                       JIP_LZII  46 reEleslqkakerlesrikelEeelk 71 
                                    r  +e+++++  +l+++++++ eelk
  gi|119719290|ref|YP_919785.1| 168 RAKIEEIRAQIPELKKKVQAINEELK 193
                                    55667777888888999999998887 PP

  == domain 4  score: 10.4 bits;  conditional E-value: 0.0043
                       JIP_LZII   3 mgkevenLikENteLletknaLnvvkddLIarvdeLtsereiLreEleslqkakerlesrikelEeel 70 
                                    + +e+ ++++E+ + +e   aL  ++d+L++r+ eL++er+ +re  ++ +++  +l s+ k l eel
  gi|119719290|ref|YP_919785.1| 188 INEELKTVVSEYLKVKEQMQALKQQRDELVKRLVELKQERDRIRETANNYHQIYISLLSEEKSLREEL 255
                                    56899************************************************999999999998887 PP

  == domain 5  score: 2.5 bits;  conditional E-value: 1.3
                       JIP_LZII  38 LtsereiLreEleslqkak 56 
                                    L se+++LreEle++   +
  gi|119719290|ref|YP_919785.1| 244 LLSEEKSLREELERISILL 262
                                    77999*******9986554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3389  (0.189023); expected 358.6 (0.02)
Passed bias filter:                     1016  (0.056668); expected 358.6 (0.02)
Passed Vit filter:                       315  (0.0175693); expected 17.9 (0.001)
Passed Fwd filter:                       250  (0.0139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):             135  [number of targets reported over threshold]
# CPU time: 2.84u 0.47s 00:00:03.30 Elapsed: 00:00:00.75
# Mc/sec: 1284.25
//
Query:       gi|119719291|ref|YP_919786.1|  [L=279]
Description: zinc finger TFIIB-type domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-17   63.2   0.1      1e-07   31.9   0.0    2.5  2  TFIIB           Transcription factor TFIIB repeat
      3e-08   33.0   0.3    5.3e-08   32.3   0.3    1.4  1  TF_Zn_Ribbon    TFIIB zinc-binding
    8.3e-05   22.7   0.0       0.17   12.0   0.0    2.5  2  Cyclin_C        Cyclin, C-terminal domain
    0.00094   19.0   0.5     0.0021   17.9   0.5    1.6  1  Zn_ribbon_SprT  SprT-like zinc ribbon domain
     0.0026   17.6   0.3     0.0055   16.6   0.3    1.5  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
     0.0027   17.1   3.7       0.35   10.3   0.2    2.3  2  zf-ribbon_3     zinc-ribbon domain
     0.0034   17.4   0.3     0.0058   16.6   0.3    1.4  1  DZR             Double zinc ribbon
  ------ inclusion threshold ------
      0.019   14.6   6.8        0.1   12.3   6.8    2.1  1  zinc_ribbon_2   zinc-ribbon domain
      0.039   14.3   0.4        9.6    6.6   0.0    3.2  3  Rrf2            Transcriptional regulator
      0.058   13.5   8.4       0.12   12.5   1.8    2.3  2  UPF0547         Uncharacterised protein family UPF0547
      0.091   12.2   0.2       0.39   10.2   0.1    2.0  2  HTH_Tnp_ISL3    Helix-turn-helix domain of transposase family
      0.092   12.9   0.1       0.25   11.5   0.1    1.7  1  Trp_repressor   Trp repressor protein
       0.13   12.8   3.1        1.2    9.7   0.3    2.6  2  zf-C2H2         Zinc finger, C2H2 type
        0.2   12.3   0.5         13    6.5   0.2    2.5  2  zf-ISL3         zinc-finger of transposase IS204/IS1001/IS109
        0.2   11.2   3.3       0.26   10.9   0.4    2.3  2  Sgf11           Sgf11 (transcriptional regulation protein)
       0.45   10.1   5.0       0.62    9.6   0.3    2.3  2  zf_C2H2_10      C2H2 type zinc-finger
       0.59    9.9   0.1       0.59    9.9   0.1    2.6  3  A2L_zn_ribbon   A2L zinc ribbon domain
       0.91    9.5   6.2       0.69    9.9   0.5    2.3  2  zf-C2HC_2       zinc-finger of a C2HC-type
        1.1    9.4   3.7        4.8    7.4   3.7    2.1  1  Zn-ribbon_8     Zinc ribbon domain
        1.6    8.7   3.5         36    4.4   0.0    2.6  2  Cys_rich_CPXG   Cysteine-rich CPXCG
        4.2    8.0   6.0        1.5    9.4   0.9    2.3  2  zf-H2C2_2       Zinc-finger double domain


Domain annotation for each model (and alignments):
>> TFIIB  Transcription factor TFIIB repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.0   1.2e-10     1e-07       1      70 [.      92     162 ..      92     163 .. 0.91
   2 !   29.0   0.0   9.8e-10   8.4e-07      29      71 .]     220     262 ..     214     262 .. 0.95

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 1.2e-10
                                    HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHH.TTTTSS--HHHHHHHSS--SHH CS
                          TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAc.rkeevkrtqkeissvlqVsekt 70 
                                    ++++a+ ++Lp    ++ ke + ++ +e++l Gr  +++aAA +y  c + ++v  ++k+   v+ Vse  
  gi|119719291|ref|YP_919786.1|  92 VESMAKSMNLPPHLIEEVKEYFTKVQKEGLLRGRNRKAVAAAIIYYVCsKEKNVSVSLKDLEGVAGVSEND 162
                                    578*****************************************8665166789*************9975 PP

  == domain 2  score: 29.0 bits;  conditional E-value: 9.8e-10
                                    TTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                          TFIIB  29 kvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                    ++l+G++p giaAA++yi + + + ++tq+ i++++ Vs+ t+
  gi|119719291|ref|YP_919786.1| 220 NLLQGKKPRGIAAAAVYIIANLLGYRKTQSLIAKIAGVSTLTL 262
                                    89************************************99875 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.3   6.2e-11   5.3e-08       1      41 [.       1      42 [.       1      44 [. 0.85

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 6.2e-11
                                   EEETTTTCEE.CHEETSTTCEEESSSSBEEEECCCCCCCHHH CS
                   TF_Zn_Ribbon  1 ykCPnCgstn.lveDpergelvCtdCGlVlednsidegpewr 41
                                   + CPnCg +   ++++e+ge+ C+ CG+V  +     g  +r
  gi|119719291|ref|YP_919786.1|  1 MSCPNCGRKVkPILNFETGEYACPYCGYVFPESLLFTGRSAR 42
                                   67*****96557*****************9998887776666 PP

>> Cyclin_C  Cyclin, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0035         3      47     113 ..     130     202 ..     125     207 .. 0.75
   2 !   12.0   0.0    0.0002      0.17      43      90 ..     226     273 ..     222     276 .. 0.93

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0035
                                    HHHHHHHHCCHHH.HS--S-HHHHHHC---HHHHHHHHHHHHHHH.....HHHHGSS--HHCCCCTCGGGCCC CS
                       Cyclin_C  47 iAaaalllarstl.nspewtetlehytgyskedlkpcvelilell.....ssapssklqavrrkyssskfhkv 113
                                    +Aaa ++ ++s   n +   + le + g+s++d+k+ ++ +l+       + + s+  + v++ + s++ ++v
  gi|119719291|ref|YP_919786.1| 130 VAAAIIYYVCSKEkNVSVSLKDLEGVAGVSENDVKKAYRVLLKKGvfelgQPHVSKPSKYVYKIVGSHELQEV 202
                                    788888877777536666779*******************999876776655556666777777777776665 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.0002
                                    -HHHHHHHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHHHHHHHHH CS
                       Cyclin_C  43 ppSliAaaalllarstlnspewtetlehytgyskedlkpcvelilell 90 
                                    +p  iAaaa+++  + l++ + ++ + ++ g+s   l+ +v+ i e+l
  gi|119719291|ref|YP_919786.1| 226 KPRGIAAAAVYIIANLLGYRKTQSLIAKIAGVSTLTLRRVVKEIDENL 273
                                    6888***************************************99876 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.5   2.4e-06    0.0021       6      31 ..       2      27 ..       2      30 .. 0.95

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.4e-06
                 Zn_ribbon_SprT  6 rCtgCgreythhlsirrhnYrCrrCk 31
                                   +C++Cgr+++ +l + +  Y C++C+
  gi|119719291|ref|YP_919786.1|  2 SCPNCGRKVKPILNFETGEYACPYCG 27
                                   6************************7 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.3   6.4e-06    0.0055      30      55 ..       2      29 ..       1      31 [. 0.94

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 6.4e-06
                 OrfB_Zn_ribbon 30 tCseCgsknke..alsgrtfkCpnCgfe 55
                                   +C++Cg+k+k+  + ++ ++ Cp Cg++
  gi|119719291|ref|YP_919786.1|  2 SCPNCGRKVKPilNFETGEYACPYCGYV 29
                                   6*************************97 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.5    0.0031       2.6       4      13 ..       2      11 ..       1      12 [. 0.69
   2 !   10.3   0.2   0.00041      0.35      16      25 ..      20      29 ..      15      30 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0031
                    zf-ribbon_3  4 rCPnCGapls 13
                                   +CPnCG +++
  gi|119719291|ref|YP_919786.1|  2 SCPNCGRKVK 11
                                   5888887555 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00041
                    zf-ribbon_3 16 dnvCpyCGtk 25
                                     +CpyCG++
  gi|119719291|ref|YP_919786.1| 20 EYACPYCGYV 29
                                   558****998 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.3   6.8e-06    0.0058      15      37 ..       3      29 ..       1      37 [. 0.70

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 6.8e-06
                            DZR 15 CseCgtklkavaa....edrCpsCgek 37
                                   C++Cg k+k+  +    e++Cp Cg+ 
  gi|119719291|ref|YP_919786.1|  3 CPNCGRKVKPILNfetgEYACPYCGYV 29
                                   777777777666677777777777776 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   6.8   0.00012       0.1       2      21 ..       3      28 ..       2      30 .. 0.96

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00012
                  zinc_ribbon_2  2 CpnCGaelqdnakF......CpyCGt 21
                                   CpnCG+++++  +F      CpyCG+
  gi|119719291|ref|YP_919786.1|  3 CPNCGRKVKPILNFetgeyaCPYCGY 28
                                   **********999999*********8 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.22   1.9e+02      27      56 ..      91     123 ..      78     126 .. 0.74
   2 ?    6.6   0.0     0.011       9.6       8      54 ..     129     175 ..     122     178 .. 0.89
   3 ?    1.5   0.0      0.46     4e+02      11      49 ..     232     269 ..     227     272 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.22
                                    -HHHHHHHHTS-HHHHHHH...HHHHHHTTSEE CS
                           Rrf2  27 sseeiaerqnispsyleki...lakLrkaglvk 56 
                                    ++e++a+++n++p+ +e +   ++k +k+gl++
  gi|119719291|ref|YP_919786.1|  91 EVESMAKSMNLPPHLIEEVkeyFTKVQKEGLLR 123
                                    68999*********9997633366667777765 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.011
                                    HHHHHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTS CS
                           Rrf2   8 eyalhallyLakeeeeepvsseeiaerqnispsylekilakLrkagl 54 
                                     +a  +++y  ++e++ +vs++++    ++s++ ++k  + L k+g+
  gi|119719291|ref|YP_919786.1| 129 AVAAAIIYYVCSKEKNVSVSLKDLEGVAGVSENDVKKAYRVLLKKGV 175
                                    678889999999999999***********************999996 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.46
                                    HHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHH CS
                           Rrf2  11 lhallyLakeeeeepvsseeiaerqnispsylekilakL 49 
                                      a++++a+  + +  + + ia+  ++s   l++++++ 
  gi|119719291|ref|YP_919786.1| 232 AAAVYIIANLLGYR-KTQSLIAKIAGVSTLTLRRVVKEI 269
                                    55666666666655.6677899999*********99876 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.6     0.039        33       3      11 ..       3      11 ..       2      12 .. 0.85
   2 ?   12.5   1.8   0.00014      0.12      16      25 ..      22      31 ..      21      32 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.039
                        UPF0547  3 CPeCeakvP 11
                                   CP C +kv+
  gi|119719291|ref|YP_919786.1|  3 CPNCGRKVK 11
                                   999999985 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00014
                        UPF0547 16 fCphCGyvFq 25
                                   +Cp+CGyvF 
  gi|119719291|ref|YP_919786.1| 22 ACPYCGYVFP 31
                                   6********7 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       1.3   1.1e+03      23      35 ..     121     132 ..     120     134 .. 0.77
   2 ?   10.2   0.1   0.00045      0.39      20      50 ..     238     268 ..     228     269 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.3
                   HTH_Tnp_ISL3  23 lllesrsvkavAr 35 
                                    ll+ + ++kavA+
  gi|119719291|ref|YP_919786.1| 121 LLRGR-NRKAVAA 132
                                    45566.******7 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00045
                   HTH_Tnp_ISL3  20 ilelllesrsvkavArqlgvSwtTVwrildr 50 
                                    i+ ll  +++ + +A++ gvS+ T++r++++
  gi|119719291|ref|YP_919786.1| 238 IANLLGYRKTQSLIAKIAGVSTLTLRRVVKE 268
                                    667778889*******************986 PP

>> Trp_repressor  Trp repressor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1    0.0003      0.25      40      75 ..     236     271 ..     231     278 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0003
                  Trp_repressor  40 qvvkeLLkeelsqreIaeelgvSiAtItRvsrsLkt 75 
                                     ++ +LL   ++q+ Ia+  gvS+ t  Rv +++  
  gi|119719291|ref|YP_919786.1| 236 YIIANLLGYRKTQSLIAKIAGVSTLTLRRVVKEIDE 271
                                    57777*************************999875 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.2       0.2   1.7e+02       2      10 ..       2      10 ..       1      13 [. 0.84
   2 ?    9.7   0.3    0.0014       1.2       1      11 [.      21      31 ..      21      37 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.2
                                   EETTTTEEE CS
                        zf-C2H2  2 kCpdCgksF 10
                                    Cp Cg++ 
  gi|119719291|ref|YP_919786.1|  2 SCPNCGRKV 10
                                   6*****975 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0014
                                   EEETTTTEEES CS
                        zf-C2H2  1 ykCpdCgksFk 11
                                   y Cp+Cg++F+
  gi|119719291|ref|YP_919786.1| 21 YACPYCGYVFP 31
                                   88********7 PP

>> zf-ISL3  zinc-finger of transposase IS204/IS1001/IS1096/IS1165
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.2     0.016        13       4      12 ..       2      10 ..       1      15 [. 0.85
   2 ?    3.6   0.0      0.13   1.1e+02       4      12 ..      22      31 ..      20      58 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.016
                        zf-ISL3  4 rCPnCgskt 12
                                    CPnCg+k+
  gi|119719291|ref|YP_919786.1|  2 SCPNCGRKV 10
                                   7*****996 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.13
                        zf-ISL3  4 rCPnCgsk.t 12
                                   +CP+Cg + +
  gi|119719291|ref|YP_919786.1| 22 ACPYCGYVfP 31
                                   6*****8754 PP

>> Sgf11  Sgf11 (transcriptional regulation protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.4    0.0003      0.26       6      15 ..       2      11 ..       1      12 [. 0.89
   2 ?    0.1   0.1       0.7   5.9e+02       5      11 ..      21      27 ..      18      27 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0003
                                   E-TTTSSEEE CS
                          Sgf11  6 tCpnCgRqia 15
                                   +CpnCgR+++
  gi|119719291|ref|YP_919786.1|  2 SCPNCGRKVK 11
                                   8*******96 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.7
                                   EE-TTTS CS
                          Sgf11  5 vtCpnCg 11
                                   + Cp+Cg
  gi|119719291|ref|YP_919786.1| 21 YACPYCG 27
                                   68****7 PP

>> zf_C2H2_10  C2H2 type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.6      0.15   1.3e+02       4      11 ..       2       9 ..       1      12 [. 0.84
   2 ?    9.6   0.3   0.00073      0.62       2      13 ..      20      31 ..      19      33 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.15
                     zf_C2H2_10  4 sCPKCqek 11
                                   sCP C+ k
  gi|119719291|ref|YP_919786.1|  2 SCPNCGRK 9 
                                   9****875 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00073
                     zf_C2H2_10  2 efsCPKCqeklP 13
                                   e++CP C+++ P
  gi|119719291|ref|YP_919786.1| 20 EYACPYCGYVFP 31
                                   79********99 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.2      0.16   1.4e+02      22      28 ..       1       7 [.       1       9 [. 0.91
   2 ?    9.9   0.1    0.0007      0.59      14      32 ..      13      31 ..      11      31 .. 0.90
   3 ?   -2.2   0.2       4.5   3.8e+03       3       7 ..     136     140 ..     135     141 .. 0.53

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.16
                  A2L_zn_ribbon 22 lvCieCg 28
                                   ++C++Cg
  gi|119719291|ref|YP_919786.1|  1 MSCPNCG 7 
                                   79****9 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0007
                  A2L_zn_ribbon 14 ilnseqgylvCieCgasfp 32
                                   iln e g++ C+ Cg++fp
  gi|119719291|ref|YP_919786.1| 13 ILNFETGEYACPYCGYVFP 31
                                   6777899***********8 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 4.5
                  A2L_zn_ribbon   3 lkvCs 7  
                                    ++vCs
  gi|119719291|ref|YP_919786.1| 136 YYVCS 140
                                    45555 PP

>> zf-C2HC_2  zinc-finger of a C2HC-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.5   0.00081      0.69       5      14 ..       3      12 ..       1      12 [. 0.87
   2 ?    2.3   0.8      0.19   1.6e+02       4       9 ..      22      27 ..      20      27 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00081
                      zf-C2HC_2  5 CpkCgRsFnp 14
                                   Cp+CgR+ +p
  gi|119719291|ref|YP_919786.1|  3 CPNCGRKVKP 12
                                   ******9876 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.19
                      zf-C2HC_2  4 pCpkCg 9 
                                    Cp+Cg
  gi|119719291|ref|YP_919786.1| 22 ACPYCG 27
                                   5****9 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   3.7    0.0056       4.8       8      33 ..       3      27 ..       1      30 [. 0.84

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0056
                    Zn-ribbon_8  8 CeeCghefevlqsisdapltaCPeCg 33
                                   C +Cg++  ++   ++  + aCP Cg
  gi|119719291|ref|YP_919786.1|  3 CPNCGRKVKPILN-FETGEYACPYCG 27
                                   *********9985.4667788****8 PP

>> Cys_rich_CPXG  Cysteine-rich CPXCG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.042        36       2      14 ..       2      14 ..       1      20 [. 0.75
   2 ?    3.5   1.6     0.078        67       1       7 [.      21      27 ..      21      32 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.042
                  Cys_rich_CPXG  2 qCPyCgeeievlv 14
                                   +CP+Cg +++  +
  gi|119719291|ref|YP_919786.1|  2 SCPNCGRKVKPIL 14
                                   7*****9987655 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.078
                  Cys_rich_CPXG  1 iqCPyCg 7 
                                   + CPyCg
  gi|119719291|ref|YP_919786.1| 21 YACPYCG 27
                                   68****9 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.4         1   8.8e+02      17      23 ..       3       9 ..       2      11 .. 0.83
   2 ?    9.4   0.9    0.0018       1.5      14      24 ..      20      30 ..      15      31 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 1
                      zf-H2C2_2 17 CplCdka 23
                                   Cp C+ +
  gi|119719291|ref|YP_919786.1|  3 CPNCGRK 9 
                                   ****976 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0018
                      zf-H2C2_2 14 pyeCplCdkaF 24
                                   +y Cp+C+++F
  gi|119719291|ref|YP_919786.1| 20 EYACPYCGYVF 30
                                   49*******99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       803  (0.0447878); expected 358.6 (0.02)
Passed bias filter:                      687  (0.0383178); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1728.57
//
Query:       gi|119719292|ref|YP_919787.1|  [L=93]
Description: gar1 - like small nucleolar RNP [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-07   31.4   0.0    1.6e-07   31.2   0.0    1.1  1  Gar1      Gar1/Naf1 RNA binding region
  ------ inclusion threshold ------
      0.037   14.1   0.0      0.051   13.7   0.0    1.3  1  PRC       PRC-barrel domain


Domain annotation for each model (and alignments):
>> Gar1  Gar1/Naf1 RNA binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.0   1.8e-11   1.6e-07      32      83 ..      14      60 ..       8      82 .. 0.84

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 1.8e-11
                                   TEEEEEE---S--B--BTT-EEEETT--EEEE--EEES-SSS-EEEEE--GG CS
                           Gar1 32 nevviksttsgekkvldfnsilflenktqiGkVdEifGpvnepyysVklnss 83
                                   +++v++++     +v+ ++  +++e+   +G V++++Gpv++p++ Vk+++s
  gi|119719292|ref|YP_919787.1| 14 KNLVVEAS-----NVPPIGEKVYDEKAMLVGYVYDVIGPVTSPFVLVKVDES 60
                                   57788887.....79**********************************943 PP

>> PRC  PRC-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   5.7e-06     0.051       9      47 ..      25      62 ..      19      73 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.7e-06
                                   -TT-EEEETTSSEEEEEEEEEEETTTTEEEEEEEEETTT CS
                            PRC  9 liGkeVytedGeklGkVkDvvidekegrvralvvsvggf 47
                                   +iG +Vy+e+   +G V+Dv i + +  ++ ++v+++++
  gi|119719292|ref|YP_919787.1| 25 PIGEKVYDEKAMLVGYVYDV-IGPVTSPFVLVKVDESRW 62
                                   69******************.887777777777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       215  (0.0119917); expected 358.6 (0.02)
Passed bias filter:                      189  (0.0105416); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 661.70
//
Query:       gi|119719293|ref|YP_919788.1|  [L=412]
Description: Pre-mRNA processing ribonucleoprotein, binding region [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.3e-73  245.0   0.0    1.3e-72  244.0   0.0    1.5  2  Nop             snoRNA binding domain, fibrillarin
  ------ inclusion threshold ------
      0.044   14.1   0.3       0.18   12.2   0.1    2.1  2  CPSase_L_D3     Carbamoyl-phosphate synthetase large chain, o
       0.09   12.9   1.5       0.14   12.3   0.1    2.0  2  Ribosomal_L38e  Ribosomal L38e protein family


Domain annotation for each model (and alignments):
>> Nop  snoRNA binding domain, fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0      0.88   5.2e+03     170     195 ..      19      41 ..      17      42 .. 0.73
   2 !  244.0   0.0   2.2e-76   1.3e-72       2     229 ..     153     378 ..     152     379 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 0.88
                                    SSCHHHCSHHHHHTS-CCCHHHHHHH CS
                            Nop 170 kyGliyhselvqkatppklkkkiaRl 195
                                    ++G i  s+++ +   +k  +kiaR+
  gi|119719293|ref|YP_919788.1|  19 EEGQILASDMITQ---DKDPEKIARF 41 
                                    6899999999984...4666777775 PP

  == domain 2  score: 244.0 bits;  conditional E-value: 2.2e-76
                                    HHHHHHHHHHHHHHHHHHHTTTSTCHHHHS-SHHHHHHHHHHCCCCHCCT.HHTT......HHHHHHHHHHHHCHHHH-S CS
                            Nop   2 ldeidkeintlhkrvrewYswhFpELeslvkdnleYakvvkligneredlekkee.....deelakevimaakvtastsm 76 
                                    ld+++k+in +++rvrewY+ hFpEL+++v+d+ +Y k+v+++g +r++++ ++      +++la+++++aa+     sm
  gi|119719293|ref|YP_919788.1| 153 LDDVNKTINLFASRVREWYGLHFPELNDIVEDHEDYFKIVSKLG-SRSNISLEKLkelgfKDDLAQKIVKAASN----SM 227
                                    799*****************************************.88998544223366655588888888888....** PP

                                    SS-S-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHCHHHHHHHHHHHHSSHHHHHCS-HHHHTTTT-H CS
                            Nop  77 gaelseedlknikelcdrvleleelrkelleYlesrmsaiAPNlsaLvGeevaarLishaGgLtnLakmPastiqilGae 156
                                    gael+e dl+ i+ l d  l+l++ r++l++Y+++ m  +APN++ LvG++++arLis aGgL++La++Pastiq+lGae
  gi|119719293|ref|YP_919788.1| 228 GAELTEFDLNAIRLLSDAGLQLYSIRRNLEKYIDEAMYDVAPNIRGLVGPTLGARLISLAGGLEKLARLPASTIQVLGAE 307
                                    ******************************************************************************** PP

                                    HHHCCCHH.T---SSSCHHHCSHHHHHTS-CCCHHHHHHHHHHHHHHHHHHHHTT----SHHHHHHHHHHHHHH CS
                            Nop 157 kalfralk.kkntpkyGliyhselvqkatppklkkkiaRllaaKvalaaRiDafsekdgslGkklreeiekklk 229
                                    kalfral+ + + pk+G+i+++++++k+ p+++++kiaR+la K+a+aaRiDaf  + +   ++lre++ek+++
  gi|119719293|ref|YP_919788.1| 308 KALFRALRfGARPPKHGVIFQHPYIHKS-PKWQRGKIARALAGKLAIAARIDAF--TGEYKADELREDLEKRIE 378
                                    ********999***************88.*************************..44455669********98 PP

>> CPSase_L_D3  Carbamoyl-phosphate synthetase large chain, oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   2.9e-05      0.18       3      82 ..     135     222 ..     133     245 .. 0.77
   2 ?   -2.2   0.0      0.82   4.9e+03      98     114 ..     351     367 ..     339     368 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.9e-05
                    CPSase_L_D3   3 lkeptdeRifaiaealrrglsveeihel..tkidpwFLekleelvelekelkkkkk......eldeellreakklGfsDk 74 
                                    +ke  ++R +++a+a+++  +v++  +l  +++ +w+  ++ el ++ ++ +++ k      + ++  l+++k+lGf+D 
  gi|119719293|ref|YP_919788.1| 135 VKEVAEKRDLYVAQAVNALDDVNKTINLfaSRVREWYGLHFPELNDIVEDHEDYFKivsklgSRSNISLEKLKELGFKDD 214
                                    7888999999****9987777776665433789****9988888888888887777777776677777***********9 PP

                    CPSase_L_D3  75 qiaellee 82 
                                      +++++ 
  gi|119719293|ref|YP_919788.1| 215 LAQKIVKA 222
                                    98888642 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.82
                    CPSase_L_D3  98 lpvykrvDtcAaeFeae 114
                                    l+   r+D   +e++a+
  gi|119719293|ref|YP_919788.1| 351 LAIAARIDAFTGEYKAD 367
                                    5566899******9985 PP

>> Ribosomal_L38e  Ribosomal L38e protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   2.3e-05      0.14      43      62 ..      66      85 ..      64      90 .. 0.92
   2 ?   -2.6   0.1         1     6e+03       2      17 ..     375     390 ..     365     400 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.3e-05
                 Ribosomal_L38e 43 YTLvvkdkekaeklkqsLpp 62
                                   YTL v+d+e a k+ qsL +
  gi|119719293|ref|YP_919788.1| 66 YTLAVEDEEVARKISQSLKE 85
                                   9*****************75 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1
                 Ribosomal_L38e   2 keikdiKeFLeiarrk 17 
                                    k i++iK++ +    k
  gi|119719293|ref|YP_919788.1| 375 KRIEEIKTLYAKPPAK 390
                                    5677777766555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1051  (0.0586201); expected 358.6 (0.02)
Passed bias filter:                      725  (0.0404373); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2597.93
//
Query:       gi|119719294|ref|YP_919789.1|  [L=233]
Description: fibrillarin [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.9e-98  326.8   0.2    5.6e-98  326.6   0.2    1.0  1  Fibrillarin  Fibrillarin
    0.00011   22.0   0.0    0.00015   21.5   0.0    1.3  1  GCD14        tRNA methyltransferase complex GCD14 subunit
     0.0076   16.0   0.0      0.015   15.0   0.0    1.7  1  PCMT         Protein-L-isoaspartate(D-aspartate) O-methyltran
  ------ inclusion threshold ------
      0.032   14.1   0.7      0.066   13.0   0.1    1.8  2  LBR_tudor    Lamin-B receptor of TUDOR domain


Domain annotation for each model (and alignments):
>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  326.6   0.2  1.2e-101   5.6e-98       2     223 ..       8     231 ..       7     233 .] 0.99

  Alignments for each domain:
  == domain 1  score: 326.6 bits;  conditional E-value: 1.2e-101
                                    EEECSSTTEEEEE.TTSSEEEEEE-SSTT--SSSSEEEEETTEEEEEE-TTTSHHHHHHHTT-S--S--TTSEEEEESTT CS
                    Fibrillarin   2 eeheklegvyivk.ekgdarlatknlvpgekvYgEklikveeeEyRvWnpfrsKlaaailkglkelpikkgskvLYlGaa 80 
                                     ehek+ g+y+v+ e+g+++lat nl+pg kvY+E li+++++E R+Wnp+rsKla+ai+kg++  pik+g kvLYlG+a
  gi|119719294|ref|YP_919789.1|   8 VEHEKFPGIYVVEyEDGTKKLATVNLAPGVKVYDETLIQHGDKELRTWNPYRSKLAGAIHKGITINPIKPGVKVLYLGVA 87 
                                    689***************************************************************************** PP

                                    TSHHHHHHHHHHTTTSEEEEEESSHHHHHHHH.HHHTTSTTEEEEES-TTSGGGGTTTS--EEEEEEESSSTTHHHHHHH CS
                    Fibrillarin  81 sGttvsHvsDivgeegvvyavefsprvlreli.evakkRknivPileDArkPekYralvekvDvifaDvaqpdqarilak 159
                                    sGtt+sHvsDi+g++gv+++vef+prv+re+i +va +R+n+vP+l+DAr+P+kY+++ve vDv++aD+aqp qa+ +a+
  gi|119719294|ref|YP_919789.1|  88 SGTTPSHVSDIIGPKGVLFGVEFAPRVMREFIeKVAVHRENVVPLLADARFPTKYAHVVELVDVVYADIAQPFQAKYVAD 167
                                    ********************************789********************************************* PP

                                    HHHHHEEEEEEEEEEEEHHHHHSSSSHHHHHHHHHHHHHHTTEEEEEEEE-TTTSTTEEEEEEE CS
                    Fibrillarin 160 naklflkeggyllisikarsidvtkepeevfkeeveklkeeglkvleqvklepyekdhalvvgk 223
                                    na++flk+ggy++++ika+sidvt++p+e++k+e+++l+e+g+kv+e+ +lepy++ ha+vv++
  gi|119719294|ref|YP_919789.1| 168 NADMFLKSGGYIMMAIKAMSIDVTATPSETYKREITHLEERGYKVKEVKHLEPYDEAHAFVVAQ 231
                                    **************************************************************97 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   3.4e-08   0.00015      38     140 ..      75     177 ..      63     225 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 3.4e-08
                          GCD14  38 lkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsqlvtvthrDvckeGfdeevsgkvDav 117
                                    +kpG +v+  G  sg+  + ++  ++P+G lf +ef  + +++ +e+   h+  ++v     D+      ++v + vD v
  gi|119719294|ref|YP_919789.1|  75 IKPGVKVLYLGVASGTTPSHVSDIIGPKGVLFGVEFAPRVMREFIEKVAVHR--ENVVPLLADARFPTKYAHVVELVDVV 152
                                    89**********************************8766665555555554..35555556776544458899****** PP

                          GCD14 118 fLDlPaPwea..iphaakalkkegg 140
                                    + D+ +P++a  + + a+++ k+gg
  gi|119719294|ref|YP_919789.1| 153 YADIAQPFQAkyVADNADMFLKSGG 177
                                    ********99444444555545554 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   3.4e-06     0.015      71     133 ..      75     136 ..      62     206 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.4e-06
                                    --TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-G CS
                           PCMT  71 lkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDG 133
                                    +k+g +vL +G  sG     ++ ++g+kg + ++e  +++++e  +++   ++env+   +D 
  gi|119719294|ref|YP_919789.1|  75 IKPGVKVLYLGVASGTTPSHVSDIIGPKGVLFGVEFAPRVMREFIEKVAV-HRENVVPLLADA 136
                                    89***************************************999999865.455666555665 PP

>> LBR_tudor  Lamin-B receptor of TUDOR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   1.5e-05     0.066      25      46 ..       5      26 ..       4      30 .. 0.94
   2 ?   -3.4   0.1         2   9.1e+03      23      40 ..     198     213 ..     198     213 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.5e-05
                      LBR_tudor 25 vkvlsfdekkqlYtVkykDGTe 46
                                   vkv+++++   +Y V y+DGT 
  gi|119719294|ref|YP_919789.1|  5 VKVVEHEKFPGIYVVEYEDGTK 26
                                   8********************6 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2
                      LBR_tudor  23 yevkvlsfdekkqlYtVk 40 
                                    y+ ++++ +e++  Y+Vk
  gi|119719294|ref|YP_919789.1| 198 YKREITHLEERG--YKVK 213
                                    566666666666..8886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1621.92
//
Query:       gi|119719295|ref|YP_919790.1|  [L=297]
Description: helix-turn-helix domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.4e-11   42.4   2.3    6.9e-11   42.0   0.5    2.2  2  HTH_3     Helix-turn-helix
    6.3e-09   36.0   0.8    1.9e-08   34.5   0.8    1.8  1  HTH_31    Helix-turn-helix domain
    4.6e-05   23.4   1.0    0.00011   22.1   0.3    2.1  2  HTH_19    Helix-turn-helix domain
     0.0024   17.7   0.1     0.0053   16.6   0.1    1.6  1  HTH_25    Helix-turn-helix domain
     0.0035   17.1   0.1      0.015   15.1   0.1    2.0  1  MerR      MerR family regulatory protein
  ------ inclusion threshold ------
      0.059   13.5   0.0       0.16   12.1   0.0    1.7  1  MerR_1    MerR HTH family regulatory protein
      0.077   12.8   0.1       0.17   11.7   0.1    1.6  1  HTH_23    Homeodomain-like domain
       0.97    9.5   3.9        6.6    6.8   1.3    3.4  3  RHH_1     Ribbon-helix-helix protein, copG family


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1       3.5   7.9e+03      21      34 ..      82      95 ..      82      96 .. 0.85
   2 !   42.0   0.5   3.1e-14   6.9e-11       1      52 [.     115     166 ..     115     168 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.5
                                   SSHHHHHHHHTTSS CS
                          HTH_3 21 vsrstisriEnGer 34
                                   vs st + + +Ger
  gi|119719295|ref|YP_919790.1| 82 VSSSTANSLLRGER 95
                                   67899999****98 PP

  == domain 2  score: 42.0 bits;  conditional E-value: 3.1e-14
                                    HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSEH CS
                          HTH_3   1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvsl 52 
                                    l+++R+  gls+  LA+++Gvs +ti+ +E G +  +le++ kl++ Lg ++
  gi|119719295|ref|YP_919790.1| 115 LRKARERMGLSRGALAREVGVSARTIAYYEEGLSDATLEIAAKLEEILGSEI 166
                                    89**********************************************9765 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.8   8.4e-12   1.9e-08       3      55 ..     112     163 ..     112     177 .. 0.94

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 8.4e-12
                         HTH_31   3 GalLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralg 55 
                                    G +Lr +Rer GLs+ ++A+ +gvs+ t+  +E G  +  +++  ++l ++lg
  gi|119719295|ref|YP_919790.1| 112 GKELRKARERMGLSRGALAREVGVSARTIAYYEEGLSD-ATLEIAAKLEEILG 163
                                    789**********************************7.99999999999887 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.3   5.1e-08   0.00011       1      53 [.     112     163 ..     112     167 .. 0.86
   2 ?   -3.7   0.0       5.6   1.3e+04      32      45 ..     260     272 ..     259     279 .. 0.60

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 5.1e-08
                         HTH_19   1 GerLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealg 53 
                                    G+ L++aRe  gl+  +la+++g+s + i+ +E g + +++ e   k+ e+lg
  gi|119719295|ref|YP_919790.1| 112 GKELRKARERMGLSRGALAREVGVSARTIAYYEEGLS-DATLEIAAKLEEILG 163
                                    6779*******************************88.776666666666665 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 5.6
                         HTH_19  32 iEngkkdvpsaell 45 
                                    i n+k  ++ +e++
  gi|119719295|ref|YP_919790.1| 260 ILNNKE-EILSEKV 272
                                    556655.5555554 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   2.4e-06    0.0053       2      33 ..     115     146 ..     114     151 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.4e-06
                                    HHHHHHTTT--HHHHHHHSS--HHHHHHHHCT CS
                         HTH_25   2 LraaRearglsleevaketkIrkdylealEed 33 
                                    Lr+aRe++gls+ ++a+e  ++++++   Ee+
  gi|119719295|ref|YP_919790.1| 115 LRKARERMGLSRGALAREVGVSARTIAYYEEG 146
                                    9***********************99877776 PP

>> MerR  MerR family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   6.6e-06     0.015       3      21 ..     127     145 ..     127     145 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 6.6e-06
                                    HHHHHHHTTTHHHHHHHHH CS
                           MerR   3 gevAeltGvsprtLRyYEr 21 
                                    g +A+ +Gvs+rt+ yYE+
  gi|119719295|ref|YP_919790.1| 127 GALAREVGVSARTIAYYEE 145
                                    789***************7 PP

>> MerR_1  MerR HTH family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0     7e-05      0.16       4      22 ..     127     145 ..     124     147 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7e-05
                                    HHHHHHHTS-HHHHHHHHH CS
                         MerR_1   4 gevakilgvtthtlrywek 22 
                                    g +a+++gv+++t+ y+e+
  gi|119719295|ref|YP_919790.1| 127 GALAREVGVSARTIAYYEE 145
                                    789**************97 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   7.7e-05      0.17      12      46 ..     116     147 ..     115     151 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7.7e-05
                         HTH_23  12 lllae..GlsvreIAreLgvsrrTvyrwlkryreeGl 46 
                                    + ++e  Gls+ + Are gvs rT+  +     eeGl
  gi|119719295|ref|YP_919790.1| 116 RKARErmGLSRGALAREVGVSARTIAYY-----EEGL 147
                                    5566679******************843.....5665 PP

>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   1.3    0.0029       6.6      12      31 ..     113     132 ..     113     133 .. 0.92
   2 ?   -0.3   0.0      0.53   1.2e+03      11      25 ..     172     186 ..     171     187 .. 0.84
   3 ?   -0.3   0.0       0.5   1.1e+03      19      29 ..     190     200 ..     190     200 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0029
                                    HHHHHHHHHHTSSHHHHHHH CS
                          RHH_1  12 erLdelarrrgrSrSelIRe 31 
                                    ++L++ ++r+g Sr++l Re
  gi|119719295|ref|YP_919790.1| 113 KELRKARERMGLSRGALARE 132
                                    5899**************98 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.53
                                    HHHHHHHHHHHTSSH CS
                          RHH_1  11 lerLdelarrrgrSr 25 
                                    ++ L+el + +++S+
  gi|119719295|ref|YP_919790.1| 172 VDSLRELTKSGRPSV 186
                                    688999999999997 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.5
                                    HHHTSSHHHHH CS
                          RHH_1  19 rrrgrSrSelI 29 
                                    ++rgr++ +lI
  gi|119719295|ref|YP_919790.1| 190 AKRGRNVEWLI 200
                                    689******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 2023.71
//
Query:       gi|119719296|ref|YP_919791.1|  [L=384]
Description: tRNA (guanine-N(2)-)-methyltransferase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.7e-92  308.8   0.0      7e-92  308.5   0.0    1.0  1  TRM              N2,N2-dimethylguanosine tRNA methyltransfera
    1.7e-07   31.2   0.0    2.7e-07   30.5   0.0    1.2  1  Met_10           Met-10+ like-protein
    0.00025   20.8   0.0     0.0004   20.2   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    0.00045   19.9   0.0    0.00073   19.2   0.0    1.2  1  Cons_hypoth95    Conserved hypothetical protein 95
  ------ inclusion threshold ------
      0.019   15.9   0.0      0.059   14.4   0.0    1.9  1  Methyltransf_24  Methyltransferase domain
      0.028   15.1   0.0       0.05   14.3   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
       0.07   12.7   0.0       0.12   11.9   0.0    1.3  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
      0.081   12.3   0.1       0.12   11.7   0.1    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
      0.087   12.1   0.0       0.13   11.6   0.0    1.1  1  DNA_methylase    C-5 cytosine-specific DNA methylase
       0.14   11.7   0.0       0.24   10.9   0.0    1.4  1  MTS              Methyltransferase small domain
       0.19   11.6   0.0       0.39   10.6   0.0    1.4  1  Methyltransf_18  Methyltransferase domain


Domain annotation for each model (and alignments):
>> TRM  N2,N2-dimethylguanosine tRNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  308.5   0.0   4.3e-95     7e-92      18     375 ..      28     381 ..      15     382 .. 0.92

  Alignments for each domain:
  == domain 1  score: 308.5 bits;  conditional E-value: 4.3e-95
                                    --SS--GGGHHHHHHHHHH....HHHHHHHH-S-EEEEESS-TTSHHHHHHHHH-S-EEEEEEE-S-HHHHHHHHHHHHH CS
                            TRM  18 eeVFYNPvqefnRDlsvlvir.qlellkkklgekikvldaLsasGlRaiRfalEvpgvkevlaNDisekAvelikeNvkl 96 
                                    ++VFYNP+++  RD+s +++  + ell++     + v+da+sa+G+R+iR+alE +gv +v++NDi+++Ave+i++Nv+l
  gi|119719296|ref|YP_919791.1|  28 APVFYNPRMRCSRDISSVIVGaYAELLGRG---GLVVVDAFSATGIRGIRYALENEGVGRVILNDINPRAVEIIRQNVDL 104
                                    79**************99965566666655...69********************************************* PP

                                    TT--GGEEEE-S-HHHHHC--SS-EEEEEE--SS--GGGHHHHHHHEEEEEEEEEEE--HHHHTTSSHHHHHHHHSSB-- CS
                            TRM  97 neveeivvineddAnvllaekkkrfdviDlDPfGspapfldsavqsvkekglLlvTaTDtavLaGaspekclrkYgaval 176
                                    n v++iv+++++dA+ lla   +  d++DlDPfGspa+++d a++++k+kglL+vTaTD+ +L G++p++c+rkY + ++
  gi|119719296|ref|YP_919791.1| 105 NGVSDIVEVRREDASSLLA-SLSGVDIVDLDPFGSPAEYVDPALRCLKHKGLLCVTATDLPPLLGKYPKTCVRKYFSKSI 183
                                    ******************5.56678******************************************************* PP

                                    -STTHHHHHHHHHHHHHHHHHHTTTEEEEEEEEEEETTEEEEEEEEEE-HHHHHHHHTTEEEEEEETTT--EEEE--GGG CS
                            TRM 177 kselcHEvalRillkavareaakYekavepllslsadfYvrvfvkvktgaakvkkvleklglvlhCsgClseekvkglak 256
                                    ++e+  E a+Rill+++areaak  ++++pl s+++++ vrv v v + + +   +++++g+v++  + l++  v  +  
  gi|119719296|ref|YP_919791.1| 184 ETEFSRELAVRILLYFIAREAAKLGRTIVPLYSYYMEHHVRVCVLVLKTESRYGGLTDSIGFVKYNPTSLERAAVPLFDF 263
                                    *****************************************************************777777555554444 PP

                                    --SB-TTT-SBEEEEEEEE-S-S--HHHHHHHHHHHCT...-TTS-HHHHHHHHHHHHHHS--SS-EEHHHHHHHHT-SS CS
                            TRM 257 fkaecehcgaklhlaGPlwlgplkdkefveevleeaekek.eeelkkrvkklLklikeElldaplyydlsqlasvlklsv 335
                                        +e+ + +  ++GPlw+ ++ ++ f + v ++ +++  ++ l ++  ++ ++i eE++  p+y+++++ as+ +l+ 
  gi|119719296|ref|YP_919791.1| 264 ---YREERSDNWVVGGPLWVKEIFQRTFADAVGRAYSSKLkAHGLCGKGWRVVSTILEEVSRPPFYFTTEKFASTYRLKE 340
                                    ...5777888999*******************999988652555699999***************************987 PP

                                    --.-HHHHHHH....TT-EE-TTSTTEEE-SS-HHHHHHHH CS
                            TRM 336 pp.lkkvvsalkelgfevsrtHakpkaikTnapleavvevl 375
                                    ++ + +v + l++ gfe srtH+ pk+++T a++ +++e++
  gi|119719296|ref|YP_919791.1| 341 EKsVVEVLEVLRARGFEGSRTHFDPKGFRTSASIGEILEAI 381
                                    551689*****************************999875 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.0   1.7e-10   2.7e-07     101     198 ..      58     157 ..      50     158 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 1.7e-10
                                    T-EEEETT-TTTCCHHHCCHHTTSS.EEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG---.TT-EEEEEE--TT CS
                         Met_10 101 gevVvdvfAGiGpfaipiakyskak.rvlaidlnPesvkylkeniklNkvekvvkpileDgrevir.eqladrvvmnlpk 178
                                    g vVvd f   G   i  a   +++ rv+ +d+nP++v+ +++n+ lN v+++v++  eD+  ++   + +d v ++   
  gi|119719296|ref|YP_919791.1|  58 GLVVVDAFSATGIRGIRYALENEGVgRVILNDINPRAVEIIRQNVDLNGVSDIVEVRREDASSLLAsLSGVDIVDLDPFG 137
                                    6699*****999999999976666448************************************99844556766688889 PP

                                    TGGGGHHHHHHHEEEEEEEE CS
                         Met_10 179 saieFldkvlaalkdggvih 198
                                    s  e++d +l++lk++g+ +
  gi|119719296|ref|YP_919791.1| 138 SPAEYVDPALRCLKHKGLLC 157
                                    99999999999999999877 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   2.4e-07    0.0004       4     113 ..      58     162 ..      56     192 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2.4e-07
                Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgp.kaevvGiDiseeaielArenaqklgld.nveFeqgdiee.leklledekfDlils 80 
                                    gl+v+D+ ++tG  +++ a   ++  ++v++ Di+++a+e  r+n + +g++  ve++++d+ + l +    + +D++  
  gi|119719296|ref|YP_919791.1|  58 GLVVVDAFSATGIRGIRYAL-ENEgVGRVILNDINPRAVEIIRQNVDLNGVSdIVEVRREDASSlLAS---LSGVDIVD- 132
                                    789****************5.4553788***********************989**********4444...47899944. PP

                Methyltransf_31  81 nevlnaladpdkileeiervlkpggilliedpr 113
                                       l+ + +p+++   + r lk +g l+++  +
  gi|119719296|ref|YP_919791.1| 133 ---LDPFGSPAEYVDPALRCLKHKGLLCVTATD 162
                                    ...5799********************999877 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   4.5e-07   0.00073      45     142 ..      61     156 ..      49     161 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 4.5e-07
                                    EEETT-TTSHHHHH.HH.HTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEEEE--S CS
                  Cons_hypoth95  45 vLDlfaGsGalglE.Al.SRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdivflDPP 122
                                    v+D f+ +G  g+  Al   g+ +++l + +++av+i+++n++  ++++ +++ +eda++ l +l    + +div lDP 
  gi|119719296|ref|YP_919791.1|  61 VVDAFSATGIRGIRyALeNEGVGRVILNDINPRAVEIIRQNVDLNGVSDIVEVRREDASSLLASL----SGVDIVDLDPF 136
                                    677788888777753443458999**********************9997777777777777666....457******85 PP

                                    SSTTCH.HHHHHHHHHTT-E CS
                  Cons_hypoth95 123 yakellieevlelleekkll 142
                                        +++  +l+ l++k+ll
  gi|119719296|ref|YP_919791.1| 137 GSPAEYVDPALRCLKHKGLL 156
                                    55555678888888888877 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   3.6e-05     0.059      14      76 ..      73     134 ..      43     158 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.6e-05
                Methyltransf_24  14 llralrrngagrlvavdhdpgaeeaaalare....aglddrvrlikadseealaslaagsiDllfiD 76 
                                    + +al++ g gr++  d +p   +a +++r+    +g++d+v+++++d++++lasl+   +D++ +D
  gi|119719296|ref|YP_919791.1|  73 IRYALENEGVGRVILNDINP---RAVEIIRQnvdlNGVSDIVEVRREDASSLLASLS--GVDIVDLD 134
                                    5678888888**********...999999999999*********************9..47765444 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   3.1e-05      0.05       2      68 ..      62     131 ..      61     154 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.1e-05
                                    EEET-TTSHHHHHHHCTS.TSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEE CS
                Methyltransf_25   2 LdlGcGtGrltlalakrl.gkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlv 68 
                                    +d+   tG   ++ a +  g ++v+  Di+++++e++r++++ +g+   ve+++ da++l    + +D+v
  gi|119719296|ref|YP_919791.1|  62 VDAFSATGIRGIRYALENeGVGRVILNDINPRAVEIIRQNVDLNGVsdIVEVRREDASSLLASLSGVDIV 131
                                    5666667765555544443689*******************99**99999********999888888887 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   7.6e-05      0.12       3      67 ..      60     127 ..      59     142 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.6e-05
                Methyltransf_15   3 vilDlfsGaGGnviqfalv...fekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklkl 67 
                                    v++D+fs +G   i +al+     +vi  +in++ ++++ +N  + gvsd + +   d  +lla+l  
  gi|119719296|ref|YP_919791.1|  60 VVVDAFSATGIRGIRYALEnegVGRVILNDINPRAVEIIRQNVDLNGVSDIVEVRREDASSLLASLSG 127
                                    689*************9997777799****************************99999999988654 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   7.5e-05      0.12     183     217 ..      81     115 ..      52     131 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7.5e-05
                           PrmA 183 gakkvvavDiDevAvkvakeNaelNkveakleval 217
                                    g  +v+  Di++ Av++ ++N++lN+v++ +ev  
  gi|119719296|ref|YP_919791.1|  81 GVGRVILNDINPRAVEIIRQNVDLNGVSDIVEVRR 115
                                    67788899***********************9953 PP

>> DNA_methylase  C-5 cytosine-specific DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   7.8e-05      0.13       8      56 ..      68     116 ..      60     133 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.8e-05
                                    -TT-HHHHHHHHTT-EEEEEEE--TTTHHHHHHH-.-SEEEES-TTTS- CS
                  DNA_methylase   8 aGiGGfrlgleaagfecvaaseidkkaaktYeanfkkvsigDitkidkk 56 
                                     Gi G+r++le+ g+  v+ ++i++ a+++ ++n       Di +++ +
  gi|119719296|ref|YP_919791.1|  68 TGIRGIRYALENEGVGRVILNDINPRAVEIIRQNVDLNGVSDIVEVRRE 116
                                    3999******************************985555555554443 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00015      0.24      35      93 ..      61     122 ..      50     164 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00015
                                    EEEET-TTSHHHHHHHHHTTC.E.EEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTTS CS
                            MTS  35 vlDlGcGaGvlgaalakespeae.vtlvdvdarAlesakenleankle..vevvasdvleev 93 
                                    v+D  + +G+ g+  a e++ +  v l d++ rA+e+ ++n+  n+++  vev+ +d+ + +
  gi|119719296|ref|YP_919791.1|  61 VVDAFSATGIRGIRYALENEGVGrVILNDINPRAVEIIRQNVDLNGVSdiVEVRREDASSLL 122
                                    66777778888888888888876699*********************999999999987755 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00024      0.39      31      80 ..      75     124 ..      66     133 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00024
                Methyltransf_18  31 ylvkegkakkviasDinegplekakeniekagledkievrlsdGleklke 80 
                                    y+++++ + +vi  Din+ ++e  ++n++ +g++d +evr  d  + l +
  gi|119719296|ref|YP_919791.1|  75 YALENEGVGRVILNDINPRAVEIIRQNVDLNGVSDIVEVRREDASSLLAS 124
                                    7889999*********************************9998777664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.54u 0.23s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2725.87
//
Query:       gi|119719297|ref|YP_919792.1|  [L=141]
Description: translation initiation factor IF5 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-30  104.7   0.0      3e-30  104.5   0.0    1.0  1  eIF-5_eIF-2B     Domain found in IF2B/IF5
     0.0023   17.4   0.6     0.0036   16.8   0.6    1.3  1  TF_Zn_Ribbon     TFIIB zinc-binding
     0.0043   17.1   0.5     0.0081   16.2   0.5    1.4  1  Elf1             Transcription elongation factor Elf1 like
     0.0076   16.6   1.1      0.014   15.8   1.1    1.4  1  Lar_restr_allev  Restriction alleviation protein Lar
  ------ inclusion threshold ------
       0.01   15.7   0.2       0.12   12.3   0.0    2.2  2  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
      0.013   15.2   0.7      0.024   14.4   0.7    1.3  1  Ribosomal_S27e   Ribosomal protein S27
      0.033   14.3   0.7      0.055   13.6   0.7    1.3  1  DUF2387          Probable metal-binding protein (DUF2387)
      0.083   13.0   1.2        4.3    7.5   0.1    2.6  2  zf-ACC           Acetyl-coA carboxylase zinc finger domain
       0.13   12.5   0.4       0.19   11.9   0.4    1.3  1  IBR              IBR domain, a half RING-finger domain
       0.48    9.9   2.6         14    5.2   0.2    2.2  2  zf-ribbon_3      zinc-ribbon domain
        0.5   10.6   2.4        1.1    9.5   2.4    1.6  1  Auto_anti-p27    Sjogren's syndrome/scleroderma autoantigen 1
       0.52   10.3   2.8        4.5    7.3   0.2    2.6  3  zinc_ribbon_4    zinc-ribbon domain
        1.7    8.6   5.8        2.7    7.9   0.8    2.3  2  DUF3797          Domain of unknown function (DUF3797)


Domain annotation for each model (and alignments):
>> eIF-5_eIF-2B  Domain found in IF2B/IF5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.5   0.0   2.2e-33     3e-30       5     116 ..      25     134 ..      20     135 .. 0.96

  Alignments for each domain:
  == domain 1  score: 104.5 bits;  conditional E-value: 2.2e-33
                                    CSSSS--SSTT--EEEETT.EEEETTHHHHHHHHTTSHHHHHHHHHHHHTSEEEESETTEEEESSSSSCCHHHHHHHHHH CS
                   eIF-5_eIF-2B   5 edkkerykmpklqvkvegkkktvivNfeeiakaLnrdpehvlkyllkelgtqgsidengrlilngkfeakkleklldkyi 84 
                                    +++ er+ +p+ +v ++gk k+ i+Nf+++a++Lnr+p  +l+++lke++  g + eng+++++g+++a++l+kll+++ 
  gi|119719297|ref|YP_919792.1|  25 RSTGERFVLPTFEVSKTGK-KVYIHNFKDVAEKLNREPPVLLRFILKEIALPGVY-ENGTAVIHGEVSAQTLNKLLERFY 102
                                    46789**************.***********************************.9*********************** PP

                                    HHHTSTSSSTSTCEEECCSSSCEEEEESSSTC CS
                   eIF-5_eIF-2B  85 eeyVlCkeCkspetelekeerllvlkCkaCga 116
                                    +eyV C+ C+ p+t l+ke++l+++kC+aCga
  gi|119719297|ref|YP_919792.1| 103 NEYVKCPVCEAPDTILVKEKKLMYIKCTACGA 134
                                    *******************************7 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.6   2.6e-06    0.0036       2      29 ..     107     136 ..     106     140 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.6e-06
                                    EETTTTCEE.CHEETSTTCE.EESSSSBEE CS
                   TF_Zn_Ribbon   2 kCPnCgstn.lveDpergel.vCtdCGlVl 29 
                                    kCP+C  ++ +++ ++   +  Ct+CG+V 
  gi|119719297|ref|YP_919792.1| 107 KCPVCEAPDtILVKEKKLMYiKCTACGAVS 136
                                    9******998999999999978******96 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.5   5.9e-06    0.0081      14      53 ..      97     134 ..      89     139 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5.9e-06
                           Elf1  14 kkkk.lptkFdCpfCnheksvevkldkkekiaevsCkvCge 53 
                                      ++ ++++ +Cp+C++ +++ vk   ++k  +++C+ Cg+
  gi|119719297|ref|YP_919792.1|  97 LLERfYNEYVKCPVCEAPDTILVK---EKKLMYIKCTACGA 134
                                    45555778889*******999886...556799******97 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   1.1   9.9e-06     0.014       5      37 ..     107     135 ..     103     140 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 9.9e-06
                Lar_restr_allev   5 pCPfCggravlersqrvvaeigqcvyCadCgas 37 
                                     CP C  ++++   +++      ++ C+ Cga+
  gi|119719297|ref|YP_919792.1| 107 KCPVCEAPDTILVKEKKLM----YIKCTACGAV 135
                                    7**********99999998....*********4 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1      0.34   4.7e+02      27      33 ..     107     113 ..     100     116 .. 0.67
   2 ?   12.3   0.0   8.4e-05      0.12       5      20 ..     120     135 ..     119     140 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.34
                        DUF35_N  27 vCphCgs 33 
                                     Cp C +
  gi|119719297|ref|YP_919792.1| 107 KCPVCEA 113
                                    6888865 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 8.4e-05
                        DUF35_N   5 aegrLvgqrCpdCGtv 20 
                                    +e +L++ +C++CG+v
  gi|119719297|ref|YP_919792.1| 120 KEKKLMYIKCTACGAV 135
                                    5789**********99 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.7   1.7e-05     0.024       8      35 ..     106     135 ..     101     139 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.7e-05
                                    EE-TTTS-EEEEESS-S..S-EEESSSTCE CS
                 Ribosomal_S27e   8 vkCpdCenetvvFshaa..tvvkCisCgkv 35 
                                    vkCp Ce+  ++  + +   ++kC  Cg v
  gi|119719297|ref|YP_919792.1| 106 VKCPVCEAPDTILVKEKklMYIKCTACGAV 135
                                    9*******9998866551268*******86 PP

>> DUF2387  Probable metal-binding protein (DUF2387)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.7     4e-05     0.055      10      37 ..     107     133 ..     100     139 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4e-05
                        DUF2387  10 vCPrCsemDkirmweedeveyrECvsCg 37 
                                     CP C++ D+i + +e +  y+ C++Cg
  gi|119719297|ref|YP_919792.1| 107 KCPVCEAPDTILV-KEKKLMYIKCTACG 133
                                    6**********87.777899*******9 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1     0.047        64       2       9 ..     106     113 ..     105     114 .. 0.85
   2 ?    7.5   0.1    0.0031       4.3       2      10 ..     127     135 ..     126     135 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.047
                         zf-ACC   2 tKCpsCge 9  
                                    +KCp C++
  gi|119719297|ref|YP_919792.1| 106 VKCPVCEA 113
                                    79**9987 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0031
                         zf-ACC   2 tKCpsCgem 10 
                                    +KC++Cg++
  gi|119719297|ref|YP_919792.1| 127 IKCTACGAV 135
                                    8******86 PP

>> IBR  IBR domain, a half RING-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.4   0.00014      0.19       8      45 ..      94     133 ..      88     136 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00014
                            IBR   8 lkksles.dpnlkwCprpdCe...aiieksegcksvtCskCg 45 
                                    l+k le   +++++Cp   Ce   +i+ k+++  +++C+ Cg
  gi|119719297|ref|YP_919792.1|  94 LNKLLERfYNEYVKCP--VCEapdTILVKEKKLMYIKCTACG 133
                                    66777777778*****..89855566688888999******8 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.2     0.012        17       2      11 ..     105     114 ..     104     116 .. 0.80
   2 ?    5.2   0.2      0.01        14       3      11 ..     127     135 ..     125     140 .. 0.65

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.012
                    zf-ribbon_3   2 tvrCPnCGap 11 
                                    +v+CP C ap
  gi|119719297|ref|YP_919792.1| 105 YVKCPVCEAP 114
                                    689****887 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.01
                    zf-ribbon_3   3 vrCPnCGap 11 
                                    ++C +CGa+
  gi|119719297|ref|YP_919792.1| 127 IKCTACGAV 135
                                    566666664 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   2.4    0.0008       1.1      18      40 .]     108     133 ..     106     133 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0008
                  Auto_anti-p27  18 CpvC...gvPLmrdrkggkvyCvaCd 40 
                                    CpvC    ++L++++k   + C aC+
  gi|119719297|ref|YP_919792.1| 108 CPVCeapDTILVKEKKLMYIKCTACG 133
                                    ***************888999****6 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       3.2   4.5e+03      12      26 ..      31      45 ..      29      45 .. 0.76
   2 ?    2.4   0.1      0.11   1.5e+02      26      32 ..     106     112 ..     105     116 .. 0.68
   3 ?    7.3   0.2    0.0033       4.5       1      11 [.     125     135 ..     119     139 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.2
                  zinc_ribbon_4 12 yeiddeklpakgvkv 26
                                   + ++   ++++g+kv
  gi|119719297|ref|YP_919792.1| 31 FVLPTFEVSKTGKKV 45
                                   667777889999987 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.11
                  zinc_ribbon_4  26 vrCskCg 32 
                                    v+C+ C 
  gi|119719297|ref|YP_919792.1| 106 VKCPVCE 112
                                    5666664 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0033
                  zinc_ribbon_4   1 MkitCpsCkak 11 
                                    M i C +C+a+
  gi|119719297|ref|YP_919792.1| 125 MYIKCTACGAV 135
                                    66666666664 PP

>> DUF3797  Domain of unknown function (DUF3797)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.8     0.002       2.7      11      20 ..     103     112 ..      92     118 .. 0.80
   2 ?    3.3   0.3     0.056        77       8      20 ..     118     133 ..     114     136 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.002
                        DUF3797  11 ekYvqCPeCg 20 
                                    + Yv+CP+C 
  gi|119719297|ref|YP_919792.1| 103 NEYVKCPVCE 112
                                    35*******6 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.056
                        DUF3797   8 kLdek...YvqCPeCg 20 
                                       ek   Y++C  Cg
  gi|119719297|ref|YP_919792.1| 118 LVKEKklmYIKCTACG 133
                                    45555689*******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      603  (0.0336327); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1089.44
//
Query:       gi|119719298|ref|YP_919793.1|  [L=196]
Description: hypothetical protein Tpen_0381 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-13   51.8   0.0    1.6e-13   51.1   0.0    1.3  1  Peptidase_C92  Permuted papain-like amidase enzyme, YaeF/YiiX
    1.6e-06   28.1   0.0    5.2e-05   23.2   0.0    2.2  2  NLPC_P60       NlpC/P60 family
     0.0029   17.9   0.0     0.0039   17.5   0.0    1.3  1  LRAT           Lecithin retinol acyltransferase
  ------ inclusion threshold ------
        0.1   12.3   0.2        2.2    7.9   0.1    2.0  2  DUF1287        Domain of unknown function (DUF1287)
       0.13   11.9   0.3       0.25   11.0   0.3    1.4  1  DSX_dimer      Doublesex dimerisation domain


Domain annotation for each model (and alignments):
>> Peptidase_C92  Permuted papain-like amidase enzyme, YaeF/YiiX, C92 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.1   0.0   4.4e-17   1.6e-13       2     166 ..      44     191 ..      43     192 .. 0.85

  Alignments for each domain:
  == domain 1  score: 51.1 bits;  conditional E-value: 4.4e-17
                  Peptidase_C92   2 lekGdiifqtsraslseainpatasefkHvgivvgeegderlvveaaakegvrvtpLseflar.rssiavyrlkealtae 80 
                                    l++Gdii+++ +      i+p   ++++H+ +++g+     +vv+a  + gv v+++ + +++  s++ +yr+k++    
  gi|119719298|ref|YP_919793.1|  44 LQPGDIILTRGK---LASIIP---GYYSHAILYIGN----GMVVHA-VSDGVVVQSIYDAISSdVSAVGIYRVKTS--SY 110
                                    689*****9994...457899...9*****999986....489***.699*******9999988999********7..68 PP

                  Peptidase_C92  81 qrqkaaeaalrrlgkpYdfgFele.......ddrlYCsklVakaykealgikvktvellgklllknpdsklklleletvl 153
                                     +  a++ al+++g pYd+++ +         +++YCs+lV+++y   l +  +++ +   ++l         ++ + v+
  gi|119719298|ref|YP_919793.1| 111 IKLAAVQWALSKVGYPYDYSWLVYpggkqvyGSSYYCSELVWASY---LAVGGPDLDANPGFTL---------KYGYNVA 178
                                    8999****************9887777777789************...4455677777777777.........5678999 PP

                  Peptidase_C92 154 pqslaespalelv 166
                                    pq++a+++ ++lv
  gi|119719298|ref|YP_919793.1| 179 PQEIADDNDVYLV 191
                                    ****999999887 PP

>> NLPC_P60  NlpC/P60 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   1.4e-08   5.2e-05      43      97 ..      37      95 ..       8     103 .. 0.83
   2 ?    2.9   0.0     0.032   1.1e+02      12      44 ..     143     176 ..     127     190 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1.4e-08
                                   EE..EEGGG--TTEEEEESG......TGGESEEEEEEETTEEEEEETTEEEEEETTSTTBH CS
                       NLPC_P60 43 kkkeiskselkrGDLvffkt......kkgisHvgiYlgngkmlhassekvsvsslsekywk 97
                                    k  i  s l++GD++++++       +  sH+ +Y+gng+++ha s++v v+s++ ++++
  gi|119719298|ref|YP_919793.1| 37 YK--IDLSLLQPGDIILTRGklasiiPGYYSHAILYIGNGMVVHAVSDGVVVQSIYDAISS 95
                                   44..888999*********98887777889***********************99988765 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.032
                                    TEB-HHHHHHHHHHTT.T----SSHHHHCCCSEE CS
                       NLPC_P60  12 sgfDCsglvryafaka.gielprssgeqeaagkk 44 
                                    s + Cs lv +++  + g +l  ++g + ++g +
  gi|119719298|ref|YP_919793.1| 143 SSYYCSELVWASYLAVgGPDLDANPGFTLKYGYN 176
                                    4778************999999998888666666 PP

>> LRAT  Lecithin retinol acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.1e-06    0.0039       4      46 ..      52      97 ..      43     140 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.1e-06
                                   -TT-EEEEE-SSSEEEEEEEETTEEEEEE-SB..........-GCG CS
                           LRAT  4 krGdllevsRtlyeHhgiyvGdgkVvHltpes...tsekskieksv 46
                                    rG l ++    y+H  +y+G+g+VvH   +    +s  ++i++ v
  gi|119719298|ref|YP_919793.1| 52 TRGKLASIIPGYYSHAILYIGNGMVVHAVSDGvvvQSIYDAISSDV 97
                                   456666677799****************988844433333333322 PP

>> DUF1287  Domain of unknown function (DUF1287)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.029     1e+02     104     163 ..      42     104 ..      26     105 .. 0.66
   2 ?    7.9   0.1   0.00061       2.2       4      50 ..     115     163 ..     112     167 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.029
                        DUF1287 104 edeyqpGdivvfkleekleHigivsdkrekkgvplvihnigagqkeedlle....kskitghyr 163
                                    +   qpGdi++ + +  +   g  s+     g+ +v+h +++g   +++      + + +g yr
  gi|119719298|ref|YP_919793.1|  42 SL-LQPGDIILTRGKLASIIPGYYSHAILYIGNGMVVHAVSDGVVVQSIYDaissDVSAVGIYR 104
                                    44.89*****999744444446677777777999999998888775555433334566666666 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00061
                        DUF1287   4 arkevekkvkYdskYvkigYPnGd.vpeeeGvCtDvviralrka.gidL 50 
                                    a + + +kv Y  +Y  + YP+G  v  ++  C+ +v+ ++ ++ g dL
  gi|119719298|ref|YP_919793.1| 115 AVQWALSKVGYPYDYSWLVYPGGKqVYGSSYYCSELVWASYLAVgGPDL 163
                                    5566678999***********99537788889********998855565 PP

>> DSX_dimer  Doublesex dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.3     7e-05      0.25       8      26 ..     116     134 ..     110     142 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 7e-05
                      DSX_dimer   8 aqWlleklGyPWemmPlmy 26 
                                     qW l k+GyP++   l+y
  gi|119719298|ref|YP_919793.1| 116 VQWALSKVGYPYDYSWLVY 134
                                    5***********9988888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1358.21
//
Query:       gi|119719299|ref|YP_919794.1|  [L=198]
Description: hypothetical protein Tpen_0382 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       695  (0.038764); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1536.83
//
Query:       gi|119719300|ref|YP_919795.1|  [L=186]
Description: phosphoribosyltransferase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.5e-27   94.9   0.0    4.9e-27   94.4   0.0    1.1  1  Pribosyltran  Phosphoribosyl transferase domain
    1.2e-05   24.9   0.0    1.6e-05   24.4   0.0    1.1  1  UPRTase       Uracil phosphoribosyltransferase
     0.0085   15.6   0.0      0.011   15.3   0.0    1.2  1  PRTase_2      Phosphoribosyl transferase
  ------ inclusion threshold ------
       0.18   11.7   0.0       0.27   11.1   0.0    1.2  1  Colicin       Colicin pore forming domain


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.4   0.0   1.1e-30   4.9e-27      14     151 ..      17     148 ..       8     155 .. 0.85

  Alignments for each domain:
  == domain 1  score: 94.4 bits;  conditional E-value: 1.1e-30
                                    EEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE.........EE----TTSEEEE CS
                   Pribosyltran  14 avarlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaar.gssdesrlledpagkkVli 92 
                                    +  +l+++i+e+ +++pd++v+iargG++++ il+d L v+ a+ +  k+++++++   r +++ e  l  d++g+kVl+
  gi|119719300|ref|YP_919795.1|  17 DSVQLSKKIIEN-GYRPDILVAIARGGWVLGRILSDLLSVRDAVALTMKFYEEVGSHKERpVLVQE--LNVDLRGRKVLL 93 
                                    6667999*****.**************************997766666666665555555055554..************ PP

                                    E-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-HHHHHHHHHH-TTS.....EEEEEE CS
                   Pribosyltran  93 VDDildtGgTllaalelLkekgpeevriavlvdkpateeevdknakrvfslspdnfvav 151
                                    VDDi+d+G Tl++a+++L++++p evr+a+l+ k  + +++d+++k++     ++ v++
  gi|119719300|ref|YP_919795.1|  94 VDDIVDSGATLREAVNHLRKAEPLEVRTATLYVKTWSPFKPDFYVKELS----EWVVFP 148
                                    *******************************************999887....777765 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   3.6e-09   1.6e-05      70     147 ..      34     114 ..      20     126 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 3.6e-09
                        UPRTase  70 alVpilRaGegmeealrellpearvghlglqree...etlepveyynkLPkkiaertvlllDpviaTGgsaaaaiqlLke 146
                                    +lV+i R+G  + + l++ll     + l ++  e   +++e    ++ L  +++ r+vll+D ++ +G+++ +a+++L++
  gi|119719300|ref|YP_919795.1|  34 ILVAIARGGWVLGRILSDLLSVRDAVALTMKFYEevgSHKERPVLVQELNVDLRGRKVLLVDDIVDSGATLREAVNHLRK 113
                                    68*****************88775555555443311223344467889*******************************9 PP

                        UPRTase 147 r 147
                                    +
  gi|119719300|ref|YP_919795.1| 114 A 114
                                    5 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   2.4e-06     0.011      87     150 ..      57     117 ..      37     144 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.4e-06
                       PRTase_2  87 ekvagveelleFeEeHSHAtdhllyaedeellaaakelvLvDDEistGktalnliralqeklpr 150
                                    ++v  + ++  +eE  SH  + +l++e +  l++ ++++LvDD + +G t+ + +++l+++ p 
  gi|119719300|ref|YP_919795.1|  57 DAV--ALTMKFYEEVGSHKERPVLVQELNVDLRG-RKVLLVDDIVDSGATLREAVNHLRKAEPL 117
                                    444..23334457778999999999888777765.6699*******************998775 PP

>> Colicin  Colicin pore forming domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   6.1e-05      0.27       9      65 ..      55     109 ..      50     122 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 6.1e-05
                        Colicin   9 lkdavkfiidfyekvtkklGekakelarelaedarGkkirslsdalksfekikrnln 65 
                                    ++dav ++++fye+v  +  +    l +el  d+rG+k+  ++d + s    ++++n
  gi|119719300|ref|YP_919795.1|  55 VRDAVALTMKFYEEVGSH--KERPVLVQELNVDLRGRKVLLVDDIVDSGATLREAVN 109
                                    79*************998..566789*************999999888777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1443.73
//
Query:       gi|119719301|ref|YP_919796.1|  [L=331]
Description: translation initiation factor IF-2B subunit delta [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-81  274.2   0.3    1.3e-81  274.0   0.3    1.0  1  IF-2B     Initiation factor 2 subunit family


Domain annotation for each model (and alignments):
>> IF-2B  Initiation factor 2 subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  274.0   0.3     7e-86   1.3e-81       1     282 []      24     302 ..      24     302 .. 0.97

  Alignments for each domain:
  == domain 1  score: 274.0 bits;  conditional E-value: 7e-86
                                    SS-SHHHHHHHHHHHHHHHHHHCCCSTHHHHHHHHHHHHHHHHTSSTS-HHHHHHHHHHHHHHHCCTTTSSHHHHHHHHH CS
                          IF-2B   1 kvrGspaiaiaalevllevikdaktskvaeLkeelrkaidlLkkarPtavslgnairrllkeiselksssdvkeakksli 80 
                                    ++rG+ +ia aa+e+l++++ +++ +  +e+ke++ k ++lL ++rPtavsl na++++  + ++     ++++a++ ++
  gi|119719301|ref|YP_919796.1|  24 EIRGAGRIAKAAAEALRIAALKYEGESCEEFKEYMLKVAELLVSTRPTAVSLPNAVNYVVSQ-LKKPGIDSLEKARSLVV 102
                                    589**********************************************************4.555666778999999** PP

                                    HHHHHHHHHHHHHHHHHHHHHHTTC-TTEEEEEES--SHHHHHHHHHHHTTEEEEEEEEEXTTTTHHHTHHHHHHHTTXE CS
                          IF-2B  81 ekikelikeieeadekigdiaaelikdgdtilTicnsktvlevlraaakekkkfkVivvEsrPrlqGrltakeLvqagip 160
                                    +++ ++i+ + +a  ki++++++ i dgdtilT+cns +++++l  a+k++k+++V+++E+rP++qG  ta++L ++g+ 
  gi|119719301|ref|YP_919796.1| 103 SRASRFIEYADQALSKISEFGEKVIRDGDTILTHCNSAAATGILVLAHKKGKDITVYATETRPKFQGYITAESLLREGVR 182
                                    ******************************************************************************** PP

                                    EEEEEGGGHHHHHHCTESEEEEEXSEEETTSEEEEETTHHHHHHHHHHTTXEEEEEXXGGGBESTSSSGGGSSXXBEXTH CS
                          IF-2B 161 vtlitdsavayvmseevdkvivGAdrilenGaiankiGTsslAvlAkefnipvlvvaeslkfservqldedifieerdpe 240
                                    v +i+ sav+ +m++ +dkv+vGAd++++nGa++nk+GTs +A++A+e+ i+++v++e++kfs+ + +++ + ie+r++ 
  gi|119719301|ref|YP_919796.1| 183 VRIIPESAVRSIMKR-IDKVVVGADTVAANGAVVNKVGTSLIALAARERGIDFFVATETFKFSPFTLIGDIVPIEFRAET 261
                                    ***************.**************************************************************** PP

                                    HHHEETTEESSTTTEEEEEBSEEEEEGGGXSEEEETTEEEXC CS
                          IF-2B 241 ellnitgeriaeeelkvvnpafDvtPpelItliITevGvlpp 282
                                    e++  +     + +l+v+npafDvtPp++It+iITe+G++pp
  gi|119719301|ref|YP_919796.1| 262 EIVDEEMLARHP-KLRVLNPAFDVTPPDFITGIITEIGIIPP 302
                                    ****99988878.***************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 2544.12
//
Query:       gi|119719302|ref|YP_919797.1|  [L=319]
Description: initiation factor 2B related [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-53  181.0   0.2    3.2e-53  180.8   0.2    1.1  1  IF-2B     Initiation factor 2 subunit family


Domain annotation for each model (and alignments):
>> IF-2B  Initiation factor 2 subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.8   0.2   1.8e-57   3.2e-53       7     282 .]      19     283 ..      13     283 .. 0.88

  Alignments for each domain:
  == domain 1  score: 180.8 bits;  conditional E-value: 1.8e-57
                                    HHHHHHHHHHHHHHHHCCCSTHHHHHHHHHHHHHHHHTSSTS-HHHHHHHHHHHHHHHCCTTTSSHHHHHHHHHHHHHHH CS
                          IF-2B   7 aiaiaalevllevikdaktskvaeLkeelrkaidlLkkarPtavslgnairrllkeiselksssdvkeakksliekikel 86 
                                    ++ i al +l +v+k+++        +   + ++ +  +r t+  l+n +r +l e+ + +++s v e  ++  ++ ++ 
  gi|119719302|ref|YP_919797.1|  19 ETVIYALDLLNTVVKQKD-------PSLFIEVTEKILRSRVTSAMLQNIMRIILGELVAAQPRSFV-ELGEAFQKQYERA 90 
                                    555666666666666666.......3444566788999*****************98877777655.5555666666666 PP

                                    HHHHHHHHHHHHHHHHTTC-TTEEEEEES--SHHHHHHHHHHHTTEEEEEEEEEXTTTTHHHTHHHHHHHTTXEEEEEEG CS
                          IF-2B  87 ikeieeadekigdiaaelikdgdtilTicnsktvlevlraaakekkkfkVivvEsrPrlqGrltakeLvqagipvtlitd 166
                                    +++ +e  e  + ia+ +i++gd++lT ++s  v +++++a +++k++kV+v+EsrP  +G  +a eL++ g+++ li+d
  gi|119719302|ref|YP_919797.1|  91 TSRLREDVERSASIASRRISNGDVLLTNSYSLFVKKTIEKALRDGKELKVYVTESRPTGEGVRFAAELADMGVDTYLIVD 170
                                    666666666667889***************************************************************** PP

                                    GGHHHHHHCTESEEEEEXSEEETTSEEEEETTHHHHHHHHHHTTXEEEEEXXGGGBESTSSSGGGSSXXBEXTHHHHEET CS
                          IF-2B 167 savayvmseevdkvivGAdrilenGaiankiGTsslAvlAkefnipvlvvaeslkfservqldedifieerdpeellnit 246
                                    sa++++m+e vdkv+   ++i +nGa++nk+GTs +A++A+e+++ v+vv  +lkfs+++ ++e + i e +  e ++  
  gi|119719302|ref|YP_919797.1| 171 SAARFFMKE-VDKVLFSSEAISANGAVVNKVGTSLIALAAHEARVRVYVVSSTLKFSPETIIGELVEIPEIEFTEYIPSG 249
                                    *********.********************************************************99999999999999 PP

                                    TEESSTTTEEEEEBSEEEEEGGGXSEEEETTEEEXC CS
                          IF-2B 247 geriaeeelkvvnpafDvtPpelItliITevGvlpp 282
                                     e+   ++lk ++p+fDvtPp++I++iITe+Gv++p
  gi|119719302|ref|YP_919797.1| 250 WENL--RKLKPRSPLFDVTPPSYIDAIITEKGVIAP 283
                                    9887..78*************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       668  (0.0372581); expected 358.6 (0.02)
Passed bias filter:                      588  (0.032796); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2350.37
//
Query:       gi|119719303|ref|YP_919798.1|  [L=275]
Description: ribose-phosphate pyrophosphokinase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-16   59.8   0.0      8e-16   58.0   0.0    1.8  2  Pribosyltran_N  N-terminal domain of ribose phosphate pyropho
    6.1e-11   42.1   0.2    4.3e-10   39.3   0.1    2.1  2  Pribosyltran    Phosphoribosyl transferase domain
      2e-09   37.7   0.7    5.1e-08   33.2   0.2    2.4  3  Pribosyl_synth  Phosphoribosyl synthetase-associated domain
  ------ inclusion threshold ------
      0.016   14.7   0.0      0.027   14.0   0.0    1.3  1  PRTase_2        Phosphoribosyl transferase
       0.11   11.9   0.1       0.28   10.6   0.0    1.6  2  UPRTase         Uracil phosphoribosyltransferase


Domain annotation for each model (and alignments):
>> Pribosyltran_N  N-terminal domain of ribose phosphate pyrophosphokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.0   0.0   2.2e-19     8e-16      20     114 ..       2      97 ..       1      98 [. 0.95
   2 ?   -1.0   0.0      0.47   1.7e+03      19      56 ..     163     199 ..     146     224 .. 0.59

  Alignments for each domain:
  == domain 1  score: 58.0 bits;  conditional E-value: 2.2e-19
                 Pribosyltran_N  20 lgvelgkakvsrfadgEikveieesvrgkdvfiiqslskpvndnlmelllmidalrrasakritaViPylgysrqdrk.k 98 
                                    lg++   a+v+ f+dgE +v++ + +++++v +++   + +n++l e +l ++ lr++ a+++++V Pyl+y rqd + +
  gi|119719303|ref|YP_919798.1|   2 LGLKYEVARVRSFPDGELYVRLPQGLKDEEVAYVVCYGRRPNEALAETVLAVEGLREKGAEKVVLVAPYLPYLRQDAEfT 81 
                                    5666777899********************************************************************** PP

                 Pribosyltran_N  99 srepisaklvaklLea 114
                                    + e +s++++a+lL +
  gi|119719303|ref|YP_919798.1|  82 PGEVVSSRVIARLLAK 97 
                                    *************986 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.47
                 Pribosyltran_N  19 rlgvelgkakvsrfadgEikveieesvrgkdvfiiqsl 56 
                                     +g +    + +r+ d+ ++v+     rg++ +i+ ++
  gi|119719303|ref|YP_919798.1| 163 TIGAPYFVFEKQRMGDEIVSVT-GAVKRGETAVIVDDI 199
                                    5555555555444444333332.333356666666555 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.11   4.1e+02     106     124 ..      52      70 ..      47      86 .. 0.82
   2 !   39.3   0.1   1.2e-13   4.3e-10      14     124 ..     128     227 ..     115     262 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.11
                                    HHHHHHCC-BSEEEEEEEE CS
                   Pribosyltran 106 alelLkekgpeevriavlv 124
                                    a+e L+ekg+e+v +++++
  gi|119719303|ref|YP_919798.1|  52 AVEGLREKGAEKVVLVAPY 70 
                                    8999*******99888876 PP

  == domain 2  score: 39.3 bits;  conditional E-value: 1.2e-13
                                    EEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE----TTSEEEEE CS
                   Pribosyltran  14 avarlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdesrlledpagkkVliV 93 
                                     +  l+a  +++ ++   vvv+++  +  +ak  ad +++p+++ +k++  ++  +++           + ++g++ +iV
  gi|119719303|ref|YP_919798.1| 128 SAMPLLAAFFQK-EHGTGVVVAPDEEAERWAKTFADTIGAPYFVFEKQRMGDEIVSVTG----------AVKRGETAVIV 196
                                    555555555555.56667*****************************999998888885..........679******** PP

                                    -SEESSSHHHHHHHHHHHCC-BSEEEEEEEE CS
                   Pribosyltran  94 DDildtGgTllaalelLkekgpeevriavlv 124
                                    DDi++tGgTl ++++ L e+g   + ++v +
  gi|119719303|ref|YP_919798.1| 197 DDIVSTGGTLGEVAQKLLEAGFRDIYACVTH 227
                                    ***************9999998855555544 PP

>> Pribosyl_synth  Phosphoribosyl synthetase-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.051   1.8e+02      99     120 ..      49      70 ..      44     112 .. 0.72
   2 ?   -2.4   0.0       1.2   4.2e+03       5      24 ..     144     163 ..     141     172 .. 0.88
   3 !   33.2   0.2   1.4e-11   5.1e-08      75     148 ..     181     255 ..     170     274 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.051
                                    HHHHHHHHHHTT--EEEEEEEE CS
                 Pribosyl_synth  99 fvaaaevlkerGaykiyvlath 120
                                     v a e l+e+Ga k++ +a +
  gi|119719303|ref|YP_919798.1|  49 TVLAVEGLREKGAEKVVLVAPY 70 
                                    5778999*********999865 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.2
                                    EEEEESSGGGHHHHHHHHHH CS
                 Pribosyl_synth   5 avivakspgsakkatsyaer 24 
                                     v+va + ++ + a+++a+ 
  gi|119719303|ref|YP_919798.1| 144 GVVVAPDEEAERWAKTFADT 163
                                    5999999999999****996 PP

  == domain 3  score: 33.2 bits;  conditional E-value: 1.4e-11
                                    --EES--T.TSEEEEEEEEE-S-HHHHHHHHHHHHTT--EEEEEEEEE---TTHHHHHHHSS--EEEEESSS--H CS
                 Pribosyl_synth  75 ltvvGdvg.GriaiivddliddvesfvaaaevlkerGaykiyvlathGllssdaprlleesaidevvvtntiphe 148
                                    ++v G v+ G  a+ivdd++    ++ + a+ l e G   iy+ +th ll +da +++  s ++e + t+++ + 
  gi|119719303|ref|YP_919798.1| 181 VSVTGAVKrGETAVIVDDIVSTGGTLGEVAQKLLEAGFRDIYACVTHALLVQDAEARIFGSGVKEFISTDSVHNP 255
                                    5678888549************************************************************99765 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   7.6e-06     0.027     117     158 ..     186     227 ..     179     245 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.6e-06
                       PRTase_2 117 llaaakelvLvDDEistGktalnliralqeklprkryvvvsl 158
                                    ++++ ++ v+vDD +stG t+ +++++l e+  r+ y++v+ 
  gi|119719303|ref|YP_919798.1| 186 AVKRGETAVIVDDIVSTGGTLGEVAQKLLEAGFRDIYACVTH 227
                                    56778899**********************999998888874 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       2.1   7.5e+03     110     124 ..      18      32 ..      15      36 .. 0.72
   2 ?   10.6   0.0   7.9e-05      0.28     122     150 ..     191     219 ..     175     239 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 2.1
                        UPRTase 110 eyynkLPkkiaertv 124
                                    e y +LP+ +++++v
  gi|119719303|ref|YP_919798.1|  18 ELYVRLPQGLKDEEV 32 
                                    679999999955554 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 7.9e-05
                        UPRTase 122 rtvlllDpviaTGgsaaaaiqlLkergvg 150
                                    +t++++D +++TGg++ ++ q+L+e+g++
  gi|119719303|ref|YP_919798.1| 191 ETAVIVDDIVSTGGTLGEVAQKLLEAGFR 219
                                    689**********************8875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1764.71
//
Query:       gi|119719304|ref|YP_919799.1|  [L=106]
Description: hypothetical protein Tpen_0387 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 812.66
//
Query:       gi|119719305|ref|YP_919800.1|  [L=259]
Description: RNase P/RNase MRP subunit p30-like [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-15   57.5   0.0    1.5e-15   57.3   0.0    1.1  1  RNase_P_p30  RNase P subunit p30
  ------ inclusion threshold ------
      0.037   14.7   0.0      0.067   13.8   0.0    1.4  1  Bin3         Bicoid-interacting protein 3 (Bin3)


Domain annotation for each model (and alignments):
>> RNase_P_p30  RNase P subunit p30
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.3   0.0   1.7e-19   1.5e-15      21     201 ..      37     217 ..      20     232 .. 0.77

  Alignments for each domain:
  == domain 1  score: 57.3 bits;  conditional E-value: 1.7e-19
                                    HHHHHH-SEEEEEEEEEESS---HHHHH.......HHHHHHHH....HHSSEEEEEEES-H..HHHHHHHHH--EEEEE- CS
                    RNase_P_p30  21 tlaelgytgvainftveaekekkpnasepikeelkelkkelsg..lkllsRvtlvvsdpskl.qrlskvrqkfdllavrP 97 
                                    ++++ gy+g ++   v  ++ +   +    +++++e+  +l++  ++ +sR+ l +s +s l ++l+ +r  fd+++v+ 
  gi|119719305|ref|YP_919800.1|  37 RARKAGYHGCVFVARVGNQEWSLYRE----AKRFDETARKLREsgIECYSRCHLQISAQSLLkKALRMLRPLFDVISVEA 112
                                    56677777555555555333333333....335555555555555***************666***************** PP

                                    -SHHHHHHHHHT.T-SEEE-TTTTSSS-S--HHHHHHHHHHT-EEEEESHHHHHS-H.HHHHHHHHHHHHHHH.HHHH.- CS
                    RNase_P_p30  98 ttekalraacenldvDiisidltsrlpfglkhktiraAvergvafEinyspllrdsg.laRrnfisnarkllr.ltrg.k 174
                                     t ++  +   +++vD+i+++ ++  p +lk   i   +++g ++Ei++   + +      +  ++++r+ ++ l+++  
  gi|119719305|ref|YP_919800.1| 113 ETRAITAFGSRDHRVDLITLPQRN-IPEILK-GDIDEILKQGKFVEITLDRFFLGGSkPLDVAQVARVRETVKpLVDKgV 190
                                    **********************75.888776.679****************9887763344566777777665355556* PP

                                    -EEEE--BSSGGG---HHHHHHHHHHH CS
                    RNase_P_p30 175 gvviSSgAesplelRnpydiinLlktl 201
                                    g+viSSg++sp++ R p+ +i++++++
  gi|119719305|ref|YP_919800.1| 191 GIVISSGPSSPYSPRDPRAVISFGEVF 217
                                    ***********************9875 PP

>> Bin3  Bicoid-interacting protein 3 (Bin3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   7.5e-06     0.067      18      62 ..      23      73 ..      21     120 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.5e-06
                           Bin3 18 gDeglkrlfkkiyellkpgGv....li..lEpqewksYkkkkklseelken 62
                                    D+ l++lf++iy+  ++ G+    ++  +  qew+ Y+++k+ +e++++ 
  gi|119719305|ref|YP_919800.1| 23 RDDELLSLFREIYARARKAGYhgcvFVarVGNQEWSLYREAKRFDETARKL 73
                                   5999***********99966555447755678***********98887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1805.97
//
Query:       gi|119719306|ref|YP_919801.1|  [L=150]
Description: hypothetical protein Tpen_0389 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-35  121.9   0.4      2e-35  121.6   0.4    1.1  1  RNA_binding  RNA binding


Domain annotation for each model (and alignments):
>> RNA_binding  RNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.6   0.4   1.1e-39     2e-35       2     117 ..       4     124 ..       3     126 .. 0.97

  Alignments for each domain:
  == domain 1  score: 121.6 bits;  conditional E-value: 1.1e-39
                                    EEEEEEE-TTC-HHHHHHHHHTTSTTS.....E---EEEEEE-CCC-EEEEEEEEESSHHH.HHHHHHHHHHHCCCCHHH CS
                    RNA_binding   2 ievrafvhaTEdeekVlealsnllpee.....eveieeeeaeGhygnpitileaelekkka.kkvlkkllellreeeike 75 
                                    +e+++fvhaTEdee+Vl+a+sn+lpe      ev ++++ + G++gn it++++ ++++ + ++++++++++++e+++++
  gi|119719306|ref|YP_919801.1|   4 LELSTFVHATEDEERVLQAVSNVLPERmrgslEVYLSKNVVLGYHGNAITVMKFFIDEEVEaQEAFEHIVRRMEESDFNY 83 
                                    689**********************99***999899******************************************** PP

                                    HHHCCHCCB-TTSEEEEEEEHHHHHTT---BESSSSEEEEEE CS
                    RNA_binding  76 LlkeleervdekgklylrldKQaaylgklslvegddvIkvki 117
                                    +l++le+r++ +g++ylr+dKQ+aylg+++++egddvI+v++
  gi|119719306|ref|YP_919801.1|  84 FLDSLEDRFE-HGRIYLRVDKQEAYLGNIRISEGDDVIRVTA 124
                                    **********.****************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1071.93
//
Query:       gi|119719307|ref|YP_919802.1|  [L=187]
Description: 50S ribosomal protein L15e [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.8e-64  214.6   2.7    1.3e-63  214.2   2.7    1.1  1  Ribosomal_L15e  Ribosomal L15


Domain annotation for each model (and alignments):
>> Ribosomal_L15e  Ribosomal L15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  214.2   2.7   7.1e-68   1.3e-63       1     156 [.       2     155 ..       2     167 .. 0.96

  Alignments for each domain:
  == domain 1  score: 214.2 bits;  conditional E-value: 7.1e-68
                                    -SHHHHHHHTTSTTSHHHHHHHHHHHHHHTTS-SEEEESS-SSHHHHHHHT--SSTTEEEEEEEEE-SS---..---SS- CS
                 Ribosomal_L15e   1 gaykylrelwkkkqsdvlrellrerlweyrqepavvrverptrldrArrLGYkakqGivvvrvrvrrGgrkkkvskgktg 80 
                                    g+yky++e+wk++ + ++ +l+rer++ +r+ep+vvr+ rptr++rAr+LGYkakqG++v+rvrvr+Gg ++  ++  +g
  gi|119719307|ref|YP_919802.1|   2 GYYKYMAEIWKRPFKGEHGQLMRERFMLWRREPTVVRIPRPTRINRARALGYKAKQGYIVARVRVRKGGLNR--PRPSSG 79 
                                    68**********************************************************************..****** PP

                                    --GGGG-SSS---SS-HHHHHHHHHHHHSTTSEEEEEEEEEEESSEEEEEEEEE-TTSHHHHT-TTTGGGGSGGGT CS
                 Ribosomal_L15e  81 rkpkrqgvnklkpakslqaiaeervgrklpnlrvLnSYwvgeDgtykyyEvilvDpshkairndkkinwickkvhk 156
                                    r+pkr+gv+ ++p+ks q+iaeer++rk+pnl vL+SY+vgeDg yk+yEv++vDp+h+a+++d + +w++  ++k
  gi|119719307|ref|YP_919802.1|  80 RRPKRMGVYGYSPHKSAQQIAEERAARKFPNLVVLGSYYVGEDGVYKWYEVVMVDPHHPAVKRDIERRWVAGFKKK 155
                                    **********************************************************************966655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1421.71
//
Query:       gi|119719308|ref|YP_919803.1|  [L=334]
Description: small GTP-binding protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.1e-27   94.1   0.1    1.3e-26   93.5   0.1    1.3  1  NOG1_N        NOG1 N-terminal helical domain
    2.7e-19   69.3   0.0    4.6e-19   68.6   0.0    1.4  1  MMR_HSR1      50S ribosome-binding GTPase
    1.4e-17   63.1   0.0    3.3e-17   62.0   0.0    1.7  1  NOG1          Nucleolar GTP-binding protein 1 (NOG1)
    2.9e-11   43.1   0.0    8.7e-11   41.6   0.0    1.8  1  FeoB_N        Ferrous iron transport protein B
    1.5e-06   28.2   0.1    3.1e-06   27.2   0.1    1.5  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
    0.00023   21.1   0.5       0.94    9.4   0.0    2.7  2  RsgA_GTPase   RsgA GTPase
     0.0026   17.2   0.0     0.0048   16.4   0.0    1.4  1  SRPRB         Signal recognition particle receptor beta subun
     0.0049   16.5   0.1      0.045   13.3   0.1    2.2  1  Ras           Ras family
     0.0067   16.5   0.3        2.1    8.4   0.0    2.4  2  Dynamin_N     Dynamin family
  ------ inclusion threshold ------
       0.13   12.9   0.0       0.28   11.7   0.0    1.6  1  AAA_18        AAA domain


Domain annotation for each model (and alignments):
>> NOG1_N  NOG1 N-terminal helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.5   0.1   7.1e-30   1.3e-26       7     160 .]      14     165 ..       9     165 .. 0.96

  Alignments for each domain:
  == domain 1  score: 93.5 bits;  conditional E-value: 7.1e-30
                         NOG1_N   7 vptseelidkalrrakraakttkkkkneikrlrnlearkvrtasntlsdkLeeivkkfPnldelhpFyrelldvlvdkde 86 
                                    + ++eel++ a+r  kr+++++  +k e++r+r le    + a+ +ls +L+++    P l++lhpFyr+l+ + +d+d 
  gi|119719308|ref|YP_919803.1|  14 PQSVEELFELAVRSCKRKSSAKGVDKVETRRIRALECV--KLAAGVLSSRLRDVALTSPFLEDLHPFYRSLVTIDLDVDL 91 
                                    56789******************999******888765..778999********************************** PP

                         NOG1_N  87 lkksLaqvkwarklirkigkeyvnklkkaddkkeakelrreafgrvasvlkkvdkaldfLedvrkkLrkLpaiD 160
                                    +k++ +++ +a+k+i+kig e+  ++++a++ +e+   ++++fgr+ svl++ +++l +L++ + + +kLp+iD
  gi|119719308|ref|YP_919803.1|  92 YKSCTSRLYSASKIIKKIGLEQRVRIRRAKTYEEIVSAEKAFFGRALSVLRELEECLPMLRKFQLTFAKLPEID 165
                                    *************************************************************************9 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.6   0.0   2.6e-22   4.6e-19       2      86 ..     171     258 ..     170     289 .. 0.79

  Alignments for each domain:
  == domain 1  score: 68.6 bits;  conditional E-value: 2.6e-22
                                    EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSS...HHHHHH..HHHHHHHHHHC. CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGlie...gaseek..glgkaflalee. 75 
                                    v+i+G pNvGKS+L+++lt++k +v+ +p+tT++ + g++++   +i+lvDtpGl++   +   ek   + ka+ al+  
  gi|119719308|ref|YP_919803.1| 171 VIIAGAPNVGKSSLLKSLTRAKPEVKPYPFTTKELIVGHIEHPLGKIQLVDTPGLLDrplE---EKnpIELKAVVALKHi 247
                                    89***************************************66689********9864222...2234566666667776 PP

                                    TSEEEEEEETT CS
                       MMR_HSR1  76 adlillvvdas 86 
                                    + l+l+vvd +
  gi|119719308|ref|YP_919803.1| 248 TGLVLFVVDPT 258
                                    79*******54 PP

>> NOG1  Nucleolar GTP-binding protein 1 (NOG1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.0   0.0   1.8e-20   3.3e-17       2      58 .]     236     291 ..     235     291 .. 0.96

  Alignments for each domain:
  == domain 1  score: 62.0 bits;  conditional E-value: 1.8e-20
                           NOG1   2 IEkqAiaALkhladavlFllDpseecgysleeQlsLleeikelfankpvivvlnKiD 58 
                                    IE++A++ALkh+ ++vlF++Dp+e+cg++l+ Q+++++ +k+ ++  +  +v+nK D
  gi|119719308|ref|YP_919803.1| 236 IELKAVVALKHITGLVLFVVDPTETCGFTLDFQYAVYRGVKSFIS-SEAWIVVNKLD 291
                                    9********************************************.67888999*98 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6   0.0   4.8e-14   8.7e-11       2     156 .]     170     328 ..     169     328 .. 0.77

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 4.8e-14
                                    EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHH..CTSS CS
                         FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsayseeekvardfll..eeep 79 
                                    tv+++G pnvGk++l+ +lt ak +v  +p +t e   g++++   ++++vD PG  +  +  e + +  + ++  ++ +
  gi|119719308|ref|YP_919803.1| 170 TVIIAGAPNVGKSSLLKSLTRAKPEVKPYPFTTKELIVGHIEHPLGKIQLVDTPGLLDR-PLEEKNPIELKAVValKHIT 248
                                    6899**************************************999**********9773.33333334333333226667 PP

                                    SEEEEEEEGGGHH.HHHHHHHHHHH.....TTSSEEEEEETHHHHHHTTEEE-HHHHHHHHT.S-EEEEBTTTTBTHHHH CS
                         FeoB_N  80 dvvvnvvdatnle.rnLyLtlqlle.....lgvpvvlalnmideaekkgieidlkkLsekLg.vpvvktsakkkegieel 152
                                     +v+ vvd t+    +L +   +       ++ +  +++n++d a+++++    +++++ +g v+ v++sa+kk g+++l
  gi|119719308|ref|YP_919803.1| 249 GLVLFVVDPTETCgFTLDFQYAVYRgvksfISSEAWIVVNKLDIAQTEHM----DNFRRVFGaVDYVAVSAEKKIGVDNL 324
                                    89999***887531344444444332222245678899******999976....578888886899************** PP

                                    HHHH CS
                         FeoB_N 153 lkai 156
                                    +++i
  gi|119719308|ref|YP_919803.1| 325 KEKI 328
                                    9986 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.1   1.7e-09   3.1e-06      58     103 ..     283     331 ..     265     333 .. 0.89

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 1.7e-09
                   MMR_HSR1_Xtn  58 clyvlNKiDlisleeldelare...pnsvviSaekelnldeLkekiwee 103
                                    + +v+NK D ++ e++d+++r     ++v +Saek++++d+Lkeki e+
  gi|119719308|ref|YP_919803.1| 283 AWIVVNKLDIAQTEHMDNFRRVfgaVDYVAVSAEKKIGVDNLKEKIIEK 331
                                    679******************65657********************886 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.1   0.00071       1.3     100     122 ..     169     191 ..     155     229 .. 0.79
   2 !    9.4   0.0   0.00053      0.94      48      99 ..     282     330 ..     276     333 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00071
                                    SEEEEECSTTSSHHHHHHHHCTT CS
                    RsgA_GTPase 100 ktsvlvGqSGvGKStLinallpe 122
                                     t++++G   vGKS+L+++l+  
  gi|119719308|ref|YP_919803.1| 169 PTVIIAGAPNVGKSSLLKSLTRA 191
                                    6899***************9875 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00053
                                    EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTT CS
                    RsgA_GTPase  48 epvivlnKiDlleeeeeleelkeelealgyevllvsaktkegleelkellkd 99 
                                    e  iv+nK+D++++e+ +++++  + a++y  ++vsa++k g+++lke++ +
  gi|119719308|ref|YP_919803.1| 282 EAWIVVNKLDIAQTEH-MDNFRRVFGAVDY--VAVSAEKKIGVDNLKEKIIE 330
                                    578************9.9999999999976..566778889*****998866 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   2.7e-06    0.0048       4      86 ..     169     258 ..     167     261 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.7e-06
                                    -EEEEE-STTSSHHHHHHHHHHS..S---B---SS-EEETTG...GGTT-SEEEETT......-GCCSHHHHHHHHHHGG CS
                          SRPRB   4 pavllvGlsdsGKTslftrLttd..svkktvtSqessaalkvksekgskltliDfPG......heklrqklleklkakss 75 
                                    p+v+++G  + GK sl++ Lt    +vk+     ++ ++ ++ ++   k++l+D PG      +ek   +l+   +a ++
  gi|119719308|ref|YP_919803.1| 169 PTVIIAGAPNVGKSSLLKSLTRAkpEVKPYPFTTKELIVGHI-EHPLGKIQLVDTPGlldrplEEKNPIELKAV-VALKH 246
                                    79*******************987678888888899999999.7888899******944222223333334333.44445 PP

                                    EEEE.EEEEETT CS
                          SRPRB  76 lkgl.vfvvDSt 86 
                                    + gl +fvvD t
  gi|119719308|ref|YP_919803.1| 247 ITGLvLFVVDPT 258
                                    555425888865 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.1   2.5e-05     0.045       2     159 ..     171     331 ..     170     334 .] 0.73

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.5e-05
                                    EEEEESTTSSHHHHHHHHHHSSCSSSCTTTSSEEEEEEEEEETTEEEEEEEEEETT.....SGGGH..HHHHHHHTTESE CS
                            Ras   2 lvlvGdsavGKtslllrfvkdkFkeeyesTigvdfytkeievdgkevkleiwDTAG.....qeefk..slrelyyrdaeg 74 
                                    +++ G  +vGK+sll + ++ k + +  +    +  + +ie      k+++ DT G      ee +  +l+  +  +   
  gi|119719308|ref|YP_919803.1| 171 VIIAGAPNVGKSSLLKSLTRAKPEVKPYPFTTKELIVGHIEHP--LGKIQLVDTPGlldrpLEEKNpiELKAVVALKHIT 248
                                    68999**************999876655544366666666554..55678899999544442444411344444445555 PP

                                    EEEEEETTBHHHHHTHHHHHHHHHHHST..TTSEEEEEEETTTGGGG-SS-HHHHHHHHHHHT.SEEEEEBTTTTCTHHH CS
                            Ras  75 illvyditsresfenvkkwveeikrvae..envpivLvGnKvDleekravsteegeelakelg.lkfletSAktnenvee 151
                                     l+++ ++ +e+     ++   + r ++   + +  +v nK D+++     te+  ++ + +g + ++ +SA+++ +v++
  gi|119719308|ref|YP_919803.1| 249 GLVLFVVDPTETCGFTLDFQYAVYRGVKsfISSEAWIVVNKLDIAQ-----TEHMDNFRRVFGaVDYVAVSAEKKIGVDN 323
                                    68999999988877776666666666664534689999*******7.....78888999999999**************9 PP

                                    HHHHHHHH CS
                            Ras 152 afeellre 159
                                    + e+++++
  gi|119719308|ref|YP_919803.1| 324 LKEKIIEK 331
                                    99999887 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0    0.0011       2.1       1      38 [.     171     207 ..     171     214 .. 0.81
   2 !    6.1   0.0     0.006        11     102     120 ..     216     234 ..     209     257 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0011
                                    EEEEEBTTTTHHHHHHHHHTS--S---SSS---S-EEE CS
                      Dynamin_N   1 iavvGsqSsGKSSvlnaLlgedilprgpnptTrrplel 38 
                                    +++ G+ + GKSS+l +L++++   ++p p T + l++
  gi|119719308|ref|YP_919803.1| 171 VIIAGAPNVGKSSLLKSLTRAK-PEVKPYPFTTKELIV 207
                                    67889999***********999.668888888776665 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.006
                                    SEEEEE---B-SSSGTTSH CS
                      Dynamin_N 102 gltlvDlPGldsvnkrdqe 120
                                    ++ lvD+PGl +++ ++++
  gi|119719308|ref|YP_919803.1| 216 KIQLVDTPGLLDRPLEEKN 234
                                    789*******999888774 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00015      0.28       1      21 [.     171     191 ..     171     222 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00015
                         AAA_18   1 IlltGtpGvGKttlakeLskr 21 
                                    ++++G+p vGK++l k L + 
  gi|119719308|ref|YP_919803.1| 171 VIIAGAPNVGKSSLLKSLTRA 191
                                    79***************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2224.45
//
Query:       gi|119719309|ref|YP_919804.1|  [L=204]
Description: proteasome endopeptidase complex [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    8.8e-55  185.1   0.3    1.1e-54  184.8   0.3    1.0  1  Proteasome  Proteasome subunit


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.8   0.3   6.2e-59   1.1e-54       5     190 .]       6     184 ..       4     184 .. 0.93

  Alignments for each domain:
  == domain 1  score: 184.8 bits;  conditional E-value: 6.2e-59
                                    -EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSGTCHHHH CS
                     Proteasome   5 ttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrpipverl 84 
                                    +t+vGi+ +dgvvlaa+kr+++g +l+sks  +K+++i d++g+a aGl aD++tl+r+++ae++ly+l+ +  ++v   
  gi|119719309|ref|YP_919804.1|   6 GTTVGIRVSDGVVLAAEKRVSYGLYLMSKS-GKKVYRILDKMGMASAGLMADMQTLARIVEAEMRLYELDSNISPKVW-- 82 
                                    6999**********************8888.7************************************8888777777.. PP

                                    HHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHHSTTBSHHHHH CS
                     Proteasome  85 varvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekeykedltleeav 164
                                       va++l+  +++++  p++++++++g+deeg  +Ly++dp+G++ie++ +va Gsg++ a++++e++yk+d++l+ea+
  gi|119719309|ref|YP_919804.1|  83 --TVAKLLSYILYERRLFPYYAEIVVGGLDEEG-SHLYSLDPIGAIIEDD-YVALGSGTQLAISIVESNYKKDMSLDEAL 158
                                    ..555555555556666*************999.8**************6.***************************** PP

                                    HHHHHHHHHHHHHBTTSCSSEEEEEE CS
                     Proteasome 165 elavkalkealerdklsgknievavi 190
                                     la+k++++a++rd++sg++++v vi
  gi|119719309|ref|YP_919804.1| 159 SLALKSVYAAMKRDAASGDGVDVLVI 184
                                    ***********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1404.44
//
Query:       gi|119719310|ref|YP_919805.1|  [L=794]
Description: DNA polymerase II [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.8e-69  232.7   0.0    8.8e-69  232.4   0.0    1.1  1  DNA_pol_B       DNA polymerase family B
    3.3e-39  135.0   0.0    4.4e-38  131.3   0.0    2.3  1  DNA_pol_B_exo1  DNA polymerase family B, exonuclease domain
    3.3e-10   40.0   0.1      6e-10   39.2   0.1    1.3  1  DNA_pol_B_exo2  Predicted 3'-5' exonuclease related to the ex
    1.2e-07   31.8   0.0    3.7e-07   30.3   0.0    1.8  1  RNase_H_2       RNase_H superfamily
  ------ inclusion threshold ------
      0.047   12.6   0.1      0.085   11.7   0.1    1.3  1  DNA_pol_B_2     DNA polymerase type B, organellar and viral


Domain annotation for each model (and alignments):
>> DNA_pol_B  DNA polymerase family B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  232.4   0.0   2.5e-72   8.8e-69       3     457 ..     377     772 ..     375     774 .. 0.88

  Alignments for each domain:
  == domain 1  score: 232.4 bits;  conditional E-value: 2.5e-72
                                    HHHHHHS-HHHHHHHHHHHHHHHTTBE-B-----.--SS.-S----BE----EEESS-EEEEEETTHHHHHHHHTT-STT CS
                      DNA_pol_B   3 lsrvledgqqirveslLlrlakeegfilpdrtekkgkeeegYqGatVlePkkglydkpvlvlDFaSLYPsiiqahNlcyt 82 
                                    l +v++ +   rve +L+r+a   +  +p+++e  g+e+  Y+Ga Vl+Pk g+++k ++vlDF+S+YP+i++++N+++ 
  gi|119719310|ref|YP_919805.1| 377 LDQVFAASVGNRVEWFLIRQAFVFNELVPNSRER-GEET--YKGAIVLKPKPGVHKK-IAVLDFSSMYPNIMIKYNISPD 452
                                    5667777778899999999999999999955544.6666..*************975.99******************** PP

                                    TCE-HCCHCCT--BTT...TEEE-TCC-EEE-TTS---HHHHHHHHHHHHHHHHHHHHHCS--H.HHHHHHHHHHHHHHH CS
                      DNA_pol_B  83 tlvaseeeakeleaedeyleveveprlvefvkksvregllpklLkdllakRkaikkelkeekde.fekalldkqQlalKv 161
                                    t v  ee+++   +++    v v+p+  +  + +   g + k+L++ll++R+++++++k+     +e +++d++Q+a+Kv
  gi|119719310|ref|YP_919805.1| 453 TYVPPEEHVD---PSE----VWVAPEVGHR-FRKHPPGFYRKVLESLLEARRRLREKMKTLDPRsEEYRIYDERQKAIKV 524
                                    ***9998755...443....6677765444.366789**********************6554415899*********** PP

                                    HHHHHHHHHTSTTSTT--HHHHHHHHHHHHHHHHHHHHHHHHT...SSGGGT-SS.....T-EEEEEBSSEEEEE-S-SS CS
                      DNA_pol_B 162 taNsvYGftGvansrlpclalAasvTtiGRemLektkelvekkaellskllalpeeaeeeklkviYGDTDSvfielkvkd 241
                                    + N++YG+ G +  r +  ++A+  T+ GRe +++t +  ++                  +l++iYGDTDS+f++++ ++
  gi|119719310|ref|YP_919805.1| 525 ITNATYGYSGWSMARWYKREVAEATTAWGRELIKATIKKAQSL-----------------GLSIIYGDTDSIFVQFDEEK 587
                                    **********************************999988876.................9***************9887 PP

                                    HHHHHHHHHHHHHHHHT.TSTTT--EEEEEEEEEEEEE.ETTEEEEEEEEESSTTSEEEEESSGGGSTTS-HHHHHHHHH CS
                      DNA_pol_B 242 veellkigkelaeevseklfkkplklefekvykkllLi.sKKkYaglkvektskanklliKGvdlvRrdncklvkevikk 320
                                    + +l+       e+v+++l ++   ++++kvy+k+ ++ sKKkY gl  +     ++++  G + vR d+++++ke+ ++
  gi|119719310|ref|YP_919805.1| 588 IGRLV-------EYVEKELGFE---IKLDKVYEKVFFTeSKKKYCGLLAD-----GRVDLVGFEAVRGDWAEISKEIQER 652
                                    76554.......6788866666...8889******99857**********.....99*********************** PP

                                    HHHHHSSS....S-HHHHHHHHHHHHHHHHHHHHTT-S-GGGG-EEEEESS.CCCSSGCCSHHHHHHHHHHHHCSS---T CS
                      DNA_pol_B 321 vlelllkdeteersleeglealksilkdvleeleenkvplekfvlskelskepenyksknlphlevakrlkkrneeapev 400
                                    v+e +lk+    +++ ++++++++++    +el e+++plek+v+ k+lsk+ ++y+  + ph+ va++lk+  + ++  
  gi|119719310|ref|YP_919805.1| 653 VVEIVLKE----EDPWKAVDFVRKTI----TELSEGRIPLEKLVIWKTLSKDLDEYEVDA-PHVVVARELKRL-GYRVGK 722
                                    ********....**************....9*************************9988.***999998766.789999 PP

                                    TCEEEEEEBETSS.....SS-GGGTEEEHHHHHHCCSEB-HHHHHH.TTHHHHHHHHT CS
                      DNA_pol_B 401 gdrisYvivekkkevkkknllaseraedpeyvleknlpidieyYls.qllkevarlle 457
                                    g +i Y++v+ +        ++se+a+ p +  ++  ++d++yY++ q+++++ r+le
  gi|119719310|ref|YP_919805.1| 723 GAKIGYIVVKGAG-------KVSEKAK-PLISVKSPDEVDTDYYVKrQIVPAALRILE 772
                                    ***********75.......6777665.6666677789*****************997 PP

>> DNA_pol_B_exo1  DNA polymerase family B, exonuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.3   0.0   1.2e-41   4.4e-38       2     336 ..      33     310 ..      32     311 .. 0.81

  Alignments for each domain:
  == domain 1  score: 131.3 bits;  conditional E-value: 1.2e-41
                                    ECTTSEEEEEEEE---EEEEEESSCGGHHHHHHHHHHHCCTTCCCEEEEEEEECCCCEECCTSSCCHHCEEEEEESSTCH CS
                 DNA_pol_B_exo1   2 teegksvcvnvfgfkpyfYceapdgkeleevkeelkelyeelskkvtkivkvelvlkkslygyekkpvpylkvsvsnpne 81 
                                    te g++++v + +f+pyfY+ +++     +++  l e ++    ++ k+ +v  ++ ++l+g   +   +lkv++++p++
  gi|119719310|ref|YP_919805.1|  33 TESGERIVVAEKNFRPYFYLVPEN-----AISDALVERVRTALHTF-KVLSVN-AIERKLFGRTLN---VLKVTITDPRD 102
                                    899********************3.....34444444444444444.477887.88899*******...*********** PP

                                    HHHHHHHHHHCCCCCCCCSSS--HHHHHHHHCTS-TTCEEEEE..TEEEEGCC--C-.SEEEEEETTTSCEETTTCC.S- CS
                 DNA_pol_B_exo1  82 lkkirkelspleeivdvyeydvdylerflidnkivgfgwysvk..kylvraegkisncdveidcdvddliakpkese.pp 158
                                    ++k+r+   ++  i dv e+d+ +++r+++d +i +++w   k   ++v+   ++++      ++ ++      +++ p+
  gi|119719310|ref|YP_919805.1| 103 VPKAREVAAKIPGIRDVLEADIRFYMRYMVDTGISPSSWVLAKvrSAPVPNGWRVDEFFE--LVEAPRSLD---KKStPR 177
                                    ***************************************999933333333334444322..222233332...3335** PP

                                    EEEEEEEEEETEETTSEETTTT..--EEEEEEEECCTC.SS.SEEEEEEECCCTSS----EE--SSTCSTTEEEEEESSH CS
                 DNA_pol_B_exo1 159 lrvlsFDIeckskkgkfpdaensedpiiqIscvldglgekepearklftlrecaseeeedfeltpkpeypgvkvlefdsE 238
                                    l+  +FDIec+ ++g  pd+e+  dp+  Is + ++ +       ++f+ +e +                        sE
  gi|119719310|ref|YP_919805.1| 178 LKTYAFDIECYNRYG-EPDPER--DPVLVISRTGEDGT-------VIFSQDEGS------------------------SE 223
                                    ***************.9*****..**********9988.......899999999........................9* PP

                                    HHHHHHHHHHHHHH--SEEEESSTTTTHHHHHHHHHHHCCTCCHCG.SCCSCTCEECCCCESEEEEEECEEEETTSEEEE CS
                 DNA_pol_B_exo1 239 kelLqaflefikqydPdvitgYNidnFDlpYilnRakelykvklsklgrlnkggrskvseigfskqarekvkisgrihlD 318
                                    k+lL++f++ + qydPdvi+gYN + FD+pY+l+Ra+ ++ vkl       + gr+ ++ ++     +++ ++ gr ++D
  gi|119719310|ref|YP_919805.1| 224 KKLLEEFVNDLVQYDPDVILGYNSNRFDWPYLLQRAR-VNGVKL-------SIGRNLGEPSQS---VYGHFSVVGRANVD 292
                                    *************************************.555553.......556655544444...59999********* PP

                                    HHHHHHHHSSSSG-SHHH CS
                 DNA_pol_B_exo1 319 lyrvvkrklklpsYkLna 336
                                    ly+++++    +  +L++
  gi|119719310|ref|YP_919805.1| 293 LYDYASELQEVKVKTLEN 310
                                    *****9987777666666 PP

>> DNA_pol_B_exo2  Predicted 3'-5' exonuclease related to the exonuclease domain of PolB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   0.1   1.7e-13     6e-10      28     169 ..     215     358 ..     201     365 .. 0.84

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 1.7e-13
                 DNA_pol_B_exo2  28 kslgeeessekelikkffegvekkkpqlV.sfngrgfDlpvleyralkhgvsapkyfdegdedrekkwnnylsrystrhl 106
                                    +s ++e ssek+l+++f + + ++ p ++ ++n++ fD p l +ra ++gv+     + g+   +  +   +s   +  +
  gi|119719310|ref|YP_919805.1| 215 FS-QDEGSSEKKLLEEFVNDLVQYDPDVIlGYNSNRFDWPYLLQRARVNGVKLSIGRNLGEP-SQSVYG-HFSVVGRANV 291
                                    33.556789****************986449*********************9999999993.445555.78888899** PP

                 DNA_pol_B_exo2 107 DLmdllseygaranakLdelakllglPGKlg...vdGskVaelyqegklke.ireYcetDvlnTYlv 169
                                    DL+d+ se +  + + L+++++ lg+  K +   +d +kV+e++++ + ++ + +Y   D+ +TYl+
  gi|119719310|ref|YP_919805.1| 292 DLYDYASELQEVKVKTLENVSEFLGVMKKSErvlIDTNKVYEYWDSKDKRSlLLRYAGDDARSTYLL 358
                                    *************************9999765559*********98766551789**********97 PP

>> RNase_H_2  RNase_H superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.0     1e-10   3.7e-07       3     161 ..     183     358 ..     181     362 .. 0.71

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 1e-10
                      RNase_H_2   3 fDiEttGlspkknl..iyliGvldvdekeiekltqllaeepeeekailelflellekk..kalvtfngksFDvpflkrlf 78 
                                    fDiE++  +++++   + ++ + ++ e+ ++ ++q  +e+ +e+k ++e++ ++l ++  + ++ +n ++FD+p+l +++
  gi|119719310|ref|YP_919805.1| 183 FDIECYNRYGEPDPerDPVLVISRTGEDGTVIFSQ--DEGSSEKKLLEEFV-NDLVQYdpDVILGYNSNRFDWPYLLQRA 259
                                    99999999776665435677677667777666776..77777777777755.5555553356889************999 PP

                      RNase_H_2  79 ..kkyklde.................eefrhiDLlkelrk.kklesysLksvekelgierreedlsGsqavklyqeylrt 138
                                      + +kl+                    +  +DL+  +++ ++++   L++v ++lg+  ++e +   ++ k+y+ +   
  gi|119719310|ref|YP_919805.1| 260 rvNGVKLSIgrnlgepsqsvyghfsvVGRANVDLYDYASElQEVKVKTLENVSEFLGVMKKSERV-LIDTNKVYEYW--- 335
                                    77555555577888888777766666555999***98865344455579999999***9995444.34455666666... PP

                      RNase_H_2 139 gdeellekilaYNedDvralatl 161
                                     ++++   +l+Y  dD r+++ l
  gi|119719310|ref|YP_919805.1| 336 DSKDKRSLLLRYAGDDARSTYLL 358
                                    566667779***********988 PP

>> DNA_pol_B_2  DNA polymerase type B, organellar and viral
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   2.4e-05     0.085     212     248 ..     414     449 ..     412     464 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.4e-05
                    DNA_pol_B_2 212 ayrGGrc.ypsvlgiyeeniyvyDvnSlYPsamthypm 248
                                     y G ++ +p+  g + ++i v D+ S+YP++m +y +
  gi|119719310|ref|YP_919805.1| 414 TYKGAIVlKPK-PG-VHKKIAVLDFSSMYPNIMIKYNI 449
                                    68888887666.44.569****************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (794 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.74u 0.31s 00:00:01.05 Elapsed: 00:00:00.49
# Mc/sec: 4908.76
//
Query:       gi|119719311|ref|YP_919806.1|  [L=217]
Description: hypothetical protein Tpen_0394 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    7.4e-07   28.7   2.4     0.0015   18.0   0.1    2.0  2  PhoU_div    Protein of unknown function DUF47
     0.0086   16.0   0.2       0.15   11.9   0.2    2.3  2  DNA_meth_N  DNA methylase N-terminal domain
     0.0089   15.8   2.9      0.011   15.5   1.0    2.2  2  DASH_Duo1   DASH complex subunit Duo1


Domain annotation for each model (and alignments):
>> PhoU_div  Protein of unknown function DUF47
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.3   2.3e-05      0.13     125     213 ..      24     109 ..      11     110 .. 0.84
   2 !   18.0   0.1   2.4e-07    0.0015     107     213 ..     113     214 ..     105     215 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.3e-05
                       PhoU_div 125 eaiealaevieeleklletalskk..diveeieslEdeiDqlqrklikklfsredasnplevlllveiieklenvsdrae 202
                                    ++ e++ +v++ ++   e++l+ +  + +e i++   ++  lq + i  l +     + +    +v i   +  v+d+  
  gi|119719311|ref|YP_919806.1|  24 DILEEIRRVVKTIN---EQGLRDEqrERIERIQKTKSQTQTLQTEYIDYLTKA--SRGLMHREEWVRIGSRVMSVVDKLS 98 
                                    56666777777777...8888876779******************99888773..36*********************** PP

                       PhoU_div 203 dvadrisiill 213
                                     +++r+  +++
  gi|119719311|ref|YP_919806.1|  99 GISYRLGFLIE 109
                                    *****988775 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 2.4e-07
                       PhoU_div 107 efpeelkdeflallkktveaiealaevieeleklletalskkdiveeieslEdeiDqlqrklikklfsredasnplevll 186
                                     +pe++  +f a+ + ++ ++  l++++++l     +al+    + +i++ E  iD+l+r  i + +   + ++   +ll
  gi|119719311|ref|YP_919806.1| 113 VVPEKVASNFAAMCDNLSMMVSTLDQAMNKLLSSPPQALE---DLRKISEYESTIDSLYRSTIFEVLG--SNISSSTMLL 187
                                    48999*********************99999988888888...69***************98877666..3466677889 PP

                       PhoU_div 187 lveiieklenvsdraedvadrisiill 213
                                    l  i e le  sd   d+ + + iill
  gi|119719311|ref|YP_919806.1| 188 LLGIAEMLEDSSDILYDLVSNLYIILL 214
                                    999999999999999999999999987 PP

>> DNA_meth_N  DNA methylase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.2   2.6e-05      0.15      13      53 ..      30      70 ..      25      72 .. 0.90
   2 ?    1.2   0.0      0.06   3.6e+02      17      34 ..     152     169 ..     149     178 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.6e-05
                     DNA_meth_N 13 KtvaeeLrkvgeseWsretLnRwvkgksaarrLteaEvalL 53
                                   ++v+++ ++ g ++  re++ R++k+ks+ ++L+ + +++L
  gi|119719311|ref|YP_919806.1| 30 RRVVKTINEQGLRDEQRERIERIQKTKSQTQTLQTEYIDYL 70
                                   89*****************************9998777666 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.06
                     DNA_meth_N  17 eeLrkvgeseWsretLnR 34 
                                    e Lrk++e e + ++L R
  gi|119719311|ref|YP_919806.1| 152 EDLRKISEYESTIDSLYR 169
                                    78*************999 PP

>> DASH_Duo1  DASH complex subunit Duo1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   1.0   1.8e-06     0.011       6      55 ..      23      74 ..      15      87 .. 0.85
   2 ?   -1.2   0.0      0.29   1.8e+03       4       4 ..     149     149 ..     123     171 .. 0.59

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.8e-06
                      DASH_Duo1  6 leqLrkinevienvies.Lkkak.sniervketvestntLLdkWirIlsqte 55
                                    + L++i++v+++++e+ L++ + + ier+++t ++t+tL  ++i+ l +++
  gi|119719311|ref|YP_919806.1| 23 QDILEEIRRVVKTINEQgLRDEQrERIERIQKTKSQTQTLQTEYIDYLTKAS 74
                                   578999*******99755*99999**********************999886 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.29
                      DASH_Duo1   4 k 4  
                                    +
  gi|119719311|ref|YP_919806.1| 149 Q 149
                                    1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1188  (0.0662614); expected 358.6 (0.02)
Passed bias filter:                      617  (0.0344135); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1415.94
//
Query:       gi|119719312|ref|YP_919807.1|  [L=92]
Description: hypothetical protein Tpen_0395 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.6e-05   22.5   0.0     0.0002   21.3   0.0    1.6  1  Molydop_binding  Molydopterin dinucleotide binding domain
     0.0032   17.6   0.0     0.0051   17.0   0.0    1.5  1  CDC48_N          Cell division protein 48 (CDC48), N-terminal


Domain annotation for each model (and alignments):
>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   2.2e-08    0.0002      22      92 ..      14      82 ..       4      91 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2.2e-08
                                   HHHHCSSS.-EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESSB-TTEEEEESSHCC.....S-GHC CS
                Molydop_binding 22 lrlakpep.evveinpedAaalGikdGdlVevesrrGsvevrakvtervrpGvvfmpfgwweagekggnaNa 92
                                   lr++++ p  ++ +np ++++lGi+   +V+++ +  ++ + a+ +e+v+p  v+ ++ + +   kg++ N+
  gi|119719312|ref|YP_919807.1| 14 LRRRDEVPeGRAFMNPSTMNELGISSEIEVVIAGK-KKLYFAAMPSESVPPNEVWCNTDELK--TKGVADNS 82
                                   3444444466********************88765.59*****************9998877..66666655 PP

>> CDC48_N  Cell division protein 48 (CDC48), N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   5.7e-07    0.0051      10      53 ..      18      61 ..      11      87 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 5.7e-07
                                   -CSSTTEEEE-HHHHHHHTS-TTSEEEEECCCCEEEEEEEBSTT CS
                        CDC48_N 10 edvgrgivridpedmeelglepgdvveiegkrkTvaivwpaepe 53
                                    +v  g++ ++p++m+elg+++   v i gk+k +  ++p+e  
  gi|119719312|ref|YP_919807.1| 18 DEVPEGRAFMNPSTMNELGISSEIEVVIAGKKKLYFAAMPSESV 61
                                   467889*****************99*******999999998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 658.84
//
Query:       gi|119719313|ref|YP_919808.1|  [L=85]
Description: hypothetical protein Tpen_0396 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.35s 00:00:00.82 Elapsed: 00:00:00.54
# Mc/sec: 477.49
//
Query:       gi|119719314|ref|YP_919809.1|  [L=325]
Description: hypothetical protein Tpen_0397 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.3e-13   50.3   0.0    5.8e-13   49.5   0.0    1.4  1  DUF87          Helicase HerA, central domain
    5.3e-07   28.9   0.0    3.1e-06   26.4   0.0    1.9  2  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
    5.6e-05   22.6   0.0    0.00011   21.7   0.0    1.4  1  FtsK_SpoIIIE   FtsK/SpoIIIE family
    0.00018   20.2   0.0    0.00028   19.6   0.0    1.2  1  DUF853         Bacterial protein of unknown function (DUF853)
    0.00068   18.8   0.1     0.0011   18.0   0.1    1.3  1  T2SSE          Type II/IV secretion system protein
      0.003   17.3   0.3       0.15   11.8   0.1    2.2  2  DEAD           DEAD/DEAH box helicase
     0.0051   15.8   0.0       0.37    9.7   0.0    2.0  2  AAA_10         AAA-like domain
  ------ inclusion threshold ------
      0.014   15.6   0.7      0.064   13.5   0.2    2.1  2  AAA_22         AAA domain
      0.028   14.8   0.1      0.066   13.6   0.1    1.6  1  AAA_19         AAA domain
      0.044   13.3   0.0      0.068   12.7   0.0    1.2  1  AAA_7          P-loop containing dynein motor region
       0.13   12.2   0.0       0.26   11.2   0.0    1.5  1  NTPase_1       NTPase
       0.14   12.5   2.0       0.24   11.7   0.1    2.1  2  AAA_16         AAA ATPase domain
       0.16   12.4   0.1        1.5    9.3   0.1    2.1  2  AAA            ATPase family associated with various cellular
       0.17   11.8   0.0        0.3   11.0   0.0    1.4  1  MobB           Molybdopterin guanine dinucleotide synthesis p
        0.2   10.6   0.0       0.32    9.9   0.0    1.3  1  AAA_6          Hydrolytic ATP binding site of dynein motor re


Domain annotation for each model (and alignments):
>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.5   0.0   4.9e-16   5.8e-13       5      69 ..       8      76 ..       6     135 .. 0.78

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 4.9e-16
                          DUF87  5 rllsgsevpvyldlnklv...trHlAilgsTGsGKSntvavLleellekkgatililDpHGEYgkal..e 69
                                    ll +++++v+l + ++v   + H+ + g TGsGK+ntv+vLl  l  ++g++ l+lD HGEYg +   e
  gi|119719314|ref|YP_919809.1|  8 MLLAERGLRVRLGALSAVslkQGHIVVAGPTGSGKTNTVKVLLCGLK-RRGIPFLVLDFHGEYGEFGrlE 76
                                   56666666666655444411157************************.****************998553 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0   2.6e-09   3.1e-06      13      56 ..      27      70 ..      19      85 .. 0.89
   2 ?   -0.1   0.0      0.29   3.5e+02     264     287 ..     243     266 ..     237     273 .. 0.84

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 2.6e-09
                  TrwB_AAD_bind 13 retqhilivGttGsGKtqalekllrairargdraivlDltGafv 56
                                     + hi+++G tGsGKt++++ ll ++++rg   +vlD++G++ 
  gi|119719314|ref|YP_919809.1| 27 LKQGHIVVAGPTGSGKTNTVKVLLCGLKRRGIPFLVLDFHGEYG 70
                                   6789*************************************984 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.29
                  TrwB_AAD_bind 264 llaegRkfGgavvlglqsiaqlre 287
                                    l  e+RkfG  vv+ +q    l e
  gi|119719314|ref|YP_919809.1| 243 LFLELRKFGEVVVAVAQRLDDLSE 266
                                    56799************9988765 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   8.8e-08   0.00011      40      64 ..      30      54 ..      17      77 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 8.8e-08
                                   .SEEEE--TTSSHHHHHHHHHHHHH CS
                   FtsK_SpoIIIE 40 shllvaGatgsGKStalntLilSla 64
                                   +h++vaG tgsGK++++++L+++l 
  gi|119719314|ref|YP_919809.1| 30 GHIVVAGPTGSGKTNTVKVLLCGLK 54
                                   8*********************985 PP

>> DUF853  Bacterial protein of unknown function (DUF853)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   2.4e-07   0.00028      18      62 ..      26      70 ..      18      86 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.4e-07
                         DUF853 18 klanrhGliaGatGtGktvtLqvlaeslseaGvpvfladvkGdLs 62
                                   +l   h ++aG tG Gkt t++vl  +l + G+p ++ d  G+  
  gi|119719314|ref|YP_919809.1| 26 SLKQGHIVVAGPTGSGKTNTVKVLLCGLKRRGIPFLVLDFHGEYG 70
                                   5567799*********************************99875 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1   9.5e-07    0.0011     127     154 ..      27      54 ..      12      63 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 9.5e-07
                          T2SSE 127 rerglilvsGgTgsGKttllyallkein 154
                                     ++g i+v+G+TgsGKt ++ +ll  ++
  gi|119719314|ref|YP_919809.1|  27 LKQGHIVVAGPTGSGKTNTVKVLLCGLK 54 
                                    4699***************999987665 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.1   0.00013      0.15      12      31 ..      27      46 ..      21      58 .. 0.84
   2 ?    3.5   0.0     0.045        54      94     134 ..     247     284 ..     220     298 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00013
                                   HTTCEEEEEESTTSSHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxx RF
                           DEAD 12 lgggdvlvaaeTGsGKTlaf 31
                                   l++g+++va++TGsGKT   
  gi|119719314|ref|YP_919809.1| 27 LKQGHIVVAGPTGSGKTNTV 46
                                   67899************875 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.045
                                    HHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  94 ldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrll 134
                                    l++  ++vv+  +rlddl + +   l++ +++Vl  a r  
  gi|119719314|ref|YP_919809.1| 247 LRKFGEVVVAVAQRLDDLSE-RV--LRNASLVVLHDASRAD 284
                                    4455799**********664.55..9999****98887765 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0   0.00031      0.37      21      67 ..      29      75 ..      21      93 .. 0.86
   2 ?    4.1   0.0     0.015        18     236     299 ..     211     276 ..     189     291 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00031
                         AAA_10 21 asasliiGdlGnGKSvlakllvlyisllggkaliiDpkkerekfket 67
                                     + ++ G++G GK  ++k+l   +  +g   l++D   e  +f + 
  gi|119719314|ref|YP_919809.1| 29 QGHIVVAGPTGSGKTNTVKVLLCGLKRRGIPFLVLDFHGEYGEFGRL 75
                                   57899*******************************99999888765 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.015
                         AAA_10 236 sdkkefkvvifDEawift...ssaeGkkllkelvRiGRsynaavylvtqsadDvlkeelknniglkl 299
                                    +++++ +v+++ Eaw         e   l + l    R++   v+ v+q  dD+++  l+n  +l++
  gi|119719314|ref|YP_919809.1| 211 KSQEIAHVTVIEEAWQVLpyrARWEAPSLAERLFLELRKFGEVVVAVAQRLDDLSERVLRN-ASLVV 276
                                    4788999********865111556899999****99*****************98777665.44554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2   5.3e-05     0.064       4      26 ..      28      50 ..      26      63 .. 0.87
   2 ?   -0.6   0.0       1.3   1.5e+03      77     100 ..     197     224 ..     171     259 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.3e-05
                         AAA_22  4 tagilvvtGesGtGKTtllrrll 26
                                   ++g++vv G++G+GKT +++ ll
  gi|119719314|ref|YP_919809.1| 28 KQGHIVVAGPTGSGKTNTVKVLL 50
                                   689*************9998776 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.3
                         AAA_22  77 ellealeqalrarav....ielliiDEa 100
                                     ll++l++a+ ar++     ++ +i+Ea
  gi|119719314|ref|YP_919809.1| 197 VLLKHLYDAAMARGKsqeiAHVTVIEEA 224
                                    4567888888888877787889999998 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   5.5e-05     0.066       4      36 ..      24      55 ..      21      64 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.5e-05
                         AAA_19  4 avealkekvllvtaGpGtGKTrvlkhivallve 36
                                   av  lk+++++v ++ G+GKT ++k  +  l++
  gi|119719314|ref|YP_919809.1| 24 AV-SLKQGHIVVAGPTGSGKTNTVKVLLCGLKR 55
                                   77.8999*****************998776665 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   5.7e-05     0.068      30      69 ..      26      65 ..      16      69 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.7e-05
                          AAA_7 30 lknkkpvllvGptGtGKtviikdllkkldkekylsltinf 69
                                     ++ ++++ GptG+GKt ++k ll  l+++ + +l++ f
  gi|119719314|ref|YP_919809.1| 26 SLKQGHIVVAGPTGSGKTNTVKVLLCGLKRRGIPFLVLDF 65
                                   345668999**************99999988777776666 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00022      0.26       1      29 [.      31      59 ..      31      94 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00022
                                   EEEEE--TTSSHHHHHHHHHHHH...GGG CS
                       NTPase_1  1 kvfiTGppGvGKtTlvkkvlellkssgvk 29
                                   ++++ Gp G+GKt  vk +l+ lk++g++
  gi|119719314|ref|YP_919809.1| 31 HIVVAGPTGSGKTNTVKVLLCGLKRRGIP 59
                                   799**********************9986 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1    0.0002      0.24      15      54 ..      21      59 ..      15      78 .. 0.79
   2 ?   -0.3   0.1         1   1.3e+03     106     126 ..     226     250 ..     137     290 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0002
                         AAA_16 15 alervrsgrpelvllsGesGvGKsslvrellralekdggi 54
                                   al++v+  + + +++ G+ G+GK+  v+ ll  l+++g+ 
  gi|119719314|ref|YP_919809.1| 21 ALSAVSLKQ-GHIVVAGPTGSGKTNTVKVLLCGLKRRGIP 59
                                   566666666.6899*************9999888887644 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1
                         AAA_16 106 a....avpelagaeasrllellkrl 126
                                    +     ++  a+++a+rl+ +l+++
  gi|119719314|ref|YP_919809.1| 226 QvlpyRARWEAPSLAERLFLELRKF 250
                                    2333333333334444454444444 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1    0.0012       1.5       2      27 ..      33      61 ..      32      76 .. 0.77
   2 ?    0.6   0.0      0.61   7.2e+02      60     121 ..     217     270 ..     199     277 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0012
                                   EEESSTTSSHHHHHHHHHHHHT...HEEE CS
                            AAA  2 llyGppGtGKTllakavakelg...vefl 27
                                   ++ Gp G GKT ++k +   l+   ++fl
  gi|119719314|ref|YP_919809.1| 33 VVAGPTGSGKTNTVKVLLCGLKrrgIPFL 61
                                   689*************9988852235555 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.61
                                    EEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS CS
                            AAA  60 silfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr 121
                                    ++ +i+E+ ++ + r   ++ e+ ++++ L+ el ++ +     +v+++++r d+l++ +lr
  gi|119719314|ref|YP_919809.1| 217 HVTVIEEAWQVLPYR---ARWEAPSLAERLFLELRKFGE-----VVVAVAQRLDDLSERVLR 270
                                    555555555555555...445555556666666666655.....899999999999999986 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00025       0.3       2      62 ..      32      95 ..      31     120 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00025
                           MobB  2 lgivgksgsGKTtLleklipelkarglrvgtiKhahhgfd..vdkpgkD.syrhrkAGAkevlv 62
                                   + ++g  gsGKT  ++ l+  lk+rg+   ++  + +  +    +pgkD s+++ + G  e +v
  gi|119719314|ref|YP_919809.1| 32 IVVAGPTGSGKTNTVKVLLCGLKRRGIPFLVLDFHGEYGEfgRLEPGKDlSFNVLSTGDIEFVV 95
                                   568899*********************9999988876544227899999888888888777666 PP

>> AAA_6  Hydrolytic ATP binding site of dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00027      0.32      27      52 ..      23      49 ..      14      64 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00027
                          AAA_6 27 qAlklklgg.apaGpagtGKtEtvkdL 52
                                   +A++lk g   +aGp+g GKt tvk L
  gi|119719314|ref|YP_919809.1| 23 SAVSLKQGHiVVAGPTGSGKTNTVKVL 49
                                   6777777752479************88 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                       107  (0.00596798); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2020.04
//
Query:       gi|119719315|ref|YP_919810.1|  [L=171]
Description: nucleic acid binding, OB-fold, tRNA/helicase-type [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-08   34.1   0.5      2e-08   34.1   0.5    1.6  2  tRNA_anti-codon  OB-fold nucleic acid binding domain


Domain annotation for each model (and alignments):
>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0      0.52   9.2e+03      45      53 ..      27      35 ..      23      37 .. 0.68
   2 !   34.1   0.5   1.1e-12     2e-08       3      67 ..      52     113 ..      50     137 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 0.52
                                   TS-TTSEEE CS
                tRNA_anti-codon 45 nlkeGdvvr 53
                                    +k+G+vv+
  gi|119719315|ref|YP_919810.1| 27 AVKRGSVVY 35
                                   467788876 PP

  == domain 2  score: 34.1 bits;  conditional E-value: 1.1e-12
                                    EEEEEEEEEEEEETTEEEEEEEETTEEEEEEEETHHHHHHHTT..S-TTSEEEEEEEEEECTTSSEE CS
                tRNA_anti-codon   3 vaGrvtsisdrsggkvifidlrDgtgriqvvlfreeatklaen..lkeGdvvrvtGrvkrrpggele 67 
                                    v+Grv+ +   +g k+ +i+l Dg+g+++v +++ e++ l+e+  l eG+  +v G ++++++g  +
  gi|119719315|ref|YP_919810.1|  52 VVGRVQGV--VHGDKFTDIVLGDGSGTVTVRFWS-EKKGLLEDkgLAEGSTAKVLGVLRESREG--T 113
                                    99******..************************.6666666667****************988..3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 1088.63
//
Query:       gi|119719316|ref|YP_919811.1|  [L=106]
Description: hypothetical protein Tpen_0399 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 745.63
//
Query:       gi|119719317|ref|YP_919812.1|  [L=108]
Description: hypothetical protein Tpen_0400 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.096   12.1   0.0        1.2    8.6   0.0    2.1  2  HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family I
       0.12   12.6   0.0       0.28   11.4   0.0    1.6  2  SelB-wing_2   Elongation factor SelB, winged helix


Domain annotation for each model (and alignments):
>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0   0.00014       1.2      10      29 ..      39      57 ..      38      61 .. 0.91
   2 ?    1.2   0.0     0.027   2.4e+02      10      21 ..      94     105 ..      93     108 .] 0.89

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00014
                   HTH_Tnp_ISL3 10 sriTlrleayilelllesrs 29
                                   +++T++ e++i+e++++s s
  gi|119719317|ref|YP_919812.1| 39 AFFTEDVERMIVEEVTRS-S 57
                                   68**************98.4 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.027
                   HTH_Tnp_ISL3  10 sriTlrleayil 21 
                                    +r++  le+y++
  gi|119719317|ref|YP_919812.1|  94 RRFSPELEEYVI 105
                                    8*********97 PP

>> SelB-wing_2  Elongation factor SelB, winged helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.69   6.2e+03      26      36 ..      33      38 ..      21      51 .. 0.54
   2 ?   11.4   0.0   3.1e-05      0.28      16      51 ..      59      95 ..      57      97 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.69
                                   CSSSS-HCCHH CS
                    SelB-wing_2 26 laprlpaklfq 36
                                   +apr+     q
  gi|119719317|ref|YP_919812.1| 33 AAPRV-----Q 38
                                   23333.....3 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 3.1e-05
                                   -EEHHHHHHH.CSSSS-HCCHHHHHHHHHHTTSEEE- CS
                    SelB-wing_2 16 GmskeeLrsr.laprlpaklfqallealvargilave 51
                                   G+ + eL  r   +++++  f   l  l+ +g l+++
  gi|119719317|ref|YP_919812.1| 59 GVTRSELYKRvTGRGVKPVEFYRALTNLLGKGVLKRR 95
                                   99********666*********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 875.01
//
Query:       gi|119719318|ref|YP_919813.1|  [L=302]
Description: signal-transduction protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-42  143.5  17.4    1.2e-11   44.9   0.4    4.4  4  CBS       CBS domain


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.3   2.2e-12   3.9e-08       2      55 ..      11      62 ..       5      64 .. 0.85
   2 !   42.2   0.4   4.7e-15   8.4e-11       8      56 ..      94     142 ..      87     143 .. 0.92
   3 !   44.9   0.4   6.6e-16   1.2e-11       1      55 [.     150     203 ..     150     205 .. 0.92
   4 !   33.4   0.4   2.5e-12   4.5e-08       5      55 ..     229     278 ..     225     280 .. 0.91

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 2.2e-12
                                   HHHSBSSCEEEETTSB.HHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                            CBS  2 gdimtrdvvtvppdtt.leealelmrekgvsrlPVVdedgklvGivtlrDllral 55
                                   g +   +++ v p+++ + ++l  m +++v+++P Vde g l G+v+ rDl+++l
  gi|119719318|ref|YP_919813.1| 11 GRF---PPLAVVPSSSrVLDVLVAMGRNRVRHVPLVDERGVLKGMVSARDLVDFL 62
                                   555...56666666666********9999***********999*********998 PP

  == domain 2  score: 42.2 bits;  conditional E-value: 4.7e-15
                                    SCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                            CBS   8 dvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                    d+++v+  ++l+e++elm+e+g+++l VVded ++vGiv++r+++++l+
  gi|119719318|ref|YP_919813.1|  94 DPPYVYTRSDLREVIELMVERGIGALAVVDEDLRVVGIVSERHVISLLA 142
                                    78999999*********************9888*************997 PP

  == domain 3  score: 44.9 bits;  conditional E-value: 6.6e-16
                                    HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                            CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                    V++imt++vv+++p ++l e ++ m e++++rlP V   ++l Givt +D+l+++
  gi|119719318|ref|YP_919813.1| 150 VKEIMTSEVVYLSPMDSLFEGMRVMSERRIRRLPLVS-GEELRGIVTIKDVLSYV 203
                                    89***********************9999*******4.446************97 PP

  == domain 4  score: 33.4 bits;  conditional E-value: 2.5e-12
                                    SBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                            CBS   5 mtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                     +++v+ v  d +++ a+ lm+++g+++l VV  dgk+ Givt+rD+l  l
  gi|119719318|ref|YP_919813.1| 229 SSKPVLAVEDDVDVGLAVSLMKKHGIGAL-VVTHDGKPRGIVTERDVLTRL 278
                                    578999999999*********9999****.9889**************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2313.05
//
Query:       gi|119719319|ref|YP_919814.1|  [L=194]
Description: hypothetical protein Tpen_0402 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1574.70
//
Query:       gi|119719320|ref|YP_919815.1|  [L=126]
Description: hypothetical protein Tpen_0403 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 863.73
//
Query:       gi|119719321|ref|YP_919816.1|  [L=450]
Description: UbiD family decarboxylase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-91  305.5   0.0    6.6e-91  305.2   0.0    1.0  1  UbiD      3-octaprenyl-4-hydroxybenzoate carboxy-lyase


Domain annotation for each model (and alignments):
>> UbiD  3-octaprenyl-4-hydroxybenzoate carboxy-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  305.2   0.0   3.7e-95   6.6e-91       6     405 ..      31     406 ..      28     407 .. 0.93

  Alignments for each domain:
  == domain 1  score: 305.2 bits;  conditional E-value: 3.7e-95
                                    CTTSEEEEESEB-TBTHHHHHHHHHHHHT--EEEEEEBTTB.TT-EEEE-TTS-HCHHHHHHTS-GHHHHHHHHHHHHHS CS
                           UbiD   6 kagelvrikeevdpelEiaeiarrvleeggpallFenvkgkgskfpvltnlfgtrervalalglssleeileklaellep 85 
                                    k g l++ ++ v  e+E+a  +++      p+l+ ++        ++++n+++ re v  + g +s  e+++k+ +++e+
  gi|119719321|ref|YP_919816.1|  31 KLGRLKQLQKMVELEFEAAYYMKKYQ--PDPVLMNTRY------GRLISNVLARRETVYEVVGGKSDSEVYAKFLRAMEN 102
                                    6799********************98..3344444444......49******************99*************8 PP

                                    ..----EE--GCG-GGGSEEECCCCC--HHHS---BSSTTSSS-EEECEEEEEE-TTTT-EEEEEEEEEEEETTEEEE-- CS
                           UbiD  86 kppippkvvesekapcqeevvlegddvdLskLPvltlwpgDgGpyitlglvitrdpetgkrnlgiyRmqvldknklglhw 165
                                      p p  ++es+++  + ev     +vdL +LPv++++++DgG+yit+g++i++dp tg  n++i+R+++ld+++l++++
  gi|119719321|ref|YP_919816.1| 103 --PQPLSRIESSTG-LK-EV-----AVDLFRLPVPKFFERDGGRYITAGVFIAKDPLTGAVNASIHRAMILDEESLAVRL 173
                                    ..577888877664.55.55.....59***************************************************** PP

                                    TTTHCHHHHHHHHHHCCT--EEEEEEES--HHHHHHCTS--TTT-TCHHHHHHHHTS--EEEE-SSSSSEEETT-SEEEE CS
                           UbiD 166 qihkggaehlrkakkkggeplpvavaiGvdPaltlaAvaplPeglsElefaGalrgepvelvkcetvdlevpadAEivle 245
                                    ++++  ++ +r+a+k+g ++lp+a+ iG++P+++l+A+ + P g+ E+e+a al g ++  +++   ++ +p   E+vl 
  gi|119719321|ref|YP_919816.1| 174 VPRHLYQI-HRNAEKAG-RNLPAAILIGAPPLVYLCAASSPPFGVYEVEVANALAGGRLTGTDSLLDGVVLPLPVEVVLL 251
                                    *8877666.999*****.8*********************************************9988************ PP

                                    EEEECCEEEECTTTC-TTSCEEC--CCEEEEEEEEEEE-TT-EEEE-SSSCCSHHHHCHHHHHHHHHHHHHHCCSTTEEE CS
                           UbiD 246 GeidpgetapEGPfgdhtGyysevrdefpvfkVtaithRkdpiypttvvgkppeedallgkalealflpllkkqvpevkd 325
                                    Ge  +g++a+EGPf+d++G+y+ vr+e pvf+V++i +R+dp+++++++    e+ +l+g+++ea ++ + +++   v++
  gi|119719321|ref|YP_919816.1| 252 GEFIAGRRAKEGPFVDILGTYDIVREE-PVFRVESILTRQDPLFYSILPSGL-EHILLMGFPREAAIWSVASRTATGVRK 329
                                    *********************999996.*******************66666.******************999999*** PP

                                    EEE-GGGTTTCEEEEECHHHTCCHHHHHHHHHHCCTTGGC-SEEEEEEETTS-TTSHHHHHHHHHHC--CCCCEEEECCC CS
                           UbiD 326 vhlpeeggfhllavvsikkrypghakkvmealwalkqqlsltKlvivvDedvdvrdlkevlwaiatrvdpdrDlviiegt 405
                                    v+l++ gg++l+av+s++k+++g+ k+v+ a++a+++  sl K+v+vvD+dvd++d+ +v+wa+atr++pd+D+vii+g+
  gi|119719321|ref|YP_919816.1| 330 VRLTPGGGGWLHAVISMEKTTEGDPKNVILAAFAAHP--SL-KTVVVVDADVDPDDPLDVEWALATRMQPDEDIVIIKGA 406
                                    *************************************..99.***********************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       230  (0.0128284); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 3384.38
//
Query:       gi|119719322|ref|YP_919817.1|  [L=157]
Description: NusG antitermination factor [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      8e-21   73.7   0.0    1.2e-20   73.2   0.0    1.3  1  Spt5-NGN  Early transcription elongation factor of RNA pol II
    2.1e-07   30.7   0.9    7.6e-07   28.9   0.9    2.0  1  KOW       KOW motif
  ------ inclusion threshold ------
      0.083   13.4   0.0        1.6    9.3   0.0    2.3  1  NusG      Transcription termination factor nusG


Domain annotation for each model (and alignments):
>> Spt5-NGN  Early transcription elongation factor of RNA pol II, NGN section
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.2   0.0   1.9e-24   1.2e-20       1      84 []      10      89 ..      10      89 .. 0.96

  Alignments for each domain:
  == domain 1  score: 73.2 bits;  conditional E-value: 1.9e-24
                       Spt5-NGN  1 siwavkctagqErevalslmkkilelakkenleIkSvfapdelkGyiyvEAdrkaaveralegipnvrgvvqglvpikEved 82
                                   +++a+++t+gqE +va  l+++    a++ +++++S++++++lkG+++vE+d  + ++r+  g+++vrgvv+g v+++E+e 
  gi|119719322|ref|YP_919817.1| 10 RFYALRVTSGQEYNVAQLLYRR----AASGKYKVYSILVVPGLKGMVFVESDALYEAQRLAYGLKHVRGVVRGAVSLQEMEG 87
                                   58********************....778889************************************************98 PP

                       Spt5-NGN 83 ll 84
                                   ll
  gi|119719322|ref|YP_919817.1| 88 LL 89
                                   86 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.9   1.3e-10   7.6e-07       1      32 []     100     131 ..     100     132 .. 0.94

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 1.3e-10
                                    TTSEEEESSSTTTTCEEEEEEEETTTTEEEEE CS
                            KOW   1 pGdhVkVvsGphkGktGkVvkvdqhkvrVfvd 32 
                                    +Gd V++++Gp+ G  G++v +d+ ++ V v+
  gi|119719322|ref|YP_919817.1| 100 VGDFVEIIRGPFTGMRGRIVGIDKSRNEVKVE 131
                                    7*************************888775 PP

>> NusG  Transcription termination factor nusG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00026       1.6       3      56 ..      11      57 ..       9      97 .. 0.57

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00026
                                   EEEEEE-TTTHHHHHHHH...HHHCT-EEE-SCEEEEEEETTEEE.......CSSTTEEEEEE- CS
                                   xxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxx RF
                           NusG  3 WYvlqvepgkekkvkenL...leeeglevivPaeekveirqgkkk.......klfpgyifikad 56
                                   +Y+l+v +g+e +v++ L   + + ++                 k       + ++g++f++ d
  gi|119719322|ref|YP_919817.1| 11 FYALRVTSGQEYNVAQLLyrrAASGKY-----------------KvysilvvPGLKGMVFVESD 57
                                   789999999999998888322222222.................12222222555666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 1166.60
//
Query:       gi|119719323|ref|YP_919818.1|  [L=89]
Description: hypothetical protein Tpen_0406 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0012   18.8   2.2     0.0033   17.3   0.1    2.0  2  SecE             SecE/Sec61-gamma subunits of protein translo
  ------ inclusion threshold ------
        3.7    7.6   6.2        1.1    9.2   0.2    2.3  2  Gram_pos_anchor  LPXTG cell wall anchor motif


Domain annotation for each model (and alignments):
>> SecE  SecE/Sec61-gamma subunits of protein translocation complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   3.7e-07    0.0033       9      48 ..      11      50 ..       5      54 .. 0.90
   2 ?    1.3   0.2     0.037   3.3e+02      27      40 ..      70      83 ..      64      84 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.7e-07
                                   HHHHCCCCCHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           SecE  9 aElkKVtWPtrkEllkttvvVlvfvvimglflflvDlvfs 48
                                   + l+ V +Pt +E+  +  vVl++  ++g ++f++ l+ s
  gi|119719323|ref|YP_919818.1| 11 RLLRMVDKPTIEEYKLMLRVVLLGLGLLGTVGFFFQLLGS 50
                                   5799******************************987765 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.037
                                   HHHHHHHHHHHHHH CS
                           SecE 27 vvVlvfvvimglfl 40
                                   ++V+++++ ++l+l
  gi|119719323|ref|YP_919818.1| 70 IIVIAATLALALYL 83
                                   68888888888875 PP

>> Gram_pos_anchor  LPXTG cell wall anchor motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   1.7     0.091   8.2e+02      20      31 ..      32      43 ..      30      46 .. 0.51
   2 ?    9.2   0.2   0.00013       1.1      20      41 ..      65      88 ..      63      88 .. 0.65

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.091
                                   XXXXXXXXXXXX CS
                Gram_pos_anchor 20 ltaaGllallgg 31
                                   l+ +Gll ++g 
  gi|119719323|ref|YP_919818.1| 32 LLGLGLLGTVGF 43
                                   445555555554 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00013
                                   XXXXXXXXXXXXXXX..XXXXXXX CS
                Gram_pos_anchor 20 ltaaGllallggllL..lvkrRKk 41
                                   ++++G+++++++l+L  +++ R k
  gi|119719323|ref|YP_919818.1| 65 TLFGGIIVIAATLALalYLRSREK 88
                                   566676666666666668888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 710.63
//
Query:       gi|119719324|ref|YP_919819.1|  [L=323]
Description: ornithine carbamoyltransferase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-49  166.7   0.0      6e-49  166.1   0.0    1.2  1  OTCace    Aspartate/ornithine carbamoyltransferase, Asp/Orn b
    1.9e-43  148.0   0.0    2.7e-43  147.5   0.0    1.2  1  OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl


Domain annotation for each model (and alignments):
>> OTCace  Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.1   0.0   6.7e-53     6e-49       2     156 ..     153     303 ..     152     304 .. 0.95

  Alignments for each domain:
  == domain 1  score: 166.1 bits;  conditional E-value: 6.7e-53
                                    C.EEEEESSTTSHHHHHHHHHHHHCT-EEEEES-TTSSH-HHHHHHHHHHHHHHT-EEEEESSCHHHHTT-SEEEE--SS CS
                         OTCace   2 glkiafvGdkknnvanslikllarlgmdvvlvaPkglepdkevleeakknakksggsititedleeavkgaDvvytdvwv 81 
                                    g+++af+Gd+  nv+nsl+++ ++lg+ ++++aP ++ p +e+l +         ++i++ ed+eeav +aDvvytdv+v
  gi|119719324|ref|YP_919819.1| 153 GVTLAFIGDGTDNVFNSLAIAGVKLGVRIRVAAPREYMPSEELLGRDV------LSRIEVYEDPEEAVRDADVVYTDVFV 226
                                    89**********************************999999995543......479*********************** PP

                                    ETTCCGGHHHHHHHHCC.CSB-HHHHHHS-T.T-EEEE-S---BTTTB-HHHHTSTTBHHHHHHHHHHHHHHHHHHH CS
                         OTCace  82 smgeekereerlkklkd.yqvteellklakk.daivlHcLPakrgeEvtdeVfdsprsvvfeqaeNrlhtikAllvl 156
                                    smg+ekere rlk + + yqv+++ll+     d+i++HcLPa+rgeEvtd+V++sp+svvf+qaeNrlht k++l++
  gi|119719324|ref|YP_919819.1| 227 SMGQEKEREYRLKVFLPkYQVNSQLLRSVGReDFIFMHCLPAHRGEEVTDDVIESPQSVVFDQAENRLHTSKSVLLH 303
                                    ***************************99998******************************************986 PP

>> OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.5   0.0     3e-47   2.7e-43       2     148 .]       6     146 ..       5     146 .. 0.96

  Alignments for each domain:
  == domain 1  score: 147.5 bits;  conditional E-value: 3e-47
                                    -BSSGGGS-HHHHHHHHHHHHHHHHHHHT.TT-STTTTT-EEEEEESS--HHHHHHHHHHHHHTTSEEEEEESTTTSCTT CS
                       OTCace_N   2 hllsledlskeeieelldlaaelkekvkk.ekkekllkgktlallFeepStRTrvSfevAakrlGgkvlslseaediqls 80 
                                    hll+l+d+ ++eie+l++ a  lk+ +k   k+ +ll+g+++a++Fe+pStRTr+Sf vAa++lG+ ++s s ++++ql 
  gi|119719324|ref|YP_919819.1|   6 HLLTLRDYAADEIESLIRDAVLLKKLRKLgLKRLNLLNGRSVAMIFEKPSTRTRASFTVAAYELGAFPVSYS-SSELQLA 84 
                                    9***********************988767899999************************************.7799998 PP

                                    TGGSTTSSCHHHHHHHHHHHTSEEEEEESSHHHHHHHHHHHSSEEEEEEETSSB-HHHHHHHHHHHHH CS
                       OTCace_N  81 svskgrkEsleDtarvlsryvdaiviRhpgaeeleelakyasvpviNagdgdgeHPtQaLaDlltire 148
                                         r+E+++D+arvl+ry d+i++R++ +e+leela+y+ vpv+N + +d++HP+QaLaD +ti e
  gi|119719324|ref|YP_919819.1|  85 -----RGEPVKDVARVLARYHDLIAARVYRHEDLEELARYSGVPVVNLL-SDKYHPLQALADYMTIFE 146
                                    .....77******************************************.****************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2257.73
//
Query:       gi|119719325|ref|YP_919820.1|  [L=452]
Description: seryl-tRNA synthetase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.9e-33  113.6   0.0    1.7e-32  112.8   0.0    1.3  1  tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, 
    9.9e-19   67.6   6.5    2.3e-18   66.4   6.5    1.6  2  Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
  ------ inclusion threshold ------
       0.27   11.8   5.6       0.69   10.4   5.6    1.7  1  APG6_N        Apg6 coiled-coil region
        1.5    9.2   7.5        5.5    7.4   0.1    2.5  2  HalX          HalX domain


Domain annotation for each model (and alignments):
>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.8   0.0   3.8e-36   1.7e-32       8     179 .]     244     422 ..     238     422 .. 0.94

  Alignments for each domain:
  == domain 1  score: 112.8 bits;  conditional E-value: 3.8e-36
                                    SEEEEE-SSSHHHHHHHHHHHEEEBGGSSEEEEEEEEEEBTTTS....TBCTTTB-SEEEEEEEEEEESGGGHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2b   8 dreyiLkPtneetfvelirdevlrskrLPlklyqiqtkyRdEks....dsrGLlRvreFhqkdgyvfhaeaslddslrdl 83 
                                    +++++L+ t+e+++++l+  evl +k+LPl ++ ++  +R+E+     d++G++Rv+ F++ +++vf++++++++  ++l
  gi|119719325|ref|YP_919820.1| 244 GEDLYLIGTAEHPIAALHAGEVLAEKELPLLYAGVSESFRKEAGahgkDTKGIFRVHHFEKVEQFVFSHPDESWEWHEKL 323
                                    589******************9*********************77899******************************** PP

                                    HHHHHHHHHHTT.SCEEEEEEGTTSCBTTSEEEEEEEEETTTSEEEEEEEEEEEETHHHHHTTEEEECTTS..SEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxx RF
                   tRNA-synt_2b  84 ikaisriferlglefraiielmsaksadykdkkefeavsesltkgieigtiqklgtrlserlgatvldenn..reksvim 161
                                    i+ ++++++ l +++r +    ++  + +++k+++ea+++ ++k++e+++++++ + +s rl++++++  +  ++  v++
  gi|119719325|ref|YP_919820.1| 324 IRNAEELWQGLEIPYRIVNIASGDLGVVAAKKYDLEAWMPAQGKYREMVSCSNCTDWQSYRLNIRYAEVRGgpSKGYVHT 403
                                    **************885555599999****************************************99998667789*** PP

                                    EEEE.EEHHHHHHHHHHHH CS
                                    xxxx.xxxxxxxxxxxxxx RF
                   tRNA-synt_2b 162 icaa.igveRllsaileqn 179
                                    ++ + ++++R++ ai+e++
  gi|119719325|ref|YP_919820.1| 404 LNSTaLAIQRTITAIVENH 422
                                    **999************86 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.4   6.5   5.2e-22   2.3e-18       5     107 ..       6     106 ..       5     107 .. 0.97
   2 ?   -3.0   0.0       1.9   8.4e+03       5      22 ..     130     147 ..     129     155 .. 0.76

  Alignments for each domain:
  == domain 1  score: 66.4 bits;  conditional E-value: 5.2e-22
                                    HHHHH-HHHHHHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHH CS
                   Seryl_tRNA_N   5 klirenpeavkeklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelk 84 
                                     l+r+npe++ e++k+R+ d+++v+  ++ld ++r+ ++e +el+++ Ne+s+++ +   +  ++e+li e++el+ +++
  gi|119719325|ref|YP_919820.1|   6 YLLRNNPEKLIENMKARFMDPSLVENAIKLDVEWRAKKKEYDELKHRLNEVSAKVRSSTGQ--EREKLILEARELSSKVS 83 
                                    69******************************************************99976..7**************** PP

                                    HHHHHHHHHHHHHHHHHCTS--- CS
                   Seryl_tRNA_N  85 aleaelkeleaeleklllaiPNi 107
                                     le+el+elea+ e +l+++PN+
  gi|119719325|ref|YP_919820.1|  84 LLEKELAELEAKRELALRRLPNV 106
                                    **********************8 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.9
                                    HHHHH-HHHHHHHHCCCT CS
                   Seryl_tRNA_N   5 klirenpeavkeklkkRg 22 
                                    k +re++e + +  k++g
  gi|119719325|ref|YP_919820.1| 130 KVFREHLEGFLKETKEKG 147
                                    889999999999998886 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   5.6   0.00015      0.69      14      78 ..      35      97 ..      32     110 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00015
                         APG6_N 14 ldkqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekere 78
                                   ld + ++ +ke d+++  l+++ ++ ++++   +e+e+l  e ++l+++ + l++eL+ele++re
  gi|119719325|ref|YP_919820.1| 35 LDVEWRAKKKEYDELKHRLNEVSAKVRSST--GQEREKLILEARELSSKVSLLEKELAELEAKRE 97
                                   677888899999999999999999977755..899999999999999999999999999999987 PP

>> HalX  HalX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1    0.0012       5.5      31      56 ..      40      65 ..      34      72 .. 0.83
   2 ?    3.1   3.6     0.027   1.2e+02      14      31 ..      77      94 ..      69     103 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0012
                           HalX 31 LadseeYqeLearleelraqldetld 56
                                   +a   eY+eL+ rl+e+ a++     
  gi|119719325|ref|YP_919820.1| 40 RAKKKEYDELKHRLNEVSAKVRSSTG 65
                                   67889**************9987765 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.027
                           HalX 14 aLasKravLeaekseaeL 31
                                   +L+sK+++Le e++e e 
  gi|119719325|ref|YP_919820.1| 77 ELSSKVSLLEKELAELEA 94
                                   79*******998776543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (452 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       867  (0.0483574); expected 358.6 (0.02)
Passed bias filter:                      628  (0.0350271); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 3088.40
//
Query:       gi|119719326|ref|YP_919821.1|  [L=132]
Description: translation initiation factor IF-5A [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-12   47.2   0.2    2.6e-12   46.7   0.2    1.3  1  eIF-5a    Eukaryotic elongation factor 5A hypusine, DNA-bindi
    6.9e-07   29.2   0.2    1.3e-06   28.3   0.2    1.5  1  EFP_N     Elongation factor P (EF-P) KOW-like domain
  ------ inclusion threshold ------
      0.012   15.7   0.2       0.92    9.7   0.0    2.6  2  YcgR_2    Flagellar protein YcgR
      0.033   14.2   0.3      0.061   13.4   0.3    1.4  1  EFP       Elongation factor P (EF-P) OB domain


Domain annotation for each model (and alignments):
>> eIF-5a  Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.7   0.2   5.8e-16   2.6e-12       1      69 []      69     131 ..      69     131 .. 0.97

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 5.8e-16
                                    --EEEEEEEEEE-SS.EEEEEE.TT--EEE.EEGG..GB-HHHHTT--TT-E..EEEEEETTEEEEEEE- CS
                         eIF-5a   1 nVkrkeyqLidIqdDgflsLmd.ddgetkeDlklpegelgkqikekfeegkdvlVtVlsamGeekiiavK 69 
                                    ++k++++q+++  +D  ++Lm+ +d++t+e +++p    +++ik+k+ eg +  V+V+++mG+ ki++v+
  gi|119719326|ref|YP_919821.1|  69 IIKKFTAQVVAFVGD-NVQLMNlEDYSTFE-IPMP---QEEEIKSKLSEGVE--VEVWEVMGRHKIMRVR 131
                                    69*************.9*************.****...789***********..*************997 PP

>> EFP_N  Elongation factor P (EF-P) KOW-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.2     3e-10   1.3e-06       2      33 ..       8      39 ..       7      45 .. 0.92

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 3e-10
                                   GGG--TT-EEEETTEEEEEEEEEEEEETTS-- CS
                          EFP_N  2 aselkkGlvieidgklyvVlefehvkpGkGqa 33
                                   a ++k G +i idg++++V+e+e +k Gk ++
  gi|119719326|ref|YP_919821.1|  8 AGNIKVGSFIVIDGEPCKVVEVEKSKTGKHGS 39
                                   889*************************9764 PP

>> YcgR_2  Flagellar protein YcgR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0    0.0087        39      46      80 ..      69      88 ..      23      92 .. 0.55
   2 ?    9.7   0.0   0.00021      0.92      25      59 ..      89     123 ..      84     132 .] 0.79

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0087
                                   --TT-EEEEEEE-TSSEEEEEEEEEEEEETTCEEE CS
                         YcgR_2 46 lregtevevrfiseggvyaFrsrvlgrikdpipll 80
                                   +                 +F+++v+  + d++ l+
  gi|119719326|ref|YP_919821.1| 69 II---------------KKFTAQVVAFVGDNVQLM 88
                                   33...............345566666555555555 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00021
                                    EE.-TTEEEEEEEEET-SB----TT-EEEEEEE-T CS
                         YcgR_2  25 dikgddyliislPieegrlvplregtevevrfise 59 
                                      ++ +++ i +P+ee+    l eg evev+ + +
  gi|119719326|ref|YP_919821.1|  89 NLEDYSTFEIPMPQEEEIKSKLSEGVEVEVWEVMG 123
                                    555678899*********************86655 PP

>> EFP  Elongation factor P (EF-P) OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.3   1.4e-05     0.061      10      47 ..      82     119 ..      76     124 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.4e-05
                                    TTEEEEEETTT--EEEEEHHHHTTGCGG--TT-EEEEE CS
                            EFP  10 gdeyvFMdnetYeqielpkeqlgdaakfLkEgmevtvl 47 
                                    gd++ +M+ e+Y  +e+p  q ++ +  L Eg ev+v+
  gi|119719326|ref|YP_919821.1|  82 GDNVQLMNLEDYSTFEIPMPQEEEIKSKLSEGVEVEVW 119
                                    89*******************98888999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 956.05
//
Query:       gi|119719327|ref|YP_919822.1|  [L=168]
Description: phosphopantetheine adenylyltransferase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-08   34.2   0.0    3.1e-08   33.9   0.0    1.2  1  CTP_transf_like  Cytidylyltransferase-like


Domain annotation for each model (and alignments):
>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.0   1.7e-12   3.1e-08       1     139 [.      20     153 ..      20     157 .. 0.73

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 1.7e-12
                                    EEEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST.-.SCSSTHHHHHHHHHHH.TTCTTEEEEEEESEHHHHH CS
                CTP_transf_like   1 lagGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkk.k.kplasaeeRlemlela.kevdevisvdpweltrevl 77 
                                    ++gGtF ++H GH rll+ a+   +e l+vgv+sde +k   k +p+ ++e R   +  + k vd+    +p  +++ + 
  gi|119719327|ref|YP_919822.1|  20 VVGGTFSLLHRGHRRLLRFALLCSQE-LLVGVTSDEYVKERgKsHPVEPYEVRALSVLTFlKTVDP---SRPVAIVP-ID 94 
                                    579******************99999.**************659*********9999888777777...45555554.55 PP

                                    HHTTT.......TEEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEEHTTCEEEEEEECCTTTCSHHH CS
                CTP_transf_like  78 kklkp.......dklylvigadvledfsewkeleeilgnvklvvvsrpekqanvllkaekrtngiSstk 139
                                    ++++p       d  ++ ++++++  + + + l+++ g  +l ++ ++        + + +    Sst+
  gi|119719327|ref|YP_919822.1|  95 DEYGPatsdpcaD--CIFVSEETFPGAVKVNMLRRLRGLPPLKIFAVE--------LVTVEGVRLSSTY 153
                                    5555544434445..777777777777777777777777777777555........3334444455555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1246.60
//
Query:       gi|119719328|ref|YP_919823.1|  [L=77]
Description: hypothetical protein Tpen_0411 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.015   14.6   3.3      0.015   14.5   3.3    1.1  1  Herpes_BMRF2  Herpesvirus BMRF2 protein


Domain annotation for each model (and alignments):
>> Herpes_BMRF2  Herpesvirus BMRF2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   3.3   8.5e-07     0.015     261     322 ..      14      74 ..       1      76 [. 0.72

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 8.5e-07
                   Herpes_BMRF2 261 vsravlvvlltlavvlillvhvlldkadllliksvLvivilvlylsavgceieiirkKLkka 322
                                     s  vl   l l ++l+++  v l+ +  +l++++L +++l++++  +++  e++r+KL++a
  gi|119719328|ref|YP_919823.1|  14 LSSLVLLAWLELIAFLLIVENVALK-VANSLVRGLLGVLLLFTWVLLMAVAAEALRRKLARA 74 
                                    3444444444444555555555555.56679****************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       913  (0.0509231); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 557.06
//
Query:       gi|119719329|ref|YP_919824.1|  [L=341]
Description: glycosyl transferase family protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.4e-31  107.0  18.7      2e-30  105.9  18.7    1.6  1  Glycos_transf_4  Glycosyl transferase family 4


Domain annotation for each model (and alignments):
>> Glycos_transf_4  Glycosyl transferase family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.9  18.7   1.1e-34     2e-30       2     159 ..      84     244 ..      83     245 .. 0.88

  Alignments for each domain:
  == domain 1  score: 105.9 bits;  conditional E-value: 1.1e-34
                Glycos_transf_4   2 llllltillilllGflDDvlglkarlKlilqilaalililtld.....lslttlgllltqvlielglilavlltllvivg 76 
                                    l++l+t++l++++G+lDD l lk +lK++l++l+++++++++      + + +  +++  + ++++ +++++l+ + i+g
  gi|119719329|ref|YP_919824.1|  84 LAVLATSALCFAVGLLDDKLVLKGVLKTFLTALSIIPILVVALtypaaIDWGRPVVPI-IGRMRMT-VIYWVLFPISIAG 161
                                    6899********************************9988777666552222222233.3667788.778899999**** PP

                Glycos_transf_4  77 vtNavNliDGldGlaagvsiiialalvvlaavdgrsellllalallgallGfllfNrypAkvFmGDsgslflGlvlavla 156
                                     +N+vN++D l+G+  g+++++++al+v+ a++g+  ll++al+ ++ ll++++fN+ypA+vF GDsgslf+G++l+++a
  gi|119719329|ref|YP_919824.1| 162 SANVVNMLDVLNGIVPGTALVAFAALAVIGALSGDGLLLVIALVAVAILLAYYPFNAYPARVFNGDSGSLFIGGLLGAIA 241
                                    *****************************************88888888******************************* PP

                Glycos_transf_4 157 ilg 159
                                    +++
  gi|119719329|ref|YP_919824.1| 242 VVF 244
                                    986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.36
# Mc/sec: 2833.04
//
Query:       gi|119719330|ref|YP_919825.1|  [L=328]
Description: putative deoxyhypusine synthase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-82  276.0   0.0    3.7e-82  275.8   0.0    1.0  1  DS        Deoxyhypusine synthase


Domain annotation for each model (and alignments):
>> DS  Deoxyhypusine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  275.8   0.0   2.1e-86   3.7e-82       2     285 ..      30     318 ..      29     321 .. 0.96

  Alignments for each domain:
  == domain 1  score: 275.8 bits;  conditional E-value: 2.1e-86
                             DS   2 llesyeki.gfqatslgeaidilnkmrkdekctiflgltsnlissGlreiiadlvkeklvdvivtTaggieeDlikalgk 80 
                                    +l+sy++  gf+a+ + ea+++l ++  +    i +++ +nl+++Glr++iad ++++l+d++vtT+g+ ++D+++ +g+
  gi|119719330|ref|YP_919825.1|  30 VLKSYRRLgGFSARYIVEAAELLWEAY-SGGGRIAVAFPANLVATGLRGLIADSIRRGLLDLVVTTGGTFDHDIARGTGH 108
                                    6899****9*****************5.5677************************************************ PP

                             DS  81 ktylgdfelddeeLrekginRignllvpneny.ckfedwvreildkleeeqkvwspselikelGkeindeeSilywAykn 159
                                    k+y+g+fe+dd  L+e gi+R+gn+l+p eny   +e++++e+l++l++ +++wspsel  e Gk+++de Sil++ y++
  gi|119719330|ref|YP_919825.1| 109 KYYVGRFEIDDVFLKELGIHRLGNILIPVENYgPPIERFTHEMLEELSALKSSWSPSELAVESGKRLRDELSILRAVYEK 188
                                    ********************************99********************************************** PP

                             DS 160 dipvfcpaltDgslGdqlllfhsv...k.ekkklkldivkDirelndialkakktgaiilGGGvpKhhilnanlmrngad 235
                                    +    +p++ D+++G+++++f++    + + + ++ld+++D r+++d +++a+k + ++lGGG++Khh+++++++r g+d
  gi|119719330|ref|YP_919825.1| 189 GRLLVSPGVLDSAFGTAIVTFNDKaraSsTARFVELDLISDERRIADYMYEAEKLAGLMLGGGISKHHLIWWAQFRGGLD 268
                                    *********************97545433566689********************************************* PP

                             DS 236 yavyittaqefdGslsgatldEavSwgkikaeaksvkvyaDaTivlPLlv 285
                                    yav+it   e+dGslsga+++EavSwgkik+ea++v+v +D+T++lPL++
  gi|119719330|ref|YP_919825.1| 269 YAVQITSTPEWDGSLSGARTREAVSWGKIKPEARHVTVPGDVTVILPLIL 318
                                    ************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 2236.16
//
Query:       gi|119719331|ref|YP_919826.1|  [L=69]
Description: DNA-directed RNA polymerase subunit E, RpoE2 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.2e-14   52.4   0.2    4.9e-14   52.2   0.2    1.1  1  Spt4            Spt4/RpoE2 zinc finger
      7e-05   22.1   1.4    9.8e-05   21.6   1.4    1.2  1  zf-ribbon_3     zinc-ribbon domain
    0.00074   19.1   0.8    0.00074   19.1   0.8    1.6  2  zf-RRN7         Zinc-finger of RNA-polymerase I-specific TFII
     0.0054   16.7   0.6     0.0079   16.2   0.6    1.2  1  DZR             Double zinc ribbon
  ------ inclusion threshold ------
       0.01   15.5   0.3      0.014   15.1   0.3    1.2  1  zinc_ribbon_2   zinc-ribbon domain
      0.022   15.5   0.3       0.03   15.1   0.3    1.2  1  zinc_ribbon_15  zinc-ribbon family
      0.027   14.3   1.5       0.05   13.5   1.5    1.4  1  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
      0.029   13.9   2.7      0.048   13.2   0.2    2.2  2  TF_Zn_Ribbon    TFIIB zinc-binding
      0.041   14.2   0.7       0.16   12.2   0.6    1.7  2  DUF2072         Zn-ribbon containing protein
       0.16   12.0   3.1       0.98    9.5   0.5    2.2  2  YhfH            YhfH-like protein
       0.32   11.2   2.7        5.1    7.3   3.0    2.1  2  Zn-ribbon_8     Zinc ribbon domain
       0.98    9.6   6.5        2.3    8.4   0.5    2.4  2  DUF2256         Uncharacterized protein conserved in bacteria


Domain annotation for each model (and alignments):
>> Spt4  Spt4/RpoE2 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.2   0.2   3.3e-17   4.9e-14       1      77 []       9      69 .]       9      69 .] 0.97

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 3.3e-17
                           Spt4  1 lrACllCklvktedqFeeegCpnCeilelkgdkekvsectseefeGlvaildpekSwvAkwqrldkkvpglYAlkve 77
                                   l+AC++Ck++++++    + Cp+C           +s++++++++G+va++dpekS+ Ak   l+ k++g Y +kv+
  gi|119719331|ref|YP_919826.1|  9 LKACVKCKALVEDSV---DVCPVC-----------GSREFTDDWDGFVAVIDPEKSEAAKL--LSLKQKGAYSVKVR 69
                                   59************9...******...........**************************..99999*******96 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   1.4   6.6e-08   9.8e-05       3      24 ..      10      31 ..       8      32 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 6.6e-08
                    zf-ribbon_3  3 vrCPnCGaplssddnvCpyCGt 24
                                   + C +C+a++++++ vCp CG+
  gi|119719331|ref|YP_919826.1| 10 KACVKCKALVEDSVDVCPVCGS 31
                                   68******99***********8 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       2.3   3.5e+03       6      10 ..      11      15 ..      10      19 .. 0.65
   2 !   19.1   0.8     5e-07   0.00074       3      21 ..      22      41 ..      20      42 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2.3
                        zf-RRN7  6 pCgvC 10
                                   +C  C
  gi|119719331|ref|YP_919826.1| 11 ACVKC 15
                                   56666 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 5e-07
                        zf-RRN7  3 kgppCgvCgcrsftl.ddGf 21
                                    + +C+vCg+r+ft   dGf
  gi|119719331|ref|YP_919826.1| 22 SVDVCPVCGSREFTDdWDGF 41
                                   5789**********977887 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.6   5.3e-06    0.0079      28      49 .]       9      30 ..       2      30 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5.3e-06
                            DZR 28 edrCpsCgekvdpearfCpeCG 49
                                    ++C++C++ v+    +Cp CG
  gi|119719331|ref|YP_919826.1|  9 LKACVKCKALVEDSVDVCPVCG 30
                                   579******************9 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.3   9.3e-06     0.014       2      21 ..      12      31 ..      11      32 .. 0.96

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 9.3e-06
                  zinc_ribbon_2  2 CpnCGaelqdnakFCpyCGt 21
                                   C +C a ++d +  Cp CG+
  gi|119719331|ref|YP_919826.1| 12 CVKCKALVEDSVDVCPVCGS 31
                                   9******************7 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.3     2e-05      0.03      66      86 .]      10      30 ..       2      30 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2e-05
                 zinc_ribbon_15 66 keCknCgkeveeefkyCpkCg 86
                                   k C +C++ ve++++ Cp Cg
  gi|119719331|ref|YP_919826.1| 10 KACVKCKALVEDSVDVCPVCG 30
                                   79******************9 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   1.5   3.4e-05      0.05       7      36 ..       5      34 ..       2      35 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.4e-05
                        DUF35_N  7 grLvgqrCpdCGtvqfPPr.avCphCgsddl 36
                                    rL +  C +C ++ +     vCp Cgs+++
  gi|119719331|ref|YP_919826.1|  5 RRLPLKACVKCKAL-VEDSvDVCPVCGSREF 34
                                   5999999*******.58888*********98 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.2      0.24   3.5e+02      22      31 ..      12      21 ..      11      24 .. 0.51
   2 ?   13.2   0.2   3.2e-05     0.048       2      14 ..      25      37 ..      25      53 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.24
                                   ESSSSBEEEE CS
                   TF_Zn_Ribbon 22 CtdCGlVled 31
                                   C +C +++ed
  gi|119719331|ref|YP_919826.1| 12 CVKCKALVED 21
                                   6666333333 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 3.2e-05
                                   EETTTTCEECHEE CS
                   TF_Zn_Ribbon  2 kCPnCgstnlveD 14
                                   +CP+Cgs++++ D
  gi|119719331|ref|YP_919826.1| 25 VCPVCGSREFTDD 37
                                   7******998544 PP

>> DUF2072  Zn-ribbon containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.6   0.00011      0.16       3      30 ..      11      34 ..       9      36 .. 0.91
   2 ?   -0.4   0.0      0.83   1.2e+03     114     127 ..      55      68 ..      45      69 .] 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00011
                        DUF2072  3 kCtkCekvfedgskeilkGCpsCGgkkF 30
                                    C+kC+ + ed+ +     Cp+CG + F
  gi|119719331|ref|YP_919826.1| 11 ACVKCKALVEDSVD----VCPVCGSREF 34
                                   6**********988....7*******99 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.83
                        DUF2072 114 vmalkeegkYvvdl 127
                                    +++lk++g Y v++
  gi|119719331|ref|YP_919826.1|  55 LLSLKQKGAYSVKV 68 
                                    57888999998875 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.5   0.00065      0.98       9      19 ..       5      15 ..       4      21 .. 0.93
   2 ?    2.8   0.1      0.08   1.2e+02      15      21 ..      25      31 ..      24      35 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00065
                           YhfH  9 rnLPkKkCteC 19
                                   r+LP K C++C
  gi|119719331|ref|YP_919826.1|  5 RRLPLKACVKC 15
                                   89********* PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.08
                           YhfH 15 kCteCGk 21
                                   +C+ CG+
  gi|119719331|ref|YP_919826.1| 25 VCPVCGS 31
                                   5*****7 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1     0.059        88      23      36 ..       6      19 ..       1      23 [. 0.75
   2 ?    7.3   3.0    0.0034       5.1      23      35 ..      20      33 ..      11      36 .. 0.64

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.059
                    Zn-ribbon_8 23 dapltaCPeCgsev 36
                                   + pl+aC +C++ v
  gi|119719331|ref|YP_919826.1|  6 RLPLKACVKCKALV 19
                                   55788999998755 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0034
                    Zn-ribbon_8 23 dapltaCPeCgs.e 35
                                   +++  +CP Cgs e
  gi|119719331|ref|YP_919826.1| 20 EDSVDVCPVCGSrE 33
                                   344456*****955 PP

>> DUF2256  Uncharacterized protein conserved in bacteria (DUF2256)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.5    0.0016       2.3       2      14 ..       4      16 ..       3      21 .. 0.89
   2 ?    4.3   0.9      0.03        45       9      18 ..      25      35 ..      22      41 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0016
                        DUF2256  2 KselpsKiCavCg 14
                                   K++lp K C+ C+
  gi|119719331|ref|YP_919826.1|  4 KRRLPLKACVKCK 16
                                   899*********8 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.03
                        DUF2256  9 iCavCg.rpft 18
                                   +C+vCg r+ft
  gi|119719331|ref|YP_919826.1| 25 VCPVCGsREFT 35
                                   6****857787 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 495.14
//
Query:       gi|119719332|ref|YP_919827.1|  [L=222]
Description: DNA-directed RNA polymerase subunit E' [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-17   63.4   0.0    3.5e-17   62.5   0.0    1.5  1  SHS2_Rpb7-N    SHS2 domain found in N terminus of Rpb7p/Rpc25
    3.3e-11   43.3   3.1    3.3e-11   43.3   3.1    1.9  2  S1             S1 RNA binding domain
  ------ inclusion threshold ------
      0.082   13.1   0.1       0.16   12.2   0.0    1.5  2  RNA_pol_Rbc25  RNA polymerase III subunit Rpc25


Domain annotation for each model (and alignments):
>> SHS2_Rpb7-N  SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.5   0.0   5.9e-21   3.5e-17       2      70 .]      36     104 ..      35     104 .. 0.99

  Alignments for each domain:
  == domain 1  score: 62.5 bits;  conditional E-value: 5.9e-21
                                    EEEEE-GGGTTSTHHHHHHHHHHHHHTTBEETTTEEEEEEEEEEEECCEEE-TTTSSEEEEEEEEEEEE CS
                    SHS2_Rpb7-N   2 dtvrlePsylgstledallerllekyegkvvpslGvivavldiaeysegkvlggsGsvyvrVtfralvF 70 
                                    d++r++P  +g++l++a le+l+e +eg+vv+ +G+++++ld + ++eg  + g+G++y++++f+alvF
  gi|119719332|ref|YP_919827.1|  36 DVIRIPPRLFGQPLKEASLEILKESFEGRVVQGVGLVISILDAEVSEEGFLTWGDGASYHEARFTALVF 104
                                    89******************************************************************9 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1      0.52   3.1e+03       8      16 ..      61      69 ..      58      81 .. 0.56
   2 !   43.3   3.1   5.6e-15   3.3e-11       5      75 .]     109     191 ..     105     191 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.52
                                   EEEEEEEEE CS
                             S1  8 veGeVtsvt 16
                                   +eG V++ +
  gi|119719332|ref|YP_919827.1| 61 FEGRVVQGV 69
                                   555555544 PP

  == domain 2  score: 43.3 bits;  conditional E-value: 5.6e-15
                                    TCEEEEEEEEEETTEEEEEETTTEEEEEEGGGSSSS.............CEESCHHHCEETTEEEEEEEEEEETTTTEEE CS
                             S1   5 gevveGeVtsvtkgGafVelgngvegfvpaselsrd.............arvedpdevlkvGdevkvkvlkvdkdrrrii 71 
                                    +evveGeV  v++ G+ V+lg +vegfv++s++                  +e++++++++Gd v+ +v +v +d+ r +
  gi|119719332|ref|YP_919827.1| 109 NEVVEGEVDLVENIGLTVRLG-PVEGFVHKSQIYPSrnitydrengvviIQDEKGTRTIRKGDVVRGRVVGVSYDEQRGQ 187
                                    89*******************.***********76668***********99*************************9988 PP

                                    EEEC CS
                             S1  72 lsik 75 
                                    l i+
  gi|119719332|ref|YP_919827.1| 188 LKIR 191
                                    8775 PP

>> RNA_pol_Rbc25  RNA polymerase III subunit Rpc25
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.3   7.8e+03      23      39 ..      32      48 ..      28      50 .. 0.79
   2 ?   12.2   0.0   2.7e-05      0.16       1      80 [.     106     185 ..     106     217 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.3
                                   BTTBSEEEEECCCCSTT CS
                  RNA_pol_Rbc25 23 lgffddifvpkelLfep 39
                                   ++f d i +p++l+ +p
  gi|119719332|ref|YP_919827.1| 32 VEFADVIRIPPRLFGQP 48
                                   48999999999987666 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 2.7e-05
                                    -STTSEEEEEEEEEETTCEEEEBTTBSEEEEECCCCS..TTEEEECCCTCEEEEESSSEEEEE-TTSEEEEEEEEEEE-- CS
                  RNA_pol_Rbc25   1 PfvgevltgkiksstregikvslgffddifvpkelLf..epsefdeeeqawvweveeeeelyldvgeeirfrveeeifvd 78 
                                    P+ +ev++g +   ++ g+ v+lg ++  fv k+++    +  +d+e+ + + +  e+ +  + +g+ +r rv+ +++ +
  gi|119719332|ref|YP_919827.1| 106 PVNNEVVEGEVDLVENIGLTVRLGPVEG-FVHKSQIYpsRNITYDRENGVVIIQD-EKGTRTIRKGDVVRGRVVGVSYDE 183
                                    8899********************9987.67777775226889**9999988887.7777789**************955 PP

                                    -- CS
                  RNA_pol_Rbc25  79 vk 80 
                                    ++
  gi|119719332|ref|YP_919827.1| 184 QR 185
                                    54 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 1496.17
//
Query:       gi|119719333|ref|YP_919828.1|  [L=320]
Description: DNA-cytosine methyltransferase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-51  175.1   0.0    1.1e-33  117.0   0.0    2.0  2  DNA_methylase    C-5 cytosine-specific DNA methylase
  ------ inclusion threshold ------
      0.018   14.6   0.0      0.027   14.0   0.0    1.2  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
      0.026   14.3   0.0       0.04   13.7   0.0    1.4  1  Met_10           Met-10+ like-protein


Domain annotation for each model (and alignments):
>> DNA_methylase  C-5 cytosine-specific DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.0   0.0   1.9e-37   1.1e-33       2     159 ..       6     174 ..       5     191 .. 0.89
   2 !   56.5   0.0   4.5e-19   2.7e-15     266     335 .]     248     317 ..     182     317 .. 0.84

  Alignments for each domain:
  == domain 1  score: 117.0 bits;  conditional E-value: 1.9e-37
                                    EEEEES-TT-HHHHHHHHTT-EEEEEEE--TTTHHHHHHH-...-SEEEES-TTTS-......GS--.-SEEEE---GGG CS
                  DNA_methylase   2 kfidLfaGiGGfrlgleaagfecvaaseidkkaaktYeanfk..kvsigDitkidkk......klpediDlLvgGfPCqp 73 
                                    +++dLfaG+GGf+ g+++ gf++v a+e d+ aa+ ++ nf+  +v ++D++++  +       ++    +++gG+PC +
  gi|119719333|ref|YP_919828.1|   6 TVLDLFAGAGGFSRGFAEEGFSIVGAVEVDPLAAEAFRLNFPgaRVFEEDVREVHSRdillglGFR--PRVIIGGPPCEA 83 
                                    789****************************************99999999999999776644444..89********** PP

                                    TECTSE.......E--TTSGGGHHHHHHHHHHHHH--SEEEEEEEGGGGGGCCSHHHHHHHHHHHHHTEE.EEEEEEEGG CS
                  DNA_methylase  74 fSvaGk.......qkgfedtrgtLffeiiriikekkPkvfllENVkgLlkhdkgktlkvilekleelGYe.vsykllnas 145
                                    +S a          +  +d+ g+L   +iri+ + +P+vf++ENV+g+l++  g   +v+ e+++ +GY+ v++++l a+
  gi|119719333|ref|YP_919828.1|  84 YSRANPrrereplDRLYKDPVGSLVLHYIRIVGDLEPEVFVMENVPGILDEGLG---EVLREEFSRVGYHdVYFNVLVAE 160
                                    ****985555555566789999*****************************765...56679******97699******* PP

                                    GTT-SB--EEEEEE CS
                  DNA_methylase 146 dyGvpQnReRvfiv 159
                                    +yG+p  R Rvfi 
  gi|119719333|ref|YP_919828.1| 161 HYGTPSHRVRVFIS 174
                                    ************96 PP

  == domain 2  score: 56.5 bits;  conditional E-value: 4.5e-19
                                    --EEEETTEEE--T.TTGGG--B-BHHHHHHHHT--TT-----SBHHHHHHHHTS--HHHHHHHHHHHHH CS
                  DNA_methylase 266 eagklqknkerfkpviekkriRrLtprEaarlqGfPddfefgskksaaykqiGnsVpvpvieaiakeikk 335
                                    + +++  +++ + +++++ ++R Lt+rE arl+GfPd+  f ++k+a++ q+G++Vpvp+++aia+e+kk
  gi|119719333|ref|YP_919828.1| 248 HPYRVAPTVMGSSRFVHPFENRLLTVREQARLMGFPDTHVFVGSKEAQFNQVGEAVPVPLARAIAREVKK 317
                                    445566667777779***************************************************9976 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   4.5e-06     0.027       3      32 ..       6      36 ..       4      57 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.5e-06
                Methyltransf_15  3 vilDlfsGaGGnviqfalv.fekviaieinl 32
                                   ++lDlf+GaGG +  fa++ f+ v a+e+++
  gi|119719333|ref|YP_919828.1|  6 TVLDLFAGAGGFSRGFAEEgFSIVGAVEVDP 36
                                   58****************9899999999986 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   6.7e-06      0.04     103     165 ..       6      61 ..       1     117 [. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.7e-06
                                    EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG--- CS
                         Met_10 103 vVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDgrevir 165
                                    +V+d+fAG G f+   a     ++v a++++P + + +    +lN    +v  ++eD+rev  
  gi|119719333|ref|YP_919828.1|   6 TVLDLFAGAGGFSRGFAE-EGFSIVGAVEVDPLAAEAF----RLNFPGARV--FEEDVREVHS 61 
                                    79***************9.5567899******997655....566555555..7777777754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2233.19
//
Query:       gi|119719334|ref|YP_919829.1|  [L=69]
Description: hypothetical protein Tpen_0417 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.049   13.7   0.4      0.066   13.3   0.4    1.2  1  Mis12     Mis12 protein


Domain annotation for each model (and alignments):
>> Mis12  Mis12 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.4   3.7e-06     0.066      26      67 ..      26      66 ..      21      68 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.7e-06
                                   HHHHHHHHHHH........TTSTHHHH-HHHHHHHHHHHHHH CS
                          Mis12 26 yravdavekvLdkkleedeeeekaaeesteeieeGtakletl 67
                                    +a+da+e++L+   +  + + +++ee ++e+eeG+++l++l
  gi|119719334|ref|YP_919829.1| 26 VEALDAIEEFLA-SVHGATPQVEEDEELARELEEGVEELREL 66
                                   689********5.55555566888999************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       696  (0.0388198); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 500.40
//
Query:       gi|119719335|ref|YP_919830.1|  [L=474]
Description: hypothetical protein Tpen_0418 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.064   13.0   0.3       0.67    9.7   0.1    2.4  2  Get5_C    Get5 C-terminal domain


Domain annotation for each model (and alignments):
>> Get5_C  Get5 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1   3.7e-05      0.67      26      38 .]     176     188 ..     174     188 .. 0.91
   2 ?    0.2   0.0     0.035   6.3e+02      14      32 ..     450     468 ..     443     468 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 3.7e-05
                         Get5_C  26 vleRLqKGWeltk 38 
                                    vl+ LqKGW lt+
  gi|119719335|ref|YP_919830.1| 176 VLQSLQKGWVLTD 188
                                    99********996 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.035
                         Get5_C  14 knkfkndaearavleRLqK 32 
                                    k+k +  ++a +++eRL K
  gi|119719335|ref|YP_919830.1| 450 KAKAEQYPKAWELVERLEK 468
                                    455555588999*****87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (474 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 3104.96
//
Query:       gi|119719336|ref|YP_919831.1|  [L=174]
Description: hypothetical protein Tpen_0419 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.7e-32  109.7   0.1    1.1e-30  106.1   0.1    2.0  2  DUF2122         RecB-family nuclease (DUF2122)
     0.0014   18.8   0.0     0.0017   18.5   0.0    1.1  1  SpoU_methylase  SpoU rRNA Methylase family


Domain annotation for each model (and alignments):
>> DUF2122  RecB-family nuclease (DUF2122)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.042   3.8e+02       8      26 ..      19      37 ..      14      39 .. 0.86
   2 !  106.1   0.1   1.3e-34   1.1e-30       1     105 [.      41     154 ..      41     155 .. 0.96

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.042
                        DUF2122  8 ipevlklalklgksllvlp 26
                                   ++ev ++a+ lg + lvl+
  gi|119719336|ref|YP_919831.1| 19 VAEVARIAYGLGYNTLVLS 37
                                   99***********999986 PP

  == domain 2  score: 106.1 bits;  conditional E-value: 1.3e-34
                        DUF2122   1 GaAAqsGipevlklalklgksllvlpdlkDalellkpekvlllsk.ee.geelleeeel.......eekgrvllvfsgad 71 
                                    G AAq Gipe++klal+++++l+vl+dl +++ell+p+++l++ + ++ g+el+e+ ++        e +r+++vf+ga+
  gi|119719336|ref|YP_919831.1|  41 GPAAQVGIPEAQKLALRHNCNLIVLSDLPEVVELLRPNVILVAVPgKYgGRELSEVLKElegktsgGEASRIAVVFGGAE 120
                                    78*****************************************9978899999999888999999999************ PP

                        DUF2122  72 egfskkelelgetvkvegveadvgelaelavvly 105
                                    +g+s+ke+++ge v+++gve+d+g+++ +av+ly
  gi|119719336|ref|YP_919831.1| 121 PGLSQKEMKTGELVHPDGVEEDIGSTGVAAVTLY 154
                                    *********************************9 PP

>> SpoU_methylase  SpoU rRNA Methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.9e-07    0.0017       5     114 ..       9     129 ..       5     135 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.9e-07
                                    EEES-SSHHHHHHHHHHHHHTT-SEEEEESGSSC..TCGSHHHHHHCTTHHHHHHEEEESSHHHHHHHHCCCTEEEEEES CS
                 SpoU_methylase   5 vlveiedpgNlGaiaRtakafgaselvlvkprsa..dllnpeakraaagalevlelkvvdsleealkelkeegfalvats 82 
                                    vl ++++ + +  +aR a+ +g ++lvl++  +   ++  pea+++a+ +    +l v ++l e+++ l+ + + lva+ 
  gi|119719336|ref|YP_919831.1|   9 VLHNTNSSQRVAEVARIAYGLGYNTLVLSRVYGPaaQVGIPEAQKLALRHN--CNLIVLSDLPEVVELLRPN-VILVAVP 85 
                                    8999999999******************87644311345566666665544..44779************99.9999998 PP

                                    T..T-SEGCCS..HHH........TTEEEEEEBTTTBS-HHHHC CS
                 SpoU_methylase  83 l..kgkslsei..dlk........ekvalvfGnEdkGlsnelle 114
                                    +  +g++lse+  +l+        +++a+vfG  + Gls+++++
  gi|119719336|ref|YP_919831.1|  86 GkyGGRELSEVlkELEgktsggeaSRIAVVFGGAEPGLSQKEMK 129
                                    899999999885522255677888****************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       231  (0.0128842); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 1107.15
//
Query:       gi|119719337|ref|YP_919832.1|  [L=63]
Description: 50S ribosomal protein L37e [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.5e-24   84.1  12.6    6.2e-24   83.9  12.6    1.0  1  Ribosomal_L37e  Ribosomal protein L37e
     0.0071   16.5   1.5     0.0084   16.2   1.5    1.3  1  NOB1_Zn_bind    Nin one binding (NOB1) Zn-ribbon like
     0.0099   15.7   5.9      0.018   14.9   5.9    1.4  1  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
  ------ inclusion threshold ------
      0.063   13.0   1.5      0.063   13.0   1.5    2.3  2  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
       0.62    9.6   4.4        2.2    7.8   4.4    1.8  1  zf-ribbon_3     zinc-ribbon domain
        1.5    8.6   7.4         13    5.6   0.6    2.3  2  Rubredoxin_2    Rubredoxin metal binding domain


Domain annotation for each model (and alignments):
>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.9  12.6   2.1e-27   6.2e-24       2      53 ..       3      55 ..       2      56 .. 0.98

  Alignments for each domain:
  == domain 1  score: 83.9 bits;  conditional E-value: 2.1e-27
                 Ribosomal_L37e  2 kGtssfGkrqkkktHilCrrCgkrsyhvqkktCascGy.psaklrkynWsaKa 53
                                   kGt+sfGkr ++ tHi+CrrCg++s++v+k +Ca+cG+ +s+++r+y+W++K+
  gi|119719337|ref|YP_919832.1|  3 KGTTSFGKRGRNITHIRCRRCGHHSFNVRKGYCAHCGFgRSKRIRRYSWQNKK 55
                                   9**************************************************97 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   1.5   2.8e-06    0.0084       9      39 ..      18      48 ..      10      62 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.8e-06
                   NOB1_Zn_bind  9 lrChaCfkvtkdmtkkFCpkCGnktLkrvav 39
                                   +rC+ C +   + +k +C +CG    kr+  
  gi|119719337|ref|YP_919832.1| 18 IRCRRCGHHSFNVRKGYCAHCGFGRSKRIRR 48
                                   79********************766555543 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   5.9   5.9e-06     0.018      13      32 ..      19      39 ..      18      44 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.9e-06
                        DUF35_N 13 rCpdCGtvqfPPr.avCphCg 32
                                   rC+ CG++ f  r  +C hCg
  gi|119719337|ref|YP_919832.1| 19 RCRRCGHHSFNVRkGYCAHCG 39
                                   9*******************5 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   1.5   2.1e-05     0.063      17      27 ..      17      27 ..      13      29 .. 0.86
   2 ?    2.5   0.7      0.04   1.2e+02      20      25 ..      35      40 ..      34      43 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.1e-05
                                   ----SSS---- CS
                 DNA_RNApol_7kD 17 piRCkeCGhRi 27
                                    iRC+ CGh +
  gi|119719337|ref|YP_919832.1| 17 HIRCRRCGHHS 27
                                   59*******76 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.04
                                   -SSS-- CS
                 DNA_RNApol_7kD 20 CkeCGh 25
                                   C +CG+
  gi|119719337|ref|YP_919832.1| 35 CAHCGF 40
                                   778886 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   4.4   0.00072       2.2       2      24 ..      17      40 ..      16      41 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00072
                    zf-ribbon_3  2 tvrCPnCGa.plssddnvCpyCGt 24
                                   ++rC +CG+     +   C++CG 
  gi|119719337|ref|YP_919832.1| 17 HIRCRRCGHhSFNVRKGYCAHCGF 40
                                   689******556666667*****5 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   7.4      0.01        31       2      21 ..      19      39 ..      19      39 .. 0.82
   2 ?    5.6   0.6    0.0045        13       3      11 ..      35      43 ..      34      46 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.01
                   Rubredoxin_2  2 vCsqCGfesakwf.GrCpsCg 21
                                   +C++CG+ s  +  G C +Cg
  gi|119719337|ref|YP_919832.1| 19 RCRRCGHHSFNVRkGYCAHCG 39
                                   8*****988766449999997 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0045
                   Rubredoxin_2  3 CsqCGfesa 11
                                   C +CGf  +
  gi|119719337|ref|YP_919832.1| 35 CAHCGFGRS 43
                                   *****9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       752  (0.0419432); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 410.11
//
Query:       gi|119719338|ref|YP_919833.1|  [L=73]
Description: like-Sm ribonucleoprotein, core [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-23   80.5   0.3    5.8e-23   80.4   0.3    1.0  1  LSM       LSM domain
  ------ inclusion threshold ------
      0.034   14.3   0.0      0.036   14.2   0.0    1.1  1  SM-ATX    Ataxin 2 SM domain
      0.052   13.7   0.1      0.065   13.4   0.1    1.3  1  DUF150_C  RimP C-terminal SH3 domain


Domain annotation for each model (and alignments):
>> LSM  LSM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.4   0.3   9.8e-27   5.8e-23       2      67 .]       8      71 ..       7      71 .. 0.96

  Alignments for each domain:
  == domain 1  score: 80.4 bits;  conditional E-value: 9.8e-27
                                   HHHHTTTSEEEEEETTSEEEEEEEEEEETTSEEEEEEEEEEETTETEEEEEEEEEEEGGGEEEEEE CS
                            LSM  2 flkklinkkvtvelkngrelrGtLkgfDqfmNlvLedveetlkdkkekrklglvliRGnnivlisl 67
                                    l+++++k+v+v+lk+gre+rG+Lk++D ++NlvLe++ee++ +  ++r+lg++++RG+n++l+s+
  gi|119719338|ref|YP_919833.1|  8 VLAESLEKNVLVKLKGGREIRGQLKSYDYHLNLVLENAEEIRGT--RTRQLGTIIVRGDNVILVSP 71
                                   6999*************************************976..8****************986 PP

>> SM-ATX  Ataxin 2 SM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   6.1e-06     0.036      14      51 ..      15      50 ..       4      69 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6.1e-06
                                   SEEEEEETTS-EEEEEEEEE-T..T--EEEEEEEETTS CS
                         SM-ATX 14 kevevtvknGevyeGifstvslekdfsvvLkmarkvkk 51
                                   k+v v++k G  ++G +++++    +++vL++a +++ 
  gi|119719338|ref|YP_919833.1| 15 KNVLVKLKGGREIRGQLKSYDY--HLNLVLENAEEIRG 50
                                   789*******************..***********998 PP

>> DUF150_C  RimP C-terminal SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   1.1e-05     0.065      10      52 ..      12      51 ..       9      67 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.1e-05
                       DUF150_C 10 flGelVkvklklpvegrkkftGkivevd.eetitlevdgkkrkk 52
                                   +l ++V vklk    g+++++G+++++d   +++le  ++ r+ 
  gi|119719338|ref|YP_919833.1| 12 SLEKNVLVKLK----GGREIRGQLKSYDyHLNLVLENAEEIRGT 51
                                   6789999**99....*************7777888877666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 516.04
//
Query:       gi|119719339|ref|YP_919834.1|  [L=131]
Description: ribosomal protein S6e [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-36  125.1   0.0    1.8e-36  124.9   0.0    1.0  1  Ribosomal_S6e  Ribosomal protein S6e


Domain annotation for each model (and alignments):
>> Ribosomal_S6e  Ribosomal protein S6e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.9   0.0     1e-40   1.8e-36       1     118 [.       7     121 ..       7     126 .. 0.98

  Alignments for each domain:
  == domain 1  score: 124.9 bits;  conditional E-value: 1e-40
                                    -EEEEEETTTTEEEEEE-CHHHCTTCTT-BSSEEEECCTTTSSSTS-EEEEEEEEETTC-BB-TTS-SSSEEEEEEETTS CS
                  Ribosomal_S6e   1 mklnisdpatgkqklievdekklrtligkrigeevdgdalGeelkgyvlkitggsdkqGfpmkqgvltpgrvrlLlskgg 80 
                                    +k++isdp+tgk++++ev+++++ +lig +ig+ +dg+++G   +g++l+i ggs ++G pm++++ ++++  +Lls+  
  gi|119719339|ref|YP_919834.1|   7 FKVVISDPKTGKAEQVEVSGEQALRLIGLKIGDIIDGGLVG--KPGVKLQIRGGSGRAGEPMRPDIEGARKGYFLLSG-P 83 
                                    79***************************************..**********************************9.* PP

                                    SSS-SSSSS-EEEEEEE-SB--SSEEEEEEEEEE--SS CS
                  Ribosomal_S6e  81 vgyrprrkGerkrksvrGcivsadisqlnlvivkkgek 118
                                    +gy pr+kGer+r+ vrG+++s+di+q+n+viv  +ek
  gi|119719339|ref|YP_919834.1|  84 PGYWPREKGERRRRFVRGNVISDDIVQINTVIVYDEEK 121
                                    *********************************88887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 882.04
//
Query:       gi|119719340|ref|YP_919835.1|  [L=482]
Description: hypothetical protein Tpen_0423 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (482 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 3176.39
//
Query:       gi|119719341|ref|YP_919836.1|  [L=105]
Description: translation initiation factor eIF-1A [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-22   77.6   0.0    5.7e-22   77.3   0.0    1.1  1  eIF-1a    Translation initiation factor 1A / IF-1
     0.0052   16.5   0.1     0.0083   15.9   0.1    1.3  1  RsgA_N    RsgA N-terminal domain
  ------ inclusion threshold ------
       0.03   14.9   0.0      0.042   14.4   0.0    1.2  1  Renin_r   Renin receptor-like protein


Domain annotation for each model (and alignments):
>> eIF-1a  Translation initiation factor 1A / IF-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.3   0.0   9.5e-26   5.7e-22       4      64 .]      23      82 ..      20      82 .. 0.96

  Alignments for each domain:
  == domain 1  score: 77.3 bits;  conditional E-value: 9.5e-26
                                   EEEEEEEETTTEEEEEE.SSSSBEEEEE-HHHHCT----TT-EEEEEE-TT-TTEEEEES- CS
                         eIF-1a  4 igkViealgnnlfrVelpdngkevlaeipgkfRnkiwikrGdyVlVelspydltkGrIvyr 64
                                    +++ ++lg ++ rV ++d gk +l++ipgkf++++w+k Gd+VlV ++++++++G+I+yr
  gi|119719341|ref|YP_919836.1| 23 LCVIQQLLGFDRARVFCSD-GKVRLCRIPGKFKKRMWMKVGDVVLVAPWDFQPERGDIIYR 82
                                   699**************85.****************************************8 PP

>> RsgA_N  RsgA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   1.4e-06    0.0083      16      44 ..      40      67 ..      25      73 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.4e-06
                         RsgA_N 16 eegeiyecRaRGkFRkkkisplVGDrVef 44
                                   ++g++  cR+ GkF+k+ + + VGD V +
  gi|119719341|ref|YP_919836.1| 40 SDGKVRLCRIPGKFKKR-MWMKVGDVVLV 67
                                   6789999********88.5667***9976 PP

>> Renin_r  Renin receptor-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   7.1e-06     0.042      71      97 ..      64      90 ..      56      91 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 7.1e-06
                        Renin_r 71 aivvalasmdPgrDSiiYRmtttrlkk 97
                                   ++ va ++  P+r  iiYR t++ l+k
  gi|119719341|ref|YP_919836.1| 64 VVLVAPWDFQPERGDIIYRYTSNELQK 90
                                   567888****************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 694.97
//
Query:       gi|119719342|ref|YP_919837.1|  [L=112]
Description: thioredoxin domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.2e-20   71.7   0.1    4.7e-20   71.5   0.1    1.1  1  Thioredoxin    Thioredoxin
    5.3e-08   32.9   0.2    7.1e-08   32.5   0.2    1.2  1  Thioredoxin_7  Thioredoxin-like
      7e-08   32.9   0.9    2.6e-07   31.1   0.9    1.7  1  Thioredoxin_2  Thioredoxin-like domain
    1.5e-05   25.2   0.8    0.00028   21.2   0.6    2.0  2  Thioredoxin_8  Thioredoxin-like
    0.00021   21.1   0.1    0.00024   20.9   0.1    1.0  1  DIM1           Mitosis protein DIM1
    0.00027   20.8   0.4     0.0011   18.9   0.4    1.7  1  AhpC-TSA       AhpC/TSA family
      0.005   17.1   0.1     0.0064   16.8   0.1    1.1  1  DUF5091        Domain of unknown function (DUF5091)
  ------ inclusion threshold ------
      0.023   14.4   0.3      0.042   13.6   0.3    1.4  1  Redoxin        Redoxin
      0.023   14.0   0.0      0.027   13.8   0.0    1.0  1  OST3_OST6      OST3 / OST6 family, transporter family
      0.025   14.5   0.0      0.029   14.3   0.0    1.1  1  HyaE           Hydrogenase-1 expression protein HyaE


Domain annotation for each model (and alignments):
>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.5   0.1   2.6e-23   4.7e-20      14      93 ..      17      98 ..       9     110 .. 0.84

  Alignments for each domain:
  == domain 1  score: 71.5 bits;  conditional E-value: 2.6e-23
                                   HTTTSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTT..TSEEEEEETTTSHHHHHHTT-SSSSEEEEEETTEEEEEEESS-H CS
                    Thioredoxin 14 vakekklvlveFyApwCghCkalaPeleklaeelkd..kvklakvdvdenedlakkyevegiPtlklfkngkevkkyegare 93
                                   + +ekk v+v+FyA+wC +Ck +  +l ++ + ++    v ++kv+vd+++++a++y+v g+Pt+++f +gkevk+y+g   
  gi|119719342|ref|YP_919837.1| 17 LLSEKKVVVVDFYADWCIPCKVVDDMLLRVEKLFERydSVCFVKVNVDTEKEVAAEYDVLGLPTVIVFAAGKEVKRYTGVPR 98
                                   45679*****************9998766555555555****************************************9843 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.2     4e-11   7.1e-08      12      82 ..      16      85 ..      11      86 .. 0.88

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 4e-11
                                   HHHHHT--EEEEE--TT-HHHHHHHHHHHH-HHHHH.HHHT-EEEEESS--S-GGG.-TT---SSEEEEE- CS
                  Thioredoxin_7 12 kaaergkpvlvffgaswcftCqalerdflsdeevkaalaekfvllrvdvterdanileldeqgvPvvafld 82
                                    + +++k v v+f a+wc +C+++++++l  e++ +   + + +++v+v+++++   e+d  g+P+v+++ 
  gi|119719342|ref|YP_919837.1| 16 GLLSEKKVVVVDFYADWCIPCKVVDDMLLRVEKLFE-RYDSVCFVKVNVDTEKEVAAEYDVLGLPTVIVFA 85
                                   677899*************************99999.77**********99998665777788*****996 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.9   1.4e-10   2.6e-07       3      99 ..      19      96 ..      17     102 .. 0.85

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 1.4e-10
                  Thioredoxin_2  3 gngkpvlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtPt. 83
                                   +++k v+v+f++++C  Ck   + l  ++++ +r     +++ + ++ v+++++ke+             a +y+v g+Pt 
  gi|119719342|ref|YP_919837.1| 19 SEKKVVVVDFYADWCIPCKVVDDMLLRVEKLFER-----YDS-VCFVKVNVDTEKEV-------------AAEYDVLGLPTv 81
                                   689********************99999777777.....655.68888888888887.............599********6 PP

                  Thioredoxin_2 84 ivfldgkeivarlpGy 99
                                   ivf  gk +v r++G 
  gi|119719342|ref|YP_919837.1| 82 IVFAAGK-EVKRYTGV 96
                                   6688888.999**995 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.6   1.6e-07   0.00028       2      48 ..      22      68 ..      21      73 .. 0.86
   2 !    8.6   0.1    0.0013       2.4      62      90 ..      57      85 ..      53      90 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.6e-07
                                   SEEEEEE--SSSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-SS-HH CS
                  Thioredoxin_8  2 kvvlLyfgaswcppckaftpklkelyeklkkkkkveivyvsldkkee 48
                                   kvv++ f+a+wc pck +   l ++++ ++  + v +v v++d ++e
  gi|119719342|ref|YP_919837.1| 22 KVVVVDFYADWCIPCKVVDDMLLRVEKLFERYDSVCFVKVNVDTEKE 68
                                   9**************999888888888887789**********8765 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0013
                                   EE.EE-TT-HHHHTT-S--TT-SEEEEE- CS
                  Thioredoxin_8 62 lsvpfddkkrnklkkkynvkaiPtlvvld 90
                                   ++v ++ +  ++++ +y+v ++Pt++v  
  gi|119719342|ref|YP_919837.1| 57 CFVKVNVDTEKEVAAEYDVLGLPTVIVFA 85
                                   6788999999****************986 PP

>> DIM1  Mitosis protein DIM1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.1   1.4e-07   0.00024       6      88 ..       7      91 ..       3      99 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.4e-07
                                   -SHHHHHHHHHH-SSSEEEEEEE-TT-HHHHHHHHHHHHHHHHTTTTEEEEEE..ETTT--TTSCCCTT-SSSEEEEEETTE CS
                           DIM1  6 etkeevdqailseeerlvviRFGrdedaeClklDelLakiaeklknfaviylv..didevpdfnkmyeledpvtilffyrnk 85
                                    +  +v+   l  e+++vv+ F  d+   C  +D++L ++ +  +++  +  v  ++d+ ++    y++    t+++f  +k
  gi|119719342|ref|YP_919837.1|  7 PSVSHVELKGLLSEKKVVVVDFYADWCIPCKVVDDMLLRVEKLFERYDSVCFVkvNVDTEKEVAAEYDVLGLPTVIVFAAGK 88
                                   566777777777899********************************9887761156688999999**99777777777777 PP

                                   EEE CS
                           DIM1 86 hmk 88
                                    +k
  gi|119719342|ref|YP_919837.1| 89 EVK 91
                                   766 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.4   5.9e-07    0.0011      17     102 ..      11      98 ..       6     107 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 5.9e-07
                                    EEECHHH..TTSEEEEEEESTST-CCHH...HHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHHHH-H.SSEEEE-TT CS
                       AhpC-TSA  17 tvslsdy..kgkpvvlffypkdwcpvCt...telpalaklyeefkergvevigvsvdspeshkkfiekeslnfpllsDee 91 
                                     v+l+ +  ++k+vv+ fy+  wc +C+   + l + +kl+e+++   v  + v+vd+++++++  +  +l+  ++    
  gi|119719342|ref|YP_919837.1|  11 HVELKGLlsEKKVVVVDFYAD-WCIPCKvvdDMLLRVEKLFERYD--SVCFVKVNVDTEKEVAAEYDVLGLPTVIVFAAG 87 
                                    5788888867799******99.***99833356777777777777..7899************99999999999999888 PP

                                    SHHHHHTT-EE CS
                       AhpC-TSA  92 gkvakaygvlk 102
                                    ++v +  gv++
  gi|119719342|ref|YP_919837.1|  88 KEVKRYTGVPR 98 
                                    88888777775 PP

>> DUF5091  Domain of unknown function (DUF5091)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   3.6e-06    0.0064      81     132 ..      19      70 ..      10      77 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.6e-06
                        DUF5091  81 kedkifsieidfdpeidsevgieilkeiekylkgcDalfFmtyfvdidkeiL 132
                                     e+k++ ++  +d  i  +v  ++l ++ek +   D++ F+   vd++ke+ 
  gi|119719342|ref|YP_919837.1|  19 SEKKVVVVDFYADWCIPCKVVDDMLLRVEKLFERYDSVCFVKVNVDTEKEVA 70 
                                    5779**********************************************85 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.3   2.3e-05     0.042      21     104 ..      12      97 ..       8     108 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.3e-05
                                    EEHHH.HTTSEEEEEEESTTT-HHHHHTHH...HHHTHHHHHHCSTTTEEEEEESSSHHHHHHHHHTT-TSEEEE-TTSH CS
                        Redoxin  21 vslse.fkgkkvvvnfvpgafcPtCsaehp...yleklaellkekgvdvvavvadndafvkefwgkeglkfpvlsDgsaa 96 
                                    v+l+  + +kkvvv+ + + +c +C+        +ekl e+     v +v v++d++  v +  + +gl+ +++  ++++
  gi|119719342|ref|YP_919837.1|  12 VELKGlLSEKKVVVVDFYADWCIPCKVVDDmllRVEKLFER--YDSVCFVKVNVDTEKEVAAEYDVLGLPTVIVFAAGKE 89 
                                    77888878888777666666*****9866644666666555..3446677788888888888888899998888888888 PP

                                    HHHHTT-T CS
                        Redoxin  97 ftkalGlr 104
                                    + +  G++
  gi|119719342|ref|YP_919837.1|  90 VKRYTGVP 97 
                                    88887765 PP

>> OST3_OST6  OST3 / OST6 family, transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.5e-05     0.027      46     109 ..      33      91 ..      26     108 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.5e-05
                      OST3_OST6  46 CelCrefepefelvakswrkdekskskklfFakvdfdegkdvFqklglnsaPhlllfppkkgpk 109
                                    C +C+ +++ +  v k + +      +++ F+kv++d  k+v +++ +  +P +++f + k+ k
  gi|119719342|ref|YP_919837.1|  33 CIPCKVVDDMLLRVEKLFERY-----DSVCFVKVNVDTEKEVAAEYDVLGLPTVIVFAAGKEVK 91 
                                    899999999999999999999.....69*****************************9966544 PP

>> HyaE  Hydrogenase-1 expression protein HyaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.6e-05     0.029      10      96 ..       5      90 ..       1      97 [. 0.75

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.6e-05
                                   TEEEE-CCCHHHHHHHHSEEEEEESS-SS-SSSSS-HCHHHHHHHCT-TTS-EEEEEE.THHHHHHHHHCCT-TSSSEEEEE CS
                           HyaE 10 glaevdadtlddflkaagdavlllagDpkrfpEvsDvaVvlpEllkaFpnalraavva.dreqeealaerfgvlktPsllfl 90
                                   gl+ v+  +l+ +l+++   v+ + +D      v+D   +l  + k F+ ++    v+ + + e+++a ++ vl  P+++++
  gi|119719342|ref|YP_919837.1|  5 GLPSVSHVELKGLLSEKKVVVVDFYADWCIPCKVVDD--MLLRVEKLFERYDSVCFVKvNVDTEKEVAAEYDVLGLPTVIVF 84
                                   6666666667777777766666666666666666665..555677889998888888778999******************* PP

                                   ETTEEE CS
                           HyaE 91 rdgeyl 96
                                   + g+ +
  gi|119719342|ref|YP_919837.1| 85 AAGKEV 90
                                   *99855 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 759.04
//
Query:       gi|119719343|ref|YP_919838.1|  [L=341]
Description: flap endonuclease-1 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.3e-22   78.3   0.0    9.4e-22   77.2   0.0    1.6  2  XPG_I         XPG I-region
    9.4e-16   58.1   0.0    1.6e-15   57.4   0.0    1.4  1  XPG_N         XPG N-terminal domain
    4.6e-06   27.2   0.1      4e-05   24.1   0.0    2.4  3  5_3_exonuc    5'-3' exonuclease, C-terminal SAM fold
     0.0084   16.0   0.1      0.013   15.4   0.1    1.5  1  5_3_exonuc_N  5'-3' exonuclease, N-terminal resolvase-like do
  ------ inclusion threshold ------
        0.1   12.6   0.0       0.18   11.9   0.0    1.3  1  MotCF         Bacteriophage T4 MotA, C-terminal


Domain annotation for each model (and alignments):
>> XPG_I  XPG I-region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       3.3   1.2e+04      55      61 ..      97     102 ..      82     120 .. 0.48
   2 !   77.2   0.0   2.6e-25   9.4e-22       1      94 []     141     237 ..     141     237 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3.3
                                    CTT..EE CS
                          XPG_I  55 kkkkeke 61 
                                    k++ ek+
  gi|119719343|ref|YP_919838.1|  97 KQR-EKA 102
                                    222.111 PP

  == domain 2  score: 77.2 bits;  conditional E-value: 2.6e-25
                                    HHHT--EEE-SS-HHHHHHHHHHTTSSSEEE-SSSHHHHTT-SEEEESTT..ECECTT....EEECEEEEEEHHHHHHHH CS
                          XPG_I   1 klmgipyvvApgEAEAqcayLqkkglvdaviseDsDlllFGapkvlrnls.kkkskkk..kekekkkvevidlekvlkel 77 
                                    +lmg+p+v+A  +AEAq+ayL+k+g ++av s D D+ll+G+p+++r l+ ++++     ++ +k  +e ++le++l+ +
  gi|119719343|ref|YP_919838.1| 141 RLMGFPVVDAVHDAEAQAAYLVKRGEAWAVSSMDWDSLLYGSPRLVRYLTlTGFEWLPskQKARKLIPELVTLEELLSGH 220
                                    68***********************************************97776665576677788899*********** PP

                                    T--HHHHHHHHHHHCET CS
                          XPG_I  78 gltreqlidlaillgcD 94 
                                    g+t  ql+d+ail+g+D
  gi|119719343|ref|YP_919838.1| 221 GITLRQLVDIAILVGTD 237
                                    ****************9 PP

>> XPG_N  XPG N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.4   0.0   4.6e-19   1.6e-15      11     100 ..      10     101 ..       1     102 [. 0.89

  Alignments for each domain:
  == domain 1  score: 57.4 bits;  conditional E-value: 4.6e-19
                                    HHH-GEEEEEGGGGTTEEEEEEHHHHHHHHHHHSE.ETTEE-BS.....-HHHHHHHHHHHHHH.HTTEEEEEEE--S-- CS
                          XPG_N  11 kevaairsvsiealegkklaiDaslwlyrfliavreqlgnalen.....tshlmglfsrllrll.dfgikPifVFdgkap 84 
                                    k+ +    + ++   g++la+Da  ++y+fl  vr++ g+  +n     tshl gl+sr++rl  ++  + ifVFdg + 
  gi|119719343|ref|YP_919838.1|  10 KPKK----IGLQGVRGRVLAVDALNSVYQFLALVRDERGMLFTNsrgevTSHLIGLLSRYSRLAyEYDASFIFVFDGSPH 85 
                                    4444....66777889**********************************************97369************* PP

                                    GGGHHHHHHHHHHHHH CS
                          XPG_N  85 dlkkeelekrserrqe 100
                                    +lk+ elekr+++r++
  gi|119719343|ref|YP_919838.1|  86 PLKARELEKRKKQREK 101
                                    ************9987 PP

>> 5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0         2   7.1e+03      55      65 ..      97     107 ..      78     137 .. 0.56
   2 ?   -0.8   0.0      0.67   2.4e+03      28      46 ..     200     218 ..     199     220 .. 0.85
   3 !   24.1   0.0   1.1e-08     4e-05       4      49 ..     225     268 ..     222     288 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2
                     5_3_exonuc  55 klkekLeenke 65 
                                    k++ek +++  
  gi|119719343|ref|YP_919838.1|  97 KQREKAKQEYA 107
                                    33333332222 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.67
                     5_3_exonuc  28 ektAakLlkeygsleeile 46 
                                    +++A kL+ e  +lee+l+
  gi|119719343|ref|YP_919838.1| 200 KQKARKLIPELVTLEELLS 218
                                    56899********999985 PP

  == domain 3  score: 24.1 bits;  conditional E-value: 1.1e-08
                     5_3_exonuc   4 eqiidlkaLvGDssDnipGvpgiGektAakLlkeygsleeilenld 49 
                                    +q++d++ LvG   D  +Gv+g+G+  A k++k+ygsle++  ++ 
  gi|119719343|ref|YP_919838.1| 225 RQLVDIAILVGT--DYNEGVKGVGPLRALKMIKRYGSLENLPVSVR 268
                                    6999*******5..6678**********************977664 PP

>> 5_3_exonuc_N  5'-3' exonuclease, N-terminal resolvase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   3.8e-06     0.013       3      84 ..      24     111 ..      22     176 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.8e-06
                   5_3_exonuc_N   3 lLiDgsslifRayyal........lttsdgeptnavygflnmllklleeekpthlavvfDakkktfRhelypeYKanRee 74 
                                    l +D+ + +++ + al        +t+s+ge t+ + g+l+   +l  e++  ++++vfD +++  +   +++ K++Re+
  gi|119719343|ref|YP_919838.1|  24 LAVDALNSVYQ-FLALvrdergmlFTNSRGEVTSHLIGLLSRYSRLAYEYDA-SFIFVFDGSPHPLKARELEKRKKQREK 101
                                    66777777775.444447888888899*********************9996.9******8777899999********99 PP

                   5_3_exonuc_N  75 tpeelkeqlp 84 
                                    +++e +e l 
  gi|119719343|ref|YP_919838.1| 102 AKQEYAELLS 111
                                    9999877554 PP

>> MotCF  Bacteriophage T4 MotA, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0     5e-05      0.18       9      47 ..     301     339 ..     295     341 .] 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5e-05
                                    HHHHHHHHHHTT--EEEEEEETTEEEEEEEEEETTEEEE CS
                          MotCF   9 kdlmlklldkngfvlkkveiyrsnylailekrtngirnf 47 
                                    + lm  l+d+n f  k+ve+y     a  e+r  g+  f
  gi|119719343|ref|YP_919838.1| 301 EGLMKFLVDENDFSPKRVEVYLRRLEAAYERRKGGLTRF 339
                                    34777799*************************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.23s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 2495.57
//
Query:       gi|119719344|ref|YP_919839.1|  [L=531]
Description: DNA ligase I, ATP-dependent Dnl1 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.8e-48  163.9   0.0    6.2e-48  163.1   0.0    1.4  1  DNA_ligase_A_M  ATP dependent DNA ligase domain
    9.5e-23   81.4   0.0    1.8e-19   70.7   0.0    3.0  2  DNA_ligase_A_N  DNA ligase N terminus
    7.3e-19   68.2   0.1    1.6e-18   67.1   0.1    1.6  1  DNA_ligase_A_C  ATP dependent DNA ligase C terminal region


Domain annotation for each model (and alignments):
>> DNA_ligase_A_M  ATP dependent DNA ligase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.1   0.0     1e-51   6.2e-48       1     204 []     198     393 ..     198     393 .. 0.95

  Alignments for each domain:
  == domain 1  score: 163.1 bits;  conditional E-value: 1e-51
                                    -EEEEEESCHHHHHHHTTTSEEEEEEEESSEEEEEEEETTEEEEEETTS-B-GGGCHHHHHHHHHHBSTTESEEEEEEEE CS
                 DNA_ligase_A_M   1 pmLAeslksiekalkkleekafivEiKyDGeRaqvhkegdkvklfSRrlkditaakpelvkalkeafkkdeksvilDGEl 80 
                                    pmLA  + ++ ++++++ ++++++E+KyDG R+q+h+ ++kv++fSRrl dit++ p++v+++ e +   ++++++DGE+
  gi|119719344|ref|YP_919839.1| 198 PMLADMAYNVDELFQEH-GSPLHLEYKYDGLRVQIHMGRGKVRVFSRRLSDITEYVPDVVERAVEGLH--VEEAVVDGEA 274
                                    9***************7.9*******************************************988885..569******* PP

                                    EEEETTTTCBEHHHHHCHHHHCHCCTHHHHHHSEEEEEEEEEEEETTEEHTTSCHHHHHHHHHHHB--BTTTEEE--EEE CS
                 DNA_ligase_A_M  81 vavdketgeilpfqklasrkkkkkkveeklkeaelclfvFDiLyldgesltdeplkeRrklLeeilkesedrvelaesle 160
                                    vav    g+++pfq+l +r+++k + e+ lk+ +  l +FD++yl+g+sl++ep++ R +lL+ei+   ++++ la++++
  gi|119719344|ref|YP_919839.1| 275 VAV--IGGAPVPFQELLRRVRRKNEREDFLKSLPFELHLFDVIYLNGKSLVREPYSTRSRLLREIV--VSEEI-LAKKTV 349
                                    **6..678************9999999999************************************..55555.899999 PP

                                    ESSHHHHHHHHHHHHHTTECEEEEEETT-CC-TTCEEEEEEEEE CS
                 DNA_ligase_A_M 161 vkdveeleelleeaiseglEGlvvKnpdskYepgkrsknwlKvK 204
                                     ++ +e+ e++e a+++g EG++ K  +s+Y+pg r+++wlK+K
  gi|119719344|ref|YP_919839.1| 350 AYTRQEALEFYESAVRSGNEGVMSKRHSSVYKPGIRGSDWLKLK 393
                                    ******************************************99 PP

>> DNA_ligase_A_N  DNA ligase N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.7   0.0     3e-23   1.8e-19       2     172 ..       4     150 ..       2     151 .. 0.88
   2 !    4.7   0.0    0.0058        35      63     101 ..     145     183 ..     143     216 .. 0.76

  Alignments for each domain:
  == domain 1  score: 70.7 bits;  conditional E-value: 3e-23
                                    CHHHHHHHHHHCC.-.--HHHHHHHHHHHHHTS-..SHHHHHHHHHH....SS-CCCS------HHHHHHHHHHHHT--H CS
                 DNA_ligase_A_N   2 Faelaelfekieest.kkrlekrailanffrkvesagpedlypalrL....llPdydgreygigesllakalaealglsk 76 
                                    F+el+e+ e+    + + r+ek++il++f+    + +pe++ +a+r+    ++P+yd+re+g+g sl+++al  + + + 
  gi|119719344|ref|YP_919839.1|   4 FRELVEAAEAAG--RvSGRKEKVRILSEFL---GRLSPEEASIAARFlaghVFPEYDNRELGVGYSLVREALKVLDQKP- 77 
                                    455555555555..458899**********...5557999*******************************98777666. PP

                                    HHHHHHHHHHS-HHHHHHHHHCCHHHH------BHHHHHHHHHHHHH-.STTHHHHHHHHHHHHHHHS-HHHHHHHHHHH CS
                 DNA_ligase_A_N  77 kkikdalakvgDlgevaeevlskrstlakkspltieevnelLdklaaa.gkgsedekkkilkkllkraspeEakylirii 155
                                                l  v            +++p +i ev++lL+++a   g+gs+++k k+l++l++r+s +E+ yl ri+
  gi|119719344|ref|YP_919839.1|  78 ------------LFLV------------EPQPPAITEVYRLLERIAGVsGEGSREKKLKLLEGLFSRLSRKEVEYLLRIL 133
                                    ............3466............78899************9888******************************* PP

                                    CT---SS--HHHHHHHH CS
                 DNA_ligase_A_N 156 lkdlriglsektvldal 172
                                     ++ rig+s++++l+a+
  gi|119719344|ref|YP_919839.1| 134 FGEVRIGASTGLLLEAI 150
                                    ***************98 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0058
                                    HHHHHHHHHHT--HHHHHHHHHHHS-HHHHHHHHHCCHH CS
                 DNA_ligase_A_N  63 llakalaealglskkkikdalakvgDlgevaeevlskrs 101
                                    ll +a+++++g++  ++ +a+  + D+g+va+++l++  
  gi|119719344|ref|YP_919839.1| 145 LLLEAISRLSGVPYGDVLHAYMVLSDVGDVAFKALESPA 183
                                    6899*********88788888889*********996443 PP

>> DNA_ligase_A_C  ATP dependent DNA ligase C terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.1   0.1   2.7e-22   1.6e-18       1      99 []     412     504 ..     412     504 .. 0.96

  Alignments for each domain:
  == domain 1  score: 67.1 bits;  conditional E-value: 2.7e-22
                                    GGGSEEEEEEEEEE..TTEEEEEEEE-SS--HHHHHHHHHHHGGGEECTTCESS---HHHHTTEEE-TT-EEEEEESEEE CS
                 DNA_ligase_A_C   1 rgglvgslllgvyd..dgkleyvgkvgtGfsdaeleelrkklkelerkkppfaekvpeeekrdvWvePelvveVkfaeit 78 
                                    r+g+++ + lgvyd  +g++ +vgk+  G+sdae ee++k+l +l+ +++ +           v+v+Pe+vveV ++ei+
  gi|119719344|ref|YP_919839.1| 412 RSGWLSDYHLGVYDeeSGRFLSVGKTFKGLSDAEFEEMTKRLLQLKVREEGY----------VVYVKPEIVVEVDYSEIQ 481
                                    6799**********99999***********************9999999999..........48**************** PP

                                    CTSSSTT..EECT-EEEEE-TTS CS
                 DNA_ligase_A_C  79 asgkyka..slRfPrfkrlReDk 99 
                                    +s++y++  +lRf+r++r+R Dk
  gi|119719344|ref|YP_919839.1| 482 RSKRYPSgfALRFARIRRIRFDK 504
                                    **********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (531 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 3486.43
//
Query:       gi|119719345|ref|YP_919840.1|  [L=323]
Description: hypothetical protein Tpen_0428 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.9e-07   29.0   0.0    9.1e-07   28.6   0.0    1.2  1  Lactamase_B_2  Beta-lactamase superfamily domain
    1.8e-06   27.9   0.0    5.8e-06   26.3   0.0    1.7  1  Lactamase_B_3  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0     1e-10   9.1e-07       3     152 ..      29     195 ..      28     249 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 1e-10
                                    EEES--TT..............HHHHHTCGGS--SSS--..SEEEEE-SS--HHHH.GGGGCCCC.C--EE.EEEE.EEH CS
                  Lactamase_B_2   3 iLiDagpd..............lrqqalralqPvelrdelppidaVllthaHyDHl.aglltlre.lrpkk.lply.apk 64 
                                    iL+Da+ +              + +q lr +   e ++  ++ d+V ++h H DH+   + +l e lr+++  ++y ++ 
  gi|119719345|ref|YP_919840.1|  29 ILFDASSSlaprryglpphpeeFKAQ-LRVR--EEILKAASRADVVTVSHYHRDHYsPPYASLYEcLRENEyEEIYsGKV 105
                                    89999999999999999988888888.8877..33667778***************867888888755555455999999 PP

                                    HHHHHCCTTCGHHHCHTT......TTEEEEEE-..TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEE.CTTE CS
                  Lactamase_B_2  65 gvlavleanfvylaleee......pavnvheld..wgesfelgdggleitatparhksgrrldrnagdtlGlrie.gggk 135
                                     v+++ e+ + y ++ ++       + +++e++   ++ +++g  g ei+a++arh+         g +l ++++ +g  
  gi|119719345|ref|YP_919840.1| 106 VVAKHPEELINYSQRRRAeafleaVRGKAKEIHllNQGVLRFG--GTEIEAFTARHGESL------GYVLCFVVRvDGSP 177
                                    9999999999999999888777664445555552234445555..789***********9......99999999966777 PP

                                    EEEEESS-S.---HHHHH CS
                  Lactamase_B_2 136 rvyyigDtg.yipeeige 152
                                     +++++D++  +++e+ e
  gi|119719345|ref|YP_919840.1| 178 FLAFLPDVQgPVDDEVVE 195
                                    799****97456666554 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   6.5e-10   5.8e-06       9     126 ..      19     197 ..      15     222 .. 0.78

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 6.5e-10
                  Lactamase_B_3   9 sflletagarilvDPf......kanlgyeppa...................eeaDlvlisqaledHahletlkql..... 58 
                                    s+l+et++++il D        +    y+ p+                    +aD+v++s+ + dH+ ++          
  gi|119719345|ref|YP_919840.1|  19 SILVETPDVKILFDASsslaprR----YGLPPhpeefkaqlrvreeilkaaSRADVVTVSHYHRDHYSPPYASLYeclre 94 
                                    8999**********885444430....333335566777777777777788*****************996665599999 PP

                  Lactamase_B_3  59 .......................................aenvkvleegeslevggleiravatshdavggsergenngf 99 
                                                                           a+++++l+ ++ l++gg+ei+a+++ h    g+  g   +f
  gi|119719345|ref|YP_919840.1|  95 neyeeiysgkvvvakhpeelinysqrrraeafleavrgkAKEIHLLN-QGVLRFGGTEIEAFTARH----GESLGYVLCF 169
                                    99999999999998888888888888888777777777655555555.5789************99....7778888899 PP

                  Lactamase_B_3 100 lleqdgl.tiyhlGhlahelsseelkel 126
                                    ++++dg   +++l+++  + ++e  +++
  gi|119719345|ref|YP_919840.1| 170 VVRVDGSpFLAFLPDVQGPVDDEVVEKI 197
                                    9999755168999999999888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 2066.45
//
Query:       gi|119719346|ref|YP_919841.1|  [L=302]
Description: signal recognition particle-docking protein FtsY [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.2e-70  234.8   0.2    9.4e-70  234.2   0.2    1.3  1  SRP54            SRP54-type protein, GTPase domain
    4.4e-06   26.5   0.5    7.6e-06   25.8   0.5    1.3  1  AAA_30           AAA domain
    0.00012   22.5   0.1    0.00048   20.6   0.0    1.8  2  AAA_16           AAA ATPase domain
    0.00013   22.1   0.0    0.00033   20.7   0.0    1.8  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
    0.00042   19.4   0.1     0.0009   18.3   0.1    1.6  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
     0.0015   18.7   0.6     0.0033   17.6   0.6    1.6  1  SRP54_N          SRP54-type protein, helical bundle domain
     0.0023   18.4   0.0     0.0068   16.8   0.0    1.8  1  AAA              ATPase family associated with various cellul
     0.0024   17.6   0.0     0.0045   16.7   0.0    1.4  1  AAA_24           AAA domain
     0.0035   17.3   0.1      0.068   13.1   0.1    2.3  1  NTPase_1         NTPase
     0.0047   16.5   0.0      0.025   14.1   0.0    2.1  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
     0.0057   16.5   0.0      0.011   15.7   0.0    1.5  1  MobB             Molybdopterin guanine dinucleotide synthesis
     0.0088   15.6   0.0      0.014   15.0   0.0    1.3  1  GTP_EFTU         Elongation factor Tu GTP binding domain
      0.009   16.3   0.1      0.022   15.0   0.0    1.7  2  AAA_28           AAA domain
  ------ inclusion threshold ------
      0.018   15.1   0.1      0.042   13.9   0.1    1.6  1  B12-binding      B12 binding domain
       0.02   15.3   0.3       0.27   11.7   0.1    2.7  3  3HCDH_RFF        3-hydroxybutyryl-CoA dehydrogenase reduced R
      0.021   14.8   0.0       0.18   11.8   0.0    2.0  2  ResIII           Type III restriction enzyme, res subunit
      0.024   15.1   0.0      0.057   13.8   0.0    1.6  1  AAA_17           AAA domain
      0.035   14.2   0.1       0.13   12.3   0.1    2.1  2  MMR_HSR1         50S ribosome-binding GTPase
      0.043   13.7   0.0       0.13   12.2   0.0    1.5  1  AAA_31           AAA domain
       0.05   14.0   0.0       0.19   12.2   0.0    1.9  1  RNA_helicase     RNA helicase
      0.085   13.1   0.0       0.24   11.7   0.0    1.7  1  AAA_22           AAA domain
        0.1   11.8   0.0        1.6    7.9   0.0    2.1  2  ArsA_ATPase      Anion-transporting ATPase
        0.1   12.3   0.0       0.16   11.6   0.0    1.4  1  Thymidylate_kin  Thymidylate kinase
       0.12   12.9   0.0       0.18   12.3   0.0    1.4  1  ABC_tran         ABC transporter
       0.13   12.3   0.0       0.28   11.2   0.0    1.5  1  AAA_5            AAA domain (dynein-related subfamily)
       0.14   12.2   0.0       0.34   11.0   0.0    1.7  1  AAA_2            AAA domain (Cdc48 subfamily)
       0.15   11.6   0.0       0.29   10.6   0.0    1.4  1  AAA_7            P-loop containing dynein motor region


Domain annotation for each model (and alignments):
>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  234.2   0.2   1.4e-72   9.4e-70       3     195 ..     109     301 ..     107     302 .] 0.99

  Alignments for each domain:
  == domain 1  score: 234.2 bits;  conditional E-value: 1.4e-72
                                    EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEESSTTSCHHHHHHHHHHHHHHT CS
                          SRP54   3 villvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvikkkeeadpaavakeavekakee 82 
                                     il++G++G GKTtt+aKLa +++k+g++v+++aaDtfRa+ +eQ++++a+++g++v++   +adpaava+eav+k ++ 
  gi|119719346|ref|YP_919841.1| 109 SILFLGPNGHGKTTTVAKLAYRFRKQGYRVAIAAADTFRAGSIEQVSQWASRAGAEVVSLGYNADPAAVAYEAVKKGEKG 188
                                    59****************************************************************************** PP

                                    TSSEEEEEE--SSTTHHHHHHHHHHHHHHHSSSEEEEEEETTBHTHHHHHHHHHHHHSSCSEEEEESTTSSSSTTHHHHH CS
                          SRP54  83 kidvvlvDTaGrlqndkelmeelkkikkvvkpdevllvldattgqeavkqakaFkeavgitgviltklDgdakgGaalsi 162
                                    +++vvl+DTaGr++++k+lm+e+kki++v++pd +++v da++g++av+qak+F ++vg++g iltk+D+d +gGaals+
  gi|119719346|ref|YP_919841.1| 189 DFQVVLIDTAGRMHTKKNLMDEMKKIARVASPDFKVFVGDALVGNDAVEQAKTFFSEVGFDGSILTKFDADIRGGAALSV 268
                                    ******************************************************************************** PP

                                    HHHHTS-EEEEE-SSSTTGEEE--HHHHHHHHH CS
                          SRP54 163 aaelklPikfigvGekiedleefdperlvsrll 195
                                    ++ +k+P+ ++g+G+ iedl+ef+ e+++ +l+
  gi|119719346|ref|YP_919841.1| 269 VYVTKKPLLYVGTGQGIEDLKEFNVEEYLGMLF 301
                                    ***************************998886 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.5   1.1e-08   7.6e-06      22     124 ..     111     228 ..      98     242 .. 0.69

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 1.1e-08
                         AAA_30  22 vltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgieastiakllkrlk...............grarl 86 
                                    +  Gp G GKtt++++l+  ++++g+rv+++A     A  +++ ++ +++  a+++ +l+               g  + 
  gi|119719346|ref|YP_919841.1| 111 LFLGPNGHGKTTTVAKLAYRFRKQGYRVAIAAADTFRAGSIEQVSQWASRAGAEVV-SLGynadpaavayeavkkG--E- 186
                                    568*************************************9975554444444444.2223444566666543231..2. PP

                         AAA_30  87 epg.tllivDEagmvdtkq..laallkaaekag.akvilvGD 124
                                    + + +++++D ag + tk+  ++++ k+a+ a+    ++vGD
  gi|119719346|ref|YP_919841.1| 187 KGDfQVVLIDTAGRMHTKKnlMDEMKKIARVASpDFKVFVGD 228
                                    3346*********99665323666666666554344457787 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       2.2   1.4e+03      80     126 ..      50      81 ..       6      91 .. 0.43
   2 !   20.6   0.0   7.2e-07   0.00048      12     132 ..      94     220 ..      92     234 .. 0.63

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 2.2
                         AAA_16  80 ellrqlldeaesaeleawrekleealaavpelagaea...........srllellkrl 126
                                     l+++l  +                          ++           ++ll++l++l
  gi|119719346|ref|YP_919841.1|  50 ALVADLSGR--------------------------ISgkklgrfadkrKALLDELRAL 81 
                                    222222222..........................22333323333334444444444 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 7.2e-07
                         AAA_16  12 Llsalervrsgrp.elvllsGesGvGKsslvrellralekdggiflrgkcdql..esaipysalaqalareellrqllde 88 
                                    L  +++r  +g +  ++l+ G+ G GK++ v +l+ +++k+g  ++ + +d +  +s    s++a+ + +e +    +++
  gi|119719346|ref|YP_919841.1|  94 LDGLVKRGVAGKGfFSILFLGPNGHGKTTTVAKLAYRFRKQGYRVAIAAADTFraGSIEQVSQWASRAGAEVVSLGYNAD 173
                                    6677888888888899*************************888877777777324445557788888553333333333 PP

                         AAA_16  89 aesaeleawrekleealaavpelagaea....srllellkrllallsr 132
                                    +++ + ea ++  ++ ++ v  ++ a++    + l +++k++++ +s+
  gi|119719346|ref|YP_919841.1| 174 PAAVAYEAVKKGEKGDFQ-VVLIDTAGRmhtkKNLMDEMKKIARVASP 220
                                    333333333333333333.33333333334457777777777766666 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   4.9e-07   0.00033       9      37 ..     117     145 ..     114     265 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 4.9e-07
                                    TSSHHHHHHHHHHHHHHTT--EEEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           CbiA   9 GvGKTtlaanLaralarrglrVllvDaDp 37 
                                    G GKTt++a+La  + ++g+rV+   aD+
  gi|119719346|ref|YP_919841.1| 117 GHGKTTTVAKLAYRFRKQGYRVAIAAADT 145
                                    88*********************998886 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   1.4e-06    0.0009      35      67 ..     113     145 ..      99     209 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.4e-06
                                    EE-TTSSHHHHHHHHHHHHHCTT--EEEEEE-- CS
                           MeaB  35 tGvPGaGkstlvealglelrrrGkrvavlavDP 67 
                                     G  G Gk t+v +l+ ++r++G+rva+ a D 
  gi|119719346|ref|YP_919841.1| 113 LGPNGHGKTTTVAKLAYRFRKQGYRVAIAAADT 145
                                    6788*************************9984 PP

>> SRP54_N  SRP54-type protein, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.6     5e-06    0.0033       6      75 .]      11      78 ..       6      78 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 5e-06
                                   HHHHHHHCCSSCGHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHCTTSS-HHHHHHHHHHHHH CS
                        SRP54_N  6 nsalkklsgkskideedleealkeleeaLleaDVgvkvvkklienvkkkavgekklkpkqqvkkivkdeL 75
                                   ++++     ++++de++l+   +     L+ea V+++v++ l++++  +  g kkl +  + +k++ deL
  gi|119719346|ref|YP_919841.1| 11 SAIIEE-VAYTELDEKTLKRHADAFVLRLVEAGVALEVAEALVADLSGRISG-KKLGRFADKRKALLDEL 78
                                   555554.45678**********************************885555.99***********9998 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0     1e-05    0.0068       1      74 [.     110     205 ..     110     222 .. 0.61

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1e-05
                                    EEEESSTTSSHHHHHHHHHHHH..THEEEEEETTTCSSS..................STTHHHHHHHHHHHHHHHTS..T CS
                            AAA   1 vllyGppGtGKTllakavakel..gvefleisgsellsk..................yvgesekkirelfkeakeka..k 58 
                                    +l+ Gp G GKT+++  +a  +  + + + i +++ +                     +g +++  +   +++k+ +  +
  gi|119719346|ref|YP_919841.1| 110 ILFLGPNGHGKTTTVAKLAYRFrkQGYRVAIAAADTFRAgsieqvsqwasragaevvSLGYNADPAAVAYEAVKKGEkgD 189
                                    699******************84312234444444442345666666666666666633333333333333334333433 PP

                                    SEEEEEETGGGHHHHH CS
                            AAA  59 psilfiDEidalaksr 74 
                                      +++iD + ++++++
  gi|119719346|ref|YP_919841.1| 190 FQVVLIDTAGRMHTKK 205
                                    6899999999988887 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   6.7e-06    0.0045       4      91 ..     109     214 ..     107     229 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6.7e-06
                         AAA_24   4 kiliyGpsgiGKTtlakel.......gpkplfidtekGlksldadkfpdieswedfl.devvel...............a 60 
                                    +il  Gp+g GKTt++++l       g+++++   +       a  ++++++w+     evv+l               +
  gi|119719346|ref|YP_919841.1| 109 SILFLGPNGHGKTTTVAKLayrfrkqGYRVAIAAADT----FRAGSIEQVSQWASRAgAEVVSLgynadpaavayeavkK 184
                                    58899**************777777666666664444....333334444444433213344448888999999999999 PP

                         AAA_24  61 aeladyktlviDtideleelclaevirqnek 91 
                                     e+ d++++ iDt++ +   +++ +++++++
  gi|119719346|ref|YP_919841.1| 185 GEKGDFQVVLIDTAGRM-HTKKNLMDEMKKI 214
                                    9*************998.3345555555555 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.1    0.0001     0.068       5      35 ..     113     143 ..     109     226 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.0001
                                    E--TTSSHHHHHHHHHHHH...GGGEEEEEE CS
                       NTPase_1   5 TGppGvGKtTlvkkvlellkssgvkvgGfyt 35 
                                     Gp G GKtT v k++   +++g++v+   +
  gi|119719346|ref|YP_919841.1| 113 LGPNGHGKTTTVAKLAYRFRKQGYRVAIAAA 143
                                    59**********************9974444 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       4.8   3.2e+03      31      56 ..      12      38 ..       7      56 .. 0.66
   2 !   14.1   0.0   3.8e-05     0.025       4     135 ..     111     242 ..     108     259 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 4.8
                                   EEESS-SSCHCCCCCCHCCCT..EEEE CS
                           cobW 31 vivNefgevsiDaellretgve.ivel 56
                                    i+ e+  +++D++ l+++++  ++ l
  gi|119719346|ref|YP_919841.1| 12 AIIEEVAYTELDEKTLKRHADAfVLRL 38
                                   567777779999999988744434444 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 3.8e-05
                                    EEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SS.CHCCC..CCCHCCCT.EEEETTTTECCHCTT-HHHHHHHHHH CS
                           cobW   4 vltGflGsGKTtLlnhll..enraglklavivNefge.vsiDa..ellretgveivelenGciCctlredllkelealee 78 
                                    ++ G+ G GKTt + +l    +++g+++a+   +     si++  +  +++g+e+v+l     + +       + ea+++
  gi|119719346|ref|YP_919841.1| 111 LFLGPNGHGKTTTVAKLAyrFRKQGYRVAIAAADTFRaGSIEQvsQWASRAGAEVVSLGYNADPAA------VAYEAVKK 184
                                    567999************987889*********986523344311445666777888765555544......44444433 PP

                                    HH.TT-SEEEEEECTTTTHHHHHTT.SHHHHHCCCECEEEEEEETTTH.CCHCCHHHHH CS
                           cobW  79 re.erldviliEttGlaePapvaft.eeelksdltldavvavvDaknleaeeekieeka 135
                                     e ++++v+li t G ++ +  ++   +++++ +  d++v+v Da    ++  ++++++
  gi|119719346|ref|YP_919841.1| 185 GEkGDFQVVLIDTAGRMHTKKNLMDeMKKIARVASPDFKVFVGDALV-GNDAVEQAKTF 242
                                    33368**********777777744449999999*********99933.34444444444 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.6e-05     0.011       3      62 ..     111     168 ..     109     195 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.6e-05
                           MobB   3 givgksgsGKTtLleklipelkarglrvgtiKhahhgfdvdkpgkDsyrhrkAGAkevlv 62 
                                     + g +g GKTt + kl   ++++g+rv++   a++ f   + ++ s    +AGA+ v +
  gi|119719346|ref|YP_919841.1| 111 LFLGPNGHGKTTTVAKLAYRFRKQGYRVAIA--AADTFRAGSIEQVSQWASRAGAEVVSL 168
                                    688999**********************984..666777777777777777788877765 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0     2e-05     0.014       5      87 ..     109     207 ..     105     244 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2e-05
                                    EEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEE...................T CS
                       GTP_EFTU   5 nigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisle...................k 65 
                                     i ++g   hGKtT++ +L y+  +   + + a      Dt  +    +++  ++ +  e                   k
  gi|119719346|ref|YP_919841.1| 109 SILFLGPNGHGKTTTVAKLAYRFRKQGYRVAIAA----ADTFRAGSIEQVSQWASRAGAEvvslgynadpaavayeavkK 184
                                    67899999****************9999777665....333333333333333333333333455666666677779974 PP

                                    .TCSSEEEEEEEESSSGGGHHHH CS
                       GTP_EFTU  66 .etkkylinliDtPGHvdFskev 87 
                                     e+ ++++ liDt G +   k+ 
  gi|119719346|ref|YP_919841.1| 185 gEKGDFQVVLIDTAGRMHTKKNL 207
                                    69999**********76544443 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       5.3   3.5e+03      85     102 ..      16      33 ..      11      85 .. 0.55
   2 !   15.0   0.0   3.3e-05     0.022       2      33 ..     110     145 ..     109     199 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 5.3
                         AAA_28  85 tlaYarayggeaeaelea 102
                                    ++aY + ++++ +++ +a
  gi|119719346|ref|YP_919841.1|  16 EVAYTELDEKTLKRHADA 33 
                                    444444444444443333 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 3.3e-05
                         AAA_28   2 ivitGgestGKTtlleaLaar....gypvvpEaare 33 
                                    i ++G+ + GKTt++++La r    gy+v   aa +
  gi|119719346|ref|YP_919841.1| 110 ILFLGPNGHGKTTTVAKLAYRfrkqGYRVAIAAADT 145
                                    889****************54445699988555544 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   6.3e-05     0.042      17      90 ..     151     230 ..     124     240 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.3e-05
                    B12-binding  17 lavlaaalrdagfeVqllganven....edivaairaekpdvvglSal..ltsqleavkelvellkrirprvkvvvGGah 90 
                                    + ++ ++ ++ag eV+ lg+n+++     + v++ ++ +++vv++ +   + ++ + + e+ + ++ ++p++kv+vG a 
  gi|119719346|ref|YP_919841.1| 151 IEQVSQWASRAGAEVVSLGYNADPaavaYEAVKKGEKGDFQVVLIDTAgrMHTKKNLMDEMKKIARVASPDFKVFVGDAL 230
                                    678999999***************5554444555555677779996655588888888888888999*********9665 PP

>> 3HCDH_RFF  3-hydroxybutyryl-CoA dehydrogenase reduced Rossmann-fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00041      0.27      27      65 ..     129     168 ..     118     169 .. 0.85
   2 ?   -1.7   0.0       6.4   4.3e+03      18      31 ..     190     203 ..     180     207 .. 0.72
   3 ?   -0.6   0.0       2.7   1.8e+03      45      62 ..     233     250 ..     229     254 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00041
                      3HCDH_RFF  27 ldyra.atrlAlAaaaqaspqalaqavalLqalGkkvlvl 65 
                                    +++r+ + r+A+Aaa++ ++   +q+ ++  ++G +v+ l
  gi|119719346|ref|YP_919841.1| 129 YRFRKqGYRVAIAAADTFRAGSIEQVSQWASRAGAEVVSL 168
                                    555554779****************************987 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 6.4
                      3HCDH_RFF  18 rpvvlfDlaldyra 31 
                                     +vvl+D a ++ +
  gi|119719346|ref|YP_919841.1| 190 FQVVLIDTAGRMHT 203
                                    57999998877665 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 2.7
                      3HCDH_RFF  45 pqalaqavalLqalGkkv 62 
                                    + a++qa +++ + G+  
  gi|119719346|ref|YP_919841.1| 233 NDAVEQAKTFFSEVGFDG 250
                                    67899*********9975 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00027      0.18      22      54 ..     105     137 ..      66     158 .. 0.79
   2 ?    0.5   0.0      0.82   5.4e+02     128     158 ..     185     219 ..     167     227 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00027
                                    .TTSEEEEEESTTSTHHHHHHHHHHHH-S.... CS
                         ResIII  22 krdkrglikmaTGtGKTlvaaklierllkkgke 54 
                                    k+   +l+  + G GKT + akl++r++k+g++
  gi|119719346|ref|YP_919841.1| 105 KGFFSILFLGPNGHGKTTTVAKLAYRFRKQGYR 137
                                    66778899999******************9884 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.82
                                    HHTTT-SEEEEETGGGTTS.T....TTHHHHHT-- CS
                         ResIII 128 llrdrfdviiiDEaHrlgakk....swreilekfk 158
                                     +++ f+v++iD a r++ kk    ++++i++  +
  gi|119719346|ref|YP_919841.1| 185 GEKGDFQVVLIDTAGRMHTKKnlmdEMKKIARVAS 219
                                    4677899*******999997455557777766555 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   8.6e-05     0.057       1     108 [.     113     226 ..     113     229 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.6e-05
                                    EE-TTSSHHHHHHHHH...HHHTEEE.EEHHHHHHHHHHTT.T..SHSSHHHHCTSHHHHHHHHHHHHHHHHHHHH..HS CS
                         AAA_17   1 lGgPGsGKgtqceklv...ekygfth.lsaGdllreeakrg.g..lakardemrklpleekkelqkeaaekiaeea..kk 71 
                                    lG+ G GK+t ++kl+   +k g+ + + a d +r+   ++ +  +++a  e+  ++l  + +  + a e++++ +  + 
  gi|119719346|ref|YP_919841.1| 113 LGPNGHGKTTTVAKLAyrfRKQGYRVaIAAADTFRAGSIEQvSqwASRAGAEV--VSLGYNADPAAVAYEAVKKGEkgDF 190
                                    79*************955555588864899*****744333121133333333..3333344444455555544321144 PP

                                    SEEEEEE-SEEEETTEEEESSHHHHHHHH..SEEEEE CS
                         AAA_17  72 kgvlvdghprikeqagfldglpkevleelkpdaiill 108
                                    + vl+d+  r+ +++ ++d+++k + + ++pd+ +++
  gi|119719346|ref|YP_919841.1| 191 QVVLIDTAGRMHTKKNLMDEMKK-IARVASPDFKVFV 226
                                    679**********9999999986.8999999987775 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       6.3   4.2e+03      46      64 ..      48      66 ..      15      88 .. 0.58
   2 ?   12.3   0.1    0.0002      0.13       2      87 ..     110     233 ..     109     274 .. 0.60

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 6.3
                                   EEEEEEECGGCSSHHHHHH CS
                       MMR_HSR1 46 keielvDtpGliegaseek 64
                                    e  ++D+ G i+g++ ++
  gi|119719346|ref|YP_919841.1| 48 AEALVADLSGRISGKKLGR 66
                                   3455666666555444433 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.0002
                                    EEEEESTTSSHHHHHHHHHT.......STEEESSSTTSSSSEEEE.EEEETTEE.......................... CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltg.......ekaivsdkpgtTrdineg.rvklkgke.......................... 47 
                                    ++++G    GK+t + +l         ++ai+++  +    i++  +++    +                          
  gi|119719346|ref|YP_919841.1| 110 ILFLGPNGHGKTTTVAKLAYrfrkqgyRVAIAAADTFRAGSIEQVsQWA--S-Ragaevvslgynadpaavayeavkkge 186
                                    6778888888888888887422222222444444445444443330222..1.023334444444455555555555555 PP

                                    .....EEEEECGGCSSHHHHHHHHHHHHHHHHC..T.SEEEEEEETT..T CS
                       MMR_HSR1  48 .....ielvDtpGliegaseekglgkaflalee..a.dlillvvdas..e 87 
                                         ++l+Dt+G ++   ++k+l ++++++ +  + d  ++v da   +
  gi|119719346|ref|YP_919841.1| 187 kgdfqVVLIDTAGRMH---TKKNLMDEMKKIARvaSpDFKVFVGDALvgN 233
                                    55555********544...5666666666655542249999998855443 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00019      0.13      12      40 ..     117     145 ..     115     156 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00019
                         AAA_31  12 GvGKTTtsvnlaaalaklgkkvLlvDlDp 40 
                                    G GKTTt+ +la+ + k+g++v +  +D+
  gi|119719346|ref|YP_919841.1| 117 GHGKTTTVAKLAYRFRKQGYRVAIAAADT 145
                                    88********************9988886 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00028      0.19       1      56 [.     110     180 ..     110     227 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00028
                   RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl..............klkkkdsvysrnpeddfwdgYt.gqevvvid 56 
                                    i++ Gp+g GK+t++ +La ++ k+                 ++ +++ sr+ ++ +  gY+ ++++v ++
  gi|119719346|ref|YP_919841.1| 110 ILFLGPNGHGKTTTVAKLAYRFRKQGyrvaiaaadtfragSIEQVSQWASRAGAEVVSLGYNaDPAAVAYE 180
                                    6899***************9999887777777777777765555555556666666667777444444444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00036      0.24       8     116 ..     110     215 ..     108     228 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00036
                         AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka......erlsseellea 81 
                                    ++  G+ G GKTt++++l++++         r++ ++v +++  + +    e ++++ +++ a      ++++  ++   
  gi|119719346|ref|YP_919841.1| 110 ILFLGPNGHGKTTTVAKLAYRF---------RKQGYRVAIAAADTFRAGSIEQVSQWASRAGAevvslgYNADPAAVA-- 178
                                    6778*****************9.........44444444433333333333333333332222333233333333333.. PP

                         AAA_22  82 leqalrarav..ielliiDEaqhlr.seealeeLrsll 116
                                     ++a+++  +   ++++iD a ++  +++++ e ++++
  gi|119719346|ref|YP_919841.1| 179 -YEAVKKGEKgdFQVVLIDTAGRMHtKKNLMDEMKKIA 215
                                    .2222222223335777777777743355555555555 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0024       1.6       4      38 ..     110     144 ..     108     154 .. 0.91
   2 ?    1.5   0.0       0.2   1.3e+02     112     138 ..     178     203 ..     171     224 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0024
                                    EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S CS
                    ArsA_ATPase   4 ilvgGKGGVGKttvsaatavklsekgkkvllistD 38 
                                    il+ G  G GKtt  a +a++  ++g++v + + D
  gi|119719346|ref|YP_919841.1| 110 ILFLGPNGHGKTTTVAKLAYRFRKQGYRVAIAAAD 144
                                    7889999**********************998777 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.2
                                    HHHHHHHHHHCSSSSEEEEESBSCCHT CS
                    ArsA_ATPase 112 sfeellkyvkeeeydvvvlDtaPTGht 138
                                    ++e++ k  ++ ++ vv++Dta   ht
  gi|119719346|ref|YP_919841.1| 178 AYEAV-KKGEKGDFQVVLIDTAGRMHT 203
                                    45554.4457889********977666 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00024      0.16       3      28 ..     114     139 ..     112     186 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00024
                                    ESTTSSHHHHHHHHHHHHHHTTE.EE CS
                Thymidylate_kin   3 GlDGaGKttqaellkerlkeegikvv 28 
                                    G +G GKtt +++l+ r++++g++v 
  gi|119719346|ref|YP_919841.1| 114 GPNGHGKTTTVAKLAYRFRKQGYRVA 139
                                    899********************964 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00028      0.18      15      51 ..     111     147 ..     108     250 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00028
                                    EEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  15 aivGenGaGKStLlkllagllkpteGeilldgkdlke 51 
                                     ++G+nG GK+t ++ la   +++  ++ +  +d+ +
  gi|119719346|ref|YP_919841.1| 111 LFLGPNGHGKTTTVAKLAYRFRKQGYRVAIAAADTFR 147
                                    689***********99999999888788766555544 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00041      0.28       2      30 ..     110     139 ..     109     155 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00041
                                    EEEE--SSSSHHHHHHHGGGGB.S--EEEE CS
                          AAA_5   2 vlLvGppGtgKselaerlaaal.nreveyv 30 
                                    +l +Gp G gK++ + +la ++ ++ + + 
  gi|119719346|ref|YP_919841.1| 110 ILFLGPNGHGKTTTVAKLAYRFrKQGYRVA 139
                                    789*******************65544444 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00051      0.34       4      83 ..     108     204 ..     105     221 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00051
                                    --EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG---..........----THHHHHHHHHTTT-HHHHTTS... CS
                          AAA_2   4 isilllgptgvGktelakalaellfvkkekkliradaselle..........eeevehlvsrligappgyvgaeegG... 70 
                                     sil+lgp+g Gkt +  +la   + k+  ++++a a ++            + + +++vs    a p+ v++e      
  gi|119719346|ref|YP_919841.1| 108 FSILFLGPNGHGKTTTVAKLAYRFR-KQGYRVAIAAADTFRAgsieqvsqwaSRAGAEVVSLGYNADPAAVAYEAVKkge 186
                                    69*************9888888888.677777777777777655555555544555556666666666666665322447 PP

                                    .....EEEEETGGG---- CS
                          AAA_2  71 .....ivllDEidKihpk 83 
                                         +vl+D   + h k
  gi|119719346|ref|YP_919841.1| 187 kgdfqVVLIDTAGRMHTK 204
                                    778888888877777764 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00043      0.29      35      65 ..     109     139 ..     102     146 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00043
                          AAA_7  35 pvllvGptGtGKtviikdllkkldkekylsl 65 
                                    ++l+ Gp G GKt+++ +l  ++ k+ y ++
  gi|119719346|ref|YP_919841.1| 109 SILFLGPNGHGKTTTVAKLAYRFRKQGYRVA 139
                                    68****************9999999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              27  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.46
# Mc/sec: 1981.26
//
Query:       gi|119719347|ref|YP_919842.1|  [L=129]
Description: prefoldin, alpha subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-25   89.3   3.6    1.9e-25   89.1   3.6    1.1  1  Prefoldin        Prefoldin subunit
    0.00025   20.9   8.4      0.012   15.6   1.0    2.1  2  Prefoldin_2      Prefoldin subunit
    0.00092   18.7   1.0       0.26   10.8   0.1    2.5  2  KNOX2            KNOX2 domain
  ------ inclusion threshold ------
      0.015   15.4   0.9        2.3    8.4   0.0    2.2  2  DUF4055          Domain of unknown function (DUF4055)
      0.026   14.1   0.2      0.042   13.4   0.2    1.4  1  Peripla_BP_2     Periplasmic binding protein
      0.066   12.9   0.2      0.066   12.9   0.2    1.9  2  dCache_3         Double sensory domain of two-component senso
      0.081   13.0   4.0        3.4    7.8   0.3    2.1  2  DUF148           Domain of unknown function DUF148
       0.11   12.4   1.0       0.65    9.9   0.1    2.0  2  DUF1759          Protein of unknown function (DUF1759)
       0.14   12.6   2.5        1.1    9.8   0.1    2.1  2  ParB             ParB family
       0.15   12.2   0.9       0.39   10.9   0.1    1.8  2  FAA_hydrolase_N  Fumarylacetoacetase N-terminal
       0.26   11.3   4.2       0.56   10.2   0.5    2.1  2  DUF1664          Protein of unknown function (DUF1664)
       0.78    9.0   5.1        3.1    7.0   0.5    2.1  2  FmiP_Thoc5       Fms-interacting protein/Thoc5


Domain annotation for each model (and alignments):
>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.1   3.6   1.3e-28   1.9e-25       3     112 ..      17     126 ..      15     129 .] 0.97

  Alignments for each domain:
  == domain 1  score: 89.1 bits;  conditional E-value: 1.3e-28
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT.-TT-EEEEEEETTEEEEEE--STTEEEEEEETTEEEEEEHHHHHHHH CS
                      Prefoldin   3 eeleslqaelaqlkeaieelektletlktlkkedegkevlvplgaglyvkaevkdtdkvlvdlGagyyveksleeAiell 82 
                                    + +e+lq+e++  ++ i e+++++ +lk+++  ++gke+lvp++ag+yv+a++k+ +k+lv +G+++ veksl+eA+e+l
  gi|119719347|ref|YP_919842.1|  17 QVAEELQREIQLAQTLIAEVDSAILALKNISSLEDGKEILVPVSAGVYVRASIKRQEKFLVAIGSNILVEKSLDEAVEFL 96 
                                    7899**************************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Prefoldin  83 kkkleelekqlekleeeleklkdqittlea 112
                                    +k++eel++ +e   ++l+k  ++i ++e 
  gi|119719347|ref|YP_919842.1|  97 NKRKEELSQLVERRMNDLNKVVARIREIES 126
                                    **************************9997 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   1.2   0.00049      0.73       3      42 ..       8      47 ..       6      56 .. 0.87
   2 !   15.6   1.0   7.9e-06     0.012      53      99 ..      82     128 ..      69     129 .] 0.93

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00049
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS- CS
                    Prefoldin_2  3 linkfqqlqqqlqqlaqqikqletqlkelelvleelelld 42
                                   l+++++ l q  ++l+ +i+ ++t + e+++++ +l+++ 
  gi|119719347|ref|YP_919842.1|  8 LAEEYSVLAQVAEELQREIQLAQTLIAEVDSAILALKNIS 47
                                   6789**************************9988887664 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 7.9e-06
                                    TEEEEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    Prefoldin_2  53 dvlvkqdkeevkeeLeerketlekeiktlekqleklekeleelkeel 99 
                                    ++lv+++++e+ e L++rke+l++ +++  + l k+ ++++e+++++
  gi|119719347|ref|YP_919842.1|  82 NILVEKSLDEAVEFLNKRKEELSQLVERRMNDLNKVVARIREIESSI 128
                                    68****************************************99987 PP

>> KNOX2  KNOX2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   0.1     0.005       7.5      17      43 ..      13      39 ..      10      48 .. 0.79
   2 !   10.8   0.1   0.00017      0.26      28      47 ..      87     106 ..      85     107 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.005
                          KNOX2 17 dvLvkYkeeLtrpveEAteFlreieqq 43
                                    vL++  eeL+r ++ A + + e+ + 
  gi|119719347|ref|YP_919842.1| 13 SVLAQVAEELQREIQLAQTLIAEVDSA 39
                                   5889999********888877777664 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00017
                          KNOX2  28 rpveEAteFlreieqqLqsL 47 
                                    + ++EA+eFl++ +++L++L
  gi|119719347|ref|YP_919842.1|  87 KSLDEAVEFLNKRKEELSQL 106
                                    789**************988 PP

>> DUF4055  Domain of unknown function (DUF4055)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.4    0.0091        14     101     132 ..       3      34 ..       1      36 [. 0.86
   2 ?    8.4   0.0    0.0016       2.3      71     110 ..      65     103 ..      43     121 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0091
                        DUF4055 101 qaaieaeaenSvLallasnledaldqaLrwma 132
                                    q++++ ++e SvLa +a++l++ ++ a  ++a
  gi|119719347|ref|YP_919842.1|   3 QSRERLAEEYSVLAQVAEELQREIQLAQTLIA 34 
                                    67888899***************999877766 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0016
                        DUF4055  71 gkealdrlekqmaalGarlleektateTatqaaieaeaen 110
                                     +++++r ek + a+G ++l+ek+ +e+++  ++++e e 
  gi|119719347|ref|YP_919842.1|  65 VRASIKRQEKFLVAIGSNILVEKSLDEAVEFLNKRKE-EL 103
                                    5789999999999999999999999998876655444.33 PP

>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   2.8e-05     0.042      98     175 ..      12      87 ..       2     106 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.8e-05
                                    HHHHHHHHHHTT-H.HHHHHHHHHHHHHHHHHHHTS-TT.-EEEEEEEETTE..EEEE-TTSTTTHHHHTS--EESTTT CS
                   Peripla_BP_2  98 keqiralgellgle.deaeklvaeidsklaaaksaidsekpkpvlvfggadeggyvvagsnsyigdlldalgieniaae 175
                                    +  + +++e l++e + a++l+ae+ds++ a+k+  + e+ k++lv  +a   g++v +s  +  ++l a+g +++ + 
  gi|119719347|ref|YP_919842.1|  12 YSVLAQVAEELQREiQLAQTLIAEVDSAILALKNISSLEDGKEILVPVSA---GVYVRASIKRQEKFLVAIGSNILVEK 87 
                                    5557899999****999**********************99999998844...45888888887777776666666555 PP

>> dCache_3  Double sensory domain of two-component sensor kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   1.3      0.22   3.3e+02       2      44 ..       2      44 ..       1      54 [. 0.68
   2 ?   12.9   0.2   4.4e-05     0.066      15      67 ..      65     121 ..      60     126 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.22
                       dCache_3  2 nqvkeqLeaslqtaenlleqeedqllalle.lvasspgvaeais 44
                                   +q++e+L  ++  + +++++e ++  +l++ l+a+ ++ + a++
  gi|119719347|ref|YP_919842.1|  2 AQSRERLAEEYS-VLAQVAEELQREIQLAQtLIAEVDSAILALK 44
                                   688899999999.5555555555554555548888888887774 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 4.4e-05
                       dCache_3  15 aenlleqeedqllallelvasspgvaeais..egdreqlerlldsiwndlg..leqi 67 
                                    ++++++++e+ l a++ ++  + ++ ea +  ++  e+l++l+++++ndl+  +++i
  gi|119719347|ref|YP_919842.1|  65 VRASIKRQEKFLVAIGSNILVEKSLDEAVEflNKRKEELSQLVERRMNDLNkvVARI 121
                                    5689*********************************************98775554 PP

>> DUF148  Domain of unknown function DUF148
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.3    0.0023       3.4      22      65 ..       3      46 ..       1      55 [. 0.90
   2 ?    6.9   0.4    0.0043       6.4      25      73 ..      77     125 ..      66     128 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0023
                         DUF148 22 eqleawaekygvtdeykefeakvkaqkeevkknvtavisnLssv 65
                                   +  e +ae+y+v ++++e  ++  +  + + ++v+++i  L+++
  gi|119719347|ref|YP_919842.1|  3 QSRERLAEEYSVLAQVAEELQREIQLAQTLIAEVDSAILALKNI 46
                                   566899********************************999876 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0043
                         DUF148  25 eawaekygvtdeykefeakvkaqkeevkknvtavisnLssvqekleaIl 73 
                                     a  +   v++ + e  + ++++kee+++ v++ ++ L +v +++++I 
  gi|119719347|ref|YP_919842.1|  77 VAIGSNILVEKSLDEAVEFLNKRKEELSQLVERRMNDLNKVVARIREIE 125
                                    5555556788899999999**************************9995 PP

>> DUF1759  Protein of unknown function (DUF1759)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1      0.14     2e+02      98     124 ..      15      41 ..       2      59 .. 0.61
   2 ?    9.9   0.1   0.00044      0.65      51      86 ..      84     119 ..      53     129 .] 0.83

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.14
                        DUF1759  98 ivdavneivralealgeeadkydailv 124
                                    + + ++e+ r ++ +    +++d+ + 
  gi|119719347|ref|YP_919842.1|  15 LAQVAEELQREIQLAQTLIAEVDSAIL 41 
                                    344455555555555555555555443 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00044
                        DUF1759  51 lseenYeaaveaLkkrYdnkrkiirellnelmklps 86 
                                    l e++ + ave+L+kr ++  ++++  +n l k+  
  gi|119719347|ref|YP_919842.1|  84 LVEKSLDEAVEFLNKRKEELSQLVERRMNDLNKVVA 119
                                    589999************************999865 PP

>> ParB  ParB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00071       1.1      10      54 ..      10      51 ..       5      78 .. 0.80
   2 ?    3.1   0.3     0.082   1.2e+02      14      46 ..      88     120 ..      85     128 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00071
                           ParB 10 aDYklLlkvaeklekkdvelseliekvkeeiekvqsdtelaedeq 54
                                   + Y +L++vae+l+ + +  ++li++v + i ++++  ++   e+
  gi|119719347|ref|YP_919842.1| 10 EEYSVLAQVAEELQREIQLAQTLIAEVDSAILALKNI-SS--LED 51
                                   67****************************9996333.22..233 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.082
                           ParB  14 lLlkvaeklekkdvelseliekvkeeiekvqsd 46 
                                     L ++ e l+k+++els+l+e+  ++++kv ++
  gi|119719347|ref|YP_919842.1|  88 SLDEAVEFLNKRKEELSQLVERRMNDLNKVVAR 120
                                    688888999999999999999988888887665 PP

>> FAA_hydrolase_N  Fumarylacetoacetase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1      0.78   1.2e+03      81     101 ..      17      38 ..       2      54 .. 0.58
   2 ?   10.9   0.1   0.00026      0.39      13      72 ..      70     129 .]      62     129 .] 0.77

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.78
                                    T.SHHHHT-HHHHHHHEEEGGG CS
                FAA_hydrolase_N  81 a.eeelrdneelreealvplee 101
                                    + +eel+++ +l++ ++ ++++
  gi|119719347|ref|YP_919842.1|  17 QvAEELQREIQLAQTLIAEVDS 38 
                                    2444555555555555555544 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00026
                                    EESEEEEEEETTEEEEHHHHHHTTSS-STGG...SSSGTTSS..SSSHHHHHT-HHHHHHHH CS
                FAA_hydrolase_N  13 kkeprigvaIGdqvldLsalaeaglfsqleedaeekesvfsq..ptLnafaalgrevwravR 72 
                                    k++++  vaIG+ +l  + l+ea  f   ++ +ee ++++++  + Ln+ +a  re+ +++R
  gi|119719347|ref|YP_919842.1|  70 KRQEKFLVAIGSNILVEKSLDEAVEFL--NKRKEELSQLVERrmNDLNKVVARIREIESSIR 129
                                    4477899*************8877766..45556777777555799*********9999998 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.2     0.079   1.2e+02      62      91 ..      13      42 ..       1      56 [. 0.44
   2 ?   10.2   0.5   0.00038      0.56      46      89 ..      85     128 ..      81     129 .] 0.90

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.079
                        DUF1664 62 rhLssridrvdkkldeqkeiskeikeevte 91
                                     L++  ++++++++  + +++e+++ + +
  gi|119719347|ref|YP_919842.1| 13 SVLAQVAEELQREIQLAQTLIAEVDSAILA 42
                                   333333333333333333333333333333 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00038
                        DUF1664  46 vskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeev 89 
                                    v k+l++  e l++ k++Ls+ ++r  + l+++ + ++ei++ +
  gi|119719347|ref|YP_919842.1|  85 VEKSLDEAVEFLNKRKEELSQLVERRMNDLNKVVARIREIESSI 128
                                    8899*********************9999999999999998765 PP

>> FmiP_Thoc5  Fms-interacting protein/Thoc5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.4     0.014        21     102     144 ..       3      45 ..       2      52 .. 0.88
   2 ?    7.0   0.5    0.0021       3.1     105     146 ..      87     128 ..      85     129 .] 0.94

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.014
                     FmiP_Thoc5 102 eqRkelaeqlkeleekkkkleqeieekkkfLssLppkLkslkk 144
                                    + R++lae+++ l +  ++l+ ei+  +  + +  +++ +lk+
  gi|119719347|ref|YP_919842.1|   3 QSRERLAEEYSVLAQVAEELQREIQLAQTLIAEVDSAILALKN 45 
                                    57***********************999999988888777764 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0021
                     FmiP_Thoc5 105 kelaeqlkeleekkkkleqeieekkkfLssLppkLkslkkat 146
                                    k+l+e+++ l+++k++l+q +e + + L++   +++++++++
  gi|119719347|ref|YP_919842.1|  87 KSLDEAVEFLNKRKEELSQLVERRMNDLNKVVARIREIESSI 128
                                    789999*******************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1634  (0.0911373); expected 358.6 (0.02)
Passed bias filter:                      830  (0.0462937); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 911.28
//
Query:       gi|119719348|ref|YP_919843.1|  [L=85]
Description: ribosomal LX protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.5e-09   35.6   0.1    1.2e-08   35.0   0.1    1.3  1  Ribosomal_L18A  Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A
  ------ inclusion threshold ------
       0.05   14.1   0.0       0.06   13.9   0.0    1.1  1  DUF1801         Domain of unknown function (DU1801)


Domain annotation for each model (and alignments):
>> Ribosomal_L18A  Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.1   1.4e-12   1.2e-08      64     120 ..       7      59 ..       1      60 [. 0.79

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 1.4e-12
                                    ...............TEEEEEEEEEEESSHHHHHHHHHHHHHHHS---GGGEEEEEE CS
                 Ribosomal_L18A  64 tkvknygiwlrydsrsgthnfykeyrdlteegaveqvYselgsrhrakrssIqIekv 120
                                     +vk y + lry    ++++f+ ++r l+e++++e +Ys lgsrh+++r++I++e+v
  gi|119719348|ref|YP_919843.1|   7 FEVKGYMV-LRY---GERRKFTLYLRGLSEREVLESAYSLLGSRHKVTRNHIKVESV 59 
                                    33444433.344...56789***********************************99 PP

>> DUF1801  Domain of unknown function (DU1801)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   6.7e-06      0.06      34      78 ..      20      69 ..       5      74 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.7e-06
                                   SSEEEE...........HHTHHHHHH.-EEESSEEEEETTS---HHHHHH CS
                        DUF1801 34 kkhvslffkGak.....edpkgllegkkgkgkrcirfkslddideellee 78
                                    ++++l+++G +     e   +ll + ++ ++ +i+++s+ +++ e++++
  gi|119719348|ref|YP_919843.1| 20 RRKFTLYLRGLSerevlESAYSLLGSRHKVTRNHIKVESVTEVPPENVKD 69
                                   678999***999888877888888889******************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 652.48
//
Query:       gi|119719349|ref|YP_919844.1|  [L=103]
Description: hypothetical protein Tpen_0432 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 684.42
//
Query:       gi|119719350|ref|YP_919845.1|  [L=204]
Description: hypothetical protein Tpen_0433 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.5e-43  146.5   3.1    5.9e-42  143.6   3.1    2.0  1  CarS-like     CDP-archaeol synthase
    3.3e-05   23.8   0.6    3.3e-05   23.8   0.6    2.6  3  CTP_transf_1  Cytidylyltransferase family
  ------ inclusion threshold ------
      0.075   12.5   7.8      0.022   14.3   4.3    1.8  2  5TM-5TMR_LYT  5TMR of 5TMR-LYT


Domain annotation for each model (and alignments):
>> CarS-like  CDP-archaeol synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.6   3.1   9.9e-46   5.9e-42       7     175 .]      41     204 .]      38     204 .] 0.89

  Alignments for each domain:
  == domain 1  score: 143.6 bits;  conditional E-value: 9.9e-46
                      CarS-like   7 ksiylllpayvanasavlvGG.......GtpvdlGktlvdGrrliGdGvtyrGtvaGvlvGvlvgliqglleklsilald 79 
                                    +s+ ++lpayvanas v++          +p+d+G t+vdG+rl+Gd +t+ G+++G+l+Gvlvg++             
  gi|119719350|ref|YP_919845.1|  41 RSMLWVLPAYVANASPVVFSRlvrkrwrLHPMDFGLTFVDGQRLLGDNKTFEGFLGGMLSGVLVGILL------------ 108
                                    567889*************85222222257**********************************9863............ PP

                      CarS-like  80 ssgsvlefvilalllafGallGdavGsfikrrlkierGkpalildqldfvlgalllaypvkllp.ieliilivlitlvlh 158
                                    ++  ++++v  a+ll +GallGd+ G+f+krrl+i+ G+pa +ldqldfv gal+l   +  lp +e+++ +vl+t+++h
  gi|119719350|ref|YP_919845.1| 109 AYARFVDGV-SAFLLPLGALLGDLGGAFVKRRLRIKPGEPAILLDQLDFVAGALILQGLFSKLPaAEVVVAVVLLTPIVH 187
                                    467888886.69*********************************************8877666268889999******* PP

                      CarS-like 159 lsaniiayklglkdvwy 175
                                    l++n+ a+ lglkdv++
  gi|119719350|ref|YP_919845.1| 188 LLTNMAAFVLGLKDVPW 204
                                    ****************9 PP

>> CTP_transf_1  Cytidylyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.3     0.016        96      18      67 ..       7      56 ..       2      71 .. 0.64
   2 !   23.8   0.6   5.6e-09   3.3e-05     170     233 ..      88     143 ..      85     145 .. 0.90
   3 ?   -2.9   0.2      0.75   4.5e+03      18      19 ..     180     181 ..     157     199 .. 0.48

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.016
                                   TTSH.HHHHHHHHHHHHHHHHHHH.HTT--SHHHHHHHHH...HHHHHHHH CS
                   CTP_transf_1 18 lllgglvflllvavvvilalkEli.rlvrlkkrekrllllllslvllllll 67
                                    ++ gl+fl++ ++v +++  E++ ++ +  + ++++l++ l ++++  ++
  gi|119719350|ref|YP_919845.1|  7 ACFLGLYFLVFSLIVYVILGAEFLvSVLQPGNVARSMLWV-LPAYVANASP 56
                                   4556688888888888887777651444555555555555.6666665554 PP

  == domain 2  score: 23.8 bits;  conditional E-value: 5.6e-09
                                    --BHHHHHHHHHHHHHHHHHHHHHHHCTS---TTSHHHHHHHHHHHHHHHHHHHHHHHHHHT-S CS
                   CTP_transf_1 170 kKTveGfigGlvaavvvglllalvlskalalsllhllllslllslvavfGDLveSglKRafgiK 233
                                    +KT eGf+gG+++ v+vg+lla++   +         + ++ll l a +GDL    +KR+++iK
  gi|119719350|ref|YP_919845.1|  88 NKTFEGFLGGMLSGVLVGILLAYARFVD--------GVSAFLLPLGALLGDLGGAFVKRRLRIK 143
                                    8********************9987653........56678889999****************9 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 0.75
                                    TT CS
                   CTP_transf_1  18 ll 19 
                                    +l
  gi|119719350|ref|YP_919845.1| 180 VL 181
                                    11 PP

>> 5TM-5TMR_LYT  5TMR of 5TMR-LYT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1      0.22   1.3e+03      26      32 ..      15      21 ..       5      77 .. 0.62
   2 ?   14.3   4.3   3.7e-06     0.022      55     146 ..      93     178 ..      90     201 .. 0.63

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.22
                   5TM-5TMR_LYT 26 glfsilg 32
                                    +fs++ 
  gi|119719350|ref|YP_919845.1| 15 LVFSLIV 21
                                   4443322 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 3.7e-06
                   5TM-5TMR_LYT  55 GllgGplvGliagliaglhRyllgGftalacgistilagllaGlihrklkrrrkkltvlvalligllveilqmllillla 134
                                    G+lgG+l G+++g++ ++ R+ + G++a+   + ++l  l ++++ r+l+ +      ++ +++   +  +  +lil  +
  gi|119719350|ref|YP_919845.1|  93 GFLGGMLSGVLVGILLAYARF-VDGVSAFLLPLGALLGDLGGAFVKRRLRIKP-----GEPAILLDQLDFVAGALILQGL 166
                                    99*******************.9999999999999999999999988877654.....4444443333444444444333 PP

                   5TM-5TMR_LYT 135 kpfdqalalvkt 146
                                         a+++v  
  gi|119719350|ref|YP_919845.1| 167 FSKLPAAEVVVA 178
                                    333333333222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1395.74
//
Query:       gi|119719351|ref|YP_919846.1|  [L=152]
Description: hypothetical protein Tpen_0434 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.029   14.3   0.2       0.04   13.9   0.2    1.2  1  DUF1110        Protein of unknown function (DUF1110)
      0.035   14.2   0.0      0.053   13.6   0.0    1.2  1  TetR_C_29      Tetracyclin repressor-like, C-terminal domain
      0.048   14.2   0.1        0.1   13.2   0.0    1.6  2  Phage_holin_1  Bacteriophage holin


Domain annotation for each model (and alignments):
>> DUF1110  Protein of unknown function (DUF1110)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   6.8e-06      0.04       2      43 ..       9      51 ..       8      70 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.8e-06
                        DUF1110  2 Aae.aWkarfrerVvevaervesvrekLaaaearleapmrvad 43
                                   A+  aW+a+ + ++ve +e++++  ++L +a +r  + + +  
  gi|119719351|ref|YP_919846.1|  9 AEKyAWRAHRMTKIVELNELMKKYTQELSDALQRKDLDSAISR 51
                                   55579****************************9777666654 PP

>> TetR_C_29  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   8.9e-06     0.053      33     112 ..      15      94 ..       5      99 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.9e-06
                                    -TT--TTS--SS-.THHHHHHHHHHHHHHHHTTSS-SS--HHHHHHHHHHHHHHHHHTHHHHHHHH---TTSHHHHHHHH CS
                      TetR_C_29  33 rgrhlkksesirelnspliekleeilerGqaagvFrpgvdaldlyllisslcffrvsnrhtlsalfgrdlsspealerrr 112
                                    r+++++k  +++el+++ +++l++ l+r   + ++ +++  l+ +++++   ++ v n +t++++ +  + s e++ ++ 
  gi|119719351|ref|YP_919846.1|  15 RAHRMTKIVELNELMKKYTQELSDALQRKDLDSAISREIALLEALIAVAKNEIISVINDPTVKNIAESYVLSHEKTLSYA 94 
                                    678899999*********************************************************99998888776665 PP

>> Phage_holin_1  Bacteriophage holin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.7e-05       0.1      31      72 ..      41      82 ..      14      94 .. 0.70
   2 ?   -2.6   0.1       1.4   8.2e+03      42      45 ..     126     129 ..     113     141 .. 0.44

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.7e-05
                  Phage_holin_1 31 fgldltvaklaeqllqivs..avlsllaalGvvvDPttkgisDS 72
                                   + +dl++a   +  +++++  ++++   ++ v++DPt+k+i+ S
  gi|119719351|ref|YP_919846.1| 41 QRKDLDSA--ISREIALLEalIAVAKNEIISVINDPTVKNIAES 82
                                   45566666..2233334442244555679************998 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.4
                  Phage_holin_1  42 eqll 45 
                                    e + 
  gi|119719351|ref|YP_919846.1| 126 ELFS 129
                                    2222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1035  (0.0577277); expected 358.6 (0.02)
Passed bias filter:                      734  (0.0409393); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1091.23
//
Query:       gi|119719352|ref|YP_919847.1|  [L=105]
Description: hypothetical protein Tpen_0435 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-07   30.7   0.2    0.00016   21.5   0.1    2.2  2  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
     0.0027   17.8   0.0     0.0036   17.4   0.0    1.2  1  CDC48_N         Cell division protein 48 (CDC48), N-terminal 
  ------ inclusion threshold ------
      0.046   14.2   0.2       0.22   12.0   0.0    1.9  2  PrlF_antitoxin  prlF antitoxin for toxin YhaV_toxin
        0.1   12.7   0.0        0.5   10.5   0.0    1.9  2  AbrB-like       AbrB-like transcriptional regulator


Domain annotation for each model (and alignments):
>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0    0.0011       4.7       1      22 [.      21      42 ..      21      43 .. 0.93
   2 !   21.5   0.1   3.6e-08   0.00016       5      32 ..      71      98 ..      68     104 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0011
                                   EEETTEEEEEE-CCCHHHCCEE CS
                 MazE_antitoxin  1 fkvGnsgavriPkevrfelgir 22
                                   +kv ++ +v  P+ ++++lgi+
  gi|119719352|ref|YP_919847.1| 21 VKVYSNNQVLVPAQLVRSLGIQ 42
                                   68999***************96 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 3.6e-08
                                   TEEEEEE-CCCHHHCCEECTCEEEEEEC CS
                 MazE_antitoxin  5 nsgavriPkevrfelgireGdevelevd 32
                                    s + +iPkevr++ g+ +G e+e+++ 
  gi|119719352|ref|YP_919847.1| 71 DSRQFTIPKEVREKIGVAPGMEIEVVEI 98
                                   699********************99875 PP

>> CDC48_N  Cell division protein 48 (CDC48), N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   8.1e-07    0.0036      12      81 ..      24      96 ..      14     102 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 8.1e-07
                                   SSTTEEEE-HHHHHHHTS-TTSEEEEEC.CCC.EEEEEEEBSTTST.TTTEEEE-HHHHHHHT--TTEEEEEE CS
                        CDC48_N 12 vgrgivridpedmeelglepgdvveieg.krk.Tvaivwpaepede.gkgiIrmdgvtRknagvsiGdkVtVr 81
                                     ++ v +  + +++lg++ +++ ei+  + + Tv +v ++ +    +     + + +R+ +gv  G +++V 
  gi|119719352|ref|YP_919847.1| 24 YSNNQVLVPAQLVRSLGIQDIEYAEITIrHASsTVSFVARLLKTRFtDSRQFTIPKEVREKIGVAPGMEIEVV 96
                                   56899*********************9965558*******99985578999****************999985 PP

>> PrlF_antitoxin  prlF antitoxin for toxin YhaV_toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0       0.2     9e+02       4      24 ..      23      43 ..      20      63 .. 0.72
   2 ?   12.0   0.0     5e-05      0.22       3      35 ..      68     100 ..      66     105 .] 0.77

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.2
                 PrlF_antitoxin  4 ltergqttiPasvRkaLklkk 24
                                   + +  q  +Pa + + L+++ 
  gi|119719352|ref|YP_919847.1| 23 VYSNNQVLVPAQLVRSLGIQD 43
                                   556788999999988898876 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 5e-05
                 PrlF_antitoxin   3 tltergqttiPasvRkaLklkkgrdkiaytild 35 
                                    + t+  q tiP+ vR+ +++ +g +  + +i++
  gi|119719352|ref|YP_919847.1|  68 RFTDSRQFTIPKEVREKIGVAPGMEIEVVEIKP 100
                                    78999****************987433445555 PP

>> AbrB-like  AbrB-like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00011       0.5      29      65 ..      17      53 ..       2      57 .. 0.84
   2 ?   -0.2   0.0      0.25   1.1e+03      49      61 ..      83      95 ..      73      99 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00011
                      AbrB-like 29 asYrvsVqknGnLliGsaYTkklgLkpGdefeIklgr 65
                                     Y+v+V +n ++l+ +   + lg++  +  eI++++
  gi|119719352|ref|YP_919847.1| 17 LPYKVKVYSNNQVLVPAQLVRSLGIQDIEYAEITIRH 53
                                   56***********************999998988876 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.25
                      AbrB-like 49 kklgLkpGdefeI 61
                                   +k+g+ pG e e+
  gi|119719352|ref|YP_919847.1| 83 EKIGVAPGMEIEV 95
                                   7899999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 713.77
//
Query:       gi|119719353|ref|YP_919848.1|  [L=89]
Description: hypothetical protein Tpen_0436 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0057   17.3   0.0      0.008   16.8   0.0    1.2  1  AKNA           AT-hook-containing transcription factor
  ------ inclusion threshold ------
       0.11   12.2   0.0       0.11   12.1   0.0    1.1  1  Cons_hypoth95  Conserved hypothetical protein 95


Domain annotation for each model (and alignments):
>> AKNA  AT-hook-containing transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   8.9e-07     0.008      33      71 ..      50      88 ..      46      89 .] 0.92

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 8.9e-07
                           AKNA 33 gqpgkfdpsreleaeIyqlgqrleeLkdqtdqlkqkvee 71
                                   + ++kf+  r++  e+ +l  +le  k+   q++ k e+
  gi|119719353|ref|YP_919848.1| 50 TDQRKFSLARSIVNEVLRLYSMLEGVKEELPQTQGKREP 88
                                   5789******************************99887 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   1.2e-05      0.11      45      87 ..      24      65 ..      15      88 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.2e-05
                                   EEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCC CS
                  Cons_hypoth95 45 vLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleel 87
                                    +D ++G G + l A SRg + +++ve+d++ +++ +  ++e+
  gi|119719353|ref|YP_919848.1| 24 SVDDYSGGGIVILHAFSRG-RIIYAVETDQRKFSLARSIVNEV 65
                                   6899***************.999*******9999877766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       293  (0.0163422); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.30s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 607.16
//
Query:       gi|119719354|ref|YP_919849.1|  [L=350]
Description: hypothetical protein Tpen_0437 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-36  125.1   0.0    3.5e-33  115.1   0.0    2.1  1  DUF711    Uncharacterised ACR (DUF711)
  ------ inclusion threshold ------
       0.16   11.9   0.1       0.28   11.1   0.1    1.4  1  LppA      Lipoprotein confined to pathogenic Mycobacterium


Domain annotation for each model (and alignments):
>> DUF711  Uncharacterised ACR (DUF711)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.1   0.0   3.9e-37   3.5e-33       5     404 ..       5     336 ..       1     338 [. 0.85

  Alignments for each domain:
  == domain 1  score: 115.1 bits;  conditional E-value: 3.9e-37
                         DUF711   5 ekldiRtvTlgislldcasedleklaekiyekiikkaaklvktveeieeeyGievvtkRisvtpisellaeasaeeavel 84 
                                      +++R+v l ++l++  ++              +k a + ++v++ +e+ G++v tkR++ +p+     e++     + 
  gi|119719354|ref|YP_919849.1|   5 AGFKVRAVVLHVDLEKGGDS------------LEEKLAAFTEAVKAFSETTGVDVWTKRVVANPVP---PESF----EKA 65 
                                    56788888888888843333............3468999***************************...4444....567 PP

                         DUF711  85 aktldelakevgvdfiggfsal.vekgltkgdkeliesipealaetervcssvnvastkaginmdavraaaevikeiael 163
                                    +++l ++a+  g++    ++a+  +++       + e++++++ ++er++ss+         + ++ + + +++k+++e+
  gi|119719354|ref|YP_919849.1|  66 VHALYSAAEPSGIN----YVAVpQRRP------LTPEVLADVMDSYERLYSSATY-------DDNSTATLVSTVKALSER 128
                                    88999*********....****44444......45579**************666.......556777788888999987 PP

                         DUF711 164 tkdkdglgnaklvvfanvpednPFfpgAfhgvgeaeavinvGvsgpgvvkkaleeakkeasleelaeaikktafkitrlg 243
                                    ++    l +a+++v +    ++P+fp+  ++v         Gvs + +  k l+e  +   l++++e+++  a++    +
  gi|119719354|ref|YP_919849.1| 129 SP----LMAARYAVSFGGFIQTPYFPATATSV--------EGVSLSLLYPKFLSEN-P---LSKVSETFSGLAAR----A 188
                                    75....788******************99986........3777777777778777.4...56666666554433....2 PP

                         DUF711 244 elvarevakrlgvefggiDlSlaPtpavgdSvaeileelglesfGapGtlaalalltdavkkGGvmasskvgGlsGlflp 323
                                            +++   f giD+Sl+P   +++Sva ++e++   ++G+pGt+ a+  l++ +    ++ + + +G++ ++lp
  gi|119719354|ref|YP_919849.1| 189 --------EKTLPGFLGIDFSLSPW--EDESVALLVEKVSGTTLGSPGTIRAIRELNRRINL--LAHEARAVGYNEVMLP 256
                                    ........334456***********..78*********************************..89999*********** PP

                         DUF711 324 vsEDaglaeaaeegaltiekLlamsaVCsvGLDmvpipgdtsaetiaaliaDeaalavrlnKtlavRliPvpgkkaGdkv 403
                                    + ED++l e a+ g+l++++Ll +++ C  GLDmv ip  t+ + ++ +++D   +     + l+ Rli +p  ++Gd+v
  gi|119719354|ref|YP_919849.1| 257 LAEDNRLKELAKTGQLRFSHLLNYASYCVAGLDMVVIPDTTEDKVLENILLDLSEIQKLKGRILGLRLILAPA-EEGDEV 335
                                    *********************************************************************8887.678887 PP

                         DUF711 404 e 404
                                    e
  gi|119719354|ref|YP_919849.1| 336 E 336
                                    6 PP

>> LppA  Lipoprotein confined to pathogenic Mycobacterium
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   3.1e-05      0.28      66     118 ..      37      88 ..      29     109 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.1e-05
                                    SSS-TTTEEE-B---EEESS---HHHHHHHHHHHHHHHHTTT--EEE-S-BSS CS
                           LppA  66 dpyeetdgrrvalesvvsagpipddqWpqaleiVrelAakygatevevfkDep 118
                                    ++++et g  v++ ++v+a p+p++ +++a+ +  ++A+  g++ v v + +p
  gi|119719354|ref|YP_919849.1|  37 KAFSETTGVDVWT-KRVVANPVPPESFEKAVHALYSAAEPSGINYVAVPQRRP 88 
                                    5789*********.667789**********************99988877666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2445.38
//
Query:       gi|119719355|ref|YP_919850.1|  [L=370]
Description: hypothetical protein Tpen_0438 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00012   22.5   0.0    0.00027   21.4   0.0    1.5  1  AAA_17           AAA domain
    0.00033   20.7   0.0     0.0021   18.1   0.0    2.0  1  Nuc_deoxyrib_tr  Nucleoside 2-deoxyribosyltransferase


Domain annotation for each model (and alignments):
>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0     3e-08   0.00027       1     119 [.      11     135 ..      11     146 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 3e-08
                                    EE-TTSSHHHHHHHHHHHH.TEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHH.....HSSEE CS
                         AAA_17   1 lGgPGsGKgtqceklveky.gfthlsaGdllreeakrgglakardemrklpleekkelqkeaaekiaeea.....kkkgv 74 
                                    +G+ GsG   +++++  +  +++++  G  +++  ++ g +  ++++ +++    + l+++  e+i ++      +k+ v
  gi|119719355|ref|YP_919850.1|  11 TGISGSGRLSVLQEVSSEApELKVIDVGTRMYDKSRELGVVIPDGKILDMDPLALEYLRATTFEDILRDVeelrrQKQVV 90 
                                    69*************998879*************9999*98888889888888888888877777755433445566779 PP

                                    EEEE-SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHH CS
                         AAA_17  75 lvdghprikeqagfldglpkevleelkpdaiilleadpeeilerr 119
                                     + +h ++++++ +l  +    ++ + pd+ + + +++  +++ +
  gi|119719355|ref|YP_919850.1|  91 AISTHVSFRWKKHLLHAFNFYYVNRIAPDLYVNVLDNAHLVYAAL 135
                                    ******************************999988887776655 PP

>> Nuc_deoxyrib_tr  Nucleoside 2-deoxyribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   2.3e-07    0.0021      14     102 ..     221     338 ..     206     346 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.3e-07
                                    HHHHHHHHHHHHTTTTEEE-CC...............................TT-TT.......--SSHHHHHHHHHHH CS
                Nuc_deoxyrib_tr  14 kalaarlkallaengldglaPl...............................dneaelel...paeetaraiyeadial 59 
                                     +  +++k++l+e+g+ +++P+                               + +   ++   + e    +i+ +d +l
  gi|119719355|ref|YP_919850.1| 221 LEEKNEVKKRLKEAGIVVFDPIsvedsplidmayeaekagkkevefemdgrtfSLP--VSQiydAIEDIRDQIVVRDYQL 298
                                    56678899999999999999999999999999999999998888887766655222..2223447889999********* PP

                                    HHC-SEEEEE--SSSSSS--HHHHHHHHHHHHCT-EEEEE-S- CS
                Nuc_deoxyrib_tr  60 irqaDavianldpfrgpeaDsGtafEvGyavalgkpvlayttd 102
                                    i+q+D++++ +  +      +G+  E+ y +  +k v+a   +
  gi|119719355|ref|YP_919850.1| 299 INQSDIIVVFYPTTV---LSPGVLSEIKYGYTHNKHVFAIFPH 338
                                    ************999...********************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 2689.27
//
Query:       gi|119719356|ref|YP_919851.1|  [L=671]
Description: type II secretion system protein E [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-46  159.2   0.0    2.6e-46  157.9   0.0    1.6  2  T2SSE     Type II/IV secretion system protein
  ------ inclusion threshold ------
      0.011   16.2   0.0       0.03   14.8   0.0    1.7  1  ABC_tran  ABC transporter
      0.015   15.2   0.1      0.042   13.6   0.0    1.8  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
      0.025   14.3   0.0      0.055   13.2   0.0    1.5  1  AAA_29    P-loop containing region of AAA domain
      0.031   14.5   0.8       0.25   11.6   0.0    2.3  2  AAA_28    AAA domain
      0.036   14.1   0.0       0.11   12.5   0.0    1.9  1  MMR_HSR1  50S ribosome-binding GTPase
      0.098   12.4   0.7       0.34   10.6   0.0    1.9  2  AAA_15    AAA ATPase domain
       0.11   12.9   0.0       0.33   11.3   0.0    1.8  2  AAA_16    AAA ATPase domain
        1.2    9.7   4.2       0.49   10.9   0.2    2.1  2  AAA_23    AAA domain


Domain annotation for each model (and alignments):
>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.9   0.0   1.3e-49   2.6e-46       4     250 ..     151     406 ..     148     420 .. 0.93
   2 ?   -2.8   0.1       1.3   2.6e+03      12      35 ..     453     476 ..     447     502 .. 0.71

  Alignments for each domain:
  == domain 1  score: 157.9 bits;  conditional E-value: 1.3e-49
                          T2SSE   4 lleallddekvsdihvekper.vkvrervdgielreveelekaalerlisriaalakldiseerplqdarlpekgvrlrv 82 
                                    ++e l++d++  di     +r + v  r  +    ++ + +++ l+ +i ++a++a+++is   p++da lp + +rl +
  gi|119719356|ref|YP_919851.1| 151 PIEVLMRDYRLEDISCDGVDRaIHVWHRDYESIPTNIVFRSRDYLREFIVKLAHMAGKHISAAFPIVDAMLP-GRHRLAA 229
                                    6789999**************99**8888788999*************************************.8899988 PP

                          T2SSE  83 vllPvvag..ealviRkksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeinksderi 160
                                         v     +++iRk ++k l++ +++ +++l+   a+ l   +++r++ +v G+T  GKttll+a+ ++++    +i
  gi|119719356|ref|YP_919851.1| 230 TYGEEVSPrgSTFTIRKFREKPLSIVEIISSGNLDSWSAAYLWLMIENRMTAMVIGATAAGKTTLLNAIANFFKPG-FKI 308
                                    876655444699***************************************************************9.*** PP

                          T2SSE 161 vtvEDpvEiqleganqvqlnak.........kakvtfadllraaLRlrPDrimvGEiRdketleilkAvnTGHlgslsTl 231
                                    vt+E + E++l ++n vql+++          +++t+ dl++ +LR rPD i+vGE+R++e++ + +A++TGH g +sT+
  gi|119719356|ref|YP_919851.1| 309 VTIEETPELNLPHENWVQLVSResyglgeskVGEITLYDLVKVSLRYRPDYIIVGEVRGEEAFVLFQAMSTGHGG-MSTM 387
                                    ****************************998899***************************************99.**** PP

                          T2SSE 232 HansaagalerLeqlgaev 250
                                    Ha+s   a++rL    ++v
  gi|119719356|ref|YP_919851.1| 388 HADSLDRAVKRLTSPPMNV 406
                                    ************8755555 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.3
                          T2SSE  12 ekvsdihvekpervkvrervdgie 35 
                                    + v d+hv   e+  +r+ ++++ 
  gi|119719356|ref|YP_919851.1| 453 DPVKDVHVVVSESHHIRFIAEKLG 476
                                    568999999999999999888733 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   1.5e-05      0.03       9      48 ..     276     315 ..     271     335 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.5e-05
                                    ETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   9 kegekvaivGenGaGKStLlkllagllkpteGeilldgkd 48 
                                    ++  +  ++G + aGK+tLl+++a+  kp    +++++++
  gi|119719356|ref|YP_919851.1| 276 ENRMTAMVIGATAAGKTTLLNAIANFFKPGFKIVTIEETP 315
                                    556677899*****************99988888777665 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.1e-05     0.042       3      61 ..     282     320 ..     280     349 .. 0.69
   2 ?   -2.3   0.0       1.5     3e+03     140     161 ..     478     499 ..     424     530 .. 0.51

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.1e-05
                         AAA_21   3 vliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefe 61 
                                    ++iG+ ++GK++LL a+  ++                    k  +++ +++++++ ++ 
  gi|119719356|ref|YP_919851.1| 282 MVIGATAAGKTTLLNAIANFF--------------------KPGFKIVTIEETPELNLP 320
                                    79***************6554....................444444444444444444 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.5
                         AAA_21 140 fgkaltditsrawsllllldgl 161
                                    ++++l + ++r +  l+++++ 
  gi|119719356|ref|YP_919851.1| 478 RVEDLYSEIERRRLVLEWMRMK 499
                                    2222233333333333333333 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.8e-05     0.055      22      48 ..     278     304 ..     268     309 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.8e-05
                         AAA_29  22 kgatlltGpsGsGKSTllDAiqalLvp 48 
                                    + + +++G++ +GK+Tll Ai+  + p
  gi|119719356|ref|YP_919851.1| 278 RMTAMVIGATAAGKTTLLNAIANFFKP 304
                                    33789****************987766 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1      0.31   6.2e+02     112     148 ..      93     130 ..      68     134 .. 0.64
   2 ?   11.6   0.0   0.00012      0.25       3      29 ..     282     313 ..     280     318 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.31
                         AAA_28 112 vfllppapei.dddgeRredleereaiderlrealrel 148
                                    ++ ++ +p++  d + R++ ++e+++++e+ r+a+r+l
  gi|119719356|ref|YP_919851.1|  93 ILSVELEPPAsFDVELREHVVAEARRLAEKYRSAVRGL 130
                                    3333334444347888999**************99986 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00012
                         AAA_28   3 vitGgestGKTtlleaLaar...gypvv..pE 29 
                                    +++G+  +GKTtll+a+a+    g+++v  +E
  gi|119719356|ref|YP_919851.1| 282 MVIGATAAGKTTLLNAIANFfkpGFKIVtiEE 313
                                    589***************86667555443255 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.8e-05      0.11       2      21 ..     281     300 ..     280     320 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.8e-05
                                    EEEEESTTSSHHHHHHHHHT CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltg 21 
                                    ++++G + +GK+tL+na+ +
  gi|119719356|ref|YP_919851.1| 281 AMVIGATAAGKTTLLNAIAN 300
                                    689***************98 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.5      0.53   1.1e+03     134     258 ..      10      29 ..       2      98 .. 0.41
   2 ?   10.6   0.0   0.00017      0.34      26      60 ..     281     312 ..     271     328 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.53
                         AAA_15 134 ekisvekkkskkelpkekeeklekekeelkidkedlkklikkleeslkkeeelknvlksaiiklllisakRnvsdedsek 213
                                    ek++  kkk+kk +                       ++++                                       
  gi|119719356|ref|YP_919851.1|  10 EKKKPAKKKEKKAIA----------------------ETSE--------------------------------------- 28 
                                    222222222222222......................1111....................................... PP

                         AAA_15 214 kssllgklkekileealqekleeelteklkeiqeklkeidkklae 258
                                                                                +
  gi|119719356|ref|YP_919851.1|  29 --------------------------------------------K 29 
                                    ............................................1 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00017
                         AAA_15  26 tvliGkNnsGKSsilealdlFlnnkekknkkviki 60 
                                      +iG+ ++GK+++l+a+  F++     +k v+ +
  gi|119719356|ref|YP_919851.1| 281 AMVIGATAAGKTTLLNAIANFFKPG---FKIVTIE 312
                                    479*******************977...4344444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       6.1   1.2e+04     108     131 ..     108     131 ..      72     139 .. 0.53
   2 ?   11.3   0.0   0.00017      0.33      27      80 ..     281     332 ..     275     380 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 6.1
                         AAA_16 108 vpelagaeasrllellkrllalls 131
                                     +e   aea+rl+e+ +++++ ls
  gi|119719356|ref|YP_919851.1| 108 LREHVVAEARRLAEKYRSAVRGLS 131
                                    333333444666666666665555 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00017
                         AAA_16  27 vllsGesGvGKsslvrellralekd.ggiflrgkcdqlesaipysalaqalaree 80 
                                     +++G+ + GK++l++++++ ++   ++++++++ + +   +p   ++q+ +re+
  gi|119719356|ref|YP_919851.1| 281 AMVIGATAAGKTTLLNAIANFFKPGfKIVTIEETPELN---LPHENWVQLVSRES 332
                                    579****************7666555566688888888...88888999987644 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.6      0.97   1.9e+03     103     115 ..      15      27 ..       3      99 .. 0.63
   2 ?   10.9   0.2   0.00024      0.49      24      40 ..     283     299 ..     277     302 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.97
                         AAA_23 103 ttkkaklelleid 115
                                     +kk+k+ + e++
  gi|119719356|ref|YP_919851.1|  15 AKKKEKKAIAETS 27 
                                    1111111111111 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00024
                         AAA_23  24 ItGpNGaGKTTildAik 40 
                                    ++G + aGKTT+l+Ai 
  gi|119719356|ref|YP_919851.1| 283 VIGATAAGKTTLLNAIA 299
                                    68*************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (671 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1158  (0.0645881); expected 358.6 (0.02)
Passed bias filter:                      862  (0.0480785); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.75u 0.29s 00:00:01.04 Elapsed: 00:00:00.45
# Mc/sec: 4458.92
//
Query:       gi|119719357|ref|YP_919852.1|  [L=291]
Description: hypothetical protein Tpen_0440 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       255  (0.0142228); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 2069.29
//
Query:       gi|119719358|ref|YP_919853.1|  [L=138]
Description: S-adenosylmethionine decarboxylase related [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      1e-36  125.4   0.0    1.2e-36  125.2   0.0    1.0  1  AdoMet_dc  S-adenosylmethionine decarboxylase


Domain annotation for each model (and alignments):
>> AdoMet_dc  S-adenosylmethionine decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.2   0.0   6.7e-41   1.2e-36       1     106 []       9     115 ..       9     115 .. 1.00

  Alignments for each domain:
  == domain 1  score: 125.2 bits;  conditional E-value: 6.7e-41
                                    EEEEEEES--HHHCTSHHHHHHHHHHHHHHCT-EEEEEEEEE-SSS-EEEEEEETTEEEEEEEEGGGTEEEEEEEEEST. CS
                      AdoMet_dc   1 hllvdlygcdpelledaelleqilteaaeaigatvlsvafhkfepeGvsvvvliaeShlsiHtwpetgyaaiDvftcge. 79 
                                    hl+v++++cd +ll++ e ++++l +aa a++ tv+   f++f+p+G+s+ vl+aeSh+siHtwpe+gyaa+Dvftcge 
  gi|119719358|ref|YP_919853.1|   9 HLIVEMFECDGRLLDSLEVVKSALLDAAVASNSTVVGFDFYRFKPHGISGYVLVAESHISIHTWPEYGYAAVDVFTCGEh 88 
                                    9******************************************************************************* PP

                                    HHHHHHHHHHHHHHT-SEEEEEEEEEE CS
                      AdoMet_dc  80 ispekaleylieafkadrvtvdelkRG 106
                                    ++p+k le+l+e+++a++vt+ +++RG
  gi|119719358|ref|YP_919853.1|  89 TDPWKGLEILKERLRAKKVTIISIERG 115
                                    **************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       228  (0.0127168); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 961.86
//
Query:       gi|119719359|ref|YP_919854.1|  [L=474]
Description: hypothetical protein Tpen_0442 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (474 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       863  (0.0481343); expected 358.6 (0.02)
Passed bias filter:                      649  (0.0361983); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.42
# Mc/sec: 3356.76
//
Query:       gi|119719360|ref|YP_919855.1|  [L=75]
Description: hypothetical protein Tpen_0443 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0015   18.2   0.2     0.0018   18.0   0.2    1.0  1  DSHCT     DSHCT (NUC185) domain
  ------ inclusion threshold ------
      0.065   13.3   0.2      0.088   12.9   0.2    1.2  1  Mis12     Mis12 protein


Domain annotation for each model (and alignments):
>> DSHCT  DSHCT (NUC185) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.2     2e-07    0.0018     106     159 ..      18      71 ..      12      73 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2e-07
                          DSHCT 106 faellektdldeGdiVRllrrleellrqlakaakvigneeLkkkaeeaielikR 159
                                    +a++l+  +l+e  +V +l  +ee+l  +++a++v ++eeL++++ee +e ++R
  gi|119719360|ref|YP_919855.1|  18 LASTLRRDELYEARLVEALDAIEEFLASVRSAPQVEEDEELARELEEGVEELRR 71 
                                    566777789*******************************************99 PP

>> Mis12  Mis12 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   9.8e-06     0.088      25      67 ..      32      72 ..      26      73 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.8e-06
                                   HHHHHHHHHHHH........TTSTHHHH-HHHHHHHHHHHHHH CS
                          Mis12 25 lyravdavekvLdkkleedeeeekaaeesteeieeGtakletl 67
                                   l +a+da+e++L+   ++  +  +++ee ++e+eeG+++l++l
  gi|119719360|ref|YP_919855.1| 32 LVEALDAIEEFLA-SVRSAPQ-VEEDEELARELEEGVEELRRL 72
                                   5689********4.4444443.677889***********9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       864  (0.0481901); expected 358.6 (0.02)
Passed bias filter:                      579  (0.032294); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 513.78
//
Query:       gi|119719361|ref|YP_919856.1|  [L=183]
Description: hypothetical protein Tpen_0444 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-22   80.8   0.0    1.6e-22   80.5   0.0    1.1  1  AAA_18           AAA domain
    1.3e-05   25.6   0.0    2.3e-05   24.8   0.0    1.5  1  AAA              ATPase family associated with various cellul
    6.2e-05   23.4   0.1     0.0001   22.7   0.0    1.3  1  AAA_16           AAA ATPase domain
    8.4e-05   22.6   0.1    0.00024   21.1   0.0    1.7  2  AAA_5            AAA domain (dynein-related subfamily)
     0.0006   20.0   0.2      0.029   14.5   0.1    2.1  2  AAA_33           AAA domain
    0.00098   19.4   0.0     0.0018   18.5   0.0    1.6  1  AAA_28           AAA domain
     0.0014   18.5   0.6     0.0042   17.0   0.2    1.8  1  NTPase_1         NTPase
     0.0014   18.7   0.4      0.013   15.6   0.4    2.1  1  SKI              Shikimate kinase
     0.0024   17.4   0.0     0.0032   16.9   0.0    1.3  1  KTI12            Chromatin associated protein KTI12
     0.0027   17.7   0.3     0.0059   16.5   0.1    1.6  2  NACHT            NACHT domain
     0.0043   16.8   0.0     0.0058   16.4   0.0    1.2  1  AAA_30           AAA domain
     0.0046   17.4   0.4      0.022   15.2   0.4    2.0  1  AAA_17           AAA domain
     0.0053   17.0   0.1       0.01   16.1   0.1    1.5  1  AAA_22           AAA domain
     0.0055   16.6   0.0      0.011   15.6   0.0    1.5  1  AAA_3            ATPase family associated with various cellul
     0.0066   16.8   0.0     0.0098   16.3   0.0    1.4  1  RNA_helicase     RNA helicase
     0.0083   16.3   0.0     0.0094   16.1   0.0    1.2  1  Cytidylate_kin2  Cytidylate kinase-like family
  ------ inclusion threshold ------
      0.011   15.5   0.0      0.017   14.9   0.0    1.4  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      0.012   15.3   0.2      0.022   14.5   0.2    1.6  1  AAA_24           AAA domain
      0.013   15.2   1.0       0.14   11.8   0.2    2.4  3  Cytidylate_kin   Cytidylate kinase
      0.018   14.5   0.2      0.039   13.5   0.1    1.6  1  AAA_7            P-loop containing dynein motor region
      0.018   14.9   0.1      0.038   13.9   0.1    1.5  1  APS_kinase       Adenylylsulphate kinase
      0.024   14.5   0.1       0.89    9.4   0.1    2.1  2  dNK              Deoxynucleoside kinase
      0.027   14.5   0.3      0.037   14.1   0.3    1.3  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
       0.04   14.0   0.0      0.057   13.5   0.0    1.3  1  Sigma54_activ_2  Sigma-54 interaction domain
      0.043   13.0   0.0      0.043   13.0   0.0    1.2  1  TIP49            TIP49 P-loop domain
      0.059   13.4   0.0      0.081   13.0   0.0    1.2  1  AAA_14           AAA domain
      0.059   13.1   0.1      0.094   12.4   0.1    1.4  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.062   12.5   0.0       0.07   12.3   0.0    1.1  1  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.063   13.0   0.0       0.26   11.0   0.0    1.8  2  PRK              Phosphoribulokinase / Uridine kinase family
      0.071   12.3   0.0      0.087   12.0   0.0    1.3  1  ArsA_ATPase      Anion-transporting ATPase
      0.075   12.3   0.1       0.13   11.6   0.1    1.4  1  Zeta_toxin       Zeta toxin
      0.081   12.4   0.3       0.33   10.4   0.5    1.8  2  ParA             NUBPL iron-transfer P-loop NTPase
      0.083   12.6   0.1       0.13   11.9   0.1    1.3  1  Sigma54_activat  Sigma-54 interaction domain
      0.089   12.2   0.0       0.16   11.3   0.0    1.5  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
       0.11   11.5   0.1        0.2   10.6   0.1    1.4  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
       0.11   12.2   0.4       0.19   11.4   0.1    1.5  1  CoaE             Dephospho-CoA kinase
       0.13   12.4   0.2       0.27   11.3   0.2    1.6  1  MMR_HSR1         50S ribosome-binding GTPase
       0.14   12.0   0.1       0.27   11.1   0.1    1.4  1  Rad17            Rad17 P-loop domain
       0.15   11.8   0.0       0.26   11.0   0.0    1.4  1  IstB_IS21        IstB-like ATP binding protein
       0.23   11.8   0.6       0.49   10.7   0.4    1.5  1  AAA_19           AAA domain
       0.24   10.9   1.1       0.41   10.2   1.1    1.8  1  AAA_25           AAA domain
       0.34   10.5   1.3       0.45   10.1   0.4    1.7  1  SRP54            SRP54-type protein, GTPase domain


Domain annotation for each model (and alignments):
>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.5   0.0   3.7e-25   1.6e-22       1     130 []       3     122 ..       3     122 .. 0.95

  Alignments for each domain:
  == domain 1  score: 80.5 bits;  conditional E-value: 3.7e-25
                         AAA_18   1 IlltGtpGvGKttlakeLskrlgf.gvnlrdvakenglllevdpealdeskrldedkldklldaleenssaleegknlvi 79 
                                    +l+tGtpGvGKt++a+ L++ lg   v + ++a+en+l+ ++dpe   +  ++d+  + +ll+++  +++        v+
  gi|119719361|ref|YP_919856.1|   3 VLITGTPGVGKTSVAQSLASTLGKkYVDVAKLAAENNLVKGFDPE--LQAYIVDTSSVRALLEEILTCNE--------VV 72 
                                    79****************999955699999999************..**********9999999999977........** PP

                         AAA_18  80 dghlaeleseaakdikkvvLtaspeelleRlekRgyeeakikeneeaeild 130
                                    d h++e+++ + + ++ +vL+++p el++Rle+Rgy ++ki+ n eae ld
  gi|119719361|ref|YP_919856.1|  73 DTHIVECVPKRKVTHV-IVLRLNPLELKKRLEARGYPNRKIAANVEAEVLD 122
                                    *************999.*******************************985 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   5.5e-08   2.3e-05       1      48 [.       3      50 ..       3      79 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 5.5e-08
                                   EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHH CS
                            AAA  1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkire 48
                                   vl++G+pG+GKT++a+++a++lg +++ +      +++v+    ++++
  gi|119719361|ref|YP_919856.1|  3 VLITGTPGVGKTSVAQSLASTLGKKYVDVAKLAAENNLVKGFDPELQA 50
                                   799********************9999998888777755554444444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   2.4e-07    0.0001      26      85 ..       2      52 ..       1      97 [. 0.73

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 2.4e-07
                         AAA_16 26 lvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrql 85
                                   +vl++G +GvGK+s++++l+  l k+++ +++  ++ +        l++ ++  el + +
  gi|119719361|ref|YP_919856.1|  2 AVLITGTPGVGKTSVAQSLASTLGKKYVDVAKLAAENN--------LVKGFDP-ELQAYI 52
                                   69************************777766666666........5555544.333333 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   5.7e-07   0.00024       2      64 ..       3      62 ..       2      82 .. 0.77
   2 ?   -1.3   0.0       4.6     2e+03      49      70 ..     115     139 ..      92     170 .. 0.64

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 5.7e-07
                                   EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........-------- CS
                          AAA_5  2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar 64
                                   vl+ G pG+gK+++a++la+ l+++++ v+  +   e++l+ + ++ + ++  vd + vra  
  gi|119719361|ref|YP_919856.1|  3 VLITGTPGVGKTSVAQSLASTLGKKYVDVA--KLAAENNLVKGFDP-ELQAYIVDTSSVRALL 62
                                   89********************99876555..44578888888887.7777777777776655 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 4.6
                                    ........--------...G-SEEE CS
                          AAA_5  49 ngttslvdsplvraar...egeilv 70 
                                    n +++  ds+l +a++   e +++ 
  gi|119719361|ref|YP_919856.1| 115 NVEAEVLDSVLIDAVKwfgERKVFE 139
                                    6667777777777777666444443 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   6.8e-05     0.029       2      49 ..       3      52 ..       3      77 .. 0.72
   2 ?    3.6   0.0      0.16        68     100     134 ..      87     122 ..      70     126 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.8e-05
                         AAA_33  2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqsktdyt 49
                                   vl+ G pG+GK+ +a++l+  lg  +v +++ ++ ++l++  ++ ++ y+
  gi|119719361|ref|YP_919856.1|  3 VLITGTPGVGKTSVAQSLASTLGkkYVDVAKLAAENNLVKGFDPELQAYI 52
                                   6889******************9988877776666666654444444444 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.16
                         AAA_33 100 rivvvetdeetlkeRlakRaang.ddrsevpeeald 134
                                    +++v++  + +lk+Rl++R  ++ + +++v+ e+ld
  gi|119719361|ref|YP_919856.1|  87 HVIVLRLNPLELKKRLEARGYPNrKIAANVEAEVLD 122
                                    67889999999*********9984556688888887 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   4.2e-06    0.0018       2      26 ..       3      30 ..       2      70 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 4.2e-06
                         AAA_28  2 ivitGgestGKTtlleaLaar...gypv 26
                                   + itG+++ GKT++++ La++   +y+ 
  gi|119719361|ref|YP_919856.1|  3 VLITGTPGVGKTSVAQSLASTlgkKYVD 30
                                   89*****************987443443 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.2   9.8e-06    0.0042       2      31 ..       3      32 ..       2      45 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 9.8e-06
                                   EEEE--TTSSHHHHHHHHHHHH...GGGEE CS
                       NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvkvg 31
                                   v+iTG pGvGKt + + ++++l ++ v v+
  gi|119719361|ref|YP_919856.1|  3 VLITGTPGVGKTSVAQSLASTLGKKYVDVA 32
                                   89********************99988886 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.4   3.1e-05     0.013       1      29 [.       9      37 ..       9     158 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.1e-05
                                   TTSSHHHHHHHHHHHHTSEEEEHHHHHHH CS
                            SKI  1 mGaGKstvGkllAkklglefiDlDeliek 29
                                   +G+GK++v++ lA +lg +++D+ +l  +
  gi|119719361|ref|YP_919856.1|  9 PGVGKTSVAQSLASTLGKKYVDVAKLAAE 37
                                   69********************9877544 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   7.6e-06    0.0032       4      38 ..       3      37 ..       1      72 [. 0.79

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 7.6e-06
                                   EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-TH CS
                          KTI12  4 vvltGlPssGKstrakeLakaleeekrsvvvidde 38
                                   v++tG P +GK+++a+ La++l ++  +v  +  e
  gi|119719361|ref|YP_919856.1|  3 VLITGTPGVGKTSVAQSLASTLGKKYVDVAKLAAE 37
                                   89********************9977776655444 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   1.4e-05    0.0059       3      29 ..       3      29 ..       1      35 [. 0.89
   2 ?   -2.1   0.0       7.5   3.2e+03     104     123 ..      57      76 ..      43     101 .. 0.62

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.4e-05
                                   EEEEC-TTTCHHHHHHHHHHHHCTS-S CS
                          NACHT  3 vilqGeaGsGKTtLlqklalawaegkl 29
                                   v+++G +G+GKT  +q+la+++ +++ 
  gi|119719361|ref|YP_919856.1|  3 VLITGTPGVGKTSVAQSLASTLGKKYV 29
                                   89*******************999875 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 7.5
                                    .....HHHHHCTTTTT--EE CS
                          NACHT 104 pvrtlLselirkkllpeasl 123
                                    +vr lL+e+++ + +  +++
  gi|119719361|ref|YP_919856.1|  57 SVRALLEEILTCNEVVDTHI 76 
                                    55555555555544444444 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.4e-05    0.0058      21      80 ..       3      65 ..       1      91 [. 0.82

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.4e-05
                         AAA_30 21 avltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelg...ieastiakllkrl 80
                                   +++tG +G GKt + ++l+ ++ ++  +v+ lA +++  k    el+   +++s++  ll++ 
  gi|119719361|ref|YP_919856.1|  3 VLITGTPGVGKTSVAQSLASTLGKKYVDVAKLAAENNLVKGFDPELQayiVDTSSVRALLEEI 65
                                   689***********************************9999988884445888888888655 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.4   5.1e-05     0.022       1     119 [.       6     102 ..       6     121 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.1e-05
                                    EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEEEEE-S CS
                         AAA_17   1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemrklpleekkelqkeaaekiaeeakkkgvlvdghp 80 
                                    +G PG+GK+ +++ l+  +g +++     + + a++++l+k +d   +++++++  ++++++ +i       + +vd+h 
  gi|119719361|ref|YP_919856.1|   6 TGTPGVGKTSVAQSLASTLGKKYVD----VAKLAAENNLVKGFDPELQAYIVDTSSVRALLE-EILTC----NEVVDTHI 76 
                                    69**********************9....555555666666555555666677776666665.35442....34777777 PP

                                    EEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHH CS
                         AAA_17  81 rikeqagfldglpkevleelkpdaiilleadpeeilerr 119
                                    +          +pk      k++++i+l  +p e+ +r+
  gi|119719361|ref|YP_919856.1|  77 VE--------CVPK-----RKVTHVIVLRLNPLELKKRL 102
                                    52........2332.....23466666666666555555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   2.3e-05      0.01       8      30 ..       3      25 ..       1      67 [. 0.79

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.3e-05
                         AAA_22  8 lvvtGesGtGKTtllrrlleqld 30
                                   +++tG +G+GKT +++ l+++l 
  gi|119719361|ref|YP_919856.1|  3 VLITGTPGVGKTSVAQSLASTLG 25
                                   68*****************9994 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   2.7e-05     0.011       2      28 ..       3      29 ..       2      37 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.7e-05
                          AAA_3  2 vllegvPGlaktllvkalakaldlefk 28
                                   vl++g+PG++kt ++++la++l+ ++ 
  gi|119719361|ref|YP_919856.1|  3 VLITGTPGVGKTSVAQSLASTLGKKYV 29
                                   89********************99885 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   2.3e-05    0.0098       1      26 [.       3      28 ..       3      78 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.3e-05
                   RNA_helicase  1 iwlyGpsgeGKStlakeLakallkkl 26
                                   ++++G +g+GK+++a++La++l kk+
  gi|119719361|ref|YP_919856.1|  3 VLITGTPGVGKTSVAQSLASTLGKKY 28
                                   6799******************9887 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   2.2e-05    0.0094       4      71 ..       5      73 ..       2     126 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.2e-05
                Cytidylate_kin2  4 IsreyGsgGetigeaLAekLglpfydr.eiieevakelglseeeveevdersrlssflskllaarvagd 71
                                   I+++ G g++ +++ LA  Lg +++d  ++ +e    +g+++e  + + ++s+++++l+++l ++   d
  gi|119719361|ref|YP_919856.1|  5 ITGTPGVGKTSVAQSLASTLGKKYVDVaKLAAENNLVKGFDPELQAYIVDTSSVRALLEEILTCNEVVD 73
                                   899***********************9344444444458888877666667888999999998865444 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   3.9e-05     0.017      36      61 ..       3      28 ..       2      94 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.9e-05
                         RuvB_N 36 vllyGpPGlGkttlakiiakelgvkl 61
                                   vl++G PG+Gkt++a+ +a+ lg k 
  gi|119719361|ref|YP_919856.1|  3 VLITGTPGVGKTSVAQSLASTLGKKY 28
                                   89******************999875 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.2   5.2e-05     0.022       5      79 ..       3     134 ..       1     152 [. 0.56

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.2e-05
                         AAA_24   5 iliyGpsgiGKTtlakel.........gpkplfi.......dtekGlksldadkfpdieswedfldevvel......... 59 
                                    +li+G +g+GKT++a +l               +       ++ kG++    + ++d +s+ ++l+e+ +          
  gi|119719361|ref|YP_919856.1|   3 VLITGTPGVGKTSVAQSLastlgkkyvD-----VaklaaenNLVKGFDPELQAYIVDTSSVRALLEEILTCnevvdthiv 77 
                                    89***************95554333220.....12222222222222222233333333455555544444555666666 PP

                         AAA_24  60 .....................................aaeladyktlviDtidelee 79 
                                                                         + e + ++++ iD + ++ e
  gi|119719361|ref|YP_919856.1|  78 ecvpkrkvthvivlrlnplelkkrleargypnrkiaaNVEAEVLDSVLIDAVKWFGE 134
                                    666666666666666666666666666666666666555555566666666666655 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   0.00033      0.14       3      31 ..       5      33 ..       3      42 .. 0.89
   2 ?   -1.5   0.0         4   1.7e+03     180     199 ..      42      59 ..      35      79 .. 0.63
   3 ?    0.7   0.0      0.86   3.7e+02     188     205 ..     137     154 ..     132     159 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00033
                                   EE-STTSSHHHHHHHHHHHHT-EEEEHHH CS
                 Cytidylate_kin  3 iDGPagsGKssvaralaeklglkyldtga 31
                                   i G  g GK sva+ la++lg ky+d ++
  gi|119719361|ref|YP_919856.1|  5 ITGTPGVGKTSVAQSLASTLGKKYVDVAK 33
                                   678899*******************9876 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 4
                                    S-S---TT-EEEETTTS-HH CS
                 Cytidylate_kin 180 gpLklaedaliidtskltie 199
                                    +++ +   a i+dts++  +
  gi|119719361|ref|YP_919856.1|  42 KGFDPELQAYIVDTSSV--R 59 
                                    56666677888888753..2 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.86
                                    -EEEETTTS-HHHHHHHH CS
                 Cytidylate_kin 188 aliidtskltieevveki 205
                                    ++ +dt+ +++ e+v+ +
  gi|119719361|ref|YP_919856.1| 137 VFEVDTTGKSVGEIVNIV 154
                                    789************865 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   9.1e-05     0.039      35      63 ..       2      30 ..       1      39 [. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.1e-05
                          AAA_7 35 pvllvGptGtGKtviikdllkkldkekyl 63
                                    vl++G+ G+GKt+++++l ++l k+ + 
  gi|119719361|ref|YP_919856.1|  2 AVLITGTPGVGKTSVAQSLASTLGKKYVD 30
                                   69********************9965554 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   8.9e-05     0.038       4      40 ..       2      38 ..       1      54 [. 0.87

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8.9e-05
                                   EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHH CS
                     APS_kinase  4 vvwltGlsgsGKstianalekkLvekgisvylLdGdn 40
                                    v++tG  g GK+++a+ l+++L +k + v  L  +n
  gi|119719361|ref|YP_919856.1|  2 AVLITGTPGVGKTSVAQSLASTLGKKYVDVAKLAAEN 38
                                   689***********************99999987664 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.1    0.0021      0.89       3      50 ..       5      56 ..       3      85 .. 0.66
   2 ?    4.3   0.0     0.077        33     118     156 ..      78     121 ..      55     147 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0021
                                   EEESTTSSHHHHHHHHHCCST..CEEEE-HHHHCCSSSS..HHHHHHHHSHH CS
                            dNK  3 veGnIgaGKstlvklLskklg..vkvfeEpvdkwtnvqk..nlLekfYkdps 50
                                   + G+ g+GK+++++ L+ +lg  ++ +  + ++++ v++  + L+ +  d s
  gi|119719361|ref|YP_919856.1|  5 ITGTPGVGKTSVAQSLASTLGkkYVDVAKLAAENNLVKGfdPELQAYIVDTS 56
                                   88999***************96655555666666444445555555554444 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.077
                                    HHCCH..-SEEEEEE--HHHHHHHHHHCTTCCCT...TS-HHHH CS
                            dNK 118 eelak..pdlliYLkasletclerikkRgreeek...kieldYl 156
                                    e ++k  + ++i L++++ ++++r++ Rg  + k   ++e + l
  gi|119719361|ref|YP_919856.1|  78 ECVPKrkVTHVIVLRLNPLELKKRLEARGYPNRKiaaNVEAEVL 121
                                    4444455889999***************9877665556666655 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.3   8.7e-05     0.037       4      64 ..       5      63 ..       2     130 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.7e-05
                                   EESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH...CCHCCCHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxx RF
                           CbiA  4 astkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep...dlkrllelle 64
                                   + ++ GvGKT++a +La  l +  + V + ++  + n+ +   g  ++++    d +++  lle
  gi|119719361|ref|YP_919856.1|  5 ITGTPGVGKTSVAQSLASTLGK--KYVDVAKLAAENNLVK---GFDPELQAyivDTSSVRALLE 63
                                   56788****************9..7788888888755543...555544445554444444444 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   0.00013     0.057      23      59 ..       2      36 ..       1      77 [. 0.78

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00013
                                   -EEEEEETT--HHHHHHCC--TTS-EE--SSTTHHHH CS
                Sigma54_activ_2 23 pvfltGekGsgkelvArlLhknsgpwleifvverlak 59
                                    v++tG +G gk++vA+ L++  g+  + ++v++la+
  gi|119719361|ref|YP_919856.1|  2 AVLITGTPGVGKTSVAQSLASTLGK--KYVDVAKLAA 36
                                   69*****************998877..5555555554 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0    0.0001     0.043      52      85 ..       2      36 ..       1     125 [. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.0001
                                   XXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXX CS
                          TIP49 52 avLlaGpsgtGktalaiaiskelged.vpfvalsg 85
                                   avL++G +g Gkt++a +++  lg++ v  ++l++
  gi|119719361|ref|YP_919856.1|  2 AVLITGTPGVGKTSVAQSLASTLGKKyVDVAKLAA 36
                                   79**********************65155555554 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00019     0.081       4      90 ..       2      83 ..       1     107 [. 0.64

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00019
                         AAA_14  4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqevpewe.kalk 84
                                   +++itG   vGKT +++ l+++l  k  ++  ++ +++  k   dp +l  +i +          +l Ei  ++e+  +++ 
  gi|119719361|ref|YP_919856.1|  2 AVLITGTPGVGKTSVAQSLASTLGKKYVDVAKLAAENNLVKG-FDP-ELQAYIVDT----SSVRALLEEILTCNEVVdTHIV 77
                                   689*****************9988333333333333333332.234.466777764....3455788888888875414455 PP

                         AAA_14 85 slvdeg 90
                                   ++v ++
  gi|119719361|ref|YP_919856.1| 78 ECVPKR 83
                                   555555 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00022     0.094       2      59 ..       4      53 ..       3      80 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00022
                Viral_helicase1  2 vvhGvpGcGKStlirkllrtsliltvnrptaelltegkpklpnlsvrtvdsflmalvk 59
                                   ++ G pG GK+++ ++l++t      +++ + +++ ++   +n+ v+++d  l+a + 
  gi|119719361|ref|YP_919856.1|  4 LITGTPGVGKTSVAQSLAST-----LGKKYVDVAKLAA---ENNLVKGFDPELQAYIV 53
                                   799***************99.....3444333333332...33334444444444433 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00016      0.07       4      39 ..       3      36 ..       1      84 [. 0.77

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00016
                        DUF2075  4 vlVtGvaGtGKtvvllnllaeleddeeertavylsv 39
                                   vl+tG +G GKt v+ +l+ +l   +++  ++ l  
  gi|119719361|ref|YP_919856.1|  3 VLITGTPGVGKTSVAQSLASTL--GKKYVDVAKLAA 36
                                   89*****************999..444443333333 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00061      0.26       4      32 ..       5      33 ..       2      49 .. 0.85
   2 ?   -0.4   0.0       1.9   7.9e+02      12      42 ..      55      90 ..      53     125 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00061
                            PRK  4 vagsSGaGkttvarklekifgrekvkaae 32
                                   ++g  G Gkt+va+ l + +g++ v  a+
  gi|119719361|ref|YP_919856.1|  5 ITGTPGVGKTSVAQSLASTLGKKYVDVAK 33
                                   8********************98887554 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.9
                            PRK 12 kttvarklekifgrekvkaaei.....egdsflrld 42
                                   +++v + le+i+  ++v  ++i     + ++ + ++
  gi|119719361|ref|YP_919856.1| 55 TSSVRALLEEILTCNEVVDTHIvecvpKRKVTHVIV 90
                                   567777777777666665555444444223333333 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0    0.0002     0.087       4      30 ..       3      29 ..       1      77 [. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0002
                                   EEEEESTTSSHHHHHHHHHHHHHHTTS CS
                    ArsA_ATPase  4 ilvgGKGGVGKttvsaatavklsekgk 30
                                   +l++G  GVGKt+v+ ++a  l +k  
  gi|119719361|ref|YP_919856.1|  3 VLITGTPGVGKTSVAQSLASTLGKKYV 29
                                   899****************99988755 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1    0.0003      0.13      18      49 ..       2      31 ..       1      50 [. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0003
                     Zeta_toxin 18 lillgGqpGAGKselaellkdelerqgnvvrl 49
                                   ++l+ G pG GK+++a+ l+  l  ++++v +
  gi|119719361|ref|YP_919856.1|  2 AVLITGTPGVGKTSVAQSLASTL--GKKYVDV 31
                                   79******************999..6666654 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.5   0.00077      0.33       8      36 ..       4      32 ..       1      37 [. 0.85
   2 ?   -1.4   0.0         3   1.3e+03      37      60 ..     137     160 ..     134     174 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00077
                           ParA  8 vlSgKGGVGKStvavnlAlaLakkglkvg 36
                                    + g  GVGK++va +lA +L kk ++v+
  gi|119719361|ref|YP_919856.1|  4 LITGTPGVGKTSVAQSLASTLGKKYVDVA 32
                                   567888***************99988886 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3
                           ParA  37 llDaDiyGpsiprllgveeekpeq 60 
                                    ++ +D +G s+ +++++ +   e 
  gi|119719361|ref|YP_919856.1| 137 VFEVDTTGKSVGEIVNIVRLVLEG 160
                                    678999999999999987654444 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00031      0.13      24      47 ..       2      25 ..       1      43 [. 0.74

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00031
                                   -EEEECSTTSSHHHHHHHHHHHST CS
                Sigma54_activat 24 svlitGesGtGKellaraiheask 47
                                    vlitG  G+GK+ +a+++ ++  
  gi|119719361|ref|YP_919856.1|  2 AVLITGTPGVGKTSVAQSLASTLG 25
                                   79***************9876544 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00037      0.16      25      48 ..       3      26 ..       1      50 [. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00037
                   Mg_chelatase 25 lllvGppGsGKtmlakrlpsllpp 48
                                   +l++G+pG GKt +a+ l+s l +
  gi|119719361|ref|YP_919856.1|  3 VLITGTPGVGKTSVAQSLASTLGK 26
                                   799***************998865 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00046       0.2      32      64 ..       3      35 ..       1      40 [. 0.88

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00046
                                   EEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEE CS
                           MeaB 32 vGltGvPGaGkstlvealglelrrrGkrvavla 64
                                   v +tG+PG+Gk  + + l+ +l ++   va la
  gi|119719361|ref|YP_919856.1|  3 VLITGTPGVGKTSVAQSLASTLGKKYVDVAKLA 35
                                   569*******************99999998887 PP

>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00045      0.19       2      36 ..       2      37 ..       1      55 [. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00045
                                   EEEEEESTTSSHHHHHHHHHH.TT-EEEEHHHHHHH CS
                           CoaE  2 ivgltGgiasGKstvanlfad.lgvpivDaDlvArq 36
                                    v +tG  + GK+ va+ +a+ lg + vD  ++A +
  gi|119719361|ref|YP_919856.1|  2 AVLITGTPGVGKTSVAQSLAStLGKKYVDVAKLAAE 37
                                   5779****************99*******9998875 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   0.00063      0.27       2      55 ..       3      57 ..       2     106 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00063
                                   EEEEESTTSSHHHHHHHHHTS.TEEESSSTTSSSSEEEEEEEETTEEEEEEECGG CS
                       MMR_HSR1  2 vaivGrpNvGKStLinaltge.kaivsdkpgtTrdinegrvklkgkeielvDtpG 55
                                   v+i G p vGK+++ ++l  +   +  d +    + n  +    + + ++vDt  
  gi|119719361|ref|YP_919856.1|  3 VLITGTPGVGKTSVAQSLASTlGKKYVDVAKLAAENNLVKGFDPELQAYIVDTSS 57
                                   89****************9764233333333333333333221224667777665 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00064      0.27      48      75 ..       3      30 ..       1      41 [. 0.91

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00064
                          Rad17 48 LLisGPsGCgkstvvkvLskelgiklre 75
                                   +Li+G +G gk+ v + L+  lg k+ +
  gi|119719361|ref|YP_919856.1|  3 VLITGTPGVGKTSVAQSLASTLGKKYVD 30
                                   69*********************99976 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0    0.0006      0.26      50      72 ..       3      25 ..       1      45 [. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0006
                      IstB_IS21 50 ivllGpsGvGKshlaialgveav 72
                                   ++++G +GvGK+ +a +l+    
  gi|119719361|ref|YP_919856.1|  3 VLITGTPGVGKTSVAQSLASTLG 25
                                   899*************9997655 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.4    0.0012      0.49      13      36 ..       3      26 ..       1      38 [. 0.81

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0012
                         AAA_19 13 llvtaGpGtGKTrvlkhivallve 36
                                   +l+t+ pG GKT v +   + l +
  gi|119719361|ref|YP_919856.1|  3 VLITGTPGVGKTSVAQSLASTLGK 26
                                   89***********99988777665 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.1   0.00095      0.41      36      56 ..       3      23 ..       1     133 [. 0.94

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00095
                         AAA_25 36 allaGapgtGKttlaldlala 56
                                   +l++G pg+GKt +a +la +
  gi|119719361|ref|YP_919856.1|  3 VLITGTPGVGKTSVAQSLAST 23
                                   789**************9975 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.4    0.0011      0.45       4      35 ..       3      34 ..       1      45 [. 0.85

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0011
                                   EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEE CS
                          SRP54  4 illvGlqGaGKTttlaKLaallkkegkkvllv 35
                                   +l+ G+ G+GKT+ +  La  l k+  +v+  
  gi|119719361|ref|YP_919856.1|  3 VLITGTPGVGKTSVAQSLASTLGKKYVDVAKL 34
                                   799******************99997776644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                       108  (0.00602376); expected 17.9 (0.001)
Passed Fwd filter:                        42  (0.00234257); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              42  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 1229.35
//
Query:       gi|119719362|ref|YP_919857.1|  [L=604]
Description: type II secretion system protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.4e-23   80.7   1.5    1.5e-13   50.8   0.0    3.3  3  T2SSF     Type II secretion system (T2SS), protein F


Domain annotation for each model (and alignments):
>> T2SSF  Type II secretion system (T2SS), protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   0.4   1.2e-13   2.2e-09       6     124 ..     126     251 ..     122     252 .. 0.91
   2 ?   -5.3   3.6         1   1.8e+04     109     123 ..     308     322 ..     306     327 .. 0.44
   3 !   50.8   0.0   8.5e-18   1.5e-13       1     124 [.     400     526 ..     400     527 .. 0.94

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 1.2e-13
                                    HHHHHTT--HHHHHHHHHHHHS..SHHHHHHHHHHHHHHHTTS.....SHHHHHCT-TT.TS-HHHHHHHHHHHHHT-HH CS
                          T2SSF   6 atllsaGvplveaLellaeeae..ngplaeelkriarrlraGg.....slsealertpssefpelvvqlirageeggnLa 78 
                                     ++  +G+++++++e+la+  +  ++++++e ++   +++  g     +++++ +r p++ +++l+  + ++ ++gg++ 
  gi|119719362|ref|YP_919857.1| 126 TVMATGGISPYTSFERLAKAPKvlFQEIKKEAMYFFLKVKGMGqdplsAIEDSAKRVPHNGYKQLMLGYAATLRAGGDVV 205
                                    678899**********************************988653333346666************************* PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXXXX CS
                          T2SSF  79 evLerlaeyleeerelrrkllaallepllllvvallvllillaill 124
                                    ++L+r  e + +er ++ k   ++++ l++ ++a+++l  + +++l
  gi|119719362|ref|YP_919857.1| 206 HYLQRQTEVMLRERVSQMKTIGERIGALMESYMAIVLLTSMTLYVL 251
                                    ***************************************9999886 PP

  == domain 2  score: -5.3 bits;  conditional E-value: 1
                                    XXXXXXXXXXXXXXX CS
                          T2SSF 109 lvvallvllillail 123
                                    +++al +++ +++++
  gi|119719362|ref|YP_919857.1| 308 VYLALGIPITIFLFV 322
                                    444444444444433 PP

  == domain 3  score: 50.8 bits;  conditional E-value: 8.5e-18
                                    HHHHHHHHHHTT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTSSHHHHHCT-TT....TS.-HHHHHHHHHHHHHT- CS
                          T2SSF   1 flrqlatllsaGvplveaLellaeeaengplaeelkriarrlraGgslsealertps...sef.pelvvqlirageeggn 76 
                                    flr l+   ++G+ +++ +  l + + +g++++ l++ia+++ +G sl++ +er+     ++f    +  l++++e gg 
  gi|119719362|ref|YP_919857.1| 400 FLRDLVEVRKTGMAPEKCIINLKDRD-YGKFTPYLRDIAKQVGWGVSLHTIFERFSKgmkNWFaLISMFLLVESIEVGGG 478
                                    8999**********************.**************************776655668877777889********* PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXXXX CS
                          T2SSF  77 LaevLerlaeyleeerelrrkllaallepllllvvallvllillaill 124
                                     +++Le+la+y e  ++ +++++aal   +l+ +v++l++ ++++il+
  gi|119719362|ref|YP_919857.1| 479 TPQTLEALASYAETLEQVEKEKRAALRPLMLMPYVGALIITVVVLILV 526
                                    *********************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (604 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       780  (0.0435049); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.25s 00:00:00.84 Elapsed: 00:00:00.42
# Mc/sec: 4334.20
//
Query:       gi|119719363|ref|YP_919858.1|  [L=428]
Description: beta-lactamase domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.9e-16   58.3   0.0    1.4e-15   57.5   0.0    1.4  1  Beta-Casp      Beta-Casp domain
    9.7e-14   51.1   0.0    1.7e-13   50.3   0.0    1.4  1  RMMBL          Zn-dependent metallo-hydrolase RNA specificity
    4.8e-11   43.0   0.2    1.4e-10   41.5   0.2    1.8  1  Lactamase_B    Metallo-beta-lactamase superfamily
    1.5e-07   31.0   0.0    2.8e-07   30.1   0.0    1.4  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain
    3.2e-07   30.1   0.0    7.1e-07   28.9   0.0    1.6  1  Lactamase_B_2  Beta-lactamase superfamily domain
    4.5e-06   26.7   0.0    1.4e-05   25.0   0.0    1.9  1  Lactamase_B_3  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Beta-Casp  Beta-Casp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.5   0.0   4.6e-19   1.4e-15       1     109 [.     235     344 ..     235     345 .. 0.84

  Alignments for each domain:
  == domain 1  score: 57.5 bits;  conditional E-value: 4.6e-19
                                    HHHHHHHH..HCTT..TTS-S-EEEEE-HHHHHHHHHGGGGGG...........E-SHH.....HHHH..HHHS-SSEEE CS
                      Beta-Casp   1 aqellylLeelwkekkledlklpiyldsplaskatevYkeyae...........veaks.lewmeskkeelnsskgpkvi 68 
                                    aqe+l++L ++  +       +piy+d+ +a+ a ++  e ++           ve ++ +++ +++k ++   ++p vi
  gi|119719363|ref|YP_919858.1| 235 AQEILCVLAKYDLQ-------VPIYVDG-MARTANDLIAEDSHllrepslfkkaVEMSTkVKDWDHRK-KI--LSKPGVI 303
                                    69999999999844.......6******.********666666*******988844444456666664.23..569**** PP

                                    EES-TTSSSSHHHHHHHHHTTSTTSEEEESS---TTSHHHH CS
                      Beta-Casp  69 lassgmlegGrsrellkklledprntvilvgyqaegTlgrk 109
                                    ++  gml+gG+s ++++k++e+++n+vi+v+y  ++T++r+
  gi|119719363|ref|YP_919858.1| 304 ISPAGMLQGGPSEYYMEKIMENEKNAVIFVSYVIPETPARQ 344
                                    ***************************************98 PP

>> RMMBL  Zn-dependent metallo-hydrolase RNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.3   0.0   5.8e-17   1.7e-13       3      62 .]     359     418 ..     357     418 .. 0.97

  Alignments for each domain:
  == domain 1  score: 50.3 bits;  conditional E-value: 5.8e-17
                          RMMBL   3 pvkarieeidfSgHadknellelirklkprn.vilvHGeeeatsalarllkeeegidvfiP 62 
                                    pvkarie++dfS+H +++el + + + k+   v+lvHGeeea+ +la+l   + g ++f+P
  gi|119719363|ref|YP_919858.1| 359 PVKARIEWFDFSAHCGHSELVKTLDSAKKGSkVVLVHGEEEAAVKLAELS-VKAGHETFVP 418
                                    8*****************************9*******************.****999998 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5   0.2   4.6e-14   1.4e-10       4     156 ..      19     173 ..      16     209 .. 0.90

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 4.6e-14
                                    CSSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCH CS
                    Lactamase_B   4 dpvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalf 83 
                                    ++ +++l+  +g++iL D G+s e +      + l ++pk ++av ++H+HlDH G+++ l    + p +  +++a    
  gi|119719363|ref|YP_919858.1|  19 VGRSAILLGVEGKLILLDYGVSIEGEEPQ---FPLPVPPKGIHAVAISHAHLDHSGAAPLLYVSGQPPLISTPLTATLSD 95 
                                    6678999999*************999998...79********************************************** PP

                                    CHHHHHHHHHCCHH....TTCHCGCCEEEEETTTEECCCTEEEEEHE.CTTSTSCCEEEEEETTCCEEEECTTTSSHH CS
                    Lactamase_B  84 meeaddaasrkgll....lagvsadkpdvdeeeldgnaggrralyvt.ggpghghghgvveygggkvlftGDallage 156
                                       +d+    k  +    ++ +    + v++  +++++ g ++  v   g+ +g+  +++e ++ +vl+tGD +l   
  gi|119719363|ref|YP_919858.1|  96 LLIKDFMKLSKYYIpyeaPEVEKMLESLVPLGYGESYDIGSVTIRVLdAGHIPGSAMIQIETPSLNVLYTGDYSLHDT 173
                                    ****8887777777**9988888888999999999999999999888569**********************998655 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.0   9.5e-11   2.8e-07       2     180 ..      26     186 ..      25     196 .. 0.84

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 9.5e-11
                  Lactamase_B_6   2 LeldnvkiLlDvGwdeskvslesalkelekviptvdliLLshatlehlGayallyakfksklllnipvyatlpvvkLGrv 81 
                                    L +++  iLlD G++ +    e+   +l    + + ++ +sha l+h Ga +lly++       + p  +t  ++ L  +
  gi|119719363|ref|YP_919858.1|  26 LGVEGKLILLDYGVSIEG---EEPQFPLPVPPKGIHAVAISHAHLDHSGAAPLLYVSG------QPPLISTPLTATLSDL 96 
                                    667777888888888542...333345555567899****************999875......567789999999**** PP

                  Lactamase_B_6  82 slldlyaskgllgpedseeleledideafdkiktlkYsQklelkskldgltitaynaGhtlGGtiWkiskesekivYavd 161
                                    ++ d ++ ++   p++       +++++ +++ +l Y  + ++ s    +ti  + aGh +G ++ +i++ s +++Y  d
  gi|119719363|ref|YP_919858.1|  97 LIKDFMKLSKYYIPYEA-----PEVEKMLESLVPLGYGESYDIGS----VTIRVLDAGHIPGSAMIQIETPSLNVLYTGD 167
                                    ******99999999975.....599***************99996....******************************* PP

                  Lactamase_B_6 162 wnhakeshLngaalldssg 180
                                    ++     +L+ga +++ s+
  gi|119719363|ref|YP_919858.1| 168 YSLHDTCLLRGAGISEFSK 186
                                    **99999999999887544 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0   2.4e-10   7.1e-07       3     174 ..      33     204 ..      31     232 .. 0.73

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 2.4e-10
                                    EEES--TTHHHHHTCGG.S--SSS--..SEEEEE-SS--HHHHGGGGCCCC..C--EEEEEEEEHHHHHHCCTTCGHHHC CS
                  Lactamase_B_2   3 iLiDagpdlrqqalral.qPvelrdelppidaVllthaHyDHlaglltlre..lrpkklplyapkgvlavleanfvylal 79 
                                    iL+D g ++ +  +++   Pv+    ++ i+aV ++haH DH  g+  l    ++p   pl+ +  + a+l++ ++ +++
  gi|119719363|ref|YP_919858.1|  33 ILLDYGVSIEGE-EPQFpLPVP----PKGIHAVAISHAHLDHS-GAAPLLYvsGQP---PLIST-PLTATLSDLLIKDFM 102
                                    788888888777.667634444....568**************.666666635554...55533.333334444443333 PP

                                    HTT.............TTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S-- CS
                  Lactamase_B_2  80 eee.............pavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyi 146
                                    +                 +++++l  ges ++g   ++i++  a h  g          +   ie++  +v+y+gD    
  gi|119719363|ref|YP_919858.1| 103 KLSkyyipyeapevekMLESLVPLGYGESYDIG--SVTIRVLDAGHIPGS---------AMIQIETPSLNVLYTGDYSLH 171
                                    33334444444444699999************9..567888888887777.........888899************988 PP

                                    -.....HHHHHHHCT-SEEEEE-S-SSTTHHHH CS
                  Lactamase_B_2 147 p.....eeigerlggadllllditayeddemir 174
                                    +     ++   ++ +ad+++++ t+ e d + r
  gi|119719363|ref|YP_919858.1| 172 DtcllrGAGISEFSKADVVIMESTYAEYDHPPR 204
                                    8666654444799***********999887665 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   4.7e-09   1.4e-05       6      83 ..      20     103 ..      18     194 .. 0.67

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 4.7e-09
                  Lactamase_B_3   6 ghnsflletagarilvDPf......kanlgyeppaeeaDlvlisqaledHahletlkqlaenvkvleegeslevggleir 79 
                                    g +++ll ++g+ il+D++      +++  +  p++ + +v is+a+ dH  +++l  +  ++++++++ ++++ +l i+
  gi|119719363|ref|YP_919858.1|  20 GRSAILLGVEGKLILLDYGvsiegeEPQFPLPVPPKGIHAVAISHAHLDHSGAAPLLYVSGQPPLISTPLTATLSDLLIK 99 
                                    8899***************8888754488889999************************999999999666666666555 PP

                  Lactamase_B_3  80 avat 83 
                                     +  
  gi|119719363|ref|YP_919858.1| 100 DFMK 103
                                    4433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.67u 0.37s 00:00:01.04 Elapsed: 00:00:00.56
# Mc/sec: 2297.09
//
Query:       gi|119719364|ref|YP_919859.1|  [L=171]
Description: heat shock protein Hsp20 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.6e-14   53.2   2.1    1.2e-12   47.9   2.1    2.2  1  HSP20       Hsp20/alpha crystallin family
    6.5e-09   35.2   0.0    1.7e-08   33.9   0.0    1.7  1  ArsA_HSP20  HSP20-like domain found in ArsA
     0.0044   17.4   0.0     0.0071   16.7   0.0    1.2  1  PIH1_CS     PIH1 CS-like domain
  ------ inclusion threshold ------
      0.019   16.0   0.5      0.033   15.2   0.5    1.5  1  CS          CS domain
      0.065   12.6   0.3      0.065   12.6   0.3    1.8  2  DPCD        DPCD protein family


Domain annotation for each model (and alignments):
>> HSP20  Hsp20/alpha crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.9   2.1   3.3e-16   1.2e-12       2     101 ..      86     168 ..      85     171 .] 0.91

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 3.3e-16
                                    --SSEEEEEEEEE-TT--CCCEEEEEETTEEEEEEE--..---TT----SS---EEEEEE--STTB-TTT-EEEEETTEE CS
                          HSP20   2 ikeeeeefevkldvpglkkeelkvkvednrvlvkgeheeeeedekglikerssrkFsrkftLPenvdadkvkaslkdGvL 81 
                                    + +e ++++v ld+pg++k+e++v+ ++n+++v+ + e               rk+ ++++  + vd+++ ka++k+GvL
  gi|119719364|ref|YP_919859.1|  86 VFDEGDHYRVILDIPGVEKDEINVEATENSLVVSTTGE---------------RKYYKEVRFSDPVDPSTAKAQYKNGVL 150
                                    67899*****************************9999...............7788999999***************** PP

                                    EEEEEBSS--..-------- CS
                          HSP20  82 tvtvpkkepekkkkerkiqi 101
                                    tvt++kke++k  ker ++i
  gi|119719364|ref|YP_919859.1| 151 TVTIEKKEKPK--KERGVKI 168
                                    ********995..6777766 PP

>> ArsA_HSP20  HSP20-like domain found in ArsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.0   4.6e-12   1.7e-08       1      62 [.      90     153 ..      90     154 .. 0.90

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 4.6e-12
                     ArsA_HSP20   1 ddeyvlkldLPfvdkeeidlsrsgdeLtIkig...nfrRqitLPsvlarkevtsAkfedgvLeIr 62 
                                    +d+y++ ld+P+v+k+ei+++ +++ L+++     ++ +++   + ++  ++ +A++++gvL+++
  gi|119719364|ref|YP_919859.1|  90 GDHYRVILDIPGVEKDEINVEATENSLVVSTTgerKYYKEVRFSDPVDPSTA-KAQYKNGVLTVT 153
                                    69*****************************944455566**********66.**********97 PP

>> PIH1_CS  PIH1 CS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0     2e-06    0.0071      32      87 ..      92     147 ..      89     155 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2e-06
                        PIH1_CS  32 elaieielPllksikevklrvgerrleleskk.akyfLslkLpYpvdedkveAkFvk 87 
                                    ++++ +++P++ +  e++++ +e++l++ + +  ky  ++++  pvd + ++A++++
  gi|119719364|ref|YP_919859.1|  92 HYRVILDIPGV-EKDEINVEATENSLVVSTTGeRKYYKEVRFSDPVDPSTAKAQYKN 147
                                    688999*****.789*************998899*********************75 PP

>> CS  CS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.5   9.1e-06     0.033      18      76 .]      99     156 ..      91     170 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 9.1e-06
                                    -TTCTTTTTCEEEEEETTEEEEEE.TSCEEEEECEBSS-BETTTEEEEEETTEEEEEEEB CS
                             CS  18 vkkvnikkkdvkvefkerslkvki.gkeklliegeLfgpIdpeesswtieskkveitLkK 76 
                                    +++v  +k++++ve +e+sl v+  g++k ++e  + +p+dp+ ++   ++  + +t++K
  gi|119719364|ref|YP_919859.1|  99 IPGV--EKDEINVEATENSLVVSTtGERKYYKEVRFSDPVDPSTAKAQYKNGVLTVTIEK 156
                                    5555..99****************87778888888****************999999998 PP

>> DPCD  DPCD protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1      0.22   8.1e+02      26      43 ..      10      27 ..       5      42 .. 0.77
   2 ?   12.6   0.3   1.8e-05     0.065     112     165 ..     106     154 ..      93     167 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.22
                           DPCD 26 edgkemvEEYdvktdell 43
                                   +  ++m+EE+d   +e++
  gi|119719364|ref|YP_919859.1| 10 KRIRKMMEEFDKMFEEMM 27
                                   555778888887666655 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 1.8e-05
                           DPCD 112 svtvdeeereivvrTt.NkKYyKklsipdldrlklkleqealsfahanntLiisY 165
                                    +++v+++e+++vv Tt  +KYyK+++  d      +++ ++ + +++n  L ++ 
  gi|119719364|ref|YP_919859.1| 106 EINVEATENSLVVSTTgERKYYKEVRFSD------PVDPSTAKAQYKNGVLTVTI 154
                                    79999********988479*****98776......44555555555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 966.70
//
Query:       gi|119719365|ref|YP_919860.1|  [L=106]
Description: ribosomal protein S24e [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.8e-24   84.1   0.0    6.6e-24   83.7   0.0    1.2  1  Ribosomal_S24e  Ribosomal protein S24e


Domain annotation for each model (and alignments):
>> Ribosomal_S24e  Ribosomal protein S24e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.7   0.0   3.7e-28   6.6e-24       2      78 ..      24     100 ..      23     101 .. 0.98

  Alignments for each domain:
  == domain 1  score: 83.7 bits;  conditional E-value: 3.7e-28
                                    EEEE-SSS-S--HHHHHHHHHHHHTS-CTTEEEEEEEE-SSSSEEEEEEEEES-HHHHHHHS-HHHHHHTTSS---S CS
                 Ribosomal_S24e   2 vdvlHpgkatpskteireklakmykvdpdlvvvfgfrthfGggkttGfakiYdsleaakkfEpkhrlaRnglaekkk 78 
                                    v++ H+g++tps+ +++e l +m+ +    +vv+++ t++G+g +++ ++iYds  ++k fEpkh+l+Rngl ++++
  gi|119719365|ref|YP_919860.1|  24 VEIHHQGSGTPSRRDVAEALRNMLGTGGSAIVVRKLVTRYGQGVSEALIHIYDSDVKMKMFEPKHILRRNGLIQEQE 100
                                    79***********************************************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 827.00
//
Query:       gi|119719366|ref|YP_919861.1|  [L=53]
Description: ribosomal protein S27a [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.3e-14   52.4   3.3    5.1e-14   52.2   3.3    1.1  1  Ribosomal_S27    Ribosomal protein S27a
    4.7e-05   23.3   3.2    6.1e-05   22.9   3.2    1.2  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
    0.00014   21.7   0.8    0.00015   21.6   0.8    1.1  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
     0.0093   15.9   3.7      0.018   14.9   3.7    1.5  1  Zn_ribbon_SprT   SprT-like zinc ribbon domain
     0.0096   16.0   0.1     0.0099   16.0   0.1    1.1  1  zf-piccolo       Piccolo Zn-finger
     0.0097   15.8   4.9       0.03   14.2   4.9    1.8  1  Nudix_N_2        Nudix N-terminal
  ------ inclusion threshold ------
      0.013   15.5   2.6      0.039   13.9   0.2    2.2  2  YhfH             YhfH-like protein
      0.016   15.1   0.3      0.036   13.9   0.3    1.6  1  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
      0.025   14.7   1.4      0.032   14.3   1.4    1.2  1  Ribosomal_L37ae  Ribosomal L37ae protein family
      0.026   14.9   1.4      0.037   14.4   1.4    1.3  1  Lar_restr_allev  Restriction alleviation protein Lar
      0.028   14.6   3.9       0.04   14.1   3.9    1.4  1  Ribosomal_L37e   Ribosomal protein L37e
        0.1   12.8   1.0       0.14   12.4   1.0    1.2  1  DUF2387          Probable metal-binding protein (DUF2387)
       0.12   12.0   2.5       0.35   10.5   0.1    2.1  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
       0.13   12.4   3.5       0.37   10.9   0.2    2.2  2  UPF0547          Uncharacterised protein family UPF0547
       0.14   12.1   3.3        1.8    8.5   0.6    2.1  2  HalOD2           Halobacterial output domain 2
       0.14   11.5   3.7        0.9    8.9   0.4    2.1  2  zf-RanBP         Zn-finger in Ran binding protein and others
       0.17   11.7   0.0       0.21   11.5   0.0    1.2  1  VWA_3_C          von Willebrand factor type A C-terminal doma
       0.21   11.1   7.0       0.26   10.8   0.4    2.2  2  zf-ribbon_3      zinc-ribbon domain
       0.22   11.3   6.1       0.67    9.8   0.1    2.2  2  zinc_ribbon_2    zinc-ribbon domain
       0.96    9.0   4.8        5.5    6.6   0.1    2.1  2  zn-ribbon_14     Zinc-ribbon
        1.6    8.2   7.3       0.12   11.9   1.0    2.0  2  Mu-like_Com      Mu-like prophage protein Com
          2    8.0   7.3        4.9    6.7   2.0    2.8  2  TF_Zn_Ribbon     TFIIB zinc-binding
        2.9    7.7   9.4        2.7    7.8   1.2    2.2  2  Rubredoxin_2     Rubredoxin metal binding domain


Domain annotation for each model (and alignments):
>> Ribosomal_S27  Ribosomal protein S27a
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.2   3.3   6.6e-17   5.1e-14       1      45 []       4      49 ..       4      49 .. 0.95

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 6.6e-17
                                   SSSSCCESS.SSSEEESS-B-SS-S-TTSBEEECTT...EEEESSTTTE CS
                  Ribosomal_S27  1 vlkyYkvdd.sgkverlrkeCpreCGaGvfMAehkd...RkyCGkCglT 45
                                   v+++Y++d+ +g++  ++k+Cpr C  G +MA+h     R++CGkCg+T
  gi|119719366|ref|YP_919861.1|  4 VHELYEYDYkTGTIRLKNKKCPR-C--GSIMAHHLKpveRWHCGKCGYT 49
                                   799********************.*..*******97777*********9 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   3.2   7.8e-08   6.1e-05      13      46 .]      17      49 ..      15      49 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 7.8e-08
                  Zn_Tnp_IS1595 13 lrWpngfvCPhCgsrkayriktrglfqCkeCrkq 46
                                   +r +n+  CP+Cgs  a+ +k  ++++C +C+++
  gi|119719366|ref|YP_919861.1| 17 IRLKNKK-CPRCGSIMAHHLKPVERWHCGKCGYT 49
                                   5667776.***********************985 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.8   1.9e-07   0.00015      29      56 ..      22      50 ..       3      52 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.9e-07
                 OrfB_Zn_ribbon 29 ktCseCgsknke.alsgrtfkCpnCgfea 56
                                   k+C++Cgs++ +  +  ++++C +Cg++ 
  gi|119719366|ref|YP_919861.1| 22 KKCPRCGSIMAHhLKPVERWHCGKCGYTE 50
                                   89**********88899*********985 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   3.7   2.4e-05     0.018       6      31 ..      23      47 ..      23      52 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.4e-05
                 Zn_ribbon_SprT  6 rCtgCgreythhlsi.rrhnYrCrrCk 31
                                   +C++Cg+   hhl+   r  ++C++C+
  gi|119719366|ref|YP_919861.1| 23 KCPRCGSIMAHHLKPvER--WHCGKCG 47
                                   6**************999..******8 PP

>> zf-piccolo  Piccolo Zn-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   1.3e-05    0.0099      25      53 ..      18      46 ..       2      51 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.3e-05
                     zf-piccolo 25 eCkkqvCnlCGFnptphltekkeWlclnC 53
                                     k++ C  CG  +  hl+ ++ W c +C
  gi|119719366|ref|YP_919861.1| 18 RLKNKKCPRCGSIMAHHLKPVERWHCGKC 46
                                   568899*****888888888********9 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   4.9   3.9e-05      0.03       3      33 ..      24      51 ..      22      52 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.9e-05
                                   -TTT--B-EEE--TT-SS-EEEETTTTEEE- CS
                      Nudix_N_2  3 CsqCGtpvelripdgDnreRlvCpaCgtihY 33
                                   C+ CG+ +++++      eR  C +Cg++ Y
  gi|119719366|ref|YP_919861.1| 24 CPRCGSIMAHHLK---PVERWHCGKCGYTEY 51
                                   *********9996...689***********9 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2     5e-05     0.039      10      23 ..      18      31 ..      16      35 .. 0.87
   2 ?    1.6   0.2      0.37   2.9e+02      15      20 ..      42      47 ..      37      49 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5e-05
                           YhfH 10 nLPkKkCteCGkei 23
                                   +L +KkC+ CG+ +
  gi|119719366|ref|YP_919861.1| 18 RLKNKKCPRCGSIM 31
                                   6899*******988 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.37
                           YhfH 15 kCteCG 20
                                    C +CG
  gi|119719366|ref|YP_919861.1| 42 HCGKCG 47
                                   588888 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.3   4.6e-05     0.036       4      31 ..      24      50 ..      22      51 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.6e-05
                                   ESTTTSBEEEEECSCCCEEEESSSS-EE CS
                 RNA_POL_M_15KD  4 CpkCgNlLlpkedkegknfeCrqCgYee 31
                                   Cp Cg+ +    +    +  C +CgY e
  gi|119719366|ref|YP_919861.1| 24 CPRCGSIMAHHLKPVE-RWHCGKCGYTE 50
                                   ********76654333.245******76 PP

>> Ribosomal_L37ae  Ribosomal L37ae protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   1.4   4.1e-05     0.032      32      60 ..      20      49 ..      11      50 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.1e-05
                                   S-BEESSSSSS.EEEEEETTEEEETTTTEE CS
                Ribosomal_L37ae 32 akytCpfcgkt.kvkRkavgiwkCkkcgkt 60
                                   ++ +Cp+cg+  + + k v+ w+C+kcg+t
  gi|119719366|ref|YP_919861.1| 20 KNKKCPRCGSImAHHLKPVERWHCGKCGYT 49
                                   4568*****986778899**********97 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   1.4   4.8e-05     0.037       3      36 ..      21      48 ..      19      53 .] 0.77

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.8e-05
                Lar_restr_allev  3 LkpCPfCggravlersqrvvaeigqcvyCadCga 36
                                    k CP Cg+   ++  +          +C +Cg+
  gi|119719366|ref|YP_919861.1| 21 NKKCPRCGSIMAHHLKPVE------RWHCGKCGY 48
                                   599*****98777777555......569*****9 PP

>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   3.9   5.2e-05      0.04      18      43 ..      23      52 ..      13      53 .] 0.76

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.2e-05
                 Ribosomal_L37e 18 lCrrCgkr.syh...vqkktCascGypsak 43
                                   +C rCg+  + h   v++ +C++cGy + +
  gi|119719366|ref|YP_919861.1| 23 KCPRCGSImAHHlkpVERWHCGKCGYTEYR 52
                                   7*****96266633345799******8776 PP

>> DUF2387  Probable metal-binding protein (DUF2387)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   1.0   0.00018      0.14      11      42 ..      24      52 ..      21      53 .] 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00018
                        DUF2387 11 CPrCsemDkirmweedeveyrECvsCgftdel 42
                                   CPrC    +i++++  +ve   C +Cg+t+ +
  gi|119719366|ref|YP_919861.1| 24 CPRCG---SIMAHHLKPVERWHCGKCGYTEYR 52
                                   99998...59*******************975 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00045      0.35       3      17 ..      22      36 ..      20      37 .. 0.81
   2 ?    1.7   0.3      0.25     2e+02       3       9 ..      41      47 ..      39      49 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00045
                         zf_UBZ  3 ylCerCgkeipesel 17
                                     C+rCg+ + ++ +
  gi|119719366|ref|YP_919861.1| 22 KKCPRCGSIMAHHLK 36
                                   68******9998865 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.25
                         zf_UBZ  3 ylCerCg 9 
                                   + C +Cg
  gi|119719366|ref|YP_919861.1| 41 WHCGKCG 47
                                   7799998 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.2   0.00048      0.37       1      11 [.      22      32 ..      22      36 .. 0.84
   2 ?    2.6   0.4      0.19   1.5e+02      17      22 ..      43      48 ..      37      49 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00048
                        UPF0547  1 KvCPeCeakvP 11
                                   K+CP+C ++ +
  gi|119719366|ref|YP_919861.1| 22 KKCPRCGSIMA 32
                                   99****98765 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.19
                        UPF0547 17 CphCGy 22
                                   C  CGy
  gi|119719366|ref|YP_919861.1| 43 CGKCGY 48
                                   888999 PP

>> HalOD2  Halobacterial output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1     0.047        37      33      41 ..      23      31 ..      20      34 .. 0.77
   2 ?    8.5   0.6    0.0024       1.8      32      40 ..      41      49 ..      38      52 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.047
                         HalOD2 33 kCtrCGevq 41
                                   kC rCG ++
  gi|119719366|ref|YP_919861.1| 23 KCPRCGSIM 31
                                   788888875 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0024
                         HalOD2 32 WkCtrCGev 40
                                   W+C++CG +
  gi|119719366|ref|YP_919861.1| 41 WHCGKCGYT 49
                                   *******87 PP

>> zf-RanBP  Zn-finger in Ran binding protein and others
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.2     0.042        33      17      26 ..      20      29 ..      18      29 .. 0.77
   2 ?    8.9   0.4    0.0012       0.9       2      12 ..      38      48 ..      37      49 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.042
                                   SSSB-TTT-- CS
                       zf-RanBP 17 wstkCvaCqa 26
                                   ++ kC +C++
  gi|119719366|ref|YP_919861.1| 20 KNKKCPRCGS 29
                                   6789999986 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0012
                                   SSSEE-SSS-- CS
                       zf-RanBP  2 egdWdCskClv 12
                                    ++W+C kC++
  gi|119719366|ref|YP_919861.1| 38 VERWHCGKCGY 48
                                   579******96 PP

>> VWA_3_C  von Willebrand factor type A C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00027      0.21      23      34 ..      11      22 ..       1      23 [. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00027
                                   -TTT--EEE-SS CS
                        VWA_3_C 23 DpatGTVRLkkk 34
                                   D  tGT+RLk+k
  gi|119719366|ref|YP_919861.1| 11 DYKTGTIRLKNK 22
                                   899*******86 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.4   0.00033      0.26       3      11 ..      22      30 ..      20      32 .. 0.82
   2 ?    3.7   1.4     0.057        44      18      24 ..      42      48 ..      41      49 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00033
                    zf-ribbon_3  3 vrCPnCGap 11
                                   ++CP+CG++
  gi|119719366|ref|YP_919861.1| 22 KKCPRCGSI 30
                                   79*****85 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.057
                    zf-ribbon_3 18 vCpyCGt 24
                                   +C +CG+
  gi|119719366|ref|YP_919861.1| 42 HCGKCGY 48
                                   6999997 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00086      0.67      13      20 ..      21      28 ..      16      30 .. 0.68
   2 ?    3.2   2.4     0.097        76      16      21 ..      43      48 ..      42      49 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00086
                  zinc_ribbon_2 13 akFCpyCG 20
                                   +k Cp+CG
  gi|119719366|ref|YP_919861.1| 21 NKKCPRCG 28
                                   56677777 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.097
                  zinc_ribbon_2 16 CpyCGt 21
                                   C +CG+
  gi|119719366|ref|YP_919861.1| 43 CGKCGY 48
                                   666665 PP

>> zn-ribbon_14  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1     0.007       5.5       2       9 ..      23      30 ..      22      35 .. 0.85
   2 ?    3.9   1.5     0.047        37       3       8 ..      43      48 ..      42      49 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.007
                   zn-ribbon_14  2 kCerCGyl 9 
                                   kC rCG +
  gi|119719366|ref|YP_919861.1| 23 KCPRCGSI 30
                                   8*****97 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.047
                   zn-ribbon_14  3 CerCGy 8 
                                   C +CGy
  gi|119719366|ref|YP_919861.1| 43 CGKCGY 48
                                   *****9 PP

>> Mu-like_Com  Mu-like prophage protein Com
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   1.0   0.00015      0.12      26      36 ..      23      35 ..      12      39 .. 0.73
   2 ?    0.1   0.8      0.69   5.4e+02       6      10 ..      42      46 ..      35      49 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00015
                    Mu-like_Com 26 KCPRCGtL..nHl 36
                                   KCPRCG +   Hl
  gi|119719366|ref|YP_919861.1| 23 KCPRCGSImaHHL 35
                                   9*****8633455 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.69
                    Mu-like_Com  6 RCGeC 10
                                    CG+C
  gi|119719366|ref|YP_919861.1| 42 HCGKC 46
                                   47777 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   2.0    0.0063       4.9       2      27 ..      23      29 ..       3      34 .. 0.64
   2 ?    2.4   0.3      0.15   1.2e+02      22      27 ..      43      48 ..      41      50 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0063
                                   EETTTTCEECHEETSTTCEEESSSSB CS
                   TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGl 27
                                   k                   C++CG+
  gi|119719366|ref|YP_919861.1| 23 K-------------------CPRCGS 29
                                   4...................555555 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.15
                                   ESSSSB CS
                   TF_Zn_Ribbon 22 CtdCGl 27
                                   C++CG+
  gi|119719366|ref|YP_919861.1| 43 CGKCGY 48
                                   9***96 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   1.6     0.036        28      16      22 ..      23      29 ..      23      29 .. 0.89
   2 ?    7.8   1.2    0.0034       2.7       1      11 [.      41      51 ..      41      53 .] 0.81

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.036
                   Rubredoxin_2 16 rCpsCgs 22
                                   +Cp Cgs
  gi|119719366|ref|YP_919861.1| 23 KCPRCGS 29
                                   7****97 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0034
                   Rubredoxin_2  1 YvCsqCGfesa 11
                                   ++C +CG++  
  gi|119719366|ref|YP_919861.1| 41 WHCGKCGYTEY 51
                                   78999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 394.69
//
Query:       gi|119719367|ref|YP_919862.1|  [L=465]
Description: hypothetical protein Tpen_0450 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (465 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       759  (0.0423336); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.61u 0.26s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 3032.65
//
Query:       gi|119719368|ref|YP_919863.1|  [L=458]
Description: hypothetical protein Tpen_0451 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (458 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 3537.99
//
Query:       gi|119719369|ref|YP_919864.1|  [L=336]
Description: putative DNA-binding/iron metalloprotein/AP endonuclease [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.1e-80  268.8   0.0    7.2e-80  268.6   0.0    1.0  1  Peptidase_M22  Glycoprotease family
     0.0072   15.9   0.0      0.082   12.4   0.0    2.0  2  BcrAD_BadFG    BadF/BadG/BcrA/BcrD ATPase family
  ------ inclusion threshold ------
      0.058   13.1   0.1       0.13   12.0   0.1    1.6  1  DUF348         G5-linked-Ubiquitin-like domain


Domain annotation for each model (and alignments):
>> Peptidase_M22  Glycoprotease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  268.6   0.0   1.2e-83   7.2e-80       8     271 .]      34     301 ..      30     301 .. 0.96

  Alignments for each domain:
  == domain 1  score: 268.6 bits;  conditional E-value: 1.2e-83
                                    EEEEEE....SSSSHHHHHHHHHHHHHHHHHHHHHHHTSTGGGEEEEEEEEESS-HHHHHHHHHHHHHHHHHCT--EEEE CS
                  Peptidase_M22   8 asqkelhakyGGvvPelasraHserllplieealaeaglsledldaIavtkgPGlftgLrvGvsfAkglalalnkPlvgV 87 
                                    + +++++++ GG+ P++a+++Hs+  ++++ eal++ag+s+e++da+av+ gPG++++LrvG++ A+ lal+++kPlv+V
  gi|119719369|ref|YP_919864.1|  34 NVNHTYVPRHGGIKPTEAAEHHSRVAPKVLSEALQKAGISVEEVDAVAVALGPGMGPCLRVGATLARYLALKFGKPLVPV 113
                                    34455679************************************************************************ PP

                                    EHHHHHHHCCHCTSECSSCEEEEESSSTEEEEEECTTEEEEEEEESSSEHHHHHHHHHHHHT..SSCCHHHHHHHCTC.S CS
                  Peptidase_M22  88 nhleahalaarleekeefPvvllvsGghtqvylvkegryeilgetlddaagealdkvarllglpypggpkieklakeg.k 166
                                    nh +ah++  rl+++ e+Pv ++v Gg+t+v + +egry+++getld+ +g++ld +ar +gl++pg p +e+la +g +
  gi|119719369|ref|YP_919864.1| 114 NHAIAHLEISRLTTGLEDPVFVYVAGGNTMVTTFNEGRYRVFGETLDIPLGNCLDTFAREVGLGFPGVPRVEELALKGrE 193
                                    *************999******************99******************************************89 PP

                                    .......EETTEEE.CHHHHHHHHHHST.T..HHHHHHHHHHHHHHHHHHHHHHHHHHCTBSEEEEESGGGGXHHHHHCH CS
                  Peptidase_M22 167 kiefprplkgldfsfsGlktavlkelek.e..vedlaasfqeavvdhlvekteralklpkakelvilGGvaankrLreal 243
                                    +i +p+++kg+d+s+sGl t +l++ ++ +   ed+++s+ e++ ++lve++eral+++++++lv+ GGva  + L e+l
  gi|119719369|ref|YP_919864.1| 194 YIPLPYTVKGQDVSYSGLLTHALSLYRSgRarLEDVCYSLVETAYSMLVEVAERALAHTGKSQLVLTGGVARSRILLEKL 273
                                    9*************************665368************************************************ PP

                                    CCHHHHTTSEEEXXXHHHHSSXCHHHHH CS
                  Peptidase_M22 244 eeeaeelglkliiPplkyctdnaamiaw 271
                                    + + e++g  l + p++y  dn+amia+
  gi|119719369|ref|YP_919864.1| 274 RRMVEDRGGVLGVVPPEYAGDNGAMIAY 301
                                    ***9999988888888**********97 PP

>> BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.029   1.7e+02      38      68 ..      53      83 ..      20     167 .. 0.79
   2 !   12.4   0.0   1.4e-05     0.082     203     264 ..     238     298 ..     210     300 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.029
                                   ........HHHHHHHHHHT--GGGECEE..E CS
                    BcrAD_BadFG 38 eaaekvleealtealerageeeadieetylv 68
                                   e   +v  ++l+eal++ag + ++++ +++ 
  gi|119719369|ref|YP_919864.1| 53 EHHSRVAPKVLSEALQKAGISVEEVDAVAVA 83
                                   4556788899999999999999998776543 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 1.4e-05
                                    HHHHHHHHHTT---SS...EEEESGGGG-HHHHHHH.....HHHH-S-EE--GGGGGHHHHHHH CS
                    BcrAD_BadFG 203 alrvialisrsggvtde..vtltGGvakneaavkelrklvkenygevkininpdsiytgalGAa 264
                                     + + ++++r  + t +  ++ltGGva++  ++++lr +v+ + g       ++++y+g  GA+
  gi|119719369|ref|YP_919864.1| 238 YSMLVEVAERALAHTGKsqLVLTGGVARSRILLEKLRRMVEDRGGVL---GVVPPEYAGDNGAM 298
                                    44455555555444444459********************9988775...56788888888886 PP

>> DUF348  G5-linked-Ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   2.2e-05      0.13      21      40 ..      65      84 ..      58      85 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.2e-05
                                   HHHHHTT----TT-EEES-T CS
                         DUF348 21 dlLeeagitlgeqDkVsPsL 40
                                   ++L++agi+++e+D V ++L
  gi|119719369|ref|YP_919864.1| 65 EALQKAGISVEEVDAVAVAL 84
                                   8****************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2342.68
//
Query:       gi|119719370|ref|YP_919865.1|  [L=241]
Description: Mn2+-dependent serine/threonine protein kinase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.5e-11   42.3   0.0    7.5e-11   41.9   0.0    1.2  1  Pkinase      Protein kinase domain
    1.1e-08   34.8   0.0    1.8e-08   34.2   0.0    1.2  1  RIO1         RIO1 family
    3.3e-08   33.8   0.2     0.0018   18.3   0.0    2.2  2  APH          Phosphotransferase enzyme family
      3e-05   23.5   0.0    0.00041   19.8   0.0    2.1  1  Kdo          Lipopolysaccharide kinase (Kdo/WaaP) family
    0.00011   21.6   0.0    0.00014   21.2   0.0    1.1  1  Pkinase_Tyr  Protein tyrosine kinase


Domain annotation for each model (and alignments):
>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9   0.0   2.1e-14   7.5e-11       3     151 ..      20     169 ..      18     186 .. 0.82

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 2.1e-14
                                    EEEEEEEESSEEEEEEEETTTTEEEEEEE.EECHCHCHHHH.....HHHHHHHHHHHHHSCTTB--EEEEEEESSEEEEE CS
                        Pkinase   3 kleklGeGsfGkVykaveketgkivAvKk.ikkekakkkke.....kkvlrEikilkklkhpnivrlyevfeekdelylv 76 
                                     +  lG G+ ++++k+     g++v+vK  + k+ ++ + +     ++++ E +il +     +   + v+  ++e +lv
  gi|119719370|ref|YP_919865.1|  20 AEGVLGFGAEAVIVKGE--LAGEKVVVKYrVPKSYRDPRLDselrrERTVLESRILSRAAMAGVNVPVPVLVYPEEGILV 97 
                                    56789********9999..789999999626666666666633444455555555556666666666777777******* PP

                                    EE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEESSSS CS
                        Pkinase  77 leyveggeladllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFGlakeless 151
                                    + y+ g+ l+d ++    +++ ++++++ +i + l  lHs gi++ Dl ++N++++ ++   ++DFGl    +++
  gi|119719370|ref|YP_919865.1|  98 MTYIGGERLKDSMR---GIEPGTLRNVFVEIGRQLGTLHSLGIVYGDLTTSNVILSPTRTPWLVDFGLGFFSNRD 169
                                    *************8...5*************************************************98766665 PP

>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.0   5.1e-12   1.8e-08      53     150 ..      64     161 ..      41     164 .. 0.83

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 5.1e-12
                                    HHHHHHHHHHHHHHHTT--S--EEEE..ETTEEEEE--EETTEEGGB.HHHCG-HHHHHHHHHHHHHHHHHHHHTSTEEE CS
                           RIO1  53 lwaekEfrnLkrleeagvpvPkpiel..krhvlvmefigedgvaapk.lkdveeeeeaeelyeevleemrklykeaglvH 129
                                      +  E r+L+r++ agv+vP p+ +  ++ +lvm +ig  g ++++ ++ +e    +++++ e+ +++  l    g+v 
  gi|119719370|ref|YP_919865.1|  64 ERTVLESRILSRAAMAGVNVPVPVLVypEEGILVMTYIG--GERLKDsMRGIE-PGTLRNVFVEIGRQLGTLH-SLGIVY 139
                                    4555699****************99855799********..665554155555.899*********9877766.****** PP

                                    SS-STTSEEEETT.EEEE--GT CS
                           RIO1 130 aDLSeyNvlvded.kvviIDvs 150
                                    +DL   Nv+++    ++++D++
  gi|119719370|ref|YP_919865.1| 140 GDLTTSNVILSPTrTPWLVDFG 161
                                    ***********9999*****85 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   4.9e-07    0.0018      28     108 ..      52     135 ..      30     137 .. 0.78
   2 !   14.4   0.1   7.3e-06     0.026     167     238 ..     136     206 ..     134     214 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 4.9e-07
                                    E-TTS-HHHHHHHHHHH.....HHHHHTT-..B--B-CTTBS-EEETTEEEEEEE----EE-SS...HHHHHHHHHHHHH CS
                            APH  28 npparaaeeirrevall.....rlLakagv..pvPevlagdtddeeigllfalieyvpgrsllr...klsaaqlpellea 97 
                                    ++++r++ e+rre  +l        a agv  pvP++++      e+g   ++++y++g+ l +      +  l++++ +
  gi|119719370|ref|YP_919865.1|  52 YRDPRLDSELRRERTVLesrilSRAAMAGVnvPVPVLVY-----PEEG--ILVMTYIGGERLKDsmrGIEPGTLRNVFVE 124
                                    566667777777776555522255556666778888888.....5555..56***************999********** PP

                                    HHHHHCCHHCH CS
                            APH  98 lgeflaalhqv 108
                                    +g+ l+ lh++
  gi|119719370|ref|YP_919865.1| 125 IGRQLGTLHSL 135
                                    *********97 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 7.3e-06
                                    EEE-SS-SGGGEEEC..TTEEEEE---TT-EEEECCHHHHCCH....HHCSCHCC...CHCHHHHHHHHCS-HHHHCCC CS
                            APH 167 vllHgDlhpgNllvdpddgrvtGviDfedaglgpplyDlavll....rswtseld...peflaallrayeqeaglarla 238
                                    +++ gDl + N+++ p+ ++   ++Df++   +++  D +v l    r    +l    p ++++l++a    +g+a+++
  gi|119719370|ref|YP_919865.1| 136 GIVYGDLTTSNVILSPTRTPW--LVDFGLGFFSNRDEDAGVDLhlfkR----ALEsthPLQAEDLFQAFV--DGYAQIR 206
                                    6899***********999999..****************999944432....222444666666666665..5665554 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   1.1e-07   0.00041      29     207 .]      36     202 ..      21     202 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.1e-07
                            Kdo  29 naalrkyyrggllgklskdlyrfk.lgrtravrEfrllkrLeeagvavpkpvaagavkvgleyrAlllterlegaqdLed 107
                                    ++a+ k  ++  + k ++d    + l r r v E r+l r   agv+vp pv  + +        +l++  + g + L+d
  gi|119719370|ref|YP_919865.1|  36 ELAGEKVVVKYRVPKSYRDPRLDSeLRRERTVLESRILSRAAMAGVNVPVPVLVYPEE------GILVMTYIGG-ERLKD 108
                                    56666777777777778884444459999**********************9987654......4677777755.56888 PP

                            Kdo 108 llakwaelaeelkrallkavgrliaklhragvnHadlyaknillqqeeeeeaeiwliDldkarlrlradrwrekdLarLk 187
                                     ++    ++    r+ + ++gr    lh++g+  +dl   n+ l  +     + wl+D+  +     +d +   dL+  k
  gi|119719370|ref|YP_919865.1| 109 SMRG---IEPGTLRNVFVEIGRQLGTLHSLGIVYGDLTTSNVILSPTR----TPWLVDFGLGFFSN-RDEDAGVDLHLFK 180
                                    8886...666677788899****************************9....*******9888777.7778888888888 PP

                            Kdo 188 rsfl.kieltead.weallraY 207
                                    r ++ +  l+  d ++a++ +Y
  gi|119719370|ref|YP_919865.1| 181 RALEsTHPLQAEDlFQAFVDGY 202
                                    8877544444444356666666 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   3.9e-08   0.00014       5     152 ..      22     165 ..      18     185 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 3.9e-08
                                    EEEEEESSEEEEEEEEETTTTSSEEEEEEEEE.....STTSSHHH..HHHHHHHHHHHHTS-BTTB--EEEEEESSSSEE CS
                    Pkinase_Tyr   5 kklGeGafGkVvegtlkgekekkevkVavKtl.....keeateee..keelleeakimkklkhpnivkllgvctkeepll 77 
                                      lG Ga + +v+g+l        +kV+vK       ++   ++e  +e+ + e +i+++     +   + v +  e+ +
  gi|119719370|ref|YP_919865.1|  22 GVLGFGAEAVIVKGELA------GEKVVVKYRvpksyRDPRLDSElrRERTVLESRILSRAAMAGVNVPVPVLVYPEEGI 95 
                                    57999999999999999......44555554321000333222323356666678888888777777777788888999* PP

                                    EEEE--TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHHHHHHHHHTTEEEST-SGGGEEEEETTEEEE-STTTHEE CS
                    Pkinase_Tyr  78 ivteyvkgGdLlkfLrkkekekltlkdllsfalqvAkGmeyLeskklvHrdlaarNvLlsenkvvkisDfGLard 152
                                    +v+ y+ g  L++ +r       +  +l ++ +++ + +  L+s  +v  dl++ Nv+ls +++  + DfGL   
  gi|119719370|ref|YP_919865.1|  96 LVMTYIGGERLKDSMRGI-----EPGTLRNVFVEIGRQLGTLHSLGIVYGDLTTSNVILSPTRTPWLVDFGLGFF 165
                                    ********9999999885.....788899999***************************************9655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1639.68
//
Query:       gi|119719371|ref|YP_919866.1|  [L=349]
Description: hypothetical protein Tpen_0454 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-43  149.6   0.0    1.4e-43  149.2   0.0    1.2  1  NMD3            NMD3 family
  ------ inclusion threshold ------
      0.015   15.3   2.1       0.11   12.5   1.1    2.4  2  DZR             Double zinc ribbon
      0.041   14.2   0.0      0.081   13.3   0.0    1.5  1  mCpol           minimal CRISPR polymerase domain
      0.045   13.4   3.8       0.66    9.7   0.7    2.5  2  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
       0.15   12.1   0.0        4.2    7.5   0.0    2.3  2  2CSK_N          Two-component sensor kinase N-terminal
       0.16   12.4   0.3         21    5.6   0.0    2.6  3  RNA_pol_Rpb2_7  RNA polymerase Rpb2, domain 7
       0.43   10.7   6.6        5.3    7.2   0.1    3.2  2  Zn-ribbon_8     Zinc ribbon domain
        0.5   10.3   0.1        0.5   10.3   0.1    2.8  3  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)


Domain annotation for each model (and alignments):
>> NMD3  NMD3 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.2   0.0   6.1e-47   1.4e-43       1     240 [.       5     231 ..       5     234 .. 0.92

  Alignments for each domain:
  == domain 1  score: 149.2 bits;  conditional E-value: 6.1e-47
                           NMD3   1 CcrCGkeieelinglCedCllkevditegiek.ievevCkeCgrylpkgkWvkaeleseellaeclkklvekgLkvseev 79 
                                    C+ CGk++++li+glC++C++++ +i+e +   ++v+vC++Cgr ++k++W    l+s+e la  ++k + + +kv+ e+
  gi|119719371|ref|YP_919866.1|   5 CPVCGKPTDRLIDGLCPECYRRSRRIMEPKRDaLRVKVCRKCGRLYYKDEW----LSSSEELAMSVEKDLPRLVKVRGEL 80 
                                    ****************************99999******************....7889999999999988888988877 PP

                           NMD3  80 eevkvelvdaefiwtephskrikvkvtvqgevrgenetilqqevevevkvkrqqCprCsriaggyyeaivQvRqk.relt 158
                                    ++ +v l  ++            ++v+  g++++  +  +++++++++k+++++C+ C  + +++  aivQvR++ rel+
  gi|119719371|ref|YP_919866.1|  81 RSARVSLYIDK---GF-------AEVHAVGRADSGIDFFYEETLRIPLKTEYSICDWCLGKVSKKKSAIVQVRASeRELS 150
                                    77777654444...23.......367777777667999****************************************** PP

                           NMD3 159 eeehkrtfelleqlilkhdahafiskikevkeGlDfyfgsksaArklveflksevggkvkeseklvsedkksgkevyrlt 238
                                    ++e+k++ ++l +l  +++a+a   ++ke+  GlD+yf+s  aAr++v++l+++v  +v e++k v+ d + g+e+y+ t
  gi|119719371|ref|YP_919866.1| 151 NDEKKAVYKVLDELSSSGNAEALPWDVKEEAGGLDLYFSSPRAAREVVRRLSERVYFEVLETSKKVGVDGS-GHEKYQST 229
                                    ********************************************************************999.******99 PP

                           NMD3 239 ys 240
                                    + 
  gi|119719371|ref|YP_919866.1| 230 IR 231
                                    85 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.1   5.1e-05      0.11       1      37 [.       5      49 ..       2      55 .. 0.83
   2 ?    0.9   0.0      0.22   4.9e+02       9      24 ..     119     134 ..     115     152 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.1e-05
                            DZR  1 CpqCgeelppdar.fCseCgtklkavaa.......edrCpsCgek 37
                                   Cp Cg++++      C+eC  + ++  +        ++C +Cg+ 
  gi|119719371|ref|YP_919866.1|  5 CPVCGKPTDRLIDgLCPECYRRSRRIMEpkrdalrVKVCRKCGRL 49
                                   999999988765569*****9977666677899999******986 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.22
                            DZR   9 ppdarfCseCgtklka 24 
                                    + +   C++C  k+++
  gi|119719371|ref|YP_919866.1| 119 KTEYSICDWCLGKVSK 134
                                    5667789999888875 PP

>> mCpol  minimal CRISPR polymerase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.6e-05     0.081      15      74 ..     262     320 ..     254     335 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.6e-05
                          mCpol  15 alllsndeeeleklskevkeaikklkkllkdelgasvifaaGDsilakssleedllvels 74 
                                     l ls+ e+e+ +l k++  +i+ ++++ + +    v++ aGD++ ++s+  + ++v++ 
  gi|119719371|ref|YP_919866.1| 262 LLNLSSYEKEVYMLNKSLLSRISVIARANELK-MGVVVYTAGDKVHVMSNDYKVYEVDIP 320
                                    445999*******************9987777.899*************98887777765 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.7   0.00029      0.66       6      20 ..       5      19 ..       4      26 .. 0.86
   2 ?    4.3   0.1     0.014        32      20      32 .]      39      51 ..      31      51 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00029
                  zf-NADH-PPase  6 CgrCGaptepaeggw 20
                                   C+ CG pt +  +g 
  gi|119719371|ref|YP_919866.1|  5 CPVCGKPTDRLIDGL 19
                                   **********99996 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.014
                  zf-NADH-PPase 20 warvCpaCglehY 32
                                   + +vC  Cg+ +Y
  gi|119719371|ref|YP_919866.1| 39 RVKVCRKCGRLYY 51
                                   679********99 PP

>> 2CSK_N  Two-component sensor kinase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0019       4.2      33      77 ..     171     216 ..     165     251 .. 0.75
   2 ?    2.1   0.0     0.084   1.9e+02      44      62 ..     313     331 ..     297     338 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0019
                         2CSK_N  33 ralaeqvrvedge..levdlppaalellesdaedrvyyqVsdadgrl 77 
                                     al   v+ e g   l+++ p+aa+e+++ + ++rvy+ V +++ ++
  gi|119719371|ref|YP_919866.1| 171 EALPWDVKEEAGGldLYFSSPRAAREVVR-RLSERVYFEVLETSKKV 216
                                    55555666666644489999*********.89********9986654 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.084
                         2CSK_N  44 gelevdlppaalellesda 62 
                                    +  evd+pp+a++l+++++
  gi|119719371|ref|YP_919866.1| 313 KVYEVDIPPSARKLFQEEQ 331
                                    3479***********9765 PP

>> RNA_pol_Rpb2_7  RNA polymerase Rpb2, domain 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.026        58      29      69 ..      34      75 ..      28      91 .. 0.65
   2 ?   -3.4   0.0         6   1.3e+04      44      63 ..     122     141 ..     119     149 .. 0.51
   3 ?    5.6   0.0    0.0095        21      43      80 ..     298     335 ..     271     340 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.026
                                   TTTEEEEEEESSSSSCCCEE.EBTTTTCSSSEEEEEEEHHHH CS
                 RNA_pol_Rpb2_7 29 kSDavevdvcgrckllaaan.eCkivkseekiekveipeafk 69
                                   k Da++v+vc++c+ l +++ + +  ++ +   + ++p+ +k
  gi|119719371|ref|YP_919866.1| 34 KRDALRVKVCRKCGRLYYKDeWLSSSEELAMSVEKDLPRLVK 75
                                   6799**********9998774344444444444445555555 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 6
                                    CCCEEEBTTTTCSSSEEEEE CS
                 RNA_pol_Rpb2_7  44 laaaneCkivkseekiekve 63 
                                    ++++++C    s++k + v+
  gi|119719371|ref|YP_919866.1| 122 YSICDWCLGKVSKKKSAIVQ 141
                                    55556665444444443333 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.0095
                                    SCCCEEEBTTTTCSSSEEEEEEEHHHHHHHHHHHHTTB CS
                 RNA_pol_Rpb2_7  43 llaaaneCkivkseekiekveipeafklLlqeLqslgi 80 
                                    +++a ++ ++++++ k+ +v+ip +++ L+qe q++g+
  gi|119719371|ref|YP_919866.1| 298 VYTAGDKVHVMSNDYKVYEVDIPPSARKLFQEEQTVGL 335
                                    344444999***********************888776 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.1    0.0024       5.3      28      40 .]       4      16 ..       1      16 [. 0.84
   2 ?    3.5   2.4     0.036        80       8      33 ..      20      47 ..      19      53 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0024
                    Zn-ribbon_8 28 aCPeCgsevrrvi 40
                                    CP Cg+++ r+i
  gi|119719371|ref|YP_919866.1|  4 LCPVCGKPTDRLI 16
                                   4********9987 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.036
                    Zn-ribbon_8  8 CeeCghefevlqsis.daplta.CPeCg 33
                                   C eC ++  ++++ + da  ++ C +Cg
  gi|119719371|ref|YP_919866.1| 20 CPECYRRSRRIMEPKrDALRVKvCRKCG 47
                                   7888888887776665666666788887 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1       0.3   6.6e+02      27      33 ..       4      10 ..       2      13 .. 0.70
   2 ?   -1.0   0.3      0.76   1.7e+03      27      32 ..      19      24 ..      17      27 .. 0.74
   3 ?   10.3   0.1   0.00022       0.5       5      22 ..      34      51 ..      32      55 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.3
                        DUF35_N 27 vCphCgs 33
                                    Cp Cg 
  gi|119719371|ref|YP_919866.1|  4 LCPVCGK 10
                                   5888874 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.76
                        DUF35_N 27 vCphCg 32
                                    Cp C 
  gi|119719371|ref|YP_919866.1| 19 LCPECY 24
                                   699995 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00022
                        DUF35_N  5 aegrLvgqrCpdCGtvqf 22
                                   ++  L++  C++CG++++
  gi|119719371|ref|YP_919866.1| 34 KRDALRVKVCRKCGRLYY 51
                                   56689**********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      583  (0.0325172); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2366.94
//
Query:       gi|119719372|ref|YP_919867.1|  [L=89]
Description: hypothetical protein Tpen_0455 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-09   36.9   0.0    5.8e-09   36.1   0.0    1.4  1  DUF424           Protein of unknown function (DUF424)
  ------ inclusion threshold ------
       0.03   14.5   0.0       0.03   14.4   0.0    1.1  1  Cdc13_OB4_dimer  Cdc13 OB4 dimerization domain


Domain annotation for each model (and alignments):
>> DUF424  Protein of unknown function (DUF424)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.0   6.5e-13   5.8e-09       9      92 .]       1      86 [.       1      86 [. 0.88

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 6.5e-13
                                   EEEEEEGGGTT-EEEETTEEEE--HHHH--EEE..-HHHHHHHHHHHEEEEEESHHHHHHHHHTTSS-GGG-EEETTEEEEE CS
                         DUF424  9 lvavcdkellgktfkegelllnvsegfyggela..seeeaikeLekatiaNivgeeavvlavkaGlvdpdsVlvidgvphaq 88
                                   ++a+cd++llg +++ +++++++++ f+gg+l+  ++e + ke++ a+ +  +ge++ +l  +     +++ l+++gvp++q
  gi|119719372|ref|YP_919867.1|  1 MLAICDEKLLGVELEYNNVRVKITRDFFGGSLVllDDELLRKEIAGADSITAFGEDSLSLLEEIYPSVRKASLRVAGVPYVQ 82
                                   79*******************************999999******************9998454445567778888888888 PP

                                   EEE- CS
                         DUF424 89 igkl 92
                                   ++++
  gi|119719372|ref|YP_919867.1| 83 VFRI 86
                                   8875 PP

>> Cdc13_OB4_dimer  Cdc13 OB4 dimerization domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   3.4e-06      0.03      16      72 ..       6      63 ..       1      83 [. 0.80

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.4e-06
                                   EEEEEEEEEETTTEEEEEESS---T--B-.GGG-EEEEEESHHHHHHHHSSS---GGG CS
                Cdc13_OB4_dimer 16 kakilsvevdedkvelyvtndlilkkkvd.pkeiLkveilGkenvnyFlgdeealedi 72
                                   + k+l ve+++++v++++t d   +  v    e+L+ ei G + +  F  d   l ++
  gi|119719372|ref|YP_919867.1|  6 DEKLLGVELEYNNVRVKITRDFFGGSLVLlDDELLRKEIAGADSITAFGEDSLSLLEE 63
                                   6799*******************9777651678***************8755444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       186  (0.0103743); expected 358.6 (0.02)
Passed bias filter:                      181  (0.0100954); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 596.17
//
Query:       gi|119719373|ref|YP_919868.1|  [L=285]
Description: putative circadian clock protein, KaiC [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.2e-57  192.0   0.0    1.1e-56  191.8   0.0    1.0  1  ATPase           KaiC
      7e-05   21.6   0.0    0.00011   20.9   0.0    1.2  1  GvpD             GvpD gas vesicle protein
    0.00024   20.7   0.2    0.00092   18.8   0.2    1.9  1  AAA_25           AAA domain
     0.0024   17.7   0.0     0.0037   17.1   0.0    1.3  1  MEDS             MEDS: MEthanogen/methylotroph, DcmR Sensory 
  ------ inclusion threshold ------
      0.012   15.7   0.0      0.017   15.1   0.0    1.2  1  ResIII           Type III restriction enzyme, res subunit
      0.021   14.6   0.0       0.03   14.1   0.0    1.4  1  DEAD             DEAD/DEAH box helicase
      0.022   14.1   0.0      0.034   13.5   0.0    1.2  1  DnaB_C           DnaB-like helicase C terminal domain
      0.032   14.5   0.5      0.073   13.3   0.5    1.8  1  AAA_22           AAA domain
      0.069   12.2   0.0       0.13   11.3   0.0    1.4  1  T2SSE            Type II/IV secretion system protein
      0.073   12.3   0.0       0.13   11.5   0.0    1.3  1  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.076   12.7   0.0       0.14   11.9   0.0    1.3  1  Sigma54_activat  Sigma-54 interaction domain
      0.091   12.3   0.0       0.17   11.4   0.0    1.3  1  AAA_7            P-loop containing dynein motor region
       0.14   12.3   0.0       0.27   11.3   0.0    1.5  1  QCR10            Ubiquinol-cytochrome-c reductase complex sub
       0.25   11.0   0.3       0.45   10.2   0.3    1.5  1  AAA_24           AAA domain


Domain annotation for each model (and alignments):
>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.8   0.0   8.4e-60   1.1e-56       2     228 ..      49     277 ..      48     280 .. 0.97

  Alignments for each domain:
  == domain 1  score: 191.8 bits;  conditional E-value: 8.4e-60
                         ATPase   2 ktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekleeeg 81 
                                    k g+eglDe + gG+ +gr++l+tGe+GtGKt+f+l+Fl++g+++ +epg++v v+e+ +d+ + +  +Gwd+e + ++g
  gi|119719373|ref|YP_919868.1|  49 KLGVEGLDERI-GGLLRGRTYLVTGETGTGKTMFSLTFLMEGLRS-NEPGIYVLVDEEYSDFMNGVYDFGWDFESYIRSG 126
                                    679*******9.******************************999.********************************** PP

                         ATPase  82 klaiidasesaeesaee.kdkedleelieelaeaikeikakrvviDsitgl.ayeekeavaReilrqlvrvl.kklgvTa 158
                                    +l i+ ++ +  e+ ++    + ++++++ + +  ++i+a+r+viD++++l  +e + a +Re+++ l+  l k +g T+
  gi|119719373|ref|YP_919868.1| 127 QLRILTLMPDFVERMKNkPVDTVVRSIVDGILQEARAIRAQRLVIDPVAPLiVNEGDLAWTREYIKSLIINLeKRIGATT 206
                                    ************9999855677899**************************9999999**************99****** PP

                         ATPase 159 ilvsekssseeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIte.egikvle 228
                                    ++vse++++++a +++gveef++ gv+vL  ++++++++Rtl ++kmR+ ++ +++++f+I + +g++v  
  gi|119719373|ref|YP_919868.1| 207 LIVSEIPTGSTALSRFGVEEFLAAGVFVLGIERVRNTFYRTLYVRKMRWRPVPPQIFVFDIVRgKGVVVKG 277
                                    *******************************************************************9975 PP

>> GvpD  GvpD gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0     9e-08   0.00011      10     211 ..      65     273 ..      62     282 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 9e-08
                           GvpD  10 GktllikGaPGtGktlftlrgl.dvlrresdvlyvstrvdde.tvseay...fsgeaeld..ktalldllkdpleldldv 82 
                                    G+t l+ G+ GtGkt+f l +l + lr +++ +yv    + +  ++ +y    + e+ +   +  +l l+ d +e    +
  gi|119719373|ref|YP_919868.1|  65 GRTYLVTGETGTGKTMFSLTFLmEGLRSNEPGIYVLVDEEYSdFMNGVYdfgWDFESYIRsgQLRILTLMPDFVE--RMK 142
                                    99*******************8468*********97665544144556676656666666447778888877654..555 PP

                           GvpD  83 dvPiekldlesllefvdeiaaiatkliialdswelvyeylaerydsPediktvkndlvvlaresgvrlvlvletaansr. 161
                                    + P+++  + s+++ + + a +     + +d    v   + ++ d     + +k  ++ l +  g+  ++v+e  + s+ 
  gi|119719373|ref|YP_919868.1| 143 NKPVDT-VVRSIVDGILQEARAIRAQRLVIDP---VAPLIVNEGDLAWTREYIKSLIINLEKRIGATTLIVSEIPTGSTa 218
                                    667754.4777776554444444444455677...6777778888888889999999999999****999*998765532 PP

                           GvpD 162 l......eyivdGvvtlnvkeddrgrlrrdlrleklrGvrignrlqPftladGkfk 211
                                    l      e+++ Gv  l ++   r    r l + k+r   + ++++ f +  Gk  
  gi|119719373|ref|YP_919868.1| 219 LsrfgveEFLAAGVFVLGIERV-RNTFYRTLYVRKMRWRPVPPQIFVFDIVRGKGV 273
                                    2333555899*******99887.999***********9999999999999988854 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.2   7.2e-07   0.00092      23     186 ..      56     209 ..      38     211 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 7.2e-07
                         AAA_25  23 rwlvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgeal...rd 99 
                                    +  ++gll +g + l++G +gtGKt++ l    + ++          e+g  ++v+ E s  ++ + ++  g ++    +
  gi|119719373|ref|YP_919868.1|  56 DERIGGLL-RGRTYLVTGETGTGKTMFSLTFLMEGLRSN--------EPGIYVLVDEEYS--DFMNGVYDFGWDFesyIR 124
                                    66789998.8*******************9998888633........5666666665544..599999999855444477 PP

                         AAA_25 100 darllvldlagveslpLfakdrggtlltadvdaleaaieevegvrlvviDplsralgg..densnsdv.galvealeria 176
                                     ++l++l+l+  + +  ++++  +t++ + vd + ++++++  ++ +viDp++ +  +  d    ++  ++l+    +++
  gi|119719373|ref|YP_919868.1| 125 SGQLRILTLMP-DFVERMKNKPVDTVVRSIVDGILQEARAIR-AQRLVIDPVAPLIVNegDLAWTREYiKSLII---NLE 199
                                    89999999955.34444567777777999***********86.9********9976551122222222233333...344 PP

                         AAA_25 177 rrtgaavllv 186
                                    +r ga++l+v
  gi|119719373|ref|YP_919868.1| 200 KRIGATTLIV 209
                                    4666666655 PP

>> MEDS  MEDS: MEthanogen/methylotroph, DcmR Sensory domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   2.9e-06    0.0037      19     108 ..      84     173 ..      79     194 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.9e-06
                           MEDS  19 pfikaglargekvlyvasastldelrealrkagldvdaalesgqleildaeetylrgggfdp..ermlealrralakala 96 
                                     f+ +gl+++e+ +yv+ ++++++ ++ + + g d +++ +sgql+il+    +++  + +p  + + + +   l++a+a
  gi|119719373|ref|YP_919868.1|  84 TFLMEGLRSNEPGIYVLVDEEYSDFMNGVYDFGWDFESYIRSGQLRILTLMPDFVERMKNKPvdTVVRSIVDGILQEARA 163
                                    79*********************************************999877777766666533444455555555555 PP

                           MEDS  97 dgyaglrvigem 108
                                       +  r+++++
  gi|119719373|ref|YP_919868.1| 164 I--RAQRLVIDP 173
                                    5..555666665 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   1.4e-05     0.017      24      63 ..      65     103 ..      26     107 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.4e-05
                                    TSEEEEEESTTSTHHHHH.HHHHHHH-S.....-EEEEESS CS
                         ResIII  24 dkrglikmaTGtGKTlva.aklierllkkgkeekflflvpr 63 
                                     + +l+  +TGtGKT+ + + l+e l+++++   + +lv++
  gi|119719373|ref|YP_919868.1|  65 GRTYLVTGETGTGKTMFSlTFLMEGLRSNEP--GIYVLVDE 103
                                    568999************7778888888744..89999986 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.4e-05      0.03      10      75 ..      61     124 ..      56     210 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.4e-05
                                    HHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  10 lilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyid 75 
                                     +l+g+  lv +eTG+GKT+  l  +++ +    +++g  +l+ e     ++ +++    f +yi+
  gi|119719373|ref|YP_919868.1|  61 GLLRGRTYLVTGETGTGKTMFSLTFLMEGLR--SNEPGIYVLVDEEYSDFMNGVYDFGWDFESYIR 124
                                    57899**************998888888774..478887777777666666666666666666555 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.6e-05     0.034       5      43 ..      51      89 ..      48     107 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.6e-05
                                   STHHHHHHCTSBXTTXEEEEEEXTTSSHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         DnaB_C  5 gfkdLDkltsGlqkgdliiiAarpsmGktalalniaena 43
                                   g + LD+ ++Gl +g  +++ +  ++Gkt++ l++  + 
  gi|119719373|ref|YP_919868.1| 51 GVEGLDERIGGLLRGRTYLVTGETGTGKTMFSLTFLMEG 89
                                   7889****************************9987654 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.5   5.7e-05     0.073       7      29 ..      67      89 ..      63     208 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.7e-05
                         AAA_22  7 ilvvtGesGtGKTtllrrlleql 29
                                     +vtGe+GtGKT+   ++l++ 
  gi|119719373|ref|YP_919868.1| 67 TYLVTGETGTGKTMFSLTFLMEG 89
                                   579***********988888764 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   9.9e-05      0.13     117     151 ..      58      87 ..      23     103 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 9.9e-05
                          T2SSE 117 kiaevlrkavrerglilvsGgTgsGKttllyallk 151
                                    +i  +lr       + lv+G Tg+GKt +  + l 
  gi|119719373|ref|YP_919868.1|  58 RIGGLLRGR-----TYLVTGETGTGKTMFSLTFLM 87 
                                    455555555.....789**********98766554 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   9.9e-05      0.13       3      40 ..      67     102 ..      65     111 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9.9e-05
                        DUF2075   3 vvlVtGvaGtGKtvvllnllaeleddeeertavylsvN 40 
                                     +lVtG++GtGKt+  l++l e    ++++  +y++v 
  gi|119719373|ref|YP_919868.1|  67 TYLVTGETGTGKTMFSLTFLMEG--LRSNEPGIYVLVD 102
                                    689**************999998..6777777777665 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00011      0.14      24      54 ..      67      97 ..      60     108 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                                   -EEEECSTTSSHHHHHHHHHHHSTTTTS-EE CS
                Sigma54_activat 24 svlitGesGtGKellaraiheaskrkekpfv 54
                                   + l+tGe+GtGK++++ +   +  r+++p +
  gi|119719373|ref|YP_919868.1| 67 TYLVTGETGTGKTMFSLTFLMEGLRSNEPGI 97
                                   679************9888777777777655 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00013      0.17      33      58 ..      65      91 ..      62     100 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00013
                          AAA_7 33 kkpvllvGptGtGKtviikd.llkkld 58
                                   ++  l++G+tGtGKt+   + l++ l 
  gi|119719373|ref|YP_919868.1| 65 GRTYLVTGETGTGKTMFSLTfLMEGLR 91
                                   6789************99997777766 PP

>> QCR10  Ubiquinol-cytochrome-c reductase complex subunit (QCR10)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00021      0.27      14      52 ..     217     255 ..     204     261 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00021
                          QCR10  14 ptlalfGgaagvavlfftsgvPrvqkdiLqkiPvigsyf 52 
                                    + l  fG+    a+ +f+ g+ rv++++++ + v + ++
  gi|119719373|ref|YP_919868.1| 217 TALSRFGVEEFLAAGVFVLGIERVRNTFYRTLYVRKMRW 255
                                    67889************************9876666666 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.3   0.00035      0.45       3      23 ..      66      89 ..      64     150 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00035
                         AAA_24  3 lkiliyGpsgiGKTtlakel...g 23
                                   + +l++G+ g+GKT++ +++   g
  gi|119719373|ref|YP_919868.1| 66 RTYLVTGETGTGKTMFSLTFlmeG 89
                                   6789**************995550 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2101.23
//
Query:       gi|119719374|ref|YP_919869.1|  [L=519]
Description: radical SAM domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-13   51.7   0.0    2.2e-13   50.9   0.0    1.5  1  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.9   0.0   1.3e-17   2.2e-13       1     166 [.     225     385 ..     225     386 .. 0.85

  Alignments for each domain:
  == domain 1  score: 50.9 bits;  conditional E-value: 1.3e-17
                                    EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiri 80 
                                    v+++rgC ++C fC  ++     + +r+++ e++ ++v+e++a +++++v l++   +++++  ++le l+ +   g   
  gi|119719374|ref|YP_919869.1| 225 VETSRGCFRMCAFCLEGH---IFRGVRERPFEQVRRIVEEGSAGNRTRHVKLVSLSFFDHSEADRILEWLVNE---G--Y 296
                                    5789*************9...6*******************96666*****************9999999998...4..4 PP

                                    EEEECSSCHG...HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET.EEEEEEEBTTTS CS
                                    xxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
                    Radical_SAM  81 tvetngtlpd...eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikr.vvdrivglpGen 156
                                    +++++ ++ d   e+ le ++  g  ++++  e++++      +++  +++ + e+   +r++g     v+ +vg+pGe 
  gi|119719374|ref|YP_919869.1| 297 SFSIPSLRADtlnERRLEYIRLGGQKTLTVAPETLSPS-LAIAIRKHIGYSLIRELSLSARKLGYTGlKVYLMVGIPGER 375
                                    5555666655667*********99**************.666666666677777777777777766666*********** PP

                                    HHHHHHHHHH CS
                                    xxxxxxxxxx RF
                    Radical_SAM 157 deeleellel 166
                                    +e+l+ ++e 
  gi|119719374|ref|YP_919869.1| 376 EEDLRLTAEK 385
                                    ****999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (519 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 3148.43
//
Query:       gi|119719375|ref|YP_919870.1|  [L=371]
Description: metal dependent phosphohydrolase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.6e-14   52.7   0.7    1.1e-13   51.5   0.7    1.7  1  HD              HD domain
    0.00018   21.1   0.1    0.00045   19.7   0.0    1.6  2  HDOD            HDOD domain
  ------ inclusion threshold ------
      0.035   14.1   0.3        0.2   11.7   0.0    2.2  2  Sulfolobus_pRN  Sulfolobus plasmid regulatory protein


Domain annotation for each model (and alignments):
>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.5   0.7   1.8e-17   1.1e-13       1     121 [.      25     128 ..      25     129 .. 0.77

  Alignments for each domain:
  == domain 1  score: 51.5 bits;  conditional E-value: 1.8e-17
                                    HHHHHHHHHHHHHHHHHHHHH..HHHHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHHHHH. CS
                             HD   1 rleHsleVaklarrlaedlge..eedrellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrlgld. 77 
                                    r+ Hsl++++la+r+a++ g   e ++e l+laaLlHD+G++pf++a +          +Hekv+ e++r  +++l  + 
  gi|119719375|ref|YP_919870.1|  25 RFSHSLGTLYLAERIAKSAGIedEGEVESLRLAALLHDVGHMPFSHALS---------SNHEKVSQEVVRSMLGDLLGKd 95 
                                    799****************999************************666.........3688888888888887772223 PP

                                    .HHHHHHHHHTTCCHHHHHHHHHHHHCCTSCHHHHHHHHHHHHHH CS
                             HD  78 .ledvaklirehheswegkkrprglaerqlslearivklaDrlaa 121
                                        v+++ +  ++ +            ++  ++ +++++D+l +
  gi|119719375|ref|YP_919870.1|  96 lKHGVIDILAGSSRLS------------PILASEVDADRLDYLLR 128
                                    4444555555555555............57777777777777765 PP

>> HDOD  HDOD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   7.6e-08   0.00045      96     151 ..      26      84 ..      14      93 .. 0.89
   2 ?   -2.3   0.0      0.43   2.6e+03      90     161 ..     217     289 ..     193     295 .. 0.57

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 7.6e-08
                                    HHHHHHHHHHHHHHHHHTT-S-H...HHHHHHHHTTTHHHHHHHHHSHHHHHHHHHHHH CS
                           HDOD  96 wehslavAlvarelaeelgledp...eeaflaGLLhdiGklvllsllpeeleellekva 151
                                     +hsl + ++a+++a+++g ed+   e + la+LLhd+G + + ++l+ + e++ ++v 
  gi|119719375|ref|YP_919870.1|  26 FSHSLGTLYLAERIAKSAGIEDEgevESLRLAALLHDVGHMPFSHALSSNHEKVSQEVV 84 
                                    589***************9999767899*********************9999988765 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.43
                                    S-HHHHHHHHHHHHHH.HHHHHHHTT-S-HHHHHHHHHTTTHHHHHHHHHSHHHHHHHHHHHHHH---HHHHH CS
                           HDOD  90 adlkklwehslavAlv.arelaeelgledpeeaflaGLLhdiGklvllsllpeeleellekvaeeelslleae 161
                                    ++ k+lw +  ++ ++ a + a++ + ++ +e+ ++ LL++  klv+  +l++   e+ ++   e+  + +ae
  gi|119719375|ref|YP_919870.1| 217 LEEKELWCMFDDCMVIeALKRARKSEEDRLKELATSFLLRKPPKLVFEAYLSDGPGEGFRRELYEHALKGTAE 289
                                    5555555555555433122334444444457777777887777777777777777776666555555555555 PP

>> Sulfolobus_pRN  Sulfolobus plasmid regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1      0.29   1.7e+03       8      29 ..     219     240 ..     216     252 .. 0.75
   2 ?   11.7   0.0   3.4e-05       0.2      22      49 ..     290     317 ..     283     321 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.29
                 Sulfolobus_pRN   8 ekillilsrrcatleeleektG 29 
                                    ek l  +   c+ +e l+    
  gi|119719375|ref|YP_919870.1| 219 EKELWCMFDDCMVIEALKRARK 240
                                    7777888899*****9986554 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 3.4e-05
                 Sulfolobus_pRN  22 eeleektGiekeellvyltrlykrGlis 49 
                                    e l ek G++   llvyl+r+   G + 
  gi|119719375|ref|YP_919870.1| 290 ELLVEKCGVPEGCLLVYLARIVPIGNVN 317
                                    5578****************98777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2508.91
//
Query:       gi|119719376|ref|YP_919871.1|  [L=458]
Description: hypothetical protein Tpen_0459 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (458 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 3176.23
//
Query:       gi|119719377|ref|YP_919872.1|  [L=177]
Description: hypothetical protein Tpen_0460 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-09   36.1   0.0    7.2e-09   35.6   0.0    1.2  1  Methyltrn_RNA_2  Putative SAM-dependent RNA methyltransferase


Domain annotation for each model (and alignments):
>> Methyltrn_RNA_2  Putative SAM-dependent RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.0     4e-13   7.2e-09      31     113 ..      20     101 ..      16     119 .. 0.90

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 4e-13
                                    HHHHHHHHHHBESSSB-TTEEEEEEEEESSSS-EEEEEETTT--S--SSHHHHHHHHHHHHCHCC..TGCCSEEEEETTE CS
                Methyltrn_RNA_2  31 vlarcvsaalfvshgiRedvvvylvLegtpdpprtikieasevkkvspderniailikkalkave..eikkqekkvrpgl 108
                                    +++r v  a+f+sh+iR+dv++  v+   pd   ++ +  s +++v+ de+++a+l +++ +a+   e +   ++ ++g+
  gi|119719377|ref|YP_919872.1|  20 LVCRVVTSAIFLSHDIRRDVTLRFVM---PDAGLSVSFLSSRLRHVHVDEQSFAGLHRRIVRAMWevESEGGARHPHSGI 96 
                                    79*********************997...59999*************************9999974556667899999** PP

                                    EEE-- CS
                Methyltrn_RNA_2 109 tVrke 113
                                     V+++
  gi|119719377|ref|YP_919872.1|  97 SVERI 101
                                    99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 1123.99
//
Query:       gi|119719378|ref|YP_919873.1|  [L=338]
Description: putative rRNA pseudouridine synthase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-25   90.9   0.0    4.7e-22   78.9   0.0    3.1  1  TruB_N    TruB family pseudouridylate synthase (N terminal do
    1.2e-22   79.8   0.0    2.2e-22   79.0   0.0    1.4  1  TruB_C_2  tRNA pseudouridylate synthase B C-terminal domain
    2.6e-19   69.0   0.4    4.4e-19   68.2   0.4    1.4  1  PUA       PUA domain
    1.3e-16   60.4   0.1    4.6e-16   58.6   0.0    2.0  3  DKCLD     DKCLD (NUC011) domain
     0.0027   18.0   0.0      0.014   15.7   0.0    2.3  3  UPF0113   UPF0113 PUA domain


Domain annotation for each model (and alignments):
>> TruB_N  TruB family pseudouridylate synthase (N terminal domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.9   0.0   1.3e-25   4.7e-22       1     149 []      62     175 ..      62     175 .. 0.95

  Alignments for each domain:
  == domain 1  score: 78.9 bits;  conditional E-value: 1.3e-25
                                    HHHTT-S-EEESS---TT-EEEEEEEEGGGGGGHHHCTTS-EEEEEEEEETEEETTSBTTS-EEE-.--TT--HHHHHHH CS
                         TruB_N   1 krllkakkvGhtGtLDplatGvLvvavgeaTklleylleadKeYeatirlgaetdteDaegeileeekveklteekleev 80 
                                    ++ll+++++ h+GtLDp+++GvL++ +++a ++l +ll++dKeY++++rl+ + d                   e+le+v
  gi|119719378|ref|YP_919873.1|  62 RKLLGIERIAHAGTLDPKVSGVLPITLNNAVRVLPVLLKEDKEYVCVMRLHGDVDP------------------ERLERV 123
                                    799***********************************************865543..................56999* PP

                                    HHHC-EEE---------------------------------EEEEEEEEEEEEEEEEEEEEEESTTTTH CS
                         TruB_N  81 lkkftGeieqvppmySAvkvnGkrlyelaregeeverkkrkvtiyelelleveepevelevecskGtYi 149
                                    +++f+G+i+q+pp  SAvk                 r+ r  +iy+++lle++e+++ l+v c++GtY+
  gi|119719378|ref|YP_919873.1| 124 VSMFKGRIYQRPPLRSAVK-----------------REVRIRQIYDIRLLEFNERTALLHVWCEAGTYM 175
                                    *******************.................899*****************************6 PP

>> TruB_C_2  tRNA pseudouridylate synthase B C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.0   0.0   6.2e-26   2.2e-22       1      63 [.     176     242 ..     176     243 .. 0.92

  Alignments for each domain:
  == domain 1  score: 79.0 bits;  conditional E-value: 6.2e-26
                                    HHHHHHHHHHTTS-EEEEEEEEEEETTE.GG-..B-HHHHHHHHHHHHT..--H.HHHHEEEGGGGG CS
                       TruB_C_2   1 RtLcdDiGeaLgcgAhveeLRRtrvgpf.deedmvtledLedavllyke..dee.LdrlllPlesal 63 
                                    R+Lc+DiGe Lg+gAh++eLRR+r+g++ ++ ++ t++d+ da++++ke   +  L+++ lP+e+a+
  gi|119719378|ref|YP_919873.1| 176 RKLCHDIGEILGVGAHMQELRRIRSGSLyEDRNCSTMHDVVDAYYIWKErgIDHfLRQVFLPVEAAI 242
                                    9**************************779999****************763337*********996 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.2   0.4   1.2e-22   4.4e-19       1      73 [.     246     318 ..     246     319 .. 0.98

  Alignments for each domain:
  == domain 1  score: 68.2 bits;  conditional E-value: 1.2e-22
                                    CEEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEEEE CS
                            PUA   1 grvvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveierv 73 
                                    ++v++ d+Av+a+++ga L +pG+v+ eg ++ + +Vai++ +gelva+G+a++++e + +   g++v++e+v
  gi|119719378|ref|YP_919873.1| 246 PKVWIRDSAVDAVCHGAPLAVPGIVKLEGGIKVNSTVAILTLKGELVAIGKAQMTTEKMLTESSGIAVKTEHV 318
                                    69**********************************************************************8 PP

>> DKCLD  DKCLD (NUC011) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.6   0.0   1.3e-19   4.6e-16      12      58 .]      12      58 ..       6      58 .. 0.96
   2 ?   -3.7   0.0       3.6   1.3e+04       4      15 ..      95     106 ..      94     108 .. 0.79
   3 ?   -3.6   0.0       3.4   1.2e+04       8      21 ..     305     318 ..     303     326 .. 0.74

  Alignments for each domain:
  == domain 1  score: 58.6 bits;  conditional E-value: 1.3e-19
                                   X-EEESS-----TTSS--GGG--HHHHHHTEEEEEEE-SSS-HHHHH CS
                          DKCLD 12 dkllvrtehytplpaGssPlkRpieeyikyGvinLDKPsnPsSHEVV 58
                                   +++ vr+e +t+ ++G+ P +Rp e ++ky+vinLDKP +PsSHEVV
  gi|119719378|ref|YP_919873.1| 12 REIYVRSEDETDFSYGWLPEERPPEVLLKYSVINLDKPVGPSSHEVV 58
                                   7899******************************************9 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 3.6
                                    XX....XXX-EE CS
                          DKCLD   4 wpllLknydkll 15 
                                    +p+lLk+ ++++
  gi|119719378|ref|YP_919873.1|  95 LPVLLKEDKEYV 106
                                    699999988765 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 3.4
                                    ..XXX-EEESS--- CS
                          DKCLD   8 Lknydkllvrtehy 21 
                                    L++ + + v+teh 
  gi|119719378|ref|YP_919873.1| 305 LTESSGIAVKTEHV 318
                                    56667788999986 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       3.4   1.2e+04      20      52 ..      40      71 ..      38      79 .. 0.60
   2 ?   -3.2   0.0       2.9     1e+04      43      54 ..     183     194 ..     182     204 .. 0.72
   3 !   15.7   0.0   3.8e-06     0.014       1      75 [.     247     327 ..     247     328 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 3.4
                        UPF0113 20 kesilkitesvkenqvvvVlnengeplGiGkir 52
                                   k s+++++++v  +   vV  + +++lGi +i+
  gi|119719378|ref|YP_919873.1| 40 KYSVINLDKPVGPSSHEVV-AWLRKLLGIERIA 71
                                   5566666666665444444.4556777776665 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.9
                        UPF0113  43 geplGiGkirkd 54 
                                    ge+lG+G   ++
  gi|119719378|ref|YP_919873.1| 183 GEILGVGAHMQE 194
                                    689999987664 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 3.8e-06
                        UPF0113   1 kvvvkekaeklFLYGrdvlkesilkitesvkenqvvvVlnengeplGiGkirkdt..k.aspgkivvkn...laDiGeYl 74 
                                    kv+++ +a   +  G  +   +i+k+++++k n  v++l  +ge+++iGk++  t     ++++i vk+   ++D G+Y 
  gi|119719378|ref|YP_919873.1| 247 KVWIRDSAVDAVCHGAPLAVPGIVKLEGGIKVNSTVAILTLKGELVAIGKAQMTTekMlTESSGIAVKTehvVMDPGTYP 326
                                    79*************************************************99889745778888887634457888887 PP

                        UPF0113  75 R 75 
                                    R
  gi|119719378|ref|YP_919873.1| 327 R 327
                                    6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 2162.19
//
Query:       gi|119719379|ref|YP_919874.1|  [L=98]
Description: 50S ribosomal protein L14e [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00016   21.5   0.3    0.00028   20.7   0.3    1.4  1  KOW             KOW motif
    0.00039   20.8   0.0    0.00051   20.5   0.0    1.2  1  Ribosomal_L14e  Ribosomal protein L14
  ------ inclusion threshold ------
        0.1   12.4   0.0        1.4    8.8   0.0    2.1  2  WIYLD           Ubiquitin-binding WIYLD domain


Domain annotation for each model (and alignments):
>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.3   4.7e-08   0.00028       1      31 [.       6      35 ..       6      37 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 4.7e-08
                                   TTSEEEESSSTTTTCEEEEEEEETTTTEEEE CS
                            KOW  1 pGdhVkVvsGphkGktGkVvkvdqhkvrVfv 31
                                   +G+++  +sG+ +G ++++v++++++ +V+v
  gi|119719379|ref|YP_919874.1|  6 VGRICVKTSGREAGLKCVIVDIIDDN-FVLV 35
                                   6999**********************.4444 PP

>> Ribosomal_L14e  Ribosomal protein L14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   8.6e-08   0.00051       1      39 [.      45      83 ..      45      89 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 8.6e-08
                 Ribosomal_L14e  1 pRqaiplkrlkLtkivlklprgartgavkkawekadvee 39
                                   +R  +++++l+  ++++++++ga+ + vk+a+eka++ e
  gi|119719379|ref|YP_919874.1| 45 KRRRANIRHLEPLEYKISISKGASDEEVKAALEKAGLIE 83
                                   5999*******************************9865 PP

>> WIYLD  Ubiquitin-binding WIYLD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.046   2.7e+02       4      21 ..      43      60 ..      40      62 .. 0.86
   2 ?    8.8   0.0   0.00024       1.4       3      30 ..      67      94 ..      65      96 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.046
                          WIYLD  4 gkeRidaAidamkelGfs 21
                                   g +R +a i+++++l ++
  gi|119719379|ref|YP_919874.1| 43 GVKRRRANIRHLEPLEYK 60
                                   67899999*******996 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00024
                          WIYLD  3 sgkeRidaAidamkelGfskeqvrpvlk 30
                                   +++e ++aA+++   + f ke+v+p++ 
  gi|119719379|ref|YP_919874.1| 67 ASDEEVKAALEKAGLIEFMKEKVKPTVS 94
                                   57899********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 615.71
//
Query:       gi|119719380|ref|YP_919875.1|  [L=87]
Description: hypothetical protein Tpen_0463 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-32  110.6   0.5    3.3e-32  110.4   0.5    1.0  1  UPF0147   Uncharacterised protein family (UPF0147)


Domain annotation for each model (and alignments):
>> UPF0147  Uncharacterised protein family (UPF0147)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.4   0.5   1.8e-36   3.3e-32       4      81 .]       7      84 ..       5      84 .. 0.98

  Alignments for each domain:
  == domain 1  score: 110.4 bits;  conditional E-value: 1.8e-36
                                   HHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHHHH CS
                        UPF0147  4 kikevielLeeiiedtsvPrniRraakeakekLkdekeslavraataisiLdeisnDpnmPlhaRtliwevvskLEti 81
                                   +ik++ielL++i++d+ +PrniRr+a+e++e L+d +++++++aat+is L++is+Dpn+Pl+aRt+iw+++s LE++
  gi|119719380|ref|YP_919875.1|  7 QIKNAIELLKQIADDRGIPRNIRRVATESIEVLMDPQMTPGLKAATVISKLEDISSDPNTPLFARTKIWQIISLLEQV 84
                                   699*************************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 620.40
//
Query:       gi|119719381|ref|YP_919876.1|  [L=353]
Description: radical SAM domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.7e-07   29.6   0.1    2.5e-06   27.9   0.1    2.0  1  Radical_SAM  Radical SAM superfamily
    0.00011   22.4   0.0    0.00022   21.3   0.0    1.5  1  Fer4_14      4Fe-4S single cluster domain
     0.0022   18.3   0.0     0.0042   17.4   0.0    1.5  1  Fer4_12      4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.052   13.5   0.0        2.5    8.1   0.0    2.9  3  TFIID_30kDa  Transcription initiation factor TFIID 23-30kDa s


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.1   5.7e-10   2.5e-06       4     107 ..      35     144 ..      32     253 .. 0.92

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 5.7e-10
                                    ESEESS--TTTSCCTT.....HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC.CCT CS
                                    xxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx RF
                    Radical_SAM   4 trgCnlrCsfCarpet.....vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla.vpg 77 
                                    t  C+++C +C+ +       v     +++ ++ e   ++k+   + g  +  l+gg+pl+   + +++++  k+   +g
  gi|119719381|ref|YP_919876.1|  35 TGLCPYNCFYCPLSNYrkqrdVTFVNEVEVYDPGEYFTLLKAEILRSGSLGASLTGGDPLVKQSLSVETAKFLKEVfGKG 114
                                    667***********999999988888888888888888887776788899***********988888888888877999* PP

                                    EEEEEEECSSCHGHHHHHHHHHTT-SEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  78 iritvetngtlpdeeklerllelgvdrvsl 107
                                    ++i+v t g+l++ e l  l+e+g+d + +
  gi|119719381|ref|YP_919876.1| 115 FHIHVYTTGLLLRHETLNSLVEAGLDELRI 144
                                    ************************998766 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   4.9e-08   0.00022       2      92 ..      33     126 ..      32     141 .. 0.68

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 4.9e-08
                        Fer4_14   2 fvrlsgCnlsCkgCdnketwkselgkpqteelle....qilk..dlkkseikiqglvltGGePLhyenkk.ellklvkrl 74 
                                    f+ ++ C+ +C  C  ++ ++++    +++e+++    + ++  +++  ++   g +ltGG+PL  ++ + e  k++k++
  gi|119719381|ref|YP_919876.1|  33 FL-TGLCPYNCFYCPLSN-YRKQRDVTFVNEVEVydpgEYFTllKAEILRSGSLGASLTGGDPLVKQSLSvETAKFLKEV 110
                                    66.899********9444.4443333333333321111222212444555666789********9988773578999999 PP

                        Fer4_14  75 keeypekkiwletngtle 92 
                                      ++  ++i+++t g+l 
  gi|119719381|ref|YP_919876.1| 111 FGKG--FHIHVYTTGLLL 126
                                    9999..*******99875 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   9.4e-07    0.0042       4      98 ..      26     128 ..      23     144 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 9.4e-07
                        Fer4_12   4 eGvrlslfvsg.CnlsCkgCfnketwsfk......sgkeft.kelleeiiedlkkesiegltllGGEPllpena.ealle 74 
                                    +G+ +++f++g C+ +C +C   + ++ +      + + ++  e    + +++  +   g +l+GG+Pl+ +    + ++
  gi|119719381|ref|YP_919876.1|  26 QGLKTVIFLTGlCPYNCFYCPLSNYRKQRdvtfvnEVEVYDpGEYFTLLKAEILRSGSLGASLTGGDPLVKQSLsVETAK 105
                                    688889996666********877777555333332333343355555556666667789***********7766457899 PP

                        Fer4_12  75 lvkevkeekpekdiwlytgytlee 98 
                                    ++kev  +++   ++ +tg  l +
  gi|119719381|ref|YP_919876.1| 106 FLKEVFGKGF-HIHVYTTGLLLRH 128
                                    9999999999.5799999987754 PP

>> TFIID_30kDa  Transcription initiation factor TFIID 23-30kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0   0.00056       2.5      20      46 ..      91     117 ..      77     120 .. 0.83
   2 ?   -1.5   0.0      0.55   2.4e+03      27      38 ..     270     281 ..     263     281 .. 0.81
   3 ?    1.3   0.0     0.075   3.4e+02      27      39 ..     300     312 ..     297     321 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00056
                    TFIID_30kDa  20 sDprlarlvsLaaqKFisdiaadAyqy 46 
                                     Dp +++ +s+ + KF+ ++  + ++ 
  gi|119719381|ref|YP_919876.1|  91 GDPLVKQSLSVETAKFLKEVFGKGFHI 117
                                    79*****************98777665 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.55
                    TFIID_30kDa  27 lvsLaaqKFisd 38 
                                    ++s a++++++d
  gi|119719381|ref|YP_919876.1| 270 VLSAATHQYVTD 281
                                    589999***998 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.075
                    TFIID_30kDa  27 lvsLaaqKFisdi 39 
                                    + sL a KFi   
  gi|119719381|ref|YP_919876.1| 300 VASLYADKFIHPM 312
                                    779*******755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 2249.37
//
Query:       gi|119719382|ref|YP_919877.1|  [L=137]
Description: hypothetical protein Tpen_0465 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       268  (0.0149478); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 998.77
//
Query:       gi|119719383|ref|YP_919878.1|  [L=108]
Description: regulatory protein, ArsR [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.5e-13   48.6   0.1    8.5e-13   48.0   0.1    1.3  1  HTH_5            Bacterial regulatory protein, arsR family
    1.5e-09   37.7   0.1    2.9e-09   36.9   0.1    1.5  1  HTH_20           Helix-turn-helix domain
    3.1e-06   27.0   0.2    4.9e-06   26.3   0.2    1.3  1  TrmB             Sugar-specific transcriptional regulator Trm
     0.0011   18.7   0.0     0.0019   17.9   0.0    1.4  1  HTH_IclR         IclR helix-turn-helix domain
     0.0012   18.7   0.7     0.0019   18.1   0.1    1.7  2  MarR_2           MarR family
     0.0039   17.5   0.0     0.0065   16.8   0.0    1.5  1  Rrf2             Transcriptional regulator
      0.004   17.1   0.8       0.11   12.5   0.0    2.1  2  HTH_29           Winged helix-turn helix
     0.0046   17.3   0.0     0.0062   16.9   0.0    1.2  1  Penicillinase_R  Penicillinase repressor
  ------ inclusion threshold ------
      0.065   12.8   1.6       0.11   12.1   0.1    2.1  2  HTH_24           Winged helix-turn-helix DNA-binding
      0.095   12.6   0.0       0.12   12.2   0.0    1.2  1  TFIIE_alpha      TFIIE alpha subunit


Domain annotation for each model (and alignments):
>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.0   0.1   4.7e-16   8.5e-13       1      46 [.      21      66 ..      21      67 .. 0.97

  Alignments for each domain:
  == domain 1  score: 48.0 bits;  conditional E-value: 4.7e-16
                                   SHHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_5  1 dptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                   +p RlkI++lL  g++ v+e+++ lg +q+ vS+HL+ Lre G+V+
  gi|119719383|ref|YP_919878.1| 21 HPLRLKIISLLYAGPRNVSEIVNSLGEPQPVVSRHLALLREKGVVR 66
                                   589*****************************************96 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.1   1.6e-12   2.9e-09       6      60 ..      11      71 ..       6      72 .. 0.89

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 1.6e-12
                                   H.......HS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                         HTH_20  6 A.......LahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvreg 60
                                   A       L hP R++i ++L  a+++ +se+   l+ ++  +s+HL+ L+e g v+ +r g
  gi|119719383|ref|YP_919878.1| 11 AqaefcksLCHPLRLKIISLL-YAGPRNVSEIVNSLGEPQPVVSRHLALLREKGVVRAERRG 71
                                   5555555599***********.***********************************99987 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.2   2.7e-09   4.9e-06      16      64 ..      29      77 ..      28      82 .. 0.91

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 2.7e-09
                                   HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE CS
                           TrmB 16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYra 64
                                    Ll  gp +++ei + lg p++ v + L  L +kG+V+ e++ +++Y +
  gi|119719383|ref|YP_919878.1| 29 SLLYAGPRNVSEIVNSLGEPQPVVSRHLALLREKGVVRAERRGTNVYYY 77
                                   799**************************************99887765 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.1e-06    0.0019       7      50 ..      26      67 ..      25      69 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.1e-06
                                   HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                       HTH_IclR  7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                    i+ +l ++p+   +se+ + +g p + v+R+L+ L e G v+ 
  gi|119719383|ref|YP_919878.1| 26 KIISLLYAGPRN--VSEIVNSLGEPQPVVSRHLALLREKGVVRA 67
                                   567777777775..9**************************985 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1     1e-06    0.0019      13      54 ..      30      68 ..      20      73 .. 0.84
   2 ?   -1.6   0.1       1.4   2.6e+03      41      45 ..      93      97 ..      82     108 .] 0.57

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1e-06
                                   HHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                         MarR_2 13 aLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                    L+++p+   +v+e++  lg +++ vsr+l+ L ++G v+ +
  gi|119719383|ref|YP_919878.1| 30 LLYAGPR---NVSEIVNSLGEPQPVVSRHLALLREKGVVRAE 68
                                   4566664...*****************************866 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.4
                                   HHHHH CS
                         MarR_2 41 ilkrL 45
                                   +++++
  gi|119719383|ref|YP_919878.1| 93 VIRKM 97
                                   33333 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   3.6e-06    0.0065      26      69 ..      36      80 ..      23      94 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.6e-06
                                   B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE.ETTT-TCEEESS CS
                           Rrf2 26 vsseeiaerqnispsylekilakLrkaglvks.vrGkgGGyrLak 69
                                    +++ei ++ + +++++++ la Lr++g+v++ +rG +  y La 
  gi|119719383|ref|YP_919878.1| 36 RNVSEIVNSLGEPQPVVSRHLALLREKGVVRAeRRGTNVYYYLAY 80
                                   5789**************************983579888888775 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   6.3e-05      0.11       1      46 [.      24      69 ..      24      75 .. 0.87
   2 ?    3.3   0.2     0.048        85      29      46 ..      90     107 ..      88     108 .] 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.3e-05
                         HTH_29  1 RaqallllaeGvstvsqiAkllglsrrtvyrwlkrfeegGlaalld 46
                                   R++++ ll+ G  +vs+i+  lg   + v r+l + +e+G+  + +
  gi|119719383|ref|YP_919878.1| 24 RLKIISLLYAGPRNVSEIVNSLGEPQPVVSRHLALLREKGVVRAER 69
                                   899********77***************************765543 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.048
                         HTH_29  29 vyrwlkrfeegGlaalld 46 
                                    v+r+++ + e++++al++
  gi|119719383|ref|YP_919878.1|  90 VRRVIRKMIEERAQALQR 107
                                    9**************997 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   3.5e-06    0.0062      15      89 ..      33     103 ..      24     107 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.5e-06
                                    HS-EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTEEEEE----XXXXXXXXXXXXXXXXXXXXXX CS
                Penicillinase_R  15 kgeatvkevveeleeekelaysTVktllrrLvkKgllsrekegrafiYsplvseeeavasavkqlldklfegsvk 89 
                                    +g+ +v+e+v+ l e+    +  V   l  L +Kg++++e+ g    Y+ +  e e   + v+ +++k++e++ +
  gi|119719383|ref|YP_919878.1|  33 AGPRNVSEIVNSLGEP----QPVVSRHLALLREKGVVRAERRGTNVYYYLAYPELEEACRIVRRVIRKMIEERAQ 103
                                    58899***********....788999****************988888888877777777888888888875554 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1     6e-05      0.11       4      48 .]      23      66 ..      21      66 .. 0.90
   2 ?   -1.5   0.2       1.1     2e+03      34      44 ..      90     100 ..      90     100 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6e-05
                         HTH_24  4 tdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                   +++kI++lL++ +  + +e+   lg +++ v+r+l  L e+G+++
  gi|119719383|ref|YP_919878.1| 23 LRLKIISLLYA-GPRNVSEIVNSLGEPQPVVSRHLALLREKGVVR 66
                                   57899999999.666899*************************97 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.1
                         HTH_24  34 vnrrlkrLeee 44 
                                    v+r +++++ee
  gi|119719383|ref|YP_919878.1|  90 VRRVIRKMIEE 100
                                    78999999986 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   6.7e-05      0.12      32      95 ..      40     100 ..      24     107 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.7e-05
                                    HHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEEEEEECCCHCCCHHHHHHHHHHH CS
                    TFIIE_alpha  32 dlakelkidlnelrklLnrLyearlvkykrrrdeekswykyywrinyeklvdvvkrkleevvkk 95 
                                    ++ + l+  ++++ + L+ L+e+++v   rr   ++++y y  +++ e++  +v+r +++++ +
  gi|119719383|ref|YP_919878.1|  40 EIVNSLGEPQPVVSRHLALLREKGVVRAERR---GTNVYYYLAYPELEEACRIVRRVIRKMIEE 100
                                    6777788888999999*********988886...79999999999***********99999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 839.48
//
Query:       gi|119719384|ref|YP_919879.1|  [L=255]
Description: methyltransferase type 11 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.3e-34  117.5   0.0      2e-33  116.1   0.0    1.6  2  GCD14            tRNA methyltransferase complex GCD14 subunit
    1.9e-11   44.1   0.0    2.7e-11   43.6   0.0    1.1  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    2.4e-07   30.5   0.2    4.8e-07   29.5   0.2    1.5  1  GCD14_N          tRNA methyltransferase complex GCD14 subunit
    2.4e-07   30.7   0.0    3.3e-07   30.2   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
      1e-05   24.8   0.0    1.5e-05   24.2   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
    2.9e-05   24.7   0.0    5.5e-05   23.7   0.0    1.5  1  Methyltransf_11  Methyltransferase domain
    5.9e-05   23.7   0.0    9.8e-05   23.0   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
     0.0021   17.6   0.0     0.0086   15.6   0.0    2.0  2  MTS              Methyltransferase small domain
     0.0043   16.4   0.0     0.0057   16.0   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
  ------ inclusion threshold ------
      0.013   14.7   0.0      0.018   14.2   0.0    1.2  1  Methyltransf_3   O-methyltransferase
      0.015   15.3   0.0       0.02   14.9   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
      0.018   15.8   0.0      0.044   14.5   0.0    1.7  1  Methyltransf_12  Methyltransferase domain
      0.028   14.4   0.0      0.054   13.4   0.0    1.4  1  Methyltransf_18  Methyltransferase domain
      0.037   15.1   0.0        0.1   13.7   0.0    1.7  2  Methyltransf_24  Methyltransferase domain
      0.062   13.0   0.0       0.14   11.9   0.0    1.5  1  Met_10           Met-10+ like-protein


Domain annotation for each model (and alignments):
>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.1   0.0   1.7e-36     2e-33      17     178 ..      74     230 ..      71     245 .. 0.94
   2 ?   -1.0   0.0      0.96   1.1e+03     230     246 ..     237     253 ..     231     254 .. 0.79

  Alignments for each domain:
  == domain 1  score: 116.1 bits;  conditional E-value: 1.7e-36
                          GCD14  17 LphrtqilytaDisliimkLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsqlvtv 96 
                                    L   tq++y +D + i+++ ++ pGs+vve+GtG+g l+  +a  v P G+++t+e  ++ +e a+e+++e +l  +v  
  gi|119719384|ref|YP_919879.1|  74 LRRFTQVIYPKDAAYIVVSANIGPGSRVVEAGTGTGFLTAILAWYVRPSGRVYTYEIRKDFYEAALENLKEVGLLPYVEA 153
                                    5567**************************************************************************** PP

                          GCD14  97 thrDvckeGfdeevsgkvDavfLDlPaPweaiphaakalkkeggrlCsfsPCieqvqrtceaLrelgfteietlevllrt 176
                                    +++D+ k G de   ++vDav LD+P Pw+  ++a +al ++gg l  f P + q+ r + a+r++gf+ ie +ev +r+
  gi|119719384|ref|YP_919879.1| 154 KNKDIRK-GIDE---SDVDAVVLDMPDPWNVAEEAYNAL-THGGILAVFVPTVTQLERVIVAVRKSGFKVIEPVEVNVRK 228
                                    ****975.7733...467*********************.99************************************** PP

                          GCD14 177 ye 178
                                    y+
  gi|119719384|ref|YP_919879.1| 229 YK 230
                                    97 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.96
                          GCD14 230 kPvselkghtgyLtfat 246
                                    +P +  + htgyL+ a+
  gi|119719384|ref|YP_919879.1| 237 RPETLGVLHTGYLLTAR 253
                                    66666677*****9997 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6   0.0   2.2e-14   2.7e-11      64     193 ..      88     219 ..      77     235 .. 0.83

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 2.2e-14
                                    HHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTC.SEEEEES-GGGTTGGG-S CS
                           PCMT  64 lalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldle.nvivvvgDGrkGyeekaP 142
                                    +++   ++ +g+rv+e G+G+G+lta+la +v+++grv + e  k+++e+a +nlk+ +l   v  +  D rkG +e + 
  gi|119719384|ref|YP_919879.1|  88 YIVVSANIGPGSRVVEAGTGTGFLTAILAWYVRPSGRVYTYEIRKDFYEAALENLKEVGLLpYVEAKNKDIRKGIDE-SD 166
                                    5555556899*************************************************9879***********986.67 PP

                                    EEEEEESSBBS.S--HHHHHTEEEEEEEEEEESB..SSSEEEEEEEEETTTEEE CS
                           PCMT 143 Ydaihvgaaap.eiPealidQLkeGGrlvvPvge..eeeQvlklvdkkadgkvv 193
                                     da+++    p ++ e+  + L +GG+l v v +  + e v+  v+k++  kv+
  gi|119719384|ref|YP_919879.1| 167 VDAVVLDMPDPwNVAEEAYNALTHGGILAVFVPTvtQLERVIVAVRKSG-FKVI 219
                                    8999998876659**************9887765536666677777766.4444 PP

>> GCD14_N  tRNA methyltransferase complex GCD14 subunit N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.2     4e-10   4.8e-07       5      50 ..       6      51 ..       3      52 .. 0.91

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 4e-10
                        GCD14_N  5 raGdrVqLtDaKgrkhtitLepGgefhthrGaieHDdlIGrpeGsV 50
                                   + Gd+V L    + ++t+  e+G+ +ht++G+++  +++G+  G  
  gi|119719384|ref|YP_919879.1|  6 KTGDWVLLYHDEKHRYTVKVEEGRVYHTTHGSVNLTEVVGKRYGET 51
                                   68******9888889*************************998865 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   2.7e-10   3.3e-07       4     113 ..      98     200 ..      95     228 .. 0.89

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 2.7e-10
                Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdiee.leklledekfDlilsn 81 
                                    g rv+++G+GtG+lt  la  ++p ++v+  +i ++  e A en+++ gl   ve +  di + ++++     +D ++  
  gi|119719384|ref|YP_919879.1|  98 GSRVVEAGTGTGFLTAILAWYVRPSGRVYTYEIRKDFYEAALENLKEVGLLpYVEAKNKDIRKgIDES----DVDAVVL- 172
                                    789**********************************************9999*************54....4777666. PP

                Methyltransf_31  82 evlnaladpdkileeiervlkpggilliedpr 113
                                        +++dp ++ ee+ ++l+ ggil++  p 
  gi|119719384|ref|YP_919879.1| 173 ----DMPDPWNVAEEAYNALTHGGILAVFVPT 200
                                    ....7*********************997766 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   1.3e-08   1.5e-05      20      73 ..      87     143 ..      78     161 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 1.3e-08
                                    HHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-...SEEEEE-S-HHHHHHHHCHTT CS
                         RrnaAD  20 neIldklnleekltvleigpGkGilTeeLakra...kqvvvlElderLakllqkkls 73 
                                    + I++ +n+ +   v+e g+G+G+lT++La ++     v  +E+++++++   ++l+
  gi|119719384|ref|YP_919879.1|  87 AYIVVSANIGPGSRVVEAGTGTGFLTAILAWYVrpsGRVYTYEIRKDFYEAALENLK 143
                                    679******************************87778999********98777665 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   4.6e-08   5.5e-05       2      96 .]     103     196 ..     102     196 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 4.6e-08
                                    EET-TTSHHHHHHHHTT...SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCT..SS-TT-EEEEEEES-CCC-CC CS
                Methyltransf_11   2 dvGcGtGrlaealakrg...arvvgvDlskemlklakekaseeglkvefvvadaekl..pfednsfDlvvssevlhhved 76 
                                    ++G+GtG l++ la ++   +rv++ ++ k + ++a e+ +e gl + +v+a  +++   + ++ +D+vv+      ++d
  gi|119719384|ref|YP_919879.1| 103 EAGTGTGFLTAILAWYVrpsGRVYTYEIRKDFYEAALENLKEVGL-LPYVEAKNKDIrkGIDESDVDAVVLD-----MPD 176
                                    78************444566************************8.6677777776542699999****988.....59* PP

                                    HHHHHHHHHHHEEEEEEEEE CS
                Methyltransf_11  77 pekalkeiaRvLkpgGllvi 96 
                                    p  + +e++  L  gG+l++
  gi|119719384|ref|YP_919879.1| 177 PWNVAEEAYNALTHGGILAV 196
                                    *****************975 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   8.2e-08   9.8e-05       1      97 []     101     192 ..     101     192 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 8.2e-08
                                    EEEET-TTSHHHHHHHCTS.TSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEEESTGGGS CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrl.gkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvssgalhhl 77 
                                    v+++G+GtG lt+ la  + ++++v+  +i +++ eaa e+++e gl   ve  ++d+++   +++ +D+vv+       
  gi|119719384|ref|YP_919879.1| 101 VVEAGTGTGFLTAILAWYVrPSGRVYTYEIRKDFYEAALENLKEVGLlpYVEAKNKDIRKGI-DESDVDAVVLD------ 173
                                    899*************999769*********************9888999********9954.3457*****93...... PP

                                    SHHHHHHHHHHHHHHEEEEE CS
                Methyltransf_25  78 sdedlekalkeiarvLkpgG 97 
                                      +d  ++ +e++++L+ gG
  gi|119719384|ref|YP_919879.1| 174 -MPDPWNVAEEAYNALTHGG 192
                                    .3566789999999999998 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       4.6   5.5e+03     110     136 ..      49      75 ..      47      79 .. 0.80
   2 !   15.6   0.0   7.2e-06    0.0086      33     106 ..      99     175 ..      88     220 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 4.6
                                    TCHCHHHHHHHHHHHHHHHEEEEEEEE CS
                            MTS 110 gkatelavaeeliaeAkeaLkegGeLl 136
                                    g+ +++++ e+l+ + ++ L+  G+L+
  gi|119719384|ref|YP_919879.1|  49 GETVRTNIGEDLVVSRANLLDRLGSLR 75 
                                    566788899999999999999988885 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 7.2e-06
                                    SEEEEET-TTSHHHHHHH.HHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTTSTTS-EEEEEE--- CS
                            MTS  33 gkvlDlGcGaGvlgaala.kespeaevtlvdvdarAlesakenleankle..vevvasdvleeveekkfdlivsNPP 106
                                     +v+  G+G+G+l+a la    p+ +v  +++ +   e+a enl++ +l   ve+ ++d+ + ++e ++d++v   P
  gi|119719384|ref|YP_919879.1|  99 SRVVEAGTGTGFLTAILAwYVRPSGRVYTYEIRKDFYEAALENLKEVGLLpyVEAKNKDIRKGIDESDVDAVVLDMP 175
                                    67999*********999845789999**********************9999********************97644 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   4.8e-06    0.0057      43     152 ..      93     197 ..      59     221 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.8e-06
                                    --S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEE CS
                Ubie_methyltran  43 vavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvtv 122
                                     +  +g++v++  +Gtg l++ l+  v+ +g+v   +i ++  + + + lke g   + ++ a+ +++    d  Dv +v
  gi|119719384|ref|YP_919879.1|  93 ANIGPGSRVVEAGTGTGFLTAILAWYVRPSGRVYTYEIRKDFYEAALENLKEVGL--LPYVEAKNKDIRKGIDESDVDAV 170
                                    45567999*********************************************98..57999999999888777787777 PP

                                    ES-GGG-S-HHHHHHHHHHHEEEEEEEEEE CS
                Ubie_methyltran 123 sfGlrnvtDklkaLkeayrvlkpGGrlvvl 152
                                       + +++D  ++ +eay  l  GG+l v+
  gi|119719384|ref|YP_919879.1| 171 ---VLDMPDPWNVAEEAYNALTHGGILAVF 197
                                    ...5689******************99886 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.5e-05     0.018      37     114 ..      87     164 ..      73     174 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.5e-05
                                    HHHHHHHHHHT--EEEEE--TTSHHHHHHHTTS-TT-EEEEEES-HHHHHHHHHHHHHTT-GGGEEEEES-HHHHHHH CS
                 Methyltransf_3  37 qfLslLvklvnakrvleiGvftGyslLatalalPeDGkilaididreayeialkfiqkagvaekieliegdalkvLee 114
                                     ++ +  ++    rv+e G+ tG+    +a  + + G++ + +i ++ ye al+ ++  g+   +e ++ d +k ++e
  gi|119719384|ref|YP_919879.1|  87 AYIVVSANIGPGSRVVEAGTGTGFLTAILAWYVRPSGRVYTYEIRKDFYEAALENLKEVGLLPYVEAKNKDIRKGIDE 164
                                    55555666777789**********************************************999999888888877776 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   1.7e-05      0.02      26      90 ..      98     159 ..      76     191 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.7e-05
                Methyltransf_32  26 altvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkrlsfaelsie 90 
                                      +vv++G G g+L+ +la   ++ + +v+  +++++  e+a +  +++g  +   ++ ++++i+
  gi|119719384|ref|YP_919879.1|  98 GSRVVEAGTGTGFLTAILAW-YVRPSGRVYTYEIRKDFYEAALENLKEVG--LLPYVEAKNKDIR 159
                                    568****************9.66789****************99999988..5455555555555 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   3.7e-05     0.044       1      99 []     102     194 ..     102     194 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.7e-05
                Methyltransf_12   1 LeiGcGtGsllrallekl.pdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhl 79 
                                    +e G+GtG l++ l+ +  p  +++ ++i +++ e+a e l++ + +    ve +++d+ +  ++s +D+vv+      +
  gi|119719384|ref|YP_919879.1| 102 VEAGTGTGFLTAILAWYVrPSGRVYTYEIRKDFYEAALENLKEVGLLP--YVEAKNKDIRKGIDESDVDAVVL-----DM 174
                                    589*********999999999************************977..66666666666666679999975.....35 PP

                Methyltransf_12  80 kdirevldnirklLkpgGrl 99 
                                    +d+  v ++++++L+ gG+l
  gi|119719384|ref|YP_919879.1| 175 PDPWNVAEEAYNALTHGGIL 194
                                    88899999999999998876 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   4.5e-05     0.054       9      87 ..      92     171 ..      89     173 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.5e-05
                Methyltransf_18   9 aslvekgsrvaDiGtDHgylpiylv.kegkakkviasDinegplekakeniekagledkievrlsdGleklkeeevdtvv 87 
                                     + + +gsrv+  Gt  g+l++ l+   +   +v+  +i++  +e+a en+++ gl   +e+   d  + ++e++vd+vv
  gi|119719384|ref|YP_919879.1|  92 SANIGPGSRVVEAGTGTGFLTAILAwYVRPSGRVYTYEIRKDFYEAALENLKEVGLLPYVEAKNKDIRKGIDESDVDAVV 171
                                    56788899************988873667889***************************************9999*9998 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       5.5   6.5e+03      72      86 ..      12      26 ..       6      74 .. 0.74
   2 ?   13.7   0.0   8.4e-05       0.1       1      99 [.     102     192 ..     102     196 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 5.5
                Methyltransf_24 72 llfiDgghaaeavle 86
                                   ll+ D  h ++   e
  gi|119719384|ref|YP_919879.1| 12 LLYHDEKHRYTVKVE 26
                                   667777777655444 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 8.4e-05
                Methyltransf_24   1 vEiGvysGvstlwllralrrngagrlvavdhdpg.aeeaaalareaglddrvrlikadseealaslaagsiDllfiDggh 79 
                                    vE G+  G+ t++l+  +r  g+  +++ +  ++  e+a ++++e gl  +v+  ++d ++ + +   +++D +++D++ 
  gi|119719384|ref|YP_919879.1| 102 VEAGTGTGFLTAILAWYVRPSGR--VYTYEIRKDfYEAALENLKEVGLLPYVEAKNKDIRKGIDE---SDVDAVVLDMP- 175
                                    89******************996..8888877755677888888889999888888887777654...66*******98. PP

                Methyltransf_24  80 aaeavledleallprlapgg 99 
                                       +  +  e + + l+ gg
  gi|119719384|ref|YP_919879.1| 176 ---DPWNVAEEAYNALTHGG 192
                                    ...44444445555555555 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00011      0.14      97     194 ..      94     191 ..      85     196 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                                    T--TT-EEEETT-TTTCCHHHCCHHTTSS.EEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG---TT-EEEEEE- CS
                         Met_10  97 lveegevVvdvfAGiGpfaipiakyskak.rvlaidlnPesvkylkeniklNkvekvvkpileDgrevireqladrvvmn 175
                                     + +g +Vv+   G G+++  +a y +++ rv++ ++  + ++   en+k   +  +v++ ++D r+ i e+ +d vv++
  gi|119719384|ref|YP_919879.1|  94 NIGPGSRVVEAGTGTGFLTAILAWYVRPSgRVYTYEIRKDFYEAALENLKEVGLLPYVEAKNKDIRKGIDESDVDAVVLD 173
                                    47899******************99997549************************************************9 PP

                                    -TTTGGGGHHHHHHHEEEE CS
                         Met_10 176 lpksaieFldkvlaalkdg 194
                                    +p+   +  +++++al++g
  gi|119719384|ref|YP_919879.1| 174 MPD-PWNVAEEAYNALTHG 191
                                    995.455555566655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 1843.27
//
Query:       gi|119719385|ref|YP_919880.1|  [L=432]
Description: hypothetical protein Tpen_0468 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.19   11.6   0.0       0.33   10.8   0.0    1.3  1  Glyco_H_20C_C  Glycoside Hydrolase 20C C-terminal domain


Domain annotation for each model (and alignments):
>> Glyco_H_20C_C  Glycoside Hydrolase 20C C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   1.9e-05      0.33     129     151 ..     401     423 ..     385     431 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 1.9e-05
                  Glyco_H_20C_C 129 elWmkenkpfGfevldiRlGGll 151
                                    + W +e +++G++v  +R+GG+ 
  gi|119719385|ref|YP_919880.1| 401 SGWVEEARAQGWDVRVVRMGGVG 423
                                    67*******************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       258  (0.0143901); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 2826.72
//
Query:       gi|119719386|ref|YP_919881.1|  [L=69]
Description: hypothetical protein Tpen_0469 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.011   16.4   0.4      0.011   16.3   0.4    1.1  1  DnaG_DnaB_bind  DNA primase DnaG DnaB-binding


Domain annotation for each model (and alignments):
>> DnaG_DnaB_bind  DNA primase DnaG DnaB-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.3   0.4   6.3e-07     0.011      31      96 ..       3      66 ..       1      69 [] 0.90

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 6.3e-07
                 DnaG_DnaB_bind 31 glallreliealaaepelntaaLlerlrgtpeeallaeLaveelqveeeeelerefadalarLqeq 96
                                   ++ +l +l++ +  +++l  a L+e+l     e++l+ + +   qvee+eelere+++++++L+e 
  gi|119719386|ref|YP_919881.1|  3 TIGALSRLLASTLRRDGLYEARLVEALDA--IEEFLTSVRGATPQVEEDEELERELKGCVEELREL 66
                                   5678999999998899999999****998..689*****************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 531.35
//
Query:       gi|119719387|ref|YP_919882.1|  [L=163]
Description: 30S ribosomal protein S19e [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.8e-51  172.4   0.0    4.4e-51  172.2   0.0    1.0  1  Ribosomal_S19e  Ribosomal protein S19e
    3.1e-05   23.7   0.0     0.0092   15.8   0.0    2.8  3  RuvB_C          RuvB C-terminal winged helix domain
    0.00015   21.6   0.1    0.00029   20.7   0.1    1.5  1  HTH_12          Ribonuclease R winged-helix domain
  ------ inclusion threshold ------
       0.02   14.9   0.0      0.033   14.2   0.0    1.3  1  HTH_45          Winged helix-turn-helix
      0.058   13.1   0.1       0.14   11.8   0.1    1.7  1  GntR            Bacterial regulatory proteins, gntR family
      0.069   13.2   0.0        2.9    8.0   0.0    2.5  3  HTH_20          Helix-turn-helix domain
      0.074   13.2   0.1       0.31   11.2   0.1    2.0  2  Mrr_N           Mrr N-terminal domain


Domain annotation for each model (and alignments):
>> Ribosomal_S19e  Ribosomal protein S19e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.2   0.0   1.7e-54   4.4e-51       3     136 ..       5     138 ..       3     139 .. 0.96

  Alignments for each domain:
  == domain 1  score: 172.2 bits;  conditional E-value: 1.7e-54
                                    SSHHHHHHHHHS--S--.-S-SSS-SSSS-SS-S-SS-SSTTTHHHHHHHHHHHTS--TTSGGGGS----SS-SSS---- CS
                 Ribosomal_S19e   3 kdVpaeelikalaeeLk.ksgklevPewadlvKtgsakelapededWfyvRaAsilRkvylrgpvGverlrkvYGgkkrr 81 
                                    k Vp++ li++la++Lk + +++++Pewa ++Ktg ++e++p+d+dW+y R+A++lRk+yl+gpvG+erlr++YGg++++
  gi|119719387|ref|YP_919882.1|   5 KFVPPRLLIEELAAYLKeNVKEIQPPEWALYAKTGPTRERPPQDPDWWYKRCAALLRKIYLEGPVGLERLRTAYGGRTKN 84 
                                    779**************77899********************************************************** PP

                                    ---THHHHHHHHHTTSSS--SSS---SS-HHHHHTHHHHH--SS--S--XXXXXX CS
                 Ribosomal_S19e  82 gvrpshfvkasgsvirkilqqLeklglvkkekkkgrrltkkGqrlldriaeevak 136
                                     v+++hf+ka gs irk+lqqLe++glv k+ + gr++t+kG++l+d++a +++k
  gi|119719387|ref|YP_919882.1|  85 TVKRKHFKKAGGSAIRKALQQLESAGLVAKTPR-GRVITEKGRALVDTTALRIFK 138
                                    ****************************77755.****************99987 PP

>> RuvB_C  RuvB C-terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.53   1.4e+03      23      40 ..      10      27 ..       1      29 [. 0.76
   2 ?    4.4   0.0     0.013        34      14      35 ..      59      80 ..      54      89 .. 0.78
   3 !   15.8   0.0   3.6e-06    0.0092      51      69 ..     109     127 ..     105     130 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.53
                                   -B-HHHHHHHTT--HHHH CS
                         RuvB_C 23 pvglktlaailgeeketi 40
                                    + ++ laa l+e+ ++i
  gi|119719387|ref|YP_919882.1| 10 RLLIEELAAYLKENVKEI 27
                                   566899999999999888 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.013
                                   HHHHT.TT--B-HHHHHHHTT- CS
                         RuvB_C 14 llkekfkggpvglktlaailge 35
                                   ll + + +gpvgl+ l ++ g 
  gi|119719387|ref|YP_919882.1| 59 LLRKIYLEGPVGLERLRTAYGG 80
                                   688899*********9887764 PP

  == domain 3  score: 15.8 bits;  conditional E-value: 3.6e-06
                                    TTSEEEETTEEEE-HHHHH CS
                         RuvB_C  51 eglIertsrGRilTkkglk 69 
                                     gl+ +t+rGR +T+kg  
  gi|119719387|ref|YP_919882.1| 109 AGLVAKTPRGRVITEKGRA 127
                                    69**************975 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.1   1.1e-07   0.00029      29      64 ..      93     127 ..      83     129 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.1e-07
                         HTH_12  29 digeravRyrLrkleergltrrvgyagreltEkGle 64 
                                    + g  a+R  L+ le  gl+ +  ++ r +tEkG  
  gi|119719387|ref|YP_919882.1|  93 KAGGSAIRKALQQLESAGLVAKTPRG-RVITEKGRA 127
                                    56778*******************98.******975 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.3e-05     0.033      37      68 ..     100     131 ..      97     141 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.3e-05
                         HTH_45  37 nkYLdmLvekglikkskekYvlTekGlellek 68 
                                    +k L++L + gl+ k+    v+TekG+ l+++
  gi|119719387|ref|YP_919882.1| 100 RKALQQLESAGLVAKTPRGRVITEKGRALVDT 131
                                    6889************************9986 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   5.6e-05      0.14      39      60 ..      97     118 ..      92     121 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.6e-05
                                    HHHHHHHHHHHHTTSEEEETTC CS
                           GntR  39 ttvReALrrLeaeglverrqgr 60 
                                    + +R+AL++Le++glv   +++
  gi|119719387|ref|YP_919882.1|  97 SAIRKALQQLESAGLVAKTPRG 118
                                    569*************877765 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       2.4   6.1e+03      35      41 ..      80      86 ..      58      93 .. 0.58
   2 ?    8.0   0.0    0.0011       2.9      40      61 .]      98     119 ..      95     119 .. 0.86
   3 ?    2.4   0.0     0.064   1.6e+02       5      32 ..     126     153 ..     123     161 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.4
                                   TS-HHHH CS
                         HTH_20 35 dlskntl 41
                                   + +knt+
  gi|119719387|ref|YP_919882.1| 80 GRTKNTV 86
                                   4667774 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0011
                                    HHHHHHHHHHHCTTEEEECTEE CS
                         HTH_20  40 tlsyHLrvLeeagLvevvregr 61 
                                     +++ L++Le+agLv  +  gr
  gi|119719387|ref|YP_919882.1|  98 AIRKALQQLESAGLVAKTPRGR 119
                                    568889*********9998886 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.064
                                    HHHS-HHHHHHHHHHSTCTTB-HHHHHH CS
                         HTH_20   5 eALahPvRrrilraLaraegltaselae 32 
                                    +AL + + +ri++ L ++++   + la+
  gi|119719387|ref|YP_919882.1| 126 RALVDTTALRIFKKLVEERPELSKYLAK 153
                                    699999*********6666555544444 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.78     2e+03      21      47 ..      14      41 ..      11      46 .. 0.79
   2 ?   11.2   0.1   0.00012      0.31      57      85 ..     102     129 ..      84     131 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.78
                          Mrr_N 21 keirervaerf.glseeeraellpsgkq 47
                                   +e+ ++++e++ ++++ e+a + ++g +
  gi|119719387|ref|YP_919882.1| 14 EELAAYLKENVkEIQPPEWALYAKTGPT 41
                                   5778888888888999999999888854 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00012
                          Mrr_N  57 artyLkkagllespkrgvwkiTekGrevl 85 
                                    a+++L  agl+ ++ rg + iTekGr+++
  gi|119719387|ref|YP_919882.1| 102 ALQQLESAGLVAKTPRGRV-ITEKGRALV 129
                                    899**************86.9*****986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       641  (0.0357521); expected 358.6 (0.02)
Passed bias filter:                      582  (0.0324614); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1177.96
//
Query:       gi|119719388|ref|YP_919883.1|  [L=116]
Description: DNA-binding TFAR19-related protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.3e-22   78.5  13.2    4.9e-22   78.3  13.2    1.0  1  dsDNA_bind       Double-stranded DNA-binding domain
  ------ inclusion threshold ------
       0.14   12.7   1.5        0.2   12.2   1.1    1.5  2  WAC_Acf1_DNA_bd  ATP-utilising chromatin assembly and remodel
        0.2   11.7   3.9       0.24   11.5   3.9    1.1  1  MAS20            MAS20 protein import receptor
       0.25   11.4   5.3        2.6    8.1   5.3    2.0  1  SurA_N           SurA N-terminal domain


Domain annotation for each model (and alignments):
>> dsDNA_bind  Double-stranded DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.3  13.2   1.1e-25   4.9e-22       1     109 [.      13     113 ..       8     115 .. 0.85

  Alignments for each domain:
  == domain 1  score: 78.3 bits;  conditional E-value: 1.1e-25
                                    XXXXXXXXXXXXXXXXXXXX...XXXX--SS..S--SSHHHHTTS--HHHHHHHHHHTTT-HHHHHHHHHHHHHHHH--S CS
                     dsDNA_bind   1 irkarlaelqaqagsssgsggaseqqeqqqeaseeeakqaiLsqiLepeAreRLsrirlvkperaeavenrLiqlaqsGq 80 
                                    i++++l e q+  +++        + +++q+a+ee+++q+iL++iL+peAr+RLs+++lvkpe +ea+e +Liqla+s  
  gi|119719388|ref|YP_919883.1|  13 IKRRKLLEYQRALEAE--------KAKEEQKAREEAMRQEILRRILTPEARARLSNLKLVKPELVEALEIQLIQLAESRS 84 
                                    5666666666655432........33333444699********************************************* PP

                                    S-----HHHHHHHHHHHS---XXXXX..X CS
                     dsDNA_bind  81 lrskvteeqLkeLLeqvaekkketkivis 109
                                    +r  +++e+Lk++L ++ e +++ +++++
  gi|119719388|ref|YP_919883.1|  85 VRVPIDDETLKQILARLYEAQRAREVKFR 113
                                    *******************9999999985 PP

>> WAC_Acf1_DNA_bd  ATP-utilising chromatin assembly and remodelling N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.1   4.5e-05       0.2      33      82 ..      12      60 ..      10      75 .. 0.76
   2 ?    0.8   0.2      0.16   7.3e+02      62      81 ..      39      59 ..      32     109 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.5e-05
                WAC_Acf1_DNA_bd 33 eitgksnltyfeAlesEkeaskeleekfpealkkpvlelvqf.strsrldd 82
                                   ei+ ++ l y+ Ale Ek+++++   + +ea+++++l+ + + + r rl++
  gi|119719388|ref|YP_919883.1| 12 EIKRRKLLEYQRALEAEKAKEEQK--AREEAMRQEILRRILTpEARARLSN 60
                                   5778899**********8766654..4789999999998854044455555 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.16
                WAC_Acf1_DNA_bd 62 ealkkpvlelvqf.strsrld 81
                                   ea+++++l+ + + + r rl+
  gi|119719388|ref|YP_919883.1| 39 EAMRQEILRRILTpEARARLS 59
                                   444444444442202222232 PP

>> MAS20  MAS20 protein import receptor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   3.9   5.4e-05      0.24      18      88 ..      14      86 ..      12     109 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.4e-05
                          MAS20 18 kRrsdpefkkklrerrkkqakaakeeeeaekaekkk.kealeeakeelp.tdaeevekfFleevqlGEellaq 88
                                   kRr+  e+++ l+ ++ k++++a+ee+ +++  ++  +  +++  ++l+  ++e ve+  ++ +ql+E+ + +
  gi|119719388|ref|YP_919883.1| 14 KRRKLLEYQRALEAEKAKEEQKAREEAMRQEILRRIlTPEARARLSNLKlVKPELVEALEIQLIQLAESRSVR 86
                                   9***********9999998866655554444444435323333344455689999999999999999988776 PP

>> SurA_N  SurA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   5.3   0.00059       2.6      38      81 ..      60     103 ..      10     114 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00059
                         SurA_N  38 peavLerqvlerlilekiqlqeaektgirvddeelnqaiaeiAk 81 
                                    + + ++ +++e l ++ iql+e++ + + +dde+l+q +a++ +
  gi|119719388|ref|YP_919883.1|  60 NLKLVKPELVEALEIQLIQLAESRSVRVPIDDETLKQILARLYE 103
                                    555667799****************************9998755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1613  (0.089966); expected 358.6 (0.02)
Passed bias filter:                      651  (0.0363099); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 841.52
//
Query:       gi|119719389|ref|YP_919884.1|  [L=50]
Description: ribosomal protein L39e [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-14   53.1   7.8      2e-14   53.0   7.8    1.1  1  Ribosomal_L39  Ribosomal L39 protein


Domain annotation for each model (and alignments):
>> Ribosomal_L39  Ribosomal L39 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.0   7.8   1.1e-18     2e-14       1      41 [.       9      48 ..       9      49 .. 0.97

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 1.1e-18
                  Ribosomal_L39  1 kKlrLaKalkqNrpvPaWvrlktdrkvrynpkrRhWRrtkL 41
                                   kKlrLa a+++N +vP+Wv+ kt  kvr++p rR+WRr+ +
  gi|119719389|ref|YP_919884.1|  9 KKLRLAAAVRSNEQVPIWVISKTLGKVRRKP-RRNWRRSRM 48
                                   7******************************.******987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.44
# Mc/sec: 341.80
//
Query:       gi|119719390|ref|YP_919885.1|  [L=103]
Description: ribosomal protein L31e [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-18   67.1   0.2    1.7e-18   66.6   0.2    1.1  1  Ribosomal_L31e  Ribosomal protein L31e


Domain annotation for each model (and alignments):
>> Ribosomal_L31e  Ribosomal protein L31e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.6   0.2   9.6e-23   1.7e-18       3      76 ..      10      83 ..       9      85 .. 0.96

  Alignments for each domain:
  == domain 1  score: 66.6 bits;  conditional E-value: 9.6e-23
                 Ribosomal_L31e  3 vtreytInihkrihgvgfkkraprAlkeikkfamkemgtpdv.ridtrLnkavwakgirnvpyrirvrlsrkrne 76
                                   +tr y+In  +r++++ +kkra+ A+++i++f++++++ pd  +i ++Ln  vw+++i+++p++++v +s k ++
  gi|119719390|ref|YP_919885.1| 10 YTRTYVIN-LRRVYSAPRKKRAKVAVRAIRDFIARHLRFPDRiKISPELNLIVWSRSIEKPPRKVKVDVSFKVED 83
                                   69******.89*******************************9****************************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 762.29
//
Query:       gi|119719391|ref|YP_919886.1|  [L=223]
Description: translation initiation factor IF-6 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.6e-63  212.5   0.9    4.7e-63  212.2   0.9    1.1  1  eIF-6        eIF-6 family
  ------ inclusion threshold ------
       0.11   12.7   0.1       0.27   11.5   0.0    1.7  2  PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/bet


Domain annotation for each model (and alignments):
>> eIF-6  eIF-6 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  212.2   0.9   5.2e-67   4.7e-63       2     197 .]       7     203 ..       6     203 .. 0.98

  Alignments for each domain:
  == domain 1  score: 212.2 bits;  conditional E-value: 5.2e-67
                                    E-BTTB--HHHH-EE-SSEEEE-TTS-HHHHHHHHHHHT-EEEE--BTTBS-HHHH-EE-SSEEEEETT--HHHHHHHHH CS
                          eIF-6   2 lsiegsseiGvfarltnkyalvpegveeefvkaieeeLkvevvettiagsrlvGslvvgNsngllvpstvtdeeleklke 81 
                                    +s++g+++iGv++++++++al+p +++e+  ++i+e+L+v+++++++ag+rlvG++++gN+ngl+vp+ + d+ele+lk+
  gi|119719391|ref|YP_919886.1|   7 ISLYGTPNIGVYIFANDRFALIPYDAPEKLDRKIAENLSVDAFRVSVAGTRLVGIFLAGNNNGLVVPRVILDSELEHLKS 86 
                                    6899**************************************************************************** PP

                                    HHH---EEE-.-SS--HHHHEEE-SSEEEE-GGGGG.GHHHHHHHHTSEEEE--BTTBS-TTTSEEE-SSEEEE-TT--H CS
                          eIF-6  82 slkleverle.ekltAlGNvilaNDkvAlvhpdlsketveiiadvLgvevvrgtiagiktvGsaavvtnkgllvhpkate 160
                                     l++++ +le  + t +GN++laND++++ ++ l k++v+ iad+Lgve+++++i++++ vGs++v+tn+g+ + p ate
  gi|119719391|ref|YP_919886.1|  87 LLDVNIVVLEdVRETGIGNLVLANDNGCVASQILPKSAVDRIADALGVECIQMSIGDVPFVGSLSVATNRGVALPPLATE 166
                                    ******99983599****************************************************************** PP

                                    HHHHHHHHHHT-SEEE--BTTTBS-GGGTEEE-SS-E CS
                          eIF-6 161 eeleeleellkveveagTvNrGsklvgsglvaNdkga 197
                                    ee++ +ee lkv++++ TvNrG+ ++++glvaN+kga
  gi|119719391|ref|YP_919886.1| 167 EEIKSVEEALKVKANVLTVNRGKMFLRTGLVANSKGA 203
                                    ***********************************96 PP

>> PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0     3e-05      0.27      21      56 ..     112     147 ..      91     160 .. 0.80
   2 ?   -2.8   0.0      0.79     7e+03      44      73 ..     181     212 ..     169     216 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3e-05
                                    TCEEEEETTS-THHHHHHHHTT-EEEEESSSCHHHH CS
                    PGM_PMM_III  21 gagvvktvmtslalervakklgiklvetkvGdkyvl 56 
                                    ++ v++++   +a++r+a++lg++++++ +Gd  ++
  gi|119719391|ref|YP_919886.1| 112 NGCVASQILPKSAVDRIADALGVECIQMSIGDVPFV 147
                                    33699999999********************97665 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.79
                                    EEEEESSSCHHHHHHHHHTT..ECEEEETTCE CS
                    PGM_PMM_III  44 klvetkvGdkyvleemkeeg..avlGgEeSgh 73 
                                    +++ ++ G  ++   + +++  a++G    gh
  gi|119719391|ref|YP_919886.1| 181 NVLTVNRGKMFLRTGLVANSkgALVGEDTTGH 212
                                    55566666666666555542224444333344 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1442.65
//
Query:       gi|119719392|ref|YP_919887.1|  [L=567]
Description: radical SAM domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.7e-14   54.6   0.0    3.2e-14   53.6   0.0    1.5  1  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.6   0.0   1.8e-18   3.2e-14       9     166 ..     205     391 ..     193     392 .. 0.85

  Alignments for each domain:
  == domain 1  score: 53.6 bits;  conditional E-value: 1.8e-18
                                    S--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEE...............SSTGGGSTTHHHHHHHHHHT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...............xxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM   9 lrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilg...............ggepllypdfvellerlakl 73 
                                    ++CsfC+ p    r gr+ ++   +i eev++l +e gv+ + lg                  p  +p  +e+l r ++l
  gi|119719392|ref|YP_919887.1| 205 GGCSFCIEP----RLGRVVFREAKSIGEEVRAL-YELGVRAFRLGrqadflaykakgvneVEFPEPDPSSIEELMRTVRL 279
                                    68*******....69******************.8**********97777777777777766666668888888888888 PP

                                    C...CCTEEEEEEECSSCHG.....HHHHHHHHHTT..-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSE CS
                                    x...xxxxxxxxxxxxxxxx.....xxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  74 a...vpgiritvetngtlpd.....eeklerllelg..vdrvslgleaaddekvlklmnrghtfeevlealeklreagik 143
                                    a    + i+i  + ++t        +e l+ +++++   d+ ++gle+ad+  v k +n g++ e vlea+++ +e+g +
  gi|119719392|ref|YP_919887.1| 280 AapsAETIHIDNVNPATIYIhkekaREALKSIVKYHtpGDVAAFGLESADPV-VVKQNNLGNDAEGVLEAIKIVNEVGAR 358
                                    8898555555555555543355688**************************9.88888899*****************88 PP

                                    T..........EEEEEEEBTTTSHHHHHHHHHH CS
                                    x..........xxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM 144 r..........vvdrivglpGendeeleellel 166
                                    r           v++++glpGe+ +++++  e+
  gi|119719392|ref|YP_919887.1| 359 RgwngspellpGVNFVLGLPGETAKTYRANKEF 391
                                    88888889999*************998876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (567 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 3947.82
//
Query:       gi|119719393|ref|YP_919888.1|  [L=312]
Description: thiamine-phosphate kinase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-17   63.1   0.0    5.8e-17   62.1   0.0    1.5  1  AIRS      AIR synthase related protein, N-terminal domain
     0.0024   18.0   0.1      0.004   17.3   0.1    1.5  1  AIRS_C    AIR synthase related protein, C-terminal domain


Domain annotation for each model (and alignments):
>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.1   0.0   6.4e-21   5.8e-17       1      93 [.      22     133 ..      22     134 .. 0.87

  Alignments for each domain:
  == domain 1  score: 62.1 bits;  conditional E-value: 6.4e-21
                                    SSSEE........EEEEEEEE.EECCTCCCC...HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC......HHHHHHHHHH CS
                           AIRS   1 dDaav........vvttdshnrpvlvepvhf...iGakavavnlsDlaamGArPlalllslalp......wleevvrgla 63 
                                    dDaav        vv +ds+++ + + p+ +   +G++a+ + +sD+++ GA+Pl++l+sl +p       lee++rgl 
  gi|119719393|ref|YP_919888.1|  22 DDAAVlsleetslVVNVDSFESGIHLYPFLPpriAGRRAAVGSISDVLVKGAKPLGILVSLRVPstadlgFLEEFYRGLL 101
                                    8999445555555999997776666666555999********************************************** PP

                                    HHHHHTT-EEEEEEEEEESS..EEEEEEEEEE CS
                           AIRS  64 eaaeelgvplvgGdtsfsne..ptisvtavGl 93 
                                    ea+ ++g+ ++gGdt +s+   + + v+a+G+
  gi|119719393|ref|YP_919888.1| 102 EAGTRFGARILGGDTDVSSTcyLRVDVVAIGV 133
                                    *****************977688889999986 PP

>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   4.5e-07     0.004      58     152 ..     198     290 ..     145     294 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.5e-07
                                    HTTECEEEE--TTHHHHHHHHHHHTTTEEEEEECGTHHHHHHHH......HHHHHHHCSTTTEEEEEEEHGGHHHHHHHH CS
                         AIRS_C  58 kglvkaahDvTgGGLlgalaemapasgvgaeidldkvpifdele......splemllsensGrllvavppeeadavlail 131
                                    k+l ++a D ++ GL+ +l  +a+ sgvg+++++  v ++++ +       ++ ++ s +    ++++p+e++    +++
  gi|119719393|ref|YP_919888.1| 198 KELLTSAIDNSD-GLALSLYYLAESSGVGIVVEELPVHAVAKEClprerlVDAVLYASGEDYNFIFTFPEEAE----EEV 272
                                    688999999999.7*********************99999998888887666666666888888888888888....555 PP

                                    HHTTCCCEEEEEEEEESSSEE CS
                         AIRS_C 132 eeeglpeaavIGevtakeels 152
                                    ++ g   a++IG+vt++e++ 
  gi|119719393|ref|YP_919888.1| 273 RKTG---ATIIGRVTEGEGVF 290
                                    6665...89*******99775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 2062.35
//
Query:       gi|119719394|ref|YP_919889.1|  [L=81]
Description: hypothetical protein Tpen_0477 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0036   17.3   0.8     0.0041   17.1   0.8    1.1  1  Colicin_V  Colicin V production protein
  ------ inclusion threshold ------
      0.012   15.5   0.5      0.013   15.4   0.5    1.1  1  DctQ       Tripartite ATP-independent periplasmic transporter
        3.9    7.2   6.3        5.9    6.6   6.3    1.3  1  SPC25      Microsomal signal peptidase 25 kDa subunit (SPC25)


Domain annotation for each model (and alignments):
>> Colicin_V  Colicin V production protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.8   6.8e-07    0.0041      23      77 ..      10      65 ..       8      79 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 6.8e-07
                      Colicin_V 23 revlsllgwvvafvvasllypslaellae.......lilspalaaiiaflllfllvllivsl 77
                                   r vl++l +v+a+v+a++ y++la +l+        l      aa   ++ +++ +++i++ 
  gi|119719394|ref|YP_919889.1| 10 RAVLGVLTVVLAVVFAYYSYKTLAYILNWekppgdpL------AAYTTYVQVMIYSIFILTS 65
                                   679**************************86555443......4444444444433333332 PP

>> DctQ  Tripartite ATP-independent periplasmic transporters, DctQ component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.5   2.2e-06     0.013      59     129 ..       3      75 ..       1      78 [. 0.71

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.2e-06
                           DctQ  59 prvrrlleliadllallfaavliwagwlevaaalfeettpvlg..lplwwvylvlpigaallalvalarllrl 129
                                     r r   +++  +l++++a+v++++++   a++l++e+ p       + +v++++   ++l  +++l +++ +
  gi|119719394|ref|YP_919889.1|   3 DRKRFTSRAVLGVLTVVLAVVFAYYSYKTLAYILNWEKPPGDPlaAYTTYVQVMIYSIFILTSVFLLHETFSS 75 
                                    5667777888889**************5566666666666555125566666777777788888888877765 PP

>> SPC25  Microsomal signal peptidase 25 kDa subunit (SPC25)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   6.3   0.00099       5.9      29      77 ..      10      71 ..       3      79 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.00099
                          SPC25 29 rLalGylavaiaavaflydykv.....eFee......skpvlaiavvlY..filsgiltlys 77
                                   r +lG+l v++a+v  +y+yk+      +e+        +++ + v++Y  fil++++ l++
  gi|119719394|ref|YP_919889.1| 10 RAVLGVLTVVLAVVFAYYSYKTlayilNWEKppgdplAAYTTYVQVMIYsiFILTSVFLLHE 71
                                   889******************99889988882222222344444445553344555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1013  (0.0565006); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.30s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 533.62
//
Query:       gi|119719395|ref|YP_919890.1|  [L=588]
Description: DEAD_2 domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.5e-21   76.1   0.0    8.3e-21   74.9   0.0    1.6  2  Helicase_C_2  Helicase C-terminal domain
    1.5e-14   54.0   0.0    2.3e-14   53.4   0.0    1.3  1  DEAD_2        DEAD_2
      3e-08   33.6   0.0      5e-08   32.9   0.0    1.3  1  HBB           Helical and beta-bridge domain
    0.00091   19.0   0.1       0.12   12.2   0.1    2.5  2  DEAD          DEAD/DEAH box helicase
  ------ inclusion threshold ------
      0.036   14.1   0.1       0.68    9.9   0.1    2.2  1  ResIII        Type III restriction enzyme, res subunit
      0.096   12.4   0.1          2    8.1   0.0    2.7  2  GntR          Bacterial regulatory proteins, gntR family


Domain annotation for each model (and alignments):
>> Helicase_C_2  Helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       3.3   9.9e+03      85     115 ..       5      35 ..       3      43 .. 0.77
   2 !   74.9   0.0   2.8e-24   8.3e-21      10     157 ..     425     568 ..     419     577 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 3.3
                   Helicase_C_2  85 lraviivglPfpnpkdpeveakreyldekgk 115
                                    lra +   +P++ + + ++e+  e+ +++ +
  gi|119719395|ref|YP_919890.1|   5 LRAQVEALIPYKTVRKGQLELALEVAKAYAE 35 
                                    6666667799999999999998888877654 PP

  == domain 2  score: 74.9 bits;  conditional E-value: 2.8e-24
                   Helicase_C_2  10 ggvlvffpSyklleevverlkeeleskkieifveekeesrekvleeykekkkkgaillavcrGklsEGidfs...ddllr 86 
                                     ++l+ fpSy+++  v+ +++++      +++ e+ +++  ++l ++ e   ++a+ll v+rGk+ EG++f+     l+ 
  gi|119719395|ref|YP_919890.1| 425 RRALAIFPSYSFMMGVYPYIRSK------PVIIERRDSTIGSMLGKVLE--LEKALLLVVARGKFAEGVEFTvlgKSLID 496
                                    57899****************86......578877999***********..********************988789999 PP

                   Helicase_C_2  87 aviivglPfpnpkdpeveakreyldekgk..knsgkewylpealravnQaiGRliRhkdDygaivllDeRfak 157
                                     ++i glP p+p + e+e   e l+e+ +  + ++k++yl++a+ +v Q+iGR +R+++D+  +++lDeR+  
  gi|119719395|ref|YP_919890.1| 497 TIVIAGLPVPEP-SVENEKLYELLQERLGdrDLAWKYVYLYPAFMQVVQGIGRGVRSEKDKVKVFILDERMIG 568
                                    ************.67778888888887774445699**********************************865 PP

>> DEAD_2  DEAD_2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.4   0.0   7.6e-18   2.3e-14       1     175 [.      67     228 ..      67     229 .. 0.86

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 7.6e-18
                                    EEESSHHHHHHHHHHHHHHHHHCHHHS---EEEE--CCCC-SCHHCCCHHCCCCHHHHHHHHHCCHHCCHTTTTTT-SCC CS
                         DEAD_2   1 ycsRThsqleqvvkelkklesykkkkekvkvviLgSRknlCineevkkekkekavneaCkelkkkkaeekeekCsffenl 80 
                                    y +R +sq +  ++e+k+l +      +v +v+L  +kn+C+   ++     ++  ++C+ ++         +C++ +++
  gi|119719395|ref|YP_919890.1|  67 YLARSKSQFQAPLREVKRLLER---GISVPTVVLVNKKNYCLLRGALPLD-YEEFLHFCRVKRFTG------ACPYSSEF 136
                                    889****************753...579***************9999965.777889**9888777......6***9888 PP

                                    CCHHHHHHHHHHC---CHHHHHHHHHCT--HHHHHHHHHCCTSEEEEEHHHHTSCCCHHHHH...T..GCGCEEEECTCC CS
                         DEAD_2  81 eelkklkkllleevvdiedlvelgeklklCPYylsrelledadiiilpYqyLldekireslk...gislknsivilDEAh 157
                                    e+           +v+     +lg kl++CP+ l+ ++l +a +++++Y y++ e  r+ l    g  +   ++++DEAh
  gi|119719395|ref|YP_919890.1| 137 ED------AEIPVLVTPKSARSLGAKLGVCPFELAWKALRKARLVVASYPYVFREDLRRLLVeslGTPMDVLMLVVDEAH 210
                                    43......345677788888999***********************************99876555556667789***** PP

                                    CHHHHHHHCC-EEEECHH CS
                         DEAD_2 158 Niedvceeaasveisees 175
                                    N+ d+++e++ + +s+ +
  gi|119719395|ref|YP_919890.1| 211 NLPDHIAESTAIAVSDAT 228
                                    ***********9999876 PP

>> HBB  Helical and beta-bridge domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.0   1.7e-11     5e-08      96     189 ..     305     401 ..     276     402 .. 0.87

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 1.7e-11
                                    HHHHHHHTS.TTTEEEEEE.STT.EECCCCS-TCCHHH.HHHHCHCCCCCCTS-SSHHHHHHHHT.....EEE.S..S.. CS
                            HBB  96 efllawlssdeedYvrlvskeegesLeavcldPskalr.flkerlssllmsgtltpleeysdiiGle.aklkkfpspf.p 172
                                     f +a  ++ +e  v  vs++ + sL++v + P k+ r +  +++s++lms tl p+e y +++G++  +++    pf  
  gi|119719395|ref|YP_919890.1| 305 AFAEALRRASHEYLVTAVSSDGSVSLKLVLINPGKVSReVFPKVRSAVLMSSTLMPAEYYVAVLGFPgERVREVSYPFvW 384
                                    45556666666677889999999************98637799*************************999999998735 PP

                                    GGHCCCCCCCCCSHTCC CS
                            HBB 173 kEnlivlfatdVsTkyk 189
                                    +En  v+ ++ +s++y 
  gi|119719395|ref|YP_919890.1| 385 SENVDVVIVKGISSRYV 401
                                    9*************995 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.1   3.9e-05      0.12      12      76 ..      34      92 ..      24     106 .. 0.79
   2 ?    4.1   0.0     0.012        34     120     136 ..     199     215 ..     158     234 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.9e-05
                                   HTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTT.STS CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx RF
                           DEAD 12 lgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkky.idl 76
                                    ++  +l++ +TG GKT+a l  +l        + +pk+++++ +++  +  l+++k++++  i++
  gi|119719395|ref|YP_919890.1| 34 AEKAILLARYPTGIGKTAAVLAGAL-------ASGAPKVVYLARSKSQFQAPLREVKRLLERgISV 92
                                   4555678999***********9999.......57899******99999999999999999864554 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.012
                                    TTEEEEEEETHHHHHHT CS
                                    xxxxxxxxxxxxxxxxx RF
                           DEAD 120 sqvrflVlDEadrlldq 136
                                     +v +lV+DEa++l d 
  gi|119719395|ref|YP_919890.1| 199 MDVLMLVVDEAHNLPDH 215
                                    56889********9876 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   0.00023      0.68       3      75 ..      17     115 ..      15     239 .. 0.49

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00023
                                    EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHG........ CS
                         ResIII   3 elreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleef........ 74 
                                    ++r+ Q e   ++++++   ++  +l   +TG GKT     l+ +l++ +   k++ l+ +ks  +  l+e+        
  gi|119719395|ref|YP_919890.1|  17 TVRKGQLELALEVAKAY--AEKAILLARYPTGIGKTAAV--LAGALASGA--PKVVYLARSKSQFQAPLREVkrllergi 90 
                                    57899999999999888..477777899*******9655..444444432..3777777777777666666633333333 PP

                                    ........................G CS
                         ResIII  75 ........................k 75 
                                                            +
  gi|119719395|ref|YP_919890.1|  91 svptvvlvnkknycllrgalpldyE 115
                                    3333333333333333333333331 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0   0.00067         2      32      53 ..     220     241 ..     212     243 .. 0.90
   2 ?    0.7   0.0      0.14     4e+02      43      61 ..     308     326 ..     306     328 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00067
                                    HHHTS-HHHHHHHHHHHHHTTS CS
                           GntR  32 aefgVsrttvReALrrLeaegl 53 
                                    ++++Vs  t+R+A+++L a+g+
  gi|119719395|ref|YP_919890.1| 220 TAIAVSDATLRRAISELRAAGI 241
                                    5789**************9986 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.14
                                    HHHHHHHHTTSEEEETTCE CS
                           GntR  43 eALrrLeaeglverrqgrG 61 
                                    eALrr + e lv++ +  G
  gi|119719395|ref|YP_919890.1| 308 EALRRASHEYLVTAVSSDG 326
                                    9************987666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (588 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.47
# Mc/sec: 3775.86
//
Query:       gi|119719396|ref|YP_919891.1|  [L=202]
Description: sugar isomerase (SIS) [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.1e-17   62.2   0.6    7.4e-17   61.4   0.4    1.5  2  SIS        SIS domain
    2.7e-11   43.7   5.1      2e-06   27.9   1.9    2.3  2  SIS_2      SIS domain
     0.0088   15.9   2.0       0.09   12.6   0.1    2.2  2  PRMT5      PRMT5 arginine-N-methyltransferase
  ------ inclusion threshold ------
      0.073   12.8   0.1       0.14   11.9   0.1    1.4  1  PGM_PMM_I  Phosphoglucomutase/phosphomannomutase, alpha/beta/


Domain annotation for each model (and alignments):
>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.4   0.4   1.6e-20   7.4e-17       2     110 ..      39     141 ..      38     156 .. 0.92
   2 ?   -2.1   0.0      0.72   3.2e+03      46      61 ..     160     175 ..     143     176 .. 0.78

  Alignments for each domain:
  == domain 1  score: 61.4 bits;  conditional E-value: 1.6e-20
                                    HCTSSEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHHTTS CS
                            SIS   2 LakakriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelakerga 81 
                                    La + +i+v+GaG+s+ +ak +a+ l+++g++v++v ++ +      + i+e+d++i++s sg t  ++ +a  ak+ +a
  gi|119719396|ref|YP_919891.1|  39 LATKSKILVVGAGRSGLVAKAFAMRLMHLGFNVYVVGETIT------PSISEGDVLIAVSGSGSTQVVLSVASAAKRAKA 112
                                    77889**********************************99......88******************************* PP

                                    EEEEEESSTTSHHHHHSSEEEEEEEECHC CS
                            SIS  82 kiiaITdskgsplareadlalyinaepet 110
                                     ++aIT+ ++spl + +d+++ ++   ++
  gi|119719396|ref|YP_919891.1| 113 VVVAITSFAESPLGKISDHIVVVPGRTKV 141
                                    *******************9998877776 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.72
                                    TGGGG-STTCEEEEEE CS
                            SIS  46 gvlalideddlvilis 61 
                                     +l+++ ed+++++++
  gi|119719396|ref|YP_919891.1| 160 APLGTLFEDTVMVFFD 175
                                    4788999999999986 PP

>> SIS_2  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   9.4e-07    0.0042       8      59 ..      14      66 ..       9      76 .. 0.85
   2 !   27.9   1.9   4.4e-10     2e-06      91     138 .]      74     119 ..      69     119 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 9.4e-07
                                   HHHHHHHHH.SHHHHHHHHHHHHHHHHTT--EEEEESGGGHHHHHHTSSSTT- CS
                          SIS_2  8 eilerivet.qaeaiekaaeliadslenggkvlvfGsGhSaalaeelaaragg 59
                                   +++e+++ + ++e++++  ++++++l+++ k+lv G+G S + a+ +a r+  
  gi|119719396|ref|YP_919891.1| 14 SYIEKVAGElDKESVNRFLKILTSALATKSKILVVGAGRSGLVAKAFAMRLMH 66
                                   55666654438999***********************************9875 PP

  == domain 2  score: 27.9 bits;  conditional E-value: 4.4e-10
                                    HHHHHHHHTT--TT-EEEEE-SS--SHHHHHHHHHHHHHT-EEEEEE- CS
                          SIS_2  91 yakqilrlvrlkpgDvLlviSnsGnnavvveaaeaakergmkviAlts 138
                                    ++++i  +  +++gDvL+ +S sG+ +vv+ +a aak+  + v+A+ts
  gi|119719396|ref|YP_919891.1|  74 VGETITPS--ISEGDVLIAVSGSGSTQVVLSVASAAKRAKAVVVAITS 119
                                    55666666..99***********************************8 PP

>> PRMT5  PRMT5 arginine-N-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.1     2e-05      0.09      62      86 ..      33      63 ..       6      77 .. 0.68
   2 ?    2.9   0.3     0.019        86      63      96 ..      84     117 ..      72     124 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2e-05
                                   C.......-EEEEEEES-TTSHHHHHHHHHH CS
                          PRMT5 62 s......ekklvilvvGaGRGplvdralkal 86
                                   +       +k  ilvvGaGR +lv +a+ + 
  gi|119719396|ref|YP_919891.1| 33 KiltsalATKSKILVVGAGRSGLVAKAFAMR 63
                                   034444456779**************99765 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.019
                                    .-EEEEEEES-TTSHHHHHHHHHHHHHCCCEEEE CS
                          PRMT5  63 ekklvilvvGaGRGplvdralkaleetkvtkvki 96 
                                    e ++ i+v G+G   +v ++ +a++++k   v i
  gi|119719396|ref|YP_919891.1|  84 EGDVLIAVSGSGSTQVVLSVASAAKRAKAVVVAI 117
                                    57899**********9999999999988555554 PP

>> PGM_PMM_I  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   3.1e-05      0.14      14      83 ..      20      83 ..      13      87 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.1e-05
                                   CHCTBSCCHHHHHHHHHHHHCHHCSTS-EEEEEE-S-TTHHHHHHHHHHHHHCCT-CEEEEEEB-HHHHH CS
                      PGM_PMM_I 14 gegeltpelveklgqaiaeylkaeakkkkvvvGrDtRvssrelaealaaglaanGvevillgllptPavs 83
                                     gel++e v ++ + + ++l+ +   k +vvG  +R  s  +a+a+a  l++ G++v+++g + tP +s
  gi|119719396|ref|YP_919891.1| 20 A-GELDKESVNRFLKILTSALATK--SKILVVG-AGR--SGLVAKAFAMRLMHLGFNVYVVGETITPSIS 83
                                   3.6899999999999999999984..5555555.555..89*********************99999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       769  (0.0428914); expected 358.6 (0.02)
Passed bias filter:                      584  (0.0325729); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1369.70
//
Query:       gi|119719397|ref|YP_919892.1|  [L=75]
Description: hypothetical protein Tpen_0480 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.013   15.2   0.1      0.014   15.0   0.1    1.0  1  DSHCT     DSHCT (NUC185) domain


Domain annotation for each model (and alignments):
>> DSHCT  DSHCT (NUC185) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1     8e-07     0.014     106     157 ..      18      69 ..      12      71 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 8e-07
                          DSHCT 106 faellektdldeGdiVRllrrleellrqlakaakvigneeLkkkaeeaieli 157
                                    +a++l+  +l+e  +V +l  +ee+l  +++a++v ++eeL++++ee +e +
  gi|119719397|ref|YP_919892.1|  18 LASTLRRDELYEARLVEALDAIEEFLASVRSAPQVEEDEELARELEEGVEEL 69 
                                    566777789**************************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       776  (0.0432818); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 549.29
//
Query:       gi|119719398|ref|YP_919893.1|  [L=474]
Description: hypothetical protein Tpen_0481 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.12   12.4   0.0       0.75    9.8   0.0    2.2  1  IMS       impB/mucB/samB family


Domain annotation for each model (and alignments):
>> IMS  impB/mucB/samB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   4.2e-05      0.75     114     148 ..     229     335 ..      26     336 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 4.2e-05
                                    S........................................................................HHHHHHH CS
                            IMS 114 e........................................................................gaalake 121
                                    +                                                                        + ++ak 
  gi|119719398|ref|YP_919893.1| 229 RnapkewrlrkeekqsvilseikaanegeidifravriatyyaadgkypgpntakrllefgvgnepywirvegAVRIAKL 308
                                    055555555555555566666666666666666666666666666677777777777777777777777777789***** PP

                                    HHHHHHHHH---EEEEEESSHHHHHHH CS
                            IMS 122 lrkaikeelgltvsiGiasnkllAKla 148
                                    l +++ + l + +s+G+ + ++lA+la
  gi|119719398|ref|YP_919893.1| 309 LHEEVPQLLAFMCSAGCKKARYLARLA 335
                                    *************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (474 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       596  (0.0332422); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 2813.85
//
Query:       gi|119719399|ref|YP_919894.1|  [L=228]
Description: hypothetical protein Tpen_0482 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.042   13.8   0.0      0.082   12.9   0.0    1.4  1  Hjc       Archaeal holliday junction resolvase (hjc)
      0.078   13.5   0.0       0.12   12.8   0.0    1.4  1  NERD      Nuclease-related domain


Domain annotation for each model (and alignments):
>> Hjc  Archaeal holliday junction resolvase (hjc)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   9.1e-06     0.082      29      87 ..     113     174 ..     107     180 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.1e-06
                                    SS-SEEEEETTEEEEEEEEEESSSEE.EE...EHHHHHHHHHHHHHHTCEEEEEEEETTTEEE CS
                            Hjc  29 plpDviAirgdvvlviEvKsskkeri.yl...kkeqvekllefarkaggelllavklqgkewk 87 
                                      +D+iA   + vlv+ +K  ++ ++  l    k  +e+ l +a+k +  + ++++l gk+ k
  gi|119719399|ref|YP_919894.1| 113 FEVDLIAASDNLVLVVDCKRWRRAPPsSLkkaAKAHLERCLALADKMKSGADIGIRL-GKQAK 174
                                    568****************999885514555577889999****************8.44444 PP

>> NERD  Nuclease-related domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.4e-05      0.12      12      55 ..      91     134 ..      80     159 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.4e-05
                           NERD  12 eLkelkedeylvlhdvrlrpg.tg.eiDhlvispkgifviEvKnws 55 
                                    +L+  ++ + +  +++r+++  ++ e+D+++ s + ++v+++K w+
  gi|119719399|ref|YP_919894.1|  91 YLA--ESFGLRTKRNLRFKNLgRRfEVDLIAASDNLVLVVDCKRWR 134
                                    555..56677777889995555337********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1508.52
//
Query:       gi|119719400|ref|YP_919895.1|  [L=141]
Description: 50S ribosomal protein L14P [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.9e-35  120.3   0.0    5.9e-35  120.0   0.0    1.0  1  Ribosomal_L14  Ribosomal protein L14p/L23e
  ------ inclusion threshold ------
      0.098   13.0   0.0       0.19   12.1   0.0    1.5  1  PAS_3          PAS fold


Domain annotation for each model (and alignments):
>> Ribosomal_L14  Ribosomal protein L14p/L23e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.0   0.0   6.6e-39   5.9e-35       4     121 ..      23     140 ..      21     141 .] 0.95

  Alignments for each domain:
  == domain 1  score: 120.0 bits;  conditional E-value: 6.6e-39
                                    SS-EEE--SSSSBSEEEEEEETT-.....---EE-SSSEEEEEESSS-T...TTSSCEEEEEEEE-SS-EE-TTS-EEEE CS
                  Ribosomal_L14   4 lktrlkvaDNsgakevecikvlggk....krkaasvGdiivvsvkkakpkgkvkkgdvvkavvvrtkkevrrkdGsvirf 79 
                                    +++ +kvaDNsga  +++i v ++k    + + a vGdi++vs++ +kp   + +++v++a+v+r+++++rr+dGs+i f
  gi|119719400|ref|YP_919895.1|  23 MESLVKVADNSGATLAKVIGVPHYKavwrRIPGAAVGDIVIVSIRAGKP---ELRKQVMRAIVIRQRRPYRRPDGSWIAF 99 
                                    7999*******************99777455******************...99************************** PP

                                    SS-EEEEB-TTS-BSS-.B-SBEEHHHHHH.-HHHHHTBSBE CS
                  Ribosomal_L14  80 ddnaaVllnkkgeplGtrifgpvarelrekkflkivslApev 121
                                    +dna+V+++ +gep+Gt+i gp a+e++e+ ++k+ ++A+ +
  gi|119719400|ref|YP_919895.1| 100 EDNAVVIITPEGEPKGTEIRGPLAKEAAER-WPKLSAMASII 140
                                    *****************************9.********977 PP

>> PAS_3  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.1e-05      0.19      58      83 ..      89     114 ..      69     117 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.1e-05
                          PAS_3  58 irrkdGeyrwveararvirdengkpv 83 
                                    +rr+dG+++ +e+ a+vi   +g+p 
  gi|119719400|ref|YP_919895.1|  89 YRRPDGSWIAFEDNAVVIITPEGEPK 114
                                    59****************99999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       249  (0.0138881); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1022.67
//
Query:       gi|119719401|ref|YP_919896.1|  [L=111]
Description: ribosomal protein S17 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.5e-17   61.9   4.1    5.7e-17   61.6   4.1    1.1  1  Ribosomal_S17  Ribosomal protein S17


Domain annotation for each model (and alignments):
>> Ribosomal_S17  Ribosomal protein S17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.6   4.1   3.2e-21   5.7e-17       3      67 ..      41     106 ..      40     107 .. 0.97

  Alignments for each domain:
  == domain 1  score: 61.6 bits;  conditional E-value: 3.2e-21
                                    EEE--STTEEEEEEEEEEEETTTTEEEEEEEEEEEE-TTTS.--TT-EEEEEEECECSSSEEEEEE CS
                  Ribosomal_S17   3 VvsdkmdkTvvVrverlvkhpkykkyvkrrkkylahdenns.vkvGDiVrieecrPlSktkrfvvv 67 
                                    V + km+  +v  +e+l++++kyk+y+ rrkk ++  ++++ vk+GD V ++e+rPl+k+++fvv+
  gi|119719401|ref|YP_919896.1|  41 VEKVKMHNVAVAVHEYLYYNEKYKRYEVRRKKKHVRVPPCIpVKPGDEVIVAETRPLAKSVSFVVI 106
                                    7788************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.44
# Mc/sec: 765.20
//
Query:       gi|119719402|ref|YP_919897.1|  [L=94]
Description: ribonuclease P, Rpp29 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-19   68.5   0.0    3.8e-19   68.4   0.0    1.0  1  UPF0086   Domain of unknown function UPF0086


Domain annotation for each model (and alignments):
>> UPF0086  Domain of unknown function UPF0086
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.4   0.0   2.1e-23   3.8e-19       2      84 .]       7      89 ..       6      89 .. 0.98

  Alignments for each domain:
  == domain 1  score: 68.4 bits;  conditional E-value: 2.1e-23
                                   HHCCSXXSS-EEEEEECSSTTTTTEEEEEEEEETTEEEEEECTTEEEEEESTTCEEEEEE.TTEEEEEECCCCSSXHHHHHC CS
                        UPF0086  2 kLlkadlhGaeveVvrsknpslvgikGiVvkEtkntlkivtkksrvktvpKegsvFefevkdvlevevdGsqlryrpadRae 83
                                   ++l+++l+G+e  Vv+sknps+vgi G++++Et +t++i  +    k++ K++ v+++++ d  e+ vdG  l  rp++R +
  gi|119719402|ref|YP_919897.1|  7 NILRHELIGLEACVVKSKNPSQVGICGLILDETYKTIVIGVPGGPKKRIFKAQVVLRIKLPDGKELLVDGAFLVGRPEERLK 88
                                   89**********************************************************9999****************98 PP

                                   H CS
                        UPF0086 84 r 84
                                   r
  gi|119719402|ref|YP_919897.1| 89 R 89
                                   7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       220  (0.0122706); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.44
# Mc/sec: 641.67
//
Query:       gi|119719403|ref|YP_919898.1|  [L=84]
Description: ribosomal protein L29 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      4e-17   61.9   8.8    5.4e-17   61.5   8.8    1.1  1  Ribosomal_L29   Ribosomal L29 protein
     0.0016   18.7   6.5     0.0018   18.5   6.5    1.2  1  DUF4355         Domain of unknown function (DUF4355)
  ------ inclusion threshold ------
      0.023   14.7   3.2      0.023   14.7   3.2    2.2  2  DUF1192         Protein of unknown function (DUF1192)
       0.04   14.4   4.1      0.051   14.0   4.1    1.3  1  Enkurin         Calmodulin-binding
      0.079   13.2   3.6        0.1   12.9   3.6    1.1  1  DUF29           Domain of unknown function DUF29
       0.17   11.6   0.7       0.21   11.4   0.7    1.3  1  DUF2299         Uncharacterized conserved protein (DUF2299)
       0.51    9.9   5.3       0.55    9.7   5.3    1.1  1  Vps5            Vps5 C terminal like
        1.7    9.3   4.1        2.9    8.5   3.8    1.6  1  Arg_decarbox_C  Arginine decarboxylase C-terminal helical ext


Domain annotation for each model (and alignments):
>> Ribosomal_L29  Ribosomal L29 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.5   8.8   2.4e-20   5.4e-17       2      56 ..      10      64 ..       9      64 .. 0.98

  Alignments for each domain:
  == domain 1  score: 61.5 bits;  conditional E-value: 2.4e-20
                                   HHHHS-HHHHHHHHHHHHHHHHHHHHHHHHTSSS-CHHHHHHHHHHHHHHHHHHH CS
                  Ribosomal_L29  2 elrelsdeeLkeklkelkkeLfnLrfqkatgqlenpsrirkvRkdIARikTvlre 56
                                   elr++s ee +++l+el+ eL +L+ q+  g+len + irk++++IARi+T+ +e
  gi|119719403|ref|YP_919898.1| 10 ELRKMSREERQKRLQELRGELARLKAQAHRGSLENVASIRKIKREIARILTIENE 64
                                   9****************************************************98 PP

>> DUF4355  Domain of unknown function (DUF4355)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   6.5   7.9e-07    0.0018      32      75 ..       4      46 ..       1      69 [. 0.88

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 7.9e-07
                        DUF4355 32 ikkeakklakmnaeekaeyeleklqkeleelkaelarkelkaea 75
                                   + k+a++l km++ee+++  l++l+ el+ lka++ r  l++ a
  gi|119719403|ref|YP_919898.1|  4 MAKQAEELRKMSREERQK-RLQELRGELARLKAQAHRGSLENVA 46
                                   5689**************.*****************99988755 PP

>> DUF1192  Protein of unknown function (DUF1192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   3.2     1e-05     0.023      11      45 ..       5      39 ..       1      47 [. 0.87
   2 ?    1.6   3.5      0.13     3e+02      29      46 ..      48      68 ..      41      74 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1e-05
                        DUF1192 11 heigqDLslLSveELeerIalLeaEIaRleaaiak 45
                                   + + ++L ++S eE ++r ++L+ E aRl+a+  +
  gi|119719403|ref|YP_919898.1|  5 AKQAEELRKMSREERQKRLQELRGELARLKAQAHR 39
                                   56789*************************99765 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.13
                        DUF1192 29 IalLeaEIaRl...eaaiakk 46
                                   I + + EIaR+   e+++++k
  gi|119719403|ref|YP_919898.1| 48 IRKIKREIARIltiENELRRK 68
                                   88999*****72225555555 PP

>> Enkurin  Calmodulin-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   4.1   2.3e-05     0.051      29      76 ..       5      53 ..       1      68 [. 0.80

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.3e-05
                        Enkurin 29 keappgmrllseeerqellegLkkkweelnkeyqslpl.lidtlskrqr 76
                                   +++ +++r +s+eerq+ l++L+ ++ +l+ + ++ +l ++ +++k +r
  gi|119719403|ref|YP_919898.1|  5 AKQAEELRKMSREERQKRLQELRGELARLKAQAHRGSLeNVASIRKIKR 53
                                   333579**************************99999856777777665 PP

>> DUF29  Domain of unknown function DUF29
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   3.6   4.5e-05       0.1      31      96 ..       8      70 ..       4      75 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.5e-05
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTTTTHHHHHHHHHHHHHHHHHH-..-GGGG--H. CS
                          DUF29 31 ieEiedlgrsekrelesrlavllehlLkwqyqpekrsrswrseireqrkeieklledspsLksyle 96
                                   +eE+ +++r+e+++  + l+  l+    ++ q ++ s +  ++ir+ ++ei+++l  +++L+++++
  gi|119719403|ref|YP_919898.1|  8 AEELRKMSREERQKRLQELRGELA---RLKAQAHRGSLENVASIRKIKREIARILTIENELRRKAP 70
                                   79******9999876666665555...4556666899999****************9**9999876 PP

>> DUF2299  Uncharacterized conserved protein (DUF2299)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.7   9.2e-05      0.21      60      90 ..       6      36 ..       3      68 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9.2e-05
                                   HHHHHHHHS-HHHHHHHHHHHHHHHTTTT-E CS
                        DUF2299 60 ehkkalsslkeeerkeflselkrdLlrlcvd 90
                                   ++ + l+++++eer++ l+el+ +L+rl+ +
  gi|119719403|ref|YP_919898.1|  6 KQAEELRKMSREERQKRLQELRGELARLKAQ 36
                                   56799**********************9876 PP

>> Vps5  Vps5 C terminal like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   5.3   0.00025      0.55     143     199 ..       3      57 ..       1      69 [. 0.91

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00025
                           Vps5 143 elskkkeqleKlekaaksqqdklqqlkkeveelerkvqeaekeFeeisetikkEler 199
                                     ++k+ e+l K++++  ++q++lq+l+ e++ l++++++ + e     ++ik+E++r
  gi|119719403|ref|YP_919898.1|   3 RMAKQAEELRKMSRE--ERQKRLQELRGELARLKAQAHRGSLENVASIRKIKREIAR 57 
                                    578899999999999..7889**********************99999******987 PP

>> Arg_decarbox_C  Arginine decarboxylase C-terminal helical extension
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   3.8    0.0013       2.9      16      45 ..       1      30 [.       1      33 [. 0.90

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0013
                 Arg_decarbox_C 16 lerlrrqveaagrLtpeerqalleeleagL 45
                                   ++r+ +q+e+  +++ eerq+ l+el+  L
  gi|119719403|ref|YP_919898.1|  1 MKRMAKQAEELRKMSREERQKRLQELRGEL 30
                                   68999999999***************9766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1510  (0.0842211); expected 358.6 (0.02)
Passed bias filter:                      651  (0.0363099); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 649.66
//
Query:       gi|119719404|ref|YP_919899.1|  [L=187]
Description: ribosomal protein S3 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-23   83.5   1.6    1.6e-23   83.0   0.7    1.7  2  Ribosomal_S3_C  Ribosomal protein S3, C-terminal domain
    8.1e-10   38.4   0.1    1.4e-09   37.6   0.1    1.5  1  KH_2            KH domain
     0.0002   21.1   0.7      0.034   14.0   0.1    2.8  3  KH_1            KH domain
      0.003   17.6   0.4     0.0053   16.8   0.4    1.5  1  KH_5            NusA-like KH domain
  ------ inclusion threshold ------
      0.048   13.6   0.0      0.094   12.6   0.0    1.5  1  KH_4            KH domain


Domain annotation for each model (and alignments):
>> Ribosomal_S3_C  Ribosomal protein S3, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.7   5.9e+03      60      82 ..       9      31 ..       6      32 .. 0.76
   2 !   83.0   0.7   4.4e-27   1.6e-23       1      83 []      85     168 ..      85     168 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.7
                                   HHH-EEEEEEEEETTEEEEEEEE CS
                 Ribosomal_S3_C 60 radidyavaeaktkyGiiGvkVw 82
                                   r+ ++  + +a+     iG kV 
  gi|119719404|ref|YP_919899.1|  9 RQLVRANYVHAQFFKTPIGTKVI 31
                                   56677788888888888888886 PP

  == domain 2  score: 83.0 bits;  conditional E-value: 4.4e-27
                                    HHHHHHTT--HHHHHHHHHHHHHHCC-SEEEEEEEC-SS.TTT--EEEEEEC----..TCHHHH-EEEEEEEEETTEEEE CS
                 Ribosomal_S3_C   1 iaeqlekrvsfRramkkairramkagakGikiqvsGrLggaeiarsekykeGrvpl..htlradidyavaeaktkyGiiG 78 
                                    +a++l ++v+fRra+  a++r+m aga+G++i++sG+L+ +++ r+ek+++G+vp+  ++ ++ +d+a+ ++ +k G++G
  gi|119719404|ref|YP_919899.1|  85 VARALVRGVRFRRAALVALNRIMAAGARGAEIVISGKLT-SQRHRTEKFTRGYVPKsgEPGEELVDEAIVHVLLKLGMYG 163
                                    6899***********************************.**************************************** PP

                                    EEEEE CS
                 Ribosomal_S3_C  79 vkVwI 83 
                                    vkV+I
  gi|119719404|ref|YP_919899.1| 164 VKVRI 168
                                    ***98 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6   0.1     4e-13   1.4e-09       4      75 ..       5      73 ..       2      76 .. 0.83

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 4e-13
                                   HHHHHHTECETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEEEEEEEETT CS
                           KH_2  4 eslaveikkagvskveIertanrviiviresqpgivIGkgGsnikkigkelrkdieklegkkVklnivkVkk 75
                                   e+l++++  a + +    +t+ +++++++++ pg+vIG++G+nik+i + l+++++ +e+ ++   +v+V +
  gi|119719404|ref|YP_919899.1|  5 EYLQRQLVRANYVHAQFFKTPIGTKVIVYAGVPGLVIGRKGANIKAIAEVLEREFG-IENPQID--VVEVPN 73
                                   56666665666666666678889********************************8.*****99..778766 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.1   9.6e-06     0.034      12      27 ..      38      53 ..      28      55 .. 0.91
   2 ?   -2.4   0.0       1.2   4.3e+03      47      52 ..     115     120 ..     103     128 .. 0.61
   3 !    4.6   0.0    0.0079        28      30      53 ..     163     184 ..     160     186 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 9.6e-06
                                   HHHHTGGGHHHHHHHH CS
                           KH_1 12 griIGkgGsnIkeIre 27
                                   g++IG++G+nIk I e
  gi|119719404|ref|YP_919899.1| 38 GLVIGRKGANIKAIAE 53
                                   89***********987 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.2
                                    EEEEEE CS
                           KH_1  47 evtisG 52 
                                    e++isG
  gi|119719404|ref|YP_919899.1| 115 EIVISG 120
                                    455555 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.0079
                                    T-EEEEESSTT...T.-EEEEEE.S CS
                           KH_1  30 gakIkvpksedegsderevtisG.s 53 
                                    g+k++++k+ +   +++++ i+G +
  gi|119719404|ref|YP_919899.1| 163 GVKVRIMKPAK---MPDTILIKGvT 184
                                    9*****96333...89*******66 PP

>> KH_5  NusA-like KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.4   1.5e-06    0.0053       5      47 ..      28      71 ..      26      95 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.5e-06
                           KH_5  5 tkvaVkshnpnvdpvGaivgkkGsrikavsseLk......gekidvvew 47
                                   tkv+V+++       G ++g+kG++ika+ + L+      + +idvve 
  gi|119719404|ref|YP_919899.1| 28 TKVIVYAGV-----PGLVIGRKGANIKAIAEVLErefgieNPQIDVVEV 71
                                   799999999.....9*******************99999999*****96 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.6e-05     0.094      40      55 ..      37      52 ..       9      57 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.6e-05
                           KH_4 40 lGrvIGkrGrtldAlq 55
                                    G+vIG++G +++A+ 
  gi|119719404|ref|YP_919899.1| 37 PGLVIGRKGANIKAIA 52
                                   69************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1419.02
//
Query:       gi|119719405|ref|YP_919900.1|  [L=127]
Description: ribosomal protein L22 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.9e-25   87.8   0.1    5.5e-25   87.6   0.1    1.0  1  Ribosomal_L22  Ribosomal protein L22p/L17e


Domain annotation for each model (and alignments):
>> Ribosomal_L22  Ribosomal protein L22p/L17e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.6   0.1   3.1e-29   5.5e-25       8     102 ..       1     123 [.       1     124 [. 0.97

  Alignments for each domain:
  == domain 1  score: 87.6 bits;  conditional E-value: 3.1e-29
                                    S-HHHHHHHHHHHTTSBHHHHHHHHHT..-SST..........................THHHHHHHHHHHHHHHH..HT CS
                  Ribosomal_L22   8 vsfkklrevarlIrgmkveeAlkyLkf..skkk..........................aakfvlklLknaeanaelkgl 59 
                                    +s k + e++rlI+g+++eeA ++L +  + k+                          +ak +lklL n e+nae kgl
  gi|119719405|ref|YP_919900.1|   1 MSYKLTVETLRLIKGKSIEEARRILTEiaEMKRsvplkrynkkvghrsdvpgpgrypvkVAKNLLKLLDNLENNAEFKGL 80 
                                    68999**********************9877779********************************************** PP

                                    -GGGEEEEEEEEEEEEEEEEEEEESTTEEEEEEEEEEEEEEEE CS
                  Ribosomal_L22  60 dvdslvIeeiqvnkgpklkrrtyrArGrinpirkspchievvl 102
                                    +v++l I+++ ++kg k++++ +rA Gr++p+  + +h+e++ 
  gi|119719405|ref|YP_919900.1|  81 NVENLRIVHAAAHKGMKIRNYLPRAFGRATPYYDQLVHVEIIA 123
                                    *****************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 896.94
//
Query:       gi|119719406|ref|YP_919901.1|  [L=91]
Description: 50S ribosomal protein L37Ae [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.5e-32  108.9   3.0    1.1e-31  108.7   3.0    1.0  1  Ribosomal_L37ae  Ribosomal L37ae protein family
     0.0032   17.1   3.5       0.57   10.0   0.8    2.3  2  Rubredoxin_2     Rubredoxin metal binding domain
     0.0036   17.3   0.2     0.0054   16.8   0.2    1.3  1  Elf1             Transcription elongation factor Elf1 like
     0.0067   16.6   0.3     0.0089   16.2   0.3    1.1  1  IBR              IBR domain, a half RING-finger domain
      0.007   15.7   3.7      0.025   13.9   3.7    1.9  1  zf-TFIIB         Transcription factor zinc-finger
  ------ inclusion threshold ------
      0.013   15.4   0.7      0.021   14.7   0.7    1.4  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.018   14.9   6.5       0.86    9.6   2.8    2.3  2  Zn_ribbon_SprT   SprT-like zinc ribbon domain
      0.022   14.3   0.2       0.03   13.8   0.2    1.2  1  TF_Zn_Ribbon     TFIIB zinc-binding
      0.023   14.6   2.5       0.31   11.0   2.5    2.3  1  zinc_ribbon_4    zinc-ribbon domain
      0.044   13.7   4.1      0.068   13.2   4.1    1.3  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
      0.074   13.2   1.2          4    7.6   0.3    2.3  2  Zn-ribbon_8      Zinc ribbon domain
      0.087   12.8   2.1        1.5    8.8   0.2    2.3  2  Nudix_N_2        Nudix N-terminal
       0.11   12.4   0.9       0.42   10.6   0.9    1.7  1  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon
       0.15   12.0   1.1       0.51   10.2   0.1    1.9  2  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
        0.3   10.7   2.1        6.1    6.5   0.2    2.1  2  zf_C2H2_10       C2H2 type zinc-finger
       0.35   10.2   3.7        2.7    7.4   0.3    2.2  2  zf-RanBP         Zn-finger in Ran binding protein and others
       0.35   11.0   5.7        2.7    8.1   0.3    2.3  2  UPF0547          Uncharacterised protein family UPF0547
        4.7    7.8   6.9    1.1e+02    3.5   5.4    2.6  2  zf-H2C2_2        Zinc-finger double domain


Domain annotation for each model (and alignments):
>> Ribosomal_L37ae  Ribosomal L37ae protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.7   3.0   1.1e-34   1.1e-31       1      77 [.       4      81 ..       4      87 .. 0.97

  Alignments for each domain:
  == domain 1  score: 108.7 bits;  conditional E-value: 1.1e-34
                                   XXXXXX-GGGGTTSS-HHHHHHHHHHHHHHHS-BEESSSSSS.EEEEEETTEEEETTTTEEEE-BSSSSS-HHHHHHH CS
                Ribosomal_L37ae  1 rtkkvgiaGkygtrYGaslrkrvkkieisqhakytCpfcgkt.kvkRkavgiwkCkkcgktvaGgAytpettsaktvk 77
                                   +t++vg aG++g+rYGa+lrk+v+ ie +++a+++Cp+c+   +vkR+++giw C+kcg+++aGgA+ p+t++++t++
  gi|119719406|ref|YP_919901.1|  4 HTRVVGPAGRFGARYGATLRKKVAAIERKMKARHKCPRCQAVgTVKRESIGIWVCRKCGYKFAGGAWLPRTEAGRTFS 81
                                   799**************************************99********************************986 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.1    0.0027       2.7      16      27 ..      38      49 ..      38      50 .. 0.89
   2 !   10.0   0.8   0.00057      0.57       1      11 [.      56      66 ..      56      71 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0027
                   Rubredoxin_2 16 rCpsCgsWntlk 27
                                   +Cp C++ +t+k
  gi|119719406|ref|YP_919901.1| 38 KCPRCQAVGTVK 49
                                   7******99986 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00057
                   Rubredoxin_2  1 YvCsqCGfesa 11
                                   +vC++CG+++a
  gi|119719406|ref|YP_919901.1| 56 WVCRKCGYKFA 66
                                   89******987 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.2   5.4e-06    0.0054      15      56 ..      30      66 ..      17      76 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.4e-06
                           Elf1 15 kkklptkFdCpfCnheksvevkldkkekiaevsCkvCgesfe 56
                                    +k++ + +Cp+C++  +v     k+e+i++  C++Cg +f 
  gi|119719406|ref|YP_919901.1| 30 ERKMKARHKCPRCQAVGTV-----KRESIGIWVCRKCGYKFA 66
                                   34588999******99666.....7899**********9885 PP

>> IBR  IBR domain, a half RING-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.3     9e-06    0.0089      11      48 ..      28      65 ..      17      67 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 9e-06
                            IBR 11 sles.dpnlkwCprpdCeaiiekseg.cksvtCskCgfef 48
                                    +e  ++ + +Cp   C+a+   + +  +   C+kCg++f
  gi|119719406|ref|YP_919901.1| 28 AIERkMKARHKCP--RCQAVGTVKREsIGIWVCRKCGYKF 65
                                   366657789****..8**77666555456688******99 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   3.7   2.5e-05     0.025       1      34 [.      38      75 ..      38      78 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.5e-05
                       zf-TFIIB  1 kCPkCqdeleeserggveidyCpqCr.....GvWldrge 34
                                   kCP+Cq+   +++r  + i++C +C+     G Wl r e
  gi|119719406|ref|YP_919901.1| 38 KCPRCQA-VGTVKRESIGIWVCRKCGykfagGAWLPRTE 75
                                   8****96.6799*************54444488888876 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.7   2.2e-05     0.021      29      56 ..      37      65 ..      19      66 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.2e-05
                 OrfB_Zn_ribbon 29 ktCseCgsknke.alsgrtfkCpnCgfea 56
                                    +C++C ++++  + s   ++C++Cg+++
  gi|119719406|ref|YP_919901.1| 37 HKCPRCQAVGTVkRESIGIWVCRKCGYKF 65
                                   58*****99998899***********985 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   2.8   0.00086      0.86      11      33 ..      15      45 ..      15      50 .. 0.87
   2 ?    8.3   2.8    0.0021       2.1       6      31 ..      38      62 ..      38      69 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00086
                 Zn_ribbon_SprT 11 greythhlsirrhn........YrCrrCkgt 33
                                   g +y+++l+++ ++        + C+rC+ +
  gi|119719406|ref|YP_919901.1| 15 GARYGATLRKKVAAierkmkarHKCPRCQAV 45
                                   5789999*****99**************965 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0021
                 Zn_ribbon_SprT  6 rCtgCgreythhlsirrhn...YrCrrCk 31
                                   +C++C+    +  +++r++   + Cr+C+
  gi|119719406|ref|YP_919901.1| 38 KCPRCQ----AVGTVKRESigiWVCRKCG 62
                                   599999....566888888999******8 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2     3e-05      0.03       2      27 ..      38      63 ..      37      66 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3e-05
                                   EETTTTCEECHEETSTTCEEESSSSB CS
                   TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGl 27
                                   kCP C    +v  ++ g  vC +CG+
  gi|119719406|ref|YP_919901.1| 38 KCPRCQAVGTVKRESIGIWVCRKCGY 63
                                   9******99****************8 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   2.5   0.00031      0.31       4      35 ..      38      65 ..      33      66 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00031
                  zinc_ribbon_4  4 tCpsCkakyeiddeklpakgvkvrCskCghvF 35
                                    Cp+C+a+ ++  e +    +   C kCg +F
  gi|119719406|ref|YP_919901.1| 38 KCPRCQAVGTVKRESI----GIWVCRKCGYKF 65
                                   5***********9744....444599999888 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   4.1   6.8e-05     0.068      17      45 ..      35      63 ..      30      64 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.8e-05
                  Zn_Tnp_IS1595 17 ngfvCPhCgsrkayrikt..rglfqCkeCrk 45
                                   +++ CP+C+     ++k+   g + C++C++
  gi|119719406|ref|YP_919901.1| 35 ARHKCPRCQAV--GTVKResIGIWVCRKCGY 63
                                   5789*****55..44444448********98 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.3     0.004         4      21      37 ..      33      49 ..      23      51 .. 0.66
   2 ?    4.5   0.0     0.039        39       7      15 ..      57      65 ..      56      84 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.004
                    Zn-ribbon_8 21 isdaplta.CPeCgs..evr 37
                                   ++     + CP+C++  +v+
  gi|119719406|ref|YP_919901.1| 33 MK---ARHkCPRCQAvgTVK 49
                                   44...3344****9974444 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.039
                    Zn-ribbon_8  7 rCeeCghef 15
                                    C++Cg +f
  gi|119719406|ref|YP_919901.1| 57 VCRKCGYKF 65
                                   59****998 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.2    0.0015       1.5      20      31 ..      34      45 ..      19      46 .. 0.76
   2 ?    3.6   0.2     0.065        64      24      30 ..      57      63 ..      56      65 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0015
                                   S-EEEETTTTEE CS
                      Nudix_N_2 20 reRlvCpaCgti 31
                                   + R+ Cp+C+++
  gi|119719406|ref|YP_919901.1| 34 KARHKCPRCQAV 45
                                   68*******987 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.065
                                   EETTTTE CS
                      Nudix_N_2 24 vCpaCgt 30
                                   vC +Cg+
  gi|119719406|ref|YP_919901.1| 57 VCRKCGY 63
                                   7888876 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.9   0.00042      0.42       4      27 ..      38      63 ..      38      66 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00042
                 PhnA_Zn_Ribbon  4 kCplCaSeytY..edgallvCpeCah 27
                                   kCp C++  t   e   ++vC +C++
  gi|119719406|ref|YP_919901.1| 38 KCPRCQAVGTVkrESIGIWVCRKCGY 63
                                   8******9999999999*******98 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1      0.67   6.6e+02      23      29 ..      38      44 ..      30      46 .. 0.67
   2 ?   10.2   0.1   0.00052      0.51      19      31 ..      57      65 ..      47      66 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.67
                                   EESSSS- CS
                 RNA_POL_M_15KD 23 eCrqCgY 29
                                    C  C++
  gi|119719406|ref|YP_919901.1| 38 KCPRCQA 44
                                   4777776 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00052
                                   CCEEEESSSS-EE CS
                 RNA_POL_M_15KD 19 gknfeCrqCgYee 31
                                   +    Cr+CgY++
  gi|119719406|ref|YP_919901.1| 57 V----CRKCGYKF 65
                                   3....******97 PP

>> zf_C2H2_10  C2H2 type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.2    0.0062       6.1       3      10 ..      37      44 ..      35      46 .. 0.85
   2 ?    4.1   0.1     0.034        34       3      11 ..      56      64 ..      55      66 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0062
                     zf_C2H2_10  3 fsCPKCqe 10
                                   + CP+Cq 
  gi|119719406|ref|YP_919901.1| 37 HKCPRCQA 44
                                   99****96 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.034
                     zf_C2H2_10  3 fsCPKCqek 11
                                   + C KC++k
  gi|119719406|ref|YP_919901.1| 56 WVCRKCGYK 64
                                   57******8 PP

>> zf-RanBP  Zn-finger in Ran binding protein and others
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.3     0.033        33      19      27 ..      37      45 ..      35      46 .. 0.82
   2 ?    7.4   0.3    0.0027       2.7       3      13 ..      54      64 ..      52      64 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.033
                                   SB-TTT--B CS
                       zf-RanBP 19 tkCvaCqap 27
                                    kC +Cqa+
  gi|119719406|ref|YP_919901.1| 37 HKCPRCQAV 45
                                   69*****96 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0027
                                   SSEE-SSS--E CS
                       zf-RanBP  3 gdWdCskClvq 13
                                   g W C kC+++
  gi|119719406|ref|YP_919901.1| 54 GIWVCRKCGYK 64
                                   77******985 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.8     0.021        21       2       8 ..      38      44 ..      37      45 .. 0.85
   2 ?    8.1   0.3    0.0027       2.7      16      24 ..      57      65 ..      55      66 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.021
                        UPF0547  2 vCPeCea 8 
                                   +CP+C+a
  gi|119719406|ref|YP_919901.1| 38 KCPRCQA 44
                                   7****86 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0027
                        UPF0547 16 fCphCGyvF 24
                                   +C+ CGy F
  gi|119719406|ref|YP_919901.1| 57 VCRKCGYKF 65
                                   6******99 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0         8   7.9e+03       4       8 ..       3       7 ..       2      10 .. 0.78
   2 ?    3.5   5.4      0.11   1.1e+02      14      25 ..      55      66 ..      29      66 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 8
                      zf-H2C2_2 4 rHirk 8
                                  rH+r+
  gi|119719406|ref|YP_919901.1| 3 RHTRV 7
                                  78875 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.11
                      zf-H2C2_2 14 pyeCplCdkaFk 25
                                   ++ C +C+++F+
  gi|119719406|ref|YP_919901.1| 55 IWVCRKCGYKFA 66
                                   478******995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       725  (0.0404373); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 630.47
//
Query:       gi|119719407|ref|YP_919902.1|  [L=270]
Description: ribosomal RNA adenine methylase transferase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.8e-35  120.0   0.0    1.1e-34  119.7   0.0    1.1  1  RrnaAD           Ribosomal RNA adenine dimethylase
    8.2e-05   23.2   0.0    0.00015   22.4   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
    0.00023   20.8   0.0    0.00033   20.2   0.0    1.2  1  MTS              Methyltransferase small domain
     0.0059   17.2   0.0      0.012   16.2   0.0    1.5  1  Methyltransf_11  Methyltransferase domain


Domain annotation for each model (and alignments):
>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.7   0.0   2.6e-38   1.1e-34       4     238 ..      15     235 ..      13     264 .. 0.88

  Alignments for each domain:
  == domain 1  score: 119.7 bits;  conditional E-value: 2.6e-38
                                    CXXGCG--EE--HHHHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTT..TCCCEEEE CS
                         RrnaAD   4 lrksygqnflknkkvineIldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkkls..kdeklkvv 81 
                                     ++++gq+fl++ +v+ +I + +n      v+e+g G G lT +L +r+  v   E+de+La +l+ +l     +++ ++
  gi|119719407|ref|YP_919902.1|  15 YKRRLGQHFLVDDTVASRIASFVN---GEDVYEVGCGLGSLTLPLSERSAYVFCCEKDEALALFLSRELYrrGIGNVDIM 91 
                                    5899***************98877...678*************************************99888889***** PP

                                    -S-CCGHHHHHHHCTTTCCCCEEEEEEE--TTTHHHHHHHHHHGGGGCEEEEEEEEEHHHHHHHH--TTSTT-SHHHHHH CS
                         RrnaAD  82 hqDflkfetpeevtekdsihqeflvvanlPyeistqlvkqlleesrfglvkmllwlqkefarrllarpgskkrsrlsvlr 161
                                      D+l  ++              lvv+n+P +is+qlv++l   +  gl k++l lq+e+a+rl a+pg ++++rlsv++
  gi|119719407|ref|YP_919902.1|  92 VGDALRIDLSR---------SSHLVVSNTPFNISSQLVVKLC--YDEGLLKAYLGLQREVAERLYAKPGTREYGRLSVIS 160
                                    ***********.........778******************9..89999******************************* PP

                                    HHHEEEEEEEEC-GGCECS--SSSEEEEEEEE-SS-S--S-HHHHHHHHHHHHCTTTSBCCCHCCCTSTCHHHHHCT CS
                         RrnaAD 162 eaftdvklvakveksifsPppkvdsalvelerkdedlpqkdlkkyesvvrkllnrkrktlstslksllpggelqals 238
                                    ++ ++++ +  v++++f Pppkv  + v+l +       +d++  e + r ++   ++ + t+l  ++ g +++ + 
  gi|119719407|ref|YP_919902.1| 161 QLCFSIERLFDVPPNAFLPPPKVFTSFVRLVPLRRL-GAEDVRLVEEFSRRIFPYINRVVTTALR-IGLGVNREVAE 235
                                    ********************************9996.899*************999999999987.54444444443 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   3.3e-08   0.00015       1      76 [.      42     115 ..      42     126 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 3.3e-08
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEEEST.GGG CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvssga.lhh 76 
                                    v ++GcG G ltl l++r   a v +++ +e++     +++ ++g+ nv++++gda ++++   s +lvvs+ + +++
  gi|119719407|ref|YP_919902.1|  42 VYEVGCGLGSLTLPLSERS--AYVFCCEKDEALALFLSRELYRRGIgNVDIMVGDALRIDLSR-SSHLVVSN-TpFNI 115
                                    779***************5..**********999999999989999*************9875.99999995.43654 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   7.4e-08   0.00033      32     112 ..      39     118 ..      19     127 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 7.4e-08
                                    CSEEEEET-TTSHHHHHHHHHTTC.EEEEEESB.HHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEEEE---STTT CS
                            MTS  32 sgkvlDlGcGaGvlgaalakespeaevtlvdvd.arAlesakenleanklevevvasdvleeveekkfdlivsNPPfhag 110
                                     ++v  +GcG G l++ l ++s    v ++++d a Al +++e +++   +v+++  d+l     ++  l+vsN Pf  +
  gi|119719407|ref|YP_919902.1|  39 GEDVYEVGCGLGSLTLPLSERSAY--VFCCEKDeALALFLSRELYRRGIGNVDIMVGDALRIDLSRSSHLVVSNTPFNIS 116
                                    567999**************9888..7888876267999999999999999*********98888************877 PP

                                    CH CS
                            MTS 111 ka 112
                                    ++
  gi|119719407|ref|YP_919902.1| 117 SQ 118
                                    66 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   2.7e-06     0.012       2      66 ..      44     108 ..      43     120 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.7e-06
                                    EET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-TT-EEEEE CS
                Methyltransf_11   2 dvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl.kvefvvadaeklpfednsfDlvv 66 
                                    +vGcG G+l+ +l +r a v++++ ++++    +++  ++g+ +v+++v+da ++ +   s  lvv
  gi|119719407|ref|YP_919902.1|  44 EVGCGLGSLTLPLSERSAYVFCCEKDEALALFLSRELYRRGIgNVDIMVGDALRIDLSR-SSHLVV 108
                                    79**********************9999998888888888999**********999987.444555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       267  (0.0148921); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1953.85
//
Query:       gi|119719408|ref|YP_919903.1|  [L=129]
Description: 50S ribosomal protein L7Ae [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-29  102.0   0.4    1.5e-29  101.6   0.4    1.2  1  Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 famil
    1.4e-05   24.9   0.2    3.2e-05   23.7   0.2    1.7  2  PELOTA_1        PELOTA RNA binding domain
     0.0015   18.6   0.0     0.0017   18.4   0.0    1.1  1  RNase_P_pop3    RNase P subunit Pop3


Domain annotation for each model (and alignments):
>> Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.6   0.4   2.5e-33   1.5e-29       2      94 ..      19     112 ..      18     113 .. 0.96

  Alignments for each domain:
  == domain 1  score: 101.6 bits;  conditional E-value: 2.5e-33
                                    HHHHHHHHHHHHTE.EEESHHHHHHHHHTTTESEEEEETTSSSGGHHHHHHHHHHHTTEEEEEESCHHHHHHHTTSSSEC CS
                 Ribosomal_L7Ae   2 aieevlkkakkagk.lvlGlkevtkalergeaklvilAedvepeekkkllealckekevpyvkvkskkeLGelvgkkrpv 80 
                                    +++++l++a+++g+ +++G++e+tka+erg aklv++A dv+p+e +++l+ lc+ek+vpyv+v+sk++LG+++g ++++
  gi|119719408|ref|YP_919903.1|  19 KAYQALSLAREKGGkIKKGTNETTKAVERGLAKLVLIATDVDPPEVVAHLPLLCEEKKVPYVYVPSKERLGKAAGINVAA 98 
                                    789999999999888***************************************************************** PP

                                    SEEEEEESTTTHHH CS
                 Ribosomal_L7Ae  81 salaikdegdskdl 94 
                                    +a+ai ++g++  l
  gi|119719408|ref|YP_919903.1|  99 AAAAILEPGEAASL 112
                                    *********99876 PP

>> PELOTA_1  PELOTA RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.59   3.5e+03      68      80 ..      16      28 ..      13      29 .. 0.77
   2 !   23.7   0.2   5.3e-09   3.2e-05      21      71 ..      33      85 ..      17      94 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.59
                       PELOTA_1 68 vpdlpYsavglik 80
                                    ++++Y+a++l +
  gi|119719408|ref|YP_919903.1| 16 LAEKAYQALSLAR 28
                                   5678999999876 PP

  == domain 2  score: 23.7 bits;  conditional E-value: 5.3e-09
                       PELOTA_1 21 liKPgigEaTRvlLRRvPekvlvrdeee..pdlahlllLakekgvpveevpdl 71
                                    iK g  E+T+++ R   + vl++ + +  + +ahl lL++ek+vp++ vp++
  gi|119719408|ref|YP_919903.1| 33 KIKKGTNETTKAVERGLAKLVLIATDVDppEVVAHLPLLCEEKKVPYVYVPSK 85
                                   69**********************988865679**************999876 PP

>> RNase_P_pop3  RNase P subunit Pop3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   2.8e-07    0.0017      39     151 ..      17     123 ..      12     127 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.8e-07
                   RNase_P_pop3  39 lkklvrlleskeneeseltvglneivelLecsesddvvllvcnkDtPsvLlsqlpllvavanltvklvqlpksaqaklde 118
                                    ++k  ++l++   +  ++  g ne  +  e  + ++ vl++ + D P   + +lpll++ ++  v+ v +p +  ++l +
  gi|119719408|ref|YP_919903.1|  17 AEKAYQALSLAREKGGKIKKGTNETTKAVE-RGLAKLVLIATDVD-PPEVVAHLPLLCEEKK--VPYVYVPSK--ERLGK 90 
                                    556667777677788899************.999999********.77789*********99..999988865..56666 PP

                   RNase_P_pop3 119 klGlskagmllvrkdasldkklaklvskkveel 151
                                    + G + a + +   +     +l++ + k+v++l
  gi|119719408|ref|YP_919903.1|  91 AAGINVAAAAAAILEPGEAASLVDEIIKEVNNL 123
                                    666655533222222222235666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 974.12
//
Query:       gi|119719409|ref|YP_919904.1|  [L=389]
Description: Fmu (Sun) domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.6e-42  143.2   0.0    1.2e-41  142.6   0.0    1.3  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
    3.3e-11   43.0   1.5      7e-11   41.9   1.5    1.6  1  PUA              PUA domain
    6.5e-10   39.0   0.0      1e-09   38.3   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    2.9e-06   27.9   0.1    4.2e-05   24.2   0.1    2.4  1  Methyltransf_25  Methyltransferase domain
    3.9e-06   27.1   0.0    7.1e-06   26.2   0.0    1.5  1  FtsJ             FtsJ-like methyltransferase
    7.9e-05   22.2   0.0      0.011   15.2   0.0    2.3  2  Methyltransf_4   Putative methyltransferase
     0.0002   21.2   0.0    0.00057   19.7   0.0    1.7  2  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    0.00027   21.5   0.1     0.0024   18.5   0.1    2.4  1  Methyltransf_11  Methyltransferase domain
    0.00097   18.7   0.0        1.5    8.3   0.0    2.2  2  MTS              Methyltransferase small domain
     0.0017   17.7   0.0      0.021   14.2   0.0    2.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
     0.0025   17.8   0.0       0.24   11.4   0.0    2.9  2  ADH_zinc_N       Zinc-binding dehydrogenase
     0.0046   17.4   0.0       0.27   11.8   0.0    2.4  2  Methyltr_RsmF_N  N-terminal domain of 16S rRNA methyltransfer
  ------ inclusion threshold ------
      0.029   14.0   0.0      0.052   13.2   0.0    1.3  1  Cons_hypoth95    Conserved hypothetical protein 95
      0.082   12.1   0.0       0.13   11.5   0.0    1.2  1  DUF43            Branched-chain polyamine synthase A C-termin
       0.11   11.6   0.0       0.27   10.3   0.0    1.6  2  Fibrillarin      Fibrillarin


Domain annotation for each model (and alignments):
>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.6   0.0   9.9e-45   1.2e-41       3     199 ..     196     386 ..     194     387 .. 0.90

  Alignments for each domain:
  == domain 1  score: 142.6 bits;  conditional E-value: 9.9e-45
                                    HH---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC..EEE CS
                Methyltr_RsmB-F   3 lLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlggelfDr 82 
                                    lL+pq++ t+lD+caaPGgKTth a+lm ++g+v+Avd+ k++++ ++e  +rLg+++++ l +D r+i+++l ++ +D 
  gi|119719409|ref|YP_919904.1| 196 LLDPQPGWTVLDMCAAPGGKTTHAAQLMGDHGEVIAVDRTKSKVDTIMEHARRLGLKSVKGLVYDSRYISEYLDKDSVDA 275
                                    89****************************************************************************** PP

                                    EEEEE--CCGGGTTT-TCHHHH--HHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEES--STTTTHHHHHHHHHH-TTEEE CS
                Methyltr_RsmB-F  83 iLlDaPCsgtgvirrdpdvklrrkekdiaqlaklqkellsaaidllkkgGvlvYsTCsvlveEneevieeaLkkredvel 162
                                    +++D PC+++gv   +p++ ++r   d+ +l+  q++ l  a+++l++gG l+++TC++ + Ene  +  a +     + 
  gi|119719409|ref|YP_919904.1| 276 VIIDPPCTALGV---RPKLWYERGFDDVLKLSDYQRQFLREAAKVLRRGGRLLFTTCTISPYENEFNVIFAASYL-GLKP 351
                                    ***********9...6889999*******************************************9886554443.4444 PP

                                    ESSBSTTSTTSSECEECTSEEE-TTTTSS-SEEEEEE CS
                Methyltr_RsmB-F 163 vetelsepkglklgeeagtlrllPhtenkdgffiakl 199
                                     ++++   k   lg++   l+++Ph++++ gffia +
  gi|119719409|ref|YP_919904.1| 352 LPLSFPPVKSGLLGTG--SLQFVPHEHDTPGFFIALF 386
                                    4444444444445555..5****************87 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9   1.5   5.9e-14     7e-11       1      72 [.      94     164 ..      94     166 .. 0.94

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 5.9e-14
                                    CEEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEEE CS
                            PUA   1 grvvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveier 72 
                                    g+v vd+  ++ +  ga+++apGv++ve   +egd V +++++g++va G+  ++ + + +  +g +v++ r
  gi|119719409|ref|YP_919904.1|  94 GKVYVDKKTAESVYVGANVFAPGVTKVEN-AREGDLVSVIAPGGRVVAEGVLSMDPSRVFSERKGLAVRVVR 164
                                    79*************************98.*************************99999988888888765 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.3   0.0   8.7e-13     1e-09       4     113 ..     202     330 ..     199     353 .. 0.91

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 8.7e-13
                Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsn.. 81 
                                    g +vlD  ++ G +t  +a+++g+++ev+ +D+++  +    e+a++lgl+ v+  + d   +++ l ++++D ++ +  
  gi|119719409|ref|YP_919904.1| 202 GWTVLDMCAAPGGKTTHAAQLMGDHGEVIAVDRTKSKVDTIMEHARRLGLKSVKGLVYDSRYISEYLDKDSVDAVIIDpp 281
                                    678***************************************************9999888877546669********99 PP

                Methyltransf_31  82 .................evlnaladpdkileeiervlkpggilliedpr 113
                                                     +vl +   + ++l+e+ +vl+ gg+ll +++ 
  gi|119719409|ref|YP_919904.1| 282 ctalgvrpklwyergfdDVLKLSDYQRQFLREAAKVLRRGGRLLFTTCT 330
                                    9999999999999999999999999*********************997 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.1   3.5e-08   4.2e-05       1      97 []     205     322 ..     205     322 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 3.5e-08
                                    EEEET-TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBS..SSTTTEEEEEE...... CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlg.kakvtgvDiseemleaareraeeegl.nvefvqgdaedlp..fedgsfDlvvs...... 70 
                                    vLd+++ +G  t ++a+ +g +++v++vD +++ ++++ e+a++ gl +v+ ++ d + ++  ++++s+D+v++      
  gi|119719409|ref|YP_919904.1| 205 VLDMCAAPGGKTTHAAQLMGdHGEVIAVDRTKSKVDTIMEHARRLGLkSVKGLVYDSRYISeyLDKDSVDAVIIdppcta 284
                                    9*****************9779**********************9999*********9998545889******9766555 PP

                                    ....ESTGG...........GSSHHHHHHHHHHHHHHEEEEE CS
                Methyltransf_25  71 ....sgalh...........hlsdedlekalkeiarvLkpgG 97 
                                                         ls + ++++l+e+a+vL+ gG
  gi|119719409|ref|YP_919904.1| 285 lgvrP---KlwyergfddvlKLS-DYQRQFLREAAKVLRRGG 322
                                    44440...044444444431233.345789999999999988 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0     6e-09   7.1e-06      19     137 ..     197     330 ..     162     348 .. 0.73

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 6e-09
                                    S-..TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS........HHHTTEEEECS-CCCSSHHHHHCHCHHHSSE CS
                           FtsJ  19 fk..pgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm........aplpgvttiqgditdpetiekikealserkv 88 
                                    ++  pg tv+D +aaPGg +  ++q +g +g v+avD  +         a + g+++++g + d + i + +   ++  v
  gi|119719409|ref|YP_919904.1| 197 LDpqPGWTVLDMCAAPGGKTTHAAQLMGDHGEVIAVDRTKSkvdtimehARRLGLKSVKGLVYDSRYISEYL---DKDSV 273
                                    43347799********************99********8887887776555589999999998887766555...57899 PP

                                    EEEEE--S-.......SS-CHHHHHHHHH.CCCCHHHHCCHCCCCECCCEEEECCCH CS
                           FtsJ  89 dlvvsDgap.......dvsgvhdldeylq.sqLllaalelalkllkpggtfvlkifr 137
                                    d v+ D          +    + +d +l+ s+  ++ l+ a k+l++gg +++ +++
  gi|119719409|ref|YP_919904.1| 274 DAVIIDPPCtalgvrpKLWYERGFDDVLKlSDYQRQFLREAAKVLRRGGRLLFTTCT 330
                                    999999543111111133334444555553466666666677888888888877776 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   9.1e-06     0.011       4      78 ..     204     278 ..     202     281 .. 0.91
   2 ?    4.4   0.0     0.019        23      96     120 ..     307     332 ..     306     346 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 9.1e-06
                                    EEEEET-TTSHHHHHHHHHSTTS.EEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCCHHHHCS-TTSEEEEEE CS
                 Methyltransf_4   4 vvleiGcGkGeflvalAkknPdk.nflGiEirvkvvakvlkkiealelkNlrilrgdalkvllelledgslekifi 78 
                                    +vl+++ + G+ + + A+   d  ++++++  ++ v+++++++++l+lk ++ l  d  ++++e+l ++s++ + i
  gi|119719409|ref|YP_919904.1| 204 TVLDMCAAPGGKTTHAAQLMGDHgEVIAVDRTKSKVDTIMEHARRLGLKSVKGLVYDS-RYISEYLDKDSVDAVII 278
                                    5899999999999999998776438********************************8.************99987 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.019
                                    SHHHHHHHHHHEEEEEEEEEEES.HH CS
                 Methyltransf_4  96 qpellkelarvLkkgGvlelaTD.ve 120
                                    q+++l e+a+vL+ gG l + T  ++
  gi|119719409|ref|YP_919904.1| 307 QRQFLREAAKVLRRGGRLLFTTCtIS 332
                                    789***************99996444 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       3.3   3.9e+03       4      43 ..      56      97 ..      54     115 .. 0.62
   2 !   19.7   0.0   4.8e-07   0.00057      28     132 ..     162     260 ..     153     276 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3.3
                                   HHHHHHHHHTT..S---HHHHHHHHHS-GGGGSSCGGGGGTT CS
                           PCMT  4 ealieelkkkg..viksdkvaealeevdReefvpesfkekaY 43
                                   e+l+eel+++g  v ++d+  ea+     + f  + ++ k+Y
  gi|119719409|ref|YP_919904.1| 56 EDLLEELREEGlkVYRHDRLPEAFYVPVEGPFEVRLLPGKVY 97
                                   678888888873345677777776544444455554555555 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 4.8e-07
                                    S-GGGGSSCGGGGGTTSSS-EEEETTEEE--HHHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESB CS
                           PCMT  28 vdReefvpesfkekaYedaplsigynatiSaphmvalalellelkkgarvLevGsGsGyltavlarlvgekgrvvsieri 107
                                    v R+++   s++e+ Y d  l i      S p+mva+   ll+ ++g  vL++ +  G +t   a+l+g++g v++++r+
  gi|119719409|ref|YP_919904.1| 162 VVRSVYRAVSLRETRYFDEGL-IYH---QSLPSMVAV--RLLDPQPGWTVLDMCAAPGGKTTHAAQLMGDHGEVIAVDRT 235
                                    668888888888888988888.433...488999985..78*************************************** PP

                                    HHHHHHHHHHHHHCTTCSEEEEES- CS
                           PCMT 108 kelveeakrnlkkldlenvivvvgD 132
                                    k+ v++  ++ ++l+l++v+  v D
  gi|119719409|ref|YP_919904.1| 236 KSKVDTIMEHARRLGLKSVKGLVYD 260
                                    *************999999876666 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1     2e-06    0.0024       9      96 .]     217     326 ..     206     326 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2e-06
                                    HHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCT.S.S-TT-EEEEEEES........-CCC-C CS
                Methyltransf_11   9 rlaealakrg..arvvgvDlskemlklakekaseegl.kvefvvadaekl.p.fednsfDlvvsse........vlhhve 75 
                                     +a++l+  g  ++v++vD +k  +++  e+a++ gl +v+ +v d + +   + ++s+D+v++               +
  gi|119719409|ref|YP_919904.1| 217 THAAQLM--GdhGEVIAVDRTKSKVDTIMEHARRLGLkSVKGLVYDSRYIsEyLDKDSVDAVIIDPpctalgvrP----K 290
                                    2333333..3558**********************9877677777777775535557******999554455550....1 PP

                                    ...............CHHHHHHHHHHHEEEEEEEEE CS
                Methyltransf_11  76 ...............dpekalkeiaRvLkpgGllvi 96 
                                                    ++++l+e+a+vL+ gG+l++
  gi|119719409|ref|YP_919904.1| 291 lwyergfddvlklsdYQRQFLREAAKVLRRGGRLLF 326
                                    444555555555555******************986 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0    0.0015       1.7      25     107 ..     195     282 ..     188     294 .. 0.80
   2 !    8.3   0.0    0.0013       1.5     117     154 ..     306     343 ..     297     347 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0015
                                    HHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.E.EEEEESBHHHHHHHHHHHHHTTGC...EEEEE-STTTT.STTS-EE CS
                            MTS  25 etlpkelsgkvlDlGcGaGvlgaalakespeae.vtlvdvdarAlesakenleankle...vevvasdvlee.veekkfd 99 
                                    + l+ +   +vlD+++  G  ++++a+   ++  v +vd  +  ++   e +++ +l+   + v+ s  ++e ++++++d
  gi|119719409|ref|YP_919904.1| 195 RLLDPQPGWTVLDMCAAPGGKTTHAAQLMGDHGeVIAVDRTKSKVDTIMEHARRLGLKsvkGLVYDSRYISEyLDKDSVD 274
                                    56666777789****9999999998887766544*************9999999999887666777766666156899** PP

                                    EEEE---S CS
                            MTS 100 livsNPPf 107
                                    +++  PP 
  gi|119719409|ref|YP_919904.1| 275 AVIIDPPC 282
                                    *******6 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0013
                                    HHHHHHHHHHHHEEEEEEEEEEEETTSCHHHHHHHHHS CS
                            MTS 117 vaeeliaeAkeaLkegGeLliVanrklgyeslleelfg 154
                                      +++++eA+++L+ gG+Ll+ + +  +ye+  + +f 
  gi|119719409|ref|YP_919904.1| 306 YQRQFLREAAKVLRRGGRLLFTTCTISPYENEFNVIFA 343
                                    5689*****************99999999998887775 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   1.7e-05     0.021      41     150 ..     195     325 ..     182     346 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.7e-05
                                    HH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TT..S-T-EE CS
                Ubie_methyltran  41 klvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpf..eddsfD 118
                                    +l  +++g +vlD+++  g  + + ++ +g++g+v+ +D  ++ +++  +++++ g ++++ l+ ++  + +  ++ds D
  gi|119719409|ref|YP_919904.1| 195 RLLDPQPGWTVLDMCAAPGGKTTHAAQLMGDHGEVIAVDRTKSKVDTIMEHARRLGLKSVKGLVYDSRYISEylDKDSVD 274
                                    556678899****************************************************9998888776422569999 PP

                                    EEEE.....ES-GG.............G-S-HHH.HHHHHHHHEEEEEEEE CS
                Ubie_methyltran 119 vvtv.....sfGlr.............nvtDklk.aLkeayrvlkpGGrlv 150
                                     v +     + G+r              ++D+++  L+ea +vl+ GGrl+
  gi|119719409|ref|YP_919904.1| 275 AVIIdppctALGVRpklwyergfddvlKLSDYQRqFLREAAKVLRRGGRLL 325
                                    998744433467763333333222222345555324777777777777765 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.12   1.4e+02      76      96 ..     129     149 ..     123     178 .. 0.75
   2 !   11.4   0.0    0.0002      0.24       9      94 ..     219     336 ..     213     352 .. 0.67

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.12
                                    HHCEEEEEEEEECSCTSSEEE CS
                     ADH_zinc_N  76 lkllkpgGrlvvvGggkgeee 96 
                                    +++++pgGr+v  G+++++ +
  gi|119719409|ref|YP_919904.1| 129 VSVIAPGGRVVAEGVLSMDPS 149
                                    789***********9555443 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.0002
                                    HHHHTT-..EEEEEESSHHHH....HHHHHTTESEEEET............TTCHHHHHHHHHT...........TTSSE CS
                     ADH_zinc_N   9 lAkalGa..eviavdsseekl....elakklGadeviny............keadlverikelt...........ggegv 59 
                                    +A  +G   eviavd++++k+    e a++lG + v               k+ ++++ i +              ++g+
  gi|119719409|ref|YP_919904.1| 219 AAQLMGDhgEVIAVDRTKSKVdtimEHARRLGLKSVKGLvydsryiseyldKD-SVDAVIIDPPctalgvrpklwYERGF 297
                                    6777777789*********9955556666666554433333345555454322.333333333377777777776789** PP

                                    EEEEESSC.SHHHHHHHHHCEEEEEEEEECSC...TSSE CS
                     ADH_zinc_N  60 dvvfecvG.sgatleaalkllkpgGrlvvvGg...gkge 94 
                                    d v+  +  + + l++a k+l++gGrl +      ++++
  gi|119719409|ref|YP_919904.1| 298 DDVLKLSDyQRQFLREAAKVLRRGGRLLFTTCtisPYEN 336
                                    *******956678899**********9987655544444 PP

>> Methyltr_RsmF_N  N-terminal domain of 16S rRNA methyltransferase RsmF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   0.00022      0.27       5      68 ..      17      84 ..      15     100 .. 0.76
   2 ?    3.2   0.0      0.11   1.3e+02      73      90 .]     174     191 ..     163     191 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00022
                                   HHHHHHHHHGG.GHHHHHHHHH--.---EEE--TTS..TTHHHHHHH..-SS--B-TT-TTEEES--- CS
                Methyltr_RsmF_N  5 Fiekmkellge.eaeaflaaleep.rkkglRvNtlKisveeleklse..efelepvpwceeGfyleee 68
                                   F+e++ +++    +e+++++le+p +++ +RvNtlK+++e+l +  +  + ++ + +  +e+fy++ e
  gi|119719409|ref|YP_919904.1| 17 FVEYLARFFSLgYIEDLFRSLETPgSRYFFRVNTLKVRPEDLLEELReeGLKVYRHDRLPEAFYVPVE 84
                                   777777777776779999999665267899**********9877555367777778888888888765 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.11
                                    TSHHHHTTS-EE--TTTH CS
                Methyltr_RsmF_N  73 khplheaGlyYiQEpSam 90 
                                    ++ ++ +Gl+Y Q   +m
  gi|119719409|ref|YP_919904.1| 174 ETRYFDEGLIYHQSLPSM 191
                                    6789*********99888 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.3e-05     0.052      44     123 ..     204     282 ..     195     291 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.3e-05
                                    EEEETT-TTSHHHHHH..HHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEEEE-- CS
                  Cons_hypoth95  44 rvLDlfaGsGalglEA..lSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdivflDP 121
                                    +vLD++a  G+    A  l  +  ++++v++ k+ v ++ e+ ++l+l++ ++ l+ d+    + l   k ++d v +DP
  gi|119719409|ref|YP_919904.1| 204 TVLDMCAAPGGKTTHAaqLMGDHGEVIAVDRTKSKVDTIMEHARRLGLKS-VKGLVYDSRYISEYL--DKDSVDAVIIDP 280
                                    67888887777777772234567799*********************997.999999998888877..56789******* PP

                                    SS CS
                  Cons_hypoth95 122 Py 123
                                    P 
  gi|119719409|ref|YP_919904.1| 281 PC 282
                                    *5 PP

>> DUF43  Branched-chain polyamine synthase A C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0    0.0001      0.13      59     134 ..     218     296 ..     214     305 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0001
                                    HHHHHHT--SEEEEE-S-HHHHHHHHHHHHHHT--.EEEE---TTS---TTTSS-BSEEEE---SSHHHHH..HHHHHH CS
                          DUF43  59 lalaLtglpkkvvvvDiDeRlikfiervakelglk.ieaivyDlrkplpeelkekFdvfitDPpetvealk..aFlgRG 134
                                     a+ L g   +v+ vD  +  ++ i + a++lglk ++ +vyD r       k+  d +i DPp t  +++  ++  RG
  gi|119719409|ref|YP_919904.1| 218 HAAQLMGDHGEVIAVDRTKSKVDTIMEHARRLGLKsVKGLVYDSRYISEYLDKDSVDAVIIDPPCTALGVRpkLWYERG 296
                                    577888888899999**999***********************9976555557789************99622555565 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00022      0.27      69     135 ..     200     268 ..     185     281 .. 0.80
   2 ?   -2.9   0.0       2.5     3e+03     191     222 ..     312     343 ..     305     345 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00022
                                    -TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHTTS..TTEEEEES-TTSGGGGT CS
                    Fibrillarin  69 kkgskvLYlGaasGttvsHvsDivgeegvvyavefsprvlrelievakkR..knivPileDArkPekYr 135
                                    ++g  vL + aa G    H + ++g++g v av+ ++  +  ++e a++   k +  ++ D r+ ++Y 
  gi|119719409|ref|YP_919904.1| 200 QPGWTVLDMCAAPGGKTTHAAQLMGDHGEVIAVDRTKSKVDTIMEHARRLglKSVKGLVYDSRYISEYL 268
                                    78999*******************************999999998887533367777777777777775 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.5
                                    HHHHHHHHHTTEEEEEEEE-TTTSTTEEEEEE CS
                    Fibrillarin 191 keeveklkeeglkvleqvklepyekdhalvvg 222
                                    +e  + l++ g     ++++ pye+++ ++++
  gi|119719409|ref|YP_919904.1| 312 REAAKVLRRGGRLLFTTCTISPYENEFNVIFA 343
                                    44555666666667778899999999988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 2667.67
//
Query:       gi|119719410|ref|YP_919905.1|  [L=77]
Description: 30S ribosomal protein S28e [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.5e-31  106.1   5.9    7.3e-31  106.0   5.9    1.0  1  Ribosomal_S28e  Ribosomal protein S28e


Domain annotation for each model (and alignments):
>> Ribosomal_S28e  Ribosomal protein S28e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.0   5.9     4e-35   7.3e-31       2      64 .]      12      74 ..      11      74 .. 0.98

  Alignments for each domain:
  == domain 1  score: 106.0 bits;  conditional E-value: 4e-35
                                   --EEEEEEEEEE---SSSSEEEEEEEE-S-SS-S-EEEEEEES---TT-EEEES--S--TT-- CS
                 Ribosomal_S28e  2 eaklAeVikvlgrtGsrGevtqVrvellegkdkgriiiRnVkGPvreGDiLtLlEterEArrL 64
                                   +a++AeV++++grtG++GevtqVrv++leg+dkgri++RnV GPvr+GDi++L+EterEAr++
  gi|119719410|ref|YP_919905.1| 12 DAVPAEVVQIIGRTGITGEVTQVRVRVLEGRDKGRILTRNVRGPVRVGDIVMLRETEREARKI 74
                                   689**********************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 533.45
//
Query:       gi|119719411|ref|YP_919906.1|  [L=182]
Description: hypothetical protein Tpen_0496 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.9e-09   36.1   3.3      1e-08   35.6   3.3    1.2  1  Sld5            GINS complex protein
  ------ inclusion threshold ------
      0.025   14.1   0.1        2.8    7.4   0.0    2.2  2  Porphobil_deam  Porphobilinogen deaminase, dipyromethane cofa


Domain annotation for each model (and alignments):
>> Sld5  GINS complex protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   3.3   1.1e-12     1e-08       2     108 ..      43     157 ..      42     158 .. 0.82

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 1.1e-12
                                    EEEHHHHHHHHHTTSCCCHHCHHHCHHHHHHCCCHHTTSSSSTTTTTTHHHHH...HHHHHHHT..........HCHHHH CS
                           Sld5   2 eLPlWlaelLkrqrrveieppewlspesleailedetkssdlpslpphflela...vkllelard.........ldelkr 69 
                                     LPl+lae+L ++  +e ++++ +++++l++ l +e k++ l+ l + f+  +   v+ le +++         l+elk 
  gi|119719411|ref|YP_919906.1|  43 KLPLFLAEELVESEVAEYVEEDLVKKAELKKQLWAEGKNEKLERLDDSFYLKFrlyVRALERRKNagdrnaekeLEELKT 122
                                    79*************************************888888887776663225555555557788899******** PP

                                    HHHHHHHHHHHHHHHTHCHHHHHHHTS-TCCHCCS-HHH CS
                           Sld5  70 llrdllevRlakirkfaenledaagggggellsglseeE 108
                                    l  dl+++R++ki  +a    + +     +   +++ eE
  gi|119719411|ref|YP_919906.1| 123 LFTDLVRSRMRKIAILAVLSPEVS----RDHIANMTREE 157
                                    *************99997777766....56666666666 PP

>> Porphobil_deam  Porphobilinogen deaminase, dipyromethane cofactor binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0   0.00031       2.8      58      88 ..       5      35 ..       2      85 .. 0.84
   2 ?    5.2   0.1    0.0014        13      29      64 ..     101     134 ..      58     143 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00031
                 Porphobil_deam 58 leeaLlegeidlaVhSlKDlptelpeglela 88
                                   l + Ll  ++++aV +lKD  + lp gle+ 
  gi|119719411|ref|YP_919906.1|  5 LARTLLYYDVEIAVKALKDKTVRLPGGLEVR 35
                                   778999*******************999986 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0014
                 Porphobil_deam  29 eivtiktkGDkildkpLakiggkglFtkeleeaLle 64 
                                     ++  k  GD++ +k+L+++  k lFt+ ++ ++ +
  gi|119719411|ref|YP_919906.1| 101 ALERRKNAGDRNAEKELEEL--KTLFTDLVRSRMRK 134
                                    67788999***********9..99***999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       721  (0.0402142); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1215.42
//
Query:       gi|119719412|ref|YP_919907.1|  [L=693]
Description: MCM family protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   2.1e-103  344.3   0.0   5.4e-103  342.9   0.0    1.7  2  MCM              MCM P-loop domain
    1.8e-38  131.2   0.2    3.2e-38  130.4   0.2    1.4  1  MCM_OB           MCM OB domain
    5.4e-31  106.9   5.1    5.8e-31  106.8   3.0    2.2  2  MCM_lid          MCM AAA-lid domain
    1.3e-16   61.1   0.5    1.5e-15   57.7   0.0    2.4  2  MCM_N            MCM N-terminal domain
    3.1e-08   33.2   0.1    6.8e-05   22.3   0.0    2.4  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    9.2e-07   28.9   0.0    2.9e-06   27.3   0.0    1.9  1  AAA_5            AAA domain (dynein-related subfamily)
    1.5e-05   24.9   0.0    4.2e-05   23.4   0.0    1.7  1  AAA_3            ATPase family associated with various cellul
     0.0046   16.3   0.1     0.0086   15.4   0.1    1.4  1  EAP30            EAP30/Vps36 family
  ------ inclusion threshold ------
       0.01   15.9   1.0      0.022   14.9   1.0    1.6  1  Zn-ribbon_8      Zinc ribbon domain
      0.013   15.5   0.5      0.021   14.8   0.5    1.3  1  DZR              Double zinc ribbon
      0.017   15.2   0.0      0.038   14.0   0.0    1.5  1  HypA             Hydrogenase/urease nickel incorporation, met
      0.032   14.5   0.0         15    5.9   0.0    2.6  2  Inhibitor_I10    Serine endopeptidase inhibitors
      0.033   13.9   0.1        0.2   11.3   0.1    2.1  1  Sigma54_activat  Sigma-54 interaction domain
      0.042   14.0   0.2      0.091   12.9   0.2    1.5  1  Bot1p            Eukaryotic mitochondrial regulator protein
      0.088   13.2   0.3       0.31   11.4   0.0    2.1  2  AAA_16           AAA ATPase domain
       0.25   11.0   1.1       0.53   10.0   0.1    1.9  2  MAGE             MAGE family


Domain annotation for each model (and alignments):
>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  342.9   0.0  4.9e-106  5.4e-103       2     224 .]     278     500 ..     277     500 .. 0.99
   2 ?   -2.0   0.0       1.4   1.6e+03      50     109 ..     606     665 ..     579     678 .. 0.75

  Alignments for each domain:
  == domain 1  score: 342.9 bits;  conditional E-value: 4.9e-106
                                    HHHHHHHHTSSTHHHHHHHHSSTTSSS-HHHHHHHHHHHH---EBBBSSSSBBCSS-EEEEEESSTSTHHHHHHHHHHHS CS
                            MCM   2 veeikelakekdiieklvksiapsiyghedvkkaillqlfggvkkkledktklrgdinvllvgdpgtaKsqlLkyvekla 81 
                                    +++i el++++d+ e++++siapsiyg++++k+ai+l+lfggv k ++d++++rgdi++ll+gdpgtaKsqlL+yv+++a
  gi|119719412|ref|YP_919907.1| 278 EKKILELSRREDLEEIIINSIAPSIYGYKEIKTAIALLLFGGVPKIHPDGIRVRGDIHILLIGDPGTAKSQLLRYVASIA 357
                                    789***************************************************************************** PP

                                    SSEEEEESSSSSSSHSSSEEEEESSSSSEEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEESSSCEEEE CS
                            MCM  82 pravytsgkgssaagLtaavvrdeetgefvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisiaKaGivatL 161
                                    pr+ ytsgkg+saagLtaavv+++++gef+leaGalvlad+Gv+ciDefdkm+ +dr+++hEamEqqt+siaKaGivatL
  gi|119719412|ref|YP_919907.1| 358 PRGLYTSGKGASAAGLTAAVVKEKNSGEFYLEAGALVLADGGVACIDEFDKMEAKDRVSIHEAMEQQTVSIAKAGIVATL 437
                                    ******************************************************************************** PP

                                    E--EEEEEEE--SSSSCCTTS-HHHHSSSSHHHHHHSSEEEEE-SSTTHHHHHHHHHHHHHHH CS
                            MCM 162 nartsvlaAanpkagrydkkksvaeninlsaalLsrFDlifvllDkvdeekDeelaehivslh 224
                                    nar+s+laAanp++gry + ++++eni+l+ ++LsrFDlifv++D++++e+D+ela+++v+ h
  gi|119719412|ref|YP_919907.1| 438 NARASILAAANPAFGRYLPGRNISENIDLPVTILSRFDLIFVVRDTPNAERDRELAQYVVDFH 500
                                    ************************************************************976 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.4
                                    SSSBBCSS-EEEEEESSTSTHHHHHHHHHHHSSSEEEEESSSSSSSHSSSEEEEESSSSS CS
                            MCM  50 dktklrgdinvllvgdpgtaKsqlLkyveklapravytsgkgssaagLtaavvrdeetge 109
                                    d +++  di+ ++ g p  ++ +l+  + ++ +     +g+  ++++L     ++   ++
  gi|119719412|ref|YP_919907.1| 606 DTQTMTIDIDTIMTGQPKSQREKLIAVLDTVKNLVRQNNGEPIKEEDLYSELEKNGIDRN 665
                                    445677899999999999999999998888888877778887777777777766665555 PP

>> MCM_OB  MCM OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.4   0.2   2.9e-41   3.2e-38       1     124 [.     108     238 ..     108     240 .. 0.93

  Alignments for each domain:
  == domain 1  score: 130.4 bits;  conditional E-value: 2.9e-41
                                    XXGG--GGGTTSEEEEEEEEEEE---EEEEEEEEEEETTT-.-EEE.....S----SB-..TTT-HHH....-EEE-GGG CS
                         MCM_OB   1 slRdlrsehigklvkveGivtrasevkpklkkavfeckkcgktvev.....eleePrkCeekeCeskd....pfkletek 71 
                                    ++R++r++h+g+lv veGivt++s vk++l++ vf+ck+cg++++v      l++P++C  + C++++     f+l +ek
  gi|119719412|ref|YP_919907.1| 108 KIRNIRARHLGRLVAVEGIVTKISPVKQELVEGVFKCKTCGTELTVpqgpeGLTKPTTC--PVCSENGvksaGFVLLPEK 185
                                    58****************************************9998888866888****..999944444459******* PP

                                    SEEEEEEEEEEE-------------EEEEEEEGGGTT---TT-EEEEEEEEEE CS
                         MCM_OB  72 skfvdfqklklQEspeevpaGelPrslevileddlvdkvkPGdrvevtGiyra 124
                                    skfvd qk  lQE+pee+p+G+lPrs+ev++++dlvd v+PGdr +v+G +r+
  gi|119719412|ref|YP_919907.1| 186 SKFVDLQKFVLQEKPEELPPGQLPRSIEVLVREDLVDVVRPGDRATVVGFLRM 238
                                    *************************************************9987 PP

>> MCM_lid  MCM AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       4.3   4.9e+03       9      27 ..     264     282 ..     258     287 .. 0.60
   2 !  106.8   3.0   5.1e-34   5.8e-31       2      85 ..     516     598 ..     515     600 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 4.3
                                    HHHHTT--BETCHHHHHHH CS
                        MCM_lid   9 yarekikPklseeakekls 27 
                                     a+e++   +++e+++k+ 
  gi|119719412|ref|YP_919907.1| 264 SAKENLDVEITPEDEKKIL 282
                                    2566666667766666664 PP

  == domain 2  score: 106.8 bits;  conditional E-value: 5.1e-34
                                    HHHHHHHHHHHTT--BETCHHHHHHHHHHHHHHHHHTSSTSSSST--HHHHHHHHHHHHHHHHHHTSSSE-HHHHHHHHH CS
                        MCM_lid   2 llrkYiayarekikPklseeakeklseaYvelRkeeedskrksipitvRqLesliRLseAlAklrlsevvteedveeair 81 
                                    +l+kYiayar++++P+ls+eak k++e+Yv++Rk++ed+ ++ i it+RqLe+liRLseA+A+++l++vvt++d+e ai+
  gi|119719412|ref|YP_919907.1| 516 TLKKYIAYARRHVRPRLSPEAKSKIVEYYVNMRKKSEDA-SSPIAITPRQLEALIRLSEAHARMHLRDVVTARDAEVAIS 594
                                    89********************************99755.99************************************** PP

                                    HHHH CS
                        MCM_lid  82 llke 85 
                                    l++ 
  gi|119719412|ref|YP_919907.1| 595 LMEY 598
                                    *985 PP

>> MCM_N  MCM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.7   0.0   1.3e-18   1.5e-15       2      86 ..      11      90 ..      10     135 .. 0.90
   2 ?    0.8   0.1      0.65   7.2e+02      48      86 ..     487     526 ..     485     562 .. 0.77

  Alignments for each domain:
  == domain 1  score: 57.7 bits;  conditional E-value: 1.3e-18
                          MCM_N  2 ekFedFLeefkddsededgekkYrdqlqemaerekttLevdlddLaafdeeLaeailenpkeylplleealkevvkklepsy 83
                                   e++ +FL+ f     + dg+ kYrd +++m  + + +L +d+ddL  fd+eLa+ +le p ++l++ ++a+ ev+k   p+y
  gi|119719412|ref|YP_919907.1| 11 ERITEFLKRF-----TVDGREKYRDAIRRMSIERSISLVIDFDDLLLFDKELADILLERPHDFLDAASKAIMEVLKIENPDY 87
                                   7999******.....7889********************************************************9999999 PP

                          MCM_N 84 kdd 86
                                   +++
  gi|119719412|ref|YP_919907.1| 88 AKE 90
                                   987 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.65
                          MCM_N  48 afdeeLaeailenpkeylpl.leealkevvkklepsykdd 86 
                                    + d+eLa+ +++   e +p+ le++l+    k + +y+++
  gi|119719412|ref|YP_919907.1| 487 ERDRELAQYVVDFHGETYPVsLEKVLDAQTLKKYIAYARR 526
                                    6789**************9989999999998888888877 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0013       1.5      19      48 ..     330     359 ..     327     364 .. 0.89
   2 !   22.3   0.0   6.1e-08   6.8e-05      95     159 ..     386     450 ..     374     463 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0013
                   Mg_chelatase  19 aaGgHnlllvGppGsGKtmlakrlpsllpp 48 
                                    + G  ++ll+G pG+ K+ l + ++s+ p+
  gi|119719412|ref|YP_919907.1| 330 VRGDIHILLIGDPGTAKSQLLRYVASIAPR 359
                                    67899******************9999885 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 6.1e-08
                   Mg_chelatase  95 skpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpc 159
                                       + G++ la  Gv  +DE+ ++++k   ++ e +e+++v+i++a   ++  ar  ++aa+Np+
  gi|119719412|ref|YP_919907.1| 386 FYLEAGALVLADGGVACIDEFDKMEAKDRVSIHEAMEQQTVSIAKAGIVATLNARASILAAANPA 450
                                    46789***********************************************************7 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   2.6e-09   2.9e-06       1     123 [.     335     450 ..     335     464 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 2.6e-09
                                    EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--...........--------G-SEEEEESGGG-- CS
                          AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik..ngttslvdsplvraaregeilvlDEverae 78 
                                    ++lL+G+pGt+Ks+l +++a+   r + +    ++ +++ l+  +  +  +g+  l+ ++lv     g ++++DE++++e
  gi|119719412|ref|YP_919907.1| 335 HILLIGDPGTAKSQLLRYVASIAPRGLYT--SGKGASAAGLTAAVVKEknSGEFYLEAGALV--LADGGVACIDEFDKME 410
                                    79********************9777655..45556666666666644557999********..89************** PP

                                    HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS- CS
                          AAA_5  79 sevlnsLlslleerrllleeggelvkaknddllerfrviatanpl 123
                                     +   s +  +e++++++++ g +   ++       +++a+anp+
  gi|119719412|ref|YP_919907.1| 411 AKDRVSIHEAMEQQTVSIAKAGIVATLNAR-----ASILAAANPA 450
                                    999999***********9999888877775.....8899999986 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   3.7e-08   4.2e-05       1     113 [.     335     450 ..     335     455 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 3.7e-08
                          AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvf.an..llladeinrappk 77 
                                    h+ll g PG+ak +l + +a++    +           + ++ + v e+++ ef +++G+++ a+  +   de ++ ++k
  gi|119719412|ref|YP_919907.1| 335 HILLIGDPGTAKSQLLRYVASIAPRGLYTS--GKGASAAGLTAAVVKEKNSGEFYLEAGALVlADggVACIDEFDKMEAK 412
                                    9******************99876655432..3345678899999999999********976243448999********* PP

                          AAA_3  78 tqsalleameerqvtvege..thklpepflvlatqnPi 113
                                     + ++ eame+++v+++++    +l+    +la+ nP 
  gi|119719412|ref|YP_919907.1| 413 DRVSIHEAMEQQTVSIAKAgiVATLNARASILAAANPA 450
                                    **************998662267999**********95 PP

>> EAP30  EAP30/Vps36 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   7.7e-06    0.0086     101     233 ..     539     681 ..     535     682 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 7.7e-06
                          EAP30 101 qivevclatraeng..............glisleelyalvnrarggvalvspdDllraiekl....lvlgsglsvlqvgg 162
                                    +ive+  + r+++                li l+e  a++   r   + v+  D + ai+++    ++ g   + ++++ 
  gi|119719412|ref|YP_919907.1| 539 KIVEYYVNMRKKSEdasspiaitprqleALIRLSEAHARMH-LR---DVVTARDAEVAISLMeyflRNVGIDTQTMTIDI 614
                                    67777777766666777777777777778888888888887.56...69*************988888886666666555 PP

                          EAP30 163 kkvvrSvptelntdqvevlevakrlvsllaekssgggvtaselaeeeenlgwsvarakeaLeelereGllw 233
                                     +++   p++++++  +vl ++k+l   ++++++ + +++++l +e e+ g++++ a++a+e+l+++G l+
  gi|119719412|ref|YP_919907.1| 615 DTIMTGQPKSQREKLIAVLDTVKNL---VRQNNG-EPIKEEDLYSELEKNGIDRNFARKAIEKLLEQGELM 681
                                    6666666666666655555555555...666666.489999999998899******************997 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   1.0   1.9e-05     0.022       6      34 ..     142     171 ..     141     176 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.9e-05
                    Zn-ribbon_8   6 YrCeeCghefevlqsis.dapltaCPeCgs 34 
                                    ++C+ Cg+e +v q      ++t+CP C +
  gi|119719412|ref|YP_919907.1| 142 FKCKTCGTELTVPQGPEgLTKPTTCPVCSE 171
                                    9*************9886555666****87 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.5   1.9e-05     0.021      10      37 ..     139     172 ..     134     179 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.9e-05
                            DZR  10 pdarfCseCgtklkavaa.......edrCpsCgek 37 
                                    ++   C++Cgt+l  + +       +++Cp C+e 
  gi|119719412|ref|YP_919907.1| 139 EGVFKCKTCGTELTVP-QgpegltkPTTCPVCSEN 172
                                    55667********855.4599***********987 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   3.4e-05     0.038      56      98 ..     127     175 ..      78     178 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.4e-05
                                    TTTT-EEEEEEE--EEEETTTS-EEECHH..HHH.....S-TTTSSS-EE CS
                           HypA  56 vlegaeLeieevpvkvrCreCgkefelee..kal.....rCpkCgsadve 98 
                                    v++ + ++ e v+ +++C++Cg+e ++ +  +       +Cp C++++v+
  gi|119719412|ref|YP_919907.1| 127 VTKISPVKQELVEGVFKCKTCGTELTVPQgpE-GltkptTCPVCSENGVK 175
                                    455566778999**************876442.1455669*****99886 PP

>> Inhibitor_I10  Serine endopeptidase inhibitors
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.016        18       5      34 ..     240     268 ..     238     284 .. 0.76
   2 ?    5.9   0.0     0.014        15       4      27 ..     438     462 ..     436     466 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.016
                  Inhibitor_I10   5 aekdlnanAvPFFARfLegQeceelsdeev 34 
                                    ++k+l  nA P F  +Le  +  e+s  e 
  gi|119719412|ref|YP_919907.1| 240 EDKKLVKNAPPIFHAYLEANY-VEVSAKEN 268
                                    578899**************9.55554443 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.014
                  Inhibitor_I10   4 naekdlnanAvPFFARfLegQe.ce 27 
                                    na++ + a A P F R+L g + +e
  gi|119719412|ref|YP_919907.1| 438 NARASILAAANPAFGRYLPGRNiSE 462
                                    56778889**********9998554 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00018       0.2      22     143 ..     333     449 ..     327     464 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00018
                                    SS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEBSSSSSTTTSS-BEHHHHHTTTSEEEEET CS
                Sigma54_activat  22 dlsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGhekGaFtGAekekkGlfekadgGtlfLDe 101
                                    d+++l+ G+ Gt K+ l r + +  +r    + +   +a ++ l ++ +   ++G F      ++G++  adgG+  +De
  gi|119719412|ref|YP_919907.1| 333 DIHILLIGDPGTAKSQLLRYVASIAPR---GLYTSGKGASAAGLTAAVVKEKNSGEF----YLEAGALVLADGGVACIDE 405
                                    566677777777776666666555543...344555566666666665544455544....4578*************** PP

                                    GGGS-HHHHHHHHHHHHHSEE..ESBTSSSEEE--EEEEEEESS CS
                Sigma54_activat 102 igelplelQekLlrvlqegev..ervGsskeikvdvriiaatne 143
                                      +++++  + + +++++++v   + G  ++ ++   i+aa+n 
  gi|119719412|ref|YP_919907.1| 406 FDKMEAKDRVSIHEAMEQQTVsiAKAGIVATLNARASILAAANP 449
                                    ****************9997522689999999999999999886 PP

>> Bot1p  Eukaryotic mitochondrial regulator protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   8.1e-05     0.091      15      67 ..     530     582 ..     526     626 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.1e-05
                          Bot1p  15 pvlseelreeIyeevakkgksvrevSvkygvkikRveAivrLkelekkwknkg 67 
                                    p ls e++ +I+e +++  k  ++ S+   + ++ +eA++rL e   +++ + 
  gi|119719412|ref|YP_919907.1| 530 PRLSPEAKSKIVEYYVNMRKKSEDASSPIAITPRQLEALIRLSEAHARMHLRD 582
                                    5699****************************************999986554 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       5.1   5.7e+03     126     154 ..      31      60 ..      11      92 .. 0.61
   2 ?   11.4   0.0   0.00028      0.31      26      63 ..     335     370 ..     329     443 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 5.1
                         AAA_16 126 llallsrderp..lvlvlDdlqwadeaslql 154
                                    +++++s  er   lv+ +Ddl  +d + +++
  gi|119719412|ref|YP_919907.1|  31 AIRRMSI-ERSisLVIDFDDLLLFDKELADI 60 
                                    3444444.33212555555555555544444 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00028
                         AAA_16  26 lvllsGesGvGKsslvrellralekdggiflrgkcdql 63 
                                     +ll+G++G+ Ks l+r ++ ++  + g++++gk  + 
  gi|119719412|ref|YP_919907.1| 335 HILLIGDPGTAKSQLLRYVA-SIAPR-GLYTSGKGASA 370
                                    689*****************.78888.67777776655 PP

>> MAGE  MAGE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1       1.3   1.5e+03     142     209 ..     490     552 ..     484     555 .. 0.73
   2 ?   10.0   0.1   0.00047      0.53      85     171 ..     596     673 ..     565     681 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.3
                           MAGE 142 qeLekyLkrlgldenstskeitklklkldelLkklvkqgYlvreke...s.kasdeeeekveyrvGpRakvE 209
                                    +eL +y   ++ ++           ++l+++L+  + ++Y+   +    +  + +++ ++vey v  R k E
  gi|119719412|ref|YP_919907.1| 490 RELAQYVVDFHGETY---------PVSLEKVLDAQTLKKYIAYARRhvrPrLSPEAKSKIVEYYVNMRKKSE 552
                                    556666666666655.........248999999999999998777777744567888999999999887766 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00047
                           MAGE  85 ksyiLvstlpeeyreaaaiiapskiesealeekeaaykGiltvvlslills.ggsiseqeLekyLkrlgldenstskeit 163
                                     +y+L+++  +++     +i+ + i + +++ + ++++++l +v  l+  + g+ i+e++L++ L++ g+d+n   ++  
  gi|119719412|ref|YP_919907.1| 596 MEYFLRNVGIDTQT---MTIDIDTIMTGQPKSQREKLIAVLDTVKNLVRQNnGEPIKEEDLYSELEKNGIDRNFA-RK-- 669
                                    56888888777544...6677777777788999999*************997888*****************954.32.. PP

                           MAGE 164 klklklde 171
                                         +++
  gi|119719412|ref|YP_919907.1| 670 ----AIEK 673
                                    ....4444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (693 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.68u 0.28s 00:00:00.96 Elapsed: 00:00:00.45
# Mc/sec: 4584.51
//
Query:       gi|119719413|ref|YP_919908.1|  [L=739]
Description: DEAD/DEAH box helicase domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-24   86.1   0.0    2.4e-23   82.8   0.0    2.4  2  DEAD             DEAD/DEAH box helicase
    4.7e-13   49.5   0.3    1.9e-12   47.6   0.1    2.3  1  HHH_5            Helix-hairpin-helix domain
    2.4e-10   40.7   0.0      4e-10   40.0   0.0    1.3  1  ResIII           Type III restriction enzyme, res subunit
    2.7e-10   40.6   0.0    1.2e-08   35.3   0.0    3.2  2  Helicase_C       Helicase conserved C-terminal domain
    1.3e-07   31.6   0.0    9.7e-06   25.6   0.0    2.6  2  HHH_2            Helix-hairpin-helix motif
    1.6e-06   27.6   0.0      0.075   12.9   0.0    3.7  3  HHH              Helix-hairpin-helix motif
    0.00033   20.4   0.0     0.0071   16.2   0.0    2.8  2  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
     0.0018   18.5   0.0        4.2    7.9   0.0    2.8  2  IMS_HHH          IMS family HHH motif
     0.0065   16.5   0.1      0.024   14.7   0.1    2.1  1  HemN_C           HemN C-terminal domain
      0.008   15.9   0.0      0.026   14.2   0.0    1.9  2  AAA_30           AAA domain
  ------ inclusion threshold ------
      0.028   14.7   0.0       0.28   11.5   0.0    2.3  2  HHH_3            Helix-hairpin-helix motif
      0.032   14.5   0.0        8.4    6.7   0.0    2.6  2  Cdd1             Pathogenicity locus
       0.11   12.3   0.0        0.4   10.4   0.0    2.0  1  S4               S4 domain


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.8   0.0   1.7e-26   2.4e-23       6     170 ..      35     188 ..      30     193 .. 0.85
   2 ?    0.2   0.0      0.41   5.7e+02      45      73 ..     247     275 ..     235     348 .. 0.71

  Alignments for each domain:
  == domain 1  score: 82.8 bits;  conditional E-value: 1.7e-26
                                    HHHHH.HHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETT CS
                                    xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD   6 eaipl.ilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliigg 84 
                                    +a++  +l+g++++++a+T+sGKTl++ +++l+++      +g k+l+++P+r+La + ++++k+f+ + ++r +l +g+
  gi|119719413|ref|YP_919908.1|  35 AAVEKgVLDGKNIVLSAPTASGKTLVAELAALKHL-----LNGGKVLYLAPLRALASEKFKEFKEFFGEFGYRSVLSTGD 109
                                    555541569***********************999.....5689*************************99998877664 PP

                                    SSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  85 vaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrqviv 164
                                      ++     l  ++d++v+t ++ d+ll+     + +v++++ DE++ l +++++ +++ +l+++    ++ + q  ++ 
  gi|119719413|ref|YP_919908.1| 110 --YDTADPSL-GKYDVIVTTNEKADSLLRHSAPWFPDVTLVIADEVHLLGSEKRGATLEVLLTRI--LLSEDPPQ--ILG 182
                                    ..33444556.678**************766767*******************************..45555545..*** PP

                                    EESSBS CS
                                    xxxxxx RF
                           DEAD 165 lSATlp 170
                                    lSAT+ 
  gi|119719413|ref|YP_919908.1| 183 LSATIG 188
                                    ****96 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.41
                                    STS-EEEEEESSHHHHHHHHHHHHHHTTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  45 ktgpkalivePtreLaeqtlnnlkkfkky 73 
                                    +++ +al+ +Ptr  a   +++l+ ++ +
  gi|119719413|ref|YP_919908.1| 247 REEGQALVFSPTRRAASSDAKKLSVYTRK 275
                                    55668999999998888777777666554 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.6   0.1   1.4e-15   1.9e-12       3      55 ..     659     711 ..     655     713 .. 0.95

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 1.4e-15
                                    HHHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHH CS
                          HHH_5   3 eLlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriilel 55 
                                    eL s+ GiG+++A++l+++G++s+ dl+ ad+ +L++ipGiG+ +A++i+ +l
  gi|119719413|ref|YP_919908.1| 659 ELVSLRGIGRVRARRLYEHGYKSLVDLILADERDLTRIPGIGPNLARSIKRQL 711
                                    7889*********************************************9988 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   0.0   2.9e-13     4e-10      21     169 ..      26     187 ..      10     189 .. 0.78

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 2.9e-13
                                    .................TTSEEEEEESTTSTHHHHH.HHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG.... CS
                         ResIII  21 s...............krdkrglikmaTGtGKTlva.aklierllkkgkeekflflvprkslleqtleefkkflseayke 84 
                                    +                + k++++ ++T +GKTlva +++ ++ll+ g+  k+l l+p ++l +   +efk+f+ e    
  gi|119719413|ref|YP_919908.1|  26 IktlyptqvaavekgvLDGKNIVLSAPTASGKTLVAeLAALKHLLN-GG--KVLYLAPLRALASEKFKEFKEFFGEFGY- 101
                                    44444444444444445678999*************8888888887.55..8*********************998543. PP

                                    GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-S..EEEEETGGGTTS.T.......TTHHHHH CS
                         ResIII  85 igkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfd..viiiDEaHrlgakk.......swreile 155
                                     +   +gd ++a   +  + +++vtt +++d+ +        +  + + d  ++i DE+H lg++k         ++il 
  gi|119719413|ref|YP_919908.1| 102 RSVLSTGDYDTA-DPSLGKYDVIVTTNEKADSLL-------RHSAPWFPDvtLVIADEVHLLGSEKrgatlevLLTRILL 173
                                    666677777777.8899*****************.......2333333335599**********8677777778888888 PP

                                    T---SEEEEEESS- CS
                         ResIII 156 kfkeavllglTATp 169
                                    + ++  +lgl+AT+
  gi|119719413|ref|YP_919908.1| 174 SEDPPQILGLSATI 187
                                    8899*********7 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.97   1.3e+03      11      50 ..      67     110 ..      58     134 .. 0.60
   2 !   35.3   0.0   8.6e-12   1.2e-08      14     109 ..     247     388 ..     235     390 .. 0.66

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.97
                                    HHTTTTSEEEEEESSHH.HHHHHHHHHHHT...TSTEEEESTTS CS
                     Helicase_C  11 kleeeggkilifvntid.rlekvklllekk...gikvavlhgel 50 
                                    k+  +ggk+l  ++ +    ek+k ++e +   g++++  +g+ 
  gi|119719413|ref|YP_919908.1|  67 KHLLNGGKVLYLAPLRAlASEKFKEFKEFFgefGYRSVLSTGDY 110
                                    55568888888888888533333444222233367766666654 PP

  == domain 2  score: 35.3 bits;  conditional E-value: 8.6e-12
                                    TTTSEEEEEESSHH....HHHH....HHHH.......................HHHT.......TSTEEEESTTSTHHHH CS
                     Helicase_C  14 eeggkilifvntid....rlek....vkll.......................lekk.......gikvavlhgelpqner 55 
                                    +e+g++l+f++t++    +++k    ++ +                       l             va +h+ l+ + r
  gi|119719413|ref|YP_919908.1| 247 REEGQALVFSPTRRaassDAKKlsvyTRKFlrdserrhlkeaarkvlsshadkL--TnelaelmLHGVAFHHAGLSGDAR 324
                                    567777777777774433221122231111344444433333333333333321..022334446788889999****** PP

                                    HHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEEESSSS.SSH..........HHHHHHHTTSSS CS
                     Helicase_C  56 eeileqfnkgesdvLiatdvaerGidipkvnlVinfdlp.rnv..........tsyiqriGRtgR 109
                                    e + + f++g  + ++at  ++ G+++p ++ Vi+ d+  +nv           +y+q++GR+gR
  gi|119719413|ref|YP_919908.1| 325 ETVEQLFREGFLKTVVATPTLAAGVNLP-ARRVIITDYRrYNVelgyhesipvMEYKQMAGRAGR 388
                                    ***************************9.889999999974556666666777************ PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.074     1e+02      39      59 ..     230     250 ..     229     254 .. 0.89
   2 !   25.6   0.0     7e-09   9.7e-06       6      53 ..     661     709 ..     656     713 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.074
                          HHH_2  39 evddiGeeiAqsivefFenek 59 
                                    +v+d+G   A+ +++ +++e 
  gi|119719413|ref|YP_919908.1| 230 SVEDVGSALANLVHDVLREEG 250
                                    69*************999875 PP

  == domain 2  score: 25.6 bits;  conditional E-value: 7e-09
                          HHH_2   6 LGIrhVGektAklLakr.FksldaLkkasleeLlevddiGeeiAqsive 53 
                                     ++r +G   A+ L ++ +ksl  L  a++ +L+ +++iG+  A+si++
  gi|119719413|ref|YP_919908.1| 661 VSLRGIGRVRARRLYEHgYKSLVDLILADERDLTRIPGIGPNLARSIKR 709
                                    578************998*****************************75 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.28   3.9e+02      15      29 ..     230     244 ..     229     245 .. 0.89
   2 !    8.8   0.0    0.0011       1.5      12      29 ..     659     676 ..     659     677 .. 0.91
   3 !   12.9   0.0   5.5e-05     0.075       2      28 ..     682     708 ..     681     709 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.28
                                    TSTT-SHHHHHHHHH CS
                            HHH  15 alPGVGpktAeaIls 29 
                                    +++ VG + A+ +++
  gi|119719413|ref|YP_919908.1| 230 SVEDVGSALANLVHD 244
                                    799********9997 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0011
                                    HHHTSTT-SHHHHHHHHH CS
                            HHH  12 eLlalPGVGpktAeaIls 29 
                                    eL++l G+G+ +A++ ++
  gi|119719413|ref|YP_919908.1| 659 ELVSLRGIGRVRARRLYE 676
                                    8*************9876 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 5.5e-05
                                    HHHHHTSSHHHHHTSTT-SHHHHHHHH CS
                            HHH   2 leglipasreeLlalPGVGpktAeaIl 28 
                                    l  li a++ +L+ +PG+Gp  A++I 
  gi|119719413|ref|YP_919908.1| 682 LVDLILADERDLTRIPGIGPNLARSIK 708
                                    6778899999**************995 PP

>> DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   5.1e-06    0.0071       8      36 ..     665     694 ..     659     700 .. 0.82
   2 ?    1.8   0.0      0.16   2.2e+02       3      16 ..     693     706 ..     691     712 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5.1e-06
                DNA_pol_lambd_f   8 GVGpktAkkwyakGirtledlra.krakLt 36 
                                    G+G+++A+++y+ G+++l dl   ++ +Lt
  gi|119719413|ref|YP_919908.1| 665 GIGRVRARRLYEHGYKSLVDLILaDERDLT 694
                                    9*******************9765445555 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.16
                DNA_pol_lambd_f   3 FtkvyGVGpktAkk 16 
                                    +t++ G+Gp  A+ 
  gi|119719413|ref|YP_919908.1| 693 LTRIPGIGPNLARS 706
                                    89********9986 PP

>> IMS_HHH  IMS family HHH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.0    0.0041       5.6      11      31 ..     658     678 ..     655     679 .. 0.88
   2 !    7.9   0.0     0.003       4.2      10      27 ..     690     707 ..     680     712 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0041
                        IMS_HHH  11 lpitkipGiGgklgekLeklG 31 
                                    l++ +++GiG++ + +L  +G
  gi|119719413|ref|YP_919908.1| 658 LELVSLRGIGRVRARRLYEHG 678
                                    47889************9888 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.003
                        IMS_HHH  10 plpitkipGiGgklgekL 27 
                                    ++++t ipGiG+ l+  +
  gi|119719413|ref|YP_919908.1| 690 ERDLTRIPGIGPNLARSI 707
                                    689*********999874 PP

>> HemN_C  HemN C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   1.8e-05     0.024      26      65 ..     461     501 ..     451     502 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.8e-05
                         HemN_C  26 feqrfgld.leellaaaleklqeqGLLeldggrlrltprGr 65 
                                    f+ +fg   l+ l +++l++l e GL+el+g+ l++t  Gr
  gi|119719413|ref|YP_919908.1| 461 FALKFGTFsLSTLSRKVLRRLVEGGLVELNGEALKPTFLGR 501
                                    56666665688889**********************98877 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   1.9e-05     0.026       2     112 ..      29     167 ..      28     185 .. 0.70
   2 ?   -2.8   0.0       3.1   4.3e+03      39      66 ..     243     269 ..     236     290 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.9e-05
                         AAA_30   2 lnaeQaaavealltsgdrvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkv.Lae................ 64 
                                    l + Q aave+ + +g+   vl +p  +GKt + + ++  +  +gg+v+ lAp  + A +  +e                
  gi|119719413|ref|YP_919908.1|  29 LYPTQVAAVEKGVLDGK-NIVLSAPTASGKTLVAELAALKHLLNGGKVLYLAPLRALASEkFKEfkeffgefgyrsvlst 107
                                    7899*******999997.789999999****9988887777777*********998887658855556665555544433 PP

                         AAA_30  65 ........elgieastiakllkrlk..............grarlepg.tllivDEagmvdtkqlaallkaa 112
                                            +           l +++              + a + p+ tl+i DE+ ++++++  a l+ +
  gi|119719413|ref|YP_919908.1| 108 gdydtadpS-----------LGKYDvivttnekadsllrHSAPWFPDvTLVIADEVHLLGSEKRGATLEVL 167
                                    333333331...........3333344444445555555666788888*******9999998887777766 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.1
                         AAA_30  39 reaweaaggrviglAptgkaAkvLaeel 66 
                                     ++++++ g+ ++++pt +aA   a++l
  gi|119719413|ref|YP_919908.1| 243 HDVLREE-GQALVFSPTRRAASSDAKKL 269
                                    4444444.47888999999998655555 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.72   9.9e+02      15      33 ..     659     677 ..     655     681 .. 0.85
   2 ?   11.5   0.0    0.0002      0.28       6      30 ..     683     707 ..     678     710 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.72
                          HHH_3  15 eLqklpGlgpklAknIvay 33 
                                    eL  l G+g + A+++ ++
  gi|119719413|ref|YP_919908.1| 659 ELVSLRGIGRVRARRLYEH 677
                                    788999*******998776 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.0002
                          HHH_3   6 vdiNtAsaeeLqklpGlgpklAknI 30 
                                    vd+  A++ +L+++pG+gp+lA+ I
  gi|119719413|ref|YP_919908.1| 683 VDLILADERDLTRIPGIGPNLARSI 707
                                    777789*****************98 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0    0.0087        12       3      39 ..     655     691 ..     653     694 .. 0.87
   2 ?    6.7   0.0    0.0061       8.4       6      26 ..     691     712 ..     687     723 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0087
                           Cdd1   3 kalkelqdiPniGkalaedlvelGirsveelkgedpe 39 
                                    ++l el ++ +iG+  a+ l+e G++s+ +l   d  
  gi|119719413|ref|YP_919908.1| 655 EELLELVSLRGIGRVRARRLYEHGYKSLVDLILADER 691
                                    67889999**********************9877765 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0061
                           Cdd1   6 kelqdiPniGkalaedlv.elG 26 
                                    ++l++iP+iG++la+ +  +lG
  gi|119719413|ref|YP_919908.1| 691 RDLTRIPGIGPNLARSIKrQLG 712
                                    589***********99864666 PP

>> S4  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00029       0.4      15      38 ..     474     496 ..     472     499 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00029
                                    SHHHHHHHHHTTTEEETTEEE--T CS
                             S4  15 srreArqlIehGrVlVNGkvvkdp 38 
                                    sr+  r+l+e+G V +NG+  k p
  gi|119719413|ref|YP_919908.1| 474 SRKVLRRLVEGGLVELNGEALK-P 496
                                    8999**************9887.5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (739 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.67u 0.27s 00:00:00.94 Elapsed: 00:00:00.43
# Mc/sec: 5120.93
//
Query:       gi|119719414|ref|YP_919909.1|  [L=601]
Description: translation initiation factor IF-2 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      4e-33  113.2   2.8      4e-33  113.2   2.8    2.3  2  GTP_EFTU_D4  Elongation factor Tu domain 4
    4.1e-31  108.0   0.0    4.2e-30  104.7   0.0    2.1  2  GTP_EFTU     Elongation factor Tu GTP binding domain
    1.9e-19   69.7   0.2      4e-19   68.7   0.2    1.5  1  IF-2         Translation-initiation factor 2
    1.7e-08   34.7   8.8    3.5e-08   33.7   0.0    3.0  3  GTP_EFTU_D2  Elongation factor Tu domain 2
    1.3e-07   31.7   0.0    5.2e-07   29.7   0.0    2.1  2  MMR_HSR1     50S ribosome-binding GTPase
    0.00021   21.5   0.0    0.00058   20.1   0.0    1.8  2  Roc          Ras of Complex, Roc, domain of DAPkinase
     0.0003   20.7   0.0     0.0032   17.3   0.0    2.3  2  ATP_bind_1   Conserved hypothetical ATP binding protein
     0.0032   17.5   0.0      0.011   15.8   0.0    1.9  2  Dynamin_N    Dynamin family
     0.0053   16.5   0.2       0.84    9.4   0.0    3.0  3  PduV-EutP    Ethanolamine utilisation - propanediol utilisati
  ------ inclusion threshold ------
      0.033   13.6   0.1          1    8.8   0.0    2.7  2  Arf          ADP-ribosylation factor family
      0.045   13.4   0.0       0.26   10.9   0.0    2.1  1  Ras          Ras family
      0.072   13.0   0.4        2.7    7.8   0.0    2.9  3  RsgA_GTPase  RsgA GTPase
      0.095   12.4   0.4       0.18   11.5   0.4    1.5  1  DUF1741      Domain of unknown function (DUF1741)


Domain annotation for each model (and alignments):
>> GTP_EFTU_D4  Elongation factor Tu domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       2.1   2.9e+03      41      52 ..     336     347 ..     310     376 .. 0.58
   2 !  113.2   2.8   2.9e-36     4e-33       2      86 .]     472     557 ..     471     557 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2.1
                                    E.EEEEEEEEEE CS
                    GTP_EFTU_D4  41 GrevGeilqiqd 52 
                                     +evG+++q+ +
  gi|119719414|ref|YP_919909.1| 336 EEEVGRLKQLVE 347
                                    345555555433 PP

  == domain 2  score: 113.2 bits;  conditional E-value: 2.9e-36
                                    -CEEEEEEEEEEETCCCEEEEEEEEEEEEETT-EEEETTE.EEEEEEEEEETTEEESEEETT-EEEEEEESS-.TTTS-- CS
                    GTP_EFTU_D4   2 PgkikilpgvvfrrsdpaivGvevlgGvikpgvklikedGrevGeilqiqdkgkkleeakaGqevaisiegki.vGrqik 80 
                                    P+ ++ilpg+vfrr+dp+ivGv+v++G+i++gv+li++dGre+Gei+qi++++k l+++++G+evaisi++k  vGrq+k
  gi|119719414|ref|YP_919909.1| 472 PAVVQILPGYVFRRRDPIIVGVRVVCGRIRSGVPLITKDGREIGEIMQIKEHDKVLDVVSEGAEVAISIRSKAiVGRQVK 551
                                    99*********************************************************************988****** PP

                                    TT-EEE CS
                    GTP_EFTU_D4  81 egdily 86 
                                    egd+ly
  gi|119719414|ref|YP_919909.1| 552 EGDYLY 557
                                    *****9 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.7   0.0     3e-33   4.2e-30       5     189 ..      14     220 ..      11     225 .. 0.80
   2 ?    0.5   0.0      0.28   3.8e+02      26      63 ..     510     547 ..     505     560 .. 0.79

  Alignments for each domain:
  == domain 1  score: 104.7 bits;  conditional E-value: 3e-33
                                    EEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHH..HHHSTHCHSHHHHHHTSCSSCEEEEEETTCSSEEEEEEEESSSGG CS
                       GTP_EFTU   5 nigiighvDhGKtTLtdrLlyktgaiskkgeka..eeervlDtlkeErergiTiksaaisleketkkylinliDtPGHvd 82 
                                     ++++ghvD+GKtTL+d++  ++ a ++ g+ +   ++++l + + E   g  ++   ++         + +iDtPGH+ 
  gi|119719414|ref|YP_919909.1|  14 IVVVLGHVDAGKTTLLDKIRGTAVAKREPGTMTqhIGASFLPWKALEAVCGSLVSQIRAE----VVIPGFLVIDTPGHEA 89 
                                    689****************99888888877766343488999999999877655555555....5589999********* PP

                                    GHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGST...........HHHHHHHHHHHHHHHH CS
                       GTP_EFTU  83 FskevirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrl...........kaelkeiveevkqkls 151
                                    Fs+   rg +++D+a+lvvd+ +G e+qt e + ++++++vp+iv++NK+D++            +++k++ e+++ kl 
  gi|119719414|ref|YP_919909.1|  90 FSNLRRRGGSIADIAILVVDVLRGLEQQTFESIDILRERKVPFIVAVNKIDKIpgwksfpntpfVESVKRQSEAAQLKL- 168
                                    ********************************************************99996666555555555555555. PP

                                    HHHHHHHHHHHTTT.................TTEEEEEEBTTTTBTHHHHHHHHH CS
                       GTP_EFTU 152 rkeeklekygekge.................kevpvvfgSalkgegvktllealv 189
                                       e+l +y  ++                  +   +v++Sa++geg+ +ll +l 
  gi|119719414|ref|YP_919909.1| 169 ---EELLSYIIQQFaslgfrsdrydrirdftRVLALVPVSAVTGEGIPDLLLVLA 220
                                    ...33334433333444555567788887778999**************998876 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.28
                                    HTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEE CS
                       GTP_EFTU  26 ktgaiskkgekaeeervlDtlkeErergiTiksaaisl 63 
                                    +  +i +  + +e+++vlD  +e  e  i+i s+ai  
  gi|119719414|ref|YP_919909.1| 510 DGREIGEIMQIKEHDKVLDVVSEGAEVAISIRSKAIVG 547
                                    5566777777778899*****************99865 PP

>> IF-2  Translation-initiation factor 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.7   0.2   2.9e-22     4e-19       3     104 ..     348     450 ..     346     451 .. 0.90

  Alignments for each domain:
  == domain 1  score: 68.7 bits;  conditional E-value: 2.9e-22
                                    CHHHCCCSCSSCCEEEEEESSHHHHHHHHHHHHCTT.SSTEEEECEEEESSB-HHHHHHHHHST......EEEEEESSSC CS
                           IF-2   3 elfeeikeegkelnviikaDvqGsleAlkeaLekleseevkvkvihsgvGaitesDvelasasn......aiiigFnvkv 76 
                                    e+++ +k e + ++v++kaD+ G+leAl  +L+k       +++  +++G++ ++Dv  as  +      a i++Fnvk+
  gi|119719414|ref|YP_919909.1| 348 EEISGVKFERDVVGVVVKADTLGTLEALVGYLKKQ-----GIPIRVADIGPVVKRDVVQASMVKekdplyAAILAFNVKI 422
                                    5566667677999*********************8.....499999**************9943357999********** PP

                                    THHHHHCCCCCTSEEEEESSHHHHHHHH CS
                           IF-2  77 skkakklaekegvkirlynvIYkliddv 104
                                     ++a+++a+++g+ +++ +++Ykl++++
  gi|119719414|ref|YP_919909.1| 423 LPEAQDEAARHGIPVFQERIMYKLVENY 450
                                    *************************987 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   0.0   2.6e-11   3.5e-08       1      73 [.     252     330 ..     252     331 .. 0.93
   2 ?   -2.0   0.1       3.6     5e+03      48      65 ..     354     371 ..     335     377 .. 0.61
   3 ?    4.0   2.3     0.048        66       3      63 ..     490     545 ..     489     557 .. 0.83

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 2.6e-11
                                    EEEEEEEEEESEEETTEEEEEEC.TCTTSEEEEEEEEEEEEETEEESEE...........ETTSEEEEEEEESSCCSGSS CS
                    GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilg.ndtskkeivtrissletfhededea...........vaganaGvivaikgledaii 68 
                                    G +a+ ++y+G++++Gd v+ +g  +   +   tr+++l+++ +++de+           +  a+aGv++ + gle+a +
  gi|119719414|ref|YP_919909.1| 252 GMTATLILYDGVIRRGDIVVTGGiEGA-FS---TRVRALLMP-KPLDEMrspedrfleveRIVAAAGVKLVAEGLEKA-V 325
                                    678999***************997764.88...*********.88***************999**************8.9 PP

                                    TTCEE CS
                    GTP_EFTU_D2  69 vGdtl 73 
                                     G++l
  gi|119719414|ref|YP_919909.1| 326 PGAPL 330
                                    99987 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.6
                                    EETTSEEEEEEEESSCCS CS
                    GTP_EFTU_D2  48 avaganaGvivaikgled 65 
                                      + +++Gv v+++ l +
  gi|119719414|ref|YP_919909.1| 354 KFERDVVGVVVKADTLGT 371
                                    366778888888877655 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.048
                                    EEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSC CS
                    GTP_EFTU_D2   3 valgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikgl 63 
                                    ++++rv+ G ++ G  +    +d  +  ++++i ++  + + +d + +ga + + ++ k +
  gi|119719414|ref|YP_919909.1| 490 IVGVRVVCGRIRSGVPLIT--KDG-R--EIGEIMQIKEHDKVLDVVSEGAEVAISIRSKAI 545
                                    699***********99998..762.3..69**********************999987766 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.0   3.8e-10   5.2e-07       2     114 .]      15     138 ..      14     138 .. 0.75
   2 ?   -2.2   0.0       3.2   4.4e+03      33      58 ..     371     396 ..     352     435 .. 0.67

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 3.8e-10
                                    EEEEESTTSSHHHHHHHHHTSTEEESSSTTS.SSSEEEEEEEETTEE..................EEEEECGGCSSHHHH CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgt.Trdinegrvklkgke..................ielvDtpGliegase 62 
                                    v+++G+  +GK+tL+ ++ g+ a ++++pgt T++i    + +k  e                  + ++DtpG  e    
  gi|119719414|ref|YP_919909.1|  15 VVVLGHVDAGKTTLLDKIRGT-AVAKREPGTmTQHIGASFLPWKALEavcgslvsqiraevvipgFLVIDTPG-HE---- 88 
                                    899***************996.4555666652777765555566433566667777777788888********.44.... PP

                                    HHHHHHHHHHHHC.TSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                       MMR_HSR1  63 ekglgkaflalee.adlillvvdaseeklkpldeeleelleeakkplilvlnk 114
                                       +++  ++  + ad+++lvvd+  ++l+++  e  ++l+e+k p+i+++nk
  gi|119719414|ref|YP_919909.1|  89 --AFSNLRRRGGSiADIAILVVDVL-RGLEQQTFESIDILRERKVPFIVAVNK 138
                                    ..3333333333457********66.7799**9******************98 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.2
                                    SSSEEEEEEEETTEEEEEEECGGCSS CS
                       MMR_HSR1  33 TrdinegrvklkgkeielvDtpGlie 58 
                                    T++   g +k++g +i+++D+  +++
  gi|119719414|ref|YP_919909.1| 371 TLEALVGYLKKQGIPIRVADIGPVVK 396
                                    66666677777777888888776554 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   4.2e-07   0.00058       2     120 .]      15     141 ..      14     141 .. 0.71
   2 ?   -3.1   0.0       6.5     9e+03      92     104 ..     447     459 ..     435     464 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 4.2e-07
                                    EEEESSTTSSHHHHHHCHCT-CCC-EE....ETTTTEEEEEEECGGSG.GCTTBTTTTCEE...EEEEEE-SGGCTTTT- CS
                            Roc   2 vvlvGdsgvGKtsllkrfvedkfseke....kstigvdfltkevtkik.gvendkkvkkvk...lniWDtaGqerfrslh 73 
                                    vv++G   +GKt+ll+++    + ++e    ++ ig++fl +++ +   g   ++   +v    + + Dt G+e f++l+
  gi|119719414|ref|YP_919909.1|  15 VVVLGHVDAGKTTLLDKIRGTAVAKREpgtmTQHIGASFLPWKALEAVcGSLVSQIRAEVVipgFLVIDTPGHEAFSNLR 94 
                                    799**************998887766422226789*****998765432322222223333123799************* PP

                                    HHHHCTSCEEEEEEEGHHHHCHHHHHHHHHHHCS.SS-EEEEEE-TTT CS
                            Roc  74 plylreaalailvydsrssenlkeWlkelkkvag.kspvilvgnkiDl 120
                                    +   + a++ailv+d  +  +  + +++++  ++ k p+i+ +nkiD+
  gi|119719414|ref|YP_919909.1|  95 RRGGSIADIAILVVDVLRGLEQ-QTFESIDILRErKVPFIVAVNKIDK 141
                                    ***************5544332.23556665554156899999**995 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 6.5
                                    HHCHHHHHHHHHH CS
                            Roc  92 senlkeWlkelkk 104
                                     en ++Wl+e ++
  gi|119719414|ref|YP_919909.1| 447 VENYQKWLQETRD 459
                                    4788999999876 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.28   3.9e+02       1      21 [.      17      37 ..      17      59 .. 0.82
   2 !   17.3   0.0   2.3e-06    0.0032      92     234 ..      78     201 ..      56     224 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.28
                     ATP_bind_1  1 vvGpaGsGKttfvgalseile 21
                                   v+G++ +GKtt+  ++  ++ 
  gi|119719414|ref|YP_919909.1| 17 VLGHVDAGKTTLLDKIRGTAV 37
                                   89**********998876655 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 2.3e-06
                     ATP_bind_1  92 dyllfDtPGQielfthseslakiveeLesefalvvvyLvDsqrltdptkfisgllsalsamlrlelPhvvvlnkfDllke 171
                                     +l++DtPG   + +++  +         ++a +++ +vD+ r  +  +f s       ++ + ++P++v++nk+D +  
  gi|119719414|ref|YP_919909.1|  78 GFLVIDTPGHEAFSNLRRRGG--------SIADIAILVVDVLRGLEQQTFESI-----DILRERKVPFIVAVNKIDKIP- 143
                                    689*******99999999999........8999************99999888.....99*****************88. PP

                     ATP_bind_1 172 klekeleffedvealslllekeeekykklaeaiaelleefalvlrflplssekeesiedllsl 234
                                          + f+++  ++ ++ + e ++ kl+e ++ ++++fa    f  +  ++   ++++l+l
  gi|119719414|ref|YP_919909.1| 144 ----GWKSFPNTPFVESVKRQSEAAQLKLEELLSYIIQQFASL-GFRSDRYDRIRDFTRVLAL 201
                                    ....777777777777777777766666666666666666655.5555544444444444444 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   7.9e-06     0.011       1      34 [.      15      48 ..      15      50 .. 0.95
   2 ?   -3.3   0.0       6.1   8.3e+03     104     112 ..      80      88 ..      76      95 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 7.9e-06
                                   EEEEEBTTTTHHHHHHHHHTS--S---SSS---S CS
                      Dynamin_N  1 iavvGsqSsGKSSvlnaLlgedilprgpnptTrr 34
                                   ++v+G++ +GK+++l+++ g ++  r+p+ +T+ 
  gi|119719414|ref|YP_919909.1| 15 VVVLGHVDAGKTTLLDKIRGTAVAKREPGTMTQH 48
                                   79*****************************986 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 6.1
                                    EEEE---B- CS
                      Dynamin_N 104 tlvDlPGld 112
                                     ++D+PG  
  gi|119719414|ref|YP_919909.1|  80 LVIDTPGHE 88 
                                    589****65 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0   0.00061      0.84       4      26 ..      15      37 ..      12      50 .. 0.86
   2 ?   -3.4   0.0       5.3   7.3e+03      40      46 ..      81      87 ..      80     109 .. 0.79
   3 ?    3.7   0.0     0.036        49      87     103 ..     354     370 ..     338     388 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00061
                      PduV-EutP  4 illiGkvgsGKttLtqalkgeel 26
                                   ++++G+v++GKttL  +++g ++
  gi|119719414|ref|YP_919909.1| 15 VVVLGHVDAGKTTLLDKIRGTAV 37
                                   899***************99876 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 5.3
                      PduV-EutP 40 viDtPGe 46
                                   viDtPG 
  gi|119719414|ref|YP_919909.1| 81 VIDTPGH 87
                                   79***95 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.036
                      PduV-EutP  87 vfnkeviGiitkidlae 103
                                     f+++v+G++ k+d+  
  gi|119719414|ref|YP_919909.1| 354 KFERDVVGVVVKADTLG 370
                                    699***********873 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00072         1      17      45 ..      15      43 ..       5      53 .. 0.86
   2 ?    1.5   0.0      0.13   1.7e+02     113     127 ..     127     141 ..      78     221 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00072
                                   EEEEESTTSSHHHHHHHHHHSSCEECSSS CS
                            Arf 17 illlGLDnaGKtTilkklkleelvttvPT 45
                                   +++lG   aGKtT+l k++   +++  P 
  gi|119719414|ref|YP_919909.1| 15 VVVLGHVDAGKTTLLDKIRGTAVAKREPG 43
                                   7899***************9999998884 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.13
                                    CTTSEEEEEEE-TTS CS
                            Arf 113 lkevallvlaNKqDl 127
                                     ++v+++v  NK+D 
  gi|119719414|ref|YP_919909.1| 127 ERKVPFIVAVNKIDK 141
                                    467888888888885 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00019      0.26       3      93 ..      16     125 ..      14     170 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00019
                                    EEEESTTSSHHHHHHHHHHSSCSSSCTTTSSEE................EEEEEEEETTEEEEEEEEEETTSGGGHHHHH CS
                            Ras   3 vlvGdsavGKtslllrfvkdkFkeeyesTigvd................fytkeievdgkevkleiwDTAGqeefkslre 66 
                                    v++G    GKt+ll +       ++   T+                   +++++i+++     + + DT G e f++lr+
  gi|119719414|ref|YP_919909.1|  16 VVLGHVDAGKTTLLDKIRGTAVAKREPGTMTQHigasflpwkaleavcgSLVSQIRAEVVIPGFLVIDTPGHEAFSNLRR 95 
                                    6666666666666655444444443333332222233444444433333444444444555567799************* PP

                                    HHHTTESEEEEEEETT...BHHHHHTHHHH CS
                            Ras  67 lyyrdaegillvydit...sresfenvkkw 93 
                                       + a+ ++lv d+    ++++fe+++ +
  gi|119719414|ref|YP_919909.1|  96 RGGSIADIAILVVDVLrglEQQTFESIDIL 125
                                    ***************722246677666543 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0     0.002       2.7      95     125 ..       8      38 ..       3      51 .. 0.84
   2 ?    0.6   0.0      0.34   4.8e+02     152     164 ..      78      90 ..      71      93 .. 0.81
   3 ?    0.3   0.0      0.41   5.7e+02      17      60 ..     102     143 ..      87     171 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.002
                                    HHCTTSEEEEECSTTSSHHHHHHHHCTT--- CS
                    RsgA_GTPase  95 ellkdktsvlvGqSGvGKStLinallpelel 125
                                    + l+  ++v++G+  +GK+tL++++++++ +
  gi|119719414|ref|YP_919909.1|   8 QFLRAPIVVVLGHVDAGKTTLLDKIRGTAVA 38 
                                    5678889******************997644 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.34
                                    TEEEESS-SSSS- CS
                    RsgA_GTPase 152 gglliDtPGfrel 164
                                    g l+iDtPG +++
  gi|119719414|ref|YP_919909.1|  78 GFLVIDTPGHEAF 90 
                                    679******8876 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.41
                                    -EEEEEEESTTTT--HHHHHHHHHHHHHTT-EEEEEEE-GGG-- CS
                    RsgA_GTPase  17 dqllivvslkepelslnlldrfLvlaeekgiepvivlnKiDlle 60 
                                    d +++vv +    l++++ +  + ++ e++++ ++++nKiD + 
  gi|119719414|ref|YP_919909.1| 102 DIAILVVDVL-RGLEQQTFE-SIDILRERKVPFIVAVNKIDKIP 143
                                    5555555555.445444444.455678899***********886 PP

>> DUF1741  Domain of unknown function (DUF1741)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.4   0.00013      0.18     180     225 ..     541     589 ..     436     594 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00013
                        DUF1741 180 ltpeqvlevIkqg...YetLslkalqegLdkwekyreedektflkkivr 225
                                     +++ v + +k+g   Y  Ls+++++  L+k+eky  e+ek+ l+k++r
  gi|119719414|ref|YP_919909.1| 541 RSKAIVGRQVKEGdylYSNLSIEEINRLLEKYEKYLAENEKSYLRKLMR 589
                                    45555666667666669*****************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (601 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       696  (0.0388198); expected 358.6 (0.02)
Passed bias filter:                      601  (0.0335211); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.72u 0.32s 00:00:01.04 Elapsed: 00:00:00.49
# Mc/sec: 3671.15
//
Query:       gi|119719415|ref|YP_919910.1|  [L=63]
Description: ribosomal protein L24E [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.5e-18   65.6   1.0      4e-18   65.4   1.0    1.0  1  Ribosomal_L24e  Ribosomal protein L24e
    9.1e-05   22.3   0.9    0.00012   21.9   0.9    1.2  1  zf-FCS          MYM-type Zinc finger with FCS sequence motif
     0.0013   18.8   1.1     0.0037   17.3   1.1    1.7  1  zf-MYND         MYND finger
  ------ inclusion threshold ------
      0.021   15.1   0.2      0.021   15.1   0.2    1.7  2  zf-C6H2         zf-MYND-like zinc finger, mRNA-binding
      0.035   14.0   3.9       0.19   11.6   0.4    2.1  2  zf-HIT          HIT zinc finger
       0.11   12.5   2.3        2.2    8.3   0.1    2.1  2  DUF2116         Uncharacterized protein containing a Zn-ribbo
       0.41   10.5   4.7        1.2    9.1   4.7    1.8  1  VATC            Vms1-associating treble clef domain


Domain annotation for each model (and alignments):
>> Ribosomal_L24e  Ribosomal protein L24e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.4   1.0   1.6e-21     4e-18       2      53 ..       3      55 ..       2      60 .. 0.94

  Alignments for each domain:
  == domain 1  score: 65.4 bits;  conditional E-value: 1.6e-21
                                   XX-B-TTT-SB--SS--EEEE-TTS-EEEESSHHH.HHHHHTT--GGGSTTST CS
                 Ribosomal_L24e  2 ktekCsFsgykiyPGhGkrfvrnDgkvfrFlssKc.eklfkqkrnPrklkWTk 53
                                   ++  C+F+g++i PG+G+ +v+nDg+v+r++ssKc ++++k +r Pr+ kW +
  gi|119719415|ref|YP_919910.1|  3 RIVYCAFCGSPIKPGEGISYVKNDGTVLRYCSSKCfKSAIKYHRDPRRQKWVR 55
                                   6778*******************************9999************76 PP

>> zf-FCS  MYM-type Zinc finger with FCS sequence motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.9   4.8e-08   0.00012       5      40 ..       6      40 ..       3      40 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 4.8e-08
                         zf-FCS  5 rCwfCkkyikgkpeftyvlendgvvgqFCStsClds 40
                                    C fC+  ik ++    ++ ndg v ++CS+ C++s
  gi|119719415|ref|YP_919910.1|  6 YCAFCGSPIKPGE-GISYVKNDGTVLRYCSSKCFKS 40
                                   6************.689*****************97 PP

>> zf-MYND  MYND finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   1.1   1.4e-06    0.0037      13      35 ..       7      46 ..       3      48 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.4e-06
                                   -TTT.................S-SEESSHHHHHHCHHHHC CS
                        zf-MYND 13 CagC.................ksvfYCskeCqradwksHk 35
                                   Ca C                    +YCs++C +++ k+H+
  gi|119719415|ref|YP_919910.1|  7 CAFCgspikpgegisyvkndgTVLRYCSSKCFKSAIKYHR 46
                                   6666666666666666666555669**************9 PP

>> zf-C6H2  zf-MYND-like zinc finger, mRNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.2         2   5.2e+03      27      30 ..       8      11 ..       4      14 .. 0.64
   2 ?   15.1   0.2   8.3e-06     0.021      27      42 ..      31      46 ..      21      60 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2
                        zf-C6H2 27 fFCs 30
                                    FC+
  gi|119719415|ref|YP_919910.1|  8 AFCG 11
                                   4564 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 8.3e-06
                        zf-C6H2 27 fFCsqeCFkknwkkHk 42
                                    +Cs +CFk++ k H+
  gi|119719415|ref|YP_919910.1| 31 RYCSSKCFKSAIKYHR 46
                                   69**********9997 PP

>> zf-HIT  HIT zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.2     0.023        59       4      11 ..       6      13 ..       4      16 .. 0.82
   2 ?   11.6   0.4   7.5e-05      0.19      21      30 .]      30      39 ..      26      39 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.023
                                   B-TTT-SB CS
                         zf-HIT  4 lCgvCgfp 11
                                    C++Cg p
  gi|119719415|ref|YP_919910.1|  6 YCAFCGSP 13
                                   5****986 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 7.5e-05
                                   -EESSHHHHH CS
                         zf-HIT 21 tryCSLrCyk 30
                                    ryCS +C+k
  gi|119719415|ref|YP_919910.1| 30 LRYCSSKCFK 39
                                   69******98 PP

>> DUF2116  Uncharacterized protein containing a Zn-ribbon (DUF2116)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1   0.00086       2.2       6      17 ..       7      18 ..       5      23 .. 0.90
   2 ?    4.3   0.2     0.015        38      19      40 ..      32      53 ..      27      59 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00086
                        DUF2116  6 CivCGkaIplde 17
                                   C+ CG +I ++e
  gi|119719415|ref|YP_919910.1|  7 CAFCGSPIKPGE 18
                                   *********998 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.015
                        DUF2116 19 fCsekCqeeyekkrkkvarsqq 40
                                    Cs kC +   k  +  +r+++
  gi|119719415|ref|YP_919910.1| 32 YCSSKCFKSAIKYHRDPRRQKW 53
                                   7*****8765444444444443 PP

>> VATC  Vms1-associating treble clef domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   4.7   0.00045       1.2       5      33 ..       6      39 ..       3      52 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00045
                           VATC  5 rCsiCgeslegkv..yFekfd...frYCstkClr 33
                                    C +Cg+ +++ +   + k d    rYCs kC +
  gi|119719415|ref|YP_919910.1|  6 YCAFCGSPIKPGEgiSYVKNDgtvLRYCSSKCFK 39
                                   69999999997554488888733359******75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       715  (0.0398795); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 466.78
//
Query:       gi|119719416|ref|YP_919911.1|  [L=426]
Description: DNA primase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-09   38.4   0.2    4.3e-09   36.7   0.2    1.9  1  Toprim_4  Toprim domain
    1.4e-06   28.6   0.0    3.3e-06   27.4   0.0    1.7  1  Toprim_2  Toprim-like
    1.2e-05   25.5   0.2      9e-05   22.7   0.0    2.6  2  Toprim    Toprim domain


Domain annotation for each model (and alignments):
>> Toprim_4  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.2   7.2e-13   4.3e-09       2      79 ..     172     236 ..     171     243 .. 0.84

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 7.2e-13
                       Toprim_4   2 eiiiVEgyaDvlalekagiknvvavlggalspldgirpeklktenlveaekkvkevilaldgDaeGeataerlaelll 79 
                                    ++i+VEg+aDv +l + g+knv+a  g  +  ++ i+ +  +           k+vil++dgD  Ge  a  ++++l+
  gi|119719416|ref|YP_919911.1| 172 TVILVEGRADVQNLLRHGYKNVIALGGATI--PKSIK-SLVEN----------KKVILFVDGDRGGELIARNVINALK 236
                                    89**********************777677..67777.24555..........9*****************9999663 PP

>> Toprim_2  Toprim-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   5.5e-10   3.3e-06       1      81 [.     174     245 ..     174     282 .. 0.88

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 5.5e-10
                       Toprim_2   1 vvfEgaiDalSlaqlgikektnvvalgGtalteaalkllerypekkvvlalDnDkaGrkaakrlaellreagvrekirel 80 
                                    +++Eg  D+  l+++g k   nv+algG    ++ +k l ++  kkv+l +D D+ G+  a+++++ l+   v+  +r +
  gi|119719416|ref|YP_919911.1| 174 ILVEGRADVQNLLRHGYK---NVIALGGA-TIPKSIKSLVEN--KKVILFVDGDRGGELIARNVINALK---VDFVARAP 244
                                    699**************8...********.888888888888..89*******************9995...44455544 PP

                       Toprim_2  81 p 81 
                                    p
  gi|119719416|ref|YP_919911.1| 245 P 245
                                    4 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   1.5e-08     9e-05       2      90 ..     173     239 ..     172     252 .. 0.86
   2 ?   -1.1   0.0      0.37   2.2e+03      46      46 ..     341     341 ..     251     401 .. 0.60

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.5e-08
                                    EEEESSHHHHHHHHHTHTSTEEEEEEESSSSEEEHSTTEEEEEECTTTHHHHHHHHHHHHHHSEEEEECSSSHHHHHHHH CS
                         Toprim   2 lvivEgpsdaktiakalgsgfqavtaslGhildletefkpvyeeiedkkkvlkalkelakradeiilatDpDreGeaiaw 81 
                                    +++vEg +d++++ +    g+++v+a+ G  +                        +++ + +++il  D+Dr Ge ia 
  gi|119719416|ref|YP_919911.1| 173 VILVEGRADVQNLLRH---GYKNVIALGGATIPKSI--------------------KSLVENKKVILFVDGDRGGELIAR 229
                                    79**************...9*********9998776....................4555889***************** PP

                                    HHHHHHT.HH CS
                         Toprim  82 ellevlk.el 90 
                                     ++++lk ++
  gi|119719416|ref|YP_919911.1| 230 NVINALKvDF 239
                                    ***9988544 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.37
                                    C CS
                         Toprim  46 i 46 
                                    +
  gi|119719416|ref|YP_919911.1| 341 K 341
                                    1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1196  (0.0667076); expected 358.6 (0.02)
Passed bias filter:                      775  (0.0432261); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.45
# Mc/sec: 2860.42
//
Query:       gi|119719417|ref|YP_919912.1|  [L=431]
Description: GTP-binding signal recognition particle [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-69  232.9   0.1    3.4e-69  232.4   0.1    1.2  1  SRP54            SRP54-type protein, GTPase domain
    2.6e-24   85.7   3.8    3.3e-24   85.4   2.3    2.0  1  SRP_SPB          Signal peptide binding domain
      2e-11   43.9   1.3    7.7e-11   42.1   1.3    2.1  1  SRP54_N          SRP54-type protein, helical bundle domain
    7.8e-07   28.8   0.2    2.5e-05   23.9   0.2    2.4  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
    1.4e-06   28.2   1.6    3.4e-06   26.9   0.8    2.0  2  AAA_30           AAA domain
    3.2e-05   24.0   0.0     0.0001   22.3   0.0    2.1  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
      5e-05   23.3   0.1    0.00019   21.5   0.1    2.0  1  MMR_HSR1         50S ribosome-binding GTPase
    7.2e-05   21.9   0.2    0.00057   18.9   0.0    2.3  3  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
    0.00032   21.0   0.0     0.0017   18.7   0.0    2.2  2  AAA_22           AAA domain
    0.00033   21.1   0.1     0.0011   19.4   0.1    2.0  1  AAA_17           AAA domain
    0.00037   20.4   0.0     0.0012   18.7   0.0    1.9  1  MobB             Molybdopterin guanine dinucleotide synthesis
     0.0006   19.2   0.2     0.0021   17.4   0.1    1.9  1  Zeta_toxin       Zeta toxin
     0.0011   19.4   0.2      0.022   15.2   0.1    2.8  2  AAA              ATPase family associated with various cellul
     0.0013   18.5   1.1      0.011   15.5   0.0    2.8  3  Thymidylate_kin  Thymidylate kinase
     0.0016   18.6   0.0     0.0044   17.2   0.0    1.9  1  AAA_33           AAA domain
     0.0019   18.6   0.0     0.0061   17.0   0.0    1.9  1  AAA_16           AAA ATPase domain
     0.0026   18.0   0.3      0.039   14.2   0.0    2.9  3  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
      0.003   17.5   0.1     0.0082   16.1   0.1    1.7  1  NTPase_1         NTPase
     0.0033   17.2   0.0        1.2    8.9   0.0    2.6  2  CLP1_P           mRNA cleavage and polyadenylation factor CLP
     0.0047   16.1   0.1     0.0088   15.2   0.1    1.4  1  LpxK             Tetraacyldisaccharide-1-P 4'-kinase
     0.0052   17.0   0.1        2.7    8.2   0.0    2.4  2  TPM_phosphatase  TPM domain
     0.0057   16.5   0.1      0.015   15.1   0.1    1.7  1  ATP_bind_1       Conserved hypothetical ATP binding protein
     0.0057   16.2   0.2      0.017   14.7   0.2    1.9  1  GTP_EFTU         Elongation factor Tu GTP binding domain
  ------ inclusion threshold ------
      0.015   15.2   0.0       0.03   14.2   0.0    1.5  1  APS_kinase       Adenylylsulphate kinase
       0.02   15.3   0.4      0.081   13.4   0.2    2.0  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain
      0.022   14.8   0.0      0.039   13.9   0.0    1.6  1  ResIII           Type III restriction enzyme, res subunit
      0.023   14.1   0.1        3.5    7.0   0.0    2.4  2  SRPRB            Signal recognition particle receptor beta su
      0.023   14.1   0.1       0.22   10.9   0.0    2.4  2  Arf              ADP-ribosylation factor family
      0.024   14.8   0.7         11    6.3   0.1    3.6  3  HGTP_anticodon   Anticodon binding domain
      0.025   13.9   0.0      0.053   12.9   0.0    1.5  1  Gtr1_RagA        Gtr1/RagA G protein conserved region
      0.042   14.1   0.2       0.11   12.7   0.2    1.9  1  AAA_28           AAA domain
       0.05   13.6   0.0       0.43   10.6   0.0    2.3  2  Glyco_transf_4   Glycosyltransferase Family 4
      0.063   13.0   0.0       0.38   10.5   0.0    2.2  2  TPP_enzyme_M     Thiamine pyrophosphate enzyme, central domai
      0.065   12.7   0.0       0.11   11.9   0.0    1.3  1  AAA_7            P-loop containing dynein motor region
      0.067   12.5   0.0       0.12   11.7   0.0    1.4  1  6PF2K            6-phosphofructo-2-kinase
      0.092   12.5   0.0        3.5    7.4   0.0    2.5  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
        0.1   12.0   0.0       0.18   11.2   0.0    1.5  1  ParA             NUBPL iron-transfer P-loop NTPase
       0.11   12.3   0.6        1.9    8.3   0.1    2.4  2  AAA_26           AAA domain
       0.12   11.5   0.0       0.24   10.5   0.0    1.4  1  G-alpha          G-protein alpha subunit
       0.16   12.2   0.3        4.1    7.7   0.0    2.7  3  Roc              Ras of Complex, Roc, domain of DAPkinase


Domain annotation for each model (and alignments):
>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  232.4   0.1   7.6e-72   3.4e-69       2     196 .]     100     294 ..      99     294 .. 0.99

  Alignments for each domain:
  == domain 1  score: 232.4 bits;  conditional E-value: 7.6e-72
                                    EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEESSTTSCHHHHHHHHHHHHHH CS
                          SRP54   2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvikkkeeadpaavakeavekake 81 
                                      +++vGl+G+GKTtt+aK+a+++k++g++v +vaaDt+R++A+eQL+ laek+gvp+++  +e+d++++a ++v+   +
  gi|119719417|ref|YP_919912.1| 100 FKVMFVGLEGSGKTTTVAKVANYYKRKGYRVGVVAADTYRPGAYEQLRSLAEKVGVPFYGDPQERDAVSLALRGVKVLSD 179
                                    579***************************************************************************** PP

                                    TTSSEEEEEE--SSTTHHHHHHHHHHHHHHHSSSEEEEEEETTBHTHHHHHHHHHHHHSSCSEEEEESTTSSSSTTHHHH CS
                          SRP54  82 ekidvvlvDTaGrlqndkelmeelkkikkvvkpdevllvldattgqeavkqakaFkeavgitgviltklDgdakgGaals 161
                                    ++i+++l+DTaGr++ +++lmee+k++ + vkpd v+lv+dat g+++++qa+aF+ea+ ++ vi++k+Dg+akgG+als
  gi|119719417|ref|YP_919912.1| 180 KGIQMILIDTAGRHKDEEALMEEVKTLYREVKPDAVVLVVDATQGSAVARQARAFQEAMPFGYVIVAKMDGSAKGGGALS 259
                                    ******************************************************************************** PP

                                    HHHHHTS-EEEEE-SSSTTGEEE--HHHHHHHHHT CS
                          SRP54 162 iaaelklPikfigvGekiedleefdperlvsrllg 196
                                    ++a++k  ++fig+Gekiedleef+p+++v rllg
  gi|119719417|ref|YP_919912.1| 260 AVASSKARVIFIGTGEKIEDLEEFNPKKFVARLLG 294
                                    *********************************95 PP

>> SRP_SPB  Signal peptide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.4   2.3   7.3e-27   3.3e-24       2      99 .]     324     416 ..     323     416 .. 0.91

  Alignments for each domain:
  == domain 1  score: 85.4 bits;  conditional E-value: 7.3e-27
                                    SCTHHHHHHHHHHHCCCCCCHHHHCCC.....H...CCCCCHHHHHHHHHTTSBHHHHHSGCG-..HHHHHHHHHHTTS- CS
                        SRP_SPB   2 ftlrdlleqlqqikkmGplskllsmiPgmsaeakaeeeaekklkrieaiidSMTkeErdspekllkesRkrRiArGsGts 81 
                                     tl dl+eql+ ++kmGplsk+++m+   + +    +e++ +++++  i++SMT eE+ +pe ++++sR+rRiArGsG+s
  gi|119719417|ref|YP_919912.1| 324 ITLLDLKEQLEGLRKMGPLSKIAEMMGL-QVKV---SEEDLNIDKWINIMNSMTMEELLNPE-IIDSSRMRRIARGSGVS 398
                                    6899**********************85.3222...334789********************.9999************* PP

                                    HHHHHHHHHHHHHHHHHT CS
                        SRP_SPB  82 vqevnellkqfeqmkkmm 99 
                                     ++v++ll+ +++mkk+m
  gi|119719417|ref|YP_919912.1| 399 PRDVKQLLEAYRNMKKVM 416
                                    ****************98 PP

>> SRP54_N  SRP54-type protein, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   1.3   1.7e-13   7.7e-11       1      75 []       4      81 ..       4      81 .. 0.93

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 1.7e-13
                                   HHHHHHHHHHHHCCSSCGHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHCTTS....S-HHHHHHHHHHHHH CS
                        SRP54_N  1 LgkklnsalkklsgkskideedleealkeleeaLleaDVgvkvvkklienvkkkavgekk....lkpkqqvkkivkdeL 75
                                   L+++l +++++++++  +d   ++ +++el++aLl+aDV v +v ++ e++kk+  + ++     ++k+ ++ki+++eL
  gi|119719417|ref|YP_919912.1|  4 LKESLMGVVSRIRSSVLLDSREVDLVIRELQRALLKADVDVGLVLSVSERIKKRFFE-EEqppgFSKKEVLVKILYEEL 81
                                   678999*********************************************995555.55699999************8 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.2   5.6e-08   2.5e-05       4     152 ..     103     250 ..     100     268 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 5.6e-08
                                    EEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SSCHCCCCCCHCCCT.EEEETTTTECCHCTT-HHHHHHHHHHHH. CS
                           cobW   4 vltGflGsGKTtLlnhll..enraglklavivNefgevsiDaellretgveivelenGciCctlredllkelealeere. 80 
                                    +++G  GsGKTt + ++    +r+g+++ v+  + +  +  ++l + +  e v +   + +   r+ ++ +l+ ++ ++ 
  gi|119719417|ref|YP_919912.1| 103 MFVGLEGSGKTTTVAKVAnyYKRKGYRVGVVAADTYRPGAYEQLRSLA--EKVGVPFYGDPQE-RDAVSLALRGVKVLSd 179
                                    678999************9999**************866666655444..3466666666766.6777777776655544 PP

                                    TT-SEEEEEECTTTTHHHH.HTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HHH CS
                           cobW  81 erldviliEttGlaePapv.afteeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKtDl 152
                                    + +++ili t G  +  +  + + ++l ++++ davv vvDa++  ++  ++++ +++ + +   +++ K+D 
  gi|119719417|ref|YP_919912.1| 180 KGIQMILIDTAGRHKDEEAlMEEVKTLYREVKPDAVVLVVDATQG-SAVARQARAFQEAMPFG-YVIVAKMDG 250
                                    57**********66666662666999****************886.56777777788777775.566778886 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.8   7.6e-09   3.4e-06      22     137 ..     103     234 ..      94     250 .. 0.72
   2 ?   -1.4   0.0       3.6   1.6e+03     109     126 ..     258     275 ..     246     340 .. 0.59

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 7.6e-09
                         AAA_30  22 vltGpAGtGKttalkalreaweaaggrviglAptg.k..aAkvLa...eelgi.....eastiakllkrlk.grarlepg 89 
                                    + +G  G+GKtt+++++++ ++++g+rv ++A    +  a ++L+   e++g+     + ++ a  l   +  ++  ++g
  gi|119719417|ref|YP_919912.1| 103 MFVGLEGSGKTTTVAKVANYYKRKGYRVGVVAADTyRpgAYEQLRslaEKVGVpfygdPQERDAVSLAL-RgVKVLSDKG 181
                                    6799************************87776542332334444333899986666544444444433.3444556777 PP

                         AAA_30  90 .tllivDEagmv..dtkqlaallkaaekag.akvilvGDerQlasVea.Ggvl 137
                                     +++++D ag      + ++++ +  ++ +   v+lv D  Q ++V +  +++
  gi|119719417|ref|YP_919912.1| 182 iQMILIDTAGRHkdEEALMEEVKTLYREVKpDAVVLVVDATQGSAVARqARAF 234
                                    9*********9965555677777777775449999999********8744555 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.6
                         AAA_30 109 lkaaekagakvilvGDer 126
                                    l+a+++++a+vi++G  +
  gi|119719417|ref|YP_919912.1| 258 LSAVASSKARVIFIGTGE 275
                                    455666678888887544 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   2.3e-07    0.0001       9      55 ..     109     250 ..     105     426 .. 0.70

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 2.3e-07
                                    TSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH.................................. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................................. RF
                           CbiA   9 GvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep.................................. 54 
                                    G+GKTt++a+ a + +r+g+rV +v aD+ ++ +   e+l+    +                                  
  gi|119719417|ref|YP_919912.1| 109 GSGKTTTVAKVANYYKRKGYRVGVVAADTYRPGAY--EQLRSLA-Ekvgvpfygdpqerdavslalrgvkvlsdkgiqmi 185
                                    9***************************9988865..3333222.24667778878888777777777777777777777 PP

                                    ................................................................C CS
                                    ................................................................x RF
                           CbiA  55 ................................................................d 55 
                                                                                                    +
  gi|119719417|ref|YP_919912.1| 186 lidtagrhkdeealmeevktlyrevkpdavvlvvdatqgsavarqarafqeampfgyvivakmdG 250
                                    77777777777777777777777777777777775555444444444444444444444444441 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.1   4.3e-07   0.00019       1      98 [.     101     232 ..     101     247 .. 0.63

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 4.3e-07
                                    EEEEEESTTSSHHHHHHHHHT....STEEESSSTTSSSSE.EEEEEE...ETTEE......................... CS
                       MMR_HSR1   1 evaivGrpNvGKStLinaltg....ekaivsdkpgtTrdi.negrvk...lkgke......................... 47 
                                    +v++vG   +GK+t + +  +    +  +v+  +  T  +  +++++   +   +                         
  gi|119719417|ref|YP_919912.1| 101 KVMFVGLEGSGKTTTVAKVANyykrKGYRVGVVAADTYRPgAYEQLRslaE---Kvgvpfygdpqerdavslalrgvkvl 177
                                    699****************98553224699999999999966666664331...13344444444555555555666666 PP

                                    ......EEEEECGGCSSHHHHHH.HHHHHHHHHHCTSEEEEEEETTTTCSHHHHHHHH CS
                       MMR_HSR1  48 ......ielvDtpGliegaseek.glgkaflaleeadlillvvdaseeklkpldeele 98 
                                          ++l+Dt+G  ++++e   ++ k++ +  + d+++lvvda+++  +++ ++  
  gi|119719417|ref|YP_919912.1| 178 sdkgiqMILIDTAG-RHKDEEALmEEVKTLYREVKPDAVVLVVDATQG--SAVARQAR 232
                                    666666********.553333333344444444556********9854..33334333 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   1.3e-06   0.00057      32      67 ..     102     137 ..      94     145 .. 0.90
   2 ?   -1.2   0.0       1.7   7.8e+02     113     144 ..     173     204 ..     164     213 .. 0.80
   3 ?   -1.9   0.0       2.9   1.3e+03     200     235 ..     384     419 ..     355     425 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.3e-06
                                    EEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE-- CS
                           MeaB  32 vGltGvPGaGkstlvealglelrrrGkrvavlavDP 67 
                                    v + G+ G+Gk t+v +++  ++r+G+rv+v+a D 
  gi|119719417|ref|YP_919912.1| 102 VMFVGLEGSGKTTTVAKVANYYKRKGYRVGVVAADT 137
                                    668899***************************995 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.7
                                    HHHHHHHTT-SEEEEEEESSTTHHHHHHTT-S CS
                           MeaB 113 vvllleaaGfDvvlietvGvGqsevdvaevvd 144
                                     v++l   G  ++li+t G  + e +++e v+
  gi|119719417|ref|YP_919912.1| 173 GVKVLSDKGIQMILIDTAGRHKDEEALMEEVK 204
                                    578888999999*****999888877776655 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 2.9
                                    BTTB--EEEEEBCCCTBSHHHHHHHHHHHHHHHHHT CS
                           MeaB 200 ekeWrpkvlktsavegeGidelvdaieehrevlkkt 235
                                    +++   ++ + s+v  + +++l++a ++ ++v+++ 
  gi|119719417|ref|YP_919912.1| 384 DSSRMRRIARGSGVSPRDVKQLLEAYRNMKKVMRQL 419
                                    445556788889999999999999999999988875 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   3.7e-06    0.0017      10     117 ..     104     208 ..     101     224 .. 0.76
   2 ?   -1.6   0.0       6.5   2.9e+03     117     136 ..     282     301 ..     261     302 .. 0.66

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 3.7e-06
                         AAA_22  10 vtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseellealeqalrar 89 
                                     +G  G+GKTt+++++++ ++     +  r++vv  +   ++  ++ lr l++++g++  +   ++++ +++  + ++  
  gi|119719417|ref|YP_919912.1| 104 FVGLEGSGKTTTVAKVANYYK----RKGYRVGVVAADTYRPGAYEQ-LRSLAEKVGVPFYG-DPQERDAVSLALRGVKVL 177
                                    689***************995....445799999999888885555.48899999998888.666666666666666666 PP

                         AAA_22  90 av..ielliiDEaqhlr.seealeeLrslln 117
                                    ++  i++++iD a +   +e+++ee+++l+ 
  gi|119719417|ref|YP_919912.1| 178 SDkgIQMILIDTAGRHKdEEALMEEVKTLYR 208
                                    66667********998545899999999887 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 6.5
                         AAA_22 117 nlsrkgvqliLvGtpelrkl 136
                                    +++ k++   L G+p+l+ l
  gi|119719417|ref|YP_919912.1| 282 EFNPKKFVARLLGMPDLEAL 301
                                    33467777778888888766 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1   2.5e-06    0.0011       1     118 [.     105     229 ..     105     237 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 2.5e-06
                                    EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHCTS......HHHHHHHHHHHHHHHHHHHH..HSS CS
                         AAA_17   1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemrkl......pleekkelqkeaaekiaeea..kkk 72 
                                    +G+ GsGK+t ++k++  y+ + +  G +  ++ ++g  ++ r+  +k+      + +e++    +a + ++  +  + +
  gi|119719417|ref|YP_919912.1| 105 VGLEGSGKTTTVAKVANYYKRKGYRVGVVAADTYRPGAYEQLRSLAEKVgvpfygDPQERD-AVSLALRGVKVLSdkGIQ 183
                                    79*************************9999999888878888888864444433333333.344555555555511556 PP

                                    EEEEEE-SEEEETTEEEESSHHHHHHHH..SEEEE.EE--HHHHHHH CS
                         AAA_17  73 gvlvdghprikeqagfldglpkevleelkpdaiil.leadpeeiler 118
                                     +l+d+  r k+++ ++++++    +e+kpda++l ++a +   ++r
  gi|119719417|ref|YP_919912.1| 184 MILIDTAGRHKDEEALMEEVK-TLYREVKPDAVVLvVDATQGSAVAR 229
                                    69*******988888778777.589*****99998455555555555 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   2.7e-06    0.0012       2      34 ..     102     134 ..     101     139 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.7e-06
                           MobB   2 lgivgksgsGKTtLleklipelkarglrvgtiK 34 
                                    + +vg +gsGKTt + k+ +  k++g+rvg++ 
  gi|119719417|ref|YP_919912.1| 102 VMFVGLEGSGKTTTVAKVANYYKRKGYRVGVVA 134
                                    679***************************995 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   4.6e-06    0.0021      12     122 ..      95     208 ..      87     241 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.6e-06
                     Zeta_toxin  12 sqerPklillgGqpGAGKselaellkdele.rqgnvvrldpDdlRelh.Peyeeilka.dpkkaseltqkdaselvekll 88 
                                     +++P  ++ +G  G+GK+++ ++++++ + ++ +v ++ +D++R+    + +++ ++  +  + +  ++da  l+ + +
  gi|119719417|ref|YP_919912.1|  95 VSSTPFKVMFVGLEGSGKTTTVAKVANYYKrKGYRVGVVAADTYRPGAyEQLRSLAEKvGVPFYGDPQERDAVSLALRGV 174
                                    45889999*********************945556668999****86503444444455888889999999999999999 PP

                     Zeta_toxin  89 qeaiengyn.iivegtlrspdvvkklaealkkaGY 122
                                    + + ++g+  i+++++ r+ d+ + l+e++k   +
  gi|119719417|ref|YP_919912.1| 175 KVLSDKGIQmILIDTAGRHKDEEA-LMEEVKTLYR 208
                                    999999987345688888888776.7777776544 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   4.8e-05     0.022       1     117 [.     102     282 ..     102     293 .. 0.65
   2 ?   -1.4   0.0       6.6   2.9e+03      27      56 ..     383     412 ..     356     417 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.8e-05
                                    EEEESSTTSSHHHHHHHHHHHHTHE.........................................EEEEETTTCSSS.. CS
                            AAA   1 vllyGppGtGKTllakavakelgve.........................................fleisgsellsk.. 37 
                                    v+++G  G GKT+++  va+  +++                                          l + g ++ls+  
  gi|119719417|ref|YP_919912.1| 102 VMFVGLEGSGKTTTVAKVANYYKRKgyrvgvvaadtyrpgayeqlrslaekvgvpfygdpqerdavSLALRGVKVLSDkg 181
                                    689******************97665555555555555666666666666666666666666665534444444442256 PP

                                    ..........STTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS....... CS
                            AAA  38 ..........yvgesekkirelfkeakeka.kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkk....... 99 
                                                ++ e+ ++e+ +  +e + + ++l++D     a +r+ ++ +e++    ++++++dg  k        
  gi|119719417|ref|YP_919912.1| 182 iqmilidtagRHKDEEALMEEVKTLYREVKpDAVVLVVDATQGSAVARQARAFQEAMPFGYVIVAKMDGSAKGggalsav 261
                                    66666666653333444444443334444333388888888888888866666777777778888888888888888999 PP

                                    ...SSTEEEEEEESSGGGSTH CS
                            AAA 100 ...eskvivigatnrpdkldp 117
                                       +++vi+ig++ ++++l++
  gi|119719417|ref|YP_919912.1| 262 assKARVIFIGTGEKIEDLEE 282
                                    998888999999988888876 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 6.6
                                    EEEETTTCSSSSTTHHHHHHHHHHHHHHHT CS
                            AAA  27 leisgsellskyvgesekkirelfkeakek 56 
                                    +  s ++ +    g s++++++l+++ +++
  gi|119719417|ref|YP_919912.1| 383 IDSSRMRRIARGSGVSPRDVKQLLEAYRNM 412
                                    333333333446677777777777666555 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   2.4e-05     0.011       3      27 ..     106     130 ..     104     139 .. 0.90
   2 ?   -0.8   0.0       2.4   1.1e+03     103     127 ..     199     220 ..     189     241 .. 0.59
   3 ?   -1.4   0.1       3.5   1.6e+03     131     164 ..     387     421 ..     381     425 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.4e-05
                                    ESTTSSHHHHHHHHHHHHHHTTE.E CS
                Thymidylate_kin   3 GlDGaGKttqaellkerlkeegikv 27 
                                    Gl+G+GKtt ++++++++k++g++v
  gi|119719417|ref|YP_919912.1| 106 GLEGSGKTTTVAKVANYYKRKGYRV 130
                                    9*********************984 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.4
                                    TCHHHHHHGGGTTSE-SEEEEEESS CS
                Thymidylate_kin 103 dldlvlslnedvllkPdltflldvd 127
                                    +++ v++l ++v  kPd+++l+  d
  gi|119719417|ref|YP_919912.1| 199 LMEEVKTLYREV--KPDAVVLVV-D 220
                                    344444444454..777777754.2 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 3.5
                                    HHTSCCTTSS.TTTSHHHHHHHHHHHHHHHHHHHH CS
                Thymidylate_kin 131 alkRlakrde.ldeeeeeqldflrkvrerylelak 164
                                    +++R+a+++  + +++++ l+ +r++++++ +l +
  gi|119719417|ref|YP_919912.1| 387 RMRRIARGSGvSPRDVKQLLEAYRNMKKVMRQLSR 421
                                    67888888776779999999999999999988875 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   9.8e-06    0.0044       2      38 ..     102     143 ..     102     238 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 9.8e-06
                         AAA_33   2 vllvGlpGsGKstlaerl...lkklg..avllssdtlrrrlf 38 
                                    v++vGl GsGK+t + ++   +k+ g  + +++ dt+r   +
  gi|119719417|ref|YP_919912.1| 102 VMFVGLEGSGKTTTVAKVanyYKRKGyrVGVVAADTYRPGAY 143
                                    89************9998443555556666688888765544 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   1.4e-05    0.0061      27     145 ..     102     223 ..      92     247 .. 0.61

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.4e-05
                         AAA_16  27 vllsGesGvGKsslvrellralekd..ggiflrgkcdqlesaipysalaqalareellrqllde....aesaeleawrek 100
                                    v+++G  G+GK++ v +++++++++  ++ ++++++ +           ++l r +l ++++ +    ++++++   + +
  gi|119719417|ref|YP_919912.1| 102 VMFVGLEGSGKTTTVAKVANYYKRKgyRVGVVAADTYRP---G----AYEQL-R-SLAEKVGVPfygdPQERDAVSLALR 172
                                    7899*********************43333344443333...2....44444.3.4444444332221222233333333 PP

                         AAA_16 101 leeala........avpelagaeasrllellkrllallsrderplvlvlDdlq 145
                                      ++l+        +  + + +++++l e++k l +  ++ +  +vlv+D  q
  gi|119719417|ref|YP_919912.1| 173 GVKVLSdkgiqmilIDTAGRHKDEEALMEEVKTLYREVKP-DA-VVLVVDATQ 223
                                    3333336666665433334444448999999999988887.55.899999888 PP

>> PFOR_II  Pyruvate:ferredoxin oxidoreductase core domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   8.8e-05     0.039      13      52 ..     114     153 ..     102     159 .. 0.88
   2 ?   -1.0   0.0       4.8   2.2e+03      54      89 ..     183     218 ..     173     230 .. 0.66
   3 ?   -1.5   0.0         7   3.2e+03      45      99 ..     298     355 ..     296     357 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 8.8e-05
                                    HHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT- CS
                        PFOR_II  13 gtaksavdelReegikvGllrlrtlrPFPeeelkellkkv 52 
                                     t+ ++++ ++++g++vG++   t+rP  +e+l++l++kv
  gi|119719417|ref|YP_919912.1| 114 TTVAKVANYYKRKGYRVGVVAADTYRPGAYEQLRSLAEKV 153
                                    5788899****************************99876 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 4.8
                                    EEEEEE-S--TT-G-HHHHHHHHHTGGGTSEEEEEE CS
                        PFOR_II  54 kvvvldrnisfgseGqlveevkaalkkskvkvvnfv 89 
                                    +++ +d +     e +l+eevk+   + k+++v +v
  gi|119719417|ref|YP_919912.1| 183 QMILIDTAGRHKDEEALMEEVKTLYREVKPDAVVLV 218
                                    556667666666668899999998877766555444 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 7
                                    HHHHSTT-SEEEEEE-S--TT-G..-HHHHHHHHHTGGG.TSEEEEEE--GGG----H CS
                        PFOR_II  45 lkellkkvkkvvvldrnisfgse..Gqlveevkaalkks.kvkvvnfvaglgGrditv 99 
                                    l+ ll+++++++ l+++ +  ++   + + + k++l++  k+ +++ +a + G +++v
  gi|119719417|ref|YP_919912.1| 298 LEALLQRFSEFARLEKERARAIAsgKITLLDLKEQLEGLrKMGPLSKIAEMMGLQVKV 355
                                    6777888888888876655444442667788888888877777777777777777766 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   1.8e-05    0.0082       2      39 ..     102     139 ..     101     146 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.8e-05
                                    EEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE- CS
                       NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgGfyteevr 39 
                                    v+  G  G+GKtT v kv++  k++g++vg + +  +r
  gi|119719417|ref|YP_919912.1| 102 VMFVGLEGSGKTTTVAKVANYYKRKGYRVGVVAADTYR 139
                                    5667999**********************877777666 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0    0.0027       1.2       3      32 ..     108     137 ..     106     143 .. 0.90
   2 ?    5.6   0.0     0.027        12      67     150 ..     157     231 ..     146     248 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0027
                         CLP1_P   3 kdsGKSTlarlLlNyalrkgrkpvyvDlDv 32 
                                      sGK+T ++  +Ny  rkg+++ +v +D 
  gi|119719417|ref|YP_919912.1| 108 EGSGKTTTVAKVANYYKRKGYRVGVVAADT 137
                                    689***********************9996 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.027
                         CLP1_P  67 ffGdtspsdnpslylalvkelareveekleenkkakasgliIntpGwvkglg..aellleliealepdvvvvldqeelln 144
                                    f+Gd + +d++sl l+ vk l ++           + + ++I+t G  k++   +e  + l + ++pd+vv++ +  + +
  gi|119719417|ref|YP_919912.1| 157 FYGDPQERDAVSLALRGVKVLSDK-----------GIQMILIDTAGRHKDEEalMEEVKTLYREVKPDAVVLVVDATQGS 225
                                    555555555555555555555554...........4589*********987523699999*******9999987766666 PP

                         CLP1_P 145 elkrdl 150
                                     + r++
  gi|119719417|ref|YP_919912.1| 226 AVARQA 231
                                    665555 PP

>> LpxK  Tetraacyldisaccharide-1-P 4'-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1     2e-05    0.0088      28      72 ..      93     134 ..      72     139 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2e-05
                                    S--B--SS-EEEEEESBSS-HSHHHHHHHHHHHTTTS..-EEEEE CS
                           LpxK  28 lkserlpvpVivVGNitvGGtGKTPlvialvkllqarglkvgvlS 72 
                                    lk  ++p +V+ VG     G+GKT +v+ ++++++++g++vgv++
  gi|119719417|ref|YP_919912.1|  93 LKVSSTPFKVMFVG---LEGSGKTTTVAKVANYYKRKGYRVGVVA 134
                                    56677889999998...79************************95 PP

>> TPM_phosphatase  TPM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.024        11      12      89 ..     111     186 ..     106     192 .. 0.68
   2 !    8.2   0.0    0.0061       2.7      12      87 ..     195     279 ..     192     282 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.024
                                    HHHHHHHHHHHHHHTT--EEEEEEESB-...TT--HHHHHHHHHHHHST...TTTS-SSEEEEEEETTTTEEEEEE-STT CS
                TPM_phosphatase  12 eeaeleeklaalekktgvqivvvtvdsl...dgediedyadelfdkwgl...gkkkkdngvllliavddrkvrietgygl 85 
                                     +++  +k a+++k++g+++ vv  d+        + +    l++k g+   g+ ++++ v l++    r v +  ++g+
  gi|119719417|ref|YP_919912.1| 111 GKTTTVAKVANYYKRKGYRVGVVAADTYrpgA---Y-EQLRSLAEKVGVpfyGDPQERDAVSLAL----RGVKVLSDKGI 182
                                    567778999*****************984322...2.2233445555543125555668888888....88888888888 PP

                                    TTT- CS
                TPM_phosphatase  86 egal 89 
                                    + +l
  gi|119719417|ref|YP_919912.1| 183 QMIL 186
                                    7665 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0061
                                    HHHHHHHHHHHHHHTT--EEEEEEESB-TT--HHHHHHHHHHHHSTTT.......TS-S.SEEEEEEETT.TTEEEEEE- CS
                TPM_phosphatase  12 eeaeleeklaalekktgvqivvvtvdsldgediedyadelfdkwglgk.......kkkd.ngvllliavd.drkvrietg 82 
                                    +e++l e+ ++l+++ + + vv++vd ++g    + a  + +++ +g+       ++++  g+l ++a +  r + i tg
  gi|119719417|ref|YP_919912.1| 195 DEEALMEEVKTLYREVKPDAVVLVVDATQGSAVARQARAFQEAMPFGYvivakmdGSAKgGGALSAVASSkARVIFIGTG 274
                                    688999**********************9999877776664444446654433322233478888887554588888888 PP

                                    STTTT CS
                TPM_phosphatase  83 ygleg 87 
                                    +++e+
  gi|119719417|ref|YP_919912.1| 275 EKIED 279
                                    88875 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   3.3e-05     0.015       2      33 ..     105     136 ..     104     142 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.3e-05
                     ATP_bind_1   2 vGpaGsGKttfvgalseilelrgrsvavvNLD 33 
                                    vG  GsGKtt v +++++++ +g++v vv  D
  gi|119719417|ref|YP_919912.1| 105 VGLEGSGKTTTVAKVANYYKRKGYRVGVVAAD 136
                                    899*************************9776 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.2   3.7e-05     0.017      11     135 ..     107     251 ..     100     413 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.7e-05
                                    STTSSHHHHHHHHHHHTTSSCHHHHHHHHHST..................HCHSHHHHHHTSCSSCEEEEEETTCSSEEE CS
                       GTP_EFTU  11 hvDhGKtTLtdrLlyktgaiskkgekaeeerv..................lDtlkeErergiTiksaaisleketkkyli 72 
                                       +GKtT++ ++  + ++   +  +  ++++                      ++Er   ++     +++  + k  ++
  gi|119719417|ref|YP_919912.1| 107 LEGSGKTTTVAKVANYYKRKGYRVGVVAADTYrpgayeqlrslaekvgvpFYGDPQERD-AVSLALRGVKVL-SDKGIQM 184
                                    55678888888888777776665555543333445555555555555533222333332.355555555555.89999** PP

                                    EEEEESS.SGG...GHHHHHHHHH..T-SEEEEEEETTTBSTHHHHHHHHHHHHTTTE.EEEEEESCGST CS
                       GTP_EFTU  73 nliDtPG.Hvd...Fskevirglr..vlDgavlvvdaveGvepqteevlrlalkegvp.iivfiNKmDrl 135
                                     liDt G H+d    ++ev + +r  + D +vlvvda++G  +  +     a +e +p   v++ KmD  
  gi|119719417|ref|YP_919912.1| 185 ILIDTAGrHKDeeaLMEEVKTLYRevKPDAVVLVVDATQGSAVARQA---RAFQEAMPfGYVIVAKMDGS 251
                                    *******766656678888888762257**********995443322...34567777667888888876 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   6.6e-05      0.03       2      49 ..      99     146 ..      98     152 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6.6e-05
                                    -EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT- CS
                     APS_kinase   2 gvvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdL 49 
                                    ++ v++ Gl gsGK+t   +++++ ++kg++v ++  d+ R g +++L
  gi|119719417|ref|YP_919912.1|  99 PFKVMFVGLEGSGKTTTVAKVANYYKRKGYRVGVVAADTYRPGAYEQL 146
                                    57799**********************************998877776 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       5.5   2.5e+03     118     141 ..      29      55 ..      18      65 .. 0.60
   2 ?   13.4   0.2   0.00018     0.081       2      92 ..     111     232 ..     110     264 .. 0.65

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 5.5
                Glyco_trans_4_4 118 lyralerrllrr...adavlvvseaea 141
                                    ++r+l+r+ll+    + +vl+vse + 
  gi|119719417|ref|YP_919912.1|  29 VIRELQRALLKAdvdVGLVLSVSERIK 55 
                                    345666666655544444555555554 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00018
                Glyco_trans_4_4   2 GigryvaelaraLaarGheVtvltpapapg.apeleedgvrvhrlpvprrpspladlaalralrrl.............. 66 
                                    G ++ va +a  + + G++V v++++ +++ a+e+ +  ++ +++p++  p+   + a + alr++              
  gi|119719417|ref|YP_919912.1| 111 GKTTTVAKVANYYKRKGYRVGVVAADTYRPgAYEQLRSLAEKVGVPFYGDPQ--ERDAVSLALRGVkvlsdkgiqmilid 188
                                    6688999****************96655552556667777777777777776..44444444444433344444444444 PP

                Glyco_trans_4_4  67 ..............l..rqrrerpdvvh.ahs.ptaglaarlar 92 
                                                  +    r+ +pd v+ + +  +++++ar+ar
  gi|119719417|ref|YP_919912.1| 189 tagrhkdeealmeeVktLYREVKPDAVVlVVDaTQGSAVARQAR 232
                                    44444444444444233357999996662445356888899998 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   8.8e-05     0.039      22      62 ..      97     135 ..      49     245 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8.8e-05
                                    .TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEES CS
                         ResIII  22 krdkrglikmaTGtGKTlvaaklierllkkgkeekflflvp 62 
                                        +++++   G+GKT + ak++ ++++kg+  ++ +++ 
  gi|119719417|ref|YP_919912.1|  97 STPFKVMFVGLEGSGKTTTVAKVANYYKRKGY--RVGVVAA 135
                                    566789999999******************99..6666654 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.045        20       5      25 ..     101     121 ..      97     137 .. 0.83
   2 ?    7.0   0.0    0.0079       3.5      42      87 ..     175     223 ..     163     238 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.045
                                    EEEEE-STTSSHHHHHHHHHH CS
                          SRPRB   5 avllvGlsdsGKTslftrLtt 25 
                                    +v++vGl  sGKT+   ++ +
  gi|119719417|ref|YP_919912.1| 101 KVMFVGLEGSGKTTTVAKVAN 121
                                    699**********98887765 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0079
                                    TG...GGTT-SEEEETT-GCCSHHHHHHHHHHGG.EE..EEEEEEETTS CS
                          SRPRB  42 kvksekgskltliDfPGheklrqklleklkakss.lk..glvfvvDSti 87 
                                    kv s+kg ++ liD  G +k    l+e++k+  + +k  ++v vvD+t 
  gi|119719417|ref|YP_919912.1| 175 KVLSDKGIQMILIDTAGRHKDEEALMEEVKTLYReVKpdAVVLVVDATQ 223
                                    56799**********************9998655465559******985 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0    0.0005      0.22       9      35 ..      94     120 ..      89     126 .. 0.84
   2 ?   -0.4   0.0       1.5   6.6e+02      81      95 ..     211     225 ..     174     239 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0005
                                    TT.TTEEEEEEEESTTSSHHHHHHHHH CS
                            Arf   9 klkkkelrilllGLDnaGKtTilkklk 35 
                                    k ++  ++++++GL+++GKtT + k+ 
  gi|119719417|ref|YP_919912.1|  94 KVSSTPFKVMFVGLEGSGKTTTVAKVA 120
                                    5566789**************999875 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.5
                                    TESEEEEEEETT-CT CS
                            Arf  81 ktdavifvvDsadre 95 
                                    k dav+ vvD+++ +
  gi|119719417|ref|YP_919912.1| 211 KPDAVVLVVDATQGS 225
                                    235666666665544 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.1     0.024        11      14      47 ..      26      60 ..      16      63 .. 0.86
   2 ?    2.7   0.0      0.32   1.4e+02      16      55 ..     114     157 ..     101     158 .. 0.79
   3 ?    1.7   0.0      0.64   2.8e+02      10      58 ..     193     243 ..     163     247 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.024
                                   HHHHHHHHHHHHHTTTSEEEEES.SSSTHHHHHHH CS
                 HGTP_anticodon 14 leeyakklaeeLraagirveldd.snesigkkire 47
                                   +  + ++l+++L++a+++v l    +e+i+k++ e
  gi|119719417|ref|YP_919912.1| 26 VDLVIRELQRALLKADVDVGLVLsVSERIKKRFFE 60
                                   5667899*************************966 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.32
                                    HHHHHHHHHHHTTTSEEEEES.SSSTHH..HHHHH.HHHTT-SE CS
                 HGTP_anticodon  16 eyakklaeeLraagirveldd.snesig..kkire.adllgipf 55 
                                    + + k+a+ ++++g+rv +   +++++g  +++r  a+++g+pf
  gi|119719417|ref|YP_919912.1| 114 TTVAKVANYYKRKGYRVGVVAaDTYRPGayEQLRSlAEKVGVPF 157
                                    678899***********999999999997755554377788887 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.64
                                    S..HHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEE CS
                 HGTP_anticodon  10 k..aeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavv 58 
                                    +  +e+l+e++k l++e + + +  ++d  ++s   + ++a +   pf  v
  gi|119719417|ref|YP_919912.1| 193 HkdEEALMEEVKTLYREVKPDAVVLVVDATQGSAVARQARAFQEAMPFGYV 243
                                    244778999999999999999998888888887777777777777777655 PP

>> Gtr1_RagA  Gtr1/RagA G protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00012     0.053       1     102 [.     101     238 ..     101     248 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00012
                      Gtr1_RagA   1 kvLLmGksgsGKtsmrsiiFdnylardtlrlgati...................................dveksevrfl 45 
                                    kv+++G +gsGKt+    + +ny  r   r+g+ +                                    ++  +v   
  gi|119719417|ref|YP_919912.1| 101 KVMFVGLEGSGKTTTVAKV-ANYYKRKGYRVGVVAadtyrpgayeqlrslaekvgvpfygdpqerdavslALRGVKVLSD 179
                                    89**********9876666.899999999999999999****************************99554455555555 PP

                      Gtr1_RagA  46 gnltlnlwDcgGqeafveeylssqkeeifrnvg..vliyVfDvesre.leedletlkeil 102
                                    + +++ l+D  G+++  e  l ++ ++++r+v+  +++ V+D+++ + + ++ + ++e++
  gi|119719417|ref|YP_919912.1| 180 KGIQMILIDTAGRHKDEEA-LMEEVKTLYREVKpdAVVLVVDATQGSaVARQARAFQEAM 238
                                    679**********997655.79999*******8889*******98866999999999987 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   0.00025      0.11       1      33 [.     101     140 ..     101     240 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00025
                         AAA_28   1 kivitGgestGKTtlleaLaar....gyp..vv.pEaare 33 
                                    k++++G e++GKTt++++ a+     gy+  vv ++++r 
  gi|119719417|ref|YP_919912.1| 101 KVMFVGLEGSGKTTTVAKVANYykrkGYRvgVVaADTYRP 140
                                    6899****************65555788844333555554 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0       1.7   7.5e+02       7      33 ..      29      58 ..      26      86 .. 0.68
   2 ?   10.6   0.0   0.00095      0.43       3      76 ..     111     185 ..     109     194 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 1.7
                 Glyco_transf_4  7 hvleLaraLarrGheVtvv...tpgddgpl 33
                                   +++eL raL ++ ++V +v   + + ++++
  gi|119719417|ref|YP_919912.1| 29 VIRELQRALLKADVDVGLVlsvSERIKKRF 58
                                   689999999999999988866433333333 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00095
                 Glyco_transf_4   3 GverhvleLaraLarrGheVtvvtpgddgpleeev.elvvrvprvplpllkrllrslaflrrlrrllkrekpDvv 76 
                                    G  + v  +a++  r+G++V vv+ ++ +p ++e+ + + + ++vp+ ++++ +  ++ ++r  ++l   ++  +
  gi|119719417|ref|YP_919912.1| 111 GKTTTVAKVANYYKRKGYRVGVVAADTYRPGAYEQlRSLAEKVGVPFYGDPQERDAVSLALRGVKVLSDKGIQMI 185
                                    55788999***************9988888888877888888888888888888878777777777777777666 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00084      0.38      18      53 ..     133     168 ..     116     177 .. 0.83
   2 ?   -1.0   0.0       3.1   1.4e+03       4      24 ..     257     277 ..     256     284 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00084
                                    E-CHHCHTTGHHHHHHHHHHHT-EEEEEGGGTTSS- CS
                   TPP_enzyme_M  18 vGggvarsgaseelrelaeklgiPvvttlmgkgvip 53 
                                    v   + r ga e+lr+laek+g+P+   ++ +++++
  gi|119719417|ref|YP_919912.1| 133 VAADTYRPGAYEQLRSLAEKVGVPFYGDPQERDAVS 168
                                    55566789******************9999999886 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3.1
                                    HHHHHHH-SSEEEEE-CHHCH CS
                   TPP_enzyme_M   4 aaellkaakrpvilvGggvar 24 
                                    a+++++++k  vi++G g + 
  gi|119719417|ref|YP_919912.1| 257 ALSAVASSKARVIFIGTGEKI 277
                                    67789999********99665 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00025      0.11      34      66 ..     100     132 ..      94     165 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00025
                          AAA_7  34 kpvllvGptGtGKtviikdllkkldkekylslt 66 
                                     +v++vG +G+GKt+++ ++ + ++++ y + +
  gi|119719417|ref|YP_919912.1| 100 FKVMFVGLEGSGKTTTVAKVANYYKRKGYRVGV 132
                                    689****************99999988887655 PP

>> 6PF2K  6-phosphofructo-2-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00027      0.12      10      58 ..      96     144 ..      88     157 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00027
                                    ..S-EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHHHHHHS CS
                          6PF2K  10 knsklvivlvGLpargKtyiskkltrylkwlgvrtkvFnvgkyrreask 58 
                                    +++++ +++vGL   gKt++  k+  y k  g+r  v  +  yr  a +
  gi|119719417|ref|YP_919912.1|  96 SSTPFKVMFVGLEGSGKTTTVAKVANYYKRKGYRVGVVAADTYRPGAYE 144
                                    567899****************************999999999876655 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0    0.0078       3.5       3      23 ..     101     121 ..     100     153 .. 0.77
   2 ?    2.1   0.0      0.33   1.5e+02      40      80 ..     186     228 ..     179     262 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0078
                      PduV-EutP   3 killiGkvgsGKttLtqalkg 23 
                                    k++++G  gsGKtt   ++ +
  gi|119719417|ref|YP_919912.1| 101 KVMFVGLEGSGKTTTVAKVAN 121
                                    89***********98877665 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.33
                      PduV-EutP  40 viDtPGeylenrklysalivtsaea..dvialvqdateeesvf 80 
                                    +iDt G + +++ l++ ++++  e+  d ++lv+dat+ + v 
  gi|119719417|ref|YP_919912.1| 186 LIDTAGRHKDEEALMEEVKTLYREVkpDAVVLVVDATQGSAVA 228
                                    69*************9999886654338999999999876654 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00041      0.18      14      47 ..     109     142 ..     101     221 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00041
                           ParA  14 GVGKStvavnlAlaLakkglkvgllDaDiyGpsi 47 
                                    G GK+t+ +++A   ++kg++vg++ aD y p  
  gi|119719417|ref|YP_919912.1| 109 GSGKTTTVAKVANYYKRKGYRVGVVAADTYRPGA 142
                                    89**************************998765 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1    0.0042       1.9      10      34 ..     108     132 ..     102     149 .. 0.94
   2 ?    1.6   0.1      0.46   2.1e+02      78     112 ..     190     227 ..     181     235 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0042
                         AAA_26  10 tgvGKTvvslgLvralkrkgvkvgy 34 
                                    +g+GKT++ + +++++krkg++vg+
  gi|119719417|ref|YP_919912.1| 108 EGSGKTTTVAKVANYYKRKGYRVGV 132
                                    58*********************98 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.46
                         AAA_26  78 aarqegedidlekiv...kelekdadivvVEGagglgv 112
                                    a+r+++e+  +e++    +e++ da ++vV++++g  v
  gi|119719417|ref|YP_919912.1| 190 AGRHKDEEALMEEVKtlyREVKPDAVVLVVDATQGSAV 227
                                    77889999999999999889999*******99998765 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00053      0.24      21      50 ..      97     126 ..      85     152 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00053
                                    ..EEEEEEEESTTSSHHHHHHHHHHHCS-- CS
                        G-alpha  21 krevkllllGqseSGKsTilkqlkllykkg 50 
                                    ++++k++++G ++SGK+T++ ++  +yk +
  gi|119719417|ref|YP_919912.1|  97 STPFKVMFVGLEGSGKTTTVAKVANYYKRK 126
                                    5689****************9999888655 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0091       4.1       1      22 [.     101     122 ..     101     145 .. 0.82
   2 ?    1.4   0.0      0.78   3.5e+02      54     103 ..     180     235 ..     162     249 .. 0.65
   3 ?   -2.1   0.0       9.5   4.3e+03      89     106 ..     356     373 ..     342     378 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0091
                                    EEEEESSTTSSHHHHHHCHCT- CS
                            Roc   1 KvvlvGdsgvGKtsllkrfved 22 
                                    Kv++vG +g+GKt+ + ++ + 
  gi|119719417|ref|YP_919912.1| 101 KVMFVGLEGSGKTTTVAKVANY 122
                                    9*************99998764 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.78
                                    TCEEEEEEEE-SGGC.....TTTT-HHHHC.TSCEEEEEEEGHHHHCHHHHHHHHH CS
                            Roc  54 kkvklniWDtaGqer.....frslhplylr.eaalailvydsrssenlkeWlkelk 103
                                    k +++ + DtaG  +     ++++++ly + + ++++lv+d+++ + + +  + ++
  gi|119719417|ref|YP_919912.1| 180 KGIQMILIDTAGRHKdeealMEEVKTLYREvKPDAVVLVVDATQGSAVARQARAFQ 235
                                    45777788999965422223556778888635678888999887777655555555 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 9.5
                                    GHHHHCHHHHHHHHHHHC CS
                            Roc  89 srssenlkeWlkelkkva 106
                                    s+++ n+++W++ +++++
  gi|119719417|ref|YP_919912.1| 356 SEEDLNIDKWINIMNSMT 373
                                    566679999999888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       779  (0.0434492); expected 358.6 (0.02)
Passed bias filter:                      672  (0.0374812); expected 358.6 (0.02)
Passed Vit filter:                       141  (0.00786435); expected 17.9 (0.001)
Passed Fwd filter:                        40  (0.00223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              40  [number of targets reported over threshold]
# CPU time: 0.71u 0.29s 00:00:01.00 Elapsed: 00:00:00.45
# Mc/sec: 2890.06
//
Query:       gi|119719418|ref|YP_919913.1|  [L=401]
Description: beta-lactamase domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-06   28.9   0.0    2.2e-06   28.0   0.0    1.5  1  Flavodoxin_1   Flavodoxin
    1.2e-06   28.6   1.9    3.4e-06   27.2   0.9    2.0  2  Lactamase_B    Metallo-beta-lactamase superfamily
    0.00031   20.3   0.0     0.0076   15.8   0.0    2.2  2  Lactamase_B_2  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Flavodoxin_1  Flavodoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   3.6e-10   2.2e-06       1     129 [.     258     380 ..     258     394 .. 0.86

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 3.6e-10
                                    EEEETSSSHHHHHHHHHHHHHHHTTTEEEEEEEEGTTSC.....GGGGGTHSEEEEEEEEETTTBEEGGGHHHHHHHHHH CS
                   Flavodoxin_1   1 ilYgSetGnteklAkqlaeelgehgfnadvvslsdydes.....lseieeealllvvtsTfgnGdppengesffqdllel 75 
                                    ++Y S++G  e l     eel+++gf+++v+ + d ++      l e+ + +ll+++ +T+  G  p       ++l+++
  gi|119719418|ref|YP_919913.1| 258 VVYVSMYGFVERLVSLAIEELSQRGFETRVYAFTDTSRPrisdiLGELADAELLVLGGATYEAGVQPVLD--YVVRLIAE 335
                                    89***********************************999889999999***************877432..34777777 PP

                                    HCHHGCCSTTTTEEEEEEEEECTTSSSTTHHHHHHHHHHHHTTCEEESSSEEEE CS
                   Flavodoxin_1  76 kgdeledgdlsgvrfavfglGdsayenFcaagkkldekleelGaerllkllegd 129
                                    k +++        + av+ l ++++ +   agk + e l++ G++r+   +e++
  gi|119719418|ref|YP_919913.1| 336 KLEYR------SDKLAVLLLSSYGWAG--TAGKLVAEALKGHGFQRVSS-VEVQ 380
                                    75444......46899***********..******************97.5554 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.9   5.7e-10   3.4e-06       7     160 ..      39     177 ..      34     228 .. 0.85
   2 ?    0.1   0.0      0.11   6.8e+02      97     156 ..     257     321 ..     206     350 .. 0.74

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 5.7e-10
                                    EEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHH CS
                    Lactamase_B   7 nsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmee 86 
                                    n+yl+ +++g++++D    +  ++++ e  ++ ++  d+++v++ H+ +DH G ++++ +    +v+  + +a  ++   
  gi|119719418|ref|YP_919913.1|  39 NAYLLLTGEGAVVFDGWKKWFSELFL-EKIREIVDYGDIRYVVVHHAEPDHSGSVPDVLRVSEKAVALGHPIAGRMLSSF 117
                                    9**************99999999987.599999************************************99999999999 PP

                                    HHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCCC CS
                    Lactamase_B  87 addaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallagetgri 160
                                     +  + r              ++++++++ +g+r    v+   +h +  +  ++++++vl++ Da+ + + + +
  gi|119719418|ref|YP_919913.1| 118 YGVTRFR--------------PVKDGEELKVGERSIHFVYTPWLHWPETIMSYLRDDGVLLSCDAFGSYSVPAL 177
                                    9887777..............8888888888888888888888999*******************998777665 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.11
                                    H.....TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHH CS
                    Lactamase_B  97 l.....lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallage 156
                                           +g++++ +   +eel   +++ r + +t +  +  +++  e+ ++ +l+ G a++++ 
  gi|119719418|ref|YP_919913.1| 257 VvvyvsMYGFVERLVSLAIEELSQRGFETRVYAFTDTSRPRISDILGELADAELLVLGGATYEAG 321
                                    14445556788888888999999999999999999999999999999999999999998888654 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.3e-06    0.0076      27     116 ..      72     152 ..      50     164 .. 0.82
   2 ?    2.3   0.0     0.017     1e+02     113     168 ..     266     319 ..     197     323 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.3e-06
                                    -..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTTTTEEEEEE-TTSEEEECSTTEEEE CS
                  Lactamase_B_2  27 elppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleeepavnvheldwgesfelgdggleit 106
                                    +  +i  V++ ha+ DH   ++++ + ++k +  ++++  ++ l++          + +++++++ ge++++g+  +++ 
  gi|119719418|ref|YP_919913.1|  72 DYGDIRYVVVHHAEPDHSGSVPDVLRVSEKAV-ALGHPIAGRMLSSFY--------GVTRFRPVKDGEELKVGERSIHFV 142
                                    45799*********************877654.449999999999995........356999************9***** PP

                                    EEEE-EE--C CS
                  Lactamase_B_2 107 atparhksgr 116
                                     tp  h+ ++
  gi|119719418|ref|YP_919913.1| 143 YTPWLHWPET 152
                                    ***9999766 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.017
                                    E--CTCCE-TTTSEEEEEE.....CTTEEEEEESS-S---.HHHHHHHCT-SEEEEE-S-SS CS
                  Lactamase_B_2 113 ksgrrldrnagdtlGlrie.....gggkrvyyigDtgyip.eeigerlggadllllditaye 168
                                    + +r         ++l+ie     g + rvy  +Dt +    +i  +l++a+ll+l +  ye
  gi|119719418|ref|YP_919913.1| 266 FVER--------LVSLAIEelsqrGFETRVYAFTDTSRPRiSDILGELADAELLVLGGATYE 319
                                    5555........67777775554445567********888889999*********9998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2714.73
//
Query:       gi|119719419|ref|YP_919914.1|  [L=152]
Description: heat shock protein Hsp20 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-14   54.3   1.9    1.6e-14   53.9   1.9    1.2  1  HSP20            Hsp20/alpha crystallin family
    1.2e-09   37.6   0.1    2.2e-09   36.7   0.1    1.5  1  ArsA_HSP20       HSP20-like domain found in ArsA
     0.0091   17.0   0.1      0.015   16.3   0.1    1.4  1  CS               CS domain
  ------ inclusion threshold ------
      0.017   15.5   0.0      0.047   14.1   0.0    1.7  2  PIH1_CS          PIH1 CS-like domain
      0.057   13.3   0.1        3.4    7.6   0.0    2.4  2  Glyco_hydro_65C  Glycosyl hydrolase family 65, C-terminal dom


Domain annotation for each model (and alignments):
>> HSP20  Hsp20/alpha crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.9   1.9   4.5e-18   1.6e-14       2      93 ..      51     146 ..      50     152 .] 0.87

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 4.5e-18
                                    --SSEEEEEEEEE-TT--CCCEEEEEETTEEEEEEE--......---TT----SS---EEEEEE--STTB-TTT-EEEEE CS
                          HSP20   2 ikeeeeefevkldvpglkkeelkvkvednrvlvkgehe....eeeedekglikerssrkFsrkftLPenvdadkvkaslk 77 
                                    i +  ++ +v +d+pg++k+e+k+ v+++++ v +e+     + e+++k++ ++r +++  +k++LP  v +++ +a ++
  gi|119719419|ref|YP_919914.1|  51 IEDRGDSLAVYVDLPGFRKNEIKIRVTEDSLEVFAEKSeervKDEDSRKYIQRQRLYKQVYKKISLPVKVRPEQARARFE 130
                                    667788999************************99988777777777888888999999********************* PP

                                    TTEEEEEEEBSS--.. CS
                          HSP20  78 dGvLtvtvpkkepekk 93 
                                    dGvL v vpk+ +ek+
  gi|119719419|ref|YP_919914.1| 131 DGVLVVLVPKSGAEKE 146
                                    **********999854 PP

>> ArsA_HSP20  HSP20-like domain found in ArsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.1   6.1e-13   2.2e-09       2      61 ..      56     136 ..      55     137 .. 0.95

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 6.1e-13
                     ArsA_HSP20   2 deyvlkldLPfvdkeeidlsrsgdeLtIkig......................nfrRqitLPsvlarkevtsAkfedgvL 59 
                                    d   + +dLP++ k ei+++ ++d L + ++                      +  ++i+LP +++ +++ +A+fedgvL
  gi|119719419|ref|YP_919914.1|  56 DSLAVYVDLPGFRKNEIKIRVTEDSLEVFAEkseervkdedsrkyiqrqrlykQVYKKISLPVKVRPEQA-RARFEDGVL 134
                                    567799****************************************999999999999**********88.********* PP

                     ArsA_HSP20  60 eI 61 
                                    ++
  gi|119719419|ref|YP_919914.1| 135 VV 136
                                    97 PP

>> CS  CS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   4.3e-06     0.015       6      75 ..      52     139 ..      47     140 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.3e-06
                                    EEETTEEEEEEE-TTCTTTTTCEEEEEETTEEEEEETS.CEEEEECE...................BSS-BETTTEEEEE CS
                             CS   6 yQtldeVvvtiyvkkvnikkkdvkvefkerslkvkigk.eklliege...................LfgpIdpeesswti 65 
                                      + d++ v++ +++   +k+++k++ +e+sl+v  +k e+ +++++                   L  ++ pe+++ ++
  gi|119719419|ref|YP_919914.1|  52 EDRGDSLAVYVDLPGF--RKNEIKIRVTEDSLEVFAEKsEERVKDEDsrkyiqrqrlykqvykkisLPVKVRPEQARARF 129
                                    5567999********9..******************554555555557*****************************999 PP

                                    ETTEEEEEEE CS
                             CS  66 eskkveitLk 75 
                                    e+  + +++ 
  gi|119719419|ref|YP_919914.1| 130 EDGVLVVLVP 139
                                    9888777665 PP

>> PIH1_CS  PIH1 CS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.3e-05     0.047      31      86 ..      56     130 ..      48     139 .. 0.81
   2 ?   -2.0   0.0       1.4     5e+03      36      52 ..     135     151 ..     132     152 .] 0.79

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.3e-05
                        PIH1_CS  31 kelaieielPllksikevklrvgerrlel....................eskk..akyfLslkLpYpvdedkveAkFv 86 
                                    ++la+ ++lP+    +e+k+rv+e++le+                    +  +  ++   +++Lp +v  +++ A+F+
  gi|119719419|ref|YP_919914.1|  56 DSLAVYVDLPGF-RKNEIKIRVTEDSLEVfaekseervkdedsrkyiqrQ--RlyKQVYKKISLPVKVRPEQARARFE 130
                                    6899********.679**********************999877776431..23323333699999999999999996 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.4
                        PIH1_CS  36 eielPllksikevklrv 52 
                                     + +P+  + kev+++v
  gi|119719419|ref|YP_919914.1| 135 VVLVPKSGAEKEVEVKV 151
                                    56788888999999988 PP

>> Glyco_hydro_65C  Glycosyl hydrolase family 65, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0   0.00096       3.4      16      36 ..      67      87 ..      66      93 .. 0.86
   2 ?    3.4   0.0     0.021        74      13      36 ..     108     131 ..     107     151 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00096
                                   ETTEEEEEEEESSEEEEEEES CS
                Glyco_hydro_65C 16 yRGrrLrVrvtpeevtvtles 36
                                   +R + +++rvt ++++v +e+
  gi|119719419|ref|YP_919914.1| 67 FRKNEIKIRVTEDSLEVFAEK 87
                                   899**************9986 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.021
                                    EEEETTEEEEEEEESSEEEEEEES CS
                Glyco_hydro_65C  13 rlryRGrrLrVrvtpeevtvtles 36 
                                    +  y+   L V+v+pe+++ + e+
  gi|119719419|ref|YP_919914.1| 108 KQVYKKISLPVKVRPEQARARFED 131
                                    66899999*********9977776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       981  (0.0547158); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 967.37
//
Query:       gi|119719420|ref|YP_919915.1|  [L=120]
Description: translation initiation factor SUI1 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-21   76.7   0.1    1.9e-21   76.4   0.1    1.1  1  SUI1         Translation initiation factor SUI1
     0.0078   16.5   0.1      0.014   15.7   0.1    1.6  1  Img2         Mitochondrial large subunit ribosomal protein (I
  ------ inclusion threshold ------
      0.039   14.4   0.4      0.064   13.7   0.4    1.3  1  GTP_EFTU_D2  Elongation factor Tu domain 2
      0.092   12.6   0.0       0.12   12.3   0.0    1.3  1  DUF4032      Domain of unknown function (DUF4032)


Domain annotation for each model (and alignments):
>> SUI1  Translation initiation factor SUI1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.4   0.1   4.3e-25   1.9e-21       2      77 .]      42     113 ..      41     113 .. 0.95

  Alignments for each domain:
  == domain 1  score: 76.4 bits;  conditional E-value: 4.3e-25
                           SUI1   2 kpkihirleqrggrKkvTtvsgleafgidlkklakelkkkfacsgsvvkdggeeiqvQGdqrkkvaelLtekygvp 77 
                                    ++ i+ir+e+r+g + vT+++gl+ ++ +l ++++e+k kfac+g++ kd+   +++QGd+r kv+e+L+ + g+p
  gi|119719420|ref|YP_919915.1|  42 QQLIKIRVEKRKGHRDVTIITGLDVKDPELRRMVSEMKAKFACGGTI-KDD--HVELQGDHRYKVKEFLVLN-GFP 113
                                    789*******************************************9.777..8***************998.876 PP

>> Img2  Mitochondrial large subunit ribosomal protein (Img2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   3.1e-06     0.014      21      80 .]      52     112 ..      14     112 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.1e-06
                           Img2  21 rggtkkltvirkieGDiaalredLrkalee.lvkvnevtgkieikGdrveevkkfLeskgF 80 
                                    r+g + +t+i   +    +lr+ ++++ ++ ++  + +  ++e++Gd++ +vk+fL  +gF
  gi|119719420|ref|YP_919915.1|  52 RKGHRDVTIITGLDVKDPELRRMVSEMKAKfACGGTIKDDHVELQGDHRYKVKEFLVLNGF 112
                                    4444444554444444444444444444433344455899*****************9999 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.4   1.4e-05     0.064       8      65 ..      34      91 ..      33      96 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.4e-05
                                   EEESEEETTEEEEEECTCTTSEE..EEEEEEEEEEETEEESEEETTSEEEEEEEESSCCS CS
                    GTP_EFTU_D2  8 vysGtlkkGdevrilgndtskke..ivtrissletfhededeavaganaGvivaikgled 65
                                   +  G++k+ + ++i     ++k+   vt i++l +  ++++ +v +  a + +++   +d
  gi|119719420|ref|YP_919915.1| 34 ILKGVFKEQQLIKI--RVEKRKGhrDVTIITGLDVKDPELRRMVSEMKAKFACGGTIKDD 91
                                   789***********..555455567****************************9976666 PP

>> DUF4032  Domain of unknown function (DUF4032)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.6e-05      0.12      53      86 ..      48      80 ..      17     107 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.6e-05
                        DUF4032 53 kvvdaghhrrrLlrLTGldveenQArrlLndles 86
                                   + v+++  +r ++ +TGldv++   rr+++++++
  gi|119719420|ref|YP_919915.1| 48 R-VEKRKGHRDVTIITGLDVKDPELRRMVSEMKA 80
                                   3.556666788999******************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 828.29
//
Query:       gi|119719421|ref|YP_919916.1|  [L=472]
Description: hypothetical protein Tpen_0506 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.14   11.9   0.3          3    7.7   0.0    2.6  2  Get5_C    Get5 C-terminal domain


Domain annotation for each model (and alignments):
>> Get5_C  Get5 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0   0.00016         3      26      38 .]     175     187 ..     169     187 .. 0.87
   2 ?    1.4   0.1     0.015   2.7e+02      14      32 ..     449     467 ..     442     467 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00016
                         Get5_C  26 vleRLqKGWeltk 38 
                                    vl  LqKGW lt+
  gi|119719421|ref|YP_919916.1| 175 VLRSLQKGWVLTD 187
                                    7888******996 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.015
                         Get5_C  14 knkfkndaearavleRLqK 32 
                                    k+k +  ++a+ ++eRL K
  gi|119719421|ref|YP_919916.1| 449 KAKAEQYPKAQSLVERLEK 467
                                    555566689********87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (472 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 3427.98
//
Query:       gi|119719422|ref|YP_919917.1|  [L=69]
Description: hypothetical protein Tpen_0507 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       842  (0.046963); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 518.44
//
Query:       gi|119719423|ref|YP_919918.1|  [L=309]
Description: putative agmatinase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-63  214.0   0.0    3.6e-63  213.7   0.0    1.1  1  Arginase  Arginase family


Domain annotation for each model (and alignments):
>> Arginase  Arginase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  213.7   0.0     2e-67   3.6e-63       3     277 ..      28     286 ..      26     289 .. 0.91

  Alignments for each domain:
  == domain 1  score: 213.7 bits;  conditional E-value: 2e-67
                                    EEEEEEE--TTTSSSGGGGGHHHHHHHHHHTSBTHCHEETTTTE.SCCSEEEEEEEEE--SSCHHHHHHHHHHHHHHHHH CS
                       Arginase   3 vallGvPfdaagsgrpGarfGPraireasarleealeynlelgv.leelkivdlgdvavtpvdneevleqieeavaeilk 81 
                                     +++G+Pfd++ +g pG rf+P+ ire s +le+   + ++l++  e+l ++d+gd++v + + e +++ +   ++e+l+
  gi|119719423|ref|YP_919918.1|  28 YVVVGAPFDSTATGVPGQRFAPQRIREVSVELET---FLPDLQIdVERLAVNDAGDLPVLT-SVEALIDILGGVAREVLS 103
                                    689******************************7...44444555889***********86.99989************* PP

                                    TTCEEEEEESSGGGHHHHHHHHHHHHSTTEEEEEESSS----SSCTTTBSSSTTSHHHHHHHHTSECGCEEEEEEE-STC CS
                       Arginase  82 agklpivlGGDHsialgilralaekygkplgvihfDAHaDlrtpetegsgnshGtpfrraaeegllkpkklvqiGirsvd 161
                                    +gk  i+lGGDH  ++++l  +a +++ +lgv+ fDAH+Dlr+++  + ++sh+t+frr +  + +k+  +++   r+++
  gi|119719423|ref|YP_919918.1| 104 SGKGLIMLGGDHFSSFPVLVEAAGNVD-ELGVLVFDAHLDLRDEYPVKCRYSHATVFRRLI--EQTKNVYIAYYKPRGWS 180
                                    ***********************9998.6********************************..55777899999****** PP

                                    SHHHHHHHHTTSEEEEHHHHHHHHHHHHHHHHHHHHTCTTSEEEEEEEGGGBBTTTSTSSSS-BSS-B-HHHHHHHHHH. CS
                       Arginase 162 neeyelakelgirvitmreidelglkavveeilervgaeedpvylSfDiDvlDpavaPGtGtpepgGltlrellallre. 240
                                    +eeye++++      + r++  l+     ee+++ v+ e++ vy+S+DiD+lDpa+aPGtGtpep Gl +rel + lr+ 
  gi|119719423|ref|YP_919918.1| 181 SEEYEFMRQ------SPRKLAVLNT---REEVESWVK-EHRTVYVSIDIDALDPAYAPGTGTPEPIGLAPRELVDSLRAa 250
                                    *******96......6666666555...788999996.668**************************************8 PP

                                    HHCHSEEEEEEEE-B-GGGSSTTTHHHHHHHHHHHHH CS
                       Arginase 241 laeklnlvgaDvvEvnPaldteaeqtarlaarlvrel 277
                                    + ++++l g+DvvEvnP  d ++  t+r+aa+++ e+
  gi|119719423|ref|YP_919918.1| 251 VLGSEKLLGIDVVEVNPLVDVNN-LTSRVAAKILLEA 286
                                    7788*****************55.**********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.21s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 2437.56
//
Query:       gi|119719424|ref|YP_919919.1|  [L=62]
Description: DNA-directed RNA polymerase subunit P [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.3e-05   22.2   5.2    0.00019   21.1   5.2    1.6  1  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
    0.00015   21.8   1.5    0.00021   21.3   1.5    1.2  1  Zn-ribbon_8      Zinc ribbon domain
     0.0008   18.7   0.8       0.18   11.3   0.2    2.2  2  zf-ribbon_3      zinc-ribbon domain
     0.0031   17.5   0.1      0.004   17.1   0.1    1.1  1  zf-C2HC5         Putative zinc finger motif, C2HC5-type
     0.0051   16.8   0.2     0.0057   16.7   0.2    1.2  1  HypA             Hydrogenase/urease nickel incorporation, met
     0.0053   16.3   1.3       0.16   11.6   0.2    2.2  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
  ------ inclusion threshold ------
      0.011   16.0   0.2      0.013   15.8   0.2    1.1  1  DUF2072          Zn-ribbon containing protein
      0.012   15.2   1.2       0.72    9.4   0.1    2.1  2  TF_Zn_Ribbon     TFIIB zinc-binding
      0.016   15.6   2.5        1.3    9.6   0.2    2.2  2  zf-C2H2          Zinc finger, C2H2 type
      0.018   14.8   0.7        1.2    9.0   0.0    2.3  2  zinc_ribbon_5    zinc-ribbon domain
       0.02   14.9   0.6      0.045   13.8   0.8    1.4  1  DZR              Double zinc ribbon
       0.02   14.8   1.0       0.88    9.6   0.1    2.2  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
      0.025   14.4   0.2      0.031   14.2   0.2    1.2  1  C1_1             Phorbol esters/diacylglycerol binding domain
      0.025   14.4   6.1        0.6   10.0   0.5    2.2  2  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
      0.028   15.2   1.8          5    8.2   0.2    2.3  2  zf-C2H2_4        C2H2-type zinc finger
      0.029   14.3   0.6        3.1    7.8   0.1    2.1  2  YhfH             YhfH-like protein
       0.04   13.7   2.2       0.57   10.0   0.1    2.1  2  zinc_ribbon_10   Predicted integral membrane zinc-ribbon meta
      0.042   14.2   0.3      0.049   14.0   0.3    1.2  1  DUF4379          Probable Zinc-ribbon domain
       0.05   13.3   1.2       0.55   10.0   0.1    2.2  2  zinc_ribbon_2    zinc-ribbon domain
      0.054   13.7   0.2      0.066   13.4   0.2    1.1  1  IBR              IBR domain, a half RING-finger domain
      0.061   13.3   0.8       0.12   12.3   0.8    1.5  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.069   12.8   1.6       0.71    9.5   0.1    2.2  2  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
      0.074   13.0   5.4       0.87    9.6   5.4    2.1  2  Zn_ribbon_SprT   SprT-like zinc ribbon domain
      0.082   12.8   3.7        2.1    8.4   0.2    2.4  2  zinc_ribbon_4    zinc-ribbon domain
      0.082   13.2   1.4       0.28   11.5   1.4    1.8  2  zinc_ribbon_9    zinc-ribbon
      0.089   12.8   1.2        8.6    6.4   0.1    2.1  2  CpXC             CpXC protein
       0.16   11.8   3.5       0.19   11.5   0.4    2.1  2  zf-C2H2_11       zinc-finger C2H2-type
       0.27   11.4   2.8        6.7    7.0   0.1    2.1  2  zf-AN1           AN1-like Zinc finger
       0.34   10.7   2.8       0.51   10.1   2.8    1.3  1  zf-CSL           CSL zinc finger
       0.55   10.2   3.4         12    5.9   0.4    2.1  2  PyrI_C           Aspartate carbamoyltransferase regulatory ch


Domain annotation for each model (and alignments):
>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   5.2   3.1e-07   0.00019       1      32 []      18      52 ..      18      52 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 3.1e-07
                                   -B-SSS--B----SSS-...---SSS-----B--- CS
                 DNA_RNApol_7kD  1 YiCgeCgaevslkkgdp...iRCkeCGhRilYKkR 32
                                   Y C +Cg+ ++ ++++    +RC +CG+Ri+ K R
  gi|119719424|ref|YP_919919.1| 18 YRCLRCGQVFTKEEQERlpgVRCPYCGFRIVEKVR 52
                                   99******9998888754459**********8877 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   1.5   3.6e-07   0.00021       6      38 ..      18      50 ..      15      51 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 3.6e-07
                    Zn-ribbon_8  6 YrCeeCghefevlqsisdapltaCPeCgs.evrr 38
                                   YrC +Cg++f++  +  + p + CP Cg   v++
  gi|119719424|ref|YP_919919.1| 18 YRCLRCGQVFTKEEQ-ERLPGVRCPYCGFrIVEK 50
                                   ***********6663.4667788****9755555 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0      0.01       6.1       2      15 ..      17      31 ..      16      33 .. 0.78
   2 !   11.3   0.2    0.0003      0.18       3       9 ..      38      44 ..      36      50 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.01
                    zf-ribbon_3  2 tvrCPnCGa.plssd 15
                                   t+rC +CG+   +++
  gi|119719424|ref|YP_919919.1| 17 TYRCLRCGQvFTKEE 31
                                   899******666665 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.0003
                    zf-ribbon_3  3 vrCPnCG 9 
                                   vrCP+CG
  gi|119719424|ref|YP_919919.1| 38 VRCPYCG 44
                                   5666666 PP

>> zf-C2HC5  Putative zinc finger motif, C2HC5-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   6.6e-06     0.004      19      46 ..      19      49 ..      11      53 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 6.6e-06
                       zf-C2HC5 19 nClnCGkiiCakegls...kpCsfCgsplls 46
                                    Cl CG++  + e+      +C++Cg  +++
  gi|119719424|ref|YP_919919.1| 19 RCLRCGQVFTKEEQERlpgVRCPYCGFRIVE 49
                                   7*********9998888889*****987765 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.2   9.5e-06    0.0057      69      97 ..      16      48 ..       2      53 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 9.5e-06
                                   -EEEETTTS-EEECHHH.HH...S-TTTSSS-E CS
                           HypA 69 vkvrCreCgkefeleek.al...rCpkCgsadv 97
                                    ++rC +Cg+ f++ee+ +l   rCp Cg + v
  gi|119719424|ref|YP_919919.1| 16 KTYRCLRCGQVFTKEEQeRLpgvRCPYCGFRIV 48
                                   5689*********7764322555*****97655 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.2   0.00027      0.16       2      16 ..      17      31 ..      16      33 .. 0.85
   2 ?    3.8   0.0     0.071        42       4      13 ..      39      48 ..      37      53 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00027
                         zf_UBZ  2 tylCerCgkeipese 16
                                   ty C rCg+ +  +e
  gi|119719424|ref|YP_919919.1| 17 TYRCLRCGQVFTKEE 31
                                   9*********98876 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.071
                         zf_UBZ  4 lCerCgkeip 13
                                    C+ Cg +i 
  gi|119719424|ref|YP_919919.1| 39 RCPYCGFRIV 48
                                   7*****9996 PP

>> DUF2072  Zn-ribbon containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.8   0.2   2.1e-05     0.013       3      29 ..      19      47 ..      17      58 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.1e-05
                        DUF2072  3 kCtkCekvfedgskeilkG..CpsCGgkk 29
                                   +C +C++vf   ++e l G  Cp CG + 
  gi|119719424|ref|YP_919919.1| 19 RCLRCGQVFTKEEQERLPGvrCPYCGFRI 47
                                   8***************99999*****875 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.1    0.0012      0.72      12      29 ..      10      27 ..       4      34 .. 0.84
   2 ?    5.0   0.2     0.029        17       2       7 ..      39      44 ..      38      50 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0012
                                   HEETSTTCEEESSSSBEE CS
                   TF_Zn_Ribbon 12 veDpergelvCtdCGlVl 29
                                   + D++  +++C +CG V 
  gi|119719424|ref|YP_919919.1| 10 EADYSLKTYRCLRCGQVF 27
                                   7899999********996 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.029
                                   EETTTT CS
                   TF_Zn_Ribbon  2 kCPnCg 7 
                                   +CP+Cg
  gi|119719424|ref|YP_919919.1| 39 RCPYCG 44
                                   688888 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.2    0.0022       1.3       1      12 [.      18      29 ..      18      32 .. 0.87
   2 ?    6.2   0.2     0.027        16       2       8 ..      39      45 ..      38      50 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0022
                                   EEETTTTEEESS CS
                        zf-C2H2  1 ykCpdCgksFkr 12
                                   y+C  Cg++F+ 
  gi|119719424|ref|YP_919919.1| 18 YRCLRCGQVFTK 29
                                   9*********86 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.027
                                   EETTTTE CS
                        zf-C2H2  2 kCpdCgk 8 
                                   +Cp+Cg 
  gi|119719424|ref|YP_919919.1| 39 RCPYCGF 45
                                   7****96 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0     0.002       1.2      27      36 ..      19      28 ..      10      29 .. 0.89
   2 ?    4.4   0.1     0.053        32       3      12 ..      38      45 ..      37      52 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.002
                  zinc_ribbon_5 27 rCakCaevFd 36
                                   rC +C++vF+
  gi|119719424|ref|YP_919919.1| 19 RCLRCGQVFT 28
                                   9********8 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.053
                  zinc_ribbon_5  3 irCpdCdtkF 12
                                   +rCp C+  F
  gi|119719424|ref|YP_919919.1| 38 VRCPYCG--F 45
                                   5888887..5 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.8   7.6e-05     0.045      28      49 .]      17      44 ..       3      44 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.6e-05
                            DZR 28 edrCpsCgekvdpearf......CpeCG 49
                                    +rC +Cg+  ++e++       Cp+CG
  gi|119719424|ref|YP_919919.1| 17 TYRCLRCGQVFTKEEQErlpgvrCPYCG 44
                                   7899999999777776668999999998 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1     0.058        35      32      44 ..      15      24 ..       4      26 .. 0.76
   2 ?    9.6   0.1    0.0015      0.88      18      27 ..      37      46 ..      31      58 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.058
                  Zn_Tnp_IS1595 32 iktrglfqCkeCr 44
                                   +   + ++C +C+
  gi|119719424|ref|YP_919919.1| 15 L---KTYRCLRCG 24
                                   4...559999997 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0015
                  Zn_Tnp_IS1595 18 gfvCPhCgsr 27
                                   g++CP+Cg r
  gi|119719424|ref|YP_919919.1| 37 GVRCPYCGFR 46
                                   678*****76 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.2   5.2e-05     0.031       9      37 ..      15      46 ..       7      50 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.2e-05
                                   SS--B-TTT-SB-..-S.SSS-EEEETTT--E CS
                           C1_1  9 kqptfCkhCgefl..wg.kekqglkCswCkll 37
                                    ++ +C  Cg+ +  ++ ++++g++C  C+++
  gi|119719424|ref|YP_919919.1| 15 LKTYRCLRCGQVFtkEEqERLPGVRCPYCGFR 46
                                   56779********995569**********987 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.5     0.001       0.6       5      21 ..      11      27 ..      10      31 .. 0.90
   2 ?    8.0   0.6    0.0044       2.6       6      20 ..      32      46 ..      27      52 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.001
                        DUF35_N  5 aegrLvgqrCpdCGtvq 21
                                   a++ L   rC  CG+v+
  gi|119719424|ref|YP_919919.1| 11 ADYSLKTYRCLRCGQVF 27
                                   67899999*******96 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0044
                        DUF35_N  6 egrLvgqrCpdCGtv 20
                                   + rL g rCp CG  
  gi|119719424|ref|YP_919919.1| 32 QERLPGVRCPYCGFR 46
                                   679999999999976 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.2    0.0083         5       1      13 [.      18      29 ..      18      34 .. 0.82
   2 ?    6.6   0.1     0.028        17       2      10 ..      39      45 ..      38      53 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0083
                      zf-C2H2_4  1 fkCpiCgksFssk 13
                                   ++C  Cg++F +k
  gi|119719424|ref|YP_919919.1| 18 YRCLRCGQVF-TK 29
                                   89********.54 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.028
                      zf-C2H2_4  2 kCpiCgksF 10
                                   +Cp+C   F
  gi|119719424|ref|YP_919919.1| 39 RCPYC--GF 45
                                   7****..55 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.2     0.025        15      15      24 ..      19      28 ..      13      34 .. 0.74
   2 ?    7.8   0.1    0.0053       3.1       9      26 ..      33      50 ..      30      52 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.025
                           YhfH 15 kCteCGkeie 24
                                    C  CG+++ 
  gi|119719424|ref|YP_919919.1| 19 RCLRCGQVFT 28
                                   6******963 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0053
                           YhfH  9 rnLPkKkCteCGkeieEq 26
                                   ++LP   C+ CG  i E+
  gi|119719424|ref|YP_919919.1| 33 ERLPGVRCPYCGFRIVEK 50
                                   5799999*****999886 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00095      0.57      37      52 ..      10      25 ..       1      27 [. 0.74
   2 ?    4.8   0.2     0.039        23      39      53 ..      31      46 ..      24      47 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00095
                 zinc_ribbon_10 37 keeleevkyrCpkCga 52
                                   + +++  +yrC  Cg+
  gi|119719424|ref|YP_919919.1| 10 EADYSLKTYRCLRCGQ 25
                                   5677777*******97 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.039
                 zinc_ribbon_10 39 eleev.kyrCpkCgal 53
                                   e e++   rCp+Cg+ 
  gi|119719424|ref|YP_919919.1| 31 EQERLpGVRCPYCGFR 46
                                   555555569****975 PP

>> DUF4379  Probable Zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.3   8.2e-05     0.049      30      56 .]      18      43 ..       3      43 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 8.2e-05
                        DUF4379 30 WkCakCgheWeasvsnrtkgsskCpkC 56
                                    +C +Cg+ + ++ ++r  g + Cp+C
  gi|119719424|ref|YP_919919.1| 18 YRCLRCGQVFTKEEQERLPGVR-CPYC 43
                                   69****************9998.**** PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1      0.25   1.5e+02       2       6 ..      20      24 ..      17      26 .. 0.68
   2 ?   10.0   0.1   0.00092      0.55      16      22 ..      40      46 ..      38      52 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.25
                  zinc_ribbon_2  2 CpnCG 6 
                                   C +CG
  gi|119719424|ref|YP_919919.1| 20 CLRCG 24
                                   66666 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00092
                  zinc_ribbon_2 16 CpyCGtp 22
                                   CpyCG+ 
  gi|119719424|ref|YP_919919.1| 40 CPYCGFR 46
                                   8888864 PP

>> IBR  IBR domain, a half RING-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   0.00011     0.066      18      47 ..      17      46 ..       4      47 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00011
                            IBR 18 lkwCprpdCeaiiekseg..cksvtCskCgfe 47
                                   +  C    C++++ k+e+     v+C+ Cgf+
  gi|119719424|ref|YP_919919.1| 17 TYRCL--RCGQVFTKEEQerLPGVRCPYCGFR 46
                                   55799..8*****99999544449******97 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.8   0.00021      0.12      29      55 ..      18      46 ..       3      49 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00021
                 OrfB_Zn_ribbon 29 ktCseCgsknke..alsgrtfkCpnCgfe 55
                                    +C +Cg++ ++  +     ++Cp Cgf+
  gi|119719424|ref|YP_919919.1| 18 YRCLRCGQVFTKeeQERLPGVRCPYCGFR 46
                                   57******9999555555679******97 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1    0.0012      0.71       5      15 ..      16      26 ..      13      28 .. 0.85
   2 ?    2.4   0.1       0.2   1.2e+02       8      16 ..      39      48 ..      33      51 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0012
                                   -EEE-TTT--E CS
                Desulfoferrod_N  5 evYkCevCGni 15
                                     Y+C  CG++
  gi|119719424|ref|YP_919919.1| 16 KTYRCLRCGQV 26
                                   68*******98 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.2
                                   E-TTT-.-EE CS
                Desulfoferrod_N  8 kCevCG.niV 16
                                   +C  CG  iV
  gi|119719424|ref|YP_919919.1| 39 RCPYCGfRIV 48
                                   8*****4455 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.8    0.0019       1.1       4      12 ..      17      25 ..       9      31 .. 0.72
   2 ?    9.6   5.4    0.0014      0.87       4      35 ..      17      48 ..      17      51 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0019
                 Zn_ribbon_SprT  4 vYrCtgCgr 12
                                   +YrC +Cg+
  gi|119719424|ref|YP_919919.1| 17 TYRCLRCGQ 25
                                   567777764 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0014
                 Zn_ribbon_SprT  4 vYrCtgCgreythhlsirrhn...YrCrrCkgtLr 35
                                   +YrC +Cg    +  +   ++    rC++C+ +++
  gi|119719424|ref|YP_919919.1| 17 TYRCLRCG---QVFTKEEQERlpgVRCPYCGFRIV 48
                                   7*******...5544447777777******98876 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.2    0.0035       2.1      27      36 .]      19      28 ..      15      28 .. 0.90
   2 ?    5.5   0.2     0.027        16      26      33 ..      38      45 ..      34      48 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0035
                  zinc_ribbon_4 27 rCskCghvFr 36
                                   rC +Cg+vF+
  gi|119719424|ref|YP_919919.1| 19 RCLRCGQVFT 28
                                   9********7 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.027
                  zinc_ribbon_4 26 vrCskCgh 33
                                   vrC+ Cg 
  gi|119719424|ref|YP_919919.1| 38 VRCPYCGF 45
                                   66777764 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1      0.13        75      22      32 ..      19      28 ..       3      30 .. 0.70
   2 ?   11.5   1.4   0.00047      0.28       3      34 ..      18      50 ..      16      51 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.13
                  zinc_ribbon_9 22 vlCPhCgggFV 32
                                     C +Cg+ F 
  gi|119719424|ref|YP_919919.1| 19 R-CLRCGQVFT 28
                                   3.999999886 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00047
                  zinc_ribbon_9  3 yWChqCdrfVsvspdedsd..vlCPhCgggFVEe 34
                                   y C +C + ++  +++++   v CP+Cg   VE 
  gi|119719424|ref|YP_919919.1| 18 YRCLRCGQVFTK-EEQERLpgVRCPYCGFRIVEK 50
                                   668899988875.4555555658*****999995 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.1     0.019        12      33      49 ..      13      29 ..       5      33 .. 0.84
   2 ?    6.4   0.1     0.014       8.6      34      47 ..      34      47 ..      31      57 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.019
                           CpXC 33 gslfeatCpkCgatakl 49
                                    sl +++C +Cg+ ++ 
  gi|119719424|ref|YP_919919.1| 13 YSLKTYRCLRCGQVFTK 29
                                   58999*******99875 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.014
                           CpXC 34 slfeatCpkCgata 47
                                   +l  ++Cp+Cg ++
  gi|119719424|ref|YP_919919.1| 34 RLPGVRCPYCGFRI 47
                                   667789*****876 PP

>> zf-C2H2_11  zinc-finger C2H2-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.4   0.00031      0.19       4      15 ..      17      28 ..      14      30 .. 0.89
   2 ?    1.0   0.2      0.62   3.7e+02       5      11 ..      38      44 ..      37      46 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00031
                     zf-C2H2_11  4 tcqCleCGlcft 15
                                   t++Cl CG  ft
  gi|119719424|ref|YP_919919.1| 17 TYRCLRCGQVFT 28
                                   9*******9998 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.62
                     zf-C2H2_11  5 cqCleCG 11
                                   ++C  CG
  gi|119719424|ref|YP_919919.1| 38 VRCPYCG 44
                                   69****9 PP

>> zf-AN1  AN1-like Zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.3     0.038        23      13      23 ..      17      27 ..       9      30 .. 0.81
   2 ?    7.0   0.1     0.011       6.7       9      20 ..      32      44 ..      28      47 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.038
                         zf-AN1 13 pfkCryCgkvF 23
                                    ++C +Cg+vF
  gi|119719424|ref|YP_919919.1| 17 TYRCLRCGQVF 27
                                   399******99 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.011
                         zf-AN1  9 kdflp.fkCryCg 20
                                   ++ lp ++C+yCg
  gi|119719424|ref|YP_919919.1| 32 QERLPgVRCPYCG 44
                                   457889******8 PP

>> zf-CSL  CSL zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   2.8   0.00085      0.51      18      50 ..      17      43 ..       6      50 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00085
                                   EEEE.TTSSEEEEEHHHHHTT....--EEEETTS CS
                         zf-CSL 18 yypC.RCgdeFelteedleegaegaevvvqCssC 50
                                   +y C RCg+ F  +e++   g       v+C+ C
  gi|119719424|ref|YP_919919.1| 17 TYRClRCGQVFTKEEQERLPG-------VRCPYC 43
                                   79*********9999998887.......778777 PP

>> PyrI_C  Aspartate carbamoyltransferase regulatory chain, metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.4      0.02        12      28      47 ..      12      31 ..       4      32 .. 0.81
   2 ?    5.6   0.3     0.025        15      34      44 ..      38      48 ..      30      51 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.02
                                   ETTTTEEEETTT--EEEHHH CS
                         PyrI_C 28 dkekvklkCkYCekeiseee 47
                                   d +  +++C  C++++++ee
  gi|119719424|ref|YP_919919.1| 12 DYSLKTYRCLRCGQVFTKEE 31
                                   556679***********986 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.025
                                   EEETTT--EEE CS
                         PyrI_C 34 lkCkYCekeis 44
                                   ++C YC+  i 
  gi|119719424|ref|YP_919919.1| 38 VRCPYCGFRIV 48
                                   79****97765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); expected 358.6 (0.02)
Passed Vit filter:                       104  (0.00580066); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              30  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 451.31
//
Query:       gi|119719425|ref|YP_919920.1|  [L=297]
Description: methyltransferase type 11 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-07   30.0   0.0    5.8e-07   29.4   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    5.5e-07   30.1   0.1    2.4e-06   28.1   0.0    2.1  2  Methyltransf_11  Methyltransferase domain
    7.1e-07   29.8   0.0    1.8e-06   28.6   0.0    1.7  1  Methyltransf_25  Methyltransferase domain
    1.9e-06   27.7   0.0    2.7e-06   27.1   0.0    1.2  1  Cons_hypoth95    Conserved hypothetical protein 95
    2.6e-05   23.8   0.0      4e-05   23.2   0.0    1.2  1  MTS              Methyltransferase small domain
    2.7e-05   24.0   0.0    0.00032   20.5   0.0    2.0  2  Met_10           Met-10+ like-protein
    0.00016   21.0   0.0    0.00024   20.5   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
    0.00024   20.7   0.0    0.00036   20.2   0.0    1.2  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
    0.00048   19.9   0.0    0.00091   19.0   0.0    1.4  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    0.00076   19.4   0.0     0.0014   18.5   0.0    1.5  1  Methyltransf_30  S-adenosyl-L-methionine-dependent methyltran
  ------ inclusion threshold ------
       0.02   14.0   0.0      0.028   13.5   0.0    1.1  1  RrnaAD           Ribosomal RNA adenine dimethylase
      0.028   13.8   0.0       0.07   12.5   0.0    1.5  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
      0.031   14.1   0.0       0.18   11.6   0.0    2.4  2  Methyltransf_23  Methyltransferase domain
      0.061   13.0   0.0        0.1   12.3   0.0    1.4  1  N6_N4_Mtase      DNA methylase
       0.07   12.8   0.0       0.14   11.8   0.0    1.4  2  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
      0.077   11.9   0.0       0.25   10.2   0.0    1.7  2  Methyltransf_9   Protein of unknown function (DUF1698)
      0.094   12.1   0.0       0.13   11.6   0.0    1.3  1  Spermine_synth   Spermine/spermidine synthase domain
       0.14   13.2   0.0       0.26   12.3   0.0    1.4  1  Methyltransf_24  Methyltransferase domain
        0.2   11.0   0.0       0.29   10.5   0.0    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm


Domain annotation for each model (and alignments):
>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   6.1e-10   5.8e-07       4     107 ..     145     248 ..     143     265 .. 0.91

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 6.1e-10
                Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfDlilsne 82 
                                    g +vlD+ +G G+ ++++ e+   +aevv+i+ +++++  A+ n  + +l++++   gd+++   + l +e fD +l + 
  gi|119719425|ref|YP_919920.1| 145 GEKVLDVCTGLGYTAIRALER---GAEVVSIEKDPNVLYIAEHNPFSEKLSRASILLGDAFDvVGE-LPEEYFDKVLHDP 220
                                    679****************66...79************************************8777.57789******98 PP

                Methyltransf_31  83 vl...naladpdkileeiervlkpggil 107
                                    ++   +    +++++ ++ rvlk+gg++
  gi|119719425|ref|YP_919920.1| 221 PVfafAGHLYSAEFYTRLWRVLKKGGRV 248
                                    88777666678999************97 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       7.2   6.8e+03      19      39 ..     122     142 ..     109     147 .. 0.70
   2 !   28.1   0.0   2.5e-09   2.4e-06       1      95 [.     149     249 ..     149     250 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 7.2
                                    SEEEEEES-HHHHHHHHHHCC CS
                Methyltransf_11  19 arvvgvDlskemlklakekas 39 
                                    ++++g+D+   + + +++ ++
  gi|119719425|ref|YP_919920.1| 122 HNITGIDPLSDAERKVRMLGV 142
                                    789999998887777776665 PP

  == domain 2  score: 28.1 bits;  conditional E-value: 2.5e-09
                                    EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCT..SS-TT-EEEEEEES-CCC-... CS
                Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl.kvefvvadaekl..pfednsfDlvvssevlhhv... 74 
                                    Ldv +G G+ a    +rga+vv ++ ++++l +a+++   e+l + +++ +da ++   +++++fD v+    ++ +   
  gi|119719425|ref|YP_919920.1| 149 LDVCTGLGYTAIRALERGAEVVSIEKDPNVLYIAEHNPFSEKLsRASILLGDAFDVvgELPEEYFDKVLHDPPVFAFagh 228
                                    899999999999999*********************9999999*999********6567**********98844444355 PP

                                    CCHHHHHHHHHHHEEEEEEEE CS
                Methyltransf_11  75 edpekalkeiaRvLkpgGllv 95 
                                       +++   ++RvLk+gG+++
  gi|119719425|ref|YP_919920.1| 229 LYSAEFYTRLWRVLKKGGRVF 249
                                    589***************986 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0   1.9e-09   1.8e-06       1      97 []     148     246 ..     148     246 .. 0.88

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 1.9e-09
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGB..SSSTTTEEEEEEEST.GGG CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedl..pfedgsfDlvvssga.lhh 76 
                                    vLd+++G G +++++++r+  a+v+ ++ +++ l +a+++  +e+l +++++ gda d+  +++++ fD v+     + +
  gi|119719425|ref|YP_919920.1| 148 VLDVCTGLGYTAIRALERG--AEVVSIEKDPNVLYIAEHNPFSEKLsRASILLGDAFDVvgELPEEYFDKVLHDPPvFAF 225
                                    9*****************5..********************999999*********9973458999******94444444 PP

                                    SSHHHHHHHHHHHHHHEEEEE CS
                Methyltransf_25  77 lsdedlekalkeiarvLkpgG 97 
                                      +   ++++ +++rvLk+gG
  gi|119719425|ref|YP_919920.1| 226 AGHLYSAEFYTRLWRVLKKGG 246
                                    44455678************9 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0   2.9e-09   2.7e-06      41     122 ..     144     221 ..     122     250 .. 0.88

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 2.9e-09
                                    CC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEEEE- CS
                  Cons_hypoth95  41 egarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdivflD 120
                                    +g++vLD++ G G  ++ Al Rga ++v +ekd++++ i ++n  + kl+ ++++l  da++ + +l   +e+fd v  D
  gi|119719425|ref|YP_919920.1| 144 RGEKVLDVCTGLGYTAIRALERGA-EVVSIEKDPNVLYIAEHNPFSEKLS-RASILLGDAFDVVGEL--PEEYFDKVLHD 219
                                    6789*******************6.6899**************9999988.59***********999..5779******* PP

                                    -S CS
                  Cons_hypoth95 121 PP 122
                                    PP
  gi|119719425|ref|YP_919920.1| 220 PP 221
                                    ** PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   4.2e-08     4e-05      28     135 ..     141     248 ..     132     254 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 4.2e-08
                                    HCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-...STTTTSTTS-EEEEEE CS
                            MTS  28 pkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvas...dvleeveekkfdlivs 103
                                      ++ +kvlD+++G G+ ++ ++++  e  v+ +++d + l +a++n  ++kl+ ++++     dv+ e++e+ fd ++ 
  gi|119719425|ref|YP_919920.1| 141 GVARGEKVLDVCTGLGYTAIRALERGAE--VVSIEKDPNVLYIAEHNPFSEKLSrASILLGdafDVVGELPEEYFDKVLH 218
                                    5557889**************9998877..9****************9999999888876611156667889******** PP

                                    ---STTTCHCHHHHHHHHHHHHHHHEEEEEEE CS
                            MTS 104 NPPfhagkatelavaeeliaeAkeaLkegGeL 135
                                     PP+ a     +    e+ +   ++Lk+gG+ 
  gi|119719425|ref|YP_919920.1| 219 DPPVFAFAG--HLYSAEFYTRLWRVLKKGGRV 248
                                    ***988766..556667777777888888775 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.23   2.1e+02      34      92 ..      49     110 ..      38     131 .. 0.76
   2 !   20.5   0.0   3.4e-07   0.00032      89     177 ..     133     221 ..     128     251 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.23
                                    S-SCEEEE-S-SBTTTTB--...EEEEEES-.SEEEEEETTEEEEEETTTS---GGGHHHHH CS
                         Met_10  34 kvktvlrkvsevegefRtfe...levlaGsdstetihkEngcrfklDvskvyfsskleaEre 92 
                                     vktv +   ++eg + + +   le laGsd++  +  E  +  ++   k y+  k   Er 
  gi|119719425|ref|YP_919920.1|  49 AVKTVSEVSLNLEGATHRLTlgiLERLAGSDKLLYVGPEGVYFVEVRDEKGYYKLKYLGERV 110
                                    688888888888888777662225889****9999999999999999999999999988864 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 3.4e-07
                                    HHHHHHHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG---... CS
                         Met_10  89 aErerlaklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDgrevir... 165
                                    aEr+  +  v  ge V+dv  G G+ ai +    ++ +v++i+++P+     ++n    k+++    +l+D+ +v+    
  gi|119719425|ref|YP_919920.1| 133 AERKVRMLGVARGEKVLDVCTGLGYTAIRALE--RGAEVVSIEKDPNVLYIAEHNPFSEKLSRAS-ILLGDAFDVVGelp 209
                                    455555555999****************9998..999*********9887777777777777654.67788888876565 PP

                                    TT-EEEEEE--T CS
                         Met_10 166 eqladrvvmnlp 177
                                    e+ +d+v+ + p
  gi|119719425|ref|YP_919920.1| 210 EEYFDKVLHDPP 221
                                    677776665555 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   2.5e-07   0.00024      54     166 ..     136     252 ..     130     276 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.5e-07
                                    HHTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG---.....-- CS
                           CMAS  54 ileklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedlde.....kv 128
                                     ++ l++  G+++Ld+ +G G++++ra er +++vv++    +    a+++  ++ l+ +++++l d  d+ +      +
  gi|119719425|ref|YP_919920.1| 136 KVRMLGVARGEKVLDVCTGLGYTAIRALER-GAEVVSIEKDPNVLYIAEHNPFSEKLS-RASILLGDAFDVVGelpeeYF 213
                                    567899************************.*******99999988888877766655.566666665554332444689 PP

                                    SEEEEE.S-GGGTSGGGHHHHHHHHHHHS-TT-EEEEEE CS
                           CMAS 129 drvvsv.gafehvgkenydtffkklkkllkedGllllht 166
                                    d+v     +f   g+   ++f+ +l ++lk++G++   t
  gi|119719425|ref|YP_919920.1| 214 DKVLHDpPVFAFAGHLYSAEFYTRLWRVLKKGGRVFHYT 252
                                    999865156666788888899999999999999987666 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   3.8e-07   0.00036       3      81 ..     147     222 ..     145     231 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 3.8e-07
                Methyltransf_15   3 vilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklklekikvdlvflSpPw 81 
                                     +lD+++G G  +i   + + +v++ie++++ l++a+hN  + +  ++  + lgd f+++ +l +e    d v+  pP+
  gi|119719425|ref|YP_919920.1| 147 KVLDVCTGLGYTAIRALERGAEVVSIEKDPNVLYIAEHNPFS-EKLSRASILLGDAFDVVGELPEEYF--DKVLHDPPV 222
                                    79*************9999********************755.5789999**********99877766..999999985 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   9.6e-07   0.00091      67     132 ..     138     200 ..     127     217 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 9.6e-07
                                    HHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES- CS
                           PCMT  67 ellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgD 132
                                     +l + +g++vL+v +G Gy +    r +++ + vvsie+ +++   a++n   ++l++ ++  gD
  gi|119719425|ref|YP_919920.1| 138 RMLGVARGEKVLDVCTGLGYTAI---RALERGAEVVSIEKDPNVLYIAEHNPFSEKLSRASILLGD 200
                                    5688999*************764...678899999****************999999998888888 PP

>> Methyltransf_30  S-adenosyl-L-methionine-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.5e-06    0.0014      27      93 ..     188     255 ..     173     286 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.5e-06
                                    TTTTEEEEEEES-HHHHHHHC-.T-EEEEEE-SS-TTTSGGGCSHHHHHHHHHHEEEEEEEEES---H CS
                Methyltransf_30  27 aaeevtlklligdarealkeld.ekadawFlDgFsPaknPelwseellkelarllkkkgtlatyssAg 93 
                                    +++  +  +l+gda +++ el+ e++d + +D+   a +  l+s e++ +l r+lkk+g++  y+ A 
  gi|119719425|ref|YP_919920.1| 188 SEKLSRASILLGDAFDVVGELPeEYFDKVLHDPPVFAFAGHLYSAEFYTRLWRVLKKGGRVFHYTGAP 255
                                    555667899************9899********999999**************************985 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.9e-05     0.028      30      95 ..     144     213 ..     132     239 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.9e-05
                                    TTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTT..TCCCEEEE-S-CCGH..HHHHHHC CS
                         RrnaAD  30 ekltvleigpGkGilTeeLakrakqvvvlElderLakllqkkls..kdeklkvvhqDflkf..etpeevt 95 
                                       +vl++ +G G +  + ++r  +vv++E+d++ + + +++++  k ++  ++  D+ +   e+pee+ 
  gi|119719425|ref|YP_919920.1| 144 RGEKVLDVCTGLGYTAIRALERGAEVVSIEKDPNVLYIAEHNPFseKLSRASILLGDAFDVvgELPEEYF 213
                                    6689******************************999999988856667777888887765335555555 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   7.4e-05      0.07      41     150 ..     138     249 ..     132     252 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.4e-05
                                    HH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-..TTS-T-EE CS
                Ubie_methyltran  41 klvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeL..pfeddsfD 118
                                    ++ +v rg+kvlDv++G g  a++   ++++  +vv ++ ++n+L ++e+    e  ++   l ++a ++  +  ++ fD
  gi|119719425|ref|YP_919920.1| 138 RMLGVARGEKVLDVCTGLGYTAIR---ALERGAEVVSIEKDPNVLYIAEHNPFSEKLSRASILLGDAFDVvgELPEEYFD 214
                                    677899*************99986...45667799999************999999999999999998763355678888 PP

                                    EEEEES-GGG-S-...HHHHHHHHHHHEEEEEEEE CS
                Ubie_methyltran 119 vvtvsfGlrnvtD...klkaLkeayrvlkpGGrlv 150
                                     v     +  ++      +    ++rvlk GGr++
  gi|119719425|ref|YP_919920.1| 215 KVLHDPPVFAFAGhlySAEFYTRLWRVLKKGGRVF 249
                                    88765444444441105566778899999999885 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00019      0.18      21      66 ..     143     188 ..      96     259 .. 0.78
   2 ?   -1.6   0.0       2.2     2e+03     108     119 ..     241     252 ..     227     280 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00019
                Methyltransf_23  21 raggrvLdiGcGtGillevlrengfsvtgvDlspeaveiaekakka 66 
                                     +g +vLd+ +G G+++  + e+g++v+ ++ +p+   iae  +++
  gi|119719425|ref|YP_919920.1| 143 ARGEKVLDVCTGLGYTAIRALERGAEVVSIEKDPNVLYIAEHNPFS 188
                                    45669*****************************988777533333 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.2
                Methyltransf_23 108 llkpgGylllse 119
                                     lk gG++++ +
  gi|119719425|ref|YP_919920.1| 241 VLKKGGRVFHYT 252
                                    455555544432 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00011       0.1     190     230 ..     143     183 ..     119     184 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00011
                                    -TT-EEEETT-TTTHHHHHHHHTT-EEEEEESSHHHHHHHH CS
                    N6_N4_Mtase 190 kkgdivlDpFaGSGtTavaakelgrkfiGieieeeyvelae 230
                                      g+ vlD   G G+Ta+ a+e g + ++ie++++ +++ae
  gi|119719425|ref|YP_919920.1| 143 ARGEKVLDVCTGLGYTAIRALERGAEVVSIEKDPNVLYIAE 183
                                    56999*****************************9999886 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00015      0.14       3      89 ..     139     222 ..     137     227 .. 0.89
   2 ?   -3.4   0.0       6.5   6.2e+03     123     138 ..     237     252 ..     232     255 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00015
                                    HH---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC..EEE CS
                Methyltr_RsmB-F   3 lLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlggelfDr 82 
                                    +L    +e++lD+c++ G   t i +l +  ++vv ++++ + l   ++n     +  + +l +Da  +   l +e fD+
  gi|119719425|ref|YP_919920.1| 139 MLGVARGEKVLDVCTGLG--YTAIRAL-ERGAEVVSIEKDPNVLYIAEHNPFSEKLSRASILLGDAFDVVGELPEEYFDK 215
                                    56677899*******988..4789999.999*******************998889999*********9999999***** PP

                                    EEEEE-- CS
                Methyltr_RsmB-F  83 iLlDaPC 89 
                                    +L D P 
  gi|119719425|ref|YP_919920.1| 216 VLHDPPV 222
                                    ****995 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 6.5
                                    HHCCCEEEEEEEEEEE CS
                Methyltr_RsmB-F 123 aaidllkkgGvlvYsT 138
                                     ++ +lkkgG +   T
  gi|119719425|ref|YP_919920.1| 237 RLWRVLKKGGRVFHYT 252
                                    579999***9987655 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.1     1e+03     124     151 ..      96     123 ..      89     143 .. 0.72
   2 ?   10.2   0.0   0.00027      0.25     112     157 ..     141     187 ..     131     217 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.1
                                    -TTSHHHHHHHHCT-SEEEEE---HHHH CS
                 Methyltransf_9 124 cgnGyhlwrmvgegaklvvGidPselfl 151
                                     ++Gy+  + +ge  + ++ i+  +++ 
  gi|119719425|ref|YP_919920.1|  96 DEKGYYKLKYLGERVAPTLEINGVHMHN 123
                                    5689999999999999888888766654 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00027
                                    .--TT-EEEEET-TTSHHHHHHHHCT-SEE.EEE---HHHHHHHHHH CS
                 Methyltransf_9 112 sdlkgrtildvGcgnGyhlwrmvgegaklv.vGidPselfliqfeav 157
                                       +g ++ldv  g Gy   r + +ga++v +  dP+ l++   +  
  gi|119719425|ref|YP_919920.1| 141 GVARGEKVLDVCTGLGYTAIRALERGAEVVsIEKDPNVLYIAEHNPF 187
                                    5568999********************97647789**9999877655 PP

>> Spermine_synth  Spermine/spermidine synthase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00014      0.13      73     133 ..     192     252 ..     147     282 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00014
                                    TTEEEEESTCHHHHCTCSS.-EEEEEEECCSTTCSSCG.CSSHHHHHHHHHTEEEEEEEEEEE CS
                 Spermine_synth  73 arvklvlgdgfkflkayek.kfdvvivdsldpvgpaen.lFskeffdllkkvlkedGviilqa 133
                                    +r  ++lgd+f ++ ++ +  fd v  d   pv   +  l+s ef+  l +vlk++G ++  +
  gi|119719425|ref|YP_919920.1| 192 SRASILLGDAFDVVGELPEeYFDKVLHDP--PVFAFAGhLYSAEFYTRLWRVLKKGGRVFHYT 252
                                    688999***********997888877665..55555556******************776655 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00028      0.26      15     101 ..     160     248 ..     151     250 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00028
                Methyltransf_24  15 lralrrngagrlvavdhdpgaeeaaalare...aglddrvrlikadseealaslaagsiDllfiDgghaa....eavled 87 
                                     ral+r +  ++v++++dp   ++  +a+    ++  +r+ ++ +d+++++++l ++ +D ++ D +  a       +e+
  gi|119719425|ref|YP_919920.1| 160 IRALERGA--EVVSIEKDP---NVLYIAEHnpfSEKLSRASILLGDAFDVVGELPEEYFDKVLHDPPVFAfaghLYSAEF 234
                                    45677777..5********...88888888666556677**************************653333322234556 PP

                Methyltransf_24  88 leallprlapggvv 101
                                    +  l+++l++gg v
  gi|119719425|ref|YP_919920.1| 235 YTRLWRVLKKGGRV 248
                                    78899999999976 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00031      0.29     159     211 ..     142     193 ..     130     218 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00031
                           PrmA 159 vkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkvea 211
                                    v +ge+vlDv tG G  ai a+  ga +vv +  D+  + +a++N    k+++
  gi|119719425|ref|YP_919920.1| 142 VARGEKVLDVCTGLGYTAIRALERGA-EVVSIEKDPNVLYIAEHNPFSEKLSR 193
                                    56899*******************98.5899*************976666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2064.05
//
Query:       gi|119719426|ref|YP_919921.1|  [L=197]
Description: putative RNA-processing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.7e-15   54.3   1.3    2.1e-08   33.9   0.0    2.2  2  KH_1      KH domain
    4.9e-05   23.1   2.0     0.0038   17.0   0.0    2.4  2  KH_2      KH domain


Domain annotation for each model (and alignments):
>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.0   2.3e-12   2.1e-08       4      65 ..      16      75 ..      13      76 .. 0.84
   2 !   18.2   1.5   1.8e-07    0.0016      12      62 ..     116     161 ..     111     165 .. 0.80

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 2.3e-12
                                   EEEGGGHHHHHHTGGGHHHHHHHHHH.T-EEEEESSTT...T.-EEEE...EE.SHHHHHHHHHHHH CS
                           KH_1  4 ilvPsslvgriIGkgGsnIkeIreet.gakIkvpksedegsderevti...sG.speavekAkelie 65
                                   ++v +s +g+iIGk Gsn ++++e t ++k +v+ s        +v +    G +p++v +Ak+++e
  gi|119719426|ref|YP_919921.1| 16 VPVEQSRIGYIIGKDGSNKRRLEE-TfNVKLDVD-SA-----TGVVYVepgEGaTPYNVFRAKKALE 75
                                   5677889*****************.66*****87.54.....479***5555***********9987 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 1.8e-07
                                    HHHHTGGGHHHHHHHHHHT-EEEEESSTT...T.-EEEEEESHHH...HHHHHH CS
                           KH_1  12 griIGkgGsnIkeIreetgakIkvpksedegsderevtisGspea...vekAke 62 
                                     riIG  G+  k +++ tga+I++  +      e+ v i+G+ e+   v++A+e
  gi|119719426|ref|YP_919921.1| 116 ARIIGTEGRFKKTLEDMTGARIVI--G------EKAVGIIGDFEQnkvVKEALE 161
                                    69*********************5..3......457*****9998455555555 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   4.3e-07    0.0038      31      59 ..      18      46 ..       8      57 .. 0.84
   2 !    4.8   0.9    0.0027        24      36      64 ..     115     142 ..     112     161 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.3e-07
                                   EEESCHHHHHTGGGHHHHHHHHHHHHHHH CS
                           KH_2 31 iresqpgivIGkgGsnikkigkelrkdie 59
                                   +  s+ g +IGk Gsn ++++++++ +++
  gi|119719426|ref|YP_919921.1| 18 VEQSRIGYIIGKDGSNKRRLEETFNVKLD 46
                                   7789******************9988774 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0027
                                    HHHHHTGGGHHHHHHHHHHHHHHHHHHTT CS
                           KH_2  36 pgivIGkgGsnikkigkelrkdieklegk 64 
                                    ++++IG +G+  k+++   + +i ++ +k
  gi|119719426|ref|YP_919921.1| 115 KARIIGTEGRFKKTLEDMTGARI-VIGEK 142
                                    789***************99999.34444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1362.07
//
Query:       gi|119719427|ref|YP_919922.1|  [L=241]
Description: protein of unknown function RIO1 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-56  190.8   0.0    2.1e-56  190.5   0.0    1.1  1  RIO1            RIO1 family
    5.7e-10   39.5   0.2    2.4e-06   27.7   0.0    2.7  2  APH             Phosphotransferase enzyme family
      0.001   18.7   0.0     0.0025   17.5   0.0    1.7  2  Choline_kinase  Choline/ethanolamine kinase
      0.004   16.6   0.0      0.013   14.8   0.0    1.7  2  Pkinase         Protein kinase domain
  ------ inclusion threshold ------
      0.011   15.1   0.0        2.2    7.6   0.0    2.2  2  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family
      0.028   13.2   0.0       0.03   13.1   0.0    1.2  1  Pkinase_fungal  Fungal protein kinase


Domain annotation for each model (and alignments):
>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.5   0.0     7e-60   2.1e-56       2     182 ..      48     226 ..      47     232 .. 0.96

  Alignments for each domain:
  == domain 1  score: 190.5 bits;  conditional E-value: 7e-60
                                    EEEEEETTTEEEEEEEE-S---SS-H.HHHCTTTSTTSTCG--GS-HHHHHHHHHHHHHHHHHHHHHTT--S--EEEEET CS
                           RIO1   2 VyhavsedgkevaiKiyktstteFkk.rkkyvsgekrfkdrksktnprklvklwaekEfrnLkrleeagvpvPkpielkr 80 
                                    Vy++ ++dg+++a+Kiy + t+eF++ r ky+ g++rf+    +   r+l+ +wa+kE+rnL+r+++ g+p+Pkpi++ +
  gi|119719427|ref|YP_919922.1|  48 VYWGKDRDGRDLAVKIYLIVTAEFRRgRLKYILGDPRFEGA--SLRGRELIYAWARKEYRNLRRASQFGIPCPKPIAVYE 125
                                    9*************************999*********966..8999********************************* PP

                                    TEEEEE--EETTEEGGBHHHCG-HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETTEEEE--GTTEEETTSTTH CS
                           RIO1  81 hvlvmefigedgvaapklkdveeeeeaeelyeevleemrklykeaglvHaDLSeyNvlvdedkvviIDvsQaveldhpna 160
                                    ++lvmefig+dgv+ap lkd +  +   e+++e+ +++++++ eaglvHaDLSeyN+lv++d++viID++ av  +hpna
  gi|119719427|ref|YP_919922.1| 126 NILVMEFIGRDGVPAPLLKDSP-PSRPYEAFRELQSYIERMVLEAGLVHADLSEYNILVEDDRLVIIDWGSAVLSSHPNA 204
                                    **********************.889999*************************************************** PP

                                    HHHHHHHHHHHHHHHHTTC--- CS
                           RIO1 161 lefLerDveniikfFrrkgvek 182
                                    +efL  D++n+ +fFr  gv++
  gi|119719427|ref|YP_919922.1| 205 EEFLLNDIRNVYRFFRELGVDT 226
                                    *****************99884 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.1   0.00036       1.1       7      72 ..      42     131 ..      39     148 .. 0.60
   2 !   27.7   0.0     8e-10   2.4e-06     140     199 ..     142     199 ..     133     201 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00036
                                    -.SSCEEEEEEETT.--EEEEE.............................E-TTS-HHHHHHHHHHHHHHHHTT-B--B CS
                            APH   7 ggasnrtylvttpa.gryvlrr.............................npparaaeeirrevallrlLakagvpvPe 56 
                                     g + r+y+ ++ + +++++++                              +    ++ +r+e++ lr  ++ g+p+P+
  gi|119719427|ref|YP_919922.1|  42 TGKEARVYWGKDRDgRDLAVKIylivtaefrrgrlkyilgdprfegaslrgRE--LIYAWARKEYRNLRRASQFGIPCPK 119
                                    56677777777777557777775555555555555555555444444322111..224445677778888888888**** PP

                                    -CTTBS-EEETTEEEE CS
                            APH  57 vlagdtddeeigllfa 72 
                                    ++a     +e+ l+++
  gi|119719427|ref|YP_919922.1| 120 PIAV----YENILVME 131
                                    ***4....44444444 PP

  == domain 2  score: 27.7 bits;  conditional E-value: 8e-10
                                    CTCC.....HHHHHHHHHHHHHHHH--SSS-EEEE-SS-SGGGEEEC..TTEEEEE---TT-EEE CS
                            APH 140 elld.....lleeleeqvlaalaallpgelptvllHgDlhpgNllvdpddgrvtGviDfedaglg 199
                                    +l+d     ++e+++e +   +++ ++   +++l+H Dl+  N+lv+  d+r+  +iD++ a+l+
  gi|119719427|ref|YP_919922.1| 142 LLKDsppsrPYEAFRE-LQSYIERMVL---EAGLVHADLSEYNILVE--DDRL-VIIDWGSAVLS 199
                                    4444555556788888.8889999999...9****************..5555.5*****99875 PP

>> Choline_kinase  Choline/ethanolamine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.2   3.5e+03      29      46 ..      26      43 ..      11      47 .. 0.73
   2 !   17.5   0.0   8.2e-07    0.0025     130     171 ..     154     193 ..     147     239 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.2
                                   HHHHTTSSS-EEEEETTE CS
                 Choline_kinase 29 llserglgpklygifenG 46
                                    l++rg+ +klyg+ + G
  gi|119719427|ref|YP_919922.1| 26 HLMNRGVLAKLYGTVSTG 43
                                   467788889999988776 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 8.2e-07
                                    HHHTHHHHHHCHGG-EEEE-S--SGGGEEE.-CTTEEEE--G CS
                 Choline_kinase 130 elekleklleelespvvfcHnDlqegNillnkeekklvlIDF 171
                                     + +l++++e++  +  + H Dl e Nil+  e+++lv+ID+
  gi|119719427|ref|YP_919922.1| 154 AFRELQSYIERMVLEAGLVHADLSEYNILV--EDDRLVIIDW 193
                                    57789999999999999*************..*********9 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.37   1.1e+03       8      31 ..      41      63 ..      18      70 .. 0.83
   2 !   14.8   0.0   4.5e-06     0.013     116     151 ..     168     202 ..     153     213 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.37
                                   EEESSEEEEEEEETTTTEEEEEEE CS
                        Pkinase  8 GeGsfGkVykaveketgkivAvKk 31
                                    +G+ ++Vy ++ +++g+  AvK+
  gi|119719427|ref|YP_919922.1| 41 STGKEARVYWGK-DRDGRDLAVKI 63
                                   578999999999.58889999997 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 4.5e-06
                                    HTTEE-SS-SGGGEEEETTTEEEE-SGTTSEESSSS CS
                        Pkinase 116 skgiiHrDlKpeNiLidekgelKitDFGlakeless 151
                                    ++g++H Dl   NiL++ ++ l i+D+G a   ++ 
  gi|119719427|ref|YP_919922.1| 168 EAGLVHADLSEYNILVE-DDRLVIIDWGSAVLSSHP 202
                                    5789*************.999*******99876654 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0   0.00073       2.2      56      83 ..      98     125 ..      87     131 .. 0.87
   2 ?    5.5   0.0    0.0032       9.7     130     169 ..     161     196 ..     143     228 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00073
                            Kdo  56 travrEfrllkrLeeagvavpkpvaaga 83 
                                    + a++E+r+l+r  + g++ pkp+a ++
  gi|119719427|ref|YP_919922.1|  98 AWARKEYRNLRRASQFGIPCPKPIAVYE 125
                                    56899*******************9875 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0032
                            Kdo 130 liaklh.ragvnHadlyaknillqqeeeeeaeiwliDldka 169
                                     i+++  +ag+ Hadl   nil++ +      +++iD   a
  gi|119719427|ref|YP_919922.1| 161 YIERMVlEAGLVHADLSEYNILVEDDR-----LVIIDWGSA 196
                                    566664269**************9885.....888886555 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0     1e-05      0.03     299     367 ..     142     204 ..      73     223 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1e-05
                 Pkinase_fungal 299 iekaespkellealrDaIkghrsLflkagiLHrDiSenNilitdskkegerkglLiDLDlakelsddss 367
                                    + k + p++  ea+r+     ++++l+ag++H D Se+Nil+       +++ ++iD   a+  s++++
  gi|119719427|ref|YP_919922.1| 142 LLKDSPPSRPYEAFRELQSYIERMVLEAGLVHADLSEYNILVE------DDRLVIIDWGSAVLSSHPNA 204
                                    55555566666666766667778899****************9......77888888877777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1776.41
//
Query:       gi|119719428|ref|YP_919923.1|  [L=465]
Description: phosphoesterase domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-12   48.4   0.4    2.9e-10   40.7   0.1    2.6  2  DHHA1     DHHA1 domain
    8.4e-05   22.8   0.0    0.00015   21.9   0.0    1.4  1  DHH       DHH family


Domain annotation for each model (and alignments):
>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.7   0.0     0.002        18      10      77 ..     254     322 ..     245     332 .. 0.68
   2 !   40.7   0.1   3.3e-14   2.9e-10      11     132 ..     333     463 ..     323     465 .] 0.79

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.002
                                    HHHHHHHCHHHHHHHHHHHHHH.HTCEEECTCEEEEEECHCCHHHHHHHHHHHHHHT..HGBTTCEEEEEE CS
                          DHHA1  10 elekeleelkealaklkaeell.ekaeevkgvkvlvaevgeewdagalgiaadklks..klkkpvivfvak 77 
                                    e  k+l  + e  ++++ ++l  ++a+++ g+++++a  ++e   ++l+++a  l+   ++++ +++++++
  gi|119719428|ref|YP_919923.1| 254 EEVKKL--ATELVKYMLSAGLSvKDAQKIIGYNYYLASEKPESPLRDLREYAYILNAlgRMENYEVAVAIN 322
                                    455566..56666666666654144555559999999999*************999954445555555555 PP

  == domain 2  score: 40.7 bits;  conditional E-value: 3.3e-14
                                    HHHHHHCHHHHHHHHHHHHHHHTCEEEC...TCEEEEEECHCCHHHHHHHHHHHHHHT....HG...BT.TCEEEEEEEE CS
                          DHHA1  11 lekeleelkealaklkaeellekaeevk...gvkvlvaevgeewdagalgiaadklks....kl...kk.pvivfvakee 79 
                                    +e+  +++++ la+l ++ l  + e+vk   g   ++ ev  +++++ +g + + l s    k+   k   v++ ++ke+
  gi|119719428|ref|YP_919923.1| 333 AEDVSNNYRKTLARLIESVLSGDSEKVKvyeGRISVIIEV-RDANPKLTGPLSSILASllsqKFrdkKLlGVAAPLSKED 411
                                    6777889999***********9999999**9777777777.788888777775555553334557633345555555555 PP

                                    CTEEEEEEEESSHSS-HHHHHHHHHHHTTCCEEEETCEEEEEEEHCHHHHHHH CS
                          DHHA1  80 gdkvkvsarskkdgvdagelakeaaaklgggGGGHdlAaGagipaekleeale 132
                                      + k+s+r   + vd+g  ++++aak+g  GGGH+ A Ga ++ +kl+++le
  gi|119719428|ref|YP_919923.1| 412 S-TLKISFRRLTEEVDIGRTLQDIAAKIGIEGGGHPAAGGAVVSRDKLKALLE 463
                                    5.******99877*************************************998 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   1.7e-08   0.00015       2      93 ..      25     153 ..      24     161 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.7e-08
                                    EEEE-ECSSSHHHHHH.HHHHHH................................CECS--TCGGCGCCHHCCCSEEEEE CS
                                    xxxxxxxxxxxxxxxx.xxxxxx................................xxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DHH   2 ilivghknpDtDsigS.aialan................................llvDhneksqavegeakeeaedvii 48 
                                    +l+  + ++D+D++ S +++l+                                 + +D ++  +  ++   +e+++++ 
  gi|119719428|ref|YP_919923.1|  25 VLV--VSHYDADGLSSlSLMLYFlwshgvpfharlveqvdprtleelplgeydyaIFLDLGSGYKHLIE-RYAEGKNILL 101
                                    455..89*********76666666666666666666666666666666666666668888888777777.889999**** PP

                                    EE-S---S........S---SS--EEEE-SSS-HHHHHHHHHHHTT----HHH CS
                                    xxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DHH  49 iDHHrlge........efetlapilflnepvgstaeivaelleekkeeiskei 93 
                                    iDHH +++        e++ + ++ +  ++ +s++++ + ll+  +e+++k +
  gi|119719428|ref|YP_919923.1| 102 IDHHVPSSpkgeeccvEINPY-RVGLNGSEEASASTLTYLLLRSLDEKVEKMV 153
                                    ******989999988755555.5566677788888898888887666655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (465 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 3122.85
//
Query:       gi|119719429|ref|YP_919924.1|  [L=148]
Description: 30S ribosomal protein S15P [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.4e-25   87.2   0.3    1.4e-24   85.9   0.2    1.8  2  Ribosomal_S13_N  Ribosomal S13/S15 N-terminal domain
    2.4e-18   66.1   0.2    3.7e-18   65.5   0.2    1.2  1  Ribosomal_S15    Ribosomal protein S15
  ------ inclusion threshold ------
      0.043   14.3   0.1        7.5    7.0   0.0    2.1  2  RecX             RecX family
      0.078   13.0   0.0       0.12   12.4   0.0    1.2  1  DUF4186          Domain of unknown function (DUF4186)


Domain annotation for each model (and alignments):
>> Ribosomal_S13_N  Ribosomal S13/S15 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.9   0.2   3.2e-28   1.4e-24       5      60 .]       3      58 ..       1      58 [. 0.97
   2 ?   -2.5   0.0       1.2   5.5e+03      29      44 ..     116     131 ..     108     135 .. 0.60

  Alignments for each domain:
  == domain 1  score: 85.9 bits;  conditional E-value: 3.2e-28
                                   SSSSS--------S-SS--TTS---HHHHHHHHHHHHHTT--HHHHHHHHHHCCT- CS
                Ribosomal_S13_N  5 hsrgkGkSgSarPyrreapsWlklskeeveelivklakkGltpSqIGviLRDqyGv 60
                                   +s++kG+SgS+rP + ++p+W+k+ +eeveel+v l +kG++pS+IGviLRDqyG+
  gi|119719429|ref|YP_919924.1|  3 KSKEKGRSGSTRPPQLKKPEWVKMRPEEVEELVVSLYRKGYPPSMIGVILRDQYGI 58
                                   5899***************************************************9 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.2
                                    -HHHHHHHHHHHHHTT CS
                Ribosomal_S13_N  29 skeeveelivklakkG 44 
                                     ++++  l+  ++++G
  gi|119719429|ref|YP_919924.1| 116 IESKIHRLVKYYKREG 131
                                    4455555555555665 PP

>> Ribosomal_S15  Ribosomal protein S15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.5   0.2   8.2e-22   3.7e-18       4      79 ..      72     145 ..      70     146 .. 0.93

  Alignments for each domain:
  == domain 1  score: 65.5 bits;  conditional E-value: 8.2e-22
                                    HHHHHSSSTT-TSSHHHHHHHHHHHHHHHHHHHHCTTT-HHHHHHHHHHHHHHHHHHHHHHHH-H..HHHHHHHHHCT CS
                  Ribosomal_S15   4 likefqrhekDtGspevqiallterInnltehlkenkkDkhsrrgLlklvskRrkllkYLkrkdv..erYkklieklg 79 
                                    +++e + ++    ++++++++l++r+ ++++hl+e++kD+hs+rgL++++sk+++l+kY+kr+ +  +++k+  +k+ 
  gi|119719429|ref|YP_919924.1|  72 ILRERGLAP----EIPEDLMNLMKRAIRVRKHLEEHPKDYHSKRGLQLIESKIHRLVKYYKREGIlpPDWKYEPSKIA 145
                                    677888888....99*************************************************9999***9988865 PP

>> RecX  RecX family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0    0.0017       7.5      86     117 ..      21      53 ..       4      57 .. 0.82
   2 ?    5.4   0.1    0.0053        24      47      88 ..      68     109 ..      61     131 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0017
                                    T.TTS-HHHHHHHHHHHHHHTT--HHHHHHHHH CS
                           RecX  86 l.kkeedekekqklvrfLarrGFssevirevlk 117
                                    + + + +++e + lv  L+r+G++ ++i  +l+
  gi|119719429|ref|YP_919924.1|  21 PeWVKMRPEEVEELVVSLYRKGYPPSMIGVILR 53 
                                    4455666888899999************99987 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0053
                                    HHHHHHHTTT--HHHHHHHHTTS-HHHHHHHHHHHHHHHTTT CS
                           RecX  47 rikqeLkqkGiseelieqaleeldeeeqarelaekklkklkk 88 
                                     + q L+++G+++e+ e+ ++ +++  ++r+ +e + k +++
  gi|119719429|ref|YP_919924.1|  68 SVLQILRERGLAPEIPEDLMNLMKRAIRVRKHLEEHPKDYHS 109
                                    57789****************999999999999998888843 PP

>> DUF4186  Domain of unknown function (DUF4186)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   2.7e-05      0.12       4      45 ..      86     127 ..      84     144 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.7e-05
                        DUF4186   4 lerlskskfrskFklkekdkeyikekglekikehardliakr 45 
                                    l +l k+++r + +l+e+ k+y +++gl+ i+++ + l++  
  gi|119719429|ref|YP_919924.1|  86 LMNLMKRAIRVRKHLEEHPKDYHSKRGLQLIESKIHRLVKYY 127
                                    567999*****************************9999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1175.86
//
Query:       gi|119719430|ref|YP_919925.1|  [L=372]
Description: Fis family transcriptional regulator [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.7e-37  127.9   0.0    8.5e-37  126.7   0.0    1.5  2  ATP-grasp_2  ATP-grasp domain
      6e-13   48.9   0.1    9.7e-13   48.2   0.1    1.3  1  Ligase_CoA   CoA-ligase
    0.00091   18.7   0.0     0.0074   15.8   0.0    2.1  1  ATP-grasp_5  ATP-grasp domain
  ------ inclusion threshold ------
       0.11   12.0   0.0       0.23   10.9   0.0    1.5  1  CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP bindin
       0.18   11.5   0.0       0.37   10.5   0.0    1.5  1  GARS_A       Phosphoribosylglycinamide synthetase, ATP-grasp 


Domain annotation for each model (and alignments):
>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.7   0.0   2.4e-40   8.5e-37       3     201 ..       4     192 ..       3     193 .. 0.91
   2 ?   -2.8   0.0         1   3.7e+03     151     170 ..     340     359 ..     317     370 .. 0.71

  Alignments for each domain:
  == domain 1  score: 126.7 bits;  conditional E-value: 2.4e-40
                                    -HHHHHHHHHCTT----SEEEESSH..HHHHHHHHHHTSSSEEEEE--SSSTCCCTTCEEEESSHHHHHHHHHCCTTSEE CS
                    ATP-grasp_2   3 hEyqakeilakygvkvpegevaesa..eeaeeaakklgekelvvKaQvlaGGRGKagGvklvkskeeakeaakellgkel 80 
                                    +E++ k+i++k++v+v+++ + +++  ++    +k l +  l+vKaQv   GRGKag vk ++++eea ++a+e++  e 
  gi|119719430|ref|YP_919925.1|   4 YEFEVKDIFEKFQVPVEKSCLLTHEalKDSLGCIKGLRTP-LIVKAQVRGWGRGKAGLVKSAENPEEALKVAQEFFLREF 82 
                                    79***************99876543113444455666555.5**********************************9999 PP

                                    E-TTS-TT-EEE--EEEEE---ECEEEEEEEEEETTTTEEEEEEESSTTS-HHHHHHH-GGGEEEEEEBTTTB--HHHHH CS
                    ATP-grasp_2  81 vtkqtgkeGkkvekvlveealdikkElYlsivlDraskkvvviaSseGGvdiEevaakkPekiikvaidpakglkeeqar 160
                                            G+k+  vlv+e+  i +E+Yls+++  +  +++++aS++GGvd+Ee+  k+P  + k+ idp +gl+++++r
  gi|119719430|ref|YP_919925.1|  83 N-------GEKIRYVLVSERKRILREMYLSFMVSSNPPGFLLLASKHGGVDVEELS-KTPGGLLKIFIDPFEGLRDYMVR 154
                                    9.......**********************************************96.79********************* PP

                                    HHHHHCT--CHHHHHHHHHHHHHHHHHHHTTEEEEEEEEEE CS
                    ATP-grasp_2 161 eiakklglekelvkkaakiikklyklfveldatlvEiNPLv 201
                                    ++a  lg+++e   ++ ki+  l+++f+e++ tl+E+NPL+
  gi|119719430|ref|YP_919925.1| 155 TVAGYLGVPQE---HIEKILRSLWQIFREYNFTLLEVNPLA 192
                                    *********86...6678999*******************7 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1
                                    TTB--HHHHHHHHHHCT--C CS
                    ATP-grasp_2 151 akglkeeqareiakklglek 170
                                      g++e++ r+i++++gl++
  gi|119719430|ref|YP_919925.1| 340 LSGFMEDEGRRILREAGLSA 359
                                    46888889999999999875 PP

>> Ligase_CoA  CoA-ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.2   0.1   2.7e-16   9.7e-13       3     148 ..     254     368 ..     252     370 .. 0.96

  Alignments for each domain:
  == domain 1  score: 48.2 bits;  conditional E-value: 2.7e-16
                                    SSHHHHHHHHHHHHHT..............T--BSEEEE-TSS--..........HHHHHHHHHHHHS-TT-SEEEEEEE CS
                     Ligase_CoA   3 nGGtLayeamdlikealgdvasnkklknvlgseqheiidlGddaftkGrpHPmiDptkriealkklaadpevkvilldiv 82 
                                    nG++L+++++d++ ea              g+ +  ++dlG++a            +++ eal  ++++++++ ill+i 
  gi|119719430|ref|YP_919925.1| 254 NGAGLTMATLDAVLEA--------------GARPGLFLDLGGGAD----------AERVREALLLVLKQQNISKILLNIL 309
                                    8***************..............*************98..........7************************ PP

                                    ESSSEHHHHHHHHHHHHHHTT...--S-EEEEEECTTHH.....HHHHHHHTTTSSEEE-SSHHHH CS
                     Ligase_CoA  83 lGygahedpaaellkaikeakaegrelpvvarvaGteadpqelseqakaleeagveiasskaqalr 148
                                    +G+ +++++a ++++a+++ak     + v +r+ G  +d     e++++l+eag+   +s ++a++
  gi|119719430|ref|YP_919925.1| 310 GGITRCDEVARGVVQALSSAK--PSSVKVAVRLSGFMED-----EGRRILREAGLSAFDSLEEAVA 368
                                    ********************9..99999***********.....***************9999986 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   2.1e-06    0.0074      11     218 ..       4     203 ..       2     207 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.1e-06
                    ATP-grasp_5  11 teaeakelleaygipvvetrl..assaeeaveaaeeigypvvlKivspdilhKtdvgGvrlnlkdaeevraaaeeilerv 88 
                                    +e+e+k+++e + +pv +++l  ++  ++ +  ++ +  p  +K ++++   + ++g v+   +++ee  + a+e+   +
  gi|119719430|ref|YP_919925.1|   4 YEFEVKDIFEKFQVPVEKSCLltHEALKDSLGCIKGLRTPLIVKAQVRGW-GRGKAGLVKS-AENPEEALKVAQEF---F 78 
                                    689*****************9778888999***************99986.6778888888.44444444444444...4 PP

                    ATP-grasp_5  89 kekspeariegvlVqemakr.ggrElivgvteDpvFGpvilfGlGGtavevlkdvavalpplnstlareliertkaskll 167
                                     +++ +++i+ vlV e ++  +++ l   v+  p    +++  +GG+ ve l+++  +l  +     + l +   + + +
  gi|119719430|ref|YP_919925.1|  79 LREFNGEKIRYVLVSERKRIlREMYLSFMVSSNPPGFLLLASKHGGVDVEELSKTPGGLLKIFIDPFEGLRD--YMVRTV 156
                                    44567899*********997666666666666665445666668***********88888876666655532..344555 PP

                    ATP-grasp_5 168 kgvrgekkadlaaleellvrlsqLvvdlpeIreldinPllveeegvvalDa 218
                                     g+ g      + +e++l  l q+ +++ + + l++nPl  +e+gv+alD 
  gi|119719430|ref|YP_919925.1| 157 AGYLGV---PQEHIEKILRSLWQIFREY-NFTLLEVNPLALTEDGVLALDR 203
                                    566665...5668999999999*****5.6899****************95 PP

>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   6.4e-05      0.23       6      72 ..       9      76 ..       6      90 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 6.4e-05
                                   HHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTT.EEEESSHHHHHHHHHHHHH CS
                    CPSase_L_D2  6 kealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkG.mrvarneeelaelvkkala 72
                                   k++ +k++vpv +s   + e l+++l + k +  P i+ka + + G+G  +++++ e+ +e++k a++
  gi|119719430|ref|YP_919925.1|  9 KDIFEKFQVPVEKSCLLTHEALKDSLGCIKGLRTPLIVKAQVRGWGRGkAGLVKSAENPEEALKVAQE 76
                                   77899*******************************************45899999998888887765 PP

>> GARS_A  Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0    0.0001      0.37       7      88 ..       9      95 ..       5     122 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0001
                                   HHHHHHTT--B--EEEESS..HHHHHHHHHHHSSSEEEEEES..C-GGGT-EEEE..SSHHHHHHHHHHHCTS-TTCCCCSS CS
                         GARS_A  7 kdllkkagiptaeyeaftd..peeakeyieeatakalVvKad..glaagKgviva..kseeealkavkeilekkkfGeagek 82
                                   kd+++k ++p  +   +t+   ++    i+ + ++  +vKa+  g   gK   v   ++ eealk+++e++ ++  Ge  + 
  gi|119719430|ref|YP_919925.1|  9 KDIFEKFQVPVEKSCLLTHeaLKDSLGCIKGLRTPL-IVKAQvrGWGRGKAGLVKsaENPEEALKVAQEFFLREFNGEKIRY 89
                                   889999999988776665422677777899999999.99996447888887666533889************9999****** PP

                                   EEEEE- CS
                         GARS_A 83 vviEel 88
                                   v++ e+
  gi|119719430|ref|YP_919925.1| 90 VLVSER 95
                                   *99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2523.74
//
Query:       gi|119719431|ref|YP_919926.1|  [L=294]
Description: succinyl-CoA synthetase, alpha subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.9e-31  108.0   1.8    5.9e-31  107.0   1.2    1.9  2  CoA_binding    CoA binding domain
      8e-18   64.6   0.0    1.4e-17   63.8   0.0    1.4  1  Succ_CoA_lig   Succinyl-CoA ligase like flavodoxin domain
    6.4e-11   42.3   0.0    1.1e-10   41.5   0.0    1.5  1  Ligase_CoA     CoA-ligase
    9.7e-08   32.5   0.2    2.3e-07   31.3   0.2    1.6  1  CoA_binding_2  CoA binding domain
  ------ inclusion threshold ------
      0.013   15.5   0.0      0.022   14.8   0.0    1.3  1  CIF            Cycle inhibiting factor (CIF)
      0.023   14.4   0.0      0.041   13.6   0.0    1.4  1  PurK_C         Phosphoribosylaminoimidazole carboxylase C-ter


Domain annotation for each model (and alignments):
>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.0   1.2     2e-34   5.9e-31       1      96 []       6     100 ..       6     100 .. 0.98
   2 ?   -2.0   0.0       2.1   6.2e+03      27      47 ..     170     186 ..     145     207 .. 0.61

  Alignments for each domain:
  == domain 1  score: 107.0 bits;  conditional E-value: 2e-34
                                    CTTEEEEEETTTSHHHHHHHHHHHHHHECEEEEEEC-TTTTTCEETTEEEESCHHHHHHHC.TTTEEEEES-HHHHHHHH CS
                    CoA_binding   1 dkdtkviviGagglgiaglyhfkeklkygikavfgvnprkvgtevlglpvyksvdeleekt.evdvavitvPaesaqeav 79 
                                    d++t+v+v+G++g+  +g++h++++l+yg+++v+gv+p+k+g+++ g+pvy++v+e+++k+ e+++++++vPa+ a +av
  gi|119719431|ref|YP_919926.1|   6 DEKTRVLVQGITGK--QGMLHTEQMLRYGTRIVAGVTPGKGGSTIVGVPVYNTVAEAVDKHpEINTSIVFVPAPYAPDAV 83 
                                    689***********..*********************************************77***************** PP

                                    HHHHHTT-SEEEEESST CS
                    CoA_binding  80 delveagikgiviiteg 96 
                                     e+++agik +v+ite+
  gi|119719431|ref|YP_919926.1|  84 YEALDAGIKKVVVITEH 100
                                    ***************95 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.1
                                    HECEEEEEEC-TTTTTCEETT CS
                    CoA_binding  27 kygikavfgvnprkvgtevlg 47 
                                    ++g++ ++g++++     v g
  gi|119719431|ref|YP_919926.1| 170 GFGVSTAVGIGGD----PVTG 186
                                    4555555555544....4444 PP

>> Succ_CoA_lig  Succinyl-CoA ligase like flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.8   0.0   4.8e-21   1.4e-17       1     135 [.     146     286 ..     146     289 .. 0.87

  Alignments for each domain:
  == domain 1  score: 63.8 bits;  conditional E-value: 4.8e-21
                   Succ_CoA_lig   1 pGkialisqSGalalalldwaasrglgfskvvslGn..eadvdvadlleylaedpetkvillylEsird.grkflsaarr 77 
                                    pG+++++s SG+l  ++  ++ ++g+g+s++v +G    + ++++d+ e +a+d+et++++l+ E  +   ++f++   +
  gi|119719431|ref|YP_919926.1| 146 PGNVGVVSRSGTLTYEVSLRLLASGFGVSTAVGIGGdpVTGLSFEDVYELFARDDETRLVVLVGEIGGTkEERFAEYYAK 225
                                    79*********************************9556889***********************6665389******** PP

                   Succ_CoA_lig  78 aarkkpvvvlksGrseagaraaashtgala....gsdavvdaafrqaGvlrvdsleelfdaa 135
                                    ++ kkpvv++ +G+s+   r    h ga++    gs++    a+r++G+++++sl+e+++++
  gi|119719431|ref|YP_919926.1| 226 LSSKKPVVAFIAGKSAPPGRKM-GHAGAIVfgseGSYESKVNALRRSGIYVAQSLREIAEIV 286
                                    **************88777664.5666654433366666678***************99987 PP

>> Ligase_CoA  CoA-ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5   0.0   3.8e-14   1.1e-10       1     150 [.     152     271 ..     152     281 .. 0.93

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 3.8e-14
                                    EESSHHHHHHHHHHHHHT..............T--BSEEEE-TSS--..........HHHHHHHHHHHHS-TT-SEEEEE CS
                     Ligase_CoA   1 lvnGGtLayeamdlikealgdvasnkklknvlgseqheiidlGddaftkGrpHPmiDptkriealkklaadpevkvilld 80 
                                    ++++GtL+ye    +  +              g + ++ +++G+d  t         + ++ +  + +a+d+e++ ++l 
  gi|119719431|ref|YP_919926.1| 152 VSRSGTLTYEVSLRLLAS--------------GFGVSTAVGIGGDPVT---------GLSFEDVYELFARDDETRLVVLV 208
                                    689999999999999888..............9***************.........*********************** PP

                                    EEESSSEHHHHHHHHHHHHHHTT...--S-EEEEEECTTHH.....HHHHHHHTTTSSEEE-SSHHHHHH CS
                     Ligase_CoA  81 ivlGygahedpaaellkaikeakaegrelpvvarvaGteadpqelseqakaleeagveiasskaqalraa 150
                                    +++G g++e+  ae+ +++++ k      pvva++aG +a+p++ +++a+a+  ++   ++sk +alr +
  gi|119719431|ref|YP_919926.1| 209 GEIG-GTKEERFAEYYAKLSSKK------PVVAFIAGKSAPPGRKMGHAGAIVFGSEGSYESKVNALRRS 271
                                    ****.****99999999888887......***********************999999999999888865 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.2   7.6e-11   2.3e-07      14     114 ..      19     129 ..      10     131 .. 0.88

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 7.6e-11
                                    SHHHHHHHHHHHHT--EEE.ESSS-..SEETTEES----T.......T--EEEE-S-HHHHGGGHHHHHHH--SEEEE-T CS
                  CoA_binding_2  14 kfgykvlryllehglpvvp.Vnpke..eeilgekvyaslae.d..pepvdlvdvftppeatpeivkealalgakavwlqp 87 
                                    k g   ++++l+ g ++v+ V+p +  ++i g++vy ++ae      ++ +  vf+p+  +p+ v eal++g+k v++  
  gi|119719431|ref|YP_919926.1|  19 KQGMLHTEQMLRYGTRIVAgVTPGKggSTIVGVPVYNTVAEaVdkHPEINTSIVFVPAPYAPDAVYEALDAGIKKVVVIT 98 
                                    5666667889999988886599999999************8435778888***************************999 PP

                                    T....---HHHHHHHHHTT-EEE.ES-HHHH CS
                  CoA_binding_2  88 g....sedeeaaelaeeagirvvgdrCilve 114
                                    +     e  e++++a +++  ++g++ ++v+
  gi|119719431|ref|YP_919926.1|  99 EhipvHETIEFVRYALSKQAVIIGPNTPGVI 129
                                    99999999999999999**********9997 PP

>> CIF  Cycle inhibiting factor (CIF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   7.3e-06     0.022      26      81 ..     182     237 ..     177     264 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 7.3e-06
                                    -B-HHHHHHHHHHHHH-SSS---CCCCHHHS-ECCCHHHHHHCCS-TTSEEEEEEE CS
                            CIF  26 epvcglsaqnifklmtekevavdpveieqtgklentefaesvdtldsaknyvvlvn 81 
                                    +pv gls ++++ l++ ++ +   v +   g  +++ fae   +l+s+k  v+++ 
  gi|119719431|ref|YP_919926.1| 182 DPVTGLSFEDVYELFARDDETRLVVLVGEIGGTKEERFAEYYAKLSSKKPVVAFIA 237
                                    79******************999999*9*9*********************99886 PP

>> PurK_C  Phosphoribosylaminoimidazole carboxylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.4e-05     0.041      18      43 ..     226     250 ..     207     258 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.4e-05
                         PurK_C  18 llaipgahlHlYgKeearpgRKmGHi 43 
                                    l + + +  ++ gK+ a pgRKmGH 
  gi|119719431|ref|YP_919926.1| 226 LSSKKPVVAFIAGKS-APPGRKMGHA 250
                                    555555666666999.*********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1994.03
//
Query:       gi|119719432|ref|YP_919927.1|  [L=232]
Description: uridylate kinase, putative [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.9e-27   94.6   0.1    2.9e-26   92.5   0.1    1.8  1  AA_kinase  Amino acid kinase family
  ------ inclusion threshold ------
       0.14   12.4   0.2       0.37   11.0   0.2    1.7  1  DUF2537    Protein of unknown function (DUF2537)


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.5   0.1   3.3e-30   2.9e-26       3     240 ..       7     208 ..       5     209 .. 0.88

  Alignments for each domain:
  == domain 1  score: 92.5 bits;  conditional E-value: 3.3e-30
                                    EEEEE-TTCCC.CTCC...HHHHHHHHHHHHH.HHHTTEEEEEE--HHHHHHHHHH..TCCCCCHHHC....E..HHHHH CS
                      AA_kinase   3 vVvKlGGsslt.dkee...aslrrlaeqiaal.kesgnklvvVhGggsftdgllal..ksglssgelaaglrstleeage 75 
                                     VvKlGGs+l  d++     ++r ++++++++ +es+ ++vvV+Ggg +++++++l  + g+++g l             
  gi|119719432|ref|YP_919927.1|   7 AVVKLGGSLLFeDEGSlkeGYVRGFLRELREYlAESNGRVVVVVGGGRYARNYIQLgrRLGVNEGVL------------- 73 
                                    7*******666377769**999*******99988899*******************77777777777............. PP

                                    HHHHHHHHHHHHHHHHHHHHTTH.GEEEE-GGGTCEECCCE..HHHTTTCEEECCHHHHHHHTT.-EEEEESEEEEETTT CS
                      AA_kinase  76 vatrdalaslgerlvaallaagl.pavglsaaaldateagrdegsdgnvesvdaeaieelleag.vvpvltgfigldeeg 153
                                        d+l++l +rl+aa + a++ ++ +l ++ l+                     +++ll++g  v+ ++g++    +g
  gi|119719432|ref|YP_919927.1|  74 ----DYLGILVSRLNAATMYAAFyNSPPLIPETLL--------------------DVHKLLASGlRVVFMGGLQ----PG 125
                                    ....9**************9999344444444444....................59*******6666666666....99 PP

                                    EEEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHH.CSSS.TTTHHHHCHHHHHHHHHC CS
                      AA_kinase 154 elgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaee.saselatgGmkvkhpaalaaarr 232
                                    +    s+ t+aal+Ae l+  +lii+tdV+G+y++dpk +p a+l +++sv+e++   + e + g  + ++   l++++r
  gi|119719432|ref|YP_919927.1| 126 Q----STTTTAALVAESLNG-SLIIATDVEGIYTDDPKRNPAATLMERVSVEELRRmFQREQVAGEYRMIDVLSLNVIQR 200
                                    9....9**************.************************************99999****************** PP

                                    TT-EEEEE CS
                      AA_kinase 233 ggipvvIt 240
                                    ++++v+++
  gi|119719432|ref|YP_919927.1| 201 SKVKVFVL 208
                                    *****997 PP

>> DUF2537  Protein of unknown function (DUF2537)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.2   4.1e-05      0.37       6      50 ..      77     125 ..      75     136 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4.1e-05
                        DUF2537   6 Gltvavfvavvvavavva....lslalaevhpllavvvnvvvvaGlaPt 50 
                                    G+ v+ + a+ + +a +     + ++l +vh lla ++ vv  +Gl P 
  gi|119719432|ref|YP_919927.1|  77 GILVSRLNAATMYAAFYNspplIPETLLDVHKLLASGLRVVFMGGLQPG 125
                                    78888888888888888778878899********************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1720.98
//
Query:       gi|119719433|ref|YP_919928.1|  [L=410]
Description: peptide chain release factor 1 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-44  151.0   0.0    4.3e-44  150.1   0.0    1.5  1  eRF1_2           eRF1 domain 2
    6.6e-35  120.0   0.7    6.6e-35  120.0   0.7    2.2  3  eRF1_3           eRF1 domain 3
    6.7e-17   62.0   0.1    1.4e-14   54.6   0.0    2.6  2  baeRF_family10   Bacterial archaeo-eukaryotic release factor 
    1.5e-14   54.4   0.4    6.5e-14   52.3   0.0    2.2  2  acVLRF1          Actinobacteria/chloroflexi VLRF1 release fac
      2e-10   40.8   0.0    3.3e-10   40.1   0.0    1.3  1  eRF1_1           eRF1 domain 1
    2.3e-05   24.4   2.3    2.3e-05   24.4   2.3    1.8  1  Zn-ribbon_8      Zinc ribbon domain
    3.1e-05   24.0   0.7    5.7e-05   23.1   0.3    1.7  1  HypA             Hydrogenase/urease nickel incorporation, met
     0.0036   16.6   1.6      0.025   13.9   2.0    2.2  2  zf-TFIIB         Transcription factor zinc-finger
     0.0042   17.4   1.1     0.0085   16.4   1.1    1.5  1  DUF4379          Probable Zinc-ribbon domain
     0.0057   16.7   2.8       0.59   10.2   0.1    2.7  2  baeRF_family2    Bacterial archaeo-eukaryotic release factor 
  ------ inclusion threshold ------
      0.018   15.1   0.4      0.035   14.1   0.4    1.4  1  Elf1             Transcription elongation factor Elf1 like
      0.018   15.2   0.6        2.2    8.4   0.3    2.6  2  FUR              Ferric uptake regulator family
      0.025   14.5   1.4        1.8    8.6   0.1    2.4  2  zinc_ribbon_4    zinc-ribbon domain
      0.044   13.7   0.5      0.087   12.8   0.5    1.4  1  Anti-TRAP        Tryptophan RNA-binding attenuator protein in
       0.05   14.0   0.5       0.13   12.6   0.1    1.8  2  Lar_restr_allev  Restriction alleviation protein Lar
      0.081   13.2   0.0       0.17   12.2   0.0    1.5  1  HAD_SAK_2        HAD domain in Swiss Army Knife RNA repair pr
      0.085   13.1   0.4       0.17   12.1   0.4    1.4  1  DUF2072          Zn-ribbon containing protein
        0.1   12.5   1.9       0.13   12.2   0.1    2.0  2  Zn_ribbon_SprT   SprT-like zinc ribbon domain
        0.3   10.9   0.8        4.6    7.1   0.0    2.3  2  A2L_zn_ribbon    A2L zinc ribbon domain
        1.5    8.7   4.3        7.8    6.4   0.3    2.3  2  TFIIS_C          Transcription factor S-II (TFIIS)


Domain annotation for each model (and alignments):
>> eRF1_2  eRF1 domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.1   0.0   4.8e-47   4.3e-44       2     133 .]     140     270 ..     139     270 .. 0.98

  Alignments for each domain:
  == domain 1  score: 150.1 bits;  conditional E-value: 4.8e-47
                                    EEEEEEETTEEEEEEEESSCEEEEEEEE------BSTTBSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCHTTTESEEE CS
                         eRF1_2   2 vglivldegeAtigllkgsrtevlkkievsvPkKhkrGgqsarrfeRlreekleeflkkvaeaankafllvdkdklkgii 81 
                                    +gliv++++eA i++l+g++ ev+++++  vP+Kh+ GgqsarrfeR++e+ ++ef+k+v+e+ank fl   kd+l+gii
  gi|119719433|ref|YP_919928.1| 140 YGLIVIERDEAAIAILRGKSLEVVDELTAGVPGKHRSGGQSARRFERIIEQLVHEFYKRVGEHANKIFLP-LKDELRGII 218
                                    8********************************************************************3.69******* PP

                                    EEESSTHHHHHHHHHHHHHHHHTCCEEEEE-S-TSCHHHHHHHHCCHHHHCC CS
                         eRF1_2  82 lagpgfvkeefldkdlldaelkkkviklvdvsyggesglnevlekaaevlkd 133
                                    ++gpgf k+ef ++d+l++el++k++ l+dv+ygg sgl e+lek+++ +kd
  gi|119719433|ref|YP_919928.1| 219 IGGPGFSKKEFAEGDYLHYELRQKILGLFDVGYGGVSGLYELLEKSKDLIKD 270
                                    ***********************************************99987 PP

>> eRF1_3  eRF1 domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       9.5   8.5e+03       6      20 ..       8      22 ..       3      31 .. 0.65
   2 ?   -2.0   0.0       5.4   4.8e+03      58      77 ..     159     194 ..     127     206 .. 0.51
   3 !  120.0   0.7   7.4e-38   6.6e-35       1     113 []     273     408 ..     273     408 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 9.5
                                   HHHHHHHHHHHCTCS CS
                         eRF1_3  6 klleefleelakdtg 20
                                     le+++eel+k +g
  gi|119719433|ref|YP_919928.1|  8 YKLEKLVEELKKKEG 22
                                   456666666666554 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 5.4
                                    S...............-HHH-HHHHHH.HHHHHHHH CS
                         eRF1_3  58 v...............ketgeelelve.lieelven 77 
                                                    ++ g+ +++ e +ie+lv++
  gi|119719433|ref|YP_919928.1| 159 SlevvdeltagvpgkhRSGGQSARRFErIIEQLVHE 194
                                    233333333444443334445555555555555544 PP

  == domain 3  score: 120.0 bits;  conditional E-value: 7.4e-38
                                    HHHHHHHHHHHHHHHHCTCSSEEESHHHHHHHHHTT-EEEEEEEHCHHTSSSHHHHHS....................-H CS
                         eRF1_3   1 liqekklleefleelakdtgkavYGveevlkalemgAvetLLvseelersrdtlkekv....................ke 60 
                                    +++e++++++fl +la+dtg+avYG+ ev++al+++Ave+LL+se+le+ r+ +k++                     ++
  gi|119719433|ref|YP_919928.1| 273 FMKEREAVNQFLYHLARDTGLAVYGEAEVREALQLNAVEKLLLSEDLEKIRVRAKCTSckhefeatlhsesevaqlkcPK 352
                                    689************************************************88666657********************* PP

                                    HH-HHHHHH...HHHHHHHHHHHTT-EEEEE-TTSHHHHHHHHHTTTEEEEESS-- CS
                         eRF1_3  61 tgeelelve...lieelvenveesgakveiisseseeGeqlvkafgGiaaiLRykv 113
                                    +g e+e++e   ++eel+e +e++ga+v+++s++s+eG+++ k+fgGi+aiLRy++
  gi|119719433|ref|YP_919928.1| 353 CGGEVEIIEnrsVVEELAELAEKTGAEVVLVSTQSAEGKEFFKTFGGIGAILRYRL 408
                                    ******************************************************85 PP

>> baeRF_family10  Bacterial archaeo-eukaryotic release factor family 10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.6   0.0   1.5e-17   1.4e-14       6     123 ..     130     250 ..     126     267 .. 0.90
   2 ?    4.7   0.1     0.037        33      74     104 ..     363     393 ..     361     398 .. 0.88

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 1.5e-17
                 baeRF_family10   6 LlealdeyerygvvlvdreraRlfevylgeleeveevegevpgrtktggwksqdrfqrreeeqaerhlkevAellaklle 85 
                                    L e ++  e yg+++++r++a+++  ++ +le v+e+++ vpg+++ gg+ s +rf+r  e+ +++++k+v+e+++k++ 
  gi|119719433|ref|YP_919928.1| 130 LEEMIRVKEVYGLIVIERDEAAIAILRGKSLEVVDELTAGVPGKHRSGGQ-SARRFERIIEQLVHEFYKRVGEHANKIFL 208
                                    78889999******************************************.****************************9 PP

                 baeRF_family10  86 erg..verlvlgGdeeetaall..drlpkalrarvvgtlplp 123
                                    + +  ++ +++gG+   +++++  d l+ +lr+++ g ++++
  gi|119719433|ref|YP_919928.1| 209 PLKdeLRGIIIGGPGFSKKEFAegDYLHYELRQKILGLFDVG 250
                                    87777*********9999999744689999999999988776 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.037
                 baeRF_family10  74 kevAellaklleergverlvlgGdeeetaal 104
                                    + v+e la+l+e+ g+e ++++ + +e +++
  gi|119719433|ref|YP_919928.1| 363 RSVVEELAELAEKTGAEVVLVSTQSAEGKEF 393
                                    5799******************999888877 PP

>> acVLRF1  Actinobacteria/chloroflexi VLRF1 release factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.3   0.0   7.2e-17   6.5e-14       3      94 ..     140     234 ..     138     265 .. 0.90
   2 ?   -1.2   0.0       2.7   2.4e+03      66      90 ..     280     306 ..     259     325 .. 0.63

  Alignments for each domain:
  == domain 1  score: 52.3 bits;  conditional E-value: 7.2e-17
                        acVLRF1   3 lgvllvrrggfavgvveggelvaskvgtrdvqgrtaaGGwSqqRfaRrrenqadalleavaeaaarllaeesae...vvl 79 
                                    +g++++ r+  a+++++g+ l+ + + t  v g+++ GG+S +Rf+R +e+ + + +++v e+a++++ + ++e   +++
  gi|119719433|ref|YP_919928.1| 140 YGLIVIERDEAAIAILRGKSLEVVDELTAGVPGKHRSGGQSARRFERIIEQLVHEFYKRVGEHANKIFLPLKDElrgIII 219
                                    7899****************************************************************888887888*** PP

                        acVLRF1  80 gGdrslvaevledar 94 
                                    gG+    +e++e   
  gi|119719433|ref|YP_919928.1| 220 GGPGFSKKEFAEGDY 234
                                    ***999999988754 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.7
                        acVLRF1  66 aarll..aeesaevvlgGdrslvaevl 90 
                                    +++ l   +++  +++ G+ +++++++
  gi|119719433|ref|YP_919928.1| 280 VNQFLyhLARDTGLAVYGEAEVREALQ 306
                                    333331113333377777777777665 PP

>> eRF1_1  eRF1 domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.1   0.0   3.6e-13   3.3e-10       2     128 ..      12     133 ..      11     134 .. 0.95

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 3.6e-13
                                    EEEEE..CTBTTSCCEEEEEE-SCHHHHHHHHHCHTTHEEEEEEEECHHH.......--CEEEEEEEEEEEEEEECTT.. CS
                         eRF1_1   2 kllkr..dlekdgsgsvtLipeddedlwhlynliapgdsvrastvrkvqresstgsreservklkLtikvekvdfdkd.. 77 
                                    kl+++  + e++g+++v+L+++    ++++ n +  ++s++++++ +v+r         ++v+ +L   ++++++  +  
  gi|119719433|ref|YP_919928.1|  12 KLVEElkKKEGRGTELVSLYIPAGRPISDVLNTLYYEYSTASNIKDRVTR---------HHVLDALATIINRLKLFREtp 82 
                                    7777776889**************************************99.........9****************9999 PP

                                    .SSEEEEEEEEEEGGGG--TTSEEEEEE-TTSEEEEEECE.ESHHHHHHHHHH CS
                         eRF1_1  78 .agvlrisGkvieenehvklgafhtldlelkrpftiikee.wdsfalerLkea 128
                                     +g++++ G v+ + +    +++    +e+++++++  ++ +++f++e+L+e+
  gi|119719433|ref|YP_919928.1|  83 pNGLIVFAGYVAGDVP--GREKMEVHLIEPPQKLNVWLYRcDSRFYTEILEEM 133
                                    99**************..69999999************999**********98 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   2.3   2.5e-08   2.3e-05       7      37 ..     327     358 ..     326     360 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 2.5e-08
                    Zn-ribbon_8   7 rCeeCghefe.vlqsisdapltaCPeCgsevr 37 
                                    +C++C+hefe  l+s s+ ++ +CP+Cg+ev+
  gi|119719433|ref|YP_919928.1| 327 KCTSCKHEFEaTLHSESEVAQLKCPKCGGEVE 358
                                    7*********7677666999999******986 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.3   6.4e-08   5.7e-05      63     103 ..     318     363 ..     280     371 .. 0.74

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 6.4e-08
                                    EEEEE--EEEETTTS-EEECHH....H..HHS-TTTSSS-EEEEESS CS
                           HypA  63 eieevpvkvrCreCgkefelee....k..alrCpkCgsadveivsGe 103
                                    ++e+++v+++C++C++efe +     +  +l+CpkCg+ +vei++ +
  gi|119719433|ref|YP_919928.1| 318 DLEKIRVRAKCTSCKHEFEATLhsesEvaQLKCPKCGG-EVEIIENR 363
                                    3899***************554333214455******9.68887766 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   2.0   2.8e-05     0.025       1      27 [.     327     355 ..     327     356 .. 0.84
   2 !    7.8   0.3    0.0022         2       1      16 [.     349     364 ..     349     366 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.8e-05
                       zf-TFIIB   1 kCPkCqdeleeser..ggveidyCpqCrG 27 
                                    kC +C++e+e + +  ++v   +Cp+C+G
  gi|119719433|ref|YP_919928.1| 327 KCTSCKHEFEATLHseSEVAQLKCPKCGG 355
                                    8*********9999555566667*****9 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0022
                       zf-TFIIB   1 kCPkCqdeleesergg 16 
                                    kCPkC+ e e++e + 
  gi|119719433|ref|YP_919928.1| 349 KCPKCGGEVEIIENRS 364
                                    8*******99998765 PP

>> DUF4379  Probable Zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   1.1   9.5e-06    0.0085      31      56 .]     327     353 ..     318     353 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 9.5e-06
                        DUF4379  31 kCakCgheWeasvsnrtkgssk.CpkC 56 
                                    kC  C+he+ea++++  +  +  CpkC
  gi|119719433|ref|YP_919928.1| 327 KCTSCKHEFEATLHSESEVAQLkCPKC 353
                                    9***************9443335**** PP

>> baeRF_family2  Bacterial archaeo-eukaryotic release factor family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.1   0.00065      0.59      78     136 ..     142     200 ..     130     207 .. 0.89
   2 ?    5.7   0.4     0.016        14      61      81 ..     363     383 ..     361     385 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00065
                  baeRF_family2  78 lVvlaGDvrarsllrdeLpervrelvvevegggraagadrealaeevaealaerrarrr 136
                                    l+v+  D  a ++lr +  e v el+  v+g+ r+ g + + +++ ++++++e+ +r  
  gi|119719433|ref|YP_919928.1| 142 LIVIERDEAAIAILRGKSLEVVDELTAGVPGKHRSGGQSARRFERIIEQLVHEFYKRVG 200
                                    677777999999****************************************9988765 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.016
                  baeRF_family2  61 eavAeevdrlvresgaelVvl 81 
                                    + v ee+++l++++gae+V++
  gi|119719433|ref|YP_919928.1| 363 RSVVEELAELAEKTGAEVVLV 383
                                    6799***************99 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.4     4e-05     0.035      16      57 ..     320     359 ..     313     369 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4e-05
                           Elf1  16 kklptkFdCpfCnheksvevkldkkekiaevsCkvCgesfet 57 
                                    +k+  + +C  C+he   e +l+ ++++a+++C +Cg ++e+
  gi|119719433|ref|YP_919928.1| 320 EKIRVRAKCTSCKHE--FEATLHSESEVAQLKCPKCGGEVEI 359
                                    56777789*******..*******************988875 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.061        55      13      54 ..      38      80 ..      35      85 .. 0.89
   2 ?    8.4   0.3    0.0025       2.2      62     113 ..     327     381 ..     312     386 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.061
                                   HHHHHHHHSS.SBEHHHHHHHHHHTTTT--HHHHHHHHHHHHH CS
                            FUR 13 ilevleksee.hlsaeevykelkeedpeislaTVYrtLkllee 54
                                   i +vl++    + +a ++ +++ +++    laT+ + Lkl++e
  gi|119719433|ref|YP_919928.1| 38 ISDVLNTLYYeYSTASNIKDRVTRHHVLDALATIINRLKLFRE 80
                                   66777777666******************************98 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0025
                                    EETTSEEEEEESS..SSSEEEEEETTT-.-EEEE--HHHHHHHHHHHHHTT-EEE CS
                            FUR  62 efedgesryelak..kehhdhlicekCg.kviefkddeiekiqeeiaekegfklv 113
                                    + ++ +  +e +   +++ + l c kCg +v+ +++ ++ +  +e aek+g ++v
  gi|119719433|ref|YP_919928.1| 327 KCTSCKHEFEATLhsESEVAQLKCPKCGgEVEIIENRSVVEELAELAEKTGAEVV 381
                                    45556677776655588999*******6489999*****************9986 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.1     0.002       1.8      19      35 ..     319     335 ..     315     336 .. 0.82
   2 ?    4.4   0.1     0.039        35      24      32 ..     346     354 ..     342     356 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.002
                  zinc_ribbon_4  19 lpakgvkvrCskCghvF 35 
                                    l + +v+++C+ C+h F
  gi|119719433|ref|YP_919928.1| 319 LEKIRVRAKCTSCKHEF 335
                                    5666889********98 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.039
                  zinc_ribbon_4  24 vkvrCskCg 32 
                                    + ++C+kCg
  gi|119719433|ref|YP_919928.1| 346 AQLKCPKCG 354
                                    578999997 PP

>> Anti-TRAP  Tryptophan RNA-binding attenuator protein inhibitory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.5   9.7e-05     0.087      11      39 ..     326     356 ..     317     362 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.7e-05
                                    EE-TTTTTTSEE..TTE......E-TTTTTS CS
                      Anti-TRAP  11 tkCdaCngsGki..epeeprasleCPkCsGk 39 
                                     kC  C+   ++   +e + a l+CPkC+G+
  gi|119719433|ref|YP_919928.1| 326 AKCTSCKHEFEAtlHSESEVAQLKCPKCGGE 356
                                    58999988765511566889**********7 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       5.7   5.1e+03      29      36 ..     326     333 ..     297     349 .. 0.65
   2 ?   12.6   0.1   0.00015      0.13       5      24 ..     349     368 ..     346     381 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 5.7
                Lar_restr_allev  29 vyCadCga 36 
                                      C+ C+ 
  gi|119719433|ref|YP_919928.1| 326 AKCTSCKH 333
                                    56777766 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00015
                Lar_restr_allev   5 pCPfCggravlersqrvvae 24 
                                     CP Cgg+ +++++ +vv+e
  gi|119719433|ref|YP_919928.1| 349 KCPKCGGEVEIIENRSVVEE 368
                                    7*************999986 PP

>> HAD_SAK_2  HAD domain in Swiss Army Knife RNA repair proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00019      0.17      26      57 ..     353     391 ..     328     404 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00019
                      HAD_SAK_2  26 a......ldpe.averlkriveatgakiVlsstWrrred 57 
                                           ++++ +ve+l++++e+tga++Vl st  ++ +
  gi|119719433|ref|YP_919928.1| 353 CggeveiIENRsVVEELAELAEKTGAEVVLVSTQSAEGK 391
                                    044555567766*********************887766 PP

>> DUF2072  Zn-ribbon containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.4   0.00019      0.17       3      42 ..     327     369 ..     326     394 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00019
                        DUF2072   3 kCtkCekvfe....dgskeilkGCpsCGgkkFlyvkeeekkedv 42 
                                    kCt+C+++fe    + s++ +  Cp+CGg+  + +++++  e+ 
  gi|119719433|ref|YP_919928.1| 327 KCTSCKHEFEatlhSESEVAQLKCPKCGGEV-EIIENRSVVEEL 369
                                    8********93332345556679*****974.555555555544 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.2       2.8   2.5e+03       3       7 ..     117     121 ..     116     122 .. 0.85
   2 ?   12.2   0.1   0.00014      0.13       5      36 ..     326     359 ..     325     361 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2.8
                 Zn_ribbon_SprT   3 yvYrC 7  
                                    + YrC
  gi|119719433|ref|YP_919928.1| 117 WLYRC 121
                                    99**9 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00014
                 Zn_ribbon_SprT   5 YrCtgCgreythhlsi.rrhn..YrCrrCkgtLrg 36 
                                    ++Ct+C+ e++++l +   +     C++C+g+ ++
  gi|119719433|ref|YP_919928.1| 326 AKCTSCKHEFEATLHSeS-EVaqLKCPKCGGEVEI 359
                                    79*******999999953.4347*******99765 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1      0.26   2.4e+02       5      12 ..     327     334 ..     326     338 .. 0.88
   2 ?    7.1   0.0    0.0051       4.6       4      20 ..     348     364 ..     346     365 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.26
                  A2L_zn_ribbon   5 vCsvCggn 12 
                                    +C+ C+++
  gi|119719433|ref|YP_919928.1| 327 KCTSCKHE 334
                                    8******8 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0051
                  A2L_zn_ribbon   4 kvCsvCggngilnseqg 20 
                                     +C +Cgg+++++ +++
  gi|119719433|ref|YP_919928.1| 348 LKCPKCGGEVEIIENRS 364
                                    58**********98876 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.3    0.0088       7.8      26      38 ..     323     335 ..     320     336 .. 0.82
   2 ?    3.4   0.4     0.077        69       2       9 ..     349     356 ..     348     358 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0088
                        TFIIS_C  26 tvfykCtkCghrW 38 
                                     v  kCt+C+h++
  gi|119719433|ref|YP_919928.1| 323 RVRAKCTSCKHEF 335
                                    57789******98 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.077
                        TFIIS_C   2 kCpkCgsr 9  
                                    kCpkCg++
  gi|119719433|ref|YP_919928.1| 349 KCPKCGGE 356
                                    8****975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1070  (0.0596798); expected 358.6 (0.02)
Passed bias filter:                      920  (0.0513135); expected 358.6 (0.02)
Passed Vit filter:                       130  (0.00725082); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.65u 0.27s 00:00:00.92 Elapsed: 00:00:00.47
# Mc/sec: 2605.02
//
Query:       gi|119719434|ref|YP_919929.1|  [L=210]
Description: methyltransferase small [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-09   38.1   0.0    1.6e-09   37.6   0.0    1.2  1  MTS              Methyltransferase small domain
    4.4e-08   33.7   0.1    8.6e-08   32.8   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    9.4e-08   32.0   0.0    1.2e-07   31.7   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    1.3e-06   28.0   0.1    1.7e-06   27.6   0.1    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    6.1e-06   26.0   0.1     0.0002   21.1   0.1    2.2  1  UPF0020          Putative RNA methylase family UPF0020
    1.7e-05   25.4   0.0    3.5e-05   24.4   0.0    1.5  1  Methyltransf_11  Methyltransferase domain
    2.1e-05   24.2   0.0    2.8e-05   23.8   0.0    1.1  1  Cons_hypoth95    Conserved hypothetical protein 95
     0.0017   18.1   0.1     0.0026   17.5   0.1    1.3  1  Methyltransf_16  Lysine methyltransferase
     0.0031   17.4   0.0     0.0036   17.2   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
     0.0056   16.0   0.0     0.0071   15.7   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
  ------ inclusion threshold ------
      0.032   13.6   0.0      0.046   13.1   0.0    1.2  1  TehB             Tellurite resistance protein TehB
      0.083   12.5   0.0        0.1   12.1   0.0    1.3  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
        0.1   13.4   0.0       0.16   12.7   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
       0.15   12.0   0.0       0.22   11.5   0.0    1.2  1  Methyltransf_32  Methyltransferase domain


Domain annotation for each model (and alignments):
>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6   0.0   1.2e-12   1.6e-09      25     111 ..      45     133 ..      36     150 .. 0.81

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 1.2e-12
                                    HHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTT.ST.TS-EEE CS
                            MTS  25 etlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasdvlee.ve.ekkfdl 100
                                    e++++   +kvlDlGcG+G lg+ +a       v+++d d+ A+  ak  + + ++   v+++  dv    +     fd+
  gi|119719434|ref|YP_919929.1|  45 EHFQDISGKKVLDLGCGTGRLGIGAALLGGI--VVMLDLDFSAVSEAKSAAIRLGVYerVDLLVADVRLIpLReGILFDT 122
                                    6788878999**************9998777..9***************99998887788888888754303314469** PP

                                    EEE---STTTC CS
                            MTS 101 ivsNPPfhagk 111
                                    +v NPPf  + 
  gi|119719434|ref|YP_919929.1| 123 VVENPPFGVHA 133
                                    *******6654 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.0   6.7e-11   8.6e-08       1      70 [.      55     125 ..      55     147 .. 0.90

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 6.7e-11
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTT.TEEEEEE CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedg.sfDlvvs 70 
                                    vLdlGcGtGrl + +a   g + v+++D++ +++ +a++ a + g+  +v+++++d++ +p+ +g  fD vv 
  gi|119719434|ref|YP_919929.1|  55 VLDLGCGTGRLGIGAALL-G-GIVVMLDLDFSAVSEAKSAAIRLGVyeRVDLLVADVRLIPLREGiLFDTVVE 125
                                    9***************88.5.9*********************999***************988879999986 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.0   9.1e-11   1.2e-07       3      83 ..      51     128 ..      49     172 .. 0.82

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 9.1e-11
                Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieeleklled.ekfDlils 80 
                                    +g++vlDlGCGtG+l++ +a +lg  + vv +D +  a++ A++ a +lg+  +v + ++d+  ++    +   fD ++ 
  gi|119719434|ref|YP_919929.1|  51 SGKKVLDLGCGTGRLGIGAA-LLG--GIVVMLDLDFSAVSEAKSAAIRLGVYeRVDLLVADVRLIPL--REgILFDTVVE 125
                                    689*****************.665..689*****************9999655**********9994..33367898888 PP

                Methyltransf_31  81 nev 83 
                                    n +
  gi|119719434|ref|YP_919929.1| 126 NPP 128
                                    744 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.1   1.3e-09   1.7e-06     161     215 ..      51     104 ..      33     126 .. 0.76

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 1.3e-09
                           PrmA 161 egeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklev 215
                                    +g++vlD+G+G+G L i+aa+Lg   vv +D+D  Av+ ak+ a + +v +++++
  gi|119719434|ref|YP_919929.1|  51 SGKKVLDLGCGTGRLGIGAALLGGI-VVMLDLDFSAVSEAKSAAIRLGVYERVDL 104
                                    679********************86.677************99888888887766 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.1   1.6e-07    0.0002      29     134 ..      52     132 ..      30     138 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.6e-07
                                    TS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEE CS
                        UPF0020  29 gepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelklygsDldrrvvqgareNaekagvgdliefs 108
                                    g++ lD  CG+G + I aallg  ++                           +Dld ++v  a++ a + gv +++++ 
  gi|119719434|ref|YP_919929.1|  52 GKKVLDLGCGTGRLGIGAALLGGIVV--------------------------MLDLDFSAVSEAKSAAIRLGVYERVDLL 105
                                    56677777888888888888777776..........................68************************** PP

                                    E--GGG--STTS.---EEEE------- CS
                        UPF0020 109 qadaakLrlkeg.evdvivtnpPYGer 134
                                    +ad++ ++l+eg  +d++v npP+G  
  gi|119719434|ref|YP_919929.1| 106 VADVRLIPLREGiLFDTVVENPPFGVH 132
                                    ********888889***********75 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   2.7e-08   3.5e-05       1      66 [.      56     124 ..      56     127 .. 0.95

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 2.7e-08
                                    EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT.-EEEEE CS
                Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl..kvefvvadaeklpfedn.sfDlvv 66 
                                    Ld+GcGtGrl    a  g+ vv +Dl+  ++  ak++a + g+  +v+++vad++ +p++++  fD vv
  gi|119719434|ref|YP_919929.1|  56 LDLGCGTGRLGIGAALLGGIVVMLDLDFSAVSEAKSAAIRLGVyeRVDLLVADVRLIPLREGiLFDTVV 124
                                    8***************************************999************99****87899987 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   2.2e-08   2.8e-05      35     143 ..      41     148 ..      34     171 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 2.2e-08
                                    HHCCC....HCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--S CS
                  Cons_hypoth95  35 ilaae....iegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakk 110
                                    ++a+e    i g++vLDl +G+G lg+ A+  g   +v+++ d +av+  k    +l++ e+++ l+ d     l++   
  gi|119719434|ref|YP_919929.1|  41 WIAQEhfqdISGKKVLDLGCGTGRLGIGAALLG-GIVVMLDLDFSAVSEAKSAAIRLGVYERVDLLVADVRLIPLRE--- 116
                                    55555566799******************9999.899************************9999999988877777... PP

                                    S-EEEEEEE--SSSTTCH.HHHHHHHHHTT-EE CS
                  Cons_hypoth95 111 keefdivflDPPyakellieevlelleekkllk 143
                                    +  fd v  +PP+  ++     ++ l +  +l+
  gi|119719434|ref|YP_919929.1| 117 GILFDTVVENPPFGVHAR-GSDITFLSRAVMLA 148
                                    899**********99875.77777777555554 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1     2e-06    0.0026      32      78 ..      42      81 ..      30     104 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2e-06
                Methyltransf_16 32 lekklakelganelsklsvlELGsGtGlvGlavaellpeakviltDl 78
                                   +++      + ++ s+++vl+LG GtG  G+ +a+l  +  v++ Dl
  gi|119719434|ref|YP_919929.1| 42 IAQ-----EHFQDISGKKVLDLGCGTGRLGIGAALL--GGIVVMLDL 81
                                   433.....478999********************99..444444454 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.8e-06    0.0036      20      62 ..      49     102 ..      25     174 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.8e-06
                Methyltransf_23  20 lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae...........k 62 
                                    + +g++vLd+GcGtG+l   ++  g  v++ Dl++ av++a+            
  gi|119719434|ref|YP_919929.1|  49 DISGKKVLDLGCGTGRLGIGAALLGGIVVMLDLDFSAVSEAKsaairlgvyerV 102
                                    66789************9999999999999999999999987555555555540 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   5.5e-06    0.0071      44     120 ..      48     123 ..      40     165 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 5.5e-06
                                    -S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSS.TEEEEE--TTT-TTS-T.-EEEE CS
                Ubie_methyltran  44 avkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegki.nieflqanaeeLpfedd.sfDvv 120
                                     + +g+kvlD+ +Gtg l +  +      g vv+lD++ + +++++  + + g++ ++++l+a+   +p  ++  fD+v
  gi|119719434|ref|YP_919929.1|  48 QDISGKKVLDLGCGTGRLGIGAA---LLGGIVVMLDLDFSAVSEAKSAAIRLGVYeRVDLLVADVRLIPLREGiLFDTV 123
                                    56789************999754...45688999***************99999989*******999999885246765 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   3.6e-05     0.046      28      61 ..      49      82 ..      40     111 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.6e-05
                                   CS-S-EEEEES-TTSHHHHHHHHTT-EEEEEES- CS
                           TehB 28 ivkpgkvldlgcgqgrnslylsllgydvtawdkn 61
                                    ++  kvldlgcg gr  +  +llg  v  +d +
  gi|119719434|ref|YP_919929.1| 49 DISGKKVLDLGCGTGRLGIGAALLGGIVVMLDLD 82
                                   57889************99999999877777755 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   8.1e-05       0.1       3      82 ..      54     130 ..      52     169 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.1e-05
                Methyltransf_15   3 vilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklklekikvdlvflSpPwG 82 
                                     +lDl +G+G   i  al +  v+ ++ + + +  a+  a   gv ++++l ++dv      l++  + +d v+  pP G
  gi|119719434|ref|YP_919929.1|  54 KVLDLGCGTGRLGIGAALLGGIVVMLDLDFSAVSEAKSAAIRLGVYERVDLLVADVRL--IPLREGIL-FDTVVENPPFG 130
                                    79*****************************************************974..45556655.99999999988 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00012      0.16       1      54 [.      56     105 ..      56     141 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00012
                Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvele 54 
                                    L++GcGtG+l    +    +  ++ +D++ sa+  ak   a+++    ++v+l 
  gi|119719434|ref|YP_919929.1|  56 LDLGCGTGRLGIGAALL--GGIVVMLDLDFSAVSEAKS--AAIRLGVYERVDLL 105
                                    8**********999999..99999*****999944444..44444444444444 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00018      0.22      23      77 ..      49      98 ..      33     112 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00018
                Methyltransf_32 23 esgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkk 77
                                   + + ++v+D+G+G g L+   al    ++  vv +d+  + v++a+  a +lg  
  gi|119719434|ref|YP_919929.1| 49 DISGKKVLDLGCGTGRLGIGAAL----LGGIVVMLDLDFSAVSEAKSAAIRLG-V 98
                                   456789***************99....6999***************9999999.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1559.74
//
Query:       gi|119719435|ref|YP_919930.1|  [L=188]
Description: RNA-binding S1 domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.1e-06   25.7   0.0    1.6e-05   24.6   0.0    1.6  1  ECR1_N          Exosome complex exonuclease RRP4 N-terminal r
    0.00079   20.0   0.0     0.0014   19.2   0.0    1.4  1  EXOSC1          Exosome component EXOSC1/CSL4
  ------ inclusion threshold ------
      0.041   13.8   0.5      0.069   13.1   0.5    1.3  1  Prok-RING_1     Prokaryotic RING finger family 1
      0.061   13.3   0.5      0.095   12.7   0.5    1.2  1  zinc-ribbons_6  zinc-ribbons
       0.12   12.4   1.0        0.2   11.7   1.0    1.3  1  DZR             Double zinc ribbon
       0.42   11.0   3.6        1.1    9.6   0.8    2.6  2  S1              S1 RNA binding domain
       0.51   10.5   4.4       0.95    9.7   4.4    1.4  1  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 


Domain annotation for each model (and alignments):
>> ECR1_N  Exosome complex exonuclease RRP4 N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   6.2e-09   1.6e-05       1      34 [.       6      41 ..       6      43 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 6.2e-09
                                   EE-TT-EEEETTTSEE-TTEEEETTE..EEESSSEE CS
                         ECR1_N  1 iVtPGevlttdeefmrGhGTYvrggt..iyAsvaGt 34
                                   +V+PGe ++ +ee+++G+++Yv++ t  + A  +G+
  gi|119719435|ref|YP_919930.1|  6 VVIPGENVGVAEEYLPGENVYVDEETgdLKAKRVGV 41
                                   69*******************965443367776666 PP

>> EXOSC1  Exosome component EXOSC1/CSL4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   5.6e-07    0.0014       4      58 ..      64     124 ..      61     148 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 5.6e-07
                                    TT-EEEEEEEEEESSEEEEEEEEECTB.....SBCCCEEECCCTTSS--STS.TTSSCCHC CS
                         EXOSC1   4 egdvVLarvtrlrkkqalveilsvege.....nnvlsdsgvgangegavkei.eaggglds 58 
                                    +gdvV a v ++r   a+vei  ve++      +  ++++v++ +++ v+ + ++ g++d 
  gi|119719435|ref|YP_919930.1|  64 KGDVVYAVVKQIRDPVAIVEIFYVENKrrkliPPLTGILHVSNASSSRVRLLsDVIGYGDV 124
                                    59*************************7766666779************999888888887 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.5   2.7e-05     0.069       5      27 ..     151     173 ..     148     178 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.7e-05
                    Prok-RING_1   5 kkCpvCgkelkeedDiVvCpeCg 27 
                                     kCp C  ++++   i  Cp+C 
  gi|119719435|ref|YP_919930.1| 151 AKCPSCMTPMRKRGVILLCPNCR 173
                                    69********************5 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.5   3.7e-05     0.095       2      28 ..     152     178 ..     151     183 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.7e-05
                                    --SSS-S--EE-SSEEE-TTT--EEEE CS
                 zinc-ribbons_6   2 kCpeCqqelekrgeqyhCeaCqedlkk 28 
                                    kCp+C ++++krg  + C +C+ + ++
  gi|119719435|ref|YP_919930.1| 152 KCPSCMTPMRKRGVILLCPNCRYKTRR 178
                                    8********************987765 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.0   7.9e-05       0.2      15      39 ..     153     177 ..     150     181 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7.9e-05
                            DZR  15 CseCgtklkavaaedrCpsCgekvd 39 
                                    C+ C t++++      Cp+C +k+ 
  gi|119719435|ref|YP_919930.1| 153 CPSCMTPMRKRGVILLCPNCRYKTR 177
                                    99*****99888899*****99865 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       1.6   4.2e+03      48      59 ..      17      28 ..       4      41 .. 0.72
   2 ?    9.6   0.8   0.00043       1.1       3      27 ..      63      90 ..      61     132 .. 0.67

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.6
                                   HCEETTEEEEEE CS
                             S1 48 evlkvGdevkvk 59
                                   e++ +G+ v+v 
  gi|119719435|ref|YP_919930.1| 17 EEYLPGENVYVD 28
                                   677778877775 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00043
                                   TTTCEEEEEEEEEETTEEEEEET...TT CS
                             S1  3 ekgevveGeVtsvtkgGafVelg...ng 27
                                    kg+vv ++V+++ +  a+Ve++   n+
  gi|119719435|ref|YP_919930.1| 63 GKGDVVYAVVKQIRDPVAIVEIFyveNK 90
                                   69*******************9854433 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   4.4   0.00037      0.95      17      39 ..     152     172 ..     150     173 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00037
                  Auto_anti-p27  17 tCpvCgvPLmrdrkggkvyCvaC 39 
                                     Cp C +P+ + r g+ ++C++C
  gi|119719435|ref|YP_919930.1| 152 KCPSCMTPMRK-R-GVILLCPNC 172
                                    5*******666.5.7******** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1392.65
//
Query:       gi|119719436|ref|YP_919931.1|  [L=211]
Description: hypothetical protein Tpen_0522 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-45  154.4   1.7    2.9e-45  154.1   1.7    1.1  1  DUF2067   Uncharacterized protein conserved in archaea (DUF20


Domain annotation for each model (and alignments):
>> DUF2067  Uncharacterized protein conserved in archaea (DUF2067)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.1   1.7   1.6e-49   2.9e-45       1     185 [.       8     192 ..       8     193 .. 0.96

  Alignments for each domain:
  == domain 1  score: 154.1 bits;  conditional E-value: 1.6e-49
                        DUF2067   1 iklndeeeleeflekisekiksaeevkievegn.rllievyGtekei........kdiirrikellre.klkkekrglfk 70 
                                    +++nd+ e+++fl+++++++           g+ rl+ e++G++ ++        +di+rr+k+l+re ++k+ +++ +k
  gi|119719436|ref|YP_919931.1|   8 FTFNDSGEAVSFLSMLKKEL-----------GDaRLYGEIKGKKLKVfipegertDDIVRRVKTLYREiHEKTLTVRPRK 76 
                                    79******************...........444788888888888888888888************************* PP

                        DUF2067  71 yslsdllreag..apvppdvLvdaLkllGykaelreenvlktnapleevvelaerlseiykelrfknlskaakrvvavvs 148
                                    +++s++l++a+  +++p+++L+d+L++ G ka lr +++l+tna+l+e+ve+ae+ls++yk+l +++l+++a+r+ av+s
  gi|119719436|ref|YP_919931.1|  77 LGVSTILSMANleVAIPVPALADVLNMVGKKAVLR-GEYLETNASLKEAVEFAEKLSRAYKSLLHEPLTATARRLAAVAS 155
                                    ***********************************.******************************************** PP

                        DUF2067 149 vltgldpdevieellekGlLeeeegkivlrkewkkal 185
                                    v+ g++pd++++ l++kG+L+++eg+++l++e++k+l
  gi|119719436|ref|YP_919931.1| 156 VVLGTEPDKAVDLLVSKGILKQVEGNVSLSEEYTKSL 192
                                    **********************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       829  (0.0462379); expected 358.6 (0.02)
Passed bias filter:                      670  (0.0373696); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1481.85
//
Query:       gi|119719437|ref|YP_919932.1|  [L=292]
Description: NAD(+) kinase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.2e-25   90.3   0.1    2.9e-25   89.1   0.1    1.5  1  NAD_kinase  ATP-NAD kinase


Domain annotation for each model (and alignments):
>> NAD_kinase  ATP-NAD kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.1   0.1   1.6e-29   2.9e-25      72     291 ..      51     257 ..      45     258 .. 0.88

  Alignments for each domain:
  == domain 1  score: 89.1 bits;  conditional E-value: 1.6e-29
                                    -TTTTTSSSEEEEEE-HHHHHHHHHHHHHCT-EEEEEESSS--SS-SEEGGGHHHHHHHHHHT-SEEEEEEEEEEEEEET CS
                     NAD_kinase  72 eafadagvdliivvGGDGTaldvarllqkaeiPvlgvnaGvkgfltefepeaaaellekllegeirvekrevldavimrs 151
                                     ++  +++dl ivvGGDGT l+ ++  +++ +P+lg++  ++g+l   + + a+e+le++l+g++  e    l  +i  +
  gi|119719437|ref|YP_919932.1|  51 SELEAREADLGIVVGGDGTLLRTVQKSNAVLPPILGFSSDSLGYLLPHRVDVAREVLEEVLRGNYS-ERDVALGEFIAGE 129
                                    56678899******************************************************9997.5556666688777 PP

                                    TE......EEEEEEESSEEEEEESSSSS-EEEEEEETTEEEEEEEESEEEEE-TGGGGTHHHHTT--EE-TT---EEEEE CS
                     NAD_kinase 152 kgeediadiviensvlnevviirgpgstlielelyvdtelleadqldglivstPtGstayslsaGgplisPgvlailivp 231
                                     ++            lnev++  +pg+ + e+e+ +++e l  ++ dg+iv+tP Gst++++s Ggp+i  + ++ ++  
  gi|119719437|ref|YP_919932.1| 130 RAG----------VFLNEVCVWSEPGK-IVEFEVLLNDESLYRVRGDGVIVATPAGSTGHAFSYGGPVIIDTGQR-ALEV 197
                                    773..........569****9999875.679************************************99888887.7888 PP

                                    ESESSS-..---EEE-TT-EEEEEE-.SS--EEEEETTTEEEEE-TT-EEEEEEESSEEEEEE CS
                     NAD_kinase 232 icPhsls..srpiVvssssklrirva.srseallaldGseelelspgdevrvtasdkkfklir 291
                                    ++P +ls   rp++v   s   i v+   + a l++dG+   +l++   v+v+ s+k+ ++i 
  gi|119719437|ref|YP_919932.1| 198 VFPGALSplIRPLIVHGGS---IAVKvIAHPANLVVDGQVYSKLQEASKVTVRPSSKSLRFIY 257
                                    8887776336*****9988...444556999*****************************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1981.10
//
Query:       gi|119719438|ref|YP_919933.1|  [L=364]
Description: putative circadian clock protein, KaiC [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.1e-67  225.6   0.0    6.1e-67  225.3   0.0    1.1  1  ATPase    KaiC
    1.1e-06   28.3   0.0    1.6e-06   27.8   0.0    1.2  1  AAA_25    AAA domain
    4.5e-05   22.9   0.1      0.001   18.4   0.0    2.1  2  Rad51     Rad51
     0.0047   16.3   0.0     0.0077   15.6   0.0    1.4  1  DnaB_C    DnaB-like helicase C terminal domain
  ------ inclusion threshold ------
      0.035   12.7   0.1       0.12   11.0   0.0    1.7  2  GvpD      GvpD gas vesicle protein
      0.074   12.8   0.0        0.5   10.1   0.0    2.0  2  DEAD      DEAD/DEAH box helicase


Domain annotation for each model (and alignments):
>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  225.3   0.0     2e-70   6.1e-67       2     229 ..     119     352 ..     118     354 .. 0.94

  Alignments for each domain:
  == domain 1  score: 225.3 bits;  conditional E-value: 2e-70
                         ATPase   2 ktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekleeeg 81 
                                    +tgI+glDeil gG+ +g+++l++Ge+G+GKtif+ qFli+ga + gepg++++++ep ++l +  k +Gwdl +l +  
  gi|119719438|ref|YP_919933.1| 119 PTGIPGLDEILAGGFLRGKTYLVAGEAGCGKTIFSIQFLINGALN-GEPGLYIAIDEPTNQLLRGLKLFGWDLGDLISAR 197
                                    8********************************************.********************************** PP

                         ATPase  82 klaiidasesaeesaee..kdkedleelieelaeaikeikakrvviDsitglayeekeav...aReilrqlvrvl.kklg 155
                                    kl+++d+ ++ +++  +  +++ +++ +ie++ +a k+i+akr+viD+i++l y  ke+    aRe lr++v  + k  +
  gi|119719438|ref|YP_919933.1| 198 KLMFLDMRTHFSKIYMRdeRKHIEPRYIIEQILNAAKKINAKRLVIDPIAPLVYGGKEEDvlyAREFLREMVFAIeKTGE 277
                                    ***********9988776677788899*************************655444432569***********78888 PP

                         ATPase 156 vTailvsekssseeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIte.egikvlee 229
                                    +T+i++se+++++++ +++gveef+++g+ivL  +ei ++++R++ i+k R++++++ +++f+I + +gi++ e+
  gi|119719438|ref|YP_919933.1| 278 LTTIMTSEIPTGSTKLSRFGVEEFLASGIIVLGIEEIYGNVERVMYIRKARWAPVKPSKYIFDIVSgKGIVIREP 352
                                    9***********************************************************************987 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.0   5.5e-10   1.6e-06      22     161 ..     125     257 ..     109     283 .. 0.77

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 5.5e-10
                         AAA_25  22 rrwlvk.gllpagelallaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgeal.. 97 
                                    ++ ++  g+l +g++ l+aG  g+GKt + ++  +  a  G+           + ly++ +++ ++l r l+  g +l  
  gi|119719438|ref|YP_919933.1| 125 LDEILAgGFL-RGKTYLVAGEAGCGKTIFSIQFLINGAlNGE-----------PGLYIAIDEPTNQLLRGLKLFGWDLgd 192
                                    5555552665.9**************************6666...........67*****************99977765 PP

                         AAA_25  98 .rddarllvldlagv.eslpLfakdrggtl.ltadvdaleaaieevegvrlvviDplsr.alggdens 161
                                        ++l +ld  +   ++ +   d + ++     ++++ +a+++++ ++ +viDp++  ++gg e++
  gi|119719438|ref|YP_919933.1| 193 lISARKLMFLDMRTHfSKIYM--RDERKHIePRYIIEQILNAAKKIN-AKRLVIDPIAPlVYGGKEED 257
                                    555788999998777555544..334444435566999*******86.***********666667766 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   3.4e-07     0.001      14      61 ..     113     160 ..      98     172 .. 0.80
   2 ?    2.1   0.1     0.031        93      18      46 ..     285     318 ..     254     320 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 3.4e-07
                                    HSS-EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHT CS
                          Rad51  14 sellqlttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtv 61 
                                    ++ l   tG   lDe+L GG+  g+   + Ge ++Gkt ++ ++ +  
  gi|119719438|ref|YP_919933.1| 113 KRALYAPTGIPGLDEILAGGFLRGKTYLVAGEAGCGKTIFSIQFLING 160
                                    33455789********************************99987765 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.031
                                    EE--S-HHH.....HHHHTSSEESSSEEEEEEST CS
                          Rad51  18 qlttGskkl.....DelLgGGietgsiteifGef 46 
                                    ++ tGs+kl     +e L  Gi +  i ei+G+ 
  gi|119719438|ref|YP_919933.1| 285 EIPTGSTKLsrfgvEEFLASGIIVLGIEEIYGNV 318
                                    48899988733333679***************75 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   2.6e-06    0.0077       3      63 ..     119     179 ..     118     246 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.6e-06
                                    XSSTHHHHHHC.TSBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHH CS
                                    xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         DnaB_C   3 stgfkdLDklt.sGlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeql 63 
                                    +tg   LD+++ +G+ +g+ +++A+ +++Gkt + +++  n a + + p +++ ++ +++ql
  gi|119719438|ref|YP_919933.1| 119 PTGIPGLDEILaGGFLRGKTYLVAGEAGCGKTIFSIQFLINGALNGE-PGLYIAIDEPTNQL 179
                                    68889999876268***********************9999887544.66666666666666 PP

>> GvpD  GvpD gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0     4e-05      0.12      10      32 ..     136     158 ..     129     175 .. 0.83
   2 ?   -1.4   0.0      0.23   6.8e+02     163     210 ..     300     346 ..     293     352 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4e-05
                           GvpD  10 GktllikGaPGtGktlftlrgld 32 
                                    Gkt l+ G+ G Gkt+f +++l 
  gi|119719438|ref|YP_919933.1| 136 GKTYLVAGEAGCGKTIFSIQFLI 158
                                    9********************95 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.23
                           GvpD 163 eyivdGvvtlnvkeddrgrlrrdlrleklrGvrignrlqPftladGkf 210
                                    e+++ G++ l ++e   g + r + + k r   +++  + f +  Gk 
  gi|119719438|ref|YP_919933.1| 300 EFLASGIIVLGIEEI-YGNVERVMYIRKARWAPVKPSKYIFDIVSGKG 346
                                    8999*******9988.999*******9*99999999999999999885 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00017       0.5      11      60 ..     133     180 ..     126     184 .. 0.86
   2 ?    0.1   0.0       0.2   6.1e+02      58      88 ..     224     257 ..     220     298 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00017
                                    HHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  11 ilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLa 60 
                                    +l+g+  lva+e G GKT   +  +++  ++  g++g  + i ePt +L 
  gi|119719438|ref|YP_919933.1| 133 FLRGKTYLVAGEAGCGKTIFSIQFLINGALN--GEPGLYIAIDEPTNQLL 180
                                    468999************9888888887776..99999999999999986 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.2
                                    HHHHHHHHHHHHHTTT...STSEEEEEETTSSHH CS
                                    xxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxx RF
                           DEAD  58 eLaeqtlnnlkkfkky...idlrvlliiggvaar 88 
                                     ++eq+ln +kk+  +   id  + l++gg++++
  gi|119719438|ref|YP_919933.1| 224 YIIEQILNAAKKINAKrlvIDPIAPLVYGGKEED 257
                                    5689999999999885444665555778877663 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2360.05
//
Query:       gi|119719439|ref|YP_919934.1|  [L=103]
Description: hypothetical protein Tpen_0525 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-09   37.0   0.2    3.5e-09   36.7   0.2    1.1  1  Pcc1      Transcription factor Pcc1


Domain annotation for each model (and alignments):
>> Pcc1  Transcription factor Pcc1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.2   1.9e-13   3.5e-09       8      65 ..      22      80 ..      17      87 .. 0.90

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 1.9e-13
                                   -SSHHHHHHHHHHHHHHCHC-TTE.CEEEEEEETTEEEEEEEESSHHHHHHHHHHHHHH CS
                           Pcc1  8 fpterlAsialrtLqvDkelspla.vkrslslegnvLqveykAttnrmLRvavngfles 65
                                   + te++ si++r+L+++ e  p   +k+sls+eg  L++++ ++   +LR+++n++ + 
  gi|119719439|ref|YP_919934.1| 22 LGTEEEVSIIYRSLKPETEEVPRYrSKVSLSVEGGSLTLTIVSSKVSSLRASLNTYSRI 80
                                   57999************88889888*****************************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 699.87
//
Query:       gi|119719440|ref|YP_919935.1|  [L=166]
Description: hypothetical protein Tpen_0526 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       249  (0.0138881); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1318.55
//
Query:       gi|119719441|ref|YP_919936.1|  [L=784]
Description: SMC domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.9e-16   58.8   1.8    9.9e-16   58.8   1.8    4.7  2  AAA_23           AAA domain
    1.7e-13   50.5   0.0    1.1e-12   47.9   0.0    1.9  1  SMC_N            RecF/RecN/SMC N terminal domain
    3.3e-11   43.5   0.0    4.2e-06   26.7   0.0    3.6  2  AAA_15           AAA ATPase domain
    1.3e-06   28.4  11.1    0.00093   19.1   0.0    2.9  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    1.1e-05   25.3  24.8       0.27   11.1   0.6    4.9  5  Phage_GP20       Phage minor structural protein GP20
    1.3e-05   25.6   9.9      0.047   14.2   0.1    6.1  5  NPV_P10          Nucleopolyhedrovirus P10 protein
    3.1e-05   23.6   0.0    6.3e-05   22.6   0.0    1.4  1  AAA_29           P-loop containing region of AAA domain
    9.9e-05   22.9   1.9       0.42   11.1   0.0    4.5  3  ABC_tran         ABC transporter
    0.00011   21.0  25.8    0.00073   18.3  11.8    2.7  2  AAA_13           AAA domain
     0.0012   19.1  31.6       0.14   12.5   2.0    6.1  6  BLOC1_2          Biogenesis of lysosome-related organelles co
     0.0019   18.5  44.9      0.047   13.9  13.2    4.3  4  ATG16            Autophagy protein 16 (ATG16)
      0.003   17.2  31.9       0.31   10.6   0.4    5.7  5  PI3K_P85_iSH2    Phosphatidylinositol 3-kinase regulatory sub
     0.0064   16.5   7.7     0.0064   16.5   7.7    6.3  6  DHR10            Designed helical repeat protein 10 domain
      0.008   15.6  50.8      0.046   13.1   4.6    4.6  4  GAS              Growth-arrest specific micro-tubule binding
     0.0081   16.9  32.7       0.18   12.6   1.8    5.7  6  Occludin_ELL     Occludin homology domain
     0.0093   16.0  30.0      0.073   13.2   4.8    5.2  4  Med9             RNA polymerase II transcription mediator com
  ------ inclusion threshold ------
      0.017   15.4   2.5      0.075   13.3   0.1    3.3  2  AAA_22           AAA domain
      0.017   15.2  18.2      0.058   13.5   0.2    4.9  5  DUF2730          Protein of unknown function (DUF2730)
      0.031   14.3  27.1       0.72    9.9   0.7    6.1  7  Laminin_II       Laminin Domain II
      0.034   14.0   1.2        0.4   10.6   0.2    2.9  2  DUF1952          Domain of unknown function (DUF1952)
      0.037   13.6   0.0      0.037   13.6   0.0    2.9  2  AAA_27           AAA domain
      0.054   13.5  19.2          4    7.5   2.0    5.5  5  DUF1664          Protein of unknown function (DUF1664)
      0.057   13.7   0.0       0.13   12.5   0.0    1.6  1  SbcCD_C          Putative exonuclease SbcCD, C subunit
      0.061   12.6  25.8        1.3    8.3   0.5    4.7  4  DUF3450          Protein of unknown function (DUF3450)
      0.096   12.0  18.3       0.76    9.1   1.3    3.8  2  DUF4407          Domain of unknown function (DUF4407)
       0.13   12.4  14.6       0.18   12.0   0.9    4.5  4  GCN5L1           GCN5-like protein 1 (GCN5L1)
       0.16   11.5   0.2       0.39   10.3   0.2    1.6  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
       0.18   12.3  43.1       0.68   10.4  10.3    4.3  4  Fez1             Fez1
       0.27   10.9  17.2        1.6    8.4   0.2    4.2  4  DUF745           Protein of unknown function (DUF745)
       0.28    9.1  27.3     0.0084   14.1   2.6    3.7  4  V_ATPase_I       V-type ATPase 116kDa subunit family
       0.32   11.4  37.5      0.071   13.5   1.2    6.5  6  Snapin_Pallidin  Snapin/Pallidin
       0.33   10.8  19.5       0.66    9.8   1.3    5.0  5  Sec34            Sec34-like family
       0.33   11.4   7.4         74    3.8   1.2    4.4  4  T3SSipB          Type III cell invasion protein SipB
       0.43    9.8  15.7        0.2   10.9   0.6    4.0  4  HemX             HemX, putative uroporphyrinogen-III C-methyl
       0.57   10.0  18.2      0.086   12.7   1.6    3.6  3  Spc29            Spindle Pole Component 29
       0.61    9.0  33.9       0.37    9.7   3.2    4.2  4  IFT57            Intra-flagellar transport protein 57
       0.64    8.8  57.3        2.1    7.2  13.6    4.3  4  Spc7             Spc7 kinetochore protein
       0.87    9.6  12.1      0.026   14.6   2.0    3.4  4  LOH1CR12         Tumour suppressor protein
        1.1    7.1  17.8      0.073   11.0   0.5    3.0  3  Prominin         Prominin
        1.2    9.4   5.2        2.3    8.5   0.1    3.3  2  NdhM             Cyanobacterial and plastid NDH-1 subunit M
        1.9    8.0  31.9        2.2    7.8   5.9    4.0  3  Exonuc_VII_L     Exonuclease VII, large subunit
        2.3    6.7  47.1       0.41    9.2   7.5    4.2  4  FapA             Flagellar Assembly Protein A
          3    7.9  44.7        2.8    8.0   2.4    5.1  4  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
        3.7    7.6  14.8        9.6    6.3   0.5    3.9  3  FlxA             FlxA-like protein
        4.3    6.3  44.0        1.6    7.7  22.8    4.7  1  Atg14            Vacuolar sorting 38 and autophagy-related su
        4.4    7.1  12.9       0.18   11.6   1.6    3.7  4  LemA             LemA family
        4.9    7.7   6.0        1.2    9.6   0.4    2.9  1  DUF3140          Protein of unknown function (DUF3140)
        5.2    6.9  18.8        8.1    6.3   0.2    5.1  5  Sec8_exocyst     Sec8 exocyst complex component specific doma
          6    6.4  22.9        2.5    7.6   0.5    5.9  6  Fzo_mitofusin    fzo-like conserved region
        6.3    7.2  19.8        4.4    7.6   0.1    5.8  6  KxDL             Uncharacterized conserved protein
        6.4    5.9  23.8       0.92    8.7   2.1    4.0  4  TMPIT            TMPIT-like protein
        7.9    6.5  11.5        1.5    8.8   0.2    4.7  5  Sec20            Sec20
        9.5    6.4  40.4          2    8.5   0.8    4.9  4  BRE1             BRE1 E3 ubiquitin ligase


Domain annotation for each model (and alignments):
>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.8   1.8   2.9e-18   9.9e-16       3     193 ..       2     251 ..       1     284 [. 0.61
   2 ?   -0.6   7.2       4.8   1.6e+03     117     196 ..     300     388 ..     271     392 .. 0.55

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 2.9e-18
                         AAA_23   3 kienfrsfrd.qeidFskgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiesegkvkayveltfen 81 
                                    ++e++r f+d + ++F++g+t+I Gp G+GK+++l A+ +aLyg  +  +r  +   +k+ v+   +++ +  +el++e 
  gi|119719441|ref|YP_919936.1|   2 EVEGYRFFKDpFRVEFGDGVTVIAGPVGSGKSSLLSAVEYALYGTDSYIER--RVYTKKDLVNS-ASASLRVLLELEVEG 78 
                                    689*****87478*******************************8777666..34455555554.344555558888877 PP

                         AAA_23  82 kdgrytrsiererelskkkgkttkkaklellei.deleqfisellgskki........il.nlilflgqer......... 142
                                    ++    ++ier+ ++   + +++   ++ +l++ ++  ++++ellg ++         +  +l+l+ + ++         
  gi|119719441|ref|YP_919936.1|  79 EGV---YRIERRLSKEGRERVEVLLPDGGILREsSKVLEKVEELLGMDFFefsrsvsiNYvTLFLLAHGSQsvrsrvldr 155
                                    777...88888888888888888888888887768888999998886644366666642223333333333577777777 PP

                         AAA_23 143 ....................feefelkdkke...................rleelekeleeledekkllekl........ 175
                                                                  e                           l+ l +e++ le++        
  gi|119719441|ref|YP_919936.1| 156 llgidaveklaraitakpilD---------EmrslkgdvdflrsagfseeN-------LNILREEERRLEQEliegerll 219
                                    777777666655555544441.........033334445555323222221.......3444443333333334443333 PP

                         AAA_23 176 ..............eqekekekeleeleeele 193
                                                  ++ +e + el+++e+ le
  gi|119719441|ref|YP_919936.1| 220 eglkkeasdlegaaKKYQELKSELNAKEKLLE 251
                                    33333343333333222233333333333333 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 4.8
                         AAA_23 117 leqfisellgskkiilnlilflgqerfeefelkdkkerleelekeleeledekkllekl...........eqekekekel 185
                                    +e +++e ++ +++ +++++ + +e+    e k  + ++e +ek+l+e+e +   le++           e++k++    
  gi|119719441|ref|YP_919936.1| 300 SEYNLREVFSAFERVFHQLDEIYSEKY--REIKGLSAQVEVYEKQLREIESRLVGLEEHvsdyeraeseiEKIKSEYGDE 377
                                    444444444444444444433333332..122444458888888888888888877777777655543333333333355 PP

                         AAA_23 186 eeleeeleeil 196
                                    ++l+ee+  ++
  gi|119719441|ref|YP_919936.1| 378 NKLREEIGRLE 388
                                    66666665555 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.9   0.0   3.2e-15   1.1e-12       6     204 ..       2     772 ..       1     783 [. 0.93

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 3.2e-15
                                    EEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHC.TT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N   6 eienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvL.Gersakklrseklsdlihkskekasvkkaeveitfd 84 
                                    e+e+++ ++ +   ++f +++t+i Gp GSGKs+ll A+ + L G++s+ + r  + +dl+++        +a++ ++++
  gi|119719441|ref|YP_919936.1|   2 EVEGYRFFK-DPFRVEFGDGVTVIAGPVGSGKSSLLSAVEYALyGTDSYIERRVYTKKDLVNS-------ASASLRVLLE 73 
                                    799999997.9******************************9978889988999999999997.......3344444333 PP

                                    ETTEESSSSSSCEEEEEEEETTSEEEEEE........TTEEE-HHHHHHHHHCTT-STT..................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxx..................... RF
                          SMC_N  85 nedkklkiekeevsisrrvkrkgeseyki........ngkevtkkevsellesagiske..................... 135
                                     e +     +  + i+rr++++g+ ++++         +++   ++v+ell +  ++ +                     
  gi|119719441|ref|YP_919936.1|  74 LEVEG----EGVYRIERRLSKEGRERVEVllpdggilRESSKVLEKVEELLGMDFFEFSrsvsinyvtlfllahgsqsvr 149
                                    22222....3367899999999987766655755544444444577777777777777689999999************* PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                          SMC_N 136 ................................................................................ 135
                                                                                                                    
  gi|119719441|ref|YP_919936.1| 150 srvldrllgidaveklaraitakpildemrslkgdvdflrsagfseenlnilreeerrleqeliegerlleglkkeasdl 229
                                    ******************************************************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                          SMC_N 136 ................................................................................ 135
                                                                                                                    
  gi|119719441|ref|YP_919936.1| 230 egaakkyqelkselnakeklledlrdrvkgvlsldalvvgleelrdkllraaekllppsklikeiegievseynlrevfs 309
                                    ******************************************************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                          SMC_N 136 ................................................................................ 135
                                                                                                                    
  gi|119719441|ref|YP_919936.1| 310 afervfhqldeiysekyreikglsaqvevyekqlreiesrlvgleehvsdyeraeseiekikseygdenklreeigrles 389
                                    ******************************************************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                          SMC_N 136 ................................................................................ 135
                                                                                                                    
  gi|119719441|ref|YP_919936.1| 390 elgmlqrrselercvssvrrvlaeevakkgeaecyvcgnrlseefldwvrekvsksvkelkdveesigklrerinvlkkk 469
                                    ******************************************************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                          SMC_N 136 ................................................................................ 135
                                                                                                                    
  gi|119719441|ref|YP_919936.1| 470 ledlreykltlinyeaayeeyqrlleerknlqaaldaereeleraksglsvigaelkvvredflrlrtsysklplldeik 549
                                    ******************************************************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                          SMC_N 136 ................................................................................ 135
                                                                                                                    
  gi|119719441|ref|YP_919936.1| 550 kleqevsslrselqrlepqynkylelekriealsreiedkrhrlegirkdidekramlesfeerlarerrleevlgkvrr 629
                                    ******************************************************************************** PP

                                    ........................................................................CS-HHHHH CS
                                    ........................................................................xxxxxxxx RF
                          SMC_N 136 ........................................................................lLSgGekt 143
                                                                                                             LS G+kt
  gi|119719441|ref|YP_919936.1| 630 vkealievhadlrsqkimelnkvvneivrgiypytdieevrvrvvspsrrvggrsiyqvevkvggewypyssRLSDGQKT 709
                                    ******************************************************************************** PP

                                    HHHHHHHHHHHCC..S--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC CS
                                    xxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 144 LvalaLlfAiqkv..kpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlek 204
                                    +v l+Ll+ +++   k+  + +lDe   + D++  + + + +   +   Q iv++  e++  +
  gi|119719441|ref|YP_919936.1| 710 VVFLSLLIGLNRLlnKRVGFLVLDEPVPNVDDAIKASLLKSMLLVTGLRQAIVTTQAEDIAGR 772
                                    *********987533899*******777777665555555444455589****9988877655 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0   1.3e-08   4.2e-06       7     291 ..       2     510 ..       1     522 [. 0.54
   2 !    9.6   0.0     0.002      0.66     151     332 ..     540     735 ..     525     736 .. 0.77

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 1.3e-08
                         AAA_15   7 kikNFRslkd.veidlseeltvliGkNnsGKSsilealdlFlnnkekkn............................... 54 
                                    +++ +R +kd + +++ + +tv+ G+ +sGKSs+l a ++ l  ++++                                
  gi|119719441|ref|YP_919936.1|   2 EVEGYRFFKDpFRVEFGDGVTVIAGPVGSGKSSLLSAVEYALYGTDSYIerrvytkkdlvnsasaslrvllelevegegv 81 
                                    799************************************99999977774555555555555555555555555555555 PP

                         AAA_15  55 ..............kkvikiekedleifeniseskdikIdvef..................................... 83 
                                                  +                           +                                     
  gi|119719441|ref|YP_919936.1|  82 yrierrlskegrerV---------------------------Evllpdggilresskvlekveellgmdffefsrsvsin 134
                                    555555555555550...........................05555555555555555555555555555555555555 PP

                         AAA_15  84 ................................................................................ 83 
                                                                                                                    
  gi|119719441|ref|YP_919936.1| 135 yvtlfllahgsqsvrsrvldrllgidaveklaraitakpildemrslkgdvdflrsagfseenlnilreeerrleqelie 214
                                    55599*************************************99999999999876666666666665555555555544 PP

                         AAA_15  84 ..........................................aekekakeyektlkskekkkadlllkkkesdlkktikd 121
                                                                                                                    
  gi|119719441|ref|YP_919936.1| 215 gerlleglkkeasdlegaakkyqelkselnakeklledlrdrV------------------------------------- 257
                                    4444444444433333333333333333333333333333330..................................... PP

                         AAA_15 122 kklklkknelsdekisvekkks....................kkelpkekeeklekekeelkidkedlkklikkleeslk 181
                                                         +                    +   + +  +kl ke+e +++   +l+++ + +e  + 
  gi|119719441|ref|YP_919936.1| 258 ---------------------KgvlsldalvvgleelrdkllRAAEKLLPPSKLIKEIEGIEVSEYNLREVFSAFERVFH 316
                                    .....................03334444445555555555444444445555555666666666666666666666664 PP

                         AAA_15 182 keeelknvlksaiiklllisakRnvsdedsekkssllgklkekileealqekl........................... 234
                                    + +   +++++++++++  sa+ +v +++  +++s l  l e  +++  +e+                            
  gi|119719441|ref|YP_919936.1| 317 QLD---EIYSEKYREIKGLSAQVEVYEKQLREIESRLVGLEEHVSDYERAESEiekikseygdenklreeigrleselgm 393
                                    444...55555555555555555555544444444444444444443222222333333333322222233333333333 PP

                         AAA_15 235 .......................................................eeelteklkeiqeklkeidkklaee 259
                                                                                            ++++e + ++ e ++ ++kkl++ 
  gi|119719441|ref|YP_919936.1| 394 lqrrselercvssvrrvlaeevakkgeaecyvcgnrlseefldwvrekvsksvkeLKDVEESIGKLRERINVLKKKLEDL 473
                                    33333333333333333333333333333333333333333344455555555555555555556666666666666555 PP

                         AAA_15 260 lkkilkkkidkikkfnykgkkneeieik.....ddee 291
                                     +++l+ +  +  +++y++  +e ++++     + ee
  gi|119719441|ref|YP_919936.1| 474 REYKLTLINYEAAYEEYQRLLEERKNLQaaldaEREE 510
                                    5566666666666666666666666666666555555 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.002
                         AAA_15 151 keeklekekeelkidkedlkklikkleeslkkeeelknvlksaiiklllisakRnvsd...edsekkssllgklkekile 227
                                    ++ +l  e+++l+ + ++l++ +++le + +k+ el++ ++++   ++ i++kR+  +   +d ++k+ +l++  e++ +
  gi|119719441|ref|YP_919936.1| 540 SKLPLLDEIKKLEQEVSSLRSELQRLEPQYNKYLELEKRIEAL---SREIEDKRHRLEgirKDIDEKRAMLESFEERLAR 616
                                    5566667777888888888888888888888888555555554...4556666666664444445555555555555555 PP

                         AAA_15 228 ealqekleeelteklkeiqeklkeidkklaeelkkilkkkidkikkfnykgkkneeieik.................... 287
                                    e    +  ee+  k  +++e+l e   +l +++  +l+k +++i+ + y++ + ee++++                    
  gi|119719441|ref|YP_919936.1| 617 E----RRLEEVLGKVRRVKEALIEVHADLRSQKIMELNKVVNEIVRGIYPYTDIEEVRVRvvspsrrvggrsiyqvevkv 692
                                    4....4466777777777777777777777777788888999999999********9999******************** PP

                         AAA_15 288 .ddeelplnknGsGvqrllllillileaekkdekeeknvilliEEP 332
                                      + + + ++ ++G++  ++l+lli  ++     +++  +l+++EP
  gi|119719441|ref|YP_919936.1| 693 gGEWYPYSSRLSDGQKTVVFLSLLIGLNRLL---NKRVGFLVLDEP 735
                                    88888899999**************999999...999999999999 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   2.7e-06   0.00093       1      97 [.      21     116 ..      21     220 .. 0.73
   2 !   10.6   6.6     0.001      0.35     125     297 ..     532     765 ..     437     767 .. 0.65

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 2.7e-06
                         AAA_21   1 lnvliGpNgsGKSnLLdaldllarl..drdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrl 78 
                                    ++v+ Gp gsGKS+LL a +++         ++  ++++  ++ +   + l + + e++++++ie  ls++ r r ++ l
  gi|119719441|ref|YP_919936.1|  21 VTVIAGPVGSGKSSLLSAVEYALYGtdSYIERRVYTKKDLVNSASASLRVLLELEVEGEGVYRIERRLSKEGRERVEVLL 100
                                    79*****************9985436333333333344444444455555666666666666666666666666666666 PP

                         AAA_21  79 ersqveeklssvetllesg 97 
                                     + ++   l ++ ++le+ 
  gi|119719441|ref|YP_919936.1| 101 PDGGI---LRESSKVLEKV 116
                                    66666...44444444444 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.001
                         AAA_21 125 fslkelsvsepndlqfgkaltditsrawsllllldglrkerigllnifadyfgfakekrllqrlvrslklveielsdlge 204
                                    f +   s+s+   l+ +k l   +s ++s l+ l+ ++              ++ ++ ++++ l+r++ + + +l+ +++
  gi|119719441|ref|YP_919936.1| 532 FLRLRTSYSKLPLLDEIKKLEQEVSSLRSELQRLEPQY-------------NKYLELEKRIEALSREIEDKRHRLEGIRK 598
                                    33333333333333333333333333333333333333.............33333333333333333333333333333 PP

                         AAA_21 205 geeliasvderlrer................................................................. 219
                                     +++     e   er                                                                 
  gi|119719441|ref|YP_919936.1| 599 DIDEKRAMLESFEERlarerrleevlgkvrrvkealievhadlrsqkimelnkvvneivrgiypytdieevrvrvvspsr 678
                                    3333333333333334444444444566777777777777777777999999999999********************** PP

                         AAA_21 220 .....gvvflengdgqelparel..SdGtkrllalltallralkkg...sllliDEpEngLHPkllrrllellkelsrng 289
                                          ++++e + g+e+ +++   SdG+k + +l +++   +  +   ++l++DEp  + + ++ ++ll+ + + +  +
  gi|119719441|ref|YP_919936.1| 679 rvggrSIYQVEVKVGGEWYPYSSrlSDGQKTVVFLSLLIGLNRLLNkrvGFLVLDEPVPNVDDAIKASLLKSMLLVTG-L 757
                                    *******************999888*******75555555555555669********999999999999999988888.9 PP

                         AAA_21 290 aQviltTH 297
                                     Q i+tT+
  gi|119719441|ref|YP_919936.1| 758 RQAIVTTQ 765
                                    99999995 PP

>> Phage_GP20  Phage minor structural protein GP20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   3.7    0.0022      0.75      17      70 ..     195     248 ..     178     258 .. 0.89
   2 ?    5.4   0.8     0.044        15      28      67 ..     237     276 ..     232     295 .. 0.80
   3 !   11.0   0.1   0.00082      0.28      19      70 ..     328     379 ..     313     393 .. 0.82
   4 ?    5.3   1.7     0.048        16      18      74 ..     440     496 ..     425     518 .. 0.68
   5 !   11.1   0.6   0.00078      0.27      25      96 ..     546     617 ..     539     631 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0022
                     Phage_GP20  17 kakldeveeerdtlkeqlkdrdkqLedLkkkakdneeLqkqieelqaknkkaka 70 
                                    +++l+ + ee+  l+++l + +  Le+Lkk+a d e   k+ +el+ +++++++
  gi|119719441|ref|YP_919936.1| 195 EENLNILREEERRLEQELIEGERLLEGLKKEASDLEGAAKKYQELKSELNAKEK 248
                                    77889999****************************************999887 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.044
                     Phage_GP20  28 dtlkeqlkdrdkqLedLkkkakdneeLqkqieelqaknkk 67 
                                    ++lk++l++++k LedL + +k++ +L + +  l++  +k
  gi|119719441|ref|YP_919936.1| 237 QELKSELNAKEKLLEDLRDRVKGVLSLDALVVGLEELRDK 276
                                    689*********************9999887777765555 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00082
                     Phage_GP20  19 kldeveeerdtlkeqlkdrdkqLedLkkkakdneeLqkqieelqaknkkaka 70 
                                    +++ + ++++ +++ql + ++ L +L++ + d e  + +ie+++ ++ ++++
  gi|119719441|ref|YP_919936.1| 328 EIKGLSAQVEVYEKQLREIESRLVGLEEHVSDYERAESEIEKIKSEYGDENK 379
                                    4566778999999999999999999999999999999999999999888443 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.048
                     Phage_GP20  18 akldeveeerdtlkeqlkdrdkqLedLkkkakdneeLqkqieelqaknkkakaeyea 74 
                                    +k+++  +e ++++e++++  + ++ Lkkk +d  e + ++ +++a++++ +   e+
  gi|119719441|ref|YP_919936.1| 440 EKVSKSVKELKDVEESIGKLRERINVLKKKLEDLREYKLTLINYEAAYEEYQRLLEE 496
                                    456666677888888888888888888888888888888888888877774443333 PP

  == domain 5  score: 11.1 bits;  conditional E-value: 0.00078
                     Phage_GP20  25 eerdtlkeqlkdrdkqLedLkkkakdneeLqkqieelqaknkkakaeyeakiadlkldnaielaLkeakakn 96 
                                    +e ++l++++    ++L+ L+ +++   eL+k ie l  +++++    e   +d++   a+ ++++e  a++
  gi|119719441|ref|YP_919936.1| 546 DEIKKLEQEVSSLRSELQRLEPQYNKYLELEKRIEALSREIEDKRHRLEGIRKDIDEKRAMLESFEERLARE 617
                                    57899****************************************999999999999988888888877766 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.1     0.055        18      23      61 ..     222     260 ..     216     279 .. 0.89
   2 ?    2.1   0.0       0.8   2.7e+02      16      49 ..     332     355 ..     314     416 .. 0.62
   3 ?    3.6   0.1      0.27        91      20      56 ..     442     475 ..     435     495 .. 0.67
   4 !   14.2   0.1   0.00014     0.047       9      61 ..     544     596 ..     542     608 .. 0.91
   5 ?    0.2   0.1       3.1   1.1e+03      19      61 ..     626     656 ..     593     666 .. 0.52

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.055
                        NPV_P10  23 lqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenI 61 
                                    l+++  d++   ++ +el+++L+a  + L++l + v+ +
  gi|119719441|ref|YP_919936.1| 222 LKKEASDLEGAAKKYQELKSELNAKEKLLEDLRDRVKGV 260
                                    677788999999*********************999865 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.8
                        NPV_P10  16 vddkVdalqqqvddvqenlpdvtelnekLdaqsa 49 
                                    ++ +V++ ++q+ ++++ l           ++ +
  gi|119719441|ref|YP_919936.1| 332 LSAQVEVYEKQLREIESRL----------VGLEE 355
                                    3333333333333333333..........22222 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.27
                        NPV_P10  20 VdalqqqvddvqenlpdvtelnekLdaqsaqLaelet 56 
                                    V   +++v+++++  + + +l e+++ + ++L++l +
  gi|119719441|ref|YP_919936.1| 442 V---SKSVKELKDVEESIGKLRERINVLKKKLEDLRE 475
                                    3...455555555555566677777777777777765 PP

  == domain 4  score: 14.2 bits;  conditional E-value: 0.00014
                        NPV_P10   9 IradikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenI 61 
                                     +++ik++++ V++l +++++++ + ++  el+++++a+s ++++    +e I
  gi|119719441|ref|YP_919936.1| 544 LLDEIKKLEQEVSSLRSELQRLEPQYNKYLELEKRIEALSREIEDKRHRLEGI 596
                                    5899*************************************999887777776 PP

  == domain 5  score: 0.2 bits;  conditional E-value: 3.1
                        NPV_P10  19 kVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenI 61 
                                    kV  +++++ +v+             d  s+++ el++ v++I
  gi|119719441|ref|YP_919936.1| 626 KVRRVKEALIEVH------------ADLRSQKIMELNKVVNEI 656
                                    2222222222222............233444444555555544 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   1.9e-07   6.3e-05      16      50 ..      14      47 ..       4      51 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.9e-07
                         AAA_29 16 tieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                   ++e+  +g+t+++Gp GsGKS+ll A+ + L+++ 
  gi|119719441|ref|YP_919936.1| 14 RVEFG-DGVTVIAGPVGSGKSSLLSAVEYALYGTD 47
                                   45555.569**********************9975 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0    0.0012      0.42      13      42 ..      21      50 ..      13     130 .. 0.77
   2 ?    1.2   0.1       1.5     5e+02      60     122 ..     335     403 ..     307     413 .. 0.60
   3 ?    4.8   0.9      0.11        38     106     135 ..     698     735 ..     358     737 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0012
                                   EEEEEESTTSSHHHHHHHHTTSS--SEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran 13 kvaivGenGaGKStLlkllagllkpteGei 42
                                   +++i G+ G+GKS+Ll+++   l  t   i
  gi|119719441|ref|YP_919936.1| 21 VTVIAGPVGSGKSSLLSAVEYALYGTDSYI 50
                                   689*************98766655555544 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 1.5
                                    CEEEE-SS.--S-TTSBHHHH............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHH CS
                                    xxxxxxxx.xxxxxxxxxxxx............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  60 eigvlpqe.pqlfpeltvren............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalara 122
                                    +++v++++  ++ +      +             +++eiek+ s++g++++  + +++  s+L    ++r +l r+
  gi|119719441|ref|YP_919936.1| 335 QVEVYEKQlREIES------RlvgleehvsdyeRAESEIEKIKSEYGDENKLREEIGRLESELGML-QRRSELERC 403
                                    33333333233333......1333333566666677779999999999888888888777777443.334455555 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.11
                                    S..GGS-HHHHH......HHHHHHHHHHTSSEEEEEST CS
                                    x..xxxxxxxxx......xxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran 106 p..ssLSgGqkq......rvalarallkkpkllllDEp 135
                                    p  s LS Gqk        + l r+l k+  +l+lDEp
  gi|119719441|ref|YP_919936.1| 698 PysSRLSDGQKTvvflslLIGLNRLLNKRVGFLVLDEP 735
                                    14488999999944444444567888888999999999 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   6.9    0.0072       2.4     288     453 ..     222     391 ..     193     398 .. 0.49
   2 !   18.3  11.8   2.2e-06   0.00073     252     456 ..     417     610 ..     377     630 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0072
                         AAA_13 288 LekliekveskkselleklkavsdeasensafeedkeelkaeaealeeqLkglqraleaKrkepfksvelesvkakie.. 365
                                    L+k ++++                     + ++++++elk+e++a e+ L+ l+++++      +  v le++ +k+   
  gi|119719441|ref|YP_919936.1| 222 LKKEASDL---------------------EGAAKKYQELKSELNAKEKLLEDLRDRVKGVLSLDALVVGLEELRDKLLra 280
                                    22222222.....................333333444444444444444444444444433333333444444444322 PP

                         AAA_13 366 ......................sikklvaeineliakhNekvanleeekeeakkklelhl..veeleseldeykkkykkl 421
                                                          ++ +  ++++++  +  e+ ++  +e + +  ++e ++  + e+es l  +++++++ 
  gi|119719441|ref|YP_919936.1| 281 aekllppsklikeiegievseyNLREVFSAFERVFHQLDEIYSEKYREIKGLSAQVEVYEkqLREIESRLVGLEEHVSDY 360
                                    33333333333333333344446666666666666666666666666666665555555533566666666666666666 PP

                         AAA_13 422 ekaieklekelkeeeaelkkleeeikeLekql 453
                                    e+a ++ e ++k e+ + +kl+eei  Le +l
  gi|119719441|ref|YP_919936.1| 361 ERAESEIE-KIKSEYGDENKLREEIGRLESEL 391
                                    65555555.56666666666666666666665 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 2.2e-06
                         AAA_13 252 eassdtCpFCgqplpaerkaaLeahFddefeekqerLekliekveskkselleklkavsdeasensafeedkeelka... 328
                                    ++ + +C  Cg+ l++e+     +  +++++e  ++ e+ i k+ ++++ l++kl+++ +++   +++e ++ee+++   
  gi|119719441|ref|YP_919936.1| 417 KKGEAECYVCGNRLSEEFLDWVREKVSKSVKE-LKDVEESIGKLRERINVLKKKLEDLREYKLTLINYEAAYEEYQRlle 495
                                    444789**********************9998.8999***********999999****9998888888888666666444 PP

                         AAA_13 329 eaealeeqLkglqraleaKrkepfk.svelesvkakiesikklvaeineliakhNekvanleeekeeakkklelhlveel 407
                                    e ++l+++L++ +++le+ +  ++   +el++v ++  ++  + +++  l       +++le+e+++++++l++ + + +
  gi|119719441|ref|YP_919936.1| 496 ERKNLQAALDAEREELERAKSGLSViGAELKVVREDFLRLRTSYSKLPLL-----DEIKKLEQEVSSLRSELQRLEPQ-Y 569
                                    88999999**9999999888777776899999999999999999987544.....44566666666666666662222.2 PP

                         AAA_13 408 eseldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrde 456
                                    +        ky +lek ie l +e++++  +l+ ++++i e+++ l++ 
  gi|119719441|ref|YP_919936.1| 570 N--------KYLELEKRIEALSREIEDKRHRLEGIRKDIDEKRAMLESF 610
                                    1........3334444444444444444444444444444444444332 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   2.2    0.0046       1.5      18      82 ..     194     258 ..     190     284 .. 0.81
   2 ?    7.7   1.0     0.012       4.2      47      92 ..     323     368 ..     289     371 .. 0.82
   3 ?    0.3   0.1       2.7     9e+02      45      77 ..     362     394 ..     359     406 .. 0.75
   4 ?    6.5   0.6      0.03        10      45      78 ..     441     474 ..     433     483 .. 0.70
   5 ?   -0.8   0.1       5.7   1.9e+03      35      70 ..     486     521 ..     475     528 .. 0.59
   6 !   12.5   2.0   0.00042      0.14      34      92 ..     546     608 ..     518     611 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0046
                        BLOC1_2  18 tvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavs 82 
                                    + e++++L +  ++ +++  + ++ +++l+k++++l+   ++ q++++++++ ek +++L + v+
  gi|119719441|ref|YP_919936.1| 194 SEENLNILREEERRLEQELIEGERLLEGLKKEASDLEGAAKKYQELKSELNAKEKLLEDLRDRVK 258
                                    56888999999999999999999999999999999999999999999999988888888887765 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.012
                        BLOC1_2  47 ekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLE 92 
                                    ++k  +++ ++++++ y +q+ +ie ++  Lee vs  +   +e+E
  gi|119719441|ref|YP_919936.1| 323 SEKYREIKGLSAQVEVYEKQLREIESRLVGLEEHVSDYERAESEIE 368
                                    4566677788889999999999999999999999998777777766 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 2.7
                        BLOC1_2  45 slekkleklnekyeelqpylqqidqiekqvteL 77 
                                     +e+++ek++++y   +++ ++i ++e ++  L
  gi|119719441|ref|YP_919936.1| 362 RAESEIEKIKSEYGDENKLREEIGRLESELGML 394
                                    467788888888888888888888888776655 PP

  == domain 4  score: 6.5 bits;  conditional E-value: 0.03
                        BLOC1_2  45 slekkleklnekyeelqpylqqidqiekqvteLe 78 
                                    +++k++++l+  +e++ ++ ++i+ ++k++++L 
  gi|119719441|ref|YP_919936.1| 441 KVSKSVKELKDVEESIGKLRERINVLKKKLEDLR 474
                                    5666667777777777777777777777776665 PP

  == domain 5  score: -0.8 bits;  conditional E-value: 5.7
                        BLOC1_2  35 kykklkdvaaslekkleklnekyeelqpylqqidqi 70 
                                     y+++++ +++ ++   +l+++ eel+  ++ +  i
  gi|119719441|ref|YP_919936.1| 486 AYEEYQRLLEERKNLQAALDAEREELERAKSGLSVI 521
                                    355555555555555555556666666666666555 PP

  == domain 6  score: 12.5 bits;  conditional E-value: 0.00042
                        BLOC1_2  34 ekykklkdvaaslekkleklnekyeelqpylqqidqiekqvte....LeeavseLDeyskeLE 92 
                                     ++kkl+++++sl+++l++l+ +y++  ++ ++i+++ +++++    Le + + +De    LE
  gi|119719441|ref|YP_919936.1| 546 DEIKKLEQEVSSLRSELQRLEPQYNKYLELEKRIEALSREIEDkrhrLEGIRKDIDEKRAMLE 608
                                    5789*****************************998888876422226666666666655555 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   5.6   0.00068      0.23      93     159 ..     187     256 ..     176     286 .. 0.85
   2 ?    3.5   2.4      0.22        74     112     172 ..     330     396 ..     301     415 .. 0.55
   3 ?    6.3   1.0      0.03        10     108     144 ..     439     475 ..     432     479 .. 0.89
   4 !   13.9  13.2   0.00014     0.047      17     161 ..     483     635 ..     481     648 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00068
                          ATG16  93 lyksrgelaqrllelneelqkleeklkedeerlaeleaeraale...tklkdreeelrekeklvqdlqDE 159
                                     ++s g +++ l+ l ee ++le++l e e+ l+ l++e ++le   +k+++++ el+ kekl++dl+D 
  gi|119719441|ref|YP_919936.1| 187 FLRSAGFSEENLNILREEERRLEQELIEGERLLEGLKKEASDLEgaaKKYQELKSELNAKEKLLEDLRDR 256
                                    57899999999********************************833345566677999**********95 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.22
                          ATG16 112 qkleeklkedeerlaeleaeraaletklkdreeelrekeklvq......dlqDElsaLqlqlnqaEe 172
                                    + l ++ +  e++l+e+e++   le+ ++d e +  e ek         +l++E+  L+ +l ++  
  gi|119719441|ref|YP_919936.1| 330 KGLSAQVEVYEKQLREIESRLVGLEEHVSDYERAESEIEKIKSeygdenKLREEIGRLESELGMLQR 396
                                    2223333333344444444444444444444444444444333444444566666666666665554 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.03
                          ATG16 108 neelqkleeklkedeerlaeleaeraaletklkdree 144
                                     e+++k  ++lk  ee++ +l++++++l++kl+d++e
  gi|119719441|ref|YP_919936.1| 439 REKVSKSVKELKDVEESIGKLRERINVLKKKLEDLRE 475
                                    678899999************************9986 PP

  == domain 4  score: 13.9 bits;  conditional E-value: 0.00014
                          ATG16  17 faeliqaynrLldrtsaleaenaklekaaasaks.....sksskksakekeasasq......snskqsakiqsleqklaq 85 
                                    +++ ++ y+rLl+  + l+a   + +++ ++aks      +  k +++              s+    ++i++leq++++
  gi|119719441|ref|YP_919936.1| 483 YEAAYEEYQRLLEERKNLQAALDAEREELERAKSglsviGAELKVVREDF-----LrlrtsySKLPLLDEIKKLEQEVSS 557
                                    567789999*9999777666655555555555555545633333333333.....033334678999************* PP

                          ATG16  86 lreelael...yksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDEls 161
                                    lr+el+ l   y +  el++r+ +l+ e+++++ +l+  ++ ++e +a+ ++ e++l+ re +l+e    v  ++++l+
  gi|119719441|ref|YP_919936.1| 558 LRSELQRLepqYNKYLELEKRIEALSREIEDKRHRLEGIRKDIDEKRAMLESFEERLA-RERRLEEVLGKVRRVKEALI 635
                                    *****998555677789**************************************986.45555555555555555554 PP

>> PI3K_P85_iSH2  Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.4      0.21        72       8      37 ..     225     254 ..     194     264 .. 0.76
   2 !    7.5   3.5    0.0085       2.9      55     139 ..     313     398 ..     303     403 .. 0.84
   3 ?    4.0   0.7       0.1        34      80     111 ..     446     477 ..     430     489 .. 0.80
   4 !   10.3   1.0    0.0012       0.4      20     101 ..     484     566 ..     477     569 .. 0.85
   5 !   10.6   0.4    0.0009      0.31      17      59 ..     570     612 ..     567     615 .. 0.96

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.21
                  PI3K_P85_iSH2   8 kegdleklseklrevskqlqekskeydqlk 37 
                                    + +dle  ++k++e++++l+ k+k ++ l 
  gi|119719441|ref|YP_919936.1| 225 EASDLEGAAKKYQELKSELNAKEKLLEDLR 254
                                    456777777777777777777777776665 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0085
                  PI3K_P85_iSH2  55 eaFneaikmFeeqiklqekfskeaqehEie..klqenleqlksrlkelhsskekLeedlkqqkeeereleReinalkpel 132
                                    ++F    +++ e+ + +  +s +++  E++  ++++ l  l+++++  + + +++e ++k++  +e +l  ei +l +el
  gi|119719441|ref|YP_919936.1| 313 RVFHQLDEIYSEKYREIKGLSAQVEVYEKQlrEIESRLVGLEEHVSDYERAESEIE-KIKSEYGDENKLREEIGRLESEL 391
                                    4677777777777777777777776555555599********************96.79********************* PP

                  PI3K_P85_iSH2 133 lqLqkrk 139
                                     +Lq+r 
  gi|119719441|ref|YP_919936.1| 392 GMLQRRS 398
                                    ****985 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.1
                  PI3K_P85_iSH2  80 ehEieklqenleqlksrlkelhsskekLeedl 111
                                     +E ++++e++ +l++r++ l+++ e+L e+ 
  gi|119719441|ref|YP_919936.1| 446 VKELKDVEESIGKLRERINVLKKKLEDLREYK 477
                                    47999999****************99999875 PP

  == domain 4  score: 10.3 bits;  conditional E-value: 0.0012
                  PI3K_P85_iSH2  20 revskqlqekskeydqlkeeynkiseeiqlkrqaleaFneaikmFeeq.iklqekfskeaqehEieklqenleqlksrlk 98 
                                    +   +++q   +e+ +l+ +  + +ee++  +  l + +   k+ +e  ++l  ++sk +   Ei+kl++ ++ l+s l+
  gi|119719441|ref|YP_919936.1| 484 EAAYEEYQRLLEERKNLQAALDAEREELERAKSGLSVIGAELKVVREDfLRLRTSYSKLPLLDEIKKLEQEVSSLRSELQ 563
                                    5556788888899999999999****************9777776654389**********9999999999999999999 PP

                  PI3K_P85_iSH2  99 elh 101
                                     l+
  gi|119719441|ref|YP_919936.1| 564 RLE 566
                                    886 PP

  == domain 5  score: 10.6 bits;  conditional E-value: 0.0009
                  PI3K_P85_iSH2  17 eklrevskqlqekskeydqlkeeynkiseeiqlkrqaleaFne 59 
                                    +k+ e++k ++  s+e + +    + i+++i++kr  le F+e
  gi|119719441|ref|YP_919936.1| 570 NKYLELEKRIEALSREIEDKRHRLEGIRKDIDEKRAMLESFEE 612
                                    7999*************************************98 PP

>> DHR10  Designed helical repeat protein 10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   5.3     0.034        11      30      79 ..     207     256 ..     198     261 .. 0.90
   2 ?    7.0   1.1     0.017       5.9      59     107 ..     315     363 ..     288     366 .. 0.73
   3 ?    2.4   0.9      0.47   1.6e+02      43      81 ..     361     399 ..     357     412 .. 0.87
   4 ?    6.4   1.1     0.026       8.8      62      99 ..     438     475 ..     431     478 .. 0.85
   5 ?    3.2   7.8      0.26        86       4      76 ..     456     528 ..     453     541 .. 0.87
   6 !   16.5   7.7   1.9e-05    0.0064      47     109 ..     546     608 ..     544     616 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.034
                          DHR10  30 vvekdlrsciklleeieaelakleeakkklkelrdaleekeielrelerk 79 
                                    ++e++l +  +lle +++e   le a kk +el+ +l+ ke+ l++l  +
  gi|119719441|ref|YP_919936.1| 207 RLEQELIEGERLLEGLKKEASDLEGAAKKYQELKSELNAKEKLLEDLRDR 256
                                    56788888889*******************************99999766 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.017
                          DHR10  59 lkelrdaleekeielrelerkeerlqrqlenaeeklerlreqaeekrea 107
                                      +l + ++ek +e + l+++ e  ++ql   e +l  l+e+ ++ ++a
  gi|119719441|ref|YP_919936.1| 315 FHQLDEIYSEKYREIKGLSAQVEVYEKQLREIESRLVGLEEHVSDYERA 363
                                    4556677788888888888888888888888888888888887776655 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.47
                          DHR10  43 eeieaelakleeakkklkelrdaleekeielrelerkee 81 
                                    e +e+e++k +++  + ++lr+++  +e el  l+r+ e
  gi|119719441|ref|YP_919936.1| 361 ERAESEIEKIKSEYGDENKLREEIGRLESELGMLQRRSE 399
                                    568999***********************9999998876 PP

  == domain 4  score: 6.4 bits;  conditional E-value: 0.026
                          DHR10  62 lrdaleekeielrelerkeerlqrqlenaeeklerlre 99 
                                     r+++++  +el+++e  +  l+ +++  ++kle lre
  gi|119719441|ref|YP_919936.1| 438 VREKVSKSVKELKDVEESIGKLRERINVLKKKLEDLRE 475
                                    57888999999999999999999999999999999987 PP

  == domain 5  score: 3.2 bits;  conditional E-value: 0.26
                          DHR10   4 laeekeelaelErkarelqakidalqvvekdlrsciklleeieaelakleeakkklkelrdaleekeielrel 76 
                                    + + +e ++ l +k  +l++   +l ++e+  ++  +llee ++ +a+l+ ++++l++++  l+  ++el+ +
  gi|119719441|ref|YP_919936.1| 456 IGKLRERINVLKKKLEDLREYKLTLINYEAAYEEYQRLLEERKNLQAALDAEREELERAKSGLSVIGAELKVV 528
                                    566789999***************************************************9999888877765 PP

  == domain 6  score: 16.5 bits;  conditional E-value: 1.9e-05
                          DHR10  47 aelakleeakkklkelrdaleekeielrelerkeerlqrqlenaeeklerlreqaeekreaak 109
                                    +e++kle++ + l +  ++le + ++  ele+++e l r +e ++ +le  r++ +ekr+  +
  gi|119719441|ref|YP_919936.1| 546 DEIKKLEQEVSSLRSELQRLEPQYNKYLELEKRIEALSREIEDKRHRLEGIRKDIDEKRAMLE 608
                                    699999****************************************************98766 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   4.6   0.00014     0.046      25     106 ..     175     255 ..     168     284 .. 0.87
   2 !    8.1   2.5    0.0045       1.5      44     114 ..     324     397 ..     292     432 .. 0.60
   3 !    8.2   9.6    0.0041       1.4      48     125 ..     441     518 ..     437     521 .. 0.90
   4 ?    6.3   6.6     0.016       5.5      61     124 ..     546     602 ..     536     616 .. 0.53

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00014
                            GAS  25 LelIkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdl 104
                                    L+  +slK ++  l+      e +l+ + +e +rl+++L + e+ +e L+k++ + e   +++++lk++l+  ek l+dl
  gi|119719441|ref|YP_919936.1| 175 LDEMRSLKGDVDFLRSAGF-SEENLNILREEERRLEQELIEGERLLEGLKKEASDLEGAAKKYQELKSELNAKEKLLEDL 253
                                    5667777777777776554.5678999***************************************************99 PP

                            GAS 105 kw 106
                                    + 
  gi|119719441|ref|YP_919936.1| 254 RD 255
                                    85 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0045
                            GAS  44 rnekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarl...kelekelkdlkwehevleqr 114
                                    ++ +e++ +s++ + ++++L++ e  +  L++++ +ye+  ++++++k+++   ++l +e+ +l+ e  +l+ r
  gi|119719441|ref|YP_919936.1| 324 EKYREIKGLSAQVEVYEKQLREIESRLVGLEEHVSDYERAESEIEKIKSEYgdeNKLREEIGRLESELGMLQRR 397
                                    34444444555555555555555555555555555555555555555555422233444444444444444333 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0041
                            GAS  48 elseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrfekvekerdel 125
                                    ++s+  +e k+ +e + k++e ++ L+k+l++ ++ k  l n +a ++e ++ l++ k  +  l  + e++e+++  l
  gi|119719441|ref|YP_919936.1| 441 KVSKSVKELKDVEESIGKLRERINVLKKKLEDLREYKLTLINYEAAYEEYQRLLEERKNLQAALDAEREELERAKSGL 518
                                    567788999999***********************************9999999999999999999999999998766 PP

  == domain 4  score: 6.3 bits;  conditional E-value: 0.016
                            GAS  61 epLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrfekvekerde 124
                                    +       e+++L++++   +++ q+l+ + +++ elek +++l+ e e +++r+e + k++de
  gi|119719441|ref|YP_919936.1| 546 D-------EIKKLEQEVSSLRSELQRLEPQYNKYLELEKRIEALSREIEDKRHRLEGIRKDIDE 602
                                    3.......44444444445555555555555555555555555555555555555555554444 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.3         1   3.5e+02      26      62 ..     207     243 ..     198     260 .. 0.65
   2 !   12.6   1.8   0.00052      0.18      15      90 ..     320     392 ..     312     400 .. 0.74
   3 ?    5.0   0.8      0.12        41      59      93 ..     439     474 ..     428     479 .. 0.83
   4 ?    6.0   2.6     0.059        20      16      91 ..     482     564 ..     474     566 .. 0.72
   5 ?    7.7   3.3     0.017       5.8      29      79 ..     553     604 ..     522     620 .. 0.51
   6 !    9.3   2.0    0.0056       1.9      19      81 ..     567     629 ..     562     656 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 1
                   Occludin_ELL  26 elhaeleevskkfseLerelkelkegskeykkieeei 62 
                                    +l++el e ++ ++ L++e ++l+   k+y+++++e+
  gi|119719441|ref|YP_919936.1| 207 RLEQELIEGERLLEGLKKEASDLEGAAKKYQELKSEL 243
                                    5556666666666677777777777777777776663 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00052
                   Occludin_ELL  15 aeFnkeYkeYkelhaeleevskkfseLerelkelkegskeykkieeeilqeykklkkdpeyqekkkrceyLkekLs 90 
                                    + ++++Y+e k l a++e ++k+++e+e++l  l+e+ + y+++e+ei +  ++     +  + ++++  L+++L 
  gi|119719441|ref|YP_919936.1| 320 EIYSEKYREIKGLSAQVEVYEKQLREIESRLVGLEEHVSDYERAESEIEKIKSE---YGDENKLREEIGRLESELG 392
                                    56899**********************************999999884332222...2333344445555555555 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.12
                   Occludin_ELL  59 eeeilqeykklkk.dpeyqekkkrceyLkekLshiK 93 
                                     e++ ++ k+lk  +++  + ++r+++Lk+kL+ ++
  gi|119719441|ref|YP_919936.1| 439 REKVSKSVKELKDvEESIGKLRERINVLKKKLEDLR 474
                                    577888888888878899999***********9876 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.059
                   Occludin_ELL  16 eFnkeYkeYkelhaeleevskkfseLerelkelkegsk....eykkieee...ilqeykklkkdpeyqekkkrceyLkek 88 
                                    ++++ Y+eY++l +e +++++ +   ++el+++k g +    e k + e+   +  +y+kl    e ++ ++++  L+++
  gi|119719441|ref|YP_919936.1| 482 NYEAAYEEYQRLLEERKNLQAALDAEREELERAKSGLSvigaELKVVREDflrLRTSYSKLPLLDEIKKLEQEVSSLRSE 561
                                    58999999999999999999999999999999998888666555555543111455666666677777777777777777 PP

                   Occludin_ELL  89 Lsh 91 
                                    L+ 
  gi|119719441|ref|YP_919936.1| 562 LQR 564
                                    765 PP

  == domain 5  score: 7.7 bits;  conditional E-value: 0.017
                   Occludin_ELL  29 aeleevskkfseLerelkelkegskeykkieeeilqeykklkk.dpeyqekk 79 
                                    +e++++++++++Le + +++ e +k+++ + +ei ++ ++l+   ++  ek+
  gi|119719441|ref|YP_919936.1| 553 QEVSSLRSELQRLEPQYNKYLELEKRIEALSREIEDKRHRLEGiRKDIDEKR 604
                                    3333444444444433333333333333333333333333333333333333 PP

  == domain 6  score: 9.3 bits;  conditional E-value: 0.0056
                   Occludin_ELL  19 keYkeYkelhaeleevskkfseLerelkelkegskeykkieeeilqeykklkkdpeyqekkkr 81 
                                     +Y++Y el++++e++s+++++ +++l+  +++ +e + + e+  +++++ ++ +e + k +r
  gi|119719441|ref|YP_919936.1| 567 PQYNKYLELEKRIEALSREIEDKRHRLEGIRKDIDEKRAMLESFEERLARERRLEEVLGKVRR 629
                                    69****************************999999999999888888877776666555554 PP

>> Med9  RNA polymerase II transcription mediator complex subunit 9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.9      0.13        44      57      80 .]     234     257 ..     216     257 .. 0.85
   2 ?    3.9   0.3      0.16        55      43      77 ..     327     361 ..     316     363 .. 0.92
   3 !    8.2   3.4    0.0074       2.5      13      72 ..     442     500 ..     437     516 .. 0.76
   4 !   13.2   4.8   0.00022     0.073      10      79 ..     545     613 ..     537     614 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.13
                           Med9  57 aeieeleeqlakKrelLkkyknrv 80 
                                    ++ +el+ +l +K++lL+++++rv
  gi|119719441|ref|YP_919936.1| 234 KKYQELKSELNAKEKLLEDLRDRV 257
                                    67799***************9886 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.16
                           Med9  43 relpgidrsveeqeaeieeleeqlakKrelLkkyk 77 
                                    re++g++  ve  e++++e e +l   +e  ++y 
  gi|119719441|ref|YP_919936.1| 327 REIKGLSAQVEVYEKQLREIESRLVGLEEHVSDYE 361
                                    899**********************9999999996 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0074
                           Med9  13 iekdpnlsskdletktgelrhkLkkarelirelpgidrsveeqeaeieeleeqlakKrel 72 
                                    ++k   ++ kd+e ++g+lr +++  ++ ++ l +   +  + ea  ee++  l+ +++l
  gi|119719441|ref|YP_919936.1| 442 VSKSV-KELKDVEESIGKLRERINVLKKKLEDLREYKLTLINYEAAYEEYQRLLEERKNL 500
                                    56666.899***********************9996666666666666666555555544 PP

  == domain 4  score: 13.2 bits;  conditional E-value: 0.00022
                           Med9  10 lksiekdpnlsskdletktgelrhkLkkarelirelpgidrsveeqeaeieeleeqlakKrelLkkyknr 79 
                                    l +i+k + +++  l ++++ l  +++k  el + ++ ++r +e+   ++e  ++ ++ Kr++L+++ +r
  gi|119719441|ref|YP_919936.1| 545 LDEIKKLE-QEVSSLRSELQRLEPQYNKYLELEKRIEALSREIEDKRHRLEGIRKDIDEKRAMLESFEER 613
                                    55555555.67777777777777777788888888888****************************9987 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   0.00022     0.075       4      38 ..      18      91 ..      15     204 .. 0.60
   2 ?   -0.8   0.0       4.9   1.7e+03     105     136 ..     246     276 ..     225     320 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00022
                         AAA_22  4 tagilvvtGesGtGKTtllrrlleqldeeakaee...........................................e 38
                                   ++g++v+ G++G+GK+ ll  + + l       +                                           e
  gi|119719441|ref|YP_919936.1| 18 GDGVTVIAGPVGSGKSSLLSAVEYALYGT----DsyierrvytkkdlvnsasaslrvllelevegegvyrierrlskE 91
                                   7899*****************99988321....112223334444444333333333333333333333333333333 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 4.9
                         AAA_22 105 seealeeLrsllnlsrkgvqliLvGtpelrkl 136
                                    +e++le+Lr++++ +  ++  ++vG +elr+ 
  gi|119719441|ref|YP_919936.1| 246 KEKLLEDLRDRVK-GVLSLDALVVGLEELRDK 276
                                    3667777777776.555666666666666654 PP

>> DUF2730  Protein of unknown function (DUF2730)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   1.0       2.3   7.8e+02      55      96 ..     218     250 ..     194     263 .. 0.52
   2 ?   13.5   0.2   0.00017     0.058      22      96 ..     315     394 ..     305     399 .. 0.83
   3 ?    2.2   0.1      0.55   1.9e+02      33      59 ..     447     473 ..     414     499 .. 0.73
   4 ?    7.3   0.2     0.014       4.8      51      87 ..     534     570 ..     513     582 .. 0.85
   5 ?   -0.6   0.1       4.1   1.4e+03      36      57 ..     580     601 ..     569     642 .. 0.59

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 2.3
                        DUF2730  55 kvenLPtakdlekLkllladlrgelkaleaevrqlshqvdLL 96 
                                              le Lk++ +dl+g  k+ ++  ++l+ + +LL
  gi|119719441|ref|YP_919936.1| 218 L---------LEGLKKEASDLEGAAKKYQELKSELNAKEKLL 250
                                    3.........44455555555555555554444444444443 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00017
                        DUF2730  22 lllldskYakr.edleklaekveendkrlteletkvenLPta.kdlekLkllladlr...gelkaleaevrqlshqvdLL 96 
                                      +ld+ Y  +  +++ l  +ve ++k+l e+e+++  L  + +d e+ + ++++++   g+ ++l++e+ +l+  +++L
  gi|119719441|ref|YP_919936.1| 315 FHQLDEIYSEKyREIKGLSAQVEVYEKQLREIESRLVGLEEHvSDYERAESEIEKIKseyGDENKLREEIGRLESELGML 394
                                    45688888755389*************************976379***********944456689999******999998 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.55
                        DUF2730  33 edleklaekveendkrlteletkvenL 59 
                                    ++l+ ++e++ + ++r++ l+ k+e+L
  gi|119719441|ref|YP_919936.1| 447 KELKDVEESIGKLRERINVLKKKLEDL 473
                                    345555555555555555555555544 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.014
                        DUF2730  51 eletkvenLPtakdlekLkllladlrgelkaleaevr 87 
                                    +l t+ ++LP  ++++kL+ +++ lr el+ le++ +
  gi|119719441|ref|YP_919936.1| 534 RLRTSYSKLPLLDEIKKLEQEVSSLRSELQRLEPQYN 570
                                    67788899**********************9998865 PP

  == domain 5  score: -0.6 bits;  conditional E-value: 4.1
                        DUF2730  36 eklaekveendkrlteletkve 57 
                                    e l  ++e++++rl+ +   ++
  gi|119719441|ref|YP_919936.1| 580 EALSREIEDKRHRLEGIRKDID 601
                                    3344444455555544444443 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.6     0.067        23      26      82 ..     222     277 ..     207     299 .. 0.64
   2 ?    4.4   0.3       0.1        34      43      94 ..     318     369 ..     288     373 .. 0.49
   3 ?    5.1   0.3     0.062        21       9      77 ..     319     393 ..     312     413 .. 0.59
   4 ?    9.9   0.7    0.0021      0.72      42      81 ..     437     476 ..     430     482 .. 0.89
   5 ?    4.5   2.2     0.095        32       7      84 ..     485     571 ..     479     590 .. 0.62
   6 ?    4.0   0.8      0.13        46      15      55 ..     575     615 ..     569     655 .. 0.71
   7 ?    0.1   0.1       2.1   7.3e+02       5      43 ..     620     656 ..     615     668 .. 0.66

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.067
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHH CS
                     Laminin_II  26 lentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqle 82 
                                    l+++ ++l++++++ +e + +++++ k ++d r+ vk +   ++ L+  l+el+ + 
  gi|119719441|ref|YP_919936.1| 222 LKKEASDLEGAAKKYQELKSELNAKEKLLEDLRDRVKGVL-SLDALVVGLEELRDKL 277
                                    5666677777777777777777777777777777777653.3455555555554443 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.1
                                    XXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH...HHHHHHH CS
                     Laminin_II  43 tnekvkdankairdArrsvkkLeklapqLldklkelkqleeassslsdnise 94 
                                     +e  +++ + i+  + +v   ek++ +++++l  l+++ +  +    +i++
  gi|119719441|ref|YP_919936.1| 318 LDEIYSEKYREIKGLSAQVEVYEKQLREIESRLVGLEEHVSDYERAESEIEK 369
                                    3333334444444444444444444444444444444444444444445555 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.062
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX......XXXXX--TTTTTGGGHHH CS
                     Laminin_II   9 netakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArr......svkkLeklapqLldklke 77 
                                    +e+ +e  + +++ls+++e  +++l ei++ +   +e+v+d+ +a  + ++         kL +++ +L++ l  
  gi|119719441|ref|YP_919936.1| 319 DEIYSEKYREIKGLSAQVEVYEKQLREIESRLVGLEEHVSDYERAESEIEKikseygDENKLREEIGRLESELGM 393
                                    566666667778888888888888888888888888888877666555443111111334455555555555444 PP

  == domain 4  score: 9.9 bits;  conditional E-value: 0.0021
                                    XXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHH CS
                     Laminin_II  42 etnekvkdankairdArrsvkkLeklapqLldklkelkql 81 
                                     + ekv+++ k ++d+++s+ kL + +++L +kl+ l++ 
  gi|119719441|ref|YP_919936.1| 437 WVREKVSKSVKELKDVEESIGKLRERINVLKKKLEDLREY 476
                                    57899******************************99875 PP

  == domain 5  score: 4.5 bits;  conditional E-value: 0.095
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.........XXXX--TTTTTGGGHHH CS
                     Laminin_II   7 eanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrs.........vkkLeklapqLldklke 77 
                                    +a e  +  le  ++l++ l+ ++e+l+++++ +  + +++k   +     r+s         +kkLe+++  L + l++
  gi|119719441|ref|YP_919936.1| 485 AAYEEYQRLLEERKNLQAALDAEREELERAKSGLSVIGAELKVVREDFLRLRTSysklplldeIKKLEQEVSSLRSELQR 564
                                    67777788888888888888888888888888888888888866666665555511111111155556666666666555 PP

                                    HHHHHHH CS
                     Laminin_II  78 lkqleea 84 
                                    l+ + ++
  gi|119719441|ref|YP_919936.1| 565 LEPQYNK 571
                                    5555444 PP

  == domain 6  score: 4.0 bits;  conditional E-value: 0.13
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                     Laminin_II  15 vleqlaplsqnlentkeklseinrsveetnekvkdankair 55 
                                     ++ +++ls ++e  +  l++i+++++e  + ++++ + ++
  gi|119719441|ref|YP_919936.1| 575 LEKRIEALSREIEDKRHRLEGIRKDIDEKRAMLESFEERLA 615
                                    57788899999999999999999999999888888876554 PP

  == domain 7  score: 0.1 bits;  conditional E-value: 2.1
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                     Laminin_II   5 aaeanetakevleqlaplsqnlentkeklseinrsveet 43 
                                    ++e++ ++  v+e l +++++l   ++k+ e+n+ v+e+
  gi|119719441|ref|YP_919936.1| 620 LEEVLGKVRRVKEALIEVHADLR--SQKIMELNKVVNEI 656
                                    45666677777777777777665..45666666665555 PP

>> DUF1952  Domain of unknown function (DUF1952)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1       1.9   6.3e+02      51      66 ..      72      87 ..      59      92 .. 0.70
   2 ?   10.6   0.2    0.0012       0.4      32      58 ..     668     695 ..     657     704 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.9
                        DUF1952 51 leveveGeeaerWaer 66
                                   le+eveGe   r   r
  gi|119719441|ref|YP_919936.1| 72 LELEVEGEGVYRIERR 87
                                   6777777776666555 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0012
                        DUF1952  32 vvrfreleP.lkvGslrisrleveveGe 58 
                                     vr r + P ++vG+ +i ++ev v+Ge
  gi|119719441|ref|YP_919936.1| 668 EVRVRVVSPsRRVGGRSIYQVEVKVGGE 695
                                    59*****98679***************7 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   0.00011     0.037      21      57 ..      17      50 ..       2     126 .. 0.77
   2 ?   -2.1   0.1       7.3   2.5e+03     156     197 ..     556     600 ..     545     610 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00011
                         AAA_27 21 fsaeeadlhliyGpNEAGKstalrAisdllfGipert 57
                                   f    +++++i Gp  +GKs++l+A++  l+G +   
  gi|119719441|ref|YP_919936.1| 17 F---GDGVTVIAGPVGSGKSSLLSAVEYALYGTDSYI 50
                                   4...37899***********************87543 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 7.3
                         AAA_27 156 aslrevleaLeaeadelfkprkskk...rainealeeleeakkel 197
                                    +slr+ l++Le + +++ + +k+ +   r+i +++++le  +k +
  gi|119719441|ref|YP_919936.1| 556 SSLRSELQRLEPQYNKYLELEKRIEalsREIEDKRHRLEGIRKDI 600
                                    456666666666666665555554433455555555555555555 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       8.9     3e+03      88     117 ..     228     257 ..     203     272 .. 0.58
   2 ?    6.3   0.2     0.027       9.2      41     120 ..     309     394 ..     295     398 .. 0.67
   3 ?    5.7   0.1     0.042        14      83     120 ..     436     473 ..     400     477 .. 0.79
   4 ?    4.8   0.2      0.08        27      55     120 ..     491     558 ..     486     569 .. 0.68
   5 ?    7.5   2.0     0.012         4      39     118 ..     551     615 ..     545     632 .. 0.52

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 8.9
                        DUF1664  88 evtevredlseigedvesvkeavegleskl 117
                                    +++ + ++ +e+++++++ +++ e+l  ++
  gi|119719441|ref|YP_919936.1| 228 DLEGAAKKYQELKSELNAKEKLLEDLRDRV 257
                                    333334444444444444444444444333 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.027
                        DUF1664  41 davesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevte...vredlseigedv...esvkeavegle 114
                                    +a e+v +ql++++++  +  + Ls++++  +k+l e +     ++e+v++   +++++++i+++    ++++e +  le
  gi|119719441|ref|YP_919936.1| 309 SAFERVFHQLDEIYSEKYREIKGLSAQVEVYEKQLREIESRLVGLEEHVSDyerAESEIEKIKSEYgdeNKLREEIGRLE 388
                                    57778888888888888888888888888888888888888888888877611134455555554322256666666666 PP

                        DUF1664 115 skleri 120
                                    s+l  +
  gi|119719441|ref|YP_919936.1| 389 SELGML 394
                                    666655 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.042
                        DUF1664  83 keikeevtevredlseigedvesvkeavegleskleri 120
                                      ++e+v++  ++l++++e + +++e ++ l++kle++
  gi|119719441|ref|YP_919936.1| 436 DWVREKVSKSVKELKDVEESIGKLRERINVLKKKLEDL 473
                                    55677777777788888888888888888888887776 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.08
                        DUF1664  55 eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvk..eavegleskleri 120
                                    + l + +++L++ +d   ++l+  k   + i +e++ vred  ++++  +++   + +++le++++++
  gi|119719441|ref|YP_919936.1| 491 QRLLEERKNLQAALDAEREELERAKSGLSVIGAELKVVREDFLRLRTSYSKLPllDEIKKLEQEVSSL 558
                                    66778889999999999999999999999999999999998888776555432113344444444444 PP

  == domain 5  score: 7.5 bits;  conditional E-value: 0.012
                        DUF1664  39 lsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskle 118
                                    l++ v+s+ ++l+++  + ++   +L++ri+ + +++++  +               l+ i++d+++ +++ e++e++l+
  gi|119719441|ref|YP_919936.1| 551 LEQEVSSLRSELQRLEPQYNK-YLELEKRIEALSREIEDKRHR--------------LEGIRKDIDEKRAMLESFEERLA 615
                                    333344444444444333332.234555555555555555555..............55555555555555555555543 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0    0.0004      0.13      25      86 ..     695     749 ..     681     752 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.0004
                        SbcCD_C  25 elsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatlle 86 
                                    e++  s++lS G+k +++ l l+ +l  l+++      ++++++LDE   ++D+   a+ll+
  gi|119719441|ref|YP_919936.1| 695 EWYPYSSRLSDGQK-TVVFLSLLIGLNRLLNK------RVGFLVLDEPVPNVDDAIKASLLK 749
                                    3578899*******.999************99......69*************998888876 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.4     0.039        13      35     102 ..     194     261 ..     182     278 .. 0.78
   2 ?    7.9   1.1    0.0051       1.7      39      97 ..     315     373 ..     301     414 .. 0.92
   3 ?    8.3   0.5    0.0038       1.3      20      98 ..     437     518 ..     424     534 .. 0.52
   4 ?    4.8   4.3     0.043        15      44     109 ..     546     614 ..     537     657 .. 0.60

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.039
                        DUF3450  35 sqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeierelvpll 102
                                    s+++ + l +e + l++e+ + ++ le l+++ + le   ++ ++  ++l+ + + +e ++++++ +l
  gi|119719441|ref|YP_919936.1| 194 SEENLNILREEERRLEQELIEGERLLEGLKKEASDLEGAAKKYQELKSELNAKEKLLEDLRDRVKGVL 261
                                    67778888888888999999999999999999999998888888888888888888888888886554 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0051
                        DUF3450  39 idklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeiere 97 
                                      +ld+  +e  +e++ l++++e  e++ ++ e+ +  +e+ +++ e+  +eie+i++e
  gi|119719441|ref|YP_919936.1| 315 FHQLDEIYSEKYREIKGLSAQVEVYEKQLREIESRLVGLEEHVSDYERAESEIEKIKSE 373
                                    568888889999999999999999999999999999******************99987 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0038
                        DUF3450  20 qalkeaekavaaaaqsqkkidklddekqellaeyralkeelesl...evyneqlerlvasqeqeiasleeqieeieeier 96 
                                     ++++ +k+v++ +++++ i kl +  + l++++++l+e +  l   e+  e+++rl+++ ++  a l+ + ee+e+ ++
  gi|119719441|ref|YP_919936.1| 437 WVREKVSKSVKELKDVEESIGKLRERINVLKKKLEDLREYKLTLinyEAAYEEYQRLLEERKNLQAALDAEREELERAKS 516
                                    55555555666666666666666665555555555544433333000333334444444444444444444444444444 PP

                        DUF3450  97 el 98 
                                    +l
  gi|119719441|ref|YP_919936.1| 517 GL 518
                                    44 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.043
                        DUF3450  44 dekqellaeyralkeeleslevyneq...lerlvasqeqeiasleeqieeieeierelvpllekmidrL 109
                                    de ++l++e+ +l++el++le + ++   le+ ++++ +ei++ + ++e i++  +e   +le+  +rL
  gi|119719441|ref|YP_919936.1| 546 DEIKKLEQEVSSLRSELQRLEPQYNKyleLEKRIEALSREIEDKRHRLEGIRKDIDEKRAMLESFEERL 614
                                    455566666666666666666433321113455555555555555555555554444444444444444 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7  10.0       2.1     7e+02     187     240 ..     432     518 ..     193     532 .. 0.59
   2 ?    9.1   1.3    0.0022      0.76     138     214 ..     544     622 ..     523     651 .. 0.61

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 2.1
                        DUF4407 187 e...................kkaqldaaqaelaelkakld..............atarlaalraelaeleaerakeraas 233
                                    e                    ++ + +++++++ lk+kl+              a ++ ++l +e++ l+a++++er++ 
  gi|119719441|ref|YP_919936.1| 432 EefldwvrekvsksvkelkdVEESIGKLRERINVLKKKLEdlreykltlinyeaAYEEYQRLLEERKNLQAALDAEREEL 511
                                    12222222222222222222555555555555555555555656556555555555555555555555555555555555 PP

                        DUF4407 234 qaaaaad 240
                                    ++a+++ 
  gi|119719441|ref|YP_919936.1| 512 ERAKSGL 518
                                    5555555 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0022
                        DUF4407 138 leaqiaalqaeidaaearldalraeaqkeldgtk.........gtgttgvaGkgpaakekkaqldaaqaelaelkaklda 208
                                    l ++i++l++e+++++++l++l+ +++k l+ +k          ++  + +G  +  +ek+a+l+  +++la        
  gi|119719441|ref|YP_919936.1| 544 LLDEIKKLEQEVSSLRSELQRLEPQYNKYLELEKriealsreiEDKRHRLEGIRKDIDEKRAMLESFEERLAR------- 616
                                    568999*********************9999855554443333222233333333333333333333333333....... PP

                        DUF4407 209 tarlaa 214
                                    + rl++
  gi|119719441|ref|YP_919936.1| 617 ERRLEE 622
                                    333333 PP

>> GCN5L1  GCN5-like protein 1 (GCN5L1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1       7.5   2.5e+03      55      72 ..     328     345 ..     309     389 .. 0.67
   2 ?    7.6   0.2     0.012       4.1      14      71 ..     414     471 ..     405     476 .. 0.77
   3 ?   -1.6   0.1       8.5   2.9e+03      44      66 ..     485     507 ..     482     530 .. 0.74
   4 ?   12.0   0.9   0.00052      0.18      49     111 ..     548     610 ..     497     613 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 7.5
                         GCN5L1  55 eakalqanvakfakqtdq 72 
                                    e+k l+a+v+ ++kq ++
  gi|119719441|ref|YP_919936.1| 328 EIKGLSAQVEVYEKQLRE 345
                                    455555555555555433 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.012
                         GCN5L1  14 eeqekakkeaiesaaaltealvdklnsgvaeayanqkklekeakalqanvakfakqtd 71 
                                    e ++k  +e+ +  ++l+e+ +d ++++v+++ ++ k +e+ + +l+++++ ++k+ +
  gi|119719441|ref|YP_919936.1| 414 EVAKKGEAECYVCGNRLSEEFLDWVREKVSKSVKELKDVEESIGKLRERINVLKKKLE 471
                                    5555666777778888888888888888888888888888888888888888888754 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 8.5
                         GCN5L1  44 eayanqkklekeakalqanvakf 66 
                                    +ay++ ++l +e k+lqa++++ 
  gi|119719441|ref|YP_919936.1| 485 AAYEEYQRLLEERKNLQAALDAE 507
                                    57888888888888888776654 PP

  == domain 4  score: 12.0 bits;  conditional E-value: 0.00052
                         GCN5L1  49 qkklekeakalqanvakfakqtdqWlalvesfnsalkeiGDvenWaktienDlksitealeyv 111
                                     kkle+e+ +l++++++++ q +++l+l ++++   +ei D ++  + i +D+ +  + le  
  gi|119719441|ref|YP_919936.1| 548 IKKLEQEVSSLRSELQRLEPQYNKYLELEKRIEALSREIEDKRHRLEGIRKDIDEKRAMLESF 610
                                    59************************************************9999888888765 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.2    0.0012      0.39       2      19 ..      21      38 ..      20      45 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0012
                                   EEEEEESTTCCHHHHHHH CS
                           cobW  2 vtvltGflGsGKTtLlnh 19
                                   vtv++G++GsGK++Ll++
  gi|119719441|ref|YP_919936.1| 21 VTVIAGPVGSGKSSLLSA 38
                                   89**************86 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   1.3      0.35   1.2e+02      36      85 ..     201     253 ..     164     293 .. 0.57
   2 ?   10.4  10.3     0.002      0.68      27     148 ..     323     474 ..     314     484 .. 0.59
   3 ?    9.1  13.4    0.0048       1.6      31     163 ..     488     619 ..     471     620 .. 0.76
   4 ?    7.8   5.2     0.013       4.2      31     111 ..     570     649 ..     567     680 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.35
                           Fez1  36 lkaqlrelrakleekeeeikeleesleektle...levcenelqrkkseaell 85 
                                    l+ + r l+++l e e+ ++ l++++++ +      +++++el+ k++  e l
  gi|119719441|ref|YP_919936.1| 201 LREEERRLEQELIEGERLLEGLKKEASDLEGAakkYQELKSELNAKEKLLEDL 253
                                    33333333333333333333333333332222000122222222222222222 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.002
                           Fez1  27 tqklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkse...aellrekvekleeelkelre.. 101
                                    ++k  ei  l aq+   +++l+e e+++  lee++++ ++     e+e+++ kse   ++ lre++++le+el  l++  
  gi|119719441|ref|YP_919936.1| 323 SEKYREIKGLSAQVEVYEKQLREIESRLVGLEEHVSDYERA----ESEIEKIKSEygdENKLREEIGRLESELGMLQRrs 398
                                    67888999999999999999999999999999888765444....44444433321115667777888888887774411 PP

                           Fez1 102 elselsleeeeaa..............................lesdeakaqrqeaeeleelkreverlraeLkeer 148
                                    el++  + + + +                              + s+++k+ ++ +e++++l+++++ l+++L+  r
  gi|119719441|ref|YP_919936.1| 399 ELERCVS-SVRRVlaeevakkgeaecyvcgnrlseefldwvreKVSKSVKELKDVEESIGKLRERINVLKKKLEDLR 474
                                    3443322.222223455555555556777777666665444433333334444445666666666666666665544 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0048
                           Fez1  31 seivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellr..ekvekleeelkelreelselsl 108
                                    +e+  l  + ++l+a+l+++ ee++++++ l+   +el+v+ +++ r +++ + l   ++++kle+e+++lr+el++l++
  gi|119719441|ref|YP_919936.1| 488 EEYQRLLEERKNLQAALDAEREELERAKSGLSVIGAELKVVREDFLRLRTSYSKLPllDEIKKLEQEVSSLRSELQRLEP 567
                                    5667777889999999*99999999****************9998888655554322266***************99776 PP

                           Fez1 109 eeeeaalesdeakaqrqeaeeleelkreverlraeLkeerqkkeeqassFeqERr 163
                                    + ++  le ++ + +   ++e+e+ ++++e +r+ + e+r   e+ ++  ++ERr
  gi|119719441|ref|YP_919936.1| 568 QYNK-YLELEK-RIEA-LSREIEDKRHRLEGIRKDIDEKRAMLESFEERLARERR 619
                                    5443.333333.3333.34678888888888888888888888888888888886 PP

  == domain 4  score: 7.8 bits;  conditional E-value: 0.013
                           Fez1  31 seivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelselslee 110
                                    + +++l  ++  l+ ++e+k ++++ +++ ++ek + le  e++l+r++  +e+l + v++++e l e++ +l++++  e
  gi|119719441|ref|YP_919936.1| 570 NKYLELEKRIEALSREIEDKRHRLEGIRKDIDEKRAMLESFEERLARERRLEEVLGK-VRRVKEALIEVHADLRSQKIME 648
                                    67899999999**************************************99999987.9999999999999998876655 PP

                           Fez1 111 e 111
                                     
  gi|119719441|ref|YP_919936.1| 649 L 649
                                    4 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.2    0.0046       1.6      88     152 ..     194     261 ..     187     282 .. 0.68
   2 ?   -1.0   0.1       3.6   1.2e+03      62     119 ..     334     363 ..     305     418 .. 0.62
   3 ?    6.0   1.3     0.025       8.6      81     164 ..     438     534 ..     429     542 .. 0.54
   4 ?    5.8   0.5     0.031        10      82     159 ..     548     624 ..     540     635 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0046
                         DUF745  88 seanakaaakaakqaqqqlealkallkaakenlenaeqva...agaqqelaektqlleaAkkRveeLk 152
                                    se+n+++ ++  +  +q+l   ++ll+  k++++++e +a   ++ ++el++k++lle+ + Rv+ + 
  gi|119719441|ref|YP_919936.1| 194 SEENLNILREEERRLEQELIEGERLLEGLKKEASDLEGAAkkyQELKSELNAKEKLLEDLRDRVKGVL 261
                                    677777777777777777755555555555555555555511166778***************98765 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3.6
                         DUF745  62 qlveqleqelreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaaken 119
                                    + ve +e++lre e+ +   +                            + +  ++ +
  gi|119719441|ref|YP_919936.1| 334 AQVEVYEKQLREIESRLVGLE----------------------------EHVSDYERA 363
                                    334455555555554433222............................222222222 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.025
                         DUF745  81 ekkslqsseanakaaakaakqaqqqlealkallkaake...nlenaeqvaagaqqelaektql..........leaAkkR 147
                                    + +++++s + +k ++++  + ++ +++lk+ l+  +e   +l n+e++ ++ q+ l+e+++l          le Ak+ 
  gi|119719441|ref|YP_919936.1| 438 VREKVSKSVKELKDVEESIGKLRERINVLKKKLEDLREyklTLINYEAAYEEYQRLLEERKNLqaaldaereeLERAKSG 517
                                    55566666666666666666666666666666544333111566666666666666666666622222222225556666 PP

                         DUF745 148 veeLkkqlkearkdlek 164
                                    +  +  +lk +r+d+ +
  gi|119719441|ref|YP_919936.1| 518 LSVIGAELKVVREDFLR 534
                                    66666666666666655 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.031
                         DUF745  82 kkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaektqlleaAkkRveeLkkqlkear 159
                                     k+l++  +++++  +  +   +++  l++ ++a + ++e+ ++  +g  ++++ek+++le+ ++R+++ +++l+e+ 
  gi|119719441|ref|YP_919936.1| 548 IKKLEQEVSSLRSELQRLEPQYNKYLELEKRIEALSREIEDKRHRLEGIRKDIDEKRAMLESFEERLAR-ERRLEEVL 624
                                    55666666666666666777778888999999999***************************9999876.55555555 PP

>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.4      0.74   2.5e+02      37     105 ..     196     263 ..     185     283 .. 0.63
   2 ?    1.1   1.0       0.2        69      60     119 ..     318     377 ..     288     392 .. 0.62
   3 ?   14.1   2.6   2.5e-05    0.0084      30     130 ..     395     508 ..     391     535 .. 0.73
   4 ?    8.8   3.0   0.00098      0.33      74     185 ..     544     661 ..     526     685 .. 0.65

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.74
                     V_ATPase_I  37 rklrfleeeieklekavikeeeaeesleapeekeldeleeelekleeelkelnenleklkkelnelvel 105
                                    ++l++l+ee ++le++ i+ e+   +  ++e+++l+   ++ ++l++el+  ++ le+l+++++ ++ l
  gi|119719441|ref|YP_919936.1| 196 ENLNILREEERRLEQELIEGER-LLEGLKKEASDLEGAAKKYQELKSELNAKEKLLEDLRDRVKGVLSL 263
                                    5566666666665555555555.3334445555666666777777777777777777776666665555 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.2
                     V_ATPase_I  60 eesleapeekeldeleeelekleeelkelnenleklkkelnelvelkavlekakefleee 119
                                     ++  +++ +e++ l++++e +e++l+e+++ l  l++++++ + +++ +ek+k+ + +e
  gi|119719441|ref|YP_919936.1| 318 LDEIYSEKYREIKGLSAQVEVYEKQLREIESRLVGLEEHVSDYERAESEIEKIKSEYGDE 377
                                    344555666677777777777777777777777777777777776666666666555443 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 2.5e-05
                     V_ATPase_I  30 rrcdemerklrfleeeieklekavikeeea..............eesleapeekeldeleeelekleeelkelnenlekl 95 
                                    +r  e+er ++ +++ ++++  ++ ++e                ++++ +++ kel+++ee++ kl e+++ l+++le+l
  gi|119719441|ref|YP_919936.1| 395 QRRSELERCVSSVRRVLAEEVAKKGEAE-CyvcgnrlseefldwVREKVSKSVKELKDVEESIGKLRERINVLKKKLEDL 473
                                    5666666666555555554222222222.135566899999999889999999*************************** PP

                     V_ATPase_I  96 kkelnelvelkavlekakefleeeeeeeeeeesee 130
                                    ++ + +l++++a +e+ +++lee+++ +++  +e+
  gi|119719441|ref|YP_919936.1| 474 REYKLTLINYEAAYEEYQRLLEERKNLQAALDAER 508
                                    *********************98744444322222 PP

  == domain 4  score: 8.8 bits;  conditional E-value: 0.00098
                     V_ATPase_I  74 leeelekleeelkelnenleklkkelnelvelkavlekakefleee.eeeeeeeeseeeeeekeeeeeeeseeeeeeell 152
                                    l +e++kle+e+++l+++l++l+ ++n+ +el++ +e  ++ +e++ ++ e  +++ +e    ++++ e++ee+ ++e +
  gi|119719441|ref|YP_919936.1| 544 LLDEIKKLEQEVSSLRSELQRLEPQYNKYLELEKRIEALSREIEDKrHRLEGIRKDIDE----KRAMLESFEERLARERR 619
                                    5678999*************************999999999998763222222222222....22222222222221111 PP

                     V_ATPase_I 153 eeeee............lsfvaGvikrekveaferilwralrgnl 185
                                        e            l  v   ++++k++++++++  ++rg  
  gi|119719441|ref|YP_919936.1| 620 L---EevlgkvrrvkeaLIEVHADLRSQKIMELNKVVNEIVRGIY 661
                                    1...01223334444446668888888888888888888888854 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   3.2      0.18        61      19      87 ..     195     258 ..     194     260 .. 0.90
   2 ?    0.6   0.1       2.3   7.9e+02      54      79 ..     332     357 ..     304     371 .. 0.69
   3 ?    1.2   0.1       1.5   5.1e+02      27      56 ..     375     405 ..     360     412 .. 0.77
   4 ?   13.5   1.2   0.00021     0.071       2      51 ..     429     478 ..     428     502 .. 0.86
   5 ?    0.6   0.3       2.3   7.6e+02      23      47 ..     491     515 ..     484     521 .. 0.83
   6 ?    9.4   4.2    0.0042       1.4      21      87 ..     547     615 ..     544     616 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.18
                Snapin_Pallidin  19 deklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqklkkRae 87 
                                    +e+l+ lr++ + L ++l +  + L+ l+++++     dl+  akK +++k ++++ ++ l+ l++R++
  gi|119719441|ref|YP_919936.1| 195 EENLNILREEERRLEQELIEGERLLEGLKKEAS-----DLEGAAKKYQELKSELNAKEKLLEDLRDRVK 258
                                    578889999999999999999999998888777.....*****************************86 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 2.3
                Snapin_Pallidin  54 vlpdlkeyakKLvnikkrmsslnerl 79 
                                    + ++++ y k L++i+ r+  l+e +
  gi|119719441|ref|YP_919936.1| 332 LSAQVEVYEKQLREIESRLVGLEEHV 357
                                    44567777777777777776666655 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 1.5
                Snapin_Pallidin  27 qsQeeLleqldrlnekLkeleeaqe.aevlp 56 
                                       ++L+e++ rl ++L  l++  e + +++
  gi|119719441|ref|YP_919936.1| 375 GDENKLREEIGRLESELGMLQRRSElERCVS 405
                                    56789************99999888555554 PP

  == domain 4  score: 13.5 bits;  conditional E-value: 0.00021
                Snapin_Pallidin   2 aLaegllellepkldeldeklkelrqsQeeLleqldrlnekLkeleeaqe 51 
                                     L+e++l+ +  k+ +  ++lk++++s  +L+e+++ l++kL++l+e++ 
  gi|119719441|ref|YP_919936.1| 429 RLSEEFLDWVREKVSKSVKELKDVEESIGKLRERINVLKKKLEDLREYKL 478
                                    69*******************************************99876 PP

  == domain 5  score: 0.6 bits;  conditional E-value: 2.3
                Snapin_Pallidin  23 kelrqsQeeLleqldrlnekLkele 47 
                                    + l ++ + L++ ld ++e+L++++
  gi|119719441|ref|YP_919936.1| 491 QRLLEERKNLQAALDAEREELERAK 515
                                    667888899************9876 PP

  == domain 6  score: 9.4 bits;  conditional E-value: 0.0042
                Snapin_Pallidin  21 klkelrqsQeeLleqldrlnekLkeleeaqe..aevlpdlkeyakKLvnikkrmsslnerlqklkkRae 87 
                                    ++k+l+q+ + L+++l+rl  +++++ e+++  +++  +++  + +L  i+k++ +    l++ ++R+ 
  gi|119719441|ref|YP_919936.1| 547 EIKKLEQEVSSLRSELQRLEPQYNKYLELEKriEALSREIEDKRHRLEGIRKDIDEKRAMLESFEERLA 615
                                    6899999999*********************95555668**************************9997 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.6      0.71   2.4e+02      14      66 ..     207     259 ..     195     284 .. 0.68
   2 ?    1.8   0.2      0.61   2.1e+02      33      66 ..     326     359 ..     294     398 .. 0.52
   3 ?    6.8   0.7     0.017       5.7       3      78 ..     447     508 ..     430     535 .. 0.46
   4 ?    9.8   1.3     0.002      0.66      10      73 ..     546     612 ..     543     631 .. 0.81
   5 ?    0.4   0.0       1.6   5.5e+02      26      87 ..     620     679 ..     604     687 .. 0.67

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.71
                          Sec34  14 elleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeiee 66 
                                    +l +++ e +++Le l+++ ++ +   ++ +e   +l +++k le+l + ++ 
  gi|119719441|ref|YP_919936.1| 207 RLEQELIEGERLLEGLKKEASDLEGAAKKYQELKSELNAKEKLLEDLRDRVKG 259
                                    55555556666666666666666666666666666666666666666666654 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.61
                          Sec34  33 fksvsektsslheaceqlleeqkrleelaeeiee 66 
                                    +++++  + +++   +ql e ++rl  l e +++
  gi|119719441|ref|YP_919936.1| 326 YREIKGLSAQVEVYEKQLREIESRLVGLEEHVSD 359
                                    3333333333333333333333333333333322 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.017
                          Sec34   3 dqLeskeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLkyFeeldpit 78 
                                    ++L++ ee++ +l e+++ ++++Le+l+e +k    + ++  e+ ++llee+k+l+   +                
  gi|119719441|ref|YP_919936.1| 447 KELKDVEESIGKLRERINVLKKKLEDLRE-YKLTLINYEAAYEEYQRLLEERKNLQAALD-------------AER 508
                                    23333333333333333333333333332.233333333333333333333333333333.............333 PP

  == domain 4  score: 9.8 bits;  conditional E-value: 0.002
                          Sec34  10 eecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieek...LkyFee 73 
                                    +e+++l ++++++ ++L+ le ++++  e  +++++ + ++ ++++rle + ++i+ek   L+ Fee
  gi|119719441|ref|YP_919936.1| 546 DEIKKLEQEVSSLRSELQRLEPQYNKYLELEKRIEALSREIEDKRHRLEGIRKDIDEKramLESFEE 612
                                    5788999999999999999999999999999999999999999999999999999987333555555 PP

  == domain 5  score: 0.4 bits;  conditional E-value: 1.6
                          Sec34  26 LeeleekfksvsektsslheaceqlleeqkrleelaeeieekLkyFeeldpitrkLnspgss 87 
                                    Lee+  k+++v+e   ++h++     ++  +l+++++ei   +  +++++++  +  sp+  
  gi|119719441|ref|YP_919936.1| 620 LEEVLGKVRRVKEALIEVHADLR--SQKIMELNKVVNEIVRGIYPYTDIEEVRVRVVSPSRR 679
                                    44445555555555555544333..3566789999999999999999999998888877765 PP

>> T3SSipB  Type III cell invasion protein SipB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.2      0.25        84      51      93 ..     218     260 ..     204     284 .. 0.85
   2 ?    0.8   0.0       1.8     6e+02      56     109 ..     316     369 ..     294     383 .. 0.76
   3 ?    2.8   0.6      0.44   1.5e+02      61     137 ..     441     514 ..     428     522 .. 0.55
   4 ?    3.8   1.2      0.22        74      75     111 ..     547     583 ..     452     629 .. 0.61

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.25
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT- CS
                        T3SSipB  51 alseakgatddleaaiekadqaksaadaatkkvdeaqkrlkeL 93 
                                    +l+  k+ + dle a++k++++ks+ +a +k +++   r+k++
  gi|119719441|ref|YP_919936.1| 218 LLEGLKKEASDLEGAAKKYQELKSELNAKEKLLEDLRDRVKGV 260
                                    55566677889999************99999999999988764 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 1.8
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---------CHHHHHHH CS
                        T3SSipB  56 kgatddleaaiekadqaksaadaatkkvdeaqkrlkeLaPdePekakleaaeqQ 109
                                    +++ + + ++  +++ + ++++  +k++ e+  rl +L+    ++ ++e + + 
  gi|119719441|ref|YP_919936.1| 316 HQLDEIYSEKYREIKGLSAQVEVYEKQLREIESRLVGLEEHVSDYERAESEIEK 369
                                    445667888888999999999999999999999999998877778777776554 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.44
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---------CHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHH CS
                        T3SSipB  61 dleaaiekadqaksaadaatkkvdeaqkrlkeLaPdePekakleaaeqQagaa.adalqadealqKkldaasklseka 137
                                    ++ ++++++++++  + ++ ++++  +k+l++L     e++    + + a +  +  l+  ++lq +lda +   e+a
  gi|119719441|ref|YP_919936.1| 441 KVSKSVKELKDVEESIGKLRERINVLKKKLEDL----REYKLTLINYEAAYEEyQRLLEERKNLQAALDAEREELERA 514
                                    556667777777777777777777777777777....22222222222222222344444555555555555444444 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.22
                                    HHHHHHHHHHHHHHHHTT---------CHHHHHHHHH CS
                        T3SSipB  75 aadaatkkvdeaqkrlkeLaPdePekakleaaeqQag 111
                                    +++++++ v+     l+ L+P+  ++ +le+  + + 
  gi|119719441|ref|YP_919936.1| 547 EIKKLEQEVSSLRSELQRLEPQYNKYLELEKRIEALS 583
                                    3444444444444466666666666666655544444 PP

>> HemX  HemX, putative uroporphyrinogen-III C-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.3      0.13        45      49      99 ..     210     260 ..     191     286 .. 0.50
   2 ?    0.6   0.1       0.8   2.7e+02      43      78 ..     335     370 ..     307     414 .. 0.45
   3 ?    3.3   0.4      0.12        41      33      94 ..     452     513 ..     437     530 .. 0.81
   4 ?   10.9   0.6   0.00059       0.2      36     109 ..     547     620 ..     537     623 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.13
                           HemX  49 qqlaqveaekeqkqeleerlqqlaeklealekeleqlqkqleelqqqlskv 99 
                                    q+l + e + e  ++ +++l+ +a+k ++l++el++++k le l+++++ v
  gi|119719441|ref|YP_919936.1| 210 QELIEGERLLEGLKKEASDLEGAAKKYQELKSELNAKEKLLEDLRDRVKGV 260
                                    333332233333333344445555555555555555555555555555544 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.8
                           HemX  43 qlaaleqqlaqveaekeqkqeleerlqqlaekleal 78 
                                    q++  e+ql ++e+     +e  ++++ +++++e+ 
  gi|119719441|ref|YP_919936.1| 335 QVEVYEKQLREIESRLVGLEEHVSDYERAESEIEKI 370
                                    222222222222222222222222222222222222 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.12
                           HemX  33 ltaevaelqqqlaaleqqlaqveaekeqkqeleerlqqlaeklealekeleqlqkqleelqq 94 
                                     + ++ +l+++++ l+++l+ +++ k +  + e+++++ +  le++++++++l+++ eel++
  gi|119719441|ref|YP_919936.1| 452 VEESIGKLRERINVLKKKLEDLREYKLTLINYEAAYEEYQRLLEERKNLQAALDAEREELER 513
                                    44556889999999999999999999999999999999999999998888888888887765 PP

  == domain 4  score: 10.9 bits;  conditional E-value: 0.00059
                           HemX  36 evaelqqqlaaleqqlaqveaekeqkqeleerlqqlaeklealekeleqlqkqleelqqqlskvsgaerkdWlL 109
                                    e+++l+q++++l ++l+++e + ++  ele+r+++l+ ++e+++++le   k+++e ++ l+  + + +++++L
  gi|119719441|ref|YP_919936.1| 547 EIKKLEQEVSSLRSELQRLEPQYNKYLELEKRIEALSREIEDKRHRLEGIRKDIDEKRAMLESFEERLARERRL 620
                                    45677777888888888777777777788888888888888888888888888887777777777776666666 PP

>> Spc29  Spindle Pole Component 29
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.4      0.34   1.1e+02      85     167 ..     279     363 ..     267     394 .. 0.62
   2 ?    4.5   1.3      0.08        27      80     153 ..     407     483 ..     395     513 .. 0.72
   3 ?   12.7   1.6   0.00025     0.086      79     196 ..     532     663 ..     521     684 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.34
                          Spc29  85 ReglsrkPppkissp..glapsdesrldsiyssvkki.velekklddqkleIkeLkreleqqrtvnseLqekvaeleeev 161
                                    R     +Pp+k+ +   g   s e +l  ++s  +++  +l+ +  ++  eIk L  ++e  +   +e+ +++  lee+v
  gi|119719441|ref|YP_919936.1| 279 RAAEKLLPPSKLIKEieGIEVS-EYNLREVFSAFERVfHQLDEIYSEKYREIKGLSAQVEVYEKQLREIESRLVGLEEHV 357
                                    4444444666653330033333.334666666665541344444445556888888888888888888888888888888 PP

                          Spc29 162 krlaal 167
                                      ++  
  gi|119719441|ref|YP_919936.1| 358 SDYERA 363
                                    665544 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.08
                          Spc29  80 LRrQLReglsrkPppkisspglapsdesrldsiyssvkkivelek....klddqkleIkeLkreleqqrtvnseLqek 153
                                     Rr L e +++k +++    g   s+e  ld ++++v+k v+  k     + + +++I+ Lk++le+ r    +L + 
  gi|119719441|ref|YP_919936.1| 407 VRRVLAEEVAKKGEAECYVCGNRLSEEF-LDWVREKVSKSVKELKdveeSIGKLRERINVLKKKLEDLREYKLTLINY 483
                                    5777777777887777777777766665.88888777765543333333999999**********9998877776654 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 0.00025
                          Spc29  79 kLRrQLReglsrkPp.pkis.spglapsdesrldsiyssvkkivelek.......klddqkleIkeLkreleqqrtvnse 149
                                    +LR  LR+  s++P   +i+ +     s +s+l+++  + +k  elek        ++d++ +++ +++ ++++r++ + 
  gi|119719441|ref|YP_919936.1| 532 FLR--LRTSYSKLPLlDEIKkLEQEVSSLRSELQRLEPQYNKYLELEKriealsrEIEDKRHRLEGIRKDIDEKRAMLES 609
                                    555..7888888864123330233445678888999888888888888788888799*********************** PP

                          Spc29 150 Lqekvae...leeev....krlaalehSnrkfrsyssapsnsttkefvgslyen 196
                                      e++a+   lee +    +  +al++ +  +rs + +  n+  +e v ++y  
  gi|119719441|ref|YP_919936.1| 610 FEERLARerrLEEVLgkvrRVKEALIEVHADLRSQKIMELNKVVNEIVRGIYPY 663
                                    **9998522377766555444467777777799999999999999999888865 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.3       0.2        66     258     314 ..     198     257 ..     170     262 .. 0.70
   2 ?    9.7   3.2    0.0011      0.37     253     360 ..     289     396 ..     286     398 .. 0.89
   3 ?    2.5  10.0      0.17        58     230     319 ..     432     516 ..     363     526 .. 0.58
   4 ?    7.0   5.2    0.0073       2.5     224     333 ..     509     619 ..     508     637 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.2
                          IFT57 258 lekiesrEkylnsql...eellqeyreaqeelsevkekykqlsegvseltrelaeiseel 314
                                    l+ + + E++l+++l   e ll+ +++    l+ + +ky++l+++++++++ l+++ +++
  gi|119719441|ref|YP_919936.1| 198 LNILREEERRLEQELiegERLLEGLKKEASDLEGAAKKYQELKSELNAKEKLLEDLRDRV 257
                                    455556666666666333456666777777788888888888888888877777776665 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0011
                          IFT57 253 disktlekiesrEkylnsqleellqeyreaqeelsevkekykqlsegvseltrelaeiseelekvkqemeergssmtDgs 332
                                    ++ k++e ie  E++l + ++   + ++++ e +se  +++k ls++v+ ++++l+ei+ +l  +++ + + +   ++ +
  gi|119719441|ref|YP_919936.1| 289 KLIKEIEGIEVSEYNLREVFSAFERVFHQLDEIYSEKYREIKGLSAQVEVYEKQLREIESRLVGLEEHVSDYERAESEIE 368
                                    5678999*********************************************************9999999999887776 PP

                          IFT57 333 plvkikkaltklkkEikqmdvrigVlqh 360
                                     + +     +kl++Ei  ++   g lq+
  gi|119719441|ref|YP_919936.1| 369 KIKSEYGDENKLREEIGRLESELGMLQR 396
                                    6665556668999999999999998885 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.17
                          IFT57 230 kkhkksieeslpetksqlkklhedisktlekiesrEkylnsqleellqeyreaqeelsevkekykqlsegvseltrelae 309
                                    +++ + ++e+++++ ++lk+++e i k  e+i+   k l+      l+ey+ +  +++++ e+y+ l e+ ++l+  l+ 
  gi|119719441|ref|YP_919936.1| 432 EEFLDWVREKVSKSVKELKDVEESIGKLRERINVLKKKLED-----LREYKLTLINYEAAYEEYQRLLEERKNLQAALDA 506
                                    45555667777777777777777777777777766666653.....3455555555555555555555555555555555 PP

                          IFT57 310 iseelekvkq 319
                                      eele++k+
  gi|119719441|ref|YP_919936.1| 507 EREELERAKS 516
                                    5555555554 PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.0073
                          IFT57 224 ahleqmkkhkksieeslpetksqlkklhedisk..tlekiesrEkylnsqleellqeyreaqeelsevkekykqlsegvs 301
                                    ++le+ k+  + i ++l+ +++ + +l +  sk   l++i++ E+ +  +l+++lq ++ + +++ e++++++ ls++++
  gi|119719441|ref|YP_919936.1| 509 EELERAKSGLSVIGAELKVVREDFLRLRTSYSKlpLLDEIKKLEQEVS-SLRSELQRLEPQYNKYLELEKRIEALSREIE 587
                                    567777777778888888888888888888888444899999999985.5888889999999999999999999999999 PP

                          IFT57 302 eltrelaeiseelekvkqemeergssmtDgsp 333
                                    ++++ l+ i +++++    +e+ +++++  + 
  gi|119719441|ref|YP_919936.1| 588 DKRHRLEGIRKDIDEKRAMLESFEERLARERR 619
                                    99999999999999888888877776665555 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   8.9     0.022       7.5     145     211 ..     195     260 ..     191     295 .. 0.65
   2 ?    6.5   8.0    0.0099       3.3     138     281 ..     312     455 ..     302     458 .. 0.84
   3 ?    7.2  13.6    0.0061       2.1     137     255 ..     446     567 ..     435     571 .. 0.81
   4 ?    6.6  11.5    0.0089         3     170     271 ..     549     649 ..     542     660 .. 0.39

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.022
                           Spc7 145 eenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelael 211
                                    eenl++l+e++++Le++  e ++ll+ l++e ++le  ++k qe + el++ +++ Le lr++++ +
  gi|119719441|ref|YP_919936.1| 195 EENLNILREEERRLEQELIEGERLLEGLKKEASDLEGAAKKYQELKSELNA-KEKLLEDLRDRVKGV 260
                                    567777777777777777777777777777777777777777777776544.555677777766544 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0099
                           Spc7 138 egLkegleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidke..eLeelreelaelkaei 215
                                    e + ++l+e++++  ++ + L++q e  ++ l e+e++   lee + + ++a+ e+e+i++e  + ++lree+ +l++e+
  gi|119719441|ref|YP_919936.1| 312 ERVFHQLDEIYSEKYREIKGLSAQVEVYEKQLREIESRLVGLEEHVSDYERAESEIEKIKSEygDENKLREEIGRLESEL 391
                                    677889999999999999999999999999999****************999999999886511578999******9999 PP

                           Spc7 216 eekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevkaleel 281
                                      + ++ +el++ + +++  ++e  ++k e+e  +   +r+ ee  +w ++ vs+  +e+k++ee 
  gi|119719441|ref|YP_919936.1| 392 GML-QRRSELERCVSSVRRVLAEEVAKKGEAECYVC-GNRLSEEFLDWVREKVSKSVKELKDVEES 455
                                    955.45688888888888888888888888776666.88888888888888888888888888875 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0061
                           Spc7 137 legLkegleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesid..keeLeelreelaelkae 214
                                    +++Lk  +ee + +l+e  ++L+k+ e l e++  l +++a+ ee  + l+e+++  +++d  +eeLe +++ l+ + ae
  gi|119719441|ref|YP_919936.1| 446 VKELK-DVEESIGKLRERINVLKKKLEDLREYKLTLINYEAAYEEYQRLLEERKNLQAALDaeREELERAKSGLSVIGAE 524
                                    55555.46888889999999999999999999999998888877777777776666666555599*************** PP

                           Spc7 215 ieekkkelaelqeqleel..eekieelkeqkseleeeiaeaer 255
                                    ++  +++  +l++   +l   ++i++l+++ s+l++e+++ e 
  gi|119719441|ref|YP_919936.1| 525 LKVVREDFLRLRTSYSKLplLDEIKKLEQEVSSLRSELQRLEP 567
                                    ************9998853279999999999999999998875 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.0089
                           Spc7 170 peleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleee 249
                                    ++le+e ++l++el++l+ ++++  ++ ++++e+l +e+++    +e  +k+++e+++ le+ ee+++  + + +e+  +
  gi|119719441|ref|YP_919936.1| 549 KKLEQEVSSLRSELQRLEPQYNKYLEL-EKRIEALSREIEDKRHRLEGIRKDIDEKRAMLESFEERLAR-ERRLEEVLGK 626
                                    344445555555555555544443222.23344444444444444444444444444444444444422.2223333322 PP

                           Spc7 250 iae.aervleeckgwsesevsrl 271
                                    +++ +e ++e + + +++ + +l
  gi|119719441|ref|YP_919936.1| 627 VRRvKEALIEVHADLRSQKIMEL 649
                                    22212223333333333333333 PP

>> LOH1CR12  Tumour suppressor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       6.5   2.2e+03      65      99 ..     246     280 ..     217     299 .. 0.59
   2 ?   -1.4   0.1       6.7   2.3e+03      79     122 ..     319     362 ..     288     367 .. 0.63
   3 ?   -1.3   0.2       6.1     2e+03      55      80 ..     446     471 ..     435     512 .. 0.57
   4 ?   14.6   2.0   7.6e-05     0.026      54     124 ..     544     621 ..     539     628 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 6.5
                       LOH1CR12  65 iitllaelrekqkqyasyaealskvnelsdqlsri 99 
                                     ++ll++lr++ k   s  + + +++el d+l r 
  gi|119719441|ref|YP_919936.1| 246 KEKLLEDLRDRVKGVLSLDALVVGLEELRDKLLRA 280
                                    24556666666666666666666666666555554 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 6.7
                       LOH1CR12  79 yasyaealskvnelsdqlsriqiiledivpllEtlnelLdedeR 122
                                     + y e+  +++ ls+q+   ++ l +i   l  l e + + eR
  gi|119719441|ref|YP_919936.1| 319 DEIYSEKYREIKGLSAQVEVYEKQLREIESRLVGLEEHVSDYER 362
                                    34577777888888888777777777766666666665555555 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 6.1
                       LOH1CR12  55 verikevdakiitllaelrekqkqya 80 
                                    v++ k+v+++i +l + ++  +k+ +
  gi|119719441|ref|YP_919936.1| 446 VKELKDVEESIGKLRERINVLKKKLE 471
                                    44555555555555444444443332 PP

  == domain 4  score: 14.6 bits;  conditional E-value: 7.6e-05
                       LOH1CR12  54 lverikevdakiitllaelrekqkqyasyaealskvnelsdql.......sriqiiledivpllEtlnelLdedeRLe 124
                                    l ++ik++++++++l +el+  + qy++y e  ++++ ls ++         i++ ++++ ++lE + e L  + RLe
  gi|119719441|ref|YP_919936.1| 544 LLDEIKKLEQEVSSLRSELQRLEPQYNKYLELEKRIEALSREIedkrhrlEGIRKDIDEKRAMLESFEERLARERRLE 621
                                    5678**************************998888888766511111115677888999999999999999999998 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.7      0.56   1.9e+02     230     285 ..     204     259 ..     190     285 .. 0.60
   2 ?   11.0   0.5   0.00021     0.073     181     327 ..     303     456 ..     295     465 .. 0.71
   3 ?    3.8   5.7     0.033        11     591     704 ..     464     589 ..     438     614 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.56
                       Prominin 230 lesnvlpaLaelerllenlkeakeqLeqvnklekeLrksgsqLrdglrgvkrdlnq 285
                                     e  + + L e erlle lk+    Le   k  +eL+++ +  ++ l++ +++++ 
  gi|119719441|ref|YP_919936.1| 204 EERRLEQELIEGERLLEGLKKEASDLEGAAKKYQELKSELNAKEKLLEDLRDRVKG 259
                                    33344444555566666666666666666666666666665555555555555554 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00021
                       Prominin 181 gledlrtflkdvpqhidhvlvqnyeele......khvsddLddagkhlgldladtlesnvlpaLaelerllenlkeakeq 254
                                    +l+++ +  + v+ ++d++  + y+e++      +  +++L ++++ l++ l++++++   +a +e+e++  +  + +++
  gi|119719441|ref|YP_919936.1| 303 NLREVFSAFERVFHQLDEIYSEKYREIKglsaqvEVYEKQLREIESRLVG-LEEHVSDY-ERAESEIEKIKSEYGDENKL 380
                                    6667777788999************9982221112234677777777765.44444443.48889999999999999999 PP

                       Prominin 255 LeqvnklekeLrksg..sqLrdglrgvkrdlnqalsnlCqseeCskilssleiekldtskcl..dqlpnvdevleal 327
                                     e++ +le+eL + +  s+L++++++v+r l + ++++ + +eC+   ++l+ e+ld  ++   ++++++++v e++
  gi|119719441|ref|YP_919936.1| 381 REEIGRLESELGMLQrrSELERCVSSVRRVLAEEVAKKGE-AECYVCGNRLSEEFLDWVREKvsKSVKELKDVEESI 456
                                    9999999999976542279******************666.99**99999999999976555344444444433333 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.033
                       Prominin 591 eeerkdLeklresglskihsslyleqlckkltkvnletlaekleelanelsngk...knlkqslkneaqdlraiqqel.v 666
                                    +  +k+Le+lre +l  i+++   e+ ++ l +   ++l++ l++  +el+++k   ++++ +lk   +d+ ++ + +  
  gi|119719441|ref|YP_919936.1| 464 NVLKKKLEDLREYKLTLINYEAAYEEYQRLLEER--KNLQAALDAEREELERAKsglSVIGAELKVVREDFLRLRTSYsK 541
                                    455899*********************9998774..45666677777777776677788888888888887777665514 PP

                       Prominin 667 lplessvkklkksvkklde..........ensdlqesikkllaavera 704
                                    lpl  ++kkl+++v +l +          +  +l+++i+ l +++e+ 
  gi|119719441|ref|YP_919936.1| 542 LPLLDEIKKLEQEVSSLRSelqrlepqynKYLELEKRIEALSREIEDK 589
                                    678888888888888888833333323333333555666655555555 PP

>> NdhM  Cyanobacterial and plastid NDH-1 subunit M
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.1    0.0067       2.3      53      82 ..     289     318 ..     275     327 .. 0.90
   2 ?    0.7   0.6       1.8   6.1e+02      36      83 ..     448     495 ..     439     510 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0067
                           NdhM  53 elvesyegedlteynlrriGsdlehfirkl 82 
                                    +l+++ eg +++eynlr++ s +e++ ++l
  gi|119719441|ref|YP_919936.1| 289 KLIKEIEGIEVSEYNLREVFSAFERVFHQL 318
                                    799*********************988876 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1.8
                           NdhM  36 efvWeeealkkvyekfdelvesyegedlteynlrriGsd..lehfirkll 83 
                                    e++  ee++ k++e+ + l  +++ edl ey+l  i  +   e++ r l 
  gi|119719441|ref|YP_919936.1| 448 ELKDVEESIGKLRERINVL--KKKLEDLREYKLTLINYEaaYEEYQRLLE 495
                                    5555667777777777655..566789*****999975411566666554 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   7.4      0.09        30     148     274 ..     269     409 ..     160     429 .. 0.70
   2 ?    4.5   6.9     0.066        22     160     261 ..     452     567 ..     412     568 .. 0.41
   3 ?    7.8   5.9    0.0065       2.2     169     255 ..     549     640 ..     539     659 .. 0.59

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.09
                   Exonuc_VII_L 148 qleelerrlekaikrll................eekkqrleklasrlkspeellerkrqrldeleerleralkkqlkkkr 211
                                     leel+++l +a+++ll                 + ++ ++++++ +++ +e++++k ++++ l++++e   +kql++ +
  gi|119719441|ref|YP_919936.1| 269 GLEELRDKLLRAAEKLLppsklikeiegievseYNLREVFSAFERVFHQLDEIYSEKYREIKGLSAQVEV-YEKQLREIE 347
                                    3466666777777766677766776666655554444445555555566667777777777777777777.666777777 PP

                   Exonuc_VII_L 212 erleelkerlkekleekkerlkklkerlelleekkerleeleeklealsplkvLkrGyaivrk 274
                                    +rl  l+e+++ ++e+++++++k+k++    ++ +e++ +le++l  l+ ++ L+r  + vr+
  gi|119719441|ref|YP_919936.1| 348 SRLVGLEEHVS-DYERAESEIEKIKSEYGDENKLREEIGRLESELGMLQRRSELERCVSSVRR 409
                                    77777776663.455666666666666666667777777777777777777777776666554 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.066
                   Exonuc_VII_L 160 ikrlleekkqrleklasrl...kspeellerkrqrldeleerlera..lkkqlkkkrerleelkerlk...ekleekker 231
                                    +++ + + ++r++ l+++l   ++ +  l + + +++e+++ le++  l+ +l+++re+le++k+ l+   ++l+  +e+
  gi|119719441|ref|YP_919936.1| 452 VEESIGKLRERINVLKKKLedlREYKLTLINYEAAYEEYQRLLEERknLQAALDAEREELERAKSGLSvigAELKVVRED 531
                                    11122222222222222221111111122222222222222222211122234455555555554443345444444444 PP

                   Exonuc_VII_L 232 lkklkerle......lleekkerleeleeklealsp 261
                                    + +l+++ +      ++++ ++++++l ++l+ l+p
  gi|119719441|ref|YP_919936.1| 532 FLRLRTSYSklplldEIKKLEQEVSSLRSELQRLEP 567
                                    444433333555555577777777777777777777 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0065
                   Exonuc_VII_L 169 qrleklasrlkspeellerkrqrldeleerleralkkqlkkkrerleelkerl.k..ekleekkerlkklkerle....l 241
                                    ++le+  s+l+s  ++le + +++ ele+r+e+ l+++++ kr+rle +++ + +  + le+ +erl++  +rle    +
  gi|119719441|ref|YP_919936.1| 549 KKLEQEVSSLRSELQRLEPQYNKYLELEKRIEA-LSREIEDKRHRLEGIRKDIdEkrAMLESFEERLARE-RRLEevlgK 626
                                    344555555667777888888888888888888.888888888888888865543443344444444222.233333334 PP

                   Exonuc_VII_L 242 leekkerleeleek 255
                                    +++ ke+l e+++ 
  gi|119719441|ref|YP_919936.1| 627 VRRVKEALIEVHAD 640
                                    44444444443333 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   6.1     0.072        25     336     410 ..     195     259 ..     185     301 .. 0.85
   2 ?    5.5   3.7     0.016       5.4     336     409 ..     326     399 ..     316     422 .. 0.77
   3 ?    9.2   7.5    0.0012      0.41     335     414 ..     438     516 ..     427     530 .. 0.75
   4 ?    6.6   6.5    0.0076       2.6     323     438 ..     532     656 ..     518     668 .. 0.53

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.072
                           FapA 336 keklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeeles 410
                                     e+l+ l+ee ++le+el + ++ ++ l+k+           ++l+ + +++++lk+el++ e+ l++l ++++ 
  gi|119719441|ref|YP_919936.1| 195 EENLNILREEERRLEQELIEGERLLEGLKKE----------ASDLEGAAKKYQELKSELNAKEKLLEDLRDRVKG 259
                                    5778999**********************93..........3788888888888888888888888888888775 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.016
                           FapA 336 keklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeele 409
                                     +++k l  ++e +e++l+++++++  l++   +++  +   e++k+   + +kl+ee+  le el  l+ + e
  gi|119719441|ref|YP_919936.1| 326 YREIKGLSAQVEVYEKQLREIESRLVGLEEHVSDYERAESEIEKIKSEYGDENKLREEIGRLESELGMLQRRSE 399
                                    45678999999999**********99999944477666666666666666669*******99999998876554 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0012
                           FapA 335 lkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeeleskkee 414
                                    ++ek+++  +el+++ee++ kl+++i+ l+k+ ++ +  +  +  ++ + e++++l ee ++l++ l++  eele+  ++
  gi|119719441|ref|YP_919936.1| 438 VREKVSKSVKELKDVEESIGKLRERINVLKKKLEDLREYKLTLINYEAAYEEYQRLLEERKNLQAALDAEREELERA-KS 516
                                    56777777788888888888888888888885445555566677888888888888889999999888888888887.33 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.0076
                           FapA 323 kteievgldepelkeklkeleeeleeleeeleklkkkikklpklka.ekqlesekkeqlkklletkeklkeeleeleeel 401
                                     ++++ + +++ l +++k+le+e+ +l++el++l+ +++k  +l++  ++l+ e++++ ++l+  ++ + e+ + le   
  gi|119719441|ref|YP_919936.1| 532 FLRLRTSYSKLPLLDEIKKLEQEVSSLRSELQRLEPQYNKYLELEKrIEALSREIEDKRHRLEGIRKDIDEKRAMLES-- 609
                                    556666667777888889999999999999999999977777755533333333333333333333333333222222.. PP

                           FapA 402 kelkeelesk............keeakikvnkeiypgvkikigkkklii 438
                                       +e+l++              +ea i+v+  + +   ++++k +++i
  gi|119719441|ref|YP_919936.1| 610 --FEERLARErrleevlgkvrrVKEALIEVHADLRSQKIMELNKVVNEI 656
                                    ..22222222322233333343334455555555555555555555555 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   2.4    0.0082       2.8      35      91 ..     198     254 ..     191     260 .. 0.88
   2 ?    4.6   3.2     0.096        32       8      81 ..     327     399 ..     321     421 .. 0.83
   3 ?    7.4   8.0     0.013       4.2       8      89 ..     440     520 ..     435     541 .. 0.82
   4 ?    4.3   7.5      0.11        39      25      98 ..     549     618 ..     543     644 .. 0.56

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0082
                     TPR_MLP1_2  35 aeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesakaeleese 91 
                                     +i++e +++ e+el++ +  ++ l++  ++l+ + ++++elk+e+++ ++ le  +
  gi|119719441|ref|YP_919936.1| 198 LNILREEERRLEQELIEGERLLEGLKKEASDLEGAAKKYQELKSELNAKEKLLEDLR 254
                                    57899999999**********************************999999998765 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.096
                     TPR_MLP1_2   8 eeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeae 81 
                                     eik l+++ e +e++l+++++ l   +e +++ ++  e+e+ k +++  + ++lree+ +l++e+  l+ + e
  gi|119719441|ref|YP_919936.1| 327 REIKGLSAQVEVYEKQLREIESRLVGLEEHVSDYER-AESEIEKIKSEYGDENKLREEIGRLESELGMLQRRSE 399
                                    588899999999999999999999999999999888.8999999999999999999999999988887776554 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.013
                     TPR_MLP1_2   8 eeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesakael 87 
                                    e++++  +e ++ e+ + kl+e ++  ++ +++  + Y+  l++ +++ +e q+l ee ++l+a +   ++e+e+ak+ l
  gi|119719441|ref|YP_919936.1| 440 EKVSKSVKELKDVEESIGKLRERINVLKKKLEDLRE-YKLTLINYEAAYEEYQRLLEERKNLQAALDAEREELERAKSGL 518
                                    666677778889999999999999999999999988.9999999999999999999999999999999999999999988 PP

                     TPR_MLP1_2  88 ee 89 
                                    + 
  gi|119719441|ref|YP_919936.1| 519 SV 520
                                    75 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.11
                     TPR_MLP1_2  25 qklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesakaeleeseesweeqk 98 
                                    +kl++++ + ++++++ + +Y + l    e  k ++al  e+++ + +++ ++++ ++ +a le  ee +++++
  gi|119719441|ref|YP_919936.1| 549 KKLEQEVSSLRSELQRLEPQYNKYL----ELEKRIEALSREIEDKRHRLEGIRKDIDEKRAMLESFEERLARER 618
                                    4555555555555555555444444....333555556666666666666666666666666655555554433 PP

>> FlxA  FlxA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1     0.086        29      17      40 ..     327     355 ..     322     402 .. 0.72
   2 ?    5.2   0.4     0.061        20      13      39 ..     450     476 ..     441     516 .. 0.73
   3 ?    6.3   0.5     0.028       9.6      18      60 ..     547     588 ..     537     612 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.086
                           FlxA  17 sqiasLqkQiknlqkqLkelses.....d 40 
                                     +i+ L  Q++ ++kqL+e+ +      +
  gi|119719441|ref|YP_919936.1| 327 REIKGLSAQVEVYEKQLREIESRlvgleE 355
                                    57999999999999999999887444432 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.061
                           FlxA  13 sgsasqiasLqkQiknlqkqLkelses 39 
                                    ++ ++ i +L++ i+ l+k+L++l e 
  gi|119719441|ref|YP_919936.1| 450 KDVEESIGKLRERINVLKKKLEDLREY 476
                                    56788999****************987 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.028
                           FlxA  18 qiasLqkQiknlqkqLkelsesdeltkeekkkqqqliqaQIqq 60 
                                    +i++L++++++l  +L+ l  + ++  e  +k+++ ++ +I++
  gi|119719441|ref|YP_919936.1| 547 EIKKLEQEVSSLRSELQRLEPQYNKYLE-LEKRIEALSREIED 588
                                    6777777777777777777777444444.55666666666665 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7  22.8    0.0048       1.6      35     166 ..     505     653 ..     431     657 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0048
                          Atg14  35 ksekeslkkkiekalegke...........................eaeqledkiknkkakleelksliadlrer...lq 84 
                                     +e+e+l           e                           ++  l d+ik++ + +++l+s+ ++l+ +     
  gi|119719441|ref|YP_919936.1| 505 DAEREEL-----------EraksglsvigaelkvvredflrlrtsySKLPLLDEIKKLEQEVSSLRSELQRLEPQynkYL 573
                                    2222222...........12333444444456666666777777777778888999999999999988888876622266 PP

                          Atg14  85 elkdklsqlkkeieekkkklaklsdklkkRrsdleslqneleerrkkqiaklqdaikrieqklsslssktlesrsslcse 164
                                    el+++++ l +eie+k+++l++ ++++ ++r+ les +++l+  r++ +++++ +++r+++ l +++ ++ +++++++  
  gi|119719441|ref|YP_919936.1| 574 ELEKRIEALSREIEDKRHRLEGIRKDIDEKRAMLESFEERLA--RERRLEEVLGKVRRVKEALIEVHADLRSQKIMELNK 651
                                    89**************************************97..55679******************9999888887776 PP

                          Atg14 165 la 166
                                    ++
  gi|119719441|ref|YP_919936.1| 652 VV 653
                                    65 PP

>> LemA  LemA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       7.1   2.4e+03      70      96 ..     232     249 ..     213     283 .. 0.68
   2 ?   -0.9   0.1       4.1   1.4e+03      71      97 ..     323     350 ..     288     387 .. 0.64
   3 ?   11.6   1.6   0.00054      0.18      35     116 ..     491     574 ..     463     581 .. 0.87
   4 ?    0.7   0.1       1.3   4.3e+02      47      92 ..     607     651 ..     577     664 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 7.1
                           LemA  70 vaEnYPdLkanenfleLqeelegtEnr 96 
                                     a +Y         +eL++el+  E+ 
  gi|119719441|ref|YP_919936.1| 232 AAKKY---------QELKSELNAKEKL 249
                                    33444.........4444444444433 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 4.1
                           LemA  71 aEnYPdLka.nenfleLqeelegtEnri 97 
                                    +E+Y ++k  +++++   ++l ++E+r+
  gi|119719441|ref|YP_919936.1| 323 SEKYREIKGlSAQVEVYEKQLREIESRL 350
                                    4444444432333333444444444443 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.00054
                           LemA  35 eevteaRaka..aeaesveekaeaenqlssalsrllavaEnYPdLkanenfleLqeelegtEnriavaRrrYneavreyn 112
                                    +++ e R+++  a  ++ ee ++a++ ls    +l +v E++  L+++ + l L +e++++E++++  R++ ++   +yn
  gi|119719441|ref|YP_919936.1| 491 QRLLEERKNLqaALDAEREELERAKSGLSVIGAELKVVREDFLRLRTSYSKLPLLDEIKKLEQEVSSLRSELQRLEPQYN 570
                                    5566666666333367789999****************************************************999999 PP

                           LemA 113 tkie 116
                                    +++e
  gi|119719441|ref|YP_919936.1| 571 KYLE 574
                                    9875 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 1.3
                           LemA  47 aesveekaeaenqlssalsrllavaEnYPdLkanenfleLqeeleg 92 
                                     es+ee+ + e++l++ l+++  v E+  + +a+ + ++++e l++
  gi|119719441|ref|YP_919936.1| 607 LESFEERLARERRLEEVLGKVRRVKEALIEVHADLRSQKIME-LNK 651
                                    478899999999999999999999999988888877777663.444 PP

>> DUF3140  Protein of unknown function (DUF3140)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.4    0.0035       1.2      10      64 ..     431     483 ..     426     512 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0035
                        DUF3140  10 akeLeeWLkteeSkevgekkdggesvghesGrkiveilrkkkadltdddlehmrk 64 
                                    ++e  +W +++ Sk+v e kd +es+g+   r  +++l+kk +dl +  l  ++ 
  gi|119719441|ref|YP_919936.1| 431 SEEFLDWVREKVSKSVKELKDVEESIGKLRER--INVLKKKLEDLREYKLTLINY 483
                                    78999**************999*****98655..9**********9988776654 PP

>> Sec8_exocyst  Sec8 exocyst complex component specific domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.3      0.78   2.6e+02      78     115 ..     219     256 ..     202     278 .. 0.72
   2 ?   -0.0   0.1       2.2   7.4e+02      74     126 ..     315     367 ..     299     403 .. 0.70
   3 ?    3.1   0.3      0.24        81      99     133 ..     439     474 ..     431     481 .. 0.58
   4 ?    5.7   0.3     0.037        13      72     140 ..     488     556 ..     481     558 .. 0.88
   5 ?    6.3   0.2     0.024       8.1      74     134 ..     572     632 ..     566     640 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.78
                   Sec8_exocyst  78 lssiqesqekvselKesleeakkklstkkkeLkelnar 115
                                    l+ +++ ++++++  ++ +e k++l++k+k L++l +r
  gi|119719441|ref|YP_919936.1| 219 LEGLKKEASDLEGAAKKYQELKSELNAKEKLLEDLRDR 256
                                    55666666666666677777777777777777777665 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 2.2
                   Sec8_exocyst  74 YskilssiqesqekvselKesleeakkklstkkkeLkelnarsakykevieiL 126
                                    ++++ +  +e  +++++l  ++e  +k+l + ++ L  l+++ + y++  + +
  gi|119719441|ref|YP_919936.1| 315 FHQLDEIYSEKYREIKGLSAQVEVYEKQLREIESRLVGLEEHVSDYERAESEI 367
                                    55555555555566666666677777777777777777766666666554444 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.24
                   Sec8_exocyst  99 kkklstkkkeLkelnarsakykevieiLd.aieelk 133
                                    ++k+s+  keLk+++++  k++e i++L+ ++e+l+
  gi|119719441|ref|YP_919936.1| 439 REKVSKSVKELKDVEESIGKLRERINVLKkKLEDLR 474
                                    555566666666666666666666666641344444 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.037
                   Sec8_exocyst  72 asYskilssiqesqekvselKesleeakkklstkkkeLkelnarsakykevieiLdaieelkkvpdkie 140
                                      Y+ +l+  ++ q  + + +e+le ak+ ls   +eLk + ++ ++++   + L  ++e+kk+ +++ 
  gi|119719441|ref|YP_919936.1| 488 EEYQRLLEERKNLQAALDAEREELERAKSGLSVIGAELKVVREDFLRLRTSYSKLPLLDEIKKLEQEVS 556
                                    56778888888888899999*******************************999999999999998876 PP

  == domain 5  score: 6.3 bits;  conditional E-value: 0.024
                   Sec8_exocyst  74 YskilssiqesqekvselKesleeakkklstkkkeLkelnarsakykevieiLdaieelkk 134
                                    Y ++ + i+   +++++ +++le  +k++ +k+++L+  ++r a+ +++ e+L ++  +k+
  gi|119719441|ref|YP_919936.1| 572 YLELEKRIEALSREIEDKRHRLEGIRKDIDEKRAMLESFEERLARERRLEEVLGKVRRVKE 632
                                    67777889999999***************************************99998876 PP

>> Fzo_mitofusin  fzo-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.3       1.7   5.8e+02     114     153 ..     205     244 ..     170     261 .. 0.62
   2 ?    2.6   0.1      0.27        90      89     143 ..     297     348 ..     280     363 .. 0.74
   3 ?    2.4   0.1      0.31     1e+02     120     156 ..     359     395 ..     353     398 .. 0.85
   4 ?    7.6   0.5    0.0075       2.5     122     157 ..     440     475 ..     401     479 .. 0.86
   5 ?   -1.1   0.0       3.6   1.2e+03     104     148 ..     491     535 ..     487     548 .. 0.69
   6 ?    5.6   0.7     0.032        11     115     154 ..     549     588 ..     544     594 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.7
                  Fzo_mitofusin 114 ekeleeeikelekeiekleevqkkakllrnkaslleseLe 153
                                    e+ le+e+ e e+ +e l++  + ++   +k ++l+seL+
  gi|119719441|ref|YP_919936.1| 205 ERRLEQELIEGERLLEGLKKEASDLEGAAKKYQELKSELN 244
                                    3444444444444444444444444444444444444444 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.27
                  Fzo_mitofusin  89 ancshqvqqelsstfarlcqqvdetekeleeeikelekeiekleevqkkakllrn 143
                                     ++s+   +e+ s+f+r+ +q de  +e  +eik l++++e  e+   +++ +  
  gi|119719441|ref|YP_919936.1| 297 IEVSEYNLREVFSAFERVFHQLDEIYSEKYREIKGLSAQVEVYEK---QLREIES 348
                                    56666677899999999999***9999999999999999876554...4444444 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.31
                  Fzo_mitofusin 120 eikelekeiekleevqkkakllrnkaslleseLekfe 156
                                    + ++ e+eiek+++     ++lr++  +leseL + +
  gi|119719441|ref|YP_919936.1| 359 DYERAESEIEKIKSEYGDENKLREEIGRLESELGMLQ 395
                                    56788999999999999999*********99998766 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.0075
                  Fzo_mitofusin 122 kelekeiekleevqkkakllrnkaslleseLekfee 157
                                    ++++k++++l++v+++  +lr++ + l+++Le+ +e
  gi|119719441|ref|YP_919936.1| 440 EKVSKSVKELKDVEESIGKLRERINVLKKKLEDLRE 475
                                    678999*************************99765 PP

  == domain 5  score: -1.1 bits;  conditional E-value: 3.6
                  Fzo_mitofusin 104 arlcqqvdetekeleeeikelekeiekleevqkkakllrnkasll 148
                                    +rl ++ ++ ++ l++e +ele+  + l  +  ++k++r+   +l
  gi|119719441|ref|YP_919936.1| 491 QRLLEERKNLQAALDAEREELERAKSGLSVIGAELKVVREDFLRL 535
                                    566666667777777777777777777777777777777655555 PP

  == domain 6  score: 5.6 bits;  conditional E-value: 0.032
                  Fzo_mitofusin 115 keleeeikelekeiekleevqkkakllrnkaslleseLek 154
                                    k+le+e+++l++e+++le   +k   l ++ + l++e+e+
  gi|119719441|ref|YP_919936.1| 549 KKLEQEVSSLRSELQRLEPQYNKYLELEKRIEALSREIED 588
                                    6899999999999999999999999999999999999886 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.6      0.39   1.3e+02      43      81 ..     208     246 ..     194     258 .. 0.68
   2 ?    1.4   0.0       1.2     4e+02      32      78 ..     304     350 ..     295     373 .. 0.79
   3 ?    7.6   0.1     0.013       4.4      36      79 ..     428     471 ..     426     473 .. 0.94
   4 ?   -1.0   0.1       6.5   2.2e+03      62      80 ..     546     564 ..     486     569 .. 0.48
   5 ?    3.3   1.4       0.3     1e+02      38      79 ..     574     615 ..     544     618 .. 0.71
   6 ?    2.6   0.4      0.48   1.6e+02      25      69 ..     600     644 ..     596     655 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.39
                           KxDL  43 laklrarfkqgtkllkevkkdLesifkkirslkaklakk 81 
                                    l++   + ++  + lk+  +dLe   kk + lk++l++k
  gi|119719441|ref|YP_919936.1| 208 LEQELIEGERLLEGLKKEASDLEGAAKKYQELKSELNAK 246
                                    444444445555556666678888888888888888765 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 1.2
                           KxDL  32 LlelnalsqerlaklrarfkqgtkllkevkkdLesifkkirslkakl 78 
                                    L e+    ++ +++l + + ++ + +k + ++ e   k++r ++++l
  gi|119719441|ref|YP_919936.1| 304 LREVFSAFERVFHQLDEIYSEKYREIKGLSAQVEVYEKQLREIESRL 350
                                    66666667777888888888888888888888888888888888765 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.013
                           KxDL  36 nalsqerlaklrarfkqgtkllkevkkdLesifkkirslkakla 79 
                                    n ls+e l  +r+++ + +k lk+v + + +++++i+ lk+kl+
  gi|119719441|ref|YP_919936.1| 428 NRLSEEFLDWVREKVSKSVKELKDVEESIGKLRERINVLKKKLE 471
                                    6788999999********************************97 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 6.5
                           KxDL  62 kdLesifkkirslkaklak 80 
                                    ++++++ + ++sl+++l++
  gi|119719441|ref|YP_919936.1| 546 DEIKKLEQEVSSLRSELQR 564
                                    3344444555555555555 PP

  == domain 5  score: 3.3 bits;  conditional E-value: 0.3
                           KxDL  38 lsqerlaklrarfkqgtkllkevkkdLesifkkirslkakla 79 
                                    ++++r + l+ +++++ + l  ++kd++  +  ++s++++la
  gi|119719441|ref|YP_919936.1| 574 ELEKRIEALSREIEDKRHRLEGIRKDIDEKRAMLESFEERLA 615
                                    456677777777777777777777777777777777666665 PP

  == domain 6  score: 2.6 bits;  conditional E-value: 0.48
                           KxDL  25 lnkknreLlelnals..qerlaklrarfkqgtkllkevkkdLesifk 69 
                                    + +k ++L+ + + +  ++rl+++  ++++ +++l ev +dL+s  +
  gi|119719441|ref|YP_919936.1| 600 IDEKRAMLESFEERLarERRLEEVLGKVRRVKEALIEVHADLRS--Q 644
                                    67788889988886633689**********************86..4 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1      0.69   2.3e+02      40      85 ..     206     253 ..     180     285 .. 0.63
   2 ?    5.3   0.8      0.03        10       7      83 ..     304     382 ..     292     400 .. 0.75
   3 ?    3.5   2.1       0.1        34      22      81 ..     439     503 ..     428     542 .. 0.52
   4 ?    8.7   2.1    0.0027      0.92      21      93 ..     548     618 ..     524     639 .. 0.60

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.69
                          TMPIT  40 kkqkkrlkelksslkklkksvk..eeeeeeveelkeelkerkkvlkev 85 
                                    ++ +++l e ++ l+ lkk+++  e  +++++elk+el+ ++k l+++
  gi|119719441|ref|YP_919936.1| 206 RRLEQELIEGERLLEGLKKEASdlEGAAKKYQELKSELNAKEKLLEDL 253
                                    344444444444444444443333344455555555555555555543 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.03
                          TMPIT   7 lekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk..eeeeeeveelkeelkerkkvlk 83 
                                    l++ f ++e  ++++ +   e  + ++ +s +++  +k+l+e++s+l  l+++v+  e+ e+e+e++k+e  +++k  +
  gi|119719441|ref|YP_919936.1| 304 LREVFSAFERVFHQLDEIYSEKYREIKGLSAQVEVYEKQLREIESRLVGLEEHVSdyERAESEIEKIKSEYGDENKLRE 382
                                    4555666666677777777777788888888889999999999999999998877666777788888888776665554 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.1
                          TMPIT  22 kqkleelsklqskcskeikkqkkrlkelksslkklkksvk.....eeeeeeveelkeelkerkkv 81 
                                    ++k+ +  k  +++ ++i k ++r++ lk++l++l++ +      e   ee+++l ee k+ ++ 
  gi|119719441|ref|YP_919936.1| 439 REKVSKSVKELKDVEESIGKLRERINVLKKKLEDLREYKLtlinyEAAYEEYQRLLEERKNLQAA 503
                                    44555555555555555555555555555555555544223322322222222222222222222 PP

  == domain 4  score: 8.7 bits;  conditional E-value: 0.0027
                          TMPIT  21 ykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlkevesllpkkn 93 
                                    +k+  +e+s+l s++ ++++ q +++ el+++++ l++++ e++++++e ++++++e++++l++ e+ l +++
  gi|119719441|ref|YP_919936.1| 548 IKKLEQEVSSLRSEL-QRLEPQYNKYLELEKRIEALSREI-EDKRHRLEGIRKDIDEKRAMLESFEERLARER 618
                                    222233333333333.233334444555666666666654.57777888888888888888888888776653 PP

>> Sec20  Sec20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.2    0.0043       1.5      10      63 ..     201     254 ..     195     269 .. 0.91
   2 ?    0.5   0.0       1.7   5.9e+02      37      72 ..     269     304 ..     259     315 .. 0.78
   3 ?   -1.8   0.0         9     3e+03      16      54 ..     331     369 ..     316     374 .. 0.75
   4 ?   -0.8   0.2       4.2   1.4e+03      17      58 ..     459     500 ..     439     515 .. 0.61
   5 ?   -0.1   0.1       2.7     9e+02      19      53 ..     546     580 ..     538     620 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0043
                          Sec20  10 lraisqllsqevqqSeenleeldastkslekleeeykqvedvlsrskklvkkle 63 
                                    lr+ ++ l qe  + e  le l++ + +le +  +y+++++ l+  +kl++ l 
  gi|119719441|ref|YP_919936.1| 201 LREEERRLEQELIEGERLLEGLKKEASDLEGAAKKYQELKSELNAKEKLLEDLR 254
                                    7888999******************************************98775 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1.7
                          Sec20  37 slekleeeykqvedvlsrskklvkklerrdktdkll 72 
                                     le+l +++   ++ l    kl+k +e  +++++ l
  gi|119719441|ref|YP_919936.1| 269 GLEELRDKLLRAAEKLLPPSKLIKEIEGIEVSEYNL 304
                                    689999999999999999999*****9999998853 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 9
                          Sec20  16 llsqevqqSeenleeldastkslekleeeykqvedvlsr 54 
                                     ls++v+  e+ l e+++    le+  ++y   e+ +++
  gi|119719441|ref|YP_919936.1| 331 GLSAQVEVYEKQLREIESRLVGLEEHVSDYERAESEIEK 369
                                    577888888888888888888888888888777777665 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 4.2
                          Sec20  17 lsqevqqSeenleeldastkslekleeeykqvedvlsrskkl 58 
                                    l + ++  ++ le+l++   +l + e  y + + +l+  k+l
  gi|119719441|ref|YP_919936.1| 459 LRERINVLKKKLEDLREYKLTLINYEAAYEEYQRLLEERKNL 500
                                    444455555556666666666666666666666666666665 PP

  == domain 5  score: -0.1 bits;  conditional E-value: 2.7
                          Sec20  19 qevqqSeenleeldastkslekleeeykqvedvls 53 
                                    +e+++ e+ + +l++  + le   ++y ++e+ ++
  gi|119719441|ref|YP_919936.1| 546 DEIKKLEQEVSSLRSELQRLEPQYNKYLELEKRIE 580
                                    56666666677777777777776666666666554 PP

>> BRE1  BRE1 E3 ubiquitin ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   4.2      0.18        61      30      86 ..     195     251 ..     189     258 .. 0.90
   2 ?    8.5   0.8    0.0059         2       2      57 ..     326     384 ..     325     405 .. 0.83
   3 ?    4.2   5.6      0.13        44       3      70 ..     447     513 ..     445     535 .. 0.81
   4 ?    6.0   7.1     0.036        12       2      78 ..     545     624 ..     544     650 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.18
                           BRE1  30 eekklrleaekakadqkyfaamrskdalenelkkLnkllsKsselieqLkelekefv 86 
                                    ee+++ l  e  + +q+  + +r  + l++e   L    +K +el ++L+  ek + 
  gi|119719441|ref|YP_919936.1| 195 EENLNILREEERRLEQELIEGERLLEGLKKEASDLEGAAKKYQELKSELNAKEKLLE 251
                                    88899999999999***********************************99888765 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0059
                           BRE1   2 qkELvklekafeelseqlskkvkeltileekkl...rleaekakadqkyfaamrskdal 57 
                                    + E++ l+++ e  ++ql++  + l  lee ++   r+e+e++k + +y + ++ ++ +
  gi|119719441|ref|YP_919936.1| 326 YREIKGLSAQVEVYEKQLREIESRLVGLEEHVSdyeRAESEIEKIKSEYGDENKLREEI 384
                                    689**************************9986444899**********9988887765 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.13
                           BRE1   3 kELvklekafeelseqlskkvkeltileekklrleaekakadqkyfaamrskdalenelkkLnkllsK 70 
                                    kEL+++e+ + +l+e ++ ++k+l++l e kl l +  + a ++y  +  ++++l++ l + ++ l++
  gi|119719441|ref|YP_919936.1| 447 KELKDVEESIGKLRERINVLKKKLEDLREYKLTLIN-YEAAYEEYQRLLEERKNLQAALDAEREELER 513
                                    7*****************************999865.5666677777777777777666666655555 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.036
                           BRE1   2 qkELvklekafeelseqlskk...vkeltileekklrleaekakadqkyfaamrskdalenelkkLnkllsKsselieqL 78 
                                     +E++kle++   l+++l+ +   ++++  le+++  l+ e++  +     +++++d  ++ l    + l++++ l e L
  gi|119719441|ref|YP_919936.1| 545 LDEIKKLEQEVSSLRSELQRLepqYNKYLELEKRIEALSREIEDKRHRLEGIRKDIDEKRAMLESFEERLARERRLEEVL 624
                                    57999999999999998888633367778899999999999999999999999999998888888888888887776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (784 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1812  (0.101065); expected 358.6 (0.02)
Passed bias filter:                      887  (0.0494729); expected 358.6 (0.02)
Passed Vit filter:                       192  (0.0107089); expected 17.9 (0.001)
Passed Fwd filter:                       123  (0.00686039); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              53  [number of targets reported over threshold]
# CPU time: 1.81u 0.37s 00:00:02.18 Elapsed: 00:00:00.61
# Mc/sec: 3866.84
//
Query:       gi|119719442|ref|YP_919937.1|  [L=73]
Description: hypothetical protein Tpen_0528 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 516.44
//
Query:       gi|119719443|ref|YP_919938.1|  [L=249]
Description: hypothetical protein Tpen_0529 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0011   18.8   0.0       0.88    9.5   0.0    2.7  3  L51_S25_CI-B8  Mitochondrial ribosomal protein L51 / S25 / CI
  ------ inclusion threshold ------
      0.031   14.0   0.3        1.8    8.3   0.1    2.1  2  MoeA_N         MoeA N-terminal region (domain I and II)


Domain annotation for each model (and alignments):
>> L51_S25_CI-B8  Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.32   2.9e+03      29      40 ..     137     148 ..     134     176 .. 0.81
   2 !    6.1   0.0    0.0012        10       9      22 ..     194     207 ..     191     209 .. 0.91
   3 !    9.5   0.0   9.8e-05      0.88       7      28 ..     226     247 ..     225     249 .] 0.86

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.32
                                    SS-EEEEE-SS- CS
                  L51_S25_CI-B8  29 dgPallaiYfng 40 
                                    ++Pa+l+ Y  +
  gi|119719443|ref|YP_919938.1| 137 KHPAALGGYSSE 148
                                    799999999877 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0012
                                    THHHHTT-TTSEEE CS
                  L51_S25_CI-B8   9 LprlkykNPavpiv 22 
                                    Lp++++ NP+++i+
  gi|119719443|ref|YP_919938.1| 194 LPSFARDNPWLRIL 207
                                    9**********996 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 9.8e-05
                                    TTTHHHHTT-TTSEEEEEESS- CS
                  L51_S25_CI-B8   7 knLprlkykNPavpivvrrrsg 28 
                                    + Lp++++ NP++ ++ rrr g
  gi|119719443|ref|YP_919938.1| 226 SELPSFARDNPWLDFLSRRRGG 247
                                    68*************9998755 PP

>> MoeA_N  MoeA N-terminal region (domain I and II)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1    0.0002       1.8      42      58 ..      31      47 ..      15      94 .. 0.77
   2 ?    4.0   0.0    0.0042        37      34      90 ..     125     193 ..     106     197 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0002
                                   BSSS-EESSSEEEEEEB CS
                         MoeA_N 42 vPpfdnSamDGYAvrae 58
                                    Ppfd+Sa+DG  vr++
  gi|119719443|ref|YP_919938.1| 31 EPPFDASAVDGSGVRVA 47
                                   5**********999654 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.0042
                                    S-EE-SS-BSSS-E.ESSSEEEEEEBTTB--........................-S---TT-.EEEE-TTS CS
                         MoeA_N  34 edvvApedvPpfdn.SamDGYAvraeagsgaseeep.............saageeperllpgg.avrimTGa 90 
                                    e + Ap  +P ++  +a  GY  +++a +      p             ++a+e+++ ++pgg a+ + TG+
  gi|119719443|ref|YP_919938.1| 125 EIIPAPLRTPSYKHpAALGGYSSESRAQQLPP---PlgysptrdlsvgaEQARETRAVSVPGGeATGVSTGD 193
                                    55778888888865488899998766666653...13447788899998889999999999999*******6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 2020.77
//
Query:       gi|119719444|ref|YP_919939.1|  [L=428]
Description: actin/actin family protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.8e-17   60.8   0.0      1e-14   54.0   0.0    2.1  1  Actin     Actin


Domain annotation for each model (and alignments):
>> Actin  Actin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.0   0.0   5.8e-19     1e-14     118     336 ..     149     355 ..      74     404 .. 0.76

  Alignments for each domain:
  == domain 1  score: 54.0 bits;  conditional E-value: 5.8e-19
                          Actin 118 fEkfkvpalylaksavlsafasgkstglvvDsGasvtsvvpVldGyvLkkairrsdlgGkaLteqlkellssknvevtpr 197
                                     E+  v+a+ +  ++  +a a+   t +vv+sG+++t ++p+   y++++ai+ ++ gG   +   +e+l++        
  gi|119719444|ref|YP_919939.1| 149 AEEKVVKAVTIIPQPLAVAIAEKTVTCVVVESGHGNTQITPIS-MYPIRNAIVALNRGGAEADAIAAEILRDL------- 220
                                    477889***********************************97.6**************************95....... PP

                          Actin 198 ylikkkkvveaessaekeelekltesyktleeeevleeiKesvcevsedpeg...deeksssspeksYeLPDg....sei 270
                                                           +++ +   ee+ ++++Ke+v  + +d ++   +++ + +++++++ +P      +  
  gi|119719444|ref|YP_919939.1| 221 -----------------------GYE-DRAREEKFVRQFKEAVGLIPRDLNQaieKARREPERFRTVFSIPGTviqvDMG 276
                                    .......................222.5678999****************99665555556999999****883333355 PP

                          Actin 271 klgeeRfkvpEiLFdpsligsesaleee.............kskllgiselivaainacdvdlrpeLlanivvtGGnsl 336
                                    ++g +Rf + Ei+F+p+    es +++               + ++ + + i+++++++ ++l+p L++ i+++GGn  
  gi|119719444|ref|YP_919939.1| 277 NMGWARFLIGEIIFNPEHEIFESYYKRGmprpkdtvvggerVRGTMPLVQAITHSVSRTSTELQPALYKDIILSGGNFA 355
                                    67779************999998877779999******999999999*****************************964 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2912.85
//
Query:       gi|119719445|ref|YP_919940.1|  [L=502]
Description: hypothetical protein Tpen_0531 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (502 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 3891.40
//
Query:       gi|119719446|ref|YP_919941.1|  [L=76]
Description: hypothetical protein Tpen_0532 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.39
# Mc/sec: 588.61
//
Query:       gi|119719447|ref|YP_919942.1|  [L=135]
Description: hypothetical protein Tpen_0533 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.46
# Mc/sec: 880.29
//
Query:       gi|119719448|ref|YP_919943.1|  [L=128]
Description: hypothetical protein Tpen_0534 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 937.66
//
Query:       gi|119719449|ref|YP_919944.1|  [L=93]
Description: DNA-binding protein Alba [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-19   69.6   1.3    1.5e-19   69.6   1.3    1.8  2  Alba      Alba
     0.0017   18.3   0.6     0.0037   17.2   0.2    1.6  2  Rpp20     Rpp20 subunit of nuclear RNase MRP and P


Domain annotation for each model (and alignments):
>> Alba  Alba
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.6   1.3   1.7e-23   1.5e-19       3      66 ..       8      69 ..       6      70 .. 0.94
   2 ?    0.2   0.1     0.075   6.7e+02      40      53 ..      79      92 ..      77      93 .] 0.83

  Alignments for each domain:
  == domain 1  score: 69.6 bits;  conditional E-value: 1.7e-23
                                   EEE-STS-HHHHHHHHHHHHTHTTESEEEEEEETTHHHHHHHHHHHHHHHTCTT.EEEEEEEEE CS
                           Alba  3 iyVsskspimsyvkralklLsnkkeeeVvlkatGraIskAvsvaeilkrrfgkglyqvnvltss 66
                                   + V++ +++m+yv++a+ ++ n++++ V +ka+GraIs+Av+vaei+++rf+k+++ v  ++++
  gi|119719449|ref|YP_919944.1|  8 VLVGN-KSVMNYVLAAVIQF-NQGAKKVSIKARGRAISRAVDVAEIVRSRFLKDEVDVSSIKIG 69
                                   67888.**************.*************************************999876 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.075
                                   HHHHHHHHHHHHHT CS
                           Alba 40 skAvsvaeilkrrf 53
                                   ++++s+ ei+ +r 
  gi|119719449|ref|YP_919944.1| 79 ERTISTIEIVLERK 92
                                   5899*****98875 PP

>> Rpp20  Rpp20 subunit of nuclear RNase MRP and P
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.2   4.2e-07    0.0037      58      95 ..      27      63 ..      21      73 .. 0.76
   2 ?   -1.1   0.0      0.19   1.7e+03     126     136 ..      77      87 ..      67      88 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.2e-07
                          Rpp20 58 elkkeeVfvkatGrAiekalsvgrwfqekeeykvrvet 95
                                   ++  ++V +ka GrAi +a+ v++  +++  +k +v+ 
  gi|119719449|ref|YP_919944.1| 27 NQGAKKVSIKARGRAISRAVDVAEIVRSR-FLKDEVDV 63
                                   56789******************998766.33333333 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.19
                          Rpp20 126 trtRwvsmvev 136
                                     ++R++s++e+
  gi|119719449|ref|YP_919944.1|  77 GKERTISTIEI 87 
                                    58899999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 733.89
//
Query:       gi|119719450|ref|YP_919945.1|  [L=530]
Description: ATPase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-09   37.4   0.0    2.2e-09   36.8   0.0    1.2  1  T2SSE            Type II/IV secretion system protein
    0.00024   21.6   0.0    0.00074   20.1   0.0    1.9  1  AAA_18           AAA domain
    0.00026   21.0   0.0    0.00072   19.6   0.0    1.7  1  AAA_14           AAA domain
    0.00034   21.0   0.0    0.00062   20.2   0.0    1.4  1  AAA_16           AAA ATPase domain
    0.00081   19.2   0.0      0.021   14.6   0.0    2.4  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
     0.0027   17.4   0.0     0.0044   16.8   0.0    1.3  1  IstB_IS21        IstB-like ATP binding protein
     0.0034   17.8   0.0     0.0099   16.3   0.0    1.8  1  AAA              ATPase family associated with various cellul
     0.0045   17.0   0.0     0.0077   16.2   0.0    1.4  1  ResIII           Type III restriction enzyme, res subunit
     0.0051   17.1   0.0      0.011   16.0   0.0    1.7  1  AAA_28           AAA domain
     0.0074   15.7   0.0      0.012   14.9   0.0    1.3  1  DnaB_C           DnaB-like helicase C terminal domain
  ------ inclusion threshold ------
      0.011   15.7   0.0      0.021   14.8   0.0    1.4  1  AAA_5            AAA domain (dynein-related subfamily)
      0.015   14.9   0.0      0.024   14.2   0.0    1.3  1  SRP54            SRP54-type protein, GTPase domain
      0.016   15.2   0.0      0.033   14.2   0.0    1.5  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.017   14.7   0.0      0.038   13.6   0.0    1.7  1  AAA_25           AAA domain
      0.019   14.9   0.0      0.037   14.0   0.0    1.5  1  NACHT            NACHT domain
      0.021   14.9   0.0      0.042   14.0   0.0    1.4  1  Sigma54_activ_2  Sigma-54 interaction domain
      0.022   14.0   0.0      0.045   13.0   0.0    1.4  1  Zeta_toxin       Zeta toxin
      0.032   13.9   0.1       0.18   11.5   0.0    2.2  2  Thymidylate_kin  Thymidylate kinase
      0.044   13.9   0.0       0.12   12.5   0.0    1.8  1  AAA_33           AAA domain
      0.045   13.2   0.0        0.1   12.0   0.0    1.6  1  KTI12            Chromatin associated protein KTI12
      0.049   12.6   0.0      0.085   11.8   0.0    1.3  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
      0.052   13.2   0.0       0.11   12.2   0.0    1.4  1  Sigma54_activat  Sigma-54 interaction domain
      0.054   13.4   0.0       0.15   11.9   0.0    1.8  1  NTPase_1         NTPase
      0.055   13.3   0.0        0.1   12.5   0.0    1.4  1  AAA_3            ATPase family associated with various cellul
      0.064   13.0   0.0       0.13   12.0   0.0    1.5  1  ATP_bind_1       Conserved hypothetical ATP binding protein
      0.067   13.5   0.0       0.17   12.2   0.0    1.7  1  AAA_22           AAA domain
      0.085   13.3   0.0       0.34   11.3   0.0    2.0  2  RNA_helicase     RNA helicase
        0.1   12.3   0.3        0.2   11.4   0.1    1.5  1  AAA_24           AAA domain
        0.1   12.9   0.0       0.19   12.1   0.0    1.5  1  AAA_19           AAA domain
       0.12   11.6   0.0       0.21   10.7   0.0    1.3  1  DUF815           Protein of unknown function (DUF815)
       0.12   12.1   0.0       0.26   11.0   0.0    1.5  1  AAA_30           AAA domain
       0.14   11.5   0.0       0.25   10.7   0.0    1.3  1  FtsK_SpoIIIE     FtsK/SpoIIIE family
       0.18   12.3   0.0       0.34   11.4   0.0    1.4  1  ABC_tran         ABC transporter
       0.21   10.8   0.0       0.35   10.0   0.0    1.3  1  NB-ARC           NB-ARC domain


Domain annotation for each model (and alignments):
>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.8   0.0   4.1e-12   2.2e-09      79     243 ..     221     374 ..     178     395 .. 0.76

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 4.1e-12
                          T2SSE  79 rlrvvllPvvag.ealviRkksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeinksd 157
                                    r+ +  +P + g e  + R   +++l+l+d+   ++l   i++ l+k       il++G+ g GKtt++ al ++   + 
  gi|119719450|ref|YP_919945.1| 221 RIVITKPPFSDGiEITATR--PVARLRLEDYNLPKKL---IER-LEKQ---AEGILIAGAPGMGKTTFAQALAEYYYRKG 291
                                    5566666666665555555..4556677777655443...333.3333...5889**********************999 PP

                          T2SSE 158 erivtvEDpvEiql.eganqvqlnakkakvtfadllraaLRlrPDrimvGEiRdketlei.lkAvnTGHlgslsTlHans 235
                                    + + t+E p+ ++l +++ q + n      t ++    +L  rPD  +  E+Rd+  +e+       G  g ++ +Ha s
  gi|119719450|ref|YP_919945.1| 292 KVVKTIESPRDMHLpADITQYSRNY----ATSEEIHDVLLLSRPDYTFFDEMRDTKDFELyADLRLAG-VGMVGVVHATS 366
                                    9999*********944455554444....4666666667899******************54444555.55599****** PP

                          T2SSE 236 aagalerL 243
                                    +++a++r 
  gi|119719450|ref|YP_919945.1| 367 PIDAVQRF 374
                                    ******97 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   1.4e-06   0.00074       1      60 [.     266     326 ..     266     345 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.4e-06
                         AAA_18   1 IlltGtpGvGKttlakeLskrlgf..gvnlrdvakenglllevdpealdeskrldedkldkl 60 
                                    Il++G+pG GKtt+a++L++   +  g +++ + + +++ l+ d  +++++    e+ +d+l
  gi|119719450|ref|YP_919945.1| 266 ILIAGAPGMGKTTFAQALAEYY-YrkGKVVKTIESPRDMHLPADITQYSRNYATSEEIHDVL 326
                                    99****************9872.377777777777777777777777777777777776655 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   1.4e-06   0.00072       5      81 ..     266     347 ..     262     354 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.4e-06
                         AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklke.........ekktylflDEiqe 75 
                                    ++i Ga  +GKTt+++ l++ ++  ++  +  +++++rd  l   +++ ++ ++ +++         ++  y f+DE+  
  gi|119719450|ref|YP_919945.1| 266 ILIAGAPGMGKTTFAQALAEYYY--RKGKVVKTIESPRDMHLP--ADITQYSRNYATSeeihdvlllSRPDYTFFDEMRD 341
                                    7899***************9999..666666677888874322..2222222222111223346666799********** PP

                         AAA_14  76 vpewek 81 
                                     +++e 
  gi|119719450|ref|YP_919945.1| 342 TKDFEL 347
                                    *99986 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   1.2e-06   0.00062      16      55 ..     256     294 ..     249     379 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.2e-06
                         AAA_16  16 lervrsgrpelvllsGesGvGKsslvrellralekdggif 55 
                                    +er+ ++  e +l+ G++G+GK++ +++l++++ ++g ++
  gi|119719450|ref|YP_919945.1| 256 IERLEKQA-EGILIAGAPGMGKTTFAQALAEYYYRKGKVV 294
                                    55555554.89*******************9999995333 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0     4e-05     0.021      31      59 ..     261     289 ..     253     327 .. 0.77
   2 ?    1.8   0.0      0.34   1.8e+02      94     138 ..     463     507 ..     460     524 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4e-05
                         RuvB_N  31 ealdhvllyGpPGlGkttlakiiakelgv 59 
                                    ++ + +l++G+PG+Gktt+a+ +a+    
  gi|119719450|ref|YP_919945.1| 261 KQAEGILIAGAPGMGKTTFAQALAEYYYR 289
                                    567889****************9986544 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.34
                         RuvB_N  94 hrlsraveevlysamedfrldivigkGpsarsikldlpkftlvga 138
                                    +++++a+e  l++ + d   ++vi++ +s   ik+ ++ f  ++ 
  gi|119719450|ref|YP_919945.1| 463 YKMKNALEKALFKMLGDGGYELVIDENESLVVIKVPVDGFNYLAG 507
                                    679999*****************************9999987665 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   8.3e-06    0.0044      45      80 ..     261     296 ..     247     348 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 8.3e-06
                      IstB_IS21  45 ekkenivllGpsGvGKshlaialgveavraglsvlf 80 
                                    +++e+i++ G +G+GK+ +a al+    r+g+ v  
  gi|119719450|ref|YP_919945.1| 261 KQAEGILIAGAPGMGKTTFAQALAEYYYRKGKVVKT 296
                                    57899*********************9999998865 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.9e-05    0.0099       1      23 [.     266     288 ..     266     340 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.9e-05
                                    EEEESSTTSSHHHHHHHHHHHHT CS
                            AAA   1 vllyGppGtGKTllakavakelg 23 
                                    +l+ G pG+GKT++a+a+a+   
  gi|119719450|ref|YP_919945.1| 266 ILIAGAPGMGKTTFAQALAEYYY 288
                                    6899***************9874 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.5e-05    0.0077      13      56 ..     253     295 ..     242     338 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.5e-05
                                    HHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....- CS
                         ResIII  13 enlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeek 56 
                                    ++l+e l+ k+ + +li+ a G+GKT  a +l+e++++kgk  k
  gi|119719450|ref|YP_919945.1| 253 KKLIERLE-KQAEGILIAGAPGMGKTTFAQALAEYYYRKGKVVK 295
                                    67889998.9999*************************988554 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   2.1e-05     0.011       2      25 ..     266     289 ..     265     338 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.1e-05
                         AAA_28   2 ivitGgestGKTtlleaLaargyp 25 
                                    i i G+++ GKTt ++aLa+  y+
  gi|119719450|ref|YP_919945.1| 266 ILIAGAPGMGKTTFAQALAEYYYR 289
                                    789****************98543 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   2.4e-05     0.012      20      48 ..     264     292 ..     254     305 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.4e-05
                                    XEEEEEEXTTSSHHHHHHHHHHHHHHCST CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         DnaB_C  20 dliiiAarpsmGktalalniaenaavkek 48 
                                    + i+iA+ p+mGkt++a  +ae    k k
  gi|119719450|ref|YP_919945.1| 264 EGILIAGAPGMGKTTFAQALAEYYYRKGK 292
                                    5699*****************98776544 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0     4e-05     0.021       2      41 ..     266     309 ..     265     340 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4e-05
                                    EEEE--SSSSHHHHHHHGGGGB...S--EEEEE--TT--.HHHH CS
                          AAA_5   2 vlLvGppGtgKselaerlaaal...nreveyvqltrdtt.eedl 41 
                                    +l+ G+pG gK+++a+ la+ +   ++ v ++  +rd+  ++d+
  gi|119719450|ref|YP_919945.1| 266 ILIAGAPGMGKTTFAQALAEYYyrkGKVVKTIESPRDMHlPADI 309
                                    7999******************9888888888888888534444 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   4.6e-05     0.024       4      32 ..     266     294 ..     263     322 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.6e-05
                                    EEEEESTTSSHHHHHHHHHHHHHHTTS-E CS
                          SRP54   4 illvGlqGaGKTttlaKLaallkkegkkv 32 
                                    il++G  G+GKTt +  La+++ ++gk v
  gi|119719450|ref|YP_919945.1| 266 ILIAGAPGMGKTTFAQALAEYYYRKGKVV 294
                                    89**********************98866 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   6.2e-05     0.033       9      51 ..     254     300 ..     246     301 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6.2e-05
                                    HHHHHHHHCHTEEEEEEESTTSSHHHHHHHHHHHTT--.....----T CS
                           TsaE   9 algkklakalgdvilLeGdLGaGKTtlvrglakalgve.....evkSP 51 
                                    +l ++l k  ++ il+ G  G+GKTt++++la+ +  +     +++SP
  gi|119719450|ref|YP_919945.1| 254 KLIERLEK-QAEGILIAGAPGMGKTTFAQALAEYYYRKgkvvkTIESP 300
                                    33344433.2345*******************9874333222356666 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   7.3e-05     0.038      23      54 ..     253     284 ..     239     390 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.3e-05
                         AAA_25  23 rwlvkgllpagelallaGapgtGKttlaldla 54 
                                    ++l+++l    e +l+aGapg GKtt+a  la
  gi|119719450|ref|YP_919945.1| 253 KKLIERLEKQAEGILIAGAPGMGKTTFAQALA 284
                                    67888888888889**************9998 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0     7e-05     0.037       3      22 ..     266     285 ..     264     293 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7e-05
                                    EEEEC-TTTCHHHHHHHHHH CS
                          NACHT   3 vilqGeaGsGKTtLlqklal 22 
                                    +++ G++G+GKTt++q la+
  gi|119719450|ref|YP_919945.1| 266 ILIAGAPGMGKTTFAQALAE 285
                                    789**************986 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0     8e-05     0.042      14      67 ..     256     312 ..     251     324 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 8e-05
                                    HHHHHT-SS-EEEEEETT--HHHHHHCC--T...TS-EE--SSTTHHHH-HHHHHHH CS
                Sigma54_activ_2  14 LeqaaqsklpvfltGekGsgkelvArlLhkn...sgpwleifvverlaklpldlleq 67 
                                    +e ++++   ++++G++G gk+++A++L++    +g++++  +  r+++lp+d+ + 
  gi|119719450|ref|YP_919945.1| 256 IERLEKQAEGILIAGAPGMGKTTFAQALAEYyyrKGKVVKTIESPRDMHLPADITQY 312
                                    6788888899*******************9622245555555666677888888765 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   8.5e-05     0.045      18      48 ..     265     295 ..     252     304 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.5e-05
                     Zeta_toxin  18 lillgGqpGAGKselaellkdelerqgnvvr 48 
                                     il++G+pG GK++ a++l+++  r+g+vv+
  gi|119719450|ref|YP_919945.1| 265 GILIAGAPGMGKTTFAQALAEYYYRKGKVVK 295
                                    59********************999999986 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00034      0.18       3      45 ..     270     312 ..     268     329 .. 0.71
   2 ?   -0.3   0.0       1.4   7.5e+02     110     126 ..     322     339 ..     310     344 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00034
                                    ESTTSSHHHHHHHHHHHHHHTTE.EEEESSSTTSHHHHHHHHH CS
                Thymidylate_kin   3 GlDGaGKttqaellkerlkeegikvvltrepggteiGekirel 45 
                                    G  G GKtt+a++l+e++ ++g+ v +   p++  +   i ++
  gi|119719450|ref|YP_919945.1| 270 GAPGMGKTTFAQALAEYYYRKGKVVKTIESPRDMHLPADITQY 312
                                    7789******************644444556666666666666 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.4
                                    HGGGTTS.E-SEEEEEES CS
                Thymidylate_kin 110 lnedvll.kPdltflldv 126
                                    +++ +ll +Pd+tf+ ++
  gi|119719450|ref|YP_919945.1| 322 IHDVLLLsRPDYTFFDEM 339
                                    44445559*******875 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00023      0.12       2      21 ..     266     285 ..     266     323 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00023
                         AAA_33   2 vllvGlpGsGKstlaerllk 21 
                                    +l+ G+pG+GK+t+a+ l++
  gi|119719450|ref|YP_919945.1| 266 ILIAGAPGMGKTTFAQALAE 285
                                    5789************9984 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00019       0.1       4      37 ..     266     299 ..     265     371 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00019
                                    EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-T CS
                          KTI12   4 vvltGlPssGKstrakeLakaleeekrsvvvidd 37 
                                    +++ G P  GK+t+a+ La++   +++ v  i++
  gi|119719450|ref|YP_919945.1| 266 ILIAGAPGMGKTTFAQALAEYYYRKGKVVKTIES 299
                                    799*******************999998887763 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00016     0.085      28      61 ..     262     295 ..     243     299 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00016
                                    -SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EE CS
                           MeaB  28 raqvvGltGvPGaGkstlvealglelrrrGkrva 61 
                                    +a+ + + G PG Gk t+ +al++ + r+Gk v 
  gi|119719450|ref|YP_919945.1| 262 QAEGILIAGAPGMGKTTFAQALAEYYYRKGKVVK 295
                                    4677889***********************9886 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0    0.0002      0.11      13      52 ..     254     293 ..     247     303 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0002
                                    HHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS- CS
                Sigma54_activat  13 eqikkvaktdlsvlitGesGtGKellaraiheaskrkekp 52 
                                    + i+++ k+   +li G  G GK+++a+a+ e   rk k 
  gi|119719450|ref|YP_919945.1| 254 KLIERLEKQAEGILIAGAPGMGKTTFAQALAEYYYRKGKV 293
                                    567788888899******************9988877764 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00029      0.15       2      31 ..     266     295 ..     265     301 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00029
                                    EEEE--TTSSHHHHHHHHHHHH...GGGEE CS
                       NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvg 31 
                                    ++i G pG+GKtT+ + ++e   ++g  v+
  gi|119719450|ref|YP_919945.1| 266 ILIAGAPGMGKTTFAQALAEYYYRKGKVVK 295
                                    789****************99988887765 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00019       0.1       2      44 ..     266     312 ..     265     324 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00019
                          AAA_3   2 vllegvPGlaktllvkalakaldle...fkriqftpdl.lPsdilGt 44 
                                    +l+ g+PG++kt++++ala+    +   +k i    d+ lP+di+  
  gi|119719450|ref|YP_919945.1| 266 ILIAGAPGMGKTTFAQALAEYYYRKgkvVKTIESPRDMhLPADITQY 312
                                    799****************9876551125566667787689999865 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00025      0.13       1      30 [.     268     297 ..     268     322 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00025
                     ATP_bind_1   1 vvGpaGsGKttfvgalseilelrgrsvavv 30 
                                    ++G +G GKttf +al+e++  +g+ v+++
  gi|119719450|ref|YP_919945.1| 268 IAGAPGMGKTTFAQALAEYYYRKGKVVKTI 297
                                    68******************9999888776 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00032      0.17       4      29 ..     262     287 ..     258     322 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00032
                         AAA_22   4 tagilvvtGesGtGKTtllrrlleql 29 
                                    +a  +++ G +G+GKTt ++ l+e +
  gi|119719450|ref|YP_919945.1| 262 QAEGILIAGAPGMGKTTFAQALAEYY 287
                                    677799***************99876 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00065      0.34       1      26 [.     266     291 ..     266     351 .. 0.80
   2 ?   -1.5   0.0       6.2   3.2e+03      29      64 ..     396     435 ..     382     442 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00065
                   RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl 26 
                                    i++ G++g GK+t+a+ La+   +k 
  gi|119719450|ref|YP_919945.1| 266 ILIAGAPGMGKTTFAQALAEYYYRKG 291
                                    6899*************998776554 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 6.2
                   RNA_helicase  29 kkkdsvysrnpeddfwdgYt....gqevvvidDfgqvkde 64 
                                     + ++vys +++ ++ +g +      +vvv+ Df+  + e
  gi|119719450|ref|YP_919945.1| 396 GRVEKVYSLETTVKIPHGLKeedlARPVVVVRDFMTGEPE 435
                                    5567788888888888888733233579999999876655 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00037       0.2       5      22 ..     266     283 ..     262     294 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00037
                         AAA_24   5 iliyGpsgiGKTtlakel 22 
                                    ili G +g+GKTt+a  l
  gi|119719450|ref|YP_919945.1| 266 ILIAGAPGMGKTTFAQAL 283
                                    89*************977 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00036      0.19       8      40 ..     261     293 ..     253     348 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00036
                         AAA_19   8 lkekvllvtaGpGtGKTrvlkhivallvelggv 40 
                                     +++ +l+ + pG+GKT+  ++  +++ + g+v
  gi|119719450|ref|YP_919945.1| 261 KQAEGILIAGAPGMGKTTFAQALAEYYYRKGKV 293
                                    5667789999************99999988876 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00039      0.21      51      89 ..     261     301 ..     252     319 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00039
                         DUF815  51 lpannvLLwGarGtGKSslvkallneyaeeg..Lrlievek 89 
                                    ++a+ +L+ Ga G+GK +  +al + y ++g  ++ ie  +
  gi|119719450|ref|YP_919945.1| 261 KQAEGILIAGAPGMGKTTFAQALAEYYYRKGkvVKTIESPR 301
                                    68999**********************99997778777655 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00049      0.26      19      49 ..     264     294 ..     253     305 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00049
                         AAA_30  19 rvavltGpAGtGKttalkalreaweaaggrv 49 
                                       ++ G++G GKtt  +al+e + ++g+ v
  gi|119719450|ref|YP_919945.1| 264 EGILIAGAPGMGKTTFAQALAEYYYRKGKVV 294
                                    467899******************9998655 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00047      0.25      36      59 ..     260     283 ..     246     284 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00047
                                    GGS-.SEEEE--TTSSHHHHHHHH CS
                   FtsK_SpoIIIE  36 kkmashllvaGatgsGKStalntL 59 
                                     k a  +l+aGa+g GK+t+ ++L
  gi|119719450|ref|YP_919945.1| 260 EKQAEGILIAGAPGMGKTTFAQAL 283
                                    5566689*************9998 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00065      0.34      11      44 ..     263     294 ..     260     347 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00065
                                    TSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  11 gekvaivGenGaGKStLlkllagllkpteGeill 44 
                                     e + i G  G GK+t++++la+ +   +G++ +
  gi|119719450|ref|YP_919945.1| 263 AEGILIAGAPGMGKTTFAQALAEYYY-RKGKV-V 294
                                    567889***************99886.78998.2 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00066      0.35      10      40 ..     253     283 ..     249     330 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00066
                                    HHHHCTTTSCSEEEEEEESTTSSHHHHHHHH CS
                         NB-ARC  10 ekLlekdelqslvvalvGmgGvGKttlakqi 40 
                                    +kL e  e q   + + G +G+GKtt a+  
  gi|119719450|ref|YP_919945.1| 253 KKLIERLEKQAEGILIAGAPGMGKTTFAQAL 283
                                    67777777777789************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (530 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      619  (0.0345251); expected 358.6 (0.02)
Passed Vit filter:                       130  (0.00725082); expected 17.9 (0.001)
Passed Fwd filter:                        34  (0.00189637); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              34  [number of targets reported over threshold]
# CPU time: 0.70u 0.32s 00:00:01.02 Elapsed: 00:00:00.50
# Mc/sec: 3212.70
//
Query:       gi|119719451|ref|YP_919946.1|  [L=130]
Description: hypothetical protein Tpen_0537 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 892.61
//
Query:       gi|119719452|ref|YP_919947.1|  [L=202]
Description: XRE family transcriptional regulator [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-20   73.4   1.2    1.4e-09   38.2   0.0    2.3  2  CBS             CBS domain
    3.2e-13   49.5   2.0    7.5e-13   48.3   0.8    2.2  2  HTH_3           Helix-turn-helix
    1.5e-12   47.6   0.9    1.5e-12   47.6   0.9    2.0  2  HTH_31          Helix-turn-helix domain
    3.7e-07   30.1   0.2    1.1e-06   28.5   0.2    1.9  1  HTH_19          Helix-turn-helix domain
    9.3e-05   22.8   0.3     0.0004   20.8   0.1    2.0  2  HTH_26          Cro/C1-type HTH DNA-binding domain
    0.00093   19.0   0.5     0.0028   17.5   0.3    1.9  2  HTH_25          Helix-turn-helix domain
     0.0019   17.7   0.9     0.0081   15.7   0.4    2.4  3  HTH_24          Winged helix-turn-helix DNA-binding
     0.0058   16.4   1.9      0.041   13.7   0.2    2.9  4  HTH_38          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.015   15.2   0.1      0.046   13.7   0.1    1.8  1  HTH_37          Helix-turn-helix domain
      0.015   15.1   0.9       0.45   10.4   0.2    3.1  4  HTH_23          Homeodomain-like domain
      0.021   15.5   0.0      0.042   14.5   0.0    1.5  1  DUF4936         Domain of unknown function (DUF4936)
      0.022   14.5   0.1       0.18   11.5   0.0    2.3  2  HTH_Tnp_4       Helix-turn-helix of DDE superfamily endonucle
      0.022   14.2   0.9      0.046   13.2   0.2    1.9  2  Sigma70_r4      Sigma-70, region 4
      0.028   14.4   0.1      0.069   13.1   0.1    1.7  1  Pou             Pou domain - N-terminal to homeobox domain
      0.035   14.2   0.0      0.064   13.4   0.0    1.4  1  MqsA_antitoxin  Antitoxin component of bacterial toxin-antito
      0.049   13.7   0.2        0.2   11.7   0.1    2.0  2  Thioredoxin_3   Thioredoxin domain
      0.084   12.8   0.8       0.27   11.2   0.4    2.0  2  MarR_2          MarR family


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2   0.0   1.3e-12   1.4e-09       3      55 ..      80     133 ..      78     135 .. 0.92
   2 !   33.6   0.6   3.7e-11     4e-08       2      56 ..     146     198 ..     145     199 .. 0.89

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 1.3e-12
                                    HHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEE.ETTTBEEEEEEHHHHHHHH CS
                            CBS   3 dimtrdvvtvppdttleealelmrekgvsrlPVV.dedgklvGivtlrDllral 55 
                                    ++m++++v+v+p+t+l e++++m ekg+s+lPV+ d++++ +G v + D+lra 
  gi|119719452|ref|YP_919947.1|  80 EVMSSPLVYVKPSTSLLEVARIMWEKGFSQLPVIdDSSNENLGTVFDDDVLRAF 133
                                    89********************98999*******777779***********985 PP

  == domain 2  score: 33.6 bits;  conditional E-value: 3.7e-11
                                    HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                            CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                    +d+m+++++ ++  t ++ +++++  +gv ++  V+++ k+ Gi+t++D++++l+
  gi|119719452|ref|YP_919947.1| 146 ADVMSDPLPIISCGTKIRVVARML-GRGVPAV-LVEDEMKIKGIITKSDIAKLLV 198
                                    79**********************.7556666.588899************9985 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3   0.8   7.1e-16   7.5e-13       1      48 [.      21      68 ..      21      70 .. 0.96
   2 ?   -1.3   0.0       2.2   2.3e+03       9      22 ..     187     200 ..     181     202 .] 0.77

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 7.1e-16
                                   HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHH CS
                          HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaL 48
                                   l+ lR+ +gl+q eLA+++Gvs+s i+riE G+ nP+++tl k+ +aL
  gi|119719452|ref|YP_919947.1| 21 LRLLRLRAGLTQVELAQRAGVSQSLIARIEAGKVNPRVSTLMKIYRAL 68
                                   799****************************************98777 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.2
                                    THHHHHHHHHHTSS CS
                          HTH_3   9 glsqeeLAeklGvs 22 
                                     +++ ++A++l vs
  gi|119719452|ref|YP_919947.1| 187 IITKSDIAKLLVVS 200
                                    58899999999887 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.6   0.9   1.5e-15   1.5e-12       5      55 ..      20      69 ..      18      78 .. 0.92
   2 ?   -2.0   0.1       4.5   4.7e+03      20      20 ..     148     148 ..     129     176 .. 0.55

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 1.5e-15
                         HTH_31  5 lLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralg 55
                                   +Lr lR raGL+q e+A+r+gvs+s + r+E G+  +p+ ++l ++ ral 
  gi|119719452|ref|YP_919947.1| 20 ELRLLRLRAGLTQVELAQRAGVSQSLIARIEAGKV-NPRVSTLMKIYRALE 69
                                   8**********************************.6******99999986 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.5
                         HTH_31  20 v 20 
                                    v
  gi|119719452|ref|YP_919947.1| 148 V 148
                                    2 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.2   1.1e-09   1.1e-06       4      53 ..      21      69 ..      19      78 .. 0.92

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 1.1e-09
                         HTH_19  4 LkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealg 53
                                   L+ +R  +gltq ela+r+g+s+s i+ iE gk  +p  ++l ki++al+
  gi|119719452|ref|YP_919947.1| 21 LRLLRLRAGLTQVELAQRAGVSQSLIARIEAGKV-NPRVSTLMKIYRALE 69
                                   899999**************************99.*******99999997 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.1   3.8e-07    0.0004       2      51 ..      21      69 ..      20      76 .. 0.90
   2 ?   -0.4   0.0       1.5   1.6e+03       6      23 ..     182     200 ..     179     202 .] 0.81

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 3.8e-07
                         HTH_26  2 LrelmadrgitkseLargtgisaatlsrlvkgkpervsldtLdkiCdaLg 51
                                   Lr l    g+t+ eLa+++g+s++ ++r+  gk+ +++ +tL+ki +aL+
  gi|119719452|ref|YP_919947.1| 21 LRLLRLRAGLTQVELAQRAGVSQSLIARIEAGKV-NPRVSTLMKIYRALE 69
                                   5666667789***********************6.**********99997 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.5
                         HTH_26   6 madrgi.tkseLargtgis 23 
                                    m+ +gi tks+ a+ + +s
  gi|119719452|ref|YP_919947.1| 182 MKIKGIiTKSDIAKLLVVS 200
                                    7889999***999987665 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.3   2.7e-06    0.0028       2      35 ..      21      54 ..      20      56 .. 0.94
   2 ?   -2.3   0.0       4.1   4.3e+03      44      60 ..     130     146 ..     123     148 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.7e-06
                                   HHHHHHTTT--HHHHHHHSS--HHHHHHHHCT-- CS
                         HTH_25  2 LraaRearglsleevaketkIrkdylealEeddf 35
                                   Lr  R+++gl+  e+a++  ++++++ ++E++++
  gi|119719452|ref|YP_919947.1| 21 LRLLRLRAGLTQVELAQRAGVSQSLIARIEAGKV 54
                                   8999***************************986 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4.1
                                    HHHHHHHHHHHTT--HH CS
                         HTH_25  44 lrgylrnYArlLgldpe 60 
                                    lr+++r+  r+ +l ++
  gi|119719452|ref|YP_919947.1| 130 LRAFIRENTRAAQLTAA 146
                                    78888887777666655 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.4   7.7e-06    0.0081       9      36 ..      21      48 ..      21      49 .. 0.92
   2 ?   -3.2   0.0       6.2   6.6e+03      19      33 ..     161     175 ..     159     177 .. 0.69
   3 ?   -2.5   0.0       3.7   3.9e+03      18      26 ..     188     196 ..     185     200 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 7.7e-06
                         HTH_24  9 LelLqknprisqreLAerlglSpstvnr 36
                                   L+lL+  ++++q eLA+r g+S+s + r
  gi|119719452|ref|YP_919947.1| 21 LRLLRLRAGLTQVELAQRAGVSQSLIAR 48
                                   7899999****************98876 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 6.2
                         HTH_24  19 sqreLAerlglSpst 33 
                                     +r +A++lg  +++
  gi|119719452|ref|YP_919947.1| 161 KIRVVARMLGRGVPA 175
                                    567889999866655 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 3.7
                         HTH_24  18 isqreLAer 26 
                                    i+ +++A+ 
  gi|119719452|ref|YP_919947.1| 188 ITKSDIAKL 196
                                    888999986 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.2   3.9e-05     0.041      16      39 ..      24      48 ..      19      49 .. 0.86
   2 ?   -1.9   0.0       2.9     3e+03      14      23 ..     100     109 ..      97     109 .. 0.75
   3 ?    0.3   0.1      0.57     6e+02      23      32 ..     162     171 ..     158     172 .. 0.87
   4 ?   -3.5   0.0       8.8   9.3e+03      25      30 ..     192     197 ..     190     200 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.9e-05
                         HTH_38 16 l.laeGlslreIArrLgrspsTIsR 39
                                   l l +Gl++ e A+r g+s s I+R
  gi|119719452|ref|YP_919947.1| 24 LrLRAGLTQVELAQRAGVSQSLIAR 48
                                   5368********************9 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.9
                         HTH_38  14 erllaeGlsl 23 
                                     +++++G s+
  gi|119719452|ref|YP_919947.1| 100 RIMWEKGFSQ 109
                                    5789999986 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.57
                         HTH_38  23 lreIArrLgr 32 
                                    +r +Ar Lgr
  gi|119719452|ref|YP_919947.1| 162 IRVVARMLGR 171
                                    7999*****9 PP

  == domain 4  score: -3.5 bits;  conditional E-value: 8.8
                         HTH_38  25 eIArrL 30 
                                    +IA++L
  gi|119719452|ref|YP_919947.1| 192 DIAKLL 197
                                    789887 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   4.4e-05     0.046      29      67 ..      27      64 ..      20      71 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.4e-05
                                   HCT--HHHHHHHHT--HHHHHHHHTT--TT--HHHHHHH CS
                         HTH_37 29 krelsqseaaqllgiaqPkvsrllrgklsrfsldkLlnl 67
                                   + +l+q e+aq+ g++q+ + r++ gk++  ++++L+++
  gi|119719452|ref|YP_919947.1| 27 RAGLTQVELAQRAGVSQSLIARIEAGKVNP-RVSTLMKI 64
                                   679***********************9974.56666665 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.2   0.00043      0.45       8      37 ..      21      49 ..      19      52 .. 0.86
   2 ?   -2.5   0.0       4.7     5e+03      33      44 ..      63      74 ..      60      77 .. 0.76
   3 ?    1.1   0.0      0.34   3.6e+02      17      31 ..     159     173 ..     134     177 .. 0.76
   4 ?   -1.9   0.0         3   3.1e+03      19      27 ..     189     197 ..     188     201 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00043
                         HTH_23  8 lrillllaeGlsvreIAreLgvsrrTvyrw 37
                                   lr l+l a Gl++ e A++ gvs++ + r+
  gi|119719452|ref|YP_919947.1| 21 LRLLRLRA-GLTQVELAQRAGVSQSLIARI 49
                                   56677777.****************99998 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.7
                         HTH_23 33 Tvyrwlkryree 44
                                    +yr l+ + ee
  gi|119719452|ref|YP_919947.1| 63 KIYRALESFMEE 74
                                   589999999776 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.34
                         HTH_23  17 GlsvreIAreLgvsr 31 
                                    G  +r +Ar+Lg+  
  gi|119719452|ref|YP_919947.1| 159 GTKIRVVARMLGRGV 173
                                    667899*****9866 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 3
                         HTH_23  19 svreIAreL 27 
                                    ++++IA++L
  gi|119719452|ref|YP_919947.1| 189 TKSDIAKLL 197
                                    7899**998 PP

>> DUF4936  Domain of unknown function (DUF4936)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0     4e-05     0.042      21      61 ..      31      71 ..      18      90 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4e-05
                        DUF4936 21 lqaalaartgvagrLlrrlddpesqdglaTwMEvYedvdda 61
                                    q +la+r gv+  L  r+++++ +  ++T+M +Y++ +  
  gi|119719452|ref|YP_919947.1| 31 TQVELAQRAGVSQSLIARIEAGKVNPRVSTLMKIYRALESF 71
                                   57799******************************998765 PP

>> HTH_Tnp_4  Helix-turn-helix of DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00017      0.18      13      39 ..      23      49 ..      21      49 .. 0.92
   2 ?   -0.1   0.0      0.72   7.6e+02      33      52 ..      58      77 ..      57      78 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00017
                      HTH_Tnp_4 13 LvyLRlnltyqdLayrFgvsestvsri 39
                                   L +LR +lt+  La+r gvs+s + ri
  gi|119719452|ref|YP_919947.1| 23 LLRLRAGLTQVELAQRAGVSQSLIARI 49
                                   89********************88776 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.72
                      HTH_Tnp_4 33 estvsrifhkwvdlLaerlk 52
                                   +st  +i ++++ +++e+l+
  gi|119719452|ref|YP_919947.1| 58 VSTLMKIYRALESFMEEELT 77
                                   58889999*******99986 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   4.4e-05     0.046      15      41 ..      24      50 ..      17      52 .. 0.83
   2 ?   -3.1   0.0       5.6   5.9e+03      17      26 ..      71      81 ..      66      81 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.4e-05
                                   HHHTTT--HHHHHHHHTS-HHHHHHHH CS
                     Sigma70_r4 15 lrfgeglTleEIgerlgiSrerVrqie 41
                                   lr   glT+ E+++r g+S++ + +ie
  gi|119719452|ref|YP_919947.1| 24 LRLRAGLTQVELAQRAGVSQSLIARIE 50
                                   344689***************999998 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5.6
                                   H.TTT--HHHH CS
                     Sigma70_r4 17 f.geglTleEI 26
                                   f +e+lT +E+
  gi|119719452|ref|YP_919947.1| 71 FmEEELTACEV 81
                                   45899998886 PP

>> Pou  Pou domain - N-terminal to homeobox domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   6.6e-05     0.069      11      70 ..      19      74 ..      17      75 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.6e-05
                            Pou 11 kefkqkRiklgltQadvglaLgklygkefSqttIcrFEkLdlslk..nmlklkplLekWLee 70
                                   +e++  R++ gltQ ++++         +Sq+ I r+E+ +++++   ++k++  Le+ +ee
  gi|119719452|ref|YP_919947.1| 19 EELRLLRLRAGLTQVELAQR------AGVSQSLIARIEAGKVNPRvsTLMKIYRALESFMEE 74
                                   689999********998876......689*********998886422677888888887776 PP

>> MqsA_antitoxin  Antitoxin component of bacterial toxin-antitoxin system, MqsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   6.1e-05     0.064      71     122 ..      18      70 ..      13      76 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.1e-05
                 MqsA_antitoxin  71 pafiarvrkkleldqreaaeifGgGvnafsryekGkvrppla.lvkllklldr 122
                                    p++++ +r + +l+q e+a+  G+     +r e+Gkv+p ++ l+k+++ l+ 
  gi|119719452|ref|YP_919947.1|  18 PEELRLLRLRAGLTQVELAQRAGVSQSLIARIEAGKVNPRVStLMKIYRALES 70 
                                    67778889999****************************98747899998875 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       4.2   4.5e+03      40      54 ..      74      88 ..      61      90 .. 0.67
   2 ?   11.7   0.1   0.00019       0.2      49      75 ..     172     197 ..     162     198 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 4.2
                                   HHHHHCT-SSSSEEE CS
                  Thioredoxin_3 40 eeiekygVmsvPalv 54
                                   ee+   +Vms P ++
  gi|119719452|ref|YP_919947.1| 74 EELTACEVMSSPLVY 88
                                   344677788888775 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00019
                                    SSSEEECTTCEEEESS---CCHHHHHH CS
                  Thioredoxin_3  49 svPalvidgkvvvsGkvpseeeirkll 75 
                                     vPa++++++++++G + ++ +i+kll
  gi|119719452|ref|YP_919947.1| 172 GVPAVLVEDEMKIKG-IITKSDIAKLL 197
                                    69*************.********997 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.4   0.00026      0.27      11      41 ..      21      49 ..      20      50 .. 0.91
   2 ?   -2.1   0.0       3.6   3.8e+03      22      31 ..     188     197 ..     163     200 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00026
                                   HHHHHCTTTSEEEHHHHHHHHTSSHHHHHHH CS
                         MarR_2 11 LaaLgrrpgrdltvgelarrlglsksavsri 41
                                   L  L+ r g  lt+ ela+r g+s+s + ri
  gi|119719452|ref|YP_919947.1| 21 LRLLRLRAG--LTQVELAQRAGVSQSLIARI 49
                                   667899999..***************99887 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.6
                                    EEHHHHHHHH CS
                         MarR_2  22 ltvgelarrl 31 
                                    +t +++a+ l
  gi|119719452|ref|YP_919947.1| 188 ITKSDIAKLL 197
                                    3556666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1497.83
//
Query:       gi|119719453|ref|YP_919948.1|  [L=444]
Description: 4-aminobutyrate aminotransferase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   5.4e-134  446.9   0.0   6.6e-134  446.6   0.0    1.0  1  Aminotran_3    Aminotransferase class-III
     0.0052   16.0   0.0     0.0081   15.4   0.0    1.3  1  Aminotran_1_2  Aminotransferase class I and II
  ------ inclusion threshold ------
       0.19   10.6   0.0         47    2.8   0.0    2.9  3  Aminotran_5    Aminotransferase class-V


Domain annotation for each model (and alignments):
>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  446.6   0.0  1.1e-137  6.6e-134      10     404 ..      35     435 ..      28     437 .. 0.96

  Alignments for each domain:
  == domain 1  score: 446.6 bits;  conditional E-value: 1.1e-137
                                    CEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT-..S. CS
                    Aminotran_3  10 llvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklapkgld. 88 
                                    +lv+++a+Gv+++dvdg+ ylD+ s+i v+n+Gh+hPkvvka+keqa+ l h s+  + +e+ +klaekl++++p+ +  
  gi|119719453|ref|YP_919948.1|  35 PLVAKRAHGVWVEDVDGNVYLDFNSGIGVTNTGHCHPKVVKAIKEQAERLLHYSLTDFLYEEPVKLAEKLVSITPGRFPk 114
                                    4899************************************************************************9977 PP

                                    EEEEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEEEE-TTBGGGT CS
                    Aminotran_3  89 kvflansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevvrlkypdeevl 168
                                    kvf+ nsG+e++e+A+K+ar     + +  +++iiaf g+fHGrt+g+ls+t+sk+  ++ +gp+lp+v +++yp+++++
  gi|119719453|ref|YP_919948.1| 115 KVFYTNSGTESIEAAIKTARG----HFRGTRPYIIAFAGSFHGRTYGSLSLTSSKPVQRRHLGPLLPGVFHAPYPYCYRC 190
                                    9********************....33778************************************************** PP

                                    B-HHHHHHHHHHHHHHHH......CHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE-TTTTTTTTS CS
                    Aminotran_3 169 keneeeeaalleeleale......kkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivDEvqtGfGrTG 242
                                    +++++  ++ l ++  +e       +  +evaA++vEpi gegG++v++pef+++lrel++k+++ll+vDEvq+GfGrTG
  gi|119719453|ref|YP_919948.1| 191 PFRQKYPECNLWCVDFIEewmlkkYVPPEEVAAFVVEPIAGEGGYIVPPPEFFKRLRELADKYGILLVVDEVQSGFGRTG 270
                                    ****9999999999999888776666789*************************************************** PP

                                    SSSGGGGCTS--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTSB--TTTT-HHHHHHHHHHHHHHHHTTHHHHHHHHHH CS
                    Aminotran_3 243 klfAlehagvspDlmtlaKaltgGlplsavlataevmqalapgshgsTfgGnplacavalavleiieeekllenaqelga 322
                                    k+fA+eh+gv+pD++++aK++++Glpl a++++aevm+   pgsh+sTfgGnp+ ca+ala++e+ieeekll+na ++g+
  gi|119719453|ref|YP_919948.1| 271 KWFAIEHFGVEPDIIAVAKGIASGLPLGAIIGRAEVMDLP-PGSHASTFGGNPVSCAAALATIEVIEEEKLLDNATRVGE 349
                                    **************************************98.*************************************** PP

                                    HHHHHHHHHCTT-TTEEEEEEETTEEEEEEBCCCETTC....HHHHHHHHHCTEE-EEETTTEEEE---TT--HHHHHHH CS
                    Aminotran_3 323 alkegLeelqkkyevikevRgkGlmiaielkeeaevke....keilkkakekGvlilsaGdnvirllppliitdeeidel 398
                                    +  ++L+elq++  +i++vRgkGlmi++el +++   +    ++ l+ a +kG+l+++aG ++ir++ppliit++e++ +
  gi|119719453|ref|YP_919948.1| 350 YAMKRLRELQEEIPYIGDVRGKGLMIGVELIARDGSPNpkllQKTLEIAFKKGLLVIGAGVSTIRIAPPLIITQQEMETG 429
                                    *******************************9988555789988999999****************************** PP

                                    HHHHHH CS
                    Aminotran_3 399 leilkk 404
                                    l il++
  gi|119719453|ref|YP_919948.1| 430 LRILEE 435
                                    *99987 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.4e-06    0.0081     164     241 ..     237     308 ..     236     417 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.4e-06
                                    B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHH CS
                  Aminotran_1_2 164 vatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilgnaavvs 241
                                    v+++e  + l +la+ky++ll+vDe+ +gf  + + ++  +++ve+++    +   + a Gl+    G+i+g a+v +
  gi|119719453|ref|YP_919948.1| 237 VPPPEFFKRLRELADKYGILLVVDEVQSGFGRTGKWFAIEHFGVEPDII---AVAKGIASGLPL---GAIIGRAEVMD 308
                                    7899999*************************98744333999988644...433333445555...77777776665 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.008        48      58      88 ..     110     140 ..      66     151 .. 0.82
   2 ?    2.8   0.0    0.0079        47     158     179 ..     243     264 ..     219     270 .. 0.86
   3 ?    1.0   0.0     0.026   1.6e+02     259     297 ..     323     361 ..     320     408 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.008
                                    -STGGGEEEESSHHHHHHHHHHHCCCC-TTT CS
                    Aminotran_5  58 aeseeeiiftsGtteainlvalslarslkpg 88 
                                     +  +++ +t ++te+i++++++++ +++  
  gi|119719453|ref|YP_919948.1| 110 GRFPKKVFYTNSGTESIEAAIKTARGHFRGT 140
                                    5667899**************9998776655 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.0079
                                    HHHHHHHHHHTT-EEEEE-TTT CS
                    Aminotran_5 158 veeigklakkkgalvlvDaaqa 179
                                    ++++ +la k+g+l++vD +q+
  gi|119719453|ref|YP_919948.1| 243 FKRLRELADKYGILLVVDEVQS 264
                                    5678889999***********8 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.026
                                    HHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCTSTTE CS
                    Aminotran_5 259 iglgaaleyleeigleaiekhekelaeyllerlkslpgv 297
                                    ++++aal  +e i+ e+    +++  ey+++rl++l++ 
  gi|119719453|ref|YP_919948.1| 323 VSCAAALATIEVIEEEKLLDNATRVGEYAMKRLRELQEE 361
                                    68999******************************9864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (444 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 3181.43
//
Query:       gi|119719454|ref|YP_919949.1|  [L=185]
Description: pyruvate/ketoisovalerate oxidoreductase, gamma subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-30  106.7   0.6    1.8e-30  106.3   0.6    1.1  1  POR              Pyruvate ferredoxin/flavodoxin oxidoreductas
  ------ inclusion threshold ------
      0.029   14.2   0.0      0.068   13.0   0.0    1.7  1  Biotin_lipoyl_2  Biotin-lipoyl like


Domain annotation for each model (and alignments):
>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.3   0.6     2e-34   1.8e-30       1     176 [.      13     178 ..      13     179 .. 0.91

  Alignments for each domain:
  == domain 1  score: 106.3 bits;  conditional E-value: 2e-34
                                    CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHH..HHGGGEEE CS
                            POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetls..ehldglkp 78 
                                    GGqG+vta+ +la+aa+  G+y++a +++g+e+rG++++++ ri+d  i ++ +v + d+l +ld+++l   ++ + lkp
  gi|119719454|ref|YP_919949.1|  13 GGQGAVTAASLLAQAAVLRGKYALAIPFFGAERRGAPVFAYTRIADGTILSRARVKRGDILAVLDPSLLGqvNVESLLKP 92 
                                    9*********************************************8899****************99988999999*** PP

                                    EEEEEEECTCGTT-CCHHHCTS-HHHHHHHT-EEEEE-HHHHHHHCCC....CCHHHHHHHHHHHHHHT.S-HHHHHHHH CS
                            POR  79 ggiiiynseelkpdelkkakeeerelkerlgvrvygvdatkiakeiggn...eraaNtvmlGalaallg.lplealeeai 154
                                    gg i++n++    ++ ++              + y vda  ia+ +g      +++N+ m+Ga+ ++ g ++l +le a+
  gi|119719454|ref|YP_919949.1|  93 GGRIVINTGGRRIEVGARG-------------EAYCVDAVSIADSLGLRlagIVLVNMPMVGAVGRVYGgVGLPDLESAV 159
                                    ********87433333332.............259*********666656669*************************** PP

                                    HCCS-CH.HHHHHHHHHHHHHH CS
                            POR 155 kkrfpkkkeviekNlkafragy 176
                                    k+ ++     +e+N++a+++g 
  gi|119719454|ref|YP_919949.1| 160 KEVIKV---HVERNVEAVKRGW 178
                                    *****6...5*********995 PP

>> Biotin_lipoyl_2  Biotin-lipoyl like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   7.6e-06     0.068      23      36 ..      66      79 ..      65      87 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.6e-06
                Biotin_lipoyl_2 23 rVkaGdvLaelDsr 36
                                   rVk Gd+La+lD++
  gi|119719454|ref|YP_919949.1| 66 RVKRGDILAVLDPS 79
                                   8***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 1235.97
//
Query:       gi|119719455|ref|YP_919950.1|  [L=87]
Description: pyruvate ferredoxin/flavodoxin oxidoreductase, delta subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.6e-15   54.4  14.6    2.8e-08   33.2   4.4    2.3  2  Fer4        4Fe-4S binding domain
    7.2e-11   42.5  16.9    5.1e-09   36.6   8.5    1.6  2  Fer4_7      4Fe-4S dicluster domain
    6.1e-10   38.7  13.5    5.7e-06   26.2   3.0    2.4  3  Fer4_6      4Fe-4S binding domain
    8.6e-10   38.6  19.3    7.5e-07   29.2   9.6    1.7  2  Fer4_10     4Fe-4S dicluster domain
    7.2e-09   35.7   7.4    9.3e-09   35.3   7.4    1.2  1  Fer4_21     4Fe-4S dicluster domain
    1.1e-07   31.9   7.4    1.6e-07   31.4   7.4    1.3  1  Fer4_9      4Fe-4S dicluster domain
    3.4e-07   31.1   6.8      0.002   19.0   2.1    2.1  2  Fer4_16     4Fe-4S double cluster binding domain
    3.8e-07   30.8  11.5     0.0039   17.9   2.7    2.5  2  Fer4_15     4Fe-4S single cluster domain
    3.8e-06   27.3   2.7      0.043   14.4   0.5    2.1  2  Fer4_17     4Fe-4S dicluster domain
    5.3e-06   26.2  14.1     0.0031   17.5   4.0    2.4  2  Fer4_2      4Fe-4S binding domain
    6.9e-05   23.0  13.3      0.013   15.9   4.0    2.2  2  Fer4_4      4Fe-4S binding domain
    0.00036   21.0   8.6      0.035   14.7   0.7    2.2  2  Fer4_13     4Fe-4S single cluster domain of Ferredoxin I
     0.0025   18.2  10.6       0.13   12.7   2.9    2.1  3  Fer4_8      4Fe-4S dicluster domain
  ------ inclusion threshold ------
       0.15   12.2   1.6       0.18   12.0   1.6    1.2  1  ETF_QO      Electron transfer flavoprotein-ubiquinone oxidore
       0.88   10.5  10.9       0.52   11.2   2.0    2.1  3  Fer4_22     4Fe-4S dicluster domain
          3    7.9   3.7        1.7    8.7   0.3    1.9  2  IBD         Transcription-initiator DNA-binding domain IBD


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   2.6   2.3e-09   2.6e-06       1      24 []      27      50 ..      27      50 .. 0.95
   2 !   33.2   4.4   2.5e-11   2.8e-08       1      24 []      58      81 ..      58      81 .. 0.95

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 2.3e-09
                                   EEEETTTSSS-THHHHHSTTTEEE CS
                           Fer4  1 vvideekCigCGaCvevCPvgAIt 24
                                   +v+d++kC  CG C   CP g+I+
  gi|119719455|ref|YP_919950.1| 27 PVVDMSKCRLCGVCWLYCPDGVIE 50
                                   69********************96 PP

  == domain 2  score: 33.2 bits;  conditional E-value: 2.5e-11
                                   EEEETTTSSS-THHHHHSTTTEEE CS
                           Fer4  1 vvideekCigCGaCvevCPvgAIt 24
                                   v+id++ C gCG C+  CP+ AI+
  gi|119719455|ref|YP_919950.1| 58 VKIDYDYCKGCGVCAAECPFKAIS 81
                                   68********************96 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   1.2   7.3e-06    0.0081      27      52 .]      23      48 ..      11      48 .. 0.86
   2 !   36.6   8.5   4.5e-12   5.1e-09       1      52 []      33      79 ..      33      79 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 7.3e-06
                         Fer4_7 27 gtekveidpekClgCgaCvavCPtga 52
                                   +te++++d++kC  Cg+C   CP g+
  gi|119719455|ref|YP_919950.1| 23 RTERPVVDMSKCRLCGVCWLYCPDGV 48
                                   457889*****************885 PP

  == domain 2  score: 36.6 bits;  conditional E-value: 4.5e-12
                         Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                   +C  Cg C  +Cp ++ie+de+      + v+id+++C gCg+C+a+CP++a
  gi|119719455|ref|YP_919950.1| 33 KCRLCGVCWLYCPDGVIEIDED-----ARLVKIDYDYCKGCGVCAAECPFKA 79
                                   7*******************98.....45699*****************987 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   1.9     1e-06    0.0012       2      24 .]      27      49 ..      26      49 .. 0.95
   2 ?   -0.4   0.0       1.2   1.4e+03       1       8 [.      48      55 ..      48      55 .. 0.85
   3 !   26.2   3.0   5.1e-09   5.7e-06       2      24 .]      58      80 ..      57      80 .. 0.95

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1e-06
                         Fer4_6  2 veidpdkCigCgdCvrvCPegai 24
                                   +++d +kC  Cg C   CP g+i
  gi|119719455|ref|YP_919950.1| 27 PVVDMSKCRLCGVCWLYCPDGVI 49
                                   89******************998 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.2
                         Fer4_6  1 vveidpdk 8 
                                   v+eid+d+
  gi|119719455|ref|YP_919950.1| 48 VIEIDEDA 55
                                   79***995 PP

  == domain 3  score: 26.2 bits;  conditional E-value: 5.1e-09
                         Fer4_6  2 veidpdkCigCgdCvrvCPegai 24
                                   v id+d C gCg C++ CP++ai
  gi|119719455|ref|YP_919950.1| 58 VKIDYDYCKGCGVCAAECPFKAI 80
                                   78*******************98 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   9.6   6.7e-10   7.5e-07       2      56 .]      27      76 ..      26      76 .. 0.94
   2 !   20.7   2.1   3.1e-07   0.00034       2      23 ..      58      79 ..      57      86 .. 0.84

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 6.7e-10
                        Fer4_10  2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                   +v+d ++C  Cg C   CP      g+++++++   v+++++ C gcg C+++CP
  gi|119719455|ref|YP_919950.1| 27 PVVDMSKCRLCGVCWLYCPD-----GVIEIDEDARLVKIDYDYCKGCGVCAAECP 76
                                   57899***************.....99999999999999***************9 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 3.1e-07
                        Fer4_10  2 vvidddtCirCgkCvkaCPadl 23
                                   v+id d C +Cg C + CP+++
  gi|119719455|ref|YP_919950.1| 58 VKIDYDYCKGCGVCAAECPFKA 79
                                   789****************955 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   7.4   8.3e-12   9.3e-09       2      59 .]      28      82 ..      27      82 .. 0.86

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 8.3e-12
                        Fer4_21  2 ridedkCigCgkCliaCedtshqaieidakt.vlkvvedeCvGCnlCssvCPvedciem 59
                                   ++d +kC  Cg C + C+d     ieid+++  +k+  d C GC +C++ CP  ++i+m
  gi|119719455|ref|YP_919950.1| 28 VVDMSKCRLCGVCWLYCPD---GVIEIDEDArLVKIDYDYCKGCGVCAAECPF-KAISM 82
                                   6899**************9...7888887761557779**************7.99988 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   7.4   1.4e-10   1.6e-07       1      51 []      33      80 ..      33      80 .. 0.93

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 1.4e-10
                         Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                   kC  Cg C   Cp gv++ d+ +r ++++  +   C gCg C++ Cp +ai
  gi|119719455|ref|YP_919950.1| 33 KCRLCGVCWLYCPDGVIEIDEDARLVKIDY-D--YCKGCGVCAAECPFKAI 80
                                   7**************************965.3..5************9987 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.2   3.4e-05     0.038       1      23 [.      33      55 ..      33      62 .. 0.85
   2 !   19.0   2.1   1.8e-06     0.002       2      21 ..      65      84 ..      64      87 .] 0.88

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.4e-05
                        Fer4_16  1 rCgtCgkCaevCPtnaikekkek 23
                                   +C  Cg C   CP ++i+ ++++
  gi|119719455|ref|YP_919950.1| 33 KCRLCGVCWLYCPDGVIEIDEDA 55
                                   5****************988555 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 1.8e-06
                        Fer4_16  2 CgtCgkCaevCPtnaikekk 21
                                   C++Cg Ca  CP +ai++ +
  gi|119719455|ref|YP_919950.1| 65 CKGCGVCAAECPFKAISMVR 84
                                   ****************9875 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   1.5   4.6e-06    0.0051       2      27 ..      28      54 ..      28      56 .. 0.87
   2 !   17.9   2.7   3.5e-06    0.0039       1      19 [.      58      76 ..      58      82 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.6e-06
                        Fer4_15  2 vvDrdaCigcglCvaea.pevfelded 27
                                   vvD ++C  cg+C+  + + v+e+ded
  gi|119719455|ref|YP_919950.1| 28 VVDMSKCRLCGVCWLYCpDGVIEIDED 54
                                   69***************4468999987 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 3.5e-06
                        Fer4_15  1 VvvDrdaCigcglCvaeap 19
                                   V++D d C gcg+C+ae+p
  gi|119719455|ref|YP_919950.1| 58 VKIDYDYCKGCGVCAAECP 76
                                   89****************8 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.1   6.8e-05     0.076      41      60 ..      29      48 ..       5      49 .. 0.76
   2 !   14.4   0.5   3.8e-05     0.043       2      14 ..      65      77 ..      52      86 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.8e-05
                        Fer4_17 41 ekaslCieCgeCerkCPqgl 60
                                     +s+C  Cg C  +CP g+
  gi|119719455|ref|YP_919950.1| 29 VDMSKCRLCGVCWLYCPDGV 48
                                   4799*************986 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 3.8e-05
                        Fer4_17  2 CiqCgyClpeCps 14
                                   C +Cg C++eCp+
  gi|119719455|ref|YP_919950.1| 65 CKGCGVCAAECPF 77
                                   7777777777776 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   2.5     3e-05     0.034       1      21 [.      25      45 ..      25      46 .. 0.87
   2 !   17.5   4.0   2.8e-06    0.0031       3      21 ..      58      76 ..      48      77 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3e-05
                         Fer4_2  1 apvvvdtdrCigCgaCvsa.CP 21
                                   +++vvd  +C  Cg C +  CP
  gi|119719455|ref|YP_919950.1| 25 ERPVVDMSKCRLCGVC-WLyCP 45
                                   589*************.55599 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 2.8e-06
                         Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                                   v++d d C gCg C   CP
  gi|119719455|ref|YP_919950.1| 58 VKIDYDYCKGCGVCAAECP 76
                                   899***********999** PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   1.9   0.00015      0.17       2      17 .]      32      47 ..      31      47 .. 0.90
   2 !   15.9   4.0   1.2e-05     0.013       1      16 [.      62      77 ..      62      78 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00015
                         Fer4_4  2 erCigCgsCvaaCPqg 17
                                   ++C  Cg+C  +CP+g
  gi|119719455|ref|YP_919950.1| 32 SKCRLCGVCWLYCPDG 47
                                   69************86 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.2e-05
                         Fer4_4  1 qerCigCgsCvaaCPq 16
                                   ++ C gCg+C a CP+
  gi|119719455|ref|YP_919950.1| 62 YDYCKGCGVCAAECPF 77
                                   589************8 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.7   3.1e-05     0.035       1      18 [.      29      46 ..      29      59 .. 0.84
   2 !   10.7   1.7   0.00054      0.61       1      17 [.      60      76 ..      60      78 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.1e-05
                        Fer4_13  1 VDrdtCiacgaCvelaPd 18
                                   VD ++C  cg+C+  +Pd
  gi|119719455|ref|YP_919950.1| 29 VDMSKCRLCGVCWLYCPD 46
                                   89***************9 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00054
                        Fer4_13  1 VDrdtCiacgaCvelaP 17
                                   +D d C +cg+C++ +P
  gi|119719455|ref|YP_919950.1| 60 IDYDYCKGCGVCAAECP 76
                                   7999************9 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   1.4    0.0011       1.3      47      64 ..      30      47 ..       5      48 .. 0.75
   2 !    7.0  11.2    0.0069       7.7       2      64 ..      31      78 ..      30      80 .. 0.57
   3 !   12.7   2.9   0.00012      0.13       3      17 ..      63      77 ..      61      86 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0011
                         Fer4_8 47 alwsCttcgaCtevCpvg 64
                                    + +C  cg C   Cp g
  gi|119719455|ref|YP_919950.1| 30 DMSKCRLCGVCWLYCPDG 47
                                   467788888888777765 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0069
                         Fer4_8  2 lekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64
                                   ++kC  Cg C   Cp      +   dar       ++ +        ++C +cg C+ +Cp +
  gi|119719455|ref|YP_919950.1| 31 MSKCRLCGVCWLYCPDG--VIEIDEDARL------VKID-------YDYCKGCGVCAAECPFK 78
                                   56777777777777711..1111122222......2222.......48899999999999965 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 0.00012
                         Fer4_8  3 ekCieCgaCqsaCpv 17
                                   ++C +Cg C ++Cp+
  gi|119719455|ref|YP_919950.1| 63 DYCKGCGVCAAECPF 77
                                   567778888887874 PP

>> ETF_QO  Electron transfer flavoprotein-ubiquinone oxidoreductase, 4Fe-4S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.6   0.00016      0.18      44      92 ..      38      82 ..      22      86 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00016
                                   -THHHH-TTS-EEEEETTTTSSEEEEE-CCC--S--HHHHH-TT--EEE CS
                         ETF_QO 44 gpeqryCPagvyeivedeeakekklqinaqnCvhCktCdikdpsqniew 92
                                   g++  yCP gv ei ed+      ++i+   C  C +C    p + i+ 
  gi|119719455|ref|YP_919950.1| 38 GVCWLYCPDGVIEIDEDA----RLVKIDYDYCKGCGVCAAECPFKAISM 82
                                   66778********98777....5789************99999998876 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   1.8     0.047        52      80      94 ..      32      46 ..      19      49 .. 0.67
   2 ?    3.7   1.9       0.1   1.1e+02       1      14 [.      33      46 ..      33      56 .. 0.83
   3 ?   11.2   2.0   0.00046      0.52      76      94 ..      59      77 ..      48      79 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.047
                        Fer4_22 80 sgCvGCgRCieacpv 94
                                   s+C  Cg C   cp 
  gi|119719455|ref|YP_919950.1| 32 SKCRLCGVCWLYCPD 46
                                   556666666666654 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.1
                        Fer4_22  1 rClsCgaCtlvCpt 14
                                   +C  Cg C l Cp 
  gi|119719455|ref|YP_919950.1| 33 KCRLCGVCWLYCPD 46
                                   68899999999985 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.00046
                        Fer4_22 76 kfgesgCvGCgRCieacpv 94
                                   k++   C GCg C + cp 
  gi|119719455|ref|YP_919950.1| 59 KIDYDYCKGCGVCAAECPF 77
                                   568899***********96 PP

>> IBD  Transcription-initiator DNA-binding domain IBD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.3    0.0015       1.7      44      60 ..      26      42 ..      18      60 .. 0.74
   2 ?    0.8   0.3      0.43   4.8e+02      49      60 ..      62      73 ..      51      78 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0015
                                   -HH....HHHHHTEEES CS
                            IBD 44 hpeddwkrclvcGicwl 60
                                    p  d  +c +cG+cwl
  gi|119719455|ref|YP_919950.1| 26 RPVVDMSKCRLCGVCWL 42
                                   56667889********6 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.43
                                   ..HHHHHTEEES CS
                            IBD 49 wkrclvcGicwl 60
                                    ++c+ cG+c  
  gi|119719455|ref|YP_919950.1| 62 YDYCKGCGVCAA 73
                                   459******975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.48
# Mc/sec: 544.08
//
Query:       gi|119719456|ref|YP_919951.1|  [L=388]
Description: pyruvate flavodoxin/ferredoxin oxidoreductase domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.4e-65  219.7   0.0    5.5e-65  219.3   0.0    1.1  1  POR_N            Pyruvate flavodoxin/ferredoxin oxidoreductas
    2.9e-27   95.0   0.1    5.3e-27   94.1   0.1    1.5  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
    8.9e-05   22.4   0.2    0.00035   20.4   0.1    2.1  2  Transketolase_C  Transketolase, C-terminal domain


Domain annotation for each model (and alignments):
>> POR_N  Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  219.3   0.0   9.2e-69   5.5e-65       2     229 ..      19     242 ..      18     244 .. 0.95

  Alignments for each domain:
  == domain 1  score: 219.3 bits;  conditional E-value: 9.2e-69
                                    HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCCHHH CS
                          POR_N   2 aaiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmienlgl 81 
                                    aa  a++dv++aYPITP+++++e++a+++a+ge+ ++++v++esE++a++a iGAa aGar+ TaTS+qGl +m+e +++
  gi|119719456|ref|YP_919951.1|  19 AARDADPDVVSAYPITPQTPVIEKIADFIASGEL-NAKFVRVESEHSAMAALIGAASAGARTYTATSSQGLFYMYEVVWW 97 
                                    78899****************************9.7******************************************** PP

                                    HHHTT--EEEEEEEEE-STTBEEEEE--TTCHHHHS---EEEE-SSHHHHHHHHHHHHHHHHH..CTSEEEEEEEHHHH. CS
                          POR_N  82 aageelPvvivvvaRalpstglsirtdqsDlmaardtglivlasenvqeafdlalvAfnlAek..vrvPvivlfDgflls 159
                                    aag++lP+v+ +v+Ral  + ++i+ ++sD++a+rd+g+ +++++++qe++dl+l+ + ++e+  v +P  v  D+f +s
  gi|119719456|ref|YP_919951.1|  98 AAGARLPIVMGIVTRALGPP-WNIWSEHSDFYAIRDSGWNMFFASSAQEVYDLTLISYGVSENpdVLLPSAVGWDAFEVS 176
                                    ********************.*********************************************************** PP

                                    HEEEEEEC-SGG.GS-----SBXXXXXXXXSXXXBXXTXXTSSXXEEESBXBXTTSXBXXXXHHHHHHHH CS
                          POR_N 160 hevekvelpdeedelklikekleeyerkeyaldpekpiargtaanpdtglehrekgneaedaaekvveev 229
                                    h++e+v+++ +e     +++ l+++ + ++ l+pe p   g  a+p+ + e+r++++ea ++a  v +ev
  gi|119719456|ref|YP_919951.1| 177 HTYEPVHVLGRE----EASKILPPKGAWKPPLTPEDPSSLGNLAYPEEYAEVRRTLREASEKALGVFREV 242
                                    ************....566666666677789*****************************9987777766 PP

>> PFOR_II  Pyruvate:ferredoxin oxidoreductase core domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.1   0.1   8.9e-31   5.3e-27       1     102 []     266     369 ..     266     369 .. 0.99

  Alignments for each domain:
  == domain 1  score: 94.1 bits;  conditional E-value: 8.9e-31
                                    -SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHHHHTGG CS
                        PFOR_II   1 AevvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevkaalkk 80 
                                    A+ +i++mGs++g++ +avd lRe+g++vG l+l+++rPFP+ee++++l++vk vv++ r+  fgs ++l+ +v++a++ 
  gi|119719456|ref|YP_919951.1| 266 ADALIIGMGSIIGEVYRAVDLLRERGERVGALKLWVYRPFPYEEVARRLENVKLVVTVARASVFGSLSPLGLDVASAITL 345
                                    89****************************************************************************99 PP

                                    G..TSEEEEEE--GGG----HHHH CS
                        PFOR_II  81 s..kvkvvnfvaglgGrditvedi 102
                                       +vk+v++ ag+gG d+++ed+
  gi|119719456|ref|YP_919951.1| 346 GglDVKLVDYAAGVGGVDVYAEDV 369
                                    999*****************9997 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       0.7   4.2e+03      10      19 ..     147     156 ..     143     157 .. 0.81
   2 !   20.4   0.1   5.9e-08   0.00035      10      77 ..     266     333 ..     261     372 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.7
                                    SSEEEEEETT CS
                Transketolase_C  10 kdvtlvayGs 19 
                                     d+tl++yG 
  gi|119719456|ref|YP_919951.1| 147 YDLTLISYGV 156
                                    599*****96 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 5.9e-08
                                    SSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEESTTSHH CS
                Transketolase_C  10 kdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeavkrgGig 77 
                                     d +++++Gs   e+ +A++ L+++g ++  + l   +p+  e ++  +++ + +v+v  a+++g+++
  gi|119719456|ref|YP_919951.1| 266 ADALIIGMGSIIGEVYRAVDLLRERGERVGALKLWVYRPFPYEEVARRLENVKLVVTVARASVFGSLS 333
                                    699*************************************************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 2556.99
//
Query:       gi|119719457|ref|YP_919952.1|  [L=300]
Description: thiamine pyrophosphate binding domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.3e-23   81.3   0.2      1e-22   80.6   0.2    1.3  1  TPP_enzyme_C    Thiamine pyrophosphate enzyme, C-terminal TPP
     0.0029   16.9   0.0     0.0039   16.4   0.0    1.3  1  DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase
  ------ inclusion threshold ------
      0.072   12.9   0.1       0.11   12.3   0.1    1.3  1  Asp_Glu_race    Asp/Glu/Hydantoin racemase


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.6   0.2   1.7e-26     1e-22      17     147 ..      55     196 ..      45     202 .. 0.87

  Alignments for each domain:
  == domain 1  score: 80.6 bits;  conditional E-value: 1.7e-26
                                    SSSEEEC.ETTTS-TTTHHHHHHHHHHH.....STTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEEEEEEE-SBCCCHH CS
                   TPP_enzyme_C  17 rprsylt.sgglgtmGyglpaAiGakla.....kpdrevvaivGDGgflmi.lqelatavrrnlpitvvvlnNegygmtg 89 
                                     prs ++ + ++ ++  + +aA+G+  a     kp ++vv+ +GDGg+ +i lq+l+ a++r++++++++++Ne+y++tg
  gi|119719457|ref|YP_919952.1|  55 HPRSAFKvPVLHIAFAASAAAASGMVEAleklgKP-ANVVVWAGDGGTVDIgLQALSGAAERGHNLIYICYDNEAYMNTG 133
                                    37887777889*************98743333344.5******************************************* PP

                                    HH...HHHHTCCTTTTSBB.BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHH.CSSS CS
                   TPP_enzyme_C  90 gq...qepfggkrksgpagkdlkpvdfaklaealGak.garvekadveeleealkeal.ekkg 147
                                     q   ++p+ ++++++p+g+ + ++d+  ++ a+ ++ +a++++a+v++l  +l++a   k+g
  gi|119719457|ref|YP_919952.1| 134 IQksgSTPYKAWTTTTPTGNLSVKKDVPSIMVAHRVPyVATINPAYVNDLYYKLRKAAqIKGG 196
                                    ********************99999************999*****************944445 PP

>> DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   6.5e-07    0.0039     115     177 ..      71     132 ..      62     191 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6.5e-07
                 DXP_synthase_N 115 tsisaalGlavardlkgekkkvvaviGDgaltgGmafealnnigelkkkllvilNdNemsisk 177
                                    +s +aa G+++a ++ g+  +vv   GDg+ t  + ++al  ++e  ++l+ i  dNe  +++
  gi|119719457|ref|YP_919952.1|  71 ASAAAASGMVEALEKLGKPANVVVWAGDGG-TVDIGLQALSGAAERGHNLIYICYDNEAYMNT 132
                                    577899***********************9.88999*********************987655 PP

>> Asp_Glu_race  Asp/Glu/Hydantoin racemase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   1.8e-05      0.11      70     108 ..      39      77 ..       1      99 [. 0.66

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.8e-05
                                    ESEEEE--CHHHHHHHHHHHH-SSEEEECHHHHHHHHHH CS
                   Asp_Glu_race  70 adaiviaCnTahavadelqkkikiPvlgiveataealka 108
                                      +++ aC+T  ++ ++ +++ k+Pvl+i+ a+ +a+++
  gi|119719457|ref|YP_919952.1|  39 TYLVIPACCTSVIAGPHPRSAFKVPVLHIAFAASAAAAS 77 
                                    335667999999****************99999666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       692  (0.0385967); expected 358.6 (0.02)
Passed bias filter:                      618  (0.0344693); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2170.39
//
Query:       gi|119719458|ref|YP_919953.1|  [L=544]
Description: membrane protein-like [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   7.9e-104  348.0   6.6   3.2e-102  342.7   6.6    2.0  1  DUF2070   Predicted membrane protein (DUF2070)


Domain annotation for each model (and alignments):
>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  342.7   6.6  1.8e-106  3.2e-102       1     564 []      12     537 ..      12     541 .. 0.87

  Alignments for each domain:
  == domain 1  score: 342.7 bits;  conditional E-value: 1.8e-106
                        DUF2070   1 leklskyifrlPswkvsllliillalligllaflssklfgillfglp...alvaflltlpvlrilggr....ltykrs.. 71 
                                    +++ +k+i+rlP++   +l+ i ++ll  ll+     l ++ll+g+p   +l ++ll   v  +l+ +    ++ +rs  
  gi|119719458|ref|YP_919953.1|  12 FKSSYKWIIRLPAT--RVLAPISFSLL--LLS-----LGASLLLGVPpseLLHSLLLGAAVPLYLHVCdrrvFNFRRSlg 82 
                                    5789*********8..55566666666..223.....5578999999999999999999999999888888********* PP

                        DUF2070  72 lflalltelivviisllaillsallqalvllalvls.....lalvfalrllvlvavsdesllkavlpaliqpllailllv 146
                                    +fl +l++l++v+++  + +l+++l+ lv + l+++      a ++a+ ++++++v++++++  +               
  gi|119719458|ref|YP_919953.1|  83 VFLLYLAMLPLVLVLRKPPILATVLEGLVGFLLAVGilsvwKAGALAILYFLWFSVAHNDPRALY--------------- 147
                                    ********************998776666666666644444444555555555555555555444............... PP

                        DUF2070 147 lyfspesfllllllslifalavylfivvvdrplkrnlgvsaldllsaFlahileg.skelEeffeeigeeadvpvkvlsf 225
                                                 ++ +f+la+  +++vvdr++++++gvs++ +l+aFl++il+g ++e+Ee++e+i++e++ +v+v+sf
  gi|119719458|ref|YP_919953.1| 148 -------------ILSAFFLASSTVFFVVDRRIRKAAGVSGVGFLEAFLKYILSGaRSEVEEYLERISVERTLQVHVYSF 214
                                    .............444578888889999**************************************************** PP

                        DUF2070 226 rredgekallvvPniHPGPlgeiGGsnLpkilaerldelvlvlHgtatHdfNlvserevekiveavkealeeleysskas 305
                                     + d e  +lv++n+HPGPl+++G+s+Lp+++a++ d+ +l+l++++tH++Nl+  r++e+++ av + + +   + + +
  gi|119719458|ref|YP_919953.1| 215 -TADREIGRLVISNVHPGPLRDLGSSTLPQLIAKCRDTPTLFLKAPCTHSENLPRLRYSEELAGAVCSCTPS--PAVDRC 291
                                    .444599***************************************************************99..667788 PP

                        DUF2070 306 kpvrvesgdvkllgqrfgdslllvitrapegiDDiplsvglsimaeakaegfedvllVDaHNsfseeage.vlpgsedae 384
                                    ++ + +sg+v+++ ++fg+   lv+  ++  ++D+p+ v     +e++   +e  + VD HN+      + +   + +++
  gi|119719458|ref|YP_919953.1| 292 GLGYSSSGKVDVVRLAFGEIPDLVFLDPQVIMEDLPYRV----SEESH--AVEGAVAVDLHNMIAPGYLKiDEDDEIEIA 365
                                    89*************************************....33433..479**********999988854555999** PP

                        DUF2070 385 eliraaekalekleaaeeselkvgvarsetpkltpeeglGdlgiqvlvlevdgqktayvliDgNNmepglreeirealke 464
                                    e+++a+++a+e  e ++e+e+++g+ar+e  +     ++G++g++++vl++ g+k +++ iDgNNm+p+++e++++++ke
  gi|119719458|ref|YP_919953.1| 366 EIVSAIHEASE--EVEAEGEIYAGFARVEYTD---GASVGPGGVACAVLQIAGKKLLLLSIDGNNMTPDFKERVLRTFKE 440
                                    ***********..*************999775...699*****************************************9 PP

                        DUF2070 465 .vdlevevmTTDtHvvngvsl..gynpvGekvskdelielvlelvekAiadlepvevgyatervevkvfgedrfeelvst 541
                                     ++ +v v TTDtH ++g+++  +y+pvG+   +++++e+++++vekA++++++v+vgy++    v + g+ +  e+++ 
  gi|119719458|ref|YP_919953.1| 441 sFE-KVLVATTDTHLYTGLYRnvDYYPVGALS-PEKVLETCMSCVEKALKNVSKVRVGYCS----VPFRGRFMDGEMLRR 514
                                    999.*************************776.9*************************99....566666666667777 PP

                        DUF2070 542 vnsvvsvakilaaallllaills 564
                                    ++ + ++  + ++a+++la+++s
  gi|119719458|ref|YP_919953.1| 515 ISVATKKNTRDSLAVVFLAFAVS 537
                                    77777777777777777777654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (544 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.24s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 3653.56
//
Query:       gi|119719459|ref|YP_919954.1|  [L=257]
Description: RNA methyltransferase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-28   98.7   0.0    4.4e-28   98.2   0.0    1.2  1  SpoU_methylase   SpoU rRNA Methylase family
     0.0025   17.7   0.0      0.038   13.8   0.0    2.1  2  Methyltrn_RNA_4  SAM-dependent RNA methyltransferase


Domain annotation for each model (and alignments):
>> SpoU_methylase  SpoU rRNA Methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.2   0.0   4.9e-32   4.4e-28       2     142 .]      16     164 ..      15     164 .. 0.86

  Alignments for each domain:
  == domain 1  score: 98.2 bits;  conditional E-value: 4.9e-32
                                    EEEEEES-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHH.EEEESSHHHHHHHHCCCTEEEEE CS
                 SpoU_methylase   2 livvlveiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevle.lkvvdsleealkelkeegfalva 80 
                                    + v++ve+ +++N+G iaR++k+f + +l+lvkpr+      e +r a++a++++e +++v+sl e++   + +     +
  gi|119719459|ref|YP_919954.1|  16 VSVAFVEPLYEQNIGYIARSMKNFCLAKLYLVKPRCS--VGLESRRYAMHAADIVEnAVIVGSLGELVGMHDLV----AC 89 
                                    6899********************************8..888889*********************99997777....44 PP

                                    EST.T-S.EGCCS...........HHHTTEEEEEEBTTTBS-HHHHCTSSEEEE----TTSSS--HHHHHHHHHH CS
                 SpoU_methylase  81 tsl.kgk.slsei...........dlkekvalvfGnEdkGlsnelleladrlvkIpmsgeveSLNvavAvailly 142
                                    t++ kgk +l+++           + ++++++v+G+Ed+Gls e+l+ +d lv+I  ++e++SLN ++A+ai++y
  gi|119719459|ref|YP_919954.1|  90 TTGvKGKpPLRRYvspgemaslfaESTGSKLVVIGREDWGLSAEELSICDMLVTIEANPEYPSLNASHAAAIVFY 164
                                    444555515555544444454444444**********************************************98 PP

>> Methyltrn_RNA_4  SAM-dependent RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.021   1.9e+02      28      48 ..      29      49 ..      16      59 .. 0.89
   2 !   13.8   0.0   4.3e-06     0.038     114     177 ..     100     163 ..      54     168 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.021
                                   HHHHHHHHHHTT-SEEEEE-- CS
                Methyltrn_RNA_4 28 lhDiaRsartygvkkyyvvtp 48
                                   +  iaRs + + ++k+y+v+p
  gi|119719459|ref|YP_919954.1| 29 IGYIARSMKNFCLAKLYLVKP 49
                                   6679***************99 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 4.3e-06
                                    SS-B-HHHHHHHHHH--S-EEEEE--.TT---HHHHTT-SEEB--TTTTSS-----HHHHHHHHH CS
                Methyltrn_RNA_4 114 entvsyeelrelleeeekpvlllfGt.gwGlaeevlekadyiLepirgaseynHLsvrsAvaiil 177
                                    ++ vs  e+ +l++e++ + l+++G   wGl+ e l+ +d+ L  i+++ ey  L    A+ai++
  gi|119719459|ref|YP_919954.1| 100 RRYVSPGEMASLFAESTGSKLVVIGReDWGLSAEELSICDM-LVTIEANPEYPSLNASHAAAIVF 163
                                    45677889999999999999*****637***********96.678******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1746.06
//
Query:       gi|119719460|ref|YP_919955.1|  [L=168]
Description: 50S ribosomal protein L10e [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-32  112.6   0.1    1.6e-32  112.3   0.1    1.0  1  Ribosomal_L16  Ribosomal protein L16p/L10e


Domain annotation for each model (and alignments):
>> Ribosomal_L16  Ribosomal protein L16p/L10e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.3   0.1   8.8e-37   1.6e-32       4     132 .]      15     163 ..      13     163 .. 0.94

  Alignments for each domain:
  == domain 1  score: 112.3 bits;  conditional E-value: 8.8e-37
                                    SXXBSSSXXSSTSXX.XSXXXXXESX........EEEEESSXEEEEHHHHHHHHHHHCTCCCCTSXC...EEXXSXXXXE CS
                  Ribosomal_L16   4 kkyrKsrkryirgvs.tkgtklefgd........ygLvalekgqltaealeaariainrylkkkrgk...klwirvfphh 71 
                                    ++y++ +  yi+  +   + k+++g+        ++Lv++ +gq++a+aleaar+ +n+yl+ k g+    l++ vfphh
  gi|119719460|ref|YP_919955.1|  15 PPYTRLE--YIKSNPpVLIPKFDLGNpkgnfntvLKLVVMRPGQIRANALEAARQHANKYLTAKVGEanfFLRVAVFPHH 92 
                                    6899999..99999989****************999**************************8888899999******** PP

                                    EEEE-.....SS-TTTSSSS....XEEEEEEEEEXSSCEEEEE..TTXXXSHHHHHHHHHHHHTSSSXEEEE CS
                  Ribosomal_L16  72 pvtkk.....agedRmgkGk....Gkpegwvarvkigqiifei..kagvneeiakealrraasKlpiktkiv 132
                                    +++++     ag+dR+++G+    G+p g +arv++gqi++ +  +a  n ++akealrraasK+p++ +i+
  gi|119719460|ref|YP_919955.1|  93 ILRENkmmamAGADRLQDGMrlsfGTPVGRAARVEAGQIVMLVkvDA-KNIDHAKEALRRAASKIPLPSRII 163
                                    *******************************************6433.4889****************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 1078.35
//
Query:       gi|119719461|ref|YP_919956.1|  [L=235]
Description: hypothetical protein Tpen_0547 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-81  272.4   3.0    3.3e-81  272.2   3.0    1.0  1  DUF2192   Uncharacterized protein conserved in archaea (DUF21


Domain annotation for each model (and alignments):
>> DUF2192  Uncharacterized protein conserved in archaea (DUF2192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  272.2   3.0   1.8e-85   3.3e-81       2     227 ..       3     224 ..       2     226 .. 0.98

  Alignments for each domain:
  == domain 1  score: 272.2 bits;  conditional E-value: 1.8e-85
                        DUF2192   2 elykkrievlvdllsklleeekltReelvellkkvYeekgiePlrGlskPediYdkElatlYvvgkyGlgleeelkelfd 81 
                                    e+++kriev++++++++le++  +Re+lv++l++vY+e+++eP+rG+++  +iYdkElatlY+vgkyGl+le+e+ + f+
  gi|119719461|ref|YP_919956.1|   3 EVHRKRIEVAINVWGEILEKTFENREQLVSYLEAVYRENRLEPIRGKTR-INIYDKELATLYLVGKYGLALEDEI-SSFS 80 
                                    89***********************************************.************************9.99** PP

                        DUF2192  82 kifsvEekleealeiilskkkeeavekvkevlgkidenkvarvlrlvltkvvlgfadeeelikllrkleeafpelektvk 161
                                    ++f+vE+k++++l+ +ls+  e+ +++v+++ g+++e++v+rvlrl++t+vvlgf+dee++i++l+++e+afpel+++++
  gi|119719461|ref|YP_919956.1|  81 DLFHVEIKADKVLSRVLSG--EDPRNAVVSEFGSTEEDNVFRVLRLAMTAVVLGFMDEETFIRVLESFEKAFPELDRNFT 158
                                    ******************5..8899999999************************************************* PP

                        DUF2192 162 kyarfyiAfkiaekiaegeirnrlekealkkalalrlgiekalPsdeyiaeiakevfkvpkkvlkk 227
                                    +++rfyiAf++aekia+geirnrlekea+k+al+++l++eka+P d++i+ ia +  kvp+  +++
  gi|119719461|ref|YP_919956.1| 159 SFKRFYIAFRLAEKIAAGEIRNRLEKEAYKHALCVKLNAEKAAPPDSFIRDIAVNALKVPEFKVNS 224
                                    ************************************************************987775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.32s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1522.51
//
Query:       gi|119719462|ref|YP_919957.1|  [L=97]
Description: 30S ribosomal protein S26e [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.7e-22   78.5   0.7    5.5e-22   78.3   0.7    1.0  1  Ribosomal_S26e  Ribosomal protein S26e
    0.00014   21.9   0.9      0.026   14.7   0.1    2.8  3  zf-RING_7       C4-type zinc ribbon domain
  ------ inclusion threshold ------
      0.014   15.3   0.2       0.56   10.1   0.1    2.2  2  PHD             PHD-finger
      0.055   13.4   0.1       0.11   12.4   0.1    1.5  1  Prok-RING_1     Prokaryotic RING finger family 1
      0.057   13.0   3.0       0.37   10.4   0.0    2.5  3  zf_UBZ          Ubiquitin-Binding Zinc Finger


Domain annotation for each model (and alignments):
>> Ribosomal_S26e  Ribosomal protein S26e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.3   0.7   1.5e-25   5.5e-22       1      96 [.       1      92 [.       1      96 [. 0.97

  Alignments for each domain:
  == domain 1  score: 78.3 bits;  conditional E-value: 1.5e-25
                                   X--S-SSTT----S-S---EEE-TTT--EEES----EEEEEEESS-SSSHHHHTTSBSSSS----EEEEEEE--HHHHHHTT CS
                 Ribosomal_S26e  1 mtkKRrnngrnkkgrghvkivrCsncarlvpkdKaikrfvvrniveaaavrdlseasvyeeyalPklYiklaycvscaihsk 82
                                   m+kKR+++gr+k ++g++  v+C++c+ l+p++Ka+k +     ++ + +++l+++      +lP++ ++++ c+ caih+ 
  gi|119719462|ref|YP_919957.1|  1 MPKKRKSRGRHKGDKGKEDLVQCDECGALIPRSKAVKITKPVMPIDPQLAKELRDK----GAILPQYTVTKYLCLRCAIHRG 78
                                   9******************************************************9....789******************* PP

                                   SS----TTTTS--S CS
                 Ribosomal_S26e 83 vvrvRsredrknre 96
                                   +++ R +e+rk+++
  gi|119719462|ref|YP_919957.1| 79 IIKIRPEEERKSQK 92
                                   ***********987 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   7.2e-06     0.026      18      32 ..      15      29 ..       7      30 .. 0.84
   2 !    4.7   0.0    0.0098        35       9      22 ..      45      58 ..      43      63 .. 0.85
   3 ?   -1.0   0.0      0.58   2.1e+03       7      18 ..      80      91 ..      80      92 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 7.2e-06
                                   CCSTB-EE-TTT--E CS
                      zf-RING_7 18 ragdevvtCpeCGRI 32
                                   ++++++v+C+eCG++
  gi|119719462|ref|YP_919957.1| 15 KGKEDLVQCDECGAL 29
                                   45578********97 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0098
                                   --CCHHHHHCCSTB CS
                      zf-RING_7  9 lppqvlselragde 22
                                   ++pq+ +elr ++ 
  gi|119719462|ref|YP_919957.1| 45 IDPQLAKELRDKGA 58
                                   89********9975 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.58
                                   -B--CCHHHHHC CS
                      zf-RING_7  7 melppqvlselr 18
                                   ++++p+++++++
  gi|119719462|ref|YP_919957.1| 80 IKIRPEEERKSQ 91
                                   6899**999876 PP

>> PHD  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00016      0.56       9      22 ..      14      27 ..       8      30 .. 0.80
   2 ?    3.3   0.0     0.021        75      42      50 ..      63      74 ..      45      76 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00016
                                   TSTTSCEEEETTTS CS
                            PHD  9 sdeeeelvqCdgCk 22
                                   ++ +e+lvqCd+C+
  gi|119719462|ref|YP_919957.1| 14 DKGKEDLVQCDECG 27
                                   45689********8 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.021
                                   S...TBSSTTTH CS
                            PHD 42 g...ewlCekCk 50
                                       ++lC +C 
  gi|119719462|ref|YP_919957.1| 63 YtvtKYLCLRCA 74
                                   14458******6 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   3.1e-05      0.11      16      28 ..      16      28 ..      10      35 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.1e-05
                    Prok-RING_1 16 eedDiVvCpeCgt 28
                                    ++D+V+C+eCg+
  gi|119719462|ref|YP_919957.1| 16 GKEDLVQCDECGA 28
                                   569*********8 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0    0.0001      0.37       2      15 ..      20      33 ..      19      36 .. 0.84
   2 ?   -2.3   0.1      0.99   3.5e+03      25      31 ..      49      55 ..      49      56 .. 0.79
   3 ?    2.8   0.1     0.025        89       2       8 ..      67      73 ..      66      76 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0001
                         zf_UBZ  2 tylCerCgkeipes 15
                                    ++C++Cg+ ip s
  gi|119719462|ref|YP_919957.1| 20 LVQCDECGALIPRS 33
                                   579********976 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.99
                         zf_UBZ 25 fAkdLqe 31
                                   +Ak+L +
  gi|119719462|ref|YP_919957.1| 49 LAKELRD 55
                                   59**986 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.025
                         zf_UBZ  2 tylCerC 8 
                                    ylC rC
  gi|119719462|ref|YP_919957.1| 67 KYLCLRC 73
                                   69***** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 714.78
//
Query:       gi|119719463|ref|YP_919958.1|  [L=210]
Description: hypothetical protein Tpen_0549 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.9e-24   84.7   0.0    1.5e-23   83.6   0.0    1.5  1  Methyltrn_RNA_2  Putative SAM-dependent RNA methyltransferase
     0.0099   16.1   0.0      0.017   15.3   0.0    1.3  1  SpoU_methylase   SpoU rRNA Methylase family


Domain annotation for each model (and alignments):
>> Methyltrn_RNA_2  Putative SAM-dependent RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.6   0.0   1.6e-27   1.5e-23       2     196 ..      17     203 ..      16     205 .. 0.91

  Alignments for each domain:
  == domain 1  score: 83.6 bits;  conditional E-value: 1.6e-27
                                    EEEEEEESSEESSSHHHCCCTTTTTTSHHHHHHHHHHHHBESSSB-TTEEEEEEEEESSSS-EEEEEETTT--S--SSHH CS
                Methyltrn_RNA_2   2 refvvlankapTdsdiplddlpGaagrldvlarcvsaalfvshgiRedvvvylvLegtpdpprtikieasevkkvspder 81 
                                    r fvv +n+a T + + +  l+   gr+dv+ar++ +al   ++ R +  + ++L g+p+pp  + +        ++ e 
  gi|119719463|ref|YP_919958.1|  17 RVFVVFSNTAATAPVFTVSTLATLGGRMDVVARSLINALWDLESQRFNTLLVALLNGPPNPPLGLYAWRVPAGGKRS-EG 95 
                                    78*********************99*************************************998776555544455.99 PP

                                    HHHHHHHHHHCHCCTGCCSEEEEETTEEEE-.--HHHHHHHHHCT.SEEEEESTTSEEGGGS---SSEE.EEEE-TT-SH CS
                Methyltrn_RNA_2  82 niailikkalkaveeikkqekkvrpgltVrk.egfealleelsek.ksiillkekGedisnakielnPv.FilgdHidlp 158
                                     + +li +al+++        k   gl V+k   + +++++l++  ++++ll+e+G +  n+++e +Pv F+lgdHi++p
  gi|119719463|ref|YP_919958.1|  96 FFGGLILEALSGK--------K-VDGLLVEKgARLVDVVSLLKGAgYPVYLLDENGLSYANVNLE-EPVaFVLGDHIGIP 165
                                    9*********887........3.468888762458999****9999*******************.7766********** PP

                                    HHHHHHHHCTTSEEEES-SS---HHHHHHHHHHHHHHH CS
                Methyltrn_RNA_2 159 eeeekllerlkakrvslgPlsLhadhcvtlihneldkk 196
                                    ++  + + rl +  +s+g +  +++hc+  +h++ld+ 
  gi|119719463|ref|YP_919958.1| 166 ADLLRQVTRLVDGVISIGRTPYLTSHCIAFVHELLDRS 203
                                    ***********************************985 PP

>> SpoU_methylase  SpoU rRNA Methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.9e-06     0.017      58     120 ..     115     176 ..     102     181 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.9e-06
                                    EEEESSHHHHHHHHCCCTEEEEEESTT-SEGCCSHHHTTEEEEEEBTTTBS-HHHHCTSSEEE CS
                 SpoU_methylase  58 lkvvdsleealkelkeegfalvatslkgkslseidlkekvalvfGnEdkGlsnelleladrlv 120
                                    +++ + l ++++ lk +g+ ++ ++++g s+ +++l+e+va+v+G    G++ +ll++++rlv
  gi|119719463|ref|YP_919958.1| 115 VEKGARLVDVVSLLKGAGYPVYLLDENGLSYANVNLEEPVAFVLGDH-IGIPADLLRQVTRLV 176
                                    5666789999***********************************85.9*******9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1412.02
//
Query:       gi|119719464|ref|YP_919959.1|  [L=59]
Description: hypothetical protein Tpen_0550 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       864  (0.0481901); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 410.77
//
Query:       gi|119719465|ref|YP_919960.1|  [L=472]
Description: hypothetical protein Tpen_0551 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (472 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       902  (0.0503096); expected 358.6 (0.02)
Passed bias filter:                      597  (0.033298); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 3146.78
//
Query:       gi|119719466|ref|YP_919961.1|  [L=619]
Description: HxlR family transcriptional regulator [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.4e-09   36.9   0.0    6.8e-09   35.5   0.0    1.8  1  HTH_5        Bacterial regulatory protein, arsR family
    3.8e-06   26.9   2.7    4.1e-06   26.8   0.2    2.4  2  HTH_20       Helix-turn-helix domain
    9.4e-05   22.2   1.5    0.00018   21.3   1.5    1.4  1  DUF35_N      Rubredoxin-like zinc ribbon domain (DUF35_N)
     0.0037   17.0   0.0      0.006   16.3   0.0    1.2  1  TackOD1      Thaumarchaeal output domain 1
     0.0077   16.2   0.1      0.023   14.6   0.1    1.9  1  HTH_Crp_2    Crp-like helix-turn-helix domain
  ------ inclusion threshold ------
       0.02   15.0   0.6      0.038   14.1   0.6    1.5  1  Zn-ribbon_8  Zinc ribbon domain
      0.034   14.3   0.0      0.082   13.1   0.0    1.6  1  HTH_34       Winged helix DNA-binding domain
      0.037   13.9   0.1       0.13   12.2   0.1    1.9  1  MarR_2       MarR family
      0.048   13.2   0.0      0.093   12.3   0.0    1.5  1  HTH_24       Winged helix-turn-helix DNA-binding
      0.087   12.9   0.2        0.2   11.7   0.2    1.5  1  HypA         Hydrogenase/urease nickel incorporation, metallo
       0.11   12.3   0.1       0.39   10.6   0.1    1.9  1  HxlR         HxlR-like helix-turn-helix


Domain annotation for each model (and alignments):
>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.0   4.2e-12   6.8e-09       2      45 ..      14      58 ..      13      59 .. 0.97

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 4.2e-12
                                   HHHHHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          HTH_5  2 ptRlkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLV 45
                                   + Rl+ ++lL++ ++l +++la +l++s+ ++  HL++L+eaG+V
  gi|119719466|ref|YP_919961.1| 14 EIRLQAMRLLRDrRKLRFGDLASYLDVSPEKLAFHLRQLKEAGIV 58
                                   78**********999*****************************9 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.2   2.5e-09   4.1e-06       3      57 ..       7      61 ..       6      64 .. 0.95
   2 ?   -3.8   0.2       8.5   1.4e+04      47      55 ..     188     196 ..     186     199 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 2.5e-09
                                   HHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                         HTH_20  3 iaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevv 57
                                   +++A++++ R+  +r+L++++ l +++la  ld+s+  l +HLr+L eag+v ++
  gi|119719466|ref|YP_919961.1|  7 LLKAVSNEIRLQAMRLLRDRRKLRFGDLASYLDVSPEKLAFHLRQLKEAGIVVQE 61
                                   799************************************************9876 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 8.5
                                    HHHHCTTEE CS
                         HTH_20  47 vLeeagLve 55 
                                     L+++gL+e
  gi|119719466|ref|YP_919961.1| 188 LLARVGLLE 196
                                    699999998 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   1.5   1.1e-07   0.00018      13      37 .]     558     582 ..     556     582 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.1e-07
                        DUF35_N  13 rCpdCGtvqfPPravCphCgsddle 37 
                                    +C++CG+v++ +   Cp+C+s+ +e
  gi|119719466|ref|YP_919961.1| 558 HCTACGHVFVSKALRCPKCLSTGVE 582
                                    8********************9876 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   3.7e-06     0.006      37     100 ..     519     583 ..     500     590 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.7e-06
                        TackOD1  37 ysypllealskekeeseelleelvkrglle.eelvdrirlCpsCksghlnvrevCpkCkSidiee 100
                                    +s p ++++s +  ++  +l++ +krgl + + +  ++ +C+ C +  ++    CpkC S+ +e+
  gi|119719466|ref|YP_919961.1| 519 VSVPEIRFTSLSPADMLVVLKAYAKRGLRTvTFTKTSLYHCTACGHVFVSKALRCPKCLSTGVEQ 583
                                    5667777777777799999*********9988888899**********************98775 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   1.4e-05     0.023      25      54 ..      32      62 ..       7      75 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.4e-05
                                   HHHHHHTTSSHHHHHHHHHHHHHTTSEE.ET CS
                      HTH_Crp_2 25 eelAsmlGltretvsrilseLkreglis.rg 54
                                    +lAs+l +++e +   l++Lk++g++   g
  gi|119719466|ref|YP_919961.1| 32 GDLASYLDVSPEKLAFHLRQLKEAGIVVqEG 62
                                   69************************99434 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.6   2.3e-05     0.038       6      39 ..     557     584 ..     556     585 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.3e-05
                    Zn-ribbon_8   6 YrCeeCghefevlqsisdapltaCPeCgs.evrrv 39 
                                    Y+C++Cgh+f     ++      CP+C s  v+++
  gi|119719466|ref|YP_919961.1| 557 YHCTACGHVFV----SK---ALRCPKCLStGVEQL 584
                                    9*******998....22...456****98777765 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0     5e-05     0.082       1      45 [.      15      59 ..      15      65 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5e-05
                         HTH_34  1 vRlavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYie 45
                                   +Rl+++ +L + ++  f +l + l ++  +L+ hl+ L++ag ++
  gi|119719466|ref|YP_919961.1| 15 IRLQAMRLLRDRRKLRFGDLASYLDVSPEKLAFHLRQLKEAGIVV 59
                                   8****************************************9776 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   7.9e-05      0.13      11      54 ..      20      61 ..      15      64 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.9e-05
                                   HHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                         MarR_2 11 LaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                   +  L++r    l+ g+la +l++s+  +  +l+ L +aG v+++
  gi|119719466|ref|YP_919961.1| 20 MRLLRDRRK--LRFGDLASYLDVSPEKLAFHLRQLKEAGIVVQE 61
                                   556666655..******************************876 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   5.7e-05     0.093       2      47 ..      13      58 ..      12      59 .. 0.96

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.7e-05
                         HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                   +e++++ ++lL++  ++   +LA  l++Sp  +  +l++L+e+G++
  gi|119719466|ref|YP_919961.1| 13 NEIRLQAMRLLRDRRKLRFGDLASYLDVSPEKLAFHLRQLKEAGIV 58
                                   78999999*************************************9 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   0.00012       0.2      70      98 ..     556     582 ..     536     589 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00012
                                    EEEETTTS-EEECHHHHHS-TTTSSS-EE CS
                           HypA  70 kvrCreCgkefeleekalrCpkCgsadve 98 
                                     ++C+ Cg+ f ++  alrCpkC s++ve
  gi|119719466|ref|YP_919961.1| 556 LYHCTACGHVFVSK--ALRCPKCLSTGVE 582
                                    578********987..68*****999886 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00024      0.39      17      88 ..      27      90 ..      16      92 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00024
                                   S-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHHHHHHHHHHHHHHHH CS
                           HxlR 17 gkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrslepvlqelkkwgeeyle 88
                                    k Rf++l+  l ++s + La +Lr+L++ g++ +e          Y+l+  G  + +++++l+   +eyle
  gi|119719466|ref|YP_919961.1| 27 RKLRFGDLASYL-DVSPEKLAFHLRQLKEAGIVVQE----GD---YYTLSTVGLRVLEIVDALSLETNEYLE 90
                                   678********9.9*****************98543....33...488888888888888888776666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (619 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 3829.81
//
Query:       gi|119719467|ref|YP_919962.1|  [L=123]
Description: hypothetical protein Tpen_0553 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       812  (0.0452898); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 788.83
//
Query:       gi|119719468|ref|YP_919963.1|  [L=112]
Description: hypothetical protein Tpen_0554 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       246  (0.0137208); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.29s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 797.59
//
Query:       gi|119719469|ref|YP_919964.1|  [L=336]
Description: putative RNA methylase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-28   99.5   0.0    1.3e-26   93.6   0.0    2.6  2  UPF0020          Putative RNA methylase family UPF0020
    8.5e-13   48.2   0.0    1.5e-12   47.4   0.0    1.4  1  MTS              Methyltransferase small domain
    1.7e-09   37.9   0.9    3.3e-09   37.0   0.9    1.4  1  THUMP            THUMP domain
    1.6e-07   31.9   0.0    4.7e-07   30.4   0.0    1.9  1  Methyltransf_11  Methyltransferase domain
    3.5e-07   30.8   0.0    1.3e-06   29.0   0.0    2.0  2  Methyltransf_25  Methyltransferase domain
    4.9e-07   29.7   0.0    9.2e-07   28.8   0.0    1.4  1  Methyltransf_31  Methyltransferase domain
     0.0026   17.4   0.0     0.0041   16.8   0.0    1.3  1  Cons_hypoth95    Conserved hypothetical protein 95
     0.0046   16.3   0.0     0.0078   15.6   0.0    1.3  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
  ------ inclusion threshold ------
      0.012   15.1   0.1       0.92    8.9   0.0    2.7  3  AviRa            RRNA methyltransferase AviRa
       0.15   11.7   0.0        1.8    8.2   0.0    2.1  2  N6_N4_Mtase      DNA methylase
       0.25   10.5   0.0        2.5    7.3   0.0    2.2  2  N6_Mtase         N-6 DNA Methylase


Domain annotation for each model (and alignments):
>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.93   1.5e+03     157     190 ..      35      69 ..      20      73 .. 0.75
   2 !   93.6   0.0   7.8e-30   1.3e-26       1     194 [.     161     326 ..     161     328 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.93
                                    TT..-EEEEEESSHHHHHCC---.ESEEEEEEETT CS
                        UPF0020 157 rgggrlvlltsenkalekaleer.alrkvkeknvk 190
                                    r+g+  v++  ++++l+ ++e++ +++kv++++++
  gi|119719469|ref|YP_919964.1|  35 REGSGRVIAEIDERCLAILMEKArSVEKVYLFFGE 69 
                                    56677788888899999999988788888888775 PP

  == domain 2  score: 93.6 bits;  conditional E-value: 7.8e-30
                                    -SSS-SS---SS-HHHHHHHHHHTT--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--EE CS
                        UPF0020   1 RgyRefngpapLketLAaalvrlagwkpgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelkly 80 
                                    R yR f + ++L++ +A+al r   ++ g++l DP+CGsGti++E +l +   a                       + +
  gi|119719469|ref|YP_919964.1| 161 RPYRRFIHRSALNPLIAYALCRA--VRGGKSLWDPFCGSGTIPLE-CLEVYPWA-----------------------RAV 214
                                    78******************996..89******************.45554444.......................478 PP

                                    EEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE----------HHHHHHHHHHHHHHHHHH-TT.. CS
                        UPF0020  81 gsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpPYGerlgskkalekLYseflrelkrvlrggg 160
                                    +sD +++ ++ga +N  + g +    +s+   a Lr  +g++d++vtnpP+G+r ++ + l+k Y+++ +e++rvl +gg
  gi|119719469|ref|YP_919964.1| 215 CSDVNAEFIAGALQNSLAVGKELDLVVSDIRSAPLR--SGSIDAVVTNPPFGIREKAVGGLRKVYEALFTEASRVLVQGG 292
                                    ***************998888888888887777777..88**************************************** PP

                                    -EEEEEESSHHHHHCC---ESEEEEEEETTEEEE CS
                        UPF0020 161 rlvlltsenkalekaleeralrkvkeknvklgll 194
                                    rl++lt+++k +e+++++ ++ kv e + + g+l
  gi|119719469|ref|YP_919964.1| 293 RLAVLTPHRKLVESLAQKHSFLKVGEWRLNEGGL 326
                                    *******************999999888877765 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.4   0.0   8.9e-16   1.5e-12      36     148 ..     191     307 ..     178     328 .. 0.85

  Alignments for each domain:
  == domain 1  score: 47.4 bits;  conditional E-value: 8.9e-16
                                    EEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTST.TS-EEEEEE---STTTCHCH CS
                            MTS  36 lDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeve.ekkfdlivsNPPfhagkate 114
                                     D  cG G + +++++ +p a+ ++ dv+a+ ++ a +n  a + e+++v sd+ ++    +++d++v+NPPf   +++ 
  gi|119719469|ref|YP_919964.1| 191 WDPFCGSGTIPLECLEVYPWARAVCSDVNAEFIAGALQNSLAVGKELDLVVSDIRSAPLrSGSIDAVVTNPPFGIREKAV 270
                                    5667**************************************************98754389***********8766543 PP

                                    ...HHHHHHHHHHHHHHEEEEEEEEEEEETTSCHHHH CS
                            MTS 115 ...lavaeeliaeAkeaLkegGeLliVanrklgyesl 148
                                        +v e+l++eA ++L +gG+L + + +   +esl
  gi|119719469|ref|YP_919964.1| 271 gglRKVYEALFTEASRVLVQGGRLAVLTPHRKLVESL 307
                                    223799******************9987666555554 PP

>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   0.9     2e-12   3.3e-09      22     135 ..      39     143 ..      20     147 .. 0.77

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 2e-12
                                    TEEEEECTEEEEEETHHHHHHHHHTSTTECEEEEE...EEEEESSHHHHHHHHHHHHHHHHHHCT-EEEEEEEESSSTSS CS
                          THUMP  22 grivvelkgekpeedeellkealekargiqrvipv...cevceadledileaakeivkkkfeeeketFaVrvkrrgkhfe 98 
                                    gr++ e+       de+ l  ++ekar +++v+      + +e++  d+ e+ +e+           F V+++r  k+++
  gi|119719469|ref|YP_919964.1|  39 GRVIAEI-------DERCLAILMEKARSVEKVYLFfgeAASIEEAGIDLSEKLREFSGFFR-----FFSVHAERITKDID 106
                                    4444444.......77777788999999999999966544444444456666666666333.....7************* PP

                                    SHHHHHHHHHHHHHHCCTT-EE-SSS-SEEEEEEEET CS
                          THUMP  99 ftsreinrevGkaivektglkVdlenPdivvrveiik 135
                                     ts ei+ ++G++++ +++l V+l+ Pdi v ve  k
  gi|119719469|ref|YP_919964.1| 107 LTSLEIAAKIGEMVKTRLNLDVSLDFPDIPVYVEYEK 143
                                    *********************************9766 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.0   2.9e-10   4.7e-07       5      96 .]     195     296 ..     191     296 .. 0.88

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 2.9e-10
                                    -TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES.......-CCC-. CS
                Methyltransf_11   5 cGtGrlaealakrg..arvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvsse.......vlhhv. 74 
                                    cG+G +  ++ + +  ar v+ D+++e+++ a +++   g ++++vv+d+++ p++++s+D+vv +        ++  + 
  gi|119719469|ref|YP_919964.1| 195 CGSGTIPLECLEVYpwARAVCSDVNAEFIAGALQNSLAVGKELDLVVSDIRSAPLRSGSIDAVVTNPpfgirekAVGGLr 274
                                    9999999999999999*************99977777777789***********************97666666666668 PP

                                    CCHHHHHHHHHHHEEEEEEEEE CS
                Methyltransf_11  75 edpekalkeiaRvLkpgGllvi 96 
                                    +  e+++ e+ RvL +gG+l++
  gi|119719469|ref|YP_919964.1| 275 KVYEALFTEASRVLVQGGRLAV 296
                                    899****************975 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0         4   6.6e+03      28      42 ..      44      58 ..      27      87 .. 0.59
   2 !   29.0   0.0     8e-10   1.3e-06       5      97 .]     194     292 ..     191     292 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 4
                                   ESSHHHHHHHHHHHH CS
                Methyltransf_25 28 Diseemleaarerae 42
                                   +i+e++l++  e+a+
  gi|119719469|ref|YP_919964.1| 44 EIDERCLAILMEKAR 58
                                   444555555444443 PP

  == domain 2  score: 29.0 bits;  conditional E-value: 8e-10
                                    T-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEEST.GGGSS..... CS
                Methyltransf_25   5 GcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssga.lhhls..... 78 
                                     cG+G++ l++++ ++ a+ ++ D+++e+++ a ++  + g ++++v+ d+++ p+ +gs+D+vv +   + + +     
  gi|119719469|ref|YP_919964.1| 194 FCGSGTIPLECLEVYPWARAVCSDVNAEFIAGALQNSLAVGKELDLVVSDIRSAPLRSGSIDAVVTN-PpFGIREkavgg 272
                                    5*************999********************99888************************4.447754411111 PP

                                    .HHHHHHHHHHHHHHEEEEE CS
                Methyltransf_25  79 .dedlekalkeiarvLkpgG 97 
                                     ++ +e+++ e++rvL +gG
  gi|119719469|ref|YP_919964.1| 273 lRKVYEALFTEASRVLVQGG 292
                                    13456889999999999998 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.0   5.6e-10   9.2e-07       4     124 ..     187     309 ..     185     328 .. 0.88

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 5.6e-10
                Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnev 83 
                                    g+++ D+ CG+G++ +e   e++p a+ v  D ++e i  A +n+   g  ++ + ++di +++  l   ++D +++n +
  gi|119719469|ref|YP_919964.1| 187 GKSLWDPFCGSGTIPLECL-EVYPWARAVCSDVNAEFIAGALQNSLAVGK-ELDLVVSDIRSAP--LRSGSIDAVVTNPP 262
                                    67889**************.***********************9665555.6************..889*********99 PP

                Methyltransf_31  84 l....naladpdkile....eiervlkpggilliedprllaelpakvee 124
                                    +     a+  + k++e    e++rvl +gg+l++ +p+  ++l +++ +
  gi|119719469|ref|YP_919964.1| 263 FgireKAVGGLRKVYEalftEASRVLVQGGRLAVLTPH--RKLVESLAQ 309
                                    999999999999*9999999*****************9..555544443 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   2.5e-06    0.0041      37     128 ..     176     268 ..     148     318 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.5e-06
                                    CCC......HCC-EEEETT-TTSHHHHHHHHTT.-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS-- CS
                  Cons_hypoth95  37 aae......iegarvLDlfaGsGalglEAlSRg.akkavlvekdkeavkilkenleelkleeetaelkedaleallklak 109
                                     a+        g+++ D f+GsG++ lE+l  +  ++av+ + ++e ++   +n  +++  +e + ++ d  +a l+   
  gi|119719469|ref|YP_919964.1| 176 IAYalcravRGGKSLWDPFCGSGTIPLECLEVYpWARAVCSDVNAEFIAGALQNSLAVG--KELDLVVSDIRSAPLRS-- 251
                                    4444555534556677**************7653799***********98888888888..45788888887777666.. PP

                                    SS-EEEEEEE--SSSTTCH CS
                  Cons_hypoth95 110 kkeefdivflDPPyakell 128
                                      +++d v  +PP+   + 
  gi|119719469|ref|YP_919964.1| 252 --GSIDAVVTNPPFGIREK 268
                                    ..689*********86654 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   4.8e-06    0.0078      42     164 ..     181     309 ..     173     319 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.8e-06
                                    H--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEE CS
                Ubie_methyltran  42 lvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvt 121
                                    + av+ g+++ D  +G+g + ++ ++ v    + v  D+n++ +  + +     gk ++++++++    p   +s D v 
  gi|119719469|ref|YP_919964.1| 181 CRAVRGGKSLWDPFCGSGTIPLECLE-VYPWARAVCSDVNAEFIAGALQNSLAVGK-ELDLVVSDIRSAPLRSGSIDAVV 258
                                    77899999**************9987.667788899********998888877775.89******************987 PP

                                    EE..S-GGG..-S-HHHH....HHHHHHHEEEEEEEEEEEE----SHHHHH CS
                Ubie_methyltran 122 vs..fGlrn..vtDklka....LkeayrvlkpGGrlvvlefskvelpllsq 164
                                        fG+r   v    k+    + ea rvl  GGrl vl   +  ++ l q
  gi|119719469|ref|YP_919964.1| 259 TNppFGIREkaVGGLRKVyealFTEASRVLVQGGRLAVLTPHRKLVESLAQ 309
                                    6445****8333344444111157889************988877777666 PP

>> AviRa  RRNA methyltransferase AviRa
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.1   1.8e+03      33      51 ..      40      58 ..      39      65 .. 0.79
   2 ?    8.9   0.0   0.00057      0.92      53      98 ..     186     229 ..     175     237 .. 0.83
   3 ?    3.0   0.0     0.035        57     151     232 ..     239     317 ..     232     319 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.1
                          AviRa 33 RlasEilqralellekkee 51
                                   R+  Ei +r+l++l +k++
  gi|119719469|ref|YP_919964.1| 40 RVIAEIDERCLAILMEKAR 58
                                   77889*******9988766 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00057
                          AviRa  53 apltlyDpCCGgayLltvlgllhgkkikkvlasDvdeevlelakkN 98 
                                    ++ +l+Dp CG++ +   l  l     ++ + sDv++e ++ a +N
  gi|119719469|ref|YP_919964.1| 186 GGKSLWDPFCGSGTI--PLECLEVYPWARAVCSDVNAEFIAGALQN 229
                                    5679*********87..57888889999999999999999998887 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.035
                          AviRa 151 vfkaditekeeeaekevdivitDlPYGelvswqgeseepvkqlleslaavldpeesvvaviadkkkkieherfrrlerlk 230
                                    ++  di  + +  + ++d v+t  P+G   +  g+ ++  ++l+++ ++vl  + + +av + ++k +e    ++   lk
  gi|119719469|ref|YP_919964.1| 239 LVVSDIR-SAPLRSGSIDAVVTNPPFGIREKAVGGLRKVYEALFTEASRVL-VQGGRLAVLTPHRKLVES-LAQKHSFLK 315
                                    5566776.56666777*******************999************9.667778887777666554.466666777 PP

                          AviRa 231 vG 232
                                    vG
  gi|119719469|ref|YP_919964.1| 316 VG 317
                                    76 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0    0.0011       1.8     192     211 ..     187     206 ..     164     224 .. 0.82
   2 ?    1.2   0.0      0.15   2.5e+02       1      52 [.     254     294 ..     254     316 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0011
                                    T-EEEETT-TTTHHHHHHHH CS
                    N6_N4_Mtase 192 gdivlDpFaGSGtTavaake 211
                                    g++  DpF+GSGt+  +++e
  gi|119719469|ref|YP_919964.1| 187 GKSLWDPFCGSGTIPLECLE 206
                                    78889********9888876 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.15
                                    EEEEEE--SSSSSCS.....GCCGCCHHHHHHHHHHHHHHHHHHHEEEEEEE CS
                    N6_N4_Mtase   1 vdlivtdpPYntgkdyendeqyeeedsyeeyleflekvlkevrrvLkddgsi 52 
                                    +d +vt pP+++ ++            + +  +  e  + e+ rvL ++g +
  gi|119719469|ref|YP_919964.1| 254 IDAVVTNPPFGIREK-----------AVGGLRKVYEALFTEASRVLVQGGRL 294
                                    7899999*9999988...........55555566666666666666666655 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.14   2.3e+02      43      61 ..     183     201 ..     170     210 .. 0.77
   2 ?    7.3   0.0    0.0016       2.5     124     139 ..     252     267 ..     217     309 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.14
                       N6_Mtase  43 epksgesvyDpacGsggll 61 
                                      + g+s  Dp cGsg + 
  gi|119719469|ref|YP_919964.1| 183 AVRGGKSLWDPFCGSGTIP 201
                                    5678899*********875 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0016
                       N6_Mtase 124 kkfdvvvaNppfnqke 139
                                     ++d+vv+Nppf+++e
  gi|119719469|ref|YP_919964.1| 252 GSIDAVVTNPPFGIRE 267
                                    689*********9984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2205.92
//
Query:       gi|119719470|ref|YP_919965.1|  [L=337]
Description: eRF1 domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.6e-20   71.0   0.0    2.9e-19   69.4   0.0    1.8  2  eRF1_1       eRF1 domain 1
    5.1e-10   39.8   0.3    1.5e-09   38.3   0.1    1.9  2  eRF1_3       eRF1 domain 3
  ------ inclusion threshold ------
      0.032   14.5   0.0       0.11   12.8   0.0    1.9  1  LAGLIDADG_3  LAGLIDADG-like domain
       0.11   12.8   4.3      0.069   13.4   0.9    2.4  3  acVLRF1      Actinobacteria/chloroflexi VLRF1 release factor


Domain annotation for each model (and alignments):
>> eRF1_1  eRF1 domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.4   0.0   6.4e-23   2.9e-19      19     128 ..       1     112 [.       1     113 [. 0.96
   2 ?   -0.9   0.0      0.35   1.6e+03      78      92 ..     278     307 ..     166     316 .. 0.54

  Alignments for each domain:
  == domain 1  score: 69.4 bits;  conditional E-value: 6.4e-23
                                    EE-SCHHHHHHHHHCHTTHEEEEEEEECHHH.......--CEEEEEEEEEEEEEEECTTSSEEEEEEEEEEGGGG.--TT CS
                         eRF1_1  19 ipeddedlwhlynliapgdsvrastvrkvqresstgsreservklkLtikvekvdfdkdagvlrisGkvieeneh.vklg 97 
                                    ++e  edl++l+ l+++gd v   t+r+   e++tg+   er+ + L ++vekv + k ++ lr++G+v+e  e+   +g
  gi|119719470|ref|YP_919965.1|   1 MVEVLEDLYYLFLLVRKGDVVYGWTTRQLRIERATGEERGERIPVYLGVEVEKVSYAKFSEKLRFTGRVVEAPEEvYAKG 80 
                                    68899***********************988*****************************************9994589* PP

                                    SEEEEEE-TTSEEEEEECE.ESHHHHHHHHHH CS
                         eRF1_1  98 afhtldlelkrpftiikee.wdsfalerLkea 128
                                    +fht+++ ++++++i k+   d f  ++L++a
  gi|119719470|ref|YP_919965.1|  81 SFHTIQVGVGDRVKIVKKSgIDGFTRNILEKA 112
                                    *****************888*******99987 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.35
                                    S...............SEEEEEEEEEEGGG CS
                         eRF1_1  78 a...............gvlrisGkvieene 92 
                                    +                vl++ G+v + n+
  gi|119719470|ref|YP_919965.1| 278 TlivsdallfgeesreRVLKVLGEVFSRNG 307
                                    033333333333333366666666666665 PP

>> eRF1_3  eRF1 domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       2.8   1.3e+04      69      89 ..     102     123 ..      83     128 .. 0.62
   2 !   38.3   0.1   3.3e-13   1.5e-09       7     112 ..     245     335 ..     241     336 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.8
                                    H.HHHHHHHHHHHTT-EEEEE- CS
                         eRF1_3  69 e.lieelvenveesgakveiis 89 
                                    + ++++++e++ +   +v +is
  gi|119719470|ref|YP_919965.1| 102 DgFTRNILEKAASKIRRVLLIS 123
                                    2566666676666666666666 PP

  == domain 2  score: 38.3 bits;  conditional E-value: 3.3e-13
                                    HHHHHHHHHHCTCSSEEESHHHHHHHHHTT-EEEEEEEHCHHTSSSHHHHHS-HHH-HHHHHHHHHHHHHHHHHTT-EEE CS
                         eRF1_3   7 lleefleelakdtgkavYGveevlkalemgAvetLLvseelersrdtlkekvketgeelelvelieelvenveesgakve 86 
                                     +e++l+el  ++gkav G e+v+k++e g v+tL+vs+ l   + + +e+             + +++ +v + ++k++
  gi|119719470|ref|YP_919965.1| 245 EVERVLQELFSGKGKAVAGLENVEKVAEWGIVKTLIVSDALLFGE-ESRER-------------VLKVLGEVFSRNGKIF 310
                                    58999**************************************97.45555.............899************* PP

                                    EE-TTSHHHHHHHHHTTTEEEEESS- CS
                         eRF1_3  87 iisseseeGeqlvkafgGiaaiLRyk 112
                                    i+++ese+G +l k fgG  a L y+
  gi|119719470|ref|YP_919965.1| 311 IVPEESEAGRKL-KPFGGALAELYYS 335
                                    ************.********99886 PP

>> LAGLIDADG_3  LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.5e-05      0.11      33      74 ..     190     230 ..     183     238 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.5e-05
                                    -HHHHHHHHHHHHHCT.HSCEEEEEEE-SCCCCECCCHCHCT CS
                    LAGLIDADG_3  33 skelledvqrlLlrlGIestiyekkkakgrgvyrlliisgen 74 
                                    +++l+e v+r+L +lG+++++ +  +++  g+y +l  +g++
  gi|119719470|ref|YP_919965.1| 190 NERLAEVVSRVLGELGVKARVVKVSEGGEAGIY-ELLRGGQS 230
                                    789*********************999999998.55555544 PP

>> acVLRF1  Actinobacteria/chloroflexi VLRF1 release factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.1   4.9e+03       3      19 ..      10      26 ..       9      40 .. 0.68
   2 ?   -1.3   0.0      0.56   2.5e+03      57      85 ..     107     129 ..     101     164 .. 0.67
   3 ?   13.4   0.9   1.5e-05     0.069      44     119 ..     171     252 ..     170     263 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.1
                        acVLRF1  3 lgvllvrrggfavgvve 19
                                   +++llvr+g    g   
  gi|119719470|ref|YP_919965.1| 10 YLFLLVRKGDVVYGWTT 26
                                   678999*9998777766 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.56
                        acVLRF1  57 alleavaeaaarllaeesaevvlgGdrsl 85 
                                    + le++a +++r+l      ++ +Gd+++
  gi|119719470|ref|YP_919965.1| 107 NILEKAASKIRRVL------LISVGDEEV 129
                                    55666666666666......444444433 PP

  == domain 3  score: 13.4 bits;  conditional E-value: 1.5e-05
                        acVLRF1  44 qqRfaRrrenqadalleavaeaaarllaeesae.........vvlgGdrslvaevledarlaplatlareelldvpdprr 114
                                    q+ f+  r++++d+ + av e++a+++ +  +e         v  gG+  + + ++  + ++ l+  + +  l++++  +
  gi|119719470|ref|YP_919965.1| 171 QRIFESGRAEHVDEVVVAVNERLAEVVSRVLGElgvkarvvkVSEGGEAGIYELLRGGQSRELLSSVRLP--LELAEV-E 247
                                    666999*********************7777777778888889999999999999988776665555444..455555.6 PP

                        acVLRF1 115 avLed 119
                                    +vL++
  gi|119719470|ref|YP_919965.1| 248 RVLQE 252
                                    66665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2507.23
//
Query:       gi|119719471|ref|YP_919966.1|  [L=232]
Description: ribosome biogenesis protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.6e-43  147.1   0.0    5.3e-43  146.9   0.0    1.0  1  EMG1            EMG1/NEP1 methyltransferase
     0.0092   16.0   0.1      0.053   13.5   0.2    2.0  2  Glyco_transf_4  Glycosyltransferase Family 4


Domain annotation for each model (and alignments):
>> EMG1  EMG1/NEP1 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.9   0.0   5.9e-47   5.3e-43       1     194 []       6     223 ..       6     223 .. 0.91

  Alignments for each domain:
  == domain 1  score: 146.9 bits;  conditional E-value: 5.9e-47
                                    EEEEEES--B--GG................SCGGSB--HHHHCGG.TTSTTGGGSS-CHHHHHHHHHHHCSCHHCTT.EE CS
                           EMG1   1 ivLeeasLelvkvk................kkseqLLnsddhkkilkklkreakeaRpDIvHqcLlalldspLnkagllq 64 
                                    +vL++a Lelv+++                ++ ++LL+ + h+ ++k+l++ +k++RpDIvH +Ll ++ds+Ln+ g l+
  gi|119719471|ref|YP_919966.1|   6 LVLADAGLELVPRElwshpavkshakrrgkNPGRMLLDISVHYAAMKTLNEYWKRGRPDIVHVSLLVAQDSVLNRLGYLH 85 
                                    59****************************************************************************** PP

                                    EEEEETTSEEEEE-TT----SSHHHHHHHHHHHHCCSEEEETTEE.SCEEEEC.S-HHHHCCC...SEEEEE-TTSEE-. CS
                           EMG1  65 vyihttknvlIevnpqtRiPrtfkrFagLmvqLLkklsirategeekLlkvik.npitdhlpp..gskiillsesaekkl 141
                                      iht++++l+e++p++ +Pr+++rF+gL++qLL+k+++++ +++ +L k+   +++ ++l++     ++ lse++e++ 
  gi|119719471|ref|YP_919966.1|  86 TVIHTYDGKLVELDPSMVVPRNYNRFVGLFEQLLEKGQVPPGSEK-PLAKLRTgRNLGEVLKEmgVDAVYRLSEKGEPV- 163
                                    *****************************************9998.*****88689*******877899********55. PP

                                    .................EEEE-SSSS.......---HHEEESSSS---HHHHHHHHHHHCH CS
                           EMG1 142 vdleefv.....vkpvvfvigamskgsvki...dykeeeisisnypLsaavvcskiltafE 194
                                     ++ +++     ++  +++iga+++g+ +    +++ ee+si ++ L a++v+++++ ++E
  gi|119719471|ref|YP_919966.1| 164 -KPLDLArriagSDVPAVIIGAFQRGEFSKevlSIEAEEYSIFREALPAWTVVAEVVVSLE 223
                                    .466666555775566899*******444322456667******************98876 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.2   5.9e-06     0.053      38      86 ..      28      76 ..       5     112 .. 0.74
   2 ?    0.6   0.0     0.056   5.1e+02      45      76 ..     122     153 ..      77     181 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.9e-06
                 Glyco_transf_4 38 elvvrvprvplpllkrllrslaflrrlrrllkrekpDvvHahspaalga 86
                                    + +r ++ p + l +    +a+++ l + +kr++pD+vH+   +a   
  gi|119719471|ref|YP_919966.1| 28 SHAKRRGKNPGRMLLDISVHYAAMKTLNEYWKRGRPDIVHVSLLVAQDS 76
                                   45667777888888889999999*****************998766544 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.056
                 Glyco_transf_4  45 rvplpllkrllrslaflrrlrrllkrekpDvv 76 
                                    +  +p+++++l  l+  r l ++lk+ ++D v
  gi|119719471|ref|YP_919966.1| 122 GQVPPGSEKPLAKLRTGRNLGEVLKEMGVDAV 153
                                    44558888888889999999999999999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1492.59
//
Query:       gi|119719472|ref|YP_919967.1|  [L=74]
Description: hypothetical protein Tpen_0558 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.43
# Mc/sec: 522.66
//
Query:       gi|119719473|ref|YP_919968.1|  [L=472]
Description: hypothetical protein Tpen_0559 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.15   11.8   0.2       0.29   10.8   0.2    1.4  1  DUF2937   Protein of unknown function (DUF2937)


Domain annotation for each model (and alignments):
>> DUF2937  Protein of unknown function (DUF2937)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2   1.6e-05      0.29      31      91 ..      44     103 ..      41     115 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 1.6e-05
                        DUF2937  31 LeghldelkrqlagfqatAkrffkgdlealiahyrqsedpvvradaesiqalverlerLeq 91 
                                    L++  +++ r+la+++a  +++++    +++ ++ + e++++r+  ++++++++r+++L+ 
  gi|119719473|ref|YP_919968.1|  44 LKATHEQVARELAEIKANYAQYGE-AYVEYVGRLGEGEEKAFREAEKAMREALKRVDELKI 103
                                    889999******************.999*******************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (472 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       744  (0.041497); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 3113.74
//
Query:       gi|119719474|ref|YP_919969.1|  [L=123]
Description: RNAse P, Rpr2/Rpp21 subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-13   50.4   0.0    2.4e-13   50.2   0.0    1.1  1  Rpr2            RNAse P Rpr2/Rpp21/SNM1 subunit domain
      0.006   16.7   4.0      0.047   13.9   4.0    2.1  1  zinc_ribbon_13  Nucleic-acid-binding protein containing Zn-ri
  ------ inclusion threshold ------
      0.048   13.8   0.0       0.11   12.7   0.0    1.6  1  SpdB            Mobile element transfer protein
        2.2    8.3   5.1        7.8    6.6   0.6    2.5  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain


Domain annotation for each model (and alignments):
>> Rpr2  RNAse P Rpr2/Rpp21/SNM1 subunit domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.2   0.0   5.4e-17   2.4e-13       2      90 .]      16      95 ..      15      95 .. 0.87

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 5.4e-17
                                   HHHHHHHHH.HHHHH-HHHHHHHHHHHHHHHHHCT---SSTCCCTB-TTT--B--CTTTEEEEEE-SSS-E.........EE CS
                           Rpr2  2 lnfLyqaahlqlaeaspalsrylakqlrevskkaqlrlppsvkrtvCkkCgsvlipgvtcsvrvenkskkkkkkkkkadvlv 83
                                   ++ L + a+    +  p+l+ ++++    ++kka+l+ p+ +k +vC+kCg++l+ g++++vrv+n+ k k         + 
  gi|119719474|ref|YP_919969.1| 16 IKRLLEFAAK-VYRVEPRLADRYGELSLLIAKKARLHYPDFLKARVCRKCGAFLVVGFSARVRVKNRGKMK--------YIA 88
                                   6666666665.67889************************************************9855543........478 PP

                                   EEETTTT CS
                           Rpr2 84 vtClaCg 90
                                   vtCl+Cg
  gi|119719474|ref|YP_919969.1| 89 VTCLRCG 95
                                   ******7 PP

>> zinc_ribbon_13  Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   4.0     1e-05     0.047      30      49 ..      83     102 ..      60     108 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1e-05
                 zinc_ribbon_13  30 nkkfitvsCknCgYtelYka 49 
                                    + k+i+v+C +CgYt  Y  
  gi|119719474|ref|YP_919969.1|  83 KMKYIAVTCLRCGYTRRYPL 102
                                    679************98865 PP

>> SpdB  Mobile element transfer protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.4e-05      0.11      12      39 ..      79     105 ..      70     107 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.4e-05
                           SpdB  12 drrGkekhvAaCtapkCgfSadydsrsa 39 
                                     +rGk+k++A+ t  +Cg+   y+ + +
  gi|119719474|ref|YP_919969.1|  79 KNRGKMKYIAV-TCLRCGYTRRYPLKRS 105
                                    579******98.788****999986655 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.5     0.012        56      18      26 ..      58      66 ..      46      85 .. 0.79
   2 ?    6.6   0.6    0.0017       7.8      19      34 ..      89     104 ..      72     113 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.012
                  Zn_Tnp_IS1595 18 gfvCPhCgs 26
                                    +vC +Cg 
  gi|119719474|ref|YP_919969.1| 58 ARVCRKCGA 66
                                   489****95 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0017
                  Zn_Tnp_IS1595  19 fvCPhCgsrkayrikt 34 
                                    ++C +Cg+++ y +k+
  gi|119719474|ref|YP_919969.1|  89 VTCLRCGYTRRYPLKR 104
                                    78**********9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 827.71
//
Query:       gi|119719475|ref|YP_919970.1|  [L=491]
Description: hypothetical protein Tpen_0561 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.2e-10   38.9   0.0    1.3e-09   38.1   0.0    1.5  1  DUF402     Protein of unknown function (DUF402)
    2.9e-05   23.6   0.0    4.2e-05   23.1   0.0    1.2  1  RNase_E_G  Ribonuclease E/G family


Domain annotation for each model (and alignments):
>> DUF402  Protein of unknown function (DUF402)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.0   1.4e-13   1.3e-09       7      68 .]     370     433 ..     364     433 .. 0.88

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 1.4e-13
                                    E-TT-SEEEEEEEETTTEEEEEEEEEES--EE....E.EEE-EEEEEEESEEE......-HHHH CS
                         DUF402   7 lplglwynvfhfldgdgrlqglYvDiatppev.ge.gawktiDlyLDlvvspdgevevlDedEL 68 
                                     +l +++ v+++  ++g+l+g+Yv+i+ p  + g+ +++ ++Dl +D+++ +d+e +v+D+ E+
  gi|119719475|ref|YP_919970.1| 370 TWLFGRAVVHFYTSARGELKGVYVNINAPVFFaGNaNTLGYVDLGVDVTRAADEEPKVVDLAEF 433
                                    567778888888888**************888655999************9************8 PP

>> RNase_E_G  Ribonuclease E/G family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   4.7e-09   4.2e-05       2      90 ..     149     235 ..     148     251 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 4.7e-09
                      RNase_E_G   2 laGrylVllpegkkvgvSkkiedeeererlkelleelkpeevGlIvRtaaegaseeelekdleelkkkweeilekakkrk 81 
                                    ++G+ + l+ ++++ +vS+ i+de+ r +l +l+ +  p++ G+ +R+a++ as  ++ ++++ l++k e+il++++  k
  gi|119719475|ref|YP_919970.1| 149 ITGSLVRLVQFDRH-SVSEHIRDENLRLQLLTLAMTSAPTGWGVHFRSASKRASIVDVMAEIKALSEKAEKILKEVA-PK 226
                                    56777777755555.9******************9999*************************************97.66 PP

                      RNase_E_G  82 apsllyeee 90 
                                    +p ++   e
  gi|119719475|ref|YP_919970.1| 227 EPGVVVPGE 235
                                    777766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (491 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 3250.97
//
Query:       gi|119719476|ref|YP_919971.1|  [L=167]
Description: histidine triad (HIT) protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-13   51.1   0.0    2.3e-13   50.7   0.0    1.2  1  HIT       HIT domain
    1.1e-07   32.4   0.0    1.6e-07   31.8   0.0    1.3  1  DcpS_C    Scavenger mRNA decapping enzyme C-term binding
    2.7e-06   27.2   0.1    6.7e-06   26.0   0.0    1.6  2  CwfJ_C_1  Protein similar to CwfJ C-terminus 1


Domain annotation for each model (and alignments):
>> HIT  HIT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.7   0.0   3.9e-17   2.3e-13       6      95 ..      38     128 ..      33     131 .. 0.95

  Alignments for each domain:
  == domain 1  score: 50.7 bits;  conditional E-value: 3.9e-17
                                    CCEEEE-SSEEEEE-SS-SSSSEEEEEESSTGCSGGGCCHHHHHHHHHHHHHHHHHHHTCTTCCCEEEEEEESGGGT-SS CS
                            HIT   6 stvvyeddlvlafldidpkapghlLvipkkhlselhdlteeelakllsavkkvakalqkkfknkglrvvinngahagqsv 85 
                                    + vvy+ ++++++l+  p   ghlLv p +h++++++l++eel  l +av    + l+k ++ +g++v +n g+ ag   
  gi|119719476|ref|YP_919971.1|  38 NLVVYKGEKIIVMLNRYPYNTGHLLVAPTRHVADFSQLSDEELFSLAKAVSLSLELLKKALSPDGFNVGVNLGRVAGAGL 117
                                    569**************************************************************************988 PP

                                    .SS-EEEEEEC CS
                            HIT  86 .ahlHiHvipr 95 
                                      hlH+Hv+pr
  gi|119719476|ref|YP_919971.1| 118 eSHLHVHVVPR 128
                                    46*******98 PP

>> DcpS_C  Scavenger mRNA decapping enzyme C-term binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.0   2.7e-11   1.6e-07       4     100 ..      26     126 ..      23     134 .. 0.85

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 2.7e-11
                                    HHHHHTTSS.-B-E.EEE-SSEEEEE-SS-SSSEEEEEEESS---SGGG--TTTTTHHHHHHHHHHHHHHHTT-T-EEEE CS
                         DcpS_C   4 fnilakgke.perv.vyedekfvvlkDikpkaklhllvipkrdikslrdLtkehlpllkemrekakkvieekynevdaee 81 
                                     ++ ++  e +e++ vy+ ek++v+   +p ++ hllv p r++++  +L++e+l  l++ +    +++++      ++ 
  gi|119719476|ref|YP_919971.1|  26 ICKAVESSElEENLvVYKGEKIIVMLNRYPYNTGHLLVAPTRHVADFSQLSDEELFSLAKAVSLSLELLKKAL---SPDG 102
                                    5666666665555438888**************************************************9866...6889 PP

                                    E--SCCCT-.....-S-S--EEEE CS
                         DcpS_C  82 lrvgvhyqP.....svyhlHlHvi 100
                                    ++vgv++         +hlH+Hv+
  gi|119719476|ref|YP_919971.1| 103 FNVGVNLGRvagagLESHLHVHVV 126
                                    99999988877667779******8 PP

>> CwfJ_C_1  Protein similar to CwfJ C-terminus 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   1.1e-09   6.7e-06      12      69 ..      22      81 ..      14      99 .. 0.89
   2 ?   -1.7   0.0      0.42   2.5e+03     100     108 ..     119     127 ..     113     129 .. 0.87

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 1.1e-09
                                   HH-S--..--SS---SS--S-B-SSEEEE---S-SSTT-EEEEESS--SSTTSS-HHHHH CS
                       CwfJ_C_1 12 dsClfC..lsnpklekhlivsignkvYlalpkgpLssgHvliipieHisallsldeevld 69
                                   + C+ C  +++++le++l+v  g+k+ ++l + p + gH+l+ p+ H++  ++l++e+l 
  gi|119719476|ref|YP_919971.1| 22 EGCFICkaVESSELEENLVVYKGEKIIVMLNRYPYNTGHLLVAPTRHVADFSQLSDEELF 81
                                   679999778999******************************************998765 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.42
                                    ----EEEEE CS
                       CwfJ_C_1 100 vHlaiqvip 108
                                    +Hl+++v+p
  gi|119719476|ref|YP_919971.1| 119 SHLHVHVVP 127
                                    799999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1176.37
//
Query:       gi|119719477|ref|YP_919972.1|  [L=423]
Description: translation initiation factor IF-2 subunit gamma [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-30  106.1   0.1    1.2e-29  103.3   0.1    2.0  1  GTP_EFTU      Elongation factor Tu GTP binding domain
    5.5e-29  100.3   0.1    1.2e-28   99.1   0.1    1.6  1  eIF2_C        Initiation factor eIF2 gamma, C terminal
    6.6e-07   29.6   0.9    1.8e-06   28.3   0.9    1.7  1  GTP_EFTU_D2   Elongation factor Tu domain 2
    1.8e-05   24.8   0.0    4.4e-05   23.5   0.0    1.7  1  MMR_HSR1      50S ribosome-binding GTPase
     0.0005   20.0   0.1        0.4   10.6   0.0    2.2  2  RsgA_GTPase   RsgA GTPase
  ------ inclusion threshold ------
      0.066   13.0   0.1        6.8    6.4   0.0    2.3  2  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
      0.094   12.7   0.1       0.19   11.8   0.1    1.4  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
        0.1   11.6   0.3       0.91    8.4   0.1    2.1  2  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
       0.13   11.8   0.2         19    4.8   0.0    2.7  2  FeoB_N        Ferrous iron transport protein B


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.3   0.1   5.8e-33   1.2e-29       2     193 ..      14     213 ..      13     214 .. 0.88

  Alignments for each domain:
  == domain 1  score: 103.3 bits;  conditional E-value: 5.8e-33
                                    CEEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEE................. CS
                       GTP_EFTU   2 rirnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisle................. 64 
                                    +++nig+ ghvDhGKtTL+++L+                    +++eE +rgiT k+  + +                  
  gi|119719477|ref|YP_919972.1|  14 PLVNIGTSGHVDHGKTTLIEALTGVWAS---------------RHSEELKRGITLKIGYADTAiykcpkcpppqayytsa 78 
                                    579*******************944433...............3457889999999988888888999999999999999 PP

                                    .............TTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTB.STHHHHHHHHHHHHTTTE.EEEEE CS
                       GTP_EFTU  65 .............ketkkylinliDtPGHvdFskevirglrvlDgavlvvdaveG.vepqteevlrlalkegvp.iivfi 129
                                                   +  +++++iD PGH+  ++ + +g++ +Dga+lvvda++  ++pqt+e++  ++  gv+ ++++ 
  gi|119719477|ref|YP_919972.1|  79 tmpkdgkckycgsPLEFVRKVSFIDVPGHEMLMSIMLAGAALMDGALLVVDATKEcPQPQTREHFTALSIIGVRnLVIVQ 158
                                    9*****9999884488899*********************************97769*****************9***** PP

                                    ESCGST.HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHHSH CS
                       GTP_EFTU 130 NKmDrl.kaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvktllealvellp 193
                                    NK+D + k++  e+ +e+k k+      +   ++++    p+v++Sal++ ++++l+ a+ e++p
  gi|119719477|ref|YP_919972.1| 159 NKVDVVsKERALESYNEIK-KF------IAGTWAEN---APIVPVSALHKANIDALVWAIEEYIP 213
                                    ******7788888888888.77......66666665...6***********************98 PP

>> eIF2_C  Initiation factor eIF2 gamma, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.1   0.1   6.3e-32   1.2e-28       2      85 ..     338     421 ..     337     422 .. 0.98

  Alignments for each domain:
  == domain 1  score: 99.1 bits;  conditional E-value: 6.3e-32
                                    EEEEEEEE-SBESSSSSCCC-----TTEEEEEEETTEEEEEEEEEEESSEEEEEEEEEEE-STTEEEEEEEEETTSEEEE CS
                         eIF2_C   2 eleieyellerlvgvkeekkveklkkkEvLmlniGsastggvvtsvkkdeakvkLkkPvcaekgekialsRrvekrWrLi 81 
                                    +leie++ller+vg+++ +kve+++ +E+Lm+n+G+a ++g vtsv++++a++kLk Pv+ae+g+++a+sR++ ++WrLi
  gi|119719477|ref|YP_919972.1| 338 DLEIEVNLLERVVGLDKPMKVEPVRAGEILMVNVGTALSIGAVTSVRDNVAHMKLKIPVVAETGTRVAISRQLAGKWRLI 417
                                    59****************************************************************************** PP

                                    EEEE CS
                         eIF2_C  82 GwGe 85 
                                    G+G 
  gi|119719477|ref|YP_919972.1| 418 GYGF 421
                                    **95 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.9   8.9e-10   1.8e-06       1      62 [.     245     313 ..     245     326 .. 0.90

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 8.9e-10
                                    EEEEEEEEEESEEETTEEEEEEC.TCTTSEE......EEEEEEEEEEETEEESEEETTSEEEEEEEESS CS
                    GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilg.ndtskke......ivtrissletfhededeavaganaGvivaikg 62 
                                    G+v +g++++G +++G e++i++  + +k++        t+i+sl t  ++++ a++g+ + v++ +++
  gi|119719477|ref|YP_919972.1| 245 GGVLGGTIVQGRFEVGHEIEIRPgIKIKKDGqevyepVYTTITSLKTGDQPLEKAYPGGLVAVGTTLDP 313
                                    899********************77665666*******************************9998876 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   2.2e-08   4.4e-05       2      98 ..      18     143 ..      17     167 .. 0.71

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 2.2e-08
                                    EEEEESTTSSHHHHHHHHHTS...TEEESSSTTSSSSEEEEEEEETTEE............................... CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltge...kaivsdkpgtTrdinegrvklkgke............................... 47 
                                    ++  G+   GK+tLi altg    +   + k g T++i ++  ++ + +                               
  gi|119719477|ref|YP_919972.1|  18 IGTSGHVDHGKTTLIEALTGVwasRHSEELKRGITLKIGYADTAIYKCPkcpppqayytsatmpkdgkckycgsplefvr 97 
                                    677899**************65224455666799***9999888443223555666777777777777777777788877 PP

                                    .EEEEECGGCSSHHHHHHHHHHHHHHHHC.TSEEEEEEETTTTCSHHHHHHHH CS
                       MMR_HSR1  48 .ielvDtpGliegaseekglgkaflalee.adlillvvdaseeklkpldeele 98 
                                     + ++D+pG  e      +l   +la    +d +llvvda++e  +p+ +e  
  gi|119719477|ref|YP_919972.1|  98 kVSFIDVPG-HE------MLMSIMLAGAAlMDGALLVVDATKECPQPQTREHF 143
                                    7********.44......6777777656558********99765555555443 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0     0.002       3.9      91     122 ..       4      38 ..       1      52 [. 0.78
   2 !   10.6   0.0    0.0002       0.4      13      97 ..     118     208 ..      95     213 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.002
                                    HHHHHHCTTSEEEEECSTTS...SHHHHHHHHCTT CS
                    RsgA_GTPase  91 eelkellkdktsvlvGqSGv...GKStLinallpe 122
                                    +e +e+lk++  v +G SG    GK+tLi+al++ 
  gi|119719477|ref|YP_919972.1|   4 DEFQEALKKQPLVNIGTSGHvdhGKTTLIEALTGV 38 
                                    678999*************4455*********985 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0002
                                    EES--EEEEEEESTTTT--HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHH......HHHHHHHHHHHTTSEEEE--TTT CS
                    RsgA_GTPase  13 vaNvdqllivvslkepelslnlldrfLvlaeekgiepvivlnKiDlleeee......eleelkeelealgyevllvsakt 86 
                                    +a +d +l+vv ++++  ++++ + f +l      ++viv nK+D++++e+      e++++ + + a + +++ vsa +
  gi|119719477|ref|YP_919972.1| 118 AALMDGALLVVDATKECPQPQTREHFTALSIIGVRNLVIVQNKVDVVSKERalesynEIKKFIAGTWAENAPIVPVSALH 197
                                    788899999999998888888888887777777779**************988866666666666677789999999999 PP

                                    HTTHHHHHHHC CS
                    RsgA_GTPase  87 kegleelkell 97 
                                    k+++++l  ++
  gi|119719477|ref|YP_919972.1| 198 KANIDALVWAI 208
                                    99999887665 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.016        32       8      26 ..      22      47 ..      16      66 .. 0.72
   2 ?    6.4   0.0    0.0034       6.8      40     142 ..     101     209 ..      92     210 .. 0.61

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.016
                      PduV-EutP  8 GkvgsGKttLtqalkg.......eel 26
                                   G+v+ GKttL +al+g       eel
  gi|119719477|ref|YP_919972.1| 22 GHVDHGKTTLIEALTGvwasrhsEEL 47
                                   8999**********985555555555 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0034
                      PduV-EutP  40 viDtPGeylenrklysalivtsaeadvialvqdateeesvfppgfasvfnkeviG......iitkidlaedeenieavee 113
                                    +iD PG       l+s + + +a  d   lv+dat+e +  p++  ++ +  +iG      +  k+d++++e ++e  +e
  gi|119719477|ref|YP_919972.1| 101 FIDVPGHE----MLMSIMLAGAALMDGALLVVDATKE-CPQPQTREHFTALSIIGvrnlviVQNKVDVVSKERALESYNE 175
                                    58888854....4555566666666777777777654.3444444444445555522221156799**999988887655 PP

                      PduV-EutP 114 lLk.saGa....ekifevsavekegieellkyle 142
                                      k  aG     + i  vsa++k +i+ l+  +e
  gi|119719477|ref|YP_919972.1| 176 IKKfIAGTwaenAPIVPVSALHKANIDALVWAIE 209
                                    4432344322224689***********9987776 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   9.4e-05      0.19      58     100 ..     154     208 ..     151     212 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9.4e-05
                   MMR_HSR1_Xtn  58 clyvlNKiDlisleeldelare............pnsvviSaekelnldeLkeki 100
                                     ++v NK+D +s+e   e ++e              +v++Sa ++ n+d+L+ +i
  gi|119719477|ref|YP_919972.1| 154 LVIVQNKVDVVSKERALESYNEikkfiagtwaenAPIVPVSALHKANIDALVWAI 208
                                    57899*****99887655555446678899987668999***********98766 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.11   2.1e+02      31      52 ..      17      38 ..      12      45 .. 0.85
   2 ?    8.4   0.1   0.00046      0.91     171     229 ..     155     212 ..     144     218 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.11
                                   EEEEEE-TTSSHHHHHHHHHHH CS
                           MeaB 31 vvGltGvPGaGkstlvealgle 52
                                    +G  G    Gk tl+eal+  
  gi|119719477|ref|YP_919972.1| 17 NIGTSGHVDHGKTTLIEALTGV 38
                                   589999999*********9865 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00046
                                    EEEEE---HHHHHHHHHHHHHHHHHCSTTBTTB..--EEEEEBCCCTBSHHHHHHHHHHHH CS
                           MeaB 171 iivvnkaDkkeaekaarelraaleleeekekeW..rpkvlktsavegeGidelvdaieehr 229
                                    +iv nk D    e+a + ++ + +       +W  +++++ +sa+++  id lv aiee+ 
  gi|119719477|ref|YP_919972.1| 155 VIVQNKVDVVSKERALESYNEIKKFIA---GTWaeNAPIVPVSALHKANIDALVWAIEEYI 212
                                    456699998887777777766555554...44533789*********************96 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0    0.0094        19       3      23 ..      18      38 ..      16      42 .. 0.85
   2 ?    4.4   0.0     0.013        25     106     154 ..     152     206 ..      94     208 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0094
                                   EEEEESTTSSHHHHHHHHHTT CS
                         FeoB_N  3 valvGnpnvGkttlfnaltga 23
                                   + + G  + Gkttl++altg+
  gi|119719477|ref|YP_919972.1| 18 IGTSGHVDHGKTTLIEALTGV 38
                                   567799999**********96 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.013
                                    SSEEEEEETHHHHHHTTEEE-HHHHHHHH......TS-EEEEBTTTTBTHHHHHH CS
                         FeoB_N 106 vpvvlalnmideaekkgieidlkkLsekL......gvpvvktsakkkegieellk 154
                                     ++v++ n++d+++k++     +++++ +      + p+v++sa +k +i++l+ 
  gi|119719477|ref|YP_919972.1| 152 RNLVIVQNKVDVVSKERALESYNEIKKFIagtwaeNAPIVPVSALHKANIDALVW 206
                                    4689999******9999999999999887444444589************99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      583  (0.0325172); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2811.07
//
Query:       gi|119719478|ref|YP_919973.1|  [L=635]
Description: arginyl-tRNA synthetase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.5e-31  107.5   0.0    5.4e-28   98.0   0.0    2.2  1  tRNA-synt_1d  tRNA synthetases class I (R)
    8.9e-30  103.3   0.2    2.9e-29  101.7   0.0    2.0  2  DALR_1        DALR anticodon binding domain
     0.0007   18.4   0.0      0.011   14.5   0.1    2.6  3  tRNA-synt_1g  tRNA synthetases class I (M)
     0.0041   15.4   0.4      0.054   11.7   0.1    2.5  3  tRNA-synt_1   tRNA synthetases class I (I, L, M and V)
  ------ inclusion threshold ------
      0.047   13.0   0.0       0.16   11.2   0.0    1.8  3  tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
      0.091   11.7   0.1        3.2    6.6   0.1    2.2  2  tRNA-synt_1f  tRNA synthetases class I (K)
      0.094   12.8   0.0       0.26   11.4   0.0    1.8  1  HemN_C        HemN C-terminal domain


Domain annotation for each model (and alignments):
>> tRNA-synt_1d  tRNA synthetases class I (R)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.0   0.0   2.1e-31   5.4e-28      16     347 ..     115     502 ..     102     504 .. 0.81

  Alignments for each domain:
  == domain 1  score: 98.0 bits;  conditional E-value: 2.1e-31
                                    -SST-EEEEE----BTTS--BHHHHHHHHHHHHHHHHHHHCT-EEEEEE--B-SSTCHHHHHHHHHHHTTTTTTS---.- CS
                   tRNA-synt_1d  16 srekkkvvvdfssPniakemhvGhLrstiiGdavsrlleflGydvirlnhvGDWGtqfGlLiaylekkqdekllqeqe.l 94 
                                    ++ +++++v++ s n   ++hvGhLr  ++Gd+++rll + G++v    +v D G q    +  +   + e   ++   +
  gi|119719478|ref|YP_919973.1| 115 AETRERIIVEHVSANPIHPLHVGHLRNGVLGDSLVRLLRARGHEVKAHFYVDDVGLQVAYAAKAFSIVGGEGQGKKDHfV 194
                                    567889***************************************************99988888776666544333212 PP

                                    -SCC...CHHHHHHHHCCCSHC...........................................CCHHHHHHHHHHHCT CS
                   tRNA-synt_1d  95 qdLe...afykeakkdydeeei...........................................faerarnyvvkLqsg 128
                                    + L    ++  e+kk  ++                                               + + r      ++g
  gi|119719478|ref|YP_919973.1| 195 GTLYtaiNLLIEVKKLREKAKSasgdelaeinskvseylwrlgelsekfpgliekllewvektedPEAELRRLNRMYEEG 274
                                    2222100122222222222222444555999*********************9999999888776666778888889999 PP

                                    -HHHHHHHHHHHHHHHHHHHHHHHHCT---EC.--CC...CCCCCHHHHHHHHHCTT-EEECTTCEEEEECCC....... CS
                   tRNA-synt_1d 129 dedirklwkllvditrtelqklydrldvtlie.rGes...lykeslneivkelkkkglvkesdGalvvfldef....... 197
                                    d+ + kl +++ d+  +  +++ drl ++      es   ++     +++++l+  glv+  dGalv   d         
  gi|119719478|ref|YP_919973.1| 275 DPSTVKLTRRVLDYCLEGIRETLDRLGISFDSwDWESeltVWSGATSDVIDKLRGLGLVERRDGALVFRADLLaesedvr 354
                                    999*************************9976744444469999***********************988866888999* PP

                                    ........TSSCCEECC-TTS-B-HHHHHHHHHHHHHHTT--SEEEEEEECCCHHHHHHHHHHHHCTTSSTTTSEEEEEE CS
                   tRNA-synt_1d 198 ........gkrlgvvvqksDGgylytttDiaaakerkeelkadkvlyvidsrqslhlqqiflilkkigyvpeskdlehan 269
                                             +  ++++++sDG++lytt+Dia  + ++   +ad+v+ vi  +q l   q+ l+l  +gy     +l h +
  gi|119719478|ref|YP_919973.1| 355 raagippgFTVTPMTLVRSDGTTLYTTRDIAYSIWKL--SRADRVINVIAVQQTLAQAQLRLALYALGYRDVGRRLIHYS 432
                                    *998888334456799***************999766..68****************************8889******* PP

                                    E--EE-TTSSBSBCSSSTC-BHHHHHHHHHHHHHHHHCCCCCCTS-CCCCHCHHHHHHHHHHHHCCCCTS-TTS-EE- CS
                   tRNA-synt_1d 270 fGmvlgkdkkkfktrkGetvkLadlLdealeralqlikeknkdkvlqadelekvaeavgvgaikyaDlsknrindyif 347
                                    + mv    + +++ r+G  v  +++++ea+ ra++ i+ +       + +     e vg+ga+k+  ls+   +   f
  gi|119719478|ref|YP_919973.1| 433 YEMV-NLPGTRMSSRRGVYVSADEVIEEAVARAKEEIAKRGVG---DVGDA----EKVGIGALKFFFLSQTPGKVLTF 502
                                    ****.899***************************88766555...44443....45788888887777665555555 PP

>> DALR_1  DALR anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       2.1   5.4e+03      13      54 ..     212     252 ..     201     266 .. 0.65
   2 !  101.7   0.0   1.1e-32   2.9e-29       1     119 []     518     635 .]     518     635 .] 0.96

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.1
                                    HHTTCTTCCCCHCCHCCS-SHHHHHHHHHHHTHHHHHHHHHH CS
                         DALR_1  13 rkaeeegekleeealalleeeeekeLlkalaqfpevleeaae 54 
                                    +ka+ +  ++ +e ++   +e  ++L     +fp ++e+ +e
  gi|119719478|ref|YP_919973.1| 212 EKAKSASGDELAEINSK-VSEYLWRLGELSEKFPGLIEKLLE 252
                                    44444444444444443.667777777888888888777665 PP

  == domain 2  score: 101.7 bits;  conditional E-value: 1.1e-32
                                    HHHHHHHHHHHHHHTTCTTCCCCHCCHCCS-SHHHHHHHHHHHTHHHHHHHHHHHT-THHHHHHHHHHHHHHHHHHHHCT CS
                         DALR_1   1 vqyahaRiksilrkaeeegekleeealalleeeeekeLlkalaqfpevleeaaeelephklaeylyeLaatfhkfYnker 80 
                                    vqy+++R+  ilrka ee ++ +e +      eee  L+  + +fp+v++eaa++l+p+ la+yl +La++f+++Y++ +
  gi|119719478|ref|YP_919973.1| 518 VQYSYVRALGILRKASEEHIRPDELNVGD-VGEEEHPLILLVGEFPNVVKEAADNLRPDLLASYLNTLATEFNRYYDSYP 596
                                    8*****************99887766665.899*********************************************** PP

                                    STTSCTHHH.HHHHHHHHHHHHHHHHHHHHTT----S-- CS
                         DALR_1  81 vlkeeeeelaaaRLaLvkavrqvLangLdlLGieapekm 119
                                    vl ++   ++ +RLa vk v+q+L+ng++lLGieap++m
  gi|119719478|ref|YP_919973.1| 597 VLRAPTTSKKYSRLAVVKMVEQTLKNGMKLLGIEAPQRM 635
                                    **************************************9 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   4.3e-06     0.011      13      58 ..     133     178 ..     128     204 .. 0.91
   2 ?   -2.8   0.0      0.79     2e+03      71      92 ..     290     311 ..     280     341 .. 0.69
   3 ?    0.0   0.0      0.11   2.7e+02     317     344 ..     432     459 ..     423     464 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.3e-06
                                    ---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHH CS
                   tRNA-synt_1g  13 klHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAek 58 
                                    +lH+Ghl++ + +D ++R  r+rg+ev      D  G +++ +A++
  gi|119719478|ref|YP_919973.1| 133 PLHVGHLRNGVLGDSLVRLLRARGHEVKAHFYVDDVGLQVAYAAKA 178
                                    78*************************9999999999999999986 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.79
                                    HHHHHHHHHHTT---SEEEETT CS
                   tRNA-synt_1g  71 heeikelfkklnisfdkygrtt 92 
                                     e i+e++++l+isfd+++  +
  gi|119719478|ref|YP_919973.1| 290 LEGIRETLDRLGISFDSWDWES 311
                                    5678999999******997544 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.11
                                    EE--EEE--------------HHHHHHH CS
                   tRNA-synt_1g 317 aheyltvegkKlSkSrgvvvkakealer 344
                                    + e++++ g ++S+ rgv v a+e++e+
  gi|119719478|ref|YP_919973.1| 432 SYEMVNLPGTRMSSRRGVYVSADEVIEE 459
                                    568999*****************99986 PP

>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.1   2.1e-05     0.054      38      79 ..     134     175 ..     129     195 .. 0.93
   2 ?   -1.5   0.0      0.22   5.6e+02     105     158 ..     283     335 ..     268     346 .. 0.66
   3 ?    0.1   0.0     0.072   1.8e+02     561     597 ..     440     498 ..     434     503 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.1e-05
                    tRNA-synt_1  38 lHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaieak 79 
                                    lH+Gh  + +l d ++r  r +G+ev+  + +D  Gl + ++
  gi|119719478|ref|YP_919973.1| 134 LHVGHLRNGVLGDSLVRLLRARGHEVKAHFYVDDVGLQVAYA 175
                                    8************************************98765 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.22
                    tRNA-synt_1 105 rewkaeyaeeirkqvkrlGvsvD.fdre.ylTldkeleeavkevfvrladkgliyr 158
                                    r   ++  e ir+++ rlG+s+D +d e  lT+    + a+  v+ +l   gl+ r
  gi|119719478|ref|YP_919973.1| 283 RRVLDYCLEGIRETLDRLGISFDsWDWEsELTVW---SGATSDVIDKLRGLGLVER 335
                                    55556677899********988655543124543...4455555556666666655 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.072
                    tRNA-synt_1 561 GrKmSKslgNvidpldvik......................kygadalRltlilsdvgr 597
                                    G +mS + g +++ ++vi+                      k+g  al+++ ++ + g+
  gi|119719478|ref|YP_919973.1| 440 GTRMSSRRGVYVSADEVIEeavarakeeiakrgvgdvgdaeKVGIGALKFFFLSQTPGK 498
                                    999****************9********************999******9999777665 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   6.4e-05      0.16      23     117 ..     134     252 ..     127     265 .. 0.86
   2 ?   -3.2   0.0       1.6   4.2e+03     262     287 ..     398     423 ..     390     437 .. 0.73
   3 ?   -3.1   0.0       1.5   3.9e+03      75     119 ..     580     623 ..     527     625 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6.4e-05
                                    -BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEBB--SHHHHHHHHHTTS-........................HHHHHHH CS
                   tRNA-synt_1e  23 shlGhaRslvafDilrrilqalgYdvqfvqnvtDidDkiikrareeeks........................vkelaek 78 
                                     h+Gh R+ v  D l r+l+a+g++v+    v D+  ++   a++ +                          vk+l ek
  gi|119719478|ref|YP_919973.1| 134 LHVGHLRNGVLGDSLVRLLRARGHEVKAHFYVDDVGLQVAYAAKAFSIVggegqgkkdhfvgtlytainllieVKKLREK 213
                                    7*************************988888888877777666666669999999999999999999999999999999 PP

                                    HHHHHHHHHHHTT----SB--BGGGGHHHHHHHHHHHHH CS
                   tRNA-synt_1e  79 fieefkkdleaLnvlkptleprvsekvdeiielveklie 117
                                      ++  ++l+++n + +++  r  e  ++  +l+ekl+e
  gi|119719478|ref|YP_919973.1| 214 AKSASGDELAEINSKVSEYLWRLGELSEKFPGLIEKLLE 252
                                    999999999999999999999988888888888888875 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.6
                                    -BHHHHHTTS-HHHHHHHHHSS-TTS CS
                   tRNA-synt_1e 262 itikdvlkkfdprqlRllllsahyrs 287
                                    i + +v ++  ++qlRl+l+   yr+
  gi|119719478|ref|YP_919973.1| 398 INVIAVQQTLAQAQLRLALYALGYRD 423
                                    55555566667788999999888875 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 1.5
                                    HHHHHHHHHHHHHHHTT----SB--BGGGGHHHHHHHHHHHHHTT CS
                   tRNA-synt_1e  75 laekfieefkkdleaLnvlkptleprvsekvdeiielvekliekg 119
                                      ++  +ef++ +++  vl++ ++++   ++ +++++ve+ +++g
  gi|119719478|ref|YP_919973.1| 580 YLNTLATEFNRYYDSYPVLRAPTTSKKYSRL-AVVKMVEQTLKNG 623
                                    4556678889999999999887777777776.4778888888877 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1    0.0012       3.2      36      71 ..     133     168 ..     117     171 .. 0.93
   2 ?    2.5   0.0     0.021        54     268     297 ..     430     458 ..     425     464 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0012
                   tRNA-synt_1f  36 liHiGnlrevltadlvaralrkrgeevrlilisDdm 71 
                                    ++H+G lr+ + +d ++r lr+rg+ev+  +++Dd+
  gi|119719478|ref|YP_919973.1| 133 PLHVGHLRNGVLGDSLVRLLRARGHEVKAHFYVDDV 168
                                    58********************************97 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.021
                   tRNA-synt_1f 268 kvvYelillkggekmssSkGnvltledwle 297
                                    ++ Ye++ l g   mss +G++++ ++++e
  gi|119719478|ref|YP_919973.1| 430 HYSYEMVNLPGT-RMSSRRGVYVSADEVIE 458
                                    679*******99.9************9987 PP

>> HemN_C  HemN C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0    0.0001      0.26      18      59 ..     299     341 ..     290     344 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0001
                         HemN_C  18 reGldlaafeqrfgld.leellaaaleklqeqGLLeldggrlr 59 
                                    r G++++ + ++++l+ ++ +  ++++kl+  GL+e ++g l+
  gi|119719478|ref|YP_919973.1| 299 RLGISFDSWDWESELTvWSGATSDVIDKLRGLGLVERRDGALV 341
                                    67**************555566******************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (635 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.46
# Mc/sec: 4184.79
//
Query:       gi|119719479|ref|YP_919974.1|  [L=471]
Description: hypothetical protein Tpen_0565 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.14   11.8   0.1       0.32   10.7   0.1    1.5  1  DUF2937   Protein of unknown function (DUF2937)


Domain annotation for each model (and alignments):
>> DUF2937  Protein of unknown function (DUF2937)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   1.8e-05      0.32      31      91 ..      44     103 ..      41     111 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 1.8e-05
                        DUF2937  31 LeghldelkrqlagfqatAkrffkgdlealiahyrqsedpvvradaesiqalverlerLeq 91 
                                    L++  +e+ ++la+++   +++++    +++ ++ + e++++r+  ++++++++r+++L+ 
  gi|119719479|ref|YP_919974.1|  44 LKATHEEVAQELAEIRGNYAQYGE-AYVEYVGRLGEGEEKAFREAEKAMREALKRVDELKI 103
                                    8899********************.999*******************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (471 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 3478.38
//
Query:       gi|119719480|ref|YP_919975.1|  [L=84]
Description: hypothetical protein Tpen_0567 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 585.96
//
Query:       gi|119719481|ref|YP_919976.1|  [L=977]
Description: leucyl-tRNA synthetase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.6e-61  207.6   0.0    5.4e-59  200.0   0.0    3.3  2  tRNA-synt_1    tRNA synthetases class I (I, L, M and V)
    8.5e-24   84.0   0.3    1.7e-09   36.9   0.0    4.1  4  tRNA-synt_1g   tRNA synthetases class I (M)
    6.7e-21   74.8   1.1    1.3e-20   73.9   1.1    1.5  1  Anticodon_1    Anticodon-binding domain of tRNA
    1.6e-11   44.1   0.0    2.8e-11   43.3   0.0    1.4  1  tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
    5.3e-08   32.6   0.0    2.2e-05   24.0   0.0    2.4  2  tRNA-synt_1e   tRNA synthetases class I (C) catalytic domain
      0.003   16.5   0.2      0.059   12.3   0.0    2.8  3  tRNA-synt_1f   tRNA synthetases class I (K)


Domain annotation for each model (and alignments):
>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.0   0.0   1.8e-62   5.4e-59       2     592 ..      31     687 ..      30     699 .. 0.81
   2 ?   -3.3   0.0      0.64   1.9e+03     486     524 ..     730     763 ..     717     766 .. 0.73

  Alignments for each domain:
  == domain 1  score: 200.0 bits;  conditional E-value: 1.8e-62
                    tRNA-synt_1   2 lyekWeeedvfkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaieakv. 80 
                                    ++ +Wee+++f++    + ++++f ++ + Py++  +H+G a++    di+ r+krm+G++vl+  Gw   G +i a+  
  gi|119719481|ref|YP_919976.1|  31 WQRRWEESGLFEAD--PDPSRPKFFVTFPYPYINSFPHLGTAYTVLRVDILARFKRMQGFNVLFPQGWHATGGPIVAAAl 108
                                    889*********99..7777****************************************************88865541 PP

                    tRNA-synt_1  81 ......ekklgakekkerkklgreefrekvrewkaeyaeeirkqvkrlGvsvDfdreylT..ldkeleeavkevfvrlad 152
                                          ek++ + +     +    +fr+    w++ + +  +++++r G s+D+ re +T  l++ +++ +++ ++ l +
  gi|119719481|ref|YP_919976.1| 109 rvregdEKQIRILKSIGIPDSEIPKFRDP-EYWVEFFRKGFKQDFSRYGLSIDWRREFFTtyLNPPYSKFIQWQYTVLRE 187
                                    11222233333333333334444556554.5699**************************667788************** PP

                    tRNA-synt_1 153 kgliyrgkklvnwstklktalselEv..eykdkkdalihvafpladkeevklviaTTtPeTllgdtavavnpeldyv... 227
                                    kgli rg+++v w++k + ++ + +   ey    ++   v  ++++++       T +PeT+ g + + vnpe +y    
  gi|119719481|ref|YP_919976.1| 188 KGLITRGSHPVVWCPKEHKVVGDHDRpdEYAGI-GPERVVIIKFKGEDGLVYPCLTYRPETVYGAVNIWVNPESKYLvae 266
                                    ************************998555554.554445555555566558899*********************9899 PP

                    tRNA-synt_1 228 itkeklilaeallkslvkkesekkiledergkeLegkevelplvnrkipiiaddyvdkeaGtGvVkiaPahdedDyevgk 307
                                    +++ek+++ e   ++l++++++ ki+ +++g+eL+g+++++p+++ +ip++   +v+++aGtG+V   Pah + D++  +
  gi|119719481|ref|YP_919976.1| 267 VDGEKWVIGEYGARELADQDHSVKIVGEVKGSELVGRFARNPVTGWRIPVLPAYFVQADAGTGIVMSVPAHAPYDFAGLE 346
                                    9************************************************************************9997544 PP

                    tRNA-synt_1 308 kynl................evinildedgtlteea............................................ 327
                                    + +                                +                                            
  gi|119719481|ref|YP_919976.1| 347 DLKKdpyllekfgldpaildA--------------Vrpvklidveeygglpaeevvrrlgvtsqfdrekleeatkevysk 412
                                    333233223333335544440..............3555555555556666666799999999999999*********** PP

                    tRNA-synt_1 328 .............aefeglkvfdarkkvveelkekglllkaekiehsvpfcerskkpi.iyrateqWfvrvke..ladaa 391
                                                 + + g kvf+ ++ vve+l  +g  l++ +     p+  r ++   +  +++qWf r ++   +  a
  gi|119719481|ref|YP_919976.1| 413 efykgvlkpevfgERWGGRKVFEVKEDVVENLVSRGIALRHYTLP--SPVYCRCGARThVKLVKDQWFLRYSDpeWKRRA 490
                                    ************************************988766554..444444444430445689*****99777999** PP

                    tRNA-synt_1 392 lkavekvqfvpkskekryaswleniqdWciSRqrwWGhripl...fvsketeevvvreelkelvagreeeeaekkaleke 468
                                     + +++++fvp+  ++++++++   +dW+   +r  G+++p    +v ++  + ++      l++ +++ e+   +++k 
  gi|119719481|ref|YP_919976.1| 491 HECIDRMRFVPEEVRQEFHRLVDWYEDWACTHERELGTPLPWderWVLESLSDSTIYMAYYTLAKYLQHPEKYGIDWSKL 570
                                    *****************************************555588888777777667777777777777777777765 PP

                    tRNA-synt_1 469 akdklkkekgelekdedvlDvWFsSgswpfstlgypee....dteelkkffpadmlleGlDiirgWvarlillslaltgs 544
                                     ++ +          + vl    + gs+   t g p+e     ++e+   +p dm ++G D i   +   i+  +a++ +
  gi|119719481|ref|YP_919976.1| 571 NNEFF----------DYVLLGKGDPGSVAERT-GIPKElleeMRKEFLYWYPVDMRVSGKDLIGNHLVFFIMHHVAIFPE 639
                                    55555..........23333334444443322.23333111158888889***************************999 PP

                    tRNA-synt_1 545 ePf.kevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltlil 592
                                    e + + + v+g v+   G+KmSKs gN i   + ++  gada R++ ++
  gi|119719481|ref|YP_919976.1| 640 EHWpRGIGVNGWVLV-AGKKMSKSAGNFILLREALEYWGADATRFAEAY 687
                                    87636799****996.5****************************8664 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 0.64
                    tRNA-synt_1 486 vlDvWFsSgswpfstlgypeedteelkkffpadmlleGl 524
                                     +D WF+S +    tl+   + t+e+++    ++l+eG+
  gi|119719481|ref|YP_919976.1| 730 FVDDWFESVLY--RTLE---KVTKEYEELNTKNVLVEGF 763
                                    57999999774..5666...3366677777888888886 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   0.0   9.2e-13   2.7e-09       2      57 ..      53     108 ..      52     119 .. 0.94
   2 !    3.6   0.0    0.0078        23      63     132 ..     137     210 ..     133     215 .. 0.81
   3 ?    1.5   0.3     0.034     1e+02     162     276 ..     454     567 ..     437     583 .. 0.69
   4 !   36.9   0.0   5.8e-13   1.7e-09     285     371 ..     614     703 ..     593     713 .. 0.85

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 9.2e-13
                                    EEEE--B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHH CS
                   tRNA-synt_1g   2 lvttalpYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAe 57 
                                    +vt + pY+n+ +HlG +++v+  Di+aR+kr++g +vlf  g  + G pi  +A 
  gi|119719481|ref|YP_919976.1|  53 FVTFPYPYINSFPHLGTAYTVLRVDILARFKRMQGFNVLFPQGWHATGGPIVAAAL 108
                                    89*************************************************99885 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.0078
                                    HHHHHHHHHHHHHHHHHHTT---S...EEEET.TSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-G CS
                   tRNA-synt_1g  63 peelvekvheeikelfkklnisfd...kygrt.tseehkelvqeifkklkekgliyekeieqlycpkderflpd 132
                                    pe  ve +++ +k++f+++++s d   ++ +t  +   +++ q  ++ l ekgli++++  +++cpk+++   d
  gi|119719481|ref|YP_919976.1| 137 PEYWVEFFRKGFKQDFSRYGLSIDwrrEFFTTyLNPPYSKFIQWQYTVLREKGLITRGSHPVVWCPKEHKVVGD 210
                                    66667777888999999999888855545555157788999**************************9988776 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.034
                                    ...............EEE..EEEEEE-GGGGHHHHHHHH.HH-TT.SHHHHHHHH.HHHHT----EE-ESS-SSS-EETT CS
                   tRNA-synt_1g 162 telinpksaisgskpevk.etehlffklskfekklkewieeeeke.leenvkkivkewlkegLkdlaisrdldwGipvPg 239
                                     +l  p+   +g++  vk  ++++f++ s+ e k +++ + ++ +  +e+v++  + +++   +d+a + + + G p+P 
  gi|119719481|ref|YP_919976.1| 454 YTLPSPVYCRCGARTHVKlVKDQWFLRYSDPEWKRRAHECIDRMRfVPEEVRQEFHRLVDW-YEDWACTHERELGTPLPW 532
                                    5566777777777777662467899999887666666555555555999999999999988.9****************8 PP

                                    ECCEEE-HHHHHHH..HHHHTTTTT-...TTSGGGG.G- CS
                   tRNA-synt_1g 240 aekkvlYVWldAli..gYisatkelakkkgeeekwkeyW 276
                                    +e  vl    d +i   Y +  k+l     ++ek+   W
  gi|119719481|ref|YP_919976.1| 533 DERWVLESLSDSTIymAYYTLAKYLQ----HPEKYGIDW 567
                                    88888888888776223445555544....445555444 PP

  == domain 4  score: 36.9 bits;  conditional E-value: 5.8e-13
                                    EEEEEGGGHHHHHTHHHHHHHH..TT----S-EEEE--EEE--------------HHHHHHHH-HHHHHHHHHH.HS-TT CS
                   tRNA-synt_1g 285 vhfigkdiikFHtifwPaillg..aelklpkkvvaheyltvegkKlSkSrgvvvkakealerldadllRYylaa.eapek 361
                                    + + gkd i  H +f+ +   +   e + p+ + +++++ v gkK+SkS g+++  +eale+  ad+ R+  a+  ++  
  gi|119719481|ref|YP_919976.1| 614 MRVSGKDLIGNHLVFFIMHHVAifPEEHWPRGIGVNGWVLVAGKKMSKSAGNFILLREALEYWGADATRFAEAYaGNSGL 693
                                    4677************999999988999******************************************9998556677 PP

                                    S-EEE-HHHH CS
                   tRNA-synt_1g 362 kDldfswedf 371
                                    +D +f+ e +
  gi|119719481|ref|YP_919976.1| 694 DDGNFEPEVA 703
                                    8899987655 PP

>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.9   1.1   4.4e-24   1.3e-20       1     150 [.     732     863 ..     732     865 .. 0.88

  Alignments for each domain:
  == domain 1  score: 73.9 bits;  conditional E-value: 4.4e-24
                    Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkraaqevllevletllrllaPf 80 
                                    d w+ s l++++++vt+ yee++ ++++ + +  ++n++ +wy++    + ++          evl++++e  + +laP+
  gi|119719481|ref|YP_919976.1| 732 DDWFESVLYRTLEKVTKEYEELNTKNVLVEGFFNLQNAY-RWYVKRRGGTANK----------EVLKKFVEIQTLILAPI 800
                                    78******************************9988888.9998887777754..........9**************** PP

                    Anticodon_1  81 mPfitEelwqreeeelgkkesimlaewpe.kaeelekeleeeevellkeivkairklrselkikpsselkv 150
                                    +P+i+Ee+w    e  g+ke+i++ +wp+ ++++ ++e  e++ ++   +vk+ +++ + lk+k+s  +++
  gi|119719481|ref|YP_919976.1| 801 TPHIAEEIW----EATGHKEFISRTSWPAvDKSKIKDEV-EKAESI---VVKLYEDIQEVLKLKKSGVERI 863
                                    *********....999************97776555555.667777...8999999999999999876665 PP

>> tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.3   0.0   9.3e-15   2.8e-11      25     131 ..     240     345 ..     220     392 .. 0.80

  Alignments for each domain:
  == domain 1  score: 43.3 bits;  conditional E-value: 9.3e-15
                  tRNA-synt_1_2  25 vfttrpdtlfGvtfvalapehp.lveklaekkkelaafieevkkksesereletkekeGvftglkaihPitgekipiwva 103
                                      t rp+t++G+  + + pe++ lv ++  +k  + ++ ++   +++++ ++  + k     g +a +P+tg++ip+  a
  gi|119719481|ref|YP_919976.1| 240 CLTYRPETVYGAVNIWVNPESKyLVAEVDGEKWVIGEYGARELADQDHSVKIVGEVKGSELVGRFARNPVTGWRIPVLPA 319
                                    5589***************987589999**********988777777777777666655699****************** PP

                  tRNA-synt_1_2 104 nyvlmeygtgavmavPahdqrDfeFakk 131
                                     +v ++ gtg vm+vPah   D  Fa  
  gi|119719481|ref|YP_919976.1| 320 YFVQADAGTGIVMSVPAHAPYD--FAGL 345
                                    ******************8765..5555 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.0    0.0016       4.9      22      54 ..      64      96 ..      57     453 .. 0.89
   2 !   24.0   0.0   7.2e-09   2.2e-05     205     279 ..     600     684 ..     568     690 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0016
                                   --BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEB CS
                   tRNA-synt_1e 22 ashlGhaRslvafDilrrilqalgYdvqfvqnv 54
                                     hlG a +++ +Dil+r+ +++g++v f q  
  gi|119719481|ref|YP_919976.1| 64 FPHLGTAYTVLRVDILARFKRMQGFNVLFPQGW 96
                                   67*************************997765 PP

  == domain 2  score: 24.0 bits;  conditional E-value: 7.2e-09
                                    -.........SSEEEEEEEGGGTTTHHHHHHHHHHHHSS.S--EEEEEEE--EEETTBE--TTTT---BHHHHHTTS-HH CS
                   tRNA-synt_1e 205 g.........seidihsGGiDLafPhhenelaqseaafd.kqlvkyflhnghlkiegekmsksLknfitikdvlkkfdpr 274
                                                +d+ + G+DL+  h    +  + a f  +++ +    ng++ + g+kmsks +nfi+++++l+ + + 
  gi|119719481|ref|YP_919976.1| 600 EemrkeflywYPVDMRVSGKDLIGNHLVFFIMHHVAIFPeEHWPRGIGVNGWVLVAGKKMSKSAGNFILLREALEYWGAD 679
                                    4444444445789************************98788999999****************************9999 PP

                                    HHHHH CS
                   tRNA-synt_1e 275 qlRll 279
                                    + R++
  gi|119719481|ref|YP_919976.1| 680 ATRFA 684
                                    99886 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0     0.065   1.9e+02      37     130 ..      65     163 ..      63     181 .. 0.64
   2 ?   -2.7   0.1       0.7   2.1e+03     170     203 ..     454     491 ..     430     520 .. 0.62
   3 !   12.3   0.0     2e-05     0.059     235     307 ..     612     684 ..     608     765 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.065
                   tRNA-synt_1f  37 iHiGnlrevltadlvaralrkrgeevrlilisDdmDg.....lRkvpenlpek.llekylgkpltsiPdpkgkhesyaeh 110
                                    +H+G++  vl++d++ar  r +g +v +   +    g       +v e  +++  + k +g p ++iP+ + + e ++e 
  gi|119719481|ref|YP_919976.1|  65 PHLGTAYTVLRVDILARFKRMQGFNVLFPQGWHATGGpivaaALRVREGDEKQiRILKSIGIPDSEIPKFR-DPEYWVEF 143
                                    57777777777777777666666665544444443221111133444554555566778888888888865.55888888 PP

                   tRNA-synt_1f 111 fnaelvesLdelgievefis 130
                                    f++ +++  ++ g  +++ +
  gi|119719481|ref|YP_919976.1| 144 FRKGFKQDFSRYGLSIDWRR 163
                                    88888888888888888765 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.7
                   tRNA-synt_1f 170 yspylpvcekcgrvdttevvevdaeeeeieYkc.......e 203
                                    y   +pv  +cg    t+v+ v+ +++ ++Y++       +
  gi|119719481|ref|YP_919976.1| 454 YTLPSPVYCRCGA--RTHVKLVK-DQWFLRYSDpewkrraH 491
                                    4444555557777..78888887.88888887744433333 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 2e-05
                   tRNA-synt_1f 235 VdfEpaGkDhaaaGgSvdvsskiaeilggeaPekvvYe.lillkggekmssSkGnvltledwlevaepevlrfl 307
                                    Vd+  +GkD++ +   + + +++a + + + P ++  + ++l+ g+ kms+S Gn++ l+++le+   +  rf 
  gi|119719481|ref|YP_919976.1| 612 VDMRVSGKDLIGNHLVFFIMHHVAIFPEEHWPRGIGVNgWVLVAGK-KMSKSAGNFILLREALEYWGADATRFA 684
                                    5556666666665555556666655555556666644316666666.******************999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (977 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.78u 0.30s 00:00:01.08 Elapsed: 00:00:00.50
# Mc/sec: 5890.09
//
Query:       gi|119719482|ref|YP_919977.1|  [L=81]
Description: hypothetical protein Tpen_0569 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 565.96
//
Query:       gi|119719483|ref|YP_919978.1|  [L=360]
Description: histone deacetylase superfamily protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-66  225.3   0.0    1.7e-66  224.8   0.0    1.2  1  Hist_deacetyl  Histone deacetylase domain


Domain annotation for each model (and alignments):
>> Hist_deacetyl  Histone deacetylase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  224.8   0.0   9.6e-71   1.7e-66      28     304 ..      54     313 ..      26     316 .. 0.92

  Alignments for each domain:
  == domain 1  score: 224.8 bits;  conditional E-value: 9.6e-71
                                    .EE-----HHHHTTTS-HHHHHHHHCHHHHCHHT.TTHCCHHHCCTSTSSSSSTHCTTTCCHHHHHHHHHHHHHHHHHHT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Hist_deacetyl  28 liqpseatkeellkvHskeYlelleslsnelkkkeeakekeleeiasklldddtpvspktlkaallavgavleavdavls 107
                                    + + ++  +++ll +H+keY++ ++++s+ l++               l  +dtp+ p++++ allav ++l+++d +++
  gi|119719483|ref|YP_919978.1|  54 VHEVKRYPESVLLLAHDKEYVDYVKRMSE-LGAGL-------------LDYGDTPAYPGVFEKALLAVSGTLTLADILVK 119
                                    566778889999*************9774.44443.............45799**************************8 PP

                                    TSSSEEEETT.SS--TT-BTTB-BTTBSS-HHHHHHHHHHHCC-SS-EEEEE-SSS--HHHHHHCTT-TTEEEEEEEE-C CS
                                    xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Hist_deacetyl 108 gsvkaafvlv.rPpgHHakaseasGFClvNnvaiaikylqakhelkrvailDvDvHhGnGteeafysdpdvltlSiHrye 186
                                        ++++++ ++++HHa+++ a+GFC++N+va+a++y+++  +++rvai+DvD+HhG+Gt+e++y+dp +l +S+H y+
  gi|119719483|ref|YP_919978.1| 120 A--GRGVAFNpQGGFHHARRRSAGGFCVFNDVAVAARYVRE-RGYERVAIIDVDAHHGDGTQEILYRDP-LLKVSVHGYG 195
                                    8..9*************************************.789**********************99.799******* PP

                                    CTSTTSS--TT---SGGGTTSEEEEEE-TT-BHHHHHHHHHHCHHHHHCCH--SEEEEEE-STTBTTSTT-S-BB-HHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Hist_deacetyl 187 gifyPgtgaledlgegkgkgfnlnvpleegtgdeeylkvfeeilrpvleefkPdlilvsaGfDalkgdplgelnlsvegy 266
                                     +fyPgtg +++lgeg+g  +n+nvp++  + d+ +  v++e+l p+++ ++Pd+++v+ G+Da++gdpl +l+l+ + y
  gi|119719483|ref|YP_919978.1| 196 YGFYPGTGWIDELGEGDGLCMNINVPIPLTSADDVFELVVRELLAPLISSYSPDFVIVQSGVDAYRGDPLVGLRLTDNSY 275
                                    **************999999************************************************************ PP

                                    HHHHHHHCCCHGS-G.EEEEE-S---HHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Hist_deacetyl 267 keltkklaeladkvkkvvllleGGYnlealaravtavl 304
                                    k + + l  +a ++ +v+l+++GGY++e +ar ++ +l
  gi|119719483|ref|YP_919978.1| 276 KVFAEFLSGIAARGVPVLLTGGGGYQPEVTARTWAFIL 313
                                    ***********9877******************98766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 2533.08
//
Query:       gi|119719484|ref|YP_919979.1|  [L=183]
Description: pyruvate/ketoisovalerate oxidoreductase, gamma subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-38  132.2   0.0    2.4e-38  132.0   0.0    1.0  1  POR       Pyruvate ferredoxin/flavodoxin oxidoreductase


Domain annotation for each model (and alignments):
>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.0   0.0   1.3e-42   2.4e-38       1     177 []       7     177 ..       7     177 .. 0.96

  Alignments for each domain:
  == domain 1  score: 132.0 bits;  conditional E-value: 1.3e-42
                                    CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHH..HHGGGEEE CS
                            POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetls..ehldglkp 78 
                                    GGqGvvt +++la aa r+G+ v+ ++e+g+e+rG+++ ++ ris+epi  + +++e+  +v+ d+++ +    ++gl++
  gi|119719484|ref|YP_919979.1|   7 GGQGVVTSSELLALAALREGKFVYHAPEFGPERRGAPVKAYTRISREPIELHSGIYEPSAVVVIDPSLQNdpSIASGLRK 86 
                                    9*****************************************************************999889******** PP

                                    EEEEEEECTCGTT-CCHHHCTS-HHHHHHHT-EEEEE-HHHHHHHCCC.CCHHHHHHHHHHHHHHT.S-HHHHHHHHHCC CS
                            POR  79 ggiiiynseelkpdelkkakeeerelkerlgvrvygvdatkiakeiggneraaNtvmlGalaallg.lplealeeaikkr 157
                                    gg+i++n++ + +  l  a e         g++v+ vda  ia e  g +++ Nt mlGa++++++ ++le++  +  +r
  gi|119719484|ref|YP_919979.1|  87 GGLIVVNAKSPGDVLLRSAQEK--------GAEVWYVDAYSIAMEVFG-RPFYNTPMLGAFVRASNvVSLESVVSVAMER 157
                                    ********98888888887765........6799**************.******************************* PP

                                    S-CH.HHHHHHHHHHHHHHH CS
                            POR 158 fpkkkeviekNlkafragye 177
                                    f k ++++++N+ a+r++y+
  gi|119719484|ref|YP_919979.1| 158 FSKDSKLAQLNVLAIRRAYD 177
                                    **999**************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       260  (0.0145016); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 1256.74
//
Query:       gi|119719485|ref|YP_919980.1|  [L=98]
Description: pyruvate ferredoxin/flavodoxin oxidoreductase, delta subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-14   51.8  16.3    1.2e-08   34.4   6.0    2.1  2  Fer4      4Fe-4S binding domain
    1.4e-11   44.4  10.5    1.7e-11   44.1  10.5    1.1  1  Fer4_21   4Fe-4S dicluster domain
    4.7e-10   39.1  15.8    4.8e-06   26.4   4.7    2.1  2  Fer4_6    4Fe-4S binding domain
    2.4e-09   37.6  22.6    2.2e-06   28.2  11.4    1.8  2  Fer4_7    4Fe-4S dicluster domain
    1.7e-08   34.0  12.9    0.00011   22.1   3.6    2.2  2  Fer4_2    4Fe-4S binding domain
    2.6e-08   33.8  22.8      1e-05   25.5  12.9    2.0  2  Fer4_10   4Fe-4S dicluster domain
    4.3e-07   30.8   8.6    0.00033   21.5   2.4    2.2  2  Fer4_16   4Fe-4S double cluster binding domain
    2.3e-06   27.7   9.7    7.7e-06   26.0  10.3    1.6  2  Fer4_9    4Fe-4S dicluster domain
    0.00097   19.6  12.1       0.15   12.6   2.3    2.3  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
     0.0016   18.9  12.8       0.47   11.0  12.8    2.1  1  Fer4_8    4Fe-4S dicluster domain
     0.0026   18.4  11.9       0.27   12.0   4.7    2.9  2  Fer4_15   4Fe-4S single cluster domain
     0.0048   17.4  10.8       0.29   11.7   2.3    2.2  3  Fer4_17   4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.033   14.7  11.7      0.064   13.8   3.1    2.3  2  Fer4_4    4Fe-4S binding domain
       0.36   11.0  10.3        0.8    9.9   2.1    2.1  2  Fer4_18   4Fe-4S dicluster domain
       0.68   10.8  11.7       0.37   11.7   2.2    2.1  3  Fer4_22   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   2.6   2.8e-08   3.4e-05       1      23 [.      40      62 ..      40      63 .. 0.95
   2 !   34.4   6.0     1e-11   1.2e-08       2      24 .]      71      93 ..      70      93 .. 0.94

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 2.8e-08
                                   EEEETTTSSS-THHHHHSTTTEE CS
                           Fer4  1 vvideekCigCGaCvevCPvgAI 23
                                   +vi++ kCi+C  C   CP  AI
  gi|119719485|ref|YP_919980.1| 40 PVINQAKCIRCLMCWVHCPEPAI 62
                                   69*****************9998 PP

  == domain 2  score: 34.4 bits;  conditional E-value: 1e-11
                                   EEETTTSSS-THHHHHSTTTEEE CS
                           Fer4  2 videekCigCGaCvevCPvgAIt 24
                                    +d++ C gCG+C++vCPv AI+
  gi|119719485|ref|YP_919980.1| 71 AVDYDYCKGCGICANVCPVHAIE 93
                                   69********************6 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1  10.5   1.4e-14   1.7e-11       2      59 .]      41      94 ..      40      94 .. 0.94

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 1.4e-14
                        Fer4_21  2 ridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedciem 59
                                   +i+++kCi C  C + C++    ai   ++  ++v  d C GC +C++vCPv  +iem
  gi|119719485|ref|YP_919980.1| 41 VINQAKCIRCLMCWVHCPE---PAILRGEDDSVAVDYDYCKGCGICANVCPV-HAIEM 94
                                   79****************7...88988889999******************9.99998 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   3.3   1.1e-06    0.0013       1      24 []      39      62 ..      39      62 .. 0.94
   2 !   26.4   4.7     4e-09   4.8e-06       2      24 .]      70      92 ..      69      92 .. 0.95

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.1e-06
                         Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                                   +++i++ kCi C  C ++CPe ai
  gi|119719485|ref|YP_919980.1| 39 KPVINQAKCIRCLMCWVHCPEPAI 62
                                   69******************9876 PP

  == domain 2  score: 26.4 bits;  conditional E-value: 4e-09
                         Fer4_6  2 veidpdkCigCgdCvrvCPegai 24
                                   v++d+d C gCg C++vCP  ai
  gi|119719485|ref|YP_919980.1| 70 VAVDYDYCKGCGICANVCPVHAI 92
                                   89*****************9998 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2  11.4   1.8e-09   2.2e-06       1      52 []      46      91 ..      46      91 .. 0.93
   2 !   21.1   3.4   2.8e-07   0.00034       2      21 ..      77      96 ..      76      97 .. 0.92

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 1.8e-09
                         Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                   +Ci C  C + Cp  ai   e+      ++v++d+++C gCg C++vCP+ a
  gi|119719485|ref|YP_919980.1| 46 KCIRCLMCWVHCPEPAILRGED------DSVAVDYDYCKGCGICANVCPVHA 91
                                   7************999999887......579******************976 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 2.8e-07
                         Fer4_7  2 CigCgaCvaaCpvkaielde 21
                                   C gCg C+++Cpv+aie+ +
  gi|119719485|ref|YP_919980.1| 77 CKGCGICANVCPVHAIEMVP 96
                                   ****************9976 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   1.8   2.8e-06    0.0033       2      22 .]      39      59 ..      38      59 .. 0.93
   2 !   22.1   3.6   8.9e-08   0.00011       3      21 ..      70      88 ..      68      89 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.8e-06
                         Fer4_2  2 pvvvdtdrCigCgaCvsa.CPa 22
                                   ++v++ ++Ci+C  C ++ CP+
  gi|119719485|ref|YP_919980.1| 39 KPVINQAKCIRCLMC-WVhCPE 59
                                   699************.**9**5 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 8.9e-08
                         Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                                   v+vd d C gCg+C ++CP
  gi|119719485|ref|YP_919980.1| 70 VAVDYDYCKGCGICANVCP 88
                                   789**************** PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5  12.9   8.7e-09     1e-05       2      56 .]      40      88 ..      39      88 .. 0.89
   2 !   19.8   2.2   5.4e-07   0.00065       3      23 ..      71      91 ..      69      98 .] 0.84

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 8.7e-09
                        Fer4_10  2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                   +vi++ +CirC  C   CP           + e++ v ++++ C gcg C+ +CP
  gi|119719485|ref|YP_919980.1| 40 PVINQAKCIRCLMCWVHCPE------PAILRGEDDSVAVDYDYCKGCGICANVCP 88
                                   799*****************......66667777777789**************9 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 5.4e-07
                        Fer4_10  3 vidddtCirCgkCvkaCPadl 23
                                    +d d C +Cg C ++CP+++
  gi|119719485|ref|YP_919980.1| 71 AVDYDYCKGCGICANVCPVHA 91
                                   6799***************66 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.4   0.00011      0.14       1      24 [.      46      69 ..      46      75 .. 0.84
   2 !   21.5   2.4   2.8e-07   0.00033       2      20 ..      77      95 ..      76      98 .] 0.90

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00011
                        Fer4_16  1 rCgtCgkCaevCPtnaikekkeke 24
                                   +C++C  C   CP+ ai   ++ +
  gi|119719485|ref|YP_919980.1| 46 KCIRCLMCWVHCPEPAILRGEDDS 69
                                   6****************9876555 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 2.8e-07
                        Fer4_16  2 CgtCgkCaevCPtnaikek 20
                                   C++Cg Ca+vCP++ai++ 
  gi|119719485|ref|YP_919980.1| 77 CKGCGICANVCPVHAIEMV 95
                                   ****************976 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   2.1   6.2e-05     0.074      33      51 .]      37      62 ..      17      62 .. 0.71
   2 !   26.0  10.3   6.4e-09   7.7e-06       1      51 []      46      92 ..      46      92 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.2e-05
                         Fer4_9 33 e.......eaCigCgaCveaCpkgai 51
                                   +        +Ci C  C  +Cp+ ai
  gi|119719485|ref|YP_919980.1| 37 AlkpvinqAKCIRCLMCWVHCPEPAI 62
                                   2444445578***********98765 PP

  == domain 2  score: 26.0 bits;  conditional E-value: 6.4e-09
                         Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                   kC++C  C   Cp  ++ + +    a    +    C gCg C+++Cp +ai
  gi|119719485|ref|YP_919980.1| 46 KCIRCLMCWVHCPEPAILRGEDDSVAVDYDY----CKGCGICANVCPVHAI 92
                                   7***************999999998887665....*************987 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   2.3   0.00013      0.15       1      18 [.      42      59 ..      42      60 .. 0.94
   2 !   12.3   2.4   0.00016      0.19       1      17 [.      72      88 ..      72      93 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00013
                        Fer4_13  1 VDrdtCiacgaCvelaPd 18
                                   +++ +Ci c  C+  +P+
  gi|119719485|ref|YP_919980.1| 42 INQAKCIRCLMCWVHCPE 59
                                   7899*************8 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00016
                        Fer4_13  1 VDrdtCiacgaCvelaP 17
                                   VD d C +cg+C++++P
  gi|119719485|ref|YP_919980.1| 72 VDYDYCKGCGICANVCP 88
                                   899************** PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0  12.8   0.00039      0.47       3      64 ..      45      90 ..      43      91 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00039
                         Fer4_8  3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64
                                    kCi+C +C  +Cp       ++   rge     +  +        ++C +cg C++vCpv+
  gi|119719485|ref|YP_919980.1| 45 AKCIRCLMCWVHCP-------EPAILRGEDDS--VAVD-------YDYCKGCGICANVCPVH 90
                                   69***********9.......55555666444..2333.......489************98 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.7    0.0021       2.5       2      20 ..      41      59 ..      41      69 .. 0.84
   2 !   12.0   4.7   0.00023      0.27       1      19 [.      70      88 ..      70      93 .. 0.93

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0021
                        Fer4_15  2 vvDrdaCigcglCvaeape 20
                                   v+++ +Ci c +C+  +pe
  gi|119719485|ref|YP_919980.1| 41 VINQAKCIRCLMCWVHCPE 59
                                   58999************86 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00023
                        Fer4_15  1 VvvDrdaCigcglCvaeap 19
                                   V vD d C gcg C+ ++p
  gi|119719485|ref|YP_919980.1| 70 VAVDYDYCKGCGICANVCP 88
                                   88***************98 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   2.8    0.0031       3.7      45      57 ..      46      58 ..      27      60 .. 0.73
   2 !   10.3   1.5   0.00068      0.81       1      21 [.      46      66 ..      46      76 .. 0.72
   3 !   11.7   2.3   0.00024      0.29       2      16 ..      77      91 ..      76      95 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0031
                        Fer4_17 45 lCieCgeCerkCP 57
                                   +Ci C +C   CP
  gi|119719485|ref|YP_919980.1| 46 KCIRCLMCWVHCP 58
                                   5666666666666 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00068
                        Fer4_17  1 rCiqCgyClpeCpsyeaydne 21
                                   +Ci+C +C  +Cp  ++ + e
  gi|119719485|ref|YP_919980.1| 46 KCIRCLMCWVHCPEPAILRGE 66
                                   699999999999976665555 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.00024
                        Fer4_17  2 CiqCgyClpeCpsye 16
                                   C +Cg C+++Cp ++
  gi|119719485|ref|YP_919980.1| 77 CKGCGICANVCPVHA 91
                                   999999999999865 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   1.4     0.018        22       1      15 [.      44      58 ..      44      67 .. 0.87
   2 ?   13.8   3.1   5.3e-05     0.064       2      16 ..      75      89 ..      74      90 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.018
                         Fer4_4  1 qerCigCgsCvaaCP 15
                                   q +Ci+C  C   CP
  gi|119719485|ref|YP_919980.1| 44 QAKCIRCLMCWVHCP 58
                                   569****99988888 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 5.3e-05
                         Fer4_4  2 erCigCgsCvaaCPq 16
                                   + C gCg C ++CP+
  gi|119719485|ref|YP_919980.1| 75 DYCKGCGICANVCPV 89
                                   89************5 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   1.1     0.006       7.2      57      73 ..      43      59 ..      25      67 .. 0.77
   2 ?    9.9   2.1   0.00067       0.8      50      74 ..      66      90 ..      59      94 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.006
                        Fer4_18 57 gagdcidcescvkvcPt 73
                                   ++++ci c +c   cP 
  gi|119719485|ref|YP_919980.1| 43 NQAKCIRCLMCWVHCPE 59
                                   67888888888888885 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00067
                        Fer4_18 50 keerkekgagdcidcescvkvcPtg 74
                                   +++  + +   c  c+ c +vcP++
  gi|119719485|ref|YP_919980.1| 66 EDDSVAVDYDYCKGCGICANVCPVH 90
                                   55555667778************98 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   2.2     0.052        62       1      13 [.      46      58 ..      25      61 .. 0.71
   2 ?    5.5   1.3     0.027        32       1      15 [.      46      60 ..      46      75 .. 0.82
   3 ?   11.7   2.2   0.00031      0.37      77      95 ..      72      90 ..      62      91 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.052
                        Fer4_22  1 rClsCgaCtlvCp 13
                                   +C++C  C + Cp
  gi|119719485|ref|YP_919980.1| 46 KCIRCLMCWVHCP 58
                                   4666666666665 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.027
                        Fer4_22  1 rClsCgaCtlvCptC 15
                                   +C++C  C + Cp  
  gi|119719485|ref|YP_919980.1| 46 KCIRCLMCWVHCPEP 60
                                   7***********975 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.00031
                        Fer4_22 77 fgesgCvGCgRCieacpvk 95
                                   ++   C GCg C ++cpv+
  gi|119719485|ref|YP_919980.1| 72 VDYDYCKGCGICANVCPVH 90
                                   57889***********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.46
# Mc/sec: 637.31
//
Query:       gi|119719486|ref|YP_919981.1|  [L=394]
Description: pyruvate flavodoxin/ferredoxin oxidoreductase domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.3e-73  245.3   0.0    8.2e-73  244.9   0.0    1.1  1  POR_N            Pyruvate flavodoxin/ferredoxin oxidoreductas
    4.4e-28   97.6   0.0      8e-28   96.7   0.0    1.5  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
    1.2e-05   25.2   0.0      4e-05   23.5   0.0    1.9  2  Transketolase_C  Transketolase, C-terminal domain
     0.0081   15.8   0.8     0.0081   15.8   0.8    1.9  2  TPP_enzyme_N     Thiamine pyrophosphate enzyme, N-terminal TP


Domain annotation for each model (and alignments):
>> POR_N  Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  244.9   0.0   1.8e-76   8.2e-73       2     230 ..      17     240 ..      16     241 .. 0.98

  Alignments for each domain:
  == domain 1  score: 244.9 bits;  conditional E-value: 1.8e-76
                                    HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCCHHH CS
                          POR_N   2 aaiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmienlgl 81 
                                    aa++a+vdvi+aYPITP++ i+e+lae++++ge+ d+ ++ +esE+ a sa++GA++aGar++TaTS+qGl+Lm+e l++
  gi|119719486|ref|YP_919981.1|  17 AAKQAKVDVISAYPITPQTIIVETLAEYVNNGEL-DAAFIPVESEHTALSAAVGASLAGARVFTATSSQGLALMYEILWI 95 
                                    899******************************9.9******************************************** PP

                                    HHHTT--EEEEEEEEE-STTBEEEEE--TTCHHHHS---EEEE-SSHHHHHHHHHHHHHHHHH..CTSEEEEEEEHHHH. CS
                          POR_N  82 aageelPvvivvvaRalpstglsirtdqsDlmaardtglivlasenvqeafdlalvAfnlAek..vrvPvivlfDgflls 159
                                    aag ++P+v+++ +Ral+ + ++i++++ D++aardtg++++++envqea+dl+l+Af++Ae+  v +P iv +Dgf+l+
  gi|119719486|ref|YP_919981.1|  96 AAGLRAPIVMAIGNRALSPN-INIHCSHDDAYAARDTGWLQFFAENVQEAYDLTLMAFRVAEDerVLLPTIVNLDGFILT 174
                                    *******************9.*****************************************999*************** PP

                                    HEEEEEEC-SGG.GS-----SBXXXXXXXXSXXXBXXTXXTSSXXEEESBXBXTTSXBXXXXHHHHHHHHH CS
                          POR_N 160 hevekvelpdeedelklikekleeyerkeyaldpekpiargtaanpdtglehrekgneaedaaekvveeve 230
                                    h+ e ++++++      ++ +l+++++ +  +dp++p ++g+ ++ d+++eh++ ++e ++++  vv+ev+
  gi|119719486|ref|YP_919981.1| 175 HALEGLYVLEDA----EVDAFLPKRKPIN-PIDPKNPKTYGPLDFTDWYMEHKRLQFEVYQKVGGVVREVF 240
                                    *********999....9**********99.*********************************99999986 PP

>> PFOR_II  Pyruvate:ferredoxin oxidoreductase core domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.7   0.0   1.8e-31     8e-28       1     102 []     262     366 ..     262     366 .. 0.97

  Alignments for each domain:
  == domain 1  score: 96.7 bits;  conditional E-value: 1.8e-31
                                    -SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G.-HHHHHHHHHTG CS
                        PFOR_II   1 AevvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgse.Gqlveevkaalk 79 
                                    A+ +iv++Gs+agta+ a+++l e+g+k+G++ l+ +rPFP +el+++l++++ v+vldr++sfgs+ +ql+++v++al+
  gi|119719486|ref|YP_919981.1| 262 ADKAIVILGSSAGTARFAARKLAEKGMKLGVVSLTQYRPFPVAELRKVLESFDVVAVLDRSVSFGSPgNQLFMDVSTALY 341
                                    899****************************************************************99*********** PP

                                    GG..TSEEEEEE--GGG----HHHH CS
                        PFOR_II  80 ks..kvkvvnfvaglgGrditvedi 102
                                    +s  ++ +vn+v+glgGrd+t+ ++
  gi|119719486|ref|YP_919981.1| 342 SSkkRPILVNVVYGLGGRDFTPLHV 366
                                    9998999**************9775 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.87   3.9e+03      37      54 ..      22      36 ..      13      50 .. 0.61
   2 !   23.5   0.0     9e-09     4e-05       7     102 ..     259     354 ..     256     373 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.87
                                   CEEEEE-SEEESHHHHHH CS
                Transketolase_C 37 saeVvdlrtvkplDketi 54
                                   +++V+++    p+  +ti
  gi|119719486|ref|YP_919981.1| 22 KVDVISA---YPITPQTI 36
                                   4555554...44444444 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 9e-09
                                    ETTSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEESTTSHHHHHHHHHHH CS
                Transketolase_C   7 regkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeavkrgGigsevaaalae 86 
                                     eg d ++v  Gs   +a  Aa +L+++g++  Vv+l   +p+  + +++++++ + + v++  v +g+ g ++   +++
  gi|119719486|ref|YP_919981.1| 259 VEGADKAIVILGSSAGTARFAARKLAEKGMKLGVVSLTQYRPFPVAELRKVLESFDVVAVLDRSVSFGSPGNQLFMDVST 338
                                    5899999*****************************************************************99999999 PP

                                    CCCTTCSSEEEEEEE- CS
                Transketolase_C  87 eafdgldapvkrvggp 102
                                     ++ + ++p++  +++
  gi|119719486|ref|YP_919981.1| 339 ALYSSKKRPILVNVVY 354
                                    8888888888765555 PP

>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.8   1.8e-06    0.0081       1     103 [.       8     113 ..       8     163 .. 0.83
   2 ?   -1.9   0.1      0.48   2.2e+03      44      71 ..     269     296 ..     259     299 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.8e-06
                                    EEHHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT......TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHH CS
                   TPP_enzyme_N   1 mtvaealvraLkalgvehvfgvpGsrilplldalseeq.....girvvlarhEqgaafaAdgyaratgkpgvvlvtsgpG 75 
                                    m++ +a++ a k+++v+++ ++p +  + +++ l+e       +  ++ + +E +a  aA+g + a     v+ +ts  G
  gi|119719486|ref|YP_919981.1|   8 MNGDRAVAYAAKQAKVDVISAYPITPQTIIVETLAEYVnngelDAAFIPVESEHTALSAAVGASLAGA--RVFTATSSQG 85 
                                    78999******************999999999999988888999*******************99974..4566666679 PP

                                    HHHCHHHHHHHHHHT--EEEEEEE--CC CS
                   TPP_enzyme_N  76 atnaltalaeAkvdriPllvlsgdrpts 103
                                    ++ ++  l  A+  r P+++  g+r+ s
  gi|119719486|ref|YP_919981.1|  86 LALMYEILWIAAGLRAPIVMAIGNRALS 113
                                    ********************99999865 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.48
                                    E-SSHHHHHHHHHHHHHHHTS-EEEEE- CS
                   TPP_enzyme_N  44 larhEqgaafaAdgyaratgkpgvvlvt 71 
                                    l ++ ++a faA  +a+   k+gvv +t
  gi|119719486|ref|YP_919981.1| 269 LGSSAGTARFAARKLAEKGMKLGVVSLT 296
                                    5556678999999999999999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 2574.32
//
Query:       gi|119719487|ref|YP_919982.1|  [L=311]
Description: thiamine pyrophosphate binding domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.3e-26   91.2   0.4    7.8e-26   90.7   0.2    1.4  2  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0      0.55   9.8e+03      29      50 ..      25      47 ..      13      48 .. 0.62
   2 !   90.7   0.2   4.4e-30   7.8e-26       2     152 ..      51     216 ..      50     217 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 0.55
                                   -TTTHHHHHHHHHH.HSTTSEEE CS
                   TPP_enzyme_C 29 tmGyglpaAiGakl.akpdrevv 50
                                   + G g+p  + ++l a pd +vv
  gi|119719487|ref|YP_919982.1| 25 CAGCGIPQVVRLALkAVPDPKVV 47
                                   56667776666666445666665 PP

  == domain 2  score: 90.7 bits;  conditional E-value: 4.4e-30
                                    SSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHH.........STTSEEEEEEEHHHHHHT.GGGHHHHHHT CS
                   TPP_enzyme_C   2 iGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGakla.........kpdrevvaivGDGgflmi.lqelatavrr 71 
                                    +Gcl++++  +    + +s+  + ++ ++ ++ ++A+G+++a          ++ +++++ GDGg+++i +q+l+ a +r
  gi|119719487|ref|YP_919982.1|  51 TGCLEVATTIF----PYTSWGVPWVHIAFENAAAVASGIEAAfkilskkygVEKPKIIVFGGDGGTFDIgFQALSGALER 126
                                    78999844444....445677799*****************555666555444679************************ PP

                                    T-SEEEEEEE-SBCCCHHHH...HHHHTCCTTTTSBB......BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHH CS
                   TPP_enzyme_C  72 nlpitvvvlnNegygmtggq...qepfggkrksgpagk.....dlkpvdfaklaealGak.garvekadveeleealkea 142
                                    ++++++++++Ne+y++tg q    +p+g++++++pagk      ++++++ ++a a+G++ +a++++a + ++ +++ +a
  gi|119719487|ref|YP_919982.1| 127 GHDMIYICYDNEAYMNTGIQrsgATPKGASTTTSPAGKvvpgkLERKKNLIEIAIAHGIRyAATMNPAFPVDMYNKIVKA 206
                                    ******************************************779999************888***************** PP

                                    HCSSSEEEEE CS
                   TPP_enzyme_C 143 lekkgpalie 152
                                     ++ gp++++
  gi|119719487|ref|YP_919982.1| 207 ANTPGPTVLH 216
                                    ********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2244.70
//
Query:       gi|119719488|ref|YP_919983.1|  [L=1283]
Description: reverse gyrase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-87  294.1   0.0    2.5e-87  293.6   0.0    1.2  1  Topoisom_bac    DNA topoisomerase
    2.9e-24   85.3   0.0    8.8e-24   83.7   0.0    1.9  1  Toprim          Toprim domain
    2.3e-14   52.5   0.6    2.3e-14   52.5   0.6    2.7  3  zf_Rg           Reverse gyrase zinc finger
    4.7e-12   46.0   0.0    2.4e-10   40.5   0.0    2.8  3  DEAD            DEAD/DEAH box helicase
    3.2e-09   37.1   0.0    0.00027   21.2   0.0    3.9  3  Helicase_C      Helicase conserved C-terminal domain
    1.2e-05   25.4   0.0      3e-05   24.1   0.0    1.6  1  ResIII          Type III restriction enzyme, res subunit
     0.0058   16.7   0.4     0.0058   16.7   0.4    2.6  2  Zn-ribbon_8     Zinc ribbon domain
  ------ inclusion threshold ------
      0.038   13.6   0.3       0.25   10.9   0.0    2.7  3  AAA_25          AAA domain
      0.061   13.8   0.0       0.48   10.9   0.0    2.6  2  Toprim_4        Toprim domain
      0.064   12.7   0.0       0.19   11.2   0.0    1.7  2  PhoH            PhoH-like protein
       0.07   11.8   0.0       0.22   10.2   0.0    1.7  2  SNF2_N          SNF2 family N-terminal domain
        0.5    9.9   3.6          3    7.4   0.1    3.1  3  TF_Zn_Ribbon    TFIIB zinc-binding
       0.78    9.8   5.8        0.3   11.1   0.4    2.3  2  DZR             Double zinc ribbon
        1.5    8.4   5.9        1.8    8.1   0.1    3.0  3  zf-ribbon_3     zinc-ribbon domain
        2.9    8.0   4.5       0.97    9.5   0.3    2.2  2  HypA            Hydrogenase/urease nickel incorporation, meta
        4.5    7.1   6.8         16    5.4   0.1    3.2  3  zinc_ribbon_2   zinc-ribbon domain


Domain annotation for each model (and alignments):
>> Topoisom_bac  DNA topoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  293.6   0.0   2.2e-90   2.5e-87       2     412 ..     853    1251 ..     852    1252 .. 0.87

  Alignments for each domain:
  == domain 1  score: 293.6 bits;  conditional E-value: 2.2e-90
                   Topoisom_bac    2 inenlvdaaeaRrelDwliGinlsrlltkklkgkkvlsaGRVqtptLaliveRereienFvpeeyweveatlkkekke 79  
                                     in+++v+a+ +Rr+ D+++G++ls+ l++ ++g+k+lsaGRVqtp+L++ive  ++ ++ +    + +e++   +++e
  gi|119719488|ref|YP_919983.1|  853 INDRMVEAQLVRRIEDRWLGFSLSQKLQE-CRGHKWLSAGRVQTPVLGWIVENSEKARRKKVV--FILELSR--RGAE 925 
                                     899************************97.8889*******************9999987554..5555543..2222 PP

                   Topoisom_bac   80 kekkkkkkkerikdkeeaeaileklkkkeakvesvekkekkkppplpfdtttLqkeasrklglsakktlsiaqkLYek 157 
                                      ek     ++   d +  +a+ +k+k++ ++v+ v+++ek+ ppp pf+t+tL++ea++ lgl+ ++t++iaq+L+e+
  gi|119719488|ref|YP_919983.1|  926 GEKLRVIVDNARLDGQSPAAVSNKIKEEGVTVSIVSREEKTLPPPPPFTTDTLLREANQVLGLDVDRTMRIAQDLFES 1003
                                     223345555555667777889999988779************9999*******************************7 PP

                   Topoisom_bac  158 aglitYpRTdstrlseeaelkailealakkygkeylefaekllkktkkksvvknkkveaHeAIrPteelp.klkels. 233 
                                      glitY+RTdstr+s+   ++ +++++++++++ey++        ++++    ++  +aHe+IrPt+ l+ +  +l  
  gi|119719488|ref|YP_919983.1| 1004 -GLITYHRTDSTRVSDLG-ISVARTYITERFSEEYFA--------PRRW----GEG-GAHECIRPTRPLDvD--SLMq 1064
                                     .*****************.9*********98888887........5545....445.8********999953..3334 PP

                   Topoisom_bac  234 ..............ddekklYelIvrrflaslmkdakyeettvklev...eeeefkasgktilekGfkkvykeekkee 294 
                                                   +d+ +lY+lI+rrf+as+m++ak+ e ++ ++    e+e   +++ + + +Gf+k+ + +  + 
  gi|119719488|ref|YP_919983.1| 1065 mirqgilqvqvnftRDHIRLYDLIFRRFIASQMPPAKVVEAKAVVKGpyfEKEITFIESIIEKAEGFTKILPLRTRQ- 1141
                                     568899********67777**************************9888866777777788899*******965443. PP

                   Topoisom_bac  295 eeeelpelkegeevkvkeveleekkTkppkryteasLikamekagiGtpaTraeiieklvergYverkk.kslvptel 371 
                                         +pe k +  +++       k+ +  + yt+a++i++m++++iG+p+T+++i+++l++r+Yv++ k ++lv t+l
  gi|119719488|ref|YP_919983.1| 1142 ----IPEGKYDVLLST------YKRVSEVPLYTQADVIRLMKERNIGRPSTYSKIVRTLLDRNYVVEVKgGRLVSTRL 1209
                                     ....777777776644......479*******************************************99******** PP

                   Topoisom_bac  372 Gkalvell.ekfkdlvspelTaeleekLdeIaegkadakevl 412 
                                     Gk+++e+l  +f d+vs++ Ta++ +++deI+eg+ad+ +vl
  gi|119719488|ref|YP_919983.1| 1210 GKKVYEFLsVNFGDVVSENKTADVLRRMDEIEEGRADYLDVL 1251
                                     ********8888**************************9998 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.7   0.0   7.9e-27   8.8e-24       1     103 []     653     838 ..     653     838 .. 0.90

  Alignments for each domain:
  == domain 1  score: 83.7 bits;  conditional E-value: 7.9e-27
                                    EEEEESSHHHHHHHHHTHT..................STEEEEEEESSSSEEEHS......................... CS
                         Toprim   1 elvivEgpsdaktiakalg..................sgfqavtaslGhildlet......................... 37 
                                    +lv+vE+p++a+tia+++g                  +  ++++a++Ghi+dl+t                         
  gi|119719488|ref|YP_919983.1| 653 VLVVVESPTKARTIASFFGkpsrrrvgplvaydiafsGYILTIVATQGHIFDLTTnaysynsskdlygvlvldaygaskh 732
                                    69*************************************************************************99999 PP

                                    .TTEEEEE........................................ECTTTHHHHHHHHHHHHHHSEEEEECSSSHHH CS
                         Toprim  38 .efkpvye........................................eiedkkkvlkalkelakradeiilatDpDreG 76 
                                     +f pv++                                        ++ dk ++++al++la++++e+++atDpD+eG
  gi|119719488|ref|YP_919983.1| 733 yRFVPVFNtikrcmncgaqfteyavedvprqhvqkvevekrcprcgstNVFDKAEIVEALRKLASEVEEVFVATDPDTEG 812
                                    9555555555555556666666666777777778888999999************************************* PP

                                    HHHHHHHHHHHTHHHTTTEEEEEESSS CS
                         Toprim  77 eaiawellevlkellenkigrvefsei 103
                                    e+iaw+++  l ++++  i+rvef+e+
  gi|119719488|ref|YP_919983.1| 813 EKIAWDVYLSLAPYVRV-IKRVEFHEV 838
                                    ********9999****9.*******96 PP

>> zf_Rg  Reverse gyrase zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.5   0.6     2e-17   2.3e-14       3      37 ..       2      37 ..       1      44 [. 0.90
   2 ?   -2.0   0.0       2.2   2.4e+03       8      20 ..     743     755 ..     741     758 .. 0.78
   3 ?   -0.8   0.1      0.94   1.1e+03       6      14 ..     770     778 ..     767     781 .. 0.87

  Alignments for each domain:
  == domain 1  score: 52.5 bits;  conditional E-value: 2e-17
                          zf_Rg  3 kavfeklCPNCgGdisdeRlekGLpCkrClPke.gd 37
                                   ka++++lCPNC+Gdisd Rlek LpC++ClP++  +
  gi|119719488|ref|YP_919983.1|  2 KALYKSLCPNCHGDISDFRLEKRLPCRQCLPEKdAE 37
                                   799****************************98555 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.2
                          zf_Rg   8 klCPNCgGdisde 20 
                                    k C NCg + +++
  gi|119719488|ref|YP_919983.1| 743 KRCMNCGAQFTEY 755
                                    6799**9887765 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.94
                          zf_Rg   6 feklCPNCg 14 
                                    +ek CP Cg
  gi|119719488|ref|YP_919983.1| 770 VEKRCPRCG 778
                                    6899****8 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.5   0.0   2.1e-13   2.4e-10       3     149 ..      99     243 ..      97     254 .. 0.77
   2 ?    2.1   0.0      0.13   1.4e+02      62     108 ..     374     421 ..     364     439 .. 0.82
   3 ?   -3.1   0.0       5.2   5.8e+03      98     128 ..     692     725 ..     637     748 .. 0.61

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 2.1e-13
                                    HHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEE. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                           DEAD   3 iQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlli. 81 
                                     Q+     +l++ ++++ a+TG GKT   ++ +l  +     ++g+k  iv Pt+ La+q++++++ f  ++ +++  i 
  gi|119719488|ref|YP_919983.1|  99 AQKTWARRVLRNTSFVILAPTGVGKTVFGIVMAL-FL----ASRGKKSYIVLPTTTLAQQVFEKATLFARKVAVNEGGIv 173
                                    5788888999999*************87766666.33....4789999**********************9886666442 PP

                                    ..ET...TSSHHHHHHHHHTT.CSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHS CS
                                    ..xx...xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  82 ..ig...gvaardqlskldng.vdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnql 149
                                       g   ++++++ ls+++ g   ++++t + l + ++  kl+  ++ f+ +D +d + ++  s+ i+ril+ l
  gi|119719488|ref|YP_919983.1| 174 vyHGglpQSKKEEVLSRVSGGdFSVLITTSQFLSRNFD--KLERVRFDFVFVDDVDSIIKS--SKNIDRILRLL 243
                                    3234233566666666665448*********9999775..64455556699********98..88888888876 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.13
                                    HHHHHHHHHTTTSTSEEEEEETTSSHHHHHHHHHTT.CSEEEEEHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                           DEAD  62 qtlnnlkkfkkyidlrvlliiggvaardqlskldng.vdivvgtpgrl 108
                                    + l+ l + +++ +lrv  ++g++++r+ l++++ g +d++vg  +  
  gi|119719488|ref|YP_919983.1| 374 EFLESLAEALEKSGLRVGRFYGNHNKRKLLEEFSGGnLDVLVGVASYY 421
                                    56788888899999*******************7557*****977655 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 5.2
                                    CSEEEEEHHHHHHHH.HCTSSH.CTTE.EEEEEE CS
                                    xxxxxxxxxxxxxxx.xxxxxx.xxxx.xxxxxx RF
                           DEAD  98 vdivvgtpgrlddll.stgkln.lsqv.rflVlD 128
                                    +  +v+t g ++dl+ +  + n  +++  +lVlD
  gi|119719488|ref|YP_919983.1| 692 ILTIVATQGHIFDLTtNAYSYNsSKDLyGVLVLD 725
                                    5568899999999774222233233333667777 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   2.4e-07   0.00027       6      74 ..     129     203 ..     125     241 .. 0.81
   2 !    8.4   0.0    0.0024       2.7      33      87 ..     380     435 ..     348     447 .. 0.77
   3 ?    2.3   0.0      0.18   2.1e+02      96     110 ..     561     575 ..     547     576 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 2.4e-07
                                    HHHHHHHTTTTSEEEEEESSHHHHHH....HHHHHHHT...TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESG CS
                     Helicase_C   6 llellkleeeggkilifvntidrlek....vklllekk...gikvavlhgelpqnereeileqfnkgesdvLiatd 74 
                                    +++l+ l ++g+k++i+++t++ +++    ++l+ +k    +  ++v+hg lpq+++ee+l++   g++ vLi+t+
  gi|119719488|ref|YP_919983.1| 129 VMALF-LASRGKKSYIVLPTTTLAQQvfekATLFARKVavnEGGIVVYHGGLPQSKKEEVLSRVSGGDFSVLITTS 203
                                    55665.7899************6654555456664433777889999**************************997 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0024
                                    HHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGG....GTSSSTSTTESE CS
                     Helicase_C  33 klllekkgikvavlhgelpqnereeileqfnkgesdvLiatdv....aerGidipkvnl 87 
                                       lek+g++v +++g   + ++++ le+f  g+ dvL+        + rG+d+p v  
  gi|119719488|ref|YP_919983.1| 380 AEALEKSGLRVGRFYG---NHNKRKLLEEFSGGNLDVLVGVASyygtLVRGLDLPHVVR 435
                                    33368889********...88999**************887766677889****97644 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.18
                                    SHHHHHHHHTTSSST CS
                     Helicase_C  96 nvtsyiqriGRtgRa 110
                                    +v +yiq++GRt R 
  gi|119719488|ref|YP_919983.1| 561 DVLTYIQASGRTSRL 575
                                    5678********996 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   2.6e-08     3e-05      22     141 ..     108     226 ..      85     248 .. 0.76

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 2.6e-08
                                    .TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG...........GEEEESSS-B CS
                         ResIII  22 krdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseayke.......igkkvsgdkk 94 
                                     r++ ++i ++TG+GKT+  + ++  l++ gk  k  ++ p+++l +q  e+ + f+ + + +       +g+  +++k 
  gi|119719488|ref|YP_919983.1| 108 LRNTSFVILAPTGVGKTVFGIVMALFLASRGK--KSYIVLPTTTLAQQVFEKATLFARKVAVNeggivvyHGGLPQSKK- 184
                                    4788999**********988877777777655..9**********************9988774444443222222222. PP

                                    --.........-SEEEEEHHHHHHTH........HHHTTT-SEEEEETG CS
                         ResIII  95 ka..kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEa 141
                                    ++  ++ +  + ++l+tt q l+++        ++l+r rfd++++D +
  gi|119719488|ref|YP_919983.1| 185 EEvlSRVSGGDFSVLITTSQFLSRNF-------DKLERVRFDFVFVDDV 226
                                    22677889999999999999999999.......8899999999999976 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.7      0.52   5.9e+02      29      35 ..       9      15 ..       3      30 .. 0.77
   2 !   16.7   0.4   5.2e-06    0.0058       7      36 ..     744     782 ..     733     783 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.52
                    Zn-ribbon_8 29 CPeCgse 35
                                   CP+C+++
  gi|119719488|ref|YP_919983.1|  9 CPNCHGD 15
                                   8888875 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 5.2e-06
                    Zn-ribbon_8   7 rCeeCghefe.......vlqsis.dapltaCPeCgs.ev 36 
                                    rC +Cg +f+       ++q +   + ++ CP+Cgs +v
  gi|119719488|ref|YP_919983.1| 744 RCMNCGAQFTeyavedvPRQHVQkVEVEKRCPRCGStNV 782
                                    7*********9*999997777774445666*****9665 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00023      0.25      26      62 ..     104     140 ..      84     237 .. 0.82
   2 ?   -2.8   0.0       3.5   3.9e+03     109     141 ..     460     493 ..     450     496 .. 0.72
   3 ?   -4.2   0.0       9.3     1e+04      57      85 ..     881     907 ..     875     915 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00023
                         AAA_25  26 vkgllpagelallaGapgtGKttlaldlalava.tGkp 62 
                                     +++  +++  ++ +++g+GKt++ + +al +a +Gk+
  gi|119719488|ref|YP_919983.1| 104 ARRV-LRNTSFVILAPTGVGKTVFGIVMALFLAsRGKK 140
                                    3444.4677778889******************88874 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.5
                         AAA_25 109 agv.eslpLfakdrggtlltadvdaleaaieeve 141
                                     +   +++++a++++++++++ v+ ++++++ +e
  gi|119719488|ref|YP_919983.1| 460 LQIaSNVRVVASRDDQAVIDRLVAYVRNWLQNME 493
                                    3333578889988888889999999999999876 PP

  == domain 3  score: -4.2 bits;  conditional E-value: 9.3
                         AAA_25  57 vatGkpwlg.pvapeqgkVlyvsaEdsede 85 
                                     ++G++wl       q +Vl +  E+se  
  gi|119719488|ref|YP_919983.1| 881 ECRGHKWLSaG--RVQTPVLGWIVENSE-K 907
                                    57899998843..478888888888877.3 PP

>> Toprim_4  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       4.4     5e+03      61      88 ..     366     393 ..     364     394 .. 0.83
   2 ?   10.9   0.0   0.00043      0.48      43      73 ..     787     818 ..     779     834 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 4.4
                       Toprim_4  61 ldgDaeGeataerlaellleegvkvtrl 88 
                                    + + + Ge+  e lae+l++ g++v r+
  gi|119719488|ref|YP_919983.1| 366 FAPAGTGEEFLESLAEALEKSGLRVGRF 393
                                    5666789*********9999**999886 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00043
                       Toprim_4  43 kt.enlveaekkvkevilaldgDaeGeataer 73 
                                    ++ e+l++  ++v+ev +a+d+D eGe+ a  
  gi|119719488|ref|YP_919983.1| 787 EIvEALRKLASEVEEVFVATDPDTEGEKIAWD 818
                                    4444555567889***************9865 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00017      0.19       8      54 ..      99     145 ..      96     160 .. 0.89
   2 ?   -3.8   0.0       6.6   7.4e+03      24      36 ..     365     377 ..     364     384 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00017
                                    HHHHHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEE CS
                           PhoH   8 eQkeylealkkndivfaiGpaGtGKtylavalavealkkkkvkriil 54 
                                    +Qk+ ++ + +n+  ++++p+G GKt + +++a+ + +++k + i+l
  gi|119719488|ref|YP_919983.1|  99 AQKTWARRVLRNTSFVILAPTGVGKTVFGIVMALFLASRGKKSYIVL 145
                                    6899999999999999********************99999999988 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 6.6
                                    EE--TTSSTTHHH CS
                           PhoH  24 aiGpaGtGKtyla 36 
                                    +++paGtG  +l 
  gi|119719488|ref|YP_919983.1| 365 VFAPAGTGEEFLE 377
                                    579*****99884 PP

>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0    0.0002      0.22     101     199 ..     143     239 ..     113     248 .. 0.72
   2 ?   -3.0   0.0         2   2.2e+03     149     163 ..    1146    1160 ..    1143    1177 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0002
                                    EE--H.HHHHHHHHH...HHHH-TTS-EEE--SSHHHH-----------------EEEE-HHHHHHHT......TTS-S- CS
                                    xxxxx.xxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SNF2_N 101 ivvPa.slldqWene...ierhvsssalrvlvyggqkkmkkkntkvapklladydvvittYdvlsreaelqkkrsvlkqv 176
                                    iv P+ +l++q  ++   ++r v+  +  ++vy+g+  ++kk++++++    d+ v+itt + lsr+       ++l++v
  gi|119719488|ref|YP_919983.1| 143 IVLPTtTLAQQVFEKatlFARKVAVNEGGIVVYHGGLPQSKKEEVLSRVSGGDFSVLITTSQFLSRNF------DKLERV 216
                                    677773444444333222666666666668899998888999999999999**************888......9***** PP

                                    S-SEEEES-GGGT--TTSHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxx RF
                         SNF2_N 177 ewkrvvlDEghtlknstskaaea 199
                                    + ++v +D    + +s +++  +
  gi|119719488|ref|YP_919983.1| 217 RFDFVFVDDVDSIIKSSKNIDRI 239
                                    ********999998887766655 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2
                                     ---EEEE-HHHHHHH CS
                                     xxxxxxxxxxxxxxx RF
                         SNF2_N  149 dydvvittYdvlsre 163 
                                     +ydv++ tY+++s++
  gi|119719488|ref|YP_919983.1| 1146 KYDVLLSTYKRVSEV 1160
                                     79*********9954 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1       0.2   2.3e+02       3       9 ..       9      15 ..       8      25 .. 0.79
   2 ?   -1.2   0.1       1.3   1.5e+03      22      27 ..     745     750 ..     743     759 .. 0.60
   3 ?    7.4   0.1    0.0027         3       2      15 ..     773     785 ..     773     789 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.2
                                   ETTTTCE CS
                   TF_Zn_Ribbon  3 CPnCgst 9 
                                   CPnC+++
  gi|119719488|ref|YP_919983.1|  9 CPNCHGD 15
                                   9999985 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.3
                                    ESSSSB CS
                   TF_Zn_Ribbon  22 CtdCGl 27 
                                    C +CG+
  gi|119719488|ref|YP_919983.1| 745 CMNCGA 750
                                    555554 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0027
                                    EETTTTCEECHEET CS
                   TF_Zn_Ribbon   2 kCPnCgstnlveDp 15 
                                    +CP Cgstn v+D 
  gi|119719488|ref|YP_919983.1| 773 RCPRCGSTN-VFDK 785
                                    5*******9.8885 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.7      0.54     6e+02      30      38 ..       8      16 ..       2      32 .. 0.57
   2 ?   11.1   0.4   0.00027       0.3      13      37 ..     743     780 ..     736     787 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.54
                            DZR 30 rCpsCgekv 38
                                    Cp+C+ ++
  gi|119719488|ref|YP_919983.1|  8 LCPNCHGDI 16
                                   566665443 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00027
                            DZR  13 rfCseCgtklkavaa.............edrCpsCgek 37 
                                    + C +Cg++  ++a              e+rCp+Cg+ 
  gi|119719488|ref|YP_919983.1| 743 KRCMNCGAQFTEYAVedvprqhvqkvevEKRCPRCGST 780
                                    67*******987776899999**************986 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.4      0.56   6.3e+02      19      22 ..       9      12 ..       7      16 .. 0.70
   2 ?    1.0   0.1      0.27     3e+02       4      11 ..     744     751 ..     743     754 .. 0.69
   3 ?    8.1   0.1    0.0016       1.8       2      12 ..     771     782 ..     770     787 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.56
                    zf-ribbon_3 19 CpyC 22
                                   Cp+C
  gi|119719488|ref|YP_919983.1|  9 CPNC 12
                                   7777 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.27
                    zf-ribbon_3   4 rCPnCGap 11 
                                    rC nCGa+
  gi|119719488|ref|YP_919983.1| 744 RCMNCGAQ 751
                                    78888873 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0016
                    zf-ribbon_3   2 tvrCPnCGa.pl 12 
                                    ++rCP+CG+ ++
  gi|119719488|ref|YP_919983.1| 771 EKRCPRCGStNV 782
                                    79******9775 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.5       2.4   2.7e+03      72      92 ..       8      30 ..       3      37 .. 0.68
   2 ?    9.5   0.3   0.00086      0.97      71      97 ..     743     782 ..     733     789 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.4
                                   EETTTS-EEECHH.H.HHS-TTT CS
                           HypA 72 rCreCgkefelee.k.alrCpkC 92
                                    C +C+ +++  + + +l C +C
  gi|119719488|ref|YP_919983.1|  8 LCPNCHGDISDFRlEkRLPCRQC 30
                                   68888877774433346788888 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00086
                                    EEETTTS-EEECHH.HHH............S-TTTSSS-E CS
                           HypA  71 vrCreCgkefelee.kal............rCpkCgsadv 97 
                                     rC +Cg++f++ + +++            rCp+Cgs++v
  gi|119719488|ref|YP_919983.1| 743 KRCMNCGAQFTEYAvEDVprqhvqkvevekRCPRCGSTNV 782
                                    58*******9966432336778999************876 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.3      0.62   6.9e+02       2       5 ..       9      12 ..       7      16 .. 0.69
   2 ?    3.1   0.1     0.077        86       2       8 ..     745     751 ..     742     754 .. 0.69
   3 ?    5.4   0.1     0.014        16       1       9 [.     773     781 ..     769     787 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.62
                  zinc_ribbon_2  2 CpnC 5 
                                   CpnC
  gi|119719488|ref|YP_919983.1|  9 CPNC 12
                                   5555 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.077
                  zinc_ribbon_2   2 CpnCGae 8  
                                    C nCGa+
  gi|119719488|ref|YP_919983.1| 745 CMNCGAQ 751
                                    6666654 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.014
                  zinc_ribbon_2   1 fCpnCGael 9  
                                    +Cp+CG ++
  gi|119719488|ref|YP_919983.1| 773 RCPRCGSTN 781
                                    588888777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       825  (0.0460148); expected 358.6 (0.02)
Passed bias filter:                      765  (0.0426683); expected 358.6 (0.02)
Passed Vit filter:                       103  (0.00574488); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.94u 0.33s 00:00:01.27 Elapsed: 00:00:00.49
# Mc/sec: 7902.13
//
Query:       gi|119719489|ref|YP_919984.1|  [L=180]
Description: nicotinamide-nucleotide adenylyltransferase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-10   41.8   0.0    2.2e-10   40.9   0.0    1.5  1  CTP_transf_like  Cytidylyltransferase-like


Domain annotation for each model (and alignments):
>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   0.0   1.2e-14   2.2e-10       1      74 [.       9      80 ..       9     140 .. 0.72

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 1.2e-14
                                   EEEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHH CS
                CTP_transf_like  1 lagGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkkkplasaeeRlemlelakevdevisvdpweltr 74
                                   l+ G+F+p+HlGH + l+++ +  +e ++ ++ s++ +++  ++++++ eRlem+ +  +++ ++     ++++
  gi|119719489|ref|YP_919984.1|  9 LFMGRFQPFHLGHYNALKWIVERESE-VVLAIGSAQYSHSL-RNPFTVGERLEMVYAVLREEGLLDRVLVTVVP 80
                                   699***********************.**************.*************9997777666555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       293  (0.0163422); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1170.84
//
Query:       gi|119719490|ref|YP_919985.1|  [L=81]
Description: AsnC family transcriptional regulator [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.2e-16   58.1   0.1    6.9e-16   58.0   0.1    1.0  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
     0.0001   22.3   0.2    0.00029   20.8   0.2    1.7  1  NapD            NapD protein
  ------ inclusion threshold ------
      0.076   13.6   0.6         15    6.3   0.0    2.5  2  ACT_4           ACT domain
      0.097   12.8   0.1        1.5    9.0   0.0    2.5  2  LAL_C2          L-amino acid ligase C-terminal domain 2


Domain annotation for each model (and alignments):
>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.0   0.1   1.5e-19   6.9e-16       1      74 [.      11      81 .]      11      81 .] 0.97

  Alignments for each domain:
  == domain 1  score: 58.0 bits;  conditional E-value: 1.5e-19
                                   EEEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEE CS
                 AsnC_trans_reg  1 vlvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivle 74
                                   vl+++e g+    +++ e+++++p V+e++ + G yd+++kv+ +d+ ++++ + +k++++pgv+rt t+ v e
  gi|119719490|ref|YP_919985.1| 11 VLINCEIGK---EKDVLEQIRNIPGVIEAHLLYGVYDIIVKVTGKDNVEIREMILTKIRRIPGVKRTLTMPVVE 81
                                   789999999...**********************************************************9975 PP

>> NapD  NapD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.2   6.4e-08   0.00029       2      65 ..       7      72 ..       6      77 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 6.4e-08
                           NapD  2 hIsSlvVqarperlaavkaalaalpgv.EvhasdeegklVvviEaesedeladti.eaiealpgVl 65
                                   +I+ +++++  ++ ++v+++++++pgv E h   +   ++v + +++  e+ + i ++i+++pgV 
  gi|119719490|ref|YP_919985.1|  7 NIAYVLINCEIGKEKDVLEQIRNIPGViEAHLLYGVYDIIVKVTGKDNVEIREMIlTKIRRIPGVK 72
                                   677799*******************977999999999999999999888888865267******96 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0    0.0034        15      63      78 ..      21      36 ..       1      37 [. 0.81
   2 ?    5.9   0.1    0.0043        19      60      77 ..      56      73 ..      40      74 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0034
                          ACT_4 63 srviakLraipgVisV 78
                                   ++v++++r+ipgVi++
  gi|119719490|ref|YP_919985.1| 21 KDVLEQIRNIPGVIEA 36
                                   4799*********986 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0043
                          ACT_4 60 ehLsrviakLraipgVis 77
                                   e  + +++k+r+ipgV++
  gi|119719490|ref|YP_919985.1| 56 EIREMILTKIRRIPGVKR 73
                                   44467899*******975 PP

>> LAL_C2  L-amino acid ligase C-terminal domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   0.00034       1.5      15      40 ..      22      47 ..      17      55 .. 0.83
   2 ?    1.3   0.0     0.084   3.7e+02      18      28 ..      63      73 ..      57      80 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00034
                         LAL_C2 15 eGleearalpgvveveltvkpGdevr 40
                                   + le++r++pgv e++l + + d + 
  gi|119719490|ref|YP_919985.1| 22 DVLEQIRNIPGVIEAHLLYGVYDIIV 47
                                   679*************9887766665 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.084
                         LAL_C2 18 eearalpgvve 28
                                    ++r++pgv++
  gi|119719490|ref|YP_919985.1| 63 TKIRRIPGVKR 73
                                   57889999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 522.61
//
Query:       gi|119719491|ref|YP_919986.1|  [L=175]
Description: hypothetical protein Tpen_0578 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-24   86.1   0.0    1.8e-24   85.8   0.0    1.1  1  DUF359    Protein of unknown function (DUF359)


Domain annotation for each model (and alignments):
>> DUF359  Protein of unknown function (DUF359)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.8   0.0     1e-28   1.8e-24       1     124 [.      50     170 ..      50     172 .. 0.90

  Alignments for each domain:
  == domain 1  score: 85.8 bits;  conditional E-value: 1e-28
                         DUF359   1 vtknllkagikPdlaivDgktkReeveeeekeeekekekekevievkNpaGtiteelieaikeal....eseekvlilVd 76 
                                    v+k+++++g+  d+ ivDg+t+R+        + ++ + ++e +++kN++G+i++e++e +++ l     +++k++++V+
  gi|119719491|ref|YP_919986.1|  50 VSKSFRERGL-GDFFIVDGHTRRN-------LKVEDLPGKAEAFTCKNRPGEISRECYELLRNLLtsaiGRGKKIVVYVE 121
                                    5667777777.899**********.......333458999*********************9999888899********* PP

                         DUF359  77 GEEDLavlpaillapeg.svvvYGqpdeGvvlvkvteeakeeaeellek 124
                                    GEEDL++l+a+l++p + s+v+YG+++ ++ ++++t+  ++ ae+ll k
  gi|119719491|ref|YP_919986.1| 122 GEEDLLSLVALLYCPLNdSWVIYGNFRGYLEVIPCTSFFRSVAENLLVK 170
                                    ***************98688*************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       260  (0.0145016); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 1131.05
//
Query:       gi|119719492|ref|YP_919987.1|  [L=156]
Description: AsnC family transcriptional regulator [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-17   63.0   0.1    3.3e-17   62.2   0.1    1.4  1  AsnC_trans_reg   Lrp/AsnC ligand binding domain
    2.4e-17   62.2   0.6    9.8e-17   60.3   0.1    2.2  3  HTH_24           Winged helix-turn-helix DNA-binding
      7e-17   61.0   0.0    1.8e-16   59.6   0.0    1.7  2  HTH_AsnC-type    AsnC-type helix-turn-helix domain
    2.8e-06   27.1   0.1    8.6e-06   25.6   0.1    1.8  1  HTH_11           HTH domain
    0.00012   22.0   0.2    0.00044   20.1   0.0    2.0  2  MarR             MarR family
    0.00015   21.8   0.0    0.00035   20.6   0.0    1.6  1  HTH_20           Helix-turn-helix domain
    0.00016   21.7   0.5     0.0003   20.8   0.5    1.4  1  NapD             NapD protein
    0.00018   21.1   0.1    0.00064   19.4   0.0    1.9  2  Sigma70_r4_2     Sigma-70, region 4
     0.0012   18.3   0.6     0.0031   17.0   0.1    2.0  2  GerE             Bacterial regulatory proteins, luxR family
     0.0014   18.4   0.4     0.0047   16.8   0.0    2.2  3  TrmB             Sugar-specific transcriptional regulator Trm
     0.0017   18.1   0.0     0.0038   17.0   0.0    1.5  1  HTH_IclR         IclR helix-turn-helix domain
     0.0018   18.0   0.1     0.0049   16.6   0.1    1.7  1  HTH_DeoR         DeoR-like helix-turn-helix domain
     0.0018   18.0   0.0     0.0059   16.4   0.0    1.9  1  HTH_23           Homeodomain-like domain
     0.0019   18.1   0.0     0.0052   16.6   0.0    1.7  1  MarR_2           MarR family
     0.0019   18.6   0.3      0.016   15.7   0.0    2.4  3  HTH_27           Winged helix DNA-binding domain
     0.0022   18.0   0.1     0.0049   16.9   0.1    1.6  1  HTH_Mga          M protein trans-acting positive regulator (M
     0.0027   17.6   0.1       0.03   14.3   0.0    2.4  2  HTH_Crp_2        Crp-like helix-turn-helix domain
     0.0035   17.9   0.7       0.07   13.7   0.0    2.6  2  ACT_4            ACT domain
     0.0039   17.3   0.6      0.013   15.7   0.1    2.0  2  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
     0.0057   16.5   0.1      0.013   15.4   0.1    1.6  1  HTH_5            Bacterial regulatory protein, arsR family
      0.006   16.1   0.0      0.016   14.7   0.0    1.8  1  Sigma70_r4       Sigma-70, region 4
  ------ inclusion threshold ------
      0.011   15.7   0.0      0.026   14.5   0.0    1.7  1  HTH_36           Helix-turn-helix domain
      0.013   15.6   1.3      0.045   13.8   0.1    2.1  2  DUF2250          Uncharacterized protein conserved in archaea
      0.015   15.1   0.1       0.23   11.3   0.0    2.4  2  HTH_10           HTH DNA binding domain
      0.036   13.8   0.1      0.094   12.4   0.0    1.7  1  DUF4423          Domain of unknown function (DUF4423)
      0.039   14.6   0.3       0.47   11.1   0.3    2.3  2  FtsX_ECD         FtsX extracellular domain
      0.039   13.9   0.1      0.075   13.0   0.1    1.5  1  HTH_6            Helix-turn-helix domain, rpiR family
       0.04   14.1   0.0       0.12   12.6   0.0    1.7  2  MIase            Muconolactone delta-isomerase
      0.048   13.5   0.1       0.12   12.2   0.1    1.8  1  HxlR             HxlR-like helix-turn-helix
      0.062   13.5   0.0       0.13   12.4   0.0    1.5  1  AsnC_trans_reg2  AsnC-like ligand binding domain
      0.064   13.0   0.0       0.13   12.0   0.0    1.4  1  HTH_Tnp_4        Helix-turn-helix of DDE superfamily endonucl
      0.067   13.4   0.0      0.091   12.9   0.0    1.4  1  B-block_TFIIIC   B-block binding subunit of TFIIIC
      0.076   13.1   0.4       0.18   12.0   0.0    1.7  2  DMAP1_like       Putative DMAP1-like
       0.11   12.0   0.0       0.18   11.3   0.0    1.3  1  HTH_Tnp_ISL3     Helix-turn-helix domain of transposase famil
       0.13   11.8   0.3       0.44   10.2   0.3    1.9  1  HTH_50           Helix-turn-helix domain
       0.15   12.2   0.0       0.39   10.9   0.0    1.7  1  HTH_28           Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.2   0.1   6.6e-20   3.3e-17       5      74 ..      80     145 ..      76     146 .. 0.93

  Alignments for each domain:
  == domain 1  score: 62.2 bits;  conditional E-value: 6.6e-20
                                    E-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEE CS
                 AsnC_trans_reg   5 lepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivle 74 
                                    + p++   + ++ ++l+++pe+ve+y v+G+y+ +lkv+v++ e+l  +l+e +++++gv++t+t+ vl+
  gi|119719492|ref|YP_919987.1|  80 TVPQK---YSQVLKELEKMPEIVEIYDVAGEYSTILKVRVKNKEDLASLLDE-IGKIDGVESTKTMYVLR 145
                                    44466...9*******************************************.***************97 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.3   0.1     2e-19   9.8e-17       1      48 []      10      57 ..      10      57 .. 0.99
   2 ?   -1.6   0.0       4.3   2.1e+03      35      44 ..      86      95 ..      82      95 .. 0.72
   3 ?   -2.1   0.0       5.7   2.8e+03       8      18 ..     143     153 ..     143     155 .. 0.82

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 2e-19
                         HTH_24  1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                   ld++d+kILe+Lq+n++++++++A +lg+S +tv+ r+k+L+++G+Ik
  gi|119719492|ref|YP_919987.1| 10 LDHIDKKILEILQDNAKTPYAQIASQLGISEATVHLRIKKLVSMGVIK 57
                                   79*********************************************8 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 4.3
                         HTH_24 35 nrrlkrLeee 44
                                   ++ lk+Le++
  gi|119719492|ref|YP_919987.1| 86 SQVLKELEKM 95
                                   6678999985 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 5.7
                         HTH_24   8 ILelLqknpri 18 
                                    +L++++++ ri
  gi|119719492|ref|YP_919987.1| 143 VLRVIKEDTRI 153
                                    58999999888 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.6   0.0   3.7e-19   1.8e-16       1      41 [.      10      50 ..      10      51 .. 0.99
   2 ?   -2.4   0.0       9.1   4.5e+03       9      19 ..     144     154 ..     143     155 .. 0.81

  Alignments for each domain:
  == domain 1  score: 59.6 bits;  conditional E-value: 3.7e-19
                  HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrL 41
                                   LD+iD+kILe+Lq +a+++ya++A ++G+Se+tv+ R+++L
  gi|119719492|ref|YP_919987.1| 10 LDHIDKKILEILQDNAKTPYAQIASQLGISEATVHLRIKKL 50
                                   8***************************************9 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 9.1
                  HTH_AsnC-type   9 LeaLqedaRis 19 
                                    L+ + ed Ri 
  gi|119719492|ref|YP_919987.1| 144 LRVIKEDTRIK 154
                                    78889999985 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.1   1.7e-08   8.6e-06       3      44 ..      15      55 ..      14      66 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.7e-08
                         HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                   ++ile+L + + + + +++A +L++S++tv+ +Ik+L ++gv
  gi|119719492|ref|YP_919987.1| 15 KKILEIL-QDNAKTPYAQIASQLGISEATVHLRIKKLVSMGV 55
                                   69*****.555559***********************99994 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   8.8e-07   0.00044       7      51 ..      16      60 ..      14      61 .. 0.94
   2 ?   -2.1   0.0       7.4   3.7e+03      35      43 ..      86      94 ..      85      95 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 8.8e-07
                                   HHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                           MarR  7 viLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRsk 51
                                   +iL+il ++     +++a++lg+s +tv   +++L+  G i+R +
  gi|119719492|ref|YP_919987.1| 16 KILEILQDNAKTPYAQIASQLGISEATVHLRIKKLVSMGVIKRFQ 60
                                   589999999999999****************************86 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 7.4
                                   HHHHHHHHH CS
                           MarR 35 trvldrLek 43
                                   + vl++Lek
  gi|119719492|ref|YP_919987.1| 86 SQVLKELEK 94
                                   5799***98 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0     7e-07   0.00035      14      55 ..      16      57 ..      11      58 .. 0.95

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 7e-07
                                   HHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                         HTH_20 14 rilraLaraegltaselaerldlskntlsyHLrvLeeagLve 55
                                   +il  L +++    +++a +l++s +t++ ++++L++ g ++
  gi|119719492|ref|YP_919987.1| 16 KILEILQDNAKTPYAQIASQLGISEATVHLRIKKLVSMGVIK 57
                                   799************************************997 PP

>> NapD  NapD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.5   6.1e-07    0.0003       8      71 ..      78     142 ..      72     143 .. 0.94

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 6.1e-07
                           NapD   8 Vqarperlaavkaalaalpg.vEvhasdeegklVvviEaesedeladtieaiealpgVlsaslvy 71 
                                    V + p++  +v+++l+++p+ vE++ + +e   ++ +  +++++la  +++i +++gV s++ +y
  gi|119719492|ref|YP_919987.1|  78 VITVPQKYSQVLKELEKMPEiVEIYDVAGEYSTILKVRVKNKEDLASLLDEIGKIDGVESTKTMY 142
                                    5688**************9868***************************************9888 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   1.3e-06   0.00064      28      49 ..      28      49 ..      13      51 .. 0.92
   2 ?   -1.9   0.0       5.6   2.8e+03       4      14 ..      88      98 ..      82      99 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.3e-06
                                   -HHHHHHHHT--HHHHHHHHHH CS
                   Sigma70_r4_2 28 sykEIAellgisegtVksrlsR 49
                                   +y++IA++lgise+tV  r+++
  gi|119719492|ref|YP_919987.1| 28 PYAQIASQLGISEATVHLRIKK 49
                                   8***************999875 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 5.6
                                   HHHHHTTS-HH CS
                   Sigma70_r4_2  4 lrealaeLper 14
                                   +++ l+++pe+
  gi|119719492|ref|YP_919987.1| 88 VLKELEKMPEI 98
                                   56667777775 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   6.3e-06    0.0031      21      43 ..      30      52 ..      15      63 .. 0.83
   2 ?   -1.7   0.0       4.5   2.2e+03      44      56 ..     113     125 ..     109     126 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6.3e-06
                                   HHHHHHHTS-HHHHHHHHHHHHH CS
                           GerE 21 keIAeelniSekTVkvhksnimk 43
                                    +IA++l+iSe TV+  ++ + +
  gi|119719492|ref|YP_919987.1| 30 AQIASQLGISEATVHLRIKKLVS 52
                                   69*************99998865 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 4.5
                                    HHT-SSHHHHHHH CS
                           GerE  44 KLnvksrvelvrl 56 
                                    K +vk++ +l+ l
  gi|119719492|ref|YP_919987.1| 113 KVRVKNKEDLASL 125
                                    8889999999875 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   9.4e-06    0.0047      10      56 ..      14      60 ..       6      91 .. 0.82
   2 ?   -1.8   0.0       6.1     3e+03      40      48 ..      86      94 ..      66     103 .. 0.70
   3 ?   -1.3   0.0       4.3   2.1e+03      32      32 ..     126     126 ..     105     147 .. 0.55

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 9.4e-06
                                   CCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                           TrmB 10 EakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerek 56
                                   + k+   L  + +    +ia++lg+++++v   +++L+++G+++r +
  gi|119719492|ref|YP_919987.1| 14 DKKILEILQDNAKTPYAQIASQLGISEATVHLRIKKLVSMGVIKRFQ 60
                                   666666666777777889*************************9976 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 6.1
                                   HHHHHHHHH CS
                           TrmB 40 YevLrsLed 48
                                    +vL++Le+
  gi|119719492|ref|YP_919987.1| 86 SQVLKELEK 94
                                   456777766 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 4.3
                                    T CS
                           TrmB  32 l 32 
                                    l
  gi|119719492|ref|YP_919987.1| 126 L 126
                                    2 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   7.7e-06    0.0038       8      50 ..      17      58 ..      16      58 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 7.7e-06
                                   HHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                       HTH_IclR  8 iLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                   iL++l   +     +++A ++g++ +tvh  ++ Lv +G +++
  gi|119719492|ref|YP_919987.1| 17 ILEILQDNAKT-PYAQIASQLGISEATVHLRIKKLVSMGVIKR 58
                                   89999999997.89************************99875 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   9.8e-06    0.0049       3      46 ..      15      58 ..      14      60 .. 0.95

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 9.8e-06
                       HTH_DeoR  3 eqilellkqqgklsveelvellgvSeaTiRRDLneLeeqglltR 46
                                   ++ile l++  k    +++ +lg+SeaT+   +++L+  g+++R
  gi|119719492|ref|YP_919987.1| 15 KKILEILQDNAKTPYAQIASQLGISEATVHLRIKKLVSMGVIKR 58
                                   79****************************99*********999 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.2e-05    0.0059      11      39 ..      21      49 ..      14      60 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.2e-05
                         HTH_23 11 llllaeGlsvreIAreLgvsrrTvy.rwlk 39
                                   l+  a + ++++IA +Lg+s+ Tv  r++k
  gi|119719492|ref|YP_919987.1| 21 LQDNA-KTPYAQIASQLGISEATVHlRIKK 49
                                   44444.6799***************66665 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.1e-05    0.0052      22      53 ..      27      58 ..      15      65 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.1e-05
                                   EEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                         MarR_2 22 ltvgelarrlglsksavsrilkrLvaaGLver 53
                                      +++a  lg+s ++v+ ++k+Lv+ G + r
  gi|119719492|ref|YP_919987.1| 27 TPYAQIASQLGISEATVHLRIKKLVSMGVIKR 58
                                   56689***********************9987 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   3.3e-05     0.016       8      51 ..      17      59 ..      12      64 .. 0.85
   2 ?   -1.2   0.0       6.2   3.1e+03      35      45 ..      85      95 ..      71     100 .. 0.81
   3 ?   -0.7   0.0       4.1   2.1e+03      23      40 ..     128     145 ..     114     150 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.3e-05
                         HTH_27  8 vLhlirhrrrrkkl.adlcgrlnvedshisyslkkLtekGLvert 51
                                   +L+ ++  ++ k+  a+++  l ++ ++++  +kkL+ +G+++r 
  gi|119719492|ref|YP_919987.1| 17 ILEILQ--DNAKTPyAQIASQLGISEATVHLRIKKLVSMGVIKRF 59
                                   677777..5555555***************************875 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 6.2
                         HTH_27 35 isyslkkLtek 45
                                   +s +lk+L+++
  gi|119719492|ref|YP_919987.1| 85 YSQVLKELEKM 95
                                   67899999987 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 4.1
                         HTH_27  23 dlcgrlnvedshisyslk 40 
                                    ++ +   ve++ ++y+l+
  gi|119719492|ref|YP_919987.1| 128 EIGKIDGVESTKTMYVLR 145
                                    566666788888888887 PP

>> HTH_Mga  M protein trans-acting positive regulator (MGA) HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   9.8e-06    0.0049       7      45 ..      14      51 ..       8      63 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 9.8e-06
                        HTH_Mga  7 klkLlelLteneksltldelakeLglseltlqsdiseLn 45
                                   + k+le+L + +  +++  +a++Lg+se t+  +i +L 
  gi|119719492|ref|YP_919987.1| 14 DKKILEILQD-NAKTPYAQIASQLGISEATVHLRIKKLV 51
                                   689*******.********************99998886 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0     6e-05      0.03      24      61 ..      29      64 ..      14      68 .. 0.84
   2 ?    0.2   0.0       1.5   7.7e+02      35      47 ..      82      94 ..      77     125 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6e-05
                                   HHHHHHHTTSSHHHHHHHHHHHHHTTSEEE.TEEEEES- CS
                      HTH_Crp_2 24 qeelAsmlGltretvsrilseLkreglisr.grririld 61
                                    +++As lG++  tv   +++L   g+i+r +    i d
  gi|119719492|ref|YP_919987.1| 29 YAQIASQLGISEATVHLRIKKLVSMGVIKRfQA---IID 64
                                   579*************************96233...445 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.5
                                   HHHHHHHHHHHHH CS
                      HTH_Crp_2 35 retvsrilseLkr 47
                                   ++  s++l+eL++
  gi|119719492|ref|YP_919987.1| 82 PQKYSQVLKELEK 94
                                   5666788888876 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.76   3.8e+02      61      78 ..      84     101 ..      72     102 .. 0.88
   2 !   13.7   0.0   0.00014      0.07      50      77 ..     110     137 ..     102     139 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.76
                          ACT_4  61 hLsrviakLraipgVisV 78 
                                    + s+v++ L+++p++ ++
  gi|119719492|ref|YP_919987.1|  84 KYSQVLKELEKMPEIVEI 101
                                    5789***********987 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 0.00014
                          ACT_4  50 ikitveVkdvehLsrviakLraipgVis 77 
                                      ++v Vk+ e+L+++++ + +i+gV+s
  gi|119719492|ref|YP_919987.1| 110 TILKVRVKNKEDLASLLDEIGKIDGVES 137
                                    5689**********************87 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   2.6e-05     0.013      13      52 ..      17      56 ..      15      58 .. 0.86
   2 ?   -1.8   0.1       7.3   3.7e+03      40      49 ..      86      95 ..      84      96 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.6e-05
                                   HHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                 Fe_dep_repress 13 IYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyv 52
                                   I+++  ++++   +++a+ L++s ++V   +kkL ++G +
  gi|119719492|ref|YP_919987.1| 17 ILEILQDNAKTPYAQIASQLGISEATVHLRIKKLVSMGVI 56
                                   67777777888889***********************965 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 7.3
                                   HHHHHHHHHT CS
                 Fe_dep_repress 40 semlkkLekd 49
                                   s+ lk+Lek+
  gi|119719492|ref|YP_919987.1| 86 SQVLKELEKM 95
                                   7899999997 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   2.6e-05     0.013       6      46 ..      16      57 ..      15      58 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.6e-05
                                   HHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_5  6 kILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                   kIL +L++  ++   ++a +lg+s++tv    kkL  +G+++
  gi|119719492|ref|YP_919987.1| 16 KILEILQDnAKTPYAQIASQLGISEATVHLRIKKLVSMGVIK 57
                                   89******6678889************************986 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   3.1e-05     0.016       5      43 ..      10      49 ..       9      52 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.1e-05
                                   S-HHHHHHHHHHH.TTT--HHHHHHHHTS-HHHHHHHHHH CS
                     Sigma70_r4  5 Lpererevlelrf.geglTleEIgerlgiSrerVrqiekr 43
                                   L+  ++++le      + ++++I+ +lgiS+ +V+ ++k+
  gi|119719492|ref|YP_919987.1| 10 LDHIDKKILEILQdNAKTPYAQIASQLGISEATVHLRIKK 49
                                   5556666777666677889****************99987 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   5.1e-05     0.026      28      55 .]      29      56 ..      15      56 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.1e-05
                         HTH_36 28 qetlakrlglsknTvsraikeLeqlGyi 55
                                   ++ +a++lg+s+ Tv   ik+L+  G i
  gi|119719492|ref|YP_919987.1| 29 YAQIASQLGISEATVHLRIKKLVSMGVI 56
                                   899********************99965 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   9.1e-05     0.045       3      57 ..       7      61 ..       5      73 .. 0.83
   2 ?    0.4   0.2       1.5   7.3e+02      25      57 ..     105     137 ..      83     154 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9.1e-05
                        DUF2250  3 eleedelalkvlkhlk.kanvdYaksiakeleipleevrellkkLeelGLlerveg 57
                                   e++ d+ + k+l++l+ +a+  Ya+ ia +l i+   v+  +kkL ++G ++r ++
  gi|119719492|ref|YP_919987.1|  7 EIKLDHIDKKILEILQdNAKTPYAQ-IASQLGISEATVHLRIKKLVSMGVIKRFQA 61
                                   5667777888999886257888985.8999**********************9875 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.5
                        DUF2250  25 aksiakeleipleevrellkkLeelGLlerveg 57 
                                    a  ++  l++++++ ++l   L e+G ++ ve+
  gi|119719492|ref|YP_919987.1| 105 AGEYSTILKVRVKNKEDLASLLDEIGKIDGVES 137
                                    444555556666666666666666666666654 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00046      0.23      27      46 ..      30      49 ..      24      53 .. 0.87
   2 ?    1.1   0.0      0.69   3.5e+02      26      48 ..     126     148 ..     123     151 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00046
                         HTH_10 27 keLAkelGIskstlsehLrk 46
                                   +++A +lGIs++t++ +++k
  gi|119719492|ref|YP_919987.1| 30 AQIASQLGISEATVHLRIKK 49
                                   79************999987 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.69
                         HTH_10  26 lkeLAkelGIskstlsehLrkae 48 
                                    l+e+ k+ G+  + +++ Lr ++
  gi|119719492|ref|YP_919987.1| 126 LDEIGKIDGVESTKTMYVLRVIK 148
                                    68999**************9765 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00019     0.094      35      70 ..      25      58 ..      15      63 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00019
                        DUF4423 35 fkadpeelakrlrpkisaeevekalefLlklgllkk 70
                                   +k  ++++a +l+  is++ v+  ++ L+++g++k+
  gi|119719492|ref|YP_919987.1| 25 AKTPYAQIASQLG--ISEATVHLRIKKLVSMGVIKR 58
                                   347789*******..*******************98 PP

>> FtsX_ECD  FtsX extracellular domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1      0.21   1.1e+02      76      95 ..      81     100 ..      71     101 .. 0.83
   2 ?   11.1   0.3   0.00094      0.47      39      95 ..      83     137 ..      78     138 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.21
                       FtsX_ECD  76 dpekleevaeelkklpgVee 95 
                                     p+k+++v +el+k+p++ e
  gi|119719492|ref|YP_919987.1|  81 VPQKYSQVLKELEKMPEIVE 100
                                    57999999999999999866 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00094
                       FtsX_ECD  39 ealeefkeqlgednsellegltedeNpLpdsfevklkdpekleevaeelkklpgVee 95 
                                    + + ++ ++l+ + +e++e ++      +  ++v++k+ e+l+++ +e+ k++gVe+
  gi|119719492|ref|YP_919987.1|  83 QKYSQVLKELE-KMPEIVEIYDVA-GEYSTILKVRVKNKEDLASLLDEIGKIDGVES 137
                                    56677777777.578888887765.3688999***********************96 PP

>> HTH_6  Helix-turn-helix domain, rpiR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   0.00015     0.075      13      52 ..       9      44 ..       4      55 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00015
                                   ---HHHHHHHHHHHH-S---TT--HHHHHHHTT--HHHHH CS
                          HTH_6 13 kltksekkiaeyilaspdkaielsikalAkaaavSeativ 52
                                   kl   +kki+e+++ + ++ +    +++A ++++Seat+ 
  gi|119719492|ref|YP_919987.1|  9 KLDHIDKKILEILQDNAKTPY----AQIASQLGISEATVH 44
                                   677789999999998887765....79***********95 PP

>> MIase  Muconolactone delta-isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       2.3   1.1e+03      26      49 ..      42      70 ..      23      96 .. 0.62
   2 ?   12.6   0.0   0.00023      0.12      29      70 ..      87     128 ..      77     138 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 2.3
                          MIase 26 rekaraqelqrqGklvrlwrv.....vge 49
                                   + + r+++l + G ++r+ ++     vg+
  gi|119719492|ref|YP_919987.1| 42 TVHLRIKKLVSMGVIKRFQAIidpekVGR 70
                                   45556778888888888887755554444 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00023
                          MIase  29 araqelqrqGklvrlwrvvgeyanisifdvedndeLhelLss 70 
                                    +  +el++  ++v+++ v+gey++i  ++v+++++L  lL +
  gi|119719492|ref|YP_919987.1|  87 QVLKELEKMPEIVEIYDVAGEYSTILKVRVKNKEDLASLLDE 128
                                    56689999999**************************99975 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00024      0.12      17      66 ..      25      73 ..      14      97 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00024
                                   S-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE- CS
                           HxlR 17 gkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYslt 66
                                    k  + +++ +l +is+ +   r+++L + g+i+r      P+kv  ++t
  gi|119719492|ref|YP_919987.1| 25 AKTPYAQIASQL-GISEATVHLRIKKLVSMGVIKRFQAIIDPEKVGRKVT 73
                                   556689999999.9*****************************9977666 PP

>> AsnC_trans_reg2  AsnC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00026      0.13      10      79 ..      77     145 ..      67     148 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00026
                AsnC_trans_reg2  10 vawkvpeerveevaevvaelpevtHcYeRewpynlyfmvharseeeveevlaeiaaatgledyevLpstr 79 
                                     ++ vp+ ++ +v + ++++pe+  +Y    +y     v ++++e++ + l+ei +  g+e++++++ +r
  gi|119719492|ref|YP_919987.1|  77 GVITVPQ-KYSQVLKELEKMPEIVEIYDVAGEYSTILKVRVKNKEDLASLLDEIGKIDGVESTKTMYVLR 145
                                    4666655.999**************************************************999999877 PP

>> HTH_Tnp_4  Helix-turn-helix of DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00026      0.13      21      44 ..      28      51 ..      26      54 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00026
                      HTH_Tnp_4 21 tyqdLayrFgvsestvsrifhkwv 44
                                   +y ++a + g+se tv+  ++k+v
  gi|119719492|ref|YP_919987.1| 28 PYAQIASQLGISEATVHLRIKKLV 51
                                   799*****************9998 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00018     0.091      24      55 ..      32      71 ..      29     125 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00018
                 B-block_TFIIIC 24 LakeskqdprslfyrlksLekkgLIvkqsii........d 55
                                   +a+ ++++   ++ r+k+L + g I++ ++i        +
  gi|119719492|ref|YP_919987.1| 32 IASQLGISEATVHLRIKKLVSMGVIKRFQAIidpekvgrK 71
                                   678899*********************9997666555441 PP

>> DMAP1_like  Putative DMAP1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00035      0.18      36      77 ..      10      51 ..       3      61 .. 0.86
   2 ?   -1.7   0.1       6.3   3.1e+03       5      13 ..      87      95 ..      83     132 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00035
                     DMAP1_like 36 ledkelkikeiinkkqsypnvfLaSslgfskstwnkkvekiL 77
                                   l  ++ ki ei++ + + p++ +aS+lg+s  t++  ++k++
  gi|119719492|ref|YP_919987.1| 10 LDHIDKKILEILQDNAKTPYAQIASQLGISEATVHLRIKKLV 51
                                   4567899*************************9998888765 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 6.3
                     DMAP1_like  5 kllknieel 13
                                   ++lk++e++
  gi|119719492|ref|YP_919987.1| 87 QVLKELEKM 95
                                   455554443 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00035      0.18      19      51 ..      16      50 ..      12      51 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00035
                   HTH_Tnp_ISL3 19 yilellles..rsvkavArqlgvSwtTVwrildry 51
                                   +ile l+++   + +++A qlg+S+ TV+ +++ +
  gi|119719492|ref|YP_919987.1| 16 KILEILQDNakTPYAQIASQLGISEATVHLRIKKL 50
                                   677777777777999*************9887765 PP

>> HTH_50  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.3   0.00089      0.44       9      46 ..      11      49 ..       6      50 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00089
                         HTH_50  9 eefErelikkayekYpS.tRklAkrLGvShtaianklrk 46
                                   +++++++++ +  + +     +A +LG+S +++  +++k
  gi|119719492|ref|YP_919987.1| 11 DHIDKKILEILQDNAKTpYAQIASQLGISEATVHLRIKK 49
                                   5666666665555544314579***********999997 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00079      0.39      12      35 ..      26      49 ..      16      61 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00079
                         HTH_28 12 GhsvreaArelgisrrtvyrWikr 35
                                     +++++A +lgis+ tv   ik+
  gi|119719492|ref|YP_919987.1| 26 KTPYAQIASQLGISEATVHLRIKK 49
                                   349***************877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       974  (0.0543254); expected 358.6 (0.02)
Passed bias filter:                      632  (0.0352502); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); expected 17.9 (0.001)
Passed Fwd filter:                        36  (0.00200792); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              36  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1077.54
//
Query:       gi|119719493|ref|YP_919988.1|  [L=272]
Description: exosome complex RNA-binding protein Rrp42 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    7.7e-28   97.6   0.0    1.3e-27   96.9   0.0    1.4  1  RNase_PH    3' exoribonuclease family, domain 1
      1e-17   63.9   0.1    2.6e-17   62.6   0.0    1.8  2  RNase_PH_C  3' exoribonuclease family, domain 2


Domain annotation for each model (and alignments):
>> RNase_PH  3' exoribonuclease family, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.9   0.0   1.4e-31   1.3e-27       1     132 []      33     168 ..      33     168 .. 0.93

  Alignments for each domain:
  == domain 1  score: 96.9 bits;  conditional E-value: 1.4e-31
                                    EEEEEEEEESSSSTTSEEEEEEECCEEEEEEEEEEEEEE-TCCG--CCEEEECCCCECCCCEC-C...S...HHHHHHHH CS
                       RNase_PH   1 elRslsietgvlsqanGSaylelGdtkvlasvtgpieerpseerddaegaldveveyapfasgerrregrpsdeeielsr 80 
                                    ++R++++e g++ +a+GSa++ lG+t+v+a+v++ i + p+++  ++eg+  v+ e++p+as+ ++  g p++e iel+r
  gi|119719493|ref|YP_919988.1|  33 QYREIRLEKGIIGKADGSARVFLGSTQVIAGVKLAIGT-PFPD-APNEGVQIVNAELSPVASPFFEP-GPPGEEDIELAR 109
                                    68**********************************98.7777.445699***************76.9*********** PP

                                    HHHHHHCCTC-C........CGCCTCEEEEEEEEEECCCS-CHHHCHHHHHHHHHCTCEE CS
                       RNase_PH  81 lleralrpsill........ekkpkstididitvlssdggslldalinaaslALadagip 132
                                    +++r +r+  ++        +  +++t++idi+ l++dg +l da+ +aa lAL+d+++p
  gi|119719493|ref|YP_919988.1| 110 VVDRGFRSAKVVdlaklsiiPSAKCWTLYIDIYPLDHDG-NLVDAAGLAALLALLDTKLP 168
                                    ***********6667777779999***************.******************98 PP

>> RNase_PH_C  3' exoribonuclease family, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.6   0.0   2.9e-21   2.6e-17       2      67 .]     191     256 ..     190     256 .. 0.97
   2 ?   -2.8   0.0      0.76   6.8e+03      56      65 ..     259     268 ..     258     269 .. 0.83

  Alignments for each domain:
  == domain 1  score: 62.6 bits;  conditional E-value: 2.9e-21
                                    --EEEEEEEETTEEEES--HHHHHHSSEEEEEEEETTSEEEEEEEECSSCEEHHHHHHHHHHHHHH CS
                     RNase_PH_C   2 pviavtvgkvddqfvlDptkeEedlsegdltlavagtkevvtlmkeggsqldeetlleaielAkkg 67 
                                    +v+ vtv+k+++++v+Dpt+eEe+ +++++t+ +++++e+++++k+g+++++++++l+a ++A+k+
  gi|119719493|ref|YP_919988.1| 191 LVVYVTVAKIGEYLVVDPTLEEELTADAKITFGITERGEICAIQKSGEGSFRPDEVLRARDMALKA 256
                                    899************************************************************985 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.76
                                    HHHHHHHHHH CS
                     RNase_PH_C  56 tlleaielAk 65 
                                    tl+eai+ A 
  gi|119719493|ref|YP_919988.1| 259 TLFEAIKKAV 268
                                    799***9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       235  (0.0131073); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1825.76
//
Query:       gi|119719494|ref|YP_919989.1|  [L=245]
Description: exosome complex exonuclease 1 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    7.8e-36  123.5   0.0    1.1e-35  123.1   0.0    1.2  1  RNase_PH    3' exoribonuclease family, domain 1
    3.4e-16   59.0   0.1    5.9e-16   58.3   0.1    1.4  1  RNase_PH_C  3' exoribonuclease family, domain 2


Domain annotation for each model (and alignments):
>> RNase_PH  3' exoribonuclease family, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.1   0.0   1.2e-39   1.1e-35       1     131 [.      24     152 ..      24     153 .. 0.95

  Alignments for each domain:
  == domain 1  score: 123.1 bits;  conditional E-value: 1.2e-39
                                    EEEEEEEEESSSSTTSEEEEEEECCEEEEEEEEEEEEEE-TCCG.--CCEEEECCCCECCCCEC-C...S...HHHHHHH CS
                       RNase_PH   1 elRslsietgvlsqanGSaylelGdtkvlasvtgpieerpseer.ddaegaldveveyapfasgerrregrpsdeeiels 79 
                                    e+R+l++e gvl++a+GSay+elG++kvla+v+gp+e+ p+ e+ +d    l++++ + pf+  er++  +ps++eiels
  gi|119719494|ref|YP_919989.1|  24 EMRPLRVEAGVLKNADGSAYVELGNNKVLAAVYGPREPMPRHEAlPDR-AILKCRYSMLPFSVAERKS-PQPSRREIELS 101
                                    79************************************8888887653.46**************966.79********* PP

                                    HHHHHHHCCTC-CCGCCTCEEEEEEEEEECCCS-CHHHCHHHHHHHHHCTCE CS
                       RNase_PH  80 rlleralrpsillekkpkstididitvlssdggslldalinaaslALadagi 131
                                    +++ +al p + l+++p++ i ++i++l++dg ++  a+i+a s+ALadagi
  gi|119719494|ref|YP_919989.1| 102 KVIREALAPAVFLNEYPRTSIEVYIHILEADG-GTRTASIIAGSVALADAGI 152
                                    ********************************.******************9 PP

>> RNase_PH_C  3' exoribonuclease family, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.3   0.1   6.6e-20   5.9e-16       1      67 []     156     221 ..     156     221 .. 0.98

  Alignments for each domain:
  == domain 1  score: 58.3 bits;  conditional E-value: 6.6e-20
                                    S--EEEEEEEETTEEEES--HHHHHHSSEEEEEEEETTSEEEEEEEECSSCEEHHHHHHHHHHHHHH CS
                     RNase_PH_C   1 apviavtvgkvddqfvlDptkeEedlsegdltlavagtkevvtlmkeggsqldeetlleaielAkkg 67 
                                    ++v+a++vgk+++ +vlD +  E+++++gd+++a+   + ++tl++++g  +++++++ea+ lA+k+
  gi|119719494|ref|YP_919989.1| 156 DLVAAIAVGKIGNVLVLDINGIEDQYGDGDMPIAMMPQRGEITLLQADGV-FTPQEIEEALRLAQKA 221
                                    58************************************************.*************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1815.87
//
Query:       gi|119719495|ref|YP_919990.1|  [L=237]
Description: exosome complex RNA-binding protein Rrp4 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.1e-08   32.6   0.6    1.5e-07   31.2   0.6    1.8  1  KH_1      KH domain
    1.5e-06   28.5   0.1    3.5e-06   27.2   0.1    1.7  1  KH_6      KH domain
     0.0021   17.9   0.9     0.0049   16.7   0.9    1.7  1  KH_2      KH domain
  ------ inclusion threshold ------
       0.11   12.8   3.9       0.23   11.8   0.3    2.6  2  S1        S1 RNA binding domain


Domain annotation for each model (and alignments):
>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.6   3.3e-11   1.5e-07       4      64 ..     157     211 ..     155     213 .. 0.84

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 3.3e-11
                                    EEEGGGHHHHHHTGGGHHHHHHHHHHT-EEEEESSTT...T.-EEEEEE.SHHHHHHHHHHH CS
                           KH_1   4 ilvPsslvgriIGkgGsnIkeIreetgakIkvpksedegsderevtisG.speavekAkeli 64 
                                    +++P ++v+r+IG++Gs++  I++  g+k  v  ++        +++ G +p++ve A+ ++
  gi|119719495|ref|YP_919990.1| 157 VEIPPQKVPRVIGRRGSMVSMIEDLLGVKLIVG-QN------GRIVVVGdDPQRVEIAVLAV 211
                                    69**********************77***9975.32......346666*********98766 PP

>> KH_6  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.1   7.9e-10   3.5e-06       1      38 [.     154     194 ..     154     202 .. 0.82

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 7.9e-10
                           KH_6   1 GmlfeVslslvrRll....nhvLeeLgkagpfeiavGlNGri 38 
                                    G l+e+++++v+R++    + v +++++ +++ ++vG+NGri
  gi|119719495|ref|YP_919990.1| 154 GTLVEIPPQKVPRVIgrrgSMV-SMIEDLLGVKLIVGQNGRI 194
                                    99*************7774444.77777799**********9 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.9   1.1e-06    0.0049      25      67 ..     153     195 ..     139     216 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.1e-06
                                    CEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEE CS
                           KH_2  25 nrviiviresqpgivIGkgGsnikkigkelrkdieklegkkVk 67 
                                    +++ + i   +  +vIG++Gs++ +i+  l+ ++ + +++++ 
  gi|119719495|ref|YP_919990.1| 153 RGTLVEIPPQKVPRVIGRRGSMVSMIEDLLGVKLIVGQNGRIV 195
                                    5677777888999*********************988888854 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.3     0.092   4.1e+02      45      63 ..      30      48 ..      20      59 .. 0.83
   2 ?   11.8   0.3   5.1e-05      0.23       4      75 .]      71     144 ..      69     144 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.092
                                   CHHHCEETTEEEEEEEEEE CS
                             S1 45 dpdevlkvGdevkvkvlkv 63
                                   ++++v++vG +++ kvl+v
  gi|119719495|ref|YP_919990.1| 30 VEGQVFRVGRKYYSKVLGV 48
                                   6788999999999999986 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 5.1e-05
                                    TTCEEEEEEEEEETTEEEEEETTTEEEEEEGGGSSSS...CEESCHHHCEETTEEEEEEEEEEETTTTEEEEEEC CS
                             S1   4 kgevveGeVtsvtkgGafVelgngvegfvpaselsrd...arvedpdevlkvGdevkvkvlkvdkdrrriilsik 75 
                                    +g +v G+V+++     +V++  +  + +p+se+ ++    ++ + ++ l vGd + +k+  +d  +  ++l+ik
  gi|119719495|ref|YP_919990.1|  71 EGHIVVGKVVDIGFTSWEVDINSPYVAVLPVSEVTSRpvtISRNELSRILDVGDLILAKIVSFDLSKD-PVLTIK 144
                                    7999*********************************88777777888999***********999988.888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1643.97
//
Query:       gi|119719496|ref|YP_919991.1|  [L=235]
Description: putative RNA-associated protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-21   75.7   0.1    4.3e-21   74.8   0.1    1.5  1  SBDS      Shwachman-Bodian-Diamond syndrome (SBDS) protein
    1.5e-17   63.7   0.3    2.1e-17   63.2   0.3    1.3  1  SBDS_C    SBDS protein C-terminal domain
  ------ inclusion threshold ------
      0.016   15.2   0.0      0.034   14.2   0.0    1.5  1  EFG_C     Elongation factor G C-terminus
      0.052   13.5   0.0       0.38   10.7   0.0    2.2  3  DUF4426   Domain of unknown function (DUF4426)


Domain annotation for each model (and alignments):
>> SBDS  Shwachman-Bodian-Diamond syndrome (SBDS) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.8   0.1   9.6e-25   4.3e-21       3      88 .]       8      93 ..       6      93 .. 0.98

  Alignments for each domain:
  == domain 1  score: 74.8 bits;  conditional E-value: 9.6e-25
                                   EEEEEEETTEEEEEEE-HHHHHHHHCTT---HHHHBSSSS-EEETTTTEE--HHHHHHHHS---HHHHHHHHHHHSEEE--H CS
                           SBDS  3 sivrykkgkkrFeiavyknklleyregkeidLsevlqsekiFtnaskGetaskselekafgteskdeiikeILkkGeiqvsa 84
                                   si+r+++g+kr+ei+v+ +k+  y++g++ ++ e+++ e i+ +a++G +as+sel+k+fgt++  +++++ILk+Ge+ +++
  gi|119719496|ref|YP_919991.1|  8 SIARLERGGKRYEIIVDVEKAWLYKNGEKLNVREIMEGEFIYYDANRGLKASESELKKVFGTDNIYSVAEIILKQGELLLTT 89
                                   899******************************************************************************* PP

                                   HHHH CS
                           SBDS 85 eerk 88
                                   e+r+
  gi|119719496|ref|YP_919991.1| 90 EQRR 93
                                   *996 PP

>> SBDS_C  SBDS protein C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.2   0.3   4.7e-21   2.1e-17       2      87 ..     100     182 ..      99     218 .. 0.70

  Alignments for each domain:
  == domain 1  score: 63.2 bits;  conditional E-value: 4.7e-21
                                    HHHHHHHHHHHEEBTTTTB---HHHHHHHHHHTT----TTS-CCCCHHHHHHHHTTTS-..-EE-EEEEEEEE-...CCC CS
                         SBDS_C   2 ekeiieivaeklvnpqtkrpytttmIekalkelgtsvktnksaksQalevikaLiqeip..iqrarmrlritcptsikdk 79 
                                    +++iie++++++v+p+t++p++ ++Ie al+e+++s+++ k+a+ Q+ +vikaL+  +p  i+ a m + i  +     +
  gi|119719496|ref|YP_919991.1| 100 KRQIIELISRNAVDPRTNAPIPAKRIELALEEARVSIDPFKPAELQVPDVIKALRMTLPmkIMKAIMAVYIPAA-----Y 174
                                    799****************************************************6666337777776666554.....3 PP

                                    HHHHHHHH CS
                         SBDS_C  80 ilklieqv 87 
                                    + k+++ v
  gi|119719496|ref|YP_919991.1| 175 VGKAYHAV 182
                                    33333333 PP

>> EFG_C  Elongation factor G C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   7.7e-06     0.034      10      71 ..     167     227 ..     161     231 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.7e-06
                                    EEEEECCCCCCHHHHHHHCT-EEEEEEEE.TTEEEEEEEEEGGG-TTHHHCHHHCTTTS-EE CS
                          EFG_C  10 eievpeeyvgkvisdlssrrGeiedmeqdasgrviieaeiPlaeligfateLrslTkGegsf 71 
                                     + +p  yvgk++    s+ G+++  +++++g   +e e+P+       +++ slTkG g +
  gi|119719496|ref|YP_919991.1| 167 AVYIPAAYVGKAY-HAVSKMGKVLRENYRSDGSLDLEIEVPAGLQSSIVEKVASLTKGSGDV 227
                                    6899*********.666778**********************9999*************976 PP

>> DUF4426  Domain of unknown function (DUF4426)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   8.4e-05      0.38      52      87 ..      18      53 ..       6      63 .. 0.78
   2 ?   -0.1   0.0      0.19   8.4e+02      72      96 ..      62      86 ..      53      94 .. 0.84
   3 ?   -3.8   0.0       2.7   1.2e+04      90     107 ..     193     210 ..     190     212 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 8.4e-05
                                   E--EEEEEEEE-TT--EEEE--EEEEETTEEEEEEE CS
                        DUF4426 52 avsakvsgkaknllgqskeLefrevkegdaiyylae 87
                                     ++ v ++   l ++ ++L++re+ eg+ iyy a+
  gi|119719496|ref|YP_919991.1| 18 RYEIIVDVEKAWLYKNGEKLNVREIMEGEFIYYDAN 53
                                   56677788888899999****************776 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.19
                                   --EEEEETTEEEEEEEEE--SSEEE CS
                        DUF4426 72 efrevkegdaiyylaefpieneetl 96
                                   e+++v  +d iy +ae+ +++ e l
  gi|119719496|ref|YP_919991.1| 62 ELKKVFGTDNIYSVAEIILKQGELL 86
                                   678888999*******999998876 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 2.7
                                    --SSEEEEEEEEEEETTS CS
                        DUF4426  90 ieneetltfeievkegee 107
                                    ++++ +l++eiev++g +
  gi|119719496|ref|YP_919991.1| 193 YRSDGSLDLEIEVPAGLQ 210
                                    667778889999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 1884.90
//
Query:       gi|119719497|ref|YP_919992.1|  [L=238]
Description: proteasome subunit alpha [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.4e-59  199.5   0.0    4.4e-59  199.2   0.0    1.1  1  Proteasome      Proteasome subunit
    5.9e-15   54.6   0.3    1.3e-14   53.5   0.3    1.6  1  Proteasome_A_N  Proteasome subunit A N-terminal signature


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.2   0.0   4.9e-63   4.4e-59       1     189 [.      33     214 ..      33     215 .. 0.97

  Alignments for each domain:
  == domain 1  score: 199.2 bits;  conditional E-value: 4.9e-63
                                    HHHS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSGTC CS
                     Proteasome   1 vkkGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrpip 80 
                                    vk+G t++G+k+ dgvvla++kr+   s l  + t eKi kid h+gvafaGl++Dar+l+++ar  aq++rl yg+pip
  gi|119719497|ref|YP_919992.1|  33 VKRGMTALGVKAVDGVVLAVEKRSA--SPL-VEGT-EKIKKIDSHVGVAFAGLFGDARVLIDQARIYAQSHRLVYGEPIP 108
                                    799**********************..999.5664.9******************************************* PP

                                    HHHHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHHSTTBSH CS
                     Proteasome  81 verlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekeykedltl 160
                                    +e lv+r+++ +q+ytq++g+rpfgv++l+agvd++g p+L q+dp G+y+++k a aiG g++ a  ++ key++d++ 
  gi|119719497|ref|YP_919992.1| 109 IELLVKRICDIKQVYTQHGGVRPFGVAFLFAGVDRKG-PHLIQTDPGGTYLRCK-ARAIGAGAQKALDLFVKEYHDDIKI 186
                                    **********************************888.***************8.************************* PP

                                    HHHHHHHHHHHHHHHHHBTTSCSSEEEEE CS
                     Proteasome 161 eeavelavkalkealerdklsgknievav 189
                                    eea  la++ lkea+e d ++++nie+a 
  gi|119719497|ref|YP_919992.1| 187 EEATLLALRGLKEAME-DGFTPENIELAR 214
                                    ****************.99*******985 PP

>> Proteasome_A_N  Proteasome subunit A N-terminal signature
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.5   0.3   1.4e-18   1.3e-14       1      23 []      10      32 ..      10      32 .. 0.99

  Alignments for each domain:
  == domain 1  score: 53.5 bits;  conditional E-value: 1.4e-18
                 Proteasome_A_N  1 YDrslttFSPdGRLfQVEYAmkA 23
                                   YDr++t+FSP+GRL+QVEYA++A
  gi|119719497|ref|YP_919992.1| 10 YDRAITIFSPEGRLYQVEYAFEA 32
                                   **********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1694.88
//
Query:       gi|119719498|ref|YP_919993.1|  [L=270]
Description: GTPase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.3e-49  166.5   0.0    9.8e-49  166.3   0.0    1.0  1  ATP_bind_1   Conserved hypothetical ATP binding protein
    0.00016   22.1   0.1    0.00056   20.3   0.1    2.0  1  AAA_16       AAA ATPase domain
    0.00044   19.8   0.0     0.0079   15.7   0.0    2.4  2  GTP_EFTU     Elongation factor Tu GTP binding domain
    0.00068   19.7   0.0    0.00089   19.3   0.0    1.3  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    0.00088   19.0   0.0     0.0032   17.1   0.0    1.8  2  SRP54        SRP54-type protein, GTPase domain
     0.0019   17.1   0.1     0.0031   16.5   0.1    1.2  1  AAA_PrkA     PrkA AAA domain
     0.0029   17.9   0.0     0.0094   16.2   0.0    1.8  1  AAA_22       AAA domain
      0.004   16.9   0.0      0.071   12.8   0.0    2.1  2  IstB_IS21    IstB-like ATP binding protein
     0.0042   17.0   0.3       0.13   12.1   0.0    2.8  3  RsgA_GTPase  RsgA GTPase
     0.0061   15.6   0.0        1.8    7.5   0.0    2.7  3  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
  ------ inclusion threshold ------
      0.011   16.0   0.0      0.021   15.0   0.0    1.5  1  AAA_33       AAA domain
      0.022   14.7   0.1      0.045   13.7   0.1    1.5  1  NACHT        NACHT domain
      0.024   14.5   0.0      0.064   13.0   0.0    1.7  2  CLP1_P       mRNA cleavage and polyadenylation factor CLP1 P-
      0.027   13.9   0.0      0.061   12.8   0.0    1.5  1  PhoH         PhoH-like protein
      0.031   14.0   0.0      0.043   13.5   0.0    1.3  1  AAA_30       AAA domain
      0.035   14.0   0.0      0.059   13.3   0.0    1.4  1  ATPase_2     ATPase domain predominantly from Archaea
      0.053   13.2   0.0      0.071   12.8   0.0    1.3  1  AAA_24       AAA domain
      0.067   13.2   0.0       0.16   11.9   0.0    1.7  1  AAA_5        AAA domain (dynein-related subfamily)
      0.079   13.5   0.1       0.17   12.4   0.1    1.5  1  ABC_tran     ABC transporter
      0.099   11.7   0.0       0.17   10.9   0.0    1.3  1  T2SSE        Type II/IV secretion system protein
        0.1   12.4   0.1        1.7    8.4   0.0    2.7  3  PduV-EutP    Ethanolamine utilisation - propanediol utilisati
        0.1   12.9   0.0        0.2   12.0   0.0    1.5  1  AAA_19       AAA domain
       0.11   13.1   0.0       0.29   11.7   0.0    1.7  2  AAA_18       AAA domain
       0.12   12.6   0.0       0.22   11.7   0.0    1.5  1  AAA_28       AAA domain
       0.19   10.5   0.2        2.6    6.8   0.0    2.0  2  DLIC         Dynein light intermediate chain (DLIC)
        0.2   11.8   0.0        1.5    9.0   0.0    2.3  2  MMR_HSR1     50S ribosome-binding GTPase
       0.24   10.9   0.0       0.37   10.3   0.0    1.2  1  AAA_7        P-loop containing dynein motor region


Domain annotation for each model (and alignments):
>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.3   0.0   1.5e-51   9.8e-49       2     240 ..      25     264 ..      24     265 .. 0.96

  Alignments for each domain:
  == domain 1  score: 166.3 bits;  conditional E-value: 1.5e-51
                     ATP_bind_1   2 vGpaGsGKttfvgalseilelrg.rsvavvNLDPAaeelpYeaavdirelitledvmedlglgpngalvvaleflresld 80 
                                    +GpaGsGKt++v +l +++e+++  +v +vNLDP+a  +pY+a+v+ire++++edvm + +lgpngal+ ++e+ re l 
  gi|119719498|ref|YP_919993.1|  25 LGPAGSGKTSLVASLGKWIEKKQlVPVLYVNLDPGAPYTPYAAEVNIREYVKVEDVMAREKLGPNGALIRSIELAREYLP 104
                                    7******************988735899***************************************************9 PP

                     ATP_bind_1  81 wldeelekeeddyllfDtPGQielfthseslakiveeLesefalvvvyLvDsqrltdptkfisgllsalsamlrlelPhv 160
                                    ++ e++++  + y+l+DtPGQ+elf +++ ++++ve++ + + ++ v ++D   ++ p + +s +l+a  + lrl++  +
  gi|119719498|ref|YP_919993.1| 105 EIVERIGRSPKPYVLVDTPGQMELFLFRDLGVEFVEAMRRVGYIIGVLIFDHLLAARPQDVVSLRLLATIVQLRLGVDVI 184
                                    9*****99999*****************************9*************************************** PP

                     ATP_bind_1 161 vvlnkfDllkeklekeleffedvealslllekeeekykklaeaiaelleefalvlrflplssekeesiedllslidealq 240
                                     v+nk D+ +e +e+    ++d  +l + l++e++   ++ e+++ +l+e+   +r+  +s+ + e++e+l++++ e+++
  gi|119719498|ref|YP_919993.1| 185 PVINKSDVSSETRERLSRALSDSSSLLEELKSERGLLGEMSEKVVGVLDEYRFATRVPLVSALTWEGLEELYDMLHEIFC 264
                                    ********88668888888999999999999999***************************************9999876 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.1   8.4e-07   0.00056      24      75 ..      19      69 ..       6     235 .. 0.63

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 8.4e-07
                         AAA_16 24 pelvllsGesGvGKsslvrellralekdg.giflrgkcdqlesaipysa.laqa 75
                                    ++++  G++G+GK+slv +l + +ek+  + +l+ + d     +py +  a++
  gi|119719498|ref|YP_919993.1| 19 KSIIVMLGPAGSGKTSLVASLGKWIEKKQlVPVLYVNLDPG---APYTPyAAEV 69
                                   4789999***************9999997666699999998...7775523222 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.34   2.3e+02       6      23 ..      22      39 ..      18      48 .. 0.85
   2 !   15.7   0.0   1.2e-05    0.0079      72     190 ..     117     261 ..      75     264 .. 0.65

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.34
                                   EEEEESTTSSHHHHHHHH CS
                       GTP_EFTU  6 igiighvDhGKtTLtdrL 23
                                   i+++g   +GKt+L+ +L
  gi|119719498|ref|YP_919993.1| 22 IVMLGPAGSGKTSLVASL 39
                                   7889999********998 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1.2e-05
                                    EEEEEESSSGG...G...HHHHHHHHHT-SEEE..EEEETTTBSTHHHHHHHHHH.....HHTTTEEEEEEESCGST... CS
                       GTP_EFTU  72 inliDtPGHvd...F...skevirglrvlDgav..lvvdaveGvepqteevlrla.....lkegvpiivfiNKmDrl... 135
                                    + l+DtPG ++   F     e  +++r + + +  l++d      pq    lrl+     l++gv +i +iNK D     
  gi|119719498|ref|YP_919993.1| 117 YVLVDTPGQMElflFrdlGVEFVEAMRRVGYIIgvLIFDHLLAARPQDVVSLRLLativqLRLGVDVIPVINKSDVSset 196
                                    567777777654222111346666677666554114444444444444444443311111456777*********99666 PP

                                    HHHHHHHHHHHHHHHHHH..........HHHHHHHHHTTT..........TTEEEEEEBTTTTBTHHHHHHHHHH CS
                       GTP_EFTU 136 kaelkeiveevkqklsrk..........eeklekygekge..........kevpvvfgSalkgegvktllealve 190
                                    +++l++  ++ ++ l++                      e            + v  +Sal+ eg+++l ++l e
  gi|119719498|ref|YP_919993.1| 197 RERLSRALSDSSSLLEELksergllgemS----------EkvvgvldeyrFATRVPLVSALTWEGLEELYDMLHE 261
                                    66666666666655533355556655541..........1444444444456789999**************987 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.3e-06   0.00089       3      55 ..      23     176 ..      21     238 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.3e-06
                                    EEESSTTSSHHHHHHHHHHHHHH.TT--EEEEEEEESSCCCCHHTTEB-HHHH........................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................... RF
                           CbiA   3 iastkGGvGKTtlaanLaralar.rglrVllvDaDpqannlaileglendiep........................... 54 
                                    ++ +  G+GKT+l+a+L++ + + +   Vl v +Dp a+ + +    e +i++                           
  gi|119719498|ref|YP_919993.1|  23 VMLGPAGSGKTSLVASLGKWIEKkQLVPVLYVNLDPGAPYTPY--AAEVNIREyvkvedvmareklgpngalirsielar 100
                                    5556679****************55679**************5..44444444456788889999999999999888888 PP

                                    ...........................................................................C CS
                                    ...........................................................................x RF
                           CbiA  55 ...........................................................................d 55 
                                                                                                                
  gi|119719498|ref|YP_919993.1| 101 eylpeiverigrspkpyvlvdtpgqmelflfrdlgvefveamrrvgyiigvlifdhllaarpqdvvslrllativQ 176
                                    8888888888888888888888877777777777777777777776666666666666666665543333333330 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   4.8e-06    0.0032       2      34 ..      20      52 ..      19      58 .. 0.86
   2 ?   -1.5   0.0       2.4   1.6e+03      81      95 ..     112     126 ..      96     129 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.8e-06
                                   EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEE CS
                          SRP54  2 nvillvGlqGaGKTttlaKLaallkkegkkvll 34
                                   ++i+++G+ G+GKT+ +a L ++++k++  ++l
  gi|119719498|ref|YP_919993.1| 20 SIIVMLGPAGSGKTSLVASLGKWIEKKQLVPVL 52
                                   689**********************99765554 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.4
                                    HTTSSEEEEEE--SS CS
                          SRP54  81 eekidvvlvDTaGrl 95 
                                    ++   +vlvDT G++
  gi|119719498|ref|YP_919993.1| 112 RSPKPYVLVDTPGQM 126
                                    5556689*****987 PP

>> AAA_PrkA  PrkA AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   4.6e-06    0.0031      86     117 ..      17      51 ..      11      66 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.6e-06
                       AAA_PrkA  86 erkqilyllGPvggGksslverlkklleaa...pi 117
                                    +rk i+ +lGP g+Gk+slv +l k +e++   p+
  gi|119719498|ref|YP_919993.1|  17 VRKSIIVMLGPAGSGKTSLVASLGKWIEKKqlvPV 51 
                                    699*************************9865544 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.4e-05    0.0094       5      49 ..      19      58 ..      17      76 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.4e-05
                         AAA_22  5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlps 49
                                   ++i+v  G++G+GKT l++ l ++ ++      + ++v++v+l  
  gi|119719498|ref|YP_919993.1| 19 KSIIVMLGPAGSGKTSLVASLGKWIEKK-----QLVPVLYVNLDP 58
                                   799*********************9643.....355566777655 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   0.00011     0.071      44      72 ..      16      44 ..       4      57 .. 0.79
   2 ?    1.8   0.0      0.25   1.7e+02      51     110 ..     118     178 ..     112     207 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00011
                      IstB_IS21 44 iekkenivllGpsGvGKshlaialgveav 72
                                   + +k  iv+lGp+G GK+ l ++lg+   
  gi|119719498|ref|YP_919993.1| 16 VVRKSIIVMLGPAGSGKTSLVASLGKWIE 44
                                   5678899******************7554 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.25
                      IstB_IS21  51 vllGpsGvGKshlaialgveavraglsvlfvrvedLveelkrarrdgkla.ralkrllkvd 110
                                    vl+  +G    +l   lgve v+a  +v ++    ++ +l +ar ++ ++ r l+++++ +
  gi|119719498|ref|YP_919993.1| 118 VLVDTPGQMELFLFRDLGVEFVEAMRRVGYIIGVLIFDHLLAARPQDVVSlRLLATIVQLR 178
                                    66677777778888999***************999***99999988876525556666554 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0    0.0002      0.13      94     120 ..      14      40 ..       5      59 .. 0.86
   2 ?   -1.2   0.0       2.5   1.6e+03     154     163 ..     118     127 ..     112     130 .. 0.78
   3 ?    1.5   0.0      0.38   2.5e+02      45      64 ..     179     199 ..     158     261 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0002
                                    HHHCTTSEEEEECSTTSSHHHHHHHHC CS
                    RsgA_GTPase  94 kellkdktsvlvGqSGvGKStLinall 120
                                      +++++++v++G+ G GK++L+ +l 
  gi|119719498|ref|YP_919993.1|  14 VCVVRKSIIVMLGPAGSGKTSLVASLG 40 
                                    5678999****************9986 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.5
                                    EEESS-SSSS CS
                    RsgA_GTPase 154 lliDtPGfre 163
                                    +l+DtPG  e
  gi|119719498|ref|YP_919993.1| 118 VLVDTPGQME 127
                                    79*****665 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.38
                                    TT-EEEEEEE-GGG--HHH.H CS
                    RsgA_GTPase  45 kgiepvivlnKiDlleeee.e 64 
                                     g++++ v+nK D+ +e++ +
  gi|119719498|ref|YP_919993.1| 179 LGVDVIPVINKSDVSSETReR 199
                                    456778899999999988732 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.028        18      30      72 ..      20      63 ..      11      68 .. 0.77
   2 ?   -0.5   0.0      0.71   4.7e+02      14      63 ..      98     148 ..      89     152 .. 0.83
   3 !    7.5   0.0    0.0027       1.8     171     227 ..     184     261 ..     175     267 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.028
                                   EEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEE..EE------- CS
                           MeaB 30 qvvGltGvPGaGkstlvealglelrrrGkrvavl..avDPsspft 72
                                     + + G  G+Gk  lv  lg  + +  + v vl   +DP++p+t
  gi|119719498|ref|YP_919993.1| 20 SIIVMLGPAGSGKTSLVASLGKWIEK-KQLVPVLyvNLDPGAPYT 63
                                   566778999***********987655.566666511669999987 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.71
                                    HHHHHHHHHGGG-S-SEE.EEEEE-TTSSHHHHHHHHHHHHHCTT--EEEE CS
                           MeaB  14 eakellerllakaGraqv.vGltGvPGaGkstlvealglelrrrGkrvavl 63 
                                     a+e l +++++ Gr+ +   l  +PG     l   lg+e++++ +rv+ +
  gi|119719498|ref|YP_919993.1|  98 LAREYLPEIVERIGRSPKpYVLVDTPGQMELFLFRDLGVEFVEAMRRVGYI 148
                                    588999999999999965256789999999999999999999999999854 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0027
                                    EEEEE---..HHHHHHHHHHHHHHHHHCST...................TBTTB--EEEEEBCCCTBSHHHHHHHHHH CS
                           MeaB 171 iivvnkaD..kkeaekaarelraaleleee...................kekeWrpkvlktsavegeGidelvdaiee 227
                                    i v+nk+D   +  e+ +r l+   +l+ee                   +e  + ++v  +sa++ eG++el d ++e
  gi|119719498|ref|YP_919993.1| 184 IPVINKSDvsSETRERLSRALSDSSSLLEElksergllgemsekvvgvlDEYRFATRVPLVSALTWEGLEELYDMLHE 261
                                    669*****8766778889999999999988999*************9988999********************99877 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   3.1e-05     0.021       2     104 ..      22     154 ..      21     159 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.1e-05
                         AAA_33   2 vllvGlpGsGKstlaerl...lkklg...avllssdt............lrrrlfgtdqqskt......dytrvldrlyq 57 
                                    +++ G++GsGK+ l+ +l   ++k +   +  ++ d             +r+ ++++d+   +       ++r  + +++
  gi|119719498|ref|YP_919993.1|  22 IVMLGPAGSGKTSLVASLgkwIEKKQlvpVLYVNLDPgapytpyaaevnIREYVKVEDVMAREklgpngALIRSIELARE 101
                                    89***************977755555666444555557788999988884444444333322233333467888889999 PP

                         AAA_33  58 ilnelarkalsagrnvildat......nlsrrerarflklarrlgvpvrivvv 104
                                     l e++++  ++ ++++l  t      +l+r+   +f+++ rr g+ + ++++
  gi|119719498|ref|YP_919993.1| 102 YLPEIVERIGRSPKPYVLVDTpgqmelFLFRDLGVEFVEAMRRVGYIIGVLIF 154
                                    99999999999999977766669998888888888888888888877766665 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   6.7e-05     0.045       2      27 ..      21      46 ..      20      54 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.7e-05
                                   CEEEEC-TTTCHHHHHHHHHHHHCTS CS
                          NACHT  2 lvilqGeaGsGKTtLlqklalawaeg 27
                                   ++++ G+aGsGKT L+++l   + ++
  gi|119719498|ref|YP_919993.1| 21 IIVMLGPAGSGKTSLVASLGKWIEKK 46
                                   6899*************997665555 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   9.6e-05     0.064       1      35 [.      26      61 ..      26      67 .. 0.92
   2 ?   -2.7   0.0       6.6   4.4e+03     101     115 ..     113     127 ..      93     145 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.6e-05
                         CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpv.yvDlDvGqs 35
                                   Gp  sGK++l++ L  ++ +k+  pv yv+lD+G +
  gi|119719498|ref|YP_919993.1| 26 GPAGSGKTSLVASLGKWIEKKQLVPVlYVNLDPGAP 61
                                   899***************999998888*******75 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 6.6
                         CLP1_P 101 akasgliIntpGwvk 115
                                    + +  ++++tpG ++
  gi|119719498|ref|YP_919993.1| 113 SPKPYVLVDTPGQME 127
                                    455667888888665 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   9.2e-05     0.061      17      41 ..      17      41 ..       7      54 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.2e-05
                                   HH-SEEEEE--TTSSTTHHHHHHHH CS
                           PhoH 17 kkndivfaiGpaGtGKtylavalav 41
                                    +++i++++GpaG+GKt l  +l+ 
  gi|119719498|ref|YP_919993.1| 17 VRKSIIVMLGPAGSGKTSLVASLGK 41
                                   4789*************99888774 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   6.4e-05     0.043      18      46 ..      19      47 ..      11     130 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.4e-05
                         AAA_30 18 drvavltGpAGtGKttalkalreaweaag 46
                                   + + v+ GpAG+GKt ++++l + +e+++
  gi|119719498|ref|YP_919993.1| 19 KSIIVMLGPAGSGKTSLVASLGKWIEKKQ 47
                                   5588999**************99999875 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   8.8e-05     0.059      13     125 ..      12     121 ..       3     143 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.8e-05
                       ATPase_2  13 eilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialr...eesiskldefieeeeekkklekal.giavpk 88 
                                    +i+   +++i++  Gp gsGKt+L+  + +  e+k+   + y +l     +    ++  i+   e  k+e+++  ++++ 
  gi|119719498|ref|YP_919993.1|  12 SIVCVVRKSIIVMLGPAGSGKTSLVASLGKWIEKKQLVPVLYVNLDpgaPYTPYAAEVNIR---EYVKVEDVMaREKLGP 88 
                                    555566789***************9988777766665434444443000333333333322...2222223221334444 PP

                       ATPase_2  89 aeleeilkeksklvfkaielllekikkkgkkiiiiiD 125
                                    + +   l + ++l+ +++ ++ e i ++ k + +++D
  gi|119719498|ref|YP_919993.1|  89 NGA---LIRSIELAREYLPEIVERIGRSPK-PYVLVD 121
                                    333...335566666677776666666633.555555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00011     0.071       4      38 ..      21      63 ..      18     122 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00011
                         AAA_24  4 kiliyGpsgiGKTtlakel........gpkplfidtekGlksl 38
                                    i++ Gp+g+GKT+l+++l           +l+++++ G+  +
  gi|119719498|ref|YP_919993.1| 21 IIVMLGPAGSGKTSLVASLgkwiekkqLVPVLYVNLDPGAPYT 63
                                   6899***************888887777777888888877555 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00024      0.16       2      33 ..      22      57 ..      21      94 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00024
                                   EEEE--SSSSHHHHHHHGGGGB....S--EEEEE-- CS
                          AAA_5  2 vlLvGppGtgKselaerlaaal....nreveyvqlt 33
                                   ++++Gp G+gK++l+ +l + +      +v+yv+l 
  gi|119719498|ref|YP_919993.1| 22 IVMLGPAGSGKTSLVASLGKWIekkqLVPVLYVNLD 57
                                   689***************999975444455666655 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00025      0.17       8      31 ..      16      39 ..      12      47 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00025
                                   EETTSEEEEEESTTSSHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  8 lkegekvaivGenGaGKStLlkll 31
                                   + + ++++++G+ G+GK++L++ l
  gi|119719498|ref|YP_919993.1| 16 VVRKSIIVMLGPAGSGKTSLVASL 39
                                   5678899*************9987 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00026      0.17     126     156 ..      16      46 ..       7      52 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00026
                          T2SSE 126 vrerglilvsGgTgsGKttllyallkeinks 156
                                    v ++ +i++ G+ gsGKt l+ +l k+i+k+
  gi|119719498|ref|YP_919993.1|  16 VVRKSIIVMLGPAGSGKTSLVASLGKWIEKK 46 
                                    5677899999**********99999999887 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0    0.0026       1.7       3      21 ..      21      39 ..      19      53 .. 0.85
   2 ?   -2.8   0.0         7   4.6e+03      91     104 ..     182     195 ..     171     204 .. 0.73
   3 ?    0.3   0.0      0.79   5.3e+02     124     142 ..     242     260 ..     228     261 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0026
                      PduV-EutP  3 killiGkvgsGKttLtqal 21
                                    i+++G+ gsGKt+L  +l
  gi|119719498|ref|YP_919993.1| 21 IIVMLGPAGSGKTSLVASL 39
                                   58899**********9887 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 7
                      PduV-EutP  91 eviGiitkidlaed 104
                                    +vi +i k d++++
  gi|119719498|ref|YP_919993.1| 182 DVIPVINKSDVSSE 195
                                    68888888888744 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.79
                      PduV-EutP 124 fevsavekegieellkyle 142
                                      vsa++ eg+eel ++l+
  gi|119719498|ref|YP_919993.1| 242 PLVSALTWEGLEELYDMLH 260
                                    569***********99997 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00031       0.2       7      40 ..      16      49 ..      11      70 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00031
                         AAA_19  7 alkekvllvtaGpGtGKTrvlkhivallvelggv 40
                                    ++++++++++++G+GKT ++    +++++ + v
  gi|119719498|ref|YP_919993.1| 16 VVRKSIIVMLGPAGSGKTSLVASLGKWIEKKQLV 49
                                   57889999************99998888877655 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00044      0.29       1      67 [.      22      96 ..      22     162 .. 0.64
   2 ?   -1.8   0.0       6.5   4.3e+03      16      44 ..     202     227 ..     189     239 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00044
                         AAA_18  1 IlltGtpGvGKttlakeL.....skrlgf..........gvnlrdvakenglllevdpealdeskrldedkldklldaleen 67
                                   I+  G++G+GKt+l   L     +k   +          g  ++ +a+e +++++v  e     +++ ++kl  +  +++ +
  gi|119719498|ref|YP_919993.1| 22 IVMLGPAGSGKTSLVASLgkwieKKQ--LvpvlyvnldpGAPYTPYAAEVNIREYVKVE-----DVMAREKLGPNGALIRSI 96
                                   7789**************66653333..2455777777755555555555555555555.....445444444444444444 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 6.5
                         AAA_18  16 keLskrlgfgvnlrdvakenglllevdpe 44 
                                    ++Ls++   +  l ++ +e+gll e  ++
  gi|119719498|ref|YP_919993.1| 202 RALSDS---SSLLEELKSERGLLGEMSEK 227
                                    333333...66666666666666666555 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00033      0.22       2      93 ..      22     135 ..      21     166 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00033
                         AAA_28   2 ivitGgestGKTtlleaLa.....ar..............gypvvpEa.areileekl..akgedalpwv.edllafaer 58 
                                    iv++G+ ++GKT+l++ L      ++               +p+ +E+  re+++ +   a+++   + +  + +++a++
  gi|119719498|ref|YP_919993.1|  22 IVMLGPAGSGKTSLVASLGkwiekKQlvpvlyvnldpgapYTPYAAEVnIREYVKVEDvmAREKLGPNGAlIRSIELARE 101
                                    89****************95554411344444444453334555555435666665553222222222223356666666 PP

                         AAA_28  59 vleeqleeeaaaaankvlfcDrglldtlaYarayg 93 
                                     l e +e+  + ++++++++D+    +l+  r +g
  gi|119719498|ref|YP_919993.1| 102 YLPEIVERIGR-SPKPYVLVDTPGQMELFLFRDLG 135
                                    66555544444.46666666666666555555555 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0    0.0039       2.6      26      51 ..      19      45 ..      10      60 .. 0.75
   2 ?    1.7   0.0      0.14        92     177     208 ..     162     193 ..     155     200 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0039
                           DLIC 26 ksv.lvlGedgsGkttliaklqGveee 51
                                   ks+ ++lG  gsGkt+l+a l    e+
  gi|119719498|ref|YP_919993.1| 19 KSIiVMLGPAGSGKTSLVASLGKWIEK 45
                                   6651568************99654444 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.14
                           DLIC 177 dedsvllPlgedvlttnlGldvvvvvtkcdai 208
                                     +d v l l + ++   lG+dv+ v+ k+d  
  gi|119719498|ref|YP_919993.1| 162 PQDVVSLRLLATIVQLRLGVDVIPVINKSDVS 193
                                    578899999999*****************975 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0    0.0022       1.5       2      72 ..      22     140 ..      21     189 .. 0.59
   2 ?   -2.5   0.0         8   5.3e+03      26      45 ..     231     251 ..     208     258 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0022
                                    EEEEESTTSSHHHHHHHHHT.....S...TEEESSSTTSSSSEEEEEEEETTEE.......................... CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltg.....e...kaivsdkpgtTrdinegrvklkgke.......................... 47 
                                    ++ +G   +GK++L+ +l +     +   +  v+  pg+  ++  ++v++++                            
  gi|119719498|ref|YP_919993.1|  22 IVMLGPAGSGKTSLVASLGKwiekkQlvpVLYVNLDPGAPYTPYAAEVNIREYVkvedvmareklgpngalirsielare 101
                                    56778888888888888865444332333346666667777776666664421134445555555566666666666666 PP

                                    ...............EEEEECGGCSSHHHHHHHHHHHHHH CS
                       MMR_HSR1  48 ...............ielvDtpGliegaseekglgkafla 72 
                                                   ++lvDtpG +e     ++lg +f +
  gi|119719498|ref|YP_919993.1| 102 ylpeiverigrspkpYVLVDTPGQME-LFLFRDLGVEFVE 140
                                    666666666666666********543.1222244444444 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 8
                                    E.SSSTTSSSSEEEEEEEETT CS
                       MMR_HSR1  26 v.sdkpgtTrdinegrvklkg 45 
                                    v  ++ ++Tr +    ++++g
  gi|119719498|ref|YP_919993.1| 231 VlDEYRFATRVPLVSALTWEG 251
                                    336777888888777777666 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00056      0.37      31      64 ..      17      50 ..      10      57 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00056
                          AAA_7 31 knkkpvllvGptGtGKtviikdllkkldkekyls 64
                                    +k  +++ Gp+G+GKt+++ +l k ++k+++++
  gi|119719498|ref|YP_919993.1| 17 VRKSIIVMLGPAGSGKTSLVASLGKWIEKKQLVP 50
                                   566678899*************999999887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                       108  (0.00602376); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              27  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 1750.09
//
Query:       gi|119719499|ref|YP_919994.1|  [L=396]
Description: AAA ATPase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-21   74.9   0.5    2.6e-20   72.2   0.0    2.5  2  Cdc6_C           CDC6, C terminal winged helix domain
    2.2e-14   53.9   0.0    4.4e-14   52.9   0.0    1.4  1  AAA_22           AAA domain
    5.3e-14   52.9   0.4    5.2e-11   43.2   0.1    2.5  2  AAA_16           AAA ATPase domain
    2.3e-10   41.0   0.0    4.6e-10   40.0   0.0    1.5  1  AAA              ATPase family associated with various cellul
    2.3e-07   31.0   1.2    3.5e-07   30.4   0.3    1.8  1  ATPase_2         ATPase domain predominantly from Archaea
    9.4e-05   21.4   2.0     0.0081   15.0   0.0    2.3  2  AAA_32           AAA domain
    0.00019   20.9   0.0    0.00033   20.1   0.0    1.4  1  TniB             Bacterial TniB protein
    0.00074   18.8   0.0     0.0012   18.1   0.0    1.3  1  NB-ARC           NB-ARC domain
    0.00078   18.8   0.0    0.00092   18.6   0.0    1.2  1  DUF2075          Uncharacterized conserved protein (DUF2075)
     0.0015   18.4   0.0     0.0031   17.5   0.0    1.5  1  NACHT            NACHT domain
     0.0017   17.6   0.0     0.0046   16.1   0.0    1.6  2  DUF815           Protein of unknown function (DUF815)
     0.0023   17.7   0.0     0.0052   16.5   0.0    1.7  1  Sigma54_activat  Sigma-54 interaction domain
     0.0025   17.8   0.5     0.0089   16.0   0.5    2.1  1  AAA_5            AAA domain (dynein-related subfamily)
  ------ inclusion threshold ------
      0.014   14.7   0.2       0.52    9.5   0.2    2.3  2  KAP_NTPase       KAP family P-loop domain
      0.017   14.9   1.0        5.5    6.7   0.1    2.4  2  DEAD             DEAD/DEAH box helicase
      0.018   15.6   0.6      0.052   14.1   0.2    2.0  2  AAA_18           AAA domain
       0.03   13.8   0.0      0.059   12.9   0.0    1.4  1  AAA_7            P-loop containing dynein motor region
      0.032   14.5   0.2       0.09   13.1   0.0    1.7  1  AAA_19           AAA domain
       0.04   14.3   0.2       0.11   12.8   0.2    1.8  1  Ribosomal_S13    Ribosomal protein S13/S18
      0.078   12.7   0.2        0.2   11.3   0.0    1.8  2  AAA_30           AAA domain
       0.08   12.8   0.0       0.34   10.8   0.0    1.9  2  DAO_C            C-terminal domain of alpha-glycerophosphate 
      0.082   12.9   0.1       0.19   11.8   0.1    1.5  1  AAA_14           AAA domain
      0.084   13.2   2.8       0.42   10.9   0.9    2.4  2  PIN_9            PIN like domain
      0.089   12.6   1.6        0.2   11.5   1.6    1.6  1  AAA_lid_4        RuvB AAA lid domain
      0.094   13.1   0.0        0.2   12.1   0.0    1.5  1  RNA_helicase     RNA helicase
       0.11   12.6   1.7        1.7    8.7   0.4    2.5  2  DUF87            Helicase HerA, central domain
       0.12   12.4   0.0       0.28   11.2   0.0    1.7  1  ResIII           Type III restriction enzyme, res subunit
       0.13   12.3   0.0       0.25   11.4   0.0    1.5  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.14   11.8   0.0       0.26   11.0   0.0    1.4  1  AAA_24           AAA domain


Domain annotation for each model (and alignments):
>> Cdc6_C  CDC6, C terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0         2   1.2e+03      41      61 ..     174     194 ..     162     200 .. 0.75
   2 !   72.2   0.0   4.3e-23   2.6e-20       1      83 [.     301     382 ..     301     383 .. 0.97

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 2
                                    HHHHHHHHHHHTTSEEEEEEE CS
                         Cdc6_C  41 evsdllseLemlgilelekss 61 
                                    +v  + ++L++  +l+++++s
  gi|119719499|ref|YP_919994.1| 174 SVIGITNDLKFTEFLDARVKS 194
                                    4568899*********99875 PP

  == domain 2  score: 72.2 bits;  conditional E-value: 4.3e-23
                                    HHHHHHHHCHCSSS-EEHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEESSSCHH CS
                         Cdc6_C   1 LcalvlllrksgkeevttgevyevYkslCesegvdpltqrevsdllseLemlgileleksskGrregrtrkisLnvdpdd 80 
                                    L+++ ll++++g +++ttg +y++Yk+l  + g++p+t+r++ d+l+eL+m gi+++++ s Gr +grt+ + L v+ ++
  gi|119719499|ref|YP_919994.1| 301 LASIYLLTKEGGAKTITTGLIYDKYKELVTKVGIEPVTSRRITDILNELDMAGIINARVISLGR-YGRTKVVALGVPLKN 379
                                    7899***********************************************************9.************999 PP

                                    HHH CS
                         Cdc6_C  81 vle 83 
                                    v+e
  gi|119719499|ref|YP_919994.1| 380 VEE 382
                                    976 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.9   0.0   7.1e-17   4.4e-14       6     131 ..      55     179 ..      51     183 .. 0.88

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 7.1e-17
                         AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaee..erpevvfvtlpsstsskdllrellralglelkaerlsseelleale 83 
                                    + ++++G +GtGKT + + +l++l      e+   r e+v++++ + ++s  +l el ++lg++    +l + e++++++
  gi|119719499|ref|YP_919994.1|  55 SNVFIYGLTGTGKTAVTKYVLRRLA-----EKggGRIEYVYINCRQNNTSYRVLAELGKFLGVKIPFTGLALGEVMKRIT 129
                                    5679*******************94.....33458********************************9************ PP

                         AAA_22  84 qalraravielliiDEaqhlr.s..eealeeLrsllnlsrkgvqliLvGtp 131
                                    qal+++++i ++++DE+++l  +  +++l +L +++n + +++++ ++G +
  gi|119719499|ref|YP_919994.1| 130 QALDRKHRILIVVLDEVDNLVkRngDDVLYYL-TRVNEQLTNTRVSVIGIT 179
                                    *******************9872569999999.666657788888888765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.2   0.1   8.4e-14   5.2e-11       2      74 ..      31     105 ..      30     114 .. 0.86
   2 !    7.4   0.0    0.0085       5.3     121     165 ..     123     170 ..     113     176 .. 0.79

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 8.4e-14
                         AAA_16   2 lvGReeeleqLlsalervrsgrp.elvllsGesGvGKsslvrellralekdg.gif..lrgkcdqlesaipysalaq 74 
                                    l+ R+e++++L+ +l ++ sg+  ++v+++G  G+GK+++ + +lr+l ++g g    ++ +c+q+  +++y +la+
  gi|119719499|ref|YP_919994.1|  31 LPHRDEQIKRLALTLAPALSGSRpSNVFIYGLTGTGKTAVTKYVLRRLAEKGgGRIeyVYINCRQN--NTSYRVLAE 105
                                    688*************77777766***************************6355577********..888866665 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0085
                         AAA_16 121 ellkrllallsrderplvlvlDdlq.wadeaslqllaaLlrlles..k 165
                                    e++kr+ + l r++r l++vlD+++  ++    ++l++L r  e+  +
  gi|119719499|ref|YP_919994.1| 123 EVMKRITQALDRKHRILIVVLDEVDnLVKRNGDDVLYYLTRVNEQltN 170
                                    6788899888987777*********77777888889999998887542 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   0.0   7.4e-13   4.6e-10       1     112 [.      57     182 ..      57     197 .. 0.87

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 7.4e-13
                                    EEEESSTTSSHHHHHHHHHHHH......THEEEEEETTTCSSS....................STTHHHHHHHHHHHHHH CS
                            AAA   1 vllyGppGtGKTllakavakel......gvefleisgsellsk....................yvgesekkirelfkeak 54 
                                    v +yG  GtGKT++ k v + l       +e++ i++ +   +                     +ge +k+i + +++  
  gi|119719499|ref|YP_919994.1|  57 VFIYGLTGTGKTAVTKYVLRRLaekgggRIEYVYINCRQNNTSyrvlaelgkflgvkipftglALGEVMKRITQALDR-- 134
                                    578******************97665544999999999988667999999999999***9999999999999999987.. PP

                                    HTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSG CS
                            AAA  55 ekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrp 112
                                    +++   i+++DE+d+l+k++       +++v+  L ++ +++++   +v vig+tn+ 
  gi|119719499|ref|YP_919994.1| 135 KHR-ILIVVLDEVDNLVKRN-------GDDVLYYLTRVNEQLTN--TRVSVIGITNDL 182
                                    343.68***********999.......99***************..58********84 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.3   5.7e-10   3.5e-07      16     155 ..      50     171 ..      33     191 .. 0.77

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 5.7e-10
                       ATPase_2  16 erepneiyfiYGpegsGKtaLlkeiienledkdk.yviyyialreesiskldefieeeeekkklekalgiavpkaeleei 94 
                                    + ++ + +fiYG  g GKta+ k ++ +l +k+  ++ y++   ++++++++          +l k lg ++p + l   
  gi|119719499|ref|YP_919994.1|  50 SGSRPSNVFIYGLTGTGKTAVTKYVLRRLAEKGGgRIEYVYINCRQNNTSYRVL-------AELGKFLGVKIPFTGL--- 119
                                    55666779*********************8887744445544444455555555.......4788888888888777... PP

                       ATPase_2  95 lkeksklvfkaielllekikkkgkkiiiiiDelqklidlglngaellvkeLlnliesltke 155
                                           + + ++++ +++ +k + +i+++De+ +l+  + n   ++++ L ++ e+lt+ 
  gi|119719499|ref|YP_919994.1| 120 ------ALGEVMKRITQALDRKHRILIVVLDEVDNLV--KRN-GDDVLYYLTRVNEQLTNT 171
                                    ......44788999999999**999************..766.677888899988888765 PP

>> AAA_32  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.3e-05    0.0081      32      78 ..      56     102 ..      42     108 .. 0.90
   2 ?    4.6   1.4     0.019        12     474     510 ..     244     280 ..     210     283 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.3e-05
                         AAA_32  32 NifvlGesgtGrttlvkrlleeiakkeptpdDwcYvnnfdnpeePka 78 
                                    N+f+ G +gtG+t ++k +l++ a+k     +++Y+n  +n+++ ++
  gi|119719499|ref|YP_919994.1|  56 NVFIYGLTGTGKTAVTKYVLRRLAEKGGGRIEYVYINCRQNNTSYRV 102
                                    9***********************************98888776655 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.019
                         AAA_32 474 strfseiadllrEAdywakkegaevveaehVekAlee 510
                                        +   d+l  A+ +a++e+a+ v+++hV+kA +e
  gi|119719499|ref|YP_919994.1| 244 NGDCRLALDILLKAADIAERERASEVTEAHVDKARNE 280
                                    456677899*************************876 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   5.4e-07   0.00033      25     158 ..      44     176 ..      30     185 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 5.4e-07
                           TniB  25 eLleypkrkrmpnlllvGdsnnGKtmivekFarlhppekdedaekvpvlvvqappkpdekrlyaaiLealgaplkara.r 103
                                     L  + + +r++n+ ++G + +GKt++ +   r+  +   +   +++ ++++++++ +  r  a++ + lg+++  +   
  gi|119719499|ref|YP_919994.1|  44 TLAPALSGSRPSNVFIYGLTGTGKTAVTKYVLRRLAE---KGGGRIEYVYINCRQNNTSYRVLAELGKFLGVKIPFTGlA 120
                                    455566789****************988766665443...45678999******************99999998877635 PP

                           TniB 104 vskleqqvlrll.relkvrvLiiDEihnllagsarkqreflnalksLgnelkipiv 158
                                    + +  +++ + l r+ ++ ++++DE++nl++ + ++    l  +     + +++++
  gi|119719499|ref|YP_919994.1| 121 LGEVMKRITQALdRKHRILIVVLDEVDNLVKRNGDDVLYYLTRVNEQLTNTRVSVI 176
                                    55777776666625677888899******987776666655555554445555555 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0     2e-06    0.0012      22     112 ..      56     146 ..      35     168 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2e-06
                                    EEEEEESTTSSHHHHHHHHCCSHCCCCCCBTEEEEEEEESXXHHHHHHHXXHHHHHCCCTTSSSS-STTSHHHHHHHHCC CS
                         NB-ARC  22 vvalvGmgGvGKttlakqilnksdevegrFdsvawvvvsktdkseeiletilkeLslseddleekeeveslkrklvrlLl 101
                                     v+++G  G GKt + k +l+ ++e  g    ++++   ++ +s+++l ++ k L+ +       + +e   +++ ++L 
  gi|119719499|ref|YP_919994.1|  56 NVFIYGLTGTGKTAVTKYVLRRLAEKGGGRIEYVYINCRQNNTSYRVLAELGKFLGVK-IPFTGLALGE-VMKRITQALD 133
                                    59**************************888899******************999887.5566666666.99******** PP

                                    CT.TEEE.EEEEE CS
                         NB-ARC 102 tk.rfll.vlDDV 112
                                    +k r l+ vlD V
  gi|119719499|ref|YP_919994.1| 134 RKhRILIvVLDEV 146
                                    *998876267776 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.5e-06   0.00092       3     106 ..      56     155 ..      54     270 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.5e-06
                        DUF2075   3 vvlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlrealakke..ekkkkkeafeklssfinnlsefkka 80 
                                     v++ G +GtGKt v   +l +l  ++ + +  y++ N +++++ ++ la+     + k+  +   l +++++++     
  gi|119719499|ref|YP_919994.1|  56 NVFIYGLTGTGKTAVTKYVLRRL-AEKGGGRIEYVYINCRQNNTSYRVLAELGkfLGVKIPFTGLALGEVMKRIT----- 129
                                    69*********************.888999999****************98876667777777777778888887..... PP

                        DUF2075  81 eekkeepkedvvivDEAhrlltksdq 106
                                    ++ +++ ++ +v+ DE   l +++  
  gi|119719499|ref|YP_919994.1| 130 QALDRKHRILIVVLDEVDNLVKRNGD 155
                                    77788889999999999888884443 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0     5e-06    0.0031       3      99 ..      57     155 ..      55     181 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 5e-06
                                    EEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-....-HCHHHCCCCTS--SSS-C...CHHHHCC CS
                          NACHT   3 vilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgna.rsladllfsqlpepaapvse...vwavlle 78 
                                    v++ G  G GKT+  + + + +ae+   +   ++v ++++r+ ++s ++   l ++l  + p  + +  e    ++  l 
  gi|119719499|ref|YP_919994.1|  57 VFIYGLTGTGKTAVTKYVLRRLAEKGGGR--IEYV-YINCRQNNTSYRVlAELGKFLGVKIPFTGLALGEvmkRITQALD 133
                                    899***********************666..6777.6788988888888899*******999998888882223455567 PP

                                    SCCCEE.EEEE-STT-SS-TCH CS
                          NACHT  79 lperlL.lilDglDelvtdlgq 99 
                                    +++r+L  +lD +D lv+ +g 
  gi|119719499|ref|YP_919994.1| 134 RKHRILiVVLDEVDNLVKRNGD 155
                                    8999997789*******99987 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   7.5e-06    0.0046      28      81 ..      29      82 ..      23     107 .. 0.86
   2 ?   -2.7   0.0       4.3   2.6e+03      92     120 ..     158     186 ..     150     193 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 7.5e-06
                         DUF815 28 ddLvgidkqkealventeqfleglpannvLLwGarGtGKSslvkallneyaeeg 81
                                   +dL   d+q ++l    +  l+g + +nv+++G  GtGK ++ k +l+++ae+g
  gi|119719499|ref|YP_919994.1| 29 EDLPHRDEQIKRLALTLAPALSGSRPSNVFIYGLTGTGKTAVTKYVLRRLAEKG 82
                                   5677789999999999999******************************99987 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.3
                         DUF815  92 lkelpklvellrerperfilfvDDLsFee 120
                                    l  l ++ e+l +++  +i    DL F+e
  gi|119719499|ref|YP_919994.1| 158 LYYLTRVNEQLTNTRVSVIGITNDLKFTE 186
                                    67788999999999999999999999976 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   8.4e-06    0.0052      20      64 ..      52      99 ..      32     180 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 8.4e-06
                                   TSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS...-EEEEETTTS-TT CS
                Sigma54_activat 20 ktdlsvlitGesGtGKellaraiheaskrkek...pfvavncaaipee 64
                                   + +++v+i G +GtGK+ + + + ++  +k +   ++v +nc + +++
  gi|119719499|ref|YP_919994.1| 52 SRPSNVFIYGLTGTGKTAVTKYVLRRLAEKGGgriEYVYINCRQNNTS 99
                                   34599******************99766664444599*****988765 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.5   1.4e-05    0.0089       1      77 [.      56     149 ..      56     196 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.4e-05
                                    EEEEE--SSSSHHHHHHHGGGGB......S--EEEEE--TT--HHHHH--B--...........--------........ CS
                          AAA_5   1 dvlLvGppGtgKselaerlaaal......nreveyvqltrdtteedlkgrreik..ngttslvdsplvraar........ 64 
                                    +v++ G +GtgK+ ++++++++l      + e++y++++++ t+  ++ ++  k  + +  ++  +l + ++        
  gi|119719499|ref|YP_919994.1|  56 NVFIYGLTGTGKTAVTKYVLRRLaekgggRIEYVYINCRQNNTSYRVLAELG-KflGVKIPFTGLALGEVMKritqaldr 134
                                    699***********************98888999999999888877777665.335666666666666666666688887 PP

                                    ..G-SEEEEESGGG- CS
                          AAA_5  65 ..egeilvlDEvera 77 
                                      +  i+vlDEv+++
  gi|119719499|ref|YP_919994.1| 135 khRILIVVLDEVDNL 149
                                    777778888888876 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.092        57       3      47 ..      36      81 ..      34     108 .. 0.76
   2 ?    9.5   0.2   0.00084      0.52     159     199 ..     123     163 ..     118     198 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.092
                     KAP_NTPase  3 lyasaladilseptl..atpivvgLygkWGsGKssllnkledelkef 47
                                     ++ la +l  p+l  ++p+ v +yg  G+GK+++ + + + l e+
  gi|119719499|ref|YP_919994.1| 36 EQIKRLALTLA-PALsgSRPSNVFIYGLTGTGKTAVTKYVLRRLAEK 81
                                   56677777776.55556899999999999******999887777666 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00084
                     KAP_NTPase 159 elladmektLdalqkrlVvviDdLDrceteevlqlleavkl 199
                                    e+++++ ++Ld++++ l+vv+D+ D++ + +   +l+++  
  gi|119719499|ref|YP_919994.1| 123 EVMKRITQALDRKHRILIVVLDEVDNLVKRNGDDVLYYLTR 163
                                    589***********************988887777776655 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1     0.009       5.5      15      41 ..      55      80 ..      37     103 .. 0.71
   2 ?    6.3   0.1     0.012       7.6     121     155 ..     137     170 ..     119     184 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.009
                                   CEEEEEESTTSSHHHHHHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD 15 gdvlvaaeTGsGKTlaflipvlqivye 41
                                    +v++ + TG+GKT++    vl++++e
  gi|119719499|ref|YP_919994.1| 55 SNVFIYGLTGTGKTAVTK-YVLRRLAE 80
                                   69************9954.44445555 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.012
                                    TEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD 121 qvrflVlDEadrlldqgfsdfinrilnqlpqitcd 155
                                    ++ ++VlDE+d+l +   +d++   l++++++ ++
  gi|119719499|ref|YP_919994.1| 137 RILIVVLDEVDNLVKR-NGDDVLYYLTRVNEQLTN 170
                                    56789**********9.666666667777554444 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.2   8.4e-05     0.052       1      66 [.      57     152 ..      57     177 .. 0.56
   2 ?   -1.7   0.0       6.4     4e+03      46      67 ..     263     284 ..     216     306 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.4e-05
                         AAA_18   1 IlltGtpGvGKttlakeLskrl.gf....gvnlrdvakenglllevdpe.........................aldesk 50 
                                    +++ G  G+GKt ++k++ +rl +      + +  ++++n++++ v +e                         ald+++
  gi|119719499|ref|YP_919994.1|  57 VFIYGLTGTGKTAVTKYVLRRLaEKgggrIEYVYINCRQNNTSYRVLAElgkflgvkipftglalgevmkritqALDRKH 136
                                    79***************977763335555333333444444444444443322333333344444444444444555555 PP

                         AAA_18  51 rldedkldklldalee 66 
                                    r+ + +ld++ +++++
  gi|119719499|ref|YP_919994.1| 137 RILIVVLDEVDNLVKR 152
                                    5555555555555555 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 6.4
                         AAA_18  46 ldeskrldedkldklldaleen 67 
                                     ++  ++ e  +dk+ +++e+n
  gi|119719499|ref|YP_919994.1| 263 RERASEVTEAHVDKARNEIEKN 284
                                    3444444444444444444444 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   9.5e-05     0.059      34      75 ..      55      99 ..      42     111 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.5e-05
                          AAA_7 34 kpvllvGptGtGKtviikdllkkldke...kylsltinfsaqtsa 75
                                    +v+++G tGtGKt+++k +l++l ++   ++ ++ in+ ++ ++
  gi|119719499|ref|YP_919994.1| 55 SNVFIYGLTGTGKTAVTKYVLRRLAEKgggRIEYVYINCRQNNTS 99
                                   6899*****************999854222456666666666555 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00015      0.09       9      62 ..      53     106 ..      47     169 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00015
                         AAA_19   9 kekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerl 62 
                                    + +++++ +  GtGKT v+k +++ l e gg   e +++ +  +    ++  +l
  gi|119719499|ref|YP_919994.1|  53 RPSNVFIYGLTGTGKTAVTKYVLRRLAEKGGGRIEYVYINCRQNNTSYRVLAEL 106
                                    5678999***********************999988888776555444443333 PP

>> Ribosomal_S13  Ribosomal protein S13/S18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   0.00018      0.11      28      64 ..     251     287 ..     231     302 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00018
                  Ribosomal_S13  28 akiilkkadvdedkrigelteeeiekieeivenkaqy 64 
                                      i+lk+ad+ e+ r++e+te +++k ++++e++ + 
  gi|119719499|ref|YP_919994.1| 251 LDILLKAADIAERERASEVTEAHVDKARNEIEKNLTV 287
                                    56889**************************997654 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00033       0.2      17      61 ..      53     101 ..      43     180 .. 0.57
   2 ?   -2.1   0.2       4.4   2.7e+03     142     178 ..     242     278 ..     208     290 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00033
                         AAA_30  17 gdrvavltGpAGtGKttalkal.reaweaag...grviglAptgkaAkv 61 
                                    +   +++ G  GtGKt + k + r+++e+ g   + v +   +++ + +
  gi|119719499|ref|YP_919994.1|  53 RPSNVFIYGLTGTGKTAVTKYVlRRLAEKGGgriEYVYINCRQNNTSYR 101
                                    55567899************99788888888344223333444444444 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.4
                         AAA_30 142 eaagigtaeLtevvRqkeseeraaalalregdaeeal 178
                                    +++g +   L+ + + ++ +er+ a ++ e ++++a 
  gi|119719499|ref|YP_919994.1| 242 RQNGDCRLALDILLKAADIAERERASEVTEAHVDKAR 278
                                    3344455555555555555555555555555555554 PP

>> DAO_C  C-terminal domain of alpha-glycerophosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       3.5   2.2e+03      26      69 ..      68     109 ..      48     152 .. 0.70
   2 ?   10.8   0.0   0.00056      0.34      83     118 ..     208     243 ..     195     245 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 3.5
                                    HT--HHHHHHHHHHHGGGHHHHHHHHHHTH...HHHHHTTS-HH CS
                          DAO_C  26 ygldeevaehLaerYGsraeevlelakedekpelaerlspelpy 69 
                                    + +++ v ++Lae+ G r+e v    + +++++  + l++  ++
  gi|119719499|ref|YP_919994.1|  68 TAVTKYVLRRLAEKGGGRIEYVY--INCRQNNTSYRVLAELGKF 109
                                    45777788888888888888887..5555555444444444444 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00056
                                    --SHHHHHHTTS-HHHH-HHHHHHHHHHHHHHHHHH CS
                          DAO_C  83 artlvDvlaRRtrlafldadaalealpevaelmaee 118
                                    a +l+D+l RR + af +   + +++++va++ a++
  gi|119719499|ref|YP_919994.1| 208 AIQLEDILRRRAKEAFHEGVVSDAVIKKVAAIAARQ 243
                                    789*****************************9976 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00031      0.19       5      77 ..      57     155 ..      54     189 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00031
                         AAA_14   5 lvitGaRrvGKTtllkqlikell...vkkesilyinldderd..........kkladpe............kllelilek 59 
                                    ++i G+  +GKT + k ++++l      + +++yin+ ++++                             ++++ i + 
  gi|119719499|ref|YP_919994.1|  57 VFIYGLTGTGKTAVTKYVLRRLAekgGGRIEYVYINCRQNNTsyrvlaelgkF-----LgvkipftglalgEVMKRITQA 131
                                    7899**********99999988888878899********99865555444440.....1444444554444555555555 PP

                         AAA_14  60 lke.ekktylflDEiqev.....p 77 
                                    l + ++  +++lDE+ ++     +
  gi|119719499|ref|YP_919994.1| 132 LDRkHRILIVVLDEVDNLvkrngD 155
                                    33335566699****998554443 PP

>> PIN_9  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.72   4.5e+02      24      62 ..     130     168 ..     118     184 .. 0.60
   2 ?   10.9   0.9   0.00068      0.42      28     102 ..     223     298 ..     200     308 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.72
                          PIN_9  24 rllgsvelvvpkavleELerlakagkg.kertaakvalsL 62 
                                    + l+++   ++  vl+E+++l+k++ +       +v ++L
  gi|119719499|ref|YP_919994.1| 130 QALDRK-HRILIVVLDEVDNLVKRNGDdVLYYLTRVNEQL 168
                                    444333.335567889999887766551333445555555 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00068
                          PIN_9  28 svelvvpkavleELerlakagkgkertaakv...alsLaerceiveaeeekaDdailelakeldaavlvTnDreLkkr 102
                                     +e vv +av++ ++++a++++g  r a ++   a+++aer +  e++e+++D a  e+ k+l ++v+ T  ++L  +
  gi|119719499|ref|YP_919994.1| 223 FHEGVVSDAVIKKVAAIAARQNGDCRLALDIllkAADIAERERASEVTEAHVDKARNEIEKNLTVDVIKT--MPLHVK 298
                                    56889************************99555677899999999999**************9999965..455555 PP

>> AAA_lid_4  RuvB AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.6   0.00032       0.2       1      69 [.     206     279 ..     206     284 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00032
                      AAA_lid_4   1 YeeeeLeeivkrsak.ilgveieeega....aeiarRsRGTPRianrLLrRvrDfaqvkgdgkitkevakkaLe 69 
                                    Y++ +Le+i++r ak  ++  + +++     a ia R  G  R+a  +L +  D a+ ++ +++t++ ++ka +
  gi|119719499|ref|YP_919994.1| 206 YNAIQLEDILRRRAKeAFHEGVVSDAVikkvAAIAARQNGDCRLALDILLKAADIAERERASEVTEAHVDKARN 279
                                    7888999999887753677667776642222579***********************************99966 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00032       0.2       1      36 [.      57      91 ..      57     101 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00032
                   RNA_helicase  1 iwlyGpsgeGKStlakeLakallkklklkkkdsvys 36
                                   +++yG +g+GK+ ++k++ ++l++k +    + vy+
  gi|119719499|ref|YP_919994.1| 57 VFIYGLTGTGKTAVTKYVLRRLAEKGGGR-IEYVYI 91
                                   689*******************9887333.345554 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.4    0.0027       1.7      28      54 ..      59      85 ..      56      89 .. 0.87
   2 ?    2.3   0.0      0.25   1.5e+02     160     216 ..      94     151 ..      85     154 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0027
                          DUF87 28 ilgsTGsGKSntvavLleellekkgat 54
                                   i g TG+GK+  +++ l++l+ek g++
  gi|119719499|ref|YP_919994.1| 59 IYGLTGTGKTAVTKYVLRRLAEKGGGR 85
                                   8999*****************665555 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.25
                          DUF87 160 lknqaiarlldkledllrkggsf.snsstdliallleklekegkitiidlsgvdelaq 216
                                     +n++  r+l+ l ++l  ++ f +    ++++ + + l+++++i i+ l +vd+l++
  gi|119719499|ref|YP_919994.1|  94 RQNNTSYRVLAELGKFLGVKIPFtGLALGEVMKRITQALDRKHRILIVVLDEVDNLVK 151
                                    678889999999999999998888899999999999999***************9987 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00045      0.28       5      54 ..      34      84 ..      30     173 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00045
                                   -HHHHHHHHHHT.......TTSEEEEEESTTSTHHHHHHHHHHHH-S.... CS
                         ResIII  5 reyQeeaienll.eklkskrdkrglikmaTGtGKTlvaaklierllkkgke 54
                                   r+ Q++ +  +l  +l+  r  +++i   TGtGKT v   + +rl++kg+ 
  gi|119719499|ref|YP_919994.1| 34 RDEQIKRLALTLaPALSGSRPSNVFIYGLTGTGKTAVTKYVLRRLAEKGGG 84
                                   5555555555543455558889999*************9999999999765 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0    0.0004      0.25       4      44 ..      35      79 ..      32      87 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0004
                                   HHHHHHHHHHHHHCH....TEEEEEEESTTSSHHHHHHHHHHHTT CS
                           TsaE  4 eeetealgkklakal....gdvilLeGdLGaGKTtlvrglakalg 44
                                    e++++l+ +la al     + ++++G  G+GKT+ ++ +++ l 
  gi|119719499|ref|YP_919994.1| 35 DEQIKRLALTLAPALsgsrPSNVFIYGLTGTGKTAVTKYVLRRLA 79
                                   6788999999999887654456******************99885 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00043      0.26       4      79 ..      56     151 ..      53     166 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00043
                         AAA_24   4 kiliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdie.........................swedfldevve 58 
                                    +++iyG  g+GKT + k      l    ekG  +++   +++ +                         ++ ++++ +++
  gi|119719499|ref|YP_919994.1|  56 NVFIYGLTGTGKTAVTKYV----LRRLAEKGGGRIEYVYINC-RqnntsyrvlaelgkflgvkipftglALGEVMKRITQ 130
                                    799***********99999....5566799999999998874.4488988888888899999999999999999999999 PP

                         AAA_24  59 laaeladyktlviDtidelee 79 
                                      + ++++ ++v+D +d l++
  gi|119719499|ref|YP_919994.1| 131 ALDRKHRILIVVLDEVDNLVK 151
                                    9****************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       836  (0.0466284); expected 358.6 (0.02)
Passed bias filter:                      673  (0.037537); expected 358.6 (0.02)
Passed Vit filter:                       106  (0.00591221); expected 17.9 (0.001)
Passed Fwd filter:                        29  (0.00161749); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              29  [number of targets reported over threshold]
# CPU time: 0.65u 0.27s 00:00:00.92 Elapsed: 00:00:00.44
# Mc/sec: 2712.86
//
Query:       gi|119719500|ref|YP_919995.1|  [L=386]
Description: tryptophanyl-tRNA synthetase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.3e-31  108.3   0.0    5.3e-31  108.0   0.0    1.1  1  tRNA-synt_1b  tRNA synthetases class I (W and Y)
  ------ inclusion threshold ------
       0.11   12.7   0.2       0.19   11.9   0.2    1.3  1  FYVE          FYVE zinc finger


Domain annotation for each model (and alignments):
>> tRNA-synt_1b  tRNA synthetases class I (W and Y)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.0   0.0   5.9e-35   5.3e-31       6     293 .]      78     353 ..      73     353 .. 0.93

  Alignments for each domain:
  == domain 1  score: 108.0 bits;  conditional E-value: 5.9e-35
                                    -EEEEEEETSSS.-BGGGHHHHHHHHHHHH.TTSEEEEEEEHHHHHTTTTT-SSHHHHHHHHHHHHHHHHHHHHHTCHTT CS
                   tRNA-synt_1b   6 lrvysGidPTgk.lHlGylvplkklvelqk.aghevffliaDlhAiigdpskaeerklrkreevlenaikaqlakgldpe 83 
                                    + +y+G +P+ + +H++++vp+   +++q+  g +v++ i D + ++ ++     ++l++ e++++  i +++a g+d +
  gi|119719500|ref|YP_919995.1|  78 FFLYTGRAPSNSpMHIAHIVPFIATRWFQEkFGANVYIQIPDEEKFLAKKV----ETLEEIEKYAVQDILNIIALGFDEN 153
                                    668********99****************9779***********9999998....8888888888888999********* PP

                                    TEEEEETHHHHTTH.HHHHHHHHHHTTCBHHHHHHHHHCCHHCSSSC--BHHHHHHHHHHHHHHHHTCHS.EEEEEGGGH CS
                   tRNA-synt_1b  84 kaevvlqsewlehl.elaellrdlgklgslnrmlqfksvkkrleegegislgeftYplLqaaDilllkad.lvpgGsDQk 161
                                    k+ ++  +e++++l + a l+++  ++ + + +  f+      e+    ++g++ Yp Lq    ++ k++ l p G DQ+
  gi|119719500|ref|YP_919995.1| 154 KTFIFRDTEYISKLyKPAVLVARHINFSTARAVFGFDN-----ES----TIGLIFYPALQIVPTFFEKKRpLIPCGIDQD 224
                                    *************98999999*****99999999**99.....45....69*************9999999********* PP

                                    HHHHHHHHHHHHHHHHSTTSS-EEEEET-BBSTTSSS.BTTCETTCGC-BTTCCHHHHHHHHHHCHCSTTC..SHHHHHH CS
                   tRNA-synt_1b 162 qnielgrdlarrfnkkevfkkpegltvplltgldGek.KmSKSagnsaIfLddekesvkkkiqkavtdsde..evekllk 238
                                      ++l rd+a+r+n+     k   ++ +l+ gl+G + KmS S++ +aI L+d +e+vk ki +a+t  ++  e ++ l 
  gi|119719500|ref|YP_919995.1| 225 PYFRLQRDIAPRLNRY----KAAEVLSKLVWGLKGPEtKMSASEPDTAILLSDPPETVKRKIINAYTGGRAtvEEQRRLG 300
                                    ***************9....888888898888887666*********************************8899999** PP

                                    HHHTHHHCHHHHHHHHCCSEEESSHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH CS
                   tRNA-synt_1b 239 lktelsnelierleavsgkkpkreaeellaeevtklvhggdlkkalaealnelle 293
                                    + +e++  ++  ++ + + ++ +++ e + +++t+++ +g++k +l e +n++le
  gi|119719500|ref|YP_919995.1| 301 GVPEVCT-VFHWYSVLFEDDD-KKLLERYHACRTGKLLCGECKAELVERINSFLE 353
                                    *******.9999999888888.88888889*********************9985 PP

>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   2.1e-05      0.19      21      58 ..     323     359 ..     309     365 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.1e-05
                                    SSS--EE-TTT--EE-STTS-EEE.EEGGGTEEEEEEE CS
                           FYVE  21 llrrrhhCrlCGkvvCekCssklvallekeaeeksvrv 58 
                                    ll+r h Cr+ Gk++C +C  +lv+ +++  e+++ rv
  gi|119719500|ref|YP_919995.1| 323 LLERYHACRT-GKLLCGECKAELVERINSFLERHRARV 359
                                    678999***8.**************9999888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2678.26
//
Query:       gi|119719501|ref|YP_919996.1|  [L=824]
Description: phosphoenolpyruvate synthase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.2e-121  406.0   0.0   1.8e-121  405.4   0.0    1.3  1  PPDK_N           Pyruvate phosphate dikinase, PEP/pyruvate bi
    7.9e-74  248.4   0.0    1.2e-73  247.8   0.0    1.2  1  PEP-utilizers_C  PEP-utilising enzyme, TIM barrel domain
    3.6e-25   87.5   1.4    8.2e-25   86.3   0.8    2.0  2  PEP-utilizers    PEP-utilising enzyme, mobile domain
     0.0041   17.3   0.0        4.2    7.6   0.0    3.2  3  PEP-utilisers_N  PEP-utilising enzyme, N-terminal
  ------ inclusion threshold ------
      0.096   13.1   0.4        1.3    9.3   0.0    3.1  4  Radical_SAM      Radical SAM superfamily


Domain annotation for each model (and alignments):
>> PPDK_N  Pyruvate phosphate dikinase, PEP/pyruvate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  405.4   0.0  5.1e-125  1.8e-121       2     321 ..      21     343 ..      20     349 .. 0.96

  Alignments for each domain:
  == domain 1  score: 405.4 bits;  conditional E-value: 5.1e-125
                         PPDK_N   2 elvGGKganLaellneagipvPpgfaitadafrefleengleekideelkeldvdd....vdelrkaskeirelilsael 77 
                                    ++vGGK+anL+e+ln agipvPpgfa+ta+a+++f+ee+g+++ki e++++  v +     +++ +askeir+li s+++
  gi|119719501|ref|YP_919996.1|  21 PIVGGKNANLGEMLN-AGIPVPPGFAVTAYAYKRFIEETGIRDKIYEIIRT-RVGKgaakPEDYMEASKEIRALIESVPM 98 
                                    68***********77.*********************************97.5543333399****************** PP

                         PPDK_N  78 PeeleeaikeayeelgkkfgdeelpvaVRSSataEDlpkasfaGqqdtyLnvggeeevleaikavfaSlfnerAilYrke 157
                                    P+++ee+i++ay+el++++g++e+ vaVRSSataEDlp+asfaGqq+tyLnv+ge+ev+e+++++++Slf++rAi+Yr++
  gi|119719501|ref|YP_919996.1|  99 PKDIEEEIRRAYRELCRRVGKKEEFVAVRSSATAEDLPDASFAGQQETYLNVKGEDEVIEKVRKCWSSLFTPRAIFYRES 178
                                    ******************************************************************************** PP

                         PPDK_N 158 kgldheevalavvvqkmvnsdlgasGVafsldpetGfkdevlinasyGlGeaVVaGrvtpdefvvekstrkilekkigek 237
                                    kg+ he+v ++v vqkmvns+   +GV+f+l+p tG++d+++i+  +GlGeaVV+G+vtpde +v+k+t ki+ ++i ek
  gi|119719501|ref|YP_919996.1| 179 KGFAHEKVLISVAVQKMVNSR--TAGVMFTLHPVTGDRDKIVIEGHWGLGEAVVSGKVTPDEWIVDKKTMKIIARNIVEK 256
                                    *********************..********************************************************* PP

                         PPDK_N 238 eikivydekeegtkevevpeeereklaLsdeeveeLaeiakkiekhygtpmdiEfaid...eeegklyllQaRpetrtse 314
                                    ++++v+d+ + +t+e e++ e+r++++L+deev +Lae+a kie+hyg+pmdiE+a+d   +  ++++++QaRpet++s+
  gi|119719501|ref|YP_919996.1| 257 RVELVRDPVTGRTVEREIEPERRNAPSLTDEEVLRLAELAVKIENHYGRPMDIEWAVDrdlKFPESVFIVQARPETVWSR 336
                                    *********988******999*************************************9999999*************** PP

                         PPDK_N 315 kkekkaa 321
                                    k+++ + 
  gi|119719501|ref|YP_919996.1| 337 KEAQPTG 343
                                    9987665 PP

>> PEP-utilizers_C  PEP-utilising enzyme, TIM barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  247.8   0.0   3.3e-77   1.2e-73      13     293 ..     482     783 ..     469     784 .. 0.93

  Alignments for each domain:
  == domain 1  score: 247.8 bits;  conditional E-value: 3.3e-77
                                    CHCCCXBCEEEEEESSCHHHHHHHHCTXSSEEEEEHHHHCTTS..CCHHHHHH..........HHHHHHHHHHHTTTSEE CS
                PEP-utilizers_C  13 vtkdgkkikvlaNidtpedaekalengaeGiGLlRtEflfmar..eelpteee..........qaeaykkvleamngrpv 80 
                                    v k+++++k+++N++ pe+++ +++ +++GiGL+R Ef++ +   e++ ++ e           ae ++ v++ +++rpv
  gi|119719501|ref|YP_919996.1| 482 VWKPITATKIYMNLGVPEKIKDYKDLPFDGIGLMRVEFIMASYvgEHPLYLLEsgrgdvlvnkMAEGIALVAREIYPRPV 561
                                    567899********************************9998875558888888********99**************** PP

                                    EEEXXXSSCC..GGSGGC.HHHH.XSXGGGSSXTHHHHCCS..HHHHHHHHHHHHHHCCCC...EEEEEESSXXSHHHHH CS
                PEP-utilizers_C  81 vvRtlDiggd..kelpel.keepeevNPmlGfRgirlglse..pelfetqlrAllrasaag...kleimlPmvasveele 152
                                    vvR+ D++++  ++l+ + k+ep+e NPmlG+Rg+++++s   ++ f+ +++A++++++++   ++++m P+v++++e e
  gi|119719501|ref|YP_919996.1| 562 VVRFSDFKTNeyRQLKGGeKYEPQEDNPMLGWRGVSRYISPqyEKAFRLEVKAIKKVREEMglgNVWVMAPFVRTLWEAE 641
                                    *********9889***985679*****************87669***************65566**************** PP

                                    HHHHHHHHHHHHHHHCTCTXXTTXEEEEEEXSHHHHHTHHHHCTTSSEEEEXHHHHHHHHHTXXCCCHCHHHH....SXT CS
                PEP-utilizers_C 153 eakkiieevkeelekegvkkkkkvkvGiMiEvpsaalladklakevdFfSiGtNDLtQytlavdRdneevakl....ydp 228
                                    + +k+++e+       g++ ++++kv++M Evps+++la+++ ++ d+fSiG+NDLtQ+tl+ dRd++ + k+    +d+
  gi|119719501|ref|YP_919996.1| 642 KFVKLLAEE-------GLESSRDFKVWAMAEVPSIIFLAEEFSRYFDGFSIGSNDLTQLTLGTDRDSAILPKIdpryFDE 714
                                    *****9998.......88899************************************************99999999*** PP

                                    TTCHHCCCHHHHHHHHHHCC...XEEEEESCCCC.SCCCHHHHHHCTXSEEEEXGGGHHHHHHHHHCTT CS
                PEP-utilizers_C 229 lepavlrlikevikaaeekg...lkvgiCGelag.dpsavellvglGldelSmsaasvpaaraalaqve 293
                                     +pav+ +i+++i++a++      +v+iCG++++ +p  +e+lv+ G+d++S++++ v+++r+++a++e
  gi|119719501|ref|YP_919996.1| 715 RDPAVRTAIAMLIEKAHKSPygyRTVSICGQAPSvYPDFTEFLVRQGIDSISVNPDVVAKTRELVASIE 783
                                    ******************988899**********9******************************9986 PP

>> PEP-utilizers  PEP-utilising enzyme, mobile domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.3   0.8   2.3e-28   8.2e-25       2      73 .]     383     454 ..     382     454 .. 0.97
   2 ?   -3.6   0.0       2.8   9.9e+03      39      52 ..     550     564 ..     546     571 .. 0.60

  Alignments for each domain:
  == domain 1  score: 86.3 bits;  conditional E-value: 2.3e-28
                                    --S-EEEEES---HHHHTTS-GEEEEEES--TTHHHHHHHHHHTT--EEE--SSHH.HH--TEEEEEETTTT CS
                  PEP-utilizers   2 leegvILvaeetspsdiagldkaaGivterGGmtSHaAivArelgiPaVvgvgeatielkegdlitvDgstG 73 
                                    +++g+ILv+++t+p++++ ++ aa+ivt++GGmt HaAiv+relgiP++vg++eat++l++g+  tvD++ G
  gi|119719501|ref|YP_919996.1| 383 MQPGDILVTTMTDPDWVPYMKMAAAIVTDEGGMTAHAAIVGRELGIPVIVGTREATKVLVDGKDYTVDARAG 454
                                    789******************************************************************988 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2.8
                                    HHHHHH.TT--EEE- CS
                  PEP-utilizers  39 AivAre.lgiPaVvg 52 
                                    A+vAre +  P+Vv 
  gi|119719501|ref|YP_919996.1| 550 ALVAREiYPRPVVVR 564
                                    666666234566655 PP

>> PEP-utilisers_N  PEP-utilising enzyme, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.78   2.8e+03      41      41 ..      77      77 ..      36     116 .. 0.42
   2 !    5.6   0.0    0.0047        17      60     112 ..     251     303 ..     233     305 .. 0.86
   3 !    7.6   0.0    0.0012       4.2       1      16 [.     357     377 ..     357     405 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.78
                                   H CS
                PEP-utilisers_N 41 e 41
                                   +
  gi|119719501|ref|YP_919996.1| 77 A 77
                                   1 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0047
                                    HHHHHHHHHHHT-HHHHHHHHHHHHHHT--HHHHHHHHHHHHHHHHHHTT-HH CS
                PEP-utilisers_N  60 aaifeahlmlleDpelleeveerIregglnaeaAveevveefaaqfealddey 112
                                    ++i+e   +l++Dp   + ve++I+ ++ na +  +e v ++a+   +++++y
  gi|119719501|ref|YP_919996.1| 251 RNIVEKRVELVRDPVTGRTVEREIEPERRNAPSLTDEEVLRLAELAVKIENHY 303
                                    46999999*****************************9999999988888877 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0012
                                    E-EEEE-SEEEEEEE.....- CS
                PEP-utilisers_N   1 kGiaaspGiaiGkav.....e 16 
                                    kG++aspG+a+Gka      e
  gi|119719501|ref|YP_919996.1| 357 KGLPASPGVAYGKAKiclslE 377
                                    79************9777441 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.92   3.3e+03     128     143 ..      80      94 ..      44     162 .. 0.64
   2 ?   -1.8   0.0         1   3.7e+03      67     107 ..     464     514 ..     455     515 .. 0.67
   3 ?   -2.5   0.0       1.6   5.8e+03      36      73 ..     613     650 ..     602     661 .. 0.74
   4 ?    9.3   0.0   0.00037       1.3      34     123 ..     723     807 ..     710     818 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.92
                                    HHHHHHHHHHHHTTSE CS
                                    xxxxxxxxxxxxxxxx RF
                    Radical_SAM 128 eevlealeklreagik 143
                                    e+++ea + +r++ i+
  gi|119719501|ref|YP_919996.1|  80 EDYMEASKEIRAL-IE 94 
                                    4444444444444.33 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1
                                    HHHHHHTC............CCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEE CS
                                    xxxxxxxx............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  67 lerlakla............vpgiritvetngtlpdeeklerllelgvdrvsl 107
                                    l+ ++k++            +p   + +  n ++  +ek++  ++l++d + l
  gi|119719501|ref|YP_919996.1| 464 LLGAKKEEkavaaapieivwKPITATKIYMNLGV--PEKIKDYKDLPFDGIGL 514
                                    4444444455444455577777777777777777..79999999999888765 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 1.6
                                    HHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  36 eevkelkaekgvkevilgggepllypdfvellerlakl 73 
                                    + +k++++e+g ++v+++   +   ++ +++++ la++
  gi|119719501|ref|YP_919996.1| 613 KAIKKVREEMGLGNVWVMAPFVRTLWEAEKFVKLLAEE 650
                                    55667777888888888777777777777777777665 PP

  == domain 4  score: 9.3 bits;  conditional E-value: 0.00037
                                    HHHHHHHHH.HHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSS CS
                                    xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  34 ileevkelk.aekgvkevilgggepllypdfvellerlaklavpgiritvetngtlpdeeklerllelgvdrvslgleaa 112
                                    i+ ++++++    g ++v + g+ p++ypdf+e+l r         +i+v    +  ++e ++ + ++ +   slg+e +
  gi|119719501|ref|YP_919996.1| 723 IAMLIEKAHkSPYGYRTVSICGQAPSVYPDFTEFLVRQGID-----SISVNPDVVAKTRELVASIERRVILERSLGIERY 797
                                    566777887444459999999**********9999999887.....4555555555448888999888888889999999 PP

                                    SHHHHHHHHTC CS
                                    xxxxxxxxxxx RF
                    Radical_SAM 113 ddekvlklmnr 123
                                    d++    +m+r
  gi|119719501|ref|YP_919996.1| 798 DED-LGWPMRR 807
                                    998.8888864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (824 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.66u 0.29s 00:00:00.95 Elapsed: 00:00:00.43
# Mc/sec: 5778.63
//
Query:       gi|119719502|ref|YP_919997.1|  [L=182]
Description: hydrogenase maturation protease [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.9e-05   22.7   0.0    0.00013   21.8   0.0    1.4  1  HycI      Hydrogenase maturation protease


Domain annotation for each model (and alignments):
>> HycI  Hydrogenase maturation protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   7.2e-09   0.00013      28     124 ..      46     148 ..      37     154 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 7.2e-09
                                    GGHHHHCC-SEEEEEEE--S.SS-TT-E.......EEEECCHHHHHHTTC.CGCCCHCHHHHHHHHHHCCS--SEEEEEE CS
                           HycI  28 elvgtleeadkliivDavdf.glepGev.......kiikddevpkklkakkmsaHqlplaevlklleekgeipkevillg 99 
                                      v +le  d li +D+vd   +epG v       +++  +ev    +++  saHq+  a+++ l    g ++ e+ ++g
  gi|119719502|ref|YP_919997.1|  46 TAVSHLEGVDLLIFIDVVDKsFGEPGDVvvlridpRTLSPEEVATAISFE-TSAHQVTPAHIVLLGYSSGFFRGEAYVVG 124
                                    56899999***********9889*****3333333345678***988888.***************************** PP

                                    E--S-BST.CCS--HHHHCCHHHHH CS
                           HycI 100 vqpesledvgielseevkkavekav 124
                                    v +e +++   ++s+ v +a e+a 
  gi|119719502|ref|YP_919997.1| 125 VVSEHTDF-ARKMSSRVVAAAERAC 148
                                    ********.999**99999999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1237.07
//
Query:       gi|119719503|ref|YP_919998.1|  [L=232]
Description: hypothetical protein Tpen_0590 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      0.006   16.5   0.0      0.006   16.5   0.0    2.0  2  RHH_1     Ribbon-helix-helix protein, copG family


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.5      0.45   8.1e+03      29      36 ..      10      17 ..       8      18 .. 0.71
   2 !   16.5   0.0   3.3e-07     0.006       2      36 ..      38      73 ..      37      75 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.45
                                   HHHHHHHH CS
                          RHH_1 29 IReAlrey 36
                                   +R+++r+y
  gi|119719503|ref|YP_919998.1| 10 LRRLARAY 17
                                   57788777 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 3.3e-07
                                   EEEEEEHHHHHHHHHHHHHHT.SSHHHHHHHHHHHH CS
                          RHH_1  2 vsirldeellerLdelarrrg.rSrSelIReAlrey 36
                                   + ++l++++ e +de+ar+++    ++++R++l+e 
  gi|119719503|ref|YP_919998.1| 38 IVFTLPKKEEESIDEIARKLEeAGHGDFVRALLAEK 73
                                   5689****************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1682.68
//
Query:       gi|119719504|ref|YP_919999.1|  [L=423]
Description: hydrogenase (NiFe) small subunit HydA [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-23   82.9   1.9    2.7e-23   82.1   1.9    1.4  1  NiFe_hyd_SSU_C  NiFe/NiFeSe hydrogenase small subunit C-termi
    2.3e-14   53.3   0.0    6.9e-14   51.8   0.0    1.8  2  Oxidored_q6     NADH ubiquinone oxidoreductase, 20 Kd subunit
    3.8e-05   23.4   0.3    3.8e-05   23.4   0.3    3.7  4  TAT_signal      TAT (twin-arginine translocation) pathway sig


Domain annotation for each model (and alignments):
>> NiFe_hyd_SSU_C  NiFe/NiFeSe hydrogenase small subunit C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.1   1.9   4.5e-27   2.7e-23       1      80 []     291     371 ..     291     371 .. 0.98

  Alignments for each domain:
  == domain 1  score: 82.1 bits;  conditional E-value: 4.5e-27
                                    HSSBCGGC-TTHHHHHHT-B-SSTTSH.TSBSGGGT--GGG-BSSTTTC-BTTTTB-TTTTTS----TTSTTGGGGSSST CS
                 NiFe_hyd_SSU_C   1 ygktihdnCerreyfdagefaeefgde.egClyklGCkGpvtyadcpkrkwnegvswpvkagapCigCtepgfpdkkspf 79 
                                    +g+t+h++C+r++ + ag+f   +g++   Cly +GCkGp++++ ++k  w +gv  p+++g +CigCt+pgf+d+++pf
  gi|119719504|ref|YP_919999.1| 291 FGNTVHEQCPRAGSYAAGDFRAYPGENsYRCLYAVGCKGPISNCPWNKLGWVNGVGGPTRTGGVCIGCTMPGFTDAYEPF 370
                                    899***********************9899*************************************************9 PP

                                    T CS
                 NiFe_hyd_SSU_C  80 y 80 
                                    y
  gi|119719504|ref|YP_919999.1| 371 Y 371
                                    7 PP

>> Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.8   0.0   1.2e-17   6.9e-14       1     130 [.      54     267 ..      54     268 .. 0.88
   2 ?   -3.1   0.0       1.1   6.4e+03       1      17 [.     355     372 ..     355     378 .. 0.78

  Alignments for each domain:
  == domain 1  score: 51.8 bits;  conditional E-value: 1.2e-17
                                    -SHHHHHH.T-TTTTHHHHH.HTEE........EEEETTT-S--HHH......HHHTHTTTSEEEEEESBE...E..... CS
                    Oxidored_q6   1 CtGcsisl.laleedlldll.elie........lryhetlladskee......eieakekeadvlvveGavtrkp..... 59 
                                    C+G++ +l +a+e+dl+d+l + ++        l++het++ + +e       ++++++ + +vlv+eG+ +++      
  gi|119719504|ref|YP_919999.1|  54 CAGNTTALiQATEPDLIDVLgGSFHlvgpgnvkLAFHETVMPEWGEGalsiarAAAQGKLDPFVLVLEGSFPQDEkaggp 133
                                    ********************9888889999999**********9988*****98999999***********7777***** PP

                                    ................EEHHHHHHHHGGGSSEEEEESHHHHH-TGGGSTT-T.EE......................... CS
                    Oxidored_q6  60 ................kealellkelaekakaviavGtCAafGGipaaannp.sv......................... 97 
                                                     + +e++++l ++a av+ +G+CA++GG+ a +  + ++                         
  gi|119719504|ref|YP_919999.1| 134 pgsdsycyigdengkvISCVEWMRRLLPRAVAVVTMGNCASYGGLVANK--VlERvpglpssswsdsptgavgffddpir 211
                                    **********************************************544..33445899999***************999 PP

                                    .......................-HHHHHHHC..S-E.EEE-SSS--HHHHHHHHHH CS
                    Oxidored_q6  98 .......................geevgellev.vpvdinipGCPphpeailetlla 130
                                                           + + ge+  +  p  + +pGCP++ +  l++l+a
  gi|119719504|ref|YP_919999.1| 212 gikglvstlpeaepfrrfitgqcTLKPGEIRPDcRPA-MAVPGCPANGNGQLRALAA 267
                                    9999988888877777776654425556666665666.*********9999888877 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.1
                                    -SHHHHHH.T-TTTTHHH CS
                    Oxidored_q6   1 CtGcsisl.laleedlld 17 
                                    C Gc++   ++++e++++
  gi|119719504|ref|YP_919999.1| 355 CIGCTMPGfTDAYEPFYK 372
                                    99***9866888888776 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.3   6.3e-09   3.8e-05       1      20 [.       7      26 ..       7      27 .. 0.92
   2 ?   -2.6   0.4      0.99   5.9e+03      15      25 ..     164     174 ..     163     174 .. 0.73
   3 ?   -1.4   0.3      0.42   2.5e+03      17      25 ..     248     256 ..     248     257 .. 0.84
   4 ?   -0.6   4.8      0.23   1.3e+03      12      25 ..     385     398 ..     383     399 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 6.3e-09
                     TAT_signal  1 klSRRdFLKgsAAaaAAaal 20
                                   ++SRRdFLK +++aa +a l
  gi|119719504|ref|YP_919999.1|  7 SISRRDFLKMGGVAALLASL 26
                                   59*************99976 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.99
                     TAT_signal  15 aAAaalggcaa 25 
                                     A +++g+ca+
  gi|119719504|ref|YP_919999.1| 164 VAVVTMGNCAS 174
                                    47888999985 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.42
                     TAT_signal  17 Aaalggcaa 25 
                                    A+a++gc a
  gi|119719504|ref|YP_919999.1| 248 AMAVPGCPA 256
                                    789****86 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 0.23
                     TAT_signal  12 AAaaAAaalggcaa 25 
                                    ++aa Aa+l+g+++
  gi|119719504|ref|YP_919999.1| 385 GVAAIAALLAGVGL 398
                                    78999999**9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 3054.53
//
Query:       gi|119719505|ref|YP_920000.1|  [L=596]
Description: nickel-dependent hydrogenase, large subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.2e-56  190.9   0.0    1.4e-36  126.5   0.0    2.6  2  NiFeSe_Hases  Nickel-dependent hydrogenase


Domain annotation for each model (and alignments):
>> NiFeSe_Hases  Nickel-dependent hydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.6   0.0   3.7e-21   6.6e-17       1      80 [.      42     122 ..      42     141 .. 0.92
   2 !  126.5   0.0   7.9e-41   1.4e-36     160     505 .]     174     581 ..     166     581 .. 0.73

  Alignments for each domain:
  == domain 1  score: 61.6 bits;  conditional E-value: 3.7e-21
                                    --HHHHTTTS-GGGHHHHHHTT-SSSTTHHHHHHHHHHHHHHT----HHHHHHHHHHH.HHHHHHHHHHHHHHTTGGGTS CS
                   NiFeSe_Hases   1 RGlElilkgrdprdawalvqRiCGVCttvHalasvravedAlgikipknarlirnlia.aalllhdhivhFYhLhalDwv 79 
                                    RG+E++l+gr p+da ++++RiCGVC  +Ha as++av+ A+g+ +   + ++rn+   ++ +l dh + +  L + D+ 
  gi|119719505|ref|YP_920000.1|  42 RGFEVFLRGRPPEDAVHITSRICGVCGASHANASAHAVDMAYGVAPEPLGVVLRNMAFaMTDALYDHPLILNMLGGPDYS 121
                                    9*******************************************************75156789*****99999999997 PP

                                    - CS
                   NiFeSe_Hases  80 d 80 
                                    +
  gi|119719505|ref|YP_920000.1| 122 E 122
                                    6 PP

  == domain 2  score: 126.5 bits;  conditional E-value: 7.9e-41
                                    HHHHTHHHHHHHSSSSS--.EBTTBESSGBGSBSHHHH.HHHHHHHHHHHHHHHHTH..HHHHHHHHHHTGGGGCS--GG CS
                   NiFeSe_Hases 160 qrkaakivaifggknPhpqslvvGGvtcaidllnaerl.aevkslikevkefveevy..lpDvlaiakaYkdwakigkgl 236
                                     r a ++  ++ g++ hp++l+ GG+++   l+nae l   ++  +++++++ +  y  ++D++ + +  + +++ g + 
  gi|119719505|ref|YP_920000.1| 174 SRIAREAGVLIYGRHSHPSTLIPGGISTD--LTNAEYLlIGYTYRLTKLTAWAKFLYavWQDIVWFYEERHGYKEQGLTY 251
                                    5666677778889*************998..5566654156777788888888877622579988888777788888888 PP

                                    GGT-EEEEEEEESSTT-.STT...GGE...........EEEEEEESTTETT..SEBEE-TTTEEEE-TTSSBS.TS-B-G CS
                   NiFeSe_Hases 237 gkknflsvgefpeekse.elk...esl...........llpsGvilngdls..kveevdeekitEevkhswYk.ekslhp 298
                                    + +n++s g f++ ++   l+   e++           +++ G+ +ng+l   +++e+ + +i E+v++s Y+  k++ p
  gi|119719505|ref|YP_920000.1| 252 RRHNMVSGGLFDDPEAYsALNgspEDFyknvdsamskrTIKPGAFVNGELVtkSYKEI-NLSIMEHVERSLYEdWKGKLP 330
                                    9999999999955444322222233337777888888899999999999963344555.568***********6566889 PP

                                    GG---EB---...................EEE--T......TSB-BSS-EEEE..TTB...--BESHHHHHHHHHHT.T- CS
                   NiFeSe_Hases 299 legetepkyt...................leelde......egkYswikaPry..kgk...amevGplarvlvayak.gk 347
                                    + +e++p+ +                        +      +gkY w    r+  k+    ++evGp+ar+ v+  + ++
  gi|119719505|ref|YP_920000.1| 331 IYTEKDPEGNpllwgkydvayhpwnkttiP----KpgapdwNGKYNWATHVRFvwKDGtitPFEVGPIARLTVTAYQpSD 406
                                    999999987788888888987666554440....15555559*******99973333234489*******9887655222 PP

                                    HHH...........HHHHHHHHHHHT................-HGGGGSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   NiFeSe_Hases 348 eev...........kelvdkllkklg................lkvealfstlGRtaaRaleakliaellkewldelveni 400
                                                  +          g                 ++    +tl R +aRa++    + ++ + + + ve +
  gi|119719505|ref|YP_920000.1| 407 FGSgngilrvdlprS----------GgaddlppsvveemtleWRAPPHSTTLQRVLARAFNVVADVAAAWSNVVKAVELV 476
                                    222322223333330..........23445555555555544344446799********998777777777777888889 PP

                                    HTTB---B--TT-SGGGS-SEEEEEEEEEETTEEEEEEEEEETTEEEEEEEE-HHHHHH--S-TT----HHHHHHTT-B- CS
                   NiFeSe_Hases 401 kkgdtetaneekldkkevpkeakGvglveapRGaLsHwikikdgkienYqavvPsTWnasPrdakgqkgayEaaLigtpv 480
                                    ++g t+t n +    +  p+ + Gvg++eapRG+  Hw++ + g+i nYq+  P+T n+sP+d+ g ++++E+++ +  v
  gi|119719505|ref|YP_920000.1| 477 RSGRTKTSNPW----NPPPRRTFGVGFTEAPRGTVRHWVVQEGGRIVNYQIHAPTTGNVSPKDKWG-MSPFEQSVANSVV 551
                                    99988877776....3446889*****************************************988.79*******9988 PP

                                    SSTTS-.....HHHHHHHHHT--BHHHHH- CS
                   NiFeSe_Hases 481 adpekP.....leilrtihSfDPClACavH 505
                                    +++  P     l+ +r i+SfDPC+ACavH
  gi|119719505|ref|YP_920000.1| 552 TEEVPPdswegLDFVRAIRSFDPCIACAVH 581
                                    76554444444******************* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (596 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 4013.43
//
Query:       gi|119719506|ref|YP_920001.1|  [L=263]
Description: hypothetical protein Tpen_0593 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.16   11.5  13.0       0.32   10.5   2.2    3.2  3  Nitrate_red_gam  Nitrate reductase gamma subunit
        3.1    7.3  15.3        0.3   10.7   3.3    3.0  3  Ni_hydr_CYTB     Prokaryotic cytochrome b561


Domain annotation for each model (and alignments):
>> Nitrate_red_gam  Nitrate reductase gamma subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.2    0.0097        87       3      33 ..       7      36 ..       5      47 .. 0.81
   2 ?    4.8   0.3     0.002        18      67     142 ..     129     205 ..     122     215 .. 0.77
   3 ?   10.5   2.2   3.6e-05      0.32     175     202 ..     215     242 ..     209     249 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.0097
                Nitrate_red_gam  3 llfvvlPYvalavlvvgsllryrydqftwts 33
                                    ++v+ PYv+ + l +g ++r ++  f w+ 
  gi|119719506|ref|YP_920001.1|  7 AIYVLPPYVVAT-LAFGVAYRLSRYLFLWKR 36
                                   578889998765.678999**9999999985 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.002
                Nitrate_red_gam  67 liPksvtealgvseelyqllalvaGliagvlalvGlllLllRRltnkrvr.aatsasDkvvlllLllqillGllttl 142
                                    ++P s + ++ +++    l+ ++ G ++++la++G+ + l  +l++   r ++ +a D++ l+lLl  +++G+l+t 
  gi|119719506|ref|YP_920001.1| 129 VLPASEMGWVFTNSVWGPLTLILNGDLLAILAIIGVSYKLGDKLVRLYHRlRHVRAGDFFDLALLLSILVTGFLATH 205
                                    56666666666666666677789999**********999988877654441467889***************99886 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 3.6e-05
                Nitrate_red_gam 175 vplifklHvllglllfalfPFtrLvHvl 202
                                      ++  lH+ll+ ll+al+PFt++ H +
  gi|119719506|ref|YP_920001.1| 215 YRFMLGLHILLAELLVALLPFTKFWHFV 242
                                    5677889*****************9986 PP

>> Ni_hydr_CYTB  Prokaryotic cytochrome b561
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   4.0     0.039   3.5e+02      55     111 ..      17      59 ..       6     110 .. 0.79
   2 ?    0.2   1.4     0.055   4.9e+02      41      63 ..      70      98 ..      39     141 .. 0.62
   3 ?   10.7   3.3   3.4e-05       0.3      16      64 ..     192     240 ..     189     260 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.039
                                    HHHHHHHHHH------------STTTSSSSS----------------TTTHHHHHHH CS
                   Ni_hydr_CYTB  55 alllfrllwlkkakkpspriifrqikrdltlllrgrkpeagknnplqklvhlllyvl 111
                                    a+l+f +++              ++ r+l+l++rg  ++++  ++++ lv+l++ +l
  gi|119719506|ref|YP_920001.1|  17 ATLAFGVAY--------------RLSRYLFLWKRGYSAPRRARPIGKLLVGLVVTFL 59 
                                    333444444..............4889999999999999999999999988877766 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.055
                                   -......HHHHHHHHHHHHHHHHHHHHHH CS
                   Ni_hydr_CYTB 41 k......aralHklaGlvllalllfrllw 63
                                   k      ++alH+l  + l++ll   +++
  gi|119719506|ref|YP_920001.1| 70 KsdfvggLIALHILGVIPLIFLLSQHVAM 98
                                   23334445555555444444444333333 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 3.4e-05
                                    HHHHHHHHHHHHHS------S-GGG-HHHHHHHHHHHHHHHHHHHHHHH CS
                   Ni_hydr_CYTB  16 lvvllllsgllianlhprlywgdsgkaralHklaGlvllalllfrllwl 64 
                                    l + +l++g+l ++  p++ +++  +++ lH+l++ +l+all f  +w 
  gi|119719506|ref|YP_920001.1| 192 LLLSILVTGFLATHHLPSPDVTTYRFMLGLHILLAELLVALLPFTKFWH 240
                                    5667888***************9999****************9888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1923.91
//
Query:       gi|119719507|ref|YP_920002.1|  [L=446]
Description: 4Fe-4S ferredoxin iron-sulfur binding domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.5e-08   32.3   2.6     0.0059   16.8   0.0    3.2  3  CCG       Cysteine-rich domain
      3e-07   30.8  12.4    3.3e-06   27.4   5.5    2.5  3  Fer4_8    4Fe-4S dicluster domain
    5.1e-06   26.9   7.7    0.00034   21.1   7.8    3.0  3  Fer4_17   4Fe-4S dicluster domain
    7.5e-06   26.0   3.6      0.021   14.9   0.1    3.1  3  Fer4_10   4Fe-4S dicluster domain
     0.0002   21.5   8.9      0.018   15.2   9.4    3.0  4  Fer4_9    4Fe-4S dicluster domain
    0.00036   21.1  11.3    0.00064   20.3   8.4    2.6  3  Fer4_7    4Fe-4S dicluster domain
    0.00051   20.1  10.7       0.11   12.7   0.4    3.1  3  Fer4_21   4Fe-4S dicluster domain
    0.00082   19.1  18.5     0.0067   16.2   2.9    3.3  3  Fer4      4Fe-4S binding domain
     0.0014   18.6  18.5       0.03   14.4   1.4    3.1  3  Fer4_6    4Fe-4S binding domain
     0.0016   18.5  14.8      0.019   15.0   1.4    3.2  3  Fer4_2    4Fe-4S binding domain
      0.005   17.2  16.3       0.01   16.3   0.9    3.1  3  Fer4_4    4Fe-4S binding domain
  ------ inclusion threshold ------
       0.15   13.0  10.6        2.7    9.0  11.3    2.4  2  Fer4_16   4Fe-4S double cluster binding domain
       0.47   10.7   4.0        3.5    7.9   0.1    2.7  3  Fer4_18   4Fe-4S dicluster domain
        3.2    8.7   7.1         22    6.0   0.3    3.1  3  Fer4_22   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> CCG  Cysteine-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       7.4   9.5e+03      53      74 ..     234     255 ..     226     259 .. 0.73
   2 !   16.8   0.0   4.6e-06    0.0059       1      47 [.     307     355 ..     307     370 .. 0.91
   3 !   14.3   0.0   2.8e-05     0.036      57      84 ..     394     421 ..     382     422 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 7.4
                            CCG  53 laealakrnvetaeetgadaiv 74 
                                      + +akr ++ +++ ga+++v
  gi|119719507|ref|YP_920002.1| 234 SVRVVAKRIYDYIKSIGAEYVV 255
                                    4556778888889999999998 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 4.6e-06
                            CCG   1 vayfdgChllraa..ypevrkalkkllealgveleel.ekesCCGagggr 47 
                                    ++++ +C+++r     +e+ ++l  + + ++v+l+ +   ++CCG gg  
  gi|119719507|ref|YP_920002.1| 307 ITWHSPCKMGRFGglIEEPVEVLSSI-SQNFVKLKSHgLFSKCCGGGGSI 355
                                    689***********************.9******************9976 PP

  == domain 3  score: 14.3 bits;  conditional E-value: 2.8e-05
                            CCG  57 lakrnvetaeetgadaivtacpgCllql 84 
                                     ++++v++++e ga  +vtac gC  +l
  gi|119719507|ref|YP_920002.1| 394 AGREKVQEIKESGASTVVTACIGCIHTL 421
                                    5799********************8877 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   5.5   2.6e-09   3.3e-06       2      65 .]      30     115 ..      29     115 .. 0.67
   2 !   15.6   0.5   1.3e-05     0.017       3      30 ..      99     126 ..      97     142 .. 0.80
   3 ?   -1.1   0.0       2.1   2.7e+03      45      54 ..     408     417 ..     374     419 .. 0.62

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 2.6e-09
                         Fer4_8   2 lekCieCgaCqsaCp.........vlrrtkkhlldargeaae..................dvqeeqvleeeealwsCttc 54 
                                    le+C+ C +C+ +Cp          +++    ++  rg+++                   +       +  + +++Ct+c
  gi|119719507|ref|YP_920002.1|  30 LENCVSCALCEVNCPytpvgeeygPVSKAEPLRNIYRGKVNIlprlfpwlfgaklpktkeE-----LDKWVDLAYHCTNC 104
                                    589***********86665555553333334444555555557777777777777543221.....22236789****** PP

                         Fer4_8  55 gaCtevCpvgi 65 
                                    g C   Cp gi
  gi|119719507|ref|YP_920002.1| 105 GLCYITCPFGI 115
                                    ********987 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 1.3e-05
                         Fer4_8   3 ekCieCgaCqsaCpvlrrtkkhlldarg 30 
                                    ++C++Cg+C  +Cp+  ++++++++ rg
  gi|119719507|ref|YP_920002.1|  99 YHCTNCGLCYITCPFGIHSGEMIKTLRG 126
                                    6899999999999998888876666555 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 2.1
                         Fer4_8  45 eealwsCttc 54 
                                     + + +C +c
  gi|119719507|ref|YP_920002.1| 408 STVVTACIGC 417
                                    5566666666 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   1.8   0.00011      0.14      41      58 ..      28      45 ..       6      47 .. 0.76
   2 !   21.1   7.8   2.7e-07   0.00034       1      60 [.      32     115 ..      32     116 .. 0.68
   3 ?    0.1   0.0      0.94   1.2e+03      30      49 ..     398     417 ..     374     419 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00011
                        Fer4_17 41 ekaslCieCgeCerkCPq 58
                                   +  ++C++C +Ce  CP+
  gi|119719507|ref|YP_920002.1| 28 HFLENCVSCALCEVNCPY 45
                                   67899************8 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 2.7e-07
                        Fer4_17   1 rCiqCgyClpeCpsyea...ydn.epkkllraakl...................glleeaeke.....ekaslCieCgeC 52 
                                    +C +C+ C+ +Cp+      y+   ++++lr+++                    + +e    e     + a  C++Cg+C
  gi|119719507|ref|YP_920002.1|  32 NCVSCALCEVNCPYTPVgeeYGPvSKAEPLRNIYRgkvnilprlfpwlfgaklpKTKE----EldkwvDLAYHCTNCGLC 107
                                    6************955522233323445666555445566888888888865543233....23335589********** PP

                        Fer4_17  53 erkCPqgl 60 
                                       CP g+
  gi|119719507|ref|YP_920002.1| 108 YITCPFGI 115
                                    *****987 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.94
                        Fer4_17  30 klglleeaekeekaslCieC 49 
                                    k+++++e  +++++  Ci+C
  gi|119719507|ref|YP_920002.1| 398 KVQEIKESGASTVVTACIGC 417
                                    33444444445899999999 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.3   0.00092       1.2       7      26 ..      31      48 ..      27      70 .. 0.79
   2 !   14.9   0.1   1.7e-05     0.021       8      24 ..     100     116 ..      85     138 .. 0.78
   3 ?    0.5   0.0      0.52   6.6e+02      32      48 ..     401     417 ..     378     422 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00092
                        Fer4_10  7 dtCirCgkCvkaCPadltsv 26
                                   + C+ C+ C   CP+  t v
  gi|119719507|ref|YP_920002.1| 31 ENCVSCALCEVNCPY--TPV 48
                                   579999999999999..444 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 1.7e-05
                        Fer4_10   8 tCirCgkCvkaCPadlt 24 
                                     C++Cg C   CP+ ++
  gi|119719507|ref|YP_920002.1| 100 HCTNCGLCYITCPFGIH 116
                                    69999999999999553 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.52
                        Fer4_10  32 aseeeavrkkvekCtgc 48 
                                    + +e+  +++v +C+gc
  gi|119719507|ref|YP_920002.1| 401 EIKESGASTVVTACIGC 417
                                    44555566788999998 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   1.3   0.00035      0.45      33      48 ..      21      45 ..       4      48 .. 0.67
   2 !   15.2   9.4   1.4e-05     0.018       1      49 [.      32     114 ..      32     116 .. 0.89
   3 !   10.6   1.6   0.00038      0.49       2      17 ..     101     116 ..     100     122 .. 0.69
   4 ?   -0.1   0.0      0.85   1.1e+03      33      39 ..     404     417 ..     376     419 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00035
                         Fer4_9 33 e.........eaCigCgaCveaCpk 48
                                             e+C++C  C+  Cp 
  gi|119719507|ref|YP_920002.1| 21 HltpvslhflENCVSCALCEVNCPY 45
                                   1455666777889999999999996 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 1.4e-05
                         Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase..................................eaCigCgaCveaC 46 
                                    +C++C  C+  Cp++ v e+ ++   +   ++                                     C+ Cg C+  C
  gi|119719507|ref|YP_920002.1|  32 NCVSCALCEVNCPYTPVGEEYGPVSKAEPLRNIyrgkvnilprlfpwlfgaklpktkeeldkwvdlaYHCTNCGLCYITC 111
                                    6***********999998888887776655544888999****************************99*********** PP

                         Fer4_9  47 pkg 49 
                                    p g
  gi|119719507|ref|YP_920002.1| 112 PFG 114
                                    *87 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00038
                         Fer4_9   2 CtgCgaCveaCpagvv 17 
                                    Ct+Cg C   Cp+g++
  gi|119719507|ref|YP_920002.1| 101 CTNCGLCYITCPFGIH 116
                                    7777777777777665 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 0.85
                         Fer4_9  33 e.......eaCigC 39 
                                    e       +aCigC
  gi|119719507|ref|YP_920002.1| 404 EsgastvvTACIGC 417
                                    13344566789998 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   3.4     0.001       1.3      36      50 ..      31      45 ..       9      47 .. 0.72
   2 !   20.3   8.4     5e-07   0.00064       2      52 .]      33     115 ..      32     115 .. 0.61
   3 ?   -2.1   0.1       4.7   6.1e+03       2       5 ..     414     417 ..     395     419 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.001
                         Fer4_7 36 ekClgCgaCvavCPt 50
                                   e+C++C  C+  CP+
  gi|119719507|ref|YP_920002.1| 31 ENCVSCALCEVNCPY 45
                                   667777777777775 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 5e-07
                         Fer4_7   2 CigCgaCvaaCpvkaield..eeenek..............................gtekveidpekClgCgaCvavCP 49 
                                    C+ C  C+++Cp+  +  +  ++++++                              + +k++  +  C++Cg C  +CP
  gi|119719507|ref|YP_920002.1|  33 CVSCALCEVNCPYTPVGEEygPVSKAEplrniyrgkvnilprlfpwlfgaklpktkeELDKWVDLAYHCTNCGLCYITCP 112
                                    ***********866665441122222244455555555555555555544443332233666666778************ PP

                         Fer4_7  50 tga 52 
                                    +g+
  gi|119719507|ref|YP_920002.1| 113 FGI 115
                                    *96 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 4.7
                         Fer4_7   2 CigC 5  
                                    CigC
  gi|119719507|ref|YP_920002.1| 414 CIGC 417
                                    6666 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   1.1   0.00015      0.19      38      52 ..      30      44 ..      13      48 .. 0.81
   2 !   12.7   0.4   8.4e-05      0.11      40      52 ..     100     112 ..      87     121 .. 0.74
   3 ?    0.0   0.1      0.75   9.6e+02      34      44 ..     407     417 ..     394     421 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00015
                        Fer4_21 38 edeCvGCnlCssvCP 52
                                    ++Cv C+lC   CP
  gi|119719507|ref|YP_920002.1| 30 LENCVSCALCEVNCP 44
                                   589*********9*9 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 8.4e-05
                        Fer4_21  40 eCvGCnlCssvCP 52 
                                    +C+ C lC++ CP
  gi|119719507|ref|YP_920002.1| 100 HCTNCGLCYITCP 112
                                    5777777777776 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.75
                        Fer4_21  34 lkvvedeCvGC 44 
                                    + +v   C+GC
  gi|119719507|ref|YP_920002.1| 407 ASTVVTACIGC 417
                                    45556678888 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   1.7   0.00015      0.19       6      20 ..      31      45 ..      28      46 .. 0.93
   2 !   16.2   2.9   5.3e-06    0.0067       8      21 ..     101     114 ..      98     115 .. 0.92
   3 ?    0.3   0.5      0.53   6.8e+02       7      11 ..     413     417 ..     410     417 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00015
                                   TTSSS-THHHHHSTT CS
                           Fer4  6 ekCigCGaCvevCPv 20
                                   e C+ C +C+  CP+
  gi|119719507|ref|YP_920002.1| 31 ENCVSCALCEVNCPY 45
                                   89************7 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 5.3e-06
                                    SSS-THHHHHSTTT CS
                           Fer4   8 CigCGaCvevCPvg 21 
                                    C++CG+C+  CP+g
  gi|119719507|ref|YP_920002.1| 101 CTNCGLCYITCPFG 114
                                    ************98 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.53
                                    TSSS- CS
                           Fer4   7 kCigC 11 
                                     CigC
  gi|119719507|ref|YP_920002.1| 413 ACIGC 417
                                    7**** PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   1.4   2.3e-05      0.03       7      21 ..      31      45 ..      26      49 .. 0.92
   2 !   13.9   3.0   3.3e-05     0.042       9      23 ..     101     115 ..     101     116 .. 0.94
   3 ?   -1.1   0.6       1.8   2.3e+03       8      12 ..     413     417 ..     412     417 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.3e-05
                         Fer4_6  7 dkCigCgdCvrvCPe 21
                                   ++C++C  C+++CP+
  gi|119719507|ref|YP_920002.1| 31 ENCVSCALCEVNCPY 45
                                   79************7 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 3.3e-05
                         Fer4_6   9 CigCgdCvrvCPega 23 
                                    C+ Cg C++ CP+g+
  gi|119719507|ref|YP_920002.1| 101 CTNCGLCYITCPFGI 115
                                    ************985 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1.8
                         Fer4_6   8 kCigC 12 
                                    +CigC
  gi|119719507|ref|YP_920002.1| 413 ACIGC 417
                                    7**** PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   1.6    0.0003      0.39       8      22 .]      31      45 ..      26      45 .. 0.88
   2 !   15.0   1.4   1.5e-05     0.019       4      21 ..      94     112 ..      92     113 .. 0.82
   3 ?   -0.5   0.2       1.3   1.7e+03       9      13 ..     413     417 ..     409     419 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0003
                         Fer4_2  8 drCigCgaCvsaCPa 22
                                   ++C++C  C  +CP+
  gi|119719507|ref|YP_920002.1| 31 ENCVSCALCEVNCPY 45
                                   67*******999**5 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1.5e-05
                         Fer4_2   4 vvdtd.rCigCgaCvsaCP 21 
                                    +vd + +C++Cg C+  CP
  gi|119719507|ref|YP_920002.1|  94 WVDLAyHCTNCGLCYITCP 112
                                    6674449************ PP

  == domain 3  score: -0.5 bits;  conditional E-value: 1.3
                         Fer4_2   9 rCigC 13 
                                    +CigC
  gi|119719507|ref|YP_920002.1| 413 ACIGC 417
                                    6***9 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   2.0   0.00071       0.9       2      16 ..      31      45 ..      30      51 .. 0.93
   2 !   16.3   0.9     8e-06      0.01       4      17 .]     101     114 ..      92     114 .. 0.91
   3 ?   -1.2   0.6       3.1     4e+03       3       7 ..     413     417 ..     412     417 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00071
                         Fer4_4  2 erCigCgsCvaaCPq 16
                                   e+C+ C  C+  CP+
  gi|119719507|ref|YP_920002.1| 31 ENCVSCALCEVNCPY 45
                                   89************6 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 8e-06
                         Fer4_4   4 CigCgsCvaaCPqg 17 
                                    C++Cg C+++CP+g
  gi|119719507|ref|YP_920002.1| 101 CTNCGLCYITCPFG 114
                                    ************86 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 3.1
                         Fer4_4   3 rCigC 7  
                                     CigC
  gi|119719507|ref|YP_920002.1| 413 ACIGC 417
                                    5**** PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0  11.3    0.0021       2.7       1      66 [.      32     113 ..      32     114 .. 0.68
   2 ?    8.0   2.6    0.0043       5.5       1      16 [.     100     115 ..     100     124 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0021
                        Fer4_16   1 rCgtCgkCaevCPtnaikek..kekeiearecisy................ntaekkdlaedeekckkqeaitgCdiCqd 62 
                                    +C++C  C   CP   + e+     ++e+ ++i                  +    k+ +e  +  + ++++t C+ C  
  gi|119719507|ref|YP_920002.1|  32 NCVSCALCEVNCPYTPVGEEygPVSKAEPLRNIYRgkvnilprlfpwlfgaK--LPKTKEELDKWVDLAYHCTNCGLCYI 109
                                    6*****************9933333344444544488999999999775422..22222222223335799********* PP

                        Fer4_16  63 vCPa 66 
                                    +CP+
  gi|119719507|ref|YP_920002.1| 110 TCPF 113
                                    ***9 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0043
                        Fer4_16   1 rCgtCgkCaevCPtna 16 
                                    +C++Cg C  +CP + 
  gi|119719507|ref|YP_920002.1| 100 HCTNCGLCYITCPFGI 115
                                    7999999999999765 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.2     0.067        86      59      72 ..      31      44 ..       6      49 .. 0.76
   2 ?    7.9   0.1    0.0027       3.5      56      76 ..      96     116 ..      82     124 .. 0.77
   3 ?   -2.7   0.0       5.3   6.8e+03      55      65 ..     408     418 ..     393     431 .. 0.58

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.067
                        Fer4_18 59 gdcidcescvkvcP 72
                                    +c++c  c   cP
  gi|119719507|ref|YP_920002.1| 31 ENCVSCALCEVNCP 44
                                   67888888888888 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0027
                        Fer4_18  56 kgagdcidcescvkvcPtgid 76 
                                    + a +c++c+ c   cP gi 
  gi|119719507|ref|YP_920002.1|  96 DLAYHCTNCGLCYITCPFGIH 116
                                    45668************9985 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 5.3
                        Fer4_18  55 ekgagdcidce 65 
                                    ++ ++ ci c 
  gi|119719507|ref|YP_920002.1| 408 STVVTACIGCI 418
                                    33444444443 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.5     0.034        43       1      13 [.      32      44 ..      13      48 .. 0.81
   2 ?    6.0   0.3     0.017        22      81      94 ..     100     113 ..      83     115 .. 0.70
   3 ?   -1.6   0.0       3.8   4.9e+03      76      85 ..     408     417 ..     389     421 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.034
                        Fer4_22  1 rClsCgaCtlvCp 13
                                   +C+sC+ C + Cp
  gi|119719507|ref|YP_920002.1| 32 NCVSCALCEVNCP 44
                                   4777777777776 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.017
                        Fer4_22  81 gCvGCgRCieacpv 94 
                                    +C+ Cg C  +cp 
  gi|119719507|ref|YP_920002.1| 100 HCTNCGLCYITCPF 113
                                    56666666666665 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 3.8
                        Fer4_22  76 kfgesgCvGC 85 
                                    ++  ++C+GC
  gi|119719507|ref|YP_920002.1| 408 STVVTACIGC 417
                                    4456789998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 3225.58
//
Query:       gi|119719508|ref|YP_920003.1|  [L=146]
Description: hydrogenase expression/synthesis, HypA [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.9e-28   97.4   0.0    5.5e-28   97.2   0.0    1.0  1  HypA             Hydrogenase/urease nickel incorporation, met
    0.00072   19.5   0.3        1.2    9.2   0.0    2.7  3  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
  ------ inclusion threshold ------
      0.011   15.2   0.3       0.97    9.0   0.0    2.5  2  TF_Zn_Ribbon     TFIIB zinc-binding
      0.016   15.6   0.0        2.8    8.4   0.0    2.2  2  Lar_restr_allev  Restriction alleviation protein Lar
      0.025   14.4   0.6        8.6    6.3   0.2    2.3  2  TFIIS_C          Transcription factor S-II (TFIIS)
      0.037   14.0   0.3        1.2    9.2   0.1    2.5  3  CpXC             CpXC protein
       0.04   14.0   1.3        7.1    6.8   0.2    2.4  2  Zn-ribbon_8      Zinc ribbon domain
      0.052   13.5   3.6          3    7.9   0.1    2.8  3  zinc_ribbon_4    zinc-ribbon domain
      0.098   12.1   1.0        2.6    7.6   0.0    2.2  2  zf-ribbon_3      zinc-ribbon domain
       0.11   12.5   1.6        2.8    7.9   0.0    2.6  3  Nudix_N_2        Nudix N-terminal
       0.13   12.8   0.2        2.3    8.8   0.0    2.4  2  Zn_ribbon_recom  Recombinase zinc beta ribbon domain
       0.14   12.2   0.1        3.3    7.9   0.0    2.2  2  zf-Mss51         Zinc-finger of mitochondrial splicing suppre
       0.18   12.3   1.4       0.62   10.6   0.2    2.0  2  zf-H2C2_2        Zinc-finger double domain
       0.84    9.4   6.9        1.6    8.5   0.6    2.3  2  Rubredoxin_2     Rubredoxin metal binding domain


Domain annotation for each model (and alignments):
>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.2   0.0   4.3e-31   5.5e-28       1     111 [.       1     143 [.       1     144 [. 0.96

  Alignments for each domain:
  == domain 1  score: 97.2 bits;  conditional E-value: 4.3e-31
                                    XCHHHHHHHHHHHHHHHHCCTT..EEEEEEEEEETTCT--HHHHHHHHHHHHCC.TTTT-EEEEEEE--EEEETTTS-EE CS
                           HypA   1 MHElsiaesivevveeeakeaaarkvtkvkvevGelsgvepeaLefafellaegtvlegaeLeieevpvkvrCreCgkef 80 
                                    MHE+s+++++ve++ e a +++++++++v vev e+s++e+++L+ a+++l+e+t++eg++L ie+vp++++C++Cg++f
  gi|119719508|ref|YP_920003.1|   1 MHEWSLMQAVVEALLEFAGRNGFSRISRVVVEVNEVSQLEEDILREAYSVLTENTIAEGSTLVIEKVPARFTCNSCGYTF 80 
                                    ******************999*********************************************************** PP

                                    ECHH.H.HH..............................S-TTTSSS-EEEEESSSEEEEEEE CS
                           HypA  81 elee.k.al..............................rCpkCgsadveivsGeellvksie 111
                                    +lee + al                              rCp+Cgs+d+     + l+vk +e
  gi|119719508|ref|YP_920003.1|  81 SLEEaRrALerlgeyaipdeegtldmpthyipavihgflRCPRCGSRDIWADMTSSLRVKAVE 143
                                    *88743333899***********************************************9987 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.0    0.0031         4      34      46 .]      66      79 ..      44      79 .. 0.72
   2 ?   -1.5   0.0       2.1   2.7e+03       4      13 ..      83      92 ..      81      93 .. 0.85
   3 !    9.2   0.0    0.0009       1.2      20      30 ..     120     130 ..     115     138 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0031
                  Zn_Tnp_IS1595 34 t.rglfqCkeCrkq 46
                                   + + +f C++C+++
  gi|119719508|ref|YP_920003.1| 66 KvPARFTCNSCGYT 79
                                   26889999999985 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.1
                  Zn_Tnp_IS1595  4 eearalLeal 13
                                   eear++Le+l
  gi|119719508|ref|YP_920003.1| 83 EEARRALERL 92
                                   7999999985 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0009
                  Zn_Tnp_IS1595  20 vCPhCgsrkay 30 
                                    +CP+Cgsr ++
  gi|119719508|ref|YP_920003.1| 120 RCPRCGSRDIW 130
                                    6******9766 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1     0.035        45      20      27 ..      71      78 ..      59      83 .. 0.89
   2 ?    9.0   0.0   0.00076      0.97       2      14 ..     120     132 ..     119     137 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.035
                                   EEESSSSB CS
                   TF_Zn_Ribbon 20 lvCtdCGl 27
                                   ++C +CG+
  gi|119719508|ref|YP_920003.1| 71 FTCNSCGY 78
                                   89****96 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00076
                                    EETTTTCEECHEE CS
                   TF_Zn_Ribbon   2 kCPnCgstnlveD 14 
                                    +CP Cgs+++  D
  gi|119719508|ref|YP_920003.1| 120 RCPRCGSRDIWAD 132
                                    7******997555 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.022        29      27      46 ..      61      85 ..      28      94 .. 0.68
   2 ?    8.4   0.0    0.0022       2.8       4      19 ..     119     134 ..     117     139 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.022
                Lar_restr_allev 27 q........cvyCadCgastpwfkiaed 46
                                   +         ++C  Cg+   +f+ +e+
  gi|119719508|ref|YP_920003.1| 61 TlviekvpaRFTCNSCGY---TFSLEEA 85
                                   144445555899*99**9...4444444 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0022
                Lar_restr_allev   4 kpCPfCggravlersq 19 
                                    + CP Cg+r+++  ++
  gi|119719508|ref|YP_920003.1| 119 LRCPRCGSRDIWADMT 134
                                    57********987765 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.2    0.0067       8.6      29      38 ..      71      80 ..      68      81 .. 0.87
   2 ?    6.2   0.0    0.0071         9       2      11 ..     120     129 ..     119     133 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0067
                        TFIIS_C 29 ykCtkCghrW 38
                                   ++C++Cg+++
  gi|119719508|ref|YP_920003.1| 71 FTCNSCGYTF 80
                                   89*****998 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0071
                        TFIIS_C   2 kCpkCgsrea 11 
                                    +Cp+Cgsr++
  gi|119719508|ref|YP_920003.1| 120 RCPRCGSRDI 129
                                    6******986 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       2.8   3.6e+03      18      35 ..      31      48 ..      26      52 .. 0.75
   2 ?    9.2   0.1   0.00094       1.2      33      52 ..      66      85 ..      46     103 .. 0.80
   3 ?    2.3   0.0      0.13   1.6e+02      39      46 ..     120     127 ..     117     141 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.8
                           CpXC 18 idadedpelkeklldgsl 35
                                   ++++e ++l+e++l + +
  gi|119719508|ref|YP_920003.1| 31 VEVNEVSQLEEDILREAY 48
                                   678888889998888765 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00094
                           CpXC 33 gslfeatCpkCgatakleap 52
                                   +   ++tC +Cg+t++le  
  gi|119719508|ref|YP_920003.1| 66 KVPARFTCNSCGYTFSLEEA 85
                                   555689**********9865 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.13
                           CpXC  39 tCpkCgat 46 
                                    +Cp+Cg +
  gi|119719508|ref|YP_920003.1| 120 RCPRCGSR 127
                                    57777654 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.2    0.0056       7.1       6      16 ..      71      81 ..      70      91 .. 0.81
   2 ?    5.8   0.1     0.011        15      28      34 ..     120     126 ..     115     129 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0056
                    Zn-ribbon_8  6 YrCeeCghefe 16
                                   + C++Cg +f 
  gi|119719508|ref|YP_920003.1| 71 FTCNSCGYTFS 81
                                   89*******98 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.011
                    Zn-ribbon_8  28 aCPeCgs 34 
                                     CP+Cgs
  gi|119719508|ref|YP_920003.1| 120 RCPRCGS 126
                                    4999999 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.1    0.0023         3       2      17 ..      70      85 ..      69      88 .. 0.85
   2 ?   -1.6   0.0       2.1   2.7e+03      11      17 ..      94     100 ..      94     101 .. 0.85
   3 ?    5.5   0.1     0.012        16      26      32 ..     119     125 ..     116     127 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0023
                  zinc_ribbon_4  2 kitCpsCkakyeidde 17
                                   ++tC sC+ +++++++
  gi|119719508|ref|YP_920003.1| 70 RFTCNSCGYTFSLEEA 85
                                   5799999999999886 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.1
                  zinc_ribbon_4  11 kyeidde 17 
                                    +y+i+de
  gi|119719508|ref|YP_920003.1|  94 EYAIPDE 100
                                    59****8 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.012
                  zinc_ribbon_4  26 vrCskCg 32 
                                    +rC++Cg
  gi|119719508|ref|YP_920003.1| 119 LRCPRCG 125
                                    4666665 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.3     0.058        74       4       9 ..      72      77 ..      71      80 .. 0.65
   2 ?    7.6   0.0     0.002       2.6       4      10 ..     120     126 ..     118     134 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.058
                    zf-ribbon_3  4 rCPnCG 9 
                                   +C++CG
  gi|119719508|ref|YP_920003.1| 72 TCNSCG 77
                                   466666 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.002
                    zf-ribbon_3   4 rCPnCGa 10 
                                    rCP+CG+
  gi|119719508|ref|YP_920003.1| 120 RCPRCGS 126
                                    8****97 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0022       2.8      21      31 ..      69      79 ..      62      80 .. 0.88
   2 ?   -3.1   0.0         6   7.7e+03      11      18 ..      94     101 ..      94     102 .. 0.79
   3 ?    3.0   0.1     0.074        94       3       8 ..     121     126 ..     119     129 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0022
                                   -EEEETTTTEE CS
                      Nudix_N_2 21 eRlvCpaCgti 31
                                    R++C++Cg++
  gi|119719508|ref|YP_920003.1| 69 ARFTCNSCGYT 79
                                   69*******97 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 6
                                    EEE--TT- CS
                      Nudix_N_2  11 elripdgD 18 
                                    e++ipd++
  gi|119719508|ref|YP_920003.1|  94 EYAIPDEE 101
                                    68999976 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.074
                                    -TTT-- CS
                      Nudix_N_2   3 CsqCGt 8  
                                    C+ CG+
  gi|119719508|ref|YP_920003.1| 121 CPRCGS 126
                                    666665 PP

>> Zn_ribbon_recom  Recombinase zinc beta ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.39     5e+02       7      17 ..      72      82 ..      70      97 .. 0.79
   2 ?    8.8   0.0    0.0018       2.3       4      14 ..     117     127 ..     115     143 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.39
                Zn_ribbon_recom  7 rCgeCGspmtr 17
                                    C  CG +++ 
  gi|119719508|ref|YP_920003.1| 72 TCNSCGYTFSL 82
                                   6*****99875 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0018
                Zn_ribbon_recom   4 GllrCgeCGsp 14 
                                    G lrC +CGs+
  gi|119719508|ref|YP_920003.1| 117 GFLRCPRCGSR 127
                                    89*******98 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0026       3.3      11      29 ..      65      83 ..      33      88 .. 0.80
   2 ?    2.3   0.0      0.15   1.9e+02      17      23 ..     119     125 ..     106     129 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0026
                       zf-Mss51 11 apkhvdfeCpdCGiptycs 29
                                   ++ + +f+C  CG+     
  gi|119719508|ref|YP_920003.1| 65 EKVPARFTCNSCGYTFSLE 83
                                   567899*******987655 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.15
                       zf-Mss51  17 feCpdCG 23 
                                    + Cp+CG
  gi|119719508|ref|YP_920003.1| 119 LRCPRCG 125
                                    68****9 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.2   0.00048      0.62      11      25 ..      67      81 ..      64      81 .. 0.84
   2 ?    0.3   0.1      0.91   1.2e+03      15      21 ..     119     125 ..     112     127 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00048
                      zf-H2C2_2 11 gekpyeCplCdkaFk 25
                                   ++ +++C +C+++F+
  gi|119719508|ref|YP_920003.1| 67 VPARFTCNSCGYTFS 81
                                   5667**********5 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.91
                      zf-H2C2_2  15 yeCplCd 21 
                                    + Cp C+
  gi|119719508|ref|YP_920003.1| 119 LRCPRCG 125
                                    68****8 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.6    0.0013       1.6       1      10 [.      71      80 ..      71      82 .. 0.88
   2 ?    4.1   1.0      0.03        39      16      22 ..     120     126 ..     120     128 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0013
                   Rubredoxin_2  1 YvCsqCGfes 10
                                   + C++CG+++
  gi|119719508|ref|YP_920003.1| 71 FTCNSCGYTF 80
                                   78******97 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.03
                   Rubredoxin_2  16 rCpsCgs 22 
                                    rCp Cgs
  gi|119719508|ref|YP_920003.1| 120 RCPRCGS 126
                                    8999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       721  (0.0402142); expected 358.6 (0.02)
Passed bias filter:                      660  (0.0368119); expected 358.6 (0.02)
Passed Vit filter:                       103  (0.00574488); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 968.08
//
Query:       gi|119719509|ref|YP_920004.1|  [L=248]
Description: ParA/MinD family ATPase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.7e-46  157.2   0.0    9.8e-46  156.2   0.0    1.5  1  ParA         NUBPL iron-transfer P-loop NTPase
    1.5e-14   54.1   0.0    5.2e-14   52.4   0.0    1.9  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    4.6e-10   39.2   1.8    1.4e-07   31.1   0.5    2.4  2  ArsA_ATPase  Anion-transporting ATPase
    8.7e-09   35.5   0.1    5.3e-06   26.5   0.0    2.1  2  AAA_31       AAA domain
    2.6e-08   33.5   0.1    5.5e-08   32.4   0.1    1.6  1  MipZ         ATPase MipZ
    1.3e-06   28.1   0.0      0.026   14.0   0.0    2.1  2  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
    0.00037   20.4   0.7        0.6    9.9   0.0    2.2  2  AAA_26       AAA domain
  ------ inclusion threshold ------
      0.024   13.7   0.2      0.041   12.9   0.2    1.3  1  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
      0.057   12.9   0.6       0.25   10.8   0.2    1.9  2  CBP_BcsQ     Cellulose biosynthesis protein BcsQ
      0.068   12.5   0.1      0.099   11.9   0.1    1.2  1  CTP_synth_N  CTP synthase N-terminus
       0.15   11.3   0.0       0.24   10.7   0.0    1.2  1  VirC1        VirC1 protein
       0.17   11.8   0.1        0.3   11.0   0.1    1.4  1  APS_kinase   Adenylylsulphate kinase
       0.21   11.3   0.3       0.34   10.6   0.3    1.5  1  AAA_30       AAA domain


Domain annotation for each model (and alignments):
>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.2   0.0   7.1e-49   9.8e-46       2     223 ..      18     228 ..      17     246 .. 0.89

  Alignments for each domain:
  == domain 1  score: 156.2 bits;  conditional E-value: 7.1e-49
                           ParA   2 vkkviavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekpeqsekkliPveakgikvmSigfl 81 
                                    vk+v++  SgKGGVGKS v++  AlaL++kg++vgllD+D++Gps +r+l+ e++ p+ s++++ Pv+a g+++m ++f+
  gi|119719509|ref|YP_920004.1|  18 VKRVVVFGSGKGGVGKSVVSAATALALSEKGYRVGLLDLDVHGPSSARILKPEGR-PSGSKHGIRPVNAGGVELMTVEFF 96 
                                    89****************************************************5.999999****************** PP

                           ParA  82 lesedeavvwrGpmkskaikqllkdvewgelDyLiiDlPPGtgDeqltvaqkl..plagaviVttpqevaladvkkaiem 159
                                    l   d ++   G  k++++ +ll +v+wge D+L++DlPPG gDe++  +  l    +  ++Vt+p  ++ ++v++ +++
  gi|119719509|ref|YP_920004.1|  97 LG--DLPLPLSGGAKTSLVAELLMNVDWGEKDFLVVDLPPGLGDETIVPLRVLksLAHTFLVVTSPSALSYSVVRRLLSF 174
                                    *9..9***************************************9876555553224788******************** PP

                           ParA 160 fkkvkvkvlGvveNmsgfvcpkcgekteifgkgggeklaeelgvpllgeipldpeireasdegk 223
                                    + + +v+v G+v N    v +          ++ +e+l ee+g+  l++ip+d+++  a+ e +
  gi|119719509|ref|YP_920004.1| 175 LVEERVNVGGLVVNYVSPVGE----------ESYVERLEEEFGIIALARIPFDEKMEAAISERN 228
                                    ************996443333..........356899999999999999999999988877665 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.4   0.0   3.8e-17   5.2e-14       2     124 ..      23     226 ..      22     230 .. 0.83

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 3.8e-17
                                    EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH........................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................... RF
                           CbiA   2 aiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep........................... 54 
                                    ++ s+kGGvGK++++a+ a al+++g+rV l+D+D+ ++++a    l+++ +p                           
  gi|119719509|ref|YP_920004.1|  23 VFGSGKGGVGKSVVSAATALALSEKGYRVGLLDLDVHGPSSAR--ILKPEGRPsgskhgirpvnaggvelmtvefflgdl 100
                                    6679*************************************95..44444444558888888****************** PP

                                    ..................................................................CCHCCCHHHHHHCH CS
                                    ..................................................................xxxxxxxxxxxxxx RF
                           CbiA  55 ..................................................................dlkrllellealgk 68 
                                                                                                          + +ll+ l++
  gi|119719509|ref|YP_920004.1| 101 plplsggaktslvaellmnvdwgekdflvvdlppglgdetivplrvlkslahtflvvtspsalsysV---VRRLLSFLVE 177
                                    *********************************************9999999999999996664431...2233333333 PP

                                    CHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           CbiA  69 kkalllkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeavaeapar 124
                                    +    +++ g+v+n v +   e++  e lee   ++g+  l+ ip+de+   a+++
  gi|119719509|ref|YP_920004.1| 178 E---RVNVGGLVVNYVSPV-GEESYVERLEE---EFGIIALARIPFDEKMEAAISE 226
                                    3...2899*******9987.45555555555...55************99666654 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.5   9.8e-11   1.4e-07       3      38 ..      22      57 ..      19      61 .. 0.89
   2 !    7.0   0.0    0.0021       2.9     207     252 ..     152     197 ..     145     223 .. 0.88

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 9.8e-11
                                   EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S CS
                    ArsA_ATPase  3 vilvgGKGGVGKttvsaatavklsekgkkvllistD 38
                                   v++ +GKGGVGK+ vsaata+ lsekg++v l+ +D
  gi|119719509|ref|YP_920004.1| 22 VVFGSGKGGVGKSVVSAATALALSEKGYRVGLLDLD 57
                                   46678************************9888776 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0021
                                    EEEEEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEEEE-TTCSSS CS
                    ArsA_ATPase 207 tsfrlVvipEklslkEteRaikeLkkygikvdavivNkllpeeeqe 252
                                     +f +V+ p  ls    +R+++ L +  ++v  ++vN + p  e++
  gi|119719509|ref|YP_920004.1| 152 HTFLVVTSPSALSYSVVRRLLSFLVEERVNVGGLVVNYVSPVGEES 197
                                    489**********************************998866665 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0   3.9e-09   5.3e-06       2      46 ..      20      64 ..      19      81 .. 0.91
   2 !    7.2   0.0    0.0031       4.3     109     164 ..     115     175 ..      83     182 .. 0.78

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 3.9e-09
                         AAA_31  2 kvIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanatt 46
                                   +v+++   KGGvGK+  s + a al+++g++v l DlD  + ++ 
  gi|119719509|ref|YP_920004.1| 20 RVVVFGSGKGGVGKSVVSAATALALSEKGYRVGLLDLDVHGPSSA 64
                                   7999**********************************9877665 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0031
                         AAA_31 109 ellekvk.deYDyiiiDcpPsLglltenaLva....sdsviipvqaeayaleGleqllkti 164
                                    ell +v+  e D+ ++D pP Lg  t+  L +    + ++++++ ++a++++ +++ll+++
  gi|119719509|ref|YP_920004.1| 115 ELLMNVDwGEKDFLVVDLPPGLGDETIVPLRVlkslAHTFLVVTSPSALSYSVVRRLLSFL 175
                                    55555542457************99888875433338999************999999876 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.1     4e-11   5.5e-08       1      49 [.      20      68 ..      20     170 .. 0.77

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 4e-11
                                   EEEEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHHHH CS
                           MipZ  1 hvivlgnekGGsGksttavhvavaLlkkGarvaaidldlrqrtlaryle 49
                                   +v+v+g  kGG Gks ++   a aL++kG rv+ +dld+   ++ar l+
  gi|119719509|ref|YP_920004.1| 20 RVVVFGSGKGGVGKSVVSAATALALSEKGYRVGLLDLDVHGPSSARILK 68
                                   589*************************************999999885 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   1.9e-05     0.026       7      39 ..      27      59 ..      19      73 .. 0.80
   2 !   12.3   0.0     6e-05     0.083     161     220 ..     167     226 ..     125     239 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.9e-05
                      Fer4_NifH  7 GkGGiGksttsqnlsaalaemgkkvlivGCDPk 39
                                   GkGG+Gks+ s+ ++ al+e+g +v ++  D  
  gi|119719509|ref|YP_920004.1| 27 GKGGVGKSVVSAATALALSEKGYRVGLLDLDVH 59
                                   8***********************977766655 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 6e-05
                      Fer4_NifH 161 iakgiekyaksggvrlgGliinsrkvddereliekfaeelgtkvlevvPrdeivrkaelr 220
                                    + + +  +  ++ v++gGl++n  + + e+  +e++ ee g+  l+ +P de+++ a  +
  gi|119719509|ref|YP_920004.1| 167 VVRRLLSFLVEERVNVGGLVVNYVSPVGEESYVERLEEEFGIIALARIPFDEKMEAAISE 226
                                    5566677777899*********9999**************************99876544 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.4   0.00096       1.3      11      33 ..      30      52 ..      19      54 .. 0.81
   2 !    9.9   0.0   0.00044       0.6     149     196 ..     172     222 ..     123     223 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00096
                         AAA_26 11 gvGKTvvslgLvralkrkgvkvg 33
                                   gvGK+vvs++ + al++kg++vg
  gi|119719509|ref|YP_920004.1| 30 GVGKSVVSAATALALSEKGYRVG 52
                                   7********************98 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00044
                         AAA_26 149 iealrqknvrvlGvilNkvrnp....envetlekksgipvlGvvPylpdlea 196
                                    +++l ++ v+v G+++N v +p      ve le+ +gi  l+++P ++++ea
  gi|119719509|ref|YP_920004.1| 172 LSFLVEERVNVGGLVVNYV-SPvgeeSYVERLEEEFGIIALARIPFDEKMEA 222
                                    44556899*********95.66465459******************998875 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2     3e-05     0.041      35      69 ..      26      63 ..       7      67 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3e-05
                                   EE-TTSSHHHHHHHHHHHHHCTT--EEEEEE-...--- CS
                           MeaB 35 tGvPGaGkstlvealglelrrrGkrvavlavD...Pss 69
                                    G  G+Gks +  a +l l ++G+rv++l +D   Pss
  gi|119719509|ref|YP_920004.1| 26 SGKGGVGKSVVSAATALALSEKGYRVGLLDLDvhgPSS 63
                                   6889*************************999444444 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2   0.00018      0.25       9      39 ..      27      57 ..      19      61 .. 0.87
   2 ?    0.0   0.0      0.35   4.8e+02      14      40 ..     108     134 ..     104     164 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00018
                       CBP_BcsQ  9 vRGGvGttsllaaLawalhelgesvlviDls 39
                                    +GGvG++ ++aa a al e g++v ++Dl 
  gi|119719509|ref|YP_920004.1| 27 GKGGVGKSVVSAATALALSEKGYRVGLLDLD 57
                                   58***********************999985 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.35
                       CBP_BcsQ  14 GttsllaaLawalhelgesvlviDlsp 40 
                                     +tsl+a L + ++  ++  lv+Dl p
  gi|119719509|ref|YP_920004.1| 108 AKTSLVAELLMNVDWGEKDFLVVDLPP 134
                                    468888888888888888888888765 PP

>> CTP_synth_N  CTP synthase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   7.2e-05     0.099       1      40 [.      19      58 ..      19      73 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.2e-05
                                   EEEEEEE--STTTTHHHHHHHHHHHHHCTT--EEEEEEE- CS
                    CTP_synth_N  1 kyilvtGGvvSglGkGiiaaslgallksrglkvtlikiDP 40
                                   k ++v G    g+Gk +++a+++  l ++g++v l+ +D 
  gi|119719509|ref|YP_920004.1| 19 KRVVVFGSGKGGVGKSVVSAATALALSEKGYRVGLLDLDV 58
                                   56999****************************9999986 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00017      0.24       3      43 ..      21      61 ..      19      66 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00017
                          VirC1  3 litfcslkGGaGkttalmglcsalasdgkrvalfeadenrP 43
                                   ++ f s kGG Gk+    +   al  +g rv+l++ d   P
  gi|119719509|ref|YP_920004.1| 21 VVVFGSGKGGVGKSVVSAATALALSEKGYRVGLLDLDVHGP 61
                                   68999**********9999999************9997666 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00022       0.3       3      39 ..      21      57 ..      19      60 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00022
                                   EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHH CS
                     APS_kinase  3 vvvwltGlsgsGKstianalekkLvekgisvylLdGd 39
                                   vvv+ +G  g GKs ++ a + +L ekg++v lLd d
  gi|119719509|ref|YP_920004.1| 21 VVVFGSGKGGVGKSVVSAATALALSEKGYRVGLLDLD 57
                                   78999*****************************976 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.3   0.00025      0.34       9      52 ..      11      54 ..       9     131 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00025
                         AAA_30  9 avealltsgdrvavltGpAGtGKttalkalreaweaaggrvigl 52
                                   a ++l + ++ v++  G  G GK+ + +a + a+ ++g+rv +l
  gi|119719509|ref|YP_920004.1| 11 ARRRLSSVKRVVVFGSGKGGVGKSVVSAATALALSEKGYRVGLL 54
                                   55677777889999*************************99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 1658.49
//
Query:       gi|119719510|ref|YP_920005.1|  [L=348]
Description: putative molybdenum cofactor biosynthesis protein A [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.1e-29  101.8   0.0      3e-28   99.3   0.0    2.0  2  Radical_SAM  Radical SAM superfamily
    1.9e-20   73.1   0.0    2.7e-20   72.6   0.0    1.2  1  Mob_synth_C  Molybdenum Cofactor Synthesis C
    0.00016   21.8   0.0    0.00032   20.8   0.0    1.5  1  Fer4_14      4Fe-4S single cluster domain
     0.0013   19.0   0.0     0.0029   17.9   0.0    1.6  1  Fer4_12      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.3   0.0   6.6e-32     3e-28       1     152 [.      23     166 ..      23     180 .. 0.94
   2 ?    0.0   0.0      0.22   9.7e+02      56      91 ..     282     343 ..     277     348 .] 0.73

  Alignments for each domain:
  == domain 1  score: 99.3 bits;  conditional E-value: 6.6e-32
                                    EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiri 80 
                                    ++vt+ Cn++C+fC+        +  + ls  ei+e +  + ++ gv+++ l+ggepll++d++++++ l+    +g+++
  gi|119719510|ref|YP_920005.1|  23 ITVTPQCNFNCVFCHGEG---EPPNNALLSASEIVEVASVA-HSLGVGTFKLTGGEPLLRKDLERIVAGLKSFG-RGVEV 97 
                                    689**************8...8*******************.8*****************************95.***** PP

                                    EEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEB CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  81 tvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivgl 152
                                    +++tng+ + e+ +  l+e+g+drv+++l+a+d+e++   + r ++fe+vl++le++ e+g++ v+ + v+ 
  gi|119719510|ref|YP_920005.1|  98 SLTTNGFFL-EKRVPSLVEAGLDRVNVSLHAFDPEVFEGVT-RVKGFEKVLRGLEAASEYGLP-VKLNFVLT 166
                                    *********.*************************999999.99*******************.88887765 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.22
                                    TGGGSTTHHHHHHHHHHTC..........................CCTEEEEEEECSSCHGH CS
                                    xxxxxxxxxxxxxxxxxxx..........................xxxxxxxxxxxxxxxxx RF
                    Radical_SAM  56 epllypdfvellerlakla..........................vpgiritvetngtlpde 91 
                                    +p+l+++  ++lerl++                             p +r+t+ +n+  p++
  gi|119719510|ref|YP_920005.1| 282 TPILRDEGGDKLERLREAFliansrrepffrfngekvtsfngrivCPVRRVTLLSNARGPRR 343
                                    78899999999999999888887777777777777777777777777777777777766655 PP

>> Mob_synth_C  Molybdenum Cofactor Synthesis C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.6   0.0     6e-24   2.7e-20       2     124 ..     186     309 ..     185     313 .. 0.90

  Alignments for each domain:
  == domain 1  score: 72.6 bits;  conditional E-value: 6e-24
                                    EEEEEE---B-TTSSB--SSB--HHHHHHHHHHHS-EEEE--SST-SSEEEEETTT--EEEEE-TTTS-.-GGG--EEEE CS
                    Mob_synth_C   2 elrfIElmpvgegeewrekkvvsadeilerieerlalleakketkgpakrykikdgkgeiglIapvsep.FCasCnRlRl 80 
                                    ++ +IEl p+g+g   +++ +v+ +++l ++e   ++     ++ +++++++++    ++++Ia++ +p FC+ C++lRl
  gi|119719510|ref|YP_920005.1| 186 NVNLIELIPTGKGGAVFDELYVPVENVLPQLEGMARKVYT--RPLQSRPVFELET-GIKVEVIANYCNPaFCSMCTKLRL 262
                                    789****************************988777665..789********55.559********************* PP

                                    -TTSEEESSSS-SS-.EEHHHHHHTT-..-HHHHHHHHHHHHHT--- CS
                    Mob_synth_C  81 tadGklktCLfaeee.idlrdllrega..seeeLkelikealarkke 124
                                    t dGklk+CL ++++ +dl ++lr++   + e+L+e++  a +r+++
  gi|119719510|ref|YP_920005.1| 263 THDGKLKPCLNRNDNlVDLTPILRDEGgdKLERLREAFLIANSRREP 309
                                    ************************99853445699999999999986 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0     7e-08   0.00032       5      91 ..      26     105 ..      23     123 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 7e-08
                        Fer4_14   5 lsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekkiw 84 
                                    + +Cn++C++C  + +  +++    +e ++++ +  ++   +      ltGGePL+    k+l ++v  lk  ++ +++ 
  gi|119719510|ref|YP_920005.1|  26 TPQCNFNCVFCHGEGEPPNNALLSASEIVEVASV--AHSLGV--GTFKLTGGEPLLR---KDLERIVAGLKSFGRGVEVS 98 
                                    568*********9997777777777777777777..334444..5579*******65...8999999999999999**** PP

                        Fer4_14  85 letngtl 91 
                                    l tng +
  gi|119719510|ref|YP_920005.1|  99 LTTNGFF 105
                                    ****976 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   6.5e-07    0.0029      14      99 ..      28     109 ..      19     126 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 6.5e-07
                        Fer4_12  14 gCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekp.ekdiwlyt 92 
                                     Cn++C +C+  e   +++     +e+  e+   ++   +  + l+GGEPll   +++l ++v  +k+ +   ++ + ++
  gi|119719510|ref|YP_920005.1|  28 QCNFNCVFCH-GEGEPPNNALLSASEI-VEVASVAHSLGVGTFKLTGGEPLL---RKDLERIVAGLKSFGRgVEVSLTTN 102
                                    7*********.7777777666665555.56666777778899**********...6777777766665554334677778 PP

                        Fer4_12  93 gytleel 99 
                                    g+ le+ 
  gi|119719510|ref|YP_920005.1| 103 GFFLEKR 109
                                    8777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 2119.32
//
Query:       gi|119719511|ref|YP_920006.1|  [L=253]
Description: ABC transporter related [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.2e-33  115.6   0.0    2.8e-33  115.3   0.0    1.1  1  ABC_tran      ABC transporter
    4.9e-14   52.8   2.9    3.3e-06   27.1   0.5    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    6.6e-06   26.8   0.0      7e-06   26.7   0.0    1.3  1  AAA_23        AAA domain
    1.2e-05   25.2   0.0    2.4e-05   24.2   0.0    1.4  1  AAA_15        AAA ATPase domain
    3.4e-05   23.4   0.0    0.00077   19.0   0.0    2.0  1  SMC_N         RecF/RecN/SMC N terminal domain
    5.5e-05   22.8   0.2     0.0001   21.9   0.2    1.4  1  AAA_29        P-loop containing region of AAA domain
     0.0028   17.2   0.4      0.098   12.2   0.1    2.2  2  AAA_25        AAA domain
     0.0029   16.7   0.1     0.0047   16.0   0.1    1.2  1  T2SSE         Type II/IV secretion system protein
     0.0031   17.7   0.0       0.15   12.2   0.1    2.2  2  AAA_33        AAA domain
     0.0035   17.7   0.1      0.007   16.8   0.1    1.6  1  AAA_16        AAA ATPase domain
     0.0097   15.8   0.1      0.015   15.2   0.1    1.3  1  RsgA_GTPase   RsgA GTPase
  ------ inclusion threshold ------
      0.011   15.5   0.0      0.021   14.6   0.0    1.4  1  AAA_30        AAA domain
      0.016   15.1   0.0      0.029   14.3   0.0    1.5  1  BCA_ABC_TP_C  Branched-chain amino acid ATP-binding cassette 
       0.03   14.6   0.5       0.18   12.1   0.1    2.1  2  AAA_22        AAA domain
      0.031   13.9   0.0      0.047   13.3   0.0    1.2  1  SRP54         SRP54-type protein, GTPase domain
      0.055   13.1   0.1      0.091   12.3   0.1    1.3  1  AAA_27        AAA domain
      0.058   13.4   0.0       0.15   12.1   0.0    1.6  1  AAA_5         AAA domain (dynein-related subfamily)
       0.06   12.6   0.0       0.09   12.0   0.0    1.2  1  Zeta_toxin    Zeta toxin
      0.074   13.3   0.0       0.62   10.3   0.0    2.1  2  AAA_28        AAA domain
      0.077   12.9   0.1       0.22   11.4   0.0    1.8  2  NACHT         NACHT domain
      0.087   12.4   0.2       0.15   11.6   0.2    1.4  1  cobW          CobW/HypB/UreG, nucleotide-binding domain
       0.17   10.7   0.0       0.24   10.2   0.0    1.1  1  DLIC          Dynein light intermediate chain (DLIC)
       0.18   11.1   0.0       0.42   10.0   0.0    1.6  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
       0.22   11.3   0.1       0.39   10.5   0.1    1.3  1  PduV-EutP     Ethanolamine utilisation - propanediol utilisat


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.3   0.0   3.8e-36   2.8e-33       1     136 [.      21     180 ..      21     181 .. 0.92

  Alignments for each domain:
  == domain 1  score: 115.3 bits;  conditional E-value: 3.8e-36
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvren 79 
                                    +k+vsl+l eg+++ ++G+nG+GK+tLl++++g  +p++G+i ++g+d+++  ++e++r  i+  +q pqlf  l+v en
  gi|119719511|ref|YP_920006.1|  21 VKDVSLELGEGTLTMLIGPNGSGKTTLLNIISGVIEPDSGRIVFKGRDITRlYPHERYRYGIARSFQVPQLFTSLSVLEN 100
                                    589***************************************************************************** PP

                                    ...........................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEE CS
                                    ...........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ...........................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllll 132
                                                               ++ +++ ++ls l+l++l d ++    + LSgGq + ++laral+++pkl+ll
  gi|119719511|ref|YP_920006.1| 101 vlvssrlyleedalgilftnswalkdwDQAQKAFEILSLLKLDHLWDAPA----RALSGGQMKLLELARALMSDPKLMLL 176
                                    **********************9966444444666777777777777776....************************** PP

                                    ESTT CS
                                    xxxx RF
                       ABC_tran 133 DEpt 136
                                    DEp 
  gi|119719511|ref|YP_920006.1| 177 DEPL 180
                                    ***7 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.5   4.4e-09   3.3e-06       1      23 [.      33      55 ..      33     114 .. 0.78
   2 !   26.1   0.1   8.8e-09   6.6e-06     229     287 ..     145     200 ..     100     209 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 4.4e-09
                         AAA_21  1 lnvliGpNgsGKSnLLdaldlla 23
                                   l++liGpNgsGK++LL +++++ 
  gi|119719511|ref|YP_920006.1| 33 LTMLIGPNGSGKTTLLNIISGVI 55
                                   699****************9873 PP

  == domain 2  score: 26.1 bits;  conditional E-value: 8.8e-09
                         AAA_21 229 gqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr 287
                                      + par lS G+ +ll l+ al +++   +l l+DEp +g +P+l +++++ l+++++
  gi|119719511|ref|YP_920006.1| 145 LWDAPARALSGGQMKLLELARALMSDP---KLMLLDEPLAGVNPALAHEIMQALRRARD 200
                                    4456999******************99...99**********************88776 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0   9.4e-09     7e-06      10      41 ..      18      53 ..       6     154 .. 0.87

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 9.4e-09
                         AAA_23 10 f...rdqeidF.skgltlItGpNGaGKTTildAikl 41
                                       +d+++++ +  lt ++GpNG+GKTT+l+ i  
  gi|119719511|ref|YP_920006.1| 18 VtavKDVSLELgEGTLTMLIGPNGSGKTTLLNIISG 53
                                   255588999995557*****************9975 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   3.2e-08   2.4e-05      14      44 ..      21      52 ..      20      77 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 3.2e-08
                         AAA_15 14 lkdveidlsee.ltvliGkNnsGKSsileald 44
                                    kdv+++l e  lt liG+N+sGK+++l+++ 
  gi|119719511|ref|YP_920006.1| 21 VKDVSLELGEGtLTMLIGPNGSGKTTLLNIIS 52
                                   6999******99******************96 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0     1e-06   0.00077      24     204 ..      31     218 ..       8     233 .. 0.65

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1e-06
                                    SSEEEEEESTTSSHHHHHHHHHHHCTT.TTT.TTTCHCCCCCC--.BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  24 ksftaivGpNGSGKsnlldAilFvLGersak.klrseklsdlihk.skekasvkkaeveitfdnedkklkiekeevsisr 101
                                      +t+++GpNGSGK+ ll+ i+ v+  +s +  ++ +++++l  + + +   + + +v  +f+  +       e+v +s 
  gi|119719511|ref|YP_920006.1|  31 GTLTMLIGPNGSGKTTLLNIISGVIEPDSGRiVFKGRDITRLYPHeRYRYGIARSFQVPQLFTSLSVL-----ENVLVSS 105
                                    4589*****************99998887763578888888876634444556666777777666666.....6777777 PP

                                    EEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT............CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 102 rvkrkgeseykingkevtkkevsellesagiske............lLSgGektLvalaLlfAiqkvkpaplyllDeida 169
                                    r++ +++    +  ++   k+  +  +  +i +             +LSgG+ +L+ la      + +p  l+llDe  a
  gi|119719511|ref|YP_920006.1| 106 RLYLEEDALGILFTNSWALKDWDQAQKAFEILSLlkldhlwdaparALSGGQMKLLELARA---LMSDP-KLMLLDEPLA 181
                                    7777777555554444444444444444444444444555555666888888888777644...23333.4677777777 PP

                                    TS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC CS
                                    xxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxx RF
                          SMC_N 170 aLDeknvkkvaellkekskn..aQfivislreemlek 204
                                        +  +++ + l++++++  + f+++ +r ++ +k
  gi|119719511|ref|YP_920006.1| 182 GVNPALAHEIMQALRRARDElgVSFLIVEHRLDLASK 218
                                    7777777777777777666645567777776666555 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.2   1.4e-07    0.0001      17      50 ..      26      59 ..      16      65 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.4e-07
                         AAA_29 17 ieidlkg.atlltGpsGsGKSTllDAiqalLvpak 50
                                   +e+  +g  t+l+Gp+GsGK+Tll  i+ ++ p++
  gi|119719511|ref|YP_920006.1| 26 LELG-EGtLTMLIGPNGSGKTTLLNIISGVIEPDS 59
                                   4444.3369***************99998888876 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.1   0.00013     0.098      30      50 ..      28      48 ..      21      55 .. 0.92
   2 ?    2.9   0.0     0.096        72     166     188 ..     189     211 ..     182     212 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                         AAA_25 30 lpagelallaGapgtGKttla 50
                                   l +g+l++l+G+ g+GKttl+
  gi|119719511|ref|YP_920006.1| 28 LGEGTLTMLIGPNGSGKTTLL 48
                                   5689***************97 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.096
                         AAA_25 166 galvealeriarrtgaavllvhH 188
                                     ++++al+r ++++g+ +l+v H
  gi|119719511|ref|YP_920006.1| 189 HEIMQALRRARDELGVSFLIVEH 211
                                    7899*****************99 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   6.3e-06    0.0047     133     161 ..      35      63 ..      23      65 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 6.3e-06
                          T2SSE 133 lvsGgTgsGKttllyallkeinksderiv 161
                                    ++ G+ gsGKttll+++   i+ ++ riv
  gi|119719511|ref|YP_920006.1|  35 MLIGPNGSGKTTLLNIISGVIEPDSGRIV 63 
                                    567********************999998 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.1    0.0002      0.15       1      16 [.      33      48 ..      33      52 .. 0.91
   2 ?    3.2   0.0      0.12        91      59     107 ..     160     214 ..     140     217 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0002
                         AAA_33  1 lvllvGlpGsGKstla 16
                                   l++l+G++GsGK+tl+
  gi|119719511|ref|YP_920006.1| 33 LTMLIGPNGSGKTTLL 48
                                   689***********96 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.12
                         AAA_33  59 lnelarkalsagrnvildatnls......rrerarflklarrlgvpvrivvvetd 107
                                    l elar  +s  + ++ld +++       ++ +++++++  +lgv ++iv  + d
  gi|119719511|ref|YP_920006.1| 160 LLELARALMSDPKLMLLDEPLAGvnpalaHEIMQALRRARDELGVSFLIVEHRLD 214
                                    55889999999999999888555444442777789999999*******9987766 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   9.4e-06     0.007      22      61 ..      29      69 ..      19     209 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 9.4e-06
                         AAA_16 22 grpelvllsGesGvGKsslvrellralekd.ggiflrgkcd 61
                                   g++ l++l+G+ G+GK++l++ +   +e d g i+++g+  
  gi|119719511|ref|YP_920006.1| 29 GEGTLTMLIGPNGSGKTTLLNIISGVIEPDsGRIVFKGRDI 69
                                   77799****************99988888843444444433 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   2.1e-05     0.015      91     124 ..      22      56 ..       7      72 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.1e-05
                                    HHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-- CS
                    RsgA_GTPase  91 eelkellkd.ktsvlvGqSGvGKStLinallpele 124
                                    ++++ +l +  +++l+G+ G GK+tL+n + +  e
  gi|119719511|ref|YP_920006.1|  22 KDVSLELGEgTLTMLIGPNGSGKTTLLNIISGVIE 56 
                                    5555566555899***************9988655 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   2.8e-05     0.021      17      50 ..      31      63 ..      22      70 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.8e-05
                         AAA_30 17 gdrvavltGpAGtGKttalkalreaweaaggrvi 50
                                   g  +++l Gp G+GKtt+l+ +  ++e + gr++
  gi|119719511|ref|YP_920006.1| 31 G-TLTMLIGPNGSGKTTLLNIISGVIEPDSGRIV 63
                                   3.5999*****************99998855554 PP

>> BCA_ABC_TP_C  Branched-chain amino acid ATP-binding cassette transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   3.9e-05     0.029       2      18 ..     231     247 ..     230     249 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.9e-05
                   BCA_ABC_TP_C   2 vIAeGtPaEvrndPrVi 18 
                                    vI +GtP+Ev  dP V+
  gi|119719511|ref|YP_920006.1| 231 VISSGTPDEVFEDPMVV 247
                                    9************9665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00023      0.18       5      23 ..      31      49 ..      27      61 .. 0.90
   2 ?    0.4   0.0      0.95   7.1e+02      71      96 ..     184     208 ..      85     215 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00023
                         AAA_22  5 agilvvtGesGtGKTtllr 23
                                    ++++++G+ G+GKTtll+
  gi|119719511|ref|YP_920006.1| 31 GTLTMLIGPNGSGKTTLLN 49
                                   67899***********986 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.95
                         AAA_22  71 erlsseellealeqalraravielli 96 
                                    +++  +e+++al++a ++ +v ++li
  gi|119719511|ref|YP_920006.1| 184 NPALAHEIMQALRRARDELGV-SFLI 208
                                    222223333333333333333.4444 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   6.3e-05     0.047       3      41 ..      33      71 ..      31      82 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.3e-05
                                   EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSS CS
                          SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvllvaaDtfR 41
                                   +++l+G++G+GKTt l  ++ +++ +  ++++   D+ R
  gi|119719511|ref|YP_920006.1| 33 LTMLIGPNGSGKTTLLNIISGVIEPDSGRIVFKGRDITR 71
                                   68*************999999888888888888888777 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00012     0.091      15      47 ..      22      52 ..      13      55 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00012
                         AAA_27 15 tdrsldfsaeeadlhliyGpNEAGKstalrAis 47
                                   +d sl+++  e  l++++GpN +GK+t+l+ is
  gi|119719511|ref|YP_920006.1| 22 KDVSLELG--EGTLTMLIGPNGSGKTTLLNIIS 52
                                   46666665..899***************98775 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0    0.0002      0.15       3      34 ..      35      67 ..      34      85 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0002
                                   EEE--SSSSHHHHHHHGGGGB.S--EEEEE--T CS
                          AAA_5  3 lLvGppGtgKselaerlaaal.nreveyvqltr 34
                                   +L+Gp G+gK++l   ++ ++  ++  +v   r
  gi|119719511|ref|YP_920006.1| 35 MLIGPNGSGKTTLLNIISGVIePDSGRIVFKGR 67
                                   8**************999998766666665555 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00012      0.09      18      60 ..      33      75 ..      22      93 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00012
                     Zeta_toxin 18 lillgGqpGAGKselaellkdelerqgnvvrldpDdlRelhPe 60
                                   l +l G  G+GK++l++ +   +e++++ +++++ d+ +l+P+
  gi|119719511|ref|YP_920006.1| 33 LTMLIGPNGSGKTTLLNIISGVIEPDSGRIVFKGRDITRLYPH 75
                                   6678899******************************999999 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00082      0.62       3      20 ..      35      52 ..      33      95 .. 0.81
   2 ?    0.7   0.0      0.73   5.4e+02     131     156 ..     185     210 ..     161     217 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00082
                         AAA_28  3 vitGgestGKTtlleaLa 20
                                   +++G+ ++GKTtll+ ++
  gi|119719511|ref|YP_920006.1| 35 MLIGPNGSGKTTLLNIIS 52
                                   68************9877 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.73
                         AAA_28 131 leereaiderlrealrelgipviivp 156
                                    ++ + +i ++lr a +elg++++iv+
  gi|119719511|ref|YP_920006.1| 185 PALAHEIMQALRRARDELGVSFLIVE 210
                                    67899999**************9994 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00029      0.22       3      20 ..      34      51 ..      32      58 .. 0.86
   2 ?   -2.4   0.0       5.3   3.9e+03      16      36 ..     187     206 ..     186     219 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00029
                                   EEEEC-TTTCHHHHHHHH CS
                          NACHT  3 vilqGeaGsGKTtLlqkl 20
                                    +l G++GsGKTtLl  +
  gi|119719511|ref|YP_920006.1| 34 TMLIGPNGSGKTTLLNII 51
                                   6899**********9866 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.3
                                    HHHHHHHHHCTS-SCCCC-SE CS
                          NACHT  16 Llqklalawaegklpqgafkl 36 
                                    L++++++a+++ +++ g +++
  gi|119719511|ref|YP_920006.1| 187 LAHEIMQALRRARDELG-VSF 206
                                    78888888888887665.333 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2    0.0002      0.15       3      20 ..      34      51 ..      32      61 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0002
                                   EEEEESTTCCHHHHHHHH CS
                           cobW  3 tvltGflGsGKTtLlnhl 20
                                   t+l G+ GsGKTtLln +
  gi|119719511|ref|YP_920006.1| 34 TMLIGPNGSGKTTLLNII 51
                                   8899***********965 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00032      0.24      25      55 ..      31      61 ..      21      74 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00032
                           DLIC 25 gksvlvlGedgsGkttliaklqGveeekkGr 55
                                   g   +++G +gsGkttl+  + Gv e+  Gr
  gi|119719511|ref|YP_920006.1| 31 GTLTMLIGPNGSGKTTLLNIISGVIEPDSGR 61
                                   5567899*****************9999887 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00056      0.42      26      52 ..      35      61 ..      19      98 .. 0.77
   2 ?   -2.1   0.0       2.7     2e+03     116     158 ..     185     228 ..     148     238 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00056
                   Mg_chelatase 26 llvGppGsGKtmlakrlpsllpplsee 52
                                   +l+Gp GsGKt l + +++++ p s +
  gi|119719511|ref|YP_920006.1| 35 MLIGPNGSGKTTLLNIISGVIEPDSGR 61
                                   789*************99998776655 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.7
                   Mg_chelatase 116 pefkrkvlevLRePledgevtisrakakvefpar.fqlvaamNp 158
                                    p + ++++++LR+  ++  v+    +++++  ++ + +v amN 
  gi|119719511|ref|YP_920006.1| 185 PALAHEIMQALRRARDELGVSFLIVEHRLDLASKyVDFVYAMNQ 228
                                    55667777778777777777776666666666652457777775 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00052      0.39       4      23 ..      34      53 ..      32      57 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00052
                      PduV-EutP  4 illiGkvgsGKttLtqalkg 23
                                    +liG+ gsGKttL + ++g
  gi|119719511|ref|YP_920006.1| 34 TMLIGPNGSGKTTLLNIISG 53
                                   69************988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                       111  (0.00619109); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 1476.07
//
Query:       gi|119719512|ref|YP_920007.1|  [L=238]
Description: ABC transporter related [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.3e-31  107.3   0.0    1.1e-30  106.9   0.0    1.1  1  ABC_tran         ABC transporter
    1.1e-14   55.0   1.5    2.9e-06   27.3   0.4    2.1  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    1.2e-10   41.2   0.5     0.0001   21.8   0.0    2.1  2  SMC_N            RecF/RecN/SMC N terminal domain
    0.00021   20.9   0.2    0.00051   19.7   0.2    1.6  1  AAA_29           P-loop containing region of AAA domain
    0.00024   21.4   0.2     0.0035   17.6   0.2    2.1  1  AAA_22           AAA domain
     0.0015   19.1   0.0     0.0023   18.4   0.0    1.3  1  AAA_23           AAA domain
     0.0021   17.7   0.6      0.022   14.3   0.6    2.2  1  AAA_25           AAA domain
     0.0029   17.4   0.1      0.025   14.3   0.1    1.9  2  AAA_15           AAA ATPase domain
     0.0057   16.4   0.0      0.011   15.5   0.0    1.6  1  AAA_30           AAA domain
  ------ inclusion threshold ------
      0.023   14.9   0.1      0.073   13.2   0.1    1.8  2  AAA_33           AAA domain
      0.027   14.7   0.0       0.17   12.2   0.0    2.0  1  SbcCD_C          Putative exonuclease SbcCD, C subunit
       0.03   13.9   0.1      0.049   13.2   0.1    1.3  1  AAA_27           AAA domain
      0.035   14.0   0.2      0.068   13.1   0.1    1.5  2  RsgA_GTPase      RsgA GTPase
      0.036   14.4   0.2      0.057   13.8   0.2    1.5  1  AAA_16           AAA ATPase domain
       0.04   13.8   0.2       0.13   12.1   0.2    1.8  2  NACHT            NACHT domain
      0.092   11.5   0.3          3    6.5   0.2    2.1  2  ABC_ATPase       Predicted ATPase of the ABC class
       0.13   11.4   0.1       0.25   10.5   0.1    1.4  1  NB-ARC           NB-ARC domain
       0.16   10.9   0.1       0.25   10.2   0.1    1.2  1  AAA_10           AAA-like domain
       0.16   12.1   0.0       0.32   11.1   0.0    1.5  1  MMR_HSR1         50S ribosome-binding GTPase
       0.17   11.0   0.0       0.24   10.6   0.0    1.2  1  Polysacc_deac_2  Divergent polysaccharide deacetylase
       0.19   11.6   0.1       0.91    9.4   0.0    1.8  2  ATPase_2         ATPase domain predominantly from Archaea


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.9   0.0   1.3e-33   1.1e-30       2     137 .]      20     164 ..      19     164 .. 0.95

  Alignments for each domain:
  == domain 1  score: 106.9 bits;  conditional E-value: 1.3e-33
                                    EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHHHH. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                       ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvren. 79 
                                    +nvs++l +ge +a+vG+nG+GKStLlk l gl +   G++l+dg+d+++  +++++   +g+lpq+ ++f+elt ren 
  gi|119719512|ref|YP_920007.1|  20 SNVSFTLDKGEFLAVVGPNGSGKSTLLKGLFGLADVLGGKVLFDGRDITRlAPHKRSLMGMGYLPQTGNVFEELTGRENl 99 
                                    79************************************************99**************************** PP

                                    ..........HHHTCHHHHHHHSTTGG.TTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    ..........xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ..........esdeeiekalsklglke.lkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                              + ++++e++l+ l  +  + ++++    ++LSgG++q++ala+ l++kp+l+++DEp+a
  gi|119719512|ref|YP_920007.1| 100 vlagydlpreDFERRLEEVLDFLPEVRgFLNRKA----TTLSGGERQMLALAMQLVRKPSLIMFDEPSA 164
                                    *********999999******9987764777777....*****************************75 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.4   3.4e-09   2.9e-06       2      26 ..      32      61 ..      31      92 .. 0.78
   2 !   26.4   0.0   6.6e-09   5.6e-06     233     294 ..     132     191 ..     121     192 .. 0.89

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 3.4e-09
                         AAA_21  2 nvliGpNgsGKSnLLdaldllarl.....d 26
                                    +++GpNgsGKS+LL+ l +la++     +
  gi|119719512|ref|YP_920007.1| 32 LAVVGPNGSGKSTLLKGLFGLADVlggkvL 61
                                   689******************987655442 PP

  == domain 2  score: 26.4 bits;  conditional E-value: 6.6e-09
                         AAA_21 233 parelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQvil 294
                                     a+ lS G +++lal+  l r +   sl+ +DEp + L Pk++++++e ++ l++  g+ vil
  gi|119719512|ref|YP_920007.1| 132 KATTLSGGERQMLALAMQLVRKP---SLIMFDEPSAALAPKVVEHVFERIRMLNKgLGITVIL 191
                                    56789***************988...************************9988877888876 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.3   2.3e-06    0.0019      25      48 ..      30      52 ..      19      61 .. 0.83
   2 !   21.8   0.0   1.2e-07    0.0001     135     201 ..     134     196 ..      87     210 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.3e-06
                                   SEEEEEESTTSSHHHHHHHHHHHC CS
                                   xxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 25 sftaivGpNGSGKsnlldAilFvL 48
                                   +f a+vGpNGSGKs ll  + F L
  gi|119719512|ref|YP_920007.1| 30 EFLAVVGPNGSGKSTLLKGL-FGL 52
                                   699*************9988.655 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 1.2e-07
                                    TCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 135 elLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreem 201
                                    ++LSgGe++++ala+    q v++ +l ++De  aaL  k v+ v e+++  +k   + vi +++++
  gi|119719512|ref|YP_920007.1| 134 TTLSGGERQMLALAM----QLVRKPSLIMFDEPSAALAPKVVEHVFERIRMLNKGLGITVILVEQDT 196
                                    48********99865....6799999**************************999999988877765 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.2     6e-07   0.00051      15      39 ..      22      46 ..      15      52 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 6e-07
                         AAA_29 15 htieidlkgatlltGpsGsGKSTll 39
                                    ++++d  ++  ++Gp+GsGKSTll
  gi|119719512|ref|YP_920007.1| 22 VSFTLDKGEFLAVVGPNGSGKSTLL 46
                                   667888555999************8 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.2   4.1e-06    0.0035       5     128 ..      29     192 ..      26     200 .. 0.58

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4.1e-06
                         AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaee......................................erpevv.fv 45 
                                      +l+v+G+ G+GK+tll+ l+  +d                                             ++  v+  +
  gi|119719512|ref|YP_920007.1|  29 GEFLAVVGPNGSGKSTLLKGLFGLADVL----GgkvlfdgrditrlaphkrslmgmgylpqtgnvfeeltgRENLVLaGY 104
                                    6799***************999988643....134557777777777777777777777666666666665333333466 PP

                         AAA_22  46 tlpsst......sskdllrellralglelkaerlsseellealeqalraravielliiDEaqh.lr.s..eealeeLrsl 115
                                    +lp +       +  d+l e+  +l++++ +  + ++++l++  q +r+   ++l++ DE    l  +  e ++e +r+l
  gi|119719512|ref|YP_920007.1| 105 DLPREDferrleEVLDFLPEVRGFLNRKATTLSGGERQMLALAMQLVRK---PSLIMFDEPSAaLApKvvEHVFERIRML 181
                                    6666664333334444444444444443333333333333333333333...3457777776656442456666666555 PP

                         AAA_22 116 lnlsrkgvqliLv 128
                                     +    g+++iLv
  gi|119719512|ref|YP_920007.1| 182 NK--GLGITVILV 192
                                    55..666666665 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   2.7e-06    0.0023      13      39 ..      22      49 ..      13      73 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.7e-06
                         AAA_23 13 qeidFskg.ltlItGpNGaGKTTildAi 39
                                   +++ ++kg + +++GpNG+GK+T+l  +
  gi|119719512|ref|YP_920007.1| 22 VSFTLDKGeFLAVVGPNGSGKSTLLKGL 49
                                   5566666525579************876 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.6   2.6e-05     0.022      30     157 ..      26     168 ..      18     196 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.6e-05
                         AAA_25  30 lpagelallaGapgtGKttlaldl..alavatGkpwlg........pvapeqgkVlyvsaEds.edelrrRlravgeal. 97 
                                    l +ge+ +++G+ g+GK+tl+  l   ++v+ Gk +++        p++   +   y+   ++  +el  R   v++ + 
  gi|119719512|ref|YP_920007.1|  26 LDKGEFLAVVGPNGSGKSTLLKGLfgLADVLGGKVLFDgrditrlaPHKRSLMGMGYLPQTGNvFEELTGRENLVLAGYd 105
                                    789*****************988844578888888887787776765555555555554444435566666666666666 PP

                         AAA_25  98 ..rddarllvldlagv.eslpLfakdrggtlltadvdaleaaieevegvrlvviDplsralgg 157
                                      r+d + ++  + ++  +++ f +++  tl  ++ + l+ a++ v ++ l+ +D  s+al+ 
  gi|119719512|ref|YP_920007.1| 106 lpREDFERRLEEVLDFlPEVRGFLNRKATTLSGGERQMLALAMQLVRKPSLIMFDEPSAALAP 168
                                    663344444444445555566666666666677777777777777777777777777777665 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.1     3e-05     0.025      21      43 ..      26      49 ..      19      56 .. 0.80
   2 ?    0.8   0.0      0.37   3.2e+02     323     349 ..     153     179 ..     133     184 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3e-05
                         AAA_15 21 lsee.ltvliGkNnsGKSsileal 43
                                   l++  +  ++G+N+sGKS++l+ l
  gi|119719512|ref|YP_920007.1| 26 LDKGeFLAVVGPNGSGKSTLLKGL 49
                                   44444999*************977 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.37
                         AAA_15 323 knvilliEEPEahLHpqaqkvlikllk 349
                                    k+ +++++EP a L p+  +++++ ++
  gi|119719512|ref|YP_920007.1| 153 KPSLIMFDEPSAALAPKVVEHVFERIR 179
                                    6789**********9999999988776 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.2e-05     0.011      17      58 ..      28      76 ..      21     195 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.2e-05
                         AAA_30 17 gdrvavltGpAGtGKttalkalreaweaag.......grviglAptgka 58
                                   +  + +++Gp G+GK+t+lk+l  +++  g       +++  lAp ++ 
  gi|119719512|ref|YP_920007.1| 28 KGEFLAVVGPNGSGKSTLLKGLFGLADVLGgkvlfdgRDITRLAPHKRS 76
                                   455899****************999999974667776667777777665 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   8.5e-05     0.073       4      20 ..      34      50 ..      32      76 .. 0.88
   2 ?   -1.3   0.0       2.7   2.3e+03      82      82 ..     172     172 ..     126     207 .. 0.51

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.5e-05
                         AAA_33  4 lvGlpGsGKstlaerll 20
                                   +vG++GsGKstl+++l 
  gi|119719512|ref|YP_920007.1| 34 VVGPNGSGKSTLLKGLF 50
                                   89***********9985 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.7
                         AAA_33  82 r 82 
                                    +
  gi|119719512|ref|YP_920007.1| 172 E 172
                                    2 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00019      0.17      24      86 ..     127     176 ..     107     180 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00019
                        SbcCD_C  24 kelsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatlle 86 
                                    + l+r+++tlSGGe+q+l       ala+++ +      +++l+++DE  + l ++ ++ ++e
  gi|119719512|ref|YP_920007.1| 127 GFLNRKATTLSGGERQML-------ALAMQLVR------KPSLIMFDEPSAALAPKVVEHVFE 176
                                    34899**********654.......45555555......467888888777777777776665 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   5.8e-05     0.049      19      46 ..      22      49 ..      13      58 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.8e-05
                         AAA_27 19 ldfsaeeadlhliyGpNEAGKstalrAi 46
                                   ++f  ++ ++  ++GpN +GKst+l+++
  gi|119719512|ref|YP_920007.1| 22 VSFTLDKGEFLAVVGPNGSGKSTLLKGL 49
                                   66777789999**************986 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1     8e-05     0.068      87     122 ..      16      52 ..       4      69 .. 0.80
   2 ?   -3.3   0.0       8.8   7.5e+03      72      90 ..     182     200 ..     170     214 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8e-05
                                    HTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT CS
                    RsgA_GTPase  87 kegleelkellkd.ktsvlvGqSGvGKStLinallpe 122
                                     e +++++  l++ ++ ++vG+ G GKStL++ l + 
  gi|119719512|ref|YP_920007.1|  16 MEVVSNVSFTLDKgEFLAVVGPNGSGKSTLLKGLFGL 52 
                                    566778888888889****************998765 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 8.8
                                    HHHTTSEEEE--TTTHTTH CS
                    RsgA_GTPase  72 lealgyevllvsaktkegl 90 
                                     + lg++v+lv+++t+++l
  gi|119719512|ref|YP_920007.1| 182 NKGLGITVILVEQDTRRAL 200
                                    5566677777766655544 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   6.6e-05     0.057      24      45 ..      29      50 ..      19     161 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.6e-05
                         AAA_16 24 pelvllsGesGvGKsslvrell 45
                                   +e + ++G+ G+GKs+l++ l+
  gi|119719512|ref|YP_920007.1| 29 GEFLAVVGPNGSGKSTLLKGLF 50
                                   37899*************9887 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   0.00015      0.13       3      21 ..      32      50 ..      30      58 .. 0.88
   2 ?   -2.3   0.0       4.2   3.6e+03     118     144 ..     203     229 ..     199     233 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00015
                                   EEEEC-TTTCHHHHHHHHH CS
                          NACHT  3 vilqGeaGsGKTtLlqkla 21
                                   +++ G++GsGK+tLl++l 
  gi|119719512|ref|YP_920007.1| 32 LAVVGPNGSGKSTLLKGLF 50
                                   689************9985 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4.2
                                    TT--EEEEEEECCCHHHHCTTSSCE.. CS
                          NACHT 118 lpeasllltvrpralrdleeqleeaiv 144
                                      +a ll++ r+r   d++e+l+++  
  gi|119719512|ref|YP_920007.1| 203 AEKALLLVSGRTRFYGDAGELLARKDL 229
                                    567889999999999999888888755 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.2    0.0035         3     244     264 ..      28      49 ..      21      68 .. 0.78
   2 ?    3.1   0.0      0.04        34     359     411 ..     160     209 ..     154     215 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0035
                                    SS.EEEEEE-TTSSHHHHHHHH CS
                     ABC_ATPase 244 kG.vtlIvGggfhGKsTLLeAl 264
                                    kG   ++vG++  GKsTLL+ l
  gi|119719512|ref|YP_920007.1|  28 KGeFLAVVGPNGSGKSTLLKGL 49 
                                    5656789************987 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.04
                                    -HHHHHHS-GGG--B--HHHCHHHHHHHH--EEEEEESS-GCCTTT-SEEEEE CS
                     ABC_ATPase 359 DermqelvskekepitplvdrvrelykklgvstilvvggsgdyldvAdtvilm 411
                                    De  ++l +   + ++ + +r+r l k lg+++ilv       l++A++ +l+
  gi|119719512|ref|YP_920007.1| 160 DEPSAALAP---KVVEHVFERIRMLNKGLGITVILVEQDTRRALKIAEKALLL 209
                                    555555553...34677899******************999999999999887 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00029      0.25      21      42 ..      30      51 ..      16      65 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00029
                                   EEEEEEESTTSSHHHHHHHHCC CS
                         NB-ARC 21 lvvalvGmgGvGKttlakqiln 42
                                    ++a+vG  G+GK+tl+k  + 
  gi|119719512|ref|YP_920007.1| 30 EFLAVVGPNGSGKSTLLKGLFG 51
                                   489*************998775 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00029      0.25      25      53 ..      33      61 ..      25      74 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00029
                         AAA_10 25 liiGdlGnGKSvlakllvlyisllggkal 53
                                   +++G+ G GKS l k l+  + +lggk+l
  gi|119719512|ref|YP_920007.1| 33 AVVGPNGSGKSTLLKGLFGLADVLGGKVL 61
                                   89*************************98 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00037      0.32       2      29 ..      32      60 ..      31      78 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00037
                                   EEEEESTTSSHHHHHHHHHTS.TEEESSS CS
                       MMR_HSR1  2 vaivGrpNvGKStLinaltge.kaivsdk 29
                                    a+vG   +GKStL++ l+g   +  ++ 
  gi|119719512|ref|YP_920007.1| 32 LAVVGPNGSGKSTLLKGLFGLaDVLGGKV 60
                                   589**************998434444555 PP

>> Polysacc_deac_2  Divergent polysaccharide deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00028      0.24      71     134 ..     105     171 ..      97     206 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00028
                                    TS-HHHHHHHHHHHHCCSTT-SEEEEEE-CCHHC-HHHHHHHHHH.HHHTT-EEEE..-S--TT-SH CS
                Polysacc_deac_2  71 smseeeiekrleaalsrvpgavgvnnhmGskftedeeameavlee.lkergllflD..srtsaksva 134
                                    ++++e+ e+rle++l+ +p+++g+ n   + +   e++m a+  + +++  l+++D  s + a +v+
  gi|119719512|ref|YP_920007.1| 105 DLPREDFERRLEEVLDFLPEVRGFLNRKATTLSGGERQMLALAMQlVRKPSLIMFDepSAALAPKVV 171
                                    678899*****************************99999886551568889999943333344444 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0    0.0011      0.91      20      41 ..      29      50 ..      22      68 .. 0.81
   2 ?   -0.1   0.0      0.86   7.3e+02      78     137 ..     143     204 ..      89     211 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0011
                       ATPase_2 20 neiyfiYGpegsGKtaLlkeii 41
                                    e++ + Gp gsGK++Llk + 
  gi|119719512|ref|YP_920007.1| 29 GEFLAVVGPNGSGKSTLLKGLF 50
                                   5778899***********9765 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.86
                       ATPase_2  78 lekalgiavpkaeleeilk.eksklvfkaielllekikkkgkk....iiiiiDelqklidlglng 137
                                    +   +++ v+k +l  +++    +l+ k +e ++e i+   k     +i++  +  ++   ++ +
  gi|119719512|ref|YP_920007.1| 143 MLALAMQLVRKPSLI-MFDePSAALAPKVVEHVFERIRMLNKGlgitVILVEQDTRRAL--KIAE 204
                                    333336777777774.4554777888888888888888777767743343333444444..5554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 1590.26
//
Query:       gi|119719513|ref|YP_920008.1|  [L=299]
Description: inner-membrane translocator [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-40  138.9  35.1      2e-40  138.7  35.1    1.0  1  BPD_transp_2  Branched-chain amino acid transport system / pe
  ------ inclusion threshold ------
        9.8    6.3   7.4         19    5.4   0.7    2.8  2  QCR10         Ubiquinol-cytochrome-c reductase complex subuni


Domain annotation for each model (and alignments):
>> BPD_transp_2  Branched-chain amino acid transport system / permease component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.7  35.1   2.2e-44     2e-40       3     268 .]       8     285 ..       6     285 .. 0.88

  Alignments for each domain:
  == domain 1  score: 138.7 bits;  conditional E-value: 2.2e-44
                   BPD_transp_2   3 lnlltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsllllallvallvgaavglllgllvlr.lk 81 
                                    +  l+++ +la++++Gl+l+   + v n++hg f+++G y+a +l++ l   +++ ++va+++ga+vgl++++lv   l+
  gi|119719513|ref|YP_920008.1|   8 VDALVYGNLLALLSVGLSLTLLTTEVSNFAHGDFAVIGIYIAYTLSQVLNVTPYAFIPVAFAGGALVGLAVYFLVFDpLR 87 
                                    66789999*******************************************************************96156 PP

                   BPD_transp_2  82 vdeliitllllsvlvgltlllltgitsgvkgqs..svkellgfagallsflsaviv.......llalllvlavllllrrt 152
                                     +   +tl+++s+++ ++l +  +i  +v++    ++ + + f+++ l  l+ ++        +++l l+++++++l+rt
  gi|119719513|ref|YP_920008.1|  88 DKASFVTLMIVSMALEFILRYSVQIYADVMQRLlkTFGRGFMFNDVRLALLGLHVDgvvvyssITTLSLLVLLYVFLYRT 167
                                    66678999999999999997777777777655433333333334444444333333899********************* PP

                   BPD_transp_2 153 rfGralravgeneeaaralGinvkrvklltfvisgalAglaGallalllgsippnigvglgfnaiaavvlGgagsllgtv 232
                                    ++G+a+ra+ en+++a+ lGinvk+v + ++++s+++A+ aG++l + +++ p ++g+ l ++++aav +Gg+gsl+g +
  gi|119719513|ref|YP_920008.1| 168 KTGTAMRAAIENPQLAQTLGINVKKVYAYSWMLSAGFAAAAGVFLPFKIVVNP-DTGFSLLLSMFAAVTVGGLGSLAGSL 246
                                    ************************************************99888.************************** PP

                   BPD_transp_2 233 iGaliigvvksllltllgi...ptelarvllgallilvl 268
                                    +Ga++i+++++ ++++l++   +t+++ +++++ + +vl
  gi|119719513|ref|YP_920008.1| 247 VGAYLISFSEIAATYFLSSlglSTSYRALVSFLSIAVVL 285
                                    ***********888887779999*********9998876 PP

>> QCR10  Ubiquinol-cytochrome-c reductase complex subunit (QCR10)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   1.1     0.009        81       8      31 ..      57      80 ..      50      82 .. 0.86
   2 ?    5.4   0.7    0.0021        19       3      27 ..     187     212 ..     185     217 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.009
                          QCR10  8 tltrygptlalfGgaagvavlfft 31
                                   ++t y+++ ++f+g a+v++++++
  gi|119719513|ref|YP_920008.1| 57 NVTPYAFIPVAFAGGALVGLAVYF 80
                                   7888999999**********9997 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0021
                          QCR10   3 gitlktltrygptl.alfGgaagvav 27 
                                    gi++k++  y+  l a+f++aagv++
  gi|119719513|ref|YP_920008.1| 187 GINVKKVYAYSWMLsAGFAAAAGVFL 212
                                    89999999996554288999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       734  (0.0409393); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1881.36
//
Query:       gi|119719514|ref|YP_920009.1|  [L=349]
Description: inner-membrane translocator [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-46  158.0  25.4    3.6e-46  157.5  25.4    1.2  1  BPD_transp_2  Branched-chain amino acid transport system / pe


Domain annotation for each model (and alignments):
>> BPD_transp_2  Branched-chain amino acid transport system / permease component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.5  25.4     2e-50   3.6e-46       7     268 .]      12     315 ..       6     315 .. 0.95

  Alignments for each domain:
  == domain 1  score: 157.5 bits;  conditional E-value: 2e-50
                   BPD_transp_2   7 tlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsl................................ 54 
                                    +l ++++i+A +l+l +g +G++n++ ++f+a+Ga++++ l+++l+ l                                
  gi|119719514|ref|YP_920009.1|  12 VLYSVYVILASSLNLEYGELGLPNFAKSAFFAVGAFSVGALSVRLGTLllgitmegefklksvyyatlvsqalvnspqlg 91 
                                    6779**************************************************************************** PP

                   BPD_transp_2  55 .lllallvallv..gaavglllgllvlrlkvdeliitllllsvlvgltlllltgitsgvkgqssvkellgfagallsfls 131
                                     +l++++++++v  +a++g+l  ++ lrl++d+l + l+++s+++++++ +++ + +g++g   v+ l+ +++ l   + 
  gi|119719514|ref|YP_920009.1|  92 vILFVVPLMIAVplAALLGVLASYPALRLREDYLGMLLIAFSEIIRVVARNYEPLVGGTYGAGVVDFLAWIPPPLKQVVL 171
                                    *66666666654338999*********************************************************99999 PP

                   BPD_transp_2 132 avivllalllvlavllllrrtrfGralravgeneeaaralGinvkrvklltfvisgalAglaGallalllgsipp.nigv 210
                                     +++  +++++ +++++l r++fGr lra+++ne aa +lG +v +++++++++++++A++aG+l+a++ gs++p ++ +
  gi|119719514|ref|YP_920009.1| 172 LALSSSIAFAIWLAYYRLSRSPFGRVLRAIRDNELAASVLGRDVAKMRMTVMALGSGMAAVAGVLYAFYVGSVNPdDFTI 251
                                    9999999************************************************************************* PP

                   BPD_transp_2 211 glgfnaiaavvlGgagsllgtviGaliigvvksllltllgi......ptelarvllgallilvl 268
                                      +f + ++v++Gg g+++g+++G  ++ +v+ ++ ++++       p+  ++v+lg+ lil++
  gi|119719514|ref|YP_920009.1| 252 SKTFLVALMVIIGGRGNPYGALVGPATYIAVDRSIQFVKQYlalpfdPNYASYVILGVALILIV 315
                                    *********************************77777766*999988999*********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2498.83
//
Query:       gi|119719515|ref|YP_920010.1|  [L=704]
Description: CoA-binding domain-containing protein, partial [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-78  263.8   0.1    2.3e-78  262.7   0.1    1.6  2  ATP-grasp_5    ATP-grasp domain
      9e-52  174.5   0.4    1.8e-50  170.3   0.1    2.7  3  Succ_CoA_lig   Succinyl-CoA ligase like flavodoxin domain
    8.3e-27   94.0   2.8    3.3e-26   92.1   0.2    3.1  4  CoA_binding_2  CoA binding domain
    4.9e-16   59.2   0.1    3.7e-15   56.4   0.1    2.4  2  CoA_binding    CoA binding domain
    0.00035   20.4   0.0    0.00099   18.9   0.0    1.8  1  Ligase_CoA     CoA-ligase
     0.0069   15.9   0.1      0.022   14.3   0.0    1.9  2  CPSase_L_D2    Carbamoyl-phosphate synthase L chain, ATP bind
  ------ inclusion threshold ------
      0.018   14.6   0.1      0.057   13.0   0.1    1.9  1  ATP-grasp_2    ATP-grasp domain
      0.067   13.8   0.5        1.4    9.6   0.1    3.6  3  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent


Domain annotation for each model (and alignments):
>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       3.1   6.9e+03     134     156 ..     314     336 ..     310     351 .. 0.64
   2 !  262.7   0.1     1e-81   2.3e-78       2     222 .]     480     701 ..     479     701 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 3.1
                    ATP-grasp_5 134 tavevlkdvavalpplnstlare 156
                                    +a+++l+d  ++l+ + + la++
  gi|119719515|ref|YP_920010.1| 314 MATDALEDYGIRLMDIPQDLAEK 336
                                    55556666666666665555555 PP

  == domain 2  score: 262.7 bits;  conditional E-value: 1e-81
                    ATP-grasp_5   2 alaegrtlLteaeakelleaygipvvetrlassaeeaveaaeeigypvvlKivspdilhKtdvgGvrlnlkdaeevraaa 81 
                                    al+egrt+Lt +ea++l+  ygipv+  ++a+s+eeav++a+eigypvvl + spdilhK+d+gG+ ++l++++ev++ +
  gi|119719515|ref|YP_920010.1| 480 ALKEGRTTLTPSEAAALVGYYGIPVLAKKIAKSPEEAVRIAREIGYPVVLEVESPDILHKSDIGGILVGLQSDAEVAEGY 559
                                    89****************************************************************************** PP

                    ATP-grasp_5  82 eeilervkekspeariegvlVqemakrggrElivgvteDpvFGpvilfGlGGtavevlkdvavalpplnstlareliert 161
                                    ++il++v++k+p+ar++g++V +ma+ +g E+ +gv++Dp+FGp++++G GG+ ve+++dv+++++pl+ ++a e++e+t
  gi|119719515|ref|YP_920010.1| 560 SKILDNVSKKAPSARVNGIIVRKMAE-KGKEIALGVHRDPIFGPLVMVGSGGVLVELYRDVSFRVAPLSLEDAYEMLEET 638
                                    **************************.***************************************************** PP

                    ATP-grasp_5 162 kaskllkgvrgekkadlaaleellvrlsqLvvdlpeIreldinPllvee..egvvalDarirl 222
                                    k++k+lkg+rge+++d ++++++l+rls+L++d+ eI+ +dinP +v+e  +g +a+D++++l
  gi|119719515|ref|YP_920010.1| 639 KIYKVLKGYRGEPPSDYEKVVDVLIRLSKLACDVEEIEDIDINPFFVYErgKGGIAVDVKVTL 701
                                    ************************************************95455*******986 PP

>> Succ_CoA_lig  Succinyl-CoA ligase like flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       3.6   8.1e+03      82     109 ..      96     123 ..      87     125 .. 0.74
   2 !  170.3   0.1   8.2e-54   1.8e-50       1     138 []     154     291 ..     154     291 .. 0.99
   3 ?    1.1   0.0      0.14   3.1e+02      68      93 ..     394     419 ..     363     431 .. 0.69

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 3.6
                   Succ_CoA_lig  82 kpvvvlksGrseagaraaashtgalags 109
                                    k v v+ sG +e g+    +  +++a++
  gi|119719515|ref|YP_920010.1|  96 KAVAVITSGFKEIGNVDLEQRIASIAKN 123
                                    8899999999888888887777777765 PP

  == domain 2  score: 170.3 bits;  conditional E-value: 8.2e-54
                   Succ_CoA_lig   1 pGkialisqSGalalalldwaasrglgfskvvslGneadvdvadlleylaedpetkvillylEsirdgrkflsaarraar 80 
                                    pG+ia+i+qSGal++al+ w++ +g+g+s +vs+Gn+advd++dl+e+++ed+ tkvi++ylE+++dgr+fl+aarr+ar
  gi|119719515|ref|YP_920010.1| 154 PGEIAFITQSGALGIALVGWTKLKGIGLSDLVSIGNKADVDETDLVEFFGEDQYTKVITAYLEGVSDGRRFLEAARRVAR 233
                                    79****************************************************************************** PP

                   Succ_CoA_lig  81 kkpvvvlksGrseagaraaashtgalagsdavvdaafrqaGvlrvdsleelfdaaell 138
                                    +kp++vlk+Gr  +   a +shtg+lags a+++aaf+q+G+l ++s+ elfd a+++
  gi|119719515|ref|YP_920010.1| 234 RKPIIVLKAGRGVRTIGAIKSHTGSLAGSFAAYEAAFKQSGILLARSFVELFDWATAF 291
                                    ******************************************************9876 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.14
                   Succ_CoA_lig  68 grkflsaarraarkkpvvvlksGrse 93 
                                    ++++l+a+r++  kk v++   G +e
  gi|119719515|ref|YP_920010.1| 394 AEALLRAVRETESKKTVLASFIGGEE 419
                                    57889999999999999998777655 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.1   0.2   1.5e-29   3.3e-26       2     113 ..      14     136 ..      13     138 .. 0.94
   2 ?   -0.9   0.0      0.97   2.2e+03      66     105 ..     395     434 ..     372     438 .. 0.72
   3 ?   -2.4   0.0       2.9   6.5e+03      80     106 ..     493     528 ..     451     530 .. 0.51
   4 ?   -1.4   0.0       1.5   3.3e+03      23      81 ..     616     681 ..     609     688 .. 0.63

  Alignments for each domain:
  == domain 1  score: 92.1 bits;  conditional E-value: 1.5e-29
                                    -EEEET--S-TTSHHHHHHHHHHH....HT--EEEESSS-SEETTEES----T....T--EEEE-S-HHHHGGGHHHHHH CS
                  CoA_binding_2   2 tiaVvGasdnpgkfgykvlrylle....hglpvvpVnpkeeeilgekvyaslaedpepvdlvdvftppeatpeivkeala 77 
                                    ++aVvGas np+k gy+v+++lle    ++ +++pVnp+++eilg k+y+s++e p +vdlv+v++p+ a+p ++++a++
  gi|119719515|ref|YP_920010.1|  14 SVAVVGASRNPEKIGYQVVKNLLEagfpRE-RIFPVNPNADEILGLKCYKSVSEIPYQVDLVVVAVPAPAVPGVLEDAGR 92 
                                    79**********************666555.8*********************968************************ PP

                                    H--SEEEE-TT........---HHHHHHHHHTT-EEE.ES-HHH CS
                  CoA_binding_2  78 lgakavwlqpg........sedeeaaelaeeagirvvgdrCilv 113
                                    +g+kav +  +          ++ +a++a+++g+r++g++ +++
  gi|119719515|ref|YP_920010.1|  93 KGVKAVAVITSgfkeignvDLEQRIASIAKNYGMRLLGPNIVGI 136
                                    ******999999*******9******************997665 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.97
                                    HHHGGGHHHHHHH--SEEEE-TT---HHHHHHHHHTT-EE CS
                  CoA_binding_2  66 eatpeivkealalgakavwlqpgsedeeaaelaeeagirv 105
                                    ea++  v+e +++++  + +  g+e +ea  ++ e+gi++
  gi|119719515|ref|YP_920010.1| 395 EALLRAVRETESKKTVLASFIGGEEVNEACGKLTENGIPC 434
                                    4455566666677777778888888888888888888765 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 2.9
                                    -SEEEE-TT.........---HHHHHHHHHTT-EEE CS
                  CoA_binding_2  80 akavwlqpg.........sedeeaaelaeeagirvv 106
                                    a+a++ + g            eea+++a+e g +vv
  gi|119719515|ref|YP_920010.1| 493 AAALVGYYGipvlakkiaKSPEEAVRIAREIGYPVV 528
                                    333333333444444444555677777777666655 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 1.5
                                    HHHHT--EEEESSS-.SEETT.EES----T.....T--....EEEE-S-HHHHGGGHHHHHHH--S CS
                  CoA_binding_2  23 llehglpvvpVnpke.eeilg.ekvyaslae.dpepvd....lvdvftppeatpeivkealalgak 81 
                                    +++ +++v p       e+l   k y+ l+    ep+     +vdv+++ ++++  v+e+++++++
  gi|119719515|ref|YP_920010.1| 616 YRDVSFRVAPLSLEDaYEMLEeTKIYKVLKGyRGEPPSdyekVVDVLIRLSKLACDVEEIEDIDIN 681
                                    555666666666555544444044444444322333336778999999999999999999887765 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.4   0.1   1.7e-18   3.7e-15       4      96 .]      13     104 ..      11     104 .. 0.96
   2 ?   -1.1   0.0       1.4   3.2e+03      36      58 ..     420     442 ..     396     449 .. 0.70

  Alignments for each domain:
  == domain 1  score: 56.4 bits;  conditional E-value: 1.7e-18
                                    EEEEEETTTSHHHHHH.HHHHHHHHECEE..EEEEC-TTTTTCEETTEEEESCHHHHHHHCTTTEEEEES-HHHHHHHHH CS
                    CoA_binding   4 tkviviGagglgiagl.yhfkeklkygik..avfgvnprkvgtevlglpvyksvdeleektevdvavitvPaesaqeavd 80 
                                     +v+v+Ga+++  +++  ++k+ l+ g++   +f+vnp+  ++e+lgl++yksv+e++ +  vd  v++vPa+++  + +
  gi|119719515|ref|YP_920010.1|  13 ESVAVVGASRNPEKIGyQVVKNLLEAGFPreRIFPVNPN--ADEILGLKCYKSVSEIPYQ--VDLVVVAVPAPAVPGVLE 88 
                                    68**************88999*******9889*******..*******************..****************** PP

                                    HHHHTT-SEEEEESST CS
                    CoA_binding  81 elveagikgiviiteg 96 
                                    ++ ++g+k +++it+g
  gi|119719515|ref|YP_920010.1|  89 DAGRKGVKAVAVITSG 104
                                    **************86 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.4
                                    C-TTTTTCEETTEEEESCHHHHH CS
                    CoA_binding  36 vnprkvgtevlglpvyksvdele 58 
                                    vn+  +  + +g+p+y+s +++ 
  gi|119719515|ref|YP_920010.1| 420 VNEACGKLTENGIPCYESPEKAA 442
                                    44444444556888887776665 PP

>> Ligase_CoA  CoA-ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   4.4e-07   0.00099      55     148 ..     356     443 ..     353     448 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 4.4e-07
                                    ...HHHHHHHHHHHHS-TT-SEEEEE.EEESSSEHHHHHHHHHHHHHHTT...--S-EEEEEECTTHH.....HHHHHHH CS
                     Ligase_CoA  55 miDptkriealkklaadpevkvilld.ivlGygahedpaaellkaikeakaegrelpvvarvaGteadpqelseqakale 133
                                    m D ++++ alk+l+  ++v+++l+    + + + +++a++ll+a++e++  +++ ++ +++ G e++     e+ ++l+
  gi|119719515|ref|YP_920010.1| 356 MADAEQYYGALKDLLMHDSVDAVLVLyCHTAITNPQEIAEALLRAVRETE--SKKTVLASFIGGEEVN-----EACGKLT 428
                                    99*************99999988776156889999**************9..8888888888888888.....******* PP

                                    TTTSSEEE-SSHHHH CS
                     Ligase_CoA 134 eagveiasskaqalr 148
                                    e g+  ++s ++a+ 
  gi|119719515|ref|YP_920010.1| 429 ENGIPCYESPEKAAS 443
                                    *******99999876 PP

>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       2.1   4.8e+03      51      88 ..     243     280 ..     223     283 .. 0.77
   2 !   14.3   0.0   9.9e-06     0.022      15     145 ..     503     639 ..     491     655 .. 0.70

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.1
                                    TTTEEEESSHHHHHHHHHHHHHHHHHHHSTS-EEEEE- CS
                    CPSase_L_D2  51 GkGmrvarneeelaelvkkalaeakaafgnkqvlveks 88 
                                    G+G r +   +  + +++ ++a+ +aaf ++ +l+ +s
  gi|119719515|ref|YP_920010.1| 243 GRGVRTIGAIKSHTGSLAGSFAAYEAAFKQSGILLARS 280
                                    77887777777777888888888888999999999887 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 9.9e-06
                                    BBSSEECSSBSSHHHHHHHHHHH-SSEEEEE.......TTCCTTTTEEEESSHH...HHHHHHHHHHHHHHHHHSTS-EE CS
                    CPSase_L_D2  15 pvvpssaapvetleealaiakeigyPviika.......afglGGkGmrvarnee...elaelvkkalaeakaafgnkqvl 84 
                                    pv   ++a  ++ eea++ia+eigyPv++            +GG   ++ ++ e     ++++ + +++a+ +   + + 
  gi|119719515|ref|YP_920010.1| 503 PVLAKKIA--KSPEEAVRIAREIGYPVVLEVespdilhKSDIGGILVGLQSDAEvaeGYSKILDNVSKKAP-SARVNGII 579
                                    55554445..999**************97641111111356788877776665411144566666667775.45677899 PP

                                    EEE--SSSEEEEEEEEEET.TS-EEEEEEEEECCECTCCCCEEEES-SS--HHHHHHHHHHH CS
                    CPSase_L_D2  85 vekslkgpkeiEvevlrDa.kgnvitvcerenslqlrtqkvievAPsqtLtdeerqalreaa 145
                                    v k+ ++ kei + v rD   g  ++v++   +++l  + +  vAP     ++++++l+e+ 
  gi|119719515|ref|YP_920010.1| 580 VRKMAEKGKEIALGVHRDPiFGPLVMVGSGGVLVELYRDVSFRVAPLSL--EDAYEMLEETK 639
                                    9999999999999999996369999999999999998899999999653..45677777654 PP

>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   2.6e-05     0.057       7     200 ..     493     683 ..     488     685 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.6e-05
                                    HHHHHHCTT----SEEEESSHHHHHHHHHHHTSSSEEEEE-.-SSSTCCCTTCEEE.ESSHHHHHHHHHCCTTSEEE-TT CS
                    ATP-grasp_2   7 akeilakygvkvpegevaesaeeaeeaakklgekelvvKaQ.vlaGGRGKagGvkl.vkskeeakeaakellgkelvtkq 84 
                                    a  ++  yg++v   ++a+s+eea ++a+++g  + v+      +  +   gG+ +  +s  e++e  +++l +  +   
  gi|119719515|ref|YP_920010.1| 493 AAALVGYYGIPVLAKKIAKSPEEAVRIAREIGYPV-VLEVEsPDILHKSDIGGILVgLQSDAEVAEGYSKILDNVSK--- 568
                                    6778899*************************999.55433123444556699887367788999999999987766... PP

                                    S-TT-EEE--EEEEE---ECEEEEEEEEEETTTTEEEEEEESSTTS-HHHHHHH-GGGEEEEEEBTTTB-.-HHHHHHHH CS
                    ATP-grasp_2  85 tgkeGkkvekvlveealdikkElYlsivlDraskkvvviaSseGGvdiEevaakkPekiikvaidpakgl.keeqareia 163
                                     ++   +v+ ++v ++ +  kE+ l++  D     +v++   +GGv +E        +++ ++++ a ++ +e+++ +++
  gi|119719515|ref|YP_920010.1| 569 -KAPSARVNGIIVRKMAEKGKEIALGVHRDPIFGPLVMVG--SGGVLVEL-YRDVSFRVAPLSLEDAYEMlEETKIYKVL 644
                                    .556789999999999999999999988887665555554..49998874.55666788888887776651445566666 PP

                                    HHC.T--CHHHHHHHHHHHHHHHHHHHT.TEEEEEEEEE CS
                    ATP-grasp_2 164 kkl.glekelvkkaakiikklyklfvel.datlvEiNPL 200
                                    k   g + + ++k+++++ +l kl  ++ + + ++iNP+
  gi|119719515|ref|YP_920010.1| 645 KGYrGEPPSDYEKVVDVLIRLSKLACDVeEIEDIDINPF 683
                                    655155568899999999999999887625678999997 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1   0.00062       1.4      10      92 ..      27     101 ..       6     104 .. 0.73
   2 ?   -1.8   0.0       2.2     5e+03      32      92 ..     242     303 ..     227     308 .. 0.65
   3 ?   -3.1   0.0       5.4   1.2e+04      13      36 ..     578     598 ..     575     598 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00062
                                    HHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHHHHCGHHHHTTS CS
                  F420_oxidored  10 mgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveevlselakdalkgk 89 
                                    +g  ++++ll+ag++ + i  + ++n +++  l      k+ + + +e   + d vv+av+  +v+ vl+++ ++  k  
  gi|119719515|ref|YP_920010.1|  27 IGYQVVKNLLEAGFPRERIFPV-NPNADEILGL------KCYK-SVSEIPYQVDLVVVAVPAPAVPGVLEDAGRKGVKAV 98 
                                    5556666777777666666644.6666655444......4444.566777889*****************9977777766 PP

                                    EEE CS
                  F420_oxidored  90 lvi 92 
                                     vi
  gi|119719515|ref|YP_920010.1|  99 AVI 101
                                    666 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.2
                                    EESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHHHHC.GHHHHTTSEEE CS
                  F420_oxidored  32 nsrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveevlsel.akdalkgklvi 92 
                                    + r   ++ +++++ g  + + ++ eaa ++  ++la  +  + + +++  + +  +g+ v+
  gi|119719515|ref|YP_920010.1| 242 AGRGVRTIGAIKSHTGSLAGSFAAYEAAFKQSGILLARSFVELFDWATAFaKTHIPRGENVV 303
                                    46777777777778887777777888888888888887777777766666444555555555 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 5.4
                                    HHHHHHHHTTS-GGCEEEEEESSC CS
                  F420_oxidored  13 alasgllaagaqpheivvansrnp 36 
                                     ++++++++g   +ei ++ +r+p
  gi|119719515|ref|YP_920010.1| 578 IIVRKMAEKG---KEIALGVHRDP 598
                                    5789999999...99999988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (704 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.48
# Mc/sec: 4406.93
//
Query:       gi|119719516|ref|YP_920011.1|  [L=143]
Description: hypothetical protein Tpen_0603 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-36  125.6   0.0    1.2e-36  125.4   0.0    1.1  1  UPF0047   Uncharacterised protein family UPF0047


Domain annotation for each model (and alignments):
>> UPF0047  Uncharacterised protein family UPF0047
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.4   0.0   6.6e-41   1.2e-36       1     114 [.      23     136 ..      23     137 .. 0.97

  Alignments for each domain:
  == domain 1  score: 125.4 bits;  conditional E-value: 6.6e-41
                                    E-HHHHHHHHHHHT.SEEEEEEEESSSSEEEEEEESSSHHHHHHHHHHHHHHSTTT.T-GGGTTS..THHHHHHHHHH-S CS
                        UPF0047   1 diteeveeavkesgvkeGlvlvfsrhttasltinEnadpdvqeDleealeklvpee.eYrhnaegpdnadaHlkssllgs 79 
                                    dit++ve++ +esg+++G++lvf++h+ta+++ nE+ ++++ +D+e  +++l+p + +Y hn   +dna+aH+ ss++g+
  gi|119719516|ref|YP_920011.1|  23 DITAQVERVAAESGIRNGVCLVFAPHATAAIIANEH-EEGLLKDIEGKISELFPVDqPYLHN-RIDDNAHAHIASSFIGA 100
                                    8**********************************9.******************99*****.6778************* PP

                                    EEEEEEETTEE---TTEEEEEEESS-SSE.EEEEEE CS
                        UPF0047  80 sltipvedgklalGtwqsiylveldgpre.Rkvvvq 114
                                    sl++pv++g+l  Gtwq+i+lveldgpr+ Rkvvv+
  gi|119719516|ref|YP_920011.1| 101 SLVLPVVNGRLLRGTWQNIFLVELDGPRSsRKVVVE 136
                                    ***************************888****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       269  (0.0150036); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 988.99
//
Query:       gi|119719517|ref|YP_920012.1|  [L=445]
Description: hypothetical protein Tpen_0604 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-30  105.4   0.0    3.3e-30  104.5   0.0    1.5  1  DUF1743          Domain of unknown function (DUF1743)
    2.3e-06   27.5   0.3    4.3e-06   26.6   0.3    1.4  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
     0.0022   17.9   2.1      0.004   17.0   2.1    1.3  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
     0.0038   17.2   0.9     0.0068   16.4   0.9    1.3  1  DZR              Double zinc ribbon
     0.0055   16.3   2.9       0.01   15.5   2.9    1.4  1  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
     0.0098   15.7   1.5      0.018   14.9   1.5    1.4  1  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
  ------ inclusion threshold ------
      0.039   13.4   4.3          1    8.8   0.1    2.3  2  zf-ribbon_3      zinc-ribbon domain
      0.087   12.8   0.0       0.16   12.0   0.0    1.3  1  HypA             Hydrogenase/urease nickel incorporation, met
      0.091   12.8   5.0       0.51   10.4   4.9    2.1  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
       0.14   11.9   4.1        5.7    6.8   0.5    2.3  2  zinc_ribbon_2    zinc-ribbon domain
       0.15   12.1   0.1       0.32   11.1   0.1    1.5  1  Zn_Tnp_IS91      Transposase zinc-binding domain
       0.17   11.1   0.0       0.39   10.0   0.0    1.6  2  Rsm22            Mitochondrial small ribosomal subunit Rsm22
       0.19   11.7   0.4       0.32   11.0   0.4    1.3  1  zinc-ribbons_6   zinc-ribbons
       0.23   11.3   2.6       0.42   10.5   2.6    1.4  1  HscB_4_cys       Co-chaperone HscB tetracysteine metal bindin
       0.25   10.7   3.2       0.83    9.0   3.3    1.9  1  zf-TFIIB         Transcription factor zinc-finger
       0.37   10.9   0.8       0.67   10.1   0.8    1.4  1  zf-Mss51         Zinc-finger of mitochondrial splicing suppre
        1.4    9.1   5.3         11    6.3   0.4    2.4  3  Zn-ribbon_8      Zinc ribbon domain
        1.6    8.8   4.8         18    5.4   0.2    2.5  2  DUF1610          Domain of unknown function (DUF1610)
        1.6    8.4   5.9        3.5    7.3   0.9    2.3  2  zf_C2H2_10       C2H2 type zinc-finger
        3.1    7.8   4.4         10    6.2   0.3    2.4  2  Ogr_Delta        Ogr/Delta-like zinc finger
        3.8    8.1   6.5        8.1    7.0   6.5    1.5  1  Zn_ribbon_recom  Recombinase zinc beta ribbon domain
        4.4    8.0   5.2         11    6.8   0.5    2.6  2  zf-ISL3          zinc-finger of transposase IS204/IS1001/IS10
        6.7    6.7   7.6        2.9    7.9   1.8    2.3  2  zf-HIT           HIT zinc finger


Domain annotation for each model (and alignments):
>> DUF1743  Domain of unknown function (DUF1743)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.5   0.0   4.2e-33   3.3e-30       2     116 .]     149     262 ..     148     262 .. 0.96

  Alignments for each domain:
  == domain 1  score: 104.5 bits;  conditional E-value: 4.2e-33
                                    THHHHHHHHHH-..-TTS-EEEEEEEE-GGGTT.---EEHHHHHHHHHHHTTCECTSEBTTTTCECCS-STTSSEEEEEE CS
                        DUF1743   2 rgiiGAtaalganialedstyEllaYreperwg.erevdeesvieadektypetfdnvDlshklvvlvPhtpdpvlfGir 80 
                                    rg++GA+a+lga  +led+tyEl++Yr+pe+   +r+++e+ ++e+d+k+ p +f ++D+s ++v+ vPh+pdpv+fG r
  gi|119719517|ref|YP_920012.1| 149 RGLVGAVASLGA-YPLEDYTYELIVYRSPEERSeSRDISEDLLLELDRKYRPLVFATYDYSSRRVLAVPHGPDPVIFGLR 227
                                    89**********.56789************************************************************** PP

                                    ES-HHHHHHHHHCSEE..S-EEC.EEEEEESTTS-TT CS
                        DUF1743  81 gedpeallkaakeilskeeesee.mavfrtnqgtdah 116
                                    + dpe l+++a ++l+  + s+  +++f+tnqgt ah
  gi|119719517|ref|YP_920012.1| 228 SLDPEILVNVAVDVLE--KISHAgYLLFKTNQGTSAH 262
                                    ****************..777778**********998 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.3   5.6e-09   4.3e-06       1      72 [.     278     349 ..     278     353 .. 0.89

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 5.6e-09
                                    EEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEET..HHHHHHHTTS-TTSEEEEEEEEEECTTSSEEEEEEE CS
                tRNA_anti-codon   1 VtvaGrvtsisdrsggkvifidlrDgtgriqvvlfr..eeatklaenlkeGdvvrvtGrvkrrpggelelkvee 72 
                                    V+v+G v  + +  +g+++ + ++D+tg++q+ + +  +   ++a+ l +Gd+v+v G v + + g l l++e 
  gi|119719517|ref|YP_920012.1| 278 VVVRGSVAEKPTVISGGHVIVNVCDETGCLQIAFYKetGRLNRVAKLLSRGDLVEVGGGVMKKD-G-LVLNAEY 349
                                    78999999999999*******************************************9998884.5.5666655 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   2.1   5.1e-06     0.004      31      56 ..     366     391 ..     364     393 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 5.1e-06
                 OrfB_Zn_ribbon  31 CseCgsknkealsgrtfkCpnCgfea 56 
                                    C++Cgs+++ a +g+ +kCp+Cg++a
  gi|119719517|ref|YP_920012.1| 366 CPKCGSRMTSAGKGKGYKCPKCGYRA 391
                                    ***********************986 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.9   8.7e-06    0.0068      14      42 ..     365     395 ..     358     397 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 8.7e-06
                            DZR  14 fCseCgtklkavaa..edrCpsCgekvdpea 42 
                                     C++Cg+++ ++ +   ++Cp+Cg+ +++ a
  gi|119719517|ref|YP_920012.1| 365 LCPKCGSRMTSAGKgkGYKCPKCGYRAKEAA 395
                                    7********9887799*********988765 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   2.9   1.3e-05      0.01       3      30 ..     363     390 ..     361     391 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.3e-05
                  zf-NADH-PPase   3 hrFCgrCGaptepaeggwarvCpaCgle 30 
                                    ++ C++CG+++  a  g +  Cp Cg++
  gi|119719517|ref|YP_920012.1| 363 NPLCPKCGSRMTSAGKGKGYKCPKCGYR 390
                                    578***********************97 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   1.5   2.3e-05     0.018       4      30 ..     366     390 ..     365     394 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.3e-05
                                    ESTTTSBEEEEECSCCCEEEESSSS-E CS
                 RNA_POL_M_15KD   4 CpkCgNlLlpkedkegknfeCrqCgYe 30 
                                    CpkCg+ + ++++ +g  + C +CgY 
  gi|119719517|ref|YP_920012.1| 366 CPKCGSRMTSAGKGKG--YKCPKCGYR 390
                                    ****************..89******5 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1    0.0013         1      11      25 ..     358     372 ..     356     373 .. 0.80
   2 ?    4.7   1.6     0.026        20      18      24 ..     383     389 ..     381     390 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0013
                    zf-ribbon_3  11 plssddnvCpyCGtk 25 
                                    +++   + Cp+CG++
  gi|119719517|ref|YP_920012.1| 358 NVKRLNPLCPKCGSR 372
                                    57888899*****87 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.026
                    zf-ribbon_3  18 vCpyCGt 24 
                                    +Cp+CG+
  gi|119719517|ref|YP_920012.1| 383 KCPKCGY 389
                                    4777776 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0    0.0002      0.16      66      96 ..     359     391 ..     330     397 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0002
                                    EE--EEEETTTS-EEECHHH..HHS-TTTSSS- CS
                           HypA  66 evpvkvrCreCgkefeleek..alrCpkCgsad 96 
                                     ++++  C +Cg++++++ k   ++CpkCg + 
  gi|119719517|ref|YP_920012.1| 359 VKRLNPLCPKCGSRMTSAGKgkGYKCPKCGYRA 391
                                    5566678*********88754588*****9765 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   4.9   0.00065      0.51      19      45 ..     364     389 ..     360     390 .. 0.84
   2 ?    7.9   0.6    0.0037       2.9      18      34 ..     381     399 ..     377     406 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00065
                  Zn_Tnp_IS1595  19 fvCPhCgsrkayriktrglfqCkeCrk 45 
                                    + CP+Cgsr     k+ + ++C +C++
  gi|119719517|ref|YP_920012.1| 364 PLCPKCGSRMTSAGKG-KGYKCPKCGY 389
                                    67*****997777777.88******98 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0037
                  Zn_Tnp_IS1595  18 gfvCPhCgsr..kayrikt 34 
                                    g  CP+Cg+r  +a +i +
  gi|119719517|ref|YP_920012.1| 381 GYKCPKCGYRakEAAKIYR 399
                                    678******9986666544 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.2     0.011       8.5      15      21 ..     365     371 ..     363     373 .. 0.72
   2 ?    6.8   0.5    0.0073       5.7       1       7 [.     383     389 ..     383     396 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.011
                  zinc_ribbon_2  15 FCpyCGt 21 
                                     Cp+CG+
  gi|119719517|ref|YP_920012.1| 365 LCPKCGS 371
                                    6888886 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0073
                  zinc_ribbon_2   1 fCpnCGa 7  
                                    +Cp+CG+
  gi|119719517|ref|YP_920012.1| 383 KCPKCGY 389
                                    6888886 PP

>> Zn_Tnp_IS91  Transposase zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00041      0.32      42      70 ..     366     394 ..     354     413 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00041
                    Zn_Tnp_IS91  42 CeeCghekivyfsCksrhCpsCqkkatee 70 
                                    C++Cg++ +++ + k   Cp+C+ +a+e 
  gi|119719517|ref|YP_920012.1| 366 CPKCGSRMTSAGKGKGYKCPKCGYRAKEA 394
                                    ***********************998875 PP

>> Rsm22  Mitochondrial small ribosomal subunit Rsm22
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       4.7   3.6e+03      17      43 ..      78     104 ..      74     110 .. 0.83
   2 ?   10.0   0.0    0.0005      0.39     229     273 ..     287     330 ..     263     332 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 4.7
                          Rsm22  17 avlrrvLdelaervpdflPkslldvge 43 
                                    +++ r+Ld+l er  +  P+ +l  g+
  gi|119719517|ref|YP_920012.1|  78 EAVVRALDDLSERHGKTDPAAILVKGD 104
                                    589999*******99999999986665 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0005
                          Rsm22 229 rptkvrskkvlidlCsedetlqrlvvtKrkGeaykaArkaeWGDr 273
                                    +pt ++ ++v++++C e + lq   + K+ G + + A+ ++ GD+
  gi|119719517|ref|YP_920012.1| 287 KPTVISGGHVIVNVCDETGCLQI-AFYKETGRLNRVAKLLSRGDL 330
                                    5788999************9985.688*************99997 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.4   0.00042      0.32       3      28 ..     366     393 ..     364     398 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00042
                                    -SSS-S--EE-S..SEEE-TTT--EEEE CS
                 zinc-ribbons_6   3 CpeCqqelekrg..eqyhCeaCqedlkk 28 
                                    Cp+C + +++ g  + y+C +C  + k+
  gi|119719517|ref|YP_920012.1| 366 CPKCGSRMTSAGkgKGYKCPKCGYRAKE 393
                                    ********95544599******876655 PP

>> HscB_4_cys  Co-chaperone HscB tetracysteine metal binding motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   2.6   0.00053      0.42       1      23 [.     364     387 ..     364     391 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00053
                                    -B-SSS--.B--SS-S---B-TTT CS
                     HscB_4_cys   1 PrCWnCGg.pgapgrgdefFCpqC 23 
                                    P C +CG+   ++g+g ++ Cp+C
  gi|119719517|ref|YP_920012.1| 364 PLCPKCGSrMTSAGKGKGYKCPKC 387
                                    889*****777999********** PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   3.3    0.0011      0.83       2      26 ..     366     388 ..     365     388 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0011
                       zf-TFIIB   2 CPkCqdeleeserggveidyCpqCr 26 
                                    CPkC++ ++ + +g+   ++Cp+C+
  gi|119719517|ref|YP_920012.1| 366 CPKCGSRMTSAGKGK--GYKCPKCG 388
                                    ********9998877..8******7 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.8   0.00086      0.67       1      24 [.     365     389 ..     365     399 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00086
                       zf-Mss51   1 lCPvpkhkqt.apkhvdfeCpdCGi 24 
                                    lCP + +++t a k   ++Cp+CG+
  gi|119719517|ref|YP_920012.1| 365 LCPKCGSRMTsAGKGKGYKCPKCGY 389
                                    5****999997888999*******8 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.4     0.014        11      28      36 ..     364     373 ..     355     376 .. 0.77
   2 ?    4.2   5.2     0.062        48       8      36 ..     366     391 ..     365     397 .. 0.73
   3 ?    4.3   0.6     0.057        44       6      16 ..     382     392 ..     381     403 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.014
                    Zn-ribbon_8  28 a.CPeCgsev 36 
                                    + CP+Cgs++
  gi|119719517|ref|YP_920012.1| 364 PlCPKCGSRM 373
                                    44*****965 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.062
                    Zn-ribbon_8   8 CeeCghefevlqsisdapltaCPeCgsev 36 
                                    C +Cg++ +      + +  +CP+Cg ++
  gi|119719517|ref|YP_920012.1| 366 CPKCGSRMTSAG---KGKGYKCPKCGYRA 391
                                    999997777444...55577799999655 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.057
                    Zn-ribbon_8   6 YrCeeCghefe 16 
                                    Y+C +Cg +  
  gi|119719517|ref|YP_920012.1| 382 YKCPKCGYRAK 392
                                    78888886654 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.7     0.042        33      18      23 ..     365     370 ..     365     371 .. 0.91
   2 ?    5.4   0.2     0.023        18      17      23 ..     382     388 ..     373     389 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.042
                        DUF1610  18 pCPNCG 23 
                                    +CP+CG
  gi|119719517|ref|YP_920012.1| 365 LCPKCG 370
                                    6****9 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.023
                        DUF1610  17 FpCPNCG 23 
                                    + CP+CG
  gi|119719517|ref|YP_920012.1| 382 YKCPKCG 388
                                    67****9 PP

>> zf_C2H2_10  C2H2 type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.3     0.083        65       5       9 ..     366     370 ..     365     373 .. 0.84
   2 ?    7.3   0.9    0.0044       3.5       3      12 ..     382     391 ..     381     392 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.083
                     zf_C2H2_10   5 CPKCq 9  
                                    CPKC+
  gi|119719517|ref|YP_920012.1| 366 CPKCG 370
                                    ****8 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0044
                     zf_C2H2_10   3 fsCPKCqekl 12 
                                    + CPKC++ +
  gi|119719517|ref|YP_920012.1| 382 YKCPKCGYRA 391
                                    56******86 PP

>> Ogr_Delta  Ogr/Delta-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.3     0.013        10       2      10 ..     366     374 ..     365     376 .. 0.92
   2 ?    2.9   0.4      0.14   1.1e+02       1       9 [.     383     391 ..     383     395 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.013
                      Ogr_Delta   2 CPhCgapaa 10 
                                    CP+Cg++++
  gi|119719517|ref|YP_920012.1| 366 CPKCGSRMT 374
                                    *******96 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.14
                      Ogr_Delta   1 rCPhCgapa 9  
                                    +CP+Cg +a
  gi|119719517|ref|YP_920012.1| 383 KCPKCGYRA 391
                                    6*****887 PP

>> Zn_ribbon_recom  Recombinase zinc beta ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   6.5      0.01       8.1       8      33 ..     366     391 ..     365     399 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.01
                Zn_ribbon_recom   8 CgeCGspmtrrkrkgkrhyYrCstyr 33 
                                    C +CGs+mt  ++++++ + +C+ + 
  gi|119719517|ref|YP_920012.1| 366 CPKCGSRMTSAGKGKGYKCPKCGYRA 391
                                    ***********999999998887664 PP

>> zf-ISL3  zinc-finger of transposase IS204/IS1001/IS1096/IS1165
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.5     0.013        11       3      15 ..     364     379 ..     363     383 .. 0.65
   2 ?    3.0   0.5      0.22   1.7e+02       4      13 ..     383     392 ..     380     420 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.013
                        zf-ISL3   3 hrCPnCgsktv...vk 15 
                                    + CP+Cgs++    + 
  gi|119719517|ref|YP_920012.1| 364 PLCPKCGSRMTsagKG 379
                                    67*******5322344 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.22
                        zf-ISL3   4 rCPnCgsktv 13 
                                    +CP+Cg + +
  gi|119719517|ref|YP_920012.1| 383 KCPKCGYRAK 392
                                    6*****9854 PP

>> zf-HIT  HIT zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.4      0.31   2.4e+02      16      22 ..     366     372 ..     365     374 .. 0.90
   2 ?    7.9   1.8    0.0037       2.9      13      22 ..     381     390 ..     377     392 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.31
                                    -TTT--E CS
                         zf-HIT  16 CpkCntr 22 
                                    CpkC+ r
  gi|119719517|ref|YP_920012.1| 366 CPKCGSR 372
                                    ****987 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0037
                                    SEE-TTT--E CS
                         zf-HIT  13 kYkCpkCntr 22 
                                     YkCpkC+ r
  gi|119719517|ref|YP_920012.1| 381 GYKCPKCGYR 390
                                    6******976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (445 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                       108  (0.00602376); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 2677.89
//
Query:       gi|119719518|ref|YP_920013.1|  [L=41]
Description: hypothetical protein Tpen_0605 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.42
# Mc/sec: 294.49
//
Query:       gi|119719519|ref|YP_920014.1|  [L=337]
Description: geranyltranstransferase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.2e-58  196.1   0.0    6.5e-58  195.8   0.0    1.1  1  polyprenyl_synt  Polyprenyl synthetase


Domain annotation for each model (and alignments):
>> polyprenyl_synt  Polyprenyl synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.8   0.0   3.6e-62   6.5e-58       3     255 ..      31     288 ..      29     289 .. 0.90

  Alignments for each domain:
  == domain 1  score: 195.8 bits;  conditional E-value: 3.6e-62
                                    HHHHHHHHHHHSSS--HHHHHHHHHHHHHSCGHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEETTEE-HHHCTCHHH CS
                polyprenyl_synt   3 lleealeylveagGKrlRpllvllaaealkeeeeelekaavlawivellhaasLvhDDimDdsetRRGqpcahrlvGnkl 82 
                                    ++++a+ y v  gGKr+Rp+l++++  a++ +e   e+a+ +a++vel h++sL++DDi+D+se+RRG+p++ +++G ++
  gi|119719519|ref|YP_920014.1|  31 EFQDAVLYQVRMGGKRVRPALTIASTLAVGGKE---ENALPAAAAVELAHNYSLILDDIIDHSELRRGKPTVWKKYGIST 107
                                    6788999***********************666...899***************************************** PP

                                    HHHHHHHHHHHHHHHHHHHHSTT.HHHHHHHHHHHHHHHHHHHHHHHHT..........TTTTCCC.SHHHHHHHHHHHT CS
                polyprenyl_synt  83 Aindgdfllarafellaklfeks.lellelfsevllqtveGqlldleee..........kdddlskfsleeyleivkyKT 151
                                    Ai+ +      + e l+++  ++ + + ++++e++  +  G+ ld+  e           ++ +++  l++yl+++++KT
  gi|119719519|ref|YP_920014.1| 108 AILIAVHYRESITEALNDT--PEpPVFHAIMAETIKLLTDGERLDILFEqsgrsdepyvVEQRYRAVRLDDYLRMIERKT 185
                                    *******************..77689999****************94443345555555456666899************ PP

                                    HHHCHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHSS-TSHHHHTT---.HHHHHHHHCT-HH CS
                polyprenyl_synt 152 aylfalpvalaallagasdeelealkdiglelGlaFQiqDDylDlfgdpevlgKpagtDiqegkct.lpilkalelaspe 230
                                    a l++ ++  +al ag   e leal+++g++lG+aFQ+ DD++D+fg++e++gK +g Di+e+k   +++l ale +++ 
  gi|119719519|ref|YP_920014.1| 186 AKLIETSCVFGALSAGQRGEILEALREYGYNLGMAFQVGDDIIDIFGEEEKTGKRVGGDIKEHKLGnVVVLLALE-ETR- 263
                                    ****************978999******************************************98356667777.544. PP

                                    HHHHHHHHTTSSHHHHHHHHHHHHH CS
                polyprenyl_synt 231 qrkvlkeilgkkaekeedvkealel 255
                                    ++++l +il+k+  + e+vkea+++
  gi|119719519|ref|YP_920014.1| 264 DKERLLAILRKEDVSWEEVKEAISI 288
                                    4668*********9*******9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       711  (0.0396564); expected 358.6 (0.02)
Passed bias filter:                      576  (0.0321267); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 2569.64
//
Query:       gi|119719520|ref|YP_920015.1|  [L=259]
Description: aspartate/glutamate/uridylate kinase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.1e-51  174.9   0.1    2.4e-51  174.7   0.1    1.0  1  AA_kinase  Amino acid kinase family


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  174.7   0.1   1.3e-55   2.4e-51       1     239 [.       5     237 ..       5     239 .. 0.98

  Alignments for each domain:
  == domain 1  score: 174.7 bits;  conditional E-value: 1.3e-55
                                    TEEEEEE-TTCCCCTCC......HHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHHTCCCCCHHHC....E..HHHH CS
                      AA_kinase   1 krvVvKlGGssltdkee......aslrrlaeqiaalkesgnklvvVhGggsftdgllalksglssgelaaglrstleeag 74 
                                    +++V+KlGGs++tdk++      ++l+ + + +a+l  +g+++v+VhGggsf++  +a+ + l++g+l       ++ +g
  gi|119719520|ref|YP_920015.1|   5 MLTVIKLGGSVITDKSKpytvrsSNLKTASAALAKLYGEGYDIVLVHGGGSFGHPTAAK-YRLHEGGLS-----PEKVRG 78 
                                    789**********99999*****************************************.*******97.....7999** PP

                                    HHHHHHHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE..HHHTTTCEEECCHHHHHHHTT-EEEEESEEEEETTTE CS
                      AA_kinase  75 evatrdalaslgerlvaallaaglpavglsaaaldateagrdegsdgnvesvdaeaieelleagvvpvltgfigldeege 154
                                    + +tr ++++l++ +v++ll+  +pav+l+ +a+ + ++g+       +++++ + ++e+l+++ vpvl g++++d   +
  gi|119719520|ref|YP_920015.1|  79 FSETRYWMTKLNTLVVEHLLRLNVPAVSLQTSAIAVNSGGK-------LSRISLDVLREMLARRLVPVLYGDAVIDLSRG 151
                                    ***********************************999998.......******************************** PP

                                    EEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHH...CSSS.TTTHHHHCHHHHHHHHH CS
                      AA_kinase 155 lgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaee...saselatgGmkvkhpaalaaar 231
                                    + ++s+Dt+aa +A++lgA++l+++    GVy+++p  + darll+ei+ ++++    +++ ++tgG + k+ +a+ aa+
  gi|119719520|ref|YP_920015.1| 152 FSILSGDTLAARIAVELGAKSLVYVMGAGGVYSKPPGSP-DARLLREIAENDVLTvggTHGVDVTGGLREKLAEAFYAAK 230
                                    ************************************886.**************************************** PP

                                    CTT-EEEE CS
                      AA_kinase 232 rggipvvI 239
                                    +g ++v I
  gi|119719520|ref|YP_920015.1| 231 NG-VRVCI 237
                                    **.99988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1922.27
//
Query:       gi|119719521|ref|YP_920016.1|  [L=191]
Description: ribosomal protein L6 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-24   86.1   7.5    5.8e-16   58.9   3.9    2.1  2  Ribosomal_L6  Ribosomal protein L6


Domain annotation for each model (and alignments):
>> Ribosomal_L6  Ribosomal protein L6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.9   3.9   3.2e-20   5.8e-16       1      76 []      12      85 ..      12      85 .. 0.99
   2 !   29.0   0.1   7.3e-11   1.3e-06       1      66 [.      97     161 ..      97     164 .. 0.93

  Alignments for each domain:
  == domain 1  score: 58.9 bits;  conditional E-value: 3.2e-20
                                   CSTTEEEEEETTTEEEEEESSEEEEEE-CTTSEEEEEECSTEEEEEECSESCHHHHHHHHHHHHHHHHHHHHHHTC CS
                   Ribosomal_L6  1 iPvgvrvsikggqlvlvlGpkgeltreipegvtvevkvegnkvtvivvsgidkekvAligtvrslinnmikGVteg 76
                                   iP+gv+v ++g + v v Gp g ++ +++++  + + vegn+v+v++ + ++k  + l+gt+ s+innmi GVt+g
  gi|119719521|ref|YP_920016.1| 12 IPEGVKVHVNG-KRVEVEGPLGKVEKDFSHARRISIRVEGNSVVVETFHATKKDYA-LVGTIASIINNMIIGVTKG 85
                                   8*********8.********************************************.*****************98 PP

  == domain 2  score: 29.0 bits;  conditional E-value: 7.3e-11
                                    CSTTEEEEEETTTEEEEEESSEEEEEE-CTTSEEEEEECSTEEEEEECSESCHHHH....HHHHHHHHHH CS
                   Ribosomal_L6   1 iPvgvrvsikggqlvlvlGpkgeltreipegvtvevkvegnkvtvivvsgidkekv....Aligtvrsli 66 
                                    +P+  +v+ ++  ++++lG++g + + i +g +v+++     +++++v+gid   v    A+i ++++l 
  gi|119719521|ref|YP_920016.1|  97 FPMSLKVEKDKIIIENFLGERGKRIAGIMPGAKVKIE-----KDDVIVEGIDLDAVaqtaANIHLATHLR 161
                                    79999******************************99.....9*************99999999888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1357.49
//
Query:       gi|119719522|ref|YP_920017.1|  [L=126]
Description: putative endoribonuclease L-PSP [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-41  141.6   0.0    1.2e-41  141.5   0.0    1.0  1  Ribonuc_L-PSP  Endoribonuclease L-PSP


Domain annotation for each model (and alignments):
>> Ribonuc_L-PSP  Endoribonuclease L-PSP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.5   0.0   6.8e-46   1.2e-41       2     120 ..       9     125 ..       8     126 .] 0.98

  Alignments for each domain:
  == domain 1  score: 141.5 bits;  conditional E-value: 6.8e-46
                                    TTSTTTSSS-BSEEEETTEEEEEEE-SB-TTTSCB.-SSHHHHHHHHHHHHHHHHHHTT--GGGEEEEEEEESSGGGHHH CS
                  Ribonuc_L-PSP   2 eaapaaaapYsqavkagnlvyvsGqlpldpetgelvegdveeqtrqalenlkavLaaagaslsdvVkvtvFladiedfae 81 
                                    e+ap++++pYsqavk+g lv+vsGq+p+dp++ge+v +d++eqtr++len+ka+L+a g+sl++vV   vFl +++df++
  gi|119719522|ref|YP_920017.1|   9 EKAPKPIGPYSQAVKVGSLVFVSGQIPIDPSSGEIVGKDIREQTRRVLENVKAILEATGSSLDKVVYSLVFLRNLSDFKA 88 
                                    79****************************************************************************** PP

                                    HHHHHHHHSSSSTS--EEEEEE-SBSGGG-SEEEEEEEE CS
                  Ribonuc_L-PSP  82 vnevyaeafdelkeaParsaveVaaLpkgakvEIeaiav 120
                                    +nevy+e+f+++k  Par++v++a +p+ga+vEI +ia+
  gi|119719522|ref|YP_920017.1|  89 FNEVYEEYFKNTK--PARVTVQAADIPRGALVEISVIAT 125
                                    ************8..**********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      597  (0.033298); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.28s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 944.31
//
Query:       gi|119719523|ref|YP_920018.1|  [L=408]
Description: threonine dehydratase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.2e-89  298.3   0.9    7.9e-89  297.9   0.9    1.1  1  PALP             Pyridoxal-phosphate dependent enzyme
    0.00064   20.3   0.0     0.0016   18.9   0.0    1.7  1  ACT_4            ACT domain
     0.0013   18.4   0.0     0.0048   16.6   0.0    1.9  1  ACT              ACT domain
  ------ inclusion threshold ------
      0.031   14.4   0.0      0.076   13.1   0.0    1.7  1  HTH_22           HTH domain
      0.084   12.2   0.0       0.13   11.5   0.0    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  297.9   0.9   2.2e-92   7.9e-89       3     294 .]      24     310 ..      22     310 .. 0.97

  Alignments for each domain:
  == domain 1  score: 297.9 bits;  conditional E-value: 2.2e-92
                                    GCSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-EEE CS
                           PALP   3 lgigpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallGlkvt 82 
                                     +i +TPl +++ ls+ ++ +++lKlE+l++tg+fK+Rga+y l++l++  g k vv+assGNh++++A+ a+llG+k+t
  gi|119719523|ref|YP_920018.1|  24 NVIHRTPLQASKTLSDLTNSEVYLKLENLQKTGAFKVRGAYYKLQKLARS-GVKSVVAASSGNHAQGVAYSASLLGIKST 102
                                    5789**********************************************.***************************** PP

                                    EEEETTS-HHHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHHHHTTTTEEEEE CS
                           PALP  83 ivvpadaspekvallrllGaevvevggdydeavaaaaelaaegegaylvsqfdnptviegygtiglEileqlggkpdavv 162
                                    iv+p+ ++ +kv +++++Gaevv+ g++yd+a  +a e+a++ +g  +v++f++p++i+g+gtig Ei e+l  ++d v+
  gi|119719523|ref|YP_920018.1| 103 IVMPRYTPFYKVNATKSYGAEVVLHGETYDDAYLKALEIAEK-TGSPFVHPFNDPDIIAGQGTIGVEIFEDL-SNVDLVL 180
                                    ******************************************.*****************************.5****** PP

                                    EE-SSSHHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTCCS..S.SS..B.SSS.CCSTCSCGTTCCHHHHSEEEEEEEE CS
                           PALP 163 vpvGgGgliaGiaaglkerrpdvrvigvepegsdalarslragrrvtvpvsdtiadglavgspselafelldrlvdeivt 242
                                    vpvGgGgli+Gia +lk+ +pdv+v+gv+p g++a++ s++++r v++p  ++iadg+ v++p++l++++++++vd++v 
  gi|119719523|ref|YP_920018.1| 181 VPVGGGGLISGIAVALKKLKPDVKVVGVQPRGAPAMYLSFHEKRIVETPQVNSIADGVIVKRPGDLTLRIMEEFVDDVVL 260
                                    ******************************************************************************** PP

                                    EEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHHHHHHHHCCTTCEEEEEEE-B CS
                           PALP 243 vsdeealeamrllarregivvepssaaalaalklreagelkegdrvvviltg 294
                                    v+d e+++am ll +r + v+ep++a ++aal   + +  +eg+rvv++++g
  gi|119719523|ref|YP_920018.1| 261 VDDREIARAMFLLLERVKTVAEPAGALSVAAL--TSGAVSAEGKRVVAVVSG 310
                                    ********************************..4444444558******98 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   4.6e-07    0.0016       6      71 ..     332     400 ..     328     401 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 4.6e-07
                          ACT_4   6 tvrleveaedrkglLaditqviseekanivsvnaktrkk...dglaeikitveVkdvehLsrviakLra 71 
                                    +vr++ +  d++g L+++++v+se + niv+++ +  +     g+a++++ +eV ++e  + +i kL+a
  gi|119719523|ref|YP_920018.1| 332 QVRIQGVLPDKPGQLKKVIDVVSELGLNIVEIQHERLNPllsPGMAQVTLGLEVPSREYADMLILKLKA 400
                                    7999999****************************998799999***************9999999986 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.3e-06    0.0048       7      33 ..     339     365 ..     333     368 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.3e-06
                                    EESSTTHHHHHHHHHHHTTSEEEEEEE CS
                            ACT   7 vpDrPGlLarvfgaladrgiNidsieq 33 
                                    +pD+PG L +v  +++++g+Ni+ i++
  gi|119719523|ref|YP_920018.1| 339 LPDKPGQLKKVIDVVSELGLNIVEIQH 365
                                    68**********************987 PP

>> HTH_22  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   2.1e-05     0.076       2      44 ..      22      64 ..      21      69 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.1e-05
                         HTH_22  2 lesiieevladlgkpverltkeekieivraLdekGiFllkgav 44
                                   l+++i++   + +k+++ lt++e     ++L++ G+F+++ga 
  gi|119719523|ref|YP_920018.1| 22 LRNVIHRTPLQASKTLSDLTNSEVYLKLENLQKTGAFKVRGAY 64
                                   78999999999******************************96 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   3.7e-05      0.13      36     104 ..      73     141 ..      66     146 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.7e-05
                                    HT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSSB-GGGC CS
                DegT_DnrJ_EryC1  36 lgvkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvdpdtynidpaai 104
                                     gvk ++a ssG +A  +a++a  +g + ++++p +t +  +na    ga++v+   + d+  +++ +i
  gi|119719523|ref|YP_920018.1|  73 SGVKSVVAASSGNHAQGVAYSASLLGIKSTIVMPRYTPFYKVNATKSYGAEVVLHGETYDDAYLKALEI 141
                                    699*******************555555*************************9776666666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2933.15
//
Query:       gi|119719524|ref|YP_920019.1|  [L=315]
Description: ribokinase-like domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-25   89.6   0.0    3.2e-25   89.1   0.0    1.2  1  PfkB      pfkB family carbohydrate kinase


Domain annotation for each model (and alignments):
>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.1   0.0   1.8e-29   3.2e-25      24     295 ..      17     283 ..       2     288 .. 0.82

  Alignments for each domain:
  == domain 1  score: 89.1 bits;  conditional E-value: 1.8e-29
                                    SEE.EESEEEEEEESHHHHHHHHHHHTT-EEEEEEEEESSHHHHHHHHHHHHTTEEETTEEEESSSEEEEEEEEETTT.S CS
                           PfkB  24 elv.evktveksaGGagaNvAvalarlgadvafigavGdDnfGeflleelkkegvdtdyvkidedtrtglalivvded.g 101
                                    + v e++++++s GG       a+ r+ a  +++++vG D+  +++l +l  ++vd +yv+ +    +++++ +v ++ g
  gi|119719524|ref|YP_920019.1|  17 DIVvEGGNMRRSLGGTVTFGSLAAIRHNATPHVVSKVGRDF-PDEYLMYLGRNNVDLSYVRLSRY-LPTTKFKLVYREgG 94 
                                    4444888899999999888899999****************.*******************6666.66666666666658 PP

                                    EEEEEEEEGGGGGHHHHHHHHHHHHHGCTSEEEEESEECTTSHHHHHHHHHHHHHHTTE.EEEEECESSSHH......HH CS
                           PfkB 102 ertivfnrgaaadltkeeleededlleeadllyisgllsselpeavleelaeaaknggt.fdpnlldplgaq......fk 174
                                    er ++      +d+  +    d++l +   ++++ g+l  e+p +v++e++e a+         ++  ++ +        
  gi|119719524|ref|YP_920019.1|  95 ERVLYLLSR-CEDILSS----DVPLDKLKGNIAVIGALIGEVPPSVVQEISEHASLVVSdLQGYVRRQSE-DrsivlaST 168
                                    777777776.5555553....3444445556677777999999999999999998877753333333333.336667767 PP

                                    HHHHHHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTSSEEEEEEGGGEEEEEETTEEEEEEE.SSSS-SBG CS
                           PfkB 175 eallellaladllkpneeElealtgekledieealaalhklkakgaktvvvtlGkeGalvvekdgelkvpavpkvkvvDt 254
                                    ++ + l++l+d++ +  +E++a++g     ++e+++++ +    ga++ +vtlG+ Ga+v++k+ +l+vp++p + vvD 
  gi|119719524|ref|YP_920019.1| 169 PEAKLLISLSDVVHAEVAEAKAVFGDL--PPAELAKRIVE---GGAAVALVTLGAGGAYVATKQRVLFVPSFP-TRVVDR 242
                                    7899999********************..99999999877...799*************************65.99**** PP

                                    TTHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHTSSSS CS
                           PfkB 255 tGAGDsfvggflaallegksleealrfanavAalvvqkkga 295
                                    tGAGD f+  f+  + +  +++ea+++a+a+ ++ ++k+g+
  gi|119719524|ref|YP_920019.1| 243 TGAGDVFTTVFAIEYHRLGDYREAAAYATAAVSFLIEKPGP 283
                                    **************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.56
# Mc/sec: 1696.24
//
Query:       gi|119719525|ref|YP_920020.1|  [L=734]
Description: elongation factor EF-2 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-59  200.5   0.0      3e-59  199.9   0.0    1.3  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    2.2e-29  101.7   0.0    2.5e-28   98.3   0.0    2.6  2  EFG_IV       Elongation factor G, domain IV
    1.4e-23   82.8   0.0      3e-23   81.7   0.0    1.6  1  EFG_II       Elongation Factor G, domain II
    2.2e-23   82.1   0.0    5.7e-23   80.8   0.0    1.8  1  EFG_C        Elongation factor G C-terminus
    2.8e-13   50.1   0.3    6.7e-13   48.8   0.3    1.7  1  GTP_EFTU_D2  Elongation factor Tu domain 2
  ------ inclusion threshold ------
       0.02   15.0   0.0      0.047   13.8   0.0    1.6  1  MMR_HSR1     50S ribosome-binding GTPase
       0.25   11.3   1.1         16    5.6   0.1    3.0  3  hnRNP_Q_AcD  Heterogeneous nuclear ribonucleoprotein Q acidic


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.9   0.0   1.2e-62     3e-59       2     193 ..      19     256 ..      18     257 .. 0.91

  Alignments for each domain:
  == domain 1  score: 199.9 bits;  conditional E-value: 1.2e-62
                                    CEEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEET..TCSSEEEEEEEESS CS
                       GTP_EFTU   2 rirnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaislek..etkkylinliDtPG 79 
                                    ++rnig+++hvDhGKtT++d+Ll+ +g+ s   + a+++ +lD  + E+ r++T+k+a++sl++  e+k y inl+DtPG
  gi|119719525|ref|YP_920020.1|  19 QVRNIGTLAHVDHGKTTTSDSLLMGAGILSP--KAAGQALALDYVEIEQLRQMTVKAANVSLYHewEGKPYVINLVDTPG 96 
                                    79*****************************..66788899**********************557999*********** PP

                                    SGGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGSTHHHHHHHHHHHHHHHHHH...... CS
                       GTP_EFTU  80 HvdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrlkaelkeiveevkqklsrk...... 153
                                    HvdF+  v+r+lr++Dg ++vvdaveGv++qte+v+r+al+e v++ + iNK+Drl++el+  ++e++q++ +       
  gi|119719525|ref|YP_920020.1|  97 HVDFTGHVTRSLRMMDGGIVVVDAVEGVMTQTETVVRQALSEYVRPLLYINKVDRLIKELRLEPREIQQRFVEIvkefna 176
                                    ***********************************************************************666888877 PP

                                    ..........HHHHHHHHHTTTTTEEEEEEBTTTTBTHH..................................HHHHHHH CS
                       GTP_EFTU 154 ..........eeklekygekgekevpvvfgSalkgegvk..................................tllealv 189
                                              ++k+++       + +v+fgSal+++g++                                  +ll+++v
  gi|119719525|ref|YP_920020.1| 177 lielyadkefKDKWKVDF----AKGQVAFGSALHKWGLTvpiatqkgvkfdyiidaylrdekdklaeefplyvALLDMVV 252
                                    777777433333333333....6778**********9999999999999******************************* PP

                                    HHSH CS
                       GTP_EFTU 190 ellp 193
                                    e++p
  gi|119719525|ref|YP_920020.1| 253 EHIP 256
                                    **99 PP

>> EFG_IV  Elongation factor G, domain IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       0.3   7.8e+02       2      19 ..     465     482 ..     464     493 .. 0.81
   2 !   98.3   0.0   9.8e-32   2.5e-28      12     121 .]     515     622 ..     508     622 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.3
                                    CCESCEE.SS-CCHCCCC CS
                         EFG_IV   2 qVayrEtirkpvkereek 19 
                                     V+yrEt+r++ + +e+k
  gi|119719525|ref|YP_920020.1| 465 IVRYRETVREKGQVFEGK 482
                                    69*******999877765 PP

  == domain 2  score: 98.3 bits;  conditional E-value: 9.8e-32
                                    -CCHCCCCCCCHTSSSHCCCCCEEEECCTTTTSSEEEEE--STCCCHCCCCHHHHCCCCCCTTS-TTTS--EESEEEEEE CS
                         EFG_IV  12 pvkereeklkkqsggdgqyakvileiePleegsgnefvdetkggqvpkeyieavekGfqealkeGplagepvtdvkvtLl 91 
                                    +  er+  l + +g+d ++a+ i++i+++     n++v++t+g+q+++e+++++ +Gf+++++ Gpla+epv++vkv+L+
  gi|119719525|ref|YP_920020.1| 515 DWRERATLLREYAGWDTDEARNIWDIDEN----FNVIVNKTSGIQYLREVKDTIIQGFRWTMEAGPLAQEPVRGVKVVLV 590
                                    556688999999****************7....7********************************************** PP

                                    EEE--T..TTC-HHHHHHHHCHHHHHHHHCC- CS
                         EFG_IV  92 dgslhe..vdsseaafkpaarralkeallkAs 121
                                    d++lhe   ++++a++ pa+++ ++++ll+A+
  gi|119719525|ref|YP_920020.1| 591 DAVLHEdpAHRGPAQIMPATKNSIMASLLSAK 622
                                    ****************************9985 PP

>> EFG_II  Elongation Factor G, domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.7   0.0   1.2e-26     3e-23       1      74 [.     389     462 ..     389     463 .. 0.97

  Alignments for each domain:
  == domain 1  score: 81.7 bits;  conditional E-value: 1.2e-26
                         EFG_II   1 fPePvislaiepkskadedklskaLarlleEDptlrverdeeTketilsGmGelHleivverlkreykvevelg 74 
                                    + ePv+++a+epk+++d  kl ++L++l+ EDptl+v  ++eT+e++lsG+G+lHlei++ +lk++ ++e+ ++
  gi|119719525|ref|YP_920020.1| 389 VAEPVVTIAVEPKKSSDLPKLVDVLRKLAIEDPTLKVYINQETGEYLLSGVGTLHLEITLWELKQRTGIEIVTS 462
                                    679*******************************************************************9875 PP

>> EFG_C  Elongation factor G C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.8   0.0   2.2e-26   5.7e-23       2      88 ..     625     710 ..     624     711 .. 0.97

  Alignments for each domain:
  == domain 1  score: 80.8 bits;  conditional E-value: 2.2e-26
                                    EEEEEEEEEEEEECCCCCCHHHHHHHCT-EEEEEEEE.TTEEEEEEEEEGGG-TTHHHCHHHCTTTS-EEEEEEEEEEE- CS
                          EFG_C   2 llEPivkveievpeeyvgkvisdlssrrGeiedmeqdasgrviieaeiPlaeligfateLrslTkGegsfsmefsgYeev 81 
                                    llEPi kv+++vp+++v+ v++ l+++rG+i++me++ +  +++ ae+P+ae+++ a+e+r++T+G++ f +ef ++++v
  gi|119719525|ref|YP_920020.1| 625 LLEPILKVDVKVPTQHVSGVLTVLNRHRGRILSMEER-GMVMRVLAELPVAESFNIADEMREATQGRAFFAYEFYKWAPV 703
                                    8************************************.****************************************** PP

                                    -HHHHHH CS
                          EFG_C  82 pgdklde 88 
                                    p++ l++
  gi|119719525|ref|YP_920020.1| 704 PSSQLEQ 710
                                    *998876 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.8   0.3   2.6e-16   6.7e-13       1      73 [.     305     371 ..     305     372 .. 0.94

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 2.6e-16
                                    EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEE CS
                    GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtl 73 
                                    G+va+grv+sGt+ +G+ev++  +  + +    ++ ++   +++++e  +   aG+iva+ gl++a ++G+t+
  gi|119719525|ref|YP_920020.1| 305 GHVATGRVFSGTVTEGQEVYL--LNAKDS---AKVLQVGLYMGPYREKTEQISAGNIVAMLGLDKA-RAGETV 371
                                    89*******************..666567...*********************************8.****98 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.9e-05     0.047      31     107 ..      53     142 ..      23     148 .. 0.53

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.9e-05
                                    TSSSSEEEEEEE.ETTEE....................EEEEECGGCSSHHHHHHHHHHHHHHHHCTSEEEEEEETTTTC CS
                       MMR_HSR1  31 gtTrdinegrvk.lkgke....................ielvDtpGliegaseekglgkaflaleeadlillvvdaseek 89 
                                    g  +   + +++ l  ++                    i+lvDtpG ++        g+  ++l+ +d  ++vvda e+ 
  gi|119719525|ref|YP_920020.1|  53 GQALALDYVEIEqL--RQmtvkaanvslyhewegkpyvINLVDTPGHVD------FTGHVTRSLRMMDGGIVVVDAVEGV 124
                                    44444444444420..11233333334444444444559*******666......344444445558********99555 PP

                                    SHHHHHHHHHHHHHTTSE CS
                       MMR_HSR1  90 lkpldeeleelleeakkp 107
                                    +++ +  + + l+e  +p
  gi|119719525|ref|YP_920020.1| 125 MTQTETVVRQALSEYVRP 142
                                    555555555555544455 PP

>> hnRNP_Q_AcD  Heterogeneous nuclear ribonucleoprotein Q acidic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       0.8   2.1e+03      24      40 ..      58      74 ..      53      77 .. 0.88
   2 ?    5.6   0.1    0.0062        16       9      43 ..     148     182 ..     146     189 .. 0.82
   3 ?    2.4   0.0     0.058   1.5e+02      28      51 ..     664     687 ..     653     691 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.8
                    hnRNP_Q_AcD 24 lDeraleaLkslpeegA 40
                                   lD++ +e+L+++ +++A
  gi|119719525|ref|YP_920020.1| 58 LDYVEIEQLRQMTVKAA 74
                                   89999********9998 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0062
                    hnRNP_Q_AcD   9 kLdelfrsgkltasdlDeraleaLkslpeegAlaV 43 
                                    k d+l+++ +l++ ++ +r +e+ k+++    l++
  gi|119719525|ref|YP_920020.1| 148 KVDRLIKELRLEPREIQQRFVEIVKEFNALIELYA 182
                                    6789***********************97655555 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.058
                    hnRNP_Q_AcD  28 aleaLkslpeegAlaVlkqfkesd 51 
                                    ++++L +lp+++ +++ ++++e++
  gi|119719525|ref|YP_920020.1| 664 VMRVLAELPVAESFNIADEMREAT 687
                                    6899*****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (734 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.71u 0.33s 00:00:01.04 Elapsed: 00:00:00.51
# Mc/sec: 4295.62
//
Query:       gi|119719526|ref|YP_920021.1|  [L=532]
Description: hypothetical protein Tpen_0614 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.025   14.6   6.6      0.047   13.7   6.6    1.4  1  Rootletin  Ciliary rootlet component, centrosome cohesion
      0.047   13.4   4.6      0.074   12.7   4.6    1.2  1  YkyA       Putative cell-wall binding lipoprotein
      0.084   13.1   0.4       0.19   12.0   0.4    1.6  1  DUF4381    Domain of unknown function (DUF4381)
       0.28   10.0   8.0       0.79    8.5   7.7    1.7  2  Spc7       Spc7 kinetochore protein
       0.32   10.8  10.0       0.03   14.1   3.9    2.1  2  CdvA       CdvA-like coiled-coil domain
        1.1    9.9   3.6        1.1    9.9   1.5    2.1  2  SlyX       SlyX
        1.1    9.5   2.6          3    8.2   0.2    2.4  2  DUF4806    Domain of unknown function (DUF4806)


Domain annotation for each model (and alignments):
>> Rootletin  Ciliary rootlet component, centrosome cohesion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   6.6   1.8e-05     0.047      29     128 ..     382     476 ..     377     528 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.8e-05
                      Rootletin  29 kkrcseleqrllektselektkltlllssareleeeesadleealakLeeErqrseklaqvnslLreqleearqaneaLt 108
                                    ++r+se  ++ lek s ++++     l++ +++  ++++ lee++++L++ r r + +++v s+Lr   +  r+  + L+
  gi|119719526|ref|YP_920021.1| 382 RRRISEAKAEALEK-SLSQRRG----LEELERILVSRERALEELVEQLRDLRGRKAGITKVTSVLRLMEQRNREYDKLLR 456
                                    67777766666663.2222333....356789999********************************9999999999999 PP

                      Rootletin 109 edlqkltkdwerlreeleqk 128
                                    + l+ l+ dw+++  el++ 
  gi|119719526|ref|YP_920021.1| 457 DALKGLEGDWSKIFSELDEF 476
                                    99**********99998754 PP

>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   4.6   2.9e-05     0.074      51     179 ..     384     514 ..     379     521 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.9e-05
                           YkyA  51 kikklsdealenveeReellekekesieeakeefekikeeieeie.deelkkeaeelieameeryeaydklykaYkeale 129
                                    +i++  +eale    ++  le+ + ++ + + ++e++ e++ ++   ++  ++++++   me+r   ydkl+ +  + le
  gi|119719526|ref|YP_920021.1| 384 RISEAKAEALEKSLSQRRGLEELERILVSRERALEELVEQLRDLRgRKAGITKVTSVLRLMEQRNREYDKLLRDALKGLE 463
                                    677777788777777777788889999999**************64677899**************************** PP

                           YkyA 130 ld.keLYemLkkeeltleeleeqiekiNesyeevkeaneqFneatkkynee 179
                                     d  +++++L +    +ee   ++eki ++y+  + a++++ e+ +k++ee
  gi|119719526|ref|YP_920021.1| 464 GDwSKIFSELDEFARMVEEKIRELEKIERAYRSGRLAKKEYVESAEKIEEE 514
                                    99679*******999999999999**********************99997 PP

>> DUF4381  Domain of unknown function (DUF4381)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.4   7.5e-05      0.19      20      79 ..     361     427 ..     352     463 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.5e-05
                        DUF4381  20 Gwwlllaalllllllvlalwllrrrkrn...........rreAlreLaalradeadakellaalselLkrv 79 
                                    G +ll++++lll++ ++ +  +rr   +           +r  l+eL+++     +++++l++l e L+ +
  gi|119719526|ref|YP_920021.1| 361 GVYLLAVLVLLLVMGAVYYSSRRRIS-EakaealekslsQRRGLEELERIL---VSRERALEELVEQLRDL 427
                                    77888844444444444444444333.257788888888888899999988...88888888888888865 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       0.3   7.7e+02      51      83 ..     175     207 ..     168     210 .. 0.88
   2 ?    8.5   7.7   0.00031      0.79     148     255 ..     400     513 ..     378     529 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.3
                           Spc7  51 vAaactvPlLeLYqhscreLkkyisegrkiire 83 
                                    vA++ +   L+LY+    + +  i++g+ ++++
  gi|119719526|ref|YP_920021.1| 175 VAGNASSTSLQLYKVTYLQRQILIEDGKAVFND 207
                                    677778899********************9986 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00031
                           Spc7 148 legleedkelLekqeeeldellpeleeeka......eleeeleklqeaaeelesidkeeLeelreelaelkaeieekkke 221
                                      glee ++ L ++e  l+el+++l+  +       ++++ l+ ++++++e +++ ++ L+ l  + +++ +e++e+ ++
  gi|119719526|ref|YP_920021.1| 400 RRGLEELERILVSRERALEELVEQLRDLRGrkagitKVTSVLRLMEQRNREYDKLLRDALKGLEGDWSKIFSELDEFARM 479
                                    35788888999999999999999887665545566688899999999********************************* PP

                           Spc7 222 laelqeqleeleekieelkeqkseleeeiaeaer 255
                                    ++e+ ++le++e +  + +  k+e+ e  ++ e+
  gi|119719526|ref|YP_920021.1| 480 VEEKIRELEKIERAYRSGRLAKKEYVESAEKIEE 513
                                    ******************9999999887776543 PP

>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.4      0.38   9.6e+02       2      12 ..     413     423 ..     380     428 .. 0.60
   2 ?   14.1   3.9   1.2e-05      0.03       2      97 ..     430     521 ..     429     527 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.38
                           CdvA   2 rkkALeeLvse 12 
                                    r++ALeeLv++
  gi|119719526|ref|YP_920021.1| 413 RERALEELVEQ 423
                                    44555555543 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 1.2e-05
                           CdvA   2 rkkALeeLvsegdipkstyeeikekleealkklkekakelkeklkkrlkeledqikslekalanlkisyasGEidEeaYk 81 
                                    rk  + ++ s  ++++++ +e  + l++alk l+ + +++ ++l++  + +e++i++lek    ++  y sG +  ++Y 
  gi|119719526|ref|YP_920021.1| 430 RKAGITKVTSVLRLMEQRNREYDKLLRDALKGLEGDWSKIFSELDEFARMVEEKIRELEK----IERAYRSGRLAKKEYV 505
                                    788899999**************************************************8....7999************ PP

                           CdvA  82 saieairellesalee 97 
                                    ++ e+i+e++ s+ +e
  gi|119719526|ref|YP_920021.1| 506 ESAEKIEEEILSLARE 521
                                    ********99988887 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   1.5   0.00043       1.1       8      46 ..     393     430 ..     386     454 .. 0.85
   2 ?   -1.8   0.0       1.9   4.9e+03      40      53 ..     477     490 ..     468     499 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00043
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                           SlyX   8 LEiklafqedtieeLndvvaeqqqqidrlqrqlrllaer 46 
                                    LE  l  q + +eeL ++++  ++ +++l +qlr l+ r
  gi|119719526|ref|YP_920021.1| 393 LEKSL-SQRRGLEELERILVSRERALEELVEQLRDLRGR 430
                                    55444.48899*************************987 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.9
                                    HHHHHHT-XXXXXX CS
                           SlyX  40 lrllaerlkelees 53 
                                     r+++e+++ele+ 
  gi|119719526|ref|YP_920021.1| 477 ARMVEEKIRELEKI 490
                                    56666666666654 PP

>> DUF4806  Domain of unknown function (DUF4806)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.2    0.0012         3       9      51 ..     397     439 ..     390     459 .. 0.86
   2 ?    0.5   0.2       0.3   7.6e+02      12      42 ..     484     514 ..     482     529 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0012
                        DUF4806   9 vsseeelerLEaavrtdekirqqyvnyLrkikgkkadlkkvfd 51 
                                    +s+   le+LE+ + ++e + +++v++Lr  +g+ka + kv++
  gi|119719526|ref|YP_920021.1| 397 LSQRRGLEELERILVSRERALEELVEQLRDLRGRKAGITKVTS 439
                                    567788***************************9999988873 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.3
                        DUF4806  12 eeelerLEaavrtdekirqqyvnyLrkikgk 42 
                                      ele++E+a r+ + + ++yv++  ki  +
  gi|119719526|ref|YP_920021.1| 484 IRELEKIERAYRSGRLAKKEYVESAEKIEEE 514
                                    679**********9999*****988777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (532 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1315  (0.0733449); expected 358.6 (0.02)
Passed bias filter:                      900  (0.050198); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.70u 0.36s 00:00:01.06 Elapsed: 00:00:00.50
# Mc/sec: 3215.10
//
Query:       gi|119719527|ref|YP_920022.1|  [L=565]
Description: methionyl-tRNA synthetase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   4.9e-155  516.1   0.0   5.9e-155  515.8   0.0    1.1  1  tRNA-synt_1g   tRNA synthetases class I (M)
    3.9e-12   46.4   0.2    8.2e-12   45.3   0.2    1.5  1  Anticodon_1    Anticodon-binding domain of tRNA
    1.4e-10   40.1   0.0    3.1e-07   29.1   0.0    2.7  2  tRNA-synt_1    tRNA synthetases class I (I, L, M and V)
    5.5e-05   22.7   0.0     0.0013   18.1   0.0    2.1  2  tRNA-synt_1e   tRNA synthetases class I (C) catalytic domain
  ------ inclusion threshold ------
      0.053   12.4   0.0        3.3    6.5   0.0    2.3  2  tRNA-synt_1f   tRNA synthetases class I (K)
        0.7   10.0   3.3        2.2    8.4   3.1    1.7  2  DZR            Double zinc ribbon
       0.82    9.7   5.0        6.2    6.9   1.8    2.8  2  Zn_Tnp_IS1595  Transposase zinc-ribbon domain
       0.85    9.9   5.5        2.5    8.4   0.6    2.8  2  zf-RING_7      C4-type zinc ribbon domain


Domain annotation for each model (and alignments):
>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  515.8   0.0  2.6e-158  5.9e-155       2     391 .]      10     402 ..       9     402 .. 0.99

  Alignments for each domain:
  == domain 1  score: 515.8 bits;  conditional E-value: 2.6e-158
                                    EEEE--B--SS---HHHHH.HHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHH CS
                   tRNA-synt_1g   2 lvttalpYangklHlGhll.evisaDifaRykrlrgeevlfvcgtDehGtpielkAekegvtpeelvekvheeikelfkk 80 
                                    lv +a+pYa g++HlG+l+ +v+saD+ aR+ rl g+ev+fv+g+D+hGtpie++A k+g +p++l+e++he+ikelf++
  gi|119719527|ref|YP_920022.1|  10 LVLAAWPYAYGVPHLGNLIgSVLSADVAARFLRLAGDEVVFVSGSDMHGTPIEVEALKRGESPKDLAERNHEKIKELFER 89 
                                    7889**************************************************************************** PP

                                    TT---SEEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG-EE........-TTS-EE-TTSSB-E CS
                   tRNA-synt_1g  81 lnisfdkygrttseehkelvqeifkklkekgliyekeieqlycpkderflpdryvegtCPkckseeargdqceecgkkle 160
                                    ++isfd+y++t+s +h ++vq+++++++e+g++ + +++ +ycpkd+ flpdry+ gtCP+c++++a+gdqce+cg+ le
  gi|119719527|ref|YP_920022.1|  90 WEISFDNYSKTESPTHIKFVQDFYRRVYENGYVFSDTVQLYYCPKDKIFLPDRYIVGTCPYCGYDRAYGDQCENCGRLLE 169
                                    ******************************************************************************** PP

                                    ................EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS-SSS-EET.. CS
                   tRNA-synt_1g 161 ptelinpksaisgskpevketehlffklskfekklkewieeeekeleenvkkivkewlkegLkdlaisrdldwGipvP.. 238
                                    pt l np++ai+gs+pe+++t+h+ff+l+k++++lk++i ee+++l+ n++++++++l++gLk++a++rd +wGip P  
  gi|119719527|ref|YP_920022.1| 170 PTLLLNPRCAICGSTPELRTTTHWFFDLPKLTDALKRYI-EENENLPPNARNMSLQILRDGLKPRALTRDNKWGIPAPfp 248
                                    ***************************************.77779*******************************9988 PP

                                    TECCEEE-HHHHHHHHHHHTTTTT-...TTSGGGG.G--S......EEEEEGGGHHHHHTHHHHHHHH..TT----S-EE CS
                   tRNA-synt_1g 239 gaekkvlYVWldAligYisatkelakkkgeeekwkeyWakdkevelvhfigkdiikFHtifwPaillg..aelklpkkvv 316
                                    gae+k++YVW++A++gYisat e++ +kge+ekwke+W  d+e++ v+figkd+i+FHt+++Pa+l++  +++ lp +v+
  gi|119719527|ref|YP_920022.1| 249 GAEDKTIYVWMEAVLGYISATIEYFASKGEPEKWKEFW-LDPETRSVYFIGKDNIPFHTLILPALLIAsgEKYVLPWTVA 327
                                    **************************************.89**************************9889999****** PP

                                    EE--EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-HHHHHHHHHHHCCCHHHHHHHHH. CS
                   tRNA-synt_1g 317 aheyltvegkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfswedfvervNseLadklgnlvnRvl 391
                                    ++eyl ++g K+SkSr+++v+++eale ++ad++R++l++ +pe+kD++f+we+f + vN++L+d++gn+v+Rvl
  gi|119719527|ref|YP_920022.1| 328 STEYLLFRGLKFSKSRRIGVWIDEALEVFPADYWRFVLVSLRPEQKDMSFTWEEFLRIVNNDLNDNIGNFVHRVL 402
                                    *************************************************************************85 PP

>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   0.2   3.7e-15   8.2e-12       7     139 ..     429     562 ..     423     564 .. 0.78

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 3.7e-15
                    Anticodon_1   7 elnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkraaqevllevletllrllaPfmPfitE 86 
                                    e+    +ev e +  +rf++a++++   ++ +  + yl++ kp+  +++  ++r+   + l+++++l ++l+P++P  ++
  gi|119719527|ref|YP_920022.1| 429 EILARSREVAEFMYAFRFKEALTHIL--WLSSSGNSYLNFRKPWELDSE--SARTPAFLALHAVKALAIMLYPIIPRSSQ 504
                                    56666789*****************9..67999***********86543..3344449999******************* PP

                    Anticodon_1  87 elwqreeeelgkkesimlaewpe.kaeel.ekel.e.........eeevellkeivkairklrse 139
                                    e+w    ++lg+k++i +  w e +++    +el           eee+   k++v+ i++lr++
  gi|119719527|ref|YP_920022.1| 505 EMW----KLLGYKDDIANHRWHEiNEAVPpGQELpSprplfrkisEEEL---KAAVEKIEELRAS 562
                                    ***....***************854433353333425677885554444...5588888888865 PP

>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0   1.4e-10   3.1e-07      20     112 ..       4      95 ..       1     139 [. 0.83
   2 !    8.2   0.0   0.00028      0.63     363     439 ..     176     253 ..     161     285 .. 0.83

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 1.4e-10
                    tRNA-synt_1  20 kekkefilvdgPPyvtGslHiGhalaktlk.divirykrmkGkevlyvpGwDhaGlaieakvekklgakekkerkklgre 98 
                                    k ++++ + +  Py+ G +H+G+ + ++l  d+  r+ r+ G ev +v G D++G +ie +  k+   +  k+ ++  +e
  gi|119719527|ref|YP_920022.1|   4 KARRKWLVLAAWPYAYGVPHLGNLIGSVLSaDVAARFLRLAGDEVVFVSGSDMHGTPIEVEALKR--GESPKDLAERNHE 81 
                                    567889999999****************964999************************9887776..3445577777777 PP

                    tRNA-synt_1  99 efrekvrewkaeya 112
                                    +++e    w   + 
  gi|119719527|ref|YP_920022.1|  82 KIKELFERWEISFD 95 
                                    77777776665554 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00028
                    tRNA-synt_1 363 pfcerskkpiiyrateqWfvrvkeladaalkavekvqfvpkskekryaswlen.iqdWciSRqrwWGhriplfvsket 439
                                    p c   +   + r t+ Wf  + +l+da+ + +e+ +  p  ++++  ++l++  +  ++ R+  WG + p+  ++++
  gi|119719527|ref|YP_920022.1| 176 PRCAICGSTPELRTTTHWFFDLPKLTDALKRYIEENENLPPNARNMSLQILRDgLKPRALTRDNKWGIPAPFPGAEDK 253
                                    6666667777899*********************9999999999999999998468899**********998666654 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0     6e-07    0.0013      18     125 ..      17     126 ..       5     138 .. 0.84
   2 ?    2.2   0.0      0.04        90     244     284 ..     329     369 ..     302     387 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 6e-07
                                    BTTS--BHHHH.HHHHHHHHHHHHHHHTT-EEEEEEEBB--SH.HHHHHHHHTTS-HHHHHHHHHHHHHHHHHHTT---- CS
                   tRNA-synt_1e  18 tvydashlGha.RslvafDilrrilqalgYdvqfvqnvtDidD.kiikrareeeksvkelaekfieefkkdleaLnvlkp 95 
                                     +y   hlG+   s+++ D+ +r+l+ +g +v fv+   D+    i  +a ++++s k+lae+  e+ k+ +e  ++   
  gi|119719527|ref|YP_920022.1|  17 YAYGVPHLGNLiGSVLSADVAARFLRLAGDEVVFVSGS-DMHGtPIEVEALKRGESPKDLAERNHEKIKELFERWEISFD 95 
                                    57999****972577799*****************985.6665156679****************************976 PP

                                    SB.--BGGGGHHHHHHHHHHHHHTTSEEE-T CS
                   tRNA-synt_1e  96 tl.eprvsekvdeiielvekliekgyaYavs 125
                                    ++ ++    +++ + ++  ++ e+gy ++ +
  gi|119719527|ref|YP_920022.1|  96 NYsKTESPTHIKFVQDFYRRVYENGYVFSDT 126
                                    651677889*****************98765 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.04
                                    E--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHSS- CS
                   tRNA-synt_1e 244 nghlkiegekmsksLknfitikdvlkkfdprqlRllllsah 284
                                    +++l + g k sks +  + i ++l+ f +   R++l+s +
  gi|119719527|ref|YP_920022.1| 329 TEYLLFRGLKFSKSRRIGVWIDEALEVFPADYWRFVLVSLR 369
                                    67899999***************************999865 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.016        35      35      69 ..      20      55 ..      12      59 .. 0.89
   2 ?    6.5   0.0    0.0015       3.3     279     329 ..     336     386 ..     322     392 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.016
                   tRNA-synt_1f 35 GliHiGnlr.evltadlvaralrkrgeevrlilisD 69
                                   G +H+Gnl   vl+ad+ ar lr  g+ev ++  sD
  gi|119719527|ref|YP_920022.1| 20 GVPHLGNLIgSVLSADVAARFLRLAGDEVVFVSGSD 55
                                   99*****8549*****************99998776 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0015
                   tRNA-synt_1f 279 gekmssSkGnvltledwlevaepevlrflilrrkPkka.kkldldleilrlv 329
                                    g k s+S+  ++ ++++lev + +  rf++++ +P+++ ++++ + e+lr+v
  gi|119719527|ref|YP_920022.1| 336 GLKFSKSRRIGVWIDEALEVFPADYWRFVLVSLRPEQKdMSFTWE-EFLRIV 386
                                    4499*******************************8642566666.666666 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   3.5     0.002       4.5      14      48 ..     147     181 ..     131     182 .. 0.64
   2 ?    8.4   3.1   0.00097       2.2       1      37 [.     148     184 ..     148     191 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.002
                            DZR  14 fCseCgtklkavaaedrCpsCgekvdpearf...CpeC 48 
                                    +C++Cg +       d+C +Cg+ ++p+      C  C
  gi|119719527|ref|YP_920022.1| 147 TCPYCGYDRA---YGDQCENCGRLLEPTLLLnprCAIC 181
                                    5777777654...2677777777777665553334444 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00097
                            DZR   1 CpqCgeelppdarfCseCgtklkavaa.edrCpsCgek 37 
                                    Cp Cg +   ++  C++Cg  l+++   + rC  Cg+ 
  gi|119719527|ref|YP_920022.1| 148 CPYCGYDRAYGD-QCENCGRLLEPTLLlNPRCAICGST 184
                                    889998866665.5999999997544488899999876 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   1.8    0.0028       6.2      16      30 ..     140     157 ..     135     166 .. 0.76
   2 ?    2.1   1.1     0.087     2e+02       6      34 ..     164     192 ..     161     201 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0028
                  Zn_Tnp_IS1595  16 png...fvCPhCgsrkay 30 
                                    p++    +CP+Cg+++ay
  gi|119719527|ref|YP_920022.1| 140 PDRyivGTCPYCGYDRAY 157
                                    66665567*******999 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.087
                  Zn_Tnp_IS1595   6 aralLealrWpngfvCPhCgsr.kayrikt 34 
                                    + +lLe     n + C  Cgs+ +++++++
  gi|119719527|ref|YP_920022.1| 164 CGRLLEPTLLLNPR-CAICGSTpELRTTTH 192
                                    66666666666666.******999888887 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.5     0.061   1.4e+02      25      30 ..     147     152 ..     144     152 .. 0.90
   2 ?    8.4   0.6    0.0011       2.5      25      33 .]     160     168 ..     159     168 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.061
                                    E-TTT- CS
                      zf-RING_7  25 tCpeCG 30 
                                    tCp+CG
  gi|119719527|ref|YP_920022.1| 147 TCPYCG 152
                                    8****9 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0011
                                    E-TTT--EE CS
                      zf-RING_7  25 tCpeCGRIL 33 
                                    +C++CGR+L
  gi|119719527|ref|YP_920022.1| 160 QCENCGRLL 168
                                    7******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (565 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.43
# Mc/sec: 3903.15
//
Query:       gi|119719528|ref|YP_920023.1|  [L=428]
Description: RNA modification protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.8e-26   93.5   0.1    1.6e-25   90.4   0.0    2.1  2  Radical_SAM  Radical SAM superfamily
    5.9e-24   84.0   0.0      1e-23   83.2   0.0    1.4  1  UPF0004      Uncharacterized protein family UPF0004
    2.4e-13   49.8   3.1    4.8e-13   48.9   3.1    1.5  1  TRAM         TRAM domain
    0.00012   22.1   2.5    0.00078   19.6   2.5    2.5  1  TRAM_2       TRAM domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.12   5.3e+02      91     145 ..      18      76 ..       2      86 .. 0.72
   2 !   90.4   0.0   3.6e-29   1.6e-25       5     167 .]     145     315 ..     141     315 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.12
                                    HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSET....E CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx....x RF
                    Radical_SAM  91 eeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikr....v 145
                                      ++++ll+++   v  ++e ad   +l+ +  rg+t  ++ + l+ l e++ kr    v
  gi|119719528|ref|YP_920023.1|  18 SNIMATLLKRRGHKVVESIENADVV-ILNTCAvRGDTETKIFRRLRELEELRQKRgfrlV 76 
                                    5567777777778888888888887.9999999999999999999999998888633333 PP

  == domain 2  score: 90.4 bits;  conditional E-value: 3.6e-29
                                    SEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS.....TTHHHHHHHHHHTCCCTEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM   5 rgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggeplly.....pdfvellerlaklavpgir 79 
                                     gC + C fC+ + t  r+  ++s +++ i+e v+++ ++kg++e++l+g+++ +y      +++el++r+ ++ + ++r
  gi|119719528|ref|YP_920023.1| 145 SGCLGSCAFCIEWVT--RGTGVKSYPIDVIIENVRAA-VSKGAREIFLTGQDVAAYgydlgTNLYELVKRILEEVDGEYR 221
                                    69***********98..********************.9******************99998999999999998778888 PP

                                    EEEEECSSCHG....HHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET..EEEEEEEB CS
                                    xxxxxxxxxxx....xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxx RF
                    Radical_SAM  80 itvetngtlpd....eeklerllelg.vdrvslgleaaddekvlklmnrghtfeevlealeklreagikr..vvdrivgl 152
                                    +++   ++++     +  le++++ +   +++++++++dd+ vl+lm+r++t+ee++  + ++r +g+k   v+d+ivg+
  gi|119719528|ref|YP_920023.1| 222 VRLGMMEPMLLgrflKNLLELFRDERlYRYFHIPAQSGDDK-VLRLMRRKYTVEEYKGIVNTIRGSGWKFsiVTDIIVGF 300
                                    88888888887555555555555555***************.************************************** PP

                                    TTTSHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxx RF
                    Radical_SAM 153 pGendeeleellell 167
                                    pGe ++e++++l++l
  gi|119719528|ref|YP_920023.1| 301 PGEGEAEFQNTLKFL 315
                                    ************996 PP

>> UPF0004  Uncharacterized protein family UPF0004
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.2   0.0   2.2e-27     1e-23       1      95 [.       3      98 ..       3     100 .. 0.96

  Alignments for each domain:
  == domain 1  score: 83.2 bits;  conditional E-value: 2.2e-27
                                   XEEEE--S-CCCCHHHHHHHHHTTTSSS----SSS--SEEEEEE--SSSSHHHHTHHHHHHHHTTS.T.--EEEEEEHHHHS CS
                        UPF0004  1 kvaietlGCqmNevdseelaslLkkegyelvedeeeAdvvlvnTCavrekaekkviqalrelkalk.kpekkvvvlGCmaqr 81
                                   +v+iet+GC  N+ +s+++a+lLk++g+++ve+ e+Advv++nTCavr ++e+k++++lrel++l+ k++ ++vv GC+++ 
  gi|119719528|ref|YP_920023.1|  3 RVYIETFGCWLNKGESNIMATLLKRRGHKVVESIENADVVILNTCAVRGDTETKIFRRLRELEELRqKRGFRLVVSGCLVNV 84
                                   79****************************************************************7799************ PP

                                   -HHHHHHH-TTS-E CS
                        UPF0004 82 ekeellkeepevdl 95
                                   +++++l+ +p + l
  gi|119719528|ref|YP_920023.1| 85 RPKSILDVAPSASL 98
                                   *******9998766 PP

>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.9   3.1   1.1e-16   4.8e-13       1      62 []     367     427 ..     367     427 .. 0.97

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 1.1e-16
                                    XXXXXXEEEEEEEEE-.TTSEEEEEET.TEEEEETT--T..TEEEEEEEEEE-SSEEEEEEE CS
                           TRAM   1 rsyvGstqeVlveglsksegegiGrtdngkvvfvpgdlpgIGdfVeVkItkvkrqyLrGell 62 
                                    rsyvG++ eV veg s   g+++Grt ++k+v++++ ++++G++V VkI ++++ +L G++l
  gi|119719528|ref|YP_920023.1| 367 RSYVGEEREVVVEGTS-IRGDLVGRTIEYKPVVIKDQEARVGEIVRVKIVDATPVSLIGKVL 427
                                    79**************.*******************9888*******************997 PP

>> TRAM_2  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   2.5   1.7e-07   0.00078       1      63 [.     370     426 ..     370     427 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.7e-07
                                    BTSEEEEEEEE.EETTEEEEEETTS-TTTS--EEEES---T...T-EEEEEEEEEETTEEEEEE CS
                         TRAM_2   1 iGktvevlvdg.eeeglyvGRsyadAPEvDgevyvtgaeklskvGdfvkvkItdadeyDLiGev 63 
                                    +G++ ev+v+g + +g +vGR+    P     v+++++e +  vG++v+vkI+da+ + LiG+v
  gi|119719528|ref|YP_920023.1| 370 VGEEREVVVEGtSIRGDLVGRTIEYKP-----VVIKDQEAR--VGEIVRVKIVDATPVSLIGKV 426
                                    899********97777789****9988.....889977654..6******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       587  (0.0327403); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2988.95
//
Query:       gi|119719529|ref|YP_920024.1|  [L=432]
Description: adenosylhomocysteinase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.2e-73  245.3   0.0    2.8e-72  243.4   0.0    1.7  1  AdoHcyase      S-adenosyl-L-homocysteine hydrolase
    1.4e-54  184.5   0.0    2.6e-54  183.7   0.0    1.4  1  AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD bindi
    2.9e-09   36.5   0.0    5.3e-09   35.7   0.0    1.3  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
      2e-06   27.5   0.0    4.5e-06   26.3   0.0    1.5  1  IlvN           Acetohydroxy acid isomeroreductase, NADPH-bind
     0.0055   17.0   0.1      0.014   15.6   0.1    1.8  1  TrkA_N         TrkA-N domain
  ------ inclusion threshold ------
      0.017   14.5   0.0      0.098   12.0   0.0    2.0  1  THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase,
      0.044   13.1   0.7        0.1   11.9   0.7    1.6  1  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
      0.082   13.3   0.1       0.23   11.9   0.1    1.8  2  NAD_binding_7  Putative NAD(P)-binding


Domain annotation for each model (and alignments):
>> AdoHcyase  S-adenosyl-L-homocysteine hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  243.4   0.0   1.3e-75   2.8e-72       1     285 [.       2     427 ..       2     429 .. 0.95

  Alignments for each domain:
  == domain 1  score: 243.4 bits;  conditional E-value: 1.3e-75
                                    --B-S-GGGHHHHHHHHHHHHCC-HHHHHHHHHCTTT-TTTT-EEEEES--SHHHHHHHHHHHHTT-EEEEE-SSTTT-- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      AdoHcyase   1 dykvkdislaefGrkeielaekempglmalreeyaeekplkgariaGslhmtiqtavLietLvalGaevrWasCnifstq 80 
                                    +y+vkdisla  Gr  +e ae+ m+ l +++e ++e++plkg++ia ++h+t +tavL+ tL+a Gae+  a+ n  stq
  gi|119719529|ref|YP_920024.1|   2 EYRVKDISLAPKGRLMVEWAERHMAVLRSIKESFSERQPLKGVKIAACMHVTKETAVLMLTLKAAGAEIALAASNPLSTQ 81 
                                    69****************************************************************************** PP

                                    HHHHHHHCCTTEEEE--TT--HHHHHHHHHHCHS-SSTS-S-SEEEESSSHHHHHHHHHHHHHH.....S..SHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      AdoHcyase  81 deaaaaiaeagvpvfawkgetleeywwcieqalkwaedekepnlilDdGGDltllvhkgvkeeesvlekeedeeeekvvl 160
                                    d +aa +a++gv+vfawkg+t+ ey + i +a +      ep++ +DdGGDlt ++hk       +   e++  +++v  
  gi|119719529|ref|YP_920024.1|  82 DPVAAYLASEGVSVFAWKGMTEREYFESIARAASI-----EPDITMDDGGDLTVMLHK-------LSIGEAKGLDYEVA- 148
                                    *******************************9966.....7*****************.......22222222333333. PP

                                    HHHHHHHTT.THHCCCHCC--EEEE-SHHHHHHHHHHHHTT---SEEEESTTSHHHCTTH.................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................... RF
                      AdoHcyase 161 ellkksleedkkytellkkikGvseetttGvhrLyelakkgkLlvpainvndsvtkskfD.................... 220
                                            ++   +++ k++ G +eetttGv rL  l+++gkLl p i vnds+tk  fD                    
  gi|119719529|ref|YP_920024.1| 149 --------KEIVPPDAYKRVVGGTEETTTGVIRLRALEREGKLLYPVIAVNDSMTKYMFDnrfgtgqstldgilratnil 220
                                    ........33344667788899********************************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                      AdoHcyase 221 ................................................................................ 220
                                                                                                                    
  gi|119719529|ref|YP_920024.1| 221 lagknvvvagygwvgrgiawrargmgarvivveadpikaleayyegfyvtdmreaskigdvfitatgnrdvvreehflem 300
                                    ******************************************************************************** PP

                                    ..............................................................S-HHHHHHHHHHHHHHHH CS
                                    ..............................................................xxxxxxxxxxxxxxxxxx RF
                      AdoHcyase 221 ..............................................................hpsfvmsasftnqvlaqi 238
                                                                                                  hps vm+ sf nq+la  
  gi|119719529|ref|YP_920024.1| 301 rdgailanaghfnveisvedleristskrrinenveeytlrngkklyllsegrlvnlaaaegHPSEVMDLSFGNQALAVH 380
                                    ******************************************************************************** PP

                                    HHHHTTSSS-SSEEE--CHHHHHHHHHCCCCCT-------HHHHHCC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      AdoHcyase 239 elfkkekkyekkvyvlpkklDekvarlhleklgaklteltkeqaeyi 285
                                     l+kk+ k + kvy+lp +lD ++a ++l++lg+++++lt +q ey+
  gi|119719529|ref|YP_920024.1| 381 LLWKKKGKLKPKVYRLPAQLDRRIALIKLKSLGVRIERLTPKQVEYL 427
                                    **********************************************8 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.7   0.0   1.2e-57   2.6e-54       1     161 [.     201     361 ..     201     362 .. 0.99

  Alignments for each domain:
  == domain 1  score: 183.7 bits;  conditional E-value: 1.2e-57
                                    HHHHHCCCCCHHHHHHH-S--TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHHHHHCTT-EE--HHHCTTT-S CS
                  AdoHcyase_NAD   1 nlygcreslvdgikratdvllaGkvavvaGyGdvGkGcaaslkglGarvivtevdPicalqaameGfevvtleevvkkad 80 
                                    n +g+ +s +dgi rat++llaGk++vvaGyG vG+G a   +g+Garviv e dPi al a  eGf v+ + e+ k +d
  gi|119719529|ref|YP_920024.1| 201 NRFGTGQSTLDGILRATNILLAGKNVVVAGYGWVGRGIAWRARGMGARVIVVEADPIKALEAYYEGFYVTDMREASKIGD 280
                                    679999************************************************************************** PP

                                    EEEE-SSSSSSB-HHHHCCS-TTEEEEE-SSTTTTBTHHHHHTTT-EEEEEETTEEEEE-TTS-EEEEEGGGSBCHHHTS CS
                  AdoHcyase_NAD  81 ivvtttGnkdiitlehlkkmkddaivcniGhfdseidvaaleanalkkeevkpqvdrvtlkdgkkiillaeGrllnlgca 160
                                    +++t+tGn+d+++ eh+ +m+d ai++n Ghf+ ei v+ le+ +++k +++ +v+++tl++gkk+ ll+eGrl+nl++a
  gi|119719529|ref|YP_920024.1| 281 VFITATGNRDVVREEHFLEMRDGAILANAGHFNVEISVEDLERISTSKRRINENVEEYTLRNGKKLYLLSEGRLVNLAAA 360
                                    ******************************************************************************99 PP

                                    - CS
                  AdoHcyase_NAD 161 t 161
                                     
  gi|119719529|ref|YP_920024.1| 361 E 361
                                    7 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.0   2.3e-12   5.3e-09      33     127 ..     220     310 ..     197     321 .. 0.91

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 2.3e-12
                                    -GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SEEEE-S--STTTTTSBSHH CS
                   2-Hacid_dh_C  33 elsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelvsleellaesDivslhlpltpetrhlinae 112
                                     l+gk v + G+G +G+ +a r++++g++vi+++  + k  e+  +g++++++ e+ +  D+ + ++     +r+++ +e
  gi|119719529|ref|YP_920024.1| 220 LLAGKNVVVAGYGWVGRGIAWRARGMGARVIVVEADPIKALEAYYEGFYVTDMREASKIGDVFITATG----NRDVVREE 295
                                    589*********************************9988899999**999**********9987765....99****** PP

                                    HHHCSTTTEEEEESS CS
                   2-Hacid_dh_C 113 elakmkkgailiNta 127
                                    ++ +m++gail N++
  gi|119719529|ref|YP_920024.1| 296 HFLEMRDGAILANAG 310
                                    *************98 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0     2e-09   4.5e-06       2     101 ..     221     316 ..     220     325 .. 0.90

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 2e-09
                                    HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHHHHHHHHHHT CS
                           IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDelqkevyeeei 81 
                                    l gk+++v GyG  G+  a   r  g  v+v   +   ++ +A  egf v++++ea+k  dv ++ +    +++v++ee 
  gi|119719529|ref|YP_920024.1| 221 LAGKNVVVAGYGWVGRGIAWRARGMGARVIVVEADPI-KALEAYYEGFYVTDMREASKIGDVFITAT---GNRDVVREEH 296
                                    789**************************99776666.7789*******************987765...5789999999 PP

                                    GGG--TT-EEEESSSHHHHT CS
                           IlvN  82 epnlkegkalafahGfnihf 101
                                      ++++g++la a  fn+  
  gi|119719529|ref|YP_920024.1| 297 FLEMRDGAILANAGHFNVEI 316
                                    9****************976 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   6.2e-06     0.014       1      44 [.     226     269 ..     226     301 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 6.2e-06
                                    EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSEE CS
                         TrkA_N   1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeglev 44 
                                    ++++G+G vGr +a + +  g  +v+v++ d+ ++ e+  eg+ v
  gi|119719529|ref|YP_920024.1| 226 VVVAGYGWVGRGIAWRARGmGA-RVIVVEADPIKALEAYYEGFYV 269
                                    79*****************666.6********9999999999765 PP

>> THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   4.4e-05     0.098      26     112 ..     213     314 ..     205     331 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.4e-05
                                    HHHHCT---TT-EEEEE---TTTHHHHHHHHHCTT-EEEEE-TTS.............CCHHHHHCCSSEEEE-SS-TT- CS
                  THF_DHG_CYH_C  26 llketgielegkkvvvvGrsnivgkplallLleknatVtvchskt.............kdlaeitreadivvvavGkpel 92 
                                    +l++t+i l+gk+vvv G +  vg+ +a+     +a V v++                +d++e  +  d+ ++a+G+ ++
  gi|119719529|ref|YP_920024.1| 213 ILRATNILLAGKNVVVAGYG-WVGRGIAWRARGMGARVIVVEADPikaleayyegfyvTDMREASKIGDVFITATGNRDV 291
                                    79999***********9986.89*******99999999998865443344455555557888999999************ PP

                                    B-GGGS...-TT-EEEE---EEC CS
                  THF_DHG_CYH_C  93 ikaemv...kegavviDvGinrv 112
                                    +++e++   ++ga++ + G+ +v
  gi|119719529|ref|YP_920024.1| 292 VREEHFlemRDGAILANAGHFNV 314
                                    **998645588999988887555 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.7   4.5e-05       0.1      28      66 ..     223     259 ..     199     308 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.5e-05
                                    --EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHH CS
                    AlaDh_PNT_C  28 pakvlviGgGvaGlqAiatakglgakVtvlDvrparleq 66 
                                      +v+v G G +G   ++ a+g+ga+V v++ +p +   
  gi|119719529|ref|YP_920024.1| 223 GKNVVVAGYGWVGRGIAWRARGMGARVIVVEADPIK--A 259
                                    45799************************9987743..3 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0         8   1.8e+04      26      39 ..      63      76 ..      60      98 .. 0.62
   2 ?   11.9   0.1    0.0001      0.23       5      76 ..     221     293 ..     218     319 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 8
                  NAD_binding_7 26 lleagakvtvvape 39
                                   l +aga++ + a +
  gi|119719529|ref|YP_920024.1| 63 LKAAGAEIALAASN 76
                                   55666666665554 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.0001
                  NAD_binding_7   5 lkgkkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvklaeeelekdlegad....lviaatddrelne 76 
                                    l gk+v+v+G G v+   + +    ga+v+vv  +    ++ l  + e  +  d+ +a     + i+at +r++ +
  gi|119719529|ref|YP_920024.1| 221 LAGKNVVVAGYGWVGRGIAWRARGMGARVIVVEAD---PIKALEAYYEGFYVTDMREASkigdVFITATGNRDVVR 293
                                    789********************************...66766666666555555554434448888888877644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2667.40
//
Query:       gi|119719530|ref|YP_920025.1|  [L=262]
Description: 5'-methylthioadenosine phosphorylase II [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.4e-55  185.6   0.0    9.5e-55  185.4   0.0    1.0  1  PNP_UDP_1       Phosphorylase superfamily
  ------ inclusion threshold ------
      0.067   13.1   0.0       0.34   10.8   0.0    1.9  2  NAD_binding_10  NAD(P)H-binding


Domain annotation for each model (and alignments):
>> PNP_UDP_1  Phosphorylase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.4   0.0   1.1e-58   9.5e-55       1     233 [.       5     242 ..       5     243 .. 0.96

  Alignments for each domain:
  == domain 1  score: 185.4 bits;  conditional E-value: 1.1e-58
                                    CEEEEESSHHHHHHHHHH...EEEEEEEEEE.TTEEEEEEEE.TTEEEEEEE--....SSHHHHHHHHHHHHHHHC--SE CS
                      PNP_UDP_1   1 kiaiivgspgevellaes...pleetpfgregrgfkfvtGtl.kgkpvvivstG....iGkpnaavvaeirllkefgvka 72 
                                    ki+ii+gs+   ++++     +   tp+g++  + ++v+G++ ++k+ +i ++G    i ++ ++++a+i +lke+gv++
  gi|119719530|ref|YP_920025.1|   5 KIGIIGGSGLYSPDFLTNpkeEKIYTPYGPP--SSHVVIGEIaGRKVAFIPRHGkrheIPPHKVNYRANIYALKELGVER 82 
                                    69*******8888888776667888999999..*********888888******************************** PP

                                    EEEEEEEEESSTTT-TT-EEEEEEEEESSSCCGCCTHHCCTCCCCTTSSEE--HHHHHHHHHCHHTTTTTEEE.EEEEEE CS
                      PNP_UDP_1  73 iiriGtaGglnpdlkvGDvvipddainfdgrsplygpkeegqyfpdsydapadpelrallkeaaealgikvhr.Gvvata 151
                                    +i+++++G+l++d+k+GD+v++d++i+++ ++ +++++ + + ++ ++d+ ++pelr+l+ ++a++lgi++h+ G++++ 
  gi|119719530|ref|YP_920025.1|  83 LISVSAVGSLREDYKPGDFVCTDQFIDMTKGRVYTFYDGPVVAHVSMADP-FCPELRELCIRSARKLGITMHEkGTYICI 161
                                    ****************************************999******9.***************************** PP

                                    SESS-CHHHHHHHHHHTC-CEEESSHHHHHHHHHHTT--EEEEEEEEETTTBETTCTCH.HCCCHHHHHHHHHHHHHHHH CS
                      PNP_UDP_1 152 dgfyaeteaelrllrrlgadaveMEtaavaqlArelgipfaairvvsdlaaggadaeatheeveefaqeaaknaaallla 231
                                    +g++++t+ae+rl+r++gad+++M+ ++++ lAre+ ++f+ i++v+d ++ +a+++ t  ev  +++e+ +++++ll  
  gi|119719530|ref|YP_920025.1| 162 EGPRFSTRAESRLWRQFGADIIGMTLVPEVNLAREARMCFLNIAMVTD-YDVWAEKPVTAHEVARVMAENTEKVKRLLAD 240
                                    ************************************************.899*************************998 PP

                                    HH CS
                      PNP_UDP_1 232 ll 233
                                    l+
  gi|119719530|ref|YP_920025.1| 241 LI 242
                                    76 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   3.8e-05      0.34      78     108 ..      68      98 ..      37     116 .. 0.74
   2 ?   -0.3   0.0     0.094   8.4e+02     156     179 ..     206     229 ..     202     233 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3.8e-05
                                    HHHHHHHHHHCT--EEEEEEETTTTSGCGCH CS
                 NAD_binding_10  78 aknivdaakeagvkRfvlvsaigvgdevpge 108
                                     ++ + a+ke gv+R++ vsa+g+ +e  ++
  gi|119719530|ref|YP_920025.1|  68 YRANIYALKELGVERLISVSAVGSLREDYKP 98 
                                    677799*****************99865444 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.094
                                    EEETTSS----EEEHHHHHHHHHH CS
                 NAD_binding_10 156 vvekgepfkggsisradVAdvlva 179
                                    +v++ + + ++ ++ + VA+v+++
  gi|119719530|ref|YP_920025.1| 206 MVTDYDVWAEKPVTAHEVARVMAE 229
                                    56677788889999********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.67u 0.37s 00:00:01.04 Elapsed: 00:00:00.60
# Mc/sec: 1306.40
//
Query:       gi|119719531|ref|YP_920026.1|  [L=171]
Description: tRNA-splicing endonuclease subunit alpha [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-27   94.2   0.4    5.2e-27   93.7   0.4    1.2  1  tRNA_int_endo    tRNA intron endonuclease, catalytic C-termin
    2.9e-11   42.9   0.1    4.5e-11   42.3   0.1    1.3  1  tRNA_int_endo_N  tRNA intron endonuclease, N-terminal domain


Domain annotation for each model (and alignments):
>> tRNA_int_endo  tRNA intron endonuclease, catalytic C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.7   0.4   5.8e-31   5.2e-27       1      85 []      79     164 ..      79     164 .. 0.93

  Alignments for each domain:
  == domain 1  score: 93.7 bits;  conditional E-value: 5.8e-31
                                    HHHHHHHHHHHHHTT-EEEECGGGTSSEEEETSCTTTSSCSEEEEEEETTSEEEHHHHHHHHHHHHHTTSEEEEEEE.TT CS
                  tRNA_int_endo   1 falkyavyrdLrekGyvvrsGlkFGadFrvYqrrpslehseylVvvvsedeeldwpdlsaavrlahsvkKklilaiv.da 79 
                                    f   yavy+dLr +Gyvv+sG+kFG+ F+vYq +p+ +hs +lV v++ +++ld+ ++++a+rl+hsv+K +ila+    
  gi|119719531|ref|YP_920026.1|  79 FYDAYAVYKDLRGRGYVVKSGMKFGSTFAVYQFGPGIDHSIFLVDVLKYNDKLDPIQIIRAGRLSHSVRKHFILAYRdPV 158
                                    6678************************************************************************8445 PP

                                    TSCEEE CS
                  tRNA_int_endo  80 egdvty 85 
                                    +g+++y
  gi|119719531|ref|YP_920026.1| 159 DGKIQY 164
                                    666665 PP

>> tRNA_int_endo_N  tRNA intron endonuclease, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   0.1     5e-15   4.5e-11      21      67 .]      13      69 ..       2      69 .. 0.92

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 5e-15
                                   HHHTTT-SEE.........CCTSSEEEEHHHHHHHHHTTSEEEE.TTSEEE-HHHHH CS
                tRNA_int_endo_N 21 lyekgfYGkp.........lidepLqLslvEAlYLlekGklevv.kggeplsfeell 67
                                    ++ gfYG++         +  + L+Lsl+ A+YLle+G+l+++ ++g+p+s+ el+
  gi|119719531|ref|YP_920026.1| 13 YFKGGFYGRFftvpkpklpDVRKELELSLFDAMYLLEQGCLDLKrEDGSPVSPSELF 69
                                   67899************************************************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       224  (0.0124937); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.53
# Mc/sec: 979.16
//
Query:       gi|119719532|ref|YP_920027.1|  [L=256]
Description: phosphoribosyltransferase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.7e-16   58.2   0.0    1.1e-15   57.5   0.0    1.2  1  Pribosyltran  Phosphoribosyl transferase domain
     0.0043   16.5   0.0     0.0058   16.1   0.0    1.2  1  UPRTase       Uracil phosphoribosyltransferase


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.5   0.0   1.2e-19   1.1e-15      14     141 ..      50     177 ..      40     186 .. 0.81

  Alignments for each domain:
  == domain 1  score: 57.5 bits;  conditional E-value: 1.2e-19
                                    EEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE.........EE----TTSEEEE CS
                   Pribosyltran  14 avarlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdes.rlledpagkkVli 92 
                                     +++la++  ++ +++pd+vv+iargG+++a  l d L+  + ++ +  + ++g    ++++ +       ++ gk+Vl+
  gi|119719532|ref|YP_920027.1|  50 WCRSLAEKVKSS-GFTPDIVVAIARGGYVPARLLCDFLD--VHDLASIQVLHWGRAAEITSVAHVKyPYQLNLSGKRVLL 126
                                    577788888888.**************************..567777777777777777665554467999********* PP

                                    E-SEESSSHHHHHHHH.HHHCC-BSEEEEEEEE.E-HHHHHHHHHH-TTS. CS
                   Pribosyltran  93 VDDildtGgTllaale.lLkekgpeevriavlv.dkpateeevdknakrvf 141
                                    VDDi+dtG +++ a + +L + +p+e++ia+     p  ++++d+++ +v+
  gi|119719532|ref|YP_920027.1| 127 VDDIVDTGDSVIVARDyILSNWKPAELKIAAMQwISPVAKIKPDFYVEEVK 177
                                    *****************************9875466666666766666665 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   6.4e-07    0.0058      70     155 ..      67     154 ..      14     168 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 6.4e-07
                        UPRTase  70 alVpilRaGegmeealrel...lpea..rvghlglqreeetlepveyynkLPkki..aertvlllDpviaTGgsaaaaiq 142
                                    ++V+i R+G   ++ l +       a  +v+h g   e ++        k P ++  + ++vll+D ++ TG s++ a +
  gi|119719532|ref|YP_920027.1|  67 IVVAIARGGYVPARLLCDFldvHDLAsiQVLHWGRAAEITSVA----HVKYPYQLnlSGKRVLLVDDIVDTGDSVIVARD 142
                                    5789999998655555444111333311555555555554444....3456666666899******************99 PP

                        UPRTase 143 lLkergvgeekIl 155
                                     +++ +++  +  
  gi|119719532|ref|YP_920027.1| 143 YILS-NWKPAELK 154
                                    9887.66655444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       670  (0.0373696); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1842.86
//
Query:       gi|119719533|ref|YP_920028.1|  [L=317]
Description: beta-lactamase domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.8e-11   42.0   0.0    1.5e-10   41.2   0.0    1.3  1  Lactamase_B_3    Beta-lactamase superfamily domain
    2.2e-10   40.4   0.0      1e-09   38.2   0.0    1.9  2  Lactamase_B_2    Beta-lactamase superfamily domain
    5.5e-09   36.3   0.1    1.7e-08   34.7   0.1    1.9  1  Lactamase_B      Metallo-beta-lactamase superfamily
    0.00033   20.1   0.0     0.0015   18.0   0.0    1.8  2  Lactamase_B_6    Metallo-beta-lactamase superfamily domain
     0.0035   16.6   0.0     0.0051   16.1   0.0    1.1  1  Beta_lactamase3  Putative beta-lactamase-like family


Domain annotation for each model (and alignments):
>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.2   0.0   4.2e-14   1.5e-10      13     134 ..      10     139 ..       6     147 .. 0.88

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 4.2e-14
                  Lactamase_B_3  13 etagarilvDPfkanlgyeppaeeaDlvlisqaledHahletlkql....................aenvkvleegesle 72 
                                    +++ a+++ DP++       pa ++ +v++s+a++dH+ l++l++l                     +nv ++e+ge++e
  gi|119719533|ref|YP_920028.1|  10 QGGRATVVFDPTR------TPALKPSVVIVSHAHSDHYSLRALRSLpntpivmsratreiidpslrLRNVVYIEDGEEVE 83 
                                    455599999*988......899*******************************************99************* PP

                  Lactamase_B_3  73 vggleiravatshdavggsergenngflleqdgltiyhlGhlahels.seelkelgrvDvvlt 134
                                    v+g++i a+++ h         +   fl+e +g +i++ G+   e     + +   r+Dvv++
  gi|119719533|ref|YP_920028.1|  84 VEGVRIDAFSSGH-------IVGSLQFLIELEGKRIVFTGDFNLEKRlVLKPASVVRADVVII 139
                                    **********999.......566789***************9986331344467778888886 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2   0.0   2.8e-13     1e-09      30     171 ..      27     148 ..       6     170 .. 0.86
   2 ?   -0.5   0.0       0.2   7.2e+02     177     198 ..     267     288 ..     232     289 .. 0.81

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 2.8e-13
                                    SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTTTTEEEEEE-TTSEEEECSTTEEEEEEE CS
                  Lactamase_B_2  30 pidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleeepavnvheldwgesfelgdggleitatp 109
                                    +  +V+++haH DH+  l  lr l +   p++ ++ ++++++ ++           nv+ ++ ge++e++  g++i a+ 
  gi|119719533|ref|YP_920028.1|  27 KPSVVIVSHAHSDHY-SLRALRSLPN--TPIVMSRATREIIDPSLR--------LRNVVYIEDGEEVEVE--GVRIDAFS 93 
                                    5678***********.6999999755..799999999999999953........45899**********8..899****9 PP

                                    E-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---HHHH..HHHCT-SEEEEE-S-SSTTH CS
                  Lactamase_B_2 110 arhksgrrldrnagdtlGlriegggkrvyyigDtgyipeeig..erlggadllllditayedde 171
                                      h  g          l ++ie +gkr++++gD +  +  +   + +  ad++++d+t+ ++++
  gi|119719533|ref|YP_920028.1|  94 SGHIVGS---------LQFLIELEGKRIVFTGDFNLEKRLVLkpASVVRADVVIIDGTYGSPEY 148
                                    9999999.........*******************66655445688999*********887765 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.2
                                    T---STSHHHHCTTSSSSEEEE CS
                  Lactamase_B_2 177 gHltpeeaveaaadlgakrlvl 198
                                    +H++ ++ v+ ++d ga+++++
  gi|119719533|ref|YP_920028.1| 267 SHADFSQIVRYVRDSGAEVAIP 288
                                    6888888888888888888887 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.1   4.8e-12   1.7e-08      41     161 ..      24     128 ..       7     166 .. 0.78

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 4.8e-12
                                    GGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTE CS
                    Lactamase_B  41 kpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmeeaddaasrkglllagvsadkpdvdeeeldgnaggr 120
                                    + ++++ vi++H+H+DH++ l+ l++  + p+++ +++ +   +  +                ++++  e+++++++ g+
  gi|119719533|ref|YP_920028.1|  24 PALKPSVVIVSHAHSDHYS-LRALRSLPNTPIVMSRATREIIDPSLR---------------LRNVVYIEDGEEVEVEGV 87 
                                    67899************97.555555555555555555555555555...............334889************ PP

                                    EEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCCCC CS
                    Lactamase_B 121 ralyvtggpghghghgvveygggkvlftGDallagetgrid 161
                                    r   +  g+  g++++ +e++g++++ftGD+ l+   ++ +
  gi|119719533|ref|YP_920028.1|  88 RIDAFSSGHIVGSLQFLIELEGKRIVFTGDFNLEKRLVLKP 128
                                    ******************************98876665555 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       0.2     7e+02      23      50 ..      15      42 ..       1      62 [. 0.71
   2 !   18.0   0.0   4.2e-07    0.0015     127     177 ..      83     133 ..      69     142 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.2
                  Lactamase_B_6 23 esalkelekviptvdliLLshatlehlG 50
                                   + ++++ ++ + + +++++sha ++h +
  gi|119719533|ref|YP_920028.1| 15 TVVFDPTRTPALKPSVVIVSHAHSDHYS 42
                                   4556666666678899******999976 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 4.2e-07
                  Lactamase_B_6 127 kldgltitaynaGhtlGGtiWkiskesekivYavdwnhakeshLngaalld 177
                                    +++g+ i a+++Gh +G   + i+ e ++iv+  d+n +k  +L+ a+++ 
  gi|119719533|ref|YP_920028.1|  83 EVEGVRIDAFSSGHIVGSLQFLIELEGKRIVFTGDFNLEKRLVLKPASVVR 133
                                    4689***************************************99998865 PP

>> Beta_lactamase3  Putative beta-lactamase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.4e-06    0.0051     128     197 ..      70     139 ..      54     143 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.4e-06
                Beta_lactamase3 128 krnvkfiryneliyfddltieakaagtflGWvnyllevekkkilayisslslkkklslemkpi.ksdvlll 197
                                     rnv  i+  e ++++ + i a ++g  +G  ++l+e e k+ + ++  + l+k+l l+++++ ++dv+++
  gi|119719533|ref|YP_920028.1|  70 LRNVVYIEDGEEVEVEGVRIDAFSSGHIVGSLQFLIELEGKR-IVFTGDFNLEKRLVLKPASVvRADVVII 139
                                    589999999*********************************.9***************998525566665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2243.94
//
Query:       gi|119719534|ref|YP_920029.1|  [L=389]
Description: putative DNA primase, small subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.7e-21   75.4   0.8    2.9e-20   73.0   0.0    2.2  2  DNA_primase_S   DNA primase small subunit
     0.0014   18.4   0.7     0.0032   17.2   0.7    1.7  1  TackOD1         Thaumarchaeal output domain 1
  ------ inclusion threshold ------
      0.051   13.6   2.5      0.068   13.2   1.4    1.8  2  HypA            Hydrogenase/urease nickel incorporation, meta
       0.51    9.1   2.1       0.76    8.5   2.1    1.1  1  NRDD            Anaerobic ribonucleoside-triphosphate reducta
       0.65   10.0   5.4        1.5    8.8   1.1    2.4  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
        2.5    7.9   4.3        8.7    6.2   0.3    2.3  2  zinc_ribbon_2   zinc-ribbon domain
        3.1    8.0   5.3         13    6.0   5.3    2.1  1  Zn-ribbon_8     Zinc ribbon domain
        6.2    6.6   8.1        6.5    6.6   2.8    2.6  2  Zn_Tnp_IS1      InsA N-terminal domain


Domain annotation for each model (and alignments):
>> DNA_primase_S  DNA primase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.6      0.48   1.1e+03       1      13 [.     101     114 ..     101     124 .. 0.84
   2 !   73.0   0.0   1.3e-23   2.9e-20      16     171 ..     149     315 ..     142     319 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.48
                                    EEEEEETTT-..TT CS
                  DNA_primase_S   1 FDiDmddydd.cse 13 
                                    FDiD+d+ ++ c++
  gi|119719534|ref|YP_920029.1| 101 FDIDVDHIPTpCKD 114
                                    9******9998776 PP

  == domain 2  score: 73.0 bits;  conditional E-value: 1.3e-23
                                    HHHHHHHHHHHHHHHHHHHH-----GG..GEEEEE--SEEEEEEE--TTEEES-HHHHHHHHH.H............... CS
                  DNA_primase_S  16 vcekcwkfvsvavkvldellredfgfk..dilwvfsgrrGfHcwvsdkdarpltdeeraaivn.ylnlyrplhpflsrsm 92 
                                    vc  c +++++ + +l e l++dfgf+  ++ + fsg rGfH++v  + +++l++  r++i++   +++  +  +l+ + 
  gi|119719534|ref|YP_920029.1| 149 VCSTCINVAREEMIKLVEILEDDFGFDraEMRVAFSGHRGFHLHVESEAVKDLDQDARREITDyVRGIGIDVKLYLKPA- 227
                                    89*************************************************************6677777777777777. PP

                                    .......................HCHHHHCT--------.........................---------------- CS
                  DNA_primase_S  93 lkivkpvveeiileeqdpf....eikkllrllpdkslre.......kkkweakedivlvllyprldeqvtkgikhllkap 161
                                     k++++++ +      + +    +   llrll+  +++e        ++we ++++ ++ l ++ de+vt+++k+l+++p
  gi|119719534|ref|YP_920029.1| 228 GKSLYTYKYSA---TSPGWagriAKYLLLRLLQAGENGEleslsmeYEQWEKTIKEAVSELSVKVDEKVTIDTKRLIRLP 304
                                    88888886655...5677899776666778888888888888999889999***************************** PP

                                    -....---.-- CS
                  DNA_primase_S 162 fcihgktg.nv 171
                                    +++hgktg +v
  gi|119719534|ref|YP_920029.1| 305 GSLHGKTGlKV 315
                                    ********887 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.7   1.4e-06    0.0032      33     116 ..      77     160 ..      43     168 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.4e-06
                        TackOD1  33 skelysypllealskekeeseelleelvkrglle..eelvdrirlCpsCksghlnvrevCpkCkSidieeqelihhftCg 110
                                    s+  y+yp ++ + ++     +l+ ++  + + +  ++l+dr   C+ C      +++ Cp+C+S ++e ++ + + tC 
  gi|119719534|ref|YP_920029.1|  77 SSAYYQYPSAQEMGEKGWLGADLVFDIDVDHIPTpcKDLHDR-WRCQDCGAEGWGFTKKCPSCGSERLEWSKWV-CSTCI 154
                                    445666666666655444444444444444444443444455.56************************99987.99**9 PP

                        TackOD1 111 nvgpee 116
                                    nv+ ee
  gi|119719534|ref|YP_920029.1| 155 NVAREE 160
                                    999887 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.4     3e-05     0.068      67      99 ..     115     145 ..      90     155 .. 0.84
   2 ?   -3.3   0.0         4   9.1e+03      22      42 ..     278     298 ..     266     314 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3e-05
                                    E--EEEETTTS-EEECHHHHHS-TTTSSS-EEE CS
                           HypA  67 vpvkvrCreCgkefeleekalrCpkCgsadvei 99 
                                     + + rC++Cg+e+   +k  +Cp+Cgs+++e 
  gi|119719534|ref|YP_920029.1| 115 LHDRWRCQDCGAEGWGFTK--KCPSCGSERLEW 145
                                    566899*****99985434..8******99875 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4
                                    T..EEEEEEEEEETTCT--HH CS
                           HypA  22 aarkvtkvkvevGelsgvepe 42 
                                      + v+++ v+v e  +++++
  gi|119719534|ref|YP_920029.1| 278 IKEAVSELSVKVDEKVTIDTK 298
                                    345677777777766666655 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   2.1   0.00034      0.76     509     532 ..     120     144 ..     116     151 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00034
                                    EETT.--EESS..SB-TTT--BE.EE CS
                           NRDD 509 vCnecgykgei..ekCpkCgseeeve 532
                                    +C++cg +g    +kCp+Cgse+ +e
  gi|119719534|ref|YP_920029.1| 120 RCQDCGAEGWGftKKCPSCGSER-LE 144
                                    8******76666699*****765.55 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.2     0.059   1.3e+02      44      55 ..     116     127 ..     107     129 .. 0.83
   2 ?    8.8   1.1   0.00065       1.5      29      55 ..     133     156 ..     131     162 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.059
                 OrfB_Zn_ribbon  44 grtfkCpnCgfe 55 
                                    +++++C++Cg+e
  gi|119719534|ref|YP_920029.1| 116 HDRWRCQDCGAE 127
                                    578******986 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00065
                 OrfB_Zn_ribbon  29 ktCseCgsknkealsgrtfkCpnCgfe 55 
                                    k+C+ Cgs+  e   + +++C+ C  +
  gi|119719534|ref|YP_920029.1| 133 KKCPSCGSERLE---WSKWVCSTCINV 156
                                    89*****98666...*********765 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.3     0.047   1.1e+02       1       8 [.     120     127 ..     120     128 .. 0.83
   2 ?    6.2   0.3    0.0039       8.7       1       8 [.     134     141 ..     132     143 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.047
                  zinc_ribbon_2   1 fCpnCGae 8  
                                    +C  CGae
  gi|119719534|ref|YP_920029.1| 120 RCQDCGAE 127
                                    69999987 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0039
                  zinc_ribbon_2   1 fCpnCGae 8  
                                    +Cp+CG e
  gi|119719534|ref|YP_920029.1| 134 KCPSCGSE 141
                                    68888876 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   5.3     0.006        13       7      36 ..     120     143 ..     118     144 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.006
                    Zn-ribbon_8   7 rCeeCghefevlqsisdaplta.CPeCgs.ev 36 
                                    rC++Cg   e +        t+ CP+Cgs ++
  gi|119719534|ref|YP_920029.1| 120 RCQDCG--AEGWG------FTKkCPSCGSeRL 143
                                    899999..55554......3344*****9665 PP

>> Zn_Tnp_IS1  InsA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   2.8    0.0029       6.5      26      34 ..     116     124 ..     112     125 .. 0.91
   2 ?    2.2   0.3     0.066   1.5e+02       7      14 ..     134     141 ..     132     143 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0029
                     Zn_Tnp_IS1  26 HeRfrCrdC 34 
                                    H+R+rC+dC
  gi|119719534|ref|YP_920029.1| 116 HDRWRCQDC 124
                                    ********* PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.066
                     Zn_Tnp_IS1   7 hCPrCsst 14 
                                     CP+C s+
  gi|119719534|ref|YP_920029.1| 134 KCPSCGSE 141
                                    6****985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       818  (0.0456244); expected 358.6 (0.02)
Passed bias filter:                      687  (0.0383178); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 2763.50
//
Query:       gi|119719535|ref|YP_920030.1|  [L=356]
Description: DNA primase, large subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.1e-33  114.1   0.1    2.7e-32  112.2   0.0    1.9  1  DNA_primase_lrg  Eukaryotic and archaeal DNA primase, large s


Domain annotation for each model (and alignments):
>> DNA_primase_lrg  Eukaryotic and archaeal DNA primase, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.2   0.0   1.5e-36   2.7e-32      17     219 ..     160     339 ..     139     354 .. 0.81

  Alignments for each domain:
  == domain 1  score: 112.2 bits;  conditional E-value: 1.5e-36
                                    G..GS-EETTEEEE-HHHHHHHHHHHHHHHHHH..........HHGGGSSS---HHHHHHHCT--.............TT CS
                DNA_primase_lrg  17 r..rvllkkGyaylpkeeleslllekfrkrlekalestkeslpeleeeikederekleellealsesyvaedvqeeedsk 94 
                                    +  ++ll+kGy+ ++ke +++l+++ ++k + + +e+tk ++++++++      + +ee+ +  s       +q  e+  
  gi|119719535|ref|YP_920030.1| 160 KlvNRLLDKGYVEVRKESFLRLIETGVKKYVLRLIEQTKVDEARIPPK----LYSAVEEIASIWS-------KQR-EELL 227
                                    155889**************************************9554....4444556666666.......222.2333 PP

                                    SSTTGG.SHHHHTT--HHHHCCHHHHCCCSS--CHHHHHHHHHHHHCT--CHHHHCCCHCHST..HHHHHH.HTHCHCHH CS
                DNA_primase_lrg  95 isakni.dklakesfPpCmrelleglkknghlkhegrlqltlFlkdiglsldeilelwkeaftrteekFdk.eyrynirh 172
                                    + a+n  +  ++++fPpC+r++++++ ++++l+h++r++l++Fl ++g s+de+le++k +     +++ +   ry+++h
  gi|119719535|ref|YP_920030.1| 228 TYARNAsKGKREDLFPPCIRAIIQDISAGKNLPHSARFALASFLLSVGFSVDEVLEVFKLS-----PDYREdIARYQVEH 302
                                    3344443677899***********************************************8.....*****9999***** PP

                                    HCC-STT--------HHHHHHS....TT---S.-HHHH.HHHHHHHHH CS
                DNA_primase_lrg 173 nyGkegkrtnyspysCekiltkpppgkgdahg.CpfrhdpdklktlLq 219
                                    ++G+ g+rt+y py+C+ +         +++g C    + +++++ Lq
  gi|119719535|ref|YP_920030.1| 303 IAGMRGSRTKYLPYKCDNM---------RSYGlCRW--RCENIRHPLQ 339
                                    *******************.........99999944..4555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2543.60
//
Query:       gi|119719536|ref|YP_920031.1|  [L=247]
Description: proliferating cell nuclear antigen PcnA [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-14   52.4   0.0    7.5e-13   48.3   0.0    2.2  2  PCNA_N    Proliferating cell nuclear antigen, N-terminal doma
    4.3e-09   36.6   0.0    9.8e-08   32.2   0.0    2.2  2  PCNA_C    Proliferating cell nuclear antigen, C-terminal doma
    7.2e-08   31.8   0.0     0.0028   16.8   0.0    2.0  2  Rad1      Repair protein Rad1/Rec1/Rad17
    0.00013   21.5   0.0    0.00019   21.0   0.0    1.4  1  Rad9      Rad9
  ------ inclusion threshold ------
      0.017   14.8   0.0      0.026   14.2   0.0    1.3  1  STD1      STD1/MTH1
       0.11   12.6   0.0        5.6    7.1   0.1    2.2  2  DUF1818   Domain of unknown function (DUF1818)


Domain annotation for each model (and alignments):
>> PCNA_N  Proliferating cell nuclear antigen, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3   0.0   2.5e-16   7.5e-13       6      94 ..       6      94 ..       1     116 [. 0.89
   2 ?    2.0   0.0     0.052   1.6e+02      13      43 ..     133     161 ..     124     191 .. 0.67

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 2.5e-16
                                   ESSHHHHHHHHHHHTTTCSEEEEEEETTEEEEEEE-TTSSEEEEEEEEGGGSSEEEESS-EEEEEEHHHHHHHHTTSTTTSE CS
                         PCNA_N  6 leqasllkklleaikdlvneanfdcddsGislqalDsshvaLvslelrsegfekyrCDrnlalgvnlnslskilkcanneds 87
                                   + +a   k ++e++  +v+eanf ++ +G++l+alD  ++a+v l + s+ fe+y  D++  ++  l  + k+lk a+ +d+
  gi|119719536|ref|YP_920031.1|  6 FPDAREWKYIIESLATIVDEANFVASPEGLKLRALDPGRIAMVDLFIPSNLFEEYSVDQETKISAVLDDIDKVLKRAKSDDK 87
                                   556667899************************************************************************* PP

                                   EEEEEET CS
                         PCNA_N 88 vtlkaed 94
                                   + ++  +
  gi|119719536|ref|YP_920031.1| 88 ISFEVSQ 94
                                   9887665 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.052
                                    HHHHHHHTTTCSEEEEEEETTEEEEEEE-TT CS
                         PCNA_N  13 kklleaikdlvneanfdcddsGislqalDss 43 
                                    k l ++++d +++a++   ++ ++l+a D+s
  gi|119719536|ref|YP_920031.1| 133 KMLSDTFRDALKDASLV--SESVKLKAEDES 161
                                    55667777777777653..334666666665 PP

>> PCNA_C  Proliferating cell nuclear antigen, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.065     2e+02      15      45 ..       9      39 ..       4      69 .. 0.89
   2 !   32.2   0.0   3.3e-11   9.8e-08       3     127 ..     124     244 ..     123     245 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.065
                                   HHHHHHHHHHHTTT-SEEEEEEETTEEEEEE CS
                         PCNA_C 15 ssefaricrdlsqlsdsvvisvtkegvkfsa 45
                                   + e++ i+  l+++ d+ +  ++ eg+k +a
  gi|119719536|ref|YP_920031.1|  9 AREWKYIIESLATIVDEANFVASPEGLKLRA 39
                                   678999**********************998 PP

  == domain 2  score: 32.2 bits;  conditional E-value: 3.3e-11
                                    --SS-SEEEEEEHHHHHHHHHHHTTT-SEEEEEEETTEEEEEEEETTEEEEEEE--BEESSSGGGCBEEEESS-EEEEEE CS
                         PCNA_C   3 pdseydavvklpssefaricrdlsqlsdsvvisvtkegvkfsasGdiGsasivlkqvkdvdkeeeavklelkepvtltfa 82 
                                    p +++    k+ s  f    +d s +s+sv +++  e++   a  d G+      + + + +  + v++++ke+ +  ++
  gi|119719536|ref|YP_920031.1| 124 PKLNFTVAAKMLSDTFRDALKDASLVSESVKLKAEDESLWLLARSDKGEI-----ESRFSIETGSLVEIDVKEAAEASYG 198
                                    5678888999************************************9987.....44455567789************** PP

                                    HHHHHHHG.GGGGC-SEEEEEEETTSEEEEEEEETTCEEEEEEE-B CS
                         PCNA_C  83 lkYlaeft.katsLservtlslssevPlvveykikdvgllayllak 127
                                    +++l +++ ka  +s+  +l+++ ++Pl + ++i+ +g l+ylla+
  gi|119719536|ref|YP_920031.1| 199 IDFLDKIVsKAYRISDILGLRFATNMPLEMTFDIAGGGTLKYLLAP 244
                                    ****997549**********************************98 PP

>> Rad1  Repair protein Rad1/Rec1/Rad17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   9.3e-07    0.0028      20      90 ..      21     101 ..       6     107 .. 0.81
   2 !   13.1   0.0   1.2e-05     0.037     167     257 ..     130     214 ..     118     224 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 9.3e-07
                           Rad1  20 afkdkalvqissdGlkfiv.ednrvlqaqafldkalFtsYtfenaqdd.........edeedeeedsvsfevsLsallec 89 
                                    +++d+a   +s++Glk+ + + +r+    +f++++lF++Y+++++++            ++ +++d++sfevs   l+ +
  gi|119719536|ref|YP_920031.1|  21 TIVDEANFVASPEGLKLRAlDPGRIAMVDLFIPSNLFEEYSVDQETKIsavlddidkVLKRAKSDDKISFEVSQGRLIIT 100
                                    46779999*********75389********************66666599999999855666689999999997777766 PP

                           Rad1  90 L 90 
                                    L
  gi|119719536|ref|YP_920031.1| 101 L 101
                                    6 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 1.2e-05
                           Rad1 167 lkvilkselLhsalteLdatskklkilassekkapvfalsakgelgssevefpneksvlekfevsslsessessYkfall 246
                                    +   + s+ +++al++ + +s+++k+ a++e     + l a+++ g+ e  f++e   l ++ v+   e+ e sY +  l
  gi|119719536|ref|YP_920031.1| 130 VAAKMLSDTFRDALKDASLVSESVKLKAEDE----SLWLLARSDKGEIESRFSIETGSLVEIDVK---EAAEASYGIDFL 202
                                    556689********************99996....8*********************99999999...666666999999 PP

                           Rad1 247 kka.akalalss 257
                                    +k+ +ka ++s 
  gi|119719536|ref|YP_920031.1| 203 DKIvSKAYRISD 214
                                    886256777765 PP

>> Rad9  Rad9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   6.4e-08   0.00019       4     104 ..      15     107 ..      13     236 .. 0.70

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 6.4e-08
                           Rad9   4 alqclsrigdelyleisedglelrtvnssrSayalvtlkksfFdkyekevseqirckilvKsvlsvfrslsakektvekv 83 
                                    ++++l+ i de ++ +s++gl+lr+++  r a + + + +++F++y   v+++ +++  +  + +v++      k+ +k+
  gi|119719536|ref|YP_920031.1|  15 IIESLATIVDEANFVASPEGLKLRALDPGRIAMVDLFIPSNLFEEY--SVDQETKISAVLDDIDKVLKR----AKSDDKI 88 
                                    6899******************************************..8889999999999******63....3455666 PP

                           Rad9  84 kisidekksrlivqllCkhgv 104
                                    + ++  +++rli++l  + + 
  gi|119719536|ref|YP_920031.1|  89 SFEV--SQGRLIITLSGRAER 107
                                    6655..899999999888764 PP

>> STD1  STD1/MTH1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   8.5e-06     0.026     129     173 ..      46      92 ..      11     101 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 8.5e-06
                           STD1 129 eiietLvsSdlYkEhnldysfklsvAkysvkkarklqeqs..kelsk 173
                                     +++  + S+l++E+++d+++k+s   + + k+ k+ +++   ++  
  gi|119719536|ref|YP_920031.1|  46 AMVDLFIPSNLFEEYSVDQETKISAVLDDIDKVLKRAKSDdkISFEV 92 
                                    56777889****************************99986644444 PP

>> DUF1818  Domain of unknown function (DUF1818)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.029        86      47      81 ..      73     107 ..      63     121 .. 0.78
   2 ?    7.1   0.1    0.0019       5.6      38      97 ..     128     188 ..     118     198 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.029
                                    HHHHCCHTTSSTTSEEEEEEEETTEEEEEEEETTE CS
                        DUF1818  47 eqlkalaeeLmdeEkialeaesdllwleveGdkea 81 
                                    ++++++ ++   ++ki+ e+++  l ++++G +e+
  gi|119719536|ref|YP_920031.1|  73 DDIDKVLKRAKSDDKISFEVSQGRLIITLSGRAER 107
                                    56667777778899*****************8764 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0019
                                    HHHHHHHHHHHHH.CCHTTSSTTSEEEEEEEETTEEEEEEEETTEEEEEEEE-TCS-EEEE CS
                        DUF1818  38 llrllaqLaeqlk.alaeeLmdeEkialeaesdllwleveGdkeaysLrlilsegRrvEgs 97 
                                    ++ +++ L ++++ al++  + +E+++l+ae ++lwl +  dk + + r+ +++g  vE  
  gi|119719536|ref|YP_920031.1| 128 FTVAAKMLSDTFRdALKDASLVSESVKLKAEDESLWLLARSDKGEIESRFSIETGSLVEID 188
                                    55566777777652577788899****************9999999999999998888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1630.94
//
Query:       gi|119719537|ref|YP_920032.1|  [L=109]
Description: transcription termination factor Tfs [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-17   62.3  10.7      3e-17   62.2   2.2    3.0  3  TFIIS_C          Transcription factor S-II (TFIIS)
    1.1e-08   34.8   0.4    1.1e-08   34.8   0.4    3.0  3  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
    2.8e-07   30.4   6.3     0.0011   18.9   0.4    2.3  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
      7e-05   22.7   8.7     0.0061   16.5   1.3    3.1  2  Nudix_N_2        Nudix N-terminal
    0.00039   20.0   0.2    0.00039   20.0   0.2    3.0  3  Baculo_LEF5_C    Baculoviridae late expression factor 5 C-ter
     0.0011   18.7   3.3      0.018   14.9   0.2    2.8  3  C1_1             Phorbol esters/diacylglycerol binding domain
     0.0016   18.5  10.3        3.1    8.0   4.2    3.9  3  Zn-ribbon_8      Zinc ribbon domain
     0.0024   17.8   0.0     0.0042   17.1   0.0    1.4  1  DUF2846          Protein of unknown function (DUF2846)
      0.003   17.0  13.8       0.22   11.1   3.3    3.4  2  TF_Zn_Ribbon     TFIIB zinc-binding
     0.0035   17.0  15.3          4    7.3   2.4    4.2  4  zinc_ribbon_2    zinc-ribbon domain
     0.0041   16.4   6.8      0.013   14.8   1.0    3.0  3  zf-TFIIB         Transcription factor zinc-finger
     0.0045   16.9   4.3       0.13   12.2   0.2    3.2  3  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon
     0.0049   16.7   3.5       0.26   11.2   0.0    3.4  4  HalOD2           Halobacterial output domain 2
     0.0068   17.1   8.9      0.054   14.2   0.3    3.1  3  zinc_ribbon_15   zinc-ribbon family
     0.0093   16.0   7.7      0.078   13.0   0.4    2.7  2  DZR              Double zinc ribbon
  ------ inclusion threshold ------
      0.022   15.1   3.5       0.31   11.3   1.5    2.7  2  Rpr2             RNAse P Rpr2/Rpp21/SNM1 subunit domain
      0.029   14.3  12.3          2    8.4   0.2    4.2  4  zinc_ribbon_4    zinc-ribbon domain
      0.029   14.6   6.1       0.18   12.1   1.2    2.9  2  IBR              IBR domain, a half RING-finger domain
      0.034   14.3   5.1        2.2    8.4   0.5    2.4  2  zf-MYND          MYND finger
      0.078   12.8   7.9       0.21   11.5   1.7    2.1  2  FdhE             Protein involved in formate dehydrogenase fo
      0.091   12.7  10.0       0.86    9.6   1.0    3.0  3  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.095   12.1  13.1       0.75    9.3   0.2    3.9  4  zf-ribbon_3      zinc-ribbon domain
       0.12   12.1  10.2        0.3   10.8   0.1    3.6  4  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
       0.15   12.2   4.2         31    4.9   0.1    3.5  3  zf-RING_7        C4-type zinc ribbon domain
       0.16   11.6   4.5        2.5    7.7   4.8    2.4  1  TackOD1          Thaumarchaeal output domain 1
       0.21   11.3   0.4       0.21   11.3   0.4    3.1  2  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
       0.25   11.8   7.1         54    4.3   7.1    2.6  1  Lar_restr_allev  Restriction alleviation protein Lar
       0.36   10.8   6.6          1    9.4   2.5    2.8  2  HypA             Hydrogenase/urease nickel incorporation, met
       0.42   10.7   5.2        0.5   10.5   3.0    2.2  1  Mut7-C           Mut7-C RNAse domain
       0.63    9.7  11.0         33    4.2   0.4    4.1  4  zf_UBZ           Ubiquitin-Binding Zinc Finger
       0.81   10.2   8.8         41    4.8   0.0    4.1  4  zf-H2C2_2        Zinc-finger double domain
       0.91    9.3  12.5        9.8    6.0   0.1    4.0  4  A2L_zn_ribbon    A2L zinc ribbon domain
          1    9.1  12.8        9.1    6.1   3.3    3.8  3  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
          1    9.4   6.0        1.5    8.9   0.8    2.3  2  Elf1             Transcription elongation factor Elf1 like
        1.3    9.2   8.0         13    6.0   0.1    3.2  3  UPF0547          Uncharacterised protein family UPF0547
          2    8.9   0.1          2    8.9   0.1    3.8  3  zf-IS66          zinc-finger binding domain of transposase IS
        2.2    8.5  13.1         30    4.8   0.7    4.1  4  zf-ACC           Acetyl-coA carboxylase zinc finger domain
        2.3    8.1  13.3        3.5    7.5   3.6    3.5  3  zinc_ribbon_5    zinc-ribbon domain
        2.8    7.6  10.7        4.3    7.0   0.1    3.7  4  RecR             RecR protein
        3.3    7.8   9.5        9.8    6.2   0.1    3.5  4  RNHCP            RNHCP domain
        3.6    7.6   8.2         21    5.1   0.3    3.0  3  PHD              PHD-finger
        3.8    7.5  10.9         25    4.9   0.1    4.0  4  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
        5.9    7.6  14.6        1.7    9.3   0.2    3.6  3  zf-ISL3          zinc-finger of transposase IS204/IS1001/IS10
        9.9    6.0  18.2        3.9    7.3   0.5    4.0  4  Rubredoxin_2     Rubredoxin metal binding domain


Domain annotation for each model (and alignments):
>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1      0.15        62       3       8 ..       4       9 ..       2      12 .. 0.85
   2 ?    1.2   0.1      0.85   3.4e+02      30      36 ..      23      29 ..      20      30 .. 0.69
   3 !   62.2   2.2   7.4e-20     3e-17       1      39 []      68     106 ..      68     106 .. 0.97

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.15
                        TFIIS_C 3 CpkCgs 8
                                  CpkCg+
  gi|119719537|ref|YP_920032.1| 4 CPKCGG 9
                                  ****96 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.85
                        TFIIS_C 30 kCtkCgh 36
                                   +C  Cg+
  gi|119719537|ref|YP_920032.1| 23 RCSRCGY 29
                                   6777775 PP

  == domain 3  score: 62.2 bits;  conditional E-value: 7.4e-20
                        TFIIS_C   1 akCpkCgsreayffqlQtRsaDEpmtvfykCtkCghrWr 39 
                                    +kC++Cg+++ay ++lQtR++DEp+t+fy CtkC + +r
  gi|119719537|ref|YP_920032.1|  68 FKCENCGNDKAYVYELQTRAGDEPATRFYICTKCRKVYR 106
                                    69**********************************997 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   0.4   2.7e-11   1.1e-08       1      35 [.       1      35 [.       1      36 [. 0.91
   2 ?    3.6   0.8      0.15        63      21      28 ..      66      74 ..      55      86 .. 0.72
   3 ?    0.2   0.3       1.7   7.1e+02      20      28 ..      93     102 ..      83     105 .. 0.69

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 2.7e-11
                                   EEBESTTTSBEEEEECSCCCEEEESSSS-EEESSC CS
                 RNA_POL_M_15KD  1 lkFCpkCgNlLlpkedkegknfeCrqCgYeepadq 35
                                   ++FCpkCg l+ p +   +k++ C+ CgY+ +++ 
  gi|119719537|ref|YP_920032.1|  1 MEFCPKCGGLMVPSVVNGKKVLRCSRCGYIVEKSN 35
                                   99***********9988888899*******99985 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.15
                                   E.EEESSSS CS
                 RNA_POL_M_15KD 21 n.feCrqCg 28
                                   + f C +Cg
  gi|119719537|ref|YP_920032.1| 66 VsFKCENCG 74
                                   468888887 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 1.7
                                    CE.EEESSSS CS
                 RNA_POL_M_15KD  20 kn.feCrqCg 28 
                                    ++ + C +C 
  gi|119719537|ref|YP_920032.1|  93 TRfYICTKCR 102
                                    4557788885 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.4   2.7e-06    0.0011      21      45 ..       4      29 ..       2      30 .. 0.95
   2 !   14.2   0.9   7.6e-05     0.031      19      45 ..      68     103 ..      65     104 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.7e-06
                  Zn_Tnp_IS1595 21 CPhCgsr.kayriktrglfqCkeCrk 45
                                   CP+Cg+   +  +++ ++++C++C++
  gi|119719537|ref|YP_920032.1|  4 CPKCGGLmVPSVVNGKKVLRCSRCGY 29
                                   ************************97 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 7.6e-05
                  Zn_Tnp_IS1595  19 fvCPhCgsrkayrikt.........rglfqCkeCrk 45 
                                    f C +Cg++kay ++           + + C +Crk
  gi|119719537|ref|YP_920032.1|  68 FKCENCGNDKAYVYELqtragdepaTRFYICTKCRK 103
                                    78*******666555555*******9********97 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   1.3   1.5e-05    0.0061       2      31 ..       3      30 ..       2      31 .. 0.94
   2 !    8.8   1.0    0.0036       1.5       3      31 ..      70     104 ..      70     105 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.5e-05
                                   B-TTT--B-EEE--TT-SS-EEEETTTTEE CS
                      Nudix_N_2  2 FCsqCGtpvelripdgDnreRlvCpaCgti 31
                                   FC++CG+ +   +  g +  R  C++Cg+i
  gi|119719537|ref|YP_920032.1|  3 FCPKCGGLMVPSVVNGKKVLR--CSRCGYI 30
                                   9*************9999987..******9 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0036
                                    -TTT--B-E....EE--TT-SS.-E.EEETTTTEE CS
                      Nudix_N_2   3 CsqCGtpve....lripdgDnr.eR.lvCpaCgti 31 
                                    C++CG+  +    l++ +gD+  +R ++C++C  +
  gi|119719537|ref|YP_920032.1|  70 CENCGNDKAyvyeLQTRAGDEPaTRfYICTKCRKV 104
                                    999**98444455899999996368569****987 PP

>> Baculo_LEF5_C  Baculoviridae late expression factor 5 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.2         2   8.1e+02      36      41 ..       3       8 ..       1       9 [. 0.84
   2 ?    0.2   0.6       1.5   5.9e+02      36      41 ..      23      28 ..      20      29 .. 0.84
   3 !   20.0   0.2   9.7e-07   0.00039      12      40 ..      72     101 ..      66     103 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 2
                  Baculo_LEF5_C 36 yCskCg 41
                                    C kCg
  gi|119719537|ref|YP_920032.1|  3 FCPKCG 8 
                                   6****9 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.5
                  Baculo_LEF5_C 36 yCskCg 41
                                    Cs+Cg
  gi|119719537|ref|YP_920032.1| 23 RCSRCG 28
                                   6****9 PP

  == domain 3  score: 20.0 bits;  conditional E-value: 9.7e-07
                  Baculo_LEF5_C  12 qClHdfv.tiEiQnRagDEivsfvryCskC 40 
                                     C  d   + E Q+RagDE +     C kC
  gi|119719537|ref|YP_920032.1|  72 NCGNDKAyVYELQTRAGDEPATRFYICTKC 101
                                    5777777799***********99999**** PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.2   4.4e-05     0.018      12      40 ..       2      33 ..       1      34 [. 0.89
   2 ?    2.3   0.0      0.38   1.6e+02      28      35 ..      67      74 ..      62      77 .. 0.81
   3 ?    0.7   0.0       1.2     5e+02      29      36 ..      96     103 ..      87     107 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.4e-05
                                   -B-TTT-SB-..-S.SSS-EEEETTT--EE-C CS
                           C1_1 12 tfCkhCgefl..wg.kekqglkCswCkllvHk 40
                                    fC +Cg ++  +   +k  l+Cs C+++v k
  gi|119719537|ref|YP_920032.1|  2 EFCPKCGGLMvpSVvNGKKVLRCSRCGYIVEK 33
                                   69********99667*************9965 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.38
                                   EEEETTT- CS
                           C1_1 28 glkCswCk 35
                                    +kC++C+
  gi|119719537|ref|YP_920032.1| 67 SFKCENCG 74
                                   58999997 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 1.2
                                    EEETTT-- CS
                           C1_1  29 lkCswCkl 36 
                                    + C+ C+ 
  gi|119719537|ref|YP_920032.1|  96 YICTKCRK 103
                                    55666654 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.1     0.032        13      29      35 ..       4      11 ..       1      16 [. 0.75
   2 ?    5.3   0.0     0.054        22       7      17 ..      23      33 ..      21      49 .. 0.85
   3 !    8.0   4.2    0.0075       3.1       5      33 ..      67     102 ..      64     108 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.032
                    Zn-ribbon_8 29 CPeCgs.e 35
                                   CP+Cg+  
  gi|119719537|ref|YP_920032.1|  4 CPKCGGlM 11
                                   *****944 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.054
                    Zn-ribbon_8  7 rCeeCghefev 17
                                   rC +Cg   e+
  gi|119719537|ref|YP_920032.1| 23 RCSRCGYIVEK 33
                                   9*****99996 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0075
                    Zn-ribbon_8   5 eYrCeeCghefe...vlqsis.dap...lta.CPeCg 33 
                                     ++Ce+Cg++     +lq+ + d+p       C +C 
  gi|119719537|ref|YP_920032.1|  67 SFKCENCGNDKAyvyELQTRAgDEPatrF-YiCTKCR 102
                                    69******999899999998888884433.3588885 PP

>> DUF2846  Protein of unknown function (DUF2846)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0     1e-05    0.0042      27      58 ..      15      46 ..       8      64 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1e-05
                        DUF2846 27 fvngkkigelankeYfvaevepGeykistere 58
                                    vngkk+ + ++++Y+v++ +pG+y++s + e
  gi|119719537|ref|YP_920032.1| 15 VVNGKKVLRCSRCGYIVEKSNPGTYRVSHRIE 46
                                   49*************************98864 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   3.3   0.00054      0.22       3      31 ..       4      33 ..       2      36 .. 0.81
   2 !    8.7   2.9    0.0029       1.2       1      25 [.      68     101 ..      68     104 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00054
                                   ETTTTCEEC..HEETSTTCEEESSSSBEEEE CS
                   TF_Zn_Ribbon  3 CPnCgstnl..veDpergelvCtdCGlVled 31
                                   CP+Cg+ ++  v++     l+C++CG+++e 
  gi|119719537|ref|YP_920032.1|  4 CPKCGGLMVpsVVN-GKKVLRCSRCGYIVEK 33
                                   ******65566777.77889*********96 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0029
                                    EEETTTTCEE.CHEE........TSTTCEEESSS CS
                   TF_Zn_Ribbon   1 ykCPnCgstn.lveD........pergelvCtdC 25 
                                    +kC nCg+++ +v++        p++  ++Ct+C
  gi|119719537|ref|YP_920032.1|  68 FKCENCGNDKaYVYElqtragdePATRFYICTKC 101
                                    79******998866655556667999999****9 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   2.4    0.0097         4      15      20 ..       3       8 ..       2       9 .. 0.73
   2 ?    6.6   0.1     0.016       6.5       1      10 [.      23      32 ..      19      36 .. 0.75
   3 ?    7.2   0.2      0.01       4.2       1       7 [.      69      75 ..      65      76 .. 0.79
   4 ?    3.1   0.1       0.2        81       2       6 ..      98     102 ..      93     109 .] 0.70

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0097
                  zinc_ribbon_2 15 FCpyCG 20
                                   FCp+CG
  gi|119719537|ref|YP_920032.1|  3 FCPKCG 8 
                                   777776 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.016
                  zinc_ribbon_2  1 fCpnCGaelq 10
                                   +C++CG+ ++
  gi|119719537|ref|YP_920032.1| 23 RCSRCGYIVE 32
                                   5888887666 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.01
                  zinc_ribbon_2  1 fCpnCGa 7 
                                   +C nCG+
  gi|119719537|ref|YP_920032.1| 69 KCENCGN 75
                                   6888886 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.2
                  zinc_ribbon_2   2 CpnCG 6  
                                    C++C 
  gi|119719537|ref|YP_920032.1|  98 CTKCR 102
                                    66665 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   1.0   3.2e-05     0.013       2      26 ..       4      28 ..       3      28 .. 0.98
   2 ?    1.9   0.0      0.36   1.5e+02      17      26 ..      65      74 ..      49      74 .. 0.65
   3 ?    1.7   0.1       0.4   1.6e+02      20      26 ..      96     102 ..      88     104 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.2e-05
                       zf-TFIIB  2 CPkCqdeleeserggveidyCpqCr 26
                                   CPkC+  +++s ++g ++ +C +C+
  gi|119719537|ref|YP_920032.1|  4 CPKCGGLMVPSVVNGKKVLRCSRCG 28
                                   ************************7 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.36
                       zf-TFIIB 17 veidyCpqCr 26
                                   v  ++C++C+
  gi|119719537|ref|YP_920032.1| 65 VVSFKCENCG 74
                                   67789****7 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.4
                       zf-TFIIB  20 dyCpqCr 26 
                                    + C++Cr
  gi|119719537|ref|YP_920032.1|  96 YICTKCR 102
                                    6788887 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.2      0.33   1.3e+02      22      26 ..       4       8 ..       3       9 .. 0.57
   2 ?    2.0   0.0      0.49     2e+02      17      27 ..      19      29 ..      15      29 .. 0.84
   3 !   12.2   0.2   0.00033      0.13       4      25 ..      69     101 ..      62     103 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.33
                 PhnA_Zn_Ribbon 22 CpeCa 26
                                   Cp+C+
  gi|119719537|ref|YP_920032.1|  4 CPKCG 8 
                                   55554 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.49
                 PhnA_Zn_Ribbon 17 gallvCpeCah 27
                                   + +l C+ C++
  gi|119719537|ref|YP_920032.1| 19 KKVLRCSRCGY 29
                                   67899****96 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 0.00033
                 PhnA_Zn_Ribbon   4 kCplCaSeytY...........edgallvCpeC 25 
                                    kC++C+ + +Y             +  ++C +C
  gi|119719537|ref|YP_920032.1|  69 KCENCGNDKAYvyelqtragdePATRFYICTKC 101
                                    9*****************999999999***999 PP

>> HalOD2  Halobacterial output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1       5.6   2.3e+03       5      38 ..       4       8 ..       2      12 .. 0.62
   2 !   11.2   0.0   0.00063      0.26      28      51 ..      18      41 ..      16      42 .. 0.91
   3 ?    3.8   0.0      0.13        54      32      39 ..      68      75 ..      60      80 .. 0.78
   4 ?    0.0   0.1         2   8.2e+02      34      40 ..      98     104 ..      93     107 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 5.6
                         HalOD2  5 CseCsldWttrhGdglGeGyrqLGayvWkCtrCG 38
                                   C+                             +CG
  gi|119719537|ref|YP_920032.1|  4 CP-----------------------------KCG 8 
                                   55.............................555 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00063
                         HalOD2 28 GayvWkCtrCGevqaaAdpShqrV 51
                                   G  v +C+rCG +    +p  +rV
  gi|119719537|ref|YP_920032.1| 18 GKKVLRCSRCGYIVEKSNPGTYRV 41
                                   67799*****************99 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.13
                         HalOD2 32 WkCtrCGe 39
                                   +kC +CG+
  gi|119719537|ref|YP_920032.1| 68 FKCENCGN 75
                                   68999996 PP

  == domain 4  score: 0.0 bits;  conditional E-value: 2
                         HalOD2  34 CtrCGev 40 
                                    Ct+C +v
  gi|119719537|ref|YP_920032.1|  98 CTKCRKV 104
                                    8888766 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.6      0.33   1.3e+02      80      86 .]       2       8 ..       1       8 [. 0.88
   2 !   14.2   0.3   0.00013     0.054      32      74 ..      16      76 ..      10      82 .. 0.84
   3 !    9.7   0.6    0.0035       1.4      38      75 ..      68     105 ..      50     108 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.33
                 zinc_ribbon_15 80 kyCpkCg 86
                                   ++CpkCg
  gi|119719537|ref|YP_920032.1|  2 EFCPKCG 8 
                                   8*****9 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 0.00013
                 zinc_ribbon_15 32 kkkkpylacskCkslleaskelgkeiekkesse..................kkeCknCgke 74
                                    + k++l cs+C++++e+s+  + +++++ +++                  + +C+nCg+ 
  gi|119719537|ref|YP_920032.1| 16 VNGKKVLRCSRCGYIVEKSNPGTYRVSHRIERTpkdvvtlvdvdvsvlpvvSFKCENCGND 76
                                   45589**************977777777766668899*************999*****985 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.0035
                 zinc_ribbon_15  38 lacskCkslleaskelgkeiekkessekkeCknCgkev 75 
                                    ++c++C++  +   el+++  ++ +++ ++C +C+k+ 
  gi|119719537|ref|YP_920032.1|  68 FKCENCGNDKAYVYELQTRAGDEPATRFYICTKCRKVY 105
                                    78*****99999998999999999999*******9875 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.4   0.00019     0.078      13      40 ..       2      33 ..       1      36 [. 0.77
   2 ?    5.8   1.7     0.034        14      14      37 ..      69     104 ..      60     109 .] 0.67

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00019
                            DZR 13 rfCseCgtklkavaa......edrCpsCgekvdp 40
                                   +fC++Cg  + +  +        rC++Cg+ v++
  gi|119719537|ref|YP_920032.1|  2 EFCPKCGGLMVP--SvvngkkVLRCSRCGYIVEK 33
                                   69****998542..224588899******99875 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.034
                            DZR  14 fCseCgtklkavaa............edrCpsCgek 37 
                                     C++Cg++   v +             + C +C + 
  gi|119719537|ref|YP_920032.1|  69 KCENCGNDKAYVYElqtragdepatrFYICTKCRKV 104
                                    588888884433334456677887778888888765 PP

>> Rpr2  RNAse P Rpr2/Rpp21/SNM1 subunit domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.5   0.00077      0.31      46      90 .]       2      74 ..       1      74 [. 0.80
   2 ?    2.5   0.0      0.44   1.8e+02      41      54 ..      91     104 ..      77     107 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00077
                                   TB-TTT--B--CTTTEEEEEE-SSS-E.....................................EEEEETTTT CS
                           Rpr2 46 tvCkkCgsvlipgvtcsvrvenkskkkkkkkkka............................dvlvvtClaCg 90
                                   ++C kCg +++p v    +v + s+     +k++                             v+ ++C +Cg
  gi|119719537|ref|YP_920032.1|  2 EFCPKCGGLMVPSVVNGKKVLRCSRCGYIVEKSNpgtyrvshriertpkdvvtlvdvdvsvlPVVSFKCENCG 74
                                   69***********999999977777666666666777777778888898899999998888866679*****7 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.44
                                    STCCCTB-TTT--B CS
                           Rpr2  41 psvkrtvCkkCgsv 54 
                                    p+ +  +C kC++v
  gi|119719537|ref|YP_920032.1|  91 PATRFYICTKCRKV 104
                                    55566788888877 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1      0.41   1.7e+02      28      32 ..       4       8 ..       3      12 .. 0.73
   2 ?    8.4   0.2    0.0049         2      23      33 ..      19      29 ..      14      31 .. 0.80
   3 ?    5.0   0.1     0.057        23      24      33 ..      66      75 ..      64      76 .. 0.81
   4 ?    4.6   0.6     0.076        31       5      13 ..      98     106 ..      96     106 .. 0.64

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.41
                  zinc_ribbon_4 28 CskCg 32
                                   C+kCg
  gi|119719537|ref|YP_920032.1|  4 CPKCG 8 
                                   77776 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0049
                  zinc_ribbon_4 23 gvkvrCskCgh 33
                                   ++ +rCs+Cg 
  gi|119719537|ref|YP_920032.1| 19 KKVLRCSRCGY 29
                                   4679*****97 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.057
                  zinc_ribbon_4 24 vkvrCskCgh 33
                                   v+ +C +Cg+
  gi|119719537|ref|YP_920032.1| 66 VSFKCENCGN 75
                                   5789999986 PP

  == domain 4  score: 4.6 bits;  conditional E-value: 0.076
                  zinc_ribbon_4   5 CpsCkakye 13 
                                    C +C ++y+
  gi|119719537|ref|YP_920032.1|  98 CTKCRKVYR 106
                                    666666664 PP

>> IBR  IBR domain, a half RING-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.2   0.00043      0.18      21      46 ..       4      29 ..       1      80 [. 0.54
   2 ?    0.3   3.1       2.1   8.6e+02      46      54 ..      95     103 ..      69     108 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00043
                            IBR 21 CprpdCeaiiekseg..cksvtCskCgf 46
                                   Cp  +C++++ +s    +k ++Cs+Cg+
  gi|119719537|ref|YP_920032.1|  4 CP--KCGGLMVPSVVngKKVLRCSRCGY 29
                                   55..566666444443233345555554 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 2.1
                            IBR  46 fefCfnCkk 54 
                                    f +C++C+k
  gi|119719537|ref|YP_920032.1|  95 FYICTKCRK 103
                                    334444444 PP

>> zf-MYND  MYND finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.4    0.0091       3.7       1      17 [.       4      28 ..       4      39 .. 0.79
   2 ?    8.4   0.5    0.0054       2.2       1      20 [.      70     105 ..      70     106 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0091
                                   -TTT--.........B-SCE-TTTS CS
                        zf-MYND  1 CavCgk........aealkkCagCk 17
                                   C +Cg          ++  +C++C 
  gi|119719537|ref|YP_920032.1|  4 CPKCGGlmvpsvvnGKKVLRCSRCG 28
                                   8999999999986444444*****6 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0054
                                    -TTT--...............B-SC..E-TTTS-SE CS
                        zf-MYND   1 CavCgk..............aealk..kCagCksvf 20 
                                    C++Cg+              ++a++   C++C++v+
  gi|119719537|ref|YP_920032.1|  70 CENCGNdkayvyelqtragdEPATRfyICTKCRKVY 105
                                    99***************9987777799*****9996 PP

>> FdhE  Protein involved in formate dehydrogenase formation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.7   0.00051      0.21     169     201 ..       2      28 ..       1      32 [. 0.84
   2 ?    5.3   0.5     0.039        16     206     242 ..      65     103 ..      61     108 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00051
                                    SS-TTT---EEEEEEE-------EEEEEETTT- CS
                           FdhE 169 glCPvCgsaPvasvvriggeaeglRylhCslCe 201
                                    ++CP Cg+  v svv+      g + l Cs C 
  gi|119719537|ref|YP_920032.1|   2 EFCPKCGGLMVPSVVN------GKKVLRCSRCG 28 
                                    68*************4......44588899985 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.039
                                    --TTS-TTT---SS-EEE..------C-EEEEEETTTTE CS
                           FdhE 206 vvRvkCsnCeetkelayl..sledekaavkAesCdeChs 242
                                    vv  kC nC+++k   y   +  +++ a +   C +C++
  gi|119719537|ref|YP_920032.1|  65 VVSFKCENCGNDKAYVYElqTRAGDEPATRFYICTKCRK 103
                                    6788******99988775113344456779999999975 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   1.0    0.0021      0.86      31      55 ..       4      30 ..       2      33 .. 0.89
   2 ?    7.7   0.2    0.0081       3.3      30      46 ..      23      38 ..      22      47 .. 0.78
   3 ?    6.1   2.2     0.025        10      28      55 ..      67     104 ..      64     106 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0021
                 OrfB_Zn_ribbon 31 CseCgsknke..alsgrtfkCpnCgfe 55
                                   C++Cg  + +   + +++++C++Cg+ 
  gi|119719537|ref|YP_920032.1|  4 CPKCGGLMVPsvVNGKKVLRCSRCGYI 30
                                   *******99988888999******985 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0081
                 OrfB_Zn_ribbon 30 tCseCgsknkealsgrt 46
                                   +Cs+Cg+++++  ++ t
  gi|119719537|ref|YP_920032.1| 23 RCSRCGYIVEK-SNPGT 38
                                   6*********9.54444 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.025
                 OrfB_Zn_ribbon  28 SktCseCgsknke..........alsgrtfkCpnCgfe 55 
                                    S +C +Cg  + +          ++++r + C++C  +
  gi|119719537|ref|YP_920032.1|  67 SFKCENCGNDKAYvyelqtragdEPATRFYICTKCRKV 104
                                    67899999999888989999998899999999999865 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.2    0.0018      0.75      17      24 ..       2       9 ..       1      11 [. 0.64
   2 ?    6.0   0.1      0.02         8       4      14 ..      23      33 ..      21      36 .. 0.79
   3 ?    4.0   0.4     0.083        34      19      24 ..      70      75 ..      68      78 .. 0.61
   4 ?   -0.7   0.2       2.6   1.1e+03      18      22 ..      97     101 ..      96     104 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0018
                    zf-ribbon_3 17 nvCpyCGt 24
                                    +Cp+CG+
  gi|119719537|ref|YP_920032.1|  2 EFCPKCGG 9 
                                   46777775 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.02
                    zf-ribbon_3  4 rCPnCGaplss 14
                                   rC++CG ++++
  gi|119719537|ref|YP_920032.1| 23 RCSRCGYIVEK 33
                                   8*****87676 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.083
                    zf-ribbon_3 19 CpyCGt 24
                                   C +CG 
  gi|119719537|ref|YP_920032.1| 70 CENCGN 75
                                   666664 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 2.6
                    zf-ribbon_3  18 vCpyC 22 
                                    +C++C
  gi|119719537|ref|YP_920032.1|  97 ICTKC 101
                                    69999 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00074       0.3       5      15 ..       3      13 ..       1      15 [. 0.86
   2 ?    4.7   0.2     0.058        24       6      10 ..      24      28 ..      21      31 .. 0.72
   3 ?    1.9   0.2      0.44   1.8e+02      24      29 ..      70      75 ..      67      76 .. 0.86
   4 ?   -2.3   0.1       9.1   3.7e+03      24      28 ..      98     102 ..      97     105 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00074
                  zf-NADH-PPase  5 FCgrCGaptep 15
                                   FC++CG+ ++p
  gi|119719537|ref|YP_920032.1|  3 FCPKCGGLMVP 13
                                   ******98877 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.058
                  zf-NADH-PPase  6 CgrCG 10
                                   C+rCG
  gi|119719537|ref|YP_920032.1| 24 CSRCG 28
                                   77776 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.44
                  zf-NADH-PPase 24 CpaCgl 29
                                   C++Cg+
  gi|119719537|ref|YP_920032.1| 70 CENCGN 75
                                   ****97 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 9.1
                  zf-NADH-PPase  24 CpaCg 28 
                                    C  C+
  gi|119719537|ref|YP_920032.1|  98 CTKCR 102
                                    99997 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1      0.37   1.5e+02      25      30 ..       3       8 ..       1      11 [. 0.86
   2 ?    4.6   0.1      0.09        37      19      30 ..      17      28 ..      14      31 .. 0.83
   3 ?    4.9   0.1     0.076        31      24      30 ..      68      74 ..      58      74 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.37
                                   E-TTT- CS
                      zf-RING_7 25 tCpeCG 30
                                   +Cp CG
  gi|119719537|ref|YP_920032.1|  3 FCPKCG 8 
                                   8****9 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.09
                                   CSTB-EE-TTT- CS
                      zf-RING_7 19 agdevvtCpeCG 30
                                   +g++v +C  CG
  gi|119719537|ref|YP_920032.1| 17 NGKKVLRCSRCG 28
                                   5678*******9 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.076
                                   EE-TTT- CS
                      zf-RING_7 24 vtCpeCG 30
                                   ++C++CG
  gi|119719537|ref|YP_920032.1| 68 FKCENCG 74
                                   68****9 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   4.8    0.0061       2.5      88     154 ..       2      75 ..       1     103 [. 0.72

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0061
                        TackOD1  88 evCpkCkSid....ieeqelihhftCgnvgpeee...flkegkle.CpkCktkLrhiGvDYdr.plevykCnsCks 154
                                    e CpkC+       ++ ++++ + +Cg++ ++++   +++++++e  pk   +L  ++vD +  p  ++kC++C++
  gi|119719537|ref|YP_920032.1|   2 EFCPKCGGLMvpsvVNGKKVLRCSRCGYIVEKSNpgtYRVSHRIErTPKDVVTL--VDVDVSVlPVVSFKCENCGN 75 
                                    78****986511226789***********9887433378888776245554555..45554432777888999975 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.4   0.00051      0.21       5      22 ..      20      37 ..      16      39 .. 0.87
   2 ?    8.0   0.4    0.0054       2.2       7      14 ..      68      75 ..      65      76 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00051
                                   -EEE-TTT--EEEECC-- CS
                Desulfoferrod_N  5 evYkCevCGniVeVleaG 22
                                    v +C  CG iVe  ++G
  gi|119719537|ref|YP_920032.1| 20 KVLRCSRCGYIVEKSNPG 37
                                   689**********88888 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0054
                                   EE-TTT-- CS
                Desulfoferrod_N  7 YkCevCGn 14
                                   +kCe CGn
  gi|119719537|ref|YP_920032.1| 68 FKCENCGN 75
                                   9******9 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   7.1      0.13        54       6      41 ..       4      38 ..       1     108 [. 0.75

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.13
                Lar_restr_allev  6 CPfCggravlersqrvvaeigqcvyCadCga....stpwf 41
                                   CP Cgg  v    ++++     +  C  Cg+    s+p +
  gi|119719537|ref|YP_920032.1|  4 CPKCGGLMVPSVVNGKK-----VLRCSRCGYivekSNPGT 38
                                   99999988877777666.....678888887655533333 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1      0.41   1.7e+02      89     103 ..       4      19 ..       1      22 [. 0.69
   2 ?    9.4   2.5    0.0025         1      69      99 ..      20      80 ..      14     108 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.41
                                    -TTTSSS-E.EEEESS CS
                           HypA  89 CpkCgsadv.eivsGe 103
                                    CpkCg+  v ++v+G+
  gi|119719537|ref|YP_920032.1|   4 CPKCGGLMVpSVVNGK 19 
                                    *****98662456666 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0025
                                   -EEEETTTS-EEECHHH.HH.............................S-TTTSSS-EEE CS
                           HypA 69 vkvrCreCgkefeleek.al.............................rCpkCgsadvei 99
                                    ++rC++Cg+ +e+++  ++                             +C++Cg+ +  +
  gi|119719537|ref|YP_920032.1| 20 KVLRCSRCGYIVEKSNPgTYrvshriertpkdvvtlvdvdvsvlpvvsfKCENCGNDKAYV 80
                                   5688999999999776333356788999999999999999999999999999999876554 PP

>> Mut7-C  Mut7-C RNAse domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   3.0    0.0012       0.5      61     133 ..      37     105 ..       9     107 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0012
                         Mut7-C  61 gvlltsrdveeqlreviarlglklslkpels.rCvaCngeleevekeevkervpekvyeeadeftrCekCrkvf 133
                                    g +  s+++e+  ++v+  +++++s+ p++s +C +C +  + v + +      +   e a++f+ C+kCrkv+
  gi|119719537|ref|YP_920032.1|  37 GTYRVSHRIERTPKDVVTLVDVDVSVLPVVSfKCENCGNDKAYVYELQ-----TRAGDEPATRFYICTKCRKVY 105
                                    467778888999999999999999988887658999987544444433.....3556677888**********9 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1     0.089        36       4       9 ..       3       8 ..       1      14 [. 0.81
   2 ?    3.7   0.1      0.12        48       4      10 ..      23      29 ..      21      35 .. 0.78
   3 ?    3.2   0.3      0.17        68       2       9 ..      67      74 ..      66      76 .. 0.87
   4 ?    4.2   0.4     0.081        33       3      11 ..      96     104 ..      94     108 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.089
                         zf_UBZ 4 lCerCg 9
                                  +C++Cg
  gi|119719537|ref|YP_920032.1| 3 FCPKCG 8
                                  8****9 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.12
                         zf_UBZ  4 lCerCgk 10
                                    C+rCg 
  gi|119719537|ref|YP_920032.1| 23 RCSRCGY 29
                                   5****95 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.17
                         zf_UBZ  2 tylCerCg 9 
                                   ++ Ce Cg
  gi|119719537|ref|YP_920032.1| 67 SFKCENCG 74
                                   699****9 PP

  == domain 4  score: 4.2 bits;  conditional E-value: 0.081
                         zf_UBZ   3 ylCerCgke 11 
                                    y+C +C k 
  gi|119719537|ref|YP_920032.1|  96 YICTKCRKV 104
                                    99****996 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.5       1.7     7e+02      17      21 ..       4       8 ..       3       9 .. 0.86
   2 ?    3.6   0.0      0.24     1e+02      10      22 ..      17      29 ..      14      30 .. 0.88
   3 ?    4.8   0.0       0.1        41      15      23 ..      68      78 ..      40      81 .. 0.73
   4 ?    3.4   0.4      0.29   1.2e+02      17      24 ..      98     105 ..      91     106 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 1.7
                      zf-H2C2_2 17 CplCd 21
                                   Cp+C+
  gi|119719537|ref|YP_920032.1|  4 CPKCG 8 
                                   9***6 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.24
                      zf-H2C2_2 10 tgekpyeCplCdk 22
                                    g+k + C+ C++
  gi|119719537|ref|YP_920032.1| 17 NGKKVLRCSRCGY 29
                                   58999******98 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.1
                      zf-H2C2_2 15 yeCplCd..ka 23
                                   ++C+ C+  ka
  gi|119719537|ref|YP_920032.1| 68 FKCENCGndKA 78
                                   8*****96555 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.29
                      zf-H2C2_2  17 CplCdkaF 24 
                                    C +C+k++
  gi|119719537|ref|YP_920032.1|  98 CTKCRKVY 105
                                    ******87 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.5     0.043        17      22      28 ..       2       8 ..       1       9 [. 0.92
   2 ?    1.3   0.1      0.76   3.1e+02      24      30 ..      24      30 ..      19      33 .. 0.78
   3 ?    6.0   0.1     0.024       9.8       5      13 ..      69      77 ..      68      87 .. 0.87
   4 ?    2.8   0.5      0.25     1e+02       4      10 ..      96     102 ..      95     103 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.043
                  A2L_zn_ribbon 22 lvCieCg 28
                                   ++C++Cg
  gi|119719537|ref|YP_920032.1|  2 EFCPKCG 8 
                                   8*****9 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.76
                  A2L_zn_ribbon 24 CieCgas 30
                                   C  Cg++
  gi|119719537|ref|YP_920032.1| 24 CSRCGYI 30
                                   8889987 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.024
                  A2L_zn_ribbon  5 vCsvCggng 13
                                   +C++Cg+++
  gi|119719537|ref|YP_920032.1| 69 KCENCGNDK 77
                                   7******98 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.25
                  A2L_zn_ribbon   4 kvCsvCg 10 
                                    ++C++C+
  gi|119719537|ref|YP_920032.1|  96 YICTKCR 102
                                    6899998 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   3.3     0.022       9.1       9      25 ..      13      29 ..       3      31 .. 0.71
   2 ?    3.5   0.0      0.14        57      19      24 ..      69      74 ..      58      76 .. 0.80
   3 ?    3.5   0.8      0.14        59       1       8 [.      96     103 ..      96     106 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.022
                                   B----SSS----SSS-- CS
                 DNA_RNApol_7kD  9 evslkkgdpiRCkeCGh 25
                                   +  ++ + ++RC  CG+
  gi|119719537|ref|YP_920032.1| 13 PSVVNGKKVLRCSRCGY 29
                                   445677889*******8 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.14
                                   --SSS- CS
                 DNA_RNApol_7kD 19 RCkeCG 24
                                   +C +CG
  gi|119719537|ref|YP_920032.1| 69 KCENCG 74
                                   899999 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.14
                                    -B-SSS-- CS
                 DNA_RNApol_7kD   1 YiCgeCga 8  
                                    YiC +C +
  gi|119719537|ref|YP_920032.1|  96 YICTKCRK 103
                                    9*****86 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.4       0.2        81      41      55 ..      17      31 ..       3      58 .. 0.72
   2 ?    8.9   0.8    0.0037       1.5      21      55 ..      67     105 ..      59     108 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.2
                           Elf1 41 ekiaevsCkvCgesf 55
                                   +++ +++C+ Cg  +
  gi|119719537|ref|YP_920032.1| 17 NGKKVLRCSRCGYIV 31
                                   455689999999754 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0037
                           Elf1  21 kFdCpfCnheksvevkldkkek....iaevsCkvCgesf 55 
                                    +F+C +C+++k+   +l+++ +    +    C++C++ +
  gi|119719537|ref|YP_920032.1|  67 SFKCENCGNDKAYVYELQTRAGdepaTRFYICTKCRKVY 105
                                    7***********999999999877776677799998765 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.9     0.039        16      14      21 ..       1       8 [.       1       8 [. 0.91
   2 ?    6.0   0.1     0.031        13      16      23 ..      23      30 ..      21      32 .. 0.86
   3 ?   -0.2   0.1       2.7   1.1e+03      16      21 ..      69      74 ..      63      75 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.039
                        UPF0547 14 aqfCphCG 21
                                   ++fCp CG
  gi|119719537|ref|YP_920032.1|  1 MEFCPKCG 8 
                                   78*****9 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.031
                        UPF0547 16 fCphCGyv 23
                                   +C+ CGy+
  gi|119719537|ref|YP_920032.1| 23 RCSRCGYI 30
                                   7******6 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 2.7
                        UPF0547 16 fCphCG 21
                                   +C  CG
  gi|119719537|ref|YP_920032.1| 69 KCENCG 74
                                   799998 PP

>> zf-IS66  zinc-finger binding domain of transposase IS66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.1    0.0049         2       3      13 ..       3      13 ..       2      16 .. 0.86
   2 ?    2.4   0.5      0.54   2.2e+02       4      27 ..      24      49 ..      21      55 .. 0.64
   3 ?    1.9   0.0      0.74     3e+02       3       9 ..      69      75 ..      67      86 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0049
                        zf-IS66  3 tCpcCGgllkp 13
                                    Cp+CGgl++p
  gi|119719537|ref|YP_920032.1|  3 FCPKCGGLMVP 13
                                   6******9875 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.54
                        zf-IS66  4 CpcCGg.l.lkpigedrvreeldipP 27
                                   C+ CG     +  g+ rv+ +++  P
  gi|119719537|ref|YP_920032.1| 24 CSRCGYiVeKSNPGTYRVSHRIERTP 49
                                   77777654466666666666666655 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.74
                        zf-IS66  3 tCpcCGg 9 
                                   +C +CG 
  gi|119719537|ref|YP_920032.1| 69 KCENCGN 75
                                   5999997 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.3      0.11        45       4       9 ..       4       9 ..       4      12 .. 0.76
   2 ?    1.6   0.1      0.73     3e+02       3      11 ..      23      31 ..      22      34 .. 0.82
   3 ?    4.8   0.7     0.074        30       2       9 ..      68      75 ..      68      75 .. 0.87
   4 ?    4.3   0.1       0.1        42      20      26 .]      95     101 ..      92     101 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.11
                         zf-ACC 4 CpsCge 9
                                  Cp+Cg 
  gi|119719537|ref|YP_920032.1| 4 CPKCGG 9
                                  888886 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.73
                         zf-ACC  3 KCpsCgeml 11
                                   +C +Cg ++
  gi|119719537|ref|YP_920032.1| 23 RCSRCGYIV 31
                                   6****9766 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.074
                         zf-ACC  2 tKCpsCge 9 
                                   +KC+ Cg+
  gi|119719537|ref|YP_920032.1| 68 FKCENCGN 75
                                   5*****96 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.1
                         zf-ACC  20 lyVCPkC 26 
                                    +y+C+kC
  gi|119719537|ref|YP_920032.1|  95 FYICTKC 101
                                    89***** PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   3.6    0.0086       3.5       5      34 ..       4      30 ..       3      32 .. 0.84
   2 ?    1.2   0.1      0.75   3.1e+02       4       9 ..      69      74 ..      66      76 .. 0.79
   3 ?    3.8   0.3      0.12        48      28      35 ..      98     105 ..      97     106 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0086
                  zinc_ribbon_5  5 CpdCdtkFklvdsklKksgkkV.rCakCaev 34
                                   Cp+C+    +v s   ++gkkV rC +C+ +
  gi|119719537|ref|YP_920032.1|  4 CPKCGGL--MVPSV--VNGKKVlRCSRCGYI 30
                                   8888875..67888..9****99*****976 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.75
                  zinc_ribbon_5  4 rCpdCd 9 
                                   +C++C+
  gi|119719537|ref|YP_920032.1| 69 KCENCG 74
                                   699997 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.12
                  zinc_ribbon_5  28 CakCaevF 35 
                                    C kC++v+
  gi|119719537|ref|YP_920032.1|  98 CTKCRKVY 105
                                    9****997 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0      0.22        90      17      25 ..       2      10 ..       1      12 [. 0.83
   2 ?    7.0   0.1     0.011       4.3      15      27 ..      20      32 ..      18      35 .. 0.82
   3 ?    2.5   0.5      0.26   1.1e+02      18      24 ..      69      75 ..      68      77 .. 0.90
   4 ?   -0.8   0.1       2.8   1.2e+03      19      23 ..      98     102 ..      92     106 .. 0.67

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.22
                                   EE-TTT--E CS
                           RecR 17 rhCsrCgnl 25
                                    +C++Cg l
  gi|119719537|ref|YP_920032.1|  2 EFCPKCGGL 10
                                   59****976 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.011
                                   H-EE-TTT--EES CS
                           RecR 15 kvrhCsrCgnlte 27
                                   kv +CsrCg + e
  gi|119719537|ref|YP_920032.1| 20 KVLRCSRCGYIVE 32
                                   7889*****9976 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.26
                                   E-TTT-- CS
                           RecR 18 hCsrCgn 24
                                    C++Cgn
  gi|119719537|ref|YP_920032.1| 69 KCENCGN 75
                                   5*****9 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 2.8
                                    -TTT- CS
                           RecR  19 CsrCg 23 
                                    C +C+
  gi|119719537|ref|YP_920032.1|  98 CTKCR 102
                                    55665 PP

>> RNHCP  RNHCP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.4     0.027        11      45      77 ..       6      32 ..       2      36 .. 0.74
   2 ?    6.2   0.1     0.024       9.8       3      24 ..      21      42 ..      19      46 .. 0.79
   3 ?    3.8   0.2      0.13        54       3      12 ..      67      76 ..      65      93 .. 0.73
   4 ?    0.9   0.2       1.1   4.6e+02      67      76 ..      96     105 ..      82     109 .] 0.72

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.027
                          RNHCP 45 eCkglmepiavevkkkkewvivhrCekCgelkk 77
                                   +C+glm p  v+ k       v rC++Cg + +
  gi|119719537|ref|YP_920032.1|  6 KCGGLMVPSVVNGK------KVLRCSRCGYIVE 32
                                   68999988877633......3679999997755 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.024
                          RNHCP  3 sftCeeCgkeveklaagsakrn 24
                                    ++C++Cg  vek+++g+ +  
  gi|119719537|ref|YP_920032.1| 21 VLRCSRCGYIVEKSNPGTYRVS 42
                                   5789999999999999985555 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.13
                          RNHCP  3 sftCeeCgke 12
                                   sf+Ce+Cg++
  gi|119719537|ref|YP_920032.1| 67 SFKCENCGND 76
                                   5777777764 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 1.1
                          RNHCP  67 hrCekCgelk 76 
                                    + C+kC+++ 
  gi|119719537|ref|YP_920032.1|  96 YICTKCRKVY 105
                                    5677776654 PP

>> PHD  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.3     0.052        21       1      22 [.       3      28 ..       3      31 .. 0.84
   2 ?    1.5   0.2      0.71   2.9e+02      43      50 ..      67      74 ..      56      76 .. 0.67
   3 ?    3.1   2.9      0.21        86      34      50 ..      85     102 ..      65     104 .. 0.55

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.052
                                   SBTTTTS....TTSTTSCEEEETTTS CS
                            PHD  1 rCavCkk....ksdeeeelvqCdgCk 22
                                   +C  C++    +  ++++++ C +C+
  gi|119719537|ref|YP_920032.1|  3 FCPKCGGlmvpSVVNGKKVLRCSRCG 28
                                   699999998877778999*******7 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.71
                                   TBSSTTTH CS
                            PHD 43 ewlCekCk 50
                                   ++ Ce+C 
  gi|119719537|ref|YP_920032.1| 67 SFKCENCG 74
                                   56777774 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.21
                                    HSHHSHHSS.TBSSTTTH CS
                            PHD  34 leseekpeg.ewlCekCk 50 
                                     +  ++p +  ++C+kC+
  gi|119719537|ref|YP_920032.1|  85 TRAGDEPATrFYICTKCR 102
                                    333333333589999997 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1     0.062        25      27      33 ..       3       9 ..       1      12 [. 0.83
   2 ?    3.6   0.2      0.16        64      13      18 ..      23      28 ..      20      31 .. 0.80
   3 ?    1.3   0.3      0.82   3.3e+02      14      18 ..      70      74 ..      69      77 .. 0.57
   4 ?    2.9   0.1      0.26   1.1e+02      11      21 ..      95     105 ..      86     107 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.062
                        DUF35_N 27 vCphCgs 33
                                   +Cp+Cg+
  gi|119719537|ref|YP_920032.1|  3 FCPKCGG 9 
                                   8999986 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.16
                        DUF35_N 13 rCpdCG 18
                                   rC+ CG
  gi|119719537|ref|YP_920032.1| 23 RCSRCG 28
                                   999999 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.82
                        DUF35_N 14 CpdCG 18
                                   C +CG
  gi|119719537|ref|YP_920032.1| 70 CENCG 74
                                   55555 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.26
                        DUF35_N  11 gqrCpdCGtvq 21 
                                    +  C++C +v+
  gi|119719537|ref|YP_920032.1|  95 FYICTKCRKVY 105
                                    55699998886 PP

>> zf-ISL3  zinc-finger of transposase IS204/IS1001/IS1096/IS1165
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.2    0.0043       1.7       4      20 ..       3      21 ..       2      23 .. 0.82
   2 ?    2.4   0.9      0.65   2.6e+02       4      13 ..      23      32 ..      20      55 .. 0.70
   3 ?    3.6   2.5      0.26   1.1e+02       4      16 ..      69      81 ..      67     105 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0043
                        zf-ISL3  4 rCPnCgsktv..vkhgkke 20
                                    CP+Cg  +v  v++gkk 
  gi|119719537|ref|YP_920032.1|  3 FCPKCGGLMVpsVVNGKKV 21
                                   6*******5555****985 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.65
                        zf-ISL3  4 rCPnCgsktv 13
                                   rC +Cg  + 
  gi|119719537|ref|YP_920032.1| 23 RCSRCGYIVE 32
                                   899**97655 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.26
                        zf-ISL3  4 rCPnCgsktvvkh 16
                                   +C nCg+ ++++ 
  gi|119719537|ref|YP_920032.1| 69 KCENCGNDKAYVY 81
                                   7******999875 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.7      0.86   3.5e+02      17      21 ..       4       8 ..       3       9 .. 0.82
   2 ?    6.2   0.2     0.022       8.8       2       8 ..      23      29 ..      23      33 .. 0.86
   3 ?    7.3   0.5    0.0095       3.9       1      10 [.      68      77 ..      68      81 .. 0.82
   4 ?    2.8   0.4      0.24        97       1      12 [.      96     107 ..      96     109 .] 0.81

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.86
                   Rubredoxin_2 17 CpsCg 21
                                   Cp Cg
  gi|119719537|ref|YP_920032.1|  4 CPKCG 8 
                                   99997 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.022
                   Rubredoxin_2  2 vCsqCGf 8 
                                   +Cs+CG+
  gi|119719537|ref|YP_920032.1| 23 RCSRCGY 29
                                   8*****9 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0095
                   Rubredoxin_2  1 YvCsqCGfes 10
                                   + C++CG++ 
  gi|119719537|ref|YP_920032.1| 68 FKCENCGNDK 77
                                   89*****976 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.24
                   Rubredoxin_2   1 YvCsqCGfesak 12 
                                    Y+C +C  +++ 
  gi|119719537|ref|YP_920032.1|  96 YICTKCRKVYRE 107
                                    99****887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       708  (0.0394891); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); expected 17.9 (0.001)
Passed Fwd filter:                        62  (0.00345808); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              44  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 725.76
//
Query:       gi|119719538|ref|YP_920033.1|  [L=187]
Description: cytidylate kinase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.2e-23   81.6   2.2    7.7e-21   75.0   2.2    2.1  1  Cytidylate_kin2  Cytidylate kinase-like family
    3.4e-17   63.1   0.1    6.7e-17   62.2   0.1    1.5  1  AAA_17           AAA domain
    2.9e-16   60.2   0.1    3.9e-16   59.8   0.1    1.3  1  AAA_18           AAA domain
    5.1e-12   46.0   4.0      3e-05   23.9   0.1    2.1  2  Cytidylate_kin   Cytidylate kinase
    7.2e-07   29.4   0.0    1.8e-06   28.1   0.0    1.7  2  ADK              Adenylate kinase
    1.7e-06   28.3   0.3    0.00015   21.9   0.3    2.2  1  AAA_33           AAA domain
    1.3e-05   25.3   1.5    3.4e-05   24.0   1.5    1.7  1  SKI              Shikimate kinase
    0.00018   21.8   0.1    0.00047   20.4   0.0    1.6  2  AAA_28           AAA domain
    0.00064   20.1   0.0     0.0012   19.3   0.0    1.5  1  AAA              ATPase family associated with various cellul
     0.0044   16.7   1.3        1.5    8.5   0.0    3.2  4  Thymidylate_kin  Thymidylate kinase
     0.0047   16.9   0.0     0.0089   16.0   0.0    1.6  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.005   17.1   0.0     0.0075   16.6   0.0    1.5  1  AAA_22           AAA domain
     0.0058   15.9   0.4      0.044   13.0   0.4    2.1  1  Zeta_toxin       Zeta toxin
     0.0059   17.0   0.0     0.0082   16.5   0.0    1.3  1  AAA_16           AAA ATPase domain
     0.0062   15.6   0.2       0.98    8.4   0.0    2.1  2  T2SSE            Type II/IV secretion system protein
  ------ inclusion threshold ------
      0.025   14.3   0.2      0.089   12.5   0.1    1.8  1  AAA_30           AAA domain
      0.029   14.1   0.7       0.46   10.2   0.0    2.1  2  PRK              Phosphoribulokinase / Uridine kinase family
      0.035   14.0   0.0      0.059   13.3   0.0    1.4  1  NACHT            NACHT domain
      0.038   13.7   0.3        1.9    8.1   0.0    2.3  2  CoaE             Dephospho-CoA kinase
      0.069   13.0   0.0       0.11   12.4   0.0    1.4  1  NTPase_1         NTPase
      0.075   12.2   0.0       0.12   11.6   0.0    1.5  1  NB-ARC           NB-ARC domain
      0.087   13.1   0.0       0.16   12.2   0.0    1.4  1  Hydin_ADK        Hydin Adenylate kinase-like domain
      0.089   12.5   0.0       0.21   11.3   0.0    1.6  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
       0.11   12.2   0.0       0.28   10.9   0.0    1.7  1  ATP_bind_1       Conserved hypothetical ATP binding protein
       0.12   12.8   0.0       0.17   12.4   0.0    1.5  1  ABC_tran         ABC transporter
       0.17   11.6   0.0       0.23   11.2   0.0    1.2  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase


Domain annotation for each model (and alignments):
>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.0   2.2   1.1e-23   7.7e-21       1     177 [.       7     159 ..       7     160 .. 0.94

  Alignments for each domain:
  == domain 1  score: 75.0 bits;  conditional E-value: 1.1e-23
                Cytidylate_kin2   1 iITIsreyGsgGetigeaLAekLglpfydr.eiieevakelglseeeveevdersrlssflskllaarvagdtldekldd 79 
                                    ++++s++ Gsg++t ++ +Ae+++l++++   +++e+ak+lg++   ++++ e+                    +e++d 
  gi|119719538|ref|YP_920033.1|   7 VVAVSGTPGSGKTTYARFIAERYNLRYVSSgSLFREMAKKLGVDLIRLHSMAEE--------------------NEDIDR 66 
                                    799***************************9*****************999881....................445555 PP

                Cytidylate_kin2  80 elfeaqervirelaaeesvVivGRgadliLkdrpnvlrvfltapledrvkrvaereglseeearekiketDkrrakyykk 159
                                    +    ++r+i+e+ ++ +vVi G  a  +Lkd+   ++v ++aple+r++r+a+re++  e+a e+ik ++k + ++ ++
  gi|119719538|ref|YP_920033.1|  67 A---VDSRAIEEAKKG-NVVIEGHLAVWLLKDIA-DVKVIFDAPLEVRARRIAQRESIPLEKALEEIKIREKSNYERARR 141
                                    5...6799*****877.***************99.9******************************************** PP

                Cytidylate_kin2 160 ytgqdwgdaenYdlvlnt 177
                                    y++ d+ d +  dlv+nt
  gi|119719538|ref|YP_920033.1| 142 YYNLDIRDYTVADLVVNT 159
                                    *****************8 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.2   0.1   9.7e-20   6.7e-17       2     125 ..      12     118 ..      11     129 .. 0.75

  Alignments for each domain:
  == domain 1  score: 62.2 bits;  conditional E-value: 9.7e-20
                                    E-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSH.HHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEEEEE-S CS
                         AAA_17   2 GgPGsGKgtqceklvekygfthlsaGdllreeakrgglakar.demrklpleekkelqkeaaekiaeeakkkgvlvdghp 80 
                                    G PGsGK+t+++ ++e+y++ ++s G+l+re+ak+ g +  r + m     ee++++++ +  +  eeakk++v+++gh 
  gi|119719538|ref|YP_920033.1|  12 GTPGSGKTTYARFIAERYNLRYVSSGSLFREMAKKLGVDLIRlHSM----AEENEDIDRAVDSRAIEEAKKGNVVIEGHL 87 
                                    99***********************************944331334....455666777777777788899********9 PP

                                    EEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHHTTS CS
                         AAA_17  81 rikeqagfldglpkevleelkpdaiilleadpeeilerrlkdrtr 125
                                     +            + l+++  d+ ++++a+ e +++rr+ +r++
  gi|119719538|ref|YP_920033.1|  88 AV------------WLLKDI-ADVKVIFDAPLE-VRARRIAQRES 118
                                    86............555666.466667777776.66666666665 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.8   0.1   5.6e-19   3.9e-16       1     121 [.       8     124 ..       8     147 .. 0.89

  Alignments for each domain:
  == domain 1  score: 59.8 bits;  conditional E-value: 5.6e-19
                         AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....gvnlrdvakenglllevdpealdeskrldedkldklldaleenssaleegk 75 
                                    ++++GtpG+GKtt a+ +++r ++     g   r++ak+ g  l + + + +e++ +d+ ++ +++++ ++        +
  gi|119719538|ref|YP_920033.1|   8 VAVSGTPGSGKTTYARFIAERYNLryvssGSLFREMAKKLGVDLIRLHSMAEENEDIDRAVDSRAIEEAKK--------G 79 
                                    689******************87799999999999999999999999999999999999999999998888........8 PP

                         AAA_18  76 nlvidghlaeleseaakdikkvvLtaspeelleRlekRgyeeakik 121
                                    n+vi+ghla ++  +  d k v+ +a+ e++++R+++R+  + +++
  gi|119719538|ref|YP_920033.1|  80 NVVIEGHLAVWLLKDIADVK-VIFDAPLEVRARRIAQRESIPLEKA 124
                                    99******************.*****************98766654 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.1   4.3e-08     3e-05       1      37 [.       8      44 ..       8      60 .. 0.90
   2 !   23.4   1.2   6.1e-08   4.2e-05      90     185 ..      56     148 ..      49     176 .. 0.73

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 4.3e-08
                                   EEEE-STTSSHHHHHHHHHHHHT-EEEEHHHHHHHHH CS
                 Cytidylate_kin  1 iaiDGPagsGKssvaralaeklglkyldtgalYRala 37
                                   +a+ G  gsGK + ar +ae+ +l+y+++g+l+R +a
  gi|119719538|ref|YP_920033.1|  8 VAVSGTPGSGKTTYARFIAERYNLRYVSSGSLFREMA 44
                                   7999******************************998 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 6.1e-08
                                    HHHTTSHHHHHHHHHHHHTT-BSSBEEEEESSIIIIISTT.-SEEEEEE--HHHHHHHHHHHHHHTT----HHHHHHHHH CS
                 Cytidylate_kin  90 SavaaipavRailvkklrelvkkarvvveGRDigtvvfpd.aelKifldAsveeRakRRlkqlkakgtsvsleellaeik 168
                                    S+   ++++ +++ ++  e +kk++vv+eG  ++  +++d a++K+  dA  e+Ra RR++q+++   +++lee+  +i+
  gi|119719538|ref|YP_920033.1|  56 SMAEENEDIDRAVDSRAIEEAKKGNVVIEGH-LAVWLLKDiADVKVIFDAPLEVRA-RRIAQRESIPLEKALEEI--KIR 131
                                    55566778888899999999**********7.666666666**************8.788896766666666665..566 PP

                                    HHHHHHHCTSSS-S--- CS
                 Cytidylate_kin 169 eRDklDkerevgpLkla 185
                                    e+ +  ++r++++L + 
  gi|119719538|ref|YP_920033.1| 132 EKSNYERARRYYNLDIR 148
                                    66777788888888654 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   2.7e-09   1.8e-06       1      38 [.      10      47 ..      10      87 .. 0.82
   2 ?   -1.5   0.0       3.4   2.4e+03     107     133 ..     100     133 ..      82     160 .. 0.68

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 2.7e-09
                                   EEESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHHCT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            ADK  1 llGaPgaGKGtqaeklvkkyglahlstGdllRaevksg 38
                                   + G+Pg+GK t a+ ++++y+l  +s+G l+R+  k+ 
  gi|119719538|ref|YP_920033.1| 10 VSGTPGSGKTTYARFIAERYNLRYVSSGSLFREMAKKL 47
                                   579*****************************998765 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.4
                                    EEEE--HHHHHHHHHT.......GSHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxx.......xxxxxxxxxxx RF
                            ADK 107 leldvpeevlveRltg.......DneetvkkRle 133
                                    + +d+p ev  +R+++          e++k R +
  gi|119719538|ref|YP_920033.1| 100 VIFDAPLEVRARRIAQresipleKALEEIKIREK 133
                                    4566666677777766555555544455555544 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.3   2.2e-07   0.00015       1     121 [.       7     119 ..       7     139 .. 0.71

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 2.2e-07
                         AAA_33   1 lvllvGlpGsGKstlaerllkklgavllssdtlrrrlfg...tdqqsktdytrvldrlyqilnelarkalsagrnvilda 77 
                                    +v + G pGsGK+t+a+ ++++     +ss +l+r +++    d  ++   ++ ++++ + +  +a +  ++++nv++  
  gi|119719538|ref|YP_920033.1|   7 VVAVSGTPGSGKTTYARFIAERYNLRYVSSGSLFREMAKklgVDLIRLHSMAEENEDIDRAVDSRAIE-EAKKGNVVIEG 85 
                                    78899*****************99***********999954433335555555666677777666644.44444455433 PP

                         AAA_33  78 tnlsrrerarflklarrlgvpvrivvvetdeetlkeRlakRaan 121
                                               ++l++  + ++  v+++++ e+ ++R+a+R+  
  gi|119719538|ref|YP_920033.1|  86 --------HLAVWLLK--DIADVKVIFDAPLEVRARRIAQRESI 119
                                    ........33455555..55566688888888888888888865 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   1.5     5e-08   3.4e-05       1     136 [.      14     147 ..      14     170 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 5e-08
                                    TTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHTS-HHHH.....HHHHHHHHHHHHHHHHHHHHCCCSSEEEEE-TTGGGS CS
                            SKI   1 mGaGKstvGkllAkklglefiDlDeliekrtgksiaei.....feeegeegFrelEsevlkelleeeglViatGGGavls 75 
                                    +G+GK+t ++ +A++++l+++ + +l+ + ++k   ++     ++ee e+ +r+ +s++++e  +  ++Vi         
  gi|119719538|ref|YP_920033.1|  14 PGSGKTTYARFIAERYNLRYVSSGSLFREMAKKLGVDLirlhsMAEENEDIDRAVDSRAIEEAKKG-NVVIEG------- 85 
                                    69***********************99888876544440222256889999***********9888.777766....... PP

                                    HHHHHHHH.HHSEEEEEE--HHHHHHHHHHTTSSGGGCSCHHHHHHHHHHH.HHHHHHCCSSC CS
                            SKI  76 eenrellk.ekgiviyLdvsleellerlkadkeRPllqekskeeelleela.ereplyeeaad 136
                                    + + +llk    + +  d++le+ ++r++++++ Pl ++ ++  + +e+   er + y +++ 
  gi|119719538|ref|YP_920033.1|  86 HLAVWLLKdIADVKVIFDAPLEVRARRIAQRESIPLEKALEE-IKIREKSNyERARRYYNLDI 147
                                    44555555433444666****************888888887.77787777799999988765 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   6.9e-07   0.00047       2      66 ..       8      75 ..       7      90 .. 0.72
   2 ?   -1.6   0.0         4   2.7e+03      51      67 ..     117     133 ..     101     159 .. 0.52

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 6.9e-07
                         AAA_28  2 ivitGgestGKTtlleaLaar.gypvv..pEaareileeklakgedalpwv.edllafaervleeqlee 66
                                   ++++G++++GKTt ++ +a+r + ++v     +re+ ++++ +  + l++  e+  ++ ++v   ++ee
  gi|119719538|ref|YP_920033.1|  8 VAVSGTPGSGKTTYARFIAERyNLRYVssGSLFREMAKKLGVDLIR-LHSMaEENEDIDRAVDSRAIEE 75
                                   899****************999777666689999999998855554.4444356666666655444443 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 4
                         AAA_28  51 dllafaervleeqleee 67 
                                    + + ++++++e +++e 
  gi|119719538|ref|YP_920033.1| 117 ESIPLEKALEEIKIREK 133
                                    33444444444444433 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.7e-06    0.0012       2      40 ..       9      45 ..       8      85 .. 0.64

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.7e-06
                                   EEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTT CS
                            AAA  2 llyGppGtGKTllakavakelgvefleisgsellskyvg 40
                                    ++G+pG GKT+ a+ +a+  + +++  s  +l+ ++ +
  gi|119719538|ref|YP_920033.1|  9 AVSGTPGSGKTTYARFIAERYNLRYV--SSGSLFREMAK 45
                                   589*****************766544..44444434333 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0021       1.5       3      22 ..      12      31 ..      10      47 .. 0.85
   2 ?    0.8   0.0      0.47   3.3e+02      87     108 ..      32      53 ..      30      64 .. 0.90
   3 ?   -0.3   0.0         1   7.2e+02     145     171 ..      58      83 ..      53      86 .. 0.83
   4 ?    4.6   0.4     0.033        23     119     160 ..      97     144 ..      64     169 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0021
                                   ESTTSSHHHHHHHHHHHHHH CS
                Thymidylate_kin  3 GlDGaGKttqaellkerlke 22
                                   G  G+GKtt a++++er++ 
  gi|119719538|ref|YP_920033.1| 12 GTPGSGKTTYARFIAERYNL 31
                                   778**************975 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.47
                                    S-HHHHHHHHHTTTTTTCHHHH CS
                Thymidylate_kin  87 RylfSslaYqgakegvdldlvl 108
                                    Ry+ S+ ++ ++++++++dl++
  gi|119719538|ref|YP_920033.1|  32 RYVSSGSLFREMAKKLGVDLIR 53 
                                    9****************99986 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1
                                    HHHHHHHHHHHHHHHHHHHHTTSTEEE CS
                Thymidylate_kin 145 eeeqldflrkvrerylelakederili 171
                                     ee++d+ r v  r+ e+ak +++++i
  gi|119719538|ref|YP_920033.1|  58 AEENEDIDRAVDSRAIEEAK-KGNVVI 83 
                                    6899999999********96.888776 PP

  == domain 4  score: 4.6 bits;  conditional E-value: 0.033
                                    SEEEEEESSHHHHHTSCCTTSS......TTTSHHHHHHHHHHHHHHHH CS
                Thymidylate_kin 119 dltflldvdpevalkRlakrde......ldeeeeeqldflrkvreryl 160
                                    d+ +++d + ev+++R+a+r++      l+e + ++++ +++ r++y+
  gi|119719538|ref|YP_920033.1|  97 DVKVIFDAPLEVRARRIAQRESiplekaLEEIKIREKSNYERARRYYN 144
                                    66667777*************987665555666666666666666554 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.3e-05    0.0089      19      86 ..       5      65 ..       1     103 [. 0.71

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.3e-05
                                   TEEEEEEESTTSSHHHHHHHHHHHTT------TTTTSEEEEEE..SSEEEEE-TT-SSTHHHHHCTTC CS
                           TsaE 19 gdvilLeGdLGaGKTtlvrglakalgveevkSPTFtlveeYelekeglyHfDlYRledeeeleelgle 86
                                   + v++ +G  G+GKTt +r +a+ ++++ v+S +  l++e +++    + +Dl Rl++ +e e+ +++
  gi|119719538|ref|YP_920033.1|  5 RLVVAVSGTPGSGKTTYARFIAERYNLRYVSSGS--LFREMAKK----LGVDLIRLHSMAE-ENEDID 65
                                   568999*********************99*9986..66777442....4588888865444.333333 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.1e-05    0.0075       6      64 ..       6      68 ..       2     131 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.1e-05
                         AAA_22  6 gilvvtGesGtGKTtllrrlleqldeeakaee....erpevvfvtlpsstsskdllrellral 64
                                    +++v G +G+GKTt +r ++e+++ ++        e ++ + v+l  + s ++  +++ ra+
  gi|119719538|ref|YP_920033.1|  6 LVVAVSGTPGSGKTTYARFIAERYNLRYVSSGslfrEMAKKLGVDLIRLHSMAEENEDIDRAV 68
                                   57899******************9766655556666444444555544444444444444444 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.4   6.4e-05     0.044      18     175 ..       7     164 ..       5     176 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.4e-05
                     Zeta_toxin  18 lillgGqpGAGKselaellkdelerqgnvvrldpDdlRelhPeyeeilkadpkkaseltqkdaselvekllqeaiengyn 97 
                                    ++ ++G pG+GK++ a+ ++++   + ++v  ++  +Re+  +  ++   + ++++e  ++  + +  ++++ea  ++ n
  gi|119719538|ref|YP_920033.1|   7 VVAVSGTPGSGKTTYARFIAERY--NLRYVS-SGSLFREMAKKL-GVDLIRLHSMAEENEDIDRAVDSRAIEEA--KKGN 80 
                                    67899***************998..777776.667777777553.32333555666665555566666677776..4567 PP

                     Zeta_toxin  98 iivegtlrsp..dvvkklaealkkaGYevevvvvavkk....elSrlgvldRyeeevaeg.Rlvpkeehdeafeglresv 170
                                    +++eg l+     ++++ ++ + +a  ev+++ +a+++    e + ++++ R++ + +++ R+ + ++ d ++  l  ++
  gi|119719538|ref|YP_920033.1|  81 VVIEGHLAVWllKDIAD-VKVIFDAPLEVRARRIAQREsiplEKALEEIKIREKSNYERArRYYNLDIRDYTVADLVVNT 159
                                    77777777631122222.23333557777777777766333355677777777777444447777777777777776666 PP

                     Zeta_toxin 171 ealee 175
                                      l++
  gi|119719538|ref|YP_920033.1| 160 YPLDV 164
                                    66555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.2e-05    0.0082      26      88 ..       7      58 ..       2     129 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.2e-05
                         AAA_16 26 lvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqllde 88
                                   +v +sG +G+GK++ +r ++++++ +  ++ +g   +          a+ l   +l+r    +
  gi|119719538|ref|YP_920033.1|  7 VVAVSGTPGSGKTTYARFIAERYNLR--YVSSGSLFRE--------MAKKL-GVDLIRLHSMA 58
                                   689******************99998..7888888887........55555.43444444333 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0    0.0014      0.98     129     148 ..       5      24 ..       1      32 [. 0.81
   2 ?    5.6   0.1      0.01       7.1      42     102 ..      75     137 ..      51     179 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0014
                          T2SSE 129 rglilvsGgTgsGKttllya 148
                                    r ++ vsG+ gsGKtt +  
  gi|119719538|ref|YP_920033.1|   5 RLVVAVSGTPGSGKTTYARF 24 
                                    67889***********8755 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.01
                          T2SSE  42 lekaalerlisriaalakldiseerplqdarlpekgvrl.rvvllPvvag.ealviRkksake 102
                                      k+    +  ++a+   +di++ +++ da l+ ++ r+ +   +P+ ++ e++ iR+ks+ e
  gi|119719538|ref|YP_920033.1|  75 EAKKGNVVIEGHLAVWLLKDIADVKVIFDAPLEVRARRIaQRESIPLEKAlEEIKIREKSNYE 137
                                    33344455667999999****************88877735678999999999****555543 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   0.00013     0.089      18      44 ..       5      31 ..       1      83 [. 0.66

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00013
                         AAA_30 18 drvavltGpAGtGKttalkalreawea 44
                                   ++v+++ G +G+GKtt  + ++e ++ 
  gi|119719538|ref|YP_920033.1|  5 RLVVAVSGTPGSGKTTYARFIAERYNL 31
                                   67999************9999998873 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00066      0.46       1      33 [.       7      39 ..       7      76 .. 0.72
   2 ?    2.9   0.3      0.11        77     113     152 ..      81     118 ..      53     163 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00066
                            PRK  1 vIgvagsSGaGkttvarklekifgrekvkaaei 33
                                   v++v+g  G+Gktt ar + ++ +   v + + 
  gi|119719538|ref|YP_920033.1|  7 VVAVSGTPGSGKTTYARFIAERYNLRYVSSGSL 39
                                   799******************999777775544 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.11
                            PRK 113 lviEGlhalydervaelldlkiyvdisidlelarklqRDi 152
                                    +viEG +a++   +++ +d+k+  d+  +++  r  qR  
  gi|119719538|ref|YP_920033.1|  81 VVIEGHLAVW--LLKDIADVKVIFDAPLEVRARRIAQRES 118
                                    7888877765..488999*******999999776666765 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   8.6e-05     0.059       2      25 ..       7      30 ..       6      43 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.6e-05
                                   CEEEEC-TTTCHHHHHHHHHHHHC CS
                          NACHT  2 lvilqGeaGsGKTtLlqklalawa 25
                                   +v++ G +GsGKTt ++ +a+   
  gi|119719538|ref|YP_920033.1|  7 VVAVSGTPGSGKTTYARFIAERYN 30
                                   799**************9998665 PP

>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0    0.0028       1.9       1      40 [.       6      46 ..       6      61 .. 0.81
   2 ?    3.6   0.2      0.07        48     119     156 ..      93     130 ..      70     147 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0028
                                   EEEEEEESTTSSHHHHHHHHHH.TT-EEEEHHHHHHHTTCC CS
                           CoaE  1 livgltGgiasGKstvanlfad.lgvpivDaDlvArqvvep 40
                                   l+v+++G  +sGK+t a+ +a+ +++  v    + r++ ++
  gi|119719538|ref|YP_920033.1|  6 LVVAVSGTPGSGKTTYARFIAErYNLRYVSSGSLFREMAKK 46
                                   589****************9998988888777777776655 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.07
                                    GGGSSEEEEEE--HHHHHHHHHHCCTSTHHHHHHHHHH CS
                           CoaE 119 ekliervlvvdvelelqveRlvardgvseeevkaiiaa 156
                                    ++++++ ++ d++le + +R+ +r+ +  e++ + i+ 
  gi|119719538|ref|YP_920033.1|  93 KDIADVKVIFDAPLEVRARRIAQRESIPLEKALEEIKI 130
                                    56677778889**************9988877666653 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00016      0.11       2      34 ..       8      39 ..       7      93 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00016
                                   EEEE--TTSSHHHHHHHHHHHH...GGGEEEEE CS
                       NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvkvgGfy 34
                                   v+++G pG+GKtT  + ++e  + + +  +G +
  gi|119719538|ref|YP_920033.1|  8 VAVSGTPGSGKTTYARFIAERYNLR-YVSSGSL 39
                                   789***************9998444.4445544 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00017      0.12      20      43 ..       5      28 ..       1      64 [. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00017
                                   SEEEEEEESTTSSHHHHHHHHCCS CS
                         NB-ARC 20 slvvalvGmgGvGKttlakqilnk 43
                                   +lvva++G +G+GKtt a+ i + 
  gi|119719538|ref|YP_920033.1|  5 RLVVAVSGTPGSGKTTYARFIAER 28
                                   589*************99988765 PP

>> Hydin_ADK  Hydin Adenylate kinase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00023      0.16       2      29 ..       8      35 ..       7      48 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00023
                      Hydin_ADK  2 iivhGaPlsGKtatavtLakkYeaAllt 29
                                   + v G+P sGKt+ a  +a +Y+  +++
  gi|119719538|ref|YP_920033.1|  8 VAVSGTPGSGKTTYARFIAERYNLRYVS 35
                                   7799******************988776 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0    0.0003      0.21      36      61 ..       8      33 ..       2      64 .. 0.77
   2 ?   -1.8   0.0       3.4   2.4e+03      98     134 ..     115     151 ..      76     159 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0003
                         RuvB_N 36 vllyGpPGlGkttlakiiakelgvkl 61
                                   v ++G PG Gktt a+ ia+  + + 
  gi|119719538|ref|YP_920033.1|  8 VAVSGTPGSGKTTYARFIAERYNLRY 33
                                   5689***************9876554 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.4
                         RuvB_N  98 raveevlysamedfrldivigkGpsarsikldlpkft 134
                                    +     l +a+e++++    +  ++ r  +ld+  +t
  gi|119719538|ref|YP_920033.1| 115 QRESIPLEKALEEIKIREKSNYERARRYYNLDIRDYT 151
                                    3333345556666666555555555566666666666 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00041      0.28       1      23 [.      10      32 ..      10      37 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00041
                     ATP_bind_1  1 vvGpaGsGKttfvgalseilelr 23
                                   v G++GsGKtt+ + ++e ++lr
  gi|119719538|ref|YP_920033.1| 10 VSGTPGSGKTTYARFIAERYNLR 32
                                   78**********99998887765 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00025      0.17      13      42 ..       7      39 ..       5     145 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00025
                                   EEEEEESTTSSHHHHHHHHTTSS--...SEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx...xxxxx RF
                       ABC_tran 13 kvaivGenGaGKStLlkllagllkp...teGei 42
                                   +va+ G  G+GK+t ++ +a+ ++     +G++
  gi|119719538|ref|YP_920033.1|  7 VVAVSGTPGSGKTTYARFIAERYNLryvSSGSL 39
                                   68999***************9998655555655 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00033      0.23       2      27 ..       9      33 ..       8      70 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00033
                Viral_helicase1  2 vvhGvpGcGKStlirkllrtsliltv 27
                                    v+G pG+GK+t  r +++  ++l+ 
  gi|119719538|ref|YP_920033.1|  9 AVSGTPGSGKTTYARFIAER-YNLRY 33
                                   599*********99988877.44443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       678  (0.0378158); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 1209.77
//
Query:       gi|119719539|ref|YP_920034.1|  [L=91]
Description: ribosomal protein L34e [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.9e-20   71.6   1.0    6.4e-20   71.3   1.0    1.1  1  Ribosomal_L34e  Ribosomal protein L34e
     0.0073   16.2   1.0       0.48   10.4   0.1    2.2  2  DUF4428         Domain of unknown function (DUF4428)
     0.0095   15.8   0.4       0.38   10.7   0.2    2.8  2  zf-C4_ClpX      ClpX C4-type zinc finger
  ------ inclusion threshold ------
      0.032   14.1   0.2        2.1    8.3   0.1    2.2  2  zf-C3HC4_3      Zinc finger, C3HC4 type (RING finger)
       0.14   11.7   1.6       0.36   10.4   0.1    2.2  2  Sgf11           Sgf11 (transcriptional regulation protein)


Domain annotation for each model (and alignments):
>> Ribosomal_L34e  Ribosomal protein L34e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.3   1.0   1.8e-23   6.4e-20      10      90 ..       3      80 ..       1      83 [. 0.89

  Alignments for each domain:
  == domain 1  score: 71.3 bits;  conditional E-value: 1.8e-23
                 Ribosomal_L34e 10 rlsYntrsnkvrvvktpggklvyqykkkkgkapkCgdckkkLqGipalrpkelsrlsktkktvsRaYGgslcakcvkeriv 90
                                   r++ ++rs+k+++v+tpgg+l ++ + kk+  pkC+ c++ +qG+p+l ++     ++  + ++R+YGg+lc++c+++ i+
  gi|119719539|ref|YP_920034.1|  3 RPALRSRSKKRKLVRTPGGRLALHVIDKKHDYPKCAICGRPIQGVPKLTSRLE---RRGVRMPTRPYGGYLCHECLRKGIK 80
                                   78899*****************************************8865433...345799***************9886 PP

>> DUF4428  Domain of unknown function (DUF4428)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.8   0.1    0.0075        27       1       9 [.      36      44 ..      36      52 .. 0.87
   2 !   10.4   0.1   0.00013      0.48      20      33 ..      68      81 ..      66      91 .] 0.71

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0075
                        DUF4428  1 iCaiCgkKi 9 
                                   +CaiCg  i
  gi|119719539|ref|YP_920034.1| 36 KCAICGRPI 44
                                   7*****876 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00013
                        DUF4428 20 gyvCkdClkKlsef 33
                                   gy+C++Cl K + +
  gi|119719539|ref|YP_920034.1| 68 GYLCHECLRKGIKL 81
                                   8********95433 PP

>> zf-C4_ClpX  ClpX C4-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.14     5e+02       8      22 ..       7      21 ..       7      27 .. 0.84
   2 !   10.7   0.2   0.00011      0.38       2      31 ..      36      76 ..      35      81 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.14
                     zf-C4_ClpX  8 ksesevkklIagpng 22
                                   +s+s+ +kl+  p+g
  gi|119719539|ref|YP_920034.1|  7 RSRSKKRKLVRTPGG 21
                                   689999****99976 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00011
                     zf-C4_ClpX  2 rCSFCgksesevkklIagpng...........vyICdeCve 31
                                   +C  Cg++ + v kl +  +             y C eC +
  gi|119719539|ref|YP_920034.1| 36 KCAICGRPIQGVPKLTSRLERrgvrmptrpygGYLCHECLR 76
                                   7**************99887788999999999999999976 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1   0.00057       2.1      36      49 ..      33      46 ..      25      47 .. 0.82
   2 ?    4.1   0.0     0.012        42      24      32 ..      69      77 ..      55      86 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00057
                                   TT-B-TTT--B--E CS
                     zf-C3HC4_3 36 rkkkCpiCrrpiek 49
                                     +kC iC rpi+ 
  gi|119719539|ref|YP_920034.1| 33 DYPKCAICGRPIQG 46
                                   5689********97 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.012
                                   EE-HHHHHH CS
                     zf-C3HC4_3 24 vlCeeCaek 32
                                   +lC+eC++k
  gi|119719539|ref|YP_920034.1| 69 YLCHECLRK 77
                                   47****987 PP

>> Sgf11  Sgf11 (transcriptional regulation protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1    0.0001      0.36       3      16 ..      33      46 ..      31      47 .. 0.85
   2 ?   -0.3   0.2      0.22   7.9e+02       7      13 ..      71      77 ..      69      77 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0001
                                   -EEE-TTTSSEEEG CS
                          Sgf11  3 eyvtCpnCgRqiaa 16
                                    y +C +CgR+i++
  gi|119719539|ref|YP_920034.1| 33 DYPKCAICGRPIQG 46
                                   5779********97 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.22
                                   -TTTSSE CS
                          Sgf11  7 CpnCgRq 13
                                   C  C R+
  gi|119719539|ref|YP_920034.1| 71 CHECLRK 77
                                   999*996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 608.87
//
Query:       gi|119719540|ref|YP_920035.1|  [L=421]
Description: aspartyl-tRNA synthetase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      6e-84  281.8   0.0    6.9e-84  281.6   0.0    1.0  1  tRNA-synt_2   tRNA synthetases class II (D, K and N)
    0.00059   19.4   0.1       0.02   14.3   0.0    2.9  4  tRNA-synt_2d  tRNA synthetases class II core domain (F)


Domain annotation for each model (and alignments):
>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  281.6   0.0   7.7e-88   6.9e-84       6     313 ..     108     415 ..     103     416 .. 0.94

  Alignments for each domain:
  == domain 1  score: 281.6 bits;  conditional E-value: 7.7e-88
                                    HHTHHHHCCSHHHHHHHHHHHHHHHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT.TEEE....-E-S-SHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxx RF
                    tRNA-synt_2   6 lknryldlrtekvskvlrlrstvtkavrkyleengfieietPiLsksdteegarlFkvksrekekeff....aLtqspql 81 
                                    +++ryl lr ++v++ + +rs +++ +r++++e+gf+e++tP ++k+  e+ga+lF v       ++f    +L+qspql
  gi|119719540|ref|YP_920035.1| 108 INYRYLALRLPRVRAAFLARSLIVNEIRSFFSERGFLEVHTPKIVKAGAEGGATLFEV-------DYFgvkaYLAQSPQL 180
                                    79********************************************************.......88889999******* PP

                                    HHHHHHHCTHSEEEEEEEEE--S--BTTB-S-CEEEEEEEEET-SCHH.HHHHHHHHHHHHHHHHHHCSCCCCCHTTTTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    tRNA-synt_2  82 ylellivagidrvfqiaraFRaEdsrtdrhlaEFtqieaemsfieeed.imqvleelikslvkevlessakdiefvirrn 160
                                    y+++l+ + + rvf+i++ FRaE+++t+rhl+E + +++em fi+  + +++vl +l+ +l +++ e+  + ++    + 
  gi|119719540|ref|YP_920035.1| 181 YKQMLMCG-VPRVFEIGPFFRAEKFSTTRHLNESWGLDVEMGFIKGMEdVLEVLSQLVVHLSHKLNERLGDALRGLGYNV 259
                                    ********.***********************************98877****************888877777666666 PP

                                    SEE-SSS-EEEEHHHHHHHHHTS......-SS--HHHHHHHHH...HS--SEEEEEEEBGGGSTTCBBBSTTSTTBBSEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    tRNA-synt_2 161 skdlkkpfkrltykeaieklnei......gkdldkaderalvk...keknepvfvtdfPaelkpFyarkeeddkkltesy 231
                                      ++ ++ + lty+ea+e ln+       g+d d + e+ l +   +++ + +f++d+P+e kpFy  k+++  k+  ++
  gi|119719540|ref|YP_920035.1| 260 I-KPVTSVRVLTYDEALEVLNSLgfnlkwGEDFDPKAEKSLGDyleEKGVQAYFIVDYPWESKPFYIMKKDE--KRGYAF 336
                                    5.55567*************99999999999********9976555999******************99888..89**** PP

                                    EEEETTEEEEEEEEB--SHHHHHHHHHHCCHHSSSGGGGHHHHHHHHCT--SEEEEEEEHHHHHHHHCT-SSGGGCSSS- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    tRNA-synt_2 232 DllingvElvgGslRiedpeeleeklkskgldeeaeekfswylealeyGapphgGlglGldRlvmlllgsesIrdviaFP 311
                                    Dl i+g+E+++G +R++++e+l+++l +kgl+   +e fs+ylea++yG+pphgG+glG+dRlvm++lg ++Ir++++FP
  gi|119719540|ref|YP_920035.1| 337 DLDIRGIEVASGGQREHRYEVLRQNLLEKGLN---PEDFSFYLEAFKYGMPPHGGFGLGIDRLVMTFLGVQNIRETVLFP 413
                                    ********************************...********************************************* PP

                                    XX CS
                                    xx RF
                    tRNA-synt_2 312 kl 313
                                    + 
  gi|119719540|ref|YP_920035.1| 414 RD 415
                                    96 PP

>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0     0.049   4.4e+02      22      43 ..     130     151 ..     120     156 .. 0.87
   2 ?   -3.7   0.0      0.75   6.7e+03     103     121 ..     191     209 ..     190     212 .. 0.79
   3 ?   -0.3   0.0      0.07   6.2e+02      13      39 ..     235     261 ..     227     280 .. 0.79
   4 !   14.3   0.0   2.3e-06      0.02     213     234 ..     388     409 ..     378     416 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.049
                                    HHHHHHHHHHCTTCEESSTTSE CS
                   tRNA-synt_2d  22 vleeikeiflelgfeevegpev 43 
                                    +++ei+++f e gf ev+ p++
  gi|119719540|ref|YP_920035.1| 130 IVNEIRSFFSERGFLEVHTPKI 151
                                    6799*************99988 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 0.75
                                    EEEEEEEEEBSST-SSSB- CS
                   tRNA-synt_2d 103 kiisigrvfRrdavDathl 121
                                    +++ ig  fR ++   t++
  gi|119719540|ref|YP_920035.1| 191 RVFEIGPFFRAEKFSTTRH 209
                                    78999999***99777654 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.07
                                    HSB-SHHHHHHHHHHHHHHCTTCEESS CS
                   tRNA-synt_2d  13 agklhpltkvleeikeiflelgfeeve 39 
                                    +  +h  +k+ e++ + ++ lg+++++
  gi|119719540|ref|YP_920035.1| 235 QLVVHLSHKLNERLGDALRGLGYNVIK 261
                                    56689999****************998 PP

  == domain 4  score: 14.3 bits;  conditional E-value: 2.3e-06
                                    EEEEEHHHHHHHHHT-SSGHHH CS
                   tRNA-synt_2d 213 afGlGveRlamlkygieDiRel 234
                                    +fGlG++Rl m  +g+++iRe 
  gi|119719540|ref|YP_920035.1| 388 GFGLGIDRLVMTFLGVQNIRET 409
                                    7*******************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2825.71
//
Query:       gi|119719541|ref|YP_920036.1|  [L=107]
Description: zinc finger SWIM domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.7e-06   25.1   0.2    1.6e-05   24.5   0.2    1.4  1  SWIM      SWIM zinc finger


Domain annotation for each model (and alignments):
>> SWIM  SWIM zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.2   8.9e-10   1.6e-05      12      39 ..      49      82 ..      36      83 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 8.9e-10
                           SWIM 12 lnkatCsCpefqk......ngipCkHalAvllal 39
                                   +   +CsCp+f +      ++  C H++Av la+
  gi|119719541|ref|YP_920036.1| 49 IPGVYCSCPDFLFhvhlerSRKKCYHMVAVELAI 82
                                   44789*************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 725.47
//
Query:       gi|119719542|ref|YP_920037.1|  [L=486]
Description: nucleic acid binding, OB-fold, tRNA/helicase-type [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-06   27.0   0.2    0.00044   20.2   0.1    2.6  2  tRNA_anti-codon  OB-fold nucleic acid binding domain
  ------ inclusion threshold ------
      0.023   14.3   0.0      0.048   13.3   0.0    1.4  1  DUF2240          Uncharacterized protein conserved in archaea
      0.091   13.0   0.2       0.46   10.7   0.0    2.2  3  tRNA_anti_2      OB-fold nucleic acid binding domain


Domain annotation for each model (and alignments):
>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.1   7.4e-08   0.00044       1      72 [.     101     176 ..     101     183 .. 0.92
   2 !    4.1   0.0    0.0078        47      20      43 ..     408     435 ..     402     454 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 7.4e-08
                                    EEEEEEEEEEE....EEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEE.EEEEECTTSSEEEEEEE CS
                tRNA_anti-codon   1 VtvaGrvtsis....drsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvt.Grvkrrpggelelkvee 72 
                                    V v+G v+s+     + +g+ ++ + l D++++i  v++ e+a +l   l++G+ v v+   vk+++++  el++++
  gi|119719542|ref|YP_920037.1| 101 VDVEGVVVSMYplsvTSGGKQYLRFALADREAIIWSVAWGEKALELSGMLTVGKKVLVKaVSVKKYREK-NELIIDK 176
                                    6699*******************************************************8889999887.8888876 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0078
                                    EEEEEETTEEEEEEEET....HHHHHHH CS
                tRNA_anti-codon  20 fidlrDgtgriqvvlfr....eeatkla 43 
                                    +++ +Dgt++i++v ++    ee+++l+
  gi|119719542|ref|YP_920037.1| 408 YLVFDDGTATIRAVSNSpqilEEVYELQ 435
                                    6789************955554444443 PP

>> DUF2240  Uncharacterized protein conserved in archaea (DUF2240)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0     8e-06     0.048      85     136 ..      24      76 ..      11      80 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8e-06
                        DUF2240  85 stferildaia.astgiekkevvaeinelqeelkglvdveaaalvvakkegvd 136
                                    ++ e +++ i+  +++++++++   i+e+ e+++g ++ eaa+ ++ak+ g++
  gi|119719542|ref|YP_920037.1|  24 PPEEILIEEILrHKRNLTREDLERLIREKIEDFGGVIKREAAVYLLAKEMGIN 76 
                                    44455555555146789**********************************97 PP

>> tRNA_anti_2  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   7.7e-05      0.46      18      84 ..      98     169 ..      86     177 .. 0.75
   2 ?   -3.7   0.0       2.4   1.4e+04      20      41 ..     288     311 ..     283     316 .. 0.73
   3 ?   -2.0   0.0       0.7   4.2e+03      38      56 ..     406     424 ..     402     440 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 7.7e-05
                    tRNA_anti_2  18 lkkavwvrGeisnlk..r.kasghvY..ftLkDekakisavifrsraaklkftledGmkVlvk.grlsvYepr 84 
                                    l+ +v v+G + ++   +  + g  Y  f L D +a i  v + ++a +l+  l+ G+kVlvk ++++ Y ++
  gi|119719542|ref|YP_920037.1|  98 LR-NVDVEGVVVSMYplSvTSGGKQYlrFALADREAIIWSVAWGEKALELSGMLTVGKKVLVKaVSVKKYREK 169
                                    53.48899999998766433344566337899************999999999*********72467766665 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 2.4
                    tRNA_anti_2  20 kavwvrGeisnlk..rkasghvYf 41 
                                    ++++++G +  ++  r++ g vY+
  gi|119719542|ref|YP_920037.1| 288 SRFYLEGYVLGFEifRREGGRVYL 311
                                    457888999888865555788886 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.7
                    tRNA_anti_2  38 hvYftLkDekakisavifr 56 
                                    +vY+   D +a+i+av  +
  gi|119719542|ref|YP_920037.1| 406 TVYLVFDDGTATIRAVSNS 424
                                    5899999999999999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (486 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 3088.23
//
Query:       gi|119719543|ref|YP_920038.1|  [L=195]
Description: hypothetical protein Tpen_0631 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 1217.70
//
Query:       gi|298205345|ref|YP_003717797.1|  [L=106]
Description: putative transcription elongation factor Elf1 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-17   63.9   0.2    1.2e-17   63.7   0.2    1.1  1  Elf1             Transcription elongation factor Elf1 like
    0.00053   20.3   0.4     0.0008   19.7   0.4    1.3  1  Lar_restr_allev  Restriction alleviation protein Lar
     0.0019   18.1   3.9       0.47   10.5   0.1    2.5  2  DUF1610          Domain of unknown function (DUF1610)
     0.0032   16.8   1.7       0.88    9.1   0.1    2.3  2  zf-ribbon_3      zinc-ribbon domain
     0.0054   16.4   0.2       0.01   15.5   0.2    1.5  1  zf-CSL           CSL zinc finger
      0.009   15.9   1.2      0.019   14.8   1.2    1.5  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
  ------ inclusion threshold ------
      0.035   13.8   2.1          3    7.7   0.2    2.3  2  zinc_ribbon_2    zinc-ribbon domain
      0.035   14.8   2.4        1.6    9.5   0.3    2.4  2  zf-ISL3          zinc-finger of transposase IS204/IS1001/IS10
      0.039   14.2   5.1      0.064   13.5   0.7    2.1  2  Ribosomal_L32p   Ribosomal L32p protein family
      0.049   13.8   1.8          5    7.4   0.2    2.3  2  zf-RING_7        C4-type zinc ribbon domain
      0.071   12.5   0.6       0.16   11.3   0.6    1.6  1  zf-TFIIB         Transcription factor zinc-finger
      0.077   12.9   1.0      0.088   12.7   1.0    1.1  1  FdhE             Protein involved in formate dehydrogenase fo
      0.083   12.9   0.5       0.33   11.0   0.0    2.0  2  Rubredoxin       Rubredoxin
      0.093   12.7   1.8        8.6    6.4   0.1    2.3  2  zinc_ribbon_4    zinc-ribbon domain
       0.11   12.7   3.6       0.37   11.0   0.7    2.2  2  zinc_ribbon_13   Nucleic-acid-binding protein containing Zn-r
       0.16   12.6   0.0        1.5    9.5   0.0    2.0  2  RbpA             RNA polymerase-binding protein
       0.16   11.4   0.5       0.39   10.2   0.5    1.7  1  Vps36-NZF-N      Vacuolar protein sorting 36 NZF-N zinc-finge
       0.18   11.8   0.1        9.5    6.3   0.0    2.2  2  CpXC             CpXC protein
       0.18   11.7   0.8       0.28   11.2   0.8    1.3  1  zf-DNL           DNL zinc finger
       0.24   11.4   3.0         13    5.8   4.0    2.2  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
       0.55   10.4   2.4        4.9    7.3   0.2    2.3  2  zf-Mss51         Zinc-finger of mitochondrial splicing suppre
       0.58    9.9   4.3        8.9    6.1   0.3    2.2  2  Rubredoxin_2     Rubredoxin metal binding domain
       0.61   10.2   3.8        2.9    8.0   0.5    2.3  2  zf-C3H2C3        Zinc-finger
       0.63    9.6   4.7        3.9    7.1   3.4    2.4  2  TF_Zn_Ribbon     TFIIB zinc-binding
       0.82    9.5   4.0        3.7    7.4   0.1    2.6  2  zf-HYPF          HypF finger


Domain annotation for each model (and alignments):
>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.7   0.2   1.7e-20   1.2e-17       1      77 [.       2      79 ..       2      80 .. 0.90

  Alignments for each domain:
  == domain 1  score: 63.7 bits;  conditional E-value: 1.7e-20
                              Elf1  1 gkRkkkakkrkkkkkkklptkFdCpfCnheksvevkldkkek..iaevsCkvCgesfetkvnalsepvDvYskwiDace 77
                                      g+R+kk+++r    k+klpt+F+Cp+C+++ +v v+++k  +    +vsC++Cg++++++  +  epvD +s+++D +e
  gi|298205345|ref|YP_003717797.1|  2 GRRRKKRARRVVVVKRKLPTVFQCPRCGAS-AVGVSVKKGGRenYVVVSCSNCGLKARYDYVEYLEPVDYFSRFLDDYE 79
                                      79999999999999999*************.8888888865444999*****************************997 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.4   1.1e-06    0.0008       5      36 ..      24      55 ..      20      70 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.1e-06
                   Lar_restr_allev  5 pCPfCggravlersqrvvaeigqcvyCadCga 36
                                       CP Cg  av +  +++  e   +v+C +Cg 
  gi|298205345|ref|YP_003717797.1| 24 QCPRCGASAVGVSVKKGGRENYVVVSCSNCGL 55
                                      6***************9999888********9 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.1   0.00066      0.47      15      23 ..      21      29 ..      17      30 .. 0.95
   2 !    8.2   0.7    0.0033       2.4      10      23 ..      41      54 ..      40      54 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00066
                           DUF1610 15 vvFpCPNCG 23
                                      +vF CP CG
  gi|298205345|ref|YP_003717797.1| 21 TVFQCPRCG 29
                                      89******9 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0033
                           DUF1610 10 prEravvFpCPNCG 23
                                      +rE++vv  C NCG
  gi|298205345|ref|YP_003717797.1| 41 GRENYVVVSCSNCG 54
                                      69***********9 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.1    0.0012      0.88       4      11 ..      24      31 ..      22      37 .. 0.78
   2 !    6.9   0.2    0.0058       4.1       3       9 ..      48      54 ..      47      57 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0012
                       zf-ribbon_3  4 rCPnCGap 11
                                      +CP+CGa 
  gi|298205345|ref|YP_003717797.1| 24 QCPRCGAS 31
                                      7*****96 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0058
                       zf-ribbon_3  3 vrCPnCG 9 
                                      v+C+nCG
  gi|298205345|ref|YP_003717797.1| 48 VSCSNCG 54
                                      5677777 PP

>> zf-CSL  CSL zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.2   1.4e-05      0.01      20      55 ..      24      58 ..      17      62 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.4e-05
                                      EE.TTSSE.EEEEHHHHHTT....--EEEETTSSEEEE CS
                            zf-CSL 20 pC.RCgde.FelteedleegaegaevvvqCssCSLwik 55
                                      +C RCg     ++ ++  ++     vvv Cs C L+++
  gi|298205345|ref|YP_003717797.1| 24 QCpRCGASaVGVSVKKGGRE---NYVVVSCSNCGLKAR 58
                                      8******9988888888887...69**********987 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   1.2   2.7e-05     0.019      13      60 ..       6      61 ..       3      64 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.7e-05
                    OrfB_Zn_ribbon 13 keyGikveevnpay.TSktCseCgsknke.......alsgrtfkCpnCgfeadrDv 60
                                      k++ + v++v++   T  +C++Cg+           + +  ++ C+nCg++a  D+
  gi|298205345|ref|YP_003717797.1|  6 KKRARRVVVVKRKLpTVFQCPRCGASAVGvsvkkggRENYVVVSCSNCGLKARYDY 61
                                      56677899999999999*******9988778878888889999*******998876 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.2    0.0042         3      16      21 ..      25      30 ..      21      31 .. 0.64
   2 ?    5.6   0.1     0.019        13      16      20 ..      50      54 ..      43      56 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0042
                     zinc_ribbon_2 16 CpyCGt 21
                                      Cp+CG+
  gi|298205345|ref|YP_003717797.1| 25 CPRCGA 30
                                      666665 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.019
                     zinc_ribbon_2 16 CpyCG 20
                                      C++CG
  gi|298205345|ref|YP_003717797.1| 50 CSNCG 54
                                      66666 PP

>> zf-ISL3  zinc-finger of transposase IS204/IS1001/IS1096/IS1165
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.3    0.0022       1.6       3      20 ..      23      43 ..      21      47 .. 0.77
   2 ?    5.1   0.1     0.053        38       3      15 ..      48      60 ..      46      64 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0022
                           zf-ISL3  3 hrCPnCgsktv...vkhgkke 20
                                       +CP+Cg+  v   vk+g +e
  gi|298205345|ref|YP_003717797.1| 23 FQCPRCGASAVgvsVKKGGRE 43
                                      68*******766678888766 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.053
                           zf-ISL3  3 hrCPnCgsktvvk 15
                                        C nCg k +++
  gi|298205345|ref|YP_003717797.1| 48 VSCSNCGLKARYD 60
                                      57*****999887 PP

>> Ribosomal_L32p  Ribosomal L32p protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.7   8.9e-05     0.064       9      34 ..       4      30 ..       2      41 .. 0.77
   2 ?    2.9   0.2      0.19   1.3e+02      26      33 ..      47      54 ..      41      60 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.9e-05
                                      HHHHHHHGGGT.------EEEETTTCC CS
                    Ribosomal_L32p  9 ksrrrkRrahw.klkapnlvecpncge 34
                                      + ++r Rr    k+k p++ +cp cg+
  gi|298205345|ref|YP_003717797.1|  4 RRKKRARRVVVvKRKLPTVFQCPRCGA 30
                                      345555555537**************8 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.19
                                      EEEETTTC CS
                    Ribosomal_L32p 26 lvecpncg 33
                                      +v c+ncg
  gi|298205345|ref|YP_003717797.1| 47 VVSCSNCG 54
                                      689****9 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.2     0.007         5      20      31 ..      18      30 ..       8      30 .. 0.78
   2 ?    5.8   0.1     0.022        15      22      30 ..      43      54 ..      35      54 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.007
                                      S.TB-EE-TTT-- CS
                         zf-RING_7 20 g.devvtCpeCGR 31
                                      +   v++Cp CG+
  gi|298205345|ref|YP_003717797.1| 18 KlPTVFQCPRCGA 30
                                      44569******96 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.022
                                      B...-EE-TTT- CS
                         zf-RING_7 22 e...vvtCpeCG 30
                                      e   vv C +CG
  gi|298205345|ref|YP_003717797.1| 43 EnyvVVSCSNCG 54
                                      24559******9 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.6   0.00022      0.16       1      26 [.      24      54 ..      24      54 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00022
                          zf-TFIIB  1 kCPkCqdele.....eserggveidyCpqCr 26
                                      +CP+C+++ +     +  r ++ +  C +C+
  gi|298205345|ref|YP_003717797.1| 24 QCPRCGASAVgvsvkKGGRENYVVVSCSNCG 54
                                      7******9997777777779999999**997 PP

>> FdhE  Protein involved in formate dehydrogenase formation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.0   0.00012     0.088     169     202 ..      23      55 ..       6      63 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00012
                                       SS-TTT---EEEEEEE-------EEEEEETTT-- CS
                              FdhE 169 glCPvCgsaPvasvvriggeaeglRylhCslCet 202
                                         CP Cg+ +v   v+ gg +e++  ++Cs C  
  gi|298205345|ref|YP_003717797.1|  23 FQCPRCGASAVGVSVKKGG-RENYVVVSCSNCGL 55 
                                       56*********99999999.99**********86 PP

>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00047      0.33      30      43 ..      18      31 ..      17      34 .. 0.88
   2 ?   -0.5   0.1       1.8   1.3e+03      37      43 ..      50      56 ..      48      61 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00047
                                      GS-TT-BBTTTB-B CS
                        Rubredoxin 30 dlPddWvCPdCgve 43
                                      +lP  ++CP Cg++
  gi|298205345|ref|YP_003717797.1| 18 KLPTVFQCPRCGAS 31
                                      69**********97 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.8
                                      BTTTB-B CS
                        Rubredoxin 37 CPdCgve 43
                                      C +Cg++
  gi|298205345|ref|YP_003717797.1| 50 CSNCGLK 56
                                      5566554 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1     0.012       8.6      26      33 ..      23      30 ..      17      33 .. 0.67
   2 ?    5.7   0.1     0.019        14      21      32 ..      43      54 ..      34      56 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.012
                     zinc_ribbon_4 26 vrCskCgh 33
                                       +C++Cg+
  gi|298205345|ref|YP_003717797.1| 23 FQCPRCGA 30
                                      45666654 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.019
                     zinc_ribbon_4 21 akgvkvrCskCg 32
                                      ++ v v Cs+Cg
  gi|298205345|ref|YP_003717797.1| 43 ENYVVVSCSNCG 54
                                      566789999998 PP

>> zinc_ribbon_13  Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1      0.27   1.9e+02       1      10 [.      24      33 ..      24      41 .. 0.82
   2 ?   11.0   0.7   0.00051      0.37      31      47 ..      43      59 ..      40      66 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.27
                    zinc_ribbon_13  1 kCpKCgntea 10
                                      +Cp+Cg + +
  gi|298205345|ref|YP_003717797.1| 24 QCPRCGASAV 33
                                      6****98765 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00051
                    zinc_ribbon_13 31 kkfitvsCknCgYtelY 47
                                      +++++vsC+nCg    Y
  gi|298205345|ref|YP_003717797.1| 43 ENYVVVSCSNCGLKARY 59
                                      78*********976655 PP

>> RbpA  RNA polymerase-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0    0.0021       1.5      36      61 ..       8      33 ..       3      45 .. 0.79
   2 ?    1.1   0.0      0.82   5.9e+02      51      65 ..      48      62 ..      42      69 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0021
                              RbpA 36 etevtfaaeaevPetwecrrcGkeak 61
                                      + + +   + ++P++++c+rcG++a 
  gi|298205345|ref|YP_003717797.1|  8 RARRVVVVKRKLPTVFQCPRCGASAV 33
                                      55566677889************996 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.82
                              RbpA 51 wecrrcGkeakldge 65
                                       +c +cG++a+ d  
  gi|298205345|ref|YP_003717797.1| 48 VSCSNCGLKARYDYV 62
                                      689*******98865 PP

>> Vps36-NZF-N  Vacuolar protein sorting 36 NZF-N zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.5   0.00054      0.39      30      49 ..      44      63 ..      16      65 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00054
                       Vps36-NZF-N 30 stplPpClaCGvkpdlelik 49
                                      +  +  C +CG k+ ++ ++
  gi|298205345|ref|YP_003717797.1| 44 NYVVVSCSNCGLKARYDYVE 63
                                      555678**********9885 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.013       9.5      37      46 ..      22      31 ..       7      35 .. 0.84
   2 ?    3.6   0.0      0.09        65      36      51 ..      46      61 ..      41      74 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.013
                              CpXC 37 eatCpkCgat 46
                                       ++Cp+Cga+
  gi|298205345|ref|YP_003717797.1| 22 VFQCPRCGAS 31
                                      689****987 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.09
                              CpXC 36 featCpkCgataklea 51
                                        + C +Cg +a++++
  gi|298205345|ref|YP_003717797.1| 46 VVVSCSNCGLKARYDY 61
                                      5678999998888776 PP

>> zf-DNL  DNL zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.8   0.00039      0.28       3      35 ..      22      54 ..      20      57 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00039
                            zf-DNL  3 tftCkaCetrsskeiskkaYekGvVivqCpgCk 35
                                      +f+C  C+        kk+ ++  V+v+C++C 
  gi|298205345|ref|YP_003717797.1| 22 VFQCPRCGASAVGVSVKKGGRENYVVVSCSNCG 54
                                      79**********9999****************6 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   4.0     0.018        13      16      28 ..      20      33 ..       8      53 .. 0.69
   2 ?    3.2   0.1      0.12        89      20      30 ..      48      59 ..      38      64 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.018
                     Zn_Tnp_IS1595 16 pngfvCPhCgsr.k 28
                                      p+ f CP+Cg +  
  gi|298205345|ref|YP_003717797.1| 20 PTVFQCPRCGASaV 33
                                      45588999997644 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.12
                     Zn_Tnp_IS1595 20 v.CPhCgsrkay 30
                                      v C +Cg +  y
  gi|298205345|ref|YP_003717797.1| 48 VsCSNCGLKARY 59
                                      34****987555 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.2    0.0069       4.9      14      25 ..      20      31 ..       6      38 .. 0.84
   2 ?    3.2   0.1      0.13        96      12      24 ..      43      55 ..      34      66 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0069
                          zf-Mss51 14 hvdfeCpdCGip 25
                                      +  f+Cp+CG +
  gi|298205345|ref|YP_003717797.1| 20 PTVFQCPRCGAS 31
                                      5679******76 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.13
                          zf-Mss51 12 pkhvdfeCpdCGi 24
                                      ++ v + C +CG+
  gi|298205345|ref|YP_003717797.1| 43 ENYVVVSCSNCGL 55
                                      5667889*****8 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.3     0.012       8.9      16      22 ..      24      30 ..      23      33 .. 0.59
   2 ?    5.2   0.4     0.025        18       3       9 ..      50      56 ..      49      58 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.012
                      Rubredoxin_2 16 rCpsCgs 22
                                      +Cp Cg+
  gi|298205345|ref|YP_003717797.1| 24 QCPRCGA 30
                                      5666664 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.025
                      Rubredoxin_2  3 CsqCGfe 9 
                                      Cs+CG +
  gi|298205345|ref|YP_003717797.1| 50 CSNCGLK 56
                                      *****76 PP

>> zf-C3H2C3  Zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.2      0.12        84      30      35 .]      24      29 ..      14      29 .. 0.80
   2 ?    8.0   0.5    0.0041       2.9       1      15 [.      50      64 ..      50      65 .. 0.95

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.12
                         zf-C3H2C3 30 vCPkCk 35
                                      +CP C+
  gi|298205345|ref|YP_003717797.1| 24 QCPRCG 29
                                      9****6 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0041
                         zf-C3H2C3  1 CdnCglkLdypfvay 15
                                      C nCglk  y +v y
  gi|298205345|ref|YP_003717797.1| 50 CSNCGLKARYDYVEY 64
                                      9***********998 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   3.4    0.0055       3.9       1      33 [.      23      61 ..      23      65 .. 0.71
   2 ?   -3.4   0.0       9.9   7.1e+03      11      18 ..      74      81 ..      72      82 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0055
                                      EEETTTTCEEC...HEETSTTCEE...ESSSSBEEEECC CS
                      TF_Zn_Ribbon  1 ykCPnCgstnl...veDpergelv...CtdCGlVledns 33
                                      ++CP Cg + +   v    r ++v   C++CGl   +++
  gi|298205345|ref|YP_003717797.1| 23 FQCPRCGASAVgvsVKKGGRENYVvvsCSNCGLKARYDY 61
                                      689999998777886666666664444999999866665 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 9.9
                                      CHEETSTT CS
                      TF_Zn_Ribbon 11 lveDperg 18
                                      ++ D+e g
  gi|298205345|ref|YP_003717797.1| 74 FLDDYEAG 81
                                      68899987 PP

>> zf-HYPF  HypF finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.2      0.12        84      24      29 ..      25      30 ..      21      32 .. 0.82
   2 ?    7.4   0.1    0.0052       3.7      18      28 ..      44      54 ..      40      59 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.12
                                      -TTTS- CS
                           zf-HYPF 24 CtnCGP 29
                                      C++CG 
  gi|298205345|ref|YP_003717797.1| 25 CPRCGA 30
                                      999995 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0052
                                      T-TT---TTTS CS
                           zf-HYPF 18 haqfisCtnCG 28
                                      ++  +sC nCG
  gi|298205345|ref|YP_003717797.1| 44 NYVVVSCSNCG 54
                                      67889*****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 794.81
//
Query:       gi|119719544|ref|YP_920039.1|  [L=255]
Description: geranylgeranylglyceryl phosphate synthase-like protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.9e-58  196.6   0.1    4.7e-58  196.3   0.1    1.0  1  PcrB            PcrB family
    3.9e-09   36.3   0.2    4.1e-08   33.0   0.0    2.0  2  His_biosynth    Histidine biosynthesis protein
    1.1e-06   28.1   0.9     0.0078   15.6   0.1    2.2  2  ThiG            Thiazole biosynthesis protein ThiG
     0.0001   21.3   0.7    0.00053   18.9   0.2    2.0  2  Trp_syntA       Tryptophan synthase alpha chain
    0.00012   21.3   2.3      0.021   14.0   0.2    2.3  2  NanE            Putative N-acetylmannosamine-6-phosphate epim
     0.0041   16.5   0.9       0.02   14.3   0.1    2.1  2  G3P_antiterm    Glycerol-3-phosphate responsive antiterminato
     0.0093   15.2   0.3     0.0093   15.2   0.3    1.6  2  DHO_dh          Dihydroorotate dehydrogenase
  ------ inclusion threshold ------
      0.024   13.6   0.3       0.37    9.8   0.1    2.0  2  IMPDH           IMP dehydrogenase / GMP reductase domain
      0.028   14.5   0.0      0.066   13.3   0.0    1.6  1  DpaA_N          Dipicolinate synthase subunit A N-terminal do
      0.036   13.4   0.2       0.14   11.5   0.0    1.9  2  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
      0.052   14.1   0.3       0.18   12.4   0.3    1.9  1  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
      0.066   12.6   0.1       0.56    9.6   0.0    2.0  2  BtpA            BtpA family
      0.076   12.3   0.4       0.17   11.2   0.1    1.8  2  TMP-TENI        Thiamine monophosphate synthase
       0.12   12.7   0.1       0.63   10.3   0.0    2.0  2  PucR            Purine catabolism regulatory protein-like fam
       0.17   12.3   0.0       0.44   10.9   0.0    1.7  1  HTH_Tnp_1       Transposase
       0.18   11.5   1.1         20    4.8   0.3    2.6  3  MoCF_biosynth   Probable molybdopterin binding domain


Domain annotation for each model (and alignments):
>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  196.3   0.1   4.2e-61   4.7e-58       6     216 ..      15     235 ..      10     245 .. 0.90

  Alignments for each domain:
  == domain 1  score: 196.3 bits;  conditional E-value: 4.2e-61
                                    TS...EEEEE-TTSS-CHHHHHHH...HCTT-SEEEEECSTCHHH...HHHHHHHHHHCTSSS-EEEEESSGGG--TTSS CS
                           PcrB   6 er...hltklDPeeenpdEiveiv...iesgtDavmigGsqsvtl...dntvrllkkvsriklPivlepsnvegvvryaD 76 
                                    e+   h+t++DPe+++p+ +++i+   +e gt a+m+gGs++v +   d++v ++k+   +++P++l+p+ +++++r+aD
  gi|119719544|ref|YP_920039.1|  15 EHgaiHMTLIDPEKTTPEVAARIArevAEAGTSAIMVGGSIGVSEamtDEVVLAIKRS--TEVPVILFPGSPTALSRHAD 92 
                                    33477*************9887766669*************66542227888888877..9******************* PP

                                    EEEEEEETTBSSTTTTTHHHHHHHHHHHHHHHCTEEEEEEEEEBTTTSHHHHHTTB-.B-TTHHHHHHHHHHHHHHTT-S CS
                           PcrB  77 alFvmsllnsanadWivgahalglkkvkklieseeilaegYlvvePdskvaavteak.vdlnkediaayallaakllglr 155
                                    a+++ s+lns+n+++i+ga+++g+  vk++   +e+l+ gY++v  +++v+ v+ ++ ++  k++++a+++laa+++g++
  gi|119719544|ref|YP_920039.1|  93 AVWFLSVLNSQNPYFITGAQMQGAPIVKRYG--LEVLPLGYIIVGEGGAVSIVSYTRpLPFAKPEVVAAYALAAEYMGFQ 170
                                    *******************************..*********************************************** PP

                                    EEEEE-.TTSSS-HHHHHHHHHHHSSSEEEEESS--SHHHHHHHHCC.SSEEEE-CHHHHHH..H CS
                           PcrB 156 liYlEa.sGaledveevialkkklekarlivGGGirsaEkAkevvea.ADvivvGnvveekd..e 216
                                    ++YlE  sG    + ++++++k +++  livGGGirs+E Ake ++a AD+iv+G++vee++   
  gi|119719544|ref|YP_920039.1| 171 FVYLEGgSGGEPVPPKIVKMVKGVTTLPLIVGGGIRSPEVAKELAKAgADIIVTGTIVEESEniR 235
                                    ******999888779*********************************************98443 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1      0.17   1.9e+02      43      87 ..      18      60 ..       5      73 .. 0.71
   2 !   33.0   0.0   3.7e-11   4.1e-08      40     111 ..     163     234 ..     136     245 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.17
                                   -SEEEEEEHHHHCTTHHHHHHHHHHHHHH-SSEEEEESSSSSHHH CS
                   His_biosynth 43 adelhvvDldaakegreanldlveeiaeevfipvqvGGGIrsled 87
                                   a  +h+  +d  k+  e+   + +e+ae+ +  ++vGG I   e+
  gi|119719544|ref|YP_920039.1| 18 A--IHMTLIDPEKTTPEVAARIAREVAEAGTSAIMVGGSIGVSEA 60
                                   3..455555556777888888889999999999999997765554 PP

  == domain 2  score: 33.0 bits;  conditional E-value: 3.7e-11
                                    HHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THH CS
                   His_biosynth  40 eegadelhvvDldaakegreanldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavknpel 111
                                    ++++  + +v l++ + g+++  ++v+ +   +++p+ vGGGIrs e ++el +agad ++ gt + ++ ++
  gi|119719544|ref|YP_920039.1| 163 AAEYMGFQFVYLEGGSGGEPVPPKIVKMVKGVTTLPLIVGGGIRSPEVAKELAKAGADIIVTGTIVEESENI 234
                                    55666788999***********************************************99999986555443 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.1   0.00013      0.15     136     183 ..      37      82 ..      30      95 .. 0.82
   2 !   15.6   0.1     7e-06    0.0078     156     226 ..     177     247 ..     147     254 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00013
                                    HHHHHHHTT-SEBEEBSSSTTS----S-HHHHHHHHHH-SS-BEEES- CS
                           ThiG 136 larrleevGcaavmPlaapiGsglGllnkealkiiieeakvPvivDAG 183
                                    +ar + e+G++a+m ++  iG ++ ++++ +l  i ++++vPvi+  G
  gi|119719544|ref|YP_920039.1|  37 IAREVAEAGTSAIM-VGGSIGVSEAMTDEVVL-AIKRSTEVPVILFPG 82 
                                    799***********.5667**99988776655.678899*****8665 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 7e-06
                                    TS----S-HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSHHHHHHHHHHHHHH CS
                           ThiG 156 GsglGllnkealkiiieeakvPvivDAGigspsdaaqamelGadavllntavaeakdpvamArafklavea 226
                                    Gsg   + ++ +k++   +++P+iv  Gi+sp+ a +  + Gad ++  t v e++++ +    +  a++ 
  gi|119719544|ref|YP_920039.1| 177 GSGGEPVPPKIVKMVKGVTTLPLIVGGGIRSPEVAKELAKAGADIIVTGTIVEESENIRETIGRIVRATRE 247
                                    6777777888899999999***********************************99987665555555555 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.21   2.4e+02      33     200 ..      41      76 ..       6      82 .. 0.44
   2 !   18.9   0.2   4.7e-07   0.00053     188     235 ..     186     233 ..     181     252 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.21
                                    HHHCT-SSEEEE---S--TTS-HHHHHHHHCCCCTT--HHHHHHHHHHHHHHCSSS-EEEEE-CHHHCCC-HHHHCHHHH CS
                      Trp_syntA  33 lekagadviElGlpfsdPladGPvIqaanlraLakgvtlekvlelveevrkkevevPivlltylnlvlsygeerflaelk 112
                                    +++ag++                                                                         
  gi|119719544|ref|YP_920039.1|  41 VAEAGTS------------------------------------------------------------------------- 47 
                                    3333333......................................................................... PP

                                    HCTEEEEEETTSBCCCHHHHHHHHHHTT-EEEEEE-TTS-HHHHHHHHHH--S-EEEESTTC-SSTTSSB-TTHHHHHHH CS
                      Trp_syntA 113 eagvdglivpDlPleeaeelveaakkkglelvflvapttsderlkevveqaegfvYvvsraGvTgaenavaaevdelver 192
                                                                                            ++ + G  g+++a+   +de+v +
  gi|119719544|ref|YP_920039.1|  48 --------------------------------------------------------AIMVGGSIGVSEAM---TDEVVLA 68 
                                    ........................................................33333333333333...3333444 PP

                                    HHHCTSS- CS
                      Trp_syntA 193 lkkltavP 200
                                    +k+ t+vP
  gi|119719544|ref|YP_920039.1|  69 IKRSTEVP 76 
                                    44444444 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 4.7e-07
                                    HHHHHHHHCTSS-EEEESSS-SHHHHHHHHTT-SEEEE-HHHHHHHHC CS
                      Trp_syntA 188 elverlkkltavPvavGFGistkeqvkqvakvadGvivGSalvkkiee 235
                                    ++v+ +k +t++P+ vG Gi+++e +k++ak  + +iv   +v++ e+
  gi|119719544|ref|YP_920039.1| 186 KIVKMVKGVTTLPLIVGGGIRSPEVAKELAKAGADIIVTGTIVEESEN 233
                                    57999*************************555556666678887664 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.2    0.0024       2.7     150     191 ..      25      70 ..       4      71 .. 0.72
   2 !   14.0   0.2   1.9e-05     0.021     138     184 ..     192     236 ..     155     244 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0024
                                    ES---SHHHH....HHHHTT--SEEEE-HHHH-HHHHHHHHHHHT- CS
                           NanE 150 eGrintPeka....kkaieiGvdavvvGsaitrleeiakkfveaik 191
                                    +    tPe a    +++ e G  a++vG++i   e +++  v aik
  gi|119719544|ref|YP_920039.1|  25 DPEKTTPEVAariaREVAEAGTSAIMVGGSIGVSEAMTDEVVLAIK 70 
                                    55556777651111567899***********999999988877776 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 1.9e-05
                                    HHHHHTT--EEEES---SHHHHHHHHTT--SEEEE-HHHH-HHHHHH CS
                           NanE 138 kalseaglkviaeGrintPekakkaieiGvdavvvGsaitrleeiak 184
                                    k +  + l +i+ G i +Pe ak+  + G+d +v G+ +   e+i +
  gi|119719544|ref|YP_920039.1| 192 KGV--TTLPLIVGGGIRSPEVAKELAKAGADIIVTGTIVEESENIRE 236
                                    333..35779**************************99988888865 PP

>> G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1      0.31   3.5e+02     123     154 ..      30      61 ..      11      74 .. 0.82
   2 !   14.3   0.1   1.8e-05      0.02     128     168 ..     185     225 ..     181     227 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.31
                                    ESGGGHHHHCTSTTS...EEEEESS--SHHHH CS
                   G3P_antiterm 123 lPglvpkvikeikkelkipiiaGGLietkedv 154
                                     P +++++++e+ ++ +  i+ GG i  +e +
  gi|119719544|ref|YP_920039.1|  30 TPEVAARIAREVAEAGTSAIMVGGSIGVSEAM 61 
                                    68999999999999999999999998776655 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 1.8e-05
                                    HHHHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEEE- CS
                   G3P_antiterm 128 pkvikeikkelkipiiaGGLietkedveealkaGaiavsts 168
                                    pk++k +k  +++p+i GG i++ e  +e+ kaGa+ + t+
  gi|119719544|ref|YP_920039.1| 185 PKIVKMVKGVTTLPLIVGGGIRSPEVAKELAKAGADIIVTG 225
                                    99**********************************99986 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       2.1   2.3e+03     259     276 ..      38      55 ..      32      67 .. 0.73
   2 !   15.2   0.3   8.3e-06    0.0093     219     276 ..     176     228 ..     169     243 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.1
                                    HHHHHHHTECEEEESHHH CS
                         DHO_dh 259 alekieaGAslvqvytal 276
                                    a e +eaG s++ v+  +
  gi|119719544|ref|YP_920039.1|  38 AREVAEAGTSAIMVGGSI 55 
                                    557788888888887655 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 8.3e-06
                                    EEEEEGGGHHHHHHHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHH CS
                         DHO_dh 219 GGlsGkalkdialkvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytal 276
                                    GG +G+++ +  +k++     ++  ++p+I  GGi s e a e ++aGA ++  +t +
  gi|119719544|ref|YP_920039.1| 176 GGSGGEPVPPKIVKMVKG---VT--TLPLIVGGGIRSPEVAKELAKAGADIIVTGTIV 228
                                    778888888765555543...34..49*************************999976 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.069        77     110     142 ..      39      72 ..      17      83 .. 0.60
   2 ?    9.8   0.1   0.00033      0.37     134     173 ..     186     225 ..     161     238 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.069
                                    HHHHHTT-SEEEEE-STSSSHHHHHHHH.HHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx RF
                          IMPDH 110 kalveagvdvlvvdsahghsekvleavk.eikkk 142
                                    ++++eag  +++v  + g se +++ v  +ik++
  gi|119719544|ref|YP_920039.1|  39 REVAEAGTSAIMVGGSIGVSEAMTDEVVlAIKRS 72 
                                    4455566666666666666665555433134433 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00033
                                    HHHHHHHHHTTTSEEEEEEE-SHHHHHHHHHTT-SEEEE- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH 134 eavkeikkkveeveviaGnvataegakaLieagadavkvG 173
                                    + vk +k  ++   +++G + + e ak+L++agad++  G
  gi|119719544|ref|YP_920039.1| 186 KIVKMVKGVTTLPLIVGGGIRSPEVAKELAKAGADIIVTG 225
                                    5677777666433477999999999999999999999766 PP

>> DpaA_N  Dipicolinate synthase subunit A N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   5.9e-05     0.066       3      35 ..     199     233 ..     198     244 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.9e-05
                                    EEESB-HHHHHHHHHHHHTT-EEEEES-..TSSS- CS
                         DpaA_N   3 aviGGDaRqlylarkLaekgakvslygl..eleek 35 
                                    +++GG  R  ++a++La+ ga++ + g   e++e+
  gi|119719544|ref|YP_920039.1| 199 LIVGGGIRSPEVAKELAKAGADIIVTGTivEESEN 233
                                    69************************995433333 PP

>> Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.83   9.3e+02      93      93 ..      33      33 ..       5      56 .. 0.44
   2 ?   11.5   0.0   0.00013      0.14     164     197 ..     194     228 ..     180     229 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.83
                                   T CS
                 Ribul_P_3_epim 93 h 93
                                    
  gi|119719544|ref|YP_920039.1| 33 V 33
                                   1 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00013
                                    T---EEEEESS--T.TTCHHHHHHT--EEEESHHH CS
                 Ribul_P_3_epim 164 eldlkievDGGvkl.dnieqiaeagadvlVagsav 197
                                     ++l + v GG++  + ++++a+agad++V+g+ v
  gi|119719544|ref|YP_920039.1| 194 VTTLPLIVGGGIRSpEVAKELAKAGADIIVTGTIV 228
                                    4668899*****86266789************865 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.3   0.00016      0.18       3      46 ..     199     242 ..     198     248 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00016
                                    EEECSSHHHHHHHHHHHHTTSEE....EEEESSSSSSTTSSHHHHHHH CS
                      Pyr_redox   3 vvvGgGyiglElAgalaelgkkV....tvversdkllrllDeeaskil 46 
                                    ++vGgG    E+A++la+ g+++    t+ve s++++    e++++i+
  gi|119719544|ref|YP_920039.1| 199 LIVGGGIRSPEVAKELAKAGADIivtgTIVEESENIR----ETIGRIV 242
                                    69****************9965444559999999999....7777766 PP

>> BtpA  BtpA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.23   2.6e+02     164     205 ..      37      79 ..      10      89 .. 0.70
   2 ?    9.6   0.0    0.0005      0.56     174     240 ..     170     238 ..     143     246 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.23
                           BtpA 164 vkdtvergladavilsGkatGgevdleelkla.ketvkvkvlv 205
                                    +   v  + + a+++ G    +e+ ++e++la k+  +v+v+ 
  gi|119719544|ref|YP_920039.1|  37 IAREVAEAGTSAIMVGGSIGVSEAMTDEVVLAiKRSTEVPVIL 79 
                                    3333444566788888888888888888887724445588876 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0005
                           BtpA 174 davilsGkatGgevdleelklaketvkvkvlvgsGvseenlekllsi..adGvivgtsikkdGkianai 240
                                    + v l G + G++v  + +k++k +  ++ +vg G+    ++k l    ad +++gt +    +i ++i
  gi|119719544|ref|YP_920039.1| 170 QFVYLEGGSGGEPVPPKIVKMVKGVTTLPLIVGGGIRSPEVAKELAKagADIIVTGTIVEESENIRETI 238
                                    567899999999999999*******9************9999988752357788888888887777776 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       2.1   2.4e+03     143     156 ..      39      52 ..      17      68 .. 0.54
   2 ?   11.2   0.1   0.00015      0.17      95     125 ..     197     227 ..     154     232 .. 0.67

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.1
                       TMP-TENI 143 kelaealeiPvvai 156
                                    +e+aea +  +++ 
  gi|119719544|ref|YP_920039.1|  39 REVAEAGTSAIMVG 52 
                                    33333333333333 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00015
                       TMP-TENI  95 pdliiGlSvhsleeaeeaealgadYigvGpi 125
                                      li+G  + s+e a+e++++gad i+ G+i
  gi|119719544|ref|YP_920039.1| 197 LPLIVGGGIRSPEVAKELAKAGADIIVTGTI 227
                                    3456666666666666666666666666666 PP

>> PucR  Purine catabolism regulatory protein-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00056      0.63      53     102 ..      28      82 ..      10      94 .. 0.81
   2 ?   -0.5   0.0       1.3   1.5e+03      40      66 ..     216     241 ..     183     248 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00056
                           PucR  53 kddpealaelvrelaeagvaaLviklg....r.eipeelieaadelglPlielpe 102
                                    k++pe  a++ re+aeag +a++++      +   +e ++++ ++ ++P+i +p 
  gi|119719544|ref|YP_920039.1|  28 KTTPEVAARIAREVAEAGTSAIMVGGSigvsEaMTDEVVLAIKRSTEVPVILFPG 82 
                                    668899999***************9975564246678888999999*****9997 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.3
                           PucR  40 rggeLllttglalkddpealaelvrel 66 
                                    + g  +++tg  ++ + e+++e++ ++
  gi|119719544|ref|YP_920039.1| 216 KAGADIIVTGTIVE-ESENIRETIGRI 241
                                    33333444455554.455555555555 PP

>> HTH_Tnp_1  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00039      0.44       8      38 ..      30      60 ..      26      62 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00039
                      HTH_Tnp_1  8 sdefKariVreslepgksvsevArrhgvspn 38
                                   ++e+ ari re+ e+g+s  +v  + gvs++
  gi|119719544|ref|YP_920039.1| 30 TPEVAARIAREVAEAGTSAIMVGGSIGVSEA 60
                                   78999***********************986 PP

>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.2      0.19   2.2e+02      37      78 ..      28      69 ..       7      80 .. 0.64
   2 ?    4.8   0.3     0.018        20     109     135 ..      66      92 ..      24     100 .. 0.57
   3 ?    4.2   0.0     0.028        31      21      51 ..     209     242 ..     206     250 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.19
                                   EEE-SSHHHHHHHHHHHHHTSSEEEEESS-SSSTT..--HHHHH CS
                  MoCF_biosynth 37 tvvpDdeeeikeallaaleeadviittGGtGptpd..Dvtpeal 78
                                   ++ p+  ++i++++++a  +  +i + G +G+++   D ++ a+
  gi|119719544|ref|YP_920039.1| 28 KTTPEVAARIAREVAEA--GTSAIMVGGSIGVSEAmtDEVVLAI 69
                                   47777788888888555..4478888888888764114444454 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.018
                                    GGGGE.EETTEEEEE-SSHHHHHHHHH CS
                  MoCF_biosynth 109 gailsravgktiigLPGspkavkeale 135
                                    +  ++r+++ ++i  PGsp a  + ++
  gi|119719544|ref|YP_920039.1|  66 VLAIKRSTEVPVILFPGSPTALSRHAD 92 
                                    223344446679999999998877655 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.028
                                    HHHHHHHTTSEEEEEEEEE-SSHHHHHHHH...H CS
                  MoCF_biosynth  21 llaellkelgvevskytvvpDdeeeikeal...l 51 
                                     +a++l+++g++++ ++++ ++ e i+e++    
  gi|119719544|ref|YP_920039.1| 209 EVAKELAKAGADIIVTGTIVEESENIRETIgriV 242
                                    57899************************96542 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1796.12
//
Query:       gi|119719545|ref|YP_920040.1|  [L=65]
Description: hypothetical protein Tpen_0634 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.9e-12   46.4   0.4    3.4e-12   46.2   0.4    1.1  1  Sec61_beta  Sec61beta family


Domain annotation for each model (and alignments):
>> Sec61_beta  Sec61beta family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.2   0.4   1.9e-16   3.4e-12       2      40 ..      25      63 ..      24      64 .. 0.96

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 1.9e-16
                                   XXXXXXXXX----SS-B-THHHHHHHHHHHHHHHHHTSS CS
                     Sec61_beta  2 saGLlryyeedapgikidPkvVlvlsvafiasVilLhil 40
                                   +aGLl +yeed  gik+ P+ V++ +++++++V+l+h+ 
  gi|119719545|ref|YP_920040.1| 25 AAGLLTFYEEDIGGIKVRPELVIAGTFLLVILVLLAHAG 63
                                   7************************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 466.31
//
Query:       gi|119719546|ref|YP_920041.1|  [L=69]
Description: hypothetical protein Tpen_0635 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 483.36
//
Query:       gi|119719547|ref|YP_920042.1|  [L=277]
Description: prenyltransferase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.6e-36  124.4  17.7    5.7e-36  124.1  17.7    1.1  1  UbiA      UbiA prenyltransferase family


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.1  17.7   3.2e-40   5.7e-36       9     242 ..      26     256 ..      18     272 .. 0.84

  Alignments for each domain:
  == domain 1  score: 124.1 bits;  conditional E-value: 3.2e-40
                           UbiA   9 lalaaggspdlllllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivllilgllllalll 88 
                                    + + +++++ +  ++l++l +++a ++  a+Nd+f +e+D+   + p RP+v+G+is +eal+fai+++i++++++   +
  gi|119719547|ref|YP_920042.1|  26 AGALSTQVFVADKAVLAALSAFFAETSLFAFNDVFNVEEDKV--NNPTRPIVAGEISLREALLFAIATGIMSVVFA-SAI 102
                                    33334566667889****************************..9*******************************.*** PP

                           UbiA  89 npltallgllalllyvvYtglrlKrrtllgtvvggiafglppllgwaavtgslsllalllalavflltwaialandlrdr 168
                                    +p+ +++++lal l+++Y   +lKr+++lg+++++   ++ +++g+ avt s +   ll+++  fl  ++  +++ +rd+
  gi|119719547|ref|YP_920042.1| 103 GPFPLAVIALALGLGILYD-AMLKRHGFLGNLIVAGLTAFTFPFGAIAVTASPTEKSLLFFAVAFLANVGREIVKGIRDL 181
                                    *******************.6********************************99999999999**************** PP

                           UbiA 169 egDrkagiktlpvvlGrkaaril.lalllavlllallllllalllllylllalllaalallraarlvrrrdakka 242
                                    egD kagi tlp   G+k a ++ +a++ ++++l++  l +  l  lyl+l l+  +++ + aa    + d++ a
  gi|119719547|ref|YP_920042.1| 182 EGDMKAGICTLPCEVGEKPAGVIaAAFMSLAVVLSFSGLAFVSLKHLYLALILVTDVIFAYSAAVMALKADRHHA 256
                                    *********************985444444444445566666666666666666666666666655555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1827.52
//
Query:       gi|119719548|ref|YP_920043.1|  [L=217]
Description: hypothetical protein Tpen_0637 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1412.54
//
Query:       gi|119719549|ref|YP_920044.1|  [L=210]
Description: hypothetical protein Tpen_0638 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0013   18.4   0.2       0.01   15.4   0.1    2.0  2  AAA_25    AAA domain
  ------ inclusion threshold ------
      0.021   15.2   0.1      0.037   14.4   0.1    1.5  1  AAA_16    AAA ATPase domain
      0.082   12.2   0.0      0.089   12.1   0.0    1.2  1  DnaB_C    DnaB-like helicase C terminal domain
      0.099   12.6   0.1        0.2   11.7   0.1    1.7  1  AAA_5     AAA domain (dynein-related subfamily)


Domain annotation for each model (and alignments):
>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   2.3e-06      0.01      29      57 ..      17      45 ..       3      53 .. 0.87
   2 ?    0.9   0.0     0.066     3e+02     144     186 ..      97     145 ..      60     149 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.3e-06
                         AAA_25 29 llpagelallaGapgtGKttlaldlalav 57
                                   +l + +l++++G pg+ Ktt+al la ++
  gi|119719549|ref|YP_920044.1| 17 ILSRSGLHVVYGEPGSLKTTFALLLAKSM 45
                                   67899********************9877 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.066
                         AAA_25 144 rlvviDplsralgg..densnsd...v.galvealeriarrtgaavllv 186
                                     ++v D ++++++      +++    + + + ++l ++a++ +++vl+v
  gi|119719549|ref|YP_920044.1|  97 TVIVYDGFASLTSPllTLGKSHPvlrAnTFVAAKLYEVAEKSRCTVLIV 145
                                    5555566666555544222222222223556678888899999999887 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   8.2e-06     0.037      11      85 ..      13      86 ..       5     145 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 8.2e-06
                         AAA_16 11 qLlsalervrsgrpelvllsGesGvGKsslvrellralekdg.gif..lrgkcdqlesaipysa.laqalareellrql 85
                                   +Ll++l+r     ++l +++Ge+G+ K++ +  l+++++k++ +++  ++  + +++s+ + +  +++al+++e +++l
  gi|119719549|ref|YP_920044.1| 13 RLLRILSR-----SGLHVVYGEPGSLKTTFALLLAKSMKKERkVYVglAKHAFLDFPSSFSKDFlVLRALSFKEEVAAL 86
                                   55555553.....36778***********************77999856666666654432222233333333333333 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0     2e-05     0.089      13      75 ..      15      84 ..       9     145 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2e-05
                                   CTSBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTS.....E..EEEEESSSXHHHHHHHHHHHHHTXX CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....x..xxxxxxxxxxxxxxxxxxxxxxxxx RF
                         DnaB_C 13 tsGlqkgdliiiAarpsmGktalalniaenaavkekl.....p..vavfslemsaeqlvqRllsseaeid 75
                                   ++ l ++ l ++ + p+  kt++al +a+++ +++k+     +   + f    s++ lv R ls + e+ 
  gi|119719549|ref|YP_920044.1| 15 LRILSRSGLHVVYGEPGSLKTTFALLLAKSMKKERKVyvglaKhaFLDFPSSFSKDFLVLRALSFKEEVA 84
                                   56688999**********************9987765222221123445566777778888888777774 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   4.4e-05       0.2       4      30 ..      26      53 ..      24     162 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.4e-05
                                   EE--SSSSHHHHHHHGGGGB.S--EEEE CS
                          AAA_5  4 LvGppGtgKselaerlaaal.nreveyv 30
                                   + G+pG+ K+++a  la+ + + + +yv
  gi|119719549|ref|YP_920044.1| 26 VYGEPGSLKTTFALLLAKSMkKERKVYV 53
                                   68******************54444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1546.13
//
Query:       gi|119719550|ref|YP_920045.1|  [L=115]
Description: hypothetical protein Tpen_0639 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-06   27.7   4.8      2e-06   27.4   4.8    1.0  1  OST3_OST6    OST3 / OST6 family, transporter family
  ------ inclusion threshold ------
       0.88    7.8   9.1          1    7.6   9.1    1.1  1  DUF2070      Predicted membrane protein (DUF2070)
        2.5    8.2   4.6        4.2    7.4   4.6    1.3  1  UPF0242      Uncharacterised protein family (UPF0242) N-termi
        2.6    7.7   7.4        3.4    7.3   7.4    1.2  1  Tetraspanin  Tetraspanin family
        2.9    8.2  10.2       0.34   11.2   3.6    2.0  3  DUF4149      Domain of unknown function (DUF4149)


Domain annotation for each model (and alignments):
>> OST3_OST6  OST3 / OST6 family, transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   4.8   5.6e-10     2e-06     182     284 ..      14     109 ..       7     113 .. 0.86

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 5.6e-10
                      OST3_OST6 182 lwavlslliillftsGymfnqIrgvpfvakdekggisyfaggsqnQfgaEtqivallygllallvilLiklvpriknakv 261
                                    + a++ l++ill  sG  +     +pf         + ++++ + Q + E++iv +ly++  ++++++ +      ++++
  gi|119719550|ref|YP_920045.1|  14 VLAAALLAVILLIASGVFYVLSERPPFSLGV-----QLIYPSGGGQTVSEMIIVLFLYAMAIVGLLIIYDST--KYSPQR 86 
                                    67889999*******************9965.....9*********************98888766666444..344667 PP

                      OST3_OST6 262 qrvlvivllvlifllfslllslf 284
                                    +++   +++++ ++++slll lf
  gi|119719550|ref|YP_920045.1|  87 SAFYFTLVSGVAVVAVSLLLLLF 109
                                    88889999999999999999888 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   9.1   0.00029         1      76     177 ..      14     112 ..       4     115 .] 0.64

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00029
                        DUF2070  76 lltelivviisllaillsallqalvllalvlslalvfalrllvlvavsdesllkavlpaliqpllailllvly......f 149
                                    +l++ ++++i+l+a+ ++++l++  +++l +          l++ + ++++++ ++++ +++ ++++ ll++y       
  gi|119719550|ref|YP_920045.1|  14 VLAAALLAVILLIASGVFYVLSERPPFSLGVQ---------LIYPSGGGQTVSEMIIVLFLYAMAIVGLLIIYdstkysP 84 
                                    44445555556666666666655566666666.........778888888888888888888888888888888888764 PP

                        DUF2070 150 spesfllllllslifalavylfivvvdr 177
                                    + + f+++l++ ++++++++l++ ++  
  gi|119719550|ref|YP_920045.1|  85 QRSAFYFTLVSGVAVVAVSLLLLLFIYT 112
                                    4455566666666666666666666554 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   4.6    0.0012       4.2       5      57 ..      59     114 ..      56     115 .] 0.80

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0012
                        UPF0242   5 lisiiflYllPll.llaiysiqllseqksWs..llsiGlllaaaGsLlllllllkw 57 
                                    +i+++flY + ++ ll iy     s q+s     l+ G+ ++a+  Llll++++++
  gi|119719550|ref|YP_920045.1|  59 MIIVLFLYAMAIVgLLIIYDSTKYSPQRSAFyfTLVSGVAVVAVSLLLLLFIYTNF 114
                                    6999**********999998888887777551245668899999999999999888 PP

>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   7.4   0.00096       3.4      15     105 ..      21     113 ..      12     115 .] 0.73

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00096
                                    XXXXXXXXXXXXXX..XXX.....................XXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                    xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Tetraspanin  15 igivllavGvwlrl..khaeaalacllsesaedpailaillivvGv.llfllgflGcigalkenkcllltfsllllvlfl 91 
                                    + i+l+a Gv + l  +  + +l  +l   +   ++++ ++iv+   +++++g+l ++ + k +    +++++l+  + +
  gi|119719550|ref|YP_920045.1|  21 AVILLIASGVFYVLseRPPF-SLGVQLIYPSGGGQTVSEMIIVLFLyAMAIVGLLIIYDSTKYSPQRSAFYFTLVSGVAV 99 
                                    33444444644444553333.33344455556666666777888777********************************* PP

                                    XXXXXXXXXX--HH CS
                                    xxxxxxxxxxxxxx RF
                    Tetraspanin  92 lelaagilgfvfsd 105
                                    + +++ +l+f++++
  gi|119719550|ref|YP_920045.1| 100 VAVSLLLLLFIYTN 113
                                    ***********997 PP

>> DUF4149  Domain of unknown function (DUF4149)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.4      0.15   5.4e+02      73      87 ..      17      31 ..       3      38 .. 0.50
   2 ?    0.6   0.5       0.2   7.1e+02      47      85 ..      19      29 ..      11      48 .. 0.55
   3 ?   11.2   3.6   9.6e-05      0.34      32      91 ..      54     113 ..      49     114 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.15
                        DUF4149 73 llllvvllltllnaf 87
                                    +ll+v+ll++   f
  gi|119719550|ref|YP_920045.1| 17 AALLAVILLIASGVF 31
                                   333333333333333 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.2
                        DUF4149 47 alsvlllltevavgseklaseellqlllllvvllltlln 85
                                   +l+v+ll+ +                             
  gi|119719550|ref|YP_920045.1| 19 LLAVILLIAS----------------------------G 29
                                   2222222222............................2 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 9.6e-05
                        DUF4149  32 elqsklFplyfglglalsvlllltevavgseklaseellqlllllvvllltllnafylep 91 
                                    + +s++  ++f   +a+ +ll+++   ++s + ++ +++++++++vv+++ ll  f++++
  gi|119719550|ref|YP_920045.1|  54 QTVSEMIIVLFLYAMAIVGLLIIYDSTKYSPQRSAFYFTLVSGVAVVAVSLLLLLFIYTN 113
                                    567788889999999***********99999999999********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1020  (0.0568911); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 852.24
//
Query:       gi|119719551|ref|YP_920046.1|  [L=731]
Description: oligosaccharyl transferase, STT3 subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-38  132.2  26.8    4.4e-38  131.5  26.8    1.3  1  STT3             Oligosaccharyl transferase STT3 subunit
  ------ inclusion threshold ------
       0.17   11.8   2.3       0.53   10.2   2.3    1.8  1  DUF1980          Domain of unknown function (DUF1980)


Domain annotation for each model (and alignments):
>> STT3  Oligosaccharyl transferase STT3 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.5  26.8   4.9e-42   4.4e-38      21     485 ..      41     553 ..      23     555 .. 0.80

  Alignments for each domain:
  == domain 1  score: 131.5 bits;  conditional E-value: 4.9e-42
                                    CCCCCT--S--SSCHHHHHHHCCCHHHT-C...............C.CHHSSEETTSSTTT-EEESTTCCHCCC.CHHHH CS
                           STT3  21 FtdedglsylsefDpYYnyRltenllnnGfpG..........dvvi.kkknwfdhsqyyPpGsrvdygplivlLamlasa 89 
                                     t  ++  yl efDpYY y l+e ll +G  G             + + k+++  + ++P G+ + + ++ ++    +sa
  gi|119719551|ref|YP_920046.1|  41 LTPMHWGVYLNEFDPYYEYYLSEQLLAHGN-GnyfagvawwyHWWFeNPKPRDTLF-WAPEGRDLRG-TSQPGP-AFFSA 116
                                    5678999**********************7.6566657776644441455666666.*****77765.555665.34444 PP

                                    HHCCHHC.....HHHHHHHHCCHHHHHHHHCHHHHHHHHHHS-CCCHHHHHHHCCC-CCCCCTTSTT--STCCCCHHHHH CS
                           STT3  90 iinhsld.....vsirevclwlpallgsLlaIpiyflvrelksdiaGllAAlllaiaPgYlsrtvaGfyDtdmfeivlll 164
                                     ++  l+     vs+  v  +l ++ +sL++  +y+l  elk+ +aG+lA +l+a++  Y++rt +G + +++++i ++l
  gi|119719551|ref|YP_920046.1| 117 GVYTLLRtlgfdVSLYYVHAFLVPFVASLAVFTAYLLGSELKDYRAGVLASVLIALSWAYMYRTNLG-AKHEAIAIPFML 195
                                    444444445566*******************************************************.57********** PP

                                    HHHHHHHHHHHCCSTTCHHHHHHHHHHHHHHTTSCCGGHHHHCCHHHHHHHHHCTTTS-CCHHHHH..HHHHHHHHHH.. CS
                           STT3 165 fvlffflkaiktksnkislaviaaliiflivlaWggyailiyallllfilalLiigrfelklkiav..tfsviiaflvia 242
                                    + +++flk++k+ks    l+ +a+l++ ++vlaWg+y +   +ll+l +l  L ++     +  ++  t  v+++f++  
  gi|119719551|ref|YP_920046.1| 196 LGFYLFLKGYKKKS--LLLSILAGLSLGVVVLAWGAY-VYPWNLLALVVLFWLFFHPDDTAIARSYvaTNLVVTFFVATT 272
                                    **************..*********************.******************966555555522444555555544 PP

                                    CCCCCCCTTCHHHSTTTCHHCCCCHHHHHHHHCCCHHC..CCCCCHHCCCHHTT.HHHHTT--GGGHHHHHHHHHHHHCC CS
                           STT3 243 iivllflgfqvvavseiigalgifgllqlvafgsvvvlvaelkfyqfislfqpgilsevlgligevvtalavlglialwl 322
                                        + ++f     s ++++ ++++l+ +++  ++ v  + l+ ++++  + +     ++ l  +v ++ ++lg+    +
  gi|119719551|ref|YP_920046.1| 273 PRFGPSVAFM----SFLGFLPLVATLASILVIFGIRVPSSSLGAKKTRRTLLVL----LVVL-LVVFALGTYLGVFRGLA 343
                                    4444444444....5777778888887766666666655677776666655444....2222.23333334556666666 PP

                                    CCCCTS-----TTHHHHHHHHHS---S--CCHHHCCSSST.TTTCCCHH.HCHHCCHHCTCHHHHHHHHHHHHHCCC-SC CS
                           STT3 323 gilyslldleyaklkikiiilvsvwlpvgllaltkglrfl.iftvPlgi.ifvgllleflavfvkiysvsqilfsgvvvi 400
                                    g+ + ++   ++ +  + +  v+++++ ++  l+ + +   if++ +g  +f+ ++  f   f+  ++ ++++fs+ +v+
  gi|119719551|ref|YP_920046.1| 344 GRIMAVV---MPLVREPGVTTVAEHQVPTWNQLFDDFQTSlIFAFFAGYlYFLKSKDDFNSAFISLFIATAVYFSASIVR 420
                                    6666655...8*************************99888777766666****************************** PP

                                    HCCCCCHHHHHHHCCCHHHHHHHHCCHHHHHHHHH....HHHHH.................................... CS
                           STT3 401 llmltllpvlallaavkiskifstykdekeakikv....aakav.................................... 440
                                     l+l+l+p++a+   + + +i++      e ++      a                                        
  gi|119719551|ref|YP_920046.1| 421 -LLLLLSPAVAIAGSLGLVEILDRLALPAERSYDKrhrgA---Stqttrhlailiavillllfspsilaskiplnshqpp 496
                                    .9*********************99888777777644431...266678888999999********************** PP

                                    ...........HHHHCT.TTTTHHH.TTHHHCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           STT3 441 ...........aptksnglkeslew.kantnrdsvvitwwdyghilaveadrpVtfd 485
                                                + +   +  +l+w  +n +rd+ + twwdyg+ + v   r++t d
  gi|119719551|ref|YP_920046.1| 497 liltssvplvrYDYEYMDWLSALQWiSENVPRDATIATWWDYGYWISVNTGRKTTCD 553
                                    *********999999999***********************************9998 PP

>> DUF1980  Domain of unknown function (DUF1980)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   2.3     6e-05      0.53       5      97 ..     381     488 ..     379     492 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 6e-05
                        DUF1980   5 liLlgFavllfkLhasgeisk.YInpkyapllyfamvvllilalvq.liraqkkk...............e.cghdHeek 66 
                                    li+++Fa++l+ L + ++ ++ +I   +a+ +yf++ ++ +l l    + +                      +++H  +
  gi|119719551|ref|YP_920046.1| 381 LIFAFFAGYLYFLKSKDDFNSaFISLFIATAVYFSASIVRLLLLLSpAVAIAG-SlglveildrlalpaeRsYDKRH--R 457
                                    8999**********99999744************9988888888885333333.33678888888988753355555..7 PP

                        DUF1980  67 sfikkllsylilviPlllglllptkvldssi 97 
                                    +  ++ +  l ++i+++l+ll++++ l s+i
  gi|119719551|ref|YP_920046.1| 458 GASTQTTRHLAILIAVILLLLFSPSILASKI 488
                                    88999999999*****************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (731 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       883  (0.0492498); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.77u 0.33s 00:00:01.10 Elapsed: 00:00:00.54
# Mc/sec: 4102.33
//
Query:       gi|298205346|ref|YP_003717798.1|  [L=64]
Description: H/ACA RNA-protein complex component Nop10p [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-23   83.0   1.8    1.3e-23   82.8   1.8    1.1  1  Nop10p          Nucleolar RNA-binding protein, Nop10p family
      0.006   16.4   2.4     0.0093   15.8   2.4    1.2  1  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
  ------ inclusion threshold ------
      0.017   14.7   0.4      0.025   14.2   0.4    1.2  1  RecR            RecR protein
      0.031   14.1   0.7      0.043   13.7   0.7    1.2  1  zf-C3HC4_3      Zinc finger, C3HC4 type (RING finger)
       0.06   13.0   3.5        5.1    6.8   0.1    2.2  2  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
      0.069   12.6   0.1      0.081   12.4   0.1    1.1  1  DUF1258         Protein of unknown function (DUF1258)
       0.11   10.3   0.0       0.11   10.3   0.0    1.0  1  PolC_DP2        DNA polymerase II large subunit DP2
       0.14   11.9   4.7        1.3    8.8   0.5    2.4  2  zinc_ribbon_2   zinc-ribbon domain
       0.21   11.6   0.5       0.28   11.2   0.5    1.2  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.23   11.6   3.4       0.86    9.8   3.5    1.9  1  Zn-ribbon_8     Zinc ribbon domain
       0.27   11.5   2.4       0.46   10.8   2.2    1.5  1  Ribosomal_L32p  Ribosomal L32p protein family
       0.28   10.7   6.8        1.2    8.7   6.8    1.9  1  zf-ribbon_3     zinc-ribbon domain
       0.29    9.8   1.1       0.36    9.6   1.1    1.1  1  NRDD            Anaerobic ribonucleoside-triphosphate reducta
       0.59    9.7   4.6          6    6.5   1.0    2.2  2  TF_Zn_Ribbon    TFIIB zinc-binding
        8.8    6.0   9.5        4.1    7.1   1.4    2.2  2  zf-tcix         Putative treble-clef, zinc-finger, Zn-binding


Domain annotation for each model (and alignments):
>> Nop10p  Nucleolar RNA-binding protein, Nop10p family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.8   1.8   1.1e-26   1.3e-23       5      50 ..       6      52 ..       3      54 .. 0.95

  Alignments for each domain:
  == domain 1  score: 82.8 bits;  conditional E-value: 1.1e-26
                                      -EE-TTT--EESS.SB-TTT-SB-B-SS--S--TT-TTCHHHHHCHH CS
                            Nop10p  5 lrkcgkcrvYTLk.kvcpecggptksahPaRFSPdDkyskyRralKk 50
                                      lr+c+kc+ YTL+ ++cp+cggp+k++hPa+FSPdDky++yRr++K 
  gi|298205346|ref|YP_003717798.1|  6 LRRCEKCGLYTLRqDKCPYCGGPVKTPHPAKFSPDDKYGEYRRKIKL 52
                                      89***********9*******************************95 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   2.4   7.8e-06    0.0093      10      33 ..       5      27 ..       3      30 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 7.8e-06
                           DUF35_N 10 vgqrCpdCGtvqfPPravCphCgs 33
                                      +++rC +CG +   ++  Cp+Cg+
  gi|298205346|ref|YP_003717798.1|  5 ILRRCEKCGLYTL-RQDKCPYCGG 27
                                      689********96.99******97 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.4   2.1e-05     0.025      16      34 ..       6      25 ..       3      28 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.1e-05
                                      -EE-TTT--EESS.SS-CCC CS
                              RecR 16 vrhCsrCgnltee.dlCaIC 34
                                      +r+C++Cg +t + d C+ C
  gi|298205346|ref|YP_003717798.1|  6 LRRCEKCGLYTLRqDKCPYC 25
                                      589*******977589**** PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.7   3.6e-05     0.043      26      48 ..       9      30 ..       4      31 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.6e-05
                                      -HHHHHHHHHTT-B-TTT--B-- CS
                        zf-C3HC4_3 26 CeeCaekllkrkkkCpiCrrpie 48
                                      Ce+C      r++kCp+C  p++
  gi|298205346|ref|YP_003717798.1|  9 CEKCGLYT-LRQDKCPYCGGPVK 30
                                      99999888.479*******9987 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1    0.0043       5.1      19      29 ..       4      14 ..       2      16 .. 0.80
   2 ?    6.8   0.8    0.0045       5.3       6      14 ..      22      30 ..      22      31 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0043
                     zf-NADH-PPase 19 gwarvCpaCgl 29
                                      g  r+C+ Cgl
  gi|298205346|ref|YP_003717798.1|  4 GILRRCEKCGL 14
                                      5569******8 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0045
                     zf-NADH-PPase  6 CgrCGapte 14
                                      C+ CG+p++
  gi|298205346|ref|YP_003717798.1| 22 CPYCGGPVK 30
                                      *******86 PP

>> DUF1258  Protein of unknown function (DUF1258)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   6.8e-05     0.081      17      40 ..       7      30 ..       2      36 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.8e-05
                           DUF1258 17 kfcnkcGkvvaksekcelcggkva 40
                                        c+kcG  + +++kc +cgg+v 
  gi|298205346|ref|YP_003717798.1|  7 RRCEKCGLYTLRQDKCPYCGGPVK 30
                                      57*******************985 PP

>> PolC_DP2  DNA polymerase II large subunit DP2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   9.3e-05      0.11     629     660 ..       5      36 ..       1      63 [. 0.57

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 9.3e-05
                          PolC_DP2 629 learCeeCgekteeklvCkkceeeveeekcek 660
                                       + +rCe+Cg  t  + +C+ c+  v++ +  k
  gi|298205346|ref|YP_003717798.1|   5 ILRRCEKCGLYTLRQDKCPYCGGPVKTPHPAK 36 
                                       56677777777777777777777666544333 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.3      0.02        24       2       6 ..       9      13 ..       7      14 .. 0.60
   2 ?    8.8   0.5    0.0011       1.3      16      22 ..      22      28 ..      18      29 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.02
                     zinc_ribbon_2  2 CpnCG 6 
                                      C +CG
  gi|298205346|ref|YP_003717798.1|  9 CEKCG 13
                                      55555 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0011
                     zinc_ribbon_2 16 CpyCGtp 22
                                      CpyCG p
  gi|298205346|ref|YP_003717798.1| 22 CPYCGGP 28
                                      9999966 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.5   0.00023      0.28      72      95 ..       8      28 ..       2      34 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00023
                                      EETTTS-EEECHHHHHS-TTTSSS CS
                              HypA 72 rCreCgkefeleekalrCpkCgsa 95
                                      rC++Cg  ++l+++  +Cp Cg+ 
  gi|298205346|ref|YP_003717798.1|  8 RCEKCG-LYTLRQD--KCPYCGGP 28
                                      8*****.5555645..8****985 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   3.5   0.00072      0.86       7      37 ..       8      30 ..       7      31 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00072
                       Zn-ribbon_8  7 rCeeCghefevlqsisdapltaCPeCgsevr 37
                                      rCe+Cg  ++ +q        +CP Cg++v+
  gi|298205346|ref|YP_003717798.1|  8 RCEKCG-LYTLRQ-------DKCPYCGGPVK 30
                                      8*****.777666.......35*****9885 PP

>> Ribosomal_L32p  Ribosomal L32p protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   2.2   0.00039      0.46      27      46 ..       7      26 ..       5      36 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00039
                                      EEETTTCCEECTTC-BTTTT CS
                    Ribosomal_L32p 27 vecpncgelklpHrvcpscG 46
                                       +c +cg ++l+   cp+cG
  gi|298205346|ref|YP_003717798.1|  7 RRCEKCGLYTLRQDKCPYCG 26
                                      69*****************6 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   6.8   0.00098       1.2       3      25 ..       7      28 ..       6      29 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00098
                       zf-ribbon_3  3 vrCPnCGaplssddnvCpyCGtk 25
                                      +rC +CG   + ++ +CpyCG++
  gi|298205346|ref|YP_003717798.1|  7 RRCEKCGLY-TLRQDKCPYCGGP 28
                                      589999998.89999******86 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   1.1    0.0003      0.36     508     526 ..       7      26 ..       5      33 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0003
                                       EEETT.--.EESSSB-TTT- CS
                              NRDD 508 dvCnecgy.kgeiekCpkCg 526
                                        +C++cg  +  ++kCp+Cg
  gi|298205346|ref|YP_003717798.1|   7 RRCEKCGLyTLRQDKCPYCG 26 
                                       68*****988888******9 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1     0.017        20      21      27 ..       8      14 ..       2      16 .. 0.83
   2 ?    6.5   1.0     0.005         6       2       9 ..      21      28 ..      21      33 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.017
                                      EESSSSB CS
                      TF_Zn_Ribbon 21 vCtdCGl 27
                                      +C++CGl
  gi|298205346|ref|YP_003717798.1|  8 RCEKCGL 14
                                      7*****8 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.005
                                      EETTTTCE CS
                      TF_Zn_Ribbon  2 kCPnCgst 9 
                                      kCP+Cg++
  gi|298205346|ref|YP_003717798.1| 21 KCPYCGGP 28
                                      8****985 PP

>> zf-tcix  Putative treble-clef, zinc-finger, Zn-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   1.4    0.0034       4.1       8      19 ..       3      15 ..       1      16 [. 0.79
   2 ?    3.7   1.5     0.039        46      12      17 ..      21      26 ..      16      28 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0034
                           zf-tcix  8 RGv.rkCpkCGty 19
                                      RG+ r+C kCG y
  gi|298205346|ref|YP_003717798.1|  3 RGIlRRCEKCGLY 15
                                      66449******88 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.039
                           zf-tcix 12 kCpkCG 17
                                      kCp CG
  gi|298205346|ref|YP_003717798.1| 21 KCPYCG 26
                                      9****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       662  (0.0369234); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.49
# Mc/sec: 392.66
//
Query:       gi|119719552|ref|YP_920047.1|  [L=265]
Description: translation initiation factor IF-2 subunit alpha [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.5e-20   71.6   0.0    1.2e-19   70.5   0.0    1.6  2  EIF_2_alpha  Eukaryotic translation initiation factor 2 alpha
    1.4e-11   44.6   0.8    1.5e-10   41.2   0.4    2.2  2  S1           S1 RNA binding domain
  ------ inclusion threshold ------
       0.01   14.1   0.1       0.13   10.5   0.0    2.0  2  DUF1633      Protein of unknown function (DUF1633)
      0.097   13.2   0.3       0.33   11.5   0.1    1.9  2  Dermcidin    Dermcidin, antibiotic peptide
       0.12   11.9   0.0       0.18   11.3   0.0    1.2  1  PCAF_N       PCAF (P300/CBP-associated factor) N-terminal dom


Domain annotation for each model (and alignments):
>> EIF_2_alpha  Eukaryotic translation initiation factor 2 alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       2.9     1e+04      74      84 ..      53      63 ..      51      83 .. 0.67
   2 !   70.5   0.0   3.3e-23   1.2e-19       1     114 [.     121     231 ..     121     233 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2.9
                                   HHHHHHHHHST CS
                    EIF_2_alpha 74 aIkeaLkagee 84
                                   +I+++Lk g++
  gi|119719552|ref|YP_920047.1| 53 NIRDVLKVGRK 63
                                   67888875554 PP

  == domain 2  score: 70.5 bits;  conditional E-value: 3.3e-23
                                    HHHCTHHHHTTTTS-HHHHH.HHHHSTTHHHHHTTS-TTTHHHHHHCTHHHHHHT-EEEEEEEEEEE-STTHHHHHHHHH CS
                    EIF_2_alpha   1 lyeevgwklyekyghaydaF.klaitdeevldkleipeeveeaLveiikkklkpqkvkiradieltcftkdGveaIkeaL 79 
                                    +y+e gwkl+++yg+++ ++ +++ ++ee+l +++++++++++L e +++ +kp+kvk++a i+l+c + +G+e++k+ L
  gi|119719552|ref|YP_920047.1| 121 AYREAGWKLEDHYGEIFRGLeEASARGEEALLEAGVSKQWAKVLAELARQGIKPKKVKLSALINLQCLS-KGIEGVKSTL 199
                                    599*****************9999999****************************************65.8********* PP

                                    HHHST.S..TTSSSEEEEEEEESSSSEEEEEEEES CS
                    EIF_2_alpha  80 kageeasneeeveeeeevkikliapPeYvltvetl 114
                                    ++ e+     +   + +v++++ ++P+Y+l++e++
  gi|119719552|ref|YP_920047.1| 200 TEWEN---VVSIPRDASVRVYTLGSPRYKLDIEAQ 231
                                    *5555...4456789****************9987 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.2   0.4   4.2e-14   1.5e-10       5      75 .]      12      83 ..       8      83 .. 0.94
   2 ?    1.3   0.0      0.12   4.3e+02      46      67 ..     229     250 ..     207     256 .. 0.74

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 4.2e-14
                                   TCEEEEEEEEEETTEEEEEET..TTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETTTTEEEEEEC CS
                             S1  5 gevveGeVtsvtkgGafVelg..ngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkdrrriilsik 75
                                   +e v G+V+++ ++GafV l+  +g ++++p+ e+s+    +++ +vlkvG ++ +kv++vd++++ +++s++
  gi|119719552|ref|YP_920047.1| 12 NELVVGTVIDIQDHGAFVSLDefGGLKAYIPLGEVSHS-WFKNIRDVLKVGRKYVLKVIRVDRNKKLVDVSLR 83
                                   78899********************************9.999************************9998875 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.12
                                    HHHCEETTEEEEEEEEEEETTT CS
                             S1  46 pdevlkvGdevkvkvlkvdkdr 67 
                                    + + +k+G+++ ++++ v +++
  gi|119719552|ref|YP_920047.1| 229 EAQSYKEGEKILAEIISVMEQA 250
                                    5667777777777777776654 PP

>> DUF1633  Protein of unknown function (DUF1633)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   3.5e-05      0.13     735     772 ..       7      44 ..       3      50 .. 0.91
   2 ?    1.4   0.0      0.02        72     554     605 ..     201     250 ..     171     255 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 3.5e-05
                        DUF1633 735 dlpevseilvvrpidvdeqGtpiGldefGsnkdafprG 772
                                    d+p + e++v   id+++ G+ + ldefG  k   p G
  gi|119719552|ref|YP_920047.1|   7 DVPSLNELVVGTVIDIQDHGAFVSLDEFGGLKAYIPLG 44 
                                    9*****************************99999877 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.02
                        DUF1633 554 redsslkvdserevrsgargivpgilrlkielstskdlekGyaekikimeqe 605
                                    + ++ + + ++  vr+ +        +l ie  + k+ ek  ae i +meq 
  gi|119719552|ref|YP_920047.1| 201 EWENVVSIPRDASVRVYTL--GSPRYKLDIEAQSYKEGEKILAEIISVMEQA 250
                                    5555555555555555554..34456788999999***************95 PP

>> Dermcidin  Dermcidin, antibiotic peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1      0.45   1.6e+03      34      77 ..     100     144 ..      86     161 .. 0.65
   2 ?   11.5   0.1   9.3e-05      0.33      24      91 ..     158     223 ..     139     232 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.45
                      Dermcidin  34 arqapkprkqrsslleksldgakkald.gleklgkeavedlesvg 77 
                                    a++a k     +s l+k+ld a +  +  le+   e    le++ 
  gi|119719552|ref|YP_920047.1| 100 AQRAEKILEMAASKLNKTLDDAYREAGwKLEDHYGEIFRGLEEAS 144
                                    566677777778888888887755443245555555555555554 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 9.3e-05
                      Dermcidin  24 kenagedpvlarqapkprkqrsslleksldgakkaldgleklgkeavedlesvgkgkeerawvlgapv 91 
                                    k+ a     larq  kp+k + s l  +l+   k+++g++    e  e++ s+ +    r++ lg+p 
  gi|119719552|ref|YP_920047.1| 158 KQWAKVLAELARQGIKPKKVKLSALI-NLQCLSKGIEGVKSTLTE-WENVVSIPRDASVRVYTLGSPR 223
                                    555666678**********9988886.699********9876554.6899999999999999999985 PP

>> PCAF_N  PCAF (P300/CBP-associated factor) N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   5.1e-05      0.18       8      74 ..      67     134 ..      61     158 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.1e-05
                         PCAF_N   8 qvlslprekKleklavyssCkvee.ckCngWkntesatkkkkkelkqelanlsdacrsCehslesHvs 74 
                                    +v  + r+kKl  ++       e+  k   Wk+++ a+k  +++ ++ +++l+da+r   ++le+H  
  gi|119719552|ref|YP_920047.1|  67 KVIRVDRNKKLVDVSLRRVSEKERrEKIIEWKRAQRAEKILEMAASKLNKTLDDAYREAGWKLEDHYG 134
                                    678899*********987776666599*****99999999**************************64 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1097  (0.0611858); expected 358.6 (0.02)
Passed bias filter:                      691  (0.0385409); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 1826.67
//
Query:       gi|119719553|ref|YP_920048.1|  [L=65]
Description: 30S ribosomal protein S27e [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-24   84.2   0.4      4e-24   84.1   0.4    1.0  1  Ribosomal_S27e   Ribosomal protein S27
    2.4e-06   26.8   1.7      0.015   14.7   0.3    2.2  2  zf-ribbon_3      zinc-ribbon domain
    7.9e-06   25.9   0.1    9.5e-06   25.6   0.1    1.1  1  HypA             Hydrogenase/urease nickel incorporation, met
    1.2e-05   25.1   1.2      0.081   12.8   0.1    2.1  2  DUF3797          Domain of unknown function (DUF3797)
    2.7e-05   24.0   1.5      0.082   12.9   0.4    2.2  2  zinc_ribbon_4    zinc-ribbon domain
    0.00017   21.6   2.5       0.22   11.6   0.5    2.2  2  zf-ACC           Acetyl-coA carboxylase zinc finger domain
     0.0002   21.0   1.9       0.25   11.1   0.4    2.3  2  zinc_ribbon_2    zinc-ribbon domain
    0.00026   20.7   5.1     0.0011   18.7   5.1    1.9  1  zinc_ribbon_5    zinc-ribbon domain
    0.00032   20.5   0.3     0.0032   17.3   0.5    2.0  2  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
    0.00061   19.5   2.6       0.12   12.1   0.7    2.2  2  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger
      0.001   19.2   0.4     0.0012   19.1   0.4    1.1  1  IBR              IBR domain, a half RING-finger domain
     0.0012   18.8   0.6       0.58   10.2   0.1    2.2  2  DNA_ligase_ZBD   NAD-dependent DNA ligase C4 zinc finger doma
     0.0012   18.9   2.0     0.0093   16.1   2.4    1.9  2  Auto_anti-p27    Sjogren's syndrome/scleroderma autoantigen 1
     0.0013   18.8   2.1     0.0047   17.0   2.3    1.7  2  Zn-ribbon_8      Zinc ribbon domain
     0.0015   18.5   0.2     0.0021   18.1   0.2    1.3  1  DZR              Double zinc ribbon
      0.002   18.0   0.2        2.3    8.2   0.0    2.2  2  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
     0.0022   18.2   0.4          2    8.7   0.0    2.2  2  zf-RING_7        C4-type zinc ribbon domain
     0.0022   18.0   0.5     0.0028   17.6   0.5    1.1  1  zinc_ribbon_6    Zinc-ribbon
     0.0023   17.8   0.3      0.003   17.4   0.3    1.2  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
     0.0025   17.8   2.2       0.73    9.9   0.2    2.4  2  DUF1610          Domain of unknown function (DUF1610)
     0.0033   16.9   2.2     0.0067   15.9   2.3    1.5  1  TF_Zn_Ribbon     TFIIB zinc-binding
     0.0036   16.4   0.3     0.0041   16.2   0.3    1.0  1  Tmemb_55A        Transmembrane protein 55A
      0.004   17.1   0.3     0.0049   16.9   0.3    1.1  1  Zn_Tnp_IS91      Transposase zinc-binding domain
     0.0078   16.2   0.5      0.012   15.6   0.5    1.3  1  zf-C2HC5         Putative zinc finger motif, C2HC5-type
     0.0094   16.2   2.0        3.1    8.1   0.1    2.1  2  zf-LITAF-like    LITAF-like zinc ribbon domain
  ------ inclusion threshold ------
      0.014   15.1   1.5          2    8.1   0.1    2.2  2  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
      0.016   14.9   0.7          2    8.2   0.0    2.2  2  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
       0.02   14.7   0.9        1.5    8.8   0.2    2.1  2  zf-HIT           HIT zinc finger
      0.021   14.8   3.6       0.15   12.1   3.8    1.9  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
      0.022   14.6   1.8        2.5    8.0   0.0    2.3  2  zf-FPG_IleRS     Zinc finger found in FPG and IleRS
      0.025   15.0   3.0        1.6    9.1   0.3    2.3  2  zf-IS66          zinc-finger binding domain of transposase IS
      0.027   14.5   1.3       0.44   10.6   1.3    2.1  1  zf-BED           BED zinc finger
      0.038   13.8   1.2        5.9    6.8   0.0    2.1  2  zinc_ribbon_12   Probable zinc-ribbon domain
      0.043   13.4   1.3        1.9    8.2   0.1    2.2  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
      0.043   13.5   0.2      0.053   13.2   0.2    1.1  1  TackOD1          Thaumarchaeal output domain 1
      0.045   14.2   1.1         11    6.8   0.1    2.3  2  zf-C2H2          Zinc finger, C2H2 type
      0.046   14.0   0.3      0.054   13.8   0.3    1.2  1  DUF1922          Domain of unknown function (DUF1922)
      0.047   13.2   6.5       0.65    9.5   6.7    2.0  1  Mu-like_Com      Mu-like prophage protein Com
      0.058   13.9   2.4        2.5    8.7   0.1    2.1  2  Zn_ribbon_recom  Recombinase zinc beta ribbon domain
      0.059   13.6   1.8        3.4    8.0   0.1    2.2  2  zinc_ribbon_9    zinc-ribbon
       0.06   13.3   0.6       0.16   12.0   0.6    1.4  1  zinc-ribbons_6   zinc-ribbons
      0.068   12.8   2.8        2.3    7.9   0.6    2.2  2  zf-tcix          Putative treble-clef, zinc-finger, Zn-bindin
      0.069   13.2   2.4        3.7    7.6   0.1    2.1  2  CpXC             CpXC protein
        0.1   12.7   3.2          3    8.0   0.1    2.1  2  zf-Mss51         Zinc-finger of mitochondrial splicing suppre
       0.12   12.4   2.0        6.3    6.9   0.1    2.2  2  DUF2752          Protein of unknown function (DUF2752)
       0.12   12.8   2.6        1.7    9.2   0.4    2.2  2  zf-H2C2_2        Zinc-finger double domain
       0.13   12.0   1.7          6    6.7   0.4    2.2  2  YacG             DNA gyrase inhibitor YacG
       0.13   12.9   4.2        1.7    9.4   0.1    2.5  2  zf-ISL3          zinc-finger of transposase IS204/IS1001/IS10
       0.18   11.5   3.6        4.5    7.0   0.1    2.3  2  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
       0.18   11.9   1.7         11    6.2   1.7    2.2  1  Nop10p           Nucleolar RNA-binding protein, Nop10p family
       0.19   11.1   3.5        5.5    6.4   4.4    2.1  3  zf-TFIIB         Transcription factor zinc-finger
        0.2   11.6   2.1        9.7    6.2   0.2    2.3  2  DUF951           Bacterial protein of unknown function (DUF95
       0.22   10.4   0.5        2.2    7.0   0.5    1.9  1  HECT_2           HECT-like Ubiquitin-conjugating enzyme (E2)-
       0.29   10.7   3.8          2    8.0   0.8    2.2  2  zf_C2H2_10       C2H2 type zinc-finger
       0.39   10.6   4.0        5.9    6.8   0.1    2.2  2  zf-C2H2_3        zinc-finger of acetyl-transferase ESCO
        0.5   10.1   4.4        2.3    8.0   0.1    2.5  2  Zn_Tnp_IS1       InsA N-terminal domain
       0.62   10.1   5.2        3.2    7.8   0.7    2.2  2  YhfH             YhfH-like protein
       0.66    9.9   5.3         91    3.0   5.3    2.2  1  TFIIS_C          Transcription factor S-II (TFIIS)
       0.86    9.6   4.1          3    7.9   4.0    1.8  2  Anti-TRAP        Tryptophan RNA-binding attenuator protein in
        6.7    6.6   8.6         23    4.9   0.2    2.8  3  zf-CCHC_6        Zinc knuckle


Domain annotation for each model (and alignments):
>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.1   0.4   1.3e-26     4e-24       1      54 [.      12      65 .]      12      65 .] 0.98

  Alignments for each domain:
  == domain 1  score: 84.1 bits;  conditional E-value: 1.3e-26
                                   -S--EEEEE-TTTS-EEEEESS-SS-EEESSSTCEEEEECSSSEEESSCEEEEE CS
                 Ribosomal_S27e  1 prskFldvkCpdCenetvvFshaatvvkCisCgkvLvePtGGkaklkaqilerl 54
                                   prskFl+++CpdC+n+ v++sha+t vkC +Cgk+LvePtGGka + a+ile+l
  gi|119719553|ref|YP_920048.1| 12 PRSKFLKIRCPDCGNILVTYSHASTKVKCPKCGKILVEPTGGKALIIAEILEVL 65
                                   89*************************************************985 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.1   0.00046      0.14       2      11 ..      18      28 ..      17      31 .. 0.81
   2 !   14.7   0.3   5.1e-05     0.015       2      14 ..      37      50 ..      36      51 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00046
                    zf-ribbon_3  2 tvrCPnCGa.p 11
                                   ++rCP CG+ +
  gi|119719553|ref|YP_920048.1| 18 KIRCPDCGNiL 28
                                   689*****955 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 5.1e-05
                    zf-ribbon_3  2 tvrCPnCGa.plss 14
                                   +v+CP+CG+ ++++
  gi|119719553|ref|YP_920048.1| 37 KVKCPKCGKiLVEP 50
                                   589******77876 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.1   3.2e-08   9.5e-06      69     110 ..      17      61 ..      10      63 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 3.2e-08
                                    -EEEETTTS-EEECHH..H.HHS-TTTSSS-EEEEESSSEEEEEE CS
                           HypA  69 vkvrCreCgkefelee..k.alrCpkCgsadveivsGeellvksi 110
                                    +k+rC +Cg+   + +  + +++CpkCg+  ve ++G+ l + +i
  gi|119719553|ref|YP_920048.1|  17 LKIRCPDCGNILVTYShaStKVKCPKCGKILVEPTGGKALIIAEI 61 
                                    689******9887554333688*******************9987 PP

>> DUF3797  Domain of unknown function (DUF3797)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.1   0.00027     0.081      14      30 ..      19      35 ..      14      39 .. 0.83
   2 !   12.5   0.1   0.00035      0.11      14      33 ..      38      58 ..      34      61 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00027
                        DUF3797 14 vqCPeCgNnkvlNsegk 30
                                   + CP+CgN+ v  s + 
  gi|119719553|ref|YP_920048.1| 19 IRCPDCGNILVTYSHAS 35
                                   57********9988876 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00035
                        DUF3797 14 vqCPeCgNnkvlNsegkv.ii 33
                                   v+CP+Cg + v   +gk  ii
  gi|119719553|ref|YP_920048.1| 38 VKCPKCGKILVEPTGGKAlII 58
                                   79************9997566 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0    0.0016      0.47      24      34 ..      17      27 ..       7      29 .. 0.81
   2 !   12.9   0.4   0.00027     0.082      24      34 ..      36      46 ..      32      48 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0016
                  zinc_ribbon_4 24 vkvrCskCghv 34
                                    k+rC+ Cg++
  gi|119719553|ref|YP_920048.1| 17 LKIRCPDCGNI 27
                                   58999999986 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00027
                  zinc_ribbon_4 24 vkvrCskCghv 34
                                   +kv+C+kCg++
  gi|119719553|ref|YP_920048.1| 36 TKVKCPKCGKI 46
                                   79******986 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.1    0.0024      0.72       2      11 ..      19      28 ..      19      30 .. 0.89
   2 !   11.6   0.5   0.00073      0.22       2      11 ..      38      47 ..      38      49 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0024
                         zf-ACC  2 tKCpsCgeml 11
                                   ++Cp Cg++l
  gi|119719553|ref|YP_920048.1| 19 IRCPDCGNIL 28
                                   79******98 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00073
                         zf-ACC  2 tKCpsCgeml 11
                                   +KCp+Cg +l
  gi|119719553|ref|YP_920048.1| 38 VKCPKCGKIL 47
                                   7******997 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0    0.0033      0.98       1       8 [.      20      27 ..      11      33 .. 0.78
   2 !   11.1   0.4   0.00083      0.25       1       9 [.      39      47 ..      39      50 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0033
                  zinc_ribbon_2  1 fCpnCGae 8 
                                   +Cp CG+ 
  gi|119719553|ref|YP_920048.1| 20 RCPDCGNI 27
                                   58888875 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00083
                  zinc_ribbon_2  1 fCpnCGael 9 
                                   +Cp+CG+ l
  gi|119719553|ref|YP_920048.1| 39 KCPKCGKIL 47
                                   799999966 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   5.1   3.7e-06    0.0011       1      35 [.      17      47 ..      17      48 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 3.7e-06
                  zinc_ribbon_5  1 LiirCpdCdtkFklvdsklKksgkkVrCakCaevF 35
                                   L irCpdC+    lv+        kV+C kC+++ 
  gi|119719553|ref|YP_920048.1| 17 LKIRCPDCGNI--LVTYS--HASTKVKCPKCGKIL 47
                                   78*******97..67766..699*********985 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.5   1.1e-05    0.0032       4      28 ..      21      44 ..      19      46 .. 0.92
   2 ?    7.2   0.1     0.015       4.5       4      15 ..      40      51 ..      38      57 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.1e-05
                                   ESTTTSBEEEEECSCCCEEEESSSS CS
                 RNA_POL_M_15KD  4 CpkCgNlLlpkedkegknfeCrqCg 28
                                   Cp+CgN L   +  ++k + C +Cg
  gi|119719553|ref|YP_920048.1| 21 CPDCGNILVTYSHASTK-VKCPKCG 44
                                   *********99999998.79****8 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.015
                                   ESTTTSBEEEEE CS
                 RNA_POL_M_15KD  4 CpkCgNlLlpke 15
                                   CpkCg  L  ++
  gi|119719553|ref|YP_920048.1| 40 CPKCGKILVEPT 51
                                   *****9886554 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0     0.012       3.5       2      12 ..      19      29 ..      18      33 .. 0.85
   2 !   12.1   0.7   0.00041      0.12       2      13 ..      38      49 ..      37      54 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.012
                                   EE-SSS--EEE CS
                 zf-C4_Topoisom  2 ekCPkCggdLv 12
                                   + CP Cg+ Lv
  gi|119719553|ref|YP_920048.1| 19 IRCPDCGNILV 29
                                   57*****9888 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00041
                                   EE-SSS--EEEE CS
                 zf-C4_Topoisom  2 ekCPkCggdLvl 13
                                   +kCPkCg+ Lv+
  gi|119719553|ref|YP_920048.1| 38 VKCPKCGKILVE 49
                                   79******9996 PP

>> IBR  IBR domain, a half RING-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.4   3.9e-06    0.0012      18      46 ..      18      45 ..       3      47 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 3.9e-06
                            IBR 18 lkwCprpdCeaiiekseg.cksvtCskCgf 46
                                   ++ Cp  dC++i+   ++ +++v+C+kCg+
  gi|119719553|ref|YP_920048.1| 18 KIRCP--DCGNILVTYSHaSTKVKCPKCGK 45
                                   789**..****99888886888******97 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.1     0.017         5       1      10 [.      20      29 ..      20      31 .. 0.80
   2 !   10.2   0.1     0.002      0.58       1      17 [.      39      55 ..      39      57 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.017
                 DNA_ligase_ZBD  1 hCPvCGsavv 10
                                   +CP CG  +v
  gi|119719553|ref|YP_920048.1| 20 RCPDCGNILV 29
                                   5*****7665 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.002
                 DNA_ligase_ZBD  1 hCPvCGsavvReegeai 17
                                   +CP CG  +v + g+ +
  gi|119719553|ref|YP_920048.1| 39 KCPKCGKILVEPTGGKA 55
                                   6********99888765 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   2.4   3.1e-05    0.0093      14      40 .]      17      44 ..      14      44 .. 0.87
   2 !    9.0   0.4    0.0052       1.5      17      32 ..      39      53 ..      36      56 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.1e-05
                  Auto_anti-p27 14 LaetCpvCgvPLmrdr.kggkvyCvaCd 40
                                   L   Cp+Cg +L+ +   ++kv C+ C+
  gi|119719553|ref|YP_920048.1| 17 LKIRCPDCGNILVTYShASTKVKCPKCG 44
                                   5667**********99868899*****6 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0052
                  Auto_anti-p27 17 tCpvCgvPLmrdrkgg 32
                                    Cp+Cg +L++  +gg
  gi|119719553|ref|YP_920048.1| 39 KCPKCGKILVEP-TGG 53
                                   6*********94.344 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.1     0.011       3.4      26      34 ..      18      26 ..       3      30 .. 0.74
   2 !   17.0   2.3   1.6e-05    0.0047       7      35 ..      20      47 ..      18      49 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.011
                    Zn-ribbon_8 26 ltaCPeCgs 34
                                   ++ CP+Cg 
  gi|119719553|ref|YP_920048.1| 18 KIRCPDCGN 26
                                   345999996 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 1.6e-05
                    Zn-ribbon_8  7 rCeeCghefevlqsisdaplta.CPeCgs.e 35
                                   rC +Cg   ++l++ s a+ ++ CP+Cg+  
  gi|119719553|ref|YP_920048.1| 20 RCPDCG---NILVTYSHASTKVkCPKCGKiL 47
                                   8*****...56666664455555*****844 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.2   6.9e-06    0.0021      14      38 ..      20      48 ..       6      52 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 6.9e-06
                            DZR 14 fCseCgtklkavaa...edrCpsCgek.v 38
                                    C++Cg+ l  +++   + +Cp+Cg+  v
  gi|119719553|ref|YP_920048.1| 20 RCPDCGNILVTYSHastKVKCPKCGKIlV 48
                                   59******999999999999****98744 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0    0.0079       2.4      11      19 ..      18      26 ..      12      29 .. 0.76
   2 !    8.2   0.0    0.0077       2.3      13      25 ..      39      51 ..      38      53 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0079
                        DUF35_N 11 gqrCpdCGt 19
                                     rCpdCG 
  gi|119719553|ref|YP_920048.1| 18 KIRCPDCGN 26
                                   569****95 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0077
                        DUF35_N 13 rCpdCGtvqfPPr 25
                                   +Cp+CG+  + P+
  gi|119719553|ref|YP_920048.1| 39 KCPKCGKILVEPT 51
                                   7*****9998886 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.1     0.012       3.4      24      33 .]      19      28 ..      13      28 .. 0.88
   2 !    8.7   0.0    0.0067         2      24      33 .]      38      47 ..      32      47 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.012
                                   EE-TTT--EE CS
                      zf-RING_7 24 vtCpeCGRIL 33
                                   ++Cp CG IL
  gi|119719553|ref|YP_920048.1| 19 IRCPDCGNIL 28
                                   79*****776 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0067
                                   EE-TTT--EE CS
                      zf-RING_7 24 vtCpeCGRIL 33
                                   v+Cp CG IL
  gi|119719553|ref|YP_920048.1| 38 VKCPKCGKIL 47
                                   89******98 PP

>> zinc_ribbon_6  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.5   9.5e-06    0.0028      20      54 ..       9      44 ..       3      45 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 9.5e-06
                  zinc_ribbon_6 20 peeyknkkvkilCnDCekksevkfhv.lglkCkeCg 54
                                    ++ ++k  ki C DC++   ++ h    +kC +Cg
  gi|119719553|ref|YP_920048.1|  9 IPQPRSKFLKIRCPDCGNILVTYSHAsTKVKCPKCG 44
                                   46677899***********99999972579*****7 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.3     1e-05     0.003      30      54 ..      20      45 ..      15      53 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1e-05
                 OrfB_Zn_ribbon 30 tCseCgsknke.alsgrtfkCpnCgf 54
                                   +C+ Cg ++ + + ++ ++kCp+Cg 
  gi|119719553|ref|YP_920048.1| 20 RCPDCGNILVTySHASTKVKCPKCGK 45
                                   79999999999999999999999996 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.1     0.011       3.3      19      24 .]      21      26 ..       8      26 .. 0.86
   2 !    9.9   0.2    0.0024      0.73      18      24 .]      39      45 ..      34      45 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.011
                        DUF1610 19 CPNCGE 24
                                   CP CG+
  gi|119719553|ref|YP_920048.1| 21 CPDCGN 26
                                   *****7 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0024
                        DUF1610 18 pCPNCGE 24
                                    CP+CG+
  gi|119719553|ref|YP_920048.1| 39 KCPKCGK 45
                                   6*****8 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   2.3   2.2e-05    0.0067       2      29 ..      20      47 ..      19      52 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.2e-05
                                   EETTTTCEECHEETSTTCEEESSSSBEE CS
                   TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGlVl 29
                                   +CP+Cg+  +++ ++++ + C++CG +l
  gi|119719553|ref|YP_920048.1| 20 RCPDCGNILVTYSHASTKVKCPKCGKIL 47
                                   7*****9878999999999******876 PP

>> Tmemb_55A  Transmembrane protein 55A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.3   1.4e-05    0.0041     137     176 ..       7      46 ..       2      52 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.4e-05
                      Tmemb_55A 137 pvspelqpvgvrviCghCkntflftelsrtlarCPhCrkv 176
                                    ++ p+++ +  ++ C  C n  +  +  +t  +CP+C k+
  gi|119719553|ref|YP_920048.1|   7 ALIPQPRSKFLKIRCPDCGNILVTYSHASTKVKCPKCGKI 46 
                                    56788899999*********99999999*********997 PP

>> Zn_Tnp_IS91  Transposase zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.3   1.6e-05    0.0049      37      66 ..      16      46 ..      11      54 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.6e-05
                    Zn_Tnp_IS91 37 faryeCeeCghekivyfsCksrh.CpsCqkk 66
                                   f +++C++Cg+  + y     +  Cp+C+k 
  gi|119719553|ref|YP_920048.1| 16 FLKIRCPDCGNILVTYSHASTKVkCPKCGKI 46
                                   66889*******999999888888****985 PP

>> zf-C2HC5  Putative zinc finger motif, C2HC5-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.5   3.9e-05     0.012      19      53 ..      20      56 ..      15      57 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.9e-05
                       zf-C2HC5 19 nClnCGkiiCakegls..kpCsfCgspllsseerqel 53
                                    C  CG+i+ +  + s   +C+ Cg+ l++++  ++l
  gi|119719553|ref|YP_920048.1| 20 RCPDCGNILVTYSHAStkVKCPKCGKILVEPTGGKAL 56
                                   69********9999888899******99998766655 PP

>> zf-LITAF-like  LITAF-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.1      0.01       3.1      56      69 ..      18      31 ..       9      32 .. 0.78
   2 ?    8.0   0.3     0.011       3.4       4      65 ..      36      46 ..      32      50 .. 0.58

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.01
                  zf-LITAF-like 56 ehyCpnCgallgty 69
                                   + +Cp Cg+ l ty
  gi|119719553|ref|YP_920048.1| 18 KIRCPDCGNILVTY 31
                                   66899999988887 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.011
                  zf-LITAF-like  4 tqvdCpaCqqrvvTsveyksgkltwllalllclfgcllccliPfcvdslkdvehyCpnCgal 65
                                   t+v                                                   +Cp+Cg+ 
  gi|119719553|ref|YP_920048.1| 36 TKV---------------------------------------------------KCPKCGKI 46
                                   445...................................................55555554 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.1    0.0068         2      18      24 ..      19      25 ..      15      29 .. 0.89
   2 ?    6.3   0.1     0.025       7.4      17      24 ..      37      44 ..      32      48 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0068
                                   ---SSS- CS
                 DNA_RNApol_7kD 18 iRCkeCG 24
                                   iRC +CG
  gi|119719553|ref|YP_920048.1| 19 IRCPDCG 25
                                   9*****9 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.025
                                   ----SSS- CS
                 DNA_RNApol_7kD 17 piRCkeCG 24
                                    ++C +CG
  gi|119719553|ref|YP_920048.1| 37 KVKCPKCG 44
                                   69*****9 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0    0.0067         2      21      30 ..      18      27 ..      17      28 .. 0.85
   2 ?    5.2   0.1     0.056        17      23      28 ..      39      44 ..      32      46 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0067
                  zf-NADH-PPase 21 arvCpaCgle 30
                                   + +Cp+Cg++
  gi|119719553|ref|YP_920048.1| 18 KIRCPDCGNI 27
                                   679*****86 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.056
                  zf-NADH-PPase 23 vCpaCg 28
                                    Cp Cg
  gi|119719553|ref|YP_920048.1| 39 KCPKCG 44
                                   566666 PP

>> zf-HIT  HIT zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.082        24      13      20 ..      18      25 ..      14      28 .. 0.82
   2 ?    8.8   0.2    0.0049       1.5      12      20 ..      36      44 ..      33      47 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.082
                                   SEE-TTT- CS
                         zf-HIT 13 kYkCpkCn 20
                                   k +Cp C+
  gi|119719553|ref|YP_920048.1| 18 KIRCPDCG 25
                                   789****8 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0049
                                   -SEE-TTT- CS
                         zf-HIT 12 akYkCpkCn 20
                                    k kCpkC+
  gi|119719553|ref|YP_920048.1| 36 TKVKCPKCG 44
                                   589*****8 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   3.8   0.00049      0.15      19      45 ..      19      45 ..      12      46 .. 0.90
   2 ?    7.6   0.6     0.012       3.6      18      26 ..      37      45 ..      34      52 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00049
                  Zn_Tnp_IS1595 19 fvCPhCgsr.kayriktrglfqCkeCrk 45
                                    +CP Cg+    y+ ++  + +C +C+k
  gi|119719553|ref|YP_920048.1| 19 IRCPDCGNIlVTYSHAS-TKVKCPKCGK 45
                                   68*******99999998.9*******86 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.012
                  Zn_Tnp_IS1595 18 gfvCPhCgs 26
                                   ++ CP+Cg+
  gi|119719553|ref|YP_920048.1| 37 KVKCPKCGK 45
                                   578*****6 PP

>> zf-FPG_IleRS  Zinc finger found in FPG and IleRS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0    0.0084       2.5       3      17 ..      20      34 ..      18      37 .. 0.87
   2 ?    6.0   0.3     0.037        11       3      12 ..      39      48 ..      39      51 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0084
                                   B-TTT--BBEEEECT CS
                   zf-FPG_IleRS  3 pCpRCwryiervgqa 17
                                   +Cp C++++++ ++a
  gi|119719553|ref|YP_920048.1| 20 RCPDCGNILVTYSHA 34
                                   7*********99986 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.037
                                   B-TTT--BBE CS
                   zf-FPG_IleRS  3 pCpRCwryie 12
                                   +Cp C+ +++
  gi|119719553|ref|YP_920048.1| 39 KCPKCGKILV 48
                                   8*****9876 PP

>> zf-IS66  zinc-finger binding domain of transposase IS66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.2     0.033        10       3      10 ..      20      28 ..      18      39 .. 0.77
   2 ?    9.1   0.3    0.0055       1.6       3      17 ..      39      54 ..      37      64 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.033
                        zf-IS66  3 tCpcCGg.l 10
                                    Cp+CG  l
  gi|119719553|ref|YP_920048.1| 20 RCPDCGNiL 28
                                   599**9866 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0055
                        zf-IS66  3 tCpcCGg.llkpiged 17
                                   +Cp+CG+ l+ p g++
  gi|119719553|ref|YP_920048.1| 39 KCPKCGKiLVEPTGGK 54
                                   5*****9998888876 PP

>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.3    0.0015      0.44      14      28 ..      35      49 ..      10      57 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0015
                                   SS--EETTTTEE--- CS
                         zf-BED 14 eqkavCryCgkilsr 28
                                   ++k++C  Cgkil  
  gi|119719553|ref|YP_920048.1| 35 STKVKCPKCGKILVE 49
                                   79**********975 PP

>> zinc_ribbon_12  Probable zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0      0.02       5.9      26      41 ..      13      28 ..       6      31 .. 0.81
   2 ?    6.6   0.2     0.023       6.8      28      41 ..      34      47 ..      28      49 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.02
                 zinc_ribbon_12 26 kkkqqklrCGaCsevl 41
                                   + k  k+rC  C ++l
  gi|119719553|ref|YP_920048.1| 13 RSKFLKIRCPDCGNIL 28
                                   557889******9998 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.023
                 zinc_ribbon_12 28 kqqklrCGaCsevl 41
                                     +k++C +C ++l
  gi|119719553|ref|YP_920048.1| 34 ASTKVKCPKCGKIL 47
                                   5789******9998 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1     0.095        28       4      10 ..      20      26 ..      18      31 .. 0.83
   2 ?    8.2   0.1    0.0062       1.9       3      12 ..      38      47 ..      36      51 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.095
                         zf_UBZ  4 lCerCgk 10
                                    C++Cg 
  gi|119719553|ref|YP_920048.1| 20 RCPDCGN 26
                                   7****96 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0062
                         zf_UBZ  3 ylCerCgkei 12
                                   + C++Cgk +
  gi|119719553|ref|YP_920048.1| 38 VKCPKCGKIL 47
                                   78*****976 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   0.00018     0.053     104     134 ..      19      48 ..      11      53 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00018
                        TackOD1 104 ihhftCgnvgpeeeflkegkleCpkCktkLr 134
                                    i + +Cgn+ ++ +   + k++CpkC + L 
  gi|119719553|ref|YP_920048.1|  19 IRCPDCGNILVTYSHAST-KVKCPKCGKILV 48 
                                    566677777666555443.477777766554 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1     0.035        11       2       8 ..      20      29 ..      19      36 .. 0.65
   2 ?    6.4   0.2     0.045        13       2       9 ..      39      46 ..      38      50 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.035
                                   EETTTT...E CS
                        zf-C2H2  2 kCpdCg...k 8 
                                   +CpdCg    
  gi|119719553|ref|YP_920048.1| 20 RCPDCGnilV 29
                                   8*****4433 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.045
                                   EETTTTEE CS
                        zf-C2H2  2 kCpdCgks 9 
                                   kCp+Cgk 
  gi|119719553|ref|YP_920048.1| 39 KCPKCGKI 46
                                   8*****95 PP

>> DUF1922  Domain of unknown function (DUF1922)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.3   0.00018     0.054       4      29 ..      19      47 ..      16      56 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00018
                                   EEE.TTS--E..EEETT-SEEEETTTEEE CS
                        DUF1922  4 fRC.dCGRvl..YakegaktrkCvCGkti 29
                                    RC dCG  l  Y++ ++k++   CGk +
  gi|119719553|ref|YP_920048.1| 19 IRCpDCGNILvtYSHASTKVKCPKCGKIL 47
                                   69966**98756888888887778**975 PP

>> Mu-like_Com  Mu-like prophage protein Com
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   6.7    0.0022      0.65       5      32 ..      19      45 ..      18      47 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0022
                    Mu-like_Com  5 lRCGeCaRLLaKaeAlDeltiKCPRCGt 32
                                   +RC +C  +L         ++KCP+CG 
  gi|119719553|ref|YP_920048.1| 19 IRCPDCGNILVTYSHAS-TKVKCPKCGK 45
                                   8*****99988755555.6********6 PP

>> Zn_ribbon_recom  Recombinase zinc beta ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.1    0.0083       2.5       5      16 ..      18      29 ..      17      37 .. 0.78
   2 ?    6.0   0.2     0.057        17       4      15 ..      36      47 ..      34      54 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0083
                Zn_ribbon_recom  5 llrCgeCGspmt 16
                                   ++rC +CG+ ++
  gi|119719553|ref|YP_920048.1| 18 KIRCPDCGNILV 29
                                   79******9876 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.057
                Zn_ribbon_recom  4 GllrCgeCGspm 15
                                    +++C +CG+ +
  gi|119719553|ref|YP_920048.1| 36 TKVKCPKCGKIL 47
                                   689******866 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.3     0.059        18      23      29 ..      20      26 ..       5      29 .. 0.69
   2 ?    8.0   0.1     0.011       3.4      18      33 ..      33      49 ..      26      50 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.059
                  zinc_ribbon_9 23 lCPhCgg 29
                                    CP+Cg+
  gi|119719553|ref|YP_920048.1| 20 RCPDCGN 26
                                   6****97 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.011
                  zinc_ribbon_9 18 edsd.vlCPhCgggFVE 33
                                   + s  v CP Cg   VE
  gi|119719553|ref|YP_920048.1| 33 HASTkVKCPKCGKILVE 49
                                   3333247****986665 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.6   0.00054      0.16       2      25 ..      20      46 ..      19      51 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00054
                                   --SSS-S--EE-S...SEEE-TTT--E CS
                 zinc-ribbons_6  2 kCpeCqqelekrg...eqyhCeaCqed 25
                                    Cp+C + l++ +   ++++C +C + 
  gi|119719553|ref|YP_920048.1| 20 RCPDCGNILVTYShasTKVKCPKCGKI 46
                                   699999999866556689999999875 PP

>> zf-tcix  Putative treble-clef, zinc-finger, Zn-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1     0.062        19      12      18 ..      20      26 ..      16      28 .. 0.85
   2 ?    7.9   0.6    0.0077       2.3      12      18 ..      39      45 ..      38      47 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.062
                        zf-tcix 12 kCpkCGt 18
                                   +Cp CG 
  gi|119719553|ref|YP_920048.1| 20 RCPDCGN 26
                                   5*****6 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0077
                        zf-tcix 12 kCpkCGt 18
                                   kCpkCG 
  gi|119719553|ref|YP_920048.1| 39 KCPKCGK 45
                                   9*****5 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.1     0.012       3.7      34      46 ..      15      27 ..      11      34 .. 0.83
   2 ?    5.9   0.4     0.041        12      37      45 ..      37      45 ..      31      51 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.012
                           CpXC 34 slfeatCpkCgat 46
                                   ++++++Cp+Cg+ 
  gi|119719553|ref|YP_920048.1| 15 KFLKIRCPDCGNI 27
                                   7899******975 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.041
                           CpXC 37 eatCpkCga 45
                                   +++CpkCg+
  gi|119719553|ref|YP_920048.1| 37 KVKCPKCGK 45
                                   678888887 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.1      0.01         3      13      23 ..      15      25 ..       2      35 .. 0.75
   2 ?    6.2   0.5     0.038        11      12      23 ..      33      44 ..      28      47 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.01
                       zf-Mss51 13 khvdfeCpdCG 23
                                   k  ++ CpdCG
  gi|119719553|ref|YP_920048.1| 15 KFLKIRCPDCG 25
                                   557899***** PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.038
                       zf-Mss51 12 pkhvdfeCpdCG 23
                                   +++ +++Cp+CG
  gi|119719553|ref|YP_920048.1| 33 HASTKVKCPKCG 44
                                   577899*****9 PP

>> DUF2752  Protein of unknown function (DUF2752)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1     0.053        16       5      16 ..      15      26 ..      12      32 .. 0.84
   2 ?    6.9   0.1     0.021       6.3       4      15 ..      33      44 ..      30      46 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.053
                        DUF2752  5 altGipCPGCGl 16
                                   ++  i CP CG 
  gi|119719553|ref|YP_920048.1| 15 KFLKIRCPDCGN 26
                                   67899******5 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.021
                        DUF2752  4 kaltGipCPGCG 15
                                   +a t ++CP CG
  gi|119719553|ref|YP_920048.1| 33 HASTKVKCPKCG 44
                                   6789*******9 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1      0.31        92      15      21 ..      19      25 ..       8      27 .. 0.79
   2 ?    9.2   0.4    0.0057       1.7      13      22 ..      36      45 ..      29      46 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.31
                      zf-H2C2_2 15 yeCplCd 21
                                     Cp C+
  gi|119719553|ref|YP_920048.1| 19 IRCPDCG 25
                                   69****7 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0057
                      zf-H2C2_2 13 kpyeCplCdk 22
                                   ++++Cp+C+k
  gi|119719553|ref|YP_920048.1| 36 TKVKCPKCGK 45
                                   679*****98 PP

>> YacG  DNA gyrase inhibitor YacG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.069        20       1       9 [.      19      27 ..      19      37 .. 0.72
   2 ?    6.7   0.4      0.02         6       1       8 [.      38      45 ..      38      52 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.069
                           YacG  1 vkCPtCkke 9 
                                   ++CP C++ 
  gi|119719553|ref|YP_920048.1| 19 IRCPDCGNI 27
                                   68****985 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.02
                           YacG  1 vkCPtCkk 8 
                                   vkCP+C+k
  gi|119719553|ref|YP_920048.1| 38 VKCPKCGK 45
                                   89****98 PP

>> zf-ISL3  zinc-finger of transposase IS204/IS1001/IS1096/IS1165
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.1    0.0057       1.7       3      18 ..      19      35 ..      18      39 .. 0.79
   2 ?    5.0   1.0      0.13        38       3      10 ..      38      45 ..      36      54 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0057
                        zf-ISL3  3 hrCPnCgsk.tvvkhgk 18
                                   +rCP Cg+  + + h +
  gi|119719553|ref|YP_920048.1| 19 IRCPDCGNIlVTYSHAS 35
                                   79******988899985 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.13
                        zf-ISL3  3 hrCPnCgs 10
                                    +CP+Cg+
  gi|119719553|ref|YP_920048.1| 38 VKCPKCGK 45
                                   68****97 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1     0.015       4.5       8      16 ..      20      28 ..      15      35 .. 0.86
   2 ?    5.8   0.4     0.034        10       7      16 ..      38      47 ..      32      57 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.015
                                   E-TTT--EE CS
                Desulfoferrod_N  8 kCevCGniV 16
                                   +C  CGni 
  gi|119719553|ref|YP_920048.1| 20 RCPDCGNIL 28
                                   9******96 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.034
                                   EE-TTT--EE CS
                Desulfoferrod_N  7 YkCevCGniV 16
                                    kC  CG i 
  gi|119719553|ref|YP_920048.1| 38 VKCPKCGKIL 47
                                   59******95 PP

>> Nop10p  Nucleolar RNA-binding protein, Nop10p family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   1.7     0.036        11      18      26 ..      19      29 ..      16      54 .. 0.53

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.036
                                   SB-TTT-S..B CS
                         Nop10p 18 kvcpecgg..p 26
                                    +cp+cg+   
  gi|119719553|ref|YP_920048.1| 19 IRCPDCGNilV 29
                                   55555555221 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1     0.079        24      21      26 ..      20      25 ..       6      29 .. 0.68
   2 ?    6.4   4.4     0.018       5.5       2      26 ..      21      44 ..      20      44 .. 0.88
   3 ?    6.2   0.8     0.021       6.4       1       9 [.      39      47 ..      39      57 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.079
                       zf-TFIIB 21 yCpqCr 26
                                   +Cp+C+
  gi|119719553|ref|YP_920048.1| 20 RCPDCG 25
                                   777776 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.018
                       zf-TFIIB  2 CPkCqdeleeserggveidyCpqCr 26
                                   CP C++ l+++ +   ++ +Cp+C+
  gi|119719553|ref|YP_920048.1| 21 CPDCGNILVTYSHASTKV-KCPKCG 44
                                   ***********9999888.599997 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.021
                       zf-TFIIB  1 kCPkCqdel 9 
                                   kCPkC+  l
  gi|119719553|ref|YP_920048.1| 39 KCPKCGKIL 47
                                   7****8655 PP

>> DUF951  Bacterial protein of unknown function (DUF951)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1     0.049        15      29      41 ..      17      29 ..      14      34 .. 0.87
   2 ?    6.2   0.2     0.033       9.7      27      40 ..      34      47 ..      28      51 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.049
                         DUF951 29 iklkClgcgrevm 41
                                   +k++C +cg++++
  gi|119719553|ref|YP_920048.1| 17 LKIRCPDCGNILV 29
                                   59*******9875 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.033
                         DUF951 27 adiklkClgcgrev 40
                                   a  k+kC +cg+++
  gi|119719553|ref|YP_920048.1| 34 ASTKVKCPKCGKIL 47
                                   678********986 PP

>> HECT_2  HECT-like Ubiquitin-conjugating enzyme (E2)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.5    0.0075       2.2     111     126 ..      34      49 ..       4      57 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0075
                         HECT_2 111 aetslrCrsCknvllk 126
                                    a+t+++C +C+++l++
  gi|119719553|ref|YP_920048.1|  34 ASTKVKCPKCGKILVE 49 
                                    1356666666666665 PP

>> zf_C2H2_10  C2H2 type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1      0.18        53       5      12 ..      21      28 ..      18      28 .. 0.84
   2 ?    8.0   0.8    0.0067         2       5      12 ..      40      47 ..      37      48 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.18
                     zf_C2H2_10  5 CPKCqekl 12
                                   CP C+ +l
  gi|119719553|ref|YP_920048.1| 21 CPDCGNIL 28
                                   ****9876 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0067
                     zf_C2H2_10  5 CPKCqekl 12
                                   CPKC+ +l
  gi|119719553|ref|YP_920048.1| 40 CPKCGKIL 47
                                   ****9876 PP

>> zf-C2H2_3  zinc-finger of acetyl-transferase ESCO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1      0.02       5.9       9      20 ..      14      25 ..      12      36 .. 0.83
   2 ?    5.0   1.3     0.074        22      12      20 ..      36      44 ..      29      46 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.02
                      zf-C2H2_3  9 ksfgasqCkeCg 20
                                   ++f + +C+ Cg
  gi|119719553|ref|YP_920048.1| 14 SKFLKIRCPDCG 25
                                   789999*****9 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.074
                      zf-C2H2_3 12 gasqCkeCg 20
                                   ++++C++Cg
  gi|119719553|ref|YP_920048.1| 36 TKVKCPKCG 44
                                   3477****8 PP

>> Zn_Tnp_IS1  InsA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1      0.17        49       5      11 ..      18      24 ..      17      30 .. 0.83
   2 ?    8.0   0.1    0.0076       2.3       2      11 ..      34      43 ..      33      48 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.17
                     Zn_Tnp_IS1  5 sihCPrC 11
                                    i CP C
  gi|119719553|ref|YP_920048.1| 18 KIRCPDC 24
                                   5899999 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0076
                     Zn_Tnp_IS1  2 AsVsihCPrC 11
                                   As  + CP+C
  gi|119719553|ref|YP_920048.1| 34 ASTKVKCPKC 43
                                   899******* PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.2     0.089        26      15      22 ..      20      27 ..      18      35 .. 0.87
   2 ?    7.8   0.7     0.011       3.2      15      25 ..      39      49 ..      29      51 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.089
                           YhfH 15 kCteCGke 22
                                    C++CG+ 
  gi|119719553|ref|YP_920048.1| 20 RCPDCGNI 27
                                   5*****85 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.011
                           YhfH 15 kCteCGkeieE 25
                                   kC++CGk + E
  gi|119719553|ref|YP_920048.1| 39 KCPKCGKILVE 49
                                   7*****98765 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   5.3       0.3        91       2       7 ..      39      44 ..      19      47 .. 0.54

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.3
                        TFIIS_C  2 kCpkCg 7 
                                   kCpkCg
  gi|119719553|ref|YP_920048.1| 39 KCPKCG 44
                                   344444 PP

>> Anti-TRAP  Tryptophan RNA-binding attenuator protein inhibitory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.2      0.36   1.1e+02      31      37 ..      19      25 ..       9      32 .. 0.78
   2 ?    7.9   4.0    0.0099         3      12      50 ..      20      56 ..      15      59 .. 0.61

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.36
                                   .E-TTTT CS
                      Anti-TRAP 31 leCPkCs 37
                                   + CP+C+
  gi|119719553|ref|YP_920048.1| 19 IRCPDCG 25
                                   6899996 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0099
                                   E-TTTTTTSEETTE........E-TTTTTSSEEE-HHHHHH CS
                      Anti-TRAP 12 kCdaCngsGkiepe..eprasleCPkCsGkglipTaqGqkL 50
                                    C+ C   G+i  +     + ++CPkC+   + pT  G+ L
  gi|119719553|ref|YP_920048.1| 20 RCPDC---GNILVTysHASTKVKCPKCGKILVEPT-GGKAL 56
                                   55555...66655543356679*****65444444.56555 PP

>> zf-CCHC_6  Zinc knuckle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0         4   1.2e+03      24      32 ..       4      12 ..       1      15 [. 0.59
   2 ?    4.9   0.2     0.079        23       1       9 [.      18      26 ..      18      27 .. 0.86
   3 ?    4.8   2.0     0.086        26       1       8 [.      37      44 ..      37      46 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 4
                      zf-CCHC_6 24 wngalvpqp 32
                                     +al pqp
  gi|119719553|ref|YP_920048.1|  4 ERKALIPQP 12
                                   345666666 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.079
                      zf-CCHC_6  1 rvKCknCGA 9 
                                   +++C +CG 
  gi|119719553|ref|YP_920048.1| 18 KIRCPDCGN 26
                                   79******6 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.086
                      zf-CCHC_6  1 rvKCknCG 8 
                                   +vKC +CG
  gi|119719553|ref|YP_920048.1| 37 KVKCPKCG 44
                                   8******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                       135  (0.0075297); expected 17.9 (0.001)
Passed Fwd filter:                        60  (0.00334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              60  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.55
# Mc/sec: 355.68
//
Query:       gi|119719554|ref|YP_920049.1|  [L=95]
Description: 50S ribosomal protein L44e [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-27   95.7  12.3    1.6e-27   95.7  12.3    1.4  2  Ribosomal_L44  Ribosomal protein L44
     0.0028   17.5   3.6      0.051   13.4   0.4    2.4  2  zf-FPG_IleRS   Zinc finger found in FPG and IleRS
  ------ inclusion threshold ------
      0.015   15.4   6.4          1    9.4   1.1    2.1  2  CxC5           CxC5 like cysteine cluster associated with KDZ
      0.036   14.0   4.2       0.59   10.1   0.4    2.3  2  zinc_ribbon_4  zinc-ribbon domain
      0.036   13.9   1.0       0.12   12.3   0.1    2.0  2  C1_1           Phorbol esters/diacylglycerol binding domain (
      0.039   14.0   2.3        0.2   11.7   0.3    2.2  2  Rubredoxin     Rubredoxin
      0.073   13.2   0.2       0.25   11.5   0.0    1.8  2  PHD_4          PHD-finger
       0.12   11.9   3.1       0.29   10.7   0.3    2.2  2  RecR           RecR protein
       0.19   11.8   2.4        5.9    7.0   0.2    2.1  2  CpXC           CpXC protein
       0.19   11.5   3.2        1.7    8.4   0.3    2.2  2  Rubredoxin_2   Rubredoxin metal binding domain
       0.25   11.7   5.1       0.61   10.4   5.1    1.7  1  Rpr2           RNAse P Rpr2/Rpp21/SNM1 subunit domain
        0.3   11.0   3.0        0.7    9.8   0.3    2.2  2  zf-C2H2_3      zinc-finger of acetyl-transferase ESCO
       0.63   10.2   4.6          3    8.0   4.9    1.9  1  zf-Mss51       Zinc-finger of mitochondrial splicing suppress


Domain annotation for each model (and alignments):
>> Ribosomal_L44  Ribosomal protein L44
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       3.4   4.7e+03      51      60 ..       6      15 ..       5      16 .. 0.71
   2 !   95.7  12.3   1.2e-30   1.6e-27       1      76 []      16      91 ..      16      91 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 3.4
                                   -EEEEETTT- CS
                  Ribosomal_L44 51 vlrleCteCk 60
                                   v+r  C  Ck
  gi|119719554|ref|YP_920049.1|  6 VIRTYCPRCK 15
                                   5677788887 PP

  == domain 2  score: 95.7 bits;  conditional E-value: 1.2e-30
                                   EEEEEEEEE-------SSSHHHHHHHH.H-SSSGGGGS----.--SSBB--EEEEETTT--EEE----BBS--EEE CS
                  Ribosomal_L44  1 kHtehkveqykkgkdselaqgkRrydrkqsgygGqtkpvfkkkaKttKKivlrleCteCkkkrlkalkRakkfelv 76
                                   ++teh+v+ yk+gk+++la+g+Rry rkq+gyg+++kp +k++aK+tKK vl+l+C+ C+++ +k+++R+kk+e+v
  gi|119719554|ref|YP_920049.1| 16 TYTEHEVTLYKAGKRRTLAEGQRRYLRKQKGYGSKRKPEQKRTAKVTKKQVLKLKCKVCGYTYHKEGIRLKKLEIV 91
                                   69************************************************************************96 PP

>> zf-FPG_IleRS  Zinc finger found in FPG and IleRS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.4   3.7e-05     0.051       4      15 ..      11      22 ..      11      24 .. 0.94
   2 ?    4.6   0.2     0.022        30       2      16 ..      69      83 ..      68      87 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.7e-05
                                   -TTT--BBEEEE CS
                   zf-FPG_IleRS  4 CpRCwryiervg 15
                                   CpRC++y+e+++
  gi|119719554|ref|YP_920049.1| 11 CPRCKTYTEHEV 22
                                   *********998 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.022
                                   SB-TTT--BBEEEEC CS
                   zf-FPG_IleRS  2 epCpRCwryiervgq 16
                                    +C +C+ +  ++g+
  gi|119719554|ref|YP_920049.1| 69 LKCKVCGYTYHKEGI 83
                                   59****977777765 PP

>> CxC5  CxC5 like cysteine cluster associated with KDZ transposases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   1.1   0.00075         1      46      82 ..       6      44 ..       2      52 .. 0.75
   2 ?    9.2   0.6   0.00091       1.3      41      61 ..      61      81 ..      44      90 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00075
                           CxC5 46 vlslyCpkCktrYypdyyvhdg..vrtYyggspkylqvg 82
                                   v+ +yCp+Ckt   ++ + +++   rt  +g+ +yl+ +
  gi|119719554|ref|YP_920049.1|  6 VIRTYCPRCKTYTEHEVTLYKAgkRRTLAEGQRRYLRKQ 44
                                   6789*******8777777665556777778888887654 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00091
                           CxC5 41 vlpvwvlslyCpkCktrYypd 61
                                   v + +vl l+C+ C+ +Y+ +
  gi|119719554|ref|YP_920049.1| 61 VTKKQVLKLKCKVCGYTYHKE 81
                                   555689*************86 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.3     0.014        19       3      10 ..       9      16 ..       8      18 .. 0.83
   2 ?   10.1   0.4   0.00043      0.59      18      34 ..      60      77 ..      57      79 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.014
                  zinc_ribbon_4  3 itCpsCka 10
                                   + Cp+Ck+
  gi|119719554|ref|YP_920049.1|  9 TYCPRCKT 16
                                   67999997 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00043
                  zinc_ribbon_4 18 klpakgv.kvrCskCghv 34
                                   k+++k v k++C+ Cg +
  gi|119719554|ref|YP_920049.1| 60 KVTKKQVlKLKCKVCGYT 77
                                   77766666*******987 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.1      0.61   8.5e+02      12      19 ..       9      16 ..       7      26 .. 0.72
   2 ?   12.3   0.1   8.6e-05      0.12      28      41 ..      68      81 ..      58      89 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.61
                                   -B-TTT-S CS
                           C1_1 12 tfCkhCge 19
                                   t+C  C+ 
  gi|119719554|ref|YP_920049.1|  9 TYCPRCKT 16
                                   67777765 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 8.6e-05
                                   EEEETTT--EE-CC CS
                           C1_1 28 glkCswCkllvHkk 41
                                    lkC++C++++Hk+
  gi|119719554|ref|YP_920049.1| 68 KLKCKVCGYTYHKE 81
                                   589*********96 PP

>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1      0.16   2.2e+02      37      42 ..      11      16 ..       8      20 .. 0.80
   2 ?   11.7   0.3   0.00014       0.2       1      13 [.      68      80 ..      68      84 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.16
                                   BTTTB- CS
                     Rubredoxin 37 CPdCgv 42
                                   CP C+ 
  gi|119719554|ref|YP_920049.1| 11 CPRCKT 16
                                   ****86 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00014
                                   EEEETTT-BEEET CS
                     Rubredoxin  1 kyeCkvCgyvYdp 13
                                   k++CkvCgy Y  
  gi|119719554|ref|YP_920049.1| 68 KLKCKVCGYTYHK 80
                                   679********76 PP

>> PHD_4  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.98   1.4e+03      64      67 ..      11      14 ..       7      35 .. 0.69
   2 ?   11.5   0.0   0.00018      0.25      17      50 ..      55      88 ..      44      94 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.98
                          PHD_4 64 CpkC 67
                                   Cp+C
  gi|119719554|ref|YP_920049.1| 11 CPRC 14
                                   5555 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00018
                          PHD_4 17 devveeesetpsslmeCsvCyeivHpeClkekeg 50
                                   ++ +++ ++++   + C+vC  + H+e ++ k+ 
  gi|119719554|ref|YP_920049.1| 55 QKRTAKVTKKQVLKLKCKVCGYTYHKEGIRLKKL 88
                                   3333444566666789***********9998654 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.3   0.00021      0.29      17      30 ..       9      22 ..       8      22 .. 0.90
   2 ?    1.4   0.1      0.17   2.4e+02      18      23 ..      70      75 ..      68      80 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00021
                                   EE-TTT--EESSSS CS
                           RecR 17 rhCsrCgnlteedl 30
                                   ++C+rC ++te+++
  gi|119719554|ref|YP_920049.1|  9 TYCPRCKTYTEHEV 22
                                   59*********985 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.17
                                   E-TTT- CS
                           RecR 18 hCsrCg 23
                                    C++Cg
  gi|119719554|ref|YP_920049.1| 70 KCKVCG 75
                                   599998 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.2     0.024        33       3      16 ..      11      24 ..       9      39 .. 0.69
   2 ?    7.0   0.2    0.0042       5.9      25      48 ..      56      79 ..      45      83 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.024
                           CpXC  3 CpaCgkefeaeiwt 16
                                   Cp+C++ +e e+  
  gi|119719554|ref|YP_920049.1| 11 CPRCKTYTEHEVTL 24
                                   88888888877643 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0042
                           CpXC 25 elkeklldgslfeatCpkCgatak 48
                                   +  +k+ ++++++ +C  Cg+t +
  gi|119719554|ref|YP_920049.1| 56 KRTAKVTKKQVLKLKCKVCGYTYH 79
                                   445799**************9865 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.2     0.044        61      17      22 ..      11      16 ..      10      17 .. 0.84
   2 ?    8.4   0.3    0.0012       1.7       3      12 ..      71      80 ..      70      80 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.044
                   Rubredoxin_2 17 CpsCgs 22
                                   Cp C++
  gi|119719554|ref|YP_920049.1| 11 CPRCKT 16
                                   ****97 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0012
                   Rubredoxin_2  3 CsqCGfesak 12
                                   C+ CG++++k
  gi|119719554|ref|YP_920049.1| 71 CKVCGYTYHK 80
                                   ********97 PP

>> Rpr2  RNAse P Rpr2/Rpp21/SNM1 subunit domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   5.1   0.00044      0.61      41      90 .]       4      75 ..       1      75 [. 0.69

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00044
                                   STCCCTB-TTT--B--CTTTEEEEE......................E-SSS-E..................EEEEETTTT CS
                           Rpr2 41 psvkrtvCkkCgsvlipgvtcsvrv......................enkskkkkkkkkka.........dvlvvtClaCg 90
                                   psv rt+C +C+++   +vt                           ++++         +         +vl+ +C+ Cg
  gi|119719554|ref|YP_920049.1|  4 PSVIRTYCPRCKTYTEHEVTLYKAGkrrtlaegqrrylrkqkgygskRKPE---------QkrtakvtkkQVLKLKCKVCG 75
                                   7889*********99888888766666667777777776555554442233.........14444555559999******7 PP

>> zf-C2H2_3  zinc-finger of acetyl-transferase ESCO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.2      0.19   2.6e+02      14      20 ..       9      15 ..       2      22 .. 0.71
   2 ?    9.8   0.3   0.00051       0.7       9      25 ..      64      80 ..      55      82 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.19
                      zf-C2H2_3 14 sqCkeCg 20
                                   + C+ C+
  gi|119719554|ref|YP_920049.1|  9 TYCPRCK 15
                                   34****8 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00051
                      zf-C2H2_3  9 ksfgasqCkeCgMvYnp 25
                                   k+  + +Ck+Cg +Y++
  gi|119719554|ref|YP_920049.1| 64 KQVLKLKCKVCGYTYHK 80
                                   4444456********86 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   4.9    0.0022         3       2      28 ..      11      80 ..      10      87 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0022
                       zf-Mss51  2 CPvpkhkqt...........................................apkhvdfeCpdCGiptyc 28
                                   CP +k+  +                                           +++  +++C+ CG+ ++ 
  gi|119719554|ref|YP_920049.1| 11 CPRCKTYTEhevtlykagkrrtlaegqrrylrkqkgygskrkpeqkrtakvtKKQVLKLKCKVCGYTYHK 80
                                   777765544667777777777777777777777777788888888888888788888**********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1184  (0.0660383); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 638.11
//
Query:       gi|119719555|ref|YP_920050.1|  [L=76]
Description: hypothetical protein Tpen_0645 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.064   13.3   0.2      0.088   12.9   0.2    1.1  1  Mis12     Mis12 protein


Domain annotation for each model (and alignments):
>> Mis12  Mis12 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   4.9e-06     0.088      26      67 ..      33      73 ..      28      74 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.9e-06
                                   HHHHHHHHHHH........TTSTHHHH-HHHHHHHHHHHHHH CS
                          Mis12 26 yravdavekvLdkkleedeeeekaaeesteeieeGtakletl 67
                                    +a+da+e++L+    + +   +++ee ++e+eeG+++l++l
  gi|119719555|ref|YP_920050.1| 33 VEALDAIEEFLT-SVGSATPRVEEDEELERELEEGVEELREL 73
                                   689********5.55555556888999************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       741  (0.0413297); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.30s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 495.95
//
Query:       gi|119719556|ref|YP_920051.1|  [L=708]
Description: hypothetical protein Tpen_0646 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (708 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 4977.45
//
Query:       gi|119719557|ref|YP_920052.1|  [L=433]
Description: elongation factor 1-alpha [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-53  181.3   0.0    1.6e-53  181.2   0.0    1.1  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    4.2e-37  126.9   0.0    9.5e-37  125.7   0.0    1.6  1  GTP_EFTU_D3  Elongation factor Tu C-terminal domain
    1.9e-17   63.4   0.9      4e-17   62.4   0.9    1.6  1  GTP_EFTU_D2  Elongation factor Tu domain 2
    7.8e-06   26.0   0.0    3.9e-05   23.7   0.0    2.2  1  MMR_HSR1     50S ribosome-binding GTPase
    2.2e-05   24.3   0.6    5.6e-05   23.0   0.6    1.6  1  GTP_EFTU_D4  Elongation factor Tu domain 4
  ------ inclusion threshold ------
      0.012   15.6   0.1       0.35   10.7   0.0    2.3  2  RsgA_GTPase  RsgA GTPase
      0.013   14.9   0.0      0.024   14.0   0.0    1.4  1  Gtr1_RagA    Gtr1/RagA G protein conserved region
       0.06   12.8   0.0        1.8    8.0   0.0    2.4  3  SRPRB        Signal recognition particle receptor beta subuni


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.2   0.0   7.1e-57   1.6e-53       1     182 [.       5     200 ..       5     327 .. 0.90

  Alignments for each domain:
  == domain 1  score: 181.2 bits;  conditional E-value: 7.1e-57
                                    TCEEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHH..HHHST.............HCHSHHHHHHTSCSSCEEEEEET CS
                       GTP_EFTU   1 krirnigiighvDhGKtTLtdrLlyktgaiskkgeka..eeerv.............lDtlkeErergiTiksaaislek 65 
                                    k+++n+++igh+DhGK+TL++rLly+ ga++ +  ++  e e +             lD+lkeEre+giTi+    ++e 
  gi|119719557|ref|YP_920052.1|   5 KPHLNLVVIGHIDHGKSTLMGRLLYEIGAVDPRLIQQyeE-E-AkkmgretwkyawvLDKLKEEREKGITIDLGFYKFE- 81 
                                    579*****************************99999532.3.33679999****************************. PP

                                    TCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTB.......STHHHHHHHHHHHHTTTE.EEEEEESCGST.. CS
                       GTP_EFTU  66 etkkylinliDtPGHvdFskevirglrvlDgavlvvdaveG.......vepqteevlrlalkegvp.iivfiNKmDrl.. 135
                                     tkky ++liD+PGH+dF+k++i+g++++D+a+lvv+a+eG       +  qt+e++ la+++gv  ++v+iNKmD +  
  gi|119719557|ref|YP_920052.1|  82 -TKKYFFTLIDAPGHRDFVKNMITGASQADVALLVVSAKEGefeagisPAGQTREHVFLAKTMGVDqLVVAINKMDTVny 160
                                    .*****************************************************************************99 PP

                                    .HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHH CS
                       GTP_EFTU 136 .kaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvk 182
                                     k++++ei++++ + l       + +g+k + e+p++++Sa++g +v+
  gi|119719557|ref|YP_920052.1| 161 sKERYEEIKNQLIRLL-------RMVGYKVD-EIPFIPTSAWEGVNVS 200
                                    9999999999999555.......88888885.9************997 PP

>> GTP_EFTU_D3  Elongation factor Tu C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.7   0.0   4.3e-40   9.5e-37       3     111 ..     321     427 ..     319     428 .. 0.97

  Alignments for each domain:
  == domain 1  score: 125.7 bits;  conditional E-value: 4.3e-40
                                    EEECCEEEEEEESSS..SS-BSTT-EEEEESSS-EEEEEEEEEEECCSSTTSB-BSS-SSCCSTT-CEEEEEEECCEEEE CS
                    GTP_EFTU_D3   3 kphtkfeAqvyilekerhtpitagYrpvlyirtadvtgkvveLlskldkktekvsekkpefvkpGdnvivevelikpial 82 
                                    + +++f+ ++ +l +  +t+i agY+pvl+i+ta+v ++++eLl+kld++t++v+e+kp+++k+Gd++iv+ +++kp+++
  gi|119719557|ref|YP_920052.1| 321 TVAEEFTGRIFVLYH--PTAIAAGYTPVLHIHTATVPVTFEELLQKLDPRTGSVAEEKPQYIKQGDSAIVRFKPRKPVVV 398
                                    6789***********..*************************************************************** PP

                                    --TTTHCCCCEEEEECTTCEEEEEEEEEE CS
                    GTP_EFTU_D3  83 ekgseypqlGrFaiReggrTvaaGvvtei 111
                                    ek+se+p+lGrFaiR+ grT+aaGvv ++
  gi|119719557|ref|YP_920052.1| 399 EKYSEFPPLGRFAIRDSGRTIAAGVVIDV 427
                                    **************************987 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.4   0.9   1.8e-20     4e-17       1      72 [.     247     312 ..     247     314 .. 0.94

  Alignments for each domain:
  == domain 1  score: 62.4 bits;  conditional E-value: 1.8e-20
                                    EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCE CS
                    GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdt 72 
                                    Gtv  grv++G+lk+Gd++ i  n+    + v++++s+et+h +++ea++g+n+G++v++++ ++ +++Gd+
  gi|119719557|ref|YP_920052.1| 247 GTVPVGRVETGVLKVGDKIII--NPP---KAVGEVKSIETHHTPLQEAIPGDNIGFNVKGVEKSQ-LRRGDV 312
                                    99*******************..874...358*********************************.9****9 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   1.7e-08   3.9e-05       2      87 ..      10     124 ..       9     179 .. 0.73

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.7e-08
                                    EEEEESTTSSHHHHHHHHH................T...............STEEESSSTTSSSSEEEEEEEETTEEEEE CS
                       MMR_HSR1   2 vaivGrpNvGKStLinalt................g...............ekaivsdkpgtTrdinegrvklkgkeiel 50 
                                     +++G+   GKStL+ +l+                +               +k + ++++g T+d  ++++++k+  ++l
  gi|119719557|ref|YP_920052.1|  10 LVVIGHIDHGKSTLMGRLLyeigavdprliqqyeeEakkmgretwkyawvlDKLKEEREKGITIDLGFYKFETKKYFFTL 89 
                                    689***************96666666655555555045555666666655568888999999999999999988899*** PP

                                    EECGGCSSHHHHHHHHHHHHHHHHCTSEEEEEEETT....T CS
                       MMR_HSR1  51 vDtpGliegaseekglgkaflaleeadlillvvdas....e 87 
                                    +D pG  +    +  +++ +    +ad++llvv+a+    e
  gi|119719557|ref|YP_920052.1|  90 IDAPG--H----RDFVKNMITGASQADVALLVVSAKegefE 124
                                    *****..3....23466666667779*******98844441 PP

>> GTP_EFTU_D4  Elongation factor Tu domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.6   2.5e-08   5.6e-05      20      72 ..     250     301 ..     232     312 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 2.5e-08
                                    EEEEEEEEEEEETT-EEEETTE.EEEEEEEEEETTEEESEEETT-EEEEEEES CS
                    GTP_EFTU_D4  20 ivGvevlgGvikpgvklikedGrevGeilqiqdkgkkleeakaGqevaisieg 72 
                                     vG +v +Gv+k+g k+i +  + vGe+++i++++  l+ea  G++++  ++g
  gi|119719557|ref|YP_920052.1| 250 PVG-RVETGVLKVGDKIIINPPKAVGEVKSIETHHTPLQEAIPGDNIGFNVKG 301
                                    588.9*******************************************99998 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.054   1.2e+02     103     122 ..      11      30 ..       4     101 .. 0.74
   2 ?   10.7   0.0   0.00016      0.35      13      73 ..     106     173 ..      88     189 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.054
                                    EEECSTTSSHHHHHHHHCTT CS
                    RsgA_GTPase 103 vlvGqSGvGKStLinallpe 122
                                    v++G+   GKStL+ +ll e
  gi|119719557|ref|YP_920052.1|  11 VVIGHIDHGKSTLMGRLLYE 30 
                                    78999999*****9999877 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00016
                                    EES--EEEEEEESTTTT--HH.....HHHHHHHHHHHTT-.EEEEEEE-GGG--HHH.HHHHHHHHHH CS
                    RsgA_GTPase  13 vaNvdqllivvslkepelsln.....lldrfLvlaeekgi.epvivlnKiDlleeee.eleelkeele 73 
                                    ++  d +l+vvs+ke e++       +    ++la++ g+ ++v+++nK+D ++ ++ ++ee+k++l 
  gi|119719557|ref|YP_920052.1| 106 ASQADVALLVVSAKEGEFEAGispagQTREHVFLAKTMGVdQLVVAINKMDTVNYSKeRYEEIKNQLI 173
                                    7788999*******99998652222256667888899999889999******9987765666655543 PP

>> Gtr1_RagA  Gtr1/RagA G protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.1e-05     0.024      32     161 ..      70     195 ..      62     197 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.1e-05
                      Gtr1_RagA  32 gatidveksevrflgnltlnlwDcgGqeafveeylssqkeeifrnvgvliyVfDvesreleedletlkeilealr..qys 109
                                    g+tid+   ++  +++  + l+D +G ++fv+++++       ++ +v + V+ +++ e+e  ++   ++ e++   ++ 
  gi|119719557|ref|YP_920052.1|  70 GITIDLGFYKF-ETKKYFFTLIDAPGHRDFVKNMITGA-----SQADVALLVVSAKEGEFEAGISPAGQTREHVFlaKTM 143
                                    56666666666.3567889**************86554.....5567778899999999*99999998888876511444 PP

                      Gtr1_RagA 110 peakvfvlihKmDliqedereeifeerkeeireeiekleke..eiqffaTSiwd 161
                                       ++ v i+KmD +  +  +e +ee+k+++++ ++ ++ +  ei f  TS w+
  gi|119719557|ref|YP_920052.1| 144 GVDQLVVAINKMDTV--NYSKERYEEIKNQLIRLLRMVGYKvdEIPFIPTSAWE 195
                                    45678999*******..667788999999999998866555559*********7 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.052   1.2e+02       6      29 ..      10      35 ..       5      61 .. 0.75
   2 ?    8.0   0.0   0.00081       1.8      45      72 ..      81     108 ..      65     120 .. 0.79
   3 ?   -3.3   0.0       2.2     5e+03     114     137 ..     147     172 ..     136     177 .. 0.66

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.052
                                   EEEE-STTSSHHHHHHHHHHS..S-- CS
                          SRPRB  6 vllvGlsdsGKTslftrLttd..svk 29
                                   ++++G  d GK +l+ rL+ +  +v 
  gi|119719557|ref|YP_920052.1| 10 LVVIGHIDHGKSTLMGRLLYEigAVD 35
                                   6899*************997644555 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00081
                                    ..GGTT-SEEEETT-GCCSHHHHHHHHH CS
                          SRPRB  45 sekgskltliDfPGheklrqklleklka 72 
                                    ++k+  +tliD PGh  + +++++   +
  gi|119719557|ref|YP_920052.1|  81 ETKKYFFTLIDAPGHRDFVKNMITGASQ 108
                                    5678889***********9999988443 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 2.2
                                    -EEEEEE-TTST.T---H.HHHHHHH CS
                          SRPRB 114 diliACnKqelf.laksp.klikdaL 137
                                    ++++A nK + +  +k+  + ik++L
  gi|119719557|ref|YP_920052.1| 147 QLVVAINKMDTVnYSKERyEEIKNQL 172
                                    57889999886513443224577776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2918.90
//
Query:       gi|119719558|ref|YP_920053.1|  [L=109]
Description: 30S ribosomal protein S10P [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.1e-24   84.3   0.0    5.9e-24   84.2   0.0    1.0  1  Ribosomal_S10  Ribosomal protein S10p/S20e
    0.00036   21.3   0.1    0.00072   20.3   0.1    1.5  2  PriA_C         Primosomal protein N C-terminal domain
  ------ inclusion threshold ------
      0.082   13.2   0.3         15    5.9   0.0    2.1  2  AlkA_N         AlkA N-terminal domain


Domain annotation for each model (and alignments):
>> Ribosomal_S10  Ribosomal protein S10p/S20e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.2   0.0   9.9e-28   5.9e-24       1      97 [.      13     106 ..      13     107 .. 0.98

  Alignments for each domain:
  == domain 1  score: 84.2 bits;  conditional E-value: 9.9e-28
                                    EEEEEESSHHHHHHHHHHHHHHTTSSS-EE---EEEEEEEEEEEEE--SS--.S--EEEEEEEEEEEEEEEE.E-HHHHH CS
                  Ribosomal_S10   1 rirlkSydsklLekavkkivraakelgikvkgpvplPtkrkrvtvlksphvd.kksreqfeirthkRlidisdatketid 79 
                                    rirl+S++ ++L+ ++++i ++a+++g+k++gp+plP kr rv +++ p+++  ++ ++fe+r+hkRlid+ da+++  +
  gi|119719558|ref|YP_920053.1|  13 RIRLSSTNIEDLNAVCEEIRQIAQKTGVKMRGPIPLPVKRMRVVTRRAPSGQgYETFDRFELRIHKRLIDL-DADERATR 91 
                                    8**********************************************************************.8******* PP

                                    HHS-...S---SS-EEEE CS
                  Ribosomal_S10  80 tllkllqlnlpegVsvev 97 
                                     ll+   +++p+ V ve+
  gi|119719558|ref|YP_920053.1|  92 LLLR---TRVPPTVRVEI 106
                                    ****...*********98 PP

>> PriA_C  Primosomal protein N C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.1   1.2e-07   0.00072       6      55 ..      12      57 ..      10      60 .. 0.91
   2 ?   -2.3   0.0       1.4   8.5e+03      79      92 ..      95     108 ..      79     108 .. 0.57

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.2e-07
                         PriA_C  6 alirvsgkdeekveeaaeelaellkealkleeveilgpapapiakikgry 55
                                   ++ir+s+++ e +++++ee++++ ++    ++v++ gp+p p+++++   
  gi|119719558|ref|YP_920053.1| 12 VRIRLSSTNIEDLNAVCEEIRQIAQK----TGVKMRGPIPLPVKRMRVVT 57
                                   79*********************999....6799***********98665 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.4
                         PriA_C  79 kleklkkvrvsiDv 92 
                                    +++  + vrv+i+v
  gi|119719558|ref|YP_920053.1|  95 RTRVPPTVRVEIEV 108
                                    33223367777765 PP

>> AlkA_N  AlkA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0    0.0026        16      57      81 ..      10      34 ..       4      36 .. 0.90
   2 ?    5.9   0.0    0.0026        15      79      99 ..      78      98 ..      51     105 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0026
                         AlkA_N 57 salkvrlslsdlraleaviarvrrl 81
                                   s +++rls++++++l+av +++r++
  gi|119719558|ref|YP_920053.1| 10 SKVRIRLSSTNIEDLNAVCEEIRQI 34
                                   578999*****************86 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0026
                         AlkA_N 79 rrllDLdadpeaieaaLdpll 99
                                   +rl+DLdad +a +  L+ ++
  gi|119719558|ref|YP_920053.1| 78 KRLIDLDADERATRLLLRTRV 98
                                   79*******998877775555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 742.46
//
Query:       gi|119719559|ref|YP_920054.1|  [L=200]
Description: ZPR1-related zinc finger protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-30  105.9   0.0    2.1e-30  105.7   0.0    1.1  1  zf-ZPR1          ZPR1 zinc-finger domain
  ------ inclusion threshold ------
      0.025   14.6   0.6       0.34   10.9   0.1    2.2  2  ADK_lid          Adenylate kinase, active site lid
      0.025   14.6   0.1      0.061   13.3   0.1    1.7  1  Ogr_Delta        Ogr/Delta-like zinc finger
      0.037   14.1   0.1      0.056   13.5   0.1    1.3  1  DZR              Double zinc ribbon
      0.099   13.0   0.1       0.17   12.3   0.1    1.3  1  Lar_restr_allev  Restriction alleviation protein Lar
        0.1   12.3   0.5        1.2    8.8   0.0    2.2  2  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
        0.2   11.1   3.6        5.9    6.5   0.1    2.3  2  zf-ribbon_3      zinc-ribbon domain
       0.46   10.3   2.7        9.5    6.1   0.2    2.3  2  zinc_ribbon_2    zinc-ribbon domain


Domain annotation for each model (and alignments):
>> zf-ZPR1  ZPR1 zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.7   0.0   9.6e-34   2.1e-30       3     158 ..      38     186 ..      36     187 .. 0.93

  Alignments for each domain:
  == domain 1  score: 105.7 bits;  conditional E-value: 9.6e-34
                        zf-ZPR1   3 CpsCgkengetrllltkiPyfkeviimsfeCehCgyknnevksageieekGkritlkveseedlnrqvlkSetatveipe 82 
                                    Cp Cg  + + r +   +P  ++ +++s +C +Cgyk +++ +++  ++  +r+ l+ve++edl  +v++S ta++ ipe
  gi|119719559|ref|YP_920054.1|  38 CPVCG-GPLKVREVEYMLPSLGKTLLVSKKCAKCGYKRTDIVPLSFQRH--TRVYLRVEKKEDLYIKVVRSPTARIFIPE 114
                                    ****7.99************************************99999..***************************** PP

                        zf-ZPR1  83 leleippg.tlegrlttvEGlLeqikeelekeegdqaer.ed.eekekieeflekleeliegee.pftlildDpagnSfi 158
                                    l+le+ pg   e ++t+vEG+L+ +k++l         r ++ +e+++++++++ l++++eg+  pftlildD  g S++
  gi|119719559|ref|YP_920054.1| 115 LGLELRPGlDAEMFVTNVEGVLQLFKDALL--------RlKTlDEEARVDDMVKLLDSIAEGDFtPFTLILDDVYGVSAV 186
                                    ********999******************2........223335789**************9966*************97 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00015      0.34      21      35 ..      35      49 ..      33      49 .. 0.91
   2 ?    1.7   0.0      0.12   2.6e+02      20      28 ..      63      71 ..      51      76 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00015
                                   TTB-TTT--.-B--G CS
                        ADK_lid 21 eglCDkCGepLvqRs 35
                                   e +C +CG+pL +R+
  gi|119719559|ref|YP_920054.1| 35 EDVCPVCGGPLKVRE 49
                                   789*********996 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.12
                                   STTB-TTT- CS
                        ADK_lid 20 veglCDkCG 28
                                   v  +C kCG
  gi|119719559|ref|YP_920054.1| 63 VSKKCAKCG 71
                                   567899998 PP

>> Ogr_Delta  Ogr/Delta-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   2.7e-05     0.061       2      23 ..      38      59 ..      37      75 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.7e-05
                      Ogr_Delta  2 CPhCgapaaartsrnlskdvre 23
                                   CP Cg p  +r ++++++ + +
  gi|119719559|ref|YP_920054.1| 38 CPVCGGPLKVREVEYMLPSLGK 59
                                   ****************998766 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   2.5e-05     0.056      13      37 ..      36      73 ..      28      77 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.5e-05
                            DZR 13 rfCseCgtklkavaa..............edrCpsCgek 37
                                    +C+ Cg +lk v +              +++C +Cg+k
  gi|119719559|ref|YP_920054.1| 36 DVCPVCGGPLK-VREveymlpslgktllvSKKCAKCGYK 73
                                   58********8.455699*******************97 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   7.6e-05      0.17       6      36 ..      38      72 ..      36      97 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.6e-05
                Lar_restr_allev  6 CPfCggravlersqrvvaeigq....cvyCadCga 36
                                   CP Cgg+ ++ + ++   + g+       Ca+Cg+
  gi|119719559|ref|YP_920054.1| 38 CPVCGGPLKVREVEYMLPSLGKtllvSKKCAKCGY 72
                                   **********9999999988889*99999*****9 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00056       1.2       6      19 ..      38      51 ..      37      54 .. 0.83
   2 ?    1.4   0.2      0.12   2.6e+02       6      10 ..      67      71 ..      64      73 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00056
                  zf-NADH-PPase  6 CgrCGaptepaegg 19
                                   C+ CG+p ++ e +
  gi|119719559|ref|YP_920054.1| 38 CPVCGGPLKVREVE 51
                                   *******9998765 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.12
                  zf-NADH-PPase  6 CgrCG 10
                                   C++CG
  gi|119719559|ref|YP_920054.1| 67 CAKCG 71
                                   55555 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1    0.0026       5.9       4      12 ..      37      45 ..      34      50 .. 0.65
   2 ?    5.3   0.8    0.0062        14      17      25 ..      65      73 ..      64      73 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0026
                    zf-ribbon_3  4 rCPnCGapl 12
                                    CP CG pl
  gi|119719559|ref|YP_920054.1| 37 VCPVCGGPL 45
                                   577777655 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0062
                    zf-ribbon_3 17 nvCpyCGtk 25
                                   ++C++CG+k
  gi|119719559|ref|YP_920054.1| 65 KKCAKCGYK 73
                                   58*****97 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.2     0.015        34      16      23 .]      38      45 ..      28      45 .. 0.77
   2 ?    6.1   0.2    0.0042       9.5      15      22 ..      66      73 ..      63      76 .. 0.66

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.015
                  zinc_ribbon_2 16 CpyCGtpl 23
                                   Cp CG pl
  gi|119719559|ref|YP_920054.1| 38 CPVCGGPL 45
                                   99999775 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0042
                  zinc_ribbon_2 15 FCpyCGtp 22
                                    C +CG++
  gi|119719559|ref|YP_920054.1| 66 KCAKCGYK 73
                                   56666664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1419.01
//
Query:       gi|119719560|ref|YP_920055.1|  [L=117]
Description: hypothetical protein Tpen_0650 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-13   50.0   2.3    3.3e-13   49.5   2.3    1.2  1  Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (
     0.0035   16.7   0.7      0.046   13.1   0.1    2.3  2  zf-ribbon_3    zinc-ribbon domain
     0.0062   16.0   1.3       0.01   15.3   1.3    1.4  1  TF_Zn_Ribbon   TFIIB zinc-binding
     0.0088   16.0   0.3      0.013   15.4   0.3    1.3  1  Prok-RING_1    Prokaryotic RING finger family 1
  ------ inclusion threshold ------
      0.018   15.0   0.2      0.028   14.4   0.2    1.3  1  DZR            Double zinc ribbon
      0.023   15.4   0.0      0.028   15.1   0.0    1.3  1  FYDLN_acid     Protein of unknown function (FYDLN_acid)
      0.034   14.5   0.2        6.8    7.1   0.0    2.3  2  GFA            Glutathione-dependent formaldehyde-activating 
      0.035   14.0   1.6      0.096   12.6   0.2    2.1  2  zinc_ribbon_4  zinc-ribbon domain
      0.041   13.6   0.8       0.54   10.0   0.1    2.2  2  zinc_ribbon_2  zinc-ribbon domain
      0.043   13.2   1.9        1.1    8.7   3.1    2.2  2  zf-TFIIB       Transcription factor zinc-finger
      0.049   13.4   1.0        3.4    7.5   0.0    2.3  2  zinc_ribbon_5  zinc-ribbon domain
      0.068   13.2   0.2        1.7    8.7   0.0    2.2  2  ADK_lid        Adenylate kinase, active site lid
      0.073   12.9   0.3        1.1    9.1   0.0    2.2  2  zf-C2H2_3      zinc-finger of acetyl-transferase ESCO
      0.095   13.3   1.4       0.25   11.9   1.4    1.7  1  Trm112p        Trm112p-like protein
        0.1   12.7   1.2       0.15   12.1   0.2    1.8  2  HypA           Hydrogenase/urease nickel incorporation, metal
       0.11   12.7   0.2       0.19   11.9   0.2    1.3  1  IRK_N          Inward rectifier potassium channel N-terminal
       0.12   12.5   0.1       0.18   12.0   0.1    1.3  1  DUF2318        Predicted membrane protein (DUF2318)
       0.17   12.0   3.8         33    4.7   0.3    2.4  2  Zn-ribbon_8    Zinc ribbon domain
       0.22   11.5   0.2       0.22   11.5   0.2    2.1  2  Zn_Tnp_IS1595  Transposase zinc-ribbon domain
       0.47   10.1   0.1       0.47   10.1   0.1    2.1  2  zf_UBZ         Ubiquitin-Binding Zinc Finger
       0.84    9.6   3.8        2.6    8.0   0.2    2.1  2  zf-HIT         HIT zinc finger
        1.1    9.6   3.3         41    4.5   4.2    2.2  2  zinc_ribbon_9  zinc-ribbon
          2    8.3   4.9         15    5.5   0.4    2.2  2  zf-RING_4      RING/Ubox like zinc-binding domain


Domain annotation for each model (and alignments):
>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.5   2.3   4.3e-16   3.3e-13       3      40 .]       1      37 [.       1      37 [. 0.96

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 4.3e-16
                  Auto_anti-p27  3 mgelLlkGwtMLaetCpvCgvPLmrdrkggkvyCvaCd 40
                                   m++lL  G+tML++ Cp+C vPL+r + +g+v+C+ C+
  gi|119719560|ref|YP_920055.1|  1 MANLLKSGATMLETLCPTCRVPLFRLK-SGEVVCPKCG 37
                                   99************************6.79*******6 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1      0.29   2.2e+02      18      22 ..      15      19 ..      12      23 .. 0.66
   2 !   13.1   0.1     6e-05     0.046      12      24 ..      26      38 ..      24      39 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.29
                    zf-ribbon_3 18 vCpyC 22
                                    Cp C
  gi|119719560|ref|YP_920055.1| 15 LCPTC 19
                                   56666 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 6e-05
                    zf-ribbon_3 12 lssddnvCpyCGt 24
                                   l+s+ +vCp+CG+
  gi|119719560|ref|YP_920055.1| 26 LKSGEVVCPKCGQ 38
                                   5899999****97 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   1.3   1.3e-05      0.01       3      26 ..      16      37 ..      14      39 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.3e-05
                                   ETTTTCEECHEETSTTCEEESSSS CS
                   TF_Zn_Ribbon  3 CPnCgstnlveDpergelvCtdCG 26
                                   CP C  +  ++  ++ge+vC++CG
  gi|119719560|ref|YP_920055.1| 16 CPTCRVP--LFRLKSGEVVCPKCG 37
                                   *****99..9*************9 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.3   1.6e-05     0.013       4      30 ..      13      40 ..      10      51 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.6e-05
                    Prok-RING_1  4 gkkCpvCgkel.keedDiVvCpeCgtpy 30
                                   ++ Cp C+ +l + ++  VvCp+Cg  y
  gi|119719560|ref|YP_920055.1| 13 ETLCPTCRVPLfRLKSGEVVCPKCGQRY 40
                                   678*****9861556889*******766 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.2   3.6e-05     0.028      14      37 ..      15      39 ..       8      49 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.6e-05
                            DZR 14 fCseCgtklkavaa.edrCpsCgek 37
                                    C++C+ +l + ++ e +Cp+Cg+ 
  gi|119719560|ref|YP_920055.1| 15 LCPTCRVPLFRLKSgEVVCPKCGQR 39
                                   5777777766555567777777765 PP

>> FYDLN_acid  Protein of unknown function (FYDLN_acid)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   3.6e-05     0.028      11      42 ..      15      46 ..      13      87 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.6e-05
                     FYDLN_acid 11 iCpscgakFYDLnkdPivcpkcgeefepeevl 42
                                   +Cp+c    + L+   +vcpkcg+ + + +  
  gi|119719560|ref|YP_920055.1| 15 LCPTCRVPLFRLKSGEVVCPKCGQRYVIVASE 46
                                   6*************************998773 PP

>> GFA  Glutathione-dependent formaldehyde-activating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0    0.0087       6.8      42      61 ..       6      25 ..       2      32 .. 0.82
   2 ?    6.0   0.1      0.02        15      50      72 ..      31      54 ..      27      70 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0087
                            GFA 42 dsgnkvtrsfCpeCgsplys 61
                                   +sg ++ ++ Cp+C +pl+ 
  gi|119719560|ref|YP_920055.1|  6 KSGATMLETLCPTCRVPLFR 25
                                   57899999**********95 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.02
                            GFA 50 sfCpeCgsplyse.esaapevviv 72
                                    +Cp+Cg + +   ++++++ v v
  gi|119719560|ref|YP_920055.1| 31 VVCPKCGQRYVIVaSEEEEHRVKV 54
                                   68*******998745555555555 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1      0.93   7.2e+02      28      32 ..      16      20 ..       9      22 .. 0.72
   2 ?   12.6   0.2   0.00012     0.096       3      26 ..      31      54 ..      30      55 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.93
                  zinc_ribbon_4 28 CskCg 32
                                   C+ C+
  gi|119719560|ref|YP_920055.1| 16 CPTCR 20
                                   55554 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00012
                  zinc_ribbon_4  3 itCpsCkakyeiddeklpakgvkv 26
                                   ++Cp+C+ +y i ++   +++vkv
  gi|119719560|ref|YP_920055.1| 31 VVCPKCGQRYVIVASEEEEHRVKV 54
                                   89*********9888777777776 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1      0.23   1.8e+02      14      22 ..      14      22 ..      13      23 .. 0.73
   2 ?   10.0   0.1    0.0007      0.54       9      20 ..      26      37 ..      25      39 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.23
                  zinc_ribbon_2 14 kFCpyCGtp 22
                                   + Cp C+ p
  gi|119719560|ref|YP_920055.1| 14 TLCPTCRVP 22
                                   679999866 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0007
                  zinc_ribbon_2  9 lqdnakFCpyCG 20
                                   l+ +++ Cp+CG
  gi|119719560|ref|YP_920055.1| 26 LKSGEVVCPKCG 37
                                   567889999999 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   3.1    0.0014       1.1       2      23 ..      16      37 ..      15      38 .. 0.84
   2 ?    5.9   0.1    0.0099       7.7       2      13 ..      33      44 ..      32      55 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0014
                       zf-TFIIB  2 CPkCqdeleeserggveidyCp 23
                                   CP+C+++l  +++g+v + +C 
  gi|119719560|ref|YP_920055.1| 16 CPTCRVPLFRLKSGEVVCPKCG 37
                                   ***************8766664 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0099
                       zf-TFIIB  2 CPkCqdeleese 13
                                   CPkC++  +++ 
  gi|119719560|ref|YP_920055.1| 33 CPKCGQRYVIVA 44
                                   9***99877665 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   2.1     0.048        37       3      31 ..      14      36 ..      12      36 .. 0.72
   2 ?    7.5   0.0    0.0043       3.4       4      25 ..      32      53 ..      30      55 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.048
                  zinc_ribbon_5  3 irCpdCdt.kFklvdsklKksgkkVrCakC 31
                                   + Cp C+   F+l + +       V C kC
  gi|119719560|ref|YP_920055.1| 14 TLCPTCRVpLFRLKSGE-------VVCPKC 36
                                   77****96479999888.......555555 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0043
                  zinc_ribbon_5  4 rCpdCdtkFklvdsklKksgkk 25
                                    Cp+C+  + +v s+  +  +k
  gi|119719560|ref|YP_920055.1| 32 VCPKCGQRYVIVASEEEEHRVK 53
                                   5***********9994444444 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0       0.2   1.6e+02      21      32 ..      13      24 ..       9      25 .. 0.86
   2 ?    8.7   0.0    0.0021       1.7       3      11 ..      32      40 ..      31      57 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.2
                                   TTB-TTT--.-B CS
                        ADK_lid 21 eglCDkCGepLv 32
                                   e lC  C +pL+
  gi|119719560|ref|YP_920055.1| 13 ETLCPTCRVPLF 24
                                   679****99997 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0021
                                   E-TTT--EE CS
                        ADK_lid  3 vCpkCGrsY 11
                                   vCpkCG  Y
  gi|119719560|ref|YP_920055.1| 32 VCPKCGQRY 40
                                   9*****999 PP

>> zf-C2H2_3  zinc-finger of acetyl-transferase ESCO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1      0.31   2.4e+02      15      20 ..      14      20 ..       5      21 .. 0.67
   2 ?    9.1   0.0    0.0014       1.1      12      31 ..      29      48 ..      24      51 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.31
                      zf-C2H2_3 15 q.CkeCg 20
                                   + C++C 
  gi|119719560|ref|YP_920055.1| 14 TlCPTCR 20
                                   25****6 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0014
                      zf-C2H2_3 12 gasqCkeCgMvYnpgspeDe 31
                                   g++ C++Cg  Y+    e+e
  gi|119719560|ref|YP_920055.1| 29 GEVVCPKCGQRYVIVASEEE 48
                                   6677********99877766 PP

>> Trm112p  Trm112p-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   1.4   0.00032      0.25      10      66 ..      16      43 ..      10      45 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00032
                                   -TTTHHC--HHHHHHHHHTT---S-SS----SCHHTTEECCCCEEEETTTTEEEEEE CS
                        Trm112p 10 CpackgpLdwealvevaalglnelpkekpedyellleldieegeLvCpncgraYpIk 66
                                   Cp c+ pL                             +  ++ge vCp+cg+ Y I 
  gi|119719560|ref|YP_920055.1| 16 CPTCRVPL-----------------------------FRLKSGEVVCPKCGQRYVIV 43
                                   88888888.............................88999************996 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   0.00019      0.15      69     103 ..      12      47 ..       3      56 .. 0.73
   2 ?   -1.4   0.1         3   2.4e+03       7      33 ..      66      92 ..      61     101 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00019
                                    -EEEETTTS-EEE.CHHH.HHS-TTTSSS-EEEEESS CS
                           HypA  69 vkvrCreCgkefe.leek.alrCpkCgsadveivsGe 103
                                    +++ C +C+     l+ + ++ CpkCg++ v + s e
  gi|119719560|ref|YP_920055.1|  12 LETLCPTCRVPLFrLK-SgEVVCPKCGQRYVIVASEE 47 
                                    6789****97665255.45899******987766554 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3
                                   HHHHHHHHHHHHCCTT..EEEEEEEEE CS
                           HypA  7 aesivevveeeakeaaarkvtkvkvev 33
                                   +++i ++  + a++++++++t+v   +
  gi|119719560|ref|YP_920055.1| 66 VQKISSLSASLASSETFDEITEVSRAI 92
                                   455555555556556677777776554 PP

>> IRK_N  Inward rectifier potassium channel N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   0.00024      0.19       7      22 ..      38      53 ..      37      55 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00024
                          IRK_N  7 hrYSIVSseEdglkls 22
                                    rY IV seE+ ++++
  gi|119719560|ref|YP_920055.1| 38 QRYVIVASEEEEHRVK 53
                                   59***********985 PP

>> DUF2318  Predicted membrane protein (DUF2318)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00023      0.18      36      63 ..      15      42 ..       6      54 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00023
                        DUF2318 36 aCevCekkgYvqegeelvCknCgvrfal 63
                                    C  C+   +  +  e+vC +Cg+r  +
  gi|119719560|ref|YP_920055.1| 15 LCPTCRVPLFRLKSGEVVCPKCGQRYVI 42
                                   6***********************9876 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.3     0.042        33      26      35 ..      12      22 ..       4      27 .. 0.69
   2 ?    4.5   5.0      0.05        39      25      35 ..      29      39 ..      16      43 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.042
                    Zn-ribbon_8 26 lta.CPeCgse 35
                                   l++ CP+C  +
  gi|119719560|ref|YP_920055.1| 12 LETlCPTCRVP 22
                                   4455****755 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.05
                    Zn-ribbon_8 25 pltaCPeCgse 35
                                    +++CP+Cg++
  gi|119719560|ref|YP_920055.1| 29 GEVVCPKCGQR 39
                                   3677*****85 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.3      0.68   5.3e+02      21      26 ..      16      21 ..       8      27 .. 0.84
   2 ?   11.5   0.2   0.00029      0.22      14      27 ..      25      39 ..      20      51 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.68
                  Zn_Tnp_IS1595 21 CPhCgs 26
                                   CP C +
  gi|119719560|ref|YP_920055.1| 16 CPTCRV 21
                                   ****75 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00029
                  Zn_Tnp_IS1595 14 rWpng.fvCPhCgsr 27
                                   r ++g +vCP+Cg r
  gi|119719560|ref|YP_920055.1| 25 RLKSGeVVCPKCGQR 39
                                   66777688*****77 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.2       1.5   1.2e+03       4       8 ..      15      19 ..      13      22 .. 0.85
   2 ?   10.1   0.1    0.0006      0.47       3      20 ..      31      50 ..      29      51 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.5
                         zf_UBZ  4 lCerC 8 
                                   lC+ C
  gi|119719560|ref|YP_920055.1| 15 LCPTC 19
                                   7**** PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0006
                         zf_UBZ  3 ylCerCgke..ipeselqEH 20
                                   ++C++Cg++  i  se +EH
  gi|119719560|ref|YP_920055.1| 31 VVCPKCGQRyvIVASEEEEH 50
                                   79******732444588888 PP

>> zf-HIT  HIT zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.5      0.15   1.1e+02      16      22 ..      16      22 ..      15      23 .. 0.89
   2 ?    8.0   0.2    0.0034       2.6      15      23 ..      32      40 ..      27      40 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.15
                                   -TTT--E CS
                         zf-HIT 16 CpkCntr 22
                                   Cp+C+++
  gi|119719560|ref|YP_920055.1| 16 CPTCRVP 22
                                   ****998 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0034
                                   E-TTT--EE CS
                         zf-HIT 15 kCpkCntry 23
                                    CpkC++ry
  gi|119719560|ref|YP_920055.1| 32 VCPKCGQRY 40
                                   6*******9 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.5      0.25     2e+02      22      28 ..      14      20 ..       7      24 .. 0.83
   2 ?    4.5   4.2     0.053        41      16      32 ..      25      41 ..      16      43 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.25
                  zinc_ribbon_9 22 vlCPhCg 28
                                   +lCP C+
  gi|119719560|ref|YP_920055.1| 14 TLCPTCR 20
                                   57****7 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.053
                  zinc_ribbon_9 16 pdedsdvlCPhCgggFV 32
                                   + ++ +v+CP Cg+  V
  gi|119719560|ref|YP_920055.1| 25 RLKSGEVVCPKCGQRYV 41
                                   55677888*****9876 PP

>> zf-RING_4  RING/Ubox like zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.4      0.03        23      37      45 ..      13      21 ..       5      24 .. 0.82
   2 ?    5.5   0.4     0.019        15      35      47 ..      28      40 ..      23      41 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.03
                      zf-RING_4 37 egrCPaCre 45
                                   e  CP Cr 
  gi|119719560|ref|YP_920055.1| 13 ETLCPTCRV 21
                                   679*****6 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.019
                      zf-RING_4 35 eeegrCPaCreeY 47
                                   + e +CP+C ++Y
  gi|119719560|ref|YP_920055.1| 28 SGEVVCPKCGQRY 40
                                   46889****9999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       803  (0.0447878); expected 358.6 (0.02)
Passed bias filter:                      590  (0.0329076); expected 358.6 (0.02)
Passed Vit filter:                       107  (0.00596798); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 814.21
//
Query:       gi|119719561|ref|YP_920056.1|  [L=235]
Description: DNA polymerase beta superfamily nucleotidyltransferase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-05   25.4   0.3    3.9e-05   23.9   0.3    1.8  1  NTP_transf_2  Nucleotidyltransferase domain
     0.0054   16.8   0.0     0.0097   16.0   0.0    1.5  1  Polbeta       Polymerase beta, Nucleotidyltransferase
  ------ inclusion threshold ------
      0.014   14.9   0.1       0.14   11.7   0.0    2.3  2  HTH_24        Winged helix-turn-helix DNA-binding


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.3   6.5e-09   3.9e-05      14      38 ..      40      64 ..      20      65 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 6.5e-09
                                   TSEEEEEHHHHCTTSCTTSSEEEEE CS
                   NTP_transf_2 14 vakvvlfGSyarGtalkgSDiDllv 38
                                    + v+++GS+arG+ ++ SD+Dl++
  gi|119719561|ref|YP_920056.1| 40 RIPVYVVGSVARGDVTRKSDVDLFL 64
                                   6679*******************95 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.6e-06    0.0097      16      37 ..      43      64 ..      41     106 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.6e-06
                                   TTEEEEEE-S------EEEEEE CS
                        Polbeta 16 aylFGSrakgkareeSDiDlav 37
                                   +y+ GS+a+g+ +++SD+Dl++
  gi|119719561|ref|YP_920056.1| 43 VYVVGSVARGDVTRKSDVDLFL 64
                                   89*****************985 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   2.4e-05      0.14      22      37 ..     170     185 ..     169     185 .. 0.93
   2 ?   -0.0   0.0      0.11   6.6e+02      15      27 ..     207     219 ..     204     220 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.4e-05
                         HTH_24  22 eLAerlglSpstvnrr 37 
                                    e+A+rlg+S++tv++r
  gi|119719561|ref|YP_920056.1| 170 EVARRLGISLGTVLER 185
                                    89***********987 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.11
                         HTH_24  15 nprisqreLAerl 27 
                                    +pr+s  +L +rl
  gi|119719561|ref|YP_920056.1| 207 DPRLSPEDLLRRL 219
                                    8********9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1652.32
//
Query:       gi|119719562|ref|YP_920057.1|  [L=630]
Description: type III restriction enzyme, res subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-20   73.1   0.1    7.5e-19   68.1   0.0    2.6  2  Helicase_C     Helicase conserved C-terminal domain
    1.6e-17   64.0   0.1    4.2e-16   59.4   0.0    2.2  2  ResIII         Type III restriction enzyme, res subunit
    5.1e-06   25.9   0.0    8.4e-06   25.2   0.0    1.3  1  ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
     0.0052   17.2   0.1      0.079   13.4   0.0    2.7  3  RecX           RecX family


Domain annotation for each model (and alignments):
>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.05   2.2e+02      15      59 ..     310     357 ..     299     373 .. 0.68
   2 !   68.1   0.0   1.7e-22   7.5e-19       2     107 ..     458     562 ..     457     564 .. 0.95

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.05
                                    TTSEEEEEESSHHHHHH.HHHHHHHT..TSTEEEESTTSTHHHHHHHH CS
                     Helicase_C  15 eggkilifvntidrlek.vklllekk..gikvavlhgelpqnereeil 59 
                                     ++ +++fv+t++ +e  ++++++      +++ + g  +q+ re ++
  gi|119719562|ref|YP_920057.1| 310 LRKPTIVFVTTQELVETwISYFEKYLglPRSFVGVLGGGEQKIREITV 357
                                    47899********99888888844334434444455556666666555 PP

  == domain 2  score: 68.1 bits;  conditional E-value: 1.7e-22
                                    HHHHHHHHHHHTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSST CS
                     Helicase_C   2 kleallellkleeeggkilifvntidrlekvklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGid 81 
                                    k ++lle+l +++ +gk+++++++ +++e+v  ll+++g+++ +++g++p+ +re ++++f +g+s+v+++t+v+ +Gi+
  gi|119719562|ref|YP_920057.1| 458 KKKKLLEIL-RRHADGKVIVYTQYLQTAEDVYDLLRRNGFNAEIVTGDTPAHKRELAFKNFVEGRSNVIVTTTVLDEGIT 536
                                    78899***9.9***************999855556899****************************************** PP

                                    STTESEEEESSSSSSHHHHHHHHTTS CS
                     Helicase_C  82 ipkvnlVinfdlprnvtsyiqriGRt 107
                                    +p++++ ++++   + +++iqriGR+
  gi|119719562|ref|YP_920057.1| 537 VPDADVAVIYEGTGEGRQMIQRIGRV 562
                                    *************************8 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.036   1.6e+02      97     122 ..      41      70 ..      14      84 .. 0.68
   2 !   59.4   0.0   9.3e-20   4.2e-16       2     171 .]     270     411 ..     269     411 .. 0.94

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.036
                                    .......-SEEEEEHHHHHHTH........ CS
                         ResIII  97 kekdstnkkilvttiqsldadseee....e 122
                                    +  +s++++i v++++sld+++ee     +
  gi|119719562|ref|YP_920057.1|  41 YDPESKEWRISVEKVSSLDNELEEVleklK 70 
                                    445899***************944443332 PP

  == domain 2  score: 59.4 bits;  conditional E-value: 9.3e-20
                                    -EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG. CS
                         ResIII   2 lelreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflsea 81 
                                    ++l ++Q ea +++       r++rg i + T  GK+++a+++i++l+k      ++++v +++l+e +++ f+k+l  +
  gi|119719562|ref|YP_920057.1| 270 FKLLPHQVEAYKQWT------RKRRGTISIFTRGGKSFIALEAIYSLRK-----PTIVFVTTQELVETWISYFEKYLGLP 338
                                    7899**********6......8899***********************9.....79************************ PP

                                    ...GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.TTTHHHHHT---SE CS
                         ResIII  82 ykeigkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakkswreilekfkeav 161
                                    ++++g    g++k++        +i+v+t++s+ + +        +l ++rf++ i+DEaH++ a +++++++  +++ +
  gi|119719562|ref|YP_920057.1| 339 RSFVGVLGGGEQKIR--------EITVATYSSAVKYI--------DLIKSRFELAIFDEAHHVPA-ATFKQVALGVDALY 401
                                    998887777777777........**************........9*******************.************** PP

                                    EEEEESS-S- CS
                         ResIII 162 llglTATper 171
                                    +++l+ATper
  gi|119719562|ref|YP_920057.1| 402 RMALSATPER 411
                                    ********86 PP

>> ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   1.9e-09   8.4e-06      60     150 ..     471     564 ..     456     592 .. 0.79

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 1.9e-09
                  ERCC3_RAD25_C  60 gDkiivfsDnvfaLkeya.....kklkkpyiyGetseaerlkilqkfkknpkvntiflskvgDtsiDlPeanvliqissh 134
                                    + k+iv++  + + +++      + ++ + ++G+t+ ++r   +++f +  + n+i+   v D+ i +P+a v + i   
  gi|119719562|ref|YP_920057.1| 471 DGKVIVYTQYLQTAEDVYdllrrNGFNAEIVTGDTPAHKRELAFKNFVEG-RSNVIVTTTVLDEGITVPDADVAV-IYEG 548
                                    448888876555555544000003466789*****************876.789******************987.7778 PP

                  ERCC3_RAD25_C 135 fgsrrqeaqrlGriLr 150
                                    +g  rq  qr+Gr+L 
  gi|119719562|ref|YP_920057.1| 549 TGEGRQMIQRIGRVLG 564
                                    8999**********95 PP

>> RecX  RecX family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   1.8e-05     0.079       8      66 ..      59     116 ..      53     160 .. 0.85
   2 ?   -2.1   0.0       1.2   5.2e+03      68      91 ..     204     227 ..     180     252 .. 0.50
   3 ?   -0.1   0.0      0.28   1.2e+03      74     112 ..     461     501 ..     445     503 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.8e-05
                                    HHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHH----HH.HHHHHHHTTT--HHHHHHHH CS
                           RecX   8 eevieavierlkeeglldDerfAesfvrsrlrsrgyGpr.rikqeLkqkGiseelieqal 66 
                                    ++++e+v+e+lk++  l+D++  + ++ +r   r+ G+   i ++L+ kG+++ ++e+  
  gi|119719562|ref|YP_920057.1|  59 DNELEEVLEKLKKLSTLSDADLQRVVAYTRG--RSAGRVcWIGYDLRVKGLPPTVVEALR 116
                                    6899*********************999999..788887369***********9999654 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.2
                                    TS-HHHHHHHHHHHHHHHTTTS-H CS
                           RecX  68 eldeeeqarelaekklkklkkeed 91 
                                    +++ e + +el+e+++++ + + +
  gi|119719562|ref|YP_920057.1| 204 NEEGEFEGTELVERRMRTAHVDWQ 227
                                    333333377777777777743333 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.28
                                    HHHHHHHHHHHHT..TTS-HHHHHHHHHHHHHHTT--HHHH CS
                           RecX  74 qarelaekklkkl..kkeedekekqklvrfLarrGFssevi 112
                                    +  e+++++++ +    ++  +  + ++  L r GF+ e++
  gi|119719562|ref|YP_920057.1| 461 KLLEILRRHADGKviVYTQYLQTAEDVYDLLRRNGFNAEIV 501
                                    466667777776655445668888889999*******9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (630 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       818  (0.0456244); expected 358.6 (0.02)
Passed bias filter:                      715  (0.0398795); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.43
# Mc/sec: 4414.11
//
Query:       gi|119719563|ref|YP_920058.1|  [L=207]
Description: 30S ribosomal protein S3Ae [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.9e-63  212.4   7.5    5.9e-63  212.1   7.5    1.0  1  Ribosomal_S3Ae  Ribosomal S3Ae family


Domain annotation for each model (and alignments):
>> Ribosomal_S3Ae  Ribosomal S3Ae family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  212.1   7.5   3.3e-67   5.9e-63       3     200 ..       4     190 ..       2     191 .. 0.98

  Alignments for each domain:
  == domain 1  score: 212.1 bits;  conditional E-value: 3.3e-67
                                    ----S-TCCSEEEEEEEB-TTSSSSEEEEEEEE--BSSSESHHSHTT-EEEEESHHHHTCSHTSSSEEEEEEEEEEESSE CS
                 Ribosomal_S3Ae   3 kkkvvDkfkkKeWydvkaPslfgkreiGktlvnrtqgtkiaseklkgrvvevslaDLtndekeqafrklklkieevqgkn 82 
                                    + k++Dk++ K+W +v aP+ fg +++G +++       +++ek+ gr+vevs +D+t+d  +q ++klk++i +v++  
  gi|119719563|ref|YP_920058.1|   4 RAKTKDKWSMKKWIKVLAPKAFGFANLGLIPA-------DEPEKALGRTVEVSFYDITKDV-SQLHIKLKFQIVKVDDGI 75 
                                    6799****************************.......*********************8.778*************** PP

                                    EEEEEEEEEE-HHHHHHH--SSB-EEEEEEEEEESSSEEEEEEEEEEE-STTB---HHHHHHHHHHHHHHHHHHHHHS-H CS
                 Ribosomal_S3Ae  83 altnFkgmeltrDklrslvrkwsslIeaivdvktkDgyllrvfvvafTkkrnsYakssqkkaIrkkmveilteeaseldl 162
                                    alt+ k me+trD++rslvr+++s+++ai+dv+tkDg+++rv+++a+T +r   +k+sqkkaIr++m++i++e+a++ld+
  gi|119719563|ref|YP_920058.1|  76 ALTQLKLMEMTRDYIRSLVRRGTSRVDAILDVQTKDGVKMRVMALAVTVSR---IKTSQKKAIRRIMFDIISEKAASLDF 152
                                    ***************************************************...************************** PP

                                    HHHHHHHTTTHHHHHHHHHHTTTS-EEEEEEEEEEEEE CS
                 Ribosomal_S3Ae 163 kelvkklipeslgkeiekeakkIyplrnveirKvkvlk 200
                                    ++++++ +  ++++e++ +akkIyp+++ve++K+kvl+
  gi|119719563|ref|YP_920058.1| 153 DTFIQQAVIGTMATEMQMQAKKIYPIKKVEVYKIKVLT 190
                                    *********88*************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       806  (0.0449551); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1364.87
//
Query:       gi|119719564|ref|YP_920059.1|  [L=330]
Description: phosphoesterase, DHHA1 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-10   42.1   2.6    1.5e-09   38.4   3.6    2.1  2  DHHA1     DHHA1 domain
    1.4e-08   34.8   0.0    2.7e-08   33.9   0.0    1.4  1  DHH       DHH family


Domain annotation for each model (and alignments):
>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.15   1.3e+03      52      76 ..      85     107 ..      75     120 .. 0.71
   2 !   38.4   3.6   1.7e-13   1.5e-09      14     124 ..     196     299 ..     188     318 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.15
                                    HHHHHHHHHHHHHTHGBTTCEEEEE CS
                          DHHA1  52 dagalgiaadklksklkkpvivfva 76 
                                    ++  l+++a+k+ +  ++++ v+v 
  gi|119719564|ref|YP_920059.1|  85 NPSQLRELAEKFSD--PSVTLVVVD 107
                                    66778888888888..555555444 PP

  == domain 2  score: 38.4 bits;  conditional E-value: 1.7e-13
                                    HHHCHHHHHHHHHHHHHHHTCEEECTCEEEEEECHCCHHHHHHHHHHHHHHTHGBTTCEEEEEEEECTEEEEEEEESSH. CS
                          DHHA1  14 eleelkealaklkaeellekaeevkgvkvlvaevgeewdagalgiaadklksklkkpvivfvakeegdkvkvsarskkd. 92 
                                    e    +e+laklk   l ++++ev+g+ v+++ev    +a++ + +++   +       ++v++ ++ + ++s+r++++ 
  gi|119719564|ref|YP_920059.1| 196 EP--RSEKLAKLKG-LLRASVFEVCGYIVAFTEV-SANEANVARLLVSAGAD------LAVVVGGKK-ESRLSIRVSDEl 264
                                    55..5667777664.5677888888*********.77788888888888888......444444333.679999999889 PP

                                    ...SS-HHHHHHHHHHHTTCCEEEETCEEEEEEEH CS
                          DHHA1  93 ...gvdagelakeaaaklgggGGGHdlAaGagipa 124
                                       g+dage+a+ +a++lg  GGGH+ AaG ++  
  gi|119719564|ref|YP_920059.1| 265 qkaGIDAGEIAQSVASALGAEGGGHAGAAGVKTTD 299
                                    99****************************99863 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.0     3e-12   2.7e-08       2     101 .]      14     157 ..      13     157 .. 0.79

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 3e-12
                                    EEEE-ECSSSHHHHHHHHHHHH...........................................CECS--TCGGCGCCH CS
                                    xxxxxxxxxxxxxxxxxxxxxx...........................................xxxxxxxxxxxxxxx RF
                            DHH   2 ilivghknpDtDsigSaialan...........................................llvDhneksqavege 38 
                                    ++++ h n D D++++a+++a+                                           +l+D++++sq  e +
  gi|119719564|ref|YP_920059.1|  14 VVVTSHVNTDPDGLACAYLMARlveevgleahlcfpggissvsktilgrlgmswqrecpedtrtfILCDFSNPSQLRELA 93 
                                    899*******************77777777777777777777777777777777777777777777*******9976544 PP

                                    ..HCCCSEEEEEEE-S---SS---SS--EEEE-SSS-HHHHHHHHHHHTT----HHHHHHHHHHH CS
                                    ..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DHH  39 ..akeeaedviiiDHHrlgeefetlapilflnepvgstaeivaelleekkeeiskeiaellllgi 101
                                      + ++ ++++++DHH ++ ++  la++ +++ + +s a i+a++l ++++++ +++a+l ++gi
  gi|119719564|ref|YP_920059.1|  94 ekFSDPSVTLVVVDHHFPEGKLVPLAKLAVVEREPAS-AVIAARILMDEGVNVCATLATLGIAGI 157
                                    4499**************9988888888888666555.568889888888887777777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2386.71
//
Query:       gi|119719565|ref|YP_920060.1|  [L=97]
Description: hypothetical protein Tpen_0655 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.031   14.2   0.1      0.069   13.1   0.1    1.5  2  NTase_sub_bind  Nucleotidyltransferase substrate binding prot
      0.035   14.5   0.1      0.043   14.2   0.1    1.1  1  SATase_N        Serine acetyltransferase, N-terminal


Domain annotation for each model (and alignments):
>> NTase_sub_bind  Nucleotidyltransferase substrate binding protein like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       0.3   2.7e+03       8      19 ..      23      34 ..      16      48 .. 0.62
   2 ?   13.1   0.1   7.7e-06     0.069      85     120 ..      53      88 ..      41      92 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.3
                                   HHHHHHHHHHHH CS
                 NTase_sub_bind  8 kAlasLeeavel 19
                                   + +++L+ea+++
  gi|119719565|ref|YP_920060.1| 23 EMYRELQEALSE 34
                                   455666666665 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 7.7e-06
                                    HHHHHHGCGGGTTSHHHHHHHHHTHH.HHHHHHHHH CS
                 NTase_sub_bind  85 emledRnltshtYdeetaeevveaiaeeylpelkal 120
                                    +++ d   +s+ Yd++t e+++++++++yl+++++ 
  gi|119719565|ref|YP_920060.1|  53 DFRLDVEVSSKLYDKKTLEDTLNRVVSKYLKKAEEE 88 
                                    677777889**********************99875 PP

>> SATase_N  Serine acetyltransferase, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   4.8e-06     0.043       3      70 ..      22      89 ..      20      95 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.8e-06
                                   HHHHHHHHHHHHH-GGGHHHHHHHTTT-SSHHHHHHHHHHHHH-BSSS-HHHHHHHHHHHHHH-THHH CS
                       SATase_N  3 eslraeaeeaaekepllasflyatilsheslesaLaflLanklasstlsaeqlrelfeealeadpeiv 70
                                   e++ +e +ea++++p l+  ++ ++ +    +  L   +++kl ++++++++l++++++ l++++e  
  gi|119719565|ref|YP_920060.1| 22 EEMYRELQEALSEDPELQLTIKVEVDEDWPYDFRLDVEVSSKLYDKKTLEDTLNRVVSKYLKKAEEEL 89
                                   68999********************************************************9665443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1251  (0.0697752); expected 358.6 (0.02)
Passed bias filter:                      730  (0.0407162); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.38s 00:00:00.92 Elapsed: 00:00:00.56
# Mc/sec: 517.94
//
Query:       gi|119719566|ref|YP_920061.1|  [L=113]
Description: prefoldin subunit beta [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-15   57.5   7.3    1.2e-15   57.4   7.3    1.0  1  Prefoldin_2      Prefoldin subunit
  ------ inclusion threshold ------
      0.043   13.3   8.9       0.62    9.5   4.7    2.0  2  DegS             Sensor protein DegS
      0.056   12.7   0.5      0.066   12.5   0.5    1.1  1  TcdA_TcdB        TcdA/TcdB catalytic glycosyltransferase doma
        0.1   13.0   6.0        1.7    9.1   0.2    2.2  2  Snapin_Pallidin  Snapin/Pallidin
       0.16   12.0   0.1        0.2   11.7   0.1    1.1  1  Adeno_E3A        Adenovirus E3A
       0.19   11.0   7.4        1.3    8.3   0.9    2.0  2  DUF3450          Protein of unknown function (DUF3450)
       0.22   11.2   3.5       0.39   10.5   0.1    2.1  2  DUF3287          Protein of unknown function (DUF3287)
       0.53    9.2   5.1        4.7    6.1   0.2    2.0  2  IFT57            Intra-flagellar transport protein 57
        0.6   10.6   5.2        8.1    7.0   1.2    2.2  2  DUF4140          N-terminal domain of unknown function (DUF41
          1    9.6  11.8        3.9    7.7   6.4    2.1  2  JIP_LZII         JNK-interacting protein  leucine zipper II
          1    9.3   8.4        5.8    6.8   1.9    2.3  2  Prefoldin        Prefoldin subunit
        1.1    9.5   6.9        1.8    8.9   6.9    1.3  1  DUF737           Protein of unknown function (DUF737)
        2.8    7.5   8.4        2.3    7.7   2.9    2.1  2  Fzo_mitofusin    fzo-like conserved region
        6.2    7.5   9.9          4    8.1   1.0    2.5  2  SlyX             SlyX
        6.7    7.1   8.9         14    6.1   0.5    2.2  2  DUF4078          Domain of unknown function (DUF4078)
        7.2    6.4   9.5        1.6    8.6   3.6    1.9  2  FTA4             Kinetochore complex Fta4 of Sim4 subunit, or


Domain annotation for each model (and alignments):
>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.4   7.3     1e-18   1.2e-15       1     103 [.       5     106 ..       5     109 .. 0.98

  Alignments for each domain:
  == domain 1  score: 57.4 bits;  conditional E-value: 1e-18
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-TT--EEEEETTEEEEE-HHHHHHHHHHHHHHHHHHHHH CS
                    Prefoldin_2   1 qelinkfqqlqqqlqqlaqqikqletqlkelelvleelelldedtkvyklvGdvlvkqdkeevkeeLeerketlekeikt 80 
                                    q+ i+k+qq+ ++l+++   i+q++ +l e+e +l++le+      vy+++G++l+++++eev +eL+ +ke l+ ++++
  gi|119719566|ref|YP_920061.1|   5 QQTIAKYQQTLEELRAVTLSIQQYRGRLLEIERTLKALEQSQGG-FVYRSMGNILIQTPREEVMKELNSEKELLQLRLEE 83 
                                    899***************************************99.*********************************** PP

                                    HHHHHHHHHHHHHHHHHHHHCCT CS
                    Prefoldin_2  81 lekqleklekeleelkeelqkkl 103
                                     +k+++ l+++l+ l+++l+++l
  gi|119719566|ref|YP_920061.1|  84 FTKREKLLRERLASLEKQLRSAL 106
                                    *******************9876 PP

>> DegS  Sensor protein DegS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.1    0.0054         6      40      84 ..       8      52 ..       4      62 .. 0.79
   2 ?    9.5   4.7   0.00055      0.62      75     117 ..      63     105 ..      59     112 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0054
                           DegS 40 keevsevikevdklekkerkarkrLaeVskdFkkyseeeikeaYe 84
                                     + +++++e  +++   ++ r rL+e+++  k  ++++   +Y 
  gi|119719566|ref|YP_920061.1|  8 IAKYQQTLEELRAVTLSIQQYRGRLLEIERTLKALEQSQGGFVYR 52
                                   567788999999999999************999988877666665 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00055
                           DegS  75 seeeikeaYeeakelqvelallrekEkqlrerRdelerrLkkl 117
                                    +ee +ke   e + lq++l    ++Ek lrer  +le++L+++
  gi|119719566|ref|YP_920061.1|  63 REEVMKELNSEKELLQLRLEEFTKREKLLRERLASLEKQLRSA 105
                                    5889999999999***************************986 PP

>> TcdA_TcdB  TcdA/TcdB catalytic glycosyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.5   5.9e-05     0.066     101     164 ..      45     108 ..       2     111 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.9e-05
                                    .HHHHHHHHHHHTTSTT-HHHHHHHHHHHS---HHHHHHH.............HHHHHHHHHTT CS
                      TcdA_TcdB 101 aqkafinflkakgnkntkDeirkeyLekeysldteelesykklkeinkeklaalekslneilde 164
                                     q +f+     +++ +t  e +++ L++e++l +  le+  k +++ +e+la+lek+l++ l+ 
  gi|119719566|ref|YP_920061.1|  45 SQGGFVYRSMGNILIQTPREEVMKELNSEKELLQLRLEEFTKREKLLRERLASLEKQLRSALPT 108
                                    2344544445556666668999999*********999*99999****************99875 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.2    0.0016       1.7      39      77 ..       7      44 ..       3      47 .. 0.75
   2 ?    6.2   1.6     0.012        14      16      46 ..      75     105 ..      63     110 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0016
                Snapin_Pallidin 39 lnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslne 77
                                     +k++++ e+   +v   +++y+ +L +i++ +++l++
  gi|119719566|ref|YP_920061.1|  7 TIAKYQQTLEELR-AVTLSIQQYRGRLLEIERTLKALEQ 44
                                   4455555555444.6888***************999986 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.012
                Snapin_Pallidin  16 deldeklkelrqsQeeLleqldrlnekLkel 46 
                                    + l+ +l+e ++  + L+e+l +l ++L+++
  gi|119719566|ref|YP_920061.1|  75 ELLQLRLEEFTKREKLLRERLASLEKQLRSA 105
                                    567889*********************9975 PP

>> Adeno_E3A  Adenovirus E3A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00018       0.2      14      73 ..      33      93 ..      22     101 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00018
                      Adeno_E3A 14 ldhcrrhkcfargsgefcyfelpeehiegpahgv..rlttqveltrslireftkrpllvere 73
                                   l+  r  k++ +  g f+y  + +  i+ p   v   l ++ el +  + eftkr  l+ re
  gi|119719566|ref|YP_920061.1| 33 LEIERTLKALEQSQGGFVYRSMGNILIQTPREEVmkELNSEKELLQLRLEEFTKREKLL-RE 93
                                   55668889999********************998435889999************8665.33 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.8    0.0039       4.4      47      89 ..       5      47 ..       2      52 .. 0.91
   2 ?    8.3   0.9    0.0011       1.3      51      91 ..      65     105 ..      60     111 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0039
                        DUF3450 47 qellaeyralkeeleslevyneqlerlvasqeqeiasleeqie 89
                                   q+  a+y++  eel + ++  +q++  + + e++++ le+++ 
  gi|119719566|ref|YP_920061.1|  5 QQTIAKYQQTLEELRAVTLSIQQYRGRLLEIERTLKALEQSQG 47
                                   677899*********************************9875 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0011
                        DUF3450  51 aeyralkeeleslevyneqlerlvasqeqeiasleeqieei 91 
                                    + +++l++e+e l++  e+ ++  + +++++asle+q+ ++
  gi|119719566|ref|YP_920061.1|  65 EVMKELNSEKELLQLRLEEFTKREKLLRERLASLEKQLRSA 105
                                    558999******************************99875 PP

>> DUF3287  Protein of unknown function (DUF3287)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00035      0.39      61     106 ..       8      53 ..       3      72 .. 0.86
   2 ?    1.5   1.1      0.21   2.3e+02      60      93 ..      70     103 ..      63     108 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00035
                        DUF3287  61 vekHrrlcderqklgkkrqtleaRiarveRklreleseprdWeele 106
                                    + k ++  +e + + + +q+   R+ ++eR l+ le   + +  + 
  gi|119719566|ref|YP_920061.1|   8 IAKYQQTLEELRAVTLSIQQYRGRLLEIERTLKALEQSQGGFVYRS 53 
                                    67889999999************************98877666655 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.21
                        DUF3287  60 vvekHrrlcderqklgkkrqtleaRiarveRklr 93 
                                    +  +   l ++ ++  k+ + l  R+a +e++lr
  gi|119719566|ref|YP_920061.1|  70 LNSEKELLQLRLEEFTKREKLLRERLASLEKQLR 103
                                    5555555666777888888888899999999998 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.9    0.0067       7.5     274     312 ..       6      44 ..       3      47 .. 0.92
   2 ?    6.1   0.2    0.0042       4.7     241     282 ..      64     105 ..      55     112 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0067
                          IFT57 274 ellqeyreaqeelsevkekykqlsegvseltrelaeise 312
                                    +++++y+++ eel +v+ +++q  +++ e +r+l+ +++
  gi|119719566|ref|YP_920061.1|   6 QTIAKYQQTLEELRAVTLSIQQYRGRLLEIERTLKALEQ 44 
                                    7899*****************************999876 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0042
                          IFT57 241 petksqlkklhedisktlekiesrEkylnsqleellqeyrea 282
                                    +e+ ++l+  +e ++  le+ ++rEk l ++l +l +++r+a
  gi|119719566|ref|YP_920061.1|  64 EEVMKELNSEKELLQLRLEEFTKREKLLRERLASLEKQLRSA 105
                                    67778888888899999*****************99999987 PP

>> DUF4140  N-terminal domain of unknown function (DUF4140)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.2     0.018        20      57      94 ..       6      45 ..       1      49 [. 0.68
   2 ?    7.0   1.2    0.0072       8.1      65      97 ..      64      97 ..      55     105 .. 0.60

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.018
                        DUF4140 57 vpnreaeee..elkalraeleeledelaaledelaaaear 94
                                   ++  + +++  el+a++ ++++ + +l ++e++l+a+e++
  gi|119719566|ref|YP_920061.1|  6 QTIAKYQQTleELRAVTLSIQQYRGRLLEIERTLKALEQS 45
                                   3333333334368888889999999999999999998876 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0072
                        DUF4140 65 ee.lkalraeleeledelaaledelaaaearlaf 97
                                   ee +k+l++e e l+ +l++ +++ + +++rla 
  gi|119719566|ref|YP_920061.1| 64 EEvMKELNSEKELLQLRLEEFTKREKLLRERLAS 97
                                   3336666666666666666666666666666654 PP

>> JIP_LZII  JNK-interacting protein  leucine zipper II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.2     0.022        25      46      71 .]      15      40 ..       3      40 .. 0.88
   2 ?    7.7   6.4    0.0035       3.9      36      71 .]      68     103 ..      65     103 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.022
                       JIP_LZII 46 reEleslqkakerlesrikelEeelk 71
                                    eEl++++ + ++ + r+ e+E +lk
  gi|119719566|ref|YP_920061.1| 15 LEELRAVTLSIQQYRGRLLEIERTLK 40
                                   489********************998 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0035
                       JIP_LZII  36 deLtsereiLreEleslqkakerlesrikelEeelk 71 
                                     eL+se+e L+  le+ +k  + l++r++ lE++l+
  gi|119719566|ref|YP_920061.1|  68 KELNSEKELLQLRLEEFTKREKLLRERLASLEKQLR 103
                                    599*****************************9986 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.7    0.0073       8.2       1      34 [.      11      44 ..       5      60 .. 0.66
   2 ?    6.8   1.9    0.0052       5.8      68     116 ..      56     104 ..      54     107 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0073
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                      Prefoldin  1 lkeeleslqaelaqlkeaieelektletlktlkk 34
                                   ++++le+l+a + ++++   +l +++ tlk l++
  gi|119719566|ref|YP_920061.1| 11 YQQTLEELRAVTLSIQQYRGRLLEIERTLKALEQ 44
                                   6677777777555555555555555555555544 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0052
                                    TEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Prefoldin  68 gyyveksleeAiellkkkleelekqlekleeeleklkdqittleanlaq 116
                                    ++ +  + ee ++ l+ ++e l+  le++++  + l++++ +le++l+ 
  gi|119719566|ref|YP_920061.1|  56 NILIQTPREEVMKELNSEKELLQLRLEEFTKREKLLRERLASLEKQLRS 104
                                    5667778899999999999999999999999999999999999999875 PP

>> DUF737  Protein of unknown function (DUF737)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   6.9    0.0016       1.8      85     177 ..       6     101 ..       2     109 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0016
                         DUF737  85 kikeelqkrleeeqakaeavqeelakllerEreaaq......eelteailrerlstedErlkaqllelerkarqLeekek 158
                                    ++ +  q++lee +a + ++q+   +lle Er+ ++        + +++    ++t +E+ + +   l++    L+ + +
  gi|119719566|ref|YP_920061.1|   6 QTIAKYQQTLEELRAVTLSIQQYRGRLLEIERTLKAleqsqgGFVYRSMGNILIQTPREEVMKE---LNSEKELLQLRLE 82 
                                    4455667889******99****888888888876654211113333444444444444444333...4677788999*** PP

                         DUF737 159 eLkkqdafYkeqlakLeek 177
                                    e  k++++ +e+la Le++
  gi|119719566|ref|YP_920061.1|  83 EFTKREKLLRERLASLEKQ 101
                                    *****************97 PP

>> Fzo_mitofusin  fzo-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.3     0.054        60     119     157 ..       6      44 ..       3      47 .. 0.85
   2 ?    7.7   2.9    0.0021       2.3     115     154 ..      64     104 ..      50     108 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.054
                  Fzo_mitofusin 119 eeikelekeiekleevqkkakllrnkaslleseLekfee 157
                                    + i++ ++++e+l +v+ + ++ r +  ++e+ L++ e+
  gi|119719566|ref|YP_920061.1|   6 QTIAKYQQTLEELRAVTLSIQQYRGRLLEIERTLKALEQ 44 
                                    568889999999999999999999999999999988765 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0021
                  Fzo_mitofusin 115 keleeeikelekeie.kleevqkkakllrnkaslleseLek 154
                                    +e+ +e+++ ++ ++ +lee +k+ kllr++  +le++L++
  gi|119719566|ref|YP_920061.1|  64 EEVMKELNSEKELLQlRLEEFTKREKLLRERLASLEKQLRS 104
                                    555566666555555489********************986 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   2.2       0.1   1.1e+02      12      31 ..       8      27 ..       4      49 .. 0.50
   2 ?    8.1   1.0    0.0036         4      16      55 ..      64     103 ..      61     109 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.1
                                   HHHHHHHHHHHHHHHHHHHH CS
                           SlyX 12 lafqedtieeLndvvaeqqq 31
                                   +a  ++t+eeL +v    qq
  gi|119719566|ref|YP_920061.1|  8 IAKYQQTLEELRAVTLSIQQ 27
                                   44445555555555544444 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0036
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXX CS
                           SlyX  16 edtieeLndvvaeqqqqidrlqrqlrllaerlkeleessg 55 
                                    e++++eLn +    q ++++ +++ +ll+erl++le++ +
  gi|119719566|ref|YP_920061.1|  64 EEVMKELNSEKELLQLRLEEFTKREKLLRERLASLEKQLR 103
                                    78889999999999*********************99876 PP

>> DUF4078  Domain of unknown function (DUF4078)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.5     0.013        14      38      70 ..       2      34 ..       1      46 [. 0.81
   2 ?    5.1   2.6     0.026        29      43      79 ..      62     101 ..      51     105 .. 0.63

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.013
                        DUF4078 38 skDeeeRkkqmeeLeelreeTeeqRkkreelke 70
                                   s D+++ +k +++Leelr+ T   ++ r +l e
  gi|119719566|ref|YP_920061.1|  2 SVDQQTIAKYQQTLEELRAVTLSIQQYRGRLLE 34
                                   88999999*************999888877655 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.026
                        DUF4078  43 eRkkqmeeLeelreeT...eeqRkkreelkekRkaeleer 79 
                                     R++ m+eL++++e      e+ +kre+l ++R a le++
  gi|119719566|ref|YP_920061.1|  62 PREEVMKELNSEKELLqlrLEEFTKREKLLRERLASLEKQ 101
                                    5888888888875543111344455666666666666655 PP

>> FTA4  Kinetochore complex Fta4 of Sim4 subunit, or CENP-50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   3.6    0.0014       1.6     123     178 ..       5      71 ..       1      84 [. 0.75
   2 ?    1.3   2.6      0.24   2.7e+02     129     155 ..      74     100 ..      60     111 .. 0.50

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0014
                           FTA4 123 eallerYaelrarLielserrqqlqarlarlrklkallepflgs...........edpqesvqenlv 178
                                    ++++++Y+++ ++L ++  + qq + rl + +++ + le+ +g            ++p+e+v ++l 
  gi|119719566|ref|YP_920061.1|   5 QQTIAKYQQTLEELRAVTLSIQQYRGRLLEIERTLKALEQSQGGfvyrsmgniliQTPREEVMKELN 71 
                                    7789************************************987677666655555444444444443 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.24
                           FTA4 129 YaelrarLielserrqqlqarlarlrk 155
                                     + l  rL e  +r + l++rla l+k
  gi|119719566|ref|YP_920061.1|  74 KELLQLRLEEFTKREKLLRERLASLEK 100
                                    333444555555555555555555543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1193  (0.0665402); expected 358.6 (0.02)
Passed bias filter:                      632  (0.0352502); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 748.90
//
Query:       gi|119719567|ref|YP_920062.1|  [L=658]
Description: hypothetical protein Tpen_0657 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.9e-13   48.2   9.3    5.8e-06   26.5   1.0    6.6  7  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
    9.9e-06   25.5   0.2    0.00085   19.3   0.8    3.4  3  Big_1            Bacterial Ig-like domain (group 1)
      5e-05   23.2   6.5      0.091   12.8   0.2    5.2  5  CarbopepD_reg_2  CarboxypepD_reg-like domain
  ------ inclusion threshold ------
      0.027   14.7   9.4       0.24   11.6   4.4    3.9  4  Big_3_5          Bacterial Ig-like domain (group 3)
       0.16   11.6   0.0       0.33   10.6   0.0    1.5  1  AraC_binding_2   AraC-binding-like domain


Domain annotation for each model (and alignments):
>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0       0.2     7e+02      42      78 ..      39      74 ..      36      78 .. 0.71
   2 ?   -0.2   0.0      0.34   1.2e+03      46      81 ..     119     151 ..     116     152 .. 0.75
   3 ?    1.2   0.0      0.12   4.4e+02      40      76 ..     196     230 ..     195     236 .. 0.75
   4 !   10.7   0.0   0.00014       0.5       2      58 ..     241     299 ..     240     322 .. 0.79
   5 !    5.9   0.0    0.0042        15      44      63 ..     372     392 ..     370     408 .. 0.81
   6 ?   -0.2   0.0      0.34   1.2e+03       7      55 ..     416     466 ..     410     492 .. 0.63
   7 !   26.5   1.0   1.6e-09   5.8e-06       6      74 ..     498     570 ..     493     578 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.2
                CarboxypepD_reg 42 lrglpp.gtysvtvsapGyatatreevtltagqtttld 78
                                   ++ l+  g y+vt+++     + +  v +++ +t  l+
  gi|119719567|ref|YP_920062.1| 39 IN-LTSyGVYNVTIEYLKVLVFKS-PVNISNSTTIKLR 74
                                   54.5555*********99999996.5888877765443 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.34
                CarboxypepD_reg  46 ppgtysvtvsapGyatatreevtltagqtttlditL 81 
                                    p gt++  vs+++   +   ++t++ g++t+ldi+L
  gi|119719567|ref|YP_920062.1| 119 PFGTFRYFVSFSNINRTG--SFTVD-GRSTRLDIVL 151
                                    557777788887777666..48888.9999999987 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.12
                CarboxypepD_reg  40 frlrglppgtysvtvsapGyatatreevtltagqttt 76 
                                    ++l+   +g y ++v + G   ++  ++t+++++ ++
  gi|119719567|ref|YP_920062.1| 196 YSLSYPLAGLYHLRVDYRGQTVYEG-DFTIDKNN-RR 230
                                    777777789*********9988885.79999554.44 PP

  == domain 4  score: 10.7 bits;  conditional E-value: 0.00014
                CarboxypepD_reg   2 isGrVtdasgapiagatVtvtn.adtgtvastttdadGafrlrglpp.gtysvtvsapG 58 
                                    ++ rV  a+++p+    ++++  ++ + +  +t ++dG+f+l++ p   +y+++v ++ 
  gi|119719567|ref|YP_920062.1| 241 VEIRVLTADNRPLYSDDISFEVvSPLNDRMKVTPNQDGYFSLEFCPYnWRYTLRVKSNT 299
                                    5667888888888777777665234577899****************9*******8765 PP

  == domain 5  score: 5.9 bits;  conditional E-value: 0.0042
                CarboxypepD_reg  44 glpp.gtysvtvsapGyatat 63 
                                    +lp  g+y+v+v+++Gy+ +t
  gi|119719567|ref|YP_920062.1| 372 FLPIrGRYRVVVEYAGYRWTT 392
                                    57778************8555 PP

  == domain 6  score: -0.2 bits;  conditional E-value: 0.34
                CarboxypepD_reg   7 tdasgapiagatVtvtnadtgtvastttd..adGafrlrglpp..gtysvtvs 55 
                                    +d +g+p+ g  V+++   ++ ++ +  d  ++G+  ++++p   g+ sv  s
  gi|119719567|ref|YP_920062.1| 416 VDLDGNPLYGCIVALRV--GQPSRLVFRDqlRNGQAFFSFVPSdyGSLSVNCS 466
                                    78889999999998883..3323333333225666666666665555555554 PP

  == domain 7  score: 26.5 bits;  conditional E-value: 1.6e-09
                CarboxypepD_reg   6 VtdasgapiagatVtvtnadtgt..vastttdadGafrlrglpp...gtysvtvsapGyatatreevtltagqt 74 
                                    V+   +++++ga+Vt++ + +gt  + stttd++G+  lr++p     + ++tvs+ G+ +++    + ++ q+
  gi|119719567|ref|YP_920062.1| 498 VKGWFNRALTGANVTLEVKYKGTvlTFSTTTDSTGTAVLRNVPLplgSNVTLTVSYGGFSEVRN-VYEGSPRQE 570
                                    55557899*******998877763479***************9999999**********99984.455555555 PP

>> Big_1  Bacterial Ig-like domain (group 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       0.3   1.1e+03       9      49 ..     241     281 ..     240     284 .. 0.79
   2 ?   -0.5   0.0      0.36   1.3e+03       9      30 ..     411     432 ..     409     443 .. 0.81
   3 !   19.3   0.8   2.4e-07   0.00085       8      49 ..     493     535 ..     490     537 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.3
                          Big_1   9 ltatvkDangnpvagatVtfsvsggalsassgtTdanGkat 49 
                                    + ++v  a++ p+    ++f+v +  +   ++t +++G ++
  gi|119719567|ref|YP_920062.1| 241 VEIRVLTADNRPLYSDDISFEVVSPLNDRMKVTPNQDGYFS 281
                                    6789999*************998866666677777777766 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.36
                          Big_1   9 ltatvkDangnpvagatVtfsv 30 
                                    +++ ++D +gnp+ g  V ++v
  gi|119719567|ref|YP_920062.1| 411 VRISAVDLDGNPLYGCIVALRV 432
                                    677899*******998887776 PP

  == domain 3  score: 19.3 bits;  conditional E-value: 2.4e-07
                          Big_1   8 tltatvkDangnpvagatVtfsvsg.galsassgtTdanGkat 49 
                                    t+ +tvk  ++ ++ ga+Vt++v   g++++ s+tTd+ G+a+
  gi|119719567|ref|YP_920062.1| 493 TFLVTVKGWFNRALTGANVTLEVKYkGTVLTFSTTTDSTGTAV 535
                                    788**********************99999***********96 PP

>> CarbopepD_reg_2  CarboxypepD_reg-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.4      0.22   7.8e+02      38      78 ..      39      79 ..      37      86 .. 0.82
   2 ?    2.4   0.0     0.044   1.6e+02      35      69 ..     195     229 ..     195     237 .. 0.82
   3 !    4.6   0.0    0.0088        32      25      52 ..     269     297 ..     257     303 .. 0.82
   4 ?    0.5   0.0      0.18   6.3e+02      43      56 ..     376     389 ..     373     397 .. 0.88
   5 !   12.8   0.2   2.5e-05     0.091      12      62 ..     504     563 ..     498     579 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.22
                CarbopepD_reg_2 38 lknlpagkytLvvsyvGyktqekkvtvskektldvnillke 78
                                   ++   +g y ++++y+     +  v++s+ +t++++++ ++
  gi|119719567|ref|YP_920062.1| 39 INLTSYGVYNVTIEYLKVLVFKSPVNISNSTTIKLRVNITK 79
                                   55667899999999999999999******999999887665 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.044
                CarbopepD_reg_2  35 nFelknlpagkytLvvsyvGyktqekkvtvskekt 69 
                                    +++l+++ ag y+L+v y G +  e   t++k+++
  gi|119719567|ref|YP_920062.1| 195 KYSLSYPLAGLYHLRVDYRGQTVYEGDFTIDKNNR 229
                                    58999999999*********999999999987653 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.0088
                CarbopepD_reg_2  25 kkgtvTdenGnFelknlpag.kytLvvsy 52 
                                    + +++ +++G+F+l+  p++ +ytL+v++
  gi|119719567|ref|YP_920062.1| 269 RMKVTPNQDGYFSLEFCPYNwRYTLRVKS 297
                                    567888*********98886589**9975 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 0.18
                CarbopepD_reg_2  43 agkytLvvsyvGyk 56 
                                    +g+y++vv+y Gy+
  gi|119719567|ref|YP_920062.1| 376 RGRYRVVVEYAGYR 389
                                    599**********7 PP

  == domain 5  score: 12.8 bits;  conditional E-value: 2.5e-05
                CarbopepD_reg_2  12 eplpgatVyvkgtkkgtv......TdenGnFelknlpa...gkytLvvsyvGyktqekkv 62 
                                    ++l ga+V+++ + kgtv      Td+ G+  l+n+p     ++tL+vsy G+ ++    
  gi|119719567|ref|YP_920062.1| 504 RALTGANVTLEVKYKGTVltfsttTDSTGTAVLRNVPLplgSNVTLTVSYGGFSEVRNVY 563
                                    578899988866654443333333***********997554689*********9976554 PP

>> Big_3_5  Bacterial Ig-like domain (group 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.058   2.1e+02      49      69 ..      35      55 ..      22      79 .. 0.75
   2 ?   -0.2   0.0      0.31   1.1e+03      52      74 ..     197     219 ..     180     222 .. 0.81
   3 ?   -2.0   0.0       1.2   4.3e+03      58      70 ..     376     388 ..     320     406 .. 0.72
   4 ?   11.6   4.4   6.6e-05      0.24      11      71 ..     493     557 ..     482     575 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.058
                                   EEEEEE-SS-EEEEEEEEEE- CS
                        Big_3_5 49 AtltvsalaaGthsitAtYsG 69
                                   + +t+++++ G +++t +Y  
  gi|119719567|ref|YP_920062.1| 35 VRCTINLTSYGVYNVTIEYLK 55
                                   67999999**********975 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.31
                                    EEE-SS-EEEEEEEEEE-TTS-- CS
                        Big_3_5  52 tvsalaaGthsitAtYsGdanya 74 
                                    ++s   aG +++ + Y G++ y+
  gi|119719567|ref|YP_920062.1| 197 SLSYPLAGLYHLRVDYRGQTVYE 219
                                    4444458************9997 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.2
                                    -EEEEEEEEEE-T CS
                        Big_3_5  58 aGthsitAtYsGd 70 
                                     G + ++++Y+G 
  gi|119719567|ref|YP_920062.1| 376 RGRYRVVVEYAGY 388
                                    5788888888886 PP

  == domain 4  score: 11.6 bits;  conditional E-value: 6.6e-05
                                    EEEEE--CCCCTTS--.EEEEEE..TTEE-SS-EE--TTSEEEEEEE-SS-EE.EEEEEEEE-TT CS
                        Big_3_5  11 tltatVtaasggtptG.tVtftd..ggttlgtavllsanGtAtltvsalaaGt.hsitAtYsGda 71 
                                    t+ +tV++  + + tG +Vt+ +  +gt+l   ++++++GtA l    l+ G+  ++t++Y G +
  gi|119719567|ref|YP_920062.1| 493 TFLVTVKGWFNRALTGaNVTLEVkyKGTVLTFSTTTDSTGTAVLRNVPLPLGSnVTLTVSYGGFS 557
                                    78889998888999998999998778899977777778**************9459*****9965 PP

>> AraC_binding_2  AraC-binding-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   9.3e-05      0.33      38      94 ..     177     234 ..     174     256 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 9.3e-05
                 AraC_binding_2  38 rlrygaavsi.rpselddfylvqlplsGraeveqggrevvlgpgdavvldpgrpyrlr 94 
                                    +lryg   ++ + ++l+d y +++pl+G  +++++ r  ++ +gd+++   +r+++l 
  gi|119719567|ref|YP_920062.1| 177 TLRYGERIVLkEGPPLRDKYSLSYPLAGLYHLRVDYRGQTVYEGDFTIDKNNRRVELK 234
                                    6899988888455667**********************9******9997777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (658 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       678  (0.0378158); expected 358.6 (0.02)
Passed bias filter:                      568  (0.0316805); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.45
# Mc/sec: 4374.94
//
Query:       gi|119719568|ref|YP_920063.1|  [L=336]
Description: radical SAM domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.6e-15   56.4   0.0    8.1e-15   55.6   0.0    1.4  1  Radical_SAM  Radical SAM superfamily
  ------ inclusion threshold ------
      0.033   14.3   0.0      0.061   13.5   0.0    1.4  1  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.6   0.0   9.1e-19   8.1e-15       3     166 ..      34     202 ..      32     203 .. 0.83

  Alignments for each domain:
  == domain 1  score: 55.6 bits;  conditional E-value: 9.1e-19
                                    EESEESS--TTTSCCTT..HHHHHHHHHHHHHHHHHHHHHHHHHTT...SEEEEEESSTGGGSTTHHHHHHHHHHTCCCT CS
                                    xxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM   3 vtrgCnlrCsfCarpet..vrregrgrslsveeileevkelkaekg...vkevilgggepllypdfvellerlaklavpg 77 
                                    +t +C+l C+fC++     + r+ ++  ++ e+++  +  +++ kg   ++  i   g+pl y +++el++ l+      
  gi|119719568|ref|YP_920063.1|  34 PTSFCPLSCVFCSVDAGprSTRRLTEFLVDHEYLVSWFVDVAKAKGldkAHAYIDAVGDPLTYGRIIELVRLLSSTG-VA 112
                                    899************99996666666667777777766555433332147788888*******************95.** PP

                                    EEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT..CTSHHHHHHHHHHHHHHTTSET.EEEEEEEBTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                    Radical_SAM  78 iritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn..rghtfeevlealeklreagikr.vvdrivglpG 154
                                     +it+et g l+++e +++l+++g++r++l+++a+d+    + +   +  ++ +v+ + e+++++  +    +  v +pG
  gi|119719568|ref|YP_920063.1| 113 ESITIETHGALLTRELVDKLADAGLTRINLSVDALDPS-LARTLAgtPWFDVNRVISVAEYIASST-DIdLLIAPVWVPG 190
                                    **************************************.66666433555669********99984.334********** PP

                                    TSHHHHHHHHHH CS
                                    xxxxxxxxxxxx RF
                    Radical_SAM 155 endeeleellel 166
                                    +nd+e+  ++e+
  gi|119719568|ref|YP_920063.1| 191 VNDSEIPRIIEW 202
                                    ******999988 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   6.8e-06     0.061       5      92 ..      35     124 ..      32     146 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.8e-06
                        Fer4_14   5 lsgCnlsCkgCd....nketwkselgkpqteelleqilkdlkkseikiqglvltG.GePLhyenkkellklvkrlkeeyp 79 
                                    +s C+lsC++C      ++t + +   ++ e l++  ++ +k++  +++   +   G+PL y     +++lv+ l   + 
  gi|119719568|ref|YP_920063.1|  35 TSFCPLSCVFCSvdagPRSTRRLTEFLVDHEYLVSWFVDVAKAKGLDKAHAYIDAvGDPLTY---GRIIELVRLLSSTGV 111
                                    578********987763333333333344444444445567778888888888878****99...99************9 PP

                        Fer4_14  80 ekkiwletngtle 92 
                                      +i++et g l 
  gi|119719568|ref|YP_920063.1| 112 AESITIETHGALL 124
                                    9*******98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 2057.43
//
Query:       gi|119719569|ref|YP_920064.1|  [L=431]
Description: histidyl-tRNA synthetase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.2e-63  212.5   0.0    1.2e-62  212.0   0.0    1.2  1  tRNA-synt_His   Histidyl-tRNA synthetase
    7.7e-16   58.0   0.3    1.8e-15   56.8   0.3    1.6  1  HGTP_anticodon  Anticodon binding domain
    2.1e-10   40.9   0.0    8.5e-10   38.9   0.0    2.0  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
  ------ inclusion threshold ------
      0.015   14.4   0.4        2.9    6.9   0.1    2.8  2  tRNA-synt_2     tRNA synthetases class II (D, K and N)
      0.035   13.6   0.0      0.069   12.6   0.0    1.4  1  tRNA-synt_2d    tRNA synthetases class II core domain (F)


Domain annotation for each model (and alignments):
>> tRNA-synt_His  Histidyl-tRNA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  212.0   0.0   3.3e-66   1.2e-62       1     310 []      12     318 ..      12     318 .. 0.88

  Alignments for each domain:
  == domain 1  score: 212.0 bits;  conditional E-value: 3.3e-66
                                    T---EETCHHHHHHHHHHHHHHHHHHTT-EEEE--SEEEHHHHCTTSTCC.HHHS-EEE-TTSSEEEE-SSSHHHHHHHH CS
                  tRNA-synt_His   1 glrdllpeeaekieelrrrlldlfeswGYelVspPllEyldslltgaged.ldqtfklvDqsgrllglRaDiTpqvaRia 79 
                                    g+rd lpeea +++ +++++ ++fes+GY +V++P +Eyld l ++age+  +q++ ++D+ gr lglR ++T+ +aRi+
  gi|119719569|ref|YP_920064.1|  12 GTRDWLPEEAYAKRIVSEKIREVFESYGYGEVITPAFEYLDLLKAKAGEEvVEQIYAFKDKAGRELGLRFEMTTPIARIV 91 
                                    789********************************************999456*************************** PP

                                    HHHHHTSS-EEEEEEEEEEESS-SSTT--CCEEEEEEEEESS-SHHHHHHHHHHHHHHHHHHCTSSSEEEEEEETCHHHH CS
                  tRNA-synt_His  80 ahrlnrerplRlcYaGsvlrtrpdglgrsreplQvGaEliGaegleadlEvlslllealeaaagvkelrldlghvglvra 159
                                    a rl   +plR++Y  +v+r ++ + gr re+ Q+G+El+G +++e d+Ev+ + ++al+ a+g+k++ + +++ ++v+ 
  gi|119719569|ref|YP_920064.1|  92 ASRLDLAKPLRFYYVQPVWRYEEPQRGRWREFWQAGIELFGISEPEGDAEVVAVTFDALK-AVGLKDFDIRVNDRRVVED 170
                                    ***********************************************************7.******************* PP

                                    HHHHTT--HHHHHHHHHHHHCT-HHHHHHHHHC...CTTHHHCCHCC....HCCHCCCHHHHCHCCHCTHHHHHHHHHHH CS
                  tRNA-synt_His 160 lleaaglsesleeallaalarkdlaelkelaae...aglkealrellkal.elygdaevleealealaaapalqaaldel 235
                                    l+  ag++ +l    l++l++ d  + + +++e    gl+e++++   +l +l+++   +++           q  ++ l
  gi|119719569|ref|YP_920064.1| 171 LVLGAGIPGDLLPSALRVLDKMDKFGEEYVVSElakLGLREDAATS--LLeKLKSGSLDIDTS---------TQPGREGL 239
                                    ********************99987766666551002333333222..233444444444443.........34456677 PP

                                    HHHHHHHHHHHH.H-TTEEE-TT--TTTTT--SEEEEEEETT-SS..-SEEEEEECTTTGGG.T---EEEEEEEEHHHH CS
                  tRNA-synt_His 236 eelaallealak.pevrvtlDlaelrgyeYytGlvFaayaegvgq..aiarGGrYdelgaaf.grarpAtGfsldleal 310
                                    ++la +++ l++ ++++vt+D a +rg+ YytG+vF++ a +++    ia+GGrYd+l++++ g + pA G+++ +e+l
  gi|119719569|ref|YP_920064.1| 240 RRLALVVDTLKNcYGINVTVDYAIVRGLGYYTGFVFEVKAGSSEGlgSIAGGGRYDDLVSVVgGPKIPASGMAIGVERL 318
                                    77777777777779************************998877566***************999***********987 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.8   0.3   5.1e-19   1.8e-15       1      92 [.     336     426 ..     336     427 .. 0.96

  Alignments for each domain:
  == domain 1  score: 56.8 bits;  conditional E-value: 5.1e-19
                                    SEEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTCEEE CS
                 HGTP_anticodon   1 qvvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtreqe 80 
                                    +v+vip+++ + e++ +a  +a+eLr ag++v+l  s++s+ k ++ a + g +fa+++Ge+el++g+vtvrd+   ++e
  gi|119719569|ref|YP_920064.1| 336 DVCVIPVKK-TPEILSEAVAVARELRVAGMKVVLEVSERSLSKLLEAASKRGARFAIILGERELKEGVVTVRDLYLWKEE 414
                                    69******9.999*************************************************************999999 PP

                                    EEETTHHHHHHH CS
                 HGTP_anticodon  81 rvsldelveklk 92 
                                    +v++  l e+++
  gi|119719569|ref|YP_920064.1| 415 KVARPHLYEYIR 426
                                    999998888886 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   0.0   2.4e-13   8.5e-10       1     104 [.      67     163 ..      67     325 .. 0.67

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 2.4e-13
                                    EEEEETTSEEEEE-SSSHHHHHHHHHHHEEEBGGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEESGGGHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2b   1 YkledrndreyiLkPtneetfvelirdevlrskrLPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfhaeaslddsl 80 
                                    Y ++d+ +re+ L+ + ++++++++  +    k  Pl++y++q+++R+E++ +rG  R reF q + + f+  +  ++ +
  gi|119719569|ref|YP_920064.1|  67 YAFKDKAGRELGLRFEMTTPIARIVASRLDLAK--PLRFYYVQPVWRYEEP-QRG--RWREFWQAGIELFGISE--PEGD 139
                                    89************************9955669..****************.***..***************99..999* PP

                                    HHHHHHHHHHHHHTT.SCEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2b  81 rdlikaisriferlglefraiiel 104
                                    ++++ ++ + ++++gl+ + i+  
  gi|119719569|ref|YP_920064.1| 140 AEVVAVTFDALKAVGLKDFDIRVN 163
                                    ***************998766544 PP

>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1    0.0008       2.9      28     122 ..      27     130 ..      19     137 .. 0.65
   2 ?    3.6   0.0    0.0083        30     270     299 ..     294     323 ..     290     338 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0008
                                    HHHHHHHHHHHTT-EE----SEESS-......-SSSS.--EEEEETTT.T.....EEE-E-S-SHHHHHHHHHCTHSEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxx.xxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxx RF
                    tRNA-synt_2  28 vtkavrkyleengfieietPiLsksd......teega.rlFkvksrekek.....effaLtqspqlylellivagidrvf 95 
                                    v + +r+++e+ g+ e+ tP +   d      +ee   + +  k ++  +     +f + t    +   +l  a+  r +
  gi|119719569|ref|YP_920064.1|  27 VSEKIREVFESYGYGEVITPAFEYLDllkakaGEEVVeQIYAFKDKA--GrelglRFEMTTPIARIVASRLDLAKPLRFY 104
                                    77889999999999999999876555322111222220223332222..1335555555555566666777777788999 PP

                                    EEEEEE--S--BTTB-S-CEEEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    tRNA-synt_2  96 qiaraFRaEdsrtdrhlaEFtqieaem 122
                                     + +++R E+ +  r   EF+q  +e+
  gi|119719569|ref|YP_920064.1| 105 YVQPVWRYEEPQRGRWR-EFWQAGIEL 130
                                    99999999999999988.999988886 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.0083
                                    GHHHHHHHHCT--SEEEEEEEHHHHHHHHC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    tRNA-synt_2 270 fswylealeyGapphgGlglGldRlvmlll 299
                                    +++++ ++     p +G+++G++Rl+  l 
  gi|119719569|ref|YP_920064.1| 294 YDDLVSVVGGPKIPASGMAIGVERLLEALS 323
                                    55666666667789**********998775 PP

>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.9e-05     0.069      22     127 ..      27     126 ..      17     153 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.9e-05
                                    HHHHHHHHHHCTTCEESSTTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS-ECESEEE-SSTHHHHHHHH...TTS CS
                   tRNA-synt_2d  22 vleeikeiflelgfeevegpevesefynfdaLnvpqdhpaRdmqdtFylkkpekaveekllLRthttavqirtl...ekk 98 
                                    v+e+i+e+f ++g+ ev  p        f+ L++ + ++  ++ +  y  k++    ++l LR  +t+  +r +    + 
  gi|119719569|ref|YP_920064.1|  27 VSEKIREVFESYGYGEVITPA-------FEYLDLLKAKAGEEVVEQIYAFKDKA--GRELGLRFEMTTPIARIVasrLDL 97 
                                    789***********9998876.......57777777777788877777767777..789**************9877777 PP

                                    -SSEEEEEEEEEEBSST-SSSB-SEEEEE CS
                   tRNA-synt_2d  99 kppikiisigrvfRrdavDathlaeFhqv 127
                                     +p+++  ++ v+R ++  + +  eF q+
  gi|119719569|ref|YP_920064.1|  98 AKPLRFYYVQPVWRYEEPQRGRWREFWQA 126
                                    89***************999999999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2945.53
//
Query:       gi|119719570|ref|YP_920065.1|  [L=346]
Description: bifunctional phosphoglucose/phosphomannose isomerase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.7e-38  130.6   0.0    1.2e-37  129.3   0.0    1.7  2  bact-PGI_C  Bacterial phospho-glucose isomerase C-terminal SI
    1.7e-06   27.9   0.1    8.4e-06   25.7   0.1    2.2  3  SIS         SIS domain
  ------ inclusion threshold ------
      0.019   15.0   0.0      0.043   13.8   0.0    1.6  1  SIS_2       SIS domain
      0.094   12.7   0.0       0.15   12.1   0.0    1.4  1  PAC2        PAC2 family


Domain annotation for each model (and alignments):
>> bact-PGI_C  Bacterial phospho-glucose isomerase C-terminal SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.4   6.1e+03       7      23 ..      97     113 ..      87     123 .. 0.64
   2 !  129.3   0.0   2.6e-41   1.2e-37      14     151 ..     197     332 ..     182     333 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.4
                                    HHHHHHTTSEEEEE-.. CS
                     bact-PGI_C   7 qlAlelagklpviygss 23 
                                     +A++ + k+pv++ +s
  gi|119719570|ref|YP_920065.1|  97 VVAQATQAKVPVVAVTS 113
                                    45666666666666543 PP

  == domain 2  score: 129.3 bits;  conditional E-value: 2.6e-41
                                    TSEEEEE-..TT-THHHHHHHHHHHHTT----B---.SSHHHHHHHTTSS-GGGGTTEEEEEESSHH........HHHHH CS
                     bact-PGI_C  14 gklpviygssellevaArRfknqlnenAKipafagvlpeanhneivgleaeeelkkrlrlvllrdeeehprvkkraeivk 93 
                                    g +p++y+   ++ +a +Rfk+qlnenAKi+af++ lpeanhnei+g+  +++l  ++ +vl+r +ee   + +r+++++
  gi|119719570|ref|YP_920065.1| 197 GLTPLVYS-YRPYISAGYRFKTQLNENAKIHAFYADLPEANHNEIMGW--SSPLAGKFFAVLIRGREEPFYMDARISFLR 273
                                    479*****.***************************************..68************88889*********** PP

                                    HHHTTTSSEEEEE---SSSH.HHHHHHHHHHHHHHHHHHHHHCT---S-TTTTHHHHH. CS
                     bact-PGI_C  94 elaeergvrvtevkaegesp.lerlaslillgDfvSvylAllrgvDPtpvpaIdelKee 151
                                    el+e++g+++ e k+  + p  ++l++li+++D+vSv +Al  gvDPtpv++I++lK+ 
  gi|119719570|ref|YP_920065.1| 274 ELFETQGIPFLEQKPVFDAPhTCELLQLIYMLDLVSVAVALKMGVDPTPVDTITKLKKV 332
                                    ****************99999************************************96 PP

>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.1   1.9e-09   8.4e-06      49      88 ..      74     113 ..      32     128 .. 0.74
   2 ?   -1.6   0.0       0.5   2.2e+03      37      65 ..     180     208 ..     178     223 .. 0.85
   3 ?   -3.7   0.0       2.3     1e+04      20      45 ..     212     237 ..     208     239 .. 0.75

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 1.9e-09
                                    GG-STTCEEEEEESSSHHHHHHHHHHHHHHTTSEEEEEES CS
                            SIS  49 alideddlvilisfsgetkdlvaaaelakergakiiaITd 88 
                                    a +de+ l++++s+sg+t ++++++ +a++ +++++a+T+
  gi|119719570|ref|YP_920065.1|  74 AFVDENYLLVAVSYSGNTEETIRVVAQATQAKVPVVAVTS 113
                                    689************************************5 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.5
                                    EEEHHHHHHTGGGG-STTCEEEEEESSSH CS
                            SIS  37 vedaselkhgvlalideddlvilisfsge 65 
                                    ++ ase   +v++l++++   ++ s++++
  gi|119719570|ref|YP_920065.1| 180 FSRASESAENVKSLVEKGLTPLVYSYRPY 208
                                    56788889999999999999888888887 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 2.3
                                    HHHHHHHHHHHHTSEEEEEEHHHHHH CS
                            SIS  20 akelalkleeiggivvevedaselkh 45 
                                    +  ++ +l+e ++i++++ d +e  h
  gi|119719570|ref|YP_920065.1| 212 GYRFKTQLNENAKIHAFYADLPEANH 237
                                    55678888888888888888777666 PP

>> SIS_2  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   9.7e-06     0.043     104     138 .]      79     113 ..      67     113 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9.7e-06
                                    T-EEEEE-SS--SHHHHHHHHHHHHHT-EEEEEE- CS
                          SIS_2 104 gDvLlviSnsGnnavvveaaeaakergmkviAlts 138
                                    + +L+ +S sGn +  + ++ +a +  ++v+A+ts
  gi|119719570|ref|YP_920065.1|  79 NYLLVAVSYSGNTEETIRVVAQATQAKVPVVAVTS 113
                                    557999****************************8 PP

>> PAC2  PAC2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   3.3e-05      0.15     122     200 ..      85     163 ..      13     179 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.3e-05
                                    EEEEESSHHHHHHHH...CT-CEEEEHHHHHHHHHH.HHTT-EEEEEEEEEECCC--HHHHHHHHHHHHHHHT---HCHH CS
                           PAC2 122 vtgaatdeelleele...eseyggivgitglLlsaa.kergipavgllaevphylpdPkaaaalleflskllglevdted 197
                                    v++ +++ee ++ +    +++ ++++  +g Ll+++ +++g+p+v+l    p+    P +a ++l+++   +++ +   +
  gi|119719570|ref|YP_920065.1|  85 VSYSGNTEETIRVVAqatQAKVPVVAVTSGGLLQRFaEKYGLPVVSLPMGLPPRAAFPYMA-CALSAI---VEVAIGEAN 160
                                    56667777777555333344889999999999999989***************99888888.666666...333333334 PP

                                    HHH CS
                           PAC2 198 Lee 200
                                    L +
  gi|119719570|ref|YP_920065.1| 161 LLS 163
                                    444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2403.25
//
Query:       gi|119719571|ref|YP_920066.1|  [L=91]
Description: elongation factor 1-beta [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      1e-17   64.1   0.0    1.1e-17   64.0   0.0    1.0  1  EF1_GNE      EF-1 guanine nucleotide exchange domain
  ------ inclusion threshold ------
        0.1   12.8   0.1        2.5    8.3   0.0    2.1  2  RPN13_C      UCH-binding domain
        0.1   12.9   0.1       0.19   12.1   0.1    1.4  1  Glu-tRNAGln  Glu-tRNAGln amidotransferase C subunit


Domain annotation for each model (and alignments):
>> EF1_GNE  EF-1 guanine nucleotide exchange domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.0   0.0   1.8e-21   1.1e-17       2      89 ..       6      88 ..       5      89 .. 0.94

  Alignments for each domain:
  == domain 1  score: 64.0 bits;  conditional E-value: 1.8e-21
                                   EEEEEEESSS---HHHHHHHHHH.HS-T.SEE--.--EEE-SSS-EEEEEEEEES.SS-GGGGHHHHHHTTS-S.....SEE CS
                        EF1_GNE  2 vvlevkPeddetdleelekkvksikleg.lvwgeasklepiafGlkkLqiscvie.ddkvstdeleekieeiegeledlVqs 81
                                   v+l+v P+d+et  eel kk+ + +l++ +++ + ++ epiafGl++L++ + ++ +++++t+ele  i++++g     V++
  gi|119719571|ref|YP_920066.1|  6 VLLRVLPDDAETKPEELYKKIAA-ALPEkYQVAQ-YQAEPIAFGLEALRMVILMPeETEGGTEELETIIQSVQG-----VSQ 80
                                   789********************.88777****5.*******************978899**************.....*** PP

                                   EEEEEEEE CS
                        EF1_GNE 82 veivsfnk 89
                                   v++ ++++
  gi|119719571|ref|YP_920066.1| 81 VDVLNVTR 88
                                   ****9987 PP

>> RPN13_C  UCH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.021   1.2e+02      42      63 ..       6      27 ..       2      37 .. 0.78
   2 ?    8.3   0.0   0.00041       2.5      43      75 ..      53      85 ..      17      87 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.021
                        RPN13_C 42 eLashLPeegeateeelretlr 63
                                    L+  LP++ e ++eel + ++
  gi|119719571|ref|YP_920066.1|  6 VLLRVLPDDAETKPEELYKKIA 27
                                   5788899988888888887775 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00041
                        RPN13_C 43 LashLPeegeateeelretlrSPqfrqalssls 75
                                   ++ ++Pee+e   eel+++++S q  ++++ l+
  gi|119719571|ref|YP_920066.1| 53 MVILMPEETEGGTEELETIIQSVQGVSQVDVLN 85
                                   5668999999999**********9888888775 PP

>> Glu-tRNAGln  Glu-tRNAGln amidotransferase C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   3.1e-05      0.19       3      32 ..      58      87 ..      56      90 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.1e-05
                                   HHHHHHHHHHHHHHHHHHTTCGCS--TT-- CS
                    Glu-tRNAGln  3 eeEleklakelnsildyveqLqevdttgve 32
                                   +eE e  ++el+ i++ v+ +++vd+ +v+
  gi|119719571|ref|YP_920066.1| 58 PEETEGGTEELETIIQSVQGVSQVDVLNVT 87
                                   7999999******************87885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 651.02
//
Query:       gi|119719572|ref|YP_920067.1|  [L=59]
Description: hypothetical protein Tpen_0662 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.7e-14   52.0  14.8    5.5e-13   48.6   5.5    2.5  2  DUF1610          Domain of unknown function (DUF1610)
    5.5e-06   25.9  20.0    0.00011   21.8   3.6    3.1  2  zinc_ribbon_2    zinc-ribbon domain
    9.7e-05   22.3  11.6     0.0048   16.9  11.9    2.1  1  DZR              Double zinc ribbon
    0.00065   20.0   6.7    0.00076   19.8   6.7    1.1  1  Rhodanese_C      Rhodanase C-terminal
     0.0018   18.3  11.1      0.013   15.5   0.4    2.0  2  HypA             Hydrogenase/urease nickel incorporation, met
     0.0025   17.1  16.7      0.089   12.2   0.2    4.0  4  zf-ribbon_3      zinc-ribbon domain
     0.0031   18.0   9.6      0.052   14.0  10.0    2.0  1  zf-CHY           CHY zinc finger
     0.0036   17.1  14.0      0.011   15.5   3.3    3.5  2  HscB_4_cys       Co-chaperone HscB tetracysteine metal bindin
     0.0041   17.4  11.5      0.099   13.0   3.8    2.1  2  C1_2             C1 domain
     0.0095   13.9   4.4       0.01   13.7   4.4    1.0  1  PolC_DP2         DNA polymerase II large subunit DP2
  ------ inclusion threshold ------
      0.013   15.2  16.8       0.85    9.4   3.0    3.7  3  zinc_ribbon_10   Predicted integral membrane zinc-ribbon meta
      0.015   15.4  11.0       0.47   10.6   1.4    2.9  2  DUF1272          Protein of unknown function (DUF1272)
      0.018   14.6  15.0       0.99    9.1   0.2    4.0  4  zf_UBZ           Ubiquitin-Binding Zinc Finger
       0.02   15.0  19.7        2.3    8.4   0.1    4.0  3  zf-ACC           Acetyl-coA carboxylase zinc finger domain
      0.024   14.6  11.6       0.81    9.7   6.5    3.5  2  Nudix_N_2        Nudix N-terminal
      0.025   14.7   7.5        0.2   11.8   4.8    2.5  2  zf-B_box         B-box zinc finger
      0.026   14.4  13.6        1.9    8.5   0.0    3.9  3  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
      0.026   14.5  12.7        1.3    9.1   0.1    3.7  3  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon
      0.027   14.4   5.5      0.032   14.2   5.5    1.0  1  zf-RING_9        Putative zinc-RING and/or ribbon
      0.043   14.0   5.4      0.052   13.8   5.4    1.1  1  FYVE_2           FYVE-type zinc finger
      0.049   13.6   9.6        1.2    9.2   9.8    2.1  1  zinc-ribbons_6   zinc-ribbons
      0.057   13.3  12.8        0.3   11.0   1.3    2.2  2  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.064   13.2   9.7       0.16   12.0   4.4    2.2  2  zf-C2HC5         Putative zinc finger motif, C2HC5-type
      0.067   13.1  17.6       0.49   10.4   0.2    4.0  4  zinc_ribbon_4    zinc-ribbon domain
        0.1   12.9  10.7       0.23   11.7   5.9    2.1  2  IBR              IBR domain, a half RING-finger domain
        0.1   12.7  12.1       0.33   11.1   0.6    2.1  2  zf-MYND          MYND finger
       0.12   12.5  14.2        7.3    6.8   3.0    3.1  2  zf-Mss51         Zinc-finger of mitochondrial splicing suppre
       0.13   12.3  10.9       0.29   11.1   1.7    2.3  2  Prok-RING_1      Prokaryotic RING finger family 1
       0.15   12.2  10.8          2    8.6   4.6    2.2  2  NOB1_Zn_bind     Nin one binding (NOB1) Zn-ribbon like
       0.22   11.3  21.3        0.8    9.5   0.1    3.9  3  Rubredoxin_2     Rubredoxin metal binding domain
       0.27   11.4   8.5        4.1    7.6   8.5    2.2  1  zf-UBR           Putative zinc finger in N-recognin (UBR box)
       0.32   10.8  17.7        1.1    9.1   5.4    3.8  2  A2L_zn_ribbon    A2L zinc ribbon domain
       0.43   10.2   6.6       0.21   11.2   3.4    2.0  2  DUF2321          Uncharacterized protein conserved in bacteri
       0.46   10.6  17.6       0.18   11.9   2.9    3.3  2  Zn-ribbon_8      Zinc ribbon domain
       0.47   10.4  20.8        1.4    8.8   8.0    3.3  2  zf-HIT           HIT zinc finger
       0.48   10.4  23.8        1.5    8.9   0.6    3.8  3  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
       0.53   10.3  11.8        5.6    7.0  11.8    2.4  1  zf-RING_5        zinc-RING finger domain
       0.54    9.9  17.1        1.7    8.3   0.5    3.9  4  Sgf11            Sgf11 (transcriptional regulation protein)
        0.6   10.1  20.3         31    4.6   0.3    4.0  2  Zn_ribbon_SprT   SprT-like zinc ribbon domain
       0.63    9.7   0.1       0.63    9.7   0.1    3.3  3  zf_C2H2_13       Zinc finger domain
       0.64    9.6  14.8        0.6    9.7   0.8    3.9  4  zf_C2H2_10       C2H2 type zinc-finger
       0.77   10.3  14.3        8.7    7.0   0.1    4.0  4  zf-C2H2          Zinc finger, C2H2 type
        1.4    8.8  10.6        2.8    7.8   3.0    2.9  3  ZZ               Zinc finger, ZZ type
        1.6    9.0   0.2        1.6    9.0   0.2    3.4  2  zf-RING_7        C4-type zinc ribbon domain
        1.6    8.9  14.7       0.38   10.9   1.9    2.4  2  Auto_anti-p27    Sjogren's syndrome/scleroderma autoantigen 1
        1.8    7.3  12.0        2.5    6.8   4.4    2.0  2  NRDD             Anaerobic ribonucleoside-triphosphate reduct
        2.1    8.7  11.0          3    8.2   2.8    2.5  2  zf-C6H2          zf-MYND-like zinc finger, mRNA-binding
        2.5    7.5  15.1         26    4.2   0.2    3.5  2  zf-TFIIB         Transcription factor zinc-finger
        2.6    8.2  10.4        3.4    7.8   0.6    2.0  1  Zn_Tnp_IS91      Transposase zinc-binding domain
        2.8    7.9  16.2         17    5.4   0.4    4.0  5  TFIIS_C          Transcription factor S-II (TFIIS)
        2.8    7.6   9.6       0.87    9.2   0.3    2.1  2  TackOD1          Thaumarchaeal output domain 1
        3.1    7.8  12.6        5.2    7.1   0.2    3.6  4  zf-dskA_traR     Prokaryotic dksA/traR C4-type zinc finger
        3.9    6.9   8.7        4.8    6.6   8.7    1.1  1  NMD3             NMD3 family
        4.2    7.4  11.0        6.5    6.8   1.1    2.9  3  RNHCP            RNHCP domain
        4.4    6.9  19.0        4.6    6.8   5.3    3.3  2  TF_Zn_Ribbon     TFIIB zinc-binding
        5.1    7.5   9.3        1.8    8.9   5.3    1.9  2  DUF3268          zinc-finger-containing domain
        5.5    6.8  15.5        0.4   10.4   2.4    3.3  3  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
        5.8    7.2  11.9       0.17   12.1   1.0    2.1  2  DUF2072          Zn-ribbon containing protein
        6.1    7.2  12.1    2.7e+02    1.9   7.5    3.2  2  Ribosomal_L32p   Ribosomal L32p protein family
          7    6.6  14.4    1.2e+02    2.7  14.4    3.2  1  PHD              PHD-finger
          8    6.6  12.6        8.5    6.5   0.3    3.3  3  Ribosomal_L37ae  Ribosomal L37ae protein family
        8.3    6.5  14.7       0.22   11.5   1.7    2.6  2  Anti-TRAP        Tryptophan RNA-binding attenuator protein in
        8.7    6.4  13.1         13    5.9   0.1    3.6  3  ADK_lid          Adenylate kinase, active site lid
        9.6    6.0  16.6          1    9.0   3.0    3.3  3  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
         10    6.8  18.8        9.9    6.8   1.4    3.9  4  zf-H2C2_2        Zinc-finger double domain


Domain annotation for each model (and alignments):
>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.6   5.5     2e-15   5.5e-13       1      24 []      10      33 ..      10      33 .. 0.99
   2 !   10.0   0.4    0.0024      0.67      16      23 ..      48      55 ..      43      55 .. 0.84

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 2e-15
                        DUF1610  1 CtSCGaelaprEravvFpCPNCGE 24
                                   CtSCG+++ap E+av+F CPNCGE
  gi|119719572|ref|YP_920067.1| 10 CTSCGRPIAPYEKAVSFRCPNCGE 33
                                   ***********************9 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0024
                        DUF1610 16 vFpCPNCG 23
                                   ++ CP+CG
  gi|119719572|ref|YP_920067.1| 48 KYVCPKCG 55
                                   789****9 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   3.6     4e-07   0.00011       1      22 [.       9      34 ..       9      35 .. 0.94
   2 !    8.4   8.6    0.0066       1.8       1      22 [.      38      57 ..      38      58 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 4e-07
                  zinc_ribbon_2  1 fCpnCGaelqdnakF....CpyCGtp 22
                                   +C++CG+++ + +k     Cp+CG+ 
  gi|119719572|ref|YP_920067.1|  9 KCTSCGRPIAPYEKAvsfrCPNCGEA 34
                                   8**********999999*******85 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0066
                  zinc_ribbon_2  1 fCpnCGaelqdnakF.CpyCGtp 22
                                   +C++C ++   ++k+ Cp+CG++
  gi|119719572|ref|YP_920067.1| 38 RCSKCRKQ---GNKYvCPKCGFE 57
                                   6999*998...99999*****97 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9  11.9   1.7e-05    0.0048       1      49 []      10      55 ..       8      55 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.7e-05
                            DZR  1 CpqCgeelppdar....fCseCgtklkavaaedrCpsCgekvdpearfCpeCG 49
                                   C +Cg+++ p  +     C++Cg+++       rC++C ++ ++   +Cp+CG
  gi|119719572|ref|YP_920067.1| 10 CTSCGRPIAPYEKavsfRCPNCGEAVI-----WRCSKCRKQGNKY--VCPKCG 55
                                   899999988777766667999999998.....8999999886655..899998 PP

>> Rhodanese_C  Rhodanase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   6.7   2.7e-06   0.00076      18      63 ..       7      54 ..       2      55 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 2.7e-06
                    Rhodanese_C 18 vgkCieCgkpvdelr...krnCanedCnelvl.vCeeCaeklkgvcseeC 63
                                   + kC  Cg p   ++     +C  ++C e v+  C++C+++ +++++ +C
  gi|119719572|ref|YP_920067.1|  7 LPKCTSCGRPIAPYEkavSFRC--PNCGEAVIwRCSKCRKQGNKYVCPKC 54
                                   569*********9998445566..6799988736**********988899 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.4   4.8e-05     0.013      71      95 ..       8      34 ..       1      38 [. 0.78
   2 !    9.0   4.0    0.0049       1.3      69      93 ..      35      55 ..      33      58 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.8e-05
                                   EEETTTS-EEECHHH..HHS-TTTSSS CS
                           HypA 71 vrCreCgkefeleek..alrCpkCgsa 95
                                    +C++Cg+ +   ek  ++rCp+Cg+a
  gi|119719572|ref|YP_920067.1|  8 PKCTSCGRPIAPYEKavSFRCPNCGEA 34
                                   68*******9955533789******86 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0049
                                   -EEEETTTS-EEECHHHHHS-TTTS CS
                           HypA 69 vkvrCreCgkefeleekalrCpkCg 93
                                   v  rC++C+k++++    + CpkCg
  gi|119719572|ref|YP_920067.1| 35 VIWRCSKCRKQGNK----YVCPKCG 55
                                   6789*****99984....58****9 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.3     0.044        12      18      25 ..       9      16 ..       8      18 .. 0.78
   2 !   12.2   0.2   0.00032     0.089       4      11 ..      27      35 ..      25      36 .. 0.82
   3 ?    1.4   0.4      0.85   2.3e+02       4       8 ..      38      42 ..      38      45 .. 0.86
   4 !    8.4   0.6    0.0052       1.4      18      23 ..      50      55 ..      47      57 .. 0.61

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.044
                    zf-ribbon_3 18 vCpyCGtk 25
                                   +C++CG +
  gi|119719572|ref|YP_920067.1|  9 KCTSCGRP 16
                                   79999976 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00032
                    zf-ribbon_3  4 rCPnCGa.p 11
                                   rCPnCG+ +
  gi|119719572|ref|YP_920067.1| 27 RCPNCGEaV 35
                                   8*****866 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.85
                    zf-ribbon_3  4 rCPnC 8 
                                   rC++C
  gi|119719572|ref|YP_920067.1| 38 RCSKC 42
                                   79999 PP

  == domain 4  score: 8.4 bits;  conditional E-value: 0.0052
                    zf-ribbon_3 18 vCpyCG 23
                                   vCp+CG
  gi|119719572|ref|YP_920067.1| 50 VCPKCG 55
                                   455555 PP

>> zf-CHY  CHY zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0  10.0   0.00019     0.052      22      73 ..      10      55 ..       9      57 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 0.00019
                         zf-CHY 22 CreCHeeledhelerl.evkevlcllCeteqekavlCkkCkkefaeyfCpiCk 73
                                   C +C +     ++  + ++ ++ c +C ++  +   C+kC+k+ ++y+Cp+C 
  gi|119719572|ref|YP_920067.1| 10 CTSCGR-----PIAPYeKAVSFRCPNCGEA--VIWRCSKCRKQGNKYVCPKCG 55
                                   555555.....3333314456778888885..7789****************7 PP

>> HscB_4_cys  Co-chaperone HscB tetracysteine metal binding motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   3.3   4.1e-05     0.011       1      23 [.       8      31 ..       8      32 .. 0.93
   2 ?   -1.6  11.1       9.2   2.5e+03       2      23 ..      27      54 ..      27      55 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.1e-05
                                   -B-SSS--B--SS-S---B.-TTT CS
                     HscB_4_cys  1 PrCWnCGgpgapgrgdefF.CpqC 23
                                   P+C +CG+p ap + ++ F Cp C
  gi|119719572|ref|YP_920067.1|  8 PKCTSCGRPIAPYEKAVSFrCPNC 31
                                   9************9998777**** PP

  == domain 2  score: -1.6 bits;  conditional E-value: 9.2
                                   B-SSS--B-......-SS-S---B-TTT CS
                     HscB_4_cys  2 rCWnCGgpg......apgrgdefFCpqC 23
                                   rC nCG++          +g+++ Cp+C
  gi|119719572|ref|YP_920067.1| 27 RCPNCGEAViwrcskCRKQGNKYVCPKC 54
                                   7889998752222113456788888888 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.6    0.0026      0.72      20      38 ..       9      31 ..       6      36 .. 0.87
   2 !   13.0   3.8   0.00036     0.099      19      40 ..      37      56 ..      32      57 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0026
                           C1_2 20 nCsaCgrkidgff....YsCseC 38
                                   +C  Cgr+i +++    ++C+ C
  gi|119719572|ref|YP_920067.1|  9 KCTSCGRPIAPYEkavsFRCPNC 31
                                   7*******888888999***999 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00036
                           C1_2 19 fnCsaCgrkidgffYsCseCdf 40
                                   ++Cs C+++  g++Y C++C f
  gi|119719572|ref|YP_920067.1| 37 WRCSKCRKQ--GNKYVCPKCGF 56
                                   89******9..688******98 PP

>> PolC_DP2  DNA polymerase II large subunit DP2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   4.4   3.8e-05      0.01     620     663 ..       9      56 ..       2      58 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.8e-05
                       PolC_DP2 620 kCkkCg......ketlearCeeCgekteeklvCkkceeeveeekcekcek 663
                                    kC++Cg      ++++++rC++Cge +    +C+kc+++ ++  c+kc+ 
  gi|119719572|ref|YP_920067.1|   9 KCTSCGrpiapyEKAVSFRCPNCGEAVIW--RCSKCRKQGNKYVCPKCGF 56 
                                    78888833333336788999999998876..9999999999999999975 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   3.0    0.0031      0.85      41      52 ..      22      33 ..      10      35 .. 0.79
   2 ?    7.6   0.3     0.011       3.1      41      52 ..      33      44 ..      32      46 .. 0.83
   3 ?    8.3   0.5    0.0068       1.9      43      52 ..      47      56 ..      44      57 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0031
                 zinc_ribbon_10 41 eevkyrCpkCga 52
                                   + v++rCp+Cg+
  gi|119719572|ref|YP_920067.1| 22 KAVSFRCPNCGE 33
                                   568*******97 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.011
                 zinc_ribbon_10 41 eevkyrCpkCga 52
                                   e v +rC+kC+ 
  gi|119719572|ref|YP_920067.1| 33 EAVIWRCSKCRK 44
                                   5689******86 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0068
                 zinc_ribbon_10 43 vkyrCpkCga 52
                                    ky+CpkCg+
  gi|119719572|ref|YP_920067.1| 47 NKYVCPKCGF 56
                                   58******96 PP

>> DUF1272  Protein of unknown function (DUF1272)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   2.3     0.016       4.4       7      48 ..       9      32 ..       3      35 .. 0.53
   2 ?   10.6   1.4    0.0017      0.47      32      48 ..      39      55 ..      33      57 .. 0.93

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.016
                        DUF1272  7 nCecCdkdlppdseearicsyEctFCaeCaeevlenvCPncg 48
                                   +C  C + + p +                  + ++ +CPncg
  gi|119719572|ref|YP_920067.1|  9 KCTSCGRPIAPYE------------------KAVSFRCPNCG 32
                                   5555555555544..................44444555554 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0017
                        DUF1272 32 CaeCaeevlenvCPncg 48
                                   C++C ++  + vCP cg
  gi|119719572|ref|YP_920067.1| 39 CSKCRKQGNKYVCPKCG 55
                                   9******99*******9 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1     0.064        18       5      17 ..      10      22 ..       9      23 .. 0.85
   2 ?    6.3   0.2     0.026       7.2       2      12 ..      25      35 ..      24      36 .. 0.85
   3 ?    3.2   1.2      0.24        66       3      11 ..      37      45 ..      35      45 .. 0.85
   4 ?    9.1   0.2    0.0036      0.99       2      10 ..      48      56 ..      47      59 .] 0.85

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.064
                         zf_UBZ  5 CerCgkeipesel 17
                                   C  Cg++i + e+
  gi|119719572|ref|YP_920067.1| 10 CTSCGRPIAPYEK 22
                                   ********98776 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.026
                         zf_UBZ  2 tylCerCgkei 12
                                   ++ C+ Cg+ +
  gi|119719572|ref|YP_920067.1| 25 SFRCPNCGEAV 35
                                   699*****865 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.24
                         zf_UBZ  3 ylCerCgke 11
                                   + C++C k+
  gi|119719572|ref|YP_920067.1| 37 WRCSKCRKQ 45
                                   67****985 PP

  == domain 4  score: 9.1 bits;  conditional E-value: 0.0036
                         zf_UBZ  2 tylCerCgk 10
                                    y+C++Cg 
  gi|119719572|ref|YP_920067.1| 48 KYVCPKCGF 56
                                   7******96 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.3     0.042        11       3       9 ..       9      15 ..       9      18 .. 0.85
   2 ?    8.4   0.1    0.0082       2.3       3      11 ..      27      35 ..      26      36 .. 0.86
   3 ?    3.6  10.3      0.26        72      19      26 .]      47      54 ..      37      54 .. 0.94

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.042
                         zf-ACC  3 KCpsCge 9 
                                   KC+sCg 
  gi|119719572|ref|YP_920067.1|  9 KCTSCGR 15
                                   9****95 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0082
                         zf-ACC  3 KCpsCgeml 11
                                   +Cp Cge +
  gi|119719572|ref|YP_920067.1| 27 RCPNCGEAV 35
                                   7*****986 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.26
                         zf-ACC 19 nlyVCPkC 26
                                   n+yVCPkC
  gi|119719572|ref|YP_920067.1| 47 NKYVCPKC 54
                                   9******* PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.2     0.083        23       3      10 ..      10      17 ..      10      21 .. 0.81
   2 ?    9.7   6.5    0.0029      0.81       3      30 ..      28      56 ..      27      56 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.083
                                   -TTT--B- CS
                      Nudix_N_2  3 CsqCGtpv 10
                                   C++CG p+
  gi|119719572|ref|YP_920067.1| 10 CTSCGRPI 17
                                   99999886 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0029
                                   -TTT--B-EEE--.TT-SS-EEEETTTTE CS
                      Nudix_N_2  3 CsqCGtpvelrip.dgDnreRlvCpaCgt 30
                                   C++CG++v +r      +   +vCp+Cg+
  gi|119719572|ref|YP_920067.1| 28 CPNCGEAVIWRCSkCRKQGNKYVCPKCGF 56
                                   *********8887335566679*****96 PP

>> zf-B_box  B-box zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0      0.51   1.4e+02      18      25 ..      10      17 ..       7      20 .. 0.76
   2 ?   11.8   4.8   0.00073       0.2       5      29 ..      27      54 ..      23      58 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.51
                       zf-B_box 18 CedCqqpl 25
                                   C++C+ p+
  gi|119719572|ref|YP_920067.1| 10 CTSCGRPI 17
                                   77887775 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00073
                       zf-B_box  5 kCpeHknkpatlfCedCqq....plCeeC 29
                                   +Cp+++ +  ++ C +C++    ++C++C
  gi|119719572|ref|YP_920067.1| 27 RCPNCG-EAVIWRCSKCRKqgnkYVCPKC 54
                                   8*****.**********754444899999 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0    0.0067       1.9      11      21 ..       7      17 ..       6      21 .. 0.82
   2 ?    2.0   6.0      0.71     2e+02      13      21 ..      27      35 ..      27      45 .. 0.67
   3 ?    5.0   0.1     0.083        23      27      32 ..      50      55 ..      48      57 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0067
                        DUF35_N 11 gqrCpdCGtvq 21
                                   + +C++CG+ +
  gi|119719572|ref|YP_920067.1|  7 LPKCTSCGRPI 17
                                   679*****986 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.71
                        DUF35_N 13 rCpdCGtvq 21
                                   rCp+CG  +
  gi|119719572|ref|YP_920067.1| 27 RCPNCGEAV 35
                                   788888765 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.083
                        DUF35_N 27 vCphCg 32
                                   vCp+Cg
  gi|119719572|ref|YP_920067.1| 50 VCPKCG 55
                                   567764 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   4.2     0.035       9.7       2      26 ..       7      32 ..       5      34 .. 0.86
   2 ?    3.4   1.7      0.27        74      22      26 ..      28      32 ..      27      45 .. 0.60
   3 ?    9.1   0.1    0.0046       1.3      20      28 ..      49      57 ..      44      57 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.035
                 PhnA_Zn_Ribbon  2 lpkCplCa.SeytYedgallvCpeCa 26
                                   lpkC  C+  + +Ye    + Cp+C+
  gi|119719572|ref|YP_920067.1|  7 LPKCTSCGrPIAPYEKAVSFRCPNCG 32
                                   69999997468999***********8 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.27
                 PhnA_Zn_Ribbon 22 CpeCa 26
                                   Cp+C+
  gi|119719572|ref|YP_920067.1| 28 CPNCG 32
                                   44443 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0046
                 PhnA_Zn_Ribbon 20 lvCpeCahE 28
                                   +vCp+C+ E
  gi|119719572|ref|YP_920067.1| 49 YVCPKCGFE 57
                                   8*****977 PP

>> zf-RING_9  Putative zinc-RING and/or ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   5.5   0.00012     0.032     158     201 ..      10      54 ..       5      57 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 0.00012
                      zf-RING_9 158 CelCkseellfpfqlktverCekCkavfHkeClkkkekk...ecpkc 201
                                    C  C   + + p+++    rC++C++ +  +C k +++     cpkc
  gi|119719572|ref|YP_920067.1|  10 CTSC--GRPIAPYEKAVSFRCPNCGEAVIWRCSKCRKQGnkyVCPKC 54 
                                    5555..578****************998877775444335669**** PP

>> FYVE_2  FYVE-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   5.4   0.00019     0.052      56     100 ..       9      54 ..       2      57 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00019
                         FYVE_2  56 hCilCleefk.llvnskrqCldCklnvCkkCsvenkkekvwlCkiC 100
                                    +C  C ++   + ++ +  C +C   v  +Cs+  k+ + ++C  C
  gi|119719572|ref|YP_920067.1|   9 KCTSCGRPIApYEKAVSFRCPNCGEAVIWRCSKCRKQGNKYVCPKC 54 
                                    7999999987245566789**************************9 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   9.8    0.0044       1.2       3      55 ..      10      54 ..       8      57 .. 0.42

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0044
                                   -SSS-S--E..E-SSEEE-TTT--EEEEEEE-SSS-S---EEEETTEEEE--TTT CS
                 zinc-ribbons_6  3 CpeCqqele..krgeqyhCeaCqedlkkealCpeCeqelevlkaCgavdyfCnkc 55
                                   C +C +++   ++  +++C +C e +     C +C+++ +        +y C kc
  gi|119719572|ref|YP_920067.1| 10 CTSCGRPIApyEKAVSFRCPNCGEAV--IWRCSKCRKQGN--------KYVCPKC 54
                                   66666666643333555555555532..223333333322........2222222 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   1.3    0.0011       0.3      30      54 ..       9      33 ..       8      38 .. 0.89
   2 ?   10.7   9.0    0.0014      0.38      28      55 ..      25      57 ..      25      58 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0011
                 OrfB_Zn_ribbon 30 tCseCgsknkealsgrtfkCpnCgf 54
                                   +C  Cg+   +  +   f+CpnCg 
  gi|119719572|ref|YP_920067.1|  9 KCTSCGRPIAPYEKAVSFRCPNCGE 33
                                   699****9999899999******97 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0014
                 OrfB_Zn_ribbon 28 SktCseCgsknke.....alsgrtfkCpnCgfe 55
                                   S +C++Cg+ +       +++g++++Cp+Cgfe
  gi|119719572|ref|YP_920067.1| 25 SFRCPNCGEAVIWrcskcRKQGNKYVCPKCGFE 57
                                   668*****9887778889*************97 PP

>> zf-C2HC5  Putative zinc finger motif, C2HC5-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   4.4   0.00058      0.16      16      45 ..       6      36 ..       3      44 .. 0.84
   2 ?    3.5   5.7      0.25        70      19      41 ..      27      55 ..      23      57 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00058
                       zf-C2HC5 16 aapnClnCGkiiCakegls.kpCsfCgspll 45
                                   ++p C++CG  i   e+ +  +C+ Cg+ ++
  gi|119719572|ref|YP_920067.1|  6 LLPKCTSCGRPIAPYEKAVsFRCPNCGEAVI 36
                                   589******988888877769******9887 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.25
                       zf-C2HC5 19 nClnCGkii......CakeglskpCsfCg 41
                                    C nCG  +      C k+g +  C+ Cg
  gi|119719572|ref|YP_920067.1| 27 RCPNCGEAViwrcskCRKQGNKYVCPKCG 55
                                   588999754477666888888899*9997 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1      0.21        59      27      33 ..       9      15 ..       7      18 .. 0.82
   2 ?   10.4   0.2    0.0018      0.49      22      33 ..      22      33 ..      19      36 .. 0.84
   3 ?    5.3   1.8     0.069        19      27      33 ..      38      44 ..      32      47 .. 0.78
   4 ?    4.8   0.4     0.099        27       4      10 ..      50      56 ..      48      58 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.21
                  zinc_ribbon_4 27 rCskCgh 33
                                   +C+ Cg 
  gi|119719572|ref|YP_920067.1|  9 KCTSCGR 15
                                   7999986 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0018
                  zinc_ribbon_4 22 kgvkvrCskCgh 33
                                   k+v+ rC++Cg+
  gi|119719572|ref|YP_920067.1| 22 KAVSFRCPNCGE 33
                                   789999****96 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.069
                  zinc_ribbon_4 27 rCskCgh 33
                                   rCskC++
  gi|119719572|ref|YP_920067.1| 38 RCSKCRK 44
                                   8999985 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.099
                  zinc_ribbon_4  4 tCpsCka 10
                                   +Cp+C++
  gi|119719572|ref|YP_920067.1| 50 VCPKCGF 56
                                   5888876 PP

>> IBR  IBR domain, a half RING-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   5.9   0.00085      0.23      20      54 ..       9      44 ..       5      48 .. 0.83
   2 ?    4.1   1.3       0.2        56      35      47 ..      46      57 ..      41      58 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00085
                            IBR 20 wCprpdCeaiieksegcksvtCskCgfef...CfnCkk 54
                                   +C+   C+++i + e+  s +C++Cg++    C++C+k
  gi|119719572|ref|YP_920067.1|  9 KCT--SCGRPIAPYEKAVSFRCPNCGEAViwrCSKCRK 44
                                   698..9*****9999999999*******9555666665 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.2
                            IBR 35 gcksvtCskCgfe 47
                                   g+k+  C+kCgfe
  gi|119719572|ref|YP_920067.1| 46 GNKY-VCPKCGFE 57
                                   3344.79999986 PP

>> zf-MYND  MYND finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.6    0.0012      0.33       1      18 [.      10      33 ..      10      37 .. 0.81
   2 ?    6.3   5.3     0.038        11       1      16 [.      39      54 ..      39      57 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0012
                                   -TTT--......B-SC.E-TTTS- CS
                        zf-MYND  1 CavCgk.....aealk.kCagCks 18
                                   C +Cg+     ++a + +C++C  
  gi|119719572|ref|YP_920067.1| 10 CTSCGRpiapyEKAVSfRCPNCGE 33
                                   9*******887555558*****75 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.038
                                   -TTT--.B-SC.E-TTT CS
                        zf-MYND  1 CavCgkaealk.kCagC 16
                                   C++C+k +  k  C++C
  gi|119719572|ref|YP_920067.1| 39 CSKCRK-QGNKyVCPKC 54
                                   ******.66666***** PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   7.7      0.11        30      12      26 ..      21      35 ..       9      46 .. 0.75
   2 ?    6.8   3.0     0.026       7.3      12      24 ..      44      56 ..      38      57 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.11
                       zf-Mss51 12 pkhvdfeCpdCGipt 26
                                   +k v+f Cp+CG  +
  gi|119719572|ref|YP_920067.1| 21 EKAVSFRCPNCGEAV 35
                                   789*********665 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.026
                       zf-Mss51 12 pkhvdfeCpdCGi 24
                                   ++  ++ Cp+CG+
  gi|119719572|ref|YP_920067.1| 44 KQGNKYVCPKCGF 56
                                   56789*******7 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.7    0.0011      0.29       6      27 ..       9      32 ..       7      39 .. 0.88
   2 ?    4.3   4.4      0.14        38       6      27 ..      38      55 ..      34      57 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0011
                    Prok-RING_1  6 kCpvCgkelkeedDiVv..CpeCg 27
                                   kC+ Cg+++++ + +V   Cp+Cg
  gi|119719572|ref|YP_920067.1|  9 KCTSCGRPIAPYEKAVSfrCPNCG 32
                                   8***********9999555****9 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.14
                    Prok-RING_1  6 kCpvCgkelkeedDiVvCpeCg 27
                                   +C+ C+k+ ++     vCp+Cg
  gi|119719572|ref|YP_920067.1| 38 RCSKCRKQGNKY----VCPKCG 55
                                   588898888887....9****9 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   4.6    0.0073         2      10      38 ..       9      40 ..       3      46 .. 0.75
   2 ?    8.0   3.6     0.012       3.2      14      30 ..      39      55 ..      35      58 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0073
                   NOB1_Zn_bind 10 rChaCfkvt...kdmtkkF.CpkCGnktLkrva 38
                                   +C++C + +   + +   F Cp+CG++ + r++
  gi|119719572|ref|YP_920067.1|  9 KCTSCGRPIapyE-KAVSFrCPNCGEAVIWRCS 40
                                   799**99773323.333456********99997 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.012
                   NOB1_Zn_bind 14 CfkvtkdmtkkFCpkCG 30
                                   C k  k+ +k  CpkCG
  gi|119719572|ref|YP_920067.1| 39 CSKCRKQGNKYVCPKCG 55
                                   66667799********9 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.7      0.65   1.8e+02      17      21 ..      10      14 ..       9      15 .. 0.50
   2 ?    4.1   9.2      0.14        38       1      21 [.      26      43 ..      26      46 .. 0.88
   3 ?    9.5   0.1    0.0029       0.8       1      10 [.      49      58 ..      49      59 .] 0.89

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.65
                   Rubredoxin_2 17 CpsCg 21
                                   C sCg
  gi|119719572|ref|YP_920067.1| 10 CTSCG 14
                                   55554 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.14
                   Rubredoxin_2  1 YvCsqCGfesakwfGrCpsCg 21
                                   ++C +CG    ++ +rC  C+
  gi|119719572|ref|YP_920067.1| 26 FRCPNCGE---AVIWRCSKCR 43
                                   89999996...789******7 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.0029
                   Rubredoxin_2  1 YvCsqCGfes 10
                                   YvC +CGfe 
  gi|119719572|ref|YP_920067.1| 49 YVCPKCGFEG 58
                                   9*******86 PP

>> zf-UBR  Putative zinc finger in N-recognin (UBR box)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   8.5     0.015       4.1       9      31 ..      33      55 ..      10      59 .] 0.78

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.015
                         zf-UBR  9 gevvyrCltCsldetsviCeeCf 31
                                   + v++rC +C+++ + ++C +C 
  gi|119719572|ref|YP_920067.1| 33 EAVIWRCSKCRKQGNKYVCPKCG 55
                                   37888999999998899999995 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   4.4       1.1   3.1e+02       5      28 ..       9      32 ..       5      33 .. 0.70
   2 ?    9.1   5.4    0.0039       1.1       4      30 ..      37      57 ..      35      59 .] 0.81

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 1.1
                  A2L_zn_ribbon  5 vCsvCggngilnseqgylvCieCg 28
                                   +C+ Cg++   + +     C++Cg
  gi|119719572|ref|YP_920067.1|  9 KCTSCGRPIAPYEKAVSFRCPNCG 32
                                   788888876666666666678877 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0039
                  A2L_zn_ribbon  4 kvCsvCggngilnseqgylvCieCgas 30
                                   + Cs+C+++g        +vC++Cg++
  gi|119719572|ref|YP_920067.1| 37 WRCSKCRKQGNK------YVCPKCGFE 57
                                   678888888866......*******97 PP

>> DUF2321  Uncharacterized protein conserved in bacteria (DUF2321)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1       2.1   5.8e+02      39      47 ..       9      17 ..       4      26 .. 0.65
   2 ?   11.2   3.4   0.00076      0.21      26      52 ..      25      49 ..      17      57 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 2.1
                        DUF2321 39 kcpkCstei 47
                                   kc +C+ +i
  gi|119719572|ref|YP_920067.1|  9 KCTSCGRPI 17
                                   555555555 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00076
                        DUF2321 26 eeyCekcGektitkcpkCsteirGkyy 52
                                   +  C +cGe++i +c kC+ +  G++y
  gi|119719572|ref|YP_920067.1| 25 SFRCPNCGEAVIWRCSKCRKQ--GNKY 49
                                   445***************974..5555 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   2.9   0.00066      0.18       7      36 ..       9      35 ..       9      38 .. 0.78
   2 ?    4.9  12.7       0.1        28       6      33 ..      26      55 ..      25      58 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00066
                    Zn-ribbon_8  7 rCeeCghefevlqsisdapltaCPeCgsev 36
                                   +C++Cg+   +  ++       CP+Cg++v
  gi|119719572|ref|YP_920067.1|  9 KCTSCGRPIAPYEKAV---SFRCPNCGEAV 35
                                   7*****9988777644...445****9865 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.1
                    Zn-ribbon_8  6 YrCeeCghefe.vlqsisdaplta.CPeCg 33
                                   +rC +Cg+    +  +  +  ++  CP+Cg
  gi|119719572|ref|YP_920067.1| 26 FRCPNCGEAVIwRCSKCRKQGNKYvCPKCG 55
                                   9******666644444444445666****9 PP

>> zf-HIT  HIT zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   4.9      0.14        38       5      21 ..      10      33 ..       7      35 .. 0.60
   2 ?    8.8   8.0    0.0052       1.4       4      20 ..      38      55 ..      37      57 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.14
                                   -TTT-S.B-SE......E-TTT-- CS
                         zf-HIT  5 CgvCgf.pakY......kCpkCnt 21
                                   C  Cg   a Y      +Cp+C++
  gi|119719572|ref|YP_920067.1| 10 CTSCGRpIAPYekavsfRCPNCGE 33
                                   666666644443333339****97 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0052
                                   B-TTT-S.B-SEE-TTT- CS
                         zf-HIT  4 lCgvCgf.pakYkCpkCn 20
                                    C+ C +   kY CpkC+
  gi|119719572|ref|YP_920067.1| 38 RCSKCRKqGNKYVCPKCG 55
                                   599****999*******8 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.4       1.2   3.2e+02      20      25 ..       9      14 ..       7      23 .. 0.66
   2 ?    6.0  10.4     0.042        12      19      46 .]      26      45 ..      19      45 .. 0.79
   3 ?    8.9   0.6    0.0053       1.5      16      25 ..      46      55 ..      46      59 .] 0.84

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 1.2
                  Zn_Tnp_IS1595 20 vCPhCg 25
                                    C  Cg
  gi|119719572|ref|YP_920067.1|  9 KCTSCG 14
                                   455555 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.042
                  Zn_Tnp_IS1595 19 fvCPhCgsrkayriktrglfqCkeCrkq 46
                                   f+CP+Cg       ++   ++C++Crkq
  gi|119719572|ref|YP_920067.1| 26 FRCPNCG-------EA-VIWRCSKCRKQ 45
                                   89*****.......33.67888888887 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0053
                  Zn_Tnp_IS1595 16 pngfvCPhCg 25
                                   +n+ vCP+Cg
  gi|119719572|ref|YP_920067.1| 46 GNKYVCPKCG 55
                                   5889*****9 PP

>> zf-RING_5  zinc-RING finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0  11.8      0.02       5.6       1      43 [.       9      55 ..       9      56 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.02
                      zf-RING_5  1 hCnkCfekl...skeekfyltsCgHif...CekClkkllekeavCpiCr 43
                                   +C +C +++   +k   f   +Cg  +   C+kC k+    ++vCp C+
  gi|119719572|ref|YP_920067.1|  9 KCTSCGRPIapyEKAVSFRCPNCGEAViwrCSKCRKQGN--KYVCPKCG 55
                                   699999999655555559999999885455*******99..*******6 PP

>> Sgf11  Sgf11 (transcriptional regulation protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.1    0.0079       2.2       6      15 ..       9      18 ..       7      19 .. 0.91
   2 ?    8.3   0.5     0.006       1.7       3      11 ..      24      32 ..      22      35 .. 0.82
   3 ?    0.8   0.9       1.3   3.6e+02       6      13 ..      38      45 ..      33      45 .. 0.80
   4 ?    3.5   0.4       0.2        54       5      11 ..      49      55 ..      46      55 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0079
                                   E-TTTSSEEE CS
                          Sgf11  6 tCpnCgRqia 15
                                   +C  CgR+ia
  gi|119719572|ref|YP_920067.1|  9 KCTSCGRPIA 18
                                   6********8 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.006
                                   -EEE-TTTS CS
                          Sgf11  3 eyvtCpnCg 11
                                   + ++CpnCg
  gi|119719572|ref|YP_920067.1| 24 VSFRCPNCG 32
                                   569*****8 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 1.3
                                   E-TTTSSE CS
                          Sgf11  6 tCpnCgRq 13
                                   +C  C +q
  gi|119719572|ref|YP_920067.1| 38 RCSKCRKQ 45
                                   7****886 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.2
                                   EE-TTTS CS
                          Sgf11  5 vtCpnCg 11
                                   ++Cp Cg
  gi|119719572|ref|YP_920067.1| 49 YVCPKCG 55
                                   79****7 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.3      0.11        31       6      12 ..       9      15 ..       9      19 .. 0.85
   2 ?    1.7  14.6      0.88   2.4e+02       6      32 ..      27      56 ..      25      58 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.11
                 Zn_ribbon_SprT  6 rCtgCgr 12
                                   +Ct+Cgr
  gi|119719572|ref|YP_920067.1|  9 KCTSCGR 15
                                   6*****5 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.88
                 Zn_ribbon_SprT  6 rCtgCgreythhlsirrhn...YrCrrCkg 32
                                   rC++Cg+ +  + s+ r     Y C++C+ 
  gi|119719572|ref|YP_920067.1| 27 RCPNCGEAVIWRCSKCRKQgnkYVCPKCGF 56
                                   8999999999999885544578******85 PP

>> zf_C2H2_13  Zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1    0.0023      0.63      20      28 ..      10      18 ..       9      21 .. 0.92
   2 ?    2.4   0.3      0.44   1.2e+02      12      25 ..      21      33 ..      18      39 .. 0.79
   3 ?    2.3   0.8      0.47   1.3e+02      19      24 ..      50      55 ..      43      56 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0023
                     zf_C2H2_13 20 CnkCGkPis 28
                                   C +CG+Pi+
  gi|119719572|ref|YP_920067.1| 10 CTSCGRPIA 18
                                   9*******7 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.44
                     zf_C2H2_13 12 dtnlnYRvCnkCGk 25
                                   ++++ +R C +CG 
  gi|119719572|ref|YP_920067.1| 21 EKAVSFR-CPNCGE 33
                                   6778888.999*96 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.47
                     zf_C2H2_13 19 vCnkCG 24
                                   vC kCG
  gi|119719572|ref|YP_920067.1| 50 VCPKCG 55
                                   9****9 PP

>> zf_C2H2_10  C2H2 type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.4       2.2   6.2e+02       6       9 ..       8      11 ..       7      14 .. 0.83
   2 ?    6.4   0.1     0.024       6.6       3      11 ..      26      34 ..      25      35 .. 0.84
   3 ?    1.7   0.1      0.67   1.8e+02       4      10 ..      38      44 ..      36      46 .. 0.78
   4 ?    9.7   0.8    0.0022       0.6       2      12 ..      48      58 ..      47      59 .] 0.80

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 2.2
                     zf_C2H2_10  6 PKCq 9 
                                   PKC 
  gi|119719572|ref|YP_920067.1|  8 PKCT 11
                                   9996 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.024
                     zf_C2H2_10  3 fsCPKCqek 11
                                   f CP C+e 
  gi|119719572|ref|YP_920067.1| 26 FRCPNCGEA 34
                                   88****995 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.67
                     zf_C2H2_10  4 sCPKCqe 10
                                    C KC  
  gi|119719572|ref|YP_920067.1| 38 RCSKCRK 44
                                   59***86 PP

  == domain 4  score: 9.7 bits;  conditional E-value: 0.0022
                     zf_C2H2_10  2 efsCPKCqekl 12
                                   ++ CPKC+   
  gi|119719572|ref|YP_920067.1| 48 KYVCPKCGFEG 58
                                   689****9765 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.2       0.6   1.7e+02       2       9 ..       9      16 ..       9      20 .. 0.88
   2 ?    7.0   0.1     0.032       8.7       1       8 [.      26      33 ..      26      36 .. 0.88
   3 ?    2.5   0.4      0.87   2.4e+02       2       8 ..      38      44 ..      37      48 .. 0.82
   4 ?    6.5   0.6     0.046        13       1       8 [.      49      56 ..      49      59 .] 0.88

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.6
                                   EETTTTEE CS
                        zf-C2H2  2 kCpdCgks 9 
                                   kC+ Cg++
  gi|119719572|ref|YP_920067.1|  9 KCTSCGRP 16
                                   7*****96 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.032
                                   EEETTTTE CS
                        zf-C2H2  1 ykCpdCgk 8 
                                   ++Cp Cg+
  gi|119719572|ref|YP_920067.1| 26 FRCPNCGE 33
                                   8*****97 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.87
                                   EETTTTE CS
                        zf-C2H2  2 kCpdCgk 8 
                                   +C++C k
  gi|119719572|ref|YP_920067.1| 38 RCSKCRK 44
                                   899**88 PP

  == domain 4  score: 6.5 bits;  conditional E-value: 0.046
                                   EEETTTTE CS
                        zf-C2H2  1 ykCpdCgk 8 
                                   y+Cp+Cg 
  gi|119719572|ref|YP_920067.1| 49 YVCPKCGF 56
                                   9*****96 PP

>> ZZ  Zinc finger, ZZ type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1       1.7   4.8e+02       6      14 ..       9      16 ..       8      20 .. 0.67
   2 ?    7.8   3.0      0.01       2.8       5      26 ..      26      43 ..      22      44 .. 0.90
   3 ?    4.4   0.1      0.12        34       2      12 ..      46      56 ..      45      58 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 1.7
                                   E-TTT-S.. CS
                             ZZ  6 tCdgCseap 14
                                   +C  C+  p
  gi|119719572|ref|YP_920067.1|  9 KCTSCGR-P 16
                                   5777776.5 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.01
                                   EE-TTT-S..EESSEEEESSSS CS
                             ZZ  5 ytCdgCseapligvRyhclrcs 26
                                   + C  C+e     v ++c +c+
  gi|119719572|ref|YP_920067.1| 26 FRCPNCGE----AVIWRCSKCR 43
                                   88******....99*******7 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.12
                                   SS-EE-TTT-S CS
                             ZZ  2 hkkytCdgCse 12
                                   ++ky C +C++
  gi|119719572|ref|YP_920067.1| 46 GNKYVCPKCGF 56
                                   6899*****97 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.1     0.041        11      23      31 ..       7      15 ..       4      15 .. 0.91
   2 ?    9.0   0.2    0.0058       1.6      24      30 ..      26      32 ..      21      32 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.041
                                   -EE-TTT-- CS
                      zf-RING_7 23 vvtCpeCGR 31
                                   +++C +CGR
  gi|119719572|ref|YP_920067.1|  7 LPKCTSCGR 15
                                   689*****9 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0058
                                   EE-TTT- CS
                      zf-RING_7 24 vtCpeCG 30
                                   ++Cp+CG
  gi|119719572|ref|YP_920067.1| 26 FRCPNCG 32
                                   79****9 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   1.9    0.0014      0.38      13      40 .]       5      32 ..       3      32 .. 0.90
   2 ?    3.3  11.5      0.34        95      18      40 .]      28      55 ..      27      55 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0014
                  Auto_anti-p27 13 MLaetCpvCgvPLmrdrkggkvyCvaCd 40
                                   ML   C  Cg P+  + k +   C++C+
  gi|119719572|ref|YP_920067.1|  5 MLLPKCTSCGRPIAPYEKAVSFRCPNCG 32
                                   67777***********999********6 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.34
                  Auto_anti-p27 18 CpvC..gvPLmrdr...kggkvyCvaCd 40
                                   Cp+C   v+   ++   +g+k++C+ C+
  gi|119719572|ref|YP_920067.1| 28 CPNCgeAVIWRCSKcrkQGNKYVCPKCG 55
                                   ****95555555559888999******6 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.6     0.012       3.4     509     529 ..       9      33 ..       6      38 .. 0.72
   2 ?    6.8   4.4    0.0092       2.5     509     526 ..      38      55 ..      35      58 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.012
                                    EETT.--....EESS....SB-TTT--BE CS
                           NRDD 509 vCnecgy....kgei....ekCpkCgsee 529
                                     C +cg+            ++Cp+Cg  e
  gi|119719572|ref|YP_920067.1|   9 KCTSCGRpiapY--EkavsFRCPNCG--E 33 
                                    599999987541..2456799*****..3 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0092
                                    EETT.--EESSSB-TTT- CS
                           NRDD 509 vCnecgykgeiekCpkCg 526
                                    +C +c ++g ++ CpkCg
  gi|119719572|ref|YP_920067.1|  38 RCSKCRKQGNKYVCPKCG 55 
                                    8****************9 PP

>> zf-C6H2  zf-MYND-like zinc finger, mRNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   2.3      0.18        49       9      21 ..      22      34 ..       9      40 .. 0.69
   2 ?    8.2   2.8     0.011         3       4      18 ..      40      54 ..      38      58 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.18
                        zf-C6H2  9 eassLqCptClkl 21
                                   +a s++Cp C ++
  gi|119719572|ref|YP_920067.1| 22 KAVSFRCPNCGEA 34
                                   34489*****765 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.011
                        zf-C6H2  4 seCgkeassLqCptC 18
                                   s+C k++++  Cp+C
  gi|119719572|ref|YP_920067.1| 40 SKCRKQGNKYVCPKC 54
                                   79************* PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   9.7      0.24        66       1      26 [.       9      43 ..       9      43 .. 0.91
   2 ?    4.2   0.2     0.094        26       2       6 ..      51      55 ..      49      57 .. 0.62

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.24
                       zf-TFIIB  1 kCPkCqdeleeser.........ggveidyCpqCr 26
                                   kC +C+ +  ++e+         g+  i++C +Cr
  gi|119719572|ref|YP_920067.1|  9 KCTSCGRPIAPYEKavsfrcpncGEAVIWRCSKCR 43
                                   8*********9999999999999999999999997 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.094
                       zf-TFIIB  2 CPkCq 6 
                                   CPkC+
  gi|119719572|ref|YP_920067.1| 51 CPKCG 55
                                   55554 PP

>> Zn_Tnp_IS91  Transposase zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.6     0.012       3.4      41      65 ..       9      33 ..       4      37 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.012
                    Zn_Tnp_IS91 41 eCeeCghekivyfsCksrhCpsCqk 65
                                   +C++Cg     y +  s  Cp+C++
  gi|119719572|ref|YP_920067.1|  9 KCTSCGRPIAPYEKAVSFRCPNCGE 33
                                   6999998777777777777999986 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0      0.21        59      30      35 ..       9      14 ..       5      18 .. 0.77
   2 ?    5.4   0.4      0.06        17       1       8 [.      26      33 ..      26      37 .. 0.74
   3 ?    4.1   0.4      0.15        41      27      37 ..      35      45 ..      32      47 .. 0.73
   4 ?    2.5   0.7      0.48   1.3e+02       3       8 ..      39      44 ..      37      50 .. 0.61
   5 ?    5.3   0.7     0.067        18      29      35 ..      49      55 ..      45      57 .. 0.67

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.21
                        TFIIS_C 30 kCtkCg 35
                                   kCt+Cg
  gi|119719572|ref|YP_920067.1|  9 KCTSCG 14
                                   677777 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.06
                        TFIIS_C  1 akCpkCgs 8 
                                   ++Cp+Cg+
  gi|119719572|ref|YP_920067.1| 26 FRCPNCGE 33
                                   57888886 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.15
                        TFIIS_C 27 vfykCtkCghr 37
                                   v+ +C kC ++
  gi|119719572|ref|YP_920067.1| 35 VIWRCSKCRKQ 45
                                   66788888775 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.48
                        TFIIS_C  3 CpkCgs 8 
                                   C kC++
  gi|119719572|ref|YP_920067.1| 39 CSKCRK 44
                                   555544 PP

  == domain 5  score: 5.3 bits;  conditional E-value: 0.067
                        TFIIS_C 29 ykCtkCg 35
                                   y+C kCg
  gi|119719572|ref|YP_920067.1| 49 YVCPKCG 55
                                   6666666 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.3    0.0031      0.87     143     170 ..       4      33 ..       1      36 [. 0.74
   2 ?    2.3   3.7      0.42   1.2e+02      75      94 ..      38      55 ..      33      57 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0031
                        TackOD1 143 plevykCnsCkslf..sepevkarClsCek 170
                                    ++   kC sC++     e++v++rC +C++
  gi|119719572|ref|YP_920067.1|   4 VMLLPKCTSCGRPIapYEKAVSFRCPNCGE 33 
                                    566678999998652268999999999987 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.42
                        TackOD1 75 lCpsCksghlnvrevCpkCk 94
                                    C++C+ +    ++vCpkC+
  gi|119719572|ref|YP_920067.1| 38 RCSKCRKQG--NKYVCPKCG 55
                                   577777654..566788885 PP

>> zf-dskA_traR  Prokaryotic dksA/traR C4-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.2     0.026       7.1       5      15 ..       9      19 ..       5      20 .. 0.85
   2 ?    7.1   0.2     0.019       5.2       5      13 ..      26      35 ..      19      36 .. 0.78
   3 ?   -1.5   0.2       9.3   2.6e+03       6       9 ..      39      42 ..      37      44 .. 0.75
   4 ?    2.0   0.2      0.73     2e+02       5      10 ..      49      55 ..      46      57 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.026
                   zf-dskA_traR  5 sCeeCGEpIpe 15
                                   +C  CG pI++
  gi|119719572|ref|YP_920067.1|  9 KCTSCGRPIAP 19
                                   6********86 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.019
                   zf-dskA_traR  5 s.CeeCGEpI 13
                                   + C  CGE +
  gi|119719572|ref|YP_920067.1| 26 FrCPNCGEAV 35
                                   37******86 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 9.3
                   zf-dskA_traR  6 CeeC 9 
                                   C++C
  gi|119719572|ref|YP_920067.1| 39 CSKC 42
                                   8888 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.73
                   zf-dskA_traR  5 s.CeeCG 10
                                   + C +CG
  gi|119719572|ref|YP_920067.1| 49 YvCPKCG 55
                                   35****9 PP

>> NMD3  NMD3 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   8.7     0.017       4.8       1      42 [.      10      55 ..      10      57 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.017
                           NMD3  1 CcrCGkeieeling....lCedCllkevditegiek.ievevCkeCg 42
                                   C  CG++i +  ++     C++C  + +   ++  k  +  vC++Cg
  gi|119719572|ref|YP_920067.1| 10 CTSCGRPIAPY-EKavsfRCPNCGEAVIWRCSKCRKqGNKYVCPKCG 55
                                   9*******755.444888*****999877666666669********8 PP

>> RNHCP  RNHCP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1      0.51   1.4e+02      63      74 ..       4      15 ..       2      20 .. 0.72
   2 ?    6.8   1.1     0.024       6.5       5      29 ..       9      31 ..       7      34 .. 0.80
   3 ?    4.4   2.8      0.14        38      64      80 ..      34      50 ..      32      54 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.51
                          RNHCP 63 wvivhrCekCge 74
                                   ++++ +C++Cg+
  gi|119719572|ref|YP_920067.1|  4 VMLLPKCTSCGR 15
                                   567778888875 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.024
                          RNHCP  5 tCeeCgkeveklaagsakrnHCpsC 29
                                   +C++Cg+ +++ ++       Cp+C
  gi|119719572|ref|YP_920067.1|  9 KCTSCGRPIAPYEKAV--SFRCPNC 31
                                   6999999999887766..6669999 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.14
                          RNHCP 64 vivhrCekCgelkknrv 80
                                   ++++rC+kC++  ++ v
  gi|119719572|ref|YP_920067.1| 34 AVIWRCSKCRKQGNKYV 50
                                   689******99876655 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   5.3     0.017       4.6       2      27 ..       9      33 ..       8      36 .. 0.70
   2 ?    4.0  13.0      0.13        36       1      26 [.      26      55 ..      26      56 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.017
                                   EETTTTCEECHEE.TSTTCEEESSSSB CS
                   TF_Zn_Ribbon  2 kCPnCgstnlveD.pergelvCtdCGl 27
                                   kC  Cg +  + + ++   ++C++CG+
  gi|119719572|ref|YP_920067.1|  9 KCTSCGRP--IAPyEKAVSFRCPNCGE 33
                                   78888877..66635556779999975 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.13
                                   EEETTTTCEECHEE.....TSTTCEEESSSS CS
                   TF_Zn_Ribbon  1 ykCPnCgstnlveD.....pergelvCtdCG 26
                                   ++CPnCg    ++         + +vC++CG
  gi|119719572|ref|YP_920067.1| 26 FRCPNCGEAV-IWRcskcrKQGNKYVCPKCG 55
                                   68*****985.55555554788889*****9 PP

>> DUF3268  zinc-finger-containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   4.1     0.097        27       4      36 ..       9      42 ..       6      45 .. 0.70
   2 ?    8.9   5.3    0.0065       1.8       3      37 ..      26      55 ..      24      57 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.097
                        DUF3268  4 rCpyCGekvilvsaseiYkers.kgkllylCpkC 36
                                   +C+ CG++++  ++++ ++  +  +++++ C kC
  gi|119719572|ref|YP_920067.1|  9 KCTSCGRPIAPYEKAVSFRCPNcGEAVIWRCSKC 42
                                   6888888888777777776555255677888888 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0065
                        DUF3268  3 trCpyCGekvilvsaseiYkerskgkllylCpkCd 37
                                    rCp CGe+vi++ ++     r++g   y+CpkC+
  gi|119719572|ref|YP_920067.1| 26 FRCPNCGEAVIWRCSKC----RKQG-NKYVCPKCG 55
                                   69**********98763....4455.679*****7 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   2.4    0.0015       0.4       2      25 ..       9      33 ..       9      38 .. 0.86
   2 ?    0.7   0.6       1.6   4.4e+02      19      23 ..      38      42 ..      33      44 .. 0.76
   3 ?   -0.4   5.2       3.5   9.7e+02      19      25 ..      50      56 ..      37      57 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0015
                                   B-SSS--B--.--SSS----SSS-- CS
                 DNA_RNApol_7kD  2 iCgeCgaevs.lkkgdpiRCkeCGh 25
                                   +C  Cg +    +k  + RC +CG 
  gi|119719572|ref|YP_920067.1|  9 KCTSCGRPIApYEKAVSFRCPNCGE 33
                                   699*****998888889*******6 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1.6
                                   --SSS CS
                 DNA_RNApol_7kD 19 RCkeC 23
                                   RC +C
  gi|119719572|ref|YP_920067.1| 38 RCSKC 42
                                   77777 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 3.5
                                   --SSS-- CS
                 DNA_RNApol_7kD 19 RCkeCGh 25
                                    C +CG+
  gi|119719572|ref|YP_920067.1| 50 VCPKCGF 56
                                   3777775 PP

>> DUF2072  Zn-ribbon containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.0   0.00062      0.17       3      27 ..       9      33 ..       8      37 .. 0.94
   2 ?    0.5   3.9       2.5   6.8e+02       6      27 ..      38      56 ..      36      58 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00062
                        DUF2072  3 kCtkCekvfedgskeilkGCpsCGg 27
                                   kCt+C++ +   +k +   Cp+CG 
  gi|119719572|ref|YP_920067.1|  9 KCTSCGRPIAPYEKAVSFRCPNCGE 33
                                   8***********************5 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 2.5
                        DUF2072  6 kCekvfedgskeilkGCpsCGg 27
                                   +C k  ++g+k     Cp+CG 
  gi|119719572|ref|YP_920067.1| 38 RCSKCRKQGNK---YVCPKCGF 56
                                   45555567777...66****96 PP

>> Ribosomal_L32p  Ribosomal L32p protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   2.2       1.1   2.9e+02      28      33 ..      27      32 ..       4      32 .. 0.66
   2 ?    1.9   7.5      0.97   2.7e+02      28      38 ..      27      37 ..      21      58 .. 0.50

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 1.1
                                   EETTTC CS
                 Ribosomal_L32p 28 ecpncg 33
                                   +cpncg
  gi|119719572|ref|YP_920067.1| 27 RCPNCG 32
                                   566665 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.97
                                   EETTTCCEECT CS
                 Ribosomal_L32p 28 ecpncgelklp 38
                                   +cpncge  + 
  gi|119719572|ref|YP_920067.1| 27 RCPNCGEAVIW 37
                                   67777766543 PP

>> PHD  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7  14.4      0.44   1.2e+02       2      50 ..      10      55 ..       9      57 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.44
                                   BTTTTS..TTSTTSCEEEETTTSCEEETTTSSSTHSHHSHHSSTBSSTTTH CS
                            PHD  2 CavCkk..ksdeeeelvqCdgCkrwfHqkClkppleseekpegewlCekCk 50
                                   C  C++  +  e+     C +C++++   C k  ++      ++++C+kC 
  gi|119719572|ref|YP_920067.1| 10 CTSCGRpiAPYEKAVSFRCPNCGEAVIWRCSKCRKQ-----GNKYVCPKCG 55
                                   999999877777888899**************9976.....447******6 PP

>> Ribosomal_L37ae  Ribosomal L37ae protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1       2.4   6.6e+02      53      61 ..       9      17 ..       3      21 .. 0.74
   2 ?    2.0   7.2      0.78   2.2e+02      34      60 ..      26      45 ..       7      46 .. 0.79
   3 ?    6.5   0.3     0.031       8.5      29      40 ..      44      55 ..      43      58 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 2.4
                                   EETTTTEEE CS
                Ribosomal_L37ae 53 kCkkcgktv 61
                                   kC++cg+ +
  gi|119719572|ref|YP_920067.1|  9 KCTSCGRPI 17
                                   677777665 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.78
                                   BEESSSSSSEEEEEETTEEEETTTTEE CS
                Ribosomal_L37ae 34 ytCpfcgktkvkRkavgiwkCkkcgkt 60
                                   ++Cp+cg+       + iw+C+kc+k+
  gi|119719572|ref|YP_920067.1| 26 FRCPNCGE-------AVIWRCSKCRKQ 45
                                   56777765.......459999999885 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.031
                                   HHHS-BEESSSS CS
                Ribosomal_L37ae 29 sqhakytCpfcg 40
                                   +q +ky Cp+cg
  gi|119719572|ref|YP_920067.1| 44 KQGNKYVCPKCG 55
                                   6889*******9 PP

>> Anti-TRAP  Tryptophan RNA-binding attenuator protein inhibitory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.7   0.00079      0.22      14      37 ..       8      32 ..       5      38 .. 0.82
   2 ?    0.2   5.3       2.7   7.5e+02      13      37 ..      39      55 ..      33      58 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00079
                                   TTTTTTSE.ETTE......E-TTTT CS
                      Anti-TRAP 14 daCngsGk.iepeeprasleCPkCs 37
                                   ++C   G+ i+p e+  s+ CP+C+
  gi|119719572|ref|YP_920067.1|  8 PKCTSCGRpIAPYEKAVSFRCPNCG 32
                                   5677777658999***********6 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 2.7
                                   -TTTTTTSEETTE......E-TTTT CS
                      Anti-TRAP 13 CdaCngsGkiepeeprasleCPkCs 37
                                   C +C + G+           CPkC+
  gi|119719572|ref|YP_920067.1| 39 CSKCRKQGN--------KYVCPKCG 55
                                   555554444........35689986 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   4.9      0.71     2e+02      20      34 ..      24      38 ..       8      39 .. 0.61
   2 ?   -0.3   0.2         4   1.1e+03       3       7 ..      38      42 ..      37      45 .. 0.70
   3 ?    5.9   0.1     0.047        13       3       8 ..      50      55 ..      49      56 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.71
                                   STTB-TTT--.-B-- CS
                        ADK_lid 20 veglCDkCGepLvqR 34
                                   v   C +CGe  + R
  gi|119719572|ref|YP_920067.1| 24 VSFRCPNCGEAVIWR 38
                                   555677777776655 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 4
                                   E-TTT CS
                        ADK_lid  3 vCpkC 7 
                                    C+kC
  gi|119719572|ref|YP_920067.1| 38 RCSKC 42
                                   58888 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.047
                                   E-TTT- CS
                        ADK_lid  3 vCpkCG 8 
                                   vCpkCG
  gi|119719572|ref|YP_920067.1| 50 VCPKCG 55
                                   9****9 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   3.0    0.0038         1       6      30 ..      10      34 ..      10      35 .. 0.89
   2 ?    0.3   0.5         2   5.6e+02      24      27 ..      39      42 ..      38      46 .. 0.65
   3 ?    5.1   0.6     0.063        17      23      28 ..      50      55 ..      43      57 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0038
                  zf-NADH-PPase  6 CgrCGaptepaeggwarvCpaCgle 30
                                   C  CG p +p e   + +Cp+Cg+ 
  gi|119719572|ref|YP_920067.1| 10 CTSCGRPIAPYEKAVSFRCPNCGEA 34
                                   668999999999999********85 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 2
                  zf-NADH-PPase 24 CpaC 27
                                   C+ C
  gi|119719572|ref|YP_920067.1| 39 CSKC 42
                                   5555 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.063
                  zf-NADH-PPase 23 vCpaCg 28
                                   vCp Cg
  gi|119719572|ref|YP_920067.1| 50 VCPKCG 55
                                   677776 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.4       4.5   1.2e+03      16      21 ..       9      14 ..       8      15 .. 0.83
   2 ?    6.3   0.2     0.053        15      15      22 ..      26      33 ..      19      35 .. 0.79
   3 ?    5.6   0.6     0.086        24      15      23 ..      37      45 ..      36      48 .. 0.81
   4 ?    6.8   1.4     0.036       9.9      13      21 ..      47      55 ..      44      57 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 4.5
                      zf-H2C2_2 16 eCplCd 21
                                   +C +C+
  gi|119719572|ref|YP_920067.1|  9 KCTSCG 14
                                   799997 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.053
                      zf-H2C2_2 15 yeCplCdk 22
                                   + Cp C+ 
  gi|119719572|ref|YP_920067.1| 26 FRCPNCGE 33
                                   89****86 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.086
                      zf-H2C2_2 15 yeCplCdka 23
                                   + C++C+k 
  gi|119719572|ref|YP_920067.1| 37 WRCSKCRKQ 45
                                   68*****96 PP

  == domain 4  score: 6.8 bits;  conditional E-value: 0.036
                      zf-H2C2_2 13 kpyeCplCd 21
                                   ++y Cp+C+
  gi|119719572|ref|YP_920067.1| 47 NKYVCPKCG 55
                                   67******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       846  (0.0471861); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                       129  (0.00719505); expected 17.9 (0.001)
Passed Fwd filter:                        88  (0.00490825); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              65  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.53
# Mc/sec: 334.87
//
Query:       gi|119719573|ref|YP_920068.1|  [L=158]
Description: hypothetical protein Tpen_0663 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.022   14.8   0.0      0.028   14.5   0.0    1.3  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.051   13.4   2.7      0.069   12.9   2.7    1.4  1  DUF2157         Predicted membrane protein (DUF2157)
      0.054   12.9   0.8        0.1   12.0   0.8    1.5  1  Mu-like_Com     Mu-like prophage protein Com
      0.073   13.2   0.4        2.4    8.4   0.0    2.3  2  zinc_ribbon_13  Nucleic-acid-binding protein containing Zn-ri
      0.074   12.9   0.2          7    6.6   0.0    2.3  2  TFIIS_C         Transcription factor S-II (TFIIS)
        0.1   12.4   3.3       0.12   12.1   0.4    2.2  2  zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
       0.19   11.9   2.5       0.44   10.7   2.5    1.6  1  Zn-ribbon_8     Zinc ribbon domain
       0.27   11.0   4.5        1.3    8.9   0.2    2.4  2  Rubredoxin_2    Rubredoxin metal binding domain
       0.63    9.7   4.1        1.2    8.8   4.1    1.4  1  DUF4131         Domain of unknown function (DUF4131)
       0.87    9.6   5.0          3    7.8   1.0    2.3  2  DUF1936         Domain of unknown function (DUF1936)
        5.7    6.9   5.4        3.2    7.7   0.1    2.3  2  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit


Domain annotation for each model (and alignments):
>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.7e-05     0.028      70     100 ..      82     120 ..      39     129 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.7e-05
                                    EEEETTTS-EEE.CHHHHH.........S-TTTSSS-EEEE CS
                           HypA  70 kvrCreCgkefe.leekal.........rCpkCgsadveiv 100
                                     vrC++Cg+e   l +  +         +CpkCg+ d+ +v
  gi|119719573|ref|YP_920068.1|  82 LVRCETCGYEEArLYT--EgdalfqakgTCPKCGKGDLVVV 120
                                    589*****88773333..1233578889******9988665 PP

>> DUF2157  Predicted membrane protein (DUF2157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   2.7   4.2e-05     0.069      37     102 ..      19      84 ..       6     148 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.2e-05
                        DUF2157  37 allvlGalllglGlilfvAanWqglsrlvkfllllvllllslllgavlwrdrrvpprlgealllla 102
                                    + ++l+ ll +lG+ +    +W + ++++ f  +l+ l+ls ++ ++l +  rv+++ +++l l+ 
  gi|119719573|ref|YP_920068.1|  19 IPIYLALLLATLGVTIALLRLWISTNNEQYFSAALLSLMLSSYISWYLVKVLRVKQTPRQLLTLVR 84 
                                    5689*****************************************999887788877777777664 PP

>> Mu-like_Com  Mu-like prophage protein Com
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.8   6.4e-05       0.1       5      31 ..      83     113 ..      79     118 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.4e-05
                    Mu-like_Com   5 lRCGeC....aRLLaKaeAlDeltiKCPRCG 31 
                                    +RC  C    aRL + ++Al + +  CP+CG
  gi|119719573|ref|YP_920068.1|  83 VRCETCgyeeARLYTEGDALFQAKGTCPKCG 113
                                    78888877778**********99999****9 PP

>> zinc_ribbon_13  Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0    0.0015       2.4      34      45 ..      81      92 ..      68     101 .. 0.84
   2 ?    2.9   0.1     0.074   1.2e+02       1       9 [.     108     116 ..     108     122 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0015
                 zinc_ribbon_13 34 itvsCknCgYte 45
                                   ++v C++CgY e
  gi|119719573|ref|YP_920068.1| 81 TLVRCETCGYEE 92
                                   789*******98 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.074
                 zinc_ribbon_13   1 kCpKCgnte 9  
                                    +CpKCg+ +
  gi|119719573|ref|YP_920068.1| 108 TCPKCGKGD 116
                                    5*****876 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1     0.025        41       2      12 ..      84      94 ..      81      98 .. 0.74
   2 ?    6.6   0.0    0.0043         7       2      14 ..     108     120 ..     107     125 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.025
                        TFIIS_C  2 kCpkCgsreay 12
                                   +C+ Cg +ea 
  gi|119719573|ref|YP_920068.1| 84 RCETCGYEEAR 94
                                   68888888876 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0043
                        TFIIS_C   2 kCpkCgsreayff 14 
                                    +CpkCg+ + + +
  gi|119719573|ref|YP_920068.1| 108 TCPKCGKGDLVVV 120
                                    6*****9988765 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.2      0.44   7.2e+02       3       8 ..      84      89 ..      83      93 .. 0.80
   2 ?   12.1   0.4   7.5e-05      0.12       2      13 ..     107     119 ..     106     120 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.44
                                   E-SSS- CS
                 zf-C4_Topoisom  3 kCPkCg 8 
                                    C+ Cg
  gi|119719573|ref|YP_920068.1| 84 RCETCG 89
                                   6****9 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 7.5e-05
                                    EE-SSS-.-EEEE CS
                 zf-C4_Topoisom   2 ekCPkCg.gdLvl 13 
                                    ++CPkCg gdLv+
  gi|119719573|ref|YP_920068.1| 107 GTCPKCGkGDLVV 119
                                    79*********96 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   2.5   0.00027      0.44       7      36 ..      84     117 ..      82     119 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00027
                    Zn-ribbon_8   7 rCeeCghefevlqsisdap.....ltaCPeCgs.ev 36 
                                    rCe Cg e  +l   ++ +     + +CP+Cg+ ++
  gi|119719573|ref|YP_920068.1|  84 RCETCGYEEARLY--TEGDalfqaKGTCPKCGKgDL 117
                                    8*****5555444..333334764566*****8665 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.2   0.00077       1.3       2      14 ..      84      96 ..      84      96 .. 0.92
   2 ?    3.1   0.8     0.047        77      15      21 ..     107     113 ..     104     114 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00077
                   Rubredoxin_2  2 vCsqCGfesakwf 14
                                   +C+ CG+e a+++
  gi|119719573|ref|YP_920068.1| 84 RCETCGYEEARLY 96
                                   8*******99986 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.047
                   Rubredoxin_2  15 GrCpsCg 21 
                                    G Cp Cg
  gi|119719573|ref|YP_920068.1| 107 GTCPKCG 113
                                    89****8 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   4.1   0.00072       1.2       2      51 ..      18      66 ..      17      85 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00072
                        DUF4131  2 glplalvllalllllllllllllrrrprrrvllllllllllallgfalra 51
                                   ++p++l ll++ l ++++ll l+   +++   ++++ll l++++++ ++ 
  gi|119719573|ref|YP_920068.1| 18 WIPIYLALLLATLGVTIALLRLWI-STNNEQYFSAALLSLMLSSYISWYL 66
                                   677777777777777777777766.7777778888888888888887765 PP

>> DUF1936  Domain of unknown function (DUF1936)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.2     0.047        77      24      34 .]      84      92 ..      80      92 .. 0.81
   2 ?    7.8   1.0    0.0019         3       2      10 ..     109     117 ..     108     120 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.047
                                   EES-TT---EE CS
                        DUF1936 24 RCdredCdYiE 34
                                   RC  e C+Y+E
  gi|119719573|ref|YP_920068.1| 84 RC--ETCGYEE 92
                                   66..68****9 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0019
                                    -TTTSSSBE CS
                        DUF1936   2 CPKCnvGkL 10 
                                    CPKC+ G L
  gi|119719573|ref|YP_920068.1| 109 CPKCGKGDL 117
                                    *******88 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.1     0.002       3.2      22      31 ..      83      92 ..      76      93 .. 0.83
   2 ?   -0.1   1.9      0.56   9.1e+02       4       8 ..     109     113 ..     109     114 .. 0.93

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.002
                                   EEESSSS-EE CS
                 RNA_POL_M_15KD 22 feCrqCgYee 31
                                   + C +CgYee
  gi|119719573|ref|YP_920068.1| 83 VRCETCGYEE 92
                                   56******97 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.56
                                    ESTTT CS
                 RNA_POL_M_15KD   4 CpkCg 8  
                                    CpkCg
  gi|119719573|ref|YP_920068.1| 109 CPKCG 113
                                    ****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1010  (0.0563333); expected 358.6 (0.02)
Passed bias filter:                      737  (0.0411066); expected 358.6 (0.02)
Passed Vit filter:                       113  (0.00630264); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1121.08
//
Query:       gi|119719574|ref|YP_920069.1|  [L=80]
Description: hypothetical protein Tpen_0664, partial [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0022   17.6  11.6      0.042   13.5   0.1    2.7  2  Ribosomal_S27e   Ribosomal protein S27
  ------ inclusion threshold ------
      0.034   14.2  14.9       0.24   11.5   4.0    2.8  2  DZR              Double zinc ribbon
      0.097   12.6  16.8          1    9.4  13.8    2.9  3  Prok-RING_1      Prokaryotic RING finger family 1
       0.11   12.9  18.7       0.25   11.7   8.2    3.0  3  C1_2             C1 domain
       0.18   10.5   1.3       0.21   10.3   1.3    1.1  1  tRNA-synt_1g     tRNA synthetases class I (M)
       0.25   11.4  15.0        0.1   12.6   7.1    2.8  2  ADK_lid          Adenylate kinase, active site lid
       0.26   11.3  11.1       0.54   10.3   9.5    2.3  2  zinc-ribbons_6   zinc-ribbons
       0.32   11.1   9.3       0.13   12.4   5.8    2.0  2  DUF1272          Protein of unknown function (DUF1272)
        0.4   11.1  11.9        3.7    8.0  12.3    2.4  2  Rhodanese_C      Rhodanase C-terminal
       0.65   10.1   0.0       0.65   10.1   0.0    3.2  3  DUF2752          Protein of unknown function (DUF2752)
       0.82    9.9  14.0        1.5    9.0   6.7    3.4  3  zf-B_box         B-box zinc finger
          2    8.5  18.3        2.1    8.4   7.3    2.9  3  zf-C2HC5         Putative zinc finger motif, C2HC5-type
        2.1    8.4  14.9       0.22   11.5  10.6    1.6  2  zf-RING_5        zinc-RING finger domain
        2.9    7.4  13.4        4.5    6.8   0.3    3.5  4  DUF2688          Protein of unknown function (DUF2688)
        3.6    7.4  25.4       0.11   12.2   5.4    4.0  4  zinc_ribbon_2    zinc-ribbon domain


Domain annotation for each model (and alignments):
>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.1   3.6e-05     0.042       5      36 ..       6      41 ..       3      44 .. 0.83
   2 !    5.8   7.2    0.0093        11      10      38 ..      50      78 ..      47      80 .] 0.89

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.6e-05
                                   EEEEE-TTTS-EEEEE..SS-SS-EE..ESSSTCEE CS
                 Ribosomal_S27e  5 FldvkCpdCenetvvF..shaatvvk..CisCgkvL 36
                                   Fl+  C +C++  v+     ++t v+  C+ Cgk +
  gi|119719574|ref|YP_920069.1|  6 FLKLNCMGCGESRVMLlaYVPKTLVLgrCVRCGKKI 41
                                   *************987324699*99555*****975 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0093
                                   -TTTS-EEEEESS-SS-EEESSSTCEEEE CS
                 Ribosomal_S27e 10 CpdCenetvvFshaatvvkCisCgkvLve 38
                                   C++C+         +t+ kC++Cgk+Lv+
  gi|119719574|ref|YP_920069.1| 50 CQGCGVSYCPICAKKTQGKCQICGKPLVK 78
                                   999999999889999************85 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   4.0    0.0002      0.24      15      49 .]      11      54 ..       8      54 .. 0.76
   2 ?   10.0  11.8   0.00059      0.71       1      46 [.      34      73 ..      34      79 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0002
                            DZR 15 CseCgtk....lkavaa...edrCpsCgekvdpearf..CpeCG 49
                                   C  Cg++    l  v++     rC++Cg+k+ +++++  C+ CG
  gi|119719574|ref|YP_920069.1| 11 CMGCGESrvmlLAYVPKtlvLGRCVRCGKKIYKGDEYyyCQGCG 54
                                   8889998666533333377899********98888877899998 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00059
                            DZR  1 CpqCgeelppdar..fCseCgtklkavaaedrCpsCgekvdpearfCp 46
                                   C +Cg+++ ++++  +C+ Cg +         Cp C +k++ ++++C+
  gi|119719574|ref|YP_920069.1| 34 CVRCGKKIYKGDEyyYCQGCGVSY--------CPICAKKTQGKCQICG 73
                                   99*****999988779*****997........6666666666666664 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1       0.8   9.5e+02       5      12 ..       9      16 ..       6      18 .. 0.74
   2 ?    9.4  13.8   0.00084         1       6      41 ..      33      69 ..      30      74 .. 0.90
   3 ?    7.0   0.4    0.0046       5.5       2      16 ..      64      78 ..      63      79 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.8
                    Prok-RING_1  5 kkCpvCgk 12
                                    +C  Cg+
  gi|119719574|ref|YP_920069.1|  9 LNCMGCGE 16
                                   57999986 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00084
                    Prok-RING_1  6 kCpvCgkelkeedDiVvCpeCgtpyHraCyek.agkC 41
                                   +C  Cgk++ ++d    C  Cg +y   C +k +gkC
  gi|119719574|ref|YP_920069.1| 33 RCVRCGKKIYKGDEYYYCQGCGVSYCPICAKKtQGKC 69
                                   6*****************************9835899 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0046
                    Prok-RING_1  2 ytgkkCpvCgkelke 16
                                   +t+ kC++Cgk+l +
  gi|119719574|ref|YP_920069.1| 64 KTQGKCQICGKPLVK 78
                                   6788*******9865 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.2      0.24   2.9e+02      19      27 ..       9      17 ..       5      25 .. 0.81
   2 ?   11.7   8.2   0.00021      0.25      19      47 .]      32      62 ..      22      62 .. 0.83
   3 ?    5.7   1.3     0.016        19      16      27 ..      64      75 ..      61      79 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.24
                           C1_2 19 fnCsaCgrk 27
                                    nC +Cg++
  gi|119719574|ref|YP_920069.1|  9 LNCMGCGES 17
                                   69****987 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00021
                           C1_2 19 fnCsaCgrk.idgff.YsCseCdfslhvrCa 47
                                   ++C  Cg+k  +g++ Y+C+ C +s +  Ca
  gi|119719574|ref|YP_920069.1| 32 GRCVRCGKKiYKGDEyYYCQGCGVSYCPICA 62
                                   68*******7444446***99******9998 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.016
                           C1_2 16 sesfnCsaCgrk 27
                                   + +++C++Cg++
  gi|119719574|ref|YP_920069.1| 64 KTQGKCQICGKP 75
                                   67899*****98 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.3   0.00018      0.21     129     175 ..      24      75 ..      17      80 .] 0.80

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00018
                                    EE-GGG-EE........-TTS-E...E-TTSSB-E................. CS
                   tRNA-synt_1g 129 flpdryvegtCPkckseeargdq...ceecgkklept..elinpksaisgsk 175
                                    + p   v g C  c+++  +gd+   c+ cg ++ p   + ++ k++i+g+ 
  gi|119719574|ref|YP_920069.1|  24 YVPKTLVLGRCVRCGKKIYKGDEyyyCQGCGVSYCPIcaKKTQGKCQICGKP 75 
                                    77889999*************98555699******96224567799999974 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   1.0     0.094   1.1e+02       4      32 ..      11      42 ..       9      43 .. 0.59
   2 ?   12.6   7.1   8.5e-05       0.1       3      34 ..      49      79 ..      48      80 .] 0.83

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.094
                                   -TTT--EEETTT.B--S..STTB-TTT--.-B CS
                        ADK_lid  4 CpkCGrsYhvvf.npPk..veglCDkCGepLv 32
                                   C  CG+s  + +   Pk  v g C  CG + +
  gi|119719574|ref|YP_920069.1| 11 CMGCGESRVMLLaYVPKtlVLGRCVRCGKKIY 42
                                   55566654433222355557788999998765 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 8.5e-05
                                   E-TTT--EEETTT.B--SSTTB-TTT--.-B-- CS
                        ADK_lid  3 vCpkCGrsYhvvf.npPkveglCDkCGepLvqR 34
                                    C  CG sY        k+ g+C  CG pLv+ 
  gi|119719574|ref|YP_920069.1| 49 YCQGCGVSYC--PiCAKKTQGKCQICGKPLVKK 79
                                   59*******8..324569************986 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       1.1   1.3e+03      18      24 ..      10      16 ..       4      27 .. 0.62
   2 ?   10.3   9.5   0.00045      0.54       2      47 ..      33      74 ..      32      79 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.1
                                   E-TTT-- CS
                 zinc-ribbons_6 18 hCeaCqe 24
                                   +C  C e
  gi|119719574|ref|YP_920069.1| 10 NCMGCGE 16
                                   4555544 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00045
                                   --SSS-S--EE-SSEEE-TTT--EEEEEEE-SSS-S---.EEEETTE CS
                 zinc-ribbons_6  2 kCpeCqqelekrgeqyhCeaCqedlkkealCpeCeqele.vlkaCga 47
                                    C +C +++ k +e y C+ C        +Cp C ++ + +++ Cg+
  gi|119719574|ref|YP_920069.1| 33 RCVRCGKKIYKGDEYYYCQGCGV-----SYCPICAKKTQgKCQICGK 74
                                   59*******************97.....4566666655545566654 PP

>> DUF1272  Protein of unknown function (DUF1272)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1      0.91   1.1e+03       4      13 ..       7      16 ..       4      21 .. 0.69
   2 ?   12.4   5.8   0.00011      0.13       7      55 ..      33      80 .]      29      80 .] 0.89

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.91
                        DUF1272  4 lrpnCecCdk 13
                                   l+ nC  C +
  gi|119719574|ref|YP_920069.1|  7 LKLNCMGCGE 16
                                   6667777754 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00011
                        DUF1272  7 nCecCdkdlppdseearicsyEctFCaeCaeevlenvCPncgGelvkRP 55
                                   +C +C k++ + +e  +      ++C  Ca+++ ++ C  cg  lvk+P
  gi|119719574|ref|YP_920069.1| 33 RCVRCGKKIYKGDEYYYCQGCGVSYCPICAKKT-QGKCQICGKPLVKKP 80
                                   799******999966666678889********9.************999 PP

>> Rhodanese_C  Rhodanase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0  12.3    0.0031       3.7      14      63 ..      27      72 ..       7      74 .. 0.79
   2 ?    5.0   1.2     0.026        31      16      29 ..      64      77 ..      61      79 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0031
                    Rhodanese_C 14 ksevvgkCieCgkpvdelr.krnCanedCnelvlvCeeCaeklkgvcseeC 63
                                   k+ v+g+C+ Cgk+  +   +  C+   C +   +C+ Ca+k +g c+  C
  gi|119719574|ref|YP_920069.1| 27 KTLVLGRCVRCGKKIYKGDeYYYCQ--GCGVS--YCPICAKKTQGKCQ-IC 72
                                   33499********998666799996..89865..7**********987.55 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.026
                    Rhodanese_C 16 evvgkCieCgkpvd 29
                                   ++ gkC +Cgkp  
  gi|119719574|ref|YP_920069.1| 64 KTQGKCQICGKPLV 77
                                   5789*******975 PP

>> DUF2752  Protein of unknown function (DUF2752)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00054      0.65       4      21 ..       4      21 ..       2      24 .. 0.82
   2 ?    3.6   1.5     0.059        70       9      16 ..      48      55 ..      47      57 .. 0.89
   3 ?   -1.6   0.6       2.4   2.9e+03      10      14 ..      57      61 ..      56      62 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00054
                        DUF2752  4 kaltGipCPGCGltRavh 21
                                   k +  ++C GCG  R ++
  gi|119719574|ref|YP_920069.1|  4 KIFLKLNCMGCGESRVML 21
                                   567799******999875 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.059
                        DUF2752  9 ipCPGCGl 16
                                   ++C GCG+
  gi|119719574|ref|YP_920069.1| 48 YYCQGCGV 55
                                   79*****7 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 2.4
                        DUF2752 10 pCPGC 14
                                   +CP C
  gi|119719574|ref|YP_920069.1| 57 YCPIC 61
                                   8**99 PP

>> zf-B_box  B-box zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1      0.54   6.5e+02      13      23 ..       6      16 ..       1      17 [. 0.73
   2 ?    9.0   6.7    0.0013       1.5       6      31 ..      34      63 ..      31      66 .. 0.68
   3 ?    2.7   0.1      0.12   1.4e+02       3      14 ..      66      76 ..      64      77 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.54
                       zf-B_box 13 patlfCedCqq 23
                                    ++l C  C++
  gi|119719574|ref|YP_920069.1|  6 FLKLNCMGCGE 16
                                   57889999975 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0013
                       zf-B_box  6 CpeHknkpat....lfCedCqqplCeeCst 31
                                   C ++++k ++    ++C+ C++  C+ C +
  gi|119719574|ref|YP_920069.1| 34 CVRCGKKIYKgdeyYYCQGCGVSYCPICAK 63
                                   666663333233339*************44 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.12
                       zf-B_box  3 etkCpeHknkpa 14
                                   + kC++++ kp+
  gi|119719574|ref|YP_920069.1| 66 QGKCQICG-KPL 76
                                   56888888.765 PP

>> zf-C2HC5  Putative zinc finger motif, C2HC5-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   2.5     0.021        25      18      47 ..       9      44 ..       2      48 .. 0.67
   2 ?    2.3   6.0      0.14   1.7e+02      19      41 ..      33      54 ..      20      64 .. 0.73
   3 ?    8.4   7.3    0.0018       2.1      19      46 ..      49      78 ..      45      80 .] 0.74

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.021
                       zf-C2HC5 18 pnClnCGk..iiCakegls....kpCsfCgspllss 47
                                    nC+ CG   ++  +  ++    ++C  Cg+++++ 
  gi|119719574|ref|YP_920069.1|  9 LNCMGCGEsrVMLLAYVPKtlvlGRCVRCGKKIYKG 44
                                   688888853355554444456678888888888765 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.14
                       zf-C2HC5 19 nClnCGkiiCakeglskpCsfCg 41
                                    C+ CGk i + +++   C+ Cg
  gi|119719574|ref|YP_920069.1| 33 RCVRCGKKIYKGDEY-YYCQGCG 54
                                   699999988887777.6666665 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0018
                       zf-C2HC5 19 nClnCGki...iCakeglskpCsfCgsplls 46
                                    C  CG     iCak+   ++C+ Cg+pl++
  gi|119719574|ref|YP_920069.1| 49 YCQGCGVSycpICAKKTQ-GKCQICGKPLVK 78
                                   599999872225555555.**********97 PP

>> zf-RING_5  zinc-RING finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       3.8   4.6e+03      39      42 ..      11      14 ..       8      18 .. 0.60
   2 ?   11.5  10.6   0.00018      0.22       1      44 []      33      74 ..      33      74 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.8
                      zf-RING_5 39 CpiC 42
                                   C  C
  gi|119719574|ref|YP_920069.1| 11 CMGC 14
                                   5545 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00018
                      zf-RING_5  1 hCnkCfekl.skeekfyltsCgHifCekClkkllekeavCpiCrk 44
                                   +C +C +k+ +++e +y   Cg ++C  C+kk +    +C iC+k
  gi|119719574|ref|YP_920069.1| 33 RCVRCGKKIyKGDEYYYCQGCGVSYCPICAKKTQ---GKCQICGK 74
                                   6********899999*******************...99999986 PP

>> DUF2688  Protein of unknown function (DUF2688)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.28   3.3e+02       9      18 ..      10      19 ..       6      23 .. 0.81
   2 ?    6.6   1.4    0.0043       5.2       6      19 ..      30      43 ..      27      50 .. 0.83
   3 ?   -1.0   0.4         1   1.2e+03      10      16 ..      50      56 ..      48      66 .. 0.81
   4 ?    6.8   0.3    0.0037       4.5       9      19 ..      68      78 ..      60      79 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.28
                        DUF2688  9 qCrRCGksls 18
                                   +C  CG s +
  gi|119719574|ref|YP_920069.1| 10 NCMGCGESRV 19
                                   8999**9855 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0043
                        DUF2688  6 VtTqCrRCGkslst 19
                                   V  +C RCGk + +
  gi|119719574|ref|YP_920069.1| 30 VLGRCVRCGKKIYK 43
                                   6679******9976 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1
                        DUF2688 10 CrRCGks 16
                                   C+ CG s
  gi|119719574|ref|YP_920069.1| 50 CQGCGVS 56
                                   8889977 PP

  == domain 4  score: 6.8 bits;  conditional E-value: 0.0037
                        DUF2688  9 qCrRCGkslst 19
                                   +C+ CGk+l++
  gi|119719574|ref|YP_920069.1| 68 KCQICGKPLVK 78
                                   7********97 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.4      0.29   3.5e+02      16      21 ..      11      16 ..       8      17 .. 0.82
   2 ?   12.2   5.4   9.6e-05      0.11       1      20 [.      33      54 ..      33      56 .. 0.93
   3 ?    1.6   0.6       0.2   2.4e+02       1       7 [.      57      63 ..      57      66 .. 0.61
   4 ?    5.5   0.5     0.012        14       1      10 [.      68      77 ..      68      79 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.29
                  zinc_ribbon_2 16 CpyCGt 21
                                   C  CG+
  gi|119719574|ref|YP_920069.1| 11 CMGCGE 16
                                   888987 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 9.6e-05
                  zinc_ribbon_2  1 fCpnCGaelqdnakF..CpyCG 20
                                   +C +CG+++ +++ +  C  CG
  gi|119719574|ref|YP_920069.1| 33 RCVRCGKKIYKGDEYyyCQGCG 54
                                   6********99999999****9 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.2
                  zinc_ribbon_2  1 fCpnCGa 7 
                                   +Cp C +
  gi|119719574|ref|YP_920069.1| 57 YCPICAK 63
                                   5666655 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.012
                  zinc_ribbon_2  1 fCpnCGaelq 10
                                   +C  CG++l 
  gi|119719574|ref|YP_920069.1| 68 KCQICGKPLV 77
                                   7999999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       940  (0.052429); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                        32  (0.00178482); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 480.47
//
Query:       gi|119719575|ref|YP_920070.1|  [L=614]
Description: hypothetical protein Tpen_0665 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-41  142.1   0.0    2.9e-41  141.4   0.0    1.3  1  PAPS_reduct    Phosphoadenosine phosphosulfate reductase fami
    2.9e-06   27.7  10.4    6.2e-06   26.7  10.4    1.6  1  Fer4_7         4Fe-4S dicluster domain
    6.2e-06   25.5   0.0    1.1e-05   24.7   0.0    1.3  1  NAD_synthase   NAD synthase
    1.1e-05   25.4  10.5    3.1e-05   24.0  10.6    1.7  1  Fer4_10        4Fe-4S dicluster domain
    2.3e-05   24.4   8.1      5e-05   23.4   8.1    1.5  1  Fer4_21        4Fe-4S dicluster domain
    2.9e-05   24.4   4.8     0.0041   17.5   1.1    2.5  2  Fer4_8         4Fe-4S dicluster domain
    5.8e-05   23.2  10.1    5.8e-05   23.2  10.1    1.6  1  Fer4_9         4Fe-4S dicluster domain
    0.00025   20.7  10.2     0.0034   17.1   4.1    2.5  2  Fer4           4Fe-4S binding domain
     0.0075   16.3   2.4     0.0075   16.3   2.4    2.8  2  Fer4_2         4Fe-4S binding domain
     0.0081   17.0   3.2        1.7    9.5   0.6    2.5  2  Fer4_22        4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.031   14.4   6.9       0.11   12.6   1.9    2.4  2  ETF_QO         Electron transfer flavoprotein-ubiquinone oxid
      0.056   13.6   2.2       0.11   12.6   2.2    1.4  1  Fer4_18        4Fe-4S dicluster domain
      0.065   12.7   0.0      0.065   12.7   0.0    1.8  1  QueC           Queuosine biosynthesis protein QueC
      0.065   12.0   0.0       0.12   11.1   0.0    1.4  1  tRNA_Me_trans  tRNA methyl transferase
      0.071   13.2  10.3      0.053   13.6   2.2    2.5  2  Fer4_6         4Fe-4S binding domain
      0.087   12.6   0.0        4.3    7.1   0.0    2.8  3  ATP_bind_3     PP-loop family
       0.31   11.6  13.3       0.71   10.5   3.9    2.4  2  Fer4_17        4Fe-4S dicluster domain
       0.43   11.5  12.8       0.31   12.0   1.4    2.5  2  Fer4_16        4Fe-4S double cluster binding domain
       0.76   10.9  16.7        3.7    8.7   5.7    2.7  2  Fer4_3         4Fe-4S binding domain
       0.83   10.2   8.8       0.15   12.6   0.6    2.4  2  Fer4_13        4Fe-4S single cluster domain of Ferredoxin I
        3.9    8.2  10.8       0.87   10.3   2.5    2.5  2  Fer4_4         4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.4   0.0   3.4e-44   2.9e-41       2     173 ..     233     407 ..     232     408 .. 0.97

  Alignments for each domain:
  == domain 1  score: 141.4 bits;  conditional E-value: 3.4e-44
                                    EEEE--SSCTCHHHHHHHHHHCTT..HEEEEEE-STB-HHHHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHHH-S-THHH CS
                    PAPS_reduct   2 lvvsvsgGkdslVllhLalkafkp..vpvvfvdtghefpetiefvdeleeryglrlkvyepeeevaekinaekhgsslye 79 
                                    ++vs sgGkdslV+lhLa+ka+ +  v+ +f +tg ef+et+e+  ++++ yg++l+ ++  +++++++   + + ++y+
  gi|119719575|ref|YP_920070.1| 233 VFVSLSGGKDSLVTLHLAVKALGNekVKALFNNTGLEFEETVEYARRIADYYGVELIEADAGDNFWRALPVMGPPARDYR 312
                                    589*******************995559**************************************************** PP

                                    CHHHHHHTHHHHHHHHHCT..TECEEE----CCCTTTTTTSSSEEECTTT-SCEEE-CCCT--HHHHHHHHHHCT--B-C CS
                    PAPS_reduct  80 eaaeriaKveplkkaLekl..dedalltGaRrdesksraklpiveidedfekslrvfPllnWteedvwqyilrenipynp 157
                                    + +++++K  ++ +a +k+  +  + l+G+R++es++ra  p ++++ + + ++   P+ +W+  d+w yi +e +p+n+
  gi|119719575|ref|YP_920070.1| 313 W-CCKVTKFSTISRAVKKFfpEGALSLVGQRKYESSARALSPRIWRNYWLPGVVAASPVHDWSAMDIWLYIFMERLPVNK 391
                                    *.****************99888899****************************************************** PP

                                    CCCTT-SS--BCTTB- CS
                    PAPS_reduct 158 LydqgfrsiGcvpctg 173
                                    Ly  gf+++Gc+ c++
  gi|119719575|ref|YP_920070.1| 392 LYYYGFDRLGCWLCPA 407
                                    *************985 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7  10.4   7.2e-09   6.2e-06       2      50 ..     549     592 ..     548     593 .. 0.93

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 7.2e-09
                         Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPt 50 
                                    C++C  C + Cp+k i++d e     +  +++++++C++Cg C   CP+
  gi|119719575|ref|YP_920070.1| 549 CVECLECSNWCPTKSISIDSE-----NGGIKVNESTCIHCGTCNYKCPV 592
                                    ******************997.....44699*****************7 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   1.2e-08   1.1e-05       5      80 ..     218     292 ..     215     300 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.2e-08
                                    HHHHHHHHHHHCTTSEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE-- CS
                   NAD_synthase   5 lvdflkeyvkkagakgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievktid 80 
                                     v f++e  +k+    v + lSGG DS ++  lavkalg+e+v+al   +  + ee ve a+ +a+ +g+e  + d
  gi|119719575|ref|YP_920070.1| 218 AVSFIREVAEKYRL-PVFVSLSGGKDSLVTLHLAVKALGNEKVKALFNNTGLEFEETVEYARRIADYYGVELIEAD 292
                                    56788876666665.57789****************************9*****************9999988776 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0  10.6   3.6e-08   3.1e-05       4      56 .]     544     591 ..     541     591 .. 0.92

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 3.6e-08
                        Fer4_10   4 idddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                    i +  C++C +C + CP+     + + ++se++ ++++ + C++cg C  +CP
  gi|119719575|ref|YP_920070.1| 544 IRSYFCVECLECSNWCPT-----KSISIDSENGGIKVNESTCIHCGTCNYKCP 591
                                    56667*************.....9999999999999****************9 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   8.1   5.8e-08     5e-05       3      55 ..     544     594 ..     542     597 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 5.8e-08
                        Fer4_21   3 idedkCigCgkCliaCedtshqaieidakt.vlkvvedeCvGCnlCssvCPved 55 
                                    i +  C++C +C   C+   ++ i+id+++  +kv e++C+ C  C   CPv +
  gi|119719575|ref|YP_920070.1| 544 IRSYFCVECLECSNWCP---TKSISIDSENgGIKVNESTCIHCGTCNYKCPVVE 594
                                    56667************...57888886653789******************76 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.1    0.0052       4.4      51      63 ..     549     561 ..     520     568 .. 0.76
   2 !   17.5   1.1   4.8e-06    0.0041       4      25 ..     579     600 ..     577     610 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0052
                         Fer4_8  51 CttcgaCtevCpv 63 
                                    C++c +C++ Cp+
  gi|119719575|ref|YP_920070.1| 549 CVECLECSNWCPT 561
                                    6666666666665 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 4.8e-06
                         Fer4_8   4 kCieCgaCqsaCpvlrrtkkhl 25 
                                     Ci+Cg C+ +Cpv++ t khl
  gi|119719575|ref|YP_920070.1| 579 TCIHCGTCNYKCPVVEYTFKHL 600
                                    7**************9998775 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2  10.1   6.8e-08   5.8e-05       2      48 ..     549     592 ..     548     594 .. 0.94

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 6.8e-08
                         Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpk 48 
                                    C++C +C + Cp++ ++ d+ ++ +++++     Ci+Cg+C  +Cp 
  gi|119719575|ref|YP_920070.1| 549 CVECLECSNWCPTKSISIDSENGGIKVNES---TCIHCGTCNYKCPV 592
                                    **************************9774...7***********95 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.4    0.0074       6.3       8      23 ..     549     564 ..     543     565 .. 0.89
   2 !   17.1   4.1     4e-06    0.0034       1      20 [.     573     592 ..     573     593 .. 0.94

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0074
                                    SSS-THHHHHSTTTEE CS
                           Fer4   8 CigCGaCvevCPvgAI 23 
                                    C+ C +C + CP+  I
  gi|119719575|ref|YP_920070.1| 549 CVECLECSNWCPTKSI 564
                                    ************9877 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 4e-06
                                    EEEETTTSSS-THHHHHSTT CS
                           Fer4   1 vvideekCigCGaCvevCPv 20 
                                    ++++e+ Ci+CG+C   CPv
  gi|119719575|ref|YP_920070.1| 573 IKVNESTCIHCGTCNYKCPV 592
                                    689****************8 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   1.4    0.0043       3.7       9      22 .]     548     561 ..     541     561 .. 0.87
   2 !   16.3   2.4   8.7e-06    0.0075       3      21 ..     573     591 ..     571     592 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0043
                         Fer4_2   9 rCigCgaCvsaCPa 22 
                                     C++C  C + CP+
  gi|119719575|ref|YP_920070.1| 548 FCVECLECSNWCPT 561
                                    6*******999**7 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 8.7e-06
                         Fer4_2   3 vvvdtdrCigCgaCvsaCP 21 
                                    ++v++ +Ci+Cg+C   CP
  gi|119719575|ref|YP_920070.1| 573 IKVNESTCIHCGTCNYKCP 591
                                    689***********777*9 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.1    0.0099       8.5      78      94 ..     545     561 ..     512     569 .. 0.72
   2 !    9.5   0.6     0.002       1.7       1      14 [.     579     592 ..     573     611 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0099
                        Fer4_22  78 gesgCvGCgRCieacpv 94 
                                     ++ Cv C  C+++cp+
  gi|119719575|ref|YP_920070.1| 545 RSYFCVECLECSNWCPT 561
                                    55667777777777765 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.002
                        Fer4_22   1 rClsCgaCtlvCpt 14 
                                    +C++Cg+C++ Cp 
  gi|119719575|ref|YP_920070.1| 579 TCIHCGTCNYKCPV 592
                                    48888888888886 PP

>> ETF_QO  Electron transfer flavoprotein-ubiquinone oxidoreductase, 4Fe-4S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.2     0.026        23      66      98 ..     540     572 ..     527     573 .. 0.85
   2 ?   12.6   1.9   0.00013      0.11      65      92 ..     570     597 ..     566     602 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.026
                                    EEEEE-CCC--S--HHHHH-TT--EEE---STT CS
                         ETF_QO  66 kklqinaqnCvhCktCdikdpsqniewvvPeGg 98 
                                     ++ i +  Cv C  C+   p+++i+  + +Gg
  gi|119719575|ref|YP_920070.1| 540 DRVLIRSYFCVECLECSNWCPTKSISIDSENGG 572
                                    6788999******************99988887 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00013
                                    SEEEEE-CCC--S--HHHHH-TT--EEE CS
                         ETF_QO  65 ekklqinaqnCvhCktCdikdpsqniew 92 
                                    +  +++n + C+hC tC+ k p  + ++
  gi|119719575|ref|YP_920070.1| 570 NGGIKVNESTCIHCGTCNYKCPVVEYTF 597
                                    556899**************99877666 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   2.2   0.00013      0.11      60      98 ..     548     593 ..     515     603 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00013
                        Fer4_18  60 dcidcescvkvcPtg...idirkG.lql...eciscllcidacdkv 98 
                                     c++c  c + cPt+   id  +G +++    ci c+ c   c  v
  gi|119719575|ref|YP_920070.1| 548 FCVECLECSNWCPTKsisIDSENGgIKVnesTCIHCGTCNYKCPVV 593
                                    5************9543377776535552226*******9999766 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   7.6e-05     0.065       4      55 ..     235     287 ..     232     296 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.6e-05
                                    EE--SSHHHHHHHHHHHHH-..SEEEEEEEESS-TTSHHHHHHHHHHHHT--.- CS
                           QueC   4 vllSGGlDSttvlalakkeg..kevealtfdYgqrhkkeleaakkiakelgvee 55 
                                    v lSGG DS + l la k+   ++v+al  + g   ++++e+a++ia+ +gv e
  gi|119719575|ref|YP_920070.1| 235 VSLSGGKDSLVTLHLAVKALgnEKVKALFNNTGLEFEETVEYARRIADYYGV-E 287
                                    779**********99999865689***************************9.4 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00014      0.12       3      77 ..     233     300 ..     231     312 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00014
                  tRNA_Me_trans   3 vvvalSgGVDSsvaaallkeq.gyevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdfekeykek 77 
                                    v+v lSgG DS v+++l  ++ g e ++  ++++        +   ee +++a+r+a+  g++l   d  ++++++
  gi|119719575|ref|YP_920070.1| 233 VFVSLSGGKDSLVTLHLAVKAlGNEKVKALFNNT--------GLEFEETVEYARRIADYYGVELIEADAGDNFWRA 300
                                    89************99876661444444444333........34467889************************86 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   1.2     0.082        70       9      22 ..     549     562 ..     548     564 .. 0.90
   2 ?   13.6   2.2   6.2e-05     0.053       2      20 ..     573     591 ..     573     596 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.082
                         Fer4_6   9 CigCgdCvrvCPeg 22 
                                    C+ C +C + CP++
  gi|119719575|ref|YP_920070.1| 549 CVECLECSNWCPTK 562
                                    ************97 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 6.2e-05
                         Fer4_6   2 veidpdkCigCgdCvrvCP 20 
                                    + ++++ Ci+Cg C   CP
  gi|119719575|ref|YP_920070.1| 573 IKVNESTCIHCGTCNYKCP 591
                                    579***********99999 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0     0.005       4.3       2      28 ..     233     259 ..     232     288 .. 0.79
   2 ?   -0.5   0.0         1   8.7e+02     134     161 ..     412     440 ..     403     445 .. 0.80
   3 ?    1.3   0.1       0.3   2.6e+02      34      71 ..     483     522 ..     462     546 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.005
                                    EEEE--SCHHHHHHHHHHHHHCTTTTT CS
                     ATP_bind_3   2 vlvAvSgGlDSmaLllllaklkkklgi 28 
                                    v v +SgG DS++ l+l++k   ++++
  gi|119719575|ref|YP_920070.1| 233 VFVSLSGGKDSLVTLHLAVKALGNEKV 259
                                    5799************99998665444 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1
                                    EETTCCEE-C.CCT--HHHHHHHHHHTT- CS
                     ATP_bind_3 134 eiasirlvRP.lLkvskeeleeylkekki 161
                                    e++  r+v P l++ +k+ le+y++ +++
  gi|119719575|ref|YP_920070.1| 412 ELDLLRIVKPgLYDKWKSYLESYAQMNGL 440
                                    45667899996779**********99876 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.3
                                    EEE-SSS.TCHHHHHHHHHHHHHHTT-EEEEEE--H.HHC CS
                     ATP_bind_3  34 hvdhglr.eeskeeaelvkelckklnikleiekvdv.akk 71 
                                    +v+++l+ ++ +  +e v++l ++ln +leie+v+v ++ 
  gi|119719575|ref|YP_920070.1| 483 TVEYRLHnPSVRIIEEKVRNLWHTLNKPLEIESVQVtGNA 522
                                    78999993455557899******************96333 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   1.9     0.022        19      44      58 ..     547     561 ..     522     563 .. 0.80
   2 ?   10.5   3.9   0.00084      0.71      44      57 ..     578     591 ..     564     593 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.022
                        Fer4_17  44 slCieCgeCerkCPq 58 
                                      C+eC eC+  CP 
  gi|119719575|ref|YP_920070.1| 547 YFCVECLECSNWCPT 561
                                    5699******99996 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00084
                        Fer4_17  44 slCieCgeCerkCP 57 
                                    s+Ci+Cg C++kCP
  gi|119719575|ref|YP_920070.1| 578 STCIHCGTCNYKCP 591
                                    78***********9 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.4   0.00037      0.31       1      21 [.     548     568 ..     548     579 .. 0.85
   2 ?    4.1   4.1      0.11        92       1      15 [.     579     593 ..     579     611 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00037
                        Fer4_16   1 rCgtCgkCaevCPtnaikekk 21 
                                    +C++C +C + CPt+ i+ ++
  gi|119719575|ref|YP_920070.1| 548 FCVECLECSNWCPTKSISIDS 568
                                    6****************9774 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.11
                        Fer4_16   1 rCgtCgkCaevCPtn 15 
                                    +C+ Cg C   CP+ 
  gi|119719575|ref|YP_920070.1| 579 TCIHCGTCNYKCPVV 593
                                    599999999999975 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   3.2     0.013        11       1      14 [.     549     562 ..     549     563 .. 0.91
   2 ?    8.7   5.7    0.0044       3.7       1      13 [.     580     592 ..     580     593 .. 0.96

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.013
                         Fer4_3   1 CtgCgaCvevCPvg 14 
                                    C+ C  C ++CP++
  gi|119719575|ref|YP_920070.1| 549 CVECLECSNWCPTK 562
                                    9***88******87 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0044
                         Fer4_3   1 CtgCgaCvevCPv 13 
                                    C++Cg+C   CPv
  gi|119719575|ref|YP_920070.1| 580 CIHCGTCNYKCPV 592
                                    ************6 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   2.0      0.72   6.1e+02       6      17 ..     549     560 ..     548     565 .. 0.84
   2 ?   12.6   0.6   0.00018      0.15       1      19 [.     575     593 ..     575     601 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.72
                        Fer4_13   6 CiacgaCvelaP 17 
                                    C++c  C + +P
  gi|119719575|ref|YP_920070.1| 549 CVECLECSNWCP 560
                                    889999999998 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00018
                        Fer4_13   1 VDrdtCiacgaCvelaPdv 19 
                                    V+++tCi cg+C   +P v
  gi|119719575|ref|YP_920070.1| 575 VNESTCIHCGTCNYKCPVV 593
                                    899*************965 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   1.3      0.42   3.6e+02       4      16 ..     549     561 ..     540     562 .. 0.89
   2 ?   10.3   2.5     0.001      0.87       3      15 ..     579     591 ..     577     598 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.42
                         Fer4_4   4 CigCgsCvaaCPq 16 
                                    C++C  C + CP+
  gi|119719575|ref|YP_920070.1| 549 CVECLECSNWCPT 561
                                    *******999997 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.001
                         Fer4_4   3 rCigCgsCvaaCP 15 
                                    +Ci+Cg C + CP
  gi|119719575|ref|YP_920070.1| 579 TCIHCGTCNYKCP 591
                                    7***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (614 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.66u 0.28s 00:00:00.94 Elapsed: 00:00:00.49
# Mc/sec: 3782.00
//
Query:       gi|119719576|ref|YP_920071.1|  [L=516]
Description: DNA topoisomerase VI subunit B [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.5e-59  198.1   0.0    1.4e-58  197.2   0.0    1.4  1  Topo-VIb_trans  Topoisomerase VI B subunit, transducer
    5.1e-13   49.5   0.0    8.9e-13   48.7   0.0    1.4  1  HATPase_c       Histidine kinase-, DNA gyrase B-, and HSP90-l
    8.2e-11   41.9   0.0    1.6e-10   41.0   0.0    1.4  1  HATPase_c_3     Histidine kinase-, DNA gyrase B-, and HSP90-l
     0.0022   16.8   1.1     0.0052   15.6   0.0    1.8  2  FbpA            Fibronectin-binding protein A N-terminus (Fbp
  ------ inclusion threshold ------
      0.098   12.8   0.2        0.3   11.3   0.2    1.8  1  S1FA            DNA binding protein S1FA


Domain annotation for each model (and alignments):
>> Topo-VIb_trans  Topoisomerase VI B subunit, transducer
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.2   0.0   3.9e-62   1.4e-58       1     158 [.     308     464 ..     308     465 .. 0.97

  Alignments for each domain:
  == domain 1  score: 197.2 bits;  conditional E-value: 3.9e-62
                 Topo-VIb_trans   1 PstdclspigeeliekglkkelkpefvaavtrkpkvyeghpfivEvgiayGGelekeekaeilRfaNrvPLlydegadvi 80 
                                    P+  +lsp+g++l++kg+k++lkpefvaavtr+p++y+gh+fivE++iayGGe+++++++ +lRfaN++PLlydeg dv 
  gi|119719576|ref|YP_920071.1| 308 PRPLTLSPLGADLLKKGVKSILKPEFVAAVTRPPSSYSGHAFIVEAAIAYGGEIPPQDTVMLLRFANKMPLLYDEGVDVS 387
                                    77789*************************************************************************** PP

                 Topo-VIb_trans  81 tkavksinwkrYkleqpedpvvvlvhvastkvPfksegKeaiadveeiekeiklalqevarkLkkylskkekekeeke 158
                                     k+++si+w+ Yk++ p+ pv+v+ hv+stk+Pfk++gKeaiadv+e+e+e++ a+++var+L++yls+ ek  e k+
  gi|119719576|ref|YP_920071.1| 388 RKIIDSIDWSIYKVKLPA-PVAVVTHVCSTKIPFKGVGKEAIADVPEVEHELEIAIRDVARRLRAYLSRMEKLYEVKR 464
                                    ***************998.****************************************************9888765 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.7   0.0   2.5e-16   8.9e-13       4      97 ..      28     130 ..      25     175 .. 0.71

  Alignments for each domain:
  == domain 1  score: 48.7 bits;  conditional E-value: 2.5e-16
                                    HHHHHHHHHHHHHHHHHHSTTT......EEEEEEEEEE...TEEEEEEEESSSSSTTHHHTGTCS.TTCHHCSTCHTS.. CS
                      HATPase_c   4 krLrqiisnlvdNavkfatkag......eieveikase...ddlvisveDnGiGipkedlkklfe.kfsqddstkrgg.. 71 
                                    + L+q++++lv+N++++ t+++      ++e++++  e   +++v++v DnGiGip ++++++f+  f+  +++ +++  
  gi|119719576|ref|YP_920071.1|  28 RALYQAVRELVENSLDA-TETHgilpfiDVEIRLH--EerpEWVVLRVADNGIGIPLSEVPNVFGrVFYG-SKYVVRQtr 103
                                    789*************8.54442455444477777..33578***********************99999.444444312 PP

                                    TSSSHHHHHHHHHHH.HTTTEEEEEEE CS
                      HATPase_c  72 ggtGlGlsivkklve.lmgGeiwvese 97 
                                    g +GlG++++  +++ +    i+v+s+
  gi|119719576|ref|YP_920071.1| 104 GVFGLGVKMAVLYAQmTTARPIYVKSS 130
                                    445555555544443122235555444 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   0.0   4.4e-14   1.6e-10       4      83 ..      31     116 ..      28     142 .. 0.93

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 4.4e-14
                    HATPase_c_3   4 ekAlaelvdNsldAdaen.......vkievnknrgktgeivieDdGkGmseeelknal.rlatsskeakrkstslGkkGi 75 
                                    ++A+ elv+NsldA  ++       v+i ++++r +   +++ D+G G++ +e+ n++ r+   sk+    ++++G +G+
  gi|119719576|ref|YP_920071.1|  31 YQAVRELVENSLDATETHgilpfidVEIRLHEERPEWVVLRVADNGIGIPLSEVPNVFgRVFYGSKYV--VRQTRGVFGL 108
                                    689******************************99899******************775899999995..8********* PP

                    HATPase_c_3  76 GlklAsls 83 
                                    G+k+A+l 
  gi|119719576|ref|YP_920071.1| 109 GVKMAVLY 116
                                    *****975 PP

>> FbpA  Fibronectin-binding protein A N-terminus (FbpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.4e-06    0.0052     161     237 ..     222     301 ..     217     304 .. 0.86
   2 ?   -1.4   0.7       0.2   7.3e+02     421     444 ..     467     506 ..     437     510 .. 0.58

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.4e-06
                                    SXXXSXBXTT..SXXH.HHHHHHHHH.S.XXXHHHHHHHBTTXXHHHHHHHHTTXSSSH...............HHHHHH CS
                           FbpA 161 PpsqdklnPl..eaeeleefkellsk.kekdlvkaLvkafqGlspllaeelleragldketsakelseedlerlyealqe 237
                                    Pp+  k  P   ++e l+e+  + ++ +e +l ++Lvk+f+G+++  a e l+  g+ ++t+++el+  dle l++++++
  gi|119719576|ref|YP_920071.1| 222 PPEIGKYHPRgvDVEVLKELIRATNNaSEVTLLEFLVKHFEGVGEKKATEFLQWSGFSPDTKLTELKLADLEVLASKMKT 301
                                    9999******66666666555554558999******************************************99988776 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.2
                                    H................T-.-HHHHHHHHHHHHHTTS--- CS
                           FbpA 421 e................qaesledleeikeELieegylkk 444
                                                        ++e+++++ eEL +++++kk
  gi|119719576|ref|YP_920071.1| 467 VtirkymgevssalayiVNRDPEEINALIEELLKKELAKK 506
                                    3333333333344446644588999999899888888776 PP

>> S1FA  DNA binding protein S1FA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   8.4e-05       0.3      24      51 ..     135     162 ..     125     166 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8.4e-05
                           S1FA  24 flvgnyvlyvyaqktlPprkkkPvskkk 51 
                                     +vg y+ly+   +++P+ +k  + kk 
  gi|119719576|ref|YP_920071.1| 135 RYVGEYLLYIDISRNIPHVQKMRIKKKT 162
                                    579******************9997663 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (516 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       715  (0.0398795); expected 358.6 (0.02)
Passed bias filter:                      628  (0.0350271); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.44
# Mc/sec: 3513.83
//
Query:       gi|119719577|ref|YP_920072.1|  [L=379]
Description: DNA topoisomerase VI subunit A [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-20   73.4   0.1    2.3e-20   72.3   0.1    1.6  1  TP6A_N    Type IIB DNA topoisomerase


Domain annotation for each model (and alignments):
>> TP6A_N  Type IIB DNA topoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.3   0.1   1.3e-24   2.3e-20       1      62 []      78     154 ..      78     154 .. 0.98

  Alignments for each domain:
  == domain 1  score: 72.3 bits;  conditional E-value: 1.3e-24
                                    HHHHHHHHHHHHHHHHHHTT--EEHHHHHHH...............GGGS-SSHHHHHHHHHHHHHHHTS-GGGGTE CS
                         TP6A_N   1 rkfaqllkvlelihelleegkvvTkRdiYYr...............dvelFksQaesdrliddievllgvsReeLnv 62 
                                    ++f+q++++l+li ++ +eg ++T+R++YYr                +e++++Q+es+++i+diev++g++Re+++v
  gi|119719577|ref|YP_920072.1|  78 KRFMQTVLMLSLIVQARREGDYPTIRELYYRgkrtikytdergnkaSEETWDDQRESNAVIQDIEVATGLLREHMGV 154
                                    79*****************************************9988****************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2637.87
//
Query:       gi|119719578|ref|YP_920073.1|  [L=75]
Description: AsnC family transcriptional regulator, partial [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-09   37.1   0.0    2.4e-09   37.0   0.0    1.0  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
     0.0011   19.0   0.0     0.0015   18.6   0.0    1.1  1  NapD            NapD protein


Domain annotation for each model (and alignments):
>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   0.0   2.7e-13   2.4e-09       1      72 [.       6      73 ..       6      75 .] 0.96

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 2.7e-13
                                   EEEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEE CS
                 AsnC_trans_reg  1 vlvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsiv 72
                                   +l++++pg+     +++ +l+++p V  +  + G +d+++k+ +++l++l+++++  ++ l++v++t t+++
  gi|119719578|ref|YP_920073.1|  6 ILINTRPGK---EYDVANQLKTFPFVNDVDITYGLWDIIIKIQAPSLAELDKIISM-VRGLKDVEQTVTLVA 73
                                   7899*****...******************************************99.************986 PP

>> NapD  NapD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.6e-07    0.0015       6      72 ..       6      74 ..       6      75 .] 0.85

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.6e-07
                           NapD  6 lvVqarperlaavkaalaalpgv.EvhasdeegklVvviEaesedeladtieaiealpgVls.aslvyh 72
                                   +++++rp++  +v+++l+++p v +v  + +   +++ i+a+s  el ++i+ ++ l++V + ++lv h
  gi|119719578|ref|YP_920073.1|  6 ILINTRPGKEYDVANQLKTFPFVnDVDITYGLWDIIIKIQAPSLAELDKIISMVRGLKDVEQtVTLVAH 74
                                   689******************994455555559***************************751566666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.30s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 497.48
//
Query:       gi|119719579|ref|YP_920074.1|  [L=366]
Description: hypothetical protein Tpen_0669 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.19   11.9   0.0       0.39   10.9   0.0    1.5  1  FYRC      F/Y rich C-terminus
        4.4    7.3   8.9        0.6   10.1   0.5    2.3  2  HAP       Hydrophobic abundant protein (HAP)


Domain annotation for each model (and alignments):
>> FYRC  F/Y rich C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   4.4e-05      0.39      22      77 ..     247     299 ..     243     301 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 4.4e-05
                           FYRC  22 tevWqkvlervqelrkeaglk.lklfpesisGeemfGLsepaivrlieslpgaekct 77 
                                    ++ ++k+l+ ++ l++ a l+ l    +++ G+ ++G+ ++ i +l+es   +e ++
  gi|119719579|ref|YP_920074.1| 247 KNTYEKILRILHSLQARALLNgL----TNLVGLFLLGFASSLISQLLESIARVELLQ 299
                                    56789999999999999998733....899********************9999876 PP

>> HAP  Hydrophobic abundant protein (HAP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   2.3     0.051   4.6e+02      94     149 ..     105     160 ..      81     169 .. 0.72
   2 ?   10.1   0.5   6.7e-05       0.6      99     152 ..     241     295 ..     219     305 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.051
                            HAP  94 vtgilsdlldldavlelveevlrvllaqallaglvqall.alplallvalvalteal 149
                                    v+ +   l+ l+av+ +   ++     +al  g +q +l alp+a l  l +l  al
  gi|119719579|ref|YP_920074.1| 105 VAPLTLALMTLNAVIIFTYSSVYPRELRALKVGPIQVILaALPFASLA-LLSLPPAL 160
                                    555666788888888888888888888999999999987358988774.44455544 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 6.7e-05
                            HAP  99 sdlldldavlelveevlrvllaqallaglvqallalplallval.valtealara 152
                                    + +l+l+   e +  +l++l a+all gl + +  + l    +l + l e++ar 
  gi|119719579|ref|YP_920074.1| 241 EAMLGLKNTYEKILRILHSLQARALLNGLTNLVGLFLLGFASSLiSQLLESIARV 295
                                    56899************************99765555555544426788999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2330.96
//
Query:       gi|119719580|ref|YP_920075.1|  [L=124]
Description: hypothetical protein Tpen_0670 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 942.13
//
Query:       gi|119719581|ref|YP_920076.1|  [L=84]
Description: hypothetical protein Tpen_0671 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 632.47
//
Query:       gi|119719582|ref|YP_920077.1|  [L=1003]
Description: hypothetical protein Tpen_0672 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1003 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.72u 0.28s 00:00:01.00 Elapsed: 00:00:00.48
# Mc/sec: 6273.58
//
Query:       gi|119719583|ref|YP_920078.1|  [L=186]
Description: hypothetical protein Tpen_0673 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 1259.39
//
Query:       gi|119719584|ref|YP_920079.1|  [L=86]
Description: hypothetical protein Tpen_0674 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       203  (0.0113224); expected 358.6 (0.02)
Passed bias filter:                      166  (0.00925874); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 632.03
//
Query:       gi|119719585|ref|YP_920080.1|  [L=88]
Description: hypothetical protein Tpen_0675 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.028   14.0   0.4      0.029   13.9   0.4    1.1  1  TMEM101   TMEM101 protein family
      0.039   14.4   0.2      0.042   14.3   0.2    1.0  1  DUF1689   Protein of unknown function (DUF1689)


Domain annotation for each model (and alignments):
>> TMEM101  TMEM101 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.4   3.2e-06     0.029      79     129 ..       3      54 ..       1      72 [. 0.73

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.2e-06
                        TMEM101  79 lqla.islylslsgekaeyadwlkvrvlsralaiiggylvlasglgesyRrk 129
                                    + +a i+l+ + s  + +y+  +    + r+la+i++y++l s  +++    
  gi|119719585|ref|YP_920080.1|   3 ALIAtIVLFTAVSVYTRYYGSPIYAVKVQRNLAVIAAYVMLHSNCTDVGYYL 54 
                                    34445777777777788887766555568**************999875554 PP

>> DUF1689  Protein of unknown function (DUF1689)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.2   4.6e-06     0.042      37      95 ..       3      61 ..       1      76 [. 0.88

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.6e-06
                        DUF1689 37 gwlgfsavflaptayrryktgaikgvkvprsfllGlvalvvssqlaakyaykkklkeld 95
                                   ++ ++++ f a  +y ry  + i  vkv+r++++  + +++ s+++    y +k+++ +
  gi|119719585|ref|YP_920080.1|  3 ALIATIVLFTAVSVYTRYYGSPIYAVKVQRNLAVIAAYVMLHSNCTDVGYYLSKVNSTQ 61
                                   5678999***************************9999999999999999999998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.34u 0.29s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 639.51
//
Query:       gi|119719586|ref|YP_920081.1|  [L=188]
Description: hypothetical protein Tpen_0676 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1218.36
//
Query:       gi|119719587|ref|YP_920082.1|  [L=118]
Description: hypothetical protein Tpen_0677 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.29s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 825.57
//
Query:       gi|119719588|ref|YP_920083.1|  [L=377]
Description: TGS domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.4e-18   64.3   0.0    1.5e-17   63.5   0.0    1.5  1  MMR_HSR1_Xtn   C-terminal region of MMR_HSR1 domain
    4.2e-16   58.7   0.1    1.1e-15   57.5   0.0    1.8  2  TGS            TGS domain
    3.3e-07   30.2   0.0     0.0057   16.4   0.0    2.6  2  PduV-EutP      Ethanolamine utilisation - propanediol utilisa
    1.1e-05   25.5   0.0    5.5e-05   23.2   0.0    2.2  2  MMR_HSR1       50S ribosome-binding GTPase
    4.4e-05   23.5   0.0       0.11   12.4   0.0    3.3  3  RsgA_GTPase    RsgA GTPase
    0.00015   21.9   0.0       0.11   12.7   0.0    2.5  2  YchF-GTPase_C  Protein of unknown function (DUF933)
    0.00043   19.9   0.0      0.086   12.4   0.0    2.9  3  GTP_EFTU       Elongation factor Tu GTP binding domain
     0.0025   17.3   0.0     0.0053   16.2   0.0    1.5  1  SRPRB          Signal recognition particle receptor beta subu
     0.0032   18.0   0.0     0.0077   16.8   0.0    1.6  1  ABC_tran       ABC transporter
     0.0076   15.9   0.1       0.33   10.5   0.0    2.3  2  cobW           CobW/HypB/UreG, nucleotide-binding domain
  ------ inclusion threshold ------
      0.012   15.1   0.0          1    8.9   0.1    3.0  2  FeoB_N         Ferrous iron transport protein B
      0.065   13.2   0.0       0.13   12.3   0.0    1.4  1  TsaE           Threonylcarbamoyl adenosine biosynthesis prote
       0.18   11.6   0.0        0.3   10.9   0.0    1.3  1  AAA_21         AAA domain, putative AbiEii toxin, Type IV TA 


Domain annotation for each model (and alignments):
>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.5   0.0   1.1e-20   1.5e-17       2     106 .]     194     303 ..     193     303 .. 0.87

  Alignments for each domain:
  == domain 1  score: 63.5 bits;  conditional E-value: 1.1e-20
                   MMR_HSR1_Xtn   2 gGikitstvkltkldeetvkkilkeykihnaevliredvtvDdlidviegnrvYipclyvlNKiDlisleeldelare.. 79 
                                    gG+++ ++++    + ++v ++l+ey++++a v i++++t+Dd+ d+i g+ vY p++ vl K+Dl+ ++++++l+++  
  gi|119719588|ref|YP_920083.1| 194 GGVTVVGDLE--GATVQDVVALLREYNVYHAVVRIQGRATLDDVEDAIFGSYVYRPTVAVLTKVDLAPNDHVKALKERls 271
                                    8999998855..678899***********************************************************765 PP

                   MMR_HSR1_Xtn  80 ...pnsvviSaekelnl..deLkekiweeLnL 106
                                         +  +Sa++  +l  de+ + i++eL+L
  gi|119719588|ref|YP_920083.1| 272 nygVPVYEFSAQRCRELrfDEIATYIFRELDL 303
                                    4433444599998654444***********97 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       8.8   1.2e+04      15      23 ..     203     211 ..     203     213 .. 0.81
   2 !   57.5   0.0   7.7e-19   1.1e-15       1      59 [.     304     376 ..     304     377 .] 0.96

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 8.8
                                    TTB-HHHHH CS
                            TGS  15 rgatveDfA 23 
                                    +gatv D+ 
  gi|119719588|ref|YP_920083.1| 203 EGATVQDVV 211
                                    599999985 PP

  == domain 2  score: 57.5 bits;  conditional E-value: 7.7e-19
                                    EEEEE..TTSSEEE.....EETTB-HHHHHHHHSTTHHHHEEEEEECS.......EEEETTSBB-SSEEEEEE CS
                            TGS   1 irvyt..PdGkvpd.....lprgatveDfAykIhrslakkfiyAlVnG.......qrvgldhvLedgdvveIv 59 
                                    irvyt  P+   ++     ++rga v D+A+ Ih+ l ++f+yA+V+        qrvg d vLedgd+veIv
  gi|119719588|ref|YP_920083.1| 304 IRVYTrnPKTGNVEkrpvvVKRGAKVADVAKIIHSYLYENFRYAKVWResfpfspQRVGKDFVLEDGDIVEIV 376
                                    799999999889999*********************************************************9 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   0.00016      0.22       3      24 ..      83     104 ..      81     179 .. 0.72
   2 !   16.4   0.0   4.1e-06    0.0057      83     141 ..     239     297 ..     214     299 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00016
                      PduV-EutP   3 killiGkvgsGKttLtqalkge 24 
                                    +++liG+ gsGKt+L + l+g 
  gi|119719588|ref|YP_920083.1|  83 QVVLIGSLGSGKTSLFRCLTGV 104
                                    699*************999884 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 4.1e-06
                      PduV-EutP  83 gfasvfnkeviGiitkidlaedeenieaveelLksaGaeki.fevsavekegieellkyl 141
                                     f s + ++++ ++tk+dla  +++++a +e+L++ G+    f+ + +++  ++e+ +y+
  gi|119719588|ref|YP_920083.1| 239 IFGSYVYRPTVAVLTKVDLA-PNDHVKALKERLSNYGVPVYeFSAQRCRELRFDEIATYI 297
                                    689999**************.8999************97544666666777778887776 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0     4e-08   5.5e-05       1     102 [.      83     173 ..      83     189 .. 0.70
   2 ?   -3.0   0.0       5.5   7.6e+03      33      47 ..     308     320 ..     305     344 .. 0.61

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 4e-08
                                    EEEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHCTSEEE CS
                       MMR_HSR1   1 evaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgkaflaleeadlil 80 
                                    +v+++G   +GK++L++ ltg     +d+p      + g v++ g  ++lvDtpG++       + g+ ++  ++ad+++
  gi|119719588|ref|YP_920083.1|  83 QVVLIGSLGSGKTSLFRCLTGVSKPSQDRP------VPGMVSWLGVYFQLVDTPGFLG----FTDPGRLMALARNADALI 152
                                    599******************655555544......56677777888********876....44556666666789**** PP

                                    EEEETTTTCSHHHHHHHHHHHH CS
                       MMR_HSR1  81 lvvdaseeklkpldeeleelle 102
                                    + +d++ ++ +++   + +lle
  gi|119719588|ref|YP_920083.1| 153 VTLDST-ANAEEQLAGMLRLLE 173
                                    ****65.333333344444433 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 5.5
                                    SSSEEEEEEEETTEE CS
                       MMR_HSR1  33 Trdinegrvklkgke 47 
                                    Tr++++g+v+  +++
  gi|119719588|ref|YP_920083.1| 308 TRNPKTGNVE--KRP 320
                                    8888888887..222 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.0    0.0047       6.4     100     121 ..      82     103 ..      31     111 .. 0.85
   2 ?   -0.6   0.0      0.79   1.1e+03     155     162 ..     126     133 ..     122     136 .. 0.83
   3 !   12.4   0.0   7.8e-05      0.11      50      89 ..     249     287 ..     240     303 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0047
                                    SEEEEECSTTSSHHHHHHHHCT CS
                    RsgA_GTPase 100 ktsvlvGqSGvGKStLinallp 121
                                      +vl+G+ G GK++L   l++
  gi|119719588|ref|YP_920083.1|  82 VQVVLIGSLGSGKTSLFRCLTG 103
                                    5689*************99987 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.79
                                    EESS-SSS CS
                    RsgA_GTPase 155 liDtPGfr 162
                                    l+DtPGf 
  gi|119719588|ref|YP_920083.1| 126 LVDTPGFL 133
                                    89****96 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 7.8e-05
                                    EEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTT CS
                    RsgA_GTPase  50 vivlnKiDlleeeeeleelkeelealgyevllvsaktkeg 89 
                                    v vl+K+Dl+ +++ +++lke+l+++g++v+  sa++ ++
  gi|119719588|ref|YP_920083.1| 249 VAVLTKVDLAPNDH-VKALKERLSNYGVPVYEFSAQRCRE 287
                                    669***********.******************9996544 PP

>> YchF-GTPase_C  Protein of unknown function (DUF933)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   7.9e-05      0.11       7      44 ..     313     350 ..     303     353 .. 0.90
   2 !    6.6   0.0    0.0062       8.6      66      81 ..     360     375 ..     357     377 .] 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.9e-05
                  YchF-GTPase_C   7 aGekevraWtikkgttapqaAgviHsDfekgFiraevi 44 
                                    +G+ e r   +k+g+++ + A++iHs + ++F  a+v 
  gi|119719588|ref|YP_920083.1| 313 TGNVEKRPVVVKRGAKVADVAKIIHSYLYENFRYAKVW 350
                                    578899999*************************9986 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0062
                  YchF-GTPase_C  66 legkdyvvqdgDiilf 81 
                                    + gkd+v++dgDi+++
  gi|119719588|ref|YP_920083.1| 360 RVGKDFVLEDGDIVEI 375
                                    68***********986 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0      0.04        55       5      28 ..      83     106 ..      81     113 .. 0.83
   2 !   12.4   0.0   6.3e-05     0.086      69     124 ..     121     178 ..     114     181 .. 0.87
   3 ?   -0.2   0.0      0.46   6.3e+02     124     147 ..     247     271 ..     241     340 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.04
                                    EEEEEESTTSSHHHHHHHHHHHTT CS
                       GTP_EFTU   5 nigiighvDhGKtTLtdrLlyktg 28 
                                    ++++ig + +GKt+L  +L+  ++
  gi|119719588|ref|YP_920083.1|  83 QVVLIGSLGSGKTSLFRCLTGVSK 106
                                    6899************99987665 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 6.3e-05
                                    SEEEEEEEESSSGGGHH..HHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTE CS
                       GTP_EFTU  69 kylinliDtPGHvdFsk..evirglrvlDgavlvvdaveGvepqteevlrlalkegvp 124
                                       ++l+DtPG   F++     + +r +D  ++ +d++   e+q   +lrl+ ++++ 
  gi|119719588|ref|YP_920083.1| 121 GVYFQLVDTPGFLGFTDpgRLMALARNADALIVTLDSTANAEEQLAGMLRLLEENRIS 178
                                    56799***********833566779**************************9999885 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.46
                                    EEEEEEESCGST.HHHHHHHHHHHH CS
                       GTP_EFTU 124 piivfiNKmDrl.kaelkeiveevk 147
                                    p++ +++K+D + ++ +k ++e ++
  gi|119719588|ref|YP_920083.1| 247 PTVAVLTKVDLApNDHVKALKERLS 271
                                    5789999999996555555554444 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   3.9e-06    0.0053       5      90 ..      83     162 ..      80     185 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.9e-06
                                    EEEEE-STTSSHHHHHHHHHHSS---B---SS-EEETTG...GGTT-SEEEETT-GCCSHHHHHHHHHHGGEEEEEEEEE CS
                          SRPRB   5 avllvGlsdsGKTslftrLttdsvkktvtSqessaalkvksekgskltliDfPGheklrqklleklkaksslkglvfvvD 84 
                                    +v+l+G   sGKTslf  Lt +  k+   Sq+  +   v s  g  ++l+D PG   +       +   +++ +l+  +D
  gi|119719588|ref|YP_920083.1|  83 QVVLIGSLGSGKTSLFRCLT-GVSKP---SQDRPVPGMV-SWLGVYFQLVDTPGFLGFTDPGR-LMALARNADALIVTLD 156
                                    699*************9987.44455...5544444444.5569**********999876422.2234677999999999 PP

                                    TTS-HH CS
                          SRPRB  85 Stidpk 90 
                                    St++  
  gi|119719588|ref|YP_920083.1| 157 STANAE 162
                                    999865 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   5.6e-06    0.0077      13      40 ..      83     110 ..      76     121 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.6e-06
                                    EEEEEESTTSSHHHHHHHHTTSS--SEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  13 kvaivGenGaGKStLlkllagllkpteG 40 
                                     v+++G+ G+GK++L+++l+g +kp ++
  gi|119719588|ref|YP_920083.1|  83 QVVLIGSLGSGKTSLFRCLTGVSKPSQD 110
                                    589*********************9876 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0   0.00024      0.33       3      21 ..      84     102 ..      82     112 .. 0.80
   2 ?    2.9   0.0     0.052        72     135     167 ..     240     271 ..     195     275 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00024
                                    EEEEESTTCCHHHHHHHHH CS
                           cobW   3 tvltGflGsGKTtLlnhll 21 
                                    +vl G+lGsGKT+L + l+
  gi|119719588|ref|YP_920083.1|  84 VVLIGSLGSGKTSLFRCLT 102
                                    6899**********98776 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.052
                                    HHHHHHTSSEEEEE-HHHHCHC..HHHHHHHHH CS
                           cobW 135 aedqlaaadllvlnKtDlldeeallekleerlr 167
                                    +++ +    + vl+K+Dl+++++ +++l+erl+
  gi|119719588|ref|YP_920083.1| 240 FGSYVYRPTVAVLTKVDLAPNDH-VKALKERLS 271
                                    55556666788*********995.588888775 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.1   0.00073         1       2      25 ..      83     106 ..      82     179 .. 0.90
   2 ?    2.6   0.0     0.065        90     106     148 ..     246     287 ..     243     294 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00073
                                    EEEEEESTTSSHHHHHHHHHTTSE CS
                         FeoB_N   2 tvalvGnpnvGkttlfnaltgakq 25 
                                    +v+l+G   +Gkt+lf  ltg+++
  gi|119719588|ref|YP_920083.1|  83 QVVLIGSLGSGKTSLFRCLTGVSK 106
                                    799******************875 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.065
                                    SSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTBT CS
                         FeoB_N 106 vpvvlalnmideaekkgieidlkkLsekLgvpvvktsakkkeg 148
                                     p+v +l ++d a +++++  +++Ls+  gvpv ++sa++ ++
  gi|119719588|ref|YP_920083.1| 246 RPTVAVLTKVDLAPNDHVKALKERLSN-YGVPVYEFSAQRCRE 287
                                    58999***************9999986.6********998665 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   9.2e-05      0.13      19      39 ..      80     101 ..      47     109 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9.2e-05
                                    TEE.EEEEESTTSSHHHHHHHH CS
                           TsaE  19 gdv.ilLeGdLGaGKTtlvrgl 39 
                                    gdv ++L G LG+GKT l r l
  gi|119719588|ref|YP_920083.1|  80 GDVqVVLIGSLGSGKTSLFRCL 101
                                    33359*************9976 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00022       0.3       3      29 ..      85     113 ..      84     147 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00022
                         AAA_21   3 vliGpNgsGKSnLLdaldllarl..drdv 29 
                                    vliG  gsGK++L+++l +++    dr v
  gi|119719588|ref|YP_920083.1|  85 VLIGSLGSGKTSLFRCLTGVSKPsqDRPV 113
                                    89***************988654444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       810  (0.0451782); expected 358.6 (0.02)
Passed bias filter:                      701  (0.0390987); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.46
# Mc/sec: 2445.05
//
Query:       gi|119719589|ref|YP_920084.1|  [L=718]
Description: AAA family ATPase, CDC48 subfamily protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   4.3e-102  337.8   0.0    7.6e-50  168.8   0.0    2.3  2  AAA              ATPase family associated with various cellul
    1.6e-39  133.4   2.0    3.6e-19   68.3   0.3    3.0  2  AAA_lid_3        AAA+ lid domain
    1.5e-36  124.5   1.8      2e-35  120.8   3.0    2.4  1  CDC48_N          Cell division protein 48 (CDC48), N-terminal
    2.3e-16   59.3   3.2    3.1e-16   58.9   1.4    2.2  2  CDC48_2          Cell division protein 48 (CDC48), domain 2
    1.4e-15   58.1   0.2    3.5e-06   27.5   0.0    4.3  4  AAA_16           AAA ATPase domain
    1.9e-15   56.9   0.0    1.7e-07   31.1   0.0    2.6  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    2.9e-14   53.5   0.0    9.3e-07   29.1   0.0    2.5  2  AAA_2            AAA domain (Cdc48 subfamily)
    1.3e-11   44.7   0.8    0.00026   21.0   0.1    4.0  2  AAA_5            AAA domain (dynein-related subfamily)
    2.8e-11   43.3   0.9    3.6e-06   26.9   0.0    2.8  2  Vps4_C           Vps4 C terminal oligomerisation domain
    7.1e-11   42.5   0.0    1.5e-05   25.2   0.0    2.7  2  AAA_33           AAA domain
    2.3e-10   40.9   1.4      0.019   15.2   0.1    4.2  4  AAA_22           AAA domain
    2.7e-10   40.0   0.5    0.00074   18.8   0.0    3.0  3  TIP49            TIP49 P-loop domain
    5.8e-09   36.1   0.0     0.0016   18.5   0.0    2.5  2  AAA_14           AAA domain
    1.7e-07   31.8   0.0      0.036   14.6   0.0    2.8  2  AAA_18           AAA domain
    2.6e-07   30.5   0.0      0.021   14.5   0.0    2.4  2  IstB_IS21        IstB-like ATP binding protein
    3.8e-07   30.5   0.0      0.029   14.8   0.0    2.7  2  RNA_helicase     RNA helicase
    6.3e-07   29.0   0.3      0.032   13.6   0.0    2.5  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    1.2e-06   28.8   0.0       0.03   14.6   0.0    2.7  2  AAA_28           AAA domain
    2.2e-06   27.5   0.2       0.25   11.0   0.1    3.8  2  Sigma54_activat  Sigma-54 interaction domain
    4.3e-06   26.6   0.2       0.07   12.8   0.0    2.7  2  AAA_24           AAA domain
    7.3e-06   26.1   0.1      0.036   14.0   0.0    3.2  3  ATPase_2         ATPase domain predominantly from Archaea
    8.3e-06   25.4   0.0       0.13   11.8   0.0    2.7  2  AAA_7            P-loop containing dynein motor region
    1.7e-05   24.1   0.1      0.069   12.2   0.0    2.2  2  Parvo_NS1        Parvovirus non-structural protein NS1
    3.7e-05   23.7   0.0      0.091   12.6   0.0    3.5  4  Bac_DnaA         Bacterial dnaA  protein
    4.3e-05   23.0   0.5       0.26   10.6   0.0    3.2  3  ATPase           KaiC
      5e-05   22.6   0.0       0.12   11.5   0.0    2.7  2  DUF815           Protein of unknown function (DUF815)
    5.2e-05   23.3   0.0       0.54   10.3   0.0    2.5  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    0.00011   21.7   0.8       0.43   10.0   0.0    2.5  2  PhoH             PhoH-like protein
    0.00017   21.5   0.7        1.4    8.8   0.0    3.8  4  NACHT            NACHT domain
    0.00026   20.6   5.9       0.73    9.4   0.3    4.3  3  AAA_25           AAA domain
    0.00026   20.9   0.0       0.77    9.6   0.0    2.8  2  AAA_3            ATPase family associated with various cellul
    0.00028   20.7   0.0       0.32   10.8   0.0    2.3  2  AAA_11           AAA domain
    0.00036   19.9   0.0       0.49    9.7   0.0    2.6  2  Zeta_toxin       Zeta toxin
    0.00048   20.7   0.0        1.5    9.4   0.0    2.5  2  ABC_tran         ABC transporter
    0.00048   19.6   0.0     0.0057   16.1   0.0    2.2  2  UFD1             Ubiquitin fusion degradation protein UFD1
    0.00087   18.6   0.0        1.1    8.5   0.0    2.2  2  DUF2075          Uncharacterized conserved protein (DUF2075)
     0.0013   18.0   0.0          2    7.5   0.0    2.7  2  NB-ARC           NB-ARC domain
      0.002   17.9   0.1        2.1    8.0   0.0    2.6  2  AAA_30           AAA domain
     0.0053   17.2   0.2        4.7    7.6   0.0    3.4  2  AAA_17           AAA domain
     0.0094   16.3   1.3        4.3    7.7   0.0    3.0  3  AAA_19           AAA domain
  ------ inclusion threshold ------
      0.017   14.0   0.1         11    4.7   0.0    3.2  3  AFG1_ATPase      AFG1-like ATPase
      0.023   14.7   1.1        7.6    6.7   0.1    3.4  3  DUF1905          Domain of unknown function (DUF1905)
      0.024   14.0   0.7        1.8    7.9   0.0    2.6  2  IPT              Isopentenyl transferase
      0.028   14.5   0.0         11    6.2   0.0    2.5  2  Sigma54_activ_2  Sigma-54 interaction domain
      0.059   13.1   0.1         17    5.1   0.0    2.7  2  Cytidylate_kin   Cytidylate kinase
        0.1   12.7   0.1         10    6.2   0.0    2.5  2  SKI              Shikimate kinase
        0.1   12.3   0.0         15    5.5   0.0    2.4  2  AAA_29           P-loop containing region of AAA domain
       0.12   12.1   0.2        3.7    7.1   0.0    3.1  3  Zot              Zonular occludens toxin (Zot)
       0.12   12.1   0.0         13    5.6   0.0    2.4  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
       0.22   11.5   0.4       0.83    9.7   0.1    2.1  1  Molydop_binding  Molydopterin dinucleotide binding domain
       0.28   11.1   7.9         10    6.0   0.0    4.9  5  NTPase_1         NTPase
        1.3    9.4   3.7         83    3.6   0.0    3.7  2  B5               tRNA synthetase B5 domain


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.8   0.0   2.2e-52   7.6e-50       1     131 [.     217     346 ..     217     347 .. 0.98
   2 !  166.9   0.0   8.3e-52   2.9e-49       1     131 [.     490     620 ..     490     621 .. 0.97

  Alignments for each domain:
  == domain 1  score: 168.8 bits;  conditional E-value: 2.2e-52
                                    EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCH CS
                            AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgsese 80 
                                    vl+yGppGtGKTllakava+e+g++f+ i+g+e++sk+ gese+++re+f+ea ++a p i+fiDEida+a++r++ + e
  gi|119719589|ref|YP_920084.1| 217 VLFYGPPGTGKTLLAKAVANETGAYFIAINGPEIMSKFYGESEQRLREIFEEATKNA-PAIIFIDEIDAIAPKREEVTGE 295
                                    79******************************************************9.********************** PP

                                    HHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                            AAA  81 eeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                    +e+rvv+qLl+ +dg+k++ ++vivi+atnrpd++dpal+r gRfdr+i ++
  gi|119719589|ref|YP_920084.1| 296 VEKRVVAQLLALMDGLKER-GQVIVIAATNRPDDIDPALRRpGRFDREIAFP 346
                                    ******************7.66***************************987 PP

  == domain 2  score: 166.9 bits;  conditional E-value: 8.3e-52
                                    EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH.TTCCC CS
                            AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr.sgses 79 
                                    +llyGppGtGKTllakava+e++++f+ ++g+e+lsk+vgesek +re+f++a++ a p+++f+DEid+++++r ++ +s
  gi|119719589|ref|YP_920084.1| 490 ILLYGPPGTGKTLLAKAVATESEANFIGVKGPEILSKWVGESEKAVREIFRKARQAA-PCVIFFDEIDSIVPRRgQRFDS 568
                                    69******************************************************9.****************8888** PP

                                    HHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                            AAA  80 eeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                    ++++r+vnqLlte+dg+++ e+ v+vi+atnrpd +dpallr gRfdr i+++
  gi|119719589|ref|YP_920084.1| 569 GVTDRIVNQLLTEMDGLERLEG-VVVIAATNRPDIIDPALLRpGRFDRLIYVP 620
                                    *******************877.***************************997 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.6   0.1   3.1e-20   1.1e-17       1      40 [.     369     408 ..     369     430 .. 0.78
   2 !   68.3   0.3     1e-21   3.6e-19       1      44 [.     643     688 ..     643     689 .. 0.95

  Alignments for each domain:
  == domain 1  score: 63.6 bits;  conditional E-value: 3.1e-20
                      AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgikeitm 40 
                                    dv+l+eLAe T+G++GADlaalcreAa++Alrr +++i+ 
  gi|119719589|ref|YP_920084.1| 369 DVNLDELAEITHGFTGADLAALCREAAMHALRRFLPKIDI 408
                                    9********************************6555432 PP

  == domain 2  score: 68.3 bits;  conditional E-value: 1e-21
                      AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgik..eitmedfe 44 
                                    dvdl+e+A++TeGy+GADlaa+c+eAal+Alr+  k  ++t+++fe
  gi|119719589|ref|YP_920084.1| 643 DVDLAEIARKTEGYTGADLAAVCKEAALAALREAGKptKVTKRHFE 688
                                    9********************************988745******8 PP

>> CDC48_N  Cell division protein 48 (CDC48), N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.8   3.0   5.9e-38     2e-35       2      84 ..       7      89 ..       6      90 .. 0.98

  Alignments for each domain:
  == domain 1  score: 120.8 bits;  conditional E-value: 5.9e-38
                                   EEEECCSS-CSSTTEEEE-HHHHHHHTS-TTSEEEEECCCCEEEEEEEBSTTSTTTTEEEE-HHHHHHHT--TTEEEEEEEE CS
                        CDC48_N  2 LrVaeapqedvgrgivridpedmeelglepgdvveiegkrkTvaivwpaepedegkgiIrmdgvtRknagvsiGdkVtVrka 83
                                   LrVaea+++dvgrgivrid+++m++lg+epgd+veiegk+ Tvaivwp++ edeg giIrmdg++Rknagv+iGd+V+Vrka
  gi|119719589|ref|YP_920084.1|  7 LRVAEARSRDVGRGIVRIDRNAMAKLGVEPGDIVEIEGKKVTVAIVWPQALEDEGAGIIRMDGLIRKNAGVGIGDTVKVRKA 88
                                   9********************************************************************************9 PP

                                   - CS
                        CDC48_N 84 e 84
                                   +
  gi|119719589|ref|YP_920084.1| 89 K 89
                                   7 PP

>> CDC48_2  Cell division protein 48 (CDC48), domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       5.7     2e+03      19      29 ..      34      44 ..       2      52 .. 0.64
   2 !   58.9   1.4   9.1e-19   3.1e-16       4      63 ..     110     169 ..     107     170 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 5.7
                                   E-TTEEEEECC CS
                        CDC48_2 19 vtkGdlvvfef 29
                                   v +Gd+v +e 
  gi|119719589|ref|YP_920084.1| 34 VEPGDIVEIEG 44
                                   33555555554 PP

  == domain 2  score: 58.9 bits;  conditional E-value: 9.1e-19
                                    CCCCHHHHCCCTTEEE-TTEEEEECCTCCCEEEEEEEECCCCSCEEECTSCCEEESTTCC CS
                        CDC48_2   4 gdemaylkrqFlgrpvtkGdlvvfefkgqeiklvVvstePkgpvgitetTeielgtkpve 63 
                                     d+++y+k+++ grpv  Gd+v ++ ++++++l+Vv+t P+ +v ite+Tei+++ +pv+
  gi|119719589|ref|YP_920084.1| 110 PDLVEYVKSKLIGRPVIRGDVVEIPIFSTALQLTVVTTMPAQAVQITEDTEITIRAEPVS 169
                                    68899*****************************************************98 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0     1e-08   3.5e-06      24     139 ..     214     319 ..     204     328 .. 0.76
   2 ?   -0.3   0.0       3.5   1.2e+03      70     148 ..     376     454 ..     351     476 .. 0.61
   3 !   18.8   0.0   4.7e-06    0.0016      24      51 ..     487     514 ..     463     529 .. 0.83
   4 ?    5.7   0.0     0.051        18     122     160 ..     534     580 ..     531     594 .. 0.74

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 1e-08
                         AAA_16  24 pelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqllde.aesaeleawrekle 102
                                    p  vl++G++G+GK+ l++++++   ++g++f++ +  +      +s +      e+ lr++ +e +++a +  + ++++
  gi|119719589|ref|YP_920084.1| 214 PKGVLFYGPPGTGKTLLAKAVAN---ETGAYFIAINGPEI-----MSKFYGES--EQRLREIFEEaTKNAPAIIFIDEID 283
                                    489*******************6...8889**********.....44444444..3556666655244455555666666 PP

                         AAA_16 103 ealaavpelagaeasrllellkrllallsrderplvl 139
                                    + +    e++g+ ++r+ ++l +l++ l+++++ +++
  gi|119719589|ref|YP_920084.1| 284 AIAPKREEVTGEVEKRVVAQLLALMDGLKERGQ-VIV 319
                                    66668888899999***********99999777.443 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 3.5
                         AAA_16  70 salaqalareellrqlldeaesaeleawrekleealaavpelagaea....srllellkrll.allsrderplvlvlDdl 144
                                    + ++  ++    l++l++ea+  +l+++  k++ + + +p    +e     +++ ++lk+   + l++    +++ + ++
  gi|119719589|ref|YP_920084.1| 376 AEITHGFTG-ADLAALCREAAMHALRRFLPKIDIESEKIPTEILKELkvtrEDFMQALKDVQpSALRE----VYIEVPEV 450
                                    347777766.8888888888887888888888887775555555544334444444444444222222....66666666 PP

                         AAA_16 145 qwad 148
                                    +w d
  gi|119719589|ref|YP_920084.1| 451 HWDD 454
                                    6655 PP

  == domain 3  score: 18.8 bits;  conditional E-value: 4.7e-06
                         AAA_16  24 pelvllsGesGvGKsslvrellralekd 51 
                                    p  +ll+G++G+GK+ l+++++++ e++
  gi|119719589|ref|YP_920084.1| 487 PKGILLYGPPGTGKTLLAKAVATESEAN 514
                                    589*******************987776 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.051
                         AAA_16 122 llkrllallsrderplvlvlDdlq........wadeaslql.laaLlr 160
                                    +++++++++++ + p v+++D+++        ++d++  +    +Ll+
  gi|119719589|ref|YP_920084.1| 534 AVREIFRKARQ-AAPCVIFFDEIDsivprrgqRFDSGVTDRiVNQLLT 580
                                    56788899999.999*********777777777777666554555555 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.0   4.8e-10   1.7e-07      34     103 ..     215     292 ..     190     306 .. 0.85
   2 !   23.0   0.0   1.5e-07   5.3e-05      34      97 ..     488     559 ..     450     611 .. 0.71

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 4.8e-10
                         RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrlsraveev 103
                                      vl+yGpPG Gkt lak +a+e g+ + +  gP +      e ++ l  ++ + +++   ++fidei  ++++ eev
  gi|119719589|ref|YP_920084.1| 215 KGVLFYGPPGTGKTLLAKAVANETGAYFIAINGPEImskfygESEQRLREIFEEATKNapAIIFIDEIDAIAPKREEV 292
                                    569*******************************994433334456788888877665337*************9998 PP

  == domain 2  score: 23.0 bits;  conditional E-value: 1.5e-07
                         RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleekd..vlfideihrls 97 
                                      +llyGpPG Gkt lak +a+e ++++    gP +      e ++ +  ++ + ++    v+f dei  + 
  gi|119719589|ref|YP_920084.1| 488 KGILLYGPPGTGKTLLAKAVATESEANFIGVKGPEIlskwvgESEKAVREIFRKARQAApcVIFFDEIDSIV 559
                                    469**************************9999987332222333445555555544323377777776665 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0   2.7e-09   9.3e-07       6     105 ..     217     310 ..     213     317 .. 0.87
   2 !   21.8   0.0   4.9e-07   0.00017       6     100 ..     490     579 ..     485     586 .. 0.76

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 2.7e-09
                                    EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG---- CS
                          AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKihpk 83 
                                    +l+ gp g+Gkt+laka+a+   +     +i ++  e++     + + ++++  ++   +a ++   i+++DEid i+pk
  gi|119719589|ref|YP_920084.1| 217 VLFYGPPGTGKTLLAKAVANETGA----YFIAINGPEIMS----KFYGESEQRLREIFEEATKNApaIIFIDEIDAIAPK 288
                                    689******************996....************....88888888888888888888888************9 PP

                                    .---------HHHHHHHHHHHH- CS
                          AAA_2  84 .essgadvSregVqrdLLqileg 105
                                     e+ + +v +  V+  LL +++g
  gi|119719589|ref|YP_920084.1| 289 rEEVTGEVEK-RVVAQLLALMDG 310
                                    7777777766.577778899987 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 4.9e-07
                                    EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG---- CS
                          AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKihpk 83 
                                    ill gp g+Gkt+laka+a   ++    ++i +   e+l     + + ++++  ++   +a +    ++++DEid i p+
  gi|119719589|ref|YP_920084.1| 490 ILLYGPPGTGKTLLAKAVATESEA----NFIGVKGPEILS----KWVGESEKAVREIFRKARQAApcVIFFDEIDSIVPR 561
                                    8999***************99985....************....66666666666666777777699************9 PP

                                    ..---------HHHHHHHH CS
                          AAA_2  84 ..essgadvSregVqrdLL 100
                                      ++  + v    +++ LL
  gi|119719589|ref|YP_920084.1| 562 rgQRFDSGVTDR-IVNQLL 579
                                    544444444443.444444 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.1   7.6e-07   0.00026       2     136 ..     217     335 ..     216     336 .. 0.73
   2 !   18.4   0.1   4.8e-06    0.0016       2     135 ..     490     608 ..     489     611 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 7.6e-07
                                    EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------.G-SEEEEESGGG--.. CS
                          AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar.egeilvlDEverae.. 78 
                                    vl  GppGtgK+ la+ +a  +++ +  +++++ +++  + g+ e       +   ++ +a +  ++i+++DE++ +   
  gi|119719589|ref|YP_920084.1| 217 VLFYGPPGTGKTLLAKAVANETGAYFIAINGPEIMSK--FYGESEQ------RLREIFEEATKnAPAIIFIDEIDAIApk 288
                                    899******************************8875..5555552......22244444444789*********99822 PP

                                    .HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHHT CS
                          AAA_5  79 .sevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalrs 136
                                      ev++++ +    + l l++g ++ +         + via++n++d    +++palr+
  gi|119719589|ref|YP_920084.1| 289 rEEVTGEVEKRVVAQLLALMDGLKERGQ--------VIVIAATNRPD----DIDPALRR 335
                                    2356666655555555555555555533........99*********....99999987 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 4.8e-06
                                    EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGGG--H CS
                          AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEveraes 79 
                                    +lL GppGtgK+ la+ +a   ++++  v +++      ++ ++    g+ +    ++ r+ar   ++++++DE++ + +
  gi|119719589|ref|YP_920084.1| 490 ILLYGPPGTGKTLLAKAVATESEANFIGVKGPE------ILSKWV---GESEKAVREIFRKARqaAPCVIFFDEIDSIVP 560
                                    89*****************99999999999987......888888...45555555666666668999********9999 PP

                                    HHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHH CS
                          AAA_5  80 evlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalr 135
                                       +++ s   +r +   ++ ++++  +  +le + via++n++d     ++pal+
  gi|119719589|ref|YP_920084.1| 561 RRGQRFDSGVTDRIVN--QLLTEMDGLE--RLEGVVVIAATNRPD----IIDPALL 608
                                    9999999988888887..6666666655..567799999999999....6666665 PP

>> Vps4_C  Vps4 C terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.2   0.00012     0.041      16      44 ..     410     438 ..     405     442 .. 0.88
   2 !   26.9   0.0     1e-08   3.6e-06      26      60 ..     678     713 ..     669     713 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00012
                         Vps4_C  16 wmdipsdkllePpvtlkDflkalkkarpt 44 
                                     ++ip++ l+e +vt++Df++alk ++p+
  gi|119719589|ref|YP_920084.1| 410 SEKIPTEILKELKVTREDFMQALKDVQPS 438
                                    56799999*******************98 PP

  == domain 2  score: 26.9 bits;  conditional E-value: 1e-08
                         Vps4_C  26 eP.pvtlkDflkalkkarptVskeDLekheeFTkef 60 
                                    +P +vt ++f++al+ ++p+V+keD+e++++  +ef
  gi|119719589|ref|YP_920084.1| 678 KPtKVTKRHFEQALQIVKPSVTKEDIERYKRISEEF 713
                                    5669*************************9877776 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   4.3e-08   1.5e-05       2      83 ..     217     327 ..     217     383 .. 0.70
   2 !   14.5   0.0   8.4e-05     0.029       2      43 ..     490     533 ..     490     626 .. 0.71

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 4.3e-08
                         AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt............................dytrv 51 
                                    vl+ G+pG+GK+ la+ +++++g  ++ ++ ++++++ +g+ +q+++                               +v
  gi|119719589|ref|YP_920084.1| 217 VLFYGPPGTGKTLLAKAVANETGayFIAINGPEIMSKFYGESEQRLReifeeatknapaiifideidaiapkreeVTGEV 296
                                    799********************98888***********99888888888888888888888888888888766444457 PP

                         AAA_33  52 ldrlyqilnelarkalsagrnvildatnlsrr 83 
                                    ++r+ ++l +l +   ++g+ +++ atn+ ++
  gi|119719589|ref|YP_920084.1| 297 EKRVVAQLLALMDGLKERGQVIVIAATNR-PD 327
                                    77788888788854444444444455544.44 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 8.4e-05
                         AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqq 43 
                                    +ll G+pG+GK+ la+ ++ +    ++ +  ++++++ +g+ ++
  gi|119719589|ref|YP_920084.1| 490 ILLYGPPGTGKTLLAKAVATESEanFIGVKGPEILSKWVGESEK 533
                                    6789***************9999777778888866666664333 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   0.00014     0.049       9      30 ..     218     239 ..     212     253 .. 0.81
   2 ?    6.3   0.0     0.032        11      72     118 ..     256     310 ..     244     326 .. 0.72
   3 !   15.2   0.1   5.6e-05     0.019       8      29 ..     490     511 ..     485     525 .. 0.85
   4 ?    0.4   0.0       2.2   7.4e+02      84     104 ..     537     559 ..     524     594 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00014
                         AAA_22   9 vvtGesGtGKTtllrrlleqld 30 
                                    + +G++GtGKT+l++ ++++  
  gi|119719589|ref|YP_920084.1| 218 LFYGPPGTGKTLLAKAVANETG 239
                                    679**************99874 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.032
                         AAA_22  72 rlsseellealeqalraravielliiDEaqhlr..s........eealeeLrsllnl 118
                                    + s+++l+e +e+a +++ +  ++ iDE++ +   +        ++++ +L  l++ 
  gi|119719589|ref|YP_920084.1| 256 GESEQRLREIFEEATKNAPA--IIFIDEIDAIApkReevtgeveKRVVAQLLALMDG 310
                                    57889999999999999988..*********98762344555556666666666665 PP

  == domain 3  score: 15.2 bits;  conditional E-value: 5.6e-05
                         AAA_22   8 lvvtGesGtGKTtllrrlleql 29 
                                    ++++G++GtGKT+l++ ++ + 
  gi|119719589|ref|YP_920084.1| 490 ILLYGPPGTGKTLLAKAVATES 511
                                    89***************99876 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 2.2
                         AAA_22  84 qalrarav..ielliiDEaqhlr 104
                                    + +r+++   + ++  DE++ + 
  gi|119719589|ref|YP_920084.1| 537 EIFRKARQaaPCVIFFDEIDSIV 559
                                    333333334458********986 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       5.5   1.9e+03     116     176 ..     124     182 ..     119     196 .. 0.57
   2 !   17.8   0.0   4.4e-06    0.0015      51      97 ..     215     259 ..     205     302 .. 0.87
   3 !   18.8   0.0   2.1e-06   0.00074      51     106 ..     488     542 ..     480     545 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 5.5
                                    -EEEEEEEEEEE...-SSS-..TTS--EEEEEE-SS-EEEEEE-HHHHHHHHHHT--TT-E CS
                          TIP49 116 evleGevveleveeaenplskekkikevkitlktakeekklklgskiaeellkekvkegDv 176
                                     v+ G+vve+ ++++  +l+  +++ ++ + + t+++e +++  + +  e+   +++ +D+
  gi|119719589|ref|YP_920084.1| 124 PVIRGDVVEIPIFSTALQLTVVTTMPAQAVQI-TEDTEITIRA-EPVSGEIGIPRITYEDI 182
                                    58999999999988777777444444433333.3333333332.23455555555555555 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 4.4e-06
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte 97 
                                    ++vL+ Gp+gtGkt la a+++e g    f+a++g e+ s     +e
  gi|119719589|ref|YP_920084.1| 215 KGVLFYGPPGTGKTLLAKAVANETG--AYFIAINGPEIMSKFYGESE 259
                                    89*********************99..79*********997555444 PP

  == domain 3  score: 18.8 bits;  conditional E-value: 2.1e-06
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXX CS
                          TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte.vltqalrks 106
                                    +++Ll Gp+gtGkt la a++ e  ++  f+ ++g e+ s  v  +e ++ + +rk+
  gi|119719589|ref|YP_920084.1| 488 KGILLYGPPGTGKTLLAKAVATE--SEANFIGVKGPEILSKWVGESEkAVREIFRKA 542
                                    89*******************98..5689**************99984677889997 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   4.6e-06    0.0016       5      79 ..     217     300 ..     214     326 .. 0.72
   2 !   14.9   0.0     6e-05     0.021       5      76 ..     490     558 ..     487     586 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 4.6e-06
                         AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev........ 76 
                                    ++  G+  +GKT l+k +++e       ++ in  +   k + ++e+ l++i+e+++++   ++f+DEi  +        
  gi|119719589|ref|YP_920084.1| 217 VLFYGPPGTGKTLLAKAVANETG---AYFIAINGPEIMSKFYGESEQRLREIFEEATKNAPAIIFIDEIDAIapkreevt 293
                                    56789999***********9999...89999999888887666666556666666566699********99955555555 PP

                         AAA_14  77 ....pew 79 
                                        +++
  gi|119719589|ref|YP_920084.1| 294 geveKRV 300
                                    5554444 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 6e-05
                         AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev 76 
                                    +++ G+  +GKT l+k ++ e+     +++ ++  +   k   ++ek  ++i++k+++    ++f+DEi  +
  gi|119719589|ref|YP_920084.1| 490 ILLYGPPGTGKTLLAKAVATESE---ANFIGVKGPEILSKWVGESEKAVREIFRKARQAAPCVIFFDEIDSI 558
                                    7899***************9988...9999999999999888887777777777755568999******876 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   0.00013     0.046       1      36 [.     217     273 ..     217     325 .. 0.59
   2 !   14.6   0.0    0.0001     0.036       1      25 [.     490     532 ..     490     601 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 0.00013
                         AAA_18   1 IlltGtpGvGKttlakeLskrl.gf....................gvnlrdvakeng 36 
                                    +l  G+pG+GKt lak++++++ ++                     +++ + a++n 
  gi|119719589|ref|YP_920084.1| 217 VLFYGPPGTGKTLLAKAVANETgAYfiaingpeimskfygeseqrLREIFEEATKNA 273
                                    6789****************9966688888886666666555444333333333333 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 0.0001
                         AAA_18   1 IlltGtpGvGKttlakeLskrl..gf................g 25 
                                    Ill G+pG+GKt lak+++ +   +f                 
  gi|119719589|ref|YP_920084.1| 490 ILLYGPPGTGKTLLAKAVATESeaNFigvkgpeilskwvgesE 532
                                    99****************6553224475565555555544441 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   0.00013     0.046      46      70 ..     213     237 ..     194     292 .. 0.89
   2 !   14.5   0.0   6.2e-05     0.021      47      71 ..     487     511 ..     479     519 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00013
                      IstB_IS21  46 kkenivllGpsGvGKshlaialgve 70 
                                      +++++ Gp+G+GK+ la a++ e
  gi|119719589|ref|YP_920084.1| 213 PPKGVLFYGPPGTGKTLLAKAVANE 237
                                    567899***************9976 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 6.2e-05
                      IstB_IS21  47 kenivllGpsGvGKshlaialgvea 71 
                                     ++i+l Gp+G+GK+ la a+++e 
  gi|119719589|ref|YP_920084.1| 487 PKGILLYGPPGTGKTLLAKAVATES 511
                                    5789****************99875 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   0.00031      0.11       1      26 [.     217     242 ..     217     293 .. 0.80
   2 !   14.8   0.0   8.4e-05     0.029       1      54 [.     490     550 ..     490     599 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00031
                   RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl 26 
                                    +++yGp+g+GK++lak +a++    +
  gi|119719589|ref|YP_920084.1| 217 VLFYGPPGTGKTLLAKAVANETGAYF 242
                                    689**************998876555 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 8.4e-05
                   RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl.....klkkkdsvys.rnpeddfwdgYt.gqevvv 54 
                                    i+lyGp+g+GK++lak +a++ + ++      ++ +++v    ++  +++ + +   ++v+
  gi|119719589|ref|YP_920084.1| 490 ILLYGPPGTGKTLLAKAVATESEANFigvkgPEILSKWVGEsEKAVREIFRKARqAAPCVI 550
                                    789**************99998877766666444445555444444455544443344444 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   0.00018      0.06      25      42 ..     217     234 ..     214     238 .. 0.90
   2 !   13.6   0.0   9.4e-05     0.032      25      43 ..     490     508 ..     486     513 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00018
                   Mg_chelatase  25 lllvGppGsGKtmlakrl 42 
                                    +l++GppG+GKt+lak++
  gi|119719589|ref|YP_920084.1| 217 VLFYGPPGTGKTLLAKAV 234
                                    79*************987 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 9.4e-05
                   Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                    +ll+GppG+GKt+lak+++
  gi|119719589|ref|YP_920084.1| 490 ILLYGPPGTGKTLLAKAVA 508
                                    89*************9875 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   8.7e-05      0.03       2      47 ..     217     267 ..     216     303 .. 0.69
   2 !   11.5   0.0   0.00076      0.26       2      23 ..     490     514 ..     489     553 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 8.7e-05
                         AAA_28   2 ivitGgestGKTtlleaLaar.gypvv....pEaareileeklakgedalp 47 
                                    + + G+++tGKT l++a a++ g   +    pE++ +++ e  ++ +++ +
  gi|119719589|ref|YP_920084.1| 217 VLFYGPPGTGKTLLAKAVANEtGAYFIaingPEIMSKFYGESEQRLREIFE 267
                                    6799***************76676655124555555555444444444333 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00076
                         AAA_28   2 ivitGgestGKTtlleaLaar...g 23 
                                    i + G+++tGKT l++a a +   +
  gi|119719589|ref|YP_920084.1| 490 ILLYGPPGTGKTLLAKAVATEseaN 514
                                    7899***************554332 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.1   0.00073      0.25      23      62 ..     215     251 ..     204     330 .. 0.72
   2 !   10.7   0.0   0.00089      0.31      23      51 ..     488     513 ..     478     616 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00073
                                    S-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS- CS
                Sigma54_activat  23 lsvlitGesGtGKellaraiheaskrkekpfvavncaaip 62 
                                      vl  G  GtGK+lla+a+ +++    + f+a+n  +i 
  gi|119719589|ref|YP_920084.1| 215 KGVLFYGPPGTGKTLLAKAVANET---GAYFIAINGPEIM 251
                                    569****************97654...5789999876653 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00089
                                    S-EEEECSTTSSHHHHHHHHHHHSTTTTS CS
                Sigma54_activat  23 lsvlitGesGtGKellaraiheaskrkek 51 
                                      +l+ G  GtGK+lla+a+ ++s+   +
  gi|119719589|ref|YP_920084.1| 488 KGILLYGPPGTGKTLLAKAVATESE---A 513
                                    569****************998876...3 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.1   0.00074      0.26       5      24 ..     217     238 ..     214     332 .. 0.73
   2 !   12.8   0.0    0.0002      0.07       5      22 ..     490     507 ..     487     556 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00074
                         AAA_24   5 iliyGpsgiGKTtlakel..gp 24 
                                    +l yGp+g+GKT lak    + 
  gi|119719589|ref|YP_920084.1| 217 VLFYGPPGTGKTLLAKAVanET 238
                                    789************9985433 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.0002
                         AAA_24   5 iliyGpsgiGKTtlakel 22 
                                    il+yGp+g+GKT lak  
  gi|119719589|ref|YP_920084.1| 490 ILLYGPPGTGKTLLAKAV 507
                                    89*************987 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   0.00011     0.036      17     122 ..     211     320 ..     203     326 .. 0.71
   2 ?    7.4   0.0     0.011       3.7      23      45 ..     490     512 ..     482     519 .. 0.84
   3 ?   -0.0   0.0         2   6.9e+02     107     131 ..     532     559 ..     516     597 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 0.00011
                       ATPase_2  17 repneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekal.............. 82 
                                     ep + ++ YGp g GKt L k ++++         y+ia+++ +i ++       e++++l++ +              
  gi|119719589|ref|YP_920084.1| 211 IEPPKGVLFYGPPGTGKTLLAKAVANET------GAYFIAINGPEIMSKFYG----ESEQRLREIFeeatknapaiifid 280
                                    566777889***********99999998......567888887777777776....333333333333347777777888 PP

                       ATPase_2  83 giavpkaeleeilkeksklvfkaielllekikkkgkkiii 122
                                     i+    + ee+  e  k v +++ +l++ +k++g+ i+i
  gi|119719589|ref|YP_920084.1| 281 EIDAIAPKREEVTGEVEKRVVAQLLALMDGLKERGQVIVI 320
                                    5555555566677788899999999999999999886666 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.011
                       ATPase_2  23 yfiYGpegsGKtaLlkeiienle 45 
                                    +++YGp g GKt L k +++++e
  gi|119719589|ref|YP_920084.1| 490 ILLYGPPGTGKTLLAKAVATESE 512
                                    789************99998775 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 2
                       ATPase_2 107 elllekikkkgkk...iiiiiDelqkli 131
                                    e++ ++i +k+++    +i++De+  ++
  gi|119719589|ref|YP_920084.1| 532 EKAVREIFRKARQaapCVIFFDEIDSIV 559
                                    44556666666667769999***99887 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   0.00038      0.13      31      58 ..     212     239 ..     203     293 .. 0.83
   2 !   10.7   0.0   0.00082      0.28      25      58 ..     479     512 ..     475     519 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00038
                          AAA_7  31 knkkpvllvGptGtGKtviikdllkkld 58 
                                    +  k vl++Gp GtGKt+++k + ++  
  gi|119719589|ref|YP_920084.1| 212 EPPKGVLFYGPPGTGKTLLAKAVANETG 239
                                    55688***************99888765 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00082
                          AAA_7  25 llelllknkkpvllvGptGtGKtviikdllkkld 58 
                                    + e+ ++  k +ll+Gp GtGKt+++k + ++ +
  gi|119719589|ref|YP_920084.1| 479 FREMGIDPPKGILLYGPPGTGKTLLAKAVATESE 512
                                    556666777899**************99776655 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0    0.0002     0.069     117     141 ..     217     241 ..     212     246 .. 0.89
   2 !    9.5   0.0    0.0014      0.48     117     136 ..     490     509 ..     485     514 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0002
                      Parvo_NS1 117 vwfyGpantGktnlaeaIakavply 141
                                    v+fyGp+ tGkt la+a a+ +  y
  gi|119719589|ref|YP_920084.1| 217 VLFYGPPGTGKTLLAKAVANETGAY 241
                                    89****************9977665 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0014
                      Parvo_NS1 117 vwfyGpantGktnlaeaIak 136
                                    +++yGp+ tGkt la+a a+
  gi|119719589|ref|YP_920084.1| 490 ILLYGPPGTGKTLLAKAVAT 509
                                    89***************997 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   0.00026     0.091      37     176 ..     217     358 ..     212     380 .. 0.73
   2 ?   -1.8   0.0       6.8   2.3e+03      77     111 ..     426     460 ..     422     469 .. 0.82
   3 ?    6.3   0.0     0.022       7.5      37      63 ..     490     516 ..     485     558 .. 0.90
   4 ?   -2.2   0.0       8.7     3e+03     161     179 ..     617     635 ..     572     653 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00026
                                    EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHTT-.SEEEEE-GGGGTT-HH. CS
                       Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkeklrkv.DvLliDDiqflagkek. 114
                                    +++yg+ G Gkt L ka++ne+ +       + +++ e ++++    +++  e f e  +++  ++ iD+i  +a k + 
  gi|119719589|ref|YP_920084.1| 217 VLFYGPPGTGKTLLAKAVANETGAY-----FIAINGPEIMSKFYGESEQRLREIFEEATKNApAIIFIDEIDAIAPKREe 291
                                    799***************9987655.....5668999999999999999999999999997725677*******988532 PP

                                    ........HHHHHHHHHHHHHTTT-EEEEEESS-TTT-SS--HHHHHHHHSSEEEE-----HHHHHHHHH CS
                       Bac_DnaA 115 ........tqeelfhtfnalleegkqvvlssDrsPkeleeledrlrsrfeaGlvvdieppdletrlailk 176
                                            +  +l+ +++ l e g+ +v+++   P +++        rf++ +  +   pd+  r +il+
  gi|119719589|ref|YP_920084.1| 292 vtgevekrVVAQLLALMDGLKERGQVIVIAATNRPDDIDPALR-RPGRFDREI--AFPVPDKRARREILQ 358
                                    2111111134467788888999999999***999998865433.345666544..344466666666665 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 6.8
                                    HHHHHHHHTT-HHHHHHHHTT-SEEEEE-GGGGTT CS
                       Bac_DnaA  77 nelvkalrdkkaeefkeklrkvDvLliDDiqflag 111
                                    +++++al+d + ++++e + +v  +  DDi  l++
  gi|119719589|ref|YP_920084.1| 426 EDFMQALKDVQPSALREVYIEVPEVHWDDIGGLED 460
                                    579999**************999999999988875 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.022
                                    EEEE-SSSSSHHHHHHHHHHHHHHHSS CS
                       Bac_DnaA  37 lfiygevGlGktHLlkaignevlenap 63 
                                    +++yg+ G Gkt L ka++ e ++n+ 
  gi|119719589|ref|YP_920084.1| 490 ILLYGPPGTGKTLLAKAVATESEANFI 516
                                    79*****************99888765 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 8.7
                                    EE-----HHHHHHHHHHHH CS
                       Bac_DnaA 161 vdieppdletrlailkkki 179
                                    + + ppd++ rl+ilk + 
  gi|119719589|ref|YP_920084.1| 617 IYVPPPDEKARLEILKVHT 635
                                    5678999*****9997543 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0     0.004       1.4      13      37 ..     208     232 ..     203     242 .. 0.84
   2 ?   -0.4   0.0       1.8   6.1e+02     111     152 ..     262     309 ..     249     326 .. 0.53
   3 !   10.6   0.0   0.00074      0.26      14      41 ..     482     509 ..     453     520 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.004
                         ATPase  13 kgGipegrvvlitGepGtGKtifal 37 
                                    + Gi   + vl +G pGtGKt++a+
  gi|119719589|ref|YP_920084.1| 208 HLGIEPPKGVLFYGPPGTGKTLLAK 232
                                    5588888889*************97 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.8
                         ATPase 111 laeaikeika...krvviDsitgl...ayeekeavaReilrqlvrvlk 152
                                    l+e+ +e        + iD i+++    +e + +v ++ + ql+  + 
  gi|119719589|ref|YP_920084.1| 262 LREIFEEATKnapAIIFIDEIDAIapkREEVTGEVEKRVVAQLLALMD 309
                                    444444332222356778888888321222233344555555555553 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00074
                         ATPase  14 gGipegrvvlitGepGtGKtifalqFli 41 
                                     Gi   + +l++G pGtGKt++a+  + 
  gi|119719589|ref|YP_920084.1| 482 MGIDPPKGILLYGPPGTGKTLLAKAVAT 509
                                    577777889*************987655 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0036       1.3      51      84 ..     212     245 ..     172     326 .. 0.72
   2 !   11.5   0.0   0.00036      0.12      22     114 ..     447     553 ..     429     561 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0036
                         DUF815  51 lpannvLLwGarGtGKSslvkallneyaeegLrl 84 
                                    +p + vL++G  GtGK  l ka+ ne+ +  +++
  gi|119719589|ref|YP_920084.1| 212 EPPKGVLFYGPPGTGKTLLAKAVANETGAYFIAI 245
                                    67788********************988766544 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00036
                         DUF815  22 vdevklddLvgidkqkealvente......qfleg...lpannvLLwGarGtGKSslvkallneyaeeg..Lrlieveke 90 
                                    v ev++dd+ g+++ k++l e +e      ++ +     p + +LL+G  GtGK  l ka+ +e +++   ++  e+  +
  gi|119719589|ref|YP_920084.1| 447 VPEVHWDDIGGLEDVKQQLREAVElplrhpEYFREmgiDPPKGILLYGPPGTGKTLLAKAVATESEANFigVKGPEILSK 526
                                    5577888888888888888887762222222222212257899*******************998887633555566666 PP

                         DUF815  91 dlkelpklvellr...erperfilfvD 114
                                     + e +k v+++    +++  +++f D
  gi|119719589|ref|YP_920084.1| 527 WVGESEKAVREIFrkaRQAAPCVIFFD 553
                                    666666555555311123344666666 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0    0.0016      0.54      19      50 ..     214     247 ..     183     260 .. 0.75
   2 !   10.2   0.0    0.0016      0.56      21      49 ..     489     519 ..     458     524 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0016
                                    TEEEEEEESTTSSHHHHHHHHHHHTT--..---- CS
                           TsaE  19 gdvilLeGdLGaGKTtlvrglakalgve..evkS 50 
                                     + +l++G+ G+GKT l++++a++ g    +++ 
  gi|119719589|ref|YP_920084.1| 214 PKGVLFYGPPGTGKTLLAKAVANETGAYfiAING 247
                                    3349*******************99875555555 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0016
                                    EEEEEESTTSSHHHHHHHHHHHTT--..--- CS
                           TsaE  21 vilLeGdLGaGKTtlvrglakalgve..evk 49 
                                     ilL+G+ G+GKT l++++a + + +   vk
  gi|119719589|ref|YP_920084.1| 489 GILLYGPPGTGKTLLAKAVATESEANfiGVK 519
                                    49*****************998876655555 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.1    0.0019      0.66      22      40 ..     217     235 ..     210     240 .. 0.86
   2 !   10.0   0.0    0.0013      0.43      23      42 ..     491     510 ..     482     515 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0019
                                    EEEE--TTSSTTHHHHHHH CS
                           PhoH  22 vfaiGpaGtGKtylavala 40 
                                    v   Gp GtGKt+la a+a
  gi|119719589|ref|YP_920084.1| 217 VLFYGPPGTGKTLLAKAVA 235
                                    6678***********9998 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0013
                                    EEE--TTSSTTHHHHHHHHH CS
                           PhoH  23 faiGpaGtGKtylavalave 42 
                                       Gp GtGKt+la a+a e
  gi|119719589|ref|YP_920084.1| 491 LLYGPPGTGKTLLAKAVATE 510
                                    578************99976 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1     0.015         5       3      23 ..     217     237 ..     215     240 .. 0.88
   2 ?   -0.1   0.0       2.3     8e+02      63     132 ..     256     326 ..     249     344 .. 0.61
   3 !    8.8   0.0     0.004       1.4       3      23 ..     490     510 ..     488     515 .. 0.89
   4 ?   -0.2   0.0       2.4   8.3e+02      60     112 ..     526     578 ..     521     601 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.015
                                    EEEEC-TTTCHHHHHHHHHHH CS
                          NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                    v+  G++G GKT L++ +a +
  gi|119719589|ref|YP_920084.1| 217 VLFYGPPGTGKTLLAKAVANE 237
                                    6789************99875 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 2.3
                                    TS--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH.............HHHHHCTTTTT--EEEEEEECCCH CS
                          NACHT  63 pepaapvsevwavllelperlLlilDglDelvtdlgq....kekqpvrtlLselirkkllpeasllltvrpral 132
                                     e++++ +e++++ ++++  + + +D +D ++ + ++      +++v   L  l+ + l  +  +++++ +++ 
  gi|119719589|ref|YP_920084.1| 256 GESEQRLREIFEEATKNAPAIIF-IDEIDAIAPKREEvtgeV-EKRVVAQLLALMDG-LKERGQVIVIAATNRP 326
                                    56666677766666666666666.588888888777777743.44444444466666.4445555555555555 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.004
                                    EEEEC-TTTCHHHHHHHHHHH CS
                          NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                    ++l G++G GKT L++ +a++
  gi|119719589|ref|YP_920084.1| 490 ILLYGPPGTGKTLLAKAVATE 510
                                    7899************99986 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 2.4
                                    CCCTS--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH..........HHHH CS
                          NACHT  60 sqlpepaapvsevwavllelperlLlilDglDelvtdlgq.kekqpvrtlLsel 112
                                    +   e++++v+e +   ++++   ++ +D +D +v   gq  +   +++  ++l
  gi|119719589|ref|YP_920084.1| 526 KWVGESEKAVRE-IFRKARQAAPCVIFFDEIDSIVPRRGQrFDSGVTDRIVNQL 578
                                    555677777777.444466777788999*****999999963333334444444 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0     0.014       4.7      36      53 ..     217     234 ..     210     238 .. 0.86
   2 ?    4.0   0.1     0.093        32     128     177 ..     260     309 ..     248     328 .. 0.82
   3 !    9.4   0.3    0.0021      0.73      36      54 ..     490     508 ..     484     594 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.014
                         AAA_25  36 allaGapgtGKttlaldl 53 
                                    +l++G+pgtGKt la  +
  gi|119719589|ref|YP_920084.1| 217 VLFYGPPGTGKTLLAKAV 234
                                    689**********99655 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.093
                         AAA_25 128 advdaleaaieevegvrlvviDplsralggdensnsdv.galvealeriar 177
                                    + ++++ +++++ + ++ + iD ++++ +  e+   +v +++v++l  + +
  gi|119719589|ref|YP_920084.1| 260 QRLREIFEEATK-NAPAIIFIDEIDAIAPKREEVTGEVeKRVVAQLLALMD 309
                                    456778888888.67***************999999988999999877754 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0021
                         AAA_25  36 allaGapgtGKttlaldla 54 
                                    +ll+G+pgtGKt la  +a
  gi|119719589|ref|YP_920084.1| 490 ILLYGPPGTGKTLLAKAVA 508
                                    69***********997665 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0051       1.8       2      31 ..     217     246 ..     216     328 .. 0.78
   2 !    9.6   0.0    0.0022      0.77       2      31 ..     490     519 ..     489     604 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0051
                          AAA_3   2 vllegvPGlaktllvkalakaldlefkriq 31 
                                    vl+ g PG++ktll+ka+a+  ++ f  i 
  gi|119719589|ref|YP_920084.1| 217 VLFYGPPGTGKTLLAKAVANETGAYFIAIN 246
                                    788999**************9999887765 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0022
                          AAA_3   2 vllegvPGlaktllvkalakaldlefkriq 31 
                                    +ll g PG++ktll+ka+a+  +++f  ++
  gi|119719589|ref|YP_920084.1| 490 ILLYGPPGTGKTLLAKAVATESEANFIGVK 519
                                    7999****************9999997765 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.0    0.0088         3      20      38 ..     217     235 ..     198     273 .. 0.83
   2 !   10.8   0.0   0.00092      0.32      19      73 ..     489     541 ..     461     549 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0088
                         AAA_11  20 tliqGPPGtgKTktivell 38 
                                    +l+ GPPGtgKT    ++ 
  gi|119719589|ref|YP_920084.1| 217 VLFYGPPGTGKTLLAKAVA 235
                                    7899********6655554 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00092
                         AAA_11  19 itliqGPPGtgKTktivellsqllsrrkseeeksakpriLv..CapSNaAvDeller 73 
                                      l+ GPPGtgKT    ++  +     + +  + ++p+iL    ++S++Av e+  +
  gi|119719589|ref|YP_920084.1| 489 GILLYGPPGTGKTLLAKAVATES----EANFIGVKGPEILSkwVGESEKAVREIFRK 541
                                    5699*********8888888887....345577788888743378888888888765 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0    0.0067       2.3      14      50 ..     212     246 ..     204     269 .. 0.86
   2 !    9.7   0.0    0.0014      0.49      15      49 ..     486     518 ..     477     523 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0067
                     Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvvrld 50 
                                    e Pk +l  G pG GK+ la+++++e+  +  ++ ++
  gi|119719589|ref|YP_920084.1| 212 EPPKGVLFYGPPGTGKTLLAKAVANET--GAYFIAIN 246
                                    56999999*****************98..56666665 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0014
                     Zeta_toxin  15 rPklillgGqpGAGKselaellkdelerqgnvvrl 49 
                                     Pk ill G pG GK+ la+++++e   + n++ +
  gi|119719589|ref|YP_920084.1| 486 PPKGILLYGPPGTGKTLLAKAVATES--EANFIGV 518
                                    5999********************98..6776655 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0    0.0067       2.3       6      36 ..     209     239 ..     207     318 .. 0.78
   2 !    9.4   0.0    0.0042       1.5       9      60 ..     485     534 ..     481     581 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0067
                                    EEEETTSEEEEEESTTSSHHHHHHHHTTSS- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   6 lklkegekvaivGenGaGKStLlkllagllk 36 
                                    l +++ + v + G+ G+GK+ L+k++a+++ 
  gi|119719589|ref|YP_920084.1| 209 LGIEPPKGVLFYGPPGTGKTLLAKAVANETG 239
                                    56778888999***************99875 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0042
                                    ETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   9 kegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrke 60 
                                     + + + + G+ G+GK+ L+k++a +++  +  i ++g ++ ++   +++k 
  gi|119719589|ref|YP_920084.1| 485 DPPKGILLYGPPGTGKTLLAKAVATESE--ANFIGVKGPEILSKWVGESEKA 534
                                    555668899***************9986..4555556666665554444444 PP

>> UFD1  Ubiquitin fusion degradation protein UFD1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.88     3e+02      69      97 ..      20      48 ..      15      54 .. 0.85
   2 !   16.1   0.0   1.7e-05    0.0057      69     166 ..      63     161 ..      56     167 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.88
                           UFD1 69 gtvylPewmmenlgleegdlveiesvslp 97
                                   g v + +  m +lg+e gd+veie  ++ 
  gi|119719589|ref|YP_920084.1| 20 GIVRIDRNAMAKLGVEPGDIVEIEGKKVT 48
                                   778888899**************987665 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1.7e-05
                           UFD1  69 gtvylPewmmenlgleegdlveiesvslpkgkfvklqpqsedfldis.dpkavLekaLrnfatLtkgdvieikyndkvye 147
                                    g + +   + +n g+  gd+v+++++++  +k v l p     l+++ d  +  +++L    ++ +gdv+ei   ++ ++
  gi|119719589|ref|YP_920084.1|  63 GIIRMDGLIRKNAGVGIGDTVKVRKAKVAPAKRVVLAPSYRIGLEVTpDLVEYVKSKLIGRPVI-RGDVVEIPIFSTALQ 141
                                    67778888999999*************************99999875389999*****998876.8************** PP

                           UFD1 148 lkvlevkpesavsiie.tdl 166
                                    l+v+ + p++av+i e t++
  gi|119719589|ref|YP_920084.1| 142 LTVVTTMPAQAVQITEdTEI 161
                                    *************9872444 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0031       1.1       5      40 ..     218     246 ..     214     297 .. 0.69
   2 !    8.1   0.0    0.0041       1.4       4      25 ..     490     511 ..     487     541 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0031
                        DUF2075   5 lVtGvaGtGKtvvllnllael......eddeeertavylsvN 40 
                                    l  G +GtGKt+++ ++++e                     N
  gi|119719589|ref|YP_920084.1| 218 LFYGPPGTGKTLLAKAVANETgayfiaI-------------N 246
                                    6689************999984444332.............3 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0041
                        DUF2075   4 vlVtGvaGtGKtvvllnllael 25 
                                    +l  G +GtGKt+++ ++++e 
  gi|119719589|ref|YP_920084.1| 490 ILLYGPPGTGKTLLAKAVATES 511
                                    6789***********9999987 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.0    0.0058         2      23      43 ..     217     237 ..     204     243 .. 0.84
   2 !    7.2   0.0    0.0073       2.5      23      44 ..     490     511 ..     484     518 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0058
                                    EEEEESTTSSHHHHHHHHCCS CS
                         NB-ARC  23 valvGmgGvGKttlakqilnk 43 
                                    v ++G +G GKt lak + n+
  gi|119719589|ref|YP_920084.1| 217 VLFYGPPGTGKTLLAKAVANE 237
                                    779**************9997 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0073
                                    EEEEESTTSSHHHHHHHHCCSH CS
                         NB-ARC  23 valvGmgGvGKttlakqilnks 44 
                                    + l+G +G GKt lak +  +s
  gi|119719589|ref|YP_920084.1| 490 ILLYGPPGTGKTLLAKAVATES 511
                                    679*************998874 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0     0.013       4.3      21      40 ..     217     236 ..     204     245 .. 0.82
   2 !    8.0   0.0    0.0062       2.1      22      43 ..     491     512 ..     479     524 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.013
                         AAA_30  21 avltGpAGtGKttalkalre 40 
                                    ++  Gp+GtGKt + ka+++
  gi|119719589|ref|YP_920084.1| 217 VLFYGPPGTGKTLLAKAVAN 236
                                    5678**********999875 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0062
                         AAA_30  22 vltGpAGtGKttalkalreawe 43 
                                    +l Gp+GtGKt + ka++   e
  gi|119719589|ref|YP_920084.1| 491 LLYGPPGTGKTLLAKAVATESE 512
                                    688**********999986555 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0     0.014       4.7       1      23 [.     220     242 ..     220     309 .. 0.83
   2 ?    5.7   0.1     0.052        18       1      19 [.     493     511 ..     493     547 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.014
                                    EE-TTSSHHHHHHHHHHHHTEEE CS
                         AAA_17   1 lGgPGsGKgtqceklvekygfth 23 
                                    +G+PG GK+ +++ ++ + g  +
  gi|119719589|ref|YP_920084.1| 220 YGPPGTGKTLLAKAVANETGAYF 242
                                    7************9999987544 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.052
                                    EE-TTSSHHHHHHHHHHHH CS
                         AAA_17   1 lGgPGsGKgtqceklveky 19 
                                    +G+PG GK+ +++ ++ + 
  gi|119719589|ref|YP_920084.1| 493 YGPPGTGKTLLAKAVATES 511
                                    7*********999998765 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.2     0.051        18      13      32 ..     217     236 ..     211     273 .. 0.82
   2 ?   -1.0   0.0       5.9     2e+03      99     130 ..     270     302 ..     249     313 .. 0.68
   3 ?    7.7   0.0     0.012       4.3      12      31 ..     489     508 ..     484     540 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.051
                         AAA_19  13 llvtaGpGtGKTrvlkhiva 32 
                                    +l  ++pGtGKT + k++ +
  gi|119719589|ref|YP_920084.1| 217 VLFYGPPGTGKTLLAKAVAN 236
                                    7789********98877665 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 5.9
                         AAA_19  99 klqeeellivDEfqdvdelqyrLlkallgek.k 130
                                    + ++ +++++DE+  + +   ++  ++ ++  +
  gi|119719589|ref|YP_920084.1| 270 TKNAPAIIFIDEIDAIAPKREEVTGEVEKRVvA 302
                                    333455999***999988877777766655555 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.012
                         AAA_19  12 vllvtaGpGtGKTrvlkhiv 31 
                                     +l+ ++pGtGKT + k++ 
  gi|119719589|ref|YP_920084.1| 489 GILLYGPPGTGKTLLAKAVA 508
                                    5899*********8877665 PP

>> AFG1_ATPase  AFG1-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.037        13      58      79 ..     210     231 ..     180     237 .. 0.82
   2 ?   -0.4   0.0       1.2   4.1e+02     300     345 ..     296     341 ..     269     344 .. 0.77
   3 ?    4.7   0.0     0.033        11      58      79 ..     483     504 ..     457     510 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.037
                    AFG1_ATPase  58 svepvrglYlwGgvGrGKtylm 79 
                                      ep++g+ ++G+ G GKt l 
  gi|119719589|ref|YP_920084.1| 210 GIEPPKGVLFYGPPGTGKTLLA 231
                                    568****************985 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.2
                    AFG1_ATPase 300 akedaarRfiaLvDelYdadvklvvsaevaleelyeagrlefefeR 345
                                    +++ +   + aL+D l +++  +v+ a   + ++  a r    f R
  gi|119719589|ref|YP_920084.1| 296 VEKRVVAQLLALMDGLKERGQVIVIAATNRPDDIDPALRRPGRFDR 341
                                    4455555678999999999999999999999988777666666655 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.033
                    AFG1_ATPase  58 svepvrglYlwGgvGrGKtylm 79 
                                       p++g+ l+G+ G GKt l 
  gi|119719589|ref|YP_920084.1| 483 GIDPPKGILLYGPPGTGKTLLA 504
                                    5679***************985 PP

>> DUF1905  Domain of unknown function (DUF1905)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0      0.13        43      55      81 ..      16      43 ..       7      44 .. 0.86
   2 ?    6.7   0.1     0.022       7.6      55      81 ..      60      86 ..      42      86 .. 0.81
   3 ?   -0.1   0.0       2.9   9.9e+02      14      35 ..     442     461 ..     432     466 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.13
                                   T.T-EEEEE-HHHHHHHT--TTSEEEEE CS
                        DUF1905 55 k.ggyiLpvkaavrkaigkeaGdtvtve 81
                                   + g+ i+ ++++ ++++g+e+Gd v++e
  gi|119719589|ref|YP_920084.1| 16 DvGRGIVRIDRNAMAKLGVEPGDIVEIE 43
                                   35788999*****************985 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.022
                                   TT-EEEEE-HHHHHHHT--TTSEEEEE CS
                        DUF1905 55 kggyiLpvkaavrkaigkeaGdtvtve 81
                                   +g+ i+ ++  +rk +g+  Gdtv+v+
  gi|119719589|ref|YP_920084.1| 60 EGAGIIRMDGLIRKNAGVGIGDTVKVR 86
                                   38889999999**************95 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 2.9
                                    -EEEE--S-HHHHH..-.SS-E CS
                        DUF1905  14 wtfvevPedvseelktggkgsv 35 
                                     +++evPe +++++  gg   v
  gi|119719589|ref|YP_920084.1| 442 EVYIEVPEVHWDDI--GGLEDV 461
                                    58************..776655 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0053       1.8       5      32 ..     218     245 ..     215     249 .. 0.92
   2 ?    3.6   0.1       0.1        36       5      29 ..     491     515 ..     488     519 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0053
                            IPT   5 lifGatttGKtaeaiklaketgapvivl 32 
                                    l +G+ +tGKt  a ++a+etga  i++
  gi|119719589|ref|YP_920084.1| 218 LFYGPPGTGKTLLAKAVANETGAYFIAI 245
                                    78********************998876 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.1
                            IPT   5 lifGatttGKtaeaiklaketgapv 29 
                                    l++G+ +tGKt  a ++a e  a  
  gi|119719589|ref|YP_920084.1| 491 LLYGPPGTGKTLLAKAVATESEANF 515
                                    89****************9887665 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.031        11      24      80 ..     217     284 ..     212     293 .. 0.61
   2 ?    5.5   0.0      0.05        17      24      47 ..     490     513 ..     487     561 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.031
                                    EEEEEETT--HHHHHHCC--TTS-EE.--SSTTHHHH-H.........HHHHHHT...TTSEEEEEE-TT CS
                Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgpwl.eifvverlaklp.........ldlleqa...kggtLylkdiad 80 
                                    v+  G++G+gk+l A++ +++ g    +i   e  +             +++e+a    ++++++ +i+ 
  gi|119719589|ref|YP_920084.1| 217 VLFYGPPGTGKTLLAKAVANETGAYFiAINGPEIMS--KfygeseqrlREIFEEAtknAPAIIFIDEIDA 284
                                    8999**************998776320221111111..12222233336666665444566777777765 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.05
                                    EEEEEETT--HHHHHHCC--TTS- CS
                Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgp 47 
                                    ++l G++G+gk+l A++ + +s+ 
  gi|119719589|ref|YP_920084.1| 490 ILLYGPPGTGKTLLAKAVATESEA 513
                                    799**************9988775 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.048        17       5      27 ..     221     243 ..     217     247 .. 0.91
   2 ?    5.1   0.0     0.049        17       3      27 ..     492     516 ..     490     518 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.048
                                    -STTSSHHHHHHHHHHHHT-EEE CS
                 Cytidylate_kin   5 GPagsGKssvaralaeklglkyl 27 
                                    GP g+GK  +a+a+a++ g+ ++
  gi|119719589|ref|YP_920084.1| 221 GPPGTGKTLLAKAVANETGAYFI 243
                                    9****************999876 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.049
                                    EE-STTSSHHHHHHHHHHHHT-EEE CS
                 Cytidylate_kin   3 iDGPagsGKssvaralaeklglkyl 27 
                                    + GP g+GK  +a+a+a++ +++++
  gi|119719589|ref|YP_920084.1| 492 LYGPPGTGKTLLAKAVATESEANFI 516
                                    67****************9998886 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.029        10       1      24 [.     223     246 ..     223     273 .. 0.68
   2 ?    3.9   0.0      0.15        51       1      23 [.     496     518 ..     496     546 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.029
                                    TTSSHHHHHHHHHHHHTSEEEEHH CS
                            SKI   1 mGaGKstvGkllAkklglefiDlD 24 
                                    +G+GK+ ++k++A++ g  fi + 
  gi|119719589|ref|YP_920084.1| 223 PGTGKTLLAKAVANETGAYFIAIN 246
                                    69******************9765 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.15
                                    TTSSHHHHHHHHHHHHTSEEEEH CS
                            SKI   1 mGaGKstvGkllAkklglefiDl 23 
                                    +G+GK+ ++k++A + + +fi +
  gi|119719589|ref|YP_920084.1| 496 PGTGKTLLAKAVATESEANFIGV 518
                                    69****************99965 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.097        34      21      39 ..     214     231 ..     204     236 .. 0.76
   2 ?    5.5   0.0     0.042        15      21      42 ..     487     507 ..     477     509 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.097
                         AAA_29  21 lkgatlltGpsGsGKSTll 39 
                                    +kg +l+ Gp G+GK+ l 
  gi|119719589|ref|YP_920084.1| 214 PKG-VLFYGPPGTGKTLLA 231
                                    466.9**********8765 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.042
                         AAA_29  21 lkgatlltGpsGsGKSTllDAi 42 
                                    +kg +ll Gp G+GK+ l  A+
  gi|119719589|ref|YP_920084.1| 487 PKG-ILLYGPPGTGKTLLAKAV 507
                                    355.9**********8776555 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0     0.011       3.7       4      62 ..     218     286 ..     216     320 .. 0.75
   2 ?    0.2   0.0       1.5   5.1e+02       4      17 ..     491     504 ..     490     513 .. 0.85
   3 ?   -1.5   0.0       4.7   1.6e+03      65      97 ..     531     563 ..     516     581 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.011
                            Zot   4 lvtGapGsgKts..gavkkdllp.alk.egRkiitnidGlrlerieqvlgekvs.tarlirid.....n 62 
                                    l++G+pG+gKt+  +av ++    ++  +g +i+ +  G   +r++ +++e+ + ++ +i+id      
  gi|119719589|ref|YP_920084.1| 218 LFYGPPGTGKTLlaKAVANETGAyFIAiNGPEIMSKFYGESEQRLREIFEEATKnAPAIIFIDeidaiA 286
                                    899********7224566655555333479999999999999999999999988899999999544443 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.5
                            Zot   4 lvtGapGsgKtsga 17 
                                    l +G+pG+gKt+ a
  gi|119719589|ref|YP_920084.1| 491 LLYGPPGTGKTLLA 504
                                    679********876 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 4.7
                            Zot  65 gaetlkefakwatidkgallviDEcqeifpvra 97 
                                    +++ + e++  a+ +   ++++DE   i p r 
  gi|119719589|ref|YP_920084.1| 531 SEKAVREIFRKARQAAPCVIFFDEIDSIVPRRG 563
                                    555566666666666778999999999877664 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.037        13       2      28 ..     215     241 ..     214     244 .. 0.88
   2 ?    4.0   0.0      0.11        38       2      24 ..     488     510 ..     487     514 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.037
                      PduV-EutP   2 kkilliGkvgsGKttLtqalkgeelkY 28 
                                    k +l+ G+ g+GKt L++a+ +e+  Y
  gi|119719589|ref|YP_920084.1| 215 KGVLFYGPPGTGKTLLAKAVANETGAY 241
                                    5699****************9987655 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.11
                      PduV-EutP   2 kkilliGkvgsGKttLtqalkge 24 
                                    k ill G+ g+GKt L++a+  e
  gi|119719589|ref|YP_920084.1| 488 KGILLYGPPGTGKTLLAKAVATE 510
                                    6699**************98765 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1    0.0024      0.83      24      56 ..      15      46 ..       5      53 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0024
                                   HHCSSS-EEEEEHHHHHHHT--TT-EEEEEETT CS
                Molydop_binding 24 lakpepevveinpedAaalGikdGdlVevesrr 56
                                   +   ++  v+i  + +a+lG++ Gd+Ve+e ++
  gi|119719589|ref|YP_920084.1| 15 RDVGRG-IVRIDRNAMAKLGVEPGDIVEIEGKK 46
                                   334444.9*********************9876 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       5.4   1.9e+03     103     122 ..     181     200 ..     177     205 .. 0.84
   2 ?    3.1   0.1      0.23        81       6      22 ..     221     237 ..     217     247 .. 0.84
   3 ?    1.1   0.1      0.95   3.3e+02      81     118 ..     258     296 ..     254     314 .. 0.73
   4 ?    0.1   0.0       1.9   6.6e+02     101     122 ..     452     473 ..     421     478 .. 0.76
   5 ?    6.0   0.0      0.03        10       2      33 ..     490     518 ..     489     529 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 5.4
                                    --STTGGG-HHHHHHHHHHH CS
                       NTPase_1 103 EiGkmElkskkfkeaveevL 122
                                     iG +E   +k++e+ve  L
  gi|119719589|ref|YP_920084.1| 181 DIGDLEEAKQKIREMVELPL 200
                                    69************998655 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.23
                                    --TTSSHHHHHHHHHHH CS
                       NTPase_1   6 GppGvGKtTlvkkvlel 22 
                                    GppG+GKt l k v+++
  gi|119719589|ref|YP_920084.1| 221 GPPGTGKTLLAKAVANE 237
                                    9*********9999876 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.95
                                    HHHHHHHHHHHHH.HHH-EEEE---STTGGG-HHHHHHH CS
                       NTPase_1  81 feelalealrkal.seadviviDEiGkmElkskkfkeav 118
                                     e+   e++++a  + + +i iDEi  +  k +++  +v
  gi|119719589|ref|YP_920084.1| 258 SEQRLREIFEEATkNAPAIIFIDEIDAIAPKREEVTGEV 296
                                    567777888888845556*******77666555555555 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 1.9
                                    E---STTGGG-HHHHHHHHHHH CS
                       NTPase_1 101 iDEiGkmElkskkfkeaveevL 122
                                     D iG +E   ++++eave  L
  gi|119719589|ref|YP_920084.1| 452 WDDIGGLEDVKQQLREAVELPL 473
                                    599**************98655 PP

  == domain 5  score: 6.0 bits;  conditional E-value: 0.03
                                    EEEE--TTSSHHHHHHHHHHHH...GGGEEEE CS
                       NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgGf 33 
                                    +++ GppG+GKt l k v+ + + +     G+
  gi|119719589|ref|YP_920084.1| 490 ILLYGPPGTGKTLLAKAVATESEAN---FIGV 518
                                    6788********9999998876444...3343 PP

>> B5  tRNA synthetase B5 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0      0.24        83      41      59 ..      96     114 ..      29     117 .. 0.89
   2 ?    2.5   2.3      0.53   1.8e+02      31      64 ..     667     716 ..     392     717 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.24
                                    EEE--TT-TT--SHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxx RF
                             B5  41 lVtvPswRsDlereeDliE 59 
                                     V  Ps+R  le   Dl+E
  gi|119719589|ref|YP_920084.1|  96 VVLAPSYRIGLEVTPDLVE 114
                                    5789**************9 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.53
                                    E................EESSTTCEEEE--TT.-TT--SHHHHHHHHHHH CS
                                    x...............xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx RF
                             B5  31 e...............riekdkdlllVtvPsw.RsDlereeDliEEvaRl 64 
                                    e               ++ + ++ l++  Ps  ++D+er+  + EE  R+
  gi|119719589|ref|YP_920084.1| 667 EaalaalreagkptkvTKRHFEQALQIVKPSVtKEDIERYKRISEEFRRM 716
                                    04444444444445554567777888888887689999999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (718 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                       108  (0.00602376); expected 17.9 (0.001)
Passed Fwd filter:                        52  (0.00290033); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              52  [number of targets reported over threshold]
# CPU time: 0.85u 0.36s 00:00:01.21 Elapsed: 00:00:00.53
# Mc/sec: 4049.43
//
Query:       gi|119719590|ref|YP_920085.1|  [L=303]
Description: methionine aminopeptidase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.1e-33  115.2   0.0    3.8e-33  115.0   0.0    1.1  1  Peptidase_M24  Metallopeptidase family M24


Domain annotation for each model (and alignments):
>> Peptidase_M24  Metallopeptidase family M24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.0   0.0   2.1e-37   3.8e-33       1     208 [.       3     284 ..       3     285 .. 0.86

  Alignments for each domain:
  == domain 1  score: 115.0 bits;  conditional E-value: 2.1e-37
                                    HHHHHHHHHHHHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHTTTCEESSSSEEEEGGGGGSTTTBCS.SSB..--TTEEE CS
                  Peptidase_M24   1 elirkaariasaaleavleaikpgvterelaaeieattlkrhgarglafppivasgenaavlhytpn.drv..lkegdlv 77 
                                    e++++a+++a++al+ +++  ++gv   e+a+ +e++  +r  +  +afp  v +++n  ++hytp+ +++  + +g ++
  gi|119719590|ref|YP_920085.1|   3 EQLKRAGDVAREALKLAVDISHEGVPLIEIAERVEEF--IRSRGALPAFP--VNLSINQVAAHYTPSsNDElrVPKGSVL 78 
                                    5789*************9*889*************98..55556789***..**************6466644699**** PP

                                    EEEEEEEETTEEEEEEEEEECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHHHHTTBCCGBSSCSEEEE CS
                  Peptidase_M24  78 lidagaeydgyasDitrTvlvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarevlesaglakffphglGHgv 157
                                    +id+g+++dgy++D+++Tv+    + e+r+l  a+ ea++ a  a+kp  t+ +++++++  ++++g+ k++ +++GH +
  gi|119719590|ref|YP_920085.1|  79 KIDVGVHVDGYIADCAVTVVQ---SGEYRRLALAAFEALKSAALALKPRSTAYDVGKVVEGAIRKYGY-KPIENLTGHKI 154
                                    *******************86...569*****************************************.*********** PP

                                    SS.SSSEE..EEEESSSTT.CSSB--TTBEEEEEE.........EEEEETTT............................ CS
                  Peptidase_M24 158 Gl.evhde..gpsvsresn.dgrkleeGmvftiEp.........giyfapge............................ 196
                                     + ++h +   p+v+r +  + + +  G+v+++Ep               g+                            
  gi|119719590|ref|YP_920085.1| 155 ERyNLHAGksIPNVAR-YEyRLVGINIGEVYAVEPfatngvgqvI---DSGWsniyrvvsvrrisrekdlndvlealwke 230
                                    *99***7733455554.334788899*********8888553220...23557777777777888888888888888888 PP

                                    .........................................E.EEEEBEEEEEE CS
                  Peptidase_M24 197 .........................................g.gvriedtvlvt 208
                                                                             g + ++edt++v 
  gi|119719590|ref|YP_920085.1| 231 fkglpfaerwvsrmgfsekelrglveskrvyhyprlveaggGlVSQFEDTFIVD 284
                                    999999999999999999999999999999999999999998899999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 2165.35
//
Query:       gi|119719591|ref|YP_920086.1|  [L=208]
Description: translin family protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-12   47.8   0.0    1.4e-10   41.5   0.0    2.2  1  Translin  Translin family
  ------ inclusion threshold ------
      0.071   13.3   0.1       0.12   12.6   0.1    1.4  1  DUF3102   Protein of unknown function (DUF3102)
       0.11   12.8   0.5       0.33   11.3   0.2    1.9  2  FliS      Flagellar protein FliS
       0.11   12.4   0.0        2.2    8.2   0.0    2.3  2  YfdX      YfdX protein


Domain annotation for each model (and alignments):
>> Translin  Translin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5   0.0   3.1e-14   1.4e-10       2     188 ..      18     175 ..      17     181 .. 0.82

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 3.1e-14
                                    HHHHHHHHHHHHHHHHHHHHHHHHTTGSSTTTHHHHHHH.H.HHHHHHHHHHTTSS..........GHHHHGGGTH.HHH CS
                       Translin   2 rreriikasrditaaskkiifllhrvrsekteaqdkkakik.keakeklkeiakllasvaeelqgsnayrYqrqisgglq 80 
                                    +re++  + r+it+ ++++if+lh  +         ka ++ + a+e +ke+ +l        q ++   Y+  + ++  
  gi|119719591|ref|YP_920086.1|  18 QREKMLVVTREITRRAREAIFALHHGD-------LGKAGTElERARELIKELYELK-------QTHPQLYYSGGVLNAQT 83 
                                    69***********************66.......2233322245555555555555.......4558888********** PP

                                    HHHHHHHHHHHHHHSS---HHHHHHHTT.---SSSSSS---HHHHHHHHHHHHHHHHHHHHHHHCTT--S.HHHHHHHHH CS
                       Translin  81 eliealsfahYletqtLitleevqkilealkeneedafhltpedYllGlfdLtgELmRfainsvalgdkeekplqilkfl 160
                                    e++ea ++a+ l  + L  +ee               + ++p+ Yl Gl dL+gEL R+  n + +g  + k+ +il+f+
  gi|119719591|ref|YP_920086.1|  84 EYVEASLLASLLAGEGLPGFEE---------------LLVEPQAYLAGLGDLVGELRRYVLNILREGMVD-KAWSILEFM 147
                                    *********9999988876665...............4678999*********************99987.********* PP

                                    HHHHHHHHTS----HH...HHHHHTTHH CS
                       Translin 161 relragfellnlkndsakdlrkKldvlk 188
                                    +e++ ++  ++ +      lr+K+dv +
  gi|119719591|ref|YP_920086.1| 148 EEIYVELGKFSYPEALVPGLRHKVDVAR 175
                                    *****99999999654668999999976 PP

>> DUF3102  Protein of unknown function (DUF3102)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   2.7e-05      0.12       5      46 ..       7      47 ..       4      72 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.7e-05
                        DUF3102  5 viaaEintikeqtkkilLtsaieiGrrLkEakellpyGewlk 46
                                   +ia+E+  + +q +k+l++ + ei rr +Ea   l++G+ +k
  gi|119719591|ref|YP_920086.1|  7 LIAKELDELDAQREKMLVV-TREITRRAREAIFALHHGDLGK 47
                                   79*************8765.67****************9886 PP

>> FliS  Flagellar protein FliS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   7.3e-05      0.33      18      58 ..      22      62 ..      14      68 .. 0.87
   2 ?   -2.3   0.0       1.2   5.3e+03      63      78 ..     187     202 ..     168     206 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7.3e-05
                                   HHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHH CS
                           FliS 18 vlmLydgalkflkrakeaieekdiekkgeaiskaqdIiseL 58
                                   +l++  ++ ++ ++a+ a++++d+ k+g+++++a ++i+eL
  gi|119719591|ref|YP_920086.1| 22 MLVVTREITRRAREAIFALHHGDLGKAGTELERARELIKEL 62
                                   556677899999****************************9 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.2
                                    CTTTSCHHHHHHHHHH CS
                           FliS  63 dlekggeiaknLaalY 78 
                                     +e+  ++a+++++l 
  gi|119719591|ref|YP_920086.1| 187 FFERSRDLAQRIERLL 202
                                    4455555666555554 PP

>> YfdX  YfdX protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0    0.0005       2.2       6      34 ..      34      62 ..      29      89 .. 0.85
   2 ?    1.7   0.0      0.05   2.3e+02      85     120 ..     169     204 ..     167     206 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0005
                                   HHHHHHHCTT-HHHHHHHHHHHHHHHTS- CS
                           YfdX  6 qkArlaldqgdtkeAkkllekAqgkleaa 34
                                   ++A++al++gd  +A ++le+A++ ++++
  gi|119719591|ref|YP_920086.1| 34 REAIFALHHGDLGKAGTELERARELIKEL 62
                                   6899******************9987765 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.05
                                    T-HHHHHHHHHHTT-EEEEEEEEEEHHHHHHHHHHH CS
                           YfdX  85 gdtqaArelLkllgseidittallPLatypaavkkA 120
                                    ++++ Ar +L+++++++ + + + +La+  + + +A
  gi|119719591|ref|YP_920086.1| 169 HKVDVARVILENTRNDVLFFERSRDLAQRIERLLEA 204
                                    678899***********9999999999987777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       731  (0.0407719); expected 358.6 (0.02)
Passed bias filter:                      605  (0.0337442); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 1582.66
//
Query:       gi|119719592|ref|YP_920087.1|  [L=232]
Description: deoxyribonuclease V [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-62  210.5   0.0    2.2e-62  210.3   0.0    1.0  1  Endonuclease_5  Endonuclease V
    1.6e-05   24.4   0.1    3.5e-05   23.3   0.0    1.6  2  DUF99           Protein of unknown function DUF99
  ------ inclusion threshold ------
      0.087   12.7   0.0       0.29   11.0   0.0    1.7  1  UvrC_HhH_N      UvrC Helix-hairpin-helix N-terminal


Domain annotation for each model (and alignments):
>> Endonuclease_5  Endonuclease V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.3   0.0   3.7e-66   2.2e-62       4     197 .]      23     211 ..      20     211 .. 0.94

  Alignments for each domain:
  == domain 1  score: 210.3 bits;  conditional E-value: 3.7e-66
                                    HCC-------SGG-SEEEEEEEEEEECTCEEEEEEEEEEETTTTEEEEEEEEEEE--S-SSTT-CHHHCHHHHHHHHCC- CS
                 Endonuclease_5   4 akkveledklkeklklvaGvDvsfvkeekkeavaalvvldlpslevvekavavvklsfpYipgfLaFRElpvllkalekl 83 
                                    a+ v +ed+l+e++++ aGvDv+f   + + a+aa+vv+++ps++vv+ +v++++++fpY+p++LaFRE+ ++++al++l
  gi|119719592|ref|YP_920087.1|  23 ARMVLEEDSLPESVRRAAGVDVAF---KGDYAFAAAVVVEYPSFSVVDYSVTRTEVRFPYVPTLLAFREVWPAYTALKRL 99 
                                    6678889999999***********...44446************************************************ PP

                                    SS--SEEEEEC-SSSSTTS--HHHHHHHHHTS-EEEEESS-SSSBE----SSTTEEEEEEETTEEEEEEEESSTTS--EE CS
                 Endonuclease_5  84 kqkpdvllvDGnGiaHprrlGlAshlGvlldlptiGvaKsllvgkveepekekgsvvplvsegevigaalrtkknvkpiy 163
                                    k++pdvllvDGnG +Hp ++G A+hlGvl+d ptiGvaK+llvg   e ++ k+ v+p++ +gev+g+a++t++++kp++
  gi|119719592|ref|YP_920087.1| 100 KSEPDVLLVDGNGRLHPFKAGFACHLGVLVDKPTIGVAKKLLVG---EVGSWKSGVAPVLYRGEVLGMAVKTSERSKPVF 176
                                    ********************************************...667788889999999****************** PP

                                    EEEECSS-HHHHHHHHHHCS-.T-SS-HHHHHHHH CS
                 Endonuclease_5 164 vSvGhrisletalelvlallk.kyrlPepirqAdl 197
                                    vS+Gh+isl+ta+ +v+ ++k + rlPep+r+A+l
  gi|119719592|ref|YP_920087.1| 177 VSIGHKISLNTAVWIVRMFTKrGLRLPEPLRLAHL 211
                                    ******************998578*********95 PP

>> DUF99  Protein of unknown function DUF99
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0      0.58   3.5e+03     160     175 ..      24      39 ..      13      46 .. 0.61
   2 !   23.3   0.0   5.8e-09   3.5e-05     136     181 ..     168     215 ..     157     217 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.58
                                    HHC-SSSSS-HHHHHH CS
                          DUF99 160 rkltlegriPEPlRvA 175
                                    r +  e  +PE +R A
  gi|119719592|ref|YP_920087.1|  24 RMVLEEDSLPESVRRA 39 
                                    3333445777877766 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 5.8e-09
                                    ETT....EEEEE.ESS-HHHHHHHHHHC-SSS.SS-HHHHHHHHHHHH CS
                          DUF99 136 vektgeelyvra.vGieleeaaklvrkltleg.riPEPlRvAhliAsa 181
                                    +++++++++v + + i+l++a  +vr +t++g r+PEPlR+Ahl A+a
  gi|119719592|ref|YP_920087.1| 168 TSERSKPVFVSIgHKISLNTAVWIVRMFTKRGlRLPEPLRLAHLYATA 215
                                    4445777888754789****************99************97 PP

>> UvrC_HhH_N  UvrC Helix-hairpin-helix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   4.8e-05      0.29       6     113 ..      32     139 ..      28     150 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4.8e-05
                                    -SS---EEEEEEEEEETTTEEEEEEEEEETTEE-GGG-EEEEEE.-SS.--HHHHHHHHHHHHHTTS.....---SEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     UvrC_HhH_N   6 lkekpkriecyDiShiqgtntvgsmvvfedgkpkkseyRkfkiksvke.gdDyaamrevlrRrfkrllkefsklPdLili 84 
                                    l+e+++r  ++D++  +g+++ ++ vv+e  +++  +y   + +        + a rev       +lk+ +++Pd++l+
  gi|119719592|ref|YP_920087.1|  32 LPESVRRAAGVDVAF-KGDYAFAAAVVVEYPSFSVVDYSVTRTEVRFPyVPTLLAFREVWPAYT--ALKRLKSEPDVLLV 108
                                    677788888888875.888888888888888888888877776633336777777888765432..2334678******* PP

                                    SSSHHHHHHHHHHHH.HTT-..---EEEEES. CS
                                    xxxxxxxxxxxxxxx.xxxx..xxxxxxxxxx RF
                     UvrC_HhH_N  85 DGGkgqlnaakevle.elgl..kipvvglaKd 113
                                    DG +g+l+  k+ ++ +lg+  + p +g+aK+
  gi|119719592|ref|YP_920087.1| 109 DG-NGRLHPFKAGFAcHLGVlvDKPTIGVAKK 139
                                    *8.68888888877658888889999999994 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       253  (0.0141112); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1690.92
//
Query:       gi|119719593|ref|YP_920088.1|  [L=163]
Description: hypothetical protein Tpen_0683 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-74  248.8   0.4    1.9e-74  248.6   0.4    1.0  1  Adenosine_kin  Adenosine specific kinase


Domain annotation for each model (and alignments):
>> Adenosine_kin  Adenosine specific kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  248.6   0.4     1e-78   1.9e-74       1     154 []       8     161 ..       8     161 .. 0.99

  Alignments for each domain:
  == domain 1  score: 248.6 bits;  conditional E-value: 1e-78
                                    EEE---TTEEEEEEEESSTTHHHHHHHHHHCCSTTSEEEEEEE--STT-EEEEEESSHHHHHHHHHHHHHH--TTEEEEE CS
                  Adenosine_kin   1 vkiekpeevnvilgqshfiktvedlyealvtsvpgikfglafcEasgkrLvrvegndeelvelavknalaigaghvfvil 80 
                                    v+++ p++ nvi+gq+hfik+ved+ ea+ tsvpg+kfglaf+Easg+rLvr++gnd+el+e+a+++a++igaghvfv++
  gi|119719593|ref|YP_920088.1|   8 VDVKLPSKSNVIIGQTHFIKSVEDIAEAVSTSVPGVKFGLAFNEASGDRLVRYDGNDPELIEAAIDAAKRIGAGHVFVLF 87 
                                    7899**************************************************************************** PP

                                    EEST-HHHHHHHHHHCTTCEEEEEEESSSEEEEEEEETTEEEEEEEEES---SEE--HHHHHHHHHHHHHTTS- CS
                  Adenosine_kin  81 lknafPinvlnaiksvpevvkifaAtanplevivaeteqgrgvlgvvDGfspkgveeeedkkerkellrkigYk 154
                                    +++a+Pinvln++k+v+ev++if+Atanp++vivaet+qgrgv+gv+DGf++ gve+eedkk+r e+lrkigYk
  gi|119719593|ref|YP_920088.1|  88 IRDAWPINVLNQLKNVQEVASIFCATANPVQVIVAETQQGRGVMGVIDGFTVVGVESEEDKKKRVEFLRKIGYK 161
                                    *************************************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1152.04
//
Query:       gi|119719594|ref|YP_920089.1|  [L=118]
Description: peptidyl-tRNA hydrolase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-42  144.6   0.0    1.6e-42  144.5   0.0    1.0  1  PTH2           Peptidyl-tRNA hydrolase PTH2
  ------ inclusion threshold ------
      0.083   13.2   0.3       0.23   11.8   0.4    1.8  2  SpoU_sub_bind  RNA 2'-O ribose methyltransferase substrate bi


Domain annotation for each model (and alignments):
>> PTH2  Peptidyl-tRNA hydrolase PTH2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.5   0.0   1.8e-46   1.6e-42       1     117 []       4     118 .]       4     118 .] 0.98

  Alignments for each domain:
  == domain 1  score: 144.5 bits;  conditional E-value: 1.8e-46
                                    EEEEEEEESSSSS-HHHHHHHHHHHHHHHHHHHHHH.CHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHHHTT-SEEE CS
                           PTH2   1 lkmvlvvrkDLkmskGkiaaqcahAavalvkkllkesnekellkeWeeegqkkivlkveseeeLlelaakakalglpaal 80 
                                    lk+v+v+r+DL m+kGk++aq +hA+v++v ++lk+ n+ e++++W eegq+kiv++v+seeeLl++++ka +lgl+a l
  gi|119719594|ref|YP_920089.1|   4 LKQVIVLRRDLDMGKGKMVAQGCHASVSAVLETLKR-NR-EIVERWVEEGQRKIVVRVDSEEELLSVYRKALELGLVAVL 81 
                                    59*********************************9.88.8*************************************** PP

                                    EEETSSSSSSTTCEEEEEEEEEEHHHHHHHHTTSEB- CS
                           PTH2  81 irDagrtqiepgtkTvlaigPapksivdkvtgkLkll 117
                                    ++D g tq++pgt+T+++igPa ++i+dkvtg+Lkll
  gi|119719594|ref|YP_920089.1|  82 VEDKGLTQLPPGTPTAVGIGPADEEIIDKVTGHLKLL 118
                                    ***********************************97 PP

>> SpoU_sub_bind  RNA 2'-O ribose methyltransferase substrate binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.4   2.5e-05      0.23       7      29 ..      32      54 ..      30      91 .. 0.71
   2 ?   -3.6   0.0       1.6   1.4e+04      50      59 ..     104     113 ..     102     114 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.5e-05
                  SpoU_sub_bind  7 aVleaLksgrriekllvtegrad 29
                                   aVle Lk +r+i++ +v+eg+++
  gi|119719594|ref|YP_920089.1| 32 AVLETLKRNREIVERWVEEGQRK 54
                                   8*******************333 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1.6
                  SpoU_sub_bind  50 dkekLdklsg 59 
                                    d+e++dk++g
  gi|119719594|ref|YP_920089.1| 104 DEEIIDKVTG 113
                                    7788888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 855.71
//
Query:       gi|119719595|ref|YP_920090.1|  [L=444]
Description: pseudouridylate synthase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   3.8e-127  424.5   0.0   4.4e-127  424.4   0.0    1.0  1  TruD      tRNA pseudouridine synthase D (TruD)


Domain annotation for each model (and alignments):
>> TruD  tRNA pseudouridine synthase D (TruD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  424.4   0.0  2.4e-131  4.4e-127       2     416 .]      13     433 ..      12     433 .. 0.95

  Alignments for each domain:
  == domain 1  score: 424.4 bits;  conditional E-value: 2.4e-131
                           TruD   2 lgielyvtdtegigGrlrespeDFiVeEieef....sge.e.eadegeylvlrvekrnwdtldlvrelaralgisrkrvg 75 
                                    lg e+y  d  g+gG+lr+s +DFiV+Ei+      s e + ++ +ge+++l +ekr++dt +++r++ar +g++ ++vg
  gi|119719595|ref|YP_920090.1|  13 LGLEYYGLDGAGTGGKLRSSLDDFIVREISIDgevaSPEcKyAEGAGEFTWLVLEKRKIDTVSAARAVARFFGLKLRDVG 92 
                                    799**************************6666544333223555699******************************** PP

                           TruD  76 faGtKDkrAvTtQlisi.rkvepeelealei..kdvelevvgrarrklrlGdLaGNkFeirvrdvaeeeeaakraeeile 152
                                    +aG+KD++AvT Q+isi  +v+ e++e++++  k+v+l+  +r   +l+ G L+GN F+++vr++    e+ +++e++l+
  gi|119719595|ref|YP_920090.1|  93 IAGLKDTSAVTYQFISIpGEVKMESIEEFNLshKRVKLHCPFRRPFALKPGMLYGNFFNVKVRGA----ECLECLEALLR 168
                                    *****************667********9776699*****************************4....7889******* PP

                           TruD 153 eleekggvPNyfGvQRFGsrrpvthlvGkaivkgdleeAvelyvgkpfeeesedtreareavaetgdleealeelpkslr 232
                                    el+ek++vPNy+G+QRFG++rpvth+vG++i+ g+++eAve+++ k f+ es+ +r+ar +++e+gd  +ale++pksl+
  gi|119719595|ref|YP_920090.1| 169 ELKEKKAVPNYYGYQRFGTVRPVTHVVGRMILLGEFKEAVEELIYKVFPGESQVSRRARLFLSESGDPLKALELFPKSLK 248
                                    ******************************************************************************** PP

                           TruD 233 yErallkrLaekpkdykkAlealpknLqrlFvhAyqSylFNrvlseRlerglpldepveGDvv.ifaeerlpdtdrlqlv 311
                                     Era+l++La++p+dy +Al+a+++ +++lF+ Ayq+ylFN++ls+R+ergl++  pv+GD+v if+e+r  + + + +v
  gi|119719595|ref|YP_920090.1| 249 SERAVLRHLARHPGDYVGALRAVSPYVKKLFIGAYQAYLFNKLLSKRIERGLSYYYPVPGDTVgIFREKRGGEVTGVLKV 328
                                    *************************************************************99556777799******** PP

                           TruD 312 teknveevkrliergrafvtaplvGtetelaegevgeierevleeegleledFklpklpelsskGtrRaillrvedlels 391
                                    +++nve+vkr i++g a++ +p++G++++l++g vgeiere+l+eeg++ ++F+++++pe ss+Gt+R ++l ++ l+++
  gi|119719595|ref|YP_920090.1| 329 NDANVEKVKRWIDEGFAVLLLPVFGYNSNLSHGVVGEIERELLREEGIDVSMFRVKQIPEASSAGTYRYASLVPHALNVR 408
                                    ******************************************************************************** PP

                           TruD 392 aeedeltleFsLpkGsYATvvlrEi 416
                                      +++++l+F L+kG YAT++lrE+
  gi|119719595|ref|YP_920090.1| 409 VFGNDYELTFVLNKGAYATTLLREL 433
                                    ***********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (444 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 3181.24
//
Query:       gi|119719596|ref|YP_920091.1|  [L=801]
Description: protein of unknown function DUF699, ATPase putative [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-56  191.0   0.0    3.8e-56  189.7   0.0    1.7  2  Helicase_RecD    Helicase
    6.5e-42  143.5   0.0    2.2e-27   95.9   0.0    2.3  2  GNAT_acetyltr_2  GNAT acetyltransferase 2
    1.2e-29  102.1   0.3    1.4e-28   98.6   0.0    2.9  3  DUF1726          Domain of unknown function (DUF1726)
    2.2e-05   24.3   0.6    4.2e-05   23.4   0.6    1.4  1  tRNA_bind_2      Possible tRNA binding domain
      0.002   17.9   0.0      0.013   15.2   0.0    2.1  2  AAA_30           AAA domain
     0.0076   16.5   0.0      0.021   15.0   0.0    1.8  1  Acetyltransf_1   Acetyltransferase (GNAT) family


Domain annotation for each model (and alignments):
>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.7   0.0   1.3e-59   3.8e-56       1     177 []     250     430 ..     250     430 .. 0.94
   2 ?   -4.0   0.0       3.9   1.2e+04      27      52 ..     628     653 ..     625     656 .. 0.83

  Alignments for each domain:
  == domain 1  score: 189.7 bits;  conditional E-value: 1.3e-59
                  Helicase_RecD   1 vltAdRGRGKSaalGlalaaliaegk.....snilvtapskenvktlfeflakglealglke.eekkkkaekaelrvrkq 74 
                                    vltAdRGRGKS+a+Gl +  l+++ +     ++++vtap  +nv+++f+f a+ l+  + k    +++++  ++l +++ 
  gi|119719596|ref|YP_920091.1| 250 VLTADRGRGKSSAVGLGVGWLAHRLRrakgkCKVVVTAPAVTNVQEVFRFSAAVLDLFKHKVeVLEDESGMITKLLSKGI 329
                                    79**************999998876667788*************************9988875556677777899999** PP

                  Helicase_RecD  75 rieyiapdellklkeqadllvvDEAAaiplpllkkllekfkrvvlatTvhGYEGtGrgfslkflkqlkkekkrelrelel 154
                                    +iey++p ++lk+k   dllvvDEAA+ip+pll k+l++f++vv+++T+hGYEG+Grgfsl+flk+lk+e+  +l e+e+
  gi|119719596|ref|YP_920091.1| 330 EIEYVTPLDVLKAKG--DLLVVDEAASIPVPLLFKMLKRFNKVVYSSTIHGYEGAGRGFSLRFLKRLKNEEGVKLYEYEM 407
                                    ************875..*************************************************************** PP

                  Helicase_RecD 155 eepiRyaegdplEkwlndlLlLd 177
                                    +epiRya++dp+Ekw++dlLlLd
  gi|119719596|ref|YP_920091.1| 408 SEPIRYAPEDPIEKWTFDLLLLD 430
                                    *********************97 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 3.9
                  Helicase_RecD  27 snilvtapskenvktlfeflakglea 52 
                                     +++v+ p  e++k++++ +ak++++
  gi|119719596|ref|YP_920091.1| 628 YTVIVVKPLSEKAKRIVDVIAKEFKQ 653
                                    57899999999999999999999876 PP

>> GNAT_acetyltr_2  GNAT acetyltransferase 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.9   0.0   7.5e-31   2.2e-27       2     124 ..     470     585 ..     469     590 .. 0.91
   2 !   46.5   0.0   9.3e-16   2.8e-12     175     226 ..     585     636 ..     582     637 .. 0.92

  Alignments for each domain:
  == domain 1  score: 95.9 bits;  conditional E-value: 7.5e-31
                GNAT_acetyltr_2   2 lvallvssHYknsPnDLqllsDaPahklfvLlapkkekkklpevlcvvqvalEGkiskesvknslsrgkrasGdlipwtl 81 
                                     +++++ +HY+n+PnDL ++ DaP+h l +   ++       ++++ +++a EG++ ++  k+s+ +g    G++ip+ l
  gi|119719596|ref|YP_920091.1| 470 FFGIYIMAHYRNNPNDLGIMMDAPHHFLRMVRLKNG------KIVVSLELASEGNLGEDLSKESA-KGAWLMGNIIPDRL 542
                                    5789**********************9987766454......8**************99777665.66799********* PP

                GNAT_acetyltr_2  82 sqqfqdeefaslsGaRivRiAvhpelqkmGYGsralellekyy 124
                                     ++++  +f++l G+R+vRiA+hp+++++G Gs al++le++ 
  gi|119719596|ref|YP_920091.1| 543 IKHYKILDFGNLRGIRVVRIATHPSVMGKGLGSFALSRLEEEA 585
                                    ***************************************9875 PP

  == domain 2  score: 46.5 bits;  conditional E-value: 9.3e-16
                GNAT_acetyltr_2 175 ekpekldylgvsfGltseLlkFWkragfspvylrqtaneltGEhsaimlrsl 226
                                    ++ +  d++g++fG+t eLlkFW ++g+ pv+++ ++n ++GE+++i++++l
  gi|119719596|ref|YP_920091.1| 585 ARRNGYDWVGAGFGVTYELLKFWLKNGYIPVHMSPEKNPVSGEYTVIVVKPL 636
                                    566778*******************************************997 PP

>> DUF1726  Domain of unknown function (DUF1726)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.6   0.0   4.7e-32   1.4e-28       1      93 []      91     184 ..      91     184 .. 0.98
   2 ?   -0.5   0.0      0.41   1.2e+03      70      91 ..     381     402 ..     360     404 .. 0.72
   3 ?   -3.2   0.0       2.8   8.3e+03      50      80 ..     745     776 ..     735     785 .. 0.64

  Alignments for each domain:
  == domain 1  score: 98.6 bits;  conditional E-value: 4.7e-32
                        DUF1726   1 ykesekvLGqtydllvldlfealtPnalgrlvetVrGGGliilllppleelkqlytdfhkklvveplt.eevkkrfnkrf 79 
                                    y++ ++vLG+ty ++v dl+++l+Pn+lgr++++V+GGGl+i+llp++++l ++ t+f+++l+v+ +t +++k++f+krf
  gi|119719596|ref|YP_920091.1|  91 YHKLDEVLGRTYAAAVADLVNNLEPNDLGRVMGVVEGGGLYIFLLPSFTRLLETVTRFQSNLIVPGYTdKDLKRYFEKRF 170
                                    78899*************************************************************************** PP

                        DUF1726  80 irklkehegilivd 93 
                                    i+k++eh+g++++d
  gi|119719596|ref|YP_920091.1| 171 IKKVMEHQGVAVYD 184
                                    ***********997 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.41
                        DUF1726  70 evkkrfnkrfirklkehegili 91 
                                       + f  rf+++lk+ eg+ +
  gi|119719596|ref|YP_920091.1| 381 GAGRGFSLRFLKRLKNEEGVKL 402
                                    55667999********999865 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 2.8
                        DUF1726  50 elkqlytdfhkklvveplt.eevkkrfnkrfi 80 
                                    +++ + ++++ +l+    + +++ + f k f+
  gi|119719596|ref|YP_920091.1| 745 SWHLTCQELNLSLAEATSNmKQIAQIFSKEFL 776
                                    45555555555666666666777788877775 PP

>> tRNA_bind_2  Possible tRNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.6   1.4e-08   4.2e-05      55     156 ..     682     781 ..     647     787 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.4e-08
                                    -------HHHHHHHHHHHHS---HHHHHSSSSHHHHHHHH--SSTTTS-SSSSSSHHHHHHTT---HHHHHHHHT--SSH CS
                    tRNA_bind_2  55 eldellspfDlkRLesYannllDYhvilDllptlaklyFsgrlkeevkLsavqsaiLlaiGLQrksvddlekeLnlpsnQ 134
                                    e++  l++  l R+  Ya + +  +  +D++  +++lyF ++ k   +Ls++q+ +L++  LQ ks     +eLnl+ + 
  gi|119719596|ref|YP_920091.1| 682 EVKVNLTKLQLARFLTYAWSDMTLENCIDVVGIMTRLYFLSKKK--PSLSELQELLLVSKILQAKSWHLTCQELNLSLAE 759
                                    677889999999999***999999*****************998..9********************************9 PP

                                    HHHHHHHHHHHHHHHH-HHHHH CS
                    tRNA_bind_2 135 vlalFvkiirkvskalreilek 156
                                    + + + +i + +sk +  + ++
  gi|119719596|ref|YP_920091.1| 760 ATSNMKQIAQIFSKEFLGVNSE 781
                                    9999999999999988877765 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   4.3e-06     0.013      14     113 ..     242     368 ..     224     376 .. 0.69
   2 ?   -0.1   0.0      0.21   6.3e+02      21      48 ..     374     401 ..     368     409 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.3e-06
                         AAA_30  14 ltsgdrvavltGpAGtGKttalkalreaweaa.g.....grviglAptgkaAkvLa..............eelgieasti 73 
                                    ++++++v vlt+  G GK+ a++  +  ++++        +v++ Ap  +  +++               e l+ e+  i
  gi|119719596|ref|YP_920091.1| 242 AEKEKLVFVLTADRGRGKSSAVGLGVGWLAHRlRrakgkCKVVVTAPAVTNVQEVFrfsaavldlfkhkvEVLEDESGMI 321
                                    5678899**************98755554444224455789999999877777755333333333333222333355555 PP

                         AAA_30  74 akllkrlk...........grarlepg.tllivDEagmvdtkqlaallkaae 113
                                     kll               +   l+++ +ll+vDEa+ +    l ++lk+ +
  gi|119719596|ref|YP_920091.1| 322 TKLL---SkgieieyvtplD--VLKAKgDLLVVDEAASIPVPLLFKMLKRFN 368
                                    5555...0567999**9653..455555**********99999999888766 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.21
                         AAA_30  21 avltGpAGtGKttalkalreaweaaggr 48 
                                    ++++G+ G+G  ++l+ l+++ +++g +
  gi|119719596|ref|YP_920091.1| 374 STIHGYEGAGRGFSLRFLKRLKNEEGVK 401
                                    5799****************99999865 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   7.1e-06     0.021      59      94 ..     555     590 ..     450     600 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 7.1e-06
                                    TEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTE CS
                 Acetyltransf_1  59 gvayieslaVspeyrgkGlGsaLlealeerareegi 94 
                                    + + + ++a +p+  gkGlGs  l  lee+ar++g+
  gi|119719596|ref|YP_920091.1| 555 RGIRVVRIATHPSVMGKGLGSFALSRLEEEARRNGY 590
                                    34445599**************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (801 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       624  (0.0348039); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.71u 0.29s 00:00:01.00 Elapsed: 00:00:00.45
# Mc/sec: 5385.35
//
Query:       gi|119719597|ref|YP_920092.1|  [L=346]
Description: hypothetical protein Tpen_0687 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00024   21.2   1.8    0.00039   20.5   1.8    1.2  1  Fer4_9    4Fe-4S dicluster domain
    0.00047   19.9   7.1       0.13   12.1   0.5    2.3  2  Fer4      4Fe-4S binding domain
     0.0079   16.8   3.0      0.016   15.8   3.0    1.4  1  Fer4_7    4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.016   15.3   2.5      0.026   14.6   2.5    1.2  1  Fer4_10   4Fe-4S dicluster domain
       0.15   13.0   8.6        5.1    8.3   2.6    2.3  2  Fer4_3    4Fe-4S binding domain
       0.31   12.0   3.7        5.8    7.9   0.1    2.3  2  Fer4_16   4Fe-4S double cluster binding domain
       0.81    9.9   4.0        2.1    8.5   4.0    1.6  1  Fer4_21   4Fe-4S dicluster domain
        1.4    9.1   7.1        2.9    8.1   0.5    2.3  2  Fer4_6    4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   1.8   1.8e-07   0.00039       8      48 ..     298     336 ..     296     339 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.8e-07
                         Fer4_9   8 CveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpk 48 
                                    C ++Cp+g+ ++ +a+++    a+s  +C +Cg C+  C +
  gi|119719597|ref|YP_920092.1| 298 CADVCPYGALNPLSAGETTDAVADS--RCDFCGLCLSLCRT 336
                                    **************99999988775..6***********87 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.5   5.8e-05      0.13      13      23 ..     297     307 ..     296     308 .. 0.90
   2 !   11.1   1.1   0.00013      0.28       6      19 ..     322     335 ..     319     337 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.8e-05
                                    HHHHHSTTTEE CS
                           Fer4  13 aCvevCPvgAI 23 
                                     C++vCP+gA+
  gi|119719597|ref|YP_920092.1| 297 VCADVCPYGAL 307
                                    6*********7 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00013
                                    TTSSS-THHHHHST CS
                           Fer4   6 ekCigCGaCvevCP 19 
                                    ++C +CG+C + C 
  gi|119719597|ref|YP_920092.1| 322 SRCDFCGLCLSLCR 335
                                    79********9996 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   3.0     7e-06     0.016       7      50 ..     297     336 ..     296     337 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 7e-06
                         Fer4_7   7 aCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPt 50 
                                     C+++Cp++a++   +    g  + ++  ++C +Cg C + C t
  gi|119719597|ref|YP_920092.1| 297 VCADVCPYGALNPLSA----GETTDAVADSRCDFCGLCLSLCRT 336
                                    5***********9887....4333366789************76 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   2.5   1.2e-05     0.026      14      55 ..     297     334 ..     295     335 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.2e-05
                        Fer4_10  14 kCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaC 55 
                                     C ++CP+       ++   +e ++ ++ ++C++cg C + C
  gi|119719597|ref|YP_920092.1| 297 VCADVCPY----GALNPLSAGETTDAVADSRCDFCGLCLSLC 334
                                    5*******....888888888999999************999 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.4    0.0024       5.3       7      15 .]     298     306 ..     294     306 .. 0.93
   2 ?    8.3   2.6    0.0023       5.1       1      12 [.     324     335 ..     324     337 .. 0.93

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0024
                         Fer4_3   7 CvevCPvgA 15 
                                    C +vCP+gA
  gi|119719597|ref|YP_920092.1| 298 CADVCPYGA 306
                                    ********9 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0023
                         Fer4_3   1 CtgCgaCvevCP 12 
                                    C+ Cg+C+  C+
  gi|119719597|ref|YP_920092.1| 324 CDFCGLCLSLCR 335
                                    ***********7 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.1    0.0026       5.8       7      19 ..     297     309 ..     295     322 .. 0.80
   2 ?    4.4   1.0     0.033        74       1      17 [.     323     339 ..     323     344 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0026
                        Fer4_16   7 kCaevCPtnaike 19 
                                     Ca+vCP +a++ 
  gi|119719597|ref|YP_920092.1| 297 VCADVCPYGALNP 309
                                    59******99975 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.033
                        Fer4_16   1 rCgtCgkCaevCPtnai 17 
                                    rC  Cg C++ C t+ +
  gi|119719597|ref|YP_920092.1| 323 RCDFCGLCLSLCRTARL 339
                                    6999********88765 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   4.0   0.00096       2.1      14      53 ..     298     336 ..     296     342 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00096
                        Fer4_21  14 CliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPv 53 
                                    C+ +C+ ++ + ++  ++t+ +v +++C  C lC+s C +
  gi|119719597|ref|YP_920092.1| 298 CADVCPYGALNPLSA-GETTDAVADSRCDFCGLCLSLCRT 336
                                    999999888888875.56777999**************65 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.5    0.0013       2.9      15      24 .]     298     307 ..     296     307 .. 0.91
   2 ?    4.2   1.2     0.022        50       6      21 ..     321     336 ..     318     339 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0013
                         Fer4_6  15 CvrvCPegai 24 
                                    C++vCP+ga+
  gi|119719597|ref|YP_920092.1| 298 CADVCPYGAL 307
                                    ********97 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.022
                         Fer4_6   6 pdkCigCgdCvrvCPe 21 
                                    +++C+ Cg C + C +
  gi|119719597|ref|YP_920092.1| 321 DSRCDFCGLCLSLCRT 336
                                    689*******998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2568.81
//
Query:       gi|119719598|ref|YP_920093.1|  [L=225]
Description: cytidyltransferase-like protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.6e-19   67.2   0.0      4e-18   65.3   0.0    2.0  2  DUF357           Protein of unknown function (DUF357)
    4.2e-14   53.0   0.0    7.1e-14   52.2   0.0    1.4  1  CTP_transf_like  Cytidylyltransferase-like
  ------ inclusion threshold ------
       0.13   12.2   0.0       0.24   11.3   0.0    1.5  1  FAD_syn          FAD synthetase


Domain annotation for each model (and alignments):
>> DUF357  Protein of unknown function (DUF357)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.3   0.0   6.7e-22     4e-18       1      72 [.      13      79 ..      13      80 .. 0.90
   2 ?   -1.8   0.0      0.56   3.3e+03       2      19 ..     163     177 ..     162     200 .. 0.63

  Alignments for each domain:
  == domain 1  score: 65.3 bits;  conditional E-value: 6.7e-22
                                   HHHHHHHHHHHHHH.....TS---HHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTST CS
                         DUF357  1 rYirlleealekvkiapdeesplgeaaeevlemaesYleDakyflekgdlvnAlasfsYaeGwLDagarlgl 72
                                   rYi ++e+ale++k+  +e+       ee+l++++ Y++Da+ +lekgd+++++a+ sYaeG+LDa+++lg 
  gi|119719598|ref|YP_920093.1| 13 RYIANVERALESLKVVLPEG-----GVEETLRLVRGYVSDARFYLEKGDCETSIACSSYAEGLLDALRFLGR 79
                                   8*************333332.....2389*****************************************96 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.56
                                    HHHHHHHHHHHHH..... CS
                         DUF357   2 Yirlleealekvkiapde 19 
                                    Y +++++al++vk   ++
  gi|119719598|ref|YP_920093.1| 163 YPPNFANALRRVK---PD 177
                                    6778888888888...44 PP

>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.2   0.0   1.2e-17   7.1e-14       1     141 [.      95     221 ..      95     223 .. 0.80

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 1.2e-17
                                    EEEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-..SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHHHHHH CS
                CTP_transf_like   1 lagGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkk..kplasaeeRlemlelakevdevisvdpweltrevlk 78 
                                    l+gG+FD++H GH+  l++a +l++   +v v+ d+++  +k  +pl+s+eeRleml+++k v++++  d      + l+
  gi|119719598|ref|YP_920093.1|  95 LVGGVFDLLHPGHIYFLRRASELGNV--YVVVARDKTVIDTKgrQPLFSEEERLEMLKALKFVSDAFLGDYPPNFANALR 172
                                    689*******************9995..6667777777666448*********************999998888889*** PP

                                    HTTTTEEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEEHTTCEEEEEEECCTTTCSHHHHH CS
                CTP_transf_like  79 klkpdklylvigadvledfsewkeleeilgnvklvvvsrpekqanvllkaekrtngiSstkir 141
                                    + kpd  ++ +gad+   +     +e+ + + +l v+        ++   +kr n++Sstk++
  gi|119719598|ref|YP_920093.1| 173 RVKPD--IVFLGADQGGLL---PIVEKAVQEAGLNVE--------IK-VLDKRLNDYSSTKYK 221
                                    *****..*******96665...335555555555555........11.235788899999876 PP

>> FAD_syn  FAD synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   4.1e-05      0.24       5      90 ..      90     168 ..      86     174 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.1e-05
                        FAD_syn   5 degavvtlGnFDGvHlGHqallkkaveaakekglpsvvvtFephPrevlakekaparLttleeklelleelg.vdavlvv 83 
                                     ++ v++ G FD +H GH   l++a e+    ++ + vv    + ++v+  +k +  L + ee+le+l++l  v   ++ 
  gi|119719598|ref|YP_920093.1|  90 RRKRVLVGGVFDLLHPGHIYFLRRASELG---NVYV-VVA---RDKTVID-TKGRQPLFSEEERLEMLKALKfVSDAFLG 161
                                    67889999***************999886...3333.332...3445665.44444488888888888887755666666 PP

                        FAD_syn  84 dFtkefa 90 
                                    d+  +fa
  gi|119719598|ref|YP_920093.1| 162 DYPPNFA 168
                                    6666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1487.90
//
Query:       gi|119719599|ref|YP_920094.1|  [L=287]
Description: diphthine synthase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.6e-27   96.1   0.4    3.2e-27   95.9   0.4    1.1  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.9   0.4   1.8e-31   3.2e-27       1     212 [.       1     227 [.       1     228 [. 0.81

  Alignments for each domain:
  == domain 1  score: 95.9 bits;  conditional E-value: 1.8e-31
                   TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleea..yeeiaealaealra 78 
                                    +l+++G+G++++ +++v  lr  ++ad ++ ++   ++++ + l+ e  l+   g+ ++  +++   +e a+++ e +++
  gi|119719599|ref|YP_920094.1|   1 MLVVAGLGLCGTRDISVGLLREAEDADEIFLET---YTSVSPGLRVE-DLVSVLGRGVKLVTRKdlEDESARTVLEVAAR 76 
                                    699**************************8777...44444444443.22233333333333334578888888888888 PP

                   TP_methylase  79 gkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl...lpglakeeerele 155
                                    gk ++ll++G+Pl+++t+s +v  ++a+++gi+v+v+P++s+++ ++a++g++++++g v+s++   +p+l++ +++ ++
  gi|119719599|ref|YP_920094.1|  77 GK-ALLLTIGNPLIATTHSSIV--VEAAKRGIKVRVLPAPSIIDGIIASTGLHVYKFGRVVSLVfpeDPSLKNYPYTPYS 153
                                    86.*******************..555559************************************************** PP

                   TP_methylase 156 allan....gdtlvllkaprk.............laelaelLkealyddttpvavveragtedervvrgtleel 212
                                     l +n     +t++ll+ + +             l +l e+ +e + d++t v+ v+ra+ ede+v+ g+++e+
  gi|119719599|ref|YP_920094.1| 154 VLKDNvsrgLHTIFLLDIRADegrymlfreaselLLRLEERFQENVVDENTLVIGVARATAEDEKVFAGRISEA 227
                                    *9999***9999999966664567888666444444444444666889999******************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1872.68
//
Query:       gi|119719600|ref|YP_920095.1|  [L=327]
Description: transcription initiation factor IIB [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-34  117.9   1.9    7.5e-17   61.1   0.1    2.4  2  TFIIB            Transcription factor TFIIB repeat
    3.1e-17   61.8   0.2    5.5e-17   61.0   0.2    1.4  1  TF_Zn_Ribbon     TFIIB zinc-binding
    0.00091   18.9   0.1     0.0016   18.1   0.1    1.3  1  Ribosomal_S27e   Ribosomal protein S27
     0.0014   18.1   2.8     0.0023   17.4   0.1    2.8  4  Sigma70_r4       Sigma-70, region 4
     0.0016   17.8   4.4      0.018   14.4   4.4    2.2  1  zf-ribbon_3      zinc-ribbon domain
     0.0021   17.8   2.7     0.0036   17.1   0.1    2.7  3  HTH_AsnC-type    AsnC-type helix-turn-helix domain
     0.0027   17.1   0.5      0.054   12.9   0.1    3.1  4  HTH_Tnp_ISL3     Helix-turn-helix domain of transposase famil
      0.003   17.6   0.0       0.47   10.6   0.0    2.3  2  Cyclin_C         Cyclin, C-terminal domain
     0.0032   17.5   0.6     0.0076   16.3   0.6    1.6  1  DUF2752          Protein of unknown function (DUF2752)
      0.008   16.3   0.6      0.016   15.4   0.6    1.5  1  Auto_anti-p27    Sjogren's syndrome/scleroderma autoantigen 1
  ------ inclusion threshold ------
      0.014   15.3   0.5      0.031   14.2   0.5    1.6  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
      0.015   15.6   0.2      0.032   14.6   0.2    1.5  1  Lar_restr_allev  Restriction alleviation protein Lar
      0.021   14.9   0.2      0.044   13.8   0.2    1.5  1  Zn_Tnp_IS91      Transposase zinc-binding domain
      0.025   14.3   0.2        1.6    8.5   0.2    2.2  2  Cyclin_N         Cyclin, N-terminal domain
      0.035   13.8   0.9      0.082   12.7   0.9    1.6  1  A2L_zn_ribbon    A2L zinc ribbon domain
      0.041   13.9   0.2      0.084   12.9   0.2    1.5  1  DZR              Double zinc ribbon
      0.056   13.1   0.5       0.17   11.6   0.5    1.9  1  Sigma70_r4_2     Sigma-70, region 4
      0.058   13.3   1.0       0.25   11.3   1.0    2.1  2  zinc_ribbon_4    zinc-ribbon domain
      0.072   12.8   0.9        4.8    7.0   0.1    2.3  2  zinc_ribbon_2    zinc-ribbon domain
      0.073   13.0   1.5        6.2    6.8   0.2    2.1  2  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
       0.11   12.6   0.0       0.35   10.9   0.0    1.8  1  RB_B             Retinoblastoma-associated protein B domain
       0.11   12.1   0.2       0.28   10.7   0.2    1.6  1  GerE             Bacterial regulatory proteins, luxR family
       0.11   12.6   0.1       0.25   11.5   0.1    1.5  1  DUF2318          Predicted membrane protein (DUF2318)
       0.12   12.7   1.3       0.28   11.5   1.3    1.6  1  Prim_Zn_Ribbon   Zinc-binding domain of primase-helicase
        0.3   10.8   1.1        1.8    8.3   0.2    2.3  2  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
       0.57   10.8   2.7         13    6.5   0.5    2.7  2  Trm112p          Trm112p-like protein
       0.77    9.9   2.6        2.9    8.1   0.3    2.3  2  Zn-ribbon_8      Zinc ribbon domain
        3.1    7.6   4.8         19    5.1   4.8    2.1  1  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
          9    6.1   8.1        5.6    6.7   0.3    2.7  2  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit


Domain annotation for each model (and alignments):
>> TFIIB  Transcription factor TFIIB repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.1   0.1   1.2e-19   7.5e-17       2      62 ..     144     204 ..     143     213 .. 0.93
   2 !   56.0   0.4   4.8e-18     3e-15       2      71 .]     238     307 ..     237     307 .. 0.95

  Alignments for each domain:
  == domain 1  score: 61.1 bits;  conditional E-value: 1.2e-19
                                    HHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHH CS
                          TFIIB   2 krfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeiss 62 
                                    +r+ ++l+Lp+ V d+A  ++k al+ +++ Grs ++++AA++y Acr  ++ rt+ ei+ 
  gi|119719600|ref|YP_920095.1| 144 ERLGAQLGLPKAVLDRALDIYKSALDSNLVRGRSIESVMAAAVYAACREMRLPRTLDEIAL 204
                                    578899*****************************************************85 PP

  == domain 2  score: 56.0 bits;  conditional E-value: 4.8e-18
                                    HHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                          TFIIB   2 krfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                    +r+ + l L+    ++A e++++a + ++++G+ pag+aAA++yiA++++++ rtqke++  ++V+e+t+
  gi|119719600|ref|YP_920095.1| 238 PRIGSLLRLSGATIKRAMEIIDQARNAGLTAGKDPAGLAAAAIYIAALQNGEMRTQKEVARAAKVTEVTV 307
                                    67777889999999******************************************************97 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.0   0.2     9e-20   5.5e-17       2      43 .]      28      69 ..      27      69 .. 0.98

  Alignments for each domain:
  == domain 1  score: 61.0 bits;  conditional E-value: 9e-20
                                   EETTTTCEECHEETSTTCEEESSSSBEEEECCCCCCCHHHHH CS
                   TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGlVlednsidegpewref 43
                                   +CPnCgst+l++D+ rge++C +CG+V+ ++ id g ewr+f
  gi|119719600|ref|YP_920095.1| 28 RCPNCGSTRLIYDATRGEIICANCGYVMSEREIDQGAEWRAF 69
                                   7***************************************98 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1   2.5e-06    0.0016       8      38 ..      27      57 ..      25      58 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.5e-06
                                   EE-TTTS-EEEEESS-SS-EEESSSTCEEEE CS
                 Ribosomal_S27e  8 vkCpdCenetvvFshaatvvkCisCgkvLve 38
                                    +Cp+C+ +  +++     + C  Cg v+ e
  gi|119719600|ref|YP_920095.1| 27 LRCPNCGSTRLIYDATRGEIICANCGYVMSE 57
                                   79************************99865 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       3.6   2.3e+03      23      34 ..     143     154 ..     142     155 .. 0.86
   2 ?   -2.6   0.0       6.7   4.2e+03      20      27 ..     196     203 ..     196     204 .. 0.88
   3 ?   -2.7   0.1       7.3   4.5e+03      26      40 ..     240     254 ..     239     256 .. 0.82
   4 !   17.4   0.1   3.8e-06    0.0023      18      48 ..     288     318 ..     279     319 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 3.6
                                    HHHHHHHHTS-H CS
                     Sigma70_r4  23 leEIgerlgiSr 34 
                                    le +g++lg+++
  gi|119719600|ref|YP_920095.1| 143 LERLGAQLGLPK 154
                                    7899*****985 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 6.7
                                    T--HHHHH CS
                     Sigma70_r4  20 glTleEIg 27 
                                    ++Tl EI+
  gi|119719600|ref|YP_920095.1| 196 PRTLDEIA 203
                                    68*****8 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 7.3
                                    HHHHHTS-HHHHHHH CS
                     Sigma70_r4  26 IgerlgiSrerVrqi 40 
                                    Ig  l +S  ++++ 
  gi|119719600|ref|YP_920095.1| 240 IGSLLRLSGATIKRA 254
                                    899999999999975 PP

  == domain 4  score: 17.4 bits;  conditional E-value: 3.8e-06
                                    TTT--HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                     Sigma70_r4  18 geglTleEIgerlgiSrerVrqiekrAlrkL 48 
                                    ge +T++E+++   +++ +Vr + k+ ++kL
  gi|119719600|ref|YP_920095.1| 288 GEMRTQKEVARAAKVTEVTVRNRYKELVKKL 318
                                    899*************************998 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   4.4   2.9e-05     0.018       2      25 ..      26      54 ..      25      55 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.9e-05
                    zf-ribbon_3  2 tvrCPnCGa.pl....ssddnvCpyCGtk 25
                                   + rCPnCG+  l    + + ++C++CG++
  gi|119719600|ref|YP_920095.1| 26 ELRCPNCGStRLiydaTRGEIICANCGYV 54
                                   569******865577799*********98 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       4.1   2.5e+03      20      30 ..     143     153 ..     137     159 .. 0.78
   2 ?   -1.3   0.0       3.2     2e+03      22      36 ..     239     253 ..     237     256 .. 0.84
   3 !   17.1   0.1   5.9e-06    0.0036       9      41 ..     282     314 ..     282     315 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 4.1
                  HTH_AsnC-type  20 yaeLAervGlS 30 
                                     ++L++++Gl 
  gi|119719600|ref|YP_920095.1| 143 LERLGAQLGLP 153
                                    67899999995 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 3.2
                  HTH_AsnC-type  22 eLAervGlSestvlr 36 
                                    +++  + lS +t+ r
  gi|119719600|ref|YP_920095.1| 239 RIGSLLRLSGATIKR 253
                                    6899999****9988 PP

  == domain 3  score: 17.1 bits;  conditional E-value: 5.9e-06
                  HTH_AsnC-type   9 LeaLqedaRisyaeLAervGlSestvlrRvrrL 41 
                                    ++aLq    ++ +e+A++  ++e tv++R++ L
  gi|119719600|ref|YP_920095.1| 282 IAALQNGEMRTQKEVARAAKVTEVTVRNRYKEL 314
                                    689***************************988 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0         3   1.9e+03      17      28 ..     183     197 ..     182     209 .. 0.71
   2 ?   -0.1   0.0      0.98   6.1e+02      30      39 ..     210     219 ..     203     219 .. 0.86
   3 ?   -2.5   0.0       5.7   3.5e+03      36      48 ..     243     255 ..     240     256 .. 0.81
   4 !   12.9   0.1   8.8e-05     0.054      25      52 .]     288     315 ..     276     315 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 3
                   HTH_Tnp_ISL3  17 eayilellles...r 28 
                                    +a+++++++e+   r
  gi|119719600|ref|YP_920095.1| 183 AAAVYAACREMrlpR 197
                                    688999999996334 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.98
                   HTH_Tnp_ISL3  30 vkavArqlgv 39 
                                    +k+vAr++++
  gi|119719600|ref|YP_920095.1| 210 RKDVARCYRL 219
                                    69*****996 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 5.7
                   HTH_Tnp_ISL3  36 qlgvSwtTVwril 48 
                                    +l++S  T++r++
  gi|119719600|ref|YP_920095.1| 243 LLRLSGATIKRAM 255
                                    6899999999987 PP

  == domain 4  score: 12.9 bits;  conditional E-value: 8.8e-05
                   HTH_Tnp_ISL3  25 lesrsvkavArqlgvSwtTVwrildryv 52 
                                     e+r+ k+vAr   v++ TV+++++++v
  gi|119719600|ref|YP_920095.1| 288 GEMRTQKEVARAAKVTEVTVRNRYKELV 315
                                    467********************99876 PP

>> Cyclin_C  Cyclin, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   0.00076      0.47      45      89 ..     180     223 ..     166     233 .. 0.84
   2 ?    4.8   0.0     0.047        29      44      90 ..     272     318 ..     267     327 .] 0.85

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00076
                                    HHHHHHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHHHHHHHH CS
                       Cyclin_C  45 SliAaaalllarstlnspewtetlehytgyskedlkpcvelilel 89 
                                    S++Aaa+++++r + + p   +++  yt++  +d+  c++l+l  
  gi|119719600|ref|YP_920095.1| 180 SVMAAAVYAACREM-RLPRTLDEIALYTRAGRKDVARCYRLLLRE 223
                                    77887777777777.999999********************9865 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.047
                                    HHHHHHHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHHHHHHHHH CS
                       Cyclin_C  44 pSliAaaalllarstlnspewtetlehytgyskedlkpcvelilell 90 
                                    p  +Aaaa+++a  + +++  ++++    ++++  +++ ++ +++ l
  gi|119719600|ref|YP_920095.1| 272 PAGLAAAAIYIAALQNGEMRTQKEVARAAKVTEVTVRNRYKELVKKL 318
                                    6679********99989999999999999999999999999988765 PP

>> DUF2752  Protein of unknown function (DUF2752)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.6   1.2e-05    0.0076       9      29 ..      27      47 ..      26      53 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.2e-05
                        DUF2752  9 ipCPGCGltRavhallhgdfa 29
                                   + CP CG+tR +++ ++g++ 
  gi|119719600|ref|YP_920095.1| 27 LRCPNCGSTRLIYDATRGEII 47
                                   67****************986 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.6   2.5e-05     0.016      18      40 .]      29      52 ..      26      52 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.5e-05
                  Auto_anti-p27 18 CpvC.gvPLmrdrkggkvyCvaCd 40
                                   Cp+C ++ L  d ++g+++C++C+
  gi|119719600|ref|YP_920095.1| 29 CPNCgSTRLIYDATRGEIICANCG 52
                                   ****99*****9999********6 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.5   5.1e-05     0.031      19      45 ..      27      53 ..      23      54 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.1e-05
                  Zn_Tnp_IS1595 19 fvCPhCgsrkayriktrglfqCkeCrk 45
                                    +CP+Cgs++++  +trg   C+ C++
  gi|119719600|ref|YP_920095.1| 27 LRCPNCGSTRLIYDATRGEIICANCGY 53
                                   57*******66666667********97 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.2   5.1e-05     0.032       5      37 ..      28      56 ..      24      78 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.1e-05
                Lar_restr_allev  5 pCPfCggravlersqrvvaeigqcvyCadCga..s 37
                                    CP Cg+   +  ++r+       ++Ca+Cg+  s
  gi|119719600|ref|YP_920095.1| 28 RCPNCGSTRLIYDATRGE------IICANCGYvmS 56
                                   6*************9995......9*******431 PP

>> Zn_Tnp_IS91  Transposase zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   7.2e-05     0.044      39      74 ..      26      62 ..      19      68 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.2e-05
                    Zn_Tnp_IS91 39 ryeCeeCghekivyfsCksrh.CpsCqkkateewlek 74
                                   +++C++Cg+++++y   +    C +C+   +e+ +++
  gi|119719600|ref|YP_920095.1| 26 ELRCPNCGSTRLIYDATRGEIiCANCGYVMSEREIDQ 62
                                   789***************9999*****9999987765 PP

>> Cyclin_N  Cyclin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.2    0.0026       1.6      37     116 ..     142     218 ..     111     228 .. 0.79
   2 ?    3.8   0.0     0.075        46      34     101 ..     233     299 ..     230     322 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0026
                                    HHHHHHHHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHHHHHSSS---HHHHHHHTTTSS-HHHHHHHHH CS
                       Cyclin_N  37 wlvevaekfkltpetlflavnyldRflskksvpkdklqlvgatcLllAaKveeisppkledlvyitdeafteeeilemEr 116
                                     l ++ +++ l + +l  a++++   l ++ v+ + ++ v+a++++ A++  +  p +l++++ +t     ++++ +  r
  gi|119719600|ref|YP_920095.1| 142 ELERLGAQLGLPKAVLDRALDIYKSALDSNLVRGRSIESVMAAAVYAACREMRL-PRTLDEIALYTR--AGRKDVARCYR 218
                                    37788999999999***********************************98776.9999***99985..44555555555 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.075
                                    HHHHHHHHHHHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHHHHHSSS---HHHHHHH CS
                       Cyclin_N  34 lidwlvevaekfkltpetlflavnyldRflskksvpkdklqlvgatcLllAaKveeisppkledlvyi 101
                                    ++d++ ++ + ++l+  t+  a++++d+      +  ++   ++a+++++Aa   + ++ + ++++ +
  gi|119719600|ref|YP_920095.1| 233 AADFVPRIGSLLRLSGATIKRAMEIIDQARNAGLTAGKDPAGLAAAAIYIAALQ-NGEMRTQKEVARA 299
                                    6788888999999999**************99999999*************944.3334455555544 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.9   0.00013     0.082       6      30 ..      29      54 ..      25      55 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00013
                  A2L_zn_ribbon  6 CsvCggngiln.seqgylvCieCgas 30
                                   C +Cg+  +++ +++g+ +C +Cg++
  gi|119719600|ref|YP_920095.1| 29 CPNCGSTRLIYdATRGEIICANCGYV 54
                                   999*********************97 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   0.00014     0.084      14      40 ..      28      57 ..      16      60 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00014
                            DZR 14 fCseCgtk.lkavaa...edrCpsCgekvdp 40
                                    C++Cg++ l  + a   e+ C +Cg+ +++
  gi|119719600|ref|YP_920095.1| 28 RCPNCGSTrLI-YDAtrgEIICANCGYVMSE 57
                                   69999988644.4444679999999998775 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.5   0.00028      0.17      28      54 .]     292     318 ..     289     318 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00028
                                    -HHHHHHHHT--HHHHHHHHHHHHHHH CS
                   Sigma70_r4_2  28 sykEIAellgisegtVksrlsRArkkL 54 
                                    ++kE+A+  +++e+tV++r++   kkL
  gi|119719600|ref|YP_920095.1| 292 TQKEVARAAKVTEVTVRNRYKELVKKL 318
                                    79******************9888887 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.2    0.0072       4.4      22      33 ..      23      34 ..      21      36 .. 0.79
   2 ?   11.3   1.0   0.00041      0.25       3      34 ..      27      54 ..      26      56 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0072
                  zinc_ribbon_4 22 kgvkvrCskCgh 33
                                   + +++rC++Cg 
  gi|119719600|ref|YP_920095.1| 23 EERELRCPNCGS 34
                                   568999999985 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00041
                  zinc_ribbon_4  3 itCpsCkakyeiddeklpakgvkvrCskCghv 34
                                    +Cp+C++++ i d    a+++++ C++Cg v
  gi|119719600|ref|YP_920095.1| 27 LRCPNCGSTRLIYD----ATRGEIICANCGYV 54
                                   59************....6999*******988 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1    0.0077       4.8       1       7 [.      28      34 ..      24      37 .. 0.78
   2 ?    3.9   0.1     0.075        46      16      21 ..      48      53 ..      43      59 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0077
                  zinc_ribbon_2  1 fCpnCGa 7 
                                   +CpnCG 
  gi|119719600|ref|YP_920095.1| 28 RCPNCGS 34
                                   5777775 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.075
                  zinc_ribbon_2 16 CpyCGt 21
                                   C +CG+
  gi|119719600|ref|YP_920095.1| 48 CANCGY 53
                                   666665 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.2    0.0099       6.2      40      55 ..      19      35 ..      10      43 .. 0.80
   2 ?    4.3   0.1     0.063        39      30      41 ..      47      60 ..      45      77 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0099
                 OrfB_Zn_ribbon 40 e.alsgrtfkCpnCgfe 55
                                   e + ++r+++CpnCg +
  gi|119719600|ref|YP_920095.1| 19 EdSEEERELRCPNCGST 35
                                   257799********975 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.063
                 OrfB_Zn_ribbon 30 tCseCgsknke..a 41
                                    C++Cg++++e   
  gi|119719600|ref|YP_920095.1| 47 ICANCGYVMSEreI 60
                                   699****9999543 PP

>> RB_B  Retinoblastoma-associated protein B domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00056      0.35      10      87 ..     136     211 ..     129     228 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00056
                           RB_B  10 yklaavrlrdLcerLklsselrekiwtlfehvlveetellkdRhlDqillcavYvvakvtkeelsFkeiikaYrkqpq 87 
                                    +  a++ l++L ++L l + + +++  + + +l   ++l++ R ++ ++ +avY+ ++  +  +++ ei    r   +
  gi|119719600|ref|YP_920095.1| 136 LAQAVIELERLGAQLGLPKAVLDRALDIYKSALD--SNLVRGRSIESVMAAAVYAACREMRLPRTLDEIALYTRAGRK 211
                                    6678899999999999999999999999999885..68********************99999999999765454444 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.2   0.00046      0.28      19      48 ..     292     321 ..     285     322 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00046
                                    -HHHHHHHHTS-HHHHHHHHHHHHHHHT-S CS
                           GerE  19 snkeIAeelniSekTVkvhksnimkKLnvk 48 
                                    + ke+A++  + e TV++  +++ kKL++k
  gi|119719600|ref|YP_920095.1| 292 TQKEVARAAKVTEVTVRNRYKELVKKLDIK 321
                                    679************************975 PP

>> DUF2318  Predicted membrane protein (DUF2318)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00041      0.25      37      68 ..      29      62 ..      21      71 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00041
                        DUF2318 37 CevC..ekkgYvqegeelvCknCgvrfaldsige 68
                                   C  C   +  Y  +  e++C nCg +++  +i++
  gi|119719600|ref|YP_920095.1| 29 CPNCgsTRLIYDATRGEIICANCGYVMSEREIDQ 62
                                   899943344588999*************999984 PP

>> Prim_Zn_Ribbon  Zinc-binding domain of primase-helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.3   0.00045      0.28       2      33 ..      25      52 ..      24      58 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00045
                                   EEE--TTTT-TTTEEETT....S-EEETTTTB CS
                 Prim_Zn_Ribbon  2 khspCPvCGGrDrFrfddkdgrGtwfCrqCgg 33
                                   ++  CP+CG+ +r  +d    rG  +C  C g
  gi|119719600|ref|YP_920095.1| 25 RELRCPNCGS-TRLIYDA--TRGEIICANC-G 52
                                   7888****86.7877777..789*******.4 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.2     0.003       1.8      16      29 ..      21      34 ..      19      35 .. 0.85
   2 ?    0.8   0.1      0.65     4e+02      24      29 ..      48      53 ..      46      55 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.003
                  zf-NADH-PPase 16 aeggwarvCpaCgl 29
                                   +e ++ ++Cp+Cg 
  gi|119719600|ref|YP_920095.1| 21 SEEERELRCPNCGS 34
                                   578999******95 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.65
                  zf-NADH-PPase 24 CpaCgl 29
                                   C++Cg+
  gi|119719600|ref|YP_920095.1| 48 CANCGY 53
                                   777776 PP

>> Trm112p  Trm112p-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.5      0.02        13      46      61 ..      19      34 ..       3      40 .. 0.72
   2 ?    3.9   0.1      0.14        84      47      60 ..      39      52 ..      34      54 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.02
                                   TEECCCCEEEETTTTE CS
                        Trm112p 46 eldieegeLvCpncgr 61
                                   e ++ee eL Cpncg 
  gi|119719600|ref|YP_920095.1| 19 EDSEEERELRCPNCGS 34
                                   468899********84 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.14
                                   EECCCCEEEETTTT CS
                        Trm112p 47 ldieegeLvCpncg 60
                                   +d ++ge++C ncg
  gi|119719600|ref|YP_920095.1| 39 YDATRGEIICANCG 52
                                   78899********9 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.3    0.0047       2.9      23      35 ..      23      36 ..      12      38 .. 0.70
   2 ?    1.3   0.1      0.61   3.8e+02       8      16 ..      48      56 ..      38      65 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0047
                    Zn-ribbon_8 23 dapltaCPeCgs.e 35
                                   ++ +  CP+Cgs +
  gi|119719600|ref|YP_920095.1| 23 EERELRCPNCGStR 36
                                   444556*****944 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.61
                    Zn-ribbon_8  8 CeeCghefe 16
                                   C +Cg +  
  gi|119719600|ref|YP_920095.1| 48 CANCGYVMS 56
                                   888886654 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   4.8      0.03        19       1      14 [.      23      36 ..      23      52 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.03
                        zf-RRN7  1 wekgppCgvCgcrs 14
                                   +e++ +C+ Cg+++
  gi|119719600|ref|YP_920095.1| 23 EERELRCPNCGSTR 36
                                   57999*******76 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.3    0.0091       5.6      17      29 ..      26      39 ..      19      41 .. 0.76
   2 ?    3.4   0.5       0.1        63      18      25 ..      46      53 ..      42      56 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0091
                                   ----SSS--.---B CS
                 DNA_RNApol_7kD 17 piRCkeCGh.RilY 29
                                    +RC +CG+ R++Y
  gi|119719600|ref|YP_920095.1| 26 ELRCPNCGStRLIY 39
                                   58******646655 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.1
                                   ---SSS-- CS
                 DNA_RNApol_7kD 18 iRCkeCGh 25
                                   i C +CG+
  gi|119719600|ref|YP_920095.1| 46 IICANCGY 53
                                   78999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       930  (0.0518713); expected 358.6 (0.02)
Passed bias filter:                      697  (0.0388756); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); expected 17.9 (0.001)
Passed Fwd filter:                        29  (0.00161749); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              29  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2052.56
//
Query:       gi|119719601|ref|YP_920096.1|  [L=133]
Description: PilT domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-18   66.3   0.6    3.8e-18   65.9   0.6    1.2  1  PIN_9     PIN like domain
    4.4e-06   27.0   0.4    7.9e-05   23.0   0.4    2.0  1  PIN_4     PIN domain
     0.0017   18.7   0.0     0.0027   18.0   0.0    1.3  1  Fcf1      Fcf1
     0.0022   18.5   0.5     0.0079   16.7   0.5    1.8  1  PIN       PIN domain
  ------ inclusion threshold ------
      0.078   12.7   0.0       0.13   12.0   0.0    1.5  1  DUF5615   Domain of unknown function (DUF5615)


Domain annotation for each model (and alignments):
>> PIN_9  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.9   0.6   1.1e-21   3.8e-18       1     115 [.       5     127 ..       5     128 .. 0.85

  Alignments for each domain:
  == domain 1  score: 65.9 bits;  conditional E-value: 1.1e-21
                          PIN_9   1 vilDtnaLmipvqfgvdifeelerllgsvelvvpkavleELerlakagkgkertaakvalsLaerc........eiveae 72 
                                    v++Dt+++m  ++ g+d+++ l +  +  ++vvp+avl+EL++l+ + +g++++ ak+al+L e++        e+++ e
  gi|119719601|ref|YP_920096.1|   5 VLVDTSVFMYLAEKGLDLLDVLFEREDVCRVVVPSAVLSELKHLSLSSRGAKARRAKLALKLLEEVlkrhpklfEVLDCE 84 
                                    799*****************997776889********************************9765312222112444555 PP

                          PIN_9  73 .eekaDdailelakeldaavlvTnDreLkkrllekgipvilLRq 115
                                     ++++D  +++la + +  +l+T Dr+Lkk +l++g++v++LR 
  gi|119719601|ref|YP_920096.1|  85 vGKDVDKSLVNLAFKEG-YILATADRNLKKNALQAGVEVLFLRR 127
                                    7788**********999.5666*********************6 PP

>> PIN_4  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.4   2.2e-08   7.9e-05       3     126 ..       7     121 ..       5     125 .. 0.71

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 2.2e-08
                          PIN_4   3 lDTnvlLhdpealksf.......keehdvviPitVleELdklKkgsserelarlarqanrlldellekesgrlkvqtsae 75 
                                    +DT+v+++  e    +       ++  +vv+P  Vl+EL +l  +s+    ar+a+ a++ll+e+l++ +++l ++ ++ 
  gi|119719601|ref|YP_920096.1|   7 VDTSVFMYLAEKGLDLldvlferEDVCRVVVPSAVLSELKHLSLSSR-GAKARRAKLALKLLEEVLKR-HPKL-FEVLDC 83 
                                    6777777655433333455565588889***************9999.78888889999999988875.6676.344443 PP

                          PIN_4  76 elpeeeseseknDnrIlavalelkeekpdrkvvLvskDinlrikAkalgie 126
                                    e+ +        D++ ++ a  +ke +     +L + D+nl+  A + g+e
  gi|119719601|ref|YP_920096.1|  84 EVGK------DVDKSLVNLA--FKEGY-----ILATADRNLKKNALQAGVE 121
                                    3433......5788877755..45554.....8888888888888888887 PP

>> Fcf1  Fcf1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   7.6e-07    0.0027       7      92 ..      33     127 ..      30     132 .. 0.64

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 7.6e-07
                                    EEEEEEHHHHHHHHHCT.................-HHHHHHHTT.SEEE----SS---HHHHHHHHH-BTB-TT-EEEE- CS
                           Fcf1   7 vkpliTqCviaeleklg.....kk..........lkealkiakt.ferlkCnhkkptsaddClvsvvkkkknkkryivAt 70 
                                    + +++ + v++el++l+     +k          l+e+lk   + fe+l C+   +++ d+ lv++      k+ yi+At
  gi|119719601|ref|YP_920096.1|  33 CRVVVPSAVLSELKHLSlssrgAKarraklalklLEEVLKRHPKlFEVLDCEV--GKDVDKSLVNLAF----KEGYILAT 106
                                    67778888888888888654442234444444443333333222377777776..6677777777766....79****** PP

                                    S-HHHHHHHHTSTT--EEEEE- CS
                           Fcf1  71 qDkdlrrrlrkipgvPilyikr 92 
                                     D++l++++ +  gv +l+++r
  gi|119719601|ref|YP_920096.1| 107 ADRNLKKNALQ-AGVEVLFLRR 127
                                    ******98765.4666666666 PP

>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.5   2.2e-06    0.0079       1      66 [.       5      68 ..       5     116 .. 0.62

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.2e-06
                                   EEE-HHHHHHHH.TTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHH CS
                            PIN  1 ivlDTsvliall.rgeekaeaarklleeleelvtsalvlaEllyvlarrkskrekaaelvellllls 66
                                   +++DTsv+ +l  +g +  +  +   e++ ++v++++vl+El +   +  s+  ka++ +++l ll+
  gi|119719601|ref|YP_920096.1|  5 VLVDTSVFMYLAeKGLDLLDV-LFEREDVCRVVVPSAVLSELKHLSLS--SRGAKARRAKLALKLLE 68
                                   68**********666666655.4445556***************9999..33333333333333332 PP

>> DUF5615  Domain of unknown function (DUF5615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   3.7e-05      0.13      11      64 ..      64     117 ..      60     128 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.7e-05
                        DUF5615  11 prlvellreaghdvlhvrelglegasDeeileyAkeedriivTkDkDFgellll 64 
                                     +l e++ ++ ++   v +++  +  D+  +++A +e++i+ T+D+   + +l+
  gi|119719601|ref|YP_920096.1|  64 LKLLEEVLKRHPKLFEVLDCEVGKDVDKSLVNLAFKEGYILATADRNLKKNALQ 117
                                    56667777777888888888888899*******************987766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 895.26
//
Query:       gi|119719602|ref|YP_920097.1|  [L=452]
Description: hypothetical protein Tpen_0692 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00036   20.2   0.0     0.0019   17.8   0.0    2.0  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
  ------ inclusion threshold ------
       0.01   15.5   0.0       0.02   14.6   0.0    1.4  1  Thymidylate_kin  Thymidylate kinase
      0.023   14.8   0.1        3.3    7.8   0.0    3.1  3  SKI              Shikimate kinase
      0.033   13.5   0.0      0.065   12.5   0.0    1.4  1  Zeta_toxin       Zeta toxin
      0.039   13.4   0.0      0.064   12.7   0.0    1.3  1  ParA             NUBPL iron-transfer P-loop NTPase
      0.042   13.6   0.0       0.14   11.8   0.0    1.9  2  PRK              Phosphoribulokinase / Uridine kinase family
      0.051   13.6   0.0       0.16   12.0   0.0    1.9  2  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai


Domain annotation for each model (and alignments):
>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.29   7.4e+02       5      21 ..     130     146 ..     125     159 .. 0.70
   2 !   17.8   0.0   7.5e-07    0.0019     112     176 ..     239     300 ..     226     301 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.29
                                    EEESTTCCHHHHHHHHH CS
                           cobW   5 ltGflGsGKTtLlnhll 21 
                                     ++  G+GK+t+ +++ 
  gi|119719602|ref|YP_920097.1| 130 TASRTGAGKSTVSRRVA 146
                                    45678******987776 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 7.5e-07
                                    ECEEEEEEETTTH.CCHCCHHHHH..HHHHHTSSEEEEE-HHHHCHC..HHHHHHHHHHHHTTS-EE CS
                           cobW 112 ldavvavvDaknleaeeekieeka..edqlaaadllvlnKtDlldeeallekleerlrqlnpeakvl 176
                                     d  ++vvD     ++ ++  + +     +  ad++v+nK+++++ e +++ +e+ +r++n++a ++
  gi|119719602|ref|YP_920097.1| 239 PDLYITVVDP----TRPKDVVSSYpgYVNVRLADVIVVNKVNVVSPE-SVDLVEKSVRRINERAVIV 300
                                    6889999999....445555554410567899**************9.56************99776 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   7.7e-06      0.02       6      61 ..     135     188 ..     134     205 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 7.7e-06
                                    TSSHHHHHHHHHHHHHHTTE..EEEESSSTTSHHHHHHHHHHHTCS---HHHHHHHH CS
                Thymidylate_kin   6 GaGKttqaellkerlkeegik.vvltrepggteiGekirelllkeeeleeqteallf 61 
                                    GaGK+t+++ +++ l+e g + vv++++     +G+++++++++   le++   +  
  gi|119719602|ref|YP_920097.1| 135 GAGKSTVSRRVARVLRELGVRfVVVRHPMP---YGDLLKSAVQRFASLEDLERYNCT 188
                                    9********************777777765...999999999976666666655555 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.22   5.6e+02      44      90 ..      82     128 ..      72     133 .. 0.81
   2 ?    7.8   0.0    0.0013       3.3       2      17 ..     135     150 ..     134     157 .. 0.87
   3 ?    2.1   0.0     0.074   1.9e+02      75     107 ..     192     223 ..     187     233 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.22
                                    HHHHHHHHHHHHHHHCCCSSEEEEE-TTGGGSHHHHHHHHHHSEEEE CS
                            SKI  44 eegFrelEsevlkelleeeglViatGGGavlseenrellkekgiviy 90 
                                    e+ F      + +e++e+ g V+a G   vl   + ++++++++vi 
  gi|119719602|ref|YP_920097.1|  82 EKVFLSYSDLTAEEVAEKAGRVVAAGAEFVLPGVYETMISSRKPVIA 128
                                    5666666677788999999********99999999999999998885 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0013
                                    TSSHHHHHHHHHHHHT CS
                            SKI   2 GaGKstvGkllAkklg 17 
                                    GaGKstv +++A+ l+
  gi|119719602|ref|YP_920097.1| 135 GAGKSTVSRRVARVLR 150
                                    9***********9875 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.074
                                    SHHHHHHHHHHSEEEEEE--HHHHHHHHHHTTS CS
                            SKI  75 seenrellkekgiviyLdvsleellerlkadke 107
                                    +ee+  +++ +g v+y  v+ e++l+r +++ +
  gi|119719602|ref|YP_920097.1| 192 REEYEPHIE-SGNVVYAGVDYEAILRRAEEEAD 223
                                    666777777.9****************998876 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.5e-05     0.065      10      41 ..     119     150 ..     115     181 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.5e-05
                     Zeta_toxin  10 ypsqerPklillgGqpGAGKselaellkdele 41 
                                    ++s+++P++ + +  +GAGKs++++ +++ l+
  gi|119719602|ref|YP_920097.1| 119 MISSRKPVIAVTASRTGAGKSTVSRRVARVLR 150
                                    46789*********************999885 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.5e-05     0.064       3      37 ..     124     158 ..     122     164 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.5e-05
                           ParA   3 kkviavlSgKGGVGKStvavnlAlaLakkglkvgl 37 
                                    k viav++++ G GKStv+  +A  L++ g++  +
  gi|119719602|ref|YP_920097.1| 124 KPVIAVTASRTGAGKSTVSRRVARVLRELGVRFVV 158
                                    569*************************9988665 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   5.6e-05      0.14       1      33 [.     126     159 ..     126     196 .. 0.84
   2 ?   -2.0   0.0      0.98   2.5e+03      96     116 ..     303     323 ..     266     324 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.6e-05
                            PRK   1 vIgvags.SGaGkttvarklekifgrekvkaaei 33 
                                    vI+v++s  GaGk+tv+r++  ++++ +v+ +++
  gi|119719602|ref|YP_920097.1| 126 VIAVTASrTGAGKSTVSRRVARVLRELGVRFVVV 159
                                    799998758****************999986665 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.98
                            PRK  96 teeaapdkeeliegadvlviE 116
                                    + e+  dk+eli g+ vlv+E
  gi|119719602|ref|YP_920097.1| 303 KSELYVDKPELIRGKRVLVVE 323
                                    233334677777777777776 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   6.3e-05      0.16       1      33 [.     127     159 ..     127     219 .. 0.95
   2 ?   -3.4   0.0       3.8   9.7e+03      79     100 ..     270     293 ..     252     305 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.3e-05
                                    EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllv 33 
                                    ia+++   G+GK+t++   ar l + g r ++v
  gi|119719602|ref|YP_920097.1| 127 IAVTASRTGAGKSTVSRRVARVLRELGVRFVVV 159
                                    799999*******************99998776 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 3.8
                                    EEEEEES..S...-TTCHHHHHHH CS
                                    xxxxxxx..xxxxxxxxxxxxxxx RF
                           CbiA  79 vvlnrvd..geneetllkealeel 100
                                    +v+n+v+  ++++  l +++++++
  gi|119719602|ref|YP_920097.1| 270 IVVNKVNvvSPESVDLVEKSVRRI 293
                                    677776622334444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (452 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 3089.27
//
Query:       gi|119719603|ref|YP_920098.1|  [L=553]
Description: thermosome [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   1.2e-186  621.2  13.6   1.3e-186  621.0  13.6    1.0  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  621.0  13.6  7.5e-191  1.3e-186       1     490 [.      38     529 ..      38     530 .. 0.98

  Alignments for each domain:
  == domain 1  score: 621.0 bits;  conditional E-value: 7.5e-191
                                    HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHHHHH CS
                     Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleeaekl 80 
                                    +a++vkttlGPkGmdKml++  g+++v+nDGatil e++++hP+akl+ve+a++qd+evGDGTtt+v+L+geLl+eaekl
  gi|119719603|ref|YP_920098.1|  38 VAETVKTTLGPKGMDKMLIDTLGDITVSNDGATILDEMDVQHPIAKLMVEVAKAQDKEVGDGTTTAVVLTGELLKEAEKL 117
                                    689***************************************************************************** PP

                                    HHCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHH.HCHCCCS.. CS
                     Cpn60_TCP1  81 iaagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAv.klieene.. 157
                                    +++++hpt i++gy+ka+eka e+L ++  +i+++ +d+e+L+kva+ts++sk +++ ++++++++v+Av ++ e  +  
  gi|119719603|ref|YP_920098.1| 118 LEKNIHPTIIVSGYKKAAEKAREILASK--AIKVDLNDTETLKKVAATSMRSKAVAALRDYFADIAVKAVkQVAEVVNgk 195
                                    *************************999..7777888*********************************8887777799 PP

                                    EECSCCCEECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCCSCCHHHHHHHHH CS
                     Cpn60_TCP1 158 keldlgrikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvlsdaeeleklekae 237
                                    + +d+++i+++k++gg   d++l+ G+v+dk+v++p mpk+++nak++lld +Le ekte+++++++s+++++ +++++e
  gi|119719603|ref|YP_920098.1| 196 YVVDIDNIQIIKKKGGAFLDTQLIYGIVVDKEVVHPGMPKRVTNAKIALLDAPLEVEKTEIDAEIRISSPDQMHQFLEEE 275
                                    99****************************************************************************** PP

                                    HHHHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGGGGGCGC-EEEEEEEE CS
                     Cpn60_TCP1 238 ekqleellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssledltpeelGtakkvee 317
                                    ek+l++++eki++sg+nvv+cqkgidd+a+ +lak+gila+rrvkk+d+e+la+atGa++++++ed+tpe+lG a+ vee
  gi|119719603|ref|YP_920098.1| 276 EKILRDMVEKIKESGANVVFCQKGIDDVAQYYLAKAGILAVRRVKKSDMEKLARATGARILTRVEDITPEALGRAELVEE 355
                                    ******************************************************************************** PP

                                    CCETTCCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHHHHHHHHHCCCCTSXCC CS
                     Cpn60_TCP1 318 ekigsekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatelelakklkeyaksvsge 397
                                    +k+ +ek++++e+++++k++til+rg  +  +de+er+i+dAl +v+ +++++++vpGGGa+e ela++l++ya +v g+
  gi|119719603|ref|YP_920098.1| 356 RKVADEKMVFVEGCPNPKSVTILVRGGFERAVDEAERSIKDALYAVADVLKHPYIVPGGGAIEAELARELRKYAPEVGGK 435
                                    ******************************************************************************** PP

                                    HHHHHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTX.TTEEEETTTTCEEECCCCTXEEEHHHHHHHHHHHHHH CS
                     Cpn60_TCP1 398 eqlaieafakALevipktLaeNaGldpievlaklraahnkge.kelgidvesgeiidlveagvvDplkvkrqalksAtea 476
                                    eqlaieafa+ALe+ip+tLaeN+Gldpi+++a+lraah+     ++g+dv +g ++d+++ gv++p++vk  a+k+Atea
  gi|119719603|ref|YP_920098.1| 436 EQLAIEAFANALESIPRTLAENSGLDPIDIIADLRAAHEDPSkWSYGVDVVNGGVTDMIALGVFEPATVKDHAIKVATEA 515
                                    **************************************87661469********************************** PP

                                    HHHHHCEEEEEXXX CS
                     Cpn60_TCP1 477 astiLrideiikak 490
                                    a++iLrid+ii+a 
  gi|119719603|ref|YP_920098.1| 516 AAMILRIDDIISAS 529
                                    ***********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (553 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1052  (0.0586759); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.40
# Mc/sec: 4107.91
//
Query:       gi|119719604|ref|YP_920099.1|  [L=196]
Description: dephospho-CoA kinase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.5e-16   59.6   0.0    9.5e-16   58.5   0.0    1.5  2  AAA_18           AAA domain
    1.6e-14   54.5   0.0    2.9e-14   53.6   0.0    1.4  1  AAA_17           AAA domain
    1.5e-06   28.4   0.0    2.7e-06   27.6   0.0    1.4  1  AAA_33           AAA domain
  ------ inclusion threshold ------
      0.021   15.0   0.1      0.038   14.2   0.0    1.5  2  AAA_28           AAA domain
      0.039   13.3   0.2      0.099   12.0   0.1    1.7  2  ATPase           KaiC
       0.07   13.2   0.0       0.14   12.2   0.0    1.5  1  ADK              Adenylate kinase
      0.091   12.2   0.4        4.2    6.7   0.1    2.2  2  KTI12            Chromatin associated protein KTI12
        0.1   11.9   0.4       0.18   11.1   0.2    1.9  2  Zeta_toxin       Zeta toxin
       0.11   11.8   0.5       0.15   11.2   0.5    1.6  1  DUF2075          Uncharacterized conserved protein (DUF2075)
       0.11   12.6   0.0       0.38   10.9   0.0    2.0  2  Sigma54_activ_2  Sigma-54 interaction domain
       0.13   11.3   0.2       0.25   10.4   0.2    1.4  1  T2SSE            Type II/IV secretion system protein
       0.18   12.2   0.3        0.3   11.5   0.3    1.9  1  AAA              ATPase family associated with various cellul
       0.29   11.5   3.9        2.2    8.6   0.1    2.2  2  AAA_16           AAA ATPase domain


Domain annotation for each model (and alignments):
>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.5   0.0   6.9e-19   9.5e-16       1     119 [.      13     138 ..      13     151 .. 0.90
   2 ?   -1.4   0.0       2.4   3.3e+03      30      56 ..     164     188 ..     143     194 .. 0.43

  Alignments for each domain:
  == domain 1  score: 58.5 bits;  conditional E-value: 6.9e-19
                         AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....gvnlrdvakenglllevdpe.aldeskrldedkldklldaleenssaleeg 74 
                                    Il+tG+pG+GKt +++  s++ g+     g+++r++a+e+gl   +    +++ ++r++ ++   + +++e+ +s   ++
  gi|119719604|ref|YP_920099.1|  13 ILVTGMPGAGKTVFSRVASSM-GVpvlsmGDVVRSYAAERGLPMNDASLgKISLELREKFGRAVIAERTFERLAS--IDQ 89 
                                    99******************9.5666999********************99999999999999999999999976..999 PP

                         AAA_18  75 knlvidghlaeleseaakdikk....vvLtaspeelleRlekRgyeeak 119
                                    +++vi+g+++  e  +++++      v ++as ++++eRl+kRg++++ 
  gi|119719604|ref|YP_920099.1|  90 GVVVIEGLRNLEELFYFRERASeaylVAIHASQKTRYERLRKRGRKDDP 138
                                    999****************999**********************88754 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.4
                         AAA_18  30 dvakenglllevdpealdeskrldedk 56 
                                    d+   n+  +e++ e  +e++++ ++ 
  gi|119719604|ref|YP_920099.1| 164 DIMLVNEGKTEEEFE--EECREALQKL 188
                                    333333333333333..3344444333 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.6   0.0   2.1e-17   2.9e-14       1     131 [.      16     138 ..      16     143 .. 0.77

  Alignments for each domain:
  == domain 1  score: 53.6 bits;  conditional E-value: 2.1e-17
                                    EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHH.HHHHHHH...HSSEEEE CS
                         AAA_17   1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemrklpleekkelqkeaa.ekiaeea...kkkgvlv 76 
                                    +G+PG+GK+  + +++  +g+++ls+Gd++r+ a+++gl +++  + k +le ++++ + ++ e+  e+    +++ v++
  gi|119719604|ref|YP_920099.1|  16 TGMPGAGKTVFS-RVASSMGVPVLSMGDVVRSYAAERGLPMNDASLGKISLELREKFGRAVIaERTFERLasiDQGVVVI 94 
                                    7*******9666.**************************99999999999999888866554044433323666677888 PP

                                    EE-SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHHTTST-TS-S CS
                         AAA_17  77 dghprikeqagfldglpkevleelkpdaiilleadpeeilerrlkdrtrgrdddn 131
                                    +g   + e+          + e ++   ++ ++a++++ +er+ k   rgr+dd 
  gi|119719604|ref|YP_920099.1|  95 EGLRNL-EELF-------YFRERASEAYLVAIHASQKTRYERLRK---RGRKDDP 138
                                    887754.3232.......3345666678*********99999866...7888875 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0     2e-09   2.7e-06       1     125 [.      12     138 ..      12     150 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 2e-09
                         AAA_33   1 lvllvGlpGsGKstlaerllkklg......avllssdtlrrrlfgtdqqsktdytrvldrlyq..ilnelarkalsagrn 72 
                                    l+l+ G+pG+GK+ +++ ++   g      + +++s ++ r l  +d    + + ++++++ +  i ++++++ +s  ++
  gi|119719604|ref|YP_920099.1|  12 LILVTGMPGAGKTVFSR-VASSMGvpvlsmGDVVRSYAAERGLPMNDASLGKISLELREKFGRavIAERTFERLASIDQG 90 
                                    799************98.56677855566666677777777777788777777777777755444667888888888888 PP

                         AAA_33  73 vildatnlsrrerarflklarrlgvpvrivvvetdeetlkeRlakRaangddr 125
                                    v++  ++++ +e   f++ a+    +  +v+++++++t  eRl+kR ++ dd+
  gi|119719604|ref|YP_920099.1|  91 VVVIEGLRNLEELFYFRERAS----EAYLVAIHASQKTRYERLRKRGRK-DDP 138
                                    888888888888888888886....889********************6.555 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.7e-05     0.038       2     109 ..      13     126 ..      12     152 .. 0.73
   2 ?   -3.0   0.0       5.5   7.6e+03      95     106 ..     172     183 ..     158     191 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.7e-05
                         AAA_28   2 ivitGgestGKTtlleaLaargypvv..pEaareileekl.akged.alpwv..edllafaervleeql.eeeaaaaank 74 
                                    i +tG +++GKT  ++  +++g+pv+   +++r +  e++    +d  l +   e + +f ++v++e+  e++a+ +++ 
  gi|119719604|ref|YP_920099.1|  13 ILVTGMPGAGKTVFSRVASSMGVPVLsmGDVVRSYAAERGlP-MNDaSLGKIslELREKFGRAVIAERTfERLASIDQGV 91 
                                    899*********999988899***9999**********9952.4330233332356677888888777634444446666 PP

                         AAA_28  75 vlfcDrglldtlaYarayggeaeaelea..aarekry 109
                                    v++     l++l+Y r +  e  a+l+a  a ++ ry
  gi|119719604|ref|YP_920099.1|  92 VVIEGLRNLEELFYFRERASE--AYLVAihASQKTRY 126
                                    666666788888888888776..44444324445555 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 5.5
                         AAA_28  95 eaeaeleaaare 106
                                    ++e+e+e+++re
  gi|119719604|ref|YP_920099.1| 172 KTEEEFEEECRE 183
                                    334444444433 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   7.2e-05     0.099      14      36 ..       5      27 ..       1      30 [. 0.88
   2 ?   -1.8   0.0       1.1   1.6e+03      85      85 ..     162     162 ..     106     192 .. 0.51

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.2e-05
                         ATPase 14 gGipegrvvlitGepGtGKtifa 36
                                    G+ ++  +l+tG pG+GKt+f+
  gi|119719604|ref|YP_920099.1|  5 SGVRSKFLILVTGMPGAGKTVFS 27
                                   58888899**************8 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.1
                         ATPase  85 i 85 
                                    +
  gi|119719604|ref|YP_920099.1| 162 L 162
                                    2 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0    0.0001      0.14       1      36 [.      15      49 ..      15      61 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0001
                                   EEESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            ADK  1 llGaPgaGKGtqaeklvkkyglahlstGdllRaevk 36
                                   + G PgaGK t+ +++++++g++ ls Gd++R+  +
  gi|119719604|ref|YP_920099.1| 15 VTGMPGAGK-TVFSRVASSMGVPVLSMGDVVRSYAA 49
                                   579******.88999*****************8665 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1    0.0031       4.2       3      19 ..      12      28 ..      11      34 .. 0.89
   2 ?    3.5   0.0     0.031        42     100     150 ..      91     139 ..      83     152 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0031
                                   EEEEE--TTSSHHHHHH CS
                          KTI12  3 LvvltGlPssGKstrak 19
                                   L+++tG+P +GK+ +++
  gi|119719604|ref|YP_920099.1| 12 LILVTGMPGAGKTVFSR 28
                                   9***********98875 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.031
                                    EEEEEEE--HHHHHHHHHHTT-S..S-HHHHHHHHHH---TTSS-GGGS-S CS
                          KTI12 100 lcvvyvvapldvlvkwneereekeeyekelldaLiqRyeePdsknrWDsPl 150
                                    ++v+  +++l++l+ ++e  +e+  y  ++  +   Rye   ++ r D Pl
  gi|119719604|ref|YP_920099.1|  91 VVVIEGLRNLEELFYFRERASEA--YLVAIHASQKTRYERLRKRGRKDDPL 139
                                    67777888888889999888888..9999999999***************8 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   0.00013      0.18      14      39 ..       8      32 ..       2     147 .. 0.80
   2 ?   -3.6   0.0       3.9   5.4e+03      71      89 ..     172     190 ..     164     192 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00013
                     Zeta_toxin 14 erPklillgGqpGAGKselaellkde 39
                                   +++ lil+ G pGAGK+  ++ +  +
  gi|119719604|ref|YP_920099.1|  8 RSKFLILVTGMPGAGKTVFSRVAS-S 32
                                   57789***********97766543.3 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 3.9
                     Zeta_toxin  71 kaseltqkdaselvekllq 89 
                                    k+ e ++++++e  +kll+
  gi|119719604|ref|YP_920099.1| 172 KTEEEFEEECREALQKLLA 190
                                    5556677777777777765 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.5   0.00011      0.15       3      17 ..      12      26 ..      10     135 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                        DUF2075  3 vvlVtGvaGtGKtvv 17
                                   ++lVtG +G+GKtv 
  gi|119719604|ref|YP_920099.1| 12 LILVTGMPGAGKTVF 26
                                   79***********95 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00028      0.38      19      62 ..       8      78 ..       4     104 .. 0.66
   2 ?   -2.9   0.0       4.9   6.8e+03      82      97 ..     178     193 ..     163     195 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00028
                                   T-SS-EEEEEETT--HHHHHHCC--TTS-EE--SSTTHHHH-H...........................H CS
                Sigma54_activ_2 19 qsklpvfltGekGsgkelvArlLhknsgpwleifvverlaklp...........................l 62
                                   +sk+ +++tG +G+gk++++r+ ++ + p+l++ +v r+ ++                             
  gi|119719604|ref|YP_920099.1|  8 RSKFLILVTGMPGAGKTVFSRVASSMGVPVLSMGDVVRSYAAErglpmndaslgkislelrekfgraviaE 78
                                   78999********************9999999877766654333333555555555555555555555551 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.9
                                    -HHHHHHHHHHHHHHT CS
                Sigma54_activ_2  82 skaeqkeLlellakae 97 
                                    +++    L++lla+ae
  gi|119719604|ref|YP_920099.1| 178 EEECREALQKLLARAE 193
                                    3333444445554444 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.2   0.00018      0.25     125     149 ..       6      30 ..       2      35 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00018
                          T2SSE 125 avrerglilvsGgTgsGKttllyal 149
                                     vr++ lilv+G  g GKt++  ++
  gi|119719604|ref|YP_920099.1|   6 GVRSKFLILVTGMPGAGKTVFSRVA 30 
                                    5899****************97655 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.3   0.00022       0.3       1      29 [.      13      40 ..      13     195 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00022
                                   EEEESSTTSSHHHHHHHHHHHHTHEEEEE CS
                            AAA  1 vllyGppGtGKTllakavakelgveflei 29
                                   +l++G pG GKT + + va+++gv++l++
  gi|119719604|ref|YP_920099.1| 13 ILVTGMPGAGKTVFSR-VASSMGVPVLSM 40
                                   699*********8765.899999988765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.1    0.0016       2.2      26      40 ..      12      26 ..       4      34 .. 0.86
   2 ?    3.9   0.6     0.047        65      72     130 ..     119     192 ..      72     195 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0016
                         AAA_16 26 lvllsGesGvGKssl 40
                                   l+l++G++G GK+  
  gi|119719604|ref|YP_920099.1| 12 LILVTGMPGAGKTVF 26
                                   69***********75 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.047
                         AAA_16  72 laqalareellrqlldeaesaeleawrekleeala................avpelagaea..srllellkrllall 130
                                     a++ +r e lr+ +++   +++  w e+le+ l+                 v+e + +e+  +  +e+l++lla++
  gi|119719604|ref|YP_920099.1| 119 HASQKTRYERLRKRGRK---DDPLKWEEFLERDLRelsvglgsvialadimLVNEGKTEEEfeEECREALQKLLARA 192
                                    33333455666666666...555555555555555555888877777766633333333335577777777777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       700  (0.0390429); expected 358.6 (0.02)
Passed bias filter:                      592  (0.0330191); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 1282.15
//
Query:       gi|119719605|ref|YP_920100.1|  [L=154]
Description: hypothetical protein Tpen_0695 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.3e-16   59.6   0.0    3.9e-16   59.4   0.0    1.1  1  RNA_binding  RNA binding


Domain annotation for each model (and alignments):
>> RNA_binding  RNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.4   0.0   2.2e-20   3.9e-16       1     118 [.       2     117 ..       2     118 .. 0.84

  Alignments for each domain:
  == domain 1  score: 59.4 bits;  conditional E-value: 2.2e-20
                                    EEEEEEEE-TTC-HHHHHHHHHTTSTTSE---EEEEEE-CCC-EEEEEEEEESSHHHHHHHHHHHHHHCCCCH.....HH CS
                    RNA_binding   1 kievrafvhaTEdeekVlealsnllpeeeveieeeeaeGhygnpitileaelekkkakkvlkkllellreeei.....ke 75 
                                    k+ vra +++TE  ekVl+++ nl++  +   e+  + G  + + +++e+ +++   +k l+k+++llr+++i     ++
  gi|119719605|ref|YP_920100.1|   2 KVVVRAPFYPTESLEKVLSSIFNLFDAPK---ESCAVVG--EGKGRYIECVFHN---HKPLEKFRRLLRQQRIldaarSY 73 
                                    589***********************885...2333333..55789********...****************6555555 PP

                                    HHHCCHCCB-TTSEEEEEEEHHHHHTT---BESSSS......EEEEEEE CS
                    RNA_binding  76 LlkeleervdekgklylrldKQaaylgklslvegdd......vIkvkik 118
                                    ++++l      +g++ + l+KQaa++gk+s+++ +       +I v+i+
  gi|119719605|ref|YP_920100.1|  74 VERGLR-----EGEVKFYLNKQAAFAGKVSFCTYEAgesplgSIIVVIE 117
                                    555555.....5********************99988889998888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1144.48
//
Query:       gi|119719606|ref|YP_920101.1|  [L=316]
Description: ribonuclease Z [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.8e-15   54.9   0.0    5.8e-07   29.2   0.0    2.1  2  Lactamase_B_2  Beta-lactamase superfamily domain
    7.5e-07   29.3   0.0    1.2e-06   28.7   0.0    1.4  1  Lactamase_B    Metallo-beta-lactamase superfamily
     0.0018   17.9   0.0     0.0033   17.1   0.0    1.4  1  Lactamase_B_4  tRNase Z endonuclease


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   4.6e-09   2.7e-05      33     130 ..      60     149 ..      39     157 .. 0.82
   2 !   29.2   0.0   9.7e-11   5.8e-07     133     201 .]     199     267 ..     174     267 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 4.6e-09
                                    EEE-SS--HHHHGGGGCCCC.....C--EEEEEEEEHHHHHHCCTTCGHHHCHTTTTEEEEEE-.TTSEEEECSTTEEEE CS
                  Lactamase_B_2  33 aVllthaHyDHlaglltlre.....lrpkklplyapkgvlavleanfvylaleeepavnvheld.wgesfelgdggleit 106
                                     +++th H DH+ gl  l e     +r++ l +y+p+g+++v++ +     +    +v+++el  w++ +++ +  l++ 
  gi|119719606|ref|YP_920101.1|  60 YIFVTHLHSDHYSGLIPLLEtlsllGRERALSVYGPPGLGSVVTGRR----TTGY-PVSLTELYgWEGILRFPGLPLTVS 134
                                    69*********************9888888**************993....2333.578888875888889977889999 PP

                                    EEEE-EE--CTCCE-TTTSEEEEE CS
                  Lactamase_B_2 107 atparhksgrrldrnagdtlGlri 130
                                     ++a+h+ g          l+++i
  gi|119719606|ref|YP_920101.1| 135 YVAAPHSYGA---------LSYII 149
                                    9999999887.........55555 PP

  == domain 2  score: 29.2 bits;  conditional E-value: 9.7e-11
                                    TTEEEEEESS-S---HHHHHHHCT-SEEEEE-S-SSTTHHHH.HHT---STSHHHHCTTSSSSEEEEESB CS
                  Lactamase_B_2 133 ggkrvyyigDtgyipeeigerlggadllllditayeddemir.hmgHltpeeaveaaadlgakrlvliHi 201
                                     g ++ y+gD+   + + + +    d+l++d t+++ d++++  m H+t+e+av+++++++ + lvl+H+
  gi|119719606|ref|YP_920101.1| 199 RGVKISYTGDSLPSH-RFASKAMESDVLIHDSTLLKRDWYRKpYMAHSTVEDAVAVFKATRSRLLVLTHF 267
                                    478999999998655.55666667***************999***************************7 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0     2e-10   1.2e-06       8      78 ..      26      91 ..      23     158 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 2e-10
                                   EEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHH CS
                    Lactamase_B  8 syliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaee 78
                                   ++ +   ++v+L D G   ++a++       +l+ + + ++++THlH+DH++gl  l e+     ++ a+ 
  gi|119719606|ref|YP_920101.1| 26 CIAVKMADTVFLLDVGERCQKALEC-----FHLGVNSPLYIFVTHLHSDHYSGLIPLLETLSLLGRERALS 91
                                   667777899***************8.....9***********************99999876666555555 PP

>> Lactamase_B_4  tRNase Z endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   5.5e-07    0.0033       7      63 .]      18      73 ..      14      73 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5.5e-07
                  Lactamase_B_4  7 tsDtsg.PlllLqldskrYlfGkvgEgtQRavneqkvrlsklesiFLtgkvswssigG 63
                                   t+ +++ P++++++ +  +l+ +vgE +Q+a+   ++ ++    iF+t+ + ++++ G
  gi|119719606|ref|YP_920101.1| 18 TPKSAEqPCIAVKMADTVFLL-DVGERCQKALECFHLGVNSPLYIFVTHLH-SDHYSG 73
                                   6777788**************.*****************9999*****999.777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2465.72
//
Query:       gi|119719607|ref|YP_920102.1|  [L=68]
Description: hypothetical protein Tpen_0697 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       788  (0.0439511); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 497.03
//
Query:       gi|119719608|ref|YP_920103.1|  [L=475]
Description: hypothetical protein Tpen_0698 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 3314.42
//
Query:       gi|119719609|ref|YP_920104.1|  [L=349]
Description: hypothetical protein Tpen_0699 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-92  311.0   7.5    1.3e-92  310.8   7.5    1.0  1  DUF373        Domain of unknown function (DUF373)
  ------ inclusion threshold ------
       0.11   12.3   0.0       0.14   11.9   0.0    1.1  1  RFX5_DNA_bdg  RFX5 DNA-binding domain
       0.12   11.5   0.0       0.19   10.8   0.0    1.2  1  DUF4043       Protein of unknown function (DUF4043)


Domain annotation for each model (and alignments):
>> DUF373  Domain of unknown function (DUF373)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  310.8   7.5   2.2e-96   1.3e-92       5     334 ..       2     339 ..       1     340 [. 0.93

  Alignments for each domain:
  == domain 1  score: 310.8 bits;  conditional E-value: 2.2e-96
                         DUF373   5 lcvDrDdDlgrkagvktPvvGreavleaavklaladPeDSDvNalfgaikvydeLka.egedvevavvtGdekvgveadr 83 
                                    lcvDrD+D+g+ ++vktP vG+eavl+aav+++la+P+DSD+Na+f+a+++y+eL++ +g+ veva+v+G e++gve+d+
  gi|119719609|ref|YP_920104.1|   2 LCVDRDNDVGTVLNVKTPLVGEEAVLNAAVEYSLARPDDSDSNAMFAAVQTYRELRKtYGDGVEVALVAGLEREGVEGDM 81 
                                    9********************************************************88********************* PP

                         DUF373  84 kiaeqldevlskleadsaivVsDGaeDesvlpiiqsrvkvdsvkrVvVkqsrniEstyyll....kkalkdpelrktiLv 159
                                    ki ++ld+vls+ ++d++++VsDG++De+v p+iqs+++++s++rV+V+q+r++E+t++ll    kka+++++++++ L+
  gi|119719609|ref|YP_920104.1|  82 KILQELDQVLSQGRFDGVVLVSDGPTDEAVAPLIQSKLPIVSIRRVIVQQERGVEETFVLLvnyvKKAFTEENYKRYSLG 161
                                    ******************************************************************************** PP

                         DUF373 160 plGlllliyalllllglpelalaiillllGlylllrGfgldelleelleklkesleegritfvtyvvallllligiisgy 239
                                    + Gl+l+iy+ll+ + lp++++ i++++lG++++++G++l e        ++++++++ itf +++++++l l+++i+g+
  gi|119719609|ref|YP_920104.1| 162 LTGLFLVIYSLLSYF-LPQFVWPILITALGGFMFFKGYDLGE-------YFSSIYKTKPITFASILLSIILSLLALIQGI 233
                                    *************88.9*************************.......7899*************************** PP

                         DUF373 240 islesvss....asvssglltlilafiygavewlalailtaslgkiideylkreekdiarllllpflvlaiglvlygasa 315
                                    +++ ++      +++   ll  +      av++l+l++++ +lg++id++++++ + +++  l++ ++l+++++++++++
  gi|119719609|ref|YP_920104.1| 234 YAVLKTPYidffGAIGRLLLAPVG-AQLLAVDLLVLGAVLPFLGSLIDAAIAGK-ETRYSDALVIAVILMARQLAVETAR 311
                                    **8877664554333333333333.35569*********************776.66677788999************** PP

                         DUF373 316 ylls..........lsilalslvvgivva 334
                                    +l s          +s+++ls vv++vva
  gi|119719609|ref|YP_920104.1| 312 FL-SgggdirgvltWSFVVLSSVVVMVVA 339
                                    **.559******99999999999999987 PP

>> RFX5_DNA_bdg  RFX5 DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.4e-05      0.14      91     187 ..      43     143 ..      33     157 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.4e-05
                   RFX5_DNA_bdg  91 saaavdsaqssRlpretWgsgeesnsaggserpGpvge....aekgtvlaqgqedgavskggrepssrhakeaeDkiplv 166
                                    s a   + q+ R  r t+g g e +++ g er G  g+    +e ++vl+qg+ dg+v   +       a  ++ k+p+v
  gi|119719609|ref|YP_920104.1|  43 SNAMFAAVQTYRELRKTYGDGVEVALVAGLEREGVEGDmkilQELDQVLSQGRFDGVVLVSDGPTDEAVAPLIQSKLPIV 122
                                    4455567789999**********************998444457899**********99887777788899999999999 PP

                   RFX5_DNA_bdg 167 tskvsvikgsrsqkealqlvk 187
                                    + +  +++  r  +e++ l  
  gi|119719609|ref|YP_920104.1| 123 SIRRVIVQQERGVEETFVLLV 143
                                    999999999999999877654 PP

>> DUF4043  Protein of unknown function (DUF4043)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   3.2e-05      0.19       5      38 ..      49      82 ..      46      85 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3.2e-05
                        DUF4043  5 pivrvtdlqkgaGdevtfdLvnklsgepvmgdet 38
                                    ++  ++l k+ Gd v++ Lv  l+ e+v+gd +
  gi|119719609|ref|YP_920104.1| 49 AVQTYRELRKTYGDGVEVALVAGLEREGVEGDMK 82
                                   68999**************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2339.44
//
Query:       gi|119719610|ref|YP_920105.1|  [L=374]
Description: putative RNA methylase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-15   57.1   0.0    1.3e-14   54.3   0.0    2.1  1  UPF0020          Putative RNA methylase family UPF0020
      3e-06   27.0   0.0    5.3e-06   26.2   0.0    1.3  1  Cons_hypoth95    Conserved hypothetical protein 95
    6.9e-06   25.9   0.0    1.4e-05   25.0   0.0    1.4  1  Methyltransf_31  Methyltransferase domain
    1.5e-05   24.7   0.0    2.5e-05   23.9   0.0    1.3  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
    8.7e-05   23.2   0.0     0.0002   22.0   0.0    1.7  1  Methyltransf_25  Methyltransferase domain
    0.00024   21.7   0.0    0.00077   20.1   0.0    1.9  1  Methyltransf_11  Methyltransferase domain
  ------ inclusion threshold ------
      0.021   14.5   0.0      0.068   12.9   0.0    1.7  2  N6_N4_Mtase      DNA methylase


Domain annotation for each model (and alignments):
>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.3   0.0   5.1e-18   1.3e-14       1     167 [.     184     333 ..     184     342 .. 0.87

  Alignments for each domain:
  == domain 1  score: 54.3 bits;  conditional E-value: 5.1e-18
                                    -SSS-SS---SS-HHHHHHHHHHTT--T........TS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHH CS
                        UPF0020   1 RgyRefngpapLketLAaalvrlagwkp........gepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeee 72 
                                    +++R + +p++L + L+  +++la +++        +  +lDP+CG+G++lIEaal+g + +                  
  gi|119719610|ref|YP_920105.1| 184 PERRAYSQPSALTPWLSLTILNLALATQpaggeggfDVAFLDPFCGTGGVLIEAALQGMYSV------------------ 245
                                    578999999**********99998766534443333568***********************.................. PP

                                    HHHH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE----------HHHH.HHHHHHHHHH CS
                        UPF0020  73 araelklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpPYGerlgskkal.ekLYseflre 151
                                            g+D + r v+g+++N++  g+    +++  d +kL+ + + +++ + +pPYG+   ++++   ++ +  lr 
  gi|119719610|ref|YP_920105.1| 246 --------GVDVNYRQVRGSKKNLSVLGLRAVADLVLCDSTKLPFRAEAFNAAAFDPPYGRLAPTHGRDpGEILRGALRN 317
                                    ........************************************77779************9999988888888888899 PP

                                    HHHH-TT..-EEEEEE CS
                        UPF0020 152 lkrvlrgggrlvllts 167
                                    + + ++ +gr+++ +s
  gi|119719610|ref|YP_920105.1| 318 VVESVKPRGRIAFFAS 333
                                    9999999899887654 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   2.1e-09   5.3e-06      43     124 ..     221     297 ..     211     302 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 2.1e-09
                                    -EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEEEE--S CS
                  Cons_hypoth95  43 arvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdivflDPP 122
                                      +LD f+G+G++ +EA+  g+ + v v+ + + v+  k+nl+ l+l++ +a l+  ++ +l+ +   +e f+   +DPP
  gi|119719610|ref|YP_920105.1| 221 VAFLDPFCGTGGVLIEAALQGMYS-VGVDVNYRQVRGSKKNLSVLGLRA-VADLVLCDSTKLPFR---AEAFNAAAFDPP 295
                                    569******************875.679******************997.555554444555444...578********* PP

                                    SS CS
                  Cons_hypoth95 123 ya 124
                                    y 
  gi|119719610|ref|YP_920105.1| 296 YG 297
                                    *7 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   5.3e-09   1.4e-05       5     113 ..     221     334 ..     219     364 .. 0.82

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 5.3e-09
                Methyltransf_31   5 lrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieeleklledekfDlilsnev 83 
                                    + +lD+ CGtG  ++e+a +  ++   vG+D + + ++ +++n++ lgl   + +  +d ++l+  +  e f+    + +
  gi|119719610|ref|YP_920105.1| 221 VAFLDPFCGTGGVLIEAA-L--QGMYSVGVDVNYRQVRGSKKNLSVLGLRaVADLVLCDSTKLP--FRAEAFNAAAFDPP 295
                                    578***************.4..44568***********************7788999*******..99999999888844 PP

                Methyltransf_31  84 l.....naladpdkile....eiervlkpggilliedpr 113
                                           +  dp +il+    ++ + +kp g+++    +
  gi|119719610|ref|YP_920105.1| 296 YgrlapTHGRDPGEILRgalrNVVESVKPRGRIAFFASD 334
                                    466667888899888886666777778999998877766 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   9.6e-09   2.5e-05       4      61 ..     223     280 ..     221     328 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 9.6e-09
                Methyltransf_15   4 ilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfel 61 
                                     lD+f+G+GG  i+ al++   +++++n +++  +++N  v g     +lvl+d ++l
  gi|119719610|ref|YP_920105.1| 223 FLDPFCGTGGVLIEAALQGMYSVGVDVNYRQVRGSKKNLSVLGLRAVADLVLCDSTKL 280
                                    69*****************99*********************************9873 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   7.8e-08    0.0002       2      96 ..     224     325 ..     223     326 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 7.8e-08
                                    EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEE.....EST. CS
                Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvs.....sga. 73 
                                    Ld  cGtG +++++a ++     +gvD++ ++++  +++++  gl   +++v +d ++lpf ++ f++        + a 
  gi|119719610|ref|YP_920105.1| 224 LDPFCGTGGVLIEAALQG--MYSVGVDVNYRQVRGSKKNLSVLGLraVADLVLCDSTKLPFRAEAFNAAAFdppygRLAp 301
                                    8889***********995..999*****************99888878899*********99888887665333223332 PP

                                    GGGSSHHH.HHHHHHHHHHHEEEE CS
                Methyltransf_25  74 lhhlsded.lekalkeiarvLkpg 96 
                                     h  ++ + l+ al+++ + +kp 
  gi|119719610|ref|YP_920105.1| 302 THGRDPGEiLRGALRNVVESVKPR 325
                                    333333331345666666666665 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0     3e-07   0.00077       1      65 [.     224     290 ..     224     330 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 3e-07
                                    EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEE CS
                Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlv 65 
                                    Ld  cGtG ++ + a +g+  vgvD++ ++++ +k++ s  gl    ++v +d +klpf+ + f + 
  gi|119719610|ref|YP_920105.1| 224 LDPFCGTGGVLIEAALQGMYSVGVDVNYRQVRGSKKNLSVLGLraVADLVLCDSTKLPFRAEAFNAA 290
                                    6677*************************************99998899************999775 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.6e-05     0.068     196     227 ..     224     255 ..     213     259 .. 0.91
   2 ?   -1.8   0.0      0.79     2e+03      34      65 ..     310     340 ..     292     367 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.6e-05
                                    EETT-TTTHHHHHHHHTT-EEEEEESSHHHHH CS
                    N6_N4_Mtase 196 lDpFaGSGtTavaakelgrkfiGieieeeyve 227
                                    lDpF+G+G  +++a+ +g  ++G++++ + v+
  gi|119719610|ref|YP_920105.1| 224 LDPFCGTGGVLIEAALQGMYSVGVDVNYRQVR 255
                                    9*************************987776 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.79
                                    HHHHHHHHHHHHEEEEEEEEEEE-CCCHHTHH CS
                    N6_N4_Mtase  34 flekvlkevrrvLkddgsifiniddseikkel 65 
                                     l++ l++v +  k+ g i  + +d+  ++ +
  gi|119719610|ref|YP_920105.1| 310 ILRGALRNVVESVKPRGRIAFFASDMLLQN-V 340
                                    567788889999999999999999988877.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2527.92
//
Query:       gi|119719611|ref|YP_920106.1|  [L=221]
Description: hypothetical protein Tpen_0701 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-06   27.8   1.3    4.5e-06   26.6   1.3    1.5  1  PRC              PRC-barrel domain
    3.4e-05   23.7   3.0    5.7e-05   22.9   3.0    1.4  1  CdvA             CdvA-like coiled-coil domain
  ------ inclusion threshold ------
      0.012   15.6   1.5       0.05   13.6   0.2    2.1  2  GvpG             Gas vesicle protein G
      0.023   14.8   0.2      0.065   13.3   0.2    1.9  1  E2F_TDP          E2F/DP family winged-helix DNA-binding domai
      0.029   14.1   0.0        0.1   12.4   0.0    2.0  1  PolyA_pol_RNAbd  Probable RNA and SrmB- binding site of polym
      0.054   13.4   0.1       0.16   11.8   0.0    1.8  2  OAM_alpha        D-ornithine 4,5-aminomutase alpha-subunit
       0.12   13.1   0.5       0.31   11.8   0.4    1.8  2  RsbRD_N          RsbT co-antagonist protein rsbRD N-terminal 


Domain annotation for each model (and alignments):
>> PRC  PRC-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   1.3   1.8e-09   4.5e-06       6      72 ..      47     107 ..      43     113 .. 0.92

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 1.8e-09
                                    S---TT-EEEETTSSEEEEEEEEEEETTTTEEEEEEEEETTT.....-EEEEEGG.CEECCCTEEEE CS
                            PRC   6 asdliGkeVytedGeklGkVkDvvidekegrvralvvsvggflgigekevliPfdlavkigkdriiv 72 
                                    + +++Gk Vy ++Gek+Gk+  +++ ++e ++  +v+++         ++++P + +++++++rii+
  gi|119719611|ref|YP_920106.1|  47 LEKIVGKVVYRRSGEKVGKIWKIYVSKREKQPIKVVLKTDSN-----GKIVVPPE-RIRVENNRIIL 107
                                    6799***********************************965.....9*******.******99997 PP

>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   3.0   2.2e-08   5.7e-05      37     110 ..     110     184 ..      98     197 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 2.2e-08
                           CdvA  37 kakelkeklkkrlkeledqikslekalanlkisyasGEidEeaYksaieairellesaleekeeikkllekl.sk 110
                                    + +e +  +  rl+++ +++++l   l+ l  + +sGEi+ e+Y+ a++ i++ + +++ e + +  +l+ + ++
  gi|119719611|ref|YP_920106.1| 110 HSQEAILSIIGRLSDIAEELRKLRDELLVLDEKLISGEIPREEYNVARSRIERKKVHLRMEASTLLDALNHMvQS 184
                                    55556666778*********************************************************9999333 PP

>> GvpG  Gas vesicle protein G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   1.9e-05      0.05      28      61 ..     127     160 ..     117     173 .. 0.86
   2 ?    1.1   0.1      0.16   4.1e+02      35      54 ..     173     192 ..     159     209 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.9e-05
                           GvpG  28 ddqenlrkeLaaLqqeLdaGeIdeeeFdrrEeel 61 
                                    ++ ++lr eL+ L+ +L +GeI  ee++   +++
  gi|119719611|ref|YP_920106.1| 127 EELRKLRDELLVLDEKLISGEIPREEYNVARSRI 160
                                    56689**********************9776665 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.16
                           GvpG  35 keLaaLqqeLdaGeIdeeeF 54 
                                    + L aL+   ++Ge++ ++ 
  gi|119719611|ref|YP_920106.1| 173 TLLDALNHMVQSGEVTLNKE 192
                                    55778889999999986542 PP

>> E2F_TDP  E2F/DP family winged-helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   2.6e-05     0.065      34      54 ..     175     205 ..     121     209 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.6e-05
                        E2F_TDP  34 v..........dkkdekvkkRRiYDilNVLe 54 
                                               + + +k ++RRiY+i++VL+
  gi|119719611|ref|YP_920106.1| 175 LdalnhmvqsgEVTLNKEEERRIYEIMDVLS 205
                                    133335556666677899***********95 PP

>> PolyA_pol_RNAbd  Probable RNA and SrmB- binding site of polymerase A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0     4e-05       0.1      22      44 ..      93     115 ..      92     119 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4e-05
                PolyA_pol_RNAbd  22 ispeRifeEllKlLlsghpeagl 44 
                                    ++peRi++E ++++l +h+++++
  gi|119719611|ref|YP_920106.1|  93 VPPERIRVENNRIILLDHSQEAI 115
                                    89****************99876 PP

>> OAM_alpha  D-ornithine 4,5-aminomutase alpha-subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   6.4e-05      0.16      50      91 ..      21      62 ..      10      75 .. 0.88
   2 ?   -1.5   0.0      0.85   2.2e+03      47      59 ..     159     172 ..     122     185 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.4e-05
                                   HHHHHHTT--HHHHHHHHHHHHHTTGGGG-HHHHHHHHHHHT CS
                      OAM_alpha 50 rsvLLrmGlssleakaivekvlekgllgkGaGhvvyrlakek 91
                                   +s L  m ++ +    ++ ++ +++ll+k  G+vvyr + ek
  gi|119719611|ref|YP_920106.1| 21 KSPLKHMTFEEVMRGIVLSEITDRKLLEKIVGKVVYRRSGEK 62
                                   6778899*****999**********************99876 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.85
                                    HHHH.HHHHHTT-- CS
                      OAM_alpha  47 sier.svLLrmGls 59 
                                     ier  v Lrm  s
  gi|119719611|ref|YP_920106.1| 159 RIERkKVHLRMEAS 172
                                    36663467777655 PP

>> RsbRD_N  RsbT co-antagonist protein rsbRD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.5   3.8e+03      35      51 ..     123     138 ..     108     157 .. 0.71
   2 ?   11.8   0.4   0.00012      0.31      22      75 ..     151     205 ..     125     207 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.5
                        RsbRD_N  35 aelreqlrelldallaa 51 
                                    +++ e+lr+l d+ll +
  gi|119719611|ref|YP_920106.1| 123 SDIAEELRKLRDELL-V 138
                                    456777777777777.4 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00012
                        RsbRD_N  22 atypiesag.llseaelreqlrelldallaalaseqldleseeeeelrealdels 75 
                                    ++y+  +++ + ++ +lr ++  lldal ++++s++++l++eee+ + e++d ls
  gi|119719611|ref|YP_920106.1| 151 EEYNVARSRiERKKVHLRMEASTLLDALNHMVQSGEVTLNKEEERRIYEIMDVLS 205
                                    5666656666777888******************999999999999999888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       664  (0.037035); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1387.83
//
Query:       gi|119719612|ref|YP_920107.1|  [L=363]
Description: hypothetical protein Tpen_0702 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   5.8e-123  410.4   4.2   6.5e-123  410.2   4.2    1.0  1  DUF1512        Protein of unknown function (DUF1512)
  ------ inclusion threshold ------
       0.14   12.5   0.0       0.33   11.4   0.0    1.6  1  Inhibitor_I42  Chagasin family peptidase inhibitor I42


Domain annotation for each model (and alignments):
>> DUF1512  Protein of unknown function (DUF1512)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  410.2   4.2  7.2e-127  6.5e-123       2     356 .]       6     363 .]       5     363 .] 0.96

  Alignments for each domain:
  == domain 1  score: 410.2 bits;  conditional E-value: 7.2e-127
                        DUF1512   2 isliifllllillllglnqklqlavllrdiekklakleklaeeakkkvvellkklg...kedpkklve.rl...leffvi 74 
                                    +s+i++l++l+++   ++q++q+  +++++e+++a ++ ++++a k +v+ ++k++   + ++++++e r+   +e+ +i
  gi|119719612|ref|YP_920107.1|   6 LSFIMWLVALAIF-SYITQEMQILKAISEVEGYVALFRGIRDKAVKVLVDQFSKYTassEGASRDVLEqRIlslIETRII 84 
                                    789*********9.5579***********************************9997765566667775557779***** PP

                        DUF1512  75 ePvdlePtgivkrlehllrtsedklkklvekllpeadeversnvetaleiasalnliykvvrHylllakktknlvlllql 154
                                     Pvdl+P+giv++++h+lrtse +l+k+v+++++ a+++e++++++++e+a++lnl+yk+v+Hy+l+a+k k+l+l+lql
  gi|119719612|ref|YP_920107.1|  85 LPVDLDPYGIVRKIKHVLRTSEVELEKEVSRIAKGASRTEVQRLSSLVEVARELNLVYKLVNHYYLIARKFKSLWLVLQL 164
                                    ******************************************************************************** PP

                        DUF1512 155 qmllplllklaeayekalkaflkgkPvGDgaGplvaakllekkekksleaakdtviaevelegrkvivvkaeGpgstvGr 234
                                    ++++p++l++++a+e al++f+kg+PvGD+aGplvaa l++k + + +e++kdt i++v+++g+kv++vka+Gpgst G+
  gi|119719612|ref|YP_920107.1| 165 NAQMPFVLEEVKAIEGALESFSKGIPVGDSAGPLVAALLARKYKGSFVEPVKDTEISQVTVDGKKVFIVKAKGPGSTTGH 244
                                    ******************************************************************************** PP

                        DUF1512 235 lgeavekiveklkekvdliitvDAalkLEGEetgsvaeGvGvaiGdpGvekikiErvatkygipldaviikmsleeAita 314
                                    l+ea+++i++++  kv+li++vDAalkLEGEe+gsva+G+Gva+G++Gve+++iE++ tk+g+pl av+ikms +eA++ 
  gi|119719612|ref|YP_920107.1| 245 LEEALSWIFSRE--KVSLIVSVDAALKLEGEESGSVASGYGVAMGGIGVERFEIEELSTKHGVPLFAVLIKMSEAEALSV 322
                                    ***********9..****************************************************************** PP

                        DUF1512 315 MtkeiaeavdkavervkeiikektkegetvivvGvGNtvGva 356
                                    Mt++++++v++av++v++ii++   eg++++v+GvGN++Gv+
  gi|119719612|ref|YP_920107.1| 323 MTEKVYQGVQQAVRIVEDIISR-APEGSSIVVLGVGNSLGVP 363
                                    ********************76.56699*************7 PP

>> Inhibitor_I42  Chagasin family peptidase inhibitor I42
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   3.7e-05      0.33      41      78 ..     213     253 ..     204     264 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.7e-05
                                    CCECCE...STTSSEEEEEEEEESSSEEEEEEEEEE-TTST CS
                  Inhibitor_I42  41 pdesde...lvGaggthvwtfkalkpGettiefkyarpwek 78 
                                    ++ +d+    v+++g++v+ +ka++pG+tt +++ a +w  
  gi|119719612|ref|YP_920107.1| 213 EPVKDTeisQVTVDGKKVFIVKAKGPGSTTGHLEEALSWIF 253
                                    4444445779********************99999999965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 2261.57
//
Query:       gi|119719613|ref|YP_920108.1|  [L=609]
Description: radical SAM domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.1e-19   70.5   0.5    1.7e-18   67.6   0.0    2.4  2  Radical_SAM  Radical SAM superfamily
    1.6e-06   28.3   0.2      9e-06   25.8   0.0    2.2  2  Fer4_14      4Fe-4S single cluster domain
    4.4e-06   27.0   0.2    2.3e-05   24.7   0.0    2.2  3  Fer4_12      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.7      0.19   1.1e+03       3      19 ..     131     147 ..     129     151 .. 0.84
   2 !   67.6   0.0   2.8e-22   1.7e-18       1     166 [.     154     312 ..     154     313 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.19
                                    EESEESS--TTTSCCTT CS
                                    xxxxxxxxxxxxxxxxx RF
                    Radical_SAM   3 vtrgCnlrCsfCarpet 19 
                                    vt  C+++C  C+r+++
  gi|119719613|ref|YP_920108.1| 131 VTAPCPYNCGVCTRHRS 147
                                    6777**********974 PP

  == domain 2  score: 67.6 bits;  conditional E-value: 2.8e-22
                                    EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHH.HHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCCCTE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelk.aekg.vkevilgggepllypdfvellerlaklavpgi 78 
                                    +v t+ C l C +C +  +  + g+ ++ s+e i   +++++  e+     + l+ggep+l++d+ e++++++++     
  gi|119719613|ref|YP_920108.1| 154 IVLTNRCDLSCFYCFFFAS--KSGYIYEPSLEHIRYMLRQARlTEPVkPPAIQLTGGEPTLRDDLLEIIKMAREE--GFT 229
                                    6889*************97..*********************97775588*************************..8** PP

                                    EEEEEECSSCHG..HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTS CS
                                    xxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  79 ritvetngtlpd..eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGen 156
                                    +i + tng+++   +e + + +++gv++v+++ + ++++      n+++ +e    al++lr+ag+  vv + ++++ +n
  gi|119719613|ref|YP_920108.1| 230 HIQLNTNGIRLAfdPELAVKVRQAGVNTVYMSFDGVSPF-----SNPKNHWEVP-YALDNLRKAGLG-VVLVPTVIKHYN 302
                                    **************************************9.....5575556655.9***********.************ PP

                                    HHHHHHHHHH CS
                                    xxxxxxxxxx RF
                    Radical_SAM 157 deeleellel 166
                                     +e+ +++++
  gi|119719613|ref|YP_920108.1| 303 LSEVGKIIQF 312
                                    ***9998876 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.4      0.37   2.2e+03       5      19 ..     132     146 ..     131     150 .. 0.81
   2 !   25.8   0.0   1.5e-09     9e-06       3      90 ..     155     238 ..     154     264 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.37
                        Fer4_14   5 lsgCnlsCkgCdnke 19 
                                    ++ C+ +C  C ++ 
  gi|119719613|ref|YP_920108.1| 132 TAPCPYNCGVCTRHR 146
                                    678********9765 PP

  == domain 2  score: 25.8 bits;  conditional E-value: 1.5e-09
                        Fer4_14   3 vrlsgCnlsCkgCdnketwkselgkpqteelleqilk.dlkkseikiqglvltGGePLhyenkkellklvkrlkeeypek 81 
                                    v +++C lsC  C+  ++++    +p+ e++   +l+     + +k+  + ltGGeP +    ++ll+++k+ +ee+   
  gi|119719613|ref|YP_920108.1| 155 VLTNRCDLSCFYCFFFASKSGYIYEPSLEHIR-YMLRqARLTEPVKPPAIQLTGGEPTL---RDDLLEIIKMAREEG-FT 229
                                    4589**********888777666666655554.4444356677788889********94...499***********9.78 PP

                        Fer4_14  82 kiwletngt 90 
                                    +i+l+tng 
  gi|119719613|ref|YP_920108.1| 230 HIQLNTNGI 238
                                    9******96 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1      0.59   3.5e+03       3      24 ..     121     144 ..     120     150 .. 0.80
   2 !   24.7   0.0   3.8e-09   2.3e-05       9      95 ..     154     239 ..     145     247 .. 0.73
   3 ?   -3.7   0.0       2.2   1.3e+04      90     117 ..     546     575 ..     538     582 .. 0.50

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.59
                        Fer4_12   3 GeGvrlslf..vsgCnlsCkgCfn 24 
                                    G+G ++s++  ++ C+ +C  C  
  gi|119719613|ref|YP_920108.1| 121 GKGNVISHLpvTAPCPYNCGVCTR 144
                                    78888888777889******9975 PP

  == domain 2  score: 24.7 bits;  conditional E-value: 3.8e-09
                        Fer4_12   9 slfvsgCnlsCkgCfnketwsfksgkeftkelleeii...edlkkesiegltllGGEPllpenaeallelvkevkeekpe 85 
                                    ++++++C+lsC +Cf  + +s    ++   e ++ ++   + ++  + + + l+GGEP l   +++lle++k  +ee+++
  gi|119719613|ref|YP_920108.1| 154 IVLTNRCDLSCFYCFFFASKSGYIYEPSL-EHIRYMLrqaRLTEPVKPPAIQLTGGEPTL---RDDLLEIIKMAREEGFT 229
                                    67899**********65555555444443.333333300033334555************...9***************8 PP

                        Fer4_12  86 kdiwlytgyt 95 
                                       + ++g  
  gi|119719613|ref|YP_920108.1| 230 HIQLNTNGIR 239
                                    7788888865 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 2.2
                        Fer4_12  90 lytgytleelskk..ekeellkeidvlvdG 117
                                    +y+   +e+l+ k    +   ++i+ l++G
  gi|119719613|ref|YP_920108.1| 546 SYSIKDWEKLTGKrlVEDHYKRNIKKLISG 575
                                    555555555554443223333344444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (609 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 3798.95
//
Query:       gi|119719614|ref|YP_920109.1|  [L=158]
Description: hypothetical protein Tpen_0704 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1092.58
//
Query:       gi|119719615|ref|YP_920110.1|  [L=112]
Description: hypothetical protein Tpen_0705 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.14   12.2   0.3       0.24   11.4   0.3    1.4  1  IKKbetaNEMObind  I-kappa-kinase-beta NEMO binding domain


Domain annotation for each model (and alignments):
>> IKKbetaNEMObind  I-kappa-kinase-beta NEMO binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.3   1.4e-05      0.24       4      28 ..       7      31 ..       5      35 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1.4e-05
                IKKbetaNEMObind  4 leEnqnyLsqLtslmqettkeqdsS 28
                                   +eE q++L++L s+ +e  + ++sS
  gi|119719615|ref|YP_920110.1|  7 IEEKQKLLEHLASVVEELLRNTKSS 31
                                   89***************99988888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       884  (0.0493056); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 784.22
//
Query:       gi|119719616|ref|YP_920111.1|  [L=161]
Description: PUA domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-11   43.9   0.1    3.6e-11   43.0   0.1    1.5  1  TGT_C2    Patch-forming domain C2 of tRNA-guanine transglycos
    2.1e-08   34.0   0.2      3e-08   33.5   0.2    1.2  1  PUA       PUA domain
  ------ inclusion threshold ------
      0.012   15.6   0.0       0.18   11.9   0.0    2.3  2  TruB-C_2  Pseudouridine synthase II TruB, C-terminal


Domain annotation for each model (and alignments):
>> TGT_C2  Patch-forming domain C2 of tRNA-guanine transglycosylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.0   0.1     6e-15   3.6e-11       3      66 ..      14      78 ..      12      81 .. 0.94

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 6e-15
                         TGT_C2  3 lraiadYqFGagagdaLfpedvtitrs.atgrirqvlvdgerlatlraqdgrltLsleGarrlhe 66
                                   l++++ YqFG     +  +++++++rs +tgrir+++v+++ +a++r +dg+ +++ eG r+l +
  gi|119719616|ref|YP_920111.1| 14 LQRLLLYQFGVDFDLERLGDKLSVERSrRTGRIRKIFVGDTLFASVRLSDGFIVPTPEGWRLLLS 78
                                   789999*******99999999**************************************999875 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.2   4.9e-12     3e-08       3      71 ..      85     154 ..      83     156 .. 0.94

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 4.9e-12
                                    EEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETT.SCEEEEEEESS-HHHHHHHCTSEEEEEE CS
                            PUA   3 vvvddgAvkallsgasLlapGvvevegdfeegdvVaivded.gelvavGlanysseelakikggksveie 71 
                                    v v + +++ +++g+ ++ + v+e++ ++ +gd+Va+++++  ++ + G+a++ ++ +  i +gk+++++
  gi|119719616|ref|YP_920111.1|  85 VEVPEDVARYVSQGRTVFSKHVIEADREILPGDEVAVISGEeARVSGSGKAMLPGDSMGVIRRGKAIKTR 154
                                    678889999*******************************878************************987 PP

>> TruB-C_2  Pseudouridine synthase II TruB, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0     3e-05      0.18       3      39 ..      85     128 ..      84     136 .. 0.69
   2 ?    1.5   0.0     0.053   3.1e+02       5      25 ..     137     157 ..     134     161 .] 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3e-05
                       TruB-C_2   3 veLseesakrflqGQrvkl......aaglpaeg.lVRvy.deegr 39 
                                    ve++e++a++++qG++v +      a++    g  V v+ +ee+r
  gi|119719616|ref|YP_920111.1|  85 VEVPEDVARYVSQGRTV-FskhvieADREILPGdEVAVIsGEEAR 128
                                    89***************.644455544444455566666555555 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.053
                       TruB-C_2   5 LseesakrflqGQrvklaagl 25 
                                    L+ +s++ ++ G+++k + g+
  gi|119719616|ref|YP_920111.1| 137 LPGDSMGVIRRGKAIKTRTGA 157
                                    88999999*******886655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 1341.04
//
Query:       gi|119719617|ref|YP_920112.1|  [L=134]
Description: helix-turn-helix domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.3e-13   48.6   0.4    9.7e-13   48.0   0.4    1.3  1  HTH_3     Helix-turn-helix
    7.9e-09   35.7   0.1    1.4e-08   34.9   0.1    1.4  1  HTH_31    Helix-turn-helix domain
    5.2e-07   29.6   0.2    7.9e-07   29.0   0.2    1.3  1  HTH_19    Helix-turn-helix domain
    0.00085   19.1   0.1     0.0019   18.0   0.1    1.6  1  HTH_25    Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.0   0.4   2.2e-16   9.7e-13       1      52 [.      50     101 ..      50     103 .. 0.97

  Alignments for each domain:
  == domain 1  score: 48.0 bits;  conditional E-value: 2.2e-16
                                    HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSEH CS
                          HTH_3   1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvsl 52 
                                    ++ +R+  g+++  LA+++G + sti+riE G+ +P+++ + kl+k+L+v+l
  gi|119719617|ref|YP_920112.1|  50 IRSARERMGWTRDVLAAMVGEKESTIRRIEAGQLEPTIDLARKLEKVLKVKL 101
                                    899***********************************************98 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.1   3.1e-12   1.4e-08       3      56 ..      47      99 ..      46     108 .. 0.91

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 3.1e-12
                         HTH_31  3 GalLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralgl 56
                                   G+  r +Rer G++++ +A+ +g  est++r+E G+  +p+ +  ++l  +l +
  gi|119719617|ref|YP_920112.1| 47 GEIIRSARERMGWTRDVLAAMVGEKESTIRRIEAGQL-EPTIDLARKLEKVLKV 99
                                   67789********************************.8*******99999987 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.2   1.8e-10   7.9e-07       1      63 [.      47     108 ..      47     110 .. 0.92

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 1.8e-10
                         HTH_19   1 GerLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgidleyllqge 63 
                                    Ge ++ aRe  g+t + la ++g   s i+ iE g+  +p+++l +k+ + l++ l + l+ +
  gi|119719617|ref|YP_920112.1|  47 GEIIRSARERMGWTRDVLAAMVGEKESTIRRIEAGQL-EPTIDLARKLEKVLKVKLIEELTDY 108
                                    899*********************************9.**********999999976666666 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1   4.2e-07    0.0019       2      36 ..      50      84 ..      49      87 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 4.2e-07
                                   HHHHHHTTT--HHHHHHHSS--HHHHHHHHCT--T CS
                         HTH_25  2 LraaRearglsleevaketkIrkdylealEeddfd 36
                                    r aRe++g++++ +a+    ++++++++E+++++
  gi|119719617|ref|YP_920112.1| 50 IRSARERMGWTRDVLAAMVGEKESTIRRIEAGQLE 84
                                   699*****************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 928.19
//
Query:       gi|119719618|ref|YP_920113.1|  [L=424]
Description: small GTP-binding protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.1e-26   91.8   0.0    1.2e-25   90.0   0.0    2.0  1  GTP-bdg_N     GTP-binding GTPase N-terminal
    6.2e-14   52.1   0.0    1.6e-13   50.7   0.0    1.8  1  MMR_HSR1      50S ribosome-binding GTPase
    1.1e-11   45.1   2.8    2.6e-11   43.9   2.8    1.7  1  GTP-bdg_M     GTP-binding GTPase Middle Region
    2.6e-07   30.3   0.0    6.2e-07   29.1   0.0    1.7  2  FeoB_N        Ferrous iron transport protein B
    2.5e-06   27.5   0.0      0.016   15.1   0.0    2.5  2  RsgA_GTPase   RsgA GTPase
    0.00016   21.3   0.0    0.00055   19.6   0.0    1.9  1  Ras           Ras family
    0.00027   21.5   0.5     0.0011   19.5   0.1    2.1  2  ABC_tran      ABC transporter
    0.00042   19.9   0.1      0.071   12.7   0.0    2.7  2  GTP_EFTU      Elongation factor Tu GTP binding domain
     0.0034   17.4   0.0     0.0082   16.1   0.0    1.6  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
     0.0035   17.1   0.1        4.3    7.1   0.0    2.6  2  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
     0.0061   16.2   6.3       0.13   11.8   0.8    3.2  3  cobW          CobW/HypB/UreG, nucleotide-binding domain
  ------ inclusion threshold ------
      0.049   14.0   1.5       0.15   12.4   0.6    2.4  1  AAA_16        AAA ATPase domain
      0.074   13.1   0.4       0.18   11.8   0.0    1.8  1  TsaE          Threonylcarbamoyl adenosine biosynthesis protei
      0.092   13.3   0.1        0.4   11.2   0.1    2.1  1  AAA_18        AAA domain
       0.11   12.9   0.8       0.11   12.9   0.8    2.3  2  AAA_23        AAA domain
       0.12   12.2   0.0       0.34   10.7   0.0    1.8  1  AAA_29        P-loop containing region of AAA domain
        0.2   11.1   4.2       0.91    8.9   0.1    3.1  3  Arf           ADP-ribosylation factor family
       0.27   11.5   4.6       0.34   11.2   1.0    2.8  2  DUF3618       Protein of unknown function (DUF3618)
        0.3   11.4   1.4        6.8    7.0   1.4    3.1  1  AAA_22        AAA domain
        0.3   10.8   3.2          2    8.1   0.1    2.8  3  AAA_30        AAA domain


Domain annotation for each model (and alignments):
>> GTP-bdg_N  GTP-binding GTPase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.0   0.0   1.3e-28   1.2e-25       4      89 .]      24     109 ..      22     109 .. 0.99

  Alignments for each domain:
  == domain 1  score: 90.0 bits;  conditional E-value: 1.3e-28
                      GTP-bdg_N   4 leEleeLaktaglevvgevvqkrekpdpatyiGkGkveeikelveeeeadlvifddeLspsqqrnLekelevkViDRtqL 83 
                                    l+El++L+++ag+ v+ge++qk +  dp++ iG+Gkv e+k+lvee++   v+f ++L+p+q+ nL+ke++v+ViDR +L
  gi|119719618|ref|YP_920113.1|  24 LDELRKLVEAAGYAVAGELLQKSRYEDPKYNIGRGKVLELKRLVEEKKPLKVVFLNDLKPNQAYNLSKETGVEVIDRYEL 103
                                    89****************************************************************************** PP

                      GTP-bdg_N  84 ILdIFA 89 
                                    IL+IFA
  gi|119719618|ref|YP_920113.1| 104 ILEIFA 109
                                    *****8 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.7   0.0   1.8e-16   1.6e-13       2     100 ..     196     295 ..     195     315 .. 0.78

  Alignments for each domain:
  == domain 1  score: 50.7 bits;  conditional E-value: 1.8e-16
                                    EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHC....TS CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgkaflalee....ad 77 
                                    va+ G++ +GK+tL+n ltge+  +  kp++T+ +  +r  ++g ++ ++Dt G+i+  +    l +af    +    ad
  gi|119719618|ref|YP_920113.1| 196 VALTGYTGAGKTTLFNVLTGENGYIDGKPFATLSTLSRRTYFHGFPVLVTDTIGFID--DLPDALVDAFYTTLRetlaAD 273
                                    99***************************************9************987..33445666665533334548* PP

                                    EEEEEEETTTTCSHHHHHHHHHH CS
                       MMR_HSR1  78 lillvvdaseeklkpldeeleel 100
                                    +illv+d+s ++ ++++++l + 
  gi|119719618|ref|YP_920113.1| 274 VILLVLDVS-DTPAEIRRKLTAS 295
                                    *******88.5455555555444 PP

>> GTP-bdg_M  GTP-binding GTPase Middle Region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9   2.8   2.9e-14   2.6e-11       1      79 []     111     188 ..     111     188 .. 0.90

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 2.9e-14
                                    H--SHHHHHHHHHHHHHHHHHHHCXXXXXXXXX..X..XXXXXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHH.....T CS
                      GTP-bdg_M   1 rArtkeaklQVelAqlkyllprLeglgkelsrqgGgigtrGpGetkleldrrlireriaklkkeLekvkkkrelqrkkR 79 
                                    rA ++e+klQ+elA+lk +l+   + + +l + g   g+ G G++ ++ +   ++ ri+k+++eL+k++k +e++ ++R
  gi|119719618|ref|YP_920113.1| 111 RAGSRESKLQIELAKLKRELSFA-KEYINLAKRGELHGFLGGGKYAVDAYYAYVSMRISKIEEELRKIRKMKEERIARR 188
                                    9*********************9.66666666644467***********************************999887 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0         5   4.5e+03     120     134 ..     116     130 ..      91     142 .. 0.62
   2 !   29.1   0.0   6.9e-10   6.2e-07       2     155 ..     195     355 ..     194     356 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 5
                                    HTTEEE-HHHHHHHH CS
                         FeoB_N 120 kkgieidlkkLsekL 134
                                    +++++i+l+kL+++L
  gi|119719618|ref|YP_920113.1| 116 ESKLQIELAKLKREL 130
                                    344455555555544 PP

  == domain 2  score: 29.1 bits;  conditional E-value: 6.9e-10
                                    EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SS.SSSSSHHHHHH..HHHHHCTS CS
                         FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYs.lsayseeekva..rdflleee 78 
                                    tval G   +Gkttlfn ltg + ++   p  t    + ++ ++g  v ++D  G  + l +   +   +  r++l+ + 
  gi|119719618|ref|YP_920113.1| 195 TVALTGYTGAGKTTLFNVLTGENGYIDGKPFATLSTLSRRTYFHGFPVLVTDTIGFIDdLPDALVDAFYTtlRETLAADV 274
                                    79*****************************************************8651655555554332256666666 PP

                                    SSEEEEEEEG.GGHHHHHHHHHH.HHHTTSS...EEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTBTHHHHH CS
                         FeoB_N  79 pdvvvnvvda.tnlernLyLtlq.llelgvp...vvlalnmideaekkgieidlkkLsekLgvpvvktsakkkegieell 153
                                    + +v++v d+ ++++r+L+  ++ ll+lgvp   ++l+ n+id+++++++e   ++L e  g+    +sa+++ gi+el+
  gi|119719618|ref|YP_920113.1| 275 ILLVLDVSDTpAEIRRKLTASMEvLLNLGVPptrILLVGNKIDKVSSAELEER-ERLLEDSGLRYTLISAARRIGIHELT 353
                                    66777777764589*****99984579997533267788*********99955.5566667999999************9 PP

                                    HH CS
                         FeoB_N 154 ka 155
                                    +a
  gi|119719618|ref|YP_920113.1| 354 QA 355
                                    87 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.8e-05     0.016      89     122 ..     181     216 ..     157     233 .. 0.79
   2 !    9.9   0.0   0.00072      0.65      47      97 ..     307     356 ..     263     367 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.8e-05
                                    THHHHHHHCTT..SEEEEECSTTSSHHHHHHHHCTT CS
                    RsgA_GTPase  89 gleelkellkd..ktsvlvGqSGvGKStLinallpe 122
                                    + e+++++++    t++l G +G+GK+tL n+l++e
  gi|119719618|ref|YP_920113.1| 181 KEERIARRVEAglYTVALTGYTGAGKTTLFNVLTGE 216
                                    44566666665457899****************997 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00072
                                    -EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHC CS
                    RsgA_GTPase  47 iepvivlnKiDlleeeeeleelkeelealgyevllvsaktkegleelkell 97 
                                     ++++v nKiD ++++e lee +  le+ g++ +l+sa ++ g++el++++
  gi|119719618|ref|YP_920113.1| 307 TRILLVGNKIDKVSSAE-LEERERLLEDSGLRYTLISAARRIGIHELTQAV 356
                                    3567788**********.*************************99998865 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   6.2e-07   0.00055      70     159 ..     270     359 ..     195     362 .. 0.65

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 6.2e-07
                                    TTESEEEEEEETTBHHHHHTHH.HHHHHHHHHST...TTSEEEEEEETTTGGGG-SS-HHHHHHHHHHHTSEEEEEBTTT CS
                            Ras  70 rdaegillvyditsresfenvk.kwveeikrvae...envpivLvGnKvDleekravsteegeelakelglkfletSAkt 145
                                      a++illv d++++ +  +++ k++  ++   +     + i+LvGnK+D  ++   + ee e+l ++ gl+++ +SA  
  gi|119719618|ref|YP_920113.1| 270 LAADVILLVLDVSDTPA--EIRrKLTASMEVLLNlgvPPTRILLVGNKIDKVSS--AELEERERLLEDSGLRYTLISAAR 345
                                    25789999999987654..4443555444444444467899*********9975..556677799*************** PP

                                    TCTHHHHHHHHHHH CS
                            Ras 146 nenveeafeellre 159
                                    + +++e+ +++++ 
  gi|119719618|ref|YP_920113.1| 346 RIGIHELTQAVVEM 359
                                    ******99888765 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1       3.9   3.5e+03     114     134 ..       6      26 ..       1      27 [. 0.80
   2 !   19.5   0.1   1.2e-06    0.0011      13      40 ..     195     222 ..     185     236 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 3.9
                                    HHHHHHHHHHHHTSSEEEEES CS
                                    xxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran 114 kqrvalarallkkpkllllDE 134
                                    +q v +++ l  k +l llDE
  gi|119719618|ref|YP_920113.1|   6 RQAVIVVARLSGKGDLALLDE 26 
                                    67777777899999******9 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 1.2e-06
                                    EEEEEESTTSSHHHHHHHHTTSS--SEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  13 kvaivGenGaGKStLlkllagllkpteG 40 
                                    +va++G +GaGK+tL+++l+g+     G
  gi|119719618|ref|YP_920113.1| 195 TVALTGYTGAGKTTLFNVLTGENGYIDG 222
                                    69*******************9766555 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.033        30       6      32 ..     196     222 ..     193     234 .. 0.85
   2 !   12.7   0.0   7.9e-05     0.071      88     193 ..     266     361 ..     259     362 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.033
                                    EEEEESTTSSHHHHHHHHHHHTTSSCH CS
                       GTP_EFTU   6 igiighvDhGKtTLtdrLlyktgaisk 32 
                                    +++ g + +GKtTL   L+ ++g i+ 
  gi|119719618|ref|YP_920113.1| 196 VALTGYTGAGKTTLFNVLTGENGYIDG 222
                                    67788899**********999988875 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 7.9e-05
                                    HHHHHT-SEEEEEEETTTB...STHHHHHHHHHHHHTTTE...EEEEEESCGST.HHHHHHHHHHHHHHHHHHHHHHHHH CS
                       GTP_EFTU  88 irglrvlDgavlvvdaveG...vepqteevlrlalkegvp...iivfiNKmDrl.kaelkeiveevkqklsrkeekleky 160
                                     r + ++D+ +lv+d+++    +  +    ++++l++gvp   i ++ NK+D++  ael+e  + ++++           
  gi|119719618|ref|YP_920113.1| 266 LRETLAADVILLVLDVSDTpaeIRRKLTASMEVLLNLGVPptrILLVGNKIDKVsSAELEERERLLEDSG---------- 335
                                    5667789**********8755577788889999*******99667777******7777777655554322.......... PP

                                    HHTTTTTEEEEEEBTTTTBTHHHHHHHHHHHSH CS
                       GTP_EFTU 161 gekgekevpvvfgSalkgegvktllealvellp 193
                                                +Sa +  g+ +l +a+ve+lp
  gi|119719618|ref|YP_920113.1| 336 -------LRYTLISAARRIGIHELTQAVVEMLP 361
                                    .......34556666666666666666666665 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   9.1e-06    0.0082      58     104 ..     309     360 ..     307     361 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 9.1e-06
                   MMR_HSR1_Xtn  58 clyvlNKiDlisleeldelare.....pnsvviSaekelnldeLkekiweeL 104
                                     l+v NKiD++s +el+e +r       +++ iSa++++++ eL++++ e L
  gi|119719618|ref|YP_920113.1| 309 ILLVGNKIDKVSSAELEERERLledsgLRYTLISAARRIGIHELTQAVVEML 360
                                    68999*********999999955565558999*************9987765 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0    0.0048       4.3       4      24 ..     196     216 ..     194     221 .. 0.89
   2 !    7.1   0.0    0.0048       4.3      53     140 ..     262     355 ..     253     358 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0048
                      PduV-EutP   4 illiGkvgsGKttLtqalkge 24 
                                    + l G +g+GKttL + l+ge
  gi|119719618|ref|YP_920113.1| 196 VALTGYTGAGKTTLFNVLTGE 216
                                    6799************99987 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0048
                      PduV-EutP  53 lysalivtsaeadvialvqdateeesvfppgfasvfn.........keviGiitkidlaedeenieaveelLksaGaeki 123
                                    +y++l+ t + advi lv+d++++   +  ++++ ++           ++ +  kid++ +++++e  e+lL+  G +  
  gi|119719618|ref|YP_920113.1| 262 FYTTLRET-LAADVILLVLDVSDTPAEIRRKLTASMEvllnlgvppTRILLVGNKIDKV-SSAELEERERLLEDSGLRYT 339
                                    55665544.56888888888887777766666555431111222112344455799999.999*************9865 PP

                      PduV-EutP 124 fevsavekegieellky 140
                                      +sa +++gi+el++ 
  gi|119719618|ref|YP_920113.1| 340 -LISAARRIGIHELTQA 355
                                    .59**********9876 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1         3   2.7e+03       5      13 ..     145     153 ..     144     156 .. 0.85
   2 !   11.8   0.8   0.00015      0.13       3      21 ..     196     214 ..     194     228 .. 0.86
   3 !    5.9   0.0    0.0097       8.7      85     164 ..     242     329 ..     225     337 .. 0.64

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 3
                                    EEESTTCCH CS
                           cobW   5 ltGflGsGK 13 
                                    l GflG GK
  gi|119719618|ref|YP_920113.1| 145 LHGFLGGGK 153
                                    68******9 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00015
                                    EEEEESTTCCHHHHHHHHH CS
                           cobW   3 tvltGflGsGKTtLlnhll 21 
                                    + ltG+ G+GKTtL n l+
  gi|119719618|ref|YP_920113.1| 196 VALTGYTGAGKTTLFNVLT 214
                                    679***********99887 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.0097
                                    EEEEEECTTTTHHHHHTT...SHHHHHCCCECEEEEEEETTTH......CCHCCHHHHHHHHHHTSS.EEEEE-HHHHCH CS
                           cobW  85 viliEttGlaePapvaft...eeelksdltldavvavvDaknl.....eaeeekieekaedqlaaad.llvlnKtDllde 155
                                    v++  t G  +  p a+     ++l++ l +d+++ v+D++ +      + + + e +++ ++  +  llv nK+D +++
  gi|119719618|ref|YP_920113.1| 242 VLVTDTIGFIDDLPDALVdafYTTLRETLAADVILLVLDVSDTpaeirRKLTASMEVLLNLGVPPTRiLLVGNKIDKVSS 321
                                    5666666644443332222357789999999*********888766654445555555555565555256679****999 PP

                                    C..HHHHHH CS
                           cobW 156 ealleklee 164
                                    ++l e+ e+
  gi|119719618|ref|YP_920113.1| 322 AEL-EERER 329
                                    976.55554 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.6   0.00017      0.15      18     159 ..     188     331 ..     171     405 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00017
                         AAA_16  18 rvrsgrp....elvllsGesGvGKsslvrellralekdggiflrgkcdql....esaipy.....salaqalareellrq 84 
                                    r            v l+G+ G GK++l + l     ++   ++ gk        ++ ++y     + +++++   +++ +
  gi|119719618|ref|YP_920113.1| 188 R-----VeaglYTVALTGYTGAGKTTLFNVLTG---EN--GYIDGKPFATlstlSR-RTYfhgfpVLVTDTI---GFIDD 253
                                    3.....224447899*************98884...22..3444444444222111.223222211122222...22333 PP

                         AAA_16  85 lldeaesaeleawrekleeala........avpelagaeasrllellkrllallsrderplvlvlDdlqwadeaslqlla 156
                                    l d+    +++a+ ++l+e+la        +v++ ++++++ l + +  ll+l  ++ r ++lv   ++++ +a l+  +
  gi|119719618|ref|YP_920113.1| 254 LPDA----LVDAFYTTLRETLAadvillvlDVSDTPAEIRRKLTASMEVLLNLGVPPTR-ILLVGNKIDKVSSAELEERE 328
                                    3333....555555555555555666666644455555445555555444444444333.55554444444444444444 PP

                         AAA_16 157 aLl 159
                                     Ll
  gi|119719618|ref|YP_920113.1| 329 RLL 331
                                    443 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0    0.0002      0.18       9      40 ..     184     214 ..     168     224 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0002
                                    HHHHHHHHCHTEEEEEEESTTSSHHHHHHHHH CS
                           TsaE   9 algkklakalgdvilLeGdLGaGKTtlvrgla 40 
                                    ++++++ +    +++L+G  GaGKTtl   l 
  gi|119719618|ref|YP_920113.1| 184 RIARRVEAG-LYTVALTGYTGAGKTTLFNVLT 214
                                    333333221.235**************98765 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00044       0.4       1      24 [.     196     219 ..     196     249 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00044
                         AAA_18   1 IlltGtpGvGKttlakeLskrlgf 24 
                                    ++ltG+ G+GKttl + L  ++g+
  gi|119719618|ref|YP_920113.1| 196 VALTGYTGAGKTTLFNVLTGENGY 219
                                    789***********9999766644 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.5      0.34   3.1e+02     150     197 ..     118     179 ..      30     187 .. 0.46
   2 ?   12.9   0.8   0.00013      0.11      22      40 ..     196     214 ..     190     215 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.34
                         AAA_23 150 dkkerleelekeleeledekkllekleqekekek.....................eleeleeeleeilk 197
                                    + + +l++l++el  +++ ++l ++        +                     +++++eeel +i k
  gi|119719618|ref|YP_920113.1| 118 KLQIELAKLKRELSFAKEYINLAKR-------GElhgflgggkyavdayyayvsmRISKIEEELRKIRK 179
                                    1111233333333222222222222.......2233344444444444444444444444444444443 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00013
                         AAA_23  22 tlItGpNGaGKTTildAik 40 
                                    +++tG +GaGKTT+++ ++
  gi|119719618|ref|YP_920113.1| 196 VALTGYTGAGKTTLFNVLT 214
                                    579************9876 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00038      0.34      24      39 ..     195     210 ..     181     219 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00038
                         AAA_29  24 atlltGpsGsGKSTll 39 
                                    ++ ltG +G+GK+Tl+
  gi|119719618|ref|YP_920113.1| 195 TVALTGYTGAGKTTLF 210
                                    689************8 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1      0.93   8.3e+02      93     114 ..     163     184 ..     154     191 .. 0.74
   2 ?    1.7   0.1      0.17   1.5e+02      19      37 ..     198     216 ..     193     224 .. 0.83
   3 ?    8.9   0.1     0.001      0.91      83     155 ..     273     351 ..     267     386 .. 0.67

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.93
                                    -CTTHHHHHHHHHHHCTSGCCT CS
                            Arf  93 dreRleeakeeLkalleeeelk 114
                                     ++R+++ +eeL+++ +++e +
  gi|119719618|ref|YP_920113.1| 163 VSMRISKIEEELRKIRKMKEER 184
                                    578**********998877755 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.17
                                    EEESTTSSHHHHHHHHHHS CS
                            Arf  19 llGLDnaGKtTilkklkle 37 
                                    l G  +aGKtT+ + l+ e
  gi|119719618|ref|YP_920113.1| 198 LTGYTGAGKTTLFNVLTGE 216
                                    668899******9988765 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.001
                                    SEEEEEEETT-CT.THHHHHHHHHHHCTSGCCTTSEEEEEEE-TTSTTSS-HHHHHHHTTGGGSS.....SSSSEEEEE CS
                            Arf  83 davifvvDsadre.RleeakeeLkalleeeelkevallvlaNKqDlpealseeelrellgleelk.....gkrkleiqk 155
                                    d+++ v+D++d+   ++   +   ++l +  +    +l+++NK+D  ++++ ee ++ll+ + l+     ++r++ i +
  gi|119719618|ref|YP_920113.1| 273 DVILLVLDVSDTPaEIRRKLTASMEVLLNLGVPPTRILLVGNKIDKVSSAELEERERLLEDSGLRytlisAARRIGIHE 351
                                    67777888887642344433333344444556677899******************99999886533333444444443 PP

>> DUF3618  Protein of unknown function (DUF3618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1       1.5   1.4e+03       1       9 [.     282     290 ..     282     291 .. 0.89
   2 ?   11.2   1.0   0.00038      0.34      12      36 ..     369     393 ..     361     394 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.5
                        DUF3618   1 ardpeeIer 9  
                                    +++p+eI+r
  gi|119719618|ref|YP_920113.1| 282 SDTPAEIRR 290
                                    589*****8 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00038
                        DUF3618  12 ertRaeLaeTvdeLaaradPkrlad 36 
                                    + tR+ Lae++ eL +r +++++++
  gi|119719618|ref|YP_920113.1| 369 ALTREALAEDLRELLDRCRVREVVQ 393
                                    56*******************9986 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   1.4    0.0076       6.8       8      29 ..     196     217 ..     192     403 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0076
                         AAA_22   8 lvvtGesGtGKTtllrrlleql 29 
                                    +++tG +G+GKTtl + l+ ++
  gi|119719618|ref|YP_920113.1| 196 VALTGYTGAGKTTLFNVLTGEN 217
                                    589***********98777664 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       2.1   1.9e+03      26      51 ..      15      40 ..       3      41 .. 0.71
   2 ?    8.1   0.1    0.0023         2      20      38 ..     195     213 ..     180     222 .. 0.83
   3 ?    2.1   0.1      0.16   1.4e+02     138     190 ..     339     391 ..     332     393 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.1
                         AAA_30 26 pAGtGKttalkalreaweaaggrvig 51
                                     G G   +l +lr+++eaag+ v+g
  gi|119719618|ref|YP_920113.1| 15 LSGKGDLALLDELRKLVEAAGYAVAG 40
                                   45666667899999999999999876 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0023
                         AAA_30  20 vavltGpAGtGKttalkal 38 
                                    +++ltG+ G+GKtt+ ++l
  gi|119719618|ref|YP_920113.1| 195 TVALTGYTGAGKTTLFNVL 213
                                    6789***********9887 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.16
                         AAA_30 138 rdlveaagigtaeLtevvRqkeseeraaalalregdaeealealadrgriheg 190
                                    +++ +a++ig +eLt+ v    +e  +a+lal +   +e l+ l dr r++e+
  gi|119719618|ref|YP_920113.1| 339 TLISAARRIGIHELTQAVVEMLPEKVSATLALTREALAEDLRELLDRCRVREV 391
                                    445556799********99988*************************999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (424 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       953  (0.0531541); expected 358.6 (0.02)
Passed bias filter:                      770  (0.0429472); expected 358.6 (0.02)
Passed Vit filter:                       106  (0.00591221); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.68u 0.31s 00:00:00.99 Elapsed: 00:00:00.47
# Mc/sec: 2718.08
//
Query:       gi|119719619|ref|YP_920114.1|  [L=181]
Description: hypothetical protein Tpen_0709 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-49  167.4   0.0    1.3e-49  167.0   0.0    1.1  1  Trm56     tRNA ribose 2'-O-methyltransferase, aTrm56


Domain annotation for each model (and alignments):
>> Trm56  tRNA ribose 2'-O-methyltransferase, aTrm56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.0   0.0   7.3e-54   1.3e-49       1     118 [.      59     177 ..      59     178 .. 0.97

  Alignments for each domain:
  == domain 1  score: 167.0 bits;  conditional E-value: 7.3e-54
                                    H-S--EEE.E--HHHHHHC-S...SEEEEE-TTSEEH.HHHHHHHHC-SE.EEEEE------TCHHHHSSEEEESSSS-- CS
                          Trm56   1 wGgefkvevakslkklikefkkeggivvhltmyGeni.eevieeikkkekdllvvvGaekvprevyeladynvsvgnqPh 79 
                                    wGg+fkv ++++ ++++ ++kk+ggivvhltmyGeni ee+i+ i+ + kd+lvvvG+ekvpr+++e ad+nv++gnqPh
  gi|119719619|ref|YP_920114.1|  59 WGGDFKVLTTRDPRETVANWKKNGGIVVHLTMYGENIsEELINLISGQGKDILVVVGGEKVPRWLFEEADFNVAIGNQPH 138
                                    *************************************4467899999********************************* PP

                                    -HHHHHHHHHHHHC.--TTT---TT-SSEEE--SSS-EE CS
                          Trm56  80 sevaalaifldrllegkelekefedaklkviPsergkkv 118
                                    sevaala+fldrl++g+el++ef +akl++iPs+rgk v
  gi|119719619|ref|YP_920114.1| 139 SEVAALAVFLDRLFKGEELRREFPGAKLSIIPSKRGKIV 177
                                    *************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1195.57
//
Query:       gi|119719620|ref|YP_920115.1|  [L=178]
Description: transcription factor TFIIE, alpha subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-39  133.9   1.1    2.3e-39  133.5   1.1    1.2  1  TFIIE_alpha      TFIIE alpha subunit
    6.1e-12   44.9   3.6      1e-11   44.2   3.6    1.4  1  TF_Zn_Ribbon     TFIIB zinc-binding
    0.00035   20.6   0.3       0.58   10.3   0.0    2.4  2  Zn-ribbon_8      Zinc ribbon domain
     0.0004   19.9   1.2       0.13   11.9   0.1    2.5  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
    0.00055   20.0   0.0     0.0028   17.7   0.0    1.9  2  HTH_9            RNA polymerase III subunit RPC82 helix-turn-
    0.00082   19.4   0.1     0.0013   18.7   0.1    1.3  1  HypA             Hydrogenase/urease nickel incorporation, met
     0.0021   18.0   0.8     0.0036   17.3   0.8    1.3  1  DZR              Double zinc ribbon
     0.0032   17.3   2.3      0.029   14.3   2.3    2.3  1  Zn_ribbon_SprT   SprT-like zinc ribbon domain
     0.0039   17.5   0.0     0.0097   16.2   0.0    1.6  1  Rrf2             Transcriptional regulator
     0.0041   17.5   0.4     0.0071   16.7   0.4    1.4  1  Lar_restr_allev  Restriction alleviation protein Lar
     0.0054   16.6   1.9      0.017   15.0   1.9    1.9  1  zinc_ribbon_4    zinc-ribbon domain
     0.0058   16.3   2.3       0.61    9.9   0.1    2.3  2  zinc_ribbon_2    zinc-ribbon domain
     0.0082   15.8   1.8        1.4    8.7   0.0    2.3  2  A2L_zn_ribbon    A2L zinc ribbon domain
     0.0088   15.4   0.7       0.77    9.3   0.1    2.3  2  zf-ribbon_3      zinc-ribbon domain
  ------ inclusion threshold ------
       0.02   14.8   0.8          1    9.3   0.1    2.2  2  Prok-RING_1      Prokaryotic RING finger family 1
      0.026   14.4   4.4       0.23   11.4   1.2    2.2  2  zf-HIT           HIT zinc finger
      0.028   14.9   0.4        0.6   10.6   0.1    2.2  2  Sld5             GINS complex protein
      0.033   14.1   0.1      0.097   12.6   0.0    1.9  2  HTH_5            Bacterial regulatory protein, arsR family
      0.038   14.1   0.0      0.056   13.6   0.0    1.3  1  FYVE             FYVE zinc finger
      0.038   14.0   2.7      0.072   13.1   2.7    1.4  1  ADK_lid          Adenylate kinase, active site lid
      0.048   13.9   0.3      0.081   13.2   0.3    1.4  1  IBR              IBR domain, a half RING-finger domain
       0.05   13.5   1.9        4.7    7.2   0.1    1.9  2  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.051   13.4   0.2      0.051   13.4   0.2    2.1  2  zf-C2H2_3        zinc-finger of acetyl-transferase ESCO
      0.056   13.4   0.7       0.11   12.5   0.7    1.5  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
      0.075   12.8   0.3       0.13   12.0   0.3    1.3  1  Ribosomal_S27e   Ribosomal protein S27
      0.078   12.9   0.0       0.15   12.0   0.0    1.4  1  MarR_2           MarR family
       0.09   12.9   0.1       0.21   11.7   0.1    1.7  1  Sigma70_r3       Sigma-70 region 3
      0.094   12.8   0.0       0.58   10.3   0.0    2.0  2  Ribosomal_S16    Ribosomal protein S16
      0.099   12.4   3.5        2.4    8.0   3.6    2.3  1  zinc_ribbon_10   Predicted integral membrane zinc-ribbon meta
       0.14   12.3   1.7       0.69   10.1   0.2    2.2  2  zf-UDP           Zinc-binding RING-finger
       0.21   11.9   2.3        8.5    6.8   0.2    1.9  1  C1_2             C1 domain
       0.22   12.5   1.2         16    6.7   0.1    2.4  2  zf-C2H2_4        C2H2-type zinc finger
        0.3   11.0   2.5          3    7.8   0.2    2.3  2  Nudix_N_2        Nudix N-terminal
       0.36   10.9   3.9        3.2    7.8   0.1    2.9  3  CpXC             CpXC protein
       0.45   11.1   4.3         11    6.6   0.9    2.4  2  zf-C2H2          Zinc finger, C2H2 type
       0.47   10.4   2.9        1.1    9.2   2.9    1.6  1  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
       0.54   10.4   2.9        3.4    7.8   0.2    2.2  2  zf-Mss51         Zinc-finger of mitochondrial splicing suppre
        0.6   10.2   6.2        3.1    7.9   0.4    2.7  2  zf-ACC           Acetyl-coA carboxylase zinc finger domain
        1.2    9.1   6.3        4.7    7.1   0.5    2.5  2  TFIIS_C          Transcription factor S-II (TFIIS)
          2    8.1   6.5       0.95    9.1   1.2    2.2  2  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain


Domain annotation for each model (and alignments):
>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.5   1.1     5e-42   2.3e-39       1     105 []       5     109 ..       5     109 .. 0.99

  Alignments for each domain:
  == domain 1  score: 133.5 bits;  conditional E-value: 5e-42
                                    HHHHHHHHHCS-HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEEEEEECCC CS
                    TFIIE_alpha   1 ellkevvrkfygeeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrdeekswykyywrinyek 80 
                                    e+l+e+++k++g++a++v++vL++++ev++edlak+lk+d++elrklLn+L+earlvky+r+rde+++wykyywri++e+
  gi|119719620|ref|YP_920115.1|   5 EALAEIAGKMFGDNAKKVMMVLASNVEVSDEDLAKDLKMDPPELRKLLNDLFEARLVKYRRARDENIGWYKYYWRITDEP 84 
                                    6899**************************************************************************** PP

                                    HCCCHHHHHHHHHHHHHHHHCCCTS CS
                    TFIIE_alpha  81 lvdvvkrkleevvkkLeeklekeen 105
                                    ++++++++++ +++ Le++l+ een
  gi|119719620|ref|YP_920115.1|  85 IQQILSDRKRLTLSILEKVLSLEEN 109
                                    ***********************98 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   3.6   2.2e-14     1e-11       1      41 [.     113     153 ..     113     155 .. 0.95

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 2.2e-14
                                    EEETTTTCEECHEETSTTCEEESSSSBEEEECCCCCCCHHH CS
                   TF_Zn_Ribbon   1 ykCPnCgstnlveDpergelvCtdCGlVlednsidegpewr 41 
                                    y+CP+Cg++++v ++e+++++C+ CG+Vle +++ +++e+ 
  gi|119719620|ref|YP_920115.1| 113 YVCPKCGTRYTVDEAENNNYTCEVCGEVLEPFDNTHRVEKL 153
                                    89********9999************************985 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0    0.0013      0.58      17      35 ..     102     121 ..      98     125 .. 0.73
   2 !    8.1   0.1    0.0063       2.8       6      21 ..     132     147 ..     131     155 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0013
                    Zn-ribbon_8  17 vlqsisdaplta.CPeCgse 35 
                                    ++ s  ++++t  CP+Cg +
  gi|119719620|ref|YP_920115.1| 102 KVLSLEENSETYvCPKCGTR 121
                                    55556678889999999974 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0063
                    Zn-ribbon_8   6 YrCeeCghefevlqsi 21 
                                    Y Ce Cg++ e++   
  gi|119719620|ref|YP_920115.1| 132 YTCEVCGEVLEPFDNT 147
                                    99*********98765 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.1   0.00029      0.13       1      16 [.     111     126 ..     111     128 .. 0.85
   2 ?    6.5   0.1     0.014       6.4       1      14 [.     130     143 ..     130     146 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00029
                         zf_UBZ   1 dtylCerCgkeipese 16 
                                    +ty+C++Cg++  ++e
  gi|119719620|ref|YP_920115.1| 111 ETYVCPKCGTRYTVDE 126
                                    69*******9988776 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.014
                         zf_UBZ   1 dtylCerCgkeipe 14 
                                    ++y+Ce Cg+ +++
  gi|119719620|ref|YP_920115.1| 130 NNYTCEVCGEVLEP 143
                                    58*******99876 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   6.2e-06    0.0028       5      59 ..       9      63 ..       6      65 .. 0.96
   2 ?   -0.8   0.1       3.8   1.7e+03      30      49 ..      85     105 ..      81     107 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 6.2e-06
                                   HHHHHCSTTHHHHHHHHHHHHSSBEHHHHHHHHSSTHHHHHHHHHHHHHTTSEEE CS
                          HTH_9  5 eiieehFGevvakVvetLlrkgrltlrelvkktkLsldqVkksLvvLiqhrlVqy 59
                                   ei+ ++FG+ ++kV+ +L ++   +  +l+k++k+++ + +k L  L   rlV+y
  gi|119719620|ref|YP_920115.1|  9 EIAGKMFGDNAKKVMMVLASNVEVSDEDLAKDLKMDPPELRKLLNDLFEARLVKY 63
                                   788899************************************************9 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 3.8
                                    HHHHHHHHS.STHHHHHHHHH CS
                          HTH_9  30 lrelvkktk.LsldqVkksLv 49 
                                    +++++++ k L+l+   k+L+
  gi|119719620|ref|YP_920115.1|  85 IQQILSDRKrLTLSILEKVLS 105
                                    566666666677777777765 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1     3e-06    0.0013      57      94 ..      99     139 ..      75     150 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 3e-06
                                    TTT-EEEEEEE--EEEETTTS-EEECHH..H.HHS-TTTSS CS
                           HypA  57 legaeLeieevpvkvrCreCgkefelee..k.alrCpkCgs 94 
                                    + +++L++ee + ++ C +Cg++++++e  + +++C+ Cg+
  gi|119719620|ref|YP_920115.1|  99 ILEKVLSLEENSETYVCPKCGTRYTVDEaeNnNYTCEVCGE 139
                                    4458999******************887543688*****97 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.8     8e-06    0.0036      10      42 ..     110     145 ..     105     148 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 8e-06
                            DZR  10 pdarfCseCgtklkavaa...edrCpsCgekvdpea 42 
                                    ++  +C++Cgt+    +a   +++C  Cge ++p +
  gi|119719620|ref|YP_920115.1| 110 SETYVCPKCGTRYTVDEAennNYTCEVCGEVLEPFD 145
                                    56679*******6644446799*******9988765 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   2.3   6.5e-05     0.029       4      37 ..     112     144 ..     112     145 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.5e-05
                 Zn_ribbon_SprT   4 vYrCtgCgreythhlsirrhnYrCrrCkgtLrgk 37 
                                    +Y+C+ Cg++yt+     + nY C  C+++L+++
  gi|119719620|ref|YP_920115.1| 112 TYVCPKCGTRYTVDEA-ENNNYTCEVCGEVLEPF 144
                                    7*******98887754.55589999999999876 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   2.2e-05    0.0097       8      59 ..      17      65 ..      13      68 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.2e-05
                                   HHHHHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                           Rrf2  8 eyalhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvr 59
                                   + a +++++La++ e   vs e++a+  ++ p+ l+k+l+ L +a lvk +r
  gi|119719620|ref|YP_920115.1| 17 DNAKKVMMVLASNVE---VSDEDLAKDLKMDPPELRKLLNDLFEARLVKYRR 65
                                   567789999999998...99****************************9877 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.4   1.6e-05    0.0071       2      47 ..     111     150 ..     110     162 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.6e-05
                Lar_restr_allev   2 eLkpCPfCggravlersqrvvaeigqcvyCadCgastpwfkiaede 47 
                                    e + CP Cg r ++ +++++ +      +C+ Cg +   f +++++
  gi|119719620|ref|YP_920115.1| 111 ETYVCPKCGTRYTVDEAENNNY------TCEVCGEVLEPFDNTHRV 150
                                    5689****************98......798899843334433333 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   1.9   3.9e-05     0.017       4      34 ..     114     140 ..     113     142 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.9e-05
                  zinc_ribbon_4   4 tCpsCkakyeiddeklpakgvkvrCskCghv 34 
                                    +Cp+C+++y++d++    +  + +C  Cg+v
  gi|119719620|ref|YP_920115.1| 114 VCPKCGTRYTVDEA----ENNNYTCEVCGEV 140
                                    6************4....6667777777765 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.1    0.0014      0.61      12      21 ..     110     120 ..     105     122 .. 0.70
   2 ?    6.1   0.2     0.021       9.2      10      22 ..     128     140 ..     126     141 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0014
                  zinc_ribbon_2  12 nakF.CpyCGt 21 
                                     +++ Cp+CGt
  gi|119719620|ref|YP_920115.1| 110 SETYvCPKCGT 120
                                    45557999998 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.021
                  zinc_ribbon_2  10 qdnakFCpyCGtp 22 
                                    ++n+  C+ CG+ 
  gi|119719620|ref|YP_920115.1| 128 ENNNYTCEVCGEV 140
                                    355555*****85 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0    0.0031       1.4      19      30 ..     110     121 ..     101     124 .. 0.79
   2 ?    6.4   0.4     0.017       7.4       1      10 [.     129     138 ..     129     141 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0031
                  A2L_zn_ribbon  19 qgylvCieCgas 30 
                                    +  +vC++Cg+ 
  gi|119719620|ref|YP_920115.1| 110 SETYVCPKCGTR 121
                                    5679******85 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.017
                  A2L_zn_ribbon   1 snlkvCsvCg 10 
                                    +n+++C+vCg
  gi|119719620|ref|YP_920115.1| 129 NNNYTCEVCG 138
                                    699******8 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.1    0.0017      0.77       2      10 ..     112     120 ..     111     128 .. 0.72
   2 ?    4.6   0.1     0.051        23       3      17 ..     132     146 ..     130     147 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0017
                    zf-ribbon_3   2 tvrCPnCGa 10 
                                    t+ CP+CG+
  gi|119719620|ref|YP_920115.1| 112 TYVCPKCGT 120
                                    566777775 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.051
                    zf-ribbon_3   3 vrCPnCGaplssddn 17 
                                    ++C  CG++l++ dn
  gi|119719620|ref|YP_920115.1| 132 YTCEVCGEVLEPFDN 146
                                    78999***8898665 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1    0.0023         1      15      30 ..     107     122 ..     104     125 .. 0.80
   2 ?    3.9   0.1      0.11        51       3      16 ..     130     143 ..     128     146 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0023
                    Prok-RING_1  15 keedDiVvCpeCgtpy 30 
                                    +e++   vCp+Cgt y
  gi|119719620|ref|YP_920115.1| 107 EENSETYVCPKCGTRY 122
                                    5566677*******88 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.11
                    Prok-RING_1   3 tgkkCpvCgkelke 16 
                                    ++  C+vCg+ l++
  gi|119719620|ref|YP_920115.1| 130 NNYTCEVCGEVLEP 143
                                    6889*****98875 PP

>> zf-HIT  HIT zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.2   0.00051      0.23      13      23 ..     112     122 ..     108     122 .. 0.89
   2 ?    4.0   0.1       0.1        47      13      20 ..     131     138 ..     127     142 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00051
                                    SEE-TTT--EE CS
                         zf-HIT  13 kYkCpkCntry 23 
                                     Y CpkC+try
  gi|119719620|ref|YP_920115.1| 112 TYVCPKCGTRY 122
                                    6*********9 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.1
                                    SEE-TTT- CS
                         zf-HIT  13 kYkCpkCn 20 
                                    +Y+C  C+
  gi|119719620|ref|YP_920115.1| 131 NYTCEVCG 138
                                    56666665 PP

>> Sld5  GINS complex protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1    0.0013       0.6      59      88 ..      36      69 ..      18      73 .. 0.82
   2 ?    2.5   0.0      0.44     2e+02      24      71 ..      94     157 ..      78     161 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0013
                                   HHHT.....HCHHHHHHHHHHHHHHHHHHHTHCH CS
                           Sld5 59 elard....ldelkrllrdllevRlakirkfaen 88
                                   +la+d    + el++ll+dl+e Rl k r   ++
  gi|119719620|ref|YP_920115.1| 36 DLAKDlkmdPPELRKLLNDLFEARLVKYRRARDE 69
                                   4556688889****************99887665 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.44
                                    HHCHHHHHHCCCHHTTS.............SSSTTTTTTHHHHHHHHHHHHT....HCHHHHHH CS
                           Sld5  24 wlspesleailedetks.............sdlpslpphflelavkllelard...ldelkrll 71 
                                     l+   le++l+ e++s              d    + + +e++  +le + +   +++lkr +
  gi|119719620|ref|YP_920115.1|  94 RLTLSILEKVLSLEENSetyvcpkcgtrytVDEAENNNYTCEVCGEVLEPFDNthrVEKLKRAI 157
                                    4555556666666666677778888888887788889999999999999888878888888776 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00022     0.097      19      47 .]      35      63 ..      18      63 .. 0.83
   2 ?   -2.0   0.1       7.7   3.5e+03       9      19 ..     104     115 ..      99     115 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00022
                                   HHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                          HTH_5 19 celaeelglsqstvShHLkkLreaGLVek 47
                                    +la++l++ ++ ++  L+ L ea+LV++
  gi|119719620|ref|YP_920115.1| 35 EDLAKDLKMDPPELRKLLNDLFEARLVKY 63
                                   69*************************86 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 7.7
                                    HHHTT.SSEEHH CS
                          HTH_5   9 klLae.gelcvc 19 
                                     +L+e +e++vc
  gi|119719620|ref|YP_920115.1| 104 LSLEEnSETYVC 115
                                    678887889998 PP

>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   0.00012     0.056       4      35 ..     107     141 ..     105     172 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00012
                                    -...--SB-TTT--B--SS...S--EE-TTT--EE CS
                           FYVE   4 kddsevkkCeiCakkFsll...rrrhhCrlCGkvv 35 
                                    +++se+  C++C +++++    +  + C +CG+v+
  gi|119719620|ref|YP_920115.1| 107 EENSETYVCPKCGTRYTVDeaeNNNYTCEVCGEVL 141
                                    57889999********97444499********996 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   2.7   0.00016     0.072       3      31 ..     114     141 ..     113     142 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00016
                                    E-TTT--EEETTTB--SSTTB-TTT--.- CS
                        ADK_lid   3 vCpkCGrsYhvvfnpPkveglCDkCGepL 31 
                                    vCpkCG+ Y v      ++  C +CGe L
  gi|119719620|ref|YP_920115.1| 114 VCPKCGTRYTVDE-AENNNYTCEVCGEVL 141
                                    9********9554.556999******976 PP

>> IBR  IBR domain, a half RING-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.3   0.00018     0.081      11      46 ..     105     139 ..      93     141 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00018
                            IBR  11 slesdpnlkwCprpdCeaiiekseg.cksvtCskCgf 46 
                                    sle+++++  Cp  +C++ +  +e  +++ tC+ Cg+
  gi|119719620|ref|YP_920115.1| 105 SLEENSETYVCP--KCGTRYTVDEAeNNNYTCEVCGE 139
                                    4788888999**..9*97777776656667*****96 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.1      0.01       4.7      42      57 ..     108     123 ..      99     126 .. 0.80
   2 ?    5.6   0.1     0.034        15      22      40 ..     124     143 ..     122     154 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.01
                 OrfB_Zn_ribbon  42 lsgrtfkCpnCgfead 57 
                                     +++t++Cp+Cg+++ 
  gi|119719620|ref|YP_920115.1| 108 ENSETYVCPKCGTRYT 123
                                    5889********9875 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.034
                 OrfB_Zn_ribbon  22 vnpay.TSktCseCgsknke 40 
                                    v++a     tC +Cg+++++
  gi|119719620|ref|YP_920115.1| 124 VDEAEnNNYTCEVCGEVLEP 143
                                    55555566789999988887 PP

>> zf-C2H2_3  zinc-finger of acetyl-transferase ESCO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   0.00011     0.051       4      30 ..     104     129 ..     103     132 .. 0.73
   2 ?    0.8   0.5      0.99   4.4e+02      13      20 ..     131     138 ..     127     139 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00011
                      zf-C2H2_3   4 LdlgqksfgasqCkeCgMvYnpgspeD 30 
                                    L+l  +s  +  C++Cg  Y+ +++e 
  gi|119719620|ref|YP_920115.1| 104 LSLEENS-ETYVCPKCGTRYTVDEAEN 129
                                    6665554.3345***********9985 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.99
                      zf-C2H2_3  13 asqCkeCg 20 
                                    + +C +Cg
  gi|119719620|ref|YP_920115.1| 131 NYTCEVCG 138
                                    468****8 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.7   0.00024      0.11      19      44 ..     113     138 ..     108     140 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00024
                  Zn_Tnp_IS1595  19 fvCPhCgsr.kayriktrglfqCkeCr 44 
                                     vCP+Cg r ++ + ++   + C+ C+
  gi|119719620|ref|YP_920115.1| 113 YVCPKCGTRyTVDEAEN-NNYTCEVCG 138
                                    69*****7766555565.********8 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.3   0.00029      0.13      10      36 ..     115     141 ..     113     145 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00029
                                    -TTTS-EEEEESS-SS-EEESSSTCEE CS
                 Ribosomal_S27e  10 CpdCenetvvFshaatvvkCisCgkvL 36 
                                    Cp+C+   +v +  +   +C+ Cg+vL
  gi|119719620|ref|YP_920115.1| 115 CPKCGTRYTVDEAENNNYTCEVCGEVL 141
                                    *************************98 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00032      0.15      22      56 ..      32      66 ..      20      70 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00032
                                   EEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                         MarR_2 22 ltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                   ++  +la+ l+++++ + ++l++L +a Lv +r++
  gi|119719620|ref|YP_920115.1| 32 VSDEDLAKDLKMDPPELRKLLNDLFEARLVKYRRA 66
                                   56679*************************99976 PP

>> Sigma70_r3  Sigma-70 region 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00046      0.21      20      52 ..      31      63 ..      18      70 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00046
                                   XXXHHHHHHHHTXXHHHHHHHHHHHXXXEETTX CS
                     Sigma70_r3 20 ePtpeEiAeeLglseekVrevleaarepvSldl 52
                                   e ++e++A+ L++++ ++r++l++  e++++ +
  gi|119719620|ref|YP_920115.1| 31 EVSDEDLAKDLKMDPPELRKLLNDLFEARLVKY 63
                                   789*******************98666666655 PP

>> Ribosomal_S16  Ribosomal protein S16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       2.6   1.2e+03      19      33 ..      65      75 ..      59     102 .. 0.75
   2 ?   10.3   0.0    0.0013      0.58      20      40 ..     151     171 ..     146     175 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 2.6
                                   SSTTSSESEEEEEEE CS
                  Ribosomal_S16 19 kprdgrpiEklGtYd 33
                                   ++rd    E++G+Y+
  gi|119719620|ref|YP_920115.1| 65 RARD----ENIGWYK 75
                                   5555....9999997 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0013
                                    STTSSESEEEEEEETTTTSST CS
                  Ribosomal_S16  20 prdgrpiEklGtYdPlakkke 40 
                                    ++ +r iE lG +dP +k+++
  gi|119719620|ref|YP_920115.1| 151 EKLKRAIELLGNWDPSPKQQA 171
                                    55689**********776654 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   3.6    0.0053       2.4      18      52 ..     108     139 ..     105     141 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0053
                 zinc_ribbon_10  18 knryalICskChshnGlapkeeleevkyrCpkCga 52 
                                    +n    +C+kC +    ++++e+e+ +y C  Cg+
  gi|119719620|ref|YP_920115.1| 108 ENSETYVCPKCGTR---YTVDEAENNNYTCEVCGE 139
                                    66677789999886...557899999999999997 PP

>> zf-UDP  Zinc-binding RING-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.2    0.0015      0.69      37      61 ..      99     123 ..      93     130 .. 0.84
   2 ?    1.5   0.1      0.75   3.4e+02       6      17 ..     129     140 ..     125     149 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0015
                         zf-UDP  37 vcrpcyeyerkdgnqsCPqCktryk 61 
                                    +  ++++ e    + +CP+C try+
  gi|119719620|ref|YP_920115.1|  99 ILEKVLSLEENSETYVCPKCGTRYT 123
                                    56678899999999**********7 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.75
                         zf-UDP   6 lngqiCqiCgdd 17 
                                     n+  C++Cg+ 
  gi|119719620|ref|YP_920115.1| 129 NNNYTCEVCGEV 140
                                    57789****985 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.2     0.019       8.5      13      29 ..     126     142 ..     122     145 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.019
                           C1_2  13 edssesfnCsaCgrkid 29 
                                    e ++++++C++Cg+  +
  gi|119719620|ref|YP_920115.1| 126 EAENNNYTCEVCGEVLE 142
                                    56788999999998655 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1     0.035        16       1      11 [.     113     123 ..     113     127 .. 0.84
   2 ?    4.5   0.1      0.18        80       1      10 [.     132     141 ..     132     150 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.035
                      zf-C2H2_4   1 fkCpiCgksFs 11 
                                    + Cp Cg++++
  gi|119719620|ref|YP_920115.1| 113 YVCPKCGTRYT 123
                                    89******994 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.18
                      zf-C2H2_4   1 fkCpiCgksF 10 
                                    ++C++Cg++ 
  gi|119719620|ref|YP_920115.1| 132 YTCEVCGEVL 141
                                    89****9876 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.2    0.0067         3      17      30 ..     107     120 ..     100     123 .. 0.80
   2 ?    6.4   3.3     0.019       8.6       3      31 ..     115     140 ..     114     142 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0067
                                    T-SS-EEEETTTTE CS
                      Nudix_N_2  17 gDnreRlvCpaCgt 30 
                                    ++n e +vCp+Cgt
  gi|119719620|ref|YP_920115.1| 107 EENSETYVCPKCGT 120
                                    57777899999997 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.019
                                    -TTT--B-EEE--TT-SS-EEEETTTTEE CS
                      Nudix_N_2   3 CsqCGtpvelripdgDnreRlvCpaCgti 31 
                                    C++CGt+  + + d+ +   ++C+ Cg +
  gi|119719620|ref|YP_920115.1| 115 CPKCGTR--YTV-DEAENNNYTCEVCGEV 140
                                    *****99..555.4455556999999977 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.99   4.4e+02      57      85 ..      17      54 ..      11      82 .. 0.61
   2 ?    7.8   0.1    0.0071       3.2      32      50 ..     107     125 ..      95     129 .. 0.80
   3 ?    2.1   0.1      0.42   1.9e+02      36      47 ..     130     141 ..     124     160 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.99
                           CpXC 57 dpekellillvpeserseee......eieeaeek.........e 85
                                   d +k+++++l+ + e s+e+             +         +
  gi|119719620|ref|YP_920115.1| 17 DNAKKVMMVLASNVEVSDEDlakdlkM------DppelrkllnD 54
                                   788999999999999998885433220......13333333332 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0071
                           CpXC  32 dgslfeatCpkCgatakle 50 
                                    +++  +++CpkCg++ +++
  gi|119719620|ref|YP_920115.1| 107 EENSETYVCPKCGTRYTVD 125
                                    56678999*****998876 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.42
                           CpXC  36 featCpkCgata 47 
                                    +++tC+ Cg+  
  gi|119719620|ref|YP_920115.1| 130 NNYTCEVCGEVL 141
                                    789******876 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.9     0.026        11       1      11 [.     113     123 ..     113     124 .. 0.90
   2 ?    5.4   0.1     0.065        29       1       9 [.     132     140 ..     132     148 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.026
                                    EEETTTTEEES CS
                        zf-C2H2   1 ykCpdCgksFk 11 
                                    y+Cp+Cg +++
  gi|119719620|ref|YP_920115.1| 113 YVCPKCGTRYT 123
                                    9******9986 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.065
                                    EEETTTTEE CS
                        zf-C2H2   1 ykCpdCgks 9  
                                    y+C++Cg++
  gi|119719620|ref|YP_920115.1| 132 YTCEVCGEV 140
                                    9******65 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   2.9    0.0024       1.1       4      29 ..     115     139 ..     114     146 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0024
                                    ESTTTSBEEEEECSCCCEEEESSSS- CS
                 RNA_POL_M_15KD   4 CpkCgNlLlpkedkegknfeCrqCgY 29 
                                    CpkCg    ++e++ + n+ C  Cg 
  gi|119719620|ref|YP_920115.1| 115 CPKCGTRYTVDEAENN-NYTCEVCGE 139
                                    *****99888888877.59*****95 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.2    0.0075       3.4      11      30 ..     107     126 ..      81     128 .. 0.80
   2 ?    5.1   3.3     0.053        24       2      23 ..     115     138 ..     114     142 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0075
                       zf-Mss51  11 apkhvdfeCpdCGiptycse 30 
                                    ++++ ++ Cp+CG  + ++e
  gi|119719620|ref|YP_920115.1| 107 EENSETYVCPKCGTRYTVDE 126
                                    567789*******8776665 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.053
                       zf-Mss51   2 CPvpkhkqt..apkhvdfeCpdCG 23 
                                    CP + ++ t  + ++ +++C  CG
  gi|119719620|ref|YP_920115.1| 115 CPKCGTRYTvdEAENNNYTCEVCG 138
                                    9999999888899999*******9 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.4     0.007       3.1      21      26 .]     113     118 ..     105     118 .. 0.80
   2 ?    4.3   0.9     0.099        44      17      26 .]     128     137 ..     124     140 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.007
                         zf-ACC  21 yVCPkC 26 
                                    yVCPkC
  gi|119719620|ref|YP_920115.1| 113 YVCPKC 118
                                    8***** PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.099
                         zf-ACC  17 ernlyVCPkC 26 
                                    e+n+y+C  C
  gi|119719620|ref|YP_920115.1| 128 ENNNYTCEVC 137
                                    99*****999 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.5     0.011       4.7      27      39 .]     111     123 ..     107     123 .. 0.75
   2 ?    3.8   5.3      0.12        52       3      36 ..     115     139 ..     113     141 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.011
                        TFIIS_C  27 vfykCtkCghrWr 39 
                                      y+C kCg r++
  gi|119719620|ref|YP_920115.1| 111 ETYVCPKCGTRYT 123
                                    5699999999985 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.12
                        TFIIS_C   3 CpkCgsreayffqlQtRsaDEpmtvfykCtkCgh 36 
                                    CpkCg r ++         DE +   y+C  Cg+
  gi|119719620|ref|YP_920115.1| 115 CPKCGTRYTV---------DEAENNNYTCEVCGE 139
                                    8888888887.........888888888888886 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.3      0.38   1.7e+02       3      14 ..     109     120 ..     107     127 .. 0.80
   2 ?    9.1   1.2    0.0021      0.95       3      17 ..     128     142 ..     126     145 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.38
                                    TT-EEE-TTT-- CS
                Desulfoferrod_N   3 klevYkCevCGn 14 
                                    + e Y C  CG 
  gi|119719620|ref|YP_920115.1| 109 NSETYVCPKCGT 120
                                    6799*******6 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0021
                                    TT-EEE-TTT--EEE CS
                Desulfoferrod_N   3 klevYkCevCGniVe 17 
                                    +++ Y CevCG++ e
  gi|119719620|ref|YP_920115.1| 128 ENNNYTCEVCGEVLE 142
                                    5678*******9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       945  (0.0527079); expected 358.6 (0.02)
Passed bias filter:                      774  (0.0431703); expected 358.6 (0.02)
Passed Vit filter:                       155  (0.00864521); expected 17.9 (0.001)
Passed Fwd filter:                        40  (0.00223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              40  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1241.98
//
Query:       gi|119719621|ref|YP_920116.1|  [L=213]
Description: RpiR family transcriptional regulator [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-08   34.7   0.5    2.8e-08   33.3   0.2    1.9  2  Sigma70_r4_2     Sigma-70, region 4
      9e-07   28.5   0.1    2.7e-06   27.0   0.1    1.8  1  HTH_23           Homeodomain-like domain
    6.5e-06   26.2   0.3    2.1e-05   24.6   0.1    2.0  1  HTH_28           Helix-turn-helix domain
    1.6e-05   24.5   0.1    5.8e-05   22.8   0.1    1.9  1  HTH_38           Helix-turn-helix domain
    2.4e-05   24.3   0.3    7.3e-05   22.7   0.1    1.8  2  Sigma70_ECF      ECF sigma factor
    5.6e-05   22.6   0.1    0.00014   21.3   0.1    1.7  1  Sigma70_r4       Sigma-70, region 4
      8e-05   22.5   0.2    0.00036   20.4   0.1    2.1  2  HTH_11           HTH domain
    0.00015   21.2   0.1    0.00044   19.7   0.0    1.8  1  GerE             Bacterial regulatory proteins, luxR family
    0.00049   19.9   2.6        0.3   11.0   0.1    3.1  3  TrmB             Sugar-specific transcriptional regulator Trm
    0.00062   19.7   0.0     0.0018   18.2   0.0    1.8  1  HTH_29           Winged helix-turn helix
      0.001   18.8   0.1      0.013   15.3   0.1    2.3  2  HTH_8            Bacterial regulatory protein, Fis family
     0.0013   18.7   1.1       0.04   13.9   0.2    2.4  2  DUF2089          Protein of unknown function (DUF2089)
     0.0021   18.1   0.5      0.015   15.3   0.1    2.4  2  HTH_22           HTH domain
     0.0043   17.5   0.1      0.013   15.9   0.1    2.0  1  HTH_40           Helix-turn-helix domain
     0.0051   16.6   0.1      0.049   13.4   0.0    2.2  2  HTH_30           PucR C-terminal helix-turn-helix domain
     0.0064   16.7   0.3      0.018   15.2   0.0    1.8  1  UPF0122          Putative helix-turn-helix protein, YlxM / p1
     0.0067   16.4   0.0       0.74    9.8   0.0    2.2  2  DUF1804          Protein of unknown function (DUF1804)
  ------ inclusion threshold ------
      0.013   15.5   1.9       0.06   13.3   0.1    2.7  2  HTH_6            Helix-turn-helix domain, rpiR family
      0.018   15.0   0.1          3    7.9   0.0    2.4  2  HTH_Crp_2        Crp-like helix-turn-helix domain
      0.023   14.9   0.1      0.066   13.4   0.1    1.8  1  HTH_17           Helix-turn-helix domain
      0.025   14.6   0.6       0.09   12.9   0.2    2.2  1  HTH_7            Helix-turn-helix domain of resolvase
      0.026   14.5   0.1       0.16   11.9   0.0    2.2  2  HTH_36           Helix-turn-helix domain
      0.048   13.5   0.2       0.85    9.5   0.0    2.3  2  HTH_Tnp_Tc3_1    Tc3 transposase
      0.048   13.9   0.4        0.1   12.8   0.4    1.5  1  MutS_III         MutS domain III
      0.052   13.0   0.1       0.15   11.5   0.0    1.9  2  HTH_Tnp_ISL3     Helix-turn-helix domain of transposase famil
      0.054   13.8   0.1       0.23   11.8   0.1    2.1  1  HTH_Tnp_1        Transposase
      0.061   13.2   0.0       0.16   11.8   0.0    1.8  1  Terminase_5      Putative ATPase subunit of terminase (gpP-li
      0.063   13.1   0.0       0.91    9.4   0.0    2.4  2  DUF746           Domain of Unknown Function (DUF746)
        0.1   12.2   0.2         12    5.5   0.2    2.1  2  CENP-F_N         Cenp-F N-terminal domain
       0.16   12.2   1.6         23    5.3   0.0    3.6  4  DDE_Tnp_IS66_C   IS66 C-terminal element
       0.16   12.0   1.5        3.4    7.8   0.1    2.7  2  HTH_3            Helix-turn-helix
       0.17   11.9   0.0       0.42   10.7   0.0    1.6  1  Phage_terminase  Phage terminase small subunit


Domain annotation for each model (and alignments):
>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.2   5.1e-11   2.8e-08       2      52 ..       3      53 ..       2      54 .. 0.95
   2 ?   -2.5   0.0       7.6   4.3e+03      47      53 ..     107     113 ..     103     114 .. 0.69

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 5.1e-11
                                   HHHHHHHTTS-HHHHHHHHHHHTS---HHHHHHHHT--HHHHHHHHHHHHH CS
                   Sigma70_r4_2  2 qalrealaeLperqreifllryleglsykEIAellgisegtVksrlsRArk 52
                                   ++lr+ l+ L+  +r+i++ +   g s kEIA+ll++se+tV+++l++ rk
  gi|119719621|ref|YP_920116.1|  3 DELRNVLSNLTDTERRIVEVYMQRGGSAKEIASLLNVSERTVYKALYKYRK 53
                                   6899******************************************99776 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 7.6
                                    HHHHHHH CS
                   Sigma70_r4_2  47 lsRArkk 53 
                                    ++RA+k 
  gi|119719621|ref|YP_920116.1| 107 VQRALKS 113
                                    7899986 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.1   4.9e-09   2.7e-06      14      45 ..      23      59 ..      16      63 .. 0.80

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 4.9e-09
                         HTH_23 14 lae.GlsvreIAreLgvsrrTvyrwlkryr....eeG 45
                                   + + G s +eIA +L+vs+rTvy+ l +yr    e G
  gi|119719621|ref|YP_920116.1| 23 YMQrGGSAKEIASLLNVSERTVYKALYKYRklalEQG 59
                                   666799***********************85555555 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.1   3.7e-08   2.1e-05       8      38 ..      23      53 ..      17      62 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 3.7e-08
                         HTH_28  8 llaaGhsvreaArelgisrrtvyrWikryee 38
                                   ++++G+s++e+A +l++s+rtvy+ + +y++
  gi|119719621|ref|YP_920116.1| 23 YMQRGGSAKEIASLLNVSERTVYKALYKYRK 53
                                   456899********************99997 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.1     1e-07   5.8e-05       4      41 ..      11      48 ..      10      49 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1e-07
                         HTH_38  4 hLsleeReeIerllaeGlslreIArrLgrspsTIsREl 41
                                    L+ +eR+  e   ++G s +eIA +L++s  T+++ l
  gi|119719621|ref|YP_920116.1| 11 NLTDTERRIVEVYMQRGGSAKEIASLLNVSERTVYKAL 48
                                   59********************************9865 PP

>> Sigma70_ECF  ECF sigma factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.1   1.3e-07   7.3e-05     128     176 ..       4      52 ..       1      59 [. 0.83
   2 ?   -1.8   0.0       4.3   2.4e+03     125     143 ..     147     165 ..     123     177 .. 0.58

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.3e-07
                    Sigma70_ECF 128 ealerllsldpeqarlvelrkleGlsveEiAeklgvskrtverrlalaR 176
                                    e  + l +l +  +r ve+ +  G s +EiA  l+vs+rtv++ l   R
  gi|119719621|ref|YP_920116.1|   4 ELRNVLSNLTDTERRIVEVYMQRGGSAKEIASLLNVSERTVYKALYKYR 52 
                                    3334455599********************************9986555 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.3
                    Sigma70_ECF 125 eLdealerllsldpeqarl 143
                                     L + le+l    ++ a++
  gi|119719621|ref|YP_920116.1| 147 RLSDVLEKLNYNIERLAEK 165
                                    4555555554444444333 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.1   2.6e-07   0.00014       1      37 [.       8      44 ..       8      48 .. 0.96

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2.6e-07
                                   HHHHS-HHHHHHHHHHHTTT--HHHHHHHHTS-HHHH CS
                     Sigma70_r4  1 aLasLpererevlelrfgeglTleEIgerlgiSrerV 37
                                   +L+ L++ er+++e +  +g + +EI+  l++S+ +V
  gi|119719621|ref|YP_920116.1|  8 VLSNLTDTERRIVEVYMQRGGSAKEIASLLNVSERTV 44
                                   5899******************************998 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.1   6.4e-07   0.00036       3      36 ..      17      48 ..      15      53 .. 0.84
   2 ?   -1.3   0.0         4   2.2e+03      17      26 ..     158     167 ..     147     173 .. 0.64

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 6.4e-07
                         HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdI 36
                                   + i+e  ++  g  s++e+A  LnvS+rtv++ +
  gi|119719621|ref|YP_920116.1| 17 RRIVEVYMQRGG--SAKEIASLLNVSERTVYKAL 48
                                   677777755555..*****************975 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 4
                         HTH_11  17 sgeeLAeeLn 26 
                                    ++e+LAe+++
  gi|119719621|ref|YP_920116.1| 158 NIERLAEKID 167
                                    4567777765 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   7.9e-07   0.00044       2      34 ..      11      44 ..      10      54 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 7.9e-07
                                   SS-HHHHHHHHHHCT.TS-HHHHHHHHTS-HHHH CS
                           GerE  2 sLskRErevLrllae.GksnkeIAeelniSekTV 34
                                   +L++ Er + +  ++ G s keIA+ ln+Se+TV
  gi|119719621|ref|YP_920116.1| 11 NLTDTERRIVEVYMQrGGSAKEIASLLNVSERTV 44
                                   79********976655*****************9 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.1   0.00053       0.3      22      44 ..      27      49 ..      10      54 .. 0.83
   2 ?    6.6   0.1     0.012         7      26      58 ..      94     126 ..      87     140 .. 0.76
   3 ?    0.8   0.0      0.81   4.5e+02      26      66 ..     149     189 ..     145     191 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00053
                                   CCHHCHHCCCTTSSCHCHHHHHH CS
                           TrmB 22 patadeiaeelgvprskvYevLr 44
                                     +a+eia+ l+v++ +vY++L 
  gi|119719621|ref|YP_920116.1| 27 GGSAKEIASLLNVSERTVYKALY 49
                                   5679****************995 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.012
                                    CHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                           TrmB  26 deiaeelgvprskvYevLrsLedkGlVerekgr 58 
                                    + ++e +++ + +v+++L+s+++  +V r+++r
  gi|119719621|ref|YP_920116.1|  94 ELVSELAKIVEESVQRALKSMLEDLVVPRQDQR 126
                                    669999***************997777776655 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.81
                                    CHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE-- CS
                           TrmB  26 deiaeelgvprskvYevLrsLedkGlVerekgrpklYravd 66 
                                    +++ e+l+    +  e + +L + G  + +  +p+  +a +
  gi|119719621|ref|YP_920116.1| 149 SDVLEKLNYNIERLAEKIDRLDSSGTAKAIAHEPYSWQAKP 189
                                    67888888888888888999999999999999988877776 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   3.3e-06    0.0018       9      39 ..      25      54 ..      23      65 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.3e-06
                         HTH_29  9 aeGvstvsqiAkllglsrrtvyrwlkrfeeg 39
                                    +G+s  ++iA ll++s+rtvy++l  +++ 
  gi|119719621|ref|YP_920116.1| 25 QRGGS-AKEIASLLNVSERTVYKALYKYRKL 54
                                   57997.*****************99888875 PP

>> HTH_8  Bacterial regulatory protein, Fis family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   2.3e-05     0.013       2      42 .]      12      51 ..      11      51 .. 0.91
   2 ?    0.9   0.0      0.71     4e+02      10      27 ..     148     165 ..     146     167 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.3e-05
                                   HHHHHHHHHHHHHHHTTT-HHHHHHHHTS-HHHHHHHHHHT CS
                          HTH_8  2 leevEkelIeaALertgGnkskAArlLGisRrtLyrKLkkY 42
                                   l ++E+++ e  ++r g   ++ A lL++s rt+y+ L kY
  gi|119719621|ref|YP_920116.1| 12 LTDTERRIVEVYMQRGG-SAKEIASLLNVSERTVYKALYKY 51
                                   56899999999999965.********************998 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.71
                                    HHHHHHHTTT-HHHHHHH CS
                          HTH_8  10 IeaALertgGnkskAArl 27 
                                    + ++Le+ ++n+ + A+ 
  gi|119719621|ref|YP_920116.1| 148 LSDVLEKLNYNIERLAEK 165
                                    7799*********99985 PP

>> DUF2089  Protein of unknown function (DUF2089)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.2   7.2e-05      0.04      31      72 ..       9      50 ..       5     114 .. 0.87
   2 ?    3.4   0.1      0.13        75      62      86 ..     140     164 ..     132     181 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7.2e-05
                        DUF2089 31 farLskeqlefvelfikarGnlkevekelgisYpTvrnrlde 72
                                   +++L++ + + ve++++  G+ ke+++ l++s  Tv + l +
  gi|119719621|ref|YP_920116.1|  9 LSNLTDTERRIVEVYMQRGGSAKEIASLLNVSERTVYKALYK 50
                                   678999******************************988865 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.13
                        DUF2089  62 sYpTvrnrldeileaLgyeeeeeee 86 
                                     Y  v  rl ++le+L+y+ e+ +e
  gi|119719621|ref|YP_920116.1| 140 HYDQVLYRLSDVLEKLNYNIERLAE 164
                                    5888999***********9997633 PP

>> HTH_22  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   2.8e-05     0.015      42      62 ..      28      48 ..      23      49 .. 0.92
   2 ?    0.1   0.0       1.5   8.7e+02      14      33 ..      82     100 ..      67     115 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.8e-05
                         HTH_22 42 gavekvAekLgiSraTvYryL 62
                                   g+++++A+ L++S+ TvY+ L
  gi|119719621|ref|YP_920116.1| 28 GSAKEIASLLNVSERTVYKAL 48
                                   7999**************977 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.5
                         HTH_22  14 gkpverltkeekieivraLd 33 
                                    g+p ++l  + k+e+v++L 
  gi|119719621|ref|YP_920116.1|  82 GVP-SELLESIKQELVSELA 100
                                    555.6777777888888885 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   2.3e-05     0.013       9      78 ..      23      97 ..      15     160 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.3e-05
                         HTH_40  9 l.eeglsieeIAkerglkesTIegHLaeliee..geeidlerlvseeeekeIeeaiek.....vgseklkpikealpe 78
                                   + + g s +eIA   +++e T+++ L ++ +   ++ id ++++    +k+I+ + +k     v+se l  ik++l +
  gi|119719621|ref|YP_920116.1| 23 YmQRGGSAKEIASLLNVSERTVYKALYKYRKLalEQGIDPSNFY---LRKTIAGTAAKpvqqgVPSELLESIKQELVS 97
                                   44899************************999444566667764...4444444444433335777778888888854 PP

>> HTH_30  PucR C-terminal helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   8.8e-05     0.049       4      38 ..      19      53 ..      17      65 .. 0.88
   2 ?    0.5   0.1      0.94   5.3e+02      29      46 ..     144     161 ..     136     168 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.8e-05
                                   HHHHHHHTTT-HHHHHHHHTS-HHHHHHHHHHHHH CS
                         HTH_30  4 TLraylenggnisatAkaLhvHrnTlryRLrriee 38
                                    +++y++ gg++++ A  L+v+  T+++ L + ++
  gi|119719621|ref|YP_920116.1| 19 IVEVYMQRGGSAKEIASLLNVSERTVYKALYKYRK 53
                                   689************************87766655 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.94
                                    HHHHHHHHHHHHS--TTS CS
                         HTH_30  29 lryRLrrieellgldldd 46 
                                    + yRL  + e l++++++
  gi|119719621|ref|YP_920116.1| 144 VLYRLSDVLEKLNYNIER 161
                                    889999999999998876 PP

>> UPF0122  Putative helix-turn-helix protein, YlxM / p13 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   3.3e-05     0.018      18      60 ..      12      54 ..       5      59 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.3e-05
                        UPF0122 18 LTekqanylelyyadDlSlsEiAeefnvsrqavydnikrtekl 60
                                   LT+  ++ +e+y++   S +EiA   nvs  +vy  + + +kl
  gi|119719621|ref|YP_920116.1| 12 LTDTERRIVEVYMQRGGSAKEIASLLNVSERTVYKALYKYRKL 54
                                   99*********************************99988776 PP

>> DUF1804  Protein of unknown function (DUF1804)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0    0.0013      0.74      10      83 ..      18      95 ..      13     100 .. 0.84
   2 ?    4.2   0.0     0.067        38      59     125 ..     102     169 ..      96     175 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0013
                        DUF1804 10 avRsaYvferlsleeaAkkagvseaTar....rwkreakekGdDWDklRaakrlaeggieevakqlledfvvqvqetl 83
                                   ++ + Y+++  s +e+A+ ++vse T+     ++++ a e+G D       k++a+++++ v++ + ++++  +++ l
  gi|119719621|ref|YP_920116.1| 18 RIVEVYMQRGGSAKEIASLLNVSERTVYkalyKYRKLALEQGIDPSNFYLRKTIAGTAAKPVQQGVPSELLESIKQEL 95
                                   55578999999**************9963333699************************9999999999887776655 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.067
                        DUF1804  59 laeggieevakqlledfvvqvqetleelrent.elsaedkveiLasLsdsfsktvaaakrldPelskl 125
                                    + e+ ++ + k +led+vv  q     ++  + ++   +  ++L +Lsd ++k+    +rl+ ++++l
  gi|119719621|ref|YP_920116.1| 102 IVEESVQRALKSMLEDLVVPRQDQRAPVEPVKpAVLEPHYDQVLYRLSDVLEKLNYNIERLAEKIDRL 169
                                    6677888888888888888877776666665543444455689999***9999999999999999987 PP

>> HTH_6  Helix-turn-helix domain, rpiR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   0.00011      0.06       6      53 ..       4      46 ..       1      50 [. 0.88
   2 ?    0.4   0.0       1.1   6.4e+02       3      30 ..     144     171 ..     142     180 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00011
                                   HHHHH-----HHHHHHHHHHHH-S---TT--HHHHHHHTT--HHHHHH CS
                          HTH_6  6 kiqskkekltksekkiaeyilaspdkaielsikalAkaaavSeativr 53
                                    +++  ++lt+ e++i+e+  +        s k++A  ++vSe t+ +
  gi|119719621|ref|YP_920116.1|  4 ELRNVLSNLTDTERRIVEVYMQRGG-----SAKEIASLLNVSERTVYK 46
                                   689999************9988775.....7799***********987 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.1
                                    HHHHHHHH-----HHHHHHHHHHHH-S- CS
                          HTH_6   3 llekiqskkekltksekkiaeyilaspd 30 
                                    +l +++   ekl+ + +++ae i +  +
  gi|119719621|ref|YP_920116.1| 144 VLYRLSDVLEKLNYNIERLAEKIDRLDS 171
                                    6778888999999999999999876555 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0053         3      23      47 ..      29      53 ..       6      61 .. 0.84
   2 ?    4.9   0.0     0.046        26      21      48 ..      90     117 ..      67     138 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0053
                                   HHHHHHHHTTSSHHHHHHHHHHHHH CS
                      HTH_Crp_2 23 tqeelAsmlGltretvsrilseLkr 47
                                   + +e+As+l+++  tv ++l + ++
  gi|119719621|ref|YP_920116.1| 29 SAKEIASLLNVSERTVYKALYKYRK 53
                                   668***************9987665 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.046
                                    EHHHHHHHHHTTSSHHHHHHHHHHHHHT CS
                      HTH_Crp_2  21 pltqeelAsmlGltretvsrilseLkre 48 
                                    ++ qe  +++  +  e+v r+l+ + ++
  gi|119719621|ref|YP_920116.1|  90 SIKQELVSELAKIVEESVQRALKSMLED 117
                                    6889999999*************99766 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   0.00012     0.066       4      21 ..      30      47 ..      29      58 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00012
                         HTH_17  4 veEaAelLgvsrstvyrl 21
                                    +E+A lL+vs++tvy+ 
  gi|119719621|ref|YP_920116.1| 30 AKEIASLLNVSERTVYKA 47
                                   69**************85 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   0.00016      0.09      20      42 ..      26      48 ..      15      50 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00016
                                   TT--STTTSSSS---SSSS--SS CS
                          HTH_7 20 eGisiskIAkevnisRsTvYRyl 42
                                    G s+++IA  +n+s  TvY+ l
  gi|119719621|ref|YP_920116.1| 26 RGGSAKEIASLLNVSERTVYKAL 48
                                   47899***************966 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00029      0.16      20      46 ..      25      48 ..      10      54 .. 0.88
   2 ?   -0.4   0.0         2   1.1e+03      39      48 ..     104     113 ..      86     118 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00029
                         HTH_36 20 knggcfpsqetlakrlglsknTvsrai 46
                                   ++gg   s + +a++l++s++Tv++a+
  gi|119719621|ref|YP_920116.1| 25 QRGG---SAKEIASLLNVSERTVYKAL 48
                                   5666...899***************98 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 2
                         HTH_36  39 knTvsraike 48 
                                    +++v+ra+k+
  gi|119719621|ref|YP_920116.1| 104 EESVQRALKS 113
                                    6778888874 PP

>> HTH_Tnp_Tc3_1  Tc3 transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0    0.0015      0.85       3      33 ..      10      40 ..       9      48 .. 0.89
   2 ?    1.5   0.0      0.48   2.7e+02      14      32 ..     150     168 ..     147     170 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0015
                                   ----HHHHHHHHHHHHTT--HHHHHHHHT-- CS
                  HTH_Tnp_Tc3_1  3 saLSDtEraillvmkllnvklsEiarklsRs 33
                                   s L DtEr i++v  + + + +Eia  l+ s
  gi|119719621|ref|YP_920116.1| 10 SNLTDTERRIVEVYMQRGGSAKEIASLLNVS 40
                                   679**********************999865 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.48
                                    HHHHHTT--HHHHHHHHT- CS
                  HTH_Tnp_Tc3_1  14 lvmkllnvklsEiarklsR 32 
                                    +v+ +ln ++  +a k++R
  gi|119719621|ref|YP_920116.1| 150 DVLEKLNYNIERLAEKIDR 168
                                    78999************99 PP

>> MutS_III  MutS domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.4   0.00018       0.1      67     185 ..       2     170 ..       1     173 [. 0.45

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00018
                                    HHHHHHHHTT---HHHHHHHHHTT--.-HHHHHHHHHHHHHHHTTTTT---SSTHHHHH..................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..................... RF
                       MutS_III  67 reelrellrrlpDleRllsrislgka.kardlkallealkaleelvallekeklaesee..................... 124
                                    ++elr+ l +l D+eR + +++ +++ +a+++++ll+  +++  ++ +    kla + +                     
  gi|119719621|ref|YP_920116.1|   2 SDELRNVLSNLTDTERRIVEVYMQRGgSAKEIASLLNVSERTVYKALYKY-RKLALE-Qgidpsnfylrktiagtaakpv 79 
                                    578899999999*********99997699998886444443222221111.111111.1222223344444444444444 PP

                                    .................HHHHHHHHHHB-SS--SSGGGS--B-T.............................HHHHHHH CS
                                    .................xxxxxxxxxxxxxxxxxxxxxxxxxxx.............................xxxxxxx RF
                       MutS_III 125 .................eslaelleeaideeplalekegedlra.............................iealeqe 158
                                                     ++la+++ee+                                              +e + ++
  gi|119719621|ref|YP_920116.1|  80 qqgvpsellesikqelvSELAKIVEES----------------VqralksmledlvvprqdqrapvepvkpavLEPHYDQ 143
                                    433332222222211111111111111................1122233333334444455555555554443333344 PP

                                    HHHHHHHHHHHTHHHHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       MutS_III 159 lfqelleeveealerlrrlaealaeLD 185
                                    ++ +l + +e+    ++rlae ++ LD
  gi|119719621|ref|YP_920116.1| 144 VLYRLSDVLEKLNYNIERLAEKIDRLD 170
                                    555555444444455666666666665 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00028      0.15      25      48 ..      24      48 ..      13      52 .. 0.76
   2 ?   -3.0   0.0       9.1   5.1e+03      41      48 ..     104     111 ..      96     113 .. 0.51

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00028
                   HTH_Tnp_ISL3 25 les.rsvkavArqlgvSwtTVwril 48
                                    ++  s k++A +l+vS++TV  +l
  gi|119719621|ref|YP_920116.1| 24 MQRgGSAKEIASLLNVSERTVYKAL 48
                                   455589***************8766 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 9.1
                   HTH_Tnp_ISL3  41 wtTVwril 48 
                                    + +V+r+l
  gi|119719621|ref|YP_920116.1| 104 EESVQRAL 111
                                    44555555 PP

>> HTH_Tnp_1  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1    0.0004      0.23      13      49 ..      17      58 ..      13     105 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0004
                      HTH_Tnp_1 13 ariVreslepgksvsevArrhgvspnq....LykWrrqyr.e 49
                                    riV+ +++ g s +e+A  ++vs+ +    Lyk r+++  +
  gi|119719621|ref|YP_920116.1| 17 RRIVEVYMQRGGSAKEIASLLNVSERTvykaLYKYRKLALeQ 58
                                   59*********************9864222288888887533 PP

>> Terminase_5  Putative ATPase subunit of terminase (gpP-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00029      0.16      14      39 ..      28      53 ..      14      60 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00029
                    Terminase_5 14 yrvaeIAeelglkeatVysWkkrdew 39
                                    + +eIA  l+++e+tVy    ++++
  gi|119719621|ref|YP_920116.1| 28 GSAKEIASLLNVSERTVYKALYKYRK 53
                                   5789**************87777766 PP

>> DUF746  Domain of Unknown Function (DUF746)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0    0.0016      0.91      15      46 ..      30      63 ..      28      73 .. 0.87
   2 ?    0.7   0.0      0.87   4.9e+02      37      48 ..     163     174 ..     150     177 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0016
                         DUF746 15 laeaadllgtdegiiakwvreFrewllq..LDPS 46
                                    +e+a ll ++e+++ k + ++r+++l+   DPS
  gi|119719621|ref|YP_920116.1| 30 AKEIASLLNVSERTVYKALYKYRKLALEqgIDPS 63
                                   5799**********************98445776 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.87
                         DUF746  37 rewllqLDPSGq 48 
                                     e +++LD SG 
  gi|119719621|ref|YP_920116.1| 163 AEKIDRLDSSGT 174
                                    56799*****95 PP

>> CENP-F_N  Cenp-F N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.2     0.021        12      10      56 ..      81     130 ..      75     138 .. 0.83
   2 ?    4.9   0.0      0.03        17     111     167 ..     152     209 ..     140     213 .] 0.87

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.021
                       CENP-F_N  10 eGLptkaLqki.qelesqldklkkerqqrqfq..LesLeaalqkqkqkve 56 
                                    +G+p+  L+ i qel s+l k+  e  qr  +  Le L    q q+  ve
  gi|119719621|ref|YP_920116.1|  81 QGVPSELLESIkQELVSELAKIVEESVQRALKsmLEDLVVPRQDQRAPVE 130
                                    799******9978****************986558888888888877666 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.03
                       CENP-F_N 111 iekLeqelkrykselersqqallssdvslsplstPqksfatplt.psqkksdskleel 167
                                    +ekL+ ++ r   +++r +++ +++ ++ +p+s   k ++t ++ ps+ + +  le l
  gi|119719621|ref|YP_920116.1| 152 LEKLNYNIERLAEKIDRLDSSGTAKAIAHEPYSWQAKPITTEVSmPSYVQGNPWLEIL 209
                                    79**************************************999977777777666666 PP

>> DDE_Tnp_IS66_C  IS66 C-terminal element
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       9.9   5.5e+03      17      30 ..       5      16 ..       5      21 .. 0.73
   2 ?   -1.3   0.0       4.6   2.6e+03       8      20 ..      57      70 ..      55      80 .. 0.72
   3 ?    3.5   0.1      0.15        85      17      34 ..     148     163 ..     146     170 .. 0.70
   4 ?    5.3   0.0     0.041        23       4      16 ..     173     185 ..     172     188 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 9.9
                 DDE_Tnp_IS66_C 17 LkdvLerlpdahpa 30
                                   L+ vL  l d  ++
  gi|119719621|ref|YP_920116.1|  5 LRNVLSNLTD--TE 16
                                   7899999997..33 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 4.6
                 DDE_Tnp_IS66_C  8 lNgvdPya.YLkdv 20
                                    +g+dP + YL+++
  gi|119719621|ref|YP_920116.1| 57 EQGIDPSNfYLRKT 70
                                   57999986566665 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.15
                 DDE_Tnp_IS66_C  17 LkdvLerlpdahpaedle 34 
                                    L dvLe+l +  + e+l 
  gi|119719621|ref|YP_920116.1| 148 LSDVLEKLNY--NIERLA 163
                                    889*****94..555554 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.041
                 DDE_Tnp_IS66_C   4 eTAKlNgvdPyaY 16 
                                    +TAK+  ++Py +
  gi|119719621|ref|YP_920116.1| 173 GTAKAIAHEPYSW 185
                                    6**********99 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.1     0.006       3.4       7      28 ..      25      46 ..      19      59 .. 0.86
   2 ?    2.6   0.0      0.25   1.4e+02       4      20 ..     151     167 ..     148     170 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.006
                                   HTTHHHHHHHHHHTSSHHHHHH CS
                          HTH_3  7 qlglsqeeLAeklGvsrstisr 28
                                   q+g s +e+A +l+vs +t+++
  gi|119719621|ref|YP_920116.1| 25 QRGGSAKEIASLLNVSERTVYK 46
                                   8999****************98 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.25
                                    HHHHTTHHHHHHHHHHT CS
                          HTH_3   4 lRkqlglsqeeLAeklG 20 
                                     +++l++ +e LAek++
  gi|119719621|ref|YP_920116.1| 151 VLEKLNYNIERLAEKID 167
                                    6799**********985 PP

>> Phage_terminase  Phage terminase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00075      0.42      15      41 ..      22      46 ..      17      52 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00075
                Phage_terminase 15 lykEsggtlklkdIAkvLdvsestvrk 41
                                   +y   gg    k+IA  L+vse+tv k
  gi|119719621|ref|YP_920116.1| 22 VYMQRGGS--AKEIASLLNVSERTVYK 46
                                   56666664..699***********964 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       909  (0.0507); expected 358.6 (0.02)
Passed bias filter:                      740  (0.0412739); expected 358.6 (0.02)
Passed Vit filter:                       113  (0.00630264); expected 17.9 (0.001)
Passed Fwd filter:                        32  (0.00178482); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              32  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 1322.40
//
Query:       gi|119719622|ref|YP_920117.1|  [L=243]
Description: cobalt transport protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-26   92.0  12.6    4.1e-26   92.0  12.6    1.5  1  CbiQ      Cobalt transport protein
  ------ inclusion threshold ------
        3.9    7.7  15.4       0.13   12.4   9.0    1.9  2  DUF3792   Protein of unknown function (DUF3792)


Domain annotation for each model (and alignments):
>> CbiQ  Cobalt transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.0  12.6   4.6e-30   4.1e-26       3     211 ..      14     207 ..      12     215 .. 0.84

  Alignments for each domain:
  == domain 1  score: 92.0 bits;  conditional E-value: 4.6e-30
                                    CCCCS-HHHHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHTTS---.HHHHHHHCCCHCHHHHHHHHHHE.......E CS
                           CbiQ   3 svlhrldprvkliwlfllllalvlapnlvtlliiiallllllllvilp.rvlaqalilpllflllgllillfqlittege 81 
                                    ++  rldpr+  ++   l  ++v +++ +   +i+ + +++++  + + r+l++ ++  + +++l +++ll+        
  gi|119719622|ref|YP_920117.1|  14 TPVDRLDPRTRFAISVTLAALSVYSSSALIQ-VIVLASVFAVATLARRcRLLVKGAV--GSLPILLMIFLLN-------- 82 
                                    6678999999988777776666666666555.5555555555444444255555555..5566666666665........ PP

                                    ECTTEEE...E-TTHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHHHHCCCSS--HHHHHHHHHHHHHHHHHHHHHHHHH CS
                           CbiQ  82 fvfagggqisitseGllrglllalRiltllslllllalTTppeeltsslerlgvPlelalillLayRfiflLleevqrik 161
                                    fvfa++       +G l++  +alR+l+l+s+ + +++TTppeel+ sle++gvP++ +l+++  +Rf+++L+  vq  +
  gi|119719622|ref|YP_920117.1|  83 FVFAPTP------QGALTSFAMALRFLALMSAFSVFFMTTPPEELALSLEEIGVPRDYSLLITMSFRFVPTLATDVQLVM 156
                                    9999999......******************************************************************* PP

                                    HHHHHTTTTS...SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS-SS CS
                           CbiQ 162 qAqklRlgds.klgirrslrslgkliaalflralkraervalAmeaRGYtg 211
                                    +A ++R+++  + ++r +++ +  l+++l++  ++r+  +a A+eaRGY  
  gi|119719622|ref|YP_920117.1| 157 DALRSRGLELeRGKLRVRIKNYVYLLVPLIVFEVRRSMMIAEALEARGYGS 207
                                    *************************************************76 PP

>> DUF3792  Protein of unknown function (DUF3792)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   9.0   1.5e-05      0.13      23     109 ..      25     108 ..      23     116 .. 0.85
   2 ?   -3.0   0.4       0.9     8e+03      17      21 ..     229     233 ..     219     241 .. 0.46

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.5e-05
                        DUF3792  23 lalllyftslsekvlsililiililsvfigGflagkkakkkgllnGllvGllyflillllsllikksgsafslkllikll 102
                                    +a+ ++  +ls ++ s+li++i+++svf+ + la   ++ + l++G++  l + l+++ll++++  + + + ++++++l 
  gi|119719622|ref|YP_920117.1|  25 FAISVTLAALSVYSSSALIQVIVLASVFAVATLA---RRCRLLVKGAVGSLPILLMIFLLNFVFAPTPQGALTSFAMALR 101
                                    788899999*******************999888...7778899999999999999********8888877777777777 PP

                        DUF3792 103 llllaga 109
                                    +l+l++a
  gi|119719622|ref|YP_920117.1| 102 FLALMSA 108
                                    7666665 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.9
                        DUF3792  17 lilll 21 
                                    +++++
  gi|119719622|ref|YP_920117.1| 229 VLMFF 233
                                    11111 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       692  (0.0385967); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1639.42
//
Query:       gi|119719623|ref|YP_920118.1|  [L=282]
Description: ABC transporter related [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.5e-31  107.3   0.0    1.8e-30  106.2   0.0    1.5  1  ABC_tran      ABC transporter
    1.2e-09   38.4   0.7    7.5e-06   26.0   0.0    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    1.1e-06   28.2   0.0    1.9e-06   27.5   0.0    1.3  1  SMC_N         RecF/RecN/SMC N terminal domain
    0.00052   20.6   0.0    0.00066   20.2   0.0    1.3  1  AAA_23        AAA domain
    0.00053   19.7   0.0    0.00099   18.8   0.0    1.4  1  AAA_29        P-loop containing region of AAA domain
    0.00083   19.6   0.6     0.0051   17.1   0.3    2.5  2  AAA_22        AAA domain
     0.0011   18.4   0.2       0.72    9.2   0.0    2.2  2  TniB          Bacterial TniB protein
     0.0022   18.4   0.0     0.0034   17.8   0.0    1.4  1  AAA_16        AAA ATPase domain
     0.0039   16.1   0.0     0.0056   15.6   0.0    1.2  1  DLIC          Dynein light intermediate chain (DLIC)
     0.0052   16.7   2.6      0.068   13.1   0.6    2.1  2  NTPase_1      NTPase
     0.0052   16.5   0.7      0.026   14.3   0.2    2.0  2  AAA_24        AAA domain
     0.0083   16.0   0.2      0.025   14.5   0.0    1.8  2  RsgA_GTPase   RsgA GTPase
  ------ inclusion threshold ------
      0.012   15.4   0.6       0.36   10.6   0.2    2.1  2  ATP_bind_1    Conserved hypothetical ATP binding protein
      0.016   14.9   0.0      0.026   14.2   0.0    1.3  1  AAA_15        AAA ATPase domain
      0.017   14.8   0.1       0.02   14.6   0.1    1.3  1  AAA_30        AAA domain
      0.027   14.4   0.2      0.053   13.4   0.2    1.6  1  ATPase_2      ATPase domain predominantly from Archaea
      0.031   14.5   0.2       0.07   13.3   0.2    1.5  1  Roc           Ras of Complex, Roc, domain of DAPkinase
      0.031   14.8   0.0       0.12   12.9   0.0    1.9  1  AAA_18        AAA domain
       0.05   13.6   0.1      0.094   12.7   0.1    1.4  1  TsaE          Threonylcarbamoyl adenosine biosynthesis protei
      0.052   13.3   0.0      0.078   12.7   0.0    1.3  1  PRK           Phosphoribulokinase / Uridine kinase family
      0.079   12.9   0.1       0.13   12.1   0.1    1.3  1  NACHT         NACHT domain
      0.085   12.2   0.2       0.29   10.4   0.1    1.8  2  ATPase        KaiC
       0.11   12.1   0.0        0.3   10.7   0.0    1.6  2  SRP54         SRP54-type protein, GTPase domain
       0.12   11.8   0.0       0.18   11.2   0.0    1.3  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
       0.12   11.7   0.1        0.2   10.9   0.1    1.3  1  Zeta_toxin    Zeta toxin
       0.16    9.5   0.1        0.2    9.1   0.1    1.0  1  DUF3584       Protein of unknown function (DUF3584)
       0.21   11.7   0.7       0.34   11.0   0.7    1.7  1  MMR_HSR1      50S ribosome-binding GTPase


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.2   0.0   2.7e-33   1.8e-30       1     137 []      25     171 ..      25     171 .. 0.88

  Alignments for each domain:
  == domain 1  score: 106.2 bits;  conditional E-value: 2.7e-33
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS..--S-TTSBHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxx RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe..pqlfpeltvre 78 
                                    l+ v+l++++ge +ai+GenGaGK+tL+k + g lkp +G+++++g d+++++  +l++ +g+++q+  +qlf+e+ v++
  gi|119719623|ref|YP_920118.1|  25 LRGVTLEVRRGEFIAIMGENGAGKTTLIKHFNGILKPSKGTVKVKGIDTRTKSVAELSRIVGIVFQNpdHQLFEET-VYD 103
                                    6789***************************************************************978888888.777 PP

                                    H.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    x.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  79 n.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                    +               +++++ al+ l+l+  kd+     p+sLS G+k+r+ala +l+ +p++l+lDEpta
  gi|119719623|ref|YP_920118.1| 104 EvafalrnfgysedVIERRVAWALNILDLQRYKDRS----PYSLSVGEKRRLALASVLAYDPEVLVLDEPTA 171
                                    78*******955544455566666666666655555....5*****************************97 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.3   0.00032      0.21       1      22 [.      37      58 ..      37      83 .. 0.80
   2 !   26.0   0.0   1.1e-08   7.5e-06     186     300 ..      79     203 ..      67     206 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00032
                         AAA_21  1 lnvliGpNgsGKSnLLdaldll 22
                                   + ++ G Ng+GK++L++ + ++
  gi|119719623|ref|YP_920118.1| 37 FIAIMGENGAGKTTLIKHFNGI 58
                                   56899***********988776 PP

  == domain 2  score: 26.0 bits;  conditional E-value: 1.1e-08
                         AAA_21 186 qrlvrslklveielsdlgegeeliasvderlrer.............gvvflengdgqelparelSdGtkrllalltall 252
                                     +l+r +  v+ +++  ++ e  +++v+++lr                + +l+  +++++++++lS G kr lal++ l+
  gi|119719623|ref|YP_920118.1|  79 AELSRIVGIVFQNPDHQLFEETVYDEVAFALRNFgysedvierrvawALNILDLQRYKDRSPYSLSVGEKRRLALASVLA 158
                                    556666666666666666666666666666666677777777777888889999999***************9******* PP

                         AAA_21 253 ralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSpl 300
                                    +++    +l++DEp +g ++   +++ + +++l+  g  v+++TH+ +
  gi|119719623|ref|YP_920118.1| 159 YDP---EVLVLDEPTAGQDYLQKEKISQTMNLLRLMGKTVVIVTHDVE 203
                                    999...9*************999*******9999999********976 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0   2.8e-09   1.9e-06      25     205 ..      36     208 ..      23     220 .. 0.81

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 2.8e-09
                                    SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrrvk 104
                                    +f ai+G+NG+GK+ l+     +L  ++  +++ + ++    +  ++ +  +  v i+f+n+d++l +e+   ++   + 
  gi|119719623|ref|YP_920118.1|  36 EFIAIMGENGAGKTTLIKHFNGILKPSKG-TVKVKGIDT---R-TKSVAELSRIVGIVFQNPDHQLFEETVYDEVAFALR 110
                                    699*************9999888886555.566555443...3.444555566799*********999999999999999 PP

                                    TTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 105 rkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellk 184
                                    + g se  i+++ +   ++ +l + ++ s+ +LS Gek  +ala ++A   ++p+ l +lDe  a  D  + +k+++ ++
  gi|119719623|ref|YP_920118.1| 111 NFGYSEDVIERRVAWALNILDLQRYKDRSPYSLSVGEKRRLALASVLA---YDPEVL-VLDEPTAGQDYLQKEKISQTMN 186
                                    99*************************************999998876...788865.89*****999999999999888 PP

                                    HHCTT.SEEEEE-SSHHHCCC- CS
                                    xxxxx.xxxxxxxxxxxxxxxx RF
                          SMC_N 185 ekskn.aQfivislreemleka 205
                                      +     +++++++ e+++  
  gi|119719623|ref|YP_920118.1| 187 LLRLMgKTVVIVTHDVEFVTSY 208
                                    6655436677788888777655 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   9.9e-07   0.00066      11      46 ..      26      62 ..      20     153 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 9.9e-07
                         AAA_23 11 rdqeidFsk.gltlItGpNGaGKTTildAiklaLyge 46
                                   r+++++  +  + +I G+NGaGKTT++  +  +L   
  gi|119719623|ref|YP_920118.1| 26 RGVTLEVRRgEFIAIMGENGAGKTTLIKHFNGILKPS 62
                                   66677775525789*************9988887654 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.5e-06   0.00099      13      50 ..      26      63 ..      22      68 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.5e-06
                         AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                   +g t+e+++ +++ ++G++G+GK+Tl+  ++ +L p+k
  gi|119719623|ref|YP_920118.1| 26 RGVTLEVRRGEFIAIMGENGAGKTTLIKHFNGILKPSK 63
                                   56788998777****************98888888877 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.3   7.6e-06    0.0051       4      29 ..      34      59 ..      31     205 .. 0.82
   2 ?   -1.9   0.0       5.7   3.8e+03     101     116 ..     263     278 ..     255     281 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 7.6e-06
                         AAA_22  4 tagilvvtGesGtGKTtllrrlleql 29
                                   +  +++++Ge G+GKTtl++ +   l
  gi|119719623|ref|YP_920118.1| 34 RGEFIAIMGENGAGKTTLIKHFNGIL 59
                                   6789****************998776 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 5.7
                         AAA_22 101 qhlrs.eealeeLrsll 116
                                    ++l s ee++++Lr+++
  gi|119719623|ref|YP_920118.1| 263 DYL-SpEELFNDLRRIM 278
                                    677.5599999998875 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0    0.0011      0.72      34      57 ..      34      57 ..      25      83 .. 0.82
   2 !    7.0   0.0    0.0054       3.6     101     155 ..     142     197 ..     128     200 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0011
                           TniB 34 rmpnlllvGdsnnGKtmivekFar 57
                                   r + + ++G+   GKt+++++F  
  gi|119719623|ref|YP_920118.1| 34 RGEFIAIMGENGAGKTTLIKHFNG 57
                                   556689****************85 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0054
                           TniB 101 rarvskleqqvlrllrelkvrvLiiDEihnlla.gsarkqreflnalksLgnelki 155
                                    + +v ++++ +l+   +++++vL++DE        + +k  +++n+l+ +g ++ i
  gi|119719623|ref|YP_920118.1| 142 SLSVGEKRRLALASVLAYDPEVLVLDEPTAGQDyLQKEKISQTMNLLRLMGKTVVI 197
                                    45678899999999999**********87655414788899********9987755 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   5.1e-06    0.0034      18      73 ..      31      85 ..      22     168 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 5.1e-06
                         AAA_16 18 rvrsgrpelvllsGesGvGKsslvrellralekdggif.lrgkcdqlesaipysala 73
                                    vr+g  e + + Ge G GK++l++++   l+ ++g + ++g  ++ +s +++s ++
  gi|119719623|ref|YP_920118.1| 31 EVRRG--EFIAIMGENGAGKTTLIKHFNGILKPSKGTVkVKGIDTRTKSVAELSRIV 85
                                   46666..79*******************99999876666555444444445554444 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   8.5e-06    0.0056      27      55 ..      37      65 ..      30     101 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 8.5e-06
                           DLIC 27 svlvlGedgsGkttliaklqGveeekkGr 55
                                    + ++Ge+g+Gkttli  + G+ ++ kG 
  gi|119719623|ref|YP_920118.1| 37 FIAIMGENGAGKTTLIKHFNGILKPSKGT 65
                                   5789***********************96 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.6    0.0001     0.068       2      36 ..      38      74 ..      37      88 .. 0.83
   2 ?    3.6   0.1     0.085        56      70     153 ..     137     221 ..     115     232 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.0001
                                   EEEE--TTSSHHHHHHHHHHHH.....GGGEEEEEEE CS
                       NTPase_1  2 vfiTGppGvGKtTlvkkvlellkss..gvkvgGfyte 36
                                   ++i G+ G GKtTl+k     lk s   vkv+G+ t+
  gi|119719623|ref|YP_920118.1| 38 IAIMGENGAGKTTLIKHFNGILKPSkgTVKVKGIDTR 74
                                   6899******************976446999999775 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.085
                                    EETTEEE-HHHHHHHHHHHHHHHHHHH-EEEE--..-STTGGG-HHHHHHHHHHHTTTSEEEEE--SS-.-SHHHHHHHT CS
                       NTPase_1  70 rvgkyvvdvesfeelalealrkalseadviviDE..iGkmElkskkfkeaveevLksekpvlavihrrk.dlalveeire 146
                                      + y + v +  +lal+++     +++v+v+DE   G+  l+ +k++++++ +   +k v++v h  +   + v++i  
  gi|119719623|ref|YP_920118.1| 137 DRSPYSLSVGEKRRLALASVLA--YDPEVLVLDEptAGQDYLQKEKISQTMNLLRLMGKTVVIVTHDVEfVTSYVDRIVV 214
                                    5567888888888888888865..6899*****97779999999999999876555999999999988888888998887 PP

                                    -TT-EEE CS
                       NTPase_1 147 rkdvkvf 153
                                     +++kv+
  gi|119719623|ref|YP_920118.1| 215 MSGGKVI 221
                                    7777765 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.2   3.9e-05     0.026       5      24 ..      38      56 ..      34      81 .. 0.83
   2 ?    0.4   0.0      0.71   4.7e+02     108     130 ..     178     200 ..     172     207 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.9e-05
                         AAA_24  5 iliyGpsgiGKTtlakelgp 24
                                   i+i+G++g+GKTtl+k++ +
  gi|119719623|ref|YP_920118.1| 38 IAIMGENGAGKTTLIKHF-N 56
                                   89***************9.2 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.71
                         AAA_24 108 aeefrrllkklqelrknvifiah 130
                                    +e+++++++ l+ ++k+v+++ h
  gi|119719623|ref|YP_920118.1| 178 KEKISQTMNLLRLMGKTVVIVTH 200
                                    67899999999999*****9999 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   3.8e-05     0.025      98     132 ..      34      68 ..      14      92 .. 0.77
   2 ?   -1.7   0.0       3.7   2.4e+03      20      40 ..     195     214 ..     173     222 .. 0.55

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.8e-05
                                    TTSEEEEECSTTSSHHHHHHHHCTT-----S---- CS
                    RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallpelelktgevse 132
                                    ++++++++G+ G+GK+tLi+++++ l+ + g v+ 
  gi|119719623|ref|YP_920118.1|  34 RGEFIAIMGENGAGKTTLIKHFNGILKPSKGTVKV 68 
                                    56899***************999876655555544 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.7
                                    EEEEESTTTT--HHHHHHHHH CS
                    RsgA_GTPase  20 livvslkepelslnlldrfLv 40 
                                    +++v+ +  e+ ++ +dr++v
  gi|119719623|ref|YP_920118.1| 195 VVIVTHD-VEFVTSYVDRIVV 214
                                    2333333.5555555555544 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.2   0.00055      0.36       1      34 [.      40      73 ..      40      79 .. 0.87
   2 ?    3.2   0.0     0.099        65      88     143 ..     158     213 ..     141     226 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00055
                     ATP_bind_1  1 vvGpaGsGKttfvgalseilelrgrsvavvNLDP 34
                                   ++G  G+GKtt+++ ++ il+ ++ +v+v  +D+
  gi|119719623|ref|YP_920118.1| 40 IMGENGAGKTTLIKHFNGILKPSKGTVKVKGIDT 73
                                   79*******************9999999876665 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.099
                     ATP_bind_1  88 keeddyllfDtP..GQielfthseslakiveeLesefalvvvyLvDsqrltdptkfis 143
                                     ++ + l++D P  GQ+  +   e+ ++ ++ L   +++vv++  D++++t+ ++ i 
  gi|119719623|ref|YP_920118.1| 158 AYDPEVLVLDEPtaGQD--YLQKEKISQTMNLLRLMGKTVVIVTHDVEFVTSYVDRIV 213
                                    55667888887755666..44567777778899999**************99777665 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0     4e-05     0.026      17      69 ..      28      77 ..      21     120 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4e-05
                         AAA_15 17 veidlsee.ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleife 69
                                   v++++    +  + G+N++GK+++++ ++ +l+ +    k ++k++  d++++ 
  gi|119719623|ref|YP_920118.1| 28 VTLEVRRGeFIAIMGENGAGKTTLIKHFNGILKPS----KGTVKVKGIDTRTKS 77
                                   555555555999*********************99....788888888877764 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   3.1e-05      0.02      20      69 ..      37      88 ..      24     198 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.1e-05
                         AAA_30 20 vavltGpAGtGKttalkalreaweaa.g.grviglAptgkaAkvLaeelgie 69
                                   + ++ G  G+GKtt++k+ + +++ + g  +v g+    k  ++L++ +gi 
  gi|119719623|ref|YP_920118.1| 37 FIAIMGENGAGKTTLIKHFNGILKPSkGtVKVKGIDTRTKSVAELSRIVGIV 88
                                   77899******************99944566777777777777788777764 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2     8e-05     0.053      17      82 ..      32     101 ..      27     215 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8e-05
                       ATPase_2  17 repneiyfiYGpegsGKtaLlkeiienl.edkdkyviyyialreesiskldefie...eeeekkklekal 82 
                                      + e++ i G  g GKt+L+k++   l  +k+  ++  i+ r++s ++l++ ++   ++ + + +e+++
  gi|119719623|ref|YP_920118.1|  32 VRRGEFIAIMGENGAGKTTLIKHFNGILkPSKGTVKVKGIDTRTKSVAELSRIVGivfQNPDHQLFEETV 101
                                    55678999****************9998556777889999999999999998877776333333344433 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   0.00011      0.07       2      44 ..      38      81 ..      38      91 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00011
                                   EEEESSTTSSHHHHHHCHCT.-CCC-EEETTTTEEEEEEECGGS CS
                            Roc  2 vvlvGdsgvGKtsllkrfve.dkfsekekstigvdfltkevtki 44
                                   + ++G++g+GKt+l+k+f    k s+ + +  g+d+ tk+v ++
  gi|119719623|ref|YP_920118.1| 38 IAIMGENGAGKTTLIKHFNGiLKPSKGTVKVKGIDTRTKSVAEL 81
                                   6799**************86334456677888999988887655 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00018      0.12       1      92 [.      38     132 ..      38     221 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00018
                         AAA_18   1 IlltGtpGvGKttlakeL......skrlgf........gvnlrdvakenglllevdpe.aldeskrldedkldklldale 65 
                                    I+++G  G+GKttl k+       s              ++ ++va  ++++  v+++ +++ +++ + d ++ +l+++ 
  gi|119719623|ref|YP_920118.1|  38 IAIMGENGAGKTTLIKHFngilkpS----KgtvkvkgiDTRTKSVAELSRIVGIVFQNpDHQLFEETVYDEVAFALRNFG 113
                                    89****************5555443....0445668889999**********9999998999999999999999999998 PP

                         AAA_18  66 enssaleegknlvidghlaeleseaak 92 
                                     + +        vi+ ++a+ +   + 
  gi|119719623|ref|YP_920118.1| 114 YSED--------VIERRVAWALNILDL 132
                                    8654........777777777655544 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   0.00014     0.094      19      41 ..      35      57 ..      22      68 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00014
                                   TEEEEEEESTTSSHHHHHHHHHH CS
                           TsaE 19 gdvilLeGdLGaGKTtlvrglak 41
                                   g++i++ G+ GaGKTtl++++  
  gi|119719623|ref|YP_920118.1| 35 GEFIAIMGENGAGKTTLIKHFNG 57
                                   788****************9865 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00012     0.078       1      36 [.      37      71 ..      37     123 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00012
                            PRK  1 vIgvagsSGaGkttvarklekifgrekvkaaeiegd 36
                                   +I++ g+ GaGktt+ ++++ i++  ++ +++++g+
  gi|119719623|ref|YP_920118.1| 37 FIAIMGENGAGKTTLIKHFNGILK-PSKGTVKVKGI 71
                                   69*********************9.44444555444 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1    0.0002      0.13       3      21 ..      38      56 ..      36      67 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0002
                                   EEEEC-TTTCHHHHHHHHH CS
                          NACHT  3 vilqGeaGsGKTtLlqkla 21
                                   +++ Ge+G GKTtL++++ 
  gi|119719623|ref|YP_920118.1| 38 IAIMGENGAGKTTLIKHFN 56
                                   789************9986 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00044      0.29      17      39 ..      33      55 ..      28      95 .. 0.81
   2 ?   -0.9   0.0       1.3   8.5e+02     131     163 ..     172     200 ..     117     211 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00044
                         ATPase 17 pegrvvlitGepGtGKtifalqF 39
                                    +g+ + i+Ge G+GKt++ ++F
  gi|119719623|ref|YP_920118.1| 33 RRGEFIAIMGENGAGKTTLIKHF 55
                                   58999****************99 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.3
                         ATPase 131 layeekeavaReilrqlvrvlkklgvTailvse 163
                                         ++ + +e + q ++ l+ +g T ++v+ 
  gi|119719623|ref|YP_920118.1| 172 G----QDYLQKEKISQTMNLLRLMGKTVVIVTH 200
                                    4....4455556677777777778888877765 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00046       0.3       3      39 ..      37      73 ..      36     104 .. 0.88
   2 ?   -2.3   0.0       4.2   2.8e+03     101     105 ..     180     184 ..     153     204 .. 0.47

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00046
                                   EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEEST CS
                          SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvllvaaDt 39
                                    i+++G +GaGKTt +     +lk ++ +v +   Dt
  gi|119719623|ref|YP_920118.1| 37 FIAIMGENGAGKTTLIKHFNGILKPSKGTVKVKGIDT 73
                                   5889*************99999999999988888887 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4.2
                                    HHHHH CS
                          SRP54 101 lmeel 105
                                     +++ 
  gi|119719623|ref|YP_920118.1| 180 KISQT 184
                                    22222 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00026      0.18      24      70 ..      37      81 ..      19     101 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00026
                   Mg_chelatase 24 nlllvGppGsGKtmlakrlpsllpplseeealevakiasvagkkeee 70
                                    + ++G  G+GKt l+k ++++l p + +  +  + i + +++ +e 
  gi|119719623|ref|YP_920118.1| 37 FIAIMGENGAGKTTLIKHFNGILKPSKGTVKV--KGIDTRTKSVAEL 81
                                   57789******************998755433..3333333333333 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1    0.0003       0.2      18      55 ..      37      74 ..      25      82 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0003
                     Zeta_toxin 18 lillgGqpGAGKselaellkdelerqgnvvrldpDdlR 55
                                    i + G  GAGK++l++ ++  l++ ++ v++++ d R
  gi|119719623|ref|YP_920118.1| 37 FIAIMGENGAGKTTLIKHFNGILKPSKGTVKVKGIDTR 74
                                   577889******************99999999876666 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1    0.0003       0.2       7      34 ..      25      52 ..      21      55 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0003
                        DUF3584  7 lkGrvaeldldghtnieGtNaaGKTtLl 34
                                   l+G++ e++  +   i G N+aGKTtL+
  gi|119719623|ref|YP_920118.1| 25 LRGVTLEVRRGEFIAIMGENGAGKTTLI 52
                                   78999999999***************97 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.7   0.00051      0.34       2      36 ..      38      78 ..      37     203 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00051
                                   EEEEESTTSSHHHHHHHHHT.....S.TEEESSSTTSSSSE CS
                       MMR_HSR1  2 vaivGrpNvGKStLinaltg.....e.kaivsdkpgtTrdi 36
                                   +ai+G   +GK+tLi+   g     + +++v+ +   T+ +
  gi|119719623|ref|YP_920118.1| 38 IAIMGENGAGKTTLIKHFNGilkpsKgTVKVKGIDTRTKSV 78
                                   89*************99876554421345555555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              27  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 1937.82
//
Query:       gi|119719624|ref|YP_920119.1|  [L=284]
Description: ABC transporter related [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-26   93.2   0.0    2.6e-26   92.8   0.0    1.2  1  ABC_tran      ABC transporter
    6.4e-09   36.0   1.2    0.00012   22.0   0.1    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    0.00095   18.7   0.0      0.091   12.2   0.0    2.1  2  SMC_N         RecF/RecN/SMC N terminal domain
      0.004   16.6   0.0     0.0073   15.7   0.0    1.4  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
     0.0047   17.3   0.1     0.0072   16.7   0.1    1.7  1  AAA_16        AAA ATPase domain
     0.0069   16.5   0.1      0.015   15.5   0.1    1.5  1  AAA_33        AAA domain
     0.0069   16.1   0.0       0.01   15.6   0.0    1.2  1  AAA_15        AAA ATPase domain
     0.0078   16.2   0.0       0.02   14.9   0.0    1.7  2  AAA_5         AAA domain (dynein-related subfamily)
  ------ inclusion threshold ------
      0.012   15.2   0.0      0.084   12.4   0.0    2.1  2  AAA_25        AAA domain
      0.013   15.5   0.0      0.022   14.7   0.0    1.3  1  Rad17         Rad17 P-loop domain
      0.021   14.6   0.0      0.047   13.4   0.0    1.5  1  AAA_29        P-loop containing region of AAA domain
      0.034   14.6   0.1      0.061   13.8   0.1    1.3  1  AAA_23        AAA domain
      0.034   14.6   0.1       0.13   12.6   0.1    1.9  2  AAA           ATPase family associated with various cellular 
      0.038   14.3   0.2       0.22   11.8   0.1    2.0  2  AAA_22        AAA domain
      0.079   12.9   0.0       0.14   12.0   0.0    1.4  1  RsgA_GTPase   RsgA GTPase
      0.097   12.4   0.0        1.1    9.0   0.0    2.1  2  IstB_IS21     IstB-like ATP binding protein
       0.11   12.9   0.0       0.19   12.1   0.0    1.4  1  RNA_helicase  RNA helicase
       0.12   12.6   0.0        1.6    9.0   0.0    2.2  1  SbcCD_C       Putative exonuclease SbcCD, C subunit
       0.14   11.8   0.0       0.24   11.1   0.0    1.3  1  AAA_24        AAA domain
       0.15   12.7   0.0       0.29   11.7   0.0    1.5  1  AAA_18        AAA domain
       0.15   11.4   0.0         10    5.5   0.0    2.2  2  TniB          Bacterial TniB protein
       0.15   11.9   0.1       0.37   10.7   0.0    1.7  2  NACHT         NACHT domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.8   0.0   3.2e-29   2.6e-26       1     137 []      22     173 ..      22     173 .. 0.94

  Alignments for each domain:
  == domain 1  score: 92.8 bits;  conditional E-value: 3.2e-29
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--.....SEEEEEETTCEGGGB-HHHCCHCEEEE-SS..--S-TT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxx RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp.....teGeilldgkdlkeqeleslrkeigvlpqe..pqlfpe 73 
                                    l++++++   ge+v +vG++G+GKSt+++++ gl  +       G+i + g d ++++++++   +g+++q+  +qlf +
  gi|119719624|ref|YP_920119.1|  22 LRDINFEADFGELVLLVGPSGCGKSTFARIFNGLIPNfyggeLTGRISIAGLDPRKTPTPKFAGLVGFMFQNpeNQLFFN 101
                                    6899******************************99999998999***************************66666666 PP

                                    SBHHHH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    xxxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  74 ltvren.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                    + v+++             e ++++++ l+++gl+el+++       +LSgGq+q+vala +++ kp++l+lDEpta
  gi|119719624|ref|YP_920119.1| 102 S-VERElafglenlgippeEIRRRVDETLKEYGLEELRHRSP----FELSGGQQQKVALASVMVMKPRILILDEPTA 173
                                    6.55557***********99999*************999998....*****************************97 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.1   8.2e-05     0.067       2      32 ..      35      62 ..      34      82 .. 0.76
   2 !   22.0   0.1   1.5e-07   0.00012     220     279 ..     128     185 ..      77     204 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.2e-05
                         AAA_21  2 nvliGpNgsGKSnLLdaldllarldrdvegl 32
                                    +l+Gp g+GKS++ +++ +l   ++++ g+
  gi|119719624|ref|YP_920119.1| 35 VLLVGPSGCGKSTFARIFNGL---IPNFYGG 62
                                   68*****************99...4444444 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 1.5e-07
                         AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHP.kllrrll 279
                                    ++  +  +  + ++++elS G+++  al++ +   +   ++l++DEp ++L+P +++r+l 
  gi|119719624|ref|YP_920119.1| 128 TLKEYGLEELRHRSPFELSGGQQQKVALASVMVMKP---RILILDEPTANLDPlSAMRTLG 185
                                    444445555566789******************988...**************77777665 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.025        20      26      40 ..      34      48 ..      22      52 .. 0.80
   2 !   12.2   0.0   0.00011     0.091     135     200 ..     119     204 ..      81     221 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.025
                                   EEEEEESTTSSHHHH CS
                                   xxxxxxxxxxxxxxx RF
                          SMC_N 26 ftaivGpNGSGKsnl 40
                                   +  +vGp G+GKs +
  gi|119719624|ref|YP_920119.1| 34 LVLLVGPSGCGKSTF 48
                                   5689*********86 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00011
                                    T........................CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTS CS
                                    x........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 135 e........................lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskna 190
                                    e                        +LSgG+++ vala ++    +kp  + +lDe  a+LD     +   ++ +k+ + 
  gi|119719624|ref|YP_920119.1| 119 EeirrrvdetlkeygleelrhrspfELSGGQQQKVALASVM---VMKP-RILILDEPTANLDPLSAMRTLGIVAKKTREY 194
                                    44444444444455555556666668*******99999774...3444.5789**********99999999999988887 PP

                                    EEEEE-SSHH CS
                                    xxxxxxxxxx RF
                          SMC_N 191 Qfivislree 200
                                     ++ i ++++
  gi|119719624|ref|YP_920119.1| 195 NMLTILIEHR 204
                                    7776655544 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   8.9e-06    0.0073      25      55 ..      35      65 ..      21      84 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 8.9e-06
                   Mg_chelatase 25 lllvGppGsGKtmlakrlpsllpplseeeal 55
                                   +llvGp+G+GK+  a+ +++l+p+    e  
  gi|119719624|ref|YP_920119.1| 35 VLLVGPSGCGKSTFARIFNGLIPNFYGGELT 65
                                   89*********************98777665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   8.8e-06    0.0072      24      44 ..      32      52 ..      21     242 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 8.8e-06
                         AAA_16 24 pelvllsGesGvGKsslvrel 44
                                   +elvll+G+sG+GKs+ +r +
  gi|119719624|ref|YP_920119.1| 32 GELVLLVGPSGCGKSTFARIF 52
                                   489*************99755 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   1.8e-05     0.015       1      17 [.      34      50 ..      34      52 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.8e-05
                         AAA_33  1 lvllvGlpGsGKstlae 17
                                   lvllvG++G+GKst+a+
  gi|119719624|ref|YP_920119.1| 34 LVLLVGPSGCGKSTFAR 50
                                   89*************97 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.2e-05      0.01      16      46 ..      26      55 ..      22     105 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.2e-05
                         AAA_15 16 dveidlseeltvliGkNnsGKSsilealdlF 46
                                   ++e d+ e l +l+G+ ++GKS+++++++ +
  gi|119719624|ref|YP_920119.1| 26 NFEADFGE-LVLLVGPSGCGKSTFARIFNGL 55
                                   58999999.****************998755 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   2.5e-05      0.02       2      23 ..      35      56 ..      34      65 .. 0.88
   2 ?   -3.1   0.0       8.5   6.9e+03      64      73 ..     161     170 ..     136     184 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.5e-05
                                   EEEE--SSSSHHHHHHHGGGGB CS
                          AAA_5  2 vlLvGppGtgKselaerlaaal 23
                                   vlLvGp+G+gKs++a+ +  ++
  gi|119719624|ref|YP_920119.1| 35 VLLVGPSGCGKSTFARIFNGLI 56
                                   89*************9998777 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 8.5
                                    -G-SEEEEES CS
                          AAA_5  64 regeilvlDE 73 
                                     +++il+lDE
  gi|119719624|ref|YP_920119.1| 161 MKPRILILDE 170
                                    3778888887 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0    0.0001     0.084      33      50 ..      32      49 ..      20      50 .. 0.94
   2 ?    0.2   0.0       0.6   4.9e+02      83     109 ..     118     159 ..     113     217 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0001
                         AAA_25 33 gelallaGapgtGKttla 50
                                   gel+ll+G++g+GK+t+a
  gi|119719624|ref|YP_920119.1| 32 GELVLLVGPSGCGKSTFA 49
                                   89**************97 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.6
                         AAA_25  83 edelrrRlravgeal...............rddarllvldla 109
                                     +e+rrR+ ++++++                +++++++ +++
  gi|119719624|ref|YP_920119.1| 118 PEEIRRRVDETLKEYgleelrhrspfelsgGQQQKVALASVM 159
                                    568999999999999777666655555555444444444443 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   2.7e-05     0.022      46      64 ..      33      51 ..      20      57 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.7e-05
                          Rad17 46 riLLisGPsGCgkstvvkv 64
                                   +++L+ GPsGCgkst  ++
  gi|119719624|ref|YP_920119.1| 33 ELVLLVGPSGCGKSTFARI 51
                                   689************8876 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   5.8e-05     0.047      20      38 ..      30      48 ..      22      49 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.8e-05
                         AAA_29 20 dlkgatlltGpsGsGKSTl 38
                                   d  + +ll+GpsG GKST+
  gi|119719624|ref|YP_920119.1| 30 DFGELVLLVGPSGCGKSTF 48
                                   444589************7 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   7.4e-05     0.061      15      37 ..      25      50 ..      21      63 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.4e-05
                         AAA_23 15 idF...skgltlItGpNGaGKTTild 37
                                   i+F      l+l++Gp G+GK+T+ +
  gi|119719624|ref|YP_920119.1| 25 INFeadFGELVLLVGPSGCGKSTFAR 50
                                   666544448**************875 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   0.00016      0.13       1      17 [.      35      51 ..      35      67 .. 0.93
   2 ?   -1.2   0.0       3.1   2.5e+03      54      66 ..     159     170 ..     133     203 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00016
                                   EEEESSTTSSHHHHHHH CS
                            AAA  1 vllyGppGtGKTllaka 17
                                   vll+Gp G+GK+++a+ 
  gi|119719624|ref|YP_920119.1| 35 VLLVGPSGCGKSTFARI 51
                                   79*************96 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 3.1
                                    HHTS.TSEEEEEET CS
                            AAA  54 keka.kpsilfiDE 66 
                                         kp il++DE
  gi|119719624|ref|YP_920119.1| 159 M--VmKPRILILDE 170
                                    2..24589999998 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00027      0.22       7      25 ..      34      52 ..      32      82 .. 0.90
   2 ?    0.2   0.0       1.1   8.6e+02      86      99 ..     154     170 ..      91     208 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00027
                         AAA_22  7 ilvvtGesGtGKTtllrrl 25
                                   +++++G+sG+GK+t +r +
  gi|119719624|ref|YP_920119.1| 34 LVLLVGPSGCGKSTFARIF 52
                                   6799**********99866 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.1
                         AAA_22  86 lrarav.....ielliiDE 99 
                                    + a        +++li+DE
  gi|119719624|ref|YP_920119.1| 154 ALA--SvmvmkPRILILDE 170
                                    222..13356778888888 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00018      0.14      99     117 ..      32      50 ..      10      71 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00018
                                    TSEEEEECSTTSSHHHHHH CS
                    RsgA_GTPase  99 dktsvlvGqSGvGKStLin 117
                                    +++++lvG+SG GKSt+  
  gi|119719624|ref|YP_920119.1|  32 GELVLLVGPSGCGKSTFAR 50 
                                    38899***********864 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0    0.0013       1.1      47      65 ..      32      50 ..      10      54 .. 0.76
   2 ?    0.9   0.0      0.39   3.2e+02      97     136 ..     151     189 ..     145     208 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0013
                      IstB_IS21 47 kenivllGpsGvGKshlai 65
                                    e ++l+GpsG GKs +a 
  gi|119719624|ref|YP_920119.1| 32 GELVLLVGPSGCGKSTFAR 50
                                   577999*********9985 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.39
                      IstB_IS21  97 gklaralkrllkvdllilDdlgllpldqaeaellfeviek 136
                                    +k+a a   ++k+++lilD+    +ld  +a   + +++k
  gi|119719624|ref|YP_920119.1| 151 QKVALASVMVMKPRILILDEPT-ANLDPLSAMRTLGIVAK 189
                                    55555666778999*****964.45666666555566555 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00024      0.19       1      17 [.      35      51 ..      35      66 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00024
                   RNA_helicase  1 iwlyGpsgeGKStlake 17
                                   ++l+Gpsg+GKSt+a+ 
  gi|119719624|ref|YP_920119.1| 35 VLLVGPSGCGKSTFARI 51
                                   6799**********986 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0     0.002       1.6      26      87 ..     138     186 ..     119     189 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.002
                        SbcCD_C  26 lsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllel 87 
                                     +rs  +lSGG++q++a       la+++        ++r+++LDE  ++lD+ s+ + l++
  gi|119719624|ref|YP_920119.1| 138 RHRSPFELSGGQQQKVA-------LASVMVM------KPRILILDEPTANLDPLSAMRTLGI 186
                                    56666677888885543.......3333333......4899*********999888777765 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00029      0.24       5      22 ..      35      52 ..      33      79 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00029
                         AAA_24  5 iliyGpsgiGKTtlakel 22
                                   +l++Gpsg GK+t+a+ +
  gi|119719624|ref|YP_920119.1| 35 VLLVGPSGCGKSTFARIF 52
                                   689************988 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00036      0.29       1      19 [.      35      53 ..      35      84 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00036
                         AAA_18  1 IlltGtpGvGKttlakeLs 19
                                   +ll G++G+GK+t+a+  +
  gi|119719624|ref|YP_920119.1| 35 VLLVGPSGCGKSTFARIFN 53
                                   799************9765 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.013        10      38      57 ..      35      54 ..      29      80 .. 0.88
   2 ?    3.8   0.0     0.041        34      91     127 ..     134     170 ..     123     183 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.013
                           TniB 38 lllvGdsnnGKtmivekFar 57
                                   +llvG+s +GK++ ++ F  
  gi|119719624|ref|YP_920119.1| 35 VLLVGPSGCGKSTFARIFNG 54
                                   79***********9998875 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.041
                           TniB  91 LealgaplkararvskleqqvlrllrelkvrvLiiDE 127
                                    Le+l+ +   + +  ++++ +l+    +k+r+Li+DE
  gi|119719624|ref|YP_920119.1| 134 LEELRHRSPFELSGGQQQKVALASVMVMKPRILILDE 170
                                    666777766667777888888999999********** PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00046      0.37       2      18 ..      34      50 ..      33      56 .. 0.90
   2 ?   -2.1   0.0         4   3.3e+03      69      69 ..     201     201 ..     123     222 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00046
                                   CEEEEC-TTTCHHHHHH CS
                          NACHT  2 lvilqGeaGsGKTtLlq 18
                                   lv+l G++G+GK+t+++
  gi|119719624|ref|YP_920119.1| 34 LVLLVGPSGCGKSTFAR 50
                                   799************97 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4
                                    S CS
                          NACHT  69 v 69 
                                    +
  gi|119719624|ref|YP_920119.1| 201 I 201
                                    1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1811.51
//
Query:       gi|119719625|ref|YP_920120.1|  [L=399]
Description: translation-associated GTPase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.1e-37  127.6   0.0    5.7e-37  126.7   0.0    1.4  1  MMR_HSR1_C  GTPase of unknown function C-terminal
    6.8e-17   61.6   0.0    2.5e-16   59.8   0.0    2.1  1  MMR_HSR1    50S ribosome-binding GTPase
    2.4e-09   37.1   0.0    4.6e-09   36.2   0.0    1.4  1  TGS         TGS domain
    3.1e-05   23.6   0.7      0.003   17.1   0.1    2.5  2  FeoB_N      Ferrous iron transport protein B
  ------ inclusion threshold ------
      0.084   12.6   0.0       0.14   11.8   0.0    1.4  1  DUF460      Protein of unknown function (DUF460)


Domain annotation for each model (and alignments):
>> MMR_HSR1_C  GTPase of unknown function C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.7   0.0   1.6e-40   5.7e-37       1     112 []     223     330 ..     223     330 .. 0.98

  Alignments for each domain:
  == domain 1  score: 126.7 bits;  conditional E-value: 1.6e-40
                     MMR_HSR1_C   1 alNKaDlpaadenieklkekypkdkkvvpvsAaaElaLrkaakqglikYepgdedfeikedklkeldekqkkaLekirdl 80 
                                    a+NKaDl+ +++ni++++++  ++ +vvp+sA+aElaLrka+k+gli+Y+pgd dfei ++     +++q+kaLe+ir+ 
  gi|119719625|ref|YP_920120.1| 223 AANKADLDVSEDNIKRMAKELGDRYTVVPTSAEAELALRKAEKAGLIRYIPGDPDFEIVGK----PTREQEKALEYIREK 298
                                    89*******************98889*********************************99....99************* PP

                     MMR_HSR1_C  81 vlkrygsTGVqealnaavfelldlivVYPVed 112
                                    vlkr+gsTGVq+a+++avfe l++ivV+PVe+
  gi|119719625|ref|YP_920120.1| 299 VLKRWGSTGVQKAIDTAVFEKLGMIVVFPVEN 330
                                    ******************************97 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.8   0.0     7e-20   2.5e-16       1      87 [.       4     119 ..       4     226 .. 0.86

  Alignments for each domain:
  == domain 1  score: 59.8 bits;  conditional E-value: 7e-20
                                    EEEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEE.........................EEEEECGG CS
                       MMR_HSR1   1 evaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgke.........................ielvDtpG 55 
                                    +v+ivG+pN+GKSt++ a t   ++ + +p+tT+++n g   ++  +                         +el+D++G
  gi|119719625|ref|YP_920120.1|   4 QVGIVGKPNTGKSTFFAASTLIDVKRAPYPFTTIEPNVGVGYVR-VQcvckelgvkdnprnsicidgwrfipVELIDVAG 82 
                                    59*************************************75533.123333444444556677777777777******** PP

                                    CSSHHHHHHHHHHHHHHHHC.TSEEEEEEETT....T CS
                       MMR_HSR1  56 liegaseekglgkaflalee.adlillvvdas....e 87 
                                    l+ ga e++glg+ fl++ + a ++++vvdas    e
  gi|119719625|ref|YP_920120.1|  83 LVPGAWEGRGLGNMFLDHLRrAPVLIHVVDASggtdE 119
                                    9999*************99889********9855441 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   0.0   1.3e-12   4.6e-09       4      59 ..     341     396 ..     338     397 .. 0.92

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 1.3e-12
                                    EETTSSEEEEETTB-HHHHHHHHSTTHHHHEEEEEECS..EEEETTSBB-SSEEEEEE CS
                            TGS   4 ytPdGkvpdlprgatveDfAykIhrslakkfiyAlVnG..qrvgldhvLedgdvveIv 59 
                                    ++Pd+ +  + + at++D+Ay+Ih++++++f  A+     qrv  + +L++  v++Iv
  gi|119719625|ref|YP_920120.1| 341 VLPDALL--VSKEATARDLAYQIHTDIGRRFSFAIDARtgQRVSASEKLRHRMVIKIV 396
                                    5677777..99*************************9999*****************8 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   8.2e-07     0.003       2      41 ..       4      43 ..       3      61 .. 0.88
   2 !    4.5   0.1    0.0061        22      95     148 ..     207     259 ..     186     266 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 8.2e-07
                                   EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEE CS
                         FeoB_N  2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegk 41
                                   +v +vG+pn+Gk+t+f a t  + k + +p +t+e + g 
  gi|119719625|ref|YP_920120.1|  4 QVGIVGKPNTGKSTFFAASTLIDVKRAPYPFTTIEPNVGV 43
                                   6889******************************988765 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0061
                                    HHHHHHHHHTTSSEEEEEETHHHHHHTTEEE-HHHHHHHHT..S-EEEEBTTTTBT CS
                         FeoB_N  95 LyLtlqllelgvpvvlalnmideaekkgieidlkkLsekLg..vpvvktsakkkeg 148
                                    ++L+  ++   +p+v+a n+ d   ++    ++k+++++Lg    vv+tsa+ +  
  gi|119719625|ref|YP_920120.1| 207 MHLVEYVMRKAKPMVIAANKADLDVSED---NIKRMAKELGdrYTVVPTSAEAELA 259
                                    667778888999********99765544...6788888888667899999987655 PP

>> DUF460  Protein of unknown function (DUF460)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0     4e-05      0.14      33      98 ..     176     243 ..     149     270 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4e-05
                         DUF460  33 ivGiDPGittgiavldldgevlalkssreldreevieliselGkpvivAtDvspp...petvkklarsl 98 
                                     +G+D G+ +  a+ +l+ +  + +s  + d  +++e++++  kp+++A+ +++     + +k++a++l
  gi|119719625|ref|YP_920120.1| 176 GLGVDVGV-VDKALEELSLKTKKATSWTREDLMHLVEYVMRKAKPMVIAANKADLdvsEDNIKRMAKEL 243
                                    56888886.456777788888889999999999****************87765511145566666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      639  (0.0356406); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 2576.87
//
Query:       gi|119719626|ref|YP_920121.1|  [L=325]
Description: hypothetical protein Tpen_0716 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       259  (0.0144459); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 2170.29
//
Query:       gi|119719627|ref|YP_920122.1|  [L=343]
Description: oxidoreductase domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-23   83.7   0.0    7.1e-23   81.7   0.1    1.9  2  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f
    0.00023   21.4   0.1    0.00035   20.8   0.1    1.3  1  TrkA_N          TrkA-N domain
     0.0011   19.0   0.1     0.0039   17.2   0.0    1.9  3  GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta 
     0.0011   19.5   0.1     0.0019   18.7   0.1    1.3  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
  ------ inclusion threshold ------
      0.011   15.8   0.1      0.017   15.2   0.1    1.3  1  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
      0.032   14.6   0.0      0.067   13.5   0.0    1.6  1  Gp_dh_N         Glyceraldehyde 3-phosphate dehydrogenase, NAD


Domain annotation for each model (and alignments):
>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.7   0.1   2.4e-26   7.1e-23       1     120 []       3     124 ..       3     124 .. 0.92
   2 ?   -1.3   0.0       1.2   3.6e+03      27      53 ..     204     231 ..     191     251 .. 0.68

  Alignments for each domain:
  == domain 1  score: 81.7 bits;  conditional E-value: 2.4e-26
                                    EEEEEETTSHHHHHHHHHHHHTTTTE..EEEEEECSSHHHHHHHHHHTTHE.EESSHHHHHTCT.TESEEEE-S-GGGHH CS
                   GFO_IDH_MocA   1 lrvaiiGaGkigskhlrplnesqrle..evvalldpdaeraeavaesfgve.aysdleelladp.eidavivatpngthe 76 
                                    ++va++G+G+ g++h+r l   +  +  ++v ++d d++ra  va++f v+  ys++eel++d+ + da++va+p+  h+
  gi|119719627|ref|YP_920122.1|   3 VNVAVVGVGRWGRNHVRVLSSLRGSLvgRIV-VVDADEARASSVAKQFAVDaYYSSVEELVKDEkDLDAAVVAVPTVYHF 81 
                                    58**************877777555585555.9******************88999********99************** PP

                                    HHHHHHHHTT-EEEEESSS-SSHHHHHHHHHHHHHHTS-EEEE- CS
                   GFO_IDH_MocA  77 elakaaleagkhvllEKPlattveeakelvelaekkgklvsvgy 120
                                    e+a ++l+   +vl+EKPla+t++e  +lvel +k g++++vg+
  gi|119719627|ref|YP_920122.1|  82 EVASKLLN-YADVLVEKPLAATLDEGYRLVELSRKLGRRLAVGH 124
                                    ******96.57*******************************97 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.2
                                    EEEEEECSSHHHHHHHHHHTTHE.EESS CS
                   GFO_IDH_MocA  27 evvalldpdaeraeavaesfgve.aysd 53 
                                    ev+al++ ++ r  ++++s++   +y+ 
  gi|119719627|ref|YP_920122.1| 204 EVTALYEYSQRRIATLSASWRTVpSYKH 231
                                    8999999999999998666554326655 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.1   1.2e-07   0.00035       1      49 [.       5      58 ..       5     115 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.2e-07
                                   EEEES-SHHHHHHHHHHHH.TT....EEEEEEESSHHHHHHHHHTT.SEEEES-T CS
                         TrkA_N  1 iiiiGlGrvGrslaeeLse.gg....kdvvvidkdeerveelreeg.levvvgda 49
                                   ++++G+Gr Gr+ ++ Ls+ +g    + +vv+d de+r+ ++++++ +++++ ++
  gi|119719627|ref|YP_920122.1|  5 VAVVGVGRWGRNHVRVLSSlRGslvgR-IVVVDADEARASSVAKQFaVDAYYSSV 58
                                   68*****************9889**55.***************999666766554 PP

>> GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       4.6   1.4e+04       9      19 ..      29      40 ..      26      60 .. 0.68
   2 ?   -2.1   0.0       1.3   3.8e+03      66      93 ..      53      83 ..      44      92 .. 0.70
   3 !   17.2   0.0   1.3e-06    0.0039      41     112 ..     165     232 ..     159     235 .. 0.73

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 4.6
                                   TSSEEEEEE.EE CS
                 GFO_IDH_MocA_C  9 lGevvsvdv.wt 19
                                   +G++v+vd  + 
  gi|119719627|ref|YP_920122.1| 29 VGRIVVVDAdEA 40
                                   788888864333 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.3
                                   EEEE.SEEESCTCCSCSEEE...EEEEEEEE CS
                 GFO_IDH_MocA_C 66 aalgrmrqnaeaaededaav...msvlnlek 93
                                   a + ++ +++++++d daav   + v+++e 
  gi|119719627|ref|YP_920122.1| 53 AYYSSVEELVKDEKDLDAAVvavPTVYHFEV 83
                                   5677788889999999999855544444444 PP

  == domain 3  score: 17.2 bits;  conditional E-value: 1.3e-06
                                    SHHHHTCHHHHHHHHHHHTSEEEEEEEEE.SEEESCTCCSCSEEEEEEEEEEETTEEEEEEEECCTSSSEEE CS
                 GFO_IDH_MocA_C  41 GvlgdlgiHdiDllqwLfGqppsvvaalgrmrqnaeaaededaavmsvlnlekgsgevitlesgvskglsir 112
                                    Gv+ dl++Hd D+++ ++G+pp +v+a+    ++++ +  +  +v +++ ++  ++++ ++++    ++++r
  gi|119719627|ref|YP_920122.1| 165 GVAHDLLVHDVDVVNMFLGEPPGRVFAY----KIDGGDFPFEVEVTALYEYSQRRIATLSASWRTVPSYKHR 232
                                    8899***********************9....4555555555554446666666666666666666666555 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   6.4e-07    0.0019       2      81 ..       5      87 ..       4      97 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 6.4e-07
                                   EEEETTSHHHHHHHHHHHHTTS.-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHH...H-SEEEE-S-HHHHHHHHH CS
                  F420_oxidored  2 igiiGaGnmgealasgllaaga.qpheivvansrnpekaeelaeelgvkvtavdneeaae...eadvvvlavkpedveevls 79
                                   ++++G G+ g+  ++ l++        ivv+ + ++ +a + a+++ v++  ++ ee+++   + d  v+av++ ++ ev+s
  gi|119719627|ref|YP_920122.1|  5 VAVVGVGRWGRNHVRVLSSLRGsLVGRIVVV-DADEARASSVAKQFAVDAYYSSVEELVKdekDLDAAVVAVPTVYHFEVAS 85
                                   899**********999988644599****88.***************************9766789***************9 PP

                                   HC CS
                  F420_oxidored 80 el 81
                                   +l
  gi|119719627|ref|YP_920122.1| 86 KL 87
                                   99 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.1   5.7e-06     0.017      14      83 ..       4      75 ..       1      94 [. 0.85

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.7e-06
                                   EEEEES-SHHHHHHHHHHHC...CT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-S CS
                   Shikimate_DH 14 kvlliGaGemaelvakhLla...kgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisat 83
                                   +v ++G G+ ++  ++ L++   + v ++vv+  + +ra+++a+++ ++++ + ++eel +  ++ d  ++a+
  gi|119719627|ref|YP_920122.1|  4 NVAVVGVGRWGRNHVRVLSSlrgSLVGRIVVVDADEARASSVAKQF-AVDAYYSSVEELVKDEKDLDAAVVAV 75
                                   799******999877766551116799*******************.666999******99999999888875 PP

>> Gp_dh_N  Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.3e-05     0.067       1      60 [.       3      66 ..       3      98 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.3e-05
                                   CEEEEESTSHHHHHHHHHHH..HHT.TCEEEEEE-.TS-HHHHHHHHHEETTTEC-SS-EEEET CS
                        Gp_dh_N  1 vkvainGfGRIGrlvlrall..eek.elevvaind.ltdletlayllkyDsvhgrfkgeveaee 60
                                   v+va+ G GR Gr+ +r+l   + +   ++v +    + ++++a+ +  D  + ++++ v+ e+
  gi|119719627|ref|YP_920122.1|  3 VNVAVVGVGRWGRNHVRVLSslRGSlVGRIVVVDAdEARASSVAKQFAVDAYYSSVEELVKDEK 66
                                   589****************9753333456777777679999***********999999988663 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       246  (0.0137208); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2451.82
//
Query:       gi|119719628|ref|YP_920123.1|  [L=387]
Description: geranylgeranyl reductase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-20   74.1   0.0    1.7e-20   73.5   0.0    1.2  1  FAD_binding_3   FAD binding domain
    1.3e-08   34.3   0.3    0.00015   20.9   0.1    2.1  2  Lycopene_cycl   Lycopene cyclase protein
    2.7e-08   33.8   0.8      0.001   18.7   0.1    2.5  2  DAO             FAD dependent oxidoreductase
    5.2e-08   32.0   1.2    5.3e-07   28.7   0.4    2.7  2  HI0933_like     HI0933-like protein
    6.6e-08   32.2   0.1    1.1e-06   28.2   0.1    2.1  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    6.8e-08   31.8   0.0     0.0002   20.3   0.0    2.1  2  Trp_halogenase  Tryptophan halogenase
    1.3e-06   28.5   0.0    6.8e-06   26.2   0.1    2.2  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    2.9e-06   26.7   0.3    7.6e-06   25.4   0.3    1.6  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    3.1e-05   23.3   0.1    7.3e-05   22.1   0.1    1.7  1  Thi4            Thi4 family
    4.1e-05   22.8   0.7     0.0002   20.6   0.4    2.1  2  FAD_binding_2   FAD binding domain
    0.00016   22.2   2.1      0.001   19.6   0.1    3.0  3  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
     0.0035   17.3   1.2     0.0085   16.0   0.2    2.0  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
  ------ inclusion threshold ------
      0.018   14.2   0.1      0.026   13.6   0.1    1.3  1  GIDA            Glucose inhibited division protein A
      0.072   12.4   0.0       0.12   11.7   0.0    1.3  1  Amino_oxidase   Flavin containing amine oxidoreductase
       0.11   12.5   0.1       0.27   11.2   0.1    1.7  1  NAD_binding_9   FAD-NAD(P)-binding
       0.12   12.9   0.1       0.23   12.0   0.1    1.5  1  XdhC_C          XdhC Rossmann domain
       0.14   11.5   0.7       0.21   10.9   0.7    1.3  1  FAD_oxidored    FAD dependent oxidoreductase
       0.15   12.0   0.6        1.7    8.6   0.0    2.4  2  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
       0.22   11.5   0.6         33    4.5   0.0    2.7  3  Sdh5            Flavinator of succinate dehydrogenase


Domain annotation for each model (and alignments):
>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.5   0.0   1.9e-23   1.7e-20       2     309 ..       3     287 ..       2     316 .. 0.82

  Alignments for each domain:
  == domain 1  score: 73.5 bits;  conditional E-value: 1.9e-23
                                    EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS--EEEHHHHHHHHHTT-HHHHHHHSEECCCCEEEEEEECC CS
                  FAD_binding_3   2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpradglnqrtmellrqlGledrilaegapnelmgealynels 81 
                                    +d ++VGaGpaGlm a++L+++G rv ++ek +t +v+p ++g++ r   +l+++ + ++  ++ +++++ g ++ ++  
  gi|119719628|ref|YP_920123.1|   3 YDAAVVGAGPAGLMFARVLASKGFRVAVLEKNETLAVKPCGEGISAR---VLQTAEINRSDTQRFVSHAIKGAVVVAP-- 77 
                                    6889****************************************998...6777778888888888888999999999.. PP

                                    CCCEEEEEHHCHHCST-CEE--HHHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEEEEEE- CS
                  FAD_binding_3  82 dtpkaradlelesspervtvypqteleriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetvrakYlvGa 161
                                           ++ ++ ++e  +v+   +++r++ e a++ g+++++k+ v+ +   + + t ++r        +++a+ lvGa
  gi|119719628|ref|YP_920123.1|  78 ----NGRKVVIKEEGELGYVIDKRNFLRVMGEYAASYGADIYMKEPVKEVVFKNGHWTVRARTV------ELEARLLVGA 147
                                    ....44445557999*********************************7777777766666655......699******* PP

                                    -GTT-HHHHHHTGGEEEEEEEEEEEEEEEEEEC-SCCCTTCCEEEEE..CCTTEEEEEECCETEEEEEEEEECCE-GGGS CS
                  FAD_binding_3 162 DGgrStvrktlgiefegeetvyeagvldvlfdadlsdiveplvlils..aesrgvmviPlentlerfyvqvearaekeer 239
                                    DG+ S ++k+lg+e +ge++v + +v  v+++++l+d+    +++++  a+++ v + P +       ++++++  +++ 
  gi|119719628|ref|YP_920123.1| 148 DGYLSYTAKALGLEKPGERRV-IPTVQYVMPNVELEDPDMTYFFLGNevAPKGYVWIFPKDG------RLANVGIGVQGA 220
                                    *******************99.667777888889997777766666522566777999*999......888899999999 PP

                                    CCCHHHHHHHHHHHHHHTTSSCEEEEEEEEEEEEEEEEESSSEETTEEE-GGGTEEE-STTSHHHHHHHH CS
                  FAD_binding_3 240 sekfteeevkarlreivgektldveieevsawtvaqrvaekyrkgrvflaGDAaHihpPtgGqGlNtaiq 309
                                    s+k   ++ +++ ++i+g++++     +  a+t++ ++  +  ++  +l+G Aa  + P +G G+ t+i 
  gi|119719628|ref|YP_920123.1| 221 SPKAYLDKFIKNNPSIFGKARILE--FRGAAVTIGGMLS-EIVSEHAMLVGEAAGQVIPLTGGGIHTSIA 287
                                    99****************999875..3445556665544.455667899******************996 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.1   1.6e-07   0.00015       1     144 [.       4     152 ..       4     167 .. 0.75
   2 !   11.5   0.0   0.00012      0.11     245     303 ..     250     309 ..     246     346 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.6e-07
                  Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlieaspsllfpn......nyvWsdefedlgaleecvehsWsgtivylddgkk 74 
                                    D +v+GaGpAgl  A  l  a +g +v ++e  + l   +       +v +  + + +  +++v+h  +g++v +++g+k
  gi|119719628|ref|YP_920123.1|   4 DAAVVGAGPAGLMFARVL--ASKGFRVAVLEKNETLAVKPcgegisARVLQTAEINRSDTQRFVSHAIKGAVVVAPNGRK 81 
                                    789***************..9**********99998653211111134444444444449*******************9 PP

                  Lycopene_cycl  75 illg....raYgrvsskrlkeellerlv.engvklleakvesveeeeageslvvleggrkirarlvvdarglasl 144
                                    + +     + Y  + ++++ +++ e  +  ++ ++++  v++v+ ++      v +  ++++arl v a g   +
  gi|119719628|ref|YP_920123.1|  82 VVIKeegeLGYV-IDKRNFLRVMGEYAAsYGADIYMKEPVKEVVFKNG--HWTVRARTVELEARLLVGADG-YLS 152
                                    998877778886.56666666777777736667899999999999988..555666778999999999999.333 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00012
                  Lycopene_cycl 245 vtlggslprleqk.vlaiGaaaglvhPaTGYsvarslaeapllasaiaaalresslsara 303
                                    vt gg l+++ ++  + +G aag v P TG  +  s+a  ++ a++ ++al+e +ls++ 
  gi|119719628|ref|YP_920123.1| 250 VTIGGMLSEIVSEhAMLVGEAAGQVIPLTGGGIHTSIAGGKIAAEVASKALAEGDLSKKR 309
                                    67899***999987899************************9999999999987544433 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   1.1e-06     0.001       1      32 [.       4      37 ..       4      53 .. 0.91
   2 !   13.6   0.1   3.9e-05     0.037     142     350 ..      93     293 ..      44     295 .. 0.61

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.1e-06
                                   EEEEECTSHHHHHHHHHHHHTT..EEEEESSSST CS
                            DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdia 32
                                   d +++G+G +Gl  A+ La +g  V++lek++ +
  gi|119719628|ref|YP_920123.1|  4 DAAVVGAGPAGLMFARVLASKGfrVAVLEKNETL 37
                                   789****************99*********9765 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 3.9e-05
                                    EEEHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEE.EECTEEEEEEEEEEE--GGGHHHHHTT...CTTTSEE CS
                            DAO 142 qvdpakltaalaraaealGveilegtevtgleeedgkvwgve.rttpgendaadavVnaaGawsdllgll...keldlpi 217
                                    ++d + +++ + + a++ G++i+ +++v+++  ++g  w+v+ rt  +   +a+ +V a G  s  ++ l   k+ ++++
  gi|119719628|ref|YP_920123.1|  93 VIDKRNFLRVMGEYAASYGADIYMKEPVKEVVFKNGH-WTVRaRTV-EL--EARLLVGADGYLSYTAKALgleKPGERRV 168
                                    569999************************9666655.***54332.44..36899999997765442222233334666 PP

                                    EEEEEEEEEEEECCTHSTGSGCSEEEEE...EEETTTTEEEEEETTSEEE.EEESSEEETTCSSTSCSHHHHHHHHHHHH CS
                            DAO 218 spvrgqvlvlkplseklvspaailpvpe...tdddgrgvyvtprkdgrvl.vGgtadeesgdddpevdeedidellealr 293
                                     p+  +v+   +l++    p+  +++++    + ++++v ++p  dgr+  vG         +  + + + +d++++   
  gi|119719628|ref|YP_920123.1| 169 IPTVQYVMPNVELED----PD--MTYFFlgnEVAPKGYVWIFPK-DGRLAnVGIG------VQG-ASPKAYLDKFIKNNP 234
                                    665555544433333....22..222223347777777777775.6766533432......222.333444445555555 PP

                                    HHSGG.....GCGEEEEEEEEEE.E.TTSSEEEEEEETEEEEEEEEECTTTHHHHHHHHHHHHH CS
                            DAO 294 klfPq.....lgdvlrkwaGlrp.l.pdglpligetpgvkglylatGhsghGltlapatGklla 350
                                     +f +     ++    +  G++      +  l+ge+     ++ +tG    G+ +++a Gk++a
  gi|119719628|ref|YP_920123.1| 235 SIFGKarileFRGAAVTIGGMLSeIvSEHAMLVGEA--AGQVIPLTGG---GIHTSIAGGKIAA 293
                                    555332211112222355555553224556666664..3445555444...6666666666665 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.4   5.6e-10   5.3e-07       2      38 ..       4      40 ..       3     159 .. 0.87
   2 ?   -0.8   0.0       0.5   4.8e+02     348     370 ..     243     265 ..     232     272 .. 0.85

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 5.6e-10
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HH CS
                    HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklgrK 38
                                   d +v+G+G+AGlm A  +a++g rV++lek+++l+ K
  gi|119719628|ref|YP_920123.1|  4 DAAVVGAGPAGLMFARVLASKGFRVAVLEKNETLAVK 40
                                   789*****************************99877 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.5
                                    --TTT-SEEEEEE-GGGB-TTT- CS
                    HI0933_like 348 eglrkaevTaGGVdlkevssktm 370
                                     ++r a vT GG   + vs++ m
  gi|119719628|ref|YP_920123.1| 243 LEFRGAAVTIGGMLSEIVSEHAM 265
                                    57899********9999999999 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.1   1.1e-09   1.1e-06       2     139 ..       7     155 ..       6     178 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 1.1e-09
                    Pyr_redox_3   2 IiGaGPaGlaaaielkkagledylilEkgni......gnsiyrypkemtfispsftse..kleipdlnaiseetspafsl 73 
                                    ++GaGPaGl +a  l  +g+ ++ +lEk++       g+ i+    ++  i  s t++  +  i++  +++++    + +
  gi|119719628|ref|YP_920123.1|   7 VVGAGPAGLMFARVLASKGF-RVAVLEKNETlavkpcGEGISARVLQTAEINRSDTQRfvSHAIKGAVVVAPNGRK-VVI 84 
                                    8*******************.8******963233333777888888888887776655112345566666666654.344 PP

                    Pyr_redox_3  74 kee.....klsrkealeYlrevaksfelpiklfeeVesvkkedegfevetsketyeAkkviiAtGefdkPn 139
                                    kee      + ++++l+ + e+a+s+  +i ++e V++v  ++++ +v++++ ++eA+ ++ A G+ ++  
  gi|119719628|ref|YP_920123.1|  85 KEEgelgyVIDKRNFLRVMGEYAASYGADIYMKEPVKEVVFKNGHWTVRARTVELEARLLVGADGYLSYTA 155
                                    43322443678999***************************************************987754 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.1   0.00046      0.43       3      44 ..       6      45 ..       4      57 .. 0.82
   2 !   20.3   0.0   2.1e-07    0.0002     144     389 ..      87     340 ..      51     371 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00046
                                   EEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS---.SS-EE CS
                 Trp_halogenase  3 vivGGGtaGwlaAaalakalkgklevtlveseeigtv.gvGea 44
                                    +vG+G+aG + A +la  +   ++v ++e++e+  v   Ge+
  gi|119719628|ref|YP_920123.1|  6 AVVGAGPAGLMFARVLASKG---FRVAVLEKNETLAVkPCGEG 45
                                   69***************999...99*****9776544156765 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 2.1e-07
                                    -S--EEEE-HHHHHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-SEEEE-SGGG-IIIIIIT---EE CS
                 Trp_halogenase 144 alsyAyhldaalyakfLrrvaearGvtrvegkvvevqldedgrveslrledgreveadlfiDcsGfrgllieqaLktgfe 223
                                    + + +y +d++++ +++ ++a + G ++   + v+ ++ ++g+ + +r     e+ea+l + + G+ +   ++aL  +  
  gi|119719628|ref|YP_920123.1|  87 EGELGYVIDKRNFLRVMGEYAASYGADIYMKEPVKEVVFKNGHWT-VRA-RTVELEARLLVGADGYLSY-TAKALGLEKP 163
                                    4577899********************999998888888888754.333.45679**********9986.5788999999 PP

                                    E-TTT----EEEEEEEE--H---SSEE..EEE-SSEEEEEEEETTEEEE.EEEE-TTTS-HHHHHHHHHHH....CT--T CS
                 Trp_halogenase 224 dwsdvLltdrAlavqveseelvepytr..ataekaGWtWkiPLqhrlgn.GyvyssahadddeAlaellae....ldgkl 296
                                       +v++t + +  +ve e++  +y         +G +W  P  +rl n G+ +    a+    l++++++    ++++ 
  gi|119719628|ref|YP_920123.1| 164 GERRVIPTVQYVMPNVELEDPDMTYFFlgNEVAPKGYVWIFPKDGRLANvGIGVQG--ASPKAYLDKFIKNnpsiFGKAR 241
                                    99*****9999999999999555554334788899************998776643..3444445555555111044444 PP

                                    TTS-EEEE---E.EES-SEETTEEE-CCCTEE--CCCS-HHHHHHH....HHHHHHHT--BTT--HHHHHHHHHHHHHHH CS
                 Trp_halogenase 297 eaeprkirfttG.rrkqawvknvvalGlasgfvePlestsihliqa....alrrLlallpdksdepaaiaefnrevarel 371
                                      e r   +t G + +++ ++  +++G+a+g v Pl + +ih+  a    a++   + l+++  ++  ++e+ + +++ +
  gi|119719628|ref|YP_920123.1| 242 ILEFRGAAVTIGgMLSEIVSEHAMLVGEAAGQVIPLTGGGIHTSIAggkiAAEVASKALAEGDLSKKRLEEYKKLYNEYW 321
                                    4444777777651578899999*********************99989999999**********************9999 PP

                                    H.HHHHHHHHHHHT----S CS
                 Trp_halogenase 372 e.rvrdfiilhYkatkred 389
                                    + r+rd ++  + + k +d
  gi|119719628|ref|YP_920123.1| 322 GkRIRDSLKGLHAIEKMSD 340
                                    6369999888877777776 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.1   7.2e-09   6.8e-06       1      31 [.       7      37 ..       7      43 .. 0.95
   2 ?   -2.2   0.0       5.2   4.9e+03      41      54 ..     104     117 ..      78     124 .. 0.68

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 7.2e-09
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSS CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrl 31
                                   +vGaG +Gl +A+ La +gf+v +lek++ l
  gi|119719628|ref|YP_920123.1|  7 VVGAGPAGLMFARVLASKGFRVAVLEKNETL 37
                                   8**************************9865 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5.2
                                    TTCEECTS---EEE CS
                  NAD_binding_8  41 pgvrvdygahifhg 54 
                                    +++++ yga i+++
  gi|119719628|ref|YP_920123.1| 104 GEYAASYGADIYMK 117
                                    56888888888876 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.3     8e-09   7.6e-06       2      58 ..       4      85 ..       3     165 .. 0.67

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 8e-09
                                   SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHH..HCHHHHHHHHHHHHH.......................H CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxx.......................x RF
                    Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcll..skallgvaedaeias.......................e 58
                                   d +v+G+GpAGl +a+ la +g++v+++e+++t+    c    s  +l++ae  +  +                       +
  gi|119719628|ref|YP_920123.1|  4 DAAVVGAGPAGLMFARVLASKGFRVAVLEKNETLAVKPCGEgiSARVLQTAEINRSDTqrfvshaikgavvvapngrkvviK 85
                                   789*************************777777666665544444444444444333455544444444444444444440 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.1   7.7e-08   7.3e-05      17      50 ..       2      34 ..       1      86 [. 0.91

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 7.7e-08
                                   EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESS CS
                           Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailers 50
                                   + D ++vGaG++GL  a++la k +++va+le++
  gi|119719628|ref|YP_920123.1|  2 QYDAAVVGAGPAGLMFARVLASK-GFRVAVLEKN 34
                                   57999******************.********86 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.4   2.1e-07    0.0002       1      33 [.       4      36 ..       4      48 .. 0.94
   2 ?   -0.5   0.0      0.54   5.1e+02     137     182 ..      93     142 ..      80     174 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.1e-07
                                   SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSG CS
                  FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqe 33
                                   D+ V+G+G AGL+ A  +a +G +vav+ek + 
  gi|119719628|ref|YP_920123.1|  4 DAAVVGAGPAGLMFARVLASKGFRVAVLEKNET 36
                                   899***************************875 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.54
                                    ..HHHHHHHHHHHHHHTCTEEEEESEEEEEEEECTT....EEEEEEEEET CS
                  FAD_binding_2 137 lvtghallarlvesarkagvdfqerteadeLivedg....rvtGavvenp 182
                                    +++ ++ l ++ e+a ++g d++ + +++e++ ++g    r++++++e +
  gi|119719628|ref|YP_920123.1|  93 VIDKRNFLRVMGEYAASYGADIYMKEPVKEVVFKNGhwtvRARTVELEAR 142
                                    5667788999999999*****************99999777777777654 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   1.1e-06     0.001       2      50 ..       5      54 ..       4      87 .. 0.90
   2 ?   -1.3   0.0       3.4   3.2e+03      45      67 ..     102     124 ..      78     136 .. 0.67
   3 ?    0.3   0.1       1.1     1e+03       7      22 ..     288     303 ..     286     336 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.1e-06
                                   EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS.TTSSHHHHHHHHHHH CS
                      Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll.rllDeeaskilqekl 50
                                   ++vvG+G  gl++A +la  g +V v+e +++l  + ++e +s+++ +  
  gi|119719628|ref|YP_920123.1|  5 AAVVGAGPAGLMFARVLASKGFRVAVLEKNETLAvKPCGEGISARVLQTA 54
                                   58********************************9999999999887655 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 3.4
                                    HHHHHHHHTTEEEECSEEEEEEE CS
                      Pyr_redox  45 ilqeklekngievllntkveeie 67 
                                    ++ e+    g ++++++ v+e++
  gi|119719628|ref|YP_920123.1| 102 VMGEYAASYGADIYMKEPVKEVV 124
                                    45556666666777777777766 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 1.1
                                    SSHHHHHHHHHHHHTT CS
                      Pyr_redox   7 gGyiglElAgalaelg 22 
                                    gG i+ E+A+ + + g
  gi|119719628|ref|YP_920123.1| 288 GGKIAAEVASKALAEG 303
                                    8999****99876655 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.2     9e-06    0.0085       2      48 ..       5      52 ..       4      76 .. 0.74
   2 ?   -0.7   0.0       1.2   1.2e+03      39      71 ..     322     354 ..     286     365 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 9e-06
                                   EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHH.HHHHHHHHHHHHC CS
                        3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseeal.ekalekiekslek 48
                                    av+GaG  G   a v+as+g++V +++ +e  + + + e i++++ +
  gi|119719628|ref|YP_920123.1|  5 AAVVGAGPAGLMFARVLASKGFRVAVLEKNETLAvKPCGEGISARVLQ 52
                                   69**************************98875404455556654444 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.2
                                    HHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEES CS
                        3HCDH_N  39 lekieksleklvekgklkeeeveaalarisftt 71 
                                     ++i++sl+ l++ +k+++ee +++++ +s+++
  gi|119719628|ref|YP_920123.1| 322 GKRIRDSLKGLHAIEKMSDEELNQLAEILSPQD 354
                                    567888999999999999999988877777655 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   2.8e-05     0.026       2      44 ..       5      46 ..       4     106 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.8e-05
                                   EEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT--SSSSEE CS
                           GIDA  2 viViGgGhAGceAAlaaarlGakvlLithkldtiaelsCnpsi 44
                                     V+G+G AG+  A  +a +G++v+ + +k +t+a  +C + i
  gi|119719628|ref|YP_920123.1|  5 AAVVGAGPAGLMFARVLASKGFRVAVL-EKNETLAVKPCGEGI 46
                                   67************************9.999999999997765 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00012      0.12       2      24 ..      13      35 ..      12      37 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00012
                                   HHHHHHHHHHHTTEEEEEEESSS CS
                  Amino_oxidase  2 aGLaaArqLlsaGfdVtvlEard 24
                                   aGL+ Ar L+s+Gf+V vlE ++
  gi|119719628|ref|YP_920123.1| 13 AGLMFARVLASKGFRVAVLEKNE 35
                                   9*******************875 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00029      0.27       1      36 [.       6      36 ..       6      51 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00029
                  NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsep 36
                                   a+vGaGp+Gl++++ L+++      +++ + +++e+
  gi|119719628|ref|YP_920123.1|  6 AVVGAGPAGLMFARVLASK-----GFRVAVLEKNET 36
                                   89**********9999988.....588888888776 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00024      0.23       2      35 ..       6      60 ..       5      84 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00024
                                   EEE--STTHHHHHHHHHHHTEEEEEEES-GGGG.....................- CS
                         XdhC_C  2 vifGaghvaqalarlaaalgfrvtvvdpreefa.....................t 35
                                   +++Gag+ +   ar++a+ gfrv v++++e++a                     +
  gi|119719628|ref|YP_920123.1|  6 AVVGAGPAGLMFARVLASKGFRVAVLEKNETLAvkpcgegisarvlqtaeinrsD 60
                                   599***************************9887777777666555444333332 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.7   0.00023      0.21       1     126 [.       4     135 ..       4     157 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00023
                   FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvl.....GGlltsglvatdignkaee..qvvtgiareflerlrqrgga 73 
                                    D  VvG+gpaG++ A   a +G +v+++e+++ l     G   ++ +++t + n++ +  +v + i + ++ + + r+  
  gi|119719628|ref|YP_920123.1|   4 DAAVVGAGPAGLMFARVLASKGFRVAVLEKNETLavkpcGEGISARVLQTAEINRSDTqrFVSHAIKGAVVVAPNGRKVV 83 
                                    668***************************99983333233334444444444443334444444444444444332222 PP

                   FAD_oxidored  74 rlkkrskw..ntfepevakavleemlaeagvtvllntrlvevekegkriesvtve 126
                                       k++++   + + + + +v+ e  a +g ++++++ ++ev+ ++   + v+++
  gi|119719628|ref|YP_920123.1|  84 I--KEEGElgYVIDKRNFLRVMGEYAASYGADIYMKEPVKEVVFKN-GHWTVRAR 135
                                    2..2222212478888888888888888888888888888888875.45555554 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0    0.0018       1.7       3      35 ..       6      38 ..       4      83 .. 0.80
   2 ?    1.3   0.1      0.33   3.1e+02     120     146 ..     273     302 ..     247     312 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0018
                                   EEE--SHHHHHHHHHHHTTT--EEEE-S-HHHH CS
                 NAD_Gly3P_dh_N  3 avlGaGswGtalAkvlaenghevrlwvreeeli 35
                                   av+GaG  G  +A+vla++g +v +  ++e l+
  gi|119719628|ref|YP_920123.1|  6 AVVGAGPAGLMFARVLASKGFRVAVLEKNETLA 38
                                   8************************99999443 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.33
                                    HHH-S--...EEEEESS--HHHHHTT--EE CS
                 NAD_Gly3P_dh_N 120 eelkeek...vavlsGpslAeEvakgkpta 146
                                    ++++ +     + ++G  +A Eva + +++
  gi|119719628|ref|YP_920123.1| 273 QVIPLTGggiHTSIAGGKIAAEVASKALAE 302
                                    555544444456799*********998876 PP

>> Sdh5  Flavinator of succinate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.047        44      44      62 ..     180     198 ..     179     203 .. 0.87
   2 ?   -2.4   0.1       5.1   4.8e+03      30      44 ..     304     318 ..     300     319 .. 0.84
   3 ?    4.5   0.0     0.035        33      27      47 ..     334     354 ..     332     361 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.047
                                    TS--HHHHHHHHT-.---S CS
                           Sdh5  44 dleDpdLldwltgrkeepe 62 
                                    +leDpd+ ++++g++ +p+
  gi|119719628|ref|YP_920123.1| 180 ELEDPDMTYFFLGNEVAPK 198
                                    79************88886 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.1
                                    T--HHHHHHHHHHHT CS
                           Sdh5  30 tlseeeldaferLLd 44 
                                    +ls++ l+++++L +
  gi|119719628|ref|YP_920123.1| 304 DLSKKRLEEYKKLYN 318
                                    6899999***99976 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.035
                                    HTTT--HHHHHHHHHHHTS-- CS
                           Sdh5  27 hlatlseeeldaferLLdleD 47 
                                     ++++s+eel+++ ++L  +D
  gi|119719628|ref|YP_920123.1| 334 AIEKMSDEELNQLAEILSPQD 354
                                    689**************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 2285.64
//
Query:       gi|119719629|ref|YP_920124.1|  [L=146]
Description: HxlR family transcriptional regulator [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.3e-07   28.6   0.1    1.4e-06   28.0   0.1    1.4  1  HxlR          HxlR-like helix-turn-helix
    8.7e-05   22.3   0.3    0.00019   21.3   0.3    1.6  1  HTH_5         Bacterial regulatory protein, arsR family
    0.00011   22.0   1.4    0.00022   21.1   0.3    1.9  2  MarR_2        MarR family
    0.00038   20.3   0.3     0.0012   18.7   0.1    1.9  2  MarR          MarR family
    0.00041   19.8   0.3     0.0015   18.0   0.1    2.0  2  HTH_24        Winged helix-turn-helix DNA-binding
     0.0007   19.4   1.6     0.0015   18.4   0.2    2.0  2  TrmB          Sugar-specific transcriptional regulator TrmB
    0.00077   19.5   1.7     0.0016   18.5   1.5    1.7  1  HTH_20        Helix-turn-helix domain
     0.0015   18.5   0.0     0.0047   16.9   0.0    1.8  2  HTH_45        Winged helix-turn-helix
      0.002   18.6   0.1     0.0038   17.7   0.1    1.5  1  HTH_27        Winged helix DNA-binding domain
      0.007   16.1   0.0      0.012   15.3   0.0    1.4  1  AphA_like     Putative AphA-like transcriptional regulator
      0.007   16.3   0.1      0.015   15.3   0.1    1.6  1  PadR          Transcriptional regulator PadR-like family
     0.0073   16.4   0.2     0.0092   16.1   0.2    1.2  1  Replic_Relax  Replication-relaxation
  ------ inclusion threshold ------
      0.015   15.7   0.6      0.074   13.4   0.2    2.1  2  Rrf2          Transcriptional regulator
       0.02   14.8   1.4      0.036   14.0   1.1    1.8  1  HTH_Crp_2     Crp-like helix-turn-helix domain
      0.048   13.6   0.1      0.099   12.6   0.1    1.6  1  HTH_11        HTH domain
      0.072   12.9   1.4       0.24   11.2   1.0    2.0  2  HTH_IclR      IclR helix-turn-helix domain
      0.074   13.2   0.1       0.13   12.4   0.1    1.3  1  HTH_34        Winged helix DNA-binding domain
       0.11   12.7   0.2        1.3    9.3   0.0    2.3  2  Rio2_N        Rio2, N-terminal
       0.12   12.1   0.0       0.19   11.5   0.0    1.3  1  DUF4364       Domain of unknown function (DUF4364)


Domain annotation for each model (and alignments):
>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.1   1.5e-09   1.4e-06       3      76 ..      56     129 ..      54     144 .. 0.85

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 1.5e-09
                                    HSTTHHHHHHHHTT.S-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHHHH CS
                           HxlR   3 ggkWkllilvellk.gkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrslepvl 76 
                                     +k  l +l++ll  g+  f+ + +   ++ +++L++rL++L+++gl+ ++  + v     Y lte+G++ + + 
  gi|119719629|ref|YP_920124.1|  56 AKKGVLEVLYTLLLlGPLSFTRILEST-GLNRRTLSTRLKQLQSEGLVVKVREEGVEGSSRYALTEAGKATALLA 129
                                    566677799998877********9998.9***************************************9866554 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.3     2e-07   0.00019       3      45 ..      59     102 ..      57     104 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2e-07
                                    HHHHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          HTH_5   3 tRlkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLV 45 
                                    + l++L+ L   g+l+++ + e +gl++ t+S  Lk+L  +GLV
  gi|119719629|ref|YP_920124.1|  59 GVLEVLYTLLLlGPLSFTRILESTGLNRRTLSTRLKQLQSEGLV 102
                                    679999999999*******************************9 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.7   1.6e+03      23      44 ..      26      47 ..      18      49 .. 0.58
   2 !   21.1   0.3   2.3e-07   0.00022       9      56 ..      62     107 ..      59     111 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.7
                                   EHHHHHHHHTSSHHHHHHHHHH CS
                         MarR_2 23 tvgelarrlglsksavsrilkr 44
                                   t +e ++r +ls + + ril++
  gi|119719629|ref|YP_920124.1| 26 TLREFVERENLSVADAKRILEE 47
                                   4455555555555555555555 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 2.3e-07
                                    HHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                         MarR_2   9 rvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56 
                                     vL+ L   ++  l+ + + + +gl + ++s +lk L++ GLv++++ 
  gi|119719629|ref|YP_920124.1|  62 EVLYTLLLLGP--LSFTRILESTGLNRRTLSTRLKQLQSEGLVVKVRE 107
                                    59999999999..******************************99865 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       2.9   2.7e+03      21      37 ..      28      44 ..      24      49 .. 0.54
   2 !   18.7   0.1   1.3e-06    0.0012       7      51 ..      62     106 ..      59     109 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.9
                                   HHHHHHHTS-HHHHHHH CS
                           MarR 21 seLakklgvskstvtrv 37
                                    e  ++ ++s + + r+
  gi|119719629|ref|YP_920124.1| 28 REFVERENLSVADAKRI 44
                                   45555555555555555 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 1.3e-06
                                    HHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                           MarR   7 viLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRsk 51 
                                    ++L++l   gpls + + +  g+++ t+++ l++L  +Gl+ + +
  gi|119719629|ref|YP_920124.1|  62 EVLYTLLLLGPLSFTRILESTGLNRRTLSTRLKQLQSEGLVVKVR 106
                                    7999************************************98766 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       1.3   1.2e+03      29      41 ..      36      48 ..      26      49 .. 0.58
   2 !   18.0   0.1   1.6e-06    0.0015      16      47 ..      71     102 ..      60     103 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.3
                         HTH_24 29 lSpstvnrrlkrL 41
                                   lS++  +r l++L
  gi|119719629|ref|YP_920124.1| 36 LSVADAKRILEEL 48
                                   5555444444444 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 1.6e-06
                         HTH_24  16 prisqreLAerlglSpstvnrrlkrLeeeGlI 47 
                                    + +s + + e +gl + t+++rlk+L++eGl+
  gi|119719629|ref|YP_920124.1|  71 GPLSFTRILESTGLNRRTLSTRLKQLQSEGLV 102
                                    5689999***********************98 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1       0.9   8.5e+02      22      46 ..      24      48 ..      10      50 .. 0.73
   2 !   18.4   0.2   1.6e-06    0.0015      12      59 ..      62     113 ..      61     135 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.9
                                   CCHHCHHCCCTTSSCHCHHHHHHHH CS
                           TrmB 22 patadeiaeelgvprskvYevLrsL 46
                                   +at +e  e+ +++ + + ++L++L
  gi|119719629|ref|YP_920124.1| 24 EATLREFVERENLSVADAKRILEEL 48
                                   5677777777777777777777776 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 1.6e-06
                                    CHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST....T CS
                           TrmB  12 kvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr....p 59 
                                    +v  +Ll lgp++ + i e +g+ r +    L++L + GlV +++++     
  gi|119719629|ref|YP_920124.1|  62 EVLYTLLLLGPLSFTRILESTGLNRRTLSTRLKQLQSEGLVVKVREEgvegS 113
                                    67889999*********************************99998755553 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   1.5   1.7e-06    0.0016      20      60 ..      68     108 ..      41     109 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.7e-06
                                    STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                         HTH_20  20 araegltaselaerldlskntlsyHLrvLeeagLvevvreg 60 
                                       ++l+++ + e  +l + tls +L++L++ gLv  vre+
  gi|119719629|ref|YP_920124.1|  68 LLLGPLSFTRILESTGLNRRTLSTRLKQLQSEGLVVKVREE 108
                                    466999****************************7777764 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       1.7   1.6e+03      24      44 ..      29      49 ..      18      64 .. 0.76
   2 !   16.9   0.0     5e-06    0.0047      18      64 ..      71     124 ..      57     129 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.7
                         HTH_45 24 kimykanLsykllnkYLdmLv 44
                                   + + + nLs   +++ L+ L 
  gi|119719629|ref|YP_920124.1| 29 EFVERENLSVADAKRILEELA 49
                                   556677888888888888875 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 5e-06
                         HTH_45  18 geakkTkimykanLsykllnkYLdmLvekgli.......kkskekYvlTekGle 64 
                                    g  + T+i+ +  L+ ++l+  L++L+++gl+        + ++ Y lTe G+ 
  gi|119719629|ref|YP_920124.1|  71 GPLSFTRILESTGLNRRTLSTRLKQLQSEGLVvkvreegVEGSSRYALTEAGKA 124
                                    66788**************************9999998888999********86 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1     4e-06    0.0038       9      68 .]      64     122 ..      59     122 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4e-06
                         HTH_27   9 LhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68 
                                    L ++   +++ + +++ + + ++  + s  lk+L   GLv++ + e   +++r++lT++G
  gi|119719629|ref|YP_920124.1|  64 LYTLL-LLGPLSFTRILESTGLNRRTLSTRLKQLQSEGLVVKVREEGVEGSSRYALTEAG 122
                                    55555.677888899999999999****************9999999999********99 PP

>> AphA_like  Putative AphA-like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.3e-05     0.012      51      85 ..      91     125 ..      79     138 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.3e-05
                      AphA_like  51 sslellreeGLveavdGeGmednalLaiteaGrre 85 
                                    + l +l+ eGLv  v  eG+e + + a+teaG++ 
  gi|119719629|ref|YP_920124.1|  91 TRLKQLQSEGLVVKVREEGVEGSSRYALTEAGKAT 125
                                    67899***************************974 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   1.5e-05     0.015      33      72 ..      88     125 ..      75     127 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.5e-05
                                    HHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHH CS
                           PadR  33 slYpaLkrLekeglveseweesgegpprkyYrlTdaGrre 72 
                                    +l + Lk+L+ eglv++ +ee +eg  r  Y+lT+aG+++
  gi|119719629|ref|YP_920124.1|  88 TLSTRLKQLQSEGLVVKVREEGVEGSSR--YALTEAGKAT 125
                                    66789*************9998777777..*******985 PP

>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.2   9.8e-06    0.0092      16      67 ..      76     124 ..      61     143 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 9.8e-06
                   Replic_Relax  16 arllfashra..tarrrLarLrelgllsrlrkrvggarggsepyvYaLtpkGar 67 
                                    +r+l+ ++ +  t+++rL++L+++gl+ ++r++  g++g   + +YaLt++G++
  gi|119719629|ref|YP_920124.1|  76 TRILESTGLNrrTLSTRLKQLQSEGLVVKVREE--GVEG---SSRYALTEAGKA 124
                                    5555555444457*****************999..6666...579*******76 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.86   8.1e+02      26      51 ..      25      50 ..      18      64 .. 0.77
   2 ?   13.4   0.2   7.9e-05     0.074      25      63 ..      72     112 ..      60     132 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.86
                                   B-HHHHHHHHTS-HHHHHHHHHHHHH CS
                           Rrf2 26 vsseeiaerqnispsylekilakLrk 51
                                   ++++e  er n+s   +++il++L+ 
  gi|119719629|ref|YP_920124.1| 25 ATLREFVERENLSVADAKRILEELAP 50
                                   67788889999999999999999875 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 7.9e-05
                                    -B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET..TT-T CS
                           Rrf2  25 pvsseeiaerqnispsylekilakLrkaglvksvr..GkgG 63 
                                    p+s + i e+++++++ l+  l++L+ +glv  vr  G++G
  gi|119719629|ref|YP_920124.1|  72 PLSFTRILESTGLNRRTLSTRLKQLQSEGLVVKVReeGVEG 112
                                    689999*************************8876446666 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   1.1   3.8e-05     0.036      29      54 ..      80     106 ..      41     121 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.8e-05
                                    HHTTSSHHHHHHHHHHHHHTTSEE.ET CS
                      HTH_Crp_2  29 smlGltretvsrilseLkreglis.rg 54 
                                    +  Gl+r t+s  l++L+ egl+   +
  gi|119719629|ref|YP_920124.1|  80 ESTGLNRRTLSTRLKQLQSEGLVVkVR 106
                                    678*******************99534 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1    0.0001     0.099      14      46 ..      71     103 ..      60     111 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0001
                         HTH_11  14 gpisgeeLAeeLnvSrrtvrrdIkaLeelgvpI 46 
                                    gp+s  ++ e +++ rrt   ++k+L++ g+ +
  gi|119719629|ref|YP_920124.1|  71 GPLSFTRILESTGLNRRTLSTRLKQLQSEGLVV 103
                                    4699999***********************443 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       1.6   1.5e+03      20      42 ..      26      48 ..      21      49 .. 0.78
   2 ?   11.2   1.0   0.00026      0.24      17      50 ..      71     104 ..      61     106 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.6
                                   BHHHHHHHHTS-HHHHHHHHHHH CS
                       HTH_IclR 20 tlselArrtglpkStvhRlLqtL 42
                                   tl+e  +r  l+ + + R+L  L
  gi|119719629|ref|YP_920124.1| 26 TLREFVERENLSVADAKRILEEL 48
                                   78888888888889999999877 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00026
                                    SS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                       HTH_IclR  17 qeltlselArrtglpkStvhRlLqtLvelGyveq 50 
                                    ++l+++ + + tgl++ t +  L+ L+ +G+v +
  gi|119719629|ref|YP_920124.1|  71 GPLSFTRILESTGLNRRTLSTRLKQLQSEGLVVK 104
                                    579****************************976 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00014      0.13       3      68 ..      61     125 ..      60     129 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00014
                         HTH_34   3 lavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGrea 68 
                                    l+vl +L+     +f+++ e+++++   Ls+ lk L++ g + v+   +g      + +T++G++ 
  gi|119719629|ref|YP_920124.1|  61 LEVLYTLLLLGPLSFTRILESTGLNRRTLSTRLKQLQSEGLV-VKVREEGVEGSSRYALTEAGKAT 125
                                    6888899999999**************************965.55555666668999999999975 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1      0.43     4e+02       5      22 ..      13      30 ..       9      70 .. 0.70
   2 ?    9.3   0.0    0.0014       1.3      27      70 ..      75     122 ..      72     131 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.43
                         Rio2_N  5 skedfrvLtavEmgmrnh 22
                                   +k+  rv+++vE + r++
  gi|119719629|ref|YP_920124.1| 13 EKKVSRVIEGVEATLREF 30
                                   666678888888887754 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0014
                         Rio2_N  27 telieeisrlkeeevkkrlsrllkaklisr.ktakydG...YkLtyeG 70 
                                    +++i e ++l++  ++ rl++l  ++l+++ ++   +G   Y+Lt +G
  gi|119719629|ref|YP_920124.1|  75 FTRILESTGLNRRTLSTRLKQLQSEGLVVKvREEGVEGssrYALTEAG 122
                                    6789999***********************999999986667777665 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0    0.0002      0.19      26      73 ..      79     129 ..      63     142 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0002
                        DUF4364  26 leneytnYfdlqqalseLvesglieeeek...enktlykiTekGketlelf 73 
                                    le   +n  +l+  l++L ++gl+ + ++   e++++y++Te+Gk t+ l 
  gi|119719629|ref|YP_920124.1|  79 LESTGLNRRTLSTRLKQLQSEGLVVKVREegvEGSSRYALTEAGKATALLA 129
                                    555666667889999********99884437799***********998665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1053.39
//
Query:       gi|119719630|ref|YP_920125.1|  [L=351]
Description: hypothetical protein Tpen_0720 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-09   37.9   0.0      3e-09   37.3   0.0    1.3  1  DUF87          Helicase HerA, central domain
    0.00013   21.1   0.0     0.0002   20.4   0.0    1.3  1  AAA_10         AAA-like domain
    0.00034   20.0   0.0    0.00059   19.3   0.0    1.3  1  FtsK_SpoIIIE   FtsK/SpoIIIE family
    0.00054   19.0   0.0    0.00082   18.4   0.0    1.2  1  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
    0.00072   19.8   0.3      0.034   14.4   0.3    2.3  1  AAA_22         AAA domain
     0.0037   17.2   0.3      0.066   13.1   0.1    2.2  2  NACHT          NACHT domain
  ------ inclusion threshold ------
      0.012   15.8   0.0       0.28   11.4   0.0    2.2  2  AAA_28         AAA domain
      0.022   13.4   0.0       0.15   10.6   0.0    1.9  2  DUF853         Bacterial protein of unknown function (DUF853)
      0.033   14.7   0.0       0.23   12.0   0.0    2.1  2  AAA_18         AAA domain
      0.061   13.7   0.1       0.14   12.5   0.1    1.9  1  AAA_16         AAA ATPase domain
      0.078   13.5   0.1       0.14   12.7   0.1    1.3  1  ABC_tran       ABC transporter
      0.078   11.8   0.0       0.13   11.0   0.0    1.3  1  Adeno_IVa2     Adenovirus IVa2 protein


Domain annotation for each model (and alignments):
>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.0     2e-12     3e-09       9      68 ..      49     109 ..      41     165 .. 0.84

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 2e-12
                          DUF87   9 gsevpvyldlnklvtrHlAilgsTGsGKSntvavLleellekkgatililDpHGE..Ygkal 68 
                                    +++  vyl+ +kl ++H  ilg+TGsGKS +++ ++ e+  + g+t  ++DpH+E  Y k++
  gi|119719630|ref|YP_920125.1|  49 DRGRNVYLNPEKLPNMHGVILGTTGSGKSSLARHIMLEAR-RLGVTSWVIDPHSEatYRKLF 109
                                    55568***********************************.*************96666666 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   1.4e-07    0.0002      17      61 ..      59     104 ..      52     124 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.4e-07
                         AAA_10  17 sktnasasliiGdlGnGKSvlakllvlyisllggkaliiDpkke.r 61 
                                    +k  +++ +i+G +G GKS la+ ++l ++ lg  + +iDp  e +
  gi|119719630|ref|YP_920125.1|  59 EKLPNMHGVILGTTGSGKSSLARHIMLEARRLGVTSWVIDPHSEaT 104
                                    56678999***********************************942 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   3.9e-07   0.00059      22      61 ..      45      85 ..      37      88 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 3.9e-07
                                   EEEETTS-EEEEEGGGS-..SEEEE--TTSSHHHHHHHHHH CS
                   FtsK_SpoIIIE 22 lgkeisgnplvldlkkma.shllvaGatgsGKStalntLil 61
                                   lg++ +g++++l+  k +  h++++G+tgsGKS   + ++l
  gi|119719630|ref|YP_920125.1| 45 LGRDDRGRNVYLNPEKLPnMHGVILGTTGSGKSSLARHIML 85
                                   677779999*********99**************9998887 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   5.5e-07   0.00082      14      56 ..      62     104 ..      55     112 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 5.5e-07
                  TrwB_AAD_bind  14 etqhilivGttGsGKtqalekllrairargdraivlDltGafv 56 
                                     ++h +i+GttGsGK+  +++++ ++r+ g +  v+D++ + +
  gi|119719630|ref|YP_920125.1|  62 PNMHGVILGTTGSGKSSLARHIMLEARRLGVTSWVIDPHSEAT 104
                                    57899********************************998766 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.3   2.3e-05     0.034       7      58 ..      65     110 ..      61     277 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.3e-05
                         AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevv..fvtlpsstsskdllr 58 
                                    ++v+ G +G+GK+ l+r ++ ++         r +v    +++ s+ + ++l++
  gi|119719630|ref|YP_920125.1|  65 HGVILGTTGSGKSSLARHIMLEAR--------RLGVTswVIDPHSEATYRKLFE 110
                                    89******************9984........3333344666666666666654 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.1   4.4e-05     0.066       4      25 ..      67      88 ..      66      94 .. 0.90
   2 ?    1.7   0.0      0.14   2.1e+02      42     115 ..     187     264 ..     171     292 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.4e-05
                                   EEEC-TTTCHHHHHHHHHHHHC CS
                          NACHT  4 ilqGeaGsGKTtLlqklalawa 25
                                   ++ G  GsGK+ L+++++l+++
  gi|119719630|ref|YP_920125.1| 67 VILGTTGSGKSSLARHIMLEAR 88
                                   689***************9986 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.14
                                    TTTTTTS-...-HCHHHCCCCTS--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH................HHHHHC CS
                          NACHT  42 lrelsrsgnarsladllfsqlpepaapvsevwavllelperlLlilDglDelvtdlgq.......kekqpvrtlLselir 114
                                    l+++   + a s+a+l ++++    a vs+  ++l+   + lLl+l g+ +++   +        +e+  v++ + +l++
  gi|119719630|ref|YP_920125.1| 187 LSRIHSNEGA-SIAELTRDVYFYYPALVSR--EFLALSSQILLLLLEGYMRTKGARHRlehlvvlEEAHLVKDYILSLFK 263
                                    5555555556.9999999999999999988..888888888899999999888877767777777777777777777776 PP

                                    T CS
                          NACHT 115 k 115
                                    +
  gi|119719630|ref|YP_920125.1| 264 Q 264
                                    6 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00019      0.28       3      40 ..      67     109 ..      66     117 .. 0.80
   2 ?    1.9   0.0      0.16   2.3e+02       7      43 ..     125     170 ..     119     199 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00019
                         AAA_28   3 vitGgestGKTtlleaLa..ar..g.ypvvpEaareileekla 40 
                                    vi+G+ ++GK++l++++   ar  g +++v +++ e +  kl+
  gi|119719630|ref|YP_920125.1|  67 VILGTTGSGKSSLARHIMleARrlGvTSWVIDPHSEATYRKLF 109
                                    89************99776555686377998888888877765 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.16
                         AAA_28   7 gestGKTtlleaLaar........gypvv.pEaareileeklakge 43 
                                    +++ G + l+++L++         gy+ + +E+  + +ee++ + +
  gi|119719630|ref|YP_920125.1| 125 APGWGASELASELSRYieaiygfpGYRSIlREILKRCFEEGSLEFF 170
                                    8999**********77777896666665557777777777764443 PP

>> DUF853  Bacterial protein of unknown function (DUF853)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0    0.0001      0.15       8      56 ..      49      98 ..      43     103 .. 0.79
   2 ?    0.5   0.0      0.11   1.7e+02     267     309 ..     244     286 ..     149     293 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0001
                         DUF853  8 eaeqelalal.klanrhGliaGatGtGktvtLqvlaeslseaGvpvflad 56
                                   ++ ++++l++ kl n hG+i G tG Gk    +++  +  + Gv+ ++ d
  gi|119719630|ref|YP_920125.1| 49 DRGRNVYLNPeKLPNMHGVILGTTGSGKSSLARHIMLEARRLGVTSWVID 98
                                   55666776652678***************999999888888888877766 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.11
                         DUF853 267 hLLfndapkallekveqvvrLirskGvGvyfvtqnPldlPdtv 309
                                    hL+  + ++ + + +  + + +r  G G+  vtq P ++   v
  gi|119719630|ref|YP_920125.1| 244 HLVVLEEAHLVKDYILSLFKQVRKYGWGLLAVTQLPREMDPRV 286
                                    5555555555667777778888999999999999999876555 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00016      0.23       2      22 ..      67      90 ..      67     114 .. 0.78
   2 ?   -0.1   0.0      0.82   1.2e+03       7      25 ..     126     149 ..     125     198 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00016
                         AAA_18  2 lltGtpGvGKttlakeL...skrl 22
                                   ++ Gt G+GK++la+++   ++rl
  gi|119719630|ref|YP_920125.1| 67 VILGTTGSGKSSLARHImleARRL 90
                                   589*************96665555 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.82
                         AAA_18   7 pGvGKttlakeLskrl.gf....g 25 
                                    pG G ++la eLs+   ++    g
  gi|119719630|ref|YP_920125.1| 126 PGWGASELASELSRYIeAIygfpG 149
                                    888999999999987533364441 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   9.5e-05      0.14      28      69 ..      67     105 ..      58     262 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.5e-05
                         AAA_16  28 llsGesGvGKsslvrellralekdggiflrgkcdqlesaipy 69 
                                    ++ G  G+GKssl+r+++ ++++ g   ++ +  + +s+++y
  gi|119719630|ref|YP_920125.1|  67 VILGTTGSGKSSLARHIMLEARRLG---VTSWVIDPHSEATY 105
                                    699***************6555543...33333333344445 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   9.3e-05      0.14      15      34 ..      67      86 ..      61      96 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.3e-05
                                   EEEESTTSSHHHHHHHHTTS CS
                                   xxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran 15 aivGenGaGKStLlkllagl 34
                                   +i+G +G+GKS+L++ ++ +
  gi|119719630|ref|YP_920125.1| 67 VILGTTGSGKSSLARHIMLE 86
                                   79*************99865 PP

>> Adeno_IVa2  Adenovirus IVa2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   8.6e-05      0.13      76     108 ..      51      84 ..      44     103 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 8.6e-05
                     Adeno_IVa2  76 GelsslnyglqP.viGviyGPtGsGksqllrnli 108
                                    G+   ln ++ P + Gvi G tGsGks l r ++
  gi|119719630|ref|YP_920125.1|  51 GRNVYLNPEKLPnMHGVILGTTGSGKSSLARHIM 84 
                                    555567777666367***************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2381.16
//
Query:       gi|119719631|ref|YP_920126.1|  [L=354]
Description: hypothetical protein Tpen_0721 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2406.22
//
Query:       gi|119719632|ref|YP_920127.1|  [L=865]
Description: hypothetical protein Tpen_0722 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (865 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.49
# Mc/sec: 5346.68
//
Query:       gi|119719633|ref|YP_920128.1|  [L=257]
Description: hypothetical protein Tpen_0723 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1990.43
//
Query:       gi|119719634|ref|YP_920129.1|  [L=174]
Description: hypothetical protein Tpen_0724 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        1.5    7.7   4.6        5.9    5.8   0.2    2.2  2  PalH      PalH/RIM21


Domain annotation for each model (and alignments):
>> PalH  PalH/RIM21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.2   0.00033       5.9     286     308 ..       3      25 ..       1      30 [. 0.80
   2 ?    3.9   0.7    0.0013        22     182     220 ..      90     141 ..      50     145 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.00033
                           PalH 286 vlkllitvivWewierieklerk 308
                                    +l+ll++ ivWew+ r  k+ r+
  gi|119719634|ref|YP_920129.1|   3 TLRLLAVKIVWEWVMRNVKRLRE 25 
                                    7899**********987666555 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.0013
                           PalH 182 iilvGlaliildtilsalllfsk..............kfldalpalsylfela 220
                                    i ++G+alii+d +ls ++   +              ++l ++p+++  ++++
  gi|119719634|ref|YP_920129.1|  90 IGIIGFALIIVDALLSWFTGG-SfgrslavgkflkaaETLAIIPIIFLSVQIM 141
                                    67999*****99999999876.2234466666777778888888888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.51
# Mc/sec: 1035.02
//
Query:       gi|119719635|ref|YP_920130.1|  [L=237]
Description: chromosome partitioning ATPase protein-like [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.5e-08   34.0   0.0    1.7e-07   31.3   0.0    2.0  1  AAA_31       AAA domain
    6.3e-06   25.8   1.9      2e-05   24.2   1.9    1.7  1  ParA         NUBPL iron-transfer P-loop NTPase
    1.3e-05   25.2   0.0    2.5e-05   24.4   0.0    1.5  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    3.3e-05   23.5   0.4       0.21   11.0   0.3    2.2  2  CBP_BcsQ     Cellulose biosynthesis protein BcsQ
     0.0002   20.7   0.1       0.38   10.0   0.1    2.6  3  MipZ         ATPase MipZ
     0.0068   15.6   1.2       0.02   14.1   1.2    1.9  1  ArsA_ATPase  Anion-transporting ATPase
     0.0096   15.4   0.0      0.016   14.7   0.0    1.3  1  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif


Domain annotation for each model (and alignments):
>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.0   6.6e-11   1.7e-07       3     154 ..       5     146 ..       3     153 .. 0.84

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 6.6e-11
                         AAA_31   3 vIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgiekneiektlyevlieeknikeaiiktkvenld 82 
                                    v  ++  KGG GK+  s   +  la++g kvLlvDl   +++t+ + + ++     l + +  +++ +++i+ +  e+l 
  gi|119719635|ref|YP_920130.1|   5 VAFVSGSKGGTGKSVLSSLASFELASMGRKVLLVDLGELGSSTQLC-LAEDPGPPYLSDFFQGKASWRDVIVASPWEKLF 83 
                                    5556789*******************************99999955.5677788999***99****************** PP

                         AAA_31  83 lipssidLaeaeielvelekkeeilkellekvkdeYDyiiiDcpPsLglltenaLvasdsviipvqaeayal 154
                                    + pss +   ++          + l+ lle+v+   D++++D+p   g+l +   + ++ +  ++++++++ 
  gi|119719635|ref|YP_920130.1|  84 VAPSSKQQGPVDA---------DSLEYLLEAVDGYVDFVVLDMPAYPGTLYDPVAALAEVLALVMNPDKLSF 146
                                    ****988666654.........45788999999999999999998888888877777777777777777765 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   1.9   7.8e-09     2e-05       5     123 ..       5     123 ..       2     149 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 7.8e-09
                           ParA   5 viavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekpeqsekkli.PveakgikvmSi.gfll 82 
                                    v  v+ +KGG GKS +++  +++La++g kv l+D+   G s    l  +   p  s+  ++   + +++ v S  + l 
  gi|119719635|ref|YP_920130.1|   5 VAFVSGSKGGTGKSVLSSLASFELASMGRKVLLVDLGELGSSTQLCLAEDPGPPYLSD-FFQgKASWRDVIVASPwEKLF 83 
                                    5678889**********************************99888877777777776.444244458888887424443 PP

                           ParA  83 esedeavvwrGpmkskaikqllkdvewgelDyLiiDlP..PGt 123
                                         +   +Gp+ +  ++ ll+ v+ g +D++++D+P  PGt
  gi|119719635|ref|YP_920130.1|  84 V--APSSKQQGPVDADSLEYLLEAVD-GYVDFVVLDMPayPGT 123
                                    3..3444569************9998.89*********88888 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   9.6e-09   2.5e-05       3      69 ..       8     109 ..       6     151 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 9.6e-09
                                    EEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH............................ CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................ RF
                           CbiA   3 iastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep............................ 54 
                                    + + kGG+GK++l+    + la  g++VllvD++  ++++     l +d  p                            
  gi|119719635|ref|YP_920130.1|   8 VSGSKGGTGKSVLSSLASFELASMGRKVLLVDLGELGSSTQ--LCLAEDPGPpylsdffqgkaswrdvivaspweklfva 85 
                                    6789******************************9999998..3343333335667777777777778888888888888 PP

                                    .........CCHCCCHHHHHHCHC CS
                                    .........xxxxxxxxxxxxxxx RF
                           CbiA  55 .........dlkrllellealgkk 69 
                                             d+++l+ llea+++ 
  gi|119719635|ref|YP_920130.1|  86 psskqqgpvDADSLEYLLEAVDGY 109
                                    888888888888877777777766 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.3   8.3e-05      0.21       5      38 ..       7      40 ..       3      52 .. 0.88
   2 !   10.5   0.0   0.00012      0.31     101     149 ..      95     143 ..      69     149 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 8.3e-05
                       CBP_BcsQ  5 alqGvRGGvGttsllaaLawalhelgesvlviDl 38
                                    ++G +GG+G++ l++  +  l ++g +vl++Dl
  gi|119719635|ref|YP_920130.1|  7 FVSGSKGGTGKSVLSSLASFELASMGRKVLLVDL 40
                                   57899******99999999**************8 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00012
                       CBP_BcsQ 101 kaeallaalkelkeqyrwillDlpagasaltrellaladlvllvvepda 149
                                    +a++l   l+++ +  ++++lD+pa++ +l   + ala++  lv++pd 
  gi|119719635|ref|YP_920130.1|  95 DADSLEYLLEAVDGYVDFVVLDMPAYPGTLYDPVAALAEVLALVMNPDK 143
                                    5667777788888999*******************************97 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.1   0.00015      0.38       4      38 ..       7      41 ..       4      53 .. 0.89
   2 !    7.6   0.0   0.00079         2      84     132 ..      94     142 ..      62     151 .. 0.82
   3 ?   -1.1   0.0      0.37   9.4e+02     154     180 ..     201     227 ..     186     232 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00015
                                   EE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE-- CS
                           MipZ  4 vlgnekGGsGksttavhvavaLlkkGarvaaidld 38
                                    ++  kGG+Gks  +      L+++G +v  +dl 
  gi|119719635|ref|YP_920130.1|  7 FVSGSKGGTGKSVLSSLASFELASMGRKVLLVDLG 41
                                   56778****************************95 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00079
                                    HHHHHHHHHHHHHHHH-SEEEEE--SS--HHHHHHHHT-SEEEEEEESS CS
                           MipZ  84 aevaeleelvadleaeldfividtPGsdsalsrlahsladtlvtPlnds 132
                                     +  +le l++++   +df+v+d P    +l   +++la+ l   +n  
  gi|119719635|ref|YP_920130.1|  94 VDADSLEYLLEAVDGYVDFVVLDMPAYPGTLYDPVAALAEVLALVMNPD 142
                                    3445899*******************99999999999999988888755 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.37
                                    HHHHHHHHHHHTTTTT-SS--EEEEEE CS
                           MipZ 154 lyaelvwearkkrakaerkevdWvvlr 180
                                     y+e++ +a+k+ +k+ r+ev  +v r
  gi|119719635|ref|YP_920130.1| 201 AYTETIADAHKHLSKKTREEVKLLVQR 227
                                    577777777777777777777666654 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   1.2   7.8e-06      0.02       2      35 ..       4      38 ..       3      65 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.8e-06
                                   EEEEEEE.STTSSHHHHHHHHHHHHHHTTS-EEEE CS
                    ArsA_ATPase  2 kvilvgG.KGGVGKttvsaatavklsekgkkvlli 35
                                   +v +v+G KGG GK+ +s+  + +l+ +g+kvll+
  gi|119719635|ref|YP_920130.1|  4 RVAFVSGsKGGTGKSVLSSLASFELASMGRKVLLV 38
                                   67788877**************************9 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   6.3e-06     0.016       7      48 ..      11      52 ..       4      76 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 6.3e-06
                      Fer4_NifH  7 GkGGiGksttsqnlsaalaemgkkvlivGCDPkaDstrlllg 48
                                    kGG Gks+ s+  s  la+mg+kvl+v       st+l l 
  gi|119719635|ref|YP_920130.1| 11 SKGGTGKSVLSSLASFELASMGRKVLLVDLGELGSSTQLCLA 52
                                   49**************************99888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1627.22
//
Query:       gi|119719636|ref|YP_920131.1|  [L=118]
Description: hypothetical protein Tpen_0726 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.027   14.2   0.2      0.029   14.1   0.2    1.2  1  FAM184    Family with sequence similarity 184, A and B
      0.048   13.4   0.0      0.054   13.2   0.0    1.1  1  LXG       LXG domain of WXG superfamily
       0.16   11.8   0.0       0.22   11.4   0.0    1.1  1  Sec34     Sec34-like family


Domain annotation for each model (and alignments):
>> FAM184  Family with sequence similarity 184, A and B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.2   4.9e-06     0.029     168     207 ..      75     114 ..      43     118 .] 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.9e-06
                         FAM184 168 ekhkaeveklkeeveelekekkklveeyEeklakqkafye 207
                                    + +++ev++++e++ +le+e+ +l +e+E+ l  +kaf e
  gi|119719636|ref|YP_920131.1|  75 RSIADEVARINERISALEQERGRLLAERERLLRLLKAFSE 114
                                    34578*************************9999999876 PP

>> LXG  LXG domain of WXG superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0     9e-06     0.054     126     185 ..      53     112 ..      40     118 .] 0.90

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9e-06
                            LXG 126 lasvsdivslpelddsevkdslqkakkkvqetiekledfdqeqksalanlesdlkalkty 185
                                    l+ v d v+l++   ++vk++l++  ++v +++e + +++qe  ++la+ e  l+ lk++
  gi|119719636|ref|YP_920131.1|  53 LKAVLDAVGLDPGIAEKVKEKLRSIADEVARINERISALEQERGRLLAERERLLRLLKAF 112
                                    667999************************************************999986 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   3.6e-05      0.22      20      63 ..      68     111 ..      65     115 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.6e-05
                          Sec34  20 dealeqLeeleekfksvsektsslheaceqlleeqkrleelaee 63 
                                    ++++e+L+++ +++ +++e+ s+l+++  +ll+e++rl +l ++
  gi|119719636|ref|YP_920131.1|  68 EKVKEKLRSIADEVARINERISALEQERGRLLAERERLLRLLKA 111
                                    7899*********************************9988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       995  (0.0554967); expected 358.6 (0.02)
Passed bias filter:                      706  (0.0393775); expected 358.6 (0.02)
Passed Vit filter:                       115  (0.00641419); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.32s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 758.04
//
Query:       gi|119719637|ref|YP_920132.1|  [L=392]
Description: type II secretion system protein E [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-17   63.6   0.0    3.4e-17   62.4   0.0    1.7  1  T2SSE            Type II/IV secretion system protein
    2.3e-05   24.8   0.0    5.6e-05   23.6   0.0    1.6  1  AAA_16           AAA ATPase domain
     0.0002   21.9   0.0    0.00034   21.2   0.0    1.4  1  AAA_18           AAA domain
    0.00024   20.7   0.2     0.0009   18.9   0.1    1.9  2  AAA_25           AAA domain
    0.00035   20.8   0.0    0.00059   20.1   0.0    1.3  1  AAA_28           AAA domain
    0.00045   20.0   0.0      0.001   18.9   0.0    1.5  1  AAA_30           AAA domain
    0.00071   19.9   0.0     0.0018   18.6   0.0    1.6  1  AAA_19           AAA domain
     0.0015   18.2   0.0     0.0028   17.3   0.0    1.4  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
     0.0027   17.7   0.0      0.005   16.8   0.0    1.5  1  AAA_5            AAA domain (dynein-related subfamily)
     0.0028   17.6   0.0     0.0054   16.7   0.0    1.6  1  NTPase_1         NTPase
     0.0031   17.5   0.0     0.0051   16.8   0.0    1.4  1  Glyco_transf_4   Glycosyltransferase Family 4
     0.0071   16.6   0.0      0.015   15.6   0.0    1.5  1  AAA_22           AAA domain
     0.0079   16.1   0.0      0.015   15.2   0.0    1.4  1  NACHT            NACHT domain
      0.008   15.9   0.0      0.015   15.0   0.0    1.4  1  AAA_29           P-loop containing region of AAA domain
     0.0085   16.5   0.0      0.015   15.8   0.0    1.4  1  AAA              ATPase family associated with various cellul
     0.0096   16.1   0.0      0.043   14.0   0.0    1.9  2  AAA_33           AAA domain
  ------ inclusion threshold ------
      0.011   15.5   0.0      0.016   15.0   0.0    1.2  1  AAA_11           AAA domain
      0.014   15.9   0.0      0.027   15.0   0.0    1.4  1  ABC_tran         ABC transporter
      0.014   14.6   0.0      0.021   14.1   0.0    1.2  1  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.018   14.4   0.0      0.035   13.4   0.0    1.4  1  Zeta_toxin       Zeta toxin
      0.018   15.5   0.0       0.03   14.8   0.0    1.2  1  AAA_23           AAA domain
      0.028   14.8   0.0      0.052   14.0   0.0    1.4  1  AAA_17           AAA domain
      0.052   13.7   0.0        1.7    8.8   0.0    2.5  2  Sigma54_activ_2  Sigma-54 interaction domain
      0.064   13.6   0.0       0.12   12.7   0.0    1.5  1  RNA_helicase     RNA helicase
      0.066   13.1   0.0       0.11   12.4   0.0    1.3  1  Rad17            Rad17 P-loop domain
      0.066   12.9   0.0      0.098   12.4   0.0    1.2  1  AAA_24           AAA domain
      0.092   12.1   0.0       0.16   11.3   0.0    1.3  1  FtsK_SpoIIIE     FtsK/SpoIIIE family
      0.099   12.7   0.0       0.17   12.0   0.0    1.4  1  MMR_HSR1         50S ribosome-binding GTPase
        0.1   11.8   0.0       0.13   11.5   0.0    1.2  1  KAP_NTPase       KAP family P-loop domain
       0.12   11.3   0.0       0.21   10.5   0.0    1.3  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
       0.13   11.6   0.0       0.22   11.0   0.0    1.3  1  KTI12            Chromatin associated protein KTI12
       0.13   12.0   0.0        1.7    8.5   0.0    2.1  2  CPT              Chloramphenicol phosphotransferase-like prot
       0.16   11.7   0.0       0.23   11.2   0.0    1.2  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
       0.17   11.3   0.0       0.33   10.3   0.0    1.4  1  SMC_N            RecF/RecN/SMC N terminal domain
       0.19   11.6   0.0       0.34   10.8   0.0    1.3  1  ATPase_2         ATPase domain predominantly from Archaea
       0.21   11.0   0.0       0.31   10.5   0.0    1.2  1  Pox_A32          Poxvirus A32 protein


Domain annotation for each model (and alignments):
>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.4   0.0   6.8e-20   3.4e-17     127     245 ..     171     287 ..      59     312 .. 0.87

  Alignments for each domain:
  == domain 1  score: 62.4 bits;  conditional E-value: 6.8e-20
                          T2SSE 127 rerglilvsGgTgsGKttllyallkeinks..derivtvEDpvEiqleganqvqlnakkakvtfadllraaLR.lrPDri 203
                                     +  +++++G+ gsGKtt+l al+k +++     +i +vE  +E+  +g   +q++++    ++a+++r a+R lrPD +
  gi|119719637|ref|YP_920132.1| 171 VRPSTVVITGPPGSGKTTVLSALVKAVADFfpWLHIAIVEKYRELSFRGGWFTQVVSE----NLAEGVRYAMRyLRPDLL 246
                                    445799**********************987789************************....9**********77***** PP

                          T2SSE 204 mvGEiRdketleilkAvnTGHlgslsTlHansaagalerLeq 245
                                    +vGEi  ++  ++l+    G +  ++T Ha sa+ al+ L++
  gi|119719637|ref|YP_920132.1| 247 VVGEILAEDFWSLLEPTRAGIPT-VTTFHAPSAQRALKSLSD 287
                                    ***********************.*************99986 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   1.1e-07   5.6e-05      23     122 ..     172     288 ..     161     307 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 1.1e-07
                         AAA_16  23 rpelvllsGesGvGKsslvrellralekd...................ggiflrgkcdqlesaipysa.laqalareell 82 
                                    rp+ v+++G++G+GK++++ +l +a+  d                   gg+f++   + l ++++y++ +++      ++
  gi|119719637|ref|YP_920132.1| 172 RPSTVVITGPPGSGKTTVLSALVKAVA-DffpwlhiaivekyrelsfrGGWFTQVVSENLAEGVRYAMrYLRPD-L-LVV 248
                                    6899*******************7555.5599999999999999998778887777777788899988666666.4.788 PP

                         AAA_16  83 rqlldeaesaeleawrekleeala........avpelagaeasrllel 122
                                     ++l+e+  ++le+ r+ ++++++        a         ++l ++
  gi|119719637|ref|YP_920132.1| 249 GEILAEDFWSLLEPTRAGIPTVTTfhapsaqrAL--------KSLSDA 288
                                    9999999999999999999998884433322222........333333 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   6.9e-07   0.00034       1      25 [.     176     205 ..     176     248 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 6.9e-07
                         AAA_18   1 IlltGtpGvGKttlakeLskrl.gf....g 25 
                                    +++tG+pG+GKtt+  +L k    f    +
  gi|119719637|ref|YP_920132.1| 176 VVITGPPGSGKTTVLSALVKAVaDFfpwlH 205
                                    79****************999656667663 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   1.8e-06    0.0009      29      65 ..     169     205 ..     147     221 .. 0.84
   2 ?   -1.5   0.0       3.2   1.6e+03     101     140 ..     331     371 ..     320     387 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.8e-06
                         AAA_25  29 llpagelallaGapgtGKttlaldlalavatGkpwlg 65 
                                    ll++ ++++++G+pg+GKtt+++ l+ ava   pwl+
  gi|119719637|ref|YP_920132.1| 169 LLVRPSTVVITGPPGSGKTTVLSALVKAVADFFPWLH 205
                                    66788999**********************9999987 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.2
                         AAA_25 101 arllvldlagv.eslpLfakdrggtlltadvdaleaaieev 140
                                    +rl  ++l+g+  + +Lf+k   ++l  +d+ ++e++++e+
  gi|119719637|ref|YP_920132.1| 331 QRLVPVYLEGEhAEEDLFKKALPDKLYVGDLVNVEKTLRER 371
                                    66666666677677777777766666556666666666664 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   1.2e-06   0.00059       2      41 ..     176     218 ..     175     240 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.2e-06
                         AAA_28   2 ivitGgestGKTtlleaLaar...gypvvpEaareileeklak 41 
                                    +vitG++++GKTt+l+aL +     +p+++ a  e ++e++++
  gi|119719637|ref|YP_920132.1| 176 VVITGPPGSGKTTVLSALVKAvadFFPWLHIAIVEKYRELSFR 218
                                    9*****************9655557777755555555444444 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0     2e-06     0.001      20      43 ..     175     198 ..     165     209 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2e-06
                         AAA_30  20 vavltGpAGtGKttalkalreawe 43 
                                    ++v+tGp+G+GKtt+l+al++a++
  gi|119719637|ref|YP_920132.1| 175 TVVITGPPGSGKTTVLSALVKAVA 198
                                    789****************99876 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   3.7e-06    0.0018       9      35 ..     172     198 ..     165     209 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 3.7e-06
                         AAA_19   9 kekvllvtaGpGtGKTrvlkhivallv 35 
                                    + +++++t++pG+GKT+vl + v+ + 
  gi|119719637|ref|YP_920132.1| 172 RPSTVVITGPPGSGKTTVLSALVKAVA 198
                                    66899****************999876 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   5.6e-06    0.0028       2      23 ..     175     196 ..     174     210 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5.6e-06
                                    EEEEEESTTCCHHHHHHHHHCT CS
                           cobW   2 vtvltGflGsGKTtLlnhllen 23 
                                    ++v+tG++GsGKTt+l++l++ 
  gi|119719637|ref|YP_920132.1| 175 TVVITGPPGSGKTTVLSALVKA 196
                                    589**************99965 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0     1e-05     0.005       2      74 ..     176     251 ..     175     302 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1e-05
                                    EEEE--SSSSHHHHHHHGGGGB..S--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESG CS
                          AAA_5   2 vlLvGppGtgKselaerlaaal..nreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEv 74 
                                    v++ GppG+gK+++   l +a+    +++ +++ ++++e  ++g++ ++   + l +++ + a+r  ++++lv++E+
  gi|119719637|ref|YP_920132.1| 176 VVITGPPGSGKTTVLSALVKAVadFFPWLHIAIVEKYRELSFRGGWFTQVVSENLAEGVRY-AMRylRPDLLVVGEI 251
                                    799*******************9999********************997777777777777.888998888888887 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.1e-05    0.0054       2      24 ..     176     198 ..     175     231 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.1e-05
                                    EEEE--TTSSHHHHHHHHHHHH. CS
                       NTPase_1   2 vfiTGppGvGKtTlvkkvlellk 24 
                                    v+iTGppG+GKtT+++ ++++++
  gi|119719637|ref|YP_920132.1| 176 VVITGPPGSGKTTVLSALVKAVA 198
                                    89*************99998875 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0     1e-05    0.0051      64     144 ..     234     313 ..     176     324 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1e-05
                 Glyco_transf_4  64 lrrllkrekpDvv.HahspaalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrradrviavSe 142
                                    +r +++  +pD++      a  +++ll   r  gip+V+t+H + +  +  + l+ + r+       +l+  d ++++S+
  gi|119719637|ref|YP_920132.1| 234 VRYAMRYLRPDLLvVGEILAEDFWSLLEPTR-AGIPTVTTFHAPSA-QRALKSLSDALRVHLGGATNVLNYLDVLVVTSK 311
                                    4556677789998455556666888777776.*************5.344444444444444555556899999999998 PP

                 Glyco_transf_4 143 at 144
                                     +
  gi|119719637|ref|YP_920132.1| 312 VI 313
                                    65 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0     3e-05     0.015       7      27 ..     175     195 ..     171     202 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3e-05
                         AAA_22   7 ilvvtGesGtGKTtllrrlle 27 
                                     +v+tG++G+GKTt+l  l++
  gi|119719637|ref|YP_920132.1| 175 TVVITGPPGSGKTTVLSALVK 195
                                    579*************99986 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0     3e-05     0.015       2      25 ..     175     198 ..     174     200 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3e-05
                                    CEEEEC-TTTCHHHHHHHHHHHHC CS
                          NACHT   2 lvilqGeaGsGKTtLlqklalawa 25 
                                    +v+++G++GsGKTt l  l+ a a
  gi|119719637|ref|YP_920132.1| 175 TVVITGPPGSGKTTVLSALVKAVA 198
                                    89*****************99877 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   3.1e-05     0.015      24      43 ..     175     194 ..     165     198 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.1e-05
                         AAA_29  24 atlltGpsGsGKSTllDAiq 43 
                                    ++++tGp GsGK+T+l A+ 
  gi|119719637|ref|YP_920132.1| 175 TVVITGPPGSGKTTVLSALV 194
                                    489*************9875 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   2.9e-05     0.015       1      23 [.     176     198 ..     176     251 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.9e-05
                                    EEEESSTTSSHHHHHHHHHHHHT CS
                            AAA   1 vllyGppGtGKTllakavakelg 23 
                                    v+++GppG GKT++ +a++k + 
  gi|119719637|ref|YP_920132.1| 176 VVITGPPGSGKTTVLSALVKAVA 198
                                    5789**************99963 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       5.3   2.6e+03      70     100 ..      42      72 ..      38      75 .. 0.83
   2 !   14.0   0.0   8.6e-05     0.043       2      23 ..     176     197 ..     176     211 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 5.3
                         AAA_33  70 grnvildatnlsrrerarflklarrlgvpvr 100
                                    +++++l  ++++++ + +f  ++   +v+++
  gi|119719637|ref|YP_920132.1|  42 KNDTLLVLPFRRHEVWGAFAPIFTSSKVEEA 72 
                                    78899999***********999998887765 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 8.6e-05
                         AAA_33   2 vllvGlpGsGKstlaerllkkl 23 
                                    v++ G+pGsGK+t++  l+k+ 
  gi|119719637|ref|YP_920132.1| 176 VVITGPPGSGKTTVLSALVKAV 197
                                    6789*************99875 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   3.3e-05     0.016      17      41 ..     173     197 ..     165     239 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.3e-05
                         AAA_11  17 seitliqGPPGtgKTktivellsql 41 
                                    ++ ++i GPPG+gKT+++ +l++++
  gi|119719637|ref|YP_920132.1| 173 PSTVVITGPPGSGKTTVLSALVKAV 197
                                    55689***************99987 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   5.5e-05     0.027      12      34 ..     174     196 ..     165     199 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 5.5e-05
                                    SEEEEEESTTSSHHHHHHHHTTS CS
                                    xxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  12 ekvaivGenGaGKStLlkllagl 34 
                                    ++v+i+G+ G+GK+t+l++l + 
  gi|119719637|ref|YP_920132.1| 174 STVVITGPPGSGKTTVLSALVKA 196
                                    789****************9875 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   4.3e-05     0.021       3      26 ..     175     205 ..     173     242 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.3e-05
                        DUF2075   3 vvlVtGvaGtGKtvvllnllael.......e 26 
                                     v++tG +G+GKt vl++l+ ++       +
  gi|119719637|ref|YP_920132.1| 175 TVVITGPPGSGKTTVLSALVKAVadffpwlH 205
                                    699****************999844444443 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0     7e-05     0.035      15      40 ..     172     197 ..     169     209 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7e-05
                     Zeta_toxin  15 rPklillgGqpGAGKselaellkdel 40 
                                    rP  +++ G pG+GK++++++l +++
  gi|119719637|ref|YP_920132.1| 172 RPSTVVITGPPGSGKTTVLSALVKAV 197
                                    899*****************998875 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0     6e-05      0.03      21      39 ..     175     193 ..     166     202 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 6e-05
                         AAA_23  21 ltlItGpNGaGKTTildAi 39 
                                     ++ItGp G+GKTT+l A+
  gi|119719637|ref|YP_920132.1| 175 TVVITGPPGSGKTTVLSAL 193
                                    689*************998 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0    0.0001     0.052       1      18 [.     179     196 ..     179     208 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 0.0001
                                    EE-TTSSHHHHHHHHHHH CS
                         AAA_17   1 lGgPGsGKgtqceklvek 18 
                                    +G+PGsGK+t+++ lv+ 
  gi|119719637|ref|YP_920132.1| 179 TGPPGSGKTTVLSALVKA 196
                                    7**************986 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0    0.0034       1.7      10      45 ..     162     197 ..     160     234 .. 0.78
   2 ?    2.1   0.0       0.4     2e+02      54      85 ..     337     368 ..     312     373 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0034
                                    HHHHHHHHHT-SS-EEEEEETT--HHHHHHCC--TT CS
                Sigma54_activ_2  10 lkerLeqaaqsklpvfltGekGsgkelvArlLhkns 45 
                                    l++rL  +  + + v +tG++Gsgk++v  +L k  
  gi|119719637|ref|YP_920132.1| 162 LATRLVLLLVRPSTVVITGPPGSGKTTVLSALVKAV 197
                                    56788888889999*************988887654 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.4
                                    TTHHHH-HHHHHHHTTTSEEEEEE-TT--HHH CS
                Sigma54_activ_2  54 verlaklpldlleqakggtLylkdiadlskae 85 
                                    + ++ ++  dl+++a +  Ly+ d+ + +k +
  gi|119719637|ref|YP_920132.1| 337 YLEGEHAEEDLFKKALPDKLYVGDLVNVEKTL 368
                                    336778999***************99988876 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00025      0.12       1      26 [.     176     201 ..     176     227 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00025
                   RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl 26 
                                    ++++Gp+g GK+t+   L+ka+++ +
  gi|119719637|ref|YP_920132.1| 176 VVITGPPGSGKTTVLSALVKAVADFF 201
                                    689******************99765 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00021      0.11      47      69 ..     175     197 ..     154     219 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00021
                          Rad17  47 iLLisGPsGCgkstvvkvLskel 69 
                                     ++i+GP+G gk+tv+  L k  
  gi|119719637|ref|YP_920132.1| 175 TVVITGPPGSGKTTVLSALVKAV 197
                                    568****************9965 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0    0.0002     0.098       4      22 ..     175     193 ..     172     201 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0002
                         AAA_24   4 kiliyGpsgiGKTtlakel 22 
                                     ++i+Gp+g+GKTt+++ l
  gi|119719637|ref|YP_920132.1| 175 TVVITGPPGSGKTTVLSAL 193
                                    699************9987 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00032      0.16      39      63 ..     173     197 ..     155     199 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00032
                                    -.SEEEE--TTSSHHHHHHHHHHHH CS
                   FtsK_SpoIIIE  39 ashllvaGatgsGKStalntLilSl 63 
                                    +s +++ G +gsGK+t+l +L+ ++
  gi|119719637|ref|YP_920132.1| 173 PSTVVITGPPGSGKTTVLSALVKAV 197
                                    46699****************9765 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00034      0.17       2      24 ..     176     198 ..     175     218 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00034
                                    EEEEESTTSSHHHHHHHHHTSTE CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltgeka 24 
                                    v+i G p +GK+t+++al++++a
  gi|119719637|ref|YP_920132.1| 176 VVITGPPGSGKTTVLSALVKAVA 198
                                    89*****************9755 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00026      0.13      19      49 ..     172     220 ..     161     327 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00026
                     KAP_NTPase  19 tpivvgLygkWGsGKssllnkledelkefa..................k 49 
                                    +p++v+++g+ GsGK+++l  l ++  +f                    
  gi|119719637|ref|YP_920132.1| 172 RPSTVVITGPPGSGKTTVLSALVKAVADFFpwlhiaivekyrelsfrgG 220
                                    789*******************999999965555555555555555550 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00042      0.21      28      53 ..     172     197 ..     148     208 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00042
                                    -SEEEEEEE-TTSSHHHHHHHHHHHH CS
                           MeaB  28 raqvvGltGvPGaGkstlvealglel 53 
                                    r   v +tG PG+Gk t+++al+  +
  gi|119719637|ref|YP_920132.1| 172 RPSTVVITGPPGSGKTTVLSALVKAV 197
                                    667899***************98765 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00044      0.22       4      27 ..     176     199 ..     174     218 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00044
                                    EEEE--TTSSHHHHHHHHHHHHHH CS
                          KTI12   4 vvltGlPssGKstrakeLakalee 27 
                                    vv+tG P sGK+t+ + L ka+++
  gi|119719637|ref|YP_920132.1| 176 VVITGPPGSGKTTVLSALVKAVAD 199
                                    9****************9998765 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0    0.0034       1.7       4      34 ..     176     208 ..     174     217 .. 0.86
   2 ?    1.0   0.0      0.65   3.3e+02      69     132 ..     315     375 ..     276     385 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0034
                                    EEEEE-TTSSHHHHHHHHHHHSSS..-EEEEEH CS
                            CPT   4 ilLnGgsssGKsslaralqevlde..pwlhlgv 34 
                                    +++ G + sGK+++  al + +++  pwlh+++
  gi|119719637|ref|YP_920132.1| 176 VVITGPPGSGKTTVLSALVKAVADffPWLHIAI 208
                                    7889**************999997779***986 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.65
                                    HHHHHHHHHH.HHHTT-EEEEEE--TTTHH.HHHHHHHHHTTS-EEEEEEE--HHHHHHHHHHHTS CS
                            CPT  69 laalyeavaa.maraGnnvivDdvilekew.lvdllrrllsgldvllVGvrcplevlerRelergd 132
                                     +++ ++v a ++  G++++   v+le+e+   dl+++ l   d l+VG  +++e    Re+ r+d
  gi|119719637|ref|YP_920132.1| 315 SSGVSRGVSAvYLSDGQRLV--PVYLEGEHaEEDLFKKAL--PDKLYVGDLVNVEK-TLRERFRPD 375
                                    56778888873478899988..478888886788999999..78899998888874.345666666 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00046      0.23       2      22 ..     177     197 ..     176     253 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00046
                Viral_helicase1   2 vvhGvpGcGKStlirkllrts 22 
                                    v+ G pG+GK+t++  l++  
  gi|119719637|ref|YP_920132.1| 177 VITGPPGSGKTTVLSALVKAV 197
                                    89************9999884 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00067      0.33      20      44 ..     169     193 ..     162     197 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00067
                                    EETTSSEEEEEESTTSSHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  20 lpfsksftaivGpNGSGKsnlldAi 44 
                                    l + +s  +i+Gp GSGK+ +l A+
  gi|119719637|ref|YP_920132.1| 169 LLVRPSTVVITGPPGSGKTTVLSAL 193
                                    55778999**************998 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00067      0.34      22      43 ..     175     196 ..     168     213 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00067
                       ATPase_2  22 iyfiYGpegsGKtaLlkeiien 43 
                                     ++i+Gp gsGKt++l  +++ 
  gi|119719637|ref|YP_920132.1| 175 TVVITGPPGSGKTTVLSALVKA 196
                                    689*************999876 PP

>> Pox_A32  Poxvirus A32 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00062      0.31      10      44 ..     170     204 ..     166     227 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00062
                        Pox_A32  10 lkkpFrlalvGgsGsGktvyLlsLlrtlvkkykhi 44 
                                    l +p  ++++G  GsGkt+ L +L++ + + + ++
  gi|119719637|ref|YP_920132.1| 170 LVRPSTVVITGPPGSGKTTVLSALVKAVADFFPWL 204
                                    5667789******************9999888544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                       112  (0.00624686); expected 17.9 (0.001)
Passed Fwd filter:                        36  (0.00200792); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              36  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 2647.68
//
Query:       gi|119719638|ref|YP_920133.1|  [L=471]
Description: helicase c2 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.7e-06   27.2   0.0    7.5e-05   23.0   0.0    2.3  1  Helicase_C_2  Helicase C-terminal domain


Domain annotation for each model (and alignments):
>> Helicase_C_2  Helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   4.2e-09   7.5e-05      60     158 ..     358     441 ..     326     445 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 4.2e-09
                   Helicase_C_2  60 kkkgaillavcrGklsEGidfsddllraviivglPfpnpkdpeveakreyldekgkknsgkewylpealravnQaiGRli 139
                                    + ++ +ll +  G++ EG+d++   + +v++ g P+ +p    v+a+   +  k +     ++    a  +  Q +GR+ 
  gi|119719638|ref|YP_920133.1| 358 EWNRGVLLLLSHGRYAEGVDLP---ADCVVMAGAPYLPPY---VSARLAAVGLKPD-----DV---VA-ITTVQNVGRAT 422
                                    556677888888**********...99*********9984...6677555433333.....33...33.45569****** PP

                   Helicase_C_2 140 RhkdDygaivllDeRfake 158
                                    R+      ivl DeR+a+ 
  gi|119719638|ref|YP_920133.1| 423 RTPSASPFIVLADERYARL 441
                                    ****************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (471 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 3124.97
//
Query:       gi|119719639|ref|YP_920134.1|  [L=116]
Description: hypothetical protein Tpen_0729 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1192  (0.0664845); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 844.66
//
Query:       gi|119719640|ref|YP_920135.1|  [L=165]
Description: hypothetical protein Tpen_0730 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.014   15.4   0.1       0.47   10.6   0.0    2.9  3  TolA_bind_tri  TolA binding protein trimerisation
      0.014   15.0   0.2      0.022   14.4   0.2    1.3  1  PAS_12         UPF0242 C-terminal PAS-like domain
      0.016   14.1   3.0       0.02   13.8   3.0    1.1  1  Spc7           Spc7 kinetochore protein
      0.029   14.2   1.6      0.044   13.6   1.6    1.3  1  Ph1570         Ph1570 protein
      0.084   13.0   3.7        0.2   11.8   0.1    2.4  2  bZIP_2         Basic region leucine zipper
       0.24   11.8   5.8        1.1    9.7   0.3    2.9  3  FlaC_arch      Flagella accessory protein C (FlaC)
       0.52   10.5   8.8        1.5    9.0   2.8    2.6  2  DMPK_coil      DMPK coiled coil domain like
       0.78   10.0   7.0       0.58   10.4   0.4    3.2  3  Lge1           Transcriptional regulatory protein LGE1
        1.1    9.1   0.0        1.1    9.1   0.0    4.0  4  SHOCT          Short C-terminal domain
        2.9    8.4  13.0        2.6    8.6  10.7    2.0  1  APG6_N         Apg6 coiled-coil region


Domain annotation for each model (and alignments):
>> TolA_bind_tri  TolA binding protein trimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.63   1.1e+03      51      66 ..       7      22 ..       3      31 .. 0.81
   2 ?    0.3   0.1      0.41   7.3e+02      30      49 ..      43      62 ..      38      68 .. 0.65
   3 ?   10.6   0.0   0.00026      0.47      26      49 ..      81     104 ..      77     110 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.63
                  TolA_bind_tri 51 leerQrdlYldlDerl 66
                                   ++er + lY + D + 
  gi|119719640|ref|YP_920135.1|  7 VIERLKGLYDKADDLW 22
                                   7899999**9999875 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.41
                  TolA_bind_tri 30 lqqelreLRGqiEelqyqle 49
                                   l +el+eL+ ++E     le
  gi|119719640|ref|YP_920135.1| 43 LLSELSELKAKLESDLKALE 62
                                   45677777777776555554 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00026
                  TolA_bind_tri  26 qlealqqelreLRGqiEelqyqle 49 
                                    ++ +l++e+ +LRG++E l   le
  gi|119719640|ref|YP_920135.1|  81 KIGELESEVEKLRGEVESLWVALE 104
                                    56789************9866665 PP

>> PAS_12  UPF0242 C-terminal PAS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.2   1.2e-05     0.022      84     140 ..      18      75 ..       6      82 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.2e-05
                         PAS_12  84 sdkflqdfseivqegleeWk.ralaklsskteskirlvlKtKagqevllncllgiips 140
                                    +d++  ++ e v+ ++ eW+ ++l+ ls   e k++l+   Ka +e++l++ lg++++
  gi|119719640|ref|YP_920135.1|  18 ADDLWGEYVESVKAAVREWElSKLDLLSELSELKAKLESDLKALEELKLKVELGLVDK 75 
                                    688999999**********9668*********************************97 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   3.0   1.1e-05      0.02     162     276 ..      26     136 ..       3     142 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.1e-05
                           Spc7 162 eeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelke 241
                                     e +++++ e e  k +l +el +l+++ e    +d + Leel+ +++   ++ e+ +k++ el++++e+l+ ++e+l  
  gi|119719640|ref|YP_920135.1|  26 VESVKAAVREWELSKLDLLSELSELKAKLE----SDLKALEELKLKVELGLVDKEKAEKKIGELESEVEKLRGEVESLWV 101
                                    455666666666666777777777777443....5999999999999999999999999999999999999999999988 PP

                           Spc7 242 qkseleeeiaeaervleeckgwsesevsrlkeevk 276
                                      +e+  +   + +      g +e++v + +e++k
  gi|119719640|ref|YP_920135.1| 102 ALEEFTLRSLTHSKRAGLPLGLTEEDVASKQETLK 136
                                    88888888777777777777777777777777665 PP

>> Ph1570  Ph1570 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   1.6   2.4e-05     0.044      55     114 ..      16      79 ..      11      93 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.4e-05
                         Ph1570  55 ecakefwgiyldasevkgeeaelkplkflse..svkskle...kvleeidapievkelielekae 114
                                    + a ++wg y+++ +    e el+ l +lse   +k+kle   k lee++  +e+  l++ ekae
  gi|119719640|ref|YP_920135.1|  16 DKADDLWGEYVESVKAAVREWELSKLDLLSElsELKAKLEsdlKALEELKLKVEL-GLVDKEKAE 79 
                                    67899************************98545899999555678899999999.899999997 PP

>> bZIP_2  Basic region leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.5      0.18   3.3e+02      34      52 ..      44      62 ..      30      64 .. 0.80
   2 ?   11.8   0.1   0.00011       0.2      27      51 ..      75      99 ..      72     100 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.18
                                   HHHHHHHHHHHHHHHHHHH CS
                         bZIP_2 34 vkeLeeeNaqLrqkveqLe 52
                                   + eL+e +a+L+  +++Le
  gi|119719640|ref|YP_920135.1| 44 LSELSELKAKLESDLKALE 62
                                   5688888888888888887 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00011
                                   HHHHHHHHHHHHHHHHHHHHHHHHH CS
                         bZIP_2 27 eeeleervkeLeeeNaqLrqkveqL 51
                                   +e+ e+++ eLe+e ++Lr +ve+L
  gi|119719640|ref|YP_920135.1| 75 KEKAEKKIGELESEVEKLRGEVESL 99
                                   7899******************987 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.4      0.03        54       7      37 ..      36      68 ..      26      74 .. 0.78
   2 ?    9.7   0.3   0.00063       1.1       1      24 [.      81     104 ..      76     108 .. 0.68
   3 ?   -3.0   0.0       5.6     1e+04      18      26 ..     151     159 ..     146     162 .. 0.47

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.03
                      FlaC_arch  7 nklsklst..eletvkkeneelsksveelkenV 37
                                    +lskl+   el+ +k+++e+  k +eelk +V
  gi|119719640|ref|YP_920135.1| 36 WELSKLDLlsELSELKAKLESDLKALEELKLKV 68
                                   567777766688888888888888888887666 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00063
                      FlaC_arch   1 ridelEnklsklsteletvkkene 24 
                                    +i+elE++++kl  e+e++   +e
  gi|119719640|ref|YP_920135.1|  81 KIGELESEVEKLRGEVESLWVALE 104
                                    677777777777777777654444 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 5.6
                      FlaC_arch  18 tvkkeneel 26 
                                     +++++e+l
  gi|119719640|ref|YP_920135.1| 151 AIRSTLEQL 159
                                    344444433 PP

>> DMPK_coil  DMPK coiled coil domain like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   1.1     0.022        40      35      59 ..      34      59 ..      28      61 .. 0.83
   2 ?    9.0   2.8   0.00082       1.5      24      58 ..      62      99 ..      54     102 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.022
                      DMPK_coil 35 keaEkknreLeeeleqLkkemEe.lr 59
                                   +e E    +L++el +Lk ++E  l+
  gi|119719640|ref|YP_920135.1| 34 REWELSKLDLLSELSELKAKLESdLK 59
                                   67788899*************97555 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00082
                      DMPK_coil 24 kaanlafeskLke...aEkknreLeeeleqLkkemEel 58
                                    + +l++e  L +   aEkk  eLe+e+e+L+ e+E l
  gi|119719640|ref|YP_920135.1| 62 EELKLKVELGLVDkekAEKKIGELESEVEKLRGEVESL 99
                                   5555555555544223889999*************976 PP

>> Lge1  Transcriptional regulatory protein LGE1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.9      0.21   3.8e+02      25      36 ..      54      65 ..      26      75 .. 0.52
   2 ?   10.4   0.4   0.00033      0.58      26      59 ..      76     109 ..      72     136 .. 0.94
   3 ?   -0.2   0.0      0.63   1.1e+03      18      18 ..     135     135 ..     110     165 .] 0.54

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.21
                           Lge1 25 iesldkqleelk 36
                                   +es  k+leelk
  gi|119719640|ref|YP_920135.1| 54 LESDLKALEELK 65
                                   222223444444 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00033
                           Lge1  26 esldkqleelklkvlkleleldlleeqierdaLr 59 
                                    e++ k++ el+ +v+kl  e+ +l+   e ++Lr
  gi|119719640|ref|YP_920135.1|  76 EKAEKKIGELESEVEKLRGEVESLWVALEEFTLR 109
                                    8999***************************998 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.63
                           Lge1  18 i 18 
                                    +
  gi|119719640|ref|YP_920135.1| 135 L 135
                                    2 PP

>> SHOCT  Short C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1     0.054        97       3      12 ..       8      17 ..       8      17 .. 0.92
   2 ?   -0.3   0.4      0.54   9.7e+02       3      12 ..      44      53 ..      42      55 .. 0.71
   3 ?   -2.5   0.6       2.8     5e+03       2       7 ..      60      65 ..      58      66 .. 0.70
   4 ?    9.1   0.0   0.00062       1.1       4      27 ..     133     156 ..     130     157 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.054
                          SHOCT  3 LekLkeLyar 12
                                   +e+Lk Ly++
  gi|119719640|ref|YP_920135.1|  8 IERLKGLYDK 17
                                   79******97 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.54
                          SHOCT  3 LekLkeLyar 12
                                   L +L eL+a+
  gi|119719640|ref|YP_920135.1| 44 LSELSELKAK 53
                                   6777777775 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 2.8
                          SHOCT  2 aLekLk 7 
                                   aLe+Lk
  gi|119719640|ref|YP_920135.1| 60 ALEELK 65
                                   677776 PP

  == domain 4  score: 9.1 bits;  conditional E-value: 0.00062
                          SHOCT   4 ekLkeLyarGeIteEEFeakKakL 27 
                                    e+Lk+ ++rG+I e  ++a +  L
  gi|119719640|ref|YP_920135.1| 133 ETLKKAFERGVIGETAYNAIRSTL 156
                                    89***********99999988766 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6  10.7    0.0015       2.6      12     116 ..       9     114 ..       7     119 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0015
                         APG6_N  12 eeldkqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkeleke.......reeleael 84 
                                    e+l+  +++a++ + +Y e  k   +e +       +  +l  el++l+++ e+ l+ L+el+ +       +e+ e+++
  gi|119719640|ref|YP_920135.1|   9 ERLKGLYDKADDLWGEYVESVKAAVREWEL------SKLDLLSELSELKAKLESDLKALEELKLKvelglvdKEKAEKKI 82 
                                    566666666666666666666666655333......33445555555555555555555555442222222288899999 PP

                         APG6_N  85 aaleeelealeeeeerfwreynelqlellele 116
                                     +le+e e+l  e e  w    e+ l  l + 
  gi|119719640|ref|YP_920135.1|  83 GELESEVEKLRGEVESLWVALEEFTLRSLTHS 114
                                    99999999999999999999999988877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1362  (0.0759663); expected 358.6 (0.02)
Passed bias filter:                      776  (0.0432818); expected 358.6 (0.02)
Passed Vit filter:                       104  (0.00580066); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1100.22
//
Query:       gi|119719641|ref|YP_920136.1|  [L=260]
Description: hypothetical protein Tpen_0731 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-12   46.3  10.5    2.3e-06   27.4   2.0    2.2  2  CdvA            CdvA-like coiled-coil domain
      4e-05   23.2  18.1    0.00026   20.6   2.4    3.5  3  SHOCT           Short C-terminal domain
      0.003   17.5   1.4      0.003   17.5   1.4    2.9  3  GvpG            Gas vesicle protein G
      0.008   15.1  12.4       0.12   11.3   8.4    2.2  2  Spc7            Spc7 kinetochore protein
  ------ inclusion threshold ------
       0.01   15.6   7.7       0.11   12.3   0.2    3.3  3  TACC_C          Transforming acidic coiled-coil-containing pr
       0.15   12.4   5.2       0.83   10.0   0.9    3.0  2  BLOC1_2         Biogenesis of lysosome-related organelles com
        0.2   11.8   0.8         10    6.3   0.3    2.5  3  Fib_alpha       Fibrinogen alpha/beta chain family
       0.43    9.8   5.5          5    6.4   5.4    2.2  1  DUF3450         Protein of unknown function (DUF3450)
       0.59   10.0  15.9         34    4.2  15.9    2.7  1  Apolipoprotein  Apolipoprotein A1/A4/E domain
        4.1    8.1  10.9       0.97   10.1   1.4    2.7  3  GTP-bdg_M       GTP-binding GTPase Middle Region
        4.7    7.3  20.8        0.1   12.7   5.3    2.7  3  TPR_MLP1_2      TPR/MLP1/MLP2-like protein
        5.1    7.6  17.3        1.6    9.2   7.3    2.7  2  APG6_N          Apg6 coiled-coil region


Domain annotation for each model (and alignments):
>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   1.5     2e-08   2.9e-05      22     110 ..     108     196 ..      96     201 .. 0.95
   2 !   27.4   2.0   1.6e-09   2.3e-06      48     102 ..     206     260 .]     203     260 .] 0.95

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 2e-08
                           CdvA  22 eikekleealkklkekakelkeklkkrlkeledqikslekalanlkisyasGEidEeaYksaieairellesaleekeei 101
                                     i e++++a +++ e+ ++++e+++++l+ ++  i++    l  l+   +sG i Ee+Y + + ++++ l   ++e+ee+
  gi|119719641|ref|YP_920136.1| 108 RIWEEYDRAAREVVERWEDVRERISRELAGVDATITAYVDELERLEKMRESGVIGEEEYGELKASLERRLAEKNKEREEL 187
                                    6789**************************************************************************** PP

                           CdvA 102 kklleklsk 110
                                    +++l+ l+ 
  gi|119719641|ref|YP_920136.1| 188 SRVLADLDR 196
                                    ****99976 PP

  == domain 2  score: 27.4 bits;  conditional E-value: 1.6e-09
                           CdvA  48 rlkeledqikslekalanlkisyasGEidEeaYksaieairellesaleekeeik 102
                                    +++e++ +i++l+ ala+l+ +++sG i+Ee Y++ +++++e ++++++ kee++
  gi|119719641|ref|YP_920136.1| 206 KVAEVKPEIAKLKVALAKLEERFKSGGISEEVYEKLRSELEERIKRLEKIKEEVE 260
                                    6899*********************************************999985 PP

>> SHOCT  Short C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.7       3.8   5.6e+03      18      23 ..     111     116 ..     111     119 .. 0.81
   2 !   20.6   2.4   1.7e-07   0.00026       1      27 [.     147     173 ..     147     174 .. 0.93
   3 !   12.8   1.4   5.1e-05     0.076       2      27 ..     220     245 ..     220     246 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3.8
                          SHOCT  18 EEFeak 23 
                                    EE++++
  gi|119719641|ref|YP_920136.1| 111 EEYDRA 116
                                    9**996 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 1.7e-07
                          SHOCT   1 daLekLkeLyarGeIteEEFeakKakL 27 
                                    d+Le+L +++++G+I eEE+ + Ka L
  gi|119719641|ref|YP_920136.1| 147 DELERLEKMRESGVIGEEEYGELKASL 173
                                    89*******************999866 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 5.1e-05
                          SHOCT   2 aLekLkeLyarGeIteEEFeakKakL 27 
                                    aL+kL e++ +G I+eE +e+ + +L
  gi|119719641|ref|YP_920136.1| 220 ALAKLEERFKSGGISEEVYEKLRSEL 245
                                    79***************888888887 PP

>> GvpG  Gas vesicle protein G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.6   2.5e+03      52      70 ..     111     129 ..     103     140 .. 0.72
   2 ?    2.8   3.3     0.081   1.2e+02      35      70 ..     147     182 ..     124     189 .. 0.79
   3 !   17.5   1.4     2e-06     0.003      31      74 ..     215     258 ..     206     260 .] 0.90

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.6
                           GvpG  52 eeFdrrEeelLdrLealer 70 
                                    ee+dr   e+ +r e +++
  gi|119719641|ref|YP_920136.1| 111 EEYDRAAREVVERWEDVRE 129
                                    7888888888888776654 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.081
                           GvpG  35 keLaaLqqeLdaGeIdeeeFdrrEeelLdrLealer 70 
                                     eL +L++  ++G I eee+ +    l  rL + ++
  gi|119719641|ref|YP_920136.1| 147 DELERLEKMRESGVIGEEEYGELKASLERRLAEKNK 182
                                    5899****************9988888888876554 PP

  == domain 3  score: 17.5 bits;  conditional E-value: 2e-06
                           GvpG  31 enlrkeLaaLqqeLdaGeIdeeeFdrrEeelLdrLealerleae 74 
                                    ++l+  La+L+ ++++G I+ee +++  +el +r++ le+ ++e
  gi|119719641|ref|YP_920136.1| 215 AKLKVALAKLEERFKSGGISEEVYEKLRSELEERIKRLEKIKEE 258
                                    578999****************************9999998766 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   3.9    0.0014       2.1     150     259 ..      91     186 ..      72     190 .. 0.43
   2 !   11.3   8.4   7.9e-05      0.12     150     259 ..     144     258 ..     137     260 .] 0.78

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0014
                           Spc7 150 gleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeql 229
                                    +l +++e L ++  el ++ +e+++   e+ e+ e+ +e               + +ela ++a+i +  +el++l++ +
  gi|119719641|ref|YP_920136.1|  91 SLVSEAEALIERAGELARIWEEYDRAAREVVERWEDVRE--------------RISRELAGVDATITAYVDELERLEKMR 156
                                    333333333333333333333333333333333333333..............333344444444444444444444444 PP

                           Spc7 230 eeleekieelkeqkseleeeiaeaervlee 259
                                    e+     ee  e k++le ++ae+++ +ee
  gi|119719641|ref|YP_920136.1| 157 ESGVIGEEEYGELKASLERRLAEKNKEREE 186
                                    444444444444444444444444444433 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 7.9e-05
                           Spc7 150 gleedkelLekqeeeldellpeleeekaeleeeleklqeaaeeles....idkeeLeelr.eelaelkaeieekkkelae 224
                                    +  ++ e+Lek +e      +e+ e ka+le++l++ ++++eel+     +d+  L  ++  ++ae+k ei+++k  la+
  gi|119719641|ref|YP_920136.1| 144 AYVDELERLEKMRESGVIGEEEYGELKASLERRLAEKNKEREELSRvladLDRVVLPHFKrVKVAEVKPEIAKLKVALAK 223
                                    55566667777777766667777777777777777777777776655544889999887526999*************** PP

                           Spc7 225 lqeqleeleekieelkeqkseleeeiaeaervlee 259
                                    l+e+ ++   + e  ++ +selee+i++ e+++ee
  gi|119719641|ref|YP_920136.1| 224 LEERFKSGGISEEVYEKLRSELEERIKRLEKIKEE 258
                                    ******99999999999**************9997 PP

>> TACC_C  Transforming acidic coiled-coil-containing protein (TACC), C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.016        25      23      89 ..      88     154 ..      73     159 .. 0.84
   2 ?   12.3   0.2   7.2e-05      0.11     177     200 ..     171     194 ..     167     194 .. 0.93
   3 ?    0.9   1.2      0.22   3.3e+02      91     129 ..     214     252 ..     203     260 .] 0.51

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.016
                         TACC_C  23 eiqelkkkveelkkenqemkkivaefektiaqlieekqkqkelakkeiqkvleekeqlladlnsvek 89 
                                    e + l ++ e l ++  e+ +i +e++++  +++e  +  +e  ++e++ v +   +   +l+ +ek
  gi|119719641|ref|YP_920136.1|  88 EHASLVSEAEALIERAGELARIWEEYDRAAREVVERWEDVRERISRELAGVDATITAYVDELERLEK 154
                                    4456888888999999999999999999999999999999999999999888888888888888777 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 7.2e-05
                         TACC_C 177 qSLeksleqKtkeneeLtkiCdeL 200
                                     SLe++l +K+ke eeL ++  +L
  gi|119719641|ref|YP_920136.1| 171 ASLERRLAEKNKEREELSRVLADL 194
                                    69******************9987 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.22
                         TACC_C  91 fsdlfkryekqkevlegykkneeslkkcaeeylarvkke 129
                                    +++l   + k+ e ++     ee++ k ++e+ +r+k+ 
  gi|119719641|ref|YP_920136.1| 214 IAKLKVALAKLEERFKSGGISEEVYEKLRSELEERIKRL 252
                                    444444444444444444445555555555555555544 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.9   0.00055      0.83      11      70 ..     138     197 ..     132     230 .. 0.85
   2 ?    3.0   0.9     0.086   1.3e+02      53      80 ..     238     255 ..     201     260 .] 0.43

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00055
                        BLOC1_2  11 leaeleatvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqi 70 
                                    ++a+++a v++++ Lek+ e+     +++ +  asle+ l + n++ eel+  l  +d++
  gi|119719641|ref|YP_920136.1| 138 VDATITAYVDELERLEKMRESGVIGEEEYGELKASLERRLAEKNKEREELSRVLADLDRV 197
                                    78999****************99999****************************999987 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.086
                        BLOC1_2  53 lnekyeelqpylqqidqiekqvteLeea 80 
                                    ++++            ++e+++++Le++
  gi|119719641|ref|YP_920136.1| 238 YEKLRS----------ELEERIKRLEKI 255
                                    222222..........344444444443 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.19   2.8e+02      65     110 ..     110     155 ..      94     161 .. 0.62
   2 ?    3.8   0.1     0.039        59      28     116 ..     137     226 ..     126     230 .. 0.61
   3 ?    6.3   0.3     0.007        10      64      95 ..     223     254 ..     181     260 .] 0.75

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.19
                                    HHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHH CS
                      Fib_alpha  65 lrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnv 110
                                    ++e  + +++  +  +++++++ +e + +++ti+a + +++ L ++
  gi|119719641|ref|YP_920136.1| 110 WEEYDRAAREVVERWEDVRERISRELAGVDATITAYVDELERLEKM 155
                                    4444444444455556666666667777777777777766666655 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.039
                                    CCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCH..HHHH CS
                      Fib_alpha  28 kyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqe..snir 105
                                     ++ +++  +++le +le++++s    ee   e+k sl+++ ++k+++ + ++++  +l++ +l   ++++  e   +i 
  gi|119719641|ref|YP_920136.1| 137 GVDATITAYVDELE-RLEKMRESGVIGEEEYGELKASLERRLAEKNKEREELSRVLADLDRVVLPHFKRVKVAEvkPEIA 215
                                    45555555566665.36666666666778888888888888888888788888888888755554444333332235666 PP

                                    HHHHHHHHHHH CS
                      Fib_alpha 106 vLqnvlesneq 116
                                    +L+  l ++e+
  gi|119719641|ref|YP_920136.1| 216 KLKVALAKLEE 226
                                    66666655554 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.007
                                    HHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHH CS
                      Fib_alpha  64 slrekqkskkdndnvikksskeleeeilrlke 95 
                                    +l+e+ ks   +++v++k+++elee+i rl++
  gi|119719641|ref|YP_920136.1| 223 KLEERFKSGGISEEVYEKLRSELEERIKRLEK 254
                                    345555555556999*********99999886 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   5.4    0.0033         5      19      99 ..     115     195 ..      92     260 .] 0.93

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0033
                        DUF3450  19 dqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeierel 98 
                                    ++a+++ e++ + +++++++   +d   + +++e+++l++  es  + +e++ +l as+e+++a+ +++ ee++++ ++l
  gi|119719641|ref|YP_920136.1| 115 RAAREVVERWEDVRERISRELAGVDATITAYVDELERLEKMRESGVIGEEEYGELKASLERRLAEKNKEREELSRVLADL 194
                                    5789999******************************************************************9987776 PP

                        DUF3450  99 v 99 
                                     
  gi|119719641|ref|YP_920136.1| 195 D 195
                                    5 PP

>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2  15.9     0.023        34      61     181 ..      89     252 ..      82     260 .] 0.38

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.023
                                    HHCCCHHHHHHHHHCCHHHHHHHHHHHHCHHCCHHCHCCHCHHHHHHHHHHHHHHHHHHCHHHHHHH............. CS
                 Apolipoprotein  61 qeqlgqnleelrqrlapyteelrerlaadaeelqeqlavyaeelrerlerhvealkarlapyveelr............. 127
                                    ++ l +++e+l +r  ++++       ++++ + + + +  e++rer++r++  + a++++yv+el              
  gi|119719641|ref|YP_920136.1|  89 HASLVSEAEALIERAGELARIW-----EEYDRAAREVVERWEDVRERISRELAGVDATITAYVDELErlekmresgvige 163
                                    4444444444444433333333.....33444444444445555555555555555555555555554444444444444 PP

                                    .....................HHHHHHHHHHHH-----..---.--SSSHHHHHHHTS-T.............TSHHHHH CS
                 Apolipoprotein 128 .....................qklaerleelkeslaphaeeve.erlssrveelreklee.............qaeelre 172
                                                         ++l + l +l + + ph ++v+ +++  ++  l+ +l++               e+lr 
  gi|119719641|ref|YP_920136.1| 164 eeygelkaslerrlaeknkerEELSRVLADLDRVVLPHFKRVKvAEVKPEIAKLKVALAKleerfksggiseeVYEKLRS 243
                                    44444444444444444333333444444444444444333333222222222222222222222224433333334444 PP

                                    S--XXXXXX CS
                 Apolipoprotein 173 rleanleel 181
                                    +le+ +++l
  gi|119719641|ref|YP_920136.1| 244 ELEERIKRL 252
                                    444333333 PP

>> GTP-bdg_M  GTP-binding GTPase Middle Region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1       2.3   3.4e+03      58      58 ..     142     142 ..     111     158 .. 0.59
   2 ?    3.3   1.3     0.087   1.3e+02      29      59 ..     153     183 ..     134     197 .. 0.67
   3 ?   10.1   1.4   0.00065      0.97      11      63 ..     205     254 ..     203     260 .] 0.75

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.3
                                    H CS
                      GTP-bdg_M  58 i 58 
                                    i
  gi|119719641|ref|YP_920136.1| 142 I 142
                                    3 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.087
                                    XXXXX..X..XXXXXXXXXHHHHHHHHHHHH CS
                      GTP-bdg_M  29 elsrqgGgigtrGpGetkleldrrlireria 59 
                                    e  r +G ig    Ge k  l+rrl ++  +
  gi|119719641|ref|YP_920136.1| 153 EKMRESGVIGEEEYGELKASLERRLAEKNKE 183
                                    3345578899999999999999998876432 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.00065
                                    HHHHHHHHHHHHHC.XXXXXXXXX..X..XXXXXXXXXHHHHHHHHHHHHHHHH CS
                      GTP-bdg_M  11 VelAqlkyllprLe.glgkelsrqgGgigtrGpGetkleldrrlireriaklkk 63 
                                    V++A++k ++ +L+  l+k  +r + g    G  e  +e  r +++eri++l+k
  gi|119719641|ref|YP_920136.1| 205 VKVAEVKPEIAKLKvALAKLEERFKSG----GISEEVYEKLRSELEERIKRLEK 254
                                    667777777777742444446777666....9*******************998 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.2         3   4.5e+03      33      48 ..      45      60 ..      44      65 .. 0.68
   2 ?   12.7   5.3   6.8e-05       0.1       2     109 ..      88     195 ..      87     198 .. 0.96
   3 ?    4.5   2.7     0.023        35      72     117 ..     213     254 ..     203     260 .] 0.42

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3
                     TPR_MLP1_2 33 kqaeiakeaqqkYere 48
                                   +qa+ a+ea+ k e+ 
  gi|119719641|ref|YP_920136.1| 45 QQAKKAEEAKPKAEEV 60
                                   5777777777666654 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 6.8e-05
                     TPR_MLP1_2   2 elksleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeae 81 
                                    e +sl +e+++l e++ e+++  +++ +  ++  e++++  ++ +rel    +++++  +  e+l+++++     ++e  
  gi|119719641|ref|YP_920136.1|  88 EHASLVSEAEALIERAGELARIWEEYDRAAREVVERWEDVRERISRELAGVDATITAYVDELERLEKMRESGVIGEEEYG 167
                                    77899*************************************************************************** PP

                     TPR_MLP1_2  82 sakaeleeseesweeqkeelekelsele 109
                                    ++ka+le+  ++ ++++eel + l++l 
  gi|119719641|ref|YP_920136.1| 168 ELKASLERRLAEKNKEREELSRVLADLD 195
                                    ********************99998876 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.023
                     TPR_MLP1_2  72 eiaelkaeaesakaeleeseesweeqkeelekelselekriedlne 117
                                    eia+lk ++    a+lee  +s    +e +ek  sele+ri+ l++
  gi|119719641|ref|YP_920136.1| 213 EIAKLKVAL----AKLEERFKSGGISEEVYEKLRSELEERIKRLEK 254
                                    333333222....333333333333455555555555555554443 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   2.1     0.059        88      45      78 ..     124     157 ..      43     160 .. 0.69
   2 ?    9.2   7.3    0.0011       1.6      13      99 ..     172     257 ..     166     260 .] 0.83

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.059
                         APG6_N  45 qdeeleeleeeleklekeeeelleeLkelekere 78 
                                    +++ +e++ +el+ ++++  + + eL++lek re
  gi|119719641|ref|YP_920136.1| 124 WEDVRERISRELAGVDATITAYVDELERLEKMRE 157
                                    4556667777777777777777777777777665 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0011
                         APG6_N  13 eldkqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeele 92 
                                     l+++l++ +ker+++++ l+ l++       ++ +++e + e++kl+ + ++l+e  k     +e  e+ +++lee  +
  gi|119719641|ref|YP_920136.1| 172 SLERRLAEKNKEREELSRVLADLDRVVLPHF-KRVKVAEVKPEIAKLKVALAKLEERFKSGGISEEVYEKLRSELEERIK 250
                                    6899********************9965555.79999*********************9987777777777777777777 PP

                         APG6_N  93 aleeeee 99 
                                    +le+ +e
  gi|119719641|ref|YP_920136.1| 251 RLEKIKE 257
                                    7776544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1707  (0.0952089); expected 358.6 (0.02)
Passed bias filter:                      890  (0.0496402); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.46
# Mc/sec: 1690.78
//
Query:       gi|119719642|ref|YP_920137.1|  [L=486]
Description: hypothetical protein Tpen_0732 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
        1.4    8.8   6.4         18    5.2   3.8    2.7  2  Peptidase_M48_N  CAAX prenyl protease N-terminal, five membra


Domain annotation for each model (and alignments):
>> Peptidase_M48_N  CAAX prenyl protease N-terminal, five membrane helices
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0    0.0046        83     145     178 ..     101     134 ..      97     136 .. 0.90
   2 ?    5.2   3.8   0.00099        18     120     165 ..     231     276 ..     226     284 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.0046
                Peptidase_M48_N 145 iiewggeyfylylwlfllvfslllmtiyPtlIaP 178
                                    +++++g+ f+l++ ++++++s   + ++  l+ P
  gi|119719642|ref|YP_920137.1| 101 MLRNMGDGFFLVALAITTAVSAASLALFKALVTP 134
                                    57899*****************999999888887 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.00099
                Peptidase_M48_N 120 fikdklkslllalviglpllaallwiiewggeyfylylwlfllvfs 165
                                    + +++  + ++ +  gl +la++l +++ +g  f++y  +f +++ 
  gi|119719642|ref|YP_920137.1| 231 WGVKTSRGAAVIISAGLYVLAGMLSFFTLFGAGFVFYQAVFAVLVL 276
                                    556666788899999*************************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (486 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       722  (0.04027); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 3138.79
//
Query:       gi|119719643|ref|YP_920138.1|  [L=109]
Description: hypothetical protein Tpen_0733 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 845.49
//
Query:       gi|119719644|ref|YP_920139.1|  [L=157]
Description: ribosomal protein L13 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.4e-10   38.6   0.0    9.4e-10   38.6   0.0    1.7  2  Ribosomal_L13e  Ribosomal protein L13e
     0.0015   18.3   0.7     0.0029   17.4   0.7    1.5  1  Ribosomal_L15e  Ribosomal L15
  ------ inclusion threshold ------
      0.026   13.8   0.0      0.041   13.1   0.0    1.3  1  LegC3_N         LegC3 N-terminal coiled-coil domain


Domain annotation for each model (and alignments):
>> Ribosomal_L13e  Ribosomal protein L13e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.6   0.0   1.6e-13   9.4e-10      60     116 ..      28      84 ..       3      86 .. 0.82
   2 ?   -2.3   1.2      0.59   3.5e+03      20      35 ..     130     145 ..     106     154 .. 0.55

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 1.6e-13
                 Ribosomal_L13e  60 tkvraGrGFtleElkaagiskklArtiGIavDhRrknkseeslkaNveRLkeYkskL 116
                                    + ++ GrGF+  E+ka g++ k Ar +GI vD+Rrk    e+++a  + Lk+ k++L
  gi|119719644|ref|YP_920139.1|  28 RPLKVGRGFSEGEVKALGLTVKEARLLGIYVDERRKTVHPENVEALRSWLKALKEHL 84 
                                    56899********************************99999988877777777665 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.59
                 Ribosomal_L13e  20 dqparkkrRrearqak 35 
                                     +  + k+++++r  k
  gi|119719644|ref|YP_920139.1| 130 THHYKWKKKQRERLLK 145
                                    3333333333333333 PP

>> Ribosomal_L15e  Ribosomal L15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.7   4.8e-07    0.0029     153     188 ..     102     137 ..      96     152 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.8e-07
                                    GGGTTGGGGT-SHHHHHHTT-S-SS.TT-TTTSS-T CS
                 Ribosomal_L15e 153 kvhkhRelrGltsagkksRGlrkkglkgaekirgsr 188
                                    k   hR+++G+t ag+++RGl +  +++++++++ +
  gi|119719644|ref|YP_920139.1| 102 KPDIHRVFKGKTMAGRRARGLLSVKYRYTHHYKWKK 137
                                    45679****************999999999988765 PP

>> LegC3_N  LegC3 N-terminal coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   6.8e-06     0.041     266     296 ..      55      85 ..      52      86 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.8e-06
                                    HHHHHH--S---HHHHHHHHHHHHHHHT-S- CS
                        LegC3_N 266 ekyLnkkssqlssQeaeALkavlklmkkhle 296
                                     +y +++++++ + ++eAL++ lk +k+hle
  gi|119719644|ref|YP_920139.1|  55 GIYVDERRKTVHPENVEALRSWLKALKEHLE 85 
                                    6799999***********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       725  (0.0404373); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1050.72
//
Query:       gi|119719645|ref|YP_920140.1|  [L=62]
Description: hypothetical protein Tpen_0735 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-09   37.5   1.7    1.8e-09   37.1   1.7    1.1  1  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
     0.0009   18.9   1.0        0.3   10.8   0.2    2.2  2  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
     0.0017   18.3   0.6     0.0025   17.7   0.6    1.4  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
  ------ inclusion threshold ------
      0.012   15.1   0.6      0.018   14.6   0.6    1.4  1  TF_Zn_Ribbon     TFIIB zinc-binding
      0.013   15.4   0.9       0.02   14.8   0.9    1.2  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.016   14.9   1.6       0.03   14.1   1.6    1.3  1  A2L_zn_ribbon    A2L zinc ribbon domain
      0.027   14.8   0.9       0.65   10.4   1.1    2.0  2  Lar_restr_allev  Restriction alleviation protein Lar
       0.03   14.2   5.8       0.12   12.3   5.8    1.8  1  zf-HIT           HIT zinc finger
       0.04   13.9   1.2       0.29   11.2   1.3    1.9  2  DZR              Double zinc ribbon
       0.04   14.0   0.2      0.043   13.9   0.2    1.1  1  DUF2318          Predicted membrane protein (DUF2318)
      0.042   14.2   0.5      0.047   14.0   0.5    1.2  1  C1_2             C1 domain
      0.051   13.7   0.8      0.059   13.5   0.8    1.1  1  zf-RRPl_C4       Putative ribonucleoprotein zinc-finger pf C4
       0.21   11.9   2.9        2.5    8.4   0.3    2.1  2  Cas_CXXC_CXXC    CRISPR-associated protein (Cas_CXXC_CXXC)
       0.48   10.2   4.7        2.1    8.2   0.7    2.2  2  zinc_ribbon_2    zinc-ribbon domain
       0.55   10.4   4.5        3.4    7.8   0.3    2.0  3  Zn-ribbon_8      Zinc ribbon domain


Domain annotation for each model (and alignments):
>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   1.7   1.5e-12   1.8e-09       3      29 ..      12      39 ..      10      41 .. 0.84

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 1.5e-12
                        zf-RRN7  3 kgppCgvCgcrsftl.ddGfyyCrrCht 29
                                    +p+C vCg+r+++  ++G+yyC  C++
  gi|119719645|ref|YP_920140.1| 12 PEPRCSVCGSRDVFAkIEGKYYCFKCGS 39
                                   68********655555**********97 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0    0.0037       4.4      19      29 ..      15      25 ..      10      27 .. 0.86
   2 !   10.8   0.2   0.00025       0.3       1      18 [.      32      49 ..      32      50 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0037
                                   --SSS-----B CS
                 DNA_RNApol_7kD 19 RCkeCGhRilY 29
                                   RC  CG+R ++
  gi|119719645|ref|YP_920140.1| 15 RCSVCGSRDVF 25
                                   9******9665 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00025
                                   -B-SSS--B----SSS-- CS
                 DNA_RNApol_7kD  1 YiCgeCgaevslkkgdpi 18
                                   Y C +Cg++  +++++ i
  gi|119719645|ref|YP_920140.1| 32 YYCFKCGSRLVIEHSEKI 49
                                   99***********99987 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.6   2.1e-06    0.0025      17      44 ..      12      38 ..       4      44 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.1e-06
                  Zn_Tnp_IS1595 17 ngfvCPhCgsr.kayriktrglfqCkeCr 44
                                     ++C  Cgsr  + +i++  ++ C +C+
  gi|119719645|ref|YP_920140.1| 12 PEPRCSVCGSRdVFAKIEG--KYYCFKCG 38
                                   4599*******99999997..*******8 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.6   1.5e-05     0.018       2      27 ..      15      39 ..      14      53 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.5e-05
                                   EETTTTCEECHEETSTTCEEESSSSB CS
                   TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGl 27
                                   +C +Cgs++ v+   +g ++C +CG+
  gi|119719645|ref|YP_920140.1| 15 RCSVCGSRD-VFAKIEGKYYCFKCGS 39
                                   6******97.888889*********7 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.9   1.7e-05      0.02      30      54 ..      15      39 ..      14      42 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.7e-05
                 OrfB_Zn_ribbon 30 tCseCgsknkealsgrtfkCpnCgf 54
                                   +Cs+Cgs++  a+ + +++C++Cg 
  gi|119719645|ref|YP_920140.1| 15 RCSVCGSRDVFAKIEGKYYCFKCGS 39
                                   6**********************97 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   1.6   2.5e-05      0.03       6      29 ..      16      39 ..      15      40 .. 0.97

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.5e-05
                  A2L_zn_ribbon  6 CsvCggngilnseqgylvCieCga 29
                                   CsvCg+  ++ +  g ++C +Cg+
  gi|119719645|ref|YP_920140.1| 16 CSVCGSRDVFAKIEGKYYCFKCGS 39
                                   ***********************7 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   1.1   0.00055      0.65       5      32 ..      15      38 ..      14      39 .. 0.90
   2 ?    8.1   0.1     0.003       3.6       6      25 ..      34      53 ..      31      58 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00055
                Lar_restr_allev  5 pCPfCggravlersqrvvaeigqcvyCa 32
                                    C  Cg+r+v  + +++++    c+ C 
  gi|119719645|ref|YP_920140.1| 15 RCSVCGSRDVFAKIEGKYY----CFKCG 38
                                   599**************99....99995 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.003
                Lar_restr_allev  6 CPfCggravlersqrvvaei 25
                                   C  Cg+r v+e+s++ v+e+
  gi|119719645|ref|YP_920140.1| 34 CFKCGSRLVIEHSEKIVEEY 53
                                   779*************9985 PP

>> zf-HIT  HIT zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   5.8    0.0001      0.12       1      22 [.      12      40 ..      12      41 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0001
                                   ---B-TTT-S.......B-SEE-TTT--E CS
                         zf-HIT  1 prklCgvCgf.......pakYkCpkCntr 22
                                   p++ C+vCg        ++kY C kC+ r
  gi|119719645|ref|YP_920140.1| 12 PEPRCSVCGSrdvfakiEGKYYCFKCGSR 40
                                   6789*****99999999**********98 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1     0.063        75      29      36 ..      14      21 ..       3      29 .. 0.70
   2 ?   11.2   1.3   0.00024      0.29       1      23 [.      16      42 ..      16      53 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.063
                            DZR 29 drCpsCge 36
                                    rC+ Cg+
  gi|119719645|ref|YP_920140.1| 14 PRCSVCGS 21
                                   56666665 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00024
                            DZR  1 CpqCgee....lppdarfCseCgtklk 23
                                   C+ Cg+       +++ +C++Cg++l 
  gi|119719645|ref|YP_920140.1| 16 CSVCGSRdvfaKIEGKYYCFKCGSRLV 42
                                   666776666655567778999988874 PP

>> DUF2318  Predicted membrane protein (DUF2318)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   3.6e-05     0.043      36      65 ..      15      45 ..       3      52 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.6e-05
                        DUF2318 36 aCevC.ekkgYvqegeelvCknCgvrfalds 65
                                    C+vC +++ + + + +  C +Cg+r+ +++
  gi|119719645|ref|YP_920140.1| 15 RCSVCgSRDVFAKIEGKYYCFKCGSRLVIEH 45
                                   5****77888999*************99876 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.5     4e-05     0.047      20      39 ..      15      38 ..       4      47 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4e-05
                           C1_2 20 nCsaCgrk.idgff...YsCseCd 39
                                   +Cs+Cg   ++ +    Y+C +C 
  gi|119719645|ref|YP_920140.1| 15 RCSVCGSRdVFAKIegkYYCFKCG 38
                                   8*****99744444678******5 PP

>> zf-RRPl_C4  Putative ribonucleoprotein zinc-finger pf C4 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.8     5e-05     0.059       3      37 ..      15      50 ..      13      59 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5e-05
                     zf-RRPl_C4  3 kCkyClskkl.knlnetvyCeaCeiyfkvknekqkv 37
                                   +C+ C s+++  +++ ++yC +C + + ++ +++ v
  gi|119719645|ref|YP_920140.1| 15 RCSVCGSRDVfAKIEGKYYCFKCGSRLVIEHSEKIV 50
                                   7*****9876267899*********99876655443 PP

>> Cas_CXXC_CXXC  CRISPR-associated protein (Cas_CXXC_CXXC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.2     0.025        30       5      20 ..      13      25 ..      11      31 .. 0.75
   2 ?    8.4   0.3    0.0021       2.5       3      17 ..      29      43 ..      27      61 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.025
                  Cas_CXXC_CXXC  5 kgnCitCgeRnvkqlk 20
                                   ++ C +Cg R+   ++
  gi|119719645|ref|YP_920140.1| 13 EPRCSVCGSRD---VF 25
                                   578*****995...44 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0021
                  Cas_CXXC_CXXC  3 dkkgnCitCgeRnvk 17
                                   + k+ C+ Cg R v 
  gi|119719645|ref|YP_920140.1| 29 EGKYYCFKCGSRLVI 43
                                   679*******99554 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.2      0.04        48      16      21 ..      16      21 ..      13      22 .. 0.66
   2 ?    8.2   0.7    0.0018       2.1      15      22 ..      33      40 ..      29      41 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.04
                  zinc_ribbon_2 16 CpyCGt 21
                                   C+ CG+
  gi|119719645|ref|YP_920140.1| 16 CSVCGS 21
                                   777774 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0018
                  zinc_ribbon_2 15 FCpyCGtp 22
                                   +C +CG+ 
  gi|119719645|ref|YP_920140.1| 33 YCFKCGSR 40
                                   79999976 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.3    0.0029       3.4      23      36 ..      10      24 ..       3      28 .. 0.78
   2 ?    7.6   4.0    0.0035       4.2       7      36 ..      15      41 ..      13      44 .. 0.85
   3 ?    4.1   0.4     0.043        52       6      14 ..      32      40 ..      31      50 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0029
                    Zn-ribbon_8 23 dapltaCPeCgs.ev 36
                                     p++ C  Cgs +v
  gi|119719645|ref|YP_920140.1| 10 AGPEPRCSVCGSrDV 24
                                   468899*****9665 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0035
                    Zn-ribbon_8  7 rCeeCghefevlqsisdaplta.CPeCgsev 36
                                   rC  Cg   +v+++i     +  C +Cgs++
  gi|119719645|ref|YP_920140.1| 15 RCSVCG-SRDVFAKIE---GKYyCFKCGSRL 41
                                   8*****.999**9987...5666*****965 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.043
                    Zn-ribbon_8  6 YrCeeCghe 14
                                   Y C +Cg++
  gi|119719645|ref|YP_920140.1| 32 YYCFKCGSR 40
                                   777788765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       767  (0.0427799); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.43u 0.31s 00:00:00.74 Elapsed: 00:00:00.49
# Mc/sec: 381.99
//
Query:       gi|119719646|ref|YP_920141.1|  [L=100]
Description: like-Sm ribonucleoprotein, core [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.7e-19   66.8   0.1    1.2e-18   66.5   0.1    1.1  1  LSM       LSM domain
    0.00077   19.6   0.0    0.00085   19.4   0.0    1.2  1  SM-ATX    Ataxin 2 SM domain


Domain annotation for each model (and alignments):
>> LSM  LSM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.5   0.1   1.4e-22   1.2e-18       2      66 ..       6      70 ..       5      71 .. 0.96

  Alignments for each domain:
  == domain 1  score: 66.5 bits;  conditional E-value: 1.4e-22
                                   HHHHTTTSEEEEEETTSEEEEEEEEEEETTSEEEEEEEEEEETTETEEEEEEEEEEEGGGEEEEE CS
                            LSM  2 flkklinkkvtvelkngrelrGtLkgfDqfmNlvLedveetlkdkkekrklglvliRGnnivlis 66
                                    l++  +k v v+lk+g e+ G+L+  D  mNlvL+d++e  +++k +++lg+v+iRG+n +++s
  gi|119719646|ref|YP_920141.1|  6 HLRNQSGKGVFVKLKDGSEYMGKLRMTDAAMNLVLDDAKELTETNKVVAQLGTVFIRGSNLLFVS 70
                                   589999***************************************9****************998 PP

>> SM-ATX  Ataxin 2 SM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   9.5e-08   0.00085      10      55 ..       9      50 ..       4      83 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 9.5e-08
                                   TTTTSEEEEEETTS-EEEEEEEEE-T..T--EEEEEEEETTS.... CS
                         SM-ATX 10 slvGkevevtvknGevyeGifstvslekdfsvvLkmarkvkkansk 55
                                   +  Gk v v++k+G+ y G ++ ++    +++vL+ a+++++   +
  gi|119719646|ref|YP_920141.1|  9 NQSGKGVFVKLKDGSEYMGKLRMTDA--AMNLVLDDAKELTE--TN 50
                                   66799*********************..************99..22 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 722.63
//
Query:       gi|119719647|ref|YP_920142.1|  [L=406]
Description: S-adenosylmethionine synthetase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   2.5e-166  553.4   0.1   2.8e-166  553.2   0.1    1.0  1  AdoMet_Synthase  S-adenosylmethionine synthetase (AdoMet synt
  ------ inclusion threshold ------
       0.14   12.8   0.1       0.51   11.0   0.0    1.9  2  S-AdoMet_synt_N  S-adenosylmethionine synthetase, N-terminal 


Domain annotation for each model (and alignments):
>> AdoMet_Synthase  S-adenosylmethionine synthetase (AdoMet synthetase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  553.2   0.1  3.1e-170  2.8e-166       1     395 [.       4     401 ..       4     402 .. 0.98

  Alignments for each domain:
  == domain 1  score: 553.2 bits;  conditional E-value: 3.1e-170
                                    --EEEEE-TTS-GTTSSEEEEEEE-TTSHHHHHHHHHHHHHHHHHHHHHHHHSS---EEEEEEEEE--EEEEETTEEEEE CS
                AdoMet_Synthase   1 rnivveelkkkpveeqevEivErKGiGHPDsiaDgiaeavsralskeylekfgailhhniDkvllvaGesepkfgGGevi 80 
                                    +nivve+++  p ++  vEivErKG+GHPD+iaD+i+ea+sr+ls++yle++gailhhn+Dkvl+v+G+s+p+fgGGev+
  gi|119719647|ref|YP_920142.1|   4 KNIVVEKSSYIPPSRLPVEIVERKGTGHPDYIADSISEAASRELSRYYLEHYGAILHHNLDKVLVVGGQSSPRFGGGEVV 83 
                                    69****************************************************************************** PP

                                    E-EEEEEEEEEEEEE.....EEE--HHHHHHHHHHHHHHHH-SS--TTTSEEEEEEEEEEEEHHHHHHCH-SS..-BESS CS
                AdoMet_Synthase  81 epieillsgratkev....egekipveeialeaakeylkenlraldlekdvivdvklgkgsadLkdvferkkkevplaND 156
                                    +pi+il+sgrat+ev    ++e++pv+ i+l+a+++++k+n+r+ld++++vivd+++gkgsadL+d+++r+ +  p aND
  gi|119719647|ref|YP_920142.1|  84 QPIYILVSGRATTEVvsegGRESVPVGPIILKATRDWIKSNIRFLDPDTHVIVDYRVGKGSADLVDIYNRRGS-YPGAND 162
                                    ***************99888899***********************************************766.8***** PP

                                    SEEEEEEES--HHHHHHHHHHHHHTSHHHHHH-TTEEEEEEEEEEEETTEEEEEEEEEEEGGG--SHHHHHHHHHHHHHH CS
                AdoMet_Synthase 157 tSfgvgyaplseleklvleterllnskelkkklpevGeDiKvmglRekkkielTvavalvdrlvkdleeYlevkeeikee 236
                                    tS+g+gyapls +e++vleterllns+++kk+lp+vGeD+Kvmg+R+++k++lTva+a+++r+v+++eeYl+ kee+k+ 
  gi|119719647|ref|YP_920142.1| 163 TSMGIGYAPLSPTERAVLETERLLNSEKVKKELPAVGEDVKVMGVRKGNKLTLTVAMAVISRFVHSTEEYLSLKEEVKKL 242
                                    ******************************************************************************** PP

                                    HHHHHHHHSTTSEEEEEE-TT-BGG...GTB--EESSSSGGGTT--EETTSS--TTSSB-TTS----S--TTS-TTT-HH CS
                AdoMet_Synthase 237 veelakkltkerevevevNtaDkke...eesvyltvtGtsaEegDdGsvGRGNRvnGlitpnrpmslEAaaGKNPvsHvG 313
                                    v+e+a+++t+  +vev+vNt D+++   ++++yltvtGtsaE+gDdG++GRGNR+nGlitp rpmslEA+aGKNPvsH+G
  gi|119719647|ref|YP_920142.1| 243 VKEHAASITD-LDVEVYVNTGDDPSrgdKGGLYLTVTGTSAEHGDDGATGRGNRANGLITPFRPMSLEATAGKNPVSHIG 321
                                    *********9.***********99767799************************************************** PP

                                    HHHHHHHHHHHHHHHHH-TTEEEEEEEEEE-TTSBTTS-SEEEEEEEESSS---HHSHHHHHHHHHHHHT-HHHHHHHHT CS
                AdoMet_Synthase 314 KiYnvlaneiakeiveevegvkevyvrllsqiGkpidePlvasvqvilekgvsleevekeveeiideelekieeiteeli 393
                                    K+Ynv+a + a+ei+  +++v+evy++l+sqiGkpi++Pl+a + + + +   l++v++++ee+++++l++i+ ++e+++
  gi|119719647|ref|YP_920142.1| 322 KLYNVVAFQAASEICG-LDHVNEVYIKLISQIGKPINQPLLAYIAINAPD-DVLARVKHQAEEVLAKHLDRINVLWESIL 399
                                    **************98.9****************************6655.57899***********************9 PP

                                    TT CS
                AdoMet_Synthase 394 eg 395
                                    +g
  gi|119719647|ref|YP_920142.1| 400 KG 401
                                    98 PP

>> S-AdoMet_synt_N  S-adenosylmethionine synthetase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   5.7e-05      0.51      10      24 ..      28      42 ..      22      54 .. 0.87
   2 ?   -3.4   0.0       1.8   1.6e+04      56      73 ..     228     245 ..     211     250 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 5.7e-05
                S-AdoMet_synt_N 10 seGHPDkvadqisda 24
                                     GHPD +ad+is+a
  gi|119719647|ref|YP_920142.1| 28 GTGHPDYIADSISEA 42
                                   68***********97 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.8
                S-AdoMet_synt_N  56 ttkakvdiekivrevike 73 
                                    +t+ ++++++ v++ +ke
  gi|119719647|ref|YP_920142.1| 228 STEEYLSLKEEVKKLVKE 245
                                    445566777777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); expected 358.6 (0.02)
Passed bias filter:                      603  (0.0336327); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.21s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 3047.86
//
Query:       gi|119719648|ref|YP_920143.1|  [L=662]
Description: hypothetical protein Tpen_0738 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-46  157.3   0.0    9.3e-46  155.0   0.0    2.0  2  DUF460           Protein of unknown function (DUF460)
    7.3e-05   22.0   3.8    0.00011   21.5   3.8    1.2  1  Atg14            Vacuolar sorting 38 and autophagy-related su
  ------ inclusion threshold ------
      0.017   14.5   2.7      0.029   13.7   2.7    1.3  1  DUF4763          Domain of unknown function (DUF4763)
      0.023   13.7   0.1      0.038   13.1   0.1    1.2  1  TelA             Toxic anion resistance protein (TelA)
      0.074   13.5   8.0       0.21   12.0   8.0    1.8  1  CENP-H           Centromere protein H (CENP-H)
      0.085   12.6   0.2      0.085   12.6   0.2    2.1  2  MctB             Copper transport outer membrane protein, Mct
       0.11   12.6   9.2      0.077   13.2   5.8    2.3  2  Cnn_1N           Centrosomin N-terminal motif 1
       0.12   11.2   7.1       0.17   10.7   7.1    1.2  1  PV-1             PV-1 protein (PLVAP)
       0.28   11.6   9.6       0.61   10.5   9.6    1.6  1  Uso1_p115_C      Uso1 / p115 like vesicle tethering protein, 
       0.32   10.3   3.6       0.81    9.0   3.6    1.7  1  DUF4407          Domain of unknown function (DUF4407)
       0.33   11.4   1.5        5.2    7.6   0.5    3.2  3  Acetyltransf_11  Udp N-acetylglucosamine O-acyltransferase; D
       0.51    8.8   7.8       0.85    8.1   7.8    1.3  1  FUSC             Fusaric acid resistance protein family
       0.53   10.4   6.2       0.51   10.4   2.1    2.2  2  DivIVA           DivIVA protein
        0.9   10.2   3.6        2.7    8.7   3.6    1.7  1  AATF-Che1        Apoptosis antagonizing transcription factor
          1    9.6  15.9        3.5    7.8  15.9    1.9  1  ATG16            Autophagy protein 16 (ATG16)
        1.3    9.3   7.1          4    7.8   7.0    1.8  1  DUF641           Plant protein of unknown function (DUF641)
        1.4    9.4   7.6        8.7    6.9   2.0    2.5  2  UPF0449          Uncharacterised protein family UPF0449
        1.5    8.1  10.7        3.8    6.8  10.7    1.6  1  GAS              Growth-arrest specific micro-tubule binding
          3    6.6  12.5        2.5    6.9   9.2    1.7  1  Spc7             Spc7 kinetochore protein
        4.3    7.3   7.5        3.8    7.5   0.0    3.0  3  Prefoldin_2      Prefoldin subunit
        9.9    5.9  12.9         26    4.6  12.9    1.7  1  OEP              Outer membrane efflux protein


Domain annotation for each model (and alignments):
>> DUF460  Protein of unknown function (DUF460)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       1.6   1.4e+03      45     108 ..      26      87 ..      23      92 .. 0.78
   2 !  155.0   0.0   1.1e-48   9.3e-46       3     141 .]     221     365 ..     219     365 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.6
                         DUF460  45 avldldgevlalkssreldreevieliselGkpvivAtDvspppetvkklarslkavlyvPeed 108
                                    avl +dg+v   +  re++ e+v++l ++ G  ++    v +   tv+ la+ l+     P + 
  gi|119719648|ref|YP_920143.1|  26 AVLLVDGRVE--QRVREASLEDVVRLATSGGVEALALDNVFELAPTVEGLAEFLRLFPGRPPRL 87 
                                    5666666664..457999**********999999988889999999999988877766666665 PP

  == domain 2  score: 155.0 bits;  conditional E-value: 1.1e-48
                         DUF460   3 kskdvkvevesvekdkiefeplkkkr......kkklivGiDPGittgiavldldgevlalkssreldreevieliselGk 76 
                                    +++d+ v+ve++++d++ef+pl ++       ++ livG+DPG+ tg+avld++g+vla++s+r l r+++++ ++ +G+
  gi|119719648|ref|YP_920143.1| 221 EGHDLFVRVEPARRDRVEFRPLGSRLhralsqERLLIVGVDPGMATGFAVLDFSGRVLAVDSRRLLGRGQLVRELYGFGR 300
                                    789****************8874433556666999********************************************* PP

                         DUF460  77 pvivAtDvspppetvkklarslkavlyvPeedlsveeKeelaeklsekekvkykddHeRDalaAA 141
                                    p+ivAtDv+ppp++vkkla++l+avlyvP+++lsveeK++la +++ ++ v+++++HeRD+laAA
  gi|119719648|ref|YP_920143.1| 301 PAIVATDVNPPPAYVKKLASTLGAVLYVPSRSLSVEEKRRLALEAAGQQGVRLRTSHERDSLAAA 365
                                    ****************************************************************9 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   3.8   1.3e-07   0.00011      21     111 ..     437     527 ..     413     571 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.3e-07
                          Atg14  21 perlyelrerlaklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieek 100
                                    +e l+e r  l  l+ e+ +l++++e+a+e+ +++e++ + + + ++ ++ l s+ a+lr+r+++l+  l++ ++e++ek
  gi|119719648|ref|YP_920143.1| 437 EEELEEVRRALSELLRENVELRRRLEEAEERARRSEEALRGLLRAREVARGLESEYAKLRARIELLQSELDSFRRELAEK 516
                                    578999999999******************************************************************** PP

                          Atg14 101 kkklaklsdkl 111
                                     + l++l d+l
  gi|119719648|ref|YP_920143.1| 517 ERALESLGDAL 527
                                    *****998765 PP

>> DUF4763  Domain of unknown function (DUF4763)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   2.7   3.4e-05     0.029      68     162 ..     413     514 ..     403     520 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.4e-05
                        DUF4763  68 lrskLalnvpecPei...decvdedlelelltseqpeileLqrnnhkLrqqlaelqqhlkasrkslkel...reslcqek 141
                                    lr+++++++p    i   +e ++ +  +e+l+++  ++ eL r+n+ Lr +l+e++++ ++s+++l+ l   re  + + 
  gi|119719648|ref|YP_920143.1| 413 LRRQVGVKIP---RIelqKEAEEPRRVEEELEEVRRALSELLRENVELRRRLEEAEERARRSEEALRGLlraREVARGLE 489
                                    7888888875...443334555555555666669********************************98844455666778 PP

                        DUF4763 142 krlrklqkrln....eldsfkrkle 162
                                    +  +kl++r++    eldsf+r+l+
  gi|119719648|ref|YP_920143.1| 490 SEYAKLRARIEllqsELDSFRRELA 514
                                    8888898888544447888888865 PP

>> TelA  Toxic anion resistance protein (TelA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   4.4e-05     0.038      51     130 ..     455     531 ..     428     533 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.4e-05
                           TelA  51 seLvkelkeldpdelkeekkl.gllplfkkaknkieklfakYekaeeqidkIvkeLekgqdellkdnaaLdqlyeknley 129
                                    +eL+++l+e + +  + e+ l gll+    a++ ++ l ++Y+k+++ i+ +  eL++ ++el +  +aL++l +++l y
  gi|119719648|ref|YP_920143.1| 455 VELRRRLEEAEERARRSEEALrGLLR----AREVARGLESEYAKLRARIELLQSELDSFRRELAEKERALESLGDALLSY 530
                                    47888888888887777777777777....99999*****************************************9999 PP

                           TelA 130 f 130
                                    +
  gi|119719648|ref|YP_920143.1| 531 L 531
                                    6 PP

>> CENP-H  Centromere protein H (CENP-H)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   8.0   0.00025      0.21      14      87 ..     425     504 ..     423     520 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00025
                         CENP-H  14 ellklsqelrelqeeltevekenlrlkrknrelaaellelakekesek......eklkeelekleaelkksrqrwrvvkn 87 
                                    el+k ++e r ++eel+ev++   +l r+n+el ++l+e ++ +++ +       +++e    le+e+ k r+r+++++ 
  gi|119719648|ref|YP_920143.1| 425 ELQKEAEEPRRVEEELEEVRRALSELLRENVELRRRLEEAEERARRSEealrglLRAREVARGLESEYAKLRARIELLQS 504
                                    678889999****************************6555555555578988866888889999999999999998886 PP

>> MctB  Copper transport outer membrane protein, MctB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   1.0      0.41   3.5e+02      37      87 ..     436     485 ..     432     485 .. 0.76
   2 ?   12.6   0.2   9.9e-05     0.085      32      92 ..     483     542 ..     477     554 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.41
                           MctB  37 legqveelreekeelraeadaleaqleaaddfaaavaprlvagrLtgrsVa 87 
                                    +e++ ee+r+  +el +e+ +l+++le+a++ a++  +++++g L+ r+Va
  gi|119719648|ref|YP_920143.1| 436 VEEELEEVRRALSELLRENVELRRRLEEAEERARRS-EEALRGLLRAREVA 485
                                    577888888888888888888888888888877664.56778888887775 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 9.9e-05
                           MctB  32 nlldtlegqveelreekeelraeadaleaqleaaddfaaavaprlvagrLtgrsVavvttp 92 
                                    +++ +le++ ++lr++ e l++e d+ +++l+++++  ++++++l++  L+g+ V+ v+++
  gi|119719648|ref|YP_920143.1| 483 EVARGLESEYAKLRARIELLQSELDSFRRELAEKERALESLGDALLS-YLSGEAVVAVRLS 542
                                    68899**************************************9997.69****9999875 PP

>> Cnn_1N  Centrosomin N-terminal motif 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1       1.5   1.3e+03      38      64 ..     409     435 ..     401     443 .. 0.80
   2 ?   13.2   5.8     9e-05     0.077       4      72 ..     442     519 ..     439     520 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.5
                         Cnn_1N  38 keellkenielkveveslqkelkekkk 64 
                                    +ee+l+  + +k+ + +lqke +e ++
  gi|119719648|ref|YP_920143.1| 409 VEEALRRQVGVKIPRIELQKEAEEPRR 435
                                    688999999999999999999888666 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 9e-05
                         Cnn_1N   4 EqeeqidkLkKENFdLKLriyfLeerleklse.........eqkeellkenielkveveslqkelkekkkllreaeka 72 
                                    E    +++L +EN  L+ r+ + eer  +++e         e  + l++e  +l+ ++e lq el++ +++l e e+a
  gi|119719648|ref|YP_920143.1| 442 EVRRALSELLRENVELRRRLEEAEERARRSEEalrgllrarEVARGLESEYAKLRARIELLQSELDSFRRELAEKERA 519
                                    677889**********************************9999******************************9997 PP

>> PV-1  PV-1 protein (PLVAP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   7.1    0.0002      0.17     282     377 ..     435     525 ..     407     582 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0002
                           PV-1 282 kveelarslragiervarensdlqrqkleaeqslrasqeakekvekeaqareaklqaecarq.tqlaleekaalrkerdn 360
                                    +vee   ++r ++ ++ ren +l+r+ +eae+ +r s+ea   +   a++ +  l++e a+  +++       l+ e d+
  gi|119719648|ref|YP_920143.1| 435 RVEEELEEVRRALSELLRENVELRRRLEEAEERARRSEEALRGLL-RAREVARGLESEYAKLrARIE-----LLQSELDS 508
                                    68888889999999999***************9999999987665.578888889999887313332.....59****** PP

                           PV-1 361 lakeleekkreveqlkl 377
                                    +++el+ek r +e l  
  gi|119719648|ref|YP_920143.1| 509 FRRELAEKERALESLGD 525
                                    ***********999865 PP

>> Uso1_p115_C  Uso1 / p115 like vesicle tethering protein, C terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   9.6   0.00071      0.61       2      83 ..     439     521 ..     425     528 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00071
                    Uso1_p115_C   2 kaseleseaaslkdeneklkaelqslskalesleqk.eakkaaesqakeleaenkklekeleklraelkeekekekekqk 80 
                                    +++e+ +  ++l +en +l  +l++++++++ +e++   +  a+++a+ le+e  kl+ ++e l++el+  + +  ek+ 
  gi|119719648|ref|YP_920143.1| 439 ELEEVRRALSELLRENVELRRRLEEAEERARRSEEAlRGLLRAREVARGLESEYAKLRARIELLQSELDSFRRELAEKER 518
                                    568999999***************************999********************999999999987777666655 PP

                    Uso1_p115_C  81 Eld 83 
                                     l+
  gi|119719648|ref|YP_920143.1| 519 ALE 521
                                    555 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   3.6   0.00095      0.81     131     210 ..     443     517 ..     420     653 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00095
                        DUF4407 131 ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaqldaaqaelaelkakldata 210
                                     +  l+el +++ +l++ +++ae+r+++ +++++  l        +  +G + ++ + +a ++ +q el++++++l +++
  gi|119719648|ref|YP_920143.1| 443 VRRALSELLRENVELRRRLEEAEERARRSEEALRGLLRA-----REVARGLESEYAKLRARIELLQSELDSFRRELAEKE 517
                                    556666666666666666666666666666666655553.....123455556666666666666666666555544222 PP

>> Acetyltransf_11  Udp N-acetylglucosamine O-acyltransferase; Domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       2.2   1.9e+03      29      53 ..     355     379 ..     351     394 .. 0.74
   2 ?    7.6   0.5    0.0061       5.2      30      66 ..     437     473 ..     433     490 .. 0.81
   3 ?   -0.7   0.0       2.4   2.1e+03      50      80 ..     566     590 ..     555     592 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 2.2
                                    -HHHHHHHHHHHHHHHSSSS-HHHH CS
                Acetyltransf_11  29 seeeikalkkayrllyrsglsleea 53 
                                    ++ e+++l +ay+ + +    +ee 
  gi|119719648|ref|YP_920143.1| 355 TSHERDSLAAAYKAFLSYRELFEEV 379
                                    5778999999**9997655444443 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0061
                                    HHHHHHHHHHHHHHHSSSS-HHHHHHHHHHHTTTSCC CS
                Acetyltransf_11  30 eeeikalkkayrllyrsglsleealeeleeeaeespe 66 
                                    eee++++++a   l r++ +l+ +lee+ee+a+ s+e
  gi|119719648|ref|YP_920143.1| 437 EEELEEVRRALSELLRENVELRRRLEEAEERARRSEE 473
                                    6899************************887777666 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 2.4
                                    HHHHHHHHHHHTTTSCCHHHHHHHHHH-SS- CS
                Acetyltransf_11  50 leealeeleeeaeespevqelldFieaskRG 80 
                                    l+  leel+      p  ++l++F+e + RG
  gi|119719648|ref|YP_920143.1| 566 LRRVLEELK------PPGSHLIAFFEGAARG 590
                                    444455554......6689*******99999 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   7.8     0.001      0.85     195     318 ..     414     530 ..     395     587 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.001
                           FUSC 195 adilalealrsqaayesprirararalrrllsrmlallallsslarllarlraeeaaavpelaallaelaaleaaaaaea 274
                                    ++ +++   r  +  e ++ r+  + l + ++++ +ll+   +l+r+l++  ++ ++++++l+ ll++ +       a +
  gi|119719648|ref|YP_920143.1| 414 RRQVGVKIPRIELQKEAEEPRRVEEELEEVRRALSELLRENVELRRRLEEAEERARRSEEALRGLLRAREV------ARG 487
                                    55555666666777788999999999999999999999999999999999998888886556666655555......999 PP

                           FUSC 275 leaalaalrarlralrraleadadtaalllarlaellaelaqll 318
                                    le + a lrar++ l+++l+ ++ ++ +  +r++e l++++  +
  gi|119719648|ref|YP_920143.1| 488 LESEYAKLRARIELLQSELD-SFRRELAEKERALESLGDALLSY 530
                                    99999999999999999999.44444444444444444443333 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   2.1    0.0006      0.51      20      61 ..     433     474 ..     432     486 .. 0.87
   2 ?    1.1   0.1      0.46   3.9e+02      33      69 ..     491     527 ..     482     530 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0006
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCTXXXXXXX CS
                         DivIVA  20 edeVdeFLdqvakdyeallkeneelkekvkeleeklkeykel 61 
                                    +  V+e L++v + + +ll+en el+++++e+ee+  + +e+
  gi|119719648|ref|YP_920143.1| 433 PRRVEEELEEVRRALSELLRENVELRRRLEEAEERARRSEEA 474
                                    67899****************************998776655 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.46
                                    HHHHHHHHHHHHHHHHHCCCCTXXXXXXXXXXXXXXX CS
                         DivIVA  33 dyeallkeneelkekvkeleeklkeykeleetLkktl 69 
                                    +y +l  + e l+++++  +++l+e + + e+L ++l
  gi|119719648|ref|YP_920143.1| 491 EYAKLRARIELLQSELDSFRRELAEKERALESLGDAL 527
                                    5666666666677777777777777777777776666 PP

>> AATF-Che1  Apoptosis antagonizing transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   3.6    0.0031       2.7      44     133 ..     430     514 ..     418     530 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0031
                      AATF-Che1  44 flesseefeealeeaekalkklleslleLreelleqne..ikklaeskeeeekkkskrkrkkkkkeetsleelwkelekl 121
                                      e+   +ee+lee++ al++ll++ +eLr  l e+ e   +      +ee+  +  r r+  +  e ++++l  ++e l
  gi|119719648|ref|YP_920143.1| 430 A-EEPRRVEEELEEVRRALSELLRENVELRRRL-EEAEerAR-----RSEEALRGLLRAREVARGLESEYAKLRARIELL 502
                                    3.3467899************************.33331222.....222455566666666677777777777788888 PP

                      AATF-Che1 122 ekalkpfrnatl 133
                                    +++l++fr++  
  gi|119719648|ref|YP_920143.1| 503 QSELDSFRRELA 514
                                    888888887654 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8  15.9    0.0041       3.5      61     160 ..     428     527 ..     357     531 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0041
                          ATG16  61 keasasqsnskqsakiqsleqklaqlreelaelyksrgelaqrllelneelqkl...eeklkedeerlaeleaeraalet 137
                                    kea++     + ++++++   +l++l  e  el ++ +e ++r ++ +e+l+ l   +e ++  e++ a+l+a+++ l+ 
  gi|119719648|ref|YP_920143.1| 428 KEAEEP---RRVEEELEEVRRALSELLRENVELRRRLEEAEERARRSEEALRGLlraREVARGLESEYAKLRARIELLQS 504
                                    222222...23444444445555555555555555555555555555555443222144566678889999999999999 PP

                          ATG16 138 klkdreeelrekeklvqdlqDEl 160
                                    +l++ + el+eke++++ l D+l
  gi|119719648|ref|YP_920143.1| 505 ELDSFRRELAEKERALESLGDAL 527
                                    99999999999999999999887 PP

>> DUF641  Plant protein of unknown function (DUF641)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   7.0    0.0047         4      37     125 ..     438     523 ..     418     525 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0047
                         DUF641  37 ekiqaADkavvseLkklselkrlyrkkqkkkaseaeeseleaeiqeqrsllktyeitvkkleaelkakdseieeLkekLe 116
                                    e++++  +a+ + L++  el+r+  + ++      +++e  + + + r++ + +e    kl+a ++  +se+++ +++L+
  gi|119719648|ref|YP_920143.1| 438 EELEEVRRALSELLRENVELRRRLEEAEERA---RRSEEALRGLLRAREVARGLESEYAKLRARIELLQSELDSFRRELA 514
                                    4555556666667788888888888876544...3456666667778********************************* PP

                         DUF641 117 eaeksnkkl 125
                                    e e++ ++l
  gi|119719648|ref|YP_920143.1| 515 EKERALESL 523
                                    *99987765 PP

>> UPF0449  Uncharacterised protein family UPF0449
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   2.0      0.01       8.7      24      89 ..     411     476 ..     406     484 .. 0.82
   2 ?    5.1   0.4     0.035        30      57      95 ..     488     527 ..     479     531 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.01
                        UPF0449  24 napedDvvftilsdsveedkkassseeedleaeveelYeqvrtylelnerLeeakeeLkqkceeLk 89 
                                    +a    v ++i   + +++++++ + ee+le+ +  l e +r+++el +rLeea+e+ ++ +e L+
  gi|119719648|ref|YP_920143.1| 411 EALRRQVGVKIPRIELQKEAEEPRRVEEELEEVRRALSELLRENVELRRRLEEAEERARRSEEALR 476
                                    55555566666666667788888888888888899999999*******************999997 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.035
                        UPF0449  57 veelYeqvrtylel.nerLeeakeeLkqkceeLktageeL 95 
                                     e+ Y ++r+ +el + +L + + eL +k+  L+++g+ L
  gi|119719648|ref|YP_920143.1| 488 LESEYAKLRARIELlQSELDSFRRELAEKERALESLGDAL 527
                                    788999999999963679*****************99987 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8  10.7    0.0045       3.8      48     129 ..     432     513 ..     423     525 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0045
                            GAS  48 elseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrfekvekerdelyk 127
                                    e   +++e ++ +  L ++ +e+ eLr++l++ e+   + +++ + l ++ +  + l+ e+  l+ r+e +++e d +++
  gi|119719648|ref|YP_920143.1| 432 EPRRVEEELEEVRRALSELLRENVELRRRLEEAEERARRSEEALRGLLRAREVARGLESEYAKLRARIELLQSELDSFRR 511
                                    44567788888888888888888888888888888888888888888888888888888888888888888888887766 PP

                            GAS 128 kf 129
                                    + 
  gi|119719648|ref|YP_920143.1| 512 EL 513
                                    54 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   9.2     0.003       2.5     196     281 ..     421     505 ..     403     509 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.003
                           Spc7 196 idkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlkeev 275
                                    i + eL++  ee +++++e+ee ++ l+el ++  el+ ++ee++e+ ++ ee+++   r +e  +g + se  +l+++ 
  gi|119719648|ref|YP_920143.1| 421 IPRIELQKEAEEPRRVEEELEEVRRALSELLRENVELRRRLEEAEERARRSEEALRGLLRAREVARGLE-SEYAKLRARI 499
                                    667788999999999999999999999999999999999999999999999999999999999999975.6888999999 PP

                           Spc7 276 kaleel 281
                                    + l+++
  gi|119719648|ref|YP_920143.1| 500 ELLQSE 505
                                    998876 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       2.8   2.4e+03      53      70 ..     167     184 ..     166     185 .. 0.88
   2 ?    0.7   2.6      0.57   4.9e+02      66      97 ..     435     466 ..     423     481 .. 0.61
   3 ?    7.5   0.0    0.0044       3.8       6      39 ..     491     524 ..     484     534 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2.8
                                    TEEEEE-HHHHHHHHHHH CS
                    Prefoldin_2  53 dvlvkqdkeevkeeLeer 70 
                                    +vlvk+++ e+ e L+ +
  gi|119719648|ref|YP_920143.1| 167 EVLVKRKVREIAEALQRK 184
                                    599********9999875 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.57
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    Prefoldin_2  66 eLeerketlekeiktlekqleklekeleelke 97 
                                    ++ee++e++   +++l ++  +l+++lee +e
  gi|119719648|ref|YP_920143.1| 435 RVEEELEEVRRALSELLRENVELRRRLEEAEE 466
                                    45555555555555555555555555555554 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0044
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    Prefoldin_2   6 kfqqlqqqlqqlaqqikqletqlkelelvleele 39 
                                    ++++l+++++ l++++++ +++l e e +le l 
  gi|119719648|ref|YP_920143.1| 491 EYAKLRARIELLQSELDSFRRELAEKERALESLG 524
                                    6888999999999999999999999998888775 PP

>> OEP  Outer membrane efflux protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6  12.9      0.03        26      96     186 ..     433     523 ..     423     524 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.03
                            OEP  96 eaqleqarqqlrlevaqaylqlllakeqlelaeealklaekalelaearykaGlislldvlqaqvrllqaraelaeaeqq 175
                                      + e+ ++++r ++++++ + + ++++le aee ++++e+al++  ++ ++ +  +++++  ++r   +++el +++++
  gi|119719648|ref|YP_920143.1| 433 PRRVEEELEEVRRALSELLRENVELRRRLEEAEERARRSEEALRGLLRAREVARGLESEYAKLRARIELLQSELDSFRRE 512
                                    5677899999***********************************************99********************* PP

                            OEP 176 lqlaraqLeyl 186
                                    l+  + +Le l
  gi|119719648|ref|YP_920143.1| 513 LAEKERALESL 523
                                    **999999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (662 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1279  (0.0713369); expected 358.6 (0.02)
Passed bias filter:                      849  (0.0473534); expected 358.6 (0.02)
Passed Vit filter:                       147  (0.00819901); expected 17.9 (0.001)
Passed Fwd filter:                        34  (0.00189637); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.91u 0.33s 00:00:01.24 Elapsed: 00:00:00.47
# Mc/sec: 4213.06
//
Query:       gi|119719649|ref|YP_920144.1|  [L=301]
Description: protein of unknown function RIO1 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-46  158.6   0.0    1.8e-46  158.1   0.0    1.1  1  RIO1            RIO1 family
    3.1e-20   72.2   0.3    5.2e-20   71.5   0.3    1.4  1  Rio2_N          Rio2, N-terminal
    4.5e-08   33.3   0.1     0.0028   17.6   0.0    2.9  2  APH             Phosphotransferase enzyme family
     0.0019   17.6   0.0        1.6    8.0   0.0    2.2  2  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family
     0.0035   17.0   0.0     0.0081   15.8   0.0    1.6  1  HrcA_DNA-bdg    Winged helix-turn-helix transcription repress
  ------ inclusion threshold ------
      0.024   15.0   0.0      0.053   13.9   0.0    1.6  1  Rrf2            Transcriptional regulator
       0.18   11.1   0.0         14    4.9   0.0    2.1  2  Pkinase         Protein kinase domain
       0.27   10.0   0.0       0.36    9.6   0.0    1.1  1  Pkinase_fungal  Fungal protein kinase


Domain annotation for each model (and alignments):
>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.1   0.0     8e-50   1.8e-46       2     181 ..     110     280 ..     109     287 .. 0.96

  Alignments for each domain:
  == domain 1  score: 158.1 bits;  conditional E-value: 8e-50
                                    EEEEEETTTEEEEEEEE-S---SS-HHHHCTTTSTTSTCG--GS-HHHHHHHHHHHHHHHHHHHHHTT--S--EEEEETT CS
                           RIO1   2 VyhavsedgkevaiKiyktstteFkkrkkyvsgekrfkdrksktnprklvklwaekEfrnLkrleeagvpvPkpielkrh 81 
                                    Vy + +  g+ va+K+++ ++t+F+k k+ + + ++    k + ++++ ++l+a+ Ef++L+ l + gv+vP+p++++rh
  gi|119719649|ref|YP_920144.1| 110 VYLGKTPGGRVVAVKFHRAGRTSFRKTKRVRGYAAD----KRHVSWLYQARLAAKSEFEALRILWKGGVSVPEPVDWNRH 185
                                    8999999999***********************999....6799************************************ PP

                                    EEEEE--EETTEEGGBHHHCG-HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETT.EEEE--GTTEEETTSTTH CS
                           RIO1  82 vlvmefigedgvaapklkdveeeeeaeelyeevleemrklykeaglvHaDLSeyNvlvded.kvviIDvsQaveldhpna 160
                                    v+v  +++  gv++++l ++    + e  ++  + e+ k+y eag+vH+DLSeyNvlv e+ k+v+ID++Q v+ +hp+a
  gi|119719649|ref|YP_920144.1| 186 VVVAGYVE--GVELYTLPELG---DPEGFLAAAVGEVGKAY-EAGVVHGDLSEYNVLVAEGeKPVLIDWPQWVPSSHPSA 259
                                    ********..***********...8999*************.*******************9****************** PP

                                    HHHHHHHHHHHHHHHHTTC-- CS
                           RIO1 161 lefLerDveniikfFrrkgve 181
                                      +L+rD+e ++ fF+rk+  
  gi|119719649|ref|YP_920144.1| 260 GFYLRRDLERLASFFSRKYGV 280
                                    ****************99764 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.5   0.3   2.3e-23   5.2e-20       2      82 .]      11      91 ..      10      91 .. 0.97

  Alignments for each domain:
  == domain 1  score: 71.5 bits;  conditional E-value: 2.3e-23
                         Rio2_N  2 ryLskedfrvLtavEmgmrnhevVptelieeisrlkeeevkkrlsrllkaklisrktakydGYkLtyeGyDyLALktlvkr 82
                                   + L  +d+r+L avE gm nhe+V +el+++is+l+++   +rl+rl   +l++r   +++GY Lt  GyD+LAL  lvkr
  gi|119719649|ref|YP_920144.1| 11 KVLRLDDYRLLVAVERGMINHEYVDVELVASISGLDADYAAERLKRLNGLGLVQRYRGPFTGYILTTRGYDALALYVLVKR 91
                                   678899*************************************************999********************998 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.1   4.4e-05     0.099       6      99 ..     103     211 ..      99     222 .. 0.64
   2 !   17.6   0.0   1.3e-06    0.0028     164     193 ..     221     248 ..     210     255 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.4e-05
                                    --.SSCEEEEEEETT--EE.EEE.......................E-TT...S-HHHHHHHHHHHHHHHHTT-B--B-C CS
                            APH   6 sggasnrtylvttpagryv.lrr.......................nppa...raaeeirrevallrlLakagvpvPevl 58 
                                    + g ++ +yl +tp+gr+v +++                       +  +   +a   + +e++ lr L k gv+vPe++
  gi|119719649|ref|YP_920144.1| 103 GEGKESEVYLGKTPGGRVVaVKFhragrtsfrktkrvrgyaadkrhV--SwlyQARLAAKSEFEALRILWKGGVSVPEPV 180
                                    56778888888888854443788666666666666666666554330..233335566677777**************** PP

                                    TTBS-EEETTEEEEEEE----EE-SSHHHHHHHHHHHHHHH CS
                            APH  59 agdtddeeigllfalieyvpgrsllrklsaaqlpellealg 99 
                                    ++      ++ ++++  yv+g  l++    ++l++  + l+
  gi|119719649|ref|YP_920144.1| 181 DW------NR-HVVVAGYVEGVELYT---LPELGDPEGFLA 211
                                    94......33.466666677766666...445555444444 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 1.3e-06
                                    S-EEEE-SS-SGGGEEEC..TTEEEEE--- CS
                            APH 164 lptvllHgDlhpgNllvdpddgrvtGviDf 193
                                     +++++HgDl+  N+lv +++ +v  +iD+
  gi|119719649|ref|YP_920144.1| 221 YEAGVVHGDLSEYNVLVAEGEKPV--LIDW 248
                                    67899*************999**9..**** PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0   0.00073       1.6      39      80 ..     140     181 ..     108     191 .. 0.71
   2 !    7.5   0.0     0.001       2.3     131     187 ..     217     271 ..     209     290 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00073
                            Kdo  39 gllgklskdlyrfk.lgrtravrEfrllkrLeeagvavpkpva 80 
                                    +  +   +  +++    r+ a  Ef++l+ L + gv vp+pv 
  gi|119719649|ref|YP_920144.1| 140 RGYAADKRH-VSWLyQARLAAKSEFEALRILWKGGVSVPEPVD 181
                                    334333344.55655789999********************96 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.001
                            Kdo 131 iaklhragvnHadlyaknillqqeeeeeaeiwliDldkarlrlr..adrwrekdLarLk 187
                                    + k  +agv H+dl   n+l+ ++e    + +liD  +  + +   a     +dL+rL 
  gi|119719649|ref|YP_920144.1| 217 VGKAYEAGVVHGDLSEYNVLVAEGE----KPVLIDWPQWVPSSHpsAGFYLRRDLERLA 271
                                    5667789****************99....999999877666555334556666666665 PP

>> HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor, HrcA DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   3.6e-06    0.0081      26      75 ..      36      85 ..      21      88 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.6e-06
                   HrcA_DNA-bdg 26 geeiAevlkrneGtvRNqlqsLkalgLvegvpGPkGGYkPtlkayealki 75
                                    e +A++ + +  +    l+ L  lgLv+   GP  GY+ t++ y+al +
  gi|119719649|ref|YP_920144.1| 36 VELVASISGLDADYAAERLKRLNGLGLVQRYRGPFTGYILTTRGYDALAL 85
                                   556666667777777788999*************************9975 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.4e-05     0.053      25      69 ..      33      77 ..      17      88 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.4e-05
                                   -B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT-TCEEESS CS
                           Rrf2 25 pvsseeiaerqnispsylekilakLrkaglvksvrGkgGGyrLak 69
                                    v +e +a+  ++ + y++  l++L+  glv+  rG+  Gy L+ 
  gi|119719649|ref|YP_920144.1| 33 YVDVELVASISGLDADYAAERLKRLNGLGLVQRYRGPFTGYILTT 77
                                   388999999*********************************975 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1     0.014        30       8      41 ..     103     135 ..      98     142 .. 0.83
   2 ?    4.9   0.0    0.0063        14     115     142 ..     221     248 ..     209     250 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.014
                                    EEESSEEEEEEEETTTTEEEEEEEEECHCHCHHH CS
                        Pkinase   8 GeGsfGkVykaveketgkivAvKkikkekakkkk 41 
                                    GeG+ ++Vy ++ +  g+ vAvK  +  +++ +k
  gi|119719649|ref|YP_920144.1| 103 GEGKESEVYLGK-TPGGRVVAVKFHRAGRTSFRK 135
                                    9***********.79********98877666555 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0063
                                    HHTTEE-SS-SGGGEEEETTTEEEE-SG CS
                        Pkinase 115 HskgiiHrDlKpeNiLidekgelKitDF 142
                                    +++g++H Dl   N+L+ e ++  ++D+
  gi|119719649|ref|YP_920144.1| 221 YEAGVVHGDLSEYNVLVAEGEKPVLIDW 248
                                    789***************8888888886 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00016      0.36     323     355 ..     221     247 ..     192     259 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00016
                 Pkinase_fungal 323 flkagiLHrDiSenNilitdskkegerkglLiD 355
                                    + +ag++H D Se+N+l+      +++k +LiD
  gi|119719649|ref|YP_920144.1| 221 Y-EAGVVHGDLSEYNVLVA-----EGEKPVLID 247
                                    5.89**************9.....455666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1957.99
//
Query:       gi|119719650|ref|YP_920145.1|  [L=238]
Description: metallophosphoesterase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.5e-13   50.2   0.0    5.8e-13   49.8   0.0    1.1  1  Metallophos     Calcineurin-like phosphoesterase
    4.1e-12   46.6   0.0    1.5e-10   41.5   0.0    2.0  1  Metallophos_2   Calcineurin-like phosphoesterase superfamily 
  ------ inclusion threshold ------
       0.12   12.2   0.1       0.22   11.4   0.1    1.4  1  Ribosomal_L21e  Ribosomal protein L21e


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.8   0.0   9.7e-17   5.8e-13       1     203 [.       1     198 [.       1     199 [. 0.73

  Alignments for each domain:
  == domain 1  score: 49.8 bits;  conditional E-value: 9.7e-17
                                    EEEEEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHH..TSEEEEEC-TTSCHH CS
                    Metallophos   1 lrilvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvky..pipvylllGNHegfe 78 
                                    +r+l ++D+H   ++ + + l++ l +l+ e ++ lvl+aGD+v rg++  + +   a l ++  ++p y + GN + fe
  gi|119719650|ref|YP_920145.1|   1 MRVLAFADTH---APKHVSLLAESLGRLRLE-GVELVLVAGDVVARGEWAACRQVE-AVLRRFlpGVPAYGTFGNED-FE 74 
                                    89********...999999999999999777.***************999955544.333333669***********.44 PP

                                    HHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTE.EEEEEEESECEEETHHHHHHHHHHHSCHHHHCC.......... CS
                    Metallophos  79 eellnkygylgifsepwrsdaevfnnlplaslgsgs.lkvlllhGgspellvsldklgslnleleapepg.......... 147
                                     e+  + +++ +        + +++   + + ++g+ ++++  +G              l+++++++e +          
  gi|119719650|ref|YP_920145.1|  75 -EVRGRIREECT-E------VVWLEDEAVDVEVGGTrVRIVGTPGV-------------LDRPTRWQERNvpgirgvyea 133
                                    .44444333332.3......44444455555556667888888888.............555555555555555556656 PP

                                    .....HHHHHHHHHHTTCSEEEEEESSESS....CSSSCSCCHHHHH....HHHHHTTESEEEEESSSS CS
                    Metallophos 148 .....dewlkdlekrekadwvivlgHsply....rgsgylfgdeale....dllkkygvdlvisGHtHv 203
                                          e+l++      +  +i+++H p+     rg  + f++e        +    gvdlv++GH H+
  gi|119719650|ref|YP_920145.1| 134 rlervRELLSH----PSGSLKILVTHYPPRcgtlRGEDPRFWEEMSSarlaGVVAGSGVDLVVHGHLHR 198
                                    65556888888....***************8888666666666555577779999999**********7 PP

>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5   0.0   2.6e-14   1.5e-10       1     135 [.       1     204 [.       1     228 [. 0.75

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 2.6e-14
                  Metallophos_2   1 MklaiiSDlH..snldaleavlealkevgvdaiihaGDl....eeeepevleellela....pvlaVrGNnD........ 62 
                                    M++++++D+H  +++++l++ l +l+ +gv+++++aGD+    e ++   +e++l+++    p +  +GN D        
  gi|119719650|ref|YP_920145.1|   1 MRVLAFADTHapKHVSLLAESLGRLRLEGVELVLVAGDVvargEWAACRQVEAVLRRFlpgvPAYGTFGNEDfeevrgri 80 
                                    9*************************************864332233346666666667888**********99999999 PP

                  Metallophos_2  63 ........................eevveedvlreaaelgtdl...............peeaelel.....agekvlliH 98 
                                                             +v    vl+++++++++                 e     l     +  k+l++H
  gi|119719650|ref|YP_920145.1|  81 reectevvwledeavdvevggtrvRIVGTPGVLDRPTRWQERNvpgirgvyearlervRE-----LlshpsGSLKILVTH 155
                                    899988888888888888887665333666777777777777788888766554432222.....1445668889***** PP

                  Metallophos_2  99 gdpl..............gvkdalaellkeaeegsdvvvcGHtHvpeveke 135
                                    + p                 +++la ++  a +g+d+vv+GH H+  v ++
  gi|119719650|ref|YP_920145.1| 156 YPPRcgtlrgedprfweeMSSARLAGVV--AGSGVDLVVHGHLHRSVVHRD 204
                                    *988*****9888776443444444444..569************988776 PP

>> Ribosomal_L21e  Ribosomal protein L21e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   3.6e-05      0.22      36      80 ..     184     227 ..     175     232 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.6e-05
                                    TT-EEEE---TT--SS---GGGTT-EEEE..EEEETTEEEEEEEE CS
                 Ribosomal_L21e  36 kGdkVdikidpsvqkgmphkryhGktgrvynvtkravgvivnkkv 80 
                                     G  Vd++++++ ++   h+ y G t  vynv+  av   v ++v
  gi|119719650|ref|YP_920145.1| 184 AGSGVDLVVHGHLHRSVVHRDYIGSTP-VYNVSLPAVKSAVIIEV 227
                                    5889**********************8.89**9988855555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1576.18
//
Query:       gi|119719651|ref|YP_920146.1|  [L=173]
Description: methyltransferase type 11 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-09   38.3   0.1    2.2e-09   37.9   0.1    1.2  1  Methyltransf_25  Methyltransferase domain
    2.6e-09   37.6   0.2    4.5e-09   36.8   0.2    1.4  1  Methyltransf_11  Methyltransferase domain
    0.00069   19.5   0.0     0.0017   18.2   0.0    1.6  1  Methyltransf_23  Methyltransferase domain
     0.0011   19.7   0.0     0.0014   19.3   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
     0.0041   16.9   0.0     0.0054   16.5   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
  ------ inclusion threshold ------
      0.024   14.4   0.0      0.032   14.0   0.0    1.2  1  MoeA_N           MoeA N-terminal region (domain I and II)


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   0.1   7.5e-13   2.2e-09       1      76 [.      46     114 ..      46     130 .. 0.87

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 7.5e-13
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGG CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhh 76 
                                    vLd+GcGtG l++ l    g + ++++D s +mle  r+r    ++ ++ vq+d++  pf +  fD v ++ a+h 
  gi|119719651|ref|YP_920146.1|  46 VLDAGCGTGILSEFLG---G-SYYVCLDSSRGMLEVFRARR---RCFCDAVQADMQLPPFRELAFDGVACVTAVHE 114
                                    9************997...3.77***************999...589***********************877664 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.8   0.2   1.5e-12   4.5e-09       1      95 [.      47     133 ..      47     134 .. 0.88

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 1.5e-12
                                    EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHHHH CS
                Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedpeka 80 
                                    Ld+GcGtG+l+e l   g+ +v++D s  ml++ +++ +     ++ v+ad++  pf++  fD v +  ++h       a
  gi|119719651|ref|YP_920146.1|  47 LDAGCGTGILSEFLG--GSYYVCLDSSRGMLEVFRARRRCF---CDAVQADMQLPPFRELAFDGVACVTAVHEA---PGA 118
                                    8**************..999************998777765...889******779***********9998877...478 PP

                                    HHHHHHHEEEEEEEE CS
                Methyltransf_11  81 lkeiaRvLkpgGllv 95 
                                    l  +a ++k +G+lv
  gi|119719651|ref|YP_920146.1| 119 LGVLAGLVKAEGVLV 133
                                    888888888888877 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   5.7e-07    0.0017       7     119 ..      28     136 ..      20     152 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 5.7e-07
                Methyltransf_23   7 eelsdklerllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae..kakkaqkdqfdeqeaaepqgkfd 84 
                                    e+++++l+  ++ l+    vLd GcGtGil+e l      ++  D s+ + e  +   + +   +q+d q  ++ +  fd
  gi|119719651|ref|YP_920146.1|  28 EQYKKNLAASSA-LKGLPVVLDAGCGTGILSEFLGGS--YYVCLDSSRGMLEVFRarRRCFCDAVQADMQLPPFRELAFD 104
                                    555566665444.777789***********9988333..45666776666655444455555666666666666777888 PP

                Methyltransf_23  85 lIvlrevlehvpdppellrqiatllkpgGylllse 119
                                     + +      v+  p +l  +a l+k +G+l++s+
  gi|119719651|ref|YP_920146.1| 105 GVACVT---AVHEAPGALGVLAGLVKAEGVLVVSV 136
                                    776654...45666677777777777777777776 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   4.7e-07    0.0014       1      82 [.      47     118 ..      47     144 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 4.7e-07
                Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlk 80 
                                    L+ GcGtG l++ l  +     y+++D s+ ++    e +++r++ +++ v+ + +    ++   +fD v +  ++h  +
  gi|119719651|ref|YP_920146.1|  47 LDAGCGTGILSEFLGGS----YYVCLDSSRGML----EVFRARRRCFCDAVQADMQLPPFREL--AFDGVACVTAVHEAP 116
                                    89**********99877....999*********....66666666666666666555555555..999999998888754 PP

                Methyltransf_12  81 di 82 
                                      
  gi|119719651|ref|YP_920146.1| 117 GA 118
                                    33 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.8e-06    0.0054       6     109 ..      45     134 ..      40     145 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.8e-06
                Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnevln 85 
                                    +vlD+GCGtG l+  l      ++ +v +D s  ++e+ r+++++     +   q+d++  +  + +  fD + +   + 
  gi|119719651|ref|YP_920146.1|  45 VVLDAGCGTGILSEFLG-----GSYYVCLDSSRGMLEVFRARRRC----FCDAVQADMQLPP--FRELAFDGVAC---VT 110
                                    79********9999999.....677***************99884....5778999999988..88899999999...45 PP

                Methyltransf_31  86 aladpdkileeiervlkpggilli 109
                                    a+ + + +l+ +  ++k +g+l++
  gi|119719651|ref|YP_920146.1| 111 AVHEAPGALGVLAGLVKAEGVLVV 134
                                    666666667766777777777776 PP

>> MoeA_N  MoeA N-terminal region (domain I and II)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.1e-05     0.032      23      63 ..      77     115 ..      64     144 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.1e-05
                                    GGCG-TT-BBSS-EE-SS-BSSS-EESSSEEEEEEBTTB-- CS
                         MoeA_N  23 laaealgrvlaedvvApedvPpfdnSamDGYAvraeagsga 63 
                                    +  +a  r  ++ v+A++++Ppf+  a DG A  ++a ++a
  gi|119719651|ref|YP_920146.1|  77 V-FRARRRCFCDAVQADMQLPPFRELAFDGVAC-VTAVHEA 115
                                    4.567789999*********************8.4444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       256  (0.0142785); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1235.78
//
Query:       gi|119719652|ref|YP_920147.1|  [L=1711]
Description: hypothetical protein Tpen_0742 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.8e-11   42.3  43.1    3.6e-07   30.3   3.6   10.0 11  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
    0.00014   22.4   3.6       0.25   11.7   0.0    5.4  5  DUF4198          Domain of unknown function (DUF4198)
    0.00021   21.2   6.0       0.06   13.4   0.3    4.5  4  CarbopepD_reg_2  CarboxypepD_reg-like domain
    0.00027   20.9  47.3       0.25   11.4   1.2   11.4 11  Big_1            Bacterial Ig-like domain (group 1)
  ------ inclusion threshold ------
      0.035   14.0   4.9       0.19   11.6   0.1    3.8  4  DUF4493          Domain of unknown function (DUF4493)
      0.051   13.9   4.4         54    4.2   0.3    5.2  4  Big_3            Bacterial Ig-like domain (group 3)
       0.12   12.5   0.1        2.2    8.5   0.0    2.9  2  Peptidase_M60_C  Peptidase M60 C-terminal domain
       0.64    9.9   3.4        2.5    8.0   0.2    3.5  3  PEGA             PEGA domain
        3.6    8.0  26.1       0.28   11.5   0.2    6.8  8  SpaA             Prealbumin-like fold domain


Domain annotation for each model (and alignments):
>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1       0.3     6e+02       9      48 ..      39      83 ..      35      95 .. 0.76
   2 ?   -2.6   0.0       3.5   7.1e+03      29      43 ..     396     410 ..     386     427 .. 0.72
   3 ?   -0.7   0.0      0.89   1.8e+03      12      39 ..     431     456 ..     424     461 .. 0.83
   4 ?   -1.6   0.1       1.7   3.4e+03      12      46 ..     663     700 ..     660     715 .. 0.65
   5 ?   -0.4   1.0      0.72   1.4e+03      18      36 ..     898     916 ..     895     917 .. 0.92
   6 ?   -0.3   0.1      0.66   1.3e+03      27      72 ..    1006    1049 ..     970    1057 .. 0.63
   7 ?   -0.3   0.3      0.67   1.3e+03      17      43 ..    1164    1192 ..    1154    1200 .. 0.67
   8 ?    4.1   0.0     0.027        55       2      51 ..    1278    1332 ..    1277    1342 .. 0.74
   9 !    6.1   0.1    0.0065        13      42      74 ..    1454    1486 ..    1452    1497 .. 0.84
  10 !   20.5   0.4   2.1e-07   0.00043       7      54 ..    1507    1553 ..    1502    1575 .. 0.88
  11 !   30.3   3.6   1.8e-10   3.6e-07       2      81 ..    1583    1654 ..    1582    1655 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.3
                CarboxypepD_reg  9 asgapiagatVtvtn.adtg....tvastttdadGafrlrglppg 48
                                   ++g+p a+ +V++   ++tg    + a  ttd++G+ +l+  +pg
  gi|119719652|ref|YP_920147.1| 39 PNGQPFANQQVIIVYfNETGncilAYAIGTTDSTGKITLTIAQPG 83
                                   689999999999865355554553345569999999999887775 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.5
                CarboxypepD_reg  29 vastttdadGafrlr 43 
                                    +  t t+++G ++ +
  gi|119719652|ref|YP_920147.1| 396 TPFTLTGSNGVYTAT 410
                                    556899999999976 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.89
                CarboxypepD_reg  12 apiagatVtvtnadtgtvastttdadGa 39 
                                    +p+ ga V ++  +     +t tda+G+
  gi|119719652|ref|YP_920147.1| 431 QPLQGAIVQIS--PLVGDPNTYTDANGN 456
                                    69999999999..55567899*****97 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 1.7
                CarboxypepD_reg  12 apiagatVtvtnadtgt...vastttdadGafrlrglp 46 
                                    +p+ +++V ++    g+     s +t+ dG+ +++ +p
  gi|119719652|ref|YP_920147.1| 663 EPLVNVSVLLEYFKAGArtyYESHVTGCDGTVTFTKVP 700
                                    68888888887633332111456688888888888776 PP

  == domain 5  score: -0.4 bits;  conditional E-value: 0.72
                CarboxypepD_reg  18 tVtvtnadtgtvastttda 36 
                                    tV+++n+ tg+++++ td+
  gi|119719652|ref|YP_920147.1| 898 TVVLFNETTGATRTVETDK 916
                                    8****************95 PP

  == domain 6  score: -0.3 bits;  conditional E-value: 0.66
                CarboxypepD_reg   27 gtvastttdadGafrlrglppgtysvtvsapGyatatreevtltag 72  
                                      +  s++t++dG+ +l+ ++  + +++     +  +  ++vt+ ag
  gi|119719652|ref|YP_920147.1| 1006 AVAWSAVTGSDGKASLP-VAIWQPKLKLANVKFGASI-TNVTVLAG 1049
                                     36789999999999887.6666666666666666555.45666665 PP

  == domain 7  score: -0.3 bits;  conditional E-value: 0.67
                CarboxypepD_reg   17 atVtvtnadtgtv..astttdadGafrlr 43  
                                     +tVtv  a++ +   as+ t++dG+ +++
  gi|119719652|ref|YP_920147.1| 1164 VTVTVLGASGASAafASAATGSDGTVTIS 1192
                                     56666644333223488999999998875 PP

  == domain 8  score: 4.1 bits;  conditional E-value: 0.027
                CarboxypepD_reg    2 isGrVtdasgapiagatVtvtnadtgt....vastttdadGafrlrglpp..gtys 51  
                                     i+ +V d sg+p++++ V++   +  +    ++   t+++G+  l  +pp  ++y+
  gi|119719652|ref|YP_920147.1| 1278 IKVTVFDWSGKPLKNMMVAAILREPRAkaipSTAGFTAENGSVILY-VPPgtQKYQ 1332
                                     8899***************875443322333577799999999985.999444455 PP

  == domain 9  score: 6.1 bits;  conditional E-value: 0.0065
                CarboxypepD_reg   42 lrglppgtysvtvsapGyatatreevtltagqt 74  
                                     +++ p g y+vtv  +G  t +++++ +++g+ 
  gi|119719652|ref|YP_920147.1| 1454 ISQAPLGAYKVTVNLAGVGTLAVQTIKIEKGRF 1486
                                     566677**********************99974 PP

  == domain 10  score: 20.5 bits;  conditional E-value: 2.1e-07
                CarboxypepD_reg    7 tdasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtv 54  
                                     t++ g+p+agatVt+t +++gt+ +   d++G+ +++ +ppg+ + tv
  gi|119719652|ref|YP_920147.1| 1507 TSPFGTPLAGATVTIT-KPDGTSITDSLDSSGSITVKEVPPGNLQYTV 1553
                                     7789************.6999999*******************99999 PP

  == domain 11  score: 30.3 bits;  conditional E-value: 1.8e-10
                CarboxypepD_reg    2 isGrVtdasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatreevtltagqtttldi 79  
                                     ++ +V  a g++i+gatV+++      v + ttda+G  +l+ lp gty vt+s+ G   ++    t+++g++t  ++
  gi|119719652|ref|YP_920147.1| 1583 LTVKVLGARGQGIEGATVAIE-----NVGTFTTDASGIVSLE-LPSGTYAVTASKGGRTASAT--ATVSDGKETVTEL 1652
                                     5779999**************.....59*************7.**********9999887774..7999999887777 PP

                CarboxypepD_reg   80 tL 81  
                                     +L
  gi|119719652|ref|YP_920147.1| 1653 KL 1654
                                     66 PP

>> DUF4198  Domain of unknown function (DUF4198)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   0.00012      0.25     158     203 ..      38      83 ..      22      84 .. 0.84
   2 ?    1.6   0.1      0.15   3.1e+02     163     201 ..    1158    1195 ..    1157    1197 .. 0.76
   3 ?   -0.7   0.0      0.79   1.6e+03     151     197 ..    1276    1322 ..    1272    1328 .. 0.70
   4 ?   -1.1   0.0         1     2e+03     161     175 ..    1511    1525 ..    1487    1554 .. 0.62
   5 ?    3.6   0.1     0.038        77     153     209 ..    1583    1629 ..    1578    1631 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00012
                        DUF4198 158 lldGkPlagaeveveyggtryrdapdeikv.ktdadGvvtftlpkaG 203
                                    l +G+P a+ +v ++y ++   +   ++ + +td+ G++t+t+ ++G
  gi|119719652|ref|YP_920147.1|  38 LPNGQPFANQQVIIVYFNE-TGNCILAYAIgTTDSTGKITLTIAQPG 83 
                                    569************9885.45555555559**************99 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.15
                        DUF4198  163 Plagaeveveyggtryrdapdeikv..ktdadGvvtftlpk 201 
                                     Pla+  v+v+  g++   a+   ++   t++dG vt+ ++k
  gi|119719652|ref|YP_920147.1| 1158 PLANQPVTVTVLGASGASAA---FAsaATGSDGTVTISPDK 1195
                                     99*********997333332...33359*********9986 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.79
                        DUF4198  151 eelevqvl.ldGkPlagaeveveyggtryrdapdeikv.ktdadGvvtf 197 
                                     ++++v+v+   GkPl++  v ++ ++ r +  p +  +  t ++G v +
  gi|119719652|ref|YP_920147.1| 1276 DAIKVTVFdWSGKPLKNMMVAAILREPRAKAIPST--AgFTAENGSVIL 1322
                                     67788888899**********99876433333332..347777777765 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 1
                        DUF4198  161 GkPlagaeveveygg 175 
                                     G Plaga+v++++ +
  gi|119719652|ref|YP_920147.1| 1511 GTPLAGATVTITKPD 1525
                                     667777777766432 PP

  == domain 5  score: 3.6 bits;  conditional E-value: 0.038
                        DUF4198  153 levqvl.ldGkPlagaeveveyggtryrdapdeikvktdadGvvtftlpkaGlwllea 209 
                                     l+v+vl  +G+  +ga+v +e  g           ++tda G+v++ lp +G++ ++a
  gi|119719652|ref|YP_920147.1| 1583 LTVKVLgARGQGIEGATVAIENVG----------TFTTDASGIVSLELP-SGTYAVTA 1629
                                     556666666666666666665443..........359***********9.68887776 PP

>> CarbopepD_reg_2  CarboxypepD_reg-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.083   1.6e+02      12      37 ..     431     458 ..     425     463 .. 0.83
   2 ?   -2.4   0.0       2.4   4.8e+03      38      67 ..    1454    1484 ..    1453    1493 .. 0.68
   3 ?    4.6   0.1     0.016        32      11      47 ..    1511    1550 ..    1506    1555 .. 0.74
   4 !   13.4   0.3     3e-05      0.06      10      73 ..    1591    1651 ..    1586    1657 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.083
                CarbopepD_reg_2  12 eplpgatVyvkgt..kkgtvTdenGnFe 37 
                                    +pl ga V++       +t+Td+nGn  
  gi|119719652|ref|YP_920147.1| 431 QPLQGAIVQISPLvgDPNTYTDANGNVA 458
                                    79999999998863379********955 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.4
                CarbopepD_reg_2   38 lknlpagkytLvvsyvGykt.qekkvtvske 67  
                                     +++ p g y+++v+  G  t + ++++++k+
  gi|119719652|ref|YP_920147.1| 1454 ISQAPLGAYKVTVNLAGVGTlAVQTIKIEKG 1484
                                     6677888899999998888844456666554 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.016
                CarbopepD_reg_2   11 keplpgatVyvkgtkkgtvT...denGnFelknlpagkyt 47  
                                     ++pl+gatV++++     +T   d++G+ ++k++p+g+ +
  gi|119719652|ref|YP_920147.1| 1511 GTPLAGATVTITKPDGTSITdslDSSGSITVKEVPPGNLQ 1550
                                     57*********88666666622267999999999999754 PP

  == domain 4  score: 13.4 bits;  conditional E-value: 3e-05
                CarbopepD_reg_2   10 tkeplpgatVyvkgtkkgtvTdenGnFelknlpagkytLvvsyvGyktqekkvtvskektldvn 73  
                                      ++ ++gatV +++ ++  +Td++G  +l+ lp+g+y +++s  G +t++ + tvs++k++ ++
  gi|119719652|ref|YP_920147.1| 1591 RGQGIEGATVAIENVGT-FTTDASGIVSLE-LPSGTYAVTASKGG-RTASATATVSDGKETVTE 1651
                                     4689********87665.569********6.*******9999866.555788999877665544 PP

>> Big_1  Bacterial Ig-like domain (group 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.1    0.0027       5.4      17      52 ..      40      79 ..      39      82 .. 0.86
   2 ?    0.4   0.8      0.34   6.7e+02       4      15 ..     254     265 ..     246     275 .. 0.86
   3 ?    0.2   0.0      0.38   7.5e+02       2      23 ..     287     308 ..     287     332 .. 0.90
   4 ?    1.7   1.8      0.14   2.7e+02      36      53 ..     388     412 ..     378     421 .. 0.73
   5 ?   -2.2   0.0       2.1   4.2e+03      39      47 ..     448     456 ..     435     458 .. 0.72
   6 ?   -3.5   0.0       5.3   1.1e+04      20      51 ..     664     697 ..     663     697 .. 0.68
   7 ?   -0.2   0.1      0.52     1e+03      37      50 ..    1008    1021 ..     996    1024 .. 0.79
   8 !   11.4   1.2   0.00013      0.25      19      50 ..    1157    1191 ..    1153    1193 .. 0.86
   9 ?    3.9   0.0     0.026        52       9      48 ..    1278    1320 ..    1276    1324 .. 0.83
  10 !   10.5   0.3   0.00024      0.48       8      50 ..    1501    1541 ..    1497    1542 .. 0.79
  11 ?    4.8   4.4     0.014        28       8      63 ..    1582    1628 ..    1581    1650 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0027
                          Big_1 17 ngnpvagatVtfsvsg..gals..assgtTdanGkatvtl 52
                                   ng+p a+++V +   +  g+ +   + gtTd+ Gk+t t+
  gi|119719652|ref|YP_920147.1| 40 NGQPFANQQVIIVYFNetGNCIlaYAIGTTDSTGKITLTI 79
                                   89********9999885555558999***********998 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.34
                          Big_1   4 vdtntltatvkD 15 
                                    ++t tltatvkD
  gi|119719652|ref|YP_920147.1| 254 SATDTLTATVKD 265
                                    578899999999 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.38
                          Big_1   2 dGvdtntltatvkDangnpvag 23 
                                    d+  t  l++ vkD  gn +++
  gi|119719652|ref|YP_920147.1| 287 DNAHTFLLQVAVKDICGNSLNN 308
                                    6778999***********9987 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.14
                          Big_1  36 s.......assgtTdanGkatvtlt 53 
                                    +       ++ + T++nG++t+t++
  gi|119719652|ref|YP_920147.1| 388 TytkpvsfTPFTLTGSNGVYTATIK 412
                                    3334444588899**********97 PP

  == domain 5  score: -2.2 bits;  conditional E-value: 2.1
                          Big_1  39 sgtTdanGk 47 
                                    ++ TdanG+
  gi|119719652|ref|YP_920147.1| 448 NTYTDANGN 456
                                    556666665 PP

  == domain 6  score: -3.5 bits;  conditional E-value: 5.3
                          Big_1  20 pvagatVtfsvsg.gals.assgtTdanGkatvt 51 
                                    p+ +++V ++  + ga +   s +T+ +G++t+t
  gi|119719652|ref|YP_920147.1| 664 PLVNVSVLLEYFKaGARTyYESHVTGCDGTVTFT 697
                                    5566666666656555555778899999999987 PP

  == domain 7  score: -0.2 bits;  conditional E-value: 0.52
                          Big_1   37 assgtTdanGkatv 50  
                                     a s++T+++Gka+ 
  gi|119719652|ref|YP_920147.1| 1008 AWSAVTGSDGKASL 1021
                                     6689********86 PP

  == domain 8  score: 11.4 bits;  conditional E-value: 0.00013
                          Big_1   19 npvagatVtfsvsg..gals.assgtTdanGkatv 50  
                                      p+a+++Vt++v g  ga +  +s+ T+++G++t+
  gi|119719652|ref|YP_920147.1| 1157 VPLANQPVTVTVLGasGASAaFASAATGSDGTVTI 1191
                                     59************8655558************98 PP

  == domain 9  score: 3.9 bits;  conditional E-value: 0.026
                          Big_1    9 ltatvkDangnpvagatVtfsvsg..gals.assgtTdanGka 48  
                                     +++tv D +g+p+++  V        ++++ ++ g T +nG +
  gi|119719652|ref|YP_920147.1| 1278 IKVTVFDWSGKPLKNMMVAAILREprAKAIpSTAGFTAENGSV 1320
                                     79****************9988887555558888999999876 PP

  == domain 10  score: 10.5 bits;  conditional E-value: 0.00024
                          Big_1    8 tltatvkDangnpvagatVtfsvsggalsassgtTdanGkatv 50  
                                      ++ t +  +g+p+agatVt++ ++g+ +  +   d++G +tv
  gi|119719652|ref|YP_920147.1| 1501 DVKLTFTSPFGTPLAGATVTITKPDGTSI--TDSLDSSGSITV 1541
                                     678899999****************8885..455566666665 PP

  == domain 11  score: 4.8 bits;  conditional E-value: 0.014
                          Big_1    8 tltatvkDangnpvagatVtfsvsg.galsassgtTdanGkatvtltstkagtvtvt 63  
                                     +lt+ v  a g+ ++gatV ++  + g     + tTda+G+++ +l s   gt+ vt
  gi|119719652|ref|YP_920147.1| 1582 KLTVKVLGARGQGIEGATVAIE--NvG-----TFTTDASGIVSLELPS---GTYAVT 1628
                                     58*****************988..323.....4478888888888863...444444 PP

>> DUF4493  Domain of unknown function (DUF4493)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       3.1   6.2e+03     129     196 ..     470     525 ..     469     544 .. 0.57
   2 ?    1.7   0.1       0.1     2e+02     149     197 ..     674     717 ..     661     725 .. 0.81
   3 ?   -2.1   0.0       1.5   2.9e+03     101     138 ..    1493    1530 ..    1451    1539 .. 0.69
   4 ?   11.6   0.1   9.3e-05      0.19      41      90 ..    1599    1650 ..    1566    1651 .. 0.72

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 3.1
                        DUF4493 129 vstgaggsltfdktetrkagYfkageesstltvtlkgtkkngktvtketeeittvkagdhykltlkvk 196
                                    v +g+g+++    ++t+ +gY++++          +g  ++gk +t+ t  +  + +g++y + ++++
  gi|119719652|ref|YP_920147.1| 470 VGDGSGKPIIVRSGATN-PGYLPVP----------YGLWSTGKVFTY-TVRVLWALPGTEYYVDVTPD 525
                                    55555666666666666.7777777..........443334556666.66666666666666666653 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.1
                        DUF4493 149 Yfkageesstltvtlkgtkkngktvtketeeittvkagdhykltlkvke 197
                                    Yfkag      +++ ++t   + tvt+ t++  +v+a+ ++++t+++  
  gi|119719652|ref|YP_920147.1| 674 YFKAG---ARTYYESHVTGC-DGTVTF-TKVPFKVAANSKITVTITTRP 717
                                    99999...555555555555.789999.99**************99863 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1.5
                        DUF4493  101 vtCklaNvkvsvefdeefkeyfsdykvtvstgaggslt 138 
                                      + +l    v+++f++ f + +  ++vt++  +g+s+t
  gi|119719652|ref|YP_920147.1| 1493 FEVRLDIFDVKLTFTSPFGTPLAGATVTITKPDGTSIT 1530
                                     44555555678888888888888888888777766665 PP

  == domain 4  score: 11.6 bits;  conditional E-value: 9.3e-05
                        DUF4493   41 egevrsyatyaelpea...ieLpvGtYtvkaesgdssaagfdkpyyeGsetft 90  
                                     +  +++ +t+++  +    +eLp+GtY v+a+ g+ + a+ ++ +  G+et+t
  gi|119719652|ref|YP_920147.1| 1599 TVAIENVGTFTTDASGivsLELPSGTYAVTASKGGRT-ASATATVSDGKETVT 1650
                                     3445555555555544677***************655.688888888888886 PP

>> Big_3  Bacterial Ig-like domain (group 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.3     0.027        54      48      68 .]     243     263 ..     240     263 .. 0.94
   2 ?   -2.9   0.0       4.3   8.6e+03      50      61 ..    1161    1172 ..    1146    1179 .. 0.77
   3 ?    4.1   0.0     0.029        57      42      60 ..    1453    1471 ..    1445    1482 .. 0.82
   4 ?    2.0   0.1      0.13   2.6e+02      48      68 .]    1622    1642 ..    1616    1643 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.027
                          Big_3  48 aGeytvtvtykgvsatftVtV 68 
                                    +G+ +vt++y++++ t+t tV
  gi|119719652|ref|YP_920147.1| 243 VGKENVTLSYDSATDTLTATV 263
                                    699***************998 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.3
                          Big_3   50 eytvtvtykgvs 61  
                                      ++vtvt  g+s
  gi|119719652|ref|YP_920147.1| 1161 NQPVTVTVLGAS 1172
                                     689****99954 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.029
                          Big_3   42 svdstkaGeytvtvtykgv 60  
                                     ++++++ G+y+vtv + gv
  gi|119719652|ref|YP_920147.1| 1453 TISQAPLGAYKVTVNLAGV 1471
                                     578999**********996 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.13
                          Big_3   48 aGeytvtvtykgvsatftVtV 68  
                                      G+y+vt +  g +a++t tV
  gi|119719652|ref|YP_920147.1| 1622 SGTYAVTASKGGRTASATATV 1642
                                     7***********888888777 PP

>> Peptidase_M60_C  Peptidase M60 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.44   8.7e+02      32      59 ..     405     432 ..     388     436 .. 0.78
   2 ?    8.5   0.0    0.0011       2.2      31      65 .]    1496    1530 ..    1475    1530 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.44
                                    EEEEECCCEEE--TCS..TTEEEEEEEC CS
                Peptidase_M60_C  32 lvyfsnrftFtvpssvslagaklyaVqa 59 
                                     vy ++  +  vp ++ ++  +l aVq+
  gi|119719652|ref|YP_920147.1| 405 GVYTATIKVSIVPTKITIKTSGLIAVQP 432
                                    46666666667999************96 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0011
                                     EEEEEECCCEEE--TCS..TTEEEEEEECTTEEEE CS
                Peptidase_M60_C   31 klvyfsnrftFtvpssvslagaklyaVqaDGkrit 65  
                                     +l  f  ++tFt p + +laga++++ ++DG+ it
  gi|119719652|ref|YP_920147.1| 1496 RLDIFDVKLTFTSPFGTPLAGATVTITKPDGTSIT 1530
                                     5667999*************************996 PP

>> PEGA  PEGA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1       2.7   5.4e+03      23      41 ..     394     412 ..     389     414 .. 0.83
   2 ?    0.0   0.0      0.41   8.1e+02      28      56 ..    1453    1483 ..    1448    1496 .. 0.74
   3 ?    8.0   0.2    0.0013       2.5      11      66 ..    1596    1654 ..    1595    1656 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.7
                           PEGA  23 GkTPvtlsleaGnyslrve 41 
                                      TP tl+  +G y+ +++
  gi|119719652|ref|YP_920147.1| 394 SFTPFTLTGSNGVYTATIK 412
                                    57**********9997775 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.41
                           PEGA   28 tls.leaGnyslrvekeGYedl.ektvtvta 56  
                                     t+s  + G y+++v++ G  +l ++t+++++
  gi|119719652|ref|YP_920147.1| 1453 TISqAPLGAYKVTVNLAGVGTLaVQTIKIEK 1483
                                     567889999****999987775256666665 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0013
                           PEGA   11 eGatVyidGkylG......kTPvtlsleaGnyslrvekeGYedlektvtvtagetvklnltL 66  
                                     eGatV i  +++G      +  v+l+l++G+y ++ +k G +++++t tv++g+++  +l+L
  gi|119719652|ref|YP_920147.1| 1596 EGATVAI--ENVGtfttdaSGIVSLELPSGTYAVTASKGG-RTASATATVSDGKETVTELKL 1654
                                     6888888..56777644433447889**************.6*********99888777766 PP

>> SpaA  Prealbumin-like fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0         1     2e+03      37      53 ..      66      82 ..      42      95 .. 0.80
   2 ?   -4.2   0.7         9   1.8e+04      38      55 ..     254     270 ..     233     278 .. 0.54
   3 ?   -1.6   0.0       1.7   3.4e+03      35      52 ..     683     700 ..     659     711 .. 0.83
   4 ?   -3.2   0.0       5.6   1.1e+04      28      41 ..     898     915 ..     835     929 .. 0.44
   5 ?   -0.8   1.6      0.98     2e+03      32      48 ..    1005    1021 ..     970    1082 .. 0.61
   6 ?   -2.0   0.0       2.3   4.6e+03      35      49 ..    1178    1192 ..    1147    1212 .. 0.79
   7 ?   10.2   0.1   0.00036      0.73       3      59 ..    1511    1554 ..    1510    1560 .. 0.88
   8 ?   11.5   0.2   0.00014      0.28      32      59 ..    1602    1628 ..    1574    1654 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1
                                   EEE-BTTSEEEEEEEES CS
                           SpaA 37 tlttdenGkatfegLpl 53
                                     ttd++Gk+t +  ++
  gi|119719652|ref|YP_920147.1| 66 IGTTDSTGKITLTIAQP 82
                                   579*******9985555 PP

  == domain 2  score: -4.2 bits;  conditional E-value: 9
                                    EE-BTTSEEEEEEEESEE CS
                           SpaA  38 lttdenGkatfegLplGt 55 
                                      td + +at+++L+ Gt
  gi|119719652|ref|YP_920147.1| 254 SATD-TLTATVKDLATGT 270
                                    3333.3334444444443 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 1.7
                                    ESEEE-BTTSEEEEEEEE CS
                           SpaA  35 vttlttdenGkatfegLp 52 
                                    +++ +t+ +G++tf+++p
  gi|119719652|ref|YP_920147.1| 683 YESHVTGCDGTVTFTKVP 700
                                    56778999******9987 PP

  == domain 4  score: -3.2 bits;  conditional E-value: 5.6
                                    T.....TTCCEESEEE-B CS
                           SpaA  28 a....kktgtevttlttd 41 
                                    +    ++t+  + t++td
  gi|119719652|ref|YP_920147.1| 898 TvvlfNETTGATRTVETD 915
                                    133333344444444454 PP

  == domain 5  score: -0.8 bits;  conditional E-value: 0.98
                                     CCEESEEE-BTTSEEEE CS
                           SpaA   32 gtevttlttdenGkatf 48  
                                     g+++++++t+++Gka+ 
  gi|119719652|ref|YP_920147.1| 1005 GAVAWSAVTGSDGKASL 1021
                                     45556666666666654 PP

  == domain 6  score: -2.0 bits;  conditional E-value: 2.3
                                     ESEEE-BTTSEEEEE CS
                           SpaA   35 vttlttdenGkatfe 49  
                                      +++ t+++G++t++
  gi|119719652|ref|YP_920147.1| 1178 FASAATGSDGTVTIS 1192
                                     467889999999986 PP

  == domain 7  score: 10.2 bits;  conditional E-value: 0.00036
                                     CCB-TS-EEEEEETTTSCCCHCHHTT.TTCCEESEEE-BTTSEEEEEEEESE..EEEEE CS
                           SpaA    3 gkpLaGaeFtlykvdtttdgkdaleakktgtevttlttdenGkatfegLplG..tYllv 59  
                                     g+pLaGa+ t++k d                ++ t   d+ G +t++++p+G  +Y+++
  gi|119719652|ref|YP_920147.1| 1511 GTPLAGATVTITKPD---------------GTSITDSLDSSGSITVKEVPPGnlQYTVK 1554
                                     69*************...............5577788899************6669997 PP

  == domain 8  score: 11.5 bits;  conditional E-value: 0.00014
                                     CCEESEEE-BTTSEEEEEEEESEEEEEE CS
                           SpaA   32 gtevttlttdenGkatfegLplGtYllv 59  
                                      ++v+t+ttd+ G ++ e Lp GtY ++
  gi|119719652|ref|YP_920147.1| 1602 IENVGTFTTDASGIVSLE-LPSGTYAVT 1628
                                     56789*************.******996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1711 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       766  (0.0427241); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 1.01u 0.26s 00:00:01.27 Elapsed: 00:00:00.45
# Mc/sec: 11383.84
//
Query:       gi|119719653|ref|YP_920148.1|  [L=250]
Description: Rad51-like [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-53  180.6   0.0    6.3e-53  179.7   0.0    1.4  1  Rad51     Rad51
      9e-08   31.9   0.2    1.3e-07   31.4   0.2    1.2  1  AAA_25    AAA domain
    3.7e-06   26.5   0.1    4.7e-06   26.1   0.1    1.3  1  ATPase    KaiC
    0.00013   22.2   0.0    0.00018   21.8   0.0    1.2  1  AAA_22    AAA domain
     0.0031   17.0   0.3     0.0075   15.8   0.3    1.7  1  RecA      recA bacterial DNA recombination protein
     0.0044   16.9   0.0     0.0089   15.9   0.0    1.6  1  DUF3215   Protein of unknown function (DUF3215)
     0.0045   17.5   0.0     0.0081   16.7   0.0    1.4  1  ABC_tran  ABC transporter
  ------ inclusion threshold ------
      0.011   14.9   0.0      0.019   14.1   0.0    1.3  1  PAXNEB    PAXNEB protein
       0.06   13.7   0.0       0.58   10.5   0.0    2.5  2  DUF1805   Domain of unknown function (DUF1805)
       0.17   12.3   0.0       0.33   11.4   0.0    1.4  1  AAA       ATPase family associated with various cellular acti


Domain annotation for each model (and alignments):
>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.7   0.0   3.5e-56   6.3e-53      15     254 ..      26     249 ..      16     250 .] 0.93

  Alignments for each domain:
  == domain 1  score: 179.7 bits;  conditional E-value: 3.5e-56
                                    SS-EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEESSS---GGGGHHHHHH CS
                          Rad51  15 ellqlttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavyidtegtfrperlveiaer 94 
                                    e  +++tG ++lD+lL+GGie+gsite +Gef++Gktq+ch+l+v+vqlp+++gG + +a+y+dtegtfrper+v+ia  
  gi|119719653|ref|YP_920148.1|  26 ESARISTGVRSLDDLLEGGIEVGSITEFIGEFGAGKTQICHQLSVMVQLPKDKGGLNARALYVDTEGTFRPERIVQIARA 105
                                    5568**************************************************************************** PP

                                    TT--HHHHGGGEEEEE--STTHHHHHHHHTHHHHHHS-EEEEEEETTTGGGCH-------THHHHHHHHHHHHHHHHHHH CS
                          Rad51  95 ykldkeevlenvayaRaytiehqeellqqaaallaedkfallivDsvtalyRtdfsgrgelakRqqklgkllrtLrklad 174
                                     +ld+e++len+ yaRay+    eell++a a++++  ++l+++D +t l R+   g g   +R +  + ++++L+ +a+
  gi|119719653|ref|YP_920148.1| 106 RGLDPEKTLENIIYARAYSLGGLEELLSKALAEVVKGDVGLVVLDEATRLVRASGLGAG---ERARAYAAIVSSLEAVAE 182
                                    *****************************************************877776...588899**********97 PP

                                    HH--EEEEEEE-------.------------HHHHHHHH-SEEEEEEE-STTEEEEEEES-SSS-S-EEEEEEETTEEE- CS
                          Rad51 175 efevavvitnqvvaqvdgqaalfsadpkkPigGlvlahasttRlalrkgkgeeRivkvvdsPnlpeleavfaigeeGied 254
                                      + avv++ qvv           +d  +P gG  l   ++  + l k +g+ R ++v++sP      a fa++eeG++d
  gi|119719653|ref|YP_920148.1| 183 -AGSAVVVARQVVF----------GDGVRPAGGAALDGYAHLSVFLSK-RGSAREARVLSSPWRGGV-ALFAVSEEGVVD 249
                                    .5889****99974..........6778************99999986.8************98765.789******998 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.2   7.3e-11   1.3e-07       4     184 ..      19     189 ..      16     193 .. 0.74

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 7.3e-11
                         AAA_25   4 plelsavsvadlaapppprrwlvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdse 83 
                                    p++++  + a++ +  +++++l++g +  g+++ ++G  g+GKt ++ +l++ v + k   g     +++ lyv++E++ 
  gi|119719653|ref|YP_920148.1|  19 PARRVYEESARISTGVRSLDDLLEGGIEVGSITEFIGEFGAGKTQICHQLSVMVQLPKDKGG----LNARALYVDTEGTF 94 
                                    566666777888999999*************************************6664434....689**********9 PP

                         AAA_25  84 delrrRlravgeal..rddarllvldlagveslpLfakdrggtl..ltadvdaleaaieevegvrlvviDplsralgg.. 157
                                       ++R+ ++ +a+  ++ ++l  + +a+      ++      l  l++ + +  a++ +  +v+lvv+D  +r++++  
  gi|119719653|ref|YP_920148.1|  95 --RPERIVQIARARglDPEKTLENIIYARA-----YS------LggLEELLSKALAEVVK-GDVGLVVLDEATRLVRAsg 160
                                    ..6888888887773333333322222222.....22......12355666666666666.69***********999855 PP

                         AAA_25 158 ..densnsdvgalvealeriarrtgaavl 184
                                        +++++ +a+v+ le +a++  a v+
  gi|119719653|ref|YP_920148.1| 161 lgAGERARAYAAIVSSLEAVAEAGSAVVV 189
                                    65566666679********9766555554 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.1   2.6e-09   4.7e-06       1      79 [.      30     115 ..      30     154 .. 0.76

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 2.6e-09
                         ATPase   1 vktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaek.....ygepgvfvtveepa..edlrenakslGwd 73 
                                    ++tg+  lD++l+gGi  g+++   Ge G+GKt ++ q  +           + + ++v +e +   e + + a++ G d
  gi|119719653|ref|YP_920148.1|  30 ISTGVRSLDDLLEGGIEVGSITEFIGEFGAGKTQICHQLSVMVQLPkdkggLNARALYVDTEGTFrpERIVQIARARGLD 109
                                    58**********************************99755322220111133455677777654447777777777777 PP

                         ATPase  74 leklee 79 
                                     ek  e
  gi|119719653|ref|YP_920148.1| 110 PEKTLE 115
                                    666655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0     1e-07   0.00018       6     104 ..      49     156 ..      45     189 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1e-07
                         AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaee.erpevvfvtlpsstsskdllrellralglelka...........erl 73 
                                    +i+  +Ge G+GKT  + +l    +  ++     +++ ++v+  +   ++ +  +++ra gl+ ++           + +
  gi|119719653|ref|YP_920148.1|  49 SITEFIGEFGAGKTQICHQLSVMVQLPKDK-GgLNARALYVDTEGTFRPERI-VQIARARGLDPEKtleniiyaraySLG 126
                                    677789****************98544444.36**************88888.68999999999999************* PP

                         AAA_22  74 sseellealeqalraravielliiDEaqhlr 104
                                     +eell++    + + +v +l+++DEa +l 
  gi|119719653|ref|YP_920148.1| 127 GLEELLSKALAEVVKGDV-GLVVLDEATRLV 156
                                    ******888888888888.9*******9985 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.3   4.2e-06    0.0075      32     108 ..      28     113 ..      19     229 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.2e-06
                                    -EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHH..HHHHHHHHH.TT--...EEEEESS----H....HHHHHT CS
                           RecA  32 etissGslaldialGiGGlpkGriieiyGpessGkttla..lhaiaeaqk.kggv...aafidaehaldp....kyakkl 101
                                      is+G  +ld  l  GG+  G i+e  G   +Gkt ++  l+++++  k kgg+   a ++d+e ++ p    + a++ 
  gi|119719653|ref|YP_920148.1|  28 ARISTGVRSLDDLLE-GGIEVGSITEFIGEFGAGKTQIChqLSVMVQLPKdKGGLnarALYVDTEGTFRPerivQIARAR 106
                                    579********9987.********************99633677777766256652225699**9999882222357777 PP

                                    T--GGG- CS
                           RecA 102 Gvdidel 108
                                    G+d ++ 
  gi|119719653|ref|YP_920148.1| 107 GLDPEKT 113
                                    7775543 PP

>> DUF3215  Protein of unknown function (DUF3215)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0     5e-06    0.0089       1      29 [.     136     165 ..     136     194 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5e-06
                                    HHHHHHH-SEEEEEETTS-EEEEEEGGG.C CS
                        DUF3215   1 LaellpkaiGtltfDennnlvdasGiGk.e 29 
                                    Lae++   +G++++De  +lv asG+G  e
  gi|119719653|ref|YP_920148.1| 136 LAEVVKGDVGLVVLDEATRLVRASGLGAgE 165
                                    78999*********************9862 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   4.5e-06    0.0081       7     117 ..      44     169 ..      39     179 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.5e-06
                                    EEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHHHH...... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx...... RF
                       ABC_tran   7 klkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvren...... 79 
                                     ++ g+++ ++Ge GaGK+ ++  l+ +++  +++  l+ + l   +e ++  ++i  +     l+pe+t+ en      
  gi|119719653|ref|YP_920148.1|  44 GIEVGSITEFIGEFGAGKTQICHQLSVMVQLPKDKGGLNARALYVdTEGTFRPERIVQIARARGLDPEKTL-ENiiyara 122
                                    68899*********************999996666666766665546888889999999999*******76.55598888 PP

                                    .........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHH CS
                                    .........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 .........esdeeiekalsklglkelkdtvvksspssLSgGqkqrv 117
                                              s++ +e +   +gl+ l++ +   ++s L  G++ r 
  gi|119719653|ref|YP_920148.1| 123 yslggleelLSKALAEVVKGDVGLVVLDEATRLVRASGLGAGERARA 169
                                    88876665544444666666666666555444467799999998886 PP

>> PAXNEB  PAXNEB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.1e-05     0.019      19      39 ..      30      50 ..      21      57 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.1e-05
                         PAXNEB 19 tStGtpsLDklLgGGLplGsi 39
                                   +StG++sLD+lL GG+ +Gsi
  gi|119719653|ref|YP_920148.1| 30 ISTGVRSLDDLLEGGIEVGSI 50
                                   8*******************8 PP

>> DUF1805  Domain of unknown function (DUF1805)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00033      0.58      24      39 ..      27      46 ..      14      61 .. 0.73
   2 ?   -0.4   0.0      0.86   1.5e+03      20      41 ..     117     139 ..     107     142 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00033
                                   .....-S--SHHHHHHSB-S CS
                        DUF1805 24 g....sGVrtledllaapve 39
                                   +    +GVr+l+dll++ +e
  gi|119719653|ref|YP_920148.1| 27 SarisTGVRSLDDLLEGGIE 46
                                   233569**********9887 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.86
                                    -.....-S--SHHHHHHSB-SEE CS
                        DUF1805  20 vivag.sGVrtledllaapvesv 41 
                                    +i a+  +   le+ll++ +++v
  gi|119719653|ref|YP_920148.1| 117 IIYARaYSLGGLEELLSKALAEV 139
                                    45566677778999999999987 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00019      0.33       3     104 ..      53     188 ..      52     192 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00019
                                    EESSTTSSHHHHHHHHHHHHTHE.......................EEEEETTTCSSS...................... CS
                            AAA   3 lyGppGtGKTllakavakelgve.......................fleisgsellsk...................... 37 
                                    ++G  G GKT +++++   ++ +                       +                                 
  gi|119719653|ref|YP_920148.1|  53 FIGEFGAGKTQICHQLSVMVQLPkdkgglnaralyvdtegtfrperI----------Vqiarargldpektleniiyara 122
                                    68999**********99997433333444444444444444444444..........04444444555789999999888 PP

                                    .STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEE CS
                            AAA  38 .yvgesekkirelfkeakekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvi 104
                                      +g  e+ +++ ++e+ +      +++DE+ +l++++ g   +e+ r+ +++++ l+ v +  s v+
  gi|119719653|ref|YP_920148.1| 123 ySLGGLEELLSKALAEVVKGD-VGLVVLDEATRLVRAS-GLGAGERARAYAAIVSSLEAVAEAGSAVV 188
                                    788888888888888877776.8************999.77888999999999999998888655443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1861.07
//
Query:       gi|119719654|ref|YP_920149.1|  [L=173]
Description: hypothetical protein Tpen_0744 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       228  (0.0127168); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 1313.33
//
Query:       gi|119719655|ref|YP_920150.1|  [L=610]
Description: hypothetical protein Tpen_0745 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.2e-26   91.4   0.0    9.6e-26   90.6   0.0    1.4  1  NFACT-R_1  NFACT protein RNA binding domain
    1.3e-19   70.4   0.0    1.3e-18   67.0   0.0    2.0  1  FbpA       Fibronectin-binding protein A N-terminus (FbpA)
    0.00083   19.5   0.0     0.0016   18.6   0.0    1.4  1  NFACT-R_2  NFACT protein RNA binding domain
  ------ inclusion threshold ------
      0.037   14.0   0.0      0.074   13.0   0.0    1.5  1  H2TH       Formamidopyrimidine-DNA glycosylase H2TH domain


Domain annotation for each model (and alignments):
>> NFACT-R_1  NFACT protein RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.6   0.0   2.1e-29   9.6e-26       2     109 .]     410     519 ..     409     519 .. 0.95

  Alignments for each domain:
  == domain 1  score: 90.6 bits;  conditional E-value: 2.1e-29
                      NFACT-R_1   2 vfwFkssdgylvimGkDkqeneelikkyleesdvwfhvdkessahvylrlsegeleeipeelleeaaqlakanSia.gnk 80 
                                    +++F +s+g+lv++G+ + +ne l+++y+e +d+++h+d++++a v+l+ + g+  +  e+ + eaaq+a++ S+a +  
  gi|119719655|ref|YP_920150.1| 410 FRFFFTSNGFLVVAGRSAGQNELLVRRYMEPGDIFLHADIHGAAAVVLK-TGGK--QPGEADIAEAAQFAACFSSAwKGG 486
                                    78999********************************************.6666..688999****************** PP

                      NFACT-R_1  81 lssvdvvyvpasnlsktap....ldtGsvgfkg 109
                                    l +vdv++vpa+++sk++p    l++Gs++++g
  gi|119719655|ref|YP_920150.1| 487 LYAVDVFWVPAEQVSKKPPsgeyLAKGSFMVYG 519
                                    ******************************986 PP

>> FbpA  Fibronectin-binding protein A N-terminus (FbpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.0   0.0   2.9e-22   1.3e-18      80     406 ..      80     392 ..      78     396 .. 0.74

  Alignments for each domain:
  == domain 1  score: 67.0 bits;  conditional E-value: 2.9e-22
                                    HTTXEEEEEEEXTTSSEEEEEEEEEXTTSXEEEEEEEEEXXGGGXEEEEEETTTEEEEESSXBXXXSSXSXXBSTTXBXX CS
                           FbpA  80 LkgarivsieqlgfdRivelsiekrdElgdeeeytLivEimgrhSNiiLvdeenkIidaikhvspkqsrvReilpgekYe 159
                                    ++g r++++eq+  dR+v +++  r         +L++E     +N++L+d  ++I++a+++ + +   +R + pg++Y+
  gi|119719655|ref|YP_920150.1|  80 VEGRRVEAVEQVSGDRVVAFELGPR---------RLVLEWVRE-GNLLLLDGGGRILRALRQREMR---DRALKPGHQYV 146
                                    79***********************.........*******99.*******************888...9********** PP

                                    XSXXXSXBXTTSXXH.HHHHHHHHHS.XXXHHHHHHHBTTXXHHHHHHHHTTXSSSH...............HHHHHHHH CS
                           FbpA 160 lPpsqdklnPleaeeleefkellskkekdlvkaLvkafqGlspllaeelleragldketsakelseedlerlyealqell 239
                                    +Pp     + ++ +      +l  + +++ + + v+ +  l  +l+ e+++r+gld+  +a++l e+ ++r+ ++  e++
  gi|119719655|ref|YP_920150.1| 147 PPPR--VGDAFSDDPGYLYAKL-GEYSGRAAVTAVSLVASLPAELVYEAMYRLGLDPSAKARALGEDAFRRVLSKSVEIF 223
                                    ****..5555655553333443.45468888889999999**************************************** PP

                                    TXXX....XXEE.....XSSSEESSXXTTXX..SSXXXXSXHHHHHHHHTTTXXX--SHHHHHHHHHHHHHHHHHHHHHH CS
                           FbpA 240 eeleeekfepqlvlkeekpeefsvvplksls.elekesfdslsealdeyYakkaerdrveqkrsdlekrveneleklekk 318
                                    ee       p   ++     e+++++ ++l  ++e     s+ + + +y     +rd   ++ +  ++ +++++e l +k
  gi|119719655|ref|YP_920150.1| 224 EEAL---ADPDRGFRV--SGEVYAFNPEHLGaGAE---EVSFAREFPAYVLGLIKRDLQPEEGAGAQEAIRRAVEELSRK 295
                                    9987...345332332..55666666555553544...456666666777666666666666666666666666666666 PP

                                    HHHHHHHHHCCGGH.......HHHHCCHH-----------------------.--..........--------------- CS
                           FbpA 319 lkklekelekaeka.......enyrligelltaylyaikkgmsevelenyydege..........evtIpLdprkspsen 381
                                     + l++  ++ ++           rl+  l  a l++  +  ++v+                   +v++++d + s+ +n
  gi|119719655|ref|YP_920150.1| 296 AELLSRHSATVDEVlaayrglVASRLQWSLVEARLKEAYPIVKSVD--------ParsrlvleleGVEVEVDASRSALSN 367
                                    6666655444333332233335555555666666655555544444........03334444444*************** PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHH CS
                           FbpA 382 AqkyfkkykKlkraveaveeqieet 406
                                    A +yf+k+k +kr+ +++  + e+ 
  gi|119719655|ref|YP_920150.1| 368 AASYFEKAKSAKRKLAEASAAVERS 392
                                    *****************99998876 PP

>> NFACT-R_2  NFACT protein RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   3.6e-07    0.0016       2      77 ..     411     490 ..     411     504 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 3.6e-07
                      NFACT-R_2   2 RhfrlsekaklIvgReeeEnkflk.gll.kkdfvslrakshkGplvlid..g.elseedlelaarivarYskgkeeeeve 76 
                                    R f +s+++ ++ gR ++ n+ l  +++  +d++ l+a  h ++ v+++  g ++ e+d+  aa+++a +s++ +   ++
  gi|119719655|ref|YP_920150.1| 411 RFFFTSNGFLVVAGRSAGQNELLVrRYMePGDIF-LHADIHGAAAVVLKtgGkQPGEADIAEAAQFAACFSSAWKGGLYA 489
                                    789999***************9861566677777.777777777777745536888***************987666555 PP

                      NFACT-R_2  77 v 77 
                                    v
  gi|119719655|ref|YP_920150.1| 490 V 490
                                    5 PP

>> H2TH  Formamidopyrimidine-DNA glycosylase H2TH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.7e-05     0.074      44      83 ..     189     228 ..     178     237 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.7e-05
                                    HHHHHHHTT--TTSBGGGS-HHHHHHHHHHHHHHHHHHHH CS
                           H2TH  44 adEvLfrakihPerlakslskeelellhqeikevlkeaie 83 
                                    + E+++r +++P+ +a+ l +  +++++++ +e+++ea++
  gi|119719655|ref|YP_920150.1| 189 VYEAMYRLGLDPSAKARALGEDAFRRVLSKSVEIFEEALA 228
                                    569***********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (610 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.65u 0.33s 00:00:00.98 Elapsed: 00:00:00.50
# Mc/sec: 3691.69
//
Query:       gi|119719656|ref|YP_920151.1|  [L=233]
Description: hypothetical protein Tpen_0746 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0032   17.9   1.2       0.12   12.8   0.0    3.4  4  CBS       CBS domain


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0     0.035   6.2e+02      14      42 ..      14      39 ..       7      40 .. 0.73
   2 ?   -2.4   0.0      0.38   6.8e+03      19      36 ..      65      79 ..      54      83 .. 0.62
   3 !   12.8   0.0   6.8e-06      0.12       9      54 ..     115     159 ..     107     162 .. 0.82
   4 ?   -0.3   0.0     0.084   1.5e+03      27      36 ..     173     184 ..     165     194 .. 0.67

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.035
                                   TTSBHHHHHHHHHHHTSSEEEEEETTTBE CS
                            CBS 14 pdttleealelmrekgvsrlPVVdedgkl 42
                                     ++lee++++    gv +l VV  dg+l
  gi|119719656|ref|YP_920151.1| 14 SFASLEELVRRA-AGGV-SL-VVSLDGRL 39
                                   557899999997.4558.88.88667876 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.38
                                   HHHHHHHHHHTSSEEEEE CS
                            CBS 19 eealelmrekgvsrlPVV 36
                                   e al++    + +r++VV
  gi|119719656|ref|YP_920151.1| 65 ERALREA---ARGRYLVV 79
                                   4444444...33788788 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 6.8e-06
                                    CEEEETTSBHHHHHHHHHHHTSSEEEE.EETTTBEEEEEEHHHHHHH CS
                            CBS   9 vvtvppdttleealelmrekgvsrlPV.VdedgklvGivtlrDllra 54 
                                     ++v p+t++++a+ l++e   +++ V V + g++  ++t  D + +
  gi|119719656|ref|YP_920151.1| 115 APSVAPNTSVKKAVSLLEE--SGAIAVgVRSRGRISKVLTVVDFAGY 159
                                    579**************66..68999*99999999999998887765 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 0.084
                                    HHT.SSEE.EEE CS
                            CBS  27 ekg.vsrl.PVV 36 
                                    +   vsr+ PVV
  gi|119719656|ref|YP_920151.1| 173 DPTpVSRVdPVV 184
                                    445578888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1835.95
//
Query:       gi|119719657|ref|YP_920152.1|  [L=192]
Description: hypothetical protein Tpen_0747 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.8e-33  114.1   0.0    6.9e-33  113.8   0.0    1.1  1  Mut7-C       Mut7-C RNAse domain
     0.0065   16.4   0.1       0.01   15.8   0.1    1.3  1  zf_CopZ      Zinc binding domain
  ------ inclusion threshold ------
      0.016   15.3   2.1        1.1    9.5   0.0    2.4  2  Zn-ribbon_8  Zinc ribbon domain
      0.063   13.3   0.0       0.11   12.5   0.0    1.4  1  DZR          Double zinc ribbon
        2.9    7.9   5.5        2.7    7.9   1.1    2.3  2  DUF35_N      Rubredoxin-like zinc ribbon domain (DUF35_N)


Domain annotation for each model (and alignments):
>> Mut7-C  Mut7-C RNAse domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.8   0.0   1.9e-36   6.9e-33       3     145 ..      33     178 ..      31     179 .. 0.94

  Alignments for each domain:
  == domain 1  score: 113.8 bits;  conditional E-value: 1.9e-36
                         Mut7-C   3 fllDamlgklakyLRllGydalyasdvedeellal.aakekrillTrdreLlkraklkkg..vlltsrdveeqlreviar 79 
                                    +++D mlgklak+LR+lG+ aly + ++d+++ +l ++ e+ ++lTrdr+L++r   k    vl+ +   e+ql+ v+ r
  gi|119719657|ref|YP_920152.1|  33 VVADGMLGKLAKWLRILGVRALYVRGAPDSDVEELlSRLEDPVFLTRDRALYARLASKGFkaVLVPEAPAEAQLAFVLPR 112
                                    799**********************999999998626679**************88875578999*************** PP

                         Mut7-C  80 lglklslkpelsrCvaCngeleevekeevkervpekvyeeadeftrCekCrkvfWkGshwerveel 145
                                    lg+++ l+   + C  C + l++v+  ev++ vpe v + +def+rC+ C++v+W+G+h+ +++++
  gi|119719657|ref|YP_920152.1| 113 LGVEPVLDMSRTLCPLCGSSLKRVDVREVEGLVPEGVLSAYDEFYRCTGCGQVYWRGTHFYEMKRK 178
                                    ***************************************************************987 PP

>> zf_CopZ  Zinc binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   2.9e-06      0.01       2      49 ..     124     167 ..     123     176 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.9e-06
                                    -B-TTT--B-EEE-HHHHHHHB-GGGGGG--S-EE.E---TT-SEEEE CS
                        zf_CopZ   2 kkCPvCgkkGkkVkliTvkhllkpellekvkeedYylCknedCdVvYF 49 
                                    + CP Cg++ k+V+   v+ l+ + +l+    +++y C+   C  vY+
  gi|119719657|ref|YP_920152.1| 124 TLCPLCGSSLKRVDVREVEGLVPEGVLSA--YDEFYRCT--GCGQVYW 167
                                    57************************985..66688886..5666665 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00029       1.1      21      39 ..     121     136 ..     114     136 .. 0.77
   2 ?    5.0   0.5    0.0073        26       6      14 ..     157     165 ..     156     177 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00029
                    Zn-ribbon_8  21 isdapltaCPeCgsevrrv 39 
                                    +s    t CP Cgs ++rv
  gi|119719657|ref|YP_920152.1| 121 MS---RTLCPLCGSSLKRV 136
                                    44...677********997 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0073
                    Zn-ribbon_8   6 YrCeeCghe 14 
                                    YrC+ Cg++
  gi|119719657|ref|YP_920152.1| 157 YRCTGCGQV 165
                                    9******87 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   3.1e-05      0.11      11      37 ..     122     165 ..     116     172 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.1e-05
                            DZR  11 darfCseCgtklkavaa.................edrCpsCgek 37 
                                    +   C+ Cg++lk+v                    +rC  Cg+ 
  gi|119719657|ref|YP_920152.1| 122 SRTLCPLCGSSLKRVDVreveglvpegvlsaydeFYRCTGCGQV 165
                                    5568********9777799***********************87 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.2     0.073   2.6e+02      25      33 ..     123     131 ..     122     134 .. 0.85
   2 ?    7.9   1.1   0.00076       2.7      12      22 ..     157     167 ..     155     167 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.073
                        DUF35_N  25 ravCphCgs 33 
                                    r  Cp Cgs
  gi|119719657|ref|YP_920152.1| 123 RTLCPLCGS 131
                                    678****99 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00076
                        DUF35_N  12 qrCpdCGtvqf 22 
                                     rC+ CG+v++
  gi|119719657|ref|YP_920152.1| 157 YRCTGCGQVYW 167
                                    59*******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1411.03
//
Query:       gi|119719658|ref|YP_920153.1|  [L=213]
Description: AMMECR1 domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-53  180.2   0.0    2.6e-53  180.0   0.0    1.0  1  AMMECR1   AMMECR1
  ------ inclusion threshold ------
       0.14   12.3   0.0       0.24   11.5   0.0    1.3  1  DUF4884   Domain of unknown function (DUF4884)


Domain annotation for each model (and alignments):
>> AMMECR1  AMMECR1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.0   0.0   2.9e-57   2.6e-53       1     166 []      13     196 ..      13     196 .. 0.93

  Alignments for each domain:
  == domain 1  score: 180.0 bits;  conditional E-value: 2.9e-57
                                    HHHHHHHHHHHTTSS-S-H..H---HHHHSEEEEEEEEE..EE...........CCECCCECEEEEEEHHHHHHHHHHHH CS
                        AMMECR1   1 lklareaieealkeekkle..eeakeelkekaglFVtlk..ekkg.........eLRGCiGtleperpLaeevaenAlaa 67 
                                    ++lar+a+ee+l++ +++e  ++++++l+ek+g+FVt++               eLRGCiG+ ep  pLae+ +++A+aa
  gi|119719658|ref|YP_920153.1|  13 VRLARRAVEEYLENARVIEppRDTPPSLREKSGVFVTIEkiL--VdplarrarrELRGCIGYPEPVLPLAEATIHAAIAA 90 
                                    689****************9999999************9441..1566777788************************** PP

                                    HHT-TTS----HHHHTTEEEEEEEE---EE-...-....GGG--TTT-EEEEEETTEEEEE-THHHHHTT--HHHHHHHH CS
                        AMMECR1  68 AfeDpRFspvtaeElpeleveVsvLtepepi...v....ledlevgkhGliiekgsrsatlLPqvaveqgwdkeeflasl 140
                                    A+eDpRF+p+t++El+++ +eVsvLt+pep+   +    +++++vg++Gli+e+g  +++lLPqvav++gwd+eefl+ +
  gi|119719658|ref|YP_920153.1|  91 ATEDPRFPPMTPRELDTVVFEVSVLTKPEPVdyrSpeelPDKIKVGRDGLIVEYGAARGLLLPQVAVDEGWDPEEFLSYA 170
                                    *******************************65515566888************************************** PP

                                    HHHHTS-TTCCCSTTSEEEEE-EEEE CS
                        AMMECR1 141 lrKaglrpdewkdseikltryevekf 166
                                    + Kaglr+d+w++  +k++r+++++f
  gi|119719658|ref|YP_920153.1| 171 CLKAGLRDDAWRHGGLKVYRFQAQIF 196
                                    ********99*************986 PP

>> DUF4884  Domain of unknown function (DUF4884)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   2.7e-05      0.24      12      36 ..     182     205 ..     179     207 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.7e-05
                        DUF4884  12 eHeGvkVYRFyDmgsYvYFTtrGDv 36 
                                     H G+kVYRF     +v  T +GDv
  gi|119719658|ref|YP_920153.1| 182 RHGGLKVYRFQ-AQIFVETTPKGDV 205
                                    7********96.5678888889998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       183  (0.0102069); expected 358.6 (0.02)
Passed bias filter:                      163  (0.00909142); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1598.93
//
Query:       gi|119719659|ref|YP_920154.1|  [L=270]
Description: hypothetical protein Tpen_0749 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-07   31.2   0.0      3e-07   30.4   0.0    1.4  1  Thioredoxin_3  Thioredoxin domain
    1.9e-06   28.2   0.0    3.1e-06   27.6   0.0    1.2  1  ArsD           Arsenical resistance operon trans-acting repre
    0.00047   20.3   0.0    0.00075   19.6   0.0    1.2  1  DUF1525        Protein of unknown function (DUF1525)


Domain annotation for each model (and alignments):
>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.0     5e-11     3e-07      40      75 ..      67     102 ..      57     103 .. 0.94

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 5e-11
                                    HHHHHCT-SSSSEEECTTCEEEESS---CCHHHHHH CS
                  Thioredoxin_3  40 eeiekygVmsvPalvidgkvvvsGkvpseeeirkll 75 
                                    +e+++yg++s Pa+v+dg+ v +G+ ps+eeir++l
  gi|119719659|ref|YP_920154.1|  67 REVKEYGIQSLPAVVVDGEKVLEGRYPSREEIRRIL 102
                                    7899*****************************997 PP

>> ArsD  Arsenical resistance operon trans-acting repressor ArsD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   5.1e-10   3.1e-06      65     106 ..      69     110 ..      63     119 .. 0.88

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 5.1e-10
                           ArsD  65 lekkgaeaLPlvlvdgeivktgrYptreelaewlgleeeele 106
                                    +++ g + LP v+vdge v++grYp+ree+ ++lgl+ + + 
  gi|119719659|ref|YP_920154.1|  69 VKEYGIQSLPAVVVDGEKVLEGRYPSREEIRRILGLPPRPAP 110
                                    6789*******************************9987665 PP

>> DUF1525  Protein of unknown function (DUF1525)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   1.2e-07   0.00075      39      97 ..      29      90 ..      11      99 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.2e-07
                        DUF1525 39 lpadpeqaaalvrqrlnspd.waaleeqieqayqgva..dawqlgikkiPAVvvdrraVvYG 97
                                   lp+ +    ++   +l++p+ ++ + eq+e+ y gv   ++ ++gi+ +PAVvvd ++V  G
  gi|119719659|ref|YP_920154.1| 29 LPKPERPKLKVKLFKLKDPSnFKSYLEQLEELYGGVYtrEVKEYGIQSLPAVVVDGEKVLEG 90
                                   34333333444444466654378999*********9633689*****************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1763.79
//
Query:       gi|119719660|ref|YP_920155.1|  [L=601]
Description: ATP-dependent DNA ligase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-64  217.5   0.0    2.1e-64  216.9   0.0    1.3  1  DNA_ligase_A_M   ATP dependent DNA ligase domain
    6.5e-39  134.0   0.0    1.1e-38  133.3   0.0    1.4  1  DNA_ligase_A_N   DNA ligase N terminus
    9.1e-22   77.5   0.0      2e-21   76.5   0.0    1.6  1  DNA_ligase_A_C   ATP dependent DNA ligase C terminal region
    6.9e-05   23.2   0.1    0.00011   22.6   0.1    1.3  1  RNA_ligase       RNA ligase
  ------ inclusion threshold ------
      0.017   15.1   0.1      0.054   13.5   0.0    1.9  2  DNA_ligase_OB_2  DNA ligase OB-like domain


Domain annotation for each model (and alignments):
>> DNA_ligase_A_M  ATP dependent DNA ligase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  216.9   0.0   5.8e-68   2.1e-64       1     204 []     240     440 ..     240     440 .. 0.98

  Alignments for each domain:
  == domain 1  score: 216.9 bits;  conditional E-value: 5.8e-68
                                    -EEEEEESCHHHHHHHTTTSEEEEEEEESSEEEEEEEETTEEEEEETTS-B-GGGCHHHHHHHHHHBSTTESEEEEEEEE CS
                 DNA_ligase_A_M   1 pmLAeslksiekalkkleekafivEiKyDGeRaqvhkegdkvklfSRrlkditaakpelvkalkeafkkdeksvilDGEl 80 
                                    pmLAe+l++  ++l+kl +++ ++E+KyDGeR+q hk+gdkv lfSRrl++it+++p++v+ +k++      ++i++GE+
  gi|119719660|ref|YP_920155.1| 240 PMLAERLSDPAEILEKL-GGKCLAEYKYDGERVQAHKSGDKVLLFSRRLENITHHYPDVVEYVKRLKVR---EAIVEGEI 315
                                    9***************9.77777****************************************999987...59****** PP

                                    EEEETTTTCBEHHHHHCHHHHCHCCTHHHHHHSEEEEEEEEEEEETTEEHTTSCHHHHHHHHHHHB--BTTTEEE--EEE CS
                 DNA_ligase_A_M  81 vavdketgeilpfqklasrkkkkkkveeklkeaelclfvFDiLyldgesltdeplkeRrklLeeilkesedrvelaesle 160
                                    va++++tge+lpfq+l++r ++k++ve+++ke+++++++FD++y+dge+l+++pl++Rr +Le+i+ e ++++ l+++++
  gi|119719660|ref|YP_920155.1| 316 VAYNPDTGEMLPFQELMHR-RRKYDVEKAMKEYPVRVYLFDVIYMDGEELIEKPLDQRRLILEKIVPEGDEDILLSTAKV 394
                                    *******************.9*********************************************************** PP

                                    ESSHHHHHHHHHHHHHTTECEEEEEE..TT-CC-TTCEEEEEEEEE CS
                 DNA_ligase_A_M 161 vkdveeleelleeaiseglEGlvvKn..pdskYepgkrsknwlKvK 204
                                    v d+++l  ++e+aiseg+EG+++K+  p s+Y+ g r++ w+K+K
  gi|119719660|ref|YP_920155.1| 395 VGDAKDLLHFFEQAISEGCEGVMCKSigPGSIYQMGARGWLWIKFK 440
                                    **************************999****************9 PP

>> DNA_ligase_A_N  DNA ligase N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.3   0.0     3e-42   1.1e-38       1     173 []       8     189 ..       8     189 .. 0.96

  Alignments for each domain:
  == domain 1  score: 133.3 bits;  conditional E-value: 3e-42
                                    BCHHHHHHHHHHCC.---HHHHHHHHHHHHHTS-..SHHHHHHHHHH....SS-CCCS------HHHHHHHHHHHHT--H CS
                 DNA_ligase_A_N   1 pFaelaelfekieestkkrlekrailanffrkvesagpedlypalrL....llPdydgreygigesllakalaealglsk 76 
                                    p++ la+++e+ie+ t++rl+++++l ++f+k+   +pe + ++++L    l Pdy+g e+g+ e+l  +ala+a+g+  
  gi|119719660|ref|YP_920155.1|   8 PYSVLADFYERIES-TSSRLAMTDYLVALFKKT---PPEVIDKVVYLtqgqLRPDYEGVELGVAEKLALRALAKASGRHL 83 
                                    799***********.99*************775...799****************************************9 PP

                                    HHHHHHHHHHS-HHHHHHHHHCCHHHH........------BHHHHHHHHHHHHH-.STTHHHHHHHHHHHHHHHS-HHH CS
                 DNA_ligase_A_N  77 kkikdalakvgDlgevaeevlskrstl........akkspltieevnelLdklaaa.gkgsedekkkilkkllkraspeE 147
                                    k+++d ++k+gD+g vae++l               +k++lt+++v++ L k+a+a g+g +++k+++l  ll+ a+p+E
  gi|119719660|ref|YP_920155.1|  84 KDVEDLYKKTGDIGAVAEKLLTAPGGGlleffgtpVQKKELTVSQVYSALMKIAQAsGEGAQETKVNTLVALLQDAKPKE 163
                                    99*****************99655555899999999******************999*********************** PP

                                    HHHHHHHHCT---SS--HHHHHHHHH CS
                 DNA_ligase_A_N 148 akyliriilkdlriglsektvldala 173
                                    a+y+ r++l++lr+g+++ t+ldala
  gi|119719660|ref|YP_920155.1| 164 ARYILRTVLGRLRLGIADMTILDALA 189
                                    ************************97 PP

>> DNA_ligase_A_C  ATP dependent DNA ligase C terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.5   0.0   5.5e-25     2e-21       1      99 []     465     575 ..     465     575 .. 0.91

  Alignments for each domain:
  == domain 1  score: 76.5 bits;  conditional E-value: 5.5e-25
                                    GGGSEEEEEEEEEE..TTEEEEEEEE-SS--HHHHHHHHHHHG..GGEECTTCESS---HHHHTTEEE-TT-EEEEEESE CS
                 DNA_ligase_A_C   1 rgglvgslllgvyd..dgkleyvgkvgtGfsdaeleelrkklk..elerkkppfaekvpeeekrdvWvePelvveVkfae 76 
                                    r+g++g+ll+++yd  ++++++v+kvgtGf+d++l++l + l+  +++ ++p++ +k +++    vW+ P++v+e+ +ae
  gi|119719660|ref|YP_920155.1| 465 RAGTYGALLMAAYDpeTDTFKTVCKVGTGFTDEDLAKLPELLDpyKIPHRHPRVFSKIEAD----VWFVPAVVLEIIGAE 540
                                    6799**********99999***********************9666666677777777766....9************** PP

                                    EECTSSSTT...........EECT-EEE.EE-TTS CS
                 DNA_ligase_A_C  77 itasgkyka...........slRfPrfk.rlReDk 99 
                                    it s+ +++           ++RfPrf+ r+R Dk
  gi|119719660|ref|YP_920155.1| 541 ITLSPLHTCalnkleegaglAIRFPRFTgRYRFDK 575
                                    **************************997899997 PP

>> RNA_ligase  RNA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.1     3e-08   0.00011       3     147 ..     260     422 ..     258     440 .. 0.60

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 3e-08
                                    EEEEEE-SSEEEEEEEE..TTEEEEETTCEB..CTTTHHHHHHTHHHHHHHHHHHHH..ECCEEEEEEEES......... CS
                     RNA_ligase   3 vvvtEKlDGtnfriylv..kevgvasRsqil..pfgeekfkefkrwaaalrkklkeklaneelilyGElig......... 69 
                                    + ++ K DG++++ +++  k v ++sR+ +   +   +     +  ++    ++ ++l+++e i+ GE++          
  gi|119719660|ref|YP_920155.1| 260 CLAEYKYDGERVQAHKSgdK-VLLFSRRLENitH---H-----YPDVV----EYVKRLKVREAIVEGEIVAynpdtgeml 326
                                    67899***********9633.******9999421...1.....22222....2335677789*********877666555 PP

                                    .......SS.........TTSS.......EEEEEEEEEEE.CTT.....BECE--HHHH.HHHHHCCT..B..EEEEE.S CS
                     RNA_ligase  70 ......hsi.......kygglpk......efyvFdifdir.dke.....eqrylspdev.ealakglg..tvpvlyegkf 121
                                          h         k     +        y+Fd++ ++ ++      +qr l  +++ ++  +++   t++v++    
  gi|119719660|ref|YP_920155.1| 327 pfqelmH-RrrkydveK-----AmkeypvRVYLFDVIYMDgEELiekplDQRRLILEKIvPEGDEDILlsTAKVVG---- 396
                                    5544442.046334441.....1444455*********99554434444444444444434444443255555553.... PP

                                    SHHHHHCCC..HHHHTC--EEEEEESS CS
                     RNA_ligase 122 laaeellell.lskgnkrEGlVikpes 147
                                     +a++ll ++ +  ++ +EG+ +k+  
  gi|119719660|ref|YP_920155.1| 397 -DAKDLLHFFeQAISEGCEGVMCKSIG 422
                                    .4555666644433459*****99764 PP

>> DNA_ligase_OB_2  DNA ligase OB-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.5e-05     0.054       2      36 ..     461     501 ..     460     511 .. 0.77
   2 ?   -3.5   0.1       3.2   1.1e+04      57      63 ..     562     568 ..     559     569 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.5e-05
                                    ...EEEEEEEEEEEEE.T......TEEEEE-SS--HHHHHH CS
                DNA_ligase_OB_2   2 GkGkykgmlGallvetkk......gkrfkiGsGlsdaqRen 36 
                                    G+Gk +g+ Gall+   +      ++  k+G+G++d++ ++
  gi|119719660|ref|YP_920155.1| 461 GRGKRAGTYGALLMAAYDpetdtfKTVCKVGTGFTDEDLAK 501
                                    9*************997533333333599*******98655 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3.2
                                    -EEEEEE CS
                DNA_ligase_OB_2  57 pRfPsfl 63 
                                     RfP+f 
  gi|119719660|ref|YP_920155.1| 562 IRFPRFT 568
                                    59**995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (601 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.46
# Mc/sec: 3887.83
//
Query:       gi|119719661|ref|YP_920156.1|  [L=189]
Description: hypothetical protein Tpen_0751 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.26   11.7   2.1       0.35   11.3   2.1    1.2  1  CCDC53    Subunit CCDC53 of WASH complex


Domain annotation for each model (and alignments):
>> CCDC53  Subunit CCDC53 of WASH complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   2.1     2e-05      0.35      12      80 ..       8      78 ..       1      94 [. 0.65

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2e-05
                         CCDC53 12 LNrFatecEekLvevekrlqrleitlalLEakLsSip..gleeveaeaaeastsddnaarkgppppppsse 80
                                   L +  +  E++L e+ ++   +e +l+l++  LsS+   +++e+ a+++ +++++++a   ++++++p+ e
  gi|119719661|ref|YP_920156.1|  8 LAEVKSYLEKRLEELRREERLIESMLKLVDEALSSASfvKASELVAARQPEAAEARQAVARHTVEEKPTEE 78
                                   55667788**************************9987755555555444444444433333333332222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1090  (0.0607954); expected 358.6 (0.02)
Passed bias filter:                      644  (0.0359195); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1194.13
//
Query:       gi|119719662|ref|YP_920157.1|  [L=310]
Description: ribokinase-like domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-48  164.1   0.1    7.7e-48  163.3   0.1    1.3  1  PfkB      pfkB family carbohydrate kinase


Domain annotation for each model (and alignments):
>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.3   0.1   4.3e-52   7.7e-48       5     298 ..       7     279 ..       3     282 .. 0.90

  Alignments for each domain:
  == domain 1  score: 163.3 bits;  conditional E-value: 4.3e-52
                                    EEEEEEEEEEEEECSSH..TTSEEEESEEEEEEESHHHHHHHHHHHTT-EEEEEEEEESSHHHHHHHHHHHHTTEEETTE CS
                           PfkB   5 vviGealidliavsekl..egelvevktveksaGGagaNvAvalarlgadvafigavGdDnfGeflleelkkegvdtdyv 82 
                                    +v G a+ d+++v+e++  ++e+ve+ +++ + GGa+ NvAvalarlg+ ++f+g+vG+D+ G+++l+el  +gvdt yv
  gi|119719662|ref|YP_920157.1|   7 AVSGNANLDVYLVVERIpgPDEAVEAVETRSYVGGAATNVAVALARLGVYARFLGFVGGDDEGARVLKELGGNGVDTGYV 86 
                                    78899*************999999*****************************************************999 PP

                                    EEESSSEEEEEEEEETTTSEEEEEEEEGGGGGHHHHHHHHHHHHHGCTSEEEEESEECTTSHHHHHHHHHHHHHHTTE.. CS
                           PfkB  83 kidedtrtglalivvdedgertivfnrgaaadltkeeleededlleeadllyisgllsselpeavleelaeaaknggt.. 160
                                    +++   +tg  ++++d++g+r +v+ rga+ +l++ ++ + e+ l+ +d+l++s+      p  +  +l+ea++ g    
  gi|119719662|ref|YP_920157.1|  87 QMSSL-PTGRVIVLLDRQGRRAMVALRGANTELKPGCF-NAESVLGGVDHLHLSS----THPGYTAWLLQEAKRLGLSts 160
                                    96555.*****************************877.***************9....666677777777777777667 PP

                                    EEEEECESSSHHHHHHHHHHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTSSEEEEEEGGGEEEEEETTEE CS
                           PfkB 161 fdpnlldplgaqfkeallellaladllkpneeElealtgekledieealaalhklkakgaktvvvtlGkeGalvvekdge 240
                                     dp +   + +   +++l++ + ad+l++ne+E eal g         +++       g+++vvv++G+eG+ +      
  gi|119719662|ref|YP_920157.1| 161 WDPGMAVVSRS--PQEVLKAARSADVLFLNEREYEALRGGL-------AEL-------GETLVVVKRGEEGSEAP--RLG 222
                                    78887777776..366777788*****************99.......233.......6689**********999..556 PP

                                    EEEEE.SSSS-SBGTTHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHTSSSSSTC CS
                           PfkB 241 lkvpavpkvkvvDttGAGDsfvggflaallegksleealrfanavAalvvqkkgaias 298
                                    +kv+a + v +vDttGAGD+f ++fl+a+  g s+e++l ++na++al v+++ga +s
  gi|119719662|ref|YP_920157.1| 223 VKVKA-FRVSPVDTTGAGDTFDASFLVAWKLGLSVEDCLLLGNAAGALKVTRMGAHSS 279
                                    78999.67**********************************************9864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       283  (0.0157845); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2375.34
//
Query:       gi|119719663|ref|YP_920158.1|  [L=113]
Description: hypothetical protein Tpen_0753 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       802  (0.044732); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 792.92
//
Query:       gi|119719664|ref|YP_920159.1|  [L=608]
Description: threonyl-tRNA synthetase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-50  170.3   0.0    4.3e-50  169.3   0.0    1.5  1  tRNA-Thr_ED      Archaea-specific editing domain of threonyl-
    2.8e-24   85.1   1.0    9.2e-24   83.4   0.9    2.0  2  HGTP_anticodon   Anticodon binding domain
      6e-18   65.4   0.1    8.1e-17   61.8   0.2    2.3  2  tRNA-synt_2b     tRNA synthetase class II core domain (G, H, 
  ------ inclusion threshold ------
      0.023   14.5   0.1      0.054   13.3   0.1    1.6  1  INT_SG_DDX_CT_C  INTS6/SAGE1/DDX26B/CT45 C-terminus


Domain annotation for each model (and alignments):
>> tRNA-Thr_ED  Archaea-specific editing domain of threonyl-tRNA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.3   0.0   9.5e-54   4.3e-50       1     137 []       1     137 [.       1     137 [. 0.98

  Alignments for each domain:
  == domain 1  score: 169.3 bits;  conditional E-value: 9.5e-54
                                    -EEEEEEEEEEEEEEEEESSSS-..SS---EEEESSEEEEEEE-BTT--H...HHHHHHHHHHHHHHHHHT-SEEEEEE- CS
                    tRNA-Thr_ED   1 mrlLlihadeleyeakkkalkeae.eeeekegrleealvvFiavEkeDeeekekvvekavkeikkvakkvkakkvvlypy 79 
                                    m++Lliha+++eyea++kal+ ae  + +++g++e+alvvF++vEk+D + +++vve+a++++ +v+++v+a++vv+ypy
  gi|119719664|ref|YP_920159.1|   1 MKTLLIHAKHFEYEAREKALDAAEsIDGNRSGSFENALVVFVTVEKGDGS-SQDVVEEAAADVLDVFRRVGASRVVVYPY 79 
                                    9**********************9878899*******************9.789************************** PP

                                    STS-SSB--HHHHHHHHHHHHHHHHTT.-EEEE--SSEEEEEEEEE--STTSEEEEE- CS
                    tRNA-Thr_ED  80 aHLssslaspevakeilkkleeklkekglevkraPFGwykefeisckGhpLaelsrei 137
                                    aHLs++la+pe ak++l++l e+++++g+ v+raPFGwyk f+++c+GhpL+elsr+i
  gi|119719664|ref|YP_920159.1|  80 AHLSDDLADPEEAKRVLSQLAERISSAGVPVSRAPFGWYKRFSVECYGHPLSELSRTI 137
                                    ********************************************************97 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.6   7.2e+03      12      30 ..      90     108 ..      74     111 .. 0.73
   2 !   83.4   0.9   2.1e-27   9.2e-24       1      92 [.     496     583 ..     496     585 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.6
                                    HHHHHHHHHHHHHHHTTTS CS
                 HGTP_anticodon  12 eeleeyakklaeeLraagi 30 
                                    ee++ + ++lae+++ ag+
  gi|119719664|ref|YP_920159.1|  90 EEAKRVLSQLAERISSAGV 108
                                    4566778888888888886 PP

  == domain 2  score: 83.4 bits;  conditional E-value: 2.1e-27
                                    SEEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTCEEE CS
                 HGTP_anticodon   1 qvvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtreqe 80 
                                    qv vip ++   e++++a+++a++L+++girv++dd++es+ k+ir+a+ ++ip++vvvG++e+e+g++tvr r  + q+
  gi|119719664|ref|YP_920159.1| 496 QVRVIPHSS---EYLKLADSIADKLEEQGIRVDVDDREESLAKRIRDAEVKWIPYVVVVGKREAESGKLTVRVRGQG-QY 571
                                    89*******...9*************************************************************555.68 PP

                                    EEETTHHHHHHH CS
                 HGTP_anticodon  81 rvsldelveklk 92 
                                    ++sl+elv+ l 
  gi|119719664|ref|YP_920159.1| 572 EMSLEELVGRLV 583
                                    ********9875 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0     0.079   3.5e+02      73     102 ..      48      77 ..      34     195 .. 0.81
   2 !   61.8   0.2   1.8e-20   8.1e-17       1     177 [.     270     474 ..     270     476 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.079
                                    GGGHHHHHHHHHHHHHHHHHHTT.SCEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2b  73 easlddslrdlikaisriferlglefraii 102
                                    ++s++d++++   ++ ++f+r+g +  ++ 
  gi|119719664|ref|YP_920159.1|  48 DGSSQDVVEEAAADVLDVFRRVGASRVVVY 77 
                                    37899999***************8855554 PP

  == domain 2  score: 61.8 bits;  conditional E-value: 1.8e-20
                                    EEEEETTSEEEEE-SSSHHHHHHHHHHHEEEBGGSSEEEEEEEEEEBTTTS.TBCTTTB-SEEEEEEEEEEES.GGGHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                   tRNA-synt_2b   1 YkledrndreyiLkPtneetfvelirdevlrskrLPlklyqiqtkyRdEks.dsrGLlRvreFhqkdgyvfha.easldd 78 
                                    Y++e ++ +++iL+  +++   ++++d+ +  ++LP+  +++   yR E++ ++   +R+r+F + d +vf++  a++ +
  gi|119719664|ref|YP_920159.1| 270 YQMEVDE-KKLILRYAACHQQFAMVKDWEISYRDLPFGAFEVADSYRLEQPgELLLCFRLRKFYMPDLHVFCKdLAEAME 348
                                    6666554.89******************777788****************97777679**************94354444 PP

                                    HHHHHHHHHHHHHHHTT.SCEEEEEEGTTSC...........................BTTSEEEEEEEEETTTSEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........................xxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2b  79 slrdlikaisriferlglefraiielmsaks...........................adykdkkefeavsesltkgiei 131
                                    +   +  +i++  ++lg  +  i +l++ +                                   e ++++e l++ +ei
  gi|119719664|ref|YP_920159.1| 349 VSFRIHSKIYEEIRKLGRDYVSIYNLTRSFLeqhrdylkrlvemegkpvllhfvpegkYYWVINVEYNIIDE-LGRPREI 427
                                    444444444444466688888888886533356777788888888888888877443222222344445555.******* PP

                                    EEEEEEETHHHHHTTEEEECTTSSEEEEEEEEEE.EE.HHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx.xxxxxxxxxx RF
                   tRNA-synt_2b 132 gtiqklgtrlserlgatvldennreksvimicaa.ig.veRllsaile 177
                                    gt q +  + +er+g+t++denn ++ +++i+ a ig +eR + a+l+
  gi|119719664|ref|YP_920159.1| 428 GTFQID-VGNAERFGITYVDENNTRRYPVIIHTAiIGsLERYVFAVLD 474
                                    ******.9************************************9997 PP

>> INT_SG_DDX_CT_C  INTS6/SAGE1/DDX26B/CT45 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   1.2e-05     0.054       5      27 ..     352     374 ..     348     379 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.2e-05
                INT_SG_DDX_CT_C   5 eikkqlvkevRrpgrnyekiFkl 27 
                                    +i +++++e+R+ gr+y  i++l
  gi|119719664|ref|YP_920159.1| 352 RIHSKIYEEIRKLGRDYVSIYNL 374
                                    78999***************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (608 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 4005.17
//
Query:       gi|119719665|ref|YP_920160.1|  [L=397]
Description: radical SAM domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-11   44.9   0.1    1.2e-09   38.8   0.0    3.1  3  Radical_SAM    Radical SAM superfamily
  ------ inclusion threshold ------
      0.084   13.4   0.0       0.99    9.9   0.0    2.3  2  CoA_binding_2  CoA binding domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.0   1.3e-13   1.2e-09       4     166 ..      53     221 ..      50     222 .. 0.89
   2 ?    2.3   0.0     0.022     2e+02      76     103 ..     224     251 ..     216     289 .. 0.81
   3 ?    1.2   0.1     0.047   4.2e+02      11      67 ..     325     383 ..     322     393 .. 0.58

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 1.3e-13
                                    ESEESS--TTTSCCTT..HHHHHHHHHHHHHHHHHHHHHHH.H...HTTSEEEEEESSTGGGSTTHHHHHHHHHHTC..C CS
                                    xxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx.x...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..x RF
                    Radical_SAM   4 trgCnlrCsfCarpet..vrregrgrslsveeileevkelk.a...ekgvkevilgggepllypdfvellerlakla..v 75 
                                      gC++ Cs+C+ p +  + re++++ l+ ee+   + ++  +   + g    + + gep++ p+ + ++ ++++     
  gi|119719665|ref|YP_920160.1|  53 AVGCTYSCSYCYLPDMgiSFREVHVYGLTGEEVSYALLKNPyFlptRFGSQIAVGSVGEPFASPEAASKTMEYIASFekY 132
                                    67****************99****************99986435557777777888*****************9999999 PP

                                    CTEEEEEEECSSCHGHHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  76 pgiritvetngtlpdeeklerllelg.vdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpG 154
                                     g  + ++t ++l+ ee +  l+++  +    +++ ++d+ k l++  + + + e+le+++++r++g+++  +  +++pG
  gi|119719665|ref|YP_920160.1| 133 LGNPVQFSTKAVLD-EETAGWLAQRKvPVNPLVTVVTLDKYKELEP--GAPPPYERLESMRRMRKKGLRPMLFLRPLIPG 209
                                    9************7.*********9999999********9855555..567888888*********************** PP

                                    TSHHHHHHHHHH CS
                                    xxxxxxxxxxxx RF
                    Radical_SAM 155 endeeleellel 166
                                    ++ ee ee+le+
  gi|119719665|ref|YP_920160.1| 210 VTSEEAEEILEE 221
                                    ********9986 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.022
                                    CTEEEEEEECSSCHGHHHHHHHHHTT-S CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  76 pgiritvetngtlpdeeklerllelgvd 103
                                    +   + v++ g+++++ +l+rl ++gvd
  gi|119719665|ref|YP_920160.1| 224 RHGAVGVVIGGLRVTPSILARLEKAGVD 251
                                    3677889999999999999999999966 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.047
                                    -TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHH.H.....HTTSEEEEEESSTGGGSTTHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x.....xxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  11 CsfCarpetvrregrgrslsveeileevkelk.a.....ekgvkevilgggepllypdfvell 67 
                                    C+ C+++          +++++e+ e+++++  +     e + +++ ++gg + l ++ v l+
  gi|119719665|ref|YP_920160.1| 325 CTACPVGC----PSLKTEVDPDEVREIIEKFTgVkgvkvEVDDRYIRVTGGKVRLKKHHVYLI 383
                                    55555554....344445555555555555532222222555777888888887777776665 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00011      0.99      22     104 ..     152     251 ..     147     259 .. 0.83
   2 ?    0.4   0.0     0.098   8.8e+02      83     110 ..     270     297 ..     254     301 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00011
                                    HHHHHT--EEEESSS-SEETTEES----T.....T--......................EEEE-S-HHHHGGGHHHHHHH CS
                  CoA_binding_2  22 yllehglpvvpVnpkeeeilgekvyaslae.dpepvd......................lvdvftppeatpeivkealal 78 
                                    +l +++   vpVnp  + +   ++y++l++ +p                           +   + +e+++ei++ea++ 
  gi|119719665|ref|YP_920160.1| 152 WLAQRK---VPVNPLVTVVTL-DKYKELEPgAPP--PyerlesmrrmrkkglrpmlflrPLIPGVTSEEAEEILEEAKRH 225
                                    555555...899999877776.899999943333..355999999999999999999986777788************** PP

                                    --SEEEE-TT---HHHHHHHHHTT-E CS
                  CoA_binding_2  79 gakavwlqpgsedeeaaelaeeagir 104
                                    ga +v++    + + +++++e+ag++
  gi|119719665|ref|YP_920160.1| 226 GAVGVVIGGLRVTPSILARLEKAGVD 251
                                    *******999************9986 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.098
                                    EEE-TT---HHHHHHHHHTT-EEE.ES- CS
                  CoA_binding_2  83 vwlqpgsedeeaaelaeeagirvvgdrC 110
                                    v l +g  ++e++e+a+++g+     +C
  gi|119719665|ref|YP_920160.1| 270 VPLPLGDLKREVLEIARSKGLVPFLSAC 297
                                    556678999*********9997554555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 2472.61
//
Query:       gi|119719666|ref|YP_920161.1|  [L=83]
Description: hypothetical protein Tpen_0756 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-10   40.9   0.0      3e-10   40.7   0.0    1.1  1  MJ1316    MJ1316 RNA cyclic group end recognition domain
  ------ inclusion threshold ------
      0.071   13.2   0.0       0.12   12.4   0.0    1.4  1  bPH_4     Bacterial PH domain


Domain annotation for each model (and alignments):
>> MJ1316  MJ1316 RNA cyclic group end recognition domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7   0.0   3.3e-14     3e-10       6      76 .]       3      77 ..       1      77 [. 0.80

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 3.3e-14
                         MJ1316  6 dvlnRirWdkeldkskfvvgyldR..fkgikevpleeiswied..flleeeegelaIPlHRiryikrkgevvWdR 76
                                   + lnR++Wdk ldks +vv ++ R   ++     ++++ ++ +  ++++ e  e +IP+ Ri +i+ +g+vv+++
  gi|119719666|ref|YP_920161.1|  3 NYLNRLLWDKTLDKSSVVVKFISRsaVSDEGSFLGTQVLRVTRdgVVISVEGFEKFIPFTRITEIEENGRVVFSK 77
                                   679*********************763333333344444444457799999989*******************87 PP

>> bPH_4  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.4e-05      0.12       7      41 ..      45      79 ..      40      81 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.4e-05
                          bPH_4  7 egvLliksGfirkkIpiedIkkirktksplsspal 41
                                    +  +i+   ++k Ip+ +I++i++++ +++s+ l
  gi|119719666|ref|YP_920161.1| 45 RDGVVISVEGFEKFIPFTRITEIEENGRVVFSKKL 79
                                   55555666669****************99998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       253  (0.0141112); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.45
# Mc/sec: 555.72
//
Query:       gi|119719667|ref|YP_920162.1|  [L=342]
Description: glyceraldehyde-3-phosphate dehydrogenase, type I [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-63  213.3   0.0    1.8e-63  212.8   0.0    1.2  1  Gp_dh_C   Glyceraldehyde 3-phosphate dehydrogenase, C-termina
    2.5e-35  120.8   0.0    8.1e-35  119.2   0.0    1.9  2  Gp_dh_N   Glyceraldehyde 3-phosphate dehydrogenase, NAD bindi


Domain annotation for each model (and alignments):
>> Gp_dh_C  Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  212.8   0.0     2e-67   1.8e-63       1     158 []     161     320 ..     161     320 .. 0.99

  Alignments for each domain:
  == domain 1  score: 212.8 bits;  conditional E-value: 2e-67
                                    HHHHHHHHHHHHEEEEEEEEEEEECTTTSBSSSS--.SSTTTTSBTTCSSEEEE-THHHHHHHHSGGGTTTEEEEEEEES CS
                        Gp_dh_C   1 LaplakvlndkfgikkglmttvhaytndQkllDgpskkdlrraraaaeniiptstgaakavglVlpelkgkldglAvrVP 80 
                                    Lap+++vl ++fg++ g+mttvhaytndQ++lD  + +d+rr+raaa niipt+tgaa+a++lV+pe+kgkldg+A+rVP
  gi|119719667|ref|YP_920162.1| 161 LAPVVYVLLKNFGLEWGFMTTVHAYTNDQRVLDLIHPEDFRRTRAAALNIIPTTTGAARALHLVIPEVKGKLDGMAMRVP 240
                                    8******************************************************************************* PP

                                    SSSEEEEEEEEEESSTS-HHHHHHHHHHHHHTTTTTTEEEEHSHHHGGGGTTGCSSEEEEGGGCEEET..TTEEEEEEEE CS
                        Gp_dh_C  81 tpnvsvvdlvvelekevtveevnaalkeaaegalkgilsyteeelvssDlvgdphssifdaketivve..enlvkvvawy 158
                                    + ++svvdlv ++ +e t+ee  aa+keaae++lkgil+y +e++vssD+vg+phssi+da++++v+   +n+vkvvawy
  gi|119719667|ref|YP_920162.1| 241 VADGSVVDLVAQIGREITKEELDAAFKEAAETYLKGILEYVDEPIVSSDIVGNPHSSIYDAQASMVLGgkSNKVKVVAWY 320
                                    *******************************************************************98899*******9 PP

>> Gp_dh_N  Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.2   0.0     9e-39   8.1e-35       1     100 [.       3     106 ..       3     107 .. 0.94
   2 ?   -2.4   0.0      0.68   6.1e+03      53      77 ..     295     321 ..     278     335 .. 0.63

  Alignments for each domain:
  == domain 1  score: 119.2 bits;  conditional E-value: 9e-39
                                    CEEEEESTSHHHHHHHHHHHHHT....TCEEEEEE-TS-HHHHHHHHHEETTTEC-SS-EEEETTEEEETTEEEEEE--S CS
                        Gp_dh_N   1 vkvainGfGRIGrlvlralleek....elevvaindltdletlayllkyDsvhgrfkgeveaeeealvvngkkikvlaek 76 
                                    ++v+inGfGRIGr++lra+l+++    ++e+vaindl+++++layllkyDsv+gr++++ve+++++lvv+g ++ vl+e+
  gi|119719667|ref|YP_920162.1|   3 IRVGINGFGRIGRNFLRAALKNEkffdKFEIVAINDLGSPKMLAYLLKYDSVFGRLPNKVEVKDNKLVVDGMEMLVLNEA 82 
                                    69******************443234589*************************************************** PP

                                    SGGGS-CHHHTSSEEEE-SSS--S CS
                        Gp_dh_N  77 dpeelpwkelgvdlVvestGvftd 100
                                    +pe+lpwk+lgvd+ +e+tG ftd
  gi|119719667|ref|YP_920162.1|  83 SPEKLPWKDLGVDVALEATGRFTD 106
                                    **********************98 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.68
                                    SS-EEEETTEEEETTE..EEEEE--SS CS
                        Gp_dh_N  53 kgeveaeeealvvngk..kikvlaekd 77 
                                    ++++   ++++v++gk  k+kv+a  d
  gi|119719667|ref|YP_920162.1| 295 HSSIYDAQASMVLGGKsnKVKVVAWYD 321
                                    455555566777777544666666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 2169.25
//
Query:       gi|119719668|ref|YP_920163.1|  [L=425]
Description: metallophosphoesterase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.7e-12   46.1   0.1      1e-11   45.3   0.1    1.4  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    4.4e-10   40.4   3.5    2.2e-09   38.1   3.5    2.0  1  Metallophos    Calcineurin-like phosphoesterase
     0.0074   15.6   0.0       0.68    9.2   0.0    2.3  2  Metallophos_3  Metallophosphoesterase, calcineurin superfamil
  ------ inclusion threshold ------
      0.083   12.8   2.0       0.17   11.8   2.0    1.5  1  DUF35_N        Rubredoxin-like zinc ribbon domain (DUF35_N)


Domain annotation for each model (and alignments):
>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   0.1   2.3e-15     1e-11       2     162 ..       5     207 ..       4     209 .. 0.71

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 2.3e-15
                  Metallophos_2   2 klaiiSDlHsnldaleavlealkevg..vdaiihaGDl.eeeepevleellela......pvlaVrGNnD.......... 62 
                                    +++++SD+H++ d++++++e +++ +  +d ++ aGD+ + + p +++++l+         v++V+GN+D          
  gi|119719668|ref|YP_920163.1|   5 RFLAVSDVHGKEDLVDKFIEWVQRDSlpYDFVVAAGDMgNPQRPGSMCRILKKIasslkkNVYYVKGNWDiegscgdpav 84 
                                    799******99999999999998854338*********877777777777766568889***********7666655444 PP

                  Metallophos_2  63 .........eevveedvlreaaelgtdl.........peeaelel...agekvlliHgdpl.................gv 104
                                                               +           ++  ++   ++++vl++H+ p+                 ++
  gi|119719668|ref|YP_920163.1|  85 ldldetgplF-----------------FgnivlvghgRRAEPYDIpraNNVTVLVTHYPPYsildrgkvidsnhrslhAG 147
                                    4443333330.................13334444432333333332355558888887778888888887777777788 PP

                  Metallophos_2 105 kdalaellkeaeegsdvvvcGHtHvp..evekeggvlvvnPGsvgeprdgdpe..tyaildt 162
                                      ++ +l++   ++ +v ++GH+H       +++gv++vn   + +  +  +    ya++d+
  gi|119719668|ref|YP_920163.1| 148 VVDINYLIDV--YRPRVHIFGHSHSYggLDVEHNGVVYVNVARLDRLLKNGESigNYAVIDV 207
                                    8889999999..8889**********864444569*****9888887555544567777775 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   3.5   4.9e-13   2.2e-09       2     204 .]       5     171 ..       4     171 .. 0.73

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 4.9e-13
                                    EEEEEESBTBTTCCTHHHHHHHHHHHHHHH.TTESEEEEESTSSSSSHHHHHHHHHHHHHHHH.TSEEEEEC-TTSCHHH CS
                    Metallophos   2 rilvigDlHlalgggqlddllkllddllre.ekpdlvllaGDlvdrgdlekellellaalvky.pipvylllGNHegfee 79 
                                    r+l ++D+H     g  d ++k++++++r+    d+v+ aGD  +   + + + + l++  ++ +++vy ++GN +  e 
  gi|119719668|ref|YP_920163.1|   5 RFLAVSDVH-----GKEDLVDKFIEWVQRDsLPYDFVVAAGDMGNPQRPGS-MCRILKKIASSlKKNVYYVKGNWD-IEG 77 
                                    89*******.....*************6662555888888**999998888.77776666666779**********.333 PP

                                    HHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESECEEETHHHHHHHHHHHSCHHHHCCHHHHHHHHHHTT CS
                    Metallophos  80 ellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGgspellvsldklgslnleleapepgdewlkdlekrek 159
                                    ++  +    +        d +  + l           vl+ hG  +e                     +++ +       
  gi|119719668|ref|YP_920163.1|  78 SCGDP----A-----VL-DLDETGPLFFGN------IVLVGHGRRAEP--------------------YDIPRA------ 115
                                    44444....1.....11.122223333333......566667774444....................555555...... PP

                                    CSEEEEEESSESS...........CSSSCSCCHHHHHHHHHHTTESEEEEESSSSE CS
                    Metallophos 160 adwvivlgHsply...........rgsgylfgdealedllkkygvdlvisGHtHvy 204
                                    + ++++++H p+y           ++ + + g   +  l + y++ + i+GH+H y
  gi|119719668|ref|YP_920163.1| 116 NNVTVLVTHYPPYsildrgkvidsNHRSLHAGVVDINYLIDVYRPRVHIFGHSHSY 171
                                    89***************8888876666666666666677***************86 PP

>> Metallophos_3  Metallophosphoesterase, calcineurin superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0   0.00015      0.68       7      46 ..       5      46 ..       1      75 [. 0.86
   2 !    4.3   0.0    0.0048        21     190     221 ..     139     170 ..     114     210 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00015
                                   EEEEEE--TT-GGGHHHHHHHHHHH..--SEEEEES-----H CS
                  Metallophos_3  7 kvlaisdlkgevellerlveviedk..dpDllvlvGdlvkae 46
                                   + la+sd++g+ +l+++ +e ++      D +v  Gd+ +++
  gi|119719668|ref|YP_920163.1|  5 RFLAVSDVHGKEDLVDKFIEWVQRDslPYDFVVAAGDMGNPQ 46
                                   78******************997552467********96554 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0048
                                    BTTBS---S-HHHHHHHHHH--SEEEE-SS-- CS
                  Metallophos_3 190 adkglkekgsevvaelvktlnPevvvvghavk 221
                                     ++   ++g   ++ l+  ++P+v + gh++ 
  gi|119719668|ref|YP_920163.1| 139 SNHRSLHAGVVDINYLIDVYRPRVHIFGHSHS 170
                                    333446899999*****************986 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   2.0   3.7e-05      0.17      13      32 ..     226     248 ..     225     252 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.7e-05
                        DUF35_N  13 rCpdCGtvqfPPr..avCphC.g 32 
                                    rC+ CG+v++ P+  a C++C +
  gi|119719668|ref|YP_920163.1| 226 RCAGCGRVVHIPEkwALCRRCaH 248
                                    9***********99888999944 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      579  (0.032294); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.34s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 2554.21
//
Query:       gi|119719669|ref|YP_920164.1|  [L=233]
Description: hypothetical protein Tpen_0759 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1496.46
//
Query:       gi|119719670|ref|YP_920165.1|  [L=874]
Description: redoxin domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.8e-16   58.1   4.1    6.2e-09   36.0   0.9    3.8  4  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
      1e-08   35.0   0.0    2.3e-05   24.3   0.0    2.7  2  CarbopepD_reg_2  CarboxypepD_reg-like domain
    1.9e-07   31.3   0.0      5e-07   29.9   0.0    1.8  1  Thioredoxin_8    Thioredoxin-like
    4.5e-05   23.4   0.0     0.0097   15.9   0.0    2.6  2  Thioredoxin      Thioredoxin
    4.7e-05   23.2   0.0       0.04   13.8   0.0    2.6  2  PEGA             PEGA domain
    7.2e-05   22.7   0.0     0.0002   21.3   0.0    1.7  2  AhpC-TSA         AhpC/TSA family
    0.00043   20.7   0.0      0.002   18.6   0.0    2.0  2  Thioredoxin_2    Thioredoxin-like domain
     0.0031   17.4   0.0     0.0061   16.5   0.0    1.4  1  SCO1-SenC        SCO1/SenC
     0.0035   17.1   0.0     0.0079   15.9   0.0    1.6  1  Redoxin          Redoxin
     0.0089   16.0   0.1       0.27   11.3   0.0    2.8  2  Big_1            Bacterial Ig-like domain (group 1)
  ------ inclusion threshold ------
      0.024   14.7   0.4       0.38   10.8   0.1    2.5  2  Thioredoxin_3    Thioredoxin domain


Domain annotation for each model (and alignments):
>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0         2   3.3e+03      24      69 ..     119     161 ..     114     167 .. 0.74
   2 !   20.2   0.0   3.3e-07   0.00054       2      73 ..     387     453 ..     386     460 .. 0.80
   3 !   36.0   0.9   3.8e-12   6.2e-09       3      82 .]     470     544 ..     468     544 .. 0.92
   4 ?   -1.3   0.0       1.6   2.7e+03      11      28 ..     556     573 ..     545     618 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2
                CarboxypepD_reg  24 adtgtvastttdadGafrlrglppgtysvtvsapGyatatreevtl 69 
                                    +d++ v ++   +dG+f    l+  +y+++   + y +a+   v+l
  gi|119719670|ref|YP_920165.1| 119 SDENYVEGAALSRDGRFLA--LKV-KYTLVYNNNKYSEARLAVVDL 161
                                    5677788888889999985..444.689998888888888776665 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 3.3e-07
                CarboxypepD_reg   2 isGrVtdasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatreevtltagq 73 
                                    ++ rV d+ g+ ++ga+++++ +++      + +++G  +l+ lppg y+v v ++G+ ++ ++ + lt ++
  gi|119719670|ref|YP_920165.1| 387 LTIRVLDEAGNILPGAQLIIRGKGG---PLLRNAEQGVVQLE-LPPGVYEVSVARQGFSPVDYP-LNLTSDT 453
                                    6789*****************4333...33455689999997.******************996.7777554 PP

  == domain 3  score: 36.0 bits;  conditional E-value: 3.8e-12
                CarboxypepD_reg   3 sGrVtdasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatreevtltagqtttlditLe 82 
                                       V  ++g+p+++a+V +    + +v st+td+ G+  + ++p g+y+v v+a  y+ ++ + +++ a+ t  +++tL+
  gi|119719670|ref|YP_920165.1| 470 VVAVFGETGEPLPEANVKLV---GPEVVSTRTDSRGYAGF-NVPIGNYTVIVEAGRYERYEGR-ISVGANFTDPIRVTLK 544
                                    5568899*************...799**************.5*******************86.***9999999999995 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 1.6
                CarboxypepD_reg  11 gapiagatVtvtnadtgt 28 
                                    g ++ g++V + + +tg+
  gi|119719670|ref|YP_920165.1| 556 GDGVQGVKVYAVSMSTGE 573
                                    445555555555554443 PP

>> CarbopepD_reg_2  CarboxypepD_reg-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0    0.0018         3       5      86 ..     391     469 ..     390     473 .. 0.79
   2 !   24.3   0.0   1.4e-08   2.3e-05       9      78 ..     476     545 ..     470     555 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0018
                CarbopepD_reg_2   5 VvdketkeplpgatVyvkgtkkgtv.TdenGnFelknlpagkytLvvsyvGyktqekkvtvskektldvnillkeealel 83 
                                    V+d+  ++ lpga+ ++ g++       e+G  +l+ lp+g y++ v   G+ ++   +++++++ l+++  l+ ea + 
  gi|119719670|ref|YP_920165.1| 391 VLDEA-GNILPGAQLIIRGKGGPLLrNAEQGVVQLE-LPPGVYEVSVARQGFSPVDYPLNLTSDTFLELR--LSREAPKR 466
                                    88876.58***********98665515579*****6.9***********************999988866..44444444 PP

                CarbopepD_reg_2  84 eev 86 
                                      v
  gi|119719670|ref|YP_920165.1| 467 VSV 469
                                    444 PP

  == domain 2  score: 24.3 bits;  conditional E-value: 1.4e-08
                CarbopepD_reg_2   9 etkeplpgatVyvkgtk.kgtvTdenGnFelknlpagkytLvvsyvGyktqekkvtvskektldvnillke 78 
                                    et+eplp a+V + g + + t Td+ G+  + n+p g+yt++v++  y+  e +++v  + t  ++++lk 
  gi|119719670|ref|YP_920165.1| 476 ETGEPLPEANVKLVGPEvVSTRTDSRGYAGF-NVPIGNYTVIVEAGRYERYEGRISVGANFTDPIRVTLKL 545
                                    689**********997648999*********.6************************99876555554443 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.0   3.1e-10     5e-07       1      95 []     676     764 ..     676     764 .. 0.93

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 3.1e-10
                                    .SEEEEEE--SSSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-SS-HHHHHHHGGGS-TTSEE.EE-TT-HHHHTT-S-- CS
                  Thioredoxin_8   1 gkvvlLyfgaswcppckaftpklkelyeklkkkkkveivyvsldkkeeefekylkknkkpwlsvpfddkkrnklkkkynv 80 
                                    g+++++ f+ ++c  ck  +p lk++ e+ +    v+ ++vs   ++e  ++y+++n+ +wl  + +d+    l + +nv
  gi|119719670|ref|YP_920165.1| 676 GRILVIEFFYTQCTGCKYLLPVLKRIAESGN--ATVVSLSVSPLDTNEVLRRYIEENNVTWLVGRAGDD----LVQAFNV 749
                                    6889999***********************9..9********9999***********999**9777755....9****** PP

                                    TT-SEEEEE-TT-BE CS
                  Thioredoxin_8  81 kaiPtlvvldkngev 95 
                                    +a+Pt+vv+d ++ v
  gi|119719670|ref|YP_920165.1| 750 SAFPTVVVIDGDRVV 764
                                    **********99875 PP

>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0     6e-06    0.0097      18      56 ..     676     714 ..     670     734 .. 0.79
   2 ?    4.4   0.0     0.022        37      62      96 ..     741     773 ..     738     780 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 6e-06
                                    SSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEE CS
                    Thioredoxin  18 kklvlveFyApwCghCkalaPeleklaeelkdkvklakv 56 
                                     + +++eF+ + C+ Ck l P+l+++ae  +++v+ + v
  gi|119719670|ref|YP_920165.1| 676 GRILVIEFFYTQCTGCKYLLPVLKRIAESGNATVVSLSV 714
                                    67899***********************99886655554 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.022
                                    HHHHHHTT-SSSSEEEEEETTEEEEEEESS-HHHH CS
                    Thioredoxin  62 edlakkyevegiPtlklfkngkevkkyegarekek 96 
                                    +dl++ ++v+++Pt++++  ++ v    ga+e  +
  gi|119719670|ref|YP_920165.1| 741 DDLVQAFNVSAFPTVVVIDGDRVVFVGMGAKE--E 773
                                    58899**********88877765554444443..4 PP

>> PEGA  PEGA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5   0.0    0.0047       7.6      27      62 ..     422     457 ..     421     463 .. 0.84
   2 !   13.8   0.0   2.5e-05      0.04      31      67 ..     508     544 ..     505     548 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0047
                           PEGA  27 vtlsleaGnyslrvekeGYedlektvtvtagetvkl 62 
                                    v+l+l++G y++ v   G++++    ++t+++ ++l
  gi|119719670|ref|YP_920165.1| 422 VQLELPPGVYEVSVARQGFSPVDYPLNLTSDTFLEL 457
                                    5788*****************999999888776665 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 2.5e-05
                           PEGA  31 leaGnyslrvekeGYedlektvtvtagetvklnltLe 67 
                                    ++ Gny++ ve+  Ye +e +++v a+ t  + +tL+
  gi|119719670|ref|YP_920165.1| 508 VPIGNYTVIVEAGRYERYEGRISVGANFTDPIRVTLK 544
                                    788**********************998866666655 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0         8   1.3e+04      58      71 ..     560     573 ..     559     576 .. 0.81
   2 !   21.3   0.0   1.2e-07    0.0002      12     121 ..     662     764 ..     656     766 .. 0.85

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 8
                                    TTEEEEEEESSSCH CS
                       AhpC-TSA  58 rgvevigvsvdspe 71 
                                    +gv+v++vs+ + e
  gi|119719670|ref|YP_920165.1| 560 QGVKVYAVSMSTGE 573
                                    69*******97765 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 1.2e-07
                                    STTCEEEECHHH.TTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEES.SSCHHHHHHHHH-H.SSEEEE- CS
                       AhpC-TSA  12 nadgetvslsdy.kgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsv.dspeshkkfiekeslnfpllsD 89 
                                      +  t sl d+ +g+++v+ f+ + +c +C+  lp l++ + e  ++ v  + vs+ d+ e ++++ie++++++ +   
  gi|119719670|ref|YP_920165.1| 662 LYNSSTLSLRDVqRGRILVIEFFYT-QCTGCKYLLPVLKRIA-ESGNATVVSLSVSPlDTNEVLRRYIEENNVTWLVG-R 738
                                    4456799*****999*********9.*******999998866.5566788899999999************9888554.4 PP

                                    TTSHHHHHTT-EETTTTECSCEEEEE-TTSBE CS
                       AhpC-TSA  90 eegkvakaygvlkeekglalratfvidkegki 121
                                       ++++a++v       a ++++vid + ++
  gi|119719670|ref|YP_920165.1| 739 AGDDLVQAFNVS------AFPTVVVIDGDRVV 764
                                    688999******......99*******99876 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       3.2   5.2e+03      12      30 ..     196     214 ..     189     232 .. 0.75
   2 !   18.6   0.0   1.2e-06     0.002       4     106 ..     675     775 ..     673     777 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3.2
                  Thioredoxin_2  12 ftdpdCpyCkklkkelkel 30 
                                      d++C  C+   ++++ +
  gi|119719670|ref|YP_920165.1| 196 TIDTKCELCQYTDNKIEVY 214
                                    44999****9999888766 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 1.2e-06
                  Thioredoxin_2   4 ngkpvlvvftdpdCpyCkklkkelkel.ddvtvrvllfp...lkpsfepkavaiwcakekkkafkdieenvelarkygvr 79 
                                     g+ +++ f  ++C  Ck l  +lk + ++ + +v+      l+ +   ++ + + +++ + ++    +  +l+++++v+
  gi|119719670|ref|YP_920165.1| 675 RGRILVIEFFYTQCTGCKYLLPVLKRIaESGNATVVSLSvspLDTN---EVLRRYIEENNV-TWLVGRAGDDLVQAFNVS 750
                                    57788889999****************9666666555554467766...444444444443.4555689999******** PP

                  Thioredoxin_2  80 gtPtivfldgkeivarlpGyvpaeele 106
                                    ++Pt+v++dg+++  + +G+  +eele
  gi|119719670|ref|YP_920165.1| 751 AFPTVVVIDGDRV--VFVGMGAKEELE 775
                                    ***********55..566777777765 PP

>> SCO1-SenC  SCO1/SenC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   3.8e-06    0.0061       8      83 ..     662     731 ..     656     752 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.8e-06
                      SCO1-SenC   8 dqdgeavteedl.egkpslvffgFthCpdvCpttlanmaevldalgeeaekvqplfiTvDPerDtpevlkeyleafd 83 
                                      +  + + +d+ +g++ ++ f++t+C+  C   l+ ++++ +  +      ++++ +v P  Dt evl++y+e+ +
  gi|119719670|ref|YP_920165.1| 662 LYNSSTLSLRDVqRGRILVIEFFYTQCTG-CKYLLPVLKRIAESGN-----ATVVSLSVSPL-DTNEVLRRYIEENN 731
                                    555555555555279************75.9998888877765544.....469*******7.**********9765 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   4.9e-06    0.0079      18     127 ..     665     764 ..     655     781 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.9e-06
                                    EEEEEHHH.HTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHHHHHHHHH..TT-TSEEEE-.T CS
                        Redoxin  18 gnsvslse.fkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndafvkefwgk..eglkfpvlsD.g 93 
                                     +++sl++ ++g+ +v+ f+ + +c  C+  +p l+ +ae    ++ +vv ++++  +  +e++ +  e+++++ l+  +
  gi|119719670|ref|YP_920165.1| 665 SSTLSLRDvQRGRILVIEFFYT-QCTGCKYLLPVLKRIAES---GNATVVSLSVSPLD-TNEVLRRyiEENNVTWLVGrA 739
                                    6789****99************.******988777777665...44444444444333.444444444444788888866 PP

                                    TSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEE CS
                        Redoxin  94 saaftkalGlrleedaseglrtpryavidedgkv 127
                                    + ++++a+++          + p+++vid d +v
  gi|119719670|ref|YP_920165.1| 740 GDDLVQAFNVS---------AFPTVVVIDGDRVV 764
                                    99*******88.........********998766 PP

>> Big_1  Bacterial Ig-like domain (group 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   0.00017      0.27       5      36 ..     383     414 ..     381     423 .. 0.83
   2 ?    1.3   0.1      0.21   3.4e+02      11      51 ..     471     507 ..     466     509 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00017
                          Big_1   5 dtntltatvkDangnpvagatVtfsvsggals 36 
                                    ++++lt++v D+ gn ++ga+  ++  gg l+
  gi|119719670|ref|YP_920165.1| 383 TSVKLTIRVLDEAGNILPGAQLIIRGKGGPLL 414
                                    6899****************998887777665 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.21
                          Big_1  11 atvkDangnpvagatVtfsvsggalsassgtTdanGkatvt 51 
                                    + v  + g p++ a+V++  +       s++Td+ G a ++
  gi|119719670|ref|YP_920165.1| 471 VAVFGETGEPLPEANVKLVGPE----VVSTRTDSRGYAGFN 507
                                    6666678999999999988666....346799999998766 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0       0.3     5e+02       5      30 ..     683     708 ..     679     715 .. 0.81
   2 ?   10.8   0.1   0.00023      0.38      16      72 ..     719     775 ..     713     778 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.3
                                    EESSSSTTCHHHHHHHHHHCHCCTCE CS
                  Thioredoxin_3   5 vlgpgCakCpklekavkeaaaekgik 30 
                                     + ++C+ C+ l  ++k++a++ + +
  gi|119719670|ref|YP_920165.1| 683 FFYTQCTGCKYLLPVLKRIAESGNAT 708
                                    56799*********999999987755 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00023
                                    HHHHHHHHCHCCTCECEEECCTTHHHH.HHCT-SSSSEE.ECT.TCEEEESS---CCHHH CS
                  Thioredoxin_3  16 lekavkeaaaekgikaevekvtdfeei.ekygVmsvPal.vid.gkvvvsGkvpseeeir 72 
                                    ++++++++++e++++  v ++ d  ++ + ++V + P++ vid ++vv++G +  +ee++
  gi|119719670|ref|YP_920165.1| 719 TNEVLRRYIEENNVTWLVGRAGD--DLvQAFNVSAFPTVvVIDgDRVVFVG-MGAKEELE 775
                                    67888999999999999998854..44477*********999*889*****.88888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (874 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.68u 0.28s 00:00:00.96 Elapsed: 00:00:00.44
# Mc/sec: 5903.38
//
Query:       gi|119719671|ref|YP_920166.1|  [L=141]
Description: hypothetical protein Tpen_0761 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-05   24.4   1.7    2.1e-05   24.4   1.7    1.8  2  DUF2205          Short coiled-coil protein
    0.00012   22.0   3.0      0.061   13.2   0.9    2.2  2  Prefoldin        Prefoldin subunit
    0.00097   18.6   0.5     0.0012   18.3   0.5    1.1  1  Not3             Not1 N-terminal domain, CCR4-Not complex com
     0.0045   17.2   0.4      0.069   13.4   0.2    2.2  2  FliJ             Flagellar FliJ protein
     0.0063   17.0   1.3       0.52   10.8   0.1    2.1  2  Spectrin         Spectrin repeat
     0.0076   16.4   4.9       0.15   12.2   4.8    2.0  1  Uds1             Up-regulated During Septation
  ------ inclusion threshold ------
      0.011   16.2   3.6       0.67   10.5   3.6    2.3  1  NPV_P10          Nucleopolyhedrovirus P10 protein
      0.015   14.5   0.7      0.094   11.8   0.2    1.9  2  RmuC             RmuC family
      0.017   15.6   3.9        1.2    9.6   1.0    2.2  2  Snapin_Pallidin  Snapin/Pallidin
       0.02   14.0   0.4      0.024   13.8   0.4    1.0  1  Rota_NSP3        Rotavirus non-structural protein NSP3
      0.029   14.1   3.5      0.075   12.8   1.0    2.1  2  DivIC            Septum formation initiator
      0.033   14.8   1.0        7.9    7.2   0.0    2.3  2  ThiS             ThiS family
      0.042   14.2   1.9      0.042   14.2   1.9    2.1  2  BLOC1_2          Biogenesis of lysosome-related organelles co
       0.06   13.6   2.4        1.9    8.8   0.3    2.1  2  THOC7            Tho complex subunit 7
      0.062   11.6   0.3      0.071   11.4   0.3    1.1  1  FBPase_2         Firmicute fructose-1,6-bisphosphatase
      0.064   13.2   4.2      0.059   13.3   2.5    1.7  1  DASH_Spc19       Spc19
      0.076   13.6   0.0       0.11   13.2   0.0    1.3  1  3HCDH            3-hydroxyacyl-CoA dehydrogenase, C-terminal 
      0.078   12.5   0.3      0.091   12.3   0.3    1.2  1  Vmethyltransf_C  Viral methyltransferase C-terminal
       0.13   12.6   6.5       0.12   12.6   2.7    2.2  2  ABC_tran_CTD     ABC transporter C-terminal domain
       0.15   12.2   4.0       0.28   11.4   4.0    1.4  1  Fib_alpha        Fibrinogen alpha/beta chain family
       0.18   11.6   0.8         12    5.8   0.1    2.8  3  DASH_Dam1        DASH complex subunit Dam1
       0.19   11.1   1.6        1.2    8.5   0.1    2.1  2  DUF639           Plant protein of unknown function (DUF639)
       0.22   11.3   4.2       0.11   12.3   1.0    1.8  2  OEP              Outer membrane efflux protein
       0.26   11.3   3.5       0.75    9.8   0.6    2.1  2  DUF1664          Protein of unknown function (DUF1664)
       0.39   10.8   7.3       0.41   10.7   2.7    2.1  2  DHR10            Designed helical repeat protein 10 domain
       0.41    9.9   6.2       0.46    9.7   4.7    1.7  2  DUF3450          Protein of unknown function (DUF3450)
       0.42   10.6   8.4       0.51   10.3   2.8    2.7  3  Prefoldin_2      Prefoldin subunit
       0.59    9.0   6.9        1.2    7.9   7.0    1.5  1  Spc7             Spc7 kinetochore protein
       0.68   10.6   6.3        2.4    8.8   1.2    2.5  2  SlyX             SlyX
        2.9    7.1   6.2         21    4.3   6.2    1.9  1  CorA             CorA-like Mg2+ transporter protein
          3    8.1   5.6        4.4    7.6   5.6    1.3  1  zf-C4H2          Zinc finger-containing protein


Domain annotation for each model (and alignments):
>> DUF2205  Short coiled-coil protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   1.7   3.7e-08   2.1e-05      20      62 ..      17      59 ..      12      68 .. 0.90
   2 ?   -0.9   0.1       2.9   1.7e+03      32      43 ..      98     109 ..      77     118 .. 0.48

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 3.7e-08
                        DUF2205 20 rLqqqakeLqssLqaLaervdeVkeehdKLesenrfLqqYIgd 62
                                    L++q+++Lq++L++L +r ++Vk   +K++   r+L +  g+
  gi|119719671|ref|YP_920166.1| 17 YLDSQIESLQKTLEQLEQRYEAVKVRAEKMREIERVLEELMGE 59
                                   6899*********************************987776 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.9
                        DUF2205  32 LqaLaervdeVk 43 
                                    L++L++  d+++
  gi|119719671|ref|YP_920166.1|  98 LDSLVNVRDAIQ 109
                                    333333222222 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.9   0.00011     0.061      80     114 ..      16      50 ..      11      62 .. 0.86
   2 !    8.8   0.0    0.0025       1.4       4      58 ..      83     140 ..      81     141 .] 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00011
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Prefoldin  80 ellkkkleelekqlekleeeleklkdqittleanl 114
                                    ++l+ ++e+l+k+le+le+  e  k ++++++++ 
  gi|119719671|ref|YP_920166.1|  16 KYLDSQIESLQKTLEQLEQRYEAVKVRAEKMREIE 50 
                                    89999999999999999999999999888887665 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0025
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT....-TT-EEEEEEETTEEEEEE--ST CS
                      Prefoldin   4 eleslqaelaqlkeaieelektletlktlkk...edegkevlvplgaglyvkaevkdt 58 
                                    el+ l++++++ ++ +++l ++++++++l++   + +g+ +lv+l  g+ v++ +k+t
  gi|119719671|ref|YP_920166.1|  83 ELAVLEETIESQRDILDSLVNVRDAIQKLSEhlqGYDGIPILVQLVNGVPVRILLKET 140
                                    6777999999**********************9999*********9999888877776 PP

>> Not3  Not1 N-terminal domain, CCR4-Not complex component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.5   2.1e-06    0.0012     123     214 ..      13     106 ..      11     123 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.1e-06
                           Not3 123 earewlkdaideLneqvekleaeieklsskkkkkkk.skeka.rveeleklierhkfhieklelllrlleneelepeeve 200
                                    e+ ++l+++i++L++ +e+le+ +e ++++ +k ++ ++  +  + e  + +++  +   kl    r++++ ++ +e++e
  gi|119719671|ref|YP_920166.1|  13 ELLKYLDSQIESLQKTLEQLEQRYEAVKVRAEKMREiERVLEeLMGEKLSPLNEVDYMGLKLVINARAIDELAVLEETIE 92 
                                    5679***********************999888875444333233344444555566666666677889999999999*9 PP

                           Not3 201 kikedieyyvesnq 214
                                    + ++ ++  v+  +
  gi|119719671|ref|YP_920166.1|  93 SQRDILDSLVNVRD 106
                                    99999998887654 PP

>> FliJ  Flagellar FliJ protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.2   0.00012     0.069      45      87 ..       6      48 ..       2      67 .. 0.77
   2 ?    1.9   0.0      0.42   2.5e+02       8      33 ..      85     110 ..      74     123 .. 0.53

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00012
                           FliJ 45 aelrnyqafisaldeaiaqqkqelaqaekqvekareewqearq 87
                                   +++  + + +++ld++i++++++l+q+e++ e+ + +  + r 
  gi|119719671|ref|YP_920166.1|  6 YQFNGFGELLKYLDSQIESLQKTLEQLEQRYEAVKVRAEKMRE 48
                                   566677789999*****************99988766555555 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.42
                           FliJ   8 aeaqrelqqaeekleeleqyrqeyqk 33 
                                    a  +  +++++  l++l + r+  qk
  gi|119719671|ref|YP_920166.1|  85 AVLEETIESQRDILDSLVNVRDAIQK 110
                                    33344444444444444444444433 PP

>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.1    0.0009      0.52      68     100 ..      15      47 ..       7      49 .. 0.85
   2 ?    5.4   0.1     0.045        26      13      69 ..      53     110 ..      50     119 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0009
                                    HHTTHTTHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Spectrin  68 ldeghsaseeieerleelnerWeeLkelaaerk 100
                                    l++ +s+ e ++++le+l++r+e++k +a++++
  gi|119719671|ref|YP_920166.1|  15 LKYLDSQIESLQKTLEQLEQRYEAVKVRAEKMR 47 
                                    5666788899*****************999887 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.045
                                    HHHHHHHHHHHHCCSSC.SSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Spectrin  13 leeWieekeellssedl.gkdleevqallkkhkaleaelaaqqervkalnelaeklld 69 
                                    lee + ek   l++ d+ g +l    + ++++  le+++++q++ +++l  + +++++
  gi|119719671|ref|YP_920166.1|  53 LEELMGEKLSPLNEVDYmGLKLVINARAIDELAVLEETIESQRDILDSLVNVRDAIQK 110
                                    7888999999999999999999999999999999*********999999866666643 PP

>> Uds1  Up-regulated During Septation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   4.8   0.00027      0.15      22     112 ..      21     105 ..      15     114 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00027
                           Uds1  22 eVeelkkelkaLeerlealrkkLaletklrdaarsLsrlyssskksakssaarsnskssreslakaeeelaeserkvdel 101
                                    ++e+l+k l++Le+r ea++ +     k+r+  r L++l+ ++++     ++ +    +   +a+a +ela +e+ ++  
  gi|119719671|ref|YP_920166.1|  21 QIESLQKTLEQLEQRYEAVKVR---AEKMREIERVLEELMGEKLSP---LNEVDYMGLKLVINARAIDELAVLEETIESQ 94 
                                    79********************...***************766666...2222233333345677777777777777766 PP

                           Uds1 102 aselekleera 112
                                     + l +l + +
  gi|119719671|ref|YP_920166.1|  95 RDILDSLVNVR 105
                                    66666555555 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   3.6    0.0012      0.67      14      55 ..      16      57 ..      13     124 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0012
                        NPV_P10 14 kavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaele 55
                                   k +d+++++lq+ ++++++  + v+   ek+ ++   L+el 
  gi|119719671|ref|YP_920166.1| 16 KYLDSQIESLQKTLEQLEQRYEAVKVRAEKMREIERVLEELM 57
                                   679*********************************999985 PP

>> RmuC  RmuC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   0.00016     0.094     241     285 ..       7      50 ..       4      55 .. 0.93
   2 ?    1.1   0.0       0.3   1.7e+02     223     250 ..      89     116 ..      72     120 .. 0.51

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00016
                           RmuC 241 kfekfgedleklgkklekaqksydkavkklegnilrkaeklkelg 285
                                    +f++fge l+ l +++e++qk++++  +++ + +  +aek++e++
  gi|119719671|ref|YP_920166.1|   7 QFNGFGELLKYLDSQIESLQKTLEQ-LEQRYEAVKVRAEKMREIE 50 
                                    799**********************.99999**********9986 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.3
                           RmuC 223 aqeknaeeiaellgelydkfekfgedle 250
                                    +  + +++i++ l ++ d ++k+ e+l+
  gi|119719671|ref|YP_920166.1|  89 ETIESQRDILDSLVNVRDAIQKLSEHLQ 116
                                    3334444444444444444444444443 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   1.0     0.002       1.2      34      75 ..      16      56 ..      12      65 .. 0.64
   2 ?    6.8   0.1     0.015       8.7      22      51 ..      87     116 ..      79     129 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.002
                Snapin_Pallidin 34 eqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmssl 75
                                   + ld++ e+L+++ e  e +  + +k  a+K+++i++ +++l
  gi|119719671|ref|YP_920166.1| 16 KYLDSQIESLQKTLEQLE-QRYEAVKVRAEKMREIERVLEEL 56
                                   445555555554444333.44558889999999998876665 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.015
                Snapin_Pallidin  22 lkelrqsQeeLleqldrlnekLkeleeaqe 51 
                                    l+e+++sQ++ l++l + ++++++l+e+ +
  gi|119719671|ref|YP_920166.1|  87 LEETIESQRDILDSLVNVRDAIQKLSEHLQ 116
                                    788999999999999999999999998877 PP

>> Rota_NSP3  Rotavirus non-structural protein NSP3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.4   4.2e-05     0.024     158     245 ..      21     113 ..      16     124 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.2e-05
                      Rota_NSP3 158 dtedlkskieeleqiidal....ekykdivldldkmneevkldqnsisynsaailvstilgaelkvyneklerlld.vGs 232
                                    + e+l++ +e+leq+++a+    ek ++i   l+++ +e  +  n + y   ++++++    el v +e  e + d + s
  gi|119719671|ref|YP_920166.1|  21 QIESLQKTLEQLEQRYEAVkvraEKMREIERVLEELMGEKLSPLNEVDYMGLKLVINARAIDELAVLEETIESQRDiLDS 100
                                    678999************************99999999999999**********9999999***********99997789 PP

                      Rota_NSP3 233 ltsskeiieksie 245
                                    l++ ++ i+k  e
  gi|119719671|ref|YP_920166.1| 101 LVNVRDAIQKLSE 113
                                    9999999988655 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.0   0.00013     0.075      21      58 ..      17      53 ..       3      56 .. 0.83
   2 ?    1.8   0.1      0.37   2.1e+02      20      54 ..      85     118 ..      69     121 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00013
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXXX CS
                          DivIC 21 qlkqeiaalqaelaklkaeneeLeaevkdLksdedyie 58
                                    l+++i+ lq++l++l ++ e+ + + ++++ + +++ 
  gi|119719671|ref|YP_920166.1| 17 YLDSQIESLQKTLEQLEQRYEAVKVRAEKMR-EIERVL 53
                                   5899*************************97.444443 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.37
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXX CS
                          DivIC  20 kqlkqeiaalqaelaklkaeneeLeaevkdLksde 54 
                                      l++ i+ + + l++l + +++ ++  + L +++
  gi|119719671|ref|YP_920166.1|  85 AVLEETIESQRDILDSLVNVRDAIQKLSEHL-QGY 118
                                    4567777777777777777777777777777.565 PP

>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.2     0.023        13      17      40 ..      18      45 ..       6      70 .. 0.79
   2 ?    7.2   0.0     0.014       7.9       7      54 ..      87     134 ..      81     141 .] 0.82

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.023
                                   EESSTSBHHHHHHHHHHHTCHHG....T CS
                           ThiS 17 elaegstvaelleaLgerypela....l 40
                                   ++++ ++++  le+L++ry++ +     
  gi|119719671|ref|YP_920166.1| 18 LDSQIESLQKTLEQLEQRYEAVKvraeK 45
                                   4678899************888765440 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.014
                                    CHHHHTCEEEEESSTSBHHHHHHHHHHHTCHHGTTTTEEEEETTEEEG CS
                           ThiS   7 lrelageeelelaegstvaelleaLgerypelalerrvavavNgeivp 54 
                                    l e+ +++ + l++  +v++++++L+e+ +++  ++ ++ +vNg  v+
  gi|119719671|ref|YP_920166.1|  87 LEETIESQRDILDSLVNVRDAIQKLSEHLQGYDGIPILVQLVNGVPVR 134
                                    55666688889999***************9999889999999987766 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   1.9   7.2e-05     0.042      39      77 ..      18      56 ..      12      61 .. 0.91
   2 ?    1.6   0.1       0.6   3.4e+02      53      77 ..      87     111 ..      66     120 .. 0.48

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.2e-05
                        BLOC1_2 39 lkdvaaslekkleklnekyeelqpylqqidqiekqvteL 77
                                   l+++++sl+k+le+l+++ye+++   +++ +ie+ ++eL
  gi|119719671|ref|YP_920166.1| 18 LDSQIESLQKTLEQLEQRYEAVKVRAEKMREIERVLEEL 56
                                   67899****************************999998 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.6
                        BLOC1_2  53 lnekyeelqpylqqidqiekqvteL 77 
                                    l+e+ e+ +  l+++ ++ + +++L
  gi|119719671|ref|YP_920166.1|  87 LEETIESQRDILDSLVNVRDAIQKL 111
                                    2222222233333333333333333 PP

>> THOC7  Tho complex subunit 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.3    0.0032       1.9      80     119 ..      18      57 ..       9      68 .. 0.82
   2 ?    4.9   0.1     0.051        29      72      99 ..      89     116 ..      72     119 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0032
                          THOC7  80 ieseieavreeieelkaqLeearatranrkeydelaekIt 119
                                    ++s+ie++++  e+l+++ e+ +   +  +e++++ e+++
  gi|119719671|ref|YP_920166.1|  18 LDSQIESLQKTLEQLEQRYEAVKVRAEKMREIERVLEELM 57 
                                    6899999999999999999999988888888888888775 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.051
                          THOC7  72 ryeaekeeieseieavreeieelkaqLe 99 
                                    +  + +++i++++ +vr+ i++l ++L+
  gi|119719671|ref|YP_920166.1|  89 ETIESQRDILDSLVNVRDAIQKLSEHLQ 116
                                    3333445566999*********999997 PP

>> FBPase_2  Firmicute fructose-1,6-bisphosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.3   0.00012     0.071     101     163 ..      16      76 ..       9     111 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00012
                       FBPase_2 101 ewykitlkrlievakkvsskytrskvrkalpkefayiieeLlhekeeeenkeeYyeeiietii 163
                                    +++  ++++l + ++++ ++y   kvr +  +e++ ++eeL+ ek +  n+ +Y+   ++ +i
  gi|119719671|ref|YP_920166.1|  16 KYLDSQIESLQKTLEQLEQRYEAVKVRAEKMREIERVLEELMGEKLSPLNEVDYMG--LKLVI 76 
                                    567889999************************************99999999985..33344 PP

>> DASH_Spc19  Spc19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   2.5    0.0001     0.059      67     106 ..      13      52 ..      12      92 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.0001
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH......H CS
                     DASH_Spc19  67 ellekaekeleklerreetLkaklelqegrlsnaesskke 106
                                    ell+ +++++e+l++  e+L++++e  ++r +++++ ++ 
  gi|119719671|ref|YP_920166.1|  13 ELLKYLDSQIESLQKTLEQLEQRYEAVKVRAEKMREIERV 52 
                                    68999****************************8776654 PP

>> 3HCDH  3-hydroxyacyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00018      0.11      19      85 ..      39     106 ..      26     117 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00018
                                    HHTTSS-HHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHH.HHHHHTTTHGGHH-HHHHHHHHTT- CS
                          3HCDH  19 veegvaspediDaamrlglGlpmGpfelldlvgldvakkile.vlaeelgerayapsplleklveagr 85 
                                    v+    ++++i++++++ +G +++p+  +d++gl ++ +++     ++l+e+   + ++l++lv+  +
  gi|119719671|ref|YP_920166.1|  39 VKVRAEKMREIERVLEELMGEKLSPLNEVDYMGLKLVINARAiDELAVLEETIESQRDILDSLVNVRD 106
                                    444445699****************************9999965555566664445688888887665 PP

>> Vmethyltransf_C  Viral methyltransferase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.3   0.00016     0.091      77     134 ..      24      81 ..      14     113 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00016
                Vmethyltransf_C  77 nvkGflldleelDvkvklyeekerekervsrsivseklgvlasvkdtelGavlagksl 134
                                    + +  l++le+  + vk   ek re erv ++++ ekl+ l +v+   l  v++++ +
  gi|119719671|ref|YP_920166.1|  24 SLQKTLEQLEQRYEAVKVRAEKMREIERVLEELMGEKLSPLNEVDYMGLKLVINARAI 81 
                                    555667777777778******************************9999999988865 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   2.7   0.00021      0.12      20      61 ..      18      57 ..      11      60 .. 0.74
   2 ?    1.2   0.1      0.79   4.6e+02      16      48 ..      83     113 ..      79     119 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00021
                   ABC_tran_CTD 20 LEeeiaeleaeladpelysdpeklaelsaeleeleaeLeely 61
                                   L+ +i++l++ l++ e  +++e+++   +++ e+e  Leel+
  gi|119719671|ref|YP_920166.1| 18 LDSQIESLQKTLEQLE--QRYEAVKVRAEKMREIERVLEELM 57
                                   6777777777777777..777778888888888888888776 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.79
                   ABC_tran_CTD  16 eIeaLEeeiaeleaeladpelysdpeklaelsa 48 
                                    e++ LEe i++  + l +    +  +++++ls+
  gi|119719671|ref|YP_920166.1|  83 ELAVLEETIESQRDILDSLV--NVRDAIQKLSE 113
                                    45556666666665555332..22244555555 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   4.0   0.00049      0.28      24     113 ..      16     107 ..      12     117 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00049
                                    HCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHCCCHHHHHHHCC CS
                      Fib_alpha  24 dlllkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikks...skeleeeilrlketidaq 100
                                    ++l+++ ++++k+le+le++ e ++ + ++++e+ + +++ + ek +  ++ d +  k+   ++ ++ e + l+eti +q
  gi|119719671|ref|YP_920166.1|  16 KYLDSQIESLQKTLEQLEQRYEAVKVRAEKMREIERVLEELMGEKLSPLNEVDYMGLKLvinARAID-ELAVLEETIESQ 94 
                                    6777777788888888888888888888888888888888887777777765444333211145555.777777777777 PP

                                    HHHHHHHHHHHHH CS
                      Fib_alpha 101 esnirvLqnvles 113
                                       +  L nv ++
  gi|119719671|ref|YP_920166.1|  95 RDILDSLVNVRDA 107
                                    6666665554433 PP

>> DASH_Dam1  DASH complex subunit Dam1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.1     0.021        12       5      29 ..      15      39 ..       5      47 .. 0.65
   2 ?    5.3   0.1      0.03        18       1      29 [.      25      53 ..      18      66 .. 0.62
   3 ?    3.0   0.0      0.15        88       5      34 ..      84     113 ..      80     118 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.021
                      DASH_Dam1  5 faeLaDsletLdknledLqqihesL 29
                                   ++ L  ++e L+k le+L+q  e++
  gi|119719671|ref|YP_920166.1| 15 LKYLDSQIESLQKTLEQLEQRYEAV 39
                                   4555666666666666666655555 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.03
                      DASH_Dam1  1 lepafaeLaDsletLdknledLqqihesL 29
                                   l++++++L+   e+++ + e++ +i+  L
  gi|119719671|ref|YP_920166.1| 25 LQKTLEQLEQRYEAVKVRAEKMREIERVL 53
                                   34555666666666666666666665555 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.15
                      DASH_Dam1   5 faeLaDsletLdknledLqqihesLsdfNe 34 
                                    +a L++ +e  ++ l+ L ++++++++++e
  gi|119719671|ref|YP_920166.1|  84 LAVLEETIESQRDILDSLVNVRDAIQKLSE 113
                                    666777777777777777777777777666 PP

>> DUF639  Plant protein of unknown function (DUF639)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1      0.27   1.6e+02     126     154 ..      21      49 ..      17      54 .. 0.84
   2 ?    8.5   0.1    0.0021       1.2     111     143 ..      82     117 ..      67     125 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.27
                         DUF639 126 kivavqdglseLeqllqkvnvvlLklRal 154
                                    +i + q++l++Leq    v v   k+R +
  gi|119719671|ref|YP_920166.1|  21 QIESLQKTLEQLEQRYEAVKVRAEKMREI 49 
                                    67788999999999999999999998876 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0021
                         DUF639 111 davkv...saepdsntiekivavqdglseLeqllqk 143
                                    d++ v   + e++ ++++++v v+d++++L ++lq 
  gi|119719671|ref|YP_920166.1|  82 DELAVleeTIESQRDILDSLVNVRDAIQKLSEHLQG 117
                                    455442215578999******************995 PP

>> OEP  Outer membrane efflux protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.0   0.00018      0.11     114     147 ..       5      38 ..       2      61 .. 0.87
   2 ?   -0.3   0.1       1.4     8e+02     123     139 ..      83      99 ..      76     114 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00018
                            OEP 114 ylqlllakeqlelaeealklaekalelaearyka 147
                                    ++q+    e+l+ ++ ++++++k+le+ e+ry+a
  gi|119719671|ref|YP_920166.1|   5 LYQFNGFGELLKYLDSQIESLQKTLEQLEQRYEA 38 
                                    78899999999999*****************997 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.4
                            OEP 123 qlelaeealklaekale 139
                                    +l+++ee++++++++l+
  gi|119719671|ref|YP_920166.1|  83 ELAVLEETIESQRDILD 99 
                                    56667777777776665 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.6    0.0013      0.75      46      87 ..      14      55 ..       8      74 .. 0.81
   2 ?    2.5   0.1      0.25   1.4e+02      75     103 ..      87     115 ..      74     121 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0013
                        DUF1664 46 vskqleqvseslaatkrhLssridrvdkkldeqkeiskeike 87
                                   + k l++  esl++t ++L++r + v  + +++ ei + ++e
  gi|119719671|ref|YP_920166.1| 14 LLKYLDSQIESLQKTLEQLEQRYEAVKVRAEKMREIERVLEE 55
                                   557789999999999999999999999999999999876655 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.25
                        DUF1664  75 ldeqkeiskeikeevtevredlseigedv 103
                                    l+e++e +++i + + +vr+ +++++e +
  gi|119719671|ref|YP_920166.1|  87 LEETIESQRDILDSLVNVRDAIQKLSEHL 115
                                    56666666666666666666666665554 PP

>> DHR10  Designed helical repeat protein 10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   2.7   0.00071      0.41      74     106 ..      16      48 ..      12      57 .. 0.82
   2 ?    2.5   0.2      0.25   1.5e+02      41      72 ..      83     114 ..      78     119 .. 0.45

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00071
                          DHR10  74 relerkeerlqrqlenaeeklerlreqaeekre 106
                                    + l++++e lq+ le+ e+++e ++ +ae+ re
  gi|119719671|ref|YP_920166.1|  16 KYLDSQIESLQKTLEQLEQRYEAVKVRAEKMRE 48 
                                    5688999***************99999987776 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.25
                          DHR10  41 lleeieaelakleeakkklkelrdaleekeie 72 
                                     l  +e+ ++++++  + l + rda+++++++
  gi|119719671|ref|YP_920166.1|  83 ELAVLEETIESQRDILDSLVNVRDAIQKLSEH 114
                                    34444444444444444444444444444433 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   4.7    0.0008      0.46      61     111 ..      16      66 ..       6      94 .. 0.88
   2 ?   -0.2   0.1      0.84   4.9e+02      70      98 ..      87     115 ..      69     118 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0008
                        DUF3450  61 eslevyneqlerlvasqeqeiasleeqieeieeierelvpllekmidrLeq 111
                                    + l+ + e l++ ++++eq+ + ++ + e+++eier l+ l+ + ++ L++
  gi|119719671|ref|YP_920166.1|  16 KYLDSQIESLQKTLEQLEQRYEAVKVRAEKMREIERVLEELMGEKLSPLNE 66 
                                    6688999***********************************998888776 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.84
                        DUF3450  70 lerlvasqeqeiasleeqieeieeierel 98 
                                    le+ ++sq+  ++sl +  + i++++++l
  gi|119719671|ref|YP_920166.1|  87 LEETIESQRDILDSLVNVRDAIQKLSEHL 115
                                    55666666666666666666666666555 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   2.8   0.00088      0.51      65      95 ..      16      46 ..      11      49 .. 0.50
   2 ?    6.5   4.8     0.013       7.8       4      38 ..      22      56 ..      20      62 .. 0.55
   3 ?    1.7   0.1      0.44   2.5e+02      38      56 ..      84     102 ..      64     120 .. 0.52

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00088
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    Prefoldin_2 65 eeLeerketlekeiktlekqleklekeleel 95
                                   + L+ ++e+l+k +++le+++e ++ + e++
  gi|119719671|ref|YP_920166.1| 16 KYLDSQIESLQKTLEQLEQRYEAVKVRAEKM 46
                                   4444555555555555555555555555544 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.013
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    Prefoldin_2  4 inkfqqlqqqlqqlaqqikqletqlkelelvleel 38
                                   i+ +q++ +ql+q  + +k   ++++e+e vleel
  gi|119719671|ref|YP_920166.1| 22 IESLQKTLEQLEQRYEAVKVRAEKMREIERVLEEL 56
                                   44444444444444445555556666666666666 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.44
                                    HHHS-TT--EEEEETTEEE CS
                    Prefoldin_2  38 lelldedtkvyklvGdvlv 56 
                                    l  l+e+ + ++ + d lv
  gi|119719671|ref|YP_920166.1|  84 LAVLEETIESQRDILDSLV 102
                                    3333333333333322222 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   7.0    0.0021       1.2     156     206 ..      16      66 ..       7     117 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0021
                           Spc7 156 elLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelre 206
                                    + L++q e l++ l++le+++++++ ++ek++e ++ le++  e+L  l e
  gi|119719671|ref|YP_920166.1|  16 KYLDSQIESLQKTLEQLEQRYEAVKVRAEKMREIERVLEELMGEKLSPLNE 66 
                                    568899999999999999999999999999999998888877777766643 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   1.2    0.0041       2.4      15      45 ..      18      48 ..      13      66 .. 0.51
   2 ?    4.2   0.3      0.11        66       5      39 ..      84     114 ..      80     118 .. 0.48

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0041
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           SlyX 15 qedtieeLndvvaeqqqqidrlqrqlrllae 45
                                   ++ +ie+L++++ + +q+ ++ + + ++++e
  gi|119719671|ref|YP_920166.1| 18 LDSQIESLQKTLEQLEQRYEAVKVRAEKMRE 48
                                   4444444444444444444444444444443 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.11
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           SlyX   5 leeLEiklafqedtieeLndvvaeqqqqidrlqrq 39 
                                    l  LE+ +  q d +++L +     ++ i++l ++
  gi|119719671|ref|YP_920166.1|  84 LAVLEETIESQRDILDSLVN----VRDAIQKLSEH 114
                                    34455555555555555444....44444444444 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   6.2     0.037        21     112     207 ..      14     114 ..       5     120 .. 0.45

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.037
                           CorA 112 lyrlldeivdrlfellekleeeldeledel.edstkkeilrelaqlr....rrlvklrralapnrevlkrllakaddkll 186
                                    l++ ld+ +++l ++le+le++ + +  +  + ++ +  l+el+  +     ++ ++   l  n +++++l   +++ + 
  gi|119719671|ref|YP_920166.1|  14 LLKYLDSQIESLQKTLEQLEQRYEAVKVRAeKMREIERVLEELMGEKlsplNEVDYMGLKLVINARAIDELAVLEETIES 93 
                                    34445555555555555555555555555543333333444444433333344444444444455555444443333333 PP

                           CorA 187 ddedkeylrdlldelerllem 207
                                     ++  + l +++d +++l+e+
  gi|119719671|ref|YP_920166.1|  94 QRDILDSLVNVRDAIQKLSEH 114
                                    333333344444444444444 PP

>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   5.6    0.0076       4.4       3      54 ..      16      67 ..      14     118 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0076
                        zf-C4H2  3 keirektleleklknklakevealekeekcleeykkelelLeqEkmaHveeL 54
                                   k + +++++l+k  ++l +  ea++   + ++e+++ le+L+ Ek++ ++e+
  gi|119719671|ref|YP_920166.1| 16 KYLDSQIESLQKTLEQLEQRYEAVKVRAEKMREIERVLEELMGEKLSPLNEV 67
                                   566788999************************************9988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1845  (0.102906); expected 358.6 (0.02)
Passed bias filter:                     1198  (0.0668191); expected 358.6 (0.02)
Passed Vit filter:                       227  (0.0126611); expected 17.9 (0.001)
Passed Fwd filter:                        31  (0.00172904); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              31  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 962.76
//
Query:       gi|119719672|ref|YP_920167.1|  [L=268]
Description: undecaprenyl diphosphate synthase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.8e-77  259.2   0.0    3.3e-77  259.0   0.0    1.0  1  Prenyltransf  Putative undecaprenyl diphosphate synthase


Domain annotation for each model (and alignments):
>> Prenyltransf  Putative undecaprenyl diphosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  259.0   0.0   1.8e-81   3.3e-77       1     224 []      42     267 ..      42     267 .. 0.92

  Alignments for each domain:
  == domain 1  score: 259.0 bits;  conditional E-value: 1.8e-81
                                    EE--HHHHHHHTT.S-HHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEEGGGG.GS-HHHHHHHHHHHH...HHHHHHHH CS
                   Prenyltransf   1 imDGNrRwAkkrgleereeGhkaGaealkeilelclelgvkvvtvYafSteNf.kRskeevdalmellk...eellkeel 76 
                                    i+DGNrRwA++rg+ +   Gh+ Gae++ e+l++c++lgv +vt+Y++SteN+ +Rskee+++++ +l+   +el+++e 
  gi|119719672|ref|YP_920167.1|  42 ILDGNRRWARRRGFPPWM-GHRFGAEKVDEVLDWCYDLGVVTVTLYVLSTENLeRRSKEELENIFGILRekiDELASSE- 119
                                    89***********77777.**********************************456899*********85554455555. PP

                                    HHHHHTTEEEEEESSGGGS-HHHHHHHHHHHHHHT.TTTSEEEEEEEEE-HHHHHHHHHHHHHHTT..SSSG.GGHSHHH CS
                   Prenyltransf  77 kellkegvrvrviGdlellpedvlealekaeeatkknnkklvlniavnYgsrdeiveavrelvkekseekkk.eeideet 155
                                     el++++vrv++iGd+++lp d++e+++++ee+t++ nk   lniav+Yg+r+ei+eavr+++ e+ + + + eeide+ 
  gi|119719672|ref|YP_920167.1| 120 -ELHRRQVRVKFIGDIKRLPVDIQEKMRELEERTRSYNK-RYLNIAVAYGGRHEILEAVRQIAVEVRSGRLSpEEIDEKL 197
                                    .9*********************************8877.9*********************887765555448899*** PP

                                    HHCTSTT..T.SSS-SEEEEESS--S-TTSSTTTTTT-EEEEESSSGGG--HHHHHHHHHHHHHCHHHTT CS
                   Prenyltransf 156 lekhlytaka.lpdpDlliRtsGeeRlSnFllwqlayselyfldvlWPdfskedllealleyqkrerrfg 224
                                    ++k+lyt ++  p+pDl+iRtsGe R+SnFllwq+aysel+fldv+WPdf++ d+l+a+++yq+r+rr g
  gi|119719672|ref|YP_920167.1| 198 FAKYLYTGDEpHPEPDLVIRTSGEVRISNFLLWQIAYSELVFLDVYWPDFRRIDFLRAIRTYQSRQRRKG 267
                                    *******88899*******************************************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       891  (0.049696); expected 358.6 (0.02)
Passed bias filter:                      719  (0.0401026); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 1926.64
//
Query:       gi|119719673|ref|YP_920168.1|  [L=242]
Description: deoxyribose-phosphate aldolase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-14   54.1   0.1    2.1e-14   53.7   0.1    1.1  1  DeoC      DeoC/LacD family aldolase


Domain annotation for each model (and alignments):
>> DeoC  DeoC/LacD family aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.7   0.1   1.2e-18   2.1e-14      25     205 ..      37     205 ..      23     214 .. 0.83

  Alignments for each domain:
  == domain 1  score: 53.7 bits;  conditional E-value: 1.2e-18
                                    HHHHHHHHHHHGGGSSEEEEETTTHHHHHHCSCT..TSEEEEETECSSCCTTSTTEEEETTCHHHHHHHTT-SEEEEEEE CS
                           DeoC  25 edlkalvkealtpgasavlldpgviasaskeyak..diallvkldkgtyllkskqrdvdevasveeakalGAdavkvvvy 102
                                    ++l+++++ea+  g  a ++   ++ +a k  +   ++ +++++++g+     k      va+v++a++ GAd+v+vvv+
  gi|119719673|ref|YP_920168.1|  37 KELEKTCREAVDYGFYACCVPGFFVEKAVKIVDGaaKVVTVAGFPHGNSPRAVK------VAEVKAAFEKGADEVDVVVN 110
                                    577888888888877777775555555443332245999999999888766666......******************** PP

                                    EHTTTTCHHHHHHHHHHHHHHHHHHHT..EEEEEE.EEE-CTTBSSTTCHHHHHHHHHHHHTCCT-SEEEE--SSCC.B. CS
                           DeoC 103 yradgseeeqqklaeikrvkeacheeg..lplile.lylrdeaikdekvdpdlvaeAarvsaelGaDiiKvevpkevvna 179
                                    +   +s+  ++ + e++++   ++e g  l++ile +yl  e+          v++  r  a +G+ ++K++++     a
  gi|119719673|ref|YP_920168.1| 111 ISLVKSGLLEEAVSEVQEILDVANESGgvLKVILEtGYLTAEE----------VYRLGRELARIGVHFLKTSTGFGPRGA 180
                                    ************************8876799999999998888..........*********************88899* PP

                                    HHHHHHHHHHHHHCHSSTEEEEETTS CS
                           DeoC 180 teedaevfkdvikaapvpgvvlsGGv 205
                                    t+ed+ v+++++++++   ++ +GG+
  gi|119719673|ref|YP_920168.1| 181 TPEDILVMRRAVEGTRTK-LKAAGGI 205
                                    *****************9.******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1621.87
//
Query:       gi|119719674|ref|YP_920169.1|  [L=346]
Description: hypothetical protein Tpen_0764 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.3e-12   46.0   0.0    9.1e-12   45.0   0.0    1.6  1  ACP_syn_III_C   3-Oxoacyl-[acyl-carrier-protein (ACP)] syntha
    1.6e-06   27.6   0.0    2.5e-06   27.1   0.0    1.2  1  Thiolase_N      Thiolase, N-terminal domain
    5.5e-05   22.9   1.3    0.00036   20.3   0.6    2.3  2  ACP_syn_III     3-Oxoacyl-[acyl-carrier-protein (ACP)] syntha
    0.00058   19.6   0.1      0.032   13.9   0.0    2.2  2  HMG_CoA_synt_C  Hydroxymethylglutaryl-coenzyme A synthase C t
     0.0045   16.9   0.0     0.0069   16.3   0.0    1.3  1  HMG_CoA_synt_N  Hydroxymethylglutaryl-coenzyme A synthase N t


Domain annotation for each model (and alignments):
>> ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.0   0.0   2.5e-15   9.1e-12       2      83 ..     220     301 ..     219     308 .. 0.91

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 2.5e-15
                                    HHTT--GGG-SEEEE-SSSHHHHHHHHHHHT--GGGB--TH..HHH-B-GGGHHHHHHHHHHHTTSS-TT-EEEEEEEET CS
                  ACP_syn_III_C   2 ekagltpedidalvphqanlriidavakklglpeekvvvnl..deyGntsaasiplaLdeaveegklkpgdlvllvgfGa 79 
                                    e++gl+p+d+ + v+hq n ++ + v   lg+++e+    l   e+Gnt aa +++ L + ++    kpg+++l+v+fG 
  gi|119719674|ref|YP_920169.1| 220 EETGLKPSDFAYAVFHQPNVKFPQRVGAMLGFKPEQLKLGLlsGEIGNTYAAASLIGLTNVLD--HAKPGERILVVSFGS 297
                                    789********************************777666669*******************..99************* PP

                                    TTEE CS
                  ACP_syn_III_C  80 Gltw 83 
                                    G   
  gi|119719674|ref|YP_920169.1| 298 GAGS 301
                                    9765 PP

>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0   6.9e-10   2.5e-06      23     113 ..      49     139 ..      32     153 .. 0.94

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 6.9e-10
                                    HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCTTSTSCHHHHHHHHTTS-TTSEEEEEEHGGGHHHHHHHHHHHHHHTT CS
                     Thiolase_N  23 aeeLlaealkallekagvdpeevdevivGnvlqagegqniarqaalkagipeevpavtvnkvcsSglkavalaaqsiaag 102
                                    +  ++ ea k++l++a +dp ev+ +++G      + +  a  +a ++g++++ + + ++ +c  g +a++ +a+ +++g
  gi|119719674|ref|YP_920169.1|  49 SLTMAYEASKNALKRARLDPREVQALYIGSESPPYAVKPSATVVAEALGLSRKLYGIDMEFACKAGTTALISVAGLVKSG 128
                                    5678999************************************************************************* PP

                                    SHSEEEEEEEE CS
                     Thiolase_N 103 eadvvvagGvE 113
                                     +   +a+G+ 
  gi|119719674|ref|YP_920169.1| 129 IITYGLAVGTD 139
                                    *********86 PP

>> ACP_syn_III  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.6     1e-07   0.00036       2      65 ..     106     166 ..     105     178 .. 0.88
   2 ?    0.5   0.0      0.15   5.4e+02      39      60 ..     279     303 ..     272     323 .. 0.67

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1e-07
                                    EEE-GGGHHHHHHHHHHHHHHTTS-SEEEEEEEEEGGGCS-TTTHHHHTTB-EEEEEEEEEEES CS
                    ACP_syn_III   2 DlnaaCsgfvyalsvAdaliesgaakrvLvigaetlskilDwkdrstavlfGDGAgAvvlease 65 
                                    D++ aC++ ++al  +++l++sg + + L +g++t      +   +  ++ G GA+A+v+++  
  gi|119719674|ref|YP_920169.1| 106 DMEFACKAGTTALISVAGLVKSGIITYGLAVGTDTAQG---RPGDELEYTAGAGAAAFVVSPVR 166
                                    999********************************777...5667889999*********9874 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.15
                                    GCS-TTT...HHHHTTB-EEEEEEE CS
                    ACP_syn_III  39 kilDwkd...rstavlfGDGAgAvv 60 
                                    ++lD ++   r  +v fG GAg   
  gi|119719674|ref|YP_920169.1| 279 NVLDHAKpgeRILVVSFGSGAGSDA 303
                                    5566653333778889999999633 PP

>> HMG_CoA_synt_C  Hydroxymethylglutaryl-coenzyme A synthase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.012        45      68      92 ..     227     251 ..     206     258 .. 0.78
   2 !   13.9   0.0   8.8e-06     0.032     150     206 ..     261     313 ..     254     329 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.012
                                    GG-SEEEE--SSHHHHHHHHHHHHH CS
                 HMG_CoA_synt_C  68 ddfdyvifhsPfcklvqkslarlly 92 
                                     df y +fh P  k+ q+  a l +
  gi|119719674|ref|YP_920169.1| 227 SDFAYAVFHQPNVKFPQRVGAMLGF 251
                                    5899**********99998777765 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 8.8e-06
                                    HHHHH---GGGHHHHHHHHHHHHS-HHHHTT-EEEEEEEETTTEEEEEEEEE-S--S CS
                 HMG_CoA_synt_C 150 vptevGnmYtaslyaalasllskvsadelagkriglfsYGsGlaaslfslrvkqdvs 206
                                    ++ e+Gn Y a+    l+ +l +++     g+ri++ s+GsG  +  +s+ v++  +
  gi|119719674|ref|YP_920169.1| 261 LSGEIGNTYAAASLIGLTNVLDHAK----PGERILVVSFGSGAGSDALSIVVEEGIE 313
                                    67899******99999999995555....599******************9987655 PP

>> HMG_CoA_synt_N  Hydroxymethylglutaryl-coenzyme A synthase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.9e-06    0.0069      50     171 ..      46     164 ..       4     167 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.9e-06
                 HMG_CoA_synt_N  50 redinslsltvvqkllertkldydaigrlevgtetiidksksvksvlmqlfeesgntdiegidtlnacyggtaalfnavn 129
                                     ed  +++    ++ l+r +ld   +  l +g+e+     k   +v+ + ++      + gid   ac  gt+al+  + 
  gi|119719674|ref|YP_920169.1|  46 DEDSLTMAYEASKNALKRARLDPREVQALYIGSESPPYAVKPSATVVAEALGL--SRKLYGIDMEFACKAGTTALISVAG 123
                                    5777888888889999******************9988888888898888887..56799******************** PP

                 HMG_CoA_synt_N 130 wiessawdgryalvvagdiaiydsgna.rptggagavalligp 171
                                     ++s      y l v  d a    g+    t gaga a+++ p
  gi|119719674|ref|YP_920169.1| 124 LVKSGII--TYGLAVGTDTAQGRPGDElEYTAGAGAAAFVVSP 164
                                    ***9986..6999*******99988762689*******99988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       260  (0.0145016); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2503.14
//
Query:       gi|119719675|ref|YP_920170.1|  [L=388]
Description: acetyl-CoA acetyltransferase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-22   80.4   0.0    3.3e-22   79.1   0.0    1.7  1  Thiolase_N       Thiolase, N-terminal domain
      1e-12   47.8   1.4    4.8e-11   42.4   0.3    3.2  3  Thiolase_C       Thiolase, C-terminal domain
    1.5e-06   28.0   3.8    0.00014   21.5   2.4    2.8  2  ketoacyl-synt    Beta-ketoacyl synthase, N-terminal domain
    2.2e-05   24.5   0.4     0.0051   16.8   0.0    3.6  4  Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
    4.7e-05   23.2   0.6       0.01   15.7   0.2    2.4  2  ACP_syn_III      3-Oxoacyl-[acyl-carrier-protein (ACP)] synth


Domain annotation for each model (and alignments):
>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.1   0.0   9.3e-26   3.3e-22      20     259 ..      19     223 ..       4     224 .. 0.86

  Alignments for each domain:
  == domain 1  score: 79.1 bits;  conditional E-value: 9.3e-26
                                    TS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCT.TSTSC.HHHHHHHHTTS-TTSEEEEEEHGGGHHHHHHHHHHH CS
                     Thiolase_N  20 dlsaeeLlaealkallekagvdpeevdevivGnvlqa.gegqn.iarqaalkagipeevpavtvnkvcsSglkavalaaq 97 
                                    + + ++L  ea  ++l +ag+++ +v+ ++vGn+ ++  +gq  +   +a  +g+   v+a  v+ +c+Sg +a ++a  
  gi|119719675|ref|YP_920170.1|  19 ERPLRDLMLEASLKALRDAGLSKRDVEAIFVGNMSSGyLQGQEhLGSLLATWLGV-PGVAANKVEAACGSGGAAFHNAFL 97 
                                    5567899999***************************99***999999*******.6899******************** PP

                                    HHHTTSHSEEEEEEEEESTTS-EEETCTTTTGGSSSSEEEEEHHHHHHTEETTTTSEHHHHHHHHHHHHT--HHHHHHHH CS
                     Thiolase_N  98 siaageadvvvagGvEsmsnaptaestdvrsglklgdekakdllipdgladafneehmGltaenlakkykisReeqdefA 177
                                    ++++g +d+v+a+GvE++++a+t ++t++   +  +d++ + +        ++     +l  + + kky++  e+ + fA
  gi|119719675|ref|YP_920170.1|  98 AVKSGLYDCVLAVGVEKLTDATTPDATSA--LIMAEDQEYVAFAG------FSFVALNALVYKAYMKKYGAKQEDIALFA 169
                                    ***********************998544..33333333333332......3334466888999**************** PP

                                    HHHHHHHHHHHHTTTTTTTBE-EEEEESSSEEEE-S-TTS-TT--HHHHHTS-BSSSTTSS-BTTSB--BEEEEEEEEEE CS
                     Thiolase_N 178 vkshqkaaaaqkagkFkdeivPvkvkgkkgkktvdkdeairsevtaekLaklkpaFkkeGtvtAgnasqisDGaaavllm 257
                                    v+ h+ a++++ a+ + + +              + +e ++s+++a++L+ l             ++ ++ DGaaa ll+
  gi|119719675|ref|YP_920170.1| 170 VHDHKYAVNNPLAQ-YPRAV--------------TLEEVLSSPMVADPLRLL-------------ESAPLGDGAAAALLC 221
                                    **************.77755..............89****************.............9************** PP

                                    EH CS
                     Thiolase_N 258 se 259
                                    se
  gi|119719675|ref|YP_920170.1| 222 SE 223
                                    98 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0     0.075   2.7e+02      27      47 ..      29      49 ..      25      91 .. 0.81
   2 ?    1.0   0.0     0.089   3.2e+02      24      49 ..     147     172 ..     126     179 .. 0.79
   3 !   42.4   0.3   1.3e-14   4.8e-11      22     115 ..     259     370 ..     216     381 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.075
                                   HHHHHHHHHT--GGGESEEEE CS
                     Thiolase_C 27 aikkvlkkagltvedidlfEi 47
                                   a+ k+l +agl+ +d++++ +
  gi|119719675|ref|YP_920170.1| 29 ASLKALRDAGLSKRDVEAIFV 49
                                   77899***********98754 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.089
                                    HHHHHHHHHHHHT--GGGESEEEE-- CS
                     Thiolase_C  24 PayaikkvlkkagltvedidlfEinE 49 
                                     a + k+ +kk g + edi lf +++
  gi|119719675|ref|YP_920170.1| 147 NALVYKAYMKKYGAKQEDIALFAVHD 172
                                    567788999*************9986 PP

  == domain 3  score: 42.4 bits;  conditional E-value: 1.3e-14
                                    GHHHHHHHHHHHHHT--GGGESEEEE--SBHHHHHHHHHHHT--G..................GGBSTT--HHHH-B-TT CS
                     Thiolase_C  22 lgPayaikkvlkkagltvedidlfEinEAFaaqaLavakaldldl..................ekvNvnGGaialGHPlG 83 
                                     + + a++k+   ag++ +d+d++E+++AF++  +  +++l++++                    +N  GG  a GHP+G
  gi|119719675|ref|YP_920170.1| 259 SATVKASRKAYAMAGIEPKDVDVLEVHDAFTVLGVIHLEDLGFAEkgagwkllkegqlekdgdLPTNTMGGLKARGHPVG 338
                                    567899****************************************************99987789************** PP

                                    THHHHHHHHHHHHHHHCTTSEEEEEEEETTTE CS
                     Thiolase_C  84 asGaRivvtllselkkeggklgvaalCigggq 115
                                    a+G  ++  ++ +l+ e gk  v  +  g +q
  gi|119719675|ref|YP_920170.1| 339 ATGIYQIYDIAVQLRGEAGKNQVDGAEVGLAQ 370
                                    ***************99998888776666655 PP

>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   2.4     4e-08   0.00014     156     220 ..      65     130 ..      19     141 .. 0.76
   2 ?   -2.5   0.0      0.85     3e+03      93     111 ..     262     280 ..     250     316 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 4e-08
                                    HHHHHHHT--SSEE.EEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---SHHHHHHHHHTTBB CS
                  ketoacyl-synt 156 grisyalglrGpsv.tvdtACsSslvavhaavqslrsgeadvalaGGvellltpeavagfsaagll 220
                                    + ++ +lg+ G++   v++AC S+ +a h a  +++sg  d++la Gve l+ + +  + sa+ + 
  gi|119719675|ref|YP_920170.1|  65 SLLATWLGVPGVAAnKVEAACGSGGAAFHNAFLAVKSGLYDCVLAVGVEKLTDATTPDATSALIMA 130
                                    5678888888876427*********************************99888777766666555 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.85
                                    HHHHHHHHHHHTS-HHTCT CS
                  ketoacyl-synt  93 leaawealedagltpeeld 111
                                    ++a+++a + ag++p+++d
  gi|119719675|ref|YP_920170.1| 262 VKASRKAYAMAGIEPKDVD 280
                                    5678888888899888874 PP

>> Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.048   1.7e+02      26      49 ..      26      49 ..       6      61 .. 0.81
   2 ?   -2.0   0.0      0.94   3.4e+03      29      51 ..     150     172 ..     141     180 .. 0.80
   3 !   16.8   0.0   1.4e-06    0.0051      21      56 ..     256     291 ..     235     293 .. 0.77
   4 ?    0.1   0.0      0.22   7.8e+02      88     107 ..     334     353 ..     326     362 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.048
                                   HHHHHHHHHHHHT--GGGEEEEE- CS
                Ketoacyl-synt_C 26 qaraiekalaeagvdpedvdyvea 49
                                   + +a  kal++ag++++dv+ +  
  gi|119719675|ref|YP_920170.1| 26 MLEASLKALRDAGLSKRDVEAIFV 49
                                   5677889************99865 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.94
                                    HHHHHHHHHT--GGGEEEEE-SS CS
                Ketoacyl-synt_C  29 aiekalaeagvdpedvdyveahg 51 
                                    ++++ +++ g + ed+ +   h+
  gi|119719675|ref|YP_920170.1| 150 VYKAYMKKYGAKQEDIALFAVHD 172
                                    67788899999999999988887 PP

  == domain 3  score: 16.8 bits;  conditional E-value: 1.4e-06
                                    TTHHHHHHHHHHHHHHHT--GGGEEEEE-SS-SSHH CS
                Ketoacyl-synt_C  21 pngeaqaraiekalaeagvdpedvdyveahgtgtpl 56 
                                       +a  +a +ka+a+ag++p+dvd++e h++ t l
  gi|119719675|ref|YP_920170.1| 256 TTLSATVKASRKAYAMAGIEPKDVDVLEVHDAFTVL 291
                                    456788899*********************987766 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 0.22
                                    -B-GGGHHHHHHHHHHHHHH CS
                Ketoacyl-synt_C  88 GHleaAaGvaelikvvlalk 107
                                    GH  +A G+ ++  ++ +l+
  gi|119719675|ref|YP_920170.1| 334 GHPVGATGIYQIYDIAVQLR 353
                                    9**********999988887 PP

>> ACP_syn_III  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.2   2.8e-06      0.01       3      47 ..      81     125 ..      80     138 .. 0.86
   2 !    5.5   0.0    0.0043        16      52      65 ..     211     224 ..     192     245 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.8e-06
                                    EE-GGGHHHHHHHHHHHHHHTTS-SEEEEEEEEEGGGCS-TTTHH CS
                    ACP_syn_III   3 lnaaCsgfvyalsvAdaliesgaakrvLvigaetlskilDwkdrs 47 
                                    ++aaC +  +a ++A  +++sg + +vL +g e+l++ + ++  s
  gi|119719675|ref|YP_920170.1|  81 VEAACGSGGAAFHNAFLAVKSGLYDCVLAVGVEKLTDATTPDATS 125
                                    689*******************************99977665444 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0043
                                    B-EEEEEEEEEEES CS
                    ACP_syn_III  52 fGDGAgAvvlease 65 
                                    +GDGA+A++l  ++
  gi|119719675|ref|YP_920170.1| 211 LGDGAAAALLCSEK 224
                                    8********98763 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 2963.43
//
Query:       gi|119719676|ref|YP_920171.1|  [L=135]
Description: hypothetical protein Tpen_0766 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-18   66.0   3.5    2.9e-18   65.6   3.5    1.2  1  OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
    1.5e-09   37.5   0.4    2.8e-09   36.7   0.4    1.4  1  DUF35_N        Rubredoxin-like zinc ribbon domain (DUF35_N)
    0.00055   19.9   0.2     0.0009   19.2   0.2    1.3  1  HypA           Hydrogenase/urease nickel incorporation, metal
     0.0012   18.6   0.2     0.0016   18.1   0.2    1.1  1  TackOD1        Thaumarchaeal output domain 1
     0.0025   17.9   2.8     0.0066   16.6   2.8    1.7  1  Zn-ribbon_8    Zinc ribbon domain
  ------ inclusion threshold ------
      0.012   15.6   0.3      0.017   15.1   0.3    1.2  1  DZR            Double zinc ribbon
      0.066   12.7   2.6       0.88    9.1   0.1    2.4  2  TF_Zn_Ribbon   TFIIB zinc-binding
       0.14   11.9   6.0       0.47   10.2   0.3    2.0  2  zinc_ribbon_2  zinc-ribbon domain
       0.15   12.0   0.2       0.15   12.0   0.2    2.1  2  Zn_Tnp_IS1595  Transposase zinc-ribbon domain
       0.19   11.2   3.4       0.62    9.6   0.2    2.2  2  zf-ribbon_3    zinc-ribbon domain
       0.28    9.9   0.2       0.32    9.7   0.2    1.1  1  NRDD           Anaerobic ribonucleoside-triphosphate reductas
       0.45   10.6   2.6         18    5.4   0.2    2.3  2  ADK_lid        Adenylate kinase, active site lid
        4.5    7.9   5.6       0.97   10.0   1.3    1.9  2  zf-C2H2        Zinc finger, C2H2 type


Domain annotation for each model (and alignments):
>> OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.6   3.5   2.1e-21   2.9e-18       2      65 .]      50     113 ..      49     113 .. 0.98

  Alignments for each domain:
  == domain 1  score: 65.6 bits;  conditional E-value: 2.1e-21
                                    EEE-GG-EEEEEEEEEE-TTS-EEEEEEEEEEEE-TT...-EE-EEEEEEES..TT-B-EEE-S CS
                  OB_aCoA_assoc   2 velsgrGtvysftvvhrappgfaeeaPyvvgvVeLdegvrimarlvgvdpdevriGmrVravfr 65 
                                    v l+ rG+v+ ftvv+ +p  fa +aPyvv++V+L++g  + a++++vdpdev+ Gm+V+avfr
  gi|119719676|ref|YP_920171.1|  50 VKLPERGVVEVFTVVRSPPSDFAWQAPYVVALVRLEDGTLVPAQITDVDPDEVHEGMEVEAVFR 113
                                    899************************************************************7 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.4     2e-12   2.8e-09       7      37 .]      18      48 ..      17      48 .. 0.95

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 2e-12
                        DUF35_N  7 grLvgqrCpdCGtvqfPPravCphCgsddle 37
                                   + L+g++C+dCG+ ++P r vCp Cgs ++e
  gi|119719676|ref|YP_920171.1| 18 YQLIGGKCKDCGKSFYPYRQVCPACGSENVE 48
                                   78*************************9987 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.2   6.5e-07    0.0009      64     101 ..      16      51 ..       6      60 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 6.5e-07
                                    EEEE--EEEETTTS-EEECHHHHHS-TTTSSS-EEEEE CS
                           HypA  64 ieevpvkvrCreCgkefeleekalrCpkCgsadveivs 101
                                    i+ + +  +C++Cgk+f   ++   Cp+Cgs++ve v+
  gi|119719676|ref|YP_920171.1|  16 IKYQLIGGKCKDCGKSFYPYRQ--VCPACGSENVEEVK 51 
                                    555666789********97755..7********98765 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.2   1.2e-06    0.0016      75     102 ..      24      51 ..      11      54 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.2e-06
                        TackOD1  75 lCpsCksghlnvrevCpkCkSidieeqe 102
                                     C+ C  +   +r+vCp C+S ++ee +
  gi|119719676|ref|YP_920171.1|  24 KCKDCGKSFYPYRQVCPACGSENVEEVK 51 
                                    6***********************9865 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   2.8   4.8e-06    0.0066       7      38 ..      24      49 ..      18      50 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4.8e-06
                    Zn-ribbon_8  7 rCeeCghefevlqsisdapltaCPeCgs.evrr 38
                                   +C++Cg+ f + +       ++CP+Cgs +v+ 
  gi|119719676|ref|YP_920171.1| 24 KCKDCGKSFYPYR-------QVCPACGSeNVEE 49
                                   6*********996.......47******99986 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.3   1.3e-05     0.017      30      49 .]      24      43 ..       9      52 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.3e-05
                            DZR 30 rCpsCgekvdpearfCpeCG 49
                                   +C  Cg++  p  ++Cp+CG
  gi|119719676|ref|YP_920171.1| 24 KCKDCGKSFYPYRQVCPACG 43
                                   56666666666666666665 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.3      0.04        55       2       9 ..      24      31 ..      23      36 .. 0.77
   2 ?    9.1   0.1   0.00064      0.88       2      12 ..      38      48 ..      37      56 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.04
                                   EETTTTCE CS
                   TF_Zn_Ribbon  2 kCPnCgst 9 
                                   kC++Cg +
  gi|119719676|ref|YP_920171.1| 24 KCKDCGKS 31
                                   79999876 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00064
                                   EETTTTCEECH CS
                   TF_Zn_Ribbon  2 kCPnCgstnlv 12
                                   +CP Cgs+n++
  gi|119719676|ref|YP_920171.1| 38 VCPACGSENVE 48
                                   8******9954 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   6.6   0.00081       1.1       1      22 [.      24      45 ..      24      46 .. 0.95
   2 ?   10.2   0.3   0.00034      0.47       2      14 ..      39      51 ..      38      52 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00081
                  zinc_ribbon_2  1 fCpnCGaelqdnakFCpyCGtp 22
                                   +C+ CG+   +  + Cp CG++
  gi|119719676|ref|YP_920171.1| 24 KCKDCGKSFYPYRQVCPACGSE 45
                                   8*******************97 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00034
                  zinc_ribbon_2  2 CpnCGaelqdnak 14
                                   Cp CG e+ +++k
  gi|119719676|ref|YP_920171.1| 39 CPACGSENVEEVK 51
                                   ********99887 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.7       0.4   5.5e+02      39      45 ..      24      30 ..      21      31 .. 0.85
   2 ?   12.0   0.2   0.00011      0.15      14      29 ..      32      47 ..      30      57 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.4
                  Zn_Tnp_IS1595 39 qCkeCrk 45
                                   +Ck+C+k
  gi|119719676|ref|YP_920171.1| 24 KCKDCGK 30
                                   7999987 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00011
                  Zn_Tnp_IS1595 14 rWpngfvCPhCgsrka 29
                                   ++p ++vCP+Cgs+ +
  gi|119719676|ref|YP_920171.1| 32 FYPYRQVCPACGSENV 47
                                   67889*******9954 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.4     0.092   1.3e+02      18      24 ..      24      30 ..      24      32 .. 0.83
   2 ?    9.6   0.2   0.00045      0.62       4      13 ..      38      48 ..      36      49 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.092
                    zf-ribbon_3 18 vCpyCGt 24
                                   +C+ CG+
  gi|119719676|ref|YP_920171.1| 24 KCKDCGK 30
                                   59***97 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00045
                    zf-ribbon_3  4 rCPnCGa.pls 13
                                    CP+CG+ +++
  gi|119719676|ref|YP_920171.1| 38 VCPACGSeNVE 48
                                   58888887775 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.2   0.00024      0.32     509     533 ..      24      49 ..       2      55 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00024
                                    EETT.--EESS..SB-TTT--BE.EEE CS
                           NRDD 509 vCnecgykgei..ekCpkCgseeevev 533
                                     C++cg++ +   + Cp Cgse+ ve 
  gi|119719676|ref|YP_920171.1|  24 KCKDCGKSFYPyrQVCPACGSEN-VEE 49 
                                    488888844444488*****887.765 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.2     0.018        25      22      30 ..      23      31 ..      17      33 .. 0.73
   2 ?    5.4   0.2     0.013        18       1       8 [.      36      43 ..      36      45 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.018
                                   TB-TTT--. CS
                        ADK_lid 22 glCDkCGep 30
                                   g+C +CG  
  gi|119719676|ref|YP_920171.1| 23 GKCKDCGKS 31
                                   677777765 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.013
                                   EEE-TTT- CS
                        ADK_lid  1 RrvCpkCG 8 
                                   R vCp+CG
  gi|119719676|ref|YP_920171.1| 36 RQVCPACG 43
                                   889****9 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   1.3    0.0007      0.97       2      10 ..      24      32 ..      24      36 .. 0.90
   2 ?   -1.2   0.2       2.6   3.6e+03       2       7 ..      38      43 ..      37      45 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0007
                                   EETTTTEEE CS
                        zf-C2H2  2 kCpdCgksF 10
                                   kC+dCgksF
  gi|119719676|ref|YP_920171.1| 24 KCKDCGKSF 32
                                   7******** PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.6
                                   EETTTT CS
                        zf-C2H2  2 kCpdCg 7 
                                   +Cp Cg
  gi|119719676|ref|YP_920171.1| 38 VCPACG 43
                                   699998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                       109  (0.00607954); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1070.65
//
Query:       gi|119719677|ref|YP_920172.1|  [L=108]
Description: hypothetical protein Tpen_0767 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00057   20.0   0.9      0.001   19.1   0.9    1.3  1  Zn-ribbon_8      Zinc ribbon domain
     0.0018   18.2   0.2     0.0026   17.7   0.2    1.2  1  zf-C2HC5         Putative zinc finger motif, C2HC5-type
  ------ inclusion threshold ------
      0.034   14.1   0.1      0.045   13.8   0.1    1.3  1  HypA             Hydrogenase/urease nickel incorporation, met
       0.04   14.0   0.0      0.053   13.6   0.0    1.1  1  Toxin-deaminase  The  BURPS668_1122 family of deaminases
      0.042   13.7   1.2        0.3   11.0   0.1    2.2  2  zf-C3HC4_5       Zinc finger, C3HC4 type (RING finger)
       0.25   10.9   2.6        6.3    6.4   0.3    2.4  2  TF_Zn_Ribbon     TFIIB zinc-binding
       0.26   10.8   3.4        3.3    7.2   0.3    2.2  2  zf-ribbon_3      zinc-ribbon domain
       0.56   10.4   0.2       0.56   10.4   0.2    2.1  2  UPF0547          Uncharacterised protein family UPF0547


Domain annotation for each model (and alignments):
>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.9   4.6e-07     0.001       8      35 ..      70      96 ..      69      98 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 4.6e-07
                    Zn-ribbon_8  8 CeeCghefevlqsisdaplta.CPeCgs.e 35
                                   C +Cg +f +l ++    l+  CP C+s +
  gi|119719677|ref|YP_920172.1| 70 CASCGYVFRELEKAR---LPSrCPVCKSeR 96
                                   ************877...8888****9955 PP

>> zf-C2HC5  Putative zinc finger motif, C2HC5-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.2   1.2e-06    0.0026      17      44 ..      67      96 ..      60     104 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.2e-06
                       zf-C2HC5 17 apnClnCGkiiCakegls..kpCsfCgspl 44
                                    p+C +CG +  + e+    ++C+ C+s+ 
  gi|119719677|ref|YP_920172.1| 67 PPMCASCGYVFRELEKARlpSRCPVCKSER 96
                                   69***********9999989******9875 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1     2e-05     0.045      72      97 ..      69      97 ..      38     101 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2e-05
                                   EETTTS-EEE.CHH.H.HHS-TTTSSS-E CS
                           HypA 72 rCreCgkefe.lee.k.alrCpkCgsadv 97
                                   +C +Cg+ f+ le+ +   rCp C+s+++
  gi|119719677|ref|YP_920172.1| 69 MCASCGYVFReLEKaRlPSRCPVCKSERI 97
                                   69*****9995554335569******987 PP

>> Toxin-deaminase  The  BURPS668_1122 family of deaminases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.4e-05     0.053      91     129 ..      46      82 ..      35      87 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.4e-05
                Toxin-deaminase  91 leeiaeqleknskkegsiklftelepCdSCkgvlkqfkk 129
                                    ++++a+ +    k++g++ l+ +  +C+SC++v ++++k
  gi|119719677|ref|YP_920172.1|  46 INHVAKTIR--RKSNGKMLLMMKPPMCASCGYVFRELEK 82 
                                    344555555..9999*******************99976 PP

>> zf-C3HC4_5  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1      0.11   2.5e+02      28      33 ..      68      73 ..      45      81 .. 0.71
   2 ?   11.0   0.1   0.00013       0.3       3      21 ..      88     106 ..      86     108 .] 0.83

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.11
                     zf-C3HC4_5 28 kmCesC 33
                                    mC sC
  gi|119719677|ref|YP_920172.1| 68 PMCASC 73
                                   367777 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00013
                     zf-C3HC4_5   3 iCPvCkssrYlnpdlefli 21 
                                     CPvCks+r   p++ +++
  gi|119719677|ref|YP_920172.1|  88 RCPVCKSERIRPPSFMLVV 106
                                    6********9888887776 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1     0.015        33      22      29 ..      70      77 ..      69      80 .. 0.86
   2 ?    6.4   0.3    0.0028       6.3       2      10 ..      88      96 ..      88     102 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.015
                                   ESSSSBEE CS
                   TF_Zn_Ribbon 22 CtdCGlVl 29
                                   C +CG+V 
  gi|119719677|ref|YP_920172.1| 70 CASCGYVF 77
                                   ******96 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0028
                                   EETTTTCEE CS
                   TF_Zn_Ribbon  2 kCPnCgstn 10
                                   +CP+C+s++
  gi|119719677|ref|YP_920172.1| 88 RCPVCKSER 96
                                   5******86 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.3    0.0015       3.3      18      25 ..      69      76 ..      68      77 .. 0.86
   2 ?    4.3   0.2     0.012        27       4      10 ..      88      94 ..      87      99 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0015
                    zf-ribbon_3 18 vCpyCGtk 25
                                   +C++CG++
  gi|119719677|ref|YP_920172.1| 69 MCASCGYV 76
                                   8*****98 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.012
                    zf-ribbon_3  4 rCPnCGa 10
                                   rCP C++
  gi|119719677|ref|YP_920172.1| 88 RCPVCKS 94
                                   8****97 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.2   0.00025      0.56      17      25 ..      70      78 ..      69      79 .. 0.88
   2 ?    0.3   1.0      0.35   7.7e+02       2       8 ..      88      94 ..      88      95 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00025
                        UPF0547 17 CphCGyvFq 25
                                   C+ CGyvF 
  gi|119719677|ref|YP_920172.1| 70 CASCGYVFR 78
                                   *9******6 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.35
                        UPF0547  2 vCPeCea 8 
                                   +CP C +
  gi|119719677|ref|YP_920172.1| 88 RCPVCKS 94
                                   5998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); expected 358.6 (0.02)
Passed bias filter:                      571  (0.0318478); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 787.62
//
Query:       gi|119719678|ref|YP_920173.1|  [L=443]
Description: Fmu (Sun) domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.8e-30  104.4   0.0    8.6e-30  103.9   0.0    1.2  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F


Domain annotation for each model (and alignments):
>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.9   0.0   4.8e-34   8.6e-30      11     199 ..     253     440 ..     245     441 .. 0.91

  Alignments for each domain:
  == domain 1  score: 103.9 bits;  conditional E-value: 4.8e-34
                                    EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--S.EEEEES-CTCCHHHHCC..EEEEEEEE-- CS
                Methyltr_RsmB-F  11 tilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtn.tivleaDarkidkvlggelfDriLlDaPC 89 
                                    t +D++aaP  KT++  +  ++  +++Avd++ +R++     l  Lg+++ + +++ D r      + +lfD  L+DaPC
  gi|119719678|ref|YP_920173.1| 253 TCIDAAAAPFMKTSLYCDARRCCDEILAVDISFNRIRDSRGVL--LGCRKiVHIVNSDSRFL---ATRTLFDEGLVDAPC 327
                                    689********************************99877665..88884157888998887...44467********** PP

                                    CCGGGTTT-TCHH...HH--HHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEES--STTTTHHHHHHHHHH-TTEEEESSB CS
                Methyltr_RsmB-F  90 sgtgvirrdpdvk...lrrkekdiaqlaklqkellsaaidllkkgGvlvYsTCsvlveEneevieeaLkkredvelvete 166
                                    +  g+i +dp ++   ++ + +++a ++++q+e+l  ++ ++k+gG + YsTCsvl+eE eev++++  + e   l +  
  gi|119719678|ref|YP_920173.1| 328 TNSGAIGKDPGLRlslWELDREEVALYSTRQREILRNVLRHMKHGGRVAYSTCSVLPEEGEEVVKDVAADGESSLLRPPL 407
                                    ************94445567788999**************************************************9999 PP

                                    STTSTTSSECEECTSEEE-TTTTSS-SEEEEEE CS
                Methyltr_RsmB-F 167 lsepkglklgeeagtlrllPhtenkdgffiakl 199
                                    +++    ++g    + r +P+++  ++ffia l
  gi|119719678|ref|YP_920173.1| 408 FFDEAYPRYGLRGVATRTFPDKHRSEAFFIALL 440
                                    9**9***************************88 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (443 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 3201.49
//
Query:       gi|119719679|ref|YP_920174.1|  [L=280]
Description: hypothetical protein Tpen_0769 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-05   23.8   0.0    8.3e-05   22.6   0.0    1.6  1  HTH_20           Helix-turn-helix domain
    0.00013   22.0   0.1     0.0006   19.9   0.1    2.0  1  HTH_34           Winged helix DNA-binding domain
  ------ inclusion threshold ------
       0.02   14.8   0.0      0.037   14.0   0.0    1.4  1  MarR             MarR family
      0.054   13.5   0.2      0.099   12.6   0.2    1.4  1  HTH_45           Winged helix-turn-helix
       0.36   11.5   9.7       0.16   12.6   7.1    1.7  2  Phage_holin_4_2  Mycobacterial 4 TMS phage holin, superfamily
          3    7.7   8.1        0.8    9.6   4.3    2.0  2  DUF3955          Protein of unknown function (DUF3955)


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   2.8e-08   8.3e-05       4      49 ..      16      61 ..      13      71 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 2.8e-08
                                   HHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHH CS
                         HTH_20  4 aeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLe 49
                                    e+L++P  r ilr L ++++++++el+  l +s  +l+y+L+ +e
  gi|119719679|ref|YP_920174.1| 16 YEILGNPLKRSILRILGERGEASFTELKSSLKTSTGNLYYNLDGME 61
                                   589***************************************9885 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.1     2e-07    0.0006       4      39 ..      26      61 ..      23      88 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2e-07
                         HTH_34  4 avlsyLasvdeadfvelkealeatdgnLsvhlkkLe 39
                                   ++l +L +  ea+f+elk++l++++gnL+ +l+ +e
  gi|119719679|ref|YP_920174.1| 26 SILRILGERGEASFTELKSSLKTSTGNLYYNLDGME 61
                                   69999**************************99877 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.2e-05     0.037       7      42 ..      26      61 ..      21      69 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.2e-05
                                   HHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHH CS
                           MarR  7 viLrilyeqgplsvseLakklgvskstvtrvldrLe 42
                                   +iLril e+g++s +eL + l++s++++   ld +e
  gi|119719679|ref|YP_920174.1| 26 SILRILGERGEASFTELKSSLKTSTGNLYYNLDGME 61
                                   69*************************999999888 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   3.3e-05     0.099      17      67 ..      34      83 ..      25      90 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.3e-05
                         HTH_45 17 egeakkTkimykanLsykllnkYLdmLvekgli.kkskekYvlTekGlelle 67
                                   +gea+ T++   + L+ ++ n Y +    +g++ k++k  Y+lTekG +l++
  gi|119719679|ref|YP_920174.1| 34 RGEASFTELK--SSLKTSTGNLYYNLDGMEGFVtKNEKRRYTLTEKGIRLYR 83
                                   5556666653..344444444444444557999677999*********9986 PP

>> Phage_holin_4_2  Mycobacterial 4 TMS phage holin, superfamily IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   7.1   5.4e-05      0.16      29      97 ..     134     208 ..     104     217 .. 0.71
   2 ?   -0.8   0.1      0.82   2.4e+03      35      65 ..     210     243 ..     195     265 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.4e-05
                Phage_holin_4_2  29 fltallaalvlgllnalvkpilkllslpltiltlGlftlvinalmlllaaalvsg.......fevdgfwsallgal 97 
                                    +++ ll++++ + l a v  ++  l+lp  ++ lG+f +v+ al+lll+  lv+        ++vd  + a++++l
  gi|119719679|ref|YP_920174.1| 134 LGASLLLGALPSALGAQVVFMMDQLALPYRLIPLGFFFFVLGALVLLLVVELVQRvlgghggYSVD-YLGAFFASL 208
                                    33444455555566666667777778***********************99995444344456665.556666665 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.82
                Phage_holin_4_2  35 aalvlgllnalvk..pilk.llslpltiltlGlf 65 
                                     +  + +l+a +   p+   ll   + + tlGl+
  gi|119719679|ref|YP_920174.1| 210 PVYAFNVLQAALPwdPFTLsLLYRLVQVPTLGLL 243
                                    4445555555443112222122222233344443 PP

>> DUF3955  Protein of unknown function (DUF3955)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1         1   3.1e+03      38      47 ..     131     140 ..     123     149 .. 0.64
   2 ?    9.6   4.3   0.00027       0.8      36      56 ..     162     182 ..     158     185 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1
                        DUF3955  38 LipiGyllll 47 
                                    L+++G  lll
  gi|119719679|ref|YP_920174.1| 131 LVILGASLLL 140
                                    5666665554 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00027
                        DUF3955  36 FfLipiGylllligiislviv 56 
                                      Lip+G++++++g+++l+ v
  gi|119719679|ref|YP_920174.1| 162 YRLIPLGFFFFVLGALVLLLV 182
                                    569************887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1781.95
//
Query:       gi|119719680|ref|YP_920175.1|  [L=248]
Description: hypothetical protein Tpen_0770 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.59
# Mc/sec: 1276.07
//
Query:       gi|119719681|ref|YP_920176.1|  [L=148]
Description: hypothetical protein Tpen_0771 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0012   18.4   0.1       0.51   10.1   0.0    2.3  2  A2L_zn_ribbon   A2L zinc ribbon domain
     0.0023   17.9   0.2     0.0039   17.1   0.2    1.4  1  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
     0.0025   17.7   3.7       0.29   11.1   0.2    2.6  2  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
      0.006   16.5   0.8      0.014   15.3   0.8    1.7  1  Nudix_N_2       Nudix N-terminal
  ------ inclusion threshold ------
      0.013   15.4   1.2       0.31   11.0   0.1    2.6  2  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
      0.014   14.7   1.6       0.24   10.9   0.2    2.4  2  zf-ribbon_3     zinc-ribbon domain
      0.015   15.4   0.2        6.3    7.0   0.1    2.3  2  zf-Mss51        Zinc-finger of mitochondrial splicing suppres
      0.017   15.2   2.3       0.26   11.4   0.1    2.3  2  Zn-ribbon_8     Zinc ribbon domain
      0.053   13.4   0.1       0.09   12.7   0.1    1.4  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
      0.067   13.4   0.1        0.6   10.3   0.0    2.1  2  NOB1_Zn_bind    Nin one binding (NOB1) Zn-ribbon like
      0.073   13.5   1.7        1.2    9.6   0.1    2.4  2  zf-IS66         zinc-finger binding domain of transposase IS6
       0.18   12.1   1.0        9.4    6.6   0.3    2.2  2  Prim_Zn_Ribbon  Zinc-binding domain of primase-helicase
       0.38   10.5   4.2        1.6    8.6   0.3    2.3  2  zinc_ribbon_2   zinc-ribbon domain
       0.41   10.2   8.0        1.4    8.5   5.7    2.6  2  TF_Zn_Ribbon    TFIIB zinc-binding
       0.57    9.9   3.8         12    5.7   0.2    2.3  2  zf-RRN7         Zinc-finger of RNA-polymerase I-specific TFII
       0.61    9.9   6.5          1    9.2   0.4    2.2  2  Rubredoxin_2    Rubredoxin metal binding domain
        4.3    7.5   6.9         10    6.3   0.7    2.5  2  zf-ACC          Acetyl-coA carboxylase zinc finger domain


Domain annotation for each model (and alignments):
>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0   0.00048      0.51      17      29 ..     102     114 ..      98     114 .. 0.86
   2 !    6.0   0.0    0.0095        10      21      29 ..     129     137 ..     126     140 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00048
                  A2L_zn_ribbon  17 seqgylvCieCga 29 
                                    +++g lvC++Cg+
  gi|119719681|ref|YP_920176.1| 102 RKHGVLVCPNCGS 114
                                    78999******96 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0095
                  A2L_zn_ribbon  21 ylvCieCga 29 
                                     +vC +Cg+
  gi|119719681|ref|YP_920176.1| 129 LYVCRKCGF 137
                                    599999998 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.2   3.7e-06    0.0039      19      44 ..     107     136 ..      98     138 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.7e-06
                  Zn_Tnp_IS1595  19 fvCPhCgsr..kayrikt..rglfqCkeCr 44 
                                     vCP+Cgs   + + i +  + l+ C++C+
  gi|119719681|ref|YP_920176.1| 107 LVCPNCGSPdlERIGIPGltPTLYVCRKCG 136
                                    68******9566666666***********8 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.2   0.00028      0.29      27      37 .]     108     118 ..     106     118 .. 0.92
   2 !    7.6   0.0    0.0034       3.6      13      29 ..     131     147 ..     128     148 .] 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00028
                        DUF35_N  27 vCphCgsddle 37 
                                    vCp+Cgs dle
  gi|119719681|ref|YP_920176.1| 108 VCPNCGSPDLE 118
                                    8********98 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0034
                        DUF35_N  13 rCpdCGtvqfPPravCp 29 
                                     C++CG   + P  v p
  gi|119719681|ref|YP_920176.1| 131 VCRKCGFATYLPLEVLP 147
                                    7*********9987766 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.8   1.3e-05     0.014       3      33 ..     109     140 ..     108     141 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.3e-05
                                    -TTT--B.-EEE--TT-SS-EEEETTTTEEE- CS
                      Nudix_N_2   3 CsqCGtp.velripdgDnreRlvCpaCgtihY 33 
                                    C++CG+p +e+   +g + + +vC +Cg+ +Y
  gi|119719681|ref|YP_920176.1| 109 CPNCGSPdLERIGIPGLTPTLYVCRKCGFATY 140
                                    *******88866668*************9888 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1    0.0003      0.31      17      27 ..     104     114 ..      97     114 .. 0.90
   2 ?    2.5   0.0      0.14   1.4e+02      18      26 ..     128     136 ..     126     137 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0003
                 PhnA_Zn_Ribbon  17 gallvCpeCah 27 
                                    + +lvCp+C++
  gi|119719681|ref|YP_920176.1| 104 HGVLVCPNCGS 114
                                    789******96 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.14
                 PhnA_Zn_Ribbon  18 allvCpeCa 26 
                                    +l+vC +C+
  gi|119719681|ref|YP_920176.1| 128 TLYVCRKCG 136
                                    689*****7 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.2   0.00023      0.24      18      25 ..     108     115 ..     103     118 .. 0.64
   2 ?    2.8   0.1     0.078        82      18      23 ..     131     136 ..     125     138 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00023
                    zf-ribbon_3  18 vCpyCGtk 25 
                                    vCp+CG++
  gi|119719681|ref|YP_920176.1| 108 VCPNCGSP 115
                                    56666543 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.078
                    zf-ribbon_3  18 vCpyCG 23 
                                    vC +CG
  gi|119719681|ref|YP_920176.1| 131 VCRKCG 136
                                    7****9 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0      0.01        11      11      25 ..     101     115 ..      71     117 .. 0.86
   2 ?    7.0   0.1     0.006       6.3      17      28 ..     130     141 ..     126     144 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.01
                       zf-Mss51  11 apkhvdfeCpdCGip 25 
                                    ++kh  + Cp+CG p
  gi|119719681|ref|YP_920176.1| 101 TRKHGVLVCPNCGSP 115
                                    57888899*****98 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.006
                       zf-Mss51  17 feCpdCGiptyc 28 
                                    + C +CG+ ty 
  gi|119719681|ref|YP_920176.1| 130 YVCRKCGFATYL 141
                                    89********95 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00024      0.26      27      39 ..     107     120 ..      95     120 .. 0.79
   2 ?    3.2   0.5     0.093        98       6      12 ..     130     136 ..     129     140 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00024
                    Zn-ribbon_8  27 taCPeCgs.evrrv 39 
                                     +CP+Cgs +++r+
  gi|119719681|ref|YP_920176.1| 107 LVCPNCGSpDLERI 120
                                    45*********995 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.093
                    Zn-ribbon_8   6 YrCeeCg 12 
                                    Y C++Cg
  gi|119719681|ref|YP_920176.1| 130 YVCRKCG 136
                                    99****9 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   8.6e-05      0.09      30      55 ..     108     138 ..      94     140 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.6e-05
                 OrfB_Zn_ribbon  30 tCseCgsknke.....alsgrtfkCpnCgfe 55 
                                     C++Cgs + e      l++ +++C++Cgf 
  gi|119719681|ref|YP_920176.1| 108 VCPNCGSPDLErigipGLTPTLYVCRKCGFA 138
                                    5******99999*****************95 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00057       0.6      17      38 ..     100     121 ..      96     123 .. 0.84
   2 ?    0.4   0.0      0.68   7.2e+02      25      33 ..     131     139 ..     126     145 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00057
                   NOB1_Zn_bind  17 vtkdmtkkFCpkCGnktLkrva 38 
                                    vt++     Cp+CG++ L+r+ 
  gi|119719681|ref|YP_920176.1| 100 VTRKHGVLVCPNCGSPDLERIG 121
                                    677777888***********85 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.68
                   NOB1_Zn_bind  25 FCpkCGnkt 33 
                                     C kCG +t
  gi|119719681|ref|YP_920176.1| 131 VCRKCGFAT 139
                                    599999876 PP

>> zf-IS66  zinc-finger binding domain of transposase IS66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1    0.0011       1.2       3      15 ..     108     121 ..     107     123 .. 0.89
   2 ?    2.7   0.1      0.16   1.6e+02      40      46 .]     130     136 ..     128     141 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0011
                        zf-IS66   3 tCpcCGg.llkpig 15 
                                    +Cp+CG+ +l +ig
  gi|119719681|ref|YP_920176.1| 108 VCPNCGSpDLERIG 121
                                    7******77**999 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.16
                        zf-IS66  40 yaCpcCe 46 
                                    y C++C+
  gi|119719681|ref|YP_920176.1| 130 YVCRKCG 136
                                    8899996 PP

>> Prim_Zn_Ribbon  Zinc-binding domain of primase-helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.3    0.0089       9.4       6      13 ..     109     116 ..     103     121 .. 0.90
   2 ?    4.1   0.0     0.054        57      26      34 ..     130     137 ..     123     141 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0089
                                    -TTTT-TT CS
                 Prim_Zn_Ribbon   6 CPvCGGrD 13 
                                    CP+CG+ D
  gi|119719681|ref|YP_920176.1| 109 CPNCGSPD 116
                                    *****976 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.054
                                    EEETTTTBX CS
                 Prim_Zn_Ribbon  26 wfCrqCggg 34 
                                    ++Cr+C g 
  gi|119719681|ref|YP_920176.1| 130 YVCRKC-GF 137
                                    79****.75 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.3    0.0015       1.6      16      22 ..     109     115 ..     105     115 .. 0.63
   2 ?    3.0   0.4     0.086        90       2       6 ..     132     136 ..     130     138 .. 0.60

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0015
                  zinc_ribbon_2  16 CpyCGtp 22 
                                    Cp+CG+p
  gi|119719681|ref|YP_920176.1| 109 CPNCGSP 115
                                    6666654 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.086
                  zinc_ribbon_2   2 CpnCG 6  
                                    C +CG
  gi|119719681|ref|YP_920176.1| 132 CRKCG 136
                                    55555 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       3.8   4.1e+03      28      38 ..      82      92 ..      82      93 .. 0.84
   2 ?    8.5   5.7    0.0013       1.4       2      26 ..     108     136 ..     107     137 .. 0.67

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3.8
                                   EEEECCCCCCC CS
                   TF_Zn_Ribbon 28 Vlednsidegp 38
                                   V ed+ ++eg+
  gi|119719681|ref|YP_920176.1| 82 VREDELAVEGK 92
                                   77999999987 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0013
                                    EETTTTCEEC.......HEETSTTCEEESSSS CS
                   TF_Zn_Ribbon   2 kCPnCgstnl.......veDpergelvCtdCG 26 
                                    +CPnCgs++l       +++   + +vC +CG
  gi|119719681|ref|YP_920176.1| 108 VCPNCGSPDLerigipgLTP---TLYVCRKCG 136
                                    8*******985555444444...346777777 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.2     0.011        12       5      12 ..     107     114 ..     104     119 .. 0.82
   2 ?    5.2   0.4     0.016        17      21      28 ..     129     136 ..     129     138 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.011
                        zf-RRN7   5 ppCgvCgc 12 
                                     +C+ Cg+
  gi|119719681|ref|YP_920176.1| 107 LVCPNCGS 114
                                    69*****8 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.016
                        zf-RRN7  21 fyyCrrCh 28 
                                    +y+Cr C+
  gi|119719681|ref|YP_920176.1| 129 LYVCRKCG 136
                                    69*****9 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   1.0     0.053        56      17      22 ..     109     114 ..     108     115 .. 0.79
   2 ?    9.2   0.4   0.00095         1       1      10 [.     130     139 ..     130     141 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.053
                   Rubredoxin_2  17 CpsCgs 22 
                                    Cp+Cgs
  gi|119719681|ref|YP_920176.1| 109 CPNCGS 114
                                    999986 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00095
                   Rubredoxin_2   1 YvCsqCGfes 10 
                                    YvC++CGf +
  gi|119719681|ref|YP_920176.1| 130 YVCRKCGFAT 139
                                    9******965 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.8      0.05        53      22      26 .]     108     112 ..     106     114 .. 0.88
   2 ?    6.3   0.7    0.0098        10      20      26 .]     129     135 ..     127     135 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.05
                         zf-ACC  22 VCPkC 26 
                                    VCP+C
  gi|119719681|ref|YP_920176.1| 108 VCPNC 112
                                    89999 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0098
                         zf-ACC  20 lyVCPkC 26 
                                    lyVC+kC
  gi|119719681|ref|YP_920176.1| 129 LYVCRKC 135
                                    8****** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 1134.45
//
Query:       gi|119719682|ref|YP_920177.1|  [L=176]
Description: hypothetical protein Tpen_0772 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.5e-05   23.0   2.6    0.00016   22.2   1.5    1.8  2  DUF2569   Protein of unknown function (DUF2569)
     0.0014   18.6   2.4     0.0029   17.7   2.4    1.5  1  SpoIIM    Stage II sporulation protein M


Domain annotation for each model (and alignments):
>> DUF2569  Protein of unknown function (DUF2569)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.17   1.5e+03      85     104 ..      21      37 ..      11      56 .. 0.48
   2 !   22.2   1.5   1.8e-08   0.00016      24     100 ..      95     172 ..      71     176 .] 0.76

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.17
                        DUF2569  85 yiifllanlvlalidallls 104
                                      ++  + ++l+++ +++l 
  gi|119719682|ref|YP_920177.1|  21 ALTL--VAVFLLVA-SYVLG 37 
                                    4333..33333333.33332 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 1.8e-08
                        DUF2569  24 lelidalkalfsle.ewstlknleslltlllileiitnialvafsilllvlffkrrksfPklyiifllanlvlalida 100
                                    +  i++++++++ + + + l++++ +l ++ ++e++  ++ +a  ++l+++ff+rr++ P    + +l+ l l+ i a
  gi|119719682|ref|YP_920177.1|  95 AAYISFYSGYMDKAlQVAGLEEATGTLEAYSLIEWVALVLATAEGLMLTYAFFRRRRVSPVETLASVLLQLSLIAIVA 172
                                    44444444333333166788888889**********************************998888888887776643 PP

>> SpoIIM  Stage II sporulation protein M
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   2.4   3.2e-07    0.0029       3     145 ..      28     174 ..      21     176 .] 0.64

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.2e-07
                         SpoIIM   3 llflvgillgallaa.........snfaeqis.seskensalslflaifanNlrvalllfllGllllgiptilvl.linG 71 
                                    +l++++++lg++            ++++ +i+  + ++ ++ ++++ +f+n   v+l++      ++g +t+  + ++ G
  gi|119719682|ref|YP_920177.1|  28 FLLVASYVLGFAQNItpeearrvaQEYKGYIEgARRIK-DPDAVAFGVFVNESLVILVCNT---PVIGPVTAAYIsFYSG 103
                                    44455555555555566665554322224455533333.3347888888888888665553...3456666665656666 PP

                         SpoIIM  72 fvlGavaalvaefgglllflllilPhgilelpaiiiagaaglrlgkal..rsrrkalkeakrellklllllvplll 145
                                    ++  a+    +   gl ++ +++    ++e  a+++a+a gl l +a+  r+r+   + ++  ll+l l+ ++  l
  gi|119719682|ref|YP_920177.1| 104 YMDKAL----QV-AGLEEATGTLEAYSLIEWVALVLATAEGLMLTYAFfrRRRVSPVETLASVLLQLSLIAIVAAL 174
                                    665444....22.3388889999999**********************9666666666677777777777777443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1369.24
//
Query:       gi|119719683|ref|YP_920178.1|  [L=409]
Description: phosphoglycerate kinase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   3.4e-115  385.0   0.1   4.3e-115  384.7   0.1    1.0  1  PGK       Phosphoglycerate kinase
  ------ inclusion threshold ------
       0.13   11.7   0.1       0.37   10.3   0.0    1.7  2  Arginase  Arginase family


Domain annotation for each model (and alignments):
>> PGK  Phosphoglycerate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  384.7   0.1  4.8e-119  4.3e-115       1     375 [.      10     393 ..      10     395 .. 0.91

  Alignments for each domain:
  == domain 1  score: 384.7 bits;  conditional E-value: 4.8e-119
                                    GGGS--TT-EEEEEE-----EECT.TEES--HHHHHHHH.HHHHHHHTT-EEEEEE--S--TTS-GGG-SHHHHHHHHHH CS
                            PGK   1 vkdldlkgkrvlvRvDfNvplkke.gkitddtriraalp.TikyllekgakvvllsHlgrpkgekeklslkpvaerLsel 78 
                                    ++d+d++gk+v vRvDfN+p++ + +++ ddtrira+++ Ti++l+ek+akvv+lsH+gr kg+ + +sl+++ae Ls+l
  gi|119719683|ref|YP_920178.1|  10 LDDVDVRGKTVGVRVDFNSPVDPQtKRLLDDTRIRAHAEtTIRELVEKKAKVVVLSHQGR-KGDPDFTSLREHAEVLSRL 88 
                                    589******************998899*********98637*******************.59***************** PP

                                    HTT-EEEESSTTSHHHHHHHHT-TTT-EEEES-GGGSTTTTTT-H...H....HHHHHHHT-SEEEE--GGGTTS--TTT CS
                            PGK  79 lgkeVkfvedvvgeeveeaiaelkegevllLeNvrfykeEeknde...e....lakklasladvyVnDAFgtahrahaSt 151
                                    +  +Vkfv+d++ge++ ++i++l++gevl+LeNvr+ ++E kn +   +    l++ la l +vyV DAF++ahr haS+
  gi|119719683|ref|YP_920178.1|  89 VPARVKFVDDIFGEKAVKEIKALSPGEVLVLENVRMWDGEAKNASpeeHaktpLVQALAPLLEVYVVDAFSAAHRPHASL 168
                                    ****************************************9886555415677*************************** PP

                                    THHHHCSEE.EE-HHHHHHHHHHHHHHHS--SSEEEEEEES-HHHCHHHHHHHTTT-..SEEEEETCHHHHHHHHTT-B- CS
                            PGK 152 vgiakvlsa.aaGllmekElealskvlenperplvailGGakvsdkikvienLlekv..dkliigGgmantFlkaqglei 228
                                    vg+a v+++ +aG++me+El+al +v +nperp+v+++GGak +d  ++i+++l +   dk+++gG+ an +l+ +g +i
  gi|119719683|ref|YP_920178.1| 169 VGFAPVVKHfVAGRVMERELQALYRVRNNPERPCVYVIGGAKAEDTAEIISSVLGNNiaDKVLTGGLAANLLLHSSGKKI 248
                                    *******777********************************************98778********************* PP

                                    TTSS-....-GGGHHHHHHHHHHHHHHT-EEE--SEEEEESSSSTTS.EEE.ECCG--TT-EEEEE-HHHHHHHHHHHCC CS
                            PGK 229 gkslv....eedklelakellekakkkgvkillpvDvvvakeeaekeakvv.eveaipedemalDigpktielfaeaike 303
                                    g+  v    e+  l+l  el +  +k g++i+lpvD++v+++     ++v   v+++  +  + Dig++t+e++a++i+e
  gi|119719683|ref|YP_920178.1| 249 GDVNVsvlkEKGFLDLEPELKKLLDKYGDRIVLPVDLAVEESG----KRVEvGVDSV-PNLPIKDIGSRTAEEYARIISE 323
                                    *766644333335777777777777788************832....2333256666.5678****************** PP

                                    -SEEEEES-SS-TTSGCCCHHHHHHHHHHHHHCHTSEEEEESHHHHHHHHHTT-GGGSSEEESSSHHHHHHH CS
                            PGK 304 aktvvwnGpmGvfeiekfakGTkaiakalaeatkgalsivGGgdsaaaveklgladkvshvStGGgAsLelL 375
                                    a+tvv+nGpmGvfe ekf+ GTk++ +a+a+++  a++++GGg+++aa++klg+adk+shvStGGgA++e+L
  gi|119719683|ref|YP_920178.1| 324 ARTVVMNGPMGVFEDEKFSLGTKKVFEAMASSK--AFTLIGGGHTIAAASKLGFADKLSHVSTGGGALIEYL 393
                                    *******************************84..7**********************************98 PP

>> Arginase  Arginase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0      0.62   5.6e+03      64      89 ..      39      64 ..       7      65 .. 0.66
   2 ?   10.3   0.0   4.1e-05      0.37      71     107 ..     343     379 ..     302     391 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 0.62
                                   CHHHHHHHHHHHHHHHHHTTCEEEEE CS
                       Arginase 64 dneevleqieeavaeilkagklpivl 89
                                   d +++  ++e++++e++++++ ++vl
  gi|119719683|ref|YP_920178.1| 39 DDTRIRAHAETTIRELVEKKAKVVVL 64
                                   44455666777777777777777776 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 4.1e-05
                                    HHHHHHHHHHHTTCEEEEEESSGGGHHHHHHHHHHHH CS
                       Arginase  71 qieeavaeilkagklpivlGGDHsialgilralaeky 107
                                      +++v e++++ k   ++GG+H+ia ++  ++a+k+
  gi|119719683|ref|YP_920178.1| 343 LGTKKVFEAMASSKAFTLIGGGHTIAAASKLGFADKL 379
                                    4567888889999999*************99999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.38
# Mc/sec: 3195.12
//
Query:       gi|119719684|ref|YP_920179.1|  [L=253]
Description: hypothetical protein Tpen_0774 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-34  119.3   0.0    2.5e-34  119.1   0.0    1.0  1  PAC2      PAC2 family


Domain annotation for each model (and alignments):
>> PAC2  PAC2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.1   0.0   1.4e-38   2.5e-34       1     212 [.      20     229 ..      20     230 .. 0.89

  Alignments for each domain:
  == domain 1  score: 119.1 bits;  conditional E-value: 1.4e-38
                                    EEEESSCGGGHHHHHHHHHHHHTTEEEEEEEEHCCHSBCCCC.SEEEEETTEEE-SEEEEEETTT.SEEEEEEE...E-H CS
                           PAC2   1 LilGfpgiGnVgqlavdlLiesleaekvgeidsdyllpfvgprpvvlveegrelepprlyakdsgsrdllvlqg...rep 77 
                                    +i+G+p++G+Vg +++++L+ ++e++++g++ds + lp     pv+l++e  +l p+r+y   +++  ++vl++   + p
  gi|119719684|ref|YP_920179.1|  20 FIVGLPDVGLVGPISTSHLVKQWELREIGYLDSAS-LP-----PVILFHEYSPLFPIRFYGGYKKNDYVVVLHSdiaIPP 93 
                                    69*********************************.9*.....****************766444677888888998888 PP

                                    SCHHHHHHHHHHHHHHHTTESEEEEEEEEEESS-ES..TTS-.EEEEEESSHHHHHHHHCT.....-CEEEEHHHHHHHH CS
                           PAC2  78 ilqyeefakalldwaeelgvkevvvLggldageradvphtrpekvtgaatdeelleelees.....eyggivgitglLls 152
                                    +l    +a+ l++ + +   ++vv+Lgg++ ++r ++  ++p k+++a+ d e l+  +e+     ++g+i+g+ + +l+
  gi|119719684|ref|YP_920179.1|  94 ELVPS-MASFLTESLFRKSARRVVLLGGIAVQNRLNI--ETP-KTYAASIDAESLRYAQEKgiellKEGFIGGAYAQFLK 169
                                    88888.**************************99765..666.6666665555553333334667899************ PP

                                    HHHHTT-EEEEEEEEEECCC--HHHHHHHHHHHHHHHT---HCHHHHHHHHHHHHHHHHH CS
                           PAC2 153 aakergipavgllaevphylpdPkaaaalleflskllglevdtedLeedaeeleeqleel 212
                                    ++ +r++++++llae+   +pdP a+a++l++l+k+lg +vd+++L e+ ee++ +l el
  gi|119719684|ref|YP_920179.1| 170 EGYKRKLSVIALLAECFLNYPDPGASASALQALAKILGHDVDVKQLLEQEEEIRVKLREL 229
                                    ******************************************************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       687  (0.0383178); expected 358.6 (0.02)
Passed bias filter:                      628  (0.0350271); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.37
# Mc/sec: 2026.15
//
Query:       gi|119719685|ref|YP_920180.1|  [L=143]
Description: heat shock protein Hsp20 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    7.7e-12   45.3   0.0    1.2e-11   44.7   0.0    1.4  1  HSP20       Hsp20/alpha crystallin family
    3.5e-05   23.3   0.0    6.6e-05   22.4   0.0    1.5  1  ArsA_HSP20  HSP20-like domain found in ArsA
     0.0055   17.1   0.0       0.01   16.2   0.0    1.5  1  PIH1_CS     PIH1 CS-like domain


Domain annotation for each model (and alignments):
>> HSP20  Hsp20/alpha crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.7   0.0     2e-15   1.2e-11       5      91 ..      50     137 ..      46     143 .] 0.86

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 2e-15
                                    SEEEEEEEEE-TT--.CCCEEEEEETTEEEEEEE--..---TT----SS---EEEEEE--STTB-TTT-EEEEETTEEEE CS
                          HSP20   5 eeeefevkldvpglk.keelkvkvednrvlvkgeheeeeedekglikerssrkFsrkftLPenvdadkvkaslkdGvLtv 83 
                                    + +  ++ +d++g+k ke+++v ve+n++ +++   +    e  +       k++ ++ LP n+d +++kas+++G+L+v
  gi|119719685|ref|YP_920180.1|  50 SSDCLTIYADLAGVKrKEDVDVYVEGNVLRIEARLSKPLLFEGLVFFREGITKYKLEIPLPSNADVENIKASFRKGMLEV 129
                                    566678999******888****************996666666666667899**************************** PP

                                    EEEBSS-- CS
                          HSP20  84 tvpkkepe 91 
                                    tvp k + 
  gi|119719685|ref|YP_920180.1| 130 TVPLKVQR 137
                                    ***98775 PP

>> ArsA_HSP20  HSP20-like domain found in ArsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   1.1e-08   6.6e-05       6      62 ..      56     130 ..      51     131 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.1e-08
                     ArsA_HSP20   6 lkldLPfv.dkeeidlsrsgdeLtIkig..................nfrRqitLPsvlarkevtsAkfedgvLeIr 62 
                                    + +dL +v  ke++d++ +g+ L I++                   +++ +i+LPs  + +++ +A+f++g+Le++
  gi|119719685|ref|YP_920180.1|  56 IYADLAGVkRKEDVDVYVEGNVLRIEARlskpllfeglvffregitKYKLEIPLPSNADVENI-KASFRKGMLEVT 130
                                    67899***44558********************************************999999.**********97 PP

>> PIH1_CS  PIH1 CS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.7e-06      0.01      35      97 ..      56     134 ..      39     136 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.7e-06
                        PIH1_CS  35 ieielPllksikevklrvgerrlel................eskk.akyfLslkLpYpvdedkveAkFvkktklLkvklp 97 
                                    i  +l ++k  ++v++ v+ + l +                  ++  ky+L+++Lp + d ++++A F k     +v l+
  gi|119719685|ref|YP_920180.1|  56 IYADLAGVKRKEDVDVYVEGNVLRIearlskpllfeglvffR-EGiTKYKLEIPLPSNADVENIKASFRKGMLEVTVPLK 134
                                    555677778888888888888888888888888888888853.4458*********************876555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      608  (0.0339115); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 984.17
//
Query:       gi|119719686|ref|YP_920181.1|  [L=248]
Description: helix-turn-helix domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.2e-08   33.5   0.0    6.6e-08   32.5   0.0    1.5  1  HTH_3           Helix-turn-helix
    1.7e-06   28.3   0.0    4.8e-06   26.8   0.0    1.8  2  HTH_31          Helix-turn-helix domain
    7.2e-05   22.7   0.0    0.00016   21.6   0.0    1.6  1  HTH_19          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.011   15.9   0.0      0.018   15.1   0.0    1.3  1  MqsA_antitoxin  Antitoxin component of bacterial toxin-antito
       0.12   12.4   0.0       0.29   11.2   0.0    1.6  1  DUF1902         Domain of unknown function (DUF1902)


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.0   1.8e-11   6.6e-08       1      46 [.      33      79 ..      33      82 .. 0.90

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 1.8e-11
                                   HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTT.SSCSBHHHHHHHHH CS
                          HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriEnG.ernPsletlkklak 46
                                   ++++R++ + +q eLA  ++vs s is++E+G + +P  + + k  k
  gi|119719686|ref|YP_920181.1| 33 MRKWREKFNVTQVELASIMNVSASVISDYESGrRKSPGARFIRKFVK 79
                                   599*****************************988899888888765 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.0   1.3e-09   4.8e-06       3      51 ..      30      78 ..      30      89 .. 0.92
   2 ?   -2.2   0.0       1.5   5.5e+03      28      44 ..      93     108 ..      83     112 .. 0.51

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 1.3e-09
                         HTH_31  3 GalLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavleala 51
                                   G + r +Re+ +++q e+A   +vs+s +s++E+Grr  p  +++++++
  gi|119719686|ref|YP_920181.1| 30 GLEMRKWREKFNVTQVELASIMNVSASVISDYESGRRKSPGARFIRKFV 78
                                   6789************************************999999876 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.5
                         HTH_31  28 estlsrlEqGrrgrpsp 44 
                                     s l+r+  G   + ++
  gi|119719686|ref|YP_920181.1|  93 LSGLRRILLGSD-LLRE 108
                                    344555555555.4555 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   4.6e-08   0.00016       5      50 ..      34      79 ..      33      81 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 4.6e-08
                         HTH_19  5 keaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiae 50
                                   ++ Re+++ tq ela+   +s s is +E+g+++ p+a+ ++k+++
  gi|119719686|ref|YP_920181.1| 34 RKWREKFNVTQVELASIMNVSASVISDYESGRRKSPGARFIRKFVK 79
                                   788****************************999****99999876 PP

>> MqsA_antitoxin  Antitoxin component of bacterial toxin-antitoxin system, MqsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   5.1e-06     0.018      71     112 ..      30      71 ..       7      84 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5.1e-06
                 MqsA_antitoxin  71 pafiarvrkkleldqreaaeifGgGvnafsryekGkvrppla 112
                                    + ++++ r+k++++q e+a+i+ +     s ye+G+ ++p a
  gi|119719686|ref|YP_920181.1|  30 GLEMRKWREKFNVTQVELASIMNVSASVISDYESGRRKSPGA 71 
                                    5678999*****************************998865 PP

>> DUF1902  Domain of unknown function (DUF1902)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0     8e-05      0.29      13      41 ..     218     246 ..     214     247 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 8e-05
                                    TEEEEE-SSSTT---EESSHHHHHHHHHH CS
                        DUF1902  13 gVWvaesddipGlvteaetleeLlkklea 41 
                                    g  +a+ ++ip +vt  +t+e+L++kl+a
  gi|119719686|ref|YP_920181.1| 218 GLEIAKRENIPLAVTRVDTVENLIEKLRA 246
                                    6668999****99**************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1758.45
//
Query:       gi|119719687|ref|YP_920182.1|  [L=284]
Description: type II secretion system protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-11   43.6   4.3    2.5e-11   43.6   4.3    2.0  2  T2SSF     Type II secretion system (T2SS), protein F


Domain annotation for each model (and alignments):
>> T2SSF  Type II secretion system (T2SS), protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6   4.3   1.4e-15   2.5e-11       3     124 ..     112     238 ..     110     239 .. 0.96
   2 ?   -3.6   1.6      0.55   9.9e+03     105     119 ..     254     268 ..     252     274 .. 0.61

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 1.4e-15
                                    HHHHHHHHTT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTS.....SHHHHHCT-TT.TS-HHHHHHHHHHHHHT-H CS
                          T2SSF   3 rqlatllsaGvplveaLellaeeaengplaeelkriarrlraGg.....slsealertpssefpelvvqlirageeggnL 77 
                                     ++a l+s+G++l++ Le++    +n+++++e++ i+r+++a g     +ls+a  r+ps  +++l   l ++  ++gn 
  gi|119719687|ref|YP_920182.1| 112 SYMAALSSSGMGLERLLERAVLYESNKEIKREIALILRDIKAYGldtltALSRAALRSPSRSLAMLWLGLRETYITSGNF 191
                                    68****************9999999*******************998888899999****999***************** PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXXXX CS
                          T2SSF  78 aevLerlaeyleeerelrrkllaallepllllvvallvllillaill 124
                                      +L++ +  l  e  +  ++ +++++ +++++++l+v+++l+++++
  gi|119719687|ref|YP_920182.1| 192 KSYLSHFSGVLLSEKTQSLRRVTNTISMMAEVYTTLMVAAPLMFVTM 238
                                    *******************************************9987 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 0.55
                                    TXXXXXXXXXXXXXX CS
                          T2SSF 105 pllllvvallvllil 119
                                    p +l++v+ +v++++
  gi|119719687|ref|YP_920182.1| 254 PGILVLVLTFVVVPF 268
                                    556666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       919  (0.0512577); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2081.26
//
Query:       gi|119719688|ref|YP_920183.1|  [L=499]
Description: amidohydrolase 3 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-66  225.4   0.0      4e-66  224.4   0.0    1.4  2  Amidohydro_3  Amidohydrolase family
    0.00029   20.3   0.0      0.012   15.0   0.0    2.2  2  Amidohydro_1  Amidohydrolase family
  ------ inclusion threshold ------
      0.014   15.4   0.0      0.028   14.4   0.0    1.5  1  Pyridox_ox_2  Pyridoxamine 5'-phosphate oxidase


Domain annotation for each model (and alignments):
>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  224.4   0.0   6.7e-70     4e-66       2     419 ..      47     448 ..      46     453 .. 0.91
   2 ?   -2.3   0.0      0.39   2.4e+03     442     473 .]     456     487 ..     455     487 .. 0.87

  Alignments for each domain:
  == domain 1  score: 224.4 bits;  conditional E-value: 6.7e-70
                   Amidohydro_3   2 viDakGrlvlPGFvDsHtHlagggvnlrllrlpdarvtslegvltavrdqagttpkgrwivgeGwdeaqfaeerfpyala 81 
                                    v+D +Gr+v+PG+vD+H+Hl+++ + l +l+l++  v+sle++ +++++ ++++p+g wivg+Gwd+ ++ e+r+p ++ 
  gi|119719688|ref|YP_920183.1|  47 VVDVEGRVVVPGLVDAHMHLYSTALSLGRLDLRG--VSSLEEIREVLKAAVKEAPPGSWIVGRGWDQEKLKERRMP-TRF 123
                                    89********************************..****************************************.*** PP

                   Amidohydro_3  82 eldevledapvllaaldtHaavrnsaaldlagiteatpdpaggeilrdangegatgllregafhlvldla.plareaeaa 160
                                    ++d+v  d+pv l ++++H+a++n+ al++ g+    + ++g + l ++ g  +tg++ e+  + v   + p ++e ++ 
  gi|119719688|ref|YP_920183.1| 124 DIDDVTGDNPVVLIRVCGHVALLNTLALRKMGLL---DSERGFGALLEKEGGVPTGIVYEDLVDYVVSRIpPPPPELLKS 200
                                    ******************************9999...4445566666666666********777777777566******* PP

                   Amidohydro_3 161 avaaalaalasyGitsveagggnvsslddleplfeltaeeklplrvi......ikelldaaerlglplspgseeltigav 234
                                    ++ ++l ++ s G+t     + ++ sl++le+++++     lp+         i+el+++            ++  +++v
  gi|119719688|ref|YP_920183.1| 201 WILRVLSEYVSLGVTEL---HSMSVSLEELEAVQRVLTT--LPIGYRayvdpgIAELAARE-----------YKGLVHGV 264
                                    *****************...****************988..56555566766444444433...........4457778* PP

                   Amidohydro_3 235 klfadgvlgsrtalltepyf....tgwpdfedealaelvaaadergldvaihaigdaavddvldafeaaaekngnqdrrr 310
                                    k+fadg+ g rta+l e y+    +g+  +++e +  ++++a   gl+ a+haigd av+++l+a e+     ++    r
  gi|119719688|ref|YP_920183.1| 265 KIFADGSFGARTAALREKYSdaetRGVLRISSEGILSVARRALSLGLQTAVHAIGDLAVAEALKAAEQL----PRGSL-R 339
                                    ************************************************************888888555....66666.* PP

                   Amidohydro_3 311 lehaegvtesqiervaalqvaagvqpvfnfedelldsrlgperargstpvkellnagvkvalgsDapvgpfdpwprigaa 390
                                    +eha+ ++++ +e++ a+  +++vqp f   d ++ +rlg era++++++k+l  a+ +v ++sDapv+p++pw +++aa
  gi|119719688|ref|YP_920183.1| 340 IEHASLTPPDILEKIGAVKPEIAVQPHFILSDTWITERLG-ERAEWVYAFKSLQ-ARTRVYGSSDAPVEPINPWLGVYAA 417
                                    *************************99999999******6.8*********986.566********************** PP

                   Amidohydro_3 391 vmrktrrgg..evlrpdeelsleealalyTr 419
                                    v r   +g    +++ +e++s+ eal+lyT+
  gi|119719688|ref|YP_920183.1| 418 VERGCPEGLpvCRYTYGEKMSFVEALRLYTS 448
                                    ***9999999999999**************8 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.39
                   Amidohydro_3 442 lvvldadpldvdppelaearvrltvvdGrvvy 473
                                    +vvl+  +l   ++e    r+ +++v+G++vy
  gi|119719688|ref|YP_920183.1| 456 IVVLNSTRLPTSKKEYEALRAYAVLVGGKTVY 487
                                    8999988888888888888899********98 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0     2e-06     0.012       1      44 [.      54      98 ..      54     101 .. 0.77
   2 !    3.1   0.0     0.008        48      30     167 ..     195     332 ..     172     383 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2e-06
                                   EEEE-EEEEEEECETTECSSSGHHHHH..STTHHHHHHHHHHHHHH CS
                   Amidohydro_1  1 ivlPGlIDaHvHleqsllrgatledwl..vppetaaealesgikta 44
                                   +v+PGl+DaH Hl++++l+    +d++   + e+++e+l+ ++k+a
  gi|119719688|ref|YP_920183.1| 54 VVVPGLVDAHMHLYSTALSL-GRLDLRgvSSLEEIREVLKAAVKEA 98
                                   69***********9887622.2334448899999999999999887 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.008
                                    THHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHHHHHHHHHHHTSSSEEEEEEESSEGGSGCCCSHHHHHHHHHHHHHHHH CS
                   Amidohydro_1  30 petaaealesgiktalksGtttvadmgattstgiealleaaeelplglrilggkvsldrgsaetskasreklkagaaeti 109
                                    pe ++  + +++++ ++ G+t    m+    + +ea+ + +  lp+g+r+++       g ae    +++ l+ g+    
  gi|119719688|ref|YP_920183.1| 195 PELLKSWILRVLSEYVSLGVTELHSMSVS-LEELEAVQRVLTTLPIGYRAYVDP-----GIAELAAREYKGLVHGV---- 264
                                    56666666666666666666666666664.336666666666667777777662.....44444444555555555.... PP

                                    HHCTTTCEE.EEEEECGTCCSHHH.........HHHHHHHHHHHHTTEEEEEETSSCHHHHHHHHHHT CS
                   Amidohydro_1 110 kgkadgvvk.valapheapafsde.........elkealkeakkrdlpvaiHaletkgevedaeaafg 167
                                    k++adg +   + a +e ++  +          ++  +++ a   +l+ a+Ha ++ +  e+ +aa +
  gi|119719688|ref|YP_920183.1| 265 KIFADGSFGaRTAALREKYSDAETrgvlrisseGILSVARRALSLGLQTAVHAIGDLAVAEALKAAEQ 332
                                    44455555444444444444444444444444488888888888899999999777777766666544 PP

>> Pyridox_ox_2  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   4.8e-06     0.028      39     139 ..      30     130 ..      17     132 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.8e-06
                                    EEEEEETTSHCCHCCCT--ECEEEEEEEEEEE-SE.GG.EEE.EEEEEEEEE..EEEE--HHHHHHHCCCHHHHHSTTTG CS
                   Pyridox_ox_2  39 lyfhgakgsrlaaalrgapvcvvvtevdglvlars.fn.sln.yrSVvvrGr..aeevtdeeekaealellvekivpgrw 113
                                    ++f g++++ l   ++       v +v+g+v+     +  ++ y  ++  Gr  ++ v++ ee +e+l+++v+ + pg+w
  gi|119719688|ref|YP_920183.1|  30 IVFVGSESAALKTGAD------LVVDVEGRVVVPGlVDaHMHlYSTALSLGRldLRGVSSLEEIREVLKAAVKEAPPGSW 103
                                    6777777777777777......444556666666666666799********9666779********************** PP

                                    GCSB---CCCCCT.EEEEEEEEEEEEE CS
                   Pyridox_ox_2 114 enlrpptrkelka.tsvlrlkieevsg 139
                                       r  ++++lk+     r++i++v+g
  gi|119719688|ref|YP_920183.1| 104 IVGRGWDQEKLKErRMPTRFDIDDVTG 130
                                    ****9999999998899*******998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (499 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 3715.12
//
Query:       gi|119719689|ref|YP_920184.1|  [L=292]
Description: hypothetical protein Tpen_0779 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.074   13.3   0.0        0.2   11.9   0.0    1.7  2  baeRF_family10  Bacterial archaeo-eukaryotic release factor f


Domain annotation for each model (and alignments):
>> baeRF_family10  Bacterial archaeo-eukaryotic release factor family 10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0      0.38   6.9e+03      98     121 ..      62      85 ..      43      93 .. 0.56
   2 ?   11.9   0.0   1.1e-05       0.2      89     135 ..     154     198 ..     140     201 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.38
                 baeRF_family10  98 eeetaalldrlpkalrarvvgtlp 121
                                    ++  a+ ++  p+ +r+++  +++
  gi|119719689|ref|YP_920184.1|  62 PNTVAKAAAVSPEGWRELLYLSMH 85 
                                    444455555556666665555544 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 1.1e-05
                 baeRF_family10  89 verlvlgGdeeetaalldrlpkalrarvvgtlplpvdasaaaVleka 135
                                    +erl l+G + ++ al +r+p+alr r + +++++   s++++ ek+
  gi|119719689|ref|YP_920184.1| 154 WERLKLSGLPGYRRALIERMPRALRVRAAVDINVDL--SKNEIYEKV 198
                                    99***********************99999999999..*****9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       243  (0.0135535); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 1836.41
//
Query:       gi|119719690|ref|YP_920185.1|  [L=134]
Description: hypothetical protein Tpen_0780 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       279  (0.0155614); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.44
# Mc/sec: 917.95
//
Query:       gi|119719691|ref|YP_920186.1|  [L=623]
Description: thiamine pyrophosphate binding domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.1e-28   98.1   0.1    7.7e-28   97.2   0.1    1.5  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
    4.2e-15   56.1   0.1    2.5e-14   53.6   0.0    2.0  2  POR_N         Pyruvate flavodoxin/ferredoxin oxidoreductase, 
    4.6e-10   39.4   0.9    0.00043   19.9   0.1    2.3  2  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b
    4.4e-08   32.6  22.7      1e-05   25.1   6.3    2.9  3  Fer4          4Fe-4S binding domain
    9.1e-08   31.8  20.4    0.00018   21.4   3.1    3.0  3  Fer4_2        4Fe-4S binding domain
    8.6e-06   25.8  11.4    2.2e-05   24.5  11.4    1.6  1  Fer4_21       4Fe-4S dicluster domain
    1.1e-05   25.4  11.9    0.00014   21.9  12.2    2.3  2  Fer4_10       4Fe-4S dicluster domain
    3.9e-05   23.7   5.9    3.9e-05   23.7   5.9    2.0  2  Fer4_9        4Fe-4S dicluster domain
    6.5e-05   22.8  21.5    0.00046   20.1   4.9    3.1  3  Fer4_6        4Fe-4S binding domain
    0.00057   20.4  13.7      0.002   18.7  12.0    2.6  3  Fer4_7        4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.016   16.1  10.1      0.071   14.1   3.7    2.5  2  Fer4_16       4Fe-4S double cluster binding domain
      0.021   15.3   8.5       0.92   10.0   0.6    2.5  2  Fer4_8        4Fe-4S dicluster domain
      0.024   15.1   4.0      0.024   15.1   4.0    2.8  2  Fer4_4        4Fe-4S binding domain
      0.076   12.5   0.0       0.13   11.8   0.0    1.3  1  Orbi_VP6      Orbivirus helicase VP6
      0.082   12.8   0.0       0.21   11.4   0.0    1.7  1  CedA          Cell division activator CedA
       0.13   11.2   0.6       0.29   10.1   0.6    1.5  1  E1_dh         Dehydrogenase E1 component
        2.4    8.8  11.2        5.5    7.6   2.1    2.6  3  Fer4_17       4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.2   0.1   7.3e-31   7.7e-28       1     152 [.     395     540 ..     395     541 .. 0.94

  Alignments for each domain:
  == domain 1  score: 97.2 bits;  conditional E-value: 7.3e-31
                                    ESSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEEEEE CS
                   TPP_enzyme_C   1 diGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmi.lqelatavrrnlpitvvv 79 
                                    diGc+tl      ++++p ++ +  ++ +mG +l++++G++    +++v+a++GD++f++  ++ l++av++++p++vvv
  gi|119719691|ref|YP_920186.1| 395 DIGCYTL------GFYPPFEMAD--FTWSMGSALGIGMGISKF-SKEPVIAFIGDSTFYHAgIPGLINAVYNRIPLVVVV 465
                                    89*****......9****99999..99**************94.467********************************* PP

                                    EE-SBCCCHHHHHHHHTCCTTTTSBB.BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHH....CSSSEEEEE CS
                   TPP_enzyme_C  80 lnNegygmtggqqepfggkrksgpagkdlkpvdfaklaealGak.garvekadveeleealkeal....ekkgpalie 152
                                    ++N++++mtg+q++p  g   +gpag+  + v+++ +a+a+G++ + +v+ +dv  +++a+++a+    ek +pa+++
  gi|119719691|ref|YP_920186.1| 466 MDNGITAMTGHQPHPGSG---FGPAGEPRPVVKIEDIAKAVGVEfVEVVDAYDVPAVRDAVERAIryvvEKSRPAVVV 540
                                    ***************998...56666669***************888*****************99999999999985 PP

>> POR_N  Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.6   0.0   2.4e-17   2.5e-14       2     171 ..      24     188 ..      23     243 .. 0.85
   2 ?   -0.0   0.1      0.58   6.1e+02      76      98 ..     448     470 ..     446     476 .. 0.84

  Alignments for each domain:
  == domain 1  score: 53.6 bits;  conditional E-value: 2.4e-17
                                    HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCCHHH CS
                          POR_N   2 aaiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmienlgl 81 
                                    +a++ag+ v++aYP TPs+ei+e+lae  ++ +v   +v    +E  a + +iGA++ G ra+Ta    G+  +++ l+ 
  gi|119719691|ref|YP_920186.1|  24 GALEAGISVATAYPGTPSTEIVETLAEVGERYGV---YVEWSTNEKVALEIAIGASMMGLRALTAMKHVGVNVASDPLMS 100
                                    899************************9988886...777789*********************************9999 PP

                                    HHHTT--EEEEEEEEE-STTBEEEEE--TTCHHHHS---EEEE-SSHHHHHHHHHHHHHHHHHCTSEEEEEEEHHHH.HE CS
                          POR_N  82 aageelPvvivvvaRalpstglsirtdqsDlmaardtglivlasenvqeafdlalvAfnlAekvrvPvivlfDgfllshe 161
                                     + + +   +v+v+   p    s +++q   ++ + + + v+ +++ qea d++   + l+ek++++v++ +  ++lsh+
  gi|119719691|ref|YP_920186.1| 101 LGYTGVVGGLVIVTADDPNA-HSSQNEQDNRIYGLHSYIPVFEPSSPQEAKDMVRDLYDLSEKYSTAVFLRT-TTRLSHS 178
                                    99988877777766554444.8**********************************************9887.67888** PP

                                    EEEEEC-SGG CS
                          POR_N 162 vekvelpdee 171
                                    + +v+l +  
  gi|119719691|ref|YP_920186.1| 179 RGEVTLGELR 188
                                    **99987765 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.58
                                    CCCHHHHHHTT--EEEEEEEEE- CS
                          POR_N  76 ienlglaageelPvvivvvaRal 98 
                                    i+ l+ a+ +++P+v+vv+  ++
  gi|119719691|ref|YP_920186.1| 448 IPGLINAVYNRIPLVVVVMDNGI 470
                                    688999***********997665 PP

>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1     2e-06    0.0021       3     157 ..      17     169 ..      15     179 .. 0.83
   2 !   19.9   0.1   4.1e-07   0.00043      50     157 ..     418     539 ..     415     549 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2e-06
                                    HHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT....TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHH. CS
                   TPP_enzyme_N   3 vaealvraLkalgvehvfgvpGsrilplldalseeq...girvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatn. 78 
                                    + ea++r   ++g+ ++ ++pG+ ++++++ l+e     g+ v  + +E +a  +A g +++  +   ++ ++g+++++ 
  gi|119719691|ref|YP_920186.1|  17 GNEAIARGALEAGISVATAYPGTPSTEIVETLAEVGeryGVYVEWSTNEKVALEIAIGASMMGLRALTAMKHVGVNVASd 96 
                                    568999999999***********************99888888889****************999999999999977643 PP

                                    CHHHHHHHHHHT--EEEEEEE--CCCHHS..TC--T-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--EEEE CS
                   TPP_enzyme_N  79 altalaeAkvdriPllvlsgdrptslrgqgvlqqeldqlalfrpvtkyaervtspeelpealrrAirtalsgrpgPvyl 157
                                     l++l    v +  l+++++d p ++ +q+ + + +  l+ + pv+    +++sp+e++ ++r+ ++ + ++ +++v+l
  gi|119719691|ref|YP_920186.1|  97 PLMSLGYTGVVG-GLVIVTADDPNAHSSQNEQDNRIYGLHSYIPVF----EPSSPQEAKDMVRDLYDLS-EKYSTAVFL 169
                                    888888777777.566667777777777676666777777766766....999*********9999999.888888887 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 4.1e-07
                                    HHHHHHHHHHHHHTS-EEEEE-CHHHHHHCHHHHHHHHHHT--EEEEEEE--CCCHH............S..TC--T-CC CS
                   TPP_enzyme_N  50 gaafaAdgyaratgkpgvvlvtsgpGatnaltalaeAkvdriPllvlsgdrptslrg............qgvlqqeldql 117
                                    +a ++  g+++++++p++++    +    ++++l++A ++riPl+v+++d++ +                g + ++++++
  gi|119719691|ref|YP_920186.1| 418 SALGIGMGISKFSKEPVIAFIGDSTFYHAGIPGLINAVYNRIPLVVVVMDNGITAMTghqphpgsgfgpAGEPRPVVKIE 497
                                    678888999999999999999999999999**********************9988889999999998866666666888 PP

                                    HHHCCCSSEEEE-SSG...GGHHHHHHHHHHHHHSSS--EEEE CS
                   TPP_enzyme_N 118 alfrpvtkyaervtsp...eelpealrrAirtalsgrpgPvyl 157
                                    ++++ v  ++++v ++    +++ a++rAir    ++++P+++
  gi|119719691|ref|YP_920186.1| 498 DIAKAVGVEFVEVVDAydvPAVRDAVERAIRYV-VEKSRPAVV 539
                                    888877777666655500056667899999999.555556655 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.4       3.3   3.5e+03       7      12 ..     366     371 ..     364     371 .. 0.87
   2 !   18.2   2.4   1.5e-06    0.0016       1      16 [.     563     578 ..     563     579 .. 0.93
   3 !   25.1   6.3   9.8e-09     1e-05       1      23 [.     593     615 ..     593     616 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3.3
                                    TSSS-T CS
                           Fer4   7 kCigCG 12 
                                    +C gCG
  gi|119719691|ref|YP_920186.1| 366 LCAGCG 371
                                    699**9 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 1.5e-06
                                    EEEETTTSSS-THHHH CS
                           Fer4   1 vvideekCigCGaCve 16 
                                    +++d+e+C++CG+Cv+
  gi|119719691|ref|YP_920186.1| 563 YYVDQERCVRCGICVD 578
                                    69*************7 PP

  == domain 3  score: 25.1 bits;  conditional E-value: 9.8e-09
                                    EEEETTTSSS-THHHHHSTTTEE CS
                           Fer4   1 vvideekCigCGaCvevCPvgAI 23 
                                    vvi +e C+gCG C+ +CP  AI
  gi|119719691|ref|YP_920186.1| 593 VVILPEVCVGCGVCATICPAKAI 615
                                    6899******************9 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.3       4.3   4.5e+03      10      14 ..     367     371 ..     364     372 .. 0.88
   2 !   21.4   3.1   1.7e-07   0.00018       2      22 .]     562     584 ..     561     584 .. 0.88
   3 !   20.3   3.9   3.8e-07    0.0004       2      22 .]     592     612 ..     591     612 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 4.3
                         Fer4_2  10 CigCg 14 
                                    C gCg
  gi|119719691|ref|YP_920186.1| 367 CAGCG 371
                                    9***8 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 1.7e-07
                         Fer4_2   2 pvvvdtdrCigCgaCv..saCPa 22 
                                    p++vd +rC++Cg+Cv   +CPa
  gi|119719691|ref|YP_920186.1| 562 PYYVDQERCVRCGICVdkFSCPA 584
                                    689*************7566**8 PP

  == domain 3  score: 20.3 bits;  conditional E-value: 3.8e-07
                         Fer4_2   2 pvvvdtdrCigCgaCvsaCPa 22 
                                    +vv+ ++ C+gCg C + CPa
  gi|119719691|ref|YP_920186.1| 592 RVVILPEVCVGCGVCATICPA 612
                                    68999***************8 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5  11.4   2.1e-08   2.2e-05       3      57 ..     565     615 ..     564     616 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 2.1e-08
                        Fer4_21   3 idedkCigCgkCl..iaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedci 57 
                                    +d+++C+ Cg C+   +C+     ai  +++ ++ ++ + CvGC +C+++CP  ++i
  gi|119719691|ref|YP_920186.1| 565 VDQERCVRCGICVdkFSCP-----AIVREEDGRVVILPEVCVGCGVCATICPA-KAI 615
                                    89**********8334566.....9*999999999*****************6.666 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9  12.2   1.3e-07   0.00014       3      56 .]     564     611 ..     563     611 .. 0.93
   2 !   16.3   2.6   7.5e-06    0.0079       2      22 ..     593     613 ..     592     621 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.3e-07
                        Fer4_10   3 vidddtCirCgkCvk..aCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                    ++d+++C+rCg Cv+  +CPa          ++e+++v + +e C gcg C+ +CP
  gi|119719691|ref|YP_920186.1| 564 YVDQERCVRCGICVDkfSCPA--------IVREEDGRVVILPEVCVGCGVCATICP 611
                                    5799**********9777***........9999999*******************9 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 7.5e-06
                        Fer4_10   2 vvidddtCirCgkCvkaCPad 22 
                                    vvi ++ C++Cg C + CPa+
  gi|119719691|ref|YP_920186.1| 593 VVILPEVCVGCGVCATICPAK 613
                                    78999***************4 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       5.7     6e+03      35      40 ..     366     371 ..     352     372 .. 0.73
   2 !   23.7   5.9   3.7e-08   3.9e-05       1      51 []     569     615 ..     548     615 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 5.7
                         Fer4_9  35 aCigCg 40 
                                     C gCg
  gi|119719691|ref|YP_920186.1| 366 LCAGCG 371
                                    466665 PP

  == domain 2  score: 23.7 bits;  conditional E-value: 3.7e-08
                         Fer4_9   1 kCtgCgaCvea..CpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                    +C++Cg Cv++  Cpa v +ed    +          C+gCg C+ +Cp +ai
  gi|119719691|ref|YP_920186.1| 569 RCVRCGICVDKfsCPAIVREEDGRVVILPE------VCVGCGVCATICPAKAI 615
                                    5*******99777*9998888777766664......4************9987 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.2       1.7   1.8e+03       8      13 ..     366     371 ..     364     372 .. 0.83
   2 !   11.8   3.4   0.00019       0.2       4      21 ..     565     584 ..     564     586 .. 0.87
   3 !   20.1   4.9   4.4e-07   0.00046       2      24 .]     593     615 ..     592     615 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.7
                         Fer4_6   8 kCigCg 13 
                                    +C gCg
  gi|119719691|ref|YP_920186.1| 366 LCAGCG 371
                                    8****9 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00019
                         Fer4_6   4 idpdkCigCgdCvrv..CPe 21 
                                    +d+++C+ Cg Cv+   CP+
  gi|119719691|ref|YP_920186.1| 565 VDQERCVRCGICVDKfsCPA 584
                                    8***********98777886 PP

  == domain 3  score: 20.1 bits;  conditional E-value: 4.4e-07
                         Fer4_6   2 veidpdkCigCgdCvrvCPegai 24 
                                    v+i p+ C+gCg C+++CP++ai
  gi|119719691|ref|YP_920186.1| 593 VVILPEVCVGCGVCATICPAKAI 615
                                    6788999**************98 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0         8   8.4e+03      35      42 ..     364     371 ..     347     372 .. 0.67
   2 !    7.9   2.4    0.0045       4.7      30      49 ..     562     583 ..     543     586 .. 0.74
   3 !   18.7  12.0   1.9e-06     0.002       1      52 []     569     614 ..     569     614 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 8
                         Fer4_7  35 pekClgCg 42 
                                    p  C gCg
  gi|119719691|ref|YP_920186.1| 364 PVLCAGCG 371
                                    55677776 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0045
                         Fer4_7  30 kveidpekClgCgaCva..vCP 49 
                                     +++d+e+C+ Cg Cv+   CP
  gi|119719691|ref|YP_920186.1| 562 PYYVDQERCVRCGICVDkfSCP 583
                                    4688999999999999866677 PP

  == domain 3  score: 18.7 bits;  conditional E-value: 1.9e-06
                         Fer4_7   1 rCigCgaCvaa..CpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                    rC+ Cg Cv+   Cp+ ++e d         +v+i pe C+gCg+C++ CP++a
  gi|119719691|ref|YP_920186.1| 569 RCVRCGICVDKfsCPAIVREEDG--------RVVILPEVCVGCGVCATICPAKA 614
                                    8********85448855555443........69******************986 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.4     0.036        38       1      14 [.     569     584 ..     557     594 .. 0.75
   2 ?   14.1   3.7   6.7e-05     0.071       2      18 ..     600     616 ..     599     620 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.036
                        Fer4_16   1 rCgtCgkCae..vCPt 14 
                                    rC++Cg C++  +CP+
  gi|119719691|ref|YP_920186.1| 569 RCVRCGICVDkfSCPA 584
                                    4777777776334664 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 6.7e-05
                        Fer4_16   2 CgtCgkCaevCPtnaik 18 
                                    C++Cg Ca +CP++ai+
  gi|119719691|ref|YP_920186.1| 600 CVGCGVCATICPAKAIH 616
                                    ****************7 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.6   0.00088      0.92       2      19 ..     567     586 ..     566     595 .. 0.76
   2 ?    8.6   2.0    0.0024       2.5       5      17 ..     600     612 ..     596     617 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00088
                         Fer4_8   2 lekCieCgaCqsa..Cpvlr 19 
                                     e+C++Cg C ++  Cp++ 
  gi|119719691|ref|YP_920186.1| 567 QERCVRCGICVDKfsCPAIV 586
                                    589********6555*9654 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0024
                         Fer4_8   5 CieCgaCqsaCpv 17 
                                    C++Cg C + Cp+
  gi|119719691|ref|YP_920186.1| 600 CVGCGVCATICPA 612
                                    7777777777774 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   3.0   0.00084      0.88       1      15 [.     567     583 ..     567     587 .. 0.88
   2 ?   15.1   4.0   2.2e-05     0.024       1      16 [.     597     612 ..     597     613 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00084
                         Fer4_4   1 qerCigCgsCvaa..CP 15 
                                    qerC++Cg Cv+   CP
  gi|119719691|ref|YP_920186.1| 567 QERCVRCGICVDKfsCP 583
                                    79*********977777 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 2.2e-05
                         Fer4_4   1 qerCigCgsCvaaCPq 16 
                                    +e C+gCg+C  +CP 
  gi|119719691|ref|YP_920186.1| 597 PEVCVGCGVCATICPA 612
                                    588************6 PP

>> Orbi_VP6  Orbivirus helicase VP6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00012      0.13     115     193 ..     480     558 ..     465     569 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00012
                       Orbi_VP6 115 agvgaiganggrwvvlteeiaraieskygtkidvyrdkvpaqiieverslqkelgisregva..eqterlrdlrrkeksg 192
                                     g g   a   r vv  e+ia+a+   +   +d y  +vpa    ver+++  +  sr  v    +   l +lrrk  sg
  gi|119719691|ref|YP_920186.1| 480 PGSGFGPAGEPRPVVKIEDIAKAVGVEFVEVVDAY--DVPAVRDAVERAIRYVVEKSRPAVVvsRRPCALMELRRKRLSG 557
                                    4555555566799*********************9..7********************986511566789******9998 PP

                       Orbi_VP6 193 a 193
                                     
  gi|119719691|ref|YP_920186.1| 558 E 558
                                    6 PP

>> CedA  Cell division activator CedA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0    0.0002      0.21      10      51 ..     133     172 ..     124     181 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0002
                           CedA  10 pvisyvprvepappehavkmeeyrdvwvlknkyvafllvger 51 
                                     + sy+p  ep+ p+ a  m   rd++ l +ky + +++   
  gi|119719691|ref|YP_920186.1| 133 GLHSYIPVFEPSSPQEAKDM--VRDLYDLSEKYSTAVFLRTT 172
                                    467**************876..8**********876665544 PP

>> E1_dh  Dehydrogenase E1 component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.6   0.00027      0.29     178     220 ..     496     539 ..     483     541 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00027
                                    GGG..TTTTS-EEE.EETTSHHHHHHHHHHHHHHHHTTT--EEE CS
                          E1_dh 178 ladrargvgipglr.VdgnDplavyeAvkfAaeraregkgplli 220
                                    + d a++vg+  ++ Vd+ D+ av+ Av  A+++ +e ++p+++
  gi|119719691|ref|YP_920186.1| 496 IEDIAKAVGVEFVEvVDAYDVPAVRDAVERAIRYVVEKSRPAVV 539
                                    5566777777777637*************************986 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   2.0     0.038        40       1      13 [.     569     583 ..     541     587 .. 0.76
   2 ?    5.5   1.5     0.024        26       1      16 [.     569     586 ..     569     596 .. 0.78
   3 ?    7.6   2.1    0.0052       5.5      45      58 ..     599     612 ..     587     615 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.038
                        Fer4_17   1 rCiqCgyClp..eCp 13 
                                    rC +Cg C++  +Cp
  gi|119719691|ref|YP_920186.1| 569 RCVRCGICVDkfSCP 583
                                    455555555544454 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.024
                        Fer4_17   1 rCiqCgyClp..eCpsye 16 
                                    rC +Cg C++  +Cp   
  gi|119719691|ref|YP_920186.1| 569 RCVRCGICVDkfSCPAIV 586
                                    699999999988888755 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0052
                        Fer4_17  45 lCieCgeCerkCPq 58 
                                     C++Cg C++ CP+
  gi|119719691|ref|YP_920186.1| 599 VCVGCGVCATICPA 612
                                    58888888888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (623 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.67u 0.30s 00:00:00.97 Elapsed: 00:00:00.49
# Mc/sec: 3831.63
//
Query:       gi|119719692|ref|YP_920187.1|  [L=199]
Description: pyruvate ferredoxin/flavodoxin oxidoreductase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.6e-35  121.6   0.0    4.2e-35  121.4   0.0    1.0  1  POR            Pyruvate ferredoxin/flavodoxin oxidoreductase
  ------ inclusion threshold ------
       0.36   10.9   3.2         15    5.6   0.0    2.2  2  AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD bindi


Domain annotation for each model (and alignments):
>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.4   0.0   4.7e-39   4.2e-35       1     176 [.      12     187 ..      12     188 .. 0.94

  Alignments for each domain:
  == domain 1  score: 121.4 bits;  conditional E-value: 4.7e-39
                                    CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHHHHGGGEEEEE CS
                            POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetlsehldglkpgg 80 
                                    GGqG++t+g + a+a+ r+Gy v   +++g ++rGg++++ ++ ++ p +p +  gead+l++l+  +  + ++ l ++g
  gi|119719692|ref|YP_920187.1|  12 GGQGLITIGTVVAQALIRKGYSVRVGEVHGLSQRGGSVVVFLKYGQGPLSPIVDQGEADVLLGLELIETLRRVPLLSKEG 91 
                                    9**********************************************999****************5555********** PP

                                    EEEEECTCGTT-CCHHHCTS-HHHHHHH..T-EEEEE-HHHHHHHCCC.CCHHHHHHHHHHHHHHTS-H..HHHHHHHHC CS
                            POR  81 iiiynseelkpdelkkakeeerelkerl..gvrvygvdatkiakeiggneraaNtvmlGalaallglpl..ealeeaikk 156
                                    ++++n+  + p++ +k++++++ l+  +  g+rv+ + a ++a ++g  ++++N+vmlGal++ + ++l  e+  ++++ 
  gi|119719692|ref|YP_920187.1|  92 VVLANN-FFLPPPAAKSPSRSAVLNALKglGARVVLLEADELALKAGS-PITVNMVMLGALIGTGRIDLtlEDAADVLRS 169
                                    ******.6788888888888888887779****************888.**************99988888********* PP

                                    CS-CH.HHHHHHHHHHHHHH CS
                            POR 157 rfpkkkeviekNlkafragy 176
                                    rf++k  v+e+Nl+a+++gy
  gi|119719692|ref|YP_920187.1| 170 RFKGK--VLEMNLEALKLGY 187
                                    ***95..************9 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   1.9    0.0034        30      21      55 ..       1      40 [.       1      48 [. 0.82
   2 ?    5.6   0.0    0.0016        15      40      93 ..     115     168 ..     110     184 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0034
                                   -TTSEEEEE--SH.....HHHHHHHHHHHCT-EEEEE-S- CS
                  AdoHcyase_NAD 21 laGkvavvaGyGd.....vGkGcaaslkglGarvivtevd 55
                                   +aGk +v+aG G      +G   a++l  +G  v v ev 
  gi|119719692|ref|YP_920187.1|  1 MAGKSIVIAGVGGqglitIGTVVAQALIRKGYSVRVGEVH 40
                                   69*******999533333678899************9997 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0016
                                    HHHHHCT-EEEEE-S-HHHHHHH.HCTT-EE--HHHCTTT-SEEEE-SSSSSSB- CS
                  AdoHcyase_NAD  40 aslkglGarvivtevdPicalqa.ameGfevvtleevvkkadivvtttGnkdiit 93 
                                    ++lkglGarv++ e d + al+a +    ++v l  ++ ++ i +t   + d+++
  gi|119719692|ref|YP_920187.1| 115 NALKGLGARVVLLEADEL-ALKAgSPITVNMVMLGALIGTGRIDLTLEDAADVLR 168
                                    79**************97.455514445666677777777777777666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1524.97
//
Query:       gi|119719693|ref|YP_920188.1|  [L=375]
Description: monooxygenase, FAD-binding [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-06   28.1   1.7     0.0011   18.2   0.2    2.3  2  FAD_binding_3  FAD binding domain
    0.00033   20.0   0.1    0.00059   19.2   0.1    1.4  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
     0.0026   18.3   0.2       0.02   15.5   0.0    2.4  3  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
      0.003   17.8   1.8      0.013   15.7   0.1    2.7  3  NAD_binding_8  NAD(P)-binding Rossmann-like domain
     0.0088   15.1   0.1       0.46    9.5   0.0    2.3  2  Lycopene_cycl  Lycopene cyclase protein
  ------ inclusion threshold ------
      0.011   15.3   0.7      0.037   13.6   0.1    1.9  2  DAO            FAD dependent oxidoreductase
      0.045   12.4   0.0       0.14   10.8   0.0    1.7  2  HI0933_like    HI0933-like protein
      0.059   12.4   0.0       0.22   10.6   0.0    1.9  2  FAD_binding_2  FAD binding domain


Domain annotation for each model (and alignments):
>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.2   5.1e-07    0.0011       3      36 ..       2      35 ..       1     116 [. 0.87
   2 !    9.2   0.1   0.00029      0.65     278     304 ..     243     269 ..     236     272 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 5.1e-07
                                   EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSS CS
                  FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlvekrstt 36
                                   dVl+ G+GpaGl la++L+ +G   v v    ++
  gi|119719693|ref|YP_920188.1|  2 DVLVLGGGPAGLQLARFLKGYGDGDVYVYEEHER 35
                                   9********************9765555555555 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00029
                                    ESSSEETTEEE-GGGTEEE-STTSHHH CS
                  FAD_binding_3 278 aekyrkgrvflaGDAaHihpPtgGqGl 304
                                    ++ y  +r+fl GD+a  + Pt+G Gl
  gi|119719693|ref|YP_920188.1| 243 VDVYAGDRLFLLGDSAGQTKPTTGGGL 269
                                    6678899*****************996 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   2.6e-07   0.00059       1      31 [.       1      33 [.       1      61 [. 0.83

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2.6e-07
                                   CSEEEE--SHHHHHHHHHHHHH.TS-EEEEE.T CS
                                   xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx.x RF
                    Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaqa.gakvtlve.l 31
                                   +dv+v+GgGpAGl++a++l+ +  ++v+++e  
  gi|119719693|ref|YP_920188.1|  1 MDVLVLGGGPAGLQLARFLKGYgDGDVYVYEeH 33
                                   59*******************659******642 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   8.8e-06      0.02       2      35 ..       3      37 ..       2      47 .. 0.88
   2 ?   -1.3   0.0       1.5   3.2e+03      17      40 ..      80     104 ..      79     111 .. 0.63
   3 ?   -2.7   0.0       4.2   9.4e+03      39      66 ..     288     316 ..     280     322 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 8.8e-06
                                   EEEECSSHHHHHHHHHHHHTTS.EEEEEESSSSSS CS
                      Pyr_redox  2 vvvvGgGyiglElAgalaelgk.kVtvversdkll 35
                                   v+v+GgG  gl lA +l+ +g+ +V+v e ++++ 
  gi|119719693|ref|YP_920188.1|  3 VLVLGGGPAGLQLARFLKGYGDgDVYVYEEHERVG 37
                                   89*******************55******999987 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.5
                                    HHHHTTSEEEEEESSSSSS.TTSSH CS
                      Pyr_redox  17 alaelgkkVtvversdkll.rllDe 40 
                                    +la+ g++V  +  ++ l  +l++e
  gi|119719693|ref|YP_920188.1|  80 FLARRGSEVAAIIERKLLEeKLYEE 104
                                    6788889996555555555455555 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 4.2
                                    SHHHHHHHHHHH.HHTTEEEECSEEEEEE CS
                      Pyr_redox  39 Deeaskilqekl.ekngievllntkveei 66 
                                    +e+ ++++++ l +++++++l  + ++++
  gi|119719693|ref|YP_920188.1| 288 PEAYGEAVKRALgREMHVQLLVRKALNSL 316
                                    55666777777766777877777766665 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1     6e-06     0.013       1      32 [.       5      37 ..       5      44 .. 0.92
   2 ?   -0.5   0.0      0.68   1.5e+03      24      43 ..     113     133 ..     102     149 .. 0.74
   3 ?   -1.9   0.0       1.9   4.2e+03      19      38 ..     221     240 ..     214     257 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 6e-06
                                   EE--SHHHHHHHHHHHCC.TEEEEEE-SSSSSS CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLaka.gfdvlllekrdrlG 32
                                   ++G+G +Gl +A++L+ + + dv ++e ++r+G
  gi|119719693|ref|YP_920188.1|  5 VLGGGPAGLQLARFLKGYgDGDVYVYEEHERVG 37
                                   89****************555***********9 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.68
                                    EE-SSSSSSGGG-EECETT.C CS
                  NAD_binding_8  24 llekrdrlGGraasyevpg.v 43 
                                    ll +r+ lGG a s++  g +
  gi|119719693|ref|YP_920188.1| 113 LLGARQTLGGFALSVRKRGaI 133
                                    566889999999999987643 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.9
                                    TEEEEEE-SSSSSSGGG-EE CS
                  NAD_binding_8  19 gfdvlllekrdrlGGraasy 38 
                                    ++ v ++ + + +GG +++ 
  gi|119719693|ref|YP_920188.1| 221 RVGVKVVKRLRVFGGAVYTG 240
                                    55677888888899999886 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0   0.00021      0.46       1      18 [.       2      19 ..       2      39 .. 0.89
   2 ?    3.5   0.0     0.014        31     258     292 ..     251     285 ..     214     335 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00021
                  Lycopene_cycl  1 DvvviGaGpAglslAarl 18
                                   Dv+v G+GpAgl+lA  l
  gi|119719693|ref|YP_920188.1|  2 DVLVLGGGPAGLQLARFL 19
                                   9**************866 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.014
                  Lycopene_cycl 258 vlaiGaaaglvhPaTGYsvarslaeapllasaiaa 292
                                     + +G  ag ++P+TG  ++    +a+ l++ai +
  gi|119719693|ref|YP_920188.1| 251 LFLLGDSAGQTKPTTGGGLVYLSIAARALSDAILS 285
                                    567899**********9999988888866666543 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   1.7e-05     0.037       1      37 [.       2      43 ..       2      47 .. 0.84
   2 ?   -0.0   0.1      0.23   5.2e+02      97     168 ..      49     117 ..      33     147 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.7e-05
                                   EEEEECTSHHHHHHHHHHHHTT...EEEEESSSSTT..SSGG CS
                            DAO  1 dvviiGGGiiGlstAyeLarrg...Vtllekgdiag..sgaS 37
                                   dv++ GGG +Gl  A++L   g   V ++e ++++g  ++++
  gi|119719693|ref|YP_920188.1|  2 DVLVLGGGPAGLQLARFLKGYGdgdVYVYEEHERVGlpQHCT 43
                                   8*****************666677********9888555555 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.23
                                    HHHHHHHHHHHHTTTTEEEEEH.HHHHHHSTTSTTTSEEEEETTEEEEEHHHHHHHHHHHHHHTT-EEEESEC CS
                            DAO  97 ealdkllallleagldaellda.eevrelepalpgllgalfypdtgqvdpakltaalaraaealGveilegte 168
                                    e+l+k+++ ++  gl   +l++ + +r ++p  + +l+  ++  +++++   l   l+++a ++G+++l+g++
  gi|119719693|ref|YP_920188.1|  49 EGLRKWIGVGE-RGL---VLNRfRGARFVSPSGKVFLARRGSEVAAIIERKLLEEKLYEEAVSAGARVLLGAR 117
                                    45666666543.455...3444334555555322455666677777777777777888888889988888854 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   6.4e-05      0.14       2      36 ..       2      37 ..       1      44 [. 0.85
   2 ?   -1.6   0.0      0.37   8.4e+02     318     340 ..     309     331 ..     290     335 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 6.4e-05
                                   SEEEE--SHHHHHHHHHH.HHTT--EEEE-SSSSS- CS
                    HI0933_like  2 dviviGgGaAGlmaAisa.akrgkrVlllekakklg 36
                                   dv+v+GgG+AGl  A  + +  + +V ++e+ +++g
  gi|119719693|ref|YP_920188.1|  2 DVLVLGGGPAGLQLARFLkGYGDGDVYVYEEHERVG 37
                                   89*************9994555679*****999987 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.37
                                    -TTBGGG--HHHHHHHHHHHHSE CS
                    HI0933_like 318 edkklaqlskkelkklaealkal 340
                                      k+l++ls++el++l++alk++
  gi|119719693|ref|YP_920188.1| 309 VRKALNSLSDAELDELFQALKEV 331
                                    4578999***********99975 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   9.8e-05      0.22       1      36 [.       2      38 ..       2      48 .. 0.90
   2 ?   -0.6   0.0      0.24   5.4e+02     270     303 ..      56      95 ..      37     166 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 9.8e-05
                                   SEEEE--SHHHHHHHHHHHHTTT.-EEEEESSSGGGS CS
                  FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGl.kvavvekeqefgg 36
                                   Dv+V G+G AGL  A  ++  G  +v v e  +++g+
  gi|119719693|ref|YP_920188.1|  2 DVLVLGGGPAGLQLARFLKGYGDgDVYVYEEHERVGL 38
                                   9*******************9999****999998776 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.24
                                    HHHTT-EEE-.TTSSBTH.....GGGS-HHHHHHHHH.HH CS
                  FAD_binding_2 270 lrgeGgilvd.kdGrrFm.....nelasrdvvsraileke 303
                                      ge g++++  +G rF+       la r   ++ai+e+ 
  gi|119719693|ref|YP_920188.1|  56 GVGERGLVLNrFRGARFVspsgkVFLARRGSEVAAIIERK 95 
                                    4577777888789999999998878888888888877543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2494.87
//
Query:       gi|119719694|ref|YP_920189.1|  [L=203]
Description: PadR-like family transcriptional regulator [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00032   20.6   1.0     0.0029   17.5   1.0    2.3  1  PadR      Transcriptional regulator PadR-like family
     0.0015   19.0   0.0     0.0044   17.5   0.0    1.8  1  HTH_27    Winged helix DNA-binding domain
  ------ inclusion threshold ------
      0.022   14.7   0.0      0.047   13.6   0.0    1.5  1  MarR      MarR family
      0.098   12.3   0.0       0.18   11.4   0.0    1.4  1  ArsR      ArsR transcriptional regulator
        0.1   12.5   0.5       0.46   10.5   0.3    2.1  2  HTH_12    Ribonuclease R winged-helix domain
       0.12   12.6   0.0       0.21   11.8   0.0    1.3  1  HTH_34    Winged helix DNA-binding domain


Domain annotation for each model (and alignments):
>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   1.0   9.6e-07    0.0029      36      74 ..      74     111 ..      30     112 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 9.6e-07
                                    HHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHHH CS
                           PadR  36 paLkrLekeglveseweesgegpprkyYrlTdaGrrela 74 
                                     aL+rLe+ g++ ++++   ++++r++ rlT++G +e +
  gi|119719694|ref|YP_920189.1|  74 EALRRLEERGFIFRSRQA-YRDGERRVVRLTETGSDEAR 111
                                    69*************998.59999**********99976 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.5e-06    0.0044      34      68 .]      71     106 ..      64     106 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.5e-06
                         HTH_27  34 hisyslkkLtekGLvertgde.adrrekrvrlTdkG 68 
                                    ++s++l++L+e+G++ r++ + +d+ ++ vrlT+ G
  gi|119719694|ref|YP_920189.1|  71 AVSEALRRLEERGFIFRSRQAyRDGERRVVRLTETG 106
                                    689************55544427888899****988 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.6e-05     0.047      33      51 ..      71      89 ..      70      91 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.6e-05
                                   HHHHHHHHHHHTTSEEEEE CS
                           MarR 33 tvtrvldrLekkGlieRsk 51
                                   +v+++l+rLe++G+i Rs+
  gi|119719694|ref|YP_920189.1| 71 AVSEALRRLEERGFIFRSR 89
                                   79**************998 PP

>> ArsR  ArsR transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   5.9e-05      0.18      11      54 ..     102     145 ..      97     155 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.9e-05
                           ArsR  11 lqvfdsetkkkvyeelskeWlteeeleeklgeeveealklLkki 54 
                                    l+ ++s++ +k++++ s++Wl ++ ++ + g+ev   l+ Lkk+
  gi|119719694|ref|YP_920189.1| 102 LTETGSDEARKIFKAFSESWLLMRGVALRRGSEVLGELEALKKT 145
                                    55678999**********************************95 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.3   0.00015      0.46      33      65 ..      70     109 ..      68     110 .. 0.79
   2 ?   -1.3   0.0      0.71   2.1e+03       1      17 [.     185     201 ..     185     202 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00015
                         HTH_12  33 ravRyrLrkleergltrrvgya.......greltEkGlee 65 
                                    +av   Lr leerg++ r + a         +ltE G +e
  gi|119719694|ref|YP_920189.1|  70 EAVSEALRRLEERGFIFRSRQAyrdgerrVVRLTETGSDE 109
                                    577788********99999888778765445789988775 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.71
                         HTH_12   1 veILkilaesdkpigak 17 
                                    v+ Lk l+++ kp +++
  gi|119719694|ref|YP_920189.1| 185 VYLLKRLSKELKPTSRQ 201
                                    57899999999999986 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   6.9e-05      0.21      31      76 ..      72     117 ..      70     120 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.9e-05
                         HTH_34  31 LsvhlkkLekagYievdkefkgkkprtllriTpeGreafkkyvkaL 76 
                                     s  l+ Le+ g+i ++ +     +r ++r+T++G +++ k +ka 
  gi|119719694|ref|YP_920189.1|  72 VSEALRRLEERGFIFRSRQAYRDGERRVVRLTETGSDEARKIFKAF 117
                                    68899***********99999999**************99988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.41u 0.21s 00:00:00.62 Elapsed: 00:00:00.36
# Mc/sec: 1686.21
//
Query:       gi|119719695|ref|YP_920190.1|  [L=628]
Description: hypothetical protein Tpen_0785 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.2e-11   42.9   4.1    1.8e-06   28.1   0.1    3.6  3  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
    0.00018   21.8   0.0        0.4   11.0   0.0    2.7  2  SpaA             Prealbumin-like fold domain
     0.0015   18.5   0.0      0.023   14.7   0.0    2.2  2  PapC_N           PapC N-terminal domain
     0.0021   18.2   0.0     0.0066   16.6   0.0    1.8  1  MG4              Macroglobulin domain MG4
     0.0033   17.5   0.0      0.015   15.4   0.0    2.0  2  DUF2012          Protein of unknown function (DUF2012)
     0.0052   16.5   0.3        3.6    7.4   0.0    3.5  3  fn3_3            Polysaccharide lyase family 4, domain II
  ------ inclusion threshold ------
      0.034   14.1   0.0       0.13   12.3   0.0    1.9  2  CarbopepD_reg_2  CarboxypepD_reg-like domain
      0.039   13.9   0.0        3.4    7.7   0.0    2.9  3  Y_Y_Y            Y_Y_Y domain
      0.093   13.0   0.0          2    8.7   0.0    2.4  2  SdrD_B           SdrD B-like domain


Domain annotation for each model (and alignments):
>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1       1.1   2.2e+03      38      54 ..     383     399 ..     357     423 .. 0.81
   2 !   13.9   0.1   2.4e-05     0.049      20      73 ..     447     496 ..     432     504 .. 0.75
   3 !   28.1   0.1   9.2e-10   1.8e-06       4      65 ..     510     567 ..     507     583 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.1
                CarboxypepD_reg  38 Gafrlrglppgtysvtv 54 
                                    G+  +  l++gty+v++
  gi|119719695|ref|YP_920190.1| 383 GEAVVCPLAAGTYDVVA 399
                                    55566668999999998 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 2.4e-05
                CarboxypepD_reg  20 tvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatreevtltagq 73 
                                    +++   + ++  + + a+G   + g+ppgtys++v  ++ + a+++ v+++ ++
  gi|119719695|ref|YP_920190.1| 447 VLK---GAVELVANSSAEGLAVFHGVPPGTYSLEVYWNNTRLARYS-VEVDLKG 496
                                    455...45567789*********************99999999985.7776554 PP

  == domain 3  score: 28.1 bits;  conditional E-value: 9.2e-10
                CarboxypepD_reg   4 GrVtdasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatre 65 
                                      V++  ++p++ga V ++  ++g++++  td+ G+  +  +p+g+y++ v+ +  +++t++
  gi|119719695|ref|YP_920190.1| 510 VLVRNLLDQPVKGAVVFLE--GGGFSSTRLTDEAGRADFGLVPAGNYTLIVEGA--QPQTVR 567
                                    56888889***********..9*****************************655..555543 PP

>> SpaA  Prealbumin-like fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.1    0.0019       3.7       4      58 ..     359     476 ..     357     477 .. 0.58
   2 !   11.0   0.0    0.0002       0.4      35      75 ..     533     574 ..     501     580 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0019
                                    CB-TS-EEEEEET...........................................................TTSCCCHC CS
                           SpaA   4 kpLaGaeFtlykv...........................................................dtttdgkd 24 
                                    +pL++  F +y++                                                           +       
  gi|119719695|ref|YP_920190.1| 359 YPLNNTYFVVYRAgvpvysgiarggeavvcplaagtydvvayvasrvvgrgrvtllgdsaaeiltntttvsfQ------- 431
                                    6777777777777666666666666666666666666666666666666655555555444444333222220....... PP

                                    HHTT...............TTCCEESEEE-BTTSEEEEEEEESEEEEE CS
                           SpaA  25 alea..............kktgtevttlttdenGkatfegLplGtYll 58 
                                                        +g++   + + ++G a f g+p+GtY l
  gi|119719695|ref|YP_920190.1| 432 ---FvrqgagevltsykaVLKGAVELVANSSAEGLAVFHGVPPGTYSL 476
                                    ...0222223333334444456666778899***************87 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0002
                                    ESEEE-BTTSEEEEEEEESEEEEE.EEEE-STTEEE-SSEEE CS
                           SpaA  35 vttlttdenGkatfegLplGtYll.vEtkaPegYvldkepfe 75 
                                    + t  tde G+a f+ +p+G+Y+l vE   P  ++l +++f 
  gi|119719695|ref|YP_920190.1| 533 SSTRLTDEAGRADFGLVPAGNYTLiVEGAQPQTVRLISDTFR 574
                                    46778*****************96368888888888666665 PP

>> PapC_N  PapC N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.19   3.9e+02      26      51 ..     390     415 ..     388     433 .. 0.82
   2 !   14.7   0.0   1.1e-05     0.023      25      52 ..     468     495 ..     449     512 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.19
                                    S-SEEEEEEEEETTEEEEEEEEEEEE CS
                         PapC_N  26 vlpGeYrvdvyvNgkeigrqevefka 51 
                                    +++G+Y+v  yv  + +gr +v++  
  gi|119719695|ref|YP_920190.1| 390 LAAGTYDVVAYVASRVVGRGRVTLLG 415
                                    679****************9999654 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 1.1e-05
                                    SS-SEEEEEEEEETTEEEEEEEEEEEEC CS
                         PapC_N  25 avlpGeYrvdvyvNgkeigrqevefkae 52 
                                     v+pG+Y+++vy N+++++r++ve++ +
  gi|119719695|ref|YP_920190.1| 468 GVPPGTYSLEVYWNNTRLARYSVEVDLK 495
                                    69*********************98764 PP

>> MG4  Macroglobulin domain MG4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   3.3e-06    0.0066      16      67 ..     506     552 ..     505     566 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3.3e-06
                            MG4  16 fsikVlvkdpdgspaknvpVkiealkseteekeslttdedGtakfsintped 67 
                                    + ++Vlv + +++p+k+  V++e  +    + ++  tde G+a f + +p+ 
  gi|119719695|ref|YP_920190.1| 506 YRLQVLVRNLLDQPVKGAVVFLEG-G---GFSSTRLTDEAGRADFGL-VPAG 552
                                    89**********************.5...6889999*******9987.5554 PP

>> DUF2012  Protein of unknown function (DUF2012)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   7.5e-06     0.015      27      81 ..     459     510 ..     435     526 .. 0.79
   2 ?   -2.0   0.0       1.9   3.7e+03      25      47 ..     537     559 ..     515     562 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 7.5e-06
                        DUF2012  27 rrDGsFifrdlpegsYlLevespeyvFepyrVdvkdkgkakasklrivetaevnv 81 
                                     ++G  +f+ +p+g+Y Lev   +   + y V+v    ++ ++++  +++++++v
  gi|119719695|ref|YP_920190.1| 459 SAEGLAVFHGVPPGTYSLEVYWNNTRLARYSVEVD---LKGGRSVLSIQAYRLQV 510
                                    5667779***************************9...77777777777777766 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.9
                        DUF2012  25 lvrrDGsFifrdlpegsYlLeve 47 
                                    l+ + G   f  +p+g Y+L ve
  gi|119719695|ref|YP_920190.1| 537 LTDEAGRADFGLVPAGNYTLIVE 559
                                    5555566667789******9876 PP

>> fn3_3  Polysaccharide lyase family 4, domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.07   1.4e+02      42      55 ..     390     403 ..     378     413 .. 0.78
   2 !    7.4   0.0    0.0018       3.6      32      56 ..     459     483 ..     453     499 .. 0.76
   3 ?    2.1   0.0     0.082   1.6e+02      31      50 ..     538     557 ..     528     558 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.07
                          fn3_3  42 VkpGtYrltvYadg 55 
                                      +GtY +++Y+  
  gi|119719695|ref|YP_920190.1| 390 LAAGTYDVVAYVAS 403
                                    579********975 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0018
                          fn3_3  32 dssgsftipnVkpGtYrltvYadgl 56 
                                    +++g   ++ V pGtY+l vY ++ 
  gi|119719695|ref|YP_920190.1| 459 SAEGLAVFHGVPPGTYSLEVYWNNT 483
                                    4557788999**********98765 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.082
                          fn3_3  31 adssgsftipnVkpGtYrlt 50 
                                    +d+ g+  +  V +G+Y+l 
  gi|119719695|ref|YP_920190.1| 538 TDEAGRADFGLVPAGNYTLI 557
                                    4677**************96 PP

>> CarbopepD_reg_2  CarboxypepD_reg-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       5.3   1.1e+04      38      50 ..     466     478 ..     454     490 .. 0.80
   2 ?   12.3   0.0   6.3e-05      0.13      11      51 ..     517     559 ..     511     574 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 5.3
                CarbopepD_reg_2  38 lknlpagkytLvv 50 
                                    ++ +p+g+y L v
  gi|119719695|ref|YP_920190.1| 466 FHGVPPGTYSLEV 478
                                    6678888888876 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 6.3e-05
                CarbopepD_reg_2  11 keplpgatVyvkgtkkgtv..TdenGnFelknlpagkytLvvs 51 
                                     +p+ ga V+++g ++  +  Tde G+  +  +pag+ytL+v+
  gi|119719695|ref|YP_920190.1| 517 DQPVKGAVVFLEGGGFSSTrlTDEAGRADFGLVPAGNYTLIVE 559
                                    489**********99877777******99999********996 PP

>> Y_Y_Y  Y_Y_Y domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       4.2   8.5e+03      31      47 ..     385     401 ..     381     404 .. 0.76
   2 ?    7.7   0.0    0.0017       3.4      22      47 ..     456     480 ..     442     488 .. 0.80
   3 ?    2.5   0.0     0.073   1.4e+02      30      47 ..     543     560 ..     531     564 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 4.2
                                    EEEES--SEEEEEEEEE CS
                          Y_Y_Y  31 asytnlppGdYtlkVka 47 
                                    a   +l +G+Y + +++
  gi|119719695|ref|YP_920190.1| 385 AVVCPLAAGTYDVVAYV 401
                                    6667999****887776 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0017
                                    EEESSTS.EEEEES--SEEEEEEEEE CS
                          Y_Y_Y  22 veasdysqeasytnlppGdYtlkVka 47 
                                     ++s+ +  a +   ppG+Y l+V+ 
  gi|119719695|ref|YP_920190.1| 456 ANSSAEG-LAVFHGVPPGTYSLEVYW 480
                                    4666777.99**************95 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.073
                                    EEEEES--SEEEEEEEEE CS
                          Y_Y_Y  30 easytnlppGdYtlkVka 47 
                                     a +   p+G+Ytl V++
  gi|119719695|ref|YP_920190.1| 543 RADFGLVPAGNYTLIVEG 560
                                    6777789*******9976 PP

>> SdrD_B  SdrD B-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.19   3.8e+02      44      66 ..     458     480 ..     440     497 .. 0.80
   2 ?    8.7   0.0   0.00099         2      21      66 ..     517     560 ..     512     572 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.19
                         SdrD_B  44 TdasGkYkFtnltpGeYkVefta 66 
                                    ++a+G   F+++ pG+Y++e+  
  gi|119719695|ref|YP_920190.1| 458 SSAEGLAVFHGVPPGTYSLEVYW 480
                                    56789999**********99854 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00099
                         SdrD_B  21 ekgisgvtVtLkdakgevvatttTdasGkYkFtnltpGeYkVefta 66 
                                    ++ ++g  V L  + g   +t +Td+ G+  F  + +G+Y++ ++ 
  gi|119719695|ref|YP_920190.1| 517 DQPVKGAVVFL--EGGGFSSTRLTDEAGRADFGLVPAGNYTLIVEG 560
                                    57899999999..7788889********************987743 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (628 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 4216.88
//
Query:       gi|119719696|ref|YP_920191.1|  [L=537]
Description: lysyl-tRNA synthetase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.9e-91  305.7   0.7      1e-90  304.3   0.0    1.8  2  tRNA-synt_1f    tRNA synthetases class I (K)
  ------ inclusion threshold ------
      0.058   13.3   2.9       0.17   11.8   2.9    1.8  1  Nudix_N_2       Nudix N-terminal
      0.075   12.8   0.5       0.16   11.8   0.5    1.5  1  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal


Domain annotation for each model (and alignments):
>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  304.3   0.0   1.7e-94     1e-90       1     357 [.       1     362 [.       1     365 [. 0.93
   2 ?   -0.6   0.2     0.083     5e+02     293     340 ..     427     474 ..     421     495 .. 0.76

  Alignments for each domain:
  == domain 1  score: 304.3 bits;  conditional E-value: 1.7e-94
                   tRNA-synt_1f   1 kaWadklaeklieerkkkkaekdevvvesGispSGliHiGnlr.evltadlvaralrkrgeevrlilisDdmDglRkvpe 79 
                                    ++W++ +ae + ++ +    ek+ vv + G+s+SGl+H+G+lr e+  +d v+r lr+ g ++ + l+ +++D ++   +
  gi|119719696|ref|YP_920191.1|   1 MHWVKGVAESVASRAR----EKGVVVANGGLSVSGLQHVGRLRgEITVVDTVVRLLRREGYDAVHKLTLYTVDAWKGKEA 76 
                                    69**********4442....5799******************99******************9999**********9988 PP

                   tRNA-synt_1f  80 ...nlpek.llekylgkpltsiPdpkgkhesyaehfnaelvesLdelgievefisatelYksg..lydeaikealenrek 153
                                       ++ +   ++ y g+pl ++Pdp+g+h++++eh++ e+ + L ++  +v++++++elY+s   + +  ++ + + rek
  gi|119719696|ref|YP_920191.1|  77 qrsQFGDPeEARAYTGRPLYMVPDPHGCHANWVEHYWDEFGSHLGSFAEKVDVVTTKELYESDerMKKFVLLSVTDLREK 156
                                    7774444446**************************************************98521566677888899*** PP

                   tRNA-synt_1f 154 ikeilekyrgee.reetyspylpvcekcgrvdttevvevdaeeeeieYkceecGeeeevdiregngKLqWkvdwamrWaa 232
                                    + e ++kyrge+ ++  y+p++p+cekcgrvdtte+ evda + +++Y+c++cG+e+ +++ +  gKL+W+v+w   W+a
  gi|119719696|ref|YP_920191.1| 157 VVETINKYRGEKkLQPGYIPFQPICEKCGRVDTTEALEVDAANYRVRYVCRHCGHEGWQSLAK--GKLNWRVEWVGVWYA 234
                                    *********99978999********************************************99..7************** PP

                   tRNA-synt_1f 233 lgVdfEpaGkDhaaaGgSvdvsskia.eilggeaPekvvYelillkgge....kmssSkGnvltledwlevaepevlrfl 307
                                    lgVdfEp+GkDha++GgS d  +++a +++g+++P ++ Ye+++ ++++    +m sS + ++++++wlevae evlr++
  gi|119719696|ref|YP_920191.1| 235 LGVDFEPYGKDHATPGGSRDSCNELAeKVYGFNPPLGLAYEWVGYRKQGkdmgDMGSSDFIGFSPRQWLEVAEGEVLRYI 314
                                    ********************************************9887767889************************** PP

                   tRNA-synt_1f 308 ilrrkPkkakkldldleilrlvdeYdklerkyfaeqeeeeekekrvyels 357
                                    +l++ P +++ l+l+ e+++++d +dk+er y+   ee +++ ++ yel+
  gi|119719696|ref|YP_920191.1| 315 YLSAPPMRRIVLSLE-EVPSYYDTFDKAERVYY-GLEEGDKEAAESYELA 362
                                    ***************.****************9.7788888888888775 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.083
                   tRNA-synt_1f 293 edwlevaepevlrflilrrkPkkakkldldleilrlvdeYdklerkyf 340
                                    + wle++ pe  r  ++++ P ++++  +d  i +l+    +  +++ 
  gi|119719696|ref|YP_920191.1| 427 RRWLELYAPEYYRITVVEEPPLTEIEKVMDERISQLLAALLDSLQRLE 474
                                    679********************9999999999988776655555553 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   2.9   2.9e-05      0.17       3      30 ..     181     211 ..     180     211 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.9e-05
                                    -TTT--B.-E..EE--TT-SS-EEEETTTTE CS
                      Nudix_N_2   3 CsqCGtp.ve..lripdgDnreRlvCpaCgt 30 
                                    C++CG   ++  l++ +   r R+vC +Cg+
  gi|119719696|ref|YP_920191.1| 181 CEKCGRVdTTeaLEVDAANYRVRYVCRHCGH 211
                                    99999875434688889999**********7 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.5   2.6e-05      0.16      24      52 ..     180     211 ..     175     212 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.6e-05
                 zinc_ribbon_10  24 ICskChshnGlap...keeleevkyrCpkCga 52 
                                    IC+kC  +  +       ++ +v+y+C +Cg+
  gi|119719696|ref|YP_920191.1| 180 ICEKCGRVDTTEAlevDAANYRVRYVCRHCGH 211
                                    9****999887766656666678*******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (537 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1026  (0.0572257); expected 358.6 (0.02)
Passed bias filter:                      865  (0.0482459); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.68u 0.30s 00:00:00.98 Elapsed: 00:00:00.48
# Mc/sec: 3398.25
//
Query:       gi|119719697|ref|YP_920192.1|  [L=121]
Description: hypothetical protein Tpen_0787 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0066   16.6   1.8     0.0091   16.1   1.8    1.3  1  DHHC             DHHC palmitoyltransferase
  ------ inclusion threshold ------
      0.024   14.2   4.2      0.036   13.7   4.2    1.4  1  Ni_hydr_CYTB     Prokaryotic cytochrome b561
       0.41   10.6   4.4          2    8.4   0.0    2.4  2  Syndecan         Syndecan domain
        1.1    9.8   2.5          6    7.4   0.0    2.4  2  FeoB_associated  FeoB-associated Cys-rich membrane protein
          4    6.7   5.9         12    5.2   2.2    2.0  2  DUF4191          Domain of unknown function (DUF4191)
        7.8    6.6   9.4        1.5    9.0   1.6    2.4  2  CrgA             Cell division protein CrgA


Domain annotation for each model (and alignments):
>> DHHC  DHHC palmitoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   1.8   3.1e-06    0.0091      51     118 ..      51     120 ..      43     121 .] 0.82

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.1e-06
                           DHHC  51 F..llfllylllllilalvlllialvklveeekkseflavtllkkllsilllvlsllfllllgllllfhl 118
                                    F  l++ +  l++l+la+++++i+++   +ee ++     ++l ++l+il++++s++f+ll++++ ++++
  gi|119719697|ref|YP_920192.1|  51 FppLVYAVGSLVMLVLAVFVSFIGYTMSKDEEPEWGSKLPFKLIQALNILWVLVSVMFALLVVFIYFMRI 120
                                    555566677788888888888888888888888888888888888***************9999988765 PP

>> Ni_hydr_CYTB  Prokaryotic cytochrome b561
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   4.2   1.2e-05     0.036     104     165 ..      59     118 ..      22     121 .] 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.2e-05
                                    THHHHHHHHHHHHHHHHHHHTHHHHHHHH...HTS-THHHHHHH.HHHHHHHHHHHHHHHHH CS
                   Ni_hydr_CYTB 104 vhlllyvllvvliltGlllsfaatagfplllddkggaqlarelHellaaallafvvlHiaaa 165
                                      l+++vl v++ + G+++s+  ++ +++ + ++++ q+++ l  +l+++++a++v+ i+  
  gi|119719697|ref|YP_920192.1|  59 GSLVMLVLAVFVSFIGYTMSKDEEPEWGS-KLPFKLIQALNILW-VLVSVMFALLVVFIYFM 118
                                    56899**************9976777777.889***********.*******9999999976 PP

>> Syndecan  Syndecan domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0   0.00065         2      15      39 ..      59      81 ..      52      86 .. 0.71
   2 ?    0.4   3.6      0.21   6.2e+02      16      33 ..     102     117 ..      92     120 .. 0.51

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00065
                       Syndecan 15 gvvvgllfaillvlflvYRmrKKDE 39
                                   g  + +l++ ++v f+ Y m K DE
  gi|119719697|ref|YP_920192.1| 59 GS-LVMLVLAVFVSFIGYTMSK-DE 81
                                   44.4556666679*******65.54 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.21
                       Syndecan  16 vvvgllfaillvlflvYR 33 
                                    v+v+++fa llv+f+ Y 
  gi|119719697|ref|YP_920192.1| 102 VLVSVMFA-LLVVFI-YF 117
                                    44455554.455553.43 PP

>> FeoB_associated  FeoB-associated Cys-rich membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0     0.002         6       4      24 ..      61      81 ..      59      86 .. 0.89
   2 ?   -2.1   4.1       1.7   5.2e+03       3      16 ..     102     115 ..      99     120 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.002
                FeoB_associated  4 IVgliiaaavafvirrlikkk 24
                                   +V+l++a+ v f+ + + k+ 
  gi|119719697|ref|YP_920192.1| 61 LVMLVLAVFVSFIGYTMSKDE 81
                                   6999*************9985 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.7
                FeoB_associated   3 iIVgliiaaavafv 16 
                                    ++V ++ a++v+f+
  gi|119719697|ref|YP_920192.1| 102 VLVSVMFALLVVFI 115
                                    56777777777776 PP

>> DUF4191  Domain of unknown function (DUF4191)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1     0.013        39      25      71 ..      24      68 ..       2      84 .. 0.50
   2 ?    5.2   2.2    0.0039        12      50      72 ..      98     120 ..      88     121 .] 0.83

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.013
                        DUF4191 25 llwlllaaflvvvvvfvvlglllgslilllilgillgllvalivltr 71
                                   ++++++ ++l  +v +v+ g+ + ++ ++ +l  ++g lv+l vl+ 
  gi|119719697|ref|YP_920192.1| 24 IVVTMIPVLLDGAVWMVTEGFNV-KPRFFPPLVYAVGSLVML-VLAV 68
                                   22333333444444444445543.556666665555555433.3333 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0039
                        DUF4191  50 lilllilgillgllvalivltrr 72 
                                     il+++++++++llv++i + r 
  gi|119719697|ref|YP_920192.1|  98 NILWVLVSVMFALLVVFIYFMRI 120
                                    799****************9986 PP

>> CrgA  Cell division protein CrgA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   1.6   0.00049       1.5      25      52 ..      15      42 ..       5      65 .. 0.89
   2 ?    0.6   3.2       0.2   5.9e+02      41      83 ..      63     112 ..      41     119 .. 0.53

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00049
                           CrgA 25 kaakpsprwyvpvmlglmllGllwlvvy 52
                                   +++kps+ ++v++m+ ++l G +w+v+ 
  gi|119719697|ref|YP_920192.1| 15 EKTKPSKLLIVVTMIPVLLDGAVWMVTE 42
                                   5789*********************985 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.2
                           CrgA  41 lmllGllwlvvyYlage........eipfmaelgawNlliGfgliivGllm 83 
                                    +++l ++   + Y +++        ++p ++ ++a N+l  +  ++ +ll+
  gi|119719697|ref|YP_920192.1|  63 MLVLAVFVSFIGYTMSKdeepewgsKLP-FKLIQALNILWVLVSVMFALLV 112
                                    3444444444444444344444444444.5556666666665555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1075  (0.0599587); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.53
# Mc/sec: 692.74
//
Query:       gi|119719698|ref|YP_920193.1|  [L=529]
Description: chemotaxis sensory transducer [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.2e-07   29.4  34.4     0.0019   18.6   3.3    7.7  8  NPV_P10         Nucleopolyhedrovirus P10 protein
    4.7e-06   25.7  99.7     0.0016   17.4  19.5    5.1  5  Spc7            Spc7 kinetochore protein
    1.6e-05   24.9   9.7    1.6e-05   24.9   9.7    5.1  3  Apolipoprotein  Apolipoprotein A1/A4/E domain
    6.9e-05   22.3   7.7    6.9e-05   22.3   7.7    4.7  4  CorA            CorA-like Mg2+ transporter protein
    0.00011   21.6  18.9    0.00011   21.6  18.9    5.4  4  GAS             Growth-arrest specific micro-tubule binding
    0.00024   21.2  38.4      0.029   14.4   9.0    6.3  5  Baculo_PEP_C    Baculovirus polyhedron envelope protein, PEP,
    0.00054   20.0  52.0     0.0015   18.6   4.9    6.7  7  DUF1664         Protein of unknown function (DUF1664)
     0.0016   18.2  16.5     0.0016   18.2  16.5    6.1  5  DUF4201         Domain of unknown function (DUF4201)
      0.002   17.9   0.2      0.002   17.9   0.2    6.2  8  DASH_Duo1       DASH complex subunit Duo1
     0.0058   16.2  26.2     0.0058   16.2  26.2    4.7  4  Leu_zip         Leucine zipper
     0.0058   16.7  19.2     0.0058   16.7  19.2    6.9  7  DHR10           Designed helical repeat protein 10 domain
      0.006   16.2   2.0      0.006   16.2   2.0    7.0  6  Fzo_mitofusin   fzo-like conserved region
     0.0085   16.0  16.3     0.0085   16.0  16.3    5.0  2  FTA4            Kinetochore complex Fta4 of Sim4 subunit, or 
  ------ inclusion threshold ------
      0.012   15.9  70.5       0.27   11.6   4.2    7.8  9  BLOC1_2         Biogenesis of lysosome-related organelles com
       0.12   12.6  30.1      0.056   13.7   3.1    6.4  7  DUF948          Bacterial protein of unknown function (DUF948
       0.17   12.3   2.3       0.45   11.0   0.4    2.7  2  FidL_like       FidL-like putative membrane protein
       0.37   10.2   7.3       0.13   11.7   1.0    2.5  2  Mce4_CUP1       Cholesterol uptake porter CUP1 of Mce4, putat
       0.47    9.0  74.0     0.0028   16.4  28.8    4.0  3  AAA_13          AAA domain
        1.8    8.1  85.9      0.025   14.2  10.1    5.3  5  Filament        Intermediate filament protein
        1.9    8.3  54.4       0.22   11.4   7.2    6.6  6  Sec34           Sec34-like family
        1.9    7.8 107.9       0.02   14.3  24.1    5.9  5  DUF3552         Domain of unknown function (DUF3552)
        4.5    7.4  61.9          1    9.4   4.5    7.0  7  COG2            COG (conserved oligomeric Golgi) complex comp
        7.9    5.8 100.8        2.2    7.7  34.7    4.6  3  HMMR_N          Hyaluronan mediated motility receptor N-termi


Domain annotation for each model (and alignments):
>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1     0.015        12      16      66 ..      18      74 ..      13      77 .. 0.63
   2 !   18.6   3.3   2.4e-06    0.0019      15      66 ..      77     125 ..      75     136 .. 0.73
   3 ?    6.1   0.5     0.019        15      24      65 ..     153     195 ..     127     210 .. 0.61
   4 ?    5.8   0.2     0.024        18      11      61 ..     193     243 ..     188     246 .. 0.61
   5 !    9.4   2.1    0.0019       1.5      15      73 ..     228     288 ..     221     290 .. 0.82
   6 ?   -1.0   0.0       3.2   2.5e+03      37      50 ..     340     353 ..     311     374 .. 0.59
   7 ?    4.1   0.1      0.08        63      24      71 ..     383     430 ..     370     433 .. 0.82
   8 ?    1.4   0.1      0.58   4.5e+02      56      59 ..     489     492 ..     461     529 .] 0.54

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.015
                        NPV_P10 16 vddkVdalqqqv........ddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiLn 66
                                   +++ ++a+ + +        d +qe ++    + + L ++sa+L+el +++ ++ d+L 
  gi|119719698|ref|YP_920193.1| 18 LSEEIKAMMSTIdrristlpDTLQEPIRA--SIRTSLTQLSASLEELRASLADVLDLLQ 74
                                   55555555555522222223444444444..6889999999999999999999988886 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 2.4e-06
                        NPV_P10  15 avddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiLn 66 
                                    a++++Vd lq+q++d  + l++     e + a+++q++++++++++I++iL 
  gi|119719698|ref|YP_920193.1|  77 ATSSQVDELQKQITDEFTSLEE---KVETIHAIAEQIQKISEEIQKIDSILD 125
                                    7899******999664444444...455677888888888888888888876 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.019
                        NPV_P10  24 qqqvddv.qenlpdvtelnekLdaqsaqLaeletkvenIqdiL 65 
                                    +++ +++ + nl++++++ e L ++s++ + l+++++nI ++ 
  gi|119719698|ref|YP_920193.1| 153 DAARKELgRVNLEELNKVVESLRGISETHTLLQDSLDNIAKLI 195
                                    4444444234666666666666666666666666666665543 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.024
                        NPV_P10  11 adikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenI 61 
                                    + i+ ++  ++++++  ++++en ++  ++ e+  ++sa+ ++l  ++++ 
  gi|119719698|ref|YP_920193.1| 193 KLIESLSGSLSSVDETAKELRENAEKYAKMVEEYTQLSAKAEALTRQIKEL 243
                                    556677777777777777777777766666666666666555555555543 PP

  == domain 5  score: 9.4 bits;  conditional E-value: 0.0019
                        NPV_P10  15 avddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiLnpde..vPdl 73 
                                    +++ k +al  q+++++e  + ++e  +kL++  ++L e e+++++  + Ln+ +  +P++
  gi|119719698|ref|YP_920193.1| 228 QLSAKAEALTRQIKELEERKQLLEEQAKKLEEKEKELIEREKSMTTLLENLNKAVskIPEV 288
                                    6788999999999999999999999999999999999999998888888888666678887 PP

  == domain 6  score: -1.0 bits;  conditional E-value: 3.2
                        NPV_P10  37 vtelnekLdaqsaq 50 
                                    ++el++kL +   +
  gi|119719698|ref|YP_920193.1| 340 LQELEQKLKKWESE 353
                                    22244444443333 PP

  == domain 7  score: 4.1 bits;  conditional E-value: 0.08
                        NPV_P10  24 qqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiLnpdevP 71 
                                    +++v++ +++ ++++ l +++++    L +l +++e+ + iL ++ +P
  gi|119719698|ref|YP_920193.1| 383 EKEVAQREAKTEKLEYLLKQIEEKEGYLRKLRAEIEEKERILKEELLP 430
                                    4577888888999999999999********************977788 PP

  == domain 8  score: 1.4 bits;  conditional E-value: 0.58
                        NPV_P10  56 tkve 59 
                                    +++e
  gi|119719698|ref|YP_920193.1| 489 KALE 492
                                    3322 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   6.7   1.2e-05    0.0092     148     265 ..      15     132 ..       4     137 .. 0.76
   2 !   17.4  19.5   2.1e-06    0.0016     143     253 ..     169     281 ..     161     289 .. 0.91
   3 ?    2.1  22.2      0.09        70     158     253 ..     291     385 ..     286     395 .. 0.69
   4 ?   -0.9  11.6      0.75   5.8e+02     202     259 ..     374     426 ..     363     430 .. 0.54
   5 !    9.6  20.2   0.00047      0.37     163     256 ..     426     525 ..     424     529 .] 0.77

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.2e-05
                           Spc7 148 legleedkelLekqeeel.dellpelee.ekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelael 225
                                    +e+l e+ + +++  +   ++l + l+e  +a+++  l++l +  eel ++  + L  l+++    +++++e++k++++ 
  gi|119719698|ref|YP_920193.1|  15 IEELSEEIKAMMSTIDRRiSTLPDTLQEpIRASIRTSLTQLSASLEELRASLADVLDLLQRTA--TSSQVDELQKQITDE 92 
                                    455555544444444443033333444323568999999999999999999999999998865..556788999****** PP

                           Spc7 226 qeqleeleekieelkeqkseleeeiaeaervleeckgwse 265
                                     + lee+ e+i +++eq++++ eei++ +++l+  k++++
  gi|119719698|ref|YP_920193.1|  93 FTSLEEKVETIHAIAEQIQKISEEIQKIDSILDGLKEITA 132
                                    ******************************9998888875 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 2.1e-06
                           Spc7 143 gleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeeles..idkeeLeelreelaelkaeieekkk 220
                                    ++ e l g+ e  +lL+++ +++ +l ++l+   +++ e++++l+e ae+ ++   + ++L +  e+l+++ +e+ee+k+
  gi|119719698|ref|YP_920193.1| 169 KVVESLRGISETHTLLQDSLDNIAKLIESLSGSLSSVDETAKELRENAEKYAKmvEEYTQLSAKAEALTRQIKELEERKQ 248
                                    55678999999***********************************99999995344899******************** PP

                           Spc7 221 elaelqeqleeleekieelkeqkseleeeiaea 253
                                     l+e  ++lee+e+++ e ++++++l e++++a
  gi|119719698|ref|YP_920193.1| 249 LLEEQAKKLEEKEKELIEREKSMTTLLENLNKA 281
                                    *****************************9987 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.09
                           Spc7 158 LekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekie 237
                                    L k  e l +  +el +++ ele++ ++l++++ +++s d ee ++lr el+el++++++ + ela +++ l e+++++e
  gi|119719698|ref|YP_920193.1| 291 LVKYIEFLRQKEQELIAKQIELERREAELKSFSSKIAS-DAEEARKLRIELQELEQKLKKWESELAAREKALLEKAQAME 369
                                    56666777777788888888888888888888877554.88888888888888888888888888888888888777777 PP

                           Spc7 238 elkeqkseleeeiaea 253
                                        +k+++  + +++
  gi|119719698|ref|YP_920193.1| 370 REILEKTQALVQREKE 385
                                    6655555554444333 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 0.75
                           Spc7 202 eelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervlee 259
                                    e++ ++l++ ++e++    + + ++e+le l ++iee +   ++l++ei+e+er+l+e
  gi|119719698|ref|YP_920193.1| 374 EKT-QALVQREKEVA----QREAKTEKLEYLLKQIEEKEGYLRKLRAEIEEKERILKE 426
                                    222.23333344444....333444455555566666666678888888888888876 PP

  == domain 5  score: 9.6 bits;  conditional E-value: 0.00047
                           Spc7 163 eeldellpeleeekaeleeeleklqeaaeeles......idkeeLeelreelaelkaeieekkkelaelqeqleeleeki 236
                                    eel  ++++l +e++el +  ++l e+++el+       +++  L elre+l++ +ae+++++k l+e+ ++l+ele+++
  gi|119719698|ref|YP_920193.1| 426 EELLPAKERLLKEQEELAQWEKRLLERERELTGyqrmlaSKESALVELRERLEAREAELKSREKALEEKLKRLAELEARV 505
                                    55666778888888888888888888777777666665577888999999999999999999999999999999999999 PP

                           Spc7 237 eelkeqkseleeeiaeaerv 256
                                    ++l+++ ++l+ee+++ e+ 
  gi|119719698|ref|YP_920193.1| 506 ASLEKENASLKEELRRCEER 525
                                    99999999999988876655 PP

>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   9.7     2e-08   1.6e-05      11     170 ..      13     167 ..       7     179 .. 0.67
   2 !    9.5  16.2    0.0011      0.82      63     189 ..     129     265 ..     112     266 .. 0.79
   3 ?    3.9   8.2     0.054        42       2      44 ..     477     521 ..     476     529 .] 0.86

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 2e-08
                                    HHHCCHHHCHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHCCCHHHHHHHHHCCHHHHHHHHHHHHCH CS
                 Apolipoprotein  11 ayaeeleeqlaplaqelrdrlskeleelrarlraeleevrarlepyrdevqeqlgqnleelrqrlapyteelrerlaada 90 
                                    +++eel+e ++ +  ++  r+s  ++ l++ +ra + +   +l++ ++e+++ l++ l+ l+++ +          + ++
  gi|119719698|ref|YP_920193.1|  13 MTIEELSEEIKAMMSTIDRRISTLPDTLQEPIRASIRTSLTQLSASLEELRASLADVLDLLQRTAT----------SSQV 82 
                                    567888899998888899999999999999999999999999999999999999999998888832..........3367 PP

                                    HCCHHCHCCHCHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH......-----..-----SSSHHHHHHHTS- CS
                 Apolipoprotein  91 eelqeqlavyaeelrerlerhvealkarlapyveelrqklaerleelke......slaphaeeveerlssrveelrekle 164
                                    +elq+q++     l+e++e+   a+ ++++ ++ee+++ +++ l+ lke       ++ ++ e+ ++l + ++++r++l 
  gi|119719698|ref|YP_920193.1|  83 DELQKQITDEFTSLEEKVETI-HAIAEQIQKISEEIQK-IDSILDGLKEitartdLIDGKVTEYSTKLLEAIDAARKELG 160
                                    777777777777777777776.7777777777777774.44444433330000003344455666666666666666655 PP

                                    T.TSHHH CS
                 Apolipoprotein 165 e.qaeel 170
                                    + ++eel
  gi|119719698|ref|YP_920193.1| 161 RvNLEEL 167
                                    5444444 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0011
                                    CCCHHHHHHHHHCCHHHHHHHHHHHHCHHCCH....HCHCCHCHHHHHHHHHH......HHHHHHHHCHHHHHHHHHHHH CS
                 Apolipoprotein  63 qlgqnleelrqrlapyteelrerlaadaeelq....eqlavyaeelrerlerh......vealkarlapyveelrqklae 132
                                    +++++++ ++ ++++y+ +l e ++a+ +el     e l ++ e lr   e+h      ++++ + ++ ++ +l + ++e
  gi|119719698|ref|YP_920193.1| 129 EITARTDLIDGKVTEYSTKLLEAIDAARKELGrvnlEELNKVVESLRGISETHtllqdsLDNIAKLIESLSGSLSS-VDE 207
                                    6788889999999999999999888888888622225678888888888888888766677777777777777776.999 PP

                                    HHHHHHH-----..---..--SSSHHHHHHHTS-TTSHHHHHS--XXXXXXXXXXXXXX CS
                 Apolipoprotein 133 rleelkeslaphaeeve..erlssrveelrekleeqaeelrerleanleelkaqlealv 189
                                     ++el+e+++ +a+ ve  ++ls ++e+l ++ +e +ee ++ le+++++l+++  +l+
  gi|119719698|ref|YP_920193.1| 208 TAKELRENAEKYAKMVEeyTQLSAKAEALTRQIKE-LEERKQLLEEQAKKLEEKEKELI 265
                                    99999999999999888777888888888888877.88888999999999998877776 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.054
                                    HHHCCCCHHHHHCCHHHCHHCHHH.H.HHHHHHHHHHHHHHHHHH CS
                 Apolipoprotein   2 leesldelkayaeeleeqlaplaq.e.lrdrlskeleelrarlra 44 
                                    le + +elk++ + lee+l++la+ e  ++ l+ke ++l+++lr+
  gi|119719698|ref|YP_920193.1| 477 LEAREAELKSREKALEEKLKRLAElEaRVASLEKENASLKEELRR 521
                                    7788899*****************96699**************65 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   7.7   8.8e-08   6.9e-05     116     221 ..      15     116 ..      13     123 .. 0.73
   2 !    6.8   1.6    0.0047       3.7     120     218 ..     120     219 ..     117     226 .. 0.61
   3 ?    3.1  10.9     0.062        48     112     196 ..     180     267 ..     141     308 .. 0.75
   4 ?   -0.5   8.5      0.78   6.1e+02     151     218 ..     454     522 ..     424     529 .] 0.59

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 8.8e-08
                           CorA 116 ldeivdrlfellekleeeldeledeledstkkeilrelaqlrrrlvklrralapnrevlkrllakaddkllddedkeylr 195
                                    ++e+ +++ + ++++++++  l d+l++ ++++i+ +l+ql  +l +lr +la+  ++l+r  +++  ++l ++      
  gi|119719698|ref|YP_920193.1|  15 IEELSEEIKAMMSTIDRRISTLPDTLQEPIRASIRTSLTQLSASLEELRASLADVLDLLQRTATSSQVDELQKQI----T 90 
                                    678899999999***********************************************7777744444444443....3 PP

                           CorA 196 dlldelerllemlealrerleslqdt 221
                                    d    le  +e+++a++e++++++++
  gi|119719698|ref|YP_920193.1|  91 DEFTSLEEKVETIHAIAEQIQKISEE 116
                                    33333333444444444444444433 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0047
                           CorA 120 vdrlfellekleeeldeledeledstkkeilrelaqlrrrlvkl.....rralapnrevlk..rllakaddkllddedke 192
                                    +d++++ l+++ +++d ++  + ++ + ++l+ + + r++l+++      +++  +r + +  +ll+        d  ++
  gi|119719698|ref|YP_920193.1| 120 IDSILDGLKEITARTDLIDGKV-TEYSTKLLEAIDAARKELGRVnleelNKVVESLRGISEthTLLQ-----DSLDNIAK 193
                                    7999999999999999999999.66666777777777777777742222222222222221002222.....22223334 PP

                           CorA 193 ylrdlldelerllemlealrerlesl 218
                                    +++ l+  l++++e+++ lre +e+ 
  gi|119719698|ref|YP_920193.1| 194 LIESLSGSLSSVDETAKELRENAEKY 219
                                    57777777777777777777777654 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.062
                           CorA 112 lyrlldeivdrlfellekleeeldeledel.....edstkkeilrelaqlrrrlvklrralapnrevlkrllakaddkll 186
                                    ++ ll+  +d++++l+e l+  l  ++++      + ++ +++++e +ql  ++  l r++++++e   +ll+ + +k+l
  gi|119719698|ref|YP_920193.1| 180 THTLLQDSLDNIAKLIESLSGSLSSVDETAkelreNAEKYAKMVEEYTQLSAKAEALTRQIKELEERK-QLLE-EQAKKL 257
                                    46788999999999999999999999998888888888888999999999999999999999999999.8888.777777 PP

                           CorA 187 ddedkeylrd 196
                                    ++++ke++++
  gi|119719698|ref|YP_920193.1| 258 EEKEKELIER 267
                                    7777666443 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 0.78
                           CorA 151 relaqlrrrlvklrralapnrevlkrlla..kaddkllddedkeylrdlldelerllemlealrerlesl 218
                                    rel+ ++r l+  ++al ++re l+++ a  k+++k l+++  ++l +l+ ++++l+++  +l+e l++ 
  gi|119719698|ref|YP_920193.1| 454 RELTGYQRMLASKESALVELRERLEAREAelKSREKALEEKL-KRLAELEARVASLEKENASLKEELRRC 522
                                    455555555555555555555555544445445555555554.677888888888777777777777765 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   7.9    0.0041       3.2      27     186 ..      14     174 ..      13     182 .. 0.74
   2 !   21.6  18.9   1.5e-07   0.00011      24     132 ..     163     271 ..     157     280 .. 0.93
   3 ?    4.0  10.6     0.034        27      59     123 ..     291     355 ..     286     363 .. 0.88
   4 ?   -1.5  19.7       1.8   1.4e+03      39     123 ..     439     527 ..     430     529 .] 0.46

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0041
                            GAS  27 lIkslKeeieelkkkeernekelseisqe..nkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdl 104
                                    +I++l eei+ +    +r    l ++ qe    +++  L+++ + +eeLr+ l++     q+ +++ +++ el+k+++d 
  gi|119719698|ref|YP_920193.1|  14 TIEELSEEIKAMMSTIDRRISTLPDTLQEpiRASIRTSLTQLSASLEELRASLADVLDLLQR-TATSSQVDELQKQITDE 92 
                                    5899999999999998888888888888844567999*****************99876554.56677888888888888 PP

                            GAS 105 kwehevleqrfekvekerdelykkfeaa..iqevqqktglknllLekklkalqee.lEkkeaqleevlaaanldpaalsa 181
                                      + e + + ++++ +++++++++ ++   i +  +++  +  l+  k+++ + + lE+ +a  +e+  + nl+  +l++
  gi|119719698|ref|YP_920193.1|  93 FTSLEEKVETIHAIAEQIQKISEEIQKIdsILDGLKEITARTDLIDGKVTEYSTKlLEAIDAARKEL-GRVNLE--ELNK 169
                                    8888888888888888888888877764448888888888888888888776655145555555444.466666..5666 PP

                            GAS 182 vsekl 186
                                    v e+l
  gi|119719698|ref|YP_920193.1| 170 VVESL 174
                                    66655 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 1.5e-07
                            GAS  24 NLelIkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkd 103
                                    NLe  ++  e +  + +  +  +  l++i++  ++l+  L  ++e  +eLr+++++y k  +++++l a+ + l++++k+
  gi|119719698|ref|YP_920193.1| 163 NLEELNKVVESLRGISETHTLLQDSLDNIAKLIESLSGSLSSVDETAKELRENAEKYAKMVEEYTQLSAKAEALTRQIKE 242
                                    7888888888888888888999999******************************************************* PP

                            GAS 104 lkwehevleqrfekvekerdelykkfeaa 132
                                    l++ ++ le++ +k+e++ +el ++ +++
  gi|119719698|ref|YP_920193.1| 243 LEERKQLLEEQAKKLEEKEKELIEREKSM 271
                                    **********************9998876 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.034
                            GAS  59 lkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrfekvekerd 123
                                    l++ ++ ++++ +eL ++  + e+  ++lk+  +++ +  +e ++l+ e + leq+++k e+e  
  gi|119719698|ref|YP_920193.1| 291 LVKYIEFLRQKEQELIAKQIELERREAELKSFSSKIASDAEEARKLRIELQELEQKLKKWESELA 355
                                    5666777899999999999999999**********************************999865 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 1.8
                            GAS  39 kkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekd....kqslknlkarlkelekelkdlkwehevleqr 114
                                    +++ ++ ek+l e + e   ++  L   e  + eLr++l+  e +     ++l++  +rl ele  + +l+ e+ +l+++
  gi|119719698|ref|YP_920193.1| 439 QEELAQWEKRLLERERELTGYQRMLASKESALVELRERLEAREAElksrEKALEEKLKRLAELEARVASLEKENASLKEE 518
                                    44444444444444444444444444444444444444444332210002245555555566666666666666666666 PP

                            GAS 115 fekvekerd 123
                                    + + e+  +
  gi|119719698|ref|YP_920193.1| 519 LRRCEERLK 527
                                    666655444 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   9.0   3.7e-05     0.029      23      97 ..      46     127 ..      13     134 .. 0.67
   2 !   12.4   5.0   0.00016      0.13      22     138 ..     100     223 ..      92     225 .. 0.49
   3 !    6.8   2.6    0.0082       6.4      34      95 ..     227     283 ..     220     298 .. 0.65
   4 ?    1.2   0.3      0.46   3.6e+02      44      75 ..     337     364 ..     306     424 .. 0.59
   5 ?    4.3   0.1     0.051        39      56      99 ..     468     510 ..     456     529 .] 0.51

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.7e-05
                   Baculo_PEP_C  23 nairlqnvqilaqlatlldaietqLnalsedlk.sllaeldtrldtlltnLtdalnalq......dtlrneLtnlnsilt 95 
                                    ++ir+ ++q++a l++l ++++ +L+ l+   + s + el++++++ +t L++++ ++       +++++e++ ++sil 
  gi|119719698|ref|YP_920193.1|  46 ASIRTSLTQLSASLEELRASLADVLDLLQRTATsSQVDELQKQITDEFTSLEEKVETIHaiaeqiQKISEEIQKIDSILD 125
                                    46777777777777777777777777776544414456677777777777777777777666777777777777777776 PP

                   Baculo_PEP_C  96 nL 97 
                                     L
  gi|119719698|ref|YP_920193.1| 126 GL 127
                                    55 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00016
                   Baculo_PEP_C  22 LnairlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq.dtlrneLtnlnsiltnL... 97 
                                    +++i +   qi  ++++ +++i++ L+ l+e +++    +d ++++ +t+L +a+ a   +  r +L+ ln+++ +L   
  gi|119719698|ref|YP_920193.1| 100 VETIHAIAEQI-QKISEEIQKIDSILDGLKE-ITARTDLIDGKVTEYSTKLLEAIDAARkELGRVNLEELNKVVESLrgi 177
                                    44554444444.4444444444444444332.444444455577777777777777776433345555555555555111 PP

                   Baculo_PEP_C  98 lssvtNinstLnnllqalnnl.....dlgalsqeledaldtveeil 138
                                        t ++ +L n+ + +++l       +++++el++++++  +++
  gi|119719698|ref|YP_920193.1| 178 SETHTLLQDSLDNIAKLIESLsgslsSVDETAKELRENAEKYAKMV 223
                                    2334455555555555555553333333566666666666665555 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0082
                   Baculo_PEP_C  34 aqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtnlnsilt 95 
                                    +ql++  +a+ +q+++l+e  k+ll+e++++l++  ++L +  ++++    + L+nln+ ++
  gi|119719698|ref|YP_920193.1| 227 TQLSAKAEALTRQIKELEE-RKQLLEEQAKKLEEKEKELIEREKSMT----TLLENLNKAVS 283
                                    6777788888888888766.466677777777776666666655554....44444444443 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.46
                   Baculo_PEP_C  44 etqLnalsedlksllaeldtrldtlltnLtda 75 
                                      +L++l+++lk+     +++l++  ++L ++
  gi|119719698|ref|YP_920193.1| 337 RIELQELEQKLKK----WESELAAREKALLEK 364
                                    3333333333333....222222222222222 PP

  == domain 5  score: 4.3 bits;  conditional E-value: 0.051
                   Baculo_PEP_C  56 sllaeldtrldtlltnLtdalnalqdtlrneLtnlnsiltnLls 99 
                                    s+l el++rl++  ++L++  +al+++l+ +L  l++ +++L  
  gi|119719698|ref|YP_920193.1| 468 SALVELRERLEAREAELKSREKALEEKLK-RLAELEARVASLEK 510
                                    34444444444444444444444444442.44444444444433 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1     0.014        11      48     101 ..      13      64 ..       8      68 .. 0.84
   2 !   18.6   4.9   1.9e-06    0.0015      44     117 ..      46     120 ..      42     129 .. 0.81
   3 !    8.5   0.9    0.0026         2      45     122 ..     129     207 ..     121     218 .. 0.61
   4 ?    5.8   9.5     0.018        14      40     123 ..     178     260 ..     175     309 .. 0.78
   5 ?    3.9   2.1     0.066        51      43     122 ..     268     352 ..     261     354 .. 0.70
   6 ?    6.1   6.4     0.014        11      39     115 ..     336     412 ..     332     421 .. 0.85
   7 ?    4.2   0.9     0.053        41      63     117 ..     472     526 ..     424     529 .] 0.61

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.014
                        DUF1664  48 kqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseige 101
                                      +e++se+++a    + +ri ++ ++l+e   i ++i+  +t+++  l+e++ 
  gi|119719698|ref|YP_920193.1|  13 MTIEELSEEIKAMMSTIDRRISTLPDTLQEP--IRASIRTSLTQLSASLEELRA 64 
                                    578999*********************9886..567788899999998888776 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 1.9e-06
                        DUF1664  44 esvskqleqvseslaatkrhLssridrvdkkl..deqkeiskeikeevtevredlseigedvesvkeavegleskl 117
                                    +s+ ++l+q+s+sl++ +  L++ +d ++++    ++ e++k+i++e t+++e++++i+   e+++++ e+++ k+
  gi|119719698|ref|YP_920193.1|  46 ASIRTSLTQLSASLEELRASLADVLDLLQRTAtsSQVDELQKQITDEFTSLEEKVETIHAIAEQIQKISEEIQ-KI 120
                                    789999*********************998761156789****************999988888777655553.33 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0026
                        DUF1664  45 svskqleqvseslaatkrhLssridrvdkkldeqk.eiskeikeevtevredlseigedvesvkeavegleskleriee 122
                                    +++ + + +  ++++   +L + id   k+l  ++ e  +++ e +  ++e  + +++ ++++ +++e+l ++l++++e
  gi|119719698|ref|YP_920193.1| 129 EITARTDLIDGKVTEYSTKLLEAIDAARKELGRVNlEELNKVVESLRGISETHTLLQDSLDNIAKLIESLSGSLSSVDE 207
                                    5555556666666666666666666666666554325556666666666666666666666666666666666666654 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.018
                        DUF1664  40 sdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskler 119
                                    s+  + +  +l+++ + +++    Lss +d+  k+l e++e  +++ ee t+++ + +++ +++++++e  + le++ ++
  gi|119719698|ref|YP_920193.1| 178 SETHTLLQDSLDNIAKLIESLSGSLSS-VDETAKELRENAEKYAKMVEEYTQLSAKAEALTRQIKELEERKQLLEEQAKK 256
                                    555555666666666666666666543.6666667777777777888888888888888888888888888888888888 PP

                        DUF1664 120 ieek 123
                                    +eek
  gi|119719698|ref|YP_920193.1| 257 LEEK 260
                                    8876 PP

  == domain 5  score: 3.9 bits;  conditional E-value: 0.066
                        DUF1664  43 vesvskqleqvseslaatkr..hLssridrvdkkldeqkeiskeikeevtevredlseig...edvesvkeavegleskl 117
                                     +s+++ le++ +++++  +  +L + i+ + +k +e ++ + e+++  +e+++  s+i    e+ ++++   ++le+kl
  gi|119719698|ref|YP_920193.1| 268 EKSMTTLLENLNKAVSKIPEvgDLVKYIEFLRQKEQELIAKQIELERREAELKSFSSKIAsdaEEARKLRIELQELEQKL 347
                                    56788888888888887654338999999999999998888877776666665555555500055566777789999999 PP

                        DUF1664 118 eriee 122
                                    ++ e+
  gi|119719698|ref|YP_920193.1| 348 KKWES 352
                                    98775 PP

  == domain 6  score: 6.1 bits;  conditional E-value: 0.014
                        DUF1664  39 lsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegles 115
                                    l+  ++++ ++l++  ++laa  + L ++ + +++++ e +++  + ++ev++ + ++++++  +++++e    l +
  gi|119719698|ref|YP_920193.1| 336 LRIELQELEQKLKKWESELAAREKALLEKAQAMEREILEKTQALVQREKEVAQREAKTEKLEYLLKQIEEKEGYLRK 412
                                    6666788999*****************************************************99999986555554 PP

  == domain 7  score: 4.2 bits;  conditional E-value: 0.053
                        DUF1664  63 hLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskl 117
                                    +L +r++  +++l++ +++ +e  + ++e++  +++++++  s+ke  +  e++l
  gi|119719698|ref|YP_920193.1| 472 ELRERLEAREAELKSREKALEEKLKRLAELEARVASLEKENASLKEELRRCEERL 526
                                    3444444444444444444444444444444455555555444444444444444 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.5      0.22   1.7e+02      57     118 ..      14      77 ..      12      92 .. 0.67
   2 ?    4.6   1.0     0.031        24      65     117 ..      82     134 ..      76     151 .. 0.77
   3 ?    2.0  19.9      0.19   1.5e+02      20     175 ..     108     268 ..     101     270 .. 0.63
   4 !    7.7  26.6    0.0034       2.7      22     173 ..     275     422 ..     270     426 .. 0.82
   5 !   18.2  16.5   2.1e-06    0.0016      47     136 ..     438     527 ..     431     529 .] 0.95

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.22
                        DUF4201  57 kIeernkeLkrlkkkttktvhalthlkek..lhmleselselkkelkekeerlaklrkelykvk 118
                                    +Iee ++e+k++ +++ + + +l ++ +   +  +++ l +l  +l+e+ + la++ + l+++ 
  gi|119719698|ref|YP_920193.1|  14 TIEELSEEIKAMMSTIDRRISTLPDTLQEpiRASIRTSLTQLSASLEELRASLADVLDLLQRTA 77 
                                    6889999999999999888888865544322446677777777777777777776666666554 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.031
                        DUF4201  65 Lkrlkkkttktvhalthlkeklhmleselselkkelkekeerlaklrkelykv 117
                                    + +l+k++t++   l++  e  h+++++ ++  +e+++++  l+ l++ + ++
  gi|119719698|ref|YP_920193.1|  82 VDELQKQITDEFTSLEEKVETIHAIAEQIQKISEEIQKIDSILDGLKEITART 134
                                    56778888888888888888888888888888888888888888877777665 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.19
                        DUF4201  20 hqlakiqeklekkeelgegLtlidFeq..lqie....nqalnkkIeernkeLkrlkkkttktvhalthlkeklhmlesel 93 
                                    +q++ki+e+++k + + +gL++i   +  +  +     ++l + I+   keL r        + +l+ + e l  ++++ 
  gi|119719698|ref|YP_920193.1| 108 EQIQKISEEIQKIDSILDGLKEITARTdlIDGKvteySTKLLEAIDAARKELGRVN------LEELNKVVESLRGISETH 181
                                    68999999999999999999988654311333300114455555566666665554......455555555555555555 PP

                        DUF4201  94 selkkelkekeerlaklrkelykvklerdklrkqneklkqqggll.....rvPaLlkDYdktkekveekrksvkkLrrkv 168
                                      l+++l+++ + +++l  +l++v +  + lr+  ek  +  +++     +++aL++  ++ +e+ + ++++ kkL++k 
  gi|119719698|ref|YP_920193.1| 182 TLLQDSLDNIAKLIESLSGSLSSVDETAKELRENAEKYAKMVEEYtqlsaKAEALTRQIKELEERKQLLEEQAKKLEEKE 261
                                    55555555555555555555555555555555555555544444322222489999999999999999999999999999 PP

                        DUF4201 169 kilemrl 175
                                    k+l +r 
  gi|119719698|ref|YP_920193.1| 262 KELIERE 268
                                    9998875 PP

  == domain 4  score: 7.7 bits;  conditional E-value: 0.0034
                        DUF4201  22 lakiqeklekkeelgegLtlidFeqlq.ienqalnkkIeernkeLkrlkkkttktvhalthlkeklhmleselselkkel 100
                                    l+++++ + k  e+g+ ++ i+F+  +  e +a + ++e+r++eLk  ++k++++  +   l+  l++le++l++ ++el
  gi|119719698|ref|YP_920193.1| 275 LENLNKAVSKIPEVGDLVKYIEFLRQKeQELIAKQIELERREAELKSFSSKIASDAEEARKLRIELQELEQKLKKWESEL 354
                                    567888999999***********965516789999999****************************************** PP

                        DUF4201 101 kekeerlaklrkelykvklerdklrkqneklkqqggllrvPaLlkDYdktkekveekrksvkkLrrkvkilem 173
                                      +e+ l +  + +++  le++++  q+ek  +q +  + ++L +      +++eek+  ++kLr ++++ e+
  gi|119719698|ref|YP_920193.1| 355 AAREKALLEKAQAMEREILEKTQALVQREKEVAQREA-KTEKLEY----LLKQIEEKEGYLRKLRAEIEEKER 422
                                    **************99999999998888887777776.6666655....555566666666666666665544 PP

  == domain 5  score: 18.2 bits;  conditional E-value: 2.1e-06
                        DUF4201  47 lqienqalnkkIeernkeLkrlkkkttktvhalthlkeklhmleselselkkelkekeerlaklrkelykvklerdklrk 126
                                     q e ++ +k++ er+ eL   +++ +++  al +l+e+l + e+el+ ++k l+ek +rla+l++++ ++++e++ l++
  gi|119719698|ref|YP_920193.1| 438 EQEELAQWEKRLLERERELTGYQRMLASKESALVELRERLEAREAELKSREKALEEKLKRLAELEARVASLEKENASLKE 517
                                    588999************************************************************************** PP

                        DUF4201 127 qneklkqqgg 136
                                    + +++++++ 
  gi|119719698|ref|YP_920193.1| 518 ELRRCEERLK 527
                                    ****999876 PP

>> DASH_Duo1  DASH complex subunit Duo1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       9.1   7.1e+03      16      32 ..      15      31 ..      14      39 .. 0.53
   2 ?    0.3   0.0      0.77     6e+02       8      36 ..      51      79 ..      49      88 .. 0.73
   3 !    8.0   1.2    0.0031       2.4      15      53 ..      95     133 ..      80     137 .. 0.76
   4 ?    1.0   0.0      0.47   3.7e+02      11      44 ..     147     184 ..     146     186 .. 0.61
   5 !   17.9   0.2   2.6e-06     0.002       7      60 ..     186     239 ..     183     244 .. 0.93
   6 ?   -2.0   0.0       4.1   3.2e+03      18      29 ..     273     284 ..     250     302 .. 0.60
   7 ?   -2.2   0.1       4.5   3.5e+03      16      44 ..     396     424 ..     385     426 .. 0.64
   8 ?   -2.7   0.4       6.5   5.1e+03       2      29 ..     491     518 ..     490     527 .. 0.55

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 9.1
                      DASH_Duo1 16 ienviesLkkaksnier 32
                                   ie + e++k++ s i+r
  gi|119719698|ref|YP_920193.1| 15 IEELSEEIKAMMSTIDR 31
                                   55555555555544443 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.77
                      DASH_Duo1  8 qLrkinevienviesLkkaksniervket 36
                                   +L+++ + +e +++sL ++ + ++r +++
  gi|119719698|ref|YP_920193.1| 51 SLTQLSASLEELRASLADVLDLLQRTATS 79
                                   67778888888888888887777776654 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0031
                      DASH_Duo1  15 vienviesLkkaksniervketvestntLLdkWirIlsq 53 
                                     +e  +e+++++ ++i++++e +++ +++Ld   +I  +
  gi|119719698|ref|YP_920193.1|  95 SLEEKVETIHAIAEQIQKISEEIQKIDSILDGLKEITAR 133
                                    567778888888888888888888888888866666555 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.47
                      DASH_Duo1  11 kinevienviesLkkak.sniervket...vestntLL 44 
                                    k+ e+i++ +++L +++ +++++v e+   +++t+tLL
  gi|119719698|ref|YP_920193.1| 147 KLLEAIDAARKELGRVNlEELNKVVESlrgISETHTLL 184
                                    56677777777777777777777766522234556655 PP

  == domain 5  score: 17.9 bits;  conditional E-value: 2.6e-06
                      DASH_Duo1   7 eqLrkinevienviesLkkaksniervketvestntLLdkWirIlsqtehtqrl 60 
                                    ++L++i + ie++ +sL ++ +  +++ e+ e+  +++++++++  ++e  +r 
  gi|119719698|ref|YP_920193.1| 186 DSLDNIAKLIESLSGSLSSVDETAKELRENAEKYAKMVEEYTQLSAKAEALTRQ 239
                                    68**********************************************988775 PP

  == domain 6  score: -2.0 bits;  conditional E-value: 4.1
                      DASH_Duo1  18 nviesLkkaksn 29 
                                    ++ e+L+ka s+
  gi|119719698|ref|YP_920193.1| 273 TLLENLNKAVSK 284
                                    333333333333 PP

  == domain 7  score: -2.2 bits;  conditional E-value: 4.5
                      DASH_Duo1  16 ienviesLkkaksniervketvestntLL 44 
                                    +e + +++++ ++++ ++   +e+ +++L
  gi|119719698|ref|YP_920193.1| 396 LEYLLKQIEEKEGYLRKLRAEIEEKERIL 424
                                    45555666666666666666666666655 PP

  == domain 8  score: -2.7 bits;  conditional E-value: 6.5
                      DASH_Duo1   2 LekEleqLrkinevienviesLkkaksn 29 
                                    Le+ l+ L ++ + + +++++  + k++
  gi|119719698|ref|YP_920193.1| 491 LEEKLKRLAELEARVASLEKENASLKEE 518
                                    6666666666666665555554444444 PP

>> Leu_zip  Leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   6.4      0.66   5.1e+02     151     204 ..      81     134 ..       9     180 .. 0.47
   2 ?    4.1  20.2     0.035        27     114     227 ..     214     335 ..     184     341 .. 0.69
   3 !   16.2  26.2   7.4e-06    0.0058     137     275 ..     339     478 ..     330     479 .. 0.81
   4 ?    2.2   5.1      0.14   1.1e+02     108     157 ..     487     527 ..     477     529 .] 0.44

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.66
                        Leu_zip 151 elEkqatsaleeksklekalkelqkelgekkdekenskeiskleeklaelkldl 204
                                    ++++  +++ +e + le++++ +++ +++ ++ +e+ ++i ++ + l+e+++  
  gi|119719698|ref|YP_920193.1|  81 QVDELQKQITDEFTSLEEKVETIHAIAEQIQKISEEIQKIDSILDGLKEITART 134
                                    111112222222223333333332222222222223333333333333333333 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.035
                        Leu_zip 114 lkkkkLePlneg.....GgaeLLkkeierLkeenekLkerlkelEkqatsaleeksklekalkelqkelgekkdekensk 188
                                    ++++k + + e        ae L  +i++L+e  + L+e+ k+lE++ ++++e ++ +++ l++l+k++++  ++ +  k
  gi|119719698|ref|YP_920193.1| 214 ENAEKYAKMVEEytqlsAKAEALTRQIKELEERKQLLEEQAKKLEEKEKELIEREKSMTTLLENLNKAVSKIPEVGDLVK 293
                                    3334444333322222267899*******************************************999999988888777 PP

                        Leu_zip 189 eiskleeklael...kldlektleektasaksleedlastkh 227
                                    +i+ l++k +el   +++le+   e ++ ++++++d  ++++
  gi|119719698|ref|YP_920193.1| 294 YIEFLRQKEQELiakQIELERREAELKSFSSKIASDAEEARK 335
                                    776666665555111566677666667777777777666655 PP

  == domain 3  score: 16.2 bits;  conditional E-value: 7.4e-06
                        Leu_zip 137 rLkeenekLkerlkelEkqatsaleeksklekal.kelqkelgekkdekenskeiskleeklaelkld...lektleekt 212
                                    +L+e  +kLk+   el ++ + +le+ +++e+++ +++q+ ++ +k++++++++++kle  l++++ +   l k   e +
  gi|119719698|ref|YP_920193.1| 339 ELQELEQKLKKWESELAAREKALLEKAQAMEREIlEKTQALVQREKEVAQREAKTEKLEYLLKQIEEKegyLRKLRAEIE 418
                                    58888899999999999999999999999998861566666677788888777888877666665544222666777779 PP

                        Leu_zip 213 asaksleedlastkhelLkvqeqLelaekeLekkfqqtaayknlkemltkkneqikelRkrLs 275
                                    ++++ l+e+l  +k++lLk qe+L++ ek L  + ++ + y+   +ml++k   + elR+rL+
  gi|119719698|ref|YP_920193.1| 419 EKERILKEELLPAKERLLKEQEELAQWEKRLLERERELTGYQ---RMLASKESALVELRERLE 478
                                    99999*************************999999999896...68**************96 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.14
                        Leu_zip 108 kkeseelkkkkLePlnegGgaeLLkkeierLkeenekLkerlkelEkqat 157
                                    +++  e+   kL+ l+e      L+  ++ L++en  Lke l++ E++++
  gi|119719698|ref|YP_920193.1| 487 REKALEE---KLKRLAE------LEARVASLEKENASLKEELRRCEERLK 527
                                    3333333...3333333......455555555555555555555555543 PP

>> DHR10  Designed helical repeat protein 10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   6.2     0.089        69      27      97 ..      51     120 ..      47     134 .. 0.79
   2 ?    4.6   3.7     0.043        33       9      63 ..      91     145 ..      77     161 .. 0.66
   3 !   16.7  19.2   7.5e-06    0.0058      11     114 ..     164     267 ..     158     270 .. 0.92
   4 ?    4.1   8.4      0.06        47      50      94 ..     241     285 ..     240     288 .. 0.91
   5 ?    2.1  17.2      0.25   1.9e+02      43     112 ..     303     372 ..     288     375 .. 0.89
   6 ?    0.9  14.4      0.58   4.5e+02      55     117 .]     431     493 ..     427     493 .. 0.95
   7 ?    3.8  14.0     0.074        58      50     100 ..     475     525 ..     472     529 .] 0.91

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.089
                          DHR10  27 alqvvekdlrsciklleeieaelakleeakkklkelrdaleekeielrelerkeerlqrqlenaeeklerl 97 
                                    +l+++ + l+++ + l ++ + l+++ + +++++el++++++  + l+e   +++ +  q+++  e++++ 
  gi|119719698|ref|YP_920193.1|  51 SLTQLSASLEELRASLADVLDLLQRTAT-SSQVDELQKQITDEFTSLEEKVETIHAIAEQIQKISEEIQKI 120
                                    5677777777777777777777777654.567899999999999999999999999999999999998876 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.043
                          DHR10   9 eelaelErkarelqakidalqvvekdlrsciklleeieaelakleeakkklkelr 63 
                                    +e ++lE+k   ++a ++ +q++ ++++++  +l+ +++ +a+++  + k++e +
  gi|119719698|ref|YP_920193.1|  91 DEFTSLEEKVETIHAIAEQIQKISEEIQKIDSILDGLKEITARTDLIDGKVTEYS 145
                                    4556677777777777777777777777777777777766666666665555555 PP

  == domain 3  score: 16.7 bits;  conditional E-value: 7.5e-06
                          DHR10  11 laelErkarelqakidalqvvekdlrsciklleeieaelakleeakkklkelrdaleekeielrelerkeerlqrqlena 90 
                                    l+el +    l+   ++ + ++  l ++ kl+e ++  l +++e+ k+l e+ ++++++ +e  +l++k e l+rq++  
  gi|119719698|ref|YP_920193.1| 164 LEELNKVVESLRGISETHTLLQDSLDNIAKLIESLSGSLSSVDETAKELRENAEKYAKMVEEYTQLSAKAEALTRQIKEL 243
                                    66777777788888899999999********************************************************* PP

                          DHR10  91 eeklerlreqaeekreaakarlee 114
                                    ee+ + l+eqa++ +e+ k+ +e+
  gi|119719698|ref|YP_920193.1| 244 EERKQLLEEQAKKLEEKEKELIER 267
                                    ************999999887775 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.06
                          DHR10  50 akleeakkklkelrdaleekeielrelerkeerlqrqlenaeekl 94 
                                    ++lee k+ l+e+ ++leeke+el e e+  + l   l++a  k+
  gi|119719698|ref|YP_920193.1| 241 KELEERKQLLEEQAKKLEEKEKELIEREKSMTTLLENLNKAVSKI 285
                                    678999****************************99999998886 PP

  == domain 5  score: 2.1 bits;  conditional E-value: 0.25
                          DHR10  43 eeieaelakleeakkklkelrdaleekeielrelerkeerlqrqlenaeeklerlreqaeekreaakarl 112
                                    +e+ a++ +le  +++lk+ + ++++  +e+r+l  + + l+++l+++e +l+  ++   ek++a+++++
  gi|119719698|ref|YP_920193.1| 303 QELIAKQIELERREAELKSFSSKIASDAEEARKLRIELQELEQKLKKWESELAAREKALLEKAQAMEREI 372
                                    45556677899999****************************************************9876 PP

  == domain 6  score: 0.9 bits;  conditional E-value: 0.58
                          DHR10  55 akkklkelrdaleekeielrelerkeerlqrqlenaeeklerlreqaeekreaakarleelre 117
                                    ak++l + +++l++ e++l e er+ +  qr l+++e  l  lre+ e+++++ k+r ++l+e
  gi|119719698|ref|YP_920193.1| 431 AKERLLKEQEELAQWEKRLLERERELTGYQRMLASKESALVELRERLEAREAELKSREKALEE 493
                                    6789999************************************************99888875 PP

  == domain 7  score: 3.8 bits;  conditional E-value: 0.074
                          DHR10  50 akleeakkklkelrdaleekeielrelerkeerlqrqlenaeeklerlreq 100
                                    ++le  +++lk+ ++aleek ++l+ele++ + l++  ++ +e+l r +e+
  gi|119719698|ref|YP_920193.1| 475 ERLEAREAELKSREKALEEKLKRLAELEARVASLEKENASLKEELRRCEER 525
                                    6899999**************************************999886 PP

>> Fzo_mitofusin  fzo-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1      0.67   5.2e+02     111     131 ..      16      36 ..       6      71 .. 0.47
   2 !   16.2   2.0   7.7e-06     0.006      86     159 ..      76     148 ..      63     150 .. 0.83
   3 ?    2.4   0.1      0.13        99     101     152 ..     143     195 ..     137     203 .. 0.74
   4 ?   -0.7  10.1       1.2   9.2e+02      95     135 ..     208     247 ..     151     270 .. 0.65
   5 ?   -1.6   2.9       2.2   1.7e+03     111     148 ..     268     305 ..     248     318 .. 0.61
   6 ?    5.3   9.7     0.016        13      63     157 ..     431     524 ..     429     526 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.67
                  Fzo_mitofusin 111 detekeleeeikelekeiekl 131
                                    +e ++e+++ +++++++i++l
  gi|119719698|ref|YP_920193.1|  16 EELSEEIKAMMSTIDRRISTL 36 
                                    333333333333333333333 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 7.7e-06
                  Fzo_mitofusin  86 ltsancshqvqqelsstfarlcqqvdetekeleeeikelekeiekleevqkkakllrnkaslleseLekfeeqy 159
                                    + +++    +q++++  f  l+++v++ +  + e+i+++++ei+k++++   +k +  ++ l++ ++++++++ 
  gi|119719698|ref|YP_920193.1|  76 TATSSQVDELQKQITDEFTSLEEKVETIH-AIAEQIQKISEEIQKIDSILDGLKEITARTDLIDGKVTEYSTKL 148
                                    444444557899*************9876.5999*************************999999999888765 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.13
                  Fzo_mitofusin 101 stfarlcqqvdetekele.eeikelekeiekleevqkkakllrnkaslleseL 152
                                    ++  +l +++d ++kel   +++el+k +e+l  ++++  ll++   ++++ +
  gi|119719698|ref|YP_920193.1| 143 EYSTKLLEAIDAARKELGrVNLEELNKVVESLRGISETHTLLQDSLDNIAKLI 195
                                    55667888888888888525888888888888888888888887777766655 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 1.2
                  Fzo_mitofusin  95 vqqelsstfarlcqqvdetekeleeeikelekeiekleevq 135
                                      +el +  ++  + v+e  ++l+++ ++l+++i++lee +
  gi|119719698|ref|YP_920193.1| 208 TAKELRENAEKYAKMVEEY-TQLSAKAEALTRQIKELEERK 247
                                    3455555555555555544.346666666666666665543 PP

  == domain 5  score: -1.6 bits;  conditional E-value: 2.2
                  Fzo_mitofusin 111 detekeleeeikelekeiekleevqkkakllrnkasll 148
                                    +++ ++l e++++  ++i ++ ++ k  + lr+k ++l
  gi|119719698|ref|YP_920193.1| 268 EKSMTTLLENLNKAVSKIPEVGDLVKYIEFLRQKEQEL 305
                                    34445555566666666666666777777888887766 PP

  == domain 6  score: 5.3 bits;  conditional E-value: 0.016
                  Fzo_mitofusin  63 akEralKrQfveyatekLrlivsltsancshqvqqelsstfarlcqqvdetekeleeeikelekeiekleevqkkakllr 142
                                    akEr lK+Q  e a+ + rl  +    +  + +    +s++ +l+++ +  e+el+++ k+le+++++l+e++ +   l 
  gi|119719698|ref|YP_920193.1| 431 AKERLLKEQ-EELAQWEKRLLERERELTGYQRMLASKESALVELRERLEAREAELKSREKALEEKLKRLAELEARVASLE 509
                                    778888887.455555555555555555555556666788899************************************* PP

                  Fzo_mitofusin 143 nkaslleseLekfee 157
                                    ++  +l++eL++ ee
  gi|119719698|ref|YP_920193.1| 510 KENASLKEELRRCEE 524
                                    **********98765 PP

>> FTA4  Kinetochore complex Fta4 of Sim4 subunit, or CENP-50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   3.2     0.041        32     100     163 ..      30     130 ..       5     163 .. 0.55
   2 !   16.0  16.3   1.1e-05    0.0085      69     198 ..     102     285 ..      98     287 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.041
                           FTA4 100 eelIkeLPeswe.....................................veekeaeeepleallerYaelrarLielser 142
                                    ++ I++LP++ +                                     +++ ++ +++++++ ++ +e ++ +++++e+
  gi|119719698|ref|YP_920193.1|  30 DRRISTLPDTLQepirasirtsltqlsasleelrasladvldllqrtatSSQVDELQKQITDEFTSLEEKVETIHAIAEQ 109
                                    77888888888867777777777777777777777777777766664442222222222233334444444455555555 PP

                           FTA4 143 rqqlqarlarlrklkallepf 163
                                     q+  + +++  ++   l+++
  gi|119719698|ref|YP_920193.1| 110 IQKISEEIQKIDSILDGLKEI 130
                                    555555555555555555554 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 1.1e-05
                           FTA4  69 airhvaeQidklYlea..............edekleievnedltk................................... 99 
                                     i+ +aeQi+k+  e+                        +dl +                                   
  gi|119719698|ref|YP_920193.1| 102 TIHAIAEQIQKI-SEEiqkidsildglkeiT-------ARTDLIDgkvteystklleaidaarkelgrvnleelnkvves 173
                                    5899*******9.333466655543333330.......444444466666666777788888888888888889899999 PP

                           FTA4 100 ..................eelIkeLPesweveekeaeeepleallerYaelrarLielserrqqlqarlarlrklkalle 161
                                                       +lI++L  s ++ +++a+e  ++   e+Ya+++++ ++ls++ ++l++++++l++ k+lle
  gi|119719698|ref|YP_920193.1| 174 lrgisethtllqdsldniAKLIESLSGSLSSVDETAKELREN--AEKYAKMVEEYTQLSAKAEALTRQIKELEERKQLLE 251
                                    999999999999997777777777777777555555555444..5*********************************** PP

                           FTA4 162 pflgsedpqesvqenlvtrdgeleaElermRvLlarv 198
                                    +     ++ e+ +++l+ r++ +++ le ++  ++++
  gi|119719698|ref|YP_920193.1| 252 EQ---AKKLEEKEKELIEREKSMTTLLENLNKAVSKI 285
                                    **...88999************999999988888776 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       3.6   2.8e+03      68      82 ..      16      30 ..       9      42 .. 0.51
   2 ?    0.9   0.2      0.72   5.6e+02      48      73 ..      50      75 ..      39      91 .. 0.43
   3 ?   11.6   4.2   0.00034      0.27      39      88 ..      82     131 ..      56     137 .. 0.67
   4 ?    7.2   0.7    0.0077         6      43      91 ..     164     212 ..     140     215 .. 0.73
   5 ?   10.2   9.4   0.00095      0.74      37      91 ..     210     264 ..     205     269 .. 0.76
   6 ?    3.7   6.4     0.095        74      22      96 .]     272     348 ..     265     354 .. 0.78
   7 ?   -0.1  11.3       1.5   1.2e+03      33      94 ..     344     406 ..     330     408 .. 0.80
   8 ?    3.2   7.1      0.14   1.1e+02      24      78 ..     361     414 ..     349     426 .. 0.60
   9 ?    9.4   4.9    0.0017       1.3      41      95 ..     472     526 ..     433     527 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 3.6
                        BLOC1_2 68 dqiekqvteLeeavs 82
                                   +++ ++++ + ++++
  gi|119719698|ref|YP_920193.1| 16 EELSEEIKAMMSTID 30
                                   333333333333322 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.72
                        BLOC1_2 48 kkleklnekyeelqpylqqidqiekq 73
                                   ++l +l++  eel+  l  + ++ ++
  gi|119719698|ref|YP_920193.1| 50 TSLTQLSASLEELRASLADVLDLLQR 75
                                   33333333333333333333333222 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.00034
                        BLOC1_2  39 lkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeys 88 
                                    +++  +++++++  l+ek e+++   +qi++i ++++++ ++ + L e++
  gi|119719698|ref|YP_920193.1|  82 VDELQKQITDEFTSLEEKVETIHAIAEQIQKISEEIQKIDSILDGLKEIT 131
                                    44455566666666666666666666666666666666666666665555 PP

  == domain 4  score: 7.2 bits;  conditional E-value: 0.0077
                        BLOC1_2  43 aaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeL 91 
                                    +++l+k +e l+  +e+   + +++d+i k +++L    s +De  keL
  gi|119719698|ref|YP_920193.1| 164 LEELNKVVESLRGISETHTLLQDSLDNIAKLIESLSGSLSSVDETAKEL 212
                                    5667777777777777777777777777777777777777777777777 PP

  == domain 5  score: 10.2 bits;  conditional E-value: 0.00095
                        BLOC1_2  37 kklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeL 91 
                                    k+l+++a++ +k +e++ +++++ + + +qi+++e++ + Lee +++L+e  keL
  gi|119719698|ref|YP_920193.1| 210 KELRENAEKYAKMVEEYTQLSAKAEALTRQIKELEERKQLLEEQAKKLEEKEKEL 264
                                    6777888888888888888888888888888888888888888888888877776 PP

  == domain 6  score: 3.7 bits;  conditional E-value: 0.095
                        BLOC1_2  22 yklLeklNeaase..kykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLEakfk 96 
                                      lLe+lN+a+s+  ++ +l + ++ l++k ++l +k+ el+    +++ +  ++++  e + +L    +eLE+k+k
  gi|119719698|ref|YP_920193.1| 272 TTLLENLNKAVSKipEVGDLVKYIEFLRQKEQELIAKQIELERREAELKSFSSKIASDAEEARKLRIELQELEQKLK 348
                                    56899999988765578888888888888888888888888888888888888888888888888888888887775 PP

  == domain 7  score: -0.1 bits;  conditional E-value: 1.5
                        BLOC1_2  33 sekykklkdvaaslekkl.eklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLEak 94 
                                    ++k kk+++++a  ek l ek ++++ e+ ++ q + q ek+v++ e+  ++L+   k++E+k
  gi|119719698|ref|YP_920193.1| 344 EQKLKKWESELAAREKALlEKAQAMEREILEKTQALVQREKEVAQREAKTEKLEYLLKQIEEK 406
                                    5677788777777766651555556669*****************************999987 PP

  == domain 8  score: 3.2 bits;  conditional E-value: 0.14
                        BLOC1_2  24 lLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLe 78 
                                    lLek  +a+++++ + ++++ + ek++ + ++k e+l+ +l+qi++ e  +++L 
  gi|119719698|ref|YP_920193.1| 361 LLEKA-QAMEREILEKTQALVQREKEVAQREAKTEKLEYLLKQIEEKEGYLRKLR 414
                                    44433.4555666666666666666666666666666666666666666666665 PP

  == domain 9  score: 9.4 bits;  conditional E-value: 0.0017
                        BLOC1_2  41 dvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLEakf 95 
                                    +  + le+   +l++++++l+++l+++ ++e++v++Le+  + L e  ++ E+++
  gi|119719698|ref|YP_920193.1| 472 ELRERLEAREAELKSREKALEEKLKRLAELEARVASLEKENASLKEELRRCEERL 526
                                    5556777778899*************************99888888888888776 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1       1.7   1.3e+03      29      53 ..      16      40 ..      10      70 .. 0.50
   2 ?   13.7   3.1   7.2e-05     0.056      21      88 ..      52     121 ..      44     122 .. 0.80
   3 ?    3.0   0.2      0.16   1.2e+02      28      83 ..     127     180 ..     119     186 .. 0.67
   4 ?    9.0   0.6    0.0021       1.6      25      83 ..     185     246 ..     181     252 .. 0.74
   5 ?    3.5   1.0      0.11        89      34      80 ..     239     288 ..     233     298 .. 0.39
   6 ?    0.5   0.2      0.91   7.1e+02      40      76 ..     367     402 ..     332     415 .. 0.56
   7 ?    0.1   0.1       1.3   9.8e+02      26      49 ..     496     519 ..     481     528 .. 0.63

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.7
                         DUF948 29 deaaatieelekqvdpilkevedll 53
                                   +e+++ i+ +++ +d  +  + d+l
  gi|119719698|ref|YP_920193.1| 16 EELSEEIKAMMSTIDRRISTLPDTL 40
                                   4444444444433333333333333 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 7.2e-05
                         DUF948  21 llklkktldeaaatieelek..qvdpilkevedllakvnelledvneklekvdplteavadlgesvseln 88 
                                    l +l+  l+e++a+++++ +  q ++++ +v++l +++ +    ++ek+e++ ++ e++++++e ++++ 
  gi|119719698|ref|YP_920193.1|  52 LTQLSASLEELRASLADVLDllQRTATSSQVDELQKQITDEFTSLEEKVETIHAIAEQIQKISEEIQKID 121
                                    66778888888888888886224456778888888888888888999*******************9975 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.16
                         DUF948  28 ldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlges 83 
                                    l+e++a+ + +  +v+++++++ ++++ +++ l  v   le++++++e+++ ++e+
  gi|119719698|ref|YP_920193.1| 127 LKEITARTDLIDGKVTEYSTKLLEAIDAARKELGRV--NLEELNKVVESLRGISET 180
                                    455666666666666666666666666666655555..589999999999999987 PP

  == domain 4  score: 9.0 bits;  conditional E-value: 0.0021
                         DUF948  25 kktldeaaatieele...kqvdpilkevedllakvnelledvneklekvdplteavadlges 83 
                                    ++ ld++a+ ie+l    + vd++ ke+++  +k  +++e+ ++ ++k ++lt ++++l e 
  gi|119719698|ref|YP_920193.1| 185 QDSLDNIAKLIESLSgslSSVDETAKELRENAEKYAKMVEEYTQLSAKAEALTRQIKELEER 246
                                    56677777777777766677777777777777777788888888888888888888887765 PP

  == domain 5  score: 3.5 bits;  conditional E-value: 0.11
                         DUF948  34 tieelekqvdpilkevedllakvnelled...vneklekvdplteavadl 80 
                                    +i+ele++ + + +++++l +k +el e    ++  le++++ ++++ ++
  gi|119719698|ref|YP_920193.1| 239 QIKELEERKQLLEEQAKKLEEKEKELIEReksMTTLLENLNKAVSKIPEV 288
                                    33333333333333333333333332222000333444444444444444 PP

  == domain 6  score: 0.5 bits;  conditional E-value: 0.91
                         DUF948  40 kqvdpilkevedllakvnelledvneklekvdpltea 76 
                                       ++il+++++l++  +e +++ + k+ek++ l ++
  gi|119719698|ref|YP_920193.1| 367 AMEREILEKTQALVQREKE-VAQREAKTEKLEYLLKQ 402
                                    3333455555555555555.44445555555555555 PP

  == domain 7  score: 0.1 bits;  conditional E-value: 1.3
                         DUF948  26 ktldeaaatieelekqvdpilkev 49 
                                    k l e++a++++lek+  ++ +e+
  gi|119719698|ref|YP_920193.1| 496 KRLAELEARVASLEKENASLKEEL 519
                                    445566666666666666665555 PP

>> FidL_like  FidL-like putative membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.4   0.00057      0.45      37      76 ..      75     116 ..      66     124 .. 0.85
   2 ?   -1.3   0.0       4.1   3.2e+03      42      53 ..     203     214 ..     187     257 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00057
                      FidL_like  37 sqssissiDetpdvifdkfl..remsdskdslllevkklndn 76 
                                      + +s +De +++i d+f   +e +++ +++  +++k++++
  gi|119719698|ref|YP_920193.1|  75 RTATSSQVDELQKQITDEFTslEEKVETIHAIAEQIQKISEE 116
                                    567899*************7668999**********999876 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 4.1
                      FidL_like  42 ssiDetpdvifd 53 
                                    ss+Det +++ +
  gi|119719698|ref|YP_920193.1| 203 SSVDETAKELRE 214
                                    555555555432 PP

>> Mce4_CUP1  Cholesterol uptake porter CUP1 of Mce4, putative
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.7      0.22   1.7e+02      36      98 ..      51     115 ..      32     136 .. 0.66
   2 ?   11.7   1.0   0.00016      0.13      35     139 ..     150     254 ..     144     294 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.22
                      Mce4_CUP1  36 sltdlnevLdelNprlpqlredireladladv..YadaapdlldaLdnavttsrTiveqqaeLda 98 
                                    slt+l + L+el ++l ++ + +++ a+ ++v   ++   d ++ L++ v t ++i+eq +++++
  gi|119719698|ref|YP_920193.1|  51 SLTQLSASLEELRASLADVLDLLQRTATSSQVdeLQKQITDEFTSLEEKVETIHAIAEQIQKISE 115
                                    55666666666666666666666665555443224555556666666666666666666666554 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00016
                      Mce4_CUP1  35 esltdlnevLdelN.prlpqlredireladladvYadaapdlldaLdnavttsrTiveqqaeLdalllaavglsntgadl 113
                                    e+++++ + L ++N ++l+++ e +r + ++ ++ +d+ +++ + +++++   +++ e ++eL++   + +++ ++ ++ 
  gi|119719698|ref|YP_920193.1| 150 EAIDAARKELGRVNlEELNKVVESLRGISETHTLLQDSLDNIAKLIESLSGSLSSVDETAKELRENAEKYAKMVEEYTQ- 228
                                    678888888999995679999999*****************************************99999999998876. PP

                      Mce4_CUP1 114 lerngdnLirlaadlrptlelLakYs 139
                                    l++  + L+r +++l++  +lL++ +
  gi|119719698|ref|YP_920193.1| 229 LSAKAEALTRQIKELEERKQLLEEQA 254
                                    6888999**************98765 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.4  28.8   3.6e-06    0.0028     266     470 ..      78     285 ..       2     296 .. 0.82
   2 ?   -1.2  22.0      0.75   5.9e+02     331     462 ..     299     433 ..     288     437 .. 0.78
   3 ?    3.3   8.5     0.032        25     286     376 ..     433     524 ..     431     529 .] 0.68

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.6e-06
                         AAA_13 266 paerkaaLeahFddefe...ekqerLekliekveskkselleklkavsdeasensa.feedkeelkaeaealeeqLkglq 341
                                    +++ + +L++ ++def+   ek+e++  ++e++++ +se+++k++++ d  +e  a ++    ++++   +l e++++++
  gi|119719698|ref|YP_920193.1|  78 TSSQVDELQKQITDEFTsleEKVETIHAIAEQIQK-ISEEIQKIDSILDGLKEITArTDLIDGKVTEYSTKLLEAIDAAR 156
                                    55555666666666665111455555555555554.45677888888885444333133346677777788888888888 PP

                         AAA_13 342 ralea.Krkepfksve.lesvkakiesikklvaeineliakhNekvanleeekeeakkklelhlveeleseldeykkkyk 419
                                    ++l +   +e+ k ve l  +++  + +++++++i +li++     ++++e ++e++++ e+   +++ +e++++  k +
  gi|119719698|ref|YP_920193.1| 157 KELGRvNLEELNKVVEsLRGISETHTLLQDSLDNIAKLIESLSGSLSSVDETAKELRENAEK--YAKMVEEYTQLSAKAE 234
                                    888763578888888756777777789**********************************9..567789999999**** PP

                         AAA_13 420 klekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeeinkeLkaf 470
                                    +l+++i++le++++  e+++kklee+ keL ++ ++ +   e++nk ++++
  gi|119719698|ref|YP_920193.1| 235 ALTRQIKELEERKQLLEEQAKKLEEKEKELIEREKSMTTLLENLNKAVSKI 285
                                    **********************************************99876 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.75
                         AAA_13 331 ealeeqLkglqraleaKrkepfk.svelesvkakiesikklvaeineliakhNekvanleeekeeakkklelhlveeles 409
                                    ++ e++L + q +le++  e+ + s ++ s ++++ ++  +++e+++  +k     a  e++  e ++++e+ ++e+ ++
  gi|119719698|ref|YP_920193.1| 299 RQKEQELIAKQIELERREAELKSfSSKIASDAEEARKLRIELQELEQKLKKWESELAAREKALLEKAQAMEREILEKTQA 378
                                    56677777888888888888877666788888888899999999999999999999999999999999999999999988 PP

                         AAA_13 410 eldeykkkykklekaiekle...kelkeeeaelkkleeeikeLekqlrdekpaaee 462
                                     +++  k++++ e++ ekle   k+++e+e  l+kl++ei+e+e+ l++e  +a+e
  gi|119719698|ref|YP_920193.1| 379 LVQRE-KEVAQREAKTEKLEyllKQIEEKEGYLRKLRAEIEEKERILKEELLPAKE 433
                                    88755.57777777777777333566666667899999999999999999887775 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.032
                         AAA_13 286 erLekliekveskkselleklkavsdeasensafeedkeelkaeaealeeqLkglqraleaKrkepfk.svelesvkaki 364
                                    erL k +e++++ +++lle+  +++ +++     e++  el++++ea e++Lk+ ++ale+K k++++ ++ + s++++ 
  gi|119719698|ref|YP_920193.1| 433 ERLLKEQEELAQWEKRLLERERELTGYQRMLASKESALVELRERLEAREAELKSREKALEEKLKRLAElEARVASLEKEN 512
                                    56666667776666677777777777777777777777778888888888888888888888887777666677777777 PP

                         AAA_13 365 esikklvaeine 376
                                     s+k+++ + +e
  gi|119719698|ref|YP_920193.1| 513 ASLKEELRRCEE 524
                                    777766666554 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2  10.1   3.2e-05     0.025     123     280 ..      12     161 ..       7     172 .. 0.82
   2 ?    3.5  14.7     0.057        44     197     283 ..     188     276 ..     165     283 .. 0.72
   3 ?    2.0  18.6      0.16   1.3e+02     196     279 ..     311     394 ..     293     405 .. 0.85
   4 ?    2.5  17.3      0.12        92     195     274 ..     419     498 ..     391     509 .. 0.72
   5 ?    2.9   3.1     0.084        66      12      40 ..     497     525 ..     487     529 .] 0.61

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.2e-05
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       Filament 123 ekkvesLkeelaflkkvheeEvkelqkqvseqvlvevdaarkldLteilkeiraqyeelaeknreeaeewykskleelqe 202
                                     + +e+L ee++ + +  +  +++l  +++e +  ++  ++ + L++ l+e+ra   ++ +  ++ a    +s+++elq+
  gi|119719698|ref|YP_920193.1|  12 GMTIEELSEEIKAMMSTIDRRISTLPDTLQEPIRASIR-TSLTQLSASLEELRASLADVLDLLQRTAT---SSQVDELQK 87 
                                    5789*********************************9.56678****************99999887...68******* PP

                                    XXXXXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Filament 203 aaeknsealrsakeeitelrrqiqsleieleslkkqkasleaqlaeleerleaeleklqeklseleeelaeireemar 280
                                    +++ +  +l++  e i+ +  qiq+ + e++++ +  +     l+e+ +r +    k+ e  ++l e++  +r+e+ r
  gi|119719698|ref|YP_920193.1|  88 QITDEFTSLEEKVETIHAIAEQIQKISEEIQKIDSILD----GLKEITARTDLIDGKVTEYSTKLLEAIDAARKELGR 161
                                    ******************************99876554....555555555555555555555555666666666555 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.057
                                    XXXXXXXXXXXXXXXXX-HHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Filament 197 leelqeaaeknsealrsakeeitelrrqiqs...leieleslkkqkasleaqlaeleerleaeleklqeklseleeelae 273
                                    l+++ + +e+ s +l+s+ e  +elr + ++   +  e  +l +++++l +q++eleer +    +  +kl+e+e+el e
  gi|119719698|ref|YP_920193.1| 188 LDNIAKLIESLSGSLSSVDETAKELRENAEKyakMVEEYTQLSAKAEALTRQIKELEERKQLLE-EQAKKLEEKEKELIE 266
                                    555566666666666666666666665555500055566677889999***********88755.5557899******99 PP

                                    HHHHHHHHHH CS
                       Filament 274 ireemarqlr 283
                                      + m   l+
  gi|119719698|ref|YP_920193.1| 267 REKSMTTLLE 276
                                    9999987766 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.16
                                    XXXXXXXXXXXXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Filament 196 kleelqeaaeknsealrsakeeitelrrqiqsleieleslkkqkasleaqlaeleerleaeleklqeklseleeelaeir 275
                                     le+ + + ++ s+++ s  ee  +lr ++q+le +l++ +++ a+ e++l e  + +e+e+ +  ++l + e+e+a+  
  gi|119719698|ref|YP_920193.1| 311 ELERREAELKSFSSKIASDAEEARKLRIELQELEQKLKKWESELAAREKALLEKAQAMEREILEKTQALVQREKEVAQRE 390
                                    4556666778889999999******************************************9999999999999999876 PP

                                    HHHH CS
                       Filament 276 eema 279
                                    ++++
  gi|119719698|ref|YP_920193.1| 391 AKTE 394
                                    6554 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.12
                                    XXXXXXXXXXXXXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Filament 195 skleelqeaaeknsealrsakeeitelrrqiqsleieleslkkqkasleaqlaeleerleaeleklqeklseleeelaei 274
                                    +k   l+e+    +e l + +ee+++  +++ ++e el  ++ + as e++l el erlea  ++l++  ++lee+l+++
  gi|119719698|ref|YP_920193.1| 419 EKERILKEELLPAKERLLKEQEELAQWEKRLLERERELTGYQRMLASKESALVELRERLEAREAELKSREKALEEKLKRL 498
                                    45555666666777788888888888888888888888888888888888888888888888888888888888888765 PP

  == domain 5  score: 2.9 bits;  conditional E-value: 0.084
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       Filament  12 rlAsYidkVraLEqenkeLeakieeleek 40 
                                    rlA    +V +LE+en++L+ ++++ ee+
  gi|119719698|ref|YP_920193.1| 497 RLAELEARVASLEKENASLKEELRRCEER 525
                                    55555566666666666666666666554 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   4.8    0.0067       5.2      11      80 ..      58     133 ..      48     155 .. 0.60
   2 ?    9.2   0.8    0.0014       1.1       5      60 ..     174     229 ..     170     232 .. 0.81
   3 ?   11.4   7.2   0.00029      0.22       6      67 ..     220     281 ..     216     288 .. 0.92
   4 ?   -1.6   4.0       2.9   2.2e+03      23      39 ..     359     375 ..     308     397 .. 0.43
   5 ?    6.2   2.2     0.011       8.5       6      63 ..     390     448 ..     385     460 .. 0.87
   6 ?    4.4   1.6     0.039        31      37      87 ..     464     514 ..     454     527 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0067
                          Sec34  11 ecdelleqtdealeqLe......eleekfksvsektsslheaceqlleeqkrleelaeeieekLkyFeeldpitrk 80 
                                    +++el +++ ++l++L+      ++ e  k+++++ +sl+e+ e++++  +++++++eei++  ++ + l++it +
  gi|119719698|ref|YP_920193.1|  58 SLEELRASLADVLDLLQrtatssQVDELQKQITDEFTSLEEKVETIHAIAEQIQKISEEIQKIDSILDGLKEITAR 133
                                    3444444444444444300000033344456777788888888888888888888888888777777777777665 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0014
                          Sec34   5 LeskeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleel 60 
                                    L+  +e+ + l +++d++ +++e+l+ + +sv+e  ++l+e++e+  +  +++++l
  gi|119719698|ref|YP_920193.1| 174 LRGISETHTLLQDSLDNIAKLIESLSGSLSSVDETAKELRENAEKYAKMVEEYTQL 229
                                    555566677777889***************************99988777777766 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.00029
                          Sec34   6 eskeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieek 67 
                                     +  ee+++l ++++++ +q++elee+ +  +e+ ++l+e+ ++l+e +k++++l e++++ 
  gi|119719698|ref|YP_920193.1| 220 AKMVEEYTQLSAKAEALTRQIKELEERKQLLEEQAKKLEEKEKELIEREKSMTTLLENLNKA 281
                                    567899***************************************************99986 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 2.9
                          Sec34  23 leqLeeleekfksvsek 39 
                                    + +Le+ +   +++ ek
  gi|119719698|ref|YP_920193.1| 359 KALLEKAQAMEREILEK 375
                                    12233333333444444 PP

  == domain 5  score: 6.2 bits;  conditional E-value: 0.011
                          Sec34   6 eskeeecdelleqtdealeqLeeleekfksvsekt.sslheaceqlleeqkrleelaee 63 
                                    e+k+e+++ ll+q++e +  L++l+ + ++ +    ++l  a e+ll+eq++l +  + 
  gi|119719698|ref|YP_920193.1| 390 EAKTEKLEYLLKQIEEKEGYLRKLRAEIEEKERILkEELLPAKERLLKEQEELAQWEKR 448
                                    678999*********************99999865157999************998766 PP

  == domain 6  score: 4.4 bits;  conditional E-value: 0.039
                          Sec34  37 sektsslheaceqlleeqkrleelaeeieekLkyFeeldpitrkLnspgss 87 
                                    ++k s+l e  e+l + + +l++  +++eekLk  +el+    +L++ ++s
  gi|119719698|ref|YP_920193.1| 464 ASKESALVELRERLEAREAELKSREKALEEKLKRLAELEARVASLEKENAS 514
                                    567788888888888888888888888888888888888888888888877 PP

>> DUF3552  Domain of unknown function (DUF3552)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   6.3       1.2   9.5e+02      94     175 ..      22     101 ..       8     119 .. 0.74
   2 ?   -1.3   5.6       1.5   1.2e+03     101     131 ..      82     112 ..      45     158 .. 0.55
   3 ?   10.2  18.5   0.00047      0.37      70     143 ..     209     285 ..     191     291 .. 0.80
   4 ?    5.0   8.7     0.019        15      87     135 ..     298     346 ..     289     350 .. 0.87
   5 ?   14.3  24.1   2.6e-05      0.02      52     136 ..     425     512 ..     421     527 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.2
                        DUF3552  94 LdrkeeslekkeesleekekelkqkeqsleekeeeleelveeqrqeLerisgLtkeeAkeilleeveeelkheaAkmike 173
                                    ++  +++++++ ++l ++ +e    ++s+++  ++l++ +ee r+ L ++ +L +  A +  ++e++++++ e + +  +
  gi|119719698|ref|YP_920193.1|  22 IKAMMSTIDRRISTLPDTLQE--PIRASIRTSLTQLSASLEELRASLADVLDLLQRTATSSQVDELQKQITDEFTSLEEK 99 
                                    555566666666666666666..667889999999999999999999999999999999999999999999988876555 PP

                        DUF3552 174 ie 175
                                    +e
  gi|119719698|ref|YP_920193.1| 100 VE 101
                                    54 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.5
                        DUF3552 101 lekkeesleekekelkqkeqsleekeeelee 131
                                    +++ +++++++  +l++k +++++  e++++
  gi|119719698|ref|YP_920193.1|  82 VDELQKQITDEFTSLEEKVETIHAIAEQIQK 112
                                    2222222222222222222222222222222 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.00047
                        DUF3552  70 ekelkerrne...lqrlekRllqkeetLdrkeeslekkeesleekekelkqkeqsleekeeeleelveeqrqeLeri 143
                                     kel+e  ++   + +  ++l  k e+L r+ ++le++ + lee+ k+l++ke++l e+e+++++l+e+ ++ + +i
  gi|119719698|ref|YP_920193.1| 209 AKELRENAEKyakMVEEYTQLSAKAEALTRQIKELEERKQLLEEQAKKLEEKEKELIEREKSMTTLLENLNKAVSKI 285
                                    45555544440004445579999******************************************999988888777 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.019
                        DUF3552  87 llqkeetLdrkeeslekkeesleekekelkqkeqsleekeeeleelvee 135
                                    l+qke++L  k+ +le++e++l++  ++++++ ++ ++ + el+el ++
  gi|119719698|ref|YP_920193.1| 298 LRQKEQELIAKQIELERREAELKSFSSKIASDAEEARKLRIELQELEQK 346
                                    8899999999999999999999999999999999999999999998776 PP

  == domain 5  score: 14.3 bits;  conditional E-value: 2.6e-05
                        DUF3552  52 kealleakeeihklree...lekelkerrnelqrlekRllqkeetLdrkeeslekkeesleekekelkqkeqsleekeee 128
                                    ke ll ake + k +ee   +ek l er++el+ +++ l +ke +L +  e le +e++l+++ek l++k ++l e e++
  gi|119719698|ref|YP_920193.1| 425 KEELLPAKERLLKEQEElaqWEKRLLERERELTGYQRMLASKESALVELRERLEAREAELKSREKALEEKLKRLAELEAR 504
                                    77778888877777765222577788888888888888888888888888888888888888888888888888888877 PP

                        DUF3552 129 leelveeq 136
                                    + +l +e+
  gi|119719698|ref|YP_920193.1| 505 VASLEKEN 512
                                    77765554 PP

>> COG2  COG (conserved oligomeric Golgi) complex component, COG2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   4.5    0.0013         1      22     131 ..       9     122 ..       2     131 .. 0.64
   2 ?    3.5   1.2     0.092        71      73     102 ..      88     123 ..      80     161 .. 0.50
   3 ?    0.1   0.6         1   8.1e+02      86      86 ..     153     153 ..     107     197 .. 0.47
   4 ?    3.6  12.0     0.086        67      59     113 ..     197     250 ..     165     285 .. 0.77
   5 ?    1.7   4.1      0.33   2.6e+02      71     130 ..     243     302 ..     241     306 .. 0.79
   6 ?    3.9   8.1     0.069        54      61     131 ..     323     395 ..     316     400 .. 0.79
   7 ?    2.3  11.8      0.22   1.7e+02      63     117 ..     455     509 ..     395     528 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0013
                           COG2  22 lrhgvpLeslrrdLeaylkllekellelvnedyad.FvslSghLvglqeeleevesplaaarkkves..vreklsereee 98 
                                    +++g ++e+l+++++a+++ +++++  l ++  +    s+ ++L+ l ++lee++ +la + + ++   + ++++e +++
  gi|119719698|ref|YP_920193.1|   9 EEKGMTIEELSEEIKAMMSTIDRRISTLPDTLQEPiRASIRTSLTQLSASLEELRASLADVLDLLQRtaTSSQVDELQKQ 88 
                                    67888999999999999999999988776665555666777777777777777777777777666541134566666666 PP

                           COG2  99 veskleeake.leekrellklllkldevveklea 131
                                    ++++    +e +e   ++ + ++k++e ++k+++
  gi|119719698|ref|YP_920193.1|  89 ITDEFTSLEEkVETIHAIAEQIQKISEEIQKIDS 122
                                    6666555443133333666666666666666554 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.092
                           COG2  73 evesplaaarkkvesv......reklsereeevesk 102
                                    +++ +++++ +kve +      ++k+se +++++s 
  gi|119719698|ref|YP_920193.1|  88 QITDEFTSLEEKVETIhaiaeqIQKISEEIQKIDSI 123
                                    333333333333332200000023333333333333 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 1
                           COG2  86 e 86 
                                    +
  gi|119719698|ref|YP_920193.1| 153 D 153
                                    1 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.086
                           COG2  59 slSghLvglqeeleevesplaaarkkvesvreklsereeeveskleeakeleekr 113
                                    slSg+L +++e  +e++ + ++  k ve+ + +ls++ e+++ +++e +e ++  
  gi|119719698|ref|YP_920193.1| 197 SLSGSLSSVDETAKELRENAEKYAKMVEEYT-QLSAKAEALTRQIKELEERKQLL 250
                                    79*****************999999999875.68888888888888777665543 PP

  == domain 5  score: 1.7 bits;  conditional E-value: 0.33
                           COG2  71 leevesplaaarkkvesvreklsereeeveskleeakeleekrellklllkldevvekle 130
                                    lee ++ l++  kk+e+ +++l ere+ ++  le+ +++ +k   + +l+k++e +++ e
  gi|119719698|ref|YP_920193.1| 243 LEERKQLLEEQAKKLEEKEKELIEREKSMTTLLENLNKAVSKIPEVGDLVKYIEFLRQKE 302
                                    556666677888899999999999999999999999999888888888888888887766 PP

  == domain 6  score: 3.9 bits;  conditional E-value: 0.069
                           COG2  61 SghLvglqeeleevesplaaarkkvesvreklsereeev..eskleeakeleekrellklllkldevveklea 131
                                    S++  +  ee ++++ +l+++ +k+++ +++l++re+++  +++  e++ le++++l+++  +++++  k e+
  gi|119719698|ref|YP_920193.1| 323 SSKIASDAEEARKLRIELQELEQKLKKWESELAAREKALleKAQAMEREILEKTQALVQREKEVAQREAKTEK 395
                                    66777778999999*******************9999993344556788889999888888777776666655 PP

  == domain 7  score: 2.3 bits;  conditional E-value: 0.22
                           COG2  63 hLvglqeeleevesplaaarkkvesvreklsereeeveskleeakeleekrellk 117
                                    +L+g+q+ l   es l ++r+++e+ +++l+ re+++e+kl+  +ele+  ++l+
  gi|119719698|ref|YP_920193.1| 455 ELTGYQRMLASKESALVELRERLEAREAELKSREKALEEKLKRLAELEARVASLE 509
                                    6999999999999999999999999999999999999999999999998775543 PP

>> HMMR_N  Hyaluronan mediated motility receptor N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   9.5     0.025        19     190     259 ..      54     126 ..      21     172 .. 0.75
   2 ?    5.9  23.8    0.0098       7.6     207     321 ..     163     282 ..     127     293 .. 0.74
   3 ?    7.7  34.7    0.0028       2.2     167     322 ..     373     527 ..     371     528 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.025
                         HMMR_N 190 klqvtqknLeeskakvaqLkeklvslekekieekset...eklleyieelsnvseqlekykldiaqleellke 259
                                    +l +  ++L++s a v  L ++  ++ +  + +k+ t     l+e +e +++++eq++k +++i+++ ++l+ 
  gi|119719698|ref|YP_920193.1|  54 QLSASLEELRASLADVLDLLQRTATSSQVDELQKQITdefTSLEEKVETIHAIAEQIQKISEEIQKIDSILDG 126
                                    5555566777777888888888877766665566544223789999********************9999985 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0098
                         HMMR_N 207 qLkeklvslekek..ieekseteklleyiee.lsnvseqlekykldiaqleellkekndeiesLkssLeekeqelskqvk 283
                                    +L+e ++ +e ++   e+ +  +  l+ i++ ++++s +l    +  ++l+e++++ ++ +e+  ++L++k+++l +q+k
  gi|119719698|ref|YP_920193.1| 163 NLEELNKVVESLRgiSETHTLLQDSLDNIAKlIESLSGSLSSVDETAKELRENAEKYAKMVEEY-TQLSAKAEALTRQIK 241
                                    5666666666665324444444555555555257778888888999999999999999988875.78************* PP

                         HMMR_N 284 dlnekckllekekeelvreee...ekeqtlsaEleelkekl 321
                                    +l+e+ +lle++ ++l ++e+   e+e+++++ le+l++++
  gi|119719698|ref|YP_920193.1| 242 ELEERKQLLEEQAKKLEEKEKeliEREKSMTTLLENLNKAV 282
                                    **********7766554444412267888888888888776 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0028
                         HMMR_N 167 mklrnkleakekevsvkQedmeaklqvtqknLeeskakvaqLkeklvslekekieekset.eklleyieelsnvseqlek 245
                                    ++  + l  +ekev ++ e  + kl+ + k++ee  + +++L+  + + e+  +ee     e+ll++ eel +  ++l  
  gi|119719698|ref|YP_920193.1| 373 LEKTQALVQREKEV-AQREAKTEKLEYLLKQIEEKEGYLRKLRAEIEEKERILKEELLPAkERLLKEQEELAQWEKRLLE 451
                                    55566677788999.556666779*******************9998888876777665549****************88 PP

                         HMMR_N 246 ykldiaqleellkekndeiesLkssLeekeqelskqvkdlnekckllekekeelvreeeekeqtlsaEleelkeklk 322
                                     + +++ ++ +l++k++ +++L++ Le++e el+ + k l+ek+k l +e+e  v   e+ + +l+ El  ++e+lk
  gi|119719698|ref|YP_920193.1| 452 RERELTGYQRMLASKESALVELRERLEAREAELKSREKALEEKLKRL-AELEARVASLEKENASLKEELRRCEERLK 527
                                    899*******************************************9.5788899999999*************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (529 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3892  (0.217078); expected 358.6 (0.02)
Passed bias filter:                      940  (0.052429); expected 358.6 (0.02)
Passed Vit filter:                       332  (0.0185175); expected 17.9 (0.001)
Passed Fwd filter:                       215  (0.0119917); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 3.97u 0.50s 00:00:04.47 Elapsed: 00:00:00.93
# Mc/sec: 1717.86
//
Query:       gi|119719699|ref|YP_920194.1|  [L=470]
Description: hypothetical protein Tpen_0789 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (470 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 2842.28
//
Query:       gi|119719700|ref|YP_920195.1|  [L=42]
Description: hypothetical protein Tpen_0790 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.28s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 303.27
//
Query:       gi|119719701|ref|YP_920196.1|  [L=598]
Description: glycoside hydrolase family protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-35  120.8   0.8    4.4e-35  119.8   0.8    1.5  1  DUF1925          Domain of unknown function (DUF1925)
    3.5e-31  108.6   0.0    5.9e-31  107.9   0.0    1.4  1  Glyco_hydro_57   Glycosyl hydrolase family 57
      1e-28  100.8   0.0    1.5e-13   51.0   0.0    2.2  2  DUF1926          Domain of unknown function (DUF1926)
    4.5e-06   26.2   0.0    1.8e-05   24.3   0.0    1.8  2  Glyco_hydro_38N  Glycosyl hydrolases family 38 N-terminal dom


Domain annotation for each model (and alignments):
>> DUF1925  Domain of unknown function (DUF1925)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.8   0.8   9.7e-39   4.4e-35       1      79 [.     234     309 ..     234     310 .. 0.98

  Alignments for each domain:
  == domain 1  score: 119.8 bits;  conditional E-value: 9.7e-39
                        DUF1925   1 GiwknFlvkYeesnemhkrmlevskklkklaskkeaeealeallraqandaYWhGlFGGiYlphLRravyenlikaeal 79 
                                    G++ nFl kY+e+n+mhk+ml+v+ kl+ l   k+++ea+e++l+aq+ndaYWhGlFGG+Y+p+LR+av+e+l++ae+l
  gi|119719701|ref|YP_920196.1| 234 GYFPNFLRKYRETNNMHKKMLYVRGKLSLL---KASREAWEEYLKAQCNDAYWHGLFGGVYIPFLRQAVFEHLVRAERL 309
                                    99**************************99...899*****************************************87 PP

>> Glyco_hydro_57  Glycosyl hydrolase family 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.9   0.0   1.3e-34   5.9e-31     100     324 ..       2     220 ..       1     221 [. 0.92

  Alignments for each domain:
  == domain 1  score: 107.9 bits;  conditional E-value: 1.3e-34
                                    HHHHHHHHHHHHHHT.TT-HHHHHHHHHHCTSEEEEEE-TT-B-GGG-S-HHHHHHHHHHHHHHHHHHHSS--SBEE-GG CS
                 Glyco_hydro_57 100 nlaisgplleqiqkwlnkevlelfrelqesgqvElltspyyHpllpllpdsedieaqvkkarelyeeyfgqePrgfwlpE 179
                                    +l++sgpll ++++ l ++ l  +re + + + E+l+ +y++++l+llp  ed   q+kk+rel+ee++g++Prg+w pE
  gi|119719701|ref|YP_920196.1|   2 TLHFSGPLLMYWRE-LYPDFLARLRETVSRSEFEVLGGTYSESVLSLLPW-EDRVLQLKKGRELVEETLGVSPRGLWIPE 79 
                                    79********9965.5**********************************.***************************** PP

                                    G-B--SHHHHHHHTT--EEEE-C------------TTS-EE-TTS...-EEEE--CHH-TTTSGGG-............T CS
                 Glyco_hydro_57 180 lavspeileilaelGfeylftdelaeiledkskespyrpyllkngg..iavffRdreLsddigFryseqypleavddfin 257
                                    ++++p +++++ e+G++y+++d++    ++  k++  r++l++++g  + v+f+d+  ++ ++++        a+ +++ 
  gi|119719701|ref|YP_920196.1|  80 RVWDPTLPPAISEAGYSYVIVDDEVGYRSGLWKDDVHRAVLTEYSGrrVGVLFIDGPVRYILPWK--------APGEVLG 151
                                    ***********************88888888889**********999*****************7........9****** PP

                                    TSB...........-TT---TTT-.-BB-TT-S---HHHHHHHHHHHHHHHHHHHHHHHHHSS-EEEEE CS
                 Glyco_hydro_57 258 wlkkvkka.ksevvtialdgEnwg.hypetgkkeFleklyeeleenglielvtpsefikklkpkglikl 324
                                    ++++++ +  +  v+ + d+E++g  +     +++l++++  l+  + + l+tpse+i ++  +gl +l
  gi|119719701|ref|YP_920196.1| 152 YIRSFATEdGRLYVLWGSDAEKFGeWWDARAAEQWLRTFFGMLKGDSSVALLTPSEYILRHGYQGLAYL 220
                                    *****99988888899********45555555668888888999999*************999988665 PP

>> DUF1926  Domain of unknown function (DUF1926)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3   0.0   2.3e-16     1e-12       1      54 [.     328     383 ..     328     386 .. 0.96
   2 !   51.0   0.0   3.4e-17   1.5e-13      85     280 ..     385     593 ..     382     594 .. 0.83

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 2.3e-16
                        DUF1926   1 DfdlDgreEvlleseklvavlkpaqGGsliElddrk..kefNllntLtRrpEaYHe 54 
                                    Dfd+Dg +Evl+e+++++a++kp+ GGsl+Eld++   ke+Nll+t+ R  E+Y e
  gi|119719701|ref|YP_920196.1| 328 DFDFDGVDEVLIEEKEVNAYVKPSDGGSLFELDVKMpgKEHNLLATMSRYREPYLE 383
                                    9*********************************9778****************65 PP

  == domain 2  score: 51.0 bits;  conditional E-value: 3.4e-17
                        DUF1926  85 kkeLvyDwyerkslvDhfldeeltlesfvqg.elkeegDFanqpyeiekk.kvevvlkrdGgvy.....kkeitlrKeyt 157
                                    +k +v Dwy+r ++ +h+  ++++  ++ ++  + +++DFa ++y +e+   +++vl  +G+ +       +i+l K+y+
  gi|119719701|ref|YP_920196.1| 385 QKSVVPDWYRRVAFREHIWRKDASSADWINNtPFVDVSDFALGNYIVEAVeGNKLVLSFTGRDWsdrrrPARIHLVKTYE 464
                                    68899********************99988747*************88766889999999887778998999******** PP

                        DUF1926 158 leek.seleveyeltneske.iellfavElNlal.lalead.d.rylllndkk..lgeeleleevkefeleDevlkkkle 230
                                    +  + +++ v+y+ +n + + i     vE+ l   l++e+d d  y ++ +++  ++e ++   ++ + +e +    +++
  gi|119719701|ref|YP_920196.1| 465 VLGSqRTVRVRYRWRNMERRfIDPKLSVEVSLFPrLSYEEDsDpTYTVDGSQRlsVREGFSSPWARTVRVESP-AFPTVT 543
                                    987779************************9986244444313145555555555555555555566666666.5889** PP

                        DUF1926 231 lelsepaelwafPveTVSqsekgfelvyQgvavvllwpvdlkekeewklk 280
                                    +e+s+ ae+w  P+ +    ekg    yQg+av   + v l+++e ++++
  gi|119719701|ref|YP_920196.1| 544 VESSRHAEVWVSPILSWYRTEKGLRSEYQGLAVSFNYAVALNPGETFETE 593
                                    ******************************************99998875 PP

>> Glyco_hydro_38N  Glycosyl hydrolases family 38 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0     4e-09   1.8e-05      55     123 ..      12      79 ..       7     101 .. 0.82
   2 ?   -1.4   0.0      0.27   1.2e+03     148     186 ..     268     314 ..     243     381 .. 0.74

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 4e-09
                                    HHHCCS-CCCHHHHHHHHHCTSEEECTT-SS-B-SSSS-HHHHHHHHHCCCHHHHCCH--EESEEEESS CS
                Glyco_hydro_38N  55 rwweeapeekkelvkklvaegrlevvgGgwvenDealpsgeslirqlleGqrflkeefgvrpkvaWliD 123
                                     w e +p+  ++l ++ v    +ev gG++ e+  +l  +e+ + ql +G + ++e++gv+p+ +W + 
  gi|119719701|ref|YP_920196.1|  12 YWRELYPDFLARL-RETVSRSEFEVLGGTYSESVLSLLPWEDRVLQLKKGRELVEETLGVSPRGLWIPE 79 
                                    4555577777777.****************************************************986 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.27
                                    S-HHCHCCHHHTT-SCEEEE-TTS........TEEEEEE--TT.SS...H CS
                Glyco_hydro_38N 148 lsyndknkfaeqkhlefiWrgsdg........teilthmlpadsyd...p 186
                                      +++     +++++  +W+g  g        + ++ h++ a+  +   +
  gi|119719701|ref|YP_920196.1| 268 EAWEE---YLKAQCNDAYWHGLFGgvyipflrQAVFEHLVRAERLAeeeS 314
                                    34444...445599999999999989998888888888888765555541 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (598 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 3972.60
//
Query:       gi|119719702|ref|YP_920197.1|  [L=553]
Description: starch synthase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-27   97.0   0.0    2.3e-27   96.3   0.0    1.3  1  Glyco_transf_5   Starch synthase catalytic domain
    5.9e-24   84.5   0.0      1e-23   83.7   0.0    1.3  1  Glycos_transf_1  Glycosyl transferases group 1
    9.7e-20   71.4   0.0      2e-19   70.4   0.0    1.5  1  Glyco_trans_1_4  Glycosyl transferases group 1
    2.4e-05   24.4   3.2    0.00022   21.3   1.9    3.0  2  Glyco_transf_4   Glycosyltransferase Family 4
     0.0022   18.4   6.3     0.0026   18.2   4.1    2.3  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain
     0.0084   16.5   0.0      0.027   14.9   0.0    1.8  2  Glyco_trans_1_2  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glyco_transf_5  Starch synthase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.3   0.0   7.7e-31   2.3e-27       2     228 ..       7     227 ..       6     240 .. 0.80

  Alignments for each domain:
  == domain 1  score: 96.3 bits;  conditional E-value: 7.7e-31
                 Glyco_transf_5   2 ilfvasEvaplaktGGLadvvgaLpkaLaklghdvrvilPrygaikeekkeleevaelskaaedevevevekvkvaklkk 81 
                                    +l+va E++p++k+GGLa+v + L+k+L +lg +  + lP++    ++    e va++   ++        +v v +++ 
  gi|119719702|ref|YP_920197.1|   7 VLMVAFEATPFVKVGGLAEVPSNLAKELVALGWRAYLALPSHAPPGRR--GEEPVARFATPLG--------EVFVGRASW 76 
                                    9*****************************************555554..4588888754443........355667777 PP

                 Glyco_transf_5  82 dgvdvyfldnpeffdreglYgdkgedyednaerfalfsraalellekl.gwk...pdvihahDWhtalvpallkelyker 157
                                     gv++++++  ++ d e++Y+      e  ++++ lfs +   ll +  +++   pdvih hDWh++ + + +k+  ++ 
  gi|119719702|ref|YP_920197.1|  77 GGVTYLLFSGSALSD-ERVYAG-----EVMDQKVKLFSYGLSLLLLNAeKYGvvfPDVIHFHDWHSVYALVKVKHDFQQ- 149
                                    8***********885.57**65.....5556666666666666665543333346**************9999998654. PP

                 Glyco_transf_5 158 glfkkiktvftiHNlayqgrfpkdelaalglpaedfekldglefyg..............kvnflkagivyadavttVSp 223
                                       +k++t+f++H l  +++++++ +++lg+p  +    ++++ +g                   k g ++ad+++tVS+
  gi|119719702|ref|YP_920197.1| 150 ---RKARTLFHVH-LLVKKHVDPSIFEQLGVPLGW---RHEVRVNGrsmdltlgdvlrvsGGIAEKIGALEADRLVTVSE 222
                                    ...56********.99999*************643...4678888888999999999997777888************** PP

                 Glyco_transf_5 224 tyakE 228
                                    +y  +
  gi|119719702|ref|YP_920197.1| 223 SYLLD 227
                                    **765 PP

>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.7   0.0   3.4e-27     1e-23      15     157 ..     331     481 ..     323     488 .. 0.88

  Alignments for each domain:
  == domain 1  score: 83.7 bits;  conditional E-value: 3.4e-27
                                    -EEEEEESS-TTTTTHHHHHHHHHCCCCC....HCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHH CS
                Glycos_transf_1  15 kkiilsvgrlekeKgvdllikafallkkq....lnpnvklviaGngeeekelkklaeelelsdnviflgevsredleell 90 
                                     +++++ grl ++Kg+dl+++a++++ ++    +   ++l + G++++ ++l +l  ++e  +nv+ ++ v ++  +  +
  gi|119719702|ref|YP_920197.1| 331 GPLAITTGRLARQKGFDLMVEAVPRVLRElgeaKFVFLVLPVWGGEDYVYQLADL--QREYPENVRAVFGVAPSIYKLAH 408
                                    5788999*******************99965444555555567877777777777..999999*********88777778 PP

                                    HCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTT......SEEEE-TT-HHHHHHHHHHHHH CS
                Glycos_transf_1  91 knadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdge......tGllvkpnnaealaeairklle 157
                                     ++d+f++ps++E+fGi +lEAm+ g p +as +gg++e+v d        tG+lv p ++ +laea+r+ll 
  gi|119719702|ref|YP_920197.1| 409 LASDVFFAPSRWEPFGIMALEAMSTGNPLVASRTGGLKEIVLDVNvyaergTGILVRPDDPYELAEALRDLLA 481
                                    88*****************************************999************************996 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.4   0.0   6.6e-23     2e-19       3     132 ..     333     480 ..     331     481 .. 0.79

  Alignments for each domain:
  == domain 1  score: 70.4 bits;  conditional E-value: 6.6e-23
                                    EEEEES---GG.GTHHHHHHHHHHHH.H..H.....EEEEEES---...HHHHHHHTT-T.TEEEE---.THHHHHHH.H CS
                Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkk..d.....vrlvivGdgp.rpeeleelaagleerveftGfv.edlaella.a 72 
                                      +++Grl +++kg+dl++eavp+++++  +     + l + G+++    +l +l +++ e+v+ +  v +++ +l + a
  gi|119719702|ref|YP_920197.1| 333 LAITTGRL-ARQKGFDLMVEAVPRVLRElgEakfvfLVLPVWGGEDyV-YQLADLQREYPENVRAVFGVaPSIYKLAHlA 410
                                    56889***.677**************6665345666678889944432.4565444566789998888867777775525 PP

                                    -SEEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--...T.....TSSEE--TT-HHHHHHHHHHHH CS
                Glyco_trans_1_4  73 advfvaPs..egfglkllEamaaglpvVatdvggiaevv...g.....engllvppgdpealaeailrLl 132
                                    +dvf aPs  e fg+ +lEam+ g p Va+++gg++e+v   +      +g+lv p+dp +laea+ +Ll
  gi|119719702|ref|YP_920197.1| 411 SDVFFAPSrwEPFGIMALEAMSTGNPLVASRTGGLKEIVldvNvyaerGTGILVRPDDPYELAEALRDLL 480
                                    6*******999**************************99966233333478****************998 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   1.9   7.4e-08   0.00022       1     165 [.      20     247 ..      20     249 .. 0.74
   2 ?   -3.0   0.0         2   6.1e+03     126     143 ..     403     420 ..     399     421 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 7.4e-08
                 Glyco_transf_4   1 vGGverhvleLaraLarrGheVtvv..tpgddgpleeev..............................elvvrvprvpl 48 
                                    vGG + +  +La++L ++G++ ++   +++++g+ +ee+                                  rv +   
  gi|119719702|ref|YP_920197.1|  20 VGGLAEVPSNLAKELVALGWRAYLAlpSHAPPGRRGEEPvarfatplgevfvgraswggvtyllfsgsaLSDERVYAGEV 99 
                                    69999999*****************6666666666666699*******99999999999999999888733334444444 PP

                 Glyco_transf_4  49 pllkrllrslaflrrlrrllkre..kpDvvHahspaalgaallalrr...rlgiplVltvHglye............... 108
                                       k  l+s+  ++ l ++ k +   pDv+H h+++++ +al++ ++   ++++++ ++vH l                 
  gi|119719702|ref|YP_920197.1| 100 MDQKVKLFSYGLSLLLLNAEKYGvvFPDVIHFHDWHSV-YALVKVKHdfqQRKARTLFHVHLLVKkhvdpsifeqlgvpl 178
                                    55666666666666666666666889***********7.777788888****************9999999999988888 PP

                 Glyco_transf_4 109 ..........krllkarlkplsrllralerrllrradrviavSe.atadelreryg..vppekitVipnG 165
                                              ++        l+      e+  +  adr+++vSe ++ d+++   g  ++  k +Vi+n+
  gi|119719702|ref|YP_920197.1| 179 gwrhevrvngRSMDLTLGDVLRVSGGIAEKIGALEADRLVTVSEsYLLDDVLPFVGgeFR-GKSRVIYNA 247
                                    877766666433333333344455555566669999999999984577777776665544.677777775 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2
                 Glyco_transf_4 126 lerrllrradrviavSea 143
                                    +++ ++ ++d ++a+S++
  gi|119719702|ref|YP_920197.1| 403 IYKLAHLASDVFFAPSRW 420
                                    567788899*******97 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   4.1   8.8e-07    0.0026       1     138 [.      21     222 ..      21     225 .. 0.60
   2 ?   -1.9   0.0       1.4   4.1e+03       2      13 ..     374     385 ..     336     440 .. 0.61

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 8.8e-07
                Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvltpapapgapeleedgvrvh.rlp...vprrps.pladlaal............... 60 
                                    gG + +  +la++L+a+G++  +  p+ ap+ ++ ee+ +r   +l    v+r+++ +++ l ++               
  gi|119719702|ref|YP_920197.1|  21 GGLAEVPSNLAKELVALGWRAYLALPSHAPPGRRGEEPVARFAtPLGevfVGRASWgGVTYLLFSgsalsdervyagevm 100
                                    788888899****************9999998876665555422333444667764355555555555566655666666 PP

                Glyco_trans_4_4  61 ........ralrrll....rqrrerpdvvhahsptaglaarlar...rrrgiplvvtlh..................... 104
                                             +l  ll    +     pdv+h h++++ +a +  +   ++r+++ ++++h                     
  gi|119719702|ref|YP_920197.1| 101 dqkvklfsYGLSLLLlnaeKYGVVFPDVIHFHDWHSVYALVKVKhdfQQRKARTLFHVHllvkkhvdpsifeqlgvplgw 180
                                    65555544333333454433457779********9776665443223899*********888887777777766555433 PP

                Glyco_trans_4_4 105 ...glllrrg.........sgavrrlyral....errllrradavlvvse 138
                                             +          g v r+        e+  +  ad++++vse
  gi|119719702|ref|YP_920197.1| 181 rheV-----RvngrsmdltLGDVLRV---SggiaEKIGALEADRLVTVSE 222
                                    2210.....12111221112222222...133347777888888888887 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.4
                Glyco_trans_4_4   2 Gigryvaelara 13 
                                    G++ yv++la  
  gi|119719702|ref|YP_920197.1| 374 GGEDYVYQLADL 385
                                    333333333333 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0     9e-06     0.027       2      61 ..     414     481 ..     413     511 .. 0.85
   2 ?   -2.1   0.0       1.8   5.5e+03      63      88 ..     511     536 ..     493     538 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 9e-06
                Glyco_trans_1_2   2 vLnpsrsespnlrlfEaaacGafaltddaegleelftpgk......evilfe..dleelaekirylla 61 
                                    +++psr e +    +Ea+  G +++++++ gl e++ + +      ++il++  d+ elae++r lla
  gi|119719702|ref|YP_920197.1| 414 FFAPSRWEPFGIMALEAMSTGNPLVASRTGGLKEIVLDVNvyaergTGILVRpdDPYELAEALRDLLA 481
                                    677999999999*****************999998888778888889999999************998 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.8
                Glyco_trans_1_2  63 peerraiaeaarervlaehtydhrae 88 
                                    p+  + ++++   rv+++++++  a+
  gi|119719702|ref|YP_920197.1| 511 PDAGEILRKNCVDRVEKHFSWAASAR 536
                                    44445566777788999999987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (553 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.70u 0.34s 00:00:01.04 Elapsed: 00:00:00.55
# Mc/sec: 3016.69
//
Query:       gi|119719703|ref|YP_920198.1|  [L=143]
Description: hypothetical protein Tpen_0793 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00034   20.3   0.9    0.00056   19.6   0.1    1.8  2  HTH_38        Helix-turn-helix domain
    0.00036   20.2   0.0    0.00082   19.1   0.0    1.6  1  HTH_23        Homeodomain-like domain
     0.0016   18.8   0.3     0.0036   17.7   0.3    1.7  1  HTH_40        Helix-turn-helix domain
      0.002   17.8   0.1       0.01   15.5   0.0    2.0  2  Sigma70_r4_2  Sigma-70, region 4
     0.0062   16.4   0.0      0.014   15.3   0.0    1.5  1  Terminase_5   Putative ATPase subunit of terminase (gpP-like)
     0.0076   16.2   0.0      0.011   15.7   0.0    1.2  1  SIKE          SIKE family
     0.0086   16.4   0.6       0.02   15.3   0.3    1.7  2  FlaC_arch     Flagella accessory protein C (FlaC)
     0.0096   15.5   0.0      0.023   14.3   0.0    1.6  1  GerE          Bacterial regulatory proteins, luxR family
  ------ inclusion threshold ------
       0.01   15.5   0.0      0.018   14.7   0.0    1.4  1  HTH_DeoR      DeoR-like helix-turn-helix domain
      0.013   15.5   0.6      0.023   14.7   0.0    1.7  2  HTH_11        HTH domain
      0.059   13.2   1.1        0.1   12.4   0.0    1.9  3  HTH_IclR      IclR helix-turn-helix domain
      0.074   13.1   0.1       0.17   12.0   0.1    1.6  1  COG2          COG (conserved oligomeric Golgi) complex compon
       0.09   13.1   2.4       0.22   11.9   0.1    2.5  3  HTH_31        Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   4.1e-07   0.00056      18      41 ..      58      81 ..      40      83 .. 0.82
   2 ?   -2.2   0.1       2.7   3.7e+03      11      21 ..     113     123 ..     113     127 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 4.1e-07
                         HTH_38 18 aeGlslreIArrLgrspsTIsREl 41
                                    +G+ + +IA +Lgr   TI ++l
  gi|119719703|ref|YP_920198.1| 58 RAGYPVTKIAEELGRTEATIRNHL 81
                                   389******************998 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.7
                         HTH_38  11 eeIerllaeGl 21 
                                    ee+erl+ e++
  gi|119719703|ref|YP_920198.1| 113 EELERLRRENE 123
                                    67889988876 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0     6e-07   0.00082      13      38 ..      54      81 ..      48      87 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 6e-07
                         HTH_23 13 llae..GlsvreIAreLgvsrrTvyrwl 38
                                   l++e  G++v++IA+eLg+++ T+++ l
  gi|119719703|ref|YP_920198.1| 54 LAREraGYPVTKIAEELGRTEATIRNHL 81
                                   344457******************9855 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.3   2.6e-06    0.0036      10      42 ..      58      90 ..      53     141 .. 0.65

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.6e-06
                         HTH_40 10 eeglsieeIAkerglkesTIegHLaelieegee 42
                                   + g+ + +IA+e g +e+TI +HL    e+g+ 
  gi|119719703|ref|YP_920198.1| 58 RAGYPVTKIAEELGRTEATIRNHLQGKTEAGKI 90
                                   579999******************999999852 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   7.4e-06      0.01      25      48 ..      59      82 ..      54      82 .. 0.88
   2 ?   -0.5   0.0      0.75     1e+03      34      48 ..     123     137 ..     123     142 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 7.4e-06
                                   S---HHHHHHHHT--HHHHHHHHH CS
                   Sigma70_r4_2 25 eglsykEIAellgisegtVksrls 48
                                    g++   IAe+lg +e+t++++l+
  gi|119719703|ref|YP_920198.1| 59 AGYPVTKIAEELGRTEATIRNHLQ 82
                                   6899999***************97 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.75
                                    HHHT--HHHHHHHHH CS
                   Sigma70_r4_2  34 ellgisegtVksrls 48 
                                    e+l+ +  +Vks+l+
  gi|119719703|ref|YP_920198.1| 123 EELKKKLESVKSALQ 137
                                    578888889999886 PP

>> Terminase_5  Putative ATPase subunit of terminase (gpP-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   9.8e-06     0.014      13      33 ..      60      80 ..      59      89 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 9.8e-06
                    Terminase_5 13 GyrvaeIAeelglkeatVysW 33
                                   Gy+v++IAeelg+ eat+ + 
  gi|119719703|ref|YP_920198.1| 60 GYPVTKIAEELGRTEATIRNH 80
                                   9*****************876 PP

>> SIKE  SIKE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   7.9e-06     0.011      25     101 ..      67     141 ..      61     142 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 7.9e-06
                           SIKE  25 AdsLleqaqalnkkiesmkqyqeevkeln.eiakekprseLiagiqqenrqireLqqENreLrasleehqsaLelIms 101
                                    A++L ++  ++ ++++ ++++ + v+e     +k++++ eL++      ++++ L +EN+eL+  le  +saL+ ++s
  gi|119719703|ref|YP_920198.1|  67 AEELGRTEATIRNHLQGKTEAGKIVRETYeAFVKSGGKVELVL---PGGEELERLRRENEELKKKLESVKSALQSLLS 141
                                    6666666666666666666666666665513445667788854...456679999******************98775 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       4.2   5.8e+03       4      17 ..      65      78 ..      63      89 .. 0.68
   2 !   15.3   0.3   1.4e-05      0.02      15      42 ..     114     141 ..     104     141 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 4.2
                      FlaC_arch  4 elEnklsklstele 17
                                   ++ ++l++++ ++ 
  gi|119719703|ref|YP_920198.1| 65 KIAEELGRTEATIR 78
                                   56667777776664 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 1.4e-05
                      FlaC_arch  15 eletvkkeneelsksveelkenVkdlls 42 
                                    ele +++eneel+k++e +k   + lls
  gi|119719703|ref|YP_920198.1| 114 ELERLRRENEELKKKLESVKSALQSLLS 141
                                    8999******************999986 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   1.6e-05     0.023      16      38 ..      59      81 ..      54      83 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.6e-05
                                   TTS-HHHHHHHHTS-HHHHHHHH CS
                           GerE 16 eGksnkeIAeelniSekTVkvhk 38
                                   +G+ +++IAeel+  e T+++h+
  gi|119719703|ref|YP_920198.1| 59 AGYPVTKIAEELGRTEATIRNHL 81
                                   6999******************8 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.3e-05     0.018      17      46 ..      63      92 ..      54      95 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.3e-05
                       HTH_DeoR 17 veelvellgvSeaTiRRDLneLeeqglltR 46
                                   v++++e+lg +eaTiR+ L+  +e+g+++R
  gi|119719703|ref|YP_920198.1| 63 VTKIAEELGRTEATIRNHLQGKTEAGKIVR 92
                                   889************************998 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.6e-05     0.023      17      37 ..      62      82 ..      53      93 .. 0.85
   2 ?   -3.3   0.1       6.5   8.9e+03      19      25 ..     123     129 ..     115     130 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.6e-05
                         HTH_11 17 sgeeLAeeLnvSrrtvrrdIk 37
                                   +  ++AeeL+++++t+r++++
  gi|119719703|ref|YP_920198.1| 62 PVTKIAEELGRTEATIRNHLQ 82
                                   5679***************97 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 6.5
                         HTH_11  19 eeLAeeL 25 
                                    eeL+++L
  gi|119719703|ref|YP_920198.1| 123 EELKKKL 129
                                    4666665 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       5.7   7.9e+03      39      49 ..      22      32 ..      21      33 .. 0.65
   2 ?   12.4   0.0   7.4e-05       0.1      11      40 ..      53      82 ..      52      90 .. 0.95
   3 ?   -2.0   0.1       2.4   3.3e+03      23      41 ..     124     142 ..     115     143 .] 0.49

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 5.7
                                   HHHHHHTTSEE CS
                       HTH_IclR 39 LqtLvelGyve 49
                                   L tL++   +e
  gi|119719703|ref|YP_920198.1| 22 LGTLMRSDVLE 32
                                   77888766665 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 7.4e-05
                                   T-CTTBSS-BHHHHHHHHTS-HHHHHHHHH CS
                       HTH_IclR 11 alaeapqeltlselArrtglpkStvhRlLq 40
                                   ala+++ +  ++ +A+++g + +t +++Lq
  gi|119719703|ref|YP_920198.1| 53 ALARERAGYPVTKIAEELGRTEATIRNHLQ 82
                                   89*************************998 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 2.4
                                    HHHHHHTS-HHHHHHHHHH CS
                       HTH_IclR  23 elArrtglpkStvhRlLqt 41 
                                    el +++   kS+   lL++
  gi|119719703|ref|YP_920198.1| 124 ELKKKLESVKSALQSLLSS 142
                                    4444444445555556655 PP

>> COG2  COG (conserved oligomeric Golgi) complex component, COG2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00012      0.17      27      96 ..      62     140 ..      54     143 .] 0.70

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00012
                           COG2  27 pLeslrrdLeaylkllekell......elvnedyadFvslSgh..Lv.glqeeleevesplaaarkkvesvreklsere 96 
                                    p+ ++ ++L   ++ ++++l       ++v+e y+ Fv+ +g+  Lv    eele+++ + ++++kk+esv+++l+   
  gi|119719703|ref|YP_920198.1|  62 PVTKIAEELGRTEATIRNHLQgkteagKIVRETYEAFVKSGGKveLVlPGGEELERLRRENEELKKKLESVKSALQSLL 140
                                    5555666665555555555532222227999********99973433345689*********************99765 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       1.6   2.2e+03      17      34 ..      27      44 ..      23      45 .. 0.85
   2 ?   11.9   0.1   0.00016      0.22       9      39 ..      55      85 ..      53      98 .. 0.92
   3 ?   -0.9   0.1       1.6   2.1e+03       3      12 ..     112     121 ..     112     128 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.6
                         HTH_31 17 qeevAerlgvsestlsrl 34
                                   + +v e +++ e+++++l
  gi|119719703|ref|YP_920198.1| 27 RSDVLEKIRIAEDKITWL 44
                                   678889999999**9997 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00016
                         HTH_31  9 lReraGLsqeevAerlgvsestlsrlEqGrr 39
                                   +ReraG   +  Ae lg +e+t++   qG+ 
  gi|119719703|ref|YP_920198.1| 55 ARERAGYPVTKIAEELGRTEATIRNHLQGKT 85
                                   7***********************9999976 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1.6
                         HTH_31   3 GalLralRer 12 
                                    G++L +lR++
  gi|119719703|ref|YP_920198.1| 112 GEELERLRRE 121
                                    7888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1211  (0.0675442); expected 358.6 (0.02)
Passed bias filter:                      932  (0.0519828); expected 358.6 (0.02)
Passed Vit filter:                       172  (0.0095934); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.64u 0.39s 00:00:01.03 Elapsed: 00:00:00.56
# Mc/sec: 774.54
//
Query:       gi|119719704|ref|YP_920199.1|  [L=250]
Description: hypothetical protein Tpen_0794 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-87  291.3   0.0    4.8e-87  291.1   0.0    1.0  1  ATPase    KaiC
    1.3e-06   27.3   0.0    2.5e-06   26.4   0.0    1.3  1  GvpD      GvpD gas vesicle protein
    7.1e-05   22.5   0.0    0.00012   21.8   0.0    1.4  1  AAA_25    AAA domain
     0.0013   18.1   0.3     0.0053   16.0   0.0    1.9  2  Rad51     Rad51
     0.0036   17.2   0.0     0.0066   16.3   0.0    1.5  1  MEDS      MEDS: MEthanogen/methylotroph, DcmR Sensory domain
  ------ inclusion threshold ------
      0.014   14.7   0.0      0.018   14.3   0.0    1.3  1  DnaB_C    DnaB-like helicase C terminal domain
      0.015   14.4   0.0      0.031   13.4   0.0    1.5  1  T2SSE     Type II/IV secretion system protein
      0.023   14.4   0.0      0.053   13.2   0.0    1.5  1  AAA_24    AAA domain
      0.044   14.1   0.0      0.097   13.0   0.0    1.5  1  AAA_19    AAA domain
      0.075   11.9   0.0       0.12   11.2   0.0    1.2  1  PPV_E1_C  Papillomavirus helicase
       0.13   12.6   0.1       0.23   11.8   0.1    1.5  1  AAA_16    AAA ATPase domain
       0.18   11.3   0.0       0.36   10.3   0.0    1.4  1  AAA_7     P-loop containing dynein motor region
       0.18   11.0   0.1       0.23   10.7   0.1    1.3  1  DUF2075   Uncharacterized conserved protein (DUF2075)


Domain annotation for each model (and alignments):
>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  291.1   0.0   3.5e-90   4.8e-87       1     230 [.       7     239 ..       7     240 .. 0.99

  Alignments for each domain:
  == domain 1  score: 291.1 bits;  conditional E-value: 3.5e-90
                         ATPase   1 vktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekleee 80 
                                    vktgI+g+De+l+gGip++++vl++G+pGtGKtif++q+l+ g+++ +epgv+v++ee+++++r+n++s+Gwd++k+ee+
  gi|119719704|ref|YP_920199.1|   7 VKTGIPGFDELLYGGIPKRNIVLLSGGPGTGKTIFSQQYLFYGLQN-NEPGVLVALEEHPVQIRRNMASFGWDVRKYEES 85 
                                    79*****************************************999.********************************* PP

                         ATPase  81 gklaiidasesaeesaee......kdkedleelieelaeaikeikakrvviDsitglayeekeavaReilrqlvrvlkkl 154
                                    g++ai+da++ ++++a++      ++ +d+ el++ ++ ai+++ka+r viDs+++l y +k+a+aR+il+ql+rvl++l
  gi|119719704|ref|YP_920199.1|  86 GQFAIVDAFTGGIGEAAKreryvvTSVDDVGELVDVVKAAIRDVKAERAVIDSVSTL-YMTKPAMARSILMQLKRVLSGL 164
                                    **************9999999999999******************************.********************** PP

                         ATPase 155 gvTailvsekssseeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIteegikvleek 230
                                    g T+i+vs++s++e+++gg+gve+ ++dg+++Ldl+e+++elvR+l+++kmRgtkh++k+ pfeIt++gi+v+++k
  gi|119719704|ref|YP_920199.1| 165 GATSIFVSQVSVTERGFGGPGVEH-AADGIVRLDLDEVNGELVRSLIVWKMRGTKHDMKRRPFEITDKGIVVYPDK 239
                                    ************************.************************************************986 PP

>> GvpD  GvpD gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0   1.8e-09   2.5e-06      13     207 ..      28     230 ..      22     241 .. 0.74

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 1.8e-09
                           GvpD  13 llikGaPGtGktlftlrgl.dvlrresdvlyvstrvddetvseay......fsgeaeldktalldllkdpleldldvdvP 85 
                                    +l+ G PGtGkt+f  ++l   l+++++ + v+       +          +    e  + a++d +  +++   +++  
  gi|119719704|ref|YP_920199.1|  28 VLLSGGPGTGKTIFSQQYLfYGLQNNEPGVLVALEEHPVQIRRNMasfgwdVRKYEESGQFAIVDAFTGGIGEAAKRERY 107
                                    6889*************98357999999999998888888876555777777777777799**********998888766 PP

                           GvpD  86 iekldlesllefvdeiaaiatkliialdswelvyeylaerydsPed.iktvkndlvvl.....aresgvrlvlvletaan 159
                                    +    ++ + e vd + ++a + + a    + v++ +++ y + +   + +  +l  +     a    v  v+v+e    
  gi|119719704|ref|YP_920199.1| 108 V-VTSVDDVGELVD-VVKAAIRDVKAE---RAVIDSVSTLYMTKPAmARSILMQLKRVlsglgATSIFVSQVSVTERGFG 182
                                    6.667888888888.444555555543...34777777766554443344444444430000144445666777776544 PP

                           GvpD 160 .srleyivdGvvtlnvkeddrgrlrrdlrleklrGvrignrlqPftlad 207
                                       +e+ +dG+v l++ e   g l+r+l + k+rG + + + +Pf ++d
  gi|119719704|ref|YP_920199.1| 183 gPGVEHAADGIVRLDLDEV-NGELVRSLIVWKMRGTKHDMKRRPFEITD 230
                                    1459************987.9************************9987 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   8.5e-08   0.00012      14     189 ..       6     174 ..       2     179 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 8.5e-08
                         AAA_25  14 dlaapppprrwlvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlrav 93 
                                    ++++ +p  + l+ g +p+  ++ll G pgtGKt +  +  +  ++             + ++v++E+   ++rr ++  
  gi|119719704|ref|YP_920199.1|   6 KVKTGIPGFDELLYGGIPKRNIVLLSGGPGTGKTIFSQQYLFYGLQNN----------EPGVLVALEEHPVQIRRNMASF 75 
                                    56677888889999999************************9999866..........2679999999999********9 PP

                         AAA_25  94 geal......................rddarllvldlagveslpLfakdrggtlltadvdaleaaieevegvrlvviDpl 151
                                    g ++                      + ++r  v+++++v                + vd + aai++v+ ++  viD++
  gi|119719704|ref|YP_920199.1|  76 GWDVrkyeesgqfaivdaftggigeaAKRERYVVTSVDDV---------------GELVDVVKAAIRDVK-AERAVIDSV 139
                                    9666666666666666666666666444444444444444...............344445566666654.667788888 PP

                         AAA_25 152 sralggdensnsdvgalvealeriarrtgaavllvhHv 189
                                    s ++   +     +++++ +l+r+   +ga+ ++v +v
  gi|119719704|ref|YP_920199.1| 140 STLYMTKPA---MARSILMQLKRVLSGLGATSIFVSQV 174
                                    887765444...33555555555555566666666555 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   3.9e-06    0.0053      17      56 ..       5      44 ..       1      51 [. 0.91
   2 ?   -0.3   0.0      0.38   5.2e+02     115     148 ..     113     146 ..     100     177 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.9e-06
                                   -EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHH CS
                          Rad51 17 lqlttGskklDelLgGGietgsiteifGefrsGktqlcht 56
                                    ++ tG   +DelL GGi+  +i  + G  ++Gkt ++++
  gi|119719704|ref|YP_920199.1|  5 EKVKTGIPGFDELLYGGIPKRNIVLLSGGPGTGKTIFSQQ 44
                                   5789*******************************99876 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.38
                                    THHHHHHHHTHHHHHHS-EEEEEEETTTGGGCH- CS
                          Rad51 115 ehqeellqqaaallaedkfallivDsvtalyRtd 148
                                    ++  el++ + a + + k    ++Dsv +ly t 
  gi|119719704|ref|YP_920199.1| 113 DDVGELVDVVKAAIRDVKAERAVIDSVSTLYMTK 146
                                    5666777777788888888888999999999765 PP

>> MEDS  MEDS: MEthanogen/methylotroph, DcmR Sensory domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   4.8e-06    0.0066      20      68 ..      45      93 ..      42     133 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.8e-06
                           MEDS 20 fikaglargekvlyvasastldelrealrkagldvdaalesgqleilda 68
                                   ++  gl+++e+ ++va +++  ++r+ +++ g dv +++esgq+ i+da
  gi|119719704|ref|YP_920199.1| 45 YLFYGLQNNEPGVLVALEEHPVQIRRNMASFGWDVRKYEESGQFAIVDA 93
                                   7778******99999999****************************996 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.3e-05     0.018       2      85 ..       7      89 ..       6     178 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.3e-05
                                   BXSSTHHHHHHC.TSBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHHHHHHHHHHTXXHHHHHHT CS
                                   xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         DnaB_C  2 lstgfkdLDklt.sGlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeqlvqRllsseaeidskklrtg 82
                                   ++tg   +D+l+ +G+ k +++++ + p++Gkt +  +      + ++ p +++ le +  q+ + + s   ++++ + ++g
  gi|119719704|ref|YP_920199.1|  7 VKTGIPGFDELLyGGIPKRNIVLLSGGPGTGKTIFSQQYLFYGLQ-NNEPGVLVALEEHPVQIRRNMASFGWDVRKYE-ESG 86
                                   6788999998752789999******************99987775.55576777899999999888877766665433.445 PP

                                   TSX CS
                                   xxx RF
                         DnaB_C 83 klk 85
                                   ++ 
  gi|119719704|ref|YP_920199.1| 87 QFA 89
                                   554 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.2e-05     0.031     118     149 ..      14      45 ..       4      71 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.2e-05
                          T2SSE 118 iaevlrkavrerglilvsGgTgsGKttllyal 149
                                    ++e+l   + +r ++l+sGg g+GKt++    
  gi|119719704|ref|YP_920199.1|  14 FDELLYGGIPKRNIVLLSGGPGTGKTIFSQQY 45 
                                    67888889999****************98544 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   3.8e-05     0.053       4      91 ..      27     132 ..      24     175 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.8e-05
                         AAA_24   4 kiliyGpsgiGKTtlakel................gpkplfidtekGlksldadkfpdieswedfldevvel........ 59 
                                     +l+ G +g+GKT +  ++                +++p+ i  ++ +   d++k++      +                
  gi|119719704|ref|YP_920199.1|  27 IVLLSGGPGTGKTIFSQQYlfyglqnnepgvlvalEEHPVQIRRNMASFGWDVRKYE------E-------Sgqfaivda 93 
                                    57899**************88888775333333333333333333333233333322......2.......233444457 PP

                         AAA_24  60 .......aaeladyktlviDtideleelclaevirqnek 91 
                                           aa+ ++y +  +D ++el++ ++a +++ +  
  gi|119719704|ref|YP_920199.1|  94 ftggigeAAKRERYVVTSVDDVGELVDVVKAAIRDVKAE 132
                                    777788889999999999999999999999998877655 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0     7e-05     0.097      10      26 ..      25      41 ..      22      67 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7e-05
                         AAA_19 10 ekvllvtaGpGtGKTrv 26
                                   ++++l+ +GpGtGKT  
  gi|119719704|ref|YP_920199.1| 25 RNIVLLSGGPGTGKTIF 41
                                   6789***********76 PP

>> PPV_E1_C  Papillomavirus helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   8.6e-05      0.12     257     281 ..      20      44 ..      13      50 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 8.6e-05
                       PPV_E1_C 257 kgvPkknclvllGppntGkslfams 281
                                     g+Pk+n ++l G p tGk++f++ 
  gi|119719704|ref|YP_920199.1|  20 GGIPKRNIVLLSGGPGTGKTIFSQQ 44 
                                    489*******************875 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00017      0.23      25      66 ..      26      71 ..      16     167 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00017
                         AAA_16 25 elvllsGesGvGKsslvrellralekd...ggif.lrgkcdqlesa 66
                                   ++vllsG +G+GK+   ++ l +  ++   g+++ l+++ +q +++
  gi|119719704|ref|YP_920199.1| 26 NIVLLSGGPGTGKTIFSQQYLFYGLQNnepGVLVaLEEHPVQIRRN 71
                                   89************99977764333334445555677777777555 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00026      0.36      32      57 ..      24      50 ..      15      59 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00026
                          AAA_7 32 nkkpvllvGptGtGKtviikd.llkkl 57
                                   +++ vll G  GtGKt+  ++ l+  l
  gi|119719704|ref|YP_920199.1| 24 KRNIVLLSGGPGTGKTIFSQQyLFYGL 50
                                   67789***************9555555 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00017      0.23       2      25 ..      26      49 ..      25     117 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00017
                        DUF2075  2 avvlVtGvaGtGKtvvllnllael 25
                                   ++vl +G++GtGKt+   + l+  
  gi|119719704|ref|YP_920199.1| 26 NIVLLSGGPGTGKTIFSQQYLFYG 49
                                   6899***********988866554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1687.34
//
Query:       gi|119719705|ref|YP_920200.1|  [L=927]
Description: cytochrome c biogenesis protein, transmembrane region [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0023   18.1   0.1     0.0053   16.9   0.1    1.6  1  Glutaredoxin     Glutaredoxin
     0.0032   17.7   4.6     0.0032   17.7   0.6    2.9  3  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
  ------ inclusion threshold ------
      0.016   15.2   0.6      0.065   13.2   0.3    2.1  2  CarbopepD_reg_2  CarboxypepD_reg-like domain
       0.02   14.7   0.8      0.053   13.4   0.2    2.0  2  PEGA             PEGA domain


Domain annotation for each model (and alignments):
>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   1.2e-06    0.0053       1      45 [.     554     597 ..     554     609 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.2e-06
                                    EEEEESTSSHHHHHHHHHHHHTTGGEEEEEGCCSHHHHHHHHHHH CS
                   Glutaredoxin   1 vvlftkptCpyCkkakrlLkelgvkfeeidvdkdeeireelkels 45 
                                    vv++++  C  C+ +k+ L +lgv++++ + ++  ++ ee kel 
  gi|119719705|ref|YP_920200.1| 554 VVVYGSDACQECRLTKQQLSRLGVNYTYKETSDR-KVLEEYKELY 597
                                    89**************************999997.6666666654 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.2   5.5e+03      11      27 ..     113     129 ..     110     141 .. 0.66
   2 !   17.7   0.6   7.2e-07    0.0032       6      76 ..     392     453 ..     387     468 .. 0.78
   3 ?   -0.3   0.0       0.3   1.3e+03      45      72 ..     496     521 ..     488     524 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.2
                CarboxypepD_reg  11 gapiagatVtvtnadtg 27 
                                    +a++++a++t+++  +g
  gi|119719705|ref|YP_920200.1| 113 NAGVPEASLTLYDVTKG 129
                                    67788888888765444 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 7.2e-07
                CarboxypepD_reg   6 VtdasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatreevtltagqttt 76 
                                    V+++ g+ +   tV v     +   +   ++ G+f+l+ lp   ysvtv+a+Gy ++t++ v l+ ++ ++
  gi|119719705|ref|YP_920200.1| 392 VVNEEGERVDSFTVKVN----N---TEYRGRGGTFNLS-LPRAVYSVTVEAQGYVPSTFT-VNLSSNEYRR 453
                                    56666666666666666....2...3334789****97.*******************95.8888766554 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.3
                CarboxypepD_reg  45 lppgtysvtvsapGyatatreevtltag 72 
                                    + pg y+++v + +    +  +vt+t++
  gi|119719705|ref|YP_920200.1| 496 VVPGVYTLRVIFLNQTREW--TVTITND 521
                                    789*******999888777..3777765 PP

>> CarbopepD_reg_2  CarboxypepD_reg-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.3   1.4e-05     0.065      11      75 ..     397     457 ..     391     465 .. 0.77
   2 ?   -1.6   0.0      0.62   2.8e+03      42      68 ..     497     522 ..     490     526 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.4e-05
                CarbopepD_reg_2  11 keplpgatVyvkgtkkgtvTdenGnFelknlpagkytLvvsyvGyktqekkvtvskektldvnil 75 
                                    +e +   tV v++t+        G+F+l+ lp+  y ++v++ Gy + + +v++s+++   v ++
  gi|119719705|ref|YP_920200.1| 397 GERVDSFTVKVNNTEYRG---RGGTFNLS-LPRAVYSVTVEAQGYVPSTFTVNLSSNEYRRVVLE 457
                                    567777777777776654...57*****6.************************99988776544 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.62
                CarbopepD_reg_2  42 pagkytLvvsyvGyktqekkvtvskek 68 
                                     +g ytL+v ++  +t+e +vt+++++
  gi|119719705|ref|YP_920200.1| 497 VPGVYTLRVIFLN-QTREWTVTITNDT 522
                                    4688999999997.5557899998875 PP

>> PEGA  PEGA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0         1   4.6e+03      25      44 ..     119     139 ..     112     139 .. 0.81
   2 ?   13.4   0.2   1.2e-05     0.053      28      67 ..     420     457 ..     404     460 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1
                           PEGA  25 TPvtls.leaGnyslrvekeG 44 
                                    + +tl+ + +G+ +l+v+++G
  gi|119719705|ref|YP_920200.1| 119 ASLTLYdVTKGRATLQVVLPG 139
                                    567888899999999999998 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 1.2e-05
                           PEGA  28 tlsleaGnyslrvekeGYedlektvtvtagetvklnltLe 67 
                                    +lsl+   ys++ve+ GY + + tv+++++e+ ++   Le
  gi|119719705|ref|YP_920200.1| 420 NLSLPRAVYSVTVEAQGYVPSTFTVNLSSNEYRRVV--LE 457
                                    7889999**********************9998885..44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (927 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       757  (0.0422221); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.76u 0.29s 00:00:01.05 Elapsed: 00:00:00.49
# Mc/sec: 5745.87
//
Query:       gi|119719706|ref|YP_920201.1|  [L=393]
Description: hypothetical protein Tpen_0796 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   3.8e-131  437.5   0.0   4.3e-131  437.3   0.0    1.0  1  DUF521    Protein of unknown function (DUF521)
  ------ inclusion threshold ------
       0.11   11.7   0.0       0.29   10.2   0.0    1.6  2  Cas_Cas1  CRISPR associated protein Cas1


Domain annotation for each model (and alignments):
>> DUF521  Protein of unknown function (DUF521)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  437.3   0.0  4.8e-135  4.3e-131       1     394 [.       1     381 [.       1     388 [. 0.94

  Alignments for each domain:
  == domain 1  score: 437.3 bits;  conditional E-value: 4.8e-135
                         DUF521   1 mkLtkeeeamlnGeeGealqkameilvalGeilgAerLvpvtsahvsgvsyktigdaglefleelaekgakvrvpttlnp 80 
                                    m+L+k ee+ml+Ge Gea++ am+i+v+++ei+ AerLv++++ahvsgvsy++igd+glefle la+kg++++vptt+np
  gi|119719706|ref|YP_920201.1|   1 MYLDKFEERMLEGELGEAVALAMRIVVKIAEIFSAERLVKIKHAHVSGVSYENIGDEGLEFLEGLAAKGGRFSVPTTVNP 80 
                                    9******************************************************************************* PP

                         DUF521  81 igvdlerweelgvdeefaekqeriieayeklGveltftCtpyllgnapkkGehlawsESsavvyaNSvlGarTnreggps 160
                                     +vdle w+++gvde+++ekq ri+ a++++G+++t+tCtpyl+ +  + G+hlawsES+av++aNSv+GarTnr+ggp+
  gi|119719706|ref|YP_920201.1|  81 GAVDLELWRKMGVDESYVEKQLRIVGAFRRMGAKVTLTCTPYLY-EDISPGDHLAWSESNAVLFANSVIGARTNRDGGPL 159
                                    *******************************************9.8999******************************* PP

                         DUF521 161 alaaAitGrtpeyGlhldenRkptvlveveae...sedeadygalGylvGkkvgeriPvlk..glekpsedelKalgAal 235
                                    al+ Ai+Gr+p  GlhldenR+p+++v+ ++     +++  +++ G++vG+ +g+r+P+++  gl++++ +elK ++Aa+
  gi|119719706|ref|YP_920201.1| 160 ALMEAIAGRAPLSGLHLDENRRPSLVVDFSESsryIAENGLFSVAGLIVGRLAGNRVPLVRglGLQRKDVEELKLFLAAV 239
                                    ****************************98878998999999*******************444555599********** PP

                         DUF521 236 aasgavalfhiegvTPeaetleealgekekaekititkedleevleelskakeekvdlvalGcPhlsleElrelaellkg 315
                                    +a+g++ ++ i+gv+Pe      a  +  + e  +i  +d+++ le++     +  d+v+lGcPhls+eE++++ e + +
  gi|119719706|ref|YP_920201.1| 240 GATGGTGMVLIDGVSPE------AP-GDMPGEVEKIGVDDVKAELEKY---GGSGWDAVVLGCPHLSYEEVASIIEWF-E 308
                                    *****************......33.4556677788888****99999...9999***********************.8 PP

                         DUF521 316 kkkkvkvelwvttsrevkeeaerlglveklekaGvkvlsdtCmvvsplikkkevkkvatnSgKaahYlpgltgvkvalg 394
                                    +k +++ +++++tsrev++++++     +lek ++++++dtCmvvs l   + +++vat+SgKaa+Yl +++ ++val 
  gi|119719706|ref|YP_920201.1| 309 RKGRPRSRVYLYTSREVASRLRSD----RLEKLNIHLFADTCMVVSNLGAYA-SRSVATDSGKAAFYLASKG-YSVALL 381
                                    8888*****************987....*********************996.***************9996.777765 PP

>> Cas_Cas1  CRISPR associated protein Cas1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   3.2e-05      0.29     217     247 ..     172     201 ..     169     205 .. 0.84
   2 ?   -2.5   0.0      0.24   2.1e+03      60      85 ..     304     329 ..     301     334 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 3.2e-05
                                    -SSS--TTSS-HHHHHHHHHHHHHHCHHHHH CS
                       Cas_Cas1 217 GfLHedrpgrpsLalDLmEefRpllvDrlvl 247
                                    + LH d+++rpsL++D+ E  R  ++++ ++
  gi|119719706|ref|YP_920201.1| 172 SGLHLDENRRPSLVVDFSESSRY-IAENGLF 201
                                    569*******************8.7776665 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.24
                                    EEEE-TTS-EEEEEEESSSSTHHHHH CS
                       Cas_Cas1  60 vvflsengkylgrlepeesgnvelrr 85 
                                    + +++++g++++r++  +s++v+ r+
  gi|119719706|ref|YP_920201.1| 304 IEWFERKGRPRSRVYLYTSREVASRL 329
                                    679999********999999888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2719.03
//
Query:       gi|119719707|ref|YP_920202.1|  [L=136]
Description: hypothetical protein Tpen_0797 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-32  110.0   0.2    4.3e-32  109.7   0.2    1.1  1  DUF126    Aconitase X swivel domain


Domain annotation for each model (and alignments):
>> DUF126  Aconitase X swivel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.7   0.2   2.4e-36   4.3e-32       1      80 []      17      96 ..      17      96 .. 0.99

  Alignments for each domain:
  == domain 1  score: 109.7 bits;  conditional E-value: 2.4e-36
                                   --TTS-B-TTT-BB-S.-SSSTT-B-TTSEEEES--S--SS-TTHHHHHHHHT-S-SEEEESS--HHHHHHHHHHT--EE CS
                         DUF126  1 lSflggvdpetGkvidkghplegqsiagkiLvlpsgkGStvgsyvllelakngtaPaAlilreadpilalGaivadiPlv 80
                                   + flggvdp tG v++kghpl+gqs++gkiLv+p++kGStvgsy+ll l k+g aPa+++ ++ad+++++G+++++iP++
  gi|119719707|ref|YP_920202.1| 17 ITFLGGVDPFTGLVVEKGHPLYGQSVSGKILVFPYSKGSTVGSYILLRLSKRGLAPAGIVTSSADEVTVIGCLISNIPMM 96
                                   68****************************************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       192  (0.0107089); expected 358.6 (0.02)
Passed bias filter:                      174  (0.00970495); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 1036.11
//
Query:       gi|119719708|ref|YP_920203.1|  [L=217]
Description: phage SPO1 DNA polymerase-related protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-44  150.2   0.0    5.7e-44  149.8   0.0    1.1  1  UDG       Uracil DNA glycosylase superfamily


Domain annotation for each model (and alignments):
>> UDG  Uracil DNA glycosylase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.8   0.0   3.2e-48   5.7e-44       1     149 [.      44     192 ..      44     199 .. 0.92

  Alignments for each domain:
  == domain 1  score: 149.8 bits;  conditional E-value: 3.2e-48
                                    HHC-CTT-SEEEEESSTCHHHHHHSSSS.-STT--HHHHHHHCCCCCCCHHGCTEEEEESSS....SECGCTTCCCCTCC CS
                            UDG   1 pgegppdakvvivGeaPgaeedatglpFsgragnllrkllneaglkrdleseqgvyitnvvkcrppgnrdtptsaeikac 80 
                                    pgeg+p + vv++GeaPg++ed +g+pF+g+ag ll +l++ agl+r     ++v+itnvvkcrpp nr +p+++ei+ac
  gi|119719708|ref|YP_920203.1|  44 PGEGNPCSGVVFIGEAPGRNEDLQGRPFVGAAGALLTELISLAGLSR-----EEVFITNVVKCRPPNNR-EPREEEIAAC 117
                                    799********************************************.....*****************.********** PP

                                    HHHHHHHHHHHHSSEEEEESHHHHHH.......HH.HHSCESCCCSCT......SEEEEES-SSTTTTTTTTSHHHHHHH CS
                            UDG  81 aplleeeiellkprlivllGktaakall.....ge.klgklrgklleak.....irvlplphPsplnrnffksnpelkae 149
                                     p+l ++++++kprliv+lGk+  k++l        +++++rgk +  +     ++v+p++hP+++++n     p++++ 
  gi|119719708|ref|YP_920203.1| 118 LPYLLAQLRAIKPRLIVTLGKHSTKTILrmrgmSVdSIMSVRGKAYTVNaewgqVTVFPTLHPAAALYN-----PAMRKV 192
                                    **************************9889987444888********9778899***************.....555443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 1492.62
//
Query:       gi|119719709|ref|YP_920204.1|  [L=204]
Description: hypothetical protein Tpen_0799 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1199  (0.0668749); expected 358.6 (0.02)
Passed bias filter:                      709  (0.0395449); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1337.88
//
Query:       gi|119719710|ref|YP_920205.1|  [L=130]
Description: hypothetical protein Tpen_0800 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
       0.03   14.4   0.1      0.034   14.2   0.1    1.2  1  Replic_Relax  Replication-relaxation


Domain annotation for each model (and alignments):
>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   1.9e-06     0.034      26      73 ..      56     102 ..      20     121 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.9e-06
                   Replic_Relax  26 tarrrLarLrelgllsrlrkrvggarggsepyvYaLtpkGarllaaqr 73 
                                    ++  +L++L+e+++++ l+   gg+  + +++ YaL++ Ga++l++++
  gi|119719710|ref|YP_920205.1|  56 ELDAVLQKLAEEDYVKVLYAA-GGRFLTLYKPLYALGKRGAAALSKKE 102
                                    56789************9998.77777899**************2221 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       870  (0.0485247); expected 358.6 (0.02)
Passed bias filter:                      719  (0.0401026); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 803.00
//
Query:       gi|119719711|ref|YP_920206.1|  [L=247]
Description: hypothetical protein Tpen_0801 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-08   34.2  14.3    3.4e-05   23.9   4.8    2.9  2  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
      6e-05   23.2   2.6      6e-05   23.2   2.6    2.3  2  DUF1640          Protein of unknown function (DUF1640)
    0.00011   22.2   7.7     0.0091   16.0   4.1    3.4  2  DUF1664          Protein of unknown function (DUF1664)
     0.0002   20.4   2.7     0.0002   20.4   2.7    1.9  2  IFT57            Intra-flagellar transport protein 57
    0.00056   20.3  16.6       0.72   10.3   0.2    4.8  5  FlaC_arch        Flagella accessory protein C (FlaC)
     0.0013   18.9   0.8     0.0044   17.2   0.3    1.9  2  GM_CSF           Granulocyte-macrophage colony-stimulating fa
     0.0013   19.0  10.7       0.19   12.1   0.1    4.0  4  CLZ              C-terminal leucine zipper domain of cyclic n
     0.0015   19.1  13.9       0.24   12.0   0.1    4.0  4  SlyX             SlyX
     0.0016   18.4   8.7          3    7.8   0.1    4.0  4  Prefoldin        Prefoldin subunit
     0.0017   16.0   8.4     0.0022   15.6   8.4    1.1  1  DUF3584          Protein of unknown function (DUF3584)
     0.0026   16.5   6.4       0.38    9.3   0.1    2.0  2  AAA_13           AAA domain
     0.0038   17.6  12.5        1.3    9.5   0.1    4.1  3  NPV_P10          Nucleopolyhedrovirus P10 protein
     0.0039   16.1  15.5       0.27   10.1   4.3    2.8  3  Spc7             Spc7 kinetochore protein
     0.0051   17.0   5.3        1.5    9.1   0.4    3.7  4  WXG100           Proteins of 100 residues with WXG
     0.0051   17.0  14.4      0.013   15.7   7.7    2.1  2  Jnk-SapK_ap_N    JNK_SAPK-associated protein-1
     0.0052   17.2  15.5       0.79   10.2   5.5    3.5  3  Snapin_Pallidin  Snapin/Pallidin
     0.0072   16.0   8.9       0.57    9.7   0.1    2.2  2  Filament         Intermediate filament protein
     0.0079   16.3   1.8     0.0079   16.3   1.8    2.2  2  ApoLp-III        Apolipophorin-III precursor (apoLp-III)
     0.0085   15.5  16.1       0.14   11.5   9.7    2.1  3  GAS              Growth-arrest specific micro-tubule binding
  ------ inclusion threshold ------
       0.01   15.7   1.2          4    7.4   0.0    4.1  3  Surfac_D-trimer  Lung surfactant protein D coiled-coil trimer
       0.01   15.0  11.3      0.024   13.8   1.0    2.1  2  FH2              Formin Homology 2 Domain
      0.011   16.0   9.2      0.042   14.2   0.6    3.3  3  CCDC-167         Coiled-coil domain-containing protein 167
      0.018   15.1  13.8       0.03   14.4   3.5    3.1  3  COG2             COG (conserved oligomeric Golgi) complex com
       0.02   14.4   8.0       0.13   11.8   0.1    3.4  3  DUF4635          Domain of unknown function (DUF4635)
      0.022   13.4   6.8        1.1    7.8   0.2    2.3  2  Tweety           Tweety
      0.028   14.8   5.0      0.074   13.4   0.5    2.7  3  HrpB7            Bacterial type III secretion protein (HrpB7)
       0.03   14.2   0.5       0.03   14.2   0.5    1.8  2  PIN_8            PIN like domain
      0.034   13.5   9.2      0.023   14.1   4.4    2.4  2  YjcZ             YjcZ-like protein
       0.04   14.1   9.2       0.63   10.2   5.4    2.3  3  Fib_alpha        Fibrinogen alpha/beta chain family
       0.04   14.2   0.2       0.04   14.2   0.2    3.0  1  Fer4_24          Ferredoxin I 4Fe-4S cluster domain
      0.041   14.4   2.3      0.055   13.9   0.2    2.2  1  EspB_PE          ESX-1 secreted protein B PE domain
      0.052   13.8  10.1       0.57   10.4   0.5    3.2  3  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
      0.067   13.5   4.2        7.4    7.0   0.0    3.2  2  Tup_N            Tup N-terminal
      0.075   13.2   2.5       0.48   10.6   2.5    2.1  1  Cob_adeno_trans  Cobalamin adenosyltransferase
      0.083   13.4   6.5        2.5    8.6   0.4    2.5  2  T3SSipB          Type III cell invasion protein SipB
      0.084   13.2   9.4        1.5    9.1   0.4    3.4  3  DUF5082          Domain of unknown function (DUF5082)
      0.091   13.2   8.0        9.3    6.7   0.1    4.5  4  LPP              Lipoprotein leucine-zipper
      0.093   13.0  11.3         29    5.0   0.9    3.4  2  DUF948           Bacterial protein of unknown function (DUF94
       0.13   12.5  14.9       0.57   10.4   2.5    3.2  2  Cnn_1N           Centrosomin N-terminal motif 1
       0.14   12.3   4.2         25    5.2   0.1    3.5  3  XhlA             Haemolysin XhlA
       0.17   12.4   9.1    1.2e+02    3.3   9.1    3.0  1  DUF16            Protein of unknown function DUF16
       0.24   11.6  12.3        9.8    6.4   0.0    4.2  4  JIP_LZII         JNK-interacting protein  leucine zipper II
       0.26   11.6   2.5        6.1    7.2   0.1    3.1  2  Img2             Mitochondrial large subunit ribosomal protei
       0.32   11.4   0.1       0.32   11.4   0.1    3.1  3  UPF0184          Uncharacterised protein family (UPF0184)
        0.4   10.5  16.3        1.4    8.8   0.9    2.7  3  CEP63            Centrosomal protein of 63 kDa
       0.41   10.0  15.8       0.29   10.5   8.7    2.1  2  Rab5-bind        Rabaptin-like protein
       0.42    9.3  11.3      0.078   11.6   6.3    1.9  2  Dor1             Dor1-like family
       0.43    8.5  10.1       0.12   10.3   0.9    2.0  2  Prominin         Prominin
       0.46   10.0   8.9       0.28   10.7   4.4    2.0  2  Allexi_40kDa     Allexivirus 40kDa protein
        0.5   10.4   4.5       0.64   10.0   0.3    2.8  2  SOAR             STIM1 Orai1-activating region
       0.62    9.7   5.5       0.52   10.0   1.4    2.2  2  APP_E2           E2 domain of amyloid precursor protein
       0.66    9.8   8.6       0.69    9.7   1.5    2.6  4  Bacillus_HBL     Bacillus haemolytic enterotoxin (HBL)
        0.7   10.2  14.6        4.1    7.7   4.7    3.0  3  Muted            Organelle biogenesis, Muted-like protein
        0.7   10.0   5.4        4.7    7.4   0.3    3.2  3  POTRA_TamA_1     POTRA domain TamA domain 1
       0.71   10.0   8.0          4    7.6   0.1    3.7  3  Vps51            Vps51/Vps67
       0.74   10.3  10.7         18    5.8   0.1    3.9  4  DASH_Dad2        DASH complex subunit Dad2
       0.76    9.3  10.4          2    7.9  10.4    1.7  1  Exonuc_VII_L     Exonuclease VII, large subunit
       0.84   10.2   6.2        6.6    7.3   0.1    3.4  3  HisKA_3          Histidine kinase
       0.98    9.3   6.3        6.4    6.6   0.4    2.6  3  ACCA             Acetyl co-enzyme A carboxylase carboxyltrans
        1.1   10.0   5.0        2.9    8.6   0.1    2.8  2  DUF883           Bacterial protein of unknown function (DUF88
        1.1    8.9   9.8      0.036   13.7   2.1    2.0  2  GrpE             GrpE
        1.1    7.7   4.5       0.47    8.9   0.2    1.9  2  FUSC             Fusaric acid resistance protein family
        1.2    9.0   8.6         25    4.7   0.2    3.0  3  zf-ZPR1          ZPR1 zinc-finger domain
        1.3    9.6   6.2          6    7.4   6.2    2.0  1  Ccdc124          Coiled-coil domain-containing protein 124 /O
        1.3    9.1  13.3          4    7.6   2.2    3.3  4  DUF2730          Protein of unknown function (DUF2730)
        1.6    7.9   7.9        3.5    6.8   0.4    2.1  2  TMPIT            TMPIT-like protein
        1.8    8.7   6.1       0.64   10.2   1.1    2.2  2  CHDCT2           CHDCT2 (NUC038) domain
        1.9    8.4  15.7       0.38   10.6   3.1    2.9  3  CK2S             Casein Kinase 2 substrate
        2.7    8.5   7.6         11    6.6   2.0    2.6  2  IZUMO            Izumo sperm-egg fusion, Ig domain-associated
        2.8    6.7   9.8        1.4    7.7   0.8    2.1  2  Fmp27_WPPW       RNA pol II promoter Fmp27 protein domain
        2.9    8.3  13.1       0.77   10.2   2.0    2.6  2  DUF4200          Domain of unknown function (DUF4200)
          4    7.4  10.0        5.5    7.0   0.7    2.3  2  DUF489           Protein of unknown function (DUF489)
        4.3    7.3  14.6       0.54   10.3   2.2    2.7  3  Rootletin        Ciliary rootlet component, centrosome cohesi
        5.1    8.1  14.2         27    5.7   0.9    3.4  3  PRKG1_interact   cGMP-dependent protein kinase interacting do
        6.4    7.5  14.8          4    8.1   0.5    3.1  3  YabA             Initiation control protein YabA
        7.2    7.0  11.6        7.7    6.9   1.7    3.6  4  Rx_N             Rx N-terminal domain
        8.1    6.6   7.9       0.74    9.9   0.3    3.1  1  DUF5595          Domain of unknown function (DUF5595)


Domain annotation for each model (and alignments):
>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   4.8   1.4e-07   3.4e-05      17     119 ..      48     160 ..      42     171 .. 0.78
   2 !   18.0   8.8   9.6e-06    0.0022      39     132 ..     123     219 ..     121     236 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 1.4e-07
                   Baculo_PEP_C  17 dLtnvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldt...rldtlltnLtdalnalq.......dtlrne 86 
                                    d+  +L+a++ +n  +  +l+ +ld ++t++++l+ ++k+l ++l++   ++++  ++L +++n+++       dtl+++
  gi|119719711|ref|YP_920206.1|  48 DVALLLAALKRLNNGV-YALKVTLDFLNTRVGTLQGQIKELEEALKShleAFQAENSRLAESVNRVSrefkegtDTLTKN 126
                                    5566788999999998.889999999999999999998888888888444445556778888888888888888888777 PP

                   Baculo_PEP_C  87 Lt.nlnsiltnLlssvtNinstLnnllqalnnld 119
                                     + +l+  l  L  ++t ++ tL+ + q++ ++ 
  gi|119719711|ref|YP_920206.1| 127 VQlSLDMFLEKLSGELTRLEDTLSTITQDVSAVM 160
                                    7658999999999999999999999999998874 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 9.6e-06
                   Baculo_PEP_C  39 lldaietqLnalsedlksllaeldtrldtlltnLtdalnalq..dtlr.neLtnlnsiltnLlssvtNinstLnnllqal 115
                                    l ++++ +L+ + e+l+  l+ l++ l+t ++ +++ + +l+  + ++  + t+++s++++L  s+ N++ +Ln l q +
  gi|119719711|ref|YP_920206.1| 123 LTKNVQLSLDMFLEKLSGELTRLEDTLSTITQDVSAVMSKLKevELVStDAATAVKSDVNSLRGSMSNVELALNELSQRV 202
                                    56778888888888899989999999999999999888888877555515689*************************** PP

                   Baculo_PEP_C 116 nnldlgalsqeledald 132
                                      l++ +l++  + +l+
  gi|119719711|ref|YP_920206.1| 203 TRLEESQLAALRQYSLE 219
                                    ***99999887766554 PP

>> DUF1640  Protein of unknown function (DUF1640)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   2.6   2.6e-07     6e-05      46     143 ..      57     164 ..      40     185 .. 0.86
   2 ?    3.3   3.5      0.32        76      51      92 ..     187     228 ..     159     243 .. 0.72

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 2.6e-07
                        DUF1640  46 selekseylqkaalselrkevqise..........rsefaalrseteklqreleklkqkLreeidklkadirldlnleKg 115
                                    + l++  y  k+ l+ l + v +++          +s+ +a+++e+ +l + ++++  +++e +d+l+++++l l+   +
  gi|119719711|ref|YP_920206.1|  57 KRLNNGVYALKVTLDFLNTRVGTLQgqikeleealKSHLEAFQAENSRLAESVNRVSREFKEGTDTLTKNVQLSLDMFLE 136
                                    66778888888888888888888888888899999*************************************99999999 PP

                        DUF1640 116 rireelakleakiqelnnkidrevsalr 143
                                    +   el++le+ ++ +++ ++  +s+l+
  gi|119719711|ref|YP_920206.1| 137 KLSGELTRLEDTLSTITQDVSAVMSKLK 164
                                    9999999999999888877777777666 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.32
                        DUF1640  51 seylqkaalselrkevqisersefaalrseteklqreleklk 92 
                                    s+  ++ al el + v+ +e+s+ aalr+ + +lq+   kl+
  gi|119719711|ref|YP_920206.1| 187 SMSNVELALNELSQRVTRLEESQLAALRQYSLELQEVSLKLT 228
                                    555677889999999999999999999998888886433333 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0      0.23        54      89     122 ..      56      89 ..      48      99 .. 0.71
   2 !   16.0   4.1   3.9e-05    0.0091      49     124 .]     134     209 ..      90     215 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.23
                        DUF1664  89 vtevredlseigedvesvkeavegleskleriee 122
                                    ++++++++ +++  ++ +++ v +l+++++++ee
  gi|119719711|ref|YP_920206.1|  56 LKRLNNGVYALKVTLDFLNTRVGTLQGQIKELEE 89 
                                    4556666666777777777777777777777765 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 3.9e-05
                        DUF1664  49 qleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerieekQ 124
                                     le++s +l++  + Ls   + v + + + ke+    ++  t+v++d+++++  +++v+ a ++l ++++r+ee Q
  gi|119719711|ref|YP_920206.1| 134 FLEKLSGELTRLEDTLSTITQDVSAVMSKLKEVELVSTDAATAVKSDVNSLRGSMSNVELALNELSQRVTRLEESQ 209
                                    4566666666666666666666666666666666666677777888888888888888888888888888888776 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   2.7   8.7e-07    0.0002     236     353 ..      73     193 ..      61     202 .. 0.87
   2 !    8.4   2.5     0.004      0.93     235     306 ..     137     208 ..     134     244 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 8.7e-07
                          IFT57 236 ieeslpetksqlkklhedisktlekiesrEkylnsqleellqeyreaqeelse.vkek....ykqlsegvseltrelaei 310
                                    +++ + +++ q+k+l+e ++  le  ++  ++l ++++   +e++e  ++l++ v+ +    +++ls++++ l+++l++i
  gi|119719711|ref|YP_920206.1|  73 LNTRVGTLQGQIKELEEALKSHLEAFQAENSRLAESVNRVSREFKEGTDTLTKnVQLSldmfLEKLSGELTRLEDTLSTI 152
                                    567788999*****************************************9762444422236899************** PP

                          IFT57 311 seelekvkqemeergssmtDgsplvkikkaltklkkEikqmdv 353
                                    ++++++v ++++e +   tD++    +k  +++l+  +++ ++
  gi|119719711|ref|YP_920206.1| 153 TQDVSAVMSKLKEVELVSTDAAT--AVKSDVNSLRGSMSNVEL 193
                                    *********************98..888899988887777665 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.004
                          IFT57 235 sieeslpetksqlkklhedisktlekiesrEkylnsqleellqeyreaqeelsevkekykqlsegvseltre 306
                                    +++ +l++++  l+ + +d+s +++k+++ E   +       ++ ++++ ++s+v+  +++ls++v+ l++ 
  gi|119719711|ref|YP_920206.1| 137 KLSGELTRLEDTLSTITQDVSAVMSKLKEVELVSTDAATAVKSDVNSLRGSMSNVELALNELSQRVTRLEES 208
                                    556678888888999999999999999999988888888888889999999999999999999999887763 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0      0.57   1.3e+02       9      30 ..      70      91 ..      56      93 .. 0.72
   2 !   10.3   0.2    0.0031      0.72       2      38 ..      84     117 ..      76     118 .. 0.75
   3 ?    6.8   0.6     0.039       9.1       9      35 ..     135     161 ..     120     170 .. 0.61
   4 !    9.6   0.3    0.0051       1.2       6      36 ..     178     208 ..     175     216 .. 0.89
   5 ?    2.1   0.7       1.1   2.6e+02      22      42 ..     219     239 ..     207     239 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.57
                      FlaC_arch  9 lsklsteletvkkeneelsksv 30
                                   l+ l t+++t++ +++el++ +
  gi|119719711|ref|YP_920206.1| 70 LDFLNTRVGTLQGQIKELEEAL 91
                                   4556778888888888887655 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0031
                      FlaC_arch   2 idelEnklsklsteletvkkeneelsksveelkenVk 38 
                                    i+elE+    l++ le  ++en+ l +sv+++ +++k
  gi|119719711|ref|YP_920206.1|  84 IKELEEA---LKSHLEAFQAENSRLAESVNRVSREFK 117
                                    4444443...4459*****************998877 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.039
                      FlaC_arch   9 lsklsteletvkkeneelsksveelke 35 
                                    l+kls el+ ++++++ + ++v  +  
  gi|119719711|ref|YP_920206.1| 135 LEKLSGELTRLEDTLSTITQDVSAVMS 161
                                    455555555555555555555555444 PP

  == domain 4  score: 9.6 bits;  conditional E-value: 0.0051
                      FlaC_arch   6 Enklsklsteletvkkeneelsksveelken 36 
                                     +++++l  ++++v+  ++els+ v++l+e+
  gi|119719711|ref|YP_920206.1| 178 KSDVNSLRGSMSNVELALNELSQRVTRLEES 208
                                    578999999****************999986 PP

  == domain 5  score: 2.1 bits;  conditional E-value: 1.1
                      FlaC_arch  22 eneelsksveelkenVkdlls 42 
                                    e++e+s +++++++  ++ll+
  gi|119719711|ref|YP_920206.1| 219 ELQEVSLKLTQVNQLLQKLLE 239
                                    899***********9999985 PP

>> GM_CSF  Granulocyte-macrophage colony-stimulating factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.3   1.9e-05    0.0044      17      82 ..      85     154 ..      73     174 .. 0.83
   2 ?    0.0   0.0       3.9   9.1e+02      56      79 ..     174     197 ..     150     216 .. 0.60

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.9e-05
                                    HHHHHHH.HHHHH----HHHHTSEEEEESS--BSSS--...SHHHHHHHHHHT-SGGGGGGHHHHHHHHH CS
                         GM_CSF  17 daikeal.sllnessdlaavlneevevvseefdlqept...clqtrlklykqGlrGsltklkgaltllas 82 
                                    + ++eal s l+  ++ ++ l e+v+ vs ef+    t    +q  l+++ + l G+lt+l+++l+ +++
  gi|119719711|ref|YP_920206.1|  85 KELEEALkSHLEAFQAENSRLAESVNRVSREFKEGTDTltkNVQLSLDMFLEKLSGELTRLEDTLSTITQ 154
                                    5567787357899999999*************9877662235899*******************987765 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 3.9
                                    HHHHHHHHHT-SGGGGGGHHHHHH CS
                         GM_CSF  56 qtrlklykqGlrGsltklkgaltl 79 
                                     t +k   + lrGs+++++ al+ 
  gi|119719711|ref|YP_920206.1| 174 ATAVKSDVNSLRGSMSNVELALNE 197
                                    333444456677777777766664 PP

>> CLZ  C-terminal leucine zipper domain of cyclic nucleotide-gated channels
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.1   0.00081      0.19      27      67 ..      57      97 ..      48     101 .. 0.89
   2 ?    3.1   0.3      0.51   1.2e+02      34      62 ..      89     117 ..      83     128 .. 0.73
   3 ?    6.9   0.5     0.035       8.1      25      62 ..     127     164 ..     115     166 .. 0.89
   4 ?    5.0   0.4      0.14        32      32      70 ..     187     207 ..     170     229 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00081
                            CLZ 27 keleekverLessLeaLqtrlarLlaeyessqrkLkqRitk 67
                                   k l++ v  L+ +L+ L+tr+  L ++ ++ ++ Lk+ +++
  gi|119719711|ref|YP_920206.1| 57 KRLNNGVYALKVTLDFLNTRVGTLQGQIKELEEALKSHLEA 97
                                   567888999***************************98876 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.51
                            CLZ  34 erLessLeaLqtrlarLlaeyessqrkLk 62 
                                    e L+s+Lea+q    rL + ++ + r+ k
  gi|119719711|ref|YP_920206.1|  89 EALKSHLEAFQAENSRLAESVNRVSREFK 117
                                    67888888888888888888887777666 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.035
                            CLZ  25 eqkeleekverLessLeaLqtrlarLlaeyessqrkLk 62 
                                     q +l+  +e+L ++L  L++ l  + ++++++ +kLk
  gi|119719711|ref|YP_920206.1| 127 VQLSLDMFLEKLSGELTRLEDTLSTITQDVSAVMSKLK 164
                                    577889999************************99999 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.14
                            CLZ  32 kverLessLeaLqtrlarLlaeyessqrkLkqRitkLEk 70 
                                     ++++e +L+ L                   qR+t+LE+
  gi|119719711|ref|YP_920206.1| 187 SMSNVELALNELS------------------QRVTRLEE 207
                                    4445555555555..................55555553 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.1     0.001      0.24      11      56 ..      48      93 ..      42     109 .. 0.86
   2 ?   -0.2   0.0       6.9   1.6e+03      29      48 ..      98     117 ..      89     130 .. 0.50
   3 !    9.8   0.1    0.0051       1.2      16      52 ..     132     168 ..     126     183 .. 0.89
   4 ?    0.4   5.8       4.4     1e+03       2      41 ..     199     239 ..     177     246 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.001
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXX CS
                           SlyX 11 klafqedtieeLndvvaeqqqqidrlqrqlrllaerlkeleessga 56
                                    +a +  ++++Ln+ v++   ++d l +++  l+ ++kelee+ ++
  gi|119719711|ref|YP_920206.1| 48 DVALLLAALKRLNNGVYALKVTLDFLNTRVGTLQGQIKELEEALKS 93
                                   56777788999****************************9998765 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 6.9
                                    HHHHHHHHHHHHHHHHHT-X CS
                           SlyX  29 qqqqidrlqrqlrllaerlk 48 
                                     q + +rl + ++++ +++k
  gi|119719711|ref|YP_920206.1|  98 FQAENSRLAESVNRVSREFK 117
                                    33334444444444444433 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.0051
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXX CS
                           SlyX  16 edtieeLndvvaeqqqqidrlqrqlrllaerlkelee 52 
                                    + ++e+L+ ++++ +++++ +++ + +++ +lke+e 
  gi|119719711|ref|YP_920206.1| 132 DMFLEKLSGELTRLEDTLSTITQDVSAVMSKLKEVEL 168
                                    7789*****************************9985 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 4.4
                                    HHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           SlyX   2 eerleeLE.iklafqedtieeLndvvaeqqqqidrlqrqlr 41 
                                     +r+++LE ++la + +   eL++v  +  q  + lq+ l+
  gi|119719711|ref|YP_920206.1| 199 SQRVTRLEeSQLAALRQYSLELQEVSLKLTQVNQLLQKLLE 239
                                    57788886247777887778888888887777777777665 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1     0.027       6.3      79     105 ..      70      96 ..      63     111 .. 0.69
   2 ?    6.7   0.1     0.027       6.3      73     117 ..     114     159 ..     111     162 .. 0.84
   3 ?    7.8   0.1     0.013         3      71     112 ..     166     207 ..     165     215 .. 0.90
   4 ?   -0.0   0.6       3.4   7.9e+02       6      34 ..     211     239 ..     207     245 .. 0.49

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.027
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Prefoldin  79 iellkkkleelekqlekleeeleklkd 105
                                     ++l+ ++ +l+ q+++lee+l+   +
  gi|119719711|ref|YP_920206.1|  70 LDFLNTRVGTLQGQIKELEEALKSHLE 96 
                                    577888888888888888887765544 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.027
                                    EEHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Prefoldin  73 ksleeAiellkkkle.elekqlekleeeleklkdqittleanlaql 117
                                    ++++e +++l k+++ +l+  lekl  el+ l d++ t+ + ++++
  gi|119719711|ref|YP_920206.1| 114 REFKEGTDTLTKNVQlSLDMFLEKLSGELTRLEDTLSTITQDVSAV 159
                                    6788999999999994577889****************99988766 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.013
                                    EEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Prefoldin  71 veksleeAiellkkkleelekqlekleeeleklkdqittlea 112
                                    ve+ + +A + +k  +++l+ ++ ++e +l++l++++t le+
  gi|119719711|ref|YP_920206.1| 166 VELVSTDAATAVKSDVNSLRGSMSNVELALNELSQRVTRLEE 207
                                    56777899999***************************9985 PP

  == domain 4  score: -0.0 bits;  conditional E-value: 3.4
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                      Prefoldin   6 eslqaelaqlkeaieelektletlktlkk 34 
                                    ++l++   +l+e   +l+++ + l++l +
  gi|119719711|ref|YP_920206.1| 211 AALRQYSLELQEVSLKLTQVNQLLQKLLE 239
                                    44444444444444455555555555444 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   8.4   9.3e-06    0.0022     258     408 ..      71     222 ..      61     244 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 9.3e-06
                        DUF3584 258 eslelrLsllkgelkadeerlaekqeevqeakaelkqqlrtledelkeaidelnqels.aakaklaakeselealeeqkk 336
                                      l  r+ +l+g++k+ ee+l++++e++q+++ +l ++++    e+ke  d+l+++++  ++  l++ + el +le+   
  gi|119719711|ref|YP_920206.1|  71 DFLNTRVGTLQGQIKELEEALKSHLEAFQAENSRLAESVNRVSREFKEGTDTLTKNVQlSLDMFLEKLSGELTRLEDTLS 150
                                    556788999***********************************************984678999************999 PP

                        DUF3584 337 kyedadieklkadldqlpsirsel.eeleeeldaltekhqdvqekydrrkqkikeeleeeleklkerleaire 408
                                        +d++ +  +l +++ ++++  ++++ +++ l +++ +v+ +++++ q +    e +l+ l++   +++e
  gi|119719711|ref|YP_920206.1| 151 TIT-QDVSAVMSKLKEVELVSTDAaTAVKSDVNSLRGSMSNVELALNELSQRVTRLEESQLAALRQYSLELQE 222
                                    976.68999**********999862678999******************999999888888888877444444 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.1    0.0016      0.38     410     476 ..      48     113 ..      37     124 .. 0.83
   2 !    8.8   2.3    0.0023      0.55     266     380 ..     124     236 ..     119     242 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0016
                         AAA_13 410 eldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeeinkeLkafGlgele 476
                                    ++  +  ++k+l++ +  l+  l+  ++++ +l+++ikeLe+ l+++ +a +  n+ L++   ++ +
  gi|119719711|ref|YP_920206.1|  48 DVALLLAALKRLNNGVYALKVTLDFLNTRVGTLQGQIKELEEALKSHLEAFQAENSRLAES-VNRVS 113
                                    555666789999999*************************************999999987.55555 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0023
                         AAA_13 266 paerkaaLeahFddefeekqerLekliekveskkselleklkavsde.asensafeedkeelkaeaealeeqLkglqral 344
                                    +++ + +L+ + ++    +  rLe++++++ ++ s ++ klk+v     ++  a ++d++ l+  ++++e +L++l++++
  gi|119719711|ref|YP_920206.1| 124 TKNVQLSLDMFLEK-LSGELTRLEDTLSTITQDVSAVMSKLKEVELVsTDAATAVKSDVNSLRGSMSNVELALNELSQRV 202
                                    55555566554444.77789999999999999999999999999885366677899999999999999999999999998 PP

                         AAA_13 345 eaKrkepfksvelesvkakiesikklvaeineliak 380
                                    ++  +  ++ + l +++ ++++++ +++++n+l +k
  gi|119719711|ref|YP_920206.1| 203 TRLEE--SQLAALRQYSLELQEVSLKLTQVNQLLQK 236
                                    76543..33345666666666666666666665544 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.1    0.0057       1.3      16      61 ..      73     112 ..      51     130 .. 0.70
   2 ?    5.3   0.3      0.12        28      39      63 ..     130     154 ..     115     168 .. 0.63
   3 ?    3.4   7.7      0.47   1.1e+02       9      62 ..     152     206 ..     147     243 .. 0.48

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0057
                        NPV_P10  16 vddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenI 61 
                                    ++++V  lq q+++++e l+       +L+a +a+   l ++v+ +
  gi|119719711|ref|YP_920206.1|  73 LNTRVGTLQGQIKELEEALKS------HLEAFQAENSRLAESVNRV 112
                                    567777777777777777666......6666666666666666554 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.12
                        NPV_P10  39 elnekLdaqsaqLaeletkvenIqd 63 
                                     l   L+++s +L+ le+++++I++
  gi|119719711|ref|YP_920206.1| 130 SLDMFLEKLSGELTRLEDTLSTITQ 154
                                    4555666667777777776666654 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.47
                        NPV_P10   9 IradikavddkVdalqqqvddvqenlp.dvtelnekLdaqsaqLaeletkvenIq 62 
                                    I +d++av +k++ ++   +d ++ ++ dv+ l   + +   +L+el++ v+  +
  gi|119719711|ref|YP_920206.1| 152 ITQDVSAVMSKLKEVELVSTDAATAVKsDVNSLRGSMSNVELALNELSQRVTRLE 206
                                    6666666666655554433333332221444444444444444444444443332 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.3    0.0025      0.59     152     229 ..      46     123 ..      38     129 .. 0.78
   2 !   10.1   4.3    0.0012      0.27     172     279 ..      84     192 ..      81     194 .. 0.64
   3 ?    6.9   8.4     0.011       2.5     158     228 ..     170     240 ..     151     245 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0025
                           Spc7 152 eedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeql 229
                                    e d +lL +  + l++ + +l+   + l+ ++ +lq + +ele+  k  Le+++ e ++l + +++ ++e +e ++ l
  gi|119719711|ref|YP_920206.1|  46 EGDVALLLAALKRLNNGVYALKVTLDFLNTRVGTLQGQIKELEEALKSHLEAFQAENSRLAESVNRVSREFKEGTDTL 123
                                    567777788888888888888888888888888888888888888888888888888888888888888888877665 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0012
                           Spc7 172 leeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeie.ekkkelaelqeqleeleekieelkeqkseleeei 250
                                    ++e +++l++ le  q+++  l+++ +   +e++e  ++l ++++ ++   l++l  +l++le++++++++  s +++++
  gi|119719711|ref|YP_920206.1|  84 IKELEEALKSHLEAFQAENSRLAESVNRVSREFKEGTDTLTKNVQlSLDMFLEKLSGELTRLEDTLSTITQDVSAVMSKL 163
                                    34444455555555555555444444444445555555554444412344578888888888888888888888888888 PP

                           Spc7 251 aeaervleeckgwsesevsrlkeevkale 279
                                    +e e v        +s+v++l+ +++++e
  gi|119719711|ref|YP_920206.1| 164 KEVELVSTDAATAVKSDVNSLRGSMSNVE 192
                                    88888888888888888888888877765 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.011
                           Spc7 158 LekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeq 228
                                     ++    +++ +++l+   +++e  l++l ++++ le+++ + L+++  el+e++ ++ + ++ l++l e+
  gi|119719711|ref|YP_920206.1| 170 STDAATAVKSDVNSLRGSMSNVELALNELSQRVTRLEESQLAALRQYSLELQEVSLKLTQVNQLLQKLLEK 240
                                    445556678889999999999**************************************888888887655 PP

>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1       0.3        70      45      77 ..      94     126 ..      65     129 .. 0.67
   2 !    9.1   0.4    0.0066       1.5       7      85 ..      89     167 ..      83     168 .. 0.92
   3 ?    7.0   0.0     0.028       6.6      44      78 ..     172     206 ..     170     212 .. 0.92
   4 ?    0.6   0.1       2.9   6.8e+02      60      82 ..     213     235 ..     207     239 .. 0.60

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.3
                                    HCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         WXG100  45 aadafqaefeewkqaaqklvdaLeeisealkqa 77 
                                      +afqae  ++ ++++++ ++++e +++l+++
  gi|119719711|ref|YP_920206.1|  94 HLEAFQAENSRLAESVNRVSREFKEGTDTLTKN 126
                                    346777777778888888877777777777765 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0066
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCGCGCTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         WXG100   7 eelrqaaarfqkqaeeledelqrlkaevdalqsgWsGaaadafqaefeewkqaaqklvdaLeeisealkqaanafedaD 85 
                                    e+l ++  +fq+++++l + ++r+ +e ++ +++   + + + ++++e++  ++++l d L++i++ + ++ +++ +++
  gi|119719711|ref|YP_920206.1|  89 EALKSHLEAFQAENSRLAESVNRVSREFKEGTDTLTKNVQLSLDMFLEKLSGELTRLEDTLSTITQDVSAVMSKLKEVE 167
                                    6788999999*********************************************************999999888776 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.028
                                    HHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         WXG100  44 aaadafqaefeewkqaaqklvdaLeeisealkqaa 78 
                                    +aa+a ++  + ++ ++ ++  aL+e+s+ +++  
  gi|119719711|ref|YP_920206.1| 172 DAATAVKSDVNSLRGSMSNVELALNELSQRVTRLE 206
                                    79***************************999876 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 2.9
                                    HHHHHHHHHHHHHHHHHHHHHHH CS
                         WXG100  60 aqklvdaLeeisealkqaanafe 82 
                                    ++++  +L+e+s +l+q+++ ++
  gi|119719711|ref|YP_920206.1| 213 LRQYSLELQEVSLKLTQVNQLLQ 235
                                    45555556666666666655544 PP

>> Jnk-SapK_ap_N  JNK_SAPK-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.7      0.08        19      98     146 ..      77     115 ..      61     130 .. 0.48
   2 !   15.7   7.7   5.8e-05     0.013      52     149 ..     135     239 ..     122     244 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.08
                  Jnk-SapK_ap_N  98 veqleeenrelelkaknaadqlsrleekeaelkkeysklheretellkk 146
                                    v  l+ +++ele          ++l+++ +  + e+s+l e+ + + ++
  gi|119719711|ref|YP_920206.1|  77 VGTLQGQIKELE----------EALKSHLEAFQAENSRLAESVNRVSRE 115
                                    444444444444..........222222222222222222222222222 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 5.8e-05
                  Jnk-SapK_ap_N  52 leelreeleqLeteyerekelrkraeeeleeiedqweeerkelqekveqleeenrelelkaknaadqlsrleekeaelkk 131
                                    le+l+ el++Le  ++  +++  +   +l e+e +  + + ++++ v++l+  + ++el +++++++++rlee++    +
  gi|119719711|ref|YP_920206.1| 135 LEKLSGELTRLEDTLSTITQDVSAVMSKLKEVELVSTDAATAVKSDVNSLRGSMSNVELALNELSQRVTRLEESQLAALR 214
                                    8999***********************************************************************88888 PP

                  Jnk-SapK_ap_N 132 eysklhe.......retellkklke 149
                                    +ys   +       + ++ll+kl e
  gi|119719711|ref|YP_920206.1| 215 QYSLELQevslkltQVNQLLQKLLE 239
                                    8775544599999999999999877 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.2     0.014       3.2       8      73 ..      49     113 ..      44     117 .. 0.86
   2 ?    6.7   1.2     0.042       9.8      17      83 ..      90     157 ..      89     168 .. 0.69
   3 !   10.2   5.5    0.0034      0.79      16      84 ..     175     239 ..     169     243 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.014
                Snapin_Pallidin   8 lellepkldeldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrms 73 
                                    + ll  +l++l++ + +l+ + + L+ ++ +l+ ++keleea + + l+ ++    +L++  +r+s
  gi|119719711|ref|YP_920206.1|  49 VALLLAALKRLNNGVYALKVTLDFLNTRVGTLQGQIKELEEALK-SHLEAFQAENSRLAESVNRVS 113
                                    678899999999999999999999***************99999.778888888888888888876 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.042
                Snapin_Pallidin  17 eldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrms.slnerlqklk 83 
                                    +l+++l++ +++ + L+e+++r ++++ke  ++  ++v   l+  ++KL+    r++ +l++++q + 
  gi|119719711|ref|YP_920206.1|  90 ALKSHLEAFQAENSRLAESVNRVSREFKEGTDTLTKNVQLSLDMFLEKLSGELTRLEdTLSTITQDVS 157
                                    67889999999999999999999999998888777677777888888876544444313444444444 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.0034
                Snapin_Pallidin  16 deldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqklkk 84 
                                    +++++ +++lr s + +   l++l++++++lee q     + l++y   L+++  +++++n+ lqkl +
  gi|119719711|ref|YP_920206.1| 175 TAVKSDVNSLRGSMSNVELALNELSQRVTRLEESQL----AALRQYSLELQEVSLKLTQVNQLLQKLLE 239
                                    5789999999*******************9999887....*************************9976 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.1    0.0025      0.57     219     280 ..      57     118 ..      49     134 .. 0.78
   2 !    8.1   4.8    0.0076       1.8      63     152 ..     135     228 ..     124     241 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0025
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Filament 219 telrrqiqsleieleslkkqkasleaqlaeleerleaeleklqeklseleeelaeireemar 280
                                    + l+  + +l++ l+ l     +l+ q++elee l++ le +q++ s+l e ++++ +e + 
  gi|119719711|ref|YP_920206.1|  57 KRLNNGVYALKVTLDFLNTRVGTLQGQIKELEEALKSHLEAFQAENSRLAESVNRVSREFKE 118
                                    56777788899999999999999999999999999999999999999988888877666554 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0076
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       Filament  63 ldeltkerarlqleldnlreeledlrkkyeke....lnkreevEaelkalrkdldeatlarvdLekkvesLkeelaflkk 138
                                    l++l+ e +rl+  l+++ +++  + +k+++     +   ++v +++++lr  + +  la  +L ++v  L+e      +
  gi|119719711|ref|YP_920206.1| 135 LEKLSGELTRLEDTLSTITQDVSAVMSKLKEVelvsTDAATAVKSDVNSLRGSMSNVELALNELSQRVTRLEESQLAALR 214
                                    55566666666666666666666666666553455556667777777777777777777777777777777775444444 PP

                                    XXXXXXXXXXXXXX CS
                       Filament 139 vheeEvkelqkqvs 152
                                     ++ E++e+  +++
  gi|119719711|ref|YP_920206.1| 215 QYSLELQEVSLKLT 228
                                    57777777766653 PP

>> ApoLp-III  Apolipophorin-III precursor (apoLp-III)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   1.8   3.4e-05    0.0079      37     127 ..      72     162 ..      56     165 .. 0.76
   2 ?    3.7   5.2      0.26        60      20     112 ..     145     240 ..     134     246 .. 0.51

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.4e-05
                      ApoLp-III  37 qlkqvikslqeelkkksdeleealkevkkkieetadklseenPevkkkaqelqekvQsgvqslvkesqklaeslkensqe 116
                                     l++  ++lq ++k+  ++l++ l+ ++++ ++ a++++  + e k+  + l ++vQ ++ + ++   +   +l++  ++
  gi|119719711|ref|YP_920206.1|  72 FLNTRVGTLQGQIKELEEALKSHLEAFQAENSRLAESVNRVSREFKEGTDTLTKNVQLSLDMFLEKLSGELTRLEDTLST 151
                                    56666777888888888888888888888888888888888888888888888888888888888877777777777777 PP

                      ApoLp-III 117 akeklakaikq 127
                                    +++++++ + +
  gi|119719711|ref|YP_920206.1| 152 ITQDVSAVMSK 162
                                    77777777665 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.26
                      ApoLp-III  20 qeevvetiKensenlvdqlkqv...ikslqeelkkksdeleealkevkkkieetadklse.enPevkkkaqelqekvQsg 95 
                                     e+++ ti + ++ + ++lk+v   +  +  ++k   + l  ++++v  +++e  + ++  e+++   ++ +++ ++Q+ 
  gi|119719711|ref|YP_920206.1| 145 LEDTLSTITQDVSAVMSKLKEVelvSTDAATAVKSDVNSLRGSMSNVELALNELSQRVTRlEESQ-LAALRQYSLELQEV 223
                                    45666666666666666655541113333344455555556666666666666666666533333.33556666666665 PP

                      ApoLp-III  96 vqslvkesqklaeslke 112
                                      +l +  q l + l++
  gi|119719711|ref|YP_920206.1| 224 SLKLTQVNQLLQKLLEK 240
                                    55555544545555555 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   1.0    0.0076       1.8      75     130 ..      68     124 ..      51     130 .. 0.49
   2 !    8.8   3.3    0.0041      0.96      37     119 ..      83     167 ..      75     167 .. 0.83
   3 !   11.5   9.7   0.00059      0.14      44     153 ..     130     240 ..     117     244 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0076
                            GAS  75 kqlknyekdkqslk.nlkarlkelekelkdlkwehevleqrfekvekerdelykkfe 130
                                      l + +     l+ ++k+  + l+++l++ + e+  l + +++v++e++e +++ +
  gi|119719711|ref|YP_920206.1|  68 VTLDFLNTRVGTLQgQIKELEEALKSHLEAFQAENSRLAESVNRVSREFKEGTDTLT 124
                                    555555555555442233333344445555555555555555555555555555444 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0041
                            GAS  37 elkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdk..qslknlkarlkelekelkdlkwehevleqr 114
                                    ++k+ ee+ + +l++ ++en+rl e ++++ +e +e    l +  +    + l++l  +l++le+ l++++++   +  +
  gi|119719711|ref|YP_920206.1|  83 QIKELEEALKSHLEAFQAENSRLAESVNRVSREFKEGTDTLTKNVQLSldMFLEKLSGELTRLEDTLSTITQDVSAVMSK 162
                                    567889999999*****************999999998888776665411567899999999999999999998888888 PP

                            GAS 115 fekve 119
                                    +++ve
  gi|119719711|ref|YP_920206.1| 163 LKEVE 167
                                    88876 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.00059
                            GAS  44 rnekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkq.slknlkarlkelekelkdlkwehevleqrfekveker 122
                                    + +  l+++s e  rl+++L + +++v     +lk+ e     + +++k+ +++l   ++++++  + l+qr++++e++ 
  gi|119719711|ref|YP_920206.1| 130 SLDMFLEKLSGELTRLEDTLSTITQDVSAVMSKLKEVELVSTdAATAVKSDVNSLRGSMSNVELALNELSQRVTRLEESQ 209
                                    56677899999*************************997665167789******************************** PP

                            GAS 123 delykkfeaaiqevqqktglknllLekklka 153
                                     +  +++   +qev+ k    n lL+k l++
  gi|119719711|ref|YP_920206.1| 210 LAALRQYSLELQEVSLKLTQVNQLLQKLLEK 240
                                    **************************98876 PP

>> Surfac_D-trimer  Lung surfactant protein D coiled-coil trimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0     0.017         4       4      22 ..      73      91 ..      70     101 .. 0.88
   2 ?    3.1   0.0      0.38        88       8      23 ..     135     150 ..     130     168 .. 0.90
   3 ?    0.9   0.1       1.8   4.3e+02       3      24 ..     183     204 ..     181     216 .. 0.55

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.017
                                   HHHHHHHHHHHHHHHHHHH CS
                Surfac_D-trimer  4 LrQrveaLeGklqrLqnaf 22
                                   L  rv+ L+G+++ L+ a+
  gi|119719711|ref|YP_920206.1| 73 LNTRVGTLQGQIKELEEAL 91
                                   778*************986 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.38
                                    HHHHHHHHHHHHHHHH CS
                Surfac_D-trimer   8 veaLeGklqrLqnafs 23 
                                    +e L G+l rL+  +s
  gi|119719711|ref|YP_920206.1| 135 LEKLSGELTRLEDTLS 150
                                    5889*******99887 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 1.8
                                    HHHHHHHHHHHHHHHHHHHHHH CS
                Surfac_D-trimer   3 aLrQrveaLeGklqrLqnafsq 24 
                                    +Lr  + + e  l  L   +++
  gi|119719711|ref|YP_920206.1| 183 SLRGSMSNVELALNELSQRVTR 204
                                    5555555555444444444433 PP

>> FH2  Formin Homology 2 Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   1.0    0.0001     0.024     260     344 ..      77     159 ..      40     160 .. 0.85
   2 ?    8.1   4.6    0.0054       1.2     250     345 ..     146     238 ..     142     243 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.0001
                                    GGGHHHHTTTHHHCCTS-HHHHHHHHHHHHHHHHHHHHHHHHCCTTSSTT-THHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            FH2 260 vldfsseLknvkkaakvnleslekevkklekglkklekelessekkeepsdkflevlkeflkeaeeklkkleeelkeake 339
                                    v  ++ ++k++++a k  le++++e + l +++  +++e++++    +  +++  +l  fl++ + +l +le+ l+++++
  gi|119719711|ref|YP_920206.1|  77 VGTLQGQIKELEEALKSHLEAFQAENSRLAESVNRVSREFKEGTD--TLTKNVQLSLDMFLEKLSGELTRLEDTLSTITQ 154
                                    667888999999999999999999999999999999999999998..777777888888999999999999999888888 PP

                                    HHHHH CS
                            FH2 340 lvkel 344
                                     v ++
  gi|119719711|ref|YP_920206.1| 155 DVSAV 159
                                    87665 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0054
                                    HHHHHTTSGGGGGHHHHTTTHHHCCTS-HHHHHHHHHHHHHHHHHHHHHHHHCCTTSSTT-THHHHHHHHHHHHHHHHHH CS
                            FH2 250 vkiireklpevldfsseLknvkkaakvnleslekevkklekglkklekelessekkeepsdkflevlkeflkeaeeklkk 329
                                    ++++++ +++v+ + s+Lk+v+ ++    ++++++v+ l+ +++++e  l++ ++      ++ e+    l++ + +l++
  gi|119719711|ref|YP_920206.1| 146 EDTLSTITQDVSAVMSKLKEVELVSTDAATAVKSDVNSLRGSMSNVELALNELSQ---RVTRLEESQLAALRQYSLELQE 222
                                    566777789****************************************999999...5555555555555555555555 PP

                                    HHHHHHHHHHHHHHHH CS
                            FH2 330 leeelkeakelvkelv 345
                                    ++ +l+++++l+++l+
  gi|119719711|ref|YP_920206.1| 223 VSLKLTQVNQLLQKLL 238
                                    5555555555555554 PP

>> CCDC-167  Coiled-coil domain-containing protein 167
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1      0.19        43       3      28 ..      81     106 ..      52     131 .. 0.79
   2 ?   14.2   0.6   0.00018     0.042       5      62 ..     141     199 ..     137     216 .. 0.75
   3 ?    0.9   2.0       2.5   5.7e+02       9      45 ..     205     243 ..     200     245 .. 0.57

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.19
                       CCDC-167   3 aseIdkleeklascrerLeaverrlr 28 
                                    + +I++lee+l+s  e  +a ++rl 
  gi|119719711|ref|YP_920206.1|  81 QGQIKELEEALKSHLEAFQAENSRLA 106
                                    45777777777777777777666665 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 0.00018
                       CCDC-167   5 eIdkleeklascrerLeaverrlrkeel.seeeResleeEeaslkeqleenekeLksLr 62 
                                    e+++le++l+ + +++ av ++l+++el s+++ ++++   +sl++ +++ e  L++L 
  gi|119719711|ref|YP_920206.1| 141 ELTRLEDTLSTITQDVSAVMSKLKEVELvSTDAATAVKSDVNSLRGSMSNVELALNELS 199
                                    8899**********************983556666666777777777777776666664 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 2.5
                       CCDC-167   9 leek.lasc.rerLeaverrlrkeelseeeResleeEea 45 
                                    lee+ la++ + +Le  e +l+ +++ +   + le+E +
  gi|119719711|ref|YP_920206.1| 205 LEESqLAALrQYSLELQEVSLKLTQVNQLLQKLLEKESK 243
                                    444313333134677777777777777777777777754 PP

>> COG2  COG (conserved oligomeric Golgi) complex component, COG2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.5     0.064        15      67     112 ..      80     125 ..      69     136 .. 0.81
   2 ?   14.4   3.5   0.00013      0.03      59     130 ..     137     206 ..     121     209 .. 0.82
   3 ?    3.8   3.1      0.25        59      70     132 ..     173     233 ..     166     242 .. 0.61

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.064
                           COG2  67 lqeeleevesplaaarkkvesvreklsereeeveskleeakeleek 112
                                    lq +++e+e  l++  + +++ ++ l+e  ++v+ + +e ++   k
  gi|119719711|ref|YP_920206.1|  80 LQGQIKELEEALKSHLEAFQAENSRLAESVNRVSREFKEGTDTLTK 125
                                    6889999999999999999999999999999999999988876544 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 0.00013
                           COG2  59 slSghLvglqeeleevesplaaarkkvesvreklsereeeveskleeakeleekrellklllkldevvekle 130
                                    +lSg+L+ l++ l++++++++a+++k+++v+    ++ ++v+s ++  +   +++++  +l +l+++v +le
  gi|119719711|ref|YP_920206.1| 137 KLSGELTRLEDTLSTITQDVSAVMSKLKEVELVSTDAATAVKSDVNSLRG--SMSNVELALNELSQRVTRLE 206
                                    7******************************************9997654..45555666666666666666 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.25
                           COG2  70 eleevesplaaarkkvesvreklsereeeveskleeakeleekrellklllkldevvekleal 132
                                    +   v+s+++++r  +++v+ +l+e +++v+  lee + ++  +++l  l++++  + ++++l
  gi|119719711|ref|YP_920206.1| 173 AATAVKSDVNSLRGSMSNVELALNELSQRVTR-LEESQLAALRQYSL-ELQEVSLKLTQVNQL 233
                                    44567777888887777777777777777764.44444444444333.345555555555554 PP

>> DUF4635  Domain of unknown function (DUF4635)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1      0.05        12      94     131 ..      65     102 ..      55     105 .. 0.90
   2 ?   11.8   0.1   0.00055      0.13      77     123 ..     113     159 ..     106     170 .. 0.80
   3 ?    0.2   0.2       2.2     5e+02      94     126 ..     183     215 ..     177     224 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.05
                        DUF4635  94 nlhvflekleeevreleqlvrdleeWldallgdlklee 131
                                    +l+v l+ l+  v  l+ ++++lee l  +l+  ++e+
  gi|119719711|ref|YP_920206.1|  65 ALKVTLDFLNTRVGTLQGQIKELEEALKSHLEAFQAEN 102
                                    58999999***********************9988886 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00055
                        DUF4635  77 kepseePikvlrkWlkenlhvflekleeevreleqlvrdleeWldal 123
                                    + + +e + +l k ++ +l++flekl  e+  le  +  + + + a+
  gi|119719711|ref|YP_920206.1| 113 SREFKEGTDTLTKNVQLSLDMFLEKLSGELTRLEDTLSTITQDVSAV 159
                                    55678899999***********************9877666555555 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 2.2
                        DUF4635  94 nlhvflekleeevreleqlvrdleeWldallgd 126
                                    +l   + ++e  ++el q v  lee   a l +
  gi|119719711|ref|YP_920206.1| 183 SLRGSMSNVELALNELSQRVTRLEESQLAALRQ 215
                                    566667778889999999999999866555555 PP

>> Tweety  Tweety
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.2    0.0047       1.1      87     126 ..      59      98 ..      49     128 .. 0.79
   2 ?    7.8   3.0    0.0048       1.1     106     183 ..     121     207 ..     100     220 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0047
                         Tweety  87 tndGvlqltyslrkanhtlagikklvseteesleekleee 126
                                    +n+Gv+ l  +l+  n+ + +++ +++e+ee+l+++le  
  gi|119719711|ref|YP_920206.1|  59 LNNGVYALKVTLDFLNTRVGTLQGQIKELEEALKSHLEAF 98 
                                    79*************************9999999888753 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0048
                         Tweety 106 agikklvseteesleekleeeLtkleeifakrtd.......lletlrlvqeq.veevvqqlselp.flkkkdvsltelae 176
                                     +++k v+ + + + ekl+ eLt+le+ +++ t+        l+ ++lv +  +++v + +++l+  ++++++ l+el++
  gi|119719711|ref|YP_920206.1| 121 DTLTKNVQLSLDMFLEKLSGELTRLEDTLSTITQdvsavmsKLKEVELVSTDaATAVKSDVNSLRgSMSNVELALNELSQ 200
                                    345566666666677788889999999988877767776555566666655414555667899999999*********** PP

                         Tweety 177 qvelvel 183
                                    +v+ +e+
  gi|119719711|ref|YP_920206.1| 201 RVTRLEE 207
                                    9998876 PP

>> HrpB7  Bacterial type III secretion protein (HrpB7)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.2       0.1        23      81     118 ..      77     114 ..      59     118 .. 0.68
   2 ?   13.4   0.5   0.00032     0.074      26     112 ..      82     166 ..      79     177 .. 0.73
   3 ?    1.8   0.6       1.3   2.9e+02      81     100 ..     195     215 ..     169     241 .. 0.51

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.1
                          HrpB7  81 rdvlegrvraaeaelaaarqaldaaedavaatarkiaR 118
                                    ++ l+g+++++e++l+   +a++a++ ++a+   +++R
  gi|119719711|ref|YP_920206.1|  77 VGTLQGQIKELEEALKSHLEAFQAENSRLAESVNRVSR 114
                                    45666667777776666666666666666666666666 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00032
                          HrpB7  26 aaraalaaaea.alaaaqaqveaardavraheerlddlttgsspfsiadylacrayrdvlegrvraaeaelaaarqalda 104
                                     ++++l++a +  l+a qa+ ++ ++ v++  ++ +    g+  ++ +  l+++++++ l+g+++ +e  l   +q + a
  gi|119719711|ref|YP_920206.1|  82 GQIKELEEALKsHLEAFQAENSRLAESVNRVSREFK---EGTDTLTKNVQLSLDMFLEKLSGELTRLEDTLSTITQDVSA 158
                                    445555444330344555555555555555555555...588999*********************************99 PP

                          HrpB7 105 aedavaat 112
                                       +++++
  gi|119719711|ref|YP_920206.1| 159 VMSKLKEV 166
                                    88888766 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 1.3
                          HrpB7  81 rdvlegrvraae.aelaaarq 100
                                    + +l++rv+ +e ++laa+rq
  gi|119719711|ref|YP_920206.1| 195 LNELSQRVTRLEeSQLAALRQ 215
                                    334444444333123333333 PP

>> PIN_8  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.5   0.00013      0.03      36     136 ..      64     165 ..      48     176 .. 0.68
   2 ?   -0.2   0.2       3.2   7.5e+02     103     112 ..     195     207 ..     164     246 .. 0.36

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 0.00013
                          PIN_8  36 vPhqvalEfqrnresviskekkayedl.ekeleklkkaaekkleealkkwakkkaldteelrkelkkqleelkeelkael 114
                                    +   v l f + r  +++ + k +e++ +++le+++++ +  l+e +++ +++ +  t++l k+++ +l+ + e+l+ el
  gi|119719711|ref|YP_920206.1|  64 YALKVTLDFLNTRVGTLQGQIKELEEAlKSHLEAFQAENS-RLAESVNRVSREFKEGTDTLTKNVQLSLDMFLEKLSGEL 142
                                    4678999999999999997766666550455677776666.455555555555555589999999999999999999999 PP

                          PIN_8 115 eelkksskadkee.dpilkklee 136
                                    ++l+++ ++++++   + +kl+e
  gi|119719711|ref|YP_920206.1| 143 TRLEDTLSTITQDvSAVMSKLKE 165
                                    99999999997543344444444 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 3.2
                          PIN_8 103 leelkeel...ka 112
                                    l+el++++   ++
  gi|119719711|ref|YP_920206.1| 195 LNELSQRVtrlEE 207
                                    2222222211111 PP

>> YjcZ  YjcZ-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   4.4   9.8e-05     0.023      25     132 ..     101     206 ..      83     214 .. 0.81
   2 ?    2.9   1.9      0.25        59      33      88 ..     187     242 ..     183     246 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 9.8e-05
                           YjcZ  25 freRLlqellastqlraseinaevnaalelrLk.llekLsreldpghLALttiaqrlallsqtlaekasaapklaqalaa 103
                                      +RL  e++ +++++  e + +++++++l L  +lekLs+el + +  L+ti+q ++ +  +l+e + ++ + a a++ 
  gi|119719711|ref|YP_920206.1| 101 ENSRL-AESVNRVSREFKEGTDTLTKNVQLSLDmFLEKLSGELTRLEDTLSTITQDVSAVMSKLKEVELVSTDAATAVKS 179
                                    46899.8999**********************7369**********************9999999999988878877777 PP

                           YjcZ 104 laeefaarverkekaltqrellvqarrhs 132
                                      +++  ++++ e al   el + + r  
  gi|119719711|ref|YP_920206.1| 180 DVNSLRGSMSNVELAL--NELSQRVTRLE 206
                                    7777777777666665..56666666654 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.25
                           YjcZ  33 llastqlraseinaevnaalelrLkllekLsreldpghLALttiaqrlallsqtla 88 
                                    ++++++l   e +  v+   e +L  l + s el+   L Lt+++q l +l ++++
  gi|119719711|ref|YP_920206.1| 187 SMSNVELALNELSQRVTRLEESQLAALRQYSLELQEVSLKLTQVNQLLQKLLEKES 242
                                    55666666667777777766778888888888888888888888888877766555 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1     0.079        18      31     100 ..      57     126 ..      50     133 .. 0.61
   2 ?    8.8   1.4    0.0076       1.8      25     119 ..      72     164 ..      67     171 .. 0.46
   3 ?   10.2   5.4    0.0027      0.63      26     118 ..     131     224 ..     126     243 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.079
                                    CCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCC CS
                      Fib_alpha  31 kdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaq 100
                                    k +++ +  l+ +l+ ++ +  + +  +ke+++ l+++ +  + +++ + +s +++ +e  +  +t++++
  gi|119719711|ref|YP_920206.1|  57 KRLNNGVYALKVTLDFLNTRVGTLQGQIKELEEALKSHLEAFQAENSRLAESVNRVSREFKEGTDTLTKN 126
                                    5666677777777777777777777777777777777777666665555555555555554444444444 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0076
                                    CCCCCCCCCCHHHCCCCCCCCCC....CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCC CS
                      Fib_alpha  25 lllkyekdvkkdlekleneleei....snstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaq 100
                                    +l++   +++ ++++le+ l+++    + +++   e v++++   +e         +++k+++ +l+   ++l  ++++ 
  gi|119719711|ref|YP_920206.1|  72 FLNTRVGTLQGQIKELEEALKSHleafQAENSRLAESVNRVSREFKEGTD------TLTKNVQLSLDMFLEKLSGELTRL 145
                                    55555556666666666666555000044444444444444444444444......444444444444444444444444 PP

                                    HHHHHHHHHHHHHHHHHHH CS
                      Fib_alpha 101 esnirvLqnvlesneqkiq 119
                                    e ++  +++ +++  +k++
  gi|119719711|ref|YP_920206.1| 146 EDTLSTITQDVSAVMSKLK 164
                                    4444444444443333333 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.0027
                                    CCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCH.HHH CS
                      Fib_alpha  26 llkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqe.sni 104
                                    l+   ++++ +l++le++l++i++  + + +  ke++ + +++ +  k   n ++ s +++e   ++l +++++ e s++
  gi|119719711|ref|YP_920206.1| 131 LDMFLEKLSGELTRLEDTLSTITQDVSAVMSKLKEVELVSTDAATAVKSDVNSLRGSMSNVELALNELSQRVTRLEeSQL 210
                                    56666778889999999999999999999999999999999999999988999********************9999*** PP

                                    HHHHHHHHHHHHHH CS
                      Fib_alpha 105 rvLqnvlesneqki 118
                                     +L++   ++++  
  gi|119719711|ref|YP_920206.1| 211 AALRQYSLELQEVS 224
                                    ***98754444333 PP

>> Fer4_24  Ferredoxin I 4Fe-4S cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.2   0.00017      0.04      16      34 ..     145     163 ..     141     164 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 0.00017
                        Fer4_24  16 LErSiegvmskIdavesKL 34 
                                    LE  +++++  + av+sKL
  gi|119719711|ref|YP_920206.1| 145 LEDTLSTITQDVSAVMSKL 163
                                    9*****************9 PP

>> EspB_PE  ESX-1 secreted protein B PE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   0.00024     0.055      39      71 ..      85     117 ..      81     122 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00024
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        EspB_PE  39 nasAealrkylaageaErerLAesLrnaAkaYe 71 
                                    +   eal+++l+a +aE+ rLAes++ + + ++
  gi|119719711|ref|YP_920206.1|  85 KELEEALKSHLEAFQAENSRLAESVNRVSREFK 117
                                    555689*******************99887775 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.5    0.0024      0.57      10      99 ..      35     125 ..      24     138 .. 0.74
   2 ?    8.5   0.9    0.0097       2.3      34     104 ..      91     163 ..      89     167 .. 0.77
   3 ?    4.9   3.3      0.13        31       7     101 ..     152     238 ..     149     243 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0024
                                    -HHHHHHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT.S-TCCCCCCCHHHHHHHHHHHH CS
                   Seryl_tRNA_N  10 npeavkeklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkk.edaeeliaevkelkeelkalea 88 
                                    +p++v+      g+ ++++++l  l++   +l+v+l+ l+++  +l+ +I+++ ++     e+  ae + l e +++++ 
  gi|119719711|ref|YP_920206.1|  35 EPDEVEIVEVGEGDVALLLAALKRLNNGVYALKVTLDFLNTRVGTLQGQIKELEEALkSHLEAFQAENSRLAESVNRVSR 114
                                    667777766677778889999999999999*******************9999988775666666666666666666666 PP

                                    HHHHHHHHHHH CS
                   Seryl_tRNA_N  89 elkeleaelek 99 
                                    e ke ++ l+k
  gi|119719711|ref|YP_920206.1| 115 EFKEGTDTLTK 125
                                    66666555554 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0097
                                    HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT..S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCTS CS
                   Seryl_tRNA_N  34 ldekrrelqveleelqaerNelskeIgkakkkk..edaeeliaevkelkeelkaleaelkeleaeleklllai 104
                                    l ++ ++ q+e   l +  N++s+e+++  +    +   +l    ++l+ el +le++l+++++++ ++++++
  gi|119719711|ref|YP_920206.1|  91 LKSHLEAFQAENSRLAESVNRVSREFKEGTDTLtkNVQLSLDMFLEKLSGELTRLEDTLSTITQDVSAVMSKL 163
                                    5566677788888889999999999999988875233334555569999999999999999999999999876 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.13
                                    HHH-HHHHHHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHH CS
                   Seryl_tRNA_N   7 irenpeavkeklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkal 86 
                                    i +++ av  klk  +++    d+  ++ +   +l+  + ++    Nels+ + ++ +++      +a  ++ + el+++
  gi|119719711|ref|YP_920206.1| 152 ITQDVSAVMSKLK--EVELVSTDAATAVKSDVNSLRGSMSNVELALNELSQRVTRLEESQ------LAALRQYSLELQEV 223
                                    7778888888885..456777889999999999999999999999999999999999876......45555555555555 PP

                                    HHHHHHHHHHHHHHH CS
                   Seryl_tRNA_N  87 eaelkeleaelekll 101
                                    + +l+++++ l+kll
  gi|119719711|ref|YP_920206.1| 224 SLKLTQVNQLLQKLL 238
                                    555555555555554 PP

>> Tup_N  Tup N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0     0.032       7.4      43      73 ..      79     109 ..      58     123 .. 0.86
   2 ?    4.7   1.7      0.16        38       3      67 ..     146     221 ..     144     231 .. 0.43

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.032
                          Tup_N  43 qirqtlyeLeeahrkikqqYEeeiarLkaeL 73 
                                    +++ +++eLeea ++  ++++ e +rL + +
  gi|119719711|ref|YP_920206.1|  79 TLQGQIKELEEALKSHLEAFQAENSRLAESV 109
                                    6788899999999999999999999997765 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.16
                          Tup_N   3 nelLdavkqEfdalsqeasslkaqkdeyelkiqsqiqE...........lqqirqtlyeLeeahrkikqqYEeeia 67 
                                    ++ L  + q+ +a+ ++++ ++    +  + ++s ++            l+ + q +  Lee++ +  +qY  e++
  gi|119719711|ref|YP_920206.1| 146 EDTLSTITQDVSAVMSKLKEVELVSTDAATAVKSDVNSlrgsmsnvelaLNELSQRVTRLEESQLAALRQYSLELQ 221
                                    5555555555555555555555555555554444444311110001111344444444444444444444444444 PP

>> Cob_adeno_trans  Cobalamin adenosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   2.5     0.002      0.48      31     141 ..      69     202 ..      60     241 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.002
                                    HHHHHHHHHHHHHHHCTTTTHHHHHHHHHHHHHHHHHHHHHHT......................-BTCCG-S--HHHH. CS
                Cob_adeno_trans  31 tvDelnsaiglarallaeeeeelkeaLeeiqneLfdlgaelatp.....................ekkkekkkiteeev. 88 
                                    t+D ln  +g ++ +++e ee+lk++Le  q e  +l +++                                     + 
  gi|119719711|ref|YP_920206.1|  69 TLDFLNTRVGTLQGQIKELEEALKSHLEAFQAENSRLAESVNRVsrefkegtdtltknvqlsldmF------------Le 136
                                    789999999999999988899999999999988888888875334433333322222333322220............12 PP

                                    ......HHHHHHHHHHHHHS-....-EESEEES-S...SHHHHHHHHHHHHHHHHHHHHHHHHHHS CS
                Cob_adeno_trans  89 ......eelekeideleaelp....plksfilpgg...spaaaalhvaRtvcRraERavvelaeee 141
                                          ++le+ + +++++++    +lk+  l +    + + + ++ +R  +  +E a+ el+++ 
  gi|119719711|ref|YP_920206.1| 137 klsgelTRLEDTLSTITQDVSavmsKLKEVELVSTdaaTAVKSDVNSLRGSMSNVELALNELSQRV 202
                                    222222444444444433333333334443333331115566778888888888888887777654 PP

>> T3SSipB  Type III cell invasion protein SipB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.4     0.011       2.5      29      67 ..      90     128 ..      79     167 .. 0.66
   2 ?    6.8   2.5     0.038       8.9      43     131 ..     155     242 ..     130     246 .. 0.57

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.011
                                    HHHHHHHHTTTTT----STHHHHHHHHHHHHHHHHHHHH CS
                        T3SSipB  29 awkamskaqqeaasklSdelqtalseakgatddleaaie 67 
                                    a k+  +a q+++s+l + ++++  e k+ td l++ ++
  gi|119719711|ref|YP_920206.1|  90 ALKSHLEAFQAENSRLAESVNRVSREFKEGTDTLTKNVQ 128
                                    556667777777777777777777777777777776654 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.038
                                    ---STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---------CHHHHHHHHH...HHHHHHHH CS
                        T3SSipB  43 klSdelqtalseakgatddleaaiekadqaksaadaatkkvdeaqkrlkeLaPdePekakleaaeqQagaa.adalqade 121
                                     +S ++ ++ +     td+++a    ++++   + +++ +++e  +r+  L  +e + a+l++ +  +++     +q+++
  gi|119719711|ref|YP_920206.1| 155 DVSAVMSKLKEVELVSTDAATAVKSDVNSLRGSMSNVELALNELSQRVTRL--EESQLAALRQYSLELQEVsLKLTQVNQ 232
                                    233333332222233455555555555555556666666666666688888..777888888888777766666777777 PP

                                    HHHHHHHHHH CS
                        T3SSipB 122 alqKkldaas 131
                                     lqK l+  s
  gi|119719711|ref|YP_920206.1| 233 LLQKLLEKES 242
                                    7788776555 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.1     0.088        20      18      43 ..      76     102 ..      64     113 .. 0.69
   2 ?    9.1   0.4    0.0066       1.5      69     120 ..     114     165 ..      91     168 .. 0.81
   3 ?    2.5   1.5       0.7   1.6e+02       5      55 ..     188     239 ..     177     243 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.088
                        DUF5082  18 eiaaleekIerLkea.ktklsdekesl 43 
                                    ++ +l+ +I++L+ea k++l++ +++ 
  gi|119719711|ref|YP_920206.1|  76 RVGTLQGQIKELEEAlKSHLEAFQAEN 102
                                    566788888888865477777666554 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0066
                        DUF5082  69 dgirsnlessyqtyvdkldelidaieeEIerLenqiseaqgvldtlqsqlns 120
                                     ++ + +++ +++++  ld    +++ E +rLe ++s+ +++++   s+l++
  gi|119719711|ref|YP_920206.1| 114 REFKEGTDTLTKNVQLSLDMFLEKLSGELTRLEDTLSTITQDVSAVMSKLKE 165
                                    455667899999*******************************999998876 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.7
                        DUF5082   5 isklqaqiaelrseiaalee.kIerLkeaktklsdekeslkqkkkklekpln 55 
                                     s+++ +  el++++  lee +++ L++ + +l++++ +l q ++ l+k l 
  gi|119719711|ref|YP_920206.1| 188 MSNVELALNELSQRVTRLEEsQLAALRQYSLELQEVSLKLTQVNQLLQKLLE 239
                                    4555555666666666664336777777777777777777777777776665 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.065        15       2      32 ..      70     100 ..      69     108 .. 0.83
   2 ?    6.7   0.1      0.04       9.3       2      32 ..     135     165 ..     135     176 .. 0.86
   3 ?    1.4   0.1       1.8   4.2e+02       7      28 ..     179     200 ..     171     208 .. 0.62
   4 ?    0.3   0.2         4   9.3e+02       2      15 ..     195     208 ..     187     229 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.065
                            LPP   2 ldeLssqVsqLkskvdqlssdvnsakaaaqa 32 
                                    ld L++ V +L+ ++++l++ ++s  +a qa
  gi|119719711|ref|YP_920206.1|  70 LDFLNTRVGTLQGQIKELEEALKSHLEAFQA 100
                                    5779999***********9998887777665 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.04
                            LPP   2 ldeLssqVsqLkskvdqlssdvnsakaaaqa 32 
                                    l++Ls ++ +L++  + +++dv+++ + +++
  gi|119719711|ref|YP_920206.1| 135 LEKLSGELTRLEDTLSTITQDVSAVMSKLKE 165
                                    589******************9999887765 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 1.8
                            LPP   7 sqVsqLkskvdqlssdvnsaka 28 
                                    s+V++L   +++++  +n++++
  gi|119719711|ref|YP_920206.1| 179 SDVNSLRGSMSNVELALNELSQ 200
                                    5666666666666655555554 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 4
                            LPP   2 ldeLssqVsqLksk 15 
                                    l+eLs+ V +L++ 
  gi|119719711|ref|YP_920206.1| 195 LNELSQRVTRLEES 208
                                    56777777777653 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   7.0      0.27        63      26      80 ..     133     198 ..      49     207 .. 0.65
   2 ?    5.0   0.9      0.12        29      24      76 ..     184     236 ..     175     242 .. 0.68

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.27
                         DUF948  26 ktldeaaatieelekqvdpilkevedllakvne...........lledvneklekvdplteavadl 80 
                                      l++++  ++ le+ +  i+++v ++++k +e           + +dvn+   ++ ++  a+++l
  gi|119719711|ref|YP_920206.1| 133 MFLEKLSGELTRLEDTLSTITQDVSAVMSKLKEvelvstdaataVKSDVNSLRGSMSNVELALNEL 198
                                    334444444444444444444444444444444333322222234444444444444444444444 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.12
                         DUF948  24 lkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdpltea 76 
                                    l+  +++++ +++el ++v+ + +   ++l++    l++v+ kl +v++l ++
  gi|119719711|ref|YP_920206.1| 184 LRGSMSNVELALNELSQRVTRLEESQLAALRQYSLELQEVSLKLTQVNQLLQK 236
                                    56666667777777777777776666666666666677777777777777665 PP

>> Cnn_1N  Centrosomin N-terminal motif 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   2.5    0.0024      0.57       9      71 ..      56     114 ..      54     168 .. 0.84
   2 ?    4.7   4.7      0.15        34      21      71 ..     193     243 ..     180     244 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0024
                         Cnn_1N   9 idkLkKENFdLKLriyfLeerleklseeqkeellkenielkveveslqkelkekkkllreaek 71 
                                    +++L++  + LK  + fL+ r+  l+  q++el++    lk ++e  q e+ ++ +++++ ++
  gi|119719711|ref|YP_920206.1|  56 LKRLNNGVYALKVTLDFLNTRVGTLQG-QIKELEE---ALKSHLEAFQAENSRLAESVNRVSR 114
                                    7899999**************999998.6777766...6777777777777777666665544 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.15
                         Cnn_1N  21 LriyfLeerleklseeqkeellkenielkveveslqkelkekkkllreaek 71 
                                    L +++L +r+++l+e+q  +l +   el++   +l++ ++ ++kll++ +k
  gi|119719711|ref|YP_920206.1| 193 LALNELSQRVTRLEESQLAALRQYSLELQEVSLKLTQVNQLLQKLLEKESK 243
                                    77899*****************************************99776 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1      0.35        81      10      29 ..      74      93 ..      52     125 .. 0.64
   2 ?    3.8   0.1      0.29        68       7      38 ..     136     167 ..     132     185 .. 0.76
   3 ?    5.2   0.1      0.11        25       9      29 ..     191     211 ..     183     232 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.35
                           XhlA 10 etkldnleervdkleekaae 29
                                   +t++ +l+ ++++lee    
  gi|119719711|ref|YP_920206.1| 74 NTRVGTLQGQIKELEEALKS 93
                                   34444444444444444433 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.29
                           XhlA   7 erietkldnleervdkleekaaeaeekiknle 38 
                                    e++ ++l  le++++++ ++ + + +k+k++e
  gi|119719711|ref|YP_920206.1| 136 EKLSGELTRLEDTLSTITQDVSAVMSKLKEVE 167
                                    56666777777777777777777777777764 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.11
                           XhlA   9 ietkldnleervdkleekaae 29 
                                    +e  l++l++rv++lee +  
  gi|119719711|ref|YP_920206.1| 191 VELALNELSQRVTRLEESQLA 211
                                    67789***********98755 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   9.1       0.5   1.2e+02      35      80 ..      55     108 ..      53     243 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.5
                                    HHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH............ CS
                          DUF16  35 rLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeeln........k 80 
                                     Lk++++ v +l++ ++ l+  v +++ +ikel++  k   e+++        +
  gi|119719711|ref|YP_920206.1|  55 ALKRLNNGVYALKVTLDFLNTRVGTLQGQIKELEEALKSHLEAFQaensrlaeS 108
                                    588999999999999999999999999999999999999999999544433330 PP

>> JIP_LZII  JNK-interacting protein  leucine zipper II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0     0.042       9.8      31      71 .]      52      92 ..      50      92 .. 0.90
   2 ?    6.2   0.5     0.049        11      42      71 .]      88     117 ..      65     124 .. 0.70
   3 ?    3.2   2.6      0.44     1e+02      35      67 ..     135     167 ..      93     169 .. 0.79
   4 ?    4.5   0.2      0.17        39      40      68 ..     179     207 ..     174     210 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.042
                       JIP_LZII 31 LIarvdeLtsereiLreEleslqkakerlesrikelEeelk 71
                                   L+a +  L++   +L+  l+ l++   +l+ +ikelEe lk
  gi|119719711|ref|YP_920206.1| 52 LLAALKRLNNGVYALKVTLDFLNTRVGTLQGQIKELEEALK 92
                                   677778889999999999999*****************998 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.049
                       JIP_LZII  42 reiLreEleslqkakerlesrikelEeelk 71 
                                    +e+L++ le+ q++++rl ++++ +  e+k
  gi|119719711|ref|YP_920206.1|  88 EEALKSHLEAFQAENSRLAESVNRVSREFK 117
                                    467888888888888888888877777665 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.44
                       JIP_LZII  35 vdeLtsereiLreEleslqkakerlesrikelE 67 
                                    +++L+ e + L++ l+++++  +++ s++ke+E
  gi|119719711|ref|YP_920206.1| 135 LEKLSGELTRLEDTLSTITQDVSAVMSKLKEVE 167
                                    577888888888888888888888888888877 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.17
                       JIP_LZII  40 sereiLreEleslqkakerlesrikelEe 68 
                                    s+ ++Lr  +++++ a+++l +r++ lEe
  gi|119719711|ref|YP_920206.1| 179 SDVNSLRGSMSNVELALNELSQRVTRLEE 207
                                    6778999999****************998 PP

>> Img2  Mitochondrial large subunit ribosomal protein (Img2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.1     0.026       6.1      28      54 ..      75     109 ..      62     130 .. 0.76
   2 ?    3.2   0.2      0.46   1.1e+02      30      63 ..     135     168 ..     122     239 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.026
                           Img2  28 tvirkieGDiaalredLrkalee........lvkv 54 
                                    t +   +G i++l+e L+++le         + +v
  gi|119719711|ref|YP_920206.1|  75 TRVGTLQGQIKELEEALKSHLEAfqaensrlAESV 109
                                    788899***************96544433322333 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.46
                           Img2  30 irkieGDiaalredLrkaleelvkvnevtgkiei 63 
                                    + k +G++++l++ L++  ++ + v ++ +++e+
  gi|119719711|ref|YP_920206.1| 135 LEKLSGELTRLEDTLSTITQDVSAVMSKLKEVEL 168
                                    6788999999999999999886555555555553 PP

>> UPF0184  Uncharacterised protein family (UPF0184)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1    0.0014      0.32      28      76 ..      56     104 ..      35     111 .. 0.88
   2 ?    0.1   0.1       4.8   1.1e+03      33      59 ..     140     166 ..     118     182 .. 0.75
   3 ?    0.2   0.5       4.2   9.9e+02      31      62 ..     177     208 ..     154     225 .. 0.51

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0014
                        UPF0184  28 yeainsmLDqinsaLDalEernDdlnskLrELlesnRqiRlefaeqlde 76 
                                    ++ +n+ + ++  +LD l+ r   l+++++EL e+ +     f+++++ 
  gi|119719711|ref|YP_920206.1|  56 LKRLNNGVYALKVTLDFLNTRVGTLQGQIKELEEALKSHLEAFQAENSR 104
                                    56789999************************99999999999999985 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 4.8
                        UPF0184  33 smLDqinsaLDalEernDdlnskLrEL 59 
                                      L  ++ +L  + +    ++skL+E+
  gi|119719711|ref|YP_920206.1| 140 GELTRLEDTLSTITQDVSAVMSKLKEV 166
                                    456666667777777777888888874 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 4.2
                        UPF0184  31 insmLDqinsaLDalEernDdlnskLrELles 62 
                                    + s ++ +   + ++E   ++l  ++  L es
  gi|119719711|ref|YP_920206.1| 177 VKSDVNSLRGSMSNVELALNELSQRVTRLEES 208
                                    33333333333344444334443333333333 PP

>> CEP63  Centrosomal protein of 63 kDa
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.9    0.0058       1.4      31      99 ..      50     118 ..      45     149 .. 0.83
   2 ?    4.5   0.2      0.12        28      33     100 ..     131     198 ..     118     202 .. 0.84
   3 ?    5.3   7.2     0.068        16      43     107 ..     180     244 ..     175     246 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0058
                          CEP63  31 raletrlkireeeLasarnaldekhkEvgllrqqleelekekqelvakyeqqlqklreelsklkrsyek 99 
                                      l + lk  ++++ +++ +ld  ++ vg+l+ q++ele++ +   + ++ + ++l e +++++r ++ 
  gi|119719711|ref|YP_920206.1|  50 ALLLAALKRLNNGVYALKVTLDFLNTRVGTLQGQIKELEEALKSHLEAFQAENSRLAESVNRVSREFKE 118
                                    556677888889999999999999999****99999999999999999999999999999999998875 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.12
                          CEP63  33 letrlkireeeLasarnaldekhkEvgllrqqleelekekqelvakyeqqlqklreelsklkrsyekL 100
                                    l++ l+    eL+ + ++l   +++v     +l+e+e    ++++  + ++++lr  +s+++   + L
  gi|119719711|ref|YP_920206.1| 131 LDMFLEKLSGELTRLEDTLSTITQDVSAVMSKLKEVELVSTDAATAVKSDVNSLRGSMSNVELALNEL 198
                                    66778888889999999999999999999999999999999999999999999999998877666555 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.068
                          CEP63  43 eLasarnaldekhkEvgllrqqleelekekqelvakyeqqlqklreelsklkrsyekLqrkqlke 107
                                    +++s+r  + + +   + l q++ +le+++ ++ ++y  +lq++  +l ++++  +kL  k+ ke
  gi|119719711|ref|YP_920206.1| 180 DVNSLRGSMSNVELALNELSQRVTRLEESQLAALRQYSLELQEVSLKLTQVNQLLQKLLEKESKE 244
                                    567788888888888999*******************************************9998 PP

>> Rab5-bind  Rabaptin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.8      0.11        25      28      74 ..      84     130 ..      68     142 .. 0.67
   2 ?   10.5   8.7    0.0012      0.29      20     124 ..     137     241 ..     130     245 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.11
                      Rab5-bind  28 lqellrraneqLekerkdkkeLedslkelseetskqvselakrvkks 74 
                                    ++el +  +++Le+ + ++  L +s++ +s+e  +   +l+k v+ s
  gi|119719711|ref|YP_920206.1|  84 IKELEEALKSHLEAFQAENSRLAESVNRVSREFKEGTDTLTKNVQLS 130
                                    34566666777777777777777777777777777777777766655 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0012
                      Rab5-bind  20 elrdqvkklqellrraneqLekerkdkkeLedslkelseetskqvselakrvkksEllleeLqqafskakrniqeqlavl 99 
                                    +l  ++++l   l  + +++++ +++ ke+e    ++++ + + v+ l+  + ++El l+eL+q  ++ +++    l   
  gi|119719711|ref|YP_920206.1| 137 KLSGELTRLEDTLSTITQDVSAVMSKLKEVELVSTDAATAVKSDVNSLRGSMSNVELALNELSQRVTRLEESQLAALRQY 216
                                    56678899999999999999999999999999999999999999999999999999999999999887776655555555 PP

                      Rab5-bind 100 vksreqvedelvrLqkdyesLlGkh 124
                                      ++++v+ +l+++++  ++Ll k 
  gi|119719711|ref|YP_920206.1| 217 SLELQEVSLKLTQVNQLLQKLLEKE 241
                                    5555555555555555555555554 PP

>> Dor1  Dor1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.2      0.71   1.7e+02      63      95 ..      89     121 ..      56     134 .. 0.57
   2 ?   11.6   6.3   0.00034     0.078       7     104 ..     133     235 ..     127     240 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.71
                           Dor1  63 edLvlklpkLteectrfskkaeeisekrkenkl 95 
                                    e L ++l+ ++ e  r  ++ +++s + ke + 
  gi|119719711|ref|YP_920206.1|  89 EALKSHLEAFQAENSRLAESVNRVSREFKEGTD 121
                                    233344444444444444444444444444444 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00034
                           Dor1   7 kpleelekepelLaeeaeeilaqiqdLarknyktlidaaealeairqelediraqledLvlklpkLteectrfskkaeei 86 
                                    + le+l  e ++L  +  +i + ++++  k   + + +++a  a+ + ++++r ++ ++ l l++L++ +tr  ++    
  gi|119719711|ref|YP_920206.1| 133 MFLEKLSGELTRLEDTLSTITQDVSAVMSKLKEVELVSTDAATAVKSDVNSLRGSMSNVELALNELSQRVTRLEESQLAA 212
                                    66999999****************************************************************99876655 PP

                           Dor1  87 sek.....rkenkllldkheqll 104
                                    + +     ++ + +l ++++ l 
  gi|119719711|ref|YP_920206.1| 213 LRQyslelQEVSLKLTQVNQLLQ 235
                                    55544443444444444444444 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.9   0.00051      0.12     309     404 ..      67     166 ..      57     170 .. 0.78
   2 ?    2.5   2.7      0.12        28     572     633 ..     177     237 ..     166     247 .] 0.68

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00051
                       Prominin 309 dtskcl..dqlpnvdevlealeevletnlssivkeg...larlneipekvknqtaevvpdlkkalakgreqikklakkip 383
                                    ++  ++    +  ++ ++++lee+l++ l+    e+    +++n +++  k+ t++++++++ +l+   e+++ + +++ 
  gi|119719711|ref|YP_920206.1|  67 KVTLDFlnTRVGTLQGQIKELEEALKSHLEAFQAENsrlAESVNRVSREFKEGTDTLTKNVQLSLDMFLEKLSGELTRL- 145
                                    5555555567778888899999999988877655441224678899999999999999999999999999999999999. PP

                       Prominin 384 realdavisdlenterssktf 404
                                    +++l+++++d++ +++++k+ 
  gi|119719711|ref|YP_920206.1| 146 EDTLSTITQDVSAVMSKLKEV 166
                                    999999999999999888765 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.12
                       Prominin 572 iqkelenlkvdlsnlelLteeerkdLeklresglski.hsslyleqlckkltkvnletlaekl 633
                                     ++++++l  ++sn+el  +e  ++ + l+es+l  + ++sl l++++ klt+vn   l +kl
  gi|119719711|ref|YP_920206.1| 177 VKSDVNSLRGSMSNVELALNELSQRVTRLEESQLAALrQYSLELQEVSLKLTQVNQ--LLQKL 237
                                    56777888888888888888888888888888888772456667777777777653..33333 PP

>> Allexi_40kDa  Allexivirus 40kDa protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.2      0.65   1.5e+02      78     127 ..      68     116 ..      48     148 .. 0.49
   2 ?   10.7   4.4    0.0012      0.28      54     147 ..     149     240 ..     133     247 .] 0.77

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.65
                   Allexi_40kDa  78 tlLselrdalrtltklldklksvekklelsaetasdskllkklesietsl 127
                                     +L  l +++ tl+ ++++l++  k+  + a +a++s+l+++++ + +++
  gi|119719711|ref|YP_920206.1|  68 VTLDFLNTRVGTLQGQIKELEEALKSHLE-AFQAENSRLAESVNRVSREF 116
                                    44444444444444444444444433322.22223333333333333333 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0012
                   Allexi_40kDa  54 LthishdvdsiinklnpvsllsqttlLselrdalrtltklldklksvekklelsaetasdskllkklesietsleelhak 133
                                    L  i++dv  +++kl +v+l+s+    + ++++++ l+  + +++   ++l+++ ++ ++s+l   l     +l+e+  k
  gi|119719711|ref|YP_920206.1| 149 LSTITQDVSAVMSKLKEVELVSTD-AATAVKSDVNSLRGSMSNVELALNELSQRVTRLEESQL-AALRQYSLELQEVSLK 226
                                    7789999**********9888855.45678999999999999999999998888888888884.4788888888888888 PP

                   Allexi_40kDa 134 ldelsssetseseg 147
                                    l ++ +  ++  e+
  gi|119719711|ref|YP_920206.1| 227 LTQVNQLLQKLLEK 240
                                    88877776665554 PP

>> SOAR  STIM1 Orai1-activating region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       6.3   1.5e+03      62      91 ..      70      99 ..      64     114 .. 0.65
   2 ?   10.0   0.3    0.0027      0.64      42      95 ..     151     207 ..     137     213 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 6.3
                           SOAR 62 lddvdkkileakqaleevtkelkerqeRWq 91
                                   ld +++++ +++ +++e++++lk + e +q
  gi|119719711|ref|YP_920206.1| 70 LDFLNTRVGTLQGQIKELEEALKSHLEAFQ 99
                                   555666666666666666666666655444 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0027
                           SOAR  42 klkkkrssllgslrla...hssslddvdkkileakqaleevtkelkerqeRWqqiek 95 
                                     +++  s ++++l+ +    ++    v + + +++ ++++v+ +l+e ++R +++e+
  gi|119719711|ref|YP_920206.1| 151 TITQDVSAVMSKLKEVelvSTDAATAVKSDVNSLRGSMSNVELALNELSQRVTRLEE 207
                                    5666667788887765111556666799***************************96 PP

>> APP_E2  E2 domain of amyloid precursor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.2      0.86     2e+02      89     169 ..      99     178 ..      81     198 .. 0.54
   2 ?   10.0   1.4    0.0022      0.52     101     146 ..     200     244 ..     178     247 .] 0.87

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.86
                         APP_E2  89 aaerqqLvetHqqrveaalnekrrkalekylqalqeeppnaerilkaLkkllraeqkdrvhtlrhykhllksdpekaeqm 168
                                    +ae  +L+e   +rv   ++e   + +++ + +l+    +    l  L+  l  + +d +  +++ k++  +++++a  +
  gi|119719711|ref|YP_920206.1|  99 QAENSRLAES-VNRVSREFKEGTDTLTKNVQLSLDMFLEKLSGELTRLEDTLSTITQDVSAVMSKLKEVELVSTDAATAV 177
                                    3344444433.344444555544444444444555444444455555555555555555555555555555555555555 PP

                         APP_E2 169 k 169
                                    k
  gi|119719711|ref|YP_920206.1| 178 K 178
                                    5 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0022
                         APP_E2 101 qrveaalnekrrkalekylqalqeeppnaerilkaLkkllraeqkd 146
                                    qrv + l+e + +al +y  +lqe   +  ++ + L+kll+ e k+
  gi|119719711|ref|YP_920206.1| 200 QRV-TRLEESQLAALRQYSLELQEVSLKLTQVNQLLQKLLEKESKE 244
                                    555.479999*******************************99997 PP

>> Bacillus_HBL  Bacillus haemolytic enterotoxin (HBL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1      0.71   1.6e+02     134     173 ..      58      97 ..      45     101 .. 0.63
   2 ?    9.2   0.9    0.0043      0.99     102     175 ..      83     157 ..      65     159 .. 0.86
   3 ?    9.7   1.5     0.003      0.69      83     173 ..     115     208 ..     105     212 .. 0.83
   4 ?    1.1   0.5       1.3     3e+02     107     157 ..     195     242 ..     189     244 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.71
                   Bacillus_HBL 134 klakdsknFktdvdeltsilagdsgvisqlqneiedlqgk 173
                                    +l++ +  +k ++d l+  +++ +g+i++l++++++  ++
  gi|119719711|ref|YP_920206.1|  58 RLNNGVYALKVTLDFLNTRVGTLQGQIKELEEALKSHLEA 97 
                                    4555556666666677777777777777777777665555 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0043
                   Bacillus_HBL 102 ellellekLqeeiqqnqkevkqlikeLkklklklakdsknFktdvd.eltsilagdsgvisqlqneiedlqgkik 175
                                    +++el e+L++++   q+e  +l++ +++   ++++ + +++++v+  l+  l+  sg++  l+ +++++ + ++
  gi|119719711|ref|YP_920206.1|  83 QIKELEEALKSHLEAFQAENSRLAESVNRVSREFKEGTDTLTKNVQlSLDMFLEKLSGELTRLEDTLSTITQDVS 157
                                    566777889999999999999999999999999999999999999735899999999999999999999998876 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.003
                   Bacillus_HBL  83 kFqsyyktlveav...dkkdkaellellekLqeeiqqnqkevkqlikeLkklklklakdsknFktdvdeltsilagdsgv 159
                                    +F++  +tl ++v        ++l+  l++L++++ ++ + v +++ +Lk+ +l  +   +  k+dv+ l   +++ +  
  gi|119719711|ref|YP_920206.1| 115 EFKEGTDTLTKNVqlsLDMFLEKLSGELTRLEDTLSTITQDVSAVMSKLKEVELVSTDAATAVKSDVNSLRGSMSNVELA 194
                                    566666677777733222334788999***************************************************99 PP

                   Bacillus_HBL 160 isqlqneiedlqgk 173
                                    +++l +++++l+++
  gi|119719711|ref|YP_920206.1| 195 LNELSQRVTRLEES 208
                                    ***99999999887 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 1.3
                   Bacillus_HBL 107 lekLqeeiqqnqkevkqlikeLkklklklakdsknFktdvdeltsilagds 157
                                    l++L++ ++  ++   +++++L+++ l+l++ s ++++  + l++ l+ +s
  gi|119719711|ref|YP_920206.1| 195 LNELSQRVTRLEE---SQLAALRQYSLELQEVSLKLTQVNQLLQKLLEKES 242
                                    5666666666654...57888888888888888888888888888887665 PP

>> Muted  Organelle biogenesis, Muted-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.5      0.12        27      55     130 ..      83     118 ..      51     130 .. 0.51
   2 ?    3.8   0.2      0.28        66      55      93 ..     130     168 ..     113     191 .. 0.69
   3 ?    7.7   4.7     0.018       4.1      40      91 ..     194     244 ..     188     246 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.12
                          Muted  55 llpkclesmkenLselnkkleaalekverllqkeleeekrkseqlqekeeerkaeweeflkelqekkeevDeefee 130
                                    +++++ e++k++L+ ++++   + e+v+r+ ++                                        f+e
  gi|119719711|ref|YP_920206.1|  83 QIKELEEALKSHLEAFQAENSRLAESVNRVSRE----------------------------------------FKE 118
                                    234444444444444444444444444444443........................................333 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.28
                          Muted  55 llpkclesmkenLselnkkleaalekverllqkeleeek 93 
                                     l+++le+++ +L+ l++ l + +++v+ +++k +e e 
  gi|119719711|ref|YP_920206.1| 130 SLDMFLEKLSGELTRLEDTLSTITQDVSAVMSKLKEVEL 168
                                    466777788888888888888888888888887555554 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.018
                          Muted  40 lLenikklvnelkeqllpkclesmkenLselnkkleaalekverllqkelee 91 
                                     L+++++ v+ l+e++l  + +  + +L+e++ kl ++++  ++ll+ke++e
  gi|119719711|ref|YP_920206.1| 194 ALNELSQRVTRLEESQLAALRQY-SLELQEVSLKLTQVNQLLQKLLEKESKE 244
                                    489999*********99999988.79**********************8876 PP

>> POTRA_TamA_1  POTRA domain TamA domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.3      0.02       4.7       4      42 ..      80     118 ..      78     122 .. 0.87
   2 ?    2.0   0.0      0.98   2.3e+02       9      46 ..     121     158 ..     117     163 .. 0.83
   3 ?    1.8   0.3       1.1   2.6e+02      13      38 ..     189     215 ..     178     236 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.02
                   POTRA_TamA_1   4 ieGldgeleeNvrayLsliseeesesserlerllrraee 42 
                                    ++G  +elee  +++L++ ++e+s+  e+++r  r+ +e
  gi|119719711|ref|YP_920206.1|  80 LQGQIKELEEALKSHLEAFQAENSRLAESVNRVSREFKE 118
                                    578888*********************999998887665 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.98
                   POTRA_TamA_1   9 geleeNvrayLsliseeesesserlerllrraeeeirk 46 
                                    ++l +Nv+  L+   e+ s +++rle  l+++ +++++
  gi|119719711|ref|YP_920206.1| 121 DTLTKNVQLSLDMFLEKLSGELTRLEDTLSTITQDVSA 158
                                    68999******999999999999888888888888876 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 1.1
                   POTRA_TamA_1  13 eNvrayLsliseeesesse.rlerllr 38 
                                     Nv+ +L+++s++  + +e +l+ l++
  gi|119719711|ref|YP_920206.1| 189 SNVELALNELSQRVTRLEEsQLAALRQ 215
                                    699********9999999865555554 PP

>> Vps51  Vps51/Vps67
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0       3.5   8.2e+02      27      43 ..      76      92 ..      63     101 .. 0.61
   2 ?    4.5   0.1      0.16        37      60      84 ..     135     159 ..     129     162 .. 0.88
   3 ?    7.6   0.1     0.017         4      56      86 ..     177     207 ..     176     208 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 3.5
                          Vps51 27 veasllseiraldselk 43
                                   +  +l+ +i++l++ lk
  gi|119719711|ref|YP_920206.1| 76 RVGTLQGQIKELEEALK 92
                                   33445555555555555 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.16
                          Vps51  60 Irkmksemdkldqklselkqaiski 84 
                                    ++k+++e++ l+++ls+++q +s +
  gi|119719711|ref|YP_920206.1| 135 LEKLSGELTRLEDTLSTITQDVSAV 159
                                    6899****************99876 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.017
                          Vps51  56 asdtIrkmksemdkldqklselkqaiskiae 86 
                                    + +++++++++m++++  l+el+q++++++e
  gi|119719711|ref|YP_920206.1| 177 VKSDVNSLRGSMSNVELALNELSQRVTRLEE 207
                                    567899********************99876 PP

>> DASH_Dad2  DASH complex subunit Dad2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.1     0.079        18      11      54 ..      53      96 ..      52     102 .. 0.85
   2 ?    3.9   0.1       0.3        70      16      46 ..      83     113 ..      82     126 .. 0.87
   3 ?    5.6   1.9      0.09        21      22      61 ..     136     172 ..     115     209 .. 0.65
   4 ?    0.5   0.8       3.5     8e+02      21      41 ..     188     208 ..     179     244 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.079
                      DASH_Dad2 11 LeaLkqlrdlsdslakqleeLeeklstladgteavasVlanWqn 54
                                   L+aLk+l++   +l+  l+ L+++++tl+   +  ++ l++  +
  gi|119719711|ref|YP_920206.1| 53 LAALKRLNNGVYALKVTLDFLNTRVGTLQGQIKELEEALKSHLE 96
                                   7899************************9998888888776655 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.3
                      DASH_Dad2  16 qlrdlsdslakqleeLeeklstladgteava 46 
                                    q+++l ++l++ le+++ + s la+  + v+
  gi|119719711|ref|YP_920206.1|  83 QIKELEEALKSHLEAFQAENSRLAESVNRVS 113
                                    899999*************999988777665 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.09
                      DASH_Dad2  22 dslakqleeLeeklstladgteavasVlanWqnvlraism 61 
                                    ++l+ +l++Le+ lst++   + v++V+++ ++v  + + 
  gi|119719711|ref|YP_920206.1| 136 EKLSGELTRLEDTLSTIT---QDVSAVMSKLKEVELVSTD 172
                                    456666666666666664...4455556655555433333 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 3.5
                      DASH_Dad2  21 sdslakqleeLeeklstladg 41 
                                     ++++  l+eL+++++ l++ 
  gi|119719711|ref|YP_920206.1| 188 MSNVELALNELSQRVTRLEES 208
                                    555666677777777666654 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9  10.4    0.0085         2     154     260 ..     103     231 ..      53     244 .. 0.46

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0085
                   Exonuc_VII_L 154 rrlekaikrlleekkqrleklasrlk.speellerkrqrldeleerleralkkqlkkkrerleelkerl.k......... 222
                                    +rl ++++r  +e k+  ++l+++++ s ++ le+ + +l++le+ l++ +++ +++  ++l+e++  l +         
  gi|119719711|ref|YP_920206.1| 103 SRLAESVNRVSREFKEGTDTLTKNVQlSLDMFLEKLSGELTRLEDTLST-ITQDVSAVMSKLKEVE--LvStdaatavks 179
                                    3444444444444444444444444444444444445555554444444.4444333333333333..111222222221 PP

                   Exonuc_VII_L 223 .............ekleekkerlkklkerle.....lleekkerleeleekleals 260
                                                   l+e ++r+++l    e      l++ + +l+e++ kl++++
  gi|119719711|ref|YP_920206.1| 180 dvnslrgsmsnveLALNELSQRVTRL----EesqlaALRQYSLELQEVSLKLTQVN 231
                                    11111111111112222222333222....12222234444444444444444443 PP

>> HisKA_3  Histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.1     0.028       6.6      17      66 ..      70     119 ..      66     123 .. 0.90
   2 ?    3.7   0.1      0.39        92      36      66 ..     136     166 ..     120     189 .. 0.69
   3 ?    0.8   0.5       3.1   7.1e+02      42      63 ..     199     220 ..     169     240 .. 0.54

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.028
                                    HHHHHHHHHHHHHHTTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTH CS
                        HisKA_3  17 LsaiklqlelakrllekdpekaaeqlreieelarealqevRrllhnLrpa 66 
                                    L +++ +++++++++++ +e+++ +l++ ++  ++  + v r+++++++ 
  gi|119719711|ref|YP_920206.1|  70 LDFLNTRVGTLQGQIKELEEALKSHLEAFQAENSRLAESVNRVSREFKEG 119
                                    557889999**********************************9999865 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.39
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTH CS
                        HisKA_3  36 ekaaeqlreieelarealqevRrllhnLrpa 66 
                                    ek+  +l+++e+++++  q+v ++ ++L++ 
  gi|119719711|ref|YP_920206.1| 136 EKLSGELTRLEDTLSTITQDVSAVMSKLKEV 166
                                    3555566666666666666666666655544 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 3.1
                                    HHHHHHHHHHHHHHHHHHHHHH CS
                        HisKA_3  42 lreieelarealqevRrllhnL 63 
                                     +++ +l ++ l+ +R+ + +L
  gi|119719711|ref|YP_920206.1| 199 SQRVTRLEESQLAALRQYSLEL 220
                                    3333333333344444444433 PP

>> ACCA  Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.4     0.028       6.4      10      52 ..      79     121 ..      70     133 .. 0.53
   2 ?    5.0   0.4     0.086        20       5      60 ..     153     211 ..     149     223 .. 0.82
   3 ?    1.4   0.3       1.1   2.7e+02       4      50 ..     191     237 ..     188     243 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.028
                           ACCA  10 eleekieelkklaeesevdlseeieklekkleklkkeiyknlt 52 
                                    +l+ +i+el+++ +++   +++e ++l ++++++++e+++  +
  gi|119719711|ref|YP_920206.1|  79 TLQGQIKELEEALKSHLEAFQAENSRLAESVNRVSREFKEGTD 121
                                    5555555555555555555555555555555555555544332 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.086
                           ACCA   5 ekpiaeleekieelkklaeesevdlseeieklekkleklkk...eiyknltpwqkvqla 60 
                                     ++++ + +k++e++ +++++++ +++++++l+ ++++++    e+ +++t++++ qla
  gi|119719711|ref|YP_920206.1| 153 TQDVSAVMSKLKEVELVSTDAATAVKSDVNSLRGSMSNVELalnELSQRVTRLEESQLA 211
                                    578889999***********************998888765222777889999999988 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 1.1
                           ACCA   4 fekpiaeleekieelkklaeesevdlseeieklekkleklkkeiykn 50 
                                    +e  ++el++++++l++ +  +  ++s e+++++ kl+++++ ++k 
  gi|119719711|ref|YP_920206.1| 191 VELALNELSQRVTRLEESQLAALRQYSLELQEVSLKLTQVNQLLQKL 237
                                    56677888888888888877777777888888887777777655544 PP

>> DUF883  Bacterial protein of unknown function (DUF883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.1     0.012       2.9      17      67 ..      72     122 ..      64     129 .. 0.87
   2 ?    2.2   1.1       1.2   2.7e+02       6      53 ..     155     208 ..     136     223 .. 0.51

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.012
                         DUF883  17 llkeaadeageeaeelRerleerlerarerlrdaeeavaerakeaaeaadd 67 
                                    +l++   + + +++el e l+++le+ +++ ++++e+v + ++e  e +d+
  gi|119719711|ref|YP_920206.1|  72 FLNTRVGTLQGQIKELEEALKSHLEAFQAENSRLAESVNRVSREFKEGTDT 122
                                    566666677899********************************9999987 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 1.2
                         DUF883   6 eleslladlee...llkeaadeageeaeelR...erleerlerarerlrdaeea 53 
                                    ++ +++++l+e   +  +aa   ++++++lR   +++e +l+++ +r++++ee+
  gi|119719711|ref|YP_920206.1| 155 DVSAVMSKLKEvelVSTDAATAVKSDVNSLRgsmSNVELALNELSQRVTRLEES 208
                                    444444433321103334444445555566522223344555555555555554 PP

>> GrpE  GrpE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   2.1   0.00015     0.036      12      97 ..      86     168 ..      79     191 .. 0.84
   2 ?   -0.4   1.3       3.4     8e+02      18      43 ..     207     232 ..     167     244 .. 0.45

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00015
                                    HHHCCCCCCTTCHHHCTTSCCCCCCTTTTTTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC..HHH-HHHH CS
                           GrpE  12 deeeeleeeleelekevkelkekllrllaefenlrkrtekekeeakkfaiekfakdLLpvlDnleralksakeneeeksl 91 
                                    + ee+l++ le++++e   l e+++r   ef++ +  + k+ +   +  +ek+  +L  + D l++ ++ ++   ++ s 
  gi|119719711|ref|YP_920206.1|  86 ELEEALKSHLEAFQAENSRLAESVNRVSREFKEGTDTLTKNVQLSLDMFLEKLSGELTRLEDTLSTITQDVS---AVMSK 162
                                    567899999********************************************************9999654...44444 PP

                                    HHHHHH CS
                           GrpE  92 leGvem 97 
                                    l+ ve+
  gi|119719711|ref|YP_920206.1| 163 LKEVEL 168
                                    444444 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 3.4
                                    CCCTTCHHHCTTSCCCCCCTTTTTTT CS
                           GrpE  18 eeeleelekevkelkekllrllaefe 43 
                                    e++l++l++   el+e  l+l +  +
  gi|119719711|ref|YP_920206.1| 207 ESQLAALRQYSLELQEVSLKLTQVNQ 232
                                    22233333322233333333333333 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.2     0.002      0.47     215     329 ..      50     160 ..      37     179 .. 0.79
   2 ?    1.9   1.4      0.27        63     216     319 ..     176     235 ..     133     246 .. 0.37

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.002
                           FUSC 215 rararalrrllsrmlallallsslarllarlraeeaaavpelaallaelaaleaaaaaealeaalaalrarlralrrale 294
                                    +   +al+rl++ + al  +l+ l ++  +l+ + ++ +++l+  l++ +a       ++l++ ++++ +++++    l 
  gi|119719711|ref|YP_920206.1|  50 ALLLAALKRLNNGVYALKVTLDFLNTRVGTLQGQIKELEEALKSHLEAFQA-----ENSRLAESVNRVSREFKEGTDTLT 124
                                    555789*******************************99999999999999.....466777777777777765555555 PP

                           FUSC 295 .adadtaalllarlaellaelaqllaslraleaaia 329
                                     + +   +++l+ l  +l +l ++l ++ ++ +a  
  gi|119719711|ref|YP_920206.1| 125 kNVQLSLDMFLEKLSGELTRLEDTLSTITQDVSAVM 160
                                    466688899999999999999999988877666655 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.27
                           FUSC 216 araralrrllsrmlallallsslarllarlraeeaaavpelaallaelaaleaaaaaealeaalaalrarlralrralea 295
                                    a    +++l++ m ++   l++l ++  rl +++ aa   l+++  el++                              
  gi|119719711|ref|YP_920206.1| 176 AVKSDVNSLRGSMSNVELALNELSQRVTRLEESQLAA---LRQYSLELQE------------------------------ 222
                                    2222334444444444444444444444444444433...4444444443.............................. PP

                           FUSC 296 dadtaalllarlaellaelaqlla 319
                                               +   l ++ qll+
  gi|119719711|ref|YP_920206.1| 223 -----------VSLKLTQVNQLLQ 235
                                    ...........3333333333333 PP

>> zf-ZPR1  ZPR1 zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.3      0.13        31      92     135 ..      73     116 ..      62     132 .. 0.41
   2 ?    4.7   0.2      0.11        25      83     112 ..     129     161 ..     121     181 .. 0.70
   3 ?    4.5   0.5      0.12        28      90     140 ..     182     239 ..     175     245 .. 0.62

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.13
                        zf-ZPR1  92 legrlttvEGlLeqikeeleke.egdqaeredeekekieeflekl 135
                                    l+ r+ t+ G +++++e+l+++ e  qae+++  +e+++++ +++
  gi|119719711|ref|YP_920206.1|  73 LNTRVGTLQGQIKELEEALKSHlEAFQAENSR-LAESVNRVSREF 116
                                    44455555555555555554222222222211.222222222222 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.11
                        zf-ZPR1  83 leleippgtlegrlttvEGlLeqikeele...k 112
                                    l+l++  ++l+g+lt +E+ L+ i+++++   +
  gi|119719711|ref|YP_920206.1| 129 LSLDMFLEKLSGELTRLEDTLSTITQDVSavmS 161
                                    6666666789*****************964321 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.12
                        zf-ZPR1  90 gtlegrlttvEGlLeqikeele..keegdqaer.....edeekekieeflekleelie 140
                                    ++l+g++++vE  L+++ ++++  +e++  a r      +e   k++++ + l++l+e
  gi|119719711|ref|YP_920206.1| 182 NSLRGSMSNVELALNELSQRVTrlEESQLAALRqysleLQEVSLKLTQVNQLLQKLLE 239
                                    56899*********99999997542222222224444222566666666666666666 PP

>> Ccdc124  Coiled-coil domain-containing protein 124 /Oxs1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   6.2     0.026         6      57     126 ..     128     245 ..      78     247 .] 0.56

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.026
                        Ccdc124  57 e.............................................AsgideaiaaLsvk.k..eekldrhpekrlkAaY 88 
                                    +                                             A+ +   +++L+ + +  e  l     +r     
  gi|119719711|ref|YP_920206.1| 128 QlsldmfleklsgeltrledtlstitqdvsavmsklkevelvstdaATAVKSDVNSLRGSmSnvELAL-NELSQR----V 202
                                    15555555555555555555555555666666666666666666666667777777766321112222.222222....2 PP

                        Ccdc124  89 kafeeeeLprlke.....enpgLrlsQlkqllkkewkkspeNP 126
                                    +  ee++L++l++     ++ +L+l+Q++qll+k  +k  + P
  gi|119719711|ref|YP_920206.1| 203 TRLEESQLAALRQyslelQEVSLKLTQVNQLLQKLLEKESKEP 245
                                    4556666666655222225569****************99988 PP

>> DUF2730  Protein of unknown function (DUF2730)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.1      0.34        78      45      91 ..      66     114 ..      48     125 .. 0.61
   2 ?    3.5   0.3      0.32        74      62      93 ..     126     156 ..     104     164 .. 0.72
   3 ?    7.6   2.2     0.017         4      20      91 ..     133     207 ..     122     211 .. 0.64
   4 ?    6.5   5.5     0.038       8.9      11     100 ..     157     241 ..     156     243 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.34
                        DUF2730  45 ndkrlteletkvenLPta.kdle.kLkllladlrgelkaleaevrqlsh 91 
                                     +  l+ l+t+v +L  + k+le +Lk +l+  ++e + l+++v+++s+
  gi|119719711|ref|YP_920206.1|  66 LKVTLDFLNTRVGTLQGQiKELEeALKSHLEAFQAENSRLAESVNRVSR 114
                                    4444445555555554332455314666666666666666666666665 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.32
                        DUF2730  62 akdlekLkllladlrgelkaleaevrqlshqv 93 
                                    +++l +L++ l++l gel  le +++++ + v
  gi|119719711|ref|YP_920206.1| 126 NVQL-SLDMFLEKLSGELTRLEDTLSTITQDV 156
                                    4444.488888999999999998888887655 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.017
                        DUF2730  20 villlldskYakred.leklaekveendkrlteletkvenLPta..kdlekLkllladlrgelkaleaevrqlsh 91 
                                    ++l +l+   ++ ed l+++++ v+   ++l+e+e    +  ta  +d+++L+  +++++  l++l+++v++l+ 
  gi|119719711|ref|YP_920206.1| 133 MFLEKLSGELTRLEDtLSTITQDVSAVMSKLKEVELVSTDAATAvkSDVNSLRGSMSNVELALNELSQRVTRLEE 207
                                    555666666666555346677777777777777776655555532257777777777777777777777777764 PP

  == domain 4  score: 6.5 bits;  conditional E-value: 0.038
                        DUF2730  11 lavisvvvavilllldskYakredleklaekveendkrlteletkvenLPtakdlekLkllladlrgelkaleaevrqls 90 
                                    +av+s +  v l+  d   a ++d+++l  ++++ +  l+el ++v  L  +++l++L+    +   el++++ +++q++
  gi|119719711|ref|YP_920206.1| 157 SAVMSKLKEVELVSTDAATAVKSDVNSLRGSMSNVELALNELSQRVTRLE-ESQLAALR----QYSLELQEVSLKLTQVN 231
                                    677777777778888888899*************************9995.56777664....44556677777777777 PP

                        DUF2730  91 hqvdLLLene 100
                                    ++++ LLe+e
  gi|119719711|ref|YP_920206.1| 232 QLLQKLLEKE 241
                                    7777777776 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.4     0.015       3.5      41     112 ..      72     146 ..      50     151 .. 0.73
   2 ?    5.5   2.4     0.037       8.6       5      90 ..     143     235 ..     139     243 .. 0.60

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.015
                          TMPIT  41 kqkkrlkelksslkklkksvk...eeeeeeveelkeelkerkkvlkevesllpkknglylklvlGnvnvsllnkq 112
                                      + r+  l+ ++k+l++++k   e  + e ++l+e++++ ++ +ke  ++l+k+  l l ++l +++ +l++ +
  gi|119719711|ref|YP_920206.1|  72 FLNTRVGTLQGQIKELEEALKshlEAFQAENSRLAESVNRVSREFKEGTDTLTKNVQLSLDMFLEKLSGELTRLE 146
                                    556667777777777777765444555667788999999999999999999999999999999988777776655 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.037
                          TMPIT   5 eelekefkeleetakeykqkleels....klqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelke...elke 77 
                                    ++le+ + ++ +  + +++kl+e++       +++++++++ +  +++++ +l++l+++v++ ee++++ l++   el+e
  gi|119719711|ref|YP_920206.1| 143 TRLEDTLSTITQDVSAVMSKLKEVElvstDAATAVKSDVNSLRGSMSNVELALNELSQRVTRLEESQLAALRQyslELQE 222
                                    56666666777666677777766651111444556677777888888888888888888776666555555541114444 PP

                          TMPIT  78 rkkvlkevesllp 90 
                                     +  l +v++ll 
  gi|119719711|ref|YP_920206.1| 223 VSLKLTQVNQLLQ 235
                                    4444556666554 PP

>> CHDCT2  CHDCT2 (NUC038) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.1    0.0027      0.64      92     156 ..      94     169 ..      61     173 .. 0.57
   2 ?    1.1   0.8       1.7   3.9e+02     110     154 ..     169     214 ..     155     237 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0027
                         CHDCT2  92 slaqrfaelellaeshqkllkesaagnknanavle...........kvLnqleelLsdmkadvsrlpatlsrlrpv 156
                                    +l++  ae + laes +++++e ++g  + ++ ++             L++le+ Ls + +dvs +++ l+ ++ v
  gi|119719711|ref|YP_920206.1|  94 HLEAFQAENSRLAESVNRVSREFKEGTDTLTKNVQlsldmfleklsGELTRLEDTLSTITQDVSAVMSKLKEVELV 169
                                    2333334455555555555555555444444333333444444444778888888888888888888888877666 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 1.7
                         CHDCT2 110 llkesaagnknanavlekvLnqleelLsdmkadvsrlp.atlsrlr 154
                                    +++++a+  k+  + l+  ++++e  L+++ + v+rl  ++l+ lr
  gi|119719711|ref|YP_920206.1| 169 VSTDAATAVKSDVNSLRGSMSNVELALNELSQRVTRLEeSQLAALR 214
                                    3444444555555566666677777777777777777424455444 PP

>> CK2S  Casein Kinase 2 substrate
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.4      0.04       9.3      64     109 ..      80     125 ..      60     129 .. 0.83
   2 ?   10.6   3.1    0.0016      0.38      49     102 ..     109     165 ..      81     181 .. 0.78
   3 ?    1.3   4.6       1.2   2.8e+02      42      95 ..     190     240 ..     185     245 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.04
                           CK2S  64 qlealeevlakLrekleelqkvrdsleklvrdalqlyeekadklsl 109
                                    ++ ++ e+ + L++ le +q  +++l++ v+ + +  +e++d+l++
  gi|119719711|ref|YP_920206.1|  80 LQGQIKELEEALKSHLEAFQAENSRLAESVNRVSREFKEGTDTLTK 125
                                    45555566678999*****************999999999997765 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0016
                           CK2S  49 p...lrdfpdlqerLrekqlealeevlakLrekleelqkvrdsleklvrdalqlyee 102
                                    +    r+f++  ++L +  + +l+  l+kL+ +l++l++  +++ + v+++++ ++e
  gi|119719711|ref|YP_920206.1| 109 VnrvSREFKEGTDTLTKNVQLSLDMFLEKLSGELTRLEDTLSTITQDVSAVMSKLKE 165
                                    2333799999999***********************************999986664 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 1.2
                           CK2S  42 nvklygtplrdfpdlqerLrekqlealeevlakLrekleelqkvrdsleklvrd 95 
                                    nv+l+   l+++++  +rL e ql+al +   +L+e+  +l +v++ l+kl+++
  gi|119719711|ref|YP_920206.1| 190 NVELA---LNELSQRVTRLEESQLAALRQYSLELQEVSLKLTQVNQLLQKLLEK 240
                                    55544...7778888899999999999999999999999999999999988765 PP

>> IZUMO  Izumo sperm-egg fusion, Ig domain-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   1.2     0.075        17      34     108 ..      82     157 ..      50     162 .. 0.61
   2 ?    6.6   2.0     0.046        11      36     110 ..     146     219 ..     133     239 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.075
                                    HHHHHHHTTT---SGGGGGGSEEE..HHHHHHHHHHHHHHHHHHHHS.---HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          IZUMO  34 raealledlsekelaenkflgvvd..eetlekvasslkkelkrltds.dlkgelllkeLlwllqkqkkklkealkefq 108
                                     + ++le+   ++++ ++f+++     e +++v+ ++k+ +++lt++ +l  + +l++L   l +++++l ++ ++++
  gi|119719711|ref|YP_920206.1|  82 GQIKELEE--ALKSHLEAFQAENSrlAESVNRVSREFKEGTDTLTKNvQLSLDMFLEKLSGELTRLEDTLSTITQDVS 157
                                    22222222..33333333333322114679999999999999998774688899999999999999999998887765 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.046
                                    HHHHHTTT---SGGGGGGSEEEHHHHH..HHHHHHHHHHHHHHHS---HHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                          IZUMO  36 ealledlsekelaenkflgvvdeetle..kvasslkkelkrltdsdlkgelllkeLlwllqkqkkklkealkefqke 110
                                    e++l+ +   + + ++++ +++e +l   ++a+++k++++ l+ s  + el l+eL + + +++++   al++++ e
  gi|119719711|ref|YP_920206.1| 146 EDTLSTI---TQDVSAVMSKLKEVELVstDAATAVKSDVNSLRGSMSNVELALNELSQRVTRLEESQLAALRQYSLE 219
                                    3333333...344445566666666542267899************************9999999999999999876 PP

>> Fmp27_WPPW  RNA pol II promoter Fmp27 protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.8     0.006       1.4     171     241 ..      68     139 ..      59     174 .. 0.72
   2 ?    2.0   4.8      0.33        76     179     240 ..     180     241 ..     135     246 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.006
                     Fmp27_WPPW 171 vqkelleeRleeleeqiekleekleelelksekedeelkeeieelekeikelkekl.efletlledlkesee 241
                                    v  + l+ R+ +l+ qi++lee+l+++ +  + e+++l+e ++++++e+ke  + l + ++  l+ + e+ +
  gi|119719711|ref|YP_920206.1|  68 VTLDFLNTRVGTLQGQIKELEEALKSHLEAFQAENSRLAESVNRVSREFKEGTDTLtKNVQLSLDMFLEKLS 139
                                    66778999****************999998888899999999999999888665541456666666555554 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.33
                     Fmp27_WPPW 179 Rleeleeqiekleekleelelksekedeelkeeieelekeikelkeklefletlledlkese 240
                                     +++l+ +++++e +l+el+++  + +e+  + +++++ e++e+  kl+ +++ll++l e+e
  gi|119719711|ref|YP_920206.1| 180 DVNSLRGSMSNVELALNELSQRVTRLEESQLAALRQYSLELQEVSLKLTQVNQLLQKLLEKE 241
                                    34566666666677777777666666666666667777777777777777777777666655 PP

>> DUF4200  Domain of unknown function (DUF4200)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   2.0    0.0033      0.77      12     106 ..      74     166 ..      67     171 .. 0.73
   2 ?    2.6   3.5      0.72   1.7e+02       8      61 ..     188     241 ..     184     244 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0033
                        DUF4200  12 qealeakkeeiqrleealkqreeelekkeqeleedllkfdkflkendakraralkkaeeerklkkek.eaeikklkaeie 90 
                                    +  +++ + +i++leealk++ e++++++++l e+++++ +  ke  +      k+++   ++  ek   e+ +l++ ++
  gi|119719711|ref|YP_920206.1|  74 NTRVGTLQGQIKELEEALKSHLEAFQAENSRLAESVNRVSREFKEGTDTL---TKNVQLSLDMFLEKlSGELTRLEDTLS 150
                                    5566777889**************************77666666655554...555555555544442567788888888 PP

                        DUF4200  91 tlkseiekleekleey 106
                                    t+ ++ +    kl+e+
  gi|119719711|ref|YP_920206.1| 151 TITQDVSAVMSKLKEV 166
                                    8887777777777775 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.72
                        DUF4200   8 mfevqealeakkeeiqrleealkqreeelekkeqeleedllkfdkflkendakr 61 
                                    m+ v++al++  +   rlee++  + +++  + qe   +l ++++ l++  +k 
  gi|119719711|ref|YP_920206.1| 188 MSNVELALNELSQRVTRLEESQLAALRQYSLELQEVSLKLTQVNQLLQKLLEKE 241
                                    89999*****************99999999999999999999999999876665 PP

>> DUF489  Protein of unknown function (DUF489)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.7     0.024       5.5      43     120 ..      92     171 ..      66     179 .. 0.68
   2 ?    5.1   2.7     0.086        20      44     104 ..     180     240 ..     168     244 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.024
                                    SSHHHHTTS.GGGGHHHHHHHHHHHHT--SCHHH.HHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHTTHHHHTTS-TTSH CS
                         DUF489  43 estedvygg.lanlklGletlleqlekekkkkda.eltryalsllalerkLsknkealaklgerieqierqlehfdllhe 120
                                    +s ++ ++  +++l++ ++ +++ +++ +++ +    +++ + l +l+ +L++ +++l+++++ ++++ ++l++ +l+++
  gi|119719711|ref|YP_920206.1|  92 KSHLEAFQAeNSRLAESVNRVSREFKEGTDTLTKnVQLSLDMFLEKLSGELTRLEDTLSTITQDVSAVMSKLKEVELVST 171
                                    44455555556777777777777777776643331345666667778888888888888888888888877777766554 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.086
                                    SHHHHTTSGGGGHHHHHHHHHHHHT--SCHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHH CS
                         DUF489  44 stedvygglanlklGletlleqlekekkkkdaeltryalsllalerkLsknkealaklger 104
                                    +++++ g+ +n++l+l+ l++ +++ ++++ a l +y l+l +++ kL++ +++l+kl e+
  gi|119719711|ref|YP_920206.1| 180 DVNSLRGSMSNVELALNELSQRVTRLEESQLAALRQYSLELQEVSLKLTQVNQLLQKLLEK 240
                                    5566667799*****************999999**********************999765 PP

>> Rootletin  Ciliary rootlet component, centrosome cohesion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   2.2    0.0023      0.54      86     127 ..      84     125 ..      81     167 .. 0.85
   2 ?    1.5   0.5       1.1   2.6e+02     105     165 ..     136     196 ..     124     205 .. 0.61
   3 ?   -0.5   6.5       4.7   1.1e+03      56     101 ..     200     242 ..     153     246 .. 0.52

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0023
                      Rootletin  86 laqvnslLreqleearqaneaLtedlqkltkdwerlreeleq 127
                                    ++++ + L+ +le+ +++n +L e+++++++++++ ++ l +
  gi|119719711|ref|YP_920206.1|  84 IKELEEALKSHLEAFQAENSRLAESVNRVSREFKEGTDTLTK 125
                                    5678999**************************998887764 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 1.1
                      Rootletin 105 eaLtedlqkltkdwerlreeleqkekewreeeeafneylssehsrllsLWrevvavrrqfs 165
                                    e+L+ +l++l++ ++ +++++    ++++e e   ++  ++ +s + sL  ++++v   ++
  gi|119719711|ref|YP_920206.1| 136 EKLSGELTRLEDTLSTITQDVSAVMSKLKEVELVSTDAATAVKSDVNSLRGSMSNVELALN 196
                                    4566667777777777777666666666666666666555555555555555555555544 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 4.7
                      Rootletin  56 ssareleeeesadleealakLeeErqrseklaqvnslLreqleear 101
                                    ++  +lee++ a l +   +L   ++ s kl+qvn+lL++ le+++
  gi|119719711|ref|YP_920206.1| 200 QRVTRLEESQLAALRQYSLEL---QEVSLKLTQVNQLLQKLLEKES 242
                                    222333333333333333333...3356677778888888777765 PP

>> PRKG1_interact  cGMP-dependent protein kinase interacting domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.3      0.21        50      63      88 ..      81     107 ..      65     114 .. 0.61
   2 ?    5.7   0.9      0.11        27      13      40 ..      88     115 ..      79     137 .. 0.57
   3 ?    3.0   7.4      0.85     2e+02       7      82 ..     136     216 ..     130     246 .. 0.54

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.21
                 PRKG1_interact  63 erkiseleeelk.eleeLraenqrLkd 88 
                                    + +i+elee lk +le+ +aen+rL +
  gi|119719711|ref|YP_920206.1|  81 QGQIKELEEALKsHLEAFQAENSRLAE 107
                                    455556666655235566666666654 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.11
                 PRKG1_interact  13 nerLkreLeelekelselkseleklkqq 40 
                                    +e Lk++Le  + e s+l +++++++++
  gi|119719711|ref|YP_920206.1|  88 EEALKSHLEAFQAENSRLAESVNRVSRE 115
                                    5556666666666666665555555543 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.85
                 PRKG1_interact   7 eeekeenerLkreLeelekelselkseleklkqqrqesvskrssllelekrerrslerkisel.....eeelkeleeLra 81 
                                    e+   e  rL ++L+++++++s + s+l++++  +++  ++ +s ++  + + +++e  + el       e  +l++Lr+
  gi|119719711|ref|YP_920206.1| 136 EKLSGELTRLEDTLSTITQDVSAVMSKLKEVELVSTDAATAVKSDVNSLRGSMSNVELALNELsqrvtRLEESQLAALRQ 215
                                    56666777888888888888888888888887765553333333333333333333333333311111222233333333 PP

                 PRKG1_interact  82 e 82 
                                     
  gi|119719711|ref|YP_920206.1| 216 Y 216
                                    3 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.5     0.017         4       9      62 ..      69     119 ..      52     136 .. 0.57
   2 ?    2.4   0.1       1.1   2.5e+02       7      34 ..     139     166 ..     128     193 .. 0.58
   3 ?    3.3   4.6      0.56   1.3e+02       9      58 ..     194     244 ..     180     247 .] 0.82

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.017
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXX CS
                           YabA   9 kleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekek 62 
                                    +l+ l++++++l+ +++el+e+l++ le   ++++en++l e +++ +++ ke 
  gi|119719711|ref|YP_920206.1|  69 TLDFLNTRVGTLQGQIKELEEALKSHLE---AFQAENSRLAESVNRVSREFKEG 119
                                    3444555555555555555555555544...45667777776664333333332 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 1.1
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           YabA   7 fdkleeleeqleelleeleelkeelael 34 
                                      +l++le++l++++++++++ ++l+e+
  gi|119719711|ref|YP_920206.1| 139 SGELTRLEDTLSTITQDVSAVMSKLKEV 166
                                    3444555555555555555544444443 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.56
                                    HHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXX CS
                           YabA   9 kleeleeqleell.eeleelkeelaelleenaeLeleneklrerleeeekk 58 
                                    +l+el++++++l  ++l++l++   el e   +L+  n+ l+++le+e+k+
  gi|119719711|ref|YP_920206.1| 194 ALNELSQRVTRLEeSQLAALRQYSLELQEVSLKLTQVNQLLQKLLEKESKE 244
                                    678899999888625899999999999999999999999999999766655 PP

>> Rx_N  Rx N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.2      0.73   1.7e+02       6      39 ..      66     100 ..      63     125 .. 0.78
   2 ?    2.1   0.0         1   2.4e+02      18      38 ..     133     153 ..     112     158 .. 0.74
   3 ?    6.9   1.7     0.033       7.7       2      50 ..     156     206 ..     155     229 .. 0.76
   4 ?    1.7   1.1       1.3   3.1e+02       2      51 ..     195     244 ..     194     246 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.73
                           Rx_N   6 lqkLadllaeea.kllkgvkeeleklkdeLesiqa 39 
                                    l+   d+l  ++ +l+ ++ke  e lk+ Le+ qa
  gi|119719711|ref|YP_920206.1|  66 LKVTLDFLNTRVgTLQGQIKELEEALKSHLEAFQA 100
                                    66677888888877777777777889999998887 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 1
                           Rx_N  18 kllkgvkeeleklkdeLesiq 38 
                                      l+++ +el +l+d+L++i 
  gi|119719711|ref|YP_920206.1| 133 MFLEKLSGELTRLEDTLSTIT 153
                                    567888888999999988875 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.033
                           Rx_N   2 vsallqkLadllaeeakllkgvkeeleklkdeLesiqavLedaeerqi..k 50 
                                    vsa+++kL ++          vk+++++l+  +++++  L++ ++r +  +
  gi|119719711|ref|YP_920206.1| 156 VSAVMSKLKEVELVSTDAATAVKSDVNSLRGSMSNVELALNELSQRVTrlE 206
                                    78889999988888889999************************9766322 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 1.3
                           Rx_N   2 vsallqkLadllaeeakllkgvkeeleklkdeLesiqavLedaeerqikd 51 
                                    ++ l q+++ l +++ + l++   el++   +L +++++L++  e++ k+
  gi|119719711|ref|YP_920206.1| 195 LNELSQRVTRLEESQLAALRQYSLELQEVSLKLTQVNQLLQKLLEKESKE 244
                                    556677788888888899999999999999**********9999998876 PP

>> DUF5595  Domain of unknown function (DUF5595)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.3    0.0032      0.74      38      73 .]      80     115 ..      78     115 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0032
                        DUF5595  38 leskLkelynvdeaqlesleeeekrLeeEierleke 73 
                                    l+ ++kel ++ +++le+ ++e+ rL e ++r+ +e
  gi|119719711|ref|YP_920206.1|  80 LQGQIKELEEALKSHLEAFQAENSRLAESVNRVSRE 115
                                    677899*************************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1730  (0.0964917); expected 358.6 (0.02)
Passed bias filter:                      769  (0.0428914); expected 358.6 (0.02)
Passed Vit filter:                       141  (0.00786435); expected 17.9 (0.001)
Passed Fwd filter:                        81  (0.00451782); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              77  [number of targets reported over threshold]
# CPU time: 1.17u 0.36s 00:00:01.52 Elapsed: 00:00:00.55
# Mc/sec: 1363.08
//
Query:       gi|119719712|ref|YP_920207.1|  [L=57]
Description: hypothetical protein Tpen_0802 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.047   13.3   0.7      0.054   13.1   0.7    1.0  1  HAUS-augmin3  HAUS augmin-like complex subunit 3
      0.085   13.2   1.9       0.89   10.0   0.1    1.9  2  V-SNARE       Vesicle transport v-SNARE protein N-terminus


Domain annotation for each model (and alignments):
>> HAUS-augmin3  HAUS augmin-like complex subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.7     6e-06     0.054      36      84 ..       2      52 ..       1      55 [. 0.67

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6e-06
                   HAUS-augmin3 36 LkksGkpiLegeaLeeaLktiepsdlkq...edvellevileeeeesleaLe 84
                                   L+++G   L +++L+eaL+ ie+   +     +ve+ e+ + e+ee++e+L+
  gi|119719712|ref|YP_920207.1|  2 LVNAGA-RLYEARLAEALDAIEEFLASVrgiPQVEEDEELARELEEDVEELR 52
                                   788999.999************555444334555555555555555555554 PP

>> V-SNARE  Vesicle transport v-SNARE protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   9.9e-05      0.89      25      57 ..       5      37 ..       4      42 .. 0.86
   2 ?    3.6   1.8    0.0095        85      21      40 ..      35      54 ..      33      54 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 9.9e-05
                        V-SNARE 25 aalreiekkldeaeelldqMelEvrnlpssera 57
                                   a  r +e++l ea + ++++   vr++p+ e +
  gi|119719712|ref|YP_920207.1|  5 AGARLYEARLAEALDAIEEFLASVRGIPQVEED 37
                                   5667899*********************98765 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.0095
                        V-SNARE 21 eerkaalreiekkldeaeel 40
                                   ee  ++ re+e++++e++el
  gi|119719712|ref|YP_920207.1| 35 EEDEELARELEEDVEELREL 54
                                   6788899**********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       932  (0.0519828); expected 358.6 (0.02)
Passed bias filter:                      586  (0.0326845); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.30s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 363.82
//
Query:       gi|119719713|ref|YP_920208.1|  [L=267]
Description: hypothetical protein Tpen_0804 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2033.34
//
Query:       gi|119719714|ref|YP_920209.1|  [L=295]
Description: type II secretion system protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-13   50.1   3.3    2.5e-13   50.1   3.3    2.2  2  T2SSF         Type II secretion system (T2SS), protein F
  ------ inclusion threshold ------
      0.082   13.0   0.0       0.19   11.9   0.0    1.6  1  Spore_III_AB  Stage III sporulation protein AB (spore_III_AB)


Domain annotation for each model (and alignments):
>> T2SSF  Type II secretion system (T2SS), protein F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.9      0.82   7.4e+03     104     120 ..      13      29 ..      10      32 .. 0.51
   2 !   50.1   3.3   2.8e-17   2.5e-13       5     122 ..      95     221 ..      91     223 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.82
                                    TTXXXXXXXXXXXXXXX CS
                          T2SSF 104 epllllvvallvllill 120
                                      l++ +++++v+l+l+
  gi|119719714|ref|YP_920209.1|  13 MLLAVGAMLGAVPLFLV 29 
                                    34444555555555554 PP

  == domain 2  score: 50.1 bits;  conditional E-value: 2.8e-17
                                    HHHHHHTT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTSSHHHHHC....T-TT.TS-HHHHHHHHHHHHHT-HHHH CS
                          T2SSF   5 latllsaGvplveaLellaeeaengplaeelkriarrlraGgslseale....rtpssefpelvvqlirageeggnLaev 80 
                                    la ++++G++l eaL+++ae+   g++++ l++++   ++G ++ ea++    r+  + +++l + l++a e+gg++ ++
  gi|119719714|ref|YP_920209.1|  95 LAEAVRSGLTLPEALSSVAETL-GGEVGKMLRQVVLLTEMGVTFQEAIArafsRYRLPSLDRLGSILLTAYESGGKVIDA 173
                                    7899******************.*********************999999999777779********************* PP

                                    HHHHHHH......HHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXX CS
                          T2SSF  81 Lerlaey......leeerelrrkllaallepllllvvallvllillai 122
                                    Le  a+       +eeer+++++    +++ + +l+v+l + ++++++
  gi|119719714|ref|YP_920209.1| 174 LETSAQIfgairsYEEERATTINPHVLTIYAATILYVILSLTILYVFV 221
                                    ***997622222256666666666666777777777776666666555 PP

>> Spore_III_AB  Stage III sporulation protein AB (spore_III_AB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.1e-05      0.19      49      96 ..     103     148 ..      85     169 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.1e-05
                                    S-HHHHHHHHHHCS-TTHHHHHHHHHHHHH.STSS-HHHHHHHHHHHH CS
                   Spore_III_AB  49 tpLpealeklaeksesplseffeevaerleekegesfeeaweeavekl 96 
                                     +Lpeal+++ae  ++++++++++v    e   g +f+ea+ +a++++
  gi|119719714|ref|YP_920209.1| 103 LTLPEALSSVAETLGGEVGKMLRQVVLLTE--MGVTFQEAIARAFSRY 148
                                    579**********************98755..9***********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2048.98
//
Query:       gi|119719715|ref|YP_920210.1|  [L=441]
Description: hypothetical protein Tpen_0806 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       248  (0.0138323); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2989.06
//
Query:       gi|119719716|ref|YP_920211.1|  [L=327]
Description: hypothetical protein Tpen_0807 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-45  154.3   0.1    3.7e-45  153.9   0.1    1.1  1  TackOD1          Thaumarchaeal output domain 1
    8.7e-05   22.6  17.8       0.85    9.8   0.0    5.2  5  Zn-ribbon_8      Zinc ribbon domain
    9.5e-05   21.7  14.1        1.3    8.5   0.1    5.1  5  zf-ribbon_3      zinc-ribbon domain
     0.0001   22.3   9.6       0.12   12.4   0.1    3.6  3  HypA             Hydrogenase/urease nickel incorporation, met
    0.00016   21.6   5.7       0.03   14.3   1.6    2.5  2  zinc-ribbons_6   zinc-ribbons
    0.00057   19.9  14.3      0.055   13.5   3.6    3.1  2  DZR              Double zinc ribbon
     0.0061   16.4   3.6     0.0061   16.4   3.6    3.6  3  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
     0.0096   16.0   0.1     0.0096   16.0   0.1    2.9  2  FYVE             FYVE zinc finger
  ------ inclusion threshold ------
      0.024   14.4   8.8        1.9    8.3   2.4    3.6  3  Zn_Tnp_IS1       InsA N-terminal domain
      0.025   14.5  14.3        2.7    8.0   0.5    5.6  5  zinc_ribbon_4    zinc-ribbon domain
      0.026   14.4  14.7      0.092   12.6   0.1    4.2  4  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
      0.041   14.0   9.8        0.1   12.8   1.6    2.7  2  Ribosomal_L37e   Ribosomal protein L37e
      0.058   13.1   1.9        2.7    7.7   1.9    2.3  1  Rep_fac-A_C      Replication factor-A C terminal domain
      0.058   13.3   8.1       0.94    9.4   0.3    3.1  3  C1_1             Phorbol esters/diacylglycerol binding domain
       0.09   12.7  10.9       0.85    9.6   0.1    4.1  4  Prok-RING_1      Prokaryotic RING finger family 1
       0.18   11.7  10.2       0.59   10.1   0.2    3.5  3  DUF3797          Domain of unknown function (DUF3797)
        0.4   11.0   0.1        0.4   11.0   0.1    3.3  3  Ribosomal_L32p   Ribosomal L32p protein family
          1    9.2   4.9        8.8    6.3   0.2    3.0  3  VATC             Vms1-associating treble clef domain
        1.3    8.6  18.1       0.61    9.7   0.2    4.5  4  TF_Zn_Ribbon     TFIIB zinc-binding
        1.4    9.0  12.5        1.6    8.8   1.0    4.0  3  DNA_ligase_ZBD   NAD-dependent DNA ligase C4 zinc finger doma
        1.5    8.9  11.7        4.6    7.3   0.5    4.2  4  ADK_lid          Adenylate kinase, active site lid
        1.9    8.6   9.1       0.23   11.5   0.6    3.2  3  Elf1             Transcription elongation factor Elf1 like
          2    9.5  14.7         40    5.4   0.4    5.1  5  zf-C2H2_4        C2H2-type zinc finger
        2.3    8.1   8.1        6.7    6.6   0.2    3.1  3  Cys_rich_KTR     Cysteine-rich KTR
        3.2    7.6  12.0        4.3    7.2   0.5    3.9  4  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger
        4.2    7.0   9.1         40    3.9   0.9    3.5  3  zf_C2H2_10       C2H2 type zinc-finger
        4.5    7.5   0.0        4.5    7.5   0.0    4.1  3  zf-RING_7        C4-type zinc ribbon domain
        6.2    7.1  13.1    2.7e+03   -1.3  13.1    3.3  1  IBR              IBR domain, a half RING-finger domain
        7.8    6.4  12.2       0.95    9.3   0.9    3.5  3  zf-C2H2_11       zinc-finger C2H2-type
        9.4    6.4  11.1         13    6.0   0.1    4.1  4  Ribosomal_L37ae  Ribosomal L37ae protein family


Domain annotation for each model (and alignments):
>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.9   0.1   6.1e-48   3.7e-45       4     187 .]      18     198 ..      15     198 .. 0.91

  Alignments for each domain:
  == domain 1  score: 153.9 bits;  conditional E-value: 6.1e-48
                        TackOD1   4 rskeeteekllayllsrdeeklepvldpkskelysypllealskekeeseelleelvkrglleeelvdrirlCpsCksgh 83 
                                    r+ +++ ++l+ yl++++  +++  + +k+      p+ +   k +    +llee vkrg+l++  +d++++Cp+C + +
  gi|119719716|ref|YP_920211.1|  18 RNLARALQDLVVYLVESNLGEISIEIGKKD-----HPVKSIADKYRVPLDTLLEEGVKRGFLKAFPADKLVFCPKCGGFS 92 
                                    566778889999999999888877777776.....455444445556999****************************** PP

                        TackOD1  84 lnvrevCpkCkSidieeqelihhftCgnvgpeeef..lkegkleCpkCktkLrhiGvDYdrplevykCnsCkslfsepev 161
                                    ++vr++Cp+C+S+d+e+++l++h+tCg +g+ ee   +++gk++CpkCk++L + G D+ +++++++C+sC+++fs+p +
  gi|119719716|ref|YP_920211.1|  93 FKVRYACPNCGSFDVERNTLFSHVTCGFIGVLEEAprTVTGKVQCPKCKRELVREGDDWVKLSSTWRCRSCGTSFSYPVA 172
                                    **********************************988899**************************************** PP

                        TackOD1 162 karClsCekesesddlkvreiysykl 187
                                    +++C+sC+++++++++++r++++y++
  gi|119719716|ref|YP_920211.1| 173 SLECASCGERFDDKRAEYRAVMRYSV 198
                                    ************************97 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.1     0.022        13      26      34 ..      81      90 ..      73      97 .. 0.70
   2 !    9.8   0.0    0.0014      0.85      28      38 ..      98     109 ..      91     111 .. 0.82
   3 ?    5.4   0.3     0.034        20      26      38 ..     134     146 ..     118     147 .. 0.79
   4 ?    5.0   0.1     0.045        27       7      16 ..     159     168 ..     157     174 .. 0.85
   5 ?    6.6   0.3     0.014       8.6       7      16 ..     175     184 ..     170     201 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.022
                    Zn-ribbon_8 26 lta.CPeCgs 34
                                   + + CP+Cg+
  gi|119719716|ref|YP_920211.1| 81 KLVfCPKCGG 90
                                   4455*****8 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0014
                    Zn-ribbon_8  28 aCPeCgs.evrr 38 
                                    aCP+Cgs +v+r
  gi|119719716|ref|YP_920211.1|  98 ACPNCGSfDVER 109
                                    499999999998 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.034
                    Zn-ribbon_8  26 ltaCPeCgsevrr 38 
                                    +++CP+C+ e+ r
  gi|119719716|ref|YP_920211.1| 134 KVQCPKCKRELVR 146
                                    456****997776 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.045
                    Zn-ribbon_8   7 rCeeCghefe 16 
                                    rC++Cg+ f 
  gi|119719716|ref|YP_920211.1| 159 RCRSCGTSFS 168
                                    9******996 PP

  == domain 5  score: 6.6 bits;  conditional E-value: 0.014
                    Zn-ribbon_8   7 rCeeCghefe 16 
                                    +C +Cg++f+
  gi|119719716|ref|YP_920211.1| 175 ECASCGERFD 184
                                    8********9 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.1    0.0044       2.6      18      24 ..      84      90 ..      76      92 .. 0.73
   2 !    8.5   0.1    0.0022       1.3       4      11 ..      98     105 ..      96     110 .. 0.73
   3 !    8.1   0.1     0.003       1.8       2      16 ..     134     149 ..     133     150 .. 0.89
   4 ?    1.2   0.1      0.43   2.6e+02      19      24 ..     160     165 ..     156     167 .. 0.77
   5 ?    2.4   0.1      0.19   1.1e+02      19      25 ..     176     182 ..     175     183 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0044
                    zf-ribbon_3 18 vCpyCGt 24
                                   +Cp+CG+
  gi|119719716|ref|YP_920211.1| 84 FCPKCGG 90
                                   6666665 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0022
                    zf-ribbon_3   4 rCPnCGap 11 
                                     CPnCG+ 
  gi|119719716|ref|YP_920211.1|  98 ACPNCGSF 105
                                    58888874 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.003
                    zf-ribbon_3   2 tvrCPnCGa.plssdd 16 
                                    +v+CP+C+  +++++d
  gi|119719716|ref|YP_920211.1| 134 KVQCPKCKReLVREGD 149
                                    689*****99999987 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.43
                    zf-ribbon_3  19 CpyCGt 24 
                                    C +CGt
  gi|119719716|ref|YP_920211.1| 160 CRSCGT 165
                                    778876 PP

  == domain 5  score: 2.4 bits;  conditional E-value: 0.19
                    zf-ribbon_3  19 CpyCGtk 25 
                                    C++CG++
  gi|119719716|ref|YP_920211.1| 176 CASCGER 182
                                    9999987 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.1    0.0002      0.12      62      98 ..      74     108 ..      12     112 .. 0.62
   2 ?    2.8   0.2       0.2   1.2e+02      67      95 ..     131     143 ..     116     152 .. 0.61
   3 !   10.9   1.1   0.00057      0.34      69      95 ..     156     182 ..     150     189 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0002
                                    EEEEEE--EEEETTTS-EEECHHHHHS-TTTSSS-EE CS
                           HypA  62 LeieevpvkvrCreCgkefeleekalrCpkCgsadve 98 
                                    L+    +  v C +Cg  f+ +  ++ Cp+Cgs dve
  gi|119719716|ref|YP_920211.1|  74 LKAFPADKLVFCPKCG-GFSFKV-RYACPNCGSFDVE 108
                                    55556667799****9.555443.378******9987 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.2
                                    E--EEEETTTS-EEECHHHHHS-TTTSSS CS
                           HypA  67 vpvkvrCreCgkefeleekalrCpkCgsa 95 
                                    v  k                ++CpkC+++
  gi|119719716|ref|YP_920211.1| 131 VTGK----------------VQCPKCKRE 143
                                    3333................466666654 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00057
                                    -EEEETTTS-EEECHHHHHS-TTTSSS CS
                           HypA  69 vkvrCreCgkefeleekalrCpkCgsa 95 
                                     + rCr+Cg++f+   ++l+C +Cg++
  gi|119719716|ref|YP_920211.1| 156 STWRCRSCGTSFSYPVASLECASCGER 182
                                    5789*********776689*****985 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.1    0.0028       1.7      17      37 ..      83     104 ..      67     121 .. 0.86
   2 !   14.3   1.6     5e-05      0.03       2      39 ..     136     183 ..     135     188 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0028
                                    EE-TTT--.EEEEEEE-SSS-S CS
                 zinc-ribbons_6  17 yhCeaCqe.dlkkealCpeCeq 37 
                                    ++C +C   ++k+   Cp+C++
  gi|119719716|ref|YP_920211.1|  83 VFCPKCGGfSFKVRYACPNCGS 104
                                    789***98899*********85 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 5e-05
                                    --SSS-S--EE-S.......SEEE-TTT--EEE...EEEE-SSS-S-- CS
                 zinc-ribbons_6   2 kCpeCqqelekrg.......eqyhCeaCqedlk...kealCpeCeqel 39 
                                    +Cp+C++el+++g       ++ +C++C ++++       C  C+++ 
  gi|119719716|ref|YP_920211.1| 136 QCPKCKRELVREGddwvklsSTWRCRSCGTSFSypvASLECASCGERF 183
                                    7*********8888*****999********876222456799998876 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   7.4     0.016       9.5       1      34 [.      85     140 ..      75     151 .. 0.53
   2 !   13.5   3.6   9.2e-05     0.055       1      41 [.     137     186 ..     137     189 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.016
                            DZR   1 CpqCgeelppdarfCseCgtk.lkavaa......................edrCpsC 34 
                                    Cp+Cg    +    C++Cg+  ++  ++                      + +Cp+C
  gi|119719716|ref|YP_920211.1|  85 CPKCGGFSFKVRYACPNCGSFdVE-RNTlfshvtcgfigvleeaprtvtgKVQCPKC 140
                                    555555555555555555554222.22234444455555555555555555555555 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 9.2e-05
                            DZR   1 CpqCgee........lppdar.fCseCgtklkavaaedrCpsCgekvdpe 41 
                                    Cp+C++e        ++ ++   C  Cgt+ + + a+  C sCge  d +
  gi|119719716|ref|YP_920211.1| 137 CPKCKRElvregddwVKLSSTwRCRSCGTSFSYPVASLECASCGERFDDK 186
                                    99999998888888844333348********99999********987765 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   3.6     1e-05    0.0061      14      37 .]      85     108 ..      84     108 .. 0.97
   2 ?   -0.4   0.1       1.9   1.1e+03      14      17 ..     137     140 ..     134     144 .. 0.63
   3 ?    4.5   4.9     0.053        32      13      32 ..     159     180 ..     159     184 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1e-05
                        DUF35_N  14 CpdCGtvqfPPravCphCgsddle 37 
                                    Cp+CG + f  r +Cp+Cgs+d+e
  gi|119719716|ref|YP_920211.1|  85 CPKCGGFSFKVRYACPNCGSFDVE 108
                                    *********************987 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.9
                        DUF35_N  14 CpdC 17 
                                    Cp+C
  gi|119719716|ref|YP_920211.1| 137 CPKC 140
                                    5555 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.053
                        DUF35_N  13 rCpdCGtvqfPPravC..phCg 32 
                                    rC++CGt + +P a+     Cg
  gi|119719716|ref|YP_920211.1| 159 RCRSCGTSFSYPVASLecASCG 180
                                    9*******99998765446666 PP

>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   5.8       4.2   2.5e+03      11      34 ..      84     105 ..      76     146 .. 0.64
   2 !   16.0   0.1   1.6e-05    0.0096       2      41 ..     150     189 ..     149     234 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 4.2
                                    B-TTT--B--SSS--EE-TTT--E CS
                           FYVE  11 kCeiCakkFsllrrrhhCrlCGkv 34 
                                     C++C   Fs+ + r+ C +CG+ 
  gi|119719716|ref|YP_920211.1|  84 FCPKCGG-FSF-KVRYACPNCGSF 105
                                    6888864.665.668899999975 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 1.6e-05
                                    ---...--SB-TTT--B--SSS--EE-TTT--EE-STTS- CS
                           FYVE   2 kwkddsevkkCeiCakkFsllrrrhhCrlCGkvvCekCss 41 
                                     w++ s++ +C++C ++Fs+ +    C  CG+ + +k  +
  gi|119719716|ref|YP_920211.1| 150 DWVKLSSTWRCRSCGTSFSYPVASLECASCGERFDDKRAE 189
                                    699999**************************99866554 PP

>> Zn_Tnp_IS1  InsA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0       1.1   6.4e+02       6      11 ..      83      88 ..      81      91 .. 0.86
   2 ?    7.1   0.1    0.0074       4.4       6      19 ..      97     110 ..      93     111 .. 0.87
   3 ?    8.3   2.4    0.0032       1.9       5      34 ..     134     163 ..     130     164 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.1
                     Zn_Tnp_IS1  6 ihCPrC 11
                                   + CP+C
  gi|119719716|ref|YP_920211.1| 83 VFCPKC 88
                                   67**** PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0074
                     Zn_Tnp_IS1   6 ihCPrCsstdVyRh 19 
                                      CP C s dV R+
  gi|119719716|ref|YP_920211.1|  97 YACPNCGSFDVERN 110
                                    57*********998 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0032
                     Zn_Tnp_IS1   5 sihCPrCsstdVyRhGks.tagHeRfrCrdC 34 
                                     + CP+C+  + +R+G    +    +rCr+C
  gi|119719716|ref|YP_920211.1| 134 KVQCPKCK-RELVREGDDwVKLSSTWRCRSC 163
                                    599****9.6899***983566789*****9 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.44   2.6e+02      26      32 ..      83      89 ..      77      91 .. 0.73
   2 ?    1.9   0.1      0.36   2.1e+02       5       9 ..      99     103 ..      94     107 .. 0.73
   3 ?    8.0   0.5    0.0045       2.7      23      32 ..     132     141 ..     118     143 .. 0.81
   4 ?    4.1   0.6     0.073        44      27      35 ..     159     167 ..     156     168 .. 0.79
   5 ?    3.5   0.0      0.11        69      25      35 ..     173     183 ..     170     184 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.44
                  zinc_ribbon_4 26 vrCskCg 32
                                   v C+kCg
  gi|119719716|ref|YP_920211.1| 83 VFCPKCG 89
                                   5577776 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.36
                  zinc_ribbon_4   5 CpsCk 9  
                                    Cp+C+
  gi|119719716|ref|YP_920211.1|  99 CPNCG 103
                                    77775 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0045
                  zinc_ribbon_4  23 gvkvrCskCg 32 
                                    ++kv+C+kC+
  gi|119719716|ref|YP_920211.1| 132 TGKVQCPKCK 141
                                    5699999997 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.073
                  zinc_ribbon_4  27 rCskCghvF 35 
                                    rC  Cg++F
  gi|119719716|ref|YP_920211.1| 159 RCRSCGTSF 167
                                    788888887 PP

  == domain 5  score: 3.5 bits;  conditional E-value: 0.11
                  zinc_ribbon_4  25 kvrCskCghvF 35 
                                    ++ C+ Cg+ F
  gi|119719716|ref|YP_920211.1| 173 SLECASCGERF 183
                                    67899999888 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.9     0.026        16       2       8 ..      83      89 ..      82      91 .. 0.86
   2 ?    2.2   0.2      0.29   1.7e+02      22      29 ..      97     104 ..      92     105 .. 0.70
   3 ?   12.6   0.1   0.00015     0.092       4      29 ..     137     165 ..     137     169 .. 0.94
   4 ?    1.4   0.3      0.49   2.9e+02      22      28 ..     174     180 ..     169     184 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.026
                                   EBESTTT CS
                 RNA_POL_M_15KD  2 kFCpkCg 8 
                                    FCpkCg
  gi|119719716|ref|YP_920211.1| 83 VFCPKCG 89
                                   5*****9 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.29
                                    EEESSSS- CS
                 RNA_POL_M_15KD  22 feCrqCgY 29 
                                    ++C +Cg+
  gi|119719716|ref|YP_920211.1|  97 YACPNCGS 104
                                    88888875 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 0.00015
                                    ESTTTSBEEEEECSCCCE...EEESSSS- CS
                 RNA_POL_M_15KD   4 CpkCgNlLlpkedkegkn...feCrqCgY 29 
                                    CpkC+  L   +d+++k      Cr+Cg 
  gi|119719716|ref|YP_920211.1| 137 CPKCKRELVREGDDWVKLsstWRCRSCGT 165
                                    *****************9999******95 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.49
                                    EEESSSS CS
                 RNA_POL_M_15KD  22 feCrqCg 28 
                                    +eC++Cg
  gi|119719716|ref|YP_920211.1| 174 LECASCG 180
                                    79****8 PP

>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   1.4     0.041        25      17      38 ..      83     103 ..      79     119 .. 0.84
   2 ?   12.8   1.6   0.00017       0.1      17      39 ..     158     181 ..     153     202 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.041
                 Ribosomal_L37e  17 ilCrrCgkrsyhvqkktCascG 38 
                                    ++C +Cg  s++v+   C +cG
  gi|119719716|ref|YP_920211.1|  83 VFCPKCGGFSFKVRY-ACPNCG 103
                                    68**********985.699998 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00017
                 Ribosomal_L37e  17 ilCrrCgkr.syhvqkktCascGy 39 
                                     +Cr Cg + sy v   +CascG 
  gi|119719716|ref|YP_920211.1| 158 WRCRSCGTSfSYPVASLECASCGE 181
                                    58*****765*************4 PP

>> Rep_fac-A_C  Replication factor-A C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   1.9    0.0045       2.7      21      50 ..     137     170 ..     134     241 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0045
                                    --STT---B-EEETTTE......EEETTTTEEESS- CS
                    Rep_fac-A_C  21 CpsedCnkKvveeedge......wrCekCdkeveep 50 
                                    Cp  +C++ +v+e+d+       wrC  C ++++ p
  gi|119719716|ref|YP_920211.1| 137 CP--KCKRELVREGDDWvklsstWRCRSCGTSFSYP 170
                                    88..9********99888999999999999887665 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.6     0.025        15      10      35 ..      81     103 ..      75     105 .. 0.87
   2 ?    9.4   0.3    0.0016      0.94       6      36 ..     129     165 ..     127     168 .. 0.89
   3 ?    6.6   0.9     0.012         7       9      41 ..     155     186 ..     151     193 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.025
                                    S--B-TTT-SB--SSSS-EEEETTT- CS
                           C1_1  10 qptfCkhCgeflwgkekqglkCswCk 35 
                                    +  fC +Cg f    +k+ ++C +C+
  gi|119719716|ref|YP_920211.1|  81 KLVFCPKCGGFS---FKVRYACPNCG 103
                                    6789******99...9*********7 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0016
                                    E--SS--B-TTT-SB-......-SSSS-EEEETTT-- CS
                           C1_1   6 rnfkqptfCkhCgefl......wgkekqglkCswCkl 36 
                                    r++  +  C +C+  l      w k +  ++C+ C+ 
  gi|119719716|ref|YP_920211.1| 129 RTVTGKVQCPKCKRELvregddWVKLSSTWRCRSCGT 165
                                    66778899*************999***********86 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.012
                                    SS--B-TTT-SB--SSSS-EEEETTT--EE-CC CS
                           C1_1   9 kqptfCkhCgeflwgkekqglkCswCkllvHkk 41 
                                    +++ +C  Cg ++       l C+ C++++++k
  gi|119719716|ref|YP_920211.1| 155 SSTWRCRSCGTSF-SYPVASLECASCGERFDDK 186
                                    56779********.6677889*****9998765 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1     0.027        16      17      27 ..      79      89 ..      73      97 .. 0.85
   2 ?   -0.3   0.4       1.8   1.1e+03      23      28 ..      99     104 ..      97     105 .. 0.80
   3 ?    9.6   0.1    0.0014      0.85       4      30 ..     134     167 ..     132     169 .. 0.76
   4 ?    1.7   0.1      0.43   2.6e+02       6      17 ..     175     186 ..     171     188 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.027
                    Prok-RING_1 17 edDiVvCpeCg 27
                                   +d +V Cp+Cg
  gi|119719716|ref|YP_920211.1| 79 ADKLVFCPKCG 89
                                   5789******9 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.8
                    Prok-RING_1  23 CpeCgt 28 
                                    Cp+Cg+
  gi|119719716|ref|YP_920211.1|  99 CPNCGS 104
                                    999985 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.0014
                    Prok-RING_1   4 gkkCpvCgkelkee.dDiVv......CpeCgtpy 30 
                                    + +Cp C++el  e dD V       C  Cgt++
  gi|119719716|ref|YP_920211.1| 134 KVQCPKCKRELVREgDDWVKlsstwrCRSCGTSF 167
                                    679******9965548988445555599999985 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.43
                    Prok-RING_1   6 kCpvCgkelkee 17 
                                    +C  Cg++++++
  gi|119719716|ref|YP_920211.1| 175 ECASCGERFDDK 186
                                    7*******9875 PP

>> DUF3797  Domain of unknown function (DUF3797)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.3      0.18   1.1e+02      11      20 ..      80      89 ..      74      93 .. 0.84
   2 ?    3.8   0.6     0.092        55      15      24 ..      98     107 ..      91     112 .. 0.77
   3 ?   10.1   0.2   0.00099      0.59      14      47 ..     135     168 ..     130     169 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.18
                        DUF3797 11 ekYvqCPeCg 20
                                   +k v CP+Cg
  gi|119719716|ref|YP_920211.1| 80 DKLVFCPKCG 89
                                   57899****9 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.092
                        DUF3797  15 qCPeCgNnkv 24 
                                    +CP+Cg   v
  gi|119719716|ref|YP_920211.1|  98 ACPNCGSFDV 107
                                    7****97666 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.00099
                        DUF3797  14 vqCPeCgNnkvlNsegkviieddtfyreCkCgfn 47 
                                    vqCP+C+ + v  ++  v ++     r+C+ +f+
  gi|119719716|ref|YP_920211.1| 135 VQCPKCKRELVREGDDWVKLSSTWRCRSCGTSFS 168
                                    8***************999998777799987775 PP

>> Ribosomal_L32p  Ribosomal L32p protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00066       0.4      22      47 ..      78     104 ..      70     120 .. 0.80
   2 ?   -0.4   0.2       2.4   1.5e+03      27      33 ..     135     141 ..     127     147 .. 0.74
   3 ?   -1.2   0.1       4.4   2.6e+03      28      35 ..     175     182 ..     168     188 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00066
                                    ----EEEETTTCCEECT.TC-BTTTTB CS
                 Ribosomal_L32p  22 kapnlvecpncgelklp.HrvcpscGy 47 
                                     a +lv cp+cg ++   + +cp+cG 
  gi|119719716|ref|YP_920211.1|  78 PADKLVFCPKCGGFSFKvRYACPNCGS 104
                                    45699*******88765388*****94 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 2.4
                                    EEETTTC CS
                 Ribosomal_L32p  27 vecpncg 33 
                                    v+cp+c+
  gi|119719716|ref|YP_920211.1| 135 VQCPKCK 141
                                    7899998 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 4.4
                                    EETTTCCE CS
                 Ribosomal_L32p  28 ecpncgel 35 
                                    ec  cge 
  gi|119719716|ref|YP_920211.1| 175 ECASCGER 182
                                    89999985 PP

>> VATC  Vms1-associating treble clef domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       5.8   3.5e+03       5      14 ..     136     145 ..     135     147 .. 0.82
   2 ?    6.3   0.2     0.015       8.8       3      13 ..     157     167 ..     155     170 .. 0.88
   3 ?    3.9   0.1     0.082        49       4      15 ..     174     185 ..     171     192 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 5.8
                           VATC   5 rCsiCgesle 14 
                                    +C  C+++l+
  gi|119719716|ref|YP_920211.1| 136 QCPKCKRELV 145
                                    7999*99885 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.015
                           VATC   3 vlrCsiCgesl 13 
                                    ++rC +Cg+s+
  gi|119719716|ref|YP_920211.1| 157 TWRCRSCGTSF 167
                                    7********98 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.082
                           VATC   4 lrCsiCgesleg 15 
                                    l+C +Cge++  
  gi|119719716|ref|YP_920211.1| 174 LECASCGERFDD 185
                                    69******9975 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.2      0.15        87       3       8 ..      85      90 ..      83      96 .. 0.75
   2 ?    9.7   0.2     0.001      0.61       1      14 [.      97     110 ..      97     131 .. 0.78
   3 ?    2.9   2.9      0.13        76       2      27 ..     136     165 ..     135     175 .. 0.68
   4 ?    1.6   1.9      0.32   1.9e+02       3      31 ..     160     185 ..     158     191 .. 0.66

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.15
                                   ETTTTC CS
                   TF_Zn_Ribbon  3 CPnCgs 8 
                                   CP+Cg+
  gi|119719716|ref|YP_920211.1| 85 CPKCGG 90
                                   888886 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.001
                                    EEETTTTCEECHEE CS
                   TF_Zn_Ribbon   1 ykCPnCgstnlveD 14 
                                    y CPnCgs +++++
  gi|119719716|ref|YP_920211.1|  97 YACPNCGSFDVERN 110
                                    68*****9545554 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.13
                                    EETTTTCEE.CHEE..TSTTCE.EESSSSB CS
                   TF_Zn_Ribbon   2 kCPnCgstn.lveD..pergel.vCtdCGl 27 
                                    +CP+C+ +   + D   +   + +C +CG+
  gi|119719716|ref|YP_920211.1| 136 QCPKCKRELvREGDdwVKLSSTwRCRSCGT 165
                                    8*****875334446644444447777775 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.32
                                    ETTTTCEECHEETSTTCEEESSSSBEEEE CS
                   TF_Zn_Ribbon   3 CPnCgstnlveDpergelvCtdCGlVled 31 
                                    C  Cg++   + +  + l C +CG+  +d
  gi|119719716|ref|YP_920211.1| 160 CRSCGTS---FSYPVASLECASCGERFDD 185
                                    7778865...4455557779999876666 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   1.1      0.63   3.8e+02       2       6 ..      85      89 ..      84      90 .. 0.88
   2 ?    4.3   0.1      0.07        42       2       7 ..      99     104 ..      98     111 .. 0.88
   3 ?    8.8   1.0    0.0028       1.6       1      20 [.     136     160 ..     136     165 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.63
                 DNA_ligase_ZBD  2 CPvCG 6 
                                   CP CG
  gi|119719716|ref|YP_920211.1| 85 CPKCG 89
                                   ****9 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.07
                 DNA_ligase_ZBD   2 CPvCGs 7  
                                    CP CGs
  gi|119719716|ref|YP_920211.1|  99 CPNCGS 104
                                    *****9 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0028
                 DNA_ligase_ZBD   1 hCPvCGsavvReeg.....eaiyRC 20 
                                    +CP C  ++vRe +      + +RC
  gi|119719716|ref|YP_920211.1| 136 QCPKCKRELVREGDdwvklSSTWRC 160
                                    5**********99855555555555 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1       0.5     3e+02       3       8 ..      84      89 ..      83      95 .. 0.80
   2 ?    3.3   0.1      0.14        81       1       9 [.      96     104 ..      96     110 .. 0.90
   3 ?    1.5   0.1      0.49   2.9e+02       4       9 ..     137     142 ..     131     149 .. 0.78
   4 ?    7.3   0.5    0.0077       4.6       2      29 ..     158     181 ..     158     185 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.5
                                   E-TTT- CS
                        ADK_lid  3 vCpkCG 8 
                                    CpkCG
  gi|119719716|ref|YP_920211.1| 84 FCPKCG 89
                                   588888 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.14
                                    EEE-TTT-- CS
                        ADK_lid   1 RrvCpkCGr 9  
                                    R  Cp+CG 
  gi|119719716|ref|YP_920211.1|  96 RYACPNCGS 104
                                    889****95 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.49
                                    -TTT-- CS
                        ADK_lid   4 CpkCGr 9  
                                    CpkC+r
  gi|119719716|ref|YP_920211.1| 137 CPKCKR 142
                                    777776 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.0077
                                    EE-TTT--EEETTTB--SSTTB-TTT-- CS
                        ADK_lid   2 rvCpkCGrsYhvvfnpPkveglCDkCGe 29 
                                    + C++CG+s++  +  P +   C  CGe
  gi|119719716|ref|YP_920211.1| 158 WRCRSCGTSFS--Y--PVASLECASCGE 181
                                    66*********..6..889999999998 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.3      0.96   5.8e+02      20      30 ..      95     105 ..      90     121 .. 0.69
   2 ?   11.5   0.6   0.00039      0.23      18      63 ..     131     175 ..     123     177 .. 0.87
   3 ?    2.7   0.0      0.22   1.3e+02      43      56 ..     171     184 ..     169     194 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.96
                           Elf1  20 tkFdCpfCnhe 30 
                                     ++ Cp+C++ 
  gi|119719716|ref|YP_920211.1|  95 VRYACPNCGSF 105
                                    57899999876 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00039
                           Elf1  18 lptkFdCpfCnheksvevkldkkekiaevsCkvCgesfetkvnals 63 
                                    +  k +Cp C+ e  v+   d  +   + +C++Cg+sf++ v +l+
  gi|119719716|ref|YP_920211.1| 131 VTGKVQCPKCKRE-LVREGDDWVKLSSTWRCRSCGTSFSYPVASLE 175
                                    556779*******.99999999999***************999886 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.22
                           Elf1  43 iaevsCkvCgesfe 56 
                                    +a+++C +Cge+f+
  gi|119719716|ref|YP_920211.1| 171 VASLECASCGERFD 184
                                    6899******9986 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.4       3.1   1.9e+03       3       7 ..      85      89 ..      83      96 .. 0.71
   2 ?    4.1   0.1      0.18   1.1e+02       1      20 [.      97     116 ..      97     117 .. 0.78
   3 ?    2.0   0.1      0.86   5.1e+02       2      10 ..     136     144 ..     135     151 .. 0.80
   4 ?    5.4   0.4     0.067        40       2      12 ..     159     169 ..     158     173 .. 0.85
   5 ?    4.2   0.0      0.16        97       2      15 ..     175     188 ..     174     192 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 3.1
                      zf-C2H2_4  3 CpiCg 7 
                                   Cp Cg
  gi|119719716|ref|YP_920211.1| 85 CPKCG 89
                                   ****4 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.18
                      zf-C2H2_4   1 fkCpiCgksFs.skkaLlrHl 20 
                                    + Cp C +sF   +++L +H+
  gi|119719716|ref|YP_920211.1|  97 YACPNC-GSFDvERNTLFSHV 116
                                    89****.99975555599886 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.86
                      zf-C2H2_4   2 kCpiCgksF 10 
                                    +Cp C++  
  gi|119719716|ref|YP_920211.1| 136 QCPKCKREL 144
                                    8****8876 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.067
                      zf-C2H2_4   2 kCpiCgksFss 12 
                                    +C+ Cg+sFs 
  gi|119719716|ref|YP_920211.1| 159 RCRSCGTSFSY 169
                                    8********86 PP

  == domain 5  score: 4.2 bits;  conditional E-value: 0.16
                      zf-C2H2_4   2 kCpiCgksFsskka 15 
                                    +C  Cg++F +k+a
  gi|119719716|ref|YP_920211.1| 175 ECASCGERFDDKRA 188
                                    79*******98875 PP

>> Cys_rich_KTR  Cysteine-rich KTR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.3     0.033        20      25      33 ..      76      88 ..      69      91 .. 0.70
   2 ?   -1.8   0.2       4.6   2.7e+03       6      11 ..      99     104 ..      97     107 .. 0.81
   3 ?    6.6   0.2     0.011       6.7      30      37 ..     137     144 ..     133     149 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.033
                   Cys_rich_KTR 25 nfp....LfCPKC 33
                                    fp    +fCPKC
  gi|119719716|ref|YP_920211.1| 76 AFPadklVFCPKC 88
                                   555444379***9 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.6
                   Cys_rich_KTR   6 cPvCgn 11 
                                    cP Cg+
  gi|119719716|ref|YP_920211.1|  99 CPNCGS 104
                                    899985 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.011
                   Cys_rich_KTR  30 CPKCkqet 37 
                                    CPKCk+e 
  gi|119719716|ref|YP_920211.1| 137 CPKCKREL 144
                                    ******96 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.2      0.11        68       4       9 ..      85      90 ..      83      91 .. 0.88
   2 ?    2.9   0.1      0.15        93       4      10 ..      99     105 ..      96     118 .. 0.76
   3 ?    7.2   0.5    0.0072       4.3       2      13 ..     135     146 ..     134     148 .. 0.87
   4 ?   -1.8   0.1       4.7   2.8e+03       3      10 ..     175     182 ..     174     190 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.11
                                   -SSS-- CS
                 zf-C4_Topoisom  4 CPkCgg 9 
                                   CPkCgg
  gi|119719716|ref|YP_920211.1| 85 CPKCGG 90
                                   ****97 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.15
                                    -SSS--E CS
                 zf-C4_Topoisom   4 CPkCggd 10 
                                    CP Cg+ 
  gi|119719716|ref|YP_920211.1|  99 CPNCGSF 105
                                    *****85 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0072
                                    EE-SSS--EEEE CS
                 zf-C4_Topoisom   2 ekCPkCggdLvl 13 
                                    ++CPkC+ +Lv+
  gi|119719716|ref|YP_920211.1| 135 VQCPKCKRELVR 146
                                    68******9995 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 4.7
                                    E-SSS--E CS
                 zf-C4_Topoisom   3 kCPkCggd 10 
                                    +C +Cg+ 
  gi|119719716|ref|YP_920211.1| 175 ECASCGER 182
                                    6999*976 PP

>> zf_C2H2_10  C2H2 type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.5      0.12        69       5       9 ..      85      89 ..      83      91 .. 0.89
   2 ?    3.3   0.0     0.098        59       3       9 ..      97     103 ..      96     116 .. 0.86
   3 ?    3.9   0.9     0.066        40       5      10 ..     137     142 ..     134     144 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.12
                     zf_C2H2_10  5 CPKCq 9 
                                   CPKC+
  gi|119719716|ref|YP_920211.1| 85 CPKCG 89
                                   ****7 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.098
                     zf_C2H2_10   3 fsCPKCq 9  
                                    ++CP C+
  gi|119719716|ref|YP_920211.1|  97 YACPNCG 103
                                    89****7 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.066
                     zf_C2H2_10   5 CPKCqe 10 
                                    CPKC+ 
  gi|119719716|ref|YP_920211.1| 137 CPKCKR 142
                                    ****86 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0075       4.5      20      30 ..      79      89 ..      63      89 .. 0.86
   2 ?    3.4   0.3      0.14        86      26      31 ..      99     104 ..      97     105 .. 0.86
   3 ?    2.2   0.2      0.36   2.1e+02      24      31 ..     135     142 ..     127     142 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0075
                                   STB-EE-TTT- CS
                      zf-RING_7 20 gdevvtCpeCG 30
                                   +d++v+Cp CG
  gi|119719716|ref|YP_920211.1| 79 ADKLVFCPKCG 89
                                   399*******9 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.14
                                    -TTT-- CS
                      zf-RING_7  26 CpeCGR 31 
                                    Cp+CG 
  gi|119719716|ref|YP_920211.1|  99 CPNCGS 104
                                    ****96 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.36
                                    EE-TTT-- CS
                      zf-RING_7  24 vtCpeCGR 31 
                                    v+Cp C R
  gi|119719716|ref|YP_920211.1| 135 VQCPKCKR 142
                                    89****98 PP

>> IBR  IBR domain, a half RING-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3  13.1       4.6   2.7e+03      18      29 ..     134     144 ..      66     183 .. 0.59

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 4.6
                            IBR  18 lkwCprpdCe.ai 29 
                                    +++Cp  +C+  +
  gi|119719716|ref|YP_920211.1| 134 KVQCP--KCKrEL 144
                                    44555..555334 PP

>> zf-C2H2_11  zinc-finger C2H2-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.5      0.29   1.7e+02       5      12 ..     135     142 ..     132     143 .. 0.88
   2 ?    9.3   0.9    0.0016      0.95       2      15 ..     155     168 ..     155     172 .. 0.88
   3 ?    1.0   0.2       0.6   3.6e+02       3      14 ..     172     183 ..     170     184 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.29
                     zf-C2H2_11   5 cqCleCGl 12 
                                    +qC +C++
  gi|119719716|ref|YP_920211.1| 135 VQCPKCKR 142
                                    7*****98 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0016
                     zf-C2H2_11   2 estcqCleCGlcft 15 
                                    +st +C+ CG  f+
  gi|119719716|ref|YP_920211.1| 155 SSTWRCRSCGTSFS 168
                                    69*********998 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.6
                     zf-C2H2_11   3 stcqCleCGlcf 14 
                                    +++ C  CG  f
  gi|119719716|ref|YP_920211.1| 172 ASLECASCGERF 183
                                    6889*****776 PP

>> Ribosomal_L37ae  Ribosomal L37ae protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.1     0.021        13      31      48 ..      94     111 ..      90     119 .. 0.88
   2 ?    1.8   0.1      0.42   2.5e+02      35      60 ..     117     143 ..     112     155 .. 0.76
   3 ?    3.2   2.3      0.16        96      33      61 ..     134     167 ..     125     170 .. 0.70
   4 ?   -0.3   0.2         2   1.2e+03      40      40 ..     199     199 ..     170     243 .. 0.52

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.021
                                    HS-BEESSSSSSEEEEEE CS
                Ribosomal_L37ae  31 hakytCpfcgktkvkRka 48 
                                    + +y Cp+cg+ +v+R+ 
  gi|119719716|ref|YP_920211.1|  94 KVRYACPNCGSFDVERNT 111
                                    568************975 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.42
                                    EESSSSSS.EEEEEETTEEEETTTTEE CS
                Ribosomal_L37ae  35 tCpfcgkt.kvkRkavgiwkCkkcgkt 60 
                                    tC f g   +  R+ +g  +C kc+++
  gi|119719716|ref|YP_920211.1| 117 TCGFIGVLeEAPRTVTGKVQCPKCKRE 143
                                    566666654777888898999999865 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.16
                                    -BEESSSSSSEEEE.....EETTEEEETTTTEEE CS
                Ribosomal_L37ae  33 kytCpfcgktkvkR.....kavgiwkCkkcgktv 61 
                                    k +Cp+c+++ v+      k    w+C++cg  +
  gi|119719716|ref|YP_920211.1| 134 KVQCPKCKRELVREgddwvKLSSTWRCRSCGTSF 167
                                    668999977766532222234678******9876 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 2
                                    S CS
                Ribosomal_L37ae  40 g 40 
                                    +
  gi|119719716|ref|YP_920211.1| 199 D 199
                                    2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1001  (0.0558313); expected 358.6 (0.02)
Passed bias filter:                      829  (0.0462379); expected 358.6 (0.02)
Passed Vit filter:                       148  (0.00825478); expected 17.9 (0.001)
Passed Fwd filter:                        87  (0.00485247); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              30  [number of targets reported over threshold]
# CPU time: 0.73u 0.34s 00:00:01.07 Elapsed: 00:00:00.55
# Mc/sec: 1782.06
//
Query:       gi|119719717|ref|YP_920212.1|  [L=510]
Description: type II secretion system protein E [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-52  178.8   0.0    1.7e-52  178.2   0.0    1.2  1  T2SSE     Type II/IV secretion system protein
  ------ inclusion threshold ------
      0.062   13.8   0.0       0.14   12.7   0.0    1.5  1  ABC_tran  ABC transporter
       0.11   12.9   0.0       0.26   11.6   0.0    1.7  1  AAA_16    AAA ATPase domain
       0.14   11.9   0.0        0.3   10.9   0.0    1.5  1  AAA_29    P-loop containing region of AAA domain


Domain annotation for each model (and alignments):
>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.2   0.0   3.7e-56   1.7e-52       5     247 ..     123     370 ..     120     398 .. 0.94

  Alignments for each domain:
  == domain 1  score: 178.2 bits;  conditional E-value: 3.7e-56
                          T2SSE   5 leallddekvsdihvekper.vkvrervdgielreveelekaalerlisriaalakldiseerplqdarlpekgvrlrvv 83 
                                    ++all+d +  di     ++ v v  r  +    ++ + ++ +l+ li ++ + a+++is  +p+++++lp  g rl++ 
  gi|119719717|ref|YP_920212.1| 123 IDALLRDVELEDISCDGLGTpVYVWHRRYESLPTNIVFKDPGELASLILKLSFRAGRQISVAQPIVEGSLP-MGFRLHAT 201
                                    57899999*************999888888899**************************************.******** PP

                          T2SSE  84 llPvvag.ealviRkksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeinksderivt 162
                                    l  v++   +++iRk ++  +t+ dl+a+++++e++a+ l + v+++ ++lv G+T  GKtt+l+a+ ++i  +  +ivt
  gi|119719717|ref|YP_920212.1| 202 LEEVSRRgGTFTIRKFREVPFTIVDLVAAGTVSEELAAYLWYLVENYRSVLVVGATAGGKTTTLNAIATFIRPE-AKIVT 280
                                    ****99989***************************************************************99.***** PP

                          T2SSE 163 vEDpvEiqleganqvqlnak......kakvtfadllraaLRlrPDrimvGEiRdketleilkAvnTGHlgslsTlHansa 236
                                    +ED+ E++l ++n v l+++        +v++ dll++a+R+rPD +++GEiR++e++++ +A+ TGH g +sTlHa+s 
  gi|119719717|ref|YP_920212.1| 281 IEDTPELRLPHENWVPLVTRpsheewVRNVDLFDLLKSAMRMRPDYLIIGEIRGEEAFTLFQAIATGHSG-MSTLHAESI 359
                                    ***********************99999******************************************.********* PP

                          T2SSE 237 agalerLeqlg 247
                                      a++rL    
  gi|119719717|ref|YP_920212.1| 360 DYAVKRLVSEP 370
                                    ******97644 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0     3e-05      0.14      13      49 ..     250     286 ..     244     323 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3e-05
                                    EEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEG CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  13 kvaivGenGaGKStLlkllagllkpteGeilldgkdl 49 
                                     v +vG +  GK+t l+++a   +p++  +++++++ 
  gi|119719717|ref|YP_920212.1| 250 SVLVVGATAGGKTTTLNAIATFIRPEAKIVTIEDTPE 286
                                    6789**************************9998765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   5.8e-05      0.26      25      63 ..     249     288 ..     235     368 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.8e-05
                         AAA_16  25 elvllsGesGvGKsslvrellralekdg.giflrgkcdql 63 
                                    ++vl++G+ + GK++ ++++++ ++ +  +++++ + +  
  gi|119719717|ref|YP_920212.1| 249 RSVLVVGATAGGKTTTLNAIATFIRPEAkIVTIEDTPELR 288
                                    89********************999995366676666655 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   6.6e-05       0.3      24      51 ..     250     277 ..     241     280 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 6.6e-05
                         AAA_29  24 atlltGpsGsGKSTllDAiqalLvpakk 51 
                                    ++l++G++  GK+T l Ai++ + p+ k
  gi|119719717|ref|YP_920212.1| 250 SVLVVGATAGGKTTTLNAIATFIRPEAK 277
                                    589******************9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (510 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 3268.47
//
Query:       gi|119719718|ref|YP_920213.1|  [L=283]
Description: protein of unknown function Met10 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-61  207.6   0.0    1.9e-61  207.3   0.0    1.1  1  Met_10           Met-10+ like-protein
    2.5e-06   26.9   0.0    3.5e-06   26.4   0.0    1.1  1  TRM              N2,N2-dimethylguanosine tRNA methyltransfera
    2.1e-05   24.2   0.0    3.2e-05   23.6   0.0    1.3  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
    0.00052   19.6   0.0     0.0013   18.3   0.0    1.6  1  MTS              Methyltransferase small domain
    0.00055   20.6   0.0     0.0066   17.1   0.0    2.4  2  Methyltransf_25  Methyltransferase domain
     0.0024   17.3   0.0     0.0035   16.8   0.0    1.3  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
     0.0032   17.3   0.2     0.0071   16.2   0.0    1.6  2  PRMT5            PRMT5 arginine-N-methyltransferase
  ------ inclusion threshold ------
       0.11   13.2   0.1         31    5.3   0.0    3.4  3  Methyltransf_11  Methyltransferase domain
       0.15   12.5   0.5       0.45   11.0   0.1    2.1  3  Glyco_trans_1_4  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  207.3   0.0   9.3e-65   1.9e-61       8     199 .]      32     228 ..      21     229 .. 0.93

  Alignments for each domain:
  == domain 1  score: 207.3 bits;  conditional E-value: 9.3e-65
                                    TEEEEEB-TTSSHHHHHHHHHHHHHS.S-SCEEEE-S-SBTTTTB--EEEEEES-.SEEEEEETTEEEEEETTTS---GG CS
                         Met_10   8 dvvilnlreelkeykkvigevildkt.kvktvlrkvsevegefRtfelevlaGsdstetihkEngcrfklDvskvyfssk 86 
                                     v+i++l++el +yk+ i+e+il+++ +vk+v+rk +   ge+R++ele++ G+  te++hkE+g+r+klDv+kvyfs++
  gi|119719718|ref|YP_920213.1|  32 AVAIVELPDELLPYKEAIAEAILQVHkNVKAVYRKLGGRVGEYRVRELELIGGEPITEVVHKEHGYRLKLDVTKVYFSPR 111
                                    499***********************9**********99***************************************** PP

                                    GHHHHHHHHTT--TT-EEEETT-TTTCCHHHCCHHT.TSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG--- CS
                         Met_10  87 leaErerlaklveegevVvdvfAGiGpfaipiakys.kakrvlaidlnPesvkylkeniklNkvekvvkpileDgrevir 165
                                     ++Er+r+a++v++ge+V+ +fAG+Gp+ai+iak   + ++v+ai+lnP+++ y+ en+klNkve  v p+l+D+re +r
  gi|119719718|ref|YP_920213.1| 112 EATERQRIARQVKPGETVMVMFAGVGPYAIAIAKAQpRVEKVIAIELNPAAYAYMVENVKLNKVEGLVVPVLGDVREKAR 191
                                    *********************************94324568**************************************9 PP

                                    ..TT-EEEEEE--TTTGGGGHHHHHHHEEEE.EEEEE CS
                         Met_10 166 ..eqladrvvmnlpksaieFldkvlaalkdg.gvihy 199
                                          drvvm+lp+ a  Fld+++++lk g g ih+
  gi|119719718|ref|YP_920213.1| 192 ewYGSCDRVVMPLPRGAYMFLDEAVRCLKSGgGWIHF 228
                                    777899**********************998456665 PP

>> TRM  N2,N2-dimethylguanosine tRNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0   1.8e-09   3.5e-06      52     147 ..     128     223 ..      87     226 .. 0.85

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 1.8e-09
                                    EEEESS-TTSHHHHHHHHH-S-EEEEEEE-S-HHHHHHHHHHHHHTT--GGEEEE-S-HHHHHC--SS-EEEEEE-.-SS CS
                            TRM  52 kvldaLsasGlRaiRfalEvpgvkevlaNDisekAvelikeNvklneveeivvineddAnvllaekkkrfdviDlD.PfG 130
                                    +v+  +++ G  ai  a+  p v++v+a ++++ A++ + eNvkln+ve +vv+  +d +   +e+    d + +  P G
  gi|119719718|ref|YP_920213.1| 128 TVMVMFAGVGPYAIAIAKAQPRVEKVIAIELNPAAYAYMVENVKLNKVEGLVVPVLGDVREKAREWYGSCDRVVMPlPRG 207
                                    466678999999******************************************************99999988763666 PP

                                    --GGGHHHHHHHEEEEE CS
                            TRM 131 spapfldsavqsvkekg 147
                                     +  fld av+++k++g
  gi|119719718|ref|YP_920213.1| 208 -AYMFLDEAVRCLKSGG 223
                                    .677*********9986 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   1.6e-08   3.2e-05       3      89 ..     128     214 ..     126     222 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 1.6e-08
                Methyltransf_15   3 vilDlfsGaGGnviqfalv...fekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklklekikvdlvflSp 79 
                                    +++ +f+G G  +i++a+     ekviaie n+   a + +N ++  v+  + +vlgdv e  ++    ++  d v++  
  gi|119719718|ref|YP_920213.1| 128 TVMVMFAGVGPYAIAIAKAqprVEKVIAIELNPAAYAYMVENVKLNKVEGLVVPVLGDVREKARE-WYGSC--DRVVMPL 204
                                    56779*************9888999************************************9998.56777..9999999 PP

                Methyltransf_15  80 PwGGpsYkkq 89 
                                    P G   + ++
  gi|119719718|ref|YP_920213.1| 205 PRGAYMFLDE 214
                                    9997766665 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   6.3e-07    0.0013      35     165 ..     129     254 ..     118     256 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 6.3e-07
                                    EEEET-TTSHHHHHHHHHTTC.E.EEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTTSTT..S-EEEEEE---STT CS
                            MTS  35 vlDlGcGaGvlgaalakespeae.vtlvdvdarAlesakenleankle..vevvasdvleevee..kkfdlivsNPPfha 109
                                    v+ + +G+G+ ++a+ak++p++e v +++ + +A +   en++ nk+e  v  v  dv e++ e  +++d +v+  P+ +
  gi|119719718|ref|YP_920213.1| 129 VMVMFAGVGPYAIAIAKAQPRVEkVIAIELNPAAYAYMVENVKLNKVEglVVPVLGDVREKAREwyGSCDRVVM--PLPR 206
                                    566679****************99************************877778899999988544899****9..7878 PP

                                    TCHCHHHHHHHHHHHHHHHEEEEEEEEEEEETTSCHHHHHHHHHS--EEEEEESSE CS
                            MTS 110 gkatelavaeeliaeAkeaLkegGeLliVanrklgyeslleelfgnvevvaktkkf 165
                                    g          ++ eA ++Lk+gG ++  +    + ++l +++f+ v+++a++++f
  gi|119719718|ref|YP_920213.1| 207 GAY-------MFLDEAVRCLKSGGGWIHFYYWD-REDDLFAKAFSLVKEAAEKHGF 254
                                    877.......79999999999999876655544.4466678888888888888777 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.52     1e+03      58      79 ..      16      38 ..       5      57 .. 0.74
   2 !   17.1   0.0   3.3e-06    0.0066       6      97 .]     134     223 ..     129     223 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.52
                                   BSSSTTTEEEEEEEST.GGGSSH CS
                Methyltransf_25 58 lpfedgsfDlvvssga.lhhlsd 79
                                   lp+  +sfD+v s+ a + +++ 
  gi|119719718|ref|YP_920213.1| 16 LPLVPSSFDVVGSREAaVAIVEL 38
                                   788899*****998876665554 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 3.3e-06
                                    -TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBC.CGBSSSTTTEEEEEEESTGGGSSHHH CS
                Methyltransf_25   6 cGtGrltlalakrlg.kakvtgvDiseemleaareraeeegl..nvefvqgda.edlpfedgsfDlvvssgalhhlsded 81 
                                    +G G +++a+ak+ +  +kv+++++++++ +++ e+++ +++   v  v gd+ e+  +  gs+D vv+      l+ + 
  gi|119719718|ref|YP_920213.1| 134 AGVGPYAIAIAKAQPrVEKVIAIELNPAAYAYMVENVKLNKVegLVVPVLGDVrEKAREWYGSCDRVVMP-----LP-RG 207
                                    79999999999998458********************9998887777799***55578899********5.....33.45 PP

                                    HHHHHHHHHHHEEEEE CS
                Methyltransf_25  82 lekalkeiarvLkpgG 97 
                                    +  +l+e+ r+Lk gG
  gi|119719718|ref|YP_920213.1| 208 AYMFLDEAVRCLKSGG 223
                                    678************9 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.8e-06    0.0035     155     223 ..     119     188 ..     112     227 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.8e-06
                           PrmA 155 leklvkegeevlDv..GtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellk 223
                                    + ++vk+ge+v+ +  G G   +aia a+   +kv+a+ +++ A     eN++lNkve  + v + +++ +
  gi|119719718|ref|YP_920213.1| 119 IARQVKPGETVMVMfaGVGPYAIAIAKAQPRVEKVIAIELNPAAYAYMVENVKLNKVEGLV-VPVLGDVRE 188
                                    557799999887651155555666666677899************************9976.555566554 PP

>> PRMT5  PRMT5 arginine-N-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.6   3.2e+03      43      59 ..      45      61 ..      43      67 .. 0.74
   2 !   16.2   0.0   3.6e-06    0.0071      63     133 ..     124     190 ..      97     204 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.6
                                   HHHHHHHHHHHHCTCCG CS
                          PRMT5 43 YeeAiekalsdlkkekk 59
                                   Y+eAi++a+ +++k+ k
  gi|119719718|ref|YP_920213.1| 45 YKEAIAEAILQVHKNVK 61
                                   88888888888777655 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 3.6e-06
                                    .-EEEEEEES-TTSHHHHHHHHHHHHHCCCEEEEEEEES-HHHHHHHHHHHHHHTTCCGCEEEES-CCCCC CS
                          PRMT5  63 ekklvilvvGaGRGplvdralkaleetkvtkvkivavEKnpnavvtLqkkvneekWeekveviksdmrelk 133
                                    +   +++v+ aG Gp   ++ ka+ + +    k++a+E np+a+ ++ ++v+ +k e  v  +  d+re  
  gi|119719718|ref|YP_920213.1| 124 KPGETVMVMFAGVGPYAIAIAKAQPRVE----KVIAIELNPAAYAYMVENVKLNKVEGLVVPVLGDVREKA 190
                                    3456899999*****9998888888888....9*********************99999888888888755 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.073   1.5e+02      55      74 ..      16      35 ..       4      59 .. 0.77
   2 ?   -3.9   0.0         9   1.8e+04      83      91 ..     118     126 ..     113     130 .. 0.80
   3 ?    5.3   0.0     0.015        31      19      92 ..     151     223 ..     133     226 .. 0.52

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.073
                                   TSS-TT-EEEEEEES-CCC- CS
                Methyltransf_11 55 lpfednsfDlvvssevlhhv 74
                                   lp+  +sfD+v s+e+   +
  gi|119719718|ref|YP_920213.1| 16 LPLVPSSFDVVGSREAAVAI 35
                                   599999*****999965544 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 9
                                    HHHHHEEEE CS
                Methyltransf_11  83 eiaRvLkpg 91 
                                     iaR +kpg
  gi|119719718|ref|YP_920213.1| 118 RIARQVKPG 126
                                    688999998 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.015
                                    SEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-T..T-EEEEEEES-CCC-CCHHHHHHHHHHHEEEEE CS
                Methyltransf_11  19 arvvgvDlskemlklakekaseegl..kvefvvadaeklpfed..nsfDlvvssevlhhvedpekalkeiaRvLkpgG 92 
                                    ++v++++l++++ ++  e+++ +++   v  v +d+++   ++  +s+D vv+            +l+e++R+Lk gG
  gi|119719718|ref|YP_920213.1| 151 EKVIAIELNPAAYAYMVENVKLNKVegLVVPVLGDVREKA-REwyGSCDRVVMPLP----RGAYMFLDEAVRCLKSGG 223
                                    5666666666665555555555544443333555555421.221245555444432....223457889999999988 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       2.7   5.4e+03     115     133 ..      42      58 ..      22      59 .. 0.58
   2 ?   -2.4   0.0       2.9   5.8e+03      16      40 ..      59      85 ..      47     107 .. 0.52
   3 ?   11.0   0.1   0.00022      0.45      50      91 ..     175     216 ..     119     220 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.7
                                    E--TT-HHHHHHHHHHHHH CS
                Glyco_trans_1_4 115 lvppgdpealaeailrLle 133
                                    l+p    ea+aeail++ +
  gi|119719718|ref|YP_920213.1|  42 LLP--YKEAIAEAILQVHK 58 
                                    444..46788888888765 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.9
                                   THHHHHHHH.HHHH.HH.EEEEEES-- CS
                Glyco_trans_1_4 16 gvdllleav.pllrkkd.vrlvivGdg 40
                                   +v+ + +++  ++ + +  +l ++G++
  gi|119719718|ref|YP_920213.1| 59 NVKAVYRKLgGRVGEYRvRELELIGGE 85
                                   333333444333332232356666643 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00022
                                    HTT-T.TEEEE---.THHHHHHHH-SEEEE--.---SHHHHHHH CS
                Glyco_trans_1_4  50 aagleerveftGfv.edlaellaaadvfvaPs.egfglkllEam 91 
                                    ++gl   v ++G v e+ +e++ ++d +v+P+ +g  + l Ea 
  gi|119719718|ref|YP_920213.1| 175 VEGL--VVPVLGDVrEKAREWYGSCDRVVMPLpRGAYMFLDEAV 216
                                    2233..399*****888***************998777666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 1639.41
//
Query:       gi|119719719|ref|YP_920214.1|  [L=447]
Description: phosphomannomutase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-24   85.3   0.0    5.8e-24   84.4   0.0    1.4  1  PGM_PMM_I        Phosphoglucomutase/phosphomannomutase, alpha
    2.2e-22   79.6   0.0    4.6e-22   78.6   0.0    1.6  1  PGM_PMM_II       Phosphoglucomutase/phosphomannomutase, alpha
    5.1e-16   58.9   0.0    9.1e-16   58.1   0.0    1.4  1  PGM_PMM_III      Phosphoglucomutase/phosphomannomutase, alpha
    2.6e-12   46.8   0.8    7.9e-12   45.2   0.3    2.0  2  PGM_PMM_IV       Phosphoglucomutase/phosphomannomutase, C-ter
  ------ inclusion threshold ------
      0.012   15.8   0.0       0.12   12.7   0.0    2.2  2  Cu_amine_oxidN2  Copper amine oxidase, N2 domain
      0.015   15.7   0.0       0.11   13.0   0.0    2.1  2  DUF2218          Uncharacterized protein conserved in bacteri
      0.082   13.2   0.0       0.23   11.7   0.0    1.7  1  AlkA_N           AlkA N-terminal domain
      0.095   12.8   0.1       0.24   11.5   0.1    1.6  1  EFG_II           Elongation Factor G, domain II


Domain annotation for each model (and alignments):
>> PGM_PMM_I  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.4   0.0   2.6e-27   5.8e-24       3     130 ..       7     127 ..       5     133 .. 0.95

  Alignments for each domain:
  == domain 1  score: 84.4 bits;  conditional E-value: 2.6e-27
                                    GBBTTCEEEECCHCTBSCCHHHHHHHHHHHHCHHCSTS-EEEEEE-S-TTHHHHHHHHHHHHHCCT-CEEEEEEB-HHHH CS
                      PGM_PMM_I   3 kfgtsGlRgkvgegeltpelveklgqaiaeylkaeakkkkvvvGrDtRvssrelaealaaglaanGvevillgllptPav 82 
                                    +f+++++Rg++g++ l+p+ + ++g+a+ + ++      + +v+ DtR ss+ l++al agla +G +v++ g  p+ ++
  gi|119719719|ref|YP_920214.1|   7 IFRAYDIRGVYGVD-LNPAIAVAIGNALSRLFPG-----EYCVCSDTRSSSPALKAALSAGLAGSGSNVVDGGTGPIGMA 80 
                                    79**********77.9*****************7.....69*************************************** PP

                                    HHHHHHCCECEEEEE--TTS-TTCCCEEEEETTTCE--CHHHHHHHHH CS
                      PGM_PMM_I  83 sfairklkadagimitaSHnppeyngiKvylsnGgpispeveekIeai 130
                                     +a+++l++    ++taSH ppe ngiK++ ++G+pi +e+ +k+ + 
  gi|119719719|ref|YP_920214.1|  81 IYATKHLEYHV-AYVTASHLPPEWNGIKLFKPRGIPICEEDLKKLGEV 127
                                    ********998.9**************************999988665 PP

>> PGM_PMM_II  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.6   0.0   2.1e-25   4.6e-22      15     103 .]     161     248 ..     150     248 .. 0.91

  Alignments for each domain:
  == domain 1  score: 78.6 bits;  conditional E-value: 2.1e-25
                                    HHHHHT-EEEEE-TT-TTHHHHHHHHHHTT-EEEES-----TT-TTSS----TT-TTTTHHHHGGGGG-SEEEEE-TTS- CS
                     PGM_PMM_II  15 aikksglkvvidplhGaggeilkellkelgvdvvelnaepdpdfptkapnpeekealkllielvkkegadlglafDgDaD 94 
                                    ++++++ +vv+d+++Ga++ i+++ll++lg+dvv +n++ dp f+ + ++p+  e+ ++l ++v + +adlg++fDgD+D
  gi|119719719|ref|YP_920214.1| 161 KTSSRRTRVVVDCGNGAASLIVPRLLRSLGYDVVGINCDVDPLFSVRGSEPTL-ESTAYLKDVVLRFRADLGVSFDGDGD 239
                                    36778899**************************************9999999.999*********************** PP

                                    BEEEEETTE CS
                     PGM_PMM_II  95 RlgvvderG 103
                                    R +++de+G
  gi|119719719|ref|YP_920214.1| 240 RAIFFDEKG 248
                                    *******98 PP

>> PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.1   0.0   4.1e-19   9.1e-16      18     109 ..     264     353 ..     253     358 .. 0.87

  Alignments for each domain:
  == domain 1  score: 58.1 bits;  conditional E-value: 4.1e-19
                                    STTTCEEEEETTS-THHHHHHHHTT-EEEEESSSCHHHHHHHHHTTECEEEETTCEEEETTTBSS--HHHHHHHHHHHHH CS
                    PGM_PMM_III  18 lkpgagvvktvmtslalervakklgiklvetkvGdkyvleemkeegavlGgEeSghiifldeattkDGilaallvleila 97 
                                     +pg  v+++v +s+++e++++++g+++v+++vG  +++ e  ++++vlG E Sgh++     + +DGila+l++le+  
  gi|119719719|ref|YP_920214.1| 264 SQPGD-VIANVECSSMVEKYVASRGGRVVRVPVGRIHMIFESMKSSFVLGVESSGHYVPYGGLNLDDGILAVLQFLEAFE 342
                                    35666.****************************98877665556*************9999999*************** PP

                                    HHTS-HHHHHHH CS
                    PGM_PMM_III  98 etgkslsellee 109
                                    + g ++s l+ e
  gi|119719719|ref|YP_920214.1| 343 KLGGPVSALV-E 353
                                    *********9.4 PP

>> PGM_PMM_IV  Phosphoglucomutase/phosphomannomutase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       1.1   2.5e+03      20      42 ..     271     292 ..     253     293 .. 0.81
   2 !   45.2   0.3   3.5e-15   7.9e-12       6      72 ..     365     436 ..     358     438 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.1
                                    CTTHHCCCCCCCCGCCEEEE.EE CS
                     PGM_PMM_IV  20 lkvasikeglkilledGrrlavR 42 
                                    + v++ + ++k+++ +G r+ vR
  gi|119719719|ref|YP_920214.1| 271 ANVECSSMVEKYVASRGGRV-VR 292
                                    45557788999999999999.98 PP

  == domain 2  score: 45.2 bits;  conditional E-value: 3.5e-15
                                    HCC-TT....EECCCCCTTH....HCCCCCCCCGCCEEEE.EEEETTCCEEEEEEEESSHHHHHHHHHHHHHH CS
                     PGM_PMM_IV   6 veekak..vvaalaallkva....sikeglkilledGrrlavRpSGTepllrvyvEaksdeelarlaeevael 72 
                                    v+e+ k  +v+ l+a+++ +    ++ +g++++l  G++l vR+S+Tep++rv +Ea+++e l++l++ v+e 
  gi|119719719|ref|YP_920214.1| 365 VNEEVKfkAVEYLKAYYAGKydrvDTTDGVRVDLDYGWFL-VRASNTEPVIRVTIEASTKEDLDKLEKLVRED 436
                                    4444333345555555554488889***************.*********************99999877765 PP

>> Cu_amine_oxidN2  Copper amine oxidase, N2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.41   9.2e+02      44      73 ..     152     181 ..     150     183 .. 0.82
   2 ?   12.7   0.0   5.2e-05      0.12      46      80 ..     243     277 ..     239     283 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.41
                                    HHHHHHCH---S-EEEEEEEEETSSSSEEE CS
                Cu_amine_oxidN2  44 vlqflekgeppppRkAsvvilfGkqtkelv 73 
                                    + +fl k ++   R+ +vv+  G+    l+
  gi|119719719|ref|YP_920214.1| 152 YYKFLLKVGKTSSRRTRVVVDCGNGAASLI 181
                                    67888899999*********9988776666 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 5.2e-05
                                    HHHHCH---S-EEEEEEEEETSSSSEEEEEEEEEE CS
                Cu_amine_oxidN2  46 qflekgeppppRkAsvvilfGkqtkelvvdLatgk 80 
                                     f ekg+p++p +A vvil+G q+   + +   ++
  gi|119719719|ref|YP_920214.1| 243 FFDEKGNPLAPEQAAVVILKGSQPGDVIANVECSS 277
                                    5899*******************988777666655 PP

>> DUF2218  Uncharacterized protein conserved in bacteria (DUF2218)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.62   1.4e+03       6      41 ..     212     247 ..     207     269 .. 0.76
   2 ?   13.0   0.0   4.7e-05      0.11      23      76 ..     384     439 ..     372     444 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.62
                                    -SSHHHHHHHHHHHTTTSSEEEE-SSEEEEE-SSS- CS
                        DUF2218   6 tdrasrylkqLckHfshkveverdedagriefprgt 41 
                                    t +   ylk ++  f+  + v++d+d  r  f  ++
  gi|119719719|ref|YP_920214.1| 212 TLESTAYLKDVVLRFRADLGVSFDGDGDRAIFFDEK 247
                                    66778899999999999*******998888776654 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 4.7e-05
                                    SSEEEE-SSEEEEE-SSS..-EEEEEETTEEEEEEEESSHHHHHHHHHHHHHHHHH CS
                        DUF2218  23 kveverdedagriefprg..tcrleaeddaLtlrveaedaeslarlkavvarhLer 76 
                                    k++   + d +r++++ g   +r + ++  +++++ea+++e+l++l++ v + +er
  gi|119719719|ref|YP_920214.1| 384 KYDRVDTTDGVRVDLDYGwfLVRASNTEPVIRVTIEASTKEDLDKLEKLVREDIER 439
                                    556666788999999***555566666669********************999987 PP

>> AlkA_N  AlkA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0    0.0001      0.23      23      80 ..     373     435 ..     367     439 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0001
                         AlkA_N  23 aiegvEavdedsygRtlrldgak.....Gvvevrhepeksalkvrlslsdlraleaviarvrr 80 
                                    a+e + a  +++y R   +dg++     G++ vr ++++ +++v+++ s  ++l+++ + vr+
  gi|119719719|ref|YP_920214.1| 373 AVEYLKAYYAGKYDRVDTTDGVRvdldyGWFLVRASNTEPVIRVTIEASTKEDLDKLEKLVRE 435
                                    5666666667788888888887444444********************999999999888885 PP

>> EFG_II  Elongation Factor G, domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00011      0.24       3      25 ..     411     433 ..     410     439 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00011
                         EFG_II   3 ePvislaiepkskadedklskaL 25 
                                    ePvi ++ie+++k+d dkl+k  
  gi|119719719|ref|YP_920214.1| 411 EPVIRVTIEASTKEDLDKLEKLV 433
                                    8*****************98754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 3002.22
//
Query:       gi|119719720|ref|YP_920215.1|  [L=113]
Description: hypothetical protein Tpen_0811 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-05   25.6   0.0    1.5e-05   25.2   0.0    1.2  1  ATP-synt_F  ATP synthase (F/14-kDa) subunit


Domain annotation for each model (and alignments):
>> ATP-synt_F  ATP synthase (F/14-kDa) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   8.2e-10   1.5e-05       1      81 [.       6      88 ..       6      97 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 8.2e-10
                                   EEEEESHHHHHHHHHTTCEEEECSS...HHHHHHHHHHHHHHTTEEEEEEEHHHHCCCHHHHHHCTCS..SSSEEEEESCSC CS
                     ATP-synt_F  1 iavIGdedtvtgfrlaGvgevevtd...eeeieealkelleredigiilitekiaeeirelideykee..alPaileIPske 77
                                   ++vIG++ tv  +rl+G+++v+v +   ++e  e++ ++l   +  + l++ ++++ + e+++++ +   + P+++ IPs e
  gi|119719720|ref|YP_920215.1|  6 VVVIGSSPTVDSLRLLGFEVVRVPEklgKAEEDEVVAKIL---ESRVALVESEVYASVAERLRQVMSFvkEPPLLVVIPSSE 84
                                   78********************555444788888888888...77789999999999999999988877789********99 PP

                                   CGGS CS
                     ATP-synt_F 78 gpyd 81
                                   +   
  gi|119719720|ref|YP_920215.1| 85 KAST 88
                                   8554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 868.57
//
Query:       gi|119719721|ref|YP_920216.1|  [L=116]
Description: V-type H+-transporting ATPase subunit E [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0033   17.3  16.2     0.0043   16.9  16.2    1.1  1  Apolipoprotein  Apolipoprotein A1/A4/E domain
  ------ inclusion threshold ------
      0.013   15.1   7.2      0.015   14.9   7.2    1.0  1  Exonuc_VII_L    Exonuclease VII, large subunit
      0.024   15.2  14.9       0.59   10.8   3.6    2.1  2  DUF883          Bacterial protein of unknown function (DUF883
      0.024   15.2   2.7      0.024   15.2   2.7    2.2  2  ThiS            ThiS family
      0.025   13.8   3.6      0.028   13.7   3.6    1.0  1  PDCD9           Mitochondrial 28S ribosomal protein S30 (PDCD
       0.03   14.3   7.3      0.034   14.1   7.3    1.1  1  RRF             Ribosome recycling factor
      0.045   14.2   3.1       0.06   13.8   3.1    1.3  1  DUF3037         Protein of unknown function (DUF3037)
      0.087   13.4  15.6       0.11   13.1  15.6    1.1  1  V-ATPase_G      Vacuolar (H+)-ATPase G subunit
       0.14   12.3   7.3        0.2   11.7   7.3    1.3  1  ApoLp-III       Apolipophorin-III precursor (apoLp-III)
       0.18   11.9  16.8      0.059   13.5   9.9    2.1  2  DivIVA          DivIVA protein
       0.21   11.9   3.5       0.37   11.1   0.2    2.2  2  PqqD            Coenzyme PQQ synthesis protein D (PqqD)
       0.22   11.9  21.3       0.36   11.3  21.3    1.4  1  V-ATPase_G_2    Vacuolar (H+)-ATPase G subunit
       0.25   10.4   4.9       0.31   10.1   4.9    1.0  1  CRISPR_Cse1     CRISPR-associated protein Cse1 (CRISPR_cse1)
       0.29   11.0  12.1        1.8    8.4  12.1    1.9  1  HrpE            HrpE/YscL/FliH and V-type ATPase subunit E
       0.34   11.5  11.6        1.4    9.5   0.9    2.3  2  HisKA_3         Histidine kinase
       0.57   10.0   7.7       0.84    9.4   7.7    1.3  1  Exo84_C         Exocyst component 84 C-terminal
       0.65   10.2   6.1       0.83    9.9   6.1    1.1  1  DUF4047         Domain of unknown function (DUF4047)
       0.95   10.6   5.4        8.6    7.5   0.8    2.3  2  RNase_J_C       Ribonuclease J C-terminal domain
       0.98    9.6   5.6        1.3    9.2   5.6    1.2  1  Fib_alpha       Fibrinogen alpha/beta chain family
          1    9.0  16.9        1.2    8.8   7.7    2.1  2  GARP            Glutamic acid/alanine-rich protein of Trypano
        1.2    8.0   4.9        1.4    7.8   4.9    1.0  1  5_nucleotid     5' nucleotidase family
        1.6    7.2   5.7        1.8    7.0   5.7    1.0  1  Aldedh          Aldehyde dehydrogenase family
        1.7    8.3   6.8        1.9    8.2   6.8    1.1  1  AAA_11          AAA domain
        3.3    6.9   8.1        5.1    6.3   8.1    1.3  1  VSG_B           Trypanosomal VSG domain
        3.3    8.3   9.0        9.7    6.8   1.6    2.1  2  YtxH            YtxH-like protein
        4.1    6.1  20.4          5    5.8  20.4    1.0  1  Mitofilin       Mitochondrial inner membrane protein
        6.7    6.6   8.3        4.4    7.2   0.6    2.0  2  AIF-MLS         Mitochondria Localisation Sequence
        7.5    7.0  12.9         12    6.4  12.9    1.3  1  AAA_23          AAA domain
        7.7    6.8  13.9        5.1    7.4   6.0    2.1  2  DUF4230         Protein of unknown function (DUF4230)


Domain annotation for each model (and alignments):
>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9  16.2     7e-06    0.0043      94     172 ..      25     108 ..      20     114 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 7e-06
                                    HHCHCCHCHHHHHHHHHHHHHHHHHHCHHHHHHH.....HHHHHHHHHHHH-----..-----SSSHHHHHHHTS-TTSH CS
                 Apolipoprotein  94 qeqlavyaeelrerlerhvealkarlapyveelr.....qklaerleelkeslaphaeeveerlssrveelrekleeqae 168
                                    q++ ++  +e+++r+e+ +e+ +a+  +++ +++     +k +e +e  ++++ + ++++ee+ ss++eelr++lee+ e
  gi|119719721|ref|YP_920216.1|  25 QRKAEQRVAEAKKRAEEILERARAQAREILSKAQnveldDKAKELIESEQRRVGELLKQLEEKYSSELEELRRALEENEE 104
                                    88999999**************************555555999999999999*************************999 PP

                                    HHHH CS
                 Apolipoprotein 169 elre 172
                                    ++++
  gi|119719721|ref|YP_920216.1| 105 AIKR 108
                                    8865 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   7.2   2.4e-05     0.015     138     222 ..      21     107 ..       7     114 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.4e-05
                   Exonuc_VII_L 138 vvpdkaeleeqleelerrlekaikrlleekkqrleklas.rlk.speellerkrqrldeleerleralkkqlkkkrerle 215
                                    +++++++ e++++e+++r e+ ++r+  ++++ l+k+++ +l  +++el+e++++r+ el ++le++ +++l++ r++le
  gi|119719721|ref|YP_920216.1|  21 ILQEQRKAEQRVAEAKKRAEEILERARAQAREILSKAQNvELDdKAKELIESEQRRVGELLKQLEEKYSSELEELRRALE 100
                                    67889999******************9999999999854156559999*******************9999999999999 PP

                   Exonuc_VII_L 216 elkerlk 222
                                    e +e++k
  gi|119719721|ref|YP_920216.1| 101 ENEEAIK 107
                                    9997663 PP

>> DUF883  Bacterial protein of unknown function (DUF883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   4.6    0.0019       1.2      20      55 ..      23      58 ..      11      61 .. 0.78
   2 ?   10.8   3.6   0.00095      0.59       9      56 ..      61     108 ..      55     114 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0019
                         DUF883 20 eaadeageeaeelRerleerlerarerlrdaeeava 55
                                   + +++a++ ++e+++r+ee lerar+++r+   +++
  gi|119719721|ref|YP_920216.1| 23 QEQRKAEQRVAEAKKRAEEILERARAQAREILSKAQ 58
                                   556678888999999999999999999888766654 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00095
                         DUF883   9 slladleellkeaadeageeaeelRerleerlerarerlrdaeeavae 56 
                                    +l ++++el+++ +++ ge +++l e+ +++le++r +l++ eea+++
  gi|119719721|ref|YP_920216.1|  61 ELDDKAKELIESEQRRVGELLKQLEEKYSSELEELRRALEENEEAIKR 108
                                    577899***********************************9999877 PP

>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1       3.2     2e+03      17      32 ..      32      47 ..      19      60 .. 0.51
   2 ?   15.2   2.7     4e-05     0.024       5      55 ..      57     108 ..      53     115 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 3.2
                                   EESSTSBHHHHHHHHH CS
                           ThiS 17 elaegstvaelleaLg 32
                                   + + ++  +e+le   
  gi|119719721|ref|YP_920216.1| 32 VAEAKKRAEEILERAR 47
                                   3333444444444433 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 4e-05
                                    TCCHHHHT.CEEEEESSTSBHHHHHHHHHHHTCHHGTTTTEEEEETTEEEGC CS
                           ThiS   5 aelrelag.eeelelaegstvaelleaLgerypelalerrvavavNgeivpr 55 
                                    a+  el+   +el ++e+  v+ell++L+e+y+ + +e r a++ N+e ++r
  gi|119719721|ref|YP_920216.1|  57 AQNVELDDkAKELIESEQRRVGELLKQLEEKYSSELEELRRALEENEEAIKR 108
                                    67889999999*********************98886677777777777776 PP

>> PDCD9  Mitochondrial 28S ribosomal protein S30 (PDCD9)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   3.6   4.5e-05     0.028     121     198 ..      26     103 ..      11     110 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.5e-05
                          PDCD9 121 akaeakaeeeeasldellkelrsavadallqehqy.lkkkeefdlvekeeeltqklleqLvsallgslakknprLaeas 198
                                     kae++ +e+++ ++e+l+ +r+++ ++l +++   l + +  +l+e+e++ + +ll+qL ++  + l +   +L+e++
  gi|119719721|ref|YP_920216.1|  26 RKAEQRVAEAKKRAEEILERARAQAREILSKAQNVeLDD-KAKELIESEQRRVGELLKQLEEKYSSELEELRRALEENE 103
                                    3334444478999**************777776664555.6666*****************999999988888888776 PP

>> RRF  Ribosome recycling factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   7.3   5.5e-05     0.034      86     156 ..      27      98 ..       2     106 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.5e-05
                                    SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHCS-HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            RRF  86 lTeErrkelvkeakkaaekakvairniRrdank.klkklekkiseDdvkkaekeiqkltdkyikeidellka 156
                                      e+r  e  k+a+++ e+a+ + r+i ++a++ +l +++k++ e +++++ + +++l +ky +e++el  a
  gi|119719721|ref|YP_920216.1|  27 KAEQRVAEAKKRAEEILERARAQAREILSKAQNvELDDKAKELIESEQRRVGELLKQLEEKYSSELEELRRA 98 
                                    45677778888888888888888888888875525666666799*********************9998655 PP

>> DUF3037  Protein of unknown function (DUF3037)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   3.1   9.7e-05      0.06      14     102 ..      14      99 ..       7     114 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9.7e-05
                        DUF3037  14 EfvNvGVvlfskkegflkvrleldeaRlralfpeldlealeeelkaleeicegeka..agpiakldlaerfrwltaprst 91 
                                    E + +GV+l   ++++++ r+++ ++R +++ +++  ++ +e l + +++  ++ka    +  +++++e++++l+++ s+
  gi|119719721|ref|YP_920216.1|  14 EELDIGVILQ--EQRKAEQRVAEAKKRAEEILERA-RAQAREILSKAQNVELDDKAkeLIESEQRRVGELLKQLEEKYSS 90 
                                    6678*****9..7777888889999*******988.44455555555555533333126666669999****99999887 PP

                        DUF3037  92 viqtsevhtgl 102
                                     +   e + +l
  gi|119719721|ref|YP_920216.1|  91 EL--EELRRAL 99 
                                    54..4555555 PP

>> V-ATPase_G  Vacuolar (H+)-ATPase G subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1  15.6   0.00017      0.11       6     101 ..      18     114 ..      14     116 .] 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00017
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHSHHHHHHHHHHHHSSHHHHHHHH CS
                     V-ATPase_G   6 IqqLLqAEkeAaeivkeArkrkakrlkqAkeeAekEieeyra.kkekefkekeaeklgseeelekkieketeekikelke 84 
                                    I  +Lq  ++A++ v+eA+kr ++ l  A+++A++ + + ++ + + + ke  +++  + +el k++e++ +++++el++
  gi|119719721|ref|YP_920216.1|  18 IGVILQEQRKAEQRVAEAKKRAEEILERARAQAREILSKAQNvELDDKAKELIESEQRRVGELLKQLEEKYSSELEELRR 97 
                                    556799999************************9877766542567778887788888899******************* PP

                                    HHHHHHHHHHHHHHHHH CS
                     V-ATPase_G  85 svkknkeavvkellklv 101
                                    ++++n+ea+ + +l+++
  gi|119719721|ref|YP_920216.1|  98 ALEENEEAIKRLVLEAI 114
                                    *******9998888876 PP

>> ApoLp-III  Apolipophorin-III precursor (apoLp-III)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   7.3   0.00033       0.2      42     132 ..      25     113 ..      18     115 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00033
                      ApoLp-III  42 ikslqeelkkksdeleealkevkkkieetadklse.enPevkkkaqelqekvQsgvqslvkesqklaeslkensqeakek 120
                                    + ++++ ++++   +ee+l+ ++++  e+     + +n e+  ka+el e+ Q +v +l+k+ ++  +s  e+ + a e+
  gi|119719721|ref|YP_920216.1|  25 QRKAEQRVAEAKKRAEEILERARAQAREILS---KaQNVELDDKAKELIESEQRRVGELLKQLEEKYSSELEELRRALEE 101
                                    5667788888899999999999987666654...4578************************987777777788888888 PP

                      ApoLp-III 121 lakaikqaydda 132
                                     ++aik ++ +a
  gi|119719721|ref|YP_920216.1| 102 NEEAIKRLVLEA 113
                                    899999998776 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   9.9   9.5e-05     0.059      69     107 ..      21      59 ..      10      77 .. 0.80
   2 ?    2.2   1.2      0.28   1.7e+02      23      56 ..      77     107 ..      71     112 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.5e-05
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         DivIVA  69 lvvaqetaeevkanakkeaeliikeAekkaekiveeaee 107
                                    ++  q+ ae+  a+akk ae i++ A+++a++i+++a++
  gi|119719721|ref|YP_920216.1|  21 ILQEQRKAEQRVAEAKKRAEEILERARAQAREILSKAQN 59 
                                    6778999***************************99986 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.28
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCTXX CS
                         DivIVA  23 VdeFLdqvakdyeallkeneelkekvkeleeklk 56 
                                    V e L+q+ ++y    +e eel++ ++e+ee++k
  gi|119719721|ref|YP_920216.1|  77 VGELLKQLEEKYS---SELEELRRALEENEEAIK 107
                                    5566666655554...455556666666666655 PP

>> PqqD  Coenzyme PQQ synthesis protein D (PqqD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.4      0.55   3.4e+02      30      61 ..      26      57 ..      13      62 .. 0.58
   2 ?   11.1   0.2   0.00059      0.37      25      55 ..      69     100 ..      58     102 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.55
                                   S-HHHHHHHHHHHCT--HHHHHHHHHHHHHHH CS
                           PqqD 30 rsveeivaalaeeydvdeeeaeadvlafldqL 61
                                   r+ e+ va+ +++ ++  e+a+a  ++ l++ 
  gi|119719721|ref|YP_920216.1| 26 RKAEQRVAEAKKRAEEILERARAQAREILSKA 57
                                   44444455555555444455666666666655 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00059
                                    H-.SSSS-HHHHHHHHHHHCT--HHHHHHHHH CS
                           PqqD  25 ll.dgersveeivaalaeeydvdeeeaeadvl 55 
                                    l+ +++r v e+ ++l e+y  + ee++++++
  gi|119719721|ref|YP_920216.1|  69 LIeSEQRRVGELLKQLEEKYSSELEELRRALE 100
                                    44233567************999999999887 PP

>> V-ATPase_G_2  Vacuolar (H+)-ATPase G subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3  21.3   0.00058      0.36      15     103 ..      26     115 ..      18     116 .] 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00058
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHH CS
                   V-ATPase_G_2  15 aeLdqrlEaArkeaereveaAeaeAarilreAea.kakalqaeyeqelaeevarireeararaeaeaqavrkraearlqq 93 
                                    ++ +qr+ +A+k ae+ +e+A+a+A+ il++A++ ++   ++e  + +++ v ++ ++ +++ ++e +++r++ e+  + 
  gi|119719721|ref|YP_920216.1|  26 RKAEQRVAEAKKRAEEILERARAQAREILSKAQNvELDDKAKELIESEQRRVGELLKQLEEKYSSELEELRRALEENEEA 105
                                    455799**************************974677777888888888888899999999999999999888777444 PP

                                    HHHHHHHHH- CS
                   V-ATPase_G_2  94 AvelilkaVl 103
                                      +l+l+a+l
  gi|119719721|ref|YP_920216.1| 106 IKRLVLEAIL 115
                                    4467888876 PP

>> CRISPR_Cse1  CRISPR-associated protein Cse1 (CRISPR_cse1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   4.9   0.00049      0.31     354     447 ..      15     106 ..       9     114 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00049
                                    EEEEECHHHTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSCSSHH.....HHHHHHHHHHHHHHHHHHHHHHH CS
                    CRISPR_Cse1 354 tlplpaalledkealreaveeaveaaeevaralrsavkaaakellkkgkkka.....gdasaaraafwaalegpfrella 428
                                    +l++ + +l+++++++++v ea ++aee+ ++ r ++++++ + ++   +++     +  ++   ++ ++le+++ + l+
  gi|119719721|ref|YP_920216.1|  15 ELDIGV-ILQEQRKAEQRVAEAKKRAEEILERARAQAREILSKAQNVELDDKakeliESEQRRVGELLKQLEEKYSSELE 93 
                                    555555.4467788888**********************99887766544445667766666666667777777777777 PP

                                    CCCCCS.HCTHHHHHHHHH CS
                    CRISPR_Cse1 429 algpdddaaealkawrktl 447
                                    +l++  +      + ++++
  gi|119719721|ref|YP_920216.1|  94 ELRRALE------ENEEAI 106
                                    7765544......333333 PP

>> HrpE  HrpE/YscL/FliH and V-type ATPase subunit E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4  12.1    0.0029       1.8      27      80 ..      23      73 ..      10     115 .. 0.50

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0029
                           HrpE 27 aeslrarellaeArlqAeqllaqarekaeellevaveqAeaqFWeqAnalLrgl 80
                                   +e+++a++ +aeA++ Ae++l++ar +a+e+l +a +    +  ++A +l++  
  gi|119719721|ref|YP_920216.1| 23 QEQRKAEQRVAEAKKRAEEILERARAQAREILSKAQN---VELDDKAKELIESE 73
                                   4555555555555555555555555555555552221...22233333333333 PP

>> HisKA_3  Histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   4.0     0.015       9.1      28      62 ..      22      56 ..      10      62 .. 0.66
   2 ?    9.5   0.9    0.0023       1.4      27      62 ..      66     101 ..      63     107 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.015
                                   HHHTTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        HisKA_3 28 krllekdpekaaeqlreieelarealqevRrllhn 62
                                    ++ +k+++++ae+ +++ee +++a +++R++l++
  gi|119719721|ref|YP_920216.1| 22 LQEQRKAEQRVAEAKKRAEEILERARAQAREILSK 56
                                   45555566677777777777777777777777665 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0023
                                    HHHHTTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        HisKA_3  27 akrllekdpekaaeqlreieelarealqevRrllhn 62 
                                    ak+l+e+++ ++ e l+++ee  ++ l+e+Rr+l++
  gi|119719721|ref|YP_920216.1|  66 AKELIESEQRRVGELLKQLEEKYSSELEELRRALEE 101
                                    6788899999**********************9986 PP

>> Exo84_C  Exocyst component 84 C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   7.7    0.0014      0.84       6      95 ..      12     105 ..      10     113 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0014
                        Exo84_C   6 lldeldieiarrkFeeAVdlleklesklkklskklk.deeavlqdlislkveqrreelasklsrel..lsknevkklksn 82 
                                    l +eldi +  ++  +A +++ +++++ +++ ++++ + +++l++  +++++ +++el+++ +r++  l k+  +k +s+
  gi|119719721|ref|YP_920216.1|  12 LAEELDIGVILQEQRKAEQRVAEAKKRAEEILERARaQAREILSKAQNVELDDKAKELIESEQRRVgeLLKQLEEKYSSE 91 
                                    579****************************98876478899*****************999998854345555556677 PP

                        Exo84_C  83 vslLir.LgledkA 95 
                                    ++ L r L+++++A
  gi|119719721|ref|YP_920216.1|  92 LEELRRaLEENEEA 105
                                    77776545555555 PP

>> DUF4047  Domain of unknown function (DUF4047)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   6.1    0.0013      0.83      36     114 ..      28     108 ..      18     114 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0013
                        DUF4047  36 akqhkelilheyeemksklkvdsveei..eqalsvwkqgrekikaerealqkvyteieepynqvqeelkvnksesskqvl 113
                                    a+q     ++  ee+  + ++++ e +   q++++  + +e i +e+  + ++ +++ee y    eel+ + +e ++ + 
  gi|119719721|ref|YP_920216.1|  28 AEQRVAEAKKRAEEILERARAQAREILskAQNVELDDKAKELIESEQRRVGELLKQLEEKYSSELEELRRALEENEEAIK 107
                                    444444444555666555555555555116778888899999***************************88776665554 PP

                        DUF4047 114 s 114
                                    +
  gi|119719721|ref|YP_920216.1| 108 R 108
                                    4 PP

>> RNase_J_C  Ribonuclease J C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.6     0.054        33      13      37 ..      37      61 ..      24      67 .. 0.81
   2 ?    7.5   0.8     0.014       8.6      14      51 ..      65     102 ..      61     114 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.054
                      RNase_J_C 13 keseeLieeakkvvretieealeek 37
                                   k +ee++e a++++re++ +a++ +
  gi|119719721|ref|YP_920216.1| 37 KRAEEILERARAQAREILSKAQNVE 61
                                   6788999999999999999988865 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.014
                      RNase_J_C  14 eseeLieeakkvvretieealeekesdwnelkrkirea 51 
                                    +++eLie+ +  v e +++ +e+ +s+ +el+r++ e+
  gi|119719721|ref|YP_920216.1|  65 KAKELIESEQRRVGELLKQLEEKYSSELEELRRALEEN 102
                                    67788888888888888888888888888888887664 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   5.6    0.0021       1.3      45     121 ..      30     109 ..      15     114 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0021
                                    CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH..HHHHHHHHHHHHHCCCHHHHHHHCCH.HHHHHHHHHHHHHHHHHHHH CS
                      Fib_alpha  45 eeisnstkeaeelvkeikdslrekqkskkdn..dnvikksskeleeeilrlketidaqe.snirvLqnvlesneqkiqkL 121
                                    +++++ +k aee+ ++ + + re  +++++   d   k++ ++ ++++ +l +++ ++  s++++L+  le+ne+ i++L
  gi|119719721|ref|YP_920216.1|  30 QRVAEAKKRAEEILERARAQAREILSKAQNVelDDKAKELIESEQRRVGELLKQLEEKYsSELEELRRALEENEEAIKRL 109
                                    3444455555555555555555555544432445566666555556888999999999989*****************99 PP

>> GARP  Glutamic acid/alanine-rich protein of Trypanosoma
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   7.7    0.0019       1.2      24      62 ..      21      59 ..      15      68 .. 0.75
   2 ?    3.9   4.9     0.063        39     141     184 ..      62     105 ..      55     109 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0019
                           GARP 24 leeeaaaaaskaskAkarseeaverAesaaendteakel 62
                                   +++e ++a+++ ++Ak+r+ee +erA+++a++  + ++ 
  gi|119719721|ref|YP_920216.1| 21 ILQEQRKAEQRVAEAKKRAEEILERARAQAREILSKAQN 59
                                   56788999*******************977764433333 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.063
                           GARP 141 LeealealakltdednaeelreeaneaaeeLeeLekaaeeakea 184
                                    L++ +++l ++ + +  e l++  ++ ++eLeeL++a ee  ea
  gi|119719721|ref|YP_920216.1|  62 LDDKAKELIESEQRRVGELLKQLEEKYSSELEELRRALEENEEA 105
                                    66778889999999999999999999999999999999998877 PP

>> 5_nucleotid  5' nucleotidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   4.9    0.0022       1.4     332     415 ..      15     101 ..       9     110 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0022
                                    THHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHHHHH...T.TTHHHHHHHHHHHHHHHHHHHHHHHHHHCCS-TTT-- CS
                    5_nucleotid 332 ELeeElevleekkekeeleelekleelledelkklkss...eeeskekleeleedleelkkeirelreelkelfnkqfGs 408
                                    EL+  + ++e++k +++++e +k+ e++ ++ +    +   ++++ e +++++e +e+ ++++ el ++l+e++ +++ +
  gi|119719721|ref|YP_920216.1|  15 ELDIGVILQEQRKAEQRVAEAKKRAEEILERARAQAREilsKAQNVELDDKAKELIESEQRRVGELLKQLEEKYSSELEE 94 
                                    44444445555555577777777766666644444444554233666778889999999******************999 PP

                                    SSEETTE CS
                    5_nucleotid 409 lfrtgse 415
                                    l r+ +e
  gi|119719721|ref|YP_920216.1|  95 LRRALEE 101
                                    9998765 PP

>> Aldedh  Aldehyde dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   5.7    0.0028       1.8      22     106 ..      19     104 ..       3     113 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0028
                                    EEE-B-HHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHH.HHHTHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHH CS
                         Aldedh  22 kvpaataedvdaavaaAkeafkawaklpaeeRaeiLrkaadl.leerkeelaeletletGkplaearaeveeaidvlryy 100
                                     v   ++ ++++ va+Ak+  ++  +   ++ +eiL ka+++ l ++++el+e e++ +G  l++ +++ ++ ++ lr +
  gi|119719721|ref|YP_920216.1|  19 GVILQEQRKAEQRVAEAKKRAEEILERARAQAREILSKAQNVeLDDKAKELIESEQRRVGELLKQLEEKYSSELEELRRA 98 
                                    4556778899999******99998888899999999999985499*****************999999888888888887 PP

                                    HHHHHH CS
                         Aldedh 101 aelaek 106
                                     e+ e+
  gi|119719721|ref|YP_920216.1|  99 LEENEE 104
                                    777655 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   6.8    0.0031       1.9     106     193 ..      24     111 ..       1     114 [. 0.39

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0031
                         AAA_11 106 svsleekvekrlekee..kaqlakeiskeleklakelrafeeeeek...............eklkkskekskskleqerr 168
                                    +     k e+r ++ +    ++ ++ +++ +              +               e  + +++   + l+q ++
  gi|119719721|ref|YP_920216.1|  24 EQR---KAEQRVAEAKkrAEEILERARAQAR--------------EilskaqnvelddkakELIESEQRRVGELLKQLEE 86 
                                    222...1111111110001112111111111..............12223333322222223333334444455556666 PP

                         AAA_11 169 klkkerkelskeleeaeesleeevl 193
                                    k ++e +el++ lee ee++++ vl
  gi|119719721|ref|YP_920216.1|  87 KYSSELEELRRALEENEEAIKRLVL 111
                                    6666666666666666666666665 PP

>> VSG_B  Trypanosomal VSG domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   8.1    0.0082       5.1      71     166 ..      23     116 .]       9     116 .] 0.61

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0082
                          VSG_B  71 eeeddakatktkkaakkncgalkafWkeakkaakakkkkeltrpantrararanekiqqiaekaaeiyseikkekekakk 150
                                    +e+ +a  +++ ++akk +++  ++  + ++++ +k ++ + + + +++ +  ++ + +++++ +e ys   +e   a +
  gi|119719721|ref|YP_920216.1|  23 QEQRKA--EQRVAEAKKRAEEILERARAQAREILSKAQNVELDDKAKELIESEQRRVGELLKQLEEKYSSELEELRRALE 100
                                    444333..333444444444444444444444444444455556666666666777899999999988877777777776 PP

                          VSG_B 151 araeklkkklnkAiyG 166
                                    +++e++k+   +Ai G
  gi|119719721|ref|YP_920216.1| 101 ENEEAIKRLVLEAILG 116
                                    7789999999999988 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   3.8      0.03        19      28      66 ..      26      69 ..      22      73 .. 0.64
   2 ?    6.8   1.6     0.016       9.7      25      70 ..      61     106 ..      58     110 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.03
                           YtxH 28 kdlkekaddlkekakelleeakeka.....kekaedlkekvkek 66
                                   +++ +++ ++k++a+e+le+a+ +a     k +  +l +k+ke 
  gi|119719721|ref|YP_920216.1| 26 RKAEQRVAEAKKRAEEILERARAQAreilsKAQNVELDDKAKEL 69
                                   56777888999999999999999996665533333333333333 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.016
                           YtxH  25 etRkdlkekaddlkekakelleeakekakekaedlkekvkekadel 70 
                                    e+ +++ke  +  + ++ ell++++ek +++ e+l+ +++e  + +
  gi|119719721|ref|YP_920216.1|  61 ELDDKAKELIESEQRRVGELLKQLEEKYSSELEELRRALEENEEAI 106
                                    6678888889999999999999999999999999999998876655 PP

>> Mitofilin  Mitochondrial inner membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8  20.4     0.008         5     305     390 ..      25     110 ..      17     114 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.008
                      Mitofilin 305 skelaelkkeeekkieralekqkee.lekqeealsarleeerakeerqlrlelereleeireeyeekLrteLerqaeahe 383
                                    +++ ++  +e++k++e+ le ++++  e +++a++ +l++++++  +  +++  + l+++ e+y ++L+ eL+r+ e+ e
  gi|119719721|ref|YP_920216.1|  25 QRKAEQRVAEAKKRAEEILERARAQaREILSKAQNVELDDKAKELIESEQRRVGELLKQLEEKYSSELE-ELRRALEENE 103
                                    455555567788999999999999999999999999999999999999999999999999999999999.9999999999 PP

                      Mitofilin 384 ehLkdvl 390
                                    e++k  +
  gi|119719721|ref|YP_920216.1| 104 EAIKRLV 110
                                    9988665 PP

>> AIF-MLS  Mitochondria Localisation Sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   2.1     0.095        59      81     116 ..      22      57 ..       9      69 .. 0.65
   2 ?    7.2   0.6    0.0072       4.4      67     104 ..      70     107 ..      65     113 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.095
                        AIF-MLS  81 lkektkaelqplqgekenvaeaekasseapevsvve 116
                                    l+e+ kae + ++++k   +  e+a ++a e+ +++
  gi|119719721|ref|YP_920216.1|  22 LQEQRKAEQRVAEAKKRAEEILERARAQAREILSKA 57 
                                    566666666666666666666666666666665543 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0072
                        AIF-MLS  67 vtseqakhtehitnlkektkaelqplqgekenvaeaek 104
                                    + seq +  e +++l+ek  +el++l+   e+ +ea k
  gi|119719721|ref|YP_920216.1|  70 IESEQRRVGELLKQLEEKYSSELEELRRALEENEEAIK 107
                                    78************************999998888865 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4  12.9     0.019        12     137     199 ..      21     106 ..       4     109 .. 0.50

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.019
                         AAA_23 137 flgqerfeefelkdkke............rleelekeleeledekkllekl......................eqekeke 182
                                    +l+++r++e++ ++ k+            + e l+k+++           +                      + e+++ 
  gi|119719721|ref|YP_920216.1|  21 ILQEQRKAEQRVAEAKKraeeileraraqAREILSKAQN-----------VelddkakelieseqrrvgellkQLEEKYS 89 
                                    455666544444444442222222222222222222222...........122222322333335566665533344566 PP

                         AAA_23 183 keleeleeeleeilkel 199
                                     eleel+++lee ++ +
  gi|119719721|ref|YP_920216.1|  90 SELEELRRALEENEEAI 106
                                    69999999999988766 PP

>> DUF4230  Protein of unknown function (DUF4230)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   6.0    0.0082       5.1     103     133 ..      25      56 ..      16      59 .. 0.84
   2 ?    4.9   1.5     0.047        29      96     140 ..      56     101 ..      54     106 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0082
                        DUF4230 103 lkeaeakikeeae.englleqAeenakklleq 133
                                    +++ae+++ e+++ + ++le+A+++a+++l++
  gi|119719721|ref|YP_920216.1|  25 QRKAEQRVAEAKKrAEEILERARAQAREILSK 56 
                                    68899999996655888***********9975 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.047
                        DUF4230  96 dedeeellkeaeakikeeaeeng.lleqAeenakklleqllkslgy 140
                                    ++++ el ++a++ i+ e +  g ll+q ee+   +le+l ++l  
  gi|119719721|ref|YP_920216.1|  56 KAQNVELDDKAKELIESEQRRVGeLLKQLEEKYSSELEELRRALEE 101
                                    567789999********9997777************9999887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2888  (0.16108); expected 358.6 (0.02)
Passed bias filter:                     1106  (0.0616878); expected 358.6 (0.02)
Passed Vit filter:                       171  (0.00953762); expected 17.9 (0.001)
Passed Fwd filter:                        37  (0.0020637); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              29  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 733.82
//
Query:       gi|119719722|ref|YP_920217.1|  [L=215]
Description: H+-transporting two-sector ATPase, E subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-14   54.1  10.4    1.6e-14   53.8  10.4    1.0  1  vATP-synt_E     ATP synthase (E/31 kDa) subunit
    3.3e-05   23.9   6.8    4.4e-05   23.4   6.8    1.1  1  HrpE            HrpE/YscL/FliH and V-type ATPase subunit E
    0.00063   20.1  22.9    0.00088   19.7  20.1    2.4  2  V-ATPase_G_2    Vacuolar (H+)-ATPase G subunit
     0.0034   16.8  13.9      0.006   16.0  13.9    1.5  1  DUF3552         Domain of unknown function (DUF3552)
     0.0034   17.5   8.2     0.0034   17.5   8.2    1.8  2  DivIVA          DivIVA protein
     0.0063   16.4   2.2     0.0073   16.1   2.2    1.3  1  DUF445          Protein of unknown function (DUF445)
  ------ inclusion threshold ------
      0.012   14.5   1.6      0.019   13.9   1.6    1.3  1  Phage_min_cap2  Phage minor capsid protein 2
      0.013   15.3   0.4      0.088   12.6   0.4    1.9  1  dCache_1        Cache domain
      0.016   16.0   5.8      0.016   16.0   5.8    2.4  2  CaM_binding     Plant calmodulin-binding domain
      0.047   13.0   1.7      0.062   12.6   1.7    1.1  1  TcdA_TcdB       TcdA/TcdB catalytic glycosyltransferase domai
      0.051   11.7   4.6      0.066   11.4   4.6    1.1  1  RHD3            Root hair defective 3 GTP-binding protein (RH
       0.22   10.6   2.4       0.32   10.0   2.4    1.2  1  DUF3095         Protein of unknown function (DUF3095)
       0.22   12.1   8.5         10    6.7   7.6    2.5  2  FliG_N          FliG N-terminal domain
        5.4    7.0  17.0        4.1    7.5   1.9    1.6  2  CFAP91          Cilia- and flagella-associated protein 91
        6.8    7.0   9.8        5.6    7.3   3.3    2.5  2  TetR_C_24       Tetracyclin repressor-like, C-terminal domain


Domain annotation for each model (and alignments):
>> vATP-synt_E  ATP synthase (E/31 kDa) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.8  10.4   1.3e-17   1.6e-14       3     194 ..      19     206 ..      17     210 .. 0.94

  Alignments for each domain:
  == domain 1  score: 53.8 bits;  conditional E-value: 1.3e-17
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH. CS
                    vATP-synt_E   3 rqeAeekAeeIkakaeeefeiekaklveeeeekieeayekkeKqaelqkkiaiSnalnkarlkvLkareevleevfeea. 81 
                                    r  Aee+ ++I ++ae+e++++++++ +++e  ++e++++   +  ++   ++    ++ r +  + ++e++e+++++a 
  gi|119719722|ref|YP_920217.1|  19 RRAAEEESRRIVKEAEQEAQKIVEEAIQKAEAIKAEKLNQLLNEYRQKAMAELAPKRLELRHRAIREKHELIESALNRAi 98 
                                    678*************************************************************************9874 PP

                                    HHHHHHHTTSHHCCCCHHHHHHCCCCCCC-SSCEEEEECCCCHHCCCCTHCCCCCCHHCCSSSS--SEEEEESSEBTTSS CS
                    vATP-synt_E  82 ekkLaeveedkdeYkellkkLivqalvkleepevivrarkeDaelveealdkaaeeykaktkkktvevagdeedfledvl 161
                                    e+ ++++  + d ++++l+k + +++v+l + +++v   +  a++v ++++++a+ + + +k    +++gd       + 
  gi|119719722|ref|YP_920217.1|  99 EEAVKTILGNDDYRRTFLEKSLEKGVVALSSTDLVVHPCRGSASIVGQVVEAVAARLSK-VKPGLRLEIGDP----LGCT 173
                                    778999*****99************************9999*******99999999987.777778889999....9*** PP

                                    SEEEECCSSSCEEECCCHHHCHHHHHHHHHHCC CS
                    vATP-synt_E 162 GGvvleaadgkikvnnTlearLelvleqllpei 194
                                     Gvv++++dg+   n Tlea +  v+e+  p++
  gi|119719722|ref|YP_920217.1| 174 EGVVIVSRDGREIYNATLEAKIAEVRESVKPKV 206
                                    ***************************999988 PP

>> HrpE  HrpE/YscL/FliH and V-type ATPase subunit E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   6.8   3.7e-08   4.4e-05      15     140 ..       9     137 ..       2     158 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 3.7e-08
                           HrpE  15 vleeeilrreqlaeslrarellaeArlqAeqllaqarekaeellevaveqAeaqFWeqAnalLrglqqeRealeeqllta 94 
                                     l e+i++  + a++  +r +++eA + A++++++a +kae + +   +q ++++ ++A a   +l  +R +l+++++ +
  gi|119719722|ref|YP_920217.1|   9 TLLEVIIQELRRAAEEESRRIVKEAEQEAQKIVEEAIQKAEAIKAEKLNQLLNEYRQKAMA---ELAPKRLELRHRAIRE 85 
                                    456889999999999******************************9999999999999865...6778899999999999 PP

                           HrpE  95 veqLLsdalarlLdet......plaeRasALlRqLlksqqgearatLycHPe 140
                                      +L++ al+r ++e       ++  R + L + L k+  + + + L +HP 
  gi|119719722|ref|YP_920217.1|  86 KHELIESALNRAIEEAvktilgNDDYRRTFLEKSLEKGVVALSSTDLVVHPC 137
                                    9999999999988775222222345688888899999999999999999995 PP

>> V-ATPase_G_2  Vacuolar (H+)-ATPase G subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7  20.1   7.4e-07   0.00088      23      99 ..      21     106 ..       5     108 .. 0.79
   2 ?   -1.5   0.0       2.9   3.5e+03      57      73 ..     187     203 ..     183     214 .. 0.61

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 7.4e-07
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHH........HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCS.HHH CS
                   V-ATPase_G_2  23 aArkeaereveaAeaeAarilreAeakak........alqaeyeqelaeevarireeararaeaeaqavrkraear.lqq 93 
                                    aA +e++r v++Ae+eA++i++eA +ka+        +l +ey+q+  +e a  r e r+ra  e +++ ++a +r +++
  gi|119719722|ref|YP_920217.1|  21 AAEEESRRIVKEAEQEAQKIVEEAIQKAEaikaeklnQLLNEYRQKAMAELAPKRLELRHRAIREKHELIESALNRaIEE 100
                                    788999999999999999999998666551111111156678***********************99998888666599* PP

                                    HHHHHH CS
                   V-ATPase_G_2  94 Avelil 99 
                                    Av++il
  gi|119719722|ref|YP_920217.1| 101 AVKTIL 106
                                    ****98 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.9
                                    HHHHHHHHHHHHHHHHH CS
                   V-ATPase_G_2  57 yeqelaeevarireear 73 
                                    y++ l++++a++re ++
  gi|119719722|ref|YP_920217.1| 187 YNATLEAKIAEVRESVK 203
                                    55555666666665544 PP

>> DUF3552  Domain of unknown function (DUF3552)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0  13.9     5e-06     0.006      22      83 ..      23      81 ..       9     104 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 5e-06
                        DUF3552 22 kkiaekkiaeAeeeAkkiieeAkkeAeakkkealleakeeihklreelekelkerrnelqrl 83
                                   ++ +++ ++eAe+eA+ki+eeA ++Aea+k e+l    + + ++r+++ +el  +r el++ 
  gi|119719722|ref|YP_920217.1| 23 EEESRRIVKEAEQEAQKIVEEAIQKAEAIKAEKLN---QLLNEYRQKAMAELAPKRLELRHR 81
                                   456677899***********************996...568889************999864 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   8.2   2.8e-06    0.0034      77     128 ..      16      65 ..       9      69 .. 0.84
   2 ?   -2.9   0.1       5.7   6.9e+03      98     108 ..      86      96 ..      74     105 .. 0.49

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.8e-06
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                         DivIVA  77 eevkanakkeaeliikeAekkaekiveeaeeeakkiaeeieelkrqarlfrq 128
                                    +e++++a++e++ i+keAe++a+kiveea ++a+ i++e  +l++  + +rq
  gi|119719722|ref|YP_920217.1|  16 QELRRAAEEESRRIVKEAEQEAQKIVEEAIQKAEAIKAE--KLNQLLNEYRQ 65 
                                    6899*****************************999865..55565555555 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.7
                                    XXXXXXXXXXX CS
                         DivIVA  98 aekiveeaeee 108
                                    + +++e a ++
  gi|119719722|ref|YP_920217.1|  86 KHELIESALNR 96 
                                    33333333333 PP

>> DUF445  Protein of unknown function (DUF445)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   2.2   6.1e-06    0.0073     191     304 ..      11     125 ..       4     212 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 6.1e-06
                         DUF445 191 ltsilekvksdpdhllreeedkkvreliadllndpelaakveklkkkklsdlevqeyeealwealkdlllkdlneee... 267
                                    l++i+++++++ +++ r+  +++ +++++++ +  e+++k+e++k +kl++l ++ +++a+ e + + l+ + +      
  gi|119719722|ref|YP_920217.1|  11 LEVIIQELRRAAEEESRRIVKEA-EQEAQKIVE--EAIQKAEAIKAEKLNQLLNEYRQKAMAELAPKRLELRHRAIRekh 87 
                                    46788888877777777777666.889999998..799999999999999999999999977777766654444433345 PP

                         DUF445 268 sllrerisklleklgeklaedpklrekln.kflenaaa 304
                                     l+++ + +++e+ ++++  +++ r+++  k le+ ++
  gi|119719722|ref|YP_920217.1|  88 ELIESALNRAIEEAVKTILGNDDYRRTFLeKSLEKGVV 125
                                    78888888888888888888866666654334444333 PP

>> Phage_min_cap2  Phage minor capsid protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   1.6   1.6e-05     0.019      61     152 ..      13     103 ..       3     127 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.6e-05
                 Phage_min_cap2  61 kliskltgksekelrkllkeagdkaiksddkelaiykeaglepkplekseelqqlveaylkqtegelkNltnttal.... 136
                                     +i++l + +e+e r+++kea ++a k ++   ++ ++a+     + k e+l+ql+++y +++  el    + + l    
  gi|119719722|ref|YP_920217.1|  13 VIIQELRRAAEEESRRIVKEAEQEAQKIVE---EAIQKAE-----AIKAEKLNQLLNEYRQKAMAEL--APKRLELrhra 82 
                                    5899**********************9999...6666655.....89999************99999..45555556666 PP

                 Phage_min_cap2 137 .....tslekaYerildeava 152
                                         + +e+a +r+++eav+
  gi|119719722|ref|YP_920217.1|  83 irekhELIESALNRAIEEAVK 103
                                    666656666666666666654 PP

>> dCache_1  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.4   7.4e-05     0.088       2      72 ..      17     141 ..      16     205 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.4e-05
                       dCache_1   2 aieeqaeeqllglaeqlanniedvldslenlaetlasnpslqdlleepnra..neasreslqallksilksn........ 71 
                                    +++++aee++  +++++ ++ +  ++++ + ae +     l++ll+e+++    e+ +++l+ + + i +++        
  gi|119719722|ref|YP_920217.1|  17 ELRRAAEEESRRIVKEAEQEAQKIVEEAIQKAEAIKAE-KLNQLLNEYRQKamAELAPKRLELRHRAIREKHeliesaln 95 
                                    57899******************************875.6******9999888666677777776667666633333333 PP

                       dCache_1  72 .............................................p 72 
                                                                                 +
  gi|119719722|ref|YP_920217.1|  96 raieeavktilgnddyrrtflekslekgvvalsstdlvvhpcrgsA 141
                                    3333333333444444444444444444444444444444444440 PP

>> CaM_binding  Plant calmodulin-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.0   5.8   1.3e-05     0.016      17      96 ..      26     104 ..       6     108 .. 0.70
   2 ?    0.1   0.1       1.1   1.3e+03      79     109 ..     181     210 ..     178     211 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.3e-05
                    CaM_binding  17 swsslrklklrkrkkaleekeskke.ereslrkfnprkprelpeesek.eaekVvLrhqdveekkkaeewllnnvieeta 94 
                                    s   +++ + + +k ++   e  ++ e+ + +k n+  +++ ++ + +   ++  Lrh+ ++ek +  e  ln +iee++
  gi|119719722|ref|YP_920217.1|  26 SRRIVKEAEQEAQKIVE---EAIQKaEAIKAEKLNQLLNEYRQKAMAElAPKRLELRHRAIREKHELIESALNRAIEEAV 102
                                    33444444444444333...222333556666666777777777777779****************9999*********9 PP

                    CaM_binding  95 sk 96 
                                     +
  gi|119719722|ref|YP_920217.1| 103 KT 104
                                    76 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.1
                    CaM_binding  79 kkaeewllnnvieetaskLvearKsKVkaLV 109
                                    ++++e ++n  +e  +    e+ K KV  LV
  gi|119719722|ref|YP_920217.1| 181 RDGRE-IYNATLEAKIAEVRESVKPKVLELV 210
                                    56778.999999*999999********9998 PP

>> TcdA_TcdB  TcdA/TcdB catalytic glycosyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   1.7   5.2e-05     0.062      42     139 ..      21     129 ..      13     143 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.2e-05
                                    THHHHHHHHHHHHHHHHHHHCCCCCT--HHHHHHHHHHHHHHH.........................HHHHHHHHHHH. CS
                      TcdA_TcdB  42 laaklkkilvesasdaalqdlreaidedtkkfvkkrdeliekraekdqlkdl......ldtl..vivaqkafinflkak. 112
                                    +a + ++++v++a ++a + ++eai+       +k ++l +++ +k    +l      l      i   ++ i+ ++ + 
  gi|119719722|ref|YP_920217.1|  21 AAEEESRRIVKEAEQEAQKIVEEAIQKAEAIKAEKLNQLLNEYRQKAM-AELapkrleL--RhrAIREKHELIESALNRa 97 
                                    5778899*******************6666668999******944444.3333444342..1335555555555444320 PP

                                    TTSTT-.....HHHHHHHHHHHS---HHHHHH CS
                      TcdA_TcdB 113 gnkntk.....DeirkeyLekeysldteeles 139
                                    ++++ k     D+ r++ Lek +++ +  l s
  gi|119719722|ref|YP_920217.1|  98 IEEAVKtilgnDDYRRTFLEKSLEKGVVALSS 129
                                    33333355566**********99987766655 PP

>> RHD3  Root hair defective 3 GTP-binding protein (RHD3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   4.6   5.5e-05     0.066     350     448 ..      10     108 ..       4     127 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.5e-05
                                    HHHHHHHHHH.HCT..TTTHHHHHHHHHHHHHHHHHHHH.HTTSTTTTS--.HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           RHD3 350 llekfkeavekalk.agedFaesvkekkkklvekfdeeaeslvveqakwdasdkiilklekdieaviaklrkeelkelve 428
                                    lle + +++ +a + + +  ++ ++++++k+ve+  ++ae ++ e+++    ++ ++k   +++ +  +lr+  ++e+ e
  gi|119719722|ref|YP_920217.1|  10 LLEVIIQELRRAAEeESRRIVKEAEQEAQKIVEEAIQKAEAIKAEKLNQLL-NEYRQKAMAELAPKRLELRHRAIREKHE 88 
                                    444455555544430344788889999999999999999988888888777.799************************* PP

                                    HHHHHHHHHHHHHHHHHHTS CS
                           RHD3 429 rvekkleselseavelllek 448
                                     +e+ l+ +++eav++ l +
  gi|119719722|ref|YP_920217.1|  89 LIESALNRAIEEAVKTILGN 108
                                    **************998865 PP

>> DUF3095  Protein of unknown function (DUF3095)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   2.4   0.00027      0.32     204     328 ..       6     122 ..       2     128 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00027
                        DUF3095 204 keaelvkevieliekiyGeeekrhpvseerlklklslkklklearakagkkkllalllrrlkilletllvklllklglkl 283
                                    +e++l++ +i++ ++ + eee+r++v+e + +++   +++ ++a+a + +k     l++ l+ + ++++++l+ k +l+l
  gi|119719722|ref|YP_920217.1|   6 EEKTLLEVIIQELRR-AAEEESRRIVKEAEQEAQKIVEEAIQKAEAIKAEK-----LNQLLNEYRQKAMAELAPK-RLEL 78 
                                    567788889999998.88889999998888777766555555555444432.....3455566656667777777.6666 PP

                        DUF3095 284 gkfdlkrykekvvensDfrkyddglkmvidgdeeqrdklealLee 328
                                    ++    r k++++e++  r +++++k+++  d+ +r+ le+ Le+
  gi|119719722|ref|YP_920217.1|  79 RHRAI-REKHELIESALNRAIEEAVKTILGNDDYRRTFLEKSLEK 122
                                    66555.558999****************************99997 PP

>> FliG_N  FliG N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   7.6    0.0084        10      17      81 ..      23      96 ..      18     101 .. 0.77
   2 ?    5.0   0.1     0.029        35      52      85 ..      88     122 ..      76     126 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0084
                                   HHHHHHHHTTSXHHHHHHHHHHHHCHTTXXHHHHHHHHHHHHHHHHCC.........CCHHCHHHHHHHHHHHH CS
                         FliG_N 17 eeeaaevlkhLdeeeiekltkeiaslksvskeeveaVleefleeleaq.........eylseggeeyarelLek 81
                                   eee+ +++k+ ++e ++ + ++i + + +++e+++++l+e+++++ a+           ++++  e ++++L++
  gi|119719722|ref|YP_920217.1| 23 EEESRRIVKEAEQEAQKIVEEAIQKAEAIKAEKLNQLLNEYRQKAMAElapkrlelrHRAIREKHELIESALNR 96
                                   7999999999999999999999********************99988866666444444444444455555554 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.029
                                    HHHHHHHHHH.HCCCCHHCHHHHHHHHHHHHHHSH CS
                         FliG_N  52 aVleefleel.eaqeylseggeeyarelLekalge 85 
                                    +++e  l+++ e++ + + g ++y r+ Lek+l++
  gi|119719722|ref|YP_920217.1|  88 ELIESALNRAiEEAVKTILGNDDYRRTFLEKSLEK 122
                                    4455554444388889999************9986 PP

>> CFAP91  Cilia- and flagella-associated protein 91
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8  17.1     0.011        14      55     137 ..       6      88 ..       3     104 .. 0.82
   2 ?    7.5   1.9    0.0034       4.1      89     133 ..      62     106 ..      58     119 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.011
                         CFAP91  55 rekraleaslpplsdaaslekrkkileelElkewaereeeiqelqeeRlellkkllkk.reeeqeeanekrleklkekle 133
                                     ek  le  +++l+ aa+ e+ ++i++e E +  +  ee iq+ + ++ e l++ll++ r+++++e++ krle    +++
  gi|119719722|ref|YP_920217.1|   6 EEKTLLEVIIQELRRAAE-EESRRIVKEAEQEAQKIVEEAIQKAEAIKAEKLNQLLNEyRQKAMAELAPKRLELRHRAIR 84 
                                    688889999999999888.6777899******************************98689999********98777766 PP

                         CFAP91 134 keke 137
                                    +++e
  gi|119719722|ref|YP_920217.1|  85 EKHE 88 
                                    6544 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0034
                         CFAP91  89 aereeeiqelqeeRlellkkllkkreeeqeeanekrleklkekle 133
                                    ++r++ ++el  +Rlel ++++++++e  e a ++ +e++++ + 
  gi|119719722|ref|YP_920217.1|  62 EYRQKAMAELAPKRLELRHRAIREKHELIESALNRAIEEAVKTIL 106
                                    5799**********************************9998776 PP

>> TetR_C_24  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   3.3    0.0047       5.6      19      64 ..       4      50 ..       1      58 [. 0.77
   2 ?    3.2   0.5     0.088   1.1e+02      40      65 ..      79     104 ..      54     116 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0047
                                   HHHTHHHHHHHHHHG.GGS-HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      TetR_C_24 19 iaeereeaavllrel.raLspehreeiralrreyerllrdlieeGva 64
                                   +aee+    v+++el ra ++e+r+ +++ ++e +++++++i+++ a
  gi|119719722|ref|YP_920217.1|  4 VAEEKTLLEVIIQELrRAAEEESRRIVKEAEQEAQKIVEEAIQKAEA 50
                                   56677777777777615677888888899999999999999998765 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.088
                                    HHHHHHHHHHHHHHHHHHHHHHHHHT CS
                      TetR_C_24  40 hreeiralrreyerllrdlieeGvaa 65 
                                    ++++ir++++ +e+ l ++iee+v++
  gi|119719722|ref|YP_920217.1|  79 RHRAIREKHELIESALNRAIEEAVKT 104
                                    44569999999999999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2178  (0.121479); expected 358.6 (0.02)
Passed bias filter:                      923  (0.0514808); expected 358.6 (0.02)
Passed Vit filter:                       121  (0.00674884); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.45
# Mc/sec: 1421.71
//
Query:       gi|119719723|ref|YP_920218.1|  [L=92]
Description: hypothetical protein Tpen_0814 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0019   18.5   0.1     0.0022   18.3   0.1    1.1  1  ATP-synt_F    ATP synthase (F/14-kDa) subunit
  ------ inclusion threshold ------
      0.022   15.1   0.0      0.025   15.0   0.0    1.1  1  DUF2122       RecB-family nuclease (DUF2122)
      0.051   13.8   0.0      0.066   13.4   0.0    1.2  1  Response_reg  Response regulator receiver domain


Domain annotation for each model (and alignments):
>> ATP-synt_F  ATP synthase (F/14-kDa) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   3.7e-07    0.0022      13      73 ..      18      81 ..       6      88 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.7e-07
                                   HHHTTCEEEE.CSSHHHHHHHHHHHHHHTTEEEEEEEHHHHCCCH.HHHHHCTCS.SSSEEEEE CS
                     ATP-synt_F 13 frlaGvgeve.vtdeeeieealkelleredigiilitekiaeeir.elideykee.alPaileI 73
                                   +++ G + v  v+d+ e+e+ ++e+++++   ++l+++ +++++   +++e+k + ++Pai+e+
  gi|119719723|ref|YP_920218.1| 18 LKAGGADIVIaVNDPREAERRIEEIVREKAADLVLVDDVLVSMMGrGKLKELKYRyPYPAIIEL 81
                                   56666665556999*****************************8669***************97 PP

>> DUF2122  RecB-family nuclease (DUF2122)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   4.1e-06     0.025      23      80 ..       9      67 ..       5      87 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.1e-06
                        DUF2122 23 lvlpdlkDalellkpekvlllskee.geelleeeeleekgrvllvfsgadegfskkele 80
                                   +vlpdl+ al+   ++ v+++++ + +e+ +ee  +e+  +++lv++   + + + +l+
  gi|119719723|ref|YP_920218.1|  9 VVLPDLEKALKAGGADIVIAVNDPReAERRIEEIVREKAADLVLVDDVLVSMMGRGKLK 67
                                   8**********************765888887777788888888877665555555555 PP

>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.1e-05     0.066      14      75 ..      14      79 ..       7      86 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.1e-05
                                   HHHHHHHTTEEEEEEESSHHHHHHHH....HHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEE CS
                   Response_reg 14 lrqlleeegyeevaeaedgkealell....keekvdlillDinmpgmdGlellkeireedpelpvi 75
                                   l+++l+  g   v +++d++ea + +    +e++ dl+l+D  +  m G   lke++ + p + +i
  gi|119719723|ref|YP_920218.1| 14 LEKALKAGGADIVIAVNDPREAERRIeeivREKAADLVLVDDVLVSMMGRGKLKELKYRYPYPAII 79
                                   6778887788777789999998877755558888***********************999888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 666.52
//
Query:       gi|119719724|ref|YP_920219.1|  [L=123]
Description: hypothetical protein Tpen_0815 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.7e-14   54.1   0.5    2.4e-14   53.6   0.5    1.2  1  Trm112p    Trm112p-like protein
  ------ inclusion threshold ------
      0.032   14.4   3.2       0.28   11.4   3.2    2.3  1  zf-RING_7  C4-type zinc ribbon domain


Domain annotation for each model (and alignments):
>> Trm112p  Trm112p-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.6   0.5   2.7e-18   2.4e-14       5      68 .]       1      85 [.       1      85 [. 0.98

  Alignments for each domain:
  == domain 1  score: 53.6 bits;  conditional E-value: 2.7e-18
                                   CCC-B-TTTHH.C--HHHHHHHHH.TT---.S-SS----S..................CHHTTEECCCCEEEETTTTEEEEE CS
                        Trm112p  5 lniLaCpackg.pLdwealvevaa.lglne.lpkekpedy..................ellleldieegeLvCpncgraYpI 65
                                   +++LaCp++k+ pL++ ++ +++   ++ +  +k+ +e y                  ++++++++ +g+L+Cp+cgr+ pI
  gi|119719724|ref|YP_920219.1|  1 MDLLACPYDKHfPLELYVIETRTYkDRQVTfRRKPACELYcafrgknvseldgkdpgcDECIKVEVATGVLYCPECGRWWPI 82
                                   689***************************9***************************99********************** PP

                                   ETT CS
                        Trm112p 66 kdG 68
                                   kd+
  gi|119719724|ref|YP_920219.1| 83 KDE 85
                                   *96 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   3.2   3.1e-05      0.28      22      32 ..      65      79 ..      47      79 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.1e-05
                                   B....-EE-TTT--E CS
                      zf-RING_7 22 e....vvtCpeCGRI 32
                                   e    v +CpeCGR+
  gi|119719724|ref|YP_920219.1| 65 EvatgVLYCPECGRW 79
                                   044449********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 916.27
//
Query:       gi|119719725|ref|YP_920220.1|  [L=569]
Description: glutamyl-tRNA synthetase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-77  261.0   0.0    1.4e-77  260.7   0.0    1.1  1  tRNA-synt_1c    tRNA synthetases class I (E and Q), catalytic
    1.1e-22   80.8   0.0    1.9e-22   80.0   0.0    1.4  1  tRNA-synt_1c_C  tRNA synthetases class I (E and Q), anti-codo


Domain annotation for each model (and alignments):
>> tRNA-synt_1c  tRNA synthetases class I (E and Q), catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  260.7   0.0   1.6e-81   1.4e-77       1     313 [.     101     411 ..     101     412 .. 0.96

  Alignments for each domain:
  == domain 1  score: 260.7 bits;  conditional E-value: 1.6e-81
                                    S-EEEE---SSSS-BHHHHHHHHHHHHHHHH.TT-EEEEEE--SSC..CC--HHHHHHHHHHHHHTT---SSEEEEGGGG CS
                   tRNA-synt_1c   1 kVrtRfaPePtGyLHiGhakaallnylfAkn.nnGkfilRieDTdp..erekeeaeesiledlkwlgikwdekptyqsdr 77 
                                    kV+tRfaP+P   LH+G+a+ a+lny++Ak+ +nGkfilR+eDTdp  +r  +ea + i edl wlg  w ++ + qs+r
  gi|119719725|ref|YP_920220.1| 101 KVVTRFAPNPDFVLHLGSARPAILNYYYAKKmYNGKFILRFEDTDPrtKRPMPEAYDLIREDLRWLGTPW-DEEYIQSQR 179
                                    79***************************8758************84467889*****************.55899**** PP

                                    HHHHHHHHHHHHHTTSEEEE-STHHHHHHHHCCSSHSS-TTTTS-HHHHHHHHHHHHHTTHSTTTS-EEEESSBTTSS.G CS
                   tRNA-synt_1c  78 fdelkkyaeeLikkGkAYvcectkeeleeereeqeklgskerdrydeenlklfeeemkkgkaegekavvRlkideess.v 156
                                    ++ ++++ae Lik+G AYvc  +++e+++ r +   +  + +  + ee+++ + e+m +g++ +++av+R+k d +++  
  gi|119719725|ref|YP_920220.1| 180 MEVYYEVAEALIKSGNAYVCTHSQDEIKAFRDA--GKPDPCSFLPPEEHMERW-EKMLSGEYPEGAAVLRIKTDPAHPnP 256
                                    *******************************99..778899************.9**********************99* PP

                                    GGSSTEEEEEEESGGGSBTTTBTSTSEEE-HHHHHHHHHHHTT-SEEEEEGGGGCCHHHHHHHHHHTT-S.-EEEEEE-- CS
                   tRNA-synt_1c 157 efrDlvrgriklepqeihdlvivksdiyPtYdfavvidDaleeithvlrteefldntpkyiwllealglevppfiheylr 236
                                     +rD ++ r+  +++  h+l+++k+++ PtY+fa+++dD++ ++thvlr+ee+  nt k+  +++ +g++ pp+   + r
  gi|119719725|ref|YP_920220.1| 257 SVRDWIAFRVLDTEKTPHPLTGDKYRVWPTYNFACAVDDHMLGVTHVLRGEEHAVNTLKQEYVYRHMGWK-PPVSIHFGR 335
                                    **************999*****************************************************.7788889** PP

                                    EEETTSB-SHHHHHHHHHTTSSSSTT-TTSCBHHHHHHCTB-HHHHHHHHHHHCCCSSS.EEEEHHHHHHHHHHHHH CS
                   tRNA-synt_1c 237 lnlekkklSKRklsllvdekqvkewddlreallnflrrlGwtpekerelftreeliksfdlnresksleafdrkkLe 313
                                    +nle+ +lSK  +   +++  +   dd r+ +l++lrr+G+ pe++ +l+ + ++  s+   +++++l+af+rk+Le
  gi|119719725|ref|YP_920220.1| 336 MNLEGMVLSKSVIRRGIEKGLFSSIDDIRLGTLRALRRRGILPEAIWDLVLEVGIKPST-ARVSVDKLHAFNRKYLE 411
                                    *********************************************************99.9*************997 PP

>> tRNA-synt_1c_C  tRNA synthetases class I (E and Q), anti-codon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.0   0.0   2.1e-26   1.9e-22       1     173 [.     414     558 ..     414     559 .. 0.90

  Alignments for each domain:
  == domain 1  score: 80.0 bits;  conditional E-value: 2.1e-26
                 tRNA-synt_1c_C   1 ApRymaVldpvkvt.ienlpegkeeelevplhpknpelgtrkvpfsk.eiyiereDakrlkpgeevrLkelynikveeve 78 
                                    A+Rym+V +p kv  ie+l+   ++++ev +hp+ pe+g r+++fsk e+y+  +D+      ++vrL++l+n++v +  
  gi|119719725|ref|YP_920220.1| 414 ANRYMFVPEPAKVAsIEGLE--APITAEVIVHPSFPERGRRRITFSKpEVYLP-SDVA----SSMVRLMGLGNFEVVDG- 485
                                    89**********98799887..699*********************66****9.6743....468***********765. PP

                 tRNA-synt_1c_C  79 kdesgevtelkleydgesleearkkkg.iihWvsaeeaveaevrlYdrLfkeeededfllnpdslkvl.eeglaepalan 156
                                        g     kl+y +++++ a+k++  i++W + e++v+                  +l+  ++k+   +g++ep+la+
  gi|119719725|ref|YP_920220.1| 486 ----G----SKLRYLNNDVSFAKKHELpIVQWAPVESSVRG----------------RVLKAAGTKIEeISGYGEPSLAE 541
                                    ....2....36899999**9999*****************9................89888888754679********* PP

                 tRNA-synt_1c_C 157 lkkgdivQfeRiGyfrv 173
                                    l +g++vQf R G++rv
  gi|119719725|ref|YP_920220.1| 542 LPPGEQVQFVRLGFVRV 558
                                    ***************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (569 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.46
# Mc/sec: 3728.09
//
Query:       gi|119719726|ref|YP_920221.1|  [L=482]
Description: prolyl-tRNA synthetase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-32  112.3   0.0    7.1e-32  110.8   0.0    1.7  2  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
    5.8e-21   74.4   1.2    1.1e-20   73.6   0.4    2.0  2  HGTP_anticodon  Anticodon binding domain
    4.8e-13   49.1   0.3    1.1e-12   48.0   0.3    1.6  1  ProRS-C_1       Prolyl-tRNA synthetase, C-terminal


Domain annotation for each model (and alignments):
>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.8   0.0   1.2e-35   7.1e-32       6     177 ..     102     273 ..      93     275 .. 0.92
   2 ?   -2.7   0.1      0.85   5.1e+03      69      93 ..     382     406 ..     367     419 .. 0.60

  Alignments for each domain:
  == domain 1  score: 110.8 bits;  conditional E-value: 1.2e-35
                                    TTSEEEEE-SSSHHHHHHHHHHHEEEB.GGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEE.EEES.GGGHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx.xxxxxxxxxx RF
                   tRNA-synt_2b   6 rndreyiLkPtneetfvelirdevlrs.krLPlklyqiqtkyRdEksdsrGLlRvreFhqkdgy.vfha.easlddslrd 82 
                                    + +r+++L+Pt+e++f+ +++ + ++s ++LPlklyq  ++yR+Ek+ +r+L+R+reF + +++  f + e+ l+++ +d
  gi|119719726|ref|YP_920221.1| 102 KLERRLALRPTSETAFYYMYSYW-IQSwRDLPLKLYQSVSVYRNEKN-TRPLIRGREFLWIEAHdAFAThEEALNQIRED 179
                                    3489*****************88.***888*****************.***************9446667899******* PP

                                    HHHHHHHHHHHTT.SCEEEEEE.GTTSCBTTSEEEEEEEEETTTSEEEEEEEEEEEETHHHHHTTEEEECTTSSEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2b  83 likaisriferlglefraiiel.msaksadykdkkefeavsesltkgieigtiqklgtrlserlgatvldennreksvim 161
                                    +++  + i+e+lg++f  +++  ++++   ++d++  + +++  +++++i++ + lg+r+++++++t+ld+++++k v  
  gi|119719726|ref|YP_920221.1| 180 MENSRKVIWEKLGIPFLFLRRPpWDKF-SGAEDTYAADTIMP-DGRVLQISSTHDLGQRFAKAFNVTFLDKDGKRKYVWQ 257
                                    ****************99999987754.78999*********.9************************************ PP

                                    EEEEEEHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxx RF
                   tRNA-synt_2b 162 icaaigveRllsaile 177
                                    +c++ g+ R+ +a+++
  gi|119719726|ref|YP_920221.1| 258 TCYGPGIWRITAALIA 273
                                    **********999986 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.85
                                    EEESGGGHHHHHHHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxx RF
                   tRNA-synt_2b  69 vfhaeaslddslrdlikaisrifer 93 
                                    + h  +  +d+l++l + ++++fe+
  gi|119719726|ref|YP_920221.1| 382 ISHIRKLENDILEELKRRAKEFFES 406
                                    3333444456677777777777765 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.6   0.4   1.8e-24   1.1e-20       1      93 [.     291     387 ..     291     388 .. 0.97
   2 ?   -2.7   0.0       1.2     7e+03      26      55 ..     404     431 ..     390     432 .. 0.54

  Alignments for each domain:
  == domain 1  score: 73.6 bits;  conditional E-value: 1.8e-24
                                    SEEEEESSSS...HHHHHHHHHHHHHHHHTTTSEEEEES.SSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTT CS
                 HGTP_anticodon   1 qvvviplnek...aeeleeyakklaeeLraagirveldd.snesigkkireadllgipfavvvGekelekgtvtvrdrdt 76 
                                    qvv++p+  k   +e+++e ++kl + +r+ag+rv ld  +++++g+k+++++l+g+p++++vG +e+e+gtvtv +rd 
  gi|119719726|ref|YP_920221.1| 291 QVVIVPIYYKesdKERVLEKCRKLEAMIREAGYRVYLDArEEYTPGWKFNDWELKGVPVRLEVGVREVETGTVTVFRRDL 370
                                    8******999999999**************************************************************** PP

                                    CEEEEEETTHHHHHHHH CS
                 HGTP_anticodon  77 reqervsldelveklke 93 
                                    r +e+v+ +el++ +++
  gi|119719726|ref|YP_920221.1| 371 RVKEKVADSELISHIRK 387
                                    ************99987 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.2
                                    HTTTSEEEEESSSSTHHHHHHHHHHTT-SE CS
                 HGTP_anticodon  26 raagirvelddsnesigkkireadllgipf 55 
                                     +    ++   + e + +++r  ++++ pf
  gi|119719726|ref|YP_920221.1| 404 FESR--IVTATRREEVEEALRSGKMVKMPF 431
                                    4443..333446666666666666666666 PP

>> ProRS-C_1  Prolyl-tRNA synthetase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.0   0.3   1.8e-16   1.1e-12       2      69 .]     415     482 .]     414     482 .] 0.96

  Alignments for each domain:
  == domain 1  score: 48.0 bits;  conditional E-value: 1.8e-16
                                    HHHHHHHHTT-EEEEEESSGHHHHHHHHHHH.S-EEEEEESSB-SSCCCSB-TTT-SB-SEEEEEE-B- CS
                      ProRS-C_1   2 eefkealekkgfvlapWcgeeecEekIkeet.gakslcipfdqepseegtkCivcgkpakkwvlfgrsY 69 
                                    ee+ eal ++++v++p+cg+eec +++ke t g k+++  +d  ++ +  +C+ cg pa  +v++++sY
  gi|119719726|ref|YP_920221.1| 415 EEVEEALRSGKMVKMPFCGREECADDLKEATdGGKVRGTEIDF-KEGDYGRCAWCGAPARLIVYVAKSY 482
                                    899************************************9994.678889******************* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (482 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       720  (0.0401584); expected 358.6 (0.02)
Passed bias filter:                      608  (0.0339115); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 3550.93
//
Query:       gi|119719727|ref|YP_920222.1|  [L=156]
Description: ribosomal-protein-alanine acetyltransferase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-20   73.6   0.3      2e-20   73.2   0.3    1.2  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    1.5e-17   63.7   0.0    1.6e-17   63.6   0.0    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    6.7e-15   55.3   0.5    1.1e-14   54.6   0.2    1.5  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    3.5e-09   36.5   0.1    5.5e-09   35.9   0.1    1.3  1  FR47             FR47-like protein
      1e-06   29.0   0.1    1.4e-06   28.5   0.1    1.1  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
    2.9e-06   27.4   0.0    4.3e-05   23.6   0.0    2.1  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
    4.4e-06   26.7   0.0    7.4e-06   26.0   0.0    1.3  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
    6.5e-05   23.6   0.0    7.4e-05   23.4   0.0    1.3  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
    0.00021   21.0   0.0    0.00029   20.6   0.0    1.2  1  Acetyltransf_8   Acetyltransferase (GNAT) domain
    0.00054   19.6   0.0    0.00068   19.3   0.0    1.1  1  GNAT_acetyltran  GNAT acetyltransferase
    0.00054   20.1   0.0     0.0008   19.6   0.0    1.3  1  Acetyltransf_6   Acetyltransferase (GNAT) domain
     0.0017   18.1   0.1     0.0021   17.8   0.1    1.2  1  PanZ             Acetyltransferase (GNAT) domain, PanZ
  ------ inclusion threshold ------
      0.022   14.2   0.0       0.07   12.6   0.0    1.7  1  Acetyltransf_15  Putative acetyl-transferase
      0.041   13.4   0.7       0.19   11.2   0.5    1.9  2  C_LFY_FLO        DNA Binding Domain (C-terminal) Leafy/Floric
       0.11   12.8   0.0       0.18   12.1   0.0    1.4  1  IF3_N            Translation initiation factor IF-3, N-termin
       0.11   12.5   0.0       0.21   11.6   0.0    1.3  1  Nudix_hydro      Nudix hydrolase domain


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.2   0.3   1.7e-23     2e-20      18     117 .]      27     123 ..      12     123 .. 0.81

  Alignments for each domain:
  == domain 1  score: 73.2 bits;  conditional E-value: 1.7e-23
                                    HHHHHH..HHHHHHSTTC..EEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTT CS
                 Acetyltransf_1  18 daseee..feesfsleae..gllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareeg 93 
                                    da+  +  f+ +   + +  +++va + g ++G+i  +          +++s+aV +e rg+G+G++Lle+ +++are+g
  gi|119719727|ref|YP_920222.1|  27 DAFSLDylFYLY---NRCrdYFFVADYKGLVVGYIVSCREGS----QLHVHSVAVVEELRGRGIGRKLLEETIRIARENG 99 
                                    222222224444...555559999***********9888888....7********************************* PP

                                    ESEEEEEEETTEHHHHHHHHHTTE CS
                 Acetyltransf_1  94 ikkivlaveedndaairlYeklGF 117
                                    +k+++l+v  +n++a rlYeklGF
  gi|119719727|ref|YP_920222.1| 100 LKAVYLEVKTTNTPALRLYEKLGF 123
                                    ***********************9 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.6   0.0   1.5e-20   1.6e-17      32     117 ..      44     136 ..      22     146 .. 0.88

  Alignments for each domain:
  == domain 1  score: 63.6 bits;  conditional E-value: 1.5e-20
                Acetyltransf_10  32 lllvaeeggkivGviel.rdgs..hisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp.yavpfYeklGF 106
                                    +++va+ +g +vG+i   r+gs  h++ ++V +e rg+Gig++Lle+ ++ a+++g+k   l+v+ ++  a ++YeklGF
  gi|119719727|ref|YP_920222.1|  44 YFFVADYKGLVVGYIVScREGSqlHVHSVAVVEELRGRGIGRKLLEETIRIARENGLKAvYLEVKTTNtPALRLYEKLGF 123
                                    699************55488889*********************************************9*********** PP

                Acetyltransf_10 107 kav..geeqeenG 117
                                    k++  +e+ + +G
  gi|119719727|ref|YP_920222.1| 124 KRIgvKEKYYNDG 136
                                    ***6555555665 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.6   0.2     1e-17   1.1e-14       3      76 .]      43     125 ..      41     125 .. 0.75

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 1e-17
                                    EEEEEEEETTEEEEEEEEEEES..TCTEEEEE-GGGTTSSHHHHHHHH..TT...SEEE.EE.EEEETHHHHHHHHHHTT CS
                 Acetyltransf_7   3 gevfVaeddgkivGfialslld..aeitrlaVdpeyrgkGiGraLlea..ae...kgii.le.qlelnaekaikfYeklG 73 
                                    +++fVa+ +g +vG+i+ ++++   + + +aV +e rg+GiGr+Lle   ++   +g++ ++ ++++++++a+++YeklG
  gi|119719727|ref|YP_920222.1|  43 DYFFVADYKGLVVGYIVSCREGsqLHVHSVAVVEELRGRGIGRKLLEEtiRIareNGLKaVYlEVKTTNTPALRLYEKLG 122
                                    679***********999777777666666*****************9645114556644211223333349********* PP

                                    EEE CS
                 Acetyltransf_7  74 Fee 76 
                                    F++
  gi|119719727|ref|YP_920222.1| 123 FKR 125
                                    *95 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   0.1   4.9e-12   5.5e-09      25      80 ..      70     126 ..      55     133 .. 0.86

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 4.9e-12
                                    EEEEE-GGG-SSSHHHHHHHHHHHHHHHS-.S-EEEEEETT-HHHHHHHHHHT-EEE CS
                           FR47  25 galqvlpehrrrGlgsrlvkalakeiaerg.ktvllvvvasNtpsirlyeklGfeki 80 
                                     ++ v +e r+rG g++l ++ ++  +e+g k v l v+++Ntp+ rlyeklGf+ i
  gi|119719727|ref|YP_920222.1|  70 HSVAVVEELRGRGIGRKLLEETIRIARENGlKAVYLEVKTTNTPALRLYEKLGFKRI 126
                                    57999****************9999999884667899*****************998 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.1   1.3e-09   1.4e-06      49     147 ..      43     136 ..      29     140 .. 0.86

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 1.3e-09
                 Acetyltransf_4  49 eyvflvaesdrivGyaylgqfkkrakdwkaelsvylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqf 128
                                     y+f +++++ +vGy      +    ++    sv ++ +  + +g+gr+l++  + +++e++++  + e+  +n+++  +
  gi|119719727|ref|YP_920222.1|  43 DYFFVADYKGLVVGYIVSC--RE--GSQLHVHSVAVV-EELRGRGIGRKLLEETIRIARENGLKAVYLEVKTTNTPALRL 117
                                    6888888899999997655..44..566677788888.579*************************************** PP

                 Acetyltransf_4 129 hkalGFelvgifkkcikkn 147
                                    +++lGF+  g  +k+++++
  gi|119719727|ref|YP_920222.1| 118 YEKLGFKRIGVKEKYYNDG 136
                                    *************999876 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   3.9e-08   4.3e-05      75     126 ..      68     124 ..       4     126 .. 0.68

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 3.9e-08
                                    EEEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--.....SSHHHHHTTT-E CS
                 Acetyltransf_9  75 gvtgVavapehrgrgvlskLlaraleemreegqplsllfP.....ssipiYrrfGye 126
                                     v +Vav  e rgrg+ +kLl+++++ +re+g + ++l        + ++Y+++G++
  gi|119719727|ref|YP_920222.1|  68 HVHSVAVVEELRGRGIGRKLLEETIRIARENGLKAVYLEVkttntPALRLYEKLGFK 124
                                    5789**********************************8866543335999999997 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   6.6e-09   7.4e-06      19      61 ..      61     103 ..      43     105 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 6.6e-09
                Acetyltransf_CG  19 vrkegvldfthTeVpeelrGkGiAkkLvkaalddareeglkvv 61 
                                     r++ +l+++ + V eelrG+Gi++kL ++ +  are+glk v
  gi|119719727|ref|YP_920222.1|  61 CREGSQLHVHSVAVVEELRGRGIGRKLLEETIRIARENGLKAV 103
                                    4677799999******************************986 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   6.6e-08   7.4e-05      81     138 .]      67     124 ..       4     124 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 6.6e-08
                 Acetyltransf_3  81 aelgymla.psfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGfe 138
                                    +++  +   ++ +g+G+++  ++  +++a +e gl+ ++ +++++N+   r++eklGf+
  gi|119719727|ref|YP_920222.1|  67 LHVHSVAVvEELRGRGIGRKLLEETIRIA-RENGLKAVYLEVKTTNTPALRLYEKLGFK 124
                                    4444333327799****************.7777************************7 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   2.6e-07   0.00029      83     141 ..      70     127 ..      47     130 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.6e-07
                                    EEEESSHHHCTTTCHHHHHHHHHHHHHCCTT--EEEE--BTT-HHHHHHHHHTT-EEEE CS
                 Acetyltransf_8  83 HlligeaeargkglttallralvhylfadprtrrvvvEPdvrNerairllekaGfekek 141
                                    H +   +e rg+g++++ll++ ++ + ++ + + v +E + +N+ a+rl+ek+Gf++ +
  gi|119719727|ref|YP_920222.1|  70 HSVAVVEELRGRGIGRKLLEETIRIAREN-GLKAVYLEVKTTNTPALRLYEKLGFKRIG 127
                                    555556789**************987666.*************************9875 PP

>> GNAT_acetyltran  GNAT acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0     6e-07   0.00068     160     236 ..      46     125 ..      36     132 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 6e-07
                GNAT_acetyltran 160 vvilkngeivsgasSysvyekgieieidTkedyrrkgLAtivaaalileclkrglyPsW.Daa..neaSvaLaekLGYef 236
                                    +v+ ++g +v  ++S+   ++ +  +++  e+ r++g  +++ ++ i+ + ++gl + +   +  n+++++L+ekLG+++
  gi|119719727|ref|YP_920222.1|  46 FVADYKGLVVGYIVSCREGSQLHVHSVAVVEELRGRGIGRKLLEETIRIARENGLKAVYlEVKttNTPALRLYEKLGFKR 125
                                    67778999**********************************************98755244466*************86 PP

>> Acetyltransf_6  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   7.2e-07    0.0008      73     132 ..      45     104 ..      20     113 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 7.2e-07
                 Acetyltransf_6  73 lyvlrldgrpvAvalglrsgdrlyywlggydpelaklspgllllweliedaaeeGlrrfd 132
                                    ++v+  +g +v++++  r g  l+ + +++ +el++ ++g+ ll e+i+ a+e+Gl+ + 
  gi|119719727|ref|YP_920222.1|  45 FFVADYKGLVVGYIVSCREGSQLHVHSVAVVEELRGRGIGRKLLEETIRIARENGLKAVY 104
                                    6788889************************************************98775 PP

>> PanZ  Acetyltransferase (GNAT) domain, PanZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   1.9e-06    0.0021      41      90 ..      46      95 ..      39     132 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.9e-06
                           PanZ 41 faarFNdRlLgAvkveledkeaelsdlcVRevTRrRGVgsyLleearrqa 90
                                   f+a +     g +   +e+++ +++++ V e+ R RG+g++Llee+ r a
  gi|119719727|ref|YP_920222.1| 46 FVADYKGLVVGYIVSCREGSQLHVHSVAVVEELRGRGIGRKLLEETIRIA 95
                                   55555555555555567888999***********************9876 PP

>> Acetyltransf_15  Putative acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   6.2e-05      0.07      71     139 ..      65     126 ..      44     145 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.2e-05
                Acetyltransf_15  71 nvleiYtlyvsekyrgkGlakklLeeslkelkknYkvdnelllaLHlnpkDksMnisfalYyslgFrkg 139
                                      l + ++ v e+ rg+G+ +klLee+++  +     +  + + L +         + +lY +lgF+++
  gi|119719727|ref|YP_920222.1|  65 SQLHVHSVAVVEELRGRGIGRKLLEETIRIAR----ENGLKAVYLEVKTTN---TPALRLYEKLGFKRI 126
                                    5678999********************88663....222333444333332...235555555555554 PP

>> C_LFY_FLO  DNA Binding Domain (C-terminal) Leafy/Floricaula
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.5   0.00017      0.19      29      45 ..      29      45 ..       9      52 .. 0.77
   2 ?    0.4   0.0      0.35   3.9e+02      42      77 ..      66     101 ..      46     131 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00017
                      C_LFY_FLO 29 ngldylfhlyeqcrkfl 45
                                     ldylf ly++cr+++
  gi|119719727|ref|YP_920222.1| 29 FSLDYLFYLYNRCRDYF 45
                                   579***********986 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.35
                      C_LFY_FLO  42 rkfliqvqalakekgekcptkvtnqvfryakkagas 77 
                                    +  +  v  + + +g+    k+ ++ +r a++ g +
  gi|119719727|ref|YP_920222.1|  66 QLHVHSVAVVEELRGRGIGRKLLEETIRIARENGLK 101
                                    555555555666666666666666666666665532 PP

>> IF3_N  Translation initiation factor IF-3, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00017      0.18       3      54 ..      65     118 ..      64     125 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00017
                                    TS--SSEEEEE-SS.S-EEEEEEHHHHHHHHHHHTSEEEEEE.SSSSS-EEEEE CS
                          IF3_N   3 eqIrarevrlvded.GeqlGvistreAlrlaeekgldLVevs.pnaepPVcrim 54 
                                    +q ++  v +v+e  G  +G   ++e +r+a+e+gl+ V ++ ++++ P  r+ 
  gi|119719727|ref|YP_920222.1|  65 SQLHVHSVAVVEELrGRGIGRKLLEETIRIARENGLKAVYLEvKTTNTPALRLY 118
                                    5778999****9989************************999445577888886 PP

>> Nudix_hydro  Nudix hydrolase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00018      0.21      27      66 ..      86     125 ..      84     133 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00018
                    Nudix_hydro  27 skLkaslsqwreegkrgvwlkvpieqselvpiavkeGFef 66 
                                    + L+++++  re+g ++v+l+v++++   +    k GF+ 
  gi|119719727|ref|YP_920222.1|  86 KLLEETIRIARENGLKAVYLEVKTTNTPALRLYEKLGFKR 125
                                    6799**********************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1025.25
//
Query:       gi|119719728|ref|YP_920223.1|  [L=256]
Description: beta-lactamase domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-17   64.1   0.2    1.6e-17   63.7   0.2    1.1  1  Lactamase_B_2  Beta-lactamase superfamily domain
    7.4e-08   32.6   1.0      1e-07   32.2   1.0    1.3  1  Lactamase_B    Metallo-beta-lactamase superfamily
  ------ inclusion threshold ------
      0.052   13.4   0.0       0.15   12.0   0.0    1.7  1  Lactamase_B_3  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.7   0.2   2.6e-21   1.6e-17      26     200 ..      53     221 ..      37     222 .. 0.80

  Alignments for each domain:
  == domain 1  score: 63.7 bits;  conditional E-value: 2.6e-21
                                    --..SEEEEE-SS--HHHHGGGGCCCC.....C--EEEEEEEEHHHHHHCCTTCGHHHCHTTTTEEEEEE-TTSEEEE.. CS
                  Lactamase_B_2  26 delppidaVllthaHyDHlaglltlre.....lrpkklplyapkgvlavleanfvylaleeepavnvheldwgesfel.. 98 
                                     +l+++  +ll+h H DH  g+  l       +++k++++++p+g+++  e+ +   +l +e   +++++  ++ f+   
  gi|119719728|ref|YP_920223.1|  53 GRLDEVRIILLSHLHPDHSLGVVELLWhlwirGSGKRVEVVGPRGTRRFFERMLE--VLHPE---KFETILSHGVFREig 127
                                    457799******************9999997777777***********9999953..44444...566666666665443 PP

                                    .CSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---HHHHHHHCT-SEEEEE-S-SSTTHHHH... CS
                  Lactamase_B_2  99 .gdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyipeeigerlggadllllditayeddemir... 174
                                     gd+  + +a++a h+ +          l++r++ ++++++y+gDt   + ++ e ++g+dll++++t+    e  +   
  gi|119719728|ref|YP_920223.1| 128 pGDTVGNAKAFEALHTVEA---------LAYRLTVSDRSLCYSGDTSPSE-KLVEGFAGCDLLVHEATYPPGME--Daal 195
                                    3333335677777777776.........*******************776.5567***********99544444..447* PP

                                    HHT---STSHHHHCTTSSSSEEEEES CS
                  Lactamase_B_2 175 hmgHltpeeaveaaadlgakrlvliH 200
                                    ++gH+tp +a+ +a ++ga+rl l+H
  gi|119719728|ref|YP_920223.1| 196 RDGHSTPVHAATIALRAGARRLALVH 221
                                    ************************** PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   1.0   1.7e-11     1e-07      42     163 ..      55     189 ..      33     243 .. 0.84

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 1.7e-11
                                    GGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHHHHHHHHCCHH.TTCHCGCCEEEEETTTEECCCTE CS
                    Lactamase_B  42 pkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmeeaddaasrkgll.lagvsadkpdvdeeeldgnaggr 120
                                    +++v+ ++l+HlH+DH  g+ +l  + ++     + e   +++  + ++++ + l   +++++ +++v++e+++g++ g 
  gi|119719728|ref|YP_920223.1|  55 LDEVRIILLSHLHPDHSLGVVELLWHLWIRGSGKRVEVVGPRGTRRFFERMLEVLHpEKFETILSHGVFREIGPGDTVGN 134
                                    5789***********************************************99999999999999999999999999875 PP

                                    EEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCCCCC.............. CS
                    Lactamase_B 121 ralyvtggpghghghgvveygggkvlftGDallagetgridl.............t 163
                                     a  +   ++  ++ ++++  +++++++GD++++++ +++                
  gi|119719728|ref|YP_920223.1| 135 -AKAFEALHTVEALAYRLTVSDRSLCYSGDTSPSEKLVEGFAgcdllvheatyppG 189
                                    .7889999*************************88877665555555555555441 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.4e-05      0.15      35     132 ..      56     180 ..      12     187 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.4e-05
                  Lactamase_B_3  35 eeaDlvlisqaledHahletlkql........................aenvkvleeges......levggleiravats 84 
                                    +e+ ++l+s+ ++dH     ++ l                        ++  +vl++++         ++++    + ++
  gi|119719728|ref|YP_920223.1|  56 DEVRIILLSHLHPDHSL-GVVELLwhlwirgsgkrvevvgprgtrrffERMLEVLHPEKFetilshGVFREIGPGDTVGN 134
                                    7899***********63.33444456699999444444444444444333333333322222211122333333333333 PP

                  Lactamase_B_3  85 hdavggsergenngflleqdgltiyhlGhlahelsseelkelgrvDvv 132
                                    ++a +  +  e  +++l++++ ++++ G+++   s++  + ++  D++
  gi|119719728|ref|YP_920223.1| 135 AKAFEALHTVEALAYRLTVSDRSLCYSGDTSP--SEKLVEGFAGCDLL 180
                                    355556677999*****************996..67777777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1828.77
//
Query:       gi|119719729|ref|YP_920224.1|  [L=278]
Description: xylose isomerase domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.2e-27   94.6   0.1    6.9e-27   94.3   0.1    1.1  1  AP_endonuc_2    Xylose isomerase-like TIM barrel
     0.0045   16.7   0.2        1.3    8.8   0.0    3.5  4  AP_endonuc_2_N  AP endonuclease family 2 C terminus


Domain annotation for each model (and alignments):
>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.3   0.1   7.7e-31   6.9e-27       1     194 [.      31     222 ..      31     246 .. 0.92

  Alignments for each domain:
  == domain 1  score: 94.3 bits;  conditional E-value: 7.7e-31
                                    HHHHHHCT-SEEEEECCTCSHHHHCHHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCS...HHHHHHHHHHHHH CS
                   AP_endonuc_2   1 laaaaeaGfdgvElfgrdlvpvselsdeelrelrkaldelglriaslslftrfgypdederear...reesvdalkraie 77 
                                    ++a++e+G+dgvE++  ++v v         el+ +++e+ l+++++ +  ++ + + ++ +++   re++++++++ + 
  gi|119719729|ref|YP_920224.1|  31 VKALSELGYDGVEISVLEPVEVG--------ELALLAREHSLEVPAVGTGLNYIHYGLSLTSPDagvRERARRRIEEIVF 102
                                    5799******************6........9**************************97777788************** PP

                                    HHHHHTBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEEEEE--TTTTSSSTC..HHHHHHHHHHTTTT CS
                   AP_endonuc_2  78 laaaLGapllvlhpGtagagpkgseeeawerlaeslneladyaekegvklalEtlagsgvelgd..eelarlldavdspn 155
                                     a++  ++ ++++  +    + g+ e a+++l+e l+ la++a ++gv l lE+l++ ++ l +  ee +r+l++v+ +n
  gi|119719729|ref|YP_920224.1| 103 EASRREIKGVIVGLIRGRGDEWGDVEGARRLLVEELRGLARKAGEQGVSLFLEPLNRYESRLVNtvEEGLRVLEEVGEDN 182
                                    *************9855555556677*********************************98888**************** PP

                                    EEEEEEHHHHHHHTTTHHHHHHHHHGGEEEEEE.EESS.T CS
                   AP_endonuc_2 156 vgvclDtgHlliaeedvddalraladrikhvHikDakg.d 194
                                    + + lDt+H++i+e  ++d +r    ri+h+H++D+++  
  gi|119719729|ref|YP_920224.1| 183 LLLLLDTFHMNIEERVIEDSIRLASGRIGHFHVADSNRlA 222
                                    *********************************9998842 PP

>> AP_endonuc_2_N  AP endonuclease family 2 C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0      0.99   8.9e+03      44      55 ..      10      21 ..       7      22 .. 0.80
   2 ?    2.5   0.0     0.014   1.2e+02       5      17 ..      30      42 ..      28      46 .. 0.85
   3 ?    0.8   0.0     0.045   4.1e+02      25      52 ..      81     108 ..      81     111 .. 0.78
   4 !    8.8   0.0   0.00014       1.3       1      21 [.     229     249 ..     229     250 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 0.99
                 AP_endonuc_2_N 44 llieeseaafdw 55
                                   ++i +++a fd+
  gi|119719729|ref|YP_920224.1| 10 MVIANPKARFDA 21
                                   678999999997 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.014
                 AP_endonuc_2_N  5 ifsaLrqiGYdgp 17
                                    + aL + GYdg+
  gi|119719729|ref|YP_920224.1| 30 AVKALSELGYDGV 42
                                   5789*******97 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.045
                 AP_endonuc_2_N  25 slmsreeGare.Avaflkdkllieeseaa 52 
                                    sl+s++ G re A + ++ ++++e s+++
  gi|119719729|ref|YP_920224.1|  81 SLTSPDAGVRErARRRIE-EIVFEASRRE 108
                                    578999999874667788.5999999887 PP

  == domain 4  score: 8.8 bits;  conditional E-value: 0.00014
                 AP_endonuc_2_N   1 dwkdifsaLrqiGYdgplSiE 21 
                                    d+ +i+ aLr++GY g +S E
  gi|119719729|ref|YP_920224.1| 229 DFVRILHALRDAGYSGFVSAE 249
                                    7899***************88 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 1731.68
//
Query:       gi|119719730|ref|YP_920225.1|  [L=398]
Description: alcohol dehydrogenase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-29  102.5   0.2    2.5e-29  101.3   0.1    1.7  2  ADH_N         Alcohol dehydrogenase GroES-like domain
    1.2e-21   77.0   0.2    1.8e-21   76.4   0.2    1.3  1  ADH_zinc_N    Zinc-binding dehydrogenase
    6.3e-10   38.9   0.1    3.6e-09   36.4   0.1    2.1  1  Glu_dehyd_C   Glucose dehydrogenase C-terminus
    2.7e-05   23.6   0.3      4e-05   23.0   0.3    1.2  1  AlaDh_PNT_C   Alanine dehydrogenase/PNT, C-terminal domain
    0.00022   22.3   0.0    0.00048   21.2   0.0    1.6  1  ADH_zinc_N_2  Zinc-binding dehydrogenase
     0.0042   16.5   0.3     0.0099   15.2   0.0    1.7  2  2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, 


Domain annotation for each model (and alignments):
>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.3   0.1   8.3e-33   2.5e-29       1     108 [.      53     174 ..      53     175 .. 0.95
   2 ?   -2.5   0.0       1.6   4.8e+03      16      53 ..     289     326 ..     281     334 .. 0.59

  Alignments for each domain:
  == domain 1  score: 101.3 bits;  conditional E-value: 8.3e-33
                                    TTEEEEEEEEEEE-HHHHHHHTTS......TTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SSSHHHH CS
                          ADH_N   1 pgevlikvkaagiCgsDlhilkgg......kelevklplilGHEivGeveevgpevkklkvGdrVvvepliscgeCaaCk 74 
                                    p+e+li+vka+giCgsD+h+l+ +          +++p+++GHE++G+ve+vg +vk++k Gd+V+ e ++ cgeC+aC+
  gi|119719730|ref|YP_920225.1|  53 PDEILIRVKAVGICGSDIHFLETDsegyilYPGLTRFPVVIGHEFSGVVEKVGTNVKTFKPGDMVTSEEMFWCGECDACR 132
                                    689*******************99999998888999******************************************** PP

                                    TT-GGG-........TTBEETTTSS-SSSBSEEEECGGGEEE CS
                          ADH_N  75 egeenlC........eeakllgvsldGgfaeyvvvpekklvk 108
                                    + + n+C         e + lg++ dG++a+yvvv++k+++k
  gi|119719730|ref|YP_920225.1| 133 SVDFNHClrlndpadLEFGELGFTHDGAMADYVVVKAKYAWK 174
                                    **********99988888889999*************99887 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.6
                                    HHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS- CS
                          ADH_N  16 sDlhilkggkelevklplilGHEivGeveevgpevkkl 53 
                                     D+h+   g+  ++ + +     i G+++++g++ +++
  gi|119719730|ref|YP_920225.1| 289 ADFHVEAAGAPRHTIPQMQKSLAINGKIVQIGRAAEDV 326
                                    55555555433333333344445678888888877765 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.4   0.2   6.1e-25   1.8e-21       1     128 [.     225     359 ..     225     361 .. 0.90

  Alignments for each domain:
  == domain 1  score: 76.4 bits;  conditional E-value: 6.1e-25
                                    HHHHHHHHHHHHTT-.EEEEEESSHHHHHHHHHTTESEEEET....TTC.HHHHHHHHHTTTSSEEEEEESSCSH.HHHH CS
                     ADH_zinc_N   1 gvGlaavqlAkalGa.eviavdsseeklelakklGadeviny....kea.dlverikeltggegvdvvfecvGsg.atle 73 
                                    ++Glaa++lAka+Ga +via  +s+ ++elakk Gad+v+n+    k+  ++ e+i e tgg+g+d+ +e++G++ +t++
  gi|119719730|ref|YP_920225.1| 225 PIGLAAIALAKAAGAgKVIAFEVSPTRRELAKKVGADYVFNPvelsKNGvEPWEKIMEVTGGQGADFHVEAAGAPrHTIP 304
                                    79******************************************9988889**********************6527*** PP

                                    HHHHCEEEEEEEEECSCTSSEEEEEHHHHHHTT-EEEEE-SSCHHHHHHHHHHHH CS
                     ADH_zinc_N  74 aalkllkpgGrlvvvGggkgeeefdlrnlllkeksilGsllgslreefkealdll 128
                                    +  k+l+ +G++v +G   ++ ++ l  +  ++ +i Gs + s    f ++++l+
  gi|119719730|ref|YP_920225.1| 305 QMQKSLAINGKIVQIGRAAEDVPIYLEVFQVRRGQIFGSQGHSGFGNFGNVIRLM 359
                                    ****************988888888888889999999998887667777766665 PP

>> Glu_dehyd_C  Glucose dehydrogenase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.1   1.2e-12   3.6e-09       3     207 ..     191     391 ..     189     396 .. 0.72

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 1.2e-12
                    Glu_dehyd_C   3 vgvLvEPisiveKaielaeasrsafewep.esalvlGaGslGLLalalleaeerglervyvlgrrdrpdptidlveelGa 81 
                                     g LvEP+s++  a+     +r+   ++p + + v GaG++GL a+al +    g  +v  ++    p  + +l +++Ga
  gi|119719730|ref|YP_920225.1| 191 AGSLVEPTSVAYHAM----FTRAG-GFKPgAYVAVWGAGPIGLAAIALAK--AAGAGKVIAFEV--SPT-RRELAKKVGA 260
                                    689*******87665....44443.344526789*********9966555..467776666654..444.4579****** PP

                    Glu_dehyd_C  82 tYv....dsre...tpvdeipeas..eemdlvvEaTGsakhafeaiea.lapnGvaaLlGvpeds.evevdggelhrelv 150
                                     Yv    + ++   +p ++i e++  +  d+ vEa G+++h + ++++ la nG ++ +G  ++   + +++ ++ r   
  gi|119719730|ref|YP_920225.1| 261 DYVfnpvELSKngvEPWEKIMEVTggQGADFHVEAAGAPRHTIPQMQKsLAINGKIVQIGRAAEDvPIYLEVFQVRRG-- 338
                                    **843332233111455566665422679************998886449******9999775432666666555555.. PP

                    Glu_dehyd_C 151 leNkalvGsv.NanrrhfeaavdtLaalpeslldelvtkvvdldeleeAfedddetiK 207
                                         ++Gs   +   +f + ++ +aa + + +++++t +  lde+ +Afe+ ++ i 
  gi|119719730|ref|YP_920225.1| 339 ----QIFGSQgHSGFGNFGNVIRLMAAGKID-MTQIITARFSLDEVYKAFERAHQRID 391
                                    ....789996368999**9999877776665.679*******************9986 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.3   1.3e-08     4e-05      15      75 ..     204     263 ..     197     308 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 1.3e-08
                                    SEEETTCEETCB---EEEEESTSHHHHHHHHHHHHTT-.EEEEEESSHHHHHHHHHTTTCEC CS
                    AlaDh_PNT_C  15 gkgtlaGgvpgvepakvlviGgGvaGlqAiatakglga.kVtvlDvrparleqleslgakfv 75 
                                    ++ t aGg +    a v v G+G  Gl+Aia ak+ ga kV +++v+p+r+e  +++ga +v
  gi|119719730|ref|YP_920225.1| 204 AMFTRAGGFK--PGAYVAVWGAGPIGLAAIALAKAAGAgKVIAFEVSPTRRELAKKVGADYV 263
                                    5778899999..8899*********************978************9999999865 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   1.6e-07   0.00048       2     124 ..     259     388 ..     258     396 .. 0.71

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.6e-07
                                    T-SEEE......ETTSTTHH...HHH-TT-EEEEEES-H.HHHH.HHHHHHEEEEEEEEE----.S-EEE-CHHHCTTT- CS
                   ADH_zinc_N_2   2 GAdevi......dyrtedfe...aatggegvDvvldtvg.gealleaslkvlpggGrlvsiggpplsaallkpakkrkgr 71 
                                    GAd v+      ++  e +e   ++tgg+g D  ++++g   +++ +  k l+ +G++v+ig+      +  + ++ +++
  gi|119719730|ref|YP_920225.1| 259 GADYVFnpvelsKNGVEPWEkimEVTGGQGADFHVEAAGaPRHTIPQMQKSLAINGKIVQIGRAAEDVPIYLEVFQVRRG 338
                                    6666666554423335666689999**************9667779999999899*******755555555555544333 PP

                                    EEEE--GGG...-.-HHHHHHHHHHHHHHH----..EEEEEEGGGHHHHHHHHHS CS
                   ADH_zinc_N_2  72 svkyeflfsmkasaqadileelaalieeGklrpv..vdrvfpleeaaeAhryles 124
                                    ++  +     +++   + +  + +l+++Gk+ ++  ++ +f+l+e+ +A+++ ++
  gi|119719730|ref|YP_920225.1| 339 QIFGSQG---HSG-FGN-FGNVIRLMAAGKIDMTqiITARFSLDEVYKAFERAHQ 388
                                    3333333...345.666.************8754227778**********99765 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   3.3e-06    0.0099      37      83 ..     216     263 ..     208     272 .. 0.87
   2 ?   -2.8   0.0       1.1   3.4e+03      43      71 ..     348     377 ..     345     388 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.3e-06
                                    SEEEEES-SHHHHHHHHHHHHTT-.EEEEESSSHHHHHCHHHHTCEEC CS
                   2-Hacid_dh_C  37 ktvGiiGlGrIGqavakrlkafgm.kviaydrskkkeeeeeelgvelv 83 
                                      v+++G+G IG a++ ++ka g+ kvia+++s++++e ++++g+++v
  gi|119719730|ref|YP_920225.1| 216 AYVAVWGAGPIGLAAIALAKAAGAgKVIAFEVSPTRRELAKKVGADYV 263
                                    5699********************9*********99997888787665 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.1
                                    S-SHHHHHHHHHHH.HTT-EEEEESSSHHH CS
                   2-Hacid_dh_C  43 GlGrIGqavakrlk.afgmkviaydrskkk 71 
                                    G+G+ G+ +  +++ +++m  i++ r+  +
  gi|119719730|ref|YP_920225.1| 348 GFGNFGNVIRLMAAgKIDMTQIITARFSLD 377
                                    899999988888887788877777776554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2980.24
//
Query:       gi|119719731|ref|YP_920226.1|  [L=303]
Description: creatininase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.2e-49  166.7   0.0    7.5e-49  166.4   0.0    1.1  1  Creatininase  Creatinine amidohydrolase
  ------ inclusion threshold ------
       0.12   12.4   0.0       0.15   12.0   0.0    1.3  1  PAC2          PAC2 family


Domain annotation for each model (and alignments):
>> Creatininase  Creatinine amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.4   0.0   8.3e-53   7.5e-49       2     241 .]      24     279 ..      23     279 .. 0.83

  Alignments for each domain:
  == domain 1  score: 166.4 bits;  conditional E-value: 8.3e-53
                   Creatininase   2 eltwpeveealkeddvailPvGstEqHGphlplgtDtliaealaervaeklgakalvlPtlpyGvseeh.lgfpGTisls 80 
                                    ++t+ e+ e++k++d++++P+Gs+E HG    +g Dt+i+ ++aerva ++g  + v+P+++yG  ++h  g+pGTi ++
  gi|119719731|ref|YP_920226.1|  24 QMTMSELLERVKKNDIVLVPCGSVESHGLGQATGEDTIIGAYIAERVAFETG--ITVAPPIFYGSHPSHhYGMPGTIPIK 101
                                    79*********************************************99999..88*********7555499******** PP

                   Creatininase  81 petliavlrdileslarhGfrrivlvngHggnsaalkeaarelraehdaaavrvtaaekelaaal.kleeaae.aaeese 158
                                    +e +i++++ ++++l+++Gf++i+l+n+Hg ++++l  + +++  e  ++a+ +    +  +a++ ++ ++ +  +    
  gi|119719731|ref|YP_920226.1| 102 KEAYIDYVTSVVKWLSHAGFKKIILFNSHG-QEYVLPIVKDKAIIEEGVKALIL---VTSWWAWVrDILRQGTeLKPGLV 177
                                    ******************************.999*******9999996665532...22222222033333333444445 PP

                   Creatininase 159 eeegggHAgelEtSlmlalrpelVrmdraedpeeaklakeg...................vstaedaeels.psGvlGdp 218
                                     e+  +HA+elE S++++++p+lV+ +++++++++k+                          +  +e  + p+G++G p
  gi|119719731|ref|YP_920226.1| 178 LETPFIHADELEASVLWYVAPKLVDPSKLKESDAEKMVGVIpdkwadkagnvygrpfgwyD-ISAFMEIHHyPKGSVGYP 256
                                    56699**************************998877655588899999999998888742.333333333499999*** PP

                   Creatininase 219 skataekGealleaaveelaell 241
                                    ska++ekGe ++e+a+++++e++
  gi|119719731|ref|YP_920226.1| 257 SKASREKGEVVVETAIQRIIEFI 279
                                    *******************9986 PP

>> PAC2  PAC2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.7e-05      0.15      74     110 ..      96     134 ..      41     226 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.7e-05
                                    EE-HSCHHH..HHHHHHHHHHHHTTESEEEEEEEEEESS CS
                           PAC2  74 grepilqye..efakalldwaeelgvkevvvLggldage 110
                                    g  pi +    ++++ +++w+++ g+k+++++++ + + 
  gi|119719731|ref|YP_920226.1|  96 GTIPIKKEAyiDYVTSVVKWLSHAGFKKIILFNSHGQEY 134
                                    555555555779*********************998544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1981.94
//
Query:       gi|119719732|ref|YP_920227.1|  [L=339]
Description: glyoxylate reductase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-68  230.2   0.0    1.4e-68  229.7   0.0    1.2  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
    2.9e-37  127.3   0.0    3.4e-37  127.1   0.0    1.0  1  2-Hacid_dh     D-isomer specific 2-hydroxyacid dehydrogenase,
    1.8e-05   24.9   0.0    3.3e-05   24.1   0.0    1.4  1  NAD_binding_2  NAD binding domain of 6-phosphogluconate dehyd
     0.0014   18.7   0.0     0.0031   17.6   0.0    1.5  1  Shikimate_DH   Shikimate / quinate 5-dehydrogenase
     0.0015   18.2   0.0     0.0095   15.5   0.0    2.0  2  IlvN           Acetohydroxy acid isomeroreductase, NADPH-bind
     0.0054   16.8   0.0     0.0096   16.0   0.0    1.3  1  AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD bindi
  ------ inclusion threshold ------
      0.035   13.5   0.4       0.34   10.2   0.4    2.2  1  ThiF           ThiF family
       0.15   12.4   0.0       0.36   11.2   0.0    1.7  1  Mur_ligase     Mur ligase family, catalytic domain


Domain annotation for each model (and alignments):
>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  229.7   0.0   6.4e-72   1.4e-68       1     178 []     111     291 ..     111     291 .. 0.98

  Alignments for each domain:
  == domain 1  score: 229.7 bits;  conditional E-value: 6.4e-72
                                    HHHHHHHHTTHHHHHHHHHTTCC...HTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHH CS
                   2-Hacid_dh_C   1 lalllallrrlaeadeevregew...ksekallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeee 77 
                                    ++l+la++rr+ ead+ +r+g+w   +++  l+g el+gkt+G++GlGrIG a+akrl++f++k+++yd  ++ + e+  
  gi|119719732|ref|YP_920227.1| 111 VGLILAVTRRIVEADKIIRTGQWdkpWNPYFLTGPELKGKTIGLVGLGRIGVATAKRLSSFDVKILYYDIERRWDVETVI 190
                                    589*********************999999*******************************************8888888 PP

                                    HTCEECSHHHHHHH-SEEEE-S--STTTTTSBSHHHHHCSTTTEEEEESS-GGGB-HHHHHHHHHTTSCCEEEES--SSS CS
                   2-Hacid_dh_C  78 lgvelvsleellaesDivslhlpltpetrhlinaeelakmkkgailiNtaRGglvdeeaLleaLksgkiagaalDvfeee 157
                                     ++e+++l++ll++sDivs+h+plt+et+hlin+e+l+kmkk+a+liNtaRG++vd+eaL++aLk+g+iagaalDvfe+e
  gi|119719732|ref|YP_920227.1| 191 PNMEFTDLDTLLEKSDIVSIHVPLTKETYHLINEERLRKMKKTAYLINTARGPVVDTEALVKALKEGWIAGAALDVFEQE 270
                                    899***************************************************************************** PP

                                    SSGTCHHHHHSTTEEE-SS-T CS
                   2-Hacid_dh_C 158 plpedspllelpnviltPHia 178
                                    plp+++pl++++nv+l PHia
  gi|119719732|ref|YP_920227.1| 271 PLPPNHPLTKFDNVVLAPHIA 291
                                    ********************8 PP

>> 2-Hacid_dh  D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.1   0.0   1.5e-40   3.4e-37       3     134 .]       8     323 ..       6     323 .. 0.98

  Alignments for each domain:
  == domain 1  score: 127.1 bits;  conditional E-value: 1.5e-40
                                    EEST.CHHHHHHHHHTTE.EEEEES....CSSHHHCHHHHTTESEEEE-TTS-BSHHHHHHHTT--EEEESSSSCTTB-H CS
                                    xxxxxxxxxxxxxxxxxx.xxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     2-Hacid_dh   3 ileplreeelellkeegv.evevkd....ellteellekakdadalivrsntkvtaevlealpkLkviaragvGvDnvDl 77 
                                    +++ ++e +l  lke  + +v+v++    ++++eell+ ++d dal++  ++k++aev++a+p+Lkvi++++vG+D++D+
  gi|119719732|ref|YP_920227.1|   8 VTRIIPEPGLSMLKE--CcDVVVHEskdwPPSREELLRNIRDKDALLCLLTDKIDAEVMDAAPNLKVISTYSVGFDHIDI 85 
                                    555558888999999..55************************************************************* PP

                                    HHHHHTT-EEEE-TTTTHHHHHHHH....................................................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxx....................................................... RF
                     2-Hacid_dh  78 daakerGilVtnvpgystesvAElt....................................................... 102
                                    + a++rGi Vt++pg+ t++vAE+t                                                       
  gi|119719732|ref|YP_920227.1|  86 PEATKRGIYVTHTPGVLTDAVAEFTvglilavtrriveadkiirtgqwdkpwnpyfltgpelkgktiglvglgrigvata 165
                                    ******************************************************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                     2-Hacid_dh 103 ................................................................................ 102
                                                                                                                    
  gi|119719732|ref|YP_920227.1| 166 krlssfdvkilyydierrwdvetvipnmeftdldtlleksdivsihvpltketyhlineerlrkmkktaylintargpvv 245
                                    ******************************************************************************** PP

                                    ..............................................T-BHHHHHHHHHHHHHHHHHHHTTCCGTTBCS CS
                                    ..............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     2-Hacid_dh 103 ..............................................aaTeeaqeniaeeaaenlvaflkgespanavn 134
                                                                                  +aT ea++++ae aa nl+a+lkge p+  vn
  gi|119719732|ref|YP_920227.1| 246 dtealvkalkegwiagaaldvfeqeplppnhpltkfdnvvlaphiaSATIEARQRMAELAARNLIAVLKGEMPPALVN 323
                                    *************************************************************************99998 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   1.5e-08   3.3e-05       1     106 [.     151     256 ..     151     262 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1.5e-08
                                    EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHH.HHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHS.HCC CS
                  NAD_binding_2   1 kigfiGlGvMGsnmalnllkagykvavynrtke.kveelvaegakaaesieelvasldvvitmvkagkavdevieg.lle 78 
                                    +ig++GlG +G   a++l + + k+  y+ ++   ve+++  ++  ++++  l+++ d+v + v+ +k++ ++i++  l+
  gi|119719732|ref|YP_920227.1| 151 TIGLVGLGRIGVATAKRLSSFDVKILYYDIERRwDVETVI-PNM-EFTDLDTLLEKSDIVSIHVPLTKETYHLINEeRLR 228
                                    59***************************88761455555.444.6889999***********************99999 PP

                                    C--TT-EEEE-S---HHHHHHHHHHHHH CS
                  NAD_binding_2  79 alkkgdilidgstsspedtrelakelke 106
                                    ++kk ++li+++   + dt+ l k+lke
  gi|119719732|ref|YP_920227.1| 229 KMKKTAYLINTARGPVVDTEALVKALKE 256
                                    *********************9999987 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.4e-06    0.0031       9     101 ..     146     233 ..     142     247 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.4e-06
                                    ..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEE...EE-SSS CS
                   Shikimate_DH   9 slkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvv...isatas 85 
                                    +lk+k++ l+G G+++  +ak L++  vk   ++  ++er +++ + + +     +++++l++ll+++d+v   +  t+ 
  gi|119719732|ref|YP_920227.1| 146 ELKGKTIGLVGLGRIGVATAKRLSSFDVK---ILYYDIERRWDVETVIPN-----MEFTDLDTLLEKSDIVsihVPLTKE 217
                                    799*********************88888...9999********777744.....5999999999999999433445777 PP

                                    SS-SB-HHHHHCCHHH CS
                   Shikimate_DH  86 eepilekeeveealkk 101
                                    + +++++e++++++k 
  gi|119719732|ref|YP_920227.1| 218 TYHLINEERLRKMKKT 233
                                    8888888888887754 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0      0.25   5.6e+02      62     108 ..      49      87 ..      40     119 .. 0.62
   2 !   15.5   0.0   4.2e-06    0.0095       2      91 ..     147     236 ..     146     253 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.25
                                    SEEEE-S-HHHHHHHHHHHTGGG--TT-EEEESSSHHHHTTSS---T CS
                           IlvN  62 dvvmiliPDelqkevyeeeiepnlkegkalafahGfnihfglikppk 108
                                    d +++l+ D++ +ev+  + +pnlk        + +++ f+ i++p+
  gi|119719732|ref|YP_920227.1|  49 DALLCLLTDKIDAEVM--DAAPNLK------VISTYSVGFDHIDIPE 87 
                                    5666666666666666..3445544......3344555555555555 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 4.2e-06
                                    HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHH.HHHHTT-EEEEHHHHHHT-SEEEE-S-HHHH.HHHHHH CS
                           IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvk.kAkeegfevltvaeavkkadvvmiliPDelq.kevyee 79 
                                    lkgk+i ++G G  G a a+ l    +++    ++ ++ ++ +    ++e ++++ + +k+d+v i +P + +  ++++e
  gi|119719732|ref|YP_920227.1| 147 LKGKTIGLVGLGRIGVATAKRLSSFDVKIL--YYDIERRWDvETVIPNMEFTDLDTLLEKSDIVSIHVPLTKEtYHLINE 224
                                    89******************9966555555..55555555514556789********************65441456666 PP

                                    HTGGG--TT-EE CS
                           IlvN  80 eiepnlkegkal 91 
                                    e   ++k+ ++l
  gi|119719732|ref|YP_920227.1| 225 ERLRKMKKTAYL 236
                                    666666666654 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   4.3e-06    0.0096      21     111 ..     147     241 ..     143     263 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.3e-06
                                    -TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHHHHHCTT-EE--HHHCTTT-SEE...EE.-SSSSSSB-HHH CS
                  AdoHcyase_NAD  21 laGkvavvaGyGdvGkGcaaslkglGarvivtevdPicalqaameGfevvtleevvkkadiv...vt.ttGnkdiitleh 96 
                                    l Gk++ ++G G +G  +a+ l ++  +++  +++    + +++  +e + l+++++k+div   v  t  +  +i+ e+
  gi|119719732|ref|YP_920227.1| 147 LKGKTIGLVGLGRIGVATAKRLSSFDVKILYYDIERRWDVETVIPNMEFTDLDTLLEKSDIVsihVPlTKETYHLINEER 226
                                    679*********************************99999999999999999999999987322442445679****** PP

                                    HCCS-TTEEEEE-SS CS
                  AdoHcyase_NAD  97 lkkmkddaivcniGh 111
                                    l+kmk++a + n   
  gi|119719732|ref|YP_920227.1| 227 LRKMKKTAYLINTAR 241
                                    ********9999754 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.4   0.00015      0.34      15     138 ..     146     313 ..     142     320 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00015
                                    HHHTSEEEEE--SHHHHHHHHHHHHHTTT.................EEEEEESSB.--GGGGGTBTTS-GGGT....TSB CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................xxxxxxxxx.xxxxxxxxxxxxxxxxx....xxx RF
                           ThiF  15 kLrdskvllvGaGglGsellknLalsGvg.................kltlvDnDk.ielsNlnRqflfreedi....Gkp 72 
                                    +L+ +++ lvG+G +G   +k L    v+                 + +++D D+  e+s+ +  +   +++      + 
  gi|119719732|ref|YP_920227.1| 146 ELKGKTIGLVGLGRIGVATAKRLSSFDVKilyydierrwdvetvipNMEFTDLDTlLEKSDIVSIHVPLTKETyhliNEE 225
                                    689999******************99999888888888888888888888888873477777654332111111233222 PP

                                    HHHHHHHHHHHT-....TTSEEEEEES-C.............CGCCS-HHH........HTT-SEEEEE....SSSHHHH CS
                                    xxxxxxxxxxxxx....xxxxxxxxxxxx.............xxxxxxxxx........xxxxxxxxxx....xxxxxxx RF
                           ThiF  73 Kaevaaealqein....pdveveavteri.............tdetvleel........lesvDlVvda....lDniear 123
                                    +   +++ +  in    p v+ ea+++ +             +                l+++D Vv+a    + +iear
  gi|119719732|ref|YP_920227.1| 226 RLRKMKKTAYLINtargPVVDTEALVKALkegwiagaaldvfE-------QeplppnhpLTKFDNVVLAphiaSATIEAR 298
                                    2222222222222111133344444444433334443333331.......033333333777777777766556667777 PP

                                    HHHHHHHHHHT-EEE CS
                                    xxxxxxxxxxxxxxx RF
                           ThiF 124 rlvnracvkkgipli 138
                                      ++++++++ i ++
  gi|119719732|ref|YP_920227.1| 299 QRMAELAARNLIAVL 313
                                    777777777776665 PP

>> Mur_ligase  Mur ligase family, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00016      0.36      39      87 ..      58     109 ..      43     110 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00016
                                    T-EEEES-HGGGG.EE-T..S-TTCHHHHHHHHTTEEEEEHHHHHHHHHHCC CS
                     Mur_ligase  39 Gaaavvghdaani.vvss..iskdnpeleaakepgipvesraeaLaelaarf 87 
                                     + a v ++a n+ v+s+  +  d+  +++a+++gi+v +++ +L + +a+f
  gi|119719732|ref|YP_920227.1|  58 KIDAEVMDAAPNLkVISTysVGFDHIDIPEATKRGIYVTHTPGVLTDAVAEF 109
                                    5677788999999*9999888888*********************9998877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2359.53
//
Query:       gi|119719733|ref|YP_920228.1|  [L=261]
Description: GTP-binding protein, HSR1-related [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.5e-17   61.5   0.0      8e-13   48.5   0.0    2.2  2  MMR_HSR1      50S ribosome-binding GTPase
    8.3e-11   41.7   0.0    1.1e-05   25.0   0.0    2.1  2  FeoB_N        Ferrous iron transport protein B
    2.5e-07   30.7   0.0    7.9e-07   29.1   0.0    1.8  1  RsgA_GTPase   RsgA GTPase
    1.8e-06   27.6   0.0    3.4e-05   23.5   0.0    2.7  3  GTP_EFTU      Elongation factor Tu GTP binding domain
    0.00013   22.1   0.9      0.047   13.8   0.3    2.8  3  Dynamin_N     Dynamin family
     0.0066   16.1   0.2      0.029   13.9   0.0    1.9  2  cobW          CobW/HypB/UreG, nucleotide-binding domain
  ------ inclusion threshold ------
       0.01   15.3   0.0       0.17   11.3   0.0    2.3  2  Arf           ADP-ribosylation factor family
      0.067   13.2   0.0       0.11   12.5   0.0    1.3  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
       0.11   13.0   0.0       0.29   11.7   0.0    1.8  1  AAA_18        AAA domain
       0.21   10.5   0.4       0.63    9.0   0.1    2.0  2  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
       0.23   11.2   0.0       0.85    9.4   0.0    1.9  3  PduV-EutP     Ethanolamine utilisation - propanediol utilisat


Domain annotation for each model (and alignments):
>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0   0.00021      0.34      71     114 .]       8      50 ..       2      50 .. 0.86
   2 !   48.5   0.0   4.9e-16     8e-13       2      69 ..     105     171 ..     104     217 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00021
                                    HHHHCTSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                       MMR_HSR1  71 laleeadlillvvdaseeklkpldeeleelleeakkplilvlnk 114
                                    + + +ad+++ vvda+ + ++    e+e++  + +kpl++v+nk
  gi|119719733|ref|YP_920228.1|   8 RVIARADVVVEVVDAR-DPWATRSPEIERYAVRLGKPLLVVVNK 50 
                                    335579********88.8899999******999**********8 PP

  == domain 2  score: 48.5 bits;  conditional E-value: 4.9e-16
                                    EEEEESTTSSHHHHHHHHHTS.TEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHH.HHHHH CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltge.kaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseek.glgka 69 
                                    +a+vG pNvGKSt+in l g+  + +s +pg T+ i++ r +  g  ++++DtpG++ + s+e+  l+ a
  gi|119719733|ref|YP_920228.1| 105 AAVVGIPNVGKSTIINYLKGShSVGTSPIPGFTKSITRLRAA--G-WLRVIDTPGVVPRMSQEElALRGA 171
                                    58******************9678***************998..5.89*******876344433255444 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   1.1e-05     0.017      78     153 ..      12      87 ..       6      90 .. 0.89
   2 !   25.0   0.0   6.6e-09   1.1e-05       3      75 ..     105     173 ..     103     182 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.1e-05
                                    SSSEEEEEEEGGG..HHHHHHHHHHHHHTTSSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTBTHHHHH CS
                         FeoB_N  78 epdvvvnvvdatn..lernLyLtlqllelgvpvvlalnmideaekkgieidlkkLsekLgvpvvktsakkkegieell 153
                                    ++dvvv+vvda      r+  +    + lg+p+++++n++d + ++ +e   k L+++  +pvv +sa+k+ g++ l 
  gi|119719733|ref|YP_920228.1|  12 RADVVVEVVDARDpwATRSPEIERYAVRLGKPLLVVVNKSDLVPRDVLEKWRKVLEKH--FPVVFISATKRMGTRMLW 87 
                                    78*********9833589999**********************************997..599*******99998775 PP

  == domain 2  score: 25.0 bits;  conditional E-value: 6.6e-09
                                    EEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHH CS
                         FeoB_N   3 valvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsayseeekvardfll 75 
                                     a+vG pnvGk+t++n l g+++ vg  p     k+ ++l+ +   ++++D PG+  +  +s+ee   r  l 
  gi|119719733|ref|YP_920228.1| 105 AAVVGIPNVGKSTIINYLKGSHS-VGTSPIPGFTKSITRLR-AAGWLRVIDTPGV--VPRMSQEELALRGALR 173
                                    689*****************974.66655555556667777.66899*******8..5677777776666665 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0   4.9e-10   7.9e-07      33     161 ..      31     157 ..       3     160 .. 0.71

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 4.9e-10
                                    HHHHHHHHHHHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTT.S.........EE CS
                    RsgA_GTPase  33 nlldrfLvlaeekgiepvivlnKiDlleeeeeleelkeelealgyevllvsaktkegleelkellkd.k.........ts 102
                                      ++r+ v     g ++++v+nK Dl+ ++  le++++ le+  ++v+++sa+++ g++ l + l+            ++
  gi|119719733|ref|YP_920228.1|  31 PEIERYAVR---LGKPLLVVVNKSDLVPRDV-LEKWRKVLEKH-FPVVFISATKRMGTRMLWRSLRRvAprkprgkpvVA 105
                                    456666544...455889*************.*********99.**********99999888777531112233333378 PP

                                    EEECSTTSSHHHHHHHHCTT-----S--------------SEEEEEETTTEEEESS-SS CS
                    RsgA_GTPase 103 vlvGqSGvGKStLinallpelelktgevseklgrGkhTTtavellelaegglliDtPGf 161
                                    ++vG   vGKSt+in l++++++ t+ +       k  T+ +    l     +iDtPG+
  gi|119719733|ref|YP_920228.1| 106 AVVGIPNVGKSTIINYLKGSHSVGTSPIPGF---TKSITRLRAAGWLR----VIDTPGV 157
                                    99******************99999888764...34445544444444....7888876 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   2.1e-08   3.4e-05      86     183 ..       5      85 ..       3      96 .. 0.76
   2 ?   -1.0   0.0      0.67   1.1e+03       7      23 ..     106     122 ..     101     129 .. 0.82
   3 ?   -0.9   0.0       0.6   9.7e+02      72      81 ..     149     158 ..     136     169 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 2.1e-08
                                    HHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGST.HHHHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                       GTP_EFTU  86 evirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrl.kaelkeiveevkqklsrkeeklekygekg 164
                                    +v r ++ +D++v vvda++   +++ e+ r a ++g p+ v++NK D + ++ l++  + ++++               
  gi|119719733|ref|YP_920228.1|   5 DVKRVIARADVVVEVVDARDPWATRSPEIERYAVRLGKPLLVVVNKSDLVpRDVLEKWRKVLEKH--------------- 69 
                                    7889999******************************************9433333333333333............... PP

                                    TTTEEEEEEBTTTTBTHHH CS
                       GTP_EFTU 165 ekevpvvfgSalkgegvkt 183
                                       +pvvf+Sa k  g + 
  gi|119719733|ref|YP_920228.1|  70 ---FPVVFISATKRMGTRM 85 
                                    ...5667777766666655 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.67
                                    EEEESTTSSHHHHHHHH CS
                       GTP_EFTU   7 giighvDhGKtTLtdrL 23 
                                    +++g  + GK+T++  L
  gi|119719733|ref|YP_920228.1| 106 AVVGIPNVGKSTIINYL 122
                                    68888999****98766 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.6
                                    EEEEEESSSG CS
                       GTP_EFTU  72 inliDtPGHv 81 
                                    + +iDtPG v
  gi|119719733|ref|YP_920228.1| 149 LRVIDTPGVV 158
                                    579*****76 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.019        32     122     167 ..       6      50 ..       4      51 .. 0.93
   2 !   13.8   0.3   2.9e-05     0.047       2      39 ..     106     144 ..     105     147 .. 0.88
   3 ?    0.3   0.0       0.4   6.6e+02     103     118 ..     149     164 ..     145     177 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.019
                                    HHHHHSTTEEEEEEEETTS-CCC-CHHHHHHHHSTTBTTEEEEEE- CS
                      Dynamin_N 122 vkeyikkadiilavtsanhdlsnsealflarevdpkgkrtivvltk 167
                                    vk+ i +ad+++ v++a   ++ +++ +++r +   gk  +vv++k
  gi|119719733|ref|YP_920228.1|   6 VKRVIARADVVVEVVDARDPWA-TRSPEIERYAVRLGKPLLVVVNK 50 
                                    578899****************.89999************999998 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 2.9e-05
                                    EEEEBTTTTHHHHHHHHHTS--S---SSS.---S-EEEE CS
                      Dynamin_N   2 avvGsqSsGKSSvlnaLlgedilprgpnp.tTrrplelq 39 
                                    avvG  + GKS+++n L g++   ++p+p  T  ++ l+
  gi|119719733|ref|YP_920228.1| 106 AVVGIPNVGKSTIINYLKGSHSVGTSPIPgFTKSITRLR 144
                                    79*************************973688888776 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.4
                                    EEEEE---B-SSSGTT CS
                      Dynamin_N 103 ltlvDlPGldsvnkrd 118
                                    l ++D+PG+  +  ++
  gi|119719733|ref|YP_920228.1| 149 LRVIDTPGVVPRMSQE 164
                                    568*****97665555 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   1.8e-05     0.029     110     167 ..      11      67 ..       3      74 .. 0.84
   2 ?   -0.5   0.1       0.5   8.2e+02       2      20 ..     104     122 ..     103     129 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.8e-05
                                    CCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HHHHCHC..HHHHHHHHH CS
                           cobW 110 ltldavvavvDaknleaeeekieekaedqlaaadllvlnKtDlldeeallekleerlr 167
                                    +++d+vv vvDa+   a ++++ e +   l +  l+v+nK Dl++ + l ek +++l+
  gi|119719733|ref|YP_920228.1|  11 ARADVVVEVVDARDPWATRSPEIERYAVRLGKPLLVVVNKSDLVPRDVL-EKWRKVLE 67 
                                    6789********9998999999999********************9943.66665554 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.5
                                    EEEEEESTTCCHHHHHHHH CS
                           cobW   2 vtvltGflGsGKTtLlnhl 20 
                                    v  ++G +  GK+t++n l
  gi|119719733|ref|YP_920228.1| 104 VAAVVGIPNVGKSTIINYL 122
                                    567899999*******986 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.09   1.5e+02     116     141 ..      42      67 ..       7      88 .. 0.78
   2 ?   11.3   0.0    0.0001      0.17      18      50 ..     106     138 ..      89     148 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.09
                                    SEEEEEEE-TTSTTSS-HHHHHHHTT CS
                            Arf 116 vallvlaNKqDlpealseeelrellg 141
                                     +llv+ NK Dl      e+ r+ l+
  gi|119719733|ref|YP_920228.1|  42 KPLLVVVNKSDLVPRDVLEKWRKVLE 67 
                                    579999***99987666666666555 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.0001
                                    EEEESTTSSHHHHHHHHHHSSCEECSSSSSEEE CS
                            Arf  18 lllGLDnaGKtTilkklkleelvttvPTigfnv 50 
                                     ++G+ n GK+Ti++ lk  + v t+P  gf+ 
  gi|119719733|ref|YP_920228.1| 106 AVVGIPNVGKSTIINYLKGSHSVGTSPIPGFTK 138
                                    589************************999974 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     7e-05      0.11      56      95 ..      42      85 ..      37      91 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7e-05
                   MMR_HSR1_Xtn 56 ipclyvlNKiDlisleeldelare....pnsvviSaekelnlde 95
                                   +p l+v+NK Dl+  + l++ ++       +v+iSa k+++   
  gi|119719733|ref|YP_920228.1| 42 KPLLVVVNKSDLVPRDVLEKWRKVlekhFPVVFISATKRMGTRM 85
                                   5899*********99999999884443347889****9988655 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00018      0.29       3      21 ..     107     125 ..     106     178 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00018
                         AAA_18   3 ltGtpGvGKttlakeLskr 21 
                                    + G+p vGK+t+ ++L+ +
  gi|119719733|ref|YP_920228.1| 107 VVGIPNVGKSTIINYLKGS 125
                                    89**************655 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.46   7.5e+02     171     182 ..      45      56 ..      43      94 .. 0.61
   2 ?    9.0   0.1   0.00039      0.63      26      49 ..      99     122 ..      72     133 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.46
                                    EEEEE---..HHHH CS
                           MeaB 171 iivvnkaD..kkea 182
                                    ++vvnk+D  +   
  gi|119719733|ref|YP_920228.1|  45 LVVVNKSDlvP--R 56 
                                    57888888442..2 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00039
                                    -S-SEEEEEEE-TTSSHHHHHHHH CS
                           MeaB  26 aGraqvvGltGvPGaGkstlveal 49 
                                     G+  v  + G+P +Gkst+++ l
  gi|119719733|ref|YP_920228.1|  99 RGKPVVAAVVGIPNVGKSTIINYL 122
                                    47777889*************987 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00052      0.85      61     133 ..      10      82 ..       3      92 .. 0.75
   2 ?   -2.8   0.0         3   4.8e+03       7      23 ..     108     124 ..     106     128 .. 0.80
   3 ?   -2.5   0.0       2.4   3.9e+03      39      45 ..     150     156 ..     144     162 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00052
                      PduV-EutP  61 saeadvialvqdateeesvfppgfasv...fnkeviGiitkidlaedeenieaveelLksaGaekifevsavekeg 133
                                     a adv++ v+da +++ + +p++ +    + k+++ ++ k dl+  ++ +e+ ++ L++     +  +sa+++ g
  gi|119719733|ref|YP_920228.1|  10 IARADVVVEVVDARDPWATRSPEIERYavrLGKPLLVVVNKSDLV-PRDVLEKWRKVLEKH--FPVVFISATKRMG 82 
                                    5789*****************987554222889***********9.778888888888764..2334455555555 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3
                      PduV-EutP   7 iGkvgsGKttLtqalkg 23 
                                    +G  ++GK t+ + lkg
  gi|119719733|ref|YP_920228.1| 108 VGIPNVGKSTIINYLKG 124
                                    78888999999999887 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 2.4
                      PduV-EutP  39 eviDtPG 45 
                                    +viDtPG
  gi|119719733|ref|YP_920228.1| 150 RVIDTPG 156
                                    58****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 1901.47
//
Query:       gi|119719734|ref|YP_920229.1|  [L=283]
Description: N-glycosylase/DNA lyase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.2e-65  219.0   0.0    7.2e-65  218.8   0.0    1.0  1  AGOG      N-glycosylase/DNA lyase


Domain annotation for each model (and alignments):
>> AGOG  N-glycosylase/DNA lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  218.8   0.0     4e-69   7.2e-65       2     247 ..      14     255 ..      13     256 .. 0.95

  Alignments for each domain:
  == domain 1  score: 218.8 bits;  conditional E-value: 4e-69
                                    HHHCCCHHHHHHHHHCCTSHHHHHHHHHHCCC-H...HHHHHHHHHHHHT-SS-TT-HHHHHHHHHHHHCTS--SSHHHH CS
                           AGOG   2 ellkelgieevlkleekvDpQykaveelveklged..elfvklvilNaLvSYqLsgrGEewWkefskyfsekeiknilee 79 
                                    e+++    e  l ++e+ DpQ+ av++++ek+g +   ++v+ v   aLvSY+Ls+rGE++W e +++f       +  +
  gi|119719734|ref|YP_920229.1|  14 EIFRGSIRELSLLFVER-DPQFLAVRKILEKAGFPegGFYVAGV---ALVSYMLSKRGEDHWLEAAELFD-----GTPGA 84 
                                    78999999999******.***************997799*****...**********************8.....78899 PP

                                    HHHHHHH-TTS-TTHHHHHHHHHHHCCHHHTTTHHHHHHHH.HTHHHHHHHHHHHHTS-TTSHHHHHHHHHHHHHHHHHH CS
                           AGOG  80 fikflekskgnrrlreakikRiekivefledleleelksyl.enleelleelakilgskkesKTvvFavKmlyYalrial 158
                                    +++f+e+++++rr+re+++kRi+++v+++e++    l s++ +nle++++++a+i+g+++e+KTvvFa Kml Ya++ a+
  gi|119719734|ref|YP_920229.1|  85 LYRFVEEAESLRRFREHRVKRIKRYVASREKVLS--LLSEVpVNLERFASTVARIVGANPEDKTVVFASKMLLYACI-AA 161
                                    99****************************9994..666666**********************************9.99 PP

                                    TS-----TTS-----HHHHHHHHHTTS-SS-HHHHHHTHCCHC......S.HHHHHHHHHHHHT--HHHHHHHHHHHCCH CS
                           AGOG 159 geeiplpfeipiPvDvRiakltktsglielknekklarkelvq......eevieaWkevsreseiPplhlDsllWvlgks 232
                                    ++e++  +++piPvD+R++ +t+tsg+++ +++ +  r+++ +      eev++aW+ v+r++eiPp+ lD+ +W l++ 
  gi|119719734|ref|YP_920229.1| 162 NKEYTGGERLPIPVDYRVSLVTLTSGIAKGWSCLDDLRAHASNlrakhkEEVKAAWSLVGRQAEIPPILLDAPVW-LVGG 240
                                    999**************************************999999999*************************.7778 PP

                                    HHCCS-HCCCCCHHH CS
                           AGOG 233 aleledaevkellkk 247
                                    ++++ d+evk+++++
  gi|119719734|ref|YP_920229.1| 241 CIDRGDFEVKRIDEC 255
                                    88********98775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2010.67
//
Query:       gi|119719735|ref|YP_920230.1|  [L=452]
Description: phosphoglucomutase/phosphomannomutase alpha/beta/subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.7e-15   56.3   0.3    8.8e-15   54.6   0.1    1.9  3  PGM_PMM_I    Phosphoglucomutase/phosphomannomutase, alpha/bet
      3e-07   31.0   0.0    7.7e-07   29.7   0.0    1.7  1  PGM_PMM_II   Phosphoglucomutase/phosphomannomutase, alpha/bet
    3.4e-05   24.0   0.0     0.0001   22.4   0.0    1.8  2  PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/bet


Domain annotation for each model (and alignments):
>> PGM_PMM_I  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.6   0.1   1.5e-18   8.8e-15      11     133 ..      15     133 ..      10     137 .. 0.91
   2 ?   -4.0   0.0       1.9   1.1e+04      49      61 ..     231     243 ..     229     251 .. 0.78
   3 ?   -2.7   0.0      0.72   4.3e+03      65      85 ..     309     329 ..     305     336 .. 0.74

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 1.5e-18
                                    EECCHCTBSCCHHHHHHHHHHHHCHHCSTS-EEEEEE-S-TTHHHHHHHHHHHHHCCT-CEEEEEEB-HHHHHHHHHHCC CS
                      PGM_PMM_I  11 gkvgegeltpelveklgqaiaeylkaeakkkkvvvGrDtRvssrelaealaaglaanGvevillgllptPavsfairklk 90 
                                    g+++ ++ltpe++++lg+ ++++l +   ++ vv +rD    sr+l++a+ +gl+++G +vi+++ ++ P+++fa+++++
  gi|119719735|ref|YP_920230.1|  15 GVAN-TQLTPENMAELGAVLGTILGE---GALVVAARDLYPPSRMLKRAFTSGLMSTGNSVIDFHAATLPELAFAVKRFG 90 
                                    6777.77******************9...799************************************************ PP

                                    ECEEEEE--TTS-TTCCCEEEEETTTCE--CHHHHHHHHHHCC CS
                      PGM_PMM_I  91 adagimitaSHnppeyngiKvylsnGgpispeveekIeaiiek 133
                                    a+ag+ ++      +   +K++++ G+++s e+ + I + +e+
  gi|119719735|ref|YP_920230.1|  91 AKAGVHFSVAPYNTDGIQVKIVDAGGVELSYEKLADILDMYET 133
                                    *****99886665555559*************99999998876 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 1.9
                                    S-TTHHHHHHHHH CS
                      PGM_PMM_I  49 tRvssrelaeala 61 
                                    tR+ss+ +a+al 
  gi|119719735|ref|YP_920230.1| 231 TRASSPAFAAALS 243
                                    6888888888875 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 0.72
                                    HCCT-CEEEEEEB-HHHHHHH CS
                      PGM_PMM_I  65 aanGvevillgllptPavsfa 85 
                                    +a Gv++i +g++ t+   f+
  gi|119719735|ref|YP_920230.1| 309 VARGVKKIKAGIAATDSGEFI 329
                                    688999999999999766655 PP

>> PGM_PMM_II  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.0   1.3e-10   7.7e-07       2     103 .]     156     256 ..     155     256 .. 0.87

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 1.3e-10
                                    HHHHHGGGTS-HHHHHHHT-EEEEE-TT-TTHHHHHHHHHHTT-EEEES-----TT-TT..SS----TT-TTTTHHHHGG CS
                     PGM_PMM_II   2 aYiealkekvdseaikksglkvvidplhGaggeilkellkelgvdvvelnaepdpdfpt..kapnpeekealkllielvk 79 
                                     Y+ + ++ +d++ i+ ++  v++d+ +G ++++l+   ++lg+++v + a + p  +   + p p+   ++++l+++ +
  gi|119719735|ref|YP_920230.1| 156 IYVTSAASFIDTSPIAAKEPLVIVDVNYGPASDVLPNFVGSLGARLVAVKAGRPPPGVRpqQLPSPR---DIAMLQDITR 232
                                    599999*****9999999999***********************99998877776333323555555...5********* PP

                                    GGG-SEEEEE-TTS-BEEEEETTE CS
                     PGM_PMM_II  80 kegadlglafDgDaDRlgvvderG 103
                                    +++  +++a+  Da ++++vd++G
  gi|119719735|ref|YP_920230.1| 233 ASSPAFAAALSADASQVFIVDDKG 256
                                    *********************987 PP

>> PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.2   7.1e+03      30      51 ..     186     207 ..     181     209 .. 0.85
   2 !   22.4   0.0   1.7e-08    0.0001       2     111 ..     261     365 ..     260     367 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.2
                                    S-THHHHHHHHTT-EEEEESSS CS
                    PGM_PMM_III  30 tslalervakklgiklvetkvG 51 
                                     s++l +++ +lg++lv +k G
  gi|119719735|ref|YP_920230.1| 186 ASDVLPNFVGSLGARLVAVKAG 207
                                    6788999999999999999998 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 1.7e-08
                                    HHHHHHHHHHHHHCHCSTTTCEEEEETTS-THHHHHHHHTT-EEEEESSSCHHHHHHHHHTTECEEEETTCEEEETTTBS CS
                    PGM_PMM_III   2 gdqllallakylleeklkpgagvvktvmtslalervakklgiklvetkvGdkyvleemkeegavlGgEeSghiifldeat 81 
                                    +d+l+a +a  l     ++ga ++ + +  ++++ +a+k+++ l+++k     v++ +k+ +a ++   Sg +if+++++
  gi|119719735|ref|YP_920230.1| 261 PDKLVAAVALML-----PEGARIAVSDSAGRIVDVAAEKNKLYLLRVKGLAGDVARGVKKIKAGIAATDSGEFIFPQFSY 335
                                    677777777755.....456679999999******************9878889************************** PP

                                    S--HHHHHHHHHHHHHHHTS-HHHHHHHHH CS
                    PGM_PMM_III  82 tkDGilaallvleilaetgkslselleell 111
                                      DG+l + ++le+l++++  ls+++e l+
  gi|119719735|ref|YP_920230.1| 336 SPDGMLFIGKLLELLSTQEVRLSTIIETLP 365
                                    *************************97765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (452 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 3329.08
//
Query:       gi|119719736|ref|YP_920231.1|  [L=388]
Description: nucleotidyl transferase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-40  138.2   0.0    4.1e-40  137.9   0.0    1.1  1  NTP_transferase  Nucleotidyl transferase
    2.2e-14   52.5  12.9    8.7e-06   25.3   4.0    3.9  3  Hexapep          Bacterial transferase hexapeptide (six repea
    4.5e-12   46.6   0.0    6.2e-12   46.2   0.0    1.3  1  NTP_transf_3     MobA-like NTP transferase domain
     0.0018   17.3   0.1      0.048   12.6   0.0    2.1  2  Fucokinase       L-fucokinase
  ------ inclusion threshold ------
       0.38   10.6  13.2        5.1    6.9   0.8    4.8  4  Hexapep_2        Hexapeptide repeat of succinyl-transferase


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.9   0.0   1.1e-43   4.1e-40       2     245 ..       5     253 ..       4     256 .. 0.95

  Alignments for each domain:
  == domain 1  score: 137.9 bits;  conditional E-value: 1.1e-43
                                    EEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEEEES CS
                NTP_transferase   2 avILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlialep 81 
                                    av+LaGG+G RL+PLt t++k+l+pv++  +++++ ls l ++g+e++iv +++  + +v+  +++  + g  ++i+  p
  gi|119719736|ref|YP_920231.1|   5 AVVLAGGKGVRLRPLTLTTPKPLLPVGNV-PILDHILSLLYRHGFEKVIVAVNYLGEKIVNHLVARWMDKG--LEIVAPP 81 
                                    89***************************.*****************999999999999999999999988..6666666 PP

                                    S--.BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEECTTSBEE CS
                NTP_transferase  82 egk.gtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGvieadeegrve 160
                                     +  +tAdAv++ a ++++++     lv  gD++++++++ +  +++++++  ++++++ +v+  +++G +  d++g+v 
  gi|119719736|ref|YP_920231.1|  82 LNPaDTADAVRKCASYIDEDF-----LVTMGDVVTNMDLRSFAYFHESSGS--IASIALIEVQSLRDFGAVLLDGNGAVL 154
                                    5556*************9776.....9************************..*************************** PP

                                    EEECS-SSHSH...................CSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEE CS
                NTP_transferase 161 rfvEKPkeaka...................selassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaf 221
                                    +f EKP  ++                    ++la+sG Y f  ++l+ l    +e +   d++++++p +le+ ++    
  gi|119719736|ref|YP_920231.1| 155 HFLEKPGVQEMyvaslafaftgtsrkvnlfANLANSGFYAFRYDILDVL----RENPHLMDFGKNVFPWLLENNYRVKGW 230
                                    ************************************************9....6999*******************9999 PP

                                    CSTTEE-EEEXSSHHHHHHHHHHH CS
                NTP_transferase 222 lfkdaeyWsDvGtldslleanekl 245
                                    l++ + yW DvG ++s+l+an +l
  gi|119719736|ref|YP_920231.1| 231 LAEET-YWIDVGRPESYLTANFDL 253
                                    99996.9************99776 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.2   1.6e-08   5.9e-05       2      35 ..     271     304 ..     270     305 .. 0.95
   2 !    8.5   0.1   0.00047       1.7       2      26 ..     307     331 ..     306     342 .. 0.89
   3 !   25.3   4.0   2.4e-09   8.7e-06       1      36 []     346     381 ..     346     381 .. 0.96

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.6e-08
                                    EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                        Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                    + +G++v + p+a i ++V +Gdnv+I  ++ +g
  gi|119719736|ref|YP_920231.1| 271 VYVGEGVEVSPGARIIPPVALGDNVRISQNAEVG 304
                                    789****************************997 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00047
                                    EEEETTEEE-TTEEEETTEEE-TTE CS
                        Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnv 26 
                                    +vIGs+++Ig  a++   V  G+++
  gi|119719736|ref|YP_920231.1| 307 AVIGSDTHIGVEAHVSYSVLMGEDT 331
                                    79*********99999999999887 PP

  == domain 3  score: 25.3 bits;  conditional E-value: 2.4e-09
                                    TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEEES CS
                        Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvigg 36 
                                    s+++G++++++ ++v+g++V++ +++++g+g++igg
  gi|119719736|ref|YP_920231.1| 346 SIKVGEGAVVRENSVLGEGVVVKEGSIVGPGTRIGG 381
                                    579*******************************97 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.2   0.0   1.7e-15   6.2e-12       1     111 [.       5     122 ..       5     184 .. 0.84

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 1.7e-15
                                    EEEEEESS-TTTT.....TTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHH....TTCTS-EEE-TTSS CS
                   NTP_transf_3   1 aviLAGGrSsRmg.....gdKallplggkpllervldalraagvdevvvvggd..eevlaal....arlgvrvvededpg 69 
                                    av+LAGG++ R+      ++K+llp+g+ p+l+++l  l ++g+++v+v++++  e++ ++l     ++g+++v+ +   
  gi|119719736|ref|YP_920231.1|   5 AVVLAGGKGVRLRpltltTPKPLLPVGNVPILDHILSLLYRHGFEKVIVAVNYlgEKIVNHLvarwMDKGLEIVAPPLNP 84 
                                    79**********7554435**********************************8854444332222677*********** PP

                                    -SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCH CS
                   NTP_transf_3  70 kgplaslaaalraaadadavlvlacDmPlltpelverllaaa 111
                                    + ++ +++  ++ +  ++ +lv+++D++  t   ++ ++  +
  gi|119719736|ref|YP_920231.1|  85 ADTADAVRKCASYI--DEDFLVTMGDVV--TNMDLRSFAYFH 122
                                    ************98..799*******94..566666666554 PP

>> Fucokinase  L-fucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.015        54      51     147 ..     101     199 ..      89     207 .. 0.58
   2 !   12.6   0.0   1.3e-05     0.048     259     310 ..     321     373 ..     299     380 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.015
                     Fucokinase  51 GvlvtssDvlllf.dseeisfdka.gvtalavpstldigtnHGVfvlddqsseeeeleirsvkkflhKpseeelqasgav 128
                                     +lvt +Dv+  +   +++ f+++ g +a     +++  ++ G ++ld++         + v +fl Kp ++e+    + 
  gi|119719736|ref|YP_920231.1| 101 DFLVTMGDVVTNMdLRSFAYFHESsGSIASIALIEVQSLRDFGAVLLDGN---------GAVLHFLEKPGVQEMYVASLA 171
                                    56777777777664233334444335555555566667777777777777.........778888888888887744333 PP

                     Fucokinase 129 lkd.........ekvlldsGvvffdhkt 147
                                    +              l  sG+++f++++
  gi|119719736|ref|YP_920231.1| 172 FAFtgtsrkvnlFANLANSGFYAFRYDI 199
                                    3224555555544444556666665555 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 1.3e-05
                     Fucokinase 259 afsaiknkkekkkesavvinSvlessvsvgegsvi.ehsslkgnvsigsnsiv 310
                                    ++  +   +++ +++a v  Svl++s++vgeg+v+ e+s l+++v ++++siv
  gi|119719736|ref|YP_920231.1| 321 VSYSVLMGEDTVERGAHVRYSVLAKSIKVGEGAVVrENSVLGEGVVVKEGSIV 373
                                    44444445555689999999***********99994589999*********98 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.6    0.0057        20      14      28 ..     283     299 ..     270     305 .. 0.69
   2 ?    4.5   0.2    0.0082        29       5      17 ..     292     304 ..     288     322 .. 0.44
   3 ?    0.6   0.0      0.14     5e+02       3      15 ..     308     320 ..     306     330 .. 0.73
   4 ?    6.9   0.8    0.0014       5.1      15      32 ..     350     367 ..     337     369 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0057
                                    -EE..SEEE-TT-EE-T CS
                      Hexapep_2  14 agi..GvslGdncvvga 28 
                                    a i  +v lGdn+ ++ 
  gi|119719736|ref|YP_920231.1| 283 ARIipPVALGDNVRISQ 299
                                    44346799999998875 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0082
                                    -TT-EE-TT-EES CS
                      Hexapep_2   5 GdnCliGanagiG 17 
                                    Gdn+ i  na++G
  gi|119719736|ref|YP_920231.1| 292 GDNVRISQNAEVG 304
                                    4444444444443 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.14
                                    EE-TT-EE-TT-E CS
                      Hexapep_2   3 iIGdnCliGanag 15 
                                     IG ++ iG+ a 
  gi|119719736|ref|YP_920231.1| 308 VIGSDTHIGVEAH 320
                                    5888888888775 PP

  == domain 4  score: 6.9 bits;  conditional E-value: 0.0014
                                    EESEEE-TT-EE-TT-EE CS
                      Hexapep_2  15 giGvslGdncvvgaGvvi 32 
                                    g G  +++n+v+g Gvv+
  gi|119719736|ref|YP_920231.1| 350 GEGAVVRENSVLGEGVVV 367
                                    458889999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2677.18
//
Query:       gi|119719737|ref|YP_920232.1|  [L=172]
Description: hypothetical protein Tpen_0828 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1280.80
//
Query:       gi|119719738|ref|YP_920233.1|  [L=273]
Description: hypothetical protein Tpen_0829 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.4e-58  195.7  11.9    8.8e-58  195.5  11.9    1.0  1  DUF92        Integral membrane protein DUF92
  ------ inclusion threshold ------
        0.2   11.2   0.0       0.34   10.4   0.0    1.3  1  Mu-like_Com  Mu-like prophage protein Com


Domain annotation for each model (and alignments):
>> DUF92  Integral membrane protein DUF92
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.5  11.9   9.8e-62   8.8e-58       5     235 ..      16     262 ..      12     263 .. 0.92

  Alignments for each domain:
  == domain 1  score: 195.5 bits;  conditional E-value: 9.8e-62
                          DUF92   5 llalralrkksLtpsGalaavlvgvlialaplgllffllllvFfllgslltkvkkkvKakleeek.egaRdavqVlansl 83 
                                     la++a rkk L++s+a+a+v++  l +++++g  +f++ l+Ff+++s+ltk++++ K++++ ++ e++R+ +qV++ ++
  gi|119719738|ref|YP_920233.1|  16 PLAAYARRKKYLSRSAAAASVIFSGLYMAGGIG--VFAASLFFFFSSSALTKLGYDLKRRMNVSEpEEGRTLMQVVGAGG 93 
                                    58999********************99999888..9***********************9888885677*********** PP

                          DUF92  84 valllally......lasdlllvgivasyAavaaDTlaSElGkilskskprlittl.kkvppGtnGgVsllGllasllGa 156
                                    va+l +ll+      + +  llvg+ a++A ++aDT+aSElG+++++ kprlit+l  +v+pGt+GgV+llG l sl+G+
  gi|119719738|ref|YP_920233.1|  94 VAALYSLLSalspqsA-RVPLLVGAYAAIASSNADTWASELGSLSGR-KPRLITNLsVEVEPGTSGGVTLLGALGSLAGS 171
                                    *********8877642.67789********************88777.********889********************* PP

                          DUF92 157 lliallavlllllel.......lillltlaGllGsllDSlLGatlqasvvdkrtgkvvegegge.....kvvsGldlLdN 224
                                    ll +l+a+++ ll +        i+++++aG+lG +lDS++Gatlq +++++r+g  + ++ ++     +  sG ++++N
  gi|119719738|ref|YP_920233.1| 172 LLTGLVALIASLLGAspplgvaTIAVVVVAGWLGEVLDSVVGATLQVKYYCPRCGVLTDKKVHScgattVKYSGSSWVTN 251
                                    ****99777776666899**999999*********************************988889***9778******** PP

                          DUF92 225 naVNllsallt 235
                                    +  N++++ll 
  gi|119719738|ref|YP_920233.1| 252 EVTNIIATLLS 262
                                    ********986 PP

>> Mu-like_Com  Mu-like prophage protein Com
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   3.8e-05      0.34      23      42 ..     218     237 ..     208     244 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 3.8e-05
                    Mu-like_Com  23 ltiKCPRCGtLnHlkaesld 42 
                                    ++  CPRCG L   k  s  
  gi|119719738|ref|YP_920233.1| 218 VKYYCPRCGVLTDKKVHSCG 237
                                    4555*******988877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       718  (0.0400469); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1938.62
//
Query:       gi|119719739|ref|YP_920234.1|  [L=410]
Description: hypothetical protein Tpen_0830 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.3e-15   56.2   2.0    3.3e-15   56.2   2.0    3.3  3  NfeD      NfeD-like C-terminal, partner-binding
    0.00019   20.5   0.0    0.00033   19.8   0.0    1.3  1  SDH_sah   Serine dehydrogenase proteinase
  ------ inclusion threshold ------
      0.053   14.3   0.0       0.15   12.8   0.0    1.8  1  ASL_C2    Argininosuccinate lyase C-terminal
       0.56   10.1   2.9        1.3    8.9   1.3    2.1  2  TMEM154   TMEM154 protein family


Domain annotation for each model (and alignments):
>> NfeD  NfeD-like C-terminal, partner-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.3      0.45     2e+03      52      77 ..      38      64 ..      23      70 .. 0.63
   2 ?   -3.2   0.1       2.5   1.1e+04       3       9 ..     288     294 ..     282     305 .. 0.49
   3 !   56.2   2.0   7.3e-19   3.3e-15       4      84 .]     321     403 ..     314     403 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.45
                                   TTEEEEEE-..SSB-TT-EEEEEEE-S CS
                           NfeD 52 dGeeWsars.egeiekgerVrVveveG 77
                                   +G++++++   +e +kg  V+V++  G
  gi|119719739|ref|YP_920234.1| 38 EGAYYTVKRgLEEADKGVVVVVIRSYG 64
                                   367777743156677788888877666 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.5
                                    XXXXXXX CS
                           NfeD   3 avvsvll 9  
                                    a v++++
  gi|119719739|ref|YP_920234.1| 288 AGVALIA 294
                                    2333333 PP

  == domain 3  score: 56.2 bits;  conditional E-value: 7.3e-19
                                    XXXXXXXXXXXXXS---SSS--S..S---GGTTSEEEEEE-B..S.-EEEEETTEEEEEE-.SSB-TT-EEEEEEE-SSS CS
                           NfeD   4 vvsvlllvllrplllkklkkkek.ktnaealiGkegvvledi..g.tGrvkvdGeeWsarsegeiekgerVrVveveGlt 79 
                                    ++ vlll+++   +l + +   k ++ +e+liGk+gv+ ++i  g +G v vdGe W+a se  +e+ge V+Vv+ +Gl 
  gi|119719739|ref|YP_920234.1| 321 AILVLLLAVVISKALETVRM--KaPSLQERLIGKIGVAKTRIepGkRGVVYVDGEDWTATSEYVVEEGESVEVVALDGLF 398
                                    22222332222223333322..24588889************99668**************888**************** PP

                                    EEEEE CS
                           NfeD  80 liVep 84 
                                    l+V+p
  gi|119719739|ref|YP_920234.1| 399 LKVKP 403
                                    ***98 PP

>> SDH_sah  Serine dehydrogenase proteinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   7.3e-08   0.00033      94     178 ..      56     147 ..      43     163 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 7.3e-08
                        SDH_sah  94 idliihtpGGlvlaatqiakalkehkaktrvivp..hyamsGGtlialaadeiildenavlG.....pvdpqlgqypaas 166
                                    + ++i + GG   + ++i + l++ +a+t   vp    ++s  ++ial+a+++ + + av+G     p dp+  +y  a 
  gi|119719739|ref|YP_920234.1|  56 VVVVIRSYGGYLKSMDKIVELLVSSEARTIAWVPpgERTVSAAAVIALSAQRLYMGKGAVIGsikpyPDDPKTVEYVVAR 135
                                    45789999*************************9555799**********************555555589999999999 PP

                        SDH_sah 167 ilkvvekkeakd 178
                                    +   + kk+ +d
  gi|119719739|ref|YP_920234.1| 136 VAALLSKKGVND 147
                                    999999999766 PP

>> ASL_C2  Argininosuccinate lyase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   3.4e-05      0.15       3      31 ..     176     204 ..     175     217 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.4e-05
                                    THHHHHHHHHHCTS-HHHHHHHHHHHHHH CS
                         ASL_C2   3 tATdlADyLvrkGlpFReAHeivgravrl 31 
                                    tA  lA++L ++Gl+F   H ++g +v++
  gi|119719739|ref|YP_920234.1| 176 TADSLAELLQKEGLSFASVHYVSGDLVSD 204
                                    56779**********************87 PP

>> TMEM154  TMEM154 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.21   9.6e+02      18      80 ..     163     226 ..     155     231 .. 0.72
   2 ?    8.9   1.3   0.00029       1.3      58      77 ..     312     331 ..     309     347 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.21
                        TMEM154  18 eeesadatsaasteseslkqeeakeslssaelsnesdqlel.vlmiiiPlvllillllvviili 80 
                                    ++  a at +a  + +sl++ ++ke ls+a ++  s +l   +l +++   l +ll l++++l 
  gi|119719739|ref|YP_920234.1| 163 TSDEAVATGIADGTADSLAELLQKEGLSFASVHYVSGDLVSdLLSVLLDPALAVLLALLGAMLL 226
                                    5555667777777799999999999999999999887765437777776677777777777664 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00029
                        TMEM154  58 lvlmiiiPlvllillllvvi 77 
                                    +vl++++Pl +l+lll vvi
  gi|119719739|ref|YP_920234.1| 312 NVLVVAVPLAILVLLLAVVI 331
                                    79*******99999887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       989  (0.055162); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 2725.69
//
Query:       gi|119719740|ref|YP_920235.1|  [L=285]
Description: hypothetical protein Tpen_0831 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2136.24
//
Query:       gi|119719741|ref|YP_920236.1|  [L=289]
Description: band 7 protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.8e-33  114.2   6.6    6.8e-33  114.2   6.6    1.6  2  Band_7    SPFH domain / Band 7 family
     0.0016   18.2   0.2     0.0041   16.9   0.1    1.9  2  Band_7_1  SPFH domain-Band 7 family


Domain annotation for each model (and alignments):
>> Band_7  SPFH domain / Band 7 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.2   6.6   7.5e-37   6.8e-33       2     177 ..      26     195 ..      25     207 .. 0.96
   2 ?   -1.4   0.3      0.23     2e+03     162     177 ..     213     228 ..     195     229 .. 0.46

  Alignments for each domain:
  == domain 1  score: 114.2 bits;  conditional E-value: 7.5e-37
                         Band_7   2 iieegevgvvvrfGklsrvlepGlhfilPfgrsvtvvsvrvqtldvsvsltvptkDglpvtidvtviyrvpddapklvaa 81 
                                    i++e +++vv r G+++r+ +pGl   +Pf+++ +vv++r q+++v++ +t++t+D+ pv+id+ ++++v  d++k v +
  gi|119719741|ref|YP_920236.1|  26 IVPEYQRLVVLRLGRVVRIAGPGLVVLVPFIEQGIVVDLREQYIEVTK-QTCITRDNAPVDIDFLIYFKV-VDPKKSVVE 103
                                    79**********************************************.*********************.********* PP

                         Band_7  82 veresanldnlirrvlesalrevisemtleellsnreelaeelknelneqlrkyGvevldvritdidpppevaqalaakq 161
                                    v    ++ +     ++  +lr+v+++ +l+++l++re ++e l+++l e  +++Gv v+ v i++i pp+ev++a+ + +
  gi|119719741|ref|YP_920236.1| 104 V----QDFRGAAVGIATTTLRAVVGDIELDQVLAKREYINEVLREKLDEVTARWGVKVTAVEIREILPPKEVQDAMIKQM 179
                                    *....*************************************************************************** PP

                         Band_7 162 aaeaeaqaeiaraeae 177
                                     ae+ ++a + +ae++
  gi|119719741|ref|YP_920236.1| 180 SAERNRRAMVTEAEGK 195
                                    *****97777777654 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.23
                         Band_7 162 aaeaea....qaeiaraeae 177
                                    +    a    qa+i +ae++
  gi|119719741|ref|YP_920236.1| 213 R----AegekQAAILKAEGQ 228
                                    2....133336666666665 PP

>> Band_7_1  SPFH domain-Band 7 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0      0.61   5.4e+03      18      42 ..      26      50 ..      25      53 .. 0.82
   2 !   16.9   0.1   4.5e-07    0.0041     154     209 ..     126     181 ..      91     183 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.61
                       Band_7_1 18 ivregqeavfvneGqiaDvfapGty 42
                                   iv e q+ v ++ G++  + +pG  
  gi|119719741|ref|YP_920236.1| 26 IVPEYQRLVVLRLGRVVRIAGPGLV 50
                                   7888899999999999999999865 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 4.5e-07
                       Band_7_1 154 ipvldlaakseelaeklkealkeelaeyGlelekleienislpeevekaldkrasm 209
                                    i + ++ ak e + e l+e+l+e  a+ G++++++ei++i  p+ev+ a+ k+ s+
  gi|119719741|ref|YP_920236.1| 126 IELDQVLAKREYINEVLREKLDEVTARWGVKVTAVEIREILPPKEVQDAMIKQMSA 181
                                    555567799999*************************************9998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1005  (0.0560544); expected 358.6 (0.02)
Passed bias filter:                      631  (0.0351944); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2180.82
//
Query:       gi|119719742|ref|YP_920237.1|  [L=227]
Description: hypothetical protein Tpen_0833 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-15   57.5  13.4    2.2e-09   37.5   4.0    3.4  3  Bactofilin      Polymer-forming cytoskeletal
     0.0054   16.9   0.8      0.059   13.5   1.0    2.5  2  Pentapeptide_3  Pentapeptide repeats (9 copies)
  ------ inclusion threshold ------
      0.021   14.7   2.4        1.3    9.0   0.0    3.0  3  DUF3672         Fibronectin type III protein
      0.021   14.9   0.3         14    5.8   0.0    3.4  3  Phage_spike     Phage spike trimer
        3.2    7.6   8.1         14    5.5   0.2    2.9  3  Histone_H2A_C   C-terminus of histone H2A


Domain annotation for each model (and alignments):
>> Bactofilin  Polymer-forming cytoskeletal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.5   4.0   6.2e-13   2.2e-09      17      97 ..      19     100 ..      14     101 .. 0.88
   2 !   10.7   0.0   0.00014      0.51      41      82 ..      94     134 ..      90     145 .. 0.79
   3 !   17.3   1.3   1.2e-06    0.0043      13      48 ..     186     221 ..     181     225 .. 0.80

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 6.2e-13
                     Bactofilin  17 gdlridG..kveGdieakgklvvgeggkvegnikaeevvvaGt..vkGnveaeekvelkktakveGdikaksleieegav 92 
                                    g + i+G   v+G +++k  ++++ +g+v+g+++ae+v+v+G+  ++G+v ae kv+ +++++ +G++ka+s +++    
  gi|119719742|ref|YP_920237.1|  19 GRVTIAGsgVVSGGVYEK--VTIAGSGVVDGDLEAESVSVSGSarFEGDVSAE-KVRCAGSCRFSGSVKAESARFSGATI 95 
                                    567775533889999666..**********************97788*****9.**********************9999 PP

                     Bactofilin  93 feGkl 97 
                                    +eG+l
  gi|119719742|ref|YP_920237.1|  96 VEGEL 100
                                    99986 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00014
                     Bactofilin  41 gkvegnikaeevvvaGtvk.GnveaeekvelkktakveGdika 82 
                                    + veg++++ee++vaG+++ G v+a+  ++l+++ +v Gd++a
  gi|119719742|ref|YP_920237.1|  94 TIVEGELSSEELKVAGSLRaGRVKAR-DLRLSGSFRV-GDVEA 134
                                    56899999999999999877999999.8888877776.66655 PP

  == domain 3  score: 17.3 bits;  conditional E-value: 1.2e-06
                     Bactofilin  13 levegdlridG.kveGdieakgklvvgeggkvegnik 48 
                                    +e e+ ++++G  +eGd++ak k+v+++gg+v+gni+
  gi|119719742|ref|YP_920237.1| 186 IEAENIVDVEGvVIEGDVNAK-KVVLRRGGEVRGNIS 221
                                    677888999995559999888.999999999999987 PP

>> Pentapeptide_3  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   1.0   1.6e-05     0.059       4      37 ..      60      94 ..      56     100 .. 0.70
   2 ?   -1.9   0.0       1.1     4e+03      29      43 ..     190     204 ..     179     205 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.6e-05
                 Pentapeptide_3  4 anFsgaadFrgatFsgaasFsnadF.gsadFsgar 37
                                   a+F+g+++ ++++  g+ +Fs+++  +sa+Fsga+
  gi|119719742|ref|YP_920237.1| 60 ARFEGDVSAEKVRCAGSCRFSGSVKaESARFSGAT 94
                                   67777777777777777777777776677777766 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.1
                 Pentapeptide_3  29 gsadFsgarFtgdvd 43 
                                    + +d +g+ ++gdv+
  gi|119719742|ref|YP_920237.1| 190 NIVDVEGVVIEGDVN 204
                                    467888888888886 PP

>> DUF3672  Fibronectin type III protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1    0.0088        32      14      45 ..      23      54 ..      18      73 .. 0.75
   2 ?    9.0   0.0   0.00035       1.3      10      45 ..      75     116 ..      66     121 .. 0.77
   3 ?   -1.9   0.0      0.83     3e+03      31      45 ..     194     208 ..     188     221 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0088
                        DUF3672 14 irGsinAnsGtlnnvviaenctisGtlrAeki 45
                                   i Gs     G ++ v+ia    + G l Ae +
  gi|119719742|ref|YP_920237.1| 23 IAGSGVVSGGVYEKVTIAGSGVVDGDLEAESV 54
                                   56666667777888888888888888888765 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00035
                        DUF3672  10 knadirGsinAnsGtlnnvvi......aenctisGtlrAeki 45 
                                     +  ++Gs++A+s  +++ +i      +e+ ++ G lrA ++
  gi|119719742|ref|YP_920237.1|  75 GSCRFSGSVKAESARFSGATIvegelsSEELKVAGSLRAGRV 116
                                    5778*************9999333333456778888888776 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.83
                        DUF3672  31 aenctisGtlrAeki 45 
                                     e   i+G + A+k+
  gi|119719742|ref|YP_920237.1| 194 VEGVVIEGDVNAKKV 208
                                    455566666666665 PP

>> Phage_spike  Phage spike trimer
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1      0.22     8e+02      30      42 ..      36      48 ..      17      56 .. 0.44
   2 ?    5.3   0.0    0.0057        21      22      45 ..      45      68 ..      43     133 .. 0.91
   3 ?    5.8   0.0     0.004        14      20      44 ..     197     221 ..     191     226 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.22
                                   EEEESSEEEEES- CS
                    Phage_spike 30 tltvqgGGtikGd 42
                                   ++t+ g G + Gd
  gi|119719742|ref|YP_920237.1| 36 KVTIAGSGVVDGD 48
                                   2233333344444 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0057
                                   EEEEEEEEEEEESSEEEEES-EEE CS
                    Phage_spike 22 cTgnLtvgtltvqgGGtikGdith 45
                                   + g+L+ ++++v g +   Gd+++
  gi|119719742|ref|YP_920237.1| 45 VDGDLEAESVSVSGSARFEGDVSA 68
                                   5799*****************954 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.004
                                    EEEEEEEEEEEEEESSEEEEES-EE CS
                    Phage_spike  20 vecTgnLtvgtltvqgGGtikGdit 44 
                                    v++ g+++ +++ ++ GG+++G+i+
  gi|119719742|ref|YP_920237.1| 197 VVIEGDVNAKKVVLRRGGEVRGNIS 221
                                    788999999**************93 PP

>> Histone_H2A_C  C-terminus of histone H2A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   1.1    0.0046        16       9      18 ..      20      29 ..      19      30 .. 0.89
   2 ?    5.5   0.2     0.004        14       9      18 ..      36      45 ..      35      45 .. 0.90
   3 ?   -1.9   0.0      0.83     3e+03       7      15 ..      90      98 ..      90      98 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0046
                  Histone_H2A_C  9 gVTIAqGGVL 18
                                    VTIA+ GV+
  gi|119719742|ref|YP_920237.1| 20 RVTIAGSGVV 29
                                   6********7 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.004
                  Histone_H2A_C  9 gVTIAqGGVL 18
                                    VTIA+ GV+
  gi|119719742|ref|YP_920237.1| 36 KVTIAGSGVV 45
                                   5********7 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.83
                  Histone_H2A_C  7 LggVTIAqG 15
                                   ++g+TI +G
  gi|119719742|ref|YP_920237.1| 90 FSGATIVEG 98
                                   689***987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1484.78
//
Query:       gi|119719743|ref|YP_920238.1|  [L=45]
Description: hypothetical protein Tpen_0834 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.07   13.2   0.1      0.071   13.2   0.1    1.2  1  Ribosomal_S13_N  Ribosomal S13/S15 N-terminal domain
       0.15   12.0   0.0       0.15   12.0   0.0    1.0  1  Reticulon        Reticulon
       0.18   12.6   0.7       0.41   11.5   0.3    1.7  2  Histone_HNS      H-NS histone family


Domain annotation for each model (and alignments):
>> Ribosomal_S13_N  Ribosomal S13/S15 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   1.2e-05     0.071      19      39 ..       3      23 ..       1      39 [. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.2e-05
                                   -SS--TTS---HHHHHHHHHH CS
                Ribosomal_S13_N 19 rreapsWlklskeeveelivk 39
                                   ++e+p++++ls eeveeli k
  gi|119719743|ref|YP_920238.1|  3 EKEKPKYVDLSDEEVEELIRK 23
                                   5799***************87 PP

>> Reticulon  Reticulon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.6e-05      0.15      63      98 ..       4      39 ..       1      45 [] 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.6e-05
                      Reticulon 63 kppepelelseesvreladsllellnkalselrrla 98
                                   k++++++ ls+e+v+el+++ l +++ +ls +++++
  gi|119719743|ref|YP_920238.1|  4 KEKPKYVDLSDEEVEELIRKRLREIKDVLSDIKQIL 39
                                   67899****************************997 PP

>> Histone_HNS  H-NS histone family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1      0.11   6.6e+02      59      69 ..       5      15 ..       1      18 [. 0.73
   2 ?   11.5   0.3   6.9e-05      0.41       9      37 ..      17      44 ..       8      45 .] 0.77

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.11
                                   ---TTT-SSS. CS
                    Histone_HNS 59 vpaKYrdpete 69
                                    ++KY+d ++e
  gi|119719743|ref|YP_920238.1|  5 EKPKYVDLSDE 15
                                   689**998874 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 6.9e-05
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXX- CS
                    Histone_HNS  9 lekqeealeaeerkealaeirelaaeyGl 37
                                   +e+ + +++ +e+k++l++i+++++e G+
  gi|119719743|ref|YP_920238.1| 17 VEELI-RKRLREIKDVLSDIKQILEEAGV 44
                                   33333.3599*****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1626  (0.0906911); expected 358.6 (0.02)
Passed bias filter:                     1045  (0.0582855); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 313.36
//
Query:       gi|119719744|ref|YP_920239.1|  [L=117]
Description: hypothetical protein Tpen_0835 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.044   14.2   1.2      0.049   14.1   0.0    1.7  2  G0-G1_switch_2  G0/G1 switch protein 2
       0.11   12.4   0.1       0.19   11.6   0.1    1.3  1  Reo_sigmaC_M    Reovirus sigma C capsid protein triple beta s


Domain annotation for each model (and alignments):
>> G0-G1_switch_2  G0/G1 switch protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.2      0.56     5e+03      35      49 ..       9      23 ..       7      33 .. 0.63
   2 ?   14.1   0.0   5.4e-06     0.049      27      78 ..      48      95 ..      38     110 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.56
                 G0-G1_switch_2 35 llGvviglvetvcsp 49
                                   llGvv++ +  v  p
  gi|119719744|ref|YP_920239.1|  9 LLGVVVSALLLVYVP 23
                                   677777655555544 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 5.4e-06
                 G0-G1_switch_2 27 YvlGsvLallGvviglvetvcspFssesrlreeeeavaklqaarekeaeeke 78
                                    v+G+v+a++ +v  l     +pF  +++ re++e +++l+  r+++ +  e
  gi|119719744|ref|YP_920239.1| 48 LVVGGVIAFFSLVFNLA----EPFVGKEDPRERRELEKRLEVYRARQRAMLE 95
                                   589*******8888775....59**999888887777776655544443333 PP

>> Reo_sigmaC_M  Reovirus sigma C capsid protein triple beta spiral
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   2.1e-05      0.19       7      28 ..      19      40 ..      14      43 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.1e-05
                   Reo_sigmaC_M  7 sFspPLsladGvVSLdmDPYFC 28
                                   +   PL+l +Gv S  +DP F 
  gi|119719744|ref|YP_920239.1| 19 LVYVPLQLVQGVTSKSIDPVFA 40
                                   4556***************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1466  (0.081767); expected 358.6 (0.02)
Passed bias filter:                     1066  (0.0594567); expected 358.6 (0.02)
Passed Vit filter:                       136  (0.00758548); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 861.13
//
Query:       gi|119719745|ref|YP_920240.1|  [L=101]
Description: regulatory protein, ArsR [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-11   43.3   0.2    5.6e-11   42.1   0.2    1.7  1  HTH_5     Bacterial regulatory protein, arsR family
    1.4e-06   28.2   0.0    2.2e-06   27.6   0.0    1.2  1  HTH_20    Helix-turn-helix domain
    6.3e-05   22.8   0.2    0.00012   21.9   0.2    1.5  1  TrmB      Sugar-specific transcriptional regulator TrmB
    0.00068   19.5   0.7     0.0048   16.8   0.7    2.0  1  PadR      Transcriptional regulator PadR-like family
  ------ inclusion threshold ------
      0.018   14.6   0.0      0.053   13.1   0.0    1.9  1  HTH_24    Winged helix-turn-helix DNA-binding
      0.021   15.0   0.1      0.032   14.4   0.1    1.4  1  HTH_34    Winged helix DNA-binding domain
      0.037   14.4   0.1       0.81   10.1   0.0    2.2  2  Rrf2      Transcriptional regulator


Domain annotation for each model (and alignments):
>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   0.2   2.2e-14   5.6e-11       1      47 []      19      65 ..      19      65 .. 0.98

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 2.2e-14
                                   SHHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                          HTH_5  1 dptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                   +p Rlk+L+l a +++++ el+++l+ls + +  HL++L++aGLVe+
  gi|119719745|ref|YP_920240.1| 19 NPIRLKMLSLIAVRPRYAYELSKMLNLSYPLTYLHLSILEKAGLVES 65
                                   699******************************************96 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   8.7e-10   2.2e-06       2      56 ..      12      65 ..      11      67 .. 0.97

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 8.7e-10
                                   HHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                         HTH_20  2 qiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                                   +++ +La+P R+++l+++   +++ a el + l ls    + HL +Le+agLve+
  gi|119719745|ref|YP_920240.1| 12 EVLQVLANPIRLKMLSLI-AVRPRYAYELSKMLNLSYPLTYLHLSILEKAGLVES 65
                                   7899**************.**********************************96 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.2   4.7e-08   0.00012      17      67 ..      28      82 ..      25      83 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 4.7e-08
                                   HHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST....TTEEEE--H CS
                           TrmB 17 LlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr....pklYravdp 67
                                   L++  p  a+e++++l+++++  Y  L+ Le++GlVe    +    +++Yr  d+
  gi|119719745|ref|YP_920240.1| 28 LIAVRPRYAYELSKMLNLSYPLTYLHLSILEKAGLVESYYVEgprtKRIYRLRDF 82
                                   66778899*****************************988777787779987766 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.7   1.9e-06    0.0048       1      65 [.      25      79 ..      25      82 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.9e-06
                                   HHHHHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEE CS
                           PadR  1 iLalleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrl 65
                                   +L+l++ +p+y ye+ k l+ ++           Y  L+ Lek glves+ +e    +++++Yrl
  gi|119719745|ref|YP_920240.1| 25 MLSLIAVRPRYAYELSKMLNLSY--------PLTYLHLSILEKAGLVESYYVE--GPRTKRIYRL 79
                                   58999999*****9999887774........468****************997..578999**99 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   2.1e-05     0.053      22      48 .]      38      64 ..      19      64 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.1e-05
                         HTH_24 22 eLAerlglSpstvnrrlkrLeeeGlIk 48
                                   eL+++l+lS + +  +l  Le++Gl++
  gi|119719745|ref|YP_920240.1| 38 ELSKMLNLSYPLTYLHLSILEKAGLVE 64
                                   9************************96 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   1.3e-05     0.032       1      45 [.      21      64 ..      21      79 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.3e-05
                         HTH_34  1 vRlavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYie 45
                                   +Rl++ls L++v+   + el++ l++++   + hl++Lekag +e
  gi|119719745|ref|YP_920240.1| 21 IRLKMLS-LIAVRPRYAYELSKMLNLSYPLTYLHLSILEKAGLVE 64
                                   6888776.6677777888************************987 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00032      0.81      13      57 ..      25      65 ..      18      73 .. 0.82
   2 ?    2.4   0.0     0.078     2e+02      35      50 ..      84      99 ..      75     101 .] 0.89

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00032
                                   HHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                           Rrf2 13 allyLakeeeeepvsseeiaerqnispsylekilakLrkaglvks 57
                                   +l  +a +++     + e++++ n+s +     l+ L+kaglv+s
  gi|119719745|ref|YP_920240.1| 25 MLSLIAVRPRY----AYELSKMLNLSYPLTYLHLSILEKAGLVES 65
                                   55555555553....479**************************9 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.078
                                   HTS-HHHHHHHHHHHH CS
                           Rrf2 35 qnispsylekilakLr 50
                                   ++isp++l+k+ +kL+
  gi|119719745|ref|YP_920240.1| 84 VKISPEVLRKMGEKLE 99
                                   79*********99997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.42u 0.31s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 640.81
//
Query:       gi|119719746|ref|YP_920241.1|  [L=258]
Description: fructose-bisphosphate aldolase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.7e-32  112.3   0.1    3.5e-32  111.9   0.1    1.1  1  DeoC          DeoC/LacD family aldolase
    8.6e-06   25.3   0.0    1.7e-05   24.3   0.0    1.5  1  AP_endonuc_2  Xylose isomerase-like TIM barrel
      0.002   17.7   0.2     0.0034   17.0   0.2    1.4  1  OMPdecase     Orotidine 5'-phosphate decarboxylase / HUMPS fa
  ------ inclusion threshold ------
      0.032   13.6   0.4        5.9    6.2   0.0    2.3  2  TMP-TENI      Thiamine monophosphate synthase
      0.094   12.4   0.1       0.18   11.5   0.1    1.5  1  Pilus_CpaD    Pilus biogenesis CpaD protein (pilus_cpaD)


Domain annotation for each model (and alignments):
>> DeoC  DeoC/LacD family aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.9   0.1   9.8e-36   3.5e-32       2     235 .]      18     228 ..      17     228 .. 0.93

  Alignments for each domain:
  == domain 1  score: 111.9 bits;  conditional E-value: 9.8e-36
                                    EEEEECCSHHHHHHHHCTSSHHHHHHHHHHHHHHGGGSSEEEEETTTHHHHHHCSCTTSEEEEETECSSCCTTSTTEEEE CS
                           DeoC   2 vilavDqrvankddtasaqneqledlkalvkealtpgasavlldpgviasaskeyakdiallvkldkgtyllkskqrdvd 81 
                                    +i+a+D++  ++++ +       edl ++ + +l++ ++av+++p +i ++   ++ ++ +++++d ++   +  + d  
  gi|119719746|ref|YP_920241.1|  18 LIVALDHGRRHGPIPGL------EDLGKTLSTILQARPDAVMVTPAMIERYYGLLS-EVFIVARIDGTGAVKSLDETDDR 90 
                                    699**************......8***************************99998.88899999977766665555555 PP

                                    TTCHHHHHHHTT-SEEEEEEEEHTTTTCHHHHHHHHHHHHHHHHHHHTEEEEEEEEE-CTTBSSTTCHHHHHHHHHHHHT CS
                           DeoC  82 evasveeakalGAdavkvvvyyradgseeeqqklaeikrvkeacheeglplilelylrdeaikdekvdpdlvaeAarvsa 161
                                       sv++a+++GAdav+v+vy    gs +eq   ++++rv+e+++++g p+++e++++++++++ +   d+va A+r+++
  gi|119719746|ref|YP_920241.1|  91 LISSVKRAVRAGADAVSVMVYP---GSRNEQSLWEKLARVAEEAEDYGVPVMAEVVPKPPQFQEYG--VDVVAYASRIAV 165
                                    899*******************...************************************96666..99********** PP

                                    CCT-SEEEE--SSCC.B.HHHHHHHHHHHHHCHSSTEEEEETTS..SHHHHHHHHHHHHHHHTHCEEEESHHHHTT CS
                           DeoC 162 elGaDiiKvevpkevvnateedaevfkdvikaapvpgvvlsGGv..seedfletvedAvkeagasGvlsGRaifqk 235
                                    elGaDi+K+ +              f++v++++p p vv+ GG   s ++ l +ve+Av   ga+G+++GR+ifq+
  gi|119719746|ref|YP_920241.1| 166 ELGADIVKTVYR-----------SGFSKVTQSVPAP-VVVLGGQkaSLKETLTMVEKAV-SEGAAGAAIGRNIFQH 228
                                    ***********9...........89***********.9999**9888899999******.**************97 PP

>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   4.9e-09   1.7e-05      65     151 ..      84     163 ..      52     181 .. 0.76

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 4.9e-09
                                    HHHHHHHHHHHHHHHHHHTBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEEEEE--TTTTSSSTC.HH CS
                   AP_endonuc_2  65 reesvdalkraielaaaLGapllvlhpGtagagpkgseeeawerlaeslneladyaekegvklalEtlagsgvelgd.ee 143
                                     +e  d+l + +++a + Ga+ + +++     +++++e++ w    e+l ++a++ae++gv + +E  ++++++  +  +
  gi|119719746|ref|YP_920241.1|  84 LDETDDRLISSVKRAVRAGADAVSVMVY----PGSRNEQSLW----EKLARVAEEAEDYGVPVMAEVVPKPPQFQEYgVD 155
                                    445589********************44....5555555555....5566677777777**************9999955 PP

                                    HHHHHHHH CS
                   AP_endonuc_2 144 larlldav 151
                                    +++  +++
  gi|119719746|ref|YP_920241.1| 156 VVAYASRI 163
                                    55544444 PP

>> OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.2   9.6e-07    0.0034      81     224 ..      97     237 ..      86     238 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 9.6e-07
                                    HHHHTTESEEEEEGTGH....HHHHHHHHHHHHHTTS.EEEEEESTSSGGHHHHHHHSHHHHHHHHHHHHHHHTTESEEE CS
                      OMPdecase  81 arikewadivtvhavaG....kasvkalaeaaekwgnrgllilaqmsskgnlmlqekgytqacveaarehkaedfvmGfv 156
                                     +  ++ad+v v +++G    ++  ++la++ae+ ++ g+ + a++  k   ++qe  y  ++v  a++ + e    G+ 
  gi|119719746|ref|YP_920241.1|  97 RAVRAGADAVSVMVYPGsrneQSLWEKLARVAEEAEDYGVPVMAEVVPKPP-QFQE--YGVDVVAYASRIAVE---LGAD 170
                                    556899***********5552344578889999999999999999977666.9***..***********9977...6666 PP

                                    CCCHTHHHHHHTTCSCEEEHHHTT...EEEEECTTCCG..GGHHHHHHHTTCSEEEESHHHHTSSSHHHHHHH CS
                      OMPdecase 157 aqetlnateedaddfihltpgigl...eqggdgkgqqy..ntpekligiagadiiivGRgIlkagdpveeaer 224
                                      +t        + f ++t+ + +     gg++  +++  +++ek+++ +ga  + +GR I++ +dp++++e+
  gi|119719746|ref|YP_920241.1| 171 IVKTVY-----RSGFSKVTQSVPApvvVLGGQKASLKEtlTMVEKAVS-EGAAGAAIGRNIFQHEDPAKATEA 237
                                    666655.....4799999999999776444444444331146677777.78*******************997 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0    0.0016       5.9      11      61 ..      87     139 ..      80     141 .. 0.86
   2 ?    5.4   0.1    0.0028        10     140     179 ..     178     223 ..     148     225 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0016
                       TMP-TENI  11 kneellevveealkggvtlvqlRek..eldarellelaeklaalcrkygvpli 61 
                                     +++l++ v++a+++g+++v +     + ++++l+e+  ++a+ +++ygvp++
  gi|119719746|ref|YP_920241.1|  87 TDDRLISSVKRAVRAGADAVSVMVYpgSRNEQSLWEKLARVAEEAEDYGVPVM 139
                                    56799***********999999888667889999****************986 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0028
                       TMP-TENI 140 eglkelaealeiPvvaiGGitlenvaevl......eagadgvavvs 179
                                    +g++++ +++  Pvv++GG +++  +++         ga+g a+ +
  gi|119719746|ref|YP_920241.1| 178 SGFSKVTQSVPAPVVVLGGQKASLKETLTmvekavSEGAAGAAIGR 223
                                    67889999999********987643333333333377777777655 PP

>> Pilus_CpaD  Pilus biogenesis CpaD protein (pilus_cpaD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   4.9e-05      0.18      57     116 ..      87     145 ..      75     170 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.9e-05
                     Pilus_CpaD  57 qrarlealaeeyrregagaivisvpsgssneaaaaaaaaeiravlaaaGvpaseisvray 116
                                      +rl + +++  r ga+a+ ++v+ gs ne+   + +a++++ + ++Gvp  + +v + 
  gi|119719746|ref|YP_920241.1|  87 TDDRLISSVKRAVRAGADAVSVMVYPGSRNEQSLWEKLARVAEEAEDYGVPVMA-EVVPK 145
                                    4577788899999*************************************9876.44444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 1843.77
//
Query:       gi|119719747|ref|YP_920242.1|  [L=127]
Description: hypothetical protein Tpen_0838 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-47  159.1   0.0    3.8e-47  159.0   0.0    1.0  1  Cyclophil_like   Cyclophilin-like
     0.0003   20.7   0.0    0.00033   20.6   0.0    1.2  1  Cyclophil_like2  Cyclophilin-like family


Domain annotation for each model (and alignments):
>> Cyclophil_like  Cyclophilin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.0   0.0   4.3e-51   3.8e-47       2     119 .]       3     124 ..       2     124 .. 0.96

  Alignments for each domain:
  == domain 1  score: 159.0 bits;  conditional E-value: 4.3e-51
                                    EEEEEET..TEEEEEEEETT..HHHHHHHHC-SEEEEEEECTTEEEEE-S-----SSSEESSB-TTEEEEECCCTEEEEE CS
                 Cyclophil_like   2 kikidie..sseveveLddt..etaraikealPiesrvntWgeEiYfstpvklekeenakevveagdiaywppGkalclf 77 
                                    k+k+++    ++veveL+++  +t +ai++a P+esrvn+Wg+EiYfstp +++ +e  +evve+gd+aywppG+alc+f
  gi|119719747|ref|YP_920242.1|   3 KLKVIFPesIGVVEVELTGKnpKTLDAIVKATPFESRVNLWGDEIYFSTPARVG-QEVGQEVVEKGDVAYWPPGRALCIF 81 
                                    6788887656799****99999********************************.9************************ PP

                                    SS--TT-.TTSB--SSSEEEEEEEEC-GGGGGG--TTEEEEEE CS
                 Cyclophil_like  78 fGktPis.ddeirpaspvnviGrivedlellkkvkdgekvrve 119
                                    fG+tP+s ++eirpaspvnviGr+v+dle+lk+v++ge vrve
  gi|119719747|ref|YP_920242.1|  82 FGPTPASrGGEIRPASPVNVIGRVVGDLERLKRVRSGEPVRVE 124
                                    *****************************************97 PP

>> Cyclophil_like2  Cyclophilin-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   3.7e-08   0.00033      13      81 ..      22      87 ..      11     124 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3.7e-08
                Cyclophil_like2 13 ednaaaralleklPltltmedyngnEkiaylpeklptddapegssikaGdlayyapwgnlvlfykdfee 81
                                   ++ ++ +a+++  P++ +++  +  E +++ p ++ ++    ++ +++Gd+ay++p+  l++f++ +  
  gi|119719747|ref|YP_920242.1| 22 KNPKTLDAIVKATPFESRVNLWG-DEIYFSTPARVGQEVG--QEVVEKGDVAYWPPGRALCIFFGPTPA 87
                                   56677788888888888886555.8999998888877555..567899****************99844 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       262  (0.0146132); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 866.26
//
Query:       gi|119719748|ref|YP_920243.1|  [L=319]
Description: xylose isomerase domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-13   50.7   0.0    3.3e-13   49.6   0.0    1.5  1  AP_endonuc_2  Xylose isomerase-like TIM barrel
     0.0013   18.2   0.0      0.013   14.9   0.0    2.1  2  DUF4862       Domain of unknown function (DUF4862)


Domain annotation for each model (and alignments):
>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.6   0.0   3.6e-17   3.3e-13      27     188 ..      72     238 ..      59     255 .. 0.81

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 3.6e-17
                                    HHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHC..HTTCSHHHHHHHHHHHHHHHHHHTBSEEEEEBCCGBCTTTSGHHH CS
                   AP_endonuc_2  27 deelrelrkaldelglriaslslftrfgypded..erearreesvdalkraielaaaLGapllvlhpGtagagpkgseee 104
                                    de+ r++   +++ g+++as   +      +    + ea+r+++v++l + ++++a+ G+  + + +G  ++++++++e+
  gi|119719748|ref|YP_920243.1|  72 DEAWRAVEGFVKASGVEVASGVQPLVLMQGFNPssLVEAERKKAVSKLVEVVKTSAERGISKVAFSSG--PDPGPENREA 149
                                    55566666667777777666544443333222222233447888************************..********** PP

                                    HHHHHHHHHHHHHHHHHHHTSEEEEE--TTTTSSSTC....HHHHHHHHHHTTTT..EEEEEEHHHHHHHTTTHHHHHHH CS
                   AP_endonuc_2 105 awerlaeslneladyaekegvklalEtlagsgvelgd....eelarlldavdspn..vgvclDtgHlliaeedvddalra 178
                                    a + l++sl+e+a +a+k gv+++lEt +++          +e++++ + v+ ++  +g+ +D +H+ + +e + d l+ 
  gi|119719748|ref|YP_920243.1| 150 AKDALIKSLKEIAGEAKKFGVTVILETFDRDWDKKQLigpiREAVEVAESVREEHgnFGLLWDLSHAPMLGEKPSD-LKL 228
                                    *****************************9995555599************999999*************888888.799 PP

                                    HHGGEEEEEE CS
                   AP_endonuc_2 179 ladrikhvHi 188
                                     +++++h+Hi
  gi|119719748|ref|YP_920243.1| 229 AKSYLAHIHI 238
                                    *********9 PP

>> DUF4862  Domain of unknown function (DUF4862)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.5e-06     0.013      93     158 ..     113     184 ..     101     211 .. 0.78
   2 ?    1.6   0.0     0.016   1.5e+02     224     258 ..     202     238 ..     196     247 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.5e-06
                        DUF4862  93 arardaiaklneaagrqvvsaveihsaPsrk.....asadalarSLeell.swdwagaklviEHcDalvesq 158
                                    ++a+++  ++ ++++++ +s v   s P+++     a +dal +SL+e++ +  + g  +++E  D+  +++
  gi|119719748|ref|YP_920243.1| 113 KKAVSKLVEVVKTSAERGISKVAFSSGPDPGpenreAAKDALIKSLKEIAgEAKKFGVTVILETFDRDWDKK 184
                                    456667777788889999*********999888887777***********889999*******999955443 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.016
                        DUF4862 224 dedteyGaaWeDlhlplakdepa..asedSllteeri 258
                                    +e++++G  W  +h p+  ++p+  + ++S l + +i
  gi|119719748|ref|YP_920243.1| 202 EEHGNFGLLWDLSHAPMLGEKPSdlKLAKSYLAHIHI 238
                                    67899*****************977778888877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2373.22
//
Query:       gi|119719749|ref|YP_920244.1|  [L=293]
Description: auxin efflux carrier [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.1e-07   28.2   6.2    6.1e-07   28.2   6.2    2.0  2  Mem_trans  Membrane transport protein


Domain annotation for each model (and alignments):
>> Mem_trans  Membrane transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    1.4   0.4    0.0046        82      35     125 ..      33     115 ..       6     134 .. 0.59
   2 !   28.2   6.2   3.4e-11   6.1e-07     240     382 ..     145     280 ..     139     288 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.0046
                      Mem_trans  35 nrfVvlfavPllifhfisqnnpyemllrfiladvlvklivlillllgallskifkgslewtitlfslstlpNtlvlgipl 114
                                     r V+++++  l+f++  q  +       +++  l+   v++++++ ++l     g++e    l++ s + N + +++ +
  gi|119719749|ref|YP_920244.1|  33 ARTVLYVFLTPLLFTSTYQRLSSSPASAPLALTALSASLVVLTFAIATKL----HGDPE----LVLASMYANAGYIPLGI 104
                                    55566655555555555555555544443333333333333333333333....33333....45566666777777777 PP

                      Mem_trans 115 lkalygeygvs 125
                                     ++  g yg s
  gi|119719749|ref|YP_920244.1| 105 AQSYWGSYGAS 115
                                    77766666655 PP

  == domain 2  score: 28.2 bits;  conditional E-value: 3.4e-11
                      Mem_trans 240 lrklirnPntyssllglilslvsfkwnvimpkiiqksisilgdaglpmalfslGlfLalqpkkiacgnsvatfalavRl. 318
                                     rk +  P++y++l +  l+l ++k +    +++ + +  lg ++  +al+ lG  + ++     +   +   a + Rl 
  gi|119719749|ref|YP_920244.1| 145 PRKVLAFPPVYAILAASALALAGVKLP----ELLLSPLATLGGVAPTVALVQLGMEVGASVDANIVDGLK---AYFTRLs 217
                                    6899999******************99....***********************9999775333333333...3899986 PP

                      Mem_trans 319 ilgPlvmlvavlavgLrgslllvaivqaAlPqgivlfviAkeynvherelstllifgmlialpi 382
                                    +++Pl +l++ + +  +g   ++aiv+  +P+++ ++vi +e  +++r ++ +++ ++l++++ 
  gi|119719749|ref|YP_920244.1| 218 VSVPLTLLFVEAGLA-TGIDAKIAIVESVMPSAVSCVVISRELKLDSRRVAGVVFTSTLVSTLL 280
                                    779999999999998.99*************************************999998754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 1749.33
//
Query:       gi|119719750|ref|YP_920245.1|  [L=319]
Description: peptidase T2, asparaginase 2 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-91  306.2   0.4    2.4e-91  306.0   0.4    1.0  1  Asparaginase_2  Asparaginase
  ------ inclusion threshold ------
      0.068   12.8   0.1       0.13   11.9   0.0    1.5  2  Peptidase_M24   Metallopeptidase family M24
       0.15   12.4   0.7       0.39   11.1   0.1    2.0  2  Nitro_FeMo-Co   Dinitrogenase iron-molybdenum cofactor


Domain annotation for each model (and alignments):
>> Asparaginase_2  Asparaginase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  306.0   0.4     4e-95   2.4e-91       1     298 [.      11     307 ..      11     311 .. 0.95

  Alignments for each domain:
  == domain 1  score: 306.0 bits;  conditional E-value: 4e-95
                                    -EEEEEEEEESE-G.-HHHHHHHHHCHHHHHHHHHHHHHTT--HHHHHHHHHHHHHCTCCCSSSTTSS-BTTS---EEEE CS
                 Asparaginase_2   1 pvlvihGGAgsilk.tkereeavrkalkealeagykvLkeggsaldaVeaavrllEddplfnaGkGsvltedgeveldAs 79 
                                    p++++hGGAg+  k ++e+++++++al eal+ g ++L+ gg++ldaVe+av+++E +  fnaGkG++l+ +geveldA 
  gi|119719750|ref|YP_920245.1|  11 PTVAVHGGAGRARKiEPEEKREIENALIEALKRGLEALR-GGTSLDAVEEAVKSMEASGVFNAGKGAALNLKGEVELDAG 89 
                                    689***********9***********************6.8899************************************ PP

                                    EEETTTTEEEEEEEESSBS-HHHHHHHHHHHCS-SEEEHHHHHHHHHHTT-----CGGG--HHHHHHHHHHHHCCCHS.. CS
                 Asparaginase_2  80 imdgktlraGaVagvkrvknpislArlvmeksehvlLvgegAeefareqglelvdeesllteerlkelekakkekaekke 159
                                    im gk+l++GaVa+++r  n++slAr+vmek++hvlLvg gA+++a+ +g+e  +  s+ + +r++e+++ +++k+    
  gi|119719750|ref|YP_920245.1|  90 IMWGKDLSVGAVASLRRTWNAVSLARVVMEKTDHVLLVGPGADALAERLGFEPHPGPSPRALRRYEEYRRLLASKEYYLW 169
                                    ***********************************************************************999999665 PP

                                    B-S-BS-TTTTT--.-EEEEEE-TTS-EEEEEEE--STTB-TTEE-STTSTTTSEEEETTTEEEEEEE-HHHHCCTTHHH CS
                 Asparaginase_2 160 aknvsekelkaklg.TvGaValDsegnlAaaTSTgGltnklvGRvGDspiiGaGtYAdnkvgAvsaTGkGeeiirellaa 238
                                    ++n+s +  +  lg TvGaVa+DsegnlAaaTSTgGl  kl+GRvGDspi+GaG YA+n v+AvsaTG Ge+i+r++laa
  gi|119719750|ref|YP_920245.1| 170 SRNYSVA--EVFLGdTVGAVAIDSEGNLAAATSTGGLFLKLPGRVGDSPIPGAGVYAENGVVAVSATGIGEVILRSTLAA 247
                                    5555544..233446***************************************************************** PP

                                    HHHHHHHTTT--HHHHHHHHHHCHHHHTTT.-EEEEEEETTS-EEEEECSCCCEEEEEETT CS
                 Asparaginase_2 239 divalmeykglsleeAaekvieeklkrvkg.sgGviavdkkGevaaefnsegmlrayaked 298
                                    +i++l++  g  +e+A  +v+++ ++++++ ++Gvia+d +G++a  +n+e+++r++a+ +
  gi|119719750|ref|YP_920245.1| 248 RIASLVRS-GARVEDALREVVSSVTSKFGEnTVGVIAIDGSGSYAEYTNCEVFVRGWASVS 307
                                    ********.*******************9989**********************9998765 PP

>> Peptidase_M24  Metallopeptidase family M24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.1e-05      0.13      89     144 ..       6      68 ..       2     120 .. 0.78
   2 ?   -3.4   0.0         1   6.2e+03     122     131 ..     252     261 ..     223     278 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.1e-05
                                    EEEEEEEEEC.S......SGSH.HHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHHHHTT CS
                  Peptidase_M24  89 asDitrTvlv.G......kftp.eqrelyeavleaqeaaikavkpGvtlseidaaarevlesag 144
                                    +++i  Tv+v G      k +p e re+ +a+ ea++++++a++ G++l+++ +a+    +s g
  gi|119719750|ref|YP_920245.1|   6 CANIIPTVAVhGgagrarKIEPeEKREIENALIEALKRGLEALRGGTSLDAVEEAVKSMEAS-G 68 
                                    666666664322355665444536899*************************9998765444.4 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1
                                    C-STTSBHHH CS
                  Peptidase_M24 122 avkpGvtlse 131
                                    +v+ G+++++
  gi|119719750|ref|YP_920245.1| 252 LVRSGARVED 261
                                    3333333333 PP

>> Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.65   3.9e+03      72      91 ..      41      62 ..      23      66 .. 0.60
   2 ?   11.1   0.1   6.5e-05      0.39      47      94 ..     220     267 ..     207     268 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.65
                                   CTTTSEEEES..-SSBHHHHHH CS
                  Nitro_FeMo-Co 72 eaagievykg..aggtveealk 91
                                    ++g e+++g  +   veea+k
  gi|119719750|ref|YP_920245.1| 41 LKRGLEALRGgtSLDAVEEAVK 62
                                   3455666664445566666665 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 6.5e-05
                                    HHHHHHTT-SEEEESSSCHHHHHHHCTTTSEEEES-SSBHHHHHHHHH CS
                  Nitro_FeMo-Co  47 aqllaeegvdvvivgkiGpralakleaagievykgaggtveealkevl 94 
                                    a + ae+gv +v + +iG+  l+   aa i  ++ +g  ve+al+ev+
  gi|119719750|ref|YP_920245.1| 220 AGVYAENGVVAVSATGIGEVILRSTLAARIASLVRSGARVEDALREVV 267
                                    667789***************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2343.79
//
Query:       gi|119719751|ref|YP_920246.1|  [L=56]
Description: hypothetical protein Tpen_0842 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1760  (0.098165); expected 358.6 (0.02)
Passed bias filter:                      576  (0.0321267); expected 358.6 (0.02)
Passed Vit filter:                       119  (0.00663729); expected 17.9 (0.001)
Passed Fwd filter:                        28  (0.00156172); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 398.12
//
Query:       gi|119719752|ref|YP_920247.1|  [L=419]
Description: Glu/Leu/Phe/Val dehydrogenase, C terminal, partial [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-74  250.2   4.2      3e-74  249.8   4.2    1.2  1  ELFV_dehydrog    Glutamate/Leucine/Phenylalanine/Valine dehyd
    3.4e-55  185.5   0.0    8.3e-55  184.2   0.0    1.7  2  ELFV_dehydrog_N  Glu/Leu/Phe/Val dehydrogenase, dimerisation 
    9.1e-05   21.9   0.1    0.00016   21.1   0.1    1.4  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
  ------ inclusion threshold ------
      0.011   15.1   0.1      0.021   14.2   0.1    1.4  1  ThiF             ThiF family
      0.013   16.0   0.2      0.028   14.9   0.2    1.5  1  NAD_binding_7    Putative NAD(P)-binding
      0.079   13.0   0.4        0.2   11.7   0.4    1.7  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
       0.08   13.2   0.0       0.19   12.0   0.0    1.7  1  TrkA_N           TrkA-N domain
       0.14   12.1   0.8       0.25   11.2   0.8    1.4  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
       0.14   12.2   0.9       0.29   11.2   0.5    1.6  2  AdoHcyase_NAD    S-adenosyl-L-homocysteine hydrolase, NAD bin
       0.16   12.5   0.2       0.31   11.6   0.2    1.4  1  DUF2385          Protein of unknown function (DUF2385)


Domain annotation for each model (and alignments):
>> ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  249.8   4.2   1.7e-77     3e-74       1     243 []     182     417 ..     182     417 .. 0.97

  Alignments for each domain:
  == domain 1  score: 249.8 bits;  conditional E-value: 1.7e-77
                                    T--TTTTTHHHHHHHHHHHHHHHHTTTS-STTEEEEEE--SHHHHHHHHHHHHCT-EEEEEEESSEEEEETTEE-HHHHH CS
                  ELFV_dehydrog   1 GGsldrpeaTglGvvyyveemlkklkldslegkrvaisGsGnvgsyaallltelgakvvavsDssGviydpeGldieell 80 
                                    GG  +r  +TglG++++++e++k+  ld +e+k+va++G+Gnvg yaa+ l+e+gakvvav Ds+G +y+p Gl++eel+
  gi|119719752|ref|YP_920247.1| 182 GGLYARIVSTGLGTAIAAREAAKR-VLDGVENKTVAVQGFGNVGMYAAKYLSEWGAKVVAVTDSKGGVYNPAGLNVEELI 260
                                    999*********************.7777*************************************************** PP

                                    HHHHCSSSSTTHSHHSTSTSEEESHHSHHHHSS-SEEEE-SSTTSB-HHHHTHTHHTT-SEEE-SSSS-B-HHHHHHHHH CS
                  ELFV_dehydrog  81 elkeerksvkeykkssekkaeyieneeellelkvdilvPcAtqneideenakalikngvklvvEgANlpttqeAkeilee 160
                                    ++kee+++v++yk+      ++i+ne e+lel+vdil+P+A++n+i+++na  ++k  +k++ EgAN+ptt+eA+eil++
  gi|119719752|ref|YP_920247.1| 261 KVKEETGAVANYKD----YKKTITNE-EILELDVDILIPAAVENVITKDNAP-RVK--AKIISEGANGPTTPEADEILRK 332
                                    *************3....4579***7.*************************.999..********************** PP

                                    TT-EEE-HHHHTTHHHHHHHHHHHHHHCT----HHHHHHHHHHHHHHHHHHHHHHHHHCT-T..HHHHHHHHHHHHHHHH CS
                  ELFV_dehydrog 161 agvlvvpdkaaNaGGVtvSslEmlqnlarlswteeevdeklkkimkeifkavveeaeeykqe..lvkganiagfekvaea 238
                                    +g +vvpd++aNaGGV++S +E+++n ++   teee  ++l+k+m e f++v++e +++ +e  ++ +a+++++e+v+ a
  gi|119719752|ref|YP_920247.1| 333 KGAVVVPDILANAGGVVMSWIEWANNRMGNWLTEEEALARLEKKMVENFNTVYNEWQKRFHEypMRVAAYAIAVERVVTA 412
                                    **********************************************************888888**************** PP

                                    HHHCT CS
                  ELFV_dehydrog 239 mkaqG 243
                                    mk +G
  gi|119719752|ref|YP_920247.1| 413 MKLRG 417
                                    **998 PP

>> ELFV_dehydrog_N  Glu/Leu/Phe/Val dehydrogenase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.2   0.0   4.6e-58   8.3e-55       1     130 []      36     164 ..      36     164 .. 0.99
   2 ?   -3.2   0.0       3.9   7.1e+03      71      90 ..     244     262 ..     238     270 .. 0.81

  Alignments for each domain:
  == domain 1  score: 184.2 bits;  conditional E-value: 4.6e-58
                                    -SEEEEEEEEEE-TTSBEEEEEEEEEEEE-TTSSEEEEEEEETT--HHHHHHHHHHHHHHHHHTTSS-EEEEEEEES-GG CS
                ELFV_dehydrog_N   1 pervlqvtvpvkrdnGelevikgyraqhssalgPakGGiRfhpsvnldevkaLaalmtyKnalvdlpfGGakggvkidpk 80 
                                    per l+v++pvk dnG++ v++g+r+qh+salgP+kGGiR+hp+v++ ev aL+++mt+Knal+++p+GG+kggvk++pk
  gi|119719752|ref|YP_920247.1|  36 PERLLHVKIPVKLDNGRIAVFHGWRSQHNSALGPYKGGIRYHPNVTEGEVVALSMWMTWKNALAGIPYGGGKGGVKVNPK 115
                                    89****************************************************************************** PP

                                    GS-HHHHHHHHHHHHHHHG.GG-BTTTEEEEBBTTB-HHHHHHHHHHHHH CS
                ELFV_dehydrog_N  81 klseeeleritrrfvrelakkfiGpgiDvpApDvgtgaremawladeykk 130
                                    +ls++ele++ r++  +++ +++G++iD+pApDv+t++++maw +dey+k
  gi|119719752|ref|YP_920247.1| 116 ELSPRELEELSRKYFAAIS-RIVGEDIDIPAPDVYTNPQTMAWYMDEYSK 164
                                    *******************.****************************85 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.9
                                    EEEEEES-GGGS-HHHHHHH CS
                ELFV_dehydrog_N  71 akggvkidpkklseeeleri 90 
                                    +kggv  +p +l+ eel ++
  gi|119719752|ref|YP_920247.1| 244 SKGGV-YNPAGLNVEELIKV 262
                                    78999.89999998888775 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.1   9.1e-08   0.00016      28      70 ..     204     246 ..     186     286 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 9.1e-08
                                    CGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHH CS
                   2-Hacid_dh_C  28 allgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskk 70 
                                    +     +++ktv++ G+G++G  +ak+l+++g+kv+a+  sk 
  gi|119719752|ref|YP_920247.1| 204 KRVLDGVENKTVAVQGFGNVGMYAAKYLSEWGAKVVAVTDSKG 246
                                    45566799*****************************988754 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   1.2e-05     0.021      12      49 ..     206     243 ..     189     245 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.2e-05
                                    HHHHHHTSEEEEE--SHHHHHHHHHHHHHTTTEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ThiF  12 gqekLrdskvllvGaGglGsellknLalsGvgkltlvD 49 
                                     ++ +++++v++ G G +G +++k+L  +G + + ++D
  gi|119719752|ref|YP_920247.1| 206 VLDGVENKTVAVQGFGNVGMYAAKYLSEWGAKVVAVTD 243
                                    5566888****************************999 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.2   1.5e-05     0.028       5      58 ..     210     278 ..     208     323 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.5e-05
                  NAD_binding_7   5 lkgkkvlvvGgGevAarkvrklleagakvtvvapev.......keeleelvklaeee........lekd 58 
                                    +++k+v v G G+v++  ++ l e gakv+ v+            ++eel+k++ee+        ++k 
  gi|119719752|ref|YP_920247.1| 210 VENKTVAVQGFGNVGMYAAKYLSEWGAKVVAVTDSKggvynpaGLNVEELIKVKEETgavanykdYKKT 278
                                    689****************************99997666665544555888877665444443332222 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.4   0.00011       0.2       2      42 ..     202     242 ..     201     313 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00011
                                    HHHHHHS..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEE CS
                   Shikimate_DH   2 lakkkleslkekkvlliGaGemaelvakhLlakgvkkvvva 42 
                                     ak+ l+ +++k+v + G G+++  +ak+L++ g+k v+v+
  gi|119719752|ref|YP_920247.1| 202 AAKRVLDGVENKTVAVQGFGNVGMYAAKYLSEWGAKVVAVT 242
                                    79999*******************************99986 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00011      0.19       1      30 [.     215     244 ..     215     286 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                                    EEEES-SHHHHHHHHHHHH.TTEEEEEEESS CS
                         TrkA_N   1 iiiiGlGrvGrslaeeLse.ggkdvvvidkd 30 
                                    +++ G+G+vG+  a++Lse g  +vv++ ++
  gi|119719752|ref|YP_920247.1| 215 VAVQGFGNVGMYAAKYLSEwGA-KVVAVTDS 244
                                    5799***************888.59999876 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.8   0.00014      0.25       1      95 [.     214     305 ..     214     318 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00014
                                    EEEEE--SCCHHHHHHHHHHTT-EEEEE.-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEES-HHHHHC- CS
                        3HCDH_N   1 kvaviGaGtmGagiaavfasagleVvlv.diseealekalekieksleklvekgklkeeeveaalarisfttdleeavda 79 
                                    +vav G G +G   a+ + + g +Vv v d +    + a  ++e+ ++  +e g++   + +++ ++i+ ++++ e+ d+
  gi|119719752|ref|YP_920247.1| 214 TVAVQGFGNVGMYAAKYLSEWGAKVVAVtDSKGGVYNPAGLNVEELIKVKEETGAVA--NYKDYKKTIT-NEEILEL-DV 289
                                    69**********************987615555666667777777777777777766..6666666666.4444455.9* PP

                                    SEEEE-S-SSHHHHHH CS
                        3HCDH_N  80 dlviEavvEnlelKrk 95 
                                    d+ i a+vEn+  K +
  gi|119719752|ref|YP_920247.1| 290 DILIPAAVENVITKDN 305
                                    **********999976 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.5   0.00016      0.29      22      52 ..     211     242 ..     197     294 .. 0.79
   2 ?   -2.1   0.0         2   3.6e+03      74     105 ..     283     314 ..     266     331 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00016
                                    TTSEEEEE--SHHHHHHHHHHHHCT-EEE.EE CS
                  AdoHcyase_NAD  22 aGkvavvaGyGdvGkGcaaslkglGarvi.vt 52 
                                      k++ v G+G+vG  +a+ l + Ga+v+ vt
  gi|119719752|ref|YP_920247.1| 211 ENKTVAVQGFGNVGMYAAKYLSEWGAKVVaVT 242
                                    5699**********************986244 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2
                                    HCTT.T-SEEEE-SSSSSSB-HHHHCCS-TTEE CS
                  AdoHcyase_NAD  74 evvk.kadivvtttGnkdiitlehlkkmkddai 105
                                    e+++ ++di++ +   +++it+++  ++k + i
  gi|119719752|ref|YP_920247.1| 283 EILElDVDILIPA-AVENVITKDNAPRVKAKII 314
                                    4433245666654.5678888888888887765 PP

>> DUF2385  Protein of unknown function (DUF2385)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   0.00017      0.31      32      69 ..     357     394 ..     351     412 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00017
                        DUF2385  32 rermkelleaeaasearrarlveaFNrgyrsyasvyrt 69 
                                     +rm + l+ e+a ++ ++++ve FN+ y++ ++++++
  gi|119719752|ref|YP_920247.1| 357 NNRMGNWLTEEEALARLEKKMVENFNTVYNEWQKRFHE 394
                                    46899**************************9998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       852  (0.0475208); expected 358.6 (0.02)
Passed bias filter:                      704  (0.039266); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.49
# Mc/sec: 2555.45
//
Query:       gi|119719753|ref|YP_920248.1|  [L=196]
Description: hypothetical protein Tpen_0844 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.039   14.0   0.1       0.33   10.9   0.0    2.1  2  Pyridox_ox_2  Pyridoxamine 5'-phosphate oxidase


Domain annotation for each model (and alignments):
>> Pyridox_ox_2  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   1.8e-05      0.33      65     105 ..      65     103 ..      47     121 .. 0.74
   2 ?    0.5   0.1     0.031   5.6e+02      11      35 ..     125     149 ..     119     159 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 1.8e-05
                                    EEEEEE-SEGGEEEEEEEEEEEEEEEE--HHHHHHHCCCHH CS
                   Pyridox_ox_2  65 vdglvlarsfnslnyrSVvvrGraeevtdeeekaealellv 105
                                    v ++ +a +  + +y SVv+ G+a++ td e +++ l+ ++
  gi|119719753|ref|YP_920248.1|  65 VSNVGDAPA--ENTYLSVVAAGCAYLSTDGENWKKNLTFFL 103
                                    444444555..334*****************9999887665 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.031
                                    C-SEEEEEEEETTEEEEEEEEEEEE CS
                   Pyridox_ox_2  11 egevgrlafvddgepvilPvnyvvd 35 
                                    +g++ + a++d+ +pvi+ v ++v+
  gi|119719753|ref|YP_920248.1| 125 RGRIIVTAVADNHDPVITTVDVAVQ 149
                                    56677778999999***99999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1335.37
//
Query:       gi|119719754|ref|YP_920249.1|  [L=158]
Description: hypothetical protein Tpen_0845 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1055.81
//
Query:       gi|119719755|ref|YP_920250.1|  [L=243]
Description: membrane protein-like [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-70  237.6   6.6    1.5e-70  237.4   6.6    1.0  1  DUF2208          Predicted membrane protein (DUF2208)
     0.0003   20.8   3.1       0.21   11.6   0.0    2.1  2  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
    0.00031   20.4   0.9       0.32   10.6   0.1    2.2  2  DUF4131          Domain of unknown function (DUF4131)
  ------ inclusion threshold ------
      0.087   12.9   9.4       0.17   12.0   1.8    2.1  2  DUF5080          Domain of unknown function (DUF5080)
       0.12   12.2   4.7          1    9.2   0.2    2.1  2  DUF2975          Protein of unknown function (DUF2975)
       0.84    9.5  11.2        1.5    8.6   6.7    2.2  2  Peptidase_M48_N  CAAX prenyl protease N-terminal, five membra
          1    9.1   5.1       0.26   11.1   0.2    2.2  3  MNHE             Na+/H+ ion antiporter subunit
          2    8.8   9.0        2.5    8.4   1.4    2.2  2  YwiC             YwiC-like protein
        2.1    8.3   5.3        9.9    6.1   1.0    2.4  2  PIG-P            PIG-P
        2.3    8.5   8.6       0.43   10.8   4.4    1.9  2  DUF2838          Protein of unknown function (DUF2838)
          3    7.8  10.7       0.92    9.5   1.4    2.3  2  MARVEL           Membrane-associating domain
        5.3    7.0   5.9        1.1    9.3   1.0    2.2  3  DUF3043          Protein of unknown function (DUF3043)


Domain annotation for each model (and alignments):
>> DUF2208  Predicted membrane protein (DUF2208)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  237.4   6.6     1e-73   1.5e-70       2     231 .]       8     241 ..       7     241 .. 0.98

  Alignments for each domain:
  == domain 1  score: 237.4 bits;  conditional E-value: 1e-73
                        DUF2208   2 milisqvsiilfalvlaflpqylflviilYiivimvimsvltsrsllrerkkleevesgktLfe..EknalkliekDeel 79 
                                    ++l+++v+++lfa+++a++p++++l++ilY++++mvim+v+t+r+++++ ++leev+sg++L++  ++++lkl ekD +l
  gi|119719755|ref|YP_920250.1|   8 QYLLGLVLMVLFAYMNANYPDKTWLFFILYFTAFMVIMMVVTGRHARSVLRDLEEVKSGEILYSskPDEVLKLREKDFQL 87 
                                    689************************************************************999************** PP

                        DUF2208  80 qk.elkeqlkasmitllllliviilffl..lyryiiplassllgevleeklarflaflalFealflismflrllarrvlk 156
                                    ++ el++q+kasmi+ll+l+++i++f++  ++++++ l +s++   l+ek+a+fl+flal+++++++s+++ l+arr+++
  gi|119719755|ref|YP_920250.1|  88 TQpELMAQFKASMIPLLSLVVFILVFYIpgFREFFTGLGKSMA---LDEKTANFLSFLALYGFFYAFSLATGLYARRLQS 164
                                    *99*************************99*************...89******************************** PP

                        DUF2208 157 klvmlimatsykvtekGivlkkrtgikfplkenieiklneerkfVElrstkq....klktriRLYtkdpeklyeilerl 231
                                    k+ +li+atsy+vt+kGi++++rt +kfp+k   +i+++++rkfV+l++t+q    +++++iRLY+ +p+kl++il+++
  gi|119719755|ref|YP_920250.1| 165 KTGSLIIATSYTVTSKGIIVDERTPVKFPWK--GDIIVDSRRKFVQLNITQQimgtSITQKIRLYNPEPSKLANILKSY 241
                                    *******************************..*******************99999*******************976 PP

>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.9   0.00078       1.2      50      93 ..      10      59 ..       3      65 .. 0.63
   2 !   11.6   0.0   0.00014      0.21      10      93 ..      76     165 ..      71     178 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00078
                Phage_holin_3_6 50 alllllval.alalaa....lwlaali.vaavllvlagvlalvglkklkk 93
                                    l+l+l+ l a++ a      wl +++  +a+++++ +v ++ +++ l++
  gi|119719755|ref|YP_920250.1| 10 LLGLVLMVLfAYMNANypdkTWLFFILyFTAFMVIMMVVTGRHARSVLRD 59
                                   22222222213333324788888888867799999999999988887775 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00014
                Phage_holin_3_6  10 qlssLvrteleLakaElkeeakrags.gagllgaagvlallalllllval..alala.a..lwlaalivaavllvlagvl 83 
                                    ++ +L ++ ++L + El ++ k  ++ ++ l++  +v+ + ++  ++ +l   +al+      l++l + +++ +  ++ 
  gi|119719755|ref|YP_920250.1|  76 EVLKLREKDFQLTQPELMAQFKASMIpLLSLVVFILVFYIPGFREFFTGLgkSMALDeKtaNFLSFLALYGFFYAFSLAT 155
                                    7788889999999999887766665516667778899999999999999977689975578******************* PP

                Phage_holin_3_6  84 alvglkklkk 93 
                                    +l +++  +k
  gi|119719755|ref|YP_920250.1| 156 GLYARRLQSK 165
                                    ***9995554 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.1     0.001       1.5      12      59 ..      10      57 ..       2      77 .. 0.62
   2 !   10.6   0.1   0.00022      0.32       6     113 ..      97     229 ..      94     237 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.001
                        DUF4131 12 lllllllllllllrrrprrrvllllllllllallgfalrapqpnandl 59
                                   ll+l+l++l+++ + ++  +++l+++l++ ++++ + + + +++++ l
  gi|119719755|ref|YP_920250.1| 10 LLGLVLMVLFAYMNANYPDKTWLFFILYFTAFMVIMMVVTGRHARSVL 57
                                   455555555555555666666666666666666655555555555555 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00022
                        DUF4131   6 alvllalllllllllllllrr................rprrrvllllllllllallgfalrapqpnandlsqlles.gqe 68 
                                    ++ ++ ll l+ ++l+++                   ++ +   +l+l+ ++ a++ ++  ++++ +++  +l+   + +
  gi|119719755|ref|YP_920250.1|  97 KASMIPLLSLVVFILVFYIPGfrefftglgksmaldeKTANFLSFLALYGFFYAFSLATGLYARRLQSKTGSLIIAtSYT 176
                                    56667777777777777765577799999999999987777777888887887777777666666666655555555999 PP

                        DUF4131  69 viveGvv.aslpelt.........gsgtrfvleverv......lsagktkpvsgrvlvtvp 113
                                    v+ +G + +++  ++         +         +r        ++  + +++++++++ p
  gi|119719755|ref|YP_920250.1| 177 VTSKGIIvDERTPVKfpwkgdiivD--------SRRKfvqlniTQQIMGTSITQKIRLYNP 229
                                    *9***66343333332333333332........3333333333566666666666666655 PP

>> DUF5080  Domain of unknown function (DUF5080)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   1.0      0.01        15      29      95 ..       5      69 ..       3      91 .. 0.75
   2 ?   12.0   1.8   0.00011      0.17      16      80 ..      93     162 ..      89     187 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.01
                        DUF5080 29 lildvivfviigityifigdryddlsnflvildtgsliyaylaiknlwvkpkllkykeltesksgiv 95
                                   lil+ ++ +++ +++ ++ ++y d + +  il+  +++ + + +    ++  l +  e+   +  i+
  gi|119719755|ref|YP_920250.1|  5 LILQYLLGLVLMVLFAYMNANYPDKTWLFFILYFTAFMVIMMVVTGRHARSVLRDLEEVKSGE--IL 69
                                   67777777777789999***********************9*999999988776555554433..44 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00011
                        DUF5080  16 aallksekivvlglildvivfviigityif..igdry...ddlsnflvildtgsliyaylaiknlwvkpk 80 
                                     a +k+  i +l+l++ ++vf i g   +f  +g++    ++ +nfl +l +  ++ya+     l+++ +
  gi|119719755|ref|YP_920250.1|  93 MAQFKASMIPLLSLVVFILVFYIPGFREFFtgLGKSMaldEKTANFLSFLALYGFFYAFSLATGLYARRL 162
                                    5778999999***************6555522678878877889***************98888888765 PP

>> DUF2975  Protein of unknown function (DUF2975)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.8     0.014        21      65     109 ..       4      49 ..       1      65 [. 0.63
   2 ?    9.2   0.2    0.0007         1      20      85 ..      98     165 ..      72     184 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.014
                        DUF2975  65 aliaaalllaagivalallae.lelapgvvllllgvafaslvigll 109
                                    ali+  ll ++++v +a++++ + ++  ++ +l   af+++++++ 
  gi|119719755|ref|YP_920250.1|   4 ALILQYLLGLVLMVLFAYMNAnYPDKTWLFFILYFTAFMVIMMVVT 49 
                                    5566667778888888888884544445555555555555555544 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0007
                        DUF2975  20 vlllgvlallafvvalvq..lwkLlrsirkgevFspanvrrLrriglaliaaalllaagivalallae 85 
                                    + ++ +l l++f++++++  ++ +++ + k+++ +++ +  L  ++l  +++a++la+g+ a  l ++
  gi|119719755|ref|YP_920250.1|  98 ASMIPLLSLVVFILVFYIpgFREFFTGLGKSMALDEKTANFLSFLALYGFFYAFSLATGLYARRLQSK 165
                                    34555556666666665433899**********************************98776555555 PP

>> Peptidase_M48_N  CAAX prenyl protease N-terminal, five membrane helices
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   6.7     0.001       1.5     127     171 ..       4      48 ..       1      51 [. 0.93
   2 ?    3.1   0.1     0.051        77      21      90 ..      82     148 ..      69     161 .. 0.57

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.001
                Peptidase_M48_N 127 slllalviglpllaallwiiewggeyfylylwlfllvfslllmti 171
                                     l+l  ++gl+l++++ ++  ++ ++ +l ++l +++f++++m++
  gi|119719755|ref|YP_920250.1|   4 ALILQYLLGLVLMVLFAYMNANYPDKTWLFFILYFTAFMVIMMVV 48 
                                    5789999************************************97 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.051
                Peptidase_M48_N  21 kekfdksraYgldksrfglvsslyslilllallllgllpflwklsgkllgldaeseilqslvfllllsli 90 
                                    +++f+ ++   +++ + +++  l   ++ l++ + g+ +f+  l ++   ++ +++ +  l fl+l+ ++
  gi|119719755|ref|YP_920250.1|  82 EKDFQLTQPELMAQFKASMIPLLSLVVFILVFYIPGFREFFTGLGKS---MALDEKTANFLSFLALYGFF 148
                                    56667777777777777777666666666666666666666666555...44444444444444444433 PP

>> MNHE  Na+/H+ ion antiporter subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   0.00017      0.26      19      78 ..       6      66 ..       2      76 .. 0.72
   2 ?   -2.2   0.1       2.1   3.2e+03      55      55 ..     115     115 ..      96     157 .. 0.48
   3 ?   -0.8   0.1      0.79   1.2e+03      85     109 ..     161     185 ..     157     189 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00017
                           MNHE 19 llGlllallvalllrrll.lplrrvllrllayllvflweivkanldVakrvlrpklpirpg 78
                                   +l +ll+l++++l++ +    + + +l ++ y+  f++ +++ + + a+ vlr   ++++g
  gi|119719755|ref|YP_920250.1|  6 ILQYLLGLVLMVLFAYMNaNYPDKTWLFFILYFTAFMVIMMVVTGRHARSVLRDLEEVKSG 66
                                   5555666666666643333334556999********9999999999999999866676665 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.1
                           MNHE  55 w 55 
                                    +
  gi|119719755|ref|YP_920250.1| 115 I 115
                                    1 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.79
                           MNHE  85 rlksdlaltllansitltPGTltvd 109
                                    rl+s+++ +++a s t+t   ++vd
  gi|119719755|ref|YP_920250.1| 161 RLQSKTGSLIIATSYTVTSKGIIVD 185
                                    78999999********997666666 PP

>> YwiC  YwiC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   1.4    0.0017       2.5      61     112 ..       8      60 ..       1      64 [. 0.71
   2 ?    4.8   1.1     0.022        32      14      79 ..      90     160 ..      85     179 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0017
                           YwiC  61 lliYgavallllllalllqpa.llwwallflplvavavyeakrkreRsllndl 112
                                     ++ g+v ++l +++ + +p   +++ +l+  +++v ++ +  +  Rs+l dl
  gi|119719755|ref|YP_920250.1|   8 QYLLGLVLMVLFAYMNANYPDkTWLFFILYFTAFMVIMMVVTGRHARSVLRDL 60 
                                    44555555555555566667668888888888888889999999999999886 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.022
                           YwiC  14 PlllGlllagpvwahllllvawlvgYl..affplllllka....rrrarylkplliYgavallllllalllq 79 
                                    P l++ + a   ++ l l+v  lv Y+  ++++++ l k+    +++a +l++l++Yg+  +  l+  l+++
  gi|119719755|ref|YP_920250.1|  90 PELMAQFKA-SMIPLLSLVVFILVFYIpgFREFFTGLGKSmaldEKTANFLSFLALYGFFYAFSLATGLYAR 160
                                    556666655.45555666666666665323444444444477766999999999999988887777766655 PP

>> PIG-P  PIG-P
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   1.0    0.0066       9.9      32      61 ..      19      48 ..       2      63 .. 0.70
   2 ?    4.0   0.2     0.029        44       7      68 ..      96     159 ..      91     227 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0066
                          PIG-P 32 halgityypnryWalavpayllmlvlyiyv 61
                                    a     yp++ W +++  +  ++v++++v
  gi|119719755|ref|YP_920250.1| 19 FAYMNANYPDKTWLFFILYFTAFMVIMMVV 48
                                   44445679*****98887666655555544 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.029
                          PIG-P   7 FvlyllstlafllyllwallP..eevlhalgityypnryWalavpayllmlvlyiyvalaslnl 68 
                                    F  +++  l +++++l  ++P   e++  lg ++  + + a ++ ++ l  ++y++ + + l  
  gi|119719755|ref|YP_920250.1|  96 FKASMIPLLSLVVFILVFYIPgfREFFTGLGKSMALDEKTANFLSFLALYGFFYAFSLATGLYA 159
                                    7778888899999999999998889999999888888888888888888888888766655554 PP

>> DUF2838  Protein of unknown function (DUF2838)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   4.4   0.00029      0.43       4      43 ..       8      47 ..       6      56 .. 0.90
   2 ?   -2.2   0.1       3.2   4.8e+03      69      93 ..     148     172 ..     135     179 .. 0.52

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00029
                        DUF2838  4 sFvlgvlnvlltafllgaapellplvylvlllvllplryi 43
                                   +++lg++ ++l+a++ +++p+  +l++++ +++++++ ++
  gi|119719755|ref|YP_920250.1|  8 QYLLGLVLMVLFAYMNANYPDKTWLFFILYFTAFMVIMMV 47
                                   799***************************9999998766 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.2
                        DUF2838  69 llvlpeseklfkavfalanGplalA 93 
                                    ++++   + l+   +  ++G+l++A
  gi|119719755|ref|YP_920250.1| 148 FYAFSLATGLYARRLQSKTGSLIIA 172
                                    2222445556666666666666665 PP

>> MARVEL  Membrane-associating domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   1.4   0.00062      0.92      53      94 ..       9      50 ..       4      66 .. 0.79
   2 ?    3.1   2.4     0.057        86      16      59 ..     104     153 ..      98     178 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00062
                         MARVEL 53 flyalfllvlylfknsaftsilwplidlivdalaallwlvaf 94
                                   +l+ l+l+vl ++ n + +++ w ++ l ++a ++++++v +
  gi|119719755|ref|YP_920250.1|  9 YLLGLVLMVLFAYMNANYPDKTWLFFILYFTAFMVIMMVVTG 50
                                   4556666666555599999***********999999999865 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.057
                         MARVEL  16 faiiilgliaslia............kldqllgspssalnfavfvavfsflyalfl 59 
                                    +++++++l+ +  +            +l        +++nf  f+a ++f+ya+ l
  gi|119719755|ref|YP_920250.1| 104 LSLVVFILVFYIPGfrefftglgksmAL------DEKTANFLSFLALYGFFYAFSL 153
                                    6788888888888888777766543322......36799************97643 PP

>> DUF3043  Protein of unknown function (DUF3043)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   1.0   0.00075       1.1      74     131 ..       2      55 ..       2      67 .. 0.62
   2 ?   -3.3   0.2       5.4   8.1e+03      85     116 ..     103     111 ..      93     123 .. 0.48
   3 ?   -1.0   0.0       1.1   1.6e+03      71      82 ..     199     210 ..     186     229 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00075
                        DUF3043  74 srrnlgelflplalvvlvlllvslvkvpevqavvsllllvllllvvidgillgrkvkk 131
                                    sr  + +++l l+l+vl++++   +++p   ++  +++l++ +++vi ++++gr+++ 
  gi|119719755|ref|YP_920250.1|   2 SRALILQYLLGLVLMVLFAYMN--ANYP--DKTWLFFILYFTAFMVIMMVVTGRHARS 55 
                                    7888999999999999999443..2222..3334445555555555556666655544 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 5.4
                        DUF3043  85 lalvvlvlllvslvkvpevqavvsllllvlll 116
                                    l+ +v+++                       l
  gi|119719755|ref|YP_920250.1| 103 LLSLVVFI-----------------------L 111
                                    22222222.......................1 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1.1
                        DUF3043  71 lVDsrrnlgelf 82 
                                    +VDsrr++ +l 
  gi|119719755|ref|YP_920250.1| 199 IVDSRRKFVQLN 210
                                    69***9998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       972  (0.0542138); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1503.18
//
Query:       gi|119719756|ref|YP_920251.1|  [L=207]
Description: methyltransferase small [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.4e-08   31.8   0.0    1.3e-07   31.4   0.0    1.1  1  MTS              Methyltransferase small domain
    1.6e-05   25.5   0.0    4.9e-05   23.9   0.0    1.7  2  Methyltransf_11  Methyltransferase domain
      2e-05   25.2   0.0    3.7e-05   24.4   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    5.1e-05   22.8   0.1    6.5e-05   22.5   0.1    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    0.00017   21.4   0.0    0.00019   21.3   0.0    1.1  1  Methyltransf_31  Methyltransferase domain
    0.00036   20.3   0.0     0.0005   19.8   0.0    1.2  1  UPF0020          Putative RNA methylase family UPF0020
  ------ inclusion threshold ------
      0.018   14.9   0.0      0.028   14.3   0.0    1.2  1  Methyltransf_18  Methyltransferase domain
      0.031   14.1   0.0      0.036   13.9   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
      0.052   13.3   0.0      0.062   13.0   0.0    1.1  1  Met_10           Met-10+ like-protein
      0.072   13.8   0.0       0.14   12.9   0.0    1.5  1  Methyltransf_12  Methyltransferase domain
      0.084   12.5   0.0       0.12   12.0   0.0    1.1  1  Cons_hypoth95    Conserved hypothetical protein 95


Domain annotation for each model (and alignments):
>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.0   7.8e-11   1.3e-07      24     107 ..      47     131 ..      26     141 .. 0.87

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 7.8e-11
                                    HHHCHCC.TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTTSTTS-EEE CS
                            MTS  24 letlpke.lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasdvleeveekkfdl 100
                                     + l+++  ++ ++ +G+G+G l++ +ak+      + v+v+   l++ak+n+++n l+  +++v +d+ + +   +  l
  gi|119719756|ref|YP_920251.1|  47 SRVLEASpSAEVAVEVGTGVGTLALLAAKRGAY--AVGVEVSEPCLRAAKANARRNSLDglLDFVLCDAGSCLRSSSAGL 124
                                    34455555566689**************98887..799****************************************** PP

                                    EEE---S CS
                            MTS 101 ivsNPPf 107
                                    + +NPP+
  gi|119719756|ref|YP_920251.1| 125 VFTNPPY 131
                                    ******7 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0     3e-08   4.9e-05       2      67 ..      61     127 ..      60     139 .. 0.92
   2 ?   -1.6   0.0       2.7   4.5e+03      78      92 ..     154     168 ..     149     171 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 3e-08
                                    EET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEEEE CS
                Methyltransf_11   2 dvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlvvs 67 
                                    +vG+G G la   akrga  vgv++s+  l++ak++a+++ l   ++fv +da +  ++++s  lv+ 
  gi|119719756|ref|YP_920251.1|  61 EVGTGVGTLALLAAKRGAYAVGVEVSEPCLRAAKANARRNSLdgLLDFVLCDAGS-CLRSSSAGLVFT 127
                                    89***************************************9**99******997.588888888875 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.7
                                    HHHHHHHHHHEEEEE CS
                Methyltransf_11  78 ekalkeiaRvLkpgG 92 
                                    +k l +++R+ kpg 
  gi|119719756|ref|YP_920251.1| 154 KKMLVNAVRIAKPGA 168
                                    577889999999995 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   2.3e-08   3.7e-05       2      58 ..      60     116 ..      59     140 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 2.3e-08
                                    EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGB CS
                Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedl 58 
                                    +++G+G G+l+l +akr+  a  +gv++se +l+aa+++a++++l   ++fv +da ++
  gi|119719756|ref|YP_920251.1|  60 VEVGTGVGTLALLAAKRG--AYAVGVEVSEPCLRAAKANARRNSLdgLLDFVLCDAGSC 116
                                    69***************5..*********************999988999999998664 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.1     4e-08   6.5e-05     163     214 ..      57     107 ..      40     128 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 4e-08
                           PrmA 163 eevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveakle 214
                                    e  + vGtG G La+ aak ga  +v+v + e  +++ak+Na++N+++  l+
  gi|119719756|ref|YP_920251.1|  57 EVAVEVGTGVGTLALLAAKRGA-YAVGVEVSEPCLRAAKANARRNSLDGLLD 107
                                    45569****************9.578*******************9987554 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   1.2e-07   0.00019       5      81 ..      57     128 ..      53     189 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.2e-07
                Methyltransf_31   5 lrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdiee.leklledekfDlilsn 81 
                                     + +++G+G G+l++ +a++   +a  vG++ se  ++ A++na+++ ld  + F  +d+ + l +    ++  l+++n
  gi|119719756|ref|YP_920251.1|  57 EVAVEVGTGVGTLALLAAKR---GAYAVGVEVSEPCLRAAKANARRNSLDgLLDFVLCDAGScLRS----SSAGLVFTN 128
                                    56789*************65...688************************8899*****9996663....456677776 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   3.1e-07    0.0005      77     132 ..      78     132 ..      53     140 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 3.1e-07
                                    --EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE----- CS
                        UPF0020  77 lklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpPYG 132
                                    +  +g++  +  +++a+ Na++  +++l +f+  da +   ++++ +++ tnpPY 
  gi|119719756|ref|YP_920251.1|  78 AYAVGVEVSEPCLRAAKANARRNSLDGLLDFVLCDAGSCL-RSSSAGLVFTNPPYL 132
                                    45799*******************************9887.6779**********6 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.7e-05     0.028       8      78 ..      49     117 ..      46     126 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.7e-05
                Methyltransf_18   8 iaslvekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGlekl 78 
                                    + +  ++ ++ + +Gt  g l++ ++k+g +  ++ ++++e +l++ak+n+++++l+  ++++l+d  + l
  gi|119719756|ref|YP_920251.1|  49 VLEASPSAEVAVEVGTGVGTLALLAAKRGAY--AVGVEVSEPCLRAAKANARRNSLDGLLDFVLCDAGSCL 117
                                    5666777889999*******99998887765..9***********************99999999875555 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.2e-05     0.036      14      60 ..      47      93 ..      42     165 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.2e-05
                Methyltransf_23 14 erllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveia 60
                                    r+l+  ++    +++G+G+G+l+ +++++g+  +gv+ s+ +   a
  gi|119719756|ref|YP_920251.1| 47 SRVLEASPSAEVAVEVGTGVGTLALLAAKRGAYAVGVEVSEPCLRAA 93
                                   56666667777889*************************98766554 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   3.8e-05     0.062      93     169 ..      48     122 ..      46     165 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.8e-05
                                    HHHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG---TT-E CS
                         Met_10  93 rlaklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDgrevireqla 169
                                    r+ +     ev v+v  G+G +a+ +ak  ++   +++++     +  k n ++N ++  +  +l D+   +r++ a
  gi|119719756|ref|YP_920251.1|  48 RVLEASPSAEVAVEVGTGVGTLALLAAK--RGAYAVGVEVSEPCLRAAKANARRNSLDGLLDFVLCDAGSCLRSSSA 122
                                    677778889*******************..999999***********************999999998877776555 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   8.6e-05      0.14       1      43 [.      60     100 ..      60     122 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.6e-05
                Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakr 43 
                                    +e+G+G+G+l+   +++  ++  +gv++s+  + +ak+  +++
  gi|119719756|ref|YP_920251.1|  60 VEVGTGVGTLALLAAKR--GAYAVGVEVSEPCLRAAKANARRN 100
                                    59******998888888..99999*********5555555444 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   7.2e-05      0.12      45     125 ..      59     133 ..      48     141 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.2e-05
                                    EEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEEEE--SSS CS
                  Cons_hypoth95  45 vLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdivflDPPya 124
                                     +++  G G+l+l A+ Rga  av ve ++  +++ k+n ++  l++  + +  da + l++      +  +vf +PPy 
  gi|119719756|ref|YP_920251.1|  59 AVEVGTGVGTLALLAAKRGA-YAVGVEVSEPCLRAAKANARRNSLDGLLDFVLCDAGSCLRSS-----SAGLVFTNPPYL 132
                                    577889*************6.6789*******************9996666666666555444.....568********6 PP

                                    T CS
                  Cons_hypoth95 125 k 125
                                     
  gi|119719756|ref|YP_920251.1| 133 P 133
                                    5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1470.06
//
Query:       gi|119719757|ref|YP_920252.1|  [L=430]
Description: asparaginyl-tRNA synthetase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-87  293.6   0.0    1.8e-87  293.4   0.0    1.0  1  tRNA-synt_2      tRNA synthetases class II (D, K and N)
    6.9e-12   45.2   0.1    1.3e-11   44.3   0.1    1.5  1  tRNA_anti-codon  OB-fold nucleic acid binding domain


Domain annotation for each model (and alignments):
>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  293.4   0.0     2e-91   1.8e-87       2     313 ..     110     424 ..     109     425 .. 0.96

  Alignments for each domain:
  == domain 1  score: 293.4 bits;  conditional E-value: 2e-91
                                    CCHHHHTHHHHCCSHHHHHHHHHHHHHHHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT.TEEE-E-S-SHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    tRNA-synt_2   2 eelrlknryldlrtekvskvlrlrstvtkavrkyleengfieietPiLsksdteegarlFkvksrekekeffaLtqspql 81 
                                     e++l+ r+l +r++k+ +vl+lrstv +a+++++ +ngf+e++ P+++++++e+ga+lF vk     ++  +Ltqs+q+
  gi|119719757|ref|YP_920252.1| 110 REFLLEVRHLAVRSRKMTAVLKLRSTVFEALHEWFRSNGFYEVHCPMFISAAVEGGATLFPVKYVD--GSTVYLTQSSQF 187
                                    68899*********************************************************4443..45556******* PP

                                    HHHHHHHCTHSEEEEEEEEE--S--BTTB-S-CEEEEEEEEET-SCHHHHHHHHHHHHHHHHHHHHCSCCCCCHTTTTTS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    tRNA-synt_2  82 ylellivagidrvfqiaraFRaEdsrtdrhlaEFtqieaemsfieeedimqvleelikslvkevlessakdiefvirrns 161
                                    yle+li + +++v+++a++FRaE+srt+rhl+EF++ eae++++  e i++v eel++++v++vle++++++e   r+ +
  gi|119719757|ref|YP_920252.1| 188 YLEALIYS-LEKVYTVAPSFRAEKSRTRRHLTEFWHAEAEVAWTGLEGILKVEEELVSHIVRRVLEKNREELELLGRNLE 266
                                    ********.***********************************************************999999998887 PP

                                    ..EE-SSS-EEEEHHHHHHHHHTS......-SS--HHHHHHHHHHS--SEEEEEEEBGGGSTTCBBBSTTSTTBBSEEEE CS
                                    ..xxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    tRNA-synt_2 162 ..kdlkkpfkrltykeaieklnei......gkdldkaderalvkkeknepvfvtdfPaelkpFyarkeeddkkltesyDl 233
                                      k+++ pf+r++y++aie+l+++      g+dl  ++eral++ e  +p+f++ fP  +k Fy++++  ++++t s Dl
  gi|119719757|ref|YP_920252.1| 267 plKNVEPPFPRISYDKAIEILQGKglnvkwGDDLGADEERALTE-EFDKPFFLYGFPVGVKAFYHKNDPSRPEVTLSADL 345
                                    88999999**************99********************.999******************************** PP

                                    EET.TE.EEEEEEEB--SHHHHHHHHHHCCHHSSSGGGGHHHHHHHHCT--SEEEEEEEHHHHHHHHCT-SSGGGCSSS- CS
                                    xxx.xx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    tRNA-synt_2 234 lin.gv.ElvgGslRiedpeeleeklkskgldeeaeekfswylealeyGapphgGlglGldRlvmlllgsesIrdviaFP 311
                                    l + g+ E++gG  Rie+ eel +k+k+ gl+   ++ ++wyl++++yG++ph+G+glG+dRlv++++g+++I d i+FP
  gi|119719757|ref|YP_920252.1| 346 LAPeGYgEIIGGGERIEKLEELLDKIKQFGLN---PSDYEWYLDLRRYGTVPHAGFGLGMDRLVTWIAGLDHIVDSIPFP 422
                                    **9889**************************...********************************************* PP

                                    XX CS
                                    xx RF
                    tRNA-synt_2 312 kl 313
                                    ++
  gi|119719757|ref|YP_920252.1| 423 RT 424
                                    97 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3   0.1   1.4e-15   1.3e-11       1      75 [.      20      95 ..      20      96 .. 0.95

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 1.4e-15
                                   EEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEET.HHHHHHHTTS-TTSEEEEEEEEEEC...TTSSEEEEEEEEEE CS
                tRNA_anti-codon  1 VtvaGrvtsisdrsggkvifidlrDgtgriqvvlfr.eeatklaenlkeGdvvrvtGrvkrr...pggelelkveeiel 75
                                   Vtv+G+v ++  r+ g  +f+++rD tg+iq+v+++ +   +la ++++++ v v G ++++   pgg  e+   +ie+
  gi|119719757|ref|YP_920252.1| 20 VTVRGWVYRR--RDLGDKAFVVVRDSTGIIQAVFTPeSPGHALARKVTVESSVIVGGALREDpraPGG-KEIAGRNIEI 95
                                   9*********..**************************************************888888.8988888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 2881.36
//
Query:       gi|119719758|ref|YP_920253.1|  [L=81]
Description: FeoA family protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.5e-15   55.4   1.0    6.1e-15   55.2   1.0    1.0  1  FeoA      FeoA domain


Domain annotation for each model (and alignments):
>> FeoA  FeoA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.2   1.0   3.4e-19   6.1e-15       1      73 [.       7      76 ..       7      77 .. 0.94

  Alignments for each domain:
  == domain 1  score: 55.2 bits;  conditional E-value: 3.4e-19
                                   EEGGG--TT-EEEEEEE-TT.SSHHHHHHHHT--TT-EEEEEEE-TTS-SEEEEETTEEEEE-HHHHTTEEEE CS
                           FeoA  1 vpLsdlkeGergeiarisdedpellrrLremGlvpGarievvarapfggplvvrvgdtrvaLgreeAqaIlVe 73
                                   vpL+ +++G  ++ ++++   + +lrrL e+G+ pG + +vv  + ++gp+v++ ++ r+aLgr++A++ lVe
  gi|119719758|ref|YP_920253.1|  7 VPLALVPPGSVVRLVEVQGG-HGVLRRLFELGILPGVEFRVV-FN-GAGPTVIERNGARLALGRGIAMRLLVE 76
                                   79***************887.99*******************.54.68************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       220  (0.0122706); expected 358.6 (0.02)
Passed bias filter:                      190  (0.0105974); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.45
# Mc/sec: 546.53
//
Query:       gi|119719759|ref|YP_920254.1|  [L=695]
Description: ferrous iron transport protein B [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-56  190.7   0.1    1.7e-56  190.0   0.1    1.3  1  FeoB_N        Ferrous iron transport protein B
    8.4e-24   84.0  26.6    3.7e-16   59.4   7.2    3.4  3  Gate          Nucleoside recognition
    2.2e-20   72.8   0.0    4.1e-20   72.0   0.0    1.4  1  MMR_HSR1      50S ribosome-binding GTPase
    1.8e-11   43.5   1.1    1.8e-11   43.5   1.1    3.2  3  FeoB_C        Ferrous iron transport protein B C terminus
    3.3e-11   43.6   0.0    1.2e-10   41.7   0.0    1.9  2  FeoB_Cyto     FeoB cytosolic helical domain
    1.7e-06   27.7   0.3    1.9e-05   24.3   0.3    2.2  2  GTP_EFTU      Elongation factor Tu GTP binding domain
      7e-05   22.2   0.0    0.00011   21.7   0.0    1.2  1  AIG1          AIG1 family
    0.00015   21.7   0.2       0.34   10.8   0.2    2.3  2  RsgA_GTPase   RsgA GTPase
     0.0082   16.2   0.1        3.4    7.7   0.0    2.2  2  Dynamin_N     Dynamin family
  ------ inclusion threshold ------
      0.015   15.3   0.1      0.031   14.3   0.1    1.5  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
      0.094   12.1   0.0       0.15   11.4   0.0    1.4  1  SRPRB         Signal recognition particle receptor beta subun
       0.11   11.9   0.0       0.39   10.1   0.0    1.9  1  Arf           ADP-ribosylation factor family


Domain annotation for each model (and alignments):
>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.0   0.1   1.2e-59   1.7e-56       2     155 ..       6     159 ..       5     160 .. 0.99

  Alignments for each domain:
  == domain 1  score: 190.0 bits;  conditional E-value: 1.2e-59
                                    EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHHCTSSSE CS
                         FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsayseeekvardflleeepdv 81 
                                    +val+G pnvGk+tlfn l ga+  vgNwpG+tv++ eg+++++g +++++DlPG+Yslsa seee++ardf+++e+pd+
  gi|119719759|ref|YP_920254.1|   6 RVALAGAPNVGKSTLFNVLVGAHRFVGNWPGKTVDRYEGEVEHHGVRIRFIDLPGTYSLSAQSEEEEIARDFIVNEKPDT 85 
                                    79****************************************************************************** PP

                                    EEEEEEGGGHHHHHHHHHHHHHTTSSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTBTHHHHHHH CS
                         FeoB_N  82 vvnvvdatnlernLyLtlqllelgvpvvlalnmideaekkgieidlkkLsekLgvpvvktsakkkegieellka 155
                                    v+ vv+a ++e ++yL lq+lel  +vv+a+n+id+a k g++i++++Ls+ Lgvpvv++sa kk+g++ell+a
  gi|119719759|ref|YP_920254.1|  86 VIVVVNAVSMETTMYLALQVLELYDKVVIAVNKIDVAAKMGVHIHVERLSRLLGVPVVPISALKKTGLHELLEA 159
                                    ***********************************************************************986 PP

>> Gate  Nucleoside recognition
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.3       1.4   2.1e+03      20      49 ..     310     366 ..     287     377 .. 0.63
   2 !   33.8   5.8   2.2e-11   3.3e-08       2     106 ..     379     468 ..     378     474 .. 0.91
   3 !   59.4   7.2   2.5e-19   3.7e-16       1     107 [.     542     660 ..     542     666 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.4
                           Gate  20 s.............................ssllgrigkllepvfaplgqeldwkatvs 49 
                                                                  ssl++ +g +l+ ++a  g  ++  a+  
  gi|119719759|ref|YP_920254.1| 310 TgfpikqiaealgmeelasifeqytlsgllSSLFASLGDYLRTLLASQG--FPEWAVSL 366
                                    1455555555555555555566677777778888888888888888877..66555544 PP

  == domain 2  score: 33.8 bits;  conditional E-value: 2.2e-11
                           Gate   2 lkagpiillasiliwflssssllgrigkllepvfaplgqeldwkatvslltgfaakevvvgtlgtlytsalgellqgfdt 81 
                                    l ++p+i+l++++ +fl+++++++ri+     ++ ++g  l++ka ++ll+gf+   ++v++++ +             t
  gi|119719759|ref|YP_920254.1| 379 LSFLPLIFLVFVVFGFLEDTGIMARIAATYHNLMVRIG--LSGKALMPLLLGFG---CNVPAIMGTK---------ILST 444
                                    6789**********************************..**************...******9996.........9999 PP

                           Gate  82 pksalafllfvllytpcvatlaviv 106
                                     ++++ + l+  l +pc a+l+v+ 
  gi|119719759|ref|YP_920254.1| 445 DREKVLASLLAPL-IPCQARLVVLL 468
                                    9998888888888.59*99999875 PP

  == domain 3  score: 59.4 bits;  conditional E-value: 2.5e-19
                           Gate   1 llkagpiillasiliwflss...........ssllgrigkllepvfaplgqeldwkatvslltgfaakevvvgtlgtly. 68 
                                    l+kag ii+ +si++w+l s           +s++  ig  l+p +a  g    w+++ +ll+gf+ake v++tl+    
  gi|119719759|ref|YP_920254.1| 542 LKKAGVIIFSLSIVVWILMStgpagytqdvgTSYAYLIGTSLAPALALVG-LGKWQVALALLSGFIAKESVASTLIIATg 620
                                    79**********************************************66.55**********************55544 PP

                           Gate  69 .tsalgellqgfdtpksalafllfvllytpcvatlavivr 107
                                      +   + ++   +++++ ++++f +lytpc+at+ +++ 
  gi|119719759|ref|YP_920254.1| 621 aNTFSEAFSSLGLNTAQVASLMVFATLYTPCLATVSAFYV 660
                                    2333556677777888899***************999654 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.0   0.0   2.7e-23   4.1e-20       1     114 []       6     118 ..       6     121 .. 0.80

  Alignments for each domain:
  == domain 1  score: 72.0 bits;  conditional E-value: 2.7e-23
                                    EEEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSS..HHHHHHHHHHHHHHHHCTSE CS
                       MMR_HSR1   1 evaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGlie..gaseekglgkaflaleeadl 78 
                                    +va++G pNvGKStL+n l+g++  v+++pg+T d  eg+v+++g +i+++D+pG ++   +see++++++f  +e+ d 
  gi|119719759|ref|YP_920254.1|   6 RVALAGAPNVGKSTLFNVLVGAHRFVGNWPGKTVDRYEGEVEHHGVRIRFIDLPGTYSlsAQSEEEEIARDFIVNEKPDT 85 
                                    69****************************************999**********986645556669******9999*** PP

                                    EEEEEETT...TTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                       MMR_HSR1  79 illvvdas...eeklkpldeeleelleeakkplilvlnk 114
                                    +++vv+a    +     l  ++ el     +++++++nk
  gi|119719759|ref|YP_920254.1|  86 VIVVVNAVsmeT--TMYLALQVLEL----YDKVVIAVNK 118
                                    *****9874321..11122222222....2456666665 PP

>> FeoB_C  Ferrous iron transport protein B C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.5   1.1   1.2e-14   1.8e-11       2      52 ..     485     536 ..     484     537 .. 0.94
   2 ?   -3.4   1.3       5.3   7.9e+03       3      16 ..     548     561 ..     547     562 .. 0.75
   3 ?   -1.1   0.1         1   1.6e+03       9      21 ..     597     609 ..     589     614 .. 0.85

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 1.2e-14
                         FeoB_C   2 fslYllgilvallvalllkktt.lkgep.spfvmELPpYrlPslknvliktwe 52 
                                    +++Y+  +l++ +++++++k + +k e+ + ++ ELPpY++Psl+ ++ ++w+
  gi|119719759|ref|YP_920254.1| 485 VFIYAYALLLVAALGYVFSK-LfFKAEEePELLVELPPYHRPSLRVIWWYAWD 536
                                    789*****************.66999888***********************7 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 5.3
                         FeoB_C   3 slYllgilvallva 16 
                                    +++ l+i+v +l++
  gi|119719759|ref|YP_920254.1| 548 IIFSLSIVVWILMS 561
                                    56778999999886 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1
                         FeoB_C   9 ilvallvalllkk 21 
                                    +++all+++++k 
  gi|119719759|ref|YP_920254.1| 597 VALALLSGFIAKE 609
                                    689*******986 PP

>> FeoB_Cyto  FeoB cytosolic helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0         3   4.5e+03      29      42 ..     100     114 ..      91     134 .. 0.80
   2 !   41.7   0.0   8.2e-14   1.2e-10      13      91 .]     188     267 ..     177     267 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3
                      FeoB_Cyto  29 wlAlklLe.gDeell 42 
                                    +lAl++Le +D+ ++
  gi|119719759|ref|YP_920254.1| 100 YLALQVLElYDKVVI 114
                                    89*****96676665 PP

  == domain 2  score: 41.7 bits;  conditional E-value: 8.2e-14
                      FeoB_Cyto  13 eellkesnlkaklppRwlAlklLegDeelleelked.pelraeveearkeleaelgedledvIvdarykfiegilrevvk 91 
                                    + ++++     + p+ wlAl+lLegD++++++ +e+ p++ +e+ ++rk +e+e+g++++   ++ary++i+++l+e v+
  gi|119719759|ref|YP_920254.1| 188 SGKISKCGALGNAPQEWLALRLLEGDRQIERKAREAcPDVLEEALRLRKIVEDETGKSPSLLAASARYSLIAKVLEESVH 267
                                    556666666678899*******************9989***************************************997 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.24   3.5e+02       5      24 ..       6      25 ..       3      34 .. 0.83
   2 !   24.3   0.3   1.3e-08   1.9e-05      60     189 ..      43     161 ..      35     165 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.24
                                   EEEEEESTTSSHHHHHHHHH CS
                       GTP_EFTU  5 nigiighvDhGKtTLtdrLl 24
                                    ++++g  + GK+TL   L+
  gi|119719759|ref|YP_920254.1|  6 RVALAGAPNVGKSTLFNVLV 25
                                   678899999******99987 PP

  == domain 2  score: 24.3 bits;  conditional E-value: 1.3e-08
                                    EEEEETTCSSEEEEEEEESSSGGGHHHHHHH........HHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEES CS
                       GTP_EFTU  60 aisleketkkylinliDtPGHvdFskevirg........lrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNK 131
                                      ++e   +  +i +iD PG  + s + ++          ++ D +++vv av   ++ t  ++ ++l++  ++++++NK
  gi|119719759|ref|YP_920254.1|  43 EGEVE--HHGVRIRFIDLPGTYSLSAQSEEEeiardfivNEKPDTVIVVVNAV--SMETTMYLALQVLELYDKVVIAVNK 118
                                    44555..788899999999999887665554444556666789**********..799********************** PP

                                    CGST.HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHH CS
                       GTP_EFTU 132 mDrl.kaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvktllealv 189
                                    +D + k  +   ve +++ l                 vpvv++Salk+ g+ +llea  
  gi|119719759|ref|YP_920254.1| 119 IDVAaKMGVHIHVERLSRLL----------------GVPVVPISALKKTGLHELLEATL 161
                                    ***96666677777777666................48******************976 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   7.1e-08   0.00011       2      94 ..       6      94 ..       5     114 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 7.1e-08
                                   EEEEESSTTSSHHHHHHHHHTS--SS--TTTS---SS-EEEEEEETTEEEEEEE--SCCCTTCCHHCHHHHHHHHHHHCTT- CS
                           AIG1  2 tivlvGktgnGkSaTgNsilgkkaFesklsaqsvtkkcqkksrtwdgkkinViDTPglfdlsvsadkiskeivrclllseeg 83
                                   ++ l G   +GkS+  N ++g + F  +   ++v +   + + + +g +i  iD Pg  +ls++ +  ++ei r + ++e++
  gi|119719759|ref|YP_920254.1|  6 RVALAGAPNVGKSTLFNVLVGAHRFVGNWPGKTVDRY--EGEVEHHGVRIRFIDLPGTYSLSAQSE--EEEIARDFIVNEKP 83
                                   67899999********************988887765..5666899***************99888..89***********6 PP

                                   ESEEEEEEETT CS
                           AIG1 84 ihalllvlslg 94
                                    +++++v  ++
  gi|119719759|ref|YP_920254.1| 84 DTVIVVVNAVS 94
                                   66666664443 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0     0.001       1.6     101     122 ..       6      27 ..       1      47 [. 0.87
   2 !   10.8   0.2   0.00023      0.34      17      95 ..      84     158 ..      68     167 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.001
                                    EEEEECSTTSSHHHHHHHHCTT CS
                    RsgA_GTPase 101 tsvlvGqSGvGKStLinallpe 122
                                     ++l+G   vGKStL n+l++ 
  gi|119719759|ref|YP_920254.1|   6 RVALAGAPNVGKSTLFNVLVGA 27 
                                    57899**************986 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00023
                                    -EEEEEEESTTTT--HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHH CS
                    RsgA_GTPase  17 dqllivvslkepelslnlldrfLvlaeekgiepvivlnKiDlleeeeeleelkeelealgyevllvsaktkegleelke 95 
                                    d++++vv +++ e+++ l  ++L l+     ++vi++nKiD++ ++    +++   + lg++v+ +sa +k+gl+el e
  gi|119719759|ref|YP_920254.1|  84 DTVIVVVNAVSMETTMYLALQVLELYD----KVVIAVNKIDVAAKMGVHIHVERLSRLLGVPVVPISALKKTGLHELLE 158
                                    556666666655555555444444433....79**************555666666779**********9999998865 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.0    0.0058       8.7       1      22 [.       7      28 ..       7      36 .. 0.88
   2 !    7.7   0.0    0.0023       3.4     101     140 ..      51      94 ..      44     119 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0058
                                   EEEEEBTTTTHHHHHHHHHTS- CS
                      Dynamin_N  1 iavvGsqSsGKSSvlnaLlged 22
                                   +a+ G+ + GKS++ n L+g++
  gi|119719759|ref|YP_920254.1|  7 VALAGAPNVGKSTLFNVLVGAH 28
                                   6889999*************87 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0023
                                    -SEEEEE---B-SSSGTTS..HHHHHHH..STTEEEEEEEETTS CS
                      Dynamin_N 101 kgltlvDlPGldsvnkrdq..elvkeyi..kkadiilavtsanh 140
                                     ++ ++DlPG  s  ++ +  e+++ +i  +k d +++v++a +
  gi|119719759|ref|YP_920254.1|  51 VRIRFIDLPGTYSLSAQSEeeEIARDFIvnEKPDTVIVVVNAVS 94 
                                    57889******9955555556*******9777888888888755 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   2.1e-05     0.031      52      99 ..     106     159 ..      69     162 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.1e-05
                   MMR_HSR1_Xtn  52 nrvYipclyvlNKiDlisle....eldelare..pnsvviSaekelnldeLkek 99 
                                       Y ++++++NKiD + +     ++++l+r     +v+iSa k+++l eL+e+
  gi|119719759|ref|YP_920254.1| 106 LELYDKVVIAVNKIDVAAKMgvhiHVERLSRLlgVPVVPISALKKTGLHELLEA 159
                                    56799***********655411114444555355689**************986 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0    0.0001      0.15       4      73 ..       5      75 ..       2     123 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0001
                                   -EEEEE-STTSSHHHHHHHHHHSS---B---SS-EEETTG......GGTT-SEEEETT-GCCSHHHHHHHHHH CS
                          SRPRB  4 pavllvGlsdsGKTslftrLttdsvkktvtSqessaalkv...ksekgskltliDfPGheklrqklleklkak 73
                                    +v l+G  + GK +lf+ L   +    v     ++++++    +++g ++++iD+PG  +l  +  e+ +a+
  gi|119719759|ref|YP_920254.1|  5 VRVALAGAPNVGKSTLFNVLVGAHR--FVGNWPGKTVDRYegeVEHHGVRIRFIDLPGTYSLSAQSEEEEIAR 75
                                   57899**************997643..3333455555555444578999*************98877765554 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00026      0.39      12     169 ..       2     158 ..       1     163 [. 0.69

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00026
                                    TTEEEEEEEESTTSSHHHHHHHHH.HSSCEECSS..SSSEEEEEEEETTEEEEEEEE-SSGGGG......GGGGGGC..T CS
                            Arf  12 kkelrilllGLDnaGKtTilkklk.leelvttvP..TigfnveeleiknlkftvwDvGGqeklR......plWknYf..e 80 
                                     ke+r+ l G  n GK+T+ + l   +++v   P  T+     e+e++++++++ D+ G  +l       ++ +++   e
  gi|119719759|ref|YP_920254.1|   2 AKEVRVALAGAPNVGKSTLFNVLVgAHRFVGNWPgkTVDRYEGEVEHHGVRIRFIDLPGTYSLSaqseeeEIARDFIvnE 81 
                                    599******************99824678889995567777789*************99877651111115667776224 PP

                                    TESEEEEEEETT-CTTHHHHHHHHHHHCTSGCCTTSEEEEEEE-TTSTTSS-HHHHHHHTTGGGSSSSSSEEEEEEBTTT CS
                            Arf  81 ktdavifvvDsadreRleeakeeLkalleeeelkevallvlaNKqDlpealseeelrellgleelkgkrkleiqkcsavk 160
                                    k d+vi vv ++  e        +   l+  el + ++++  NK+D++  +  +     +++e+l+    + ++  sa+k
  gi|119719759|ref|YP_920254.1|  82 KPDTVIVVVNAVSMETT------MYLALQVLELYD-KVVIAVNKIDVAAKMGVH-----IHVERLSRLLGVPVVPISALK 149
                                    56888999888765533......333344444444.467888999998776553.....334444444456788888888 PP

                                    TBTHHHHHH CS
                            Arf 161 geglkegle 169
                                    ++gl+e le
  gi|119719759|ref|YP_920254.1| 150 KTGLHELLE 158
                                    888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (695 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       688  (0.0383736); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.44
# Mc/sec: 4697.29
//
Query:       gi|119719760|ref|YP_920255.1|  [L=265]
Description: anaerobic ribonucleoside-triphosphate reductase activating protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-15   58.4   0.0      2e-15   57.6   0.0    1.4  1  Radical_SAM  Radical SAM superfamily
    3.5e-10   40.3   0.0    5.8e-10   39.6   0.0    1.3  1  Fer4_12      4Fe-4S single cluster domain
    1.9e-06   28.0   0.0    3.3e-06   27.2   0.0    1.3  1  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.6   0.0   3.3e-19     2e-15       6     132 ..      34     162 ..      30     197 .. 0.76

  Alignments for each domain:
  == domain 1  score: 57.6 bits;  conditional E-value: 3.3e-19
                                    EESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEEC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM   6 gCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritvetn 85 
                                     Cn+rC++Ca+++  +r+  +r  +v+ei+  v +++a   v++++++ggep+l+++  e+l++++k +  g+ +++ tn
  gi|119719760|ref|YP_920255.1|  34 YCNFRCPWCANSRL-ARGLEVRRATVDEIVSAVSRARAF--VDYFHVTGGEPTLQYRRLEKLFERVKTE-VGLPLSLDTN 109
                                    7************5.999999***************844..**************************97.********** PP

                                    SSCHG.HHHHHHHHHTT-SEEEEEEBSSSHH......HHHHHHT.CTSHHHHHHH CS
                                    xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxx.xxxxxxxxxx RF
                    Radical_SAM  86 gtlpd.eeklerllelgvdrvslgleaadde......kvlklmn.rghtfeevle 132
                                    +  p+  e+l r ++  v +v+++++a+ d+      +v  + +   + + +v +
  gi|119719760|ref|YP_920255.1| 110 ASIPSaLEHLLRSVD--VEHVAVDVKAPLDDpmlysqVVGLPAKvAEKVVNDVRR 162
                                    ***755555555555..89***********9886666333333323333344444 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   0.0   9.7e-14   5.8e-10       6     118 ..      26     133 ..      23     144 .. 0.81

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 9.7e-14
                        Fer4_12   6 vrlslfvsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkk..esiegltllGGEPllpenaeallelvkevkeek 83 
                                    v ++l++s Cn++C+ C n  +    +g e+ +++ +ei+  ++     ++ + ++GGEP l  +++ l +l+++vk+e 
  gi|119719760|ref|YP_920255.1|  26 VSFTLWLSYCNFRCPWCANSRL---ARGLEVRRATVDEIVSAVSRarAFVDYFHVTGGEPTL--QYRRLEKLFERVKTEV 100
                                    6689*************99865...67888888888999888887335559***********..**************** PP

                        Fer4_12  84 pekdiwlytgytleelskkekeellkeid...vlvdGk 118
                                      +  + ++ ++  +l+      ll+ +d   v+vd+k
  gi|119719760|ref|YP_920255.1| 101 GLPLSLDTNASIPSALE-----HLLRSVDvehVAVDVK 133
                                    98889999999888886.....4555555333788877 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.0   5.6e-10   3.3e-06       5      96 ..      32     117 ..      29     133 .. 0.79

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 5.6e-10
                        Fer4_14   5 lsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekkiw 84 
                                    ls Cn+ C++C n+       g +  + ++++i++ ++  +   +   +tGGeP    + + l kl +r+k+e+  ++  
  gi|119719760|ref|YP_920255.1|  32 LSYCNFRCPWCANSR---LARGLEVRRATVDEIVSAVSRARAFVDYFHVTGGEPT--LQYRRLEKLFERVKTEV-GLPLS 105
                                    589**********99...45555556666667777777777778889*******8..667999**********9.9**** PP

                        Fer4_14  85 letngtleiele 96 
                                    l tn+++   le
  gi|119719760|ref|YP_920255.1| 106 LDTNASIPSALE 117
                                    ****99975544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1697.12
//
Query:       gi|119719761|ref|YP_920256.1|  [L=615]
Description: major facilitator transporter [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.2e-23   82.8  42.1    3.1e-13   49.4  15.8    2.1  2  MFS_1       Major Facilitator Superfamily
    2.1e-15   56.7   6.8    3.2e-15   56.0   6.8    1.2  1  PhoU_div    Protein of unknown function DUF47
  ------ inclusion threshold ------
      0.015   14.2  18.8      0.032   13.1   2.9    3.4  3  Sugar_tr    Sugar (and other) transporter
      0.067   12.0  10.5        0.1   11.4   8.7    2.3  1  MFS_1_like  MFS_1 like family
        7.2    4.8   7.0       0.91    7.7   1.5    2.0  2  OATP        Organic Anion Transporter Polypeptide (OATP) fami


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1  19.9   2.4e-13   8.6e-10      29     171 ..      38     176 ..       8     222 .. 0.72
   2 !   49.4  15.8   8.5e-17   3.1e-13       4     177 ..     218     392 ..     215     402 .. 0.88

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 2.4e-13
                          MFS_1  29 ispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll.fasslwlllvlrvlqGlgagalfpaga 107
                                    +++ ++ l ++ ++++ a + l++G  + +  rr+ ll+g l++  g+++ll ++++l  +lv+ ++ G+g+g++f+++a
  gi|119719761|ref|YP_920256.1|  38 AAGGSFLLPIVSFGAFKATFDLFTGLYAGKS-RRKSLLTGTLVYTTGAVALLlLPPPLN-FLVGNIFVGAGEGLVFATSA 115
                                    23333334455578888*************5.***************555552545555.******************** PP

                          MFS_1 108 aliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlflll 171
                                     +i+d+   e+ ++ +g++ ++  +G+ +g+ ++gl++ slg +a+ +++ + s+l++v     
  gi|119719761|ref|YP_920256.1| 116 LAIRDILGLERSSLSFGYIESACYFGYSIGAFVSGLVYGSLGAPATLFVILASSVLGVV---SA 176
                                    **********************************************9999999999966...33 PP

  == domain 2  score: 49.4 bits;  conditional E-value: 8.5e-17
                          MFS_1   4 aaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa. 82 
                                    aa ++  a si++ ++p ++  + g+++  +g++ +l  l+ + ++++++++sdr+Grr +  lgl + ++  l++l + 
  gi|119719761|ref|YP_920256.1| 218 AAHMAKVADSIAWGVIPVYM-VAKGLQVYHVGFAQSLLLLVWSSTMPFWSSFSDRVGRRALATLGLMINGAL-LIAL-Pg 294
                                    55566678899999***655.555899999******************************************.6666.33 PP

                          MFS_1  83 .sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg..Wravfyilai 159
                                      +++ +l+  +++Gl +++++p+  a +ad++p+e r +a+g++ a    G++ g+l++ l++s +     +vf+ ++ 
  gi|119719761|ref|YP_920256.1| 295 tRNFPEMLLIVLVMGLSYAMYYPILPAPVADMTPPEGRDLAVGVYRALRDSGYATGALIATLILSVAPssLDSVFIDIGS 374
                                    4777788888888************************************************99955556799******** PP

                          MFS_1 160 vsllafvlfllllpeepp 177
                                    ++++ +  f ++++e++p
  gi|119719761|ref|YP_920256.1| 375 MLVVTAAAFSIVFRETRP 392
                                    *****9988888888776 PP

>> PhoU_div  Protein of unknown function DUF47
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.0   6.8     9e-19   3.2e-15      13     212 ..     400     599 ..     393     601 .. 0.88

  Alignments for each domain:
  == domain 1  score: 56.0 bits;  conditional E-value: 9e-19
                       PhoU_div  13 lqdhlekvsetvlkliellkallegdyekveellkeiselEreADeikreirlklekglflPvdRedllelveslDeild 92 
                                    ++ h+e +  +    ++l +  + g  e+ e+ +     +Er+AD++kre+   +++gl+   +R d+ +lve++D+++ 
  gi|119719761|ref|YP_920256.1| 400 VIRHVEIIRDVLVYQQKLVEKAFGGYAEELESGIRVLKDMERKADAVKREVTWRIYSGLLPTSSRIDFERLVEEIDKVAG 479
                                    56777777777778888999999999999****************************9987789**************** PP

                       PhoU_div  93 vlediamlvtlrkvefpeelkdeflallkktveaiealaevieeleklletalskkdiveeieslEdeiDqlqrklikkl 172
                                     + +   ++   k    e+l+d  + ll+ + e i++++  ie+l  l  + l       ei+  E ++D+l++k i + 
  gi|119719761|ref|YP_920256.1| 480 AVIECNERLLWVKH--SEKLRDLKQLLLEMLNENIRLADMLIENLRVLSLSPLYAVRASIEIDAGERRVDELRIKAIHMI 557
                                    99999998888884..999999999999999999999999999999766666665566779************9988877 PP

                       PhoU_div 173 fs..redasnplevlllveiieklenvsdraedvadrisiil 212
                                     +  +e+ + ++  l l+e ++ le  sd ++d+ad i+ii+
  gi|119719761|ref|YP_920256.1| 558 RKllDENEIDIMSALSLMEAVNLLELTSDDFQDAADIIRIIS 599
                                    665568889999999*************************97 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.2    0.0015       5.2      72     127 ..      66     118 ..      42     122 .. 0.84
   2 ?    3.9   3.0    0.0055        20      44     100 ..     127     183 ..     121     197 .. 0.84
   3 ?   13.1   2.9   8.8e-06     0.032     291     393 ..     250     341 ..     206     397 .. 0.57

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0015
                                    HTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHH CS
                       Sugar_tr  72 rfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyi 127
                                      +R+ksll++++++  gav   + +       ++vg ++vG g Gl+ +++ + i
  gi|119719761|ref|YP_920256.1|  66 GKSRRKSLLTGTLVYTTGAVALLLLP---PPLNFLVGNIFVGAGEGLVFATSALAI 118
                                    468*****************999999...8999**************999998766 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.0055
                                    ...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTS CS
                       Sugar_tr  44 ssvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgkn 100
                                    ss+  g i s+ ++G  iG++++gl+   +G   +l ++ + +v g v  a ++++ 
  gi|119719761|ref|YP_920256.1| 127 SSLSFGYIESACYFGYSIGAFVSGLVYGSLGAPATLFVILASSVLGVVSAASSHETM 183
                                    677889999**********************99888888888888888877777443 PP

  == domain 3  score: 13.1 bits;  conditional E-value: 8.8e-06
                                    HHHHHHHHHHHHHHHHHHHHHHHS-SHHHHHHHHHHHHHHHHHHH..HHHHTTSS...CHHHHHHHHHHHHHHHTTTTHH CS
                       Sugar_tr 291 lvtiivgvvnfvatfvaiflvdrfGRRtllllGaagmaicfvilgivalllvakskaasivaivfialfialfalgwgpv 370
                                    ++++++ v+  ++ f +  ++dr+GRR l  lG+++  ++++      l+++ +   +  +++v+ + +++ + + ++pv
  gi|119719761|ref|YP_920256.1| 250 AQSLLLLVWSSTMPFWS-SFSDRVGRRALATLGLMINGALLIA-----LPGTRNFPEMLLIVLVMGLSYAMYYPILPAPV 323
                                    45555555555555555.5566666665555555444333333.....33444443345555555555555555555554 PP

                                    HHHHHHHHSHTTTHHHHHHHHHH CS
                       Sugar_tr 371 pwvlvsElfpqsvRskalaiava 393
                                          ++ p++ R++a  +  a
  gi|119719761|ref|YP_920256.1| 324 A-----DMTPPEGRDLAVGVYRA 341
                                    4.....44455555444444333 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   8.7   2.9e-05       0.1     147     370 ..     131     354 ..      96     362 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.9e-05
                     MFS_1_like 147 yGrqrlfGsvGyaifafitGilidhysvnllpysallyvlaallvisllvvlilnetekesklkvtksl.....qvllni 221
                                    +G +      Gy i af++G++   +     p  +l+++la+ ++ ++  +++ + +++  +   + s      + ++ +
  gi|119719761|ref|YP_920256.1| 131 FGYIESACYFGYSIGAFVSGLVYGSLGA---P-ATLFVILASSVLGVVSAASSHETMQYTLQERERFSTtmktsEIVKLL 206
                                    4444444445666666666666555555...2.23344444333333333334444444333322222244554667778 PP

                     MFS_1_like 222 lknpeviifllvalilgmswgiienFlflYLkelgasntllGslvalgvvaeiplfffaeklleklGhvklliiallayi 301
                                    ++np+ +  ll+a + +++ +i++  + +Y+  +g   + +G +  l  +    +  f +   +++G + l +++l++  
  gi|119719761|ref|YP_920256.1| 207 FSNPSTASALLAAHMAKVADSIAWGVIPVYMVAKGLQVYHVGFAQSLLLLVWSSTMPFWSSFSDRVGRRALATLGLMING 286
                                    89999999999999****999999999999999999999999887777776666666677889999************99 PP

                     MFS_1_like 302 lrfllyaiienawlvlpievLhgisfgllwaaaveyvskiapksleatgqgllsglyfglGralGsliG 370
                                    + ++ +  ++n+  +l+i +  g+s+++++ ++   v++++p++ +    g++ +l    G a G+li+
  gi|119719761|ref|YP_920256.1| 287 ALLIALPGTRNFPEMLLIVLVMGLSYAMYYPILPAPVADMTPPEGRDLAVGVYRALRD-SGYATGALIA 354
                                    9999999999999999999999********9999999999999999999999998854.4777777776 PP

>> OATP  Organic Anion Transporter Polypeptide (OATP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   1.5   0.00025      0.91     134     191 ..      95     152 ..      65     156 .. 0.91
   2 ?   -1.1   0.3      0.12   4.2e+02     140     194 ..     306     360 ..     296     377 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00025
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           OATP 134 lfflaqlllGiGatpiytlGisYidDnvkkknsplylgilyalrilGpalGfllGsll 191
                                     f+++++++G+G+ ++++     i D    ++s+l +g++ ++  +G+ +G ++++l+
  gi|119719761|ref|YP_920256.1|  95 NFLVGNIFVGAGEGLVFATSALAIRDILGLERSSLSFGYIESACYFGYSIGAFVSGLV 152
                                    589************************************************9988875 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.12
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           OATP 140 lllGiGatpiytlGisYidDnvkkknsplylgilyalrilGpalGfllGslllkl 194
                                    l++G+  +++y++  + + D + ++   l +g++ alr  G+a G l+++l+l++
  gi|119719761|ref|YP_920256.1| 306 LVMGLSYAMYYPILPAPVADMTPPEGRDLAVGVYRALRDSGYATGALIATLILSV 360
                                    7899999999999999999******************************999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (615 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       705  (0.0393218); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.44
# Mc/sec: 4216.36
//
Query:       gi|119719762|ref|YP_920257.1|  [L=358]
Description: tRNA-modifying enzyme [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      1e-19   70.6   0.0    2.7e-19   69.3   0.0    1.8  1  Wyosine_form  Wyosine base formation
    2.2e-14   54.2   1.0    2.8e-12   47.3   0.1    2.9  2  Radical_SAM   Radical SAM superfamily
  ------ inclusion threshold ------
      0.055   13.7   1.3       0.27   11.5   1.3    2.0  1  Fer4_12       4Fe-4S single cluster domain
      0.074   13.2   0.1        4.9    7.3   0.0    2.5  2  Fer4_14       4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Wyosine_form  Wyosine base formation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.3   0.0   6.1e-23   2.7e-19       2      61 ..     254     312 ..     253     314 .. 0.97

  Alignments for each domain:
  == domain 1  score: 69.3 bits;  conditional E-value: 6.1e-23
                                    HT-SEEEEEE------------------HHHHHHHHHHHHTSSS.EEEEEEETTTTEEEE CS
                   Wyosine_form   2 aepdFvEvKaytyvGssrsrLtmknvPwheevadfakrlegsaedYellaehrhSrvvll 61 
                                    ++p+FvE+K+yt+vG+s++rL ++++P+ ee+++fak+le+ ++ Y++ +e+ +Srvv+l
  gi|119719762|ref|YP_920257.1| 254 GNPMFVELKGYTWVGESQKRLPISAMPTIEELEKFAKKLEELTG-YKVKVEDDKSRVVML 312
                                    89******************************************.*************98 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.3   0.1   6.3e-16   2.8e-12       2     163 ..      64     247 ..      63     251 .. 0.74
   2 ?    3.5   0.1     0.018        81      90     139 ..     284     331 ..     257     336 .. 0.82

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 6.3e-16
                                    EEESEESS--TTTSCCTT.........................HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEE... CS
                                    xxxxxxxxxxxxxxxxxx.........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                    Radical_SAM   2 vvtrgCnlrCsfCarpet.........................vrregrgrslsveeileevkelkaekgvkevilg... 53 
                                    +v+++C ++C+fC+r +                          +r    g    +                     +   
  gi|119719762|ref|YP_920257.1|  64 PVLNFCDFACKFCWRMHLpgrfklppgwrwdepediingsivaQRLLLIGFKGNPKV-------------------Srer 124
                                    6899************99***655555444444444444444433333333333333...................3444 PP

                                    ..............SSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT..-SEEEEEEBSSSHH.. CS
                                    ..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx.. RF
                    Radical_SAM  54 ..............ggepllypdfvellerlaklavpgiritvetngtlpdeeklerllelg..vdrvslgleaadde.. 115
                                                   gep+lyp+++el+++ +++   +++ +++tng    +  le+l+++   ++ ++l+l  +++e  
  gi|119719762|ref|YP_920257.1| 125 fleamfprhftislDGEPSLYPKLAELVKKVKER---NFTAFLVTNGSI--PIRLEELVKRDaqPTNLYLSLYGPNKEvf 199
                                    44444444444445*******************8...************..589999999999***************88 PP

                                    .HHHHHHTCTSHHHHHHHHHHHHHHTTSET.EEEEEEEBTTTSHHHHHHH CS
                                    .xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM 116 .kvlklmnrghtfeevlealeklreagikr.vvdrivglpGendeeleel 163
                                      + ++   ++ +e vl++le+l +    + +v r+++++  n+ + e +
  gi|119719762|ref|YP_920257.1| 200 tATADPR-IPNAWENVLRSLELLDRFTE-SrTVLRLTMVKDLNMVDPEGY 247
                                    7444444.5699*********9998844.45*********9999887665 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.018
                                    G.HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHH CS
                                    x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  90 d.eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklre 139
                                    + e+++++l e  ++ + + +e   ++ v  l+++ + +e+ l+ +e +r+
  gi|119719762|ref|YP_920257.1| 284 ElEKFAKKLEE--LTGYKVKVEDDKSR-VVMLVRDEDVWERNLKMVEEWRA 331
                                    13566666666..88***********9.9****999***********9987 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.3     6e-05      0.27      15      95 ..      69     170 ..      57     189 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6e-05
                        Fer4_12  15 CnlsCkgCfnketw.sfk.........................sgkeftkelleeiiedlkkesiegltllGGEPllpen 68 
                                    C+++Ck+C    +  +fk                          g + + ++ +e + +++ ++ + ++l  GEP+l   
  gi|119719762|ref|YP_920257.1|  69 CDFACKFCWRMHLPgRFKlppgwrwdepediingsivaqrlllIGFKGNPKVSRERFLEAMFPRHFTISLD-GEPSL--- 144
                                    77777777755554422245555555555555555555555554444454444444444446677777765.7****... PP

                        Fer4_12  69 aeallelvkevkeekpekdiwlytgyt 95 
                                    +++l+elvk+vke++++   ++++g++
  gi|119719762|ref|YP_920257.1| 145 YPKLAELVKKVKERNFT-AFLVTNGSI 170
                                    9***************5.899999997 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1     0.024   1.1e+02       6      17 ..      67      78 ..      65      98 .. 0.87
   2 ?    7.3   0.0    0.0011       4.9      55     100 ..     139     179 ..     121     192 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.024
                        Fer4_14  6 sgCnlsCkgCdn 17
                                   + C ++Ck+C +
  gi|119719762|ref|YP_920257.1| 67 NFCDFACKFCWR 78
                                   67********86 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0011
                        Fer4_14  55 GGePLhyenkkellklvkrlkeeypekkiwletngtleielektpd 100
                                     GeP +y   ++l +lvk++ke+   +   l tng++ i le+  +
  gi|119719762|ref|YP_920257.1| 139 DGEPSLY---PKLAELVKKVKERN--FTAFLVTNGSIPIRLEELVK 179
                                    4999988...9************9..9**********999985444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2579.44
//
Query:       gi|119719763|ref|YP_920258.1|  [L=240]
Description: hypothetical protein Tpen_0854 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.5e-55  185.8   0.3    9.2e-55  185.5   0.3    1.0  1  NucS            Endonuclease NucS
    0.00031   20.9   0.0    0.00046   20.3   0.0    1.3  1  Cas_Cas4        Domain of unknown function DUF83
     0.0035   17.3   0.0     0.0048   16.9   0.0    1.3  1  HSDR_N          Type I restriction enzyme R protein N terminu
     0.0044   17.0   0.0      0.011   15.7   0.0    1.7  2  HSDR_N_2        Type I restriction enzyme R protein N terminu
  ------ inclusion threshold ------
      0.012   15.5   1.5       0.79    9.7   0.1    3.1  3  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
      0.036   14.0   0.0      0.064   13.2   0.0    1.3  1  PDDEXK_9        PD-(D/E)XK nuclease superfamily
      0.049   13.5   0.1       0.13   12.1   0.1    1.7  1  betaPIX_CC      betaPIX coiled coil
       0.17   11.6   0.3        2.7    7.7   0.0    2.3  2  Redoxin         Redoxin


Domain annotation for each model (and alignments):
>> NucS  Endonuclease NucS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.5   0.3   4.1e-58   9.2e-55       3     217 ..      15     229 ..      13     237 .. 0.95

  Alignments for each domain:
  == domain 1  score: 185.5 bits;  conditional E-value: 4.1e-58
                           NucS   3 avlvvlarCkvsyeGraksrLeegerlivikpdGaflvhkdrkvePvnWqppkssltaevedgslilksirrkpeeeLkv 82 
                                    +++v++arC+v+yeGra s+Leeg+r+i+ik dG+++vh+   +ePvn+qpp+s + +e +d+ + + + r k +e+L +
  gi|119719763|ref|YP_920258.1|  15 KLVVLVARCTVTYEGRASSKLEEGDRVILIKEDGSVIVHRPVGYEPVNYQPPGSVVSVEGDDDGFRIIVTRTKRRERLLI 94 
                                    799***************************************************************************** PP

                           NucS  83 eieevehasayeledveelvldGseaelaeliiehp.dLieeGfkpvareyav.aiGivdiLgkdeegklvivelkrrka 160
                                    e++ v+h  + +led   +++ G e +l   i+ +p ++++e  kpv  e  + ++G+ d +  d eg+lv+ve+kr ka
  gi|119719763|ref|YP_920258.1|  95 EVHSVKHFFSAKLEDSARFTMWGDEEDLRRAILADPsKMLGENLKPVGAEVSLgSAGFADAVFVDSEGNLVVVEVKREKA 174
                                    ****************************97776665379***********998357************************ PP

                           NucS 161 evdaveqLkryvellkedsvldkvrGvlvapsittdaekllkeeglefkeldppkds 217
                                     v+av qLkryve +k++++  kvrG+l+ap  t  a + lk egle++++   kd+
  gi|119719763|ref|YP_920258.1| 175 SVEAVYQLKRYVERIKRETG-RKVRGILAAPGFTVSAIRALKAEGLEYRQVS-MKDA 229
                                    ********************.9***************************998.5555 PP

>> Cas_Cas4  Domain of unknown function DUF83
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0     2e-07   0.00046      47     109 ..     143     205 ..     123     237 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2e-07
                       Cas_Cas4  47 kevelsesikiDvve.kekeklvvvEvKkskkkeeaaklQllyYlllLe.kkgveikeGvleypk 109
                                     ev+l   +  D v  +++++lvvvEvK+ k+   +a +Ql+ Y+  ++ ++g +++ G+l  p 
  gi|119719763|ref|YP_920258.1| 143 AEVSLGSAGFADAVFvDSEGNLVVVEVKREKASV-EAVYQLKRYVERIKrETGRKVR-GILAAPG 205
                                    6788866888899887899**********99955.5679**********9*******.***9876 PP

>> HSDR_N  Type I restriction enzyme R protein N terminus (HSDR_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   2.1e-06    0.0048     119     159 ..     148     188 ..      85     197 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.1e-06
                                    SS---EEEEEEETTEEEEEEEE--TT-HHHHHHHHTSS--- CS
                         HSDR_N 119 nqkrrpDivlfvnglplvviElKrpgtieeAinQikryrke 159
                                    ++  ++D v    +  lvv+E+Kr+++  eA+ Q+kry ++
  gi|119719763|ref|YP_920258.1| 148 GSAGFADAVFVDSEGNLVVVEVKREKASVEAVYQLKRYVER 188
                                    566789999999999*********98889*********966 PP

>> HSDR_N_2  Type I restriction enzyme R protein N terminus (HSDR_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       3.1     7e+03      41      58 ..      81      98 ..      74     115 .. 0.71
   2 !   15.7   0.0   4.8e-06     0.011      34      79 ..     148     190 ..     119     195 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.1
                       HSDR_N_2 41 ivvykkdkkpllivecKa 58
                                   i+v +++++ +l++e+ +
  gi|119719763|ref|YP_920258.1| 81 IIVTRTKRRERLLIEVHS 98
                                   556666667777777765 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 4.8e-06
                       HSDR_N_2  34 skkkraDivvykkdkkpllivecKapsvkiseevleqlksYlealk 79 
                                    ++ + aD+v+++++   l++ve+K+++ +++  +++qlk+Y+e +k
  gi|119719763|ref|YP_920258.1| 148 GSAGFADAVFVDSE-GNLVVVEVKREKASVE--AVYQLKRYVERIK 190
                                    567789**999988.899*********9885..7*******99875 PP

>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1   0.00035      0.79      21      44 ..      35      59 ..      30      61 .. 0.86
   2 ?   -0.0   0.1      0.39   8.8e+02      24      42 ..      67      87 ..      64      91 .. 0.69
   3 ?    2.9   0.0     0.049   1.1e+02      15      39 ..     152     178 ..     150     185 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00035
                                   EECTCEEEEEECTT.CCCCCCCHHS CS
                 MazE_antitoxin 21 ireGdevelevdgd.kiilrplksl 44
                                   ++eGd+v+l+ +++  i++rp+  +
  gi|119719763|ref|YP_920258.1| 35 LEEGDRVILIKEDGsVIVHRPVGYE 59
                                   89*******99988******99765 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.39
                                   TCEEEEEECTT..CCCCCCCH CS
                 MazE_antitoxin 24 Gdevelevdgd..kiilrplk 42
                                   G+ v +e d+d  +ii++  k
  gi|119719763|ref|YP_920258.1| 67 GSVVSVEGDDDgfRIIVTRTK 87
                                   888888888888866665544 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.049
                                    CHHHCCEEC.TCEEEEEECTT.CCCCC CS
                 MazE_antitoxin  15 vrfelgire.Gdevelevdgd.kiilr 39 
                                    ++++ +++  G+ v++ev+ +  ++ +
  gi|119719763|ref|YP_920258.1| 152 FADAVFVDSeGNLVVVEVKREkASVEA 178
                                    5666677777*********99666655 PP

>> PDDEXK_9  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.8e-05     0.064      29      88 ..     149     197 ..     134     203 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.8e-05
                       PDDEXK_9  29 nkGriDlllkpkektkkkiyifEfKylkekesekekaeealeQikekgyaekykedgkki 88 
                                    + G++D++++   + + +  ++E+K        ++++ ea+ Q+k++ +  k ++  +k+
  gi|119719763|ref|YP_920258.1| 149 SAGFADAVFV---DSEGNLVVVEVK-------REKASVEAVYQLKRYVERIKRETG-RKV 197
                                    57********...788999******.......888888*********999998875.454 PP

>> betaPIX_CC  betaPIX coiled coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   5.7e-05      0.13      27      52 ..     169     194 ..     149     200 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.7e-05
                     betaPIX_CC  27 vleekslVDtVYaLkdevqelkqenk 52 
                                    v +ek+ V +VY+Lk  v+ +k+e+ 
  gi|119719763|ref|YP_920258.1| 169 VKREKASVEAVYQLKRYVERIKRETG 194
                                    678*******************9975 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.098   2.2e+02     117     137 ..      40      61 ..      25      69 .. 0.83
   2 ?    7.7   0.0    0.0012       2.7      79     137 ..     115     174 ..     104     183 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.098
                                    EEEEEEETT.EEEEEEESSSCH CS
                        Redoxin 117 ryavidedg.kvvylevepepe 137
                                    r+++i edg ++v++ v+ ep+
  gi|119719763|ref|YP_920258.1|  40 RVILIKEDGsVIVHRPVGYEPV 61 
                                    89*******8888988888875 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0012
                                    HHHH.TT-TSEEEE-TTSHHHHHTT-TTEEE.GGG.EEE-EEEEEEETTEEEEEEESSSCH CS
                        Redoxin  79 fwgk.eglkfpvlsDgsaaftkalGlrleedaseg.lrtpryavidedgkvvylevepepe 137
                                    +wg+ e+l   +l+D+s+ + ++l+ ++ +  s g  +    + +d +g++v +ev  e+ 
  gi|119719763|ref|YP_920258.1| 115 MWGDeEDLRRAILADPSKMLGENLK-PVGAEVSLGsAGFADAVFVDSEGNLVVVEVKREKA 174
                                    677778888899*************.66666677779************888888877764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 1779.80
//
Query:       gi|119719764|ref|YP_920259.1|  [L=240]
Description: hypothetical protein Tpen_0855 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1613.70
//
Query:       gi|119719765|ref|YP_920260.1|  [L=284]
Description: 2-oxoacid ferredoxin oxidoreductase subunit beta [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.5e-33  114.6   0.1    1.7e-32  112.3   0.0    1.9  2  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
    1.1e-18   67.1   0.1    1.9e-18   66.4   0.1    1.4  1  PFO_beta_C    Pyruvate ferredoxin oxidoreductase beta subunit


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.3   0.0   1.9e-36   1.7e-32       2     153 .]      50     197 ..      49     197 .. 0.97
   2 ?   -0.4   0.0     0.097   8.7e+02     130     147 ..     223     240 ..     214     243 .. 0.83

  Alignments for each domain:
  == domain 1  score: 112.3 bits;  conditional E-value: 1.9e-36
                                    SSHHHHHHHHHHTTSSSSEEEC.ETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEEEEE CS
                   TPP_enzyme_C   2 iGcltlwaarllkvkrprsylt.sgglgtmGyglpaAiGaklakpdrevvaivGDGgflmi.lqelatavrrnlpitvvv 79 
                                    iGc+ +           + y++ +g+++ +G+ lp A+G+kla+p+ +v+  +GDG+ + i l +l +a+rrn++i+++v
  gi|119719765|ref|YP_920260.1|  50 IGCHGR----------ISDYMKtNGFHTIHGRVLPLATGIKLANPNLTVIGHSGDGDAYAIgLGHLPHAARRNIDIKLIV 119
                                    788888..........778888899******************************************************* PP

                                    EE-SBCCCHHHH...HHHHTCCTTTTSBB.BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHHCSSSEEEEEE CS
                   TPP_enzyme_C  80 lnNegygmtggq...qepfggkrksgpagkdlkpvdfaklaealGak.garvekadveeleealkealekkgpaliev 153
                                    +nN ++g+t gq   ++p g k+ks+p g+ ++p+++  la a Ga+ +ar  + +v++l+e +k+a+ +kg+a+i+v
  gi|119719765|ref|YP_920260.1| 120 HNNMVFGLTTGQvtpTTPLGVKTKSTPFGNPEHPLNPLLLALASGATfVARGFSGEVDHLKELIKRAILHKGFAFIDV 197
                                    ***********************************************999999***********************98 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.097
                                    H.HHHHHHHHHHHHCSSS CS
                   TPP_enzyme_C 130 adveeleealkealekkg 147
                                    +dv+ le+a+++a+e+++
  gi|119719765|ref|YP_920260.1| 223 HDVKSLEQAFRRAMETER 240
                                    67899*********8765 PP

>> PFO_beta_C  Pyruvate ferredoxin oxidoreductase beta subunit C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.4   0.1   2.1e-22   1.9e-18       1      63 [.     201     260 ..     201     263 .. 0.97

  Alignments for each domain:
  == domain 1  score: 66.4 bits;  conditional E-value: 2.1e-22
                                    XTTTXSSSXSXXXXX-EEEGGGST---EEHHHHHHHHT-----EEEEEEEETTS--HHHHHHT CS
                     PFO_beta_C   1 CvtFNkvnTfdwYkervykleedgyDpsdlekAlekalewgdkiplGifYkeekptyeerlee 63 
                                    CvtF  +nT+   +e+vyklee+g+D + le+A+++a+e +++ip+G+fY+ e+pt+ee +++
  gi|119719765|ref|YP_920260.1| 201 CVTF--FNTYSILREKVYKLEETGHDVKSLEQAFRRAME-TERIPIGVFYEVERPTLEEAFSH 260
                                    ****..*********************************.*******************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2093.83
//
Query:       gi|119719766|ref|YP_920261.1|  [L=569]
Description: pyruvate flavodoxin/ferredoxin oxidoreductase domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-57  194.8   0.0    2.3e-57  194.4   0.0    1.2  1  POR_N            Pyruvate flavodoxin/ferredoxin oxidoreductas
    4.1e-32  111.6   0.0    8.8e-32  110.6   0.0    1.6  1  POR              Pyruvate ferredoxin/flavodoxin oxidoreductas
    4.9e-09   36.4   0.0    8.9e-09   35.6   0.0    1.5  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
    7.5e-07   28.9   2.0    1.8e-06   27.7   1.1    1.9  2  TPP_enzyme_N     Thiamine pyrophosphate enzyme, N-terminal TP
  ------ inclusion threshold ------
      0.026   14.4   0.0      0.061   13.2   0.0    1.6  1  Transketolase_C  Transketolase, C-terminal domain


Domain annotation for each model (and alignments):
>> POR_N  Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  194.4   0.0   6.4e-61   2.3e-57       2     225 ..     211     441 ..     210     447 .. 0.92

  Alignments for each domain:
  == domain 1  score: 194.4 bits;  conditional E-value: 6.4e-61
                                    HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCCHHH CS
                          POR_N   2 aaiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmienlgl 81 
                                    +a+ ag+ ++aaYP+TP+s+i++ lae  ++ ++   +v+q esE++ai+++iGAa+aGar+++aTSg G++Lm+e+lg 
  gi|119719766|ref|YP_920261.1| 211 GALSAGLTFFAAYPMTPASPILHFLAEVQRDLGI---VVFQPESELAAINMAIGAAYAGARSMVATSGGGFSLMVEALGQ 287
                                    78999***********************999886...******************************************* PP

                                    HHHTT--EEEEEEEEE-STTBEEEEE--TTCHHHH.....S---EEEE-SSHHHHHHHHHHHHHHHHHCTSEEEEEEEHH CS
                          POR_N  82 aageelPvvivvvaRalpstglsirtdqsDlmaar.....dtglivlasenvqeafdlalvAfnlAekvrvPvivlfDgf 156
                                    aa++e+P++iv v+R +pstgl+++t+q+Dl +++     +++ +vla+++  +a+ l  v++nlA+k++vPvi+l+D++
  gi|119719766|ref|YP_920261.1| 288 AAMTETPILIVEVQRPGPSTGLPTHTAQGDLRFVIhasqgEFPRVVLAPGDPYQAYVLGNVGLNLAWKYQVPVIILSDKY 367
                                    ******************************************************************************** PP

                                    HH.HEEEEEEC-SGG..GS-----SBXXXXXXXX.....SXXXBXXTXXTSSXXEEESBXBXTTSXBXXXXHHHH CS
                          POR_N 157 llshevekvelpdee.delklikekleeyerkey.....aldpekpiargtaanpdtglehrekgneaedaaekv 225
                                    l+ +++ +++ +++  +e   +++++++    +y     +++p  ++ + +  ++++ +eh+e+g+ + d +++ 
  gi|119719766|ref|YP_920261.1| 368 LG-ESYWTLKDLPQLgVEEGKVSRESVNGTFPRYkltedGVSPMVFPGTPGSLVYANTSEHDEYGFGTIDPLKVK 441
                                    **.9999998666655766666666666666677688889999999********************999965554 PP

>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.6   0.0   2.4e-35   8.8e-32       2     177 .]      16     175 ..      13     175 .. 0.93

  Alignments for each domain:
  == domain 1  score: 110.6 bits;  conditional E-value: 2.4e-35
                                    TSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHHHHGGGEEEEEE CS
                            POR   2 GqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetlsehldglkpggi 81 
                                    G Gv   + +l+k+++r G+ v+ ++ey+s irGgh +++vr+     +++  + ++d ++ald+ +++ h+++lk+ggi
  gi|119719766|ref|YP_920261.1|  16 GAGVFASSLLLGKTLMRHGFSVFVTNEYPSLIRGGHQWAQVRAVFG-GYSYSHRKTVDAVLALDKFSAEVHIADLKNGGI 94 
                                    99****************************************9998.6677777************************** PP

                                    EEEECTCGTT-CCHHHCTS-HHHHHHHT-EEEEE-HHHHHHHCCC.CCHHHHHHHHHHHHHHTS-HHHHHHHHHCCS-CH CS
                            POR  82 iiynseelkpdelkkakeeerelkerlgvrvygvdatkiakeiggneraaNtvmlGalaallglplealeeaikkrfpkk 161
                                    +++++++ +++  ++               v+++++++i+ke gg ++a Ntv++G+l+++lgl +e  e++i ++f++k
  gi|119719766|ref|YP_920261.1|  95 VVCDEGDAPTQADPR---------------VVAFPLRRIVKEEGGPSVASNTVGVGVLLGALGLRIEIAERVIYDQFRGK 159
                                    *****7644444433...............569*********************************************** PP

                                    .HHHHHHHHHHHHHHH CS
                            POR 162 keviekNlkafragye 177
                                    ke++e+N + +r+g+e
  gi|119719766|ref|YP_920261.1| 160 KEAAELNARLLRRGFE 175
                                    **************86 PP

>> PFOR_II  Pyruvate:ferredoxin oxidoreductase core domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.0   2.5e-12   8.9e-09       3     102 .]     471     558 ..     469     558 .. 0.82

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 2.5e-12
                                    EEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHHHHTGGGT CS
                        PFOR_II   3 vvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevkaalkksk 82 
                                    v++v+ Gs+   +     e+ ++   vGll++ +l PFP++++k+++ + kk++v++ n++    Gqlv+  +++l  + 
  gi|119719766|ref|YP_920261.1| 471 VLVVTWGSTKMIV----LEALRRISGVGLLQVVWLEPFPKNKVKSAV-HGKKILVIENNMT----GQLVSLLREHLFLE- 540
                                    5666666654443....3333344689******************98.999*********5....***********876. PP

                                    SEEEEEE--GGG----HHHH CS
                        PFOR_II  83 vkvvnfvaglgGrditvedi 102
                                      + +++ +  Gr++++ed+
  gi|119719766|ref|YP_920261.1| 541 --PADVLLKYDGRQFYPEDV 558
                                    ..999************997 PP

>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   1.1   5.1e-10   1.8e-06      15     112 ..     216     316 ..     205     333 .. 0.80
   2 ?   -0.9   0.0      0.29   1.1e+03      82      97 ..     349     364 ..     322     366 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 5.1e-10
                                    T--EEEE---CCCHHHHCCHHCT....TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCHHHHHHHHHHT- CS
                   TPP_enzyme_N  15 gvehvfgvpGsrilplldalseeq...girvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnaltalaeAkvdri 91 
                                    g + + ++p +   p+l  l+e q   gi v +  +E +a+++A g a a   + +v++ sg G+  ++ al +A+ + +
  gi|119719766|ref|YP_920261.1| 216 GLTFFAAYPMTPASPILHFLAEVQrdlGIVVFQPESELAAINMAIGAAYAGA-RSMVAT-SGGGFSLMVEALGQAAMTET 293
                                    6666667777777777777777777669*********************965.666666.566***************** PP

                                    -EEEEEEE--CCCHH..S..TC- CS
                   TPP_enzyme_N  92 Pllvlsgdrptslrg..qgvlqq 112
                                    P+l++  +rp  ++g  +++ q+
  gi|119719766|ref|YP_920261.1| 294 PILIVEVQRPGPSTGlpTHTAQG 316
                                    **********9999977555554 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.29
                                    HHHHHHHHT--EEEEE CS
                   TPP_enzyme_N  82 alaeAkvdriPllvls 97 
                                    +l  A++ ++P+++ls
  gi|119719766|ref|YP_920261.1| 349 GLNLAWKYQVPVIILS 364
                                    67789********997 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.7e-05     0.061      11      72 ..     470     526 ..     463     556 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.7e-05
                                    SEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEES CS
                Transketolase_C  11 dvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeavk 72 
                                    +v++v++Gs+   +leA  +++    ++ ++ + +++p+ k+ ++ s+ + ++++v+e++++
  gi|119719766|ref|YP_920261.1| 470 EVLVVTWGSTKMIVLEALRRIS----GVGLLQVVWLEPFPKNKVK-SAVHGKKILVIENNMT 526
                                    89*****************996....999***************9.8888888888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (569 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 3901.94
//
Query:       gi|119719767|ref|YP_920262.1|  [L=165]
Description: hypothetical protein Tpen_0858 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-24   85.4   0.0    3.6e-24   85.1   0.0    1.1  1  DUF123    Domain of unknown function DUF123


Domain annotation for each model (and alignments):
>> DUF123  Domain of unknown function DUF123
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.1   0.0     2e-28   3.6e-24       2      93 ..      43     135 ..      42     136 .. 0.90

  Alignments for each domain:
  == domain 1  score: 85.1 bits;  conditional E-value: 2e-28
                         DUF123   2 elkkgvylYvGsalgsgglasRvkrHaslskkkekklhWhiDyLleseeaelaevvvaseerlEcalaeal.e.aea..p 77 
                                    +l++g+ylY+Gsa+g+ggl++Rv+rH++++    k+ hWhiD Ll+++ a++a vv+ +++  Ec l++ l e   +  p
  gi|119719767|ref|YP_920262.1|  43 TLRAGIYLYLGSAKGPGGLRARVSRHLRRE----KRVHWHIDRLLAAPGASVAYVVYGETHLPECVLTRPLeElG-CrhP 117
                                    789***********************6655....58*********************99999*********5442.3459 PP

                         DUF123  78 vagfGasDck..cesHLl 93 
                                    ++gfG+sDck  c+sHLl
  gi|119719767|ref|YP_920262.1| 118 LPGFGSSDCKhgCTSHLL 135
                                    *********999*****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1249.04
//
Query:       gi|119719768|ref|YP_920263.1|  [L=413]
Description: quinolinate phosphoribosyl transferase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-19   70.5   0.0    1.9e-19   70.1   0.0    1.2  1  QRPTase_C        Quinolinate phosphoribosyl transferase, C-te
    0.00081   19.8   0.1     0.0064   16.9   0.0    2.1  2  NAPRTase_C       Nicotinate phosphoribosyltransferase C-termi
     0.0038   17.3   0.7     0.0072   16.4   0.7    1.4  1  Zn-ribbon_8      Zinc ribbon domain
     0.0096   16.3   0.0        1.5    9.2   0.0    2.3  2  NAPRTase_N       Nicotinate phosphoribosyltransferase (NAPRTa
       0.01   15.3   0.0      0.016   14.6   0.0    1.3  1  Ribul_P_3_epim   Ribulose-phosphate 3 epimerase family
  ------ inclusion threshold ------
      0.012   15.7   0.0      0.028   14.5   0.0    1.7  1  QRPTase_N        Quinolinate phosphoribosyl transferase, N-te
      0.014   15.0   0.0       0.03   14.0   0.0    1.4  1  NAPRTase         Nicotinate phosphoribosyltransferase (NAPRTa
       0.11   12.3   0.1        1.7    8.5   0.2    2.5  3  MCM_OB           MCM OB domain
       0.26   10.9   2.1       0.47   10.1   2.1    1.4  1  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain


Domain annotation for each model (and alignments):
>> QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.1   0.0   9.5e-23   1.9e-19       1     169 []     130     323 ..     130     323 .. 0.89

  Alignments for each domain:
  == domain 1  score: 70.1 bits;  conditional E-value: 9.5e-23
                                    HHHHHHHHHHHHHCTSSEEEE-S---TTTHHHHHHHHHHTTSB.......--TSSTTTSEEE-HHHHHHH....SSHHHH CS
                      QRPTase_C   1 iAtltarmveaaksakvrildTRkttPglrllekyAvliGGgd.......nhrlgLsdmvlikdnhiaaa....gsivea 69 
                                    iAt++ar+++aa ++ v +++ R+ +P+l+++ +  ++iGG+d          lg++ + ++++  ++++    g+ +  
  gi|119719768|ref|YP_920263.1| 130 IATKAARVKKAAGDKLVLSFGARRQHPALAPFVEFYAYIGGADavsavlgAEALGIKPTGTMPHSLLIIFrafkGDHSLG 209
                                    9*************************************************9**************987763333678899 PP

                                    HHHHHHHHTTTSE.EEEEESSHHHHHHHHH.HT.....-SEEEEES--H..HHHHHHHHHH.HHHSTT....SEEEEESS CS
                      QRPTase_C  70 vksvreavdkevk.ievevesleeleevle.ae.....adiimLDnfsv..eelkkaveel.keknkr....vlievSGg 135
                                    +k+++e+++k v+ + +   + +e+eev+  a+       +++LD++ +   ++++++ e+ ++ +      v+i vSGg
  gi|119719768|ref|YP_920263.1| 210 WKAFDEVIEKDVArVALADTFFDETEEVVLaAKtlgekLWGVRLDTPGSrrGNFEDIIREVrWRLDTLgykhVKIVVSGG 289
                                    ********999999988888888888876633355544889******776689*****99967776657889******** PP

                                    --TTTHHHHHCTT-SEEEECHHCHTB----EEEE CS
                      QRPTase_C 136 vtlenveeyaksgvdvisvgalthsvkalDislk 169
                                    + +  +  +a+ g d+++vga+++ ++++D++++
  gi|119719768|ref|YP_920263.1| 290 IDEYRIPSLARAGADAFGVGAAISTAPPIDFAMD 323
                                    ********************************96 PP

>> NAPRTase_C  Nicotinate phosphoribosyltransferase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.55   1.1e+03       1      26 [.     345     366 ..     345     371 .. 0.79
   2 !   16.9   0.0   3.2e-06    0.0064      50      87 ..     374     411 ..     369     412 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.55
                     NAPRTase_C   1 rKkvyRlydkdgkalaDlialadeke 26 
                                    +K+vyR     +k ++D+++l+  ++
  gi|119719768|ref|YP_920263.1| 345 KKQVYR----CDKCMVDVVVLEGSEP 366
                                    699999....5779999999998754 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 3.2e-06
                     NAPRTase_C  50 srvekLlkkvfkdGklvyelpsleeireyvkeqlaelr 87 
                                    +++e+Ll+++++dG+ ++ ++s +e+r++v eql++l+
  gi|119719768|ref|YP_920263.1| 374 AQMEPLLETFIEDGRPTKRVESPQEVRARVLEQLSRLE 411
                                    579********************************997 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.7   3.6e-06    0.0072       6      36 ..     349     376 ..     348     379 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.6e-06
                    Zn-ribbon_8   6 YrCeeCghefevlqsisdapltaCPeCgsev 36 
                                    YrC++C  +  vl   s+  +++CP+Cg+++
  gi|119719768|ref|YP_920263.1| 349 YRCDKCMVDVVVLEG-SE--PPVCPKCGAQM 376
                                    *******77777763.33..457*****976 PP

>> NAPRTase_N  Nicotinate phosphoribosyltransferase (NAPRTase) N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0   0.00078       1.5       1      57 [.      24      81 ..      24      86 .. 0.93
   2 ?    5.0   0.0     0.016        31     100     122 ..     100     122 ..      83     125 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00078
                     NAPRTase_N  1 LdtDlYkltmaqavfkkgp.dvevvfelffRkkpfkgeyaivagleevieylenlrft 57
                                   L tD Y +    ++ k g  d+ev +e++  + p++++ +++agl+ev++ le  r+t
  gi|119719768|ref|YP_920263.1| 24 LTTDIYFVRTRRILEKYGLlDAEVHMEVTASRLPEDYRWGVFAGLREVLKLLEGKRVT 81
                                   789***9999999999999***************9*****************987776 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.016
                     NAPRTase_N 100 gepeirveGpwieaillEtplLa 122
                                    + p ++veGp  e   lEtplL 
  gi|119719768|ref|YP_920263.1| 100 KIPVLTVEGPYGEFVELETPLLG 122
                                    5689*****************95 PP

>> Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   7.9e-06     0.016     153     197 ..     267     312 ..     261     313 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 7.9e-06
                                    HHHHHHHHHHHT.---EEEEESS--TTTCHHHHHHT--EEEESHHH CS
                 Ribul_P_3_epim 153 ikkvrklideke.ldlkievDGGvkldnieqiaeagadvlVagsav 197
                                    i++vr ++d+ + +++ki v GG+++  i  +a+agad++ +g a+
  gi|119719768|ref|YP_920263.1| 267 IREVRWRLDTLGyKHVKIVVSGGIDEYRIPSLARAGADAFGVGAAI 312
                                    8999999999886789*************************99997 PP

>> QRPTase_N  Quinolinate phosphoribosyl transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.4e-05     0.028      26      89 .]      61     128 ..      47     128 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.4e-05
                                    SSEEE-SHHHHHHHHHHHTTTEEEESS-TT-EEETTE......EEEEEEEEHHHHHHHHHHHHHHHHHHH CS
                      QRPTase_N  26 eegvvaGlevaeevfellpglevellvkDGervekgd......vlleieGnarallsaERvaLnllqrlS 89 
                                     +gv+aGl ++ +++e    ++v +l ++G+ ++++d       +l++eG++ ++ + E  +L +l  +S
  gi|119719768|ref|YP_920263.1|  61 RWGVFAGLREVLKLLEGK-RVTVRAL-PEGTLFKAQDyygykiPVLTVEGPYGEFVELETPLLGFLASAS 128
                                    689******999999988.9999887.999999998855555579*********************9877 PP

>> NAPRTase  Nicotinate phosphoribosyltransferase (NAPRTase) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.5e-05      0.03      32     210 ..     168     339 ..     149     352 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.5e-05
                                    EEEESBHHH...HHHHT--B--HHHHHHHHHHHHHHCHHHHHCCHHHHHHHHHHHHHCCHIIEEECHCCTHHHHHCCS-C CS
                       NAPRTase  32 flGtdnvla...aakysikaaetsahealgkeqelsafrnnlkqfqkdaldlwvaiekgnlgiaLtdlvltdaflkdfrl 108
                                    + G d v+a   a++++ik+ +t+ h++l  +++ +      +    +a d  ++ +   +  aL d++ ++ +     +
  gi|119719768|ref|YP_920263.1| 168 IGGADAVSAvlgAEALGIKPTGTMPHSLLIIFRAFKG----DHSLGWKAFDEVIEKD--VARVALADTFFDETEEVVLAA 241
                                    56777777777799***************99988887....2233347777666555..799999999998887755554 PP

                                    C..HHHSEEEEE-S.....S-HHHHHHHHHHHHHCTCTTTCC.CSEEEEESS-SHHHHHHHHHHHHHTTCEEEEEESHHH CS
                       NAPRTase 109 e..akaylgvRpDS.....Gdpvevieklaahygstlnskgy.tkrlifsDgldvekiieilealkkkgfniaFGiGtnl 180
                                    +   ++  gvR D      G      e ++   +  l   gy ++ ++ s g+d  +i ++ +a  +     aFG+G+++
  gi|119719768|ref|YP_920263.1| 242 KtlGEKLWGVRLDTpgsrrG----NFEDIIREVRWRLDTLGYkHVKIVVSGGIDEYRIPSLARAGAD-----AFGVGAAI 312
                                    45778888*****7422334....5555555555555555888999*********************.....*******9 PP

                                    HSSECTTCTTTCCEEEEEEEEEEEEEETTE CS
                       NAPRTase 181 tqdlnrdtlefavkasalniviklvevnkd 210
                                        +     fa+ ++a++ ++++v + k+
  gi|119719768|ref|YP_920263.1| 313 STAPPI---DFAMDITAVKREGRWVPISKR 339
                                    888777...9***************99997 PP

>> MCM_OB  MCM OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.68   1.4e+03       5      30 ..     116     141 ..     113     147 .. 0.82
   2 ?   -0.7   0.0       0.6   1.2e+03      90     103 ..     187     200 ..     181     205 .. 0.85
   3 ?    8.5   0.2   0.00087       1.7      31      63 ..     345     376 ..     338     400 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.68
                                    --GGGTTSEEEEEEEEEEE---EEEE CS
                         MCM_OB   5 lrsehigklvkveGivtrasevkpkl 30 
                                    l++  +g l + +Gi t+a +vk+ +
  gi|119719768|ref|YP_920263.1| 116 LETPLLGFLASASGIATKAARVKKAA 141
                                    666678889999********999765 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.6
                                    -------EEEEEEE CS
                         MCM_OB  90 paGelPrslevile 103
                                    p+G++P+sl +i++
  gi|119719768|ref|YP_920263.1| 187 PTGTMPHSLLIIFR 200
                                    99*******99986 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.00087
                                    EEEEEEETTT-.-EE.ES----SB-..TTT-HHH CS
                         MCM_OB  31 kkavfeckkcgktve.veleePrkCeekeCeskd 63 
                                    kk v++c+kc   v  +e +eP  C  ++C+++ 
  gi|119719768|ref|YP_920263.1| 345 KKQVYRCDKCMVDVVvLEGSEPPVC--PKCGAQM 376
                                    5789*******9888569999****..99*9543 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   2.1   0.00024      0.47       3      34 ..     345     377 ..     343     379 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00024
                                    TT-EEE-TTT--EEEECC--SS-EEE..TTEE-E CS
                Desulfoferrod_N   3 klevYkCevCGniVeVleaGgGeLVC..CgepMk 34 
                                    k +vY+C  C   V+Vle G    VC  Cg  M+
  gi|119719768|ref|YP_920263.1| 345 KKQVYRCDKCMVDVVVLE-GSEPPVCpkCGAQME 377
                                    78********99999986.677778888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.51
# Mc/sec: 2446.15
//
Query:       gi|119719769|ref|YP_920264.1|  [L=114]
Description: regulatory protein, ArsR [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-10   40.7   0.2    2.9e-10   40.0   0.2    1.3  1  HTH_20         Helix-turn-helix domain
    2.1e-08   33.9   0.2    3.1e-08   33.4   0.2    1.3  1  HTH_5          Bacterial regulatory protein, arsR family
    2.2e-07   30.3   0.2    3.2e-07   29.8   0.2    1.3  1  HTH_24         Winged helix-turn-helix DNA-binding
    3.5e-05   23.6   0.3    6.5e-05   22.7   0.3    1.4  1  MarR_2         MarR family
    8.3e-05   22.7   0.0    0.00014   21.9   0.0    1.4  1  HTH_34         Winged helix DNA-binding domain
    0.00042   20.2   0.0    0.00066   19.5   0.0    1.3  1  MarR           MarR family
     0.0041   17.2   1.0      0.007   16.5   0.2    1.7  2  DprA_WH        DprA winged helix domain
  ------ inclusion threshold ------
      0.032   14.0   0.1      0.055   13.3   0.1    1.4  1  HTH_IclR       IclR helix-turn-helix domain
      0.059   13.2   0.2       0.14   12.0   0.2    1.6  1  HTH_AsnC-type  AsnC-type helix-turn-helix domain
       0.12   12.3   0.0       0.18   11.7   0.0    1.3  1  TrmB           Sugar-specific transcriptional regulator TrmB
       0.15   12.1   0.0       0.24   11.5   0.0    1.3  1  FeoC           FeoC like transcriptional regulator


Domain annotation for each model (and alignments):
>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   0.2   1.8e-13   2.9e-10       5      59 ..      10      64 ..       6      66 .. 0.96

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 1.8e-13
                                   HHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
                         HTH_20  5 eALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvre 59
                                   eAL +P Rrri  +L ++ g++  +l + l++s  +ls HL +Le++gL++ vr 
  gi|119719769|ref|YP_920264.1| 10 EALKNPLRRRIVTYLLDNPGASIRQLSRSLGVSIGSLSGHLVILERVGLIREVRN 64
                                   89**************************************************996 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.2   1.9e-11   3.1e-08       1      46 [.      14      60 ..      14      61 .. 0.97

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 1.9e-11
                                   SHHHHHHHHHHTTSS.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_5  1 dptRlkILklLaege.lcvcelaeelglsqstvShHLkkLreaGLVe 46
                                   +p R++I+ +L +++ +++ +l++ lg+s + +S HL +L+  GL++
  gi|119719769|ref|YP_920264.1| 14 NPLRRRIVTYLLDNPgASIRQLSRSLGVSIGSLSGHLVILERVGLIR 60
                                   699******************************************96 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.2     2e-10   3.2e-07       2      48 .]      14      60 ..      13      60 .. 0.93

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 2e-10
                         HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                   + ++r+I  +L +np+ s+r+L++ lg+S++ ++ +l  Le+ GlI+
  gi|119719769|ref|YP_920264.1| 14 NPLRRRIVTYLLDNPGASIRQLSRSLGVSIGSLSGHLVILERVGLIR 60
                                   6789******************************9999999999886 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.3     4e-08   6.5e-05       5      59 ..      15      65 ..      10      67 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 4e-08
                                   HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSS CS
                         MarR_2  5 paqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeD 59
                                   p  +r+  +L ++pg   ++++l r lg+s +++s +l  L++ GL++++++   
  gi|119719769|ref|YP_920264.1| 15 PLRRRIVTYLLDNPG--ASIRQLSRSLGVSIGSLSGHLVILERVGLIREVRN--S 65
                                   77899999*******..9********************************98..4 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   8.7e-08   0.00014       2      45 ..      17      60 ..      16      71 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 8.7e-08
                         HTH_34  2 RlavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYie 45
                                   R  +++yL+++  a+ ++l+ +l+++ g Ls hl +Le  g i 
  gi|119719769|ref|YP_920264.1| 17 RRRIVTYLLDNPGASIRQLSRSLGVSIGSLSGHLVILERVGLIR 60
                                   6789***********************************99884 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   4.1e-07   0.00066       7      52 ..      19      64 ..      14      67 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 4.1e-07
                                   HHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE CS
                           MarR  7 viLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRsks 52
                                   +i++ l +++++s+ +L + lgvs+++++  l  Le+ Gli+  ++
  gi|119719769|ref|YP_920264.1| 19 RIVTYLLDNPGASIRQLSRSLGVSIGSLSGHLVILERVGLIREVRN 64
                                   577788899********************************96665 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.2   4.3e-06     0.007      11      56 ..      14      60 ..       6      63 .. 0.83
   2 ?   -1.6   0.0       1.8   2.9e+03      50      59 ..      90      99 ..      90     100 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.3e-06
                        DprA_WH 11 ddlerrvLaaLgpeP.vhvDqLvrrtglpaaevsaaLleLELaGlve 56
                                    +l+rr+++ L   P  ++ qL+r +g++++++s +L+ LE  Gl++
  gi|119719769|ref|YP_920264.1| 14 NPLRRRIVTYLLDNPgASIRQLSRSLGVSIGSLSGHLVILERVGLIR 60
                                   57888888777555416999*********************999998 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.8
                        DprA_WH 50 ELaGlverlp 59
                                   E +G v+r+p
  gi|119719769|ref|YP_920264.1| 90 EADGEVARQP 99
                                   6689****98 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   3.4e-05     0.055      14      50 ..      26      61 ..      19      63 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.4e-05
                                   TTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                       HTH_IclR 14 eapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                     p+  ++++l+r +g++  + +++L  L++ G+++ 
  gi|119719769|ref|YP_920264.1| 26 DNPG-ASIRQLSRSLGVSIGSLSGHLVILERVGLIRE 61
                                   5555.49***************************986 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   8.4e-05      0.14       6      30 ..      18      42 ..      16      46 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.4e-05
                  HTH_AsnC-type  6 rkILeaLqedaRisyaeLAervGlS 30
                                   r+I+  L  ++ +s ++L++ +G+S
  gi|119719769|ref|YP_920264.1| 18 RRIVTYLLDNPGASIRQLSRSLGVS 42
                                   89**********************9 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00011      0.18      16      59 ..      23      66 ..      19      72 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00011
                                   HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTT CS
                           TrmB 16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrp 59
                                   +Ll +  a+++++++ lgv+  +    L  Le+ Gl++ ++ ++
  gi|119719769|ref|YP_920264.1| 23 YLLDNPGASIRQLSRSLGVSIGSLSGHLVILERVGLIREVRNSK 66
                                   799**********************************9998765 PP

>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00014      0.24       7      50 ..      22      65 ..      18      69 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00014
                           FeoC  7 eyleergrvslkeLsrhfkaspealeamLeqwvrkGrvekvaat 50
                                    yl  +  +s+++Lsr + +s   l + L +++r G +++v ++
  gi|119719769|ref|YP_920264.1| 22 TYLLDNPGASIRQLSRSLGVSIGSLSGHLVILERVGLIREVRNS 65
                                   57778888*******************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 788.26
//
Query:       gi|119719770|ref|YP_920265.1|  [L=744]
Description: DEAD/DEAH box helicase domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.1e-26   91.8   0.0    2.8e-25   89.1   0.0    2.1  2  DEAD           DEAD/DEAH box helicase
      3e-19   69.4   0.0    5.4e-17   62.1   0.0    2.5  2  Helicase_C     Helicase conserved C-terminal domain
    2.3e-14   53.9   0.1    5.8e-14   52.6   0.1    1.8  1  DUF1998        Domain of unknown function (DUF1998)
    5.9e-05   23.1   0.0    0.00011   22.2   0.0    1.4  1  ResIII         Type III restriction enzyme, res subunit
     0.0042   16.7   0.0      0.006   16.1   0.0    1.2  1  UvrD-helicase  UvrD/REP helicase N-terminal domain
     0.0077   16.6   0.0      0.018   15.4   0.0    1.7  1  AAA_19         AAA domain
  ------ inclusion threshold ------
       0.11   12.1   0.0       0.28   10.9   0.0    1.6  1  AAA_30         AAA domain


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.1   0.0   1.1e-28   2.8e-25       2     170 ..      58     223 ..      57     228 .. 0.88
   2 ?   -0.2   0.0      0.28   7.2e+02      84     105 ..     313     335 ..     264     350 .. 0.67

  Alignments for each domain:
  == domain 1  score: 89.1 bits;  conditional E-value: 1.1e-28
                                    HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTT.STSEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
                           DEAD   2 diQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkky.idlrvll 80 
                                    + Qaeai+ i +g++ l+ a TG+GKT+afl+p+l+++y+   +++   ++v Pt++La+++++++ ++     + rv+ 
  gi|119719770|ref|YP_920265.1|  58 RFQAEAIESIRSGNNTLIIAGTGTGKTEAFLVPILERLYR---EPEETGILVYPTKALARDQVERIYSYAGAvFGFRVS- 133
                                    68************************************97...666677*****************9999986889986. PP

                                    EETTSSHHHHHHHHHTT.CSEEEEEHHHHHHHHHCTS.SH..CTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTS CS
                                    xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx.xx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  81 iiggvaardqlskldng.vdivvgtpgrlddllstgk.ln..lsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdg 156
                                    ++ g++ +++++ l+   ++++v++p++l+  l++g+ ++  l++ +f+VlD a+ ++   f+ +++ +l+++++     
  gi|119719770|ref|YP_920265.1| 134 VYDGDTPEKEREMLQVYpPRLLVTNPDMLHLSLRRGEgVKpiLEKAKFVVLDDAHIYSGV-FGSHVHYVLKRMKRFM--- 209
                                    999***********7446************999766634478*****************8.************6553... PP

                                    TTTSEEEEEESSBS CS
                                    xxxxxxxxxxxxxx RF
                           DEAD 157 klqrqvivlSATlp 170
                                    +++  +++ SAT+ 
  gi|119719770|ref|YP_920265.1| 210 PADAVFVASSATIG 223
                                    4455699999*985 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.28
                                    TSSHHHHHHHHHTT.CSEEEEEH CS
                                    xxxxxxxxxxxxxx.xxxxxxxx RF
                           DEAD  84 gvaardqlskldng.vdivvgtp 105
                                     + +r+  +kl++g +d vv+tp
  gi|119719770|ref|YP_920265.1| 313 PSHRRSVEEKLRKGeLDAVVTTP 335
                                    35566667777766688888887 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.016        42      14      56 ..      98     145 ..      86     149 .. 0.66
   2 !   62.1   0.0   2.1e-20   5.4e-17       5     111 .]     268     372 ..     261     372 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.016
                                    TTTSEEEEEESSHH....HHHH.HHHHHHHTTSTEEEESTTSTHHHHH CS
                     Helicase_C  14 eeggkilifvntid....rlek.vklllekkgikvavlhgelpqnere 56 
                                    e +++ +++ +t+     ++e+  ++    +g++v v++g++p +ere
  gi|119719770|ref|YP_920265.1|  98 EPEETGILVYPTKAlardQVERiYSYAGAVFGFRVSVYDGDTPEKERE 145
                                    4555556666666643333332445556667****************8 PP

  == domain 2  score: 62.1 bits;  conditional E-value: 2.1e-20
                                    HHHHHHHHTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTT CS
                     Helicase_C   5 allellkleeeggkilifvntidrlekvklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipk 84 
                                    +ll+   l e++ ++l+fv + + +e++++l +++g+kv v+ + l  ++r+ + e+ +kge d +++t  +e Gidi +
  gi|119719770|ref|YP_920265.1| 268 RLLK--ILAERRLRTLLFVDSHKVAESLSVLAQREGLKVSVHRAGLLPSHRRSVEEKLRKGELDAVVTTPTLELGIDIGE 345
                                    3444..458999***********998899999999********************************************* PP

                                    ESEEEESSSSSSHHHHHHHHTTSSSTT CS
                     Helicase_C  85 vnlVinfdlprnvtsyiqriGRtgRag 111
                                    ++ V+ +++p + ++y+qr+GR+gR g
  gi|119719770|ref|YP_920265.1| 346 LDAVVLYGVPPTFSKYVQRAGRVGRRG 372
                                    *************************75 PP

>> DUF1998  Domain of unknown function (DUF1998)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.6   0.1   2.3e-17   5.8e-14       2      83 .]     630     702 ..     629     702 .. 0.96

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 2.3e-17
                        DUF1998   2 ehalinalplflqcdesdlgteckapedeprkrpariliydavpgGaGiaekaaelleellraalelieecdCeeaGCpa 81 
                                    ehali a +l+++  + d+g+ +             i+iyda pgG+G+++++ e l+e l++a +++++c+Ce +GCp+
  gi|119719770|ref|YP_920265.1| 630 EHALIYAGQLVVGAAPTDMGGISF--------PSGHIYIYDAFPGGSGVTKQLLERLKEALHKAFDIVSRCTCE-DGCPK 700
                                    8**********************7........4689*************************************8.***** PP

                        DUF1998  82 Cl 83 
                                    C+
  gi|119719770|ref|YP_920265.1| 701 CI 702
                                    *7 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   4.5e-08   0.00011       4     146 ..      56     192 ..      53     222 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 4.5e-08
                                    E-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHH.HHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG.. CS
                         ResIII   4 lreyQeeaienlleklkskrdkrglikmaTGtGKTlva.aklierllkkgkeekflflvprkslleqtleefkkflseay 82 
                                    l+  Q+eaie+++        ++ li + TGtGKT    + + erl++ ++ee  +++ p+k+l     e++ +++   +
  gi|119719770|ref|YP_920265.1|  56 LYRFQAEAIESIR------SGNNTLIIAGTGTGKTEAFlVPILERLYR-EPEETGILVYPTKALARDQVERIYSYAGAVF 128
                                    5566778888775......56789999*********995556666666.5888**************************9 PP

                                    ..GEEEESSS-B--.........-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS CS
                         ResIII  83 keigkkvsgdkkka..kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlga 146
                                     +   +++gd+ ++  ++ +    ++lvt+ ++l+ ++  ++ e  +   ++ ++++ D aH +++
  gi|119719770|ref|YP_920265.1| 129 GFRVSVYDGDTPEKerEMLQVYPPRLLVTNPDMLHLSL--RRGEGVKPILEKAKFVVLDDAHIYSG 192
                                    999999999999885555566677999********999..556777788888889999***97766 PP

>> UvrD-helicase  UvrD/REP helicase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   2.4e-06     0.006       5      51 ..      60     107 ..      56     158 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.4e-06
                                    HHHHHHS..-SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEE CS
                  UvrD-helicase   5 qreaias..lggpilveAsAGsGKTfvlaerilrlikeeeiepdrilvv 51 
                                    q eai+s  +g+++l++A+ G+GKT      il+ +  e  e + ilv 
  gi|119719770|ref|YP_920265.1|  60 QAEAIESirSGNNTLIIAGTGTGKTEAFLVPILERLYRE-PEETGILVY 107
                                    88999999899***************9999999998888.666667765 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0     7e-06     0.018       1      56 [.      60     114 ..      60     185 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 7e-06
                         AAA_19   1 qreave.alkekvllvtaGpGtGKTrv.lkhivallvelggvkpeeillvaftgrAak 56 
                                    q ea+e   + ++ l++aG GtGKT+  l+ i++ l ++     e+ +lv +t+  a+
  gi|119719770|ref|YP_920265.1|  60 QAEAIEsIRSGNNTLIIAGTGTGKTEAfLVPILERLYREP---EETGILVYPTKALAR 114
                                    7899987888899************861444444444444...345556666655444 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00011      0.28       2      59 ..      56     113 ..      55     128 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00011
                         AAA_30   2 lnaeQaaavealltsgdrvavltGpAGtGKtta..lkalreaweaaggrviglAptgkaA 59 
                                    l   Qa+a+e++ ++++  +++ ++ GtGKt a  +  l++++++ +++ i++ pt++ A
  gi|119719770|ref|YP_920265.1|  56 LYRFQAEAIESIRSGNN--TLIIAGTGTGKTEAflVPILERLYREPEETGILVYPTKALA 113
                                    5667********99997..999999******76113344666665555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (744 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.45
# Mc/sec: 4973.62
//
Query:       gi|119719771|ref|YP_920266.1|  [L=441]
Description: TIP49-like [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.3e-138  462.0   0.0   1.7e-138  461.6   0.0    1.2  1  TIP49            TIP49 P-loop domain
      1e-23   83.2   0.1    6.9e-23   80.6   0.2    2.2  2  TIP49_C          TIP49 AAA-lid domain
    1.3e-11   45.1   1.6    9.2e-09   35.8   0.0    3.1  3  AAA              ATPase family associated with various cellul
    8.4e-08   32.1   0.4    3.7e-05   23.5   0.0    2.9  3  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    4.8e-07   30.1   0.0     0.0094   16.2   0.0    2.7  2  AAA_22           AAA domain
    9.9e-06   26.0   0.3    0.00027   21.4   0.3    2.5  1  AAA_16           AAA ATPase domain
    2.5e-05   23.9   0.0    0.00028   20.5   0.0    2.1  2  AAA_7            P-loop containing dynein motor region
    8.3e-05   22.1   0.5    0.00034   20.1   0.1    1.9  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    0.00014   22.2   0.2      0.042   14.2   0.0    2.8  2  AAA_19           AAA domain
    0.00019   21.5   0.2     0.0029   17.6   0.0    2.7  3  AAA_5            AAA domain (dynein-related subfamily)
    0.00029   21.4   0.0     0.0025   18.4   0.0    2.5  2  AAA_18           AAA domain
    0.00071   19.2   2.7     0.0042   16.7   0.4    2.7  3  AAA_25           AAA domain
     0.0014   18.8   0.1      0.012   15.8   0.0    2.2  2  AAA_28           AAA domain
     0.0026   17.5   0.1     0.0055   16.5   0.1    1.5  1  IstB_IS21        IstB-like ATP binding protein
     0.0068   16.9   0.0      0.013   16.0   0.0    1.5  1  ABC_tran         ABC transporter
  ------ inclusion threshold ------
      0.011   15.0   0.0       0.03   13.7   0.0    1.6  2  DnaB_C           DnaB-like helicase C terminal domain
      0.012   15.3   0.0       0.12   12.0   0.0    2.3  2  Sigma54_activat  Sigma-54 interaction domain
      0.013   15.7   0.0      0.038   14.2   0.0    1.8  1  AAA_33           AAA domain
      0.014   15.1   1.0       0.16   11.6   0.5    2.7  2  AAA_30           AAA domain
       0.03   13.6   0.2      0.079   12.2   0.1    1.7  1  Zeta_toxin       Zeta toxin
      0.033   13.4   0.0      0.094   11.9   0.0    1.7  2  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.037   13.5   0.1      0.071   12.5   0.1    1.4  1  PhoH             PhoH-like protein
      0.049   13.3   0.0       0.69    9.6   0.0    2.4  2  AAA_24           AAA domain
       0.05   13.4   0.0       0.09   12.6   0.0    1.4  1  AAA_11           AAA domain
      0.052   14.0   0.1        0.2   12.1   0.0    2.1  2  AAA_17           AAA domain
      0.054   12.8   0.1       0.14   11.5   0.1    1.7  1  ATPase           KaiC
       0.07   13.0   0.5        8.7    6.3   0.1    3.3  3  RHH_5            CopG-like RHH_1 or ribbon-helix-helix domain
      0.093   12.7   0.0       0.18   11.8   0.0    1.4  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
        0.1   11.7   0.1       0.17   11.0   0.1    1.3  1  Parvo_NS1        Parvovirus non-structural protein NS1
       0.11   12.6   0.0        4.4    7.4   0.0    2.5  2  AAA_2            AAA domain (Cdc48 subfamily)
       0.12   12.5   0.0        4.6    7.3   0.0    2.3  2  TFIID-31kDa      Transcription initiation factor IID, 31kD su
       0.13   11.7   0.0       0.27   10.6   0.0    1.5  1  IPT              Isopentenyl transferase
       0.13   11.4   0.0       0.25   10.5   0.0    1.4  1  DUF815           Protein of unknown function (DUF815)
       0.14   12.1   0.1       0.74    9.8   0.0    2.1  2  ResIII           Type III restriction enzyme, res subunit
       0.14   12.1   0.0        2.6    8.1   0.0    2.7  3  AAA_14           AAA domain
       0.15   12.5   0.0       0.32   11.4   0.0    1.6  1  RNA_helicase     RNA helicase
       0.17   11.8   0.0       0.43   10.5   0.0    1.7  1  NACHT            NACHT domain
       0.18   11.7   0.0       0.35   10.8   0.0    1.4  1  Rad17            Rad17 P-loop domain


Domain annotation for each model (and alignments):
>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  461.6   0.0  3.7e-141  1.7e-138       1     350 [.       7     353 ..       7     354 .. 0.98

  Alignments for each domain:
  == domain 1  score: 461.6 bits;  conditional E-value: 3.7e-141
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49   1 rislhshikgLGldedgeaekeeeglvGqkkareaagvivelikekklaGravLlaGpsgtGktalaiaiskelgedvpf 80 
                                    ri++hshikgLG+ ++ e+  +++glvGq++ar+aa ++v+lik++k+aGra+Ll+Gp+gtGkta+a+ai++elg ++pf
  gi|119719771|ref|YP_920266.1|   7 RIGVHSHIKGLGIRNN-EPLPVADGLVGQIEARRAAWLVVQLIKAGKMAGRAILLVGPPGTGKTAIAVAIARELGPETPF 85 
                                    799**********988.899************************************************************ PP

                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-S-EEEEEEEEEEE...-SSS-...TTS--EEEEEE-SS-EEEEEE- CS
                          TIP49  81 valsgsevyslevkktevltqalrksigvrikeekevleGevveleveeaenpls.kekkikevkitlktakeekklklg 159
                                    +alsgse+ys+e+kktevl+qalrksigvri+e++ ++eG v +++++  ++pl+ + +     +itl+t+ke+++l+++
  gi|119719771|ref|YP_920266.1|  86 MALSGSEIYSAELKKTEVLMQALRKSIGVRIRERRWIYEGVVDKVDYKFDRHPLNpYVQVPVGGTITLRTEKETRSLRVD 165
                                    ***********************************************989999*9999999******************* PP

                                    HHHHHHHHHHT--TT-EEEEETTT--EEE-SSS-SS------S--------S---S----XXXXXXXXXXXXXXXXXXXX CS
                          TIP49 160 skiaeellkekvkegDviviekesGkvkklGrsearakefDiekdefvelPkGevekkkevvqevtLhdlDvanarpqdl 239
                                    s+i+ +ll++ v+egDvi i++e+G+v+++Gr++  a+ +D+   e+v++P+G v k+ke+v ++tLh+lD + ar+++l
  gi|119719771|ref|YP_920266.1| 166 SNIVYQLLQKGVEEGDVIWIDEETGRVTRVGRAKGAAN-YDVGVRELVDVPSGPVYKEKEFVYTLTLHQLDEMHARSESL 244
                                    *********************************98876.***************************************** PP

                                    XXXX....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49 240 lslllqllkskkteiteklreeinkkvakyveegkaeivpGvlfiDevhmlDiecfsylnraleselaPivilatnrgia 319
                                    lsl+     ++ +ei  ++r +++k+v+++v++g+ae++pGvlfiD++hmlDie+fs+l+ra+esel+Pi+ilatnrg++
  gi|119719771|ref|YP_920266.1| 245 LSLI--FGAPEYREIPPDVRAKVDKTVKEWVDSGRAELIPGVLFIDDAHMLDIEAFSFLSRAMESELSPIIILATNRGFT 322
                                    ***9..899*********************************************************************** PP

                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49 320 kirGtdiisphGipvDlldrlliiktekytk 350
                                    kirGtd+++phG+p+Dlldrlliikt++yt 
  gi|119719771|ref|YP_920266.1| 323 KIRGTDVEAPHGMPLDLLDRLLIIKTKPYTA 353
                                    *****************************86 PP

>> TIP49_C  TIP49 AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       3.5   1.7e+03      37      58 ..     309     330 ..     308     335 .. 0.89
   2 !   80.6   0.2   1.5e-25   6.9e-23       1      65 [.     359     423 ..     359     424 .. 0.99

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 3.5
                        TIP49_C  37 ltpasilakkrkkkevevedve 58 
                                    l+p  ila+ r+ +++   dve
  gi|119719771|ref|YP_920266.1| 309 LSPIIILATNRGFTKIRGTDVE 330
                                    678889***********99998 PP

  == domain 2  score: 80.6 bits;  conditional E-value: 1.5e-25
                        TIP49_C   1 IlkiRakeEgvkldeeAldlLakigtetSLRYaiqLltpasilakkrkkkevevedveeveeLFl 65 
                                    IlkiRakeEgv lde+Al+ L+++gte+SLRYa +Ll+pa+ila++r+k +v ve+v+ev+ LF+
  gi|119719771|ref|YP_920266.1| 359 ILKIRAKEEGVTLDEQALEELVRLGTERSLRYAAHLLAPAKILAEQRGKSSVGVEEVREVSTLFI 423
                                    9***************************************************************6 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   0.0     2e-11   9.2e-09       1      49 [.      58     108 ..      58     122 .. 0.83
   2 ?   -2.0   0.0       9.2   4.4e+03      48      66 ..     171     187 ..     155     190 .. 0.72
   3 ?    6.8   0.0     0.019       8.7      43     112 ..     266     321 ..     234     329 .. 0.79

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 2e-11
                                    EEEESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSSSTTHHHHHHHHH CS
                            AAA   1 vllyGppGtGKTllakavakelg..vefleisgsellskyvgesekkirel 49 
                                    +ll+GppGtGKT++a a+a+elg  ++f+ +sgse+ s  ++++e  +++l
  gi|119719771|ref|YP_920266.1|  58 ILLVGPPGTGKTAIAVAIARELGpeTPFMALSGSEIYSAELKKTEVLMQAL 108
                                    69********************77799**********76666665555444 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 9.2
                                    HHHHHHHHTSTSEEEEEET CS
                            AAA  48 elfkeakekakpsilfiDE 66 
                                    +l+++  e+    +++iDE
  gi|119719771|ref|YP_920266.1| 171 QLLQKGVEEG--DVIWIDE 187
                                    4555544443..8999999 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.019
                                    HHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS.G CS
                            AAA  43 ekkirelfkeakekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnr.p 112
                                     k ++e +++ +++  p +lfiD+++ l  +             + L ++++ + +     i+i+atnr  
  gi|119719771|ref|YP_920266.1| 266 DKTVKEWVDSGRAELIPGVLFIDDAHMLDIEA-----------FSFLSRAMESELS----PIIILATNRgF 321
                                    45566666666665568**********95555...........9999999999988....39999999854 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   7.9e-08   3.7e-05       9      60 ..      31      82 ..      25     108 .. 0.87
   2 ?   -1.6   0.0       4.3     2e+03      80      92 ..     175     187 ..     164     197 .. 0.77
   3 ?    5.3   0.0     0.032        15      87     117 ..     284     314 ..     279     325 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 7.9e-08
                         RuvB_N  9 yigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakelgvk 60
                                    +gq + +    ++++  k+ + a   +ll+GpPG Gkt++a  ia+elg +
  gi|119719771|ref|YP_920266.1| 31 LVGQIEARRAAWLVVQLIKAGKMAGRAILLVGPPGTGKTAIAVAIARELGPE 82
                                   689999999999999999999999999**********************865 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 4.3
                         RuvB_N  80 tnleekdvlfide 92 
                                    + +ee+dv++ide
  gi|119719771|ref|YP_920266.1| 175 KGVEEGDVIWIDE 187
                                    45899*******8 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.032
                         RuvB_N  87 vlfideihrlsraveevlysamedfrldivi 117
                                    vlfid+ h l+ ++  +l  ame     i+i
  gi|119719771|ref|YP_920266.1| 284 VLFIDDAHMLDIEAFSFLSRAMESELSPIII 314
                                    9**********************87666665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0     2e-05    0.0094       6      52 ..      56      99 ..      52     187 .. 0.72
   2 !   11.2   0.0   0.00069      0.33      73     133 ..     260     321 ..     197     324 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2e-05
                         AAA_22  6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst......s 52
                                   + ++++G++GtGKT  +  ++++l         +pe+ f+ l++s+      +
  gi|119719771|ref|YP_920266.1| 56 RAILLVGPPGTGKTAIAVAIAREL---------GPETPFMALSGSEiysaelK 99
                                   789********************9.........78887777777665443332 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00069
                         AAA_22  73 lsseellealeqalrarav...ielliiDEaqhlrseealeeLrsllnlsrkgvqliLvGtp.el 133
                                    + +  + +++ + +++ ++   +++l iD+a+ l   ea+++L++ ++  + + ++i+  t+ ++
  gi|119719771|ref|YP_920266.1| 260 DVRAKVDKTVKEWVDSGRAeliPGVLFIDDAHML-DIEAFSFLSRAME--SELSPIIILATNrGF 321
                                    44444456677777777778889***********.9*******99999..888888887776555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.3   5.6e-07   0.00027      24      63 ..      55      95 ..      38     315 .. 0.63

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 5.6e-07
                         AAA_16 24 pelvllsGesGvGKsslvrellralekdg.giflrgkcdql 63
                                   ++++ll+G++G+GK++++ +++r+l  +  + +l+g    +
  gi|119719771|ref|YP_920266.1| 55 GRAILLVGPPGTGKTAIAVAIARELGPETpFMALSGSEIYS 95
                                   399**********************9995233344444444 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   5.9e-07   0.00028       6      61 ..      24      83 ..      19     113 .. 0.76
   2 ?    0.9   0.0       0.6   2.8e+02     103     117 ..     284     298 ..     263     302 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 5.9e-07
                          AAA_7  6 eakfseilVptvdtvrysyllelllknkk....pvllvGptGtGKtviikdllkkldkek 61
                                    +++ + lV  ++  r  +l+ +l+k++k     +llvGp GtGKt+i+  + ++l +e+
  gi|119719771|ref|YP_920266.1| 24 PLPVADGLVGQIEARRAAWLVVQLIKAGKmagrAILLVGPPGTGKTAIAVAIARELGPET 83
                                   567888899999999******99999765222289***************9999998654 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.6
                          AAA_7 103 vvFvDDlnmpakeky 117
                                    v+F+DD +m   e +
  gi|119719771|ref|YP_920266.1| 284 VLFIDDAHMLDIEAF 298
                                    79*******999876 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.1   7.1e-07   0.00034       7      68 ..      33     101 ..      29     111 .. 0.73
   2 ?   -0.6   0.0       1.5   7.2e+02     108     133 ..     283     308 ..     278     319 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 7.1e-07
                   Mg_chelatase   7 Gqeeakra....leiaaaG...gHnlllvGppGsGKtmlakrlpsllpplseeealevakiasvagkke 68 
                                    Gq ea+ra    +++  aG   g  +llvGppG+GKt +a +++  l p +   al  ++i+s   kk+
  gi|119719771|ref|YP_920266.1|  33 GQIEARRAawlvVQLIKAGkmaGRAILLVGPPGTGKTAIAVAIARELGPETPFMALSGSEIYSAELKKT 101
                                    5555555522223445566222468********************************999999876443 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.5
                   Mg_chelatase 108 GvLfLDElpefkrkvlevLRePledg 133
                                    GvLf+D++  ++ +++  L + +e++
  gi|119719771|ref|YP_920266.1| 283 GVLFIDDAHMLDIEAFSFLSRAMESE 308
                                    9*******999999999999999875 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0     9e-05     0.042       7      34 ..      52      79 ..      46     123 .. 0.88
   2 ?    5.1   0.0     0.055        26      69     129 ..     228     308 ..     154     315 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 9e-05
                         AAA_19  7 alkekvllvtaGpGtGKTrvlkhivall 34
                                   +++ + +l++++pGtGKT + ++i ++l
  gi|119719771|ref|YP_920266.1| 52 KMAGRAILLVGPPGTGKTAIAVAIAREL 79
                                   677899**************99998876 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.055
                         AAA_19  69 atTiHrlal..........................ldfddlltealelleeaeeekklqeeellivDEfqdvdelqyrLl 122
                                    + T+H+l +                           ++d++++e++       + + +    +l++D + ++d  ++++l
  gi|119719771|ref|YP_920266.1| 228 TLTLHQLDEmharsesllslifgapeyreippdvrAKVDKTVKEWVDS----GRAELI--PGVLFIDDAHMLDIEAFSFL 301
                                    567777755566666666666666666666655444445555444433....334444..669**********9999999 PP

                         AAA_19 123 kallgek 129
                                    ++ ++++
  gi|119719771|ref|YP_920266.1| 302 SRAMESE 308
                                    8877554 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   6.1e-06    0.0029       2      32 ..      58      89 ..      57     121 .. 0.78
   2 ?   -1.2   0.0         4   1.9e+03      52      73 ..     166     187 ..     151     189 .. 0.67
   3 ?   -0.2   0.0         2   9.4e+02      64      90 ..     277     306 ..     253     312 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 6.1e-06
                                   EEEE--SSSSHHHHHHHGGGGB.S--EEEEE- CS
                          AAA_5  2 vlLvGppGtgKselaerlaaal.nreveyvql 32
                                   +lLvGppGtgK+ +a  +a+ l   + ++ + 
  gi|119719771|ref|YP_920266.1| 58 ILLVGPPGTGKTAIAVAIARELgPETPFMALS 89
                                   79******************996444444444 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 4
                                    .....--------G-SEEEEES CS
                          AAA_5  52 tslvdsplvraaregeilvlDE 73 
                                       v + l + ++eg+++ +DE
  gi|119719771|ref|YP_920266.1| 166 SNIVYQLLQKGVEEGDVIWIDE 187
                                    3444555555566999999998 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 2
                                    -...G-SEEEEESGGG--HHHHHHHHHHHH CS
                          AAA_5  64 r...egeilvlDEveraesevlnsLlslle 90 
                                    r    + +l++D+ ++++ e+++ L + +e
  gi|119719771|ref|YP_920266.1| 277 RaelIPGVLFIDDAHMLDIEAFSFLSRAME 306
                                    23347889********99999998888776 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   5.2e-06    0.0025       1      50 [.      58     102 ..      58     167 .. 0.50
   2 ?   -1.9   0.0       9.7   4.6e+03      47      77 ..     252     285 ..     236     299 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 5.2e-06
                         AAA_18   1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpealdesk 50 
                                    Ill G+pG+GKt +a +++++l      +   + +g++++  +   ++++
  gi|119719771|ref|YP_920266.1|  58 ILLVGPPGTGKTAIAVAIAREL---GPETPFMALSGSEIYSAEL--KKTE 102
                                    99******************97...2222233333333333333..3333 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 9.7
                         AAA_18  47 deskrldedkldklldaleenss...aleegknl 77 
                                    +e++++  d+++k+ ++++e+ +   a+  +++l
  gi|119719771|ref|YP_920266.1| 252 PEYREIPPDVRAKVDKTVKEWVDsgrAELIPGVL 285
                                    6788888999999999999998755544444444 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.4   8.9e-06    0.0042      22      56 ..      40      78 ..      21      88 .. 0.71
   2 ?    1.0   0.0      0.55   2.6e+02      14      31 ..     111     128 ..      98     131 .. 0.77
   3 ?   -2.0   0.0       4.7   2.2e+03      69     108 ..     177     214 ..     172     245 .. 0.57

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 8.9e-06
                         AAA_25 22 rrwlvkgllp....agelallaGapgtGKttlaldlala 56
                                     wlv  l+     ag  +ll+G+pgtGKt++a+ +a +
  gi|119719771|ref|YP_920266.1| 40 AAWLVVQLIKagkmAGRAILLVGPPGTGKTAIAVAIARE 78
                                   4566666555111156789***************99976 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.55
                         AAA_25  14 dlaapppprrwlvkgllp 31 
                                     + +++++rrw+++g++ 
  gi|119719771|ref|YP_920266.1| 111 SIGVRIRERRWIYEGVVD 128
                                    46679**********986 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 4.7
                         AAA_25  69 peqgkVlyvsaEdsedelrrRlravgealrddarllvldl 108
                                    +e g V++++ E ++  + r  ra g+a+ d +   ++d+
  gi|119719771|ref|YP_920266.1| 177 VEEGDVIWIDEETGR--VTRVGRAKGAANYDVGVRELVDV 214
                                    588999999977777..44444444444433333333333 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   2.6e-05     0.012       2      57 ..      58     116 ..      57     169 .. 0.79
   2 ?    0.4   0.0       1.5     7e+02      97     147 ..     376     428 ..     348     433 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.6e-05
                         AAA_28   2 ivitGgestGKTtlleaLaar...gypvvpEaareileeklakgedalpwv.edllafae 57 
                                    i ++G+++tGKT ++ a+a++   ++p ++ ++ ei++ +l+k+e  l ++ ++ + +++
  gi|119719771|ref|YP_920266.1|  58 ILLVGPPGTGKTAIAVAIARElgpETPFMALSGSEIYSAELKKTEV-LMQAlRKSIGVRI 116
                                    899****************9998889999**********9999986.4444354444444 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.5
                         AAA_28  97 eaelea..aarekrydlvfllppapeidddgeRredleereaiderlrealre 147
                                     +el++   +r+ ry++ +l p    +++ g    ++ee +++ ++++++ + 
  gi|119719771|ref|YP_920266.1| 376 LEELVRlgTERSLRYAAHLLAPAKILAEQRGKSSVGVEEVREVSTLFISTRES 428
                                    34444466777999999999999998888888899999999999998887665 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   1.2e-05    0.0055      48      70 ..      56      78 ..      43      83 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.2e-05
                      IstB_IS21 48 enivllGpsGvGKshlaialgve 70
                                    +i+l+Gp+G+GK+ +a+a+++e
  gi|119719771|ref|YP_920266.1| 56 RAILLVGPPGTGKTAIAVAIARE 78
                                   5799****************986 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   2.8e-05     0.013      10      75 ..      54     115 ..      48     187 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.8e-05
                                    TTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSB CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  10 egekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpelt 75 
                                    +g+ + +vG+ G+GK+ ++ ++a++l p+   + l g ++ +       k+ +vl q  +   +++
  gi|119719771|ref|YP_920266.1|  54 AGRAILLVGPPGTGKTAIAVAIARELGPETPFMALSGSEIYS----AELKKTEVLMQALRKSIGVR 115
                                    688999**********************99999888888888....44444445555444444444 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   6.4e-05      0.03      15      77 ..      51     117 ..      45     134 .. 0.80
   2 ?   -2.9   0.0       7.4   3.5e+03     103     131 ..     284     310 ..     269     314 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.4e-05
                                    SBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSE....EEEEESSSXHHHHHHHHHHHHHTXXHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         DnaB_C  15 GlqkgdliiiAarpsmGktalalniaenaavkeklp....vavfslemsaeqlvqRllsseaeidsk 77 
                                    G   g  i++ + p++Gkta+a+ ia++   ++         ++s e ++++++++ l +  +++ +
  gi|119719771|ref|YP_920266.1|  51 GKMAGRAILLVGPPGTGKTAIAVAIARELGPETPFMalsgSEIYSAELKKTEVLMQALRKSIGVRIR 117
                                    566788899*****************9988644321223499*************999988877654 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 7.4
                                    EEEEEEXSSXCHHHHHHHHHHHHHHTTEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         DnaB_C 103 klfiddtpaltvseirskarrlkkekglg 131
                                     lfidd   l ++      r +++  +l+
  gi|119719771|ref|YP_920266.1| 284 VLFIDDAHMLDIEAFSFLSRAMES--ELS 310
                                    589999999999988888887755..444 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00026      0.12      12      61 ..      45      93 ..      35     105 .. 0.76
   2 ?    0.1   0.0       1.2   5.6e+02      95     119 ..     283     307 ..     275     312 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00026
                                   HHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS CS
                Sigma54_activat 12 leqikkvaktdlsvlitGesGtGKellaraiheaskrkekpfvavncaai 61
                                   ++ ik+       +l++G  GtGK+ +a ai ++    e+pf+a+  ++i
  gi|119719771|ref|YP_920266.1| 45 VQLIKAGKMAGRAILLVGPPGTGKTAIAVAIARELG-PETPFMALSGSEI 93
                                   5666666667789******************98766.5678888877665 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.2
                                    SEEEEETGGGS-HHHHHHHHHHHHH CS
                Sigma54_activat  95 GtlfLDeigelplelQekLlrvlqe 119
                                    G+lf+D+ + l++e+ + L r++++
  gi|119719771|ref|YP_920266.1| 283 GVLFIDDAHMLDIEAFSFLSRAMES 307
                                    99***********999988888876 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0     8e-05     0.038       2      31 ..      58      91 ..      58     130 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 8e-05
                         AAA_33  2 vllvGlpGsGKstlaerllkklg....avllssd 31
                                   +llvG+pG+GK+  a  ++++lg    +  ls  
  gi|119719771|ref|YP_920266.1| 58 ILLVGPPGTGKTAIAVAIARELGpetpFMALSGS 91
                                   689*******************977774445444 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.5   0.00035      0.16      19      43 ..      56      80 ..      45     194 .. 0.62
   2 ?   -0.0   0.0       1.3   6.1e+02      76     114 ..     268     307 ..     253     316 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00035
                         AAA_30 19 rvavltGpAGtGKttalkalreawe 43
                                   r  +l+Gp+GtGKt +  a+++ + 
  gi|119719771|ref|YP_920266.1| 56 RAILLVGPPGTGKTAIAVAIARELG 80
                                   47899*********99888755443 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1.3
                         AAA_30  76 llkrlk..grarlepgtllivDEagmvdtkqlaallkaaek 114
                                     +k++   gra+l p  +l +D a m+d++ +  l +a+e+
  gi|119719771|ref|YP_920266.1| 268 TVKEWVdsGRAELIP-GVLFIDDAHMLDIEAFSFLSRAMES 307
                                    333343333334444.58899********999888888776 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00017     0.079      18      47 ..      57      86 ..      49      95 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00017
                     Zeta_toxin 18 lillgGqpGAGKselaellkdelerqgnvv 47
                                   +ill+G pG GK+++a ++++el+++  + 
  gi|119719771|ref|YP_920266.1| 57 AILLVGPPGTGKTAIAVAIARELGPETPFM 86
                                   89********************98766655 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0    0.0002     0.094       4      49 ..      58     110 ..      55     128 .. 0.69
   2 ?   -2.0   0.0       3.5   1.6e+03     147     192 ..     360     403 ..     340     423 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0002
                        DUF2075   4 vlVtGvaGtGKtvvllnllael.......eddeeertavylsvNhplvlvlre 49 
                                    +l  G +GtGKt ++++++ el         + +e +++ l + + l+++lr+
  gi|119719771|ref|YP_920266.1|  58 ILLVGPPGTGKTAIAVAIARELgpetpfmALSGSEIYSAELKKTEVLMQALRK 110
                                    6677*****************97766555333344444444444555555554 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.5
                        DUF2075 147 lkklakkleveleekvhLksqfRvaaseaviewvdalldgkkekak 192
                                    lk  ak+ +v+l+e+  L++ +R  ++e+ +++  +ll+  k+ a+
  gi|119719771|ref|YP_920266.1| 360 LKIRAKEEGVTLDEQ-ALEELVRL-GTERSLRYAAHLLAPAKILAE 403
                                    566678888999898.99999999.778888888888877766655 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   0.00015     0.071      21      41 ..      57      77 ..      40      84 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00015
                                   EEEEE--TTSSTTHHHHHHHH CS
                           PhoH 21 ivfaiGpaGtGKtylavalav 41
                                    +  +Gp GtGKt +ava+a 
  gi|119719771|ref|YP_920266.1| 57 AILLVGPPGTGKTAIAVAIAR 77
                                   57789*************995 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0    0.0015      0.69       3      23 ..      56      80 ..      54     128 .. 0.84
   2 ?    0.9   0.0       0.7   3.3e+02     143     165 ..     252     274 ..     235     276 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0015
                         AAA_24  3 lkiliyGpsgiGKTtlakel....g 23
                                   + il++Gp+g+GKT +a  +    g
  gi|119719771|ref|YP_920266.1| 56 RAILLVGPPGTGKTAIAVAIarelG 80
                                   679***********99876655553 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.7
                         AAA_24 143 akytrlepklgkktanelkeevD 165
                                    ++y  ++p+++ k+ + +ke+vD
  gi|119719771|ref|YP_920266.1| 252 PEYREIPPDVRAKVDKTVKEWVD 274
                                    57899*****************9 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00019      0.09      20      42 ..      58      80 ..      42     110 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00019
                         AAA_11 20 tliqGPPGtgKTktivellsqll 42
                                    l+ GPPGtgKT   v++ ++l 
  gi|119719771|ref|YP_920266.1| 58 ILLVGPPGTGKTAIAVAIARELG 80
                                   6899**************99985 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00042       0.2       1      39 [.      61     103 ..      61     133 .. 0.78
   2 ?   -1.5   0.1       6.7   3.1e+03      79      96 ..     422     439 ..     351     441 .] 0.59

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00042
                                    EE-TTSSHHHHHHHHHHHH....TEEEEEHHHHHHHHHHTTTS CS
                         AAA_17   1 lGgPGsGKgtqceklveky....gfthlsaGdllreeakrggl 39 
                                    +G+PG GK+ ++  +++++     f  ls +++  +e k+ + 
  gi|119719771|ref|YP_920266.1|  61 VGPPGTGKTAIAVAIARELgpetPFMALSGSEIYSAELKKTEV 103
                                    7****************99665569999988888899999885 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 6.7
                                    -SEEEETTEEEESSHHHH CS
                         AAA_17  79 hprikeqagfldglpkev 96 
                                    + +++e+a++l+++++++
  gi|119719771|ref|YP_920266.1| 422 FISTRESAQYLKEFEEKM 439
                                    455666666666666665 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1    0.0003      0.14      11      36 ..      47      72 ..      44      78 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0003
                         ATPase 11 ilkgGipegrvvlitGepGtGKtifa 36
                                   ++k G + gr++l++G pGtGKt +a
  gi|119719771|ref|YP_920266.1| 47 LIKAGKMAGRAILLVGPPGTGKTAIA 72
                                   67889999***************987 PP

>> RHH_5  CopG-like RHH_1 or ribbon-helix-helix domain, RHH_5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       3.6   1.7e+03      23      37 ..      36      50 ..      34      51 .. 0.82
   2 ?    2.7   0.0      0.24   1.1e+02      25      41 ..     160     179 ..     155     180 .. 0.78
   3 ?    6.3   0.1     0.018       8.7      10      27 ..     354     371 ..     351     376 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 3.6
                          RHH_5 23 egRsvSnlaafLvek 37
                                   e R  ++l+ +L++ 
  gi|119719771|ref|YP_920266.1| 36 EARRAAWLVVQLIKA 50
                                   778889******986 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.24
                          RHH_5  25 Rsv...SnlaafLvekalre 41 
                                    Rs+   Sn + +L++k+++e
  gi|119719771|ref|YP_920266.1| 160 RSLrvdSNIVYQLLQKGVEE 179
                                    5555559***********97 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.018
                          RHH_5  10 eelleeLeewAdeegRsv 27 
                                    +e++e L++ A+eeg+++
  gi|119719771|ref|YP_920266.1| 354 DEIREILKIRAKEEGVTL 371
                                    89*************996 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00038      0.18      16      45 ..      52      81 ..      36      89 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00038
                                   HCHTEEEEEEESTTSSHHHHHHHHHHHTT- CS
                           TsaE 16 kalgdvilLeGdLGaGKTtlvrglakalgv 45
                                   k++g++ilL G+ G+GKT+++ ++a++lg 
  gi|119719771|ref|YP_920266.1| 52 KMAGRAILLVGPPGTGKTAIAVAIARELGP 81
                                   222678********************9985 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00035      0.17     114     136 ..      55      77 ..      34      81 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00035
                      Parvo_NS1 114 rntvwfyGpantGktnlaeaIak 136
                                      +++++Gp+ tGkt +a aIa+
  gi|119719771|ref|YP_920266.1|  55 GRAILLVGPPGTGKTAIAVAIAR 77 
                                    3689999**************97 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0    0.0093       4.4       6      63 ..      58     113 ..      55     136 .. 0.80
   2 ?    2.2   0.0      0.36   1.7e+02      45      76 ..     156     187 ..     151     204 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0093
                                    EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT- CS
                          AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgy 63 
                                    ill+gp g+Gkt +a a+a+ l    e +++ +  se+  +e  ++ v +    +   
  gi|119719771|ref|YP_920266.1|  58 ILLVGPPGTGKTAIAVAIARELG--PETPFMALSGSEIYSAELKKTEVLMQALRKSIG 113
                                    899*******************7..699999999999988777777776666665555 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.36
                                    -----THHHHHHHHHTTT-HHHHTTSEEEEET CS
                          AAA_2  45 eeeevehlvsrligappgyvgaeegGivllDE 76 
                                    e+e  +  v++ i+ +   +g+eeg ++ +DE
  gi|119719771|ref|YP_920266.1| 156 EKETRSLRVDSNIVYQLLQKGVEEGDVIWIDE 187
                                    555566679999999999*************9 PP

>> TFIID-31kDa  Transcription initiation factor IID, 31kD subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0      0.26   1.2e+02      43      72 ..      88     117 ..      85     134 .. 0.91
   2 ?    7.3   0.0    0.0098       4.6      35      77 ..     387     433 ..     348     441 .] 0.74

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.26
                    TFIID-31kDa  43 LedAkvlaehakkkevslddvrlAiqsrle 72 
                                    L+ +++++++ kk+ev ++++r +i  r+ 
  gi|119719771|ref|YP_920266.1|  88 LSGSEIYSAELKKTEVLMQALRKSIGVRIR 117
                                    8899*********************99876 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0098
                    TFIID-31kDa  35 ayrytssvLedAkvlaehakkkevslddvrlA....iqsrlekqfke 77 
                                      ry +++L  Ak+lae+++k++v +++vr      i++r + q+ +
  gi|119719771|ref|YP_920266.1| 387 SLRYAAHLLAPAKILAEQRGKSSVGVEEVREVstlfISTRESAQYLK 433
                                    45*************************99843344466666665555 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00056      0.27       4      26 ..      58      80 ..      55      90 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00056
                            IPT  4 ylifGatttGKtaeaiklaketg 26
                                    l++G+ +tGKta a+++a+e g
  gi|119719771|ref|YP_920266.1| 58 ILLVGPPGTGKTAIAVAIARELG 80
                                   699*****************977 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00052      0.25      51     104 ..      53     110 ..      17     117 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00052
                         DUF815  51 lpannvLLwGarGtGKSslvkallneyaeeg....Lrlievekedlkelpklvellre 104
                                    ++ + +LL+G  GtGK ++  a+ +e+  e+    L   e+   +lk+ + l+++lr+
  gi|119719771|ref|YP_920266.1|  53 MAGRAILLVGPPGTGKTAIAVAIARELGPETpfmaLSGSEIYSAELKKTEVLMQALRK 110
                                    344679**********************999997777789*******99999999987 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0    0.0016      0.74      24      48 ..      55      79 ..      33     106 .. 0.82
   2 ?   -1.0   0.0       3.4   1.6e+03     134     146 ..     279     295 ..     234     316 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0016
                                   TSEEEEEESTTSTHHHHHHHHHHHH CS
                         ResIII 24 dkrglikmaTGtGKTlvaaklierl 48
                                    + +l++ + GtGKT +a++++++l
  gi|119719771|ref|YP_920266.1| 55 GRAILLVGPPGTGKTAIAVAIAREL 79
                                   457889***************9987 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3.4
                                    S....EEEEETGGGTTS CS
                         ResIII 134 d....viiiDEaHrlga 146
                                    +    v++iD aH l  
  gi|119719771|ref|YP_920266.1| 279 ElipgVLFIDDAHMLDI 295
                                    24455999999998765 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0    0.0055       2.6       3      58 ..      56     110 ..      54     123 .. 0.79
   2 ?   -2.3   0.0       8.9   4.2e+03      49      72 ..     166     187 ..     150     189 .. 0.49
   3 ?    0.4   0.0       1.4   6.4e+02      65      97 ..     282     314 ..     228     328 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0055
                         AAA_14   3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelile 58 
                                    ++++++G+  +GKT ++  +++el  ++  ++ ++  +   ++l+++e l++++++
  gi|119719771|ref|YP_920266.1|  56 RAILLVGPPGTGKTAIAVAIARELG-PETPFMALSGSEIYSAELKKTEVLMQALRK 110
                                    7899*****************9999.888888888888777777777666666655 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 8.9
                         AAA_14  49 pekllelilek.lkeekktylflDE 72 
                                    + ++   +l+k +  e+  ++ +DE
  gi|119719771|ref|YP_920266.1| 166 S-NIVYQLLQKgV--EEGDVIWIDE 187
                                    2.23333333324..4788899998 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 1.4
                         AAA_14  65 ktylflDEiqev.pewekalkslvdegknldviv 97 
                                      +lf+D ++++  e++++l + ++++    +i+
  gi|119719771|ref|YP_920266.1| 282 PGVLFIDDAHMLdIEAFSFLSRAMESE-LSPIII 314
                                    357999*99998448999999998877.334444 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00068      0.32       1      36 [.      58      95 ..      58     115 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00068
                   RNA_helicase  1 iwlyGpsgeGKStlakeLakallkkl..klkkkdsvys 36
                                   i+l+Gp+g+GK+ +a  +a++l  +      + +++ys
  gi|119719771|ref|YP_920266.1| 58 ILLVGPPGTGKTAIAVAIARELGPETpfMALSGSEIYS 95
                                   689******************98444334445556665 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00091      0.43       1      28 [.      56      83 ..      56      89 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00091
                                   SCEEEEC-TTTCHHHHHHHHHHHHCTS- CS
                          NACHT  1 rlvilqGeaGsGKTtLlqklalawaegk 28
                                   r ++l G++G GKT+ +  +a+++  ++
  gi|119719771|ref|YP_920266.1| 56 RAILLVGPPGTGKTAIAVAIARELGPET 83
                                   5789*****************9997666 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00075      0.35      34      90 ..      42     101 ..      35     112 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00075
                          Rad17  34 wlkadvLesrkkr..iLLisGPsGCgkstvvkvLskelgiklr.ewlnpvslkepdnqks 90 
                                    wl  + ++  k     +L+ GP+G gk+ +   +++elg++     l + ++ +++ +k+
  gi|119719771|ref|YP_920266.1|  42 WLVVQLIKAGKMAgrAILLVGPPGTGKTAIAVAIARELGPETPfMALSGSEIYSAELKKT 101
                                    55555555444323378899**********99*******976413455555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                       110  (0.00613531); expected 17.9 (0.001)
Passed Fwd filter:                        38  (0.00211947); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              38  [number of targets reported over threshold]
# CPU time: 0.66u 0.29s 00:00:00.95 Elapsed: 00:00:00.45
# Mc/sec: 2916.14
//
Query:       gi|119719772|ref|YP_920267.1|  [L=281]
Description: putative phage repressor [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.3e-08   32.5   0.2    9.9e-08   31.8   0.2    1.3  1  Peptidase_S24  Peptidase S24-like
  ------ inclusion threshold ------
       0.21   11.2   0.1       0.21   11.2   0.1    2.2  2  DUF2512        Protein of unknown function (DUF2512)


Domain annotation for each model (and alignments):
>> Peptidase_S24  Peptidase S24-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.2   1.1e-11   9.9e-08       2      60 ..     190     246 ..     189     257 .. 0.86

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 1.1e-11
                                    XXSSTTCCTXXTTXEEEEECTS---TTSEEEEEETTCE-EEEEEEEEETTEEEEE.SST CS
                  Peptidase_S24   2 vpGdSMeptlldGdlilVdkfsepkrGdivvfrlpgeeeayiKrviglpgdrvllasnn 60 
                                    v + SMep l+ Gd+++V  ++++  Gdiv+    ge  ++++r++   ++++ ++ + 
  gi|119719772|ref|YP_920267.1| 190 VSSWSMEPVLHVGDVVVVAGGNSYTLGDIVIYERGGE--LIVHRIVLSVNGKYVTKGDA 246
                                    899*****************************99999..9******8888888877665 PP

>> DUF2512  Protein of unknown function (DUF2512)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.4      0.18   1.6e+03      72      93 ..      58      79 ..      53     105 .. 0.50
   2 ?   11.2   0.1   2.4e-05      0.21       6      61 ..     174     229 ..     171     235 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.18
                        DUF2512 72 vvWlltavlldnsvsiaiasll 93
                                   ++W+++ +++ ++   +   +l
  gi|119719772|ref|YP_920267.1| 58 LLWIFSGATYSEKRYFLKKVFL 79
                                   5555555555554443333333 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 2.4e-05
                        DUF2512   6 aLliKfiatlvvlllvlglflgvsfsevllisllltlvsYlvgDlliLprtgnliA 61 
                                    +L ++f+++++v l+v++  +  ++ +v  + ++ +  sY +gD++i+ r g+li+
  gi|119719772|ref|YP_920267.1| 174 LLSLRFVLSTPVPLAVVSSWSMEPVLHVGDVVVVAGGNSYTLGDIVIYERGGELIV 229
                                    6889999999999999999999999999999*******************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.65u 0.33s 00:00:00.98 Elapsed: 00:00:00.57
# Mc/sec: 1494.41
//
Query:       gi|119719773|ref|YP_920268.1|  [L=380]
Description: peptidase M50 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-20   73.3   2.2    8.5e-20   71.1   2.2    1.9  1  Peptidase_M50  Peptidase family M50
    2.5e-11   43.7   0.0    6.6e-11   42.4   0.0    1.7  2  PDZ_2          PDZ domain
      4e-09   36.2   0.0    1.2e-08   34.7   0.0    1.9  2  PDZ_6          PDZ domain
    2.5e-08   34.1   0.0    6.7e-07   29.6   0.0    2.7  3  PDZ            PDZ domain
      0.005   16.8   0.0      0.012   15.6   0.0    1.6  1  PDZ_1          PDZ-like domain
  ------ inclusion threshold ------
      0.034   14.1   0.0      0.068   13.1   0.0    1.4  1  Tricorn_PDZ    Tricorn protease PDZ domain


Domain annotation for each model (and alignments):
>> Peptidase_M50  Peptidase family M50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.1   2.2   2.9e-23   8.5e-20       1     249 [.     118     362 ..     118     364 .. 0.74

  Alignments for each domain:
  == domain 1  score: 71.1 bits;  conditional E-value: 2.9e-23
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XX CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M50   1 afilllgilvvvHElGHflvAklcgvkveefsigfGpkllsfkkgeteYaiallpLGGyVkmageepeeelseeeakafl 80 
                                    +f+l++ + ++ HEl H++ A ++gv+++++++++                 l+p GG+ +++++e            ++
  gi|119719773|ref|YP_920268.1| 118 YFLLAVAVTLIPHELSHAFQAAAEGVRIKSMGVFL---------------AFLVP-GGFAEIDEDE------------LD 169
                                    799***************************99999...............78899.**********............99 PP

                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXX.........................-EEECECTTTSCEE-SEEEC-XXXXXX CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxx.........................xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M50  81 kkspwqrllivlAGplanfilailvfvv.........................pkkskeseeekrgviGvspkpvkkegl 135
                                    +k++ ++l++++AG +an+   +l++++                         p+   +  + +  ++ v+ +p   +  
  gi|119719773|ref|YP_920268.1| 170 SKPLRSKLRVLAAGSFANIATFLLLVALfylvlftplaprpngvlvsgviqgsPAF--QRLQPGDVIVAVNGTP---TPT 244
                                    99****************99888888888999******999999999887776422..2555566666666666...556 PP

                                    XXXXXXXXXXXX..XXXXXXXX...XXXXXXXX.XXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                    xxxxxxxxxxxx..xxxxxxxx...xxxxxxxx.xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M50 136 lealkegvektl..kvvvltvk...algklitg.klslktlggpisia.qlaseaaeaglssflqllalisvnLgilNLl 208
                                    le +++ +e+    ++++ltv+   +l++       +++   g  +i+ ++ ++  ++ l   ++++ ++  +++i+N+l
  gi|119719773|ref|YP_920268.1| 245 LEGFSKVMERSApgRLIKLTVMrgsVLVNYSLVlAQHPE-SPGRGFIGvKIDQSYSNEWLYRAFWWMLVVTSSVAIINML 323
                                    666666666553114444444433355544333123333.33333333044444455555688889999999******** PP

                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M50 209 PipvLDGghllfalleairrkplserkeevanlvglallll 249
                                    Pi +LDGg+ll++ll+a++  p +++k +v+    ++l++l
  gi|119719773|ref|YP_920268.1| 324 PIVPLDGGKLLSYLLQAVA--PGRASKVAVWACSAYMLIVL 362
                                    *******************..76666666666666555554 PP

>> PDZ_2  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.4   0.0   2.2e-14   6.6e-11      14      79 ..     211     275 ..     200     278 .. 0.90
   2 ?   -2.4   0.0         2     6e+03       2      31 ..     289     332 ..     288     336 .. 0.73

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 2.2e-14
                                    .-EEEEEE-TTSGGGGT.--TT-EEEEETTB--SSHHHHHHHHHTS-TT-EEEEEEEETTEEEEEE CS
                          PDZ_2  14 ggvlvvsVkeggPaakaglkagDvilkvdgkkvksledlislllkkkpGdtVkltvlRdgkkktve 79 
                                    +gvlv  V +g+Pa ++ l++gDvi++v+g++  +le + + + +  pG+ +kltv+R++   +++
  gi|119719773|ref|YP_920268.1| 211 NGVLVSGVIQGSPAFQR-LQPGDVIVAVNGTPTPTLEGFSKVMERSAPGRLIKLTVMRGSVLVNYS 275
                                    69***************.****************************************99877766 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2
                                    ...XX------................-EEEEEE-TTSGGGGT. CS
                          PDZ_2   2 ylGvsvsdeed..............tggvlvvsVkeggPaakag 31 
                                    ++Gv++ ++ +              t+ v +++  +  P ++ +
  gi|119719773|ref|YP_920268.1| 289 FIGVKIDQSYSnewlyrafwwmlvvTSSVAIINMLPIVPLDGGK 332
                                    78999988888788888888888888888888877777766655 PP

>> PDZ_6  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       3.9   1.2e+04      36      47 ..     130     141 ..     129     144 .. 0.75
   2 !   34.7   0.0   3.8e-12   1.2e-08       2      56 .]     215     267 ..     214     267 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 3.9
                          PDZ_6  36 advaallrgsag 47 
                                    ++++++ +++a+
  gi|119719773|ref|YP_920268.1| 130 HELSHAFQAAAE 141
                                    689999997665 PP

  == domain 2  score: 34.7 bits;  conditional E-value: 3.8e-12
                          PDZ_6   2 VtaVdpgsPAdrAGlrvGDiilsvNGqpveglsladvaallr.gsagesvvlvvrr 56 
                                    V+ V+ gsPA +  l++GD+i++vNG+p+   +l+ ++  ++ +++g+ + l+v r
  gi|119719773|ref|YP_920268.1| 215 VSGVIQGSPAFQR-LQPGDVIVAVNGTPT--PTLEGFSKVMErSAPGRLIKLTVMR 267
                                    899*********9.***************..*********************9977 PP

>> PDZ  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.26   7.8e+02      24      41 ..     146     163 ..     135     165 .. 0.78
   2 !   29.6   0.0   2.2e-10   6.7e-07      26      82 .]     211     266 ..     206     266 .. 0.93
   3 ?   -0.9   0.0      0.74   2.2e+03       7      23 ..     285     301 ..     280     329 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.26
                                    SSSSEEEEEECTTSHHHH CS
                            PDZ  24 gdkgifvsevlpggaaea 41 
                                    +++g+f + ++pgg ae 
  gi|119719773|ref|YP_920268.1| 146 KSMGVFLAFLVPGGFAEI 163
                                    459***********9986 PP

  == domain 2  score: 29.6 bits;  conditional E-value: 2.2e-10
                                    SSEEEEEECTTSHHHHHTSSTTEEEEEETTEETTTSHHHHHHHHHHTTTSEEEEEEE CS
                            PDZ  26 kgifvsevlpggaaeadglkvGDkIlsvNgvdvenvsheeavqaikgskgkvtLtil 82 
                                    +g+ vs v +g++a +  l++GD+I++vNg+++ +++   +v +   ++  ++Lt++
  gi|119719773|ref|YP_920268.1| 211 NGVLVSGVIQGSPAFQR-LQPGDVIVAVNGTPTPTLEGFSKVMERSAPGRLIKLTVM 266
                                    699**************.******************999999999999999999985 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.74
                                    STTSESSEEEEEETTSS CS
                            PDZ   7 egrgglGfslkggsdqr 23 
                                    +grg++G++++   +++
  gi|119719773|ref|YP_920268.1| 285 PGRGFIGVKIDQSYSNE 301
                                    3899*****99887765 PP

>> PDZ_1  PDZ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0     4e-06     0.012      33      73 ..     213     253 ..     204     255 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4e-06
                          PDZ_1  33 vyvsea.sgsfklsskekkgviitsinnqptpnLdefievvk 73 
                                    v vs   +gs++++   + g +i  +n++ptp+L+ f +v++
  gi|119719773|ref|YP_920268.1| 213 VLVSGViQGSPAFQR-LQPGDVIVAVNGTPTPTLEGFSKVME 253
                                    555532278899977.99**********************97 PP

>> Tricorn_PDZ  Tricorn protease PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   2.3e-05     0.068      40      79 ..     228     268 ..     226     273 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.3e-05
                                    -.TT-EEEEETTEE-BTTB-HHHHHHTTT.TSEEEEEEE-S CS
                    Tricorn_PDZ  40 vreGdlilavdgepvskekgiaelLvgka.gkeveLtvkrk 79 
                                    ++ Gd+i+av+g p+ + +g++++++  a g+ ++Ltv r+
  gi|119719773|ref|YP_920268.1| 228 LQPGDVIVAVNGTPTPTLEGFSKVMERSApGRLIKLTVMRG 268
                                    679**********************9877468899999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       587  (0.0327403); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 2297.15
//
Query:       gi|119719774|ref|YP_920269.1|  [L=235]
Description: beta-lactamase superfamily hydrolase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       181  (0.0100954); expected 358.6 (0.02)
Passed bias filter:                      174  (0.00970495); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.61u 0.35s 00:00:00.96 Elapsed: 00:00:00.58
# Mc/sec: 1218.45
//
Query:       gi|119719775|ref|YP_920270.1|  [L=131]
Description: holliday junction resolvase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.8e-14   51.4   0.5    1.1e-13   51.0   0.5    1.1  1  Hjc           Archaeal holliday junction resolvase (hjc)
  ------ inclusion threshold ------
      0.017   14.9   0.4      0.047   13.5   0.2    1.8  2  Motile_Sperm  MSP (Major sperm protein) domain
      0.019   14.9   0.2      0.023   14.7   0.2    1.1  1  HSDR_N        Type I restriction enzyme R protein N terminus 
      0.022   14.8   0.1       0.04   14.0   0.1    1.7  1  VRR_NUC       VRR-NUC domain


Domain annotation for each model (and alignments):
>> Hjc  Archaeal holliday junction resolvase (hjc)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.0   0.5   2.4e-17   1.1e-13       2      89 ..      15     109 ..      14     112 .. 0.84

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 2.4e-17
                                    HHHHHHHHHH.HTT-EEEEBSCSSSSSSSS-SEEEEET..TEEEEEEEEEESSSEEEEEHHHHHHHHHHHHHH....TCE CS
                            Hjc   2 yERelvkiLr.ergfavvRsagSggatkplpDviAirg..dvvlviEvKsskkeriylkkeqvekllefarka....gge 74 
                                    +ER lvk+L  +r+ +v R++ Sg + ++ pDv+ +++  d v+++EvK+++++++++k++qv kl +f + +      e
  gi|119719775|ref|YP_920270.1|  15 VERRLVKMLSsNRENYVFRVPVSGVG-ENFPDVFLVNNveDRVVAFEVKTTVNSKVKVKAHQVSKLFRFLEAFkkykTRE 93 
                                    8********7379************9.999**9988862266******************************95443457 PP

                                    EEEEEEE.TTTEEEEE CS
                            Hjc  75 lllavkl.qgkewkll 89 
                                    +++av + ++ +w + 
  gi|119719775|ref|YP_920270.1|  94 AVIAVWFsSEGKWVFR 109
                                    8899999667777765 PP

>> Motile_Sperm  MSP (Major sperm protein) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.55   2.5e+03      35      49 ..      19      33 ..      14      42 .. 0.72
   2 ?   13.5   0.2   1.1e-05     0.047      26      49 ..      49      72 ..      44      75 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.55
                                   EEEEEES-TTTEEEE CS
                   Motile_Sperm 35 aFkvkttapkkyrvr 49
                                    +k+ +++ ++y+ r
  gi|119719775|ref|YP_920270.1| 19 LVKMLSSNRENYVFR 33
                                   568888999999877 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 1.1e-05
                                   EEE-SSSSEEEEEEES-TTTEEEE CS
                   Motile_Sperm 26 lkNtskkrvaFkvkttapkkyrvr 49
                                   + N+ ++ vaF vktt ++k+ v+
  gi|119719775|ref|YP_920270.1| 49 VNNVEDRVVAFEVKTTVNSKVKVK 72
                                   7899999*************9997 PP

>> HSDR_N  Type I restriction enzyme R protein N terminus (HSDR_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.2     5e-06     0.023     104     180 ..      24     104 ..       5     112 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5e-06
                                    GGS-EEEEE----SSSS---EEEEEEET.TEEEEEEEE--TT-HHHHHHHHTSS---.---S...SSGGGGG-....... CS
                         HSDR_N 104 enNrfqvvnQvtvtgnqkrrpDivlfvn.glplvviElKrpgtieeAinQikryrkeksdvs...ipqlfrYl....... 172
                                    + Nr ++v  v v+g ++++pD+ l  n ++ +v +E+K   +              k +v+   +  lfr+l       
  gi|119719775|ref|YP_920270.1|  24 SSNRENYVFRVPVSGVGENFPDVFLVNNvEDRVVAFEVKTTVN-------------SKVKVKahqVSKLFRFLeafkkyk 90 
                                    5567777777888899************************532.............223333345899999997777777 PP

                                    ......-EEEEE-S CS
                         HSDR_N 173 ......qfgvisng 180
                                          +++++s g
  gi|119719775|ref|YP_920270.1|  91 treaviAVWFSSEG 104
                                    77776666666666 PP

>> VRR_NUC  VRR-NUC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   8.9e-06      0.04      49      80 ..      36      65 ..       6      98 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 8.9e-06
                                   HHHHSSTS-SEEEEETTTTE..EEEEEEE-TT CS
                        VRR_NUC 49 yrglrsGvPDLilwieeqkryvflliEvKgpg 80
                                   + g++ ++PD++l+++ ++r  + + EvK++ 
  gi|119719775|ref|YP_920270.1| 36 VSGVGENFPDVFLVNNVEDR--VVAFEVKTTV 65
                                   468999**************..99*****986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       907  (0.0505884); expected 358.6 (0.02)
Passed bias filter:                      593  (0.0330749); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 899.94
//
Query:       gi|119719776|ref|YP_920271.1|  [L=353]
Description: hypothetical protein Tpen_0867 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.7e-24   86.6   0.0    1.9e-24   86.4   0.0    1.0  1  DUF354       Protein of unknown function (DUF354)
  ------ inclusion threshold ------
      0.018   13.9   0.0      0.032   13.1   0.0    1.3  1  Epimerase_2  UDP-N-acetylglucosamine 2-epimerase


Domain annotation for each model (and alignments):
>> DUF354  Protein of unknown function (DUF354)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.4   0.0   2.1e-28   1.9e-24      12     312 ..      12     314 ..       1     341 [. 0.79

  Alignments for each domain:
  == domain 1  score: 86.4 bits;  conditional E-value: 2.1e-28
                         DUF354  12 hvryfrdlikkfekeGievlltardsGdlaklvklynfvfksiGkhG.vtlkekliesakrvinlskliaevkpdvalak 90 
                                     v  f  l  + e  G e++lt rd+     l      ++  +G+hG  t + k+ es +r  +l +l+  ++pd  ++ 
  gi|119719776|ref|YP_920271.1|  12 QVLLFSYL--QHELPGYEFFLTTRDYDLNRELAGKLWKEYYVVGRHGgRTPRGKVAESLRRQASLLRLVESKNPDAHVTF 89 
                                    55555444..3344599********97666777666678999****73799***************************** PP

                         DUF354  91 hsvelprvafGlnipvvyvldnehaeaankltlpladeiikpividendlkktGadpnrirryeGtsevinvqsyeidee 170
                                     s +  rva+G++ipvv   d  h+    +l +pla+ ++ p+ +  +   +  a+  ri+ ++G  ev+ v   + de 
  gi|119719776|ref|YP_920271.1|  90 VSPDSARVAYGVGIPVVACNDTPHSTIVSRLVIPLAEVLVVPQPVAAY--FEDYARLTRISPFRGVFEVAWVARTQPDER 167
                                    ******************************************988765..67778999********************** PP

                         DUF354 171 ilkdlnlkledektilmrpepslasyld.adchkdvltkiveklkdrid..ilviprdeeqkei....yeevdnvivike 243
                                    + + l+  le  + +++r    +a y +   +  +v  ++   +  + d  +l++pr+ eqk        +++  +v  e
  gi|119719776|ref|YP_920271.1| 168 VPRSLG--LEPLNYVIVRTGEEKAFYYKePRAALEVPLRMTRYILRKTDmkVLLYPRYPEQKTAlakgLSGYEGRLVFLE 245
                                    ******..77777777777776777665155566665566665544444459*********9762222468999999999 PP

                         DUF354 244 tvdalsll.krsdlviGaGGtmnreaallGipvvscypqkllsvdkyliekdlmirstdvdeivntalrl 312
                                      + l  l   + lvi  GGt+  e+allG+p+++ +p++ + v  yl  ++  + s    e +   lr 
  gi|119719776|ref|YP_920271.1| 246 RAEVLVHLeFFARLVITGGGTIATESALLGTPAITTFPGR-VEVHEYLRANGFPVYSGVTLENLPRILRA 314
                                    9999876615789*************************98.58999998888766665555555545554 PP

>> Epimerase_2  UDP-N-acetylglucosamine 2-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   3.6e-06     0.032     211     284 ..     210     281 ..     194     295 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.6e-06
                                    HHHH--EEEEE--..HHHHHHHHHHHHH-.TTEEEE----HHHHHHHHHC-SEEEES-HHHHHHHHHCT--EEES CS
                    Epimerase_2 211 akekdvevvvpvhnnprtrkrlleeleel.envtlieplgyldflsllknaklvltdSgGiqeEapslgvpvvnl 284
                                     +++d+  v+ +++ p+ + +l + l+++  ++ ++e  ++  +++l   a+lv+t  g+i  E+++lg+p+++ 
  gi|119719776|ref|YP_920271.1| 210 LRKTDM-KVLLYPRYPEQKTALAKGLSGYeGRLVFLERAEV--LVHLEFFARLVITGGGTIATESALLGTPAITT 281
                                    444455.57788889**************559999998776..58888899*********************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 2246.21
//
Query:       gi|119719777|ref|YP_920272.1|  [L=99]
Description: hypothetical protein Tpen_0868 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.013   14.7   0.0      0.015   14.6   0.0    1.0  1  Zip            ZIP Zinc transporter
       0.14   12.7   0.1       0.26   11.8   0.1    1.4  1  Chitin_bind_4  Insect cuticle protein


Domain annotation for each model (and alignments):
>> Zip  ZIP Zinc transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.7e-06     0.015       2      68 ..       4      80 ..       3      92 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.7e-06
                            Zip  2 llkilaiiaililsllgllgpllvpkiskl..........lsklllslllafavGvllgtaflhLlPealealeesq 68
                                   +++++a++++l++ l     pl+v  +             + + +++l ++f+v  l++ta + +l++  e+l+e+ 
  gi|119719777|ref|YP_920272.1|  4 KVVLVALLSVLAIALYWSPYPLIVGGYVLGgypwlapdgqPRSTMIALGVIFSVAFLSATAAMYVLAKKNEELGEEP 80
                                   57788999999999988888888887765589999999*99****************************99999875 PP

>> Chitin_bind_4  Insect cuticle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   2.9e-05      0.26      25      43 ..      28      46 ..      27      48 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.9e-05
                  Chitin_bind_4 25 glvvqGsYsyvdpdGktrt 43
                                   g++v G Y +++pdG++r+
  gi|119719777|ref|YP_920272.1| 28 GGYVLGGYPWLAPDGQPRS 46
                                   78999************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.50
# Mc/sec: 597.06
//
Query:       gi|119719778|ref|YP_920273.1|  [L=104]
Description: AsnC family transcriptional regulator [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.2e-12   45.6   0.1    7.7e-12   45.0   0.1    1.3  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
     0.0031   17.4   0.0      0.005   16.8   0.0    1.4  1  GYD             GYD domain


Domain annotation for each model (and alignments):
>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.0   0.1   8.6e-16   7.7e-12       4      72 ..      37     101 ..      34     104 .] 0.91

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 8.6e-16
                                    EE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEE CS
                 AsnC_trans_reg   4 slepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsiv 72 
                                    ++  g+    +++ +a++ ++ V+e+y v G+yd+++k+  + le l++++ + +++l gv+rt+t+i 
  gi|119719778|ref|YP_920273.1|  37 NVGVGR---EDDVLKAIRSMEFVEEAYIVYGEYDIVAKISLPALELLDKVVTN-IRKLGGVTRTSTLIT 101
                                    555556...79***************************************999.************996 PP

>> GYD  GYD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   5.5e-07     0.005      22      78 ..      43      98 ..      36     104 .] 0.81

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.5e-07
                            GYD 22 reeakealveslGgkleslyatlGeyDvvvivEapDdetaaalslalaasGtvrt.et 78
                                   ++++ +a+ +s++  +e+ y++ GeyD+v+ + +p  e   ++   +++ G v+   t
  gi|119719778|ref|YP_920273.1| 43 EDDVLKAI-RSMEF-VEEAYIVYGEYDIVAKISLPALELLDKVVTNIRKLGGVTRtST 98
                                   55666666.66654.89**********************************8876233 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 790.27
//
Query:       gi|119719779|ref|YP_920274.1|  [L=295]
Description: hypothetical protein Tpen_0870 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.2e-14   53.0  18.5    1.9e-07   30.2  11.6    2.2  2  Presenilin  Presenilin


Domain annotation for each model (and alignments):
>> Presenilin  Presenilin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2  11.6   1.1e-11   1.9e-07      58     206 ..      54     198 ..       8     206 .. 0.74
   2 !   27.9   0.4   5.2e-11   9.3e-07     320     391 ..     218     290 ..     194     294 .. 0.79

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 1.1e-11
                     Presenilin  58 lnsllnalililvivvvtfllvlLykyrcykvikgwlilsslllLflvsglllaev..lkaynipldyitlllllwnfgv 135
                                     ++++n++ ++l++++ t +l+++ k+r  ++i +  ++++++    +s l+++++  +++  +p+  +t +ll +    
  gi|119719779|ref|YP_920274.1|  54 RGAIVNSVLTLLLVLLGTGVLLAMIKLRKARFIPALTAFAVAFSFWGISELYFYAFsaFDQRILPIADATSILLAVTT-- 131
                                    579****************************************99999999888651044444444444444443333.. PP

                     Presenilin 136 vGviaifwkgplllqqaYlilisalmAlvfikylpewTtwvlLvvisiyDlvAVLcPkGPLrlLvelaqer 206
                                     G   i   +   l +a li+ +++    +  +lp+w+++ + vv++ yDl  V   +GPL++++e    +
  gi|119719779|ref|YP_920274.1| 132 -G-ALILKPVNATLLNALLIAYGTMAGALLFATLPSWSVFGIAVVLAAYDLYSVF--RGPLKKILESTIAQ 198
                                    .3.346677788888999999999886666666*********************8..8******9976544 PP

  == domain 2  score: 27.9 bits;  conditional E-value: 5.2e-11
                     Presenilin 320 rgvkLGLGDFiFYSvLvgkAal..sgdlntvvacfvailiGLclTLllLaifkkalPALPisialGlvfyfltr 391
                                    rg+ LG+GD   YS+L     l  +  +  +++  +a  +GL +TL +L   ++ +PALP+++a+ +  y++ +
  gi|119719779|ref|YP_920274.1| 218 RGLALGMGDVLVYSMLSPAFLLypRVSVERWILSNLALTAGLYATLEMLK-RRRYMPALPLPVAFSVAAYLAYT 290
                                    7999***********9655554556788899*****************97.5889***************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       728  (0.0406046); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1998.32
//
Query:       gi|119719780|ref|YP_920275.1|  [L=390]
Description: AAA ATPase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.1e-11   42.5   0.0    2.6e-10   40.7   0.0    1.8  2  AAA_22    AAA domain
    1.6e-05   25.4   0.3    7.3e-05   23.2   0.0    2.2  2  AAA_16    AAA ATPase domain
    2.8e-05   24.6   0.0    5.7e-05   23.6   0.0    1.5  1  AAA       ATPase family associated with various cellular acti
      5e-05   22.8   0.0    9.7e-05   21.9   0.0    1.4  1  TniB      Bacterial TniB protein
    8.2e-05   22.5   0.0    0.00022   21.1   0.0    1.7  1  Cdc6_C    CDC6, C terminal winged helix domain
      0.002   17.9   0.0     0.0039   16.9   0.0    1.4  1  AAA_24    AAA domain
     0.0039   17.2   0.0      0.017   15.2   0.0    1.7  2  ResIII    Type III restriction enzyme, res subunit
  ------ inclusion threshold ------
      0.012   14.9   0.0      0.017   14.4   0.0    1.1  1  DUF2075   Uncharacterized conserved protein (DUF2075)
      0.073   12.5   0.0       0.27   10.6   0.0    1.8  2  PhoH      PhoH-like protein
      0.081   12.7   0.0        7.4    6.3   0.0    2.3  2  DEAD      DEAD/DEAH box helicase
      0.097   12.6   0.0       0.18   11.7   0.0    1.5  1  NACHT     NACHT domain
       0.11   13.0   0.0       0.24   11.9   0.0    1.6  1  ABC_tran  ABC transporter
       0.16   11.5   0.0       0.28   10.7   0.0    1.3  1  AAA_7     P-loop containing dynein motor region


Domain annotation for each model (and alignments):
>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7   0.0   1.9e-13   2.6e-10      10     118 ..      46     162 ..      42     178 .. 0.76
   2 ?   -1.3   0.0       1.8   2.5e+03      89     104 ..     310     328 ..     244     373 .. 0.59

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 1.9e-13
                         AAA_22  10 vtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskd......llrellralglelkaerlsseell.eal 82 
                                    ++G++GtGKT +   ++++ ++++    e++++++v+l+s+ s++       +++ +l++lg + ++  ls  e++ + +
  gi|119719780|ref|YP_920275.1|  46 LIGPTGTGKTSTSLFFARSVEQQS----ENVSTIYVNLKSLRSRDAdgfpwiVYTSILSQLGAKPSR-SLSAAEVFmKVV 120
                                    89*****************97765....4*************4443333332588899999999999.889888886788 PP

                         AAA_22  83 eqalraravielliiDEaqhlr...s...eealeeLrsllnl 118
                                     + +r++++ +l+i+DEa+ l+   s    +++ +L +l +l
  gi|119719780|ref|YP_920275.1| 121 GELSRRQKKLHLVIVDEADELTgprSlqgGQIVYNLTRLPEL 162
                                    888888887************765425567777777766665 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.8
                         AAA_22  89 rav...ielliiDEaqhlr 104
                                     ++    e  +++Eaq + 
  gi|119719780|ref|YP_920275.1| 310 SDTiyvSEQRVLEEAQAIC 328
                                    3334444444556666654 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   5.3e-08   7.3e-05       1      64 [.      17      84 ..      17     173 .. 0.70
   2 ?   -1.6   0.1       2.2     3e+03      12      12 ..     300     300 ..     203     351 .. 0.63

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 5.3e-08
                         AAA_16  1 rlvGReeeleqLlsalervrsgrp..elvllsGesGvGKsslvrellralekd..ggiflrgkcdql.e 64
                                   rl+ Re ++e+L+s++  + +  p  ++v l+G+ G+GK+s    ++r++e++  ++ +++ + ++l +
  gi|119719780|ref|YP_920275.1| 17 RLPHREPQIERLASLFPELPKA-PffRVVQLIGPTGTGKTSTSLFFARSVEQQseNVSTIYVNLKSLrS 84
                                   6899************966544.347**********************999998646666666666622 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.2
                         AAA_16  12 L 12 
                                    L
  gi|119719780|ref|YP_920275.1| 300 L 300
                                    1 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   4.1e-08   5.7e-05       3      89 ..      46     156 ..      44     176 .. 0.71

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 4.1e-08
                                    EESSTTSSHHHHHHHHHHHH.....THEEEEEETTTCSSS.........................STTHHHHHHHHHHHH CS
                            AAA   3 lyGppGtGKTllakavakel.....gvefleisgsellsk.........................yvgesekkirelfke 52 
                                    l+Gp GtGKT++    a+++     +v+ + +++++l+s                             e  +k+ + +++
  gi|119719780|ref|YP_920275.1|  46 LIGPTGTGKTSTSLFFARSVeqqseNVSTIYVNLKSLRSRdadgfpwivytsilsqlgakpsrslSAAEVFMKVVGELSR 125
                                    89*********9999999985444558899999999997789*************8888777644333333333333333 PP

                                    HHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHH CS
                            AAA  53 akekakpsilfiDEidalaksrsgseseeeervvnqL 89 
                                      +++k + +++DE+d+l++ r    s ++ ++v  L
  gi|119719780|ref|YP_920275.1| 126 --RQKKLHLVIVDEADELTGPR----SLQGGQIVYNL 156
                                    ..22246***********9999....55555555555 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0     7e-08   9.7e-05      20     132 ..      25     142 ..      12     165 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 7e-08
                           TniB  20 lerLeeLley.pkrkrmpnlllvGdsnnGKtmivekFarlhppekdedaekvpvlvvqappkpdekrl....yaaiLeal 94 
                                    +erL++L+   pk+   + + l+G++ +GKt+    Far+ ++++ e+ +++ v + +++++   +++    y++iL +l
  gi|119719780|ref|YP_920275.1|  25 IERLASLFPElPKAPFFRVVQLIGPTGTGKTSTSLFFARSVEQQS-ENVSTIYVNLKSLRSRD-ADGFpwivYTSILSQL 102
                                    6888888865488888899*************9999988776655.44444444444444443.33333334******** PP

                           TniB  95 gaplkararvskleqqvlrll..relkvrvLiiDEihnll 132
                                    ga+ + + ++++   +v+  l  r+ k++++i+DE ++l 
  gi|119719780|ref|YP_920275.1| 103 GAKPSRSLSAAEVFMKVVGELsrRQKKLHLVIVDEADELT 142
                                    ***999999999988988888334567889******9986 PP

>> Cdc6_C  CDC6, C terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   1.6e-07   0.00022       1      57 [.     300     356 ..     300     358 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.6e-07
                                    HHHHHHHHCHCSSS-EEHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHTTSEEE CS
                         Cdc6_C   1 LcalvlllrksgkeevttgevyevYkslCesegvdpltqrevsdllseLemlgilel 57 
                                    L+a+++ + +s++ +v+ ++v e+ + +Ce++g+ pl +re+   l++L++lg +++
  gi|119719780|ref|YP_920275.1| 300 LAAALRAAGSSDTIYVSEQRVLEEAQAICERLGIPPLGRREIATALQRLHDLGYIKV 356
                                    56677777788888999999*********************************9975 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   2.8e-06    0.0039       4      77 ..      43     141 ..      41     145 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.8e-06
                         AAA_24   4 kiliyGpsgiGKTtlakel.........gpkplfidtekGlksldadkfpdie.................swedfldevv 57 
                                     ++++Gp g+GKT++ + +           +++++++  +l+s dad fp i                  + e f++ v 
  gi|119719780|ref|YP_920275.1|  43 VVQLIGPTGTGKTSTSLFFarsveqqseNVSTIYVNLK-SLRSRDADGFPWIVytsilsqlgakpsrslsAAEVFMKVVG 121
                                    689***********999998889999777777777775.5999999999988899**************999******** PP

                         AAA_24  58 elaaeladyktlviDtidel 77 
                                    el++ +++++ +++D +del
  gi|119719780|ref|YP_920275.1| 122 ELSRRQKKLHLVIVDEADEL 141
                                    ******************98 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.2e-05     0.017       4      56 ..      20      73 ..      17      91 .. 0.79
   2 ?   -1.2   0.0       1.2   1.7e+03     129     145 ..     126     142 ..     107     155 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.2e-05
                                   E-HHHHHHHHHHT......TTSEEE.EEESTTSTHHHHHHHHHHHH-S.....- CS
                         ResIII  4 lreyQeeaienlleklkskrdkrgl.ikmaTGtGKTlvaaklierllkkgkeek 56
                                    re Q+e + +l  +l +    r++ +  +TGtGKT +++ +++++ ++ ++  
  gi|119719780|ref|YP_920275.1| 20 HREPQIERLASLFPELPKAPFFRVVqLIGPTGTGKTSTSLFFARSVEQQSENVS 73
                                   578888888888888876666677779******************999866544 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.2
                                    HTTT-SEEEEETGGGTT CS
                         ResIII 129 lrdrfdviiiDEaHrlg 145
                                    ++++  ++i+DEa  l+
  gi|119719780|ref|YP_920275.1| 126 RQKKLHLVIVDEADELT 142
                                    3344459999*996655 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.2e-05     0.017       8     101 ..      48     142 ..      42     157 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.2e-05
                        DUF2075   8 GvaGtGKtvvllnllaeleddeeertavylsvNhplvl.........vlrealakkeekkkkkeafeklssfinnlsefk 78 
                                    G +GtGKt   l ++  +  +++ +++  ++vN + ++         +++  + ++  + k +++++  + f++ +    
  gi|119719780|ref|YP_920275.1|  48 GPTGTGKTSTSLFFARSV--EQQSENVSTIYVNLKSLRsrdadgfpwIVYTSILSQL-GAKPSRSLSAAEVFMKVVG--- 121
                                    899*****9998888888..6666666666677666555779999999999999988.7777777777777777777... PP

                        DUF2075  79 kaeekkeepkedvvivDEAhrll 101
                                      e +++++k+++vivDEA  l+
  gi|119719780|ref|YP_920275.1| 122 --ELSRRQKKLHLVIVDEADELT 142
                                    ..66799************8776 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0    0.0002      0.27      20      48 ..      42      70 ..      33      81 .. 0.81
   2 ?   -1.8   0.0       1.3   1.8e+03     122     132 ..     132     142 ..     126     158 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0002
                                   SEEEEE--TTSSTTHHHHHHHHHHHHTTS CS
                           PhoH 20 divfaiGpaGtGKtylavalavealkkkk 48
                                    +v  iGp+GtGKt  ++  a ++ ++++
  gi|119719780|ref|YP_920275.1| 42 RVVQLIGPTGTGKTSTSLFFARSVEQQSE 70
                                   58999**********99999977766644 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.3
                                    EEEE-SGGG-- CS
                           PhoH 122 fvilDEAQntt 132
                                    +vi+DEA ++t
  gi|119719780|ref|YP_920275.1| 132 LVIVDEADELT 142
                                    79*****9887 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.026        36      17      35 ..      44      62 ..      33      85 .. 0.72
   2 ?    6.3   0.0    0.0054       7.4     115     135 ..     126     143 ..      94     163 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.026
                                   EEEEESTTSSHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxx RF
                           DEAD 17 vlvaaeTGsGKTlaflipv 35
                                   v + ++TG+GKT   l+ +
  gi|119719780|ref|YP_920275.1| 44 VQLIGPTGTGKTSTSLFFA 62
                                   56789*******9855444 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0054
                                    TSSHCTTEEEEEEETHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxx RF
                           DEAD 115 gklnlsqvrflVlDEadrlld 135
                                    +    +++ ++++DEad+l  
  gi|119719780|ref|YP_920275.1| 126 R---QKKLHLVIVDEADELTG 143
                                    2...48999*********975 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00013      0.18       1      97 [.      42     145 ..      42     187 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00013
                                    SCEEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-...-HCHHHCCCCTS--SSS-C.......CH CS
                          NACHT   1 rlvilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgnarsladllfsqlpepaapvse.......vw 73 
                                    r+v l G+ G GKT     +a+   ++  +     +v + slr++  +g    + + + sql ++ +++         v+
  gi|119719780|ref|YP_920275.1|  42 RVVQLIGPTGTGKTSTSLFFARSVEQQSENVS-TIYVNLKSLRSRDADGFPWIVYTSILSQLGAKPSRSLSaaevfmkVV 120
                                    68999**********99999999988886665.46666666666666666655566666666555555544588899888 PP

                                    HHHCCSCCCE.EEEEE-STT-SS-T CS
                          NACHT  74 avllelperl.LlilDglDelvtdl 97 
                                     +l +++++l L i+D +Del    
  gi|119719780|ref|YP_920275.1| 121 GELSRRQKKLhLVIVDEADELTGPR 145
                                    888888888746899*****98754 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00017      0.24      13      43 ..      43      73 ..      40     139 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00017
                                   EEEEEESTTSSHHHHHHHHTTSS--SEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran 13 kvaivGenGaGKStLlkllagllkpteGeil 43
                                   +v+++G++G+GK++    +a+ ++++++++ 
  gi|119719780|ref|YP_920275.1| 43 VVQLIGPTGTGKTSTSLFFARSVEQQSENVS 73
                                   799*********************9999883 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0    0.0002      0.28      36      70 ..      44      80 ..      41      86 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0002
                          AAA_7 36 vllvGptGtGKtviikdllkkld..kekylsltinfs 70
                                   v l+GptGtGKt++   + ++++  +e+++++ +n++
  gi|119719780|ref|YP_920275.1| 44 VQLIGPTGTGKTSTSLFFARSVEqqSENVSTIYVNLK 80
                                   6799*********999988888733455555666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 2585.47
//
Query:       gi|119719781|ref|YP_920276.1|  [L=156]
Description: pyruvoyl-dependent arginine decarboxylase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-35  121.2   0.0      4e-35  121.0   0.0    1.0  1  PvlArgDC  Pyruvoyl-dependent arginine decarboxylase (PvlArgDC


Domain annotation for each model (and alignments):
>> PvlArgDC  Pyruvoyl-dependent arginine decarboxylase (PvlArgDC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.0   0.0   2.2e-39     4e-35       1     161 [.       3     150 ..       3     151 .. 0.87

  Alignments for each domain:
  == domain 1  score: 121.0 bits;  conditional E-value: 2.2e-39
                       PvlArgDC   1 vPkkvfltkGvgesk.eelasFdlALldAgIenfNLvkvSSilPpeaeivsveeglkelppGsivevvmarassnepgrl 79 
                                    +Pkk+f+tkG+g s+ + l++F++AL++AgI+++NLv+vSSilPpe+e    ee +++lp+Gsi +vvm++++++ p r 
  gi|119719781|ref|YP_920276.1|   3 LPKKYFVTKGKGLSNvSPLMAFNNALREAGIHQLNLVPVSSILPPEVE----EESPRRLPAGSIAFVVMSEKRAKGPAR- 77 
                                    59*************89*******************************....888899********************6. PP

                       PvlArgDC  80 iaaavgvaipkdekkgGyiaEysgfgeseeeaeeeaeelaaemlattrglleekiietkeievaaveakvekygtvlaaa 159
                                    i++++++a+ k    +Gy++E+++ ++s+e++++  +   +  l+ ++      ++e+ ++ v++ e   + yg v++a+
  gi|119719781|ref|YP_920276.1|  78 ISTGISWARGKP---HGYVIEFHDGNSSAETSSNLSAMWSEIRLRDVL------ELEEPRYLVEELEIPPGYYGSVVVAL 148
                                    ********8755...*********554444444444444444555555......55999********************* PP

                       PvlArgDC 160 vf 161
                                    vf
  gi|119719781|ref|YP_920276.1| 149 VF 150
                                    *9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1053.92
//
Query:       gi|119719782|ref|YP_920277.1|  [L=490]
Description: hypothetical protein Tpen_0873 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (490 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 3155.12
//
Query:       gi|119719783|ref|YP_920278.1|  [L=72]
Description: hypothetical protein Tpen_0874 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0074   16.0   0.1     0.0082   15.8   0.1    1.0  1  DSHCT     DSHCT (NUC185) domain


Domain annotation for each model (and alignments):
>> DSHCT  DSHCT (NUC185) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   4.6e-07    0.0082     103     157 ..      12      66 ..       8      68 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.6e-07
                          DSHCT 103 gasfaellektdldeGdiVRllrrleellrqlakaakvigneeLkkkaeeaieli 157
                                     + +a++l+   l+e  +V++l  +ee+l  ++ a++v ++eeL++++ee +e +
  gi|119719783|ref|YP_920278.1|  12 SRLLASTLKGDGLYEARLVKALDAIEEFLASVRGAPRVEEDEELAREIEENVEEL 66 
                                    556788899999*************************************988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.30s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 476.27
//
Query:       gi|119719784|ref|YP_920279.1|  [L=179]
Description: putative methylase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-18   65.8   0.0    1.3e-17   63.8   0.0    1.7  1  MTS              Methyltransferase small domain
    7.9e-13   48.9   0.4    5.8e-12   46.1   0.4    2.0  1  Methyltransf_11  Methyltransferase domain
    3.6e-10   40.4   0.1    1.7e-09   38.2   0.1    1.9  1  Methyltransf_25  Methyltransferase domain
    8.8e-09   35.3   0.0    1.1e-08   35.1   0.0    1.1  1  Methyltransf_31  Methyltransferase domain
    1.7e-06   27.9   0.0    5.7e-06   26.1   0.0    1.7  1  UPF0020          Putative RNA methylase family UPF0020
    0.00029   21.5   0.0    0.00056   20.6   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
    0.00065   19.6   0.0    0.00096   19.0   0.0    1.5  1  Methyltransf_23  Methyltransferase domain
     0.0012   18.3   0.0     0.0015   17.9   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
  ------ inclusion threshold ------
       0.02   14.3   0.0       0.45    9.8   0.0    2.0  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family
      0.053   13.2   0.1      0.089   12.4   0.1    1.4  1  TPMT             Thiopurine S-methyltransferase (TPMT)
       0.11   11.8   0.0       0.14   11.4   0.0    1.1  1  CMAS             Mycolic acid cyclopropane synthetase


Domain annotation for each model (and alignments):
>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.8   0.0   8.2e-21   1.3e-17      20     163 ..       9     165 ..       7     168 .. 0.85

  Alignments for each domain:
  == domain 1  score: 63.8 bits;  conditional E-value: 8.2e-21
                                    HHHHHHHCHCC.TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTSTTS- CS
                            MTS  20 sklLletlpke.lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvleeveekk 97 
                                    + lLl++l+   + g ++ +GcG Gv+++ + ++ +   v+ vd+ ++A+++++e ++a+k   v++v+ d+l+ + + +
  gi|119719784|ref|YP_920279.1|   9 TFLLLDCLKRGfRGGVLVEVGCGKGVVSVYASNRADY--VVGVDIAWEAVRLSRELARASKEClVDFVQADMLNPFRDSS 86 
                                    569*******96667789************9998888..9***************999988778**************** PP

                                    EEEEEE---S..........TTTCHCHHHHHHHHHHHHHHHEEEEEEEEEEEETTSCHHHH...HHHHHS--EEEEEES CS
                            MTS  98 fdlivsNPPf..........hagkatelavaeeliaeAkeaLkegGeLliVanrklgyesl...leelfgnvevvaktk 163
                                     d++ sNPP+            g +   +   +l +eA ++L+ +GeL++Va++  + e+l   l+ l+ +vev+++++
  gi|119719784|ref|YP_920279.1|  87 ADVVASNPPYlpcdyredplVCGGEDGVEFSARLAREAFRVLRRSGELFLVASSISNFERLldvLRGLYASVEVAEERR 165
                                    ********96333322111145777889999***********************9999999666788888888887766 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.1   0.4   3.6e-15   5.8e-12       2      95 ..      27     135 ..      26     136 .. 0.88

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 3.6e-15
                                    EET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-TT-EEEEEEES-CCC-C..... CS
                Methyltransf_11   2 dvGcGtGrlaealakrgarvvgvDlskemlklakekaseegl.kvefvvadaeklpfednsfDlvvssevlhhve..... 75 
                                    +vGcG+G ++ +  +r+  vvgvD++ e+++l++e a+ +++  v+fv+ad+ + pf+d+s D+v s+     ++     
  gi|119719784|ref|YP_920279.1|  27 EVGCGKGVVSVYASNRADYVVGVDIAWEAVRLSRELARASKEcLVDFVQADMLN-PFRDSSADVVASNPPYLPCDyredp 105
                                    89**************************************99*9*********9.*************955555334456 PP

                                    ..........CHHHHHHHHHHHEEEEEEEE CS
                Methyltransf_11  76 ..........dpekalkeiaRvLkpgGllv 95 
                                                +++ +e+ RvL+  G l+
  gi|119719784|ref|YP_920279.1| 106 lvcggedgveFSARLAREAFRVLRRSGELF 135
                                    66666666668999***********99987 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2   0.1     1e-12   1.7e-09       2      71 ..      26      93 ..      25     132 .. 0.83

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 1e-12
                                   EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHH.TTTTEEEEESBCCGBSSSTTTEEEEEEE CS
                Methyltransf_25  2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraee.eglnvefvqgdaedlpfedgsfDlvvss 71
                                   +++GcG+G ++ ++++r     v+gvDi+ e+++  re a++ +++ v+fvq+d+ + pf d+s D+v s+
  gi|119719784|ref|YP_920279.1| 26 VEVGCGKGVVSVYASNRA--DYVVGVDIAWEAVRLSRELARAsKECLVDFVQADMLN-PFRDSSADVVASN 93
                                   69***************6..9*****************99995666*********98.8*********995 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.0   6.5e-12   1.1e-08       6     113 ..      24     140 ..      20     168 .. 0.83

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 6.5e-12
                Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkae.vvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsn... 81 
                                    +++++GCG+G  +  +  +    a+ vvG+Di  ea++l+re a+  +   v F q+d+ + +  + d++ D++ sn   
  gi|119719784|ref|YP_920279.1|  24 VLVEVGCGKGVVSVYASNR----ADyVVGVDIAWEAVRLSRELARASKECLVDFVQADMLN-P--FRDSSADVVASNppy 96 
                                    6789********9999843....445****************999999999**********.6..779*********877 PP

                Methyltransf_31  82 .......evl.....naladpdkileeiervlkpggilliedpr 113
                                           ++l     + + +++   +e++rvl+  g+l +   +
  gi|119719784|ref|YP_920279.1|  97 lpcdyreDPLvcggeDGVEFSARLAREAFRVLRRSGELFLVASS 140
                                    77777774447799999999999999**********98765555 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   3.5e-09   5.7e-06      75     176 ..      41     148 ..      30     163 .. 0.75

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 3.5e-09
                                    HH--.EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE----------H.......HHHHHHHH CS
                        UPF0020  75 aelk.lygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpPYGerlgsk.......kalekLYs 146
                                    +++  ++g+D+ +++v+ +re + +a  + l++f+qad+ +   ++++ dv+++npPY     ++       ++  ++  
  gi|119719784|ref|YP_920279.1|  41 NRADyVVGVDIAWEAVRLSRE-LARASKECLVDFVQADMLNPF-RDSSADVVASNPPYLPCDYREdplvcggEDGVEFSA 118
                                    4455599************98.567899********9998755.6779**********8543322111111144567777 PP

                                    HHHHHHHHH-TT..-EEEEEESSHHHHHCC CS
                        UPF0020 147 eflrelkrvlrgggrlvlltsenkalekal 176
                                     ++re+ rvlr++g l l++s+ +++e++l
  gi|119719784|ref|YP_920279.1| 119 RLAREAFRVLRRSGELFLVASSISNFERLL 148
                                    777777788887777777777777777765 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   3.4e-07   0.00056       1      71 [.      26      91 ..      26      94 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3.4e-07
                Methyltransf_12  1 LeiGcGtGsllralleklpdieyt.gvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvv 71
                                   +e+GcG G ++ +  ++   ++y+ gvDi  +a+ + +++la+ ++++   v++ + d l+ +  ss D+v 
  gi|119719784|ref|YP_920279.1| 26 VEVGCGKGVVSVYASNR---ADYVvGVDIAWEAV-RLSRELARASKEC--LVDFVQADMLNPFRDSSADVVA 91
                                   69***********9999...55555*********.7777777777666..7888888888777778999996 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   5.9e-07   0.00096      16      86 ..      15      90 ..       7     164 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 5.9e-07
                Methyltransf_23 16 llpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae.....kakkaqkdqfdeqeaaepqgkfdlI 86
                                    l++ ++gg ++++GcG+G ++ +++ +   v+gvD+  eav + +     ++ + ++     +  ++ + + d++
  gi|119719784|ref|YP_920279.1| 15 CLKRGFRGGVLVEVGCGKGVVSVYASNRADYVVGVDIAWEAVRLSRelaraSKECLVDFVQADMLNPFRDSSADVV 90
                                   5677899************77776665555788****999999888777775555555555455555555555555 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   9.5e-07    0.0015     164     233 ..      24      93 ..       8      94 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 9.5e-07
                           PrmA 164 evlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkvea.klevalseellk...eekadvivaN 233
                                     ++ vG+G G+ ++ a+   a+ vv+vDi   Av+ ++e a+  k     +   +++++l+   +++adv+ +N
  gi|119719784|ref|YP_920279.1|  24 VLVEVGCGKGVVSVYASN-RADYVVGVDIAWEAVRLSRELARASKECLvDF---VQADMLNpfrDSSADVVASN 93 
                                    4569**********9987.799***************99776554322133...34444433336778888776 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00027      0.45      47     120 ..      21      90 ..       9      93 .. 0.84
   2 ?    2.5   0.0     0.048        78     136     157 ..     121     142 ..     114     158 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00027
                                    -TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEE CS
                Ubie_methyltran  47 rgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvv 120
                                    rg  +++v +G g +++  s+ ++    vv++Di  + ++ +++ ++ +    ++f+qa+ +  pf d s Dvv
  gi|119719784|ref|YP_920279.1|  21 RGGVLVEVGCGKGVVSVYASNRAD---YVVGVDIAWEAVRLSRELARASKECLVDFVQAD-MLNPFRDSSADVV 90 
                                    556788999999998887776655...699******************9999******98.556********98 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.048
                                    HHHHHHHEEEEEEEEEEEE--- CS
                Ubie_methyltran 136 LkeayrvlkpGGrlvvlefskv 157
                                     +ea+rvl+  G+l+ +  s  
  gi|119719784|ref|YP_920279.1| 121 AREAFRVLRRSGELFLVASSIS 142
                                    589**********998877654 PP

>> TPMT  Thiopurine S-methyltransferase (TPMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   5.5e-05     0.089      45      74 ..      29      58 ..      11      80 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.5e-05
                                   T-TT-HHHHHH-BTTEEEEEE-S-HHHHHH CS
                           TPMT 45 lCGkaldlvwlAeqgrevvGvelselAvek 74
                                   +CGk++  v  +++ + vvGv+++  Av+ 
  gi|119719784|ref|YP_920279.1| 29 GCGKGVVSVYASNRADYVVGVDIAWEAVRL 58
                                   8**************************986 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   8.6e-05      0.14      63     106 ..      22      64 ..      11      90 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.6e-05
                                    T-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHH CS
                           CMAS  63 GmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvd 106
                                    G  l+++GcG G + ++a +r    vvg+ +  e  +l+++   
  gi|119719784|ref|YP_920279.1|  22 GGVLVEVGCGKGVVSVYASNR-ADYVVGVDIAWEAVRLSRELAR 64 
                                    7789*****************.5579999999999888887654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1208.26
//
Query:       gi|119719785|ref|YP_920280.1|  [L=102]
Description: hypothetical protein Tpen_0876 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-22   79.0   0.5    2.8e-22   78.7   0.5    1.1  1  FeS_assembly_P  Iron-sulfur cluster assembly protein
    1.2e-06   28.6   0.4    2.1e-06   27.8   0.4    1.5  1  NifU            NifU-like domain


Domain annotation for each model (and alignments):
>> FeS_assembly_P  Iron-sulfur cluster assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.7   0.5   3.1e-26   2.8e-22       2      73 ..       8      80 ..       7      81 .. 0.97

  Alignments for each domain:
  == domain 1  score: 78.7 bits;  conditional E-value: 3.1e-26
                                   HHHHHHHTT-B-TTTSSBCCCCT---EEEE-T-EEEEEE--SSTT-TTHHHHHHHHHHHHC..STT--EEEEE CS
                 FeS_assembly_P  2 eavlaaLrtVtDPelgvdlvslglvreidieggkVsvditltypacslaeairadaeaalr.alpgvevveVe 73
                                   e+v++aL++V+DPe++ ++v+lglv++++++g kV+v++tlt ++c++ + + + +++ ++ ++p+ve+veV+
  gi|119719785|ref|YP_920280.1|  8 ERVMEALKEVYDPEIPFNVVDLGLVYGVEVDGRKVKVKMTLTAIGCPMSYFLVEMVRDVIKeKIPEVEDVEVD 80
                                   79****************************************************************9999996 PP

>> NifU  NifU-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.4   2.3e-10   2.1e-06      18      67 .]      30      78 ..      10      78 .. 0.89

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 2.3e-10
                                   -EEEEEEEETTEEEEEEESGGGG-....THHHHHHHHHHHHH-TT--EEE CS
                           NifU 18 GdielvdvdegvVkvrlqGaCsgCpsstvtlkegiekaLkeevpevkeVe 67
                                   G +  v+vd+++Vkv+++    gCp+s   + e+++  +ke++pev+ Ve
  gi|119719785|ref|YP_920280.1| 30 GLVYGVEVDGRKVKVKMTLTAIGCPMSYFLV-EMVRDVIKEKIPEVEDVE 78
                                   5555689********************9999.9**************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.20s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 836.44
//
Query:       gi|119719786|ref|YP_920281.1|  [L=246]
Description: ERCC4 domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.1e-17   62.0   0.0    1.1e-16   61.4   0.0    1.3  1  ERCC4           ERCC4 domain
      2e-08   34.7   0.0    4.5e-08   33.6   0.0    1.6  1  HHH_5           Helix-hairpin-helix domain
    2.8e-08   33.2   0.0     0.0093   15.8   0.0    2.5  2  HHH             Helix-hairpin-helix motif
    6.9e-05   23.0   0.0      0.057   13.7   0.0    2.6  2  HHH_3           Helix-hairpin-helix motif
     0.0038   17.5   0.1        2.1    8.8   0.0    2.9  3  IMS_HHH         IMS family HHH motif
  ------ inclusion threshold ------
      0.028   14.2   0.1       0.17   11.7   0.0    2.3  3  ACT_7           ACT domain
      0.076   13.1   0.0       0.18   11.9   0.0    1.7  1  HHH_2           Helix-hairpin-helix motif
       0.15   12.4   0.0       0.32   11.3   0.0    1.6  1  Transposase_20  Transposase IS116/IS110/IS902 family


Domain annotation for each model (and alignments):
>> ERCC4  ERCC4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.4   0.0     5e-20   1.1e-16       1     155 [.       8     128 ..       8     129 .. 0.91

  Alignments for each domain:
  == domain 1  score: 61.4 bits;  conditional E-value: 5e-20
                                    EEGGGCTSHHHH..HHTTTSEEEEE--SSSSE.EE...CTT...............EEEEEEEHHHHHHHHCCSHHHHHH CS
                          ERCC4   1 iDsrelksgieeylleelgvevvietlpigdyilwrrkvkaeynleldieepceekvlverksaddlvasikdgrleeqv 80 
                                    +D+re +s +  + l++lgv++ + +l++gdy  +    +                + verks  d+v+s++dgrl+eq+
  gi|119719786|ref|YP_920281.1|   8 VDDRERRSPVLSE-LARLGVRYSVARLEVGDY-DV---GGV---------------YGVERKSSGDFVNSVIDGRLFEQA 67 
                                    7****99999999.9*****************.99...888...............************************ PP

                                    HHHHH.H-SEEEEEEES..-GGGTT................THHH.HHHHHHHHHHHHS-EEEEESSHHHHHHHHHH CS
                          ERCC4  81 srlkrngykkpillveg..ldqykrknknsrnkqykakvrqinrktiesaLvqlqldfgvsilttesanetaewlan 155
                                    + l++ +y+  i++veg  +   + +      +q       ++ + + +aL++l+ + gvs+l+++s +eta +++ 
  gi|119719786|ref|YP_920281.1|  68 KYLRE-SYETAIIVVEGdlS-EEVSR------RQ-------VSLNPLFGALAALAEN-GVSVLQVRSYAETALLIYV 128
                                    *****.***********742.33333......23.......88889*********99.**************99986 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.0     2e-11   4.5e-08       4      55 ..     163     213 ..     160     215 .. 0.93

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 2e-11
                                    HHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHH CS
                          HHH_5   4 LlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriilel 55 
                                    + s++Gi +++A ++l+  + ++  +  a+++eL +i+G+G+k+ ++i++ l
  gi|119719786|ref|YP_920281.1| 163 IASLPGISREMADRILRE-FHTPRRFFTATPAELRRIHGLGPKRIQKILQVL 213
                                    579***************.*****************************9866 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   8.5e-06     0.019      13      28 ..     163     178 ..     159     180 .. 0.91
   2 !   15.8   0.0   4.1e-06    0.0093       6      29 ..     188     211 ..     184     212 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 8.5e-06
                                    HHTSTT-SHHHHHHHH CS
                            HHH  13 LlalPGVGpktAeaIl 28 
                                    +++lPG+ +++A++Il
  gi|119719786|ref|YP_920281.1| 163 IASLPGISREMADRIL 178
                                    689************9 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 4.1e-06
                                    HTSSHHHHHTSTT-SHHHHHHHHH CS
                            HHH   6 ipasreeLlalPGVGpktAeaIls 29 
                                    ++a+++eL  + G Gpk+ ++Il+
  gi|119719786|ref|YP_920281.1| 188 FTATPAELRRIHGLGPKRIQKILQ 211
                                    79********************97 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.0    0.0049        11      14      32 ..     161     179 ..     157     182 .. 0.88
   2 !   13.7   0.0   2.5e-05     0.057      10      32 ..     189     211 ..     187     215 .. 0.94

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0049
                          HHH_3  14 eeLqklpGlgpklAknIva 32 
                                     +++ lpG++  +A++I++
  gi|119719786|ref|YP_920281.1| 161 NLIASLPGISREMADRILR 179
                                    57899************85 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 2.5e-05
                          HHH_3  10 tAsaeeLqklpGlgpklAknIva 32 
                                    tA+ +eL++++Glgpk +++I++
  gi|119719786|ref|YP_920281.1| 189 TATPAELRRIHGLGPKRIQKILQ 211
                                    8********************86 PP

>> IMS_HHH  IMS family HHH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       5.4   1.2e+04      13      22 ..      40      49 ..      39      50 .. 0.75
   2 ?    5.5   0.0      0.01        23      13      31 ..     163     182 ..     163     183 .. 0.88
   3 !    8.8   0.0   0.00094       2.1      12      31 ..     194     214 ..     192     215 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 5.4
                        IMS_HHH 13 itkipGiGgk 22
                                   ++ ++G+ +k
  gi|119719786|ref|YP_920281.1| 40 VGGVYGVERK 49
                                   6778999877 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.01
                        IMS_HHH  13 itkipGiGgklgek.LeklG 31 
                                    i ++pGi + ++++ L+ ++
  gi|119719786|ref|YP_920281.1| 163 IASLPGISREMADRiLREFH 182
                                    6689**********999876 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.00094
                        IMS_HHH  12 pitkipGiGgklgek.LeklG 31 
                                    +++ i+G+G+k  +k L++l+
  gi|119719786|ref|YP_920281.1| 194 ELRRIHGLGPKRIQKiLQVLD 214
                                    589**************9996 PP

>> ACT_7  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.8   4.1e+03      43      59 ..      73      89 ..      69      91 .. 0.72
   2 ?   11.7   0.0   7.6e-05      0.17      27      51 ..     102     126 ..      99     127 .. 0.85
   3 ?   -2.4   0.0       1.9   4.3e+03      21      42 ..     203     224 ..     201     227 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.8
                                   -SS-EEEEEEGGGHHHH CS
                          ACT_7 43 tyrtdyiLVpeedlekA 59
                                   +y t +i+V+ +  e++
  gi|119719786|ref|YP_920281.1| 73 SYETAIIVVEGDLSEEV 89
                                   88899999987766655 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 7.6e-05
                                    HHHHHHTTT---EEEE-SS-EEEEE CS
                          ACT_7  27 laspLaeagIsifqiStyrtdyiLV 51 
                                      ++Lae+g+s++q+ +y    +L+
  gi|119719786|ref|YP_920281.1| 102 ALAALAENGVSVLQVRSYAETALLI 126
                                    5789**************8877766 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.9
                                    --HHHHHHHHHHTTT---EEEE CS
                          ACT_7  21 tGivaklaspLaeagIsifqiS 42 
                                    ++++ k+ ++L    +s  ++S
  gi|119719786|ref|YP_920281.1| 203 PKRIQKILQVLDTSYVSAKMLS 224
                                    6777888888888888888887 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   8.1e-05      0.18       9      57 ..     167     215 ..     159     221 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.1e-05
                          HHH_2   9 rhVGektAklLakrFksldaLkkasleeLlevddiGeeiAqsivefFen 57 
                                    + +  ++A  + ++F++  ++ +a+  eL  +++ G++  q+i + +++
  gi|119719786|ref|YP_920281.1| 167 PGISREMADRILREFHTPRRFFTATPAELRRIHGLGPKRIQKILQVLDT 215
                                    56667899******************************99999988766 PP

>> Transposase_20  Transposase IS116/IS110/IS902 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00014      0.32       2      44 ..     161     205 ..     160     207 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00014
                 Transposase_20   2 elLesipGiGpvtaaallaeigdlrrf..ksakqlaayaGlapve 44 
                                    +l+ s+pGi++ +a ++l e +++rrf   ++++l +  Gl p++
  gi|119719786|ref|YP_920281.1| 161 NLIASLPGISREMADRILREFHTPRRFftATPAELRRIHGLGPKR 205
                                    5899**********************8335667888888887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1543.23
//
Query:       gi|119719787|ref|YP_920282.1|  [L=108]
Description: 50S ribosomal protein L12P [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-19   69.3  14.7    3.7e-19   69.1  14.7    1.1  1  Ribosomal_60s  60s Acidic ribosomal protein
    0.00022   21.1   3.5       0.28   11.2   0.1    2.2  2  PepSY_2        Peptidase propeptide and YPEB domain
     0.0021   18.3   0.3     0.0054   17.1   0.0    1.7  2  EF-hand_14     EF-hand domain
  ------ inclusion threshold ------
      0.087   13.1   0.0       0.48   10.7   0.0    1.9  2  HTH_Tnp_Tc3_2  Transposase
      0.094   12.2   0.7       0.11   11.9   0.7    1.0  1  DUF2868        Protein of unknown function (DUF2868)
       0.13   12.3   0.0       0.27   11.2   0.0    1.5  1  TFIID_30kDa    Transcription initiation factor TFIID 23-30kDa
       0.22   11.8   1.4       0.31   11.3   0.0    1.8  2  PhetRS_B1      Phe-tRNA synthetase beta subunit B1 domain
       0.55   10.6   2.3       0.85   10.0   2.3    1.5  1  B5             tRNA synthetase B5 domain


Domain annotation for each model (and alignments):
>> Ribosomal_60s  60s Acidic ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.1  14.7   1.7e-22   3.7e-19       1      88 []      16     106 ..      16     106 .. 0.81

  Alignments for each domain:
  == domain 1  score: 69.1 bits;  conditional E-value: 1.7e-22
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XX-- CS
                  Ribosomal_60s   1 eptaenikkvlkaagveveaarvkllvkalegkdieellangaaklaaaaaaaaaaaaaaaaaaaaeekkkeeeeeEeed 80 
                                    e+++en+k +l+aag++v+++rvk+lv+al++++iee+l+++a  +a +a+a+a a a+a  a++++e+kkee++eE ++
  gi|119719787|ref|YP_920282.1|  16 EISEENVKRILEAAGIQVDDVRVKALVAALKEVNIEEALKTAALPVAVGAPAPATAPAQAPPAEEKKEEKKEEKKEEVKE 95 
                                    69****************************************99976666666666666666666666666666666555 PP

                                    S..S--.STTT CS
                  Ribosomal_60s  81 d..dmG.fgLF 88 
                                    +  ++G  +LF
  gi|119719787|ref|YP_920282.1|  96 EtvEEGlASLF 106
                                    55699999999 PP

>> PepSY_2  Peptidase propeptide and YPEB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.1   0.00013      0.28      28      51 ..      15      38 ..      12      43 .. 0.90
   2 !   10.4   1.1   0.00023      0.51       8      43 ..      61     101 ..      54     105 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00013
                        PepSY_2 28 dwlpreklvakleaqGykvkkiev 51
                                   +++++e+++++lea+G +v++++v
  gi|119719787|ref|YP_920282.1| 15 KEISEENVKRILEAAGIQVDDVRV 38
                                   7899******************98 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00023
                        PepSY_2   8 lalla.....aaAlAgrrdtdspkadwlpreklvakleaqG 43 
                                    +a+ a     a+A+A + +++++++++ ++e++++   ++G
  gi|119719787|ref|YP_920282.1|  61 VAVGApapatAPAQAPPAEEKKEEKKEEKKEEVKEETVEEG 101
                                    33333324467788867777777777777888888888877 PP

>> EF-hand_14  EF-hand domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   2.4e-06    0.0054      14      52 ..      14      52 ..       2      62 .. 0.84
   2 ?   -1.4   0.3       1.4     3e+03      54      65 ..      84      95 ..      77     103 .. 0.44

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.4e-06
                     EF-hand_14 14 tdklsvakllkaLaetGirkdDpRLkellkklkkvekek 52
                                    +++s ++  + L+++Gi+ dD R+k l+ +lk+v+ e+
  gi|119719787|ref|YP_920282.1| 14 GKEISEENVKRILEAAGIQVDDVRVKALVAALKEVNIEE 52
                                   56889999999***********************98775 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.4
                     EF-hand_14 54 eaeesetleldr 65
                                   e++e ++ e++ 
  gi|119719787|ref|YP_920282.1| 84 EKKEEKKEEVKE 95
                                   222233333333 PP

>> HTH_Tnp_Tc3_2  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00022      0.48      25      55 ..      12      42 ..       7      55 .. 0.85
   2 ?    0.0   0.0      0.46     1e+03      23      39 ..      85     102 ..      79     104 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00022
                  HTH_Tnp_Tc3_2 25 eeGksvsreTirrrLrkaglkkrkprkkplL 55
                                   ++Gk++s e ++r+L +ag++   +r k l+
  gi|119719787|ref|YP_920282.1| 12 HAGKEISEENVKRILEAAGIQVDDVRVKALV 42
                                   56******************99888887665 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.46
                  HTH_Tnp_Tc3_2  23 lkee.GksvsreTirrrL 39 
                                     kee  ++v+ eT+   L
  gi|119719787|ref|YP_920282.1|  85 KKEEkKEEVKEETVEEGL 102
                                    566668999999998655 PP

>> DUF2868  Protein of unknown function (DUF2868)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.7   5.1e-05      0.11     144     205 ..      24      86 ..      19     106 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.1e-05
                        DUF2868 144 ralarlpldlslpgyqaLlarlqtpsletgvnda....aapePeaapepkaeaepepasepadvle 205
                                    r l+++ +++++ +++aL+a l++  +e + ++a    a  +P++a++p +++++e+++e++   +
  gi|119719787|ref|YP_920282.1|  24 RILEAAGIQVDDVRVKALVAALKEVNIEEALKTAalpvAVGAPAPATAPAQAPPAEEKKEEK---K 86 
                                    5566666777799*********9999999999999999555555555555555555444432...1 PP

>> TFIID_30kDa  Transcription initiation factor TFIID 23-30kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00012      0.27       8      29 ..      22      43 ..      17      47 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00012
                    TFIID_30kDa  8 tayyLekaGletsDprlarlvs 29
                                   ++ +Le aG++ +D+r++ lv+
  gi|119719787|ref|YP_920282.1| 22 VKRILEAAGIQVDDVRVKALVA 43
                                   6789***************998 PP

>> PhetRS_B1  Phe-tRNA synthetase beta subunit B1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00014      0.31       7      43 ..       5      41 ..       3      66 .. 0.81
   2 ?   -2.3   1.7       2.4   5.3e+03      41      49 ..      84      92 ..      78     101 .. 0.39

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00014
                      PhetRS_B1  7 kkeaLfkalgkelteeeledllfefGlElDeiveeee 43
                                    ++ L+ + gke++ee+++ +l   G+ +D++  ++ 
  gi|119719787|ref|YP_920282.1|  5 YASLLLYHAGKEISEENVKRILEAAGIQVDDVRVKAL 41
                                   567789999**********************987665 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.4
                      PhetRS_B1 41 eeekkkadk 49
                                   e++++k+++
  gi|119719787|ref|YP_920282.1| 84 EKKEEKKEE 92
                                   222122222 PP

>> B5  tRNA synthetase B5 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   2.3   0.00038      0.85      12      32 ..      13      63 ..       9     100 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00038
                                   HTS---HHHHHHHHHHTT-E............................... CS
                                   xxxxxxxxxxxxxxxxxxxx..............................x RF
                             B5 12 lGidlseeeiikiLkrlgce..............................r 32
                                   +G ++see++++iL++ g++                              +
  gi|119719787|ref|YP_920282.1| 13 AGKEISEENVKRILEAAGIQvddvrvkalvaalkevnieealktaalpvaV 63
                                   699****************96666666666666655555555555555550 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1726  (0.0962686); expected 358.6 (0.02)
Passed bias filter:                      839  (0.0467957); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 701.93
//
Query:       gi|119719788|ref|YP_920283.1|  [L=227]
Description: peptidase A24A, prepilin type IV [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-07   31.5   6.8    3.8e-07   30.5   6.8    1.6  1  Peptidase_A24  Type IV leader peptidase family
  ------ inclusion threshold ------
          7    6.8   9.3       0.98    9.5   3.0    2.5  3  BTP            Chlorhexidine efflux transporter


Domain annotation for each model (and alignments):
>> Peptidase_A24  Type IV leader peptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   6.8   4.2e-11   3.8e-07       2      95 ..      14     106 ..      13     128 .. 0.80

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 4.2e-11
                  Peptidase_A24   2 vlltillvlsviDldtrtlpdeltlpllllgvlfa.qllllglpnlaqavlgalvgalvlllislvdeqamGgGDvklaa 80 
                                    v++  l v++++D++tr+++d+++++++ll   +    l +g   l+ ++l+ +v +++ +l   ++++  G +D+  +a
  gi|119719788|ref|YP_920283.1|  14 VVAGTLWVAAYQDFRTREIDDKVWIAGTLLATPLLaAELASGRIVLQLYLLSLAVSLALAVL--SLKLGLTGEADAIAFA 91 
                                    778899************************98887634477888888899999999999999..999************* PP

                  Peptidase_A24  81 vlgaflgwerlllav 95 
                                     lg+f +    +l+ 
  gi|119719788|ref|YP_920283.1|  92 FLGFFEPPRLSPLFA 106
                                    *****9966553332 PP

>> BTP  Chlorhexidine efflux transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.6       0.3   2.7e+03      27      46 ..      52      71 ..      39      77 .. 0.54
   2 ?   -0.7   0.9      0.17   1.5e+03      15      46 ..      61      92 ..      56      97 .. 0.67
   3 ?    9.5   3.0   0.00011      0.98      24      56 ..     100     132 ..      87     133 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.3
                            BTP 27 wllgvslleagvldiglslf 46
                                   +++g  +l+  +l++++sl 
  gi|119719788|ref|YP_920283.1| 52 LASGRIVLQLYLLSLAVSLA 71
                                   45555566666666666654 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.17
                            BTP 15 lglllllvpllawllgvslleagvldiglslf 46
                                   l ll l v l+ ++l+++l+ +g  d++ ++f
  gi|119719788|ref|YP_920283.1| 61 LYLLSLAVSLALAVLSLKLGLTGEADAIAFAF 92
                                   56677777777777777777777666666555 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.00011
                            BTP  24 llawllgvslleagvldiglslfalvwnfvyNl 56 
                                     l+ l+ v+l+++++l+++ ++f+ ++n+ +Nl
  gi|119719788|ref|YP_920283.1| 100 RLSPLFAVPLGTILLLSLVPTAFFAAYNVYWNL 132
                                    56778999************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1584.60
//
Query:       gi|119719789|ref|YP_920284.1|  [L=227]
Description: triosephosphate isomerase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-12   46.9   0.0    6.8e-12   45.3   0.0    1.7  2  TIM            Triosephosphate isomerase
     0.0002   20.8   3.5    0.00025   20.6   3.5    1.3  1  NMO            Nitronate monooxygenase
    0.00065   19.1   1.2     0.0011   18.4   0.5    1.6  1  ThiG           Thiazole biosynthesis protein ThiG
    0.00088   18.4   1.2     0.0025   16.9   0.3    2.0  2  FMN_dh         FMN-dependent dehydrogenase
      0.003   16.8   0.0     0.0058   15.8   0.0    1.4  1  IGPS           Indole-3-glycerol phosphate synthase
  ------ inclusion threshold ------
      0.029   13.8   0.3      0.093   12.2   0.1    1.8  2  His_biosynth   Histidine biosynthesis protein
      0.035   13.3   0.4      0.063   12.5   0.1    1.5  2  DHO_dh         Dihydroorotate dehydrogenase
      0.054   12.7   0.1       0.11   11.7   0.1    1.5  1  PEP_hydrolase  Phosphoenolpyruvate hydrolase-like


Domain annotation for each model (and alignments):
>> TIM  Triosephosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   0.0   3.1e-15   6.8e-12       2     123 ..       7     123 ..       6     131 .. 0.83
   2 ?   -1.1   0.0      0.43   9.6e+02     159     183 ..     139     163 ..     127     179 .. 0.69

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 3.1e-15
                                    EEEEE-TBTS-HHHHHHHHHH.HHHHCHG.CTSEEEEE--GGGHHHHHHHHTTSSECEEES--BSSSSBS-TT--BHHHH CS
                            TIM   2 liagNwKmnktleeakellkk.lkaklke.ekvevviappflylekvkklleesklklgaqnvsaeksGafTGevsaeml 79 
                                    li  N+K + + +  + l  + +++k+++ + +++++ap+++ l  +++++e   + + +q v+    G++TG v+ e +
  gi|119719789|ref|YP_920284.1|   7 LILINFKAYSEASGKRGLQLAkVAEKVSKeTGITIAVAPQLTDLAFIASQVE---IPVFSQHVDDVPPGSYTGHVTLEAV 83 
                                    6889****997776665544336666655599*************9888886...9************************ PP

                                    HHTT-SEEEES-HHHHHHST--HHHHHHHHHHHHHTT-EEEEEE CS
                            TIM  80 kdlgvkyviiGHsErrqlfkEtdelvakKvkaalksglkpilCv 123
                                    kd+g+  +++ HsErr    + d +    vk+a + gl++++C 
  gi|119719789|ref|YP_920284.1|  84 KDAGAVGTMVNHSERRVRADQVDVI----VKRARSLGLTTVVCT 123
                                    ****************987666554....566888899999997 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.43
                                    EEEE--GGGSSSS----HHHHHHHH CS
                            TIM 159 viAYePvWAiGtgktatpeqaqevh 183
                                    ++A eP   iGtg ++++ + + v 
  gi|119719789|ref|YP_920284.1| 139 MVAIEPPELIGTGIPVSKAKPEVVT 163
                                    6899999999**9776655444333 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   3.5   1.1e-07   0.00025     126     230 ..     106     212 ..      25     217 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.1e-07
                            NMO 126 eevvarlkeagvvliptissvkearkvearGaDalivqGpeaGGh.qGtpevgd.kglfaLvpqvldavd.iPviAaGGi 202
                                       v+r   +g+  ++ + + +   +++a+G+D++ ++ pe  G  ++ +++++ +  ++ v+ v+++   + v+   Gi
  gi|119719789|ref|YP_920284.1| 106 DVIVKRARSLGLTTVVCTNTPEVTAAMAALGPDMVAIEPPELIGTgIP-VSKAKpEVVTSSVELVKKVNPnVKVLCGAGI 184
                                    4567888889999999999999999**************997664144.33333334444444444444347799999** PP

                            NMO 203 idrrgvaaaLalGAsgvqigtrfLltke 230
                                      +++vaaaL+lG  gv +++  + +k+
  gi|119719789|ref|YP_920284.1| 185 TVGEDVAAALRLGTVGVLLASGVVKAKD 212
                                    *******************998887776 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.5   4.8e-07    0.0011     168     212 ..     167     212 ..     146     218 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 4.8e-07
                                    HHHHHH-.SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSS CS
                           ThiG 168 kiiieea.kvPvivDAGigspsdaaqamelGadavllntavaeakd 212
                                    +++ +   +v v+  AGi + +d+a+a+ lG+ +vll++ v +akd
  gi|119719789|ref|YP_920284.1| 167 ELVKKVNpNVKVLCGAGITVGEDVAAALRLGTVGVLLASGVVKAKD 212
                                    44444446899*********************************99 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.22     5e+02     121     143 ..     101     123 ..      73     136 .. 0.70
   2 !   16.9   0.3   1.1e-06    0.0025     262     303 ..     166     207 ..     156     214 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.22
                                    SHHHHHHHHHHHHHCTESEEEEE CS
                         FMN_dh 121 drelteellkraeaagykalvlt 143
                                      + ++ ++kra+++g++++v t
  gi|119719789|ref|YP_920284.1| 101 RADQVDVIVKRARSLGLTTVVCT 123
                                    44567778899999999998887 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 1.1e-06
                                    HHHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHH CS
                         FMN_dh 262 peiveavggrievlvDgGirrGsDvlkAlalGAdavllGRpf 303
                                     e+v++v+ +++vl+  Gi+ G+Dv+ Al lG  +vll+  +
  gi|119719789|ref|YP_920284.1| 166 VELVKKVNPNVKVLCGAGITVGEDVAAALRLGTVGVLLASGV 207
                                    4679999999**************************998665 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   2.6e-06    0.0058     144     253 ..     102     219 ..      86     220 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.6e-06
                                    HHHHHHHHHHHCCTT-EEEEEESSHHHHHHHH.HTT-SEEEEESEETTTTEE-........CHHHHHHCHCC-TTSEEEE CS
                           IGPS 144 deeleelaeaakslglevLvEvhdeeeleral.klgakiiGvNnRnLktlevd........lntteeLaklvpkdvllva 214
                                     +++  +++ a+slgl  +v +++  e+++a+ +lg +++ +   +L    +         +  + eL+k+v+ +v + +
  gi|119719789|ref|YP_920284.1| 102 ADQVDVIVKRARSLGLTTVVCTNTP-EVTAAMaALGPDMVAIEPPELIGTGIPvskakpevVTSSVELVKKVNPNVKVLC 180
                                    5678889999*******99977665.56666669************976555411111111345679999999******* PP

                                    ESSS-SHHHHHHHCCTT-SEEEESHHHHC-TTHHHHHHH CS
                           IGPS 215 eSGiktredveklkeegvnafLvGeslmrqedvekaire 253
                                      Gi+  edv +  + g  ++L  + +++++d ekai +
  gi|119719789|ref|YP_920284.1| 181 GAGITVGEDVAAALRLGTVGVLLASGVVKAKDWEKAILD 219
                                    **********************************99865 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.66   1.5e+03     148     168 ..     104     124 ..      78     128 .. 0.67
   2 ?   12.2   0.1   4.2e-05     0.093      61     117 ..     165     219 ..     155     224 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.66
                                    EHHHHHHHHHHTT-SEEEEEE CS
                   His_biosynth 148 davelakkleelgageilltd 168
                                    ++  ++k++ +lg+ ++++t+
  gi|119719789|ref|YP_920284.1| 104 QVDVIVKRARSLGLTTVVCTN 124
                                    333467899999999999986 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 4.2e-05
                                    HHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHH CS
                   His_biosynth  61 nldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavknpelikelae 117
                                      +lv+++  +  ++v  G GI   edv+++l++g   v +++ +vk +++ k +++
  gi|119719789|ref|YP_920284.1| 165 SVELVKKVNPN--VKVLCGAGITVGEDVAAALRLGTVGVLLASGVVKAKDWEKAILD 219
                                    56777777777..999*********************************99998876 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.1   2.6e+03     153     179 ..      26      53 ..      19      63 .. 0.63
   2 ?   12.5   0.1   2.8e-05     0.063     178     278 ..     105     209 ..      91     223 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.1
                                    HHHHHHHHH.SSEEEEEE-SSSSHHHHH CS
                         DHO_dh 153 llkvvkevs.kvpvlvKlaPdltdeekk 179
                                    l+kv ++vs +  + + +aP+ltd + +
  gi|119719789|ref|YP_920284.1|  26 LAKVAEKVSkETGITIAVAPQLTDLAFI 53 
                                    4555555552345667777777776554 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 2.8e-05
                                    HHHHHHHHHHHTECEEEE...BSEE--C.TTCCGCCCCTT....SSEEEEEGGGHHHHHHHHHHHHHHTTT.S-EEEESS CS
                         DHO_dh 178 kkdiadvllelkldgiivtNttvqrlai.dlkseknvkan....ktGGlsGkalkdialkvirelykrlkkeipiIgvGG 252
                                     + i++ ++ l+l+ ++ tNt     a+  l    +  ++    +t G+   + k+  +    el k+++++++++   G
  gi|119719789|ref|YP_920284.1| 105 VDVIVKRARSLGLTTVVCTNTPEVTAAMaALGPDMVAIEPpeliGT-GIPVSKAKPEVVTSSVELVKKVNPNVKVLCGAG 183
                                    44566666799*********95444433133333333333455245.599999*************************** PP

                                    --SHHHHHHHHHHTECEEEESHHHHH CS
                         DHO_dh 253 iesgeDalekieaGAslvqvytalvf 278
                                    i+ geD+   ++ G   v + +++v+
  gi|119719789|ref|YP_920284.1| 184 ITVGEDVAAALRLGTVGVLLASGVVK 209
                                    *********99999988888888755 PP

>> PEP_hydrolase  Phosphoenolpyruvate hydrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1     5e-05      0.11     141     233 ..     108     194 ..      97     222 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5e-05
                  PEP_hydrolase 141 likkAheldllttayvfneeearamaeaGadvivahlGlttggsigaktalsleeavelvqeiadaakevnpdvivlvhG 220
                                    ++k+A++l+l t+    ++e ++ama+ G d++ ++     g  i  ++a+      e v + ++ +k+vnp+v vl+ +
  gi|119719789|ref|YP_920284.1| 108 IVKRARSLGLTTVVCTNTPEVTAAMAALGPDMVAIEPPELIGTGIPVSKAK-----PEVVTSSVELVKKVNPNVKVLCGA 182
                                    4689****************************9988766665555555543.....5778888999999*****999966 PP

                  PEP_hydrolase 221 Gpiaepedaeyvl 233
                                    G i+  ed++  l
  gi|119719789|ref|YP_920284.1| 183 G-ITVGEDVAAAL 194
                                    6.77888888777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 1534.10
//
Query:       gi|119719790|ref|YP_920285.1|  [L=374]
Description: radical SAM domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.5e-13   49.9   0.0    8.1e-13   49.1   0.0    1.5  1  Radical_SAM  Radical SAM superfamily
    3.9e-06   27.2   0.0    6.9e-06   26.4   0.0    1.3  1  Fer4_12      4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.039   14.1   0.0      0.091   12.9   0.0    1.6  1  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.1   0.0   1.4e-16   8.1e-13       2     155 ..     157     303 ..     156     315 .. 0.92

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 1.4e-16
                                    EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgirit 81 
                                    +++ gC+++C++C+++  + r + g+ ++++e++ ++ +l + +g++++  +gg+p+ + + + + +r++     ++ + 
  gi|119719790|ref|YP_920285.1| 157 IFFTGCSFKCVYCQNWDISTRVDNGEKVTPQELAGIATAL-YLRGARNINYVGGNPDQQLHVILESLRYMDV---NVPLL 232
                                    6899************************************.7999***************999999999996...***** PP

                                    EEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  82 vetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGe 155
                                      +n ++   e l +ll+   d    + + ++d++ ++l + +  fe v ++ +   +ag + +++r+++lp  
  gi|119719790|ref|YP_920285.1| 233 WNSNMYMS-QEALSLLLDVV-DIWLPDFKYGNDDCARRLSGVPRYFEVVSRNHKVVCDAGRD-IIIRHLVLPSH 303
                                    *******8.*********55.*************777777799****************877.********965 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0   1.2e-09   6.9e-06       9     100 ..     156     244 ..     146     268 .. 0.88

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 1.2e-09
                        Fer4_12   9 slfvsgCnlsCkgCfnketw.sfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekd 87 
                                    ++f++gC+++C +C n ++  ++++g+++t + l+ i + l  +  + + ++GG P    +  ++le ++++  + p   
  gi|119719790|ref|YP_920285.1| 156 TIFFTGCSFKCVYCQNWDIStRVDNGEKVTPQELAGIATALYLRGARNINYVGGNPDQ--QLHVILESLRYMDVNVP--L 231
                                    69**************88753799******999********99*************99..99999999999999998..8 PP

                        Fer4_12  88 iwlytgytleels 100
                                     w ++ y+ +e +
  gi|119719790|ref|YP_920285.1| 232 LWNSNMYMSQEAL 244
                                    9999999888776 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.5e-05     0.091       2      72 ..     158     223 ..     157     243 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.5e-05
                        Fer4_14   2 fvrlsgCnlsCkgCdnke.twkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvk 72 
                                    f  + gC+++C+ C n + + + + g++ t ++l  i   + + + + +++  +GG+P   ++ +++l+ ++
  gi|119719790|ref|YP_920285.1| 158 F--FTGCSFKCVYCQNWDiSTRVDNGEKVTPQELAGIA-TALYLRGA-RNINYVGGNPD--QQLHVILESLR 223
                                    4..49*********976613455777777777776666.44444443.5599*****97..66777766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2537.56
//
Query:       gi|119719791|ref|YP_920286.1|  [L=340]
Description: diphthamide biosynthesis protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-55  188.8   0.0    1.8e-55  188.6   0.0    1.0  1  Diphthamide_syn  Putative diphthamide synthesis protein


Domain annotation for each model (and alignments):
>> Diphthamide_syn  Putative diphthamide synthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.6   0.0   9.9e-60   1.8e-55       2     294 ..      33     320 ..      32     327 .. 0.94

  Alignments for each domain:
  == domain 1  score: 188.6 bits;  conditional E-value: 9.9e-60
                Diphthamide_syn   2 PegllpdsaeiadileefgaevvilgDttYGaCcvdevaaehlgadllvHyGhscls..pvdrlpvlYvfveieldvehl 79 
                                    P+gl++ + e+a +l++ g+e +++g + +G C+v  ++a++++ad++ H Gh+ ++   vd  pv++v+v  e  + ++
  gi|119719791|ref|YP_920286.1|  33 PDGLKHVARELAARLAADGVEAYVSGGHAWGGCDVALQEARAINADAILHLGHHGFVgaRVDAPPVIFVPVYYEGLLFET 112
                                    ***************999***************************************66688**********99888888 PP

                Diphthamide_syn  80 vetlkknf..kekkkivlvstiqyahaleevkeeleeegyevvkvpqsekplspgevlgctspklkeeeeevdailyigd 157
                                     e++ +n+  k  +++ + +t q+a+ ++++ ++ e++g +v   + ++   + g v+gc++++l   +e+++a++++++
  gi|119719791|ref|YP_920286.1| 113 FEKVVRNValKGYRRVTIGTTYQHAKYFSRLVRLAEDAGLTVA--G-RHLDGYLGLVVGCNYAAL---AEDAEAVIVVAG 186
                                    888888887777999*********************8888766..3.447789************...6789******** PP

                Diphthamide_syn 158 grfhllslmlsnpklpvyrydpyskklteesydakkllrrRyaaiekakdakkvGiivgtlgvqgrlelverlkkllkea 237
                                    g fh+l+++l + + p+ r+dpy++  +    d+k +++rR   +++a +a+++ + v+++++q+r+e+++r+++ll+e+
  gi|119719791|ref|YP_920286.1| 187 GVFHALGAALWTGA-PTWRVDPYTG--DYGPVDVKPIVARRLRDLSRAIEARSFLVAVSSKTGQRRPEIARRIRDLLAER 263
                                    ************76.*********9..566889*********************************************** PP

                Diphthamide_syn 238 gkksylvlvgelnpakLanfaeidafVlvaCprlsiddgkeFekPvltpyElevalg 294
                                    g ++ l + +e++ + L n+ ++da+V++aCprl++dd + F+ Pv++p El+++l+
  gi|119719791|ref|YP_920286.1| 264 GLRAELAVFDEVTREGLLNLGSYDAYVNTACPRLAVDDPDLFPGPVVNPGELKYVLK 320
                                    *******************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2487.00
//
Query:       gi|119719792|ref|YP_920287.1|  [L=291]
Description: xylose isomerase domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      1e-19   70.8   0.4    1.5e-19   70.3   0.4    1.2  1  AP_endonuc_2  Xylose isomerase-like TIM barrel
  ------ inclusion threshold ------
      0.057   12.9   0.0      0.091   12.2   0.0    1.3  1  ComA          (2R)-phospho-3-sulfolactate synthase (ComA)


Domain annotation for each model (and alignments):
>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.3   0.4   1.7e-23   1.5e-19       4     207 ..      30     237 ..      28     240 .. 0.92

  Alignments for each domain:
  == domain 1  score: 70.3 bits;  conditional E-value: 1.7e-23
                                    HHHCT-SEEEEECCTCSHHHHCHHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCSHHHHHHHHHHHHHHHHHHT CS
                   AP_endonuc_2   4 aaeaGfdgvElfgrdlvpvselsdeelrelrkaldelglriaslslftrfgypdederearreesvdalkraielaaaLG 83 
                                    ++++G d++E+ +  +   +   d+ ++e++k+  el + ++++ +++ + ++ +   e++ ++s +++ r +e   + G
  gi|119719792|ref|YP_920287.1|  30 VKRLGLDAMEIEFVRKIFLD---DKSAQEVKKLRHELEIVLTVHAPYYVNLNSAD---ESKVKASAERVLRSAEVGFKAG 103
                                    89*****************9...78***************************887...3335899999999999999*** PP

                                    BSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHHHHT..SEEEEE--TTTTSSSTCHHHHHHHHHHTTTTEEEEEE CS
                   AP_endonuc_2  84 apllvlhpGtagagpkgseeeawerlaeslneladyaekeg..vklalEtlagsgvelgdeelarlldavdspnvgvclD 161
                                    a  + +h+G   +++++++e+a++r+ + + ++a+ +++eg  ++l  E l ++  +   ee+ rl ++v+  nv  ++D
  gi|119719792|ref|YP_920287.1| 104 AWSVCFHAG---YYGDSEPESAYARIKSEVAAIARQLRDEGveIWLRPEVLGKPSEFGSLEEVIRLSEEVE--NVLPTID 178
                                    *********...99***************************7788999999999865555***********..5****** PP

                                    HHHHHHH.......TTTHHHHHHHHHGG.......EEEEEE.EESSTTTTSSTTEESTTS CS
                   AP_endonuc_2 162 tgHllia.......eedvddalraladr.......ikhvHikDakgdlgagrdrhvpige 207
                                    ++Hl+++         d++++l+al++r         h+H++ ++  + +g+ rh+++ e
  gi|119719792|ref|YP_920287.1| 179 FAHLHARgkgalrqYQDFAAVLDALESRlgrialdNMHIHVSGIEY-GEKGEIRHLNLTE 237
                                    ****************************999998889999999988.8888888888766 PP

>> ComA  (2R)-phospho-3-sulfolactate synthase (ComA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0     1e-05     0.091      69     193 ..       8     136 ..       6     145 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1e-05
                                    EE-HHHHHHHHHTT-HHHHHHHHHHCT-SEEEE--SSS---HHHHHHHHHHHCCTTSEEEEEES-SSH.......HHHTT CS
                           ComA  69 stGgtlfEaalaqgkvdeyleeckelgfdviEvsdgtlelpeeeklrliekakkeglkvlpevgkkdg.......elese 141
                                    ++G   + + +++g v+e + e+k+lg+d++E++     + +++ ++ ++k+++e l+++  v+           e + +
  gi|119719792|ref|YP_920287.1|   8 YFGPAGIPTTVSKGGVKEGMLEVKRLGLDAMEIEFVRKIFLDDKSAQEVKKLRHE-LEIVLTVHAPYYvnlnsadESKVK 86 
                                    566666777899999******************9988888888888999999888.999999988333444444456666 PP

                                    --CCHHHHHHHHHHHHTECEEEE--TTT--SSTTB-TTS-B-HHHHHHHHTT CS
                           ComA 142 sdveklieeakrdleaGaekviiEaresGitegvydekgevrtdvvekiier 193
                                     ++e++++ a+  ++aGa+ v   a   G +e   ++  +  +++v++i+++
  gi|119719792|ref|YP_920287.1|  87 ASAERVLRSAEVGFKAGAWSVCFHAGYYGDSEP--ESAYARIKSEVAAIARQ 136
                                    999******************988876565332..34445555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 2322.43
//
Query:       gi|119719793|ref|YP_920288.1|  [L=378]
Description: KH domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.2e-33  114.6   0.0    5.8e-33  114.1   0.0    1.2  1  PhoH           PhoH-like protein
    9.7e-08   31.7   0.5    0.00047   19.9   1.0    2.5  2  KH_2           KH domain
    1.2e-06   28.3   0.2    0.00076   19.3   0.5    2.8  2  KH_1           KH domain
    1.8e-05   24.7   0.8      0.052   13.7   0.3    3.4  3  KH_5           NusA-like KH domain
     0.0022   18.3   0.0     0.0061   16.8   0.0    1.8  1  AAA_22         AAA domain
     0.0063   16.4   0.1        4.3    7.3   0.0    2.6  2  KH_4           KH domain
     0.0088   16.0   0.0      0.029   14.3   0.0    1.8  1  KH_7           KH domain
  ------ inclusion threshold ------
      0.013   15.3   0.0      0.028   14.1   0.0    1.5  1  IstB_IS21      IstB-like ATP binding protein
      0.056   13.8   0.0       0.15   12.4   0.0    1.8  2  Lipase_GDSL_2  GDSL-like Lipase/Acylhydrolase family
      0.073   13.5   0.2        0.6   10.5   0.0    2.4  2  AAA_16         AAA ATPase domain
      0.073   13.5   0.2        6.6    7.2   0.0    2.6  2  AAA            ATPase family associated with various cellular


Domain annotation for each model (and alignments):
>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.1   0.0   3.6e-36   5.8e-33       3     198 ..       6     204 ..       4     211 .. 0.92

  Alignments for each domain:
  == domain 1  score: 114.1 bits;  conditional E-value: 3.6e-36
                                    ---SHHHHHHHHHHH..H-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--TT----SS----.-----TT CS
                           PhoH   3 kpktkeQkeylealk..kndivfaiGpaGtGKtylavalavealkkkkvkriiltrpaveageelGflpgdl.eekvdpy 79 
                                    +p t++Qk +l al+  + d+v ++Gp+GtGK+++ + ++++a++++k+kr+++++p v+  ++      ++ +  +++ 
  gi|119719793|ref|YP_920288.1|   6 TPATEKQKMLLGALEspDVDLVGVFGPSGTGKSFVVLLYGLSAVRSGKYKRMVVVKPLVSLSRSKVLDSSEMgNLFFEIA 85 
                                    6899***********88889***************************************9854444444444055789** PP

                                    THHHHHHHTTTS-TTCHHHHHHTTSEEEEEGGGGTT--B-SEEEEE-SGGG--HHHHHHHHTTB-TT-EEEEEE------ CS
                           PhoH  80 lrplydaLkdllgaekvekllekgkievaplaymRGrTlndafvilDEAQnttkeqmkmfltRlGenskvvvtGdvtqid 159
                                     +++ d   d+++ ++++++++++k+ +++  ++ GrT+++++v+lD+ Q +++  + ++++R G+nsk+v++Gd+  + 
  gi|119719793|ref|YP_920288.1|  86 SSYVEDVAGDYVDLKELREMFDQRKVVFVDPDFLAGRTFDNSLVFLDDVQYASPDLVTECIIRTGKNSKLVIAGDPILQA 165
                                    ******************************************************************************** PP

                                    --------THHHHHHTTT-TTEEEEE--GGG----HHHH CS
                           PhoH 160 lpkgkksGlaealevlknvegieivelkkkdvvRhplvk 198
                                    l+ ++++  a a+e l ++e   ++++  +d+vR +  +
  gi|119719793|ref|YP_920288.1| 166 LEGKTRNTAAIARELLLGEERSLVINMGINDIVRPGSKR 204
                                    **999*****************************98765 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   1.0   2.9e-07   0.00047      25      64 ..     258     297 ..     254     315 .. 0.86
   2 !    8.7   0.0   0.00091       1.5      14      59 ..     316     359 ..     302     365 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2.9e-07
                                    CEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTT CS
                           KH_2  25 nrviiviresqpgivIGkgGsnikkigkelrkdieklegk 64 
                                     +v  v +e+   ++IGk+G++i+k ++e++ +i+++e +
  gi|119719793|ref|YP_920288.1| 258 PDVLAVAKENTLSRLIGKKGERINKAQEEAGVQIRAVELT 297
                                    5677889999999*********************998865 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00091
                                    TEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHH CS
                           KH_2  14 gvskveIertanrviiviresqpgivIGkgGsnikkigkelrkdie 59 
                                     + +veIe     + + +   + g  +Gk+Gs i+ + +++r+ ++
  gi|119719793|ref|YP_920288.1| 316 HITSVEIEG--SELAVYVNPDEYGAFVGKQGSYIRFLDAAVRRLLG 359
                                    577899988..8899**************************99985 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.5   4.6e-07   0.00076      12      37 ..     270     295 ..     263     329 .. 0.83
   2 !    5.8   0.0    0.0074        12       4      25 ..     329     350 ..     326     352 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 4.6e-07
                                    HHHHTGGGHHHHHHHHHHT-EEEEES CS
                           KH_1  12 griIGkgGsnIkeIreetgakIkvpk 37 
                                    +r+IGk+G++I++ +ee g++I+ ++
  gi|119719793|ref|YP_920288.1| 270 SRLIGKKGERINKAQEEAGVQIRAVE 295
                                    79**************99****9775 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0074
                                    EEEGGGHHHHHHTGGGHHHHHH CS
                           KH_1   4 ilvPsslvgriIGkgGsnIkeI 25 
                                    + v+ + +g+ +Gk+Gs I+ +
  gi|119719793|ref|YP_920288.1| 329 VYVNPDEYGAFVGKQGSYIRFL 350
                                    6788999************976 PP

>> KH_5  NusA-like KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.3   2.2e+03      21      34 ..     144     157 ..     138     191 .. 0.61
   2 !   13.7   0.3   3.2e-05     0.052       7      61 ..     261     309 ..     259     319 .. 0.88
   3 !    7.2   0.0    0.0033       5.4       8      31 ..     328     348 ..     323     358 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.3
                           KH_5  21 aivgkkGsrikavs 34 
                                    +++ ++G+++k v+
  gi|119719793|ref|YP_920288.1| 144 ECIIRTGKNSKLVI 157
                                    55555555555444 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 3.2e-05
                           KH_5   7 vaVkshnpnvdpvGaivgkkGsrikavsseLkgekidvvewseDlaefianalsP 61 
                                    +aV ++n     +  ++gkkG+ri++  +e  g +i+ ve ++Dl e ++ a++P
  gi|119719793|ref|YP_920288.1| 261 LAVAKEN----TLSRLIGKKGERINKAQEEA-GVQIRAVELTQDLGEIVK-AIHP 309
                                    6788887....8999***************9.*************99775.5666 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0033
                           KH_5   8 aVkshnpnvdpvGaivgkkGsrik 31 
                                    aV+ +    d+ Ga+vgk+Gs+i+
  gi|119719793|ref|YP_920288.1| 328 AVYVNP---DEYGAFVGKQGSYIR 348
                                    666666...99***********98 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   3.7e-06    0.0061      10     134 ..      29     164 ..      25     166 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.7e-06
                         AAA_22  10 vtGesGtGKTtllrrlleqldeeakaee.....erpevv...fvtlpsstsskdllrellralglelka...erlsseel 78 
                                    v+G+sGtGK++++  +  ++++  k ++     +    v   + ++  s++  +l+ e+++ + ++  +     ++++e+
  gi|119719793|ref|YP_920288.1|  29 VFGPSGTGKSFVVLLYGLSAVRSGKYKRmvvvkPL---VslsRSKVLDSSEMGNLFFEIASSYVEDVAGdyvDLKELREM 105
                                    89*****************9766555555543222...123355555555778888888888888888866666666666 PP

                         AAA_22  79 lealeqalrarav.......ielliiDEaqhlrseealeeLrsllnlsrkgvqliLvGtpelr 134
                                    +++    + + +         +l+ +D++q+  s+++++e+ ++     k+ +l+++G p l+
  gi|119719793|ref|YP_920288.1| 106 FDQRKVVFVDPDFlagrtfdNSLVFLDDVQYA-SPDLVTECIIR-T--GKNSKLVIAGDPILQ 164
                                    64444444444446888999************.9******9444.4..589999999988775 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.0    0.0052       8.4      33      51 ..     261     280 ..     249     282 .. 0.82
   2 !    7.3   0.0    0.0027       4.3      25      51 ..     321     347 ..     302     362 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0052
                           KH_4  33 lnveged.lGrvIGkrGrtl 51 
                                    l+v++e+ l r+IGk+G+ +
  gi|119719793|ref|YP_920288.1| 261 LAVAKENtLSRLIGKKGERI 280
                                    566666669********987 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0027
                           KH_4  25 eeeeveielnvegedlGrvIGkrGrtl 51 
                                    e e+ e+ ++v++++ G  +Gk+G  +
  gi|119719793|ref|YP_920288.1| 321 EIEGSELAVYVNPDEYGAFVGKQGSYI 347
                                    334789******************876 PP

>> KH_7  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   1.8e-05     0.029      20      57 ..     316     356 ..     296     359 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.8e-05
                           KH_7  20 kitdveFEGPelViYtknpklfa...engdlirklAkelrk 57 
                                    +it+ve EG+el++Y++  ++ a   ++g +ir l  ++r+
  gi|119719793|ref|YP_920288.1| 316 HITSVEIEGSELAVYVNPDEYGAfvgKQGSYIRFLDAAVRR 356
                                    79**************8666433236888888888777776 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.7e-05     0.028      51      88 ..      28      65 ..      20      79 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.7e-05
                      IstB_IS21 51 vllGpsGvGKshlaialgveavraglsvlfvrvedLve 88
                                    ++GpsG+GKs++    g +avr+g+  + v v+ Lv+
  gi|119719793|ref|YP_920288.1| 28 GVFGPSGTGKSFVVLLYGLSAVRSGKYKRMVVVKPLVS 65
                                   589**********************9988888888876 PP

>> Lipase_GDSL_2  GDSL-like Lipase/Acylhydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       2.5   4.1e+03     136     165 ..     102     130 ..      87     141 .. 0.72
   2 ?   12.4   0.0   9.5e-05      0.15      57     145 ..     172     289 ..     121     309 .. 0.68

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.5
                                    HHHHHHHCT-EEE-HHHHHHHCCCCCGGBB CS
                  Lipase_GDSL_2 136 lrevaaeegvpfvDlhdaladsgerladll 165
                                    lre  ++ +v+fvD  d+la+++ + +  +
  gi|119719793|ref|YP_920288.1| 102 LREMFDQRKVVFVDP-DFLAGRTFDNSLVF 130
                                    677778889999998.56666555555554 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 9.5e-05
                                    CTGGG-T.......SEEEEE--CCCCCTT--HHHHHHH................HHHHHHHHCCC...GEEE........ CS
                  Lipase_GDSL_2  57 dllrlkp.......dlvtiliGtNDlgrgvpaaaaaand..............nleelidalraaapgaril........ 107
                                    + +++++       + ++i++G+ND+ r+++   ++ +               +++++++   ++ap+a ++        
  gi|119719793|ref|YP_920288.1| 172 NTAAIARelllgeeRSLVINMGINDIVRPGSKRGFKLALesrlrrralseeeeKVKAILQ---SHAPDADVVtvvwlkdl 248
                                    33333333333333669********99999999999998888888877765555555555...67*****9988888888 PP

                                    ...CEEEEE-TTT-TTSTCCHHHHHHHHHHHHHHHHHHCT- CS
                  Lipase_GDSL_2 108 ...vlgplpptpeaaadarelnaviaaynealrevaaeegv 145
                                         +  +p   a a+++ l + i +  e ++++ +e gv
  gi|119719793|ref|YP_920288.1| 249 kekFGAHTAPDVLAVAKENTLSRLIGKKGERINKAQEEAGV 289
                                    88733334444444444444455555555555555555444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00037       0.6      12      42 ..      15      42 ..       9      89 .. 0.82
   2 ?   -0.2   0.0      0.69   1.1e+03     138     149 ..     128     139 ..     117     158 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00037
                         AAA_16 12 LlsalervrsgrpelvllsGesGvGKsslvr 42
                                   L   l+++ s++  lv + G+sG+GKs +v 
  gi|119719793|ref|YP_920288.1| 15 L---LGALESPDVDLVGVFGPSGTGKSFVVL 42
                                   4...4444577778999***********995 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.69
                         AAA_16 138 vlvlDdlqwade 149
                                    +++lDd+q a +
  gi|119719793|ref|YP_920288.1| 128 LVFLDDVQYASP 139
                                    79******8876 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0     0.004       6.6       3      40 ..      29      90 ..      27     135 .. 0.61
   2 ?    3.8   0.1     0.043        70      10      74 ..     168     255 ..     167     304 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.004
                                   EESSTTSSHHHHHHHHHHHH......T.....HEEEEEETTTCSSS.............STT CS
                            AAA  3 lyGppGtGKTllakavakel......g.....vefleisgsellsk.............yvg 40
                                   ++Gp GtGK+ ++     ++      +      +++++s s++l++             yv+
  gi|119719793|ref|YP_920288.1| 29 VFGPSGTGKSFVVLLYGLSAvrsgkyKrmvvvKPLVSLSRSKVLDSsemgnlffeiassYVE 90
                                   79*********998877775444332133333457777777777444666665555555333 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.043
                                    SHHHHHHHHHHHH.....THEEEEEETTTCSSS.................STTHHHHHHHHHHHHHHHTS.TSEEEEEET CS
                            AAA  10 GKTllakavakel.....gvefleisgsellsk.................yvgesekkirelfkeakeka.kpsilfiDE 66 
                                    GKT    a+a+el      + ++++   +++                    ++e e+k+++++++    a   +++++ +
  gi|119719793|ref|YP_920288.1| 168 GKTRNTAAIARELllgeeRSLVINMGINDIVRPgskrgfklalesrlrrrALSEEEEKVKAILQSHAPDAdVVTVVWLKD 247
                                    88888999999976655424456666666664456666666666666666999**********99766664449999988 PP

                                    GGGHHHHH CS
                            AAA  67 idalaksr 74 
                                    + + +++ 
  gi|119719793|ref|YP_920288.1| 248 LKEKFGAH 255
                                    87776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2528.61
//
Query:       gi|119719794|ref|YP_920289.1|  [L=631]
Description: DNA topoisomerase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   4.6e-113  378.3   0.0   5.6e-113  378.1   0.0    1.1  1  Topoisom_bac  DNA topoisomerase
      1e-15   57.8   0.0    2.3e-15   56.7   0.0    1.7  1  Toprim        Toprim domain
     0.0031   17.9   0.0     0.0093   16.4   0.0    1.8  1  Toprim_4      Toprim domain
     0.0056   17.1   0.0      0.012   16.0   0.0    1.5  1  Toprim_2      Toprim-like
  ------ inclusion threshold ------
       0.13   12.2   0.1        0.3   11.0   0.1    1.5  1  ELYS          Nuclear pore complex assembly


Domain annotation for each model (and alignments):
>> Topoisom_bac  DNA topoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  378.1   0.0  1.6e-116  5.6e-113       2     412 ..     159     570 ..     158     571 .. 0.93

  Alignments for each domain:
  == domain 1  score: 378.1 bits;  conditional E-value: 1.6e-116
                   Topoisom_bac   2 inenlvdaaeaRrelDwliGinlsrlltk...klkg.....kkvlsaGRVqtptLaliveRereienFvpeeyweveatl 73 
                                    +nenl+++a aR ++D+ iG++++r+lt+   ++ g      ++ls+G++qtp+L l+v+Re e+e+F++++y+ +++ +
  gi|119719794|ref|YP_920289.1| 159 PNENLANKAFARMVVDLTIGASFTRILTLsarRN-GgvmprGSFLSYGPCQTPVLYLVVKRELEREQFKKKKYYVLRVRF 237
                                    79***************************76422.14666799************************************9 PP

                   Topoisom_bac  74 kkekkekekkkkkkkerikdkeeaeaileklkkk.eakvesvekkekkkppplpfdtttLqkeasrklglsakktlsiaq 152
                                     ++++ +      ++ +++d+e+a+++l ++k +   +v+s e +  + +pp p++t+ L+++as  l+l++k+tlsia+
  gi|119719794|ref|YP_920289.1| 238 RSQEGVF-----TASATFEDQEKAKSALDSVKRTgVGVVVSAEFNAVEVEPPVPLNTVYLESRASLFLNLRPKETLSIAE 312
                                    7777776.....58899**************986699******************************************* PP

                   Topoisom_bac 153 kLYekaglitYpRTdstrlseeaelkailealakkygkeylefaekllkktkkksvvknkkveaHeAIrPteelpklkel 232
                                    kLY   g+i+YpRT++t ++++ +l+ i +++++   +++  +++k+l+k+  + ++++++++aH++I+Pt++++++ e 
  gi|119719794|ref|YP_920289.1| 313 KLYSF-GYISYPRTETTIYPPTLNLRGIASMFTRW--EDAGWYVAKVLAKGFTP-TRGREDDKAHPPIYPTRSASRE-EI 387
                                    ****7.****************77*********97..679********988765.6777777*********998843.22 PP

                   Topoisom_bac 233 s....ddekklYelIvrrflaslmkdakyeettvkleveeeefkasgktilekGfkkvykeekkeeeeeelpelkegeev 308
                                    +    ++ +k+Ye++vr+fla+++++a++e+++v ++v+e +++++g++++ +Gf++vyk++  ++e+  lp + egeev
  gi|119719794|ref|YP_920289.1| 388 TrrfgEKAWKVYEYVVRHFLATISENAVVERQRVVVKVGELSLQSEGRKLVYAGFYNVYKYSVPKDEP--LPYVVEGEEV 465
                                    2467799**********************************************************986..********** PP

                   Topoisom_bac 309 kvkeveleekkTkppkryteasLikamekagiGtpaTraeiieklvergYverkkkslvptelGkalvell.ekfkdlvs 387
                                    +v+++++e+++T+pp++++e++L+++m+k+giGt+aT++e+i++ +er+Y ++k+k+++pt+lG++l+ +l e++++lv 
  gi|119719794|ref|YP_920289.1| 466 EVEDAKIEARTTQPPPYLSESELLALMKKYGIGTDATMQEHIHTNIERRYFVVKNKRCIPTPLGRTLALALyETVPELVL 545
                                    *****************************************************99****************6666***** PP

                   Topoisom_bac 388 pelTaeleekLdeIaegkadakevl 412
                                    pe++ ++e +L++Ia+g+++++ev+
  gi|119719794|ref|YP_920289.1| 546 PEVRGKMEASLSKIATGERTPEEVV 570
                                    ***********************98 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.7   0.0   6.5e-19   2.3e-15       2     102 ..       6     143 ..       5     144 .. 0.89

  Alignments for each domain:
  == domain 1  score: 56.7 bits;  conditional E-value: 6.5e-19
                                    EEEESSHHHHHHHHHTHT....................STEEEEEEESSSSEEEHSTTEEEEE................. CS
                         Toprim   2 lvivEgpsdaktiakalg....................sgfqavtaslGhildletefkpvye................. 44 
                                    ++++E++s a++ia++lg                    +g+   + ++Ghild ++  +++y+                 
  gi|119719794|ref|YP_920289.1|   6 VIVAEKNSVARAIASFLGgssvrrfrvervpayeflweGGKHLSIGVSGHILDFDF--PEEYNkwesvdprvlfftnpvl 83 
                                    79************************************9999999***********..4444444455556666666668 PP

                                    .ECTTTHHHHHHHHHHHHHHSEEEEECSSSHHHHHHHHHHHHHHTHHHTT.TEEEEEESS CS
                         Toprim  45 .eiedkkkvlkalkelakradeiilatDpDreGeaiawellevlkellen.kigrvefse 102
                                      +e++  ++ alk la++ + +ila+D+D+eGeaia+e++  +k  +++ +++r++fs 
  gi|119719794|ref|YP_920289.1|  84 vTREGAYIYVRALKTLARQTSTVILALDADVEGEAIAFEVMRIMKSVNPElEFRRAWFSA 143
                                    7999*************************************999988888999****986 PP

>> Toprim_4  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   2.6e-06    0.0093      50      77 ..      99     127 ..      81     139 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.6e-06
                       Toprim_4  50 aekkvkevilaldgDaeGeataerlae.l 77 
                                       +++ vilald+D+eGea a+++++ +
  gi|119719794|ref|YP_920289.1|  99 LARQTSTVILALDADVEGEAIAFEVMRiM 127
                                    4456799******************9952 PP

>> Toprim_2  Toprim-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   3.4e-06     0.012      31      71 ..      91     130 ..      77     150 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.4e-06
                       Toprim_2  31 lteaalkllerypekkvvlalDnDkaGrkaakrlaellrea 71 
                                    +  +alk l+r+ + +v+lalD+D  G++ a ++++++++ 
  gi|119719794|ref|YP_920289.1|  91 IYVRALKTLARQ-TSTVILALDADVEGEAIAFEVMRIMKSV 130
                                    556789999999.788*******************999765 PP

>> ELYS  Nuclear pore complex assembly
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   8.4e-05       0.3     119     198 ..      94     182 ..      75     191 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 8.4e-05
                           ELYS 119 kilqvLler............gdaslalaylravkpplssseavealfvllargsvteAfsfqRslsdkekreelleelv 186
                                    + l++L+++            + ++ a +++r++k+++ + e  +a f ++ ++++ eAf   R+  ++ +++ + + +v
  gi|119719794|ref|YP_920289.1|  94 RALKTLARQtstvilaldadvEGEAIAFEVMRIMKSVNPELEFRRAWFSAVTKSDILEAFRKLREPNENLANKAFARMVV 173
                                    5677777777777777888899999***********************************99998888866666666666 PP

                           ELYS 187 elcleeaarklk 198
                                    +l++    ++++
  gi|119719794|ref|YP_920289.1| 174 DLTIG---ASFT 182
                                    66666...4455 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (631 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.48
# Mc/sec: 3936.95
//
Query:       gi|119719795|ref|YP_920290.1|  [L=197]
Description: hypothetical protein Tpen_0886 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.8e-13   49.4   0.0    8.7e-13   48.8   0.0    1.2  1  ASCH          ASCH domain
  ------ inclusion threshold ------
      0.016   14.9   0.2       0.03   14.0   0.2    1.5  1  Sigma70_r4_2  Sigma-70, region 4
      0.026   14.0   0.2       0.12   11.8   0.0    2.1  2  HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family I


Domain annotation for each model (and alignments):
>> ASCH  ASCH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.8   0.0   1.4e-16   8.7e-13       1     106 [.      16     113 ..      16     114 .. 0.92

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 1.4e-16
                                    EEE-TTHHHHHHTTS--EEEESSTTTGGGT-CEEEEEECCCCTSEEEEEEEEEEEEEEHHHHHHHHHCHCC--.-HCHHH CS
                           ASCH   1 lsfhqelaslivsGkKtaeirvwdeelpkvrgdllilaalkptgralgivevtkvevkpfeevteehalkege.sleewr 79 
                                    l f++++ + ++sG+K+++ir +    p    +++++  l ++g+++g ++v++v++++++e++ ++a  +g+ + e ++
  gi|119719795|ref|YP_920290.1|  16 LRFKAKYIDMLLSGEKVTTIRRGIVT-P---TRDEVF--LESDGKIYGTARVKSVRYTKVSELNSDDAVRDGFaDKEDLK 89 
                                    5799*****************88888.3...69****..999************************************** PP

                                    HHHHCCHHHHHCCEEEEEEEEEEEEEE CS
                           ASCH  80 evheefyeeeseeyedelvvveefelv 106
                                    ++++e+y+++++   de v+++ +e v
  gi|119719795|ref|YP_920290.1|  90 KALKEIYPDLKD---DEWVTIIFLEDV 113
                                    **********97...777887777665 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.2   4.9e-06      0.03       4      54 .]     140     190 ..     137     190 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.9e-06
                                    HHHHHTTS-HHHHHHHHHHHTS---HHHHHHHHT--HHHHHHHHHHHHHHH CS
                   Sigma70_r4_2   4 lrealaeLperqreifllryleglsykEIAellgisegtVksrlsRArkkL 54 
                                    l  a   L e+  + +l r     + k++A++lg+ e+ Vk  l++A + L
  gi|119719795|ref|YP_920290.1| 140 LALAHGVLNEKLARQVLARVALSGDVKDAARKLGVDENKVKIILAKAVEEL 190
                                    55667778888888888899999999********************98765 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.18   1.1e+03      12      27 ..      14      29 ..      10      37 .. 0.76
   2 ?   11.8   0.0     2e-05      0.12      16      47 ..     151     182 ..     149     187 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.18
                   HTH_Tnp_ISL3 12 iTlrleayilellles 27
                                    Tlr++a+ + +ll++
  gi|119719795|ref|YP_920290.1| 14 RTLRFKAKYIDMLLSG 29
                                   5999999877777765 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 2e-05
                   HTH_Tnp_ISL3  16 leayilelllesrsvkavArqlgvSwtTVwri 47 
                                    l++++l+++  s  vk++Ar lgv+++ V+ i
  gi|119719795|ref|YP_920290.1| 151 LARQVLARVALSGDVKDAARKLGVDENKVKII 182
                                    5678888888888*************999755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       786  (0.0438396); expected 358.6 (0.02)
Passed bias filter:                      617  (0.0344135); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1260.92
//
Query:       gi|119719796|ref|YP_920291.1|  [L=202]
Description: hypothetical protein Tpen_0887 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1364.33
//
Query:       gi|119719797|ref|YP_920292.1|  [L=322]
Description: phosphoesterase, DHHA1 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-05   23.9   0.3    8.6e-05   23.0   0.3    1.5  1  DHHA1     DHHA1 domain
  ------ inclusion threshold ------
      0.032   13.9   0.0      0.052   13.2   0.0    1.3  1  MecA      Negative regulator of genetic competence (MecA)
      0.094   13.0   0.8       0.26   11.6   0.8    1.7  1  DUF3253   Protein of unknown function (DUF3253)
       0.16   12.0   0.1       0.28   11.2   0.1    1.3  1  AAA_5     AAA domain (dynein-related subfamily)


Domain annotation for each model (and alignments):
>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.3   1.9e-08   8.6e-05      24     136 ..     203     317 ..     181     321 .. 0.68

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 1.9e-08
                                    HHHHHHHHHTCEEEC...TCEEEEEECHCCHHHHHHHHHHHHHHTHG..BTTCEEEEEEEECTEEEEEEEESSH.SS-HH CS
                          DHHA1  24 klkaeellekaeevk...gvkvlvaevgeewdagalgiaadklkskl..kkpvivfvakeegdkvkvsarskkd.gvdag 97 
                                    ++ +++ll +a+        k     v+ +++ + + + a++l s +  ++  i+++++  g+ + + +r+ ++ + + +
  gi|119719797|ref|YP_920292.1| 203 EKVFQDLLREARLRVvyrSEK----VVAVDMRDKRVYGFAGMLASIIasEEGRIALILSRVGEAALLTLRAPPGaKGNPS 278
                                    333444444443332432333....333356778888888888887774669999999999999999*****99999999 PP

                                    HHHHHHHHHTTCCEEEETCEEEEEEEHCHHHHHHHHHHH CS
                          DHHA1  98 elakeaaaklgggGGGHdlAaGagipaekleealealee 136
                                    + a ++a+  gg+GGGH+ Aa +++p   +e++l+++ +
  gi|119719797|ref|YP_920292.1| 279 KTAWDVASRYGGSGGGHAGAASFKVPGTYAEKVLAEIVR 317
                                    999999999****************95556666665544 PP

>> MecA  Negative regulator of genetic competence (MecA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.2e-05     0.052       5      62 ..     170     226 ..     169     233 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.2e-05
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXX CS
                           MecA   5 rinentirctltkeDLeerglklselaygsekakelFremmeeaseelgFeaediplm 62 
                                    r+ +++ir  + ++ + er +  +e+a+  ++a++ F+++++ea   + ++ e+ ++ 
  gi|119719797|ref|YP_920292.1| 170 RVRDEQIRRRILRAWITERVVVPDEVAKAASEAEKVFQDLLREARLRVVYRSEK-VVA 226
                                    789********************************************9999998.554 PP

>> DUF3253  Protein of unknown function (DUF3253)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.8   5.7e-05      0.26      10      50 ..     179     218 ..     172     232 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.7e-05
                                    HHHHHS-TT--B-HHHHHHHH...-TTS-GGGHHHHHHHHH CS
                        DUF3253  10 allaerepgkticPsevAralsaeegeeWrelmekvRevav 50 
                                    ++l++  +++ + P evA+a+s++e + +++l+ ++R  +v
  gi|119719797|ref|YP_920292.1| 179 RILRAWITERVVVPDEVAKAASEAE-KVFQDLLREARLRVV 218
                                    56777778889**********8877.68*******996554 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   6.2e-05      0.28      58     106 ..     179     227 ..     159     254 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6.2e-05
                                    -------G-SEEEEESGGG--HHHHHHHHHHHHSSEEE..-SSSEEE-- CS
                          AAA_5  58 plvraaregeilvlDEveraesevlnsLlslleerrllleeggelvkak 106
                                     + ra  + +++v DEv +a se+ ++++ ll e rl++  + e v a 
  gi|119719797|ref|YP_920292.1| 179 RILRAWITERVVVPDEVAKAASEAEKVFQDLLREARLRVVYRSEKVVAV 227
                                    445577799*****************************99998887654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2277.16
//
Query:       gi|119719798|ref|YP_920293.1|  [L=176]
Description: amino acid-binding ACT domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-07   31.5   0.1    8.6e-07   28.6   0.0    2.3  2  ACT       ACT domain
     0.0001   22.0   0.1    0.00025   20.8   0.0    1.7  2  ACT_7     ACT domain
    0.00021   21.8   0.1      0.012   16.2   0.0    2.8  2  ACT_4     ACT domain
  ------ inclusion threshold ------
      0.066   13.2   0.0       0.15   12.0   0.0    1.6  1  ACT_6     ACT domain


Domain annotation for each model (and alignments):
>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.16   7.1e+02      23      29 ..      33      39 ..      27      75 .. 0.58
   2 !   28.6   0.0   1.9e-10   8.6e-07       6      64 ..     110     166 ..     106     169 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.16
                                   HTTSEEE CS
                            ACT 23 drgiNid 29
                                   ++gi+++
  gi|119719798|ref|YP_920293.1| 33 KYGISVR 39
                                   5555554 PP

  == domain 2  score: 28.6 bits;  conditional E-value: 1.9e-10
                                    EEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHT CS
                            ACT   6 gvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkk 64 
                                      +DrPG+La v++ala+ giNi  +          ++  + +vv+  ++ ev+e++ +
  gi|119719798|ref|YP_920293.1| 110 IHEDRPGILAWVASALAEKGINILQVVAEDPNI--YREPKLYVVVSKPVPGEVIEKILQ 166
                                    457************************999999..799999999999999999998865 PP

>> ACT_7  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.1         2   9.1e+03      51      63 ..      19      31 ..      18      32 .. 0.82
   2 !   20.8   0.0   5.6e-08   0.00025       7      41 ..     104     135 ..     100     140 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2
                                   EEGGGHHHHHHHH CS
                          ACT_7 51 VpeedlekAveaL 63
                                   V++e+  ++v+ L
  gi|119719798|ref|YP_920293.1| 19 VKSEKRMNVVRLL 31
                                   8899999999887 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 5.6e-08
                                    EEEEE-S-.---SS--HHHHHHHHHHTTT---EEE CS
                          ACT_7   7 iklsvvgsglpfdvtGivaklaspLaeagIsifqi 41 
                                    ++l v+ +    d +Gi+a +as+Lae gI+i+q+
  gi|119719798|ref|YP_920293.1| 104 RCLVVEIH-E--DRPGILAWVASALAEKGINILQV 135
                                    55555555.3..79*******************97 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.044     2e+02      11      38 ..       3      31 ..       1      67 [. 0.69
   2 !   16.2   0.0   2.7e-06     0.012      13      54 ..     111     150 ..     103     174 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.044
                          ACT_4 11 veaedrkglLaditqvisee.kanivsvn 38
                                   + ++ + g ++++++v+++e ++n+v + 
  gi|119719798|ref|YP_920293.1|  3 IFVHVEGGFWRRVSEVVKSEkRMNVVRLL 31
                                   556668899999***99999788887664 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 2.7e-06
                          ACT_4  13 aedrkglLaditqviseekanivsvnaktrkkdglaeikitv 54 
                                     edr+g+La ++++++e+++ni  v a++   + + e k+ v
  gi|119719798|ref|YP_920293.1| 111 HEDRPGILAWVASALAEKGINILQVVAED--PNIYREPKLYV 150
                                    58*********************998887..45555555555 PP

>> ACT_6  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   3.5e-05      0.15      10      33 ..     112     135 ..     105     138 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.5e-05
                          ACT_6  10 pdrpGltasLtsvlaefgvnilDi 33 
                                    +drpG++a ++s+lae g+nil +
  gi|119719798|ref|YP_920293.1| 112 EDRPGILAWVASALAEKGINILQV 135
                                    6********************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1190.50
//
Query:       gi|119719799|ref|YP_920294.1|  [L=460]
Description: tryptophan synthase subunit beta [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-42  145.1   0.0    3.6e-42  144.8   0.0    1.1  1  PALP      Pyridoxal-phosphate dependent enzyme


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.8   0.0     2e-46   3.6e-42       5     294 .]      76     415 ..      72     415 .. 0.82

  Alignments for each domain:
  == domain 1  score: 144.8 bits;  conditional E-value: 2e-46
                                    SSS--EEEECCTCCCCCCE..EEEEEGGGSTTSBTTHHHHHHHHHH.HHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-EE CS
                           PALP   5 igpTPlvrlprlskelgvp..lflKlEslnptgSfKdRgaeyllar.lkegtgaktvveassGNhgralAaaaallGlkv 81 
                                     +pTPl+r+ rl+k+l +p  +++K+E+  p gS+K ++a+   ++ ++eg  a+  +e+++G++g al++a  l+Glk+
  gi|119719799|ref|YP_920294.1|  76 WRPTPLIRATRLEKALRTParIYYKYEGVSPPGSHKPNTAVAQAYYnAREG-VARLTTETGAGQWGSALSFATMLFGLKL 154
                                    69***************************************9888878888.99************************** PP

                                    EEE...EETTS-HHHHHHHHHTT-EEEEE..................CCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHH CS
                           PALP  82 tiv...vpadaspekvallrllGaevvev..................ggdydeavaaaaelaaegegaylvsqfdnptvi 140
                                    t++   v+   +p+++ l++ +Gaevv +                  +g+   a + a e a e e+  +   +   +v 
  gi|119719799|ref|YP_920294.1| 155 TVYmvrVSYQQKPYRAILMQTWGAEVVPSpsnrtkagraflekdpehPGSLGIAISEALEDAIEHEDTKYSLGSVLNHVL 234
                                    ***6666667779****************666666555555333333333333333333333333444444444355688 PP

                                    HHHHTHHHHHHHHTT...TTEEEEEEE-SSSHHHHHHHHHHHH.....HSTT.-EEEEEEECTTCGGTTCC...S..S.S CS
                           PALP 141 egygtiglEileqlg...gkpdavvvpvGgGgliaGiaaglke.....rrpd.vrvigvepegsdalarsl...ragrrv 208
                                    + ++ iglE ++q++   + pd v+ +vGgG+++aGi+ ++ +     + p+ +r+++vep+ +++++++    + g+  
  gi|119719799|ref|YP_920294.1| 235 LHQTIIGLEAIKQMQaldEFPDIVIGCVGGGSNFAGISYPFYYlvrsgKAPKkTRFLAVEPASCPSMTKGEymyDFGDTA 314
                                    88********97777777*************************9977766669*****************9777444444 PP

                                    S..B..............SSS.CCSTCSCGTTCCHHHHSEEEE.EEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHH CS
                           PALP 209 tvpvs.............dtiadglavgspselafelldrlvd.eivtvsdeealeamrllarregivvepssaaalaal 274
                                    ++++              +  a gl+ +  ++ +++ll++ +  e v+ ++ e++ea+rl+ar+egiv+ p sa+a+ a+
  gi|119719799|ref|YP_920294.1| 315 RLTPLlkmytlghdfvppPIHAGGLRYH-GAAPTLSLLKKAGIfESVAYNQVEVFEAARLFARTEGIVPAPESAHAIKAV 393
                                    4444477799***999999999999999.6666666775555569*********************************** PP

                                    ..HHHHHHCCTTCEEEEEEE-B CS
                           PALP 275 ..klreagelkegdrvvviltg 294
                                      +++ea++ +e++++++ l+g
  gi|119719799|ref|YP_920294.1| 394 idEALEAKRKGEEKVILFNLSG 415
                                    99888888888889****9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (460 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 3255.65
//
Query:       gi|119719800|ref|YP_920295.1|  [L=322]
Description: mevalonate kinase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.5e-21   74.1   0.7    1.6e-20   73.1   0.0    1.9  2  GHMP_kinases_N   GHMP kinases N terminal domain
    1.6e-15   57.3   0.8    3.4e-15   56.2   0.2    1.9  2  GHMP_kinases_C   GHMP kinases C terminal
  ------ inclusion threshold ------
      0.037   13.6   0.0      0.097   12.2   0.0    1.7  1  GalKase_gal_bdg  Galactokinase galactose-binding signature
       0.05   13.8   1.5        8.9    6.6   0.0    3.0  3  DUF2795          Protein of unknown function (DUF2795)


Domain annotation for each model (and alignments):
>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.1   0.0   3.6e-24   1.6e-20       1      66 []      93     160 ..      93     160 .. 0.94
   2 ?   -3.7   0.1       3.4   1.5e+04      17      27 ..     280     290 ..     277     291 .. 0.74

  Alignments for each domain:
  == domain 1  score: 73.1 bits;  conditional E-value: 3.6e-24
                                    EEEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEH..HHH.HHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
                 GHMP_kinases_N   1 divikseiPvgaGLGSSAAlavalvaAllallgls..lee.aklaleaerlaqggngsggDvaasvyGg 66 
                                    +++++seiP+g+G+GSSAA+ava++ A  +++g +  l+e  ++a+eae+ ++ g++sg+D+++++yGg
  gi|119719800|ref|YP_920295.1|  93 KVTVDSEIPPGSGMGSSAAVAVATTHATFRAFGEEpdLKEvSRIAFEAEKVVH-GKPSGIDNTVATYGG 160
                                    589*****************************988767667***********9.**************8 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 3.4
                                    HHHHHHHHHHH CS
                 GHMP_kinases_N  17 SAAlavalvaA 27 
                                    ++ ++valv+A
  gi|119719800|ref|YP_920295.1| 280 GGGFIVALVTA 290
                                    56778888887 PP

>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.1   5.1e+03      55      66 ..     103     114 ..     102     140 .. 0.70
   2 !   56.2   0.2   7.5e-19   3.4e-15       5      81 ..     229     302 ..     222     306 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.1
                 GHMP_kinases_C  55 GaGgGptvfalf 66 
                                    G+G G++ ++ +
  gi|119719800|ref|YP_920295.1| 103 GSGMGSSAAVAV 114
                                    888888887766 PP

  == domain 2  score: 56.2 bits;  conditional E-value: 7.5e-19
                 GHMP_kinases_C   5 lergdlellgellnlsqrselkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkdeaeqvaralre 81 
                                    le+gd+e+lg+l+n ++    +  +g+++ ele+l+  ++++Galg+kl+GaGgG++++al+ + ++ ++v++alr+
  gi|119719800|ref|YP_920295.1| 229 LEEGDYESLGRLMNVNHG--FLSAIGVSTLELEKLVYTARRAGALGSKLTGAGGGGFIVALV-TAEKEKEVVEALRQ 302
                                    567***************..699***************************************.9999999***9987 PP

>> GalKase_gal_bdg  Galactokinase galactose-binding signature
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.2e-05     0.097      15      48 ..       7      40 ..       3      41 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.2e-05
                                   EEEEEEEEE--S-TTTT-EEEEEEEEEEEEEEEE CS
                GalKase_gal_bdg 15 sAPGRvnLiGEHtDYngGfVlpmAieqdiyiavs 48
                                   sAP  v L GEH    g   +++Ai ++ ++ v 
  gi|119719800|ref|YP_920295.1|  7 SAPAKVILFGEHFVVEGQPAIAAAISLRAHVTVE 40
                                   8***************************999886 PP

>> DUF2795  Protein of unknown function (DUF2795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       2.5   1.1e+04      17      27 ..       3      13 ..       2      13 .. 0.85
   2 ?    6.6   0.0     0.002       8.9      22      41 ..     218     237 ..     215     239 .. 0.87
   3 ?    5.1   0.1    0.0059        26      13      37 ..     261     307 ..     259     309 .. 0.68

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.5
                        DUF2795 17 ArrngApdevl 27
                                   A r+ Ap +v+
  gi|119719800|ref|YP_920295.1|  3 ATRSSAPAKVI 13
                                   88999*99987 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.002
                        DUF2795  22 ApdevleaLeaLPdreYesp 41 
                                    A+  v+ea ++L++ +Yes 
  gi|119719800|ref|YP_920295.1| 218 AGRLVVEAARRLEEGDYESL 237
                                    67889*************96 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.0059
                        DUF2795  13 LveyArrngA......................pdevleaLeaLPdre 37 
                                    Lv  Arr+gA                       +ev+eaL++L  r 
  gi|119719800|ref|YP_920295.1| 261 LVYTARRAGAlgskltgaggggfivalvtaekEKEVVEALRQLSPRI 307
                                    5666666666666666666666666666666689********98775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2374.06
//
Query:       gi|119719801|ref|YP_920296.1|  [L=556]
Description: hypothetical protein Tpen_0892 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.054   12.9   0.3       0.11   11.9   0.1    1.6  2  NEL       C-terminal novel E3 ligase, LRR-interacting
       0.16   11.7   0.1        3.6    7.4   0.0    2.7  2  Get5_C    Get5 C-terminal domain


Domain annotation for each model (and alignments):
>> NEL  C-terminal novel E3 ligase, LRR-interacting
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   1.2e-05      0.11     110     139 ..      74     103 ..      56     128 .. 0.83
   2 ?   -4.3   0.0       1.1   9.8e+03      53      68 ..     512     527 ..     507     531 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.2e-05
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHT-SE CS
                            NEL 110 eaaLlslgrelfRleqleqiArekvkrlrl 139
                                    +++L  +g++++R e++e+++re+v+r+++
  gi|119719801|ref|YP_920296.1|  74 KERLSMVGEKMMRNEEVEKVVREEVWRRAA 103
                                    578999*********************976 PP

  == domain 2  score: -4.3 bits;  conditional E-value: 1.1
                                    HHHHHHHHT-HHHHHH CS
                            NEL  53 aavLqaaaqdpeLReq 68 
                                    a++++ a +d++LR +
  gi|119719801|ref|YP_920296.1| 512 ASLMEHACHDEALRIT 527
                                    4455666666666655 PP

>> Get5_C  Get5 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0    0.0004       3.6      25      38 .]     259     272 ..     255     272 .. 0.86
   2 ?    0.8   0.0     0.046   4.1e+02      15      32 ..     532     551 ..     526     551 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0004
                         Get5_C  25 avleRLqKGWeltk 38 
                                     vl  LqKGW lt+
  gi|119719801|ref|YP_920296.1| 259 DVLRSLQKGWLLTD 272
                                    68889*****9996 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.046
                         Get5_C  15 nkfknd..aearavleRLqK 32 
                                    +k+k    ++a+ ++eRL K
  gi|119719801|ref|YP_920296.1| 532 TKYKAEryPKAQSLVERLEK 551
                                    5666633689********87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (556 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 4102.10
//
Query:       gi|119719802|ref|YP_920297.1|  [L=638]
Description: acetyl-CoA synthetase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      4e-96  322.2   0.0    4.8e-96  321.9   0.0    1.1  1  AMP-binding    AMP-binding enzyme
    1.7e-30  105.8   2.6      4e-30  104.6   2.6    1.7  1  AMP-binding_C  AMP-binding enzyme C-terminal domain
    3.5e-21   74.9   1.8    4.8e-21   74.4   0.6    2.0  2  ACAS_N         Acetyl-coenzyme A synthetase N-terminus


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  321.9   0.0  8.1e-100   4.8e-96       2     422 ..      72     513 ..      71     514 .. 0.88

  Alignments for each domain:
  == domain 1  score: 321.9 bits;  conditional E-value: 8.1e-100
                                    HHHHHHST.TSEEEEE...CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEE CS
                    AMP-binding   2 eeqaaktp.dkvalvd...sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvpl 77 
                                    ++++++++ +kval++   +g+ ++++Yr+l+ +vnr+Aa L++ GvkkgdrVa++lp+ pe+ + +la++++Ga   ++
  gi|119719802|ref|YP_920297.1|  72 DRHVKTWRkNKVALIWegeDGSVKKYSYRDLYVEVNRVAALLKNFGVKKGDRVALYLPMIPELPIFMLAAARIGAPFTVI 151
                                    567777777*********9999********************************************************** PP

                                    ETTS-HHHHHHHHHHHTESEEE.........ETCTCCC.HHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTT CS
                    AMP-binding  78 nptltaeelayiledseakvli.........atvdsel.leklleaaakleavklvivldadellkeeelkeeeeseeka 147
                                     ++++++ la  l+ds+ak+l+         + v  ++ ++k+le  +   +v++v+v+ +++++ +  +++++ ++++a
  gi|119719802|ref|YP_920297.1| 152 FSGFSSDSLAKRLNDSGAKLLVtadgfwrrgRVVRLKDiADKSLE--Q-ALSVESVLVVRHAGVDVAM-QEGRDYWYHEA 227
                                    ***********************9999975423333333343333..3.3467888999988888774.44455555555 PP

                                    .S.....-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEH.HHHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHHHH CS
                    AMP-binding 148 .e.....kpeeeeelkpddlayiiYTSGTTGkPKGVmlsh.rnlvanvaslkletrfklkeddvvlsilplahifglile 220
                                     e     + +e+e+l+++++++i+YTSGTTG+PKG+ +s+ ++lv+ +++lk+   f+ +++d +++++++ +i+g+++ 
  gi|119719802|ref|YP_920297.1| 228 lEgigrnTYVEPERLDSNHPLFILYTSGTTGTPKGIYHSTgGYLVWVYWTLKW--AFNPNDEDIWWCTADIGWITGHSYV 305
                                    42677786668889**************************8889999888752..24444589***************** PP

                                    HHHHHHTT-EEEE-TTCGC.CHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHH CS
                    AMP-binding 221 lllallsGatvvllpkdaa.ldpklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspel 299
                                    ++++ll+G t  ++++ ++ + p++++  ie+++vtv+++ P++++++++ g+    ++++dlsslr++ ++gep++pe+
  gi|119719802|ref|YP_920297.1| 306 VFGPLLHGLTTLMYEGAPDyPAPDRWWSIIERHGVTVFYTSPTAIRMFMRYGSHW--VEKHDLSSLRILGSVGEPINPEA 383
                                    *******************666****************************87665..7789******************* PP

                                    HHHHHHHHTC...EEEEEEEEGGGSSECEE....CHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEET CS
                    AMP-binding 300 lrffralfge...evlegYGlTEttgvvtv....lpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgp 372
                                    ++++ +++g+   ++++++++TEt+g+++     ++l     k+gs+  plpgv++ +vD++ g+p ++g++G l+++ p
  gi|119719802|ref|YP_920297.1| 384 WEWYFKVVGKgrcPIIDTWWQTETGGFMISpaagIELVP--LKPGSATLPLPGVDADVVDDN-GNPAKPGVQGYLVIKRP 460
                                    ********99999***************66665533333..479*****************9.****************9 PP

                                    ..TS-SEBTT-HHHHHHHEEET..CCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                    AMP-binding 373 ..gvmkgYlkkpeataeafdse..grwlrTGDlgrldedGyleivgRkkdlikl 422
                                      g+  g +++pe+  ++++ +  ++++  GD +  dedGy++i+gR+++++k+
  gi|119719802|ref|YP_920297.1| 461 wpGMLLGVWGDPERYVKTYW-GrfDGYYFPGDYAMKDEDGYFWILGRADEVLKV 513
                                    778*****************.44788**************************98 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.6   2.6   6.7e-34     4e-30       1      76 []     522     600 ..     522     600 .. 0.95

  Alignments for each domain:
  == domain 1  score: 104.6 bits;  conditional E-value: 6.7e-34
                                    HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE---.---...HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
                  AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdg.sea...leeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76 
                                    e+Esalv+hpaV+eaaVvG+pd+vkGe++vafVvlk+g s +   leeeL  hv++ +gp+a+p +++fv++lpktrsGK
  gi|119719802|ref|YP_920297.1| 522 ELESALVEHPAVSEAAVVGKPDPVKGEVPVAFVVLKEGfS-PsvkLEEELSNHVAEVIGPIARPAAIIFVKKLPKTRSGK 600
                                    89**********************************9963.2357**********************************9 PP

>> ACAS_N  Acetyl-coenzyme A synthetase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.4   0.6     8e-25   4.8e-21       2      55 .]      17      70 ..      16      70 .. 0.98
   2 ?   -3.9   0.0       2.3   1.4e+04      12      22 ..     328     338 ..     327     350 .. 0.70

  Alignments for each domain:
  == domain 1  score: 74.4 bits;  conditional E-value: 8e-25
                                   HHHHHHHHH-HHHHHHHHHCCS--SB--S-SECSTTTCT-EESTT-EE-HHHHH CS
                         ACAS_N  2 kelykeSiedpeaFWaeqakeldWekpfdkvldgskgpfikWFeGGklNicyNc 55
                                   +e+ ++++edpe+FW+e a+ l+W+k +dkvld+ ++pf++WF+GG++N++yN+
  gi|119719802|ref|YP_920297.1| 17 DEMRRKALEDPESFWDEHARALEWYKIWDKVLDDGEKPFYRWFVGGRINASYNA 70
                                   79***************************************************7 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 2.3
                                    HHHHHHHHHCC CS
                         ACAS_N  12 peaFWaeqake 22 
                                    p+++W+ + ++
  gi|119719802|ref|YP_920297.1| 328 PDRWWSIIERH 338
                                    89999877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (638 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.43
# Mc/sec: 4423.19
//
Query:       gi|119719803|ref|YP_920298.1|  [L=538]
Description: glycerol kinase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.7e-70  237.4   0.0    2.6e-70  236.8   0.0    1.3  1  FGGY_N       FGGY family of carbohydrate kinases, N-terminal 
    4.6e-37  127.7   0.1      7e-37  127.1   0.1    1.2  1  FGGY_C       FGGY family of carbohydrate kinases, C-terminal 
     0.0014   18.1   0.0       0.16   11.4   0.0    2.5  2  BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
  ------ inclusion threshold ------
      0.066   13.3   0.0       0.18   11.9   0.0    1.7  1  MAGI_u1      Unstructured region on MAGI


Domain annotation for each model (and alignments):
>> FGGY_N  FGGY family of carbohydrate kinases, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  236.8   0.0   5.8e-74   2.6e-70       2     245 .]       6     251 ..       5     251 .. 0.99

  Alignments for each domain:
  == domain 1  score: 236.8 bits;  conditional E-value: 5.8e-74
                                    EEEEEEESSEEEEEEEETTS-EEEEEEEE--EB-SSTT--EE-HHHHHHHHHHHHHHHHHHCT.-GCCEEEEEEEE-SS- CS
                         FGGY_N   2 ilglDcGttstkaivldekgkvvasaqaelelsspkegwaeqdpeeiwqalaeairkvleqagisekqikaIgisgqreg 81 
                                    +l++D+Gtt +ka ++  +g ++a   +e+++++p++gwaeqdp+ +w +  e++r+vl++ag++++ +++I +s+qre+
  gi|119719803|ref|YP_920298.1|   6 LLSIDIGTTTVKAGLFHSNGSLLALDGKEYPTYYPRPGWAEQDPDDWWRTSVEVARNVLKKAGVDPSRVAGICVSSQRET 85 
                                    699***************************************************************************** PP

                                    EEEEETTTEESSEEE-TT--TTHHHHHHHHHTTCHCCHHHHHSS-SSTTSHHHHHHHHHHHSCCHHCCHCEEEEHHHHHH CS
                         FGGY_N  82 lvllDkndkpLynailwkdrrtaeiveklkeegnekklyektglvlstgftlsklkWlkenepevfekiekflliddyLi 161
                                    l+l+D +++ L+++ +w drr+++++e++k  +++ ++y ktglv+++ ft++kl W kenepev++++++ l ++dy+ 
  gi|119719803|ref|YP_920298.1|  86 LALVDSEGRSLGRVPIWMDRRSSPQAERIKSRVDPAEIYRKTGLVVDATFTATKLLWYKENEPEVLRRARLGLQPKDYVV 165
                                    ******************************************************************************** PP

                                    HHHCT--EEEHHHHCTTTSEETTTTEE-HHHHHHTT--GG..GS-EEE-TCCEEEEEECCCCCCTT.S-EEEEEEEEEHH CS
                         FGGY_N 162 wrLtgqfvtdvtnasesmlfnikklewdeellailgipee..lLPklvesseiigelkpelaaklGlkegvpvvggggDq 239
                                    +rLtg+ vtd+t as++mlfni klewd+el++ lg++e   l+P+ ++s e++g+l +e++  lGl   v v +g gD 
  gi|119719803|ref|YP_920298.1| 166 YRLTGVAVTDHTVASRTMLFNIVKLEWDRELFEELGLSEYagLFPESRYSDEVVGTLSEEASRLLGLPRSVQVLAGMGDR 245
                                    ***************************************999************************************** PP

                                    HHHHHH CS
                         FGGY_N 240 qaaalG 245
                                    qa +lG
  gi|119719803|ref|YP_920298.1| 246 QAEVLG 251
                                    **9998 PP

>> FGGY_C  FGGY family of carbohydrate kinases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.1   0.1   1.6e-40     7e-37       4     197 ..     263     456 ..     262     457 .. 0.89

  Alignments for each domain:
  == domain 1  score: 127.1 bits;  conditional E-value: 1.6e-40
                         FGGY_C   4 slGTssflllvgtkpvisehglltpvagedgkpeyalegsiavagslvawlldnl..glreeirdagev...eeslaela 78 
                                    s GT+s+  ++ + p+++e++  +  a +  ++ +++e++++ ag+++ w++d+   g++  ++++      +e l+ ++
  gi|119719803|ref|YP_920298.1| 263 STGTGSTTATMVDSPLLDEKMRFSVGA-APIRGRWVVEAGMSTAGAILRWFRDQVadGVQL-LASST-RrraYEYLD-ME 338
                                    68**************99998887777.6688**********************8763322.22222.234334444.77 PP

                         FGGY_C  79 aaeavadaggvvfvpafsglrapywdpdargtitglsssttlahiarAaleavalqlrailealekdsgkpldrlavdGG 158
                                    aa   + ++g++++p fsg r+p w+p arg+i+gl+ ++t ahi+rA +e++a+ +r ile +++  g+++ +l++ GG
  gi|119719803|ref|YP_920298.1| 339 AAYVPPGSNGLIVLPFFSGARSPRWNPYARGVIFGLTVYHTRAHIFRAMMEGIAYEIRKILEVFAEV-GVKPGELILMGG 417
                                    88888889********************************************************999.************ PP

                         FGGY_C 159 gskndllmqllAdilgvpVerpktaeatalGaAilAava 197
                                    g+k++l++++ A+++ + V+ p+  +a++ G A+lA ++
  gi|119719803|ref|YP_920298.1| 418 GAKSPLWARIKANVTKMEVVLPELLDAALAGDAMLASLK 456
                                    ************************************875 PP

>> BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   3.6e-05      0.16       3      69 ..       9      81 ..       7     265 .. 0.90
   2 !    4.4   0.1    0.0049        22     193     267 .]     382     453 ..     378     453 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.6e-05
                                   EEE-SSEEEEEEEETTTE.EEEEEEE--TTS-HHH..............HHHHHHHHHHT--GGGECEE..EE CS
                    BcrAD_BadFG  3 iDgGsTttkavlmdekge.vlgrgitnsanlesvrfeaa.....ekvleealtealerageeeadieetylvg 69
                                   iD+G+Tt+ka l+  +g+ ++  g+  ++++ +++ ++      ++  +e+ +++l++ag +++ ++ +++  
  gi|119719803|ref|YP_920298.1|  9 IDIGTTTVKAGLFHSNGSlLALDGKEYPTYYPRPGWAEQdpddwWRTSVEVARNVLKKAGVDPSRVAGICVSS 81
                                   9*****************7777999999999888766433333389999***************999888765 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0049
                                    HHHHHHHHHHHHHHHHHHH...TT---SS.EEEESGGGG-HHHHHHH.....HHHH-S-EE--GGGGGHHHHHHHHHH CS
                    BcrAD_BadFG 193 dIlaglhraialrvialis...rsggvtdevtltGGvakneaavkelrklvkenygevkininpdsiytgalGAalfA 267
                                     I++ + + ia  + ++ +   ++g  + e++l+GG ak+      l   +k n+ ++++ + p+   ++  G+a++A
  gi|119719803|ref|YP_920298.1| 382 HIFRAMMEGIAYEIRKILEvfaEVGVKPGELILMGGGAKS-----PLWARIKANVTKMEV-VLPELLDAALAGDAMLA 453
                                    566666666665555554411155666677*********9.....555668999999875.67777777778888776 PP

>> MAGI_u1  Unstructured region on MAGI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0     4e-05      0.18       3      37 ..     313     347 ..     312     348 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4e-05
                        MAGI_u1   3 tdaLqdglspssestpkRnKSyndMenAgIeppee 37 
                                    +d+  dg++ +++st++R+  y dMe A + p+++
  gi|119719803|ref|YP_920298.1| 313 RDQVADGVQLLASSTRRRAYEYLDMEAAYVPPGSN 347
                                    5899999999******************9988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (538 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 3707.49
//
Query:       gi|119719804|ref|YP_920299.1|  [L=202]
Description: hexapaptide repeat-containing transferase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-25   88.2  18.3    2.3e-08   33.4   0.2    3.6  3  Hexapep          Bacterial transferase hexapeptide (six repea
    1.3e-16   60.0  15.3    4.2e-08   32.8   3.3    3.9  4  Hexapep_2        Hexapeptide repeat of succinyl-transferase
  ------ inclusion threshold ------
      0.043   13.7   0.2       0.19   11.6   0.0    2.1  2  DUF951           Bacterial protein of unknown function (DUF95
      0.099   12.9   0.2       0.15   12.3   0.2    1.4  1  BacteriocIIc_cy  Bacteriocin class IIc cyclic gassericin A-li
       0.12   12.6   0.2       0.12   12.6   0.2    1.9  2  zf-RING_7        C4-type zinc ribbon domain
       0.14   12.4   0.8         25    5.1   0.0    3.2  3  SH3_7            SH3 domain of SH3b2 type
       0.68   10.1   3.0       0.55   10.4   0.8    2.0  3  PknG_rubred      Protein kinase G rubredoxin domain


Domain annotation for each model (and alignments):
>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.2   9.2e-12   2.3e-08       2      34 ..      19      51 ..       9      53 .. 0.93
   2 !   33.2   3.8   1.1e-11   2.8e-08       1      35 [.      54      88 ..      54      89 .. 0.95
   3 !   30.3   1.7   8.7e-11   2.2e-07       2      36 .]     105     139 ..     104     139 .. 0.95

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 9.2e-12
                                   EEEETTEEE-TTEEEETTEEE-TTEEEETTEEE CS
                        Hexapep  2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvi 34
                                   + IG+++ I++fa++++++ IG+n+ Ig  v++
  gi|119719804|ref|YP_920299.1| 19 AEIGEGTRIWHFAHVRSGARIGRNCNIGKDVYV 51
                                   78**************************87776 PP

  == domain 2  score: 33.2 bits;  conditional E-value: 1.1e-11
                                   TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                        Hexapep  1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35
                                   ++vIG+nv+I +++ ++ +V+I dnv +g+++v +
  gi|119719804|ref|YP_920299.1| 54 GAVIGNNVKIQNGVSVYRGVVIEDNVFVGPYAVFT 88
                                   68******************************987 PP

  == domain 3  score: 30.3 bits;  conditional E-value: 8.7e-11
                                    EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEES CS
                        Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvigg 36 
                                    tv+ +++ Ig++a+i  +V+IG+++ ++ag+v+++
  gi|119719804|ref|YP_920299.1| 105 TVVKEGASIGANATIVCGVTIGRYAMVAAGSVVTR 139
                                    8999*****************************85 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.81   2.1e+03      14      23 ..      13      24 ..      10      27 .. 0.59
   2 !   32.8   3.3   1.6e-11   4.2e-08       3      34 .]      38      71 ..      36      71 .. 0.95
   3 !    9.0   0.0   0.00044       1.1       2      14 ..      73      85 ..      72      88 .. 0.86
   4 !   24.3   1.3   7.7e-09     2e-05       9      34 .]     112     139 ..     104     139 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.81
                                   -EE..SEEE-TT CS
                      Hexapep_2 14 agi..GvslGdn 23
                                   a++  G ++G++
  gi|119719804|ref|YP_920299.1| 13 AVVeeGAEIGEG 24
                                   554457777765 PP

  == domain 2  score: 32.8 bits;  conditional E-value: 1.6e-11
                                   EE-TT-EE-TT-EE..SEEE-TT-EE-TT-EE-S CS
                      Hexapep_2  3 iIGdnCliGanagi..GvslGdncvvgaGvvita 34
                                   +IG nC+iG++ ++  G  +G+n+++++Gv +++
  gi|119719804|ref|YP_920299.1| 38 RIGRNCNIGKDVYVdqGAVIGNNVKIQNGVSVYR 71
                                   8******************************995 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.00044
                                   EEE-TT-EE-TT- CS
                      Hexapep_2  2 viIGdnCliGana 14
                                   v I+dn+++G+ a
  gi|119719804|ref|YP_920299.1| 73 VVIEDNVFVGPYA 85
                                   89********976 PP

  == domain 4  score: 24.3 bits;  conditional E-value: 7.7e-09
                                    EE-TT-EE..SEEE-TT-EE-TT-EE-S CS
                      Hexapep_2   9 liGanagi..GvslGdncvvgaGvvita 34 
                                     iGana+i  Gv++G+ + v+aG+v+t+
  gi|119719804|ref|YP_920299.1| 112 SIGANATIvcGVTIGRYAMVAAGSVVTR 139
                                    69*****778****************96 PP

>> DUF951  Bacterial protein of unknown function (DUF951)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.3   3.2e+03      23      34 ..      33      44 ..      25      52 .. 0.79
   2 ?   11.6   0.0   7.6e-05      0.19      31      51 ..     178     198 ..     174     201 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.3
                         DUF951 23 lRvGadiklkCl 34
                                   +R Ga i  +C+
  gi|119719804|ref|YP_920299.1| 33 VRSGARIGRNCN 44
                                   799999988885 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 7.6e-05
                         DUF951  31 lkClgcgrevmlpRskfekki 51 
                                    l+C +cgrev +p+s  ek +
  gi|119719804|ref|YP_920299.1| 178 LQCDHCGREVSIPKSIYEKAL 198
                                    89****************987 PP

>> BacteriocIIc_cy  Bacteriocin class IIc cyclic gassericin A-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2     6e-05      0.15      54      86 ..     104     136 ..      54     139 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6e-05
                                    HHHHHHH---SSTTTTTSSSSS-STHHHHTSSS CS
                BacteriocIIc_cy  54 ldavasGaslgtafaiilGvtlPawilaaaaal 86 
                                      +v  Gas+g+  +i+ Gvt+  +++ aa+++
  gi|119719804|ref|YP_920299.1| 104 PTVVKEGASIGANATIVCGVTIGRYAMVAAGSV 136
                                    356789************************975 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.3       4.3   1.1e+04      28      31 ..     160     163 ..     160     163 .. 0.87
   2 ?   12.6   0.2   4.7e-05      0.12      18      31 ..     172     185 ..     165     185 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 4.3
                                    TT-- CS
                      zf-RING_7  28 eCGR 31 
                                    +CGR
  gi|119719804|ref|YP_920299.1| 160 YCGR 163
                                    7*99 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 4.7e-05
                                    CCSTB-EE-TTT-- CS
                      zf-RING_7  18 ragdevvtCpeCGR 31 
                                    r g++v +C++CGR
  gi|119719804|ref|YP_920299.1| 172 RDGNVVLQCDHCGR 185
                                    67799********9 PP

>> SH3_7  SH3 domain of SH3b2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0    0.0099        25      13      26 ..      52      65 ..      49      71 .. 0.83
   2 ?    2.8   0.2     0.054   1.4e+02      14      24 ..      71      81 ..      68      88 .. 0.84
   3 ?    1.8   0.0       0.1   2.7e+02      13      23 ..      83      93 ..      81      99 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0099
                                   -EEEE-STTEEEE- CS
                          SH3_7 13 rfaviirdnvplyD 26
                                   +++++i++nv++++
  gi|119719804|ref|YP_920299.1| 52 DQGAVIGNNVKIQN 65
                                   78*********965 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.054
                                   EEEE-STTEEE CS
                          SH3_7 14 faviirdnvpl 24
                                   ++v+i dnv++
  gi|119719804|ref|YP_920299.1| 71 RGVVIEDNVFV 81
                                   59*******99 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.1
                                   -EEEE-STTEE CS
                          SH3_7 13 rfaviirdnvp 23
                                   ++av+++d+ p
  gi|119719804|ref|YP_920299.1| 83 PYAVFTNDKYP 93
                                   9*******976 PP

>> PknG_rubred  Protein kinase G rubredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.9   4.8e+03      83     105 ..      16      42 ..       8      48 .. 0.57
   2 ?   -1.8   0.0       1.2   3.1e+03      97     107 ..     116     130 ..     103     138 .. 0.66
   3 ?   10.4   0.8   0.00022      0.55      94     125 ..     157     188 ..     125     194 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.9
                                    -CSS---GGG-B-....TTT--B-S-- CS
                    PknG_rubred  83 ltnpvvpEskRfC....wrCGrpvGRs 105
                                     +  ++ E+ R       r G+++GR+
  gi|119719804|ref|YP_920299.1|  16 EEGAEIGEGTRIWhfahVRSGARIGRN 42 
                                    444566676664311114678888887 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.2
                                    T....T--B-S---S CS
                    PknG_rubred  97 r....CGrpvGRsek 107
                                    +    CG  +GR   
  gi|119719804|ref|YP_920299.1| 116 NativCGVTIGRYAM 130
                                    444459999999765 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00022
                                    B-TTT--B-S---SS----SEEE-TTT--EEE CS
                    PknG_rubred  94 fCwrCGrpvGRsekerkgaseGtCpkCgspys 125
                                    f   CGrp  R  +er g+    C +Cg   s
  gi|119719804|ref|YP_920299.1| 157 FVCYCGRPLKRLVGERDGNVVLQCDHCGREVS 188
                                    6678************************8765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 1273.46
//
Query:       gi|119719805|ref|YP_920300.1|  [L=111]
Description: sec-independent translocation protein mttA/Hcf106 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-15   56.4   1.1    1.6e-15   56.2   1.1    1.3  1  MttA_Hcf106     mttA/Hcf106 family
    0.00074   19.4   2.9    0.00091   19.1   0.6    2.0  2  Rho_N           Rho termination factor, N-terminal domain
     0.0067   16.7   0.2      0.012   15.9   0.2    1.5  1  Ish1            Putative stress-responsive nuclear envelope p
     0.0089   15.8   1.0      0.014   15.2   0.5    1.5  2  SAP             SAP domain
  ------ inclusion threshold ------
      0.013   15.8   0.8        2.1    8.8   0.1    2.2  2  FAM25           FAM25 family
       0.11   12.9   0.5        2.2    8.7   0.1    2.3  2  Tir_receptor_M  Translocated intimin receptor (Tir) intimin-b
       0.13   12.1   4.2       0.88    9.4   0.1    2.6  3  IF2_N           Translation initiation factor IF-2, N-termina


Domain annotation for each model (and alignments):
>> MttA_Hcf106  mttA/Hcf106 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.2   1.1   6.1e-19   1.6e-15       1      46 [.      16      61 ..      16     107 .. 0.88

  Alignments for each domain:
  == domain 1  score: 56.2 bits;  conditional E-value: 6.1e-19
                                   S-HHHHHHHHHHHHHHS-TTTHHHHHHHHHHHHHHHHHHHHHHHH- CS
                    MttA_Hcf106  1 lgapelliIlvValllFGpkkLPEvaraLGktLreFkkavkeleee 46
                                   +g++el+++ + al+lFGpkkLPE+a+a+G++ r F+++++  ++ 
  gi|119719805|ref|YP_920300.1| 16 IGPTELILLIILALILFGPKKLPELAKAAGEAVRVFREETQKVTSS 61
                                   799*************************************998875 PP

>> Rho_N  Rho termination factor, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1      0.39     1e+03       5      16 ..      35      46 ..      34      47 .. 0.79
   2 !   19.1   0.6   3.6e-07   0.00091       8      42 ..      76     109 ..      73     109 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.39
                                   S-HHHHHHHHHH CS
                          Rho_N  5 ktlseLraiAke 16
                                   k+l+eL + A e
  gi|119719805|ref|YP_920300.1| 35 KKLPELAKAAGE 46
                                   789999888765 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 3.6e-07
                                    HHHHHHHHHTT-TTGGGS-HHHHHHHHHHGGGSSS CS
                          Rho_N   8 seLraiAkelgienysrlRKqdLIfaIlkaqaekg 42 
                                    ++Lr++A++lg+  +s+  + +L+ +I+++ +ekg
  gi|119719805|ref|YP_920300.1|  76 EDLRKLAEKLGV-ETSGKSRDELVKEIIQKAKEKG 109
                                    69**********.89**************999987 PP

>> Ish1  Putative stress-responsive nuclear envelope protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.2   4.8e-06     0.012       3      32 ..      72      99 ..      71     107 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.8e-06
                           Ish1  3 tWSdsdLkkWLdshGipvskaastRdeLlk 32
                                   + Sd+dL+k  ++ G+    ++++RdeL+k
  gi|119719805|ref|YP_920300.1| 72 SISDEDLRKLAEKLGVE--TSGKSRDELVK 99
                                   669************88..89********8 PP

>> SAP  SAP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.5   5.3e-06     0.014       5      29 ..      74      99 ..      71     101 .. 0.91
   2 ?   -0.9   0.0       0.6   1.5e+03       6      18 ..      98     110 ..      98     110 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.3e-06
                                   -HHHHHHHHHHTT--TTS-.HHHHHH CS
                            SAP  5 tVaeLKeeLkkrGLptsGk.KaeLie 29
                                   +  +L+++ +k+G  tsGk + eL++
  gi|119719805|ref|YP_920300.1| 74 SDEDLRKLAEKLGVETSGKsRDELVK 99
                                   6689********************96 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.6
                                    HHHHHHHHHHTT- CS
                            SAP   6 VaeLKeeLkkrGL 18 
                                    V+e  ++ k+ GL
  gi|119719805|ref|YP_920300.1|  98 VKEIIQKAKEKGL 110
                                    7899999999998 PP

>> FAM25  FAM25 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1   0.00082       2.1      27      61 ..      40      73 ..      32      76 .. 0.75
   2 ?    5.7   0.1    0.0074        19       6      20 ..      95     109 ..      92     110 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00082
                          FAM25 27 alKkAqesgekvvKevtekvtntvtnavtHAaEgL 61
                                     K+A e+  +v +e t+kvt++v ++ t   E++
  gi|119719805|ref|YP_920300.1| 40 LAKAAGEA-VRVFREETQKVTSSVEESRTTTSESI 73
                                   44555554.5899***********99999888876 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0074
                          FAM25   6 eevvkevveHaKeaG 20 
                                    +e vke+++ aKe G
  gi|119719805|ref|YP_920300.1|  95 DELVKEIIQKAKEKG 109
                                    689*********988 PP

>> Tir_receptor_M  Translocated intimin receptor (Tir) intimin-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.078     2e+02      52      63 ..      38      49 ..      35      51 .. 0.81
   2 ?    8.7   0.1   0.00084       2.2      39      59 ..      89     109 ..      58     110 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.078
                 Tir_receptor_M 52 aeqakaaGeear 63
                                    e akaaGe  r
  gi|119719805|ref|YP_920300.1| 38 PELAKAAGEAVR 49
                                   578******876 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00084
                 Tir_receptor_M  39 PsGeLkDDvvaqiaeqakaaG 59 
                                     sG+ +D++v++i ++ak+ G
  gi|119719805|ref|YP_920300.1|  89 TSGKSRDELVKEIIQKAKEKG 109
                                    59****************987 PP

>> IF2_N  Translation initiation factor IF-2, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       2.3     6e+03       8      14 ..      39      45 ..      35      49 .. 0.69
   2 ?    9.4   0.1   0.00034      0.88      34      54 .]      68      88 ..      59      88 .. 0.91
   3 ?    3.9   0.2     0.018        47      17      30 ..      98     110 ..      95     111 .] 0.87

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.3
                          IF2_N  8 eLAkeLg 14
                                   eLAk  g
  gi|119719805|ref|YP_920300.1| 39 ELAKAAG 45
                                   7777655 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00034
                          IF2_N 34 shsssLDeetaeliaeefgik 54
                                   + s s+++e++ ++ae++g++
  gi|119719805|ref|YP_920300.1| 68 TTSESISDEDLRKLAEKLGVE 88
                                   7899**************986 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.018
                          IF2_N  17 skevikkLfkelGi 30 
                                    +ke+i+k+ ke+G 
  gi|119719805|ref|YP_920300.1|  98 VKEIIQKA-KEKGL 110
                                    79******.88995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1368  (0.076301); expected 358.6 (0.02)
Passed bias filter:                      843  (0.0470188); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 770.55
//
Query:       gi|119719806|ref|YP_920301.1|  [L=324]
Description: Fis family transcriptional regulator [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00051   19.9   0.0      0.002   17.9   0.0    1.9  2  HGD-D           2-hydroxyglutaryl-CoA dehydratase, D-componen
    0.00065   19.9   1.6      0.029   14.6   0.1    2.9  2  Retrotrans_gag  Retrotransposon gag protein
      0.003   17.5   0.3      0.003   17.5   0.3    3.2  4  CHASE3          CHASE3 domain
     0.0078   15.7   1.8      0.013   15.0   1.8    1.4  1  CAP_N           Adenylate cyclase associated (CAP) N terminal
  ------ inclusion threshold ------
      0.012   15.4   0.6       0.21   11.4   0.0    2.7  2  Synaptobrevin   Synaptobrevin
      0.013   15.3   5.3       0.34   10.7   0.0    2.6  2  DUF724          Protein of unknown function (DUF724)
      0.028   13.6   0.0      0.082   12.1   0.0    1.8  2  ArsA_ATPase     Anion-transporting ATPase
      0.032   14.3   0.4       0.11   12.5   0.1    2.1  1  LOH1CR12        Tumour suppressor protein
      0.039   11.9   0.3       0.05   11.6   0.3    1.2  1  Prominin        Prominin
      0.066   12.3   3.9        1.3    8.1   0.0    3.0  3  RmuC            RmuC family
      0.085   13.5   2.9       0.76   10.5   0.4    3.0  3  Cytochrom_B562  Cytochrome b562
      0.089   12.7   0.9       0.37   10.7   0.1    2.4  2  DUF2313         Uncharacterised protein conserved in bacteria
       0.11   12.4   2.4        6.8    6.5   0.0    2.6  2  STAT_alpha      STAT protein, all-alpha domain
       0.13   12.8   5.0      0.096   13.2   0.7    2.9  2  FliG_N          FliG N-terminal domain
       0.15   12.6   9.0       0.13   12.7   1.4    3.3  3  Spectrin        Spectrin repeat
       0.16   10.3   1.0        0.5    8.6   0.0    1.8  2  Gp58            gp58-like protein
       0.18   11.8   8.0        2.1    8.4   0.1    3.0  3  Laminin_II      Laminin Domain II
       0.19   11.4   3.0        1.3    8.7   1.0    3.4  2  LXG             LXG domain of WXG superfamily
       0.21   11.9   1.7         20    5.6   0.0    3.4  2  PqqD            Coenzyme PQQ synthesis protein D (PqqD)
       0.48    9.6   1.5          4    6.6   0.8    2.1  2  TMPIT           TMPIT-like protein
       0.48    9.7   4.9        5.2    6.4   0.9    2.7  2  Helo_like_N     Fungal N-terminal domain of STAND proteins
       0.49   10.3   2.5         23    4.9   0.2    2.9  2  DUF1759         Protein of unknown function (DUF1759)
        0.5   10.0   3.3        2.4    7.8   0.2    3.0  4  RPW8            Arabidopsis broad-spectrum mildew resistance 
       0.51   10.7   7.7        1.9    8.9   0.2    3.8  4  BLOC1_2         Biogenesis of lysosome-related organelles com
       0.67    9.5   4.9        2.6    7.6   2.3    2.2  2  Phage_GPO       Phage capsid scaffolding protein (GPO) serine
       0.81    9.8   8.0      0.079   13.1   1.2    2.1  2  UPF0242         Uncharacterised protein family (UPF0242) N-te
        1.1    8.4   4.4        0.5    9.6   1.2    1.9  2  ISG65-75        Invariant surface glycoprotein
        1.9    9.2   5.0        1.7    9.4   1.8    2.5  2  Occludin_ELL    Occludin homology domain
        2.1    8.6   3.5         24    5.1   0.8    2.9  3  Fib_alpha       Fibrinogen alpha/beta chain family
        3.4    7.1   9.1          8    5.9   9.1    1.8  1  Exonuc_VII_L    Exonuclease VII, large subunit
        7.7    6.3   8.7        9.8    6.0   4.7    2.2  2  PDDEXK_1        PD-(D/E)XK nuclease superfamily
        9.8    6.5  13.9         43    4.5   5.2    3.9  2  Rx_N            Rx N-terminal domain


Domain annotation for each model (and alignments):
>> HGD-D  2-hydroxyglutaryl-CoA dehydratase, D-component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   3.6e-06     0.002      77     178 ..      54     174 ..      23     229 .. 0.82
   2 ?    0.3   0.1      0.86   4.8e+02     182     199 ..     208     225 ..     173     307 .. 0.45

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3.6e-06
                                    T..S-EEEE---...........HHHHHHHHHHHHHHHHHHHHHHT----HHHHHHHHHHHHHHHHHHHHHHHHTTSSS- CS
                          HGD-D  77 i..ipytvldiP...........eeavkyledelenliaaleeitgkrideesleaaikeanetrellkelytllpqspa 143
                                    +  + + +l++P            e+++ + + l+++ aale+++ +  ++esl++ +++ +++ e + e+++ l +   
  gi|119719806|ref|YP_920301.1|  54 LveKTLKLLKVPeppgiseaerlAESLESYGASLQRVAAALEDLLRVVDSAESLLRRLEDVKQALESWAEVFQGLNA--- 130
                                    354458899999999**999999999999******************99**************************44... PP

                                    SS-HHHHH.HHHHHTTS......-HHHHHHHHHHHHHHHHH...H CS
                          HGD-D 144 pihgfdll.llakvvfl......gkeeatealeelleelee...r 178
                                     + g ++   + ++  l      + +e+ ++le ll+e+e+   r
  gi|119719806|ref|YP_920301.1| 131 SLYG-EIArEISRIERLpqedyqDVKEFHDKLEDLLDEAERlsaR 174
                                    5777.4444666666644666999****************96541 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.86
                                    TS-EEEEEES---TT--H CS
                          HGD-D 182 eriRllltGipvellaak 199
                                    e++Rl   G+++   +++
  gi|119719806|ref|YP_920301.1| 208 EKARLEALGSALQRVEQE 225
                                    333333333333222222 PP

>> Retrotrans_gag  Retrotransposon gag protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   5.2e-05     0.029       9      80 ..     102     172 ..      97     190 .. 0.87
   2 ?    3.8   0.2      0.12        69      26      63 ..     200     236 ..     170     265 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.2e-05
                 Retrotrans_gag   9 gaAkswlkslvarsidasesWkdlkkaflktflpserkdqleeelsslrQ.gtesvreYvtrfktladqlde.v 80 
                                    + A s l++l++ ++   esW++  + +++  +   + ++  +++ +l Q + + v+e++++++ l+d++++ +
  gi|119719806|ref|YP_920301.1| 102 DSAESLLRRLEDVKQA-LESWAEVFQGLNASLYG--EIAREISRIERLPQeDYQDVKEFHDKLEDLLDEAERlS 172
                                    6788888899888888.7****************..99999999************************999742 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.12
                 Retrotrans_gag  26 sesWkdlkkaflktflpserkdqleeelsslrQgtesv 63 
                                    +es + l ++ + + l  +  ++ e+el+slrQ  +s+
  gi|119719806|ref|YP_920301.1| 200 AESVAALHEKARLEALG-SALQRVEQELRSLRQSPRSF 236
                                    56666677777777777.778899999******77776 PP

>> CHASE3  CHASE3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       6.6   3.7e+03      60      72 ..      25      37 ..      11      49 .. 0.49
   2 !   17.5   0.3   5.3e-06     0.003      39      89 ..      78     128 ..      75     132 .. 0.94
   3 ?   -1.3   9.5       3.4   1.9e+03      51     129 ..     136     227 ..     132     232 .. 0.60
   4 ?    0.6   0.4      0.89     5e+02      39      61 ..     210     232 ..     206     270 .. 0.68

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 6.6
                         CHASE3 60 eltadnpeqqerl 72
                                   ++ta+n e  e l
  gi|119719806|ref|YP_920301.1| 25 TTTAQNMEKVEEL 37
                                   3333332222222 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 5.3e-06
                         CHASE3  39 efLepyeqaraeiqealeelreltadnpeqqerldrlealieqklaeleet 89 
                                    e Le y ++ +++ +ale+l +++ + ++ ++rl++++++ e++ ++++++
  gi|119719806|ref|YP_920301.1|  78 ESLESYGASLQRVAAALEDLLRVVDSAESLLRRLEDVKQALESWAEVFQGL 128
                                    679*******************************************99875 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 3.4
                         CHASE3  51 iqealeelreltadnpeqqer........ldrlealieqklaeleetialrreggleaalalvrsdeg......kelmde 116
                                    i ++++++++l +++ +  +         ld++e+l ++ ++e +++++l+ +  lea +++++ +e+      k++ ++
  gi|119719806|ref|YP_920301.1| 136 IAREISRIERLPQEDYQDVKEfhdkledlLDEAERLSARARSEYNKLVELALR-ELEATREVLQRAESvaalheKARLEA 214
                                    56666666666666655555555555556999999999999999999999998.66666666655555000000444444 PP

                         CHASE3 117 iraliaemrdeer 129
                                    + ++++++++e r
  gi|119719806|ref|YP_920301.1| 215 LGSALQRVEQELR 227
                                    4444444444444 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 0.89
                         CHASE3  39 efLepyeqaraeiqealeelrel 61 
                                    + Le   +a ++++++l++lr+ 
  gi|119719806|ref|YP_920301.1| 210 ARLEALGSALQRVEQELRSLRQS 232
                                    55777788888888888888875 PP

>> CAP_N  Adenylate cyclase associated (CAP) N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   1.8   2.4e-05     0.013       2     138 ..     106     235 ..     105     256 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.4e-05
                                    XXXXXXXXXXXXXXXX..........XXXXXXXXXXXXXXXXXXXXXXXSXH.HHHHHHHHHHHHHHHHHHHHHHHH-HH CS
                          CAP_N   2 tlikRLEaatsrLEdiaisessssasskasssssaaaaaaaaaakaaaaaaaaksveaFdelisgsvkefvelskkigge 81 
                                    +l++RLE++ + LE+ a   +  +a     s  ++ a++ +    +  +++  + v++F++ +++ ++e  +ls+   +e
  gi|119719806|ref|YP_920301.1| 106 SLLRRLEDVKQALESWAEVFQGLNA-----SLYGEIAREISRI--ERLPQEDYQDVKEFHDKLEDLLDEAERLSARARSE 178
                                    799999**99999999654333222.....2222222222221..2222234499************************* PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHBE---.HHHHHHHCHHHHHHHHHHHHHHHTTTT CS
                          CAP_N  82 vaeqaelvkkafeaqrkfllvaskakkPadseelqelLkplseaiqkvqeireknrk 138
                                     ++ +el  + +ea r++l+ a ++   ++++ l+ l + l++  q+ +++r++ r+
  gi|119719806|ref|YP_920301.1| 179 YNKLVELALRELEATREVLQRAESVAALHEKARLEALGSALQRVEQELRSLRQSPRS 235
                                    **********************99999976777777667777777777777777765 PP

>> Synaptobrevin  Synaptobrevin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00038      0.21       7      48 ..     135     176 ..     130     186 .. 0.93
   2 ?    1.2   0.1      0.58   3.2e+02      23      41 ..     193     211 ..     190     230 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00038
                                    HHHHHHHCCCCHHCCHHHHCHCCCCCHHHHCCCCHHHHHHHH CS
                  Synaptobrevin   7 kikaevdevkdimkeNidkvlergekldeLvdktenLqssaq 48 
                                    +i +e++ ++++ +e+ ++v e ++kl++L d++e+L++ a+
  gi|119719806|ref|YP_920301.1| 135 EIAREISRIERLPQEDYQDVKEFHDKLEDLLDEAERLSARAR 176
                                    6889**********************************9986 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.58
                                    HHHCHCCCCCHHHHCCCCH CS
                  Synaptobrevin  23 idkvlergekldeLvdkte 41 
                                     ++vl+r e +  L++k+ 
  gi|119719806|ref|YP_920301.1| 193 TREVLQRAESVAALHEKAR 211
                                    5789************973 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00061      0.34      70     143 ..      70     144 ..      51     147 .. 0.79
   2 ?    4.0   3.7     0.071        40     101     183 ..     148     228 ..     135     237 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00061
                         DUF724  70 leslkeslaeLekhGFdVkalqsrlnkLlslkdeqtklleerkklekkieeeesekrkleeeid.elekkilele 143
                                    +++  +    Le +G + + + + l++Ll + d+ ++ll++++++++ +e  ++  + l++++  e+ ++i+++e
  gi|119719806|ref|YP_920301.1|  70 ISEAERLAESLESYGASLQRVAAALEDLLRVVDSAESLLRRLEDVKQALESWAEVFQGLNASLYgEIAREISRIE 144
                                    6677778889************************************99998877777776655437777777666 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.071
                         DUF724 101 kdeqtklleerkklekkieeeesekrkleeeidel.ekkilelerqlallk.ekkeaadkeiarlkseaekleeeledve 178
                                    +++++ ++e   kle  + e+e  ++++ +e ++l e + +ele  +++l+ ++  aa +e arl++    l  +l++ve
  gi|119719806|ref|YP_920301.1| 148 QEDYQDVKEFHDKLEDLLDEAERLSARARSEYNKLvELALRELEATREVLQrAESVAALHEKARLEA----LGSALQRVE 223
                                    6778888888889999999999988888888887427788899998888875445555555555544....333344444 PP

                         DUF724 179 qeFea 183
                                    qe ++
  gi|119719806|ref|YP_920301.1| 224 QELRS 228
                                    44444 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00015     0.082     171     296 ..      22     146 ..       2     152 .. 0.72
   2 ?    0.8   0.0       0.4   2.2e+02     141     203 ..      97     163 ..      93     186 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00015
                                    CCSHCHHHHHHHHHHHHHHHHHHHHHHHHHHTSTTTEEEEEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEEE..E-TT CS
                    ArsA_ATPase 171 kllglggvsieealeeleetkeeikkveeiltdpertsfrlVvipEklslkEteRaikeLkkygikvdavivNk..llpe 248
                                    k ++++++++ e++eel+  +++  + +  l      +++l   pE   + E eR++++L++yg + + v      ll  
  gi|119719806|ref|YP_920301.1|  22 KASTTTAQNM-EKVEELYRAVQSRGSSNPLLGRLVEKTLKLLKVPEPPGISEAERLAESLESYGASLQRVAAALedLLRV 100
                                    3333333333.46777777777777778888888999*******************************997654324443 PP

                                    CSSSTSHHHHHHHHHHHHHHHHHHHHTTTSEEEEEE--SS-S-SHHHH CS
                    ArsA_ATPase 249 eeqenCeflearkkiqkkylkeieelfedlevvklplleeEvvGlekl 296
                                     +  + e l +r +  k+ l++  e f+ l+   +  +++E+  +e+l
  gi|119719806|ref|YP_920301.1| 101 VD--SAESLLRRLEDVKQALESWAEVFQGLNASLYGEIAREISRIERL 146
                                    33..35888888888888888888888888777777777777666665 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.4
                                    GGGHHHHHHHHHHHHHHHHHHHHHHHHHHCCCSHCHHHHHH...HHHHHH.HHHHHHHHHHHHHHTS CS
                    ArsA_ATPase 141 llslpevleklleklvklkeklsplakqlvkllglggvsie...ealeel.eetkeeikkveeiltd 203
                                    ll++++  e+ll++l ++k++l++ a+ +++l      +i    + +e+l +e ++++k++++ l+d
  gi|119719806|ref|YP_920301.1|  97 LLRVVDSAESLLRRLEDVKQALESWAEVFQGLNASLYGEIAreiSRIERLpQEDYQDVKEFHDKLED 163
                                    7888899999999999999999999999887765554444422433333324566677777666665 PP

>> LOH1CR12  Tumour suppressor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1    0.0002      0.11      59     124 ..      99     172 ..      68     176 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.0002
                       LOH1CR12  59 kevdakiitllaelrekqkqyasyaealskvn.....elsdqlsriqiile....divpllEtlnelLdedeRLe 124
                                    ++v  + ++ll  l + ++  +s+ae ++++n     e+  ++sri+ + +    d+ +  ++l +lLde+eRL 
  gi|119719806|ref|YP_920301.1|  99 RVV-DSAESLLRRLEDVKQALESWAEVFQGLNaslygEIAREISRIERLPQedyqDVKEFHDKLEDLLDEAERLS 172
                                    444.46799**********************96555569999****88765111044456689**********96 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.3   8.9e-05      0.05     237     401 ..      69     245 ..       6     259 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.9e-05
                       Prominin 237 aLaelerllenlkeakeqLeqvnklekeLr...ksgsqLrdglrgvkrdlnqalsn.lCq.........seeCskilssl 303
                                     ++e erl+e+l++  ++L+ v + +++L     s++ L + l++vk+ l++ ++  + +         ++e s i++  
  gi|119719806|ref|YP_920301.1|  69 GISEAERLAESLESYGASLQRVAAALEDLLrvvDSAESLLRRLEDVKQALESWAEVfQ-GlnaslygeiAREISRIERLP 147
                                    5778888889999999999888888887641223456677777788888887766632.235555543334555555555 PP

                       Prominin 304 eiekldtskcldqlpnvdevlealeevletnlssivkeglarlneipekvknqtaevvpdlkkalakgreqikklakkip 383
                                    +  + d+++  d+l+++ ++ e+l    +++++++v+ +l +l++ +e +++  +      k  l+  ++++++++++++
  gi|119719806|ref|YP_920301.1| 148 QEDYQDVKEFHDKLEDLLDEAERLSARARSEYNKLVELALRELEATREVLQRAESVAALHEKARLEALGSALQRVEQELR 227
                                    44444554444*********************************999999888877777999999999999999999996 PP

                       Prominin 384 realdavisdlenterss 401
                                    + + +  + d++ ++r++
  gi|119719806|ref|YP_920301.1| 228 SLRQSPRSFDVNGVYREL 245
                                    555555555555555555 PP

>> RmuC  RmuC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0    0.0023       1.3     227     287 ..      89     149 ..      75     153 .. 0.85
   2 ?    5.1   0.5     0.019        10     232     288 ..     151     210 ..     133     213 .. 0.51
   3 ?   -0.5   0.1      0.99   5.5e+02      10      49 ..     215     255 ..     209     266 .. 0.50

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0023
                           RmuC 227 naeeiaellgelydkfekfgedleklgkklekaqksydkavkklegnilrkaeklkelgvk 287
                                    +++  +e l ++ d  e++  +le+++++le+  + ++ +  +l g+i r++ ++++l ++
  gi|119719806|ref|YP_920301.1|  89 RVAAALEDLLRVVDSAESLLRRLEDVKQALESWAEVFQGLNASLYGEIAREISRIERLPQE 149
                                    45555666777889999999***********************************999876 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.019
                           RmuC 232 aellgelydkfekfgedleklgkklekaqksydkavkkle.......gnilrkaeklkelgvke 288
                                    ++ ++e++dk+e + ++ e+l     +a+++y+k+v+  +       +++l++ae++ +l +k+
  gi|119719806|ref|YP_920301.1| 151 YQDVKEFHDKLEDLLDEAERLSA---RARSEYNKLVEL-AlreleatREVLQRAESVAALHEKA 210
                                    33334444444444444444433...334444443321.1234448888999999888888775 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.99
                           RmuC  10 lkeklekfeekveees.keeaeeleslkeqlkelqelneql 49 
                                    l + l+++e+++++   + ++ + + + ++l+++++ ++q+
  gi|119719806|ref|YP_920301.1| 215 LGSALQRVEQELRSLRqSPRSFDVNGVYRELGRVKSEAQQV 255
                                    33444444444444443444445555555555555555555 PP

>> Cytochrom_B562  Cytochrome b562
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.55   3.1e+02      50      77 ..      76     103 ..      22     126 .. 0.65
   2 ?   10.5   0.4    0.0014      0.76      47      95 ..     147     195 ..     110     197 .. 0.84
   3 ?   -1.9   0.0       9.4   5.2e+03      13      16 ..     226     229 ..     198     270 .. 0.57

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.55
                 Cytochrom_B562  50 dseeqkdYqeGldklidqldkaealaka 77 
                                     +e  + Y + l+ + ++l+++ + +++
  gi|119719806|ref|YP_920301.1|  76 LAESLESYGASLQRVAAALEDLLRVVDS 103
                                    4555666666666666666666655553 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0014
                 Cytochrom_B562  47 lekdseeqkdYqeGldklidqldkaealakagkleeakaalkelkdlrk 95 
                                    +++d +++k++++ l++l+d+ ++++a a ++ ++ ++ al+el+++r+
  gi|119719806|ref|YP_920301.1| 147 PQEDYQDVKEFHDKLEDLLDEAERLSARARSEYNKLVELALRELEATRE 195
                                    34599*****************************************997 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 9.4
                 Cytochrom_B562  13 lkqv 16 
                                    l+++
  gi|119719806|ref|YP_920301.1| 226 LRSL 229
                                    2222 PP

>> DUF2313  Uncharacterised protein conserved in bacteria (DUF2313)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00065      0.37       8      57 ..      67     114 ..      60     126 .. 0.90
   2 ?   -0.9   0.1       2.3   1.3e+03      17      38 ..     208     229 ..     188     233 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00065
                        DUF2313   8 ppglaesrelqallegeapeldrleasaddllkelfpetatelLkdWEkv 57 
                                    ppg  e ++l++ le+++++l+r+ a+++dll+   +++a++lL++ E+v
  gi|119719806|ref|YP_920301.1|  67 PPGISEAERLAESLESYGASLQRVAAALEDLLR--VVDSAESLLRRLEDV 114
                                    888889999***********************8..568999999988875 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.3
                        DUF2313  17 lqallegeapeldrleasaddl 38 
                                     +a le+++ +l+r+e+++ +l
  gi|119719806|ref|YP_920301.1| 208 EKARLEALGSALQRVEQELRSL 229
                                    5677899999999999988776 PP

>> STAT_alpha  STAT protein, all-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.6     0.033        18       3      91 ..      89     173 ..      87     203 .. 0.86
   2 ?    6.5   0.0     0.012       6.8       6      57 ..     210     263 ..     207     307 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.033
                     STAT_alpha   3 eieqrleelrskvqeteqdirkLedeqeeFdfqyqelqkleqeraesekkelkkqkellqqmlnaLdqkRkelvdklkel 82 
                                    ++ ++le+l + v   e+ +r+Led+   ++   + +q l    + s   e++++   +++++++  q  ke+ dkl++l
  gi|119719806|ref|YP_920301.1|  89 RVAAALEDLLRVVDSAESLLRRLEDVKQALESWAEVFQGL----NASLYGEIAREISRIERLPQEDYQDVKEFHDKLEDL 164
                                    56778999999999*****************999999999....556666799999999999999888888888888888 PP

                     STAT_alpha  83 lnlleslqe 91 
                                    l+++e l +
  gi|119719806|ref|YP_920301.1| 165 LDEAERLSA 173
                                    888887765 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.012
                     STAT_alpha   6 qrleelrskvqeteqdirkLedeqeeFdfq..yqelqkleqeraesekkelkkq 57 
                                    +rle l s  q++eq++r+L +   +Fd++  y el + ++e ++  ++ l++q
  gi|119719806|ref|YP_920301.1| 210 ARLEALGSALQRVEQELRSLRQSPRSFDVNgvYRELGRVKSEAQQVLRTALSEQ 263
                                    6899************************98667777777444444444444443 PP

>> FliG_N  FliG N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.7   0.00017     0.096      20      95 ..     121     200 ..     117     208 .. 0.73
   2 ?   -1.0   0.0       4.7   2.6e+03      74      88 ..     251     265 ..     245     270 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00017
                                    HHHHHTTSXHHHHHHHHHHHHCHTTXXHHHHHHHHHHHHHHHHCC....CCHHCHHHHHHHHHHHHHHSHHHH.HHHCHH CS
                         FliG_N  20 aaevlkhLdeeeiekltkeiaslksvskeeveaVleefleeleaq....eylseggeeyarelLekalgeeka.eeller 94 
                                     aev++ L+ +   ++++ei++++++++e+ ++V +ef+++le      e ls  + +   +l e al e +a +e+l+r
  gi|119719806|ref|YP_920301.1| 121 WAEVFQGLNASLYGEIAREISRIERLPQEDYQDV-KEFHDKLEDLldeaERLSARARSEYNKLVELALRELEAtREVLQR 199
                                    599**************************88887.667755543322227777777777777888888775441456666 PP

                                    H CS
                         FliG_N  95 l 95 
                                    +
  gi|119719806|ref|YP_920301.1| 200 A 200
                                    5 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 4.7
                                    HHHHHHHHHHSHHHH CS
                         FliG_N  74 yarelLekalgeeka 88 
                                     a+++L+ al+e+++
  gi|119719806|ref|YP_920301.1| 251 EAQQVLRTALSEQEV 265
                                    455666666666554 PP

>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       8.2   4.6e+03      74      94 ..      23      43 ..      12      50 .. 0.66
   2 ?   12.7   1.4   0.00024      0.13      23     103 ..      93     182 ..      69     184 .. 0.80
   3 ?    1.5   4.8      0.72     4e+02      55      95 ..     159     200 ..     148     232 .. 0.59

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 8.2
                                   THHHHHHHHHHHHHHHHHHHH CS
                       Spectrin 74 aseeieerleelnerWeeLke 94
                                   as  + + +e+++e ++++++
  gi|119719806|ref|YP_920301.1| 23 ASTTTAQNMEKVEELYRAVQS 43
                                   555566666666666666554 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00024
                                    HHCCSSCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...........HHHHHHHHTTHTTHHHHHHHHHHHHHHHHH CS
                       Spectrin  23 llssedlgkdleevqallkkhkaleaelaaqqervkaln...........elaeklldeghsaseeieerleelnerWee 91 
                                     l  edl + ++++++ll++++++++ l+++ e ++ ln              e+l +e  ++ +e +++le+l +  e 
  gi|119719806|ref|YP_920301.1|  93 AL--EDLLRVVDSAESLLRRLEDVKQALESWAEVFQGLNaslygeiareiSRIERLPQEDYQDVKEFHDKLEDLLDEAER 170
                                    44..7777889*********************************555544444555555577779999999999999999 PP

                                    HHHHHHHHHHHH CS
                       Spectrin  92 LkelaaerkqkL 103
                                    L+++a +  +kL
  gi|119719806|ref|YP_920301.1| 171 LSARARSEYNKL 182
                                    999999888888 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.72
                                    HHHHHHHHHHHHH.HHTTHTTHHHHHHHHHHHHHHHHHHHHH CS
                       Spectrin  55 ervkalnelaekl.ldeghsaseeieerleelnerWeeLkel 95 
                                    +++++l + ae+l + +  + ++ +e  l el+   e L+++
  gi|119719806|ref|YP_920301.1| 159 DKLEDLLDEAERLsARARSEYNKLVELALRELEATREVLQRA 200
                                    555555566666655555555566666666666555555544 PP

>> Gp58  gp58-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0    0.0009       0.5     267     331 ..      88     152 ..      82     169 .. 0.86
   2 ?    0.1   0.3      0.34   1.9e+02     248     308 ..     191     237 ..     157     269 .. 0.53

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0009
                           Gp58 267 qeiknregavsrvqqdldsyqrrlqdaeknyssLtqtvkGlqstvsdpnsklesrvtqLadlieq 331
                                    q++  + +++ rv  +++s+ rrl+d ++   s  +  +Gl++++  +  +  sr+ +L +   q
  gi|119719806|ref|YP_920301.1|  88 QRVAAALEDLLRVVDSAESLLRRLEDVKQALESWAEVFQGLNASLYGEIAREISRIERLPQEDYQ 152
                                    67888889999**********************************99999999999998765544 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.34
                           Gp58 248 eskisGlqstqqstakqisqeiknregavsrvqqdldsyqrrlqdaeknyssLtqtvkGlq 308
                                    e+    lq ++  +a   + ++              +++ + lq  e++  sL+q  + ++
  gi|119719806|ref|YP_920301.1| 191 EATREVLQRAESVAALHEKARL--------------EALGSALQRVEQELRSLRQSPRSFD 237
                                    4444444444444444444444..............4555555555555555555544443 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.1    0.0037       2.1      27      98 ..      74     146 ..      56     149 .. 0.80
   2 ?    5.2   2.1     0.036        20      17      96 ..     152     230 ..     147     235 .. 0.83
   3 ?   -1.4   0.0       3.9   2.2e+03      19      49 ..     238     267 ..     235     296 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0037
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH....HHHHHHHHHHH CS
                     Laminin_II  27 entkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeasss.lsdniseikel 98 
                                    e++ e+l++  +s++++ + ++d+ +++++A++  + Le + + L++  +  + l+      + ++is+i  l
  gi|119719806|ref|YP_920301.1|  74 ERLAESLESYGASLQRVAAALEDLLRVVDSAESLLRRLEDVKQALESWAEVFQGLNASLYGeIAREISRIERL 146
                                    7788899999999999999999999999999999999999888888775544444444333799999998765 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.036
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH...HHHHHHHHH CS
                     Laminin_II  17 eqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeassslsdniseik 96 
                                    +++++ + +le + ++++++ + ++   +k+ ++     +A r+v +  + +  L +k  +l+ l +a + + +++  ++
  gi|119719806|ref|YP_920301.1| 152 QDVKEFHDKLEDLLDEAERLSARARSEYNKLVELALRELEATREVLQRAESVAALHEK-ARLEALGSALQRVEQELRSLR 230
                                    6788999999999999999999888777777788888888999999999999999999.899999999888888887776 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 3.9
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                     Laminin_II  19 laplsqnlentkeklseinrsveetnekvkd 49 
                                    ++++  +l ++k++++++ r+ +  +++vk 
  gi|119719806|ref|YP_920301.1| 238 VNGVYRELGRVKSEAQQVLRT-ALSEQEVKV 267
                                    677778888888888888777.555555553 PP

>> LXG  LXG domain of WXG superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       3.1   1.8e+03      13      34 ..      21      42 ..       7      47 .. 0.56
   2 ?    8.7   1.0    0.0024       1.3      65     157 ..      75     168 ..      69     232 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 3.1
                            LXG 13 eqlkseleelkeqleqlkkaiq 34
                                   ++ ++++++  e++e+l++a+q
  gi|119719806|ref|YP_920301.1| 21 SKASTTTAQNMEKVEELYRAVQ 42
                                   3444444555555555555554 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0024
                            LXG  65 slqdlieqyeefLkkikeales.vepssngfidedfLeqelenglkkakevteelkdeink.ilasvsdivslpelddse 142
                                    +l + +e+y ++L+ + +ale+ + + ++++     Le +++++l+   ev++ l  ++   i +++s i  lp+ d+++
  gi|119719806|ref|YP_920301.1|  75 RLAESLESYGASLQRVAAALEDlLRVVDSAESLLRRLE-DVKQALESWAEVFQGLNASLYGeIAREISRIERLPQEDYQD 153
                                    55566677777777777777776666666666667777.77777777777777777777665777777777777777777 PP

                            LXG 143 vkdslqkakkkvqet 157
                                    vk+  +k ++ ++e 
  gi|119719806|ref|YP_920301.1| 154 VKEFHDKLEDLLDEA 168
                                    776666666655543 PP

>> PqqD  Coenzyme PQQ synthesis protein D (PqqD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1      0.13        72      22      62 ..     124     162 ..     119     164 .. 0.77
   2 ?    5.6   0.0     0.036        20      32      67 .]     285     316 ..     261     316 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.13
                                    HHHH-SSSS-.HHHHHHHHHHHCT--HHHHHHHHHHHHHHHH CS
                           PqqD  22 iWklldgers.veeivaalaeeydvdeeeaeadvlafldqLr 62 
                                    +++ l+   s   ei+ +++++   + +e ++dv +f d+L+
  gi|119719806|ref|YP_920301.1| 124 VFQGLNA--SlYGEIAREISRIERLP-QEDYQDVKEFHDKLE 162
                                    5666655..33788999998887888.889*********997 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.036
                                    HHHHHHHHHHHCT--HHHHHHHHHHHHHHHHCTT-- CS
                           PqqD  32 veeivaalaeeydvdeeeaeadvlafldqLrekgli 67 
                                    + e+v+ +++++  +    +advl++l++L ++g+i
  gi|119719806|ref|YP_920301.1| 285 LTELVEYVSRRTSYP----HADVLKTLYDLSSRGVI 316
                                    667777777777555....79*************97 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.24   1.3e+02      10      79 ..      72     144 ..      69     149 .. 0.70
   2 ?    6.6   0.8    0.0072         4       8      90 ..     148     233 ..     143     274 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.24
                          TMPIT  10 efkeleetakeykqkleelsklqsk...cskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerk 79 
                                    e+++l e+ ++y ++l+++++  ++   ++ ++++  +rl+++k++l++  +  +  +++ + e+++e+++++
  gi|119719806|ref|YP_920301.1|  72 EAERLAESLESYGASLQRVAAALEDllrVVDSAESLLRRLEDVKQALESWAEVFQGLNASLYGEIAREISRIE 144
                                    5667777777777777777766665111456667777888888888888888888888888888888887766 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0072
                          TMPIT   8 ekefkeleetakeykqkleelsklqskcskeikkq....kkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlk 83 
                                    ++++++++e +++++  l+e ++l  + ++e +k      ++l++ ++ l++ ++ +  +e+ ++e l + l++ ++ l+
  gi|119719806|ref|YP_920301.1| 148 QEDYQDVKEFHDKLEDLLDEAERLSARARSEYNKLvelaLRELEATREVLQRAESVAALHEKARLEALGSALQRVEQELR 227
                                    67899999999999999999988888888877775211145666666677777777778999999999999999999999 PP

                          TMPIT  84 evesllp 90 
                                    ++ ++ p
  gi|119719806|ref|YP_920301.1| 228 SLRQS-P 233
                                    88776.3 PP

>> Helo_like_N  Fungal N-terminal domain of STAND proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.3     0.028        15      22      96 ..      95     169 ..      77     183 .. 0.74
   2 ?    6.4   0.9    0.0092       5.2      34      81 ..     178     226 ..     172     239 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.028
                    Helo_like_N  22 ksLyetvksfrsrdktvreLkeeleaLeevLesLeevavaeeeselalLklpllrCgkaCkefeqvikkcskkss 96 
                                      L ++v+s  s  +++ + k+ le+ +ev + L+     e + e++ +++  ++  +  kef++ ++++   ++
  gi|119719806|ref|YP_920301.1|  95 EDLLRVVDSAESLLRRLEDVKQALESWAEVFQGLNASLYGEIAREISRIERLPQEDYQDVKEFHDKLEDLLDEAE 169
                                    457778888888888888888999999999999988444777788888888888888888888888887777654 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0092
                    Helo_like_N  34 rdktvreL.keeleaLeevLesLeevavaeeeselalLklpllrCgkaC 81 
                                    + +++ eL  +elea +evL+  e+va+ +e++ l++L   l+r ++  
  gi|119719806|ref|YP_920301.1| 178 EYNKLVELaLRELEATREVLQRAESVAALHEKARLEALGSALQRVEQEL 226
                                    555555552589*************9999***********999988765 PP

>> DUF1759  Protein of unknown function (DUF1759)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.068        38      93     121 ..      95     123 ..      77     130 .. 0.85
   2 ?    4.9   0.2      0.04        23      76     134 ..     135     193 ..     127     205 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.068
                        DUF1759  93 sqlrrivdavneivralealgeeadkyda 121
                                    + l r+vd ++ ++r le + +  + +  
  gi|119719806|ref|YP_920301.1|  95 EDLLRVVDSAESLLRRLEDVKQALESWAE 123
                                    67899**************9999998765 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.04
                        DUF1759  76 ellnelmklpslkeedasqlrrivdavneivralealgeeadkydailvsllleKldee 134
                                    e   e+ +++ l +ed + ++++ d+++ ++   e+l+  a+     lv l l+ l++ 
  gi|119719806|ref|YP_920301.1| 135 EIAREISRIERLPQEDYQDVKEFHDKLEDLLDEAERLSARARSEYNKLVELALRELEAT 193
                                    55678888899999**********************99999988888999988888764 PP

>> RPW8  Arabidopsis broad-spectrum mildew resistance protein RPW8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1       3.5     2e+03      45      78 ..      28      61 ..       3      64 .. 0.68
   2 ?    1.9   0.0      0.28   1.6e+02      52      86 ..      81     115 ..      70     123 .. 0.59
   3 ?    7.8   0.2    0.0043       2.4      27      78 ..     118     171 ..     103     180 .. 0.79
   4 ?   -2.7   0.0       7.8   4.4e+03      52      64 ..     213     225 ..     188     235 .. 0.59

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 3.5
                           RPW8 45 tPvvkeieklnkeldrpreeieeLkklLekaekL 78
                                   + +++++e+l  +++++ +    L +l ek  kL
  gi|119719806|ref|YP_920301.1| 28 AQNMEKVEELYRAVQSRGSSNPLLGRLVEKTLKL 61
                                   4567788888888887777777777777777666 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.28
                           RPW8  52 eklnkeldrpreeieeLkklLekaekLVekcsklk 86 
                                    e+  + l+r  + +e+L +  ++ae+L+++   +k
  gi|119719806|ref|YP_920301.1|  81 ESYGASLQRVAAALEDLLRVVDSAESLLRRLEDVK 115
                                    44445555556666666666666666665554444 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0043
                           RPW8  27 sldfksilkrLestle.ritPvvkeieklnkel.drpreeieeLkklLekaekL 78 
                                      + +  ++ L++ l  +i+  + +ie+l +e  +  +e +++L++lL++ae+L
  gi|119719806|ref|YP_920301.1| 118 LESWAEVFQGLNASLYgEIAREISRIERLPQEDyQDVKEFHDKLEDLLDEAERL 171
                                    5555566777777775479999*******9999899****************98 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 7.8
                           RPW8  52 eklnkeldrpree 64 
                                    e l  +l+r ++e
  gi|119719806|ref|YP_920301.1| 213 EALGSALQRVEQE 225
                                    3333333333333 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       3.2   1.8e+03      43      61 ..      24      42 ..      18      46 .. 0.64
   2 ?    8.9   0.2    0.0033       1.9      39      88 ..      73     122 ..      70     126 .. 0.82
   3 ?    2.3   0.3      0.37   2.1e+02      31      60 ..     149     175 ..     135     198 .. 0.53
   4 ?    1.1   0.1       0.9     5e+02      12      55 ..     187     231 ..     176     239 .. 0.48

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 3.2
                        BLOC1_2 43 aaslekkleklnekyeelq 61
                                      +++++ek++e+y ++q
  gi|119719806|ref|YP_920301.1| 24 STTTAQNMEKVEELYRAVQ 42
                                   4455667777777776665 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0033
                        BLOC1_2  39 lkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeys 88 
                                     ++ a+sle+    l++  ++l+ +l+ +d  e  +++Le++ ++L+++ 
  gi|119719806|ref|YP_920301.1|  73 AERLAESLESYGASLQRVAAALEDLLRVVDSAESLLRRLEDVKQALESWA 122
                                    56778888888888999999999999999999999999999999999886 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.37
                        BLOC1_2  31 aasekykklkdvaaslekkleklnekyeel 60 
                                    +  + +k+  d++++l +++e+l+   +  
  gi|119719806|ref|YP_920301.1| 149 EDYQDVKEFHDKLEDLLDEAERLS---ARA 175
                                    333333333344444444444333...333 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.9
                        BLOC1_2  12 eaeleatvedyklLeklNe.aasekykklkdvaaslekkleklne 55 
                                      eleat+e ++  e +   +  ++ ++l ++++ +e++l  l++
  gi|119719806|ref|YP_920301.1| 187 LRELEATREVLQRAESVAAlHEKARLEALGSALQRVEQELRSLRQ 231
                                    444444444444444443212334445555555555555554444 PP

>> Phage_GPO  Phage capsid scaffolding protein (GPO) serine peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.17        98     195     250 ..      79     134 ..      13     145 .. 0.75
   2 ?    7.6   2.3    0.0046       2.6     168     248 ..     148     233 ..     136     254 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.17
                      Phage_GPO 195 rfadveeavelvAeevkelsekveallaleaelaalkkeveklkaeleaLkekLsk 250
                                       +   ++++vA+++++l   v+++++l ++l+++k+++e+ ++ ++ L+++L  
  gi|119719806|ref|YP_920301.1|  79 SLESYGASLQRVAAALEDLLRVVDSAESLLRRLEDVKQALESWAEVFQGLNASLYG 134
                                    44455566777777777777777777777777777777777777777777777654 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0046
                      Phage_GPO 168 eeeeeegeslferikallskkkksddarfadveeavelvAeevkelsekveall.....aleaelaalkkeveklkaele 242
                                    +e+ ++ +++ ++++ ll + ++ +    ++ ++ vel  +e+++++e +++++     +++a+l+al +++++ ++el+
  gi|119719806|ref|YP_920301.1| 148 QEDYQDVKEFHDKLEDLLDEAERLSARARSEYNKLVELALRELEATREVLQRAEsvaalHEKARLEALGSALQRVEQELR 227
                                    555566899******************************99999999888866666666778888888888999999998 PP

                      Phage_GPO 243 aLkekL 248
                                    +L+++ 
  gi|119719806|ref|YP_920301.1| 228 SLRQSP 233
                                    888764 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   1.2   0.00014     0.079      81     178 ..      74     174 ..      16     186 .. 0.85
   2 ?    1.4   6.7      0.54     3e+02      75     156 ..     145     231 ..     140     270 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00014
                        UPF0242  81 d...eglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelkleleeqLaekqellqeyqet 157
                                    +   e+l+    +l+ + +  e+L + +d+ e++l+rl+  +q L++ +e  +  ++ l  e+  ++ + + l qe  + 
  gi|119719806|ref|YP_920301.1|  74 ErlaESLESYGASLQRVAAALEDLLRVVDSAESLLRRLEDVKQALESWAEVFQGLNASLYGEIAREISRIERLPQEDYQD 153
                                    244466666666899999999999999***************************************************** PP

                        UPF0242 158 ieeqrsvlekrqdqieqLesk 178
                                    ++e +  le   d+ e+L ++
  gi|119719806|ref|YP_920301.1| 154 VKEFHDKLEDLLDEAERLSAR 174
                                    ***************999887 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.54
                        UPF0242  75 aklteldeglktkeealeelqeeeeeLkee.....ldakeeelerlkeenqqLqekleaiaedfeelkle.leeqLaekq 148
                                    ++ +e  +++k+ +++le+l +e e+L  +      +  e +l++l+   + Lq ++e +a+  e+ +le l ++L++ +
  gi|119719806|ref|YP_920301.1| 145 RLPQEDYQDVKEFHDKLEDLLDEAERLSARarseyNKLVELALRELEATREVLQ-RAESVAALHEKARLEaLGSALQRVE 223
                                    555666688999999999999999999888676643344556777777777777.5555444444443331556666666 PP

                        UPF0242 149 ellqeyqe 156
                                    + l  +++
  gi|119719806|ref|YP_920301.1| 224 QELRSLRQ 231
                                    65555554 PP

>> ISG65-75  Invariant surface glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       2.6   1.5e+03      90     109 ..      23      42 ..       5      47 .. 0.63
   2 ?    9.6   1.2   0.00089       0.5      63     137 ..     144     218 ..     129     231 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2.6
                       ISG65-75  90 kgtltesdaeklkkaceeAk 109
                                     +t+t++++ek+++++++++
  gi|119719806|ref|YP_920301.1|  23 ASTTTAQNMEKVEELYRAVQ 42 
                                    44555555555555555444 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00089
                       ISG65-75  63 layienakekvdyyvekleslleeakekgtltesdaeklkkaceeAkaknkkarekakkalekaekaskkakeaa 137
                                    ++  +++ + v++ ++kle+ll+ea+  +    s+ +kl +++   ++++++  ++a+ +++ +eka  +a  +a
  gi|119719806|ref|YP_920301.1| 144 ERLPQEDYQDVKEFHDKLEDLLDEAERLSARARSEYNKLVELALRELEATREVLQRAESVAALHEKARLEALGSA 218
                                    4555788999**************888788888888888777777777888888888888888888777776666 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       3.6     2e+03      63      93 ..     108     115 ..      71     144 .. 0.55
   2 ?    9.4   1.8    0.0031       1.7      18      96 ..     148     226 ..     133     231 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 3.6
                   Occludin_ELL  63 lqeykklkkdpeyqekkkrceyLkekLshiK 93 
                                    l                       ++L+ +K
  gi|119719806|ref|YP_920301.1| 108 L-----------------------RRLEDVK 115
                                    1.......................1222222 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0031
                   Occludin_ELL  18 nkeYkeYkelhaeleevskkfseLerelkelkegskeykkieeeilqeykklkkdpeyqekkkrceyLkekLshiKkli 96 
                                    +++Y+  ke h++le++ ++ ++L+++ ++  ++  e + +e e  +e  +  ++ + +++k+r+e L + L+ + + +
  gi|119719806|ref|YP_920301.1| 148 QEDYQDVKEFHDKLEDLLDEAERLSARARSEYNKLVELALRELEATREVLQRAESVAALHEKARLEALGSALQRVEQEL 226
                                    6799999999999999999999999999988888887777777777888888899999999999999999999877765 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1      0.26   1.4e+02      25     123 ..      19     113 ..       8     121 .. 0.53
   2 ?    3.6   0.1      0.12        69      34     121 ..      84     171 ..      67     181 .. 0.59
   3 ?    5.1   0.8     0.043        24      49     130 ..     149     231 ..     123     236 .. 0.59

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.26
                                    CCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHH CS
                      Fib_alpha  25 lllkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesni 104
                                    +l+k  +++ +++ek+e+  + ++++ ++   l + ++++l+  +  +++  +  ++++++le     + +++++    +
  gi|119719806|ref|YP_920301.1|  19 YLSKASTTTAQNMEKVEELYRAVQSRGSSNPLLGRLVEKTLKLLKVPEPPGISEAERLAESLE----SYGASLQRVAAAL 94 
                                    455555555555555555555555555555555555555544444444443333333333333....5555555555666 PP

                                    HHHHHHHHHHHHHHHHHHH CS
                      Fib_alpha 105 rvLqnvlesneqkiqkLeq 123
                                    + L  v++s e+ + +Le 
  gi|119719806|ref|YP_920301.1|  95 EDLLRVVDSAESLLRRLED 113
                                    6666666666666666654 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.12
                                    CHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHH CS
                      Fib_alpha  34 kkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnvles 113
                                      +l+++   le++ +   +ae+l ++++d+ ++ ++ ++  + +  ++  e+ +ei+r+++  ++  + +++  + le+
  gi|119719806|ref|YP_920301.1|  84 GASLQRVAAALEDLLRVVDSAESLLRRLEDVKQALESWAEVFQGLNASLYGEIAREISRIERLPQEDYQDVKEFHDKLED 163
                                    45566666666666666666666666666664444444443355555555555556666666666666666666666666 PP

                                    HHHHHHHH CS
                      Fib_alpha 114 neqkiqkL 121
                                    +  + ++L
  gi|119719806|ref|YP_920301.1| 164 LLDEAERL 171
                                    55555555 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.043
                                    CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHH..HHHHHHHHHHHHHHHHH CS
                      Fib_alpha  49 nstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqn..vlesneqkiqkLeqdid 126
                                    + +++++e   +++d l e+++ ++   + ++k+ +    + l+  +++ +  +++ +L +   le++ + +q+ eq+  
  gi|119719806|ref|YP_920301.1| 149 EDYQDVKEFHDKLEDLLDEAERLSARARSEYNKLVELA-LRELEATREVLQRAESVAALHEkaRLEALGSALQRVEQELR 227
                                    45566666666666666666666665555555543322.23445555566666666666431145566666666666655 PP

                                    HHHH CS
                      Fib_alpha 127 qker 130
                                    ++++
  gi|119719806|ref|YP_920301.1| 228 SLRQ 231
                                    5544 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   9.1     0.014         8     141     259 ..     103     229 ..      11     275 .. 0.61

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.014
                   Exonuc_VII_L 141 dkaeleeqleelerrlekaikrlleekkqrleklasrlkspeellerkrqrldeleerleralkkq......lkkkrerl 214
                                    + + l+++le++++ le+ ++     +++   ++a+++++ e+l +++ q ++e++++le  l+++      ++++ ++l
  gi|119719806|ref|YP_920301.1| 103 SAESLLRRLEDVKQALESWAEVFQGLNASLYGEIAREISRIERLPQEDYQDVKEFHDKLEDLLDEAerlsarARSEYNKL 182
                                    33444455555555444444333333333333333444444444444444444444444442222211111133333333 PP

                   Exonuc_VII_L 215 eelkerlk.....ekleekkerlkklkerlelleekkerleeleekleal 259
                                     el+  l+     +++ +++e++++l+e+ + le+  ++l+++e++l++l
  gi|119719806|ref|YP_920301.1| 183 VELA--LReleatREVLQRAESVAALHEKAR-LEALGSALQRVEQELRSL 229
                                    3333..1122233333333334444433333.444444444444444444 PP

>> PDDEXK_1  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1      0.29   1.6e+02      24     113 ..      36     120 ..      28     140 .. 0.49
   2 ?    6.0   4.7     0.018       9.8      39     115 ..     156     234 ..     139     266 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.29
                       PDDEXK_1  24 gl.re.eeelea.pdlGtlvHaaleefyewkkldke..dleelleeaveelwpellleeeilessarlrylaeklkevle 98 
                                     l r+  ++ ++ p lG+lv ++l+ +    +++ +  ++e+l+ e +e + ++l               +  ++ + +e
  gi|119719806|ref|YP_920301.1|  36 ELyRAvQSRGSSnPLLGRLVEKTLKLLKVP-EPP-GisEAERLA-ESLESYGASLQRVA-------AALEDLLRVVDSAE 105
                                    444445344444158999999999877662.222.234555555.44443333322222.......22233333333344 PP

                       PDDEXK_1  99 klverlaeeleakrg 113
                                    +l++rl++ ++a ++
  gi|119719806|ref|YP_920301.1| 106 SLLRRLEDVKQALES 120
                                    444444444444333 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.018
                       PDDEXK_1  39 lvHaaleefye.wkkldkedleelleeaveelwpellleeeilessarlrylaekl.kevleklverlaeeleakrg.fr 115
                                     +H+ le++ +  ++l+ ++++e+  ++ve +++el+  +e+l+  ++ + l ek+  e+l ++++r+++el++ r+  r
  gi|119719806|ref|YP_920301.1| 156 EFHDKLEDLLDeAERLSARARSEYN-KLVELALRELEATREVLQRAESVAALHEKArLEALGSALQRVEQELRSLRQsPR 234
                                    59******99977778888999999.9***************98888887777776233444445555555555444333 PP

>> Rx_N  Rx N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   5.2     0.076        43       3      84 ..      91     177 ..      50     183 .. 0.72
   2 ?    2.5   5.6      0.31   1.7e+02       5      52 ..     157     208 ..     154     237 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.076
                           Rx_N   3 sallqkLadllaeea...kllkgvkeeleklkdeLesiqavLedaeerqi..kdeavkeWlkelrdlaydaeDvlDefet 77 
                                     a+l+ L  ++ +     ++l++vk+ le++ + ++ ++a L     r+i   +   +e  +++++   ++eD+lDe e 
  gi|119719806|ref|YP_920301.1|  91 AAALEDLLRVVDSAEsllRRLEDVKQALESWAEVFQGLNASLYGEIAREIsrIERLPQEDYQDVKEFHDKLEDLLDEAER 170
                                    34444454444444456677788888888888888888888876666666323455577788888888888888888887 PP

                           Rx_N  78 ealrrks 84 
                                     ++r +s
  gi|119719806|ref|YP_920301.1| 171 LSARARS 177
                                    7777665 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.31
                           Rx_N   5 llqkLadllaeea....kllkgvkeeleklkdeLesiqavLedaeerqikde 52 
                                    + +kL+dll e      + + +  + +e   +eLe+ + vL+ ae     +e
  gi|119719806|ref|YP_920301.1| 157 FHDKLEDLLDEAErlsaRARSEYNKLVELALRELEATREVLQRAESVAALHE 208
                                    668999999998866655555566668888999********99998666444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1617  (0.0901891); expected 358.6 (0.02)
Passed bias filter:                      907  (0.0505884); expected 358.6 (0.02)
Passed Vit filter:                       109  (0.00607954); expected 17.9 (0.001)
Passed Fwd filter:                        39  (0.00217525); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              32  [number of targets reported over threshold]
# CPU time: 0.85u 0.35s 00:00:01.20 Elapsed: 00:00:00.48
# Mc/sec: 2022.25
//
Query:       gi|119719807|ref|YP_920302.1|  [L=175]
Description: cytidyltransferase-like protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.6e-13   49.1   0.0      8e-13   48.8   0.0    1.3  1  CTP_transf_like  Cytidylyltransferase-like


Domain annotation for each model (and alignments):
>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.8   0.0   4.4e-17     8e-13       1      60 [.       5      63 ..       5     115 .. 0.89

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 4.4e-17
                                   EEEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-SCSSTHHHHHHHHHHH.TT CS
                CTP_transf_like  1 lagGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkkkplasaeeRlemlela.ke 60
                                   +++G+F+p+HlGH + ++++++ ++e +ivgv+ ++ +    +++++a eR+eml++a +e
  gi|119719807|ref|YP_920302.1|  5 FYPGRFQPVHLGHVKAVRWLLERVDE-VIVGVTAAQYSYTP-ENPFTAGERIEMLRAAfRE 63
                                   589***********************.********999988.***************9744 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       248  (0.0138323); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 1122.45
//
Query:       gi|119719808|ref|YP_920303.1|  [L=213]
Description: ribonuclease HII [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.3e-48  165.5   0.0    1.5e-48  165.3   0.0    1.0  1  RNase_HII  Ribonuclease HII


Domain annotation for each model (and alignments):
>> RNase_HII  Ribonuclease HII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.3   0.0   8.2e-53   1.5e-48       1     197 [.       5     208 ..       5     209 .. 0.95

  Alignments for each domain:
  == domain 1  score: 165.3 bits;  conditional E-value: 8.2e-53
                                    EEEEEE-TT-SBS-EEEEEEEECGHHHHHHHCTTGTTGTTS-HHHHHHHHHHHH...SEEEEEEE-HHHHH...HHTTTS CS
                      RNase_HII   1 iGiDEaGrGpvlGplvvaavavekereeelkklgvkDSKkLskqkreeLaklik...kkiekrklvaeeiky..asenei 75 
                                    +GiDEaGrGp+lGp+vva v++++e+ + l+++gv DSK Ls+++r  L ++i+   ++++ r ++ +ei+   + e   
  gi|119719808|ref|YP_920303.1|   5 AGIDEAGRGPMLGPMVVAIVVCPEEKVPLLRNMGVRDSKALSPRRRLLLSRAIPsvgCSVKVRVVEPQEIDCavRGECYE 84 
                                    6**********************************************************************963334445 PP

                                    -HHHHHHHHHHHHHHHHHHTCEECCECCCE--SS.HHHHHHHHHHHHC..CEEEEETTGGGT-HHHHHHHHHHHHHHHHH CS
                      RNase_HII  76 nlneikaaltlaviklleklgvkvdeilvdgvtt.peslkkkleqiik..ikvtvekkadekyllvaaASiiAkverdee 152
                                    nln+++aa+++++i+++  +g +++ ++ d  ++ p ++++ +++ +k  +++++e+ adeky +v aASi+Ak +rde+
  gi|119719808|ref|YP_920303.1|  85 NLNHLEAAVFAQLINEVLSEG-ELEVVYMDSPDPvPSRFEERVRALLKgqVRIVAENGADEKYTIVGAASIVAKETRDEI 163
                                    99*************999887.7899****9999999***********9******************************* PP

                                    HHHHHHHCSH.--TTSSTTSHHHHHHHHHHHHH..S--TTB-TTSHH CS
                      RNase_HII 153 lellkrkpgtldkgsGyasdektrallkkgats..klpdivrlsfkt 197
                                    ++ lk+ +g  d+gsGy+sd++t  ++++++ +  ++p i+r  ++t
  gi|119719808|ref|YP_920303.1| 164 INALKKTYG--DFGSGYPSDPRTLRFAEEWVRKhgEPPPIARKEWAT 208
                                    *******98..**********************999*********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1487.26
//
Query:       gi|119719809|ref|YP_920304.1|  [L=117]
Description: hypothetical protein Tpen_0900 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.11   11.3   0.0       0.11   11.3   0.0    1.1  1  Vps16_N   Vps16, N-terminal region


Domain annotation for each model (and alignments):
>> Vps16_N  Vps16, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   5.9e-06      0.11     247     305 ..       1      60 [.       1     104 [. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.9e-06
                        Vps16_N 247 lskklleleldakdipkqiaWvgndaVvvsf.esllvlvgkagdsvqflydetanlsaEv 305
                                    +s+  +e+el++++  + +a  g + Vvv++ e+ l  + +++d +q+l +  + ls+  
  gi|119719809|ref|YP_920304.1|   1 MSQDVIEFELEEEALCEALARLGAEEVVVTMgEDILFRYPRDADVSQILSQVRSTLSILS 60 
                                    68899**************************888888899*********99999888755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.25s 00:00:00.58 Elapsed: 00:00:00.38
# Mc/sec: 931.23
//
Query:       gi|119719810|ref|YP_920305.1|  [L=319]
Description: ROK family protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.6e-59  201.1   0.0    3.1e-59  200.9   0.0    1.0  1  ROK          ROK family
     0.0033   16.5   0.0       0.13   11.2   0.0    2.2  2  Glucokinase  Glucokinase
  ------ inclusion threshold ------
      0.022   14.2   0.1        0.6    9.6   0.1    2.1  2  BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
       0.14   11.7   0.0       0.22   11.1   0.0    1.3  1  FGGY_N       FGGY family of carbohydrate kinases, N-terminal 


Domain annotation for each model (and alignments):
>> ROK  ROK family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.9   0.0   6.9e-63   3.1e-59       2     290 ..       5     308 ..       4     311 .. 0.91

  Alignments for each domain:
  == domain 1  score: 200.9 bits;  conditional E-value: 6.9e-63
                                    EEEEE-SSEEEEEEEETTS-EEEEEEEEEHC.CHHCCHHHHHHHHHHCCCHCCHTEEEEEEEEESSEEETTCCEBSSGGC CS
                            ROK   2 igidiGgtkialalvdeegeilarekvetpt.etteetlvdaiaelvdeaerkadeliavgigspGlisdksgkivstpn 80 
                                    +++diG+t++++al+++egeil+ + ++t+  + + e l++  + +++ ++++  e+ ++g+gspG+++ k+g +++  n
  gi|119719810|ref|YP_920305.1|   5 VAVDIGATQTRVALGNDEGEILELHVFKTSSfPGPDEYLRHIAGLALSLEKKHGVEVEGIGVGSPGPLDMKKGEVLKSVN 84 
                                    79*************************6654267888885555555666666777888********************** PP

                                    GCCCCTTHHHHHHHHHTS-EEEEEHHHHHHHHHHHHCTTTTTS-EEEEEESSSEEEEEEETTEEE--TTS-TT-GGGSBS CS
                            ROK  81 itwenfdlvekleerlnvpvevenDvnaaalaEavfgaskdvenviyvtvgtGvGaGviingklitGrnGvagelGHiql 160
                                    +  +  ++v++l++ ++  v ++nD+  aa++E+++ga  + en++yvt++tG+GaG+ ++g+l+ G++G+a e+GH+ +
  gi|119719810|ref|YP_920305.1|  85 MPFDRLPVVSALKSLTGKKVAFANDAVTAAVGEKYWGAGRGLENLVYVTISTGIGAGIYVDGELLLGKHGNAHEVGHVVV 164
                                    ******************************************************************************** PP

                                    -.TTS-B-TTS-BSBHHHCCSHHHHHHCHTC...............CGTTS-HHHHHHHHCTT-HHHHHHHHHHHHHHHH CS
                            ROK 161 d.pegekcgCGnqgClEtlasgralekraqq...............kgekleakeiiklaekgdevaeevverlaeylak 224
                                    d  e+  cgCG++g +E+++sg ++ ++a+                + e l+ak+++ ++++gd  a  v+er+ +  a 
  gi|119719810|ref|YP_920305.1| 165 DsGEEMTCGCGKKGHWEAYCSGSGIPRYAKFlaarnpelweksplkSREPLTAKDVFDAFREGDALARLVMERVRKFNAY 244
                                    *777788********************999999************999******************************** PP

                                    HHHHHHHHH--SEEEEEHCCC.TSTTHH.HHHHHHHHHCCTTTTCCCT-EEEE-S-STTHHHHHHHHH CS
                            ROK 225 aiadlinlfdpqaivlgGgvs.eadkll.eairklvkkylnkklevpvveivaaklgdkagllGaaaL 290
                                    + a l+n++dp+ i +gG+v  + +++l + ++++v+ky+++  +    ei+   lgdk g+lGa+aL
  gi|119719810|ref|YP_920305.1| 245 GFAVLVNVYDPEIITVGGSVAlNNPDVLlAGLKEEVEKYALNVVP----EIRLTPLGDKIGVLGALAL 308
                                    ********************7334455559999999999876544....477899***********98 PP

>> Glucokinase  Glucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0   2.9e-05      0.13       2      48 ..       6      49 ..       5     122 .. 0.79
   2 !    3.2   0.0    0.0082        37     186     235 ..     180     236 ..     174     248 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2.9e-05
                    Glucokinase  2 agDiGGTkarlalveaeeeelelleiekyasadyasleealqaflae 48
                                   a DiG T++r+al ++e+e    le ++++++ +++ +e l+++   
  gi|119719810|ref|YP_920305.1|  6 AVDIGATQTRVALGNDEGEI---LELHVFKTSSFPGPDEYLRHIAGL 49
                                   67***************999...9999************99987653 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.0082
                    Glucokinase 186 aErvlSGpGLvnlyealaaad.......kleeel.....lepaeiteaalegedplareale 235
                                    +E  +SG+G+ + +++laa++            l     l+++++ +a   ++d+lar ++e
  gi|119719810|ref|YP_920305.1| 180 WEAYCSGSGIPRYAKFLAARNpelweksP----LksrepLTAKDVFDAF-REGDALARLVME 236
                                    6899****************977765442....1344458888888876.567788888876 PP

>> BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1   0.00013       0.6       3      46 ..       7     113 ..       5     147 .. 0.61
   2 ?    3.0   0.0     0.013        60     219     265 ..     255     307 ..     209     309 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00013
                                    EEE-SSEEEEEEEETTTEEEEEEEE--..................................................... CS
                    BcrAD_BadFG   3 iDgGsTttkavlmdekgevlgrgitns..................................................... 29 
                                    +D+G+T t+++l +++ge+l   + ++                                                     
  gi|119719810|ref|YP_920305.1|   7 VDIGATQTRVALGNDEGEILELHVFKTssfpgpdeylrhiaglalslekkhgvevegigvgspgpldmkkgevlksvnmp 86 
                                    9*****************99887777735555555555555555555555555555555555555555555555555555 PP

                                    ..........TTS-HHH.........H CS
                    BcrAD_BadFG  30 ..........anlesvrfeaaekvlee 46 
                                              ++l++ +++ a + +  
  gi|119719810|ref|YP_920305.1|  87 fdrlpvvsalKSLTGKKVAFANDAVTA 113
                                    555555555555555555555555555 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.013
                                    ...EEEESGGGG-HH..HHHHH.....HHHH-S..-EE--GGGGGHHHHHHHH CS
                    BcrAD_BadFG 219 e..vtltGGvaknea..avkelrklvkenygev..kininpdsiytgalGAal 265
                                       +t+ G+va n++  ++  l++ v++  ++v  +i  +p  +  g+lGA+ 
  gi|119719810|ref|YP_920305.1| 255 PeiITVGGSVALNNPdvLLAGLKEEVEKYALNVvpEIRLTPLGDKIGVLGALA 307
                                    13488888899997622456667777776666666777777888888888875 PP

>> FGGY_N  FGGY family of carbohydrate kinases, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   4.8e-05      0.22       1      29 [.       3      31 ..       3      46 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.8e-05
                                   EEEEEEEESSEEEEEEEETTS-EEEEEEE CS
                         FGGY_N  1 lilglDcGttstkaivldekgkvvasaqa 29
                                   +++++D+G+t+t++++ + +g++++ +  
  gi|119719810|ref|YP_920305.1|  3 YAVAVDIGATQTRVALGNDEGEILELHVF 31
                                   789********************987755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2307.74
//
Query:       gi|119719811|ref|YP_920306.1|  [L=474]
Description: cysteinyl-tRNA synthetase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   1.3e-129  431.9   0.0   1.6e-129  431.6   0.0    1.1  1  tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
    2.2e-16   59.6   0.5    9.9e-11   41.0   0.2    2.1  2  tRNA-synt_1g  tRNA synthetases class I (M)
    8.5e-09   34.2   0.0    2.9e-06   25.8   0.0    2.2  2  tRNA-synt_1   tRNA synthetases class I (I, L, M and V)
    7.5e-08   32.7   0.5    3.1e-07   30.8   0.1    2.2  2  DALR_2        DALR domain
  ------ inclusion threshold ------
      0.021   13.7   0.1       0.56    9.1   0.0    2.1  2  tRNA-synt_1f  tRNA synthetases class I (K)
      0.022   13.7   0.6      0.092   11.6   0.2    2.3  2  tRNA-synt_1c  tRNA synthetases class I (E and Q), catalytic d
      0.092   11.7   0.0       0.17   10.8   0.0    1.4  1  tRNA-synt_1d  tRNA synthetases class I (R)


Domain annotation for each model (and alignments):
>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  431.6   0.0  6.3e-133  1.6e-129       2     300 ..      15     311 ..      14     312 .. 0.97

  Alignments for each domain:
  == domain 1  score: 431.6 bits;  conditional E-value: 6.3e-133
                                    ---SBTTEEEEEEEEEBTTS--BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEBB--SHHHHHHHHHTTS-HHHHHHHHHH CS
                   tRNA-synt_1e   2 vkpleekkvtlYvCGptvydashlGhaRslvafDilrrilqalgYdvqfvqnvtDidDkiikrareeeksvkelaekfie 81 
                                    ++p+ee++v++YvCGptvyd+sh+GhaR++vafD+++r+l+ +gYdv +vqn+tDidDkii+rar+e++ ++e+++++ +
  gi|119719811|ref|YP_920306.1|  15 FEPVEEGRVSIYVCGPTVYDYSHVGHARTYVAFDVIKRYLRLRGYDVVHVQNITDIDDKIINRARDEGRDWREIVDEYTK 94 
                                    68999*************************************************************************** PP

                                    HHHHHHHHTT----SB--BGGGGHHHHHHHHHHHHHTTSEEE-TTS-EEE-GGG-TTTTTTTT--HHHHHHT----S--S CS
                   tRNA-synt_1e  82 efkkdleaLnvlkptleprvsekvdeiielvekliekgyaYavsdgdvyfdvskkeeYgklskqnleelelgaegevsee 161
                                    ++ ++l++L vl  +++prv+e+++eii++v+kli+ g+aY++ +g vyfdv ++++Yg+ls +  +++ +++e   ++e
  gi|119719811|ref|YP_920306.1|  95 DYLEALQKLRVLV-DVHPRVTEHISEIIDFVQKLIDSGHAYVAPSGSVYFDVDTYPDYGRLSGRLDKKMWSQEEF--ASE 171
                                    ************8.9***********************************************9987766555554..569 PP

                                    -SSTT-EEEEEE--TTS--B--TTSSEEE-SSHHHHHHHHHHH-SSEEEEEEEGGGTTTHHHHHHHHHHHHSS.S--EEE CS
                   tRNA-synt_1e 162 kkdkkDfaLWkaskegepswdsPwgkGRPGWhieCsvmaskllgseidihsGGiDLafPhhenelaqseaafd.kqlvky 240
                                    kk++ DfaLWka k+gep wdsPwg GRPGWhieCsvm+sk+lg+++dih+GG+DL+fPhhene aqsea+f+ k++vky
  gi|119719811|ref|YP_920306.1| 172 KKNPYDFALWKARKPGEPYWDSPWGPGRPGWHIECSVMSSKYLGRRFDIHGGGTDLIFPHHENERAQSEALFGeKPWVKY 251
                                    *************************************************************************99***** PP

                                    EEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHSS-TTS-EEE-HHHHHHHH CS
                   tRNA-synt_1e 241 flhnghlkiegekmsksLknfitikdvlkkfdprqlRllllsahyrsqldfkeelleeak 300
                                    ++h+g+l++ gekmsksLkn++ ++d+++++dp ++Rl l++ahyr+ l+f++e le+ak
  gi|119719811|ref|YP_920306.1| 252 WMHTGMLQVRGEKMSKSLKNIVPLRDLFRSYDPLVVRLWLATAHYRTVLQFSDEVLEQAK 311
                                    *********************************************************998 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   0.2   3.9e-14   9.9e-11      12     122 ..      34     142 ..      25     149 .. 0.88
   2 !   16.8   0.0   8.7e-07    0.0022     315     358 ..     252     295 ..     228     317 .. 0.84

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 3.9e-14
                                    S---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHTT---SEEEET CS
                   tRNA-synt_1g  12 gklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAekegvtpeelvekvheeikelfkklnisfdkygrt 91 
                                    +  H+Gh++++++ D++ Ry rlrg++v++v        +i  +A++eg + +e+v+++++ + e ++kl +  d + r 
  gi|119719811|ref|YP_920306.1|  34 DYSHVGHARTYVAFDVIKRYLRLRGYDVVHVQNITDIDDKIINRARDEGRDWREIVDEYTKDYLEALQKLRVLVDVHPRV 113
                                    568*****************************999999***************************************999 PP

                                    TSHHHHHHHHHHHHHHHHTT-EEEEEEEEEE CS
                   tRNA-synt_1g  92 tseehkelvqeifkklkekgliyekeieqly 122
                                    t+  h +   ++++kl + g+ y   +  +y
  gi|119719811|ref|YP_920306.1| 114 TE--HISEIIDFVQKLIDSGHAYVAPSGSVY 142
                                    86..555567899999999998876665555 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 8.7e-07
                                    EEEE--EEE--------------HHHHHHHH-HHHHHHHHHHHS CS
                   tRNA-synt_1g 315 vvaheyltvegkKlSkSrgvvvkakealerldadllRYylaaea 358
                                     + +++l+v+g+K+SkS +++v  +++  ++d+ ++R +la+++
  gi|119719811|ref|YP_920306.1| 252 WMHTGMLQVRGEKMSKSLKNIVPLRDLFRSYDPLVVRLWLATAH 295
                                    56789**********************************99854 PP

>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   0.0    0.0011       2.8      26      66 ..      24      64 ..      12      72 .. 0.87
   2 !   25.8   0.0   1.1e-09   2.9e-06     518     597 ..     219     298 ..     211     303 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0011
                    tRNA-synt_1 26 ilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyv 66
                                   ++++  P v    H+Gha + +  d++ ry r++G++v +v
  gi|119719811|ref|YP_920306.1| 24 SIYVCGPTVYDYSHVGHARTYVAFDVIKRYLRLRGYDVVHV 64
                                   6777888999999***********************99765 PP

  == domain 2  score: 25.8 bits;  conditional E-value: 1.1e-09
                    tRNA-synt_1 518 dmlleGlDiirgWvarlillslaltgsePfkevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltlilsdvgr 597
                                    d+   G D i+   ++   +s al+g++P+ +  +h  +++  G KmSKsl+N++   d+ ++y   ++Rl+l+++++  
  gi|119719811|ref|YP_920306.1| 219 DIHGGGTDLIFPHHENERAQSEALFGEKPWVKYWMHTGMLQVRGEKMSKSLKNIVPLRDLFRSYDPLVVRLWLATAHYRT 298
                                    56667899999999999999******************************************************998865 PP

>> DALR_2  DALR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.1   1.2e-10   3.1e-07       1      58 [.     354     412 ..     354     416 .. 0.86
   2 ?   -1.5   0.0       1.5   3.7e+03      19      53 ..     426     457 ..     424     466 .. 0.58

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 1.2e-10
                                    HHHHHHTBT--HHHHHHHHHHHHHHHHH..HHHTT-HHHHHHHHHHHHHHHGGGT-S-S- CS
                         DALR_2   1 kFeeaMdDDFNTaeAiavlFelakeiNr..alkeedkaaasalkallrelaevLGllqee 58 
                                    +F+++MdDDFN+  A+a++ +l   + +   +k +    ++al +l++e+  vLG+l e+
  gi|119719811|ref|YP_920306.1| 354 EFYASMDDDFNASGAFAAVMKLTGLVYSqvSAKPTYLLVLRAL-RLFEEFNRVLGVLDED 412
                                    59**************************555555566666777.*************986 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.5
                                    HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHGGGT CS
                         DALR_2  19 lFelakeiNralkeedkaaasalkallrelaevLG 53 
                                    l +l+ e++++l+e+++++++   + +r+  + LG
  gi|119719811|ref|YP_920306.1| 426 LLDLIVEVRAKLREQKNYELA---DYIRSKLSSLG 457
                                    667888888855555554444...33444444444 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1     0.022        57      36      72 ..      35      71 ..      17      97 .. 0.89
   2 ?    9.1   0.0   0.00022      0.56     276     340 ..     259     322 ..     224     339 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.022
                   tRNA-synt_1f 36 liHiGnlrevltadlvaralrkrgeevrlilisDdmD 72
                                     H+G +r  +  d++ r lr rg +v ++  + d+D
  gi|119719811|ref|YP_920306.1| 35 YSHVGHARTYVAFDVIKRYLRLRGYDVVHVQNITDID 71
                                   67************************99999888888 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00022
                   tRNA-synt_1f 276 lkggekmssSkGnvltledwlevaepevlrflilrrkPkkakkldldleilrlvdeYdklerkyf 340
                                       gekms+S  n++ l+d+++ + p v+r+ ++ ++ ++ ++++ + ++ ++  + ++l+ ++ 
  gi|119719811|ref|YP_920306.1| 259 QVRGEKMSKSLKNIVPLRDLFRSYDPLVVRLWLATAHYRTVLQFSDE-VLEQAKSNLQRLRGAVQ 322
                                    33456*****************************9999999999888.88888888888877765 PP

>> tRNA-synt_1c  tRNA synthetases class I (E and Q), catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   3.6e-05     0.092      49      97 ..      89     136 ..      30     140 .. 0.91
   2 ?   -3.3   0.0       1.2   3.2e+03     146     165 ..     433     452 ..     431     455 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.6e-05
                                    -HHHHHHHHHHHHHTT---SSEEEEGGGGHHHHHHHHHHHHHTTSEEEE CS
                   tRNA-synt_1c  49 keeaeesiledlkwlgikwdekptyqsdrfdelkkyaeeLikkGkAYvc 97 
                                    + e+++  le+l+ l +  d    + +++  e+ +++++Li +G+AYv+
  gi|119719811|ref|YP_920306.1|  89 VDEYTKDYLEALQKLRVLVDV-HPRVTEHISEIIDFVQKLIDSGHAYVA 136
                                    5799999************65.66899********************97 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.2
                                    EEESSBTTSSGGGSSTEEEE CS
                   tRNA-synt_1c 146 vRlkideessvefrDlvrgr 165
                                    vR+k+ e++++e+ D +r +
  gi|119719811|ref|YP_920306.1| 433 VRAKLREQKNYELADYIRSK 452
                                    89999999999999999865 PP

>> tRNA-synt_1d  tRNA synthetases class I (R)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   6.6e-05      0.17      19      68 ..      20      69 ..       4      74 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 6.6e-05
                                   T-EEEEE----BTTS--BHHHHHHHHHHHHHHHHHHHCT-EEEEEE--B- CS
                   tRNA-synt_1d 19 kkkvvvdfssPniakemhvGhLrstiiGdavsrlleflGydvirlnhvGD 68
                                   + +v +    P +    hvGh r+ +  d++ r l + Gydv+ +  + D
  gi|119719811|ref|YP_920306.1| 20 EGRVSIYVCGPTVYDYSHVGHARTYVAFDVIKRYLRLRGYDVVHVQNITD 69
                                   55666777889999999**************************9988877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (474 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      598  (0.0333538); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.46
# Mc/sec: 3065.40
//
Query:       gi|119719812|ref|YP_920307.1|  [L=296]
Description: hypothetical protein Tpen_0903 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.063   12.1   0.0       0.11   11.3   0.0    1.4  1  Fe-ADH    Iron-containing alcohol dehydrogenase


Domain annotation for each model (and alignments):
>> Fe-ADH  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   5.9e-06      0.11      69     148 ..      48     125 ..       3     135 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.9e-06
                                    HHHHHHTTS-TT.--EEEEEESHHHHHHHHHHHHHTT...................--EEEEESS-S-S-TT-SEEEEE. CS
                         Fe-ADH  69 eveeaaalareegadvviavGGGsviDtAKaialllanpe.vedylgegkakkkkalpliaiPTtaGtGsevtplavitd 147
                                     +e++ a+++e+ga  ++++GG  ++ +AK++a    +++ +++++       k+a+++  +P  ++ +   + l  ++d
  gi|119719812|ref|YP_920307.1|  48 GLEKVHAAIHESGARRIVGLGGLPAVNAAKVLASPRLRGKsLREVYY---DERKPAVEVLLVPLEPAYCTDLSDLVLVYD 124
                                    5678889999***********************99998745666662...234678999999999998888888888885 PP

                                    - CS
                         Fe-ADH 148 e 148
                                    +
  gi|119719812|ref|YP_920307.1| 125 S 125
                                    4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1981.95
//
Query:       gi|119719813|ref|YP_920308.1|  [L=249]
Description: ABC transporter related [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.7e-34  117.1   0.0      1e-33  116.7   0.0    1.2  1  ABC_tran      ABC transporter
      3e-08   33.8   0.0    0.00054   19.9   0.0    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
      2e-05   24.2   0.2     0.0089   15.5   0.0    2.1  2  SMC_N         RecF/RecN/SMC N terminal domain
    0.00012   21.7   0.0    0.00022   20.9   0.0    1.3  1  AAA_29        P-loop containing region of AAA domain
      0.003   16.6   0.0     0.0052   15.9   0.0    1.4  1  T2SSE         Type II/IV secretion system protein
     0.0073   16.7   2.0      0.023   15.1   2.0    2.0  1  AAA_16        AAA ATPase domain
  ------ inclusion threshold ------
      0.011   15.3   0.5      0.015   14.9   0.5    1.5  1  AAA_25        AAA domain
      0.014   15.3   0.4      0.032   14.1   0.2    1.6  2  RsgA_GTPase   RsgA GTPase
      0.028   14.9   0.1         10    6.6   0.0    2.2  2  AAA           ATPase family associated with various cellular 
      0.032   14.0   0.0      0.048   13.4   0.0    1.3  1  AAA_24        AAA domain
      0.034   14.4   0.3      0.062   13.6   0.3    1.7  1  AAA_22        AAA domain
       0.05   13.3   0.0       0.11   12.1   0.0    1.6  1  AAA_30        AAA domain
      0.055   13.4   0.0       0.13   12.1   0.0    1.5  2  ATPase_2      ATPase domain predominantly from Archaea
      0.062   12.1   0.2        6.8    5.4   0.0    2.2  2  ABC_ATPase    Predicted ATPase of the ABC class
      0.064   12.6   0.0       0.69    9.3   0.0    2.0  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.085   13.0   0.1       0.18   11.9   0.1    1.6  1  AAA_33        AAA domain
      0.086   11.8   0.0       0.15   11.1   0.0    1.3  1  DUF3987       Protein of unknown function (DUF3987)
       0.09   11.5   0.0       0.13   11.0   0.0    1.1  1  RNA12         RNA12 protein
       0.11   12.4   0.1        0.2   11.6   0.1    1.4  1  NACHT         NACHT domain
        0.2   12.2   0.2       0.47   11.0   0.1    1.6  1  AAA_18        AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.7   0.0   1.1e-36     1e-33       2     137 .]      22     169 ..      21     169 .. 0.95

  Alignments for each domain:
  == domain 1  score: 116.7 bits;  conditional E-value: 1.1e-36
                                    EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG..B-HHHCCHCEEEE-SS--S-TTSBHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke..qeleslrkeigvlpqepqlfpeltvren 79 
                                    + vsl++++gekv+++G++G+GKStLlk+   l+kp +G+++ldg++l++   +l+++r++ g+++q  +lfp+++v +n
  gi|119719813|ref|YP_920308.1|  22 RGVSLSVRRGEKVVVMGPSGSGKSTLLKVAVLLVKPWKGRVWLDGEELTSgrVDLRKARAKTGFVFQSYNLFPHMKVIDN 101
                                    679***********************************************999*************************** PP

                                    ..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    ..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ..............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                                   ++e+++ +l+++gl +++++       +LSgGq+qrva+aral+ +p +l+lDEpt+
  gi|119719813|ref|YP_920308.1| 102 valplrivkgydkaRAREKAASLLRQVGLAGFEEKYP----LQLSGGQQQRVAIARALAMDPVILFLDEPTS 169
                                    **********987777777999999999999999998....*****************************96 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   0.00013      0.11       3      22 ..      35      54 ..      33      82 .. 0.85
   2 !   19.9   0.0   6.1e-07   0.00054     235     297 ..     139     198 ..      87     202 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                         AAA_21  3 vliGpNgsGKSnLLdaldll 22
                                   v+ Gp gsGKS+LL+   ll
  gi|119719813|ref|YP_920308.1| 35 VVMGPSGSGKSTLLKVAVLL 54
                                   789************99887 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 6.1e-07
                         AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                     +lS G+++  a++ al+ ++    +l++DEp + L+P+l  ++l++l e ++ g+  +++TH
  gi|119719813|ref|YP_920308.1| 139 LQLSGGQQQRVAIARALAMDP---VILFLDEPTSALDPELKGEVLDVLLEVAKQGIAMLAVTH 198
                                    367999999999999999999...69**********************888888********9 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.1    0.0036       3.2      27      42 ..      34      49 ..      23      56 .. 0.84
   2 !   15.5   0.0   9.9e-06    0.0089     136     209 ..     140     211 ..      61     220 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0036
                                   EEEEESTTSSHHHHHH CS
                                   xxxxxxxxxxxxxxxx RF
                          SMC_N 27 taivGpNGSGKsnlld 42
                                    +++Gp GSGKs ll 
  gi|119719813|ref|YP_920308.1| 34 VVVMGPSGSGKSTLLK 49
                                   5899********9975 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 9.9e-06
                                    CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-.SCEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx.xxxx RF
                          SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreemleka.dklv 209
                                    +LSgG+++ va+a  +A+    p  + +lDe  +aLD +   +v ++l e  k+   ++ ++++ ++ ++a d++v
  gi|119719813|ref|YP_920308.1| 140 QLSGGQQQRVAIARALAMD---PV-ILFLDEPTSALDPELKGEVLDVLLEVAKQgIAMLAVTHELDFAREAaDRIV 211
                                    8************999975...43.6679***************99998888776999999**9999988834444 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   2.5e-07   0.00022      15      46 ..      24      54 ..      20      61 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2.5e-07
                         AAA_29 15 htieidlkgatlltGpsGsGKSTllDAiqalL 46
                                    ++++++ + ++++GpsGsGKSTll  +++lL
  gi|119719813|ref|YP_920308.1| 24 VSLSVRRGEKVVVMGPSGSGKSTLL-KVAVLL 54
                                   56677755699*************9.444444 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   5.8e-06    0.0052     123     160 ..      25      62 ..       9      84 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.8e-06
                          T2SSE 123 rkavrerglilvsGgTgsGKttllyallkeinksderi 160
                                    + +vr+   ++v G+ gsGK+tll +++  ++  + r+
  gi|119719813|ref|YP_920308.1|  25 SLSVRRGEKVVVMGPSGSGKSTLLKVAVLLVKPWKGRV 62 
                                    567889999*****************999998776665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   2.0   2.5e-05     0.023      20      44 ..      29      51 ..      23     215 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.5e-05
                         AAA_16 20 rsgrpelvllsGesGvGKsslvrel 44
                                   r+g  e v++ G+sG+GKs+l++ +
  gi|119719813|ref|YP_920308.1| 29 RRG--EKVVVMGPSGSGKSTLLKVA 51
                                   555..5699************9654 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.5   1.6e-05     0.015      30      78 ..      28      65 ..      18     199 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.6e-05
                         AAA_25 30 lpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvs 78
                                   +++ge ++++G++g+GK+tl+    +av++ kpw g       + ++++
  gi|119719813|ref|YP_920308.1| 28 VRRGEKVVVMGPSGSGKSTLLK---VAVLLVKPWKG-------R-VWLD 65
                                   4699***************975...44555555544.......2.2222 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.2   3.6e-05     0.032      98     118 ..      30      50 ..      21      58 .. 0.86
   2 ?   -2.3   0.0         4   3.6e+03      27      63 ..     172     207 ..     168     219 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.6e-05
                                    TTSEEEEECSTTSSHHHHHHH CS
                    RsgA_GTPase  98 kdktsvlvGqSGvGKStLina 118
                                    +++ +v++G+SG GKStL+++
  gi|119719813|ref|YP_920308.1|  30 RGEKVVVMGPSGSGKSTLLKV 50 
                                    457899************975 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4
                                    TTT--HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHH CS
                    RsgA_GTPase  27 epelslnlldrfLvlaeekgiepvivlnKiDlleeee 63 
                                    +pel+ + ld +L+++ ++gi ++ v   +D + e+ 
  gi|119719813|ref|YP_920308.1| 172 DPELKGEVLD-VLLEVAKQGIAMLAVTHELDFAREAA 207
                                    4777777666.56666677777777777777666654 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0     0.011        10       1      17 [.      34      50 ..      34      89 .. 0.88
   2 ?    6.5   0.0     0.011        10      33      74 ..     132     174 ..     107     213 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.011
                                   EEEESSTTSSHHHHHHH CS
                            AAA  1 vllyGppGtGKTllaka 17
                                   v+++Gp G GK++l k 
  gi|119719813|ref|YP_920308.1| 34 VVVMGPSGSGKSTLLKV 50
                                   5789**********986 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.011
                                    TCSSSSTTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHH CS
                            AAA  33 ellskyvgesekkirelfkeakeka.kpsilfiDEidalaksr 74 
                                     + +ky  + +   ++ ++ a++ a +p+ilf+DE  +    +
  gi|119719813|ref|YP_920308.1| 132 GFEEKYPLQLSGGQQQRVAIARALAmDPVILFLDEPTSALDPE 174
                                    455667777777777778888888888********77665555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   5.3e-05     0.048       3      22 ..      32      51 ..      30      79 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.3e-05
                         AAA_24  3 lkiliyGpsgiGKTtlakel 22
                                    k++++Gpsg+GK+tl+k +
  gi|119719813|ref|YP_920308.1| 32 EKVVVMGPSGSGKSTLLKVA 51
                                   69**************9865 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.3     7e-05     0.062       8      25 ..      34      51 ..      29     188 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7e-05
                         AAA_22  8 lvvtGesGtGKTtllrrl 25
                                   +vv+G+sG+GK+tll+  
  gi|119719813|ref|YP_920308.1| 34 VVVMGPSGSGKSTLLKVA 51
                                   69************9865 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00013      0.11      20      44 ..      33      57 ..      24      71 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                         AAA_30 20 vavltGpAGtGKttalkalreawea 44
                                    +v+ Gp G+GK+t+lk+++ +++ 
  gi|119719813|ref|YP_920308.1| 33 KVVVMGPSGSGKSTLLKVAVLLVKP 57
                                   47999************99877665 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00015      0.13      22      43 ..      33      54 ..      25      68 .. 0.83
   2 ?   -2.2   0.0       3.5   3.1e+03     120     148 ..     160     186 ..     109     198 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00015
                       ATPase_2 22 iyfiYGpegsGKtaLlkeiien 43
                                    +++ Gp gsGK++Llk ++  
  gi|119719813|ref|YP_920308.1| 33 KVVVMGPSGSGKSTLLKVAVLL 54
                                   589**************98865 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.5
                       ATPase_2 120 iiiiiDelqklidlglngaellvkeLlnl 148
                                    +i+++De   + d  l+  +++++ Ll++
  gi|119719813|ref|YP_920308.1| 160 VILFLDEPTSALDPELK--GEVLDVLLEV 186
                                    77788888888877777..6666666665 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0    0.0075       6.8     240     301 ..      26      91 ..      11     101 .. 0.69
   2 ?    4.6   0.0     0.013        12     324     376 ..     142     194 ..     139     216 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0075
                                    EEE-SS.EEEEEE-TTSSHHHHHHH...HHHCCSEE-TTSS-TTEEE-TT-EEE---TT--EEEE- CS
                     ABC_ATPase 240 mgipkG.vtlIvGggfhGKsTLLeA...lekGvynhvpgDGRefvvtdktavkiraEdgrsvkgvD 301
                                    + +++G  ++++G+   GKsTLL+    l k    +v  DG e+   + ++ k ra +g   ++ +
  gi|119719813|ref|YP_920308.1|  26 LSVRRGeKVVVMGPSGSGKSTLLKVavlLVKPWKGRVWLDGEELTSGRVDLRKARAKTGFVFQSYN 91 
                                    467888667899***********9523234444556666777777667777777776666665555 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.013
                                    -HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HHHHHHS-GGG--B--H CS
                     ABC_ATPase 324 SGStsqAanimealeagakllLiDEDtsAtNlmirDermqelvskekepitpl 376
                                    SG   q ++i++al ++  +l +DE tsA    ++ e ++ l++  k++i  l
  gi|119719813|ref|YP_920308.1| 142 SGGQQQRVAIARALAMDPVILFLDEPTSALDPELKGEVLDVLLEVAKQGIAML 194
                                    99999************************877777777777776666666665 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00077      0.69      17      52 ..      26      61 ..      15      90 .. 0.77
   2 ?    1.1   0.0      0.24   2.1e+02      92     128 ..     143     185 ..     136     210 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00077
                   Mg_chelatase 17 iaaaGgHnlllvGppGsGKtmlakrlpsllpplsee 52
                                   +++  g +++++Gp+GsGK+ l k    l+ p + +
  gi|119719813|ref|YP_920308.1| 26 LSVRRGEKVVVMGPSGSGKSTLLKVAVLLVKPWKGR 61
                                   55666778999***********99888777776655 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.24
                   Mg_chelatase  92 GggskpkpGeislahn.GvLfLDEl.....pefkrkvlevLRe 128
                                    Gg+++    + +la    +LfLDE      pe+k +vl+vL e
  gi|119719813|ref|YP_920308.1| 143 GGQQQRVAIARALAMDpVILFLDEPtsaldPELKGEVLDVLLE 185
                                    554444444445555414699**95334447899999999866 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1    0.0002      0.18       2      17 ..      34      49 ..      34      75 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0002
                         AAA_33  2 vllvGlpGsGKstlae 17
                                   v++ G++GsGKstl++
  gi|119719813|ref|YP_920308.1| 34 VVVMGPSGSGKSTLLK 49
                                   6899*********987 PP

>> DUF3987  Protein of unknown function (DUF3987)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00016      0.15      39      64 ..      34      59 ..      33      68 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00016
                        DUF3987 39 tlvvapsGerKSpvdklvlrpleeie 64
                                   ++v++psG++KS+++k+++ +++++ 
  gi|119719813|ref|YP_920308.1| 34 VVVMGPSGSGKSTLLKVAVLLVKPWK 59
                                   5899*******************996 PP

>> RNA12  RNA12 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00014      0.13      20      64 ..      34      80 ..      29     107 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00014
                          RNA12 20 ivvkGPrGSGkkeLvldrvlkdrkk..vlvidCdelvkarndaelis 64
                                   +vv GP GSGk+ L+   vl  +     + +d +el++ r d ++ +
  gi|119719813|ref|YP_920308.1| 34 VVVMGPSGSGKSTLLKVAVLLVKPWkgRVWLDGEELTSGRVDLRKAR 80
                                   89************977776544333499999999999999865443 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00022       0.2       3      25 ..      34      56 ..      32      62 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00022
                                   EEEEC-TTTCHHHHHHHHHHHHC CS
                          NACHT  3 vilqGeaGsGKTtLlqklalawa 25
                                   v++ G++GsGK+tLl+  +l+ +
  gi|119719813|ref|YP_920308.1| 34 VVVMGPSGSGKSTLLKVAVLLVK 56
                                   899************87665555 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00053      0.47       1      16 [.      34      49 ..      34      61 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00053
                         AAA_18  1 IlltGtpGvGKttlak 16
                                   ++++G++G+GK+tl k
  gi|119719813|ref|YP_920308.1| 34 VVVMGPSGSGKSTLLK 49
                                   789**********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                       108  (0.00602376); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 1749.65
//
Query:       gi|119719814|ref|YP_920309.1|  [L=218]
Description: polar amino acid ABC transporter, inner membrane subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      3e-17   63.0   6.2      3e-17   63.0   6.2    1.7  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.4     0.019   3.4e+02     109     140 ..      18      45 ..      11      52 .. 0.62
   2 !   63.0   6.2   1.7e-21     3e-17      14     184 ..      45     211 ..      32     212 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.019
                   BPD_transp_1 109 piitglilafggllggavlleflgswpGlgtl 140
                                    +++t+ i ++ +llg a+ + +lg    l+++
  gi|119719814|ref|YP_920309.1|  18 VVVTLQISVISFLLGLALGIALLG----LSLT 45 
                                    456666666666666666666666....4444 PP

  == domain 2  score: 63.0 bits;  conditional E-value: 1.7e-21
                   BPD_transp_1  14 kkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalrslpkdlveaaralGas 93 
                                      l+ l r +i+ ++++P +v ++l+++ +  ++i  +++++ +++l l +a+y   i+r+al+s+p+ ++  a+ lG s
  gi|119719814|ref|YP_920309.1|  45 TSLRPLARMYIEPVRGTPLLVQLLLIYFGLPSIGIKLDAFTSSFLALGLNSAAYQAEIFRSALKSIPDVQILSAESLGFS 124
                                    6788999**************999999777777777799999************************************** PP

                   BPD_transp_1  94 rwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseisnggvlalviavlllnlvad 173
                                      q++r+v+lP+al+  i++l++ f+ ++++++l++ +g    +  l+ + +    y++ +  ++l++++++++++ ++ 
  gi|119719814|ref|YP_920309.1| 125 GSQVYRYVILPQALRISIPSLVNEFVTVVKESSLASVIG----IVELTRRGEYVAAYTYRALESYLVVAAIYFAVCYLIS 200
                                    ***************************************....******************9999999999999999999 PP

                   BPD_transp_1 174 ilqrlldprvr 184
                                     l r ++ ++r
  gi|119719814|ref|YP_920309.1| 201 YLSRRIEEKIR 211
                                    99999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 1351.79
//
Query:       gi|119719815|ref|YP_920310.1|  [L=279]
Description: extracellular solute-binding protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-59  200.4   1.4    2.9e-59  200.2   1.4    1.0  1  SBP_bac_3        Bacterial extracellular solute-binding prote
    1.4e-09   38.1   0.1    2.6e-08   34.1   0.1    2.2  1  Lig_chan-Glu_bd  Ligated ion channel L-glutamate- and glycine
    2.5e-08   33.8   0.2    5.7e-07   29.4   0.2    2.1  1  Phosphonate-bd   ABC transporter, phosphonate, periplasmic su
    8.8e-05   22.5   0.8     0.0002   21.4   0.8    1.6  1  NMT1             NMT1/THI5 like
      0.001   18.7   1.7     0.0018   17.9   1.7    1.4  1  OpuAC            Substrate binding domain of ABC-type glycine
  ------ inclusion threshold ------
      0.021   14.4   0.5       0.26   10.8   0.3    2.0  2  YhfZ_C           YhfZ C-terminal domain
      0.037   13.4   0.0        5.5    6.2   0.0    2.1  2  DctP             Bacterial extracellular solute-binding prote
       0.08   12.3   0.0          1    8.7   0.0    2.0  2  LysR_substrate   LysR substrate binding domain
      0.085   12.4   0.1       0.14   11.7   0.1    1.3  1  Glyco_hydro_4    Family 4 glycosyl hydrolase


Domain annotation for each model (and alignments):
>> SBP_bac_3  Bacterial extracellular solute-binding proteins, family 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.2   1.4   1.4e-62   2.9e-59       1     220 [.      54     269 ..      54     278 .. 0.94

  Alignments for each domain:
  == domain 1  score: 200.2 bits;  conditional E-value: 1.4e-62
                                    EEEEE-S-BTTTBEE-TTS-EESHHHHHHHHHHHHCT-EEEEEE-SGGGHHHHHHTTSSSEEESSEB--HHHHTTEEEES CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      SBP_bac_3   1 lrvgvdadypPfsykdengeltGfdvdlakaiakrlgvkvefvpvswdelipalksgkvDiaiaaititpeReekvdFsq 80 
                                    l+vg++ad+pPf+y+d+ng+++G+d+++ak ia++lgv++e++++++++li+alk+g vDi+ia++t t+eRe++vdFs 
  gi|119719815|ref|YP_920310.1|  54 LIVGTSADWPPFEYVDKNGNYAGIDIEIAKRIAQELGVQLEIKDMKFAALIEALKNGDVDIVIADMTPTAEREKVVDFSI 133
                                    78****************************************************************************** PP

                                    ESEEEEEEEEEEETTSHGTCCHSSCGCGTTSEEEEETTSHHHHHHHHHHHCTSEEEEE.SSHHHHHHHHHTTSSSEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                      SBP_bac_3  81 pyfsagqvllvrkkdaskissiksladLkgkkvgvqagstaeellkeelkkgaeivef.dtleealqaLkngrvdavvad 159
                                    py++++   ++ +++    s+iks +dL+gkk+gvq g+ +e++++++lk +aei+++   ++e++ aL+ g +da+++ 
  gi|119719815|ref|YP_920310.1| 134 PYYTSKGYAVITTAK----SDIKSEQDLYGKKIGVQLGTIQEDWANNNLKGKAEIKSYdRVYPEMVWALQRGDIDAMIVG 209
                                    *****7777766543....5799899*********************9988*****9945689***************** PP

                                    HHHHHHHHHHCCGCCEEEEECGGCECEEEEEEETTTHHHHHHHHHHHHHHHHTTHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      SBP_bac_3 160 spvlaylvkknpdkkvvlveeplsseeyaiavrkgdseLrkainkalaelkadgtlakise 220
                                    + +++ l++k+p +k+   ++++ + + a+av++g ++L+  +n+++++l ++g+++ki +
  gi|119719815|ref|YP_920310.1| 210 DKIAEALITKEPSLKIAT-YVSIPTIGGAVAVPQGAEDLKYVVNSVIEKLLESGEMNKIFQ 269
                                    ******************.****************************************88 PP

>> Lig_chan-Glu_bd  Ligated ion channel L-glutamate- and glycine-binding site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.1   1.3e-11   2.6e-08      28     111 ..      74     145 ..      53     149 .. 0.74

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 1.3e-11
                                    EESHHHHHHHHHHHHHT-EEEEEE-TT-----BETTTTEB-HHHHHHHTTS-SEE-SS-B--HHHHTTSEEESESEEE.- CS
                Lig_chan-Glu_bd  28 yeGfcidLlkelakklgfkYelklvedgkyGskkekkkewnGmigellekkadlavapltitaeReevvdFtkpfmel.g 106
                                    y G  i++ k++a++lg++ e+k             + +   +i+ l ++++d+++a++t taeRe+vvdF+ p++++ g
  gi|119719815|ref|YP_920310.1|  74 YAGIDIEIAKRIAQELGVQLEIK-------------DMKFAALIEALKNGDVDIVIADMTPTAEREKVVDFSIPYYTSkG 140
                                    55555555555555555554443.............33567799*******************************98746 PP

                                    EEEEE CS
                Lig_chan-Glu_bd 107 isili 111
                                    +++++
  gi|119719815|ref|YP_920310.1| 141 YAVIT 145
                                    66654 PP

>> Phosphonate-bd  ABC transporter, phosphonate, periplasmic substrate-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.2   2.9e-10   5.7e-07      19     179 ..      81     224 ..      79     246 .. 0.82

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 2.9e-10
                                    HHHHHHHHHSSEEEEE--SSHHHHHHHHHTTS-SEEE--HHHHHHHHHHS-E.EEEEEEEETT--SEEEEEEEEETTSS- CS
                 Phosphonate-bd  19 ladyLseelGvevelvvatdyaavvealragqvDiaflgplayvqardqagv.eplatrvrsdGsasyrsviivradsdi 97 
                                    +a+ + +elGv+ e++ +  +aa++eal++g vDi+ ++  ++++ ++  +   p  t+++         ++i++a sdi
  gi|119719815|ref|YP_920310.1|  81 IAKRIAQELGVQLEIKDM-KFAALIEALKNGDVDIVIADMTPTAEREKVVDFsIPYYTSKG--------YAVITTAKSDI 151
                                    78999*************.5***********************999987665477777776........455666679** PP

                                    -SHHHHGG-EEEE--TT-TTTTHHHHHHTCCCCT--HHHHSSEEEE--HHHHHHHHHTTSSSEEEEEHHHHHHHHHH-HH CS
                 Phosphonate-bd  98 qsledLkgktiafvspsStsGylvpaalLvkeagldpeddfsevfsgshdaavlavlsgdadaaavsadaledlvaegpe 177
                                    +s +dL gk+i++       G+ +++ +  ++++l+ +  +++ +   ++++v a+ +gd+da+ v + ++e l+ ++p+
  gi|119719815|ref|YP_920310.1| 152 KSEQDLYGKKIGVQL-----GT-IQEDW--ANNNLKGKAEIKS-YDRVYPEMVWALQRGDIDAMIVGDKIAEALITKEPS 222
                                    ************954.....33.56665..4778887777666.677799999999999999999999999999998876 PP

                                    HH CS
                 Phosphonate-bd 178 dk 179
                                     k
  gi|119719815|ref|YP_920310.1| 223 LK 224
                                    54 PP

>> NMT1  NMT1/THI5 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.8   9.9e-08    0.0002      18     148 ..      88     210 ..      73     229 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 9.9e-08
                                    HTTEEEEEE--SSTTHHHHHHHCTS-SEEEE-HHHHHHHHHTT--EEEEEEEE-S--EEEEEECCC--SSGGGGTTSEEE CS
                           NMT1  18 eeGldVeivepadpsdatelvasgkadfgvsyqesllaarakglpvvsvaallqeplsglivlkdsgikspkDLkGkrig 97 
                                    e G+++ei+ ++  +  +e++ +g++d+ +++++ ++   ++   v     ++ ++ +++i+ ++s+iks +DL Gk+ig
  gi|119719815|ref|YP_920310.1|  88 ELGVQLEIKDMKF-AALIEALKNGDVDIVIADMTPTA---EREKVVDFSIPYYTSKGYAVITTAKSDIKSEQDLYGKKIG 163
                                    6688899999866.899999***********999988...44445556677899999*********************** PP

                                    E-S-TTHHHHHHHHHHHTT--GGG-EEEE-.TT-HHHHHHCTSSSEEECEE CS
                           NMT1  98 yvgspfekallkallakdggdpsdvtlvnvggtslakalltgkvDaaiggy 148
                                    ++ + +++   +  l+     +++++  +  + +++ al +g +Da+i+g 
  gi|119719815|ref|YP_920310.1| 164 VQLGTIQEDWANNNLK----GKAEIKSYDRVYPEMVWALQRGDIDAMIVGD 210
                                    *996554444433333....2233333333356666689999999998765 PP

>> OpuAC  Substrate binding domain of ABC-type glycine betaine transport system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   1.7   8.8e-07    0.0018      18     174 ..      80     206 ..      69     210 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 8.8e-07
                                    HHHHHHHHHTTEEEEEEEEESHHHHHHHHHTTSSSEEEEEEHHHHHHHHHHHHHHHHEEEEEEEESEEECEEEEEEHHHH CS
                          OpuAC  18 eilkqllekkGykveltnlgstavlfaalasGdiDvypeewtgtayeaykkaveekkglevlgplgagnteglavpkyva 97 
                                    ei+k + +++G++ e   +   a+l++al++Gd+D++  + t+ta+        ++k++    ++++ +  g+av +   
  gi|119719815|ref|YP_920310.1|  80 EIAKRIAQELGVQLEIKDMKF-AALIEALKNGDVDIVIADMTPTAE--------REKVVD--FSIPYYTSKGYAVITTA- 147
                                    79999*******999999999.99*******************954........334444..37888888888887544. PP

                                    HHHTTTBHHHHCTHHGGTEEEEEHHCCHSTTSHHCCHHHHHHHHHHT-TTCEEEGSCEEEEHHHHHHHHHTTCSSEE CS
                          OpuAC  98 ekygiksisDLkkpaedlelgakgeflgrpdgwgcekvtegllkaYgldkvelvegseaamdaelyaaykrgepvvv 174
                                     k++iks +DL  ++       + ++ +++  w+    +++l+ + ++       +s+  +++e+  a++rg+++++
  gi|119719815|ref|YP_920310.1| 148 -KSDIKSEQDLYGKKI------GVQLGTIQEDWA----NNNLKGKAEI-------KSYDRVYPEMVWALQRGDIDAM 206
                                    .59********55555......888888888899....5566666655.......7888889999999999998876 PP

>> YhfZ_C  YhfZ C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1    0.0051        10     138     189 ..      92     143 ..      80     157 .. 0.70
   2 ?   10.8   0.3   0.00013      0.26      56     199 ..     104     240 ..     104     274 .. 0.63

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0051
                         YhfZ_C 138 dvelveisynqllelllkgkiDavvWnldevqeeeelklkelkleslkekel 189
                                    + e+ +++++ l+e+l++g++D v+  ++   e+e++   ++++++ k  ++
  gi|119719815|ref|YP_920310.1|  92 QLEIKDMKFAALIEALKNGDVDIVIADMTPTAEREKVVDFSIPYYTSKGYAV 143
                                    667888999****************999855555455544555554444443 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00013
                         YhfZ_C  56 lealkegrydfavvSrlaAeqaleegkeveialelGpetYvsah..vlllrdgekseikd..glrvgvDsnSlDqkilte 131
                                    +ealk+g +d+++      +    ++   e ++++    Y+s+   v+  ++++ ++ +d  g ++gv   ++   +  +
  gi|119719815|ref|YP_920310.1| 104 IEALKNGDVDIVIA-----DMTPTAER--EKVVDFSIPYYTSKGyaVITTAKSDIKSEQDlyGKKIGVQLGTIQEDWANN 176
                                    57778888887773.....33333333..334566666666654114445666666777799*********999999888 PP

                         YhfZ_C 132 aifegkdvelveisynqllelllkgkiDavvWnldevqeeeelklkelkleslkekelveeaseAvlv 199
                                    ++  + +++  +  y +++ +l +g+iDa++   + + e++  k    +  ++++   +  +  Av v
  gi|119719815|ref|YP_920310.1| 177 NLKGKAEIKSYDRVYPEMVWALQRGDIDAMIVGDK-IAEALITK---EPSLKIATYVSIPTIGGAVAV 240
                                    888878*************************8744.55553333...333333344444445555544 PP

>> DctP  Bacterial extracellular solute-binding protein, family 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0    0.0027       5.5      45      79 ..     102     135 ..      98     138 .. 0.82
   2 ?    5.5   0.0    0.0047       9.4     113     178 ..     136     206 ..     133     215 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0027
                                    HHHHHHHTTSSSEEEEEGGGGTTTSGGGGGGGSTT CS
                           DctP  45 eviealknGtvdivatssakleglvpeigvldlPF 79 
                                    + iealknG+vdiv+++ + +++ ++ +  +++P+
  gi|119719815|ref|YP_920310.1| 102 ALIEALKNGDVDIVIADMTPTAEREKVVD-FSIPY 135
                                    679**************999998866544.66776 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0047
                                    EEEEEEEEEEESSS--SSGGGGTTEEEEETSSHHHHHHHH.HHTSEEEE-TGGGHHH....HHHTTSSSEE CS
                           DctP 113 fwenGfrqftsnkkpinspeDlkglklRvpessvllevfk.alGanptpipfgevyt....aLqtgvvDGq 178
                                    ++++G+  +t+ k  i+s  Dl g k+ v+    ++++++  l ++++  ++ +vy+    aLq+g +D++
  gi|119719815|ref|YP_920310.1| 136 YTSKGYAVITTAKSDIKSEQDLYGKKIGVQLGTIQEDWANnNLKGKAEIKSYDRVYPemvwALQRGDIDAM 206
                                    47899*************************99999998852699999999999999766668999999997 PP

>> LysR_substrate  LysR substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0   0.00051         1      34      66 ..      90     122 ..      81     133 .. 0.84
   2 ?    1.3   0.0     0.092   1.8e+02      46      71 ..     193     218 ..     183     230 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00051
                                    TEEEEEEEESHHHHHHHHHTTSSSEEEEESSSC CS
                 LysR_substrate  34 evelelvegdseelldllaegelDlairagppe 66 
                                    +v+le++ +  ++l+++l++g++D++i+   p+
  gi|119719815|ref|YP_920310.1|  90 GVQLEIKDMKFAALIEALKNGDVDIVIADMTPT 122
                                    78999999999****************988774 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.092
                                    HHHHHHHTTSSSEEEEESSSCCTTEE CS
                 LysR_substrate  46 elldllaegelDlairagppedsgle 71 
                                    e++ +l++g++D+ i+++ ++++ ++
  gi|119719815|ref|YP_920310.1| 193 EMVWALQRGDIDAMIVGDKIAEALIT 218
                                    67889***********9988666555 PP

>> Glyco_hydro_4  Family 4 glycosyl hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1     7e-05      0.14      46      99 ..      80     137 ..      65     150 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7e-05
                                    HHHHHHHHHCTTTCEEE..EESSHHHHHT..T-SEEEE---TTHHHHHHHHHHCCHTT CS
                  Glyco_hydro_4  46 tlakklveeagadlkie..attdrkealk..dadfVitairvGlekareidekiplry 99 
                                    ++ak++ +e g++l+i+  +   + ealk  d+d+Vi+ + +  e  +++d+ ip++ 
  gi|119719815|ref|YP_920310.1|  80 EIAKRIAQELGVQLEIKdmKFAALIEALKngDVDIVIADMTPTAEREKVVDFSIPYYT 137
                                    68899999999999998224567889**855799*********************974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1711.77
//
Query:       gi|119719816|ref|YP_920311.1|  [L=228]
Description: hypothetical protein Tpen_0907 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.043   13.6   0.1      0.089   12.6   0.1    1.5  1  ACT_7     ACT domain


Domain annotation for each model (and alignments):
>> ACT_7  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1     5e-06     0.089       7      64 ..     159     217 ..     155     218 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5e-06
                                    EEEEE-S-.---SS--HHHHHHHHHHTTT---EEEE.-SS-EEEEEEGGGHHHHHHHHH CS
                          ACT_7   7 iklsvvgsglpfdvtGivaklaspLaeagIsifqiS.tyrtdyiLVpeedlekAveaLh 64 
                                    +++ + g+   + ++G+v+ ++   a  g++++ i  ++r+++++V+ +d+  A e+L+
  gi|119719816|ref|YP_920311.1| 159 AAVILTGPPEILTTPGVVSLISLSVAVRGVNLTEIVsCHRDIVLIVNGSDVALAFETLR 217
                                    56666666555679******************97766*********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1750.58
//
Query:       gi|119719817|ref|YP_920312.1|  [L=291]
Description: MRP protein-like [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.8e-95  317.4   0.0    6.8e-95  317.2   0.0    1.0  1  ParA          NUBPL iron-transfer P-loop NTPase
    3.2e-16   59.5   0.0    7.7e-16   58.3   0.0    1.7  1  CbiA          CobQ/CobB/MinD/ParA nucleotide binding domain
    1.7e-07   31.0   0.1     0.0011   18.4   0.1    2.2  2  Fer4_NifH     4Fe-4S iron sulfur cluster binding proteins, Ni
    4.1e-07   30.1   0.1    7.8e-06   25.9   0.2    2.4  3  AAA_31        AAA domain
    4.4e-05   23.4   0.7       0.17   11.7   0.0    2.2  2  AAA_26        AAA domain
    7.3e-05   22.2   0.2    0.00015   21.2   0.1    1.5  2  MipZ          ATPase MipZ
    0.00018   20.8   0.4    0.00029   20.1   0.4    1.3  1  ArsA_ATPase   Anion-transporting ATPase
      0.003   17.2   0.0     0.0059   16.2   0.0    1.5  1  AAA_25        AAA domain
  ------ inclusion threshold ------
      0.011   15.4   0.5      0.019   14.7   0.5    1.3  1  AAA_30        AAA domain
      0.023   15.1   0.1       0.05   14.0   0.1    1.6  1  AAA_16        AAA ATPase domain
      0.027   14.4   0.1       0.05   13.5   0.1    1.4  1  RsgA_GTPase   RsgA GTPase
      0.028   13.4   0.1      0.049   12.6   0.1    1.4  1  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
      0.055   13.0   0.3       0.32   10.4   0.3    2.0  2  CBP_BcsQ      Cellulose biosynthesis protein BcsQ
      0.074   12.9   0.0       0.13   12.2   0.0    1.4  1  APS_kinase    Adenylylsulphate kinase
        0.1   12.6   0.0          1    9.4   0.0    2.1  2  AAA_5         AAA domain (dynein-related subfamily)
       0.11   12.1   0.2       0.19   11.4   0.2    1.3  1  SRP54         SRP54-type protein, GTPase domain
       0.12   12.2   0.0       0.26   11.0   0.0    1.6  1  CLP1_P        mRNA cleavage and polyadenylation factor CLP1 P
       0.14   12.5   0.0       0.31   11.4   0.0    1.6  1  RNA_helicase  RNA helicase
       0.16   11.2   0.1       0.36   10.1   0.1    1.5  1  VirC1         VirC1 protein
       0.36   10.7   1.0        5.5    6.9   0.0    2.4  2  zf-CCCH_6     Chromatin remodeling factor Mit1 C-terminal Zn 


Domain annotation for each model (and alignments):
>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  317.2   0.0   7.6e-98   6.8e-95       2     245 ..      31     276 ..      30     277 .. 0.98

  Alignments for each domain:
  == domain 1  score: 317.2 bits;  conditional E-value: 7.6e-98
                           ParA   2 vkkviavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekpeqsekkliPvea.kgikvmSigf 80 
                                    vk ++avlSgKGGVGKS v++nlA+aLakkg++vg+lDaD++Gpsip+++gv+++   +   +++Pv    ++k++S ++
  gi|119719817|ref|YP_920312.1|  31 VKFKVAVLSGKGGVGKSLVTANLAAALAKKGFEVGVLDADVHGPSIPKMFGVHGQVLYAGPGGIMPVVGvGNVKIVSADL 110
                                    8999**************************************************999999999***998799******** PP

                           ParA  81 llesedeavvwrGpmkskaikqllkdvewgelDyLiiDlPPGtgDeqltvaqkl.plagaviVttpqevaladvkkaiem 159
                                    ++++ed++++wrGp+k++++++ll+ v+wg lD+L++DlPPGtgDe lt+aq + +l+ga++Vttp +++ ++vkkai++
  gi|119719817|ref|YP_920312.1| 111 MVPEEDTPLIWRGPLKTSFLRELLSMVAWGPLDFLLVDLPPGTGDEPLTIAQLIrDLSGAIVVTTPSDLTRIVVKKAITF 190
                                    ******************************************************99************************ PP

                           ParA 160 fkkvkvkvlGvveNmsgfvcpkcgekteifgkgggeklaeelgvpllgeipldpeireasdegkplvlkepeseaakale 239
                                    +k+vk+++lGvv+Nm++fvcp cg+k++ifgk+g+e+l+ee++v++l+eipldp+i+e++d+g p+vl+ p+seaak++ 
  gi|119719817|ref|YP_920312.1| 191 CKQVKMPLLGVVKNMAYFVCPVCGTKHYIFGKSGAERLSEEMNVRVLAEIPLDPRINESADNGVPFVLAYPDSEAAKSFY 270
                                    ******************************************************************************** PP

                           ParA 240 eiaekv 245
                                    ++a++v
  gi|119719817|ref|YP_920312.1| 271 KLADEV 276
                                    ***998 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.3   0.0   8.6e-19   7.7e-16       1     127 [.      35     255 ..      35     256 .. 0.92

  Alignments for each domain:
  == domain 1  score: 58.3 bits;  conditional E-value: 8.6e-19
                                    EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH.......................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......................... RF
                           CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep.......................... 54 
                                    +a+ s+kGGvGK+ ++anLa+ala++g++V ++DaD+ +++    +g+ +++                            
  gi|119719817|ref|YP_920312.1|  35 VAVLSGKGGVGKSLVTANLAAALAKKGFEVGVLDADVHGPSIPKMFGVHGQVLYagpggimpvvgvgnvkivsadlmvpe 114
                                    699**************************************9976666666666888*********************** PP

                                    ....................................................................CCHCCCHHHHHH CS
                                    ....................................................................xxxxxxxxxxxx RF
                           CbiA  55 ....................................................................dlkrllelleal 66 
                                                                                                         +k+ + +++++
  gi|119719817|ref|YP_920312.1| 115 edtpliwrgplktsflrellsmvawgpldfllvdlppgtgdepltiaqlirdlsgaivvttpsdltriVVKKAITFCKQV 194
                                    ***************************************************************99888888888888888 PP

                                    CHCHHHH....EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHHTS- CS
                                    xxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           CbiA  67 gkkkall..lkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeavaeapargep 127
                                    + +  ll  +k + + +  v g +++   k++ e+l ++++v+vl++ip d +++e++ +g p
  gi|119719817|ref|YP_920312.1| 195 KMP--LLgvVKNMAYFVCPVCGTKHYIFGKSGAERLSEEMNVRVLAEIPLDPRINESADNGVP 255
                                    866..3467777777778888999**********************************99987 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   1.3e-06    0.0011       5      37 ..      38      70 ..      33      85 .. 0.82
   2 !   10.6   0.0   0.00031      0.28     190     247 ..     222     279 ..     165     284 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.3e-06
                      Fer4_NifH  5 iyGkGGiGksttsqnlsaalaemgkkvlivGCD 37
                                   + GkGG+Gks  ++nl+aala++g  v ++  D
  gi|119719817|ref|YP_920312.1| 38 LSGKGGVGKSLVTANLAAALAKKGFEVGVLDAD 70
                                   46*********************9888666555 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00031
                      Fer4_NifH 190 reliekfaeelgtkvlevvPrdeivrkaelrkktvieyapeseqakeyrelarkilen 247
                                    +  +e++ ee++++vl+ +P+d  ++++  +    +   p+se ak + +la+++l +
  gi|119719817|ref|YP_920312.1| 222 KSGAERLSEEMNVRVLAEIPLDPRINESADNGVPFVLAYPDSEAAKSFYKLADEVLAA 279
                                    55678999*******************99999988888899999*********99865 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.2   8.7e-09   7.8e-06       4      40 ..      35      71 ..      33      81 .. 0.93
   2 ?    0.9   0.0       0.4   3.6e+02     105     138 ..     128     164 ..      95     201 .. 0.58
   3 ?   -2.2   0.0       3.6   3.3e+03      27      49 ..     229     253 ..     225     275 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 8.7e-09
                         AAA_31  4 IaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDp 40
                                   +a+   KGGvGK+  + nlaaalak+g  v + D+D 
  gi|119719817|ref|YP_920312.1| 35 VAVLSGKGGVGKSLVTANLAAALAKKGFEVGVLDADV 71
                                   789999*****************************96 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.4
                         AAA_31 105 eilkellekvkde.YDyiiiDcpPsLg..lltenaLv 138
                                    + l+ell+ v     D+ ++D pP  g   lt+  L+
  gi|119719817|ref|YP_920312.1| 128 SFLRELLSMVAWGpLDFLLVDLPPGTGdePLTIAQLI 164
                                    345777777765448*********8762235555554 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 3.6
                         AAA_31  27 a.klgkkvLl.vDlDpQanattglg 49 
                                    + +++ +vL  + lDp  n +   g
  gi|119719817|ref|YP_920312.1| 229 SeEMNVRVLAeIPLDPRINESADNG 253
                                    4477889997699999999998665 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.2   0.00056       0.5       9      34 ..      41      66 ..      34      68 .. 0.87
   2 !   11.7   0.0   0.00019      0.17     118     196 ..     158     248 ..     146     250 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00056
                         AAA_26  9 dtgvGKTvvslgLvralkrkgvkvgy 34
                                     gvGK++v++ L++al +kg++vg+
  gi|119719817|ref|YP_920312.1| 41 KGGVGKSLVTANLAAALAKKGFEVGV 66
                                   569********************997 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00019
                         AAA_26 118 llnadiaknlgapvilVargglgtinqllltiealrqknvrvlGvilNk..vrnp......e.......nvetlekksgi 182
                                    l++a++++ l   +++ ++++l  i  +  +i +++q + ++lGv+ N   +         +         e l++  ++
  gi|119719817|ref|YP_920312.1| 158 LTIAQLIRDLSGAIVVTTPSDLTRIV-VKKAITFCKQVKMPLLGVVKNMayF--VcpvcgtKhyifgksGAERLSEEMNV 234
                                    67788888888888888888887774.667889999************9441..133455515555556999******** PP

                         AAA_26 183 pvlGvvPylpdlea 196
                                    +vl+++P +p++++
  gi|119719817|ref|YP_920312.1| 235 RVLAEIPLDPRINE 248
                                    *********99875 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.1   1.6e-07   0.00015       5      46 ..      37      78 ..      33      87 .. 0.86
   2 ?   -3.8   0.0       6.9   6.2e+03     100     110 ..     142     153 ..     128     167 .. 0.71

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.6e-07
                                   E--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHH CS
                           MipZ  5 lgnekGGsGksttavhvavaLlkkGarvaaidldlrqrtlar 46
                                   +   kGG Gks ++  +a aL+kkG++v+++d d+   ++ +
  gi|119719817|ref|YP_920312.1| 37 VLSGKGGVGKSLVTANLAAALAKKGFEVGVLDADVHGPSIPK 78
                                   4567******************************98777665 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 6.9
                                    -SEEEEE--.SS CS
                           MipZ 100 ldfividtP.Gs 110
                                    ldf+++d P G+
  gi|119719817|ref|YP_920312.1| 142 LDFLLVDLPpGT 153
                                    699999986244 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.4   3.2e-07   0.00029       2      38 ..      34      70 ..      33      83 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 3.2e-07
                                   EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S CS
                    ArsA_ATPase  2 kvilvgGKGGVGKttvsaatavklsekgkkvllistD 38
                                   kv +++GKGGVGK+ v a +a+ l++kg +v ++  D
  gi|119719817|ref|YP_920312.1| 34 KVAVLSGKGGVGKSLVTANLAAALAKKGFEVGVLDAD 70
                                   67889***********************999888776 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   6.6e-06    0.0059      34      59 ..      34      59 ..       6      76 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 6.6e-06
                         AAA_25 34 elallaGapgtGKttlaldlalavat 59
                                   ++a+l G +g+GK+ ++ +la+a+a+
  gi|119719817|ref|YP_920312.1| 34 KVAVLSGKGGVGKSLVTANLAAALAK 59
                                   689*********************94 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.5   2.1e-05     0.019       4      51 ..      18      66 ..      15      71 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.1e-05
                         AAA_30  4 aeQaaaveallts.gdrvavltGpAGtGKttalkalreaweaaggrvig 51
                                    eQ++++++ l++ + +vavl G  G GK+ + + l++a++++g++v +
  gi|119719817|ref|YP_920312.1| 18 REQEEVARQRLSQvKFKVAVLSGKGGVGKSLVTANLAAALAKKGFEVGV 66
                                   689999988777625589**************************99966 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   5.5e-05      0.05      19      53 ..      28      62 ..       4      88 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.5e-05
                         AAA_16 19 vrsgrpelvllsGesGvGKsslvrellralekdgg 53
                                   +++    + +lsG  GvGKs +   l+ al k+g+
  gi|119719817|ref|YP_920312.1| 28 LSQVKFKVAVLSGKGGVGKSLVTANLAAALAKKGF 62
                                   3333448999*****************99999953 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   5.6e-05      0.05      71     122 ..       5      56 ..       2      73 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.6e-05
                                    HHHHTTSEEEE--TTTHTTHHHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT CS
                    RsgA_GTPase  71 elealgyevllvsaktkegleelkellkdktsvlvGqSGvGKStLinallpe 122
                                    + ++l +e l+   +++e +++  +++k k++vl G+ GvGKS +  +l+  
  gi|119719817|ref|YP_920312.1|   5 KERQLKLEALKKAREQEEVARQRLSQVKFKVAVLSGKGGVGKSLVTANLAAA 56 
                                    55777788888888888888888889999**************988888765 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   5.5e-05     0.049      31      66 ..      35      70 ..      11      81 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.5e-05
                                   EEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE- CS
                           MeaB 31 vvGltGvPGaGkstlvealglelrrrGkrvavlavD 66
                                   v  l G  G+Gks ++ +l++ l+++G  v+vl  D
  gi|119719817|ref|YP_920312.1| 35 VAVLSGKGGVGKSLVTANLAAALAKKGFEVGVLDAD 70
                                   556899***************************887 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.3   0.00036      0.32       5      38 ..      37      69 ..      33      73 .. 0.87
   2 ?   -0.5   0.0      0.79   7.1e+02     112     147 ..     137     176 ..     124     190 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00036
                       CBP_BcsQ  5 alqGvRGGvGttsllaaLawalhelgesvlviDl 38
                                   +l+G +GGvG++ ++a La al + g +v v+D+
  gi|119719817|ref|YP_920312.1| 37 VLSG-KGGVGKSLVTANLAAALAKKGFEVGVLDA 69
                                   5566.8***********************99997 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.79
                       CBP_BcsQ 112 lk.eqyrwillDlpagasa...ltrellaladlvllvvep 147
                                    ++ +  +++l+Dlp g+ +   +  +l++     + v++p
  gi|119719817|ref|YP_920312.1| 137 VAwGPLDFLLVDLPPGTGDeplTIAQLIRDLSGAIVVTTP 176
                                    44677899******96654111234445545555666655 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00014      0.13       5      40 ..      36      71 ..      32      81 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00014
                                   EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHH CS
                     APS_kinase  5 vwltGlsgsGKstianalekkLvekgisvylLdGdn 40
                                     l+G  g GKs ++ +l+ +L +kg +v +Ld d+
  gi|119719817|ref|YP_920312.1| 36 AVLSGKGGVGKSLVTANLAAALAKKGFEVGVLDADV 71
                                   5799*****************************985 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0    0.0011         1       3      29 ..      37      64 ..      36      72 .. 0.79
   2 ?    0.5   0.0      0.63   5.7e+02       9      70 ..     123     190 ..     122     203 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0011
                                   EEE--SSSSHHHHHHHGGGGB.S--EEE CS
                          AAA_5  3 lLvGppGtgKselaerlaaal.nrevey 29
                                   +L G+ G+gKs ++  laaal ++ +e+
  gi|119719817|ref|YP_920312.1| 37 VLSGKGGVGKSLVTANLAAALaKKGFEV 64
                                   699******************5544444 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.63
                                    SSSHHHHHHHGGGGB...S--EEEEE--TT--HHHHH--B--............--------G-SEEE CS
                          AAA_5   9 GtgKselaerlaaal...nreveyvqltrdtteedlkgrreik...ngttslvdsplvraaregeilv 70 
                                    G  K+++ ++l++++      ++ v l+ +t  e l+    i+   +   + ++s l+r + +++i++
  gi|119719817|ref|YP_920312.1| 123 GPLKTSFLRELLSMVawgPLDFLLVDLPPGTGDEPLTIAQLIRdlsGAIVVTTPSDLTRIVVKKAITF 190
                                    88999999999999988888888888888888888877666666646666677888888888777776 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   0.00021      0.19       3      39 ..      35      71 ..      33      76 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00021
                                   EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEEST CS
                          SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvllvaaDt 39
                                   v +l G  G+GK   +a Laa l k+g +v +  aD+
  gi|119719817|ref|YP_920312.1| 35 VAVLSGKGGVGKSLVTANLAAALAKKGFEVGVLDADV 71
                                   78999**************************999997 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00029      0.26       1      36 [.      40      75 ..      40      82 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00029
                         CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvGqse 36
                                   G+  +GKS ++++L+  +++kg ++ ++D+Dv  ++
  gi|119719817|ref|YP_920312.1| 40 GKGGVGKSLVTANLAAALAKKGFEVGVLDADVHGPS 75
                                   66789**************************97655 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00035      0.31       2      25 ..      37      60 ..      36      79 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00035
                   RNA_helicase  2 wlyGpsgeGKStlakeLakallkk 25
                                   +l+G+ g+GKS+++ +La+al+kk
  gi|119719817|ref|YP_920312.1| 37 VLSGKGGVGKSLVTANLAAALAKK 60
                                   689******************976 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1    0.0004      0.36       5      41 ..      36      72 ..      33      76 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0004
                          VirC1  5 tfcslkGGaGkttalmglcsalasdgkrvalfeaden 41
                                   ++ s kGG Gk+     l +ala +g  v++++ad  
  gi|119719817|ref|YP_920312.1| 36 AVLSGKGGVGKSLVTANLAAALAKKGFEVGVLDADVH 72
                                   56789*****************************965 PP

>> zf-CCCH_6  Chromatin remodeling factor Mit1 C-terminal Zn finger 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.5       0.3   2.7e+02      30      45 ..      11      26 ..       2      32 .. 0.78
   2 ?    6.9   0.0    0.0061       5.5       3      29 ..     210     237 ..     209     240 .. 0.69

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.3
                                   HHHHHT--S-HHHHHH CS
                      zf-CCCH_6 30 leaLkeStEprelvee 45
                                   leaLk+ +E++e+ ++
  gi|119719817|ref|YP_920312.1| 11 LEALKKAREQEEVARQ 26
                                   799******9998665 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0061
                                    -TTTSSB--SSSS-.-GGGSSHHHHHHH CS
                      zf-CCCH_6   3 CgLCglAHfGekrt.CPhlksetqvrrm 29 
                                    C++Cg+ H+  ++     l++e +vr++
  gi|119719817|ref|YP_920312.1| 210 CPVCGTKHYIFGKSgAERLSEEMNVRVL 237
                                    ********97754413457777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       809  (0.0451224); expected 358.6 (0.02)
Passed bias filter:                      727  (0.0405488); expected 358.6 (0.02)
Passed Vit filter:                       144  (0.00803168); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 1975.71
//
Query:       gi|119719818|ref|YP_920313.1|  [L=184]
Description: peptidase M50 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-06   27.1   6.1     0.0021   17.4   0.1    3.1  3  Peptidase_M50  Peptidase family M50


Domain annotation for each model (and alignments):
>> Peptidase_M50  Peptidase family M50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.7   0.1   0.00043       7.7       5      33 ..      44      72 ..      39      82 .. 0.75
   2 !    6.3   0.3   0.00029       5.1      87     107 ..     110     130 ..     105     132 .. 0.87
   3 !   17.4   0.1   1.2e-07    0.0021     191     220 ..     135     164 ..     129     173 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.00043
                                   XXXXXXXX.XXXXXXXXXXXXXXXXXXXXX CS
                                   xxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M50  5 llgilvvv.HElGHflvAklcgvkveefsi 33
                                   +l +l  v HEl+H ++A+  g+   ++si
  gi|119719818|ref|YP_920313.1| 44 ALAFLAYVpHELAHKFIAQYYGYPA-KYSI 72
                                   444444334*************988.6777 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.00029
                                    XXXXXXXXXXXXXXXXXXXXX CS
                                    xxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M50  87 rllivlAGplanfilailvfv 107
                                      +i +AGp++n++l++++++
  gi|119719818|ref|YP_920313.1| 110 NGIISAAGPATNIVLGLVALW 130
                                    5689************99876 PP

  == domain 3  score: 17.4 bits;  conditional E-value: 1.2e-07
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M50 191 flqllalisvnLgilNLlPipvLDGghllf 220
                                    + + +a++s  ++++NL+P+ +LDG ++++
  gi|119719818|ref|YP_920313.1| 135 LASSVASLSGWIALFNLVPFGPLDGKKIAE 164
                                    667789*********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1404.27
//
Query:       gi|119719819|ref|YP_920314.1|  [L=360]
Description: extracellular solute-binding protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    9.8e-33  114.2   0.1    1.1e-32  114.0   0.1    1.0  1  SBP_bac_8   Bacterial extracellular solute-binding protein
    6.3e-29  101.1   0.1    9.3e-29  100.5   0.1    1.1  1  SBP_bac_6   Bacterial extracellular solute-binding protein
      6e-10   39.6   7.3    6.1e-09   36.3   7.3    2.0  1  SBP_bac_1   Bacterial extracellular solute-binding protein
    3.7e-08   33.4   0.0    1.1e-07   31.9   0.0    1.7  1  SBP_bac_11  Bacterial extracellular solute-binding protein
    0.00023   20.9   0.9    0.00023   20.9   0.9    1.8  2  TAT_signal  TAT (twin-arginine translocation) pathway signal 


Domain annotation for each model (and alignments):
>> SBP_bac_8  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.0   0.1   3.1e-36   1.1e-32       2     266 ..      49     310 ..      48     330 .. 0.89

  Alignments for each domain:
  == domain 1  score: 114.0 bits;  conditional E-value: 3.1e-36
                                    HHHHHHHH-TEEEEEEE-.-SSSHHHHHHHHHHTT---SEE.EEE-HHHHHHHHHTTSB--GG..GSTTHHH-HHHHHTT CS
                      SBP_bac_8   2 lakefekktgvkvnvvta.asndleqklkaalaagtapdidvvwanedalatlaeeglladls..dldnlddltdalaav 78 
                                    ++k+fe k+gvkv + ++ + +++ +kl+     g     dv++  + ++++++++gl+a+l+   ++nl +++ ++  +
  gi|119719819|ref|YP_920314.1|  49 IIKDFESKYGVKVIYDEYeSAEEAYAKLQL--GGGG---YDVIVLTDQYVPQAVKKGLVAQLDktRIPNLGNVDRVFFEN 123
                                    89****************666677777777..3344...4677777789***********8886577********99999 PP

                                    --TS..----EEEEEEE-EEEEEHHHHHHS.---BHHHHHHHHHHH.....HHH-SEGG---GGGGGGTHHETTEE---H CS
                      SBP_bac_8  79 gydgk.lygvPyasetpyvliynkdllekaedpktwdellaaakkl.....kgkfglpdpasgwlqaallakdgkslddd 152
                                     +d    y+vPya++t +++ +n d++ +   ++++++l++   k+     kgk+ +      ++ aa l+ +g +l+d+
  gi|119719819|ref|YP_920314.1| 124 NFDPGlRYAVPYAWGT-TGIGVNRDYVAEG-EIEGYEQLFD--TKVflprhKGKVSMLEEFLEVVNAAKLY-LGIPLNDW 198
                                    8965559********9.8***********8.9*********..777788889*******99**********.******** PP

                                    ..HHH.HHHHHHHHHHHHTT-EE-S..--SSTTTTTSBSEEEE-TTHHHHHH-TTTSEEEE--S--EEEEEEEEEEBTTS CS
                      SBP_bac_8 153 ggkdglkealellkklkdngktydtgadavsefanGevaftingswdiaaaqkagkklgaivpkqgsfaggkglavpkna 232
                                     +++ + +++ell++ +d    y   + ++ ++a+G+ +++ ++s+d+ +aq ++k +++++pk+g+f++++++++p na
  gi|119719819|ref|YP_920314.1| 199 -SEESKQRIIELLREQRDFLAGYYGASVYIPALAKGDLHAAHAWSGDVVQAQSENKSVEYVLPKEGAFVWIDFMVIPVNA 277
                                    .666679***********9999988899999************************************************* PP

                                    -HHHHHHHHHHHHHTTSHHHHHHHHHH---BS-S CS
                      SBP_bac_8 233 knedlaAldFlkwltspenqaalaektgyipvnk 266
                                      +dl A +++++l++p+  a+ +  t y+++ k
  gi|119719819|ref|YP_920314.1| 278 RSPDL-AYEWINFLLDPAVAAKNSSYTYYPSPVK 310
                                    ****9.*******************999986665 PP

>> SBP_bac_6  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.5   0.1   2.6e-32   9.3e-29       4     226 ..      83     315 ..      82     326 .. 0.88

  Alignments for each domain:
  == domain 1  score: 100.5 bits;  conditional E-value: 2.6e-32
                      SBP_bac_6   4 pdlilsfdkdflekfieeglfqpldpanlpnvnkdfa..eeglkdp.dgkyypygvgplvlavnkdrlkgrpvPksWaDL 80 
                                    +d+i+ ++++++ +++++gl+++ld++++pn+ +  +   e+  dp   + +py++g++++ vn+d +++ ++ + ++ L
  gi|119719819|ref|YP_920314.1|  83 YDVIV-LTDQYVPQAVKKGLVAQLDKTRIPNLGNVDRvfFENNFDPgLRYAVPYAWGTTGIGVNRDYVAEGEI-EGYEQL 160
                                    69***.*******************666666664333556777777588888*********************.****** PP

                      SBP_bac_6  81 ld.....Peykgkvalpgnngsdlfealllalyk......dfgedgvkkllrnlkanlhpaq.mvkaagslesgepavsv 148
                                    +d     P+ kgkv++   +     +a+ l+l        ++ ++ + +llr+ ++ l  ++    ++ +l++g+  +  
  gi|119719819|ref|YP_920314.1| 161 FDtkvflPRHKGKVSMLEEFL-EVVNAAKLYLGIplndwsEESKQRIIELLREQRDFLAGYYgASVYIPALAKGD--LHA 237
                                    98778889************9.6666666666667777*7777*******************99999********..*** PP

                      SBP_bac_6 149 vpyffadilpekkkgknlkvvwPedGalvspifmlvkkg.kkkelakafidfllspevqailakaggvfPvvtnpavln 226
                                    + ++++d++++++++k+++ v P++Ga+v+++fm+++ + + ++la+++i+fll+p v+a  +  ++ +P+ ++ ++l+
  gi|119719819|ref|YP_920314.1| 238 AHAWSGDVVQAQSENKSVEYVLPKEGAFVWIDFMVIPVNaRSPDLAYEWINFLLDPAVAAKNSSYTY-YPSPVKRELLE 315
                                    *********************************************************9999999998.99966655554 PP

>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   7.3   1.7e-12   6.1e-09      10     314 ..      45     296 ..      40     297 .. 0.76

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 1.7e-12
                                    HHHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHHHHTTSSSCSEEEECGGHHHHHHHTTSBECCHHHHHHTTECTTCCT CS
                      SBP_bac_1  10 lqalvakafekehpgikVeiesvgsgslaqkltlaiaaGdgpaDviavdndwiarlakaglllpldpyvkaylapgvkda 89 
                                    ++  ++k+fe  ++g+kV ++  +s + a   +l++++G   +Dvi   + ++++ +k+gl++ ld+  +++l++++  +
  gi|119719819|ref|YP_920314.1|  45 INPDIIKDFES-KYGVKVIYDEYESAEEAY-AKLQLGGGG--YDVIVLTDQYVPQAVKKGLVAQLDKTRIPNLGNVDRVF 120
                                    56667799*99.78***9999886666666.567777777..8*****888888*******************9998777 PP

                                    EEEEHHHHTHHHHCEEEES.EEEE.EEEEEEEETTTHHCTTGGGSHBHHHHHHHHHHHHHHCTCTHCCHCCEEHHHHHHH CS
                      SBP_bac_1  90 adklsssvlpkildskvly.vPly.aargliYNkdlfekagldppwtWdelveaakklkekgkkpiggarggsasgtayy 167
                                    + ++    ++  l     y vP+  +++g+ +N d++++ +++    +++l +  + l    +k       +  +    +
  gi|119719819|ref|YP_920314.1| 121 FENN----FDPGLR----YaVPYAwGTTGIGVNRDYVAEGEIE---GYEQLFDTKVFLPRHKGKV-----SMLEEFLEVV 184
                                    7774....444444....77****55************76666...6666666666666666666.....1222222222 PP

                                    HHHHHHHHHTGGGEECCCTHHCSHHHHS.HHHHHHHHHHHHHHHHHHHTTEEECSSHHHHHHHHHTTSCSEEEEEHHHHH CS
                      SBP_bac_1 168 falalakslggkvfdkdgggldnpegvt.aatylvklyavanltkelkgkgaenkdgaaalalfeaGeaamaivglwaal 246
                                    +a  l+++                     ++   + ++ + +l +e+++  a  ++ + + +++++G+  +a ++++++ 
  gi|119719819|ref|YP_920314.1| 185 NAAKLYLGI------------------PlNDWSEESKQRIIELLREQRDFLAGYYGASVYIPALAKGDLHAAHAWSGDVV 246
                                    222222222..................134455566666667789*********************************88 PP

                                    HHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEEEEEEEEEEBTTCSTHHHHHHHHHHHTSHHHH CS
                      SBP_bac_1 247 aamkvapkvafaadkekpkeelgvaplPagkggkpgilgayglaipkgsknpeaAkkFldfllspeaq 314
                                    +a ++++ v ++ +ke++                    + + ++ip ++  p+ A ++++fll p+ +
  gi|119719819|ref|YP_920314.1| 247 QAQSENKSVEYVLPKEGAFV------------------WIDFMVIPVNARSPDLAYEWINFLLDPAVA 296
                                    88777777777777777755..................99************************9975 PP

>> SBP_bac_11  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.0     3e-11   1.1e-07      13     222 ..      46     297 ..      36     304 .. 0.81

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 3e-11
                                    HHHHHHHHHHHH---EEEE.ESSHHHHHHHHHHH...-SEEEESSH.HHHHHHHHGGGGG.................... CS
                     SBP_bac_11  13 lrelaaaFeahtgvkvevs.aggsgklarqiadga.rpDvwipassawlellaaaglvqa.................... 70 
                                      +++++Fe+++gvkv +  + ++ +++++++ g   +Dv++++++ ++ +++++glv++                    
  gi|119719819|ref|YP_920314.1|  46 NPDIIKDFESKYGVKVIYDeYESAEEAYAKLQLGGgGYDVIVLTDQ-YVPQAVKKGLVAQldktripnlgnvdrvffenn 124
                                    45899**********96653888999*****88877********95.8999999************************** PP

                                    .....GG-EEEEEEEEEEEESTT-TT..---SHHHHHHSS--EEEE--T-TTTTH.H.HHHHGGG--......HHHHHHH CS
                     SBP_bac_11  71 .....esavplassplviavpkgnpk..kikgwadLlkpglklavadPttspsGl.aalalleaaga......qellkal 136
                                           avp+a  +  i v+++  +   i g ++L +   k+ ++  + + s l   l++++aa        +++ ++ 
  gi|119719819|ref|YP_920314.1| 125 fdpglRYAVPYAWGTTGIGVNRDYVAegEIEGYEQLFDT--KVFLPRHKGKVSMLeEFLEVVNAAKLylgiplNDWSEES 202
                                    ***********************85546899****9976..566666666555555777888888666667775566666 PP

                                    HHTEEEEESSHHHHHHH..........HHTTT-SEEEEEHHHHH...HSTTSSEEEE--TTT--...EEEEEEEE-TT-- CS
                     SBP_bac_11 137 ekkvvklgessrqllta..........veageadagivyeseakaa.engdkleavylpeglnldpldypaavlkkaakr 205
                                    ++++  l    r+ l+           ++ g+  a+ ++  ++ +a ++ + +e+v ++eg  +  +d+ ++++ +a+++
  gi|119719819|ref|YP_920314.1| 203 KQRIIELLREQRDFLAGyygasvyipaLAKGDLHAAHAWSGDVVQAqSENKSVEYVLPKEGAFV-WIDF-MVIPVNARSP 280
                                    666555555555555555555555577999*********9988666268889**********98.8999.669999**** PP

                                    HHHHHHHHHTTSHHHHH CS
                     SBP_bac_11 206 eaAraFlafLrspeaqa 222
                                      A ++++fL+ p++ a
  gi|119719819|ref|YP_920314.1| 281 DLAYEWINFLLDPAVAA 297
                                    *************9987 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.9   6.4e-08   0.00023       1      22 [.       2      23 ..       2      25 .. 0.92
   2 ?   -1.7   0.0      0.85   3.1e+03       5      10 ..     214     219 ..     214     219 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 6.4e-08
                     TAT_signal  1 klSRRdFLKgsAAaaAAaalgg 22
                                   kl+RR+FL   +AaaA+a  g+
  gi|119719819|ref|YP_920314.1|  2 KLTRRQFLASLGAAAALASIGA 23
                                   68****************9997 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.85
                     TAT_signal   5 RdFLKg 10 
                                    RdFL g
  gi|119719819|ref|YP_920314.1| 214 RDFLAG 219
                                    9***76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.22s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 2847.15
//
Query:       gi|119719820|ref|YP_920315.1|  [L=263]
Description: binding-protein-dependent transport systems inner membrane component [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-14   54.3   8.5    1.4e-14   54.3   8.5    1.9  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    2.7   0.7    0.0051        91     113     181 ..      12      87 ..       5      88 .. 0.46
   2 !   54.3   8.5   7.8e-19   1.4e-14       2     171 ..      75     246 ..      74     256 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.0051
                   BPD_transp_1 113 glilafggllggavlleflgs..wpG......lgtllleailgydyseisnggvlalviavlllnlvadilqrlldp 181
                                     l+laf ++  +++++  + +  +pG      l   +  a  +  +++++  g++++v++  l +++  + + ++++
  gi|119719820|ref|YP_920315.1|  12 ALLLAFLYAPLAFIVVQSFNAakYPGawrgftLEWYFELARDSEILQAAA-NGLAVAVLSATLSTVLGGVAAYYFSK 87 
                                    44444444444444444332211222333244444444444444444444.66777777777776666666666666 PP

  == domain 2  score: 54.3 bits;  conditional E-value: 7.8e-19
                   BPD_transp_1   2 illGilaa.lnrnkkldkllrpliivllslPsfv..laillvlvfvilsilghlilpviillllsaapyvrlirraalrs 78 
                                    ++lG +aa +++++  + + + +++++  +P +v  + +l++   + + ++  +++ v++  + +++ y+++  +  +++
  gi|119719820|ref|YP_920315.1|  75 TVLGGVAAyYFSKRGSSGAADSFFYAPIVIPEIVesVSLLML---YYSAGVELGFWTVLVGHTAYNVSYAYVALKPQFKV 151
                                    57899999566666677899**************88444444...4689******************************* PP

                   BPD_transp_1  79 lpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis.... 154
                                     +++ + aa++lGa+++ +f++v +P+alp i+++l+++f+ ++ ++v + f++ +pG+  +l  +i+++     +    
  gi|119719820|ref|YP_920315.1| 152 TSRSVEDAAYTLGARPFDVFVRVYFPMALPGIVASLLITFAMSFDDFVKTAFTT-GPGF-KTLPLVIWARAARGRAttel 229
                                    ******************************************************.5664.45555555555554443343 PP

                   BPD_transp_1 155 nggvlalviavlllnlv 171
                                    n+++  ++++ l+ + v
  gi|119719820|ref|YP_920315.1| 230 NALASLMILVSLAASYV 246
                                    35555555555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1891.12
//
Query:       gi|119719821|ref|YP_920316.1|  [L=256]
Description: binding-protein-dependent transport systems inner membrane component [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.4e-15   55.2  14.3    7.4e-15   55.2  14.3    2.1  2  BPD_transp_1     Binding-protein-dependent transport system i
  ------ inclusion threshold ------
        1.9    8.4  14.1       0.37   10.7   6.5    2.7  2  Peptidase_M48_N  CAAX prenyl protease N-terminal, five membra


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   2.1     0.047   4.3e+02      43     168 ..      32      70 ..       8      88 .. 0.40
   2 !   55.2  14.3   8.2e-19   7.4e-15      26     174 ..      96     246 ..      92     252 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.047
                   BPD_transp_1  43 f...................vilsilghlilpviillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvl 103
                                    f                   +                                                           
  gi|119719821|ref|YP_920316.1|  32 FeslrgggvsvyyqvvtnedY----------------------------------------------------------- 52 
                                    234444444433333333321........................................................... PP

                   BPD_transp_1 104 PnalppiitglilafggllggavlleflgswpGlgtllleailgydyseisnggvlalviavlll 168
                                                                                    +i++ + l++vi++++ 
  gi|119719821|ref|YP_920316.1|  53 -----------------------------------------------LAIIAYSGLIAVIVTAVT 70 
                                    ...............................................222211111111111111 PP

  == domain 2  score: 55.2 bits;  conditional E-value: 8.2e-19
                   BPD_transp_1  26 vllslPsfv.......laillvlvf...vilsilghlilpviillllsaapyvrlirraalrslpkdlveaaralGasrw 95 
                                    v ++lP++v               +   + l +l +++ +v+i +++ ++p+++l +++ ++ +++ l eaa++lGa++ 
  gi|119719821|ref|YP_920316.1|  96 VAFTLPMLVnfllrayA-------LmniFSLLGLANSFQAVVIGMVYEYFPLMLLPVYSTFERVERRLLEAAETLGAKPH 168
                                    67889999944444431.......3433455788899999**************************************** PP

                   BPD_transp_1  96 qifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis.nggvlalviavlllnlvadi 174
                                    q + +v++P ++p i++g+ l+f  +++++v++ +lg+    g+++    +   + + + ++g++ ++i++++ +l++++
  gi|119719821|ref|YP_920316.1| 169 QAVLRVLVPVSAPGILSGVTLVFLMAFTEFVVPAMLGGV--YGYTVGYLVWDLFLKYRNwAAGSALALIITAASLLAVYA 246
                                    *************************************55..566666666666666555334444444444444444444 PP

>> Peptidase_M48_N  CAAX prenyl protease N-terminal, five membrane helices
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   6.5   4.1e-05      0.37      56     139 ..      38     117 ..      18     149 .. 0.73
   2 ?    0.3   2.0     0.061   5.5e+02      88     149 ..     182     251 ..     131     254 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 4.1e-05
                Peptidase_M48_N  56 gllpflwklsgkllgldaeseilqslvfllllslistlislPfslYstFviEekhGfnkqtlklfikdklkslllalvig 135
                                    g++ + ++++++    d    i+ s ++ ++++ ++ l slP+++Y  F++E + G  k  ++ f + +l ++ll +  +
  gi|119719821|ref|YP_920316.1|  38 GGVSVYYQVVTN---EDYLAIIAYSGLIAVIVTAVTLLASLPVAYYLAFYVESEEGKSKLLVA-FTLPMLVNFLLRAYAL 113
                                    555555555555...3556778899999999*************************9987665.6667777777776655 PP

                Peptidase_M48_N 136 lpll 139
                                    + + 
  gi|119719821|ref|YP_920316.1| 114 MNIF 117
                                    5444 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.061
                Peptidase_M48_N  88 slistlislPfslYstFviEekhG.fnkqtlklfikdklk.......slllalviglpllaallwiiewg 149
                                     ++s ++ + +  + +Fv+ +  G +   t++  ++d++        + +lal+i++  l+a+   ++wg
  gi|119719821|ref|YP_920316.1| 182 GILSGVTLVFLMAFTEFVVPAMLGgVYGYTVGYLVWDLFLkyrnwaaGSALALIITAASLLAVYAYMRWG 251
                                    5555555555555555555554321344444444444432011111145777777777777777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       918  (0.051202); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1840.36
//
Query:       gi|119719822|ref|YP_920317.1|  [L=361]
Description: ABC transporter related [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.7e-37  126.9   0.0    1.2e-36  126.2   0.0    1.3  1  ABC_tran         ABC transporter
    7.5e-13   48.9   1.2    2.3e-07   31.0   0.2    2.3  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    2.4e-07   30.8   0.4    9.4e-07   28.9   0.1    2.2  2  TOBE_2           TOBE domain
    0.00025   21.5   0.1     0.0009   19.8   0.0    2.1  1  CysA_C_terminal  CysA C-terminal regulatory domain
    0.00077   19.1   0.9       0.58    9.7   0.0    2.7  2  AAA_25           AAA domain
      0.001   19.3   0.1      0.015   15.5   0.1    2.3  1  SbcCD_C          Putative exonuclease SbcCD, C subunit
     0.0012   18.8   0.0     0.0019   18.2   0.0    1.2  1  Rad17            Rad17 P-loop domain
     0.0015   18.8   1.4      0.028   14.7   1.4    2.2  1  AAA_22           AAA domain
     0.0025   18.2   0.4     0.0074   16.7   0.4    1.9  2  AAA_16           AAA ATPase domain
     0.0027   18.2   0.0     0.0055   17.2   0.0    1.4  1  AAA_23           AAA domain
     0.0029   17.1   0.0       0.18   11.2   0.0    2.1  2  SMC_N            RecF/RecN/SMC N terminal domain
     0.0057   16.6   0.0     0.0091   15.9   0.0    1.5  1  ATPase_2         ATPase domain predominantly from Archaea
     0.0099   16.3   0.1      0.038   14.4   0.1    2.1  1  AAA              ATPase family associated with various cellul
  ------ inclusion threshold ------
      0.012   15.3   0.0      0.024   14.4   0.0    1.4  1  AAA_29           P-loop containing region of AAA domain
       0.04   13.3   0.0      0.056   12.9   0.0    1.1  1  HSM3_N           DNA mismatch repair protein HSM3, N terminal
      0.045   13.7   0.0      0.095   12.6   0.0    1.6  1  NACHT            NACHT domain
      0.065   12.6   0.2        2.8    7.3   0.1    2.1  2  TniB             Bacterial TniB protein
      0.095   12.6   0.0       0.21   11.5   0.0    1.5  2  RsgA_GTPase      RsgA GTPase
      0.098   12.9   0.1       0.34   11.1   0.0    1.9  2  AAA_28           AAA domain
        0.1   11.3   0.2         11    4.7   0.0    2.8  2  ABC_ATPase       Predicted ATPase of the ABC class
       0.19   11.4   0.0         13    5.3   0.0    2.0  2  AAA_15           AAA ATPase domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.2   0.0   1.4e-39   1.2e-36       1     136 [.      25     169 ..      25     170 .. 0.94

  Alignments for each domain:
  == domain 1  score: 126.2 bits;  conditional E-value: 1.4e-39
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren. 79 
                                    l+ v+l++++ge+  i+G++G+GK+tLl+++agl+ p+ G++ +dg d++   l+ +++ ig+++q+  lfp+ltv++n 
  gi|119719822|ref|YP_920317.1|  25 LRGVTLEVERGELFSILGPSGCGKTTLLRIIAGLSAPDRGKVFFDGVDVTG--LPAYERDIGMVFQDLALFPHLTVYKNv 102
                                    6789***********************************************..*************************** PP

                                    ............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    ............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                 +++++ ++l+ + l+   +  ++++ ++LSgGq+qrva+aral+++p+llllDEp+
  gi|119719822|ref|YP_920317.1| 103 afslelagvpreVAERRVREVLELVHLPF--EVFAHRKIQQLSGGQQQRVAIARALARDPRLLLLDEPF 169
                                    *********99888888999999999988..44445555*****************************7 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   4.8e-06    0.0041       3      25 ..      39      61 ..      37     115 .. 0.76
   2 !   31.0   0.2   2.6e-10   2.3e-07     219     298 ..     122     201 ..      96     206 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.8e-06
                         AAA_21  3 vliGpNgsGKSnLLdaldllarl 25
                                    + Gp g+GK++LL+++ +l+  
  gi|119719822|ref|YP_920317.1| 39 SILGPSGCGKTTLLRIIAGLSAP 61
                                   589****************9753 PP

  == domain 2  score: 31.0 bits;  conditional E-value: 2.6e-10
                         AAA_21 219 r..gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQvilt 295
                                    +   +v+l  +    + + +lS G+++  a++ al+r++   +lll+DEp ++L++k+  +l++ lk+l+r +g+  + +
  gi|119719822|ref|YP_920317.1| 122 EvlELVHLPFEVFAHRKIQQLSGGQQQRVAIARALARDP---RLLLLDEPFSHLDYKVRLELIKELKRLQReTGVTTVYV 198
                                    2456777778888888899*********9********99...************************999999******** PP

                         AAA_21 296 THS 298
                                    TH+
  gi|119719822|ref|YP_920317.1| 199 THD 201
                                    **8 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0         9   7.7e+03      27      42 ..     240     255 ..     238     259 .. 0.82
   2 !   28.9   0.1   1.1e-09   9.4e-07       2      76 .]     283     358 ..     282     358 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 9
                         TOBE_2  27 eylGsstryvvelagg 42 
                                    ++lG+s +++++  gg
  gi|119719822|ref|YP_920317.1| 240 SFLGESNLVRLRAVGG 255
                                    6999999999987766 PP

  == domain 2  score: 28.9 bits;  conditional E-value: 1.1e-09
                         TOBE_2   2 aiRPEklrla.aaggan.glsGtVedveylGsstryvvelaggqlvvvrqpnadrdsalapGdtVelswdpddavvl 76 
                                     +RPE+++l+ ++ g+   ++++V+d+++lG  t++v++  g + +++  p++d +s l++   V + +d   ++v+
  gi|119719822|ref|YP_920317.1| 283 FVRPEHVSLHpPPHGRYiEVEAVVVDRVFLGPLTKVVLDGLGDAAFEALFPSRD-ASGLEERAPVKVYIDLSETRVF 358
                                    69*******984444467**********************************99.6899999999999998888776 PP

>> CysA_C_terminal  CysA C-terminal regulatory domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   1.1e-06    0.0009       1      42 [.     246     290 ..     246     291 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.1e-06
                CysA_C_terminal   1 NlFhGrvedGklriGglalpvP....elagadgqevvayVRPhDle 42 
                                    Nl + r+ +G +++ g++l++     e++g+ g ev+++VRP+++ 
  gi|119719822|ref|YP_920317.1| 246 NLVRLRAVGGVAEFRGARLDLSllseEYKGYTG-EVTLFVRPEHVS 290
                                    677778889**********************88.*********986 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0   0.00068      0.58      28      55 ..      31      57 ..       7      78 .. 0.71
   2 !    7.1   0.2    0.0042       3.6     167     190 ..     179     202 ..     109     206 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00068
                         AAA_25 28 gllpagelallaGapgtGKttlaldlal 55
                                   ++  +gel  + G++g+GKttl+  +a 
  gi|119719822|ref|YP_920317.1| 31 EV-ERGELFSILGPSGCGKTTLLRIIAG 57
                                   55.799****************866555 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0042
                         AAA_25 167 alvealeriarrtgaavllvhHvg 190
                                    +l++ l+r++r+tg++++ v H  
  gi|119719822|ref|YP_920317.1| 179 ELIKELKRLQRETGVTTVYVTHDQ 202
                                    689*******************65 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   1.7e-05     0.015      27      86 ..     136     182 ..     131     186 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.7e-05
                        SbcCD_C  27 srssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatlle 86 
                                    +r++++lSGG++q    +a+a     ++ +      ++rl++LDE Fs lD + + +l++
  gi|119719822|ref|YP_920317.1| 136 HRKIQQLSGGQQQR---VAIA----RALAR------DPRLLLLDEPFSHLDYKVRLELIK 182
                                    78899999999953...3444....33333......59*************998877776 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   2.2e-06    0.0019      33      67 ..      23      57 ..      19     103 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.2e-06
                          Rad17 33 ewlkadvLesrkkriLLisGPsGCgkstvvkvLsk 67
                                   e+l+  +Le ++ ++  i GPsGCgk+t +++++ 
  gi|119719822|ref|YP_920317.1| 23 EALRGVTLEVERGELFSILGPSGCGKTTLLRIIAG 57
                                   67888899999999*****************9985 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   1.4   3.2e-05     0.028       7     129 ..      37     199 ..      32     207 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.2e-05
                         AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaee.................erpevvfvtlpsstsskdllrellralglelk 69 
                                    +  + G+sG+GKTtllr ++      ++  +                 ++ + vf +l+      +++++++  l+l + 
  gi|119719822|ref|YP_920317.1|  37 LFSILGPSGCGKTTLLRIIAGLSA--PD--RgkvffdgvdvtglpayeRDIGMVFQDLALFP-HLTVYKNVAFSLELAGV 111
                                    56799************9998862..22..24466777777777776533333333333333.55555555555555444 PP

                         AAA_22  70 a......................erlsseell.ealeqalrarav...ielliiDE.aqhlr...seealeeLrsllnls 119
                                                           +  + ++l   + ++ + ara    ++ll++DE + hl+   + e+++eL++l+   
  gi|119719822|ref|YP_920317.1| 112 PrevaerrvrevlelvhlpfevfAHRKIQQLSgGQQQRVAIARALardPRLLLLDEpFSHLDykvRLELIKELKRLQR-- 189
                                    488888888888888888888885555555553333333333333567779999996666988666999999999999.. PP

                         AAA_22 120 rkgvqliLvG 129
                                    ++gv+ ++v 
  gi|119719822|ref|YP_920317.1| 190 ETGVTTVYVT 199
                                    9999988875 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.4   8.7e-06    0.0074      19      51 ..      32      62 ..      17     196 .. 0.75
   2 ?   -2.2   0.0       5.5   4.7e+03      40      63 ..     180     203 ..     178     229 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 8.7e-06
                         AAA_16 19 vrsgrpelvllsGesGvGKsslvrellralekd 51
                                   v +g  el  + G+sG+GK++l+r ++     d
  gi|119719822|ref|YP_920317.1| 32 VERG--ELFSILGPSGCGKTTLLRIIAGLSAPD 62
                                   4444..8999*************9988533333 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5.5
                         AAA_16  40 lvrellralekd.ggiflrgkcdql 63 
                                    l++el+r l+++ g+ +++ + dq+
  gi|119719822|ref|YP_920317.1| 180 LIKELKR-LQREtGVTTVYVTHDQN 203
                                    6777774.55552566699999998 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   6.4e-06    0.0055      11      39 ..      26      55 ..      23      58 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 6.4e-06
                         AAA_23 11 rdqeidFsk.gltlItGpNGaGKTTildAi 39
                                   r+++++ ++  l+ I Gp G+GKTT+l+ i
  gi|119719822|ref|YP_920317.1| 26 RGVTLEVERgELFSILGPSGCGKTTLLRII 55
                                   566777755369***************987 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0      0.04        34      26      42 ..      37      53 ..      24      58 .. 0.80
   2 !   11.2   0.0   0.00021      0.18     134     202 ..     139     203 ..      80     219 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.04
                                   EEEEEESTTSSHHHHHH CS
                                   xxxxxxxxxxxxxxxxx RF
                          SMC_N 26 ftaivGpNGSGKsnlld 42
                                   + +i+Gp G+GK+ ll 
  gi|119719822|ref|YP_920317.1| 37 LFSILGPSGCGKTTLLR 53
                                   5579*********9986 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00021
                                    TTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 134 kelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreeml 202
                                    +++LSgG+++ va+a  +A    +   l llDe  ++LD k + ++ + lk+ + ++ +  + +++++ 
  gi|119719822|ref|YP_920317.1| 139 IQQLSGGQQQRVAIARALA----RDPRLLLLDEPFSHLDYKVRLELIKELKRLQRETGVTTVYVTHDQN 203
                                    349**********998876....344589*****************99999888776554443333333 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.1e-05    0.0091      15      57 ..      30      71 ..      20     191 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.1e-05
                       ATPase_2 15 lerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyial 57
                                   le e+ e   i Gp g+GKt+Ll+ i+  +   d  +++++ +
  gi|119719822|ref|YP_920317.1| 30 LEVERGELFSILGPSGCGKTTLLRIIAGLS-APDRGKVFFDGV 71
                                   5666688899*************9766555.556666776655 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1   4.4e-05     0.038       3      22 ..      40      59 ..      38     213 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.4e-05
                                   EESSTTSSHHHHHHHHHHHH CS
                            AAA  3 lyGppGtGKTllakavakel 22
                                   + Gp G+GKT+l + +a  +
  gi|119719822|ref|YP_920317.1| 40 ILGPSGCGKTTLLRIIAGLS 59
                                   57**************9875 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   2.8e-05     0.024      13      43 ..      26      56 ..      22      69 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.8e-05
                         AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDAiq 43
                                   +g t+e+++ + + + GpsG GK+Tll  i+
  gi|119719822|ref|YP_920317.1| 26 RGVTLEVERGELFSILGPSGCGKTTLLRIIA 56
                                   5678899977799*************95555 PP

>> HSM3_N  DNA mismatch repair protein HSM3, N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   6.6e-05     0.056      27      97 ..     137     207 ..     118     231 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.6e-05
                         HSM3_N  27 kcslnlstvaklkedakrllanikrllvenksedkldydlllelldklvkvssfedvlevysvddlvkalk 97 
                                    + + +ls  ++ +  + r la   rll+ +++ ++ldy++ lel+++l ++     v +vy ++d  +a+ 
  gi|119719822|ref|YP_920317.1| 137 RKIQQLSGGQQQRVAIARALARDPRLLLLDEPFSHLDYKVRLELIKELKRLQRETGVTTVYVTHDQNEAMM 207
                                    55667888888889999************************************************999875 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00011     0.095       4      22 ..      39      57 ..      36      68 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00011
                                   EEEC-TTTCHHHHHHHHHH CS
                          NACHT  4 ilqGeaGsGKTtLlqklal 22
                                    + G++G+GKTtLl+ +a 
  gi|119719822|ref|YP_920317.1| 39 SILGPSGCGKTTLLRIIAG 57
                                   589***********99885 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0      0.06        52      36      53 ..      36      53 ..      23      65 .. 0.82
   2 ?    7.3   0.1    0.0033       2.8     115     165 ..     155     203 ..     116     212 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.06
                           TniB 36 pnlllvGdsnnGKtmive 53
                                   +   ++G+s +GKt++++
  gi|119719822|ref|YP_920317.1| 36 ELFSILGPSGCGKTTLLR 53
                                   56679**********987 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0033
                           TniB 115 lrelkvrvLiiDEihnllagsarkqreflnalksLgnelkipivlvGteea 165
                                      + ++r+L++DE  + l   ++ + e++  lk+L++e  ++ v+v  ++ 
  gi|119719822|ref|YP_920317.1| 155 ALARDPRLLLLDEPFSHL--DYKVRLELIKELKRLQRETGVTTVYVTHDQN 203
                                    334579*******87777..79999*******************9976655 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00024      0.21      98     121 ..      34      57 ..       8      66 .. 0.80
   2 ?   -3.4   0.0         9   7.7e+03      65      89 ..     181     205 ..     170     217 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00024
                                    TTSEEEEECSTTSSHHHHHHHHCT CS
                    RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallp 121
                                    ++++  ++G+SG GK+tL+  +++
  gi|119719822|ref|YP_920317.1|  34 RGELFSILGPSGCGKTTLLRIIAG 57 
                                    4488899************98876 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 9
                                    HHHHHHHHHHTTSEEEE--TTTHTT CS
                    RsgA_GTPase  65 leelkeelealgyevllvsaktkeg 89 
                                    ++elk   +++g+++++v  +++e+
  gi|119719822|ref|YP_920317.1| 181 IKELKRLQRETGVTTVYVTHDQNEA 205
                                    6677777788888888776665443 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0    0.0004      0.34       3      20 ..      39      56 ..      37      73 .. 0.85
   2 ?   -1.7   0.0       3.6   3.1e+03      50      79 ..     134     166 ..     106     176 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0004
                         AAA_28  3 vitGgestGKTtlleaLa 20
                                    i+G++++GKTtll+ +a
  gi|119719822|ref|YP_920317.1| 39 SILGPSGCGKTTLLRIIA 56
                                   599***********9887 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.6
                         AAA_28  50 edllafaervleeqleee.aaa..aankvlfcD 79 
                                    +   +++++   +q + + a+a  +++++l++D
  gi|119719822|ref|YP_920317.1| 134 FAHRKIQQLSGGQQQRVAiARAlaRDPRLLLLD 166
                                    333333333333333222122233788888887 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1     0.039        33     242     264 ..      32      55 ..      22      58 .. 0.85
   2 ?    4.7   0.0     0.013        11     321     366 ..     140     185 ..     126     232 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.039
                                    E-SS.EEEEEE-TTSSHHHHHHHH CS
                     ABC_ATPase 242 ipkG.vtlIvGggfhGKsTLLeAl 264
                                    + +G ++ I G+   GK+TLL+ +
  gi|119719822|ref|YP_920317.1|  32 VERGeLFSILGPSGCGKTTLLRII 55 
                                    678889***************976 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.013
                                    SS--HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HHHHHHS CS
                     ABC_ATPase 321 edASGStsqAanimealeagakllLiDEDtsAtNlmirDermqelv 366
                                    ++ SG   q ++i++al ++ +llL+DE  s     +r e+++el 
  gi|119719822|ref|YP_920317.1| 140 QQLSGGQQQRVAIARALARDPRLLLLDEPFSHLDYKVRLELIKELK 185
                                    6679999999999999999999999999877666666555555554 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.016        13      25      44 ..      37      56 ..      24      82 .. 0.80
   2 ?    4.1   0.0     0.038        32     323     365 ..     159     201 ..     138     203 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.016
                         AAA_15 25 ltvliGkNnsGKSsileald 44
                                   l  + G+ ++GK+++l+++ 
  gi|119719822|ref|YP_920317.1| 37 LFSILGPSGCGKTTLLRIIA 56
                                   77899************996 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.038
                         AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                    ++ +ll++EP  hL ++   +lik lk+l +++   +++ TH 
  gi|119719822|ref|YP_920317.1| 159 DPRLLLLDEPFSHLDYKVRLELIKELKRLQRETGVTTVYVTHD 201
                                    5689*****************************99*******7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.49
# Mc/sec: 2205.17
//
Query:       gi|119719823|ref|YP_920318.1|  [L=148]
Description: hypothetical protein Tpen_0914 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.22   11.0   0.0       0.29   10.6   0.0    1.1  1  DUF1221   Protein of unknown function (DUF1221)


Domain annotation for each model (and alignments):
>> DUF1221  Protein of unknown function (DUF1221)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   1.6e-05      0.29      49      74 ..      98     124 ..      80     133 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 1.6e-05
                        DUF1221  49 lrelhrvvkegeaYvrqcldtkdw.wa 74 
                                    + e ++ ++e+eaYvr+ l++k + wa
  gi|119719823|ref|YP_920318.1|  98 INERFKSYRETEAYVRSLLEEKGFsWA 124
                                    234467789*************54376 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 953.69
//
Query:       gi|119719824|ref|YP_920319.1|  [L=354]
Description: hypothetical protein Tpen_0915 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-21   77.8   0.0    1.9e-14   54.1   0.0    3.1  3  Nitroreductase  Nitroreductase family
     0.0016   18.1   0.1      0.055   13.0   0.0    2.6  3  TM1586_NiRdase  Putative TM nitroreductase


Domain annotation for each model (and alignments):
>> Nitroreductase  Nitroreductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.2   0.0    0.0043        39      28      48 ..      54      74 ..      12      87 .. 0.81
   2 !   16.0   0.0   1.1e-06    0.0096      95     137 ..     105     147 ..      94     150 .. 0.90
   3 !   54.1   0.0   2.2e-18   1.9e-14       2     170 .]     193     352 ..     192     352 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0043
                                   HTS--GGG---EEEEEE.-CC CS
                 Nitroreductase 28 rraPsagnlqpwrfvvvqdke 48
                                   r++Psag ++p++++v +++e
  gi|119719824|ref|YP_920319.1| 54 RTVPSAGATYPLEVYVSSRGE 74
                                   78**************86665 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 1.1e-06
                                    EE---TTS---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EE CS
                 Nitroreductase  95 vivatldkserkaaerayryalldagaaaqnllLaAtalGlgs 137
                                    v++a++++ +++++er+yry  +++g+a+qnl L+  ++Gl+ 
  gi|119719824|ref|YP_920319.1| 105 VLTAFPGRTTTYYGERGYRYVRMELGHALQNLFLSIYSHGLAG 147
                                    4467999*********************************986 PP

  == domain 3  score: 54.1 bits;  conditional E-value: 2.2e-18
                                    HH--B---B-S----HHHHHHHHHHH........HTS--GGG---EEEEEE..-CCCH....HHHHHHHHHH..HHHHHT CS
                 Nitroreductase   2 rkRrSiRkFddepvpkeelekileaa........rraPsagnlqpwrfvvv.qdkelr....yklaeaalel..llkaea 66 
                                    + RrS+R++   ++ +e l++i++          r +P  g+ + ++ +vv ++ +      y+++ + lel  ++++e 
  gi|119719824|ref|YP_920319.1| 193 AARRSVRNYARASLGLEALDSIMKWSmgevvegaRPYPKLGGGYAVEGYVVaTSVKGVekglYRFNSSELELelVRVGEF 272
                                    68*********************9999999999899***************77666668888888766665500555555 PP

                                    T-SS-GGGGGGHHHHHHHHHHHHSSEEEEE---TTS---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GGGGG CS
                 Nitroreductase  67 qaelaqryrkeelklkaqkalagapvlivivatldkserkaaerayryalldagaaaqnllLaAtalGlgscpiggfdea 146
                                    +++l++        ++ q  +++ap+++v+             ++ + a +++ga+ qn++L A  +Glg++ ig+f+++
  gi|119719824|ref|YP_920319.1| 273 AEKLWRA-------ALMQGSVRKAPAVVVL------------TGRGPLAEVEVGAVGQNIYLNAVHEGLGTVAIGAFEDE 333
                                    5555555.......9***************............99************************************ PP

                                    HHHHHHHHT-S..SEEEEEEEEE- CS
                 Nitroreductase 147 aeevrkllglpdeeeivvliavGy 170
                                    +  v  +l+++d   +++l++vG+
  gi|119719824|ref|YP_920319.1| 334 E--VSSILEVED---PLYLMPVGK 352
                                    *..********5...99****995 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       0.2   1.8e+03      78     101 ..     123     146 ..     115     148 .. 0.81
   2 ?    1.8   0.0     0.017   1.5e+02       6      28 ..     192     214 ..     188     219 .. 0.81
   3 !   13.0   0.0   6.2e-06     0.055      40     132 ..     261     352 ..     243     354 .] 0.69

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.2
                                    HHHHHHHHHHHHHHHHHHHHTT-E CS
                 TM1586_NiRdase  78 edleekaGYygeqlvLkltalGlg 101
                                    + +++++G  +++l L + ++Gl+
  gi|119719824|ref|YP_920319.1| 123 RYVRMELGHALQNLFLSIYSHGLA 146
                                    567899***************996 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.017
                                    HHH--B---B--S---HHHHHHH CS
                 TM1586_NiRdase   6 iekRhsvRkYkdealeeelleel 28 
                                    +  R+svR+Y   +l  e l+ +
  gi|119719824|ref|YP_920319.1| 192 VAARRSVRNYARASLGLEALDSI 214
                                    678********999887777766 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 6.2e-06
                                    S-----EE.E...............-SSSSEEEE----SSHHHHHHHHHHHHHHHHHHHHTT-EEEEES--SST...... CS
                 TM1586_NiRdase  40 glelqlvidenkafks..kvaklgkfkgvpnyialvgekkedleekaGYygeqlvLkltalGlgtcWvggtykkkkakve 117
                                    +lel+lv   + a+k+  +   +g   ++p +++l g+    +e+++G +g+++ L+++ +Glgt  +g+  +++ +  +
  gi|119719824|ref|YP_920319.1| 261 ELELELVRVGEFAEKLwrAALMQGSVRKAPAVVVLTGRG-PLAEVEVGAVGQNIYLNAVHEGLGTVAIGAFEDEEVS--S 337
                                    555555555544444310333445677888888888865.79***********************999975555333..5 PP

                                    .....T-S-EEEEE- CS
                 TM1586_NiRdase 118 lkkgeklvivIalGy 132
                                    + + e+ ++++ +G+
  gi|119719824|ref|YP_920319.1| 338 ILEVEDPLYLMPVGK 352
                                    555555566666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       227  (0.0126611); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 2539.72
//
Query:       gi|119719825|ref|YP_920320.1|  [L=187]
Description: RdgB/HAM1 family non-canonical purine NTP pyrophosphatase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      1e-46  159.2   0.0    1.2e-46  159.1   0.0    1.0  1  Ham1p_like  Ham1 family


Domain annotation for each model (and alignments):
>> Ham1p_like  Ham1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.1   0.0   6.5e-51   1.2e-46       1     187 []       3     179 ..       3     179 .. 0.89

  Alignments for each domain:
  == domain 1  score: 159.1 bits;  conditional E-value: 6.5e-51
                                    EEEC-S-HHHHHHHHHHTTTECCCE.EECCCCEE----BS.SSHHHHHHHHHHHHHHHTS-EEEEEEEEEEGGGTTTBGG CS
                     Ham1p_like   1 ivfaTgNkgKlrevkeilaeellevkslkelelpeveEtq.gtfeenalkKaraaaeaglpvladDsgLevdaLnglPGv 79 
                                    ++++TgN +K++e++  l++ ++e++ l      e  E+q +++e++al  a+++   ++p++++D gL+v+aLng+PG+
  gi|119719825|ref|YP_920320.1|   3 VYVVTGNVHKVAELSLALKPFGVELEPL----RAEKLEVQsESLEKIALVAAEHLPPLDKPAIVEDAGLFVKALNGFPGP 78 
                                    589***********99999888888877....23434999999**********99877777******************* PP

                                    GTTTTTHTTCHHHHHHHHHHHHCTHTTS--EEEEEEEEEEEETTTTEEEEEEEEEEEEE-SS.--SSSSTTGGGEEETT- CS
                     Ham1p_like  80 ysarfagegaedeenlaklleeleeeeedrsArfvcvlaladpeeeeellfeGeveGeiveeprgeggfGyDpiFvpeeg 159
                                    ys++  +     + +++ ll+ +e+++ dr+A f++v+al  p +++++lf+Ge  G i+ee+rg+ggfG+Dp+F p+++
  gi|119719825|ref|YP_920320.1|  79 YSSYAYK-----TIGCRGLLKLMEGVS-DREAVFRSVIALRMP-DGSIHLFKGEAAGVITEEERGTGGFGFDPVFRPRGS 151
                                    ***9964.....446778888887545.8***********999.6666*****************************887 PP

                                    SSBTTTS.CHHHHHHSHHHHHHHHHHHH CS
                     Ham1p_like 160 ektfaelskeeknaiShRgkAlekllef 187
                                    ektfae+++eekn +ShR+kA ++l+e+
  gi|119719825|ref|YP_920320.1| 152 EKTFAEMTTEEKNLYSHRAKAARNLAEW 179
                                    88***********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1432.12
//
Query:       gi|119719826|ref|YP_920321.1|  [L=792]
Description: hypothetical protein Tpen_0917 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (792 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.64u 0.27s 00:00:00.91 Elapsed: 00:00:00.42
# Mc/sec: 5704.28
//
Query:       gi|119719827|ref|YP_920322.1|  [L=166]
Description: hypothetical protein Tpen_0918 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.028   14.4   0.0      0.048   13.7   0.0    1.3  1  DUF3219   Protein of unknown function (DUF3219)


Domain annotation for each model (and alignments):
>> DUF3219  Protein of unknown function (DUF3219)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.7e-06     0.048      43      84 ..     102     143 ..      98     150 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.7e-06
                                    BS-S-EEEEETTTTEEEEEB--S-SS--B--S-B-SSEEEEE CS
                        DUF3219  43 lyekkfdvevPekalafrGeideystsltnlyeegavgefhl 84 
                                    +y   fdv+  + +l + G  ++y t  t l e + v+  ++
  gi|119719827|ref|YP_920322.1| 102 VYRVDFDVSAGNTSLVWLGCASNYDTNTTRLVESEPVSYTYV 143
                                    69999******************************9997775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       808  (0.0450667); expected 358.6 (0.02)
Passed bias filter:                      597  (0.033298); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1105.77
//
Query:       gi|119719828|ref|YP_920323.1|  [L=411]
Description: hypothetical protein Tpen_0919 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 3185.87
//
Query:       gi|119719829|ref|YP_920324.1|  [L=161]
Description: hypothetical protein Tpen_0920 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       776  (0.0432818); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1284.40
//
Query:       gi|119719830|ref|YP_920325.1|  [L=279]
Description: hypothetical protein Tpen_0921 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1782.31
//
Query:       gi|119719831|ref|YP_920326.1|  [L=512]
Description: hypothetical protein Tpen_0922 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.012   15.8   0.1       0.45   10.7   0.0    2.8  3  DUF2057   Uncharacterized protein conserved in bacteria (DUF2
      0.026   13.9   0.1      0.086   12.2   0.1    1.9  1  DUF5305   Family of unknown function (DUF5305)
      0.043   14.1   2.7       0.38   11.0   0.0    2.9  3  CBM_35    Carbohydrate binding module (family 35)
      0.057   13.6  16.3        1.2    9.4   0.4    3.6  3  Big_3_5   Bacterial Ig-like domain (group 3)
       0.07   13.4   3.0       0.93    9.7   0.4    3.2  3  SoxY      Sulfur oxidation protein SoxY


Domain annotation for each model (and alignments):
>> DUF2057  Uncharacterized protein conserved in bacteria (DUF2057)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.61   2.2e+03      18      45 ..     331     358 ..     323     386 .. 0.74
   2 ?    1.1   0.1       0.1   3.7e+02      32      64 ..     383     412 ..     368     423 .. 0.68
   3 ?   10.7   0.0   0.00012      0.45      27      54 ..     441     466 ..     423     472 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.61
                        DUF2057  18 vksslfkgaksltLtpGkhqivvrykdl 45 
                                    v s+ f+++     ++G+ q++v+++++
  gi|119719831|ref|YP_920326.1| 331 VYSGSFSPTIYAAFPEGEAQVAVKVDSN 358
                                    5556666666667789999999999886 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.1
                        DUF2057  32 tpGkhqivvrykdlfkddsdsdsqdlvkS.dpli 64 
                                    t G  ++vvr++ l+ ++s+  ++++v S  +++
  gi|119719831|ref|YP_920326.1| 383 TAG--TLVVRVSPLY-QNSN-VDVKVVGSgGAVV 412
                                    444..69********.6676.4457888844444 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00012
                        DUF2057  27 ksltLtpGkhqivvrykdlfkddsdsds 54 
                                      l L+pG++q+v++y++++  +s++++
  gi|119719831|ref|YP_920326.1| 441 LPLSLDPGSYQVVATYNSPW--GSKTQT 466
                                    457889**************..666555 PP

>> DUF5305  Family of unknown function (DUF5305)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   2.4e-05     0.086      74     137 ..     437     510 ..     425     512 .] 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.4e-05
                        DUF5305  74 ktsrlpiplteqtyeikkdetd.eengeitetvtvkespslae.........gilliilgllaliglvvlirri 137
                                     t +lp++l+ + y++  ++++   ++++t+t tv+     a+         +il++i++++a++++vv+irr 
  gi|119719831|ref|YP_920326.1| 437 GTATLPLSLDPGSYQVVATYNSpWGSKTQTVTYTVPGATAGAQeapgalfqpIILVAIVAVVAIVIVVVVIRRR 510
                                    5789999**********999987666666666666666555557899999999999999999999999999984 PP

>> CBM_35  Carbohydrate binding module (family 35)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.2     0.065   2.3e+02      40      73 ..     233     266 ..     204     278 .. 0.88
   2 ?   -2.8   0.1       2.1   7.4e+03      57      93 ..     333     369 ..     318     392 .. 0.58
   3 ?   11.0   0.0   0.00011      0.38      48      68 ..     448     468 ..     439     492 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.065
                         CBM_35  40 lnVnvekaGeynlnvtfsapygsKentlvvnGta 73 
                                    +nVn   + e+ +nv   +p+ + ++++ v  +a
  gi|119719831|ref|YP_920326.1| 233 MNVNERRTLEFLMNVSKLGPFVKSQYSVQVKVAA 266
                                    899999999*************999999887666 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.1
                         CBM_35  57 sapygsKentlvvnGtavatvafaesdevkqttvitv 93 
                                    s+ ++   ++   +G a   v++   ++ ++t + tv
  gi|119719831|ref|YP_920326.1| 333 SGSFSPTIYAAFPEGEAQVAVKVDSNKYSPVTSRFTV 369
                                    4444444444445555555555555554444444444 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00011
                         CBM_35  48 GeynlnvtfsapygsKentlv 68 
                                    G y+++ t+++p+gsK  t+ 
  gi|119719831|ref|YP_920326.1| 448 GSYQVVATYNSPWGSKTQTVT 468
                                    99**************99874 PP

>> Big_3_5  Bacterial Ig-like domain (group 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.6   5.6e+03      10      19 ..      70      79 ..      63     124 .. 0.64
   2 ?    9.4   0.4   0.00033       1.2       1      52 [.     295     352 ..     295     367 .. 0.75
   3 ?    8.3   7.5   0.00073       2.6      29      69 ..     421     458 ..     362     476 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.6
                                   EEEEEE--CC CS
                        Big_3_5 10 vtltatVtaa 19
                                   v +t+t+t++
  gi|119719831|ref|YP_920326.1| 70 VPVTVTITEV 79
                                   4444444444 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00033
                                    -S-EETTSEEEEEEE--CCCCTTS--EEEEEETTEE-SS....-EE--T..TSEEEEE CS
                        Big_3_5   1 ptsvtagqtvtltatVtaasggtptGtVtftdggttlgt....avllsa..nGtAtlt 52 
                                    p++v+ag+ v +++ +t+  +++ + tVt++ gg+++ +    ++  +a  +G A++ 
  gi|119719831|ref|YP_920326.1| 295 PSTVVAGAYVPISIALTPPVEKDEQATVTVYWGGQPVYSgsfsPTIYAAfpEGEAQVA 352
                                    689*******************************999541111333332445666655 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.00073
                                    EEEETTEE-SS-EE--TTSEEEEEEE-SS-EEEEEEEEEE- CS
                        Big_3_5  29 tftdggttlgtavllsanGtAtltvsalaaGthsitAtYsG 69 
                                    +f  + t++  a++++  GtAtl +s+  +G+++++AtY+ 
  gi|119719831|ref|YP_920326.1| 421 SFSKTPTSIDGASAVE--GTATLPLSLD-PGSYQVVATYNS 458
                                    3444557777777776..*******997.9*********63 PP

>> SoxY  Sulfur oxidation protein SoxY
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.078   2.8e+02      17      40 ..      54      79 ..      50      98 .. 0.78
   2 ?   -3.1   0.0       2.6   9.2e+03      67      85 ..     250     268 ..     245     269 .. 0.69
   3 ?    9.7   0.4   0.00026      0.93      18      87 ..     291     363 ..     283     391 .. 0.62

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.078
                           SoxY 17 vkldaPe..iAengavVpvtvsvdlp 40
                                   v++++P   +A n   Vpvtv+++  
  gi|119719831|ref|YP_920326.1| 54 VSVKVPSelVATNEYEVPVTVTITEV 79
                                   666666533799*********99754 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.6
                           SoxY  67 lgpageaevstrirlaets 85 
                                    lgp ++ ++s+++++a t+
  gi|119719831|ref|YP_920326.1| 250 LGPFVKSQYSVQVKVAATT 268
                                    5555677778888887776 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.00026
                           SoxY  18 kldaPeiAengavVpvtvsvdlpgteadkvksiallvdkNpaplaatfelgp.....ageaevstrirlaetsnv 87 
                                    k++aP  +  ga Vp+++  + p +++++  +++++    p  +  +f+++      +gea+v++++  +++s+v
  gi|119719831|ref|YP_920326.1| 291 KVSAPSTVVAGAYVPISIALTPPVEKDEQ-ATVTVYWGGQPV-YSGSFSPTIyaafpEGEAQVAVKVDSNKYSPV 363
                                    799*****************999755544.344444333332.24444444322222244555444444445544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (512 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       945  (0.0527079); expected 358.6 (0.02)
Passed bias filter:                      629  (0.0350828); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.46
# Mc/sec: 3349.72
//
Query:       gi|119719832|ref|YP_920327.1|  [L=328]
Description: PP-loop domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.5e-12   45.4   0.0    2.2e-11   43.8   0.0    1.7  1  ATP_bind_3     PP-loop family
    4.8e-06   25.6   0.0    6.4e-06   25.2   0.0    1.1  1  tRNA_Me_trans  tRNA methyl transferase
     0.0035   16.8   2.2     0.0035   16.8   2.2    2.5  3  zn-ribbon_14   Zinc-ribbon
  ------ inclusion threshold ------
      0.095   12.8   0.0       0.42   10.7   0.0    2.0  2  QueH           Epoxyqueuosine reductase QueH
      0.099   12.2   8.3        1.3    8.7   0.8    2.7  3  RecR           RecR protein
          3    7.7   8.1        5.4    6.9   0.6    3.0  3  Ribosomal_S14  Ribosomal protein S14p/S29e


Domain annotation for each model (and alignments):
>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   0.0   7.5e-15   2.2e-11       2     156 ..      51     222 ..      50     229 .. 0.82

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 7.5e-15
                                    EEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE--H..........HHC CS
                     ATP_bind_3   2 vlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckklnikleiekvdv..........akk 71 
                                    v+vAvSgG DS++ l+l+ + + +lg++++ + vd g+    + + e++++l+ +l++++++ +++           ++ 
  gi|119719832|ref|YP_920327.1|  51 VAVAVSGGKDSLTTLYLFSRFAGELGVEVFGVAVDEGIAGYREYKLEALRSLAGRLGVEIIVGSFKEyfgftldeavKAL 130
                                    78****************************************************************99999998877444 PP

                                    TTSTCCCH....HHHHHHHHHHHCHHCCT.CEEE---BHHHHHHHHHHHHCCT--CCHH.H-S-SEEEETT..CCEE-CC CS
                     ATP_bind_3  72 kgknleea....ARelRYevlkealkkegievlllAhhadDqaEtfllrlargsglagl.agikeaseias..irlvRPl 144
                                    ++k+++ +       lR  v+++a+++ g++ l+++h+ dD +  f+++  +++    l  gi +++  ++  +  + Pl
  gi|119719832|ref|YP_920327.1| 131 REKGFKVKpcsvCGVLRRYVMNHAAREAGADKLATGHNLDDEVQVFVMNALKNHVEGILrEGIVSERAEEGdlVPRIKPL 210
                                    4555554411114567999******************************9998776443146655554433236667899 PP

                                    CT--HHHHHHHH CS
                     ATP_bind_3 145 Lkvskeeleeyl 156
                                    + +  +e+ +y 
  gi|119719832|ref|YP_920327.1| 211 YFIPEKEVLAYT 222
                                    999998888875 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   2.2e-09   6.4e-06       2     125 ..      50     168 ..      49     184 .. 0.79

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 2.2e-09
                  tRNA_Me_trans   2 kvvvalSgGVDSsvaaallkeqgyevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdfekeykekvfee 81 
                                    +v+va+SgG DS  +++l+ +      gv +  ++   +eg +   e +l+  ++ a +lg+++ v +f++ +  ++ e 
  gi|119719832|ref|YP_920327.1|  50 RVAVAVSGGKDSLTTLYLFSRFA-GELGVEVFGVAV--DEGIAGYREYKLEALRSLAGRLGVEIIVGSFKEYFGFTLDEA 126
                                    8***********99999987643.334444333333..223245778899999****************99998888777 PP

                  tRNA_Me_trans  82 fleeyeeGrTPnPdvlCNkeiKfgallekakeelgadalatGHY 125
                                    +    e+G   +P+ +C      ++++++a +e+gad+latGH 
  gi|119719832|ref|YP_920327.1| 127 VKALREKGFKVKPCSVCGV--LRRYVMNHAAREAGADKLATGHN 168
                                    7777899**********75..455678888888**********5 PP

>> zn-ribbon_14  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.4      0.97   2.9e+03       2       7 ..       3       8 ..       2      12 .. 0.80
   2 ?   -0.4   0.1      0.28   8.5e+02       3       8 ..     140     145 ..     138     146 .. 0.83
   3 !   16.8   2.2   1.2e-06    0.0035       2      19 ..     283     300 ..     282     301 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.97
                   zn-ribbon_14 2 kCerCG 7
                                  kC  CG
  gi|119719832|ref|YP_920327.1| 3 KCYVCG 8
                                  899**9 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.28
                   zn-ribbon_14   3 CerCGy 8  
                                    C+ CG 
  gi|119719832|ref|YP_920327.1| 140 CSVCGV 145
                                    *****7 PP

  == domain 3  score: 16.8 bits;  conditional E-value: 1.2e-06
                   zn-ribbon_14   2 kCerCGylSSqkiCkACv 19 
                                    +C  CG  SS ++Ck C+
  gi|119719832|ref|YP_920327.1| 283 RCAVCGEPSSRPLCKTCL 300
                                    8****************6 PP

>> QueH  Epoxyqueuosine reductase QueH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00014      0.42      22     111 ..      76     166 ..      61     188 .. 0.81
   2 ?   -2.5   0.1       1.6   4.7e+03      75      88 ..     274     287 ..     259     291 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00014
                           QueH  22 gfevtvffynpnihpeeEyekRleelkrlieelkielieed...ydleefleavkglekekekgeRCekCyelrLektae 98 
                                    g+ev ++ +++ i  ++Ey+  le+l++l+ +l++e+i ++   y   +  eavk l+++  k + C++C  lr     +
  gi|119719832|ref|YP_920327.1|  76 GVEVFGVAVDEGIAGYREYK--LEALRSLAGRLGVEIIVGSfkeYFGFTLDEAVKALREKGFKVKPCSVCGVLRRYVMNH 153
                                    56777777888999999997..799*************999322333344578899999999999*************** PP

                           QueH  99 lAkengfdafttt 111
                                     A+e g+d ++t 
  gi|119719832|ref|YP_920327.1| 154 AAREAGADKLATG 166
                                    *********9996 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.6
                           QueH  75 lekekekgeRCekC 88 
                                    ++k + k +RC +C
  gi|119719832|ref|YP_920327.1| 274 ARKPSRKPSRCAVC 287
                                    34445566899999 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.4   0.4       5.1   1.5e+04      19      23 ..       4       8 ..       3       8 .. 0.58
   2 ?    8.0   0.0   0.00069       2.1       8      25 ..     129     146 ..     123     148 .. 0.79
   3 ?    8.7   0.8   0.00043       1.3      17      34 ..     282     299 ..     278     301 .. 0.91

  Alignments for each domain:
  == domain 1  score: -4.4 bits;  conditional E-value: 5.1
                                   -TTT- CS
                           RecR 19 CsrCg 23
                                   C +Cg
  gi|119719832|ref|YP_920327.1|  4 CYVCG 8 
                                   66665 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00069
                                    HHHHHHHH-EE-TTT--E CS
                           RecR   8 aLqeakekvrhCsrCgnl 25 
                                    aL+e   kv++Cs+Cg l
  gi|119719832|ref|YP_920327.1| 129 ALREKGFKVKPCSVCGVL 146
                                    66666669*******976 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.00043
                                    EE-TTT--EESSSS-CCC CS
                           RecR  17 rhCsrCgnlteedlCaIC 34 
                                    ++C +Cg  + + lC  C
  gi|119719832|ref|YP_920327.1| 282 SRCAVCGEPSSRPLCKTC 299
                                    58**************** PP

>> Ribosomal_S14  Ribosomal protein S14p/S29e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.2      0.01        30      17      29 ..       3      15 ..       1      18 [. 0.85
   2 ?   -2.0   0.1         1   3.1e+03      18      25 ..     140     147 ..     136     152 .. 0.69
   3 ?    6.9   0.6    0.0018       5.4      10      25 ..     276     291 ..     268     294 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.01
                                   --SSS--SSSEE- CS
                  Ribosomal_S14 17 rCrvtGrprGvir 29
                                   +C v+Gr+ +v+ 
  gi|119719832|ref|YP_920327.1|  3 KCYVCGRRASVYV 15
                                   7********9996 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1
                                    -SSS--SS CS
                  Ribosomal_S14  18 CrvtGrpr 25 
                                    C v+G  r
  gi|119719832|ref|YP_920327.1| 140 CSVCGVLR 147
                                    88998644 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0018
                                    ..CTTT---SSS--SS CS
                  Ribosomal_S14  10 sptrirnrCrvtGrpr 25 
                                    +p+r   rC+v+G p 
  gi|119719832|ref|YP_920327.1| 276 KPSRKPSRCAVCGEPS 291
                                    489999*******996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       701  (0.0390987); expected 358.6 (0.02)
Passed bias filter:                      610  (0.0340231); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 2004.84
//
Query:       gi|119719833|ref|YP_920328.1|  [L=73]
Description: thiamineS protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.1e-09   36.2   1.1    8.2e-09   36.0   1.1    1.1  1  ThiS      ThiS family
    0.00013   21.7   1.3    0.00017   21.4   1.3    1.1  1  Ub-Mut7C  Mut7-C ubiquitin
  ------ inclusion threshold ------
      0.059   13.4   0.1      0.073   13.1   0.1    1.2  1  TGS       TGS domain
      0.071   13.2   0.0      0.082   13.0   0.0    1.1  1  UPF0147   Uncharacterised protein family (UPF0147)
       0.13   12.1   2.4        1.4    8.8   0.0    2.7  3  SLBB      SLBB domain


Domain annotation for each model (and alignments):
>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   1.1   2.3e-12   8.2e-09       5      77 .]      15      73 .]       7      73 .] 0.90

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 2.3e-12
                                   TCCHHHHTCEEEEESSTSBHHHHHHHHHHHTCHHGTTTTEEEEETTEEEGCCTTTSB--TTCEEEEEESTTC- CS
                           ThiS  5 aelrelageeelelaegstvaelleaLgerypelalerrvavavNgeivprlwldtelkdgDevailppVaGG 77
                                   ++  +     ++e++ gst+++l+  Lg r         v+v v+ge+v +   d+++k+g +v +  +V+GG
  gi|119719833|ref|YP_920328.1| 15 GREVR-----KVEVPRGSTLRDLVTTLGLRV------SEVVVTVDGEVVAE---DEPVKPGTRVKLHSVVSGG 73
                                   44444.....456******************......**************...******************9 PP

>> Ub-Mut7C  Mut7-C ubiquitin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   1.3   4.6e-08   0.00017      26      75 ..      20      68 ..      11      71 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 4.6e-08
                       Ub-Mut7C 26 avafdeaatvkhviEalGVPhtEVelilvnGesvgfshiledGdrvavyp 75
                                   +v++ +++t+++++ +lG    EV +++v+Ge v  ++ +++G rv+   
  gi|119719833|ref|YP_920328.1| 20 KVEVPRGSTLRDLVTTLGLRVSEV-VVTVDGEVVAEDEPVKPGTRVKLHS 68
                                   678999******************.89******************98765 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1     2e-05     0.073       6      58 ..      16      66 ..      11      68 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2e-05
                                   TTSSEEEEETTB-HHHHHHHHSTTHHHHEEEEEECSEEEETTSBB-SSEEEEE CS
                            TGS  6 PdGkvpdlprgatveDfAykIhrslakkfiyAlVnGqrvgldhvLedgdvveI 58
                                   ++ +++++prg+t +D+   ++  + +  ++  V+G+ v  d +++ g  v++
  gi|119719833|ref|YP_920328.1| 16 REVRKVEVPRGSTLRDLVTTLGLRVSE--VVVTVDGEVVAEDEPVKPGTRVKL 66
                                   6667899***************99999..***************999988876 PP

>> UPF0147  Uncharacterised protein family (UPF0147)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.3e-05     0.082      23      76 ..      16      71 ..       7      72 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.3e-05
                                   HHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHH..HHT-TTS-HHHHHHHHHHHH CS
                        UPF0147 23 rniRraakeakekLkdekeslavraataisiLde..isnDpnmPlhaRtliwevvs 76
                                   r +R++     ++L+d  ++l++r ++++ ++d   +++D  +   +R+++ +vvs
  gi|119719833|ref|YP_920328.1| 16 REVRKVEVPRGSTLRDLVTTLGLRVSEVVVTVDGevVAEDEPVKPGTRVKLHSVVS 71
                                   89999999999*********************95447899999999********98 PP

>> SLBB  SLBB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00039       1.4      14      30 ..      21      37 ..      11      41 .. 0.90
   2 ?    2.2   0.6     0.046   1.7e+02       1       8 [.      44      51 ..      44      54 .. 0.82
   3 ?   -1.7   0.0      0.78   2.8e+03      16      22 ..      58      64 ..      57      71 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00039
                                   EEEETT-BHHHHHHTTT CS
                           SLBB 14 yevpigttlsdlieqaG 30
                                   +evp g+tl+dl+   G
  gi|119719833|ref|YP_920328.1| 21 VEVPRGSTLRDLVTTLG 37
                                   89**********98776 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.046
                                   EEEEESSB CS
                           SLBB  1 vVtVtGeV 8 
                                   vVtV GeV
  gi|119719833|ref|YP_920328.1| 44 VVTVDGEV 51
                                   7******5 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.78
                                   EETT-BH CS
                           SLBB 16 vpigttl 22
                                   v++gt++
  gi|119719833|ref|YP_920328.1| 58 VKPGTRV 64
                                   7888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 538.92
//
Query:       gi|119719834|ref|YP_920329.1|  [L=112]
Description: hypothetical protein Tpen_0925 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.7e-09   36.0   0.1      8e-09   35.5   0.1    1.2  1  CRS1_YhbY       CRS1 / YhbY (CRM) domain
  ------ inclusion threshold ------
      0.046   13.9   0.1      0.058   13.5   0.1    1.2  1  RTT107_BRCT_6   Regulator of Ty1 transposition protein 107 BR
      0.094   10.9   0.0       0.11   10.7   0.0    1.1  1  COG6            Conserved oligomeric complex COG6
       0.11   12.1   0.0       0.16   11.5   0.0    1.2  1  E3_UFM1_ligase  E3 UFM1-protein ligase 1


Domain annotation for each model (and alignments):
>> CRS1_YhbY  CRS1 / YhbY (CRM) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.1   1.8e-12     8e-09      18      81 ..      38     105 ..      30     107 .. 0.93

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 1.8e-12
                      CRS1_YhbY  18 pkvkiGkaGvtkevvdeiheklkteelvkvkc....egppalnmkrmaeiLeektgglviqrsgtsiv 81 
                                    p+v++Gk+G+ ++v++ei++ l+++ +vkvk+    ++   l+ +++a i+ +++g+++  ++g +i 
  gi|119719834|ref|YP_920329.1|  38 PVVNVGKKGLDEGVIEEINNILESRGIVKVKLlknfRETYGLSPEEVAVIISQRLGAEILGVRGFVIA 105
                                    89********************************997788899********************98885 PP

>> RTT107_BRCT_6  Regulator of Ty1 transposition protein 107 BRCT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   1.3e-05     0.058       2      41 ..      31      72 ..      30      91 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.3e-05
                  RTT107_BRCT_6  2 vFerakikkiNlvsdi..pggtevissiLkahGikevkvlsk 41
                                   vF+r ++  +N+ ++   +g +e i +iL++ Gi +vk l++
  gi|119719834|ref|YP_920329.1| 31 VFQRKDVPVVNVGKKGldEGVIEEINNILESRGIVKVKLLKN 72
                                   8***********8874237999******************96 PP

>> COG6  Conserved oligomeric complex COG6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   2.4e-05      0.11      81     122 ..      55      93 ..      44      99 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 2.4e-05
                           COG6  81 aeeLkeekkklelkqkllkaflkkFtLseeEeaaLtsgeevd 122
                                    ++++ e +  +  k kllk+f++++ Ls+eE+a++ s++ + 
  gi|119719834|ref|YP_920329.1|  55 INNILESRGIV--KVKLLKNFRETYGLSPEEVAVIISQR-LG 93 
                                    55555555554..678*******************9987.65 PP

>> E3_UFM1_ligase  E3 UFM1-protein ligase 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   3.7e-05      0.16     116     160 ..      50      97 ..      42     105 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.7e-05
                 E3_UFM1_ligase 116 siaeeineklqeagqvsi...aelakqydlpvdflkellekrlgkiik 160
                                     ++eein+ l+++g v++   +++ ++y l+ + +  ++++rlg  i 
  gi|119719834|ref|YP_920329.1|  50 GVIEEINNILESRGIVKVkllKNFRETYGLSPEEVAVIISQRLGAEIL 97 
                                    689**************944456678*****************98775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 749.48
//
Query:       gi|119719835|ref|YP_920330.1|  [L=260]
Description: phosphoesterase, putative [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.4e-07   31.0   2.1     0.0005   20.6   0.0    2.2  2  Metallophos    Calcineurin-like phosphoesterase
    4.3e-07   30.3   0.0    6.8e-07   29.6   0.0    1.2  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
  ------ inclusion threshold ------
      0.029   14.7   0.0      0.054   13.8   0.0    1.4  1  EccE           Putative type VII ESX secretion system translo


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   8.3e-08    0.0005       4      80 ..      33     122 ..      32     142 .. 0.73
   2 !   10.1   0.6   0.00014      0.83     159     203 ..     142     173 ..     127     174 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 8.3e-08
                                    EEEESBTB...........TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSS......HHHHHHHHHHHHHHHH.TS CS
                    Metallophos   4 lvigDlHl...........algggqlddllkllddllreekpdlvllaGDlvdrg......dlekellellaalvky.pi 65 
                                    l+++DlH+              + q ++ +++l   + e+++  v+++GD+ ++       ++ + +++ll++l +  ++
  gi|119719835|ref|YP_920330.1|  33 LLVADLHVgyegalaeqgvFVPPLQAREMKEALAAMIGESGAERVIILGDVKHEFgdvtrqEWRE-TIDLLEYLKRGlGV 111
                                    679999966666666666533333333334444445777899999999**999977998989999.99999999999*** PP

                                    EEEEEC-TTSCHHHH CS
                    Metallophos  66 pvylllGNHegfeee 80 
                                    +v +++GNH+    +
  gi|119719835|ref|YP_920330.1| 112 RVDVVRGNHD----N 122
                                    **********....3 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00014
                                    TCSEEEEEESSESSCSSSCSCCHHHHHHHHHHTTESEEEEESSSS CS
                    Metallophos 159 kadwvivlgHsplyrgsgylfgdealedllkkygvdlvisGHtHv 203
                                    ++dw++++gH+p +           +e   ++ +v  v +GH+H+
  gi|119719835|ref|YP_920330.1| 142 EGDWLFIHGHKPFP-----------VE--GFREDVRFVAMGHEHP 173
                                    579***********...........66..7789999********7 PP

>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0   1.1e-10   6.8e-07       4     130 ..      33     174 ..      31     203 .. 0.63

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 1.1e-10
                  Metallophos_2   4 aiiSDlH.................snldaleavlealkevgvdaiihaGDleeeep............evleellela.. 52 
                                    ++++DlH                 ++++  ea+++ + e g++++i +GD+ + e+            + le l++ +  
  gi|119719835|ref|YP_920330.1|  33 LLVADLHvgyegalaeqgvfvpplQAREMKEALAAMIGESGAERVIILGDV-KHEFgdvtrqewretiDLLEYLKRGLgv 111
                                    6899*******************999************************6.222234455555443345555555549* PP

                  Metallophos_2  53 pvlaVrGNnDeevveedvlreaaelgtdlpeeaelelagekvlliHgdplgvkdalaellkeaeegsdvvvcGHtHvp 130
                                    +v +VrGN+D ++++  + r + ++ + +       l+g + l+iHg++      +    ++  e++++v++GH H +
  gi|119719835|ref|YP_920330.1| 112 RVDVVRGNHD-NYLVVVLKRLEIPFHDPY------LLEG-DWLFIHGHK-----PFPVEGFR--EDVRFVAMGHEHPA 174
                                    **********.443333333333333333......2233.466666662.....22222222..23456666666654 PP

>> EccE  Putative type VII ESX secretion system translocon, EccE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   9.1e-06     0.054      46      86 ..      45      97 ..      36     101 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9.1e-06
                           EccE 46 aLreqGirarvleaeeldaalaalavglaaapa............dvreewrt 86
                                   aL+eqG+ + +l+a+e+++alaa+  ++ a+++             +r+ewr+
  gi|119719835|ref|YP_920330.1| 45 ALAEQGVFVPPLQAREMKEALAAMIGESGAERViilgdvkhefgdVTRQEWRE 97
                                   8************************9999999899999999999877888986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1787.59
//
Query:       gi|119719836|ref|YP_920331.1|  [L=428]
Description: hydroxymethylglutaryl-CoA reductase, degradative [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
   8.5e-115  383.7   5.5     1e-114  383.4   5.5    1.0  1  HMG-CoA_red  Hydroxymethylglutaryl-coenzyme A reductase
  ------ inclusion threshold ------
       0.05   13.6   1.3       0.17   11.9   0.2    2.4  2  DUF3759      Protein of unknown function (DUF3759)


Domain annotation for each model (and alignments):
>> HMG-CoA_red  Hydroxymethylglutaryl-coenzyme A reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  383.4   5.5  1.1e-118    1e-114       2     367 .]      18     383 ..      17     383 .. 0.97

  Alignments for each domain:
  == domain 1  score: 383.4 bits;  conditional E-value: 1.1e-118
                                    HHHHHHHHHH...S-HHHHHHH.TT----HHHHHHHSSS---------EEEEEEEETTEEEEEEE---STTHHHHHHHHH CS
                    HMG-CoA_red   2 veeRrkllee...lteeeleel.keesldeevadkmiEnviGyvqlPlGvagpllingkeylvPmAteEgslvAsasrga 77 
                                    +eeR+k+++e   lteee++ l + ++ld+++ad+miEnviG+++ P++va ++lingk+y+vPm++eE+s+vA+as++a
  gi|119719836|ref|YP_920331.1|  18 IEERLKIVAEfagLTEEEVALLkNFGNLDRKIADSMIENVIGAMSYPFAVAVNFLINGKDYIVPMVIEEASVVAAASNAA 97 
                                    799*****999999999999995559****************************************************** PP

                                    HHHHHTT-B.EEEE----EEEEEEEE.--S-HHHHHHHH.HTHHHHHHHHHHCSHH..CCT-EEEEEEE.EE-...SSEE CS
                    HMG-CoA_red  78 kainesgGvkttvlkdgmtraqvvllesvedaaelkkwi.ekkeeleelanaaest..srggglkdiev.vla...grlv 150
                                    +++++ gG+ + v+++ ++++q+++l  v+d+   +  + e+kee+ + an+++++  + ggg++d+e+ v++   g+++
  gi|119719836|ref|YP_920331.1|  98 RVMRRDGGI-KSVATQPIMIGQIQVL-GVKDPWYKRMVLlEHKEEILQKANEVDPVlvKFGGGARDLEArVVEsprGPML 175
                                    *********.8888888*********.*****99999999*****************************777799999** PP

                                    EEEEEEE-TTC--HHHHHHHHHHHHHHHHHHHTSEEEEEEE-S--GGGEEEEEEEEEHHHH..-SSTTHHHHHHHHHHHH CS
                    HMG-CoA_red 151 vlrlkvdtgDAmGaNmvnkateaaaelieeefgeeellsilsNlctdkkasainaiegrgksvvaeatigeevvekilka 230
                                    +++l vd++DAmGaN+vn+++e++a++ie+ +g+++ll+i sNl++++++++++ + ++++        geevv+ i++a
  gi|119719836|ref|YP_920331.1| 176 IVHLLVDVRDAMGANAVNTMAEKVAPMIERLTGGRVLLRIISNLADRRLVRSWVKVYKEDI-------GGEEVVDAIVDA 248
                                    ****************************************************999999888.......9*********** PP

                                    HHHHHH-HHHH..HHHHHHH.......HHHHHHHHHHTT--HHHHHHHHHHHTT.......SEEE...TTTEEEEEEEEE CS
                    HMG-CoA_red 231 saealvdlnranigtankGiggfnahaaNgiaAvflAtGqDlaaveesshaiaa.......leev...edgdlygsvtlP 300
                                     a+a++d++ra  +t+nkGi       +Ng+ Av+lAt qD +a+e+++ha+aa       l+++   +dg+l+g++++P
  gi|119719836|ref|YP_920331.1| 249 WAFAAADPYRA--ATHNKGI-------MNGVIAVALATAQDHRAIEAGAHAYAArtgrympLSTWekdQDGNLVGTLEMP 319
                                    ***********..*******.......**********************************99998667777******** PP

                                    .----SBSHHHHH-HHHHHH.HHTT---HH...HHHHHHHHHHHHHHHHHHHHHT-----HHHHHHHH CS
                    HMG-CoA_red 301 sleVGtvGGgtklppqaell.kllgvkgaknakeLaeiiaavgLAqelsalrALaaeglqkgHmklhr 367
                                     ++VGt+GG+tk++p a+++ k+lgvk+a    eLae++ avgLAq+++alrALa+eg+qkgHm+lh+
  gi|119719836|ref|YP_920331.1| 320 -MAVGTIGGATKVHPVAKIAlKILGVKTAT---ELAEVMGAVGLAQNFAALRALATEGIQKGHMRLHA 383
                                    .*****************************...*********************************96 PP

>> DUF3759  Protein of unknown function (DUF3759)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.26   2.4e+03      18      40 ..     243     265 ..     230     272 .. 0.80
   2 ?   11.9   0.2   1.9e-05      0.17      20      65 ..     357     402 ..     346     409 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.26
                        DUF3759  18 ellagAAafeAvkayedhqrkeG 40 
                                    + + +A af+A+  y+   +++G
  gi|119719836|ref|YP_920331.1| 243 DAIVDAWAFAAADPYRAATHNKG 265
                                    66888999999999998887777 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 1.9e-05
                        DUF3759  20 lagAAafeAvkayedhqrkeGkpvshafaKellAgfagaevdklve 65 
                                    ++ A  f+A++a   +  ++G+   ha    ++Ag +g  +d++ve
  gi|119719836|ref|YP_920331.1| 357 VGLAQNFAALRALATEGIQKGHMRLHARNLAIMAGATGDLIDRVVE 402
                                    566889**************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 3016.25
//
Query:       gi|119719837|ref|YP_920332.1|  [L=230]
Description: abortive infection protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-08   35.4  12.1    2.9e-08   34.0  11.4    2.2  1  CPBP      CPBP intramembrane metalloprotease


Domain annotation for each model (and alignments):
>> CPBP  CPBP intramembrane metalloprotease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0  11.4   1.6e-12   2.9e-08       8      91 ..     101     184 ..      52     185 .. 0.89

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 1.6e-12
                                    HHHHHHHHHHHHHHHHTTCHHHHHHHH.S-HHHHHHHHHHHHHCSGGG.........HHHHHHHHHHHHHHHHHHHHTT- CS
                           CPBP   8 fllalllapllEEllfRglllqllqergsstlailissilFglaHlpn.........gpsvllaalaGlvlgylylktgs 78 
                                     ll+++la + EE +fRg+ll              +++ lF+l Hl+          ++ v  ++l+Glv g+l+++ g 
  gi|119719837|ref|YP_920332.1| 101 SLLFAVLASFSEEYFFRGFLLGVA--------GNPLQAYLFALSHLALsdpvylvnsALLVPHYFLLGLVAGLLAERWG- 171
                                    5679*****************765........34699***********99999998554589*****************. PP

                                    HHHHHHHHHHHHH CS
                           CPBP  79 llaaillHallnl 91 
                                    ll++il+Ha++n+
  gi|119719837|ref|YP_920332.1| 172 LLSSILFHAAYNA 184
                                    ************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      156  (0.00870099); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 1587.73
//
Query:       gi|119719838|ref|YP_920333.1|  [L=177]
Description: hypothetical protein Tpen_0929 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.3e-06   26.2  15.9    9.4e-06   25.8  15.9    1.1  1  ECF_trnsprt  ECF transporter, substrate-specific component
  ------ inclusion threshold ------
      0.026   14.2   0.4       0.12   12.1   0.2    2.3  2  DUF4516      Domain of unknown function (DUF4516)
        1.2    8.9   6.3          1    9.2   4.0    2.1  3  PDR_assoc    Plant PDR ABC transporter associated
          9    6.8   9.5    2.3e+02    2.3   9.5    3.0  1  DUF202       Domain of unknown function (DUF202)


Domain annotation for each model (and alignments):
>> ECF_trnsprt  ECF transporter, substrate-specific component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8  15.9   2.1e-09   9.4e-06       2     168 ..      10     168 ..       9     169 .. 0.68

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 2.1e-09
                                    HHHHHHHHHHHHHHHHH...H.HEEE.STSEEESHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHCHT-SSTTHHHHHHHH CS
                    ECF_trnsprt   2 klvitglliAisivlsl...l.gyiplpnikitiihipvllggllfGpikGailgiitsvlkailtggtgalssfvpiaf 77 
                                    kl +t+l +A+++ +s+      ++ lp +k+++  +pv lg ll+G  +G+ + +  ++l+++   g  +l    ++ f
  gi|119719838|ref|YP_920333.1|  10 KLSLTALTAALALAFSVlklEaPFPVLPYLKFDLAEVPVTLGFLLCGLPYGVAAET-VHFLGLVA-RGADPLGA--FMKF 85 
                                    6789************97753355555555*************************9.79******.89998887..8888 PP

                                    HHHHCHHHHHHHHHHCCCHTTHHHHHHHHHHHHCCCCCHHHHHHHCCCHHHHS..................--HHHHHHH CS
                    ECF_trnsprt  78 lsriligliagllykkgkkknlkeivvsfilagvlgtivatllvlliilplyl.....klktakaiaiagkallaailgp 152
                                    l+ + + l a+   +++  +        ++l++ +   ++tl ++ ++++l+       lk+    +    al+a+  + 
  gi|119719838|ref|YP_920333.1|  86 LAVVSMFLGAY---RFSSAV------TRLALGVAARVAAMTLASYAYFYLLFPgflgyALKYTGSVY----ALFAYTALF 152
                                    88888888888...444444......44555555555555555555555555400000444444444....666666666 PP

                                    HHCCTTCCHHHHHHHH CS
                    ECF_trnsprt 153 iivkglieaiiaaiiv 168
                                     +++g+ +++++ ++v
  gi|119719838|ref|YP_920333.1| 153 NVIHGAATMALSMLVV 168
                                    6666666666666654 PP

>> DUF4516  Domain of unknown function (DUF4516)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       1.7   7.6e+03       6      13 ..      34      41 ..      33      42 .. 0.85
   2 ?   12.1   0.2   2.7e-05      0.12       6      25 ..      78      95 ..      77      97 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.7
                        DUF4516  6 swgeYlkf 13
                                   +++ Ylkf
  gi|119719838|ref|YP_920333.1| 34 PVLPYLKF 41
                                   8899*998 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 2.7e-05
                        DUF4516  6 swgeYlkfvtasllsMlaGA 25
                                   ++g+++kf+  +++sM++GA
  gi|119719838|ref|YP_920333.1| 78 PLGAFMKFL--AVVSMFLGA 95
                                   78999****..********9 PP

>> PDR_assoc  Plant PDR ABC transporter associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0         2     9e+03      17      31 ..      85      99 ..      81     105 .. 0.61
   2 ?   -0.6   0.1      0.25   1.1e+03      39      55 ..     123     139 ..     116     142 .. 0.79
   3 ?    9.2   4.0   0.00022         1      30      51 ..     138     159 ..     125     170 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2
                      PDR_assoc 17 vLksrglfteaywYW 31
                                   +L   ++f  ay + 
  gi|119719838|ref|YP_920333.1| 85 FLAVVSMFLGAYRFS 99
                                   555566666666655 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.25
                      PDR_assoc  39 gftiLFNilftlaLtYL 55 
                                     f +LF  +   aL+Y 
  gi|119719838|ref|YP_920333.1| 123 YFYLLFPGFLGYALKYT 139
                                    58899999999999996 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.00022
                      PDR_assoc  30 YWigvgallgftiLFNilftla 51 
                                    Y  +v al+++t LFN++   a
  gi|119719838|ref|YP_920333.1| 138 YTGSVYALFAYTALFNVIHGAA 159
                                    77799************86433 PP

>> DUF202  Domain of unknown function (DUF202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   9.5      0.05   2.3e+02      18      66 ..      17     102 ..      10     174 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.05
                         DUF202  18 lalialglallrffl.....................................tgepsalgkilglilivlgiltllvglv 60 
                                    +a++al++ +l+++                                       g +++++ +lg+++  l+++++++g++
  gi|119719838|ref|YP_920333.1|  17 TAALALAFSVLKLEApfpvlpylkfdlaevpvtlgfllcglpygvaaetvhfLGLVARGADPLGAFMKFLAVVSMFLGAY 96 
                                    45666666666666688888888888888888888888888887777777766777778899999999999999999999 PP

                         DUF202  61 rylrrq 66 
                                    r+ + +
  gi|119719838|ref|YP_920333.1|  97 RFSSAV 102
                                    997665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      196  (0.010932); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1332.20
//
Query:       gi|119719839|ref|YP_920334.1|  [L=888]
Description: ATP-dependent helicase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.9e-59  199.1   0.3    6.1e-58  195.8   0.1    2.2  2  DEAD_assoc  DEAD/H associated
    1.1e-26   93.6   0.0    4.1e-26   91.8   0.0    1.9  2  DEAD        DEAD/DEAH box helicase
    1.5e-16   60.7   0.3    1.3e-15   57.7   0.1    2.3  2  Helicase_C  Helicase conserved C-terminal domain
    1.8e-08   34.6   0.0    3.4e-08   33.7   0.0    1.5  1  ResIII      Type III restriction enzyme, res subunit
     0.0041   17.6   0.0       0.11   12.9   0.0    2.5  2  AAA         ATPase family associated with various cellular ac
  ------ inclusion threshold ------
      0.016   15.3   0.0         11    6.3   0.0    2.8  2  VP9         VP9 protein
      0.026   13.3   0.0      0.056   12.2   0.0    1.5  1  SNF2_N      SNF2 family N-terminal domain
      0.031   13.3   0.0       0.08   12.0   0.0    1.7  1  T2SSE       Type II/IV secretion system protein
      0.084   12.3   0.0       0.35   10.3   0.0    2.0  2  PhoH        PhoH-like protein
       0.19   12.1   0.3        1.2    9.5   0.1    2.4  2  AAA_19      AAA domain


Domain annotation for each model (and alignments):
>> DEAD_assoc  DEAD/H associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0       0.2   3.5e+02     133     179 ..     279     325 ..     267     332 .. 0.85
   2 !  195.8   0.1   3.4e-61   6.1e-58       2     191 .]     659     845 ..     658     845 .. 0.95

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.2
                     DEAD_assoc 133 aqLldvareypdfpllleavrevledqlDlerlaellrriaageirv 179
                                    + L++++r++  ++++  ++    + ++ l++la+   +i + +i  
  gi|119719839|ref|YP_920334.1| 279 ETLYEIVRKHRTTLIFTNTRSGTERVVFHLKQLARKRGDIPEDAIAA 325
                                    689*************************9999999888887777765 PP

  == domain 2  score: 195.8 bits;  conditional E-value: 3.4e-61
                     DEAD_assoc   2 PtdrtllvErfrdelgdwrlvvhspfGrrvnealalllaarlsrrfgidvqvaanDdgivlllpleerlpllldellell 81 
                                    P+dr +lvEr+rd  g+ + v+h++fGrr n+al+ +la+  s+r g ++++a++D+g++l++p+  + p   +  l  +
  gi|119719839|ref|YP_920334.1| 659 PSDRVVLVERYRDADGRVHHVFHTLFGRRTNDALSHALAYLASKRAGANIGIAVHDNGFALIYPPGVE-P---QVSLMDV 734
                                    9************************************************************8854333.2...2235679 PP

                     DEAD_assoc  82 spdeleedleaalnaselfkrrFrevAaralllprrypgkrkplwqqrlraaqLldvareypdfpllleavrevledqlD 161
                                     p ele++l++a+ ++el++rrFr+vA+r l+++r+y+g++ ++++q+l+a  Ll+v+r+ +dfp+l+e++re+led++D
  gi|119719839|ref|YP_920334.1| 735 APSELEDILKKAVFNTELMRRRFRHVATRGLMILRNYKGHEISVEKQQLSAGTLLRVIRKWEDFPILKETFREILEDYMD 814
                                    9******************************************************************************* PP

                     DEAD_assoc 162 lerlaellrriaageirvveve.tprpSpfA 191
                                    +++++e+l+++++gei+vv++  +++p+pfA
  gi|119719839|ref|YP_920334.1| 815 IAHAREVLEKVHSGEIEVVDIGlLDTPTPFA 845
                                    **********************9*******9 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.8   0.0   2.3e-29   4.1e-26       1     170 [.      38     222 ..      38     229 .. 0.87
   2 ?   -2.3   0.0       1.8   3.2e+03      40      73 ..     278     314 ..     254     355 .. 0.65

  Alignments for each domain:
  == domain 1  score: 91.8 bits;  conditional E-value: 2.3e-29
                                    -HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHS....TTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                           DEAD   1 tdiQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyet....kgktgpkalivePtreLaeqtlnnlkkfkkyid. 75 
                                    t+ Q+ a+  i +g++vlv+ +TG+GKTl +++ +l++++ +    + +++  +++v+P+r+L +++++nl++ + +i+ 
  gi|119719839|ref|YP_920334.1|  38 TPPQRYALIPIHEGKNVLVSSPTGTGKTLTAFLIALSELFGMarrgELEDTVYVVYVSPLRALNNDIYRNLEEPLREIRe 117
                                    6789999999*******************9999999999888999999****************************8777 PP

                                    ...........SEEEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHH....HCTSSHCTTEEEEEEETHHHHHHTTTHH CS
                                    ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  76 ...........lrvlliiggvaardqlskldngvdivvgtpgrlddll....stgklnlsqvrflVlDEadrlldqgfsd 140
                                               +r ++ +g+++ ++ +s l++ ++i+++tp+ l+ +l     ++k  l++v+++++DE++ l +++++ 
  gi|119719839|ref|YP_920334.1| 118 laekrgleipeIRHMVRTGDTSSSQRQSMLRKPPHILITTPETLAIILvapkFREK--LRSVKWVIVDEIHSLAENKRGV 195
                                    778888888778887778888888888899788*************8856543444..********************** PP

                                    HHHHHHHHSHHHCTTSTTTSEEEEEESSBS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD 141 finrilnqlpqitcdgklqrqvivlSATlp 170
                                    ++   l++l++   +   +   i lSAT++
  gi|119719839|ref|YP_920334.1| 196 HLALSLERLRELVGR---DFVRIGLSATIN 222
                                    *********776654...3458******97 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.8
                                    HHS...TTSTS-EEEEEESSHHHHHHHHHHHHHHTTT CS
                                    xxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  40 yet...kgktgpkalivePtreLaeqtlnnlkkfkky 73 
                                    yet     +++  +li + tr+ +e ++ +lk++  +
  gi|119719839|ref|YP_920334.1| 278 YETlyeIVRKHRTTLIFTNTRSGTERVVFHLKQLARK 314
                                    3334433344456788888888888888888887775 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0      0.61   1.1e+03      39      62 ..     122     150 ..     101     167 .. 0.69
   2 !   57.7   0.1   7.4e-19   1.3e-15       6     108 ..     277     388 ..     272     390 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.61
                                    T.....TSTEEEESTTSTHHHHHHHHHHH CS
                     Helicase_C  39 k.....gikvavlhgelpqnereeileqf 62 
                                    +     +i+  v +g++++++r+ +l++ 
  gi|119719839|ref|YP_920334.1| 122 RgleipEIRHMVRTGDTSSSQRQSMLRKP 150
                                    33444467777777778888887777765 PP

  == domain 2  score: 57.7 bits;  conditional E-value: 7.4e-19
                                    HHHHH.HHTTTTSEEEEEESSHHHHHH....HHHHHHHT....TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGG CS
                     Helicase_C   6 llell.kleeeggkilifvntidrlek....vklllekk....gikvavlhgelpqnereeileqfnkgesdvLiatdva 76 
                                    l+e l +  ++++++lif+nt++  e+    +k l +k+    +  +a++h++l+ n r+++ e+ ++ge + +++++ +
  gi|119719839|ref|YP_920334.1| 277 LYETLyEIVRKHRTTLIFTNTRSGTERvvfhLKQLARKRgdipEDAIAAHHSSLSRNVRLDVEEKLKRGELRAIVSSTSL 356
                                    444444445999999********66554456556655557888899********************************** PP

                                    TSSSTSTTESEEEESSSSSSHHHHHHHHTTSS CS
                     Helicase_C  77 erGidipkvnlVinfdlprnvtsyiqriGRtg 108
                                    e Gidi  +++V+ ++ p++vt++ qriGR g
  gi|119719839|ref|YP_920334.1| 357 ELGIDIGYIDVVVLVGSPKSVTRALQRIGRSG 388
                                    ******************************87 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   0.0   1.9e-11   3.4e-08       4     170 ..      10     222 ..       7     223 .. 0.67

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 1.9e-11
                                    E-HHHHHHHHHHT...........................TTSEEEEEESTTSTHHHHHHHHH.HHH-S........... CS
                         ResIII   4 lreyQeeaienlleklks.....................krdkrglikmaTGtGKTlvaakli.erllkkgkee...... 55 
                                     rey +e + ++l+ l +                     ++ k++l+  +TGtGKTl+a+ ++  +l+  +++       
  gi|119719839|ref|YP_920334.1|  10 TREYSKEEVLRVLDPLVAewfsgkfedltppqryalipiHEGKNVLVSSPTGTGKTLTAFLIAlSELFGMARRGeledtv 89 
                                    5666777777777555445555666667777777777778899****************665514566655444788877 PP

                                    -EEEEESSHHHHHHHHHHGGGGTGG.............GEEE....ESSS-B--.........-SEEEEEHHHHHHTH.. CS
                         ResIII  56 kflflvprkslleqtleefkkflseayke.........igkk....vsgdkkka..kekdstnkkilvttiqsldadsee 120
                                     ++ + p ++l +  ++++++ l e ++          +  +     +gd+ ++  ++  ++  +il+tt ++l  ++  
  gi|119719839|ref|YP_920334.1|  90 YVVYVSPLRALNNDIYRNLEEPLREIRELaekrgleipE--IrhmvRTGDTSSSqrQSMLRKPPHILITTPETLAIIL-- 165
                                    777777777777777766655544443223333444440..244445555555555555678889*************.. PP

                                    ......HHHTTT-SEEEEETGGGTTS.T.......TTHHHHHT-.--SEEEEEESS-S CS
                         ResIII 121 eeeeseellrdrfdviiiDEaHrlgakk.......swreilekf.keavllglTATpe 170
                                        + + +  + + +i+DE H l+++k       s +++ e + +++v++gl+AT++
  gi|119719839|ref|YP_920334.1| 166 -VAPKFREKLRSVKWVIVDEIHSLAENKrgvhlalSLERLRELVgRDFVRIGLSATIN 222
                                    .55555555556669***********966555566666665555466*********85 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   6.3e-05      0.11       1      80 [.      54     142 ..      54     164 .. 0.73
   2 ?    1.8   0.0      0.17     3e+02      59      74 ..     177     192 ..     154     211 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.3e-05
                                    EEEESSTTSSHHHHHHHHHHH....H........THEEEEEETTTCS.SSSTTHHHHHHHHHHHHHHHTSTSEEEEEETG CS
                            AAA   1 vllyGppGtGKTllakavake....l........gvefleisgsell.skyvgesekkirelfkeakekakpsilfiDEi 67 
                                    vl++ p GtGKTl+a  +a +    +         v+++ +s  + l +++  + e+ +re+ + a++      l i Ei
  gi|119719839|ref|YP_920334.1|  54 VLVSSPTGTGKTLTAFLIALSelfgMarrgeledTVYVVYVSPLRALnNDIYRNLEEPLREIRELAEKRG----LEIPEI 129
                                    68999*************9886555144444443477888888888856677777777777777776666....999999 PP

                                    GGHHHHHTTCCCH CS
                            AAA  68 dalaksrsgsese 80 
                                      ++++ ++s+s+
  gi|119719839|ref|YP_920334.1| 130 RHMVRTGDTSSSQ 142
                                    9999999333222 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.17
                                    SEEEEEETGGGHHHHH CS
                            AAA  59 psilfiDEidalaksr 74 
                                     + +++DEi++la+++
  gi|119719839|ref|YP_920334.1| 177 VKWVIVDEIHSLAENK 192
                                    46799*******9987 PP

>> VP9  VP9 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.006        11      31      73 ..      81     129 ..      75     133 .. 0.75
   2 ?    5.9   0.0     0.008        14      47      73 ..     192     218 ..     185     223 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.006
                            VP9  31 rkSelrdgvfiVrlkdkkvl......klknGlkrLreLtgDntLkiell 73 
                                    r+ el+d v++V +   + l      +l++ l+++reL +   L+i ++
  gi|119719839|ref|YP_920334.1|  81 RRGELEDTVYVVYVSPLRALnndiyrNLEEPLREIRELAEKRGLEIPEI 129
                                    999*********86544444221122799999999****9999999765 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.008
                            VP9  47 kkvlklknGlkrLreLtgDntLkiell 73 
                                    k+ ++l+  l+rLreL+g + ++i+l 
  gi|119719839|ref|YP_920334.1| 192 KRGVHLALSLERLRELVGRDFVRIGLS 218
                                    556899999***************987 PP

>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   3.1e-05     0.056     126     201 ..     131     200 ..     113     210 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.1e-05
                                    E--SSHHHH-----------------EEEE-HHHHHHHT......TTS-S-S-SEEEES-GGGT--TTSHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SNF2_N 126 vlvyggqkkmkkkntkvapklladydvvittYdvlsreaelqkkrsvlkqvewkrvvlDEghtlknstskaaeavs 201
                                     +v +g++++    ++ +  l +  +++itt ++l+     +k r++l +v+w  v++DE h l  +++ ++ a+s
  gi|119719839|ref|YP_920334.1| 131 HMVRTGDTSS----SQRQSMLRKPPHILITTPETLAIILVAPKFREKLRSVKW--VIVDEIHSLAENKRGVHLALS 200
                                    4555555433....333556667789**********999999**********9..9***********999988876 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   4.5e-05      0.08     125     153 ..      47      76 ..       8      96 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.5e-05
                          T2SSE 125 avrerglilvsGgTgsGKttll.yallkei 153
                                    +++e +++lvs +Tg+GKt ++  ++l+e+
  gi|119719839|ref|YP_920334.1|  47 PIHEGKNVLVSSPTGTGKTLTAfLIALSEL 76 
                                    678899*************88734555555 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0    0.0002      0.35       6      44 ..      38      76 ..      34      91 .. 0.85
   2 ?   -2.8   0.0       1.9   3.5e+03      84     111 ..     806     836 ..     791     838 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0002
                                   SHHHHHHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHH CS
                           PhoH  6 tkeQkeylealkkndivfaiGpaGtGKtylavalaveal 44
                                   t  Q+ +l  +++ + v +  p+GtGKt+ a  +a++ l
  gi|119719839|ref|YP_920334.1| 38 TPPQRYALIPIHEGKNVLVSSPTGTGKTLTAFLIALSEL 76
                                   5667777777888889999***************99865 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.9
                                    HHHHTTTS...-TTCHHHHHHTTSEEEEEGG CS
                           PhoH  84 ydaLkdll...gaekvekllekgkievapla 111
                                     + L+d++   +a++v + +++g+iev+++ 
  gi|119719839|ref|YP_920334.1| 806 REILEDYMdiaHAREVLEKVHSGEIEVVDIG 836
                                    3444444411155555555668899998875 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1   0.00067       1.2       1     115 [.      41     189 ..      41     208 .. 0.59
   2 ?   -2.7   0.0       3.7   6.7e+03      43      69 ..     289     322 ..     249     424 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00067
                         AAA_19   1 qreave.alkekvllvtaGpGtGKTrv..lkhivallvelggvkp...eeillvaftgrAakelrerlaalgaeatTiHr 74 
                                    qr a+   ++ k++lv  + GtGKT +  l +  +l+  +++ ++     ++ v++ +   + +  +l   +++ + i +
  gi|119719839|ref|YP_920334.1|  41 QRYALIpIHEGKNVLVSSPTGTGKTLTafLIALSELFGMARRGELedtVYVVYVSPLRALNNDIYRNL---EEPLREIRE 117
                                    66677668999*************98732333334433333333311133444444444444455555...777777777 PP

                         AAA_19  75 lal.................................ldfddlltealelle...........eaeeekklqeeellivDE 110
                                    la+                                 l                           + ++kl++ +++ivDE
  gi|119719839|ref|YP_920334.1| 118 LAEkrgleipeirhmvrtgdtsssqrqsmlrkpphiL-------------IttpetlaiilvAPKFREKLRSVKWVIVDE 184
                                    7667777777777777655555555555555555431.............033333334444556788887777999999 PP

                         AAA_19 111 fqdvd 115
                                    +  + 
  gi|119719839|ref|YP_920334.1| 185 IHSLA 189
                                    87766 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.7
                         AAA_19  43 eeillvaftgrAakelrerlaalgae.......a 69 
                                    ++ l+ + t+  ++++   l++l ++       a
  gi|119719839|ref|YP_920334.1| 289 RTTLIFTNTRSGTERVVFHLKQLARKrgdipedA 322
                                    4555555555555555555544444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (888 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.72u 0.29s 00:00:01.01 Elapsed: 00:00:00.44
# Mc/sec: 6084.38
//
Query:       gi|119719840|ref|YP_920335.1|  [L=539]
Description: aminopeptidase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-10   40.2   0.0    1.6e-09   37.8   0.0    2.1  2  Peptidase_M28  Peptidase family M28
      9e-07   28.8   0.0    2.3e-06   27.5   0.0    1.7  1  PA             PA domain


Domain annotation for each model (and alignments):
>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0      0.79   7.1e+03     108     142 ..     106     140 ..      98     144 .. 0.74
   2 !   37.8   0.0   1.7e-13   1.6e-09      16     188 ..     211     369 ..     204     377 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 0.79
                                    EEHHHHHHCHHHHHHHHHHHHHTT-TTSCCEEEEE CS
                  Peptidase_M28 108 lfesgdkssselekelkalakpvgraaaedpfder 142
                                    ++++ +k +++ +++++a+a+ ++  +  dpf++r
  gi|119719840|ref|YP_920335.1| 106 VVKMYGKVDEAAWQYVQAVARGAEAVVFVDPFPDR 140
                                    55777888888999999999888887777888766 PP

  == domain 2  score: 37.8 bits;  conditional E-value: 1.7e-13
                                    EEEEE--B-TTTTCCT---TTTTHHHHHHHHHHHHHCHHGGCCSSEEEEEEEESSCSG.........SSHHHHHHHH..H CS
                  Peptidase_M28  16 llgAHyDsvgvgrgpifvGAdDnAsgvaalLelarvlaasgsrpkrgvrflffdaEEa.........gllGSkafak..a 84 
                                    l++AH+D +         G +Dn  gva+++ l+r++ +s          ++f+aEE+         ++ GS+ +a   +
  gi|119719840|ref|YP_920335.1| 211 LFTAHVDKWLS-------GFTDNVLGVALVVALSRAFGESA-------GYAVFGAEEYgapghspwyWIWGSRSYADflE 276
                                    68999999997.......99******************955.......7899************************8864 PP

                                    HC.CCTTEEEEEEECS-SSSS--EEEHHHHHHCHHHHHHHHHHHHHTT-TTSCCEEEEESSTT-STTHHHHTTT--EEEE CS
                  Peptidase_M28  85 kp.elkkiaavlnlDmvgsggkellfesgdkssselekelkalakpvgraaaedpfdersgrgrsDhspflkagvpvldl 163
                                    +  el+   +v+nlD +g  g ++   sg++ + +l+k l +  + +            s ++  D ++f+ +gv +++l
  gi|119719840|ref|YP_920335.1| 277 RRgELDSLGVVVNLDVLGGAGITVS-ASGPDFQGGLGKALGEGYRYT------------SDQVIFDSFSFTMKGVAAATL 343
                                    447****************999999.588887777776665444322............334456999******999999 PP

                                    .CTSSS-TTTTSTTSSGGGB-HHHHH CS
                  Peptidase_M28 164 .aetgfpevyHtprDtldnidkdtla 188
                                      +++  +vyHt  D+++++d++++ 
  gi|119719840|ref|YP_920335.1| 344 hTFQDVLPVYHTDLDEPQRVDWEKVL 369
                                    779999****************9875 PP

>> PA  PA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0   2.5e-10   2.3e-06      20      89 .]      94     175 ..      76     175 .. 0.69

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 2.5e-10
                             PA  20 e..gvdvkGkivLvqrtf.......aeKarnAqaaGAagviiv..........ndgelgaatgasgnegepdgitiPavg 80 
                                    e  gvd++Gki++v+          a  +  A a GA++v++v          +     a ++     g p    +Pav 
  gi|119719840|ref|YP_920335.1|  94 EweGVDLEGKIAVVK--MygkvdeaAWQYVQAVARGAEAVVFVdpfpdrrrriV---VTATPDYRFGPGTP--PPVPAVA 166
                                    24499*********4..4222344467777777**********77665544441...23333344444445..9****** PP

                             PA  81 vsredgeal 89 
                                    vs edg +l
  gi|119719840|ref|YP_920335.1| 167 VSLEDGLRL 175
                                    ******987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (539 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.39
# Mc/sec: 4143.20
//
Query:       gi|119719841|ref|YP_920336.1|  [L=1187]
Description: glycoside hydrolase family protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.2e-31  108.4   0.2    1.3e-25   90.3   0.0    2.3  2  Glyco_hydro_57  Glycosyl hydrolase family 57
    7.3e-06   26.1   5.4     0.0049   16.8   1.1    3.9  3  YidC_periplas   YidC periplasmic domain
  ------ inclusion threshold ------
       0.14   12.5   0.5       0.66   10.3   0.2    2.3  2  A2M_BRD         Alpha-2-macroglobulin bait region domain


Domain annotation for each model (and alignments):
>> Glyco_hydro_57  Glycosyl hydrolase family 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   1.1e-06    0.0065       1      58 [.     702     768 ..     702     774 .. 0.89
   2 !   90.3   0.0   2.2e-29   1.3e-25     117     315 ..     797    1013 ..     773    1022 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.1e-06
                                    EEEEEE-----TTS-SSSSSHHHHHHHHHHT..........HHHHHHHHHHHHHTT----EEEEE-HH CS
                 Glyco_hydro_57   1 afvfhqHqplykkpgkgeytlpwvrehaaed..........YiklalilekfpkvhvtfeLsgsLiaq 58 
                                    +fv+h+Hq +   p+ g +  pw ++h +ed          Y+ ++ il k+p v++ ++Ls+sL+ q
  gi|119719841|ref|YP_920336.1| 702 VFVWHSHQGINAWPN-GSFHGPWAFKHTYEDefkpyyeggaYLVQPVILSKYPGVKMVYHLSPSLLWQ 768
                                    69*********9999.***********99876666666666999*********************987 PP

  == domain 2  score: 90.3 bits;  conditional E-value: 2.2e-29
                                     T-HHHHHHHHHHCTSEEEEEE-TT-B-GGG-S-.....HHHHHHHHHHHHHHHHHHHSS--SBEE-GGG-B--SHHHH CS
                 Glyco_hydro_57  117 kevlelfrelqesgqvElltspyyHpllpllpd.....sedieaqvkkarelyeeyfgqePrgfwlpElavspeilei 189 
                                     ++ lel+++l+ +gq+E+++  + Hp+  ++ d      e+++ +++ + ++ ++ +g+ ++g w pE+ +s+++++i
  gi|119719841|ref|YP_920336.1|  797 RKALELYKQLASRGQIEIFSDFFNHPIPGYVVDtypwgAEAMKIELEWGFNVTKRVLGVDAKGAWIPEMFFSEKLVPI 874 
                                     5789***************************77788899*************************************** PP

                                     HHHTT--EEEE-C.------------TTS-EE-TTS...-EEEE--CHH-TTTSGGG-................TTSB CS
                 Glyco_hydro_57  190 laelGfeylftde.laeiledkskespyrpyllkngg..iavffRdreLsddigFrys....eqypleavddfinwlk 260 
                                     l ++G +y++ d+ ++   +d  k+  y pyl + ++  i v+fRd++Ls+ i+F+      e  +++a+++f+  + 
  gi|119719841|ref|YP_920336.1|  875 LVQQGVKYIVLDYeTHYKGSDGEKRGIYTPYLYQGSQgqIIVLFRDTQLSNYISFENRfstpE-DADAAARNFVLMVA 951 
                                     ************987777888888999999999988789****************75543532.34446777766666 PP

                                     ...............-TT---TTT-..-BB-TT-S---HHHHHHHHHHH.HHHHHHHHHHHH..H CS
                 Glyco_hydro_57  261 kvkka.....ksevvtialdgEnwg..hypetgkkeFleklyeeleeng.lielvtpsefik..k 315 
                                     +           +vv+i  dgEnw+     ++ + +F e l  +le+ + +i + t+ e+++  +
  gi|119719841|ref|YP_920336.1|  952 S---RrfsdpTASVVVISADGENWMifSPTVATTGVFFERLCAYLESVKqYIVTATVAEVVEgaQ 1013
                                     3...3344789**************984455555569***********99*********988553 PP

>> YidC_periplas  YidC periplasmic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.1   0.00062       3.7      97     132 ..     128     163 ..     103     167 .. 0.89
   2 ?   -1.6   0.0      0.33     2e+03       4      19 ..     334     349 ..     333     352 .. 0.93
   3 !   16.8   1.1   8.3e-07    0.0049      81     253 ..     406     574 ..     386     589 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00062
                                    TTS-EEEEEEEEETT-SEEEEEEEEE--SSS-EEEE CS
                  YidC_periplas  97 gnGltftktytldrdsYlitvtdeveNtsgapvtla 132
                                    ++ + +t++y+++++s ++++t+++ N +++p++++
  gi|119719841|ref|YP_920336.1| 128 TSNVAVTREYVFKQGSRTFNLTVTLVNMGSSPMKIE 163
                                    46799**************************99876 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.33
                                    EE-SS-EEEEETBTTE CS
                  YidC_periplas   4 vdtdvlegsislkGgr 19 
                                    vdt v +++isl+G+r
  gi|119719841|ref|YP_920336.1| 334 VDTGVAKIKISLRGAR 349
                                    89*************8 PP

  == domain 3  score: 16.8 bits;  conditional E-value: 8.3e-07
                                    --TT-SEEEEEEEEE-TTS..-EEEEEEEEETT-SEEEEEEEEE--SSS-EEEEEEEEEEEE--.------------EEE CS
                  YidC_periplas  81 laeltdelpvtLtwdngnG..ltftktytldrdsYlitvtdeveNtsgapvtlapygqlkrdpeeaseeesmfaityega 158
                                    l  l+ e +v++t ++g+   l +tkt+t+ ++ Y ++ t +++N+++ +++     ++++d +        ++++ +g+
  gi|119719841|ref|YP_920336.1| 406 LV-LKMEADVPFTNPSGDQtvLHVTKTFTFYAGLYGFDETTQITNKGNVKAES----KVNWDRT----I-G-YTFAVTGV 474
                                    44.78899999**9999876799***********************9887777....4568833....2.3.67899999 PP

                                    EEEETTTCCEEEEHHHHHT...........T---EEEEES-..EEEEEETTEEEEEEEE.SSSEEEEEEEEEE.T..EEE CS
                  YidC_periplas 159 agvtdeeklqkvkfkdlekd.........kkakkekktggg..WvamtqkYFlsAlipdqdaetnefyarkkkkd..lyq 225
                                    +g  +     + + + ++++         +k++ + k+ ++  W++m++    + +i    +  + +       +    +
  gi|119719841|ref|YP_920336.1| 475 IGQKG-----ENDWQAWKDGaglhllspkEKLHFTWKSAQDleWIGMIDPEEGACIIAYLGTPGAGIVWLEA--StwGTE 547
                                    99654.....56666665556666566553333222222223377777655555555443332223333222..145778 PP

                                    EEEEE.--EEE-TT-EEEEEEEEEEEE- CS
                  YidC_periplas 226 agylsapavtvapgasasvtarlfaGPk 253
                                    +++   p++t++pg s+++ +r+f GP 
  gi|119719841|ref|YP_920336.1| 548 VRAE-YPPFTLNPGDSVTFVYRVFGGPV 574
                                    8888.59999999999999999999995 PP

>> A2M_BRD  Alpha-2-macroglobulin bait region domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.2   0.00011      0.66       3      80 ..     602     677 ..     600     696 .. 0.63
   2 ?   -3.0   0.0       1.4   8.3e+03      93     133 ..    1122    1175 ..    1078    1175 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00011
                                    EEESSSS--TTSEEEEEEE-SS-..EE-TT-....BSS----.-.-S...S....-EEEEEE--TT-----EE.EEEE.. CS
                                    xxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                        A2M_BRD   3 ispdkeeykvGetakltvkstfa..tverdstlylvlsrgni.vssgekveeidsstsfsfpvtadmaPnarv.vvyyir 78 
                                    +s+d+  y++G++ak++v+++++  t++++      +s+g + +  +++v+ +++ +s+ ++vt    P+++   v++ r
  gi|119719841|ref|YP_920336.1| 602 VSTDSLLYSPGQKAKFNVTASYRrgTIKGTL----TVSQGGTtL-YESEVTLSQQPQSVFVEVTVPTKPGIYSyTVAL-R 675
                                    5788889*************99744333333....667666644.333333444555777788877788877743333.3 PP

                                    E- CS
                                    xx RF
                        A2M_BRD  79 rd 80 
                                    ++
  gi|119719841|ref|YP_920336.1| 676 TQ 677
                                    33 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.4
                                     -.-GGGB-EEEEE.....EE...-SS.SEEEEEEE..E.........T-EEEEEEE CS
                                     xxxxxxxxxxxxx.....xxxxxxxx.xxxxxxxxxxx.........xxxxxxxxx RF
                        A2M_BRD   93 ekdfenklsvsle.....synetrPg.eevtlkvkasp.........gslvalaaV 133 
                                     e + ++ ++ +       +++ t+Pg +++  +++  p          + va+aaV
  gi|119719841|ref|YP_920336.1| 1122 EATRAQAVTPQPGtqqppQQQPTQPGgQQAPSEIQ--PqwlglaaliAAVVAVAAV 1175
                                     33333333333335555335556777456777777..6666666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.79u 0.29s 00:00:01.08 Elapsed: 00:00:00.47
# Mc/sec: 7617.20
//
Query:       gi|119719842|ref|YP_920337.1|  [L=544]
Description: hypothetical protein Tpen_0933 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.022   14.5   0.8        4.3    7.0   0.1    2.2  2  CagX      Conjugal transfer protein


Domain annotation for each model (and alignments):
>> CagX  Conjugal transfer protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1   0.00024       4.3     128     171 ..      63     109 ..      27     115 .. 0.87
   2 ?    5.8   0.1   0.00055       9.9     128     171 ..     335     381 ..     315     386 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00024
                           CagX 128 klnfdYsvsgsaeiaPervfdDgrfTyirfp...sankelPavfvvd 171
                                    + ++++ ++ + ++   r + Dg+  y+rf+    +nk  P v+vv 
  gi|119719842|ref|YP_920337.1|  63 RPDWNWPITSDLDVLEARLYSDGQYLYLRFKfqtLKNKYSPYVMVVM 109
                                    45688888889999999*************99999999999999986 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.00055
                           CagX 128 klnfdYsvsgsaeiaPervfdDgrfTyirfp...sankelPavfvvd 171
                                    + ++++ ++ + ++   r + Dg+  y+rf+    +n+  P ++vv 
  gi|119719842|ref|YP_920337.1| 335 RPDWNWPITSDLDVLEARLYSDGQYLYLRFKlsqLSNEYSPYIMVVM 381
                                    55788888899999999*************99877888888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (544 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       268  (0.0149478); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 3699.01
//
Query:       gi|119719843|ref|YP_920338.1|  [L=326]
Description: hypothetical protein Tpen_0934 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-07   32.0   0.1    2.7e-07   31.1   0.1    1.5  1  DHHA1     DHHA1 domain
  ------ inclusion threshold ------
      0.029   15.0   2.0      0.045   14.4   0.0    2.2  3  ABATE     Putative stress-induced transcription regulator


Domain annotation for each model (and alignments):
>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.1   3.1e-11   2.7e-07      23     137 ..     173     291 ..     162     292 .. 0.72

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 3.1e-11
                                    HHHHHHHHHHTCEEEC......TCEEEEEECHCCH...HHHHHHHHHHHHHTHGBT.TCEEEEEEEECT.EEEEEEEESS CS
                          DHHA1  23 aklkaeellekaeevk......gvkvlvaevgeew...dagalgiaadklksklkk.pvivfvakeegd.kvkvsarskk 91 
                                    ++ k +e ++++eev+        k+ v ev   +   + +    + + l++   + +  ++v++ +g  k++v a++ +
  gi|119719843|ref|YP_920338.1| 173 NDEKVKEWIARHEEVRlrteslAEKIPVEEVTVVAfrkRLKLSYRYLTILLE--RRgAKFTLVLVPRGLfKYRVYAGAQP 250
                                    4445555555555555555555333333333333300044555555667777..8889999999999999*********9 PP

                                    H.SS-HHHHHHHHHHHTTCCEEEETCEEEEEEEHCHHHHHHHHHHHH CS
                          DHHA1  92 d.gvdagelakeaaaklgggGGGHdlAaGagipaekleealealeea 137
                                    +  +da+++a++      +gGGGH++AaGa   a +l +ale++ ea
  gi|119719843|ref|YP_920338.1| 251 EsSYDASTVASR------LGGGGHKFAAGALFRATSLRQALEKALEA 291
                                    9***********......************************99886 PP

>> ABATE  Putative stress-induced transcription regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       1.1   9.6e+03      75      94 ..      27      48 ..      12      74 .. 0.45
   2 ?   -1.5   0.1      0.42   3.7e+03      26      39 ..     175     188 ..     139     214 .. 0.62
   3 ?   14.4   0.0     5e-06     0.045      41      84 ..     266     308 ..     243     314 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.1
                                   ......HHHHHHH.HHS----E CS
                          ABATE 75 paaal.aalnall.aaappapr 94
                                   +a+++  ++ a l  + +p+++
  gi|119719843|ref|YP_920338.1| 27 DAGDVdGVVSATLfKISRPSAE 48
                                   3334433333333322222222 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.42
                                    HHHHHH--TTHHHH CS
                          ABATE  26 adLaaWleaagllp 39 
                                    + + +W++++  + 
  gi|119719843|ref|YP_920338.1| 175 EKVKEWIARHEEVR 188
                                    33444444443333 PP

  == domain 3  score: 14.4 bits;  conditional E-value: 5e-06
                                    H..........HHHHHHHHHHHHHHTHHHH.........HHHHH CS
                          ABATE  41 gtaaagadaelararaLRealrallaaaaagdpppaaalaalna 84 
                                    g   ++a  +l ra +LR+al + l+aa++g++++++ + ++ +
  gi|119719843|ref|YP_920338.1| 266 GGHKFAAG-ALFRATSLRQALEKALEAAKTGAGVDPQKVVVVSD 308
                                    33334443.799*************************9987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2547.55
//
Query:       gi|119719844|ref|YP_920339.1|  [L=376]
Description: FAD dependent oxidoreductase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.4e-59  200.1   1.9    8.4e-59  199.9   1.9    1.0  1  DAO            FAD dependent oxidoreductase
    8.2e-10   38.3   5.6    8.5e-08   31.7   5.6    2.1  1  FAD_binding_2  FAD binding domain
    1.3e-06   27.9   0.5     0.0054   16.0   0.1    2.5  3  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    7.9e-06   25.5   0.4    1.8e-05   24.3   0.4    1.6  1  FAD_oxidored   FAD dependent oxidoreductase
    1.2e-05   24.2   0.1      0.039   12.6   0.1    2.1  2  HI0933_like    HI0933-like protein
    1.9e-05   24.8   2.9    4.6e-05   23.5   2.9    1.7  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    4.7e-05   22.9   0.7     0.0035   16.7   0.1    2.2  2  GMC_oxred_N    GMC oxidoreductase
    0.00035   19.9   0.2    0.00059   19.2   0.2    1.4  1  Thi4           Thi4 family
    0.00039   19.6   3.8      0.036   13.1   0.6    2.4  2  Lycopene_cycl  Lycopene cyclase protein
  ------ inclusion threshold ------
      0.013   16.0   3.2        0.2   12.2   1.4    2.5  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
      0.019   14.2   1.9      0.032   13.5   1.3    1.6  2  FAD_binding_3  FAD binding domain
      0.019   14.2   1.5      0.075   12.3   0.8    2.0  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
      0.027   13.6   0.5       0.45    9.5   0.4    2.1  2  GIDA           Glucose inhibited division protein A
        3.9    7.5   5.8        1.6    8.7   1.2    2.3  3  NAD_binding_9  FAD-NAD(P)-binding


Domain annotation for each model (and alignments):
>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.9   1.9   6.6e-62   8.4e-59       1     352 []       3     344 ..       3     344 .. 0.88

  Alignments for each domain:
  == domain 1  score: 199.9 bits;  conditional E-value: 6.6e-62
                                    EEEEECTSHHHHHHHHHHHHTT...EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTHHHHHHHHHHHHHHHHHHHHHSS CS
                            DAO   1 dvviiGGGiiGlstAyeLarrg...VtllekgdiagsgaSgrnsgllhsglrylpeaselarlslealeelreleeelgi 77 
                                    dvvi+GGGi+G+s Ay La++g   V+llekg  +g g++ r +g +++++ + ++      l+++++e++ el e+lg 
  gi|119719844|ref|YP_920339.1|   3 DVVIVGGGIVGVSLAYRLAEEGagrVLLLEKG-YLGGGSTFRCAGGIRASFTSREHI----VLMKRSIELWGELREKLG- 76 
                                    9*******************9888********.9999************99855633....8***************99. PP

                                    TTSEEEEEEEEEESSHHHHHHHHHHHHHH.HHTTTTEEEEEHHHHHHHSTTST..TTSEEEEETTEEEEEHHHHHHHHHH CS
                            DAO  78 didyrrtGllslaadeeelealdkllall.leagldaelldaeevrelepalp..gllgalfypdtgqvdpakltaalar 154
                                     + y+r+G+l+l + e++ e++ k++ ++ +++g++++++d++ v++++p ++    ++al++p +g + p+ ++     
  gi|119719844|ref|YP_920339.1|  77 -VKYERSGYLWLISRERDVERF-KEYSRVhNSFGVETRFVDEDFVKRVAPYVDtsSMVAALYDPLAGKASPFDAVYKQFL 154
                                    .78**********98999****.666666689**********99******94455888********************** PP

                                    HHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEE.EEEEEEEE--GGGHH.HHHTT.CTTTSEEEEEEEEEEEEEECC CS
                            DAO 155 aaealGveilegtevtgleeedgkvwgverttpgen.daadavVnaaGawsd.llgll.keldlpispvrgqvlvlkpls 231
                                    aa++lGve+  g+ev +++ e+g + gv     g++   a+ vV+aaGa s  ll++   el  p+ pv ++   +++  
  gi|119719844|ref|YP_920339.1| 155 AARSLGVEFAVGREVDSVRVERGEARGVV--V-GNElIPARSVVVAAGAESVfLLRRSgVEL--PLAPVPHHAALTEEFG 229
                                    ******************88888888983..2.545457799********995556666777..************5533 PP

                                    THSTGSGCSEEEEEEEETTTTEEEEEETTSEEEEEESSEEETTCSSTSCSHHHHHHHHHHHHHHS...GGGCGEEEEEEE CS
                            DAO 232 eklvspaailpvpetdddgrgvyvtprkdgrvlvGgtadeesgdddpevdeedidellealrklf...PqlgdvlrkwaG 308
                                          ++ +p+  ++d ++g y++++  g+vl+G +  ee+ + +p v  e ++++ +  +k++   P+ +++lr w+G
  gi|119719844|ref|YP_920339.1| 230 ------RLFDPL--IIDVETGAYAVQTFHGHVLMGVEV-EEEPFARPVVKLEFLEKVVSTWSKWLtwlPG-ANILRYWVG 299
                                    ......355555..678899***************998.8888999899999999977777777755577.9******** PP

                                    EEE.ETTSSEEEEEEETEEEEEEEEECTTTHHHHHHHHHHHHHHH CS
                            DAO 309 lrp.lpdglpligetpgvkglylatGhsghGltlapatGkllael 352
                                    ++  +pd+ p++g++ gv++ly+atG+sghG+++ap++++ lae+
  gi|119719844|ref|YP_920339.1| 300 YYEvTPDHHPILGPVDGVENLYVATGFSGHGFMMAPVVAEELAEW 344
                                    ***77*********999**************************97 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   5.6   6.6e-11   8.5e-08       1     200 [.       3     199 ..       3     225 .. 0.59

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 6.6e-11
                                    SEEEE--SHHHHHHHHHHHHTTT.-EEEEESSSGGGSGGGG--S-EE-TT..SSGGSTC.CHHHHHHHHHHHHTTT-S-H CS
                  FAD_binding_2   1 DviViGsGlAGLaAAleaaeaGl.kvavvekeqefggatawsqGgidavlspeqkkagikdspelhrtdtlkaldeladq 79 
                                    Dv+++G+G+ G + A+++ae+G+ +v+++ek+   gg+t+ + Ggi a+ ++       k+s+el+  ++++ l+  +++
  gi|119719844|ref|YP_920339.1|   3 DVVIVGGGIVGVSLAYRLAEEGAgRVLLLEKGYLGGGSTFRCAGGIRASFTSREHIVLMKRSIELW-GELREKLGVKYER 81 
                                    9*********************************999***********996665444444544443.3445555444443 PP

                                    HHHHHHHHTHHHHHHHHHHT.......T----BCCTS..SB-EEE-TT-SSTEEEE-.STT-......HHHHHHHHHHHH CS
                  FAD_binding_2  80 plveafveaapeavdeLeel.......gvpfsrtedg..pvdvrelGglsatartlhdaadarretlvtghallarlves 150
                                         ++++ ++ v+ ++e+       gv      d+  + +v++  ++s     ++  +d+   +  +  a+ + ++++
  gi|119719844|ref|YP_920339.1|  82 SGYLWLISR-ERDVERFKEYsrvhnsfGVETRF-VDEdfVKRVAPYVDTSSM---VAALYDPLAGKASPFDAVYKQFLAA 156
                                    333333333.22344444444434444222222.112124444444444444...4435555224444444444444432 PP

                                    HHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE--- CS
                  FAD_binding_2 151 arkagvdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatg 200
                                     r++gv+f    e+d++ ve g+++G+vv n+       i a+ vv+a+g
  gi|119719844|ref|YP_920339.1| 157 -RSLGVEFAVGREVDSVRVERGEARGVVVGNE------LIPARSVVVAAG 199
                                    .3555777777777777777777777777733......344444444444 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   4.2e-06    0.0054       1      34 [.       2      34 ..       2      81 .. 0.83
   2 !    9.7   0.0   0.00034      0.43     183     252 ..     144     213 ..     101     221 .. 0.78
   3 ?   -2.6   0.0       1.9   2.5e+03     101     149 ..     318     376 .]     312     376 .] 0.57

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.2e-06
                                   CSEEEE--SHHHHHHHHHHHHH.TS-EEEEETTHC CS
                                   xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
                    Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaqa.gakvtlvelegt 34
                                   +dvv++GgG+ G+++a +la+   ++v+l+e  + 
  gi|119719844|ref|YP_920339.1|  2 YDVVIVGGGIVGVSLAYRLAEEgAGRVLLLE--KG 34
                                   69*******************6266777774..33 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00034
                                    HHHHHHHHHHHHHT..TEEEEESCEEEEEEETTEEEE.EEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EE CS
                                    xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 183 kelsaaleealeke..Gvevklgtsvkeidgngekle.vvledgeeidadlvvvavGvrpstelleeklglel 252
                                    + + a +++ l ++  Gve+ +g +v  ++ +  +++ vv +++  i+a+ vvva+G +    l  +++g+el
  gi|119719844|ref|YP_920339.1| 144 SPFDAVYKQFLAARslGVEFAVGREVDSVRVERGEARgVVVGNE-LIPARSVVVAAGAESVFLL--RRSGVEL 213
                                    5566666666665556***********99999998885555555.59**********9988644..6788876 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1.9
                                    SEEEE---EEE-BC.TCTTC....TTBEECCSECHHHHHHCCSS-T.......SEEEEES CS
                                    xxxxxxxxxxxxxx.xxxxx...xxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxx RF
                    Pyr_redox_2 101 dklvlAtGssprdl.gipGv...aenvgklvrtldsaealklkllp.......krivvvG 149
                                    ++l +AtG+s + +   p v     +++k+    +s ea +l l +       k ++v+G
  gi|119719844|ref|YP_920339.1| 318 ENLYVATGFSGHGFmMAPVVaeeLAEWIKS-GKPKSEEAARLTLARfkegrliKELAVIG 376
                                    567789998777664333222234444444.44455555555554455777777777777 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.4   1.4e-08   1.8e-05       1     124 [.       3     183 ..       3     200 .. 0.59

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 1.4e-08
                   FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaee......qvvtgiareflerlrq...rg 71 
                                    Dvv+vGGg+ Gv  A+  a++Ga  +L+ e+g+lGG +t    + +    +++      +    +++e++e+l     r 
  gi|119719844|ref|YP_920339.1|   3 DVVIVGGGIVGVSLAYRLAEEGAGRVLLLEKGYLGGGSTFRCAGGIRASFTSRehivlmKRSIELWGELREKLGVkyeRS 82 
                                    9**********************888888899999999977776666644333467777777778888888886644333 PP

                   FAD_oxidored  72 ga......rlk..krskwn.........................................tfepevakavleeml..aea 100
                                    g+      + +  +r+  +                                         + + + + av++++l  +  
  gi|119719844|ref|YP_920339.1|  83 GYlwlisrE-RdvERF--KeysrvhnsfgvetrfvdedfvkrvapyvdtssmvaalydplAGKASPFDAVYKQFLaaRSL 159
                                    335555431.112222..02234445556666666666666666655555555553333223333333444444454445 PP

                   FAD_oxidored 101 gvtvllntrlvevekegkriesvt 124
                                    gv+   ++++++v++e ++ ++v+
  gi|119719844|ref|YP_920339.1| 160 GVEFAVGREVDSVRVERGEARGVV 183
                                    555555555555555544455555 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.1   3.1e-05     0.039       1      51 [.       2      54 ..       2      68 .. 0.84
   2 !    9.4   0.0    0.0003      0.38     119     167 ..     156     203 ..     142     220 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.1e-05
                                   -SEEEE--SHHHHHHHHHHHHTT-.-EEEE-SSS.SS-HHHHHCGGGT-EEEE CS
                    HI0933_like  1 kdviviGgGaAGlmaAisaakrgk.rVlllekak.klgrKilisGgGrcNvTn 51
                                   +dv+++GgG  G+  A ++a++g+ rVlllek+    g+ ++ +Gg r  +T 
  gi|119719844|ref|YP_920339.1|  2 YDVVIVGGGIVGVSLAYRLAEEGAgRVLLLEKGYlGGGSTFRCAGGIRASFTS 54
                                   59****************98887559******972457899999999999987 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0003
                                    HHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----SS- CS
                    HI0933_like 119 lkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGlSi 167
                                    +++ gv++ + +ev sv+ e++++  v + ++e + a+++v+A G +S+
  gi|119719844|ref|YP_920339.1| 156 ARSLGVEFAVGREVDSVRVERGEARGVVV-GNELIPARSVVVAAGAESV 203
                                    6789*******************999999.****************997 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   2.9   3.6e-08   4.6e-05       1      36 [.       6      41 ..       6      56 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 3.6e-08
                                   EE--SHHHHHHHHHHHCCTE.EEEEE-SSSSSSGGG- CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagf.dvlllekrdrlGGraa 36
                                   IvG+G+ G ++Ay+La++g+ +vlllek+ +lGG ++
  gi|119719844|ref|YP_920339.1|  6 IVGGGIVGVSLAYRLAEEGAgRVLLLEKG-YLGGGST 41
                                   9*******************9*******9.7777554 PP

>> GMC_oxred_N  GMC oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   2.8e-06    0.0035       1      33 [.       2      34 ..       2      53 .. 0.94
   2 ?    4.5   0.1     0.015        19     239     268 ..     180     211 ..     156     219 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.8e-06
                    GMC_oxred_N  1 vdelveggGsagsvvAaRLsedpstsvlvleag 33
                                   +d +++ggG++g  +A+RL+e+++ +vl+le g
  gi|119719844|ref|YP_920339.1|  2 YDVVIVGGGIVGVSLAYRLAEEGAGRVLLLEKG 34
                                   6899***************************87 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.015
                    GMC_oxred_N 239 t...vkrlvvaakevvvaaGalnsPqlLqrSGl 268
                                        v +  + a+ vvvaaGa +s  lL+rSG+
  gi|119719844|ref|YP_920339.1| 180 RgvvVGNELIPARSVVVAAGA-ESVFLLRRSGV 211
                                    444444556678999***998.899*******9 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.2   4.6e-07   0.00059      19      62 ..       3      48 ..       1      92 [. 0.68

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 4.6e-07
                                   EEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTT..TTST CS
                           Thi4 19 DvvivGaGssGLtaayylakkpdlkvailersvspGGGaw..lGGq 62
                                   DvvivG+G  G++ ay la++   +v++le+    GG +    GG 
  gi|119719844|ref|YP_920339.1|  3 DVVIVGGGIVGVSLAYRLAEEGAGRVLLLEKGYLGGGSTFrcAGGI 48
                                   9********************8899****99875555543224554 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.6   2.8e-05     0.036       1      32 [.       3      33 ..       3      37 .. 0.83
   2 !    7.0   0.1    0.0021       2.6     108     157 ..     168     251 ..     149     271 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.8e-05
                  Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvliea 32
                                   Dvv++G+G  g+slA rl+e+ +  +v+l+e 
  gi|119719844|ref|YP_920339.1|  3 DVVIVGGGIVGVSLAYRLAEEGA-GRVLLLEK 33
                                   9*****************55554.47888775 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0021
                  Lycopene_cycl 108 kvesveeeeageslvvleggrkirarlvvdarglaslk...................................karrlgl 152
                                     v+sv+ e   e + v+ g++ i+ar vv+a g+ s                                     +  +  +
  gi|119719844|ref|YP_920339.1| 168 EVDSVRVERG-EARGVVVGNELIPARSVVVAAGAESVFllrrsgvelplapvphhaalteefgrlfdpliidvETGAYAV 246
                                    4777776666.9999999***************55544666666666666666666666666666666666655555666 PP

                  Lycopene_cycl 153 QtfyG 157
                                    Qtf+G
  gi|119719844|ref|YP_920339.1| 247 QTFHG 251
                                    66666 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.4   0.00016       0.2       2      27 ..       4      30 ..       3      36 .. 0.82
   2 ?    2.8   0.0      0.13   1.7e+02      51      78 ..     157     184 ..     147     187 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00016
                                   EEEECSSHHHHHHHHHHHHTTS.EEEE CS
                      Pyr_redox  2 vvvvGgGyiglElAgalaelgk.kVtv 27
                                   vv+vGgG +g+ lA  lae g+ +V +
  gi|119719844|ref|YP_920339.1|  4 VVIVGGGIVGVSLAYRLAEEGAgRVLL 30
                                   8****************9988535555 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.13
                                    HHTTEEEECSEEEEEEEEETTSEEEEEE CS
                      Pyr_redox  51 ekngievllntkveeiegsedgvesvkl 78 
                                    + +g+e+  +++v +++ +  + ++v++
  gi|119719844|ref|YP_920339.1| 157 RSLGVEFAVGREVDSVRVERGEARGVVV 184
                                    778**************77766788876 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   1.3   2.5e-05     0.032       2      32 ..       2      33 ..       1      36 [. 0.88
   2 ?   -2.6   0.0       1.9   2.4e+03     115     166 ..     156     202 ..     151     275 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.5e-05
                                   EEEEEE--SHHHHHHHHHHHHTTHH.EEEEES CS
                  FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvr.vvlvek 32
                                   +dV+IVG+G +G++la  L+e G   v+l+ek
  gi|119719844|ref|YP_920339.1|  2 YDVVIVGGGIVGVSLAYRLAEEGAGrVLLLEK 33
                                   69*********************964667776 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.9
                                    HHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEEEEEE--GTT- CS
                  FAD_binding_3 115 aeerglqvrfktevesleqdeegvtaevrdketgeeetvrakYlvGaDGgrS 166
                                    a++ g+++  ++ev s++ +  + + +v ++e      + a+ +v a G+ S
  gi|119719844|ref|YP_920339.1| 156 ARSLGVEFAVGREVDSVRVERGEARGVVVGNE-----LIPARSVVVAAGAES 202
                                    56777778888888877777777666666553.....455555555555555 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.8   5.9e-05     0.075       1      33 [.       5      37 ..       5      43 .. 0.94
   2 ?   -0.1   0.0      0.33   4.3e+02      91     133 ..     156     199 ..      96     206 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.9e-05
                    Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgnig 33
                                   +I+G+G  G++ a+ l + g  ++l lEkg +g
  gi|119719844|ref|YP_920339.1|  5 VIVGGGIVGVSLAYRLAEEGAGRVLLLEKGYLG 37
                                   7*****************************776 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.33
                    Pyr_redox_3  91 aksfelpiklfeeVesvkke.degfevetsketyeAkkviiAtG 133
                                    a+s  ++     eV sv  e +e   v   +e + A++v++A+G
  gi|119719844|ref|YP_920339.1| 156 ARSLGVEFAVGREVDSVRVErGEARGVVVGNELIPARSVVVAAG 199
                                    44555666677788888885145567888889999999999999 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.4   0.00035      0.45       1      30 [.       3      32 ..       3      66 .. 0.79
   2 ?    1.9   0.0     0.073        93     116     150 ..     167     200 ..     160     232 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00035
                                   CEEEE-SSHHHHHHHHHHHHTT--EEEEES CS
                           GIDA  1 dviViGgGhAGceAAlaaarlGakvlLith 30
                                   dv+++GgG  G+  A+ +a+ Ga  +L+ +
  gi|119719844|ref|YP_920339.1|  3 DVVIVGGGIVGVSLAYRLAEEGAGRVLLLE 32
                                   79********************96666533 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.073
                                    S-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT CS
                           GIDA 116 eeveeliveekkvkgvvtedgetikakavviatGt 150
                                    +ev+++ ve ++ +gvv   +e i a++vv+a+G+
  gi|119719844|ref|YP_920339.1| 167 REVDSVRVERGEARGVVVG-NELIPARSVVVAAGA 200
                                    6899999999*****9875.678999********9 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   1.2    0.0012       1.6       1      40 [.       5      40 ..       5      49 .. 0.82
   2 ?    0.0   0.1      0.58   7.4e+02     104     154 ..     150     199 ..     146     201 .. 0.66
   3 ?   -3.8   0.0         9   1.1e+04      67      78 ..     339     350 ..     333     363 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0012
                  NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsepgagr 40
                                   +ivG+G+ G++++ rL+++       ++ l ++  +g g+
  gi|119719844|ref|YP_920339.1|  5 VIVGGGIVGVSLAYRLAEE----GAGRVLLLEKGYLGGGS 40
                                   7****************99....57888888886665455 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.58
                  NAD_binding_9 104 feellarlpegvtvevhraevvdleeradgqavlladgaslaadaVvLAlG 154
                                    ++++la+ + gv++  +  ev +++ ++++++ +  +++ + a++Vv+A G
  gi|119719844|ref|YP_920339.1| 150 YKQFLAARSLGVEFA-VGREVDSVRVERGEARGVVVGNELIPARSVVVAAG 199
                                    556665554444433.35577777777777766677888899******999 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 9
                  NAD_binding_9  67 ptfaeWlrerga 78 
                                    +++aeW+++ + 
  gi|119719844|ref|YP_920339.1| 339 EELAEWIKSGKP 350
                                    578888887664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2445.72
//
Query:       gi|119719845|ref|YP_920340.1|  [L=158]
Description: 4Fe-4S ferredoxin iron-sulfur binding domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-11   42.9  13.1    3.1e-08   33.1   3.1    2.4  2  Fer4      4Fe-4S binding domain
    2.2e-08   34.6   9.8    3.7e-08   33.8   9.8    1.4  1  Fer4_7    4Fe-4S dicluster domain
    3.3e-07   30.3  20.8    0.00021   21.4   1.1    2.1  2  Fer4_10   4Fe-4S dicluster domain
    3.5e-07   30.3   9.5    5.6e-07   29.6   9.5    1.3  1  Fer4_9    4Fe-4S dicluster domain
    8.9e-07   28.9   8.2    1.9e-06   27.9   8.2    1.5  1  Fer4_21   4Fe-4S dicluster domain
    1.2e-06   28.6  10.4    3.3e-05   24.1   0.6    2.3  2  Fer4_4    4Fe-4S binding domain
    2.1e-06   27.4  16.0    3.1e-05   23.8   4.3    2.3  2  Fer4_2    4Fe-4S binding domain
    1.6e-05   24.7  15.7    0.00025   21.0   2.5    2.3  2  Fer4_6    4Fe-4S binding domain
    2.8e-05   24.7   9.2    0.00012   22.7   2.1    2.7  2  Fer4_15   4Fe-4S single cluster domain
    0.00016   22.5  12.6      0.058   14.3   1.3    2.2  3  Fer4_16   4Fe-4S double cluster binding domain
  ------ inclusion threshold ------
      0.015   15.8   1.0      0.015   15.8   1.0    2.2  2  Fer4_17   4Fe-4S dicluster domain
      0.022   15.3   0.4      0.022   15.3   0.4    2.6  3  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
      0.027   14.9  10.6      0.035   14.5   0.9    2.2  3  Fer4_8    4Fe-4S dicluster domain
      0.088   13.8  20.0       0.86   10.7   7.9    2.3  2  Fer4_3    4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   2.5   1.1e-05     0.014      11      24 .]      41      54 ..      41      54 .. 0.96
   2 !   33.1   3.1   2.4e-11   3.1e-08       2      22 ..      63      83 ..      62      85 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.1e-05
                                   -THHHHHSTTTEEE CS
                           Fer4 11 CGaCvevCPvgAIt 24
                                   C+ C+++CPv AI+
  gi|119719845|ref|YP_920340.1| 41 CNVCESACPVKAIR 54
                                   ************96 PP

  == domain 2  score: 33.1 bits;  conditional E-value: 2.4e-11
                                   EEETTTSSS-THHHHHSTTTE CS
                           Fer4  2 videekCigCGaCvevCPvgA 22
                                    id+++C+gCG Cv vCP  A
  gi|119719845|ref|YP_920340.1| 63 RIDWDRCTGCGVCVGVCPGQA 83
                                   79****************988 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   9.8   2.9e-11   3.7e-08       4      51 ..      40      82 ..      34      83 .. 0.90

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 2.9e-11
                         Fer4_7  4 gCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtg 51
                                    C+ C++aCpvkai+++       + +++id ++C+gCg+Cv vCP +
  gi|119719845|ref|YP_920340.1| 40 PCNVCESACPVKAIRVEGL-----RGRPRIDWDRCTGCGVCVGVCPGQ 82
                                   6***************998.....46899*****************76 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5  12.7     3e-07   0.00038      10      56 .]      39      80 ..      29      80 .. 0.90
   2 !   21.4   1.1   1.6e-07   0.00021       3      23 ..      63      83 ..      61     125 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 3e-07
                        Fer4_10 10 irCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                   i C+ C +aCP+     +a+  +   ++ r++ ++Ctgcg Cv +CP
  gi|119719845|ref|YP_920340.1| 39 IPCNVCESACPV-----KAIRVEGLRGRPRIDWDRCTGCGVCVGVCP 80
                                   68**********.....999999999999*****************9 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 1.6e-07
                        Fer4_10  3 vidddtCirCgkCvkaCPadl 23
                                   +id d+C++Cg Cv +CP ++
  gi|119719845|ref|YP_920340.1| 63 RIDWDRCTGCGVCVGVCPGQA 83
                                   7999**************854 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   9.5   4.4e-10   5.6e-07       4      50 ..      40      83 ..      34      84 .. 0.89

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 4.4e-10
                         Fer4_9  4 gCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50
                                    C+ C++aCp ++++ +  ++  r++++   +C+gCg Cv +Cp +a
  gi|119719845|ref|YP_920340.1| 40 PCNVCESACPVKAIRVEGLRGRPRIDWD---RCTGCGVCVGVCPGQA 83
                                   4***********************9765...8************987 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   8.2   1.5e-09   1.9e-06       8      52 ..      35      80 ..      29      85 .. 0.82

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 1.5e-09
                        Fer4_21  8 Cig...CgkCliaCedtshqaieidaktvlkvv.edeCvGCnlCssvCP 52
                                   Ci+   C+ C  aC+   ++ai++++ +  + +  d+C+GC +C+ vCP
  gi|119719845|ref|YP_920340.1| 35 CIEeipCNVCESACP---VKAIRVEGLRGRPRIdWDRCTGCGVCVGVCP 80
                                   653344*********...8******9998877636************** PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   3.7    0.0024       3.1       7      16 ..      41      50 ..      33      51 .. 0.86
   2 !   24.1   0.6   2.6e-08   3.3e-05       2      15 ..      67      80 ..      66      94 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0024
                         Fer4_4  7 CgsCvaaCPq 16
                                   C +C++aCP+
  gi|119719845|ref|YP_920340.1| 41 CNVCESACPV 50
                                   9********7 PP

  == domain 2  score: 24.1 bits;  conditional E-value: 2.6e-08
                         Fer4_4  2 erCigCgsCvaaCP 15
                                   +rC+gCg+Cv +CP
  gi|119719845|ref|YP_920340.1| 67 DRCTGCGVCVGVCP 80
                                   9************* PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   3.9   0.00095       1.2       4      21 ..      30      49 ..      27      50 .. 0.85
   2 !   23.8   4.3   2.4e-08   3.1e-05       2      21 ..      61      80 ..      60      80 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00095
                         Fer4_2  4 vvdtdrCig...CgaCvsaCP 21
                                   v++t+ Ci+   C+ C saCP
  gi|119719845|ref|YP_920340.1| 30 VAVTE-CIEeipCNVCESACP 49
                                   56677.999999********* PP

  == domain 2  score: 23.8 bits;  conditional E-value: 2.4e-08
                         Fer4_2  2 pvvvdtdrCigCgaCvsaCP 21
                                   ++ +d drC+gCg Cv +CP
  gi|119719845|ref|YP_920340.1| 61 RPRIDWDRCTGCGVCVGVCP 80
                                   6789***************9 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   5.5   0.00094       1.2       9      24 .]      35      53 ..      35      53 .. 0.83
   2 !   21.0   2.5     2e-07   0.00025       2      23 ..      62      83 ..      61      84 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00094
                         Fer4_6  9 Ci...gCgdCvrvCPegai 24
                                   Ci    C+ C+++CP +ai
  gi|119719845|ref|YP_920340.1| 35 CIeeiPCNVCESACPVKAI 53
                                   665447**********998 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 2e-07
                         Fer4_6  2 veidpdkCigCgdCvrvCPega 23
                                   ++id d+C+gCg Cv vCP +a
  gi|119719845|ref|YP_920340.1| 62 PRIDWDRCTGCGVCVGVCPGQA 83
                                   67888**************776 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.7     0.015        19      57      66 .]      46      55 ..      43      55 .. 0.91
   2 !   22.7   2.1   9.7e-08   0.00012       3      33 ..      64      97 ..      63     158 .] 0.75

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.015
                        Fer4_15 57 raCPvdAIrv 66
                                   +aCPv+AIrv
  gi|119719845|ref|YP_920340.1| 46 SACPVKAIRV 55
                                   69******98 PP

  == domain 2  score: 22.7 bits;  conditional E-value: 9.7e-08
                        Fer4_15  3 vDrdaCigcglCvaea..pevfelde.dglasvl 33
                                   +D+d+C+gcg+Cv ++  + +f ld  +g a+++
  gi|119719845|ref|YP_920340.1| 64 IDWDRCTGCGVCVGVCpgQAMFLLDLsRGAAVTV 97
                                   9***************554566666545666444 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   1.3   4.5e-05     0.058       5      20 ..      41      56 ..      34      68 .. 0.84
   2 !   12.1   4.0   0.00023      0.29      52      65 ..      67      80 ..      60      82 .. 0.77
   3 !   13.2   4.0    0.0001      0.13       1      17 [.      68      84 ..      68      88 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.5e-05
                        Fer4_16  5 CgkCaevCPtnaikek 20
                                   C+ C ++CP++ai+ +
  gi|119719845|ref|YP_920340.1| 41 CNVCESACPVKAIRVE 56
                                   *************976 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00023
                        Fer4_16 52 eaitgCdiCqdvCP 65
                                    ++tgC++C+ vCP
  gi|119719845|ref|YP_920340.1| 67 DRCTGCGVCVGVCP 80
                                   56788888888888 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 0.0001
                        Fer4_16  1 rCgtCgkCaevCPtnai 17
                                   rC++Cg C+ vCP +a+
  gi|119719845|ref|YP_920340.1| 68 RCTGCGVCVGVCPGQAM 84
                                   59999999999999886 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   3.2     0.044        56      44      57 ..      33      49 ..      16      52 .. 0.76
   2 ?   15.8   1.0   1.2e-05     0.015      42      58 ..      65      81 ..      50      84 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.044
                        Fer4_17 44 slCie...CgeCerkCP 57
                                    +Cie   C+ Ce++CP
  gi|119719845|ref|YP_920340.1| 33 TECIEeipCNVCESACP 49
                                   55654444999999999 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 1.2e-05
                        Fer4_17 42 kaslCieCgeCerkCPq 58
                                    +++C++Cg C+ +CP 
  gi|119719845|ref|YP_920340.1| 65 DWDRCTGCGVCVGVCPG 81
                                   68999999999999996 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   3.1      0.37   4.7e+02       7      17 ..      39      49 ..      32      50 .. 0.85
   2 ?    3.6   1.9     0.078     1e+02      14      57 ..      46      54 ..      38      55 .. 0.61
   3 ?   15.3   0.4   1.7e-05     0.022       1      17 [.      64      80 ..      64      97 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.37
                        Fer4_13  7 iacgaCvelaP 17
                                   i c++C +++P
  gi|119719845|ref|YP_920340.1| 39 IPCNVCESACP 49
                                   67********9 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.078
                        Fer4_13 14 elaPdvFeeddeggasvvaeqptseeekadaeeAadaCPvesIg 57
                                   +                                   aCPv++I+
  gi|119719845|ref|YP_920340.1| 46 S-----------------------------------ACPVKAIR 54
                                   4...................................56666666 PP

  == domain 3  score: 15.3 bits;  conditional E-value: 1.7e-05
                        Fer4_13  1 VDrdtCiacgaCvelaP 17
                                   +D d+C++cg+Cv ++P
  gi|119719845|ref|YP_920340.1| 64 IDWDRCTGCGVCVGVCP 80
                                   799*************9 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   3.5     0.048        62       8      17 ..      41      50 ..      22      53 .. 0.70
   2 ?    4.2  13.2     0.047        60       8      62 ..      41      80 ..      31      83 .. 0.62
   3 ?   14.5   0.9   2.8e-05     0.035       3      16 ..      67      80 ..      65     135 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.048
                         Fer4_8  8 CgaCqsaCpv 17
                                   C  C+saCpv
  gi|119719845|ref|YP_920340.1| 41 CNVCESACPV 50
                                   6667777765 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.047
                         Fer4_8  8 CgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCp 62
                                   C  C+saCpv   +  +    rg+      +         +++Ct+cg C+ vCp
  gi|119719845|ref|YP_920340.1| 41 CNVCESACPVKAIR-VE--GLRGRPRI---D---------WDRCTGCGVCVGVCP 80
                                   88888888743333.22..22333222...2.........456***********9 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 2.8e-05
                         Fer4_8  3 ekCieCgaCqsaCp 16
                                   ++C++Cg C   Cp
  gi|119719845|ref|YP_920340.1| 67 DRCTGCGVCVGVCP 80
                                   56777777777776 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   4.1    0.0024       3.1       1      15 []      35      52 ..      35      52 .. 0.82
   2 ?   10.7   7.9   0.00067      0.86       1      15 []      69      83 ..      69      83 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0024
                         Fer4_3  1 Ctg...CgaCvevCPvgA 15
                                   C+    C+ C+ +CPv+A
  gi|119719845|ref|YP_920340.1| 35 CIEeipCNVCESACPVKA 52
                                   55555599********98 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00067
                         Fer4_3  1 CtgCgaCvevCPvgA 15
                                   CtgCg Cv vCP  A
  gi|119719845|ref|YP_920340.1| 69 CTGCGVCVGVCPGQA 83
                                   ************865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1044.58
//
Query:       gi|119719846|ref|YP_920341.1|  [L=469]
Description: hypothetical protein Tpen_0938 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-35  122.7   1.3    1.7e-35  122.7   1.3    1.5  2  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
    2.4e-23   82.0   0.1    6.1e-23   80.7   0.1    1.8  1  Fer2_4           2Fe-2S iron-sulfur cluster binding domain
    3.4e-13   49.5   0.0    4.2e-08   32.8   0.0    2.2  2  Pyr_redox_3      Pyridine nucleotide-disulphide oxidoreductas
    1.1e-11   44.5   8.0      3e-07   29.9   0.3    3.6  3  FAD_binding_2    FAD binding domain
    2.1e-11   43.9   4.4    2.8e-07   30.7   0.3    3.0  2  NAD_binding_8    NAD(P)-binding Rossmann-like domain
    3.1e-11   43.7  11.4    1.2e-05   25.7   2.1    5.1  4  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
    3.4e-10   40.0  14.4    0.00066   19.4   0.1    3.8  4  DAO              FAD dependent oxidoreductase
      1e-09   37.7   3.0    6.8e-05   21.7   0.1    3.4  3  HI0933_like      HI0933-like protein
    1.4e-08   34.2   5.1    0.00019   20.6   0.1    3.2  3  GIDA             Glucose inhibited division protein A
    1.5e-08   34.2   0.9    8.1e-06   25.3   0.0    2.5  2  Thi4             Thi4 family
    8.2e-08   32.0   3.8    9.1e-07   28.6   0.2    2.3  2  FAD_oxidored     FAD dependent oxidoreductase
    8.8e-08   31.8   2.7    7.1e-05   22.2   0.1    2.4  2  FAD_binding_3    FAD binding domain
    0.00014   21.1   0.2      0.065   12.4   0.0    2.3  2  K_oxygenase      L-lysine 6-monooxygenase (NADPH-requiring)
    0.00029   20.2   4.5       0.25   10.6   0.1    3.6  4  Amino_oxidase    Flavin containing amine oxidoreductase
     0.0022   18.0   5.5       0.31   11.0   0.0    3.9  4  NAD_binding_9    FAD-NAD(P)-binding
     0.0023   17.0   3.6      0.033   13.2   0.1    3.1  3  Lycopene_cycl    Lycopene cyclase protein
     0.0031   17.4   3.9       0.37   10.6   0.0    3.0  3  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
  ------ inclusion threshold ------
      0.013   15.0   0.2        5.6    6.4   0.0    2.3  2  Glu_dehyd_C      Glucose dehydrogenase C-terminus
      0.018   14.5   1.2        1.4    8.2   0.0    2.2  2  PALP             Pyridoxal-phosphate dependent enzyme
      0.024   14.3   1.0      0.037   13.7   0.1    1.9  2  ApbA             Ketopantoate reductase PanE/ApbA
      0.052   12.8   0.2      0.052   12.8   0.2    3.5  3  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
      0.089   12.6   1.8       0.17   11.7   1.8    1.4  1  DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydr
       0.11   12.5   0.1         21    5.2   0.1    2.6  2  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
       0.13   12.7   6.3       0.88   10.0   0.2    2.8  3  NAD_binding_7    Putative NAD(P)-binding


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.7   1.3   2.2e-38   1.7e-35       2     291 ..     113     412 ..     112     415 .. 0.77
   2 ?   -2.3   0.0       2.7   2.1e+03     158     184 ..     421     447 ..     419     458 .. 0.85

  Alignments for each domain:
  == domain 1  score: 122.7 bits;  conditional E-value: 2.2e-38
                                    SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHH.HCHHHHHHHHHHHHH.......HHHHCHHHHCCCCHCC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxx RF
                    Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcll.skallgvaedaeias.......evvkklnqgielllge 73 
                                    dv+viG+GpAGl+aal  a ag++v+++ ++   ++g+ +  ++++ g++e    ++        v +  ++g++  +++
  gi|119719846|ref|YP_920341.1| 113 DVMVIGSGPAGLSAALASASAGLEVHVF-ERHFRPGGQLVKqTHKFFGSGELFGGLRgfqiaerLVSEAERAGVKIHTRS 191
                                    8***************************.67777777777754466666666665667888886333445667******9 PP

                                    TCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC..TTBEECCSECHHHHHHCCSS-T.SEEEEES-S CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                    Pyr_redox_2  74 evvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGv.aenvgklvrtldsaealklkllp.krivvvGgG 151
                                    +v++  +g++ + ++  ++g   ++ ++++v+ tG+  r l+ pG     ++ +    +++   ++  +p +++vvvG+G
  gi|119719846|ref|YP_920341.1| 192 PVLGW-FGEGVFAVN--EGGRLLRVRAKAVVVGTGAVERFLPFPGNtL-PGV-MGAGAAQTLMNEYGVKPgEKAVVVGAG 266
                                    9****.999999994..56999**************999999998831.222.223444444444444446677****** PP

                                    HHHHHHHHHHHHHT-E.EEEEESSSSSSTTS-HHHHHHHH.HHHHHTTEEEEESCEEEEEEETTE..........EEEEE CS
                                    xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx..........xxxxx RF
                    Pyr_redox_2 152 yiGvElAaalaklgke.vtlveardrllraldkelsaale.ealekeGvevklgtsvkeidgnge..........klevv 219
                                    ++G+ ++ +l ++g+    +ve r+++        + +++ ++l++ Gv + ++++v++++g+g+          k    
  gi|119719846|ref|YP_920341.1| 267 NVGLIVSYQLLQAGVSvEAVVEVRPEIG-------GWFVHaAKLRRLGVPILTEHTVVRAEGRGRvervvisrvgK---- 335
                                    ***************9445899999998.......444440467777*****************965554444330.... PP

                                    ETTSCE..........EEESEEEE-S-EEES-HHCSHCCT-EE...EETTEE..E--TTSBESSTTEEE-GGGCTECCSS CS
                                    xxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 220 ledgee..........idadlvvvavGvrpstelleeklglel...derggi..vvdeflrtnvpgiyaiGDvaggkggp 284
                                                    ++adl+++avG++p+++ll  ++g  +   +e gg     d++++t++pg+y++GD      g+
  gi|119719846|ref|YP_920341.1| 336 -----DfqplkeyersVEADLLLLAVGLTPESRLL-AEMGARMtwsTELGGYvpYRDRYMETSIPGVYVAGDAS----GI 405
                                    .....34445555556*******************.99999885554545544778****************66....99 PP

                                    --HHHHH CS
                                    xxxxxxx RF
                    Pyr_redox_2 285 elaqaAv 291
                                    e a++A 
  gi|119719846|ref|YP_920341.1| 406 EEATTAL 412
                                    9999986 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.7
                                    HHHHHHHT-EEEEEESSSSSSTTS-HH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 158 Aaalaklgkevtlveardrllraldke 184
                                    +aa++ lg++  lve r++ lr+ld+ 
  gi|119719846|ref|YP_920341.1| 421 SAAIRILGERGELVEEREKALRMLDET 447
                                    678899999999*********999976 PP

>> Fer2_4  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.7   0.1   8.2e-26   6.1e-23       2      80 ..      15      92 ..      14      94 .. 0.93

  Alignments for each domain:
  == domain 1  score: 80.7 bits;  conditional E-value: 8.2e-26
                         Fer2_4  2 rpvtltfDGkevtvpeGdtvasAllangvdvp.rsckygrprgelcaggeCrnClVevegepnvracstpvedGlkvetq 80
                                    pv+++fDG+ev+++eG+++a+Al+a g++ + r      p+g++c++g C+ C+V+v+g+ +vrac  pv+dG +ve++
  gi|119719846|ref|YP_920341.1| 15 SPVKFRFDGEEVEAFEGESIAAALWASGIRDFrRGEQG--PQGPFCMIGYCSGCMVRVDGRSRVRACLEPVRDGAVVERE 92
                                   58***************************966266666..9************************************986 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.8e-05     0.014       2      30 ..     116     143 ..     115     160 .. 0.89
   2 !   32.8   0.0   5.6e-11   4.2e-08     114     305 .]     202     400 ..     167     400 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.8e-05
                    Pyr_redox_3   2 IiGaGPaGlaaaielkkagledylilEkg 30 
                                    +iG GPaGl+aa++   agl ++ + E++
  gi|119719846|ref|YP_920341.1| 116 VIGSGPAGLSAALASASAGL-EVHVFERH 143
                                    8*******************.699*9997 PP

  == domain 2  score: 32.8 bits;  conditional E-value: 5.6e-11
                    Pyr_redox_3 114 fevetske..tyeAkkviiAtGefdkPnklnipGeek.....lvkhyskvkefhkyagqkvvViGgknSavDaAlelvrk 186
                                    f v+   +   ++Ak v++ tG     ++l +pG +          +  ++e+    g+k vV+G++n +  + ++l ++
  gi|119719846|ref|YP_920341.1| 202 FAVNEGGRllRVRAKAVVVGTGA--VERFLPFPGNTLpgvmgAGAAQTLMNEYGVKPGEKAVVVGAGNVGLIVSYQLLQA 279
                                    55555554446899********8..56677777776421111122344445665667*********************** PP

                    Pyr_redox_3 187 gaeVtvvtr.gseiekeesdpsyslkpdienrleelvkeekikvlfnaevkeikekeeeykvk..tedgkkvevkddvvl 263
                                    g +V+ v++ + ei  +     ++l+    + l e    + ++++ + +v+++  + +  + +  +e +++ve  d  +l
  gi|119719846|ref|YP_920341.1| 280 GVSVEAVVEvRPEIGGWF-VHAAKLRRLGVPILTEH---TVVRAEGRGRVERVVISRVGKDFQplKEYERSVE-ADLLLL 354
                                    ****98877245566653.34446666666666663...5689999999998765555555543166655554.477788 PP

                    Pyr_redox_3 264 atGykpdlsflkk....slfeldedgrpvlteeteetnvpglflaG 305
                                    a+G +p+ ++l++    + ++++  g++ + +  +et +pg+++aG
  gi|119719846|ref|YP_920341.1| 355 AVGLTPESRLLAEmgarMTWSTELGGYVPYRDRYMETSIPGVYVAG 400
                                    8**********998854455555669*******************9 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.3     4e-10     3e-07       1      39 [.     113     151 ..     113     168 .. 0.91
   2 !   12.6   0.2     7e-05     0.052     140     235 ..     169     249 ..     165     257 .. 0.77
   3 ?    5.1   0.2     0.013       9.9       2      36 ..     260     295 ..     259     346 .. 0.91

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 4e-10
                                    SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGG CS
                  FAD_binding_2   1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggata 39 
                                    Dv ViGsG AGL+AAl+ a aGl+v v e  ++ gg+++
  gi|119719846|ref|YP_920341.1| 113 DVMVIGSGPAGLSAALASASAGLEVHVFERHFRPGGQLV 151
                                    9*****************************999999654 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 7e-05
                                    HHHHHHHHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----GG..........GSSSB CS
                  FAD_binding_2 140 ghallarlvesarkagvdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfgrallkellgaaaeaet 219
                                    g+++++rlv +a++agv++++r +++          G+ +   e+gr  r+rakavv+ tg+++r            +  
  gi|119719846|ref|YP_920341.1| 169 GFQIAERLVSEAERAGVKIHTRSPVLGWFG-----EGVFAV-NEGGRLLRVRAKAVVVGTGAVER---------FLPFPG 233
                                    899***********************9955.....444444.589*******************9.........334444 PP

                                    SSGTT-S-HHHHHHHC CS
                  FAD_binding_2 220 tnapavtGdglalalr 235
                                     ++p+v+G g a +l+
  gi|119719846|ref|YP_920341.1| 234 NTLPGVMGAGAAQTLM 249
                                    4555555555554444 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.013
                                    EEEE--SHHHHHHHHHHHHTTT-E.EEEESSSGGGS CS
                  FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkv.avvekeqefgg 36 
                                    ++V+G+G  GL  ++++ +aG +v avve  +e gg
  gi|119719846|ref|YP_920341.1| 260 AVVVGAGNVGLIVSYQLLQAGVSVeAVVEVRPEIGG 295
                                    69********************88688888888777 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.3   3.7e-10   2.8e-07       1      38 [.     116     153 ..     116     183 .. 0.91
   2 !   13.7   0.4   7.5e-05     0.056       1      34 [.     262     296 ..     262     307 .. 0.93

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 3.7e-10
                                    EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EE CS
                  NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasy 38 
                                    ++G+G +Gl+aA + a ag++v+++e++ r+GG++   
  gi|119719846|ref|YP_920341.1| 116 VIGSGPAGLSAALASASAGLEVHVFERHFRPGGQLVKQ 153
                                    8********************************98655 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 7.5e-05
                                    EE--SHHHHHHHHHHHCCTEEEE.EE-SSSSSSGG CS
                  NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvl.llekrdrlGGr 34 
                                    +vGaG  Gl   y L +ag++v+ ++e r+ +GG+
  gi|119719846|ref|YP_920341.1| 262 VVGAGNVGLIVSYQLLQAGVSVEaVVEVRPEIGGW 296
                                    8*******************985499********8 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   3.6e-05     0.027       2      35 ..     114     147 ..     113     159 .. 0.88
   2 ?    1.9   0.0      0.46   3.5e+02      41      64 ..     171     194 ..     160     205 .. 0.84
   3 !   25.7   2.1   1.7e-08   1.2e-05       1      79 [.     259     331 ..     259     336 .. 0.92
   4 ?    3.1   0.0      0.19   1.4e+02      17      44 ..     423     450 ..     398     458 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.6e-05
                                    EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                      Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35 
                                    v+v+G+G  gl +A a a  g +V+v+er+ ++ 
  gi|119719846|ref|YP_920341.1| 114 VMVIGSGPAGLSAALASASAGLEVHVFERHFRPG 147
                                    89***************************98877 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.46
                                    HHHHHHHHHHHHTTEEEECSEEEE CS
                      Pyr_redox  41 easkilqeklekngievllntkve 64 
                                    +++++l  + e+ g+++++ + v 
  gi|119719846|ref|YP_920341.1| 171 QIAERLVSEAERAGVKIHTRSPVL 194
                                    68999999***********98776 PP

  == domain 3  score: 25.7 bits;  conditional E-value: 1.7e-08
                                    EEEEECSSHHHHHHHHHHHHTTSEE.EEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEEEE CS
                      Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkV.tvversdkllrllDeeaskilqeklekngievllntkveeiegsedgvesvklk 79 
                                    k+vvvG+G++gl +   l + g +V  vve ++++          + + kl+++g+ +l++++v++ eg ++ ve+v+++
  gi|119719846|ref|YP_920341.1| 259 KAVVVGAGNVGLIVSYQLLQAGVSVeAVVEVRPEIG------GWFVHAAKLRRLGVPILTEHTVVRAEGRGR-VERVVIS 331
                                    68***********************99*********......5556689*******************9999.9999985 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.19
                                    HHHHTTSEEEEEESSSSSSTTSSHHHHH CS
                      Pyr_redox  17 alaelgkkVtvversdkllrllDeeask 44 
                                    a++ lg +  +ve ++k lr+lDe+ ++
  gi|119719846|ref|YP_920341.1| 423 AIRILGERGELVEEREKALRMLDETRRT 450
                                    3366889999*************98665 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1   8.8e-07   0.00066       1      36 [.     113     149 ..     113     162 .. 0.93
   2 !   14.2   0.4   3.4e-05     0.025     147     202 ..     171     224 ..     164     240 .. 0.76
   3 !   11.9   2.2   0.00016      0.12       2      45 ..     260     305 ..     259     318 .. 0.86
   4 ?    1.8   0.1      0.19   1.4e+02     153     203 ..     300     359 ..     294     394 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 8.8e-07
                                    EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSG CS
                            DAO   1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiagsga 36 
                                    dv +iG+G +Gls+A++ a +g  V ++e++ ++g g+
  gi|119719846|ref|YP_920341.1| 113 DVMVIGSGPAGLSAALASASAGleVHVFERHFRPG-GQ 149
                                    89*****************************9999.75 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 3.4e-05
                                    HHHHHHHHHHHHTT-EEEESECEEE.EEEEETCEEEEE.EECTEEE.E.EEEEEEE--GG CS
                            DAO 147 kltaalaraaealGveilegtevtg.leeedgkvwgve.rttpgen.d.aadavVnaaGa 202
                                    + +  l ++ae++Gv+i+++++v g +      + gv+ +++ g+  + +a+avV+ +Ga
  gi|119719846|ref|YP_920341.1| 171 QIAERLVSEAERAGVKIHTRSPVLGwF------GEGVFaVNEGGRLlRvRAKAVVVGTGA 224
                                    5677899******************55......55555323336555346688******8 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 0.00016
                                    EEEECTSHHHHHHHHHHHHTT...EEEEESSSSTTSSGGGSSEEEEE CS
                            DAO   2 vviiGGGiiGlstAyeLarrg...VtllekgdiagsgaSgrnsgllh 45 
                                     v++G+G +Gl + y+L ++g    +++e ++++g g   ++++l +
  gi|119719846|ref|YP_920341.1| 260 AVVVGAGNVGLIVSYQLLQAGvsvEAVVEVRPEIG-GWFVHAAKLRR 305
                                    69******************9998899**999999.98888887755 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.19
                                    HHHHHHTT-EEEESECEEEEEEEETCEEEEE.......EECTEEEE.........EEEEEEE--GGG CS
                            DAO 153 araaealGveilegtevtgleeedgkvwgve.......rttpgend.........aadavVnaaGaw 203
                                    a+++++lGv il++++v++ e  +g+v +v               +         +ad + +a G+ 
  gi|119719846|ref|YP_920341.1| 300 AAKLRRLGVPILTEHTVVRAEG-RGRVERVVisrvgkdF------QplkeyersvEADLLLLAVGLT 359
                                    56799************99844.4788888555444430......2444444444556688888864 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.1   9.1e-08   6.8e-05       2      36 ..     113     147 ..     112     153 .. 0.92
   2 !    9.3   0.0   0.00053       0.4     108     164 ..     169     224 ..     151     228 .. 0.85
   3 ?    5.1   0.3      0.01       7.5       2      35 ..     259     293 ..     258     300 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 9.1e-08
                                    SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                    HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakklg 36 
                                    dv+viG G+AGl aA++ a++g +V ++e+  ++g
  gi|119719846|ref|YP_920341.1| 113 DVMVIGSGPAGLSAALASASAGLEVHVFERHFRPG 147
                                    89***************************988777 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00053
                                    CHHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE..TTEEEEESEEEE---- CS
                    HI0933_like 108 aedivdallkelkeagvklrletevksvekeedgkfrvkt.kseeeleadklvlAtGG 164
                                      +i + l++e+++agvk+++++ v ++    +g+f v+      +++a+++v+ tG 
  gi|119719846|ref|YP_920341.1| 169 GFQIAERLVSEAERAGVKIHTRSPVLGW--FGEGVFAVNEgGRLLRVRAKAVVVGTGA 224
                                    5689999*********************..678999999955566899******9996 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.01
                                    SEEEE--SHHHHHHHHHHHHTT--EE.EE-SSSSS CS
                    HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVl.llekakkl 35 
                                    + +v+G+G  Gl  + ++ ++g +V  ++e  +++
  gi|119719846|ref|YP_920341.1| 259 KAVVVGAGNVGLIVSYQLLQAGVSVEaVVEVRPEI 293
                                    689********************995266666655 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.1   2.5e-07   0.00019       1      32 [.     113     144 ..     113     166 .. 0.84
   2 ?    4.7   0.5     0.017        13       2      29 ..     260     287 ..     259     305 .. 0.86
   3 !    9.6   0.0   0.00057      0.42     349     391 ..     388     429 ..     381     430 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.5e-07
                                    CEEEE-SSHHHHHHHHHHHHTT--EEEEES-G CS
                           GIDA   1 dviViGgGhAGceAAlaaarlGakvlLithkl 32 
                                    dv+ViG G AG+ AAla+a +G++v  +  ++
  gi|119719846|ref|YP_920341.1| 113 DVMVIGSGPAGLSAALASASAGLEVHVFERHF 144
                                    79***********************9995554 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.017
                                    EEEE-SSHHHHHHHHHHHHTT--EEEEE CS
                           GIDA   2 viViGgGhAGceAAlaaarlGakvlLit 29 
                                     +V+G+G  G+  ++++ ++G++v  ++
  gi|119719846|ref|YP_920341.1| 260 AVVVGAGNVGLIVSYQLLQAGVSVEAVV 287
                                    68*********************98765 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00057
                                    TSBBSSSBTEEE-CGGGTB-SHHHHHHHHHHHHHHHHHHHCTS CS
                           GIDA 349 tLetkkvkgLflAGqinGteGYeEaaaqGllAGinaarkakgk 391
                                     +et+ ++g+++AG+ +G e  + a  +G +AG+ aa ++ g+
  gi|119719846|ref|YP_920341.1| 388 YMETS-IPGVYVAGDASGIEEATTALLTGRVAGLSAAIRILGE 429
                                    57887.*************96666666**********998875 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   1.1e-08   8.1e-06      17      56 ..     111     149 ..     108     159 .. 0.91
   2 !    6.8   0.1    0.0047       3.5      20      55 ..     260     295 ..     246     305 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1.1e-08
                                    EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TT CS
                           Thi4  17 esDvvivGaGssGLtaayylakkpdlkvailersvspGGG 56 
                                    + Dv+++G+G++GL+aa   a + +l+v ++er+  pGG 
  gi|119719846|ref|YP_920341.1| 111 DVDVMVIGSGPAGLSAALASASA-GLEVHVFERHFRPGGQ 149
                                    57***************999999.**************96 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0047
                                    EEEE--SHHHHHHHHHHHHCTTS-E.EEEESSSS--T CS
                           Thi4  20 vvivGaGssGLtaayylakkpdlkv.ailersvspGG 55 
                                     v+vGaG  GL  +y l ++ ++ v a++e +  +GG
  gi|119719846|ref|YP_920341.1| 260 AVVVGAGNVGLIVSYQLLQA-GVSVeAVVEVRPEIGG 295
                                    599***************99.8887578898888887 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.2   1.2e-09   9.1e-07       1      42 [.     113     154 ..     113     186 .. 0.91
   2 ?    4.4   0.4     0.026        20       3      42 ..     261     301 ..     260     349 .. 0.87

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 1.2e-09
                   FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsgl 42 
                                    Dv+V+G+gpaG+ AA+a+a aG +v + e++ + GG+l ++ 
  gi|119719846|ref|YP_920341.1| 113 DVMVIGSGPAGLSAALASASAGLEVHVFERHFRPGGQLVKQT 154
                                    9************************************99886 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.026
                   FAD_oxidored   3 vVvGGgpaGvaAAiaAaraGakv.lLveergvlGGlltsgl 42 
                                    vVvG+g  G++  ++  +aG +v ++ve r+ +GG +  ++
  gi|119719846|ref|YP_920341.1| 261 VVVGAGNVGLIVSYQLLQAGVSVeAVVEVRPEIGGWFVHAA 301
                                    8**********************88**********887665 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.1   9.5e-08   7.1e-05       1      33 [.     111     143 ..     111     149 .. 0.95
   2 !    9.2   0.5   0.00083      0.62       4      28 ..     260     284 ..     258     293 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 9.5e-08
                                    EEEEEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                  FAD_binding_3   1 etdVlIVGaGpaGlmlallLseaGvrvvlvekr 33 
                                    ++dV+++G+GpaGl++al  ++aG +v++ e++
  gi|119719846|ref|YP_920341.1| 111 DVDVMVIGSGPAGLSAALASASAGLEVHVFERH 143
                                    689*****************************9 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00083
                                    EEEE--SHHHHHHHHHHHHTTHHEE CS
                  FAD_binding_3   4 VlIVGaGpaGlmlallLseaGvrvv 28 
                                     ++VGaG +Gl+ +  L +aGv+v 
  gi|119719846|ref|YP_920341.1| 260 AVVVGAGNVGLIVSYQLLQAGVSVE 284
                                    589*******************974 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.0    0.0059       4.4       3      36 ..     112     143 ..     111     146 .. 0.89
   2 !   12.4   0.0   8.7e-05     0.065     140     218 ..     206     284 ..     197     292 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0059
                    K_oxygenase   3 lDligiGiGpsnLsLailleevkkelkalflerq 36 
                                    +D++ iG Gp+ Ls a++++++   l+++++er+
  gi|119719846|ref|YP_920341.1| 112 VDVMVIGSGPAGLSAALASASAG--LEVHVFERH 143
                                    699***********999999988..999999975 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 8.7e-05
                    K_oxygenase 140 aegeeeelearnlvlgvG.tepkiPevleklegkervvHsseylerkeellakkriaVvGsGqSaaeifedllrrqkkve 218
                                    + g+  +++a+++v+g+G  e+ +P   ++l g      ++++l ++   + +++ +VvG+G  +  + ++ll+   +ve
  gi|119719846|ref|YP_920341.1| 206 EGGRLLRVRAKAVVVGTGaVERFLPFPGNTLPG-VMGAGAAQTLMNEYGVKPGEKAVVVGAGNVGLIVSYQLLQAGVSVE 284
                                    46788899**********88999****999996.566666777777778999********************99865544 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.1   0.00034      0.25       2      32 ..     122     152 ..     121     165 .. 0.87
   2 ?   -0.7   0.0      0.92   6.8e+02     211     258 ..     171     220 ..     155     224 .. 0.65
   3 !    7.4   0.0    0.0032       2.4       3      29 ..     269     296 ..     269     302 .. 0.92
   4 ?    1.2   0.0      0.24   1.8e+02     406     436 ..     380     410 ..     361     427 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00034
                                    HHHHHHHHHHHTTEEEEEEESSSSSBTTS-E CS
                  Amino_oxidase   2 aGLaaArqLlsaGfdVtvlEardrvGGRirt 32 
                                    aGL+aA   +saG++V v+E   r+GG +  
  gi|119719846|ref|YP_920341.1| 122 AGLSAALASASAGLEVHVFERHFRPGGQLVK 152
                                    9**************************8765 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.92
                                    HHHHHHHH..TTTTEEEETSEEEEEEEEETTCEEEEETTSTEE..EESEEEE CS
                  Amino_oxidase 211 qlpealae..elrgldirlntrVkeikregdgvtvtledgevv..eaDaVvv 258
                                    q++e+l +  e+ g++i+++++V    + g+gv    e g+ +  +a+aVvv
  gi|119719846|ref|YP_920341.1| 171 QIAERLVSeaERAGVKIHTRSPVL--GWFGEGVFAVNEGGRLLrvRAKAVVV 220
                                    4556666668999*********94..56555544444555555666666666 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0032
                                    HHHHHHHHHHTTEEE.EEEESSSSSBTT CS
                  Amino_oxidase   3 GLaaArqLlsaGfdV.tvlEardrvGGR 29 
                                    GL++ +qLl+aG++V  v+E r+ +GG+
  gi|119719846|ref|YP_920341.1| 269 GLIVSYQLLQAGVSVeAVVEVRPEIGGW 296
                                    9***********99956**********8 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.24
                                    HHHHHHHHHCHHCSTTEEE.SGGGCTTTTTS CS
                  Amino_oxidase 406 ghedydplakpegdprlffAGehtsreypgt 436
                                    g   y++ +++  +p++++AG++   e   t
  gi|119719846|ref|YP_920341.1| 380 GYVPYRDRYMETSIPGVYVAGDASGIEEATT 410
                                    5566777777778*********966444444 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0   0.00042      0.31       2      44 ..     116     153 ..     115     156 .. 0.76
   2 ?    4.6   0.0      0.04        30       5      33 ..     165     192 ..     165     230 .. 0.71
   3 ?    2.2   0.3      0.22   1.7e+02       1      20 [.     261     280 ..     261     301 .. 0.84
   4 ?   -1.1   0.0       2.2   1.6e+03     127     154 ..     330     357 ..     312     359 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00042
                  NAD_binding_9   2 ivGaGprGlavlerLlarakkkspleitlfdp.sepgagrvwrt 44 
                                    ++G Gp+Gl+++ + +     ++ le+++f++   pg g+  ++
  gi|119719846|ref|YP_920341.1| 116 VIGSGPAGLSAALASA-----SAGLEVHVFERhFRPG-GQLVKQ 153
                                    9*********985433.....568********66778.666555 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.04
                  NAD_binding_9   5 aGprGlavlerLlarakkkspleitlfdp 33 
                                    +G rG  ++erL+++a +++ ++i+   p
  gi|119719846|ref|YP_920341.1| 165 GGLRGFQIAERLVSEA-ERAGVKIHTRSP 192
                                    79*************7.888899987666 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.22
                  NAD_binding_9   1 aivGaGprGlavlerLlara 20 
                                    ++vGaG  Gl v  +Ll+  
  gi|119719846|ref|YP_920341.1| 261 VVVGAGNVGLIVSYQLLQAG 280
                                    69**************9974 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 2.2
                  NAD_binding_9 127 leeradgqavlladgaslaadaVvLAlG 154
                                    +++ ++ ++ l++ ++s++ad + LA+G
  gi|119719846|ref|YP_920341.1| 330 ISRVGKDFQPLKEYERSVEADLLLLAVG 357
                                    44455556777889999*********99 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.1   4.4e-05     0.033       1      30 [.     113     140 ..     113     150 .. 0.85
   2 ?    1.5   0.0      0.16   1.2e+02     120     143 ..     201     226 ..     165     247 .. 0.82
   3 ?    1.3   0.3      0.19   1.4e+02       3      30 ..     261     286 ..     260     325 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.4e-05
                  Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvli 30 
                                    Dv+viG+GpAgls A  +  a +gl+v + 
  gi|119719846|ref|YP_920341.1| 113 DVMVIGSGPAGLSAALAS--ASAGLEVHVF 140
                                    9**************999..7777777655 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.16
                  Lycopene_cycl 120 slvvleggr..kirarlvvdarglas 143
                                    + +v eggr  ++ra++vv+++g+ +
  gi|119719846|ref|YP_920341.1| 201 VFAVNEGGRllRVRAKAVVVGTGAVE 226
                                    46788999999999999999999765 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.19
                  Lycopene_cycl   3 vviGaGpAglslAarlteakpglkvvli 30 
                                    vv+GaG  gl +  +l   ++g++v  +
  gi|119719846|ref|YP_920341.1| 261 VVVGAGNVGLIVSYQL--LQAGVSVEAV 286
                                    89**************..6666666443 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0    0.0005      0.37       2      30 ..     114     142 ..     113     157 .. 0.91
   2 ?   -0.7   0.1       1.6   1.2e+03       8      21 ..     238     251 ..     237     255 .. 0.83
   3 !    6.9   0.1    0.0073       5.4       2      28 ..     260     286 ..     259     356 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0005
                                    EEEE--SCCHHHHHHHHHHTT-EEEEE-S CS
                        3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdi 30 
                                    v viG+G  G + a + asagleV+++++
  gi|119719846|ref|YP_920341.1| 114 VMVIGSGPAGLSAALASASAGLEVHVFER 142
                                    89************************987 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.6
                                    SCCHHHHHHHHHHT CS
                        3HCDH_N   8 GtmGagiaavfasa 21 
                                    G+mGag a+ ++++
  gi|119719846|ref|YP_920341.1| 238 GVMGAGAAQTLMNE 251
                                    9*******998765 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0073
                                    EEEE--SCCHHHHHHHHHHTT-EEEEE CS
                        3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlv 28 
                                      v+GaG +G  + +++++ag++V  v
  gi|119719846|ref|YP_920341.1| 260 AVVVGAGNVGLIVSYQLLQAGVSVEAV 286
                                    579*********************754 PP

>> Glu_dehyd_C  Glucose dehydrogenase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0    0.0075       5.6      34      70 ..     114     147 ..     107     154 .. 0.85
   2 ?    6.2   0.0    0.0083       6.2      32      57 ..     258     281 ..     244     294 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0075
                    Glu_dehyd_C  34 alvlGaGslGLLalalleaeerglervyvlgrrdrpd 70 
                                    ++v+G+G+ GL a  +l++ + gle v+v++r+ rp+
  gi|119719846|ref|YP_920341.1| 114 VMVIGSGPAGLSA--ALASASAGLE-VHVFERHFRPG 147
                                    79*********98..6666689998.******99886 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0083
                    Glu_dehyd_C  32 esalvlGaGslGLLalalleaeergl 57 
                                    e+a+v+GaG++GL+   +l +   g+
  gi|119719846|ref|YP_920341.1| 258 EKAVVVGAGNVGLIVSYQLLQ--AGV 281
                                    789***********9888864..344 PP

>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0    0.0019       1.4      57      84 ..     113     140 ..     101     195 .. 0.89
   2 ?    4.9   0.2     0.019        14      53     101 ..     255     307 ..     238     336 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0019
                                    EEEEEBSSHHHHHHHHHHHHHT-EEEEE CS
                           PALP  57 tvveassGNhgralAaaaallGlkvtiv 84 
                                     v++ +sG +g+++A+a+a +Gl+v+++
  gi|119719846|ref|YP_920341.1| 113 DVMVIGSGPAGLSAALASASAGLEVHVF 140
                                    578899*********************9 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.019
                                    TTTSEEEEEBSSHHHHHHHHHHHHHT-EEEEEEETTS-H....HHHHHHHHTT CS
                           PALP  53 tgaktvveassGNhgralAaaaallGlkvtivvpadasp....ekvallrllG 101
                                    ++++  v+ ++GN g+ +++    +G+ v+ vv+           +a+lr+lG
  gi|119719846|ref|YP_920341.1| 255 KPGEKAVVVGAGNVGLIVSYQLLQAGVSVEAVVEVRPEIggwfVHAAKLRRLG 307
                                    67899999************************987665334445555666655 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       4.5   3.3e+03       1      29 [.     114     142 ..     114     144 .. 0.83
   2 ?   13.7   0.1     5e-05     0.037       2      31 ..     261     290 ..     260     356 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 4.5
                                    EEEES-SHHHHHHHHHHHHHTHCEEEE-S CS
                           ApbA   1 iailGaGaiGsllaakLakagadvtlilr 29 
                                    + ++G+G  G   a   a ag +v++  r
  gi|119719846|ref|YP_920341.1| 114 VMVIGSGPAGLSAALASASAGLEVHVFER 142
                                    57999999999988888889999998766 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 5e-05
                                    EEES-SHHHHHHHHHHHHHTHCEEEE-SCH CS
                           ApbA   2 ailGaGaiGsllaakLakagadvtlilrsr 31 
                                    +++GaG +G ++ ++L +ag  v  ++  r
  gi|119719846|ref|YP_920341.1| 261 VVVGAGNVGLIVSYQLLQAGVSVEAVVEVR 290
                                    69********************99998766 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2     7e-05     0.052      29      62 ..     112     145 ..      95     185 .. 0.86
   2 ?   -2.9   6.2       4.5   3.4e+03      25      55 ..     253     284 ..     217     293 .. 0.75
   3 ?    6.1   0.1    0.0078       5.8      17      70 ..     396     447 ..     386     464 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7e-05
                                    -EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHH CS
                    AlaDh_PNT_C  29 akvlviGgGvaGlqAiatakglgakVtvlDvrpa 62 
                                      v+viG G aGl+A+ ++++ g +V v++   +
  gi|119719846|ref|YP_920341.1| 112 VDVMVIGSGPAGLSAALASASAGLEVHVFERHFR 145
                                    579*************************998755 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.5
                                    CB---.EEEEESTSHHHHHHHHHHHHTT-EEE CS
                    AlaDh_PNT_C  25 gvepa.kvlviGgGvaGlqAiatakglgakVt 55 
                                    gv+p+ k +v+G+G +Gl       + g +V+
  gi|119719846|ref|YP_920341.1| 253 GVKPGeKAVVVGAGNVGLIVSYQLLQAGVSVE 284
                                    5777647899*******976666666565555 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0078
                                    EETTCEETCB---EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHT CS
                    AlaDh_PNT_C  17 gtlaGgvpgvepakvlviGgGvaGlqAiatakglgakVtvlDvrparleqlesl 70 
                                    + +aG  +g+e+a++  + g vaGl+A+   + lg + ++++ r+++l+ l++ 
  gi|119719846|ref|YP_920341.1| 396 VYVAGDASGIEEATTALLTGRVAGLSAAI--RILGERGELVEEREKALRMLDET 447
                                    457899*******************9985..56778888888888888877773 PP

>> DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydroorotate dehydrogenase B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.8   0.00023      0.17       6      32 ..      58      81 ..      57      92 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00023
                                   SSSSSS-TTEEEETTCTT.CEEETTTT CS
                DHODB_Fe-S_bind  6 CGvGaClgCvvktkggdggeykrvCkd 32
                                   C +G C gC+v+++g    +++r+C +
  gi|119719846|ref|YP_920341.1| 58 CMIGYCSGCMVRVDGR---SRVRACLE 81
                                   889**********876...58999954 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.048        36      13      57 ..     112     155 ..     105     160 .. 0.89
   2 ?    5.2   0.1     0.028        21      12      37 ..     257     282 ..     244     291 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.048
                                    -EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT CS
                   Shikimate_DH  13 kkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelk 57 
                                      v++iG G  +  +a + +++g++ v v+ R ++   +l+++ +
  gi|119719846|ref|YP_920341.1| 112 VDVMVIGSGPAGLSAALASASAGLE-VHVFERHFRPGGQLVKQTH 155
                                    579**********999999999999.********99999999875 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.028
                                    T-EEEEES-SHHHHHHHHHHHCCT-C CS
                   Shikimate_DH  12 ekkvlliGaGemaelvakhLlakgvk 37 
                                    ++k++++GaG+++  v  +Ll++gv 
  gi|119719846|ref|YP_920341.1| 257 GEKAVVVGAGNVGLIVSYQLLQAGVS 282
                                    5799************9999999886 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0      0.03        22       9      39 ..     113     143 ..     111     186 .. 0.84
   2 ?   -2.1   0.3       7.2   5.4e+03       8      18 ..     215     225 ..     197     227 .. 0.67
   3 ?   10.0   0.2    0.0012      0.88       7      38 ..     257     288 ..     256     364 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.03
                  NAD_binding_7   9 kvlvvGgGevAarkvrklleagakvtvvape 39 
                                     v+v+G G+ +++ +   ++ag +v+v    
  gi|119719846|ref|YP_920341.1| 113 DVMVIGSGPAGLSAALASASAGLEVHVFERH 143
                                    699************************8777 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 7.2
                  NAD_binding_7   8 kkvlvvGgGev 18 
                                     k +vvG G v
  gi|119719846|ref|YP_920341.1| 215 AKAVVVGTGAV 225
                                    35567777765 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.0012
                  NAD_binding_7   7 gkkvlvvGgGevAarkvrklleagakvtvvap 38 
                                    g+k +vvG+G+v++   ++ll+ag  v  v +
  gi|119719846|ref|YP_920341.1| 257 GEKAVVVGAGNVGLIVSYQLLQAGVSVEAVVE 288
                                    6799********************99977654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (469 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.46
# Mc/sec: 3097.31
//
Query:       gi|119719847|ref|YP_920342.1|  [L=144]
Description: hypothetical protein Tpen_0939 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1085.84
//
Query:       gi|119719848|ref|YP_920343.1|  [L=170]
Description: hypothetical protein Tpen_0940 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.035   14.3   0.5        3.4    7.9   0.0    2.3  2  DUF402    Protein of unknown function (DUF402)


Domain annotation for each model (and alignments):
>> DUF402  Protein of unknown function (DUF402)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.2    0.0023        42      28      54 ..      67      91 ..      64     101 .. 0.72
   2 ?    7.9   0.0   0.00019       3.4      22      57 ..     121     154 ..     104     164 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0023
                                   EEEEEES--EE..E.EEE-EEEEEEES CS
                         DUF402 28 lYvDiatppevgegawktiDlyLDlvv 54
                                   +Y Dia++++++ g   +   ++D++v
  gi|119719848|ref|YP_920343.1| 67 YYADIASGEYIT-G-QVYFGRDVDVIV 91
                                   8*******9994.3.344555667765 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00019
                                    TTEEEEEEEEEES--EE..E.EEE-EEEEEEESEEE CS
                         DUF402  22 dgrlqglYvDiatppevgegawktiDlyLDlvvspd 57 
                                    + ++ g+  Dia+ ++v   +++++D y+  v+ ++
  gi|119719848|ref|YP_920343.1| 121 KREGAGWLADIAETNGVV--EIHFDDIYVKMVRDKK 154
                                    348899********9994..6********9887544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1205.09
//
Query:       gi|119719849|ref|YP_920344.1|  [L=247]
Description: beta-lactamase domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.1e-16   60.6   0.0    2.7e-16   60.2   0.0    1.1  1  Lactamase_B  Metallo-beta-lactamase superfamily


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.2   0.0   1.5e-20   2.7e-16       3     197 .]      23     219 ..      22     219 .. 0.95

  Alignments for each domain:
  == domain 1  score: 60.2 bits;  conditional E-value: 1.5e-20
                                    CCSSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCC CS
                    Lactamase_B   3 pdpvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapal 82 
                                     +++n ++i+++++++L Dt + + +a++++   ++  +p +v+++++TH ++D iG+++ +  a ++++++ +e +  +
  gi|119719849|ref|YP_920344.1|  23 QVQTNQFIIVDGDEALLADTSGRAVFAKLLS-QVSVLAPPTKVKYLFYTHQDPDVIGAAASWYTALPNAKIVLPELWVRF 101
                                    689*************************987.99999******************************************* PP

                                    HCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCCCCC CS
                    Lactamase_B  83 fmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallagetgridl 162
                                    +++   ++             + + v + + ++ +g + +  ++ +++h++g ++++++  k+l++GD+l +   ++ d 
  gi|119719849|ref|YP_920344.1| 102 LPHVFPPDVN--------IENRVVPVGDSGAELQLGNCTLKLIPAHFLHSPGNFSLYDPCSKILYSGDVLASLLPPDKDY 173
                                    *****66544........5678999999999****************************************888888888 PP

                                    ............TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                    Lactamase_B 163 ...........tlrgaevrdpsdaekyldsllklaglkaevlvpgH 197
                                                + +++ r+ ++ + + +++ ++++l++e++vp+H
  gi|119719849|ref|YP_920344.1| 174 dfapsfeehvkYMEPFHKRYMASGKALKAWVSRVKALDVETIVPQH 219
                                    99*******************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1884.86
//
Query:       gi|119719850|ref|YP_920345.1|  [L=307]
Description: signal transduction protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-25   89.0   7.7    3.4e-13   49.8   1.9    3.3  3  CBS              CBS domain
    1.4e-23   82.3   0.3    1.6e-22   78.9   0.1    2.5  2  HrcA_DNA-bdg     Winged helix-turn-helix transcription repres
    1.1e-08   35.2   0.2    3.5e-08   33.7   0.0    1.8  1  Rrf2             Transcriptional regulator
    6.2e-07   29.3   0.0    1.2e-06   28.3   0.0    1.5  1  HTH_11           HTH domain
    1.8e-05   24.2   0.0    9.8e-05   21.8   0.0    2.2  2  HTH_24           Winged helix-turn-helix DNA-binding
    5.4e-05   22.9   0.1     0.0018   18.0   0.0    2.5  2  HTH_IclR         IclR helix-turn-helix domain
    5.8e-05   22.9   0.0    0.00021   21.1   0.0    2.0  2  HTH_5            Bacterial regulatory protein, arsR family
    0.00023   21.0   0.0    0.00077   19.3   0.0    1.9  1  TrmB             Sugar-specific transcriptional regulator Trm
    0.00025   20.9   0.1     0.0012   18.7   0.0    2.2  1  MarR_2           MarR family
    0.00029   20.4   0.0     0.0011   18.6   0.0    2.0  1  GntR             Bacterial regulatory proteins, gntR family
    0.00031   20.7   0.0       0.02   14.9   0.0    2.7  2  HTH_29           Winged helix-turn helix
    0.00053   20.4   0.0      0.002   18.6   0.0    2.0  1  HTH_27           Winged helix DNA-binding domain
    0.00059   19.9   0.0     0.0041   17.1   0.0    2.3  2  HTH_20           Helix-turn-helix domain
    0.00095   19.1   0.1     0.0031   17.4   0.1    1.8  1  HTH_15           Helix-turn-helix domain of alkylmercury lyas
  ------ inclusion threshold ------
      0.012   15.1   0.2      0.087   12.4   0.0    2.5  3  Sigma70_r4       Sigma-70, region 4
      0.015   15.1   0.4        6.9    6.5   0.1    2.4  2  HTH_38           Helix-turn-helix domain
      0.015   15.2   0.0      0.051   13.6   0.0    1.9  1  HTH_Crp_2        Crp-like helix-turn-helix domain
      0.016   15.4   0.0      0.036   14.3   0.0    1.6  1  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
      0.017   15.2   0.0      0.044   13.9   0.0    1.7  1  Sigma70_r3       Sigma-70 region 3
      0.021   14.6   0.0       0.41   10.5   0.0    2.5  2  HTH_23           Homeodomain-like domain
      0.041   13.6   0.1        0.4   10.4   0.1    2.4  2  Sigma70_r4_2     Sigma-70, region 4
      0.056   13.8   0.0       0.17   12.3   0.0    1.8  1  FaeA             FaeA-like protein
      0.069   12.9   0.0        0.2   11.4   0.0    1.8  1  LexA_DNA_bind    LexA DNA binding domain
      0.091   13.1   0.0       0.29   11.5   0.0    1.8  2  Penicillinase_R  Penicillinase repressor
       0.14   11.9   0.0       0.23   11.1   0.0    1.3  1  DUF4423          Domain of unknown function (DUF4423)
       0.15   12.4   0.0       0.39   11.1   0.0    1.7  1  BDM              Putative biofilm-dependent modulation protei


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.63   4.3e+02      23      37 ..      88     102 ..      79     106 .. 0.75
   2 !   39.3   0.1   9.4e-13   6.5e-10       1      54 [.     173     226 ..     173     229 .. 0.93
   3 !   49.8   1.9   4.9e-16   3.4e-13       1      55 [.     236     290 ..     236     292 .. 0.96

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.63
                                    HHHHHHTSSEEEEEE CS
                            CBS  23 elmrekgvsrlPVVd 37 
                                    +l ++ +vsrl+VV+
  gi|119719850|ref|YP_920345.1|  88 RLVVDGRVSRLYVVE 102
                                    6666888******93 PP

  == domain 2  score: 39.3 bits;  conditional E-value: 9.4e-13
                                    HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                            CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54 
                                    ++d+mt+++  ++  ++++e+++l++++++++lPVVde+g l G+v+  ++ +a
  gi|119719850|ref|YP_920345.1| 173 ARDVMTPRPERATRGMSMREVARLIVSRNIRALPVVDEEGVLEGLVSAQHVSKA 226
                                    58***********************9**************999****9998766 PP

  == domain 3  score: 49.8 bits;  conditional E-value: 4.9e-16
                                    HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                            CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                    V+d+m rdv tv pd+++  ++++m+e++ +r+ VVd +g++ Gi+t++D+l al
  gi|119719850|ref|YP_920345.1| 236 VEDYMDRDVATVEPDEDILRIMRIMVERNAGRVVVVDQSGRPQGIITRTDILMAL 290
                                    89************************9999***889****************997 PP

>> HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor, HrcA DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.9   0.1   2.4e-25   1.6e-22       8      74 ..       9      75 ..       4      78 .. 0.96
   2 ?   -0.0   0.0         1   6.9e+02       6      19 ..     283     296 ..     280     303 .. 0.82

  Alignments for each domain:
  == domain 1  score: 78.9 bits;  conditional E-value: 2.4e-25
                   HrcA_DNA-bdg  8 eilqaLielyrkkkravKgeeiAevlkrneGtvRNqlqsLkalgLvegvpGPkGGYkPtlkayealk 74
                                   eil a+++ y+  +r+v + eiAe++++ +GtvRN++++Lka+gLve+++GP GGY+Pt+k  ea+k
  gi|119719850|ref|YP_920345.1|  9 EILVAVVNAYEATGRPVTSSEIAEAVGKSDGTVRNVISALKAMGLVEAKTGPGGGYVPTVKGVEAVK 75
                                   8************************************************************999876 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1
                   HrcA_DNA-bdg   6 qkeilqaLielyrk 19 
                                    + +il aL+ ly+ 
  gi|119719850|ref|YP_920345.1| 283 RTDILMALTRLYEV 296
                                    679*********86 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   0.0   5.1e-11   3.5e-08      18      66 ..      17      65 ..       8      68 .. 0.90

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 5.1e-11
                                   HHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT-TCEE CS
                           Rrf2 18 akeeeeepvsseeiaerqnispsylekilakLrkaglvksvrGkgGGyr 66
                                   a e++++pv+s+eiae ++ s+  ++ +++ L+  glv+++ G+gGGy+
  gi|119719850|ref|YP_920345.1| 17 AYEATGRPVTSSEIAEAVGKSDGTVRNVISALKAMGLVEAKTGPGGGYV 65
                                   45667889****************************************6 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0   1.8e-09   1.2e-06      12      54 ..      20      64 ..      14      65 .. 0.90

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 1.8e-09
                         HTH_11 12 argp.isgeeLAeeLnvSrrtvrrdIkaLeelgvpIesepgr..GY 54
                                   a+g  ++++e+Ae  + S  tvr+ I aL+++g  +e++ g+  GY
  gi|119719850|ref|YP_920345.1| 20 ATGRpVTSSEIAEAVGKSDGTVRNVISALKAMG-LVEAKTGPggGY 64
                                   55555****************************.********8777 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   1.4e-07   9.8e-05      10      48 .]      16      55 ..       7      55 .. 0.88
   2 ?   -0.8   0.0       1.7   1.2e+03      16      25 ..     186     195 ..     183     197 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.4e-07
                         HTH_24 10 elLqknpr.isqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                   ++ ++ +r  + +e+Ae++g S +tv+  +  L+ +Gl++
  gi|119719850|ref|YP_920345.1| 16 NAYEATGRpVTSSEIAEAVGKSDGTVRNVISALKAMGLVE 55
                                   6667788889****************************96 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.7
                         HTH_24  16 prisqreLAe 25 
                                     ++s+re+A+
  gi|119719850|ref|YP_920345.1| 186 RGMSMREVAR 195
                                    589******8 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   2.6e-06    0.0018       8      49 ..      14      55 ..       9      57 .. 0.88
   2 ?    2.1   0.1      0.25   1.7e+02      14      27 ..     183     196 ..     182     197 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.6e-06
                                   HHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                       HTH_IclR  8 iLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                   + +a +++++++t se+A++ g +  tv++ ++ L  +G+ve
  gi|119719850|ref|YP_920345.1| 14 VVNAYEATGRPVTSSEIAEAVGKSDGTVRNVISALKAMGLVE 55
                                   55556678999******************************8 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.25
                                    TTBSS-BHHHHHHH CS
                       HTH_IclR  14 eapqeltlselArr 27 
                                    +a+++++ +e+Ar 
  gi|119719850|ref|YP_920345.1| 183 RATRGMSMREVARL 196
                                    899*********96 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   3.1e-07   0.00021      14      46 ..      23      55 ..       9      56 .. 0.92
   2 ?   -2.6   0.0       7.5   5.2e+03       3      11 ..     282     290 ..     282     292 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 3.1e-07
                                   SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_5 14 gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                   ++ +++e+ae++g+s +tv+   ++L+ +GLVe
  gi|119719850|ref|YP_920345.1| 23 RPVTSSEIAEAVGKSDGTVRNVISALKAMGLVE 55
                                   67899***************************7 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 7.5
                                    HHHHHHHHH CS
                          HTH_5   3 tRlkILklL 11 
                                    tR +IL++L
  gi|119719850|ref|YP_920345.1| 282 TRTDILMAL 290
                                    7999***99 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.1e-06   0.00077      22      58 ..      24      60 ..      10      71 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.1e-06
                                   CCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                           TrmB 22 patadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                   p t +eiae++g +  +v +v++ L+ +GlVe + g 
  gi|119719850|ref|YP_920345.1| 24 PVTSSEIAEAVGKSDGTVRNVISALKAMGLVEAKTGP 60
                                   7899****************************99876 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   1.7e-06    0.0012      19      58 ..      22      61 ..      11      63 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.7e-06
                                   TSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSS CS
                         MarR_2 19 grdltvgelarrlglsksavsrilkrLvaaGLverrpgpe 58
                                   gr++t +e+a++ g s ++v +++  L a GLve ++gp+
  gi|119719850|ref|YP_920345.1| 22 GRPVTSSEIAEAVGKSDGTVRNVISALKAMGLVEAKTGPG 61
                                   5569*******************************99986 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.5e-06    0.0011      21      61 ..      22      61 ..      16      63 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.5e-06
                                   TSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTCE CS
                           GntR 21 GdkLPsereLaaefgVsrttvReALrrLeaeglverrqgrG 61
                                   G +  + +e+a++ g s  tvR +++ L+a glve++ g G
  gi|119719850|ref|YP_920345.1| 22 GRPV-TSSEIAEAVGKSDGTVRNVISALKAMGLVEAKTGPG 61
                                   6666.789*****************************9976 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   2.8e-05      0.02       6      51 ..      15      63 ..      11      67 .. 0.86
   2 ?    2.8   0.0      0.17   1.2e+02      38      63 .]     210     238 ..     207     238 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.8e-05
                         HTH_29  6 lllaeGvs...tvsqiAkllglsrrtvyrwlkrfeegGlaalldrrrsg 51
                                    +++e+ +   t s+iA+++g s  tv++++ +  + Gl  ++ ++++g
  gi|119719850|ref|YP_920345.1| 15 VNAYEATGrpvTSSEIAEAVGKSDGTVRNVISALKAMGLVEAKTGPGGG 63
                                   566666667799**************************99999888776 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.17
                         HTH_29  38 egG.laalld.rrrsgrprn.rlseeqea 63 
                                    e+G l++l + ++ s+++++ rl++++e+
  gi|119719850|ref|YP_920345.1| 210 EEGvLEGLVSaQHVSKAYADgRLDARVED 238
                                    44449999999999***********9996 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   2.9e-06     0.002      10      54 ..      16      60 ..       8      66 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.9e-06
                         HTH_27 10 hlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgde 54
                                   +  + ++r+++ +++++++  +d ++ +++++L ++GLve ++ +
  gi|119719850|ref|YP_920345.1| 16 NAYEATGRPVTSSEIAEAVGKSDGTVRNVISALKAMGLVEAKTGP 60
                                   3333899********************************887766 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0     6e-06    0.0041      19      55 ..      11      55 ..       2      59 .. 0.85
   2 ?   -1.0   0.0       2.7   1.8e+03       9      34 ..     152     197 ..     151     205 .. 0.52

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 6e-06
                                   H........STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                         HTH_20 19 L........araegltaselaerldlskntlsyHLrvLeeagLve 55
                                   L        a+++++t se+ae+++ s+ t+++ + +L   gLve
  gi|119719850|ref|YP_920345.1| 11 LvavvnayeATGRPVTSSEIAEAVGKSDGTVRNVISALKAMGLVE 55
                                   455566666789********************************9 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.7
                                    -HHHHHHHHHH....................STCTTB-HHHHHHHH CS
                         HTH_20   9 hPvRrrilraL....................araegltaselaerl 34 
                                    +P Rr++l +                     +  +g++  e+a+++
  gi|119719850|ref|YP_920345.1| 152 NPARRELLVEVdsmvavprlrardvmtprpeRATRGMSMREVARLI 197
                                    5667766655555555554444444444444444555555555555 PP

>> HTH_15  Helix-turn-helix domain of alkylmercury lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   4.5e-06    0.0031      31      59 ..      20      48 ..       4      57 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.5e-06
                         HTH_15 31 akGepVtveeLAaatgrsveevrqaLaal 59
                                   a G+pVt  e+A+a+g+s+  vr++++al
  gi|119719850|ref|YP_920345.1| 20 ATGRPVTSSEIAEAVGKSDGTVRNVISAL 48
                                   78*********************988775 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00013     0.087      17      40 ..      18      44 ..       9      49 .. 0.82
   2 ?   -1.2   0.0       2.2   1.5e+03       1      16 [.      79      94 ..      79     100 .. 0.82
   3 ?   -2.4   0.0       5.2   3.6e+03      18      28 ..     185     195 ..     172     197 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                                   H...TTT--HHHHHHHHTS-HHHHHHH CS
                     Sigma70_r4 17 f...geglTleEIgerlgiSrerVrqi 40
                                   +   g++ T +EI+e  g S ++Vr  
  gi|119719850|ref|YP_920345.1| 18 YeatGRPVTSSEIAEAVGKSDGTVRNV 44
                                   367799*******************76 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.2
                                   HHHHS-HHHHHHHHHH CS
                     Sigma70_r4  1 aLasLpererevlelr 16
                                   aL++L e +r v+  r
  gi|119719850|ref|YP_920345.1| 79 ALDKLWEPQRLVVDGR 94
                                   7999999999998765 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 5.2
                                    TTT--HHHHHH CS
                     Sigma70_r4  18 geglTleEIge 28 
                                     +g+++ E+++
  gi|119719850|ref|YP_920345.1| 185 TRGMSMREVAR 195
                                    68899999986 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.012       8.3      24      41 ..      28      45 ..      20      46 .. 0.89
   2 ?    6.5   0.1      0.01       6.9      19      30 ..     186     197 ..     183     198 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.012
                         HTH_38 24 reIArrLgrspsTIsREl 41
                                   +eIA  +g+s +T+ + +
  gi|119719850|ref|YP_920345.1| 28 SEIAEAVGKSDGTVRNVI 45
                                   59************9987 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.01
                         HTH_38  19 eGlslreIArrL 30 
                                    +G+s+re+Ar++
  gi|119719850|ref|YP_920345.1| 186 RGMSMREVARLI 197
                                    8*********86 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   7.3e-05     0.051      20      53 ..      23      57 ..       7      68 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.3e-05
                                   EEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.E CS
                      HTH_Crp_2 20 lpltqeelAsmlGltretvsrilseLkreglis.r 53
                                    p+t  e+A+ +G +  tv  ++s+Lk  gl++ +
  gi|119719850|ref|YP_920345.1| 23 RPVTSSEIAEAVGKSDGTVRNVISALKAMGLVEaK 57
                                   599*****************************963 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   5.3e-05     0.036      15      55 ..      16      57 ..       9      61 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.3e-05
                                   HHHH.HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                 Fe_dep_repress 15 tlse.ekkvvktkdlaerLnvspssVsemlkkLekdGyveye 55
                                    + e ++ +v+ +++ae+ + s  +V   ++ L+ +G+ve +
  gi|119719850|ref|YP_920345.1| 16 NAYEaTGRPVTSSEIAEAVGKSDGTVRNVISALKAMGLVEAK 57
                                   566778999******************************976 PP

>> Sigma70_r3  Sigma-70 region 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   6.4e-05     0.044      15      55 ..      19      59 ..       9      63 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.4e-05
                                   HHHSSXXXHHHHHHHHTXXHHHHHHHHHHHXXXEETTXBSS CS
                     Sigma70_r3 15 qelgrePtpeEiAeeLglseekVrevleaarepvSldlpvg 55
                                   + +gr  t  EiAe++g s   Vr+v+ a +   +++ + g
  gi|119719850|ref|YP_920345.1| 19 EATGRPVTSSEIAEAVGKSDGTVRNVISALKAMGLVEAKTG 59
                                   578************************99888777777666 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0    0.0006      0.41      20      45 ..      27      52 ..      25      57 .. 0.86
   2 ?    1.1   0.0      0.54   3.7e+02      16      26 ..     186     196 ..     171     201 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0006
                         HTH_23 20 vreIAreLgvsrrTvyrwlkryreeG 45
                                    +eIA++ g s  Tv++++++ ++ G
  gi|119719850|ref|YP_920345.1| 27 SSEIAEAVGKSDGTVRNVISALKAMG 52
                                   58*****************9987666 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.54
                         HTH_23  16 eGlsvreIAre 26 
                                    +G+s re+Ar+
  gi|119719850|ref|YP_920345.1| 186 RGMSMREVARL 196
                                    39*******97 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00058       0.4      28      45 ..      26      43 ..      25      50 .. 0.88
   2 ?   -0.0   0.0         1   7.1e+02      26      36 ..     187     197 ..     183     204 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00058
                                   -HHHHHHHHT--HHHHHH CS
                   Sigma70_r4_2 28 sykEIAellgisegtVks 45
                                   +  EIAe  g s+gtV++
  gi|119719850|ref|YP_920345.1| 26 TSSEIAEAVGKSDGTVRN 43
                                   568*************98 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1
                                    ---HHHHHHHH CS
                   Sigma70_r4_2  26 glsykEIAell 36 
                                    g+s +E+A+l+
  gi|119719850|ref|YP_920345.1| 187 GMSMREVARLI 197
                                    9*******986 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00024      0.17      13      46 ..      22      55 ..       7      67 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00024
                                   S----HHHHHHHHTS-HHHHHHHHHHHHHHSSEE CS
                           FaeA 13 kapckTreiAdalglsaYQaRyYLeqLekegkik 46
                                   + p++ +eiA+a+g s+  +R  +  L++ g ++
  gi|119719850|ref|YP_920345.1| 22 GRPVTSSEIAEAVGKSDGTVRNVISALKAMGLVE 55
                                   679**************************99987 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0    0.0003       0.2      10      61 ..       9      59 ..       5      61 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0003
                                   HHHHHHHHHHHHHSS---HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE-GGG CS
                  LexA_DNA_bind 10 evldlikasieetgypPsireiaralglkSpsaveehLkaLerKGyierdpg 61
                                   e+l  +++  e tg p +  eia+a+g kS  +v +   aL+  G++e + g
  gi|119719850|ref|YP_920345.1|  9 EILVAVVNAYEATGRPVTSSEIAEAVG-KSDGTVRNVISALKAMGLVEAKTG 59
                                   566667777789***************.89*****************98765 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00043      0.29      15      74 ..      17      76 ..       8      86 .. 0.75
   2 ?   -1.9   0.0         6   4.1e+03      64     101 ..     206     245 ..     200     263 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00043
                                   HS-EEHHHHHHT.--GGG---HHHHHHHHHHHHHTTS-EEEEETTEEEEE----XXXXXXX CS
                Penicillinase_R 15 kgeatvkevvee.leeekelaysTVktllrrLvkKgllsrekegrafiYsplvseeeavas 74
                                   + eat + v +  ++e    ++ TV+ +++ L + gl+++++ g    Y p+v+  eav++
  gi|119719850|ref|YP_920345.1| 17 AYEATGRPVTSSeIAEAVGKSDGTVRNVISALKAMGLVEAKT-GPGGGYVPTVKGVEAVKG 76
                                   444444444443355555566*****************9987.99999*****99998876 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 6
                                    ----XXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                Penicillinase_R  64 plvseeeavasa..vkqlldklfegsvkelvaafveeekl 101
                                    p+v+ee ++++   ++++ + + +g++ + v + ++++ +
  gi|119719850|ref|YP_920345.1| 206 PVVDEEGVLEGLvsAQHVSKAYADGRLDARVEDYMDRDVA 245
                                    5666666666541145666666777777777777777633 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00034      0.23      38      84 ..      26      72 ..      10      81 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00034
                        DUF4423 38 dpeelakrlrpkisaeevekalefLlklgllkkded..gkyrqtekslt 84
                                   + +e+a++++   s   v++ ++ L+ +gl++ +    g y++t+k ++
  gi|119719850|ref|YP_920345.1| 26 TSSEIAEAVG--KSDGTVRNVISALKAMGLVEAKTGpgGGYVPTVKGVE 72
                                   6789******..9*******************9988899******9987 PP

>> BDM  Putative biofilm-dependent modulation protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00057      0.39      20      49 ..     271     299 ..     263     305 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00057
                            BDM  20 ieqGlraelGvvteddilmeltkwveasdn 49 
                                    ++q  r  +G++t  dilm lt+  e +d 
  gi|119719850|ref|YP_920345.1| 271 VDQSGRP-QGIITRTDILMALTRLYEVADS 299
                                    5666665.59**************999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2218.14
//
Query:       gi|119719851|ref|YP_920346.1|  [L=418]
Description: hypothetical protein Tpen_0943 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-93  313.6   0.0    1.8e-93  313.3   0.0    1.1  1  Nre_N     Archaeal Nre, N-terminal
    2.1e-31  108.1   0.0    3.9e-31  107.2   0.0    1.4  1  Nre_C     Archaeal Nre, C-terminal


Domain annotation for each model (and alignments):
>> Nre_N  Archaeal Nre, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  313.3   0.0     2e-97   1.8e-93       1     269 [.      27     294 ..      27     295 .. 0.98

  Alignments for each domain:
  == domain 1  score: 313.3 bits;  conditional E-value: 2e-97
                          Nre_N   1 Lcglkkcpileklravekakkki.sskeleGsspPsvfVGrygYPkVsvgplvppveg.dasvldspekwl.glsledii 77 
                                    Lcgl++cpil ++r+++ + +++  ++ele+ spPsv+VG++gYP ++vg+++   e+ ++s +++p +w+ +l+l +++
  gi|119719851|ref|YP_920346.1|  27 LCGLPYCPILVRARELAGVYERVrGRRELEAPSPPSVLVGEKGYPYIRVGVNLVGGEEgSPSLYEDPGAWWgRLDLYEVL 106
                                    8**********************999************************998887777********************* PP

                          Nre_N  78 klrlslvrgekkvkvkkakedklleeiqelalsekpvdvevelekkpkaklkfdevlaPvGpsaeleklkvaenpkvprk 157
                                    +lr+s+v ++  ++ ++a   ++ e+++e+als kpv++e+ ++++p+++++fd  l+PvG sae+e+l+v++np +pr+
  gi|119719851|ref|YP_920346.1| 107 RLRASMVYSYGVYSASRAV-GRVGESVREAALSLKPVESEAVFRRPPDFSMRFDPLLKPVGFSAEVERLSVVSNPYIPRR 185
                                    ****************998.999********************************************************* PP

                          Nre_N 158 veklveDtdlkAeeavveLyrsgvdvykiqrlLSvGlLGekkkrrlVPTrWsITAvddivgkelkkeikdlpeidevevf 237
                                    v++l+eD  +kA++a veLy++g+dvy+iqr+LS G+LG+  ++++VPTrW+ITAvd+ +g++l+ ++k +pe++++e++
  gi|119719851|ref|YP_920346.1| 186 VDQLIED-RVKASRAAVELYERGFDVYYIQRVLSSGALGV--SKKFVPTRWAITAVDRLIGDYLLGKVKGYPEVSSYELY 262
                                    *******.*******************************9..************************************** PP

                          Nre_N 238 sgeylgNrflviLaPgkwsfelvEawapgslw 269
                                    +++y+gN++ ++L+Pgkws+e+vE+w p+s+w
  gi|119719851|ref|YP_920346.1| 263 HSSYIGNYYSLLLMPGKWSLEMVEVWLPNSVW 294
                                    ******************************** PP

>> Nre_C  Archaeal Nre, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.2   0.0   4.3e-35   3.9e-31      12     110 .]     316     414 ..     307     414 .. 0.96

  Alignments for each domain:
  == domain 1  score: 107.2 bits;  conditional E-value: 4.3e-35
                          Nre_C  12 iaGaYyaarlavleaLekikrqakvivlreitpeYwaPvGvWqvReavrkalekkpkefesleealeevseklklplkkl 91 
                                     +G+Y a rlavle+L+k++r a+v+ +reitpeY+aPvG+Wq+Re+vr+al++  ++f sl eale+++ekl++pl+ +
  gi|119719851|ref|YP_920346.1| 316 EDGGYEAIRLAVLEHLAKRGRVASVLAVREITPEYFAPVGNWQIRESVRAALRGGGESFPSLGEALEALKEKLRVPLNLV 395
                                    47****************************************************************************** PP

                          Nre_C  92 lkkskllkelkkqktLddF 110
                                    l++s+ll+  ++q+++++F
  gi|119719851|ref|YP_920346.1| 396 LSRSTLLAARTRQRSITEF 414
                                    *****************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2810.72
//
Query:       gi|119719852|ref|YP_920347.1|  [L=281]
Description: aldo/keto reductase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-57  195.2   0.0    1.6e-55  188.4   0.0    2.0  1  Aldo_ket_red  Aldo/keto reductase family
  ------ inclusion threshold ------
       0.16   12.3   0.0       0.25   11.7   0.0    1.3  1  TINF2_N       TERF1-interacting nuclear factor 2 N-terminus


Domain annotation for each model (and alignments):
>> Aldo_ket_red  Aldo/keto reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.4   0.0   1.8e-59   1.6e-55       2     290 ..      20     273 ..      19     275 .. 0.94

  Alignments for each domain:
  == domain 1  score: 188.4 bits;  conditional E-value: 1.8e-59
                                    EEEE-SSS-ST.....TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH-TTTGGG-EEEEEE--SSSTT CS
                   Aldo_ket_red   2 lglGtwqlgsk....eeiskeealellrraleaGinffDtAevYgkgqseellGealkksrkkreeviiatKvdlrdaei 77 
                                    lg+Gtw +g++    ++  ++e + +lrr le G++++DtAe+Yg g+see++Gea+k   ++r+ev+i++Kv      +
  gi|119719852|ref|YP_920347.1|  20 LGMGTWGIGGGywspDTSGDAEWVSALRRGLELGMTLIDTAEMYGGGHSEEVVGEAVKG--FDRDEVFIVSKV------W 91 
                                    89********8655555555666666*********************************..************......* PP

                                    SSSS-HHHHHHHHHHHHHHHT-S-EEEEEE-S--TTS-.HHHHHHHHHHHHHTTSEEEEEEES--HHHHHHH.HHTTT-- CS
                   Aldo_ket_red  78 ksglskeniresleeslkrLgtdyvDllllHrpdpslpsieevldaleelvkeGkiraiGvSnfsveqleka.kkkkkvk 156
                                    + + ++++++++ e+s++rLgt  +Dl+l+H+p  ++p ++e+++ lee+v+ G++r iGvSnf  e +e+a    +  +
  gi|119719852|ref|YP_920347.1|  92 PTHARRDDVVKAAEASVRRLGT-FMDLYLIHWPPAEVP-LCETMRGLEEVVRRGLARFIGVSNFGLELIEEArACLSRED 169
                                    *********************6.9**************.*********************************87788889 PP

                                    EEEEE-B-BTT-HHHHTTHHHHHHHTT-EEEEBSTTGGGTTGTTTSS---SSSCCC-------TS-HHHHHHHHHHHHHH CS
                   Aldo_ket_red 157 ivavqveynllreleeegllelckkkgvpliaysplggGlltgkyqseedkedkeprkdlkrdertsknldaaeelsela 236
                                    ++av+++++ll++++e+ ++++++ +g+   ay+pl +G l                              +++ l e++
  gi|119719852|ref|YP_920347.1| 170 VAAVENKFSLLDRRDESSVVPYAEREGMLYLAYTPLEKGQLA-----------------------------RDSFLAEVG 220
                                    ***************************************998.............................67789**** PP

                                    HHTT--HHHHHHHHHTTSTT-SEEEE--SSHHHHHHHHGGGG----HHHHHHHH CS
                   Aldo_ket_red 237 kehgvslaqlalryalsqpavgivipgasnieqlednldalelklseeevaeld 290
                                    +++g++ aq+al+++++  + +++ip+as+++++e+n++a+ ++ls+e+++++ 
  gi|119719852|ref|YP_920347.1| 221 RKYGKTAAQVALNWLIK-LNPVVPIPKASSLAHVEENAGAMGWRLSDEDWRAIS 273
                                    ****************6.66679***************************9996 PP

>> TINF2_N  TERF1-interacting nuclear factor 2 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   2.7e-05      0.25      97     145 ..     199     247 ..     181     249 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.7e-05
                        TINF2_N  97 sLledpeerekflqeefpeeYGekfdaalekLllefLsrLeqlLpvpdl 145
                                     L+  p e+ +  ++ f +e G+k+ +   +  l++L++L+ ++p+p++
  gi|119719852|ref|YP_920347.1| 199 YLAYTPLEKGQLARDSFLAEVGRKYGKTAAQVALNWLIKLNPVVPIPKA 247
                                    57888999999***********************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       267  (0.0148921); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1993.95
//
Query:       gi|119719853|ref|YP_920348.1|  [L=192]
Description: PEBP family protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-31  109.9   0.0    1.4e-31  109.6   0.0    1.1  1  PBP       Phosphatidylethanolamine-binding protein


Domain annotation for each model (and alignments):
>> PBP  Phosphatidylethanolamine-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.6   0.0   7.6e-36   1.4e-31       2     132 .]      56     189 ..      55     189 .. 0.93

  Alignments for each domain:
  == domain 1  score: 109.6 bits;  conditional E-value: 7.6e-36
                                    --GGG..CSBGGS-EEEEES--TTSSEEEEEEEETTSCCTCTTEEEEEEEEEETTSSEE-TTC.........EE-B-TTS CS
                            PBP   2 lpkky..egentsPplswsdvpegtksyalvviDpDapkvsetflHwvvtnipasvtslpega.........vqgknslg 70 
                                    +p++y  +g + sP +sw ++p gt+s++l+++DpDap +++ f+Hwv++n+pas+t++p+            qg n++g
  gi|119719853|ref|YP_920348.1|  56 MPREYtcDGADESPDVSWGELPPGTRSLVLLCVDPDAP-RGT-FVHWVLYNVPASATRVPRSLpkapttpfgLQGVNDFG 133
                                    7888888999****************************.666.***************9986677899************ PP

                                    SCCCCS---B--STTS..EEEEEEEEEESSSG--BGSS-SHHHHHHHHCTTEEEEEEEEEEE CS
                            PBP  71 eesesgYlgpcPpkgdgkHrYvfllyaldvealdlkagftraelgaaiaghvlakatlagnY 132
                                        +gY+gpcPp g+  HrYvf+l ald e  +l+ g++   +  +  ghv++  +++ +Y
  gi|119719853|ref|YP_920348.1| 134 F---TGYGGPCPPSGT--HRYVFVLLALDSEL-ALSGGADALTVLSKASGHVIGYGEVVLTY 189
                                    *...************..***********995.7899988889999999******9999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1423.59
//
Query:       gi|119719854|ref|YP_920349.1|  [L=143]
Description: hypothetical protein Tpen_0946 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
       0.14   11.8   0.2        0.2   11.3   0.2    1.2  1  ChitinaseA_N  Chitinase A, N-terminal domain


Domain annotation for each model (and alignments):
>> ChitinaseA_N  Chitinase A, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   1.1e-05       0.2      51      98 ..      87     136 ..      67     140 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.1e-05
                   ChitinaseA_N  51 agdkakvlldgvkvaegaas..akesatfkvkkgGryqlevelCdaeGCs 98 
                                    +++ + ++++++ v++g  +    +sa++    + +   +v++C  +GC 
  gi|119719854|ref|YP_920349.1|  87 ETELVSLYFNDTLVWSGYLDlkVGQSAQVCTPLTSKGTYRVKACSYTGCF 136
                                    457789***********999433345566666667777799********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       674  (0.0375927); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.37s 00:00:00.99 Elapsed: 00:00:00.58
# Mc/sec: 736.99
//
Query:       gi|119719855|ref|YP_920350.1|  [L=730]
Description: hypothetical protein Tpen_0947 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-23   83.7   0.1    6.6e-23   81.1   0.0    2.4  2  DUF2341   Domain of unknown function (DUF2341)
    2.8e-05   24.3   1.6      0.017   15.3   0.3    2.9  2  CARDB     CARDB
    0.00015   21.9   0.1     0.0005   20.2   0.1    1.9  1  DUF1080   Domain of Unknown Function (DUF1080)
  ------ inclusion threshold ------
      0.038   13.8   0.5       0.48   10.3   0.2    2.7  2  FlgD_ig   FlgD Ig-like domain


Domain annotation for each model (and alignments):
>> DUF2341  Domain of unknown function (DUF2341)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.1   0.0   1.5e-26   6.6e-23       1      73 [.     439     514 ..     439     532 .. 0.92
   2 ?   -1.4   0.0       0.8   3.6e+03      15      60 ..     634     678 ..     626     702 .. 0.73

  Alignments for each domain:
  == domain 1  score: 81.1 bits;  conditional E-value: 1.5e-26
                        DUF2341   1 dgsdiRf....vdsdgttLpywieswdantekaliWvkvpsip.angnktikiyygnptatstsngdatfelFDdfsg 73 
                                    d++d+Rf     d ++ ++pyw+es  ++ ++a++Wvkvpsip + g+++i++yygnp+ats+sng+atf++F+dfs+
  gi|119719855|ref|YP_920350.1| 439 DFGDLRFsylqPDGREVAIPYWVES--VSGGCATVWVKVPSIPaSPGTARIYVYYGNPSATSESNGAATFIYFNDFSS 514
                                    799*****9888888888******6..9***************8899*****************************98 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.8
                        DUF2341  15 Lpywiesw.dantekaliWvkvpsipangnktikiyygnptatstsn 60 
                                    Lp  +e++  + + +a  W k++       + i +y++++++ +  +
  gi|119719855|ref|YP_920350.1| 634 LPSEVEPVhVYYSLQANTWYKLEM--RLYGGHITVYVNDSKVIDWTD 678
                                    666666665556668888888865..556778888888888876555 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0    0.0016         7      17      71 ..     196     251 ..     185     267 .. 0.84
   2 !   15.3   0.3   3.9e-06     0.017      15      82 ..     299     365 ..     286     378 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0016
                                    TTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEE.SEE-CTEEEEEEEEEE- CS
                          CARDB  17 vgeentitvtvkNqGtaasgatkvalyldgelvgtvtv.psLaagesttvsftwtt 71 
                                    v ++  +++ v+N G + ++   v+ + ++  +g + v   L++g+s+tvs+ ++ 
  gi|119719855|ref|YP_920350.1| 196 VYNSTGFYAIVANGGPGHAYIYAVWAVTSEAPTGRIAVnRLLEPGDSVTVSVPIPS 251
                                    5667778999****************************55689*******997765 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 3.9e-06
                                    EETTSEEEEEEEEEE-SSS-EEEEEEEEEE.TTEEEEEEEESEE-CTEEEEEEEEEE-S-S-CEEEEEE CS
                          CARDB  15 afvgeentitvtvkNqGtaasgatkvalyl.dgelvgtvtvpsLaagesttvsftwtteategevtltv 82 
                                      +g+  ++ ++vkN G+a sg+++v++y   g+lvg++++ sL++g+  + s+t+t + ++g++t  v
  gi|119719855|ref|YP_920350.1| 299 GATGSLKRFVASVKNVGNA-SGTVSVEVYDhAGSLVGKTSL-SLSPGQVGEASITITLPGQPGTYTWMV 365
                                    5667777899*******86.789999999625777899999.9**********************9655 PP

>> DUF1080  Domain of Unknown Function (DUF1080)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.1   1.1e-07    0.0005     120     162 ..     643     685 ..     524     708 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.1e-07
                                    S--S--TTSEEEEEEEEETTEEEEEETTEEEEEEETTSHHHHH CS
                        DUF1080 120 akaakppgeWntyeiivkgdrvtvwlNGvlvldftdldaetek 162
                                    + ++ ++++W ++e + +g ++tv++N+ +v+d td+++ t+ 
  gi|119719855|ref|YP_920350.1| 643 VYYSLQANTWYKLEMRLYGGHITVYVNDSKVIDWTDSSPITSG 685
                                    56678899******************************98743 PP

>> FlgD_ig  FlgD Ig-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.2   0.00011      0.48      14      54 ..     309     352 ..     294     370 .. 0.73
   2 ?    0.0   0.0      0.17   7.8e+02      55      75 ..     534     554 ..     532     558 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00011
                                    EEEE..ESSSEEEEEEEE-SS--EE..EEEEEEESSSEEEEEEE CS
                        FlgD_ig  14 lgve.lpeaadevtvtikDasGevV..rtidlgaqsaGvvsftW 54 
                                    ++v+ + +a+ +v+v+++D +G +V   +++l + + G+ s+t 
  gi|119719855|ref|YP_920350.1| 309 ASVKnVGNASGTVSVEVYDHAGSLVgkTSLSLSPGQVGEASITI 352
                                    55667788999**************6555666666667777665 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.17
                                    -SB-TTS-B--SEEEEEEEEE CS
                        FlgD_ig  55 dGtdndGnkladGaYtvkvta 75 
                                    dG d++G +l +Ga + +vt 
  gi|119719855|ref|YP_920350.1| 534 DGSDSSGWQLFQGALKHRVTV 554
                                    9************98777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (730 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.49
# Mc/sec: 4446.37
//
Query:       gi|119719856|ref|YP_920351.1|  [L=460]
Description: thymidylate synthase-like [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-10   39.3   0.0    6.4e-10   38.6   0.0    1.3  1  Thymidylat_synt  Thymidylate synthase
    2.2e-06   27.7   0.1    5.2e-06   26.5   0.1    1.7  1  DUF4346          Domain of unknown function (DUF4346)
  ------ inclusion threshold ------
      0.024   15.0   0.6       0.27   11.6   0.0    3.1  4  GHMP_kinases_C   GHMP kinases C terminal


Domain annotation for each model (and alignments):
>> Thymidylat_synt  Thymidylate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.6   0.0   1.1e-13   6.4e-10      88     218 ..     234     365 ..     163     386 .. 0.80

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 1.1e-13
                                    TB-SSSHHHHHHHBTSTTTSSB-HHHHHHHHHHHSTT-ST-EEE---GGGGGGSSS--SEEEEEEEE..SEETEEEEEEE CS
                Thymidylat_synt  88 gdlgpvYGkqwrkfkaeegkkidqlakvidqlkenpdsRriivsawnpaeldkmaLppChvlfqfyvkdkkegkLslqly 167
                                    g+ g+vY++  r   +++++  dq+++++++l ++pd Rr i   w+ a   + + ppC v +q + + ++    +    
  gi|119719856|ref|YP_920351.1| 234 GEEGAVYSYGDRL--RRHREAGDQVRRIVERLASSPDTRRAIALTWDFATDTNSQDPPCLVAVQGDLSGDT---YNQVAF 308
                                    6667776665555..3478999*************************99955699************7443...799999 PP

                                    EEEEETTTHHHHHHHHHHHHHHHHHHHHT......-EEEEEEEEEEEEEEEGGGHHH CS
                Thymidylat_synt 168 qRSaDvflGvpFNiasyalLthmlaqvtg......lkpgelihtigdaHiYsnhveq 218
                                     RS D   + p N     +L+  +a +        +kpg l+   +  H+Y+     
  gi|119719856|ref|YP_920351.1| 309 FRSHDAYAAWPLNAYGLLALMRRVAGELSertgraVKPGWLVVYSSSLHVYEHDWGR 365
                                    *************9988888888886543333366899*************977655 PP

>> DUF4346  Domain of unknown function (DUF4346)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.1   8.7e-10   5.2e-06      93     118 .]     433     458 ..     384     458 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 8.7e-10
                        DUF4346  93 dhaaYlGRelqraeaaLlsgkeYiqD 118
                                     haaYl Rel rae aL +g eY+qD
  gi|119719856|ref|YP_920351.1| 433 GHAAYLSRELYRAEKALREGGEYVQD 458
                                    5************************9 PP

>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       1.9   1.1e+04      39      50 ..      26      37 ..      24      39 .. 0.82
   2 ?   -1.4   0.0      0.52   3.1e+03      48      69 ..      69      86 ..      63      94 .. 0.78
   3 ?   11.6   0.0   4.5e-05      0.27       1      38 [.     114     149 ..     114     151 .. 0.90
   4 ?   -3.6   0.0       2.5   1.5e+04       7      22 ..     360     375 ..     358     382 .. 0.68

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.9
                 GHMP_kinases_C 39 llealselGalg 50
                                   ++e l++lG+lg
  gi|119719856|ref|YP_920351.1| 26 VVERLEKLGVLG 37
                                   789999999998 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.52
                 GHMP_kinases_C 48 algaklsGaGgGptvfalfkdk 69
                                   ++ga l G+  G +++ lf  k
  gi|119719856|ref|YP_920351.1| 69 VFGADLMGS--GEALVKLF--K 86
                                   78999****..99999888..4 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 4.5e-05
                 GHMP_kinases_C   1 llealergdlellgellnlsqrselkavvgilppelee 38 
                                    l+ea++rgd+++l++++ ++ r  + a+++  p ++ee
  gi|119719856|ref|YP_920351.1| 114 LREAFKRGDWGALARAIEENYR--PGARRPAAPLRMEE 149
                                    689*******************..89999988888887 PP

  == domain 4  score: -3.6 bits;  conditional E-value: 2.5
                 GHMP_kinases_C   7 rgdlellgellnlsqr 22 
                                    ++d+++  +l+ ++++
  gi|119719856|ref|YP_920351.1| 360 EHDWGRALRLVQENAA 375
                                    5677777777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (460 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.53
# Mc/sec: 2602.67
//
Query:       gi|119719857|ref|YP_920352.1|  [L=412]
Description: SufS subfamily cysteine desulfurase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   3.9e-133  444.0   0.0   4.4e-133  443.8   0.0    1.0  1  Aminotran_5      Aminotransferase class-V
    3.1e-08   33.2   0.0    4.3e-08   32.7   0.0    1.2  1  Aminotran_1_2    Aminotransferase class I and II
    1.9e-06   26.7   0.0    5.6e-06   25.1   0.0    1.7  2  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    0.00012   21.5   0.0    0.00014   21.2   0.0    1.2  1  Beta_elim_lyase  Beta-eliminating lyase
     0.0042   16.1   0.2      0.011   14.7   0.2    1.6  1  SelA             L-seryl-tRNA selenium transferase
  ------ inclusion threshold ------
      0.027   13.2   0.0       0.05   12.3   0.0    1.3  1  Pyridoxal_deC    Pyridoxal-dependent decarboxylase conserved 


Domain annotation for each model (and alignments):
>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  443.8   0.0  1.5e-136  4.4e-133       1     371 []      24     399 ..      24     399 .. 0.98

  Alignments for each domain:
  == domain 1  score: 443.8 bits;  conditional E-value: 1.5e-136
                                    EEEBTTTS----HHHHHHHHHHHHCTCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHH CS
                    Aminotran_5   1 iyldsaAttqkpqeVldalqeyytdynanvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtteainlvals 80 
                                    +y+d+aAt+q p +V++a++ +y++ nan+ rsvh+lg +at+a+e+ r+ va++i+a+  ee++ft++tte+inl+a+s
  gi|119719857|ref|YP_920352.1|  24 VYFDNAATSQRPLQVVEAVESFYKSLNANIGRSVHELGLRATEAYEDSRKIVAAFIGAKP-EELVFTKNTTESINLAAYS 102
                                    7**********************************************************7.******************* PP

                                    CCCC..-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTEB--H CS
                    Aminotran_5  81 lars..lkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvtGtiqpv 158
                                    l+ s  +++gd ivvt++ehh+nl+pw+++ak  ga+++v+ +d+eg+l+lde+ek+l+  +k+va+thvsnvtG+++pv
  gi|119719857|ref|YP_920352.1| 103 LLVSglISRGDAIVVTRMEHHSNLLPWVRVAKLAGAELRVVDVDDEGRLRLDEYEKALSRGAKIVAVTHVSNVTGVVNPV 182
                                    **99**************************************************************************** PP

                                    HHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTTTTSSTT-EEEEEEHHHHHTS..SS.STTSEEEEET.T CS
                    Aminotran_5 159 eeigklakkkgalvlvDaaqavghipidvkklgvDflafsghKllgPtGiGvlyvrkellekleplllggemveevsl.e 237
                                    +e+++la+++ga+ lvD+aq+ +h+++dvk++g+Df+afsghK+lgP G+G ly+r +l e+lep  +gg+ ++ vs  e
  gi|119719857|ref|YP_920352.1| 183 KELCRLAHDAGAFCLVDGAQSTPHMRVDVKDIGADFFAFSGHKMLGPMGTGGLYIRGDLAERLEPPFPGGGAISLVSCaE 262
                                    *****************************************************************************965 PP

                                    EEE...EHCTTGGGS.SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-CTCBSEEEE CS
                    Aminotran_5 238 ett...faeapskfeaGTpnvagiiglgaaleyleeigleaiekhekelaeyllerlkslpgvrlygpdkaerrasivsf 314
                                    ++    +  +p+kfeaGTpnvag++gl++a+eyl+++g+e +e+hek+l+++lle l+ ++  r+ygp++ + r ++vsf
  gi|119719857|ref|YP_920352.1| 263 DSCsaeWLHPPHKFEAGTPNVAGAVGLAKAVEYLRSVGMEDVEEHEKRLTAKLLEVLEGVGA-RIYGPRDMKDRLGVVSF 341
                                    444566889************************************************99965.699************** PP

                                    EETTCSHHHHHHHHHHTTEEEEEE-TTTHHHHHHTT.S.-EEEEE--TTS-HHHHHHH CS
                    Aminotran_5 315 nfkgvhaedvatlLdeegIavrsGhhcaqplmkrlale.gtvRaSlyiynteeevdrl 371
                                    n++g+ +++va++Ld egIavrsGhhca pl+krl+ + gtvRaSly+ynt eev+++
  gi|119719857|ref|YP_920352.1| 342 NLDGLTPHEVASMLDLEGIAVRSGHHCALPLVKRLGSPmGTVRASLYLYNTPEEVEYF 399
                                    **************************************9****************986 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.0   1.4e-11   4.3e-08      43     188 ..      65     200 ..      27     204 .. 0.81

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 1.4e-11
                                    TTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHH....HTTT-EEEEEESS-TH....HHHHHHHTT CS
                  Aminotran_1_2  43 idglpeleealakflgrseklklkreaavvvgsGagaliealifllk....lnpgdeilvpdptyas....yknilrlsg 114
                                    ++ + + ++ +a f+g       k+e ++v++  +++ i++++  l     + +gd+i+v +  + s      ++++l+g
  gi|119719857|ref|YP_920352.1|  65 TEAYEDSRKIVAAFIG------AKPE-ELVFTKNTTESINLAAYSLLvsglISRGDAIVVTRMEHHSnllpWVRVAKLAG 137
                                    5556778899999***......8999.88888888877776655443355589**********99763333689****** PP

                                    SEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEE CS
                  Aminotran_1_2 115 gevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDe 188
                                    +e++ + ++  ++ +l l+++e+al++        k+++v+ ++N tG+v + +el+ l   a+  +++ +vD 
  gi|119719857|ref|YP_920352.1| 138 AELRVVDVD--DEGRLRLDEYEKALSR------GAKIVAVTHVSNVTGVVNPVKELCRL---AHDAGAFCLVDG 200
                                    *******87..99**************......889***********************...999999999996 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   1.9e-09   5.6e-06      77     201 ..      98     228 ..      90     239 .. 0.89
   2 ?   -2.7   0.0      0.55   1.6e+03     292     313 ..     330     352 ..     329     365 .. 0.72

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.9e-09
                                    HHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEESTTS.....HHHHHHHCCTTEEEEEEESS-TTTT CS
                Cys_Met_Meta_PP  77 maAiaaailallkaGdeivvsddlYggtqrllkkvlkklgievkfvdtsd.....leelekaikentklvylEtptnpll 151
                                    +aA ++ +  l++ Gd ivv++  + +      +v+k  g e ++vd++d     l+e eka++   k+v +  ++n + 
  gi|119719857|ref|YP_920352.1|  98 LAAYSLLVSGLISRGDAIVVTRMEHHSNLLPWVRVAKLAGAELRVVDVDDegrlrLDEYEKALSRGAKIVAVTHVSNVTG 177
                                    699999*****************999999999999999*********9772222257889******************** PP

                                    ----HHHHHHHHHHTT-EEEEEGTTTHT.TTS-GGGGT-SEEEEETTTTTT CS
                Cys_Met_Meta_PP 152 kvvDiekiaklakkagvlvvvDntfasp.llqrplklgaDivvhSaTKylg 201
                                     v  ++++++la++ag+  +vD + ++p + +   + gaD    S+ K lg
  gi|119719857|ref|YP_920352.1| 178 VVNPVKELCRLAHDAGAFCLVDGAQSTPhMRVDVKDIGADFFAFSGHKMLG 228
                                    ****************************66677778999999999988775 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.55
                                    HHSSSG-SEEEEEESSHH.HHHH CS
                Cys_Met_Meta_PP 292 kqlkgaggvlsFelksee.ekak 313
                                    +++k+  gv+sF+l++ + ++++
  gi|119719857|ref|YP_920352.1| 330 RDMKDRLGVVSFNLDGLTpHEVA 352
                                    67899999******987643333 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   4.7e-08   0.00014      58     214 ..      99     241 ..      66     358 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 4.7e-08
                                    HHHHHHHHHH--TTEEEEEETT.-HHHHSSTTHHHHCC--EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESS CS
                Beta_elim_lyase  58 aAnsillkillqrgeevivtep.ahihfdetgaiaelagvklrdlknkeaGkmdlekleaaikevgaheekiklisltvT 136
                                    aA s+l++ l+ rg++++vt+   h        +a lag++lr ++ +++G + l++ e+a+ + ga     k++ +t  
  gi|119719857|ref|YP_920352.1|  99 AAYSLLVSGLISRGDAIVVTRMeHHSNLLPWVRVAKLAGAELRVVDVDDEGRLRLDEYEKALSR-GA-----KIVAVTHV 172
                                    5667888999*********99855666666799999****************************.55.....78888888 PP

                                    BTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CHHHHTTSSEEEEESSSTT--SS-.EEEEE-HH. CS
                Beta_elim_lyase 137 nntagGqvvsleelrevaaiakkygiplhlDgARfanaakslgeivkemfsyvDsvtmslkKdllanvG.gvlafrdde 214
                                     n+  G v ++   +e+  +a++ g   ++DgA       +++++vk++  ++D + +s+ K  l ++G g l +r d 
  gi|119719857|ref|YP_920352.1| 173 SNV-TGVVNPV---KELCRLAHDAGAFCLVDGAQS---TPHMRVDVKDI--GADFFAFSGHKM-LGPMGtGGLYIRGDL 241
                                    886.7887775...667899************965...57889*****9..6899*****997.567998888888883 PP

>> SelA  L-seryl-tRNA selenium transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.2   3.8e-06     0.011     106     232 ..     131     244 ..      61     247 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.8e-06
                                    HHHHHHTBEEE..EESBSSB--HHHHHHT--TTEEEEEEE---SEEEEES-B---HHHHHHHHHHHT--EEEEEES-B-S CS
                           SelA 106 dvmkkaGvkLv..evGttnkthlkDyekainentalllkvhtsnyrieGftkevelaeLvelgkekglpvleDlGsGllv 183
                                     v k aG++L+  +v    + +l +yeka++  + ++  +h sn  ++G ++ v  +eL +l++        D+G+  lv
  gi|119719857|ref|YP_920352.1| 131 RVAKLAGAELRvvDVDDEGRLRLDEYEKALSRGAKIVAVTHVSN--VTGVVNPV--KELCRLAH--------DAGAFCLV 198
                                    456778988861156667789999*******************9..78999877..68999997........67777777 PP

                                    -GGGGT-----BHHHHHHT.T-SEEEEETTSTT-SSS-EEEEE-HHHHHH CS
                           SelA 184 dlseyglskePtvqealae.GvdlvsfsGDkllGgpqaGiivGkkeliek 232
                                    d    g ++ P+++  +++ G+d  +fsG k+lG    G +  + +l e+
  gi|119719857|ref|YP_920352.1| 199 D----GAQSTPHMRVDVKDiGADFFAFSGHKMLGPMGTGGLYIRGDLAER 244
                                    7....667789888777655**************9888766666666655 PP

>> Pyridoxal_deC  Pyridoxal-dependent decarboxylase conserved domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.7e-05      0.05     158     274 ..     129     232 ..     115     242 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.7e-05
                                    HHHHHHHHT-EEEEE--BTTTBB-HHHHHHHHHHHHCTT.EEEEEEEEBS-TTT-BB--HHHHHHHHHHCT-EEEEE-TT CS
                  Pyridoxal_deC 158 vekaalvlgvklrvipldengklrgaalekaieedkekGlipffvvatlGttvlgaFddlkelgdicekydlwlHvDAAy 237
                                    + ++a+++g +lrv+ +d++g+lr ++ eka+ +   k   +  v++t  + v+g  + +kel  + +  +    vD A 
  gi|119719857|ref|YP_920352.1| 129 WVRVAKLAGAELRVVDVDDEGRLRLDEYEKALSRGA-K---I--VAVTHVSNVTGVVNPVKELCRLAHDAGAFCLVDGAQ 202
                                    67899*************************987543.3...4..7889999999999********************999 PP

                                    GGGGGGSGGGGGGGTTGGGESEEEEECCCCTS--SS- CS
                  Pyridoxal_deC 238 aGsaficpeirhllkgieradSitvnphKlllvlldc 274
                                           p++r  +k i  ad +++++hK+l+ +++ 
  gi|119719857|ref|YP_920352.1| 203 ST-----PHMRVDVKDIG-ADFFAFSGHKMLG-PMGT 232
                                    98.....99999999995.9*********875.4555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 2673.84
//
Query:       gi|119719858|ref|YP_920353.1|  [L=513]
Description: phenylalanyl-tRNA synthetase subunit alpha [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.1e-79  264.7   0.0    9.7e-79  264.3   0.0    1.2  1  tRNA-synt_2d     tRNA synthetases class II core domain (F)
    6.2e-05   22.5   0.0     0.0027   17.2   0.0    2.9  3  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
    9.9e-05   21.6   0.4       0.11   11.5   0.0    2.5  2  tRNA-synt_2      tRNA synthetases class II (D, K and N)
     0.0018   18.2   3.7      0.083   12.9   0.6    3.9  3  HTH_Crp_2        Crp-like helix-turn-helix domain
  ------ inclusion threshold ------
      0.076   12.9   0.3       0.34   10.8   0.1    2.1  2  TrmB             Sugar-specific transcriptional regulator Trm
      0.093   12.8   2.3        0.3   11.2   1.3    2.4  2  HTH_20           Helix-turn-helix domain
        1.1    9.8   5.9       0.97   10.1   0.2    3.0  3  PKS_DE           Polyketide synthase dimerisation element dom


Domain annotation for each model (and alignments):
>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  264.3   0.0   3.8e-82   9.7e-79       2     243 ..     229     499 ..     228     501 .. 0.97

  Alignments for each domain:
  == domain 1  score: 264.3 bits;  conditional E-value: 3.8e-82
                                    .-TSSCTSCTSHSB-SHHHHHHHHHHHHHHCTTCEESSTTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS-..... CS
                   tRNA-synt_2d   2 idvtlpgkrieagklhpltkvleeikeiflelgfeevegpevesefynfdaLnvpqdhpaRdmqdtFylkkpeka..... 76 
                                    +d++++ ++   g++hp+ ++l+ ++ei++++gfee++gp+ve e++nfdaL++ qdhpaR+++dt+++k  ++      
  gi|119719858|ref|YP_920353.1| 229 FDLSVEVPQAGFGRKHPYLEFLDWVREILVSMGFEEMKGPHVELELWNFDALFQAQDHPAREIHDTYFVKGGATGrvgde 308
                                    588889999999*********************************************************8888889**** PP

                                    ............................ECESEEE-SSTHHHHHHHH.TTS-SSEEEEEEEEEEBSST-SSSB-SEEEEE CS
                   tRNA-synt_2d  77 ............................veekllLRthttavqirtl.ekkkppikiisigrvfRrdavDathlaeFhqv 127
                                                                 + +l+LRt+ttav++rtl ++ +    ++s++rvfR +++Da+h++eF+q+
  gi|119719858|ref|YP_920353.1| 309 ellrrialthengwvtgskgwgykwdpaRALRLILRTQTTAVSARTLyARGEGEYMCFSLDRVFRPENLDAKHSMEFYQL 388
                                    ***************************9899****************99999**************************** PP

                                    EEEEEETT--HHHHHHHHHHHHHHHCTSTEEEEEEECEETTEEEEEEEEEEECCSSSSEEEEEEEEEE-HHHHHHTT-.T CS
                   tRNA-synt_2d 128 eglvvdenvsladlkgvleellkklfgaevkvrfrpsyfpftePsaevdvylvekkkkwlEllgaGmvrpevleavgide 207
                                    eg++v++ v++++l+g+++e+ ++l g   +v+++p+yfpftePs+e ++ +   k +w+E++  Gm+rpevl+++g+ +
  gi|119719858|ref|YP_920353.1| 389 EGIIVGRRVTFRNLLGFFQEMSRRL-GLG-EVKVKPAYFPFTEPSVEGFIKH--PKLGWIEVFPGGMFRPEVLAPLGL-R 463
                                    *************************.*99.**********************..9***********************.* PP

                                    TSEEEEEEEEHHHHHHHHHT-SSGHHHHTT.HHHHG CS
                   tRNA-synt_2d 208 evsgfafGlGveRlamlkygieDiRelvendlrflr 243
                                     v+++a+G+G++R+am  +g++DiR l+++dl++++
  gi|119719858|ref|YP_920353.1| 464 GVNVAAWGIGIDRIAMTVLGVDDIRVLFSQDLEYIK 499
                                    ********************************9987 PP

>> tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.63   1.6e+03     148     186 ..      98     135 ..      94     136 .. 0.86
   2 ?    1.3   0.0     0.074   1.9e+02      12      37 ..     240     265 ..     232     267 .. 0.83
   3 !   17.2   0.0   1.1e-06    0.0027      90     203 ..     356     462 ..     336     470 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.63
                tRNA_synthFbeta 148 givealleslgiekvefepaehpalhpgrsAeikvdgke 186
                                    g v al+++lg+ ++  e+a+ ++ h  r+  +++ g e
  gi|119719858|ref|YP_920353.1|  98 GEVAALARELGV-ELGEEEAQIAFSHLARAGAVSFSGDE 135
                                    668999******.999999*******9999999888776 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.074
                tRNA_synthFbeta  12 egelnkeqklrrklrdllagaGlnEv 37 
                                     g++++  ++ + +r++l+++G+ E+
  gi|119719858|ref|YP_920353.1| 240 FGRKHPYLEFLDWVREILVSMGFEEM 265
                                    45678999999*************96 PP

  == domain 3  score: 17.2 bits;  conditional E-value: 1.1e-06
                tRNA_synthFbeta  90 largnedvrlFEigkvflkd.seeelpeeerhlaivltgkreeeswsekaravdfydlkgivealleslgiekvefepae 168
                                    +arg+ +   F + +vf+++  + +   e  +l ++++g+r           v f +l g+ +++ ++lg+++v+++pa 
  gi|119719858|ref|YP_920353.1| 356 YARGEGEYMCFSLDRVFRPEnLDAKHSMEFYQLEGIIVGRR-----------VTFRNLLGFFQEMSRRLGLGEVKVKPAY 424
                                    589999999***********76667799*************...........**************************** PP

                tRNA_synthFbeta 169 hpalhpgrsAeikvdgkevGvl.....Gelhpevleafdl 203
                                     p+ +p    e  ++  ++G++     G + pevl+ ++l
  gi|119719858|ref|YP_920353.1| 425 FPFTEPS--VEGFIKHPKLGWIevfpgGMFRPEVLAPLGL 462
                                    **99995..5555556666666444546666666666666 PP

>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   4.4e-05      0.11      94     119 ..     365     389 ..     355     393 .. 0.92
   2 !    7.5   0.1   0.00072       1.8     285     306 ..     468     489 ..     460     493 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.4e-05
                                    EEEEEEEE--S--BTTB-S-CEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    tRNA-synt_2  94 vfqiaraFRaEdsrtdrhlaEFtqie 119
                                     f++ r+FR E++++++ + EF+q+e
  gi|119719858|ref|YP_920353.1| 365 CFSLDRVFRPENLDAKHSM-EFYQLE 389
                                    58999**************.****98 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00072
                                    EEEEEEHHHHHHHHCT-SSGGG CS
                                    xxxxxxxxxxxxxxxxxxxxxx RF
                    tRNA-synt_2 285 gGlglGldRlvmlllgsesIrd 306
                                    + +g+G+dR+ m++lg ++Ir 
  gi|119719858|ref|YP_920353.1| 468 AAWGIGIDRIAMTVLGVDDIRV 489
                                    669*****************95 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.6   3.2e-05     0.083      25      58 ..      30      64 ..      28      70 .. 0.84
   2 ?    3.1   0.0     0.036        92      39      64 ..     117     143 ..      83     147 .. 0.78
   3 ?   -0.9   0.0      0.66   1.7e+03      44      61 ..     170     188 ..     168     191 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.2e-05
                                   HHHHHHTTSSHHHHHHHHHHHHHTTSEEETEE.EE CS
                      HTH_Crp_2 25 eelAsmlGltretvsrilseLkreglisrgrr.ir 58
                                   +e+A +lG++re + r   eL+ +g ++ +rr ++
  gi|119719858|ref|YP_920353.1| 30 DEIAGRLGARREDLMRDVEELRARGFVEVERReVE 64
                                   69**************************5444365 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.036
                                    HHHHHHHHHTTSEE.ETEEEEES-HHH CS
                      HTH_Crp_2  39 srilseLkreglis.rgrririldlea 64 
                                      ++s+L r+g +s  g ++r+ d+e+
  gi|119719858|ref|YP_920353.1| 117 QIAFSHLARAGAVSfSGDEVRLSDPEK 143
                                    557899********6563399999997 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.66
                                    HHHHTTSEE.ETEE.EEES- CS
                      HTH_Crp_2  44 eLkreglis.rgrr.irild 61 
                                     Lkr+ l++ r+   +++l 
  gi|119719858|ref|YP_920353.1| 170 YLKRRRLVEpRR-YaVILLR 188
                                    69*******555.3376665 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00013      0.34      19      58 ..      23      62 ..      15      70 .. 0.90
   2 ?   -1.8   0.0       1.1   2.9e+03      26      34 ..     101     109 ..      84     135 .. 0.52

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00013
                                   HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                           TrmB 19 klgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                    +g ++ deia +lg  r    + +++L  +G+Ve+e+++
  gi|119719858|ref|YP_920353.1| 23 LSGASDLDEIAGRLGARREDLMRDVEELRARGFVEVERRE 62
                                   479999******************************9876 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.1
                                    CHHCCCTTS CS
                           TrmB  26 deiaeelgv 34 
                                      +a+elgv
  gi|119719858|ref|YP_920353.1| 101 AALARELGV 109
                                    334444444 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.3   0.00012       0.3      13      59 ..      16      61 ..      13      62 .. 0.91
   2 ?   -2.7   0.0       2.5   6.3e+03      17      28 ..     121     132 ..     119     149 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00012
                                   HHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
                         HTH_20 13 rrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvre 59
                                    ril+a    ++  + e+a rl+ ++  l + +++L+  g+vev+r 
  gi|119719858|ref|YP_920353.1| 16 KRILDAV-LSGASDLDEIAGRLGARREDLMRDVEELRARGFVEVERR 61
                                   6889998.89999999******999999*****************95 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.5
                                    HHHSTCTTB-HH CS
                         HTH_20  17 raLaraegltas 28 
                                    ++Lara+++++s
  gi|119719858|ref|YP_920353.1| 121 SHLARAGAVSFS 132
                                    667666666655 PP

>> PKS_DE  Polyketide synthase dimerisation element domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.2      0.21   5.5e+02      11      26 ..      27      42 ..      25      50 .. 0.81
   2 ?   -2.2   0.1       2.6   6.6e+03       8      33 ..      58      81 ..      57      82 .. 0.65
   3 ?   10.1   0.2   0.00038      0.97       7      23 ..      94     112 ..      93     124 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.21
                         PKS_DE 11 eDlaaLaatLgldada 26
                                    Dl++ a++Lg+++++
  gi|119719858|ref|YP_920353.1| 27 SDLDEIAGRLGARRED 42
                                   6**********97666 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.6
                         PKS_DE  8 VereDlaaLaatLgldadasLsavLP 33
                                   Ver  ++ L+ t +   ++ L++ LP
  gi|119719858|ref|YP_920353.1| 58 VERREVERLSLTREG--EEYLEKGLP 81
                                   899999999755444..334666666 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.00038
                         PKS_DE   7 aVereDlaaLaatLgl..d 23 
                                    aV r+ +aaLa++Lg+  +
  gi|119719858|ref|YP_920353.1|  94 AVRRGEVAALARELGVelG 112
                                    9***************542 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (513 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 3605.19
//
Query:       gi|119719859|ref|YP_920354.1|  [L=556]
Description: phenylalanyl-tRNA synthetase subunit beta [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.5e-39  134.1   0.0    6.9e-39  133.5   0.0    1.3  1  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
    5.2e-18   65.1   0.1    1.5e-12   47.6   0.1    2.8  2  B5               tRNA synthetase B5 domain
    1.1e-13   51.3   0.0      2e-13   50.4   0.0    1.4  1  B3_4             B3/4 domain
    4.6e-07   29.6   0.0    1.3e-06   28.1   0.0    1.8  1  tRNA-synt_2d     tRNA synthetases class II core domain (F)
  ------ inclusion threshold ------
       0.18   12.1   0.0       0.82    9.9   0.0    2.2  2  PhetRS_B1        Phe-tRNA synthetase beta subunit B1 domain


Domain annotation for each model (and alignments):
>> tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.5   0.0   1.9e-42   6.9e-39       9     213 ..     350     541 ..     343     542 .. 0.97

  Alignments for each domain:
  == domain 1  score: 133.5 bits;  conditional E-value: 1.9e-42
                tRNA_synthFbeta   9 pttegelnkeqklrrklrdllagaGlnEvitysfvsekeldklleddderkavelanPlsedqsvlRtsLlpglLevlar 88 
                                    p+ +g++++ + ++r+lr+ ++g+G++Ev +y ++s++ + +++   +++  ve++nP +e + +lRt ++p+lL  +++
  gi|119719859|ref|YP_920354.1| 350 PLHPGREDPIEVFTRALREGMVGLGFVEVNNYMMTSASLMFDAM-LLPRQPIVEVENPRHEAYHALRTWIVPQLLRLMSS 428
                                    5678889********************************99994.6699******************************* PP

                tRNA_synthFbeta  89 NlargnedvrlFEigkvflkd.seeelpeeerhlaivltgkreeeswsekaravdfydlkgivealleslgiekvefepa 167
                                      + g +  r+FE g+v ++d s +++++eer+la++++gk            v   d  ++++ l+++lg+ ++++e+a
  gi|119719859|ref|YP_920354.1| 429 SKHAGYP-QRVFEAGDVAIPDeSRDNRVREERRLAFAVAGKG-----------VTLTDGLAALKGLFRQLGV-SFKLEKA 495
                                    *******.**********************************...........*******************.******* PP

                tRNA_synthFbeta 168 ehpalhpgrsAeikvdgkevGvlGelhpevleafdlkqrvyvfEld 213
                                    ehp++  gr+A+++ +    G++Ge+hp+vl +f+l+ +v++ El+
  gi|119719859|ref|YP_920354.1| 496 EHPSFIAGRVARVVTEAGDAGIVGEVHPQVLVNFGLEVPVVAGELN 541
                                    *********************************************8 PP

>> B5  tRNA synthetase B5 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   7.7e-06     0.028       2      54 ..       5      57 ..       4      95 .. 0.86
   2 !   47.6   0.1   4.3e-16   1.5e-12       5      67 .]     278     340 ..     274     340 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 7.7e-06
                                   EEEHHHHHHHHTS---HHHHHHHHHHTT-E.EESSTTCEEEE--TT-TT--SH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             B5  2 slrvekinkllGidlseeeiikiLkrlgceriekdkdlllVtvPswRsDlere 54
                                   ++++  +++l+G +l+e+++ ++L rl+ce++e  ++ +  +  + R+Dl  +
  gi|119719859|ref|YP_920354.1|  5 EVKLWDLERLTGASLDESTVRDLLPRLKCEVEEVSGEDVVYEATHDRPDLYSA 57
                                   56777899**********************98888888888887778888654 PP

  == domain 2  score: 47.6 bits;  conditional E-value: 4.3e-16
                                    HHHHHHHHTS---HHHHHHHHHHTT-E.EESSTTCEEEE--TT-TT--SHHHHHHHHHHHH-G CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             B5   5 vekinkllGidlseeeiikiLkrlgceriekdkdlllVtvPswRsDlereeDliEEvaRlyGY 67 
                                    v+  + llG+dl  ee++++L+++ ++++  ++ ++ V  P +R+D+++++D++EEva+ yGY
  gi|119719859|ref|YP_920354.1| 278 VSMNRDLLGLDLGVEETVRLLRAMRMDAEPAGNGKVAVRYPYFRVDILHPVDIAEEVAMGYGY 340
                                    5556789*******************************************************9 PP

>> B3_4  B3/4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.4   0.0   5.5e-17     2e-13       2     131 ..      94     234 ..      93     245 .. 0.91

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 5.5e-17
                                    SSEEEEEEEES--.-----HHHHHHHHHTT-----HHHHHHHHHHHHHT-.....-EEEEEGGGTBTEEEEEE--TTEEE CS
                           B3_4   2 cpryaarvlrgvkktapspewlqrrLrragirpinnvVDitNyvmlelgq.....PlhafDldkiqgdivvrlakegekl 76 
                                    +p+++ +v+rgv+ + +                i  +  ++++v+l +g+      ++ +Dld i+ +++   a  + ++
  gi|119719859|ref|YP_920354.1|  94 RPYAFFAVVRGVSLDDEA---------------IRQLMQLQEKVHLTYGRnrrkvSIGLYDLDGIKLPVRYVAASPETRM 158
                                    688888888888888888...............9999****************************999998888888899 PP

                                    EBTTS-.EEEE-T...................TSEEEETEEEEE.EETTTEEBTTTB--TT--EEEEEEEE--HHH CS
                           B3_4  77 vtldgk.erelde...................edlviadsekpv.slagvmggeeskvsedTknvfleaaafdpvs 131
                                     +l+   e +l+e                   e+++i+d+e++v s +++ ++e+ +v+e+T++v++ ++  dp++
  gi|119719859|ref|YP_920354.1| 159 KPLGFAiEMTLREvlekhpkgveyghlvkghgEYPLIVDAEGKVvSFPPITNSEDFRVTESTRDVLIDVTSTDPEA 234
                                    9996555888888899999***********************999****************************965 PP

>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   3.7e-10   1.3e-06      10     218 ..     350     542 ..     343     549 .. 0.82

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 3.7e-10
                                    CTSHSB-SHHHHHHHHHHHHHHCTTCEESSTTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS-ECESEEE-SSTHH CS
                   tRNA-synt_2d  10 rieagklhpltkvleeikeiflelgfeevegpevesefynfdaLnvpqdhpaRdmqdtFylkkpekaveekllLRthtta 89 
                                    ++++g+ +p++ + + ++e ++ lgf ev++  + s    fda+ +p++ p+ ++      ++p++  e    LRt   +
  gi|119719859|ref|YP_920354.1| 350 PLHPGREDPIEVFTRALREGMVGLGFVEVNNYMMTSASLMFDAMLLPRQ-PIVEV------ENPRH--EAYHALRTWIVP 420
                                    678999****************************************986.55444......44555..55789******* PP

                                    HHHHHH...TTS-SSEEEEEEEEEEBSST-SSSB-SEEEEEEEEEEETT--HHHHHHHHHHHHHHHCTSTEEEEEEECEE CS
                   tRNA-synt_2d  90 vqirtl...ekkkppikiisigrvfRrdavDathlaeFhqveglvvdenvsladlkgvleellkklfgaevkvrfrpsyf 166
                                      +r +   ++   p++++  g v   d+    +  e   + + v++++v+l+d ++ l+ l+++l g +  ++++++  
  gi|119719859|ref|YP_920354.1| 421 QLLRLMsssKHAGYPQRVFEAGDVAIPDESRDNRVREERRLAFAVAGKGVTLTDGLAALKGLFRQL-GVS--FKLEKAEH 497
                                    ******87666669***************999999999****************************.998..77777777 PP

                                    TTEEEEEEEEEEECCSSSSEEEEEEEEEE-HHHHHHTT-.TTSEEEEEEEEH CS
                   tRNA-synt_2d 167 pftePsaevdvylvekkkkwlEllgaGmvrpevleavgideevsgfafGlGv 218
                                    p    +  + v+      +    + +G v+p+vl ++g+  ev+++a  l v
  gi|119719859|ref|YP_920354.1| 498 PSFIAGRVARVVT-----EAGDAGIVGEVHPQVLVNFGL--EVPVVAGELNV 542
                                    7666555555555.....222334445579999999999..88888865555 PP

>> PhetRS_B1  Phe-tRNA synthetase beta subunit B1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00023      0.82       1      43 [.       1      43 [.       1      69 [. 0.85
   2 ?   -3.1   0.0       2.8   9.9e+03      27      35 ..     525     533 ..     522     541 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00023
                      PhetRS_B1  1 MPtisvkkeaLfkalgkelteeeledllfefGlElDeiveeee 43
                                   MP++ vk  +L +++g +l+e+ + dll ++  E+ e+  e+ 
  gi|119719859|ref|YP_920354.1|  1 MPVVEVKLWDLERLTGASLDESTVRDLLPRLKCEVEEVSGEDV 43
                                   9************************************998887 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.8
                      PhetRS_B1  27 llfefGlEl 35 
                                    +l++fGlE+
  gi|119719859|ref|YP_920354.1| 525 VLVNFGLEV 533
                                    6889***97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (556 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       246  (0.0137208); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.24s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 3726.31
//
Query:       gi|119719860|ref|YP_920355.1|  [L=242]
Description: HAD family hydrolase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-18   66.8   0.0    4.1e-18   66.1   0.0    1.3  1  HAD_2           Haloacid dehalogenase-like hydrolase
    1.7e-12   48.1   0.0    4.4e-12   46.8   0.0    1.6  1  Hydrolase       haloacid dehalogenase-like hydrolase
    1.6e-09   37.7   0.0    1.2e-08   34.8   0.0    2.2  2  Hydrolase_like  HAD-hyrolase-like
    0.00064   20.2   0.4     0.0015   19.0   0.4    1.6  1  HAD             haloacid dehalogenase-like hydrolase
     0.0055   16.8   0.1        4.1    7.6   0.0    2.7  3  Hydrolase_6     Haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.1   0.0   1.2e-21   4.1e-18      63     177 ..      93     211 ..      70     212 .. 0.88

  Alignments for each domain:
  == domain 1  score: 66.1 bits;  conditional E-value: 1.2e-21
                          HAD_2  63 eellrkyneekkk...kevkpydgvkelLeeLkeagyklgivTsk.sreaveekleqlgiesyFdvivtsedvekkKPdp 138
                                    eel++++ e   +     vkp +g++ +Le  k++gy+l ++++  s++   e l+++g+ ++Fd +  s+ v+ +KP+p
  gi|119719860|ref|YP_920355.1|  93 EELVSEVSEAFIQpylSLVKPAEGARGFLEGAKKMGYRLVLASNTmSTRHSVELLRRHGLAELFDYMAFSDSVGFRKPHP 172
                                    445555555555555569***************************677888999************************** PP

                          HAD_2 139 eviekaleklklkkeeviyvGDsptDieaakkagikvia 177
                                    + ++ ++ + ++ + e ++vGD+  Di +ak  g k+ia
  gi|119719860|ref|YP_920355.1| 173 RFFAHIVAEAGIAPRESFFVGDEEADIRGAKLCGFKTIA 211
                                    *************************************98 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   0.0   1.2e-15   4.4e-12       3     208 ..       9     204 ..       7     206 .. 0.70

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 1.2e-15
                                    EEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHH..HHHH.HHHHH...ETTTE.......HH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxx.xxxxx...xxxxx.......xx RF
                      Hydrolase   3 tvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakar..sgal.tgfat...figrg.......ay 69 
                                     vv D+ GTL+  + s+e+  +++a+ +a+al+                 +   + + + + +   +++r        + 
  gi|119719860|ref|YP_920355.1|   9 GVVVDLWGTLLYPSVSLEEYSRERARRIAEALRAR------------GASLgeDE-VlEAYKRarrLADRVrnitmieVS 75 
                                    69**********************44444444444............44443211.123333300011111222222234 PP

                                    HHTHHHHHHHHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase  70 aigkpewltaldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetae 149
                                    ++g++ +l ++            +  +  ++ + +  +  +       k+ ++a+ +++  k++g+++vl+++  ++   
  gi|119719860|ref|YP_920355.1|  76 LEGEVVMLLDE------------LGLEPSEELVSEVSEAFIQPYLSLVKPAEGARGFLEGAKKMGYRLVLASNTMSTRHS 143
                                    44444444444............33333333333224444455556667899*********************9998888 PP

                                    .HHHHHTT.GGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHH CS
                                    .xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase 150 .raanqlG.ddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgvnDaaalaa 208
                                     +++++ G ++ fd    sd +++ kp+p+ + +++ e ++ p+e  +VGD   D+ +++ 
  gi|119719860|ref|YP_920355.1| 144 vELLRRHGlAELFDYMAFSDSVGFRKPHPRFFAHIVAEAGIAPRESFFVGDEEADIRGAKL 204
                                    89******************************************************99986 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0      0.26   9.5e+02      36      53 ..     122     139 ..     121     156 .. 0.77
   2 !   34.8   0.0   3.5e-12   1.2e-08       2      51 ..     167     214 ..     166     239 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.26
                                    HHHHHCT-EEEEESSSSS CS
                 Hydrolase_like  36 agAnnaGwksvLVltGvt 53 
                                    +gA+++G++ vL    ++
  gi|119719860|ref|YP_920355.1| 122 EGAKKMGYRLVLASNTMS 139
                                    79*******999766555 PP

  == domain 2  score: 34.8 bits;  conditional E-value: 3.5e-12
                                    .STTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESSS CS
                 Hydrolase_like   2 lgKPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVltG 51 
                                    ++KP+p ++  ++++ g++p+e++++GD  ++Di+gA+  G k+++++ G
  gi|119719860|ref|YP_920355.1| 167 FRKPHPRFFAHIVAEAGIAPRESFFVGDE-EADIRGAKLCGFKTIAYT-G 214
                                    58***************************.***************984.4 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.4   4.1e-07    0.0015       4     187 ..      13     202 ..      10     203 .. 0.55

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 4.1e-07
                            HAD   4 DfDgTL.ldgdslelllrfllrrgaprlwralreklllalfrellrldraglaellea................llagls 66 
                                    D+ gTL  ++ sle++ r ++rr a+  +ra  + l ++   e+ ++ r+ ++++ +                  l+  +
  gi|119719860|ref|YP_920355.1|  13 DLWGTLlYPSVSLEEYSRERARRIAEA-LRARGASLGEDEVLEAYKRARRLADRVRNItmievslegevvmlldELGLEP 91 
                                    555666334466666666455444433.4444444444442222222222222222222223333333333111444444 PP

                            HAD  67 .eelaaelerfvaevirpk..lldp..galellaahraaGdrvvvvSgg.lrplvepllaelgadevlatelevddrltg 140
                                     eel  e+ +++   i+p   l +p  ga+ +l+ +++ G+r+v+ S++   +   +ll+++g    la+       ++ 
  gi|119719860|ref|YP_920355.1|  92 sEELVSEVSEAF---IQPYlsLVKPaeGARGFLEGAKKMGYRLVLASNTmSTRHSVELLRRHG----LAE------LFDY 158
                                    444444444444...666655577888*******999***********964566667778***....***......4444 PP

                            HAD 141 elglegkpvrgegkvaalrewlaaegegidleevvayGDspsDlpll 187
                                        ++++ +++  ++  +     +++gi++ e++++GD ++D+  +
  gi|119719860|ref|YP_920355.1| 159 M-AFSDSVGFRKPHPRFFAH--IVAEAGIAPRESFFVGDEEADIRGA 202
                                    4.344444444444444444..44457899999**********9876 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.25   8.9e+02       1      20 [.      10      34 ..      10      44 .. 0.56
   2 !    6.1   0.0    0.0033        12      41     100 ..      30      89 ..      21      90 .. 0.90
   3 !    7.6   0.0    0.0012       4.1      14      54 ..     112     150 ..     108     162 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.25
                                   EEEESTTTSE.....ETTEE-TTHH CS
                    Hydrolase_6  1 flfDidGvLw.....rgdkaipgaa 20
                                   +++D++G+L+      ++   + a 
  gi|119719860|ref|YP_920355.1| 10 VVVDLWGTLLypsvsLEEYSRERAR 34
                                   689*****98444432444444444 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0033
                                    SS-HHHHHHHHHHTT----GGGEEEHHHHHHHHHHHHSXXXEEEEESXHHHHHHHHHTTX CS
                    Hydrolase_6  41 skseeeyakkleklgvditeeqvvtsataaaeylkkrkadkkvlvigeeglreelkeagf 100
                                    ++  + +a+ l++ g ++ e++v+ +++ a+++  + ++   + v  e ++  +l+e g+
  gi|119719860|ref|YP_920355.1|  30 RERARRIAEALRARGASLGEDEVLEAYKRARRLADRVRNITMIEVSLEGEVVMLLDELGL 89 
                                    55668899999*************************999999999999999999999987 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0012
                                    EE-TTHHHHHHHHHHTT-EEEEEE---SS-HHHHHHHHHHT CS
                    Hydrolase_6  14 kaipgaaealnalraagkpvvllTNnsskseeeyakklekl 54 
                                    k+ +ga  +l+  +++g+++vl +N  s   ++ ++ l++ 
  gi|119719860|ref|YP_920355.1| 112 KPAEGARGFLEGAKKMGYRLVLASNTMST--RHSVELLRRH 150
                                    7899*********************7433..3455555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1619.50
//
Query:       gi|119719861|ref|YP_920356.1|  [L=109]
Description: MarR family transcriptional regulator [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.4e-14   51.9   0.0    7.6e-14   51.6   0.0    1.1  1  HTH_34    Winged helix DNA-binding domain
    0.00013   21.7   0.0    0.00022   21.0   0.0    1.4  1  HTH_5     Bacterial regulatory protein, arsR family
    0.00021   21.3   0.1     0.0021   18.1   0.0    2.4  2  HTH_20    Helix-turn-helix domain
    0.00023   21.0   0.0    0.00037   20.4   0.0    1.3  1  MarR      MarR family
     0.0011   18.7   0.0     0.0019   18.0   0.0    1.4  1  HxlR      HxlR-like helix-turn-helix
     0.0025   17.7   0.0      0.006   16.4   0.0    1.7  2  TrmB      Sugar-specific transcriptional regulator TrmB
     0.0094   15.9   0.1      0.014   15.4   0.1    1.3  1  PadR      Transcriptional regulator PadR-like family
  ------ inclusion threshold ------
      0.015   15.2   0.0      0.026   14.4   0.0    1.5  1  MarR_2    MarR family
       0.12   12.5   0.1        4.1    7.5   0.0    2.2  2  DUF480    Protein of unknown function, DUF480


Domain annotation for each model (and alignments):
>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.6   0.0   3.8e-17   7.6e-14       2      78 ..      24     100 ..      23     102 .. 0.97

  Alignments for each domain:
  == domain 1  score: 51.6 bits;  conditional E-value: 3.8e-17
                         HTH_34   2 RlavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafkkyvkaLks 78 
                                    R+a++++L++v  ++  elk al+ + g L ++l+ Le+ gY++ +k +    prtl+++T++G  a+++  + L+s
  gi|119719861|ref|YP_920356.1|  24 RFAIVTLLYAVGPMTVGELKRALGFSWGDLDSKLRSLEERGYVSARKVLTLAGPRTLVELTEKGVRAYEELRARLRS 100
                                    9********************************************************************99998887 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   1.1e-07   0.00022       3      46 ..      23      67 ..      21      68 .. 0.95

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.1e-07
                                   HHHHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_5  3 tRlkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                   +R  I+ lL   g+++v+el ++lg s + ++  L+ L+e G+V+
  gi|119719861|ref|YP_920356.1| 23 KRFAIVTLLYAvGPMTVGELKRALGFSWGDLDSKLRSLEERGYVS 67
                                   68899****999********************************7 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.1e-06    0.0021      11      58 ..      23      70 ..       6      73 .. 0.90
   2 ?    1.1   0.1      0.21   4.2e+02      22      46 ..      75      99 ..      70     106 .. 0.60

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.1e-06
                                   HHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                         HTH_20 11 vRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvr 58
                                    R +i  +L   +++t++el+++l+ s   l+  Lr Lee g+v  ++
  gi|119719861|ref|YP_920356.1| 23 KRFAIVTLLYAVGPMTVGELKRALGFSWGDLDSKLRSLEERGYVSARK 70
                                   689999999999********************************9887 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.21
                                   CTTB-HHHHHHHHTS-HHH.HHHHHH CS
                         HTH_20 22 aegltaselaerldlsknt.lsyHLr 46
                                   a+++t+ el e + ++  + l+ +Lr
  gi|119719861|ref|YP_920356.1| 75 AGPRTLVELTEKG-VRAYEeLRARLR 99
                                   6677777777765.544444555553 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   1.9e-07   0.00037       2      48 ..      21      67 ..      20      70 .. 0.94

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.9e-07
                                   -HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                           MarR  2 tltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlie 48
                                   ++ +f i+++ly  gp++v eL ++lg s + +   l+ Le++G+++
  gi|119719861|ref|YP_920356.1| 21 NYKRFAIVTLLYAVGPMTVGELKRALGFSWGDLDSKLRSLEERGYVS 67
                                   6789*****************************************97 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   9.7e-07    0.0019      10      72 ..      27      90 ..      18     102 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 9.7e-07
                                   HHHHHTT.S-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEE.EEEESSSS-EEEEEE-TCGGGG CS
                           HxlR 10 ilvellk.gkkRfselkralpkisqkmLaqrLreLeqdglie.revypevPpkveYsltekGrsl 72
                                   i++ l   g++  +elkral + s   L ++Lr Le+ g ++ r+v+   +p+   +ltekG   
  gi|119719861|ref|YP_920356.1| 27 IVTLLYAvGPMTVGELKRAL-GFSWGDLDSKLRSLEERGYVSaRKVLTLAGPRTLVELTEKGVRA 90
                                   45555556999*********.889999************8864899999*************655 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0     3e-06     0.006      16      56 ..      29      70 ..      25      92 .. 0.91
   2 ?   -1.8   0.0       1.5   2.9e+03       5      17 ..      82      94 ..      79      97 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3e-06
                                   HHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                           TrmB 16 aLl.klgpatadeiaeelgvprskvYevLrsLedkGlVerek 56
                                   +Ll + gp+t+ e+ ++lg +     + LrsLe++G+V  +k
  gi|119719861|ref|YP_920356.1| 29 TLLyAVGPMTVGELKRALGFSWGDLDSKLRSLEERGYVSARK 70
                                   677789********************************9887 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.5
                                   HHHHHCCCHCHHH CS
                           TrmB  5 GLseyEakvYlaL 17
                                    L+e  +++Y  L
  gi|119719861|ref|YP_920356.1| 82 ELTEKGVRAYEEL 94
                                   4666667777655 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   6.9e-06     0.014      29      74 ..      48      92 ..      38      93 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 6.9e-06
                                   TTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHHH CS
                           PadR 29 lseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrela 74
                                   +s G l   L++Le+ g+v+++++ +   +pr + +lT++G r+++
  gi|119719861|ref|YP_920356.1| 48 FSWGDLDSKLRSLEERGYVSARKVLT-LAGPRTLVELTEKGVRAYE 92
                                   566777788**************996.8999**********99876 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.3e-05     0.026      13      54 ..      30      69 ..      20      87 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.3e-05
                                   HHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                         MarR_2 13 aLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                    L++ ++  +tvgel r+lg s + +   l+ L+++G+v  r
  gi|119719861|ref|YP_920356.1| 30 LLYAVGP--MTVGELKRALGFSWGDLDSKLRSLEERGYVSAR 69
                                   4666677..9*****************************766 PP

>> DUF480  Protein of unknown function, DUF480
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0021       4.1      87     111 ..      20      44 ..      14      68 .. 0.85
   2 ?    3.3   0.1     0.039        77      97     118 ..      71      92 ..      59     104 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0021
                                    --HHHHHHHHHHHHH-SB-HHHHHH CS
                         DUF480  87 lseaelavlalllLRGpqtageLrt 111
                                    ++ ++ a+++ll   Gp t+geL+ 
  gi|119719861|ref|YP_920356.1|  20 MNYKRFAIVTLLYAVGPMTVGELKR 44 
                                    566889*****************85 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.039
                                    HHHHH-SB-HHHHHHHHTTTS- CS
                         DUF480  97 lllLRGpqtageLrtrserlae 118
                                    +l L Gp+t  eL ++  r +e
  gi|119719861|ref|YP_920356.1|  71 VLTLAGPRTLVELTEKGVRAYE 92 
                                    78899********999988764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 802.53
//
Query:       gi|119719862|ref|YP_920357.1|  [L=196]
Description: hypothetical protein Tpen_0954 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.43    8.8   9.7       0.49    8.6   9.7    1.1  1  YfhO      Bacterial membrane protein YfhO
       0.52    8.5  11.2       0.62    8.3  11.2    1.1  1  DUF2070   Predicted membrane protein (DUF2070)
          2    8.5  12.7       0.14   12.2   1.3    2.7  2  SirB      Invasion gene expression up-regulator, SirB


Domain annotation for each model (and alignments):
>> YfhO  Bacterial membrane protein YfhO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   9.7   8.2e-05      0.49     334     434 ..      46     146 ..      27     184 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 8.2e-05
                           YfhO 334 aPvgfpyRfsfilsflllllaaealk.....elkqlkklkllaailllvlllliilllknkksynfltssqlllglllll 408
                                    +P+ + yR++ +  f+ l+++a+a++     + ++++ ++++a +l  + ++ +++++  +     ++ + l +gl+lll
  gi|119719862|ref|YP_920357.1|  46 FPELWEYRYAVLAGFTALMVVAYAVTsrfasRAPRVEVWRWVASFLAPLPVFYVVAVATGSEA-AAASAWYLYVGLFLLL 124
                                    788899********************555554555589******9999999999997775555.7777777777777777 PP

                           YfhO 409 lalllllllllkkkkkklvllllllv 434
                                    +++ + +     +++k ++++++ ++
  gi|119719862|ref|YP_920357.1| 125 VYVSFGGA----EWSKPFLVASSTML 146
                                    77777662....33333333333333 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3  11.2    0.0001      0.62      31     172 ..      35     180 ..      17     194 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0001
                        DUF2070  31 laflssk............lfgillfglpalvaflltlpvlrilggrltykrs.lflalltelivviisllaillsallq 97 
                                    l+   ++            +  +  f+  ++va ++t+++ + + +   +++   fla l  ++vv+ +  ++ ++a   
  gi|119719862|ref|YP_920357.1|  35 LTGAYFSvvwgfpelweyrYAVLAGFTALMVVAYAVTSRFASRAPRVEVWRWVaSFLAPLPVFYVVA-VATGSEAAA--- 110
                                    3333333444577777777777888888899999999999988866655666644554444444444.333333331... PP

                        DUF2070  98 alvllalvlslalvfalrllvlvavsdesllkavlpaliqpllailllvly.fspesfllllllslifalavylfi 172
                                         a+   +  v  + llv+v++++++++k  l+a+ + l+ +++++++ ++  +++ l++l l++a   ++ i
  gi|119719862|ref|YP_920357.1| 111 ---ASAW---YLYVGLFLLLVYVSFGGAEWSKPFLVASSTMLATYPAVLYLsLARGYAANLVALGLMLASYYAAGI 180
                                    ...1222...444668999**************************9999996444444455555444444333333 PP

>> SirB  Invasion gene expression up-regulator, SirB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.3   2.3e-05      0.14      75     116 ..      63     104 ..      29     108 .. 0.89
   2 ?    0.4   4.4      0.11   6.4e+02      36     114 ..     133     183 ..     108     190 .. 0.44

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.3e-05
                           SirB  75 vllvvyivlgvvalkrakskklrllafvlAlvvflyivslAl 116
                                    +++v+y v + +a +  + + +r++a +lA + ++y+v++A+
  gi|119719862|ref|YP_920357.1|  63 LMVVAYAVTSRFASRAPRVEVWRWVASFLAPLPVFYVVAVAT 104
                                    6789************************************97 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.11
                           SirB  36 kllkilphivdtlLllsgiaLlvllglspftkaWltaKlvllvvyivlgvvalkrakskklrllafvlAlvvflyivsl 114
                                    ++                            +k +l+a  ++l+ y ++ ++ l r+   +l +l+++lA    + i++l
  gi|119719862|ref|YP_920357.1| 133 EW----------------------------SKPFLVASSTMLATYPAVLYLSLARGYAANLVALGLMLASYYAAGIYAL 183
                                    12............................2235555555555555555555544444444444444444444444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       700  (0.0390429); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1420.16
//
Query:       gi|119719863|ref|YP_920358.1|  [L=117]
Description: hypothetical protein Tpen_0955 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0055   16.7   0.0     0.0069   16.4   0.0    1.1  1  Mrr_cat   Restriction endonuclease


Domain annotation for each model (and alignments):
>> Mrr_cat  Restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   3.9e-07    0.0069      14     104 ..      24     111 ..      20     116 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.9e-07
                                    HHHHHHHSSSEEE---B-TTSSB--EEEETTEEEEEEEEEEE--TS-B-HHHHHHHHHHCTTS..SEEEEEESS-..B-H CS
                        Mrr_cat  14 aellealGykeveltgrsgDggiDliakkdplgserilvqaKryknkvgvkeVqeligalkkrgadkgifvttsd..ftk 91 
                                    a+ + + G + vel   ++ g i +ia+ ++   + +++++  + +kvg++ V+ l+  +k  +a+  ++  + +  + +
  gi|119719863|ref|YP_920358.1|  24 ARRYLEAGLS-VELLHPTRHGPIHVIARGNK---QVLAIEVADKPGKVGADRVKLLLEKAKLVKAKPVLVLYSEGafLDE 99 
                                    5566778998.****************9765...89*******99*****************988877777765566889 PP

                                    HHHHHHHTT--EE CS
                        Mrr_cat  92 aAreeaeelnkie 104
                                    +Ar+  ee nk++
  gi|119719863|ref|YP_920358.1| 100 EARKLCEE-NKVK 111
                                    ******99.6554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 838.46
//
Query:       gi|119719864|ref|YP_920359.1|  [L=144]
Description: water stress/hypersensitive response protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-12   47.9   0.0    2.3e-12   47.3   0.0    1.3  1  LEA_2     Late embryogenesis abundant protein


Domain annotation for each model (and alignments):
>> LEA_2  Late embryogenesis abundant protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.3   0.0   1.3e-16   2.3e-12       2     100 ..      55     143 ..      54     144 .] 0.97

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 1.3e-16
                                    EEEEESSSS-EEEEEEEEEEEESSSEEEEEEECE-EEESSSCEEEEEEEEEEEHHHHHHHHHHHH..HCCSEEEEEEEEE CS
                          LEA_2   2 lrvrNPNsfgvrydgleldlsyngqrlasgtspqgfsqpargtttlevpvsvsaddlarelrallagevgleleytlrgr 81 
                                    ++++NP s++ ++d+ e+d++++g+ l++gt pq + +p++ t++++vp + s++ +++ l++++        + t++g+
  gi|119719864|ref|YP_920359.1|  55 IDIYNPGSITATLDRAEFDVYADGTYLGHGTIPQRIDIPPNATRRISVPFEASYAGVLSVLKGQR--------TWTIKGT 126
                                    78***************************************************************........******* PP

                                    EE.EEETTTSCEEEEEEEE CS
                          LEA_2  82 lkvlgkpilgsvtvpvkvs 100
                                    ++ +++p+ g+  vp++v+
  gi|119719864|ref|YP_920359.1| 127 AY-IDTPF-GAIAVPFEVK 143
                                    *9.89999.*******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1051.43
//
Query:       gi|119719865|ref|YP_920360.1|  [L=205]
Description: hypothetical protein Tpen_0957 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1397.21
//
Query:       gi|119719866|ref|YP_920361.1|  [L=629]
Description: AAA ATPase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-44  152.3   0.0    2.2e-44  151.5   0.0    1.4  1  AAA_12           AAA domain
    5.2e-37  128.0   0.0    8.7e-37  127.3   0.0    1.4  1  AAA_11           AAA domain
    6.7e-16   58.6   0.0    2.2e-09   37.3   0.0    2.6  2  AAA_30           AAA domain
    6.3e-14   52.5   3.8    1.2e-11   45.2   0.5    3.4  2  AAA_19           AAA domain
      3e-11   43.5   0.2    3.2e-05   23.8   0.0    3.2  3  Viral_helicase1  Viral (Superfamily 1) RNA helicase
    1.5e-05   24.7   0.0    4.2e-05   23.3   0.0    1.8  1  UvrD_C_2         UvrD-like helicase C-terminal domain
    1.8e-05   24.4   0.3     0.0045   16.6   0.1    2.4  2  UvrD-helicase    UvrD/REP helicase N-terminal domain
    2.9e-05   23.8   0.0    9.3e-05   22.1   0.0    1.9  1  SRP54            SRP54-type protein, GTPase domain
    4.6e-05   23.9   0.3    0.00015   22.2   0.3    2.0  1  AAA_16           AAA ATPase domain
    5.1e-05   23.7   0.1    0.00031   21.2   0.0    2.4  2  AAA              ATPase family associated with various cellul
      8e-05   23.2   0.0    0.00015   22.3   0.0    1.5  1  ABC_tran         ABC transporter
    0.00012   22.3   0.0    0.00049   20.3   0.0    2.2  1  AAA_33           AAA domain
    0.00033   20.1   0.0      0.074   12.4   0.0    2.6  3  UvrD_C           UvrD-like helicase C-terminal domain
    0.00036   20.0   0.0     0.0072   15.8   0.0    2.5  2  PhoH             PhoH-like protein
    0.00039   20.7   1.2     0.0025   18.1   0.4    2.7  1  AAA_22           AAA domain
     0.0015   18.5   0.0     0.0071   16.4   0.0    2.1  2  ResIII           Type III restriction enzyme, res subunit
     0.0022   17.6   0.0     0.0076   15.9   0.0    1.9  1  AAA_25           AAA domain
     0.0022   18.1   0.3     0.0072   16.4   0.3    1.9  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
     0.0026   16.8   0.6     0.0095   14.9   0.1    2.0  2  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
     0.0032   16.7   0.7      0.047   12.9   0.1    2.7  3  ArsA_ATPase      Anion-transporting ATPase
     0.0043   16.9   0.3       0.32   10.8   0.0    2.6  2  Helicase_RecD    Helicase
     0.0047   16.9   0.0       0.03   14.3   0.0    2.2  2  ATPase_2         ATPase domain predominantly from Archaea
     0.0051   16.8   0.6      0.016   15.2   0.0    2.1  2  AAA_5            AAA domain (dynein-related subfamily)
     0.0052   16.7   0.2      0.041   13.8   0.2    2.2  1  AAA_31           AAA domain
     0.0054   15.9   0.0      0.058   12.6   0.0    2.1  2  PIF1             PIF1-like helicase
      0.006   16.5   0.0      0.012   15.5   0.0    1.4  1  Rad17            Rad17 P-loop domain
     0.0083   15.9   0.0      0.019   14.7   0.0    1.5  1  IstB_IS21        IstB-like ATP binding protein
  ------ inclusion threshold ------
       0.01   14.9   0.1      0.019   14.0   0.1    1.3  1  T2SSE            Type II/IV secretion system protein
      0.012   15.6   0.1      0.038   13.9   0.0    1.9  1  NACHT            NACHT domain
      0.012   15.5   2.4      0.029   14.3   0.2    2.6  2  NTPase_1         NTPase
      0.013   15.0   0.0      0.029   13.9   0.0    1.5  1  AAA_7            P-loop containing dynein motor region
      0.014   14.7   0.3        1.1    8.4   0.0    2.8  3  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.014   14.3   0.0      0.028   13.4   0.0    1.4  1  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
      0.021   15.1   0.2      0.087   13.1   0.1    2.2  1  AAA_28           AAA domain
      0.021   15.4   0.2      0.091   13.3   0.3    2.2  1  AAA_18           AAA domain
      0.022   14.1   0.0      0.052   12.8   0.0    1.6  1  Zeta_toxin       Zeta toxin
      0.037   13.4   0.0      0.098   12.0   0.0    1.7  1  ATPase           KaiC
      0.038   13.7   0.0       0.21   11.3   0.0    2.1  2  AAA_24           AAA domain
      0.097   12.6   0.1        0.3   11.0   0.0    1.9  1  MobB             Molybdopterin guanine dinucleotide synthesis
       0.12   11.2   1.0       0.17   10.7   1.0    1.1  1  Apt1             Golgi-body localisation protein domain
       0.13   12.3   0.0       0.32   11.0   0.0    1.6  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.14   11.5   0.0       0.49    9.7   0.0    1.8  2  Mg_chelatase     Magnesium chelatase, subunit ChlI


Domain annotation for each model (and alignments):
>> AAA_12  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.5   0.0   5.1e-47   2.2e-44       7     198 ..     413     599 ..     409     600 .. 0.90

  Alignments for each domain:
  == domain 1  score: 151.5 bits;  conditional E-value: 5.1e-47
                         AAA_12   7 erllkke.....kekvvlLdtqYRmhpeIsrfpsklfYkgkLkdaesvkkrele...aqealeepleplvfidvekseee 78 
                                     rl++ +       ++  L+  YR+hp+I+ f+ +++Y+gk+k a++ k+++l     + ++ ep +p+++i+v+++ee+
  gi|119719866|ref|YP_920361.1| 413 TRLMRFYgekggYPRTLWLRKSYRSHPDIVGFAARYVYEGKIKPAAKPKEKTLAlspGYPDFLEPRKPFTLIHVDSQEER 492
                                    555555555566677889****************************9999999877778899999999******988888 PP

                         AAA_12  79 kekkeksyiNeeEaelvvklvekllkkgseeerkkigvitpYraqvellkkklkekeeeksekeievntvdgfQGrekdv 158
                                    +     s iNe+Ea+++ +lv++l+k+g+ +  ++igvitpYraq + +k+ l+         ++evntvd+fQGrekdv
  gi|119719866|ref|YP_920361.1| 493 RG---GSRINEAEARVCYELVDALTKHGVPQ--EEIGVITPYRAQRSRIKEYLQG---F----NVEVNTVDAFQGREKDV 560
                                    87...69************************..9********************3...2....399************** PP

                         AAA_12 159 iilslVRsnekkeigflkderrlNValTRAkskliivGnk 198
                                    +i+sl  + ++ +++f +d++rlNVa+TRA++kl+ v n+
  gi|119719866|ref|YP_920361.1| 561 VIFSLTAT-REDSLAFAADANRLNVAITRARKKLLFVANA 599
                                    *****988.567789*********************9986 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.3   0.0     2e-39   8.7e-37       2     260 ..     173     399 ..     172     400 .. 0.91

  Alignments for each domain:
  == domain 1  score: 127.3 bits;  conditional E-value: 2e-39
                         AAA_11   2 lndsqreaiksalsese..itliqGPPGtgKTktivellsqllsrrkseeeksakpriLvCapSNaAvDellerllrgll 79 
                                    l++sq + ++ al+ +e  + l+ GPPGtgKT+ti+++ ++l         +++++r+L+++++N AvD+ + +l     
  gi|119719866|ref|YP_920361.1| 173 LDESQSRVVNAALELEEgeVLLVVGPPGTGKTTTIAGIAEKL---------AERGERVLISSHTNRAVDNAVGKLPI--- 240
                                    899******8877666556***********************.........89*********************866... PP

                         AAA_11  80 dsegekykpkivRvgneeeriseavksvsleekvekrlekeekaqlakeiskeleklakelrafeeeeekeklkkskeks 159
                                              +vRvg++e ++ ++++++ l++kv++ l ++       ++++++++l +++r          l+ +++ +
  gi|119719866|ref|YP_920361.1| 241 --------DFTVRVGRPE-KVLREIEPYLLSYKVKSALGER-----YADLQERINELLETIRIHRG-----YLRGKDRST 301
                                    ........579*******.9******************774.....66777778888888865544.....478889999 PP

                         AAA_11 160 kskleqerrklkkerkelskeleeaeesleeevldeaeivltTlsgagsklleklakkfdvviIDEAaqavEpstliPlr 239
                                     s le+++r++++e +el +e ++  e++++evl  a++v +Tl +++   l+++   fd+viIDEA+q   + +l ++ 
  gi|119719866|ref|YP_920361.1| 302 FSLLERSLREHERELRELLEERRKLIEEVQSEVLGGARVVGSTLIKSQLYPLRDY--PFDTVIIDEASQVSVTLALLAMV 379
                                    9999999999999999999************************************..9********************** PP

                         AAA_11 240 lgakkvvLvGDpkQLpatvis 260
                                    +g +k + vGD+kQL ++  s
  gi|119719866|ref|YP_920361.1| 380 KG-RKWIVVGDHKQLLPIFRS 399
                                    **.************998766 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.0   5.2e-12   2.2e-09       2      61 ..     173     233 ..     172     267 .. 0.90
   2 !   18.5   0.0   2.9e-06    0.0012      88     140 ..     357     405 ..     314     457 .. 0.80

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 5.2e-12
                         AAA_30   2 lnaeQaaaveallt.sgdrvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkv 61 
                                    l+++Q+++v+a+l+ ++  v +++Gp+GtGKtt++++++e ++++g+rv++ ++t++a ++
  gi|119719866|ref|YP_920361.1| 173 LDESQSRVVNAALElEEGEVLLVVGPPGTGKTTTIAGIAEKLAERGERVLISSHTNRAVDN 233
                                    8999*****9998734557***************************************987 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 2.9e-06
                         AAA_30  88 pgtllivDEagmvdtkqlaallkaaekagakvilvGDerQlasVeaGgvlrdl 140
                                    p + +i+DEa+ v+ +   all+ +  +g k i+vGD++Ql ++ + +v r+ 
  gi|119719866|ref|YP_920361.1| 357 PFDTVIIDEASQVSVTL--ALLAMV--KGRKWIVVGDHKQLLPIFRSEVAREE 405
                                    4589*********9764..677777..479**************999988765 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2   0.5   2.8e-14   1.2e-11       7     146 .]     187     398 ..     180     398 .. 0.68
   2 ?    5.0   0.0     0.067        29      33      78 ..     512     565 ..     503     620 .. 0.72

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 2.8e-14
                         AAA_19   7 alkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae.................. 68 
                                      + +vllv+++pGtGKT+++ +i + l e+g    e++l+ + t+rA+++   +l     +                  
  gi|119719866|ref|YP_920361.1| 187 LEEGEVLLVVGPPGTGKTTTIAGIAEKLAERG----ERVLISSHTNRAVDNAVGKL-----Pidftvrvgrpekvlreie 257
                                    5567899*************************....89************999887.....4112234555555555555 PP

                         AAA_19  69 .....atTiHrlal.................................................................l 78 
                                                                                                                   +
  gi|119719866|ref|YP_920361.1| 258 pyllsY-------KvksalgeryadlqerinelletirihrgylrgkdrstfsllerslreherelrelleerrklieeV 330
                                    555550.......0555555555556666666666666666677888888888888888888877766665554444440 PP

                         AAA_19  79 dfddlltealelle...............eaeeekklqeee..llivDEfqdvdelqyrLlkallgekkklllvGDpdQl 141
                                                 +               + ++  +l++    ++i+DE+++v+    +Ll  ++g+k   ++vGD++Ql
  gi|119719866|ref|YP_920361.1| 331 -------------QsevlggarvvgstliK-SQLYPLRDYPfdTVIIDEASQVSV-TLALLAMVKGRK--WIVVGDHKQL 393
                                    .............04444466666665542.3344554433359*********84.567999988554..69******** PP

                         AAA_19 142 iyvfr 146
                                     + fr
  gi|119719866|ref|YP_920361.1| 394 LPIFR 398
                                    99986 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.067
                         AAA_19  33 llvelggvkpeeillvaftgrAakelrerlaalgaeatTiHrlal.........l 78 
                                     l + +gv+ eei ++++ +   ++++e l+++++e +T+ ++           l
  gi|119719866|ref|YP_920361.1| 512 ALTK-HGVPQEEIGVITPYRAQRSRIKEYLQGFNVEVNTVDAFQGrekdvvifsL 565
                                    4444.55899*****************************9988444444444441 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.036        16       2      22 ..     194     214 ..     193     249 .. 0.72
   2 !   10.9   0.0   0.00065      0.28      51     100 ..     347     393 ..     316     407 .. 0.83
   3 !   23.8   0.0   7.4e-08   3.2e-05     175     233 ..     538     596 ..     483     597 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.036
                Viral_helicase1   2 vvhGvpGcGKStlirkllrts 22 
                                    +v G pG GK+t i  ++++ 
  gi|119719866|ref|YP_920361.1| 194 LVVGPPGTGKTTTIAGIAEKL 214
                                    78899*********9998874 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00065
                Viral_helicase1  51 dsflmalvkstkgkililDEylllhaGyill.laalskaklvilfGDplQi 100
                                    +s l +l +   ++++i+DE+ ++    + l l+a+ k +  i++GD++Q 
  gi|119719866|ref|YP_920361.1| 347 KSQLYPLRDY-PFDTVIIDEASQVS---VTLaLLAMVKGRKWIVVGDHKQL 393
                                    5555555554.79***********9...555599****************6 PP

  == domain 3  score: 23.8 bits;  conditional E-value: 7.4e-08
                Viral_helicase1 175 alkealgvrevttvhevqGltfdkVtlvllketdle.lisesrenllvAlTRhrkslvil 233
                                    + ++  +v ev+tv   qG + d+V++ l+ + +++ +++++ + l vA+TR+rk+l+++
  gi|119719866|ref|YP_920361.1| 538 EYLQGFNV-EVNTVDAFQGREKDVVIFSLTATREDSlAFAADANRLNVAITRARKKLLFV 596
                                    33334444.5***************9988854443304458899999**********997 PP

>> UvrD_C_2  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   9.9e-08   4.2e-05       5      52 .]     548     596 ..     544     596 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 9.9e-08
                       UvrD_C_2   5 ltihkaQGsefpaVivfdpdlaaarmgel....rrrlLYtavTRAreklilv 52 
                                     t+  +QG e ++Vi+   +l+a r++ l     ++ L +a+TRAr+kl  v
  gi|119719866|ref|YP_920361.1| 548 NTVDAFQGREKDVVIF---SLTATREDSLafaaDANRLNVAITRARKKLLFV 596
                                    599*************...65555656678999***************9876 PP

>> UvrD-helicase  UvrD/REP helicase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1     1e-05    0.0045       8      59 ..     184     232 ..     178     286 .. 0.86
   2 ?    5.2   0.0     0.029        12     257     300 ..     358     398 ..     348     402 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1e-05
                                    HHHS.-SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHHHH CS
                  UvrD-helicase   8 aias.lggpilveAsAGsGKTfvlaerilrlikeeeiepdrilvvTFTnkAae 59 
                                    a++   g+ +lv+  +G+GKT+++a  i+++++e+    +r+l++  Tn+A +
  gi|119719866|ref|YP_920361.1| 184 ALELeEGEVLLVVGPPGTGKTTTIAG-IAEKLAER---GERVLISSHTNRAVD 232
                                    556646777899999*********87.78888888...69**********976 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.029
                                    SSEEEESSGGG-BHHHHHHHHHHHTTTTTEEEEE-GGG--GGGG CS
                  UvrD-helicase 257 ykeiliDEyQDTnkiQyrilkllasgheelfmvGDpkQsIYgFR 300
                                    ++++ iDE+ + + +  ++l ++  ++   ++vGD kQ    FR
  gi|119719866|ref|YP_920361.1| 358 FDTVIIDEASQVSVT-LALLAMVKGRK--WIVVGDHKQLLPIFR 398
                                    8999****9888755.56788887775..9********865555 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   2.2e-07   9.3e-05       3      36 ..     192     225 ..     190     233 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 2.2e-07
                                    EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE CS
                          SRP54   3 villvGlqGaGKTttlaKLaallkkegkkvllva 36 
                                    v+l+vG+ G+GKTtt+a +a++l ++g++vl+ +
  gi|119719866|ref|YP_920361.1| 192 VLLVVGPPGTGKTTTIAGIAEKLAERGERVLISS 225
                                    89***************************99865 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.3   3.5e-07   0.00015      13      63 ..     182     230 ..     171     334 .. 0.73

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 3.5e-07
                         AAA_16  13 lsalervrsgrpelvllsGesGvGKsslvrellralekdg.giflrgkcdql 63 
                                    ++ale + +g  e++l++G++G+GK++ +  +++ l ++g  ++++ ++ + 
  gi|119719866|ref|YP_920361.1| 182 NAALE-LEEG--EVLLVVGPPGTGKTTTIAGIAEKLAERGeRVLISSHTNRA 230
                                    44444.5555..89*************************7566677776655 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   7.3e-07   0.00031       1      29 [.     193     221 ..     193     292 .. 0.72
   2 ?   -1.5   0.0       7.1     3e+03      91     127 ..     548     585 ..     521     590 .. 0.63

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 7.3e-07
                                    EEEESSTTSSHHHHHHHHHHHHTHEEEEE CS
                            AAA   1 vllyGppGtGKTllakavakelgveflei 29 
                                    +l++GppGtGKT+++  +a++l  +  ++
  gi|119719866|ref|YP_920361.1| 193 LLVVGPPGTGKTTTIAGIAEKLAERGERV 221
                                    699******************95332222 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 7.1
                                    HHHHHTTTSSST.EEEEEEESSGGGSTHHHHSTTSSEE CS
                            AAA  91 teldgvkkkesk.vivigatnrpdkldpallrgRfdrk 127
                                    + +d ++ +e++ vi+ ++++r+d+l  a   +R+++ 
  gi|119719866|ref|YP_920361.1| 548 NTVDAFQGREKDvVIFSLTATREDSLAFAADANRLNVA 585
                                    45556666544405566777889988766655666655 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   3.5e-07   0.00015       3      48 ..     182     227 ..     180     316 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 3.5e-07
                                    EEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   3 nvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkd 48 
                                    n  l+l+ege++ +vG+ G+GK+t ++ +a++l    +++l+ ++ 
  gi|119719866|ref|YP_920361.1| 182 NAALELEEGEVLLVVGPPGTGKTTTIAGIAEKLAERGERVLISSHT 227
                                    67899****************************9999999777543 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   1.1e-06   0.00049       1      33 [.     192     261 ..     192     327 .. 0.67

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.1e-06
                         AAA_33   1 lvllvGlpGsGKstlaerllkklg....avllssdt.................................l 33 
                                    ++l+vG+pG+GK+t + ++++kl+     vl+ss t                                 l
  gi|119719866|ref|YP_920361.1| 192 VLLVVGPPGTGKTTTIAGIAEKLAergeRVLISSHTnravdnavgklpidftvrvgrpekvlreiepylL 261
                                    789****************999999988888999987766666666666666666666664444444431 PP

>> UvrD_C  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       3.5   1.5e+03     213     233 ..     272     306 ..     112     335 .. 0.68
   2 !   12.4   0.0   0.00017     0.074       3     105 ..     431     553 ..     429     561 .. 0.92
   3 ?    4.7   0.1     0.038        16     329     346 ..     580     597 ..     564     600 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3.5
                                    xxxxxxxxxxxxxxxxxxxx..............x RF
                         UvrD_C 213 lfkelaeklaelkekseskr..............k 233
                                     ++ l+e ++el e+   +r              +
  gi|119719866|ref|YP_920361.1| 272 RYADLQERINELLETIRIHRgylrgkdrstfsllE 306
                                    33333333333333333333333333333333320 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00017
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx...................xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         UvrD_C   3 LekNyRStksLlkaankflenilnrrale.kek...................ktvekgekivvleaeteeeEaekiaati 62 
                                    L k yRS + +++ a +++ + + ++a + kek                     + ++++ +   ++ +e Ea+  ++++
  gi|119719866|ref|YP_920361.1| 431 LRKSYRSHPDIVGFAARYVYEGKIKPAAKpKEKtlalspgypdfleprkpftLIHVDSQEERRGGSRINEAEARVCYELV 510
                                    7788***************88888866666777899***********999999999999999999*************** PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         UvrD_C  63 kallekneklediavLvRsnkdadkiskaLkkegipfnvvdee 105
                                     al ++   +e+i v++   ++   i++ L+  ++++n+vd +
  gi|119719866|ref|YP_920361.1| 511 DALTKHGVPQEEIGVITPYRAQRSRIKEYLQGFNVEVNTVDAF 553
                                    ****************************************976 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.038
                                    xxxxxxxxxxxxxxxxxx RF
                         UvrD_C 329 RlfYVaiTRAkkrLfisy 346
                                    + + VaiTRA+k+L + +
  gi|119719866|ref|YP_920361.1| 580 NRLNVAITRARKKLLFVA 597
                                    5567********997654 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.7e-05    0.0072       7      77 ..     175     247 ..     171     298 .. 0.73
   2 ?    1.2   0.0       0.5   2.1e+02     123     157 ..     361     392 ..     354     404 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.7e-05
                                    HHHHHHHHHHH...H-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--T.T----SS--------- CS
                           PhoH   7 keQkeylealk...kndivfaiGpaGtGKtylavalavealkkkkvkriiltrpavea.geelGflpgdleekvd 77 
                                    ++Q+++++a     + +++ ++Gp GtGKt   + ++++   +++ +r++++  +  a ++ +G lp d + +v 
  gi|119719866|ref|YP_920361.1| 175 ESQSRVVNAALeleEGEVLLVVGPPGTGKTT--TIAGIAEKLAERGERVLISSHTNRAvDNAVGKLPIDFTVRVG 247
                                    67888877644355888*************6..556666666666677777666665449*******99887665 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.5
                                    EEE-SGGG--HHHHHHHHTTB-TT-EEEEEE---- CS
                           PhoH 123 vilDEAQnttkeqmkmfltRlGenskvvvtGdvtq 157
                                    vi+DEA  ++   +   l  + ++ k +v+Gd +q
  gi|119719866|ref|YP_920361.1| 361 VIIDEASQVS---VTLALLAMVKGRKWIVVGDHKQ 392
                                    999**97765...556777788999*******998 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.4   5.9e-06    0.0025       5      34 ..     190     219 ..     186     393 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 5.9e-06
                         AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeak 34 
                                      +l+v+G++GtGKTt+++ ++e+l e+ +
  gi|119719866|ref|YP_920361.1| 190 GEVLLVVGPPGTGKTTTIAGIAEKLAERGE 219
                                    6789********************976533 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.7e-05    0.0071       3     140 ..     172     365 ..     170     370 .. 0.59
   2 ?   -1.9   0.0         7     3e+03      53      82 ..     589     618 ..     581     626 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.7e-05
                                    EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHG........ CS
                         ResIII   3 elreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleef........ 74 
                                    +l e Q +++++ l +l  ++ + +l++ + GtGKT ++a ++e+l++ g+  ++l+  +++  ++ +  ++        
  gi|119719866|ref|YP_920361.1| 172 RLDESQSRVVNAAL-EL--EEGEVLLVVGPPGTGKTTTIAGIAEKLAERGE--RVLISSHTNRAVDNAVGKLpidftvrv 246
                                    56677888887777.44..5778899**********************866..999988888877777765555556666 PP

                                    ...................GGGTGG....GEEEESSS-B--............................-SEEEEEHHHH CS
                         ResIII  75 ...................kkflseaykeigkkvsgdkkka.....................kekdstnkkilvttiqsl 114
                                                       k+ l e y++ ++ +++  +++                      ++++ + + l+++  +l
  gi|119719866|ref|YP_920361.1| 247 grpekvlreiepyllsykvKSALGERYADLQERINELLETIrihrgylrgkdrstfsllersLREHERELRELLEERRKL 326
                                    66666666665555555553333333333222222222222233333333333345555555555555555555555555 PP

                                    HHTH.....................HHHTTT-SEEEEET CS
                         ResIII 115 dadseee.............eeeseellrdrfdviiiDE 140
                                     ++ ++e             +++   l++  fd +iiDE
  gi|119719866|ref|YP_920361.1| 327 IEEVQSEvlggarvvgstliKSQLYPLRDYPFDTVIIDE 365
                                    555555566666666666555555555555556666666 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 7
                                    ...-EEEEESSHHHHHHHHHHGGGGTGG.. CS
                         ResIII  53 keekflflvprkslleqtleefkkflseay 82 
                                     ++k lf+++ + +    l+e+++++++++
  gi|119719866|ref|YP_920361.1| 589 ARKKLLFVANANVMEHGILKEIREWAKKKK 618
                                    456999999999999999999988888775 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.8e-05    0.0076      30      65 ..     187     223 ..     173     233 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.8e-05
                         AAA_25  30 lpagelallaGapgtGKttlaldlalava.tGkpwlg 65 
                                    l +ge+ l++G+pgtGKtt    +a ++a +G+ +l 
  gi|119719866|ref|YP_920361.1| 187 LEEGEVLLVVGPPGTGKTTTIAGIAEKLAeRGERVLI 223
                                    579**********************999999988776 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.3   1.7e-05    0.0072       9      32 ..     200     223 ..     193     335 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.7e-05
                                    TSSHHHHHHHHHHHHHHTT--EEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxx RF
                           CbiA   9 GvGKTtlaanLaralarrglrVll 32 
                                    G+GKTt+ a++a  la+rg rVl 
  gi|119719866|ref|YP_920361.1| 200 GTGKTTTIAGIAEKLAERGERVLI 223
                                    9*********************96 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   2.2e-05    0.0095      29      62 ..     190     223 ..     169     232 .. 0.84
   2 ?   -0.9   0.1       1.6   6.7e+02     212     259 ..     274     321 ..     264     331 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.2e-05
                                    SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEE CS
                           MeaB  29 aqvvGltGvPGaGkstlvealglelrrrGkrvav 62 
                                     +v+ + G PG+Gk t++  ++++l++rG+rv +
  gi|119719866|ref|YP_920361.1| 190 GEVLLVVGPPGTGKTTTIAGIAEKLAERGERVLI 223
                                    5677899************************966 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.6
                                    CCCTBSHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHH CS
                           MeaB 212 avegeGidelvdaieehrevlkktGllekrrrerakeelrelvedell 259
                                    a+ +e i+el+++i+ hr +l+   + +    er+ +e  +  ++ l 
  gi|119719866|ref|YP_920361.1| 274 ADLQERINELLETIRIHRGYLRGKDRSTFSLLERSLREHERELRELLE 321
                                    7788999************99988777666666665555554444444 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.1   0.00011     0.047       3      36 ..     192     225 ..     190     230 .. 0.92
   2 ?   -0.4   0.0       1.2   5.2e+02     176     231 ..     269     320 ..     238     332 .. 0.75
   3 ?   -0.1   0.0      0.96   4.1e+02     124     152 ..     357     386 ..     343     403 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
                                    EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE CS
                    ArsA_ATPase   3 vilvgGKGGVGKttvsaatavklsekgkkvllis 36 
                                    v+lv G  G GKtt  a +a kl+e g++vl+ s
  gi|119719866|ref|YP_920361.1| 192 VLLVVGPPGTGKTTTIAGIAEKLAERGERVLISS 225
                                    7899999************************966 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.2
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHTSTTTEEEEEEEESSHHHHHHHHHHHHHHH CS
                    ArsA_ATPase 176 ggvsieealeeleetkeeikkveeiltdpertsfrlVvipEklslkEteRaikeLk 231
                                     g    +  e+++e +e+i+  +  l  ++r++f l     + sl+E eR ++eL 
  gi|119719866|ref|YP_920361.1| 269 LGERYADLQERINELLETIRIHRGYLRGKDRSTFSLL----ERSLREHERELRELL 320
                                    3344445778899999999999999999999999997....458999999888875 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.96
                                    SSSEEEEESBS.CCHTCGGGGHHHHHHHHH CS
                    ArsA_ATPase 124 eydvvvlDtaP.TGhtlrllslpevlekll 152
                                     +d+v++D a     tl ll +++  ++++
  gi|119719866|ref|YP_920361.1| 357 PFDTVIIDEASqVSVTLALLAMVKGRKWIV 386
                                    69******99725789****9999888865 PP

>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   0.00075      0.32       2      43 ..     195     235 ..     194     251 .. 0.89
   2 ?    3.5   0.0      0.14        58      91     107 ..     358     374 ..     301     388 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00075
                  Helicase_RecD   2 ltAdRGRGKSaalGlalaaliaegksnilvtapskenvktlf 43 
                                    + + +G+GK+++++ ++++l+++g+ ++l+++ ++++v++ +
  gi|119719866|ref|YP_920361.1| 195 VVGPPGTGKTTTIAGIAEKLAERGE-RVLISSHTNRAVDNAV 235
                                    56889*****************998.9*********998765 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.14
                  Helicase_RecD  91 adllvvDEAAaiplpll 107
                                     d++++DEA+++ ++l 
  gi|119719866|ref|YP_920361.1| 358 FDTVIIDEASQVSVTLA 374
                                    499********998863 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       3.9   1.6e+03     160     180 ..      72      92 ..      68     103 .. 0.82
   2 !   14.3   0.0     7e-05      0.03      12      68 ..     182     237 ..     177     292 .. 0.63

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 3.9
                       ATPase_2 160 vviclsSeglfiervynesel 180
                                    vv+ ++Se+l+ e vy++  +
  gi|119719866|ref|YP_920361.1|  72 VVLDATSETLIVENVYRKRLQ 92 
                                    67889**********998655 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 7e-05
                       ATPase_2  12 eeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldef 68 
                                    +  le e+ e++++ Gp g GKt+ +  i+e+l + +++v+ +++  +++ +++  +
  gi|119719866|ref|YP_920361.1| 182 NAALELEEGEVLLVVGPPGTGKTTTIAGIAEKLAERGERVL-ISSHTNRAVDNAVGK 237
                                    66789999*************************99997554.555444444444444 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   3.8e-05     0.016       2      38 ..     193     229 ..     192     236 .. 0.89
   2 ?   -2.0   0.1       7.7   3.3e+03      84      96 ..     315     327 ..     273     343 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.8e-05
                                    EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--H CS
                          AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtte 38 
                                    +l+vGppGtgK++ +  +a+ l  + e v++++ t++
  gi|119719866|ref|YP_920361.1| 193 LLVVGPPGTGKTTTIAGIAEKLAERGERVLISSHTNR 229
                                    689*******************888888888888765 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 7.7
                                    HHHHHHHSSEEE. CS
                          AAA_5  84 sLlslleerrlll 96 
                                    +L  lleerr l+
  gi|119719866|ref|YP_920361.1| 315 ELRELLEERRKLI 327
                                    4445555555555 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.2   9.6e-05     0.041      12      36 ..     200     224 ..     198     393 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9.6e-05
                         AAA_31  12 GvGKTTtsvnlaaalaklgkkvLlv 36 
                                    G GKTTt   +a+ la++g++vL+ 
  gi|119719866|ref|YP_920361.1| 200 GTGKTTTIAGIAEKLAERGERVLIS 224
                                    89*********************84 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   0.00014     0.058       2      56 ..     173     224 ..     172     232 .. 0.85
   2 ?    0.8   0.0      0.51   2.2e+02     141     159 ..     381     399 ..     372     408 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00014
                                    --HHHHHHHHHH......HCTS-EEEEESTTSSCHHHHHHHHHHCHCTCCCEEEE CS
                           PIF1   2 LneeQkkvfdaiieavlnekgklfFvtGsgGtgKtflwkallkklrsegkivlav 56 
                                    L e+Q +v++a+   +  e+g+++ v G  GtgKt     + +kl ++g+ vl  
  gi|119719866|ref|YP_920361.1| 173 LDESQSRVVNAA---LELEEGEVLLVVGPPGTGKTTTIAGIAEKLAERGERVLIS 224
                                    556677776666...5569********************************9975 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.51
                                    C-EEEEE--TTS-----SS CS
                           PIF1 141 GktvvlgGDfrQilPviek 159
                                    G   ++ GD +Q+lP+ + 
  gi|119719866|ref|YP_920361.1| 381 GRKWIVVGDHKQLLPIFRS 399
                                    6667889********9864 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   2.8e-05     0.012      31      70 ..     176     215 ..     169     237 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.8e-05
                          Rad17  31 vkewlkadvLesrkkriLLisGPsGCgkstvvkvLskelg 70 
                                     +  +    Le ++ ++LL+ GP+G gk+t++  ++ +l+
  gi|119719866|ref|YP_920361.1| 176 SQSRVVNAALELEEGEVLLVVGPPGTGKTTTIAGIAEKLA 215
                                    5566666788888899****************98887765 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   4.4e-05     0.019      44      80 ..     187     223 ..     159     232 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.4e-05
                      IstB_IS21  44 iekkenivllGpsGvGKshlaialgveavraglsvlf 80 
                                    +e+ e ++++Gp+G+GK+   + ++ + +++g +vl 
  gi|119719866|ref|YP_920361.1| 187 LEEGEVLLVVGPPGTGKTTTIAGIAEKLAERGERVLI 223
                                    688999***************************9985 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   4.5e-05     0.019     110     161 ..     173     222 ..     150     228 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.5e-05
                          T2SSE 110 aeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeinksderiv 161
                                     +e+++  ++++l+    e  ++lv G+ g+GKtt++  + ++++++ er++
  gi|119719866|ref|YP_920361.1| 173 LDESQSRVVNAALELE--EGEVLLVVGPPGTGKTTTIAGIAEKLAERGERVL 222
                                    4444444455555544..77899*********************99988876 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   8.8e-05     0.038       2      28 ..     192     218 ..     191     225 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8.8e-05
                                    CEEEEC-TTTCHHHHHHHHHHHHCTS- CS
                          NACHT   2 lvilqGeaGsGKTtLlqklalawaegk 28 
                                    ++++ G++G GKTt ++++a+++ae+ 
  gi|119719866|ref|YP_920361.1| 192 VLLVVGPPGTGKTTTIAGIAEKLAERG 218
                                    789*********************975 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.2   6.7e-05     0.029       2      30 ..     193     221 ..     192     223 .. 0.90
   2 ?   -0.5   0.0       2.4     1e+03      39      77 ..     499     542 ..     495     576 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.7e-05
                                    EEEE--TTSSHHHHHHHHHHHH...GGGE CS
                       NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkv 30 
                                    +++ GppG+GKtT +  ++e+l+++g +v
  gi|119719866|ref|YP_920361.1| 193 LLVVGPPGTGKTTTIAGIAEKLAERGERV 221
                                    5789*******************999766 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 2.4
                                    -------EEEEEET.T--EEEEEETT.....---SSEETTEEE- CS
                       NTPase_1  39 reggrrigFkivdlasgeegiLarve.....akreprvgkyvvd 77 
                                     e + r+++++vd  +++  +  + +       ++ r+++y   
  gi|119719866|ref|YP_920361.1| 499 NEAEARVCYELVDALTKHGVPQEEIGvitpyRAQRSRIKEYLQG 542
                                    56778888888888888888777777665554555555555433 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   6.8e-05     0.029      30      59 ..     187     216 ..     176     233 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.8e-05
                          AAA_7  30 lknkkpvllvGptGtGKtviikdllkkldk 59 
                                    l+++  +l+vGp GtGKt++i  + +kl +
  gi|119719866|ref|YP_920361.1| 187 LEEGEVLLVVGPPGTGKTTTIAGIAEKLAE 216
                                    56778899***************9999984 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0    0.0026       1.1       2      37 ..     191     224 ..     190     256 .. 0.79
   2 ?   -1.1   0.0         2   8.6e+02      78      99 ..     347     368 ..     301     396 .. 0.71
   3 ?    2.9   0.0      0.12        53     330     358 ..     558     594 ..     535     598 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0026
                        DUF2075   2 avvlVtGvaGtGKtvvllnllaeleddeeertavyl 37 
                                    +v+lV G +GtGKt     ++ +l   e+++++ + 
  gi|119719866|ref|YP_920361.1| 191 EVLLVVGPPGTGKTTTIAGIAEKL--AERGERVLIS 224
                                    589*************99999999..4444444333 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2
                        DUF2075  78 kkaeekkeepkedvvivDEAhr 99 
                                    k++    ++ ++d vi+DEA  
  gi|119719866|ref|YP_920361.1| 347 KSQLYPLRDYPFDTVIIDEASQ 368
                                    4445556677899******965 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.12
                        DUF2075 330 k........kkeseekaqkllkNayrVLLtRGrkGly 358
                                    k         ++++++a     N+++V +tR+rk l+
  gi|119719866|ref|YP_920361.1| 558 KdvvifsltATREDSLAFAADANRLNVAITRARKKLL 594
                                    3445555556778888999999***********9876 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   6.5e-05     0.028      16      50 ..     191     225 ..     181     233 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.5e-05
                  TrwB_AAD_bind  16 qhilivGttGsGKtqalekllrairargdraivlD 50 
                                    + +l+vG  G+GKt+++ ++ +++ +rg+r+++  
  gi|119719866|ref|YP_920361.1| 191 EVLLVVGPPGTGKTTTIAGIAEKLAERGERVLISS 225
                                    446789**************************965 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1    0.0002     0.087       4      26 ..     195     221 ..     192     235 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.0002
                         AAA_28   4 itGgestGKTtll....eaLaargypv 26 
                                    ++G+++tGKTt++    e+La+rg +v
  gi|119719866|ref|YP_920361.1| 195 VVGPPGTGKTTTIagiaEKLAERGERV 221
                                    79**********944445555667665 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.3   0.00021     0.091       2      39 ..     194     229 ..     193     336 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00021
                         AAA_18   2 lltGtpGvGKttlakeLskrlgfgvnlrdvakenglll 39 
                                    l+ G+pG+GKtt    ++++l   ++   v+  +++  
  gi|119719866|ref|YP_920361.1| 194 LVVGPPGTGKTTTIAGIAEKL--AERGERVLISSHTNR 229
                                    689*********999999998..444444444444444 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00012     0.052      18      51 ..     192     225 ..     180     231 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00012
                     Zeta_toxin  18 lillgGqpGAGKselaellkdelerqgnvvrldp 51 
                                    ++l++G pG GK+++++ ++++l+++g+ v ++ 
  gi|119719866|ref|YP_920361.1| 192 VLLVVGPPGTGKTTTIAGIAEKLAERGERVLISS 225
                                    789*********************9999998876 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00023     0.098      17      53 ..     188     223 ..     184     258 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00023
                         ATPase  17 pegrvvlitGepGtGKtifalqFlikgaekygepgvf 53 
                                     eg+v l++G pGtGKt+  +  + k ae+ ge++++
  gi|119719866|ref|YP_920361.1| 188 EEGEVLLVVGPPGTGKTTTIAGIAEKLAER-GERVLI 223
                                    6899**************999988888888.999876 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00049      0.21       4      22 ..     192     210 ..     189     239 .. 0.82
   2 ?   -1.0   0.0         3   1.3e+03      65      77 ..     357     369 ..     317     379 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00049
                         AAA_24   4 kiliyGpsgiGKTtlakel 22 
                                     +l++Gp+g+GKTt+++ +
  gi|119719866|ref|YP_920361.1| 192 VLLVVGPPGTGKTTTIAGI 210
                                    689************9987 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3
                         AAA_24  65 dyktlviDtidel 77 
                                    +++t++iD ++++
  gi|119719866|ref|YP_920361.1| 357 PFDTVIIDEASQV 369
                                    69******99987 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0    0.0007       0.3       1      41 [.     192     232 ..     192     237 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0007
                           MobB   1 vlgivgksgsGKTtLleklipelkarglrvgtiKhahhgfd 41 
                                    vl +vg  g+GKTt +  + ++l++rg rv +  h++ ++d
  gi|119719866|ref|YP_920361.1| 192 VLLVVGPPGTGKTTTIAGIAEKLAERGERVLISSHTNRAVD 232
                                    6889**************************98888877665 PP

>> Apt1  Golgi-body localisation protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.0    0.0004      0.17      95     151 ..     268     321 ..     248     333 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0004
                           Apt1  95 glpemvkklqerirqleeikehfqieskyldkegwedrlklekelaeceeeLfllmk 151
                                    +l e+  +lqeri +l    e  +i++ yl+ ++++ +  le+ l e e eL+ l++
  gi|119719866|ref|YP_920361.1| 268 ALGERYADLQERINEL---LETIRIHRGYLRGKDRSTFSLLERSLREHERELRELLE 321
                                    56688999********...4679*****************************97765 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00076      0.32       8      46 ..     181     217 ..     173     232 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00076
                                    HHHHHHHHHCHTEEEEEEESTTSSHHHHHHHHHHHTT-- CS
                           TsaE   8 ealgkklakalgdvilLeGdLGaGKTtlvrglakalgve 46 
                                     +++ +l +  g+v+l  G+ G+GKTt + g+a++l  +
  gi|119719866|ref|YP_920361.1| 181 VNAALELEE--GEVLLVVGPPGTGKTTTIAGIAEKLAER 217
                                    444445555..999********************99654 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0    0.0011      0.49      23      57 ..     191     225 ..     169     239 .. 0.73
   2 ?   -1.8   0.0       3.8   1.6e+03     135     153 ..     584     602 ..     579     618 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0011
                   Mg_chelatase  23 HnlllvGppGsGKtmlakrlpsllpplseeealev 57 
                                      ll+vGppG+GKt  ++ +++ l++  e+  + +
  gi|119719866|ref|YP_920361.1| 191 EVLLVVGPPGTGKTTTIAGIAEKLAERGERVLISS 225
                                    46899*********999888888877766655555 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.8
                   Mg_chelatase 135 vtisrakakvefparfqlv 153
                                    v+i+ra++k+ f a+  ++
  gi|119719866|ref|YP_920361.1| 584 VAITRARKKLLFVANANVM 602
                                    5666666666666655443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (629 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       897  (0.0500307); expected 358.6 (0.02)
Passed bias filter:                      717  (0.0399911); expected 358.6 (0.02)
Passed Vit filter:                       143  (0.0079759); expected 17.9 (0.001)
Passed Fwd filter:                        43  (0.00239835); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              42  [number of targets reported over threshold]
# CPU time: 0.84u 0.34s 00:00:01.18 Elapsed: 00:00:00.52
# Mc/sec: 3663.82
//
Query:       gi|119719867|ref|YP_920362.1|  [L=81]
Description: AbrB family transcriptional regulator [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.4e-10   39.3   2.5    7.8e-10   38.5   2.5    1.4  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
    0.00011   22.6   0.0    0.00013   22.3   0.0    1.1  1  PrlF_antitoxin  prlF antitoxin for toxin YhaV_toxin
  ------ inclusion threshold ------
      0.044   13.8   0.0      0.084   12.9   0.0    1.5  1  SymE_toxin      Toxin SymE, type I toxin-antitoxin system


Domain annotation for each model (and alignments):
>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.5   2.5   1.3e-13   7.8e-10       1      45 [.       7      51 ..       7      52 .. 0.95

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 1.3e-13
                                   EEETTEEEEEE-CCCHHHCCEECTCEEEEEECTTCCCCCCCHHSX CS
                 MazE_antitoxin  1 fkvGnsgavriPkevrfelgireGdevelevdgdkiilrplkslp 45
                                   ++v++ ++v+iP  vr+elgi++Gd++ ++v+g +iil+p+ ++p
  gi|119719867|ref|YP_920362.1|  7 VRVTERYRVTIPLSVRRELGIKVGDKLRVRVEGKRIILEPIPEEP 51
                                   589**************************************9987 PP

>> PrlF_antitoxin  prlF antitoxin for toxin YhaV_toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   2.2e-08   0.00013       3      64 ..       8      66 ..       6      76 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 2.2e-08
                 PrlF_antitoxin  3 tltergqttiPasvRkaLklkkgrdkiaytilddgkvvisraeeeaeDpvleqFLeFlakdl 64
                                   ++ter+  tiP svR+ L++k   dk+  ++ ++++++++   ee  +p le  L+ l+k +
  gi|119719867|ref|YP_920362.1|  8 RVTERYRVTIPLSVRRELGIKV-GDKLRVRV-EGKRIILEPIPEEPRNP-LEDMLSILDKPV 66
                                   79*******************9.77998877.46778888887777777.577788877765 PP

>> SymE_toxin  Toxin SymE, type I toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.4e-05     0.084      32      53 ..      24      45 ..      23      46 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.4e-05
                     SymE_toxin 32 qaGFatGqpltisVmegrlvit 53
                                   ++G ++G +l+++V+ +r++++
  gi|119719867|ref|YP_920362.1| 24 ELGIKVGDKLRVRVEGKRIILE 45
                                   79******************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 536.80
//
Query:       gi|119719868|ref|YP_920363.1|  [L=93]
Description: hypothetical protein Tpen_0960 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.023   14.8   1.3       0.86    9.8   0.1    2.2  2  bZIP_1    bZIP transcription factor
      0.067   13.1   0.8       0.64    9.9   0.8    2.0  1  RHH_4     Ribbon-helix-helix domain
      0.072   12.5   0.4      0.087   12.2   0.4    1.0  1  NBP1      Fungal Nap binding protein NBP1
        1.4   10.4   9.8        4.3    9.0   2.2    2.5  2  Toxin_36  Conantokin-G mollusc-toxin


Domain annotation for each model (and alignments):
>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1     0.011        48      24      49 ..      16      41 ..       6      43 .. 0.85
   2 ?    9.8   0.1   0.00019      0.86      29      57 ..      52      80 ..      48      83 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.011
                                   HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         bZIP_1 24 KqaeieeLerrvkaLekeNksLksel 49
                                   K++e ++Le+ +k++ +  ++L++++
  gi|119719868|ref|YP_920363.1| 16 KEEEYAKLESLAKEIGTTPAALAKKI 41
                                   8999999**99999998888888876 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00019
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         bZIP_1 29 eeLerrvkaLekeNksLkseleelkkeve 57
                                     L +rv +Le+  + +++el++++k+ +
  gi|119719868|ref|YP_920363.1| 52 VTLIERVRTLEERYERMAKELGRIEKDLA 80
                                   57889*******************99876 PP

>> RHH_4  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.8   0.00014      0.64      16      45 ..      14      62 ..       9      90 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00014
                                   EEEHHHHHHHHHHHHHTT--HHHHHHHH....................H CS
                          RHH_4 16 rLEpafWdaLeeiArregltvnaLiaeid...................a 45
                                    L ++ ++ Le +A++ g+t +aL ++i                    +
  gi|119719868|ref|YP_920363.1| 14 NLKEEEYAKLESLAKEIGTTPAALAKKIVlehlgldesvtliervrtlE 62
                                   689999*********************9644444444444444444441 PP

>> NBP1  Fungal Nap binding protein NBP1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.4   1.9e-05     0.087     155     221 ..      16      82 ..       2      84 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.9e-05
                           NBP1 155 lkydkqmleqLrrgrssnkserrvslrnnnleeDqvvlLqkkikklesklkdlekeLeitkkkLkFa 221
                                    ++ + ++le L +    +  +  ++   ++l  D+ v L  +++ le++ + + keL  + k+L ++
  gi|119719868|ref|YP_920363.1|  16 KEEEYAKLESLAKEIGTTPAALAKKIVLEHLGLDESVTLIERVRTLEERYERMAKELGRIEKDLAYV 82 
                                    34444567777666666666666788999999********************************996 PP

>> Toxin_36  Conantokin-G mollusc-toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   2.2   0.00095       4.3       2      15 .]      17      29 ..      17      29 .. 0.94
   2 ?    5.6   1.0     0.011        51       2      14 ..      62      74 ..      62      74 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00095
                       Toxin_36  2 EEElqkMaeeLiRE 15
                                   EEE++k +e L+ E
  gi|119719868|ref|YP_920363.1| 17 EEEYAK-LESLAKE 29
                                   9*****.****987 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.011
                       Toxin_36  2 EEElqkMaeeLiR 14
                                   EE +  Ma+eL R
  gi|119719868|ref|YP_920363.1| 62 EERYERMAKELGR 74
                                   899********76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       995  (0.0554967); expected 358.6 (0.02)
Passed bias filter:                      657  (0.0366445); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 674.04
//
Query:       gi|119719869|ref|YP_920364.1|  [L=518]
Description: hypothetical protein Tpen_0961 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.4e-24   85.8   0.0    4.9e-24   84.8   0.0    1.6  1  AAA_14        AAA domain
      1e-11   45.0   0.1    1.9e-11   44.2   0.1    1.4  1  DUF4143       Domain of unknown function (DUF4143)
    9.3e-06   25.7   0.6    3.9e-05   23.7   0.1    2.2  3  ATPase_2      ATPase domain predominantly from Archaea
     0.0046   15.8   0.0     0.0079   15.1   0.0    1.3  1  AAA_35        AAA-like domain
  ------ inclusion threshold ------
      0.031   14.7   0.0      0.066   13.6   0.0    1.7  1  AAA_16        AAA ATPase domain
      0.088   13.1   0.1        1.2    9.5   0.0    2.2  2  AAA_19        AAA domain
      0.097   13.1   0.0       0.27   11.6   0.0    1.8  1  RNA_helicase  RNA helicase


Domain annotation for each model (and alignments):
>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.8   0.0   1.9e-27   4.9e-24       3     118 ..      58     176 ..      56     199 .. 0.82

  Alignments for each domain:
  == domain 1  score: 84.8 bits;  conditional E-value: 1.9e-27
                         AAA_14   3 kilvitGaRrvGKTtllkqlikell....vkkesilyinldderdkkladpekllelileklkeekktylflDEiqevpe 78 
                                     i++i+G+RrvGKTtl+ ++i++l+    +k+e+++yi ld +++++l+ ++ l  ++ ++l + +++y+flDE+++ ++
  gi|119719869|ref|YP_920364.1|  58 GIVTIRGPRRVGKTTLIVRIIDHLIsksgIKPENVFYIPLDYKKLESLNLFD-L-FYVTAQL-P-EEKYIFLDEASMRRD 133
                                    589******************9999********************9988883.3.3344433.5.799************ PP

                         AAA_14  79 wekalkslvd....egknldvivtGSnskllskeiatslagrva 118
                                    w  +lk+lvd    e+ +l++ivtGS+s++l + + ++l++r+ 
  gi|119719869|ref|YP_920364.1| 134 WALVLKNLVDaglvEKGKLKIIVTGSHSMDLAE-AVSKLSDRQG 176
                                    **********777644699************66.7778888876 PP

>> DUF4143  Domain of unknown function (DUF4143)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   0.1   7.4e-15   1.9e-11      18     121 ..     327     475 ..     280     476 .. 0.77

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 7.4e-15
                                    x.........................xxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.... RF
                        DUF4143  18 k.........................glverlppwse..spnskkrlrkspKlyfvDtGLlvallgldkeelleds.... 66 
                                    k                          +   l+p++e  s+ ++ ++r+  K+y++D++ ++a      +e   d+    
  gi|119719869|ref|YP_920364.1| 327 KhvtgvdeegfpsarfgfgkyleyleTTKLFLFPYREdsSQTCTPNYRADRKVYVMDPFPYYAFKAHIHNE--VDPlgfs 404
                                    155556666666666666666666663344567777778**********************9943333222..2337789 PP

                                    .......xxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxx RF
                        DUF4143  67 .......enkGallEnlVaqeLlky.......sekegaklyyyrdkngaEvDfvielk...ggkivpiEvKs 121
                                            +kG+l+E++Va++L+++       s+++++k+  y++ n++E D+v+ l+   +++ ++iE K+
  gi|119719869|ref|YP_920364.1| 405 kkllsepGFKGRLVESVVAAHLVMAqqffehvSTVDYHKVLLYSK-NEKETDYVLCLSrkgEKHRILIESKY 475
                                    9999999*****************99******9999********9.69*******7766678999******8 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.1   1.5e-08   3.9e-05      14      70 ..      51     109 ..      46     157 .. 0.78
   2 ?   -1.6   0.0      0.82   2.1e+03     145     183 ..     138     177 ..     120     181 .. 0.77
   3 ?   -1.9   0.1         1   2.6e+03     151     177 ..     447     474 ..     440     508 .. 0.66

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.5e-08
                       ATPase_2  14 ilerepneiyfiYGpegsGKtaLlkeiienledkdk...yviyyialreesiskldefie 70 
                                    + +++ + i+ i Gp+++GKt+L+ +ii  l +k+    + ++yi+l  +++++l+ f +
  gi|119719869|ref|YP_920364.1|  51 LPKQGYYGIVTIRGPRRVGKTTLIVRIIDHLISKSGikpENVFYIPLDYKKLESLNLF-D 109
                                    5567788899*********************555444789***********9999998.4 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.82
                       ATPase_2 145 LlnliesltkekhlcvviclsSeglfie.rvyneselegr 183
                                    L nl++  + ek +  +i++ S ++ +   v++ s ++gr
  gi|119719869|ref|YP_920364.1| 138 LKNLVDAGLVEKGKLKIIVTGSHSMDLAeAVSKLSDRQGR 177
                                    6678888888999999999999999665377777777776 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1
                       ATPase_2 151 sltkekhlcvviclsSeglfie.rvyne 177
                                    +  +ek++  v+cls +g  ++ +++++
  gi|119719869|ref|YP_920364.1| 447 YSKNEKETDYVLCLSRKGEKHRiLIESK 474
                                    5666777777777777777666333333 PP

>> AAA_35  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   3.1e-06    0.0079      23      58 ..      47      84 ..      37     117 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.1e-06
                         AAA_35 23 cyeeiekpGa..lirikapkkmGKtSLlarilakakqq 58
                                   +++++ k+G   +++i++p+++GKt L+ ri+++  ++
  gi|119719869|ref|YP_920364.1| 47 IVNSLPKQGYygIVTIRGPRRVGKTTLIVRIIDHLISK 84
                                   5667778887779*******************997655 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.6e-05     0.066      21      63 ..      54     102 ..      42     251 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.6e-05
                         AAA_16  21 sgrpelvllsGesGvGKsslvrellralekd......ggiflrgkcdql 63 
                                    +g  ++v ++G++ vGK++l+ ++ ++l  +      +++++  ++++l
  gi|119719869|ref|YP_920364.1|  54 QGYYGIVTIRGPRRVGKTTLIVRIIDHLISKsgikpeNVFYIPLDYKKL 102
                                    344499***************5555555544366664444466555555 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00046       1.2      15      48 ..      62      95 ..      56     106 .. 0.83
   2 ?    1.3   0.0      0.15   3.9e+02      96     116 ..     113     134 ..      95     158 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00046
                         AAA_19 15 vtaGpGtGKTrvlkhivallvelggvkpeeillv 48
                                   + ++   GKT++++ i+ +l++  g+kpe++  +
  gi|119719869|ref|YP_920364.1| 62 IRGPRRVGKTTLIVRIIDHLISKSGIKPENVFYI 95
                                   5555568*********************998766 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.15
                         AAA_19  96 eekklqeeellivDEfqdvd.e 116
                                     + +l ee++++ DE+++   +
  gi|119719869|ref|YP_920364.1| 113 VTAQLPEEKYIFLDEASMRRdW 134
                                    456787888********97643 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00011      0.27       2      36 ..      61      95 ..      60     103 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00011
                   RNA_helicase  2 wlyGpsgeGKStlakeLakallkklklkkkdsvys 36
                                    + Gp+++GK+tl+ +++++l +k++ k ++ +y+
  gi|119719869|ref|YP_920364.1| 61 TIRGPRRVGKTTLIVRIIDHLISKSGIKPENVFYI 95
                                   689**********************9998888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (518 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 3579.20
//
Query:       gi|119719870|ref|YP_920365.1|  [L=54]
Description: hypothetical protein Tpen_0962 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (54 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.29s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 357.84
//
Query:       gi|119719871|ref|YP_920366.1|  [L=291]
Description: hypothetical protein Tpen_0963 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.13   12.1   0.0        0.2   11.6   0.0    1.2  1  DUF4661   Domain of unknown function (DUF4661)


Domain annotation for each model (and alignments):
>> DUF4661  Domain of unknown function (DUF4661)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   1.1e-05       0.2     159     199 ..     229     269 ..     217     274 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.1e-05
                        DUF4661 159 gpeellqistnltlhllellasallalcsrPlraaldalGl 199
                                     +ee lq+  n    +l l+   l ++cs  l+a + +lGl
  gi|119719871|ref|YP_920366.1| 229 YTEEALQLEKNTGHTILKLVDEGLYTMCSITLKARIHSLGL 269
                                    479*************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       696  (0.0388198); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 1970.67
//
Query:       gi|119719872|ref|YP_920367.1|  [L=600]
Description: hypothetical protein Tpen_0964 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      3e-76  257.0   0.0    3.9e-76  256.6   0.0    1.1  1  DUF2075    Uncharacterized conserved protein (DUF2075)
    0.00043   20.7   0.0    0.00097   19.6   0.0    1.6  1  NERD       Nuclease-related domain
    0.00052   20.4   0.2     0.0012   19.3   0.2    1.5  1  AAA_16     AAA ATPase domain
    0.00072   19.4   0.0       0.08   12.7   0.0    2.3  2  DEAD       DEAD/DEAH box helicase
     0.0054   15.8   0.0     0.0078   15.3   0.0    1.2  1  T2SSE      Type II/IV secretion system protein
  ------ inclusion threshold ------
       0.01   16.1   0.1      0.045   14.0   0.1    2.1  1  AAA_22     AAA domain
      0.011   15.8   0.0      0.021   14.8   0.0    1.4  1  ResIII     Type III restriction enzyme, res subunit
      0.017   14.3   0.0      0.026   13.7   0.0    1.2  1  PIF1       PIF1-like helicase
      0.018   14.8   0.0      0.043   13.6   0.0    1.6  1  IstB_IS21  IstB-like ATP binding protein
       0.02   14.4   0.1       0.36   10.2   0.0    2.3  2  PhoH       PhoH-like protein
       0.15   11.4   0.1       0.34   10.2   0.1    1.5  1  ATPase     KaiC


Domain annotation for each model (and alignments):
>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  256.6   0.0   2.4e-79   3.9e-76       2     363 .]     231     583 ..     230     583 .. 0.93

  Alignments for each domain:
  == domain 1  score: 256.6 bits;  conditional E-value: 2.4e-79
                        DUF2075   2 avvlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlrealakkeekkkkkeafeklssfinnlsef.... 77 
                                    + ++V+G++G+GKt+v+l+ll+e+   +++++av++++N++l+++lr al+ ++      + + kls++i  +s++    
  gi|119719872|ref|YP_920367.1| 231 KAFFVRGGTGSGKTLVALTLLFEA--VSRGYHAVLAYKNNRLLNTLRYALSLRA-----PRGAPKLSALIVYYSTGrghg 303
                                    789*********************..************************8888.....999************99**** PP

                        DUF2075  78 ...kkaeekkeepkedvvivDEAhrlltksdqaekqseenqlkelmkrakvvvalvDegQelntgeigteeelkklakkl 154
                                       ++a+ek   +++++++ DEA+r++            ++++ +mk a v+v+++D++Q+l  +e+g +e++ ++a++l
  gi|119719872|ref|YP_920367.1| 304 lgeRRAYEKGLYRNLNLAVLDEAQRMTL-----------ENIEYTMKSAPVTVYFYDDKQILIGYEEGFRENFLEAAERL 372
                                    **999***********************...........89*************************************** PP

                        DUF2075 155 eveleekvhLksqfRvaaseaviewvdalldgkkekakplssqenfdirvfddleelkkalkeknkesgrsrlvatydak 234
                                    + +++e+ +Lk+ +Rv  +  +++ v++l+  ++ ++++    +++di+vfd+++++ +al+ek++++ +++lv++++++
  gi|119719872|ref|YP_920367.1| 373 GLAYDER-ELKTLYRV--PPGYVKLVESLVYSGAVAQQDV---QGYDIKVFDNPADMLEALQEKANKGFKVALVCAFTET 446
                                    ******9.********..************9999998885...8************************************ PP

                        DUF2075 235 rlaekkkkkskekdvkiee..gdfkl..pWnleek.elkkpwaess.dtleevgseytiQGleldyvgviiGpdlvyr.. 306
                                    r ++  ++ +++++++ ++  gd +   +W ++ek e++k+w+ +  + l++++s+y +QG+e+dyvgv++G+d+v+r  
  gi|119719872|ref|YP_920367.1| 447 RGDK--NDLNSPENRRLTVkrGDREEvvTWLMDEKeEYPKYWCGELgNPLTRCASVYGAQGFEADYVGVVWGRDMVWRcg 524
                                    **55..4444455554544235533255*******999******9989******************************99 PP

                        DUF2075 307 keedrikfrgkksedkeakskrkk..kkeseekaqkllkNayrVLLtRGrkGlyiyaed 363
                                    +  + +++++++++d+ +++++ +   +++  ka +llkN+y+++LtRG+kG+yiy ed
  gi|119719872|ref|YP_920367.1| 525 PLGCGWSVNPDAITDYVGGQYSLEklARKDPGKALELLKNRYYIMLTRGIKGTYIYPED 583
                                    888999****************98999999**************************987 PP

>> NERD  Nuclease-related domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   5.9e-07   0.00097      35      92 ..      66     119 ..      40     136 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 5.9e-07
                           NERD  35 eiDhlvispkgifviEvKnwsGwifgdkegrwtqkikkgfk.npleqakrhakalkksl 92 
                                      D++v+++++ +v+E K ws  +++   ++ +q  + + + +p  q+++++ +l k++
  gi|119719872|ref|YP_920367.1|  66 RADFVVVGRGRALVVEAKGWST-VEKL--NYVVQVDGLR-EvDPCYQVENYVSKL-KYF 119
                                    68*******************4.4433..3555554222.34*************.666 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.2   7.4e-07    0.0012       4      62 ..     211     270 ..     209     294 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 7.4e-07
                         AAA_16   4 GReeeleqLlsalervrsgrpelvllsGesGvGKsslv.rellralekdggif.lrgkcdq 62 
                                    GRe+ +  ++++le++ +g+  + +++G  G+GK+ ++ + l++a+++ +  + ++ +++ 
  gi|119719872|ref|YP_920367.1| 211 GREQLV-LVHDVLEALEAGSRKAFFVRGGTGSGKTLVAlTLLFEAVSRGYHAVlAYKNNRL 270
                                    566655.88*****************************66666666665544414444443 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   4.9e-05      0.08      14      42 ..     230     258 ..     219     295 .. 0.79
   2 ?    4.3   0.0     0.018        30     101     137 ..     294     333 ..     273     344 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.9e-05
                                    TCEEEEEESTTSSHHHHHHHHHHHHHHHS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  14 ggdvlvaaeTGsGKTlaflipvlqivyet 42 
                                     + ++v++ TGsGKTl++l  ++++v++ 
  gi|119719872|ref|YP_920367.1| 230 RKAFFVRGGTGSGKTLVALTLLFEAVSRG 258
                                    56889*****************9999654 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.018
                                    EEEEHHHHHHHHHCTSSH...CTTEEEEEEETHHHHHHTT CS
                                    xxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxx RF
                           DEAD 101 vvgtpgrlddllstgkln...lsqvrflVlDEadrlldqg 137
                                    v+  +gr + l +++  +   ++++++ VlDEa+r+  ++
  gi|119719872|ref|YP_920367.1| 294 VYYSTGRGHGLGERRAYEkglYRNLNLAVLDEAQRMTLEN 333
                                    555555555555333333344899***********98765 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   4.8e-06    0.0078     101     153 ..     201     254 ..     172     264 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.8e-06
                          T2SSE 101 keltlddlgaeealk...ekiaevlrkavrerglilvsGgTgsGKttllyallkei 153
                                    + l  + +g  +++    +++ e+l++   +r+ + v GgTgsGKt ++ +ll e 
  gi|119719872|ref|YP_920367.1| 201 RFLASEGYGLGREQLvlvHDVLEALEAG--SRKAFFVRGGTGSGKTLVALTLLFEA 254
                                    4444555555555553334555666665..9***************9998887665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   2.8e-05     0.045       4     111 ..     229     336 ..     223     362 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.8e-05
                         AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka............e 71 
                                    +++  +v G +G+GKT+++ +ll +++         ++ ++  l+ ++    ll+ l  al l++ +            +
  gi|119719872|ref|YP_920367.1| 229 SRKAFFVRGGTGSGKTLVALTLLFEAV---------SRGYHAVLAYKN--NRLLNTLRYALSLRAPRgapklsalivyyS 297
                                    56778899****************995.........444444444444..345555555555554445566889999999 PP

                         AAA_22  72 rlsseell.ealeqalraravielliiDEaqhlrseealee 111
                                    +++ + l  ++ ++    r    l ++DEaq++ + e++e+
  gi|119719872|ref|YP_920367.1| 298 TGRGHGLGeRRAYEKGLYRNL-NLAVLDEAQRM-TLENIEY 336
                                    999999999999999999999.9**********.8777776 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   1.3e-05     0.021       7      70 ..     213     274 ..     208     301 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.3e-05
                                    HHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHH CS
                         ResIII   7 yQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqt 70 
                                     Q   + ++le+l++  +k +++   TG+GKTlva+ l  +  + g+  ++++   ++ ll+ +
  gi|119719872|ref|YP_920367.1| 213 EQLVLVHDVLEALEAGSRKAFFVRGGTGSGKTLVALTLLFEAVSRGY--HAVLAYKNNRLLNTL 274
                                    577788899999997778888899***********999999888877..677777777666655 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.6e-05     0.026       2      50 ..     210     258 ..     209     266 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.6e-05
                                    --HHHHHHHHHH......HCTS-EEEEESTTSSCHHHHHHHHHHCHCTC CS
                           PIF1   2 LneeQkkvfdaiieavlnekgklfFvtGsgGtgKtflwkallkklrseg 50 
                                    L +eQ   ++ ++ea+ + + k fFv G  G+gKt +  +ll    s+g
  gi|119719872|ref|YP_920367.1| 210 LGREQLVLVHDVLEALEAGSRKAFFVRGGTGSGKTLVALTLLFEAVSRG 258
                                    6689999*****************************9888876666654 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.6e-05     0.043      47      93 ..     230     277 ..     217     287 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.6e-05
                      IstB_IS21  47 kenivllGpsGvGKshlaialgveavragl.svlfvrvedLveelkra 93 
                                    ++++ + G++G GK+ +a +l  eav +g+ +vl ++ ++L+++l+ a
  gi|119719872|ref|YP_920367.1| 230 RKAFFVRGGTGSGKTLVALTLLFEAVSRGYhAVLAYKNNRLLNTLRYA 277
                                    5678899********************99626899999*****99876 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00022      0.36      12      47 ..     221     258 ..     215     269 .. 0.84
   2 ?    1.3   0.0      0.12     2e+02     123     138 ..     321     336 ..     313     340 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00022
                                    HHHHHH..H-SEEEEE--TTSSTTHHHHHHHHHHHHTT CS
                           PhoH  12 ylealk..kndivfaiGpaGtGKtylavalavealkkk 47 
                                    +leal+  + +  f+ G +G+GKt++a++l +ea++++
  gi|119719872|ref|YP_920367.1| 221 VLEALEagSRKAFFVRGGTGSGKTLVALTLLFEAVSRG 258
                                    5677777778899****************999998876 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.12
                                    EEE-SGGG--HHHHHH CS
                           PhoH 123 vilDEAQnttkeqmkm 138
                                     +lDEAQ +t e+++ 
  gi|119719872|ref|YP_920367.1| 321 AVLDEAQRMTLENIEY 336
                                    58********999875 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00021      0.34      19      52 ..     230     262 ..     227     265 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00021
                         ATPase  19 grvvlitGepGtGKtifalqFlikgaekygepgv 52 
                                    +++  + G++G+GKt++al+ l++ +++ g+  v
  gi|119719872|ref|YP_920367.1| 230 RKAFFVRGGTGSGKTLVALTLLFEAVSR-GYHAV 262
                                    5677899******************999.99877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (600 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.46
# Mc/sec: 3938.63
//
Query:       gi|119719873|ref|YP_920368.1|  [L=124]
Description: hypothetical protein Tpen_0965 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       168  (0.00937029); expected 358.6 (0.02)
Passed bias filter:                      153  (0.00853366); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 873.12
//
Query:       gi|119719874|ref|YP_920369.1|  [L=788]
Description: hypothetical protein Tpen_0966 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.066   13.0   0.0       0.31   10.8   0.0    2.1  2  Big_3_4     Domain of unknown function
       0.14   12.6   0.0       0.35   11.3   0.0    1.6  1  SopA        SopA-like central domain
       0.15   12.0   0.1       0.31   11.0   0.1    1.4  1  Holin_BhlA  BhlA holin family


Domain annotation for each model (and alignments):
>> Big_3_4  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   5.2e-05      0.31      27      50 ..     108     131 ..      99     138 .. 0.91
   2 ?   -2.2   0.0      0.55   3.3e+03      47      88 ..     419     460 ..     415     467 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 5.2e-05
                        Big_3_4  27 pvPldedGeyvvellaedeaGnqa 50 
                                    pv l+e+G+y+v ++a d  Gn a
  gi|119719874|ref|YP_920369.1| 108 PVSLNEEGNYLVTIVARDSKGNEA 131
                                    899*******************87 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.55
                        Big_3_4  47 Gnqayiakllyvvdienicvevrpldylsekleteftieava 88 
                                    G   y+ak    + +  +c +++  +y  ++ e   +++a +
  gi|119719874|ref|YP_920369.1| 419 GSIVYVAKTDIPIAAWMLCEHLKRTPYHLKHPEVFEALNAKM 460
                                    666788888888888999999999999887766555555544 PP

>> SopA  SopA-like central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   5.9e-05      0.35      21      57 ..     494     530 ..     490     559 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.9e-05
                                    GGGHHHHHHHHTSTTTTC-HHHHHHHHHHHHHHHH-- CS
                           SopA  21 ksvaesllkilshaPYidepliaewlqeveerffaaf 57 
                                    ++ a +l k l+  P+++++l++ew+++ ++r++a +
  gi|119719874|ref|YP_920369.1| 494 TPQAGNLSKRLTILPWYNSSLLKEWIGNKNDRKIALM 530
                                    66788999**************************943 PP

>> Holin_BhlA  BhlA holin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   5.2e-05      0.31       7      53 ..      22      71 ..      19      77 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 5.2e-05
                     Holin_BhlA  7 klaitqGiwavLfvvllvYilkkqekreekqe...erekkyqeiikklte 53
                                   k+a+  G+ a+L+v++l  +l  q k   k e   ++ ++y ++++k+t+
  gi|119719874|ref|YP_920369.1| 22 KVALATGLIALLSVLALATLLYYQDKTPPKIEikeKKVDEYLSLLAKITD 71
                                   789999********877666666666555555111556678889999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (788 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.69u 0.32s 00:00:01.01 Elapsed: 00:00:00.50
# Mc/sec: 4734.32
//
Query:       gi|119719875|ref|YP_920370.1|  [L=64]
Description: hypothetical protein Tpen_0967 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.30s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 426.23
//
Query:       gi|119719876|ref|YP_920371.1|  [L=72]
Description: hypothetical protein Tpen_0968 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00023   21.0   0.2        0.2   11.6   0.1    2.2  2  zinc_ribbon_4    zinc-ribbon domain
    0.00029   20.2   0.2      0.083   12.4   0.0    2.1  2  Mu-like_Com      Mu-like prophage protein Com
      0.001   19.3   1.0       0.56   10.5   0.0    2.3  2  Prim_Zn_Ribbon   Zinc-binding domain of primase-helicase
     0.0011   18.7   0.4       0.73    9.6   0.1    2.3  2  zinc_ribbon_5    zinc-ribbon domain
     0.0014   18.6   0.8       0.95    9.5   0.1    2.1  2  CpXC             CpXC protein
     0.0014   18.5   3.8      0.024   14.6   4.1    2.1  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
     0.0018   18.3   3.7      0.017   15.2   0.2    2.2  2  UPF0547          Uncharacterised protein family UPF0547
      0.002   18.2   0.3        1.4    9.1   0.1    2.2  2  Zn-ribbon_8      Zinc ribbon domain
     0.0021   18.4   3.2       0.44   11.1   0.4    2.3  2  zf-H2C2_2        Zinc-finger double domain
     0.0023   18.6   2.0       0.71   10.9   0.2    2.4  2  zf-C2H2_4        C2H2-type zinc finger
     0.0033   16.8   2.2       0.53    9.8   0.1    2.2  2  zf-ribbon_3      zinc-ribbon domain
     0.0052   16.3   0.6       0.52    9.9   0.1    2.2  2  TF_Zn_Ribbon     TFIIB zinc-binding
     0.0079   16.2   2.4      0.019   14.9   0.1    2.1  2  ADK_lid          Adenylate kinase, active site lid
  ------ inclusion threshold ------
       0.01   15.6   0.5        2.5    8.0   0.0    2.3  2  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger
      0.013   15.3   7.3       0.68    9.9   1.1    2.4  2  zf-C2HC_2        zinc-finger of a C2HC-type
      0.023   14.5   1.0       0.89    9.5   0.1    2.2  2  TFIIS_C          Transcription factor S-II (TFIIS)
      0.024   14.3   0.2        3.5    7.4   0.0    2.2  2  Zn_Tnp_IS1       InsA N-terminal domain
      0.028   14.4   0.0      0.035   14.1   0.0    1.2  1  HypA             Hydrogenase/urease nickel incorporation, met
      0.028   15.1   0.6        6.7    7.5   0.1    2.2  2  zf-ISL3          zinc-finger of transposase IS204/IS1001/IS10
      0.035   12.7   0.2       0.04   12.5   0.2    1.0  1  Terminase_GpA    Phage terminase large subunit (GpA)
      0.036   14.1   0.3        3.8    7.7   0.0    2.1  2  zf-Mss51         Zinc-finger of mitochondrial splicing suppre
      0.049   13.4   0.6        2.9    7.7   0.1    2.3  2  A2L_zn_ribbon    A2L zinc ribbon domain
      0.054   13.6   1.2          1    9.5   0.1    2.2  2  DUF2752          Protein of unknown function (DUF2752)
      0.058   13.5   2.0          5    7.3   0.1    2.2  2  TRAF6_Z2         TNF receptor-associated factor 6 zinc finger
      0.064   13.1   1.6        5.6    7.0   0.1    2.2  2  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
      0.066   13.5   1.7        4.8    7.5   0.2    2.2  2  zinc_ribbon_9    zinc-ribbon
      0.071   13.3   1.2         11    6.3   0.2    2.1  2  zf-AN1           AN1-like Zinc finger
      0.077   12.6   1.8        2.4    7.9   0.1    2.2  2  zf-tcix          Putative treble-clef, zinc-finger, Zn-bindin
      0.085   12.6   0.1         14    5.5   0.0    2.1  2  YacG             DNA gyrase inhibitor YacG
      0.092   12.7   2.3        2.5    8.1   0.1    2.1  2  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon
      0.098   12.6   2.2       0.65   10.0   2.2    1.9  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
       0.11   12.3   6.1        1.8    8.4   0.7    2.2  2  zinc_ribbon_2    zinc-ribbon domain
       0.17   11.5   1.7        6.6    6.4   0.2    2.2  2  zf_C2H2_10       C2H2 type zinc-finger
       0.18   12.0   0.4        1.1    9.5   0.0    2.0  2  DUF2387          Probable metal-binding protein (DUF2387)
       0.19   11.7   2.3        3.7    7.5   0.2    2.2  2  Cys_rich_CPXG    Cysteine-rich CPXCG
       0.19   12.0   1.8        2.3    8.5   0.1    2.2  2  zf-RING_7        C4-type zinc ribbon domain
       0.33   11.1   2.8        7.6    6.7   0.2    2.2  2  zf-ACC           Acetyl-coA carboxylase zinc finger domain
       0.39   10.1   3.0        4.9    6.6   0.2    2.2  2  zf-RanBP         Zn-finger in Ran binding protein and others
        0.6   10.7   4.7          7    7.3   0.3    2.4  2  zf-C2H2          Zinc finger, C2H2 type
        1.3    9.0   5.1         12    5.9   5.1    2.0  1  Anti-TRAP        Tryptophan RNA-binding attenuator protein in
        1.6    8.1   6.6         17    4.8   6.7    2.2  2  zf-TFIIB         Transcription factor zinc-finger
        1.7    9.0   6.7         22    5.5   6.7    2.0  1  Lar_restr_allev  Restriction alleviation protein Lar
        2.8    8.0   5.4        9.2    6.3   0.6    2.3  2  Ogr_Delta        Ogr/Delta-like zinc finger


Domain annotation for each model (and alignments):
>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0084       3.5       3      11 ..       8      16 ..       6      27 .. 0.70
   2 !   11.6   0.1   0.00048       0.2      24      36 .]      37      49 ..      34      49 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0084
                  zinc_ribbon_4  3 itCpsCkak 11
                                   ++Cp+C+  
  gi|119719876|ref|YP_920371.1|  8 VECPHCGYS 16
                                   788888755 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00048
                  zinc_ribbon_4 24 vkvrCskCghvFr 36
                                   ++++C+kCg +F+
  gi|119719876|ref|YP_920371.1| 37 RRLQCPKCGGTFN 49
                                   789******9995 PP

>> Mu-like_Com  Mu-like prophage protein Com
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1     0.013       5.2      22      32 ..       5      15 ..       2      35 .. 0.81
   2 !   12.4   0.0    0.0002     0.083      25      44 ..      39      59 ..      32      66 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.013
                    Mu-like_Com 22 eltiKCPRCGt 32
                                   el + CP CG 
  gi|119719876|ref|YP_920371.1|  5 ELLVECPHCGY 15
                                   68899*****6 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.0002
                    Mu-like_Com 25 iKCPRCG.tLnHlkaesldae 44
                                   ++CP+CG t n   + s++ e
  gi|119719876|ref|YP_920371.1| 39 LQCPKCGgTFNYYYGVSPKGE 59
                                   68****559********9877 PP

>> Prim_Zn_Ribbon  Zinc-binding domain of primase-helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0    0.0014      0.56       4      15 ..       8      19 ..       7      27 .. 0.84
   2 ?    7.6   0.2     0.011       4.7       3      12 ..      38      47 ..      36      52 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0014
                                   E--TTTT-TTTE CS
                 Prim_Zn_Ribbon  4 spCPvCGGrDrF 15
                                   ++CP CG +Dr 
  gi|119719876|ref|YP_920371.1|  8 VECPHCGYSDRL 19
                                   69********95 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.011
                                   EE--TTTT-T CS
                 Prim_Zn_Ribbon  3 hspCPvCGGr 12
                                   +  CP CGG 
  gi|119719876|ref|YP_920371.1| 38 RLQCPKCGGT 47
                                   678*****95 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0      0.01       4.3       1      18 [.       6      23 ..       6      27 .. 0.81
   2 !    9.6   0.1    0.0017      0.73       2      12 ..      38      48 ..      38      50 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.01
                  zinc_ribbon_5  1 LiirCpdCdtkFklvdsk 18
                                   L + Cp C+   +l++ k
  gi|119719876|ref|YP_920371.1|  6 LLVECPHCGYSDRLDSFK 23
                                   6789****9988888765 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0017
                  zinc_ribbon_5  2 iirCpdCdtkF 12
                                   + +Cp+C+ +F
  gi|119719876|ref|YP_920371.1| 38 RLQCPKCGGTF 48
                                   679*******9 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0048         2      38      55 ..       8      25 ..       4      36 .. 0.76
   2 !    9.5   0.1    0.0023      0.95      35      53 ..      36      54 ..      32      71 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0048
                           CpXC 38 atCpkCgatakleaplly 55
                                   ++Cp+Cg++ +l+   l 
  gi|119719876|ref|YP_920371.1|  8 VECPHCGYSDRLDSFKLL 25
                                   689999999988765555 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0023
                           CpXC 35 lfeatCpkCgatakleapl 53
                                   +++ +CpkCg t+ + + +
  gi|119719876|ref|YP_920371.1| 36 VRRLQCPKCGGTFNYYYGV 54
                                   6778999999999887765 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   4.1   5.7e-05     0.024      20      44 ..       9      45 ..       4      47 .. 0.84
   2 !    9.1   0.4     0.003       1.3      19      30 ..      39      51 ..      29      58 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.7e-05
                  Zn_Tnp_IS1595 20 vCPhCgsr...kayrikt.........rglfqCkeCr 44
                                    CPhCg++    ++++ +          +++qC +C+
  gi|119719876|ref|YP_920371.1|  9 ECPHCGYSdrlDSFKLLRdpwrysfyeVRRLQCPKCG 45
                                   6*******96655555559*****************8 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.003
                  Zn_Tnp_IS1595 19 fvCPhCgsr.kay 30
                                     CP+Cg++  +y
  gi|119719876|ref|YP_920371.1| 39 LQCPKCGGTfNYY 51
                                   5699999987444 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.2     4e-05     0.017      16      24 ..       9      17 ..       7      18 .. 0.87
   2 ?    4.3   0.3      0.11        44      17      21 ..      41      45 ..      39      49 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4e-05
                        UPF0547 16 fCphCGyvF 24
                                   +CphCGy++
  gi|119719876|ref|YP_920371.1|  9 ECPHCGYSD 17
                                   8******96 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.11
                        UPF0547 17 CphCG 21
                                   Cp CG
  gi|119719876|ref|YP_920371.1| 41 CPKCG 45
                                   66666 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0094       3.9      27      33 ..       7      14 ..       1      19 [. 0.71
   2 !    9.1   0.1    0.0034       1.4      27      35 ..      39      47 ..      27      58 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0094
                    Zn-ribbon_8 27 ta.CPeCg 33
                                    + CP+Cg
  gi|119719876|ref|YP_920371.1|  7 LVeCPHCG 14
                                   444****9 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0034
                    Zn-ribbon_8 27 taCPeCgse 35
                                    +CP+Cg++
  gi|119719876|ref|YP_920371.1| 39 LQCPKCGGT 47
                                   347777663 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.2      0.01       4.2      15      23 ..       8      16 ..       3      16 .. 0.80
   2 !   11.1   0.4    0.0011      0.44      13      25 ..      37      49 ..      31      50 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.01
                      zf-H2C2_2 15 yeCplCdka 23
                                   +eCp C+++
  gi|119719876|ref|YP_920371.1|  8 VECPHCGYS 16
                                   79*****96 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0011
                      zf-H2C2_2 13 kpyeCplCdkaFk 25
                                   ++++Cp+C+ +F+
  gi|119719876|ref|YP_920371.1| 37 RRLQCPKCGGTFN 49
                                   568********97 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.1     0.024        10       2      12 ..       9      17 ..       8      26 .. 0.73
   2 !   10.9   0.2    0.0017      0.71       2      14 ..      40      52 ..      39      55 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.024
                      zf-C2H2_4  2 kCpiCgksFss 12
                                   +Cp+C   +s+
  gi|119719876|ref|YP_920371.1|  9 ECPHC--GYSD 17
                                   7****..6664 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0017
                      zf-C2H2_4  2 kCpiCgksFsskk 14
                                   +Cp Cg++F+ ++
  gi|119719876|ref|YP_920371.1| 40 QCPKCGGTFNYYY 52
                                   8********8776 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.1    0.0013      0.53       4       9 ..       9      14 ..       7      22 .. 0.67
   2 ?    6.9   0.5      0.01       4.2       5       9 ..      41      45 ..      39      48 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0013
                    zf-ribbon_3  4 rCPnCG 9 
                                   +CP+CG
  gi|119719876|ref|YP_920371.1|  9 ECPHCG 14
                                   566665 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.01
                    zf-ribbon_3  5 CPnCG 9 
                                   CP+CG
  gi|119719876|ref|YP_920371.1| 41 CPKCG 45
                                   66665 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.035        15       3      14 ..      10      27 ..       8      34 .. 0.65
   2 !    9.9   0.1    0.0013      0.52       2      11 ..      40      50 ..      39      60 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.035
                                   ETTTTCEE.C.....HEE CS
                   TF_Zn_Ribbon  3 CPnCgstn.l.....veD 14
                                   CP Cg ++ l     ++D
  gi|119719876|ref|YP_920371.1| 10 CPHCGYSDrLdsfklLRD 27
                                   999997664455555555 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0013
                                   EETTTTCEE.C CS
                   TF_Zn_Ribbon  2 kCPnCgstn.l 11
                                   +CP+Cg+t+ +
  gi|119719876|ref|YP_920371.1| 40 QCPKCGGTFnY 50
                                   8******9744 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.3      0.99   4.1e+02       4       8 ..      10      14 ..       8      16 .. 0.82
   2 !   14.9   0.1   4.6e-05     0.019       1      19 [.      38      57 ..      38      60 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.99
                                   -TTT- CS
                        ADK_lid  4 CpkCG 8 
                                   Cp CG
  gi|119719876|ref|YP_920371.1| 10 CPHCG 14
                                   99999 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 4.6e-05
                                   EEE-TTT--EEETTT.B--S CS
                        ADK_lid  1 RrvCpkCGrsYhvvf.npPk 19
                                   R+ CpkCG ++++ +   Pk
  gi|119719876|ref|YP_920371.1| 38 RLQCPKCGGTFNYYYgVSPK 57
                                   899*********87777777 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.1     0.024       9.9       2       9 ..       8      16 ..       7      19 .. 0.82
   2 ?    8.0   0.0     0.006       2.5       3      10 ..      40      47 ..      39      55 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.024
                                   EE-SSS-.- CS
                 zf-C4_Topoisom  2 ekCPkCg.g 9 
                                   ++CP Cg +
  gi|119719876|ref|YP_920371.1|  8 VECPHCGyS 16
                                   58****965 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.006
                                   E-SSS--E CS
                 zf-C4_Topoisom  3 kCPkCggd 10
                                   +CPkCgg 
  gi|119719876|ref|YP_920371.1| 40 QCPKCGGT 47
                                   6*****86 PP

>> zf-C2HC_2  zinc-finger of a C2HC-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.6    0.0036       1.5       2       9 ..       7      14 ..       7      14 .. 0.94
   2 ?    9.9   1.1    0.0016      0.68       3      13 ..      39      49 ..      37      50 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0036
                      zf-C2HC_2  2 lvpCpkCg 9 
                                   lv+Cp+Cg
  gi|119719876|ref|YP_920371.1|  7 LVECPHCG 14
                                   89*****9 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0016
                      zf-C2HC_2  3 vpCpkCgRsFn 13
                                    +CpkCg +Fn
  gi|119719876|ref|YP_920371.1| 39 LQCPKCGGTFN 49
                                   69*****9998 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1      0.12        50       2       8 ..       9      15 ..       6      18 .. 0.69
   2 ?    9.5   0.1    0.0021      0.89       2      14 ..      40      52 ..      39      54 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.12
                        TFIIS_C  2 kCpkCgs 8 
                                   +Cp Cg 
  gi|119719876|ref|YP_920371.1|  9 ECPHCGY 15
                                   6777774 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0021
                        TFIIS_C  2 kCpkCgsreayff 14
                                   +CpkCg++  y++
  gi|119719876|ref|YP_920371.1| 40 QCPKCGGTFNYYY 52
                                   8******988886 PP

>> Zn_Tnp_IS1  InsA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.043        18       1      12 [.       1      14 [.       1      19 [. 0.73
   2 ?    7.4   0.0    0.0084       3.5       7      25 ..      40      58 ..      37      60 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.043
                     Zn_Tnp_IS1  1 MAsVs..ihCPrCs 12
                                   MA V   + CP C 
  gi|119719876|ref|YP_920371.1|  1 MAKVEllVECPHCG 14
                                   676654489****5 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0084
                     Zn_Tnp_IS1  7 hCPrCsstdVyRhGkstag 25
                                    CP+C  t  y  G s++g
  gi|119719876|ref|YP_920371.1| 40 QCPKCGGTFNYYYGVSPKG 58
                                   7*******99999999998 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   8.5e-05     0.035      66      95 ..       3      47 ..       1      54 [. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.5e-05
                                   EE--EEEETTTS-EEECHHHHH...............S-TTTSSS CS
                           HypA 66 evpvkvrCreCgkefeleekal...............rCpkCgsa 95
                                   +v++ v+C +Cg++ +l++ +l               +CpkCg++
  gi|119719876|ref|YP_920371.1|  3 KVELLVECPHCGYSDRLDSFKLlrdpwrysfyevrrlQCPKCGGT 47
                                   68899*******99998864346889999*************985 PP

>> zf-ISL3  zinc-finger of transposase IS204/IS1001/IS1096/IS1165
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.1     0.037        16       4      10 ..       9      15 ..       7      23 .. 0.84
   2 ?    7.5   0.1     0.016       6.7      40      47 .]      37      44 ..      33      55 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.037
                        zf-ISL3  4 rCPnCgs 10
                                    CP+Cg 
  gi|119719876|ref|YP_920371.1|  9 ECPHCGY 15
                                   6****95 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.016
                        zf-ISL3 40 rRyrCkeC 47
                                   rR++C++C
  gi|119719876|ref|YP_920371.1| 37 RRLQCPKC 44
                                   55555555 PP

>> Terminase_GpA  Phage terminase large subunit (GpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   9.7e-05      0.04     196     235 ..       5      46 ..       2      50 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.7e-05
                  Terminase_GpA 196 ryyvpCphCgelqels.ferlkwpege.aeekaryvCphcgs 235
                                    +  v+CphCg    l+ f+ l+ p      e  r++Cp+cg 
  gi|119719876|ref|YP_920371.1|   5 ELLVECPHCGYSDRLDsFKLLRDPWRYsFYEVRRLQCPKCGG 46 
                                    6689**********99888887644433778899******95 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0092       3.8      17      25 ..       8      16 ..       2      27 .. 0.84
   2 ?    5.0   0.1     0.062        26      16      24 ..      38      46 ..      34      52 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0092
                       zf-Mss51 17 feCpdCGip 25
                                   +eCp+CG++
  gi|119719876|ref|YP_920371.1|  8 VECPHCGYS 16
                                   79*****96 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.062
                       zf-Mss51 16 dfeCpdCGi 24
                                   +++Cp+CG 
  gi|119719876|ref|YP_920371.1| 38 RLQCPKCGG 46
                                   679****95 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0       0.1        42      24      30 ..      10      16 ..       8      19 .. 0.90
   2 ?    7.7   0.1     0.007       2.9      22      33 .]      39      50 ..      37      50 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.1
                  A2L_zn_ribbon 24 CieCgas 30
                                   C+ Cg+s
  gi|119719876|ref|YP_920371.1| 10 CPHCGYS 16
                                   *****98 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.007
                  A2L_zn_ribbon 22 lvCieCgasfpy 33
                                   l+C++Cg +f y
  gi|119719876|ref|YP_920371.1| 39 LQCPKCGGTFNY 50
                                   79*****88865 PP

>> DUF2752  Protein of unknown function (DUF2752)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1      0.26   1.1e+02       9      15 ..       8      14 ..       6      17 .. 0.86
   2 ?    9.5   0.1    0.0025         1       3      17 ..      33      47 ..      32      48 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.26
                        DUF2752  9 ipCPGCG 15
                                   ++CP CG
  gi|119719876|ref|YP_920371.1|  8 VECPHCG 14
                                   58***** PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0025
                        DUF2752  3 fkaltGipCPGCGlt 17
                                   f+++  ++CP CG+t
  gi|119719876|ref|YP_920371.1| 33 FYEVRRLQCPKCGGT 47
                                   7788889******98 PP

>> TRAF6_Z2  TNF receptor-associated factor 6 zinc finger 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.1     0.012         5       3       9 ..       7      13 ..       6      15 .. 0.92
   2 ?    5.9   0.2     0.032        14       5      13 ..      40      48 ..      38      50 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.012
                       TRAF6_Z2  3 lVeCPQC 9 
                                   lVeCP C
  gi|119719876|ref|YP_920371.1|  7 LVECPHC 13
                                   8****** PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.032
                       TRAF6_Z2  5 eCPQCQraF 13
                                    CP C + F
  gi|119719876|ref|YP_920371.1| 40 QCPKCGGTF 48
                                   6******99 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.2     0.034        14      28      34 ..      10      17 ..       8      20 .. 0.72
   2 ?    7.0   0.1     0.013       5.6      25      34 ..      38      47 ..      32      50 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.034
                        DUF35_N 28 CphC.gsd 34
                                   CphC  sd
  gi|119719876|ref|YP_920371.1| 10 CPHCgYSD 17
                                   9***5555 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.013
                        DUF35_N 25 ravCphCgsd 34
                                   r  Cp+Cg++
  gi|119719876|ref|YP_920371.1| 38 RLQCPKCGGT 47
                                   5779999764 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.1     0.054        22      24      28 ..      10      14 ..       4      19 .. 0.86
   2 ?    7.5   0.2     0.011       4.8      24      31 ..      41      48 ..      33      48 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.054
                  zinc_ribbon_9 24 CPhCg 28
                                   CPhCg
  gi|119719876|ref|YP_920371.1| 10 CPHCG 14
                                   ****8 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.011
                  zinc_ribbon_9 24 CPhCgggF 31
                                   CP Cgg F
  gi|119719876|ref|YP_920371.1| 41 CPKCGGTF 48
                                   ******99 PP

>> zf-AN1  AN1-like Zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.028        12       9      21 ..       3      15 ..       1      16 [. 0.80
   2 ?    6.3   0.2     0.026        11      14      23 ..      39      48 ..      32      48 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.028
                         zf-AN1  9 kdflpfkCryCgk 21
                                   k+ l ++C++Cg 
  gi|119719876|ref|YP_920371.1|  3 KVELLVECPHCGY 15
                                   56678******95 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.026
                         zf-AN1 14 fkCryCgkvF 23
                                    +C++Cg++F
  gi|119719876|ref|YP_920371.1| 39 LQCPKCGGTF 48
                                   79******99 PP

>> zf-tcix  Putative treble-clef, zinc-finger, Zn-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1     0.074        31      12      17 ..       9      14 ..       7      16 .. 0.86
   2 ?    7.9   0.1    0.0056       2.4      12      17 ..      40      45 ..      36      54 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.074
                        zf-tcix 12 kCpkCG 17
                                    Cp CG
  gi|119719876|ref|YP_920371.1|  9 ECPHCG 14
                                   6***** PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0056
                        zf-tcix 12 kCpkCG 17
                                   +CpkCG
  gi|119719876|ref|YP_920371.1| 40 QCPKCG 45
                                   7****8 PP

>> YacG  DNA gyrase inhibitor YacG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.037        15       1       9 [.       8      16 ..       8      26 .. 0.83
   2 ?    5.5   0.0     0.033        14       2      12 ..      40      50 ..      39      55 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.037
                           YacG  1 vkCPtCkke 9 
                                   v+CP+C+ +
  gi|119719876|ref|YP_920371.1|  8 VECPHCGYS 16
                                   89****976 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.033
                           YacG  2 kCPtCkkevew 12
                                   +CP+C+ ++++
  gi|119719876|ref|YP_920371.1| 40 QCPKCGGTFNY 50
                                   8*****98876 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.3     0.077        32      22      27 ..      10      15 ..       5      16 .. 0.76
   2 ?    8.1   0.1     0.006       2.5       4      14 ..      40      50 ..      40      62 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.077
                 PhnA_Zn_Ribbon 22 CpeCah 27
                                   Cp+C++
  gi|119719876|ref|YP_920371.1| 10 CPHCGY 15
                                   888875 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.006
                 PhnA_Zn_Ribbon  4 kCplCaSeytY 14
                                   +Cp+C+  ++Y
  gi|119719876|ref|YP_920371.1| 40 QCPKCGGTFNY 50
                                   7*****99999 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   2.2    0.0016      0.65      30      57 ..       9      49 ..       8      50 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0016
                 OrfB_Zn_ribbon 30 tCseCgsknke.............alsgrtfkCpnCgfead 57
                                   +C++Cg+ ++                + r+++Cp+Cg +++
  gi|119719876|ref|YP_920371.1|  9 ECPHCGYSDRLdsfkllrdpwrysFYEVRRLQCPKCGGTFN 49
                                   7999999999889999999998888899*********9876 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.7    0.0042       1.8      16      21 ..      10      15 ..       8      16 .. 0.58
   2 ?    6.8   0.5     0.014       5.7      16      20 ..      41      45 ..      38      47 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0042
                  zinc_ribbon_2 16 CpyCGt 21
                                   Cp+CG+
  gi|119719876|ref|YP_920371.1| 10 CPHCGY 15
                                   555554 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.014
                  zinc_ribbon_2 16 CpyCG 20
                                   Cp+CG
  gi|119719876|ref|YP_920371.1| 41 CPKCG 45
                                   66665 PP

>> zf_C2H2_10  C2H2 type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1      0.06        25       5      10 ..      10      15 ..       9      21 .. 0.91
   2 ?    6.4   0.2     0.016       6.6       5       9 ..      41      45 ..      38      48 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.06
                     zf_C2H2_10  5 CPKCqe 10
                                   CP C++
  gi|119719876|ref|YP_920371.1| 10 CPHCGY 15
                                   *****9 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.016
                     zf_C2H2_10  5 CPKCq 9 
                                   CPKC+
  gi|119719876|ref|YP_920371.1| 41 CPKCG 45
                                   ****7 PP

>> DUF2387  Probable metal-binding protein (DUF2387)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0    0.0025       1.1      31      43 ..       8      20 ..       3      28 .. 0.82
   2 ?    0.6   0.1       1.6   6.5e+02      11      15 ..      41      45 ..      36      48 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0025
                        DUF2387 31 rECvsCgftdels 43
                                   +EC +Cg++d+l+
  gi|119719876|ref|YP_920371.1|  8 VECPHCGYSDRLD 20
                                   7999999999886 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1.6
                        DUF2387 11 CPrCs 15
                                   CP+C 
  gi|119719876|ref|YP_920371.1| 41 CPKCG 45
                                   9**96 PP

>> Cys_rich_CPXG  Cysteine-rich CPXCG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.2    0.0089       3.7       1       8 [.       8      15 ..       8      20 .. 0.82
   2 ?    4.3   0.2     0.087        36       2      11 ..      40      49 ..      39      57 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0089
                  Cys_rich_CPXG  1 iqCPyCge 8 
                                   ++CP+Cg 
  gi|119719876|ref|YP_920371.1|  8 VECPHCGY 15
                                   68****96 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.087
                  Cys_rich_CPXG  2 qCPyCgeeie 11
                                   qCP Cg +++
  gi|119719876|ref|YP_920371.1| 40 QCPKCGGTFN 49
                                   8*****8875 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.1    0.0055       2.3      23      30 ..       7      14 ..       2      14 .. 0.84
   2 ?    2.9   0.1      0.31   1.3e+02      25      30 ..      40      45 ..      33      45 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0055
                                   -EE-TTT- CS
                      zf-RING_7 23 vvtCpeCG 30
                                   +v Cp+CG
  gi|119719876|ref|YP_920371.1|  7 LVECPHCG 14
                                   799****9 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.31
                                   E-TTT- CS
                      zf-RING_7 25 tCpeCG 30
                                   +Cp CG
  gi|119719876|ref|YP_920371.1| 40 QCPKCG 45
                                   8****9 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.2     0.073        30       3       8 ..       9      14 ..       8      16 .. 0.79
   2 ?    6.7   0.2     0.018       7.6       3       9 ..      40      46 ..      39      48 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.073
                         zf-ACC  3 KCpsCg 8 
                                    Cp+Cg
  gi|119719876|ref|YP_920371.1|  9 ECPHCG 14
                                   699997 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.018
                         zf-ACC  3 KCpsCge 9 
                                   +Cp+Cg 
  gi|119719876|ref|YP_920371.1| 40 QCPKCGG 46
                                   8999996 PP

>> zf-RanBP  Zn-finger in Ran binding protein and others
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.2     0.076        32       6      12 ..       9      15 ..       9      16 .. 0.84
   2 ?    6.6   0.2     0.012       4.9       6      14 ..      40      49 ..      40      50 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.076
                                   E-SSS-- CS
                       zf-RanBP  6 dCskClv 12
                                   +C++C++
  gi|119719876|ref|YP_920371.1|  9 ECPHCGY 15
                                   5****98 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.012
                                   E-SSS-.-EE CS
                       zf-RanBP  6 dCskCl.vqN 14
                                   +C+kC+ + N
  gi|119719876|ref|YP_920371.1| 40 QCPKCGgTFN 49
                                   8****98988 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.5     0.092        39       2       9 ..       9      16 ..       8      16 .. 0.87
   2 ?    7.3   0.3     0.017         7       2      12 ..      40      50 ..      39      54 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.092
                                   EETTTTEE CS
                        zf-C2H2  2 kCpdCgks 9 
                                   +Cp+Cg+s
  gi|119719876|ref|YP_920371.1|  9 ECPHCGYS 16
                                   6*****86 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.017
                                   EETTTTEEESS CS
                        zf-C2H2  2 kCpdCgksFkr 12
                                   +Cp+Cg +F+ 
  gi|119719876|ref|YP_920371.1| 40 QCPKCGGTFNY 50
                                   8*****99986 PP

>> Anti-TRAP  Tryptophan RNA-binding attenuator protein inhibitory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   5.1      0.03        12       8      39 ..       5      47 ..       1      49 [. 0.67

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.03
                                   HCEEE-TTTTTTSEETTE.................E-TTTTTS CS
                      Anti-TRAP  8 eLEtkCdaCngsGkiepe...........eprasleCPkCsGk 39
                                   eL ++C++C  s + ++             +   l+CPkC+G 
  gi|119719876|ref|YP_920371.1|  5 ELLVECPHCGYSDRLDSFkllrdpwrysfYEVRRLQCPKCGGT 47
                                   66677777777777777666665555544334569******95 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.8      0.49     2e+02      21      26 ..       9      14 ..       6      14 .. 0.70
   2 ?    4.8   6.7     0.042        17      15      29 ..      34      48 ..       9      50 .. 0.58

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.49
                       zf-TFIIB 21 yCpqCr 26
                                    Cp+C+
  gi|119719876|ref|YP_920371.1|  9 ECPHCG 14
                                   577775 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.042
                       zf-TFIIB 15 ggveidyCpqCrGvW 29
                                    +v   +Cp+C+G +
  gi|119719876|ref|YP_920371.1| 34 YEVRRLQCPKCGGTF 48
                                   666666899999987 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   6.7     0.054        22       3      36 ..       7      46 ..       5      53 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.054
                Lar_restr_allev  3 LkpCPfCggravlersqrvvaeigq......cvyCadCga 36
                                   L  CP+Cg  + l   ++ +  + +        +C +Cg 
  gi|119719876|ref|YP_920371.1|  7 LVECPHCGYSDRLDSFKLLRDPWRYsfyevrRLQCPKCGG 46
                                   678*****99999888888776666788899999999997 PP

>> Ogr_Delta  Ogr/Delta-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.6     0.022       9.2       1       6 [.       9      14 ..       9      18 .. 0.89
   2 ?    3.9   0.4      0.12        52       2       7 ..      41      46 ..      40      49 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.022
                      Ogr_Delta  1 rCPhCg 6 
                                   +CPhCg
  gi|119719876|ref|YP_920371.1|  9 ECPHCG 14
                                   6****9 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.12
                      Ogr_Delta  2 CPhCga 7 
                                   CP+Cg 
  gi|119719876|ref|YP_920371.1| 41 CPKCGG 46
                                   ****96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                       111  (0.00619109); expected 17.9 (0.001)
Passed Fwd filter:                        43  (0.00239835); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              43  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 530.62
//
Query:       gi|119719877|ref|YP_920372.1|  [L=120]
Description: hypothetical protein Tpen_0969 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.4e-08   33.1   0.2      1e-07   32.5   0.2    1.4  1  Asp_protease_2   Aspartyl protease
    3.6e-07   30.7   0.2    5.7e-07   30.0   0.2    1.4  1  gag-asp_proteas  gag-polyprotein putative aspartyl protease
  ------ inclusion threshold ------
      0.013   15.8   0.0      0.021   15.1   0.0    1.7  1  RVP              Retroviral aspartyl protease
      0.074   12.5   0.0      0.088   12.3   0.0    1.3  1  Peptidase_A3     Cauliflower mosaic virus peptidase (A3)


Domain annotation for each model (and alignments):
>> Asp_protease_2  Aspartyl protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.2   2.3e-11     1e-07       9      65 ..      20      72 ..       6      94 .. 0.74

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 2.3e-11
                 Asp_protease_2  9 pvrfllDTGasttlispelaeklglkvreseltvrvsgaggevkarlvrldslklgg 65
                                   ++++l+DTGa+ ++i+++la++lg++v +     rv++  g v+++++++  +++ g
  gi|119719877|ref|YP_920372.1| 20 EAECLVDTGATLSVIPRSLARELGVEVVDR---DRVETGAGVVEVDRGVA-LIEVEG 72
                                   6799***********************996...5999*9***99999854.555544 PP

>> gag-asp_proteas  gag-polyprotein putative aspartyl protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.2   1.3e-10   5.7e-07      11      63 ..      22      70 ..      19     100 .. 0.73

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 1.3e-10
                                   EEEEETT-SS-EEEHHHHHHTTGGGGEB..TT--EE-TTSTT-EEEEEEEEEE CS
                gag-asp_proteas 11 kflvDTGAsstiiseelaerlglsrkedkgkvevktangeveakrvrldsvki 63
                                   + lvDTGA+ ++i+++la++lg++  +   + +v+t+ g+ve+ r+  + +++
  gi|119719877|ref|YP_920372.1| 22 ECLVDTGATLSVIPRSLARELGVEVVD---RDRVETGAGVVEVDRGV-ALIEV 70
                                   789***********************9...589*******9997652.23333 PP

>> RVP  Retroviral aspartyl protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   4.8e-06     0.021       9      32 ..       4      37 ..       1     103 [. 0.85

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.8e-06
                                   EEETTE..........EEEEEE-TTBSSEEEES- CS
                            RVP  9 vkiggk..........yieallDtGAdatvisee 32
                                   v+++ k            e l+DtGA+ +vi+ +
  gi|119719877|ref|YP_920372.1|  4 VRVKAKvcdaqgarciEAECLVDTGATLSVIPRS 37
                                   55555566677777778899***********976 PP

>> Peptidase_A3  Cauliflower mosaic virus peptidase (A3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0     2e-05     0.088      13      48 ..      13      48 ..       3     102 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2e-05
                   Peptidase_A3 13 kknykkielhcyvdtGaslciakkkvipeenWvilk 48
                                    ++ + ie  c vdtGa+l +  + +  e   ++++
  gi|119719877|ref|YP_920372.1| 13 AQGARCIEAECLVDTGATLSVIPRSLARELGVEVVD 48
                                   4677889*************9998888665555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 791.67
//
Query:       gi|119719878|ref|YP_920373.1|  [L=87]
Description: hypothetical protein Tpen_0970 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 612.91
//
Query:       gi|119719879|ref|YP_920374.1|  [L=206]
Description: hypothetical protein Tpen_0971 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0088   16.0   1.6      0.019   15.0   1.6    1.5  1  TMF_DNA_bd       TATA element modulatory factor 1 DNA binding
     0.0088   15.0   4.5      0.011   14.6   4.5    1.1  1  Spc7             Spc7 kinetochore protein
     0.0093   16.2   0.2      0.018   15.3   0.2    1.5  1  BLOC1_2          Biogenesis of lysosome-related organelles co
  ------ inclusion threshold ------
      0.011   15.2   2.0      0.015   14.8   2.0    1.3  1  LRRFIP           LRRFIP family
      0.011   15.7   0.4      0.018   15.0   0.4    1.3  1  Laminin_II       Laminin Domain II
      0.014   16.0   1.4      0.032   14.8   0.9    2.0  1  SlyX             SlyX
      0.014   15.6   0.5      0.022   15.0   0.5    1.4  1  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
      0.027   14.3   0.6       0.04   13.8   0.6    1.3  1  DUF724           Protein of unknown function (DUF724)
      0.031   14.0   1.2      0.092   12.4   0.5    2.2  1  TFA2_Winged_2    TFA2 Winged helix domain 2
      0.031   13.9   0.2      0.045   13.4   0.2    1.3  1  Dehyd-heme_bind  Quinohemoprotein amine dehydrogenase A, alph
      0.042   14.4   0.2      0.091   13.3   0.3    1.5  1  DUF16            Protein of unknown function DUF16
      0.054   13.9   2.3        0.7   10.3   1.1    2.5  2  FlaC_arch        Flagella accessory protein C (FlaC)
      0.069   13.4   0.1       0.14   12.4   0.1    1.6  1  DUF948           Bacterial protein of unknown function (DUF94
       0.08   13.1   1.4       0.11   12.6   1.4    1.2  1  Mod_r            Modifier of rudimentary (Mod(r)) protein
      0.085   12.9   2.2       0.17   12.0   2.2    1.6  1  COG2             COG (conserved oligomeric Golgi) complex com
        0.1   12.6   0.1       0.21   11.6   0.1    1.4  1  PilJ             Type IV pili methyl-accepting chemotaxis tra
       0.11   11.5   0.5       0.14   11.2   0.5    1.1  1  Atg14            Vacuolar sorting 38 and autophagy-related su
       0.13   12.5   2.3       0.26   11.5   1.6    2.0  1  Cnn_1N           Centrosomin N-terminal motif 1
        0.2   11.5   3.6       0.25   11.1   3.6    1.2  1  Yuri_gagarin     Yuri gagarin
       0.24    9.7   3.1       0.32    9.3   3.1    1.1  1  SpecificRecomb   Site-specific recombinase
       0.53   10.8   7.0        1.1    9.8   7.0    1.5  1  APG6_N           Apg6 coiled-coil region
       0.64    8.0   8.0        0.8    7.7   8.0    1.1  1  DUF5401          Family of unknown function (DUF5401)


Domain annotation for each model (and alignments):
>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   1.6   2.3e-05     0.019      29      72 ..      44      87 ..      31      97 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.3e-05
                     TMF_DNA_bd 29 lklnntikkLrkknkelekeikelkkkleklekeleeleerlke 72
                                   ++l+ ++ +Lrk+++e++k+i el +++e l++ +++ e +l++
  gi|119719879|ref|YP_920374.1| 44 VELRRSVEELRKTVEEHTKQIIELRRETEGLDERVSRVEGLLER 87
                                   45555566666666666666666666666666666555555443 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   4.5   1.4e-05     0.011     177     271 ..       3      99 ..       1     106 [. 0.87

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.4e-05
                           Spc7 177 aeleeeleklqeaaeeles..idkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeae 254
                                    a+l++el +l ++ ee+    +    Le lr +++e+   + e+++ ++el++ +ee +++i el+ + + l e++++ e
  gi|119719879|ref|YP_920374.1|   3 AQLKRELFRLLKEDEEFRYamMALLGLEDLRGSMREVRDSVVELRRSVEELRKTVEEHTKQIIELRRETEGLDERVSRVE 82 
                                    678888888888777776644668899***************************************************** PP

                           Spc7 255 rvleeckgwsesevsrl 271
                                     +le+   ++e+e + +
  gi|119719879|ref|YP_920374.1|  83 GLLERLAVSEEEEANDV 99 
                                    **999999999987765 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.2   2.2e-05     0.018      37      91 ..      37      88 ..      29      91 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.2e-05
                        BLOC1_2 37 kklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeL 91
                                    +++d++ +l++++e+l++   +++++ +qi ++ ++++ L e vs+++    +L
  gi|119719879|ref|YP_920374.1| 37 REVRDSVVELRRSVEELRK---TVEEHTKQIIELRRETEGLDERVSRVEGLLERL 88
                                   5788899999999999999...***************************999998 PP

>> LRRFIP  LRRFIP family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   2.0   1.8e-05     0.015     120     190 ..      30      98 ..       7     127 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.8e-05
                         LRRFIP 120 dlLkdkleeleeslaelqrelrekckelerlkrqlealkleldelkeklkqrdeLiedhglvlveeeatdg 190
                                    + L+ ++ e+ +s++el+r+++e +k +e+  +q+ +l++e + l e + + + L+e     + eee+ ++
  gi|119719879|ref|YP_920374.1|  30 EDLRGSMREVRDSVVELRRSVEELRKTVEEHTKQIIELRRETEGLDERVSRVEGLLERLA--VSEEEEAND 98 
                                    77999***************************************************8866..555544444 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.4   2.2e-05     0.018      18      87 ..      28      97 ..      20     107 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.2e-05
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH... CS
                     Laminin_II 18 qlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeasss 87
                                    l++l   + ++++++ e++rsvee  + v++ +k+i + rr+   L++ + +++  l++l   ee++++
  gi|119719879|ref|YP_920374.1| 28 GLEDLRGSMREVRDSVVELRRSVEELRKTVEEHTKQIIELRRETEGLDERVSRVEGLLERLAVSEEEEAN 97
                                   57888899999**************************************999998888888777666554 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.9     4e-05     0.032      15      55 ..      46      86 ..      30      97 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4e-05
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXX CS
                           SlyX 15 qedtieeLndvvaeqqqqidrlqrqlrllaerlkeleessg 55
                                   + + +eeL ++v e+ +qi +l+r+ + l er++ +e   +
  gi|119719879|ref|YP_920374.1| 46 LRRSVEELRKTVEEHTKQIIELRRETEGLDERVSRVEGLLE 86
                                   56889****************************88776554 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.5   2.8e-05     0.022      32      91 ..      37      96 ..      11     105 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.8e-05
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHH CS
                   Seryl_tRNA_N 32 leldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelk 91
                                    e+ +   el+  +eel++   e +k+I ++ ++ e  +e + +v+ l e+l+  e+e++
  gi|119719879|ref|YP_920374.1| 37 REVRDSVVELRRSVEELRKTVEEHTKQIIELRRETEGLDERVSRVEGLLERLAVSEEEEA 96
                                   57778899**************************99999999999999999999888765 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.6   4.9e-05      0.04     101     184 ..       6      88 ..       2      92 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.9e-05
                         DUF724 101 kdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaekleeeledveqe 180
                                    k e  +ll+e +++   ++ +    + l  +++e+   ++el+r  + l++  e++ k+i +l+ e+e l+e++++ve  
  gi|119719879|ref|YP_920374.1|   6 KRELFRLLKEDEEFRYAMM-ALLGLEDLRGSMREVRDSVVELRRSVEELRKTVEEHTKQIIELRRETEGLDERVSRVEGL 84 
                                    5555556666666555555.33446778899********************************************99976 PP

                         DUF724 181 Feav 184
                                     e++
  gi|119719879|ref|YP_920374.1|  85 LERL 88 
                                    6655 PP

>> TFA2_Winged_2  TFA2 Winged helix domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.5   0.00011     0.092       5      54 ..       8      75 ..       5      79 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00011
                  TFA2_Winged_2  5 eLlalLkkrp.............kaeGikvkdLkdswpdveealeeLea.....egeilvlrtkkdg.q 54
                                   eL +lLk+ +             +  G ++++++ds +  +  +eeL +     +++i+ lr + +g  
  gi|119719879|ref|YP_920374.1|  8 ELFRLLKEDEefryammallgleDLRG-SMREVRDSVVELRRSVEELRKtveehTKQIIELRRETEGlD 75
                                   666666666655554333222211222.46677777777777777777699888899999988877744 PP

>> Dehyd-heme_bind  Quinohemoprotein amine dehydrogenase A, alpha subunit, haem binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   5.5e-05     0.045      20      74 ..      58     113 ..      42     142 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.5e-05
                Dehyd-heme_bind  20 dgkleriseqrktPeGwdmtvarmq.lehgleltkaer.aeivkyladtqGlapses 74 
                                    ++++++i e r+  eG d  v+r++ l  +l++ ++e+ ++++ +l  ++Gla + +
  gi|119719879|ref|YP_920374.1|  58 EEHTKQIIELRRETEGLDERVSRVEgLLERLAVSEEEEaNDVIMHLLRQRGLAVE-T 113
                                    45678999***************963678999987665278***********974.3 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.3   0.00011     0.091      35      88 ..      35      88 ..      15      99 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00011
                                   HHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHH CS
                          DUF16 35 rLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetleli 88
                                    ++++ + v  l  ++++l ++ve+ +++i el+ e +  +e++ +v+  le +
  gi|119719879|ref|YP_920374.1| 35 SMREVRDSVVELRRSVEELRKTVEEHTKQIIELRRETEGLDERVSRVEGLLERL 88
                                   57888999999*******************************999998888755 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.1   0.00085       0.7       9      38 ..      29      62 ..      28      67 .. 0.78
   2 ?    2.7   0.1      0.21   1.7e+02      21      43 ..      62      84 ..      59      91 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00085
                      FlaC_arch  9 lsklsteletvkkeneelsksveelkenV....k 38
                                   l++l  ++  v+++  el+ sveel ++V    k
  gi|119719879|ref|YP_920374.1| 29 LEDLRGSMREVRDSVVELRRSVEELRKTVeehtK 62
                                   5678889999999999999999999999955555 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.21
                      FlaC_arch 21 keneelsksveelkenVkdllsL 43
                                   k++ el+ + e l+e+V ++ +L
  gi|119719879|ref|YP_920374.1| 62 KQIIELRRETEGLDERVSRVEGL 84
                                   67778999999999999887555 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00017      0.14      22      58 ..      44      80 ..      26     102 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00017
                         DUF948 22 lklkktldeaaatieelekqvdpilkevedllakvne 58
                                   ++l++ ++e+++t+ee +kq+ ++ +e+e+l + v +
  gi|119719879|ref|YP_920374.1| 44 VELRRSVEELRKTVEEHTKQIIELRRETEGLDERVSR 80
                                   6789999999999999999999999999999888877 PP

>> Mod_r  Modifier of rudimentary (Mod(r)) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   1.4   0.00013      0.11       6     102 ..       7     106 ..       5     114 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00013
                          Mod_r   6 eeLqelledeeklealvktlpevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqeld 85 
                                     eL +ll+++e ++  +  l  +++l+ +  e++++ ++l ++  +l++++ee  ++++e + e++ l +++ + e  l+
  gi|119719879|ref|YP_920374.1|   7 RELFRLLKEDEEFRYAMMALLGLEDLRGSMREVRDSVVELRRSVEELRKTVEEHTKQIIELRRETEGLDERVSRVEGLLE 86 
                                    699999**999999999999999*****************9999999*****************9999999999998888 PP

                          Mod_r  86 ell...qkfspdallarLqt 102
                                    +l    ++   d ++++L++
  gi|119719879|ref|YP_920374.1|  87 RLAvseEEEANDVIMHLLRQ 106
                                    88766666666666666665 PP

>> COG2  COG (conserved oligomeric Golgi) complex component, COG2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   2.2   0.00021      0.17      41     109 ..       4      74 ..       1      96 [. 0.62

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00021
                           COG2  41 llekellelvnedyad.FvslS.ghLvglqeeleevesplaaarkkvesvreklsereeeveskleeakel 109
                                    +l++el +l  ed +  +  +    L +l+ +++ev+ ++ ++r+ ve++r+ ++e+ +++ +  +e + l
  gi|119719879|ref|YP_920374.1|   4 QLKRELFRLLKEDEEFrYAMMAlLGLEDLRGSMREVRDSVVELRRSVEELRKTVEEHTKQIIELRRETEGL 74 
                                    56666666666664444444431245566667777777777777777777777777777776655554444 PP

>> PilJ  Type IV pili methyl-accepting chemotaxis transducer N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00025      0.21      31     105 ..      23      95 ..      19     100 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00025
                           PilJ  31 llaaagaydaaearaqlretiaqfdrtlaalrlgdpapgllvpaeavraqleaveqlWqelkkpaeaalaqqdda 105
                                    + a+ g +d  ++ +++r+++ +++r++++lr++ ++ + +    + r++ e+++++ ++ +  +e+++++++ +
  gi|119719879|ref|YP_920374.1|  23 MMALLGLEDLRGSMREVRDSVVELRRSVEELRKTVEEHTKQII--ELRRETEGLDERVSRVEGLLERLAVSEEEE 95 
                                    4456666889999999******************999888777..9*******************9999888765 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.5   0.00017      0.14      31     114 ..       9      81 ..       3     120 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00017
                          Atg14  31 laklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdk 110
                                    l +l++e e+++  + ++l  ++           ++ +++e +  + +lr+ ++el++++++ +k+i e +++ ++l++ 
  gi|119719879|ref|YP_920374.1|   9 LFRLLKEDEEFRYAMMALLGLED-----------LRGSMREVRDSVVELRRSVEELRKTVEEHTKQIIELRRETEGLDER 77 
                                    55555555555555555555555...........5556666666666666666666666666666666666666666666 PP

                          Atg14 111 lkkR 114
                                    +++ 
  gi|119719879|ref|YP_920374.1|  78 VSRV 81 
                                    6533 PP

>> Cnn_1N  Centrosomin N-terminal motif 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.6   0.00031      0.26      36      71 ..      34      69 ..       4      71 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00031
                         Cnn_1N 36 eqkeellkenielkveveslqkelkekkkllreaek 71
                                    +++e+ ++ +el+  ve+l+k+++e +k++ e+ +
  gi|119719879|ref|YP_920374.1| 34 GSMREVRDSVVELRRSVEELRKTVEEHTKQIIELRR 69
                                   5789999***********************999876 PP

>> Yuri_gagarin  Yuri gagarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   3.6   0.00031      0.25     117     177 ..      31      91 ..       2     113 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00031
                   Yuri_gagarin 117 elaeelkgeeeqrvelvdkyekllasfeeqckelkranrrvqslqerlsqveklqeelrte 177
                                    +l   +++  +  vel    e+l  + ee  k++ + +r  + l er+s+ve l e l   
  gi|119719879|ref|YP_920374.1|  31 DLRGSMREVRDSVVELRRSVEELRKTVEEHTKQIIELRRETEGLDERVSRVEGLLERLAVS 91 
                                    44555666677889****************************************9998765 PP

>> SpecificRecomb  Site-specific recombinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   3.1   0.00039      0.32     179     277 ..       8     106 ..       2     114 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00039
                 SpecificRecomb 179 pFlalqrelealleayeaaledeeeaeedlkhlrvlldqcreavdrvrkhleenGvs.vslvfllerlrqrleRleeLld 257
                                      ++l +e e+++ a+ a l   e+ + +++++r  + + r+ v+++rk +ee+    ++l  + e l++r++R+e Ll+
  gi|119719879|ref|YP_920374.1|   8 ELFRLLKEDEEFRYAMMA-LLGLEDLRGSMREVRDSVVELRRSVEELRKTVEEHTKQiIELRRETEGLDERVSRVEGLLE 86 
                                    455666666667666666.777888899999*********************99655279******************** PP

                 SpecificRecomb 258 llleeeeeeraralveLlke 277
                                     l+ +eeee++  +++Ll++
  gi|119719879|ref|YP_920374.1|  87 RLAVSEEEEANDVIMHLLRQ 106
                                    ***99999999999999976 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   7.0    0.0013       1.1      45     104 ..      39      98 ..       2     112 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0013
                         APG6_N  45 qdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwre 104
                                     ++++ el++++e+l+k+ ee  +++ el +e e l++ ++  e  le+l   ee++ ++
  gi|119719879|ref|YP_920374.1|  39 VRDSVVELRRSVEELRKTVEEHTKQIIELRRETEGLDERVSRVEGLLERLAVSEEEEAND 98 
                                    56788899999***************************************9999987665 PP

>> DUF5401  Family of unknown function (DUF5401)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   8.0   0.00098       0.8     416     488 ..       4      77 ..       2     130 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00098
                        DUF5401 416 eqkvemekirkeqeearqeelrrleeerar.elervreeelerqqqverlrqqeeerkrkklelekekrekkea 488
                                    + k+e+ ++ ke+ee r   +  l  e  r  +  vr+  +e ++ ve lr+  ee+ ++ +el +e +  +e 
  gi|119719879|ref|YP_920374.1|   4 QLKRELFRLLKEDEEFRYAMMALLGLEDLRgSMREVRDSVVELRRSVEELRKTVEEHTKQIIELRRETEGLDER 77 
                                    5689999999***********99987766637999****************************99998654332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1414  (0.0788666); expected 358.6 (0.02)
Passed bias filter:                     1056  (0.058899); expected 358.6 (0.02)
Passed Vit filter:                       191  (0.0106531); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.42
# Mc/sec: 1456.86
//
Query:       gi|119719880|ref|YP_920375.1|  [L=171]
Description: PaREP8 domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.4e-37  126.0   7.7    9.8e-37  125.4   7.7    1.3  1  PaREP1           Archaeal PaREP1/PaREP8 family
     0.0061   16.6   0.2      0.013   15.6   0.2    1.6  1  DUF357           Protein of unknown function (DUF357)
  ------ inclusion threshold ------
      0.013   15.6   4.3       0.04   14.1   4.3    1.9  1  HEPN             HEPN domain
      0.054   14.1   1.4       0.28   11.8   1.4    2.0  1  ParE_toxin       ParE toxin of type II toxin-antitoxin system
      0.066   13.8   0.1       0.12   12.9   0.1    1.5  1  DUF3597          Domain of unknown function (DUF3597)
       0.13   13.1   0.2       0.26   12.1   0.1    1.7  2  Ribosomal_S30AE  Sigma 54 modulation protein / S30EA ribosoma


Domain annotation for each model (and alignments):
>> PaREP1  Archaeal PaREP1/PaREP8 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.4   7.7   3.3e-40   9.8e-37       1     114 [.      41     154 ..      41     155 .. 0.98

  Alignments for each domain:
  == domain 1  score: 125.4 bits;  conditional E-value: 3.3e-40
                         PaREP1   1 arleeaekeleeAeellekGdlrqAaeKaykAvkalvkalaeknnlklleeaeekerwstkellkavaklleelgdkevv 80 
                                    arle+aek l eAee+l+kGd++qA+eK+ykAv+++vkalaek   k++eea++++rw+t++l +a+++l+++lg+++v+
  gi|119719880|ref|YP_920375.1|  41 ARLELAEKSLGEAEEYLAKGDVVQASEKLYKAVEECVKALAEKLGAKQAEEARRRGRWDTWLLGMAATDLARTLGEDRVR 120
                                    69****************************************************************************** PP

                         PaREP1  81 dlwklAldLHeyqfheaklelsdveskeeavkdl 114
                                    ++wk A+d H+++fheak++++dve++ + +++l
  gi|119719880|ref|YP_920375.1| 121 LAWKDAYDVHVWGFHEAKYRVEDVEAALPLARWL 154
                                    ***************************9999988 PP

>> DUF357  Protein of unknown function (DUF357)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.2   4.2e-06     0.013      16      54 ..      28      66 ..       9      72 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.2e-06
                                   ....TS---HHHHHHHHHHHHHHHHHHHHHHTT-HHHHH CS
                         DUF357 16 apdeesplgeaaeevlemaesYleDakyflekgdlvnAl 54
                                    p +  +    ae  le+ae+ l +a+++l+kgd v+A 
  gi|119719880|ref|YP_920375.1| 28 DPAKTLNTDPSAEARLELAEKSLGEAEEYLAKGDVVQAS 66
                                   233444445567999*********************995 PP

>> HEPN  HEPN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   4.3   1.3e-05      0.04       1      50 [.      39      88 ..      39     162 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.3e-05
                                   HHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHTT--. CS
                           HEPN  1 aeewlrrAeedleaAellleegdydlacfhaqqaaekalKAlllkkggep 50
                                   ae+ l+ Ae+ l +Ae+ l +gd   a  + + a+e ++KAl  k+g + 
  gi|119719880|ref|YP_920375.1| 39 AEARLELAEKSLGEAEEYLAKGDVVQASEKLYKAVEECVKALAEKLGAKQ 88
                                   588999************************************99998765 PP

>> ParE_toxin  ParE toxin of type II toxin-antitoxin system, parDE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   1.4   9.4e-05      0.28       6      50 ..      45      91 ..      43     148 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9.4e-05
                                   HHHHHHHHHHHHHH.CC-H.HHHHHHHHHHHHHHHHHHHTTTSEECT CS
                     ParE_toxin  6 rAlkdlkkiadyia.rdgp.aakrfldaleealellaenpalgrprr 50
                                    A+k l ++ +y+a  d   a +++ +a+ee++++lae   + +  +
  gi|119719880|ref|YP_920375.1| 45 LAEKSLGEAEEYLAkGDVVqASEKLYKAVEECVKALAEKLGAKQAEE 91
                                   699***********6666679*****************999988822 PP

>> DUF3597  Domain of unknown function (DUF3597)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   4.1e-05      0.12      62     100 ..      15      54 ..       5      87 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.1e-05
                                    HHSS---TTT-HHHHHHHT----SHHHHHHHHHH.HT--- CS
                        DUF3597  62 ksgeklnwrtSivDLlkllglDsslaaRkeLAke.Lgytg 100
                                    + ++ l+   S vD  k l+ D s +aR eLA+  Lg  +
  gi|119719880|ref|YP_920375.1|  15 AVKKGLDIEASAVDPAKTLNTDPSAEARLELAEKsLGEAE 54 
                                    4567799*************************74255444 PP

>> Ribosomal_S30AE  Sigma 54 modulation protein / S30EA ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   8.9e-05      0.26      40      78 ..      49      84 ..       6      90 .. 0.78
   2 ?   -3.0   0.0       4.4   1.3e+04      54      67 ..     139     148 ..     117     151 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.9e-05
                                   EEEEEEEEECTTEEEEEEEEESSHHHHHHHHHHHHHHHH CS
                Ribosomal_S30AE 40 kkvevtirlakgkviraeeesedlyaaidlavdklerql 78
                                      e++ +lakg+v++a   se ly+a++++v++l ++l
  gi|119719880|ref|YP_920375.1| 49 SLGEAEEYLAKGDVVQA---SEKLYKAVEECVKALAEKL 84
                                   4557777788999***9...79*************9987 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.4
                                    EEEEEEESSHHHHH CS
                Ribosomal_S30AE  54 iraeeesedlyaai 67 
                                     r+    ed++aa+
  gi|119719880|ref|YP_920375.1| 139 YRV----EDVEAAL 148
                                    233....6666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       725  (0.0404373); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1176.07
//
Query:       gi|119719881|ref|YP_920376.1|  [L=148]
Description: iron dependent repressor [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-21   76.7   2.7    2.8e-21   75.4   0.6    2.3  2  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
    5.4e-13   48.8   0.1    1.3e-12   47.6   0.1    1.6  1  Fe_dep_repr_C   Iron dependent repressor, metal binding and d
    3.3e-08   33.3   0.0    8.3e-08   32.0   0.0    1.6  1  MarR_2          MarR family
    7.1e-06   25.7   0.0    1.4e-05   24.8   0.0    1.5  1  HTH_IclR        IclR helix-turn-helix domain
    3.2e-05   24.3   0.2    7.5e-05   23.1   0.1    1.7  1  HTH_27          Winged helix DNA-binding domain
    9.4e-05   22.3   0.0    0.00022   21.1   0.0    1.7  1  MarR            MarR family
    0.00042   20.0   0.1      0.043   13.6   0.0    2.8  3  LexA_DNA_bind   LexA DNA binding domain
    0.00044   20.5   0.1    0.00091   19.5   0.1    1.5  1  Rrf2            Transcriptional regulator
    0.00078   19.0   0.1     0.0024   17.4   0.0    1.9  2  HTH_24          Winged helix-turn-helix DNA-binding
      0.001   18.9   0.2     0.0031   17.4   0.2    1.9  1  TrmB            Sugar-specific transcriptional regulator TrmB
     0.0013   18.5   0.0     0.0047   16.8   0.0    1.9  2  HTH_5           Bacterial regulatory protein, arsR family
     0.0028   16.5   0.4     0.0034   16.3   0.4    1.1  1  HTH_micro       HTH-like
     0.0041   16.8   0.7       0.13   11.9   0.0    2.4  3  DUF4423         Domain of unknown function (DUF4423)
      0.006   16.5   0.0      0.013   15.5   0.0    1.6  1  HTH_Crp_2       Crp-like helix-turn-helix domain
  ------ inclusion threshold ------
      0.019   15.5   0.1      0.032   14.8   0.1    1.6  1  AAA_assoc_C     C-terminal AAA-associated domain
      0.022   14.9   0.3      0.043   13.9   0.3    1.4  1  DUF2250         Uncharacterized protein conserved in archaea 
      0.035   14.1   0.0      0.083   12.9   0.0    1.7  1  HTH_36          Helix-turn-helix domain
      0.036   14.2   0.2        0.3   11.2   0.0    2.6  3  HTH_28          Helix-turn-helix domain
      0.042   14.0   0.2       0.11   12.7   0.0    1.8  1  AbiEi_4         Transcriptional regulator, AbiEi antitoxin
      0.046   13.8   0.1      0.081   13.0   0.1    1.3  1  UPF0302         UPF0302 domain
      0.053   13.2   0.3        2.6    7.7   0.0    2.3  2  HrcA_DNA-bdg    Winged helix-turn-helix transcription repress
      0.056   13.2   0.1       0.35   10.7   0.0    2.4  2  HTH_23          Homeodomain-like domain
      0.063   13.5   0.2       0.22   11.8   0.1    1.9  2  Rio2_N          Rio2, N-terminal
      0.086   12.7   0.0       0.23   11.3   0.0    1.8  1  HTH_10          HTH DNA binding domain
      0.095   12.4   0.1      0.099   12.3   0.1    1.1  1  DUF1848         Domain of unknown function (DUF1848)
      0.095   12.7   0.1       0.15   12.0   0.1    1.5  1  HTH_45          Winged helix-turn-helix
       0.12   12.1   0.1        1.5    8.6   0.1    2.3  1  MerR            MerR family regulatory protein


Domain annotation for each model (and alignments):
>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.4   0.6   4.3e-24   2.8e-21       3      59 ..       6      62 ..       4      63 .. 0.96
   2 ?    0.5   0.1       1.1   7.1e+02      41      49 ..     138     146 ..     137     147 .. 0.88

  Alignments for each domain:
  == domain 1  score: 75.4 bits;  conditional E-value: 4.3e-24
                                   -HHHHHHHHHHHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTTE CS
                 Fe_dep_repress  3 vestEdYLetIYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyveyekykg 59
                                   +++ EdYL++IY++ e k++v+ kd++++L+v+ps++ em++kL++ G+v+y+ky g
  gi|119719881|ref|YP_920376.1|  6 SRRSEDYLRVIYEIAEAKGYVRIKDISRALGVKPSTAVEMVRKLHELGLVDYKKYEG 62
                                   6789***************************************************99 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1.1
                                    HHHHHHHHT CS
                 Fe_dep_repress  41 emlkkLekd 49 
                                    em+k+L+k+
  gi|119719881|ref|YP_920376.1| 138 EMIKRLDKK 146
                                    8*****985 PP

>> Fe_dep_repr_C  Iron dependent repressor, metal binding and dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.6   0.1     2e-15   1.3e-12       1      60 [.      66     124 ..      66     129 .. 0.96

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 2e-15
                                    -HHHHHHHHHHHHHHHHHHHHHHHHCT--CCCHHHHCCCCGGGS-HHHHHHHHHHCT-.S CS
                  Fe_dep_repr_C   1 TekGrelAkrlvrrhrllerfLvdvlgvdweeaheeAerlEhalseelierldellgfpe 60 
                                    T +G+e+A+ +++r  + e+fL +++ v+++ a ++A+ lEh ls+e++ ++ ++++f +
  gi|119719881|ref|YP_920376.1|  66 TARGKEIAEAVKKRRDIFENFL-KIILVPENVAKRDAHILEHQLSPETVLQIARFVEFAS 124
                                    899*******************.99*******************************9976 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.0   1.2e-10   8.3e-08       8      54 ..      13      58 ..      11      69 .. 0.94

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 1.2e-10
                                   HHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                         MarR_2  8 arvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                   +rv+++++ + g+ ++++++ r+lg+++s++  ++++L + GLv ++
  gi|119719881|ref|YP_920376.1| 13 LRVIYEIAEAKGY-VRIKDISRALGVKPSTAVEMVRKLHELGLVDYK 58
                                   69**********9.9*****************************876 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   2.1e-08   1.4e-05      12      50 ..      19      57 ..      13      59 .. 0.92

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 2.1e-08
                                   -CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                       HTH_IclR 12 laeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                   +aea + +++++++r++g+ +St+  +++ L+elG+v +
  gi|119719881|ref|YP_920376.1| 19 IAEAKGYVRIKDISRALGVKPSTAVEMVRKLHELGLVDY 57
                                   79999999****************************975 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.1   1.1e-07   7.5e-05      10      67 ..      14      68 ..      11      69 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1.1e-07
                         HTH_27 10 hlir...hrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdk 67
                                   ++i+   +  + ++++d++++l v  s+++++++kL+e GLv        +++  ++lT+ 
  gi|119719881|ref|YP_920376.1| 14 RVIYeiaEAKGYVRIKDISRALGVKPSTAVEMVRKLHELGLVDY------KKYEGITLTAR 68
                                   55555557788899****************************44......44446666665 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   3.4e-07   0.00022       7      48 ..      14      56 ..       9      62 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 3.4e-07
                                   HHHHHHHHSTT.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                           MarR  7 viLrilyeqgp.lsvseLakklgvskstvtrvldrLekkGlie 48
                                   ++++ ++e  +  +++++ ++lgv++st+ +++++L + Gl++
  gi|119719881|ref|YP_920376.1| 14 RVIYEIAEAKGyVRIKDISRALGVKPSTAVEMVRKLHELGLVD 56
                                   6677777777779***************************996 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   6.5e-05     0.043       5      59 ..       6      58 ..       1      61 [. 0.87
   2 ?   -1.2   0.0       2.7   1.8e+03       4      16 ..      65      77 ..      63      80 .. 0.77
   3 ?    3.2   0.0      0.11        74      18      41 ..     102     126 ..      99     148 .] 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.5e-05
                                   -HHHHHHHHHHHHHHHHHSS---HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE-G CS
                  LexA_DNA_bind  5 TerQrevldlikasieetgypPsireiaralglkSpsaveehLkaLerKGyierd 59
                                   ++r ++ l++i +  e +gy   i++i+ralg+k ps++ e  ++L+  G+++ +
  gi|119719881|ref|YP_920376.1|  6 SRRSEDYLRVIYEIAEAKGYV-RIKDISRALGVK-PSTAVEMVRKLHELGLVDYK 58
                                   5677889*************8.79**********.9999999******9999876 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.7
                                   --HHHHHHHHHHH CS
                  LexA_DNA_bind  4 LTerQrevldlik 16
                                   LT+r +e+ + +k
  gi|119719881|ref|YP_920376.1| 65 LTARGKEIAEAVK 77
                                   8899888887776 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.11
                                    HHHHHSS--.-HHHHHHHHTS-.HH CS
                  LexA_DNA_bind  18 sieetgypP.sireiaralglkSps 41 
                                    +i e++  P ++ +iar + ++S +
  gi|119719881|ref|YP_920376.1| 102 HILEHQLSPeTVLQIARFVEFASQA 126
                                    6667777665999********9864 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.1   1.4e-06   0.00091       3      73 ..       5      71 ..       1      74 [. 0.85

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.4e-06
                                   --HHHHHHHHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT-TCEEESSHCCC CS
                           Rrf2  3 lsskteyalhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvrGkgGGyrLakppee 73
                                   +s+++e  l++++++a+ ++   v++++i++  +++ps +  +++kL + glv  ++    G++L+   +e
  gi|119719881|ref|YP_920376.1|  5 VSRRSEDYLRVIYEIAEAKG--YVRIKDISRALGVKPSTAVEMVRKLHELGLVDYKKYE--GITLTARGKE 71
                                   688899999*******9999..49*****************************988644..6666665555 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   3.7e-06    0.0024       7      47 ..      15      55 ..      10      56 .. 0.91
   2 ?   -2.7   0.1       7.1   4.7e+03      21      27 ..      70      76 ..      70      77 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.7e-06
                         HTH_24  7 kILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                    I+e+ ++++   +++++++lg+ pst  + +++L e Gl+
  gi|119719881|ref|YP_920376.1| 15 VIYEIAEAKGYVRIKDISRALGVKPSTAVEMVRKLHELGLV 55
                                   57888888*******************************98 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 7.1
                         HTH_24 21 reLAerl 27
                                   +e+Ae++
  gi|119719881|ref|YP_920376.1| 70 KEIAEAV 76
                                   79**998 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.2   4.7e-06    0.0031      21      56 ..      24      59 ..      16      78 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.7e-06
                                   CCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                           TrmB 21 gpatadeiaeelgvprskvYevLrsLedkGlVerek 56
                                   g  ++++i+++lgv  s++ e++r+L + GlV+ +k
  gi|119719881|ref|YP_920376.1| 24 GYVRIKDISRALGVKPSTAVEMVRKLHELGLVDYKK 59
                                   667899**************************8766 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0     7e-06    0.0047       6      47 .]      14      57 ..      10      57 .. 0.84
   2 ?   -2.7   0.0       8.2   5.5e+03      14      23 ..     109     118 ..     104     121 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 7e-06
                                   HHHHHHTT..SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                          HTH_5  6 kILklLae..gelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                   ++++  ae  g   + +++++lg+ +st  +  +kL+e+GLV++
  gi|119719881|ref|YP_920376.1| 14 RVIYEIAEakGYVRIKDISRALGVKPSTAVEMVRKLHELGLVDY 57
                                   5666666655556789**************************86 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 8.2
                                    SSEEHHHHHH CS
                          HTH_5  14 gelcvcelae 23 
                                    ++ +v ++a+
  gi|119719881|ref|YP_920376.1| 109 SPETVLQIAR 118
                                    5677777775 PP

>> HTH_micro  HTH-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.4   5.1e-06    0.0034      89     161 ..       8      79 ..       2     103 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5.1e-06
                      HTH_micro  89 tskeyykivdflvkakdyvkaaelraklnidpKklfYvikkLakkglieqktkeeakivikinkDesgsvvkk 161
                                     s+ y +++  + +ak yv  +++   l + p +   +++kL++ gl+++k+ e++    + ++   + v k+
  gi|119719881|ref|YP_920376.1|   8 RSEDYLRVIYEIAEAKGYVRIKDISRALGVKPSTAVEMVRKLHELGLVDYKKYEGITLTARGKE-IAEAVKKR 79 
                                    5677999999********************************************9987755444.44444444 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0    0.0002      0.13      20      72 ..      10      59 ..       7      66 .. 0.92
   2 ?    4.6   0.1     0.036        24     117     151 ..      58      92 ..      55     116 .. 0.84
   3 ?   -2.8   0.0       6.9   4.6e+03     133     143 ..     125     135 ..     120     146 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0002
                        DUF4423 20 sWyypvirellplkdfkadpeelakrlrpkisaeevekalefLlklgllkkde 72
                                   + y  vi+e++++k +   ++ ++++l+  ++ + + + ++ L +lgl++ ++
  gi|119719881|ref|YP_920376.1| 10 EDYLRVIYEIAEAKGY-VRIKDISRALG--VKPSTAVEMVRKLHELGLVDYKK 59
                                   67899***********.***********..******************98765 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.036
                        DUF4423 117 Rdissltlaiskedyekikkeirefrkkilaiaee 151
                                     ++ ++tl+   +++++++k+ r+  +++l+i+  
  gi|119719881|ref|YP_920376.1|  58 KKYEGITLTARGKEIAEAVKKRRDIFENFLKIILV 92 
                                    67999*************************99755 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 6.9
                        DUF4423 133 kikkeirefrk 143
                                    ++k+ i+efr+
  gi|119719881|ref|YP_920376.1| 125 QAKEWIDEFRN 135
                                    66777777775 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.9e-05     0.013      25      62 ..      29      68 ..      11      70 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.9e-05
                                   HHHHHHTTSSHHHHHHHHHHHHHTTSEE.ETEE.EEES-H CS
                      HTH_Crp_2 25 eelAsmlGltretvsrilseLkreglis.rgrr.irildl 62
                                   +++++ lG+ ++t   + ++L + gl++ ++++ i+++ +
  gi|119719881|ref|YP_920376.1| 29 KDISRALGVKPSTAVEMVRKLHELGLVDyKKYEgITLTAR 68
                                   79**************************755445998765 PP

>> AAA_assoc_C  C-terminal AAA-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   4.9e-05     0.032       3      60 ..      31      88 ..      29     141 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.9e-05
                    AAA_assoc_C  3 LaeelelevddLlpiveaaelLglvevee.gdielTelGrkfveadikerKeifreqll 60
                                   ++++l+++    +++v+ ++ Lglv++++   i+lT+ G++++ea +k+r++if++ l+
  gi|119719881|ref|YP_920376.1| 31 ISRALGVKPSTAVEMVRKLHELGLVDYKKyEGITLTARGKEIAEA-VKKRRDIFENFLK 88
                                   566777777778899999*********76367*********9997.7889999998765 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.3   6.4e-05     0.043       6      74 ..       8      77 ..       4      81 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.4e-05
                        DUF2250  6 edelalkvlkhlkkanvdY.aksiakeleipleevrellkkLeelGLlervegktikrteaklKkksevh 74
                                   ++e++l+v++ +++a+     k i++ l ++ + + e+++kL+elGL+++++ + i  t + +  ++ v+
  gi|119719881|ref|YP_920376.1|  8 RSEDYLRVIYEIAEAKGYVrIKDISRALGVKPSTAVEMVRKLHELGLVDYKKYEGITLTARGKEIAEAVK 77
                                   56778888888888876322589**************************999888887776665555555 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00013     0.083      26      55 .]      26      55 ..      15      55 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00013
                         HTH_36 26 psqetlakrlglsknTvsraikeLeqlGyi 55
                                      ++++++lg++ +T++  +++L +lG++
  gi|119719881|ref|YP_920376.1| 26 VRIKDISRALGVKPSTAVEMVRKLHELGLV 55
                                   5789************************85 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00045       0.3      10      41 ..      22      54 ..      13      80 .. 0.86
   2 ?   -2.3   0.0       7.8   5.2e+03      21      30 ..     105     114 ..     103     118 .. 0.79
   3 ?   -1.0   0.0         3     2e+03      28      40 ..     125     137 ..     123     147 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00045
                         HTH_28 10 aaGh.svreaArelgisrrtvyrWikryeegGi 41
                                   a+G  ++++++r+lg+ ++t    ++++ e G+
  gi|119719881|ref|YP_920376.1| 22 AKGYvRIKDISRALGVKPSTAVEMVRKLHELGL 54
                                   36878****************999999999887 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 7.8
                         HTH_28  21 elgisrrtvy 30 
                                    e+++s++tv 
  gi|119719881|ref|YP_920376.1| 105 EHQLSPETVL 114
                                    6889999985 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 3
                         HTH_28  28 tvyrWikryeegG 40 
                                    + + Wi  ++ + 
  gi|119719881|ref|YP_920376.1| 125 QAKEWIDEFRNYC 137
                                    6778999999875 PP

>> AbiEi_4  Transcriptional regulator, AbiEi antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00016      0.11       4      36 ..      17      53 ..      14      56 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00016
                        AbiEi_4  4 pelasrqvGlfttrelea.aGispsa....lrrLvrkG 36
                                    e+a + +G+++ +++ + +G+ ps+    +r+L++ G
  gi|119719881|ref|YP_920376.1| 17 YEIA-EAKGYVRIKDISRaLGVKPSTavemVRKLHELG 53
                                   4455.4559*******777*****88577777777666 PP

>> UPF0302  UPF0302 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   0.00012     0.081       4      50 ..      85     130 ..      84     134 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00012
                                    HHHHHHHHH--BSSTHHHHHHHHHHH-TTTTTTEEE-S-GGGSTTEE CS
                        UPF0302   4 eflkwfLekyqlkrreaawiLnyllsneelLervhFvekarkapral 50 
                                    +flk +L  ++  +r+a  iL++ ls e++L+  +Fve a++a++++
  gi|119719881|ref|YP_920376.1|  85 NFLKIILVPENVAKRDA-HILEHQLSPETVLQIARFVEFASQAKEWI 130
                                    8***************8.59*******************99998876 PP

>> HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor, HrcA DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0     0.004       2.6      19      54 ..      21      56 ..       6      62 .. 0.87
   2 ?    3.6   0.0     0.076        51      22      46 ..      65      89 ..      57      96 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.004
                   HrcA_DNA-bdg 19 kkkravKgeeiAevlkrneGtvRNqlqsLkalgLve 54
                                   + k  v+ ++i  +l+ ++ t   ++  L+ lgLv+
  gi|119719881|ref|YP_920376.1| 21 EAKGYVRIKDISRALGVKPSTAVEMVRKLHELGLVD 56
                                   45778999***************************8 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.076
                   HrcA_DNA-bdg 22 ravKgeeiAevlkrneGtvRNqlqs 46
                                    + +g+eiAe++k+      N l++
  gi|119719881|ref|YP_920376.1| 65 LTARGKEIAEAVKKRRDIFENFLKI 89
                                   56789********998888887765 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00053      0.35       9      39 ..      14      47 ..      13      56 .. 0.76
   2 ?   -1.2   0.0       2.9   1.9e+03       7      23 ..      59      75 ..      55      78 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00053
                         HTH_23  9 rillllae...GlsvreIAreLgvsrrTvyrwlk 39
                                   r+++  ae     ++++I+r+Lgv ++T    ++
  gi|119719881|ref|YP_920376.1| 14 RVIYEIAEakgYVRIKDISRALGVKPSTAVEMVR 47
                                   667777766777899*************865555 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.9
                         HTH_23  7 RlrillllaeGlsvreI 23
                                   +++ + l a+G+ ++e+
  gi|119719881|ref|YP_920376.1| 59 KYEGITLTARGKEIAEA 75
                                   55556666766666665 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00033      0.22      22      70 ..      23      69 ..       5      73 .. 0.85
   2 ?   -0.8   0.0       2.7   1.8e+03      10      25 ..     115     130 ..      91     146 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00033
                         Rio2_N 22 hevVptelieeisrlkeeevkkrlsrllkaklisrktakydGYkLtyeG 70
                                     +V  + i++  ++k +   + +++l++ +l+ +k  ky+G  Lt  G
  gi|119719881|ref|YP_920376.1| 23 KGYVRIKDISRALGVKPSTAVEMVRKLHELGLVDYK--KYEGITLTARG 69
                                   5678888899999999999****************8..7*******988 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.7
                         Rio2_N  10 rvLtavEmgmrnhevV 25 
                                    ++ + vE+ ++  e++
  gi|119719881|ref|YP_920376.1| 115 QIARFVEFASQAKEWI 130
                                    4445566666666665 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00035      0.23      24      46 ..      26      48 ..      19      51 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00035
                         HTH_10 24 vtlkeLAkelGIskstlsehLrk 46
                                   v++k+++ +lG+++st+ e +rk
  gi|119719881|ref|YP_920376.1| 26 VRIKDISRALGVKPSTAVEMVRK 48
                                   789*****************998 PP

>> DUF1848  Domain of unknown function (DUF1848)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00015     0.099      60     149 ..      44     132 ..       5     146 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00015
                        DUF1848  60 pllkkleelkergiklyfqfTltdyekelepnvpsleerietfkelseklgkerviwRyDPilltekltvelhl..ekfe 137
                                    ++++kl+el   ++k y  +Tlt+ +ke+ + v++ +++ e+f ++   l +e+v+ R D  +l+++l+ e+ l   +f 
  gi|119719881|ref|YP_920376.1|  44 EMVRKLHELGLVDYKKYEGITLTARGKEIAEAVKKRRDIFENFLKI--ILVPENVAKR-DAHILEHQLSPETVLqiARFV 120
                                    78999*****9********************************777..6889999999.666667776666543227899 PP

                        DUF1848 138 klaeelkgytek 149
                                    ++a++ k+ +++
  gi|119719881|ref|YP_920376.1| 121 EFASQAKEWIDE 132
                                    999888887765 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00023      0.15      24      75 ..      30      82 ..       7      84 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00023
                         HTH_45 24 kimykanLsykllnkYLdmLvekglikk.skekYvlTekGlelleklkeleel 75
                                    i  +   + +++ +++ +L e gl++  + e  +lT++G+e+ e +k+ +++
  gi|119719881|ref|YP_920376.1| 30 DISRALGVKPSTAVEMVRKLHELGLVDYkKYEGITLTARGKEIAEAVKKRRDI 82
                                   56666666667889999*********76367889************9998876 PP

>> MerR  MerR family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.1    0.0023       1.5       1      24 [.      27      54 ..      27      58 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0023
                                   EHHHHHHHHTTTHHH....HHHHHHTTS CS
                           MerR  1 tIgevAeltGvsprt....LRyYEreGL 24
                                   +I+++++++Gv p+t    +R +++ GL
  gi|119719881|ref|YP_920376.1| 27 RIKDISRALGVKPSTavemVRKLHELGL 54
                                   69*********99974444666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       802  (0.044732); expected 358.6 (0.02)
Passed bias filter:                      602  (0.0335769); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              27  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 993.35
//
Query:       gi|119719882|ref|YP_920377.1|  [L=106]
Description: FeoA family protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.8e-17   61.0   0.1    1.2e-16   60.7   0.1    1.1  1  FeoA      FeoA domain


Domain annotation for each model (and alignments):
>> FeoA  FeoA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.7   0.1   6.5e-21   1.2e-16       2      72 ..       4      73 ..       3      75 .. 0.95

  Alignments for each domain:
  == domain 1  score: 60.7 bits;  conditional E-value: 6.5e-21
                                   EGGG--TT-EEEEEEE-TT.SSHHHHHHHHT--TT-EEEEEEE-TTS-SEEEEETTEEEEE-HHHHTTEEE CS
                           FeoA  2 pLsdlkeGergeiarisdedpellrrLremGlvpGarievvarapfggplvvrvgdtrvaLgreeAqaIlV 72
                                   +Ls+lk+Ge+g+++r+     ++++rL++mGlv+G+++ v++rap+g+p+ + v++ ++++++ e + ++V
  gi|119719882|ref|YP_920377.1|  4 KLSELKPGEKGIVTRVEGP-SAVRKRLLDMGLVKGTEVVVIRRAPLGDPIELLVKGYNLSIRKAESDYVYV 73
                                   69**************766.99*******************************************999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       200  (0.0111551); expected 358.6 (0.02)
Passed bias filter:                      190  (0.0105974); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 810.49
//
Query:       gi|119719883|ref|YP_920378.1|  [L=81]
Description: FeoA family protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-20   72.3   0.4    3.1e-20   72.2   0.4    1.0  1  FeoA      FeoA domain


Domain annotation for each model (and alignments):
>> FeoA  FeoA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.2   0.4   1.8e-24   3.1e-20       2      73 ..       7      76 ..       6      77 .. 0.95

  Alignments for each domain:
  == domain 1  score: 72.2 bits;  conditional E-value: 1.8e-24
                                   EGGG--TT-EEEEEEE-TT.SSHHHHHHHHT--TT-EEEEEEE-TTS-SEEEEETTEEEEE-HHHHTTEEEE CS
                           FeoA  2 pLsdlkeGergeiarisdedpellrrLremGlvpGarievvarapfggplvvrvgdtrvaLgreeAqaIlVe 73
                                   pL++++eG +g++++++     l rrL+e+G+++Gar++v++ +p  gp++v v+++r+aLgr++A+++++ 
  gi|119719883|ref|YP_920378.1|  7 PLAMCPEGCEGIVVEVNGG-MGLIRRLAELGFTKGARVRVLHSSPP-GPVLVMVKGSRIALGRGVAMRVMIS 76
                                   9***************987.99*******************88776.9*********************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       284  (0.0158403); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 580.36
//
Query:       gi|119719884|ref|YP_920379.1|  [L=676]
Description: ferrous iron transport protein B [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.3e-66  220.7   0.8    1.2e-65  219.8   0.8    1.5  1  FeoB_N        Ferrous iron transport protein B
    9.8e-45  151.4  14.6    1.5e-31  109.0   1.3    3.1  3  Gate          Nucleoside recognition
    1.1e-17   63.5   4.2    1.1e-17   63.5   4.2    2.8  3  FeoB_C        Ferrous iron transport protein B C terminus
    1.3e-17   64.1   2.2    1.3e-17   64.1   2.2    2.1  2  FeoB_Cyto     FeoB cytosolic helical domain
    1.4e-17   63.8   0.1    2.8e-17   62.8   0.1    1.5  1  MMR_HSR1      50S ribosome-binding GTPase
    0.00013   21.5   0.0    0.00024   20.6   0.0    1.5  1  SRPRB         Signal recognition particle receptor beta subun
     0.0016   18.4   0.7       0.01   15.7   0.1    2.1  2  RsgA_GTPase   RsgA GTPase
  ------ inclusion threshold ------
      0.019   14.5   0.7      0.052   13.1   0.7    1.8  1  GTP_EFTU      Elongation factor Tu GTP binding domain
       0.05   13.7   0.8      0.099   12.8   0.8    1.4  1  DUF2634       Protein of unknown function (DUF2634)
      0.085   13.0   0.0       0.21   11.8   0.0    1.6  1  MnmE_helical  MnmE helical domain
       0.27   11.4   0.9        2.2    8.5   0.1    2.6  3  Costars       Costars


Domain annotation for each model (and alignments):
>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  219.8   0.8   7.3e-69   1.2e-65       2     156 .]       4     158 ..       3     158 .. 0.99

  Alignments for each domain:
  == domain 1  score: 219.8 bits;  conditional E-value: 7.3e-69
                                    EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHHCTSSSE CS
                         FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsayseeekvardflleeepdv 81 
                                    +val+GnpnvGkt +fn ltg k ++gNwpG+tvekkegkl ++g e++i+DlPG+Ysl+a s++e +ar+f++ee+pdv
  gi|119719884|ref|YP_920379.1|   4 RVALIGNPNVGKTLIFNDLTGGKAHIGNWPGKTVEKKEGKLLHRGVEIHITDLPGTYSLTAKSIDELIARNFIVEEKPDV 83 
                                    79****************************************************************************** PP

                                    EEEEEEGGGHHHHHHHHHHHHHTTSSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTBTHHHHHHHH CS
                         FeoB_N  82 vvnvvdatnlernLyLtlqllelgvpvvlalnmideaekkgieidlkkLsekLgvpvvktsakkkegieellkai 156
                                    vv+vvda+nlernLyL+lqllel+++vv+aln++d+ae+ g++id+++Ls+ Lgvpvv+t+a++k+gieel+++i
  gi|119719884|ref|YP_920379.1|  84 VVDVVDASNLERNLYLVLQLLELEANVVIALNKYDVAEDLGYQIDVNELSKFLGVPVVPTVATTKQGIEELKDTI 158
                                    ************************************************************************986 PP

>> Gate  Nucleoside recognition
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.2       1.7   2.7e+03      11      39 ..     290     320 ..     286     328 .. 0.74
   2 !   50.4   1.6   1.4e-16   2.3e-13       3     106 ..     349     437 ..     347     442 .. 0.95
   3 !  109.0   1.3   9.1e-35   1.5e-31       1     112 []     511     645 ..     511     645 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.7
                           Gate  11 asiliwflss..ssllgrigkllepvfaplg 39 
                                    +++l w l s  +++ + ++ l++++f++lg
  gi|119719884|ref|YP_920379.1| 290 FLALWWALFSftFNVSAPFSDLIDWFFSKLG 320
                                    5555666655557778889999******999 PP

  == domain 2  score: 50.4 bits;  conditional E-value: 1.4e-16
                           Gate   3 kagpiillasiliwflssssllgrigkllepvfaplgqeldwkatvslltgfaakevvvgtlgtlytsalgellqgfdtp 82 
                                     ++p i+++++ + +l++s++l+r+++l+++v+ +lg  l++k+++++l+gf+   ++v++++ ++         ++d++
  gi|119719884|ref|YP_920379.1| 349 AFLPPIFFLFFGLALLEDSGYLARAAFLMDKVMYKLG--LHGKSFIPMLLGFG---CNVPAVMATR---------TIDSE 414
                                    6799*********************************..**************...*********9.........***** PP

                           Gate  83 ksalafllfvllytpcvatlaviv 106
                                    ++++ ++l+  l + c a+l++++
  gi|119719884|ref|YP_920379.1| 415 EDRILTILVAPLIS-CSARLPIYI 437
                                    ************87.******997 PP

  == domain 3  score: 109.0 bits;  conditional E-value: 9.1e-35
                           Gate   1 llkagpiillasiliwflss...............ssllgrigkllepvfaplgqeldwkatvslltgfaakevvvgtlg 65 
                                    l+kag+ii+l+++ +wfls+               +s+lg +gk+lep+++plg  ++w  +v+l++gf+ake+vvgt++
  gi|119719884|ref|YP_920379.1| 511 LKKAGTIIFLGIVAVWFLSNypwesvhqgdrvvleNSYLGVLGKYLEPLVRPLG--FNWMHAVALMLGFVAKEIVVGTFA 588
                                    79****************************************************..************************ PP

                           Gate  66 tly..........tsalgellqgfdtpksalafllfvllytpcvatlavivrelgsk 112
                                    tl+          +      ++g +tp + laf+ f+l+y+pc+atla+i+re+gs+
  gi|119719884|ref|YP_920379.1| 589 TLFgltaegetseKLIDALRSSGVFTPLTGLAFMAFSLIYMPCLATLAAIRRETGSW 645
                                    *********996433334446799*******************************98 PP

>> FeoB_C  Ferrous iron transport protein B C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.5   4.2   6.6e-21   1.1e-17       1      53 []     452     506 ..     452     506 .. 0.98
   2 ?   -2.4   0.1       2.4   3.9e+03       9      19 ..     518     528 ..     515     533 .. 0.55
   3 ?   -2.8   0.1       3.3   5.4e+03      10      22 ..     570     582 ..     569     589 .. 0.81

  Alignments for each domain:
  == domain 1  score: 63.5 bits;  conditional E-value: 6.6e-21
                         FeoB_C   1 lfslYllgilvallvalllkktt..lkgepspfvmELPpYrlPslknvliktweR 53 
                                    +fs+Y+lg+++a+lval +++++  +kg+psp+++ELP Y +P+l+++li++weR
  gi|119719884|ref|YP_920379.1| 452 VFSMYVLGLVLAVLVALSFRRLLpyFKGKPSPLILELPMYAKPTLRTTLIHMWER 506
                                    79*******************9789*****************************9 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.4
                         FeoB_C   9 ilvallvalll 19 
                                    i++ +++ ++l
  gi|119719884|ref|YP_920379.1| 518 IFLGIVAVWFL 528
                                    44445555554 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 3.3
                         FeoB_C  10 lvallvalllkkt 22 
                                    +val++++++k +
  gi|119719884|ref|YP_920379.1| 570 AVALMLGFVAKEI 582
                                    6899999999986 PP

>> FeoB_Cyto  FeoB cytosolic helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       1.1   1.7e+03      29      55 ..      98     123 ..      76     165 .. 0.76
   2 !   64.1   2.2   7.9e-21   1.3e-17       1      90 [.     175     264 ..     175     265 .. 0.97

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.1
                      FeoB_Cyto  29 wlAlklLegDeelleelkedpelraev 55 
                                    +l l+lLe + ++   l++ +++++ +
  gi|119719884|ref|YP_920379.1|  98 YLVLQLLELEANVVIALNK-YDVAEDL 123
                                    7889999999999988887.6666554 PP

  == domain 2  score: 64.1 bits;  conditional E-value: 7.9e-21
                      FeoB_Cyto   1 YgeeiEkaiekleellkes.nlkaklppRwlAlklLegDeelleelkedpelraeveearkeleaelgedledvIvdary 79 
                                    Yg++iE+ i+k+ ++l+++ +l +k+p RwlA+k+Le+D+e+l+ + e   ++++v+++ +e ++ lged+  ++++ ry
  gi|119719884|ref|YP_920379.1| 175 YGKQIEEYISKMMDILQKDnELSSKYPVRWLAIKILEEDDEVLKLIDE-RPIKDAVRTLLSEAKNALGEDVGVILAERRY 253
                                    9******************99***************************.9****************************** PP

                      FeoB_Cyto  80 kfiegilrevv 90 
                                    ++i+++l + +
  gi|119719884|ref|YP_920379.1| 254 SLISEALPKIL 264
                                    *****998765 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.8   0.1   1.7e-20   2.8e-17       1     114 []       4     116 ..       4     116 .. 0.86

  Alignments for each domain:
  == domain 1  score: 62.8 bits;  conditional E-value: 1.7e-20
                                    EEEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSS..HHHHHHHHHHHHHHHHCTSE CS
                       MMR_HSR1   1 evaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGlie..gaseekglgkaflaleeadl 78 
                                    +va++G+pNvGK+ ++n ltg ka+++++pg+T + +eg++ ++g ei+++D+pG ++   +s ++ ++++f   e+ d+
  gi|119719884|ref|YP_920379.1|   4 RVALIGNPNVGKTLIFNDLTGGKAHIGNWPGKTVEKKEGKLLHRGVEIHITDLPGTYSltAKSIDELIARNFIVEEKPDV 83 
                                    69***************************************9999**********98665677777899999988889** PP

                                    EEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                       MMR_HSR1  79 illvvdaseeklkpldeeleelleeakkplilvlnk 114
                                    ++ vvdas + l+++   + +ll e + +++++lnk
  gi|119719884|ref|YP_920379.1|  84 VVDVVDAS-N-LERNLYLVLQLL-ELEANVVIALNK 116
                                    ******88.4.666655566665.477888888887 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   1.5e-07   0.00024       5      94 ..       4      99 ..       1     122 [. 0.68

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.5e-07
                                   EEEEE-STTSSHHHHHHHHHHSS---B---S...S-EEETTG...GGTT-SEEEETT-GCCSHHHHHHHHHHGG.E....EE CS
                          SRPRB  5 avllvGlsdsGKTslftrLttdsvkktvtSq...essaalkvksekgskltliDfPGheklrqklleklkakss.l....kg 78
                                   +v l+G  + GKT++f+ Lt ++++         e++  +    ++g ++++ D+PG  +l  k +++l+a++  +      
  gi|119719884|ref|YP_920379.1|  4 RVALIGNPNVGKTLIFNDLTGGKAHIGNWPGktvEKKEGK--LLHRGVEIHITDLPGTYSLTAKSIDELIARNFiVeekpDV 83
                                   6889******************877665544111333333..3599******************999988876522111134 PP

                                   EEEEEETTS-HHHHHH CS
                          SRPRB 79 lvfvvDStidpkevke 94
                                   +v vvD++  ++++  
  gi|119719884|ref|YP_920379.1| 84 VVDVVDASNLERNLYL 99
                                   6667776666666544 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.31     5e+02     102     122 ..       5      25 ..       3      58 .. 0.84
   2 !   15.7   0.1   6.4e-06      0.01      34      97 ..      92     158 ..      82     164 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.31
                                    EEEECSTTSSHHHHHHHHCTT CS
                    RsgA_GTPase 102 svlvGqSGvGKStLinallpe 122
                                    ++l+G+  vGK+ + n l++ 
  gi|119719884|ref|YP_920379.1|   5 VALIGNPNVGKTLIFNDLTGG 25 
                                    5799**************986 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 6.4e-06
                                    HHHHHHH...HHHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHC CS
                    RsgA_GTPase  34 lldrfLv...laeekgiepvivlnKiDlleeeeeleelkeelealgyevllvsaktkegleelkell 97 
                                     l+r L    ++ e ++++vi+lnK D++e+     +++e  + lg++v+ + a+tk+g+eelk+ +
  gi|119719884|ref|YP_920379.1|  92 NLERNLYlvlQLLELEANVVIALNKYDVAEDLGYQIDVNELSKFLGVPVVPTVATTKQGIEELKDTI 158
                                    45554430013457789****************666777777889******************9876 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.7   3.2e-05     0.052      92     191 ..      79     161 ..       2     164 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.2e-05
                                    HT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGST.HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEE CS
                       GTP_EFTU  92 rvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrl.kaelkeiveevkqklsrkeeklekygekgekevpv 170
                                    ++ D++v vvda+   e +   ++ ++l+++ ++++++NK D + +  ++  v+e+++ l                 vpv
  gi|119719884|ref|YP_920379.1|  79 EKPDVVVDVVDAS-NLERN-LYLVLQLLELEANVVIALNKYDVAeDLGYQIDVNELSKFL----------------GVPV 140
                                    3456666666665.34444.456677888999************8899999999999555................489* PP

                                    EEEBTTTTBTHHHHHHHHHHH CS
                       GTP_EFTU 171 vfgSalkgegvktllealvel 191
                                    v++ a +++g+++l ++++e 
  gi|119719884|ref|YP_920379.1| 141 VPTVATTKQGIEELKDTIIEA 161
                                    **************9999986 PP

>> DUF2634  Protein of unknown function (DUF2634)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.8   6.1e-05     0.099      22      70 ..     149     196 ..     143     199 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.1e-05
                        DUF2634  22 dglEalkqwiykalkTeryryliYsenYGveledligkkyskeyvesei 70 
                                    +g+E+lk +i  a +T+  + + +s nYG ++e++i+k+++   +++e+
  gi|119719884|ref|YP_920379.1| 149 QGIEELKDTIIEAARTKDKS-KKFSINYGKQIEEYISKMMDILQKDNEL 196
                                    79**************9999.*****************98877666666 PP

>> MnmE_helical  MnmE helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00013      0.21      85     159 ..      39     191 ..      35     251 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00013
                                    xxxxxxxxxxxx.................................................................... RF
                   MnmE_helical  85 akrgellreGik.................................................................... 96 
                                     k+g+ll+ G++                                                                    
  gi|119719884|ref|YP_920379.1|  39 KKEGKLLHRGVEihitdlpgtysltaksideliarnfiveekpdvvvdvvdasnlernlylvlqlleleanvvialnkyd 118
                                    578999999999999*9999999999999999999999999999999999999999999999999999999999999997 PP

                                    ...xxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                   MnmE_helical  97 ...Dllkeke.....ekeeeevlkiSaktgegieeLeeaike.leleei.eeeplltnaRhkealekaleale 159
                                       Dl  + +     +    +v+ + a+t++gieeL+++i e ++ ++  ++ ++   +   e ++k+++ l+
  gi|119719884|ref|YP_920379.1| 119 vaeDLGYQIDvnelsKFLGVPVVPTVATTKQGIEELKDTIIEaARTKDKsKKFSINYGKQIEEYISKMMDILQ 191
                                    777444444444444666777779999999**********994444332233233333344444444444443 PP

>> Costars  Costars
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.1    0.0013       2.2       3      37 ..     148     183 ..     146     192 .. 0.78
   2 ?   -0.2   0.0       0.7   1.1e+03      34      52 ..     251     269 ..     228     282 .. 0.84
   3 ?   -2.1   0.0       2.8   4.6e+03      25      48 ..     583     608 ..     579     610 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0013
                        Costars   3 dkeileLcevIkelGe.knddgkvvvtFGeLfekyt 37 
                                    ++ i+eL+++I e ++ k++++k+++++G+  e+y 
  gi|119719884|ref|YP_920379.1| 148 KQGIEELKDTIIEAARtKDKSKKFSINYGKQIEEYI 183
                                    5789*********9995667799******9876664 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.7
                        Costars  34 ekytniseklvGtLlaAkk 52 
                                    ++y+ ise+l  +L+ Ak 
  gi|119719884|ref|YP_920379.1| 251 RRYSLISEALPKILKGAKP 269
                                    6899999999999999996 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 2.8
                        Costars  25 vvvtFGeLf..ekytniseklvGtLl 48 
                                    vv tF +Lf      ++sekl++ L+
  gi|119719884|ref|YP_920379.1| 583 VVGTFATLFglTAEGETSEKLIDALR 608
                                    44589999965555678999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (676 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       973  (0.0542696); expected 358.6 (0.02)
Passed bias filter:                      624  (0.0348039); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.72u 0.29s 00:00:01.01 Elapsed: 00:00:00.48
# Mc/sec: 4277.91
//
Query:       gi|119719885|ref|YP_920380.1|  [L=167]
Description: hypothetical protein Tpen_0977 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       596  (0.0332422); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 1146.23
//
Query:       gi|119719886|ref|YP_920381.1|  [L=105]
Description: PilT domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.13   12.6   1.9       0.35   11.1   0.4    2.0  2  DUF1827   Domain of unknown function (DUF1827)


Domain annotation for each model (and alignments):
>> DUF1827  Domain of unknown function (DUF1827)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1     0.026   4.6e+02      52      73 ..      30      51 ..       9      63 .. 0.75
   2 ?   11.1   0.4     2e-05      0.35      36      71 ..      63     102 ..      60     105 .] 0.76

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.026
                                   SSS---HHHHHHHHHHHHHHTS CS
                        DUF1827 52 kkRaikeeEiefvlekllkkki 73
                                    kRai+   i  + e ++kk  
  gi|119719886|ref|YP_920381.1| 30 TKRAIRGFNIVSMSEDVIKKAL 51
                                   5788888888888888888765 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 2e-05
                                    EEEEEETTEEEEEEEESS...S---HHHHHHHH.HHHHHH CS
                        DUF1827  36 vvyteapkhveivlsnkk...RaikeeEiefvl.ekllkk 71 
                                    + + +a++ ++++++ +k   Ra+ +eEie++  e++l+k
  gi|119719886|ref|YP_920381.1|  63 IQFHSAKEVADVLITRNKrdfRAVEDEEIEVLTpEEFLEK 102
                                    679999********98872335788999998753777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 742.00
//
Query:       gi|119719887|ref|YP_920382.1|  [L=90]
Description: hypothetical protein Tpen_0979 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0028   17.3   0.2     0.0047   16.5   0.3    1.4  2  TBK1_CCD1        TANK-binding kinase 1 coiled-coil domain 1
  ------ inclusion threshold ------
      0.013   15.6   0.4      0.016   15.3   0.4    1.1  1  ADIP             Afadin- and alpha -actinin-Binding
      0.026   13.9   1.2      0.031   13.6   1.2    1.1  1  GAS              Growth-arrest specific micro-tubule binding
      0.035   14.4   6.4      0.085   13.1   6.4    1.7  1  ABC_tran_CTD     ABC transporter C-terminal domain
      0.041   14.0   1.1      0.056   13.5   1.1    1.2  1  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
      0.042   13.9   1.3      0.066   13.3   1.3    1.4  1  Med9             RNA polymerase II transcription mediator com
      0.048   14.3   1.7      0.089   13.4   1.7    1.6  1  SlyX             SlyX
      0.056   13.5   3.2      0.056   13.5   3.2    2.0  2  DUF1192          Protein of unknown function (DUF1192)
      0.057   12.5   0.1      0.058   12.5   0.1    1.0  1  Atg14            Vacuolar sorting 38 and autophagy-related su
      0.058   12.3   1.4      0.068   12.0   1.4    1.2  1  Spc7             Spc7 kinetochore protein
       0.06   13.5   1.9        0.1   12.8   1.9    1.3  1  XhlA             Haemolysin XhlA
      0.073   11.9   0.2      0.077   11.8   0.2    1.0  1  Fmp27_WPPW       RNA pol II promoter Fmp27 protein domain
      0.087   13.1   1.7      0.096   12.9   1.7    1.3  1  Spc24            Spc24 subunit of Ndc80
        0.1   13.1   2.6        0.1   13.1   2.6    2.0  2  BMFP             Membrane fusogenic activity
       0.12   12.9   6.6       0.57   10.7   1.6    2.2  2  KELK             KELK-motif containing domain of MRCK Ser/Thr
       0.14   13.1   0.1       0.39   11.7   0.0    1.8  2  LPD29            Large polyvalent protein associated domain 2
        0.2   12.0   7.0        4.8    7.6   2.8    2.4  2  HalX             HalX domain
       0.23   12.0   3.6       0.29   11.7   3.6    1.2  1  APG6_N           Apg6 coiled-coil region
       0.32   10.8   5.0        2.6    7.9   5.0    2.1  1  DivIC            Septum formation initiator
       0.46   10.5   3.6       0.39   10.8   1.3    1.9  2  Bcr-Abl_Oligo    Bcr-Abl oncoprotein oligomerisation domain
       0.47   10.8   6.3       0.85   10.0   6.3    1.7  1  CCDC-167         Coiled-coil domain-containing protein 167
       0.67   10.0   5.1         12    6.0   2.2    2.2  2  PspB             Phage shock protein B
       0.71   10.2   6.9       0.31   11.3   3.9    2.0  2  Val_tRNA-synt_C  Valyl tRNA synthetase tRNA binding arm
        1.9    9.0   4.8        6.1    7.3   4.8    1.8  1  DUF4140          N-terminal domain of unknown function (DUF41


Domain annotation for each model (and alignments):
>> TBK1_CCD1  TANK-binding kinase 1 coiled-coil domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.3   6.3e-06    0.0047      97     131 ..       4      38 ..       1      51 [. 0.90
   2 ?   -1.7   0.0       2.3   1.7e+03     150     171 ..      39      60 ..      36      65 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.3e-06
                      TBK1_CCD1  97 deiselhkkllrlssslerieeslqeiknklipee 131
                                    +eise++k+l rl+++l+r+e+ + +++ k+ +++
  gi|119719887|ref|YP_920382.1|   4 QEISEIRKRLARLREELARLERRIAQVEFKMASSG 38 
                                    69*************************99998765 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.3
                      TBK1_CCD1 150 veklkvlldkiteiykqfkkdk 171
                                    +e++k++ ++++e y  +k d+
  gi|119719887|ref|YP_920382.1|  39 EERIKAVEEELKEEYPGMKFDR 60 
                                    6888888888888887777666 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.4   2.1e-05     0.016      67     114 ..       4      52 ..       1      57 [. 0.84

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.1e-05
                           ADIP  67 aeierlqskierlktqleqlerelalvqakerql.ekklktleqklkne 114
                                     ei+  +++  rl ++l++ler++a+v++k ++  e ++k+ e+ lk+e
  gi|119719887|ref|YP_920382.1|   4 QEISEIRKRLARLREELARLERRIAQVEFKMASSgEERIKAVEEELKEE 52 
                                    6888889999999999999999999999998864378899999988876 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   1.2   4.2e-05     0.031      52     103 ..       2      51 ..       1      65 [. 0.76

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.2e-05
                            GAS  52 isqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkd 103
                                    ++qe +++++ L +++ee+++L++++++ e   +   + ++r+k +e+elk+
  gi|119719887|ref|YP_920382.1|   2 MAQEISEIRKRLARLREELARLERRIAQVEF--KMASSGEERIKAVEEELKE 51 
                                    6799999999999999999999999998876..4445566677777777665 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   6.4   0.00011     0.085       9      59 ..       5      51 ..       2      54 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00011
                   ABC_tran_CTD  9 eleeleaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeLee 59
                                   e+ e+ +++++L ee+a le ++a+ e+       +   ++++++e+eL+e
  gi|119719887|ref|YP_920382.1|  5 EISEIRKRLARLREELARLERRIAQVEFK----MASSGEERIKAVEEELKE 51
                                   67777777777777777777777777753....333334445555555554 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   1.1   7.5e-05     0.056      56     104 ..       3      52 ..       2      63 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.5e-05
                     TPR_MLP1_2  56 vkelqalreelnelkaeiaelkaeaesakaelees.eesweeqkeeleke 104
                                    ++e++++r++l++l++e+a l+ +  +++ +++ s ee ++  +eel++e
  gi|119719887|ref|YP_920382.1|   3 AQEISEIRKRLARLREELARLERRIAQVEFKMASSgEERIKAVEEELKEE 52 
                                    68899999999999999999999999998887665377888888888887 PP

>> Med9  RNA polymerase II transcription mediator complex subunit 9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   1.3   8.9e-05     0.066      25      61 ..       3      47 ..       1      53 [. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.9e-05
                           Med9 25 etktgelrhkLkkarelirelpg........idrsveeqeaeiee 61
                                    ++++e+r++L + re ++ l+         +  s ee+ + +ee
  gi|119719887|ref|YP_920382.1|  3 AQEISEIRKRLARLREELARLERriaqvefkMASSGEERIKAVEE 47
                                   689*****************9999888777777777777766654 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   1.7   0.00012     0.089      23      59 ..       3      39 ..       1      54 [. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00012
                                   HHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXXXXX CS
                           SlyX 23 ndvvaeqqqqidrlqrqlrllaerlkeleessgasea 59
                                    +++ e +++++rl+++l++l++r++++e ++++s++
  gi|119719887|ref|YP_920382.1|  3 AQEISEIRKRLARLREELARLERRIAQVEFKMASSGE 39
                                   5788999999999999999999999999988876654 PP

>> DUF1192  Protein of unknown function (DUF1192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   3.2   7.5e-05     0.056      22      45 ..       6      29 ..       4      37 .. 0.90
   2 ?   -1.0   1.0       2.5   1.9e+03      26      36 ..      39      49 ..      39      51 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.5e-05
                        DUF1192 22 veELeerIalLeaEIaRleaaiak 45
                                   ++E+++r a L++E aRle+ ia+
  gi|119719887|ref|YP_920382.1|  6 ISEIRKRLARLREELARLERRIAQ 29
                                   68******************9987 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.5
                        DUF1192 26 eerIalLeaEI 36
                                   eerI++ e+E 
  gi|119719887|ref|YP_920382.1| 39 EERIKAVEEEL 49
                                   68999999985 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   7.8e-05     0.058      95     142 ..       4      51 ..       2      78 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.8e-05
                          Atg14  95 keieekkkklaklsdklkkRrsdleslqneleerrkkqiaklqdaikr 142
                                    +ei e +k+la+l+++l++  ++++ ++++++++ ++ i+ + +++k+
  gi|119719887|ref|YP_920382.1|   4 QEISEIRKRLARLREELARLERRIAQVEFKMASSGEERIKAVEEELKE 51 
                                    789999999999999999999999999999999999999998888875 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.4   9.1e-05     0.068     199     244 ..       4      50 ..       1      64 [. 0.61

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9.1e-05
                           Spc7 199 eeLeelreelaelkaeieekkkelaelqeqleel.eekieelkeqks 244
                                    +e+ e+r++la+l +e++++++++a+++ +++++ ee+i++++e+ +
  gi|119719887|ref|YP_920382.1|   4 QEISEIRKRLARLREELARLERRIAQVEFKMASSgEERIKAVEEELK 50 
                                    45566666666666666666666666665555432455555555544 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.9   0.00014       0.1       1      43 [.       8      51 ..       8      51 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00014
                           XhlA  1 eikerlerietkldnleervdkleekaaea.eekiknleedlkk 43
                                   ei++rl+r+ ++l  le r+ ++e k+a   ee+ik +ee+lk+
  gi|119719887|ref|YP_920382.1|  8 EIRKRLARLREELARLERRIAQVEFKMASSgEERIKAVEEELKE 51
                                   79**********************9877654899******9996 PP

>> Fmp27_WPPW  RNA pol II promoter Fmp27 protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2    0.0001     0.077     176     226 ..       9      60 ..       3      78 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0001
                     Fmp27_WPPW 176 leeRleeleeqiekleekleelelkseke.deelkeeieelekeikelkekl 226
                                    +++Rl++l+e++++le+++ ++e k+ ++ +e++k+  eel++e   +k  +
  gi|119719887|ref|YP_920382.1|   9 IRKRLARLREELARLERRIAQVEFKMASSgEERIKAVEEELKEEYPGMKFDR 60 
                                    89**************************877777777777777665555444 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.7   0.00013     0.096       9      49 ..       2      47 ..       1      87 [. 0.76

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00013
                          Spc24  9 iakelsdleselesleselaelkeeleeleeeseekeser.....v 49
                                   +a+e+s++ + l +l++ela+l+++++++e +  ++ +er     +
  gi|119719887|ref|YP_920382.1|  2 MAQEISEIRKRLARLREELARLERRIAQVEFKMASSGEERikaveE 47
                                   589999999999************9999999998844444333331 PP

>> BMFP  Membrane fusogenic activity
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   2.6   0.00014       0.1      53      76 ..       8      31 ..       4      32 .. 0.88
   2 ?   -1.5   0.1       4.7   3.5e+03      58      72 ..      35      49 ..      33      51 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00014
                           BMFP 53 vqrevlartrekleaLearvaaLE 76
                                    +r+ lar re+l++Le+r+a+ E
  gi|119719887|ref|YP_920382.1|  8 EIRKRLARLREELARLERRIAQVE 31
                                   57889****************988 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 4.7
                           BMFP 58 lartrekleaLearv 72
                                   ++   e+++a e+ +
  gi|119719887|ref|YP_920382.1| 35 ASSGEERIKAVEEEL 49
                                   555556666666555 PP

>> KELK  KELK-motif containing domain of MRCK Ser/Thr protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.6   0.00076      0.57      46      72 ..       1      27 [.       1      35 [. 0.92
   2 ?    5.3   0.4     0.037        28      26      40 ..      38      52 ..      28      60 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00076
                           KELK 46 lamqefsevneklselrsqkqklsRql 72
                                   +++qe se+ ++l+ lr++  +l R++
  gi|119719887|ref|YP_920382.1|  1 MMAQEISEIRKRLARLREELARLERRI 27
                                   689**********************86 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.037
                           KELK 26 aqErlksqkkeLkda 40
                                    +Er+k+ ++eLk++
  gi|119719887|ref|YP_920382.1| 38 GEERIKAVEEELKEE 52
                                   58***********97 PP

>> LPD29  Large polyvalent protein associated domain 29
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       8.2   6.1e+03       5      14 ..       4      13 ..       2      19 .. 0.77
   2 ?   11.7   0.0   0.00053      0.39       4      23 ..      39      58 ..      36      59 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 8.2
                          LPD29  5 etakeiRkeL 14
                                   +++ eiRk+L
  gi|119719887|ref|YP_920382.1|  4 QEISEIRKRL 13
                                   5678899988 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00053
                          LPD29  4 ketakeiRkeLKaaFPgvKF 23
                                    e +k + +eLK+++Pg+KF
  gi|119719887|ref|YP_920382.1| 39 EERIKAVEEELKEEYPGMKF 58
                                   688999*************9 PP

>> HalX  HalX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   2.8    0.0064       4.8      36      57 ..       5      26 ..       3      36 .. 0.72
   2 ?    6.2   0.1     0.017        13      41      67 ..      39      65 ..      39      66 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0064
                           HalX 36 eYqeLearleelraqldetlde 57
                                   e +e++ rl++lr++l ++  +
  gi|119719887|ref|YP_920382.1|  5 EISEIRKRLARLREELARLERR 26
                                   6678888888888888776554 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.017
                           HalX 41 earleelraqldetldelddaddfeal 67
                                   e+r+ +++++l e+ + +  ++d+++l
  gi|119719887|ref|YP_920382.1| 39 EERIKAVEEELKEEYPGMKFDRDLLEL 65
                                   79***************9999999887 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   3.6   0.00039      0.29      54     101 ..       4      51 ..       1      66 [. 0.70

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00039
                         APG6_N  54 eeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerf 101
                                    +e+++++k  ++l eeL++le+  +++e ++a+  ee  +  eee ++
  gi|119719887|ref|YP_920382.1|   4 QEISEIRKRLARLREELARLERRIAQVEFKMASSGEERIKAVEEELKE 51 
                                    789999999999999999999999999888877766655554444443 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   5.0    0.0035       2.6      22      51 ..       2      31 ..       1      82 [. 0.85

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0035
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHCC-X CS
                          DivIC 22 lkqeiaalqaelaklkaeneeLeaevkdLk 51
                                   + qei ++ + la+l++e ++Le+++++ +
  gi|119719887|ref|YP_920382.1|  2 MAQEISEIRKRLARLREELARLERRIAQVE 31
                                   578999999999999999999999998874 PP

>> Bcr-Abl_Oligo  Bcr-Abl oncoprotein oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   1.3   0.00052      0.39      24      54 ..       4      34 ..       1      38 [. 0.91
   2 ?   -0.2   0.0       1.4     1e+03      40      50 ..      42      52 ..      36      63 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00052
                  Bcr-Abl_Oligo 24 dsvedieqeLerCkaslrrLekelneekfkv 54
                                   + +++i + L r +++l rLe+++++  fk+
  gi|119719887|ref|YP_920382.1|  4 QEISEIRKRLARLREELARLERRIAQVEFKM 34
                                   67899*************************9 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.4
                  Bcr-Abl_Oligo 40 lrrLekelnee 50
                                   ++++e+el+ee
  gi|119719887|ref|YP_920382.1| 42 IKAVEEELKEE 52
                                   55556665555 PP

>> CCDC-167  Coiled-coil domain-containing protein 167
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   6.3    0.0011      0.85       3      51 ..       3      49 ..       1      83 [. 0.79

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0011
                       CCDC-167  3 aseIdkleeklascrerLeaverrlrkeelseeeResleeEeaslkeql 51
                                   a+eI+++ ++la++re+L ++err+ ++e       s ee  ++++e+l
  gi|119719887|ref|YP_920382.1|  3 AQEISEIRKRLARLREELARLERRIAQVEFKMAS--SGEERIKAVEEEL 49
                                   799**********************999876552..3333333333333 PP

>> PspB  Phage shock protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   2.2     0.017        12      40      61 ..      10      31 ..       2      36 .. 0.89
   2 ?    5.2   0.0     0.029        21      50      70 ..      35      55 ..      32      57 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.017
                           PspB 40 ekrLeellekAekleeRietLE 61
                                   +krL++l+e+  +le+Ri  +E
  gi|119719887|ref|YP_920382.1| 10 RKRLARLREELARLERRIAQVE 31
                                   689***************9998 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.029
                           PspB 50 AekleeRietLEriLdaespn 70
                                   A+  eeRi+++E+ L +e p 
  gi|119719887|ref|YP_920382.1| 35 ASSGEERIKAVEEELKEEYPG 55
                                   566689*********999996 PP

>> Val_tRNA-synt_C  Valyl tRNA synthetase tRNA binding arm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   3.9   0.00042      0.31       4      32 ..       4      32 ..       2      53 .. 0.78
   2 ?   -2.5   0.0       8.6   6.4e+03      52      61 ..      75      84 ..      73      87 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00042
                Val_tRNA-synt_C  4 keraRLeKeLaklekeiervqkKLanpgF 32
                                   +e++   K+La+l+ e++r+++++a  +F
  gi|119719887|ref|YP_920382.1|  4 QEISEIRKRLARLREELARLERRIAQVEF 32
                                   67777888888888888888888888777 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 8.6
                Val_tRNA-synt_C 52 eeqaeklker 61
                                   ee +e+++e+
  gi|119719887|ref|YP_920382.1| 75 EEDEEVVREA 84
                                   5667777765 PP

>> DUF4140  N-terminal domain of unknown function (DUF4140)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   4.8    0.0082       6.1      66      92 ..       5      31 ..       2      53 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0082
                        DUF4140 66 elkalraeleeledelaaledelaaae 92
                                   e++++r++l +l++ela+le+++a +e
  gi|119719887|ref|YP_920382.1|  5 EISEIRKRLARLREELARLERRIAQVE 31
                                   477777777777777777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1402  (0.0781973); expected 358.6 (0.02)
Passed bias filter:                     1001  (0.0558313); expected 358.6 (0.02)
Passed Vit filter:                       214  (0.011936); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 645.93
//
Query:       gi|119719888|ref|YP_920383.1|  [L=209]
Description: hypothetical protein Tpen_0980 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.4e-05   23.0   1.2    0.00012   22.1   1.2    1.4  1  AbiEii         Nucleotidyl transferase AbiEii toxin, Type IV 
     0.0012   18.5   2.2      0.024   14.3   2.2    2.8  1  DUF2204        Nucleotidyl transferase of unknown function (D
     0.0025   17.5   0.5     0.0059   16.3   0.5    1.6  1  NTP_transf_5   Uncharacterised nucleotidyltransferase
  ------ inclusion threshold ------
      0.035   14.6   0.3        0.1   13.1   0.2    1.9  2  CoA_binding_2  CoA binding domain


Domain annotation for each model (and alignments):
>> AbiEii  Nucleotidyl transferase AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   1.2   2.7e-08   0.00012      16     171 ..      27     166 ..      15     201 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 2.7e-08
                         AbiEii  16 vFkGGTa.LslayglipRfSeDIDlsllrgdrkellealkealeeiaaalaeeglkvklaasigegedyeglrlrypaef 94 
                                    +  GG a + + ++   R +eD+D+++l   r++  + ++e+ +e ++ + ++ lk           +++gl        
  gi|119719888|ref|YP_920383.1|  27 AVVGGLAcILMGVR---RVTEDVDVVVLVRAREDVEKLVRELRSEGIELPSSDALKAL---------QNRGLVA------ 88 
                                    55666665555555...*********98777777777778888888888888777754.........6677777...... PP

                         AbiEii  95 ggyarqkikieigfreav..ppaerreippyleelggpafevpvysleellaeKllall......drgrdrsraRDlyDl 166
                                    +    ++++++i + +++   ++ r+ ++  ++++      v+  sle+++a Kl+ l       d+ +   ++RD  D 
  gi|119719888|ref|YP_920383.1|  89 AL--VGPLRVDIRYASTWldFETIRHAVEVNIRGE-----PVRIASLEDVVAAKLTVLRtlrdveDAVQLMVQYRDRIDW 161
                                    33..3456788888999977888888888889888.....*****************99777776666666668888887 PP

                         AbiEii 167 alLle 171
                                      L +
  gi|119719888|ref|YP_920383.1| 162 ERLRR 166
                                    77666 PP

>> DUF2204  Nucleotidyl transferase of unknown function (DUF2204)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   2.2   5.3e-06     0.024       5     164 ..      12     168 ..       8     184 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.3e-06
                        DUF2204   5 laevlkvLeekgvkfvviGgtvvelalgrkrlekDvDlFitek.sqlleedfyreiaee...edwdvgstelgtvkliak 80 
                                    + +v++ L+ + +   v+Gg  + + +g++r+++DvD+ ++    +++e+ + re+ +e      + +  +l + +l+a 
  gi|119719888|ref|YP_920383.1|  12 MVSVARALRRADLPYAVVGGL-ACILMGVRRVTEDVDVVVLVRaREDVEK-LVRELRSEgieLPSSDALKALQNRGLVAA 89 
                                    568999999999977788876.556689*********9887550555654.55566544100444445566777777777 PP

                        DUF2204  81 vekeevevdl.leNildlyvpeeiLerakeveiggvevkvislEdyivlKaraareeaeeeldeiarlikelklkldvrl 159
                                    + +  ++vd+ +        + e++ +a+ev+i g  v++ slEd +  K    r    +  d + +l+ + + ++d ++
  gi|119719888|ref|YP_920383.1|  90 LVG-PLRVDIrY---ASTWLDFETIRHAVEVNIRGEPVRIASLEDVVAAKLTVLRT-LRDVEDAV-QLMVQYRDRIDWER 163
                                    665.57888744...344566689**************************998887.23333333.33333455667666 PP

                        DUF2204 160 vkehv 164
                                    +++ v
  gi|119719888|ref|YP_920383.1| 164 LRRIV 168
                                    66665 PP

>> NTP_transf_5  Uncharacterised nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.5   1.3e-06    0.0059      63     228 ..      15     167 ..       8     171 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.3e-06
                   NTP_transf_5  63 llalleeegipvllLKGpalaqlYpdpalRemgDiDllvk...redldraeelLeelGyelesdgsekhevyyre..... 134
                                    ++++l+++++p+ ++ G+a+         R   D+D+ v    red+++  + L+++G+el s  ++ ++  +r      
  gi|119719888|ref|YP_920383.1|  15 VARALRRADLPYAVVGGLACIL---MGVRRVTEDVDVVVLvraREDVEKLVRELRSEGIELPSS-DALKALQNRGlvaal 90 
                                    6788888888888888888765...23468889999765333899***************9998.665544444477777 PP

                   NTP_transf_5 135 kkgveielhwrllppesprlepdfddlleerarpveiggksilvlspedlllylalHlakhfwnrglgLrwlvDiaallr 214
                                      ++++++    +         df+  + ++a++v+i g ++++ s ed +   a+ l+  +      Lr++ D  +l+ 
  gi|119719888|ref|YP_920383.1|  91 VGPLRVDIRYASTWL-------DFET-I-RHAVEVNIRGEPVRIASLEDVV---AAKLTVLRT-----LRDVEDAVQLMV 153
                                    888999999888865.......6765.3.469*****************76...666766666.....************ PP

                   NTP_transf_5 215 klkdeldweallar 228
                                    ++ d +dwe+l ++
  gi|119719888|ref|YP_920383.1| 154 QYRDRIDWERLRRI 167
                                    **********9876 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.2   2.2e-05       0.1      46      80 ..      39      70 ..      13      74 .. 0.77
   2 ?   -1.4   0.0      0.69   3.1e+03      19      38 ..      77      96 ..      71     154 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.2e-05
                                   ----T....T--EEEE-S-HHHHGGGHHHHHHH-- CS
                  CoA_binding_2 46 yaslaedpepvdlvdvftppeatpeivkealalga 80
                                   +++++   e+vd+v++++ +e+++++v+e+ ++g+
  gi|119719888|ref|YP_920383.1| 39 VRRVT---EDVDVVVLVRAREDVEKLVRELRSEGI 70
                                   56666...68********************99997 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.69
                                   HHHHHHHHT--EEEESSS-S CS
                  CoA_binding_2 19 vlryllehglpvvpVnpkee 38
                                   +l+ l+++gl    V p + 
  gi|119719888|ref|YP_920383.1| 77 ALKALQNRGLVAALVGPLRV 96
                                   55666666666666655443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       775  (0.0432261); expected 358.6 (0.02)
Passed bias filter:                      626  (0.0349155); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 1367.80
//
Query:       gi|119719889|ref|YP_920384.1|  [L=215]
Description: hypothetical protein Tpen_0981 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1577.42
//
Query:       gi|119719890|ref|YP_920385.1|  [L=1001]
Description: hypothetical protein Tpen_0982 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-10   39.7   0.0    9.8e-10   38.4   0.0    1.7  1  DUF1156          Protein of unknown function (DUF1156)
    5.8e-07   29.4   0.0     0.0039   16.9   0.0    2.7  2  UPF0020          Putative RNA methylase family UPF0020
    1.4e-05   24.9   0.0      0.056   13.1   0.0    2.4  2  Cons_hypoth95    Conserved hypothetical protein 95
  ------ inclusion threshold ------
      0.018   14.7   0.1        0.1   12.2   0.0    2.1  3  MethyltransfD12  D12 class N6 adenine-specific DNA methyltran
       0.11   12.2   0.0         11    5.6   0.0    2.6  2  N6_N4_Mtase      DNA methylase


Domain annotation for each model (and alignments):
>> DUF1156  Protein of unknown function (DUF1156)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.0   2.7e-13   9.8e-10       2      48 ..      14      61 ..      13      74 .. 0.87

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 2.7e-13
                        DUF1156  2 lPldkinaesakEksirhg.hlstLhlWWaRrPLaaaRAvifaqLvpd 48
                                   +P+++in++s+ Ek+ +       +  WW R+PLa aRA+i a+L+  
  gi|119719890|ref|YP_920385.1| 14 FPIESINKASKSEKTGGGRpPYWEMVFWWTRKPLAGARAIIAASLLSQ 61
                                   9*************9997766789*********************987 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.1e-06    0.0039      25      59 ..      94     128 ..      90     168 .. 0.78
   2 !    9.5   0.0   0.00021      0.74     103     137 ..     577     612 ..     570     666 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.1e-06
                                    T--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT- CS
                        UPF0020  25 gwkpgepllDPmCGsGtilIEaallganiapgllr 59 
                                    +  +g++llDP+ G G+i++Eaa lg ++ +  l 
  gi|119719890|ref|YP_920385.1|  94 EKLKGKKLLDPFAGFGSIPLEAARLGLDVTAVELL 128
                                    566899*******************9998866554 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00021
                                    GGEEEEE--GGG--.STTS---EEEE---------- CS
                        UPF0020 103 dliefsqadaakLr.lkegevdvivtnpPYGerlgs 137
                                     ++++   da+ L  l  +++d+ivt+pPY + +  
  gi|119719890|ref|YP_920385.1| 577 SRVKVLLDDATTLDmLVGEKFDLIVTDPPYADDVPY 612
                                    55666667888888655569**********987654 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   1.6e-05     0.056      38      86 ..      94     141 ..      86     165 .. 0.82
   2 !    9.1   0.0   0.00026      0.95      99     129 ..     584     612 ..     571     626 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.6e-05
                                    CCHCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCC CS
                  Cons_hypoth95  38 aeiegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenlee 86 
                                    ++++g+++LD faG G++ lEA+ R    +++ve  ++a+  lk+ le 
  gi|119719890|ref|YP_920385.1|  94 EKLKGKKLLDPFAGFGSIPLEAA-RLGLDVTAVELLPTAYVFLKAVLEY 141
                                    56899*****************7.5558899999999999999877665 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00026
                                    S-HHHHCTS--SS-EEEEEEE--SSSTTCH. CS
                  Cons_hypoth95  99 daleallklakkkeefdivflDPPyakelli 129
                                    d++  l+ l   +e+fd++  DPPya++  +
  gi|119719890|ref|YP_920385.1| 584 DDATTLDML--VGEKFDLIVTDPPYADDVPY 612
                                    444555556..4679***********98654 PP

>> MethyltransfD12  D12 class N6 adenine-specific DNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.9e-05       0.1      15      72 ..      92     148 ..      86     163 .. 0.85
   2 ?   -4.2   0.1         3   1.1e+04     179     188 ..     598     607 ..     588     609 .. 0.78
   3 ?   -1.2   0.0      0.36   1.3e+03      80     145 ..     650     714 ..     616     720 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.9e-05
                                    CS-..--SEEEETT-TTSCCHHCS...SSCEEEEES-HHHHHHHHHHCCHSHHHHHHH CS
                MethyltransfD12  15 lipkdkgktfvepFaGggaVffeakkqgkkvlinDinedlinlykaliknnveelike 72 
                                    l++k kgk++ +pFaG g++ +ea + g +v++  +++  +++ ka+++  ++e+ k+
  gi|119719890|ref|YP_920385.1|  92 LVEKLKGKKLLDPFAGFGSIPLEAARLGLDVTAVELLPTAYVFLKAVLEY-PKEYGKR 148
                                    55555899*************************************99995.6666555 PP

  == domain 2  score: -4.2 bits;  conditional E-value: 3
                                    .EEEE--S-T CS
                MethyltransfD12 179 divYlDPPYn 188
                                    d++  DPPY+
  gi|119719890|ref|YP_920385.1| 598 DLIVTDPPYA 607
                                    57778****7 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.36
                                    GGC.TSHHHHHHHHHHHH...HHH-HHHHHHHHHHHHCCBGGG---B-TTS-B---B-S-SS-.... CS
                MethyltransfD12  80 eelenereyfyelreefnkkidaireaeeaidflylnrllfsglervnkkgnfnvpygaykkp.kkv 145
                                    ee +++ e+f + + ++n   +  ++++ +i+f++l   +f++++r+ +++   v+y   kkp ++v
  gi|119719890|ref|YP_920385.1| 650 EEIKTQWETFATREVSEN--TERWKYFKLNISFSELLARAFANVTRFLDEKGLLVTYYVAKKPeAWV 714
                                    344456788888888888..77778888899999999999999999999999999998888885655 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.013        46     191     219 ..      97     125 ..      86     135 .. 0.84
   2 ?    5.6   0.0    0.0031        11       2      53 ..     598     702 ..     597     728 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.013
                                    TT-EEEETT-TTTHHHHHHHHTT-EEEEE CS
                    N6_N4_Mtase 191 kgdivlDpFaGSGtTavaakelgrkfiGi 219
                                    kg+  lDpFaG G++  +a++lg +   +
  gi|119719890|ref|YP_920385.1|  97 KGKKLLDPFAGFGSIPLEAARLGLDVTAV 125
                                    67889**********99999999776555 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0031
                                    EEEEE--SSSSSCS..........................................................GCCGCCHH CS
                    N6_N4_Mtase   2 dlivtdpPYntgkdy.....................................................endeqyeeedsy 28 
                                    dlivtdpPY     y                                                     en e ++ ++  
  gi|119719890|ref|YP_920385.1| 598 DLIVTDPPYADDVPYtelsdfyyvwlkralsdvsggkliprflpeaffdefgeeiktqwetfatrevsENTERWKYFKLN 677
                                    89********9999999999999999999999999999999999999999999999999999999999899999999999 PP

                                    HHHHHHHHHHHHHHHHHEEEEEEEE CS
                    N6_N4_Mtase  29 eeyleflekvlkevrrvLkddgsif 53 
                                      ++e+l + +++v r L + g ++
  gi|119719890|ref|YP_920385.1| 678 ISFSELLARAFANVTRFLDEKGLLV 702
                                    9999999999999999999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1001 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       729  (0.0406604); expected 358.6 (0.02)
Passed bias filter:                      646  (0.036031); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.80u 0.29s 00:00:01.09 Elapsed: 00:00:00.46
# Mc/sec: 6493.78
//
Query:       gi|119719891|ref|YP_920386.1|  [L=1019]
Description: hypothetical protein Tpen_0983 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.1e-06   24.3   0.7    0.00029   18.8   0.0    2.5  2  DUF499    Protein of unknown function (DUF499)
  ------ inclusion threshold ------
       0.16   11.1   0.0       0.29   10.4   0.0    1.3  1  PS-DH     Polyketide synthase dehydratase


Domain annotation for each model (and alignments):
>> DUF499  Protein of unknown function (DUF499)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   3.2e-08   0.00029     225     420 ..     266     442 ..     212     511 .. 0.78
   2 !    3.0   0.7    0.0018        16     642     707 ..     651     719 ..     521    1013 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 3.2e-08
                         DUF499 225 dlekeleetYPFHPeylevLreiierldlqrTRdlirItrivvrklldalEd.epelImPwHId.lvdeevrglllleka 302
                                    ++e+ l  +YPF P  l+   +++     ++TR  +++tr ++r l +a+ +   el++   ++ +++  + g ++ +  
  gi|119719891|ref|YP_920386.1| 266 EFENRLRGSYPFNPYLLDAVLQLADESLVEKTR--VQLTRGLLRILASAYVNrRGELVIFADLPePKEVVIAGDVFAG-- 341
                                    58889999*********9998999999999998..6778888888888877645566666555426667788888888.. PP

                         DUF499 303 eykdykkileaeivaeeklgklkalskpeLakkilkvifLktypydslktplkeFPtlkdiarmvYepetfekndlkPaD 382
                                    + ++   ++e++          +++s    a+ +l+ i+L t+    l+     +Pt +++  + Y+p      + kP D
  gi|119719891|ref|YP_920386.1| 342 QLNVILRLYEDD---------ARKVSGSIAALSVLRHILLATFFARLLPHR-RMYPTEEELILGSYDPA-----RVKPLD 406
                                    455444444444.........5677777778999***************99.9**************96.....4689** PP

                         DUF499 383 ikdtveeikklpklvflaesdsrfWffriasveelver 420
                                    +k  +e    +   +  ++ + r+ ++ i  +ee v+ 
  gi|119719891|ref|YP_920386.1| 407 VKMFLEDAARQGLHI--EKVNGRYMYWFIGGIEEKVRD 442
                                    ******976665555..788999999999999999954 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.0018
                         DUF499 642 elkdilkdnlgidilpgrki.kvgelinviltnpkaPmi..rekalieaikeavkkLdiaierkgkllf 707
                                     l+ ++k+    d+++   + kvg+l+ ++l n++ P i  +++++ ea++e  k  +   e++g + +
  gi|119719891|ref|YP_920386.1| 651 RLRGVVKEIFTGDLINWDSFkKVGDLWSLFLNNESFPAIpaSFEEFLEALREYCKGCNCLFEEDGEVKW 719
                                    45666777667777777444279**************9944578999***9999999999999998877 PP

>> PS-DH  Polyketide synthase dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   3.2e-05      0.29     172     238 ..     241     307 ..     234     349 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 3.2e-05
                                    G--EEEEEEETTEEEEEE---GGGSSTTTT....-SB-HHHHHHHHHHG..GG----------EEEEEEEE CS
                          PS-DH 172 Fqglralwrgdgealaelrlpeelaggesa....yvlhPallDaalQllaaalsaeaekadaaylPvaier 238
                                    + gl+ +++ + + l  + ++e l++ e++    y++ P+llDa+lQl     ++   +++++ l  ++ r
  gi|119719891|ref|YP_920386.1| 241 WAGLSGARSVELAGLKGIVTDERLREFENRlrgsYPFNPYLLDAVLQLA----DESLVEKTRVQLTRGLLR 307
                                    6677777887888888888889999998889999*************66....445555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1019 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.79u 0.30s 00:00:01.09 Elapsed: 00:00:00.48
# Mc/sec: 6447.64
//
Query:       gi|119719892|ref|YP_920387.1|  [L=132]
Description: hypothetical protein Tpen_0984 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 910.48
//
Query:       gi|119719893|ref|YP_920388.1|  [L=813]
Description: helicase domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.3e-15   57.7   0.0    3.6e-15   56.3   0.0    1.8  1  Helicase_C  Helicase conserved C-terminal domain
      2e-15   56.4   0.5    4.7e-14   51.9   0.1    2.6  2  SNF2_N      SNF2 family N-terminal domain
    9.1e-09   35.5   0.0    2.6e-08   34.1   0.0    1.7  1  ResIII      Type III restriction enzyme, res subunit
    6.1e-05   23.0   0.0    0.00027   20.9   0.0    2.2  1  DUF3883     Domain of unknown function (DUF3883)
    9.2e-05   22.4   0.1    0.00024   21.1   0.1    1.7  1  PDDEXK_5    PD-(D/E)XK endonuclease
     0.0047   16.7   0.0      0.079   12.7   0.0    2.4  1  DEAD        DEAD/DEAH box helicase
  ------ inclusion threshold ------
       0.07   13.1   0.0       0.14   12.1   0.0    1.4  1  Flavi_DEAD  Flavivirus DEAD domain


Domain annotation for each model (and alignments):
>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.3   0.0   1.4e-18   3.6e-15       2     111 .]     296     426 ..     295     426 .. 0.77

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 1.4e-18
                                    HHHHHHHHHHHTTTTSEEEEEESSHHHHHH..HHHH...........HHHT......TSTEEEESTTSTHHHHHHHHHHH CS
                     Helicase_C   2 kleallellkleeeggkilifvntidrlek..vkll...........lekk......gikvavlhgelpqnereeileqf 62 
                                    kl+al +llk + +g+k+l+f+++ +++e    kl+              +        ++ v++ + ++++r+++ ++ 
  gi|119719893|ref|YP_920388.1| 296 KLDALEKLLKDHLKGRKVLVFTEYATTAEYlfEKLVeklegckivdsG--EgyakadCSEFGVMYVTAKARDRIDVSREG 373
                                    8999**********************9865642222333343333440..034444456666677778889999888888 PP

                                    H....TTSSSEEEESGGGTSSSTSTTESEEEESSSSSSHHHHHHHHTTSSSTT CS
                     Helicase_C  63 n....kgesdvLiatdvaerGidipkvnlVinfdlprnvtsyiqriGRtgRag 111
                                         +  + vLi+td++++G++++  ++V+n+++ +++t+ +qriGR++R+g
  gi|119719893|ref|YP_920388.1| 374 AllasAYPTAVLISTDIMSEGVNLQAFDVVVNYEVVWSPTKHVQRIGRIWRFG 426
                                    7774344456*****************************************86 PP

>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.9   0.1   1.8e-17   4.7e-14      59     217 ..      35     162 ..      32     174 .. 0.85
   2 ?    1.5   0.0     0.038        98     254     316 ..     165     232 ..     161     254 .. 0.79

  Alignments for each domain:
  == domain 1  score: 51.9 bits;  conditional E-value: 1.8e-17
                                    EE---TTS--HHHHHHHHH...HHTTTS---.......S-EEEE--HHHHHHHHHHHHHH-TTS-EEE--SSHHHH---- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SNF2_N  59 iLaDemGLGKTvqvlalilaqrakeekdkekkrkdtlagptLivvPaslldqWeneierhvsssalrvlvyggqkkmkkk 138
                                    +LaD+ GLGKT+q+l  i+a+ +               + +L++vP ++++qW +e+e +  +  +     +        
  gi|119719893|ref|YP_920388.1|  35 LLADDVGLGKTIQALLYIKALLELGRV-----------NHVLVIVPRAVVEQWASELEMFEIPFYI----VE-------- 91 
                                    79*****************55553333...........349******************9888855....22........ PP

                                    -------------EEEE-HHHHHHHT......TTS-S-S-SEEEES-GGGT--TTSHHHHHHHH---S-EEEE-S--SS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SNF2_N 139 ntkvapklladydvvittYdvlsreaelqkkrsvlkqvewkrvvlDEghtlknstskaaeavskLstsnrwiltGTPiq 217
                                        +p++   + v ++t+d+ + ++     +++l +++w+ vv+DE+h+l+ +t + + a++  +++  ++lt+TP  
  gi|119719893|ref|YP_920388.1|  92 ----SPDFPLGHRVYLVTLDRAKVDS----YMEALDKINWDLVVVDEAHKLRLETLRSKVAILCRRARGCLLLTATPHT 162
                                    ....4779999************888....89**********************87777777766999*********65 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.038
                                    HHHHHHHHTT-STTEE---GGGT.....--S---EEEEEEEEE--HHHHHHHH............... CS
                                    xxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SNF2_N 254 ekgrsrLlqllqrlmlrrakkdv.....eknlPpkteeiiflklskverksYnrllevlrkkalakll 316
                                    e + + L+ l +++++rr kkdv      k +P     i+ +k +k+e  + +++l++l ++ + ++ 
  gi|119719893|ref|YP_920388.1| 165 ESSFKFLIGLANSYVVRREKKDVeeyegRKIFPSLGYWIVQVKATKEESDALHKVLKFLENDQIEQIV 232
                                    5566778889999**********877644568999999999999999999999999998888776654 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.0     1e-11   2.6e-08      23     170 ..      30     161 ..      12     162 .. 0.82

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 1e-11
                                    TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B--...... CS
                         ResIII  23 rdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseaykeigkkvsgdkkkakekdst 102
                                    ++ r+l++   G GKT+ a+  i++ll+ g+ +++l++vpr +++eq+ +e++ f  + y     +v++           
  gi|119719893|ref|YP_920388.1|  30 DEPRILLADDVGLGKTIQALLYIKALLELGRVNHVLVIVPR-AVVEQWASELEMFEIPFY-----IVESPDFPL------ 97 
                                    6779999999******************************8.799**********99876.....455555555...... PP

                                    .-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.TTTHH.H.HHT---SEEEEEESS-S CS
                         ResIII 103 nkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakkswre.i.lekfkeavllglTATpe 170
                                      +++++t ++++ ds     + e l++ + d++++DEaH+l+  ++ r+ + + + ++   l lTATp 
  gi|119719893|ref|YP_920388.1|  98 GHRVYLVTLDRAKVDS-----YMEALDKINWDLVVVDEAHKLRL-ETLRSkVaILCRRARGCLLLTATPH 161
                                    799*************.....99999999**************9.544443435555778889999**95 PP

>> DUF3883  Domain of unknown function (DUF3883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   1.1e-07   0.00027       2      83 ..     687     768 ..     686     778 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.1e-07
                        DUF3883   2 EklvlealkekekeegvewvnedvedglgYDiesvdkedgeerfIEVKtta..kgkkdfelsrnElefaqekgdkYwlyr 79 
                                    E+++ ++ ++ +++ g + v+e+ +   ++D+ + +  dg    +EVK++   k+++++  + nE++ a ++ d++++ +
  gi|119719893|ref|YP_920388.1| 687 ERAAARCIRSLLENLGYTIVEEYASIPRPFDMVVKK--DGILYTVEVKGKWvgKRDEPLSFTANEIDWASRFPDRHIVCI 764
                                    6677777777788888888888888889******99..9*9**********99999*******************99888 PP

                        DUF3883  80 Vfna 83 
                                     ++ 
  gi|119719893|ref|YP_920388.1| 765 AYVD 768
                                    7765 PP

>> PDDEXK_5  PD-(D/E)XK endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.1   9.5e-08   0.00024       5      87 ..     684     768 ..     681     812 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 9.5e-08
                                    HHHHHHHHHHHHHHHHT.T-EEEEESS.TTSS-SEEEEETTEEEEEEEEE-EEETTTSCEEEE-CEEEESSSSEEEEE-- CS
                       PDDEXK_5   5 dkGDiaeakaiadllkk.gysVltPvg.dhlpyDLvadkdgklyriQvKyawleeksgqlrvknrstktdkngvhrkkYk 82 
                                    ++ + a+a++i  ll++ gy+++  +    +p+D+v+ kdg ly + vK +w+ ++++ l++  + +   ++   r+   
  gi|119719893|ref|YP_920388.1| 684 ERTERAAARCIRSLLENlGYTIVEEYAsIPRPFDMVVKKDGILYTVEVKGKWVGKRDEPLSFTANEIDWASRFPDRHIVC 763
                                    667889999999999755****999987899******************************9988777666666554444 PP

                                    CCS-S CS
                       PDDEXK_5  83 kedfD 87 
                                       +D
  gi|119719893|ref|YP_920388.1| 764 IAYVD 768
                                    44444 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   3.1e-05     0.079      14     170 ..      31     161 ..      16     167 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.1e-05
                                    TCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  14 ggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliiggvaardqlsk 93 
                                    +  +l+a ++G GKT  +l+ + + + e    + + +l+++P r+ +eq +++l+ f  +       i+++ +       
  gi|119719893|ref|YP_920388.1|  31 EPRILLADDVGLGKTIQALLYIKALL-E--LGRVNHVLVIVP-RAVVEQWASELEMFEIPFY-----IVESPDF-----P 96 
                                    55788899999****99888877555.5..777778999999.7899999999999988643.....3333333.....4 PP

                                    HHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSEEEEEESSBS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  94 ldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrqvivlSATlp 170
                                    l ++v +v     ++d+ ++   l+  +  ++V+DEa++l  +  + ++  + ++           r +++l+AT++
  gi|119719893|ref|YP_920388.1|  97 LGHRVYLVTLDRAKVDSYME--ALDKINWDLVVVDEAHKLRLETLRSKVAILCRRA----------RGCLLLTATPH 161
                                    43446677777777777664..655677789*********9998888888877777..........45999999999 PP

>> Flavi_DEAD  Flavivirus DEAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   5.4e-05      0.14      14     137 ..      41     161 ..      31     169 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.4e-05
                                    TS-TTTTHHHHHHHHHHHTT-.-EEEEESSHHHHHHHHHHTTTS-EEE-------------SEEEEEHHHHHHHHHHT-- CS
                     Flavi_DEAD  14 GaGktrkvlpelvkeaierrl.rtlvLaPtrvvlaemeealkglevryktsavkeektgrelvdvmchatftkrllspvr 92 
                                    G Gkt + l  +       r+ + lv++P r v++  +  l+  e+ +      +   g+ +  v    + +   ++   
  gi|119719893|ref|YP_920388.1|  41 GLGKTIQALLYIKALLELGRVnHVLVIVP-RAVVEQWASELEMFEIPFYIVESPDFPLGHRVYLVTLDRAKVDSYMEALD 119
                                    67777777766554443334404555555.666677888889999998888888888888888888889999999***** PP

                                    ----SEEEEETTT--SHHHHHHHHHHHHHHHTTS-EEEEEESS-T CS
                     Flavi_DEAD  93 kknyeliimDeahflDPasiaarGyletkaeegeaalilltatPP 137
                                    k n++l+++Deah l  + + ++  +  ++ +g   ++lltatP 
  gi|119719893|ref|YP_920388.1| 120 KINWDLVVVDEAHKLRLETLRSKVAILCRRARG---CLLLTATPH 161
                                    **************9999988887777766666...789999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (813 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       850  (0.0474092); expected 358.6 (0.02)
Passed bias filter:                      712  (0.0397122); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.76u 0.34s 00:00:01.10 Elapsed: 00:00:00.53
# Mc/sec: 4613.82
//
Query:       gi|119719894|ref|YP_920389.1|  [L=312]
Description: hypothetical protein Tpen_0986 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.9e-07   29.5   0.4      2e-06   27.7   0.0    1.9  2  Peptidase_M48  Peptidase family M48
  ------ inclusion threshold ------
       0.67   10.1   3.9          2    8.6   3.9    1.8  1  SPC12          Microsomal signal peptidase 12 kDa subunit (SP


Domain annotation for each model (and alignments):
>> Peptidase_M48  Peptidase family M48
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.4      0.13   1.1e+03      85     126 ..      28      69 ..      17      84 .. 0.52
   2 !   27.7   0.0   2.3e-10     2e-06      17     165 ..     119     252 ..     107     310 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.13
                                    HHHHHHHHHHHHHHHHHTT-SHHHHHTT--S---HHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M48  85 ivsllasillllglallisraeedaagafldalavligllii 126
                                    ++    +++++ ++   ++r e+   + +l  l+ +++ll +
  gi|119719894|ref|YP_920389.1|  28 MMVFATTFAYFAAMHGGFKRLEHVLVFRILIVLGLVAALLVF 69 
                                    444444444444444444444444444444444444444444 PP

  == domain 2  score: 27.7 bits;  conditional E-value: 2.3e-10
                                    HTT-..-EEEEEEE-GGGT-EEEEESSS-EEEEEEHHHH-SSB-HHHHHHHHHHHHHHHHTTHHHHH.HHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
                  Peptidase_M48  17 eaglpkpltkvyvvnspkrNAFalgggknkrivltdgLlkqllseeelaaVlGHElGHikhrhsvvs.livsllasilll 95 
                                    e+g   +  ++ vv+s+  NA   g+     i +t++L  +  + +el+ Vl HE GH    + vv    + ll+s+++l
  gi|119719894|ref|YP_920389.1| 119 EIGG--RGYEYWVVDSDVLNACRKGRE----ICVTRKLA-EVFEVDELKVVLLHEEGHDGIFDKVVVvGRIILLSSLIIL 191
                                    4555..778999*********888888....********.******************9999998885678888889999 PP

                                    HHHHHHTT-SHHHHHTT--S---HHHHHHHHHHTTHHHHHHHHHHHHHHHHTTT.HHHHHHHHHHHHHHT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M48  96 lglallisraeedaagafldalavliglliillflalSRkrEyqADeagvellkrakdlvraliklakdl 165
                                    ++ a+++ ++  + +  ++  +        i   +  S  +E  AD  ++++   ++  vr+++k+++ +
  gi|119719894|ref|YP_920389.1| 192 ITDAFMLDAEMFFSSLSAYLLA--------IPAATLASWVNEHVADLNAAKMFP-PELVVRTFVKFWACA 252
                                    9998888877766655554222........2223468999**************.**********99755 PP

>> SPC12  Microsomal signal peptidase 12 kDa subunit (SPC12)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   3.9   0.00022         2       8      60 ..      23      77 ..      22      82 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00022
                          SPC12  8 laekllqvilvlsaviafivGyit..qdlkltlyillagvvltllvvvPpWpfYn 60
                                   la +++ v  +++a +a + G ++  + + +  +++++g+v +llv+vP+  +Y 
  gi|119719894|ref|YP_920389.1| 23 LATSVMMVFATTFAYFAAMHGGFKrlEHVLVFRILIVLGLVAALLVFVPHMVWYC 77
                                   57788999999999999999988622455555567888999************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       985  (0.0549389); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2210.62
//
Query:       gi|119719895|ref|YP_920390.1|  [L=299]
Description: partition protein, ParA-like [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.8e-26   93.1   0.0    7.1e-26   91.2   0.0    1.8  2  AAA_31       AAA domain
    4.7e-13   49.3   0.0      7e-13   48.7   0.0    1.3  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
      6e-06   25.9   0.3    9.7e-06   25.2   0.3    1.3  1  ParA         NUBPL iron-transfer P-loop NTPase
    0.00011   21.8   0.1    0.00056   19.4   0.1    1.9  2  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
    0.00023   20.4   1.2    0.00026   20.3   0.2    1.7  2  ArsA_ATPase  Anion-transporting ATPase
    0.00025   20.6   0.0     0.0012   18.4   0.0    1.9  1  CBP_BcsQ     Cellulose biosynthesis protein BcsQ
    0.00038   19.8   0.1      0.032   13.5   0.2    2.3  2  VirC1        VirC1 protein
  ------ inclusion threshold ------
      0.028   13.7   0.2      0.046   13.0   0.2    1.3  1  MipZ         ATPase MipZ
      0.058   13.0   0.3       0.12   12.0   0.3    1.5  1  AAA_25       AAA domain
       0.13   12.8   0.0       0.24   12.0   0.0    1.4  1  PRAS         Proline-rich AKT1 substrate 1


Domain annotation for each model (and alignments):
>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.2   0.0   3.9e-29   7.1e-26       1     157 [.       1     177 [.       1     195 [. 0.83
   2 ?   -0.6   0.1       0.6   1.1e+03      98     122 ..     265     289 ..     208     293 .. 0.64

  Alignments for each domain:
  == domain 1  score: 91.2 bits;  conditional E-value: 3.9e-29
                         AAA_31   1 gkvIaianqKGGvGKTTtsvnlaaalakl...gkkvLlvDlDpQanattglgiekne.....iektlyevlieeknikea 72 
                                    +k +++   KGGvGKTT +vn aa+la +    +kvL+vDlD+Qa+at+++  +k++      ++t+y +l   ++ +++
  gi|119719895|ref|YP_920390.1|   1 MKAVTFLSVKGGVGKTTLAVNTAAMLADRvggSEKVLVVDLDAQASATVYILGHKKQrgfeeSNHTVYGLLSGGVEARDC 80 
                                    7999***********************5433358***************7766665557776788999999677777777 PP

                         AAA_31  73 ii.....ktk.venldlipssidLaeaeielvelekk.....eeilkellekvkde.YDyiiiDcpPsLglltenaLvas 140
                                    ++     ++k +++l+l+p++  + e+e ++v  +        +i++++lek++ e + y++iD p +Lg+l e aL+as
  gi|119719895|ref|YP_920390.1|  81 VVnvsehTDKwSSRLYLVPGDSRVTELERRIVAESAAggygwLYIVRRALEKLSGEgFSYVFIDPPATLGVLSEAALAAS 160
                                    7633332333456669999999999999999988888888877789*******9888*********************** PP

                         AAA_31 141 dsviipvqaeayaleGl 157
                                     ++i p+ ++++    +
  gi|119719895|ref|YP_920390.1| 161 RYFILPIVPDDFGRTSF 177
                                    *********99987665 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.6
                         AAA_31  98 velekkeeilkellekvkdeYDyii 122
                                     e++k+e+++ke+ e +++ Y y++
  gi|119719895|ref|YP_920390.1| 265 KEKKKHENAIKEFEEYFDEFYEYVV 289
                                    2333334445555555555566766 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.7   0.0   3.9e-16     7e-13       2     113 ..       5     239 ..       4     261 .. 0.83

  Alignments for each domain:
  == domain 1  score: 48.7 bits;  conditional E-value: 3.9e-16
                                    EEEESSTTSSHHHHHHHHHHHHHHT...T--EEEEEEEESSCCCCHHTTEB-HHHH........................ CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxx........................ RF
                           CbiA   2 aiastkGGvGKTtlaanLaralarr...glrVllvDaDpqannlaileglendiep........................ 54 
                                    ++ s kGGvGKTtla+n a+ la+r     +Vl+vD+D qa+++ ++ g ++++                          
  gi|119719895|ref|YP_920390.1|   5 TFLSVKGGVGKTTLAVNTAAMLADRvggSEKVLVVDLDAQASATVYILGHKKQRGFeesnhtvygllsggveardcvvnv 84 
                                    68899******************9655589**************995554444444456999****************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                           CbiA  55 ................................................................................ 54 
                                                                                                                    
  gi|119719895|ref|YP_920390.1|  85 sehtdkwssrlylvpgdsrvtelerrivaesaaggygwlyivrraleklsgegfsyvfidppatlgvlseaalaasryfi 164
                                    ******************************************************************************** PP

                                    ................CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEE..EEE CS
                                    ................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxx RF
                           CbiA  55 ................dlkrllellealgkkkalllkiagvvlnrvdgeneetllkealeelkqrygvpvlg..vip 113
                                                      + +++++ ++++++  l +  g+v+n+v+++ + +++ +++ e+ +  + +++g   ip
  gi|119719895|ref|YP_920390.1| 165 lpivpddfgrtsfrlfASSFFSGVAMKIRTELGTLPLCGGIVFNKVKSNTAMEKIANSIVEEVH--KSKLYGkyPIP 239
                                    ******99777666665555556666666555555999***********888888887777765..55555544333 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.3   5.4e-09   9.7e-06       6      60 ..       4      61 ..       1      80 [. 0.80

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 5.4e-09
                           ParA  6 iavlSgKGGVGKStvavnlAlaLakk...glkvgllDaDiyGpsiprllgveeekpeq 60
                                   ++ lS KGGVGK+t+avn A++La++     kv ++D+D        +lg ++++  +
  gi|119719895|ref|YP_920390.1|  4 VTFLSVKGGVGKTTLAVNTAAMLADRvggSEKVLVVDLDAQASATVYILGHKKQRGFE 61
                                   6779*******************954332689*******9999999999988876544 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1   3.1e-07   0.00056       8      53 ..      10      58 ..       4      67 .. 0.89
   2 ?   -0.3   0.0      0.32   5.8e+02     177     200 ..     203     227 ..     180     277 .. 0.67

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 3.1e-07
                      Fer4_NifH  8 kGGiGksttsqnlsaalaemg...kkvlivGCDPkaDstrlllggkaqe 53
                                   kGG+Gk+t + n++a+la++    +kvl+v  D +a +t  +lg k+q+
  gi|119719895|ref|YP_920390.1| 10 KGGVGKTTLAVNTAAMLADRVggsEKVLVVDLDAQASATVYILGHKKQR 58
                                   9*****************8733569******************999875 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.32
                      Fer4_NifH 177 gGliinsrkvddere.liekfaeel 200
                                    gG++ n+ k ++  e +++ ++ee+
  gi|119719895|ref|YP_920390.1| 203 GGIVFNKVKSNTAMEkIANSIVEEV 227
                                    6788885444444331334455554 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.2   1.4e-07   0.00026       3      39 ..       4      43 ..       1      83 [. 0.89
   2 ?   -2.7   0.0       1.4   2.5e+03     263     278 ..     269     284 ..     249     296 .. 0.63

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.4e-07
                                   EEEEEESTTSSHHHHHHHHHHHHHHT...TS-EEEEE-ST CS
                    ArsA_ATPase  3 vilvgGKGGVGKttvsaatavklsek...gkkvllistDP 39
                                   v +++ KGGVGKtt++  ta+ l++     +kvl++ +D 
  gi|119719895|ref|YP_920390.1|  4 VTFLSVKGGVGKTTLAVNTAAMLADRvggSEKVLVVDLDA 43
                                   568999******************96443799***99985 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.4
                                    HHHHHHHHHHHHTTTS CS
                    ArsA_ATPase 263 iqkkylkeieelfedl 278
                                      ++ +ke ee+f+++
  gi|119719895|ref|YP_920390.1| 269 KHENAIKEFEEYFDEF 284
                                    3334455555555544 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   6.5e-07    0.0012       1     148 [.       1     170 [.       1     184 [. 0.65

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 6.5e-07
                       CBP_BcsQ   1 mkvlalqGvRGGvGttsllaaLawalhel...gesvlviDlspdnlLrlh.........Fnvdieqregwaraeldgapw 68 
                                    mk +++  v+GGvG+t+l++  a  l       e+vlv+Dl ++   +++         F++  ++  g+    +++++ 
  gi|119719895|ref|YP_920390.1|   1 MKAVTFLSVKGGVGKTTLAVNTAAMLADRvggSEKVLVVDLDAQASATVYilghkkqrgFEESNHTVYGLLSGGVEARDC 80 
                                    899999************98888888654232699*****9876543332112223344666667777777777777765 PP

                       CBP_BcsQ  69 rqaale....yapgldllPfGelnveeken..lqqlaekaeal....laalkelk.eqyrwillDlpagasaltrellal 137
                                      ++ e    + + l l+P G  +v+e e+  ++++a+    +     +al++l+ e ++++++D pa    l +++la 
  gi|119719895|ref|YP_920390.1|  81 VVNVSEhtdkWSSRLYLVP-GDSRVTELERriVAESAAGGYGWlyivRRALEKLSgEGFSYVFIDPPATLGVLSEAALAA 159
                                    4444440011455688888.555555544422555555544452222567788888889999999999998888888887 PP

                       CBP_BcsQ 138 adlvllvvepd 148
                                    +   +l + pd
  gi|119719895|ref|YP_920390.1| 160 SRYFILPIVPD 170
                                    76666655555 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.2   1.8e-05     0.032       1      29 [.       1      29 [.       1      45 [. 0.88
   2 ?    3.9   0.0     0.016        29      71     113 ..     125     167 ..     122     173 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.8e-05
                          VirC1  1 mklitfcslkGGaGkttalmglcsalasd 29
                                   mk +tf s+kGG Gktt  +   ++la +
  gi|119719895|ref|YP_920390.1|  1 MKAVTFLSVKGGVGKTTLAVNTAAMLADR 29
                                   899**************999999999875 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.016
                          VirC1  71 lleaayeeaegeGfdyaladtrgGsselnntiiassdllliPt 113
                                    ++  a e+  geGf y+++d       l ++ +a+s ++++P 
  gi|119719895|ref|YP_920390.1| 125 IVRRALEKLSGEGFSYVFIDPPATLGVLSEAALAASRYFILPI 167
                                    567899***********************99999999999985 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2   2.6e-05     0.046       5      48 ..       6      51 ..       2      65 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.6e-05
                                   E--SSTTSSHHHHHHHHHHHHHTT...T--EEEEE--TTT-HHHHHH CS
                           MipZ  5 lgnekGGsGksttavhvavaLlkk...Garvaaidldlrqrtlaryl 48
                                   +   kGG Gk+t av  a  L+++     +v ++dld+ q++ + y+
  gi|119719895|ref|YP_920390.1|  6 FLSVKGGVGKTTLAVNTAAMLADRvggSEKVLVVDLDA-QASATVYI 51
                                   5567*****************986432479*******8.56666665 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.3   6.5e-05      0.12      33      80 ..       2      42 ..       1      62 [. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.5e-05
                         AAA_25 33 gelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaE 80
                                   ++++ l   +g+GKttla++ a+ +a      g       kVl+v+++
  gi|119719895|ref|YP_920390.1|  2 KAVTFLSVKGGVGKTTLAVNTAAMLADRV---G----GSEKVLVVDLD 42
                                   578889999**************999433...3....34467776665 PP

>> PRAS  Proline-rich AKT1 substrate 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00013      0.24      29      74 ..     230     273 ..     213     282 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00013
                           PRAS  29 gslsedaPaksrevalkqanelqyakslpvsvPvWglkekreqake 74 
                                    ++l  + P +  +++l+  ++ +y+ksl   vP+W +kek++++++
  gi|119719895|ref|YP_920390.1| 230 SKLYGKYPIPLYKTRLH--EYIAYTKSLEEHVPLWNIKEKKKHENA 273
                                    55555666655555555..899*****************9976554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      599  (0.0334096); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2081.07
//
Query:       gi|119719896|ref|YP_920391.1|  [L=147]
Description: hypothetical protein Tpen_0988 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.076   13.5   0.0       0.11   13.0   0.0    1.3  1  NERD      Nuclease-related domain


Domain annotation for each model (and alignments):
>> NERD  Nuclease-related domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0     6e-06      0.11       7      55 ..       8      58 ..       2      71 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6e-06
                           NERD  7 ravakeLkelked..eylvlhdvrlrpgtg....eiDhlvispkgifviEvKnws 55
                                    +v ++L+  +++  + +v   + l    g    ++D+lv+  +g+f +EvK+++
  gi|119719896|ref|YP_920391.1|  8 GEVYRFLRWKLRElwGARVEERYGL----GrlspDVDLLVVAGGGVFGLEVKYFQ 58
                                   5555666622222234444444444....123469*****************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       201  (0.0112109); expected 358.6 (0.02)
Passed bias filter:                      186  (0.0103743); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1111.89
//
Query:       gi|119719897|ref|YP_920392.1|  [L=336]
Description: hypothetical protein Tpen_0989 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-24   86.3   2.6    1.1e-24   86.3   2.6    4.6  2  DUF3782          Protein of unknown function (DUF3782)
      2e-24   85.3   0.0    4.3e-24   84.2   0.0    1.6  1  PDDEXK_10        PD-(D/E)XK nuclease superfamily
    2.4e-06   27.9  16.1       0.18   12.3   1.3    5.4  6  Snapin_Pallidin  Snapin/Pallidin
    3.6e-06   26.9  23.3     0.0003   20.7  17.2    2.4  2  KASH_CCD         Coiled-coil region of CCDC155 or KASH
    3.1e-05   24.6  16.6      0.084   13.5   0.9    3.4  3  YabA             Initiation control protein YabA
    4.5e-05   23.5  29.1     0.0023   18.0  13.1    2.3  2  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
    6.3e-05   23.1  19.6      0.022   14.8   4.8    2.4  2  Mod_r            Modifier of rudimentary (Mod(r)) protein
    7.8e-05   22.6  29.1       0.14   12.1   7.9    3.9  5  TMF_DNA_bd       TATA element modulatory factor 1 DNA binding
    0.00013   22.3   0.1         17    5.9   0.0    4.9  6  LPP              Lipoprotein leucine-zipper
    0.00023   21.5  41.7       0.29   11.6   7.7    4.4  4  ZapB             Cell division protein ZapB
    0.00057   20.1   6.7       0.27   11.5   0.8    3.8  5  DUF4709          Domain of unknown function (DUF4709)
    0.00059   19.9   7.7      0.081   13.0   1.6    2.6  2  DUF1664          Protein of unknown function (DUF1664)
    0.00059   20.4  42.6       0.11   13.0  14.6    3.2  4  APG6_N           Apg6 coiled-coil region
    0.00065   19.7  23.0          1    9.5   4.3    4.7  4  bZIP_1           bZIP transcription factor
     0.0015   18.5  33.9        0.3   11.0  10.2    3.1  3  JAKMIP_CC3       JAKMIP CC3 domain
     0.0016   17.8   2.6       0.12   11.6   0.1    2.7  2  ATP-synt_10      ATP10 protein
     0.0017   18.1  11.5       0.14   11.9   1.3    3.6  4  SKA2             Spindle and kinetochore-associated protein 2
     0.0018   17.9  16.3      0.061   12.9  10.7    2.3  2  PI3K_P85_iSH2    Phosphatidylinositol 3-kinase regulatory sub
     0.0028   16.4  11.7      0.049   12.2   3.1    2.1  2  FapA             Flagellar Assembly Protein A
     0.0033   17.4  17.1      0.057   13.4   3.0    3.6  4  DUF2205          Short coiled-coil protein
     0.0036   17.2   4.2        1.3    8.9   0.3    3.0  3  Sec34            Sec34-like family
     0.0043   16.5  16.8       0.18   11.1   4.4    2.2  2  DUF2353          Uncharacterized coiled-coil protein (DUF2353
     0.0053   15.6  18.4      0.031   13.0   1.1    4.0  5  Tektin           Tektin family
     0.0056   17.0  13.5       0.14   12.4   3.6    2.1  2  zf-C4H2          Zinc finger-containing protein
  ------ inclusion threshold ------
      0.012   14.7  10.4       0.75    8.8   0.5    3.2  3  TelA             Toxic anion resistance protein (TelA)
      0.013   15.4  17.5       0.21   11.4   4.6    2.2  2  DUF724           Protein of unknown function (DUF724)
      0.013   15.7  19.5       0.15   12.3   7.8    2.8  2  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
      0.016   15.7  15.2        1.1    9.7   1.5    3.7  3  DUF16            Protein of unknown function DUF16
      0.022   15.0   0.5       0.52   10.5   0.1    2.4  2  COG5             Golgi transport complex subunit 5
      0.029   14.7  25.9        5.4    7.5   8.7    4.4  4  Latarcin         Latarcin precursor
      0.037   13.8   2.9        1.2    8.9   0.5    2.4  3  Lectin_N         Hepatic lectin, N-terminal domain
      0.059   13.0  16.5      0.069   12.8   4.2    3.2  3  DUF2968          Protein of unknown function (DUF2968)
        0.1   12.9   0.2         13    6.1   0.0    2.8  2  DUF948           Bacterial protein of unknown function (DUF94
        0.1   12.7   8.5       0.49   10.5   2.3    2.5  2  ApoLp-III        Apolipophorin-III precursor (apoLp-III)
       0.11   12.5   0.1        6.4    6.8   0.0    2.5  2  LOH1CR12         Tumour suppressor protein
       0.15   11.8  20.7       0.76    9.6   0.8    5.7  5  Rbsn             Rabenosyn Rab binding domain
       0.18    9.7   6.0       0.17    9.8   1.2    2.1  2  Prominin         Prominin
        0.2   11.7  18.1         29    4.7   0.4    7.5  7  UCR_UQCRX_QCR9   Ubiquinol-cytochrome C reductase, UQCRX/QCR9
        0.2   10.3   4.5       0.61    8.7   2.8    2.2  2  Dor1             Dor1-like family
       0.23   11.2  18.6        2.3    8.0   5.7    3.0  3  DUF4201          Domain of unknown function (DUF4201)
       0.26   11.1  29.3          3    7.7   2.3    4.6  6  DivIC            Septum formation initiator
       0.33   11.1  28.4        3.7    7.8   1.9    4.8  4  JIP_LZII         JNK-interacting protein  leucine zipper II
       0.36   10.0  25.5        1.2    8.3   9.7    2.1  2  HAP1_N           HAP1 N-terminal conserved region
       0.39    9.9  13.1       0.56    9.4   3.6    2.1  2  TMPIT            TMPIT-like protein
       0.39    8.5  20.3      0.036   11.9   6.5    2.3  2  Nup88            Nuclear pore component
        0.5   10.6  17.6         11    6.4   0.1    7.4  7  VPS11_C          Vacuolar protein sorting protein 11 C termin
       0.52   10.7  15.2        8.9    6.7   0.8    4.6  3  DUF4061          Domain of unknown function (DUF4061)
       0.61    8.2   5.5        2.3    6.3   0.5    2.1  2  COG6             Conserved oligomeric complex COG6
       0.73    8.7  22.3        4.9    6.0   4.0    2.0  2  Spc7             Spc7 kinetochore protein
       0.76    7.9  15.9          2    6.5   5.4    2.9  3  EzrA             Septation ring formation regulator, EzrA
       0.82    9.8  14.9         14    5.8   2.3    4.0  4  COG2             COG (conserved oligomeric Golgi) complex com
       0.96    8.8   6.3        4.2    6.7   4.6    2.0  2  RNase_E_G        Ribonuclease E/G family
          1    9.3   4.9    1.2e+02    2.5   4.9    2.5  1  Cauli_AT         Aphid transmission protein
          1    9.0   8.7       0.66    9.6   5.7    1.6  2  YkyA             Putative cell-wall binding lipoprotein
        1.3    9.4  21.4    1.8e+04   -5.4  21.4    3.0  0  Uso1_p115_C      Uso1 / p115 like vesicle tethering protein, 
        1.4    9.0  18.3        4.9    7.2   6.2    2.3  2  ADIP             Afadin- and alpha -actinin-Binding
        1.4    8.5  12.9        1.4    8.5   1.9    2.4  2  PTRF_SDPR        PTRF/SDPR family
        1.4    9.2  24.7        2.5    8.4   1.1    6.0  7  HALZ             Homeobox associated leucine zipper
        1.5    8.9  23.3        4.2    7.4   9.6    2.3  2  UPF0242          Uncharacterised protein family (UPF0242) N-t
        1.6    8.0  15.4          1    8.6   3.1    2.4  2  DUF4763          Domain of unknown function (DUF4763)
        2.2    8.3   8.7         10    6.1   0.7    3.3  4  DUF4446          Protein of unknown function (DUF4446)
        2.3    6.0   9.8         37    2.0   9.8    2.0  1  V_ATPase_I       V-type ATPase 116kDa subunit family
        2.4    7.5  26.7        1.1    8.6  10.7    2.3  2  GAS              Growth-arrest specific micro-tubule binding
        3.1    7.4  15.6        2.4    7.7   3.0    2.7  2  DUF4795          Domain of unknown function (DUF4795)
        4.1    7.7  11.4         35    4.7   2.6    3.7  5  Ntox28           Bacterial toxin 28
        4.7    8.0   9.1         26    5.6   1.7    3.3  3  Occludin_ELL     Occludin homology domain
        4.8    6.5  17.3        3.2    7.1   1.0    3.1  2  DUF4618          Domain of unknown function (DUF4618)
          5    7.6  10.8         59    4.2   0.1    4.4  4  FlaC_arch        Flagella accessory protein C (FlaC)
        5.5    6.1   6.4         21    4.3   0.4    2.1  2  DUF1394          Protein of unknown function (DUF1394)
        5.5    7.5  17.6        8.4    6.9   4.3    3.4  3  UPF0449          Uncharacterised protein family UPF0449
        6.2    6.6  32.7        6.8    6.4  16.5    2.2  2  ERM              Ezrin/radixin/moesin family
        6.3    7.2  16.1        5.9    7.3   2.4    3.6  4  TSNAXIP1_N       Translin-associated factor X-interacting N-t
        7.4    6.1  11.3        2.5    7.6   1.6    2.9  2  AAA_27           AAA domain
        8.5    5.4  25.6       0.93    8.6   8.1    2.2  2  Taxilin          Myosin-like coiled-coil protein
        9.7    6.2   6.9        3.7    7.5   2.4    2.2  2  LURAP            Leucine rich adaptor protein


Domain annotation for each model (and alignments):
>> DUF3782  Protein of unknown function (DUF3782)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1       6.7   1.6e+03       8      20 ..      58      70 ..      35      84 .. 0.51
   2 !   86.3   2.6   4.7e-27   1.1e-24       1      78 []     184     262 ..     177     262 .. 0.97

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 6.7
                        DUF3782  8 eeeeetkedleel 20
                                   +++e++ e+++ l
  gi|119719897|ref|YP_920392.1| 58 RNQEKLWEEVKSL 70
                                   2233333333322 PP

  == domain 2  score: 86.3 bits;  conditional E-value: 4.7e-27
                        DUF3782   1 eelekleeeeeetkedleelekeieklertigaLGaRWGlvsEeafReglkeiLeealgv.kVekwlyyDkeGeVygyP 78 
                                    ee+ kl++e ++++e+   l ++++++er++ aLGaRWG+ sE+afRe++++++ee+lg+ +V +w+yyD++GeV+gyP
  gi|119719897|ref|YP_920392.1| 184 EEQGKLWKEVKSLREEQGILARKMDSFERRLIALGARWGIESEAAFREAMRGVVEEILGAgEVLRWVYYDEDGEVLGYP 262
                                    6788999999999999999***********************************************************9 PP

>> PDDEXK_10  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.2   0.0   1.8e-26   4.3e-24       1      74 []     263     331 ..     263     331 .. 0.99

  Alignments for each domain:
  == domain 1  score: 84.2 bits;  conditional E-value: 1.8e-26
                      PDDEXK_10   1 sevelDvvvkdgkvilvEiksslkrgDlavikrkkelYekakgvkvdrlivvtpfiddrnpervkavAerlgie 74 
                                    s+ve+D+++kd++++l+E+k s ++gD+a+++r ++lYek++g+k +rl++vtpfi+++    + ++A++lgie
  gi|119719897|ref|YP_920392.1| 263 SRVEADILIKDKVHVLIEVKPSASSGDIAKLWRLGRLYEKKTGTK-PRLVLVTPFIEEE----ALKAAKQLGIE 331
                                    79*******************************************.*************....**********7 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.5     0.036       8.5      14      51 ..      38      75 ..      30      91 .. 0.70
   2 ?    7.9   0.5     0.017       4.1      17      42 ..      90     115 ..      81     125 .. 0.81
   3 !   12.3   1.3   0.00074      0.18      20      54 ..     128     161 ..     119     175 .. 0.68
   4 ?    5.8   0.2     0.079        19      18      42 ..     161     185 ..     159     189 .. 0.87
   5 ?    6.2   0.2     0.056        13      18      42 ..     175     199 ..     171     212 .. 0.86
   6 ?    2.8   0.0      0.67   1.6e+02      20      43 ..     191     214 ..     187     219 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.036
                Snapin_Pallidin 14 kldeldeklkelrqsQeeLleqldrlnekLkeleeaqe 51
                                   k+d++ +++++lr+ Qe+L  + ++l e++k+l+e q 
  gi|119719897|ref|YP_920392.1| 38 KMDATLNEIRALREGQEQLWRNQEKLWEEVKSLREGQG 75
                                   56777777778888888888888888887777777665 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.017
                Snapin_Pallidin  17 eldeklkelrqsQeeLleqldrlnek 42 
                                    +l e++k+lr++Qe+L e+++ l+e+
  gi|119719897|ref|YP_920392.1|  90 RLWEEVKALRENQEKLWEEVRALRED 115
                                    667899**************999876 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 0.00074
                Snapin_Pallidin  20 eklkelrqsQeeLleqldrlnekLkeleeaqeaev 54 
                                    e++k+lr+ Qe+L e++++l e++k l+e+qe ++
  gi|119719897|ref|YP_920392.1| 128 EEVKALREGQEKLWEEVRKLWEEVKALRENQE-KL 161
                                    67777777777777777777777777777776.33 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.079
                Snapin_Pallidin  18 ldeklkelrqsQeeLleqldrlnek 42 
                                    l e++k+lr+ Qe+L e+++ l+e+
  gi|119719897|ref|YP_920392.1| 161 LWEEVKALREGQEKLWEEVKALREE 185
                                    56899***************99886 PP

  == domain 5  score: 6.2 bits;  conditional E-value: 0.056
                Snapin_Pallidin  18 ldeklkelrqsQeeLleqldrlnek 42 
                                    l e++k+lr++Q +L +++++l+e+
  gi|119719897|ref|YP_920392.1| 175 LWEEVKALREEQGKLWKEVKSLREE 199
                                    568899*************999886 PP

  == domain 6  score: 2.8 bits;  conditional E-value: 0.67
                Snapin_Pallidin  20 eklkelrqsQeeLleqldrlnekL 43 
                                    +++k+lr++Q  L+ ++d+  ++L
  gi|119719897|ref|YP_920392.1| 191 KEVKSLREEQGILARKMDSFERRL 214
                                    689***************987776 PP

>> KASH_CCD  Coiled-coil region of CCDC155 or KASH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   6.0    0.0024      0.56       9      82 ..      45     115 ..      36     119 .. 0.60
   2 !   20.7  17.2   1.3e-06    0.0003       6     124 ..      91     213 ..      86     220 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0024
                       KASH_CCD   9 tvadLqlnNkkLaeenskLkkavetaeetnakLteeieeLkkklkstQqalqkaklleeEleelkalvkeleEk 82 
                                     +  L+ +  +L  + +kL + v +  e   kL ee+++L++  +   ++ ++ k+l e  e l + v+ l E 
  gi|119719897|ref|YP_920392.1|  45 EIRALREGQEQLWRNQEKLWEEVKSLREGQGKLWEEVKALREDQR---RLWEEVKALRENQEKLWEEVRALRED 115
                                    455566666666666666666666666666666666666666543...44555566666666666666555554 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 1.3e-06
                       KASH_CCD   6 listvadLqlnNkkLaeenskLkkavetaeetnakLteeieeLkk...kl.kstQqalqkaklleeEleelkalvkeleE 81 
                                    l   v+ L+ n  kL ee++ L++   +  e  ++L ee+++L++   kl   + ++ ++ k+l e  e l + vk l E
  gi|119719897|ref|YP_920392.1|  91 LWEEVKALRENQEKLWEEVRALREDQGKLWEGQQRLWEEVKALREgqeKLwEEVRKLWEEVKALRENQEKLWEEVKALRE 170
                                    55678899999999999999999999999999999999999998631133234677788899999999999999999999 PP

                       KASH_CCD  82 krarlkaqnkqlekenqsLiakiesLqeenikllaekdelkkk 124
                                     +++l  + k l  e+  L ++++sL ee   l+   d  +++
  gi|119719897|ref|YP_920392.1| 171 GQEKLWEEVKALREEQGKLWKEVKSLREEQGILARKMDSFERR 213
                                    9999999999999999999999999999988777777766665 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.9     0.042        10      11      52 ..      33      74 ..      29      90 .. 0.71
   2 !   13.5   0.9   0.00035     0.084       2      53 ..      87     138 ..      86     146 .. 0.91
   3 !   12.6   3.3    0.0007      0.17       4      59 ..     145     200 ..     138     218 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.042
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           YabA 11 eeleeqleelleeleelkeelaelleenaeLeleneklrerl 52
                                   ++l e+++++l+e+++l+e  ++l  + ++L  e ++lre +
  gi|119719897|ref|YP_920392.1| 33 RDLLEKMDATLNEIRALREGQEQLWRNQEKLWEEVKSLREGQ 74
                                   567778888888888888888888888888888888888866 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00035
                                    -HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHX CS
                           YabA   2 dkkelfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerle 53 
                                    d++ l +++++l e+ e+l ee+++l+e+  +l e  ++L  e + lre +e
  gi|119719897|ref|YP_920392.1|  87 DQRRLWEEVKALRENQEKLWEEVRALREDQGKLWEGQQRLWEEVKALREGQE 138
                                    78899*******************************************9874 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 0.0007
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXX CS
                           YabA   4 kelfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekke 59 
                                    ++l +++++l e+ e+l ee+++l+e  ++l ee ++L+ e+ kl +++++ ++++
  gi|119719897|ref|YP_920392.1| 145 RKLWEEVKALRENQEKLWEEVKALREGQEKLWEEVKALREEQGKLWKEVKSLREEQ 200
                                    57888888999999999999999999999999999999988888888875544443 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   8.1    0.0012      0.28      18      91 ..      38     111 ..      32     121 .. 0.86
   2 !   18.0  13.1   9.6e-06    0.0023       5      95 ..     123     213 ..     120     220 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0012
                 CENP-F_leu_zip  18 kadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelqk 91 
                                    k d   + + +L    e++ +nqek+  e+ + ++   +l ee++ l+e  r+l  +++alr+++e+L +e++ 
  gi|119719897|ref|YP_920392.1|  38 KMDATLNEIRALREGQEQLWRNQEKLWEEVKSLREGQGKLWEEVKALREDQRRLWEEVKALRENQEKLWEEVRA 111
                                    556667889999999999999**********9999999******************************887654 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 9.6e-06
                 CENP-F_leu_zip   5 klhvlekLKeserkadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekee 84 
                                    ++++ e+ K+ ++ +++L + v +L  e++ + enqek+  e+   ++  e+l ee++ l+ee  +l  ++++lr+e+  
  gi|119719897|ref|YP_920392.1| 123 QQRLWEEVKALREGQEKLWEEVRKLWEEVKALRENQEKLWEEVKALREGQEKLWEEVKALREEQGKLWKEVKSLREEQGI 202
                                    788999************************************************************************** PP

                 CENP-F_leu_zip  85 Lekelqkkqer 95 
                                    L++++    +r
  gi|119719897|ref|YP_920392.1| 203 LARKMDSFERR 213
                                    *9998876665 PP

>> Mod_r  Modifier of rudimentary (Mod(r)) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   4.8   9.4e-05     0.022       9      90 ..      27     108 ..      24     116 .. 0.87
   2 !   13.4   7.9   0.00026     0.063      26      90 ..     128     192 ..     106     214 .. 0.57

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 9.4e-05
                          Mod_r   9 qelledeeklealvktlpevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqeldell 88 
                                      ll   ++le++  tl+e+++l+e +e+l   +e+l e+  sl++   +l +e+++ +e  ++l +e++++ +++++l 
  gi|119719897|ref|YP_920392.1|  27 AGLLGFRDLLEKMDATLNEIRALREGQEQLWRNQEKLWEEVKSLREGQGKLWEEVKALREDQRRLWEEVKALRENQEKLW 106
                                    5677778999999999******************************9999999999999999999999999999998887 PP

                          Mod_r  89 qk 90 
                                    ++
  gi|119719897|ref|YP_920392.1| 107 EE 108
                                    54 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00026
                          Mod_r  26 pevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqeldellqk 90 
                                    +evk+l+e +e+l +e ++l e+  +l++  e+l +e+++ +e  ++l +e++++ +e+ +l ++
  gi|119719897|ref|YP_920392.1| 128 EEVKALREGQEKLWEEVRKLWEEVKALRENQEKLWEEVKALREGQEKLWEEVKALREEQGKLWKE 192
                                    66666666666666666666666666666666666666666665555555555555555554433 PP

>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   7.8    0.0024      0.56      12      71 ..      44     103 ..      33     105 .. 0.89
   2 !    9.4   1.9    0.0042         1      16      55 ..      76     115 ..      75     123 .. 0.86
   3 ?    7.2   5.2     0.021         5      12      71 ..      93     152 ..      89     155 .. 0.90
   4 !   10.5   8.3    0.0019      0.46      12      68 ..     128     184 ..     124     185 .. 0.93
   5 !   12.1   7.9    0.0006      0.14      15      70 ..     159     214 ..     149     217 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0024
                     TMF_DNA_bd  12 eqIaqLmeEGekLskkelklnntikkLrkknkelekeikelkkkleklekeleeleerlk 71 
                                     +I +L+e  e+L  ++ kl + +k+Lr+   +l +e+k l +  ++l +e++ l+e ++
  gi|119719897|ref|YP_920392.1|  44 NEIRALREGQEQLWRNQEKLWEEVKSLREGQGKLWEEVKALREDQRRLWEEVKALRENQE 103
                                    68******************************************9999999999988765 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0042
                     TMF_DNA_bd  16 qLmeEGekLskkelklnntikkLrkknkelekeikelkkk 55 
                                    +L eE ++L+  +++l + +k Lr+  ++l +e++ l + 
  gi|119719897|ref|YP_920392.1|  76 KLWEEVKALREDQRRLWEEVKALRENQEKLWEEVRALRED 115
                                    5889999999999999999999999999999999998765 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.021
                     TMF_DNA_bd  12 eqIaqLmeEGekLskkelklnntikkLrkknkelekeikelkkkleklekeleeleerlk 71 
                                    e++++L+e+ ekL  + ++l++ + kL +  + l +e+k l +  ekl +e+ +l e+ k
  gi|119719897|ref|YP_920392.1|  93 EEVKALRENQEKLWEEVRALREDQGKLWEGQQRLWEEVKALREGQEKLWEEVRKLWEEVK 152
                                    78999***********************9999999*****99999999999988877766 PP

  == domain 4  score: 10.5 bits;  conditional E-value: 0.0019
                     TMF_DNA_bd  12 eqIaqLmeEGekLskkelklnntikkLrkknkelekeikelkkkleklekeleelee 68 
                                    e++++L+e  ekL  + +kl + +k Lr+  ++l +e+k l +  ekl +e++ l+e
  gi|119719897|ref|YP_920392.1| 128 EEVKALREGQEKLWEEVRKLWEEVKALRENQEKLWEEVKALREGQEKLWEEVKALRE 184
                                    78999**999********************************999999999999886 PP

  == domain 5  score: 12.1 bits;  conditional E-value: 0.0006
                     TMF_DNA_bd  15 aqLmeEGekLskkelklnntikkLrkknkelekeikelkkkleklekeleeleerl 70 
                                    ++L eE ++L+  + kl + +k Lr++  +l ke+k+l ++   l +++++ e+rl
  gi|119719897|ref|YP_920392.1| 159 EKLWEEVKALREGQEKLWEEVKALREEQGKLWKEVKSLREEQGILARKMDSFERRL 214
                                    57888888888888888888888888888888888888888888888888888887 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0       3.9   9.3e+02       1      32 [.      38      69 ..      38      73 .. 0.71
   2 ?    5.2   0.0      0.12        28       4      36 ..      62      94 ..      59     102 .. 0.77
   3 ?    3.6   0.0      0.38        91       6      29 ..      92     115 ..      88     125 .. 0.84
   4 ?    3.2   0.0      0.48   1.2e+02       7      35 ..     128     156 ..     101     160 .. 0.73
   5 ?    5.9   0.0     0.073        17       2      28 ..     144     170 ..     136     180 .. 0.62
   6 ?    2.6   0.0      0.74   1.8e+02       4      28 ..     174     198 ..     171     204 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 3.9
                            LPP  1 kldeLssqVsqLkskvdqlssdvnsakaaaqa 32
                                   k+d   +++ +L + ++ql  +++++ +++++
  gi|119719897|ref|YP_920392.1| 38 KMDATLNEIRALREGQEQLWRNQEKLWEEVKS 69
                                   56666688888888888888887777666655 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.12
                            LPP  4 eLssqVsqLkskvdqlssdvnsakaaaqaakeE 36
                                   +L ++V++L + + +l ++v++++++     eE
  gi|119719897|ref|YP_920392.1| 62 KLWEEVKSLREGQGKLWEEVKALREDQRRLWEE 94
                                   677889999999999999999999988777666 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.38
                            LPP   6 ssqVsqLkskvdqlssdvnsakaa 29 
                                     ++V++L +++++l ++v +++++
  gi|119719897|ref|YP_920392.1|  92 WEEVKALRENQEKLWEEVRALRED 115
                                    578999999999999999999988 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.48
                            LPP   7 sqVsqLkskvdqlssdvnsakaaaqaake 35 
                                    ++V++L + +++l ++v ++ ++++a +e
  gi|119719897|ref|YP_920392.1| 128 EEVKALREGQEKLWEEVRKLWEEVKALRE 156
                                    56667777777777777666666666554 PP

  == domain 5  score: 5.9 bits;  conditional E-value: 0.073
                            LPP   2 ldeLssqVsqLkskvdqlssdvnsaka 28 
                                    + +L ++V++L +++++l ++v+++++
  gi|119719897|ref|YP_920392.1| 144 VRKLWEEVKALRENQEKLWEEVKALRE 170
                                    345555666666666666666666655 PP

  == domain 6  score: 2.6 bits;  conditional E-value: 0.74
                            LPP   4 eLssqVsqLkskvdqlssdvnsaka 28 
                                    +L ++V++L +++ +l ++v+s+++
  gi|119719897|ref|YP_920392.1| 174 KLWEEVKALREEQGKLWKEVKSLRE 198
                                    6778999999999999999999876 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0  13.6     0.016       3.9       9      65 ..      35      98 ..      31     112 .. 0.73
   2 ?    3.9  13.5       0.3        71      12      65 ..      94     147 ..      76     147 .. 0.56
   3 !   11.6   7.7    0.0012      0.29      21      65 ..     124     168 ..     118     168 .. 0.91
   4 !    9.0   6.0    0.0078       1.9      16      64 ..     161     209 ..     159     214 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.016
                           ZapB  9 LEskiqkaidtitlLqmeieeLkeeneelkeenrele.......eeneqlkeereawqerlkkL 65
                                   L +k ++++++i++L++  e+L + +e+l ee + l+       ee+++l+e++  + e +k+L
  gi|119719897|ref|YP_920392.1| 35 LLEKMDATLNEIRALREGQEQLWRNQEKLWEEVKSLRegqgklwEEVKALREDQRRLWEEVKAL 98
                                   5679999999999999999999999999999999999999999955555555555544444433 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.3
                           ZapB  12 kiqkaidtitlLqmeieeLkeeneelkeenreleeeneqlkeereawqerlkkL 65 
                                     ++++ ++ ++L +e+++L+e++ +l e +++l ee+++l+e +e++ e ++kL
  gi|119719897|ref|YP_920392.1|  94 EVKALRENQEKLWEEVRALREDQGKLWEGQQRLWEEVKALREGQEKLWEEVRKL 147
                                    333444444555555555555555555555555588888888888877777765 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.0012
                           ZapB  21 tlLqmeieeLkeeneelkeenreleeeneqlkeereawqerlkkL 65 
                                    ++L +e+++L+e +e+l ee r+l ee+++l+e++e++ e +k+L
  gi|119719897|ref|YP_920392.1| 124 QRLWEEVKALREGQEKLWEEVRKLWEEVKALRENQEKLWEEVKAL 168
                                    67999*******************************998888776 PP

  == domain 4  score: 9.0 bits;  conditional E-value: 0.0078
                           ZapB  16 aidtitlLqmeieeLkeeneelkeenreleeeneqlkeereawqerlkk 64 
                                    + +++++L++  e+L ee+++l ee+ +l +e++ l+ee+  + +++++
  gi|119719897|ref|YP_920392.1| 161 LWEEVKALREGQEKLWEEVKALREEQGKLWKEVKSLREEQGILARKMDS 209
                                    557788888888888888888888888888*********9888888775 PP

>> DUF4709  Domain of unknown function (DUF4709)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.54   1.3e+02      31      59 ..      55      83 ..      30      91 .. 0.71
   2 ?    4.3   0.1       0.2        47      28      59 ..      66      97 ..      53     102 .. 0.74
   3 !   11.5   0.8    0.0011      0.27      28      91 ..      94     159 ..      91     164 .. 0.88
   4 ?    5.0   0.6      0.12        28      28      54 ..     150     176 ..     129     184 .. 0.54
   5 ?    5.0   0.1      0.12        28      28      65 ..     178     214 ..     175     217 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.54
                        DUF4709 31 eltevtqkLvkevkslkrdfeflkqllqa 59
                                   +l ++ +kL +evksl++ ++ l++ ++a
  gi|119719897|ref|YP_920392.1| 55 QLWRNQEKLWEEVKSLREGQGKLWEEVKA 83
                                   56777778888888888877777776665 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.2
                        DUF4709 28 elkeltevtqkLvkevkslkrdfeflkqllqa 59
                                   e+k+l e   kL +evk+l++d++ l++ ++a
  gi|119719897|ref|YP_920392.1| 66 EVKSLREGQGKLWEEVKALREDQRRLWEEVKA 97
                                   57777777888888888888888887776665 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.0011
                        DUF4709  28 elkeltevtqkLvkevkslkrdfeflkqllqakyee..klkeealelytrlndklkeleklykekv 91 
                                    e+k l e+ +kL +ev++l++d++ l++  q  +ee   l+e   +l++++++  +e++ l ++++
  gi|119719897|ref|YP_920392.1|  94 EVKALRENQEKLWEEVRALREDQGKLWEGQQRLWEEvkALREGQEKLWEEVRKLWEEVKALRENQE 159
                                    699*******************************9643799********99998888887776655 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.12
                        DUF4709  28 elkeltevtqkLvkevkslkrdfeflk 54 
                                    e+k l e+ +kL +evk+l++ +e l+
  gi|119719897|ref|YP_920392.1| 150 EVKALRENQEKLWEEVKALREGQEKLW 176
                                    344444445555555555544444444 PP

  == domain 5  score: 5.0 bits;  conditional E-value: 0.12
                        DUF4709  28 elkeltevtqkLvkevkslkrdfeflkqllqakyeekl 65 
                                    e+k l e+  kL kevksl++++++l + ++ ++e++l
  gi|119719897|ref|YP_920392.1| 178 EVKALREEQGKLWKEVKSLREEQGILARKMD-SFERRL 214
                                    6899********************9999987.477766 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.6    0.0038       0.9      41     124 .]      34     116 ..      30     116 .. 0.77
   2 !   13.0   1.6   0.00034     0.081      55     124 .]     131     200 ..     123     213 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0038
                        DUF1664  41 davesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleri 120
                                    d +e++   l+++  +l++ +++L ++ +++ +++++  e + ++ eev+++red +++ e+v++++e  e+l ++++ +
  gi|119719897|ref|YP_920392.1|  34 DLLEKMDATLNEI-RALREGQEQLWRNQEKLWEEVKSLREGQGKLWEEVKALREDQRRLWEEVKALRENQEKLWEEVRAL 112
                                    5555666666655.467888888888889999999999999999999999999999999999999999888888888877 PP

                        DUF1664 121 eekQ 124
                                     e Q
  gi|119719897|ref|YP_920392.1| 113 REDQ 116
                                    7666 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00034
                        DUF1664  55 eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerieekQ 124
                                    ++l++ +++L +++ ++ +++++  e ++++ eev+++re+ +++ e+v++++e   +l ++++++ e+Q
  gi|119719897|ref|YP_920392.1| 131 KALREGQEKLWEEVRKLWEEVKALRENQEKLWEEVKALREGQEKLWEEVKALREEQGKLWKEVKSLREEQ 200
                                    5677888899999999999999999999999999999999999999999999999999988888888777 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5  15.3    0.0056       1.3      45     122 ..      35     112 ..       8     113 .. 0.81
   2 ?    6.8  22.9     0.037       8.9      10     115 ..      35     140 ..      35     145 .. 0.79
   3 ?    7.7  16.9      0.02       4.9      45     108 ..     105     168 ..      98     173 .. 0.88
   4 !   13.0  14.6   0.00048      0.11      49     125 ..     137     213 ..     133     220 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0056
                         APG6_N  45 qdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynelqlelleleeeldsl 122
                                      e+++++ +e+++l++ +e+l ++ ++l +e ++l++   +l+ee +al e+++r w+e ++l+ ++++l ee ++l
  gi|119719897|ref|YP_920392.1|  35 LLEKMDATLNEIRALREGQEQLWRNQEKLWEEVKSLREGQGKLWEEVKALREDQRRLWEEVKALRENQEKLWEEVRAL 112
                                    556888999999999999999999999999999999999999999999999999999999999999999998887765 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.037
                         APG6_N  10 LleeldkqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaalee 89 
                                    Lle++d  l++ ++ r+  e+  ++ +k  +e ++ +e   +l ee+++l++++++l ee k+l +++e+l +e++al+e
  gi|119719897|ref|YP_920392.1|  35 LLEKMDATLNEIRALREGQEQLWRNQEKLWEEVKSLREGQGKLWEEVKALREDQRRLWEEVKALRENQEKLWEEVRALRE 114
                                    5666666666666666666666666665544444478888999999********************************** PP

                         APG6_N  90 elealeeeeerfwreynelqlellel 115
                                       +l e ++r w+e ++l+  +++l
  gi|119719897|ref|YP_920392.1| 115 DQGKLWEGQQRLWEEVKALREGQEKL 140
                                    **************999987666655 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.02
                         APG6_N  45 qdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynel 108
                                      ee+++l+e+  kl + +++l ee k+l + +e+l +e+++l+ee +al e++e+ w+e ++l
  gi|119719897|ref|YP_920392.1| 105 LWEEVRALREDQGKLWEGQQRLWEEVKALREGQEKLWEEVRKLWEEVKALRENQEKLWEEVKAL 168
                                    34789999999999*********************************************99876 PP

  == domain 4  score: 13.0 bits;  conditional E-value: 0.00048
                         APG6_N  49 leeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynelqlelleleeeldsleaq 125
                                     e+l ee++kl +e ++l e+ ++l +e ++l++  ++l+ee +al ee+ + w+e ++l+ e+  l  ++ds e +
  gi|119719897|ref|YP_920392.1| 137 QEKLWEEVRKLWEEVKALRENQEKLWEEVKALREGQEKLWEEVKALREEQGKLWKEVKSLREEQGILARKMDSFERR 213
                                    57778888888888888888888888888888888888888888888888888888888888888888888887765 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.6     0.035       8.5      27      61 ..      52      86 ..      47      91 .. 0.73
   2 ?    5.4   2.2     0.083        20      26      59 ..      86     119 ..      85     135 .. 0.79
   3 !    9.0   2.7    0.0063       1.5      26      57 ..     135     166 ..     120     170 .. 0.57
   4 !    9.5   4.3    0.0043         1      32      63 ..     162     193 ..     155     208 .. 0.54

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.035
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         bZIP_1 27 eieeLerrvkaLekeNksLkseleelkkevekLks 61
                                    +e+L r  ++L +e ksL++  ++l +ev+ L++
  gi|119719897|ref|YP_920392.1| 52 GQEQLWRNQEKLWEEVKSLREGQGKLWEEVKALRE 86
                                   57777777777777777777777777777777765 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.083
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         bZIP_1  26 aeieeLerrvkaLekeNksLkseleelkkevekL 59 
                                    + + +L ++vkaL +  ++L +e+  l+++  kL
  gi|119719897|ref|YP_920392.1|  86 EDQRRLWEEVKALRENQEKLWEEVRALREDQGKL 119
                                    5677888888888888888888888888876555 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0063
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         bZIP_1  26 aeieeLerrvkaLekeNksLkseleelkkeve 57 
                                    + +e+L ++v +L +e k+L++  e+l +ev+
  gi|119719897|ref|YP_920392.1| 135 EGQEKLWEEVRKLWEEVKALRENQEKLWEEVK 166
                                    34555555555555555555555555555555 PP

  == domain 4  score: 9.5 bits;  conditional E-value: 0.0043
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         bZIP_1  32 errvkaLekeNksLkseleelkkevekLkskv 63 
                                     ++vkaL +  ++L +e++ l++e  kL ++v
  gi|119719897|ref|YP_920392.1| 162 WEEVKALREGQEKLWEEVKALREEQGKLWKEV 193
                                    55555555555555555555554444444333 PP

>> JAKMIP_CC3  JAKMIP CC3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0  10.2    0.0012       0.3     126     183 ..      34      93 ..       8     104 .. 0.78
   2 ?    3.8   3.9       0.2        48     153     183 ..      90     121 ..      87     135 .. 0.74
   3 !    8.4  19.4    0.0079       1.9      77     185 ..     103     206 ..      98     216 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0012
                     JAKMIP_CC3 126 dLeeaLaqkGqdskwveekQalikrnqe.LvekikkleeeeskLkqeiqdlr.dqnelLE 183
                                    dL e +    ++ + + e Q  + rnqe L e +k+l+e ++kL +e+++lr dq++l E
  gi|119719897|ref|YP_920392.1|  34 DLLEKMDATLNEIRALREGQEQLWRNQEkLWEEVKSLREGQGKLWEEVKALReDQRRLWE 93 
                                    55566666678999999999999999999**********************944777877 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.2
                     JAKMIP_CC3 153 eLvekikkleeeeskLkqeiqdlrd.qnelLE 183
                                     L e +k l+e++ kL +e+++lr+ q +l E
  gi|119719897|ref|YP_920392.1|  90 RLWEEVKALRENQEKLWEEVRALREdQGKLWE 121
                                    48899999999999999999999962555655 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0079
                     JAKMIP_CC3  77 rqLlaeyqalqrayalLreklggeldaerelka.reqleselrktkskikdLeeaLaqkGqdskwveekQalikrnqeLv 155
                                    ++L +e +al+     L e      + ++ l++ +e+l +e+rk   ++k L e  ++  +++k + e Q      ++L 
  gi|119719897|ref|YP_920392.1| 103 EKLWEEVRALREDQGKLWEGQQRLWEEVKALREgQEKLWEEVRKLWEEVKALRENQEKLWEEVKALREGQ------EKLW 176
                                    68999999***999999999999999999999769***************99998777777777777765......66** PP

                     JAKMIP_CC3 156 ekikkleeeeskLkqeiqdlrdqnelLEfr 185
                                    e +k l+ee++kL +e++ lr+ + +L  +
  gi|119719897|ref|YP_920392.1| 177 EEVKALREEQGKLWKEVKSLREEQGILARK 206
                                    **********************99888655 PP

>> ATP-synt_10  ATP10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.1   0.00051      0.12      38      95 ..      76     133 ..      44     136 .. 0.78
   2 ?    5.3   0.4     0.041       9.8      34      87 ..     142     195 ..     134     202 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00051
                    ATP-synt_10  38 slgnslkdlfdeektekrrkeLeeelkksyfydlkefrktnGKlFlspksyfkadkal 95 
                                    +l++++k l +++++  ++ +  +e ++  + ++  +r+ +GKl+ + ++++ + kal
  gi|119719897|ref|YP_920392.1|  76 KLWEEVKALREDQRRLWEEVKALRENQEKLWEEVRALREDQGKLWEGQQRLWEEVKAL 133
                                    555666666666666655555566778899*************************998 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.041
                    ATP-synt_10  34 skkyslgnslkdlfdeektekrrkeLeeelkksyfydlkefrktnGKlFlspks 87 
                                    ++ ++l++++k l +++ +  ++ +  +e ++  + ++k +r+++GKl+   ks
  gi|119719897|ref|YP_920392.1| 142 EEVRKLWEEVKALRENQEKLWEEVKALREGQEKLWEEVKALREEQGKLWKEVKS 195
                                    5667777888888777555555555556778899**************986655 PP

>> SKA2  Spindle and kinetochore-associated protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.83     2e+02      42      76 ..      34      68 ..      15      78 .. 0.80
   2 !    8.7   1.8     0.006       1.4      22      77 ..      60     111 ..      29     121 .. 0.66
   3 !   11.9   1.3   0.00059      0.14      22      77 ..     123     181 ..     122     194 .. 0.71
   4 !    9.9   1.9    0.0026      0.61      23      76 ..     138     194 ..     137     216 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.83
                           SKA2 42 kLlerlkkvkeelqaLkeqceellaekkelidkir 76
                                    Lle++ +  +e+ aL+e  e+l  ++++l ++++
  gi|119719897|ref|YP_920392.1| 34 DLLEKMDATLNEIRALREGQEQLWRNQEKLWEEVK 68
                                   68888888888888888888888888888877665 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.006
                           SKA2  22 qhrLekefqqsypdnaeNpvkLlerlkkvkeelqaLkeqceellaekkelidkirt 77 
                                    q++L +e++   + ++    kL e++k+++e+   L e++++l +++++l +++r+
  gi|119719897|ref|YP_920392.1|  60 QEKLWEEVKSLREGQG----KLWEEVKALREDQRRLWEEVKALRENQEKLWEEVRA 111
                                    4444444444444443....788888888888888888888888888888877776 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 0.00059
                           SKA2  22 qhrLekefqqsypdna...eNpvkLlerlkkvkeelqaLkeqceellaekkelidkirt 77 
                                    q+rL +e+++  + ++   e+++kL e++k+++e  ++L e++++l + +++l +++++
  gi|119719897|ref|YP_920392.1| 123 QQRLWEEVKALREGQEklwEEVRKLWEEVKALRENQEKLWEEVKALREGQEKLWEEVKA 181
                                    56777777766655556678888888888888888888888888888888887777665 PP

  == domain 4  score: 9.9 bits;  conditional E-value: 0.0026
                           SKA2  23 hrLekefqqsypdna...eNpvkLlerlkkvkeelqaLkeqceellaekkelidkir 76 
                                    ++L +e+++  ++ +   eN  kL e++k+++e  ++L e++++l +e+ +l ++++
  gi|119719897|ref|YP_920392.1| 138 EKLWEEVRKLWEEVKalrENQEKLWEEVKALREGQEKLWEEVKALREEQGKLWKEVK 194
                                    667777777777766777788888888888888888888888888888877766654 PP

>> PI3K_P85_iSH2  Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   2.2     0.021         5      79     132 ..      49     102 ..      32     108 .. 0.83
   2 !   12.9  10.7   0.00026     0.061      57     148 ..     106     216 ..      93     221 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.021
                  PI3K_P85_iSH2  79 qehEieklqenleqlksrlkelhsskekLeedlkqqkeeereleReinalkpel 132
                                     ++ +e+l  n e+l + +k+l++ + kL e++k+  e++r l  e+ al+ + 
  gi|119719897|ref|YP_920392.1|  49 LREGQEQLWRNQEKLWEEVKSLREGQGKLWEEVKALREDQRRLWEEVKALRENQ 102
                                    4677899999******************************99999999988765 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00026
                  PI3K_P85_iSH2  57 FneaikmFeeqiklqekfskeaq...................ehEieklqenleqlksrlkelhsskekLeedlkqqkee 117
                                    ++e+  + e+q kl e  ++  +                    +E++ l en e+l + +k l++ +ekL e++k+  ee
  gi|119719897|ref|YP_920392.1| 106 WEEVRALREDQGKLWEGQQRLWEevkalregqeklweevrklWEEVKALRENQEKLWEEVKALREGQEKLWEEVKALREE 185
                                    45555555555555555444442333444444555555555589************************************ PP

                  PI3K_P85_iSH2 118 ereleReinalkpellqLqkrkdkylewLkt 148
                                    + +l +e+ +l+ e   L+++ d + ++L  
  gi|119719897|ref|YP_920392.1| 186 QGKLWKEVKSLREEQGILARKMDSFERRLIA 216
                                    ************************9999865 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   2.1    0.0011      0.27     334     428 ..      34     131 ..      17     133 .. 0.68
   2 !   12.2   3.1    0.0002     0.049     334     419 ..     139     204 ..     115     248 .. 0.56

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0011
                           FapA 334 elkeklkeleeeleeleeeleklkkk.ikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeelesk. 411
                                    +l ek+++  +e+++l+e +e+l ++  k+ ++ k   + + +  e++k l+e++ +l ee+++l+e++++l ee++   
  gi|119719897|ref|YP_920392.1|  34 DLLEKMDATLNEIRALREGQEQLWRNqEKLWEEVKSLREGQGKLWEEVKALREDQRRLWEEVKALRENQEKLWEEVRALr 113
                                    55556666666666666666666666422222333344445677899999999999999999999999999999999885 PP

                           FapA 412 keea.kikvnkeiypgvk 428
                                    ++++  ++ +++++ +vk
  gi|119719897|ref|YP_920392.1| 114 EDQGkLWEGQQRLWEEVK 131
                                    334446777777777765 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.0002
                           FapA 334 elkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeeleskke 413
                                    +l e++++l ee+++l+e++                    ++  e++k l+e +ekl ee+++l+ee+ +l +e++s +e
  gi|119719897|ref|YP_920392.1| 139 KLWEEVRKLWEEVKALRENQ--------------------EKLWEEVKALREGQEKLWEEVKALREEQGKLWKEVKSLRE 198
                                    22233344444444444444....................4555556666666666666666666666666665555533 PP

                           FapA 414 eakikv 419
                                    e+ i +
  gi|119719897|ref|YP_920392.1| 199 EQGILA 204
                                    333333 PP

>> DUF2205  Short coiled-coil protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   1.9     0.022       5.2      17      58 ..      59     100 ..      36     107 .. 0.82
   2 !    9.9   1.1    0.0029       0.7      13      53 ..      83     123 ..      78     128 .. 0.85
   3 ?    2.9   2.7      0.46   1.1e+02      16      52 ..     121     157 ..     107     161 .. 0.78
   4 !   13.4   3.0   0.00024     0.057      12      56 ..     152     196 ..     143     203 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.022
                        DUF2205  17 arerLqqqakeLqssLqaLaervdeVkeehdKLesenrfLqq 58 
                                    ++e+L + +k+L ++  +L e v + +e++ +L  e + L +
  gi|119719897|ref|YP_920392.1|  59 NQEKLWEEVKSLREGQGKLWEEVKALREDQRRLWEEVKALRE 100
                                    578888899999999999999999999999999888887765 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0029
                        DUF2205  13 lerearerLqqqakeLqssLqaLaervdeVkeehdKLesen 53 
                                    + re++ rL + +k+L +  ++L e v + +e++ KL    
  gi|119719897|ref|YP_920392.1|  83 ALREDQRRLWEEVKALRENQEKLWEEVRALREDQGKLWEGQ 123
                                    4579999*****************************96655 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.46
                        DUF2205  16 earerLqqqakeLqssLqaLaervdeVkeehdKLese 52 
                                    e ++rL + +k+L ++ ++L e v +  ee + L+ +
  gi|119719897|ref|YP_920392.1| 121 EGQQRLWEEVKALREGQEKLWEEVRKLWEEVKALREN 157
                                    6678888889999988888888888888888777765 PP

  == domain 4  score: 13.4 bits;  conditional E-value: 0.00024
                        DUF2205  12 klerearerLqqqakeLqssLqaLaervdeVkeehdKLesenrfL 56 
                                    k+ re++e+L + +k+L ++ ++L e v + +ee+ KL  e + L
  gi|119719897|ref|YP_920392.1| 152 KALRENQEKLWEEVKALREGQEKLWEEVKALREEQGKLWKEVKSL 196
                                    45689*********************************9998877 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.1     0.066        16      13      65 ..      33      85 ..      29      89 .. 0.79
   2 ?    5.2   0.1     0.075        18      17      59 ..      79     121 ..      64     143 .. 0.48
   3 !    8.9   0.3    0.0054       1.3      11      63 ..     143     195 ..     128     234 .. 0.55

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.066
                          Sec34 13 delleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeie 65
                                   ++lle++d++l++++ l+e  ++   + ++l e+ ++l e q +l e +++++
  gi|119719897|ref|YP_920392.1| 33 RDLLEKMDATLNEIRALREGQEQLWRNQEKLWEEVKSLREGQGKLWEEVKALR 85
                                   57888888999999999988888888888888888888888888877666655 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.075
                          Sec34  17 eqtdealeqLeeleekfksvsektsslheaceqlleeqkrlee 59 
                                    e+++++ e+ + l e++k+  e+ ++l e+   l e+q +l e
  gi|119719897|ref|YP_920392.1|  79 EEVKALREDQRRLWEEVKALRENQEKLWEEVRALREDQGKLWE 121
                                    4444444444444444444444444444444444444433333 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0054
                          Sec34  11 ecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaee 63 
                                    e+++l e+++++ e+ e+l e++k+  e  ++l e+ + l eeq +l + +++
  gi|119719897|ref|YP_920392.1| 143 EVRKLWEEVKALRENQEKLWEEVKALREGQEKLWEEVKALREEQGKLWKEVKS 195
                                    34444444444444444444444444444444444444444444444444444 PP

>> DUF2353  Uncharacterized coiled-coil protein (DUF2353)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   7.8    0.0018      0.43      47     152 ..      44     147 ..      31     152 .. 0.48
   2 !   11.1   4.4   0.00076      0.18      37     105 ..     132     200 ..     122     220 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0018
                        DUF2353  47 eeekakaadlkeekekekklsqlleesreenkalkleveeLrqklkeaqgDiklLReqlarqrlglkdedlletrhssae 126
                                    +e  a ++ +++  ++++kl + ++  re + +l +ev++Lr+  + + + +k+LRe++++     +++ l e++ +  e
  gi|119719897|ref|YP_920392.1|  44 NEIRALREGQEQLWRNQEKLWEEVKSLREGQGKLWEEVKALREDQRRLWEEVKALRENQEKL--WEEVRALREDQGKLWE 121
                                    22233333333334556666666666666666666666666666666666666666443332..2233333333333455 PP

                        DUF2353 127 ereelvkqlEklkekiqqlerdlkav 152
                                     +++l +++  l+e +++l  +++++
  gi|119719897|ref|YP_920392.1| 122 GQQRLWEEVKALREGQEKLWEEVRKL 147
                                    55555555555555555555555554 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00076
                        DUF2353  37 erlsalkkqleeekakaadlkeekekekklsqlleesreenkalkleveeLrqklkeaqgDiklLReql 105
                                       ++++k  ee  + +++ k  +e+++kl + ++  re +++l +ev++Lr+    + + +k LRe++
  gi|119719897|ref|YP_920392.1| 132 ALREGQEKLWEEVRKLWEEVKALRENQEKLWEEVKALREGQEKLWEEVKALREEQGKLWKEVKSLREEQ 200
                                    344445555566666666666668888888888888888888888888888888888888888888432 PP

>> Tektin  Tektin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.6     0.079        19     122     159 ..      43      80 ..      38      85 .. 0.84
   2 !    9.4   0.7    0.0016      0.39     319     362 ..      88     131 ..      83     136 .. 0.92
   3 !   13.0   1.1   0.00013     0.031     319     362 ..     123     166 ..     120     170 .. 0.89
   4 !    9.1   2.1     0.002      0.47     319     362 ..     137     180 ..     133     185 .. 0.91
   5 ?    3.7   0.3     0.089        21     319     359 ..     172     212 ..     167     217 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.079
                         Tektin 122 lkEveliegvqellkrtleqaeeqlrllraakhkLekd 159
                                    l+E+  +++ qe+l r  e+++e++++lr+ + kL ++
  gi|119719897|ref|YP_920392.1|  43 LNEIRALREGQEQLWRNQEKLWEEVKSLREGQGKLWEE 80 
                                    57999999999999999999999999999988877655 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0016
                         Tektin 319 qyrLveEvkeleetieaLkeklaeaeaslkaLertrleleedia 362
                                    q rL eEvk l+e+ e+L e++++ ++   +L + +++l e+++
  gi|119719897|ref|YP_920392.1|  88 QRRLWEEVKALRENQEKLWEEVRALREDQGKLWEGQQRLWEEVK 131
                                    89************************************999987 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 0.00013
                         Tektin 319 qyrLveEvkeleetieaLkeklaeaeaslkaLertrleleedia 362
                                    q+rL eEvk l+e  e+L e++++  +++kaL++++ +l e+++
  gi|119719897|ref|YP_920392.1| 123 QQRLWEEVKALREGQEKLWEEVRKLWEEVKALRENQEKLWEEVK 166
                                    89999999999999999999999999999999999999999886 PP

  == domain 4  score: 9.1 bits;  conditional E-value: 0.002
                         Tektin 319 qyrLveEvkeleetieaLkeklaeaeaslkaLertrleleedia 362
                                    q++L eEv++l e+++aL+e+ ++  +++kaL++ + +l e+++
  gi|119719897|ref|YP_920392.1| 137 QEKLWEEVRKLWEEVKALRENQEKLWEEVKALREGQEKLWEEVK 180
                                    899***********************************999987 PP

  == domain 5  score: 3.7 bits;  conditional E-value: 0.089
                         Tektin 319 qyrLveEvkeleetieaLkeklaeaeaslkaLertrlelee 359
                                    q++L eEvk l+e+  +L ++++  +++   L r++ + e+
  gi|119719897|ref|YP_920392.1| 172 QEKLWEEVKALREEQGKLWKEVKSLREEQGILARKMDSFER 212
                                    77888888888888888888888888777777776666554 PP

>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   2.9     0.005       1.2      23     104 ..      36     117 ..      29     130 .. 0.83
   2 !   12.4   3.6    0.0006      0.14      33     106 ..     130     203 ..     118     220 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.005
                        zf-C4H2  23 vealekeekcleeykkelelLeqEkmaHveeLrlIhaDinalEsvikeaeeekekslekakklyeeykklkeevnelrse 102
                                    +e ++++ + ++  ++  e+L + +++  ee++ +++   +l + +k  +e++++ +e++k l e+ +kl eev  lr++
  gi|119719897|ref|YP_920392.1|  36 LEKMDATLNEIRALREGQEQLWRNQEKLWEEVKSLREGQGKLWEEVKALREDQRRLWEEVKALRENQEKLWEEVRALRED 115
                                    56777777888888888889988888889999999999999999999999999999999999999999999999999988 PP

                        zf-C4H2 103 lg 104
                                     g
  gi|119719897|ref|YP_920392.1| 116 QG 117
                                    66 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.0006
                        zf-C4H2  33 leeykkelelLeqEkmaHveeLrlIhaDinalEsvikeaeeekekslekakklyeeykklkeevnelrselgle 106
                                    ++  ++  e+L +E ++  ee++ +++  ++l + +k  +e +ek +e++k l ee  kl +ev +lr+e g+ 
  gi|119719897|ref|YP_920392.1| 130 VKALREGQEKLWEEVRKLWEEVKALRENQEKLWEEVKALREGQEKLWEEVKALREEQGKLWKEVKSLREEQGIL 203
                                    55566777889999999999999999999999999999999999999999999999999999999999998875 PP

>> TelA  Toxic anion resistance protein (TelA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   1.1     0.036       8.7     102     132 ..      81     111 ..      32     116 .. 0.50
   2 ?    5.2   0.3      0.04       9.6     104     147 ..     118     161 ..     115     167 .. 0.85
   3 ?    8.8   0.5    0.0031      0.75     102     152 ..     165     215 ..     158     220 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.036
                           TelA 102 vkeLekgqdellkdnaaLdqlyeknleyfke 132
                                    vk+L++ q++l + ++aL + +ek++e +++
  gi|119719897|ref|YP_920392.1|  81 VKALREDQRRLWEEVKALRENQEKLWEEVRA 111
                                    3444444444444444444444444444444 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.04
                           TelA 104 eLekgqdellkdnaaLdqlyeknleyfkeLekyiaaGekkleel 147
                                    +L +gq++l + ++aL + +ek++e +++L + + a +++ e+l
  gi|119719897|ref|YP_920392.1| 118 KLWEGQQRLWEEVKALREGQEKLWEEVRKLWEEVKALRENQEKL 161
                                    68899*************************99999988866655 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0031
                           TelA 102 vkeLekgqdellkdnaaLdqlyeknleyfkeLekyiaaGekkleeldekll 152
                                    vk+L++gq++l + ++aL +++ k+++ +k L++   +  +k++  +++l+
  gi|119719897|ref|YP_920392.1| 165 VKALREGQEKLWEEVKALREEQGKLWKEVKSLREEQGILARKMDSFERRLI 215
                                    689*****************************9987777777777777666 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   4.6   0.00086      0.21      90     181 ..      39     130 ..      30     134 .. 0.91
   2 ?    9.5   6.5    0.0032      0.77      93     180 ..     125     213 ..     121     219 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00086
                         DUF724  90 lqsrlnkLlslkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaek 169
                                    + + ln++ +l++ q++l ++++kl ++++  ++ + kl ee++ l +  ++l ++ ++l+e++e+ ++e+ +l+ ++ k
  gi|119719897|ref|YP_920392.1|  39 MDATLNEIRALREGQEQLWRNQEKLWEEVKSLREGQGKLWEEVKALREDQRRLWEEVKALRENQEKLWEEVRALREDQGK 118
                                    6789***********************************************************************99999 PP

                         DUF724 170 leeeledveqeF 181
                                    l e  ++  +e+
  gi|119719897|ref|YP_920392.1| 119 LWEGQQRLWEEV 130
                                    877766665555 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0032
                         DUF724  93 rl.nkLlslkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaekle 171
                                    rl +++ +l++ q+kl ee +kl ++++  +++++kl ee++ l +   +l ++ ++l+e++ + +ke+++l+ e+  l 
  gi|119719897|ref|YP_920392.1| 125 RLwEEVKALREGQEKLWEEVRKLWEEVKALRENQEKLWEEVKALREGQEKLWEEVKALREEQGKLWKEVKSLREEQGILA 204
                                    554778899**********************************************************************9 PP

                         DUF724 172 eeledveqe 180
                                    +++++ e++
  gi|119719897|ref|YP_920392.1| 205 RKMDSFERR 213
                                    999999886 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   7.8   0.00061      0.15      14      99 ..      64     153 ..      45     154 .. 0.85
   2 ?    9.6   4.1    0.0044         1       4      60 ..     151     208 ..     149     240 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00061
                                    HHHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT....S-TCCCCCCCHHHHHHHHHHHHH CS
                   Seryl_tRNA_N  14 vkeklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkk....edaeeliaevkelkeelkaleae 89 
                                     +e    R+++ ++ +e+ +l e +r+l  e+ +l++++ +l +e+  + +++    e  ++l +evk+l e  ++l +e
  gi|119719897|ref|YP_920392.1|  64 WEEVKSLREGQGKLWEEVKALREDQRRLWEEVKALRENQEKLWEEVRALREDQgklwEGQQRLWEEVKALREGQEKLWEE 143
                                    33344457799999***********************************998889************************* PP

                                    HHHHHHHHHH CS
                   Seryl_tRNA_N  90 lkeleaelek 99 
                                    +++l +e+++
  gi|119719897|ref|YP_920392.1| 144 VRKLWEEVKA 153
                                    *999998875 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0044
                                    HHHHHH-HHHHHHHHCC.CTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC CS
                   Seryl_tRNA_N   4 iklirenpeavkeklkk.RgedkadvdelleldekrrelqveleelqaerNelskeIg 60 
                                    +k +ren e++ e +k+ R++++++ +e+ +l e++ +l +e+ +l++e+  l++++ 
  gi|119719897|ref|YP_920392.1| 151 VKALRENQEKLWEEVKAlREGQEKLWEEVKALREEQGKLWKEVKSLREEQGILARKMD 208
                                    5889999999888887636689999999999999999999999999999877776665 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   2.8      0.12        28      41      80 ..      65     104 ..      32     126 .. 0.59
   2 ?    9.7   1.5    0.0048       1.1      41      80 ..     128     167 ..     107     171 .. 0.82
   3 ?    9.3   0.7    0.0066       1.6      46      99 ..     161     214 ..     159     218 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.12
                                    HHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.... CS
                          DUF16  41 akvdklgeqinkleqkvekqgekikelkveqkaqgeelnk 80 
                                    ++v++l e + kl ++v+++ e  ++l +e+ka +e+ +k
  gi|119719897|ref|YP_920392.1|  65 EEVKSLREGQGKLWEEVKALREDQRRLWEEVKALRENQEK 104
                                    3444555555555555555555555555555555553333 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0048
                                    HHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.... CS
                          DUF16  41 akvdklgeqinkleqkvekqgekikelkveqkaqgeelnk 80 
                                    ++v++l e ++kl ++v+k+ e++k l+++q++  ee+++
  gi|119719897|ref|YP_920392.1| 128 EEVKALREGQEKLWEEVRKLWEEVKALRENQEKLWEEVKA 167
                                    5678888889999999999999999999999998888775 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0066
                                    ..HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHHHHHHH CS
                          DUF16  46 lgeqinkleqkvekqgekikelkveqkaqgeelnkvdetleliletLqkinkRl 99 
                                    l e++++l +  ek+ e++k l++eq +  +e++++ e   ++++ +++++ Rl
  gi|119719897|ref|YP_920392.1| 161 LWEEVKALREGQEKLWEEVKALREEQGKLWKEVKSLREEQGILARKMDSFERRL 214
                                    5678999999999999**********9999999999999999999999999998 PP

>> COG5  Golgi transport complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1      0.41        99      71     119 ..      64     112 ..      37     116 .. 0.58
   2 ?   10.5   0.1    0.0022      0.52      55     121 ..     100     170 ..      96     176 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.41
                                    XXXXXXXXXXXXXXXXXXXXXX-TTHHHHHHHHHHHHHHHHHHHHHHHH CS
                           COG5  71 ssvlselksslesLsasyerlkskvlepyeeaeklqsalkrlhqtldLl 119
                                     + +++l++   +L + ++ l+++  + +ee++ l++ +++l++ ++ l
  gi|119719897|ref|YP_920392.1|  64 WEEVKSLREGQGKLWEEVKALREDQRRLWEEVKALRENQEKLWEEVRAL 112
                                    3334444555555555555555555555555555555555555555555 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0022
                                    XXXXXXXXXXXXXXXXXX.X...XXXXXXXXXXXXXXXXXXX-TTHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           COG5  55 snhleLlehlskskslss.v...lselksslesLsasyerlkskvlepyeeaeklqsalkrlhqtldLlrr 121
                                    +n+++L e+++  ++ ++ +    + l +++++L +  e+l ++v + +ee++ l++ +++l++ ++ lr+
  gi|119719897|ref|YP_920392.1| 100 ENQEKLWEEVRALREDQGkLwegQQRLWEEVKALREGQEKLWEEVRKLWEEVKALRENQEKLWEEVKALRE 170
                                    566677777776666666332224789999**********************************9999986 PP

>> Latarcin  Latarcin precursor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   8.7     0.023       5.4      13      61 ..      66     111 ..      31     115 .. 0.77
   2 ?    4.7   6.8      0.16        39      25      68 ..     104     153 ..      99     161 .. 0.63
   3 ?    7.1   1.7      0.03       7.2      22      50 ..     144     171 ..     137     175 .. 0.86
   4 ?    7.0   2.4     0.032       7.6      17      52 ..     168     201 ..     156     214 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.023
                       Latarcin  13 eLdelergainrklmemvnnlRkvqgRLeemvenlrkvedledtEEARg 61 
                                    e+  l +g+   kl e v  lR++q RL e v +lr+ ++    EE R 
  gi|119719897|ref|YP_920392.1|  66 EVKSLREGQG--KLWEEVKALREDQRRLWEEVKALRENQEK-LWEEVRA 111
                                    4444444555..99999999999999999999999966665.6788887 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.16
                       Latarcin  25 klmemvnnlRkvqgR.......LeemvenlrkvedledtEEARgafkklkd 68 
                                    kl e v  lR++qg+       L e v +lr+ ++    EE R +++++k 
  gi|119719897|ref|YP_920392.1| 104 KLWEEVRALREDQGKlwegqqrLWEEVKALREGQEK-LWEEVRKLWEEVKA 153
                                    455555555555555444444499999999965555.67*****7766653 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.03
                       Latarcin  22 inrklmemvnnlRkvqgRLeemvenlrkv 50 
                                    + rkl e v  lR+ q++L e v +lr+ 
  gi|119719897|ref|YP_920392.1| 144 V-RKLWEEVKALRENQEKLWEEVKALREG 171
                                    3.9***********************954 PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.032
                       Latarcin  17 lergainrklmemvnnlRkvqgRLeemvenlrkved 52 
                                    l +g+   kl e v  lR+ qg+L + v  lr+ ++
  gi|119719897|ref|YP_920392.1| 168 LREGQ--EKLWEEVKALREEQGKLWKEVKSLREEQG 201
                                    33333..48889999999999999999988887776 PP

>> Lectin_N  Hepatic lectin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1      0.17        41      74     117 ..      45      98 ..      32     112 .. 0.51
   2 ?    6.3   0.3     0.032       7.7      68     124 ..      74     133 ..      50     140 .. 0.75
   3 ?    8.9   0.5     0.005       1.2      51     129 ..     124     208 ..     104     210 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.17
                       Lectin_N  74 eiqalss.......qggslsekvtslea...klekkqqdlkadhselllhvkql 117
                                    ei+al+        ++++l e+v+sl+    kl ++ ++l++d+  l   vk l
  gi|119719897|ref|YP_920392.1|  45 EIRALREgqeqlwrNQEKLWEEVKSLREgqgKLWEEVKALREDQRRLWEEVKAL 98 
                                    555554433333333444444444443211144444555555555555555544 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.032
                       Lectin_N  68 ssstlaeiqalssqggslsekvtsleaklek...kqqdlkadhselllhvkqlvkdLrtL 124
                                      +   e++al+  +++l e+v+ l+ + ek   + ++l++d+ +l    ++l +++++L
  gi|119719897|ref|YP_920392.1|  74 QGKLWEEVKALREDQRRLWEEVKALRENQEKlweEVRALREDQGKLWEGQQRLWEEVKAL 133
                                    455667999999999999999999987666522266778899999999999999888887 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.005
                       Lectin_N  51 sqLqreLetLketfsnf...ssstlaeiqalssqggslsekvtslea...klekkqqdlkadhselllhvkqlvkdLrtL 124
                                    ++L +e+++L+e  + +     +   e++al+ ++++l e+v+ l+    kl ++ ++l++++ +l   vk l+++  +L
  gi|119719897|ref|YP_920392.1| 124 QRLWEEVKALREGQEKLweeVRKLWEEVKALRENQEKLWEEVKALREgqeKLWEEVKALREEQGKLWKEVKSLREEQGIL 203
                                    567788888886554441115667789****************997522266678889999************9998888 PP

                       Lectin_N 125 sCqla 129
                                    + +++
  gi|119719897|ref|YP_920392.1| 204 ARKMD 208
                                    87776 PP

>> DUF2968  Protein of unknown function (DUF2968)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   2.8      0.28        66     127     175 ..      44      92 ..      34     102 .. 0.69
   2 ?   12.8   4.2   0.00029     0.069     114     179 ..      94     159 ..      87     160 .. 0.90
   3 ?    3.2   1.5      0.25        61     123     158 ..     166     201 ..     155     220 .. 0.45

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.28
                        DUF2968 127 adlavarqQeqavaerQkqarkeaaaLeaqreaaqaqlralqrqirqLq 175
                                    ++++  r+ ++++ ++Q+++ +e+++L++ + ++ ++++al++  r+L 
  gi|119719897|ref|YP_920392.1|  44 NEIRALREGQEQLWRNQEKLWEEVKSLREGQGKLWEEVKALREDQRRLW 92 
                                    4566667777778888888888888888888777777777776655554 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00029
                        DUF2968 114 qiaasearaerLqadlavarqQeqavaerQkqarkeaaaLeaqreaaqaqlralqrqirqLqaqqe 179
                                    +++a +++ e+L ++++  r+ + ++ e Q+ + +e++aL++ +e++ +++r+l +++++L ++qe
  gi|119719897|ref|YP_920392.1|  94 EVKALRENQEKLWEEVRALREDQGKLWEGQQRLWEEVKALREGQEKLWEEVRKLWEEVKALRENQE 159
                                    55666778899**************************************************99887 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.25
                        DUF2968 123 erLqadlavarqQeqavaerQkqarkeaaaLeaqre 158
                                    ++L++ ++   +  +a+ e+Q ++ ke+++L++++ 
  gi|119719897|ref|YP_920392.1| 166 KALREGQEKLWEEVKALREEQGKLWKEVKSLREEQG 201
                                    333333333333333444444444444444444444 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1      0.27        64      49      82 ..      67     100 ..      24     133 .. 0.52
   2 ?    6.1   0.0     0.056        13      31      78 ..     133     180 ..     124     198 .. 0.48

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.27
                         DUF948  49 vedllakvnelledvneklekvdplteavadlge 82 
                                    v+ l +   +l e+v+   e+  +l e+v+ l e
  gi|119719897|ref|YP_920392.1|  67 VKSLREGQGKLWEEVKALREDQRRLWEEVKALRE 100
                                    3333333333333333333333333333333333 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.056
                         DUF948  31 aaatieelekqvdpilkevedllakvnelledvneklekvdplteava 78 
                                    +++  e+l ++v+++ +ev++l ++ ++l e+v+   e  ++l e+v+
  gi|119719897|ref|YP_920392.1| 133 LREGQEKLWEEVRKLWEEVKALRENQEKLWEEVKALREGQEKLWEEVK 180
                                    444444555555555555555555555555555543333333333333 PP

>> ApoLp-III  Apolipophorin-III precursor (apoLp-III)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   2.0    0.0082         2      30     105 ..      62     153 ..      31     156 .. 0.43
   2 ?   10.5   2.3    0.0021      0.49      42     113 ..     123     196 ..     117     209 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0082
                      ApoLp-III  30 nsenlvdqlkqvikslqeelkkksdeleealkevkkkieetadklse.................enPevkkkaqelqekv 92 
                                    +  + v++l++ +++l ee+k   +   ++++evk ++ e  +kl e                    e +k++ e qek+
  gi|119719897|ref|YP_920392.1|  62 KLWEEVKSLREGQGKLWEEVKALREDQRRLWEEVK-ALRENQEKLWEevralredqgklwegqqRLWEEVKALREGQEKL 140
                                    44444555555555555555555555555555554.24444444444111000011111112222223333333334555 PP

                      ApoLp-III  93 Qsgvqslvkesqk 105
                                     + v++l +e+++
  gi|119719897|ref|YP_920392.1| 141 WEEVRKLWEEVKA 153
                                    5555555555554 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0021
                      ApoLp-III  42 ikslqeelkkksdeleealkevkkkieetadklseenPevkkkaqel...qekvQsgvqslvkesqklaeslken 113
                                    ++ l ee+k   +  e++++ev+ k+ e ++ l+e++  + +++++l   qek+ + v++l +e  kl +++k+ 
  gi|119719897|ref|YP_920392.1| 123 QQRLWEEVKALREGQEKLWEEVR-KLWEEVKALRENQEKLWEEVKALregQEKLWEEVKALREEQGKLWKEVKSL 196
                                    66778999999999999999998.577777889995555554444442228899999999999999999999864 PP

>> LOH1CR12  Tumour suppressor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0     0.027       6.4      35     110 ..      58     133 ..      55     147 .. 0.78
   2 ?    2.9   0.0      0.45   1.1e+02      46      93 ..     153     200 ..     143     215 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.027
                       LOH1CR12  35 RlqeHlavcAkavAadqaklverikevdakiitllaelrekqkqyasyaealskvnelsdqlsriqiiledivpll 110
                                    R qe l    k     q kl e++k + ++  +l +e+++ +++ ++  e++  ++e + +l   q+ l + v+ l
  gi|119719897|ref|YP_920392.1|  58 RNQEKLWEEVKSLREGQGKLWEEVKALREDQRRLWEEVKALRENQEKLWEEVRALREDQGKLWEGQQRLWEEVKAL 133
                                    6677777777788888889999999999999999999999999999888888888888777777777777766655 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.45
                       LOH1CR12  46 avAadqaklverikevdakiitllaelrekqkqyasyaealskvnels 93 
                                    a   +q+kl e++k + +  ++l +e+++ +++  +  ++++ ++e +
  gi|119719897|ref|YP_920392.1| 153 ALRENQEKLWEEVKALREGQEKLWEEVKALREEQGKLWKEVKSLREEQ 200
                                    455677777777777777777777777777777766666666666554 PP

>> Rbsn  Rabenosyn Rab binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1       2.4   5.7e+02      22      30 ..      64      72 ..      59      84 .. 0.67
   2 ?    9.6   0.8    0.0032      0.76      18      40 ..      88     110 ..      87     112 .. 0.87
   3 ?    4.8   0.2       0.1        24      18      40 ..     123     145 ..     122     147 .. 0.84
   4 ?    7.2   0.7     0.018       4.2      22      40 ..     148     166 ..     145     168 .. 0.88
   5 ?   -0.2   0.1       3.5   8.3e+02      22      30 ..     176     184 ..     171     196 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 2.4
                           Rbsn 22 fDEvatLee 30
                                   ++Ev++L e
  gi|119719897|ref|YP_920392.1| 64 WEEVKSLRE 72
                                   789999976 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0032
                           Rbsn  18 karrfDEvatLeeNLkELqeEid 40 
                                    ++r ++Ev++L eN + L eE+ 
  gi|119719897|ref|YP_920392.1|  88 QRRLWEEVKALRENQEKLWEEVR 110
                                    67889***********9999875 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.1
                           Rbsn  18 karrfDEvatLeeNLkELqeEid 40 
                                    ++r ++Ev++L e  + L eE+ 
  gi|119719897|ref|YP_920392.1| 123 QQRLWEEVKALREGQEKLWEEVR 145
                                    7999*******998888888776 PP

  == domain 4  score: 7.2 bits;  conditional E-value: 0.018
                           Rbsn  22 fDEvatLeeNLkELqeEid 40 
                                    ++Ev++L eN + L eE++
  gi|119719897|ref|YP_920392.1| 148 WEEVKALRENQEKLWEEVK 166
                                    7*************99986 PP

  == domain 5  score: -0.2 bits;  conditional E-value: 3.5
                           Rbsn  22 fDEvatLee 30 
                                    ++Ev++L e
  gi|119719897|ref|YP_920392.1| 176 WEEVKALRE 184
                                    79****986 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.3      0.16        37     242     281 ..      33      72 ..      12      96 .. 0.67
   2 ?    9.8   1.2   0.00072      0.17     625     706 ..     101     184 ..      89     212 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.16
                       Prominin 242 erllenlkeakeqLeqvnklekeLrksgsqLrdglrgvkr 281
                                    + lle++ ++ ++++++++ +++L+  +++L + +++ ++
  gi|119719897|ref|YP_920392.1|  33 RDLLEKMDATLNEIRALREGQEQLWRNQEKLWEEVKSLRE 72 
                                    4566666666666666666666666666666666655554 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00072
                       Prominin 625 nletlaekleelanelsngkknlkqslkneaqdlraiqqel...vlplessvkklkksvkkldeensdlqesikkllaav 701
                                    n e+l e++++l +++ +  ++ +q+l++e++ lr+ q++l   v +l ++vk l+++ +kl ee + l+e  +kl ++v
  gi|119719897|ref|YP_920392.1| 101 NQEKLWEEVRALREDQGKL-WEGQQRLWEEVKALREGQEKLweeVRKLWEEVKALRENQEKLWEEVKALREGQEKLWEEV 179
                                    5566777788888888666.999************999876111445666677777788888887777777777777777 PP

                       Prominin 702 eraen 706
                                    +++ +
  gi|119719897|ref|YP_920392.1| 180 KALRE 184
                                    76654 PP

>> UCR_UQCRX_QCR9  Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1       0.4        95      40      50 ..      58      68 ..      49      70 .. 0.88
   2 ?    2.5   0.0       0.6   1.4e+02      42      51 ..      74      83 ..      72      84 .. 0.89
   3 ?    2.7   0.0      0.52   1.3e+02      40      51 ..     100     111 ..      89     112 .. 0.85
   4 ?   -1.3   0.2       8.8   2.1e+03      43      50 ..     124     131 ..     116     134 .. 0.62
   5 ?    0.3   0.1       2.9     7e+02      44      51 ..     139     146 ..     135     155 .. 0.55
   6 ?    3.4   0.1       0.3        73      40      51 ..     156     167 ..     144     168 .. 0.79
   7 ?    4.7   0.4      0.12        29      42      50 ..     186     194 ..     173     196 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.4
                                   HTTTTSHHHHT CS
                 UCR_UQCRX_QCR9 40 iNkGKlWkDIk 50
                                    N+ KlW+++k
  gi|119719897|ref|YP_920392.1| 58 RNQEKLWEEVK 68
                                   59*******99 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.6
                                   TTTSHHHHTG CS
                 UCR_UQCRX_QCR9 42 kGKlWkDIkh 51
                                   +GKlW+++k+
  gi|119719897|ref|YP_920392.1| 74 QGKLWEEVKA 83
                                   6*******96 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.52
                                    HTTTTSHHHHTG CS
                 UCR_UQCRX_QCR9  40 iNkGKlWkDIkh 51 
                                     N+ KlW+++++
  gi|119719897|ref|YP_920392.1| 100 ENQEKLWEEVRA 111
                                    5999****9986 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 8.8
                                    TTSHHHHT CS
                 UCR_UQCRX_QCR9  43 GKlWkDIk 50 
                                     +lW+++k
  gi|119719897|ref|YP_920392.1| 124 QRLWEEVK 131
                                    36677766 PP

  == domain 5  score: 0.3 bits;  conditional E-value: 2.9
                                    TSHHHHTG CS
                 UCR_UQCRX_QCR9  44 KlWkDIkh 51 
                                    KlW+++++
  gi|119719897|ref|YP_920392.1| 139 KLWEEVRK 146
                                    44554443 PP

  == domain 6  score: 3.4 bits;  conditional E-value: 0.3
                                    HTTTTSHHHHTG CS
                 UCR_UQCRX_QCR9  40 iNkGKlWkDIkh 51 
                                     N+ KlW+++k+
  gi|119719897|ref|YP_920392.1| 156 ENQEKLWEEVKA 167
                                    599*****9996 PP

  == domain 7  score: 4.7 bits;  conditional E-value: 0.12
                                    TTTSHHHHT CS
                 UCR_UQCRX_QCR9  42 kGKlWkDIk 50 
                                    +GKlWk++k
  gi|119719897|ref|YP_920392.1| 186 QGKLWKEVK 194
                                    7******99 PP

>> Dor1  Dor1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.4     0.059        14      53     105 ..      44     107 ..      29     128 .. 0.58
   2 ?    8.7   2.8    0.0026      0.61      15     105 ..      66     163 ..      58     185 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.059
                           Dor1  53 qelediraqledLvlklpkLteectrfskkaeeisek...........rkenkllldkheqlle 105
                                    +e+ ++r+  e+L  + +kL+ee++  ++   ++ e+            +e+k+l +++e+l+e
  gi|119719897|ref|YP_920392.1|  44 NEIRALREGQEQLWRNQEKLWEEVKSLREGQGKLWEEvkalredqrrlWEEVKALRENQEKLWE 107
                                    4444555555555555566666666555555555555555544443333345555555555554 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0026
                           Dor1  15 epelLaeeaeeilaqiqdLarknyktlid...aaealeairqelediraqledLvlklpkLteectrfskkaeeisek.. 89 
                                    e ++L+e + ++ +++++L  + ++   +     e++e++ +e+ ++r++  +L +   +L+ee++  ++  e++ e+  
  gi|119719897|ref|YP_920392.1|  66 EVKSLREGQGKLWEEVKALREDQRRLWEEvkaLRENQEKLWEEVRALREDQGKLWEGQQRLWEEVKALREGQEKLWEEvr 145
                                    55666666666666666666666654422100235677777777777777777777777777777777777777777775 PP

                           Dor1  90 ..rkenkllldkheqlle 105
                                       +e+k+l +++e+l+e
  gi|119719897|ref|YP_920392.1| 146 klWEEVKALRENQEKLWE 163
                                    555567777777777776 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.2      0.16        39     130     175 ..      21      67 ..      11      69 .. 0.79
   2 ?    4.5   5.9      0.11        26      63     131 ..      79     147 ..      61     155 .. 0.68
   3 ?    8.0   5.7    0.0094       2.3      64     139 ..     129     204 ..     128     207 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.16
                        DUF4201 130 klkqq.ggllrvPaLlkDYdktkekveekrksvkkLrrkvkilemrl 175
                                    +l++   gll+  +Ll+ +d t +++  +r+  ++L r  ++l + +
  gi|119719897|ref|YP_920392.1|  21 ELRYAlAGLLGFRDLLEKMDATLNEIRALREGQEQLWRNQEKLWEEV 67 
                                    555441589999999999*************9999999988886655 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.11
                        DUF4201  63 keLkrlkkkttktvhalthlkeklhmleselselkkelkekeerlaklrkelykvklerdklrkqnekl 131
                                    +e+k+l++   +   +++ l+e+   l +e+++l+++  ++ e +++l++e+  +++  +kl ++ +kl
  gi|119719897|ref|YP_920392.1|  79 EEVKALREDQRRLWEEVKALRENQEKLWEEVRALREDQGKLWEGQQRLWEEVKALREGQEKLWEEVRKL 147
                                    566777777777777777777777777777777777777777777777777777777777766665555 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0094
                        DUF4201  64 eLkrlkkkttktvhalthlkeklhmleselselkkelkekeerlaklrkelykvklerdklrkqneklkqqggllr 139
                                    e+k+l++   k   ++  l e  ++l++++++l +e k + e ++kl++e+  +++e  kl k+ + l+++ g+l 
  gi|119719897|ref|YP_920392.1| 129 EVKALREGQEKLWEEVRKLWEEVKALRENQEKLWEEVKALREGQEKLWEEVKALREEQGKLWKEVKSLREEQGILA 204
                                    5556666666666666677778888888999999999999999999999999999999999999999988888875 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.8      0.12        29      19      53 ..      39      73 ..      26      77 .. 0.84
   2 ?    7.5   3.4     0.015       3.5      16      54 ..      78     116 ..      75     121 .. 0.85
   3 ?    3.0   3.5      0.35        84      21      62 ..     104     145 ..      99     147 .. 0.85
   4 ?    5.6   3.8     0.057        14      21      57 ..     125     161 ..     116     169 .. 0.65
   5 ?    7.4   3.4     0.016       3.7      23      55 ..     141     173 ..     137     178 .. 0.88
   6 ?    7.7   2.3     0.012         3      16      54 ..     162     200 ..     159     206 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.12
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXX CS
                          DivIC 19 ykqlkqeiaalqaelaklkaeneeLeaevkdLksd 53
                                   + ++ +ei al +  ++l   +e+L +evk L+ +
  gi|119719897|ref|YP_920392.1| 39 MDATLNEIRALREGQEQLWRNQEKLWEEVKSLREG 73
                                   55667899999999999999999999999999865 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.015
                                    XXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXX CS
                          DivIC  16 llaykqlkqeiaalqaelaklkaeneeLeaevkdLksde 54 
                                    +  +k+l+++  +l +e+++l++ +e+L +ev+ L+ d+
  gi|119719897|ref|YP_920392.1|  78 WEEVKALREDQRRLWEEVKALRENQEKLWEEVRALREDQ 116
                                    566788999999999999999999999999999998775 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.35
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXXXXXXX CS
                          DivIC  21 qlkqeiaalqaelaklkaeneeLeaevkdLksdedyieerAR 62 
                                    +l +e+ al ++  kl + +++L +evk L+ +++ + e  R
  gi|119719897|ref|YP_920392.1| 104 KLWEEVRALREDQGKLWEGQQRLWEEVKALREGQEKLWEEVR 145
                                    6678999999999999999***********999998888877 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.057
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXX CS
                          DivIC  21 qlkqeiaalqaelaklkaeneeLeaevkdLksdedyi 57 
                                    +l +e++al +  +kl +e ++L +evk L+ +++ +
  gi|119719897|ref|YP_920392.1| 125 RLWEEVKALREGQEKLWEEVRKLWEEVKALRENQEKL 161
                                    5666777777777777777777777777776666544 PP

  == domain 5  score: 7.4 bits;  conditional E-value: 0.016
                                    HHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXX CS
                          DivIC  23 kqeiaalqaelaklkaeneeLeaevkdLksded 55 
                                     +e+ +l +e+++l++ +e+L +evk L+ +++
  gi|119719897|ref|YP_920392.1| 141 WEEVRKLWEEVKALRENQEKLWEEVKALREGQE 173
                                    58999999********************99887 PP

  == domain 6  score: 7.7 bits;  conditional E-value: 0.012
                                    XXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXX CS
                          DivIC  16 llaykqlkqeiaalqaelaklkaeneeLeaevkdLksde 54 
                                    +  +k+l++  ++l +e+++l++e+ +L +evk L+ ++
  gi|119719897|ref|YP_920392.1| 162 WEEVKALREGQEKLWEEVKALREEQGKLWKEVKSLREEQ 200
                                    667888999999999********************7544 PP

>> JIP_LZII  JNK-interacting protein  leucine zipper II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   1.5      0.05        12      29      66 ..      33      70 ..       7      74 .. 0.88
   2 ?    7.8   1.9     0.016       3.7      32      68 ..      78     114 ..      74     118 .. 0.88
   3 ?    6.6   6.7     0.037       8.9      10      69 ..     126     185 ..     123     187 .. 0.87
   4 ?    5.0   4.6      0.12        28      32      68 ..     162     198 ..     154     217 .. 0.50

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.05
                       JIP_LZII 29 ddLIarvdeLtsereiLreEleslqkakerlesrikel 66
                                   +dL+++ d   +e  +Lre  e+l  ++e+l +++k l
  gi|119719897|ref|YP_920392.1| 33 RDLLEKMDATLNEIRALREGQEQLWRNQEKLWEEVKSL 70
                                   79*****************************9999987 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.016
                       JIP_LZII  32 IarvdeLtsereiLreEleslqkakerlesrikelEe 68 
                                     ++v  L +++  L eE+++l++++e+l +++++l e
  gi|119719897|ref|YP_920392.1|  78 WEEVKALREDQRRLWEEVKALRENQEKLWEEVRALRE 114
                                    5678999**********************99999866 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.037
                       JIP_LZII  10 LikENteLletknaLnvvkddLIarvdeLtsereiLreEleslqkakerlesrikelEee 69 
                                    L +E + L+e +++L    + L ++v  L +++e L eE+++l++ +e+l +++k+l ee
  gi|119719897|ref|YP_920392.1| 126 LWEEVKALREGQEKLWEEVRKLWEEVKALRENQEKLWEEVKALREGQEKLWEEVKALREE 185
                                    6677788888888887777889999******************************99887 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.12
                       JIP_LZII  32 IarvdeLtsereiLreEleslqkakerlesrikelEe 68 
                                     ++v  L + +e L eE+++l++++ +l +++k l e
  gi|119719897|ref|YP_920392.1| 162 WEEVKALREGQEKLWEEVKALREEQGKLWKEVKSLRE 198
                                    3334444444444444444444444444444444433 PP

>> HAP1_N  HAP1 N-terminal conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5  12.3     0.034       8.2     206     306 ..      34     134 ..      29     140 .. 0.76
   2 ?    8.3   9.7    0.0049       1.2     230     300 ..     128     198 ..     115     213 .. 0.55

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.034
                         HAP1_N 206 dcveqlseanqqiaelseelarkleelerqqeeissLlaqivdlqqklkelgveneelkqhLaaskeaqrqLtaELqdlq 285
                                    d+ e++  + ++i  l e  ++   ++e+  ee++sL+    +l + +k l +++  l ++ +a +e+q++L +E++ l+
  gi|119719897|ref|YP_920392.1|  34 DLLEKMDATLNEIRALREGQEQLWRNQEKLWEEVKSLREGQGKLWEEVKALREDQRRLWEEVKALRENQEKLWEEVRALR 113
                                    67778888888888888888888888888899999999999999999999999999999999999999999999966666 PP

                         HAP1_N 286 ekyaevegmLheaqeevkelr 306
                                    e      +  +   eevk lr
  gi|119719897|ref|YP_920392.1| 114 EDQGKLWEGQQRLWEEVKALR 134
                                    555554444445555555555 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0049
                         HAP1_N 230 eelerqqeeissLlaqivdlqqklkelgveneelkqhLaaskeaqrqLtaELqdlqekyaevegmLheaqe 300
                                    ee++  +e  ++L  ++ +l + +k l +++e+l ++ +a +e q++L +E++ l+e      +  ++ +e
  gi|119719897|ref|YP_920392.1| 128 EEVKALREGQEKLWEEVRKLWEEVKALRENQEKLWEEVKALREGQEKLWEEVKALREEQGKLWKEVKSLRE 198
                                    55555555555555555555555555555555555555555555555555555555444333333333333 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   3.0     0.038       9.1      12      73 ..      54     114 ..      43     140 .. 0.48
   2 ?    9.4   3.6    0.0024      0.56       2      60 ..     142     200 ..     127     242 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.038
                          TMPIT  12 keleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelke 73 
                                    ++l  +++++ +++++l + q k+ +e+k  +++ ++l++++k l+++++ +  eev+ l+e
  gi|119719897|ref|YP_920392.1|  54 EQLWRNQEKLWEEVKSLREGQGKLWEEVKALREDQRRLWEEVKALRENQE-KLWEEVRALRE 114
                                    55555555555555555555555555555555555555555555554432.22222222222 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0024
                          TMPIT   2 eeweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksv 60 
                                    ee+++l +e+k+l+e+++++ ++++ l + q+k+ +e+k  +++  +l++++k+l++++
  gi|119719897|ref|YP_920392.1| 142 EEVRKLWEEVKALRENQEKLWEEVKALREGQEKLWEEVKALREEQGKLWKEVKSLREEQ 200
                                    46666777777777777777777777777777777777777777777777777776664 PP

>> Nup88  Nuclear pore component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   6.2       0.2        48     569     636 ..      41     107 ..      32     124 .. 0.61
   2 ?   11.9   6.5   0.00015     0.036     558     631 ..     128     200 ..     119     226 .. 0.69

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.2
                          Nup88 569 qqleelqsleeerkslseraeklAekyeeikdkQeklvrrvkkvlkrlnsklpvlseaeremkkelek 636
                                      l+e++ l+e +++l  + ekl e+    ++ Q kl + vk+ l++ + +l   ++a re +++l++
  gi|119719897|ref|YP_920392.1|  41 ATLNEIRALREGQEQLWRNQEKLWEEVKSLREGQGKLWEEVKA-LREDQRRLWEEVKALRENQEKLWE 107
                                    5566777777777777777777777777777777777776665.344555555555555555555443 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00015
                          Nup88 558 krvkllkkqkeqqleelqsleeerkslseraeklAekyeeikdkQeklvrrvkkvlkrlnsklpvlseaeremk 631
                                      vk+l++ +e+  ee+++l ee k l+e+ ekl e+    ++ Qekl + vk+ l++ + kl + +++ re +
  gi|119719897|ref|YP_920392.1| 128 EEVKALREGQEKLWEEVRKLWEEVKALRENQEKLWEEVKALREGQEKLWEEVKA-LREEQGKLWKEVKSLREEQ 200
                                    467888888888888888888888888888888888888888888888888775.4555555555555555543 PP

>> VPS11_C  Vacuolar protein sorting protein 11 C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1     0.044        11       2      24 ..      44      66 ..      43      75 .. 0.81
   2 ?   -0.2   0.0       5.1   1.2e+03       2      13 ..      79      90 ..      78      91 .. 0.87
   3 ?    2.0   0.1         1   2.4e+02       2      14 ..      93     105 ..      92     109 .. 0.88
   4 ?    1.0   0.0       2.2   5.3e+02       2      14 ..     128     140 ..     127     143 .. 0.88
   5 ?    2.0   0.2       1.1   2.6e+02       2      14 ..     149     161 ..     148     164 .. 0.88
   6 ?    1.3   0.1       1.7   4.2e+02       2      14 ..     163     175 ..     162     185 .. 0.86
   7 ?    2.7   0.0      0.62   1.5e+02       3      25 ..     192     214 ..     190     215 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.044
                        VPS11_C  2 etirelrraQeesadrhdlFkaa 24
                                   ++ir+lr+ Qe++  + + +  +
  gi|119719897|ref|YP_920392.1| 44 NEIRALREGQEQLWRNQEKLWEE 66
                                   79**********98888877555 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 5.1
                        VPS11_C  2 etirelrraQee 13
                                   e++++lr++Q++
  gi|119719897|ref|YP_920392.1| 79 EEVKALREDQRR 90
                                   689*******97 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 1
                        VPS11_C   2 etirelrraQees 14 
                                    e++++lr++Qe++
  gi|119719897|ref|YP_920392.1|  93 EEVKALRENQEKL 105
                                    689********86 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 2.2
                        VPS11_C   2 etirelrraQees 14 
                                    e++++lr+ Qe++
  gi|119719897|ref|YP_920392.1| 128 EEVKALREGQEKL 140
                                    689********86 PP

  == domain 5  score: 2.0 bits;  conditional E-value: 1.1
                        VPS11_C   2 etirelrraQees 14 
                                    e++++lr++Qe++
  gi|119719897|ref|YP_920392.1| 149 EEVKALRENQEKL 161
                                    689********86 PP

  == domain 6  score: 1.3 bits;  conditional E-value: 1.7
                        VPS11_C   2 etirelrraQees 14 
                                    e++++lr+ Qe++
  gi|119719897|ref|YP_920392.1| 163 EEVKALREGQEKL 175
                                    689********87 PP

  == domain 7  score: 2.7 bits;  conditional E-value: 0.62
                        VPS11_C   3 tirelrraQeesadrhdlFkaaL 25 
                                    +++ lr++Q  +a + d F+  L
  gi|119719897|ref|YP_920392.1| 192 EVKSLREEQGILARKMDSFERRL 214
                                    799****************9766 PP

>> DUF4061  Domain of unknown function (DUF4061)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.8     0.037       8.9      28      64 ..      40      76 ..      37     100 .. 0.68
   2 ?    1.0   6.5       2.3   5.6e+02      26      63 ..     122     159 ..      73     182 .. 0.63
   3 ?    3.8   1.8      0.31        74      41      80 ..     158     196 ..     150     214 .. 0.47

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.037
                        DUF4061 28 dcsleqleeiReqQekLarlhfeldaeeeelaekeed 64
                                   d +l+++ ++Re Qe+L r + +l +e ++l+e + +
  gi|119719897|ref|YP_920392.1| 40 DATLNEIRALREGQEQLWRNQEKLWEEVKSLREGQGK 76
                                   5689999**************9999999888743333 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 2.3
                        DUF4061  26 GkdcsleqleeiReqQekLarlhfeldaeeeelaekee 63 
                                    G++   e+++++Re QekL +   +l +e + l+e++e
  gi|119719897|ref|YP_920392.1| 122 GQQRLWEEVKALREGQEKLWEEVRKLWEEVKALRENQE 159
                                    44445566666666666666555555555555554444 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.31
                        DUF4061  41 QekLarlhfeldaeeeelaekeedalresdenlkkLvskL 80 
                                    QekL +    l + +e+l e e +alre++ +l k v++L
  gi|119719897|ref|YP_920392.1| 158 QEKLWEEVKALREGQEKLWE-EVKALREEQGKLWKEVKSL 196
                                    44444444444444443332.3333333333333333333 PP

>> COG6  Conserved oligomeric complex COG6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.5     0.043        10      26      89 ..      54     117 ..      35     133 .. 0.64
   2 ?    6.3   0.5    0.0095       2.3      33      92 ..     145     204 ..     130     211 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.043
                           COG6  26 kellkineefleefqpvaeqLkriesdveklnelcdemkkklssakeetsdlleeaeeLkeekk 89 
                                    ++l +++e+  ee + ++e   ++ ++v++l e   ++ +++++ +e++++l ee+ +L+e++ 
  gi|119719897|ref|YP_920392.1|  54 EQLWRNQEKLWEEVKSLREGQGKLWEEVKALREDQRRLWEEVKALRENQEKLWEEVRALREDQG 117
                                    4555566666666666666666777777777777777777777777777777777777766554 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0095
                           COG6  33 eefleefqpvaeqLkriesdveklnelcdemkkklssakeetsdlleeaeeLkeekkkle 92 
                                    ++  ee ++++e+ +++ ++v++l e  +++ +++++ +ee+++l +e+++L+ee+  l 
  gi|119719897|ref|YP_920392.1| 145 RKLWEEVKALRENQEKLWEEVKALREGQEKLWEEVKALREEQGKLWKEVKSLREEQGILA 204
                                    556677788888888888888888888888888888888888888888888888876665 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4  15.0      0.03       7.2     137     262 ..      36     156 ..      32     160 .. 0.71
   2 ?    6.0   4.0      0.02       4.9     143     190 ..     153     200 ..     145     216 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.03
                           Spc7 137 legLkegleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeie 216
                                    le++  +l+ ++ +l+e +e+L +++e+l e +++l+e + +l ee++ l+e ++ l     ee+++lre+ ++l +e++
  gi|119719897|ref|YP_920392.1|  36 LEKMDATLN-EIRALREGQEQLWRNQEKLWEEVKSLREGQGKLWEEVKALREDQRRL----WEEVKALRENQEKLWEEVR 110
                                    555555554.45778888888888899998889999999999999999999977774....4577777777777777777 PP

                           Spc7 217 ekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckg 262
                                    +++++  +l e  ++l e++++l+e  ++l ee+++  + +++ ++
  gi|119719897|ref|YP_920392.1| 111 ALREDQGKLWEGQQRLWEEVKALREGQEKLWEEVRKLWEEVKALRE 156
                                    7777777777777777777777777777777777765555544444 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.02
                           Spc7 143 gleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaa 190
                                     l+en e+l e+ + L + +e+l e +++l+ee+ +l +e+++l+e++
  gi|119719897|ref|YP_920392.1| 153 ALRENQEKLWEEVKALREGQEKLWEEVKALREEQGKLWKEVKSLREEQ 200
                                    578888899999999999999999999999999999999999998854 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   3.2      0.03       7.1     105     404 ..      76     111 ..      44     136 .. 0.50
   2 ?    3.6   5.8     0.064        15     345     426 ..      87     168 ..      85     170 .. 0.87
   3 ?    6.5   5.4    0.0085         2     101     157 ..     142     198 ..     128     218 .. 0.55

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.03
                                    HHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHHHHHHHHHHT--TTTTHHHHHHHHHHHHHHHH----------- CS
                           EzrA 105 eleeeldeveekikkileelkelteseeknreeieklkekYrelrkkllanrfsygealeelekqleniekefsefeelt 184
                                    +l ee++ ++                                                                      
  gi|119719897|ref|YP_920392.1|  76 KLWEEVKALR---------------------------------------------------------------------- 85 
                                    2222222222...................................................................... PP

                                    -----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTTSHHHHHHHHHHHHHSTTS--SGGGSSSSSHHHHHHHHHHHH CS
                           EzrA 185 engdyveakeilkkleeeideleevieeiPelleelkkelpkqleelkegykemkeegYaleelniekeieelekkieei 264
                                                                                                                    
  gi|119719897|ref|YP_920392.1|   - --------------------------------------------------------------------------------   -
                                    ................................................................................ PP

                                    HHHHTT--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTSSSSSHHHHT--HHHHTTGGG-TTTS-GGGSSTTTST CS
                           EzrA 265 lerlkeleledveeelktieeeidsLyddlekEveAkkeveknlkelkeklehlekqnkelkeeldrlkqsYeLseeele 344
                                                                                                                    
  gi|119719897|ref|YP_920392.1|   - --------------------------------------------------------------------------------   -
                                    ................................................................................ PP

                                    THHHHHHHHHHHHHHHHHHHHHHS-SS---STTGGGTHHHHHHHHHHHHHHHHHHHHHHH CS
                           EzrA 345 klrelekelkelekdyeeleekleekkvaYSelqeeleeleekleeieekqeeileslks 404
                                                                      e++++l e+++++ e+qe+++e++++
  gi|119719897|ref|YP_920392.1|  86 ----------------------------------EDQRRLWEEVKALRENQEKLWEEVRA 111
                                    ..................................23333333333333333333333333 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.064
                                    THHHHHHHHHHHHHHHHHHHHHHS-SS---STTGGGTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           EzrA 345 klrelekelkelekdyeeleekleekkvaYSelqeeleeleekleeieekqeeileslkslrkdEkrAreqldeikkelk 424
                                     +r l +e+k l+++ e+l e++++      +l e +++l e+++++ e qe+++e++++l ++ k  re+ +++ +e+k
  gi|119719897|ref|YP_920392.1|  87 DQRRLWEEVKALRENQEKLWEEVRALREDQGKLWEGQQRLWEEVKALREGQEKLWEEVRKLWEEVKALRENQEKLWEEVK 166
                                    56778889999999999999999999999999999999999999999999999999999999999999999999888777 PP

                                    HH CS
                           EzrA 425 ei 426
                                     +
  gi|119719897|ref|YP_920392.1| 167 AL 168
                                    65 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.0085
                                    HHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHHHHHHHHHHT--TTTT CS
                           EzrA 101 kklaeleeeldeveekikkileelkelteseeknreeieklkekYrelrkkllanrf 157
                                    +++++l ee++ ++e+ +k+ ee+k l+e +ek  ee+++l+e+  +l k++++ r+
  gi|119719897|ref|YP_920392.1| 142 EEVRKLWEEVKALRENQEKLWEEVKALREGQEKLWEEVKALREEQGKLWKEVKSLRE 198
                                    344455555555555555555555555555555555555555555555555544444 PP

>> COG2  COG (conserved oligomeric Golgi) complex component, COG2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.1      0.32        76      63     107 ..      28      71 ..      11      77 .. 0.84
   2 ?    5.4   0.6     0.075        18      69     102 ..      79     112 ..      64     127 .. 0.57
   3 ?    5.8   2.3     0.059        14      77     114 ..     122     163 ..     107     177 .. 0.64
   4 ?    4.1   2.2      0.19        45      69     106 ..     163     200 ..     150     219 .. 0.56

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.32
                           COG2  63 hLvglqeeleevesplaaarkkvesvreklsereeeveskleeak 107
                                     L g+++ le+++  l+++r  +++ +e+l +++e++ ++++  +
  gi|119719897|ref|YP_920392.1|  28 GLLGFRDLLEKMDATLNEIR-ALREGQEQLWRNQEKLWEEVKSLR 71 
                                    58899999999999999987.588888888888888888887665 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.075
                           COG2  69 eeleevesplaaarkkvesvreklsereeevesk 102
                                    ee++ ++ +  +++++v+++re+ ++  eev++ 
  gi|119719897|ref|YP_920392.1|  79 EEVKALREDQRRLWEEVKALRENQEKLWEEVRAL 112
                                    4455555555555555555555555555555544 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.059
                           COG2  77 plaaarkkvesvreklsereeeveskleeakeleekr....e 114
                                      ++++++v+++re  ++  eev++  ee k+l+e++    e
  gi|119719897|ref|YP_920392.1| 122 GQQRLWEEVKALREGQEKLWEEVRKLWEEVKALRENQeklwE 163
                                    566777777777777777777777777777777777743332 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.19
                           COG2  69 eeleevesplaaarkkvesvreklsereeeveskleea 106
                                    ee++ ++   ++++++v+++re+  +  +ev+s  ee+
  gi|119719897|ref|YP_920392.1| 163 EEVKALREGQEKLWEEVKALREEQGKLWKEVKSLREEQ 200
                                    44555555555555555555555555555555555544 PP

>> RNase_E_G  Ribonuclease E/G family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.2      0.13        31      85     155 ..      34     103 ..       6     113 .. 0.57
   2 ?    6.7   4.6     0.018       4.2      51     148 ..      97     194 ..      78     209 .. 0.63

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.13
                      RNase_E_G  85 llyeeedlllrvlrdllnedieeivvddkelyeeikeyleevapeleekvelyeeee.plfelysiekqiek 155
                                     l e+ d +l+ +r  l+e  e+++ ++++l+ee+k+  e  + +l e+v+  +e++ +l e+++  ++ ++
  gi|119719897|ref|YP_920392.1|  34 DLLEKMDATLNEIRA-LREGQEQLWRNQEKLWEEVKSLREG-QGKLWEEVKALREDQrRLWEEVKALRENQE 103
                                    566666677777776.4555577777777777777665444.444444466555544456665554444333 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.018
                      RNase_E_G  51 aegaseeelekdleelkkkweeilekakk.rkapsllyeeedlllrvlrdllnedieeivvddkelyeeikeyleevape 129
                                    a  +++e+l ++++ l+++  ++ e +++  ++ + l e ++ l + +r+ l e+++ +  ++++l+ee+k+   e +++
  gi|119719897|ref|YP_920392.1|  97 ALRENQEKLWEEVRALREDQGKLWEGQQRlWEEVKALREGQEKLWEEVRK-LWEEVKALRENQEKLWEEVKALR-EGQEK 174
                                    34445555666666666655555555543345577888888888888888.57788888888888888887754.44555 PP

                      RNase_E_G 130 leekvelyeeee.plfelys 148
                                    l e+v+  +ee+ +l ++++
  gi|119719897|ref|YP_920392.1| 175 LWEEVKALREEQgKLWKEVK 194
                                    55557777665556666665 PP

>> Cauli_AT  Aphid transmission protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   4.9       0.5   1.2e+02     161     161 ..      98      98 ..      30     207 .. 0.58

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.5
                       Cauli_AT 161 i 161
                                    +
  gi|119719897|ref|YP_920392.1|  98 L 98 
                                    2 PP

>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   5.7    0.0028      0.66      42     182 ..      36     174 ..      31     178 .. 0.81
   2 ?    7.2   1.8     0.016       3.8      44     108 ..     135     198 ..     116     213 .. 0.57

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0028
                           YkyA  42 ielgmde.fdkikklsdealenveeReellekekesieeakeefekikeeieei..edeelkkeaeelieameeryeayd 118
                                    +e +md  +++i +l +   ++  ++e+l e+    +++ +e   k+ ee++ +  ++  l +e+++l e+ e+  e   
  gi|119719897|ref|YP_920392.1|  36 LE-KMDAtLNEIRALREGQEQLWRNQEKLWEE----VKSLREGQGKLWEEVKALreDQRRLWEEVKALRENQEKLWEEVR 110
                                    44.34444777888887777777778777777....66666666666677777742234788****************** PP

                           YkyA 119 klykaYkealeldkeLYemLkkeeltleeleeqiekiNesyeevkeaneqFneatkkyneekke 182
                                    +l ++  ++ e ++ L e+ k     +e+l e++ k+ e+ + ++e+ e++ e+ k+  e +++
  gi|119719897|ref|YP_920392.1| 111 ALREDQGKLWEGQQRLWEEVKALREGQEKLWEEVRKLWEEVKALRENQEKLWEEVKALREGQEK 174
                                    ***************************************************9999999887766 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.016
                           YkyA  44 lgmde.fdkikklsdealenveeReellekekesieeakeefekikeeieei..edeelkkeaeelie 108
                                     g+++  +++ kl +e+ ++ e++e+l e+    +++ +e  ek+ ee++ +  e+ +l ke+++l e
  gi|119719897|ref|YP_920392.1| 135 EGQEKlWEEVRKLWEEVKALRENQEKLWEE----VKALREGQEKLWEEVKALreEQGKLWKEVKSLRE 198
                                    355555667777777777777777777777....4444444444444444442222344455555543 PP

>> Uso1_p115_C  Uso1 / p115 like vesicle tethering protein, C terminal region
   [No individual domains that satisfy reporting thresholds (although complete target did)]

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   5.0     0.027       6.5      44     131 ..      12     101 ..      10     118 .. 0.70
   2 ?    7.2   6.2     0.021       4.9      54     138 ..     122     206 ..     109     214 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.027
                           ADIP  44 Llqardrdleqreslneti..rkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrl 121
                                    L++a+++d+e r +l+  +  r+l   ++   ++i+ l +  eql r  + + ++ ++l+  + +l + +k ++e+ +rl
  gi|119719897|ref|YP_920392.1|  12 LVKALEEDRELRYALAGLLgfRDLLEKMDATLNEIRALREGQEQLWRNQEKLWEEVKSLREGQGKLWEEVKALREDQRRL 91 
                                    67777777777777776543367777777777777777777777777777777777777777777777777777777777 PP

                           ADIP 122 knalqqiktq 131
                                       +++++  
  gi|119719897|ref|YP_920392.1|  92 WEEVKALREN 101
                                    7777776654 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.021
                           ADIP  54 qreslnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrlknalqqiktqya 133
                                     ++ l e+++ l+   e+l  ++++l +++++l+   + + ++ + l+  +++l + +k ++ee  +l + +++++  + 
  gi|119719897|ref|YP_920392.1| 122 GQQRLWEEVKALREGQEKLWEEVRKLWEEVKALRENQEKLWEEVKALREGQEKLWEEVKALREEQGKLWKEVKSLREEQG 201
                                    57778888899999999999999999999999999888888899999999999999999999999999999999888776 PP

                           ADIP 134 helkk 138
                                       +k
  gi|119719897|ref|YP_920392.1| 202 ILARK 206
                                    55555 PP

>> PTRF_SDPR  PTRF/SDPR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   2.5     0.047        11      10      98 ..      35     119 ..      31     124 .. 0.72
   2 ?    8.5   1.9    0.0058       1.4      61      99 ..     138     176 ..     123     183 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.047
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      PTRF_SDPR  10 lLdkvvgivdsvqesqkrlEerqaelenavksiqgdllkLakshssTsntvnklleksrkvsvnvkevrerlekqavqvk 89 
                                    lL+k+ + ++++++    l e q++l ++ + +  ++  L   + +  + v+ l e  r+   +vk +re+ ek   +v+
  gi|119719897|ref|YP_920392.1|  35 LLEKMDATLNEIRA----LREGQEQLWRNQEKLWEEVKSLREGQGKLWEEVKALREDQRRLWEEVKALRENQEKLWEEVR 110
                                    55665555555543....3344444555555555666666667777778899999********************99999 PP

                                    HHHHHHHHH CS
                      PTRF_SDPR  90 klEaneael 98 
                                     l +++ +l
  gi|119719897|ref|YP_920392.1| 111 ALREDQGKL 119
                                    999988877 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0058
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                      PTRF_SDPR  61 nklleksrkvsvnvkevrerlekqavqvkklEaneaelL 99 
                                    +kl e +rk   +vk +re+ ek   +vk l + +++l 
  gi|119719897|ref|YP_920392.1| 138 EKLWEEVRKLWEEVKALRENQEKLWEEVKALREGQEKLW 176
                                    8******************************99999885 PP

>> HALZ  Homeobox associated leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.3      0.63   1.5e+02      22      40 ..      54      72 ..      44      74 .. 0.84
   2 ?    6.6   0.4     0.038       9.1      20      40 ..      80     100 ..      75     103 .. 0.86
   3 ?    4.7   1.2      0.15        36      24      40 ..      84     100 ..      82     116 .. 0.62
   4 ?    0.7   0.1       2.6   6.2e+02      24      40 ..     119     135 ..     111     138 .. 0.77
   5 ?    1.9   1.5       1.1   2.6e+02      17      40 ..     133     156 ..     124     159 .. 0.66
   6 ?    3.7   0.8      0.31        75      20      40 ..     150     170 ..     145     173 .. 0.85
   7 ?    8.4   1.1      0.01       2.5      10      40 ..     168     198 ..     166     200 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.63
                           HALZ 22 dsLkkenekLkaelqeLke 40
                                   ++L +  ekL  e+++L+e
  gi|119719897|ref|YP_920392.1| 54 EQLWRNQEKLWEEVKSLRE 72
                                   7788899**********98 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.038
                           HALZ  20 dydsLkkenekLkaelqeLke 40 
                                    ++ +L+++ ++L  e++ L+e
  gi|119719897|ref|YP_920392.1|  80 EVKALREDQRRLWEEVKALRE 100
                                    6779***************98 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.15
                           HALZ  24 LkkenekLkaelqeLke 40 
                                    L+++ ++L  e++ L+e
  gi|119719897|ref|YP_920392.1|  84 LREDQRRLWEEVKALRE 100
                                    66666666666666665 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 2.6
                           HALZ  24 LkkenekLkaelqeLke 40 
                                    L +  ++L  e++ L+e
  gi|119719897|ref|YP_920392.1| 119 LWEGQQRLWEEVKALRE 135
                                    556679*********98 PP

  == domain 5  score: 1.9 bits;  conditional E-value: 1.1
                           HALZ  17 LksdydsLkkenekLkaelqeLke 40 
                                    L+   + L +e +kL  e++ L+e
  gi|119719897|ref|YP_920392.1| 133 LREGQEKLWEEVRKLWEEVKALRE 156
                                    444446666777777777777776 PP

  == domain 6  score: 3.7 bits;  conditional E-value: 0.31
                           HALZ  20 dydsLkkenekLkaelqeLke 40 
                                    ++ +L++  ekL  e++ L+e
  gi|119719897|ref|YP_920392.1| 150 EVKALRENQEKLWEEVKALRE 170
                                    567999999**********98 PP

  == domain 7  score: 8.4 bits;  conditional E-value: 0.01
                           HALZ  10 LKasYdaLksdydsLkkenekLkaelqeLke 40 
                                    L+   ++L  ++ +L++e  kL +e+++L+e
  gi|119719897|ref|YP_920392.1| 168 LREGQEKLWEEVKALREEQGKLWKEVKSLRE 198
                                    5555678888999****************98 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   8.6     0.071        17      86     161 ..      41     116 ..       9     129 .. 0.45
   2 ?    7.4   9.6     0.018       4.2      83     170 ..     122     208 ..     112     214 .. 0.65

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.071
                        UPF0242  86 tkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelkleleeqLaekqellqeyqetieeq 161
                                       ++++ l+e +e+L +++++  ee++ l+e + +L e+ +a  ed  +l  e+++  +++++l +e ++  e+q
  gi|119719897|ref|YP_920392.1|  41 ATLNEIRALREGQEQLWRNQEKLWEEVKSLREGQGKLWEEVKALREDQRRLWEEVKALRENQEKLWEEVRALREDQ 116
                                    3333333333334444444444444444444333344433333333333333333333333333333333333333 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.018
                        UPF0242  83 glktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelkleleeqLaekqellqeyqetieeqr 162
                                    g +   e+++ l+e +e+L ee+ +  ee++ l+e++++L e+ +a  ++ +e + e  ++L+e+q +l +  +++ e +
  gi|119719897|ref|YP_920392.1| 122 GQQRLWEEVKALREGQEKLWEEVRKLWEEVKALRENQEKLWEEVKA-LREGQEKLWEEVKALREEQGKLWKEVKSLREEQ 200
                                    4466667888888888888888888888888888888888877776.445555555555566666666666666666666 PP

                        UPF0242 163 svlekrqd 170
                                      l ++ d
  gi|119719897|ref|YP_920392.1| 201 GILARKMD 208
                                    66666655 PP

>> DUF4763  Domain of unknown function (DUF4763)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   3.9     0.075        18     100     153 ..      65     118 ..      45     129 .. 0.74
   2 ?    8.6   3.1    0.0044         1     100     160 ..     149     213 ..     137     216 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.075
                        DUF4763 100 peileLqrnnhkLrqqlaelqqhlkasrkslkelreslcqekkrlrklqkrlne 153
                                     e++ L+  + kL  +++ l +  ++ ++++k+lre + ++ + +r+l++  ++
  gi|119719897|ref|YP_920392.1|  65 EEVKSLREGQGKLWEEVKALREDQRRLWEEVKALRENQEKLWEEVRALREDQGK 118
                                    477778888888888888888888888888888888888888888877766555 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0044
                        DUF4763 100 peileLqrnnhkLrqqlaelqqhlkasrkslkelreslcqekkrlrklqkr....lneldsfkrk 160
                                     e++ L+ n+ kL  +++ l +  ++ ++++k+lre++ ++ k +++l+++    + ++dsf+r+
  gi|119719897|ref|YP_920392.1| 149 EEVKALRENQEKLWEEVKALREGQEKLWEEVKALREEQGKLWKEVKSLREEqgilARKMDSFERR 213
                                    5899********************************************98822223456666665 PP

>> DUF4446  Protein of unknown function (DUF4446)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1       1.2     3e+02      41      77 ..      33      69 ..      18      75 .. 0.82
   2 ?    4.2   0.9      0.16        39      39      84 ..      66     111 ..      41     121 .. 0.68
   3 ?    6.1   0.7     0.042        10      38      84 ..     135     181 ..     118     186 .. 0.79
   4 ?    5.1   0.8     0.088        21      41      73 ..     152     184 ..     138     231 .. 0.57

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 1.2
                        DUF4446 41 ksleellkekleeveelkeeseelekeieeleeklkk 77
                                   ++l e++  +l+e+++l+e +e+l +++e+l e++k+
  gi|119719897|ref|YP_920392.1| 33 RDLLEKMDATLNEIRALREGQEQLWRNQEKLWEEVKS 69
                                   5677888999999999999999999999998888765 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.16
                        DUF4446  39 dgksleellkekleeveelkeeseelekeieeleeklkkslqkvgl 84 
                                    + ksl e   +  eev++l+e++++l +e+++l+e+++k  ++v+ 
  gi|119719897|ref|YP_920392.1|  66 EVKSLREGQGKLWEEVKALREDQRRLWEEVKALRENQEKLWEEVRA 111
                                    4566666666777777777777777777777777777777666654 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.042
                        DUF4446  38 kdgksleellkekleeveelkeeseelekeieeleeklkkslqkvgl 84 
                                    + +++l e +++  eev++l+e++e+l +e+++l+e ++k  ++v+ 
  gi|119719897|ref|YP_920392.1| 135 EGQEKLWEEVRKLWEEVKALRENQEKLWEEVKALREGQEKLWEEVKA 181
                                    35678888999999999999999999999999999999888877765 PP

  == domain 4  score: 5.1 bits;  conditional E-value: 0.088
                        DUF4446  41 ksleellkekleeveelkeeseelekeieelee 73 
                                    k l e  ++  eev++l+e +e+l +e+++l+e
  gi|119719897|ref|YP_920392.1| 152 KALRENQEKLWEEVKALREGQEKLWEEVKALRE 184
                                    223333333333333333333333333333333 PP

>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   9.8      0.15        37      23     119 ..      89     178 ..      31     230 .. 0.47

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.15
                     V_ATPase_I  23 rkfvkevrrcdemerklrfleeeieklekavikeeeaeesleapeekeldeleeelekleeelkelnenleklkkelnel 102
                                    r+  +ev+ + e ++kl    + +++ + +         + +++  +e++ l e  ekl ee+++l e+ ++l++++++l
  gi|119719897|ref|YP_920392.1|  89 RRLWEEVKALRENQEKLWEEVRALREDQGK-------LWEGQQRLWEEVKALREGQEKLWEEVRKLWEEVKALRENQEKL 161
                                    222222222222222222211222221222.......2222223333333334444444444444444444444444444 PP

                     V_ATPase_I 103 velkavlekakefleee 119
                                     e+ + l++ +e l ee
  gi|119719897|ref|YP_920392.1| 162 WEEVKALREGQEKLWEE 178
                                    44444444444333333 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6  12.1     0.019       4.5      23     137 ..      34     145 ..      32     148 .. 0.88
   2 ?    8.6  10.7    0.0045       1.1      29     122 ..     124     214 ..     120     221 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.019
                            GAS  23 nNLelIkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelk 102
                                    + Le+ +   +ei  l++ +e+  ++ +++ +e k+l+e   k+ eev+ Lr++ ++  +   + k+l+++ ++l +e++
  gi|119719897|ref|YP_920392.1|  34 DLLEKMDATLNEIRALREGQEQLWRNQEKLWEEVKSLREGQGKLWEEVKALREDQRRLWE---EVKALRENQEKLWEEVR 110
                                    6788888888999**************************************987766655...66677778888899*** PP

                            GAS 103 dlkwehevleqrfekvekerdelykkfeaaiqevq 137
                                    +l++++  l +  +++ +e ++l++ +e+  +ev+
  gi|119719897|ref|YP_920392.1| 111 ALREDQGKLWEGQQRLWEEVKALREGQEKLWEEVR 145
                                    **************************999999986 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0045
                            GAS  29 kslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkweh 108
                                    ++l ee++ l++ +e+   e+ ++ +e k l+e+ +k+ eev+ Lr+    +ek  ++ k+l+++  +l ke+k+l++e+
  gi|119719897|ref|YP_920392.1| 124 QRLWEEVKALREGQEKLWEEVRKLWEEVKALRENQEKLWEEVKALRE---GQEKLWEEVKALREEQGKLWKEVKSLREEQ 200
                                    67889999999999999999999999999999999999999999996...567777888999999999999********* PP

                            GAS 109 evleqrfekveker 122
                                     +l  ++++ e+  
  gi|119719897|ref|YP_920392.1| 201 GILARKMDSFERRL 214
                                    99999999988865 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   6.0      0.27        64     106     158 ..      52     107 ..      30     135 .. 0.40
   2 ?    7.7   3.0      0.01       2.4      10      60 ..     138     188 ..     121     209 .. 0.65

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.27
                        DUF4795 106 eqeealkkaldtLqeelkekld.....rlelepLkeqleerlkelqkelqeamekedk 158
                                    +qe+ ++   ++L ee+k+  +       e++ L+e   + ++e++ +l+e  ek+ +
  gi|119719897|ref|YP_920392.1|  52 GQEQLWRN-QEKLWEEVKSLREgqgklWEEVKALREDQRRLWEEVK-ALRENQEKLWE 107
                                    44444432.2333333333333333333333333333333333332.22222222222 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.01
                        DUF4795  10 kklqeaieklqeelekleekvkelekrledkekklealkkqieelekvkad 60 
                                    +kl e+++kl ee++ l e +++l ++ +++++  e l++++++l+++ ++
  gi|119719897|ref|YP_920392.1| 138 EKLWEEVRKLWEEVKALRENQEKLWEEVKALREGQEKLWEEVKALREEQGK 188
                                    444466666666666666666666666666666666666666666666544 PP

>> Ntox28  Bacterial toxin 28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.9      0.17        39      47      85 ..      43      82 ..      34     101 .. 0.75
   2 ?    2.0   0.9         1   2.4e+02      45      74 ..     104     133 ..      71     138 .. 0.52
   3 ?    3.6   2.3      0.31        75      30      75 ..     112     155 ..      85     161 .. 0.54
   4 ?    4.7   2.6      0.15        35      46      79 ..     140     173 ..     110     196 .. 0.54
   5 ?   -0.2   0.0       4.9   1.2e+03      43      67 ..     186     210 ..     176     217 .. 0.58

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.17
                         Ntox28 47 ydHvkeltdaqkGLenvrralekelenppdsdteR.evLe 85
                                    + ++ l++ q+ L + +++l++e++ +++++ +  e+++
  gi|119719897|ref|YP_920392.1| 43 LNEIRALREGQEQLWRNQEKLWEEVKSLREGQGKLwEEVK 82
                                   578999*********************9999887643333 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 1
                         Ntox28  45 tpydHvkeltdaqkGLenvrralekelenp 74 
                                      ++ v+ l++ q  L + ++ l++e++ +
  gi|119719897|ref|YP_920392.1| 104 KLWEEVRALREDQGKLWEGQQRLWEEVKAL 133
                                    345555555555555555555555555555 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.31
                         Ntox28  30 rRelqGevvarkPDGtpydHvkeltdaqkGLenvrralekelenpp 75 
                                    +Re qG+    +     ++ vk l++ q+ L +  r+l++e++ ++
  gi|119719897|ref|YP_920392.1| 112 LREDQGKLWEGQ--QRLWEEVKALREGQEKLWEEVRKLWEEVKALR 155
                                    333333333222..23455555555555555555555555555444 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.15
                         Ntox28  46 pydHvkeltdaqkGLenvrralekelenppdsdt 79 
                                     ++ v+ l +  k L + +++l++e++ +++++ 
  gi|119719897|ref|YP_920392.1| 140 LWEEVRKLWEEVKALRENQEKLWEEVKALREGQE 173
                                    3555555555555555555555555555555443 PP

  == domain 5  score: -0.2 bits;  conditional E-value: 4.9
                         Ntox28  43 DGtpydHvkeltdaqkGLenvrral 67 
                                     G  +  vk l++ q  L +  + +
  gi|119719897|ref|YP_920392.1| 186 QGKLWKEVKSLREEQGILARKMDSF 210
                                    4666666666666665555555555 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.2       1.1   2.5e+02      27      54 ..      35      66 ..      30      90 .. 0.48
   2 ?    3.5   1.4       0.5   1.2e+02      24      73 ..      67     116 ..      51     140 .. 0.62
   3 ?    5.6   1.7      0.11        26      33      70 ..     139     183 ..     124     212 .. 0.47

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 1.1
                   Occludin_ELL 27 lhaeleevskkfseLerelkelkegsk....e 54
                                   l ++++++ ++++ L++  ++l ++++    e
  gi|119719897|ref|YP_920392.1| 35 LLEKMDATLNEIRALREGQEQLWRNQEklweE 66
                                   55555555555555554444444444322211 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.5
                   Occludin_ELL  24 YkelhaeleevskkfseLerelkelkegskeykkieeeilqeykklkkdp 73 
                                     k+l +   +++++++ L+++ ++l e+ k  ++ +e++++e + l++d+
  gi|119719897|ref|YP_920392.1|  67 VKSLREGQGKLWEEVKALREDQRRLWEEVKALRENQEKLWEEVRALREDQ 116
                                    55555566666666666666666666666666666666666666655533 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.11
                   Occludin_ELL  33 evskkfseLerelkelkegsk.......eykkieeeilqeykklk 70 
                                    ++++++++L +e+k+l+e+++         ++ +e++++e k l+
  gi|119719897|ref|YP_920392.1| 139 KLWEEVRKLWEEVKALRENQEklweevkALREGQEKLWEEVKALR 183
                                    444444444444444444433222211033333444444444333 PP

>> DUF4618  Domain of unknown function (DUF4618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   3.3      0.12        28      42     109 ..      34     100 ..      29     114 .. 0.51
   2 ?    7.1   1.0     0.013       3.2     188     226 ..     123     161 ..     110     167 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.12
                        DUF4618  42 klLqqyeklktvisileksskkqleqakaeLqeweekeekklekLeqqleqlnakvqklqeelnvLst 109
                                    +lL++ +   + i  l +  ++ql + +++L e  + + +   kL +++++l +  + l ee++ L+ 
  gi|119719897|ref|YP_920392.1|  34 DLLEKMDATLNEIRALRE-GQEQLWRNQEKLWEEVKSLREGQGKLWEEVKALREDQRRLWEEVKALRE 100
                                    555555555555555533.3444555555555555555555555555555555555555555555543 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.013
                        DUF4618 188 nqvlkkeiekfrefieeleeeipeLkaeveqLqaqaeep 226
                                    +q+l +e++  re  e+l ee+ +L +ev++L++++e+ 
  gi|119719897|ref|YP_920392.1| 123 QQRLWEEVKALREGQEKLWEEVRKLWEEVKALRENQEKL 161
                                    355668999999999999999999999999999887755 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.2      0.29        69       7      40 ..      37      70 ..      33      72 .. 0.87
   2 ?    1.4   0.1       1.8   4.2e+02      11      33 ..      90     112 ..      75     119 .. 0.63
   3 ?    4.2   0.1      0.25        59      15      40 ..     129     154 ..     124     165 .. 0.85
   4 ?    3.2   1.2      0.48   1.1e+02       7      35 ..     142     170 ..     138     217 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.29
                      FlaC_arch  7 nklsklsteletvkkeneelsksveelkenVkdl 40
                                   +k++ +  e+  +++ +e+l  + e+l e+Vk l
  gi|119719897|ref|YP_920392.1| 37 EKMDATLNEIRALREGQEQLWRNQEKLWEEVKSL 70
                                   67777778999*******************9976 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 1.8
                      FlaC_arch  11 klsteletvkkeneelsksveel 33 
                                    +l  e++ +++++e+l ++v  l
  gi|119719897|ref|YP_920392.1|  90 RLWEEVKALRENQEKLWEEVRAL 112
                                    44446666677777776666665 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.25
                      FlaC_arch  15 eletvkkeneelsksveelkenVkdl 40 
                                    e++ +++ +e+l ++v +l e+Vk l
  gi|119719897|ref|YP_920392.1| 129 EVKALREGQEKLWEEVRKLWEEVKAL 154
                                    78889999999999999999999876 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.48
                      FlaC_arch   7 nklsklsteletvkkeneelsksveelke 35 
                                    +++ kl  e++ +++++e+l ++v+ l e
  gi|119719897|ref|YP_920392.1| 142 EEVRKLWEEVKALRENQEKLWEEVKALRE 170
                                    56666667777777777777777766654 PP

>> DUF1394  Protein of unknown function (DUF1394)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.4     0.086        21      16      87 ..      61     130 ..      53     140 .. 0.77
   2 ?    4.1   1.0     0.096        23      15      69 ..     144     196 ..     140     202 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.086
                        DUF1394  16 revyeeveevlkeaeeileelksYkgaeeeireaisnpsdeeaqekawkavlplvaklkefyefssklekvv 87 
                                    ++++eev+++ + + ++ ee+k+ ++ ++ + e +++ +  e+qek w+ v  l + + + +e  ++l ++v
  gi|119719897|ref|YP_920392.1|  61 EKLWEEVKSLREGQGKLWEEVKALREDQRRLWEEVKALR--ENQEKLWEEVRALREDQGKLWEGQQRLWEEV 130
                                    578888888888888888888888888888888888877..8888888888887777777776666665555 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.096
                        DUF1394  15 ErevyeeveevlkeaeeileelksYkgaeeeireaisnpsdeeaqekawkavlpl 69 
                                     r+++eev+++ +++e++ ee+k+ ++ +e++ e +++ +  e+q k wk v +l
  gi|119719897|ref|YP_920392.1| 144 VRKLWEEVKALRENQEKLWEEVKALREGQEKLWEEVKALR--EEQGKLWKEVKSL 196
                                    5789999999999999999999999999999999999888..7888889888665 PP

>> UPF0449  Uncharacterised protein family UPF0449
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   8.7       2.4   5.6e+02      43      99 ..      88     144 ..      18     153 .. 0.71
   2 ?    6.9   4.3     0.035       8.4      51     100 ..     131     180 ..     111     187 .. 0.74
   3 ?    6.1   2.0     0.065        15      51      97 ..     152     198 ..     144     201 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 2.4
                        UPF0449  43 kkassseeedleaeveelYeqvrtylelnerLeeakeeLkqkceeLktageeLeeei 99 
                                    + +  +e ++l++++e+l+e+vr++ e + +L e +++L ++++ L+   e+L ee+
  gi|119719897|ref|YP_920392.1|  88 QRRLWEEVKALRENQEKLWEEVRALREDQGKLWEGQQRLWEEVKALREGQEKLWEEV 144
                                    333333445555666666666666666666666666666666666666666666555 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.035
                        UPF0449  51 edleaeveelYeqvrtylelnerLeeakeeLkqkceeLktageeLeeeie 100
                                    ++l++ +e+l+e+vr++ e  + L+e++e+L ++++ L+   e+L ee++
  gi|119719897|ref|YP_920392.1| 131 KALREGQEKLWEEVRKLWEEVKALRENQEKLWEEVKALREGQEKLWEEVK 180
                                    44555578888888888888888888888888888888888888777765 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.065
                        UPF0449  51 edleaeveelYeqvrtylelnerLeeakeeLkqkceeLktageeLee 97 
                                    ++l++++e+l+e+v+++ e +e+L e+ + L+++  +L +  ++L+e
  gi|119719897|ref|YP_920392.1| 152 KALRENQEKLWEEVKALREGQEKLWEEVKALREEQGKLWKEVKSLRE 198
                                    45677899999999999999999999999999999999999888876 PP

>> ERM  Ezrin/radixin/moesin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9  11.2      0.17        40      41     110 ..      45     114 ..      33     118 .. 0.50
   2 ?    6.4  16.5     0.028       6.8      20     111 ..     108     199 ..     104     227 .. 0.53

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.17
                            ERM  41 karraeeeaelLeqkaaeaeeeiqrlkesaekeeeekeklerklreaeleaarleeeserkeeeaerLke 110
                                    + r ++e +e+L ++++++ ee + l+e + k  ee ++l ++ r+  +e++ l+e++e+  ee++ L+e
  gi|119719897|ref|YP_920392.1|  45 EIRALREGQEQLWRNQEKLWEEVKSLREGQGKLWEEVKALREDQRRLWEEVKALRENQEKLWEEVRALRE 114
                                    3344455555555555555555555555555555555555555555555555555555555555555554 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.028
                            ERM  20 eaekaqeaLreseetaelLaekarraeeeaelLeqkaaeaeeeiqrlkesaekeeeekeklerklreaeleaarleeese 99 
                                    e+++ +e+  +  e  ++L e+ + ++e +e+L ++ +++ ee ++l+e++ek  ee ++l +  ++  +e++ l+ee+ 
  gi|119719897|ref|YP_920392.1| 108 EVRALREDQGKLWEGQQRLWEEVKALREGQEKLWEEVRKLWEEVKALRENQEKLWEEVKALREGQEKLWEEVKALREEQG 187
                                    34444444444444445555555555555555555555555555555555555555555555555555555555555555 PP

                            ERM 100 rkeeeaerLkee 111
                                    +  +e++ L+ee
  gi|119719897|ref|YP_920392.1| 188 KLWKEVKSLREE 199
                                    555555555554 PP

>> TSNAXIP1_N  Translin-associated factor X-interacting N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.3      0.15        36      50     111 .]       8      71 ..       6      71 .. 0.81
   2 ?    7.3   2.4     0.025       5.9      55     111 .]      46      99 ..      29     113 .. 0.68
   3 ?    6.0   2.2     0.064        15      67     111 .]     125     169 ..     103     169 .. 0.78
   4 ?    1.1   0.6       2.1     5e+02      87     111 .]     172     197 ..     158     197 .. 0.61

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.15
                     TSNAXIP1_N  50 EYelyiahllesqreaqylkakl...ktlsessdkraleleekreelralekeskalleeidklr 111
                                    E+e  +++l+e  re++y  a l   + l e+ d + +e++  re  ++l +++++l ee++ lr
  gi|119719897|ref|YP_920392.1|   8 EWERLVKALEE-DRELRYALAGLlgfRDLLEKMDATLNEIRALREGQEQLWRNQEKLWEEVKSLR 71 
                                    67777777665.56888885555499888899999999**********************99997 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.025
                     TSNAXIP1_N  55 iahllesqreaqylkaklktlsessdkraleleekreelralekeskalleeidklr 111
                                    i +l+e+q+++   ++kl++  +s  + + +l e+   ++al++++++l ee++ lr
  gi|119719897|ref|YP_920392.1|  46 IRALREGQEQLWRNQEKLWEEVKSLREGQGKLWEE---VKALREDQRRLWEEVKALR 99 
                                    67788888888888888866666666555455444...6666666666666666554 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.064
                     TSNAXIP1_N  67 ylkaklktlsessdkraleleekreelralekeskalleeidklr 111
                                     l +++k l e ++k   e+++  ee++al++++++l ee++ lr
  gi|119719897|ref|YP_920392.1| 125 RLWEEVKALREGQEKLWEEVRKLWEEVKALRENQEKLWEEVKALR 169
                                    335667888888888888999999999999999999999998887 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 2.1
                     TSNAXIP1_N  87 eek.reelralekeskalleeidklr 111
                                    +ek  ee++al++e+ +l +e++ lr
  gi|119719897|ref|YP_920392.1| 172 QEKlWEEVKALREEQGKLWKEVKSLR 197
                                    44455677777777777777777765 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   1.6      0.01       2.5     128     192 ..      47     114 ..      42     124 .. 0.79
   2 ?    1.8   2.8      0.63   1.5e+02     137     176 ..     154     193 ..     120     218 .. 0.54

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.01
                         AAA_27 128 erLreGGealleaegelgqlLfeasaGlaslrevleaLeaeadelfkprkskk...rainealeelee 192
                                    ++LreG e+l +++++l + + + + G  +l e ++aL++++++l+++ k+ +   ++++e+ ++l+e
  gi|119719897|ref|YP_920392.1|  47 RALREGQEQLWRNQEKLWEEVKSLREGQGKLWEEVKALREDQRRLWEEVKALRenqEKLWEEVRALRE 114
                                    579*******************************************9987666111334444443333 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.63
                         AAA_27 137 lleaegelgqlLfeasaGlaslrevleaLeaeadelfkpr 176
                                    l e++++l + + + + G ++l e ++aL++e+ +l+k+ 
  gi|119719897|ref|YP_920392.1| 154 LRENQEKLWEEVKALREGQEKLWEEVKALREEQGKLWKEV 193
                                    2233333333333333444444444455555555555544 PP

>> Taxilin  Myosin-like coiled-coil protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   8.1    0.0039      0.93      28     103 ..      33     108 ..      10     121 .. 0.93
   2 ?    1.8  10.4      0.45   1.1e+02      20     104 ..     109     193 ..     105     199 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0039
                        Taxilin  28 aelleerkrlqkqlkklkkkleqlqkekeqlqaelskaalaksKLekLcRelqkqnkklkeeskqrareeeekrke 103
                                     +lle++  +  ++++l++ +eql +++e+l +e +     + KL +  + l + +++l+ee k++ +++e+  +e
  gi|119719897|ref|YP_920392.1|  33 RDLLEKMDATLNEIRALREGQEQLWRNQEKLWEEVKSLREGQGKLWEEVKALREDQRRLWEEVKALRENQEKLWEE 108
                                    689**************************************************************99999876655 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.45
                        Taxilin  20 leaLvkkyaelleerkrlqkqlkklkkkleqlqkekeqlqaelskaalaksKLekLcRelqkqnkklkeeskqrareeee 99 
                                    + aL +   +l e ++rl +++k+l++ +e+l +e  +l +e +     ++KL +  + l + ++kl+ee k++ +e+ +
  gi|119719897|ref|YP_920392.1| 109 VRALREDQGKLWEGQQRLWEEVKALREGQEKLWEEVRKLWEEVKALRENQEKLWEEVKALREGQEKLWEEVKALREEQGK 188
                                    56677777778888888888999999999999999999999999988888888888999999999999999988888766 PP

                        Taxilin 100 krkel 104
                                      ke+
  gi|119719897|ref|YP_920392.1| 189 LWKEV 193
                                    66655 PP

>> LURAP  Leucine rich adaptor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.2       2.3   5.5e+02      24      59 ..      77     116 ..      47     138 .. 0.53
   2 ?    7.5   2.4     0.016       3.7      12      79 ..     135     206 ..     127     213 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 2.3
                          LURAP  24 lklelanlraidvkllqqllainegi....eavkWlleek 59 
                                    l  e+  lr    +l + + a++e      e v+ l e++
  gi|119719897|ref|YP_920392.1|  77 LWEEVKALREDQRRLWEEVKALRENQeklwEEVRALREDQ 116
                                    4444444444444444444444443211112333333333 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.016
                          LURAP  12 selkrleeklrklklelanlraidvkllqqllainegie....avkWlleekgtltsrcssltsslysldes 79 
                                     ++++l e +rkl  e+  lr    kl + + a++eg e     vk l ee+g+l  + +sl   +  l  +
  gi|119719897|ref|YP_920392.1| 135 EGQEKLWEEVRKLWEEVKALRENQEKLWEEVKALREGQEklweEVKALREEQGKLWKEVKSLREEQGILARK 206
                                    567889999****************************7522227999*******999999998888777554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1375  (0.0766914); expected 358.6 (0.02)
Passed bias filter:                      647  (0.0360868); expected 358.6 (0.02)
Passed Vit filter:                       182  (0.0101512); expected 17.9 (0.001)
Passed Fwd filter:                       117  (0.00652574); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              75  [number of targets reported over threshold]
# CPU time: 1.58u 0.37s 00:00:01.95 Elapsed: 00:00:00.58
# Mc/sec: 1739.22
//
Query:       gi|119719898|ref|YP_920393.1|  [L=114]
Description: hypothetical protein Tpen_0990 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-34  117.1   4.6    5.4e-34  117.0   4.6    1.0  1  YbjQ_1    Putative heavy-metal-binding
  ------ inclusion threshold ------
      0.023   15.0   0.2       0.08   13.3   0.1    1.9  2  DUF4156   Domain of unknown function (DUF4156)


Domain annotation for each model (and alignments):
>> YbjQ_1  Putative heavy-metal-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.0   4.6     6e-38   5.4e-34       1     104 []       6     108 ..       6     108 .. 0.99

  Alignments for each domain:
  == domain 1  score: 117.0 bits;  conditional E-value: 6e-38
                         YbjQ_1   1 mivtttesiegkeivevlgivtgetvrsrnvlkdilaglrslvGGelkayeeeleeareeAlerlkeeAeelGAnAvvgv 80 
                                    +i++tt+s++g+++v+vlgivtg  vr+r vl +++a+++ lvGG+ +ay eel++ar+eAl+++++eA++lGAnAv+gv
  gi|119719898|ref|YP_920393.1|   6 VIISTTHSVPGYRVVKVLGIVTGMRVRTRGVLGRLAASVEALVGGRGEAYIEELKKARDEALQDMVAEASKLGANAVIGV 85 
                                    699***************************************************************************** PP

                         YbjQ_1  81 rldtseigekgmlevlayGTAVkv 104
                                    +++tsei e g+++v+a+GTAV++
  gi|119719898|ref|YP_920393.1|  86 NFETSEILE-GFIVVTATGTAVVI 108
                                    *******99.************86 PP

>> DUF4156  Domain of unknown function (DUF4156)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.12   1.1e+03       7      33 ..       3      32 ..       1      46 [. 0.65
   2 ?   13.3   0.1   8.9e-06      0.08      40      71 ..      57      88 ..      36     107 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.12
                        DUF4156  7 geaVki..vdskpa.seCqllGevtgsqgn 33
                                   +e+V i  ++s p+ +  + lG vtg ++ 
  gi|119719898|ref|YP_920393.1|  3 AEHVIIstTHSVPGyRVVKVLGIVTGMRVR 32
                                   555555223444555566789999998765 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 8.9e-06
                        DUF4156 40 tsnkelvrgaandLrneAaalGgntivlvtst 71
                                   ++ k+   +a++d+  eA++lG+n +++v+ +
  gi|119719898|ref|YP_920393.1| 57 EELKKARDEALQDMVAEASKLGANAVIGVNFE 88
                                   44566677899****************99866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 742.72
//
Query:       gi|119719899|ref|YP_920394.1|  [L=111]
Description: DNA polymerase beta subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-11   43.7   0.0    2.8e-11   43.5   0.0    1.2  1  NTP_transf_2    Nucleotidyltransferase domain
    1.4e-05   25.1   0.0    1.5e-05   25.0   0.0    1.2  1  Polbeta         Polymerase beta, Nucleotidyltransferase
    0.00037   20.7   0.0    0.00043   20.5   0.0    1.1  1  DNA_pol_B_palm  DNA polymerase beta palm
  ------ inclusion threshold ------
      0.032   14.0   0.2      0.054   13.3   0.2    1.3  1  MdcG            Phosphoribosyl-dephospho-CoA transferase MdcG
        0.2   11.5   0.0        0.2   11.5   0.0    1.1  1  Adenyl_cycl_N   Adenylate cyclase NT domain


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.5   0.0   7.8e-15   2.8e-11       4      70 ..      22      84 ..      19     108 .. 0.77

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 7.8e-15
                                   HHHHHHHHTTTSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEE CS
                   NTP_transf_2  4 lleelkelepvakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellgle 70
                                   ++++ k+l+p+a+v+++GS+a G a+  SDiD+lvvl++  +++    +++  a i +  +e   l+
  gi|119719899|ref|YP_920394.1| 22 VAKAAKDLRPDAEVYVVGSVAEGRATVLSDIDILVVLEKAGNED----RKYLPADIVDRAVEKYSLP 84
                                   67999***********************************8764....4444444444444444444 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   4.2e-09   1.5e-05      16      57 ..      35      75 ..      20      98 .. 0.79

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 4.2e-09
                                   TTEEEEEE-S------EEEEEEEESS---HHHHHHHHHHHHH CS
                        Polbeta 16 aylFGSrakgkareeSDiDlavllkekldleeelelaaeled 57
                                   +y+ GS+a+g+a+  SDiD+ v+l++    e++  l a++ d
  gi|119719899|ref|YP_920394.1| 35 VYVVGSVAEGRATVLSDIDILVVLEKA-GNEDRKYLPADIVD 75
                                   89***********************99.44444445555444 PP

>> DNA_pol_B_palm  DNA polymerase beta palm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   1.2e-07   0.00043       9      68 ..      17      79 ..      13     109 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.2e-07
                                   HHHHHHHHHHHHH-TT-EEEE-HHHHTT-SEE.SSEEEEEEBTTBSTTSS-..-HHHHHHHHH CS
                 DNA_pol_B_palm  9 alealvkkaakeldpevevivcGSYRRgaess.GDvDvlitkkdakseskk..lkklleklvk 68
                                   + +++v kaak+l p++ev+v+GS   g+++   D+D+l+  ++a +e++k    +++++ v+
  gi|119719899|ref|YP_920394.1| 17 EYAEAVAKAAKDLRPDAEVYVVGSVAEGRATVlSDIDILVVLEKAGNEDRKylPADIVDRAVE 79
                                   67899**********************9887549*****998888775322113355555554 PP

>> MdcG  Phosphoribosyl-dephospho-CoA transferase MdcG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   1.5e-05     0.054      89     188 ..      13     109 ..       6     110 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.5e-05
                           MdcG  89 laaraalaalaallaal..glawgvyGSlgwqlatglpylhesSDLDLlirvasalqlarlldllaaleaaa....vrlD 162
                                     ++r+ ++a+a+++++l  ++++ v+GS++   at l      SD+D+l+ +++a + +r     + +++a     + +D
  gi|119719899|ref|YP_920394.1|  13 RRWREYAEAVAKAAKDLrpDAEVYVVGSVAEGRATVL------SDIDILVVLEKAGNEDRKYLPADIVDRAVekysLPVD 86 
                                    568888888888888555599********99998876......9********9999988876555555554334459999 PP

                           MdcG 163 geielpsggavalrElaaaaaqvlvK 188
                                    + +e+      + +Ela++a + ++K
  gi|119719899|ref|YP_920394.1|  87 APVEIHV---ASREELARWAGKAMIK 109
                                    9888876...4556666777666666 PP

>> Adenyl_cycl_N  Adenylate cyclase NT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   5.7e-05       0.2      74     126 ..      15      66 ..       3     106 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.7e-05
                  Adenyl_cycl_N  74 larsaeekekkekakeaaieglylmGStgsiaqsekSDlDiWvchrselsaee 126
                                      ++ae+  k++k +  +   +y++GS++    +  SD+Di v+ ++  ++++
  gi|119719899|ref|YP_920394.1|  15 WREYAEAVAKAAK-DLRPDAEVYVVGSVAEGRATVLSDIDILVVLEKAGNEDR 66 
                                    4444444444443.34455679********************99887655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 753.24
//
Query:       gi|119719900|ref|YP_920395.1|  [L=138]
Description: HEPN domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.1e-19   70.7   1.2    1.4e-19   70.4   1.2    1.1  1  HEPN       HEPN domain
  ------ inclusion threshold ------
       0.11   12.9   0.1       0.19   12.1   0.1    1.4  1  FlaC_arch  Flagella accessory protein C (FlaC)
       0.18   12.2   0.9       0.31   11.4   0.1    1.8  2  PLAC9      Placenta-specific protein 9
        4.8    7.5  10.7    4.2e+02    1.3  10.7    2.3  1  DUF4129    Domain of unknown function (DUF4129)


Domain annotation for each model (and alignments):
>> HEPN  HEPN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.4   1.2   3.1e-23   1.4e-19       2     117 ..       7     130 ..       6     131 .. 0.93

  Alignments for each domain:
  == domain 1  score: 70.4 bits;  conditional E-value: 3.1e-23
                                    HHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHTT--.SSCCHHHHHHCCHHHT............... CS
                           HEPN   2 eewlrrAeedleaAellleegdydlacfhaqqaaekalKAlllkkggeppkthdlreLleelkkelke............ 69 
                                     +++rrA ++l++A   l+++  dla+f  +qaa++++KA ll++ g+  ++h++reLl++l++el++            
  gi|119719900|ref|YP_920395.1|   7 ARLKRRALDFLDEA---LSAKNADLAAFFLEQAAQLYVKATLLELVGRETRGHGVRELLGLLARELESygfgeaagrilg 83 
                                    57899999999987...899999*******************************************99999999999999 PP

                                    .-HHHHHHHHHHHCCCHHCCCTSS--S--HHHHHHHHHHHHHHHHHHHH CS
                           HEPN  70 .seelreeleeLekayiesrYpdakeeyteedaeealkdaeevlelvee 117
                                      +  r+el  Le+ay+ srY++a++  + +d+e++  +++ +++l++e
  gi|119719900|ref|YP_920395.1|  84 fVDGRRRELVLLEEAYTASRYGEAEY--SAKDVERLAATVKDLIKLLDE 130
                                    999999999****************9..***************998765 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   4.3e-05      0.19      24      51 ..     108     135 ..     101     136 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.3e-05
                      FlaC_arch  24 eelsksveelkenVkdllsLYEvVsnqv 51 
                                    e   k+ve+l  +Vkdl++L + V++ v
  gi|119719900|ref|YP_920395.1| 108 EYSAKDVERLAATVKDLIKLLDEVAENV 135
                                    66789***************99999865 PP

>> PLAC9  Placenta-specific protein 9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       1.1   4.9e+03      41      50 ..      57      66 ..      43      74 .. 0.59
   2 ?   11.4   0.1     7e-05      0.31      34      60 ..     110     136 ..     106     138 .] 0.88

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.1
                          PLAC9 41 leaevkGllg 50
                                      e+ Gll+
  gi|119719900|ref|YP_920395.1| 57 GVRELLGLLA 66
                                   3344444443 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 7e-05
                          PLAC9  34 vektvehleaevkGllgqleelawnlP 60 
                                      k ve l a vk l+ +l+e+a n+ 
  gi|119719900|ref|YP_920395.1| 110 SAKDVERLAATVKDLIKLLDEVAENVK 136
                                    5799*******************9975 PP

>> DUF4129  Domain of unknown function (DUF4129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3  10.7     0.093   4.2e+02      34      66 ..      71     119 ..       2     122 .. 0.67

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.093
                        DUF4129  34 s................paaalaalaelfeearYGgrpasaeeyrrlve 66 
                                    s                 +++l  l e++++ rYG  + sa +++rl +
  gi|119719900|ref|YP_920395.1|  71 SygfgeaagrilgfvdgRRRELVLLEEAYTASRYGEAEYSAKDVERLAA 119
                                    233333333333333334457777999*******************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.52
# Mc/sec: 805.18
//
Query:       gi|119719901|ref|YP_920396.1|  [L=155]
Description: hypothetical protein Tpen_0993 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 1037.95
//
Query:       gi|119719902|ref|YP_920397.1|  [L=71]
Description: hypothetical protein Tpen_0994 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 499.55
//
Query:       gi|119719903|ref|YP_920398.1|  [L=121]
Description: hypothetical protein Tpen_0995 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.1e-14   52.4   0.0    6.1e-14   52.1   0.0    1.0  1  Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor


Domain annotation for each model (and alignments):
>> Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.1   0.0   3.4e-18   6.1e-14       3      93 ..      26     117 ..      24     118 .. 0.93

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 3.4e-18
                                    SCB-STCCC-SEEEEEEESSSCEEEEEEEE.GCCCTSSCSSTHHHHHHHHTT-SEEEESSSCHHHHHHHCTTTSEEEES. CS
                  Nitro_FeMo-Co   3 srvdqhFGrapyFaiyeveegevkivenrveeaadaegggggklaqllaeegvdvvivgkiGpralakleaagievykg. 81 
                                      v+++F+r+p+++i+++ +g+++ ve   +++a+++gg g ++ q+l ++gv+vv++ + Gp+  + l +ag++v ++ 
  gi|119719903|ref|YP_920398.1|  26 APVSARFARTPFLTIVDIVDGRATRVEPMPNAFASGAGGVGAAVGQWLLSSGVSVVVAPSLGPNISMILGQAGVRVEVVp 105
                                    679****************9977766666799***********************************************9 PP

                                    -SSBHHHHHHHH CS
                  Nitro_FeMo-Co  82 aggtveealkev 93 
                                    +g ++ ealk++
  gi|119719903|ref|YP_920398.1| 106 PGVPLGEALKRL 117
                                    *********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 970.09
//
Query:       gi|119719904|ref|YP_920399.1|  [L=288]
Description: cobyrinic acid a,c-diamide synthase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.2e-16   59.6   0.0    4.7e-16   59.0   0.0    1.2  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    5.6e-14   51.3  12.2    6.8e-07   28.8   3.4    2.5  2  Fer4         4Fe-4S binding domain
    5.2e-12   45.7   0.0    3.4e-06   26.7   0.0    3.0  2  ParA         NUBPL iron-transfer P-loop NTPase
    1.7e-07   31.3   0.0      0.004   17.1   0.0    2.1  2  AAA_31       AAA domain
    2.8e-07   31.0   8.6    5.7e-07   30.0   8.6    1.5  1  Fer4_7       4Fe-4S dicluster domain
    1.4e-06   28.1  11.8     0.0048   16.9   0.9    2.5  2  Fer4_6       4Fe-4S binding domain
    2.8e-06   28.2   4.6      0.021   15.8   2.0    2.3  2  Fer4_16      4Fe-4S double cluster binding domain
    1.2e-05   25.3   2.8    1.2e-05   25.3   2.8    1.7  2  Fer4_21      4Fe-4S dicluster domain
    1.7e-05   24.9   6.1    2.9e-05   24.2   6.1    1.4  1  Fer4_9       4Fe-4S dicluster domain
    9.1e-05   22.5   6.8     0.0076   16.3   8.8    2.4  2  Fer4_10      4Fe-4S dicluster domain
    0.00067   19.6  11.3      0.059   13.5   0.7    2.6  2  Fer4_2       4Fe-4S binding domain
     0.0044   17.7   5.1       0.33   11.7   0.1    2.7  2  Fer4_15      4Fe-4S single cluster domain
     0.0062   15.8   0.4      0.011   15.0   0.4    1.3  1  ArsA_ATPase  Anion-transporting ATPase
  ------ inclusion threshold ------
      0.044   13.3   0.1      0.097   12.2   0.1    1.5  1  GTP_EFTU     Elongation factor Tu GTP binding domain
      0.071   12.4   0.0       0.12   11.6   0.0    1.4  1  MipZ         ATPase MipZ
      0.075   12.5   0.0        3.4    7.0   0.0    2.3  2  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
      0.085   11.7   0.0       0.12   11.2   0.0    1.1  1  DUF2791      P-loop Domain of unknown function (DUF2791)
      0.099   12.1   0.1       0.15   11.5   0.1    1.2  1  PhoH         PhoH-like protein
       0.12   12.0   0.1       0.26   10.8   0.1    1.6  1  AAA_25       AAA domain
       0.13   11.4   0.0       0.19   10.9   0.0    1.1  1  PIF1         PIF1-like helicase
       0.26   11.7   7.8        3.3    8.2   2.5    2.5  2  Fer4_8       4Fe-4S dicluster domain
       0.85   10.2   6.9        9.1    6.9   1.6    2.3  3  Fer4_17      4Fe-4S dicluster domain
        4.9    7.8   7.8         28    5.4   0.1    2.8  2  Fer4_13      4Fe-4S single cluster domain of Ferredoxin I


Domain annotation for each model (and alignments):
>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.0   0.0     6e-19   4.7e-16       1     128 []       3     266 ..       3     266 .. 0.93

  Alignments for each domain:
  == domain 1  score: 59.0 bits;  conditional E-value: 6e-19
                                    EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH.HTTEB-HHHH......................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx......................... RF
                           CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlai.leglendiep......................... 54 
                                    +++as+kGG+GKT+++ nLa++l +rg  V + DaD++a+   + l    + ++                          
  gi|119719904|ref|YP_920399.1|   3 VVVASGKGGTGKTFFSSNLAVYLRDRGGCV-AADADVEAPDFLLaL---GGARRVlwreefrgvrrpvvdysacvkcwac 78 
                                    689**********************66655.67*******987532...222222456888889999************* PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                           CbiA  55 ................................................................................ 54 
                                                                                                                    
  gi|119719904|ref|YP_920399.1|  79 vdacqfnairrgpegpvvdydrceglgtcafvcpagaigfaeerageiyaaetehgvtvvtgdlelgggasgrlvyelke 158
                                    ******************************************************************************** PP

                                    ...............................................CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS. CS
                                    ...............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           CbiA  55 ...............................................dlkrllellealgkkkalllkiagvvlnrvdge 87 
                                                                                   ++ rlle++ al+ k       a  v+n++d +
  gi|119719904|ref|YP_920399.1| 159 rarrlssgaaryvvvdaapgigcpvvssvagadllvvvveptpqsakGAARLLEVAGALRVK-------AVAVVNKYDLN 231
                                    ************************************************************99.......9********99 PP

                                    ..-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHHTS-H CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           CbiA  88 neetllkealeelkqrygvpvlgviprdeavaeapargepv 128
                                        +    le ++   gv v g ip+deava+++a+ +p+
  gi|119719904|ref|YP_920399.1| 232 ---PSYAARLEGEL---GVDVAGRIPYDEAVARSYAEMKPL 266
                                    ...77888888887...*******************99875 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   3.4   8.7e-10   6.8e-07       1      24 []      65      88 ..      65      88 .. 0.96
   2 !   27.3   1.5   2.7e-09   2.1e-06       1      23 [.      94     116 ..      94     117 .. 0.96

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 8.7e-10
                                   EEEETTTSSS-THHHHHSTTTEEE CS
                           Fer4  1 vvideekCigCGaCvevCPvgAIt 24
                                   +v+d++ C++C aCv++C ++AI+
  gi|119719904|ref|YP_920399.1| 65 PVVDYSACVKCWACVDACQFNAIR 88
                                   69*********************6 PP

  == domain 2  score: 27.3 bits;  conditional E-value: 2.7e-09
                                    EEEETTTSSS-THHHHHSTTTEE CS
                           Fer4   1 vvideekCigCGaCvevCPvgAI 23 
                                    +v+d+++C g G+C+ vCP gAI
  gi|119719904|ref|YP_920399.1|  94 PVVDYDRCEGLGTCAFVCPAGAI 116
                                    69********************9 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0   4.3e-09   3.4e-06       6      51 ..       3      47 ..       1      86 [. 0.86
   2 !   12.6   0.0   8.5e-05     0.066     112     243 ..     168     284 ..     155     286 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 4.3e-09
                           ParA  6 iavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprll 51
                                   ++v+SgKGG GK+ +++nlA+ L+++g  v+  DaD+  p+    l
  gi|119719904|ref|YP_920399.1|  3 VVVASGKGGTGKTFFSSNLAVYLRDRGGCVA-ADADVEAPDFLLAL 47
                                   79*************************9998.69999988765555 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 8.5e-05
                           ParA 112 lDyLiiDlPPGtgDeqltvaqklplagaviVttpqevaladvkkaiemfkkvkvkvlGvveNmsgfvcpkcgekteifgk 191
                                      y+++D  PG g   ++ +   +    v+V  p   +++ + + +e++  ++vk ++vv+                 + 
  gi|119719904|ref|YP_920399.1| 168 ARYVVVDAAPGIGCPVVSSVAGAD--LLVVVVEPTPQSAKGAARLLEVAGALRVKAVAVVNKYDL-------------NP 232
                                    568899999999987777666664..566677777778889999999999999999999975432.............33 PP

                           ParA 192 gggeklaeelgvpllgeipldpeireasdegkplvlkepeseaakaleeiae 243
                                    + +++l  elgv++ g+ip d++++++  e kpl+++ p+s+aa+al ++++
  gi|119719904|ref|YP_920399.1| 233 SYAARLEGELGVDVAGRIPYDEAVARSYAEMKPLIVAYPSSKAARALLDVFS 284
                                    467889999*********************************9999988865 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.1   0.00016      0.13       4      31 ..       3      30 ..       1      40 [. 0.85
   2 !   17.1   0.0   5.2e-06     0.004     120     167 ..     170     217 ..     151     228 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00016
                         AAA_31  4 IaianqKGGvGKTTtsvnlaaalaklgk 31
                                   +++a  KGG GKT  s nla+ l  +g 
  gi|119719904|ref|YP_920399.1|  3 VVVASGKGGTGKTFFSSNLAVYLRDRGG 30
                                   568899*****************99886 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 5.2e-06
                         AAA_31 120 yiiiDcpPsLglltenaLvasdsviipvqaeayaleGleqllktieev 167
                                    y+++D+ P +g+ ++++++ +d ++++v++++ + +G+++ll+    +
  gi|119719904|ref|YP_920399.1| 170 YVVVDAAPGIGCPVVSSVAGADLLVVVVEPTPQSAKGAARLLEVAGAL 217
                                    8****************************************9987655 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   8.6   7.3e-10   5.7e-07       1      52 []      71     115 ..      71     115 .. 0.95

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 7.3e-10
                         Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                    +C++C aCv+aC  +ai+  +e    g   +++d+++C g g C+ vCP+ga
  gi|119719904|ref|YP_920399.1|  71 ACVKCWACVDACQFNAIRRGPE----G---PVVDYDRCEGLGTCAFVCPAGA 115
                                    5******************987....5...899*****************97 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   4.2   1.7e-05     0.013       2      24 .]      65      87 ..      64      87 .. 0.95
   2 !   16.9   0.9   6.1e-06    0.0048       2      24 .]      94     116 ..      94     116 .. 0.97

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.7e-05
                         Fer4_6  2 veidpdkCigCgdCvrvCPegai 24
                                   +++d+++C+ C +Cv++C ++ai
  gi|119719904|ref|YP_920399.1| 65 PVVDYSACVKCWACVDACQFNAI 87
                                   89****************99997 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 6.1e-06
                         Fer4_6   2 veidpdkCigCgdCvrvCPegai 24 
                                    +++d+d+C g g C+ vCP+gai
  gi|119719904|ref|YP_920399.1|  94 PVVDYDRCEGLGTCAFVCPAGAI 116
                                    79********************8 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   2.0   2.7e-05     0.021       2      31 ..      72     102 ..      71     104 .. 0.86
   2 !   14.7   0.1   5.7e-05     0.044       1      26 [.     100     125 ..     100     141 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.7e-05
                        Fer4_16   2 CgtCgkCaevCPtnaikek.kekeieareci 31 
                                    C++C +C+++C  nai+   + +++++++c+
  gi|119719904|ref|YP_920399.1|  72 CVKCWACVDACQFNAIRRGpEGPVVDYDRCE 102
                                    ****************976477888988885 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 5.7e-05
                        Fer4_16   1 rCgtCgkCaevCPtnaikekkekeie 26 
                                    rC + g Ca vCP++ai   +e+  e
  gi|119719904|ref|YP_920399.1| 100 RCEGLGTCAFVCPAGAIGFAEERAGE 125
                                    69999************988555444 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   2.8   1.5e-08   1.2e-05       2      57 ..      66     116 ..      65     118 .. 0.87
   2 ?   -2.8   0.0       9.1   7.1e+03      42      47 ..     179     184 ..     166     188 .. 0.56

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1.5e-08
                        Fer4_21   2 ridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedci 57 
                                    ++d + C++C  C+ aC+    +ai+  ++    v  d+C G   C+ vCP  ++i
  gi|119719904|ref|YP_920399.1|  66 VVDYSACVKCWACVDACQ---FNAIRRGPEGP-VVDYDRCEGLGTCAFVCPA-GAI 116
                                    68999*************...8***9876654.6789**************5.777 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 9.1
                        Fer4_21  42 vGCnlC 47 
                                    +GC + 
  gi|119719904|ref|YP_920399.1| 179 IGCPVV 184
                                    455443 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   6.1   3.7e-08   2.9e-05       1      51 []      71     116 ..      71     116 .. 0.95

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 3.7e-08
                         Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                    +C++C aCv+aC+++++++   +  + ++     +C g g+C+ +Cp gai
  gi|119719904|ref|YP_920399.1|  71 ACVKCWACVDACQFNAIRRGPEGPVVDYD-----RCEGLGTCAFVCPAGAI 116
                                    6*************************995.....5*************987 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   8.8   9.8e-06    0.0076       3      56 .]      66     112 ..      64     112 .. 0.91
   2 !   13.7   0.1   6.4e-05      0.05       3      24 ..      95     121 ..      93     140 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 9.8e-06
                        Fer4_10   3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                    v+d + C++C +Cv+aC       + ++++ + e   +++++C+g g C+ +CP
  gi|119719904|ref|YP_920399.1|  66 VVDYSACVKCWACVDAC-------QFNAIRRGPEGPVVDYDRCEGLGTCAFVCP 112
                                    7899*************.......568899999999999**************9 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 6.4e-05
                        Fer4_10   3 vidddtCirCgkCvkaCPadl.....t 24 
                                    v+d d+C + g+C  +CPa +     +
  gi|119719904|ref|YP_920399.1|  95 VVDYDRCEGLGTCAFVCPAGAigfaeE 121
                                    7899***************55444432 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   4.0   0.00096      0.75       2      20 ..      64      82 ..      63      84 .. 0.93
   2 !   13.5   0.7   7.6e-05     0.059       3      22 .]      94     113 ..      92     113 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00096
                         Fer4_2  2 pvvvdtdrCigCgaCvsaC 20
                                   ++vvd  +C+ C aCv+aC
  gi|119719904|ref|YP_920399.1| 64 RPVVDYSACVKCWACVDAC 82
                                   79***************** PP

  == domain 2  score: 13.5 bits;  conditional E-value: 7.6e-05
                         Fer4_2   3 vvvdtdrCigCgaCvsaCPa 22 
                                    +vvd drC g g+C  +CPa
  gi|119719904|ref|YP_920399.1|  94 PVVDYDRCEGLGTCAFVCPA 113
                                    899******99********8 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   1.3     0.013        10       2      19 ..      66      83 ..      66      92 .. 0.88
   2 !   11.7   0.1   0.00042      0.33       2      20 ..      95     113 ..      95     144 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.013
                        Fer4_15  2 vvDrdaCigcglCvaeap 19
                                   vvD +aC  c +Cv++++
  gi|119719904|ref|YP_920399.1| 66 VVDYSACVKCWACVDACQ 83
                                   69**************95 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00042
                        Fer4_15   2 vvDrdaCigcglCvaeape 20 
                                    vvD d+C+g g C+ ++p 
  gi|119719904|ref|YP_920399.1|  95 VVDYDRCEGLGTCAFVCPA 113
                                    69*************9974 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.4   1.4e-05     0.011       1      28 [.       1      28 [.       1      32 [. 0.90

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.4e-05
                                   -EEEEEEESTTSSHHHHHHHHHHHHHHT CS
                    ArsA_ATPase  1 lkvilvgGKGGVGKttvsaatavklsek 28
                                   ++v++ +GKGG GKt  s+ +av+l + 
  gi|119719904|ref|YP_920399.1|  1 MEVVVASGKGGTGKTFFSSNLAVYLRDR 28
                                   7899*******************99776 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00012     0.097      87     135 ..     183     231 ..     128     245 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00012
                                    HHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGST CS
                       GTP_EFTU  87 virglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrl 135
                                    v  +++ +D+ v+vv+ +        ++l++a +++v+ + ++NK D  
  gi|119719904|ref|YP_920399.1| 183 VVSSVAGADLLVVVVEPTPQSAKGAARLLEVAGALRVKAVAVVNKYDLN 231
                                    56788899***************************************86 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00016      0.12       3      34 ..       3      34 ..       1      59 [. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00016
                                   EEE--SSTTSSHHHHHHHHHHHHHTTT--EEE CS
                           MipZ  3 ivlgnekGGsGksttavhvavaLlkkGarvaa 34
                                   +v++  kGG+Gk+  +  +av L ++G  vaa
  gi|119719904|ref|YP_920399.1|  3 VVVASGKGGTGKTFFSSNLAVYLRDRGGCVAA 34
                                   89*************************99986 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0    0.0044       3.4       5      28 ..       6      29 ..       2      42 .. 0.87
   2 ?    3.0   0.0     0.076        59     174     235 ..     217     277 ..     200     285 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0044
                      Fer4_NifH  5 iyGkGGiGksttsqnlsaalaemg 28
                                     GkGG Gk++ s+nl+  l ++g
  gi|119719904|ref|YP_920399.1|  6 ASGKGGTGKTFFSSNLAVYLRDRG 29
                                   56***************9999887 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.076
                      Fer4_NifH 174 vrlgGl.iinsrkvddereliekfaeelgtkvlevvPrdeivrkaelrkktvieyapeseqak 235
                                    +r+  + ++n  k d +   + ++  elg++v   +P de v ++ ++ k +i   p+s+ a 
  gi|119719904|ref|YP_920399.1| 217 LRVKAVaVVN--KYDLNPSYAARLEGELGVDVAGRIPYDEAVARSYAEMKPLIVAYPSSKAAR 277
                                    4554441444..4677777788888899****************9999888877777776655 PP

>> DUF2791  P-loop Domain of unknown function (DUF2791)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00015      0.12      55     104 ..       7      57 ..       2      64 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00015
                        DUF2791  55 rGeYGsGKtFllqllreralerg.fvvaeadls.perrLhgtkgqlealYre 104
                                     G+ G+GKtF+ + l+ + ++rg +v+a+ad+  p+  L+  +g  + l+re
  gi|119719904|ref|YP_920399.1|   7 SGKGGTGKTFFSSNLAVYLRDRGgCVAADADVEaPDFLLA-LGGARRVLWRE 57 
                                    6889**************9998538999****96666554.77777776666 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00019      0.15      20      43 ..       2      25 ..       1      31 [. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00019
                                   SEEEEE--TTSSTTHHHHHHHHHH CS
                           PhoH 20 divfaiGpaGtGKtylavalavea 43
                                   ++v+a G+ GtGKt+++  lav +
  gi|119719904|ref|YP_920399.1|  2 EVVVASGKGGTGKTFFSSNLAVYL 25
                                   699***************999965 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00033      0.26      34      55 ..       2      23 ..       1      34 [. 0.90

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00033
                         AAA_25 34 elallaGapgtGKttlaldlal 55
                                   e+++  G +gtGKt++ ++la+
  gi|119719904|ref|YP_920399.1|  2 EVVVASGKGGTGKTFFSSNLAV 23
                                   688999**************98 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00024      0.19      27      57 ..       6      36 ..       2      49 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00024
                                   EEESTTSSCHHHHHHHHHHCHCTCCCEEEEE CS
                           PIF1 27 vtGsgGtgKtflwkallkklrsegkivlavA 57
                                    +G gGtgKtf+  +l  +lr +g  v+a A
  gi|119719904|ref|YP_920399.1|  6 ASGKGGTGKTFFSSNLAVYLRDRGGCVAADA 36
                                   68*********************99998866 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   2.5    0.0043       3.3       3      17 ..      70      84 ..      68      97 .. 0.79
   2 ?    6.1   0.2     0.019        15      49      64 ..      99     114 ..      92     115 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0043
                         Fer4_8  3 ekCieCgaCqsaCpv 17
                                   ++C++C aC +aC +
  gi|119719904|ref|YP_920399.1| 70 SACVKCWACVDACQF 84
                                   7899*****999964 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.019
                         Fer4_8  49 wsCttcgaCtevCpvg 64 
                                    ++C + g C+ vCp g
  gi|119719904|ref|YP_920399.1|  99 DRCEGLGTCAFVCPAG 114
                                    78************86 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   2.1     0.029        23      45      57 ..      71      83 ..      52      87 .. 0.70
   2 ?    6.9   1.6     0.012       9.1       1      19 [.      71      89 ..      71      99 .. 0.81
   3 ?    5.8   0.2     0.026        20      44      59 ..      99     114 ..      92     116 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.029
                        Fer4_17 45 lCieCgeCerkCP 57
                                    C++C  C+ +C 
  gi|119719904|ref|YP_920399.1| 71 ACVKCWACVDACQ 83
                                   4555555555553 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.012
                        Fer4_17  1 rCiqCgyClpeCpsyeayd 19
                                   +C +C +C+++C ++++++
  gi|119719904|ref|YP_920399.1| 71 ACVKCWACVDACQFNAIRR 89
                                   5999999999999887755 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.026
                        Fer4_17  44 slCieCgeCerkCPqg 59 
                                    ++C + g C+ +CP+g
  gi|119719904|ref|YP_920399.1|  99 DRCEGLGTCAFVCPAG 114
                                    799***********86 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   4.0      0.16   1.2e+02       1      16 [.      67      82 ..      67      84 .. 0.94
   2 ?    5.4   0.1     0.035        28       1      18 [.      96     113 ..      96     140 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.16
                        Fer4_13  1 VDrdtCiacgaCvela 16
                                   VD + C+ c aCv+++
  gi|119719904|ref|YP_920399.1| 67 VDYSACVKCWACVDAC 82
                                   8999**********99 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.035
                        Fer4_13   1 VDrdtCiacgaCvelaPd 18 
                                    VD d+C + g+C+ ++P 
  gi|119719904|ref|YP_920399.1|  96 VDYDRCEGLGTCAFVCPA 113
                                    899*************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2076.74
//
Query:       gi|119719905|ref|YP_920400.1|  [L=292]
Description: cobyrinic acid a,c-diamide synthase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-18   66.6   0.0    3.1e-18   66.0   0.0    1.2  1  CbiA          CobQ/CobB/MinD/ParA nucleotide binding domain
    1.7e-15   57.2   0.0    1.7e-08   34.2   0.2    2.2  2  ParA          NUBPL iron-transfer P-loop NTPase
    1.1e-12   48.3   0.0    4.5e-08   33.2   0.0    2.2  2  AAA_31        AAA domain
    1.1e-09   38.1   0.0    0.00012   21.6   0.3    2.2  2  CBP_BcsQ      Cellulose biosynthesis protein BcsQ
    1.8e-09   37.0  14.9    8.3e-08   31.7   3.4    2.2  2  Fer4          4Fe-4S binding domain
    1.5e-08   34.4  11.0    6.6e-06   26.0   2.4    2.3  2  Fer4_6        4Fe-4S binding domain
    1.9e-08   33.9  11.4    2.1e-05   24.3   3.1    2.4  2  Fer4_2        4Fe-4S binding domain
    1.4e-07   31.0   0.4    1.1e-05   24.8   0.6    2.7  3  ArsA_ATPase   Anion-transporting ATPase
    1.7e-07   31.3   7.7    4.6e-07   29.9   7.9    1.6  1  Fer4_9        4Fe-4S dicluster domain
    5.2e-06   26.5  11.6     0.0033   17.5  13.2    2.2  2  Fer4_10       4Fe-4S dicluster domain
    8.1e-06   25.9   6.5    1.3e-05   25.3   6.5    1.3  1  Fer4_21       4Fe-4S dicluster domain
    9.3e-06   26.5   8.8      0.023   15.6   2.9    2.3  2  Fer4_16       4Fe-4S double cluster binding domain
    2.4e-05   24.8  25.4    0.00093   19.7  14.2    2.1  3  Fer4_7        4Fe-4S dicluster domain
    3.8e-05   24.0   2.9      0.012   16.0   0.5    2.4  2  Fer4_8        4Fe-4S dicluster domain
    0.00033   20.0   0.0     0.0092   15.3   0.1    2.1  2  MipZ          ATPase MipZ
    0.00057   20.4   7.3      0.032   14.8   1.1    2.3  2  Fer4_17       4Fe-4S dicluster domain
     0.0035   17.7  12.0     0.0095   16.4   2.3    2.3  2  Fer4_4        4Fe-4S binding domain
  ------ inclusion threshold ------
      0.017   14.7   0.0      0.024   14.2   0.0    1.3  1  GTP_EFTU      Elongation factor Tu GTP binding domain
      0.035   13.7   0.1       0.05   13.2   0.1    1.2  1  SRP54         SRP54-type protein, GTPase domain
      0.096   12.1   0.0        2.2    7.6   0.0    2.1  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
        0.1   11.2   0.6       0.19   10.3   0.6    1.3  1  DUF853        Bacterial protein of unknown function (DUF853)
       0.11   12.1   1.1       0.44   10.1   0.2    2.2  2  AAA_25        AAA domain
       0.12   12.3   0.3         16    5.5   0.1    2.9  2  YAcAr         YspA, cpYpsA-related SLOG family
       0.15   11.4   0.2       0.22   10.8   0.2    1.2  1  CTP_synth_N   CTP synthase N-terminus
       0.15   12.8   6.5        3.4    8.5   1.6    2.6  2  Fer4_15       4Fe-4S single cluster domain
       0.17   11.6   2.6       0.75    9.5   0.4    2.4  2  AAA_30        AAA domain
       0.19   12.7  21.0       0.58   11.2   7.3    2.3  2  Fer4_3        4Fe-4S binding domain
       0.27   11.2   0.0        1.3    9.0   0.1    1.8  2  ResIII        Type III restriction enzyme, res subunit
       0.32   10.2   0.2       0.47    9.6   0.2    1.1  1  DUF2075       Uncharacterized conserved protein (DUF2075)
       0.98    9.6   5.5        2.5    8.3   5.5    1.6  1  Fer4_18       4Fe-4S dicluster domain
        1.4    9.9   6.4        6.8    7.6   0.7    2.3  2  Fer4_22       4Fe-4S dicluster domain
        7.8    7.1  15.2       0.91   10.1   3.6    2.3  2  Fer4_13       4Fe-4S single cluster domain of Ferredoxin I


Domain annotation for each model (and alignments):
>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.0   0.0   5.6e-21   3.1e-18       1     128 []       5     267 ..       5     267 .. 0.96

  Alignments for each domain:
  == domain 1  score: 66.0 bits;  conditional E-value: 5.6e-21
                                    EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH.......................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......................... RF
                           CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep.......................... 54 
                                    +a++++kGG+GKT++aa+Lar+l+++g r+llvD+D++ + + +l g e   ++                          
  gi|119719905|ref|YP_920400.1|   5 VAVTGGKGGTGKTVVAASLARLLSDAGARTLLVDLDVENPCSYTLLGAELGSAEevalfspviveekctlcgacasacpa 84 
                                    69****************************************9988888888888999********************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                           CbiA  55 ................................................................................ 54 
                                                                                                                    
  gi|119719905|ref|YP_920400.1|  85 halvlipgkrllfleplcescatclyacpagavargrkvvgwvkkgraggvdlvvgelkpgsrqhhevmertldyasstw 164
                                    ******************************************************************************** PP

                                    ........................................CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS...-TTCH CS
                                    ........................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           CbiA  55 ........................................dlkrllellealgkkkalllkiagvvlnrvdgeneetllk 94 
                                                                            d  r+  l+++ g +         +vln+++ +    +++
  gi|119719905|ref|YP_920400.1| 165 ngydvavldlppgsgkgirsalkradlallvaeptrlslaDTRRVHSLAREAGVR-------EVLVLNKYGLPGGVDSEI 237
                                    *************************************999999988888777776.......89**************** PP

                                    HHHHHHHHHCTS-EEEEEE--CCHCCCCHHTS-H CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           CbiA  95 ealeelkqrygvpvlgviprdeavaeapargepv 128
                                    ea++  +   g+ ++ ++++d+a+aea+arge+v
  gi|119719905|ref|YP_920400.1| 238 EAFAASE---GLALV-KVRYDSALAEAYARGELV 267
                                    ***9997...78777.8**************975 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.2   3.1e-11   1.7e-08       4      68 ..       3      66 ..       1      77 [. 0.86
   2 !   21.0   0.0   3.2e-07   0.00018     106     168 ..     161     221 ..     148     284 .. 0.88

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 3.1e-11
                           ParA  4 kviavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekpeqsekkliPv 68
                                   kv+av+ gKGG GK+ va++lA  L++ g+++ l+D+D+  p   +llg+e  ++e+ +  + Pv
  gi|119719905|ref|YP_920400.1|  3 KVVAVTGGKGGTGKTVVAASLARLLSDAGARTLLVDLDVENPCSYTLLGAELGSAEEVA-LFSPV 66
                                   799*********************************************99976555443.45565 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 3.2e-07
                           ParA 106 dvewgelDyLiiDlPPGtgDeqltvaqklplagaviVttpqevaladvkkaiemfkkvkvkvl 168
                                    + +w+  D+ ++DlPPG g    + +++   + a++V+ p +++lad+++  ++++++ v+ +
  gi|119719905|ref|YP_920400.1| 161 SSTWNGYDVAVLDLPPGSGKGIRSALKRA--DLALLVAEPTRLSLADTRRVHSLAREAGVREV 221
                                    568****************9888888877..5799*********************9998755 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   0.0     8e-11   4.5e-08       2      46 ..       3      47 ..       2      97 .. 0.74
   2 !   13.0   0.0   0.00013     0.071     104     157 ..     150     206 ..     138     218 .. 0.80

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 8e-11
                         AAA_31  2 kvIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanatt 46
                                   kv+a++  KGG GKT  +  la  l+ +g ++LlvDlD  +  + 
  gi|119719905|ref|YP_920400.1|  3 KVVAVTGGKGGTGKTVVAASLARLLSDAGARTLLVDLDVENPCSY 47
                                   9*************************************9876665 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00013
                         AAA_31 104 eeilkellekvkde...YDyiiiDcpPsLglltenaLvasdsviipvqaeayaleGl 157
                                    +e+++++l+  +++   YD+ ++D pP  g   ++aL  +d  + + +++ ++l   
  gi|119719905|ref|YP_920400.1| 150 HEVMERTLDYASSTwngYDVAVLDLPPGSGKGIRSALKRADLALLVAEPTRLSLADT 206
                                    55556666554443334*********************************9998765 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.3   2.2e-07   0.00012       2      42 ..       3      43 ..       2      49 .. 0.95
   2 !   14.2   0.0   4.1e-05     0.023     114     221 ..     165     276 ..     139     289 .. 0.70

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 2.2e-07
                       CBP_BcsQ  2 kvlalqGvRGGvGttsllaaLawalhelgesvlviDlspdn 42
                                   kv+a++G +GG+G+t ++a+La+ l   g + l++Dl ++n
  gi|119719905|ref|YP_920400.1|  3 KVVAVTGGKGGTGKTVVAASLARLLSDAGARTLLVDLDVEN 43
                                   789**********************************9988 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 4.1e-05
                       CBP_BcsQ 114 eqyrwillDlpagasaltrellaladlvllvvepdanc...hvrLhqqalpa..aellLiNqfeaasqlqqDllqlWlqs 188
                                    + y+  +lDlp g  +  r++l++adl llv+ep   +     r h  a +a  +e+l +N++     + +++  +    
  gi|119719905|ref|YP_920400.1| 165 NGYDVAVLDLPPGSGKGIRSALKRADLALLVAEPTRLSladTRRVHSLAREAgvREVLVLNKYGLPGGVDSEIEAFA--A 242
                                    7899*****************************986541113456655444322789999***99999999998874..4 PP

                       CBP_BcsQ 189 lrrllPlvihrDealaEalaak.qPlgeyrpdsl 221
                                     + l  ++++ D alaEa a   + +g+ +p ++
  gi|119719905|ref|YP_920400.1| 243 SEGLALVKVRYDSALAEAYARGeLVVGSKAPSAA 276
                                    56677789999******99975144555555544 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   3.4   1.5e-10   8.3e-08       1      23 [.      65      87 ..      65      88 .. 0.94
   2 !   11.0   3.8   0.00053       0.3       7      23 ..     101     117 ..      98     118 .. 0.93

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 1.5e-10
                                   EEEETTTSSS-THHHHHSTTTEE CS
                           Fer4  1 vvideekCigCGaCvevCPvgAI 23
                                   +vi eekC+ CGaC+++CP  A+
  gi|119719905|ref|YP_920400.1| 65 PVIVEEKCTLCGACASACPAHAL 87
                                   689*****************997 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00053
                                    TSSS-THHHHHSTTTEE CS
                           Fer4   7 kCigCGaCvevCPvgAI 23 
                                    +C  C +C  +CP gA 
  gi|119719905|ref|YP_920400.1| 101 LCESCATCLYACPAGAV 117
                                    6**************95 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   2.4   1.2e-08   6.6e-06       2      24 .]      65      87 ..      64      87 .. 0.93
   2 !   13.3   1.5   0.00012     0.067       6      23 ..      99     116 ..      96     117 .. 0.91

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 1.2e-08
                         Fer4_6  2 veidpdkCigCgdCvrvCPegai 24
                                   ++i ++kC+ Cg+C+++CP+ a+
  gi|119719905|ref|YP_920400.1| 65 PVIVEEKCTLCGACASACPAHAL 87
                                   7999****************986 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.00012
                         Fer4_6   6 pdkCigCgdCvrvCPega 23 
                                    + +C +C  C  +CP+ga
  gi|119719905|ref|YP_920400.1|  99 EPLCESCATCLYACPAGA 116
                                    679*************98 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   3.1   3.7e-08   2.1e-05       3      22 .]      65      84 ..      63      84 .. 0.94
   2 !   14.4   1.2   5.4e-05      0.03       5      22 .]      97     114 ..      93     114 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 3.7e-08
                         Fer4_2  3 vvvdtdrCigCgaCvsaCPa 22
                                   +v+++++C+ CgaC saCPa
  gi|119719905|ref|YP_920400.1| 65 PVIVEEKCTLCGACASACPA 84
                                   7899***************8 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 5.4e-05
                         Fer4_2   5 vdtdrCigCgaCvsaCPa 22 
                                    + +  C +C +C+ aCPa
  gi|119719905|ref|YP_920400.1|  97 FLEPLCESCATCLYACPA 114
                                    55667************8 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.6   1.9e-08   1.1e-05       5      38 ..       7      40 ..       2      45 .. 0.90
   2 ?   -0.2   0.0      0.82   4.6e+02     122     140 ..     164     183 ..     149     186 .. 0.74
   3 ?    2.2   0.0      0.15        86     210     258 ..     193     241 ..     180     261 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 1.9e-08
                                   EEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S CS
                    ArsA_ATPase  5 lvgGKGGVGKttvsaatavklsekgkkvllistD 38
                                   + gGKGG GKt v+a++a  ls+ g ++ll+ +D
  gi|119719905|ref|YP_920400.1|  7 VTGGKGGTGKTVVAASLARLLSDAGARTLLVDLD 40
                                   4689***************************988 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.82
                                    CSSSSEEEEESBS.CCHTCG CS
                    ArsA_ATPase 122 eeeydvvvlDtaP.TGhtlr 140
                                     + ydv vlD +P  G+ +r
  gi|119719905|ref|YP_920400.1| 164 WNGYDVAVLDLPPgSGKGIR 183
                                    478*********94466655 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.15
                                    EEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEEE.E-TTCSSSTSHHHH CS
                    ArsA_ATPase 210 rlVvipEklslkEteRaikeLkkygikvdavivNk.llpeeeqenCefle 258
                                     lV  p +lsl +t+R ++   + g++ + ++ Nk  lp  ++++ e ++
  gi|119719905|ref|YP_920400.1| 193 LLVAEPTRLSLADTRRVHSLAREAGVR-EVLVLNKyGLPGGVDSEIEAFA 241
                                    58999***********99999999987.5677788668887777666655 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   7.9   8.2e-10   4.6e-07       1      50 [.      71     116 ..      71     118 .. 0.95

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 8.2e-10
                         Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50 
                                    kCt CgaC +aCpa++ v   ++r   l+      C +C +C+ aCp ga
  gi|119719905|ref|YP_920400.1|  71 KCTLCGACASACPAHALVLIPGKRLLFLEP----LCESCATCLYACPAGA 116
                                    7**************************988....5************987 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5  13.2   5.9e-06    0.0033       3      56 .]      66     113 ..      64     113 .. 0.86
   2 !   12.1   1.5   0.00029      0.16       8      31 ..     101     121 ..      94     136 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 5.9e-06
                        Fer4_10   3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                    vi +++C+ Cg+C +aCPa            ++++       C+ c  C  aCP
  gi|119719905|ref|YP_920400.1|  66 VIVEEKCTLCGACASACPA------HALVLIPGKRLLFLEPLCESCATCLYACP 113
                                    7889***************......66677777777788888***********9 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00029
                        Fer4_10   8 tCirCgkCvkaCPadltsvgakge 31 
                                     C  C++C  aCPa   + +a+g 
  gi|119719905|ref|YP_920400.1| 101 LCESCATCLYACPA---GAVARGR 121
                                    6*************...4444443 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   6.5   2.2e-08   1.3e-05       2      57 ..      66     117 ..      65     119 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 2.2e-08
                        Fer4_21   2 ridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedci 57 
                                    +i e+kC  Cg C+ aC+     a+ + + ++l  +e  C  C+ C+  CP  +++
  gi|119719905|ref|YP_920400.1|  66 VIVEEKCTLCGACASACP---AHALVLIPGKRLLFLEPLCESCATCLYACPA-GAV 117
                                    6889**************...356666677778999***************5.655 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   2.9   4.1e-05     0.023       1      18 [.      71      88 ..      71      94 .. 0.90
   2 !   14.3   0.4   0.00011      0.06       2      20 ..     102     120 ..     101     137 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.1e-05
                        Fer4_16  1 rCgtCgkCaevCPtnaik 18
                                   +C+ Cg+Ca++CP++a+ 
  gi|119719905|ref|YP_920400.1| 71 KCTLCGACASACPAHALV 88
                                   5**************986 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 0.00011
                        Fer4_16   2 CgtCgkCaevCPtnaikek 20 
                                    C +C  C+ +CP++a+   
  gi|119719905|ref|YP_920400.1| 102 CESCATCLYACPAGAVARG 120
                                    ***************8766 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   3.4   4.8e-06    0.0027      30      52 .]      64      86 ..      42      86 .. 0.79
   2 !   19.7  14.2   1.7e-06   0.00093       1      52 []      71     116 ..      71     116 .. 0.93
   3 !    8.8   3.7    0.0045       2.5       2      16 ..     102     116 ..     101     130 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 4.8e-06
                         Fer4_7 30 kveidpekClgCgaCvavCPtga 52
                                   +++i++ekC+ CgaC+++CP+ a
  gi|119719905|ref|YP_920400.1| 64 SPVIVEEKCTLCGACASACPAHA 86
                                   56889999999999999999865 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 1.7e-06
                         Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                    +C+ CgaC++aCp++a+ l +       +++ + +  C +C  C  +CP+ga
  gi|119719905|ref|YP_920400.1|  71 KCTLCGACASACPAHALVLIPG------KRLLFLEPLCESCATCLYACPAGA 116
                                    7******************885......67999999**************97 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0045
                         Fer4_7   2 CigCgaCvaaCpvka 16 
                                    C  C  C  aCp++a
  gi|119719905|ref|YP_920400.1| 102 CESCATCLYACPAGA 116
                                    555666666666555 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.5   2.2e-05     0.012      50      63 ..      71      84 ..      57      89 .. 0.74
   2 !    7.9   0.1    0.0074       4.1       5      18 ..     102     115 ..     100     164 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.2e-05
                         Fer4_8 50 sCttcgaCtevCpv 63
                                   +Ct cgaC+++Cp 
  gi|119719905|ref|YP_920400.1| 71 KCTLCGACASACPA 84
                                   46666666666665 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0074
                         Fer4_8   5 CieCgaCqsaCpvl 18 
                                    C  C  C  aCp+ 
  gi|119719905|ref|YP_920400.1| 102 CESCATCLYACPAG 115
                                    77777777777743 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   1.6e-05    0.0092       2      42 ..       4      44 ..       3      68 .. 0.86
   2 ?    2.6   0.0      0.13        70      93     124 ..     160     191 ..     139     207 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.6e-05
                                   EEEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT- CS
                           MipZ  2 vivlgnekGGsGksttavhvavaLlkkGarvaaidldlrqr 42
                                   v+ ++  kGG+Gk+ +a  +a  L+++Gar   +dld+   
  gi|119719905|ref|YP_920400.1|  4 VVAVTGGKGGTGKTVVAASLARLLSDAGARTLLVDLDVENP 44
                                   6788999******************************8765 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.13
                                    HHHHHHH-SEEEEE--SS--HHHHHHHHT-SE CS
                           MipZ  93 vadleaeldfividtPGsdsalsrlahsladt 124
                                    ++++ + +d+ v+d P    + +r+a ++ad 
  gi|119719905|ref|YP_920400.1| 160 ASSTWNGYDVAVLDLPPGSGKGIRSALKRADL 191
                                    44556789*******9999999********96 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   1.1   5.8e-05     0.032      44      59 ..      70      85 ..      45      86 .. 0.85
   2 !    8.9   0.6     0.004       2.2      46      59 ..     102     115 ..     100     129 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.8e-05
                        Fer4_17 44 slCieCgeCerkCPqg 59
                                   ++C+ Cg C+++CP++
  gi|119719905|ref|YP_920400.1| 70 EKCTLCGACASACPAH 85
                                   78************87 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.004
                        Fer4_17  46 CieCgeCerkCPqg 59 
                                    C +C  C ++CP+g
  gi|119719905|ref|YP_920400.1| 102 CESCATCLYACPAG 115
                                    66666666666654 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   2.3   1.7e-05    0.0095       2      15 ..      70      83 ..      69      87 .. 0.94
   2 ?    6.4   2.3     0.028        15       4      17 .]     102     115 ..      99     120 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.7e-05
                         Fer4_4  2 erCigCgsCvaaCP 15
                                   e+C+ Cg+C +aCP
  gi|119719905|ref|YP_920400.1| 70 EKCTLCGACASACP 83
                                   89************ PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.028
                         Fer4_4   4 CigCgsCvaaCPqg 17 
                                    C  C  C +aCP g
  gi|119719905|ref|YP_920400.1| 102 CESCATCLYACPAG 115
                                    889*********65 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   4.3e-05     0.024      66     133 ..     163     228 ..     142     277 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.3e-05
                                    TCSSEEEEEEEES.SSGGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCG CS
                       GTP_EFTU  66 etkkylinliDtP.GHvdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmD 133
                                    +++ y ++++D P G     k +  +l+ +D+a+lv + ++   + t++v  la++ gv+ ++++NK  
  gi|119719905|ref|YP_920400.1| 163 TWNGYDVAVLDLPpGS---GKGIRSALKRADLALLVAEPTRLSLADTRRVHSLAREAGVREVLVLNKYG 228
                                    4677777777764244...4566778*****************************************75 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1     9e-05      0.05       4      39 ..       5      41 ..       2      65 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9e-05
                                   EEEE.ESTTSSHHHHHHHHHHHHHHTTS-EEEEEEST CS
                          SRP54  4 illv.GlqGaGKTttlaKLaallkkegkkvllvaaDt 39
                                   +++  G  G+GKT  +a La+ll++ g ++llv +D+
  gi|119719905|ref|YP_920400.1|  5 VAVTgGKGGTGKTVVAASLARLLSDAGARTLLVDLDV 41
                                   444415667************************9997 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0    0.0039       2.2      29      54 ..      10      35 ..       5     108 .. 0.79
   2 ?    2.4   0.0      0.16        89      29      71 ..     174     220 ..     158     236 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0039
                   Mg_chelatase 29 GppGsGKtmlakrlpsllpplseeea 54
                                   G  G+GKt++a+ l+ ll++   +  
  gi|119719905|ref|YP_920400.1| 10 GKGGTGKTVVAASLARLLSDAGARTL 35
                                   889***************99877655 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.16
                   Mg_chelatase  29 GppGsGKtmla....krlpsllpplseeealevakiasvagkkeeek 71 
                                     ppGsGK +      + l+ l+++ ++    ++++++s+a++   ++
  gi|119719905|ref|YP_920400.1| 174 LPPGSGKGIRSalkrADLALLVAEPTRLSLADTRRVHSLAREAGVRE 220
                                    59****976431211347788899999999999*****998666555 PP

>> DUF853  Bacterial protein of unknown function (DUF853)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.6   0.00033      0.19      27      57 ..       9      39 ..       3      44 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00033
                         DUF853 27 aGatGtGktvtLqvlaeslseaGvpvfladv 57
                                    G  GtGktv    la  ls+aG   +l+d+
  gi|119719905|ref|YP_920400.1|  9 GGKGGTGKTVVAASLARLLSDAGARTLLVDL 39
                                   47789*********************99996 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.2   0.00079      0.44      34      55 ..       4      25 ..       2      48 .. 0.86
   2 ?    0.2   0.0      0.84   4.7e+02      54      83 ..     114     144 ..     107     224 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00079
                         AAA_25 34 elallaGapgtGKttlaldlal 55
                                    +a+  G +gtGKt++a +la 
  gi|119719905|ref|YP_920400.1|  4 VVAVTGGKGGTGKTVVAASLAR 25
                                   688999**************97 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.84
                         AAA_25  54 alavatGkpwlg.pvap.eqgkVlyvsaEdse 83 
                                    a ava+G+++ g   +  + g V +v++E + 
  gi|119719905|ref|YP_920400.1| 114 AGAVARGRKVVGwV-KKgRAGGVDLVVGELKP 144
                                    66888999998842.23488888888888664 PP

>> YAcAr  YspA, cpYpsA-related SLOG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1     0.029        16       2      33 ..       4      34 ..       3      38 .. 0.86
   2 ?    3.8   0.0     0.096        54      41      63 ..     232     254 ..     213     271 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.029
                          YAcAr  2 rVlvtGgrdfadleliwatLdklhaeapidmv 33
                                   +V+vtGg++ + ++++ a L +l+  a+   +
  gi|119719905|ref|YP_920400.1|  4 VVAVTGGKGGTGKTVVAASLARLLSDAGA-RT 34
                                   69*********************999985.44 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.096
                          YAcAr  41 GaDrlAarWAaergvelvrfpaD 63 
                                    G+D+ ++++Aa++g +lv+++ D
  gi|119719905|ref|YP_920400.1| 232 GVDSEIEAFAASEGLALVKVRYD 254
                                    99***************998876 PP

>> CTP_synth_N  CTP synthase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2   0.00039      0.22       1      39 [.       3      40 ..       3      43 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00039
                                   EEEEEEE--STTTTHHHHHHHHHHHHHCTT--EEEEEEE CS
                    CTP_synth_N  1 kyilvtGGvvSglGkGiiaaslgallksrglkvtlikiD 39
                                   k + vtGG   g Gk ++aasl++ll   g++  l+ +D
  gi|119719905|ref|YP_920400.1|  3 KVVAVTGGK-GGTGKTVVAASLARLLSDAGARTLLVDLD 40
                                   678999996.79******************998887776 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   1.6    0.0061       3.4       5      20 ..      69      84 ..      66      87 .. 0.88
   2 ?    6.3   0.2     0.028        16       7      21 ..     101     115 ..      99     143 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0061
                        Fer4_15  5 rdaCigcglCvaeape 20
                                   +++C+ cg+C+ ++p 
  gi|119719905|ref|YP_920400.1| 69 EEKCTLCGACASACPA 84
                                   589***********95 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.028
                        Fer4_15   7 aCigcglCvaeapev 21 
                                    +C++c+ C+ ++p  
  gi|119719905|ref|YP_920400.1| 101 LCESCATCLYACPAG 115
                                    7***********964 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.4    0.0013      0.75      20      50 ..       5      35 ..       2      43 .. 0.85
   2 ?    1.5   0.1      0.37   2.1e+02      85     121 ..     185     222 ..     118     226 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0013
                         AAA_30 20 vavltGpAGtGKttalkalreaweaaggrvi 50
                                   vav  G  GtGKt + ++l++++ +ag r +
  gi|119719905|ref|YP_920400.1|  5 VAVTGGKGGTGKTVVAASLARLLSDAGARTL 35
                                   67778899****************9987665 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.37
                         AAA_30  85 rlepg.tllivDEagmvdtkqlaallkaaekagakvil 121
                                    +l+++   l+v E   ++ ++++++ + a++ag++ +l
  gi|119719905|ref|YP_920400.1| 185 ALKRAdLALLVAEPTRLSLADTRRVHSLAREAGVREVL 222
                                    34444245677777777777777777777777776555 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   7.3     0.001      0.58       1      15 []      72      86 ..      72      86 .. 0.95
   2 ?    7.3   5.7     0.018        10       1      15 []     102     116 ..     102     116 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.001
                         Fer4_3  1 CtgCgaCvevCPvgA 15
                                   Ct CgaC  +CP +A
  gi|119719905|ref|YP_920400.1| 72 CTLCGACASACPAHA 86
                                   ************887 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.018
                         Fer4_3   1 CtgCgaCvevCPvgA 15 
                                    C  C +C+ +CP gA
  gi|119719905|ref|YP_920400.1| 102 CESCATCLYACPAGA 116
                                    888*9*******998 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1    0.0024       1.3      34      59 ..      13      36 ..       9      39 .. 0.85
   2 ?   -0.7   0.0       2.2   1.2e+03      12      43 ..     153     186 ..     144     216 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0024
                                   TSTHHHHHHHHHHHH-S.....-EEE CS
                         ResIII 34 GtGKTlvaaklierllkkgkeekflf 59
                                   GtGKT+vaa+l++ l+ +g   ++l+
  gi|119719905|ref|YP_920400.1| 13 GTGKTVVAASLARLLSDAGA--RTLL 36
                                   9*************999876..5665 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.2
                                    HHHHT........TTSEEEEEESTTSTHHHHHHH CS
                         ResIII  12 ienlleklks..krdkrglikmaTGtGKTlvaak 43 
                                    +e++l+  +s  ++   +++ ++ G+GK + +a 
  gi|119719905|ref|YP_920400.1| 153 MERTLDYASStwNGYDVAVLDLPPGSGKGIRSAL 186
                                    555555554455666677899999***9887755 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.2   0.00084      0.47       2      25 ..       4      27 ..       3      46 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00084
                        DUF2075  2 avvlVtGvaGtGKtvvllnllael 25
                                   +v +  G+ GtGKtvv+ +l+  l
  gi|119719905|ref|YP_920400.1|  4 VVAVTGGKGGTGKTVVAASLARLL 27
                                   4445557799********998877 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   5.5    0.0045       2.5      59      96 ..      70     113 ..      65     128 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0045
                        Fer4_18  59 gdcidcescvkvcPtgidi....rkGlqle..ciscllcidacd 96 
                                     +c+ c++c + cP +  +    +  l le  c sc+ c+ ac 
  gi|119719905|ref|YP_920400.1|  70 EKCTLCGACASACPAHALVlipgKRLLFLEplCESCATCLYACP 113
                                    68************99544212234444555599*********6 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.7     0.012       6.8      81      94 ..      71      84 ..      58      86 .. 0.66
   2 ?    5.0   0.7     0.081        45       2      15 ..     102     115 ..     101     132 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.012
                        Fer4_22 81 gCvGCgRCieacpv 94
                                   +C+ Cg C +acp+
  gi|119719905|ref|YP_920400.1| 71 KCTLCGACASACPA 84
                                   55555555555554 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.081
                        Fer4_22   2 ClsCgaCtlvCptC 15 
                                    C sC++C ++Cp+ 
  gi|119719905|ref|YP_920400.1| 102 CESCATCLYACPAG 115
                                    999********975 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   3.6    0.0016      0.91       1      18 [.      68      84 ..      68      85 .. 0.91
   2 ?    2.5   3.8       0.4   2.2e+02       6      18 ..     102     114 ..      99     115 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0016
                        Fer4_13  1 VDrdtCiacgaCvelaPd 18
                                   V+ ++C+ cgaC++++P 
  gi|119719905|ref|YP_920400.1| 68 VE-EKCTLCGACASACPA 84
                                   66.9*************7 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.4
                        Fer4_13   6 CiacgaCvelaPd 18 
                                    C +c++C  ++P 
  gi|119719905|ref|YP_920400.1| 102 CESCATCLYACPA 114
                                    99**********5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                       107  (0.00596798); expected 17.9 (0.001)
Passed Fwd filter:                        32  (0.00178482); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              32  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2018.72
//
Query:       gi|119719906|ref|YP_920401.1|  [L=151]
Description: DNA polymerase beta subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.3e-08   33.7   0.0    4.3e-08   33.3   0.0    1.4  1  NTP_transf_2   Nucleotidyltransferase domain
    7.4e-07   29.2   0.0      1e-06   28.8   0.0    1.2  1  Polbeta        Polymerase beta, Nucleotidyltransferase
    7.9e-05   22.5   0.0    0.00011   22.0   0.0    1.2  1  DUF294         Putative nucleotidyltransferase DUF294
  ------ inclusion threshold ------
       0.18   11.7   0.0       0.25   11.2   0.0    1.1  1  Adenyl_cycl_N  Adenylate cyclase NT domain


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.0   9.6e-12   4.3e-08       4      48 ..       6      69 ..       2     127 .. 0.72

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 9.6e-12
                                   HHHHHHHHTT..TSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHH.................H CS
                   NTP_transf_2  4 lleelkelep..vakvvlfGSyarGtalkgSDiDllvvlpeevsre.................k 48
                                   ++ +l++l+   v+ v +fGS+arG+ ++ SD+Dllv+++  + ++                 +
  gi|119719906|ref|YP_920401.1|  6 VKSRLSSLRDpcVKAVLVFGSVARGEQGERSDLDLLVLHEGCAIEDpvarrryfyallreavgD 69
                                   455667777689**************************99886555555555444444444440 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.0   2.2e-10     1e-06      11      43 ..      16      51 ..       7      87 .. 0.74

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 2.2e-10
                                   HHHHSTTEEEEEE-S------EEEEEEEESS-...- CS
                        Polbeta 11 keielaylFGSrakgkareeSDiDlavllkek...l 43
                                   + ++++++FGS+a+g++ e+SD+Dl vl +     +
  gi|119719906|ref|YP_920401.1| 16 PCVKAVLVFGSVARGEQGERSDLDLLVLHEGCaieD 51
                                   4699***********************988765542 PP

>> DUF294  Putative nucleotidyltransferase DUF294
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   2.5e-08   0.00011      46      98 ..      15      70 ..       2      72 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 2.5e-08
                         DUF294 46 ppvpfallvmGSeGReEqtlktDqDnalvled...eeeeaareyfaelaervneaL 98
                                   +p+  a+lv+GS +R+Eq  ++D D   ++e    e+  a r+yf +l ++ + +L
  gi|119719906|ref|YP_920401.1| 15 DPCVKAVLVFGSVARGEQGERSDLDLLVLHEGcaiEDPVARRRYFYALLREAVGDL 70
                                   68999********************98888889999999******99988777665 PP

>> Adenyl_cycl_N  Adenylate cyclase NT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   5.5e-05      0.25      88     119 ..      14      45 ..       3      57 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.5e-05
                  Adenyl_cycl_N  88 keaaieglylmGStgsiaqsekSDlDiWvchr 119
                                    ++++++++ + GS++   q e+SDlD+ v h+
  gi|119719906|ref|YP_920401.1|  14 RDPCVKAVLVFGSVARGEQGERSDLDLLVLHE 45 
                                    67899**********************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       204  (0.0113782); expected 358.6 (0.02)
Passed bias filter:                      197  (0.0109878); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1101.95
//
Query:       gi|119719907|ref|YP_920402.1|  [L=143]
Description: hypothetical protein Tpen_0999 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.6e-09   37.2   0.1    3.1e-09   37.0   0.1    1.1  1  HEPN       HEPN domain
  ------ inclusion threshold ------
      0.014   15.6   0.1      0.023   14.8   0.1    1.4  2  HEPN_AbiV  AbiV


Domain annotation for each model (and alignments):
>> HEPN  HEPN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   0.1   3.5e-13   3.1e-09       2     113 ..       9     130 ..       8     135 .. 0.83

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 3.5e-13
                                    HHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHTT--.SSCCHHHHHHC....CHHHT.......-HHH CS
                           HEPN   2 eewlrrAeedleaAellleegdydlacfhaqqaaekalKAlllkkggeppkthdlreLle....elkkelke....seel 73 
                                    ++ +r A e le Ae+l++ gd++ ++ ++q a+e  +KA+ +  +  p +  d +  l+     +     e     eel
  gi|119719907|ref|YP_920402.1|   9 RYRYRLAVEHLERAERLFSLGDWAGVVAYSQLAVENFAKAVVAVFEV-PTWSYDPSNQLRslldAVPL---EarreAEEL 84 
                                    6788999**********************************999877.46666666666531114444...244479*** PP

                                    HHHHHHHHCCCHHCCCTSS--S......--HHHHHHHHHHHHHHHH CS
                           HEPN  74 reeleeLekayiesrYpdakee......yteedaeealkdaeevle 113
                                    +++++ L +    + Y++   +      y++e a eal++ ++  e
  gi|119719907|ref|YP_920402.1|  85 ANIARDLAPEHGRTSYGEPSAGlvpsdiYKREHAVEALEKGRRARE 130
                                    *********************9****************99887665 PP

>> HEPN_AbiV  AbiV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   2.6e-06     0.023      13      56 ..      15      59 ..      11      95 .. 0.83
   2 ?   -3.3   0.0      0.99   8.9e+03     142     155 ..     108     121 ..     103     124 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.6e-06
                      HEPN_AbiV 13 AeeLledAelLaengsyarAysLlilaiEElgKall.lydalegf 56
                                   A+e+le Ae L+  g +a  ++ ++la E ++Ka++ ++++ +++
  gi|119719907|ref|YP_920402.1| 15 AVEHLERAERLFSLGDWAGVVAYSQLAVENFAKAVVaVFEVPTWS 59
                                   89*******************************986145555555 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 0.99
                      HEPN_AbiV 142 sPseviskeaaeei 155
                                    +Ps++ ++e+a e 
  gi|119719907|ref|YP_920402.1| 108 VPSDIYKREHAVEA 121
                                    69999999988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1047.01
//
Query:       gi|119719908|ref|YP_920403.1|  [L=342]
Description: hypothetical protein Tpen_1000 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-08   35.0   7.8    1.8e-08   34.5   7.8    1.2  1  KASH_CCD        Coiled-coil region of CCDC155 or KASH
    4.8e-07   29.9   0.8    4.8e-07   29.9   0.8    2.3  2  JIP_LZII        JNK-interacting protein  leucine zipper II
    5.9e-07   29.8  12.2    9.3e-05   22.8   3.8    3.4  3  ZapB            Cell division protein ZapB
      6e-07   28.1   3.4    7.9e-07   27.7   3.4    1.0  1  FPP             Filament-like plant protein, long coiled-coil
    1.8e-06   28.1  11.7    2.4e-05   24.5   3.6    3.6  3  HALZ            Homeobox associated leucine zipper
    4.2e-06   27.1  11.8    7.2e-06   26.4  11.8    1.4  1  ATG16           Autophagy protein 16 (ATG16)
    1.8e-05   24.5   2.9     0.0026   17.6   0.8    2.6  2  Shugoshin_N     Shugoshin N-terminal coiled-coil region
    1.8e-05   24.7  10.9     0.0011   19.1   2.9    3.5  5  bZIP_1          bZIP transcription factor
      9e-05   22.0   2.9    0.00013   21.5   2.9    1.1  1  DUF2353         Uncharacterized coiled-coil protein (DUF2353)
    0.00016   21.0   7.5     0.0003   20.1   6.3    1.8  2  HAP1_N          HAP1 N-terminal conserved region
    0.00022   21.3   5.8    0.00022   21.3   5.8    1.6  1  JAKMIP_CC3      JAKMIP CC3 domain
    0.00022   21.2  11.4     0.0018   18.3   4.7    2.3  2  CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein C
    0.00025   21.2   7.0      0.016   15.5   2.2    2.4  2  Seryl_tRNA_N    Seryl-tRNA synthetase N-terminal domain
    0.00027   19.5   1.5    0.00037   19.0   1.5    1.1  1  MAD             Mitotic checkpoint protein
     0.0003   20.9   8.0     0.0083   16.2   2.0    2.2  2  ADIP            Afadin- and alpha -actinin-Binding
    0.00033   20.7   0.6    0.00099   19.2   0.6    1.8  1  Baculo_PEP_C    Baculovirus polyhedron envelope protein, PEP,
    0.00045   19.6   9.1     0.0011   18.4   3.7    2.1  2  GAS             Growth-arrest specific micro-tubule binding
    0.00054   20.6   2.6      0.015   16.0   2.5    2.9  1  YabA            Initiation control protein YabA
    0.00095   18.9   4.4     0.0018   18.0   4.1    1.6  1  SHE3            SWI5-dependent HO expression protein 3
      0.001   19.3   5.8       0.25   11.7   1.2    3.2  3  BLOC1_2         Biogenesis of lysosome-related organelles com
     0.0012   18.5   5.7     0.0027   17.4   5.7    1.5  1  Lebercilin      Ciliary protein causing Leber congenital amau
     0.0013   19.5   6.0      0.014   16.1   1.8    2.3  2  DUF4472         Domain of unknown function (DUF4472)
     0.0014   18.7  12.6     0.0024   17.9   2.6    3.5  3  bZIP_2          Basic region leucine zipper
     0.0014   18.7  15.5      0.002   18.2  11.8    2.1  2  TPR_MLP1_2      TPR/MLP1/MLP2-like protein
     0.0016   18.2   2.3     0.0039   17.0   2.4    1.5  1  DUF4201         Domain of unknown function (DUF4201)
     0.0028   18.1   8.1      0.005   17.3   8.1    1.4  1  Fez1            Fez1
     0.0029   18.1  15.4      0.031   14.8  15.4    2.1  1  APG6_N          Apg6 coiled-coil region
     0.0031   16.5   7.8      0.017   14.1   7.6    1.8  1  CALCOCO1        Calcium binding and coiled-coil domain (CALCO
     0.0032   17.7   5.1     0.0032   17.7   5.1    2.4  3  TMF_TATA_bd     TATA element modulatory factor 1 TATA binding
     0.0049   16.9   0.5      0.012   15.6   0.5    1.7  1  NEMO            NF-kappa-B essential modulator NEMO
     0.0054   17.0   2.5      0.037   14.3   2.0    2.2  2  KLRAQ           Predicted coiled-coil domain-containing prote
     0.0054   15.7   9.0        1.1    8.0   2.3    2.1  1  Spc7            Spc7 kinetochore protein
     0.0059   16.5   0.5      0.033   14.1   0.1    2.0  2  STAT_alpha      STAT protein, all-alpha domain
     0.0075   15.6   2.6     0.0075   15.6   2.6    2.6  2  DUF3450         Protein of unknown function (DUF3450)
  ------ inclusion threshold ------
      0.011   16.2   2.7      0.011   16.2   2.7    2.2  2  CENP-H          Centromere protein H (CENP-H)
      0.011   16.0   8.5      0.054   13.7   8.5    1.9  1  Jnk-SapK_ap_N   JNK_SAPK-associated protein-1
      0.012   15.5   0.2      0.022   14.6   0.2    1.5  1  ArAE_2          Aromatic acid exporter family member 2
      0.013   13.1   4.1      0.018   12.6   4.1    1.2  1  DUF3584         Protein of unknown function (DUF3584)
      0.013   14.6   1.4      0.016   14.3   0.3    1.6  1  APG17           Autophagy protein Apg17
      0.014   15.5  10.1      0.045   13.9   4.9    2.1  2  Tropomyosin_1   Tropomyosin like
      0.014   15.4   2.0        0.5   10.5   0.2    2.8  2  TolA_bind_tri   TolA binding protein trimerisation
      0.015   15.1   9.8      0.033   13.9   1.4    3.5  3  DivIC           Septum formation initiator
      0.015   15.7   3.0       0.18   12.2   0.6    3.1  4  FlaC_arch       Flagella accessory protein C (FlaC)
      0.016   13.4   3.0       0.18    9.9   1.8    1.9  2  EzrA            Septation ring formation regulator, EzrA
      0.017   14.7   2.5      0.095   12.3   0.1    2.3  2  Fzo_mitofusin   fzo-like conserved region
      0.018   15.1   0.6       0.21   11.7   0.1    2.2  2  DUF1664         Protein of unknown function (DUF1664)
      0.019   15.3   1.8       0.19   12.0   0.5    2.6  2  TSC22           TSC-22/dip/bun family
      0.025   14.2   7.8       0.29   10.7   1.8    2.1  2  Filament        Intermediate filament protein
      0.027   14.4   8.1        2.5    8.2   0.1    3.5  3  Bap31_Bap29_C   Bap31/Bap29 cytoplasmic coiled-coil domain
      0.028   14.1   0.5        0.1   12.2   0.4    2.0  1  SLATT_4         SMODS and SLOG-associating 2TM effector domai
      0.028   13.9   3.0      0.039   13.4   3.0    1.2  1  Golgin_A5       Golgin subfamily A member 5
      0.032   12.8   6.9       0.48    8.9   6.9    2.0  1  Macoilin        Macoilin family
      0.037   13.8   3.4      0.083   12.7   3.4    1.7  1  DUF724          Protein of unknown function (DUF724)
      0.039   12.1   6.4       0.34    9.0   6.6    1.9  1  HOOK            HOOK protein
      0.047   12.8  10.6     0.0087   15.2   6.9    1.7  1  Atg14           Vacuolar sorting 38 and autophagy-related sub
      0.068   12.5   6.8       0.11   11.8   6.8    1.4  1  Tropomyosin     Tropomyosin
      0.071   12.6   4.5       0.26   10.7   4.6    1.8  1  Leu_zip         Leucine zipper
      0.079   12.1   7.3       0.24   10.5   7.3    1.5  1  CCDC144C        CCDC144C protein coiled-coil region
      0.081   12.8   3.3        4.3    7.2   1.0    2.4  3  Sec34           Sec34-like family
      0.082   13.4   0.9         13    6.3   0.2    2.6  2  DUF16           Protein of unknown function DUF16
      0.087   12.8   8.1       0.22   11.5   8.2    1.5  1  Rootletin       Ciliary rootlet component, centrosome cohesio
      0.095   11.6   1.9       0.22   10.5   1.9    1.7  1  IFT57           Intra-flagellar transport protein 57
      0.097   12.9   9.4       0.92    9.8   3.2    2.7  2  ABC_tran_CTD    ABC transporter C-terminal domain
        0.1   12.2   2.1       0.16   11.6   2.1    1.3  1  DUF4795         Domain of unknown function (DUF4795)
        0.1   11.9   0.7       0.18   11.1   0.7    1.3  1  CorA            CorA-like Mg2+ transporter protein
       0.12   12.4  12.4       0.85    9.7   7.0    2.7  2  TMF_DNA_bd      TATA element modulatory factor 1 DNA binding
       0.13   11.2   0.2       0.21   10.5   0.2    1.4  1  Seadorna_VP6    Seadornavirus VP6 protein
       0.14   12.3   4.6       0.47   10.5   4.6    1.9  1  UPF0242         Uncharacterised protein family (UPF0242) N-te
       0.14   12.1   1.5        1.8    8.5   1.7    2.2  1  EMP24_GP25L     emp24/gp25L/p24 family/GOLD
       0.15   10.6   1.3       0.23   10.0   1.3    1.3  1  FapA            Flagellar Assembly Protein A
       0.15   11.4   0.6       0.21   10.9   0.6    1.2  1  FAM76           FAM76 protein
       0.16   11.8   6.8        1.2    9.0   1.5    2.7  2  CdvA            CdvA-like coiled-coil domain
       0.17   13.1   7.5        1.7    9.8   3.9    2.7  2  SOGA            Protein SOGA
       0.17   12.2   4.0       0.81   10.0   4.0    2.3  1  Mto2_bdg        Micro-tubular organiser Mto1 C-term Mto2-bind
       0.17   12.2   1.3        2.3    8.6   0.2    2.8  2  Tup_N           Tup N-terminal
       0.17   12.8   9.5          3    8.8   1.6    2.6  2  PRKG1_interact  cGMP-dependent protein kinase interacting dom
       0.18   11.9  14.8      0.039   14.0   8.5    2.5  2  Cep57_CLD_2     Centrosome localisation domain of PPC89
       0.19   11.6   4.6       0.13   12.1   2.6    1.7  1  DUF4515         Domain of unknown function (DUF4515)
        0.2   10.5   5.2       0.46    9.3   5.2    1.5  1  DUF812          Protein of unknown function (DUF812)
       0.21   11.8   1.2       0.44   10.8   0.3    1.9  1  Flu_M1_C        Influenza Matrix protein (M1) C-terminal doma
       0.23   11.6   8.7       0.49   10.5   1.4    3.0  3  BRE1            BRE1 E3 ubiquitin ligase
       0.23   11.6   4.7       0.14   12.4   1.4    2.1  2  Cnn_1N          Centrosomin N-terminal motif 1
       0.24   10.7   4.4        1.2    8.3   4.4    1.9  1  DUF4763         Domain of unknown function (DUF4763)
       0.24   10.9   6.5       0.34   10.4   6.5    1.4  1  Exonuc_VII_L    Exonuclease VII, large subunit
       0.26   10.9   5.3        1.9    8.1   5.3    2.2  1  PI3K_P85_iSH2   Phosphatidylinositol 3-kinase regulatory subu
       0.28   10.4   2.1        0.3   10.3   0.8    1.6  1  TMPIT           TMPIT-like protein
       0.33   10.0   6.3       0.48    9.5   6.3    1.1  1  DUF4686         Domain of unknown function (DUF4686)
       0.35   11.1   8.7          5    7.4   4.2    3.2  3  Spc24           Spc24 subunit of Ndc80
       0.38   10.8   3.2       0.89    9.6   2.6    1.9  1  CtIP_N          Tumour-suppressor protein CtIP N-terminal dom
       0.39   11.1   8.5       0.77   10.1   1.7    2.9  3  Csm1_N          Csm1 N-terminal domain
       0.41   11.4   1.8         12    6.6   0.3    2.4  2  Occludin_ELL    Occludin homology domain
       0.42    9.9   6.8        2.8    7.1   0.6    2.1  2  FmiP_Thoc5      Fms-interacting protein/Thoc5
       0.42   10.4   3.1        1.1    9.1   3.1    1.7  1  Yuri_gagarin    Yuri gagarin
        0.5   10.5   8.2       0.94    9.6   0.3    3.4  3  MbeD_MobD       MbeD/MobD like
       0.53   10.1  14.4        2.3    7.9  14.2    1.9  1  ERM             Ezrin/radixin/moesin family
       0.53   10.4  10.5        0.6   10.2   6.1    2.2  2  Mod_r           Modifier of rudimentary (Mod(r)) protein
       0.58    8.9   1.7       0.94    8.2   0.7    1.5  2  Fmp27_WPPW      RNA pol II promoter Fmp27 protein domain
        0.7   10.1   4.5        1.2    9.3   1.3    2.5  2  HMMR_C          Hyaluronan mediated motility receptor C-termi
       0.73   10.0   5.0          2    8.6   2.5    2.2  2  CREPT           Cell-cycle alteration and expression-elevated
       0.92    9.8  12.2        3.6    7.9   4.6    2.7  2  DUF4164         Domain of unknown function (DUF4164)
          1    9.4   9.0        9.7    6.3   9.0    2.2  1  Nup54           Nucleoporin complex subunit 54
        1.6    9.2   6.8        2.3    8.6   1.7    2.4  2  DUF4200         Domain of unknown function (DUF4200)
        1.8    8.8   6.6         18    5.6   2.6    3.2  3  K-box           K-box region
        1.9    8.5   9.8       0.87    9.6   1.6    3.4  3  DUF2205         Short coiled-coil protein
        2.6    8.5   9.5        8.9    6.8   1.8    3.2  4  CLZ             C-terminal leucine zipper domain of cyclic nu
          3    8.6   5.9        9.4    7.0   0.5    2.9  2  FliD_N          Flagellar hook-associated protein 2 N-terminu
        3.3    7.7   4.5        4.3    7.3   0.1    2.9  2  Pox_A_type_inc  Viral A-type inclusion protein repeat
        3.4    8.4  15.3       0.45   11.2   1.0    3.9  2  SlyX            SlyX
        3.4    7.9   5.4        4.7    7.4   3.5    2.2  1  IFT20           Intraflagellar transport complex B, subunit 2
          4    8.3  14.1          3    8.7   0.3    4.1  4  Rho_Binding     Rho Binding
        4.1    8.1   7.6        4.3    8.0   1.7    2.7  2  BST2            Bone marrow stromal antigen 2
        4.1    7.9  11.2         81    3.7   8.8    3.1  1  DUF4140         N-terminal domain of unknown function (DUF414
        4.2    6.9  13.1         12    5.4  13.0    1.7  1  HAUS-augmin3    HAUS augmin-like complex subunit 3
        4.5    7.9   7.8         13    6.3   7.8    1.8  1  Striatin        Striatin family
        4.5    7.7  16.7    5.2e+02    1.0  16.7    2.6  1  Uso1_p115_C     Uso1 / p115 like vesicle tethering protein, C
          5    7.6  14.9         15    6.0   2.5    4.4  2  LPP             Lipoprotein leucine-zipper
        5.1    7.0   6.6         11    6.0   0.2    3.1  3  GIT_CC          GIT coiled-coil Rho guanine nucleotide exchan
        5.2    7.5  11.8        4.5    7.7   6.1    3.2  3  Nnf1            Nnf1
        7.7    6.7   6.7        7.6    6.7   2.2    3.0  2  Swi5            Swi5
        8.7    6.3   9.6        1.3    9.0   4.6    2.2  2  LURAP           Leucine rich adaptor protein
        9.2    7.4   6.5         38    5.4   0.1    3.1  3  DUF5320         Family of unknown function (DUF5320)


Domain annotation for each model (and alignments):
>> KASH_CCD  Coiled-coil region of CCDC155 or KASH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   7.8   1.2e-10   1.8e-08      18     145 ..     168     299 ..     157     303 .. 0.91

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 1.2e-10
                       KASH_CCD  18 kkLaeenskLkkavetaeetnakLteeieeLkkklkstQq....alqkaklleeEleelkalvkeleEkrarlkaqnkql 93 
                                     +Lae++s+L + v + e + a  +   ++L ++l+s+      + +ka +l+ E++ lka v+ele ++arl  +   l
  gi|119719908|ref|YP_920403.1| 168 DRLAEQVSQLSQRVRSLEIALANESGKCSALGEQLRSVSSewgaLKEKAGALKAENDALKARVSELESENARLRSELASL 247
                                    69******************99999***********987522224577889***************************** PP

                       KASH_CCD  94 ekenqsLiakiesLqeenikllaekdelkkklkeLlkekaeLkkqlheleel 145
                                    + e+ sL ++++s qe  + ll+e   l++k + L+   + L+  l  l ++
  gi|119719908|ref|YP_920403.1| 248 KEEKGSLASRLTSVQESYQSLLTELGSLRQKYESLSFVASALQAALVALAAV 299
                                    *******************************************998776665 PP

>> JIP_LZII  JNK-interacting protein  leucine zipper II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1       9.3   1.4e+03      48      67 ..     166     185 ..     158     189 .. 0.72
   2 !   29.9   0.8   3.2e-09   4.8e-07       2      69 ..     197     264 ..     196     266 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 9.3
                       JIP_LZII  48 EleslqkakerlesrikelE 67 
                                    E ++l ++ ++l +r++ lE
  gi|119719908|ref|YP_920403.1| 166 EADRLAEQVSQLSQRVRSLE 185
                                    66667777777777777777 PP

  == domain 2  score: 29.9 bits;  conditional E-value: 3.2e-09
                       JIP_LZII   2 GmgkevenLikENteLletknaLnvvkddLIarvdeLtsereiLreEleslqkakerlesrikelEee 69 
                                    ++g+++ ++ +E   L+e   aL    d L arv eL se+  Lr+El sl+++k +l sr++ ++e 
  gi|119719908|ref|YP_920403.1| 197 ALGEQLRSVSSEWGALKEKAGALKAENDALKARVSELESENARLRSELASLKEEKGSLASRLTSVQES 264
                                    5799999999*****************************************************99875 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.7      0.16        24       7      51 ..     168     212 ..     149     217 .. 0.63
   2 !   22.8   3.8   6.3e-07   9.3e-05      16      65 ..     212     261 ..     200     261 .. 0.88
   3 ?    7.3   0.0     0.043       6.4       9      44 ..     261     296 ..     258     330 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.16
                           ZapB   7 eqLEskiqkaidtitlLqmeieeLkeeneelkeenreleeeneql 51 
                                    ++L ++++++ +++++L   ++    + ++l e+ r +++e  +l
  gi|119719908|ref|YP_920403.1| 168 DRLAEQVSQLSQRVRSLEIALANESGKCSALGEQLRSVSSEWGAL 212
                                    455555555555555555555555555566666665555555555 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 6.3e-07
                           ZapB  16 aidtitlLqmeieeLkeeneelkeenreleeeneqlkeereawqerlkkL 65 
                                    + ++  +L+ e+++Lk++++el++en++l++e+  lkee+ ++ +rl ++
  gi|119719908|ref|YP_920403.1| 212 LKEKAGALKAENDALKARVSELESENARLRSELASLKEEKGSLASRLTSV 261
                                    5577789***************************************9875 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.043
                           ZapB   9 LEskiqkaidtitlLqmeieeLkeeneelkeenrel 44 
                                     ++++q++++++ +L++++e L    ++l+    +l
  gi|119719908|ref|YP_920403.1| 261 VQESYQSLLTELGSLRQKYESLSFVASALQAALVAL 296
                                    5899******************98888888766555 PP

>> FPP  Filament-like plant protein, long coiled-coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   3.4   5.3e-09   7.9e-07     656     788 ..     160     293 ..     141     299 .. 0.83

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 5.3e-09
                            FPP 656 ssnecaeisklssekei.pselplvsgsneskkeenkllkeeleelksekenlevelksatenleslkaqlqesEqllae 734
                                     +++++e+++l ++  + ++++ + + +  +++ ++  l e+l+++ se   l+ +    ++++++lka+ +e E   a 
  gi|119719908|ref|YP_920403.1| 160 AQRKAYEADRLAEQVSQlSQRVRSLEIALANESGKCSALGEQLRSVSSEWGALKEKAGALKAENDALKARVSELESENAR 239
                                    3455555555554443303344455555666678899999**************************************** PP

                            FPP 735 lkseLeslkeskslaetqlkcmkesyesletrateleaelnelkqkieaLeveL 788
                                    l+seL+slke k+ + + l + +esy+sl t +  l+++ ++l   ++aL++ L
  gi|119719908|ref|YP_920403.1| 240 LRSELASLKEEKGSLASRLTSVQESYQSLLTELGSLRQKYESLSFVASALQAAL 293
                                    ***********************************9999999998888888776 PP

>> HALZ  Homeobox associated leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0       5.3   7.8e+02      27      41 ..     166     180 ..     164     182 .. 0.84
   2 !   24.5   3.6   1.6e-07   2.4e-05       9      41 ..     218     250 ..     216     252 .. 0.95
   3 ?    6.3   0.2     0.076        11      16      41 ..     253     278 ..     252     280 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 5.3
                           HALZ  27 enekLkaelqeLkek 41 
                                    e ++L  ++ +L+++
  gi|119719908|ref|YP_920403.1| 166 EADRLAEQVSQLSQR 180
                                    6689********976 PP

  == domain 2  score: 24.5 bits;  conditional E-value: 1.6e-07
                           HALZ   9 vLKasYdaLksdydsLkkenekLkaelqeLkek 41 
                                    +LKa  daLk+++  L+ en +L++el++Lke 
  gi|119719908|ref|YP_920403.1| 218 ALKAENDALKARVSELESENARLRSELASLKEE 250
                                    8******************************97 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.076
                           HALZ  16 aLksdydsLkkenekLkaelqeLkek 41 
                                    +L+s+  s+++  ++L++el +L++k
  gi|119719908|ref|YP_920403.1| 253 SLASRLTSVQESYQSLLTELGSLRQK 278
                                    7999999****************998 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4  11.8   4.9e-08   7.2e-06      25     138 ..     168     292 ..     152     299 .. 0.80

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 4.9e-08
                          ATG16  25 nrLldrtsaleaenaklekaaasaks.......sksskksakekeasasq....snskqsakiqsleqklaqlreelael 93 
                                     rL++++s+l+++ ++le a a+++        + +s +s+   +++++     +n + +a++++le++ a+lr+ela l
  gi|119719908|ref|YP_920403.1| 168 DRLAEQVSQLSQRVRSLEIALANESGkcsalgeQLRSVSSEWGALKEKAGalkaENDALKARVSELESENARLRSELASL 247
                                    5899999999999999999988888778777663333333444444444477789999********************** PP

                          ATG16  94 yksrgelaqrllelneelqkleeklkedeerlaeleaeraaletk 138
                                      ++g la+rl++++e+ q l ++l + +++ ++l+   +al+ +
  gi|119719908|ref|YP_920403.1| 248 KEEKGSLASRLTSVQESYQSLLTELGSLRQKYESLSFVASALQAA 292
                                    ************************999999999998777777766 PP

>> Shugoshin_N  Shugoshin N-terminal coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.064       9.4      12      27 ..     170     185 ..     168     189 .. 0.89
   2 !   17.6   0.8   1.8e-05    0.0026      16      42 ..     223     249 ..     221     250 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.064
                    Shugoshin_N  12 LAKsNsalslkirele 27 
                                    LA + s+ls+++r+le
  gi|119719908|ref|YP_920403.1| 170 LAEQVSQLSQRVRSLE 185
                                    78899**********9 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 1.8e-05
                    Shugoshin_N  16 NsalslkirelekevseLlsENlnLRe 42 
                                    N al+++++ele+e+++L+sE  +L+e
  gi|119719908|ref|YP_920403.1| 223 NDALKARVSELESENARLRSELASLKE 249
                                    899******************999987 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   1.1     0.083        12      22      59 ..     161     198 ..     154     204 .. 0.81
   2 !   18.1   1.1   1.5e-05    0.0022      30      63 ..     211     244 ..     206     245 .. 0.91
   3 !   19.1   2.9   7.1e-06    0.0011      25      61 ..     220     256 ..     219     259 .. 0.90
   4 ?    8.6   0.4     0.013         2      30      62 ..     239     271 ..     238     273 .. 0.93
   5 ?    2.8   0.3      0.85   1.3e+02      27      59 ..     250     282 ..     248     283 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.083
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         bZIP_1  22 qRKqaeieeLerrvkaLekeNksLkseleelkkevekL 59 
                                    qRK  e ++L+++v++L++   sL   l + + +++ L
  gi|119719908|ref|YP_920403.1| 161 QRKAYEADRLAEQVSQLSQRVRSLEIALANESGKCSAL 198
                                    89****************99999988887776666655 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 1.5e-05
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         bZIP_1  30 eLerrvkaLekeNksLkseleelkkevekLkskv 63 
                                    +L++++ aL++eN +Lk +++el+ e++ L+s++
  gi|119719908|ref|YP_920403.1| 211 ALKEKAGALKAENDALKARVSELESENARLRSEL 244
                                    799***************************9986 PP

  == domain 3  score: 19.1 bits;  conditional E-value: 7.1e-06
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         bZIP_1  25 qaeieeLerrvkaLekeNksLkseleelkkevekLks 61 
                                    +ae ++L+ rv++Le+eN+ L+sel +lk+e  +L s
  gi|119719908|ref|YP_920403.1| 220 KAENDALKARVSELESENARLRSELASLKEEKGSLAS 256
                                    688999************************9887765 PP

  == domain 4  score: 8.6 bits;  conditional E-value: 0.013
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         bZIP_1  30 eLerrvkaLekeNksLkseleelkkevekLksk 62 
                                    +L ++ + L++e  sL+s+l + ++ +++L+++
  gi|119719908|ref|YP_920403.1| 239 RLRSELASLKEEKGSLASRLTSVQESYQSLLTE 271
                                    689999************************987 PP

  == domain 5  score: 2.8 bits;  conditional E-value: 0.85
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         bZIP_1  27 eieeLerrvkaLekeNksLkseleelkkevekL 59 
                                    e   L++r    ++  +sL  el++l+ ++e+L
  gi|119719908|ref|YP_920403.1| 250 EKGSLASRLTSVQESYQSLLTELGSLRQKYESL 282
                                    444566677777777777777777777777765 PP

>> DUF2353  Uncharacterized coiled-coil protein (DUF2353)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   2.9   8.7e-07   0.00013      23     146 ..     165     283 ..     151     292 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 8.7e-07
                        DUF2353  23 qerdqyklmaeqLqerlsalkkqleeekakaadlkeekekekklsqlleesreenkalkleveeLrqklkeaqgDiklLR 102
                                     e d+++  + qL +r+++l+  l++e+ k + l    e+ +++s+     +e+  alk e ++L+ +++e++  +  LR
  gi|119719908|ref|YP_920403.1| 165 YEADRLAEQVSQLSQRVRSLEIALANESGKCSAL---GEQLRSVSSEWGALKEKAGALKAENDALKARVSELESENARLR 241
                                    3566666667777777776666665555444444...5788889999999****************************** PP

                        DUF2353 103 eqlarqrlglkdedlletrhss.aeereelvkqlEklkekiqqle 146
                                     +la+ + +   +++l +r +s +e++++l+ +l +l++k+++l 
  gi|119719908|ref|YP_920403.1| 242 SELASLKEE---KGSLASRLTSvQESYQSLLTELGSLRQKYESLS 283
                                    888877544...66677766665999***************9986 PP

>> HAP1_N  HAP1 N-terminal conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.2       1.2   1.7e+02     229     257 ..     157     185 ..     148     197 .. 0.58
   2 !   20.1   6.3     2e-06    0.0003     181     290 ..     169     281 ..     164     291 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 1.2
                         HAP1_N 229 leelerqqeeissLlaqivdlqqklkelg 257
                                    l e++r+  e  +L  q+ +l q++++l 
  gi|119719908|ref|YP_920403.1| 157 LAEAQRKAYEADRLAEQVSQLSQRVRSLE 185
                                    44455555555555555555555555543 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 2e-06
                         HAP1_N 181 kLreeasqLktetdtlE...ekEqqLvldcveqlseanqqiaelseelarkleelerqqeeissLlaqivdlqqklkelg 257
                                    +L e+ sqL++   +lE   ++E    + + eql++++++   l+e+    + e++  +  +s+L ++   l+  l +l+
  gi|119719908|ref|YP_920403.1| 169 RLAEQVSQLSQRVRSLEialANESGKCSALGEQLRSVSSEWGALKEKAGALKAENDALKARVSELESENARLRSELASLK 248
                                    56667777777776666444567777888999***************999999999999********************* PP

                         HAP1_N 258 veneelkqhLaaskeaqrqLtaELqdlqekyae 290
                                    +e+  l ++L++ +e  ++L +EL  l++ky+ 
  gi|119719908|ref|YP_920403.1| 249 EEKGSLASRLTSVQESYQSLLTELGSLRQKYES 281
                                    ******************************986 PP

>> JAKMIP_CC3  JAKMIP CC3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   5.8   1.5e-06   0.00022      89     189 ..     149     261 ..     143     268 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.5e-06
                     JAKMIP_CC3  89 ayalLreklggeldaerelkareqleselrktkskikdLeeaLaqk..............GqdskwveekQalik.rnqe 153
                                    +y +L   l    +a+r++ + ++l +++++   +++ Le aLa++               ++   ++ek   +k +n  
  gi|119719908|ref|YP_920403.1| 149 TYGELSAAL---AEAQRKAYEADRLAEQVSQLSQRVRSLEIALANEsgkcsalgeqlrsvSSEWGALKEKAGALKaENDA 225
                                    566665555...79********************************9******999998777777788887555416666 PP

                     JAKMIP_CC3 154 LvekikkleeeeskLkqeiqdlrdqnelLEfrilel 189
                                    L  ++++le+e+ +L++e+  l++ +  L  r  + 
  gi|119719908|ref|YP_920403.1| 226 LKARVSELESENARLRSELASLKEEKGSLASRLTSV 261
                                    ***********************9987776666655 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.8     0.028       4.2      42      87 ..     155     200 ..     149     214 .. 0.77
   2 !   18.3   4.7   1.2e-05    0.0018      28     101 ..     197     270 ..     192     284 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.028
                 CENP-F_leu_zip  42 kvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLek 87 
                                    ++  ea  +  e+  l e++ +l+++ r le+ L++ +     L +
  gi|119719908|ref|YP_920403.1| 155 AALAEAQRKAYEADRLAEQVSQLSQRVRSLEIALANESGKCSALGE 200
                                    555666666677888*******************987665555555 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 1.2e-05
                 CENP-F_leu_zip  28 nLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelqkkqervseLes 101
                                    +L  +l  + ++  +++  a   kae  +lk+ + el++e  +l+++L++l++ek +L+  l   qe  ++L +
  gi|119719908|ref|YP_920403.1| 197 ALGEQLRSVSSEWGALKEKAGALKAENDALKARVSELESENARLRSELASLKEEKGSLASRLTSVQESYQSLLT 270
                                    55556666666666667777778999999999999999999999999999999999999999888887776644 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.2     0.016       2.4      54      93 ..     152     191 ..     146     199 .. 0.87
   2 !   15.5   2.2   0.00011     0.016      27     105 ..     198     273 ..     190     276 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.016
                                    HHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHH CS
                   Seryl_tRNA_N  54 elskeIgkakkkkedaeeliaevkelkeelkaleaelkel 93 
                                    els++ ++a +k  +a++l ++v++l++++  le +l++ 
  gi|119719908|ref|YP_920403.1| 152 ELSAALAEAQRKAYEADRLAEQVSQLSQRVRSLEIALANE 191
                                    7899999****99********************9998765 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 0.00011
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCTS- CS
                   Seryl_tRNA_N  27 dvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaeleklllaiP 105
                                    + ++l ++ +++ +l+ ++ +l+ae  +l + ++++  ++   ++l+ e ++lkee   l  +l+ +++  ++ll++++
  gi|119719908|ref|YP_920403.1| 198 LGEQLRSVSSEWGALKEKAGALKAENDALKARVSELESEN---ARLRSELASLKEEKGSLASRLTSVQESYQSLLTELG 273
                                    567899999****************************865...88999*********************9999999886 PP

>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   1.5   2.5e-06   0.00037     126     247 ..     152     279 ..     142     311 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.5e-06
                            MAD 126 elsekeseleelqerldllkkklseleqliqqle....kkqkelaeaeqrikeLefeiqsqeddslivknsksel.arip 200
                                    els+   e ++   + d l +++s+l+q++ +le    +++ ++++  ++++  + e    ++++  +k+ ++ l ar++
  gi|119719908|ref|YP_920403.1| 152 ELSAALAEAQRKAYEADRLAEQVSQLSQRVRSLEialaNESGKCSALGEQLRSVSSEWGALKEKAGALKAENDALkARVS 231
                                    6677777777777788888888888888886666111134455667778888888888889999999*******999*** PP

                            MAD 201 elekelerlreenkklnelkenk.elLkEevedlkkkLereEkareel 247
                                    ele+e +rlr+e + l+e k+   + L+   e +++ L      r++ 
  gi|119719908|ref|YP_920403.1| 232 ELESENARLRSELASLKEEKGSLaSRLTSVQESYQSLLTELGSLRQKY 279
                                    ************999999988641445555555555555555555555 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.8      0.02       2.9      67     124 ..     158     215 ..     151     223 .. 0.53
   2 !   16.2   2.0   5.6e-05    0.0083      54     129 ..     222     297 ..     220     317 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.02
                           ADIP  67 aeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrlkna 124
                                    ae +r+  + +rl +q++ql +++ +++ ++++   k  +l ++l++ + e   lk +
  gi|119719908|ref|YP_920403.1| 158 AEAQRKAYEADRLAEQVSQLSQRVRSLEIALANESGKCSALGEQLRSVSSEWGALKEK 215
                                    4555555555555555555555555555555555555555555555554444444444 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 5.6e-05
                           ADIP  54 qreslnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrlknalqqik 129
                                    ++ +l++++++le+e++rl+s+  +lk++  +l+++l++vq+  ++l ++l +l qk  +++  ++ l+ al +++
  gi|119719908|ref|YP_920403.1| 222 ENDALKARVSELESENARLRSELASLKEEKGSLASRLTSVQESYQSLLTELGSLRQKYESLSFVASALQAALVALA 297
                                    56789999***************************************99999999999888776666666666555 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.6   6.7e-06   0.00099      26     120 ..     182     277 ..     148     296 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 6.7e-06
                   Baculo_PEP_C  26 rlqnvqilaqlatlldaietqLnalsedlksllaeldt......rldtlltnLtdalnalq...dtlrneLtnlnsiltn 96 
                                    r++++ + a+ +    a+ +qL ++s++         +      +l++  ++L++ + +l+     lr+eL +l+ +  +
  gi|119719908|ref|YP_920403.1| 182 RSLEIAL-ANESGKCSALGEQLRSVSSEWG-------AlkekagALKAENDALKARVSELEsenARLRSELASLKEEKGS 253
                                    2222222.2223333344444444444444.......25555559***************998889************** PP

                   Baculo_PEP_C  97 LlssvtNinstLnnllqalnnldl 120
                                    L+s +t ++++ ++ll+ l +l +
  gi|119719908|ref|YP_920403.1| 254 LASRLTSVQESYQSLLTELGSLRQ 277
                                    *******************99854 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.4     0.049       7.3      69     128 ..     156     215 ..     147     218 .. 0.68
   2 !   18.4   3.7   7.2e-06    0.0011      31     104 ..     212     282 ..     210     299 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.049
                            GAS  69 eveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrfekvekerdelykk 128
                                     ++e ++++ + ++  ++  +l +r+++le  l + + +   l +++ +v++e  +l++k
  gi|119719908|ref|YP_920403.1| 156 ALAEAQRKAYEADRLAEQVSQLSQRVRSLEIALANESGKCSALGEQLRSVSSEWGALKEK 215
                                    455666666666666677777777777777777777777777777777777777777665 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 7.2e-06
                            GAS  31 lKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdl 104
                                    lKe+   lk+++++ + ++se+++en rl+ +L  ++ee+  L  +l   ++  qs   l ++l +l +++++l
  gi|119719908|ref|YP_920403.1| 212 LKEKAGALKAENDALKARVSELESENARLRSELASLKEEKGSLASRLTSVQESYQS---LLTELGSLRQKYESL 282
                                    78888888888888888888888888888888888888888888888777774443...344444444444444 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   2.5   9.9e-05     0.015       8      73 ..     200     268 ..     162     329 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 9.9e-05
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...XXXXXXXXXXXXXXXXXXXXX CS
                           YabA   8 dkleeleeqleelleeleelkeelaelleenaeLeleneklrerl...eeeekkekekkkelsegkenL 73 
                                    ++l++++++ ++l+e+ ++lk+e  +l  + +eLe en +lr++l   +ee+ + +++ ++++e++++L
  gi|119719908|ref|YP_920403.1| 200 EQLRSVSSEWGALKEKAGALKAENDALKARVSELESENARLRSELaslKEEKGSLASRLTSVQESYQSL 268
                                    455555555555555555555555555555566666677777777444334444445555556666554 PP

>> SHE3  SWI5-dependent HO expression protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   4.1   1.2e-05    0.0018      28     120 ..     197     282 ..     167     290 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.2e-05
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHH CS
                           SHE3  28 eLleklelaqkkeskflenlaslkhENdnLsslLkRKerrlkdlekelselkesveelklekkqlkkrlenssasetele 107
                                     L e+l ++ +    + e+   lk ENd L++       r+ +le+e++ l+++  +lk+ek  l  rl + ++s ++l 
  gi|119719908|ref|YP_920403.1| 197 ALGEQLRSVSSEWGALKEKAGALKAENDALKA-------RVSELESENARLRSELASLKEEKGSLASRLTSVQESYQSLL 269
                                    46666777777777777888899999999976.......99*************************************** PP

                                    HHHHHHHHHHHHH CS
                           SHE3 108 eelerlkvqYdal 120
                                     el  l+ +Y++l
  gi|119719908|ref|YP_920403.1| 270 TELGSLRQKYESL 282
                                    **********997 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.2      0.04         6      45      80 ..     152     187 ..     144     190 .. 0.85
   2 ?    4.2   0.0      0.37        55      32      78 ..     191     234 ..     188     235 .. 0.69
   3 !   11.7   1.2    0.0017      0.25      17      69 ..     211     263 ..     202     298 .. 0.59

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.04
                        BLOC1_2  45 slekkleklnekyeelqpylqqidqiekqvteLeea 80 
                                    +l++ l + ++k  e + + +q+ q+ ++v++Le a
  gi|119719908|ref|YP_920403.1| 152 ELSAALAEAQRKAYEADRLAEQVSQLSQRVRSLEIA 187
                                    678888899999999999999999999999999976 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.37
                        BLOC1_2  32 asekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLe 78 
                                     s k+ +l +++ s++++  +l+ek  +l+   +    ++++v+eLe
  gi|119719908|ref|YP_920403.1| 191 ESGKCSALGEQLRSVSSEWGALKEKAGALKAENDA---LKARVSELE 234
                                    56788888888888888888888877777665544...445555554 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.0017
                        BLOC1_2  17 atvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidq 69 
                                    a +e+   L++ N a  +++ +l+++ a l+++l  l+e++ +l++ l+++++
  gi|119719908|ref|YP_920403.1| 211 ALKEKAGALKAENDALKARVSELESENARLRSELASLKEEKGSLASRLTSVQE 263
                                    55555555666666666666666666666666666666666666655555543 PP

>> Lebercilin  Ciliary protein causing Leber congenital amaurosis disease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   5.7   1.8e-05    0.0027       5     148 ..     142     280 ..     139     288 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.8e-05
                     Lebercilin   5 vlsarllkikeLqnelaelqskleelrkEnklLkrlqkr...qekaLskyedteaeLpqllarhneEvrvlrerlRksqe 81 
                                    + +a +  + eL+  lae+q+k  e ++  + + +l  r    e aL +  ++ + L + l++ ++E  +l+e+   +++
  gi|119719908|ref|YP_920403.1| 142 IAMAPRATYGELSAALAEAQRKAYEADRLAEQVSQLSQRvrsLEIALANESGKCSALGEQLRSVSSEWGALKEKAGALKA 221
                                    6677888999**********9988777666666665554111688*********************************** PP

                     Lebercilin  82 kerelekklkekeaellrlkdklkklkkLsedknLaereeLqkkLeeleakleekeekikeLerkle 148
                                    ++++l+ ++ e e+e  rl+++l  lk+        e+  L+++L+++++ +++   ++ +L++k e
  gi|119719908|ref|YP_920403.1| 222 ENDALKARVSELESENARLRSELASLKE--------EKGSLASRLTSVQESYQSLLTELGSLRQKYE 280
                                    **********************999985........5566666677766666666666666666655 PP

>> DUF4472  Domain of unknown function (DUF4472)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   2.0     0.001      0.15      33     107 .]     170     244 ..     157     244 .. 0.92
   2 !   16.1   1.8   9.3e-05     0.014      39     103 ..     220     282 ..     215     287 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.001
                        DUF4472  33 lknkvlalenrvlelelerekaaeeiqslrerlaeleeekkeleeeyvvlkknyqalekefekekkkqqelsleL 107
                                    l  +v +l +rv +le+  ++   + ++l e+l+ + +e  +l+e+  +lk +  al++   + ++++ +l +eL
  gi|119719908|ref|YP_920403.1| 170 LAEQVSQLSQRVRSLEIALANESGKCSALGEQLRSVSSEWGALKEKAGALKAENDALKARVSELESENARLRSEL 244
                                    678999******************************************************************998 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 9.3e-05
                        DUF4472  39 alenrvlelelerekaaeeiqslrerlaeleeekkeleeeyvvlkknyqalekefekekkkqqel 103
                                    ++en+ l   +   ++++e++ lr++la l+eek +l+ ++++++++yq+l +e+ + ++k + l
  gi|119719908|ref|YP_920403.1| 220 KAENDALKARVS--ELESENARLRSELASLKEEKGSLASRLTSVQESYQSLLTELGSLRQKYESL 282
                                    555544444333..455567777777777777777777777777777777777777777776665 PP

>> bZIP_2  Basic region leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.5      0.21        31      32      52 ..     165     185 ..     155     186 .. 0.83
   2 !   17.9   2.6   1.6e-05    0.0024      24      54 .]     220     250 ..     213     250 .. 0.95
   3 ?    0.7   0.1       3.8   5.6e+02      30      51 ..     261     282 ..     253     283 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.21
                                    HHHHHHHHHHHHHHHHHHHHH CS
                         bZIP_2  32 ervkeLeeeNaqLrqkveqLe 52 
                                     ++ +L e+ +qL q+v++Le
  gi|119719908|ref|YP_920403.1| 165 YEADRLAEQVSQLSQRVRSLE 185
                                    588999***********9997 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 1.6e-05
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         bZIP_2  24 kakeeeleervkeLeeeNaqLrqkveqLeke 54 
                                    ka++  l+ rv eLe+eNa+Lr ++++L+ e
  gi|119719908|ref|YP_920403.1| 220 KAENDALKARVSELESENARLRSELASLKEE 250
                                    8999************************976 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 3.8
                                    HHHHHHHHHHHHHHHHHHHHHH CS
                         bZIP_2  30 leervkeLeeeNaqLrqkveqL 51 
                                     +e  ++L +e   Lrqk+e+L
  gi|119719908|ref|YP_920403.1| 261 VQESYQSLLTELGSLRQKYESL 282
                                    5677778888888888888877 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2  11.8   1.4e-05     0.002       9     126 ..     152     272 ..     148     275 .. 0.88
   2 !   10.7   1.5    0.0028      0.42       3      47 ..     237     281 ..     235     298 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.4e-05
                     TPR_MLP1_2   9 eikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesakaele 88 
                                    e++++++e+++ + ++  l e++ + +++++  +   ++e  k ++  ++l+++ +e   lk+++  lkae++++ka ++
  gi|119719908|ref|YP_920403.1| 152 ELSAALAEAQRKAYEADRLAEQVSQLSQRVRSLEIALANESGKCSALGEQLRSVSSEWGALKEKAGALKAENDALKARVS 231
                                    678889999999999999**********************************************************9887 PP

                     TPR_MLP1_2  89 eseeswe...eqkeelekelselekriedlneqNklLhdQl 126
                                    e e++ +   ++  +l++e+ +l +r++ ++e  + L++ l
  gi|119719908|ref|YP_920403.1| 232 ELESENArlrSELASLKEEKGSLASRLTSVQESYQSLLTEL 272
                                    777765511156667899**************999999877 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0028
                     TPR_MLP1_2   3 lksleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYer 47 
                                     ++l++e++slkeek +++++l+++qe  ++   ++    qkYe+
  gi|119719908|ref|YP_920403.1| 237 NARLRSELASLKEEKGSLASRLTSVQESYQSLLTELGSLRQKYES 281
                                    567888888888888888888888888888888888888888885 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   2.4   2.6e-05    0.0039      45     133 ..     175     263 ..     158     283 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.6e-05
                        DUF4201  45 eqlqienqalnkkIeernkeLkrlkkkttktvhalthlkeklhmleselselkkelkekeerlaklrkelykvklerdkl 124
                                     ql   + +l+  +++ + + ++l ++  + + +   lkek+ +l++e+ +lk + +e+e + a+lr el ++k+e+  l
  gi|119719908|ref|YP_920403.1| 175 SQLSQRVRSLEIALANESGKCSALGEQLRSVSSEWGALKEKAGALKAENDALKARVSELESENARLRSELASLKEEKGSL 254
                                    56667777777777777777777777777888888888888888888888888888888888888888888888888777 PP

                        DUF4201 125 rkqneklkq 133
                                      + + +++
  gi|119719908|ref|YP_920403.1| 255 ASRLTSVQE 263
                                    766665554 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   8.1   3.4e-05     0.005      27     140 ..     167     282 ..     149     323 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.4e-05
                           Fez1  27 tqklseiv.alkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelse 105
                                    + +l e v +l  ++r l+ +l ++  + + l e+l++ + e   ++++    k+e++ l+ +v++le+e ++lr+el++
  gi|119719908|ref|YP_920403.1| 167 ADRLAEQVsQLSQRVRSLEIALANESGKCSALGEQLRSVSSEWGALKEKAGALKAENDALKARVSELESENARLRSELAS 246
                                    44555544278899999999***********************************************************9 PP

                           Fez1 106 lsleeeeaalesdeakaqrqe.aeeleelkreverl 140
                                    l++e+ + a++ +++++  q+  +el++l+++ e l
  gi|119719908|ref|YP_920403.1| 247 LKEEKGSLASRLTSVQESYQSlLTELGSLRQKYESL 282
                                    998888877777776666555456677777776666 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8  15.4   0.00021     0.031      24     126 ..     161     272 ..     132     293 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 0.00021
                         APG6_N  24 erdaYeeflkklkkekkeeek...........qdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeele 92 
                                    +r+aYe+  ++l ++ ++ ++           +  ++ +l e+l+ +++e  +l e+  +l++e+++l+a +++le+e +
  gi|119719908|ref|YP_920403.1| 161 QRKAYEA--DRLAEQVSQLSQrvrsleialanESGKCSALGEQLRSVSSEWGALKEKAGALKAENDALKARVSELESENA 238
                                    4444443..22222222222244455667777455555666666666666666666666666666666666666666666 PP

                         APG6_N  93 aleeeeerfwreynelqlelleleeeldsleaqy 126
                                    +l  e +   +e  +l+  l++ +e  +sl +++
  gi|119719908|ref|YP_920403.1| 239 RLRSELASLKEEKGSLASRLTSVQESYQSLLTEL 272
                                    6666666666666666666666666555554443 PP

>> CALCOCO1  Calcium binding and coiled-coil domain (CALCOCO1) like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   7.6   0.00011     0.017      58     142 ..     159     241 ..     149     302 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 0.00011
                       CALCOCO1  58 ekekeeykrdreeldrerkelesrveelkeelkesrekveeleekqkelerlseelaeeksalleakeesearirELEeD 137
                                    e +++ y+ d  +l +++++l++rv  l+ +l++   k   l e+ + +++  ++l+e+  al +++++ +ar+ ELE +
  gi|119719908|ref|YP_920403.1| 159 EAQRKAYEAD--RLAEQVSQLSQRVRSLEIALANESGKCSALGEQLRSVSSEWGALKEKAGALKAENDALKARVSELESE 236
                                    5555555554..46788999999999999999999999999999999999999999999999999999999999999877 PP

                       CALCOCO1 138 iktlt 142
                                     + l 
  gi|119719908|ref|YP_920403.1| 237 NARLR 241
                                    66553 PP

>> TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.2       2.2   3.3e+02      12      25 ..     172     185 ..     148     190 .. 0.50
   2 ?    8.0   0.6     0.022       3.2      12      65 ..     172     225 ..     161     228 .. 0.85
   3 !   17.7   5.1   2.2e-05    0.0032      15      94 ..     196     279 ..     189     284 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 2.2
                    TMF_TATA_bd  12 qlverlsseirrlE 25 
                                    + v++ls+++r+lE
  gi|119719908|ref|YP_920403.1| 172 EQVSQLSQRVRSLE 185
                                    23444444444444 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.022
                    TMF_TATA_bd  12 qlverlsseirrlEgElaslkeelerleaerdeareeivklmkeneelkelkke 65 
                                    + v++ls+++r+lE+ la+   +++ l ++ +++++e  +l ++  +lk++++ 
  gi|119719908|ref|YP_920403.1| 172 EQVSQLSQRVRSLEIALANESGKCSALGEQLRSVSSEWGALKEKAGALKAENDA 225
                                    67899*************************999999999999888888887765 PP

  == domain 3  score: 17.7 bits;  conditional E-value: 2.2e-05
                    TMF_TATA_bd  15 erlsseirrlEgElaslkeelerleaerdeareeivklmkeneelkel....kkeleelekeleelqeryetlLellGek 90 
                                    + l+ ++r+  +E  +lke+   l+ae d++++ + +l +en +l+++    k+e  +l ++l+++qe y++lL+ lG  
  gi|119719908|ref|YP_920403.1| 196 SALGEQLRSVSSEWGALKEKAGALKAENDALKARVSELESENARLRSElaslKEEKGSLASRLTSVQESYQSLLTELGSL 275
                                    67999************************************99877651111666677888*************999975 PP

                    TMF_TATA_bd  91 sEev 94 
                                      + 
  gi|119719908|ref|YP_920403.1| 276 RQKY 279
                                    5555 PP

>> NEMO  NF-kappa-B essential modulator NEMO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.5   8.1e-05     0.012       6      52 ..     200     249 ..     196     272 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 8.1e-05
                           NEMO   6 eqlkellteNneLke...alkqsNqalkeRlEeLsawqekqkeereflee 52 
                                    eql+ +  e   Lke   alk +N+alk R+ eL+  + + + e+ +l+e
  gi|119719908|ref|YP_920403.1| 200 EQLRSVSSEWGALKEkagALKAENDALKARVSELESENARLRSELASLKE 249
                                    7777777788888887779*****************99999999988765 PP

>> KLRAQ  Predicted coiled-coil domain-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   2.0   0.00025     0.037       2      75 ..     169     242 ..     168     271 .. 0.81
   2 ?    1.6   0.1       2.3   3.4e+02      29      61 ..     259     291 ..     240     324 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 0.00025
                          KLRAQ   2 klaqeYsKlraqakvLkkavleEqskeaslkeelkekeqslrkseqEvdsLtFrNkqLekrvellqeeleveek 75 
                                    +la++ s+l    + L  a+ +E  k+++l e+l++  ++    ++   +L+  N+ L+ rv+ l  e +    
  gi|119719908|ref|YP_920403.1| 169 RLAEQVSQLSQRVRSLEIALANESGKCSALGEQLRSVSSEWGALKEKAGALKAENDALKARVSELESENARLRS 242
                                    799999999999999*************************************************9988765443 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 2.3
                          KLRAQ  29 aslkeelkekeqslrkseqEvdsLtFrNkqLek 61 
                                     s++e+ ++  ++l   +q  +sL+F  + L+ 
  gi|119719908|ref|YP_920403.1| 259 TSVQESYQSLLTELGSLRQKYESLSFVASALQA 291
                                    344555555555666677777888777766665 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   2.3    0.0076       1.1     174     255 ..     148     228 ..     140     234 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0076
                           Spc7 174 eekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaea 253
                                    + + el++ l++ q++a e ++   e++ +l +++++l+  +++ + + + l eql ++++++ +lke+   l++e  + 
  gi|119719908|ref|YP_920403.1| 148 ATYGELSAALAEAQRKAYE-ADRLAEQVSQLSQRVRSLEIALANESGKCSALGEQLRSVSSEWGALKEKAGALKAENDAL 226
                                    6677888888888887766.333489999999999999999999999999999999999999999999999888887666 PP

                           Spc7 254 er 255
                                    + 
  gi|119719908|ref|YP_920403.1| 227 KA 228
                                    55 PP

>> STAT_alpha  STAT protein, all-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0       4.5   6.6e+02     147     171 ..     161     184 ..     145     185 .. 0.77
   2 !   14.1   0.1   0.00023     0.033       5      89 ..     199     282 ..     196     294 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 4.5
                     STAT_alpha 147 qkltyeedpeltdqlpqlneqvtel 171
                                    q+  ye d  l++q++ql+++v++l
  gi|119719908|ref|YP_920403.1| 161 QRKAYEADR-LAEQVSQLSQRVRSL 184
                                    444688777.999999999988775 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 0.00023
                     STAT_alpha   5 eqrleelrskvqeteqdirkLedeqeeFdfqyqelqkleqeraesekkelkkqkellqqmlnaLdqkRkelvdklkelln 84 
                                     ++l+ ++s+   ++++   L+ e + ++ +++el+++ ++r +se ++lk++k +l++ l++++++ ++l+++l  l +
  gi|119719908|ref|YP_920403.1| 199 GEQLRSVSSEWGALKEKAGALKAENDALKARVSELESE-NARLRSELASLKEEKGSLASRLTSVQESYQSLLTELGSLRQ 277
                                    5789999999999*************************.8888999999***********************99999999 PP

                     STAT_alpha  85 llesl 89 
                                    ++esl
  gi|119719908|ref|YP_920403.1| 278 KYESL 282
                                    99987 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   2.1     0.036       5.3      19      93 ..     147     221 ..     138     228 .. 0.84
   2 !   15.6   2.6   5.1e-05    0.0075      20     102 ..     211     293 ..     203     302 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.036
                        DUF3450  19 dqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeiee 93 
                                    +++  e ++a a+a++   + d+l+++ ++l++++r+l+  l++ + + + l ++++s+ +e   l+e+   +++
  gi|119719908|ref|YP_920403.1| 147 RATYGELSAALAEAQRKAYEADRLAEQVSQLSQRVRSLEIALANESGKCSALGEQLRSVSSEWGALKEKAGALKA 221
                                    5555677888899999999999999************99999999999999999999999999999999887776 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 5.1e-05
                        DUF3450  20 qalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeierelv 99 
                                    +++++a +  a+  +  +++++l+ e + l +e+ +lkee+ sl+     ++++ +s+ +e+ sl+++ e+++ ++++l+
  gi|119719908|ref|YP_920403.1| 211 ALKEKAGALKAENDALKARVSELESENARLRSELASLKEEKGSLASRLTSVQESYQSLLTELGSLRQKYESLSFVASALQ 290
                                    56667777778888889999999999999999999999999999999999999999999999999999999988888877 PP

                        DUF3450 100 pll 102
                                      l
  gi|119719908|ref|YP_920403.1| 291 AAL 293
                                    666 PP

>> CENP-H  Centromere protein H (CENP-H)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   1.1      0.18        27       7      60 ..     166     219 ..     160     225 .. 0.83
   2 ?   16.2   2.7   7.1e-05     0.011       6      92 ..     200     289 ..     195     292 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.18
                         CENP-H   7 qrdelssellklsqelrelqeeltevekenlrlkrknrelaaellelakekese 60 
                                    + d+l++++ +lsq +r+l+ +l++   +  +l ++ r+  +e   l++++ + 
  gi|119719908|ref|YP_920403.1| 166 EADRLAEQVSQLSQRVRSLEIALANESGKCSALGEQLRSVSSEWGALKEKAGAL 219
                                    5799999999********999999999999999999999999987777776655 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 7.1e-05
                         CENP-H   6 eqrdelssellklsqelrelqeeltevekenlrlkrknrelaaellelakekesek...eklkeelekleaelkksrqrw 82 
                                    eq   +sse  +l+++  +l++e + +++   +l+ +n+ l +el+ l++ek s     + ++e+ ++l +el   rq+ 
  gi|119719908|ref|YP_920403.1| 200 EQLRSVSSEWGALKEKAGALKAENDALKARVSELESENARLRSELASLKEEKGSLAsrlTSVQESYQSLLTELGSLRQKY 279
                                    677789999999**************************************99999988888******************* PP

                         CENP-H  83 rvvknvasai 92 
                                    + +  vasa+
  gi|119719908|ref|YP_920403.1| 280 ESLSFVASAL 289
                                    ****999997 PP

>> Jnk-SapK_ap_N  JNK_SAPK-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   8.5   0.00036     0.054      38     150 ..     153     268 ..     152     282 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00036
                  Jnk-SapK_ap_N  38 LeslasrneeeeaeleelreeleqLeteyerekelrkraeeeleeiedqwe...eerkelqekveqleeenrelelkakn 114
                                    L +++++ +++  e+++l e+++qL ++      +  ++  ++  + +q++   +e  +l+ek   l+ en+ l++++++
  gi|119719908|ref|YP_920403.1| 153 LSAALAEAQRKAYEADRLAEQVSQLSQRVRSLEIALANESGKCSALGEQLRsvsSEWGALKEKAGALKAENDALKARVSE 232
                                    667889999****************99766655555555555555555555111566779999999*********99999 PP

                  Jnk-SapK_ap_N 115 aadqlsrleekeaelkkeysklheretellkklkel 150
                                    ++ + +rl ++ a+lk+e+ +l +r t + ++++ l
  gi|119719908|ref|YP_920403.1| 233 LESENARLRSELASLKEEKGSLASRLTSVQESYQSL 268
                                    999999999999999999999999999998888766 PP

>> ArAE_2  Aromatic acid exporter family member 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.2   0.00015     0.022      19     114 ..     196     294 ..     180     314 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 0.00015
                         ArAE_2  19 selgdlyckvlsfaaerlenphihikaerdqirkkilevleklaglkgllvllkfEl.slkGrwps..kkyarlqalvse 95 
                                    s lg+   +v+s ++  l+++   +kae+d + +++ e+ ++ a+l+  l+ lk E  sl++r  s  ++y+ l + +++
  gi|119719908|ref|YP_920403.1| 196 SALGEQLRSVSSEWGA-LKEKAGALKAENDALKARVSELESENARLRSELASLKEEKgSLASRLTSvqESYQSLLTELGS 274
                                    5678888899****99.99************************************9648****9854499********** PP

                         ArAE_2  96 lvqllarLlvvlkrle.pee 114
                                    l q + +L +v + l+    
  gi|119719908|ref|YP_920403.1| 275 LRQKYESLSFVASALQaALV 294
                                    ***************73333 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   4.1   0.00012     0.018     329     922 ..     168     280 ..     139     324 .. 0.47

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00012
                        DUF3584 329 ealeeqkkkyedadieklkadldqlpsirseleeleeeldaltekhqdvqekydrrkqkikeeleeeleklkerleaire 408
                                    ++l eq                                                                          
  gi|119719908|ref|YP_920403.1| 168 DRLAEQVS------------------------------------------------------------------------ 175
                                    33333332........................................................................ PP

                        DUF3584 409 ekdrlkaaieealealesqlrkqleaqkeelneeekelesrlselklrldsatateEeleqieeadealekaqeelekae 488
                                                                                                                    
  gi|119719908|ref|YP_920403.1|   - --------------------------------------------------------------------------------   -
                                    ................................................................................ PP

                        DUF3584 489 aevealqaeeeqlrkkrdeadealqkaerrleqlrqaleeleeqlsPqagsLlefLrkeapdWeesigklispelLeRtD 568
                                                                                                                    
  gi|119719908|ref|YP_920403.1|   - --------------------------------------------------------------------------------   -
                                    ................................................................................ PP

                        DUF3584 569 LdPelvessekdtlyGvsLdleridvpdyaaseeeLrerlqaleealqsaeakqkqaeeelkqlnaeleeakravaeaat 648
                                                                                                                    
  gi|119719908|ref|YP_920403.1|   - --------------------------------------------------------------------------------   -
                                    ................................................................................ PP

                        DUF3584 649 alknardtlerlqnekesekdklekaiaerkqqaeeqlqkldaqlkqleeqqkaaleelkedlseerlekkakwqevvge 728
                                                                                                                    
  gi|119719908|ref|YP_920403.1|   - --------------------------------------------------------------------------------   -
                                    ................................................................................ PP

                        DUF3584 729 ldeqlaelkkaieaartqakarlkeleeaykreLkskdvDpetvkelkrkieeLekkieriekrreevreYraflqetwl 808
                                                                                 +l++++++Le  +++ + + +++ e  + + ++w 
  gi|119719908|ref|YP_920403.1| 176 ---------------------------------------------QLSQRVRSLEIALANESGKCSALGEQLRSVSSEWG 210
                                    .............................................33333333333333333333333333333333332 PP

                        DUF3584 809 kvds....laeerpalkeqveelesaaeeleqeltrliedtklerkklekerkalekqldqldenlrklrdllsklaelk 884
                                    + ++    l+ e++alk++v+eles+ ++l+ el+ l+e                                         
  gi|119719908|ref|YP_920403.1| 211 ALKEkagaLKAENDALKARVSELESENARLRSELASLKE----------------------------------------- 249
                                    222111112222333333333333333333333322222......................................... PP

                        DUF3584 885 ldadaeqaegelaerlaaleelkrkrerlsedvkkale 922
                                           ++g+la rl  ++e  +++  + ++++++ e
  gi|119719908|ref|YP_920403.1| 250 -------EKGSLASRLTSVQESYQSLLTELGSLRQKYE 280
                                    .......2334444444444444444444444444333 PP

>> APG17  Autophagy protein Apg17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.3   0.00011     0.016     247     329 ..     198     281 ..     195     285 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 0.00011
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHHHHH CS
                          APG17 247 lqerleemekakkllsekkeeiekllsalkkaleeleevgkklpeylaifkaeeeflerw.eeekekieekleeleeLre 325
                                    l e+l++++++  +l+ek+ ++++ ++alk+ ++ele+ +++l++ la +k+e+  l+   ++ +e+ ++ l el +Lr+
  gi|119719908|ref|YP_920403.1| 198 LGEQLRSVSSEWGALKEKAGALKAENDALKARVSELESENARLRSELASLKEEKGSLASRlTSVQESYQSLLTELGSLRQ 277
                                    668899999****************************99***********999988887669****************** PP

                                    HHHH CS
                          APG17 326 fYeg 329
                                     Ye+
  gi|119719908|ref|YP_920403.1| 278 KYES 281
                                    **85 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   4.9    0.0003     0.045      53     136 ..     152     235 ..     149     236 .. 0.96
   2 ?   10.3   3.0     0.004      0.59       3      66 ..     217     280 ..     215     290 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.0003
                  Tropomyosin_1  53 kleeklkeakekaeesekkktnnealtrkiqlLEeeleesdkkLkettekLretdvkaeelERkvkaLeqerdewekkye 132
                                    +l+++l ea++ka e+++++ +  +l+++++ LE  l + + k     e+Lr ++ + + l  k  aL +e+d+   ++ 
  gi|119719908|ref|YP_920403.1| 152 ELSAALAEAQRKAYEADRLAEQVSQLSQRVRSLEIALANESGKCSALGEQLRSVSSEWGALKEKAGALKAENDALKARVS 231
                                    57899*************************************************************************99 PP

                  Tropomyosin_1 133 elee 136
                                    ele+
  gi|119719908|ref|YP_920403.1| 232 ELES 235
                                    9875 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.004
                  Tropomyosin_1   3 nsLkleaeeaqekaeeleekvKeleqenlekeqeiksLtkknqqleeevekleeklkeakekae 66 
                                     +Lk+e+++ +++++ele+++ +l +e  +  +e  sL  ++  ++e    l ++l   ++k e
  gi|119719908|ref|YP_920403.1| 217 GALKAENDALKARVSELESENARLRSELASLKEEKGSLASRLTSVQESYQSLLTELGSLRQKYE 280
                                    589********************************************99999999988888776 PP

>> TolA_bind_tri  TolA binding protein trimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.2    0.0034       0.5       1      66 [.     176     241 ..     176     249 .. 0.86
   2 ?    4.3   1.6      0.28        42      21      71 ..     231     281 ..     219     284 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0034
                  TolA_bind_tri   1 sledrvarLErilearsqlllelqqqlealqqelreLRGqiEelqyqleqleerQrdlYldlDerl 66 
                                    +l +rv +LE +l+++s     l +ql + ++e   L+ +   l+ +++ l+ r  +l  +  ++ 
  gi|119719908|ref|YP_920403.1| 176 QLSQRVRSLEIALANESGKCSALGEQLRSVSSEWGALKEKAGALKAENDALKARVSELESENARLR 241
                                    689**********************************99999999999999999877766655555 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.28
                  TolA_bind_tri  21 lelqqqlealqqelreLRGqiEelqyqleqleerQrdlYldlDerlrklea 71 
                                     el ++  +l++el++L+ +   l+ +l +++e  + l ++l ++ +k e+
  gi|119719908|ref|YP_920403.1| 231 SELESENARLRSELASLKEEKGSLASRLTSVQESYQSLLTELGSLRQKYES 281
                                    567777788888888888888888888888888888888888888777665 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.6      0.61        90      25      50 ..     159     184 ..     148     192 .. 0.58
   2 ?   13.9   1.4   0.00022     0.033      22      52 ..     212     242 ..     200     255 .. 0.60
   3 ?    7.7   0.4      0.02         3      20      51 ..     231     262 ..     230     271 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.61
                                    HHHHHHHHHHHHHHHHHHHHHHHCC- CS
                          DivIC  25 eiaalqaelaklkaeneeLeaevkdL 50 
                                    e +++  e ++l ++  +L ++v+ L
  gi|119719908|ref|YP_920403.1| 159 EAQRKAYEADRLAEQVSQLSQRVRSL 184
                                    44444445555555555555555544 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 0.00022
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHCC-XX CS
                          DivIC  22 lkqeiaalqaelaklkaeneeLeaevkdLks 52 
                                    lk++  al+ae+++lka+  eLe+e ++L+s
  gi|119719908|ref|YP_920403.1| 212 LKEKAGALKAENDALKARVSELESENARLRS 242
                                    4555555555555555555555555555554 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.02
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-X CS
                          DivIC  20 kqlkqeiaalqaelaklkaeneeLeaevkdLk 51 
                                    ++l++e a+l  ela+lk+e+ +L++++   +
  gi|119719908|ref|YP_920403.1| 231 SELESENARLRSELASLKEEKGSLASRLTSVQ 262
                                    57899999999999999999999999987764 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0       3.3   4.9e+02      22      40 ..     166     184 ..     151     186 .. 0.70
   2 ?    0.4   0.1         6     9e+02       1      30 [.     180     209 ..     173     222 .. 0.66
   3 ?    3.0   0.0      0.93   1.4e+02       5      40 ..     198     233 ..     194     233 .. 0.75
   4 ?   12.2   0.6    0.0012      0.18       1      41 [.     229     269 ..     229     283 .. 0.96

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 3.3
                      FlaC_arch  22 eneelsksveelkenVkdl 40 
                                    e + l ++v +l ++V+ l
  gi|119719908|ref|YP_920403.1| 166 EADRLAEQVSQLSQRVRSL 184
                                    4566788888888888765 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 6
                      FlaC_arch   1 ridelEnklsklsteletvkkeneelsksv 30 
                                    r+ +lE  l + s + + + +++ ++s++ 
  gi|119719908|ref|YP_920403.1| 180 RVRSLEIALANESGKCSALGEQLRSVSSEW 209
                                    566666666666666666666666666655 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.93
                      FlaC_arch   5 lEnklsklsteletvkkeneelsksveelkenVkdl 40 
                                    l ++l ++s+e + +k++   l+ + + lk +V +l
  gi|119719908|ref|YP_920403.1| 198 LGEQLRSVSSEWGALKEKAGALKAENDALKARVSEL 233
                                    556788888888888888888888888888888765 PP

  == domain 4  score: 12.2 bits;  conditional E-value: 0.0012
                      FlaC_arch   1 ridelEnklsklsteletvkkeneelsksveelkenVkdll 41 
                                    r+ elE++  +l +el+++k+e  +l + ++ ++e+ + ll
  gi|119719908|ref|YP_920403.1| 229 RVSELESENARLRSELASLKEEKGSLASRLTSVQESYQSLL 269
                                    899********************************998887 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   1.2    0.0089       1.3     345     427 ..     166     248 ..     160     250 .. 0.77
   2 ?    9.9   1.8    0.0012      0.18      99     161 ..     219     281 ..     213     285 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0089
                                    THHHHHHHHHHHHHHHHHHHHHHS-SS---STTGGGTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           EzrA 345 klrelekelkelekdyeeleekleekkvaYSelqeeleeleekleeieekqeeileslkslrkdEkrAreqldeikkelk 424
                                    +++ l +++++l++++++le +l++++   S l e+l++++++  +++ek   ++ + ++l+   ++ + + +++++el 
  gi|119719908|ref|YP_920403.1| 166 EADRLAEQVSQLSQRVRSLEIALANESGKCSALGEQLRSVSSEWGALKEKAGALKAENDALKARVSELESENARLRSELA 245
                                    577899999**********************9999999988888888887777777777777666666666666666666 PP

                                    HHH CS
                           EzrA 425 eik 427
                                    ++k
  gi|119719908|ref|YP_920403.1| 246 SLK 248
                                    555 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0012
                                    TTHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHHHHHHHHHHT--TTTTHHHH CS
                           EzrA  99 akkklaeleeeldeveekikkileelkelteseeknreeieklkekYrelrkkllanrfsyge 161
                                    +k++ ++l+++++e+e++ +++++el+ l+e +    ++ ++++e Y++l ++l + r++y++
  gi|119719908|ref|YP_920403.1| 219 LKAENDALKARVSELESENARLRSELASLKEEKGSLASRLTSVQESYQSLLTELGSLRQKYES 281
                                    566777888899999999999999999999999999999999999999999999888888876 PP

>> Fzo_mitofusin  fzo-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00064     0.095      98     153 ..     169     224 ..     155     230 .. 0.91
   2 ?    3.8   0.6      0.25        37     118     159 ..     220     265 ..     218     293 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00064
                  Fzo_mitofusin  98 elsstfarlcqqvdetekeleeeikelekeiekleevqkkakllrnkaslleseLe 153
                                    +l++ +++l+q+v+  e  l +e  + ++  e+l +v+++  +l++ka  l++e +
  gi|119719908|ref|YP_920403.1| 169 RLAEQVSQLSQRVRSLEIALANESGKCSALGEQLRSVSSEWGALKEKAGALKAEND 224
                                    789999*********************************************99865 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.25
                  Fzo_mitofusin 118 eeeikelekeieklee....vqkkakllrnkaslleseLekfeeqy 159
                                    ++e ++l++++++le+    + +++  l+++  +l+s+L++ +e+y
  gi|119719908|ref|YP_920403.1| 220 KAENDALKARVSELESenarLRSELASLKEEKGSLASRLTSVQESY 265
                                    5566666666666665111123445567888888888888877777 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0       2.9   4.2e+02      97     114 ..     168     185 ..     147     194 .. 0.54
   2 ?   11.7   0.1    0.0014      0.21      42     122 ..     194     277 ..     187     282 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 2.9
                        DUF1664  97 seigedvesvkeavegle 114
                                    +++ e+v+++++ v++le
  gi|119719908|ref|YP_920403.1| 168 DRLAEQVSQLSQRVRSLE 185
                                    333444444444444444 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.0014
                        DUF1664  42 avesvskqleqvseslaatkrh...Lssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskle 118
                                     ++ +++ql +vs++  a k++   L+++ d + +++ e +   + +++e+++++e+  ++ + ++sv+e  ++l ++l 
  gi|119719908|ref|YP_920403.1| 194 KCSALGEQLRSVSSEWGALKEKagaLKAENDALKARVSELESENARLRSELASLKEEKGSLASRLTSVQESYQSLLTELG 273
                                    58899999999997655555433339999999999999999999999999999999999999999999999999999888 PP

                        DUF1664 119 riee 122
                                    ++ +
  gi|119719908|ref|YP_920403.1| 274 SLRQ 277
                                    8876 PP

>> TSC22  TSC-22/dip/bun family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0       2.2   3.2e+02      16      35 ..     167     186 ..     165     209 .. 0.70
   2 ?   12.0   0.5    0.0013      0.19      13      41 ..     220     248 ..     211     278 .. 0.70

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 2.2
                          TSC22  16 VevLkekIkeLeernselee 35 
                                     + L e++  L +r++ le 
  gi|119719908|ref|YP_920403.1| 167 ADRLAEQVSQLSQRVRSLEI 186
                                    57899999999999999984 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.0013
                          TSC22  13 rEeVevLkekIkeLeernseleeENslLk 41 
                                    + e + Lk ++ eLe++n++l++E + Lk
  gi|119719908|ref|YP_920403.1| 220 KAENDALKARVSELESENARLRSELASLK 248
                                    33445555555555555555555555555 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   1.0     0.036       5.3     202     252 ..     158     208 ..     147     225 .. 0.83
   2 ?   10.7   1.8    0.0019      0.29      19      82 ..     229     277 ..     213     299 .. 0.45

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.036
                                    XXXXXXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Filament 202 eaaeknsealrsakeeitelrrqiqsleieleslkkqkasleaqlaeleer 252
                                     +a+++  ++ +  e++++l +++ slei l++  +++++l +ql+ +  +
  gi|119719908|ref|YP_920403.1| 158 AEAQRKAYEADRLAEQVSQLSQRVRSLEIALANESGKCSALGEQLRSVSSE 208
                                    57888889999999******************************9988765 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0019
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       Filament  19 kVraLEqenkeLeakieeleekksaevsklkelyekeleelrkqldeltkerarlqleldnlre 82 
                                    +V  LE en++L+++++ l+e+k                +l ++l ++++  + l  el++lr+
  gi|119719908|ref|YP_920403.1| 229 RVSELESENARLRSELASLKEEK---------------GSLASRLTSVQESYQSLLTELGSLRQ 277
                                    33444444444444444444433...............22222333333333333333333332 PP

>> Bap31_Bap29_C  Bap31/Bap29 cytoplasmic coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1      0.83   1.2e+02      28      42 ..     162     179 ..     158     194 .. 0.73
   2 ?    8.2   0.1     0.017       2.5       4      41 ..     196     233 ..     193     238 .. 0.87
   3 ?    7.3   1.1     0.031       4.6       2      41 ..     236     275 ..     235     282 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.83
                  Bap31_Bap29_C  28 akEY..DrLadehskl.d 42 
                                     k+Y  DrLa+++s+l +
  gi|119719908|ref|YP_920403.1| 162 RKAYeaDRLAEQVSQLsQ 179
                                    5555559********952 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.017
                  Bap31_Bap29_C   4 ekLkkeLkkkkkDlealKkQaeglakEYDrLadehskl 41 
                                    ++L ++L + +++  alK++a  l++E D L   +s+l
  gi|119719908|ref|YP_920403.1| 196 SALGEQLRSVSSEWGALKEKAGALKAENDALKARVSEL 233
                                    57889999999********************9999999 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.031
                  Bap31_Bap29_C   2 eiekLkkeLkkkkkDlealKkQaeglakEYDrLadehskl 41 
                                    e+++L++eL++ k ++  l +   +++  Y  L++e   l
  gi|119719908|ref|YP_920403.1| 236 ENARLRSELASLKEEKGSLASRLTSVQESYQSLLTELGSL 275
                                    899*********************************8877 PP

>> SLATT_4  SMODS and SLOG-associating 2TM effector domain family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.4    0.0007       0.1      84     131 ..     246     293 ..     239     317 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0007
                        SLATT_4  84 eeaqkhraaAnkLwkiRekylsLltdlksgalsleearkkrDeLqeel 131
                                    +  ++    A++L +++e+y+sLlt+l s +++ e++     +Lq++l
  gi|119719908|ref|YP_920403.1| 246 SLKEEKGSLASRLTSVQESYQSLLTELGSLRQKYESLSFVASALQAAL 293
                                    566777789******************997777777766666666655 PP

>> Golgin_A5  Golgin subfamily A member 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   3.0   0.00026     0.039      83     204 ..     169     290 ..     148     326 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00026
                      Golgin_A5  83 qqqaeaeslreqlqeleeqleeerkakeeveaelerlkeelryleee...lvrskatlqsrikdrekeieklrnqlttks 159
                                    +  +++++l +++++le +l++e+ +  ++ ++l++++ e  +l+e    l+ +   l++r+ + e+e  +lr++l++ +
  gi|119719908|ref|YP_920403.1| 169 RLAEQVSQLSQRVRSLEIALANESGKCSALGEQLRSVSSEWGALKEKagaLKAENDALKARVSELESENARLRSELASLK 248
                                    33455788899999999999999999999999999999998888887222344445566777777777777777776654 PP

                      Golgin_A5 160 lsssseselesRlkqLtesLiqKQtvlEalsteknslvlQLeRle 204
                                        ++  l sRl +  es     t l +l   ++sl +    l+
  gi|119719908|ref|YP_920403.1| 249 E---EKGSLASRLTSVQESYQSLLTELGSLRQKYESLSFVASALQ 290
                                    4...4688999***9999999999999999999999988655555 PP

>> Macoilin  Macoilin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   6.9    0.0032      0.48     400     474 ..     176     250 ..     130     293 .. 0.52

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0032
                       Macoilin 400 rLeadikkLkaeLqasrqteqelrskissltseerslkselqqlkkendllqtklhelvsakqkdkqtlqqlekr 474
                                    +L + ++ L   L+++  + + l +++ s +se  +lk++ ++lk end l++++ el s+  + + +l +l   
  gi|119719908|ref|YP_920403.1| 176 QLSQRVRSLEIALANESGKCSALGEQLRSVSSEWGALKEKAGALKAENDALKARVSELESENARLRSELASLKEE 250
                                    444455555555555555555555555555555555555555555555555555555555544444444443221 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   3.4   0.00056     0.083     102     180 ..     172     250 ..     152     285 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00056
                         DUF724 102 deqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaekleeeledveqe 180
                                    ++ ++l ++ + le  +++e+ + + l e+++ ++++   l++++ +lk++++a ++++++l+se+++l+ el + ++e
  gi|119719908|ref|YP_920403.1| 172 EQVSQLSQRVRSLEIALANESGKCSALGEQLRSVSSEWGALKEKAGALKAENDALKARVSELESENARLRSELASLKEE 250
                                    5667777888888888888888888888888888888888888888888888888888888888888888888887776 PP

>> HOOK  HOOK protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   6.6    0.0023      0.34     355     559 ..     170     243 ..     143     290 .. 0.42

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0023
                           HOOK 355 lrsqlelykkqvqelhkklseeskkadklefelkkleeklealqkekerllaerdaLketneELkcaqlqqkelsqadal 434
                                    l  q+  + ++v+ l+  l +es k+  l  +l+ +     al+     l ae daLk  + EL+  ++  ++       
  gi|119719908|ref|YP_920403.1| 170 LAEQVSQLSQRVRSLEIALANESGKCSALGEQLRSVSSEWGALKEKAGALKAENDALKARVSELESENARLRS------- 242
                                    3334444444444444444444444444444444444444444444444444444444444444433322222....... PP

                           HOOK 435 askssssgenlaaellpaevreklirLqhENKmLklkqegseeekltelqelledanrrkneLetenrlanqrileLeaq 514
                                                                                                                    
  gi|119719908|ref|YP_920403.1|   - --------------------------------------------------------------------------------   -
                                    ................................................................................ PP

                           HOOK 515 veelqkalqeqgskaedssllkkkleehleklkevqeelqkkkeq 559
                                                                                 
  gi|119719908|ref|YP_920403.1| 243 --------------------------------------------E 243
                                    ............................................1 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   6.9   5.9e-05    0.0087      36     172 ..     165     306 ..     147     323 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.9e-05
                          Atg14  36 sekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklkkRr 115
                                     e + l ++++++ ++ +   +le ++ n++ k + l  + ++ +++   lk+k   lk+e+++ k+++++l +++++ r
  gi|119719908|ref|YP_920403.1| 165 YEADRLAEQVSQLSQRVR---SLEIALANESGKCSALGEQLRSVSSEWGALKEKAGALKAENDALKARVSELESENARLR 241
                                    455555556665555555...77777888888888888888888899********************************* PP

                          Atg14 116 sdleslqneleerrkkqiaklqdaik.........rieqklsslssktlesrsslcselaklyglr 172
                                    s+l+sl++e  +  ++ ++++q++++         r+++   s+  + l++ ++ +  +a+++ l+
  gi|119719908|ref|YP_920403.1| 242 SELASLKEEKGSL-ASRLTSVQESYQslltelgslRQKYESLSFVASALQAALVALAAVAAVAFLK 306
                                    ******9998876.5778999999997777777666666666666666666666666666665555 PP

>> Tropomyosin  Tropomyosin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   6.8   0.00077      0.11     127     227 ..     151     258 ..     142     283 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00077
                    Tropomyosin 127 sdLeraeeraeaaeskiveLeeeLkvvgnnlksLevseekaseredeyeeeirtLeekLkeaeeRae..eAEr.....sv 199
                                    ++L  a + a+++  ++  L e++   ++ ++sLe++ ++ s +  +  e++r++++   + +e+a   +AE      +v
  gi|119719908|ref|YP_920403.1| 151 GELSAALAEAQRKAYEADRLAEQVSQLSQRVRSLEIALANESGKCSALGEQLRSVSSEWGALKEKAGalKAENdalkaRV 230
                                    689999999999999****************************************9986665555432256652222368 PP

                    Tropomyosin 200 qkLekevdrledeleaekekykaiseeL 227
                                    ++Le+e+ rl  el + ke++ ++   L
  gi|119719908|ref|YP_920403.1| 231 SELESENARLRSELASLKEEKGSLASRL 258
                                    99*****************998888777 PP

>> Leu_zip  Leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   4.6    0.0018      0.26     134     232 ..     166     268 ..     155     281 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0018
                        Leu_zip 134 eierLkeenekLkerlkelEkqatsaleeksklekalkelqkelgekkdeke.nskeiskleeklaelkldlek...tle 209
                                    e +rL e+ ++L++r+++lE  + +   + s+l ++l+++ +e g+ k+++   ++e   l+++++el+++  +   +l 
  gi|119719908|ref|YP_920403.1| 166 EADRLAEQVSQLSQRVRSLEIALANESGKCSALGEQLRSVSSEWGALKEKAGaLKAENDALKARVSELESENARlrsELA 245
                                    7789********************999*************9999999877663333334445555555544333111444 PP

                        Leu_zip 210 ektasaksleedlastkhelLkv 232
                                    + ++++ sl++ l+s ++ + ++
  gi|119719908|ref|YP_920403.1| 246 SLKEEKGSLASRLTSVQESYQSL 268
                                    44555555555555555554444 PP

>> CCDC144C  CCDC144C protein coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   7.3    0.0016      0.24     149     268 ..     153     275 ..     146     282 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0016
                       CCDC144C 149 LsqqLskaeska...nsLenelhetrdaLrektlllesvqrdlsqaqcqikeleqmyqneeekvnkyiakqesleerlaq 225
                                    Ls  L++a++ka    +L +++ ++++ +r   ++l +     s    q++ + +   + +ek     a++++l+ r+++
  gi|119719908|ref|YP_920403.1| 153 LSAALAEAQRKAyeaDRLAEQVSQLSQRVRSLEIALANESGKCSALGEQLRSVSSEWGALKEKAGALKAENDALKARVSE 232
                                    56666666665422245666666666666666666666666666666666666666677777777777777777777777 PP

                       CCDC144C 226 lqsenmlLrqqLedaqnkadakekvvidiqdqfqdivkkLqae 268
                                    l+sen+ Lr  L   +++  +    ++++q+ +q+ +++L + 
  gi|119719908|ref|YP_920403.1| 233 LESENARLRSELASLKEEKGSLASRLTSVQESYQSLLTELGSL 275
                                    7777777777777776666666666677777777777666544 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1      0.13        19       5      64 ..     160     219 ..     156     224 .. 0.86
   2 ?    5.9   0.5     0.071        11       5      58 ..     188     241 ..     170     250 .. 0.69
   3 ?    7.2   1.0     0.029       4.3      12      64 ..     230     282 ..     222     297 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.13
                          Sec34   5 LeskeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeei 64 
                                     ++k  e d+l eq++++ + +++le    + s k s+l e+  ++ +e   l+e a ++
  gi|119719908|ref|YP_920403.1| 160 AQRKAYEADRLAEQVSQLSQRVRSLEIALANESGKCSALGEQLRSVSSEWGALKEKAGAL 219
                                    56778899999***************9999999999999999999999988888887666 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.071
                          Sec34   5 LeskeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrle 58 
                                    L +++ +c +l eq++++ ++   l+ek  + +++  +l+++  +l +e+ rl+
  gi|119719908|ref|YP_920403.1| 188 LANESGKCSALGEQLRSVSSEWGALKEKAGALKAENDALKARVSELESENARLR 241
                                    455566677777777777777777777777777777777777777777776665 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.029
                          Sec34  12 cdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeei 64 
                                    + el ++  ++ ++L++l+e+  s +++ +s++e+ ++ll+e  +l++ +e++
  gi|119719908|ref|YP_920403.1| 230 VSELESENARLRSELASLKEEKGSLASRLTSVQESYQSLLTELGSLRQKYESL 282
                                    56666777777888888888888888888888888888888888888887765 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1      0.25        38      44      83 ..     168     207 ..     152     220 .. 0.77
   2 ?    6.3   0.2     0.091        13      44     101 ..     224     281 ..     211     283 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.25
                                    H...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH....... CS
                          DUF16  44 dklgeqinkleqkvekqgekikelkveqkaqgeelnkvde 83 
                                    d l eq+++l q v+ ++  + + + +  a ge+l +v +
  gi|119719908|ref|YP_920403.1| 168 DRLAEQVSQLSQRVRSLEIALANESGKCSALGEQLRSVSS 207
                                    4667888888888888888888888888888888876654 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.091
                                    H...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHHHHHHHHH CS
                          DUF16  44 dklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetleliletLqkinkRlDs 101
                                    d+l+ ++++le +  ++  ++  lk+e      +l +v+e+ +++l  L ++ ++  s
  gi|119719908|ref|YP_920403.1| 224 DALKARVSELESENARLRSELASLKEEKGSLASRLTSVQESYQSLLTELGSLRQKYES 281
                                    4567788888888888888888999999999999999999999999999998887766 PP

>> Rootletin  Ciliary rootlet component, centrosome cohesion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   8.2    0.0015      0.22      17     130 ..     166     277 ..     147     288 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0015
                      Rootletin  17 LvskLqaKvlqYkkrcseleqrllektselektkltlllssareleeeesadleealakLeeE....rqrseklaqvnsl 92 
                                       +L ++v q  +r+++le  l++++ ++         ++  +  ++e   l+e    L+ E    + r ++l+++n+ 
  gi|119719908|ref|YP_920403.1| 166 EADRLAEQVSQLSQRVRSLEIALANESGKCSALG-----EQL-RSVSSEWGALKEKAGALKAEndalKARVSELESENAR 239
                                    3456667777777777777777766333332222.....122.2333444455566666666622223466777777777 PP

                      Rootletin  93 LreqleearqaneaLtedlqkltkdwerlreeleqkek 130
                                    Lr +l   +++  +L + l+ +++  ++l +el +  +
  gi|119719908|ref|YP_920403.1| 240 LRSELASLKEEKGSLASRLTSVQESYQSLLTELGSLRQ 277
                                    77777777777777777777777766666666654444 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.9    0.0015      0.22     266     330 ..     196     260 ..     149     293 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0015
                          IFT57 266 kylnsqleellqeyreaqeelsevkekykqlsegvseltrelaeiseelekvkqemeergssmtD 330
                                    + l +ql++  +e+ +++e+  ++k + + l+++vsel+ e a++  el ++k+e  +  s++t 
  gi|119719908|ref|YP_920403.1| 196 SALGEQLRSVSSEWGALKEKAGALKAENDALKARVSELESENARLRSELASLKEEKGSLASRLTS 260
                                    45677888888888888888888888888888888888888888888888888776666666654 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.4     0.087        13       7      56 ..     164     208 ..     152     216 .. 0.77
   2 ?    9.8   3.2    0.0062      0.92       7      68 ..     220     283 ..     217     283 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.087
                   ABC_tran_CTD   7 qreleeleaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleae 56 
                                      e ++l ++  +L ++  +le +la+++      k ++l ++l  + +e
  gi|119719908|ref|YP_920403.1| 164 AYEADRLAEQVSQLSQRVRSLEIALANES-----GKCSALGEQLRSVSSE 208
                                    3466689999999*********9999988.....6777777777666555 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0062
                   ABC_tran_CTD   7 qreleeleaeIeaLEeeiaeleaeladpelysdp..eklaelsaeleeleaeLeelyerWeeLe 68 
                                    + e ++l a+  +LE e a l  ela+    + +   +l+ +++ ++ l +eL  l +++e L+
  gi|119719908|ref|YP_920403.1| 220 KAENDALKARVSELESENARLRSELASLKEEKGSlaSRLTSVQESYQSLLTELGSLRQKYESLS 283
                                    678899*******************987755555667899999999999999999999999886 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   2.1    0.0011      0.16      18     129 ..     169     282 ..     154     297 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0011
                        DUF4795  18 klqeelekleekvkelekrledkekklealkkqieelekvkadkeeveeelaekadkeaLatkvsrdq.....fDeakke 92 
                                     l e++++l+++v++le  l++++ k  al +q++   ++ +     e++ a+ka  +aL++ vs+ +     + + ++ 
  gi|119719908|ref|YP_920403.1| 169 RLAEQVSQLSQRVRSLEIALANESGKCSALGEQLRSVSSEWGA--LKEKAGALKAENDALKARVSELEsenarLRSELAS 246
                                    5778999999999999999999999999999999999888766..4567789************8877777778888888 PP

                        DUF4795  93 LekmleellekleeqeealkkaldtLqeelkekldrl 129
                                    L++   +l ++l++++e+ +++l +L  +l +k + l
  gi|119719908|ref|YP_920403.1| 247 LKEEKGSLASRLTSVQESYQSLLTELG-SLRQKYESL 282
                                    88888999999***************9.888888754 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.7    0.0012      0.18     120     228 ..     167     271 ..     163     273 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0012
                           CorA 120 vdrlfellekleeeldeledel.edstkkeilrelaq.lrrrlvklrralapnrevlkrllakaddkllddedkeylrdl 197
                                    +drl+e++++l+++++ le  l ++s k + l+e ++ +  + + l++ + ++++   + l+ a+ ++l++e+     +l
  gi|119719908|ref|YP_920403.1| 167 ADRLAEQVSQLSQRVRSLEIALaNESGKCSALGEQLRsVSSEWGALKEKAGALKAEN-DALK-ARVSELESEN----ARL 240
                                    689999999999999999999974444444444433325555666655444444444.3334.5777888887....99* PP

                           CorA 198 ldelerllemlealrerleslqdtyssllse 228
                                    ++el++l e+  +l++rl+s+q++y+sll+e
  gi|119719908|ref|YP_920403.1| 241 RSELASLKEEKGSLASRLTSVQESYQSLLTE 271
                                    ***************************9875 PP

>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.7      0.04         6      19      72 ..     165     218 ..     161     220 .. 0.92
   2 ?    9.7   7.0    0.0057      0.85      20      71 ..     208     259 ..     200     268 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.04
                     TMF_DNA_bd  19 eEGekLskkelklnntikkLrkknkelekeikelkkkleklekeleeleerlke 72 
                                    +E  +L+ +  +l++ + +L   +++   + + l ++l+++++e   l+e++ +
  gi|119719908|ref|YP_920403.1| 165 YEADRLAEQVSQLSQRVRSLEIALANESGKCSALGEQLRSVSSEWGALKEKAGA 218
                                    68899********************************************99876 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0057
                     TMF_DNA_bd  20 EGekLskkelklnntikkLrkknkelekeikelkkkleklekeleeleerlk 71 
                                    E  +L+ k  +l++  + L++ ++ele+e ++l ++l++l +e  +l +rl+
  gi|119719908|ref|YP_920403.1| 208 EWGALKEKAGALKAENDALKARVSELESENARLRSELASLKEEKGSLASRLT 259
                                    5556777777777788888888888888888888888888888888888876 PP

>> Seadorna_VP6  Seadornavirus VP6 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.2    0.0014      0.21      28      62 ..     204     237 ..     187     267 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0014
                   Seadorna_VP6  28 gvsfdelvalreenaklkqenealkaklhrlesdw 62 
                                     vs  e  al+e+   lk en+alka++  les+ 
  gi|119719908|ref|YP_920403.1| 204 SVS-SEWGALKEKAGALKAENDALKARVSELESEN 237
                                    555.5788************************985 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   4.6    0.0031      0.47      67     150 ..     195     281 ..     121     291 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0031
                        UPF0242  67 kskleekeaklteldeglktkeealee....lqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelklelee 142
                                     s l e+ + ++++   lk+k+ al+     l+++  eL+ e +   +el+ lkee+ +L ++l  ++e ++ l+ el  
  gi|119719908|ref|YP_920403.1| 195 CSALGEQLRSVSSEWGALKEKAGALKAendaLKARVSELESENARLRSELASLKEEKGSLASRLTSVQESYQSLLTELG- 273
                                    4445555555555554444444444430011334445566667777888888888888898888888888888887775. PP

                        UPF0242 143 qLaekqel 150
                                     L++k e 
  gi|119719908|ref|YP_920403.1| 274 SLRQKYES 281
                                    35665555 PP

>> EMP24_GP25L  emp24/gp25L/p24 family/GOLD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   1.7     0.012       1.8     101     178 ..     232     306 ..     152     307 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.012
                    EMP24_GP25L 101 asdykdsakkekletleselkkleekldsikreqkylrereerlrdtnestnsrvvwwsilqllvlvlvavlqvyyLk 178
                                    + +++++   ++l +l++e   l ++l+s+++  ++l +   +lr+ +es+    ++ s lq ++++l+av  v +Lk
  gi|119719908|ref|YP_920403.1| 232 ELESENARLRSELASLKEEKGSLASRLTSVQESYQSLLTELGSLRQKYESLS---FVASALQAALVALAAVAAVAFLK 306
                                    2225555556777777777777999999999999999999999999999986...57777888888888777777776 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   1.3    0.0016      0.23     340     411 ..     210     275 ..     152     297 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0016
                           FapA 340 keleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeelesk 411
                                     +l+e+  +l++e + lk+++++l++++      ++ +++l++l+e+k +l ++l++++e +++l  el s 
  gi|119719908|ref|YP_920403.1| 210 GALKEKAGALKAENDALKARVSELESEN------ARLRSELASLKEEKGSLASRLTSVQESYQSLLTELGSL 275
                                    3444444555555555555555555422......33445555555555555555555555555555555554 PP

>> FAM76  FAM76 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.6    0.0014      0.21     216     298 ..     168     250 ..     143     252 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0014
                          FAM76 216 dhlv.avtqLkeeiaslkkqleqkdqellekdkkitelkaellekekelreklkelekeakekieklekkirellkevae 294
                                    d+l  +v+qL ++++sl+  l++   + ++   ++ ++ +e    ++     lk+ +   k+++++le+++++l+ e+a+
  gi|119719908|ref|YP_920403.1| 168 DRLAeQVSQLSQRVRSLEIALANESGKCSALGEQLRSVSSEWGALKE-KAGALKAENDALKARVSELESENARLRSELAS 246
                                    44442588888888888888888888888888888888887766654.45668888999999*****************9 PP

                          FAM76 295 lskk 298
                                    l+++
  gi|119719908|ref|YP_920403.1| 247 LKEE 250
                                    9876 PP

>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.3      0.13        20      27      65 ..     153     190 ..     146     200 .. 0.77
   2 ?    9.0   1.5     0.008       1.2      28      67 ..     206     248 ..     196     283 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.13
                           CdvA  27 leealkklkekakelkeklkkrlkeledqikslekalan 65 
                                    l+ al++ ++ka e +++l +++++l + ++sle alan
  gi|119719908|ref|YP_920403.1| 153 LSAALAEAQRKAYE-ADRLAEQVSQLSQRVRSLEIALAN 190
                                    44555555555555.589*******************98 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.008
                           CdvA  28 eealkklkekakelk...eklkkrlkeledqikslekalanlk 67 
                                    +++  +lkeka +lk   + lk+r++ele++ ++l + la+lk
  gi|119719908|ref|YP_920403.1| 206 SSEWGALKEKAGALKaenDALKARVSELESENARLRSELASLK 248
                                    5666678888877763336799999999999999999998887 PP

>> SOGA  Protein SOGA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   1.3      0.11        17      27      92 ..     171     237 ..     164     237 .. 0.54
   2 ?    9.8   3.9     0.011       1.7      13      70 ..     220     271 ..     212     291 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.11
                           SOGA  27 eeenkqlteeLnkyksklgeeessleeee.eassdsskeaelkeeLklarlqineLsgkvvkLqven 92 
                                    +e+  ql + ++ +   l +e+++ ++ + +  s ss+  +lke+  + + + + L+ +v +L+ en
  gi|119719908|ref|YP_920403.1| 171 AEQVSQLSQRVRSLEIALANESGKCSALGeQLRSVSSEWGALKEKAGALKAENDALKARVSELESEN 237
                                    4444444444444444444444444333323344445556777777777777777777777777776 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.011
                           SOGA  13 eeEaeLlrrslseleeenkqlteeLnkyksklgeeessleeeeeassdsskeaelkee 70 
                                    + E + l+ ++sele en +l++eL+ +k + g+  s l++ +      ++ ++l  e
  gi|119719908|ref|YP_920403.1| 220 KAENDALKARVSELESENARLRSELASLKEEKGSLASRLTSVQ------ESYQSLLTE 271
                                    568888999**********************999998887622......222334444 PP

>> Mto2_bdg  Micro-tubular organiser Mto1 C-term Mto2-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   4.0    0.0054      0.81      24      51 ..     223     250 ..     212     251 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0054
                       Mto2_bdg  24 rsgarerLeelkaeNrlLkaeLerdrsh 51 
                                    +   ++r +el+ eN++L+ eL+ +++ 
  gi|119719908|ref|YP_920403.1| 223 NDALKARVSELESENARLRSELASLKEE 250
                                    56679******************99986 PP

>> Tup_N  Tup N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0       6.7     1e+03      23      43 ..     158     179 ..     149     190 .. 0.75
   2 ?    8.6   0.2     0.016       2.3       4      56 ..     200     252 ..     197     278 .. 0.63

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 6.7
                          Tup_N  23 lkaqkdeyelk.iqsqiqElqq 43 
                                     +aq++ ye+  +++q++ l q
  gi|119719908|ref|YP_920403.1| 158 AEAQRKAYEADrLAEQVSQLSQ 179
                                    5678888998778888887754 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.016
                          Tup_N   4 elLdavkqEfdalsqeasslkaqkdeyelkiqsqiqElqqirqtlyeLeeahr 56 
                                    e L  v +E+ al+++a  lka++d + +++++  +E +++r++l  L+e+  
  gi|119719908|ref|YP_920403.1| 200 EQLRSVSSEWGALKEKAGALKAENDALKARVSELESENARLRSELASLKEEKG 252
                                    56666777777777777777777776666666666666666666666665543 PP

>> PRKG1_interact  cGMP-dependent protein kinase interacting domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   6.4     0.021       3.1      11      93 ..     165     254 ..     145     254 .. 0.68
   2 ?    8.8   1.6      0.02         3       8      43 ..     232     267 ..     227     286 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.021
                 PRKG1_interact  11 eenerLkreLeelekelselkseleklkqqrqe..........svskrssllelekrerrslerkiseleeelkeleeLr 80 
                                     e +rL +++++l++++++l+  l++ + + +           +  + ++ + + k e+ +l+ ++sele+e+   ++Lr
  gi|119719908|ref|YP_920403.1| 165 YEADRLAEQVSQLSQRVRSLEIALANESGKCSAlgeqlrsvssEWGALKEKAGALKAENDALKARVSELESEN---ARLR 241
                                    5677888888888888888888777765442223344443332233334444456778888888888888876...6899 PP

                 PRKG1_interact  81 aenqrLkdEngAL 93 
                                    +e + Lk+E g+L
  gi|119719908|ref|YP_920403.1| 242 SELASLKEEKGSL 254
                                    9999999999987 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.02
                 PRKG1_interact   8 eekeenerLkreLeelekelselkseleklkqqrqe 43 
                                    e ++en rL++eL +l++e+ +l s+l++++++ q+
  gi|119719908|ref|YP_920403.1| 232 ELESENARLRSELASLKEEKGSLASRLTSVQESYQS 267
                                    5678999**************999999999876544 PP

>> Cep57_CLD_2  Centrosome localisation domain of PPC89
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   1.5      0.23        34       3      63 ..     165     225 ..     164     228 .. 0.82
   2 ?   14.0   8.5   0.00026     0.039       1      61 [.     219     279 ..     219     293 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.23
                    Cep57_CLD_2   3 aevktLqnrLdsltrklqvheeelkrLnkERdsalrqLgvAyeelneLkaevealrkELke 63 
                                    +e  +L ++ ++l++++ + e++l++ +   +    qL++  +e   Lk++  al+ E++ 
  gi|119719908|ref|YP_920403.1| 165 YEADRLAEQVSQLSQRVRSLEIALANESGKCSALGEQLRSVSSEWGALKEKAGALKAENDA 225
                                    5667788888888888888888888888888888899999999999999999999999876 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 0.00026
                    Cep57_CLD_2   1 LeaevktLqnrLdsltrklqvheeelkrLnkERdsalrqLgvAyeelneLkaevealrkEL 61 
                                    L+ae+ +L+ r + l+++++   +el++L  E  s +++L +  e  ++L  e+ +lr++ 
  gi|119719908|ref|YP_920403.1| 219 LKAENDALKARVSELESENARLRSELASLKEEKGSLASRLTSVQESYQSLLTELGSLRQKY 279
                                    789*******************************************************984 PP

>> DUF4515  Domain of unknown function (DUF4515)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   2.6   0.00089      0.13     139     199 ..     212     271 ..     200     282 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00089
                        DUF4515 139 lkkkakalklaAkkalseftrsvkreNqeLrkeLlqliketkkLekekskLeeqkqrlkee 199
                                    lk ka alk++   al+ ++ +++ eN  Lr eL+ l +e  +L+++    +e+ q l+ e
  gi|119719908|ref|YP_920403.1| 212 LKEKAGALKAE-NDALKARVSELESENARLRSELASLKEEKGSLASRLTSVQESYQSLLTE 271
                                    67777777776.5688899999999***************999999999999999888776 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   5.2    0.0031      0.46     402     490 ..     192     283 ..     148     291 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0031
                         DUF812 402 qalveasaqrlvelakqWekhRv...plieeyrelkesksekekeaerkleeikklrekmkevaeelrqkeellkqLvae 478
                                       + a  ++l +++++W + ++   +l +e  +lk + se e+e  r  +e+++l+e+   +a+ l + +e+++ L++e
  gi|119719908|ref|YP_920403.1| 192 SGKCSALGEQLRSVSSEWGALKEkagALKAENDALKARVSELESENARLRSELASLKEEKGSLASRLTSVQESYQSLLTE 271
                                    467888999999999999765542227999999**********************************************9 PP

                         DUF812 479 leklpkdvsRsa 490
                                    l +l ++ +  +
  gi|119719908|ref|YP_920403.1| 272 LGSLRQKYESLS 283
                                    999988776555 PP

>> Flu_M1_C  Influenza Matrix protein (M1) C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.3     0.003      0.44      35      91 ..     157     213 ..     143     217 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.003
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       Flu_M1_C  35 magssekaeevqklaeelrqnvqvlrslGasqksseGlkkdllevlkayqkrmGvlv 91 
                                    +a +  ka e+ +lae++ q  q +rsl     +  G    l e+l++  +  G+l 
  gi|119719908|ref|YP_920403.1| 157 LAEAQRKAYEADRLAEQVSQLSQRVRSLEIALANESGKCSALGEQLRSVSSEWGALK 213
                                    5677899****************************************9999999875 PP

>> BRE1  BRE1 E3 ubiquitin ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.7      0.19        28       3      65 ..     151     213 ..     149     216 .. 0.85
   2 ?   10.5   1.4    0.0033      0.49       4      65 ..     201     262 ..     198     267 .. 0.87
   3 ?    1.2   0.0       2.6   3.9e+02       1      29 [.     268     296 ..     268     301 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.19
                           BRE1   3 kELvklekafeelseqlskkvkeltileekklrleaekakadqkyfaamrskdalenelkkLn 65 
                                     EL    ++ +    +++ + ++++ l +++  le   a +  k+ a+  + +++  e  +L+
  gi|119719908|ref|YP_920403.1| 151 GELSAALAEAQRKAYEADRLAEQVSQLSQRVRSLEIALANESGKCSALGEQLRSVSSEWGALK 213
                                    6888888888888889999**********************9999999988888888877776 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0033
                           BRE1   4 ELvklekafeelseqlskkvkeltileekklrleaekakadqkyfaamrskdalenelkkLn 65 
                                     L +++ ++ +l+e++ ++++e  +l+ +++ le+e a+ + +  +++ +k +l   l  ++
  gi|119719908|ref|YP_920403.1| 201 QLRSVSSEWGALKEKAGALKAENDALKARVSELESENARLRSELASLKEEKGSLASRLTSVQ 262
                                    588999999999**********************9999999999999999999888776665 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 2.6
                           BRE1   1 lqkELvklekafeelseqlskkvkeltil 29 
                                    l +EL +l + +e ls  +s++++ l +l
  gi|119719908|ref|YP_920403.1| 268 LLTELGSLRQKYESLSFVASALQAALVAL 296
                                    5799************9999999998877 PP

>> Cnn_1N  Centrosomin N-terminal motif 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1       8.2   1.2e+03      37      59 ..     166     188 ..     152     207 .. 0.64
   2 ?   12.4   1.4   0.00093      0.14      10      66 ..     217     279 ..     211     283 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 8.2
                         Cnn_1N  37 qkeellkenielkveveslqkel 59 
                                    + + l ++  +l ++v sl+  l
  gi|119719908|ref|YP_920403.1| 166 EADRLAEQVSQLSQRVRSLEIAL 188
                                    35666666666666666665544 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00093
                         Cnn_1N  10 dkLkKENFdLKLriyfLeerleklse......eqkeellkenielkveveslqkelkekkkll 66 
                                     +Lk EN  LK r+ +Le++  +l++      e+k +l + ++ +++  +sl  el +++++ 
  gi|119719908|ref|YP_920403.1| 217 GALKAENDALKARVSELESENARLRSelaslkEEKGSLASRLTSVQESYQSLLTELGSLRQKY 279
                                    689999999999999999999999998888988999999999999999999999988888775 PP

>> DUF4763  Domain of unknown function (DUF4763)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   4.4    0.0083       1.2      93     152 ..     221     280 ..     152     293 .. 0.60

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0083
                        DUF4763  93 elltseqpeileLqrnnhkLrqqlaelqqhlkasrkslkelreslcqekkrlrklqkrln 152
                                     +++  +  + eL  +n++Lr +la+l++ + +  + l+ ++es+++++  l +l+++ +
  gi|119719908|ref|YP_920403.1| 221 AENDALKARVSELESENARLRSELASLKEEKGSLASRLTSVQESYQSLLTELGSLRQKYE 280
                                    333334556667777777777777777777777777777777777777777777776655 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   6.5    0.0023      0.34     116     254 ..     126     259 ..      15     292 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0023
                   Exonuc_VII_L 116 DttiaDfvAdlrapTPtaaAelvvpdkaeleeqleelerrlekaikrlleekkqrleklasrlkspeellerkrqrldel 195
                                    D+++ D + +   + P a+A  ++    el + l+e++r+  +a     ++ ++++++l++r++s e  l++++ +++ l
  gi|119719908|ref|YP_920403.1| 126 DYSVNDTARYFEYKAPIAMAPRAT--YGELSAALAEAQRKAYEA-----DRLAEQVSQLSQRVRSLEIALANESGKCSAL 198
                                    555566666666666666666666..556655555555554443.....2333566666666666666777777777777 PP

                   Exonuc_VII_L 196 eerleralkkq...lkkkrerleelkerlkekleekkerlkklkerlelleekkerleelee 254
                                     e+l++ ++++   lk+k+ +l+  +++lk++++e +++ ++l+++l++l+e+k +l++  +
  gi|119719908|ref|YP_920403.1| 199 GEQLRS-VSSEwgaLKEKAGALKAENDALKARVSELESENARLRSELASLKEEKGSLASRLT 259
                                    777766.3333344555555555555555433333333333333333322222222221111 PP

>> PI3K_P85_iSH2  Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   5.3     0.013       1.9      81     135 ..     213     268 ..     147     283 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.013
                  PI3K_P85_iSH2  81 hEie.klqenleqlksrlkelhsskekLeedlkqqkeeereleReinalkpellqL 135
                                    +E+   l+  ++ lk+r++el+s+ ++L  +l + kee+ +l  ++++++   ++L
  gi|119719908|ref|YP_920403.1| 213 KEKAgALKAENDALKARVSELESENARLRSELASLKEEKGSLASRLTSVQESYQSL 268
                                    34443778888888888888888888888888888888777777776666655555 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.8     0.002       0.3       2      74 ..     207     278 ..     200     302 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.002
                          TMPIT   2 eeweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkee 74 
                                    +ew  l++++ +l+++++ +k+++ el++ + ++++e+++ k++  +l s+l+++++s + +  +e+ +l+++
  gi|119719908|ref|YP_920403.1| 207 SEWGALKEKAGALKAENDALKARVSELESENARLRSELASLKEEKGSLASRLTSVQESYQ-SLLTELGSLRQK 278
                                    689999999999999999999999999999999999999999999999999999999854.333334444444 PP

>> DUF4686  Domain of unknown function (DUF4686)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   6.3    0.0032      0.48     147     263 ..     161     274 ..     151     293 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0032
                        DUF4686 147 earilekkqLeekikeaseneaklkqqlqeeqqkrklLdqnveeLqqqvrslrdkeaqlertnsqqqlriqqqeaqlkkl 226
                                    + ++ e ++L e++ ++s+   +l   l  e  k   L ++          l++k   l+  n  ++ r+ + e    +l
  gi|119719908|ref|YP_920403.1| 161 QRKAYEADRLAEQVSQLSQRVRSLEIALANESGKCSALGEQLRSVSSEWGALKEKAGALKAENDALKARVSELESENARL 240
                                    45677889999999999999999999999999999999999999999999999999999999999999999999999999 PP

                        DUF4686 227 enekrk.sdehlksnqeLsekLsslqqekealqeelqq 263
                                     +e    ++e+      L  +L s+q   ++l +el+ 
  gi|119719908|ref|YP_920403.1| 241 RSELASlKEEK----GSLASRLTSVQESYQSLLTELGS 274
                                    88888745554....34555555555555555544443 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.7      0.62        92       8      43 ..     169     204 ..     152     230 .. 0.63
   2 ?    7.3   1.9     0.037       5.5       5      32 ..     222     249 ..     197     251 .. 0.58
   3 ?    7.4   4.2     0.034         5       7      42 ..     224     259 ..     212     303 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.62
                          Spc24   8 riakelsdleselesleselaelkeeleeleeesee 43 
                                    r+a+++s+l + + sle  la+   ++  l e+  +
  gi|119719908|ref|YP_920403.1| 169 RLAEQVSQLSQRVRSLEIALANESGKCSALGEQLRS 204
                                    466666667777777666666666666666666555 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.037
                          Spc24   5 ekfriakelsdleselesleselaelke 32 
                                    e+ ++   +s+lese  +l+sela+lke
  gi|119719908|ref|YP_920403.1| 222 ENDALKARVSELESENARLRSELASLKE 249
                                    3333444455555555555555555554 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.034
                          Spc24   7 friakelsdleselesleselaelkeeleeleeese 42 
                                     ++   +s+lese  +l+sela+lkee   l +   
  gi|119719908|ref|YP_920403.1| 224 DALKARVSELESENARLRSELASLKEEKGSLASRLT 259
                                    455566777777777777777777777666655544 PP

>> CtIP_N  Tumour-suppressor protein CtIP N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   2.6     0.006      0.89      44     119 ..     167     244 ..     156     259 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.006
                         CtIP_N  44 nqqlreqqkalkenikvlenrLraglCdrCavtqelakkkqqefessklqs..lql.itiLtnEmntLkeenkkLkeel 119
                                     ++l eq + l++ ++ le  L a +  +C+ + e++++  +e+   k +   l+     L++  ++L+ en +L+ el
  gi|119719908|ref|YP_920403.1| 167 ADRLAEQVSQLSQRVRSLEIAL-ANESGKCSALGEQLRSVSSEWGALKEKAgaLKAeNDALKARVSELESENARLRSEL 244
                                    4678899999999999999999.678899**********9999987655441133213457777777777777777776 PP

>> Csm1_N  Csm1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.3      0.64        95      40      61 ..     164     185 ..     154     201 .. 0.59
   2 ?   -0.2   0.0       8.9   1.3e+03      35      64 ..     187     216 ..     182     222 .. 0.71
   3 ?   10.1   1.7    0.0052      0.77      27      69 ..     221     263 ..     217     264 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.64
                         Csm1_N  40 dqeiesLkeqlaeleekvkele 61 
                                      e  +L eq+ +l ++v++le
  gi|119719908|ref|YP_920403.1| 164 AYEADRLAEQVSQLSQRVRSLE 185
                                    4455555555555555555544 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 8.9
                         Csm1_N  35 kletkdqeiesLkeqlaeleekvkeleerr 64 
                                    +l + + + ++L eql ++ ++   l+e++
  gi|119719908|ref|YP_920403.1| 187 ALANESGKCSALGEQLRSVSSEWGALKEKA 216
                                    566777788888888888888777777665 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.0052
                         Csm1_N  27 hENsvLsqkletkdqeiesLkeqlaeleekvkeleerrkkqeE 69 
                                     EN  L+ +++  + e  +L+ +la+l+e+  +l +r ++ +E
  gi|119719908|ref|YP_920403.1| 221 AENDALKARVSELESENARLRSELASLKEEKGSLASRLTSVQE 263
                                    69***************************99999888877776 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1      0.64        95      24      89 ..     150     202 ..     131     222 .. 0.52
   2 ?    6.6   0.3     0.084        12      26      71 ..     225     270 ..     218     287 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.64
                   Occludin_ELL  24 YkelhaeleevskkfseLerelkelkegskeykkieeeilqeykklkkdpeyqekkkrceyLkekL 89 
                                    Y el a l+e+++k  e +r  ++ ++ s++++++e  +              ++  +c  L e+L
  gi|119719908|ref|YP_920403.1| 150 YGELSAALAEAQRKAYEADRLAEQVSQLSQRVRSLEIAL-------------ANESGKCSALGEQL 202
                                    444444444444444444444444444444444444333.............34444444444444 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.084
                   Occludin_ELL  26 elhaeleevskkfseLerelkelkegskeykkieeeilqeykklkk 71 
                                    +l+a+++e++++ ++L++el +lke++   +++  +++++y++l  
  gi|119719908|ref|YP_920403.1| 225 ALKARVSELESENARLRSELASLKEEKGSLASRLTSVQESYQSLLT 270
                                    688999999999999999*****99999999999999999998744 PP

>> FmiP_Thoc5  Fms-interacting protein/Thoc5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.6     0.019       2.8     105     170 ..     168     233 ..     160     235 .. 0.90
   2 ?    6.3   2.9     0.034       5.1     110     169 ..     222     281 ..     218     296 .. 0.62

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.019
                     FmiP_Thoc5 105 kelaeqlkeleekkkkleqeieekkkfLssLppkLkslkkatkplqealglpltkerkqhelaslL 170
                                     +laeq+++l++++++le + +++  + s+L ++L+s++++   l+e+ g   +++   ++++s+L
  gi|119719908|ref|YP_920403.1| 168 DRLAEQVSQLSQRVRSLEIALANESGKCSALGEQLRSVSSEWGALKEKAGALKAENDALKARVSEL 233
                                    589********************************************9987767888888888877 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.034
                     FmiP_Thoc5 110 qlkeleekkkkleqeieekkkfLssLppkLkslkkatkplqealglpltkerkqhelasl 169
                                    + ++l++++++le+e++  +++L sL+++  sl++ ++ +qe+ +  lt+  + +++ + 
  gi|119719908|ref|YP_920403.1| 222 ENDALKARVSELESENARLRSELASLKEEKGSLASRLTSVQESYQSLLTELGSLRQKYES 281
                                    556667777777777777777777776666666666666666665555544444444444 PP

>> Yuri_gagarin  Yuri gagarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   3.1    0.0074       1.1      93     188 ..     159     254 ..     149     293 .. 0.56

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0074
                   Yuri_gagarin  93 ennrlkeeiydlkqknceqarkvrelaeelkgeeeqrvelvdkyekllasfeeqckelkranrrvqslqerlsqveklqe 172
                                    e +r   e   l  + ++ +++vr l   l +e  +   l ++  ++++ +    ++    +   ++l+ r+s++e  + 
  gi|119719908|ref|YP_920403.1| 159 EAQRKAYEADRLAEQVSQLSQRVRSLEIALANESGKCSALGEQLRSVSSEWGALKEKAGALKAENDALKARVSELESENA 238
                                    55555666666666666666666666666666666666666666666555443322222334444566666666666555 PP

                   Yuri_gagarin 173 elrterkilreevial 188
                                     lr+e   l+ee  +l
  gi|119719908|ref|YP_920403.1| 239 RLRSELASLKEEKGSL 254
                                    5555555555554333 PP

>> MbeD_MobD  MbeD/MobD like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.3    0.0063      0.94      45      62 ..     164     185 ..     147     192 .. 0.70
   2 ?    3.2   0.1      0.64        95      28      63 ..     207     242 ..     196     249 .. 0.73
   3 ?    0.5   0.3       4.5   6.7e+02       6      20 ..     266     280 ..     258     298 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0063
                      MbeD_MobD  45 a....aLseqvtgLsqQVesLs 62 
                                    a     L eqv +Lsq V sL 
  gi|119719908|ref|YP_920403.1| 164 AyeadRLAEQVSQLSQRVRSLE 185
                                    2234489999999999999986 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.64
                      MbeD_MobD  28 safaelqrmfeltqrenaaLseqvtgLsqQVesLse 63 
                                    s +  l++  +  + en aL+++v +L     +L  
  gi|119719908|ref|YP_920403.1| 207 SEWGALKEKAGALKAENDALKARVSELESENARLRS 242
                                    555667777788888999999999999776666655 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 4.5
                      MbeD_MobD   6 kqLLsAlEqLQqdYe 20 
                                    + LL  l +L q+Ye
  gi|119719908|ref|YP_920403.1| 266 QSLLTELGSLRQKYE 280
                                    679999999999997 PP

>> ERM  Ezrin/radixin/moesin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9  14.2     0.016       2.3       7     119 ..     167     279 ..     158     330 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.016
                            ERM   7 kreleerLkqlqeeaekaqeaLreseetaelLaekarraeeeaelLeqkaaeaeeeiqrlkesaekeeeekeklerklre 86 
                                     ++l e+  ql + ++  + aL ++  +   L e++r +  e   L++ka ++++e+++lk + ++ e+e ++l  +l+ 
  gi|119719908|ref|YP_920403.1| 167 ADRLAEQVSQLSQRVRSLEIALANESGKCSALGEQLRSVSSEWGALKEKAGALKAENDALKARVSELESENARLRSELAS 246
                                    56677777777777777777777777777777777777777777777777777777777777777777777777777777 PP

                            ERM  87 aeleaarleeeserkeeeaerLkeeleeareae 119
                                     ++e   l++  +  +e  + L +el   r++ 
  gi|119719908|ref|YP_920403.1| 247 LKEEKGSLASRLTSVQESYQSLLTELGSLRQKY 279
                                    777777777766666666666666665555544 PP

>> Mod_r  Modifier of rudimentary (Mod(r)) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.7       1.1   1.6e+02      36      83 ..     167     215 ..     152     222 .. 0.65
   2 ?   10.2   6.1    0.0041       0.6      30     103 ..     218     292 ..     200     301 .. 0.68

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 1.1
                          Mod_r  36 eellaeneslaeknlsl.epeleelrselqekleelkelekefeekeqe 83 
                                     + lae++s +++   + e  l +++ ++++  e+l+++++e+ +++++
  gi|119719908|ref|YP_920403.1| 167 ADRLAEQVSQLSQRVRSlEIALANESGKCSALGEQLRSVSSEWGALKEK 215
                                    3334455544444444437788888888888888888888888777665 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0041
                          Mod_r  30 qlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqeldellqkfspd.allarLqta 103
                                    +lk+e + l a   +l ++n  l+ el  l++e  +  + l++++++++ + +el +l qk+ +  ++ + Lq+a
  gi|119719908|ref|YP_920403.1| 218 ALKAENDALKARVSELESENARLRSELASLKEEKGSLASRLTSVQESYQSLLTELGSLRQKYESLsFVASALQAA 292
                                    566677777777777777777777777777777777777788888888888888877777775541344445555 PP

>> Fmp27_WPPW  RNA pol II promoter Fmp27 protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   1.6      0.11        16     176     242 ..     177     246 ..     159     267 .. 0.41
   2 ?    8.2   0.7    0.0064      0.94     173     238 ..     223     291 ..     211     327 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.11
                     Fmp27_WPPW 176 leeRleeleeqiekleekleelelkseke...deelkeeieelekeikelkeklefletlledlkesees 242
                                    l++R+++le  +++ + k + l ++ ++      +lke+  +l+ e + lk +++ le+   +l+++ +s
  gi|119719908|ref|YP_920403.1| 177 LSQRVRSLEIALANESGKCSALGEQLRSVsseWGALKEKAGALKAENDALKARVSELESENARLRSELAS 246
                                    4445555554444444444444444433222223333333333333333333333333333333333321 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0064
                     Fmp27_WPPW 173 kelleeRleeleeqiekleekleelelkseke...deelkeeieelekeikelkeklefletlledlke 238
                                     + l+ R++ele++ ++l+++l +l++++ +     ++++e +++l +e+ +l++k+e l+ + + l++
  gi|119719908|ref|YP_920403.1| 223 NDALKARVSELESENARLRSELASLKEEKGSLasrLTSVQESYQSLLTELGSLRQKYESLSFVASALQA 291
                                    567888999999999999999988888888776666778888888888888888888888877777765 PP

>> HMMR_C  Hyaluronan mediated motility receptor C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1       5.8   8.6e+02      92     128 ..     169     205 ..     157     210 .. 0.81
   2 ?    9.3   1.3    0.0083       1.2      93     124 ..     219     250 ..     212     267 .. 0.56

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 5.8
                         HMMR_C  92 klkeenselkqevsklrsqlakekqeekklkeqlkea 128
                                    +l e+ s+l q v  l   la e  + + l eql+++
  gi|119719908|ref|YP_920403.1| 169 RLAEQVSQLSQRVRSLEIALANESGKCSALGEQLRSV 205
                                    6778889999999999999999999988888888876 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0083
                         HMMR_C  93 lkeenselkqevsklrsqlakekqeekklkeq 124
                                    lk en +lk  vs l s  a+ ++e   lke+
  gi|119719908|ref|YP_920403.1| 219 LKAENDALKARVSELESENARLRSELASLKEE 250
                                    56666666666665555555555555555443 PP

>> CREPT  Cell-cycle alteration and expression-elevated protein in tumour
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   2.5     0.013         2      41     123 ..     162     247 ..     142     249 .. 0.89
   2 ?    7.3   1.5     0.035       5.1      55     123 ..     228     296 ..     211     307 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.013
                          CREPT  41 kdkeeaekllkqveealellaeYnkrLeaeleeRkklakmledfle...aqkellakaeekleelkeklekvksvrkelk 117
                                    +   ea++l++qv++  + +      L++e  + + l ++l++  +   a+ke++   +++ + lk ++++++s+++ l+
  gi|119719908|ref|YP_920403.1| 162 RKAYEADRLAEQVSQLSQRVRSLEIALANESGKCSALGEQLRSVSSewgALKEKAGALKAENDALKARVSELESENARLR 241
                                    466799************************************99863336899999999999****************** PP

                          CREPT 118 shiqsL 123
                                    s + sL
  gi|119719908|ref|YP_920403.1| 242 SELASL 247
                                    ***998 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.035
                          CREPT  55 ealellaeYnkrLeaeleeRkklakmledfleaqkellakaeekleelkeklekvksvrkelkshiqsL 123
                                      ++ l+  n+rL +el   k+ +  l++ l++++e+ +   ++l +l++k e ++ v + l+  +  L
  gi|119719908|ref|YP_920403.1| 228 ARVSELESENARLRSELASLKEEKGSLASRLTSVQESYQSLLTELGSLRQKYESLSFVASALQAALVAL 296
                                    446678888999999999999999999999999999999999999999999999999999998877666 PP

>> DUF4164  Domain of unknown function (DUF4164)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.9      0.11        17      39      86 ..     158     205 ..     147     208 .. 0.82
   2 ?    7.9   4.6     0.024       3.6      24      66 ..     212     255 ..     210     298 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.11
                        DUF4164  39 aeiealgedrsRLaeeLdqaearaarleevnrEvsrrLkaaietirav 86 
                                    ae ++ + +  RLae+  q + r ++le++ +  s++  a+ e++r+v
  gi|119719908|ref|YP_920403.1| 158 AEAQRKAYEADRLAEQVSQLSQRVRSLEIALANESGKCSALGEQLRSV 205
                                    555566667789****************99999999999999999987 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.024
                        DUF4164  24 vdrrleaerkr.deleaeiealgedrsRLaeeLdqaearaarle 66 
                                    ++++  a +++ d+l+a++++l+++ +RL  eL + + +  +l+
  gi|119719908|ref|YP_920403.1| 212 LKEKAGALKAEnDALKARVSELESENARLRSELASLKEEKGSLA 255
                                    55666666555577888888888888888777766555554444 PP

>> Nup54  Nucleoporin complex subunit 54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   9.0     0.065       9.7      49     123 ..     220     293 ..     152     307 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.065
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SS---SSHHHHHHHHHHHHHHH CS
                          Nup54  49 rerlkeisdrleeleqkhqletsvrlekakkrhvelshRllrllrkleilrsrgyaldaeEeelrarletleaql 123
                                    +   ++++ r++ele ++++++ ++l+ +k ++  l +Rl+++    + l     +l+++ e+l+    +l+a+l
  gi|119719908|ref|YP_920403.1| 220 KAENDALKARVSELE-SENARLRSELASLKEEKGSLASRLTSVQESYQSLLTELGSLRQKYESLSFVASALQAAL 293
                                    333345556666666.77777777777777777777777777777777554555555666666665555555555 PP

>> DUF4200  Domain of unknown function (DUF4200)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.3       1.8   2.6e+02      74     103 ..     159     188 ..     151     192 .. 0.76
   2 ?    8.6   1.7     0.015       2.3      30     104 ..     206     280 ..     200     290 .. 0.64

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 1.8
                        DUF4200  74 lkkekeaeikklkaeietlkseiekleekl 103
                                    + ++k+ e  +l +++++l ++ + le +l
  gi|119719908|ref|YP_920403.1| 159 EAQRKAYEADRLAEQVSQLSQRVRSLEIAL 188
                                    556778888888888888888888887665 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.015
                        DUF4200  30 kqreeelekkeqeleedllkfdkflkendakraralkkaeeerklkkekeaeikklkaeietlkseiekleekle 104
                                    ++++ +l++k   l+ +   ++  + e +++ ar + + ++ +++k + ++ +   +++ + l +e+  l +k+e
  gi|119719908|ref|YP_920403.1| 206 SSEWGALKEKAGALKAENDALKARVSELESENARLRSELASLKEEKGSLASRLTSVQESYQSLLTELGSLRQKYE 280
                                    566666666666666666666666666666666666666666666666666666666666666666666666655 PP

>> K-box  K-box region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   2.6      0.12        18      61      92 ..     213     244 ..     155     245 .. 0.69
   2 ?    2.2   0.7       1.4     2e+02      58      87 ..     246     274 ..     230     282 .. 0.38
   3 ?    1.6   0.1       2.2   3.2e+02       5      25 ..     262     282 ..     258     290 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.12
                          K-box  61 srKeqllleeieelkkkekqleeenkeLrekl 92 
                                    ++K+  l+ e + lk + ++le en +Lr +l
  gi|119719908|ref|YP_920403.1| 213 KEKAGALKAENDALKARVSELESENARLRSEL 244
                                    56778899999999999999999999999886 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 1.4
                          K-box  58 kiRsrKeqllleeieelkkkekqleeenke 87 
                                    + +++K  l   ++  +++  ++l  e   
  gi|119719908|ref|YP_920403.1| 246 SLKEEKGSLA-SRLTSVQESYQSLLTELGS 274
                                    3333333322.2333333333333333333 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 2.2
                          K-box   5 qdeeeelkqEvskLkkeiekl 25 
                                    q+++++l  E+ +L++++e+l
  gi|119719908|ref|YP_920403.1| 262 QESYQSLLTELGSLRQKYESL 282
                                    667889999999999999998 PP

>> DUF2205  Short coiled-coil protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.2       3.7   5.5e+02       1      40 [.     144     182 ..     144     190 .. 0.64
   2 ?    9.6   1.6    0.0059      0.87      20      63 ..     211     254 ..     197     264 .. 0.84
   3 ?    2.4   0.7       1.1   1.6e+02      15      44 ..     248     277 ..     243     302 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 3.7
                        DUF2205   1 msprrnsedveklerearerLqqqakeLqssLqaLaervd 40 
                                    m pr +  +++++  ea+ +    a+ L +   +L++rv 
  gi|119719908|ref|YP_920403.1| 144 MAPRATYGELSAALAEAQRKA-YEADRLAEQVSQLSQRVR 182
                                    566666667776666666553.356667777777777764 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0059
                        DUF2205  20 rLqqqakeLqssLqaLaervdeVkeehdKLesenrfLqqYIgdL 63 
                                    +L+++a +L++  +aL +rv e  +e+ +L+se   L +  g+L
  gi|119719908|ref|YP_920403.1| 211 ALKEKAGALKAENDALKARVSELESENARLRSELASLKEEKGSL 254
                                    7999*****************************87777665555 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 1.1
                        DUF2205  15 rearerLqqqakeLqssLqaLaervdeVke 44 
                                    +e++  L ++  + q+s q+L+    + ++
  gi|119719908|ref|YP_920403.1| 248 KEEKGSLASRLTSVQESYQSLLTELGSLRQ 277
                                    688899999999999999998877766665 PP

>> CLZ  C-terminal leucine zipper domain of cyclic nucleotide-gated channels
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.4      0.84   1.2e+02      24      47 ..     165     188 ..     152     204 .. 0.63
   2 ?    3.7   0.2      0.53        79      54      70 ..     219     235 ..     188     236 .. 0.61
   3 ?    6.8   1.8      0.06       8.9      15      62 ..     212     259 ..     208     264 .. 0.69
   4 ?    6.2   1.2     0.092        14      16      60 ..     234     278 ..     233     283 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.84
                            CLZ  24 aeqkeleekverLessLeaLqtrl 47 
                                     e++ l e+v++L +++ +L+  l
  gi|119719908|ref|YP_920403.1| 165 YEADRLAEQVSQLSQRVRSLEIAL 188
                                    455666666666666666666555 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.53
                            CLZ  54 yessqrkLkqRitkLEk 70 
                                    +++ +  Lk+R+++LE+
  gi|119719908|ref|YP_920403.1| 219 LKAENDALKARVSELES 235
                                    34445567777777775 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.06
                            CLZ  15 LDeeaakagaeqkeleekverLessLeaLqtrlarLlaeyessqrkLk 62 
                                    L e+a + +ae++ l+ +v++Les+   L   la L +e  s +++L+
  gi|119719908|ref|YP_920403.1| 212 LKEKAGALKAENDALKARVSELESENARLRSELASLKEEKGSLASRLT 259
                                    556656666777778888888888877777777777777777666664 PP

  == domain 4  score: 6.2 bits;  conditional E-value: 0.092
                            CLZ  16 DeeaakagaeqkeleekverLessLeaLqtrlarLlaeyessqrk 60 
                                    + e+a  ++e  +l+e   +L s+L + q  ++ Ll+e+ s  +k
  gi|119719908|ref|YP_920403.1| 234 ESENARLRSELASLKEEKGSLASRLTSVQESYQSLLTELGSLRQK 278
                                    555666778888888888999999999999999999999888777 PP

>> FliD_N  Flagellar hook-associated protein 2 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.9       1.2   1.7e+02      23      66 ..     188     229 ..     147     257 .. 0.65
   2 ?    7.0   0.5     0.064       9.4      29      62 ..     257     291 ..     247     318 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 1.2
                                    XXXXXXXXXXXHHHHHHHHHHHHHHHHHHHHHXX.GGGGGXEEEE CS
                         FliD_N  23 leqkktklewkqsayrelnsklsnlksalsalsk.sstfsakkat 66 
                                    l ++  k ++  + +r+++s+  +lk+++ al++ +++++a    
  gi|119719908|ref|YP_920403.1| 188 LANESGKCSALGEQLRSVSSEWGALKEKAGALKAeNDALKA---R 229
                                    45555555566666777777777777766566554444422...2 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.064
                                    XXXXXHHHHHHHHHHHHHHHHHHHHHXX.GGGGGX CS
                         FliD_N  29 klewkqsayrelnsklsnlksalsalsk.sstfsa 62 
                                     l++ q+ y++l ++l +l++++++ls  +s+++a
  gi|119719908|ref|YP_920403.1| 257 RLTSVQESYQSLLTELGSLRQKYESLSFvASALQA 291
                                    678889***************99888665666543 PP

>> Pox_A_type_inc  Viral A-type inclusion protein repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1       2.9   4.3e+02       3      14 ..     174     185 ..     172     190 .. 0.81
   2 ?    7.3   0.1     0.029       4.3       4      16 ..     224     236 ..     222     236 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 2.9
                 Pox_A_type_inc   3 msrlRsRIsDLE 14 
                                    +s+l  R+++LE
  gi|119719908|ref|YP_920403.1| 174 VSQLSQRVRSLE 185
                                    788999*****9 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.029
                 Pox_A_type_inc   4 srlRsRIsDLErq 16 
                                    ++l+ R+s+LE++
  gi|119719908|ref|YP_920403.1| 224 DALKARVSELESE 236
                                    78*********97 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.0    0.0031      0.45      20      55 ..     151     189 ..     147     201 .. 0.83
   2 ?    4.9   1.2      0.28        41      19      48 ..     230     259 ..     188     289 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0031
                                    HHHHHHHHHHHH...HHHHHHHHHHHHHHT-XXXXXXXX CS
                           SlyX  20 eeLndvvaeqqq...qidrlqrqlrllaerlkeleessg 55 
                                     eL++++ae q+   + drl +q+ +l +r+++le + +
  gi|119719908|ref|YP_920403.1| 151 GELSAALAEAQRkayEADRLAEQVSQLSQRVRSLEIALA 189
                                    58999999999844457****************997755 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.28
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHT-X CS
                           SlyX  19 ieeLndvvaeqqqqidrlqrqlrllaerlk 48 
                                    + eL  + a+ + +++ l+++   la rl 
  gi|119719908|ref|YP_920403.1| 230 VSELESENARLRSELASLKEEKGSLASRLT 259
                                    233333333333333333333333333333 PP

>> IFT20  Intraflagellar transport complex B, subunit 20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   3.5     0.032       4.7      69     108 ..     211     250 ..     158     257 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.032
                          IFT20  69 llkseakqreaeqqqlqaliaekkaeleRlrvelesLqkv 108
                                    +lk+ a + +ae+++l+a+++e ++e  Rlr+el sL++ 
  gi|119719908|ref|YP_920403.1| 211 ALKEKAGALKAENDALKARVSELESENARLRSELASLKEE 250
                                    67888888999**************************975 PP

>> Rho_Binding  Rho Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.2       3.8   5.7e+02      52      61 ..      59      68 ..      54      72 .. 0.88
   2 ?    2.9   0.2       1.4     2e+02       8      39 ..     163     195 ..     152     208 .. 0.61
   3 ?    4.1   0.6      0.54        81       1      30 [.     212     241 ..     198     246 .. 0.84
   4 ?    8.7   0.3      0.02         3       1      44 [.     240     280 ..     240     283 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 3.8
                    Rho_Binding 52 lLKtqAVNKL 61
                                    LK++ VNKL
  gi|119719908|ref|YP_920403.1| 59 ALKNVTVNKL 68
                                   59*******9 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 1.4
                    Rho_Binding   8 lakekeelnkklkkleeelekak.eeeeeiekl 39 
                                    +a e + l +++++l+++++ ++ + ++e  k+
  gi|119719908|ref|YP_920403.1| 163 KAYEADRLAEQVSQLSQRVRSLEiALANESGKC 195
                                    555666666666666666655554444444444 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.54
                    Rho_Binding   1 Ltkdvenlakekeelnkklkkleeelekak 30 
                                    L+++   l+ e++ l++++++le+e ++++
  gi|119719908|ref|YP_920403.1| 212 LKEKAGALKAENDALKARVSELESENARLR 241
                                    677888899999999999999999888776 PP

  == domain 4  score: 8.7 bits;  conditional E-value: 0.02
                    Rho_Binding   1 Ltkdvenlakekeelnkklkkleeelekakeeeeeieklkasye 44 
                                    L+++++ l++ek  l ++l +++e+++ +     e+ +l+++ye
  gi|119719908|ref|YP_920403.1| 240 LRSELASLKEEKGSLASRLTSVQESYQSLL---TELGSLRQKYE 280
                                    678999*********************997...68888888887 PP

>> BST2  Bone marrow stromal antigen 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.2         1   1.5e+02      46      88 ..     149     187 ..     139     197 .. 0.60
   2 ?    8.0   1.7     0.029       4.3      38      88 ..     200     250 ..     182     253 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 1
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           BST2  46 tvvtLkasLekekaqsqkqqakvqelqgeikkLnqkLqdaeae 88 
                                    t  +L+a+L + + +      ++  l +++ +L q+++  e +
  gi|119719908|ref|YP_920403.1| 149 TYGELSAALAEAQRK----AYEADRLAEQVSQLSQRVRSLEIA 187
                                    555566666555444....444455666666666666555443 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.029
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           BST2  38 aqaatcnqtvvtLkasLekekaqsqkqqakvqelqgeikkLnqkLqdaeae 88 
                                     q  + ++    Lk+     ka++   +a+v el+ e+++L  +L   ++e
  gi|119719908|ref|YP_920403.1| 200 EQLRSVSSEWGALKEKAGALKAENDALKARVSELESENARLRSELASLKEE 250
                                    5666777777789999999999999999****************9998877 PP

>> DUF4140  N-terminal domain of unknown function (DUF4140)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   8.8      0.55        81      65      95 ..     213     251 ..     142     261 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.55
                        DUF4140  65 e........elkalraeleeledelaaledelaaaearl 95 
                                    +        e +al+a++ ele e a+l++ela++++++
  gi|119719908|ref|YP_920403.1| 213 KekagalkaENDALKARVSELESENARLRSELASLKEEK 251
                                    122233555688999999999999999999999988876 PP

>> HAUS-augmin3  HAUS augmin-like complex subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4  13.0     0.078        12      42     143 ..     163     272 ..     154     326 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.078
                   HAUS-augmin3  42 piLegeaLeeaLktie........psdlkqedvellevileeeeesleaLeqelqeLqkekalklkrlnkLqvqaaslqq 113
                                    + +e ++L+e+  +++           +++ + ++l ++l    +   aL++++ +L+ e++ +  r ++L+   a l +
  gi|119719908|ref|YP_920403.1| 163 KAYEADRLAEQVSQLSqrvrsleiALANESGKCSALGEQLRSVSSEWGALKEKAGALKAENDALKARVSELESENARLRS 242
                                    56666666666666665544442322233366777778888888888899999999999999999999999999999999 PP

                   HAUS-augmin3 114 elrkleeeekeakkklkeaqeelraenaet 143
                                    el +l+ee+ + + +l+  qe+ ++   e+
  gi|119719908|ref|YP_920403.1| 243 ELASLKEEKGSLASRLTSVQESYQSLLTEL 272
                                    999999999999999999998887765554 PP

>> Striatin  Striatin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   7.8      0.09        13      30     116 ..     153     246 ..     150     335 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.09
                       Striatin  30 mkarIakLegerrgaenlkk...dlvrrikmLEyalkqerakylkl..............kegtsaakenkkkekeeeea 92 
                                    + a  a+ ++++ +a++l +   +l +r++ LE al +e  k  +l              ke+++a           + +
  gi|119719908|ref|YP_920403.1| 153 LSAALAEAQRKAYEADRLAEqvsQLSQRVRSLEIALANESGKCSALgeqlrsvssewgalKEKAGA----------LKAE 222
                                    555666666666666666542226899***************888865544443322222111111..........1111 PP

                       Striatin  93 eeeekseeeskskekksakeslkk 116
                                    ++  k++ ++ ++e++ ++++l +
  gi|119719908|ref|YP_920403.1| 223 NDALKARVSELESENARLRSELAS 246
                                    111111112222222222222222 PP

>> Uso1_p115_C  Uso1 / p115 like vesicle tethering protein, C terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0  16.7       3.5   5.2e+02      20      98 ..     198     281 ..     147     322 .. 0.66

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 3.5
                    Uso1_p115_C  20 lkaelqslskalesleqkeakkaaesqakeleaenkklekeleklraelkeekekekek........qkEldDLLlllgD 91 
                                    l  +l+s s++   l++k    a +++++ l+a++++le+e   lr+el+  ke++  +        q+ +  LL  lg 
  gi|119719908|ref|YP_920403.1| 198 LGEQLRSVSSEWGALKEK--AGALKAENDALKARVSELESENARLRSELASLKEEKG-SlasrltsvQESYQSLLTELGS 274
                                    333333333333333333..4555555666666666666666666666665555542.2345665666666666666666 PP

                    Uso1_p115_C  92 leeKvek 98 
                                    l +K e+
  gi|119719908|ref|YP_920403.1| 275 LRQKYES 281
                                    6666554 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   2.5       0.1        15       3      21 ..     168     186 ..     166     239 .. 0.80
   2 ?    1.8   3.8       2.2   3.3e+02      11      36 ..     225     250 ..     219     303 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.1
                            LPP   3 deLssqVsqLkskvdqlss 21 
                                    d L++qVsqL++ v +l+ 
  gi|119719908|ref|YP_920403.1| 168 DRLAEQVSQLSQRVRSLEI 186
                                    7788999999999888764 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 2.2
                            LPP  11 qLkskvdqlssdvnsakaaaqaakeE 36 
                                    +Lk+ v++l+s+ + +++++++ keE
  gi|119719908|ref|YP_920403.1| 225 ALKARVSELESENARLRSELASLKEE 250
                                    45566666666666666666655555 PP

>> GIT_CC  GIT coiled-coil Rho guanine nucleotide exchange factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0       3.6   5.4e+02      40      64 ..     203     227 ..     185     229 .. 0.74
   2 ?    6.0   0.2     0.074        11      27      56 ..     218     247 ..     197     255 .. 0.50
   3 ?    4.6   0.3       0.2        29      21      56 ..     247     282 ..     242     289 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 3.6
                         GIT_CC  40 tslsdelrlLQskvqkLqaeNaqlr 64 
                                     s s e   L +k   L+aeN+ l+
  gi|119719908|ref|YP_920403.1| 203 RSVSSEWGALKEKAGALKAENDALK 227
                                    5677777788889999*****9997 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.074
                         GIT_CC  27 aseakiqqLlkvNtslsdelrlLQskvqkL 56 
                                    a  a   +L++  ++l+ e ++L s++ +L
  gi|119719908|ref|YP_920403.1| 218 ALKAENDALKARVSELESENARLRSELASL 247
                                    333333333333333333333333333333 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.2
                         GIT_CC  21 lKkalaaseakiqqLlkvNtslsdelrlLQskvqkL 56 
                                    lK++ +   ++++ ++++ +sl +el  L +k ++L
  gi|119719908|ref|YP_920403.1| 247 LKEEKGSLASRLTSVQESYQSLLTELGSLRQKYESL 282
                                    677777777777778888888888877777776665 PP

>> Nnf1  Nnf1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   6.1      0.03       4.5      77     109 ..     216     248 ..     152     249 .. 0.85
   2 ?    1.4   0.1       2.7     4e+02      79     109 ..     246     276 ..     244     277 .. 0.89
   3 ?   -0.0   0.2       7.5   1.1e+03      32      71 ..     290     329 ..     259     336 .. 0.60

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.03
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           Nnf1  77 apakkeeqeeLearlqeleaenaelaeeveeqr 109
                                    a a+k+e ++L+ar++ele+ena+l  e+++++
  gi|119719908|ref|YP_920403.1| 216 AGALKAENDALKARVSELESENARLRSELASLK 248
                                    56789***********************99875 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 2.7
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           Nnf1  79 akkeeqeeLearlqeleaenaelaeeveeqr 109
                                    ++kee+ +L  rl  ++++ ++l +e+ ++r
  gi|119719908|ref|YP_920403.1| 246 SLKEEKGSLASRLTSVQESYQSLLTELGSLR 276
                                    68999******************99998777 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 7.5
                                    HHHHHHHHHHHHHHHCCHH-T..........TTSSTTTHH CS
                           Nnf1  32 vekLneLDdlieeAkerreegeeeasrpevpphtLpPeel 71 
                                    ++ L +L ++++ A  ++++  ++ ++++  +++LpP+++
  gi|119719908|ref|YP_920403.1| 290 QAALVALAAVAAVAFLKAPRVARAVKQQSPTAQQLPPQQD 329
                                    4444444445544444444444445555555667777766 PP

>> Swi5  Swi5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.5       4.9   7.2e+02      15      15 ..     177     177 ..     147     227 .. 0.60
   2 ?    6.7   2.2     0.051       7.6       4      33 ..     222     251 ..     219     292 .. 0.68

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 4.9
                                    H CS
                           Swi5  15 l 15 
                                    l
  gi|119719908|ref|YP_920403.1| 177 L 177
                                    2 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.051
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHH.HH CS
                           Swi5   4 eikeleeqleelekelaelkeelkekkdpe 33 
                                    e+ +l+++++ele+e a l++el + k+ +
  gi|119719908|ref|YP_920403.1| 222 ENDALKARVSELESENARLRSELASLKEEK 251
                                    555666666666666666666665444333 PP

>> LURAP  Leucine rich adaptor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.7       1.6   2.4e+02      57      90 ..     214     246 ..     159     249 .. 0.53
   2 ?    9.0   4.6    0.0088       1.3       7      93 ..     202     284 ..     196     296 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 1.6
                          LURAP  57 eekgtltsrcssltsslysldesedtslrGsyns 90 
                                    e+ g+l ++ ++l +    l ese++ lr  + s
  gi|119719908|ref|YP_920403.1| 214 EKAGALKAENDALKARVSEL-ESENARLRSELAS 246
                                    33444455555554443333.4444444444444 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0088
                          LURAP   7 rrskeselkrleeklrklklelanlraidvkllqqllainegieavkWlleekgtltsrcssltsslysldesedtslrG 86 
                                     rs +se   l+ek  +lk e   l+a    l      ++  + ++k   eekg+l+sr +s+  s  sl  +e  slr 
  gi|119719908|ref|YP_920403.1| 202 LRSVSSEWGALKEKAGALKAENDALKARVSELESENARLRSELASLK---EEKGSLASRLTSVQESYQSLL-TELGSLRQ 277
                                    56777888888999999999999998888888888888888877766...9******************95.55679999 PP

                          LURAP  87 synslqd 93 
                                     y+sl+ 
  gi|119719908|ref|YP_920403.1| 278 KYESLSF 284
                                    9999975 PP

>> DUF5320  Family of unknown function (DUF5320)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1       9.1   1.4e+03      63      94 ..     155     186 ..     132     191 .. 0.66
   2 ?    5.4   0.1      0.25        38      70      99 .]     204     233 ..     190     234 .. 0.87
   3 ?    3.4   0.3       1.1   1.6e+02      68      98 ..     237     267 ..     233     268 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 9.1
                        DUF5320  63 aaetaeaskeeekelLeeqaeaLeeeleaikk 94 
                                    aa ++++ k  e++ L eq + L +++  ++ 
  gi|119719908|ref|YP_920403.1| 155 AALAEAQRKAYEADRLAEQVSQLSQRVRSLEI 186
                                    45566677777888888888888888777665 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.25
                        DUF5320  70 skeeekelLeeqaeaLeeeleaikkrlkel 99 
                                    s ++e  +L+e+a aL++e +a+k+r++el
  gi|119719908|ref|YP_920403.1| 204 SVSSEWGALKEKAGALKAENDALKARVSEL 233
                                    55677789******************9997 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 1.1
                        DUF5320  68 easkeeekelLeeqaeaLeeeleaikkrlke 98 
                                    +a  ++e + L+e++ +L ++l  ++++ ++
  gi|119719908|ref|YP_920403.1| 237 NARLRSELASLKEEKGSLASRLTSVQESYQS 267
                                    5556788999999999999999999988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1223  (0.0682135); expected 358.6 (0.02)
Passed bias filter:                      773  (0.0431145); expected 358.6 (0.02)
Passed Vit filter:                       244  (0.0136092); expected 17.9 (0.001)
Passed Fwd filter:                       127  (0.0070835); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):             121  [number of targets reported over threshold]
# CPU time: 1.25u 0.35s 00:00:01.60 Elapsed: 00:00:00.54
# Mc/sec: 1906.92
//
Query:       gi|119719909|ref|YP_920404.1|  [L=253]
Description: HhH-GPD family protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-19   70.1   0.0      3e-19   69.4   0.0    1.2  1  HhH-GPD        HhH-GPD superfamily base excision DNA repair p
    1.8e-10   40.1   0.1    9.8e-09   34.7   0.0    2.6  2  HHH            Helix-hairpin-helix motif
    0.00053   20.2   6.2     0.0012   19.1   6.2    1.6  1  EndIII_4Fe-2S  Iron-sulfur binding domain of endonuclease III
     0.0031   18.1   0.0        3.8    8.2   0.0    2.6  2  HHH_5          Helix-hairpin-helix domain
  ------ inclusion threshold ------
      0.012   15.7   0.0        1.2    9.2   0.0    2.9  3  HHH_2          Helix-hairpin-helix motif
      0.041   12.5   0.0      0.051   12.2   0.0    1.0  1  Cullin         Cullin family
      0.064   13.6   0.1       0.28   11.6   0.0    2.0  2  HHH_8          Helix-hairpin-helix domain
       0.12   12.1   0.0       0.26   11.0   0.0    1.5  1  GGDEF          Diguanylate cyclase, GGDEF domain


Domain annotation for each model (and alignments):
>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.4   0.0   1.4e-22     3e-19       4     105 ..      73     199 ..      70     202 .. 0.94

  Alignments for each domain:
  == domain 1  score: 69.4 bits;  conditional E-value: 1.4e-22
                                    HHHTTS-HHHHHHHHHHHHHHHSHCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH................. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................. RF
                        HhH-GPD   4 ilsqqtsderanriierlferfgfptpedladadeekLrelirelGfyrrKakyikelArilv................. 66 
                                     l q+t+ e++++++e++f+r   p+pe+la+ad+e+Lr+  + lG+  r+a  ++e+Ar++v                 
  gi|119719909|ref|YP_920404.1|  73 FLLQRTRAETVAKVFEEFFSR--YPSPESLANADPEELRKFFSRLGLV-RRADALREAAREIVerhggsvprskeellkl 149
                                    699******************..59***********************.******************************* PP

                                    ..............S-SSS--TTSHHHHHHHHHHTTSSSSTTHHHHHHHHHHH CS
                                    ..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        HhH-GPD  67 ..............gkpdvlivvDvhvrrilkrlrsikekktkkkvekkleel 105
                                                  ++  +++vvD++v r+l+r  +++ +   +++e+ le+l
  gi|119719909|ref|YP_920404.1| 150 kgvgpyiasavlcfAYSAPVPVVDTNVERVLGRAAGASSR---EEAEAFLERL 199
                                    **************9989*******************887...7777777655 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1     0.049   1.1e+02       2      15 ..      97     110 ..      96     110 .. 0.85
   2 !   34.7   0.0   4.4e-12   9.8e-09       1      30 []     134     163 ..     134     163 .. 0.96

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.049
                                    HHHHHTSSHHHHHT CS
                            HHH   2 leglipasreeLla 15 
                                     e+l +a++eeL +
  gi|119719909|ref|YP_920404.1|  97 PESLANADPEELRK 110
                                    6899********75 PP

  == domain 2  score: 34.7 bits;  conditional E-value: 4.4e-12
                                    SHHHHHTSSHHHHHTSTT-SHHHHHHHHHH CS
                            HHH   1 sleglipasreeLlalPGVGpktAeaIlsy 30 
                                    +++g +p+s eeLl+l+GVGp+ A a+l++
  gi|119719909|ref|YP_920404.1| 134 RHGGSVPRSKEELLKLKGVGPYIASAVLCF 163
                                    68999***********************97 PP

>> EndIII_4Fe-2S  Iron-sulfur binding domain of endonuclease III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   6.2   5.2e-07    0.0012       4      17 .]     222     235 ..     222     235 .. 0.99

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 5.2e-07
                  EndIII_4Fe-2S   4 RkPkCeaCPLaDlC 17 
                                    RkPkC +CPL+DlC
  gi|119719909|ref|YP_920404.1| 222 RKPKCPECPLSDLC 235
                                    9************* PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.0    0.0034       7.6      21      39 ..      93     110 ..      81     130 .. 0.75
   2 !    8.2   0.0    0.0017       3.8       2      19 ..     144     161 ..     142     166 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0034
                                    TT--SHHHHHHS-HHHHHT CS
                          HHH_5  21 aGiesvedlaaadveeLak 39 
                                      + s+e la+ad+eeL k
  gi|119719909|ref|YP_920404.1|  93 R-YPSPESLANADPEELRK 110
                                    4.679************98 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0017
                                    HHHHTSTT--HHHHHHHH CS
                          HHH_5   2 eeLlsvsGiGpktAlall 19 
                                    eeLl+++G+Gp +A a+l
  gi|119719909|ref|YP_920404.1| 144 EELLKLKGVGPYIASAVL 161
                                    689999999998888776 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       3.1     7e+03      14      23 ..      41      50 ..      40      52 .. 0.61
   2 ?    3.1   0.0     0.047   1.1e+02      20      38 ..      91     109 ..      80     111 .. 0.81
   3 ?    9.2   0.0   0.00055       1.2      33      54 ..     142     163 ..     140     167 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.1
                          HHH_2 14 ktAklLakrF 23
                                   ++A+ La+ +
  gi|119719909|ref|YP_920404.1| 41 EVARRLAEWY 50
                                   5677777655 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.047
                          HHH_2  20 akrFksldaLkkasleeLl 38 
                                     +r+ s + L++a+ eeL 
  gi|119719909|ref|YP_920404.1|  91 FSRYPSPESLANADPEELR 109
                                    57899999********996 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.00055
                          HHH_2  33 sleeLlevddiGeeiAqsivef 54 
                                    s eeLl+++++G+ iA+++  f
  gi|119719909|ref|YP_920404.1| 142 SKEELLKLKGVGPYIASAVLCF 163
                                    679***************9866 PP

>> Cullin  Cullin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.3e-05     0.051     201     316 ..      36     201 ..      26     205 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.3e-05
                         Cullin 201 seYlkkaeerleeEeervek.yldsstkkkllevleeelikkhleelleeelkkllede.........kledLkrlykll 270
                                    +eY +++ +rl+e  +r  + +  ++t+++ + ++ e l+++   e +++ +++ +++          + e+L+++++ l
  gi|119719909|ref|YP_920404.1|  36 EEYFEEVARRLAEWYRRRGRdFPWRHTRDPYVILATEFLLQRTRAETVAKVFEEFFSRYpspeslanaDPEELRKFFSRL 115
                                    5899*******9987776664777899999999999999998877777775666665223334455559999****9999 PP

                         Cullin 271 srvdgleeLrkaleeyikeegkaivkdake........................................kektedakky 310
                                      v + ++Lr+a +e+++++g ++ ++++e                                        ++++e+a+ +
  gi|119719909|ref|YP_920404.1| 116 GLVRRADALREAAREIVERHGGSVPRSKEEllklkgvgpyiasavlcfaysapvpvvdtnvervlgraagASSREEAEAF 195
                                    9999*********************9988899999999999999999999999999999999999999888888888888 PP

                         Cullin 311 veklLe 316
                                     e+lL 
  gi|119719909|ref|YP_920404.1| 196 LERLLR 201
                                    888885 PP

>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.5   3.4e+03       9      24 ..      44      60 ..      41      61 .. 0.81
   2 ?   11.6   0.0   0.00012      0.28      23      62 ..     119     159 ..     106     163 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.5
                                   HHHHHHHHHCT--.CCC CS
                          HHH_8  9 eeladllelkged.pfr 24
                                   ++la+++ ++g+d p+r
  gi|119719909|ref|YP_920404.1| 44 RRLAEWYRRRGRDfPWR 60
                                   57999999999875666 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00012
                                    CCHHHHHHHHCCC.CC-SS-HHHHTTHCTTSTT--HHHHHH CS
                          HHH_8  23 frvraYrrAarai.ealpeeitsleeeltklpgiGkkiaak 62 
                                     r+ a r Aar i e+++  +   +eel kl+g+G+ ia  
  gi|119719909|ref|YP_920404.1| 119 RRADALREAAREIvERHGGSVPRSKEELLKLKGVGPYIASA 159
                                    577788888887636688888888667***********986 PP

>> GGDEF  Diguanylate cyclase, GGDEF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00012      0.26      55     107 ..      35      91 ..      33     105 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00012
                                    HHHHHHHHHHHHHCCS-T..TSEEEEESSSEEEEEEECSSHH..HHHHHHHHHHHHH CS
                          GGDEF  55 GDevLqevakrLssslrk..sdlvaRlggdeFaillpetsse..eaaelaerirrll 107
                                    G+e + eva+rL+++ r+  +d+  R   d  +il +e  ++  +a+++a++ ++  
  gi|119719909|ref|YP_920404.1|  35 GEEYFEEVARRLAEWYRRrgRDFPWRHTRDPYVILATEFLLQrtRAETVAKVFEEFF 91 
                                    999***************99*****************98776335555666555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       709  (0.0395449); expected 358.6 (0.02)
Passed bias filter:                      609  (0.0339673); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 1539.24
//
Query:       gi|119719910|ref|YP_920405.1|  [L=175]
Description: hypothetical protein Tpen_1002 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 1167.89
//
Query:       gi|119719911|ref|YP_920406.1|  [L=304]
Description: chromosome partitioning ATPase protein-like [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.1e-12   46.1   0.0    8.8e-12   45.3   0.0    1.3  1  AAA_31       AAA domain
    1.3e-08   35.0   0.0    1.7e-08   34.5   0.0    1.2  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
     0.0014   17.9   0.0     0.0043   16.3   0.0    1.7  2  ArsA_ATPase  Anion-transporting ATPase
     0.0025   17.3   0.0      0.019   14.5   0.0    2.0  2  ParA         NUBPL iron-transfer P-loop NTPase
  ------ inclusion threshold ------
      0.022   15.1   0.0      0.038   14.3   0.0    1.3  1  AAA_19       AAA domain


Domain annotation for each model (and alignments):
>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   0.0   2.5e-15   8.8e-12       2     155 ..       8     181 ..       7     197 .. 0.77

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 2.5e-15
                         AAA_31   2 kvIaianqKGGvGKTTtsvnlaaalaklg....kkvLlvDlDpQanattglgiekne.....iektlyevl.....i.ee 66 
                                    +++a++   GGvGKTT sv +aa l + +      +LlvDlDp a ++  l  ++n        ktl  +        ++
  gi|119719911|ref|YP_920406.1|   8 RTLAFISASGGVGKTTLSVLFAAYLQHVKgvpaREILLVDLDPTAGLSLLLLGDENYakaedEGKTLSAAYedlfeRgRR 87 
                                    7899*********************9643244368*************94443333322223334444442333453489 PP

                         AAA_31  67 knikeaiiktkvenl..dlipssidLaeaeielvelekkeeilkellek..vkdeYDyiiiDcpPsLg.lltenaLvasd 141
                                    ++ + +i ++++++   ++++   ++ ++  el +  +  e +++lle+  v +++ y+++D  P  +  +t+ +L++sd
  gi|119719911|ref|YP_920406.1|  88 VEPERYIWEASFKDSyfKVLVPGESFPRVVEELWRPGNPGESFRRLLEElgVYSSFRYVVVDSAPFFDeRYTVLSLYSSD 167
                                    9999****99988877899999999**********************98335799***********96379********* PP

                         AAA_31 142 sviipvqaeayale 155
                                    ++ +++ ++    +
  gi|119719911|ref|YP_920406.1| 168 KYAVVLRPSIVDFR 181
                                    *****999765554 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.0   4.8e-12   1.7e-08       1      74 [.      10     271 ..      10     300 .. 0.82

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 4.8e-12
                                    EEEEESSTTSSHHHHHHHHHHHHHH.TT...--EEEEEEEESSCCCCHHTTEB-HHHH...................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxx.xx...xxxxxxxxxxxxxxxxxxxxxxxxxxx...................... RF
                           CbiA   1 iaiastkGGvGKTtlaanLaralar.rg...lrVllvDaDpqannlaileglendiep...................... 54 
                                    +a++s +GGvGKTtl++ +a++l+  +g   +++llvD+Dp a ++ +l g+en+ +                       
  gi|119719911|ref|YP_920406.1|  10 LAFISASGGVGKTTLSVLFAAYLQHvKGvpaREILLVDLDPTAGLSLLLLGDENYAKAedegktlsaayedlfergrrve 89 
                                    58899*******************976533379**************99999999988999******************* PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                           CbiA  55 ................................................................................ 54 
                                                                                                                    
  gi|119719911|ref|YP_920406.1|  90 peryiweasfkdsyfkvlvpgesfprvveelwrpgnpgesfrrlleelgvyssfryvvvdsapffderytvlslyssdky 169
                                    ***************************************99999999999999999999999999999999999999999 PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                           CbiA  55 ................................................................................ 54 
                                                                                                                    
  gi|119719911|ref|YP_920406.1| 170 avvlrpsivdfrrtlrmirylaqhhsgrlggstgafyskilavynlvdtgtreasalaergirnpegkeegkakpsqevl 249
                                    99999999988888888888888888888888888888888888888888888888888888888888888888888777 PP

                                    .CCHCCCHHHHHHCHCHHHH.. CS
                                    .xxxxxxxxxxxxxxxxxxx.x RF
                           CbiA  55 .dlkrllellealgkkkall.l 74 
                                     ++++l+ l+ ++   + ++  
  gi|119719911|ref|YP_920406.1| 250 kGIDSLSTLVGRVADYYVPAhS 271
                                    7666666666555555555453 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.2e-06    0.0043       4      44 ..      11      55 ..       8      69 .. 0.85
   2 ?   -2.1   0.0      0.46   1.6e+03     122     134 ..     140     152 ..     128     153 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.2e-06
                                   EEEEESTTSSHHHHHHHHHHHHHHTT....S-EEEEE-STTTHHH CS
                    ArsA_ATPase  4 ilvgGKGGVGKttvsaatavklsekg....kkvllistDPAhsls 44
                                    +++  GGVGKtt+s  +a++l + +    +++ll+ +DP   ls
  gi|119719911|ref|YP_920406.1| 11 AFISASGGVGKTTLSVLFAAYLQHVKgvpaREILLVDLDPTAGLS 55
                                   589999***************98864333389********98887 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.46
                                    CSSSSEEEEESBS CS
                    ArsA_ATPase 122 eeeydvvvlDtaP 134
                                     + + +vv+D+aP
  gi|119719911|ref|YP_920406.1| 140 YSSFRYVVVDSAP 152
                                    568999******9 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   5.2e-06     0.019       4      41 ..       8      49 ..       5      78 .. 0.76
   2 ?    0.4   0.0     0.099   3.6e+02      91     161 ..     121     191 ..     116     199 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.2e-06
                           ParA  4 kviavlSgKGGVGKStvavnlAlaLa....kkglkvgllDaD 41
                                   +++a +S+ GGVGK+t++v +A+ L+        ++ l+D+D
  gi|119719911|ref|YP_920406.1|  8 RTLAFISASGGVGKTTLSVLFAAYLQhvkgVPAREILLVDLD 49
                                   578899*******************94222233466666666 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.099
                           ParA  91 wrGpmkskaikqllkdv.ewgelDyLiiDlPPGtgDeqltvaqklplagaviVttpqevaladvkkaiemfk 161
                                    wr     +  ++ll++   +++  y+++D  P   De  tv++  + ++  +V  p  v +  + + i+ + 
  gi|119719911|ref|YP_920406.1| 121 WRPGNPGESFRRLLEELgVYSSFRYVVVDSAPF-FDERYTVLSLYSSDKYAVVLRPSIVDFRRTLRMIRYLA 191
                                    555555556666666652578889999999995.699********999999999998776666666555544 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0     1e-05     0.038       9      48 ..       7      46 ..       2      63 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1e-05
                         AAA_19  9 kekvllvtaGpGtGKTrvlkhivallvelggvkpeeillv 48
                                   ++++ ++ a  G GKT++ +   a+l++++gv+++eillv
  gi|119719911|ref|YP_920406.1|  7 SRTLAFISASGGVGKTTLSVLFAAYLQHVKGVPAREILLV 46
                                   567789********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2047.36
//
Query:       gi|119719912|ref|YP_920407.1|  [L=260]
Description: stationary phase survival protein SurE [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-45  155.9   0.1    1.3e-45  155.5   0.1    1.1  1  SurE      Survival protein SurE
     0.0034   17.3   0.1       0.43   10.5   0.0    2.7  3  JSRP      Junctional sarcoplasmic reticulum protein


Domain annotation for each model (and alignments):
>> SurE  Survival protein SurE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.5   0.1   1.5e-49   1.3e-45       1     185 [.       3     181 ..       3     196 .. 0.88

  Alignments for each domain:
  == domain 1  score: 155.5 bits;  conditional E-value: 1.5e-49
                                    EEEE-SS-TT-HHHHHHHHHHTTTTSEEEEEEESSS-TTCTTS--SSSEEEEEEEECSTTTCEEEESS-HHHHHHHHHHT CS
                           SurE   1 iLltNDDGieapgiralvealaaaghevvvvaPdserSgigkaltleeplrveseeeeeeeeeyavsGtPadcvklalee 80 
                                    iL+tNDDG+ +pg+  l ea++  g e +vv+P++ +S++g  ltl++plrv++ +  ++e  y vsGtP+d++ +a++ 
  gi|119719912|ref|YP_920407.1|   3 ILVTNDDGPFSPGLAILREAVRGLG-EATVVVPETPKSATGLGLTLHKPLRVNRLSL-DGEPVYLVSGTPSDVIYIAMNV 80 
                                    8*********************888.*************************996655.89******************99 PP

                                    TTTTS.SSEEEEEEEES---GGGG.GG-HHHHHHHHHHHTTSEEEEEEEESSSSS-SSS---HHHHHHHHHHHHTTETTS CS
                           SurE  81 llkekkpdlVvSGiNhGaNlgtdv.lySGTvgAaleaalegipaiAvSlaskkeeekkeedtfeaaakvaaklvekliek 159
                                    ++   kpdlVvSG+N G+Nl+ +v l+SGT+gA+l+a++eg+p+iA+S+a+++ ee +e +  + + + ++++v+ ++ +
  gi|119719912|ref|YP_920407.1|  81 ISG--KPDLVVSGVNIGDNLSVQViLTSGTLGAVLQASIEGVPGIAFSAAVDTPEELEEGEYRNFVLRSTKAIVRAVVGE 158
                                    885..6********************************************998666556564555667777788888888 PP

                                    -...SS-EEEEEEESS.GCG-SEEEE CS
                           SurE 160 lllekvellnvNvPeleeeeikgvkv 185
                                     + + v+ lnvN+P++ +++++   v
  gi|119719912|ref|YP_920407.1| 159 GFPKGVDALNVNFPSVIASDVV---V 181
                                    88************88877777...3 PP

>> JSRP  Junctional sarcoplasmic reticulum protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.6   0.0    0.0068        61      24      46 ..      13      35 ..      12      44 .. 0.87
   2 ?   -3.1   0.0      0.89     8e+03      17      33 ..     150     166 ..     150     168 .. 0.76
   3 !   10.5   0.0   4.8e-05      0.43      15      52 ..     174     210 ..     173     219 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.0068
                           JSRP 24 gsgfqllhdavrGeaeveeraPe 46
                                   ++g+  l++avrG  e++  +Pe
  gi|119719912|ref|YP_920407.1| 13 SPGLAILREAVRGLGEATVVVPE 35
                                   68999********9999988887 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.89
                           JSRP  17 AslvavLgsgfqllhda 33 
                                    A++ av+g gf +  da
  gi|119719912|ref|YP_920407.1| 150 AIVRAVVGEGFPKGVDA 166
                                    77889999999876665 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 4.8e-05
                           JSRP  15 vlAslvavLgsgfqllhdavrGeaeveeraPepwvpps 52 
                                    v+As v v+++++++++ av  +++ + r P  w+  +
  gi|119719912|ref|YP_920407.1| 174 VIASDVVVVRPALKRFSTAVVRRKDPQGR-PYYWLYGH 210
                                    89*******************99998889.99999544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1892.47
//
Query:       gi|119719913|ref|YP_920408.1|  [L=182]
Description: putative NTPase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.6e-58  195.6   0.0    6.6e-58  195.3   0.0    1.0  1  NTPase_1         NTPase
    4.6e-07   29.6   0.2    6.8e-07   29.0   0.2    1.2  1  DUF2478          Protein of unknown function (DUF2478)
    0.00017   21.6   0.3       0.17   11.9   0.1    2.2  2  AAA_5            AAA domain (dynein-related subfamily)
     0.0016   18.8   0.4      0.018   15.4   0.5    2.1  2  AAA_19           AAA domain
     0.0031   16.5   3.5     0.0045   16.0   3.5    1.4  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
     0.0063   16.9   0.2      0.022   15.2   0.2    1.8  1  AAA              ATPase family associated with various cellul
     0.0076   16.5   0.6       0.04   14.2   0.3    2.3  2  AAA_22           AAA domain
  ------ inclusion threshold ------
       0.01   15.6   2.2      0.059   13.1   2.2    2.0  1  AAA_30           AAA domain
      0.011   15.4   0.2       0.36   10.5   0.1    2.1  2  IstB_IS21        IstB-like ATP binding protein
      0.016   14.9   0.1        1.6    8.4   0.0    2.2  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
       0.02   14.6   0.0      0.039   13.7   0.0    1.6  1  AAA_24           AAA domain
      0.028   14.0   0.2      0.044   13.4   0.2    1.3  1  SRP54            SRP54-type protein, GTPase domain
      0.032   14.1   0.1      0.053   13.4   0.1    1.3  1  MobB             Molybdopterin guanine dinucleotide synthesis
      0.033   14.6   0.4       0.12   12.7   0.3    1.8  2  AAA_16           AAA ATPase domain
      0.087   12.5   0.1       0.13   11.9   0.1    1.3  1  Thymidylate_kin  Thymidylate kinase


Domain annotation for each model (and alignments):
>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.3   0.0   5.6e-61   6.6e-58       2     166 ..       6     171 ..       5     173 .. 0.98

  Alignments for each domain:
  == domain 1  score: 195.3 bits;  conditional E-value: 5.6e-61
                                    EEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE-------EEEEEET.T--EEEEEETT---SSEETTEEE-HHHH CS
                       NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgGfyteevreggrrigFkivdlasgeegiLarveakreprvgkyvvdvesf 81 
                                    +++TG+pG+GKtT+v k +ell s+gvkvgG++t+evregg+r+gFk+ dl +g+eg La+v+a  +prvgkyvv+ve++
  gi|119719913|ref|YP_920408.1|   6 FLLTGRPGIGKTTCVVKTAELLVSRGVKVGGMVTHEVREGGSRVGFKVRDLLTGREGFLAKVGAGAGPRVGKYVVHVEEL 85 
                                    79****************************************************************************** PP

                                    HHHHHHHHHHHHHHH-EEEE---STTGGG-HHHHHHHHHHHTTTSEEEEE--SS-.-SHHHHHHHT-TT-EEEE--TTTT CS
                       NTPase_1  82 eelalealrkalseadviviDEiGkmElkskkfkeaveevLksekpvlavihrrk.dlalveeirerkdvkvfevteenr 160
                                    e +++ a+ +a+sea+v+viDEiG+mEl s++f  av ++L+s+kpvla+ih+r+ ++  ++ i er dvk+++vt +nr
  gi|119719913|ref|YP_920408.1|  86 EAVGVGAILRAVSEAQVVVIDEIGPMELYSPSFLPAVLKALDSDKPVLATIHEREsSSGRLRGILERGDVKLYTVTLQNR 165
                                    *******************************************************999********************** PP

                                    TTHHHH CS
                       NTPase_1 161 dallee 166
                                    d l+ +
  gi|119719913|ref|YP_920408.1| 166 DLLPPQ 171
                                    *99876 PP

>> DUF2478  Protein of unknown function (DUF2478)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.2   5.7e-10   6.8e-07      14     133 ..      18     139 ..       7     143 .. 0.84

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 5.7e-10
                        DUF2478  14 alLaafaerlraeGlrvaGvvqenaeeaegkkcdmeledlatger...irisqdlgsgsqgCrLdpeaLaea.aaavera 89 
                                    + + ++ae l ++G++v+G+v ++ +e+ g++   +++dl tg++    ++    g++     ++ e+L+++ ++a+ ra
  gi|119719913|ref|YP_920408.1|  18 TCVVKTAELLVSRGVKVGGMVTHEVREG-GSRVGFKVRDLLTGREgflAKVGAGAGPRVGKYVVHVEELEAVgVGAILRA 96 
                                    566788999************9888865.7888*******988862225556667777778889*****98736899999 PP

                        DUF2478  90 laegadlvivnkFGkqEaeGrGlreeiaaalaagiPvltaVsek 133
                                    + ++a++v++   G  E     + +++ +al ++ Pvl +++e+
  gi|119719913|ref|YP_920408.1|  97 V-SEAQVVVIDEIGPMELYSPSFLPAVLKALDSDKPVLATIHER 139
                                    9.99************************************9986 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.1   0.00014      0.17       1      24 [.       5      29 ..       5      41 .. 0.84
   2 !    8.0   0.0    0.0022       2.7      57      94 ..      91     131 ..      76     164 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00014
                                   EEEEE--SSSSHHHHHHHGGGGB.S CS
                          AAA_5  1 dvlLvGppGtgKselaerlaaal.n 24
                                   ++lL G pG+gK++ + + a++l  
  gi|119719913|ref|YP_920408.1|  5 NFLLTGRPGIGKTTCVVKTAELLvS 29
                                   689**************99999963 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0022
                                    --------G-SEEEEESGGG--...HHHHHHHHHHHHSSEE CS
                          AAA_5  57 splvraaregeilvlDEverae...sevlnsLlslleerrl 94 
                                    +++ ra+ e++++v+DE+  +e   ++ l+++l+ l+ ++ 
  gi|119719913|ref|YP_920408.1|  91 GAILRAVSEAQVVVIDEIGPMElysPSFLPAVLKALDSDKP 131
                                    67889************965433338888888888887665 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.5   1.5e-05     0.018      10      38 ..       3      31 ..       1      41 [. 0.87
   2 ?    1.2   0.0      0.35   4.1e+02      99     125 ..      96     122 ..      65     134 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.5e-05
                         AAA_19 10 ekvllvtaGpGtGKTrvlkhivallvelg 38
                                   +k++l+t+ pG GKT+++++  +llv++g
  gi|119719913|ref|YP_920408.1|  3 AKNFLLTGRPGIGKTTCVVKTAELLVSRG 31
                                   7899*****************99999876 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.35
                         AAA_19  99 klqeeellivDEfqdvdelqyrLlkal 125
                                     + e++++++DE+  ++    ++l a+
  gi|119719913|ref|YP_920408.1|  96 AVSEAQVVVIDEIGPMELYSPSFLPAV 122
                                    455566999999987776666666555 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   3.5   3.8e-06    0.0045      33      82 ..       7      54 ..       2     105 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.8e-06
                                   EEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE----------------- CS
                           MeaB 33 GltGvPGaGkstlvealglelrrrGkrvavlavDPsspftGGsilGDklR 82
                                    ltG PG Gk t v + ++ l++rG +v+ +       ++GGs +G k+R
  gi|119719913|ref|YP_920408.1|  7 LLTGRPGIGKTTCVVKTAELLVSRGVKVGGMVT--HEVREGGSRVGFKVR 54
                                   59**************************97764..467899999999988 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.2   1.8e-05     0.022       2      67 ..       7     108 ..       6     117 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.8e-05
                                    EEESSTTSSHHHHHHHHHHHH...THEEEEEETTTCSSS....................................STTHH CS
                            AAA   2 llyGppGtGKTllakavakel...gvefleisgsellsk....................................yvges 42 
                                    ll+G pG+GKT+++   a+ l   gv++  +  +e++ +                                    +v+e 
  gi|119719913|ref|YP_920408.1|   7 LLTGRPGIGKTTCVVKTAELLvsrGVKVGGMVTHEVR-EggsrvgfkvrdlltgregflakvgagagprvgkyvvHVEEL 85 
                                    89****************9984443333333333333.145666666666666677777777777777666654444443 PP

                                    HHHHHHHHHHHHHTSTSEEEEEETG CS
                            AAA  43 ekkirelfkeakekakpsilfiDEi 67 
                                    e+   + + +a ++a   +++iDEi
  gi|119719913|ref|YP_920408.1|  86 EAVGVGAILRAVSEA--QVVVIDEI 108
                                    333333333333333..68888887 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.3   3.4e-05      0.04       6      32 ..       4      30 ..       1     132 [. 0.60
   2 ?   -1.1   0.0       1.7   2.1e+03      45      85 ..     134     175 ..     112     180 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.4e-05
                         AAA_22  6 gilvvtGesGtGKTtllrrlleqldee 32
                                   +  ++tG +G+GKTt++ + +e l+ +
  gi|119719913|ref|YP_920408.1|  4 KNFLLTGRPGIGKTTCVVKTAELLVSR 30
                                   6679*************9999998643 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.7
                         AAA_22  45 vtlpsstsskdllrellralglelkaerlsseell.ealeqa 85 
                                     t+ + +ss+  lr +l+  +++l + +l++++ll  +l++ 
  gi|119719913|ref|YP_920408.1| 134 ATIHERESSSGRLRGILERGDVKLYTVTLQNRDLLpPQLARE 175
                                    444455555556666666666666666666666665666555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   2.2   4.9e-05     0.059      22     100 ..       7     111 ..       2     132 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.9e-05
                         AAA_30  22 vltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgieastiakllkrlk.................... 81 
                                    +ltG++G GKtt + + +e++ ++g +v g+   +     ++e+    +  +  ll+  +                    
  gi|119719913|ref|YP_920408.1|   7 LLTGRPGIGKTTCVVKTAELLVSRGVKVGGMVTHE-----VREGGSRVGFKVRDLLTGREgflakvgagagprvgkyvvh 81 
                                    79***********************8887654333.....2222222222222222222223333334444555555555 PP

                         AAA_30  82 .............grarlepgtllivDEagmv 100
                                                 +  ++++++++++DE+g +
  gi|119719913|ref|YP_920408.1|  82 veeleavgvgailR--AVSEAQVVVIDEIGPM 111
                                    56788888886431..4566699999998865 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1    0.0003      0.36      47      78 ..       3      34 ..       1      44 [. 0.87
   2 ?    3.1   0.0     0.058        70     101     122 ..      92     113 ..      80     135 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0003
                      IstB_IS21 47 kenivllGpsGvGKshlaialgveavraglsv 78
                                   ++n++l+G +G+GK+   +  +   v +g++v
  gi|119719913|ref|YP_920408.1|  3 AKNFLLTGRPGIGKTTCVVKTAELLVSRGVKV 34
                                   68*************99999999999999888 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.058
                      IstB_IS21 101 ralkrllkvdllilDdlgllpl 122
                                     +l+++ +++++++D++g  +l
  gi|119719913|ref|YP_920408.1|  92 AILRAVSEAQVVVIDEIGPMEL 113
                                    568889999********97655 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0    0.0014       1.6      35      56 ..       5      25 ..       1      44 [. 0.72
   2 ?    4.6   0.0     0.021        25      75      96 ..      90     111 ..      79     128 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0014
                         RuvB_N 35 hvllyGpPGlGkttlakiiake 56
                                     ll+G PG+Gktt     ++e
  gi|119719913|ref|YP_920408.1|  5 NFLLTGRPGIGKTTCVVK-TAE 25
                                   579**********97543.334 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.021
                         RuvB_N  75 laalltnleekdvlfideihrl 96 
                                    + a+l  ++e +v+ idei  +
  gi|119719913|ref|YP_920408.1|  90 VGAILRAVSEAQVVVIDEIGPM 111
                                    679****************766 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   3.3e-05     0.039       2      73 ..       3     107 ..       2     116 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.3e-05
                         AAA_24   2 klkiliyGpsgiGKTtlakelgpkplfi.............................dtekGlksldadkfpdieswedf 52 
                                    ++++l++G +giGKTt++ +   + l+                                e+ l+++ a  +p++ ++   
  gi|119719913|ref|YP_920408.1|   3 AKNFLLTGRPGIGKTTCVVKT-AELLVSrgvkvggmvthevreggsrvgfkvrdlltGREGFLAKVGAGAGPRVGKYVVH 81 
                                    6789*************9888.6666655555555555555555555555555555555555555555555555555555 PP

                         AAA_24  53 ldevvel.....aaeladyktlviDt 73 
                                    ++e++++      ++ ++ +++viD 
  gi|119719913|ref|YP_920408.1|  82 VEELEAVgvgaiLRAVSEAQVVVIDE 107
                                    55555555555544445555555555 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   3.6e-05     0.044       3      34 ..       5      36 ..       3      47 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.6e-05
                                   EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEE CS
                          SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvll 34
                                    +ll G  G+GKTt + K a+ll ++g kv  
  gi|119719913|ref|YP_920408.1|  5 NFLLTGRPGIGKTTCVVKTAELLVSRGVKVGG 36
                                   5799**********************999864 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   4.4e-05     0.053       3      36 ..       7      41 ..       5      48 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.4e-05
                           MobB  3 givgksgsGKTtLleklipelkarglrvg.tiKha 36
                                    ++g+ g GKTt + k  + l +rg++vg ++ h+
  gi|119719913|ref|YP_920408.1|  7 LLTGRPGIGKTTCVVKTAELLVSRGVKVGgMVTHE 41
                                   578999**********************7356665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.3    0.0001      0.12      26      53 ..       5      32 ..       2      59 .. 0.82
   2 ?   -0.7   0.0       1.3   1.6e+03     137     168 ..     101     133 ..      83     148 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0001
                         AAA_16 26 lvllsGesGvGKsslvrellralekdgg 53
                                   + ll+G +G+GK++ v + ++ l  +g+
  gi|119719913|ref|YP_920408.1|  5 NFLLTGRPGIGKTTCVVKTAELLVSRGV 32
                                   689*************888887777744 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.3
                         AAA_16 137 lvlvlDdlqwadeaslqllaaLlrllesk.pll 168
                                     v+v+D++   +  s ++l+a l++l+s+ p+l
  gi|119719913|ref|YP_920408.1| 101 QVVVIDEIGPMELYSPSFLPAVLKALDSDkPVL 133
                                    378888887777777777777777777744664 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00011      0.13       5      48 ..      12      60 ..       8      71 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                                   TTSSHHHHHHHHHHHHHHTTE...EEEESS..STTSHHHHHHHHHHH.T CS
                Thymidylate_kin  5 DGaGKttqaellkerlkeegik..vvltre..pggteiGekirelll.k 48
                                    G GKtt + + +e l ++g k   ++t+e  +gg+++G k+r+ll+ +
  gi|119719913|ref|YP_920408.1| 12 PGIGKTTCVVKTAELLVSRGVKvgGMVTHEvrEGGSRVGFKVRDLLTgR 60
                                   599*******************77799999556799**********933 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1226.31
//
Query:       gi|119719914|ref|YP_920409.1|  [L=377]
Description: iron-containing alcohol dehydrogenase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   5.6e-103  344.5   0.0   6.4e-103  344.4   0.0    1.0  1  Fe-ADH    Iron-containing alcohol dehydrogenase
    6.8e-15   55.5   0.0    1.5e-11   44.5   0.0    2.1  2  Fe-ADH_2  Iron-containing alcohol dehydrogenase
  ------ inclusion threshold ------
       0.12   12.4   0.0       0.22   11.5   0.0    1.3  1  VirD1     T-DNA border endonuclease VirD1


Domain annotation for each model (and alignments):
>> Fe-ADH  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  344.4   0.0  1.1e-106  6.4e-103       1     362 [.      12     367 ..      12     369 .. 0.97

  Alignments for each domain:
  == domain 1  score: 344.4 bits;  conditional E-value: 1.1e-106
                                    -SEEEEETTGGGGHHHHHTTT-..EEEEEEEHHHH.HH.THHHHHHHHHCTT-EEEE.EEE-S---HHHHHHHHTTS-TT CS
                         Fe-ADH   1 Ptrivfgkgaleelgellkklgakralivtdkgslkksglldkvlesleeagievtvfdgvepnptleeveeaaalaree 80 
                                    Pt++vf++g+l++lgel+k lg  +al+vt+++++kk g+ + ++++le+ag+ev  f++vepnpt+e+ +++a++ar++
  gi|119719914|ref|YP_920409.1|  12 PTTVVFERGSLNRLGELVKGLG-GKALVVTGRQFAKKYGYDSLIKSQLESAGVEVYFFSEVEPNPTIETADRCAEAARKA 90 
                                    99********************.6******************************************************** PP

                                    .--EEEEEESHHHHHHHHHHHHHTT...................--EEEEESS-S-S-TT-SEEEEE.-TTSEEEEE-.. CS
                         Fe-ADH  81 gadvviavGGGsviDtAKaialllanpe.vedylgegkakkkkalpliaiPTtaGtGsevtplavitdeeegeklsifdp 159
                                    g+d+++a+GGGsviD+AKa++++++ ++  +dyl   +  ++k  pl+a+PTt GtGsevt+++v+ d e+g+k++++  
  gi|119719914|ref|YP_920409.1|  91 GVDFFVAFGGGSVIDVAKAANVVYSLGGsAKDYL-WPRNVEEKLRPLVAVPTTHGTGSEVTKYSVLVDRETGMKVAVSGS 169
                                    *************************9856*****.556667888************************************ PP

                                    SS--SEEEEEHHHHHHS-HHHHHHHHHHHHHHHHHHHHHHT---TTSSB--HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fe-ADH 160 ellPdlaivDpeltltlPkrvtaatglDalahalEayvskkanplsdalaleairliaknleravadgedleareqmlla 239
                                     llP+la++Dp ++ +lP+++ a+tglDal+ha+Ea++s++a+p++d++alea r++++ l+ av+    l+ re ml+a
  gi|119719914|ref|YP_920409.1| 170 GLLPTLAVLDPLVLKHLPSDQSASTGLDALSHAIEAFFSSRATPFTDMFALEASRIAFRKLPCAVEG--FLDCREWMLYA 247
                                    *****************************************************************77..6********** PP

                                    HHHHHHHHHSS---HHHHHHHHHHC.CGGGGGS-HHHHHHHHH..........HHHHHHT.......T--HHHHHHHHHH CS
                         Fe-ADH 240 stlaglafsnaglgavHalahalgalfgiphglanaillpavlrfnaeaaperlaqlaralggesdeeaaeeliealrel 319
                                    s+lag a++++g+++ H+l+++l+ ++++phg+an + l  +l+++ + aper + +a+ +g    ++++  l   ++el
  gi|119719914|ref|YP_920409.1| 248 SMLAGYAINYTGTNIGHGLGYPLTTRLNLPHGFANTVPLLGALEYYEKYAPERARLFAEHVG----ATGVGGLRGLFKEL 323
                                    ************************************************************95....5699999999**** PP

                                    HHHTT---SHHHHT-TT-HHHHHHHHHT-T.SGGGGSSS---HH CS
                         Fe-ADH 320 lkelglptsLselgvdeedldklaeaalkd.rslannpreltae 362
                                    ++e+g+ptsLs lgv +e+ld+ +++ lk  r+l n p+e+t+e
  gi|119719914|ref|YP_920409.1| 324 CREVGAPTSLSGLGVRREELDDYVREGLKYkRNLSNAPFEVTEE 367
                                    ******************************************98 PP

>> Fe-ADH_2  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.5   0.0   2.5e-15   1.5e-11       2      94 ..      17     110 ..      16     116 .. 0.89
   2 !    9.1   0.0   0.00016      0.94     100     224 ..     134     259 ..     117     280 .. 0.83

  Alignments for each domain:
  == domain 1  score: 44.5 bits;  conditional E-value: 2.5e-15
                       Fe-ADH_2   2 igegaleklgellkelelkkvllvadentkka..agekveeslkeagikvevveeveeeadleeveklvealreketdlv 79 
                                    +++g l++lgel+k l++k +l+v++++  k   + + ++++l++ag++v +++eve+++++e++ + +ea+r++++d++
  gi|119719914|ref|YP_920409.1|  17 FERGSLNRLGELVKGLGGK-ALVVTGRQFAKKygYDSLIKSQLESAGVEVYFFSEVEPNPTIETADRCAEAARKAGVDFF 95 
                                    67899********999886.5677888877662455779***************************************** PP

                       Fe-ADH_2  80 vavGgGtiiDiakyv 94 
                                    va GgG++iD+ak +
  gi|119719914|ref|YP_920409.1|  96 VAFGGGSVIDVAKAA 110
                                    *************87 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00016
                       Fe-ADH_2 100 vpyvsvpTaaSvDGfaspgaslvvd..gkkrtv.akaaaPlaviaDldvlaeAPrrllasGvGDllgkytaladwklane 176
                                    +p+v+vpT+    +    ++ lv +  g k+ v  +  +P+  ++D  vl++ P+   as   D+l+  +  + ++ a+ 
  gi|119719914|ref|YP_920409.1| 134 RPLVAVPTTHGTGSEVTKYSVLVDRetGMKVAVsGSGLLPTLAVLDPLVLKHLPSDQSASTGLDALSHAIEAFFSSRATP 213
                                    689999999998777777777776678999999888999*********************999***************** PP

                       Fe-ADH_2 177 vseplaklsaamvqeaaeklvedkketealeellealalsgigisrpa 224
                                    +++++a+++ ++ + ++  +v  ++     e +l a++l+g +i  ++
  gi|119719914|ref|YP_920409.1| 214 FTDMFALEASRIAFRKLPCAV--EGFLDCREWMLYASMLAGYAINYTG 259
                                    **********99988887777..4666666777777777777765554 PP

>> VirD1  T-DNA border endonuclease VirD1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   3.6e-05      0.22      79     122 ..     196     238 ..     189     244 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.6e-05
                          VirD1  79 igtlssniaallsayaenpttdlealraeriafgkafadldgll 122
                                    + +ls  i a++s+ a  p td+ al+a riaf k  + ++g+l
  gi|119719914|ref|YP_920409.1| 196 LDALSHAIEAFFSSRA-TPFTDMFALEASRIAFRKLPCAVEGFL 238
                                    5689*********998.69****************988888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 2299.66
//
Query:       gi|119719915|ref|YP_920410.1|  [L=237]
Description: 5-formyltetrahydrofolate cyclo-ligase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      8e-31  107.3   0.0    9.8e-31  107.0   0.0    1.0  1  5-FTHF_cyc-lig  5-formyltetrahydrofolate cyclo-ligase family
  ------ inclusion threshold ------
       0.01   14.6   0.0      0.014   14.2   0.0    1.1  1  TLC             TLC ATP/ADP transporter


Domain annotation for each model (and alignments):
>> 5-FTHF_cyc-lig  5-formyltetrahydrofolate cyclo-ligase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.0   0.0   1.1e-34   9.8e-31       3     187 .]       9     199 ..       6     199 .. 0.93

  Alignments for each domain:
  == domain 1  score: 107.0 bits;  conditional E-value: 1.1e-34
                                    HHHHHHHHHHHTS-HHHHHHHHHHHHHHHHTSHHHHH-.SEE........EE----TTS---HHHHHHHHHTTEEEEEEE CS
                 5-FTHF_cyc-lig   3 elRkqllaalralseeevaaesealsqrieslkesqea.krv........alyvsvkgeidtkelikklleegkevllPr 73 
                                     +R++   ++++l   + a ++ ++ +ri++++++++a +r+        a +v ++++++++ +++ +l+ gk +++  
  gi|119719915|ref|YP_920410.1|   9 RIREE---VWERLVRSGAALPPFPVRGRIPNFRGADAAaRRLvesevfrkARVVFCNPDSPQRYVREAVLRHGKTLIMAS 85 
                                    56666...9***************************9999999************************************* PP

                                    ECSSCTEECEEEEEECCCCCCCCCHCTSSCE--TTECCBCGGGG-SEEEE--SEEETTS-EE-SSTTHHHHHHHHHTS.T CS
                 5-FTHF_cyc-lig  74 vrlesgslkvvrlttlkeedslesgkyglkePeeeeerelalekldlvlvPgvAfdkeGaRlGkGkGyyDrflarlkg.g 152
                                    +rl++g+l ++    ++ee++ +s+  g +   e+   +l+  ++dl + ++vA+d+ G R+GkG+G+ D ++a l+   
  gi|119719915|ref|YP_920410.1|  86 PRLREGFLILDPGRVPEEEYRYASTIRGAFAYGEKVLDSLP--RVDLKVAGSVAVDRVGGRVGKGGGFSDLEYAILRTlN 163
                                    ***********************977777776677776666..************************************* PP

                                    -SS--EEEEE--GGGEES.-----ST----SEEE-S CS
                 5-FTHF_cyc-lig 153 agdkpltvglaldeqlve.rlPleehDvpvdevvte 187
                                    a+ +++++++++++ +v  ++P++ hDvpvd v t+
  gi|119719915|ref|YP_920410.1| 164 ALSDETPIVTTVHDLQVVeKVPMDVHDVPVDYVFTP 199
                                    ************9987776**************997 PP

>> TLC  TLC ATP/ADP transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.5e-06     0.014     427     475 ..     129     178 ..     125     191 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.5e-06
                            TLC 427 eskvkgkaaidvvgarlGKSgg.sliqqllliifatlasispllavvlll 475
                                    + kv g  a+d vg r+GK gg s ++  +l ++ +l++ +p++++v  l
  gi|119719915|ref|YP_920410.1| 129 DLKVAGSVAVDRVGGRVGKGGGfSDLEYAILRTLNALSDETPIVTTVHDL 178
                                    789****************999688999****************998644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1597.07
//
Query:       gi|119719916|ref|YP_920411.1|  [L=281]
Description: DNA polymerase beta subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      5e-08   32.9   0.0    9.1e-08   32.1   0.0    1.3  1  Polbeta       Polymerase beta, Nucleotidyltransferase
     0.0054   17.0   0.0       0.01   16.1   0.0    1.6  1  NTP_transf_2  Nucleotidyltransferase domain


Domain annotation for each model (and alignments):
>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.0     1e-11   9.1e-08      13      90 ..      21     102 ..       8     104 .. 0.83

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 1e-11
                                    HHSTTEEEEEE.-S------EEEEEEEESS---HHHHHHHHHHHHHH....SSSEEEEEETTTS-HHHHHHHHHS-EEEE CS
                        Polbeta  13 ielaylFGSra.kgkareeSDiDlavllkekldleeelelaaeledi...klgkkvDlvdlneapplllyeilkegklly 88 
                                    ++ ++lFGS a ++++++ SDi +av+++ k   ee++ +a++l            +l +l ++   l++eil+ gk+ly
  gi|119719916|ref|YP_920411.1|  21 LAGVVLFGSAArREDFTPLSDINVAVITNGKVPPEERVAIAEALGTDfsvVVLSVEELKQLASNGEFLAHEILRGGKILY 100
                                    6779*******888999**************999999999999999844333444456667767799************* PP

                                    S- CS
                        Polbeta  89 sk 90 
                                    + 
  gi|119719916|ref|YP_920411.1| 101 AD 102
                                    85 PP

>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.1e-06      0.01      13      47 ..      18      55 ..       6     110 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.1e-06
                                   T..TSEEEEEHHHH.CTTSCTTSSEEEEEEESTTCHHH CS
                   NTP_transf_2 13 p..vakvvlfGSya.rGtalkgSDiDllvvlpeevsre 47
                                   +   a vvlfGS+a r ++++ SDi ++v+++  v+ e
  gi|119719916|ref|YP_920411.1| 18 GdrLAGVVLFGSAArREDFTPLSDINVAVITNGKVPPE 55
                                   445689******863699**************998743 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.35s 00:00:00.98 Elapsed: 00:00:00.57
# Mc/sec: 1496.62
//
Query:       gi|119719917|ref|YP_920412.1|  [L=139]
Description: histidine triad (HIT) protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.6e-23   81.5   0.0    7.4e-23   81.1   0.0    1.2  1  HIT       HIT domain
    2.5e-11   44.1   0.0    3.3e-11   43.7   0.0    1.2  1  DcpS_C    Scavenger mRNA decapping enzyme C-term binding
    1.1e-05   25.3   0.0    1.7e-05   24.7   0.0    1.3  1  CwfJ_C_1  Protein similar to CwfJ C-terminus 1


Domain annotation for each model (and alignments):
>> HIT  HIT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.1   0.0   1.2e-26   7.4e-23       2      95 ..      12     105 ..      11     108 .. 0.97

  Alignments for each domain:
  == domain 1  score: 81.1 bits;  conditional E-value: 1.2e-26
                                    GCC-CCEEEE-SSEEEEE-SS-SSSSEEEEEESSTGCSGGGCCHHHHHHHHHHHHHHHHHHHTCTTCCCEEEEEEESGGG CS
                            HIT   2 keipstvvyeddlvlafldidpkapghlLvipkkhlselhdlteeelakllsavkkvakalqkkfknkglrvvinngaha 81 
                                    ++ ++++vy   +v++fld+ p ++gh Lv+pk+h++++ d++ + l++++ ++k va a ++ + ++g+r+v+n g++a
  gi|119719917|ref|YP_920412.1|  12 GQLDAHFVYVGGRVVVFLDKYPVTRGHALVVPKDHYRDVFDAPGDVLSEMVFVAKVVALAQREALGARGVRLVMNSGREA 91 
                                    67899*************************************************************************** PP

                                    T-SSSS-EEEEEEC CS
                            HIT  82 gqsvahlHiHvipr 95 
                                    gq+++h H+Hvip 
  gi|119719917|ref|YP_920412.1|  92 GQEIFHAHMHVIPY 105
                                    ************96 PP

>> DcpS_C  Scavenger mRNA decapping enzyme C-term binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.7   0.0   5.5e-15   3.3e-11       2     101 ..       4     104 ..       3     113 .. 0.89

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 5.5e-15
                                    -HHHHHHTTSS-B-EEEE-SSEEEEE-SS-SSSEEEEEEESS---SGGG--TTTTTHHHHHHHHHHHHHHHTT-T....- CS
                         DcpS_C   2 wvfnilakgkepervvyedekfvvlkDikpkaklhllvipkrdikslrdLtkehlpllkemrekakkvieekyne....v 77 
                                    +vf+++++g+  + +vy   ++vv+ D++p ++ h lv+pk++ +++ d      ++l em+ +ak v+  + ++    +
  gi|119719917|ref|YP_920412.1|   4 CVFCRIVRGQLDAHFVYVGGRVVVFLDKYPVTRGHALVVPKDHYRDVFDAP---GDVLSEMVFVAKVVALAQREAlgarG 80 
                                    9*****************************************999888876...67899998888877776665577888 PP

                                    EEEEE--SCCCT--S-S--EEEEE CS
                         DcpS_C  78 daeelrvgvhyqPsvyhlHlHvis 101
                                     +  ++ g ++ + ++h H+Hvi 
  gi|119719917|ref|YP_920412.1|  81 VRLVMNSGREAGQEIFHAHMHVIP 104
                                    9999******************96 PP

>> CwfJ_C_1  Protein similar to CwfJ C-terminus 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   2.8e-09   1.7e-05      12     118 ..       2     114 ..       1     118 [. 0.77

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 2.8e-09
                                    HH-S----SS---SS--S-B-SSEEEE---S-SSTT-EEEEESS--SSTTSS-HHHHHHHHHHHHHHHHH.HHHTT--EE CS
                       CwfJ_C_1  12 dsClfClsnpklekhlivsignkvYlalpkgpLssgHvliipieHisallsldeevldeirkfrkalvkm.ykkqdkdav 90 
                                    ++C fC     + ++  v +g +v + l k p + gH l++p +H   +  ++ +vl+e+    k ++    ++ +   v
  gi|119719917|ref|YP_920412.1|   2 EDCVFCRIVRGQLDAHFVYVGGRVVVFLDKYPVTRGHALVVPKDHYRDVFDAPGDVLSEMVFVAKVVALAqREALGARGV 81 
                                    79****8888888888899*****************************************86666555443334444444 PP

                                    EEEE-.....SSS-----EEEEE--HHHHTTHH CS
                       CwfJ_C_1  91 vfEis.....sersvHlaiqvipvpksiskkae 118
                                     + ++      ++  H++++vip   +++++ +
  gi|119719917|ref|YP_920412.1|  82 RLVMNsgreaGQEIFHAHMHVIPYGTERMDRRP 114
                                    444443445567778999999998888777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.50
# Mc/sec: 844.16
//
Query:       gi|119719918|ref|YP_920413.1|  [L=187]
Description: ATP-cone domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      4e-11   43.3   0.6    1.2e-10   41.8   0.3    1.9  2  ATP-cone    ATP cone domain
  ------ inclusion threshold ------
      0.098   11.7   0.0       0.12   11.4   0.0    1.1  1  TcA_TcB_BD  Tc toxin complex TcA C-terminal TcB-binding domai


Domain annotation for each model (and alignments):
>> ATP-cone  ATP cone domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.8   0.3   1.3e-14   1.2e-10       2      67 ..       4      72 ..       3      95 .. 0.79
   2 ?   -1.0   0.0       0.3   2.7e+03      30      47 ..     116     133 ..     104     146 .. 0.66

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 1.3e-14
                                   EEE-TTS-EEE--HHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHIIT-BHHHHHHHHHHHHH........H CS
                       ATP-cone  2 kViKRdGtvepfdvekIkraiekAcegseeeideiaeeveaevrkrlrdgisteeIqdlvektli........e 67
                                   kV+KR G+ve+fd+ek+ r+  +A  +     +e+a e+++ev+++ rdg +t+eI+  v   l+        +
  gi|119719918|ref|YP_920413.1|  4 KVVKRSGKVEEFDREKLVRSMVNAGAP-----EEVAVEIAKEVESKVRDGATTDEIRRYVLARLKvlapqayeA 72
                                   8***********************777.....66666666666888899***********99998666655542 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.3
                                    HHHHHHHHHHHHHHHHHH CS
                       ATP-cone  30 eeeideiaeeveaevrkr 47 
                                     ee++ i +e+e++++ +
  gi|119719918|ref|YP_920413.1| 116 SEEVEGILKELEEDLEYG 133
                                    556666666666666443 PP

>> TcA_TcB_BD  Tc toxin complex TcA C-terminal TcB-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   1.4e-05      0.12      23     112 ..      34     128 ..      18     138 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1.4e-05
                     TcA_TcB_BD  23 qienaeevedflrskftneeLYswlesqlsalyyqaYklalslakkaerafqfElgek.....atsfikegywdslrkgL 97 
                                    ++e a+eve+ +r+  t++e+ +++ ++l+ l  qaY++ + + + a+  + fE g+       + ++  +  d   kgL
  gi|119719918|ref|YP_920413.1|  34 AVEIAKEVESKVRDGATTDEIRRYVLARLKVLAPQAYEAWTFYDRVAKGRITFEDGKYvvvskGHLYLGREVKDVGPKGL 113
                                    6778999*************************************************9888865667888999******** PP

                     TcA_TcB_BD  98 lagekLlldLkrlea 112
                                     + e+++  Lk+le+
  gi|119719918|ref|YP_920413.1| 114 SSSEEVEGILKELEE 128
                                    *************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1260.24
//
Query:       gi|119719919|ref|YP_920414.1|  [L=301]
Description: radical SAM domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-12   48.5   0.0    3.7e-12   46.9   0.0    1.8  1  Radical_SAM  Radical SAM superfamily
    6.2e-08   32.7   0.9      0.054   13.2   0.0    2.4  2  DUF1848      Domain of unknown function (DUF1848)
  ------ inclusion threshold ------
      0.017   14.5   0.0      0.029   13.8   0.0    1.2  1  CHAT         CHAT domain
       0.18   11.2   0.0       0.24   10.8   0.0    1.2  1  DUF5131      Protein of unknown function (DUF5131)


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.9   0.0   8.3e-16   3.7e-12       1     162 [.      24     183 ..      24     188 .. 0.81

  Alignments for each domain:
  == domain 1  score: 46.9 bits;  conditional E-value: 8.3e-16
                                    EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHH.HHHH.HHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCCCT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx.xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileev.kelk.aekg.vkevilgggepllypdfvellerlaklavpg 77 
                                    v+++ gC+++C +C+ ++    ++    +++ + l+ v   l+    g + ++ ++++       ++ +++r  +lav  
  gi|119719919|ref|YP_920414.1|  24 VNPYTGCSHGCLYCYASSY--IRDFFNPRPKKDFLKVVyGDLRrIPEGsIVNISSSSDPYQPLESKYGYTRRFLELAVGR 101
                                    57899************96..88888888888888888533334566746666666664444455566666666666899 PP

                                    EEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  78 iritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdrivglpGen 156
                                    + + v+t   l+  + +++l++ g  +vs+++ + d+e v k+++ + + ++++++a+e+l eag+++v    +++pG n
  gi|119719919|ref|YP_920414.1| 102 YVVEVVTKSDLV-ARDADLLAR-GQSVVSVTITTMDNE-VAKRLEpGAPPPSRRVKAVERLSEAGVPVVLRLDPLIPGLN 178
                                    ***********9.*********.88*************.******9999******************888888******* PP

                                    HHHHHH CS
                                    xxxxxx RF
                    Radical_SAM 157 deelee 162
                                    d+e + 
  gi|119719919|ref|YP_920414.1| 179 DSE-DS 183
                                    *97.44 PP

>> DUF1848  Domain of unknown function (DUF1848)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   5.0   1.2e-05     0.054     240     265 .]      14      39 ..       8      39 .. 0.91
   2 !   13.2   0.0   1.2e-05     0.054      74     131 ..     124     183 ..     102     283 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.2e-05
                        DUF1848 240 keCgCveskDiGayntClhgCvYCYA 265
                                    + C+C     +  y  C+hgC+YCYA
  gi|119719919|ref|YP_920414.1|  14 SLCTCPFKYTVNPYTGCSHGCLYCYA 39 
                                    45***********************9 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 1.2e-05
                        DUF1848  74 klyfqfTltdyeke....lepnvpsleerietfkelseklgkerviwRyDPilltekltvel 131
                                    + ++ +T+t++++e    lep+ p+ ++r++++++lse      v++R DP++   + +++ 
  gi|119719919|ref|YP_920414.1| 124 QSVVSVTITTMDNEvakrLEPGAPPPSRRVKAVERLSEAG--VPVVLRLDPLIPGLNDSEDS 183
                                    4456666665544322249******************976..4699******9655444433 PP

>> CHAT  CHAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   6.4e-06     0.029     205     245 ..     178     218 ..     174     221 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.4e-06
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           CHAT 205 vidgegvlgLaralllaGarsviaslwpVddeatalLmkrf 245
                                    ++++++v  ++ a+++aGar+v+ s ++V+ +  a+L+k+f
  gi|119719919|ref|YP_920414.1| 178 NDSEDSVREVVEAAVGAGARHVVSSTYKVKPDNLARLLKAF 218
                                    567899999****************************9999 PP

>> DUF5131  Protein of unknown function (DUF5131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   5.3e-05      0.24       9      35 ..      22      45 ..      19     120 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 5.3e-05
                        DUF5131  9 atwnpvtGCtkvspgCdnCyaerlakr 35
                                    t+np tGC   s gC  Cya +  + 
  gi|119719919|ref|YP_920414.1| 22 YTVNPYTGC---SHGCLYCYASSYIRD 45
                                   599******...68*******986554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1925.56
//
Query:       gi|119719920|ref|YP_920415.1|  [L=62]
Description: hypothetical protein Tpen_1012 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       665  (0.0370907); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 394.67
//
Query:       gi|119719921|ref|YP_920416.1|  [L=337]
Description: oxidoreductase domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-33  115.0   0.7    5.3e-33  114.4   0.7    1.3  1  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f
      4e-09   36.5   0.0    8.4e-09   35.4   0.0    1.6  1  GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta 
    7.6e-05   23.3   0.6    0.00012   22.7   0.6    1.4  1  NAD_binding_3   Homoserine dehydrogenase, NAD binding domain
    0.00065   20.0   0.8     0.0018   18.6   0.8    1.9  1  Gp_dh_N         Glyceraldehyde 3-phosphate dehydrogenase, NAD
     0.0013   19.4   1.3        0.1   13.3   0.1    2.5  2  CoA_binding     CoA binding domain
  ------ inclusion threshold ------
      0.058   12.8   0.1       0.18   11.2   0.0    1.9  2  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase


Domain annotation for each model (and alignments):
>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.4   0.7   1.8e-36   5.3e-33       1     120 []       4     123 ..       4     123 .. 0.99

  Alignments for each domain:
  == domain 1  score: 114.4 bits;  conditional E-value: 1.8e-36
                                    EEEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S-GGGHHHHHH CS
                   GFO_IDH_MocA   1 lrvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysdleelladpeidavivatpngtheelak 80 
                                    +r+++ G+G+ig+ h++ +  + +++e+va+ d  ++ a+ v e+++v+ y++++++l+dpe+dav+++tp+++h+e++ 
  gi|119719921|ref|YP_920416.1|   4 VRIGVAGLGRIGRVHAEIILTRLENAELVAVADVVESLARSVGEKYRVKWYTNFDAMLKDPEVDAVFITTPTNLHKEMIV 83 
                                    599***************************************************************************** PP

                                    HHHHTT-EEEEESSS-SSHHHHHHHHHHHHHHTS-EEEE- CS
                   GFO_IDH_MocA  81 aaleagkhvllEKPlattveeakelvelaekkgklvsvgy 120
                                    +a+eagkhv+ EKP++ tveea+e v++aek+g++++vgy
  gi|119719921|ref|YP_920416.1|  84 KAAEAGKHVFTEKPITVTVEEAREAVRAAEKAGVKLMVGY 123
                                    **************************************98 PP

>> GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   0.0   2.8e-12   8.4e-09       1      75 [.     135     202 ..     135     231 .. 0.76

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 2.8e-12
                                    HHHHHTTTTSSEEEEEEEEECBEEECHHHHCCGGSHHCSTSHHHHTCHHHHHHHHHHHTSEEEEEEEEE.SEEES CS
                 GFO_IDH_MocA_C   1 KelIengklGevvsvdvwtldtragaeakkrwkrrkkksgGvlgdlgiHdiDllqwLfGqppsvvaalgrmrqna 75 
                                    K+ I+ g++Ge++++   + + r + +++ + + +++ sgG++ d+++Hd+D++++L+G +  +v+  g   ++a
  gi|119719921|ref|YP_920416.1| 135 KARIARGEIGEPLVF---INIARDPGPPPGWAQ-DPRLSGGIFLDMLSHDFDMARFLVGREVKEVYVKG---EAA 202
                                    789************...444444444444333.4469***********************99999886...333 PP

>> NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.6   4.2e-08   0.00012       1     115 [.      10     120 ..      10     122 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 4.2e-08
                                    --SHHHHHHHHHHHH---SSEEEEEEEEESSEEE-TTHHHHHT--CB---HHHHHHHHS-EEEEE-S--HHHHTTHHHHH CS
                  NAD_binding_3   1 GlGaiGsavleqlkrqqseielelvavadrdsllskdrkallasealtldlddliahldpdvvVEcasseavaelvlkaL 80 
                                    GlG iG+  +e+++   +  ++elvavad   +  ++   +  + + ++++d++++++++d v   ++ +  +e+++ka 
  gi|119719921|ref|YP_920416.1|  10 GLGRIGRVHAEIILTRLE--NAELVAVADVV-ESLARSVGEKYRVKWYTNFDAMLKDPEVDAVFITTPTNLHKEMIVKAA 86 
                                    9*************9998..7*******999.33344444678999*************999999*************** PP

                                    HTTEEEE-S--CGGG-HHHHHHHTSSSTTS--.EE CS
                  NAD_binding_3  81 kagkdvvtankgaladealyeeLreaaeangakiy 115
                                    +agk+v t     ++  +  +e + aae++g+k++
  gi|119719921|ref|YP_920416.1|  87 EAGKHVFTEKPITVT-VEEAREAVRAAEKAGVKLM 120
                                    *******99888888.5566666778888888876 PP

>> Gp_dh_N  Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.8     6e-07    0.0018       1      35 [.       4      39 ..       4     122 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 6e-07
                                   CEEEEESTSHHHHHHHHHHHHHT.TCEEEEEE-TS- CS
                        Gp_dh_N  1 vkvainGfGRIGrlvlralleek.elevvaindltd 35
                                   v++++ G+GRIGr+ + ++l++  + e+va+ d+++
  gi|119719921|ref|YP_920416.1|  4 VRIGVAGLGRIGRVHAEIILTRLeNAELVAVADVVE 39
                                   69******************66559******99643 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.1   3.4e-05       0.1       5      88 ..       5      91 ..       2      94 .. 0.91
   2 ?    4.4   0.1      0.02        61      68      91 ..      98     121 ..      96     124 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.4e-05
                                   EEEEETTTSHHHHHH.HHHHHHHHECEEEEEEC-TTTTTCEET...TEEEESCHHHHHHHCTTTEEEEES-HHHHHHHHHHH CS
                    CoA_binding  5 kviviGagglgiagl.yhfkeklkygikavfgvnprkvgtevl...glpvyksvdeleektevdvavitvPaesaqeavdel 82
                                   +++v G g+ g+  +     +  + +++av++v +  +++ v+    ++ y++ d + ++ evd+  it+P +  +e ++++
  gi|119719921|ref|YP_920416.1|  5 RIGVAGLGRIGRVHAeIILTRLENAELVAVADVVES-LARSVGekyRVKWYTNFDAMLKDPEVDAVFITTPTNLHKEMIVKA 85
                                   799*******************************99.6676766669999**********99******************** PP

                                   HHTT-S CS
                    CoA_binding 83 veagik 88
                                   +eag  
  gi|119719921|ref|YP_920416.1| 86 AEAGKH 91
                                   **9965 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.02
                                    EES-HHHHHHHHHHHHHTT-SEEE CS
                    CoA_binding  68 itvPaesaqeavdelveagikgiv 91 
                                    itv  e+a+eav ++ +ag+k+ v
  gi|119719921|ref|YP_920416.1|  98 ITVTVEEAREAVRAAEKAGVKLMV 121
                                    78999****************987 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   5.9e-05      0.18      37     112 ..       4      86 ..       1      91 [. 0.69
   2 ?   -3.0   0.0       1.4   4.1e+03      26      51 ..     234     259 ..     230     264 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.9e-05
                                    SEEEEES-SHHHHHHHHHHH.HT.T-EEEEESSSHHHHH...CHHHHTC.EECSHHHHHH..H-SEEEE-S--STTTTTS CS
                   2-Hacid_dh_C  37 ktvGiiGlGrIGqavakrlk.af.gmkviaydrskkkee...eeeelgv.elvsleella..esDivslhlpltpetrhl 108
                                     ++G+ GlGrIG+  a+++   + +++++a+    ++ +     e+++v  +++++++l+  e D v++++p + + + +
  gi|119719921|ref|YP_920416.1|   4 VRIGVAGLGRIGRVHAEIILtRLeNAELVAVADVVESLArsvG-EKYRVkWYTNFDAMLKdpEVDAVFITTPTNLHKEMI 82 
                                    589***********99987645514566555554443333533.444442577999999844689999999998888888 PP

                                    BSHH CS
                   2-Hacid_dh_C 109 inae 112
                                    ++a+
  gi|119719921|ref|YP_920416.1|  83 VKAA 86 
                                    7776 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.4
                                    TCCGSBS-GTTSEEEEES-SHHHHHH CS
                   2-Hacid_dh_C  26 ekallgkelsgktvGiiGlGrIGqav 51 
                                    +k++ g++l+ + +G  G+  +G++v
  gi|119719921|ref|YP_920416.1| 234 RKSVFGYDLRTEVLGTEGTVYVGSQV 259
                                    56788999999999999999999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       678  (0.0378158); expected 358.6 (0.02)
Passed bias filter:                      624  (0.0348039); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2217.84
//
Query:       gi|119719922|ref|YP_920417.1|  [L=946]
Description: DEAD/DEAH box helicase domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-27   96.4   0.0      4e-27   95.1   0.0    1.6  1  DEAD         DEAD/DEAH box helicase
    7.1e-21   74.6   0.0    1.2e-18   67.4   0.0    2.5  2  Helicase_C   Helicase conserved C-terminal domain
    3.4e-18   66.1   0.1    1.5e-17   64.0   0.0    2.2  2  DEAD_assoc   DEAD/H associated
    2.5e-05   24.4   0.0    4.4e-05   23.6   0.0    1.4  1  ResIII       Type III restriction enzyme, res subunit
     0.0048   17.2   0.0      0.042   14.2   0.0    2.5  3  AAA_19       AAA domain
  ------ inclusion threshold ------
      0.017   15.1   0.2      0.058   13.4   0.1    1.9  2  HypA         Hydrogenase/urease nickel incorporation, metallo
       0.03   13.7   0.0       0.11   11.9   0.0    2.0  1  DUF4926      Domain of unknown function (DUF4926)
        0.1   12.7   0.8        0.2   11.8   0.2    1.8  2  Zn-ribbon_8  Zinc ribbon domain


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.1   0.0   1.8e-30     4e-27       4     170 ..      44     207 ..      41     212 .. 0.85

  Alignments for each domain:
  == domain 1  score: 95.1 bits;  conditional E-value: 1.8e-30
                                    HHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEET CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD   4 QaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliig 83 
                                    Q ++++l     ++l++a+TG+GKT+a+++pvl+ ++e kg +   al+v+P+r+L +++++++ +++  ++ ++++  g
  gi|119719922|ref|YP_920417.1|  44 QVKSLELSRVYPNMLISAPTGAGKTEAAVLPVLRDLVE-KGGKPIYALYVTPLRALNRDIYDRMVELFRALGFEAEVRHG 122
                                    6666666666679***********************99.999999*************************9988886666 PP

                                    TSSHHHHHHHHHTTCSEEEEEHHHHHHHH....HCTSSH..CTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTST CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  84 gvaardqlskldngvdivvgtpgrlddll....stgkln..lsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgk 157
                                    ++++r  ++  ++ ++++++tp+  + ll         +  l++ r++V+DE+++lld++++ +++  l++l+ i+   +
  gi|119719922|ref|YP_920417.1| 123 DTPQRVRRRIAESPPHMLITTPETTQFLLvdgrY----RehLKNTRWVVVDEVHELLDDKRGAQLSLALERLRLISPGLR 198
                                    66665555555555*************8855433....334*******************************87766655 PP

                                    TTSEEEEEESSBS CS
                                    xxxxxxxxxxxxx RF
                           DEAD 158 lqrqvivlSATlp 170
                                        v+ lSATl 
  gi|119719922|ref|YP_920417.1| 199 ----VVGLSATLR 207
                                    ....*******97 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.022        49      31      62 ..     104     136 ..      76     150 .. 0.79
   2 !   67.4   0.0   5.5e-22   1.2e-18      15     108 ..     258     352 ..     249     354 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.022
                                    H..HHHHHHHT.TSTEEEESTTSTHHHHHHHHHHH CS
                     Helicase_C  31 k..vklllekk.gikvavlhgelpqnereeileqf 62 
                                    +  v+l+  +  g+++ v hg++pq+ r++i e+ 
  gi|119719922|ref|YP_920417.1| 104 DrmVELF--RAlGFEAEVRHGDTPQRVRRRIAESP 136
                                    2335667..3359*****************99876 PP

  == domain 2  score: 67.4 bits;  conditional E-value: 5.5e-22
                                    TTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEEESSS CS
                     Helicase_C  15 eggkilifvntidrlek.vklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnlVinfdl 93 
                                    +gg +++f+nt+d++e   ++l +  g++v v+hg+l+ +eree+ + f++g++d ++at+ +e G+di  ++lV++f+ 
  gi|119719922|ref|YP_920417.1| 258 RGGGVIVFTNTRDTAEFiGRVLARDYGLNVRVHHGSLSRQEREEAERLFKSGRVDAIVATSSLELGVDIGYARLVVQFGS 337
                                    7899*********9987667776666****************************************************** PP

                                    SSSHHHHHHHHTTSS CS
                     Helicase_C  94 prnvtsyiqriGRtg 108
                                    pr+  ++ qr+GR+g
  gi|119719922|ref|YP_920417.1| 338 PRQAIKLAQRVGRAG 352
                                    **************8 PP

>> DEAD_assoc  DEAD/H associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.8     4e+03      52      90 ..     277     315 ..     267     319 .. 0.63
   2 !   64.0   0.0   6.8e-21   1.5e-17       1     191 []     604     782 ..     604     782 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.8
                     DEAD_assoc  52 qvaanDdgivlll.....pleerlpllldellellspdeleedl 90 
                                    +v a D+g+ + +     +      ++ +e+ +l+++ ++++++
  gi|119719922|ref|YP_920417.1| 277 RVLARDYGLNVRVhhgslSR-----QEREEAERLFKSGRVDAIV 315
                                    67788888888776543222.....2335666777777777766 PP

  == domain 2  score: 64.0 bits;  conditional E-value: 6.8e-21
                     DEAD_assoc   1 lPtdrtllvErfrdelgdwrlvvhspfGrrvnealalllaarlsrrfgidvqvaanDdgivlll....pleerlplllde 76 
                                    +P+dr+ + E      g++ + +hs +G++ n+ lallla+ ++  +g+++++ a+++++++ +    p++        +
  gi|119719922|ref|YP_920417.1| 604 VPSDRNAVAEVASY-KGKTAITLHSYLGTKGNNLLALLLAHAVRGYTGSSARYFADPYRVLVVTeyevPDQ--------R 674
                                    8*********9943.5788*******************************************665443332........3 PP

                     DEAD_assoc  77 llellspd..eleedleaalnaselfkrrFrevAaralllprrypgkrkplwqqrlraaqLldvareyp.dfpllleavr 153
                                    +le+l++      + le+ + +s+ ++  F +vA++++++  ++ +              L++ +r+   ++pl +ea+r
  gi|119719922|ref|YP_920417.1| 675 VLESLRSGleWSLRNLEEVVRESNSYALAFSHVASKMGVVDVKKSK----------PEPGLMSSLRKRMrGTPLDREALR 744
                                    4444443221456789999*********************999877..........44455555554444********** PP

                     DEAD_assoc 154 evledqlDlerlaellrriaageirvvevetprpSpfA 191
                                     +l +++Dle+++e++r++++g+  +v  ++p+ Sp+A
  gi|119719922|ref|YP_920417.1| 745 TCLFEYFDLEAVEEFVREVSEGRRPLVFKRLPELSPLA 782
                                    ************************************98 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   1.9e-08   4.4e-05      26     170 ..      56     207 ..      30     208 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 1.9e-08
                                    EEEEEESTTSTHHHHH.HHHHHHH-S......-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B--....... CS
                         ResIII  26 rglikmaTGtGKTlva.aklierllkkgkee.kflflvprkslleqtleefkkflseaykeigkkvsgdkkka..kekds 101
                                    ++li ++TG+GKT  a + + + l +kg++   +l + p ++l    ++++ +++     ++ ++ +gd+ ++  +++++
  gi|119719922|ref|YP_920417.1|  56 NMLISAPTGAGKTEAAvLPVLRDLVEKGGKPiYALYVTPLRALNRDIYDRMVELFRALG-FEAEVRHGDTPQRvrRRIAE 134
                                    689*************8999999***999888899999988777777777666665543.46677777777777678899 PP

                                    ..-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T.......TTHHHHHT---.SEEEEEESS-S CS
                         ResIII 102 tnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk.......swreilekfke.avllglTATpe 170
                                    +  ++l+tt ++ +  +      + +   ++   +++DE+H l ++k       + ++ l+ +++   ++gl+AT++
  gi|119719922|ref|YP_920417.1| 135 SPPHMLITTPETTQFLL---VDGRYREHLKNTRWVVVDEVHELLDDKrgaqlslALER-LRLISPgLRVVGLSATLR 207
                                    9999*****99999999...66666666677779***********9744434344444.55555569999*****85 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   1.9e-05     0.042      11     114 ..      55     174 ..      44     192 .. 0.63
   2 ?   -0.9   0.0      0.81   1.8e+03      52     112 ..     608     669 ..     584     683 .. 0.58
   3 ?   -3.6   0.1       5.9   1.3e+04      12      25 ..     899     912 ..     897     916 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.9e-05
                         AAA_19  11 kvllvtaGpGtGKTrvlkh.ivallvelggvkpeeillvaftgrA....akelrerlaalgaeatTiHrlal........ 77 
                                    +++l+ a+ G GKT+  +  +++ lve gg  p   l v++ +       +++ e  +alg ea+  H+ +         
  gi|119719922|ref|YP_920417.1|  55 PNMLISAPTGAGKTEAAVLpVLRDLVEKGGK-PIYALYVTPLRALnrdiYDRMVELFRALGFEAEVRHGDTPqrvrrria 133
                                    789***********97665166667777655.666677776555400005555555555666666666543355556666 PP

                         AAA_19  78 ......ldfddlltealelle.eaeeekklqeeellivDEfqdv 114
                                          l +++++t+ l     + + +++l+++ +++vDE+ ++
  gi|119719922|ref|YP_920417.1| 134 espphmLITTPETTQFL---LvDGRYREHLKNTRWVVVDEVHEL 174
                                    66665433333332222...23556788997888******9876 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.81
                         AAA_19  52 grAakelrerlaalgaeatTiHrlalldfddlltealelle.......eaeeekklqeee.llivDEfq 112
                                    + A+ e++      g+ a T+H+   l++++ +  al ll          ++ + + + + +l+v E+ 
  gi|119719922|ref|YP_920417.1| 608 RNAVAEVASYK---GKTAITLHSY--LGTKGNNLLAL-LLAhavrgytG-SSARYFADPYrVLVVTEYE 669
                                    44555555555...7889999987..77777664443.22346667532.3334444666677777765 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 5.9
                         AAA_19  12 vllvtaGpGtGKTr 25 
                                     ++v+aG G G T+
  gi|119719922|ref|YP_920417.1| 899 AVFVLAGHGIGPTT 912
                                    5899*******997 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       4.8   1.1e+04      29      63 ..     287     321 ..     286     324 .. 0.83
   2 ?   13.4   0.1   2.6e-05     0.058      62     100 ..     811     854 ..     782     860 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 4.8
                                    EEEEEETTCT--HHHHHHHHHHHHCC.TTTT-EEE CS
                           HypA  29 vkvevGelsgvepeaLefafellaegtvlegaeLe 63 
                                    v+v+ G+ls  e e  e  f+  + + +++ ++Le
  gi|119719922|ref|YP_920417.1| 287 VRVHHGSLSRQEREEAERLFKSGRVDAIVATSSLE 321
                                    89999999999999999999988888888777776 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 2.6e-05
                                    EEEEEE--EEEETTTS-EEECHH..HHH....S-TTTSSS-EEEE CS
                           HypA  62 LeieevpvkvrCreCgkefelee..kal....rCpkCgsadveiv 100
                                     +ie+++v ++C +Cg+   + +  + +    +CpkCgs+ + ++
  gi|119719922|ref|YP_920417.1| 811 KRIENTHVLLYCVHCGNWHATMRvvE-AkaypSCPKCGSRALAVL 854
                                    35999***********6555444331.24567*******998876 PP

>> DUF4926  Domain of unknown function (DUF4926)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   4.8e-05      0.11      16      43 ..     216     244 ..     197     246 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.8e-05
                        DUF4926  16 LrrGqvGTvVevyeegeaYe..VEFsdddG 43 
                                    L+ G vGTvVe +e + aYe  VE +d++G
  gi|119719922|ref|YP_920417.1| 216 LSGGRVGTVVEWFERK-AYElvVEDIDEEG 244
                                    888**********999.9985566666666 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       7.1   1.6e+04      14      24 ..     586     596 ..     585     598 .. 0.76
   2 ?   11.8   0.2   8.9e-05       0.2       8      36 ..     822     850 ..     820     853 .. 0.73

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 7.1
                    Zn-ribbon_8  14 efevlqsisda 24 
                                     fe+l++i ++
  gi|119719922|ref|YP_920417.1| 586 AFEKLVRIIEE 596
                                    69***999854 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 8.9e-05
                    Zn-ribbon_8   8 CeeCghefevlqsisdaplta.CPeCgsev 36 
                                    C  Cg+ +  ++ + +a+  + CP+Cgs++
  gi|119719922|ref|YP_920417.1| 822 CVHCGNWHATMR-VVEAKAYPsCPKCGSRA 850
                                    999**8888887.555555555*****943 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (946 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.80u 0.29s 00:00:01.09 Elapsed: 00:00:00.50
# Mc/sec: 5717.94
//
Query:       gi|119719923|ref|YP_920418.1|  [L=260]
Description: hypothetical protein Tpen_1015 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.036   14.3   0.6        0.2   11.9   0.1    2.2  2  TBP-binding  TATA box-binding protein binding
       0.11   12.6   0.0       0.16   12.1   0.0    1.2  1  FimA         Type-1 fimbrial protein, A
       0.55   10.0   2.0       0.76    9.5   2.0    1.2  1  Pox_Ag35     Pox virus Ag35 surface protein


Domain annotation for each model (and alignments):
>> TBP-binding  TATA box-binding protein binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   3.4e-05       0.2      19      46 ..      13      40 ..      10      51 .. 0.81
   2 ?    0.1   0.0      0.16   9.8e+02      35      53 ..     211     229 ..     196     238 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.4e-05
                    TBP-binding 19 GNIdesGqLedDdvLDeeskknLssLsk 46
                                   G I e+G+L  D++LD   ++ L+sL+ 
  gi|119719923|ref|YP_920418.1| 13 GLIREKGRLTVDEILDWGQREGLNSLTL 40
                                   6799*********************974 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.16
                    TBP-binding  35 eeskknLssLskLGLgsll 53 
                                    +e +k L++L+k GL ++ 
  gi|119719923|ref|YP_920418.1| 211 KEPRKFLAELAKRGLIEVT 229
                                    5788999999999986654 PP

>> FimA  Type-1 fimbrial protein, A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.7e-05      0.16      91     124 ..     165     198 ..     161     211 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.7e-05
                           FimA  91 aaqdvqtflvsetiGsdtygatlrylaqyiasGa 124
                                    + q+v++  vs+ +G ++y+ +lryl +y+  G 
  gi|119719923|ref|YP_920418.1| 165 GVQEVDCSEVSDLLGNEAYERALRYLCTYWSIGL 198
                                    78999999*********************98885 PP

>> Pox_Ag35  Pox virus Ag35 surface protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   2.0   0.00013      0.76      48     128 ..      92     177 ..      69     192 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00013
                       Pox_Ag35  48 spkqekkkrattprkkpakkekkkke.......eekeeaaeeeeledseedeenendedeseesvqaeeeksnestedda 120
                                    +p ++++++   p+k+p+  +  +++       ee+ee+ +ee +e  ee  e+ +  +e  +++ ae ++s    ++++
  gi|119719923|ref|YP_920418.1|  92 APPRPREEKGRKPKKQPPRVKPSRERslleffgEEREEPSREEPVERGEEGGEEPERREEPAPEPAAEPRASVG--VQEV 169
                                    34455555666666665443333332111112255555556666666666666667777777777777776655..599* PP

                       Pox_Ag35 121 deldeSdL 128
                                    d+++ SdL
  gi|119719923|ref|YP_920418.1| 170 DCSEVSDL 177
                                    *******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1769.75
//
Query:       gi|119719924|ref|YP_920419.1|  [L=112]
Description: 30S ribosomal protein S25e [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.1e-14   52.6   1.8    5.5e-14   52.2   1.8    1.2  1  Ribosomal_S25  S25 ribosomal protein
    6.8e-05   22.0   0.1      8e-05   21.7   0.1    1.1  1  PORR           Plant organelle RNA recognition domain
     0.0033   16.7   0.0     0.0038   16.5   0.0    1.1  1  EAP30          EAP30/Vps36 family
  ------ inclusion threshold ------
      0.024   14.5   0.5       0.04   13.8   0.5    1.4  1  TrmB           Sugar-specific transcriptional regulator TrmB
       0.13   12.3   1.3       0.13   12.3   0.3    1.6  2  Cylicin_N      Cylicin N-terminus


Domain annotation for each model (and alignments):
>> Ribosomal_S25  S25 ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.2   1.8   1.5e-17   5.5e-14      14      99 ..      15     102 ..       4     104 .. 0.81

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 1.5e-17
                  Ribosomal_S25  14 kaggkakkKKwskgkv.kdklnna.vlfdketydkllkevpkyklitpsvvserlkingslArraLreleekgliklvsk 91 
                                    k   k++kKK + gk+ + kl+     + + +++ ++ke+   k++tp+v+++++ +++s A+++Lrele++g++  + k
  gi|119719924|ref|YP_920419.1|  15 KRVTKEEKKKEEGGKKpQMKLEAStGNLTEVSLEHVIKEIRGLKYVTPYVLASKFSLKLSRAKKVLRELESRGVVVAYDK 94 
                                    44456677777776661455553314588999************************************************ PP

                  Ribosomal_S25  92 hraqviYt 99 
                                    +++  iY+
  gi|119719924|ref|YP_920419.1|  95 NSRVPIYV 102
                                    *******7 PP

>> PORR  Plant organelle RNA recognition domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.1   2.2e-08     8e-05     164     235 ..       7      78 ..       3      89 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2.2e-08
                           PORR 164 elavsalekkkeseekeeekeeealaFplkfpkgfklkkkvrekleefqklpyvsPYedaseldpksdeaeK 235
                                    + +vs+lek+ ++eek++e++ ++++ +l+ ++g   + + +  ++e + l+yv PY  as+++ k   a+K
  gi|119719924|ref|YP_920419.1|   7 RPTVSQLEKRVTKEEKKKEEGGKKPQMKLEASTGNLTEVSLEHVIKEIRGLKYVTPYVLASKFSLKLSRAKK 78 
                                    5689******9899999999**************************************99999977666665 PP

>> EAP30  EAP30/Vps36 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.1e-06    0.0038     197     233 ..      36      90 ..       7      93 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.1e-06
                          EAP30 197 g.....................ggvtaselaeeeenlgwsvarakeaLeelereGllw 233
                                    +                     ++vt   la++   ++++ +rak++L+ele++G+++
  gi|119719924|ref|YP_920419.1|  36 EastgnltevslehvikeirglKYVTPYVLASK---FSLKLSRAKKVLRELESRGVVV 90 
                                    04444444444445555555559*******888...*******************997 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.5   1.1e-05      0.04      24      65 ..      61     104 ..      57     107 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.1e-05
                                    HHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST..TTEEEE- CS
                           TrmB  24 tadeiaeelgvprskvYevLrsLedkGlVerekgr..pklYrav 65 
                                    t + +a++  +  s++ +vLr+Le++G+V   +++    +Y++v
  gi|119719924|ref|YP_920419.1|  61 TPYVLASKFSLKLSRAKKVLRELESRGVVVAYDKNsrVPIYVPV 104
                                    6677899999999****************998877545588887 PP

>> Cylicin_N  Cylicin N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.3   3.8e-05      0.13      37      73 ..       3      38 ..       1      52 [. 0.80
   2 ?   -3.0   0.0       2.2   7.7e+03       9      19 ..     100     110 ..      93     111 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.8e-05
                      Cylicin_N 37 GkkkrskpselqetvprhdkrklkedqkpahiWirrs 73
                                   G kkr + s+l++ v++++k+k ++++kp  + ++ s
  gi|119719924|ref|YP_920419.1|  3 GGKKRPTVSQLEKRVTKEEKKKEEGGKKPQ-MKLEAS 38
                                   899*************88888877766665.566655 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.2
                      Cylicin_N   9 nyipvsesskk 19 
                                     y+pv +s kk
  gi|119719924|ref|YP_920419.1| 100 IYVPVAKSHKK 110
                                    46666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       879  (0.0490267); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 797.35
//
Query:       gi|119719925|ref|YP_920420.1|  [L=358]
Description: DNA repair and recombination protein RadA [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-96  323.0   0.0    1.4e-96  322.7   0.0    1.1  1  Rad51            Rad51
      1e-10   41.5   0.0    1.9e-10   40.7   0.0    1.3  1  RecA             recA bacterial DNA recombination protein
    2.3e-10   40.3   0.0    5.6e-10   39.0   0.0    1.7  1  ATPase           KaiC
    1.1e-06   28.3   0.0    2.2e-06   27.4   0.0    1.4  1  AAA_25           AAA domain
    5.8e-06   26.8   1.7    9.7e-05   22.9   0.1    3.0  3  HHH_5            Helix-hairpin-helix domain
    2.3e-05   24.1   0.0      0.041   13.7   0.0    2.8  2  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
    0.00097   18.4   1.8      0.038   13.1   0.3    2.2  2  PAXNEB           PAXNEB protein
     0.0059   16.9   0.1      0.029   14.7   0.0    2.0  2  AAA_22           AAA domain
  ------ inclusion threshold ------
      0.011   16.3   0.0       0.03   14.8   0.0    1.8  1  ABC_tran         ABC transporter
      0.021   15.0   0.0      0.045   14.0   0.0    1.5  1  Cdd1             Pathogenicity locus
      0.046   13.4   0.0      0.076   12.7   0.0    1.4  1  AAA_24           AAA domain
      0.049   13.5   0.0       0.15   12.0   0.0    1.9  1  HHH              Helix-hairpin-helix motif
       0.13   12.6   0.2       0.78   10.0   0.0    2.4  3  DUF4332          Domain of unknown function (DUF4332)


Domain annotation for each model (and alignments):
>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  322.7   0.0     1e-99   1.4e-96       2     255 .]     109     358 .]     108     358 .] 0.99

  Alignments for each domain:
  == domain 1  score: 322.7 bits;  conditional E-value: 1e-99
                                    S-EBHHHHHHHHHSS-EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEESSS CS
                          Rad51   2 gfvsavellekrsellqlttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavyidteg 81 
                                     f++a  l ekr+++  ++tG ++lD+lL+GGie+gsite +Gef++Gktq+ch+l+v+vqlp+++gG + +a+y+dteg
  gi|119719925|ref|YP_920420.1| 109 EFITAKTLFEKRKNIEYISTGVRSLDDLLEGGIEVGSITEFIGEFGAGKTQICHQLSVMVQLPKDKGGLNARALYVDTEG 188
                                    599***************************************************************************** PP

                                    ---GGGGHHHHHHTT--HHHHGGGEEEEE--STTHHHHHHHHTHHHHHHS-EEEEEEETTTGGGCH-------THHHHHH CS
                          Rad51  82 tfrperlveiaerykldkeevlenvayaRaytiehqeellqqaaallaedkfallivDsvtalyRtdfsgrgelakRqqk 161
                                    tfrper+v+ia   +ld+e++len+ yaRay+++hq+ l+++a + + + +++l+ivDs+++++R+++ gr++la+Rqqk
  gi|119719925|ref|YP_920420.1| 189 TFRPERIVQIARARGLDPEKTLENIIYARAYNSDHQMLLIDEAKKYIEKYNIRLIIVDSLINHFRAEYPGRENLASRQQK 268
                                    ******************************************************************************** PP

                                    HHHHHHHHHHHHHHH--EEEEEEE-------.------------HHHHHHHH-SEEEEEEE-STTEEEEEEES-SSS-S- CS
                          Rad51 162 lgkllrtLrkladefevavvitnqvvaqvdgqaalfsadpkkPigGlvlahasttRlalrkgkgeeRivkvvdsPnlpel 241
                                    l+k++++L++la  +++avv+tnqv+a++d     f ++p kP gG+++ah  t R+ lrk k+ +Ri++++dsP+ +e+
  gi|119719925|ref|YP_920420.1| 269 LNKHISQLHRLASLYNLAVVVTNQVMASPDI----FFGNPLKPAGGNIMAHGCTYRIWLRKAKEGKRIARIIDSPKHAEK 344
                                    ******************************9....99******************************************* PP

                                    EEEEEEETTEEE-- CS
                          Rad51 242 eavfaigeeGieda 255
                                    e+ fai+e+G++d+
  gi|119719925|ref|YP_920420.1| 345 EVAFAITEDGVTDV 358
                                    ***********995 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7   0.0   1.4e-13   1.9e-10      26     229 ..     118     333 ..     100     346 .. 0.79

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 1.4e-13
                                    -.-----EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHH..HHHHHHHHH.TT--...EEEEESS----H.... CS
                           RecA  26 keklkvetissGslaldialGiGGlpkGriieiyGpessGkttla..lhaiaeaqk.kggv...aafidaehaldp.... 95 
                                    ++++++e is+G  +ld  l  GG+  G i+e  G   +Gkt ++  l+++++  k kgg+   a ++d+e ++ p    
  gi|119719925|ref|YP_920420.1| 118 EKRKNIEYISTGVRSLDDLLE-GGIEVGSITEFIGEFGAGKTQIChqLSVMVQLPKdKGGLnarALYVDTEGTFRPeriv 196
                                    44689************9997.********************9963367777776625665222569*******983333 PP

                                    HHHHHTT--....GGG-EEE--SSHH.HHHHH..HHHHHTTT--SEEEEE-TTT---STT-----------HHHHHHHHH CS
                           RecA  96 kyakklGvd....idellvsqpdtGe.qalei..adalvrsgaidlivvdsvaalvpkaeieGemgdskvglqarlmsqa 168
                                    + a++ G+d    +++++ ++  + + q l i  a++ ++   i li+vds+     +ae  G   ++  + q +l  + 
  gi|119719925|ref|YP_920420.1| 197 QIARARGLDpektLENIIYARAYNSDhQMLLIdeAKKYIEKYNIRLIIVDSLINH-FRAEYPGR--ENLASRQQKL-NKH 272
                                    478999999444456777777655541555552256799************9765.58999885..5555566655.678 PP

                                    HHHHHHHHTTT--EEEEEEE-----------------HHHHHHH-SEEEEEEEES------ CS
                           RecA 169 lrkltgaisksntvvifinqirekiGvmfgnpetttGGralkfyasvrldvrrieeikeke 229
                                    + +l    s  n +v+  nq+     + fgnp   +GG+ +   ++ r+ +r+++e k+  
  gi|119719925|ref|YP_920420.1| 273 ISQLHRLASLYNLAVVVTNQVMASPDIFFGNPLKPAGGNIMAHGCTYRIWLRKAKEGKRIA 333
                                    89999999999*****************************************999877655 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   0.0     4e-13   5.6e-10       1     224 [.     126     355 ..     126     356 .. 0.77

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 4e-13
                         ATPase   1 vktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlik.gaek....ygepgvfvtveepa..edlrenakslGwd 73 
                                    ++tg+  lD++l+gGi  g+++   Ge G+GKt ++ q  +  ++ k     + + ++v +e +   e + + a++ G d
  gi|119719925|ref|YP_920420.1| 126 ISTGVRSLDDLLEGGIEVGSITEFIGEFGAGKTQICHQLSVMvQLPKdkggLNARALYVDTEGTFrpERIVQIARARGLD 205
                                    58************************************8664133221111456789*****97555************* PP

                         ATPase  74 lekleeegklaiidasesaeesaeekdkedleelieelaeaikeikakrvviDsitgl...aye......ekeavaReil 144
                                     ek  e+  +++  a++s++           + li+e +++i++++++ +++Ds+ ++   +y       ++++++ + +
  gi|119719925|ref|YP_920420.1| 206 PEKTLEN--IIYARAYNSDH----------QMLLIDEAKKYIEKYNIRLIIVDSLINHfraEYPgrenlaSRQQKLNKHI 273
                                    *******..66666666654..........488*********************87764322221111114455666678 PP

                         ATPase 145 rqlvrvlkklgvTailvsekss........seeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehp 216
                                     ql r  + +++  + ++++            + agg+  ++  ++  i L++ ++ +++ R+++       kh  ke+ 
  gi|119719925|ref|YP_920420.1| 274 SQLHRLASLYNLAVVVTNQVMAspdiffgnPLKPAGGNIMAH-GCTYRIWLRKAKEGKRIARIIDS-----PKHAEKEVA 347
                                    888777777888888888877788899876567788888888.99999999999999999999885.....558999999 PP

                         ATPase 217 feIteegi 224
                                    f Ite+g+
  gi|119719925|ref|YP_920420.1| 348 FAITEDGV 355
                                    99999887 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   1.6e-09   2.2e-06      19     188 ..     130     292 ..     113     296 .. 0.76

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 1.6e-09
                         AAA_25  19 ppprrwlvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgeal. 97 
                                     +++++l++g +  g+++ ++G  g+GKt ++ +l++ v + k   g     +++ lyv++E++    ++R+ ++ +a+ 
  gi|119719925|ref|YP_920420.1| 130 VRSLDDLLEGGIEVGSITEFIGEFGAGKTQICHQLSVMVQLPKDKGG----LNARALYVDTEGTF--RPERIVQIARARg 203
                                    5778999**999****************************6664434....689**********9..6888888887774 PP

                         AAA_25  98 .rddarllvldlagveslpLfakdrggtlltadvdaleaaieevegvrlvviDplsralgg....densnsd...vgalv 169
                                     ++ ++l  + +a+      + +d+++ l    +d+  + ie+ +++rl+++D+l   +++     en +s     ++ +
  gi|119719925|ref|YP_920420.1| 204 lDPEKTLENIIYARA-----YNSDHQMLL----IDEAKKYIEK-YNIRLIIVDSLINHFRAeypgRENLASRqqkLNKHI 273
                                    444444433333332.....444444444....5556999***.78********9887666566566655554445999* PP

                         AAA_25 170 ealeriarrtgaavllvhH 188
                                    ++l r+a  ++ av+++ +
  gi|119719925|ref|YP_920420.1| 274 SQLHRLASLYNLAVVVTNQ 292
                                    **************99876 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.1     7e-08   9.7e-05       3      55 ..      49     100 ..      47     102 .. 0.85
   2 ?    2.0   0.0      0.24   3.4e+02      19      33 ..     126     140 ..     123     155 .. 0.79
   3 ?   -3.0   0.0       8.4   1.2e+04      45      52 ..     207     214 ..     195     216 .. 0.69

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 7e-08
                                    HHHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS.-HHHHHHHHHHH CS
                          HHH_5   3 eLlsvsGiGpktAlallsaGiesvedlaaadveeLakipGi.GkktAeriilel 55 
                                     L +++G+G+ tA +l  aG+ +v dla a+++eLa +  + ++++A  ii ++
  gi|119719925|ref|YP_920420.1|  49 RLEDLEGVGRITAQKLRAAGFYTVRDLAFASAHELALV--LgSEERAMAIIRSA 100
                                    5889********************************99..52556777777666 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.24
                                    HTTT--SHHHHHHS- CS
                          HHH_5  19 lsaGiesvedlaaad 33 
                                    +s+G++s++dl++  
  gi|119719925|ref|YP_920420.1| 126 ISTGVRSLDDLLEGG 140
                                    799********9874 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 8.4
                                    HHHHHHHH CS
                          HHH_5  45 kktAerii 52 
                                    +kt e+ii
  gi|119719925|ref|YP_920420.1| 207 EKTLENII 214
                                    57888887 PP

>> DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0     3e-05     0.041       8      28 ..      55      75 ..      51      84 .. 0.93
   2 !    7.1   0.0    0.0035       4.9      17      32 ..     125     140 ..     123     147 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3e-05
                DNA_pol_lambd_f  8 GVGpktAkkwyakGirtledl 28
                                   GVG+ tA+k+ a+G+ t+ dl
  gi|119719925|ref|YP_920420.1| 55 GVGRITAQKLRAAGFYTVRDL 75
                                   9*******************9 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0035
                DNA_pol_lambd_f  17 wyakGirtledlrakr 32 
                                    +++ G+r+l+dl++++
  gi|119719925|ref|YP_920420.1| 125 YISTGVRSLDDLLEGG 140
                                    6889********9954 PP

>> PAXNEB  PAXNEB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.3   2.7e-05     0.038      19      39 ..     126     146 ..     121     156 .. 0.93
   2 ?    4.6   0.1     0.011        15     138     255 ..     157     290 ..     151     296 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.7e-05
                         PAXNEB  19 tStGtpsLDklLgGGLplGsi 39 
                                    +StG++sLD+lL GG+ +Gsi
  gi|119719925|ref|YP_920420.1| 126 ISTGVRSLDDLLEGGIEVGSI 146
                                    8*******************8 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.011
                         PAXNEB 138 sekfghqFdltkrlesesls.eisftplddskkseee...........ekeslkespryssllnqiqq.llkkesfsapt 204
                                    +++++hq  ++ +l +++   ++++  +d++ + + e           + e++ e+  y++ +n+ +q ll +e ++  +
  gi|119719925|ref|YP_920420.1| 157 KTQICHQLSVMVQLPKDKGGlNARALYVDTEGTFRPErivqiararglDPEKTLENIIYARAYNSDHQmLLIDEAKKYIE 236
                                    67899999999999999998899999999666644446677777777755555566668877776555145566666666 PP

                         PAXNEB 205 kknvlRivipsLlspllyd...yppeeskpedllkFLhsLrallrssnlvalit 255
                                    k n+  i++ sL +    +    ++ +s++++l k + +L  l++  nl +++t
  gi|119719925|ref|YP_920420.1| 237 KYNIRLIIVDSLINHFRAEypgRENLASRQQKLNKHISQLHRLASLYNLAVVVT 290
                                    688988999****99998855555678899999999999999999777777666 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       1.1   1.5e+03      93     137 .]      93     137 ..      56     137 .. 0.77
   2 !   14.7   0.0   2.1e-05     0.029       6     100 ..     145     248 ..     141     293 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.1
                         AAA_22  93 elliiDEaqhlr.seealeeLrsllnlsrkgvqliLvGtpelrkll 137
                                    ++ ii  aq+l  + e + + ++l++ +rk++  i  G ++l++ll
  gi|119719925|ref|YP_920420.1|  93 AMAIIRSAQRLVnRGEEFITAKTLFE-KRKNIEYISTGVRSLDDLL 137
                                    55666678887656777777788888.8889988888888888876 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 2.1e-05
                         AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaee.erpevvfvtlpsstsskdllrellralglelka..........erls 74 
                                    +i+  +Ge G+GKT  + +l    +  ++     +++ ++v+  +   ++ +  +++ra gl+ ++          ++ +
  gi|119719925|ref|YP_920420.1| 145 SITEFIGEFGAGKTQICHQLSVMVQLPKDK-GgLNARALYVDTEGTFRPERI-VQIARARGLDPEKtleniiyaraYNSD 222
                                    677789****************98544444.36**************88888.689999999999978888888886666 PP

                         AAA_22  75 seell.ealeqalraravielliiDEa 100
                                     + ll +   ++++++   +l+i+D  
  gi|119719925|ref|YP_920420.1| 223 HQMLLiDEAKKYIEKYNI-RLIIVDSL 248
                                    666666888888888888.88888864 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   2.2e-05      0.03       7      80 ..     140     230 ..     135     284 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.2e-05
                                    EEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHHHH...... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx...... RF
                       ABC_tran   7 klkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvren...... 79 
                                     ++ g+++ ++Ge GaGK+ ++  l+ +++  +++  l+ + l   +e ++  ++i  +     l+pe+t+ en      
  gi|119719925|ref|YP_920420.1| 140 GIEVGSITEFIGEFGAGKTQICHQLSVMVQLPKDKGGLNARALYVdTEGTFRPERIVQIARARGLDPEKTL-ENiiyara 218
                                    68899*********************99999666666676665554678888899999999999***9965.55488887 PP

                                    ...........H CS
                                    ...........x RF
                       ABC_tran  80 ...........e 80 
                                               e
  gi|119719925|ref|YP_920420.1| 219 ynsdhqmllidE 230
                                    744444444331 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   3.3e-05     0.045       7      42 ..      49      84 ..      45      93 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.3e-05
                           Cdd1  7 elqdiPniGkalaedlvelGirsveelkgedpeely 42
                                   +l+d+ ++G+ +a++l++ G+++v++l+  +++el 
  gi|119719925|ref|YP_920420.1| 49 RLEDLEGVGRITAQKLRAAGFYTVRDLAFASAHELA 84
                                   699**************************9999985 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   5.5e-05     0.076       8      79 ..     150     236 ..     148     289 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.5e-05
                         AAA_24   8 yGpsgiGKTtlakel.............gpkplfidtekGlksldadkfpdie.....swedfldevvelaaeladyktl 69 
                                    +G+ g+GKT ++ +l               ++l++dte+ +    + ++++i        e+ l+ + + +a ++d + l
  gi|119719925|ref|YP_920420.1| 150 IGEFGAGKTQICHQLsvmvqlpkdkgglNARALYVDTEGTF---RPERIVQIArarglDPEKTLENIIYARAYNSDHQML 226
                                    79*************99999999999999999******955...666666666677998889999999999999999999 PP

                         AAA_24  70 viDtidelee 79 
                                     iD + +  e
  gi|119719925|ref|YP_920420.1| 227 LIDEAKKYIE 236
                                    9998887655 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00011      0.15      13      28 ..      50      65 ..      47      67 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                                   HHTSTT-SHHHHHHHH CS
                            HHH 13 LlalPGVGpktAeaIl 28
                                   L++l+GVG+ tA++ +
  gi|119719925|ref|YP_920420.1| 50 LEDLEGVGRITAQKLR 65
                                   899**********976 PP

>> DUF4332  Domain of unknown function (DUF4332)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00056      0.78      58      96 ..      53      91 ..      48     113 .. 0.81
   2 ?   -2.1   0.0       3.1   4.2e+03      10      26 ..     124     140 ..     114     161 .. 0.75
   3 ?   -2.0   0.0         3   4.1e+03      32      56 ..     259     283 ..     246     292 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00056
                        DUF4332 58 ikgigeeyaeLLeaaGvdsvaeLaqrnpanLhqklkrln 96
                                    +g+g+  a+ L aaG  +v++La  ++++L   l+  +
  gi|119719925|ref|YP_920420.1| 53 LEGVGRITAQKLRAAGFYTVRDLAFASAHELALVLGSEE 91
                                   678999999999999999999999999999987666555 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.1
                        DUF4332  10 kLkkaGikttedLlelg 26 
                                    +  + G+++ +dLle g
  gi|119719925|ref|YP_920420.1| 124 EYISTGVRSLDDLLEGG 140
                                    55678999999999865 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 3
                        DUF4332  32 rkalaeklgisernvlklanlAdLa 56 
                                    r +la++ +   + + +l  lA L 
  gi|119719925|ref|YP_920420.1| 259 RENLASRQQKLNKHISQLHRLASLY 283
                                    5555555555555555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       744  (0.041497); expected 358.6 (0.02)
Passed bias filter:                      572  (0.0319036); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 2438.75
//
Query:       gi|119719926|ref|YP_920421.1|  [L=222]
Description: hypothetical protein Tpen_1018 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.096   12.7   0.0       0.33   11.0   0.0    1.8  2  HTH_45    Winged helix-turn-helix


Domain annotation for each model (and alignments):
>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   1.8e-05      0.33      31      75 ..      82     128 ..      72     130 .. 0.85
   2 ?   -1.7   0.0      0.17     3e+03      32      44 ..     157     169 ..     151     173 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 1.8e-05
                         HTH_45  31 LsykllnkYLdm..LvekglikkskekYvlTekGlelleklkeleel 75 
                                    + +++l+ YL     +++gl+ k+++ ++lT +Gle l  + ++ e+
  gi|119719926|ref|YP_920421.1|  82 MGFDQLDPYLIVygYISRGLLAKRSSAFQLTREGLEALTIVSDVAET 128
                                    668888888876335899********************998888765 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.17
                         HTH_45  32 sykllnkYLdmLv 44 
                                    sy  +++YL++L 
  gi|119719926|ref|YP_920421.1| 157 SYPGAEEYLKYLG 169
                                    6778899999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1564.30
//
Query:       gi|119719927|ref|YP_920422.1|  [L=344]
Description: hypothetical protein Tpen_1019 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.5e-06   25.9   0.0      0.039   13.5   0.0    2.6  2  HTH_24         Winged helix-turn-helix DNA-binding
    4.6e-05   23.2   0.0     0.0058   16.5   0.0    2.7  2  MarR_2         MarR family
     0.0066   16.4   0.0      0.015   15.2   0.0    1.6  1  MarR           MarR family
  ------ inclusion threshold ------
      0.021   14.6   0.2       0.11   12.4   0.0    2.3  2  HTH_IclR       IclR helix-turn-helix domain
      0.043   14.2   0.0       0.14   12.5   0.0    1.8  1  Rrf2           Transcriptional regulator
      0.053   13.3   0.8         10    6.1   0.4    2.6  2  HTH_AsnC-type  AsnC-type helix-turn-helix domain
      0.058   13.4   0.1       0.15   12.1   0.1    1.6  1  HTH_29         Winged helix-turn helix
       0.06   13.3   0.1        0.2   11.7   0.0    1.9  2  HTH_Crp_2      Crp-like helix-turn-helix domain
       0.13   12.0   0.2       0.36   10.7   0.2    1.6  1  HTH_23         Homeodomain-like domain


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0     2e-05     0.039      21      46 ..      22      47 ..      20      47 .. 0.94
   2 !    9.8   0.0   0.00029      0.58       2      37 ..     173     208 ..     172     209 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2e-05
                         HTH_24 21 reLAerlglSpstvnrrlkrLeeeGl 46
                                    ++A+ +g Sps   r l rLee+G+
  gi|119719927|ref|YP_920422.1| 22 VDIARSTGTSPSYAARVLARLEEKGF 47
                                   69**********************96 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00029
                         HTH_24   2 detdrkILelLqknprisqreLAerlglSpstvnrr 37 
                                    de d+ +  ++ +np +  + L+ + glS + ++++
  gi|119719927|ref|YP_920422.1| 173 DEVDLMLVAEITRNPFLKLSKLSAERGLSGQVLSYH 208
                                    899****************************99998 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   2.9e-06    0.0058      26      50 ..      23      47 ..      17      47 .. 0.95
   2 ?    3.6   0.0     0.031        61       9      40 ..     178     207 ..     175     211 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.9e-06
                                   HHHHHHTSSHHHHHHHHHHHHHTTS CS
                         MarR_2 26 elarrlglsksavsrilkrLvaaGL 50
                                   ++ar +g s+s++ r+l+rL+++G+
  gi|119719927|ref|YP_920422.1| 23 DIARSTGTSPSYAARVLARLEEKGF 47
                                   9**********************96 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.031
                                    HHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHH CS
                         MarR_2   9 rvLaaLgrrpgrdltvgelarrlglsksavsr 40 
                                    ++ a++ r+p   l  + l ++ gls + +s+
  gi|119719927|ref|YP_920422.1| 178 MLVAEITRNPF--LKLSKLSAERGLSGQVLSY 207
                                    68899*****9..9**************9997 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   7.6e-06     0.015      22      46 ..      23      47 ..      17      50 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 7.6e-06
                                   HHHHHHTS-HHHHHHHHHHHHHTTS CS
                           MarR 22 eLakklgvskstvtrvldrLekkGl 46
                                   ++a+  g+s+s++ rvl rLe+kG+
  gi|119719927|ref|YP_920422.1| 23 DIARSTGTSPSYAARVLARLEEKGF 47
                                   89**********************9 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   5.3e-05      0.11      23      47 ..      23      47 ..      18      48 .. 0.95
   2 ?   -2.7   0.1       2.7   5.4e+03       7      16 ..     282     291 ..     282     291 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.3e-05
                                   HHHHHHTS-HHHHHHHHHHHHHTTS CS
                       HTH_IclR 23 elArrtglpkStvhRlLqtLvelGy 47
                                   ++Ar tg ++S + R L+ L+e G+
  gi|119719927|ref|YP_920422.1| 23 DIARSTGTSPSYAARVLARLEEKGF 47
                                   8*********************997 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.7
                                    HHHCT-CTTB CS
                       HTH_IclR   7 aiLdalaeap 16 
                                    a+Ld+l+++p
  gi|119719927|ref|YP_920422.1| 282 ALLDLLRRHP 291
                                    6899999986 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   7.2e-05      0.14      30      54 ..      23      47 ..      13      50 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.2e-05
                                   HHHHHHTS-HHHHHHHHHHHHHTTS CS
                           Rrf2 30 eiaerqnispsylekilakLrkagl 54
                                   +ia+++++spsy++++la+L+++g+
  gi|119719927|ref|YP_920422.1| 23 DIARSTGTSPSYAARVLARLEEKGF 47
                                   8*********************996 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.4    0.0051        10      19      42 .]      20      43 ..      11      43 .. 0.90
   2 ?    4.8   0.0     0.012        25       2      31 ..     173     202 ..     173     204 .. 0.95

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0051
                  HTH_AsnC-type 19 syaeLAervGlSestvlrRvrrLe 42
                                    y ++A+ +G S+s ++r ++rLe
  gi|119719927|ref|YP_920422.1| 20 RYVDIARSTGTSPSYAARVLARLE 43
                                   689***********9999999997 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.012
                  HTH_AsnC-type   2 DeiDrkILeaLqedaRisyaeLAervGlSe 31 
                                    De+D+ +++++ +++ +  ++L+++ GlS 
  gi|119719927|ref|YP_920422.1| 173 DEVDLMLVAEITRNPFLKLSKLSAERGLSG 202
                                    9**************************996 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   7.4e-05      0.15      15      40 ..      21      46 ..      11      57 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.4e-05
                         HTH_29 15 vsqiAkllglsrrtvyrwlkrfeegG 40
                                     +iA+ +g s+++  r+l r ee+G
  gi|119719927|ref|YP_920422.1| 21 YVDIARSTGTSPSYAARVLARLEEKG 46
                                   678**********************9 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   9.9e-05       0.2      26      61 ..      23      59 ..      17      62 .. 0.82
   2 ?   -2.6   0.0       2.8   5.7e+03       1      13 [.     245     257 ..     245     266 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.9e-05
                                   HHHHHTTSSHHHHHHHHHHHHHTTSEEETEE.EEES- CS
                      HTH_Crp_2 26 elAsmlGltretvsrilseLkreglisrgrr.irild 61
                                   ++A+  G++++   r+l++L+++g   rg+   r+l+
  gi|119719927|ref|YP_920422.1| 23 DIARSTGTSPSYAARVLARLEEKGFRVRGGFdYRVLS 59
                                   8***********************8776532366665 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.8
                                    HHHHHHHHHHHCT CS
                      HTH_Crp_2   1 qRlArfLlrlaer 13 
                                    +R+A  L +l+++
  gi|119719927|ref|YP_920422.1| 245 ERVAWALSNLYYT 257
                                    5777777777443 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.2   0.00018      0.36       9      46 ..      10      47 ..       5      48 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00018
                         HTH_23  9 rillllaeGlsvreIAreLgvsrrTvyrwlkryreeGl 46
                                   ++l+++ +  ++ +IAr  g s++   r+l r +e+G+
  gi|119719927|ref|YP_920422.1| 10 EVLKAAVVARRYVDIARSTGTSPSYAARVLARLEEKGF 47
                                   677777778899*********************99996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.66u 0.34s 00:00:01.00 Elapsed: 00:00:00.58
# Mc/sec: 1787.54
//
Query:       gi|119719928|ref|YP_920423.1|  [L=146]
Description: hypothetical protein Tpen_1020 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 980.39
//
Query:       gi|119719929|ref|YP_920424.1|  [L=111]
Description: hypothetical protein Tpen_1021 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.3e-07   29.2   5.8    7.3e-07   29.2   5.8    2.1  2  DUF4234   Domain of unknown function (DUF4234)
  ------ inclusion threshold ------
      0.011   15.6   4.4      0.012   15.4   4.4    1.0  1  Bax1-I    Inhibitor of apoptosis-promoting Bax1
       0.23   11.0   3.6       0.38   10.3   3.6    1.5  1  DUF4328   Domain of unknown function (DUF4328)


Domain annotation for each model (and alignments):
>> DUF4234  Domain of unknown function (DUF4234)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   5.8   1.2e-10   7.3e-07       1      66 [.      15      71 ..      15      75 .. 0.89
   2 !   10.9   3.3   6.2e-05      0.37      18      52 ..      62      96 ..      54     107 .. 0.78

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 1.2e-10
                        DUF4234  1 rslavvilLsivTlGIYslyWlykltrelnrlsgrkkttslllvflllslitcgiysivwayklgk 66
                                   rsl++v  L + T+G+Y + Wl+ + reln+l  r    + +       li+++i +i+w+yk+ +
  gi|119719929|ref|YP_920424.1| 15 RSLLKVYALIFLTFGVYFYLWLVWTKRELNALGAR---IPTC------WLIIIPIANIYWLYKYAE 71
                                   899********************************...2223......35999**********875 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 6.2e-05
                        DUF4234 18 slyWlykltrelnrlsgrkkttslllvflllslit 52
                                   ++yWlyk ++ + ++++++++  + lvf+l+++++
  gi|119719929|ref|YP_920424.1| 62 NIYWLYKYAEGFAQVTKKESAVLYFLVFWLFTIVM 96
                                   69****************66666666666676654 PP

>> Bax1-I  Inhibitor of apoptosis-promoting Bax1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   4.4     2e-06     0.012       3      81 ..      16      97 ..      14     105 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2e-06
                         Bax1-I  3 flrkvYgllalgllltalvaavvlsspaqlflslhivlflvvilaplalv.flsls...aarlkkkssala.lallllftll 79
                                    l kvY+l++l++++ + +++v+ + +  l+     +   ++i++p+a + +l+ +   +a+ +kk sa+  +++++lft++
  gi|119719929|ref|YP_920424.1| 16 SLLKVYALIFLTFGVYFYLWLVWTKRE--LNALGARIPTCWLIIIPIANIyWLYKYaegFAQVTKKESAVLyFLVFWLFTIV 95
                                   588**********99999999996665..44444455555667778888877776633344555667777778899999999 PP

                         Bax1-I 80 eG 81
                                   + 
  gi|119719929|ref|YP_920424.1| 96 MP 97
                                   85 PP

>> DUF4328  Domain of unknown function (DUF4328)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   3.6   6.4e-05      0.38      23      87 ..      20      78 ..      14     108 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 6.4e-05
                        DUF4328 23 lalllllaaavvflvWlrraranaealapgrhrrspgwavggwlvPvvnLvlPlqvvadlwrasa 87
                                   ++ l++l+ +v f  Wl+ + ++++al   + r ++ w++   ++P++n+++ + +++   + ++
  gi|119719929|ref|YP_920424.1| 20 VYALIFLTFGVYFYLWLVWTKRELNAL---GARIPTCWLI---IIPIANIYWLYKYAEGFAQVTK 78
                                   56789*************999999988...6778888876...89*******9999988765554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       664  (0.037035); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 746.93
//
Query:       gi|119719930|ref|YP_920425.1|  [L=156]
Description: hypothetical protein Tpen_1022 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0019   18.2   0.0     0.0021   18.0   0.0    1.1  1  PDDEXK_1  PD-(D/E)XK nuclease superfamily


Domain annotation for each model (and alignments):
>> PDDEXK_1  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   1.2e-07    0.0021      98     184 ..      50     128 ..       6     146 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.2e-07
                       PDDEXK_1  98 eklverlaeeleakrgfrpvale..lefggekvrLkGriDrvd.dkegelriiDyKtgsappkskelaelkeglQlllYl 174
                                    ++l+  l   le ++ ++p+ l   ++fg+    L+G  D+v   k + + +++ K+++   + k+    +e++Q +lY 
  gi|119719930|ref|YP_920425.1|  50 SRLWGDLDWVLELEEAWTPLPLAwrFRFGW----LVGVADLVRfVKARPVAVYEVKSYD---TVKR----AERVQAALYG 118
                                    444445666667777788888887789996....*********866667********99...6666....6689****** PP

                       PDDEXK_1 175 lalaegeelk 184
                                    l+++ +   k
  gi|119719930|ref|YP_920425.1| 119 LLVELNFATK 128
                                    **99884444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1131.31
//
Query:       gi|119719931|ref|YP_920426.1|  [L=315]
Description: Rad51-like [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-67  228.0   0.0    1.3e-67  227.7   0.0    1.1  1  Rad51          Rad51
    1.4e-08   34.4   0.6    1.6e-07   30.9   0.6    2.2  1  ATPase         KaiC
    1.1e-07   32.4   0.6    2.5e-07   31.2   0.2    1.9  2  HHH_5          Helix-hairpin-helix domain
    3.4e-07   30.0   0.0    5.3e-07   29.4   0.0    1.4  1  AAA_25         AAA domain
    3.9e-06   26.5   0.0    5.4e-06   26.1   0.0    1.2  1  RecA           recA bacterial DNA recombination protein
     0.0082   15.9   0.0      0.024   14.4   0.0    1.7  1  RNA_pol_A_CTD  Bacterial RNA polymerase, alpha chain C termin
     0.0085   15.5   0.1        3.2    7.0   0.0    2.2  2  DnaB_C         DnaB-like helicase C terminal domain
  ------ inclusion threshold ------
      0.073   13.3   0.0       0.13   12.6   0.0    1.4  1  AAA_22         AAA domain
      0.088   13.3   0.0       0.16   12.5   0.0    1.5  1  HhH-GPD        HhH-GPD superfamily base excision DNA repair p
      0.098   12.4   0.0       0.19   11.5   0.0    1.4  1  AAA_24         AAA domain
       0.12   12.6   0.0       0.27   11.5   0.0    1.5  1  DUF4332        Domain of unknown function (DUF4332)


Domain annotation for each model (and alignments):
>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  227.7   0.0   8.1e-71   1.3e-67       9     254 ..      75     314 ..      57     315 .] 0.93

  Alignments for each domain:
  == domain 1  score: 227.7 bits;  conditional E-value: 8.1e-71
                                    HHHHHHSS-EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEESSS---GGGG CS
                          Rad51   9 llekrsellqlttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavyidtegtfrperl 88 
                                    ++++ s+  +lttG k+lDelL+GG+ t+ i e  Ge++sGktqlch+l+vt+qlp + gG  gk+vy+dtegtf p+r+
  gi|119719931|ref|YP_920426.1|  75 YASQLSQRESLTTGVKALDELLEGGLVTQEIYEFAGEYGSGKTQLCHQLSVTAQLPPSRGGLGGKVVYVDTEGTFSPSRI 154
                                    4455555667********************************************************************** PP

                                    HHHHHHTT--HHHHGGGEEEEE--STTHHHHHHHHTHHHHHHS-EEEEEEETTTGGGCH-------THHHHHHHHHHHHH CS
                          Rad51  89 veiaerykldkeevlenvayaRaytiehqeellqqaaallaedkfallivDsvtalyRtdfsgrgelakRqqklgkllrt 168
                                     +iaer+++++  +le v +aR  ++++ eel+ +  + l +  ++l+++Dsv+alyR++f+gr+ la Rqq+++  l  
  gi|119719931|ref|YP_920426.1| 155 ERIAERFGVEG--ALEGVYVARPISVDELEELVIKGLKPLLKGGVKLVVIDSVIALYRAQFRGREWLAMRQQRINYALDW 232
                                    ********986..79***************************************************************** PP

                                    HHHHHHHH--EEEEEEE-------.------------HHHHHHHH-SEEEEEEE-STTEEEEEEES-SSS-S.-EEEEEE CS
                          Rad51 169 LrkladefevavvitnqvvaqvdgqaalfsadpkkPigGlvlahasttRlalrkgkgeeRivkvvdsPnlpe.leavfai 247
                                    L++la  +++ vvitnqvv+ +      +    k P gG+++ahast R+ + k+ g++ ++ v+dsP lp+ + a+f i
  gi|119719931|ref|YP_920426.1| 233 LKRLARVYSIVVVITNQVVSVPSN----WGVAVKLPAGGNIIAHASTHRFLM-KKAGDSWLIEVLDSPRLPKgATAQFEI 307
                                    ********************9988....566799***************865.66788999**********945789*** PP

                                    ETTEEE- CS
                          Rad51 248 geeGied 254
                                     ++G+ d
  gi|119719931|ref|YP_920426.1| 308 RDDGLGD 314
                                    ****987 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.6   9.7e-11   1.6e-07       2      73 ..      86     164 ..      85     274 .. 0.82

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 9.7e-11
                         ATPase   2 ktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgae.....kygepgvfvtveepa..edlrenakslGwd 73 
                                     tg++ lDe+l+gG+  ++++  +Ge+G+GKt ++ q  ++          g ++v+v +e +   + + + a+++G++
  gi|119719931|ref|YP_920426.1|  86 TTGVKALDELLEGGLVTQEIYEFAGEYGSGKTQLCHQLSVTAQLppsrgGLGGKVVYVDTEGTFspSRIERIAERFGVE 164
                                    69***********************************988754311111467888888888765447777777788775 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.2   1.6e-10   2.5e-07       8      56 ..      12      60 ..       5      61 .. 0.91
   2 ?   -2.9   0.0         7   1.1e+04      21      32 ..      87      98 ..      85     110 .. 0.60

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 1.6e-10
                                   TT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHHH CS
                          HHH_5  8 sGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriilelk 56
                                   +GiG++t+ +l saGie+vedl+  ++eeL ++ Gi  ++A r++  ++
  gi|119719931|ref|YP_920426.1| 12 EGIGRVTISRLKSAGIETVEDLVLYNPEELEELAGIDFERALRLVRTAR 60
                                   8*****************************************9998776 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 7
                                   TT--SHHHHHHS CS
                          HHH_5 21 aGiesvedlaaa 32
                                   +G++ +++l++ 
  gi|119719931|ref|YP_920426.1| 87 TGVKALDELLEG 98
                                   677788888774 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   3.3e-10   5.3e-07      20     175 ..      90     233 ..      67     250 .. 0.74

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 3.3e-10
                         AAA_25  20 pprrwlvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgealrd 99 
                                    + ++ l++g l+ +e+  +aG  g+GKt l+ +l+++  +  p  g      gkV+yv++E++    + R++++ e +  
  gi|119719931|ref|YP_920426.1|  90 KALDELLEGGLVTQEIYEFAGEYGSGKTQLCHQLSVTAQL-PPSRG---GLGGKVVYVDTEGTF--SPSRIERIAERFGV 163
                                    567788898889999999****************998774.34434...369************..9***********99 PP

                         AAA_25 100 darllvldlagveslpLfakdrggtlltadvdaleaaieevegvrlvviDplsralggdensnsd..v..galvealeri 175
                                     + l  +++a+        +++ ++l + +++ l   ++   gv+lvviD++ ++++++    +   +  +++  al+++
  gi|119719931|ref|YP_920426.1| 164 EGALEGVYVAR--------PISVDELEELVIKGLKPLLKG--GVKLVVIDSVIALYRAQFRGREWlaMrqQRINYALDWL 233
                                    99999999866........345666656667777766666..8*********9999986554443332333333333333 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   3.3e-09   5.4e-06      29     189 ..      80     250 ..      68     285 .. 0.71

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 3.3e-09
                                    ----EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHH......HTT--EEEEESS----HH....HH CS
                           RecA  29 lkvetissGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaq......kkggvaafidaehaldpk....ya 98 
                                     + e++++G  ald  l  GGl    i e  G   sGkt l+ ++ + aq        gg ++++d+e ++ p+     a
  gi|119719931|ref|YP_920426.1|  80 SQRESLTTGVKALDELLE-GGLVTQEIYEFAGEYGSGKTQLCHQLSVTAQlppsrgGLGGKVVYVDTEGTFSPSrierIA 158
                                    456899********9998.*********************9866555555223222357899**********96333368 PP

                                    HHTT--..GGG-EEE--SSHHHHHHHHHH.H..HTTT--SEEEEE-TTT---STT-----------HHHHHHHHHHHHHH CS
                           RecA  99 kklGvd..idellvsqpdtGeqaleiada.l..vrsgaidlivvdsvaalvpkaeieGemgdskvglqarlmsqalrklt 173
                                    +++Gv+  ++ ++v++p + ++  e++ + l  +  g++ l+v+dsv al  +a+  G   +     q r +  al  l+
  gi|119719931|ref|YP_920426.1| 159 ERFGVEgaLEGVYVARPISVDELEELVIKgLkpLLKGGVKLVVIDSVIALY-RAQFRGR--EWLAMRQQR-INYALDWLK 234
                                    899**76689*******877665554432121134689***********96.6666663..222333333.455666666 PP

                                    HHHTTT--EEEEEEE- CS
                           RecA 174 gaisksntvvifinqi 189
                                       +   +vv+  nq+
  gi|119719931|ref|YP_920426.1| 235 RLARVYSIVVVITNQV 250
                                    5555555555555665 PP

>> RNA_pol_A_CTD  Bacterial RNA polymerase, alpha chain C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   1.5e-05     0.024      28      50 ..      22      44 ..      20      48 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.5e-05
                                   HHHTT--BHHHHHHS-HHHHTTS CS
                  RNA_pol_A_CTD 28 LkragiktvgeLvklseeeLlki 50
                                   Lk+agi+tv++Lv ++ eeL+++
  gi|119719931|ref|YP_920426.1| 22 LKSAGIETVEDLVLYNPEELEEL 44
                                   9*******************986 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0    0.0019       3.2       2      42 ..      85     126 ..      84     146 .. 0.86
   2 !    6.5   0.1    0.0028       4.6     127     178 ..     194     250 ..     145     255 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0019
                                    BXSSTHHHHHHCT.SBXTTXEEEEEEXTTSSHHHHHHHHHHH CS
                                    xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         DnaB_C   2 lstgfkdLDklts.GlqkgdliiiAarpsmGktalalniaen 42 
                                    l+tg k LD+l++ Gl  ++++  A+  + Gkt l+ ++  +
  gi|119719931|ref|YP_920426.1|  85 LTTGVKALDELLEgGLVTQEIYEFAGEYGSGKTQLCHQLSVT 126
                                    689******9885279*******************9887654 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0028
                                    HTTEEEEEEEEG.GGTBTS.CS...SSCCCHHHHHHHHHHHHHHHHCTSXEEEEEEX CS
                                    xxxxxxxxxxxx.xxxxxx.xx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         DnaB_C 127 ekglgliviDyL.qlmegs.ee...kenreqevseisrsLkalakelnvpvialsqL 178
                                    ++g++l+viD +  l +++ +       r+q +      Lk la+  ++ v++  q+
  gi|119719931|ref|YP_920426.1| 194 KGGVKLVVIDSViALYRAQfRGrewLAMRQQRINYALDWLKRLARVYSIVVVITNQV 250
                                    4899******861455544332445669************************99886 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   7.8e-05      0.13       9     100 ..     107     205 ..     101     248 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.8e-05
                         AAA_22   9 vvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka.........erlsseell 79 
                                       Ge G+GKT l+ +l  +++  ++    + +vv+v+  +  s++ + +++++ +g+e+           + +++eel+
  gi|119719931|ref|YP_920426.1| 107 EFAGEYGSGKTQLCHQLSVTAQLPPSRGGLGGKVVYVDTEGTFSPSRI-ERIAERFGVEGALegvyvarpiSVDELEELV 185
                                    5679****************977666666**************99999.9999999988777889999777777777777 PP

                         AAA_22  80 ealeqalraravielliiDEa 100
                                     +  + l + +v +l++iD +
  gi|119719931|ref|YP_920426.1| 186 IKGLKPLLKGGV-KLVVIDSV 205
                                    444444444555.79999965 PP

>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   9.6e-05      0.16      20      67 ..      21     110 ..      17     191 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.6e-05
                                    HHHHHHSHCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH................................. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................. RF
                        HhH-GPD  20 rlferfgfptpedladadeekLrelirelGfyrrKakyikelArilv................................. 66 
                                    rl+++ g  t+edl  +++e+L+el   +G    +a ++  +Ar l+                                 
  gi|119719931|ref|YP_920426.1|  21 RLKSA-GIETVEDLVLYNPEELEEL---AGIDFERALRLVRTARRLAgwevravrgdeyasqlsqreslttgvkaldell 96 
                                    55555.5789***************...777777************9888877777777777766666666666665555 PP

                                    .............S CS
                                    .............x RF
                        HhH-GPD  67 .............g 67 
                                                 g
  gi|119719931|ref|YP_920426.1|  97 egglvtqeiyefaG 110
                                    55555555555550 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00011      0.19       8      79 ..     109     210 ..     107     226 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00011
                         AAA_24   8 yGpsgiGKTtlakel.............gpkplfidtekGlksldadkfpdie..............swedfldevvel. 59 
                                     G+ g+GKT l+ +l             g k++++dte+ +    + ++++i               + +  +de++el 
  gi|119719931|ref|YP_920426.1| 109 AGEYGSGKTQLCHQLsvtaqlppsrgglGGKVVYVDTEGTF---SPSRIERIAerfgvegalegvyvARPISVDELEELv 185
                                    5999***********************************55...677777777777777777777774444455555557 PP

                         AAA_24  60 .....aaeladyktlviDtidelee 79 
                                         +  + + k +viD++  l++
  gi|119719931|ref|YP_920426.1| 186 ikglkPLLKGGVKLVVIDSVIALYR 210
                                    7779888888999999999988876 PP

>> DUF4332  Domain of unknown function (DUF4332)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00016      0.27       1      35 [.      12      44 ..       9      69 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00016
                        DUF4332  1 pgigkeeaekLkkaGikttedLlelgktekgrkal 35
                                   +gig+   ++Lk+aGi+t+edL+  +++e ++  l
  gi|119719931|ref|YP_920426.1| 12 EGIGRVTISRLKSAGIETVEDLVLYNPEELEE--L 44
                                   57888888999999999999999999988887..3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 2255.40
//
Query:       gi|119719932|ref|YP_920427.1|  [L=189]
Description: hypothetical protein Tpen_1024 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1251.77
//
Query:       gi|119719933|ref|YP_920428.1|  [L=133]
Description: hypothetical protein Tpen_1025 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 928.20
//
Query:       gi|119719934|ref|YP_920429.1|  [L=254]
Description: dTMP kinase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-44  150.6   0.0    4.6e-44  150.3   0.0    1.1  1  Thymidylate_kin  Thymidylate kinase
    5.3e-09   36.5   0.0    6.8e-09   36.2   0.0    1.1  1  AAA_28           AAA domain
    1.6e-06   28.2   0.1    1.4e-05   25.1   0.1    2.0  1  dNK              Deoxynucleoside kinase
    8.5e-05   22.7   0.0    0.00077   19.6   0.0    2.2  2  AAA_33           AAA domain
    0.00016   22.3   0.0    0.00097   19.7   0.0    2.3  1  AAA_18           AAA domain
    0.00019   21.9   3.0       0.16   12.4   0.0    3.1  4  AAA_17           AAA domain
     0.0039   17.3   0.3       0.06   13.5   0.1    2.2  2  SKI              Shikimate kinase
     0.0076   15.9   0.0      0.013   15.1   0.0    1.3  1  SRP54            SRP54-type protein, GTPase domain
  ------ inclusion threshold ------
      0.011   15.5   0.0      0.032   14.0   0.0    1.7  2  ATP_bind_1       Conserved hypothetical ATP binding protein
      0.013   15.0   0.0      0.027   13.9   0.0    1.7  1  KTI12            Chromatin associated protein KTI12
      0.058   13.3   0.0       0.11   12.3   0.0    1.4  1  APS_kinase       Adenylylsulphate kinase
      0.062   13.0   0.0        0.1   12.3   0.0    1.2  1  AAA_30           AAA domain


Domain annotation for each model (and alignments):
>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.3   0.0   3.1e-47   4.6e-44       1     185 []      59     235 ..      59     235 .. 0.97

  Alignments for each domain:
  == domain 1  score: 150.3 bits;  conditional E-value: 3.1e-47
                                    EEESTTSSHHHHHHHHHHHHHHTTE.EEEESSSTTSHHHHHHHHHHHTCS---HHHHHHHHHHHHHHTTHHHHHHHHHTT CS
                Thymidylate_kin   1 iEGlDGaGKttqaellkerlkeegikvvltrepggteiGekirelllkeeeleeqteallfaadriehleekikpalkqg 80 
                                    +EG+DG+GKttqa++l+e+l++eg +vv+ rep        i+e l  + +l+ ++e++lfaadri   +e++ p+l  g
  gi|119719934|ref|YP_920429.1|  59 LEGIDGSGKTTQAAMLYEKLSAEGFQVVIVREPW----VPAIKEFLY-KHDLDVEAEVYLFAADRIILQREVVLPSLRAG 133
                                    6********************************9....678999999.99****************************** PP

                                    -EEEEES-HHHHHHHHHTTTTTTCHHHHHHGGGTTSE-SEEEEEESSHHHHHTSCCTTSSTTTSHHHHHHHHHHHHHHHH CS
                Thymidylate_kin  81 ktvivdRylfSslaYqgakegvdldlvlslnedvllkPdltflldvdpevalkRlakrdeldeeeeeqldflrkvreryl 160
                                    k+v++dR +f slaYq+  +g d d++l +n++v   Pd+++lld+++e+a+kRl+ r    ++ +e+  + +kvr++yl
  gi|119719934|ref|YP_920429.1| 134 KIVVSDRSVFASLAYQSS-RGADQDFILAVNKSVR-FPDVVVLLDLPVEEAMKRLSSRVA--QTRFEDPGYMEKVRAKYL 209
                                    *****************5.668***********98.***********************9..9***************** PP

                                    HHHH.TTSTEEEEETTS-HHHHHHHH CS
                Thymidylate_kin 161 elak.ederiliidasksieevheeI 185
                                    +la+ ++e+++++dask+ eev +eI
  gi|119719934|ref|YP_920429.1| 210 QLAEeYPEKFIVVDASKPPEEVNREI 235
                                    ***********************998 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   0.0   4.6e-12   6.8e-09       2     156 ..      57     223 ..      56     230 .. 0.80

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 4.6e-12
                         AAA_28   2 ivitGgestGKTtll....eaLaargypvv..pEaareileeklakgedalpwvedllafaervleeqleeeaaa.aank 74 
                                    +++ G  ++GKTt +    e+L+a+g++vv  +E+    ++e l k+  + ++  ++  fa+ ++  q+e      +a+k
  gi|119719934|ref|YP_920429.1|  57 VALEGIDGSGKTTQAamlyEKLSAEGFQVVivREPWVPAIKEFLYKHDLDVEA--EVYLFAADRIILQREVVLPSlRAGK 134
                                    6888999******9933335555668887777**********99998876665..7888888887777777655459*** PP

                         AAA_28  75 vlfcDrglldtlaYarayggeaeaeleaaarekrydl.vfllp.pap.ei.....dddgeRredleereaiderlrealr 146
                                    ++++Dr+++++laY   +g + +  + a  ++ r    v+ll+ p++  +     +  ++R ed+ + e++ ++ +++ +
  gi|119719934|ref|YP_920429.1| 135 IVVSDRSVFASLAYQSSRGAD-QDFILAVNKSVRFPDvVVLLDlPVEeAMkrlssRVAQTRFEDPGYMEKVRAKYLQLAE 213
                                    *********************.7878888889996444999887655433444657788889****************** PP

                         AAA_28 147 elgipviivp 156
                                    e++ ++i+v 
  gi|119719934|ref|YP_920429.1| 214 EYPEKFIVVD 223
                                    *******994 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.1   9.1e-09   1.4e-05       2     203 ..      58     243 ..      57     244 .. 0.75

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 9.1e-09
                                    EEEESTTSSHHHHHHHHHCCSTCEEEE-..HHHHCCSSSSHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHCHHSSS-EEE CS
                            dNK   2 vveGnIgaGKstlvklLskklgvkvfeE..pvdkwtnvqknlLekfYkdpsrwsfalqtyvllsrlkqqlealatkqvvv 79 
                                    ++eG  g+GK+t + +L +kl  + f+   + + w++  k++L k   d++   + +    +  + ++ l +l+++++vv
  gi|119719934|ref|YP_920429.1|  58 ALEGIDGSGKTTQAAMLYEKLSAEGFQVviVREPWVPAIKEFLYKHDLDVEAEVYLFAADRIILQREVVLPSLRAGKIVV 137
                                    68999***************998777773345679888888888887777775555555444444455555667888877 PP

                                    EES-HHHHHHTHHHHHHHTTSS-HHHHHHHHHHHHHHHHHCCH-SEEEEEE--HHHHHHHHHHCTTCCCTTS-HHHHHHH CS
                            dNK  80 leRsiysdryiFakalaekgtlseeelkiykelldnlleelakpdlliYLkasletclerikkRgreeekkieldYlekL 159
                                     +Rs      +Fa++++++    ++++        ++++ +  pd+++ L++++e+ ++r+  R  +     +  Y+ek+
  gi|119719934|ref|YP_920429.1| 138 SDRS------VFASLAYQSSRGADQDF------ILAVNKSVRFPDVVVLLDLPVEEAMKRLSSRVAQTR-FEDPGYMEKV 204
                                    7776......67777888877777665......44555666678********************99884.45779***** PP

                                    HHHHHHHHTSGGCS-EEEEETSS.-TTTHCCHHHHHHHHHHHHH CS
                            dNK 160 hekyeewlkklnevpvlvidveeldlvaeeekredvveevkelv 203
                                      ky +  +++ e   +v+d+++      ee ++++++e+ ++v
  gi|119719934|ref|YP_920429.1| 205 RAKYLQLAEEYPEK-FIVVDASK----PPEEVNREILREIVSIV 243
                                    *****999997654.56778888....77888888888887766 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   5.2e-07   0.00077       3     126 ..      58     195 ..      57     211 .. 0.73
   2 ?    0.6   0.0      0.38   5.7e+02      82     109 ..     202     229 ..     195     237 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 5.2e-07
                         AAA_33   3 llvGlpGsGKstlaerllkklg.....avllssdt...lrrrlfgtdqq.sktdytrvldrlyqilnelarkalsagrnv 73 
                                     l G  GsGK+t a  l++kl      +v+++++    +++ l++ d +   + y  ++dr++  ++e++   l+ag+ v
  gi|119719934|ref|YP_920429.1|  58 ALEGIDGSGKTTQAAMLYEKLSaegfqVVIVREPWvpaIKEFLYKHDLDvEAEVYLFAADRII-LQREVVLPSLRAGKIV 136
                                    689***************999999998888888864534444554433312334444566666.4457888899999999 PP

                         AAA_33  74 ildat....nlsrrer....arflklarrlgvpvrivvvetdeetlkeRlakRaangddrs 126
                                    + d      ++ ++ r    + +l++ +   +p+ +v ++ + e++ +Rl  R a+  +r+
  gi|119719934|ref|YP_920429.1| 137 VSDRSvfasLAYQSSRgadqDFILAVNKSVRFPDVVVLLDLPVEEAMKRLSSRVAQ--TRF 195
                                    9999965553334444444377788888999**********************997..344 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.38
                         AAA_33  82 rrerarflklarrlgvpvrivvvetdee 109
                                    ++ ra++l+la+++  ++ +v+ + ++e
  gi|119719934|ref|YP_920429.1| 202 EKVRAKYLQLAEEYPEKFIVVDASKPPE 229
                                    67799*******6655555555555555 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   6.5e-07   0.00097       1     117 [.      57     193 ..      57     210 .. 0.59

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 6.5e-07
                         AAA_18   1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpe.aldeskrldedkldklldaleenss....aleegk 75 
                                    ++l G+ G+GKtt a  L ++l  + +  +v+  +++  +  +e  ++  + ++ ++   + d +  +++    +l+ gk
  gi|119719934|ref|YP_920429.1|  57 VALEGIDGSGKTTQAAMLYEKL--SAEGFQVVIVREPWVPAIKEfLYKHDLDVEAEVYLFAADRIILQREvvlpSLRAGK 134
                                    6899**************9999..66666666666666666666522222222222222222222222234554222222 PP

                         AAA_18  76 nlvidghlaeleseaakdikk..................vvLtaspeelleRlekRgyee 117
                                     +v++++ +    +++  ++                   v L+++ ee ++Rl+ R  ++
  gi|119719934|ref|YP_920429.1| 135 -IVVSDRSVFASLAYQSSRGAdqdfilavnksvrfpdvvVLLDLPVEEAMKRLSSRVAQT 193
                                    .24444444444444444444555555555555555555****************98665 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   0.00011      0.16       2      23 ..      61      85 ..      60      88 .. 0.85
   2 ?   -3.0   0.1       6.1   9.1e+03      98     118 ..     103     123 ..      96     126 .. 0.79
   3 !    8.6   0.0    0.0016       2.3     100     129 ..     167     196 ..     143     205 .. 0.75
   4 ?   -0.7   0.0       1.2   1.7e+03      99     120 ..     214     236 ..     193     248 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00011
                                   E-TTSSHHHHHHHHHHHH...TEEE CS
                         AAA_17  2 GgPGsGKgtqceklveky...gfth 23
                                   G+ GsGK+tq++ l ek+   gf++
  gi|119719934|ref|YP_920429.1| 61 GIDGSGKTTQAAMLYEKLsaeGFQV 85
                                   899**************96666766 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 6.1
                                    HHH..SEEEEEE--HHHHHHH CS
                         AAA_17  98 eelkpdaiilleadpeeiler 118
                                    ++l+++a ++l a +  il+r
  gi|119719934|ref|YP_920429.1| 103 HDLDVEAEVYLFAADRIILQR 123
                                    678888889999988888887 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0016
                                    H..SEEEEEE--HHHHHHHHHHHTTST-TS CS
                         AAA_17 100 lkpdaiilleadpeeilerrlkdrtrgrdd 129
                                     +pd+++ll+ + ee ++r+ ++  + r +
  gi|119719934|ref|YP_920429.1| 167 RFPDVVVLLDLPVEEAMKRLSSRVAQTRFE 196
                                    379*****************9996555543 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 1.2
                                    HH..SEEEEEE--..HHHHHHHHH CS
                         AAA_17  99 elkpdaiillead..peeilerrl 120
                                    e  p+++i+++a+  pee+ ++ l
  gi|119719934|ref|YP_920429.1| 214 E-YPEKFIVVDASkpPEEVNREIL 236
                                    3.3788888887632445444444 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.17   2.5e+02       2      18 ..      64      80 ..      63      85 .. 0.87
   2 !   13.5   0.1     4e-05      0.06      87     157 ..     171     239 ..     162     240 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.17
                                   TSSHHHHHHHHHHHHTS CS
                            SKI  2 GaGKstvGkllAkklgl 18
                                   G+GK+t + +l +kl+ 
  gi|119719934|ref|YP_920429.1| 64 GSGKTTQAAMLYEKLSA 80
                                   9*********9999875 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 4e-05
                                    EEEEEE--HHHHHHHHHHTTSSGGGCSCHHHHHHHHHHHHHHHHHCCSSCEEEECTSSHHHHHHHHHHHHH CS
                            SKI  87 iviyLdvsleellerlkadkeRPllqekskeeelleelaereplyeeaadvvvdeseeskeevaeeileal 157
                                    +v++Ld+++ee ++rl+++     ++++  +e+++ ++ +  + y e + +vvd+s+ + eev +eil+++
  gi|119719934|ref|YP_920429.1| 171 VVVLLDLPVEEAMKRLSSRVAQTRFEDPGYMEKVRAKYLQLAEEYPE-KFIVVDASKPP-EEVNREILREI 239
                                    79***************999977788888877777777744444444.45777777777.99999999876 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0     9e-06     0.013       4      35 ..      57      88 ..      55      90 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 9e-06
                                   EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEE CS
                          SRP54  4 illvGlqGaGKTttlaKLaallkkegkkvllv 35
                                   ++l G+ G+GKTt +a L ++l++eg +v++v
  gi|119719934|ref|YP_920429.1| 57 VALEGIDGSGKTTQAAMLYEKLSAEGFQVVIV 88
                                   6789*************************997 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   2.2e-05     0.032       3      49 ..      61     109 ..      59     117 .. 0.90
   2 ?   -1.3   0.0         1   1.5e+03     188     214 ..     192     218 ..     146     244 .. 0.50

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.2e-05
                     ATP_bind_1   3 GpaGsGKttfvgalseilelrgrsvavvN..LDPAaeelpYeaavdire 49 
                                    G  GsGKtt    l+e l+++g +v +v     PA +e+ Y+ ++d++ 
  gi|119719934|ref|YP_920429.1|  61 GIDGSGKTTQAAMLYEKLSAEGFQVVIVRepWVPAIKEFLYKHDLDVEA 109
                                    778*************************74468*************996 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1
                     ATP_bind_1 188 lllekee....ekykklaeaiaelleefalv 214
                                    ++    +    ++++k  ++  +l ee+ + 
  gi|119719934|ref|YP_920429.1| 192 QT----RfedpGYMEKVRAKYLQLAEEYPEK 218
                                    11....1222355555555555555555555 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.8e-05     0.027       5      48 ..      58     102 ..      56     215 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.8e-05
                                    EEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH..TTSSS- CS
                          KTI12   5 vltGlPssGKstrakeLakaleeekrsvvviddeslg.iekdsyk 48 
                                     l G+  sGK+t a+ L ++l++e+ +vv++++  +  i++  yk
  gi|119719934|ref|YP_920429.1|  58 ALEGIDGSGKTTQAAMLYEKLSAEGFQVVIVREPWVPaIKEFLYK 102
                                    5778889************************99888755555566 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   7.7e-05      0.11       3      35 ..      55      87 ..      53      91 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.7e-05
                                   EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEE CS
                     APS_kinase  3 vvvwltGlsgsGKstianalekkLvekgisvyl 35
                                   + v l G+ gsGK+t a +l +kL ++g +v++
  gi|119719934|ref|YP_920429.1| 55 LYVALEGIDGSGKTTQAAMLYEKLSAEGFQVVI 87
                                   668899**********************98865 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   6.9e-05       0.1      17      52 ..      53      88 ..      48      93 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.9e-05
                         AAA_30 17 gdrvavltGpAGtGKttalkalreaweaaggrvigl 52
                                   g ++++l+G  G+GKtt  + l e + a+g++v+++
  gi|119719934|ref|YP_920429.1| 53 GGLYVALEGIDGSGKTTQAAMLYEKLSAEGFQVVIV 88
                                   567899**************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       664  (0.037035); expected 358.6 (0.02)
Passed bias filter:                      644  (0.0359195); expected 358.6 (0.02)
Passed Vit filter:                       104  (0.00580066); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 1857.90
//
Query:       gi|119719935|ref|YP_920430.1|  [L=184]
Description: phospholipase D/transphosphatidylase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-23   83.2   0.6    1.8e-23   82.9   0.6    1.2  1  PLDc_2          PLD-like domain
    6.5e-06   26.1   0.4    1.6e-05   24.9   0.4    1.6  1  PLDc            Phospholipase D Active site motif
    8.3e-06   25.5   0.2    1.1e-05   25.1   0.2    1.2  1  PP_kinase_C_1   Polyphosphate kinase C-terminal domain 1
    7.6e-05   22.0   0.4     0.0001   21.6   0.4    1.1  1  Regulator_TrmB  Archaeal transcriptional regulator TrmB


Domain annotation for each model (and alignments):
>> PLDc_2  PLD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.9   0.6   4.1e-27   1.8e-23       1     131 [.      54     179 ..      54     181 .. 0.88

  Alignments for each domain:
  == domain 1  score: 82.9 bits;  conditional E-value: 4.1e-27
                         PLDc_2   1 liqliksAkksidiatyyfvsdrei....ldallkaakrgvkvrilldskkddagavdeaslkelkellleagvevrvfe 76 
                                    l++ i++A+ksi+ia++ f+sd ++    ++ l+ + k+gv+v+++l ++     +  +++  ++++l l +gv v++ +
  gi|119719935|ref|YP_920430.1|  54 LLDYISRANKSIYIAMFQFKSDTDViskiVELLISKNKKGVDVKVVLENT-----I--DENELTYRRL-LDNGVAVKF-D 124
                                    5789***************8888865665888899*************83.....3..3567789999.999***997.4 PP

                         PLDc_2  77 tllgslHaKlylidgktvivGSsNltkrgldlnlElnvviedkelakeleeeFer 131
                                    +++ + HaKl++idg++v+vGS+N+++ ++ +n+E+ v i+ + +a++ +++F +
  gi|119719935|ref|YP_920430.1| 125 SRSVTTHAKLVIIDGRYVFVGSHNWSYMAMMRNHEASVLIDCPSIAEQETQYFMN 179
                                    335688*********************************************9965 PP

>> PLDc  Phospholipase D Active site motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.4   3.5e-09   1.6e-05       5      25 ..     130     150 ..     128     152 .. 0.92

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 3.5e-09
                                    E---EEEETTTEEEEE---SS CS
                           PLDc   5 hHqKivivDdrvafvGgaNLc 25 
                                     H+K vi+D+r++fvG+ N+ 
  gi|119719935|ref|YP_920430.1| 130 THAKLVIIDGRYVFVGSHNWS 150
                                    5*****************995 PP

>> PP_kinase_C_1  Polyphosphate kinase C-terminal domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.2   2.4e-09   1.1e-05      38     113 ..      64     139 ..      49     181 .. 0.69

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 2.4e-09
                                    EEEEEES-S-S-....-HHHHHHHHHHHTT-EEEEEES--SSS--HHHHHHHHHHHHHT-EEEE--TT--B--EEEEEEE CS
                  PP_kinase_C_1  38 aikitlYrvakd....skivkaLieAaengkqvtvlvElkArfdeenNiewakkleeagvkvvygvvglkvhaklllvvr 113
                                    +i i++++ ++d    skiv+ Li+  +  k v v v l+  +de++   + ++l ++gv v +   ++ +hakl+++  
  gi|119719935|ref|YP_920430.1|  64 SIYIAMFQFKSDtdviSKIVELLISKNK--KGVDVKVVLENTIDENE--LTYRRLLDNGVAVKFDSRSVTTHAKLVIIDG 139
                                    4555555555551133666666666555..55555555668899855..45688999*******************9964 PP

>> Regulator_TrmB  Archaeal transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.4   2.3e-08    0.0001      16     128 ..      55     181 ..      43     183 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 2.3e-08
                                    HHHHHH-SSEEEEEE.....-GGGHHHHHHHHHHHHHTT-EEEEEESS...----GGGSSSSEEEEEE-S-..--S..EE CS
                 Regulator_TrmB  16 eelIesAenelivsl.....pselLeelreeliaaaergvtVllliyp...dedleeldleevatevrvrr..sga.pll 84 
                                     ++I+ A++ +++++     +   ++++ e li+++++gv V +++ +   +++l  ++l+++ ++v++ +    +   l
  gi|119719935|ref|YP_920430.1|  55 LDYISRANKSIYIAMfqfksDTDVISKIVELLISKNKKGVDVKVVLENtidENELTYRRLLDNGVAVKFDSrsVTThAKL 134
                                    6788888888888753333366899**********************999877777788888888888754114445788 PP

                                    EEETTTEEEEE-SSS-...EEEE--HHHHHHHHHHHHHH........ CS
                 Regulator_TrmB  85 vivDrkrgvvaprevl...rdkeeeyaiifkekelihvlshyFlttl 128
                                    vi D+++++v +++ +   + ++ e +++++ ++++ + ++yF++++
  gi|119719935|ref|YP_920430.1| 135 VIIDGRYVFVGSHNWSymaMMRNHEASVLIDCPSIAEQETQYFMNIY 181
                                    *************9889889999*********************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       765  (0.0426683); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1290.28
//
Query:       gi|119719936|ref|YP_920431.1|  [L=92]
Description: hypothetical protein Tpen_1028 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.057   13.8   0.1      0.072   13.5   0.1    1.1  1  DUF2663   Protein of unknown function (DUF2663)
      0.085   13.3   0.0       0.28   11.6   0.0    1.7  2  HMG_box   HMG (high mobility group) box
       0.13   12.3   0.2       0.15   12.1   0.2    1.1  1  DUF2614   Zinc-ribbon containing domain


Domain annotation for each model (and alignments):
>> DUF2663  Protein of unknown function (DUF2663)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   1.2e-05     0.072      13      90 ..       4      85 ..       2      87 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.2e-05
                        DUF2663 13 eklekrllllsllallvlllfliyvlik..ssslssllsallessvlllllllvallyvav...kllkkKaeKaEkefhaLr 89
                                   ++++  +ll  +++l +l ++l++++++  +  + + l al+  ++++l++  v l+++++     +++ + + E+e+ +Lr
  gi|119719936|ref|YP_920431.1|  4 DRVAGAVLLAVAASLGSLYAYLLFLAQQevQVLVMK-LTALFVVETFFLVVAWVGLTLLTSppeAKVREIERRLEEEYRKLR 84
                                   56666778889999***********77743223333.4444444444555555555555542223466677889*******9 PP

                        DUF2663 90 c 90
                                   +
  gi|119719936|ref|YP_920431.1| 85 E 85
                                   7 PP

>> HMG_box  HMG (high mobility group) box
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.39   2.3e+03       7      17 ..      23      33 ..      21      36 .. 0.79
   2 ?   11.6   0.0   4.7e-05      0.28      17      44 ..      58      85 ..      46      87 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.39
                                   HHHHHHHHHHH CS
                        HMG_box  7 afflfskeqra 17
                                   a++lf+ +q  
  gi|119719936|ref|YP_920431.1| 23 AYLLFLAQQEV 33
                                   8****998875 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 4.7e-05
                                   HHHHHHSTTS-HHHHHHHHHHHHHHSHH CS
                        HMG_box 17 aklkaenPelknaeiskklgekWkalse 44
                                    +l +  Pe+k++ei ++l+e++++l e
  gi|119719936|ref|YP_920431.1| 58 LTLLTSPPEAKVREIERRLEEEYRKLRE 85
                                   5677888******************987 PP

>> DUF2614  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   2.6e-05      0.15      12      61 ..       9      59 ..       2      71 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.6e-05
                        DUF2614 12 falllvfiglivmyigllfkeselllvlflllGlllvlast.vvyfwiGll 61
                                     ll v ++l  +y  llf +++ + vl++ l  l+v+ ++ +v  w+Gl+
  gi|119719936|ref|YP_920431.1|  9 AVLLAVAASLGSLYAYLLFLAQQEVQVLVMKLTALFVVETFfLVVAWVGLT 59
                                   567778889999****999999999999999998888876526789**985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1181  (0.0658709); expected 358.6 (0.02)
Passed bias filter:                      704  (0.039266); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 768.37
//
Query:       gi|119719937|ref|YP_920432.1|  [L=465]
Description: AIR synthase-like protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.9e-37  128.4   0.1    4.8e-37  127.1   0.0    1.7  2  ThiP_synth  Thiamine-phosphate synthase
      2e-11   44.3   0.5    1.2e-10   41.8   0.3    2.3  2  AIRS_C      AIR synthase related protein, C-terminal domain
      8e-11   42.5   0.0    2.3e-10   41.0   0.0    1.8  1  AIRS        AIR synthase related protein, N-terminal domain
  ------ inclusion threshold ------
      0.027   13.8   0.0      0.061   12.7   0.0    1.5  1  HEM4        Uroporphyrinogen-III synthase HemD


Domain annotation for each model (and alignments):
>> ThiP_synth  Thiamine-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0      0.81   3.6e+03      83     106 ..     237     261 ..     232     266 .. 0.72
   2 !  127.1   0.0   1.1e-40   4.8e-37       3     164 ..     305     458 ..     303     459 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.81
                                    EEEEEE--.HHHHHHHCCTTSEEEE CS
                     ThiP_synth  83 aainiryd.ekilealeelglkvve 106
                                    a i +  d e +l+a+ee+gl+++ 
  gi|119719937|ref|YP_920432.1| 237 AIIAVTGDaESLLSACEEKGLTCSN 261
                                    5555555547899999999999875 PP

  == domain 2  score: 127.1 bits;  conditional E-value: 1.1e-40
                                    HHHHHHHHCC--.GCC--TT-B-EEEE-ST--SGGGEEEETT-EEE-TSSEEE-S-EEETS-CHHHHHHHHHHCC-TT-- CS
                     ThiP_synth   3 eralelleeeeefakliPevgsNiayalpdAksieDvaavpGRIvrvkgrvkvvgepefgasshvarvllaamkfdpevr 82 
                                      a+e+l++++++ ++iPevg+Niaya    +s+ Dv+a++GRIv++ ++++ +g+p++gas+h+a+vl +a++++  + 
  gi|119719937|ref|YP_920432.1| 305 ALAAEELVRISRLLDVIPEVGANIAYAPGPVRSPRDVLALDGRIVKTTEGARLCGKPRYGASRHLAEVLASAREAGMPYS 384
                                    56899*************************************************************************** PP

                                    EEEEEE--HHHHHHHCCTTSEEEE--CCCS-CCCT-HHHHHHHHHHHCCS-ECEEEE--BCTB--EEEEEESSHHHHHHH CS
                     ThiP_synth  83 aainirydekilealeelglkvvefdreeepeevgstmewgvaeaieelevpdviydeGgvGkEpmiyvlgkdaeevvek 162
                                    aa+n++y+e++le+l++ gl v++  + e +          v+eai++    +v +  G+ G+E+ i++l++d+ e++e 
  gi|119719937|ref|YP_920432.1| 385 AAVNLKYSEDLLEKLKSIGLPVCDATPYEASCP--------VSEAIRSGCRAQVYFYAGKPGLEASIVLLARDPLEAIEI 456
                                    ****************************99999........899999995579*************************99 PP

                                    HH CS
                     ThiP_synth 163 vl 164
                                    ++
  gi|119719937|ref|YP_920432.1| 457 LR 458
                                    87 PP

>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.23     1e+03      74      96 ..      15      35 ..      14      81 .. 0.78
   2 !   41.8   0.3   2.6e-14   1.2e-10      50     149 ..     174     269 ..     143     276 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.23
                                   HHHHHHHHTTTEEEEEECGTHHH CS
                         AIRS_C 74 galaemapasgvgaeidldkvpi 96
                                    al e++ ++g g+e+d++  p+
  gi|119719937|ref|YP_920432.1| 15 AALRELLLGAGAGLELDAN--PL 35
                                   68999**********9998..33 PP

  == domain 2  score: 41.8 bits;  conditional E-value: 2.6e-14
                                    HHHHHHHH.HTTECEEEE--TTHHHHHHHHHHHTTTEEEEEECGTHHHHHHHHHHHHHHHCSTTTEEEEEEEHGGHHHHH CS
                         AIRS_C  50 vkralaal.kglvkaahDvTgGGLlgalaemapasgvgaeidldkvpifdelesplemllsensGrllvavppeeadavl 128
                                    +++al  + +  +k +hDv++GG++gal e+a+  gv +e+++ +v++f+ l  + e+l + + G   ++++  +a+ +l
  gi|119719937|ref|YP_920432.1| 174 AALAL--QeEPSIKLMHDVSEGGVIGALLEVAQRYGVALEVSSRDVKVFEGLPRGVEPLSAPSYG--AIIAVTGDAESLL 249
                                    33333..35699***************************************99999998766665..6777777777*** PP

                                    HHHHHTTCCCEEEEEEEEESS CS
                         AIRS_C 129 aileeeglpeaavIGevtake 149
                                    +++ee gl +++  G v + +
  gi|119719937|ref|YP_920432.1| 250 SACEEKGL-TCSNAGVVAGPG 269
                                    ********.7*****998765 PP

>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   0.0   5.1e-14   2.3e-10      19      93 ..      49     132 ..      24     133 .. 0.87

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 5.1e-14
                                    TCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEEC......HHHHHHHHHHHHHHHTT-EEEEEEEEEESS...EEEEEE CS
                           AIRS  19 epvhfiGakavavnlsDlaamGArPlalllslalp......wleevvrglaeaaeelgvplvgGdtsfsne...ptisvt 89 
                                     p + +G  a +  +s+la+  ArP  ++ls  +p       +e+v+r++ e ++++g+ lvgG+t+++ +   p++s t
  gi|119719937|ref|YP_920432.1|  49 VPEEWLGFFAYHYSASNLAVSFARPELAVLSAVFPegypgeAVERVLRSFVEECRKYGTRLVGGHTARYRGlelPLLSST 128
                                    344448999999**************99*****************************************9899******* PP

                                    EEEE CS
                           AIRS  90 avGl 93 
                                    +vG 
  gi|119719937|ref|YP_920432.1| 129 MVGR 132
                                    **96 PP

>> HEM4  Uroporphyrinogen-III synthase HemD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.4e-05     0.061     100     157 ..     362     420 ..     348     436 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.4e-05
                                    .SSSHHHHGGGS-..---EEEEEE-SS.S--HHHHHHHHHTTEEEEEE-SEEEEE-HHH CS
                           HEM4 100 eegtaegLaeelae.slagkrvlllrgeiarddlaegLeergaevdevevYetvpaeee 157
                                    + g +++Lae+la+ + ag ++ + +  + ++dl e+L++ g+ v ++++Ye +++++e
  gi|119719937|ref|YP_920432.1| 362 RYGASRHLAEVLASaREAGMPYSAAVNLKYSEDLLEKLKSIGLPVCDATPYEASCPVSE 420
                                    478899*******94455588999999999***********************777654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (465 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       264  (0.0147247); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 3396.38
//
Query:       gi|119719938|ref|YP_920433.1|  [L=240]
Description: threonyl/alanyl tRNA synthetase, SAD [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.1e-10   39.6   0.1    6.7e-10   38.9   0.1    1.4  1  tRNA_SAD      Threonyl and Alanyl tRNA synthetase second addi
    1.5e-07   30.4   0.0      2e-07   30.0   0.0    1.1  1  tRNA-synt_2c  tRNA synthetases class II (A)
  ------ inclusion threshold ------
       0.14   12.4   0.6        1.1    9.4   0.2    2.6  3  LAL_C2        L-amino acid ligase C-terminal domain 2


Domain annotation for each model (and alignments):
>> tRNA_SAD  Threonyl and Alanyl tRNA synthetase second additional domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   0.1   1.1e-13   6.7e-10       1      44 []     192     235 ..     192     235 .. 0.96

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 1.1e-13
                                    EEEEEETT.EEEEESS---SBGGGC-SEEEECCECCCTCEEEEE CS
                       tRNA_SAD   1 vrvvsiGdisvelCgGtHvpnTgeIgafkilseesiakglrRIy 44 
                                    +r+v+i  ++v++ gG+Hv+nT eIg +++ + es+++   RIy
  gi|119719938|ref|YP_920433.1| 192 LRIVEIPGVDVQADGGPHVKNTCEIGGIVLKKLESKGAKRKRIY 235
                                    69****558**********************************9 PP

>> tRNA-synt_2c  tRNA synthetases class II (A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.0   3.3e-11     2e-07     473     552 .]      13      93 ..       4      93 .. 0.91

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 3.3e-11
                                    SEEEEEEEEEETTEEEESEEXXXXS.SSSCSXXXE.EEEESSEEEEESEEEEETTEEEEEXSS.XSXXXTTSEEEEEEXH CS
                   tRNA-synt_2c 473 kefveeveegeevgvvLdrTpfYae.sGGqigDeG.liekegaefrvkdvqkakgvvlhkgkleegklkvgdkvkaevde 550
                                    kef + v++++ + v Ld+T+f +  sGG + D+G l+  +g +++v+++ +++g v h+      +lk gd+v++++d+
  gi|119719938|ref|YP_920433.1|  13 KEFDAVVTRVSGNKVFLDQTAFHPGpSGGLDTDKGwLVLPTGDRVEVVQALEEGGDVAHVLARA-VNLKPGDRVRGVIDW 91 
                                    6889999999*************9659********76777889******************996.9*************9 PP

                                    HH CS
                   tRNA-synt_2c 551 er 552
                                    er
  gi|119719938|ref|YP_920433.1|  92 ER 93 
                                    86 PP

>> LAL_C2  L-amino acid ligase C-terminal domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.2   0.00019       1.1       3      44 ..      49      90 ..      47      95 .. 0.84
   2 ?   -3.0   0.0       1.4   8.4e+03      23      39 ..     103     119 ..      99     121 .. 0.76
   3 ?   -0.5   0.0      0.24   1.5e+03      18      29 ..     170     181 ..     168     187 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00019
                         LAL_C2  3 ltaprpGrlkaveGleearalpgvveveltvkpGdevrpprs 44
                                   l+ p+  r++ v+ lee  ++++v+   ++ kpGd+vr + +
  gi|119719938|ref|YP_920433.1| 49 LVLPTGDRVEVVQALEEGGDVAHVLARAVNLKPGDRVRGVID 90
                                   56665558999999***********************98765 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.4
                         LAL_C2  23 lpgvveveltvkpGdev 39 
                                      +v+ + l++k G+ v
  gi|119719938|ref|YP_920433.1| 103 ASHVLAAVLYKKYGALV 119
                                    56788899999999877 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.24
                         LAL_C2  18 eearalpgvvev 29 
                                    +ea ++pg+v++
  gi|119719938|ref|YP_920433.1| 170 DEALKIPGIVKL 181
                                    89*******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1630.19
//
Query:       gi|119719939|ref|YP_920434.1|  [L=222]
Description: methyltransferase type 11 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.4e-10   38.9   0.0    9.7e-10   38.5   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    1.5e-09   38.3   0.0    2.5e-09   37.6   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
    6.6e-05   23.6   0.0    0.00013   22.6   0.0    1.5  1  Methyltransf_12  Methyltransferase domain
    0.00034   21.3   0.0    0.00064   20.4   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
  ------ inclusion threshold ------
       0.18   11.9   0.0       0.48   10.5   0.0    1.7  1  DUF2059          Uncharacterized protein conserved in bacteri


Domain annotation for each model (and alignments):
>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.5   0.0   2.7e-13   9.7e-10      24     164 ..      44     185 ..      23     186 .. 0.76

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 2.7e-13
                Methyltransf_23  24 grvLdiGcGtGillevl...rengf..svtgvDlspeaveiaekakkaqkdqfdeqeaaepqgkfdlIvlrevlehvpdp 98 
                                    g  +d+G+Gt ++++ l   re ++    +g+  +  a +     ++ ++ ++  +e a+   +fd++++  vle ++dp
  gi|119719939|ref|YP_920434.1|  44 GIGVDVGAGTCRFAPFLsrgREIVClePAYGMLVYGYARG-----RCEHPLCA-TSENAPLRPSFDFAYMVTVLEFLEDP 117
                                    5678999999999998843333333433444444444444.....45555555.444447788***************** PP

                Methyltransf_23  99 pellrqiatllkpgGylllseplaslkedrllldw..lylvpagrhisffsarslkelleeaGlevve 164
                                    +  l++i++ lk gG+l ++++ +++k+ +l+ +   + ++p     +f+s  ++ +ll +aG+ev e
  gi|119719939|ref|YP_920434.1| 118 ALSLTRIWEALKSGGLLAVLYVERDSKWGKLYSELaeKGADPVLARARFYSQPEVDKLLSAAGFEVRE 185
                                    *************************9999998775323333333577******************976 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6   0.0     7e-13   2.5e-09       1      96 []      47     136 ..      47     136 .. 0.94

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 7e-13
                                    EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHHHH CS
                Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedpeka 80 
                                    +dvG+Gt r+a  l  rg+++v+++++  ml +  ++++ e++    ++a+ e+ p++  sfD+ ++  vl+++edp+  
  gi|119719939|ref|YP_920434.1|  47 VDVGAGTCRFAPFLS-RGREIVCLEPAYGMLVYGYARGRCEHP----LCATSENAPLRP-SFDFAYMVTVLEFLEDPALS 120
                                    59*************.999************888888888876....9***********.******************** PP

                                    HHHHHHHEEEEEEEEE CS
                Methyltransf_11  81 lkeiaRvLkpgGllvi 96 
                                    l  i+  Lk gGll++
  gi|119719939|ref|YP_920434.1| 121 LTRIWEALKSGGLLAV 136
                                    *************975 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   3.7e-08   0.00013       1      99 []      47     134 ..      47     134 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 3.7e-08
                Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlk 80 
                                    +++G+Gt +++  l +     e++++++   +++   ++ + +++++++  +   +         sfD  ++  vl+ l+
  gi|119719939|ref|YP_920434.1|  47 VDVGAGTCRFAPFLSRG---REIVCLEPAYGMLVYGYARGRCEHPLCATSENAPLRP--------SFDFAYMVTVLEFLE 115
                                    599*****999988666...9************555555444444443333333333........9************** PP

                Methyltransf_12  81 direvldnirklLkpgGrl 99 
                                    d++ +l +i ++Lk gG l
  gi|119719939|ref|YP_920434.1| 116 DPALSLTRIWEALKSGGLL 134
                                    *****************86 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   1.8e-07   0.00064       2      97 .]      47     132 ..      47     132 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.8e-07
                                    EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHH CS
                Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsded 81 
                                    +d+G+Gt r++  l++     ++++++++ +ml +  +r + e    + +++  e+ p+   sfD+ +++ +l++l+d+ 
  gi|119719939|ref|YP_920434.1|  47 VDVGAGTCRFAPFLSRG---REIVCLEPAYGMLVYGYARGRCE----HPLCATSENAPLRP-SFDFAYMVTVLEFLEDPA 118
                                    59**********99976...8************8877777322....46999999999987.*******988****9887 PP

                                    HHHHHHHHHHHEEEEE CS
                Methyltransf_25  82 lekalkeiarvLkpgG 97 
                                    l   l +i+++Lk gG
  gi|119719939|ref|YP_920434.1| 119 LS--LTRIWEALKSGG 132
                                    65..***********9 PP

>> DUF2059  Uncharacterized protein conserved in bacteria (DUF2059)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00013      0.48      26      48 ..      20      42 ..      19      46 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00013
                                   HHHSHHHHHHHHHHHHHHHHHHH CS
                        DUF2059 26 FYkSPlGkkllekepaataesmq 48
                                   +Y SP+G+ +le e ++ +e+++
  gi|119719939|ref|YP_920434.1| 20 WYDSPAGRVVLEVEASMLDEVLP 42
                                   9****************999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1383.25
//
Query:       gi|119719940|ref|YP_920435.1|  [L=404]
Description: hypothetical protein Tpen_1032 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0014   18.6   0.1     0.0039   17.2   0.0    1.7  2  HypA            Hydrogenase/urease nickel incorporation, meta
  ------ inclusion threshold ------
       0.01   15.5   0.6        3.4    7.5   0.0    2.3  2  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal
      0.012   15.5   3.1       0.48   10.4   0.0    2.5  2  DUF1610         Domain of unknown function (DUF1610)
      0.017   14.9   0.5      0.029   14.2   0.5    1.3  1  Cys_rich_CPCC   Cysteine-rich CPCC
      0.024   14.6   0.8      0.043   13.8   0.8    1.4  1  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
      0.028   14.3   0.4      0.054   13.4   0.4    1.5  1  Zn_ribbon_SprT  SprT-like zinc ribbon domain
      0.035   13.6   1.2      0.065   12.8   1.2    1.4  1  TF_Zn_Ribbon    TFIIB zinc-binding
      0.048   13.8   3.2        2.5    8.3   0.1    2.3  2  zf-Mss51        Zinc-finger of mitochondrial splicing suppres
      0.067   12.9   4.0       0.31   10.8   4.0    1.9  1  zinc_ribbon_2   zinc-ribbon domain
      0.069   13.2   0.1       0.25   11.4   0.0    1.8  2  DUF1451         Zinc-ribbon containing domain
      0.091   12.8   0.1       0.16   12.0   0.1    1.3  1  DZR             Double zinc ribbon
       0.16   11.9   0.2       0.31   11.0   0.2    1.4  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
       0.37   10.3   8.2        7.2    6.2   1.2    2.2  2  zf-ribbon_3     zinc-ribbon domain
       0.52   10.5   3.6         16    5.8   0.0    3.3  3  zf-RING_7       C4-type zinc ribbon domain
        1.3    9.0   2.9         31    4.6   0.2    2.4  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
        3.7    7.7   6.4        5.9    7.1   0.1    2.5  2  zf-ACC          Acetyl-coA carboxylase zinc finger domain


Domain annotation for each model (and alignments):
>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   3.5e-06    0.0039      56     108 ..      63     117 ..      35     119 .. 0.73
   2 ?   -2.7   0.1       5.2   5.8e+03      24      45 ..     286     297 ..     268     310 .. 0.50

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.5e-06
                                    TTTT-EEEEE..EE--EEEETTTS-EEECHH.H.HHS-TTTSSS-EEEEESSSEEEE CS
                           HypA  56 vlegaeLeie..evpvkvrCreCgkefelee.k.alrCpkCgsadveivsGeellvk 108
                                    +l++  +++e  e +v++rC +Cg++++ +  +  + Cp Cg ++   v G+el+vk
  gi|119719940|ref|YP_920435.1|  63 ALSSQGFKVEdlELSVSFRCPSCGASINFSPeTvVYVCPYCGWSG--DVYGRELRVK 117
                                    444444455522667899********99554246789*****976..3579999987 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.2
                                    .EEEEEEEEEETTCT--HHHHH CS
                           HypA  24 rkvtkvkvevGelsgvepeaLe 45 
                                     + ++v            e+L+
  gi|119719940|ref|YP_920435.1| 286 GSLKEV----------AVESLS 297
                                    344444..........444444 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0031       3.4      42      52 ..      77      87 ..      62      89 .. 0.79
   2 ?    6.0   0.3    0.0088       9.9      40      51 ..      93     104 ..      90     106 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0031
                 zinc_ribbon_10 42 evkyrCpkCga 52
                                    v++rCp+Cga
  gi|119719940|ref|YP_920435.1| 77 SVSFRCPSCGA 87
                                   469******98 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0088
                 zinc_ribbon_10  40 leevkyrCpkCg 51 
                                    +e+v y+Cp+Cg
  gi|119719940|ref|YP_920435.1|  93 PETVVYVCPYCG 104
                                    6889*******8 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00043      0.48      10      23 ..      73      86 ..      65      87 .. 0.86
   2 ?    4.2   1.3     0.037        42      12      23 ..      94     104 ..      91     104 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00043
                        DUF1610 10 prEravvFpCPNCG 23
                                   + E +v+F CP CG
  gi|119719940|ref|YP_920435.1| 73 DLELSVSFRCPSCG 86
                                   56889********9 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.037
                        DUF1610  12 EravvFpCPNCG 23 
                                    E  vv+ CP CG
  gi|119719940|ref|YP_920435.1|  94 E-TVVYVCPYCG 104
                                    6.79*******9 PP

>> Cys_rich_CPCC  Cysteine-rich CPCC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.5   2.6e-05     0.029       2      32 ..      81     111 ..      80     122 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.6e-05
                  Cys_rich_CPCC   2 qCpcCgyltleeeegsydiCpvCfWedDlvq 32 
                                    +Cp Cg     + e+ + +Cp C W  D++ 
  gi|119719940|ref|YP_920435.1|  81 RCPSCGASINFSPETVVYVCPYCGWSGDVYG 111
                                    7*****998866666667********99865 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.8   3.8e-05     0.043       4      26 ..      81     104 ..      75     105 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.8e-05
                 PhnA_Zn_Ribbon   4 kCplCaSeytY.edgallvCpeCa 26 
                                     Cp C+++ +   ++ ++vCp C+
  gi|119719940|ref|YP_920435.1|  81 RCPSCGASINFsPETVVYVCPYCG 104
                                    7**********************7 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.4   4.9e-05     0.054       6      31 ..      81     104 ..      80     107 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.9e-05
                 Zn_ribbon_SprT   6 rCtgCgreythhlsirrhnYrCrrCk 31 
                                    rC++Cg     ++s  +  Y C++C+
  gi|119719940|ref|YP_920435.1|  81 RCPSCG--ASINFSPETVVYVCPYCG 104
                                    8*****..6****************7 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.2   5.8e-05     0.065       1      26 [.      80     104 ..      80     105 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.8e-05
                                    EEETTTTCEECHEETSTTCEEESSSS CS
                   TF_Zn_Ribbon   1 ykCPnCgstnlveDpergelvCtdCG 26 
                                    ++CP Cg + + + pe+  +vC+ CG
  gi|119719940|ref|YP_920435.1|  80 FRCPSCGAS-INFSPETVVYVCPYCG 104
                                    68*****75.9**************9 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1    0.0022       2.5      14      31 ..      77      94 ..      61      95 .. 0.85
   2 ?    7.4   3.9    0.0042       4.7       2      25 ..      82     106 ..      81     111 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0022
                       zf-Mss51 14 hvdfeCpdCGiptycsee 31
                                   +v+f Cp CG ++  s e
  gi|119719940|ref|YP_920435.1| 77 SVSFRCPSCGASINFSPE 94
                                   799*******99988765 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0042
                       zf-Mss51   2 CPvpkhkqt.apkhvdfeCpdCGip 25 
                                    CP + +  + +p+ v + Cp CG++
  gi|119719940|ref|YP_920435.1|  82 CPSCGASINfSPETVVYVCPYCGWS 106
                                    99998777789************96 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   4.0   0.00027      0.31       1      20 [.      81     104 ..      81     104 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00027
                  zinc_ribbon_2   1 fCpnCGael..qd.nakF.CpyCG 20 
                                    +Cp+CGa +  ++ ++++ CpyCG
  gi|119719940|ref|YP_920435.1|  81 RCPSCGASInfSPeTVVYvCPYCG 104
                                    6********553336666*****9 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00022      0.25     104     139 ..      69     104 ..      27     113 .. 0.84
   2 ?   -1.0   0.1       1.5   1.6e+03      37      76 ..     274     307 ..     239     309 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00022
                        DUF1451 104 yqsGevvglGtlvCekCgkelalkkteeippCpkCg 139
                                    ++  ++     ++C +Cg++++++  +++  Cp Cg
  gi|119719940|ref|YP_920435.1|  69 FKVEDLELSVSFRCPSCGASINFSPETVVYVCPYCG 104
                                    555566667789***********************8 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.5
                        DUF1451  37 elvaeylkrDleeaarsleeskeeleewlsldlelieesl 76 
                                    +++++  +r +e   ++++       e+ls+dl+++e+sl
  gi|119719940|ref|YP_920435.1| 274 AEIERSARRQVEGSLKEVA------VESLSVDLKVVEKSL 307
                                    4444444444443333333......356689999999887 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00015      0.16      15      35 ..      82     104 ..      70     111 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00015
                            DZR  15 CseCgtklkavaa..edrCpsCg 35 
                                    C+ Cg++++  ++   ++Cp Cg
  gi|119719940|ref|YP_920435.1|  82 CPSCGASINFSPEtvVYVCPYCG 104
                                    77777777655556677777776 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.2   0.00028      0.31      28      55 ..      79     106 ..      62     109 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00028
                 OrfB_Zn_ribbon  28 SktCseCgsknkealsgrtfkCpnCgfe 55 
                                    S +C+ Cg+  + ++++ +++Cp Cg +
  gi|119719940|ref|YP_920435.1|  79 SFRCPSCGASINFSPETVVYVCPYCGWS 106
                                    779*********99***********986 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   8.3    0.0082       9.2       4      23 ..      81     104 ..      79     104 .. 0.74
   2 ?    6.2   1.2    0.0064       7.2       4      10 ..      99     105 ..      96     108 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0082
                    zf-ribbon_3   4 rCPnCGa.p.lssd..dnvCpyCG 23 
                                    rCP+CGa +  s++  + vCpyCG
  gi|119719940|ref|YP_920435.1|  81 RCPSCGAsInFSPEtvVYVCPYCG 104
                                    8******776555522557****9 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0064
                    zf-ribbon_3   4 rCPnCGa 10 
                                     CP+CG+
  gi|119719940|ref|YP_920435.1|  99 VCPYCGW 105
                                    5777776 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.014        16      24      31 ..      80      87 ..      64      87 .. 0.88
   2 ?    3.0   0.4       0.1   1.2e+02      23      30 ..      97     104 ..      94     104 .. 0.83
   3 ?    0.2   0.0      0.81     9e+02       8      20 ..     267     279 ..     265     286 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.014
                                   EE-TTT-- CS
                      zf-RING_7 24 vtCpeCGR 31
                                   ++Cp+CG+
  gi|119719940|ref|YP_920435.1| 80 FRCPSCGA 87
                                   79****96 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.1
                                    -EE-TTT- CS
                      zf-RING_7  23 vvtCpeCG 30 
                                    v  Cp+CG
  gi|119719940|ref|YP_920435.1|  97 VYVCPYCG 104
                                    778****9 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.81
                                    B--CCHHHHHCCS CS
                      zf-RING_7   8 elppqvlselrag 20 
                                    e++++ ++e+ + 
  gi|119719940|ref|YP_920435.1| 267 EIDSEIYAEIERS 279
                                    79********654 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.2     0.028        31      19      26 ..      80      87 ..      59      97 .. 0.78
   2 ?    4.6   0.3     0.029        33      20      30 ..      99     110 ..      93     119 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.028
                  Zn_Tnp_IS1595 19 fvCPhCgs 26
                                   f+CP Cg 
  gi|119719940|ref|YP_920435.1| 80 FRCPSCGA 87
                                   89****95 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.029
                  Zn_Tnp_IS1595  20 vCPhCgsr.kay 30 
                                    vCP+Cg +  +y
  gi|119719940|ref|YP_920435.1|  99 VCPYCGWSgDVY 110
                                    8*****776655 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.1    0.0053       5.9       3      11 ..      81      89 ..      80      90 .. 0.86
   2 ?    1.5   2.7      0.28   3.1e+02      21      26 .]      98     103 ..      95     103 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0053
                         zf-ACC  3 KCpsCgeml 11
                                   +CpsCg+++
  gi|119719940|ref|YP_920435.1| 81 RCPSCGASI 89
                                   7*****987 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.28
                         zf-ACC  21 yVCPkC 26 
                                    yVCP C
  gi|119719940|ref|YP_920435.1|  98 YVCPYC 103
                                    9***** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       647  (0.0360868); expected 358.6 (0.02)
Passed bias filter:                      571  (0.0318478); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2759.97
//
Query:       gi|119719941|ref|YP_920436.1|  [L=292]
Description: hypothetical protein Tpen_1033 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00034   20.6   3.1      0.002   18.1   1.6    2.3  2  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
    0.00039   19.7   1.1       0.47    9.9   0.1    2.2  2  zf-ribbon_3     zinc-ribbon domain
    0.00094   18.8   2.6       0.87    9.4   0.2    2.4  2  zinc_ribbon_2   zinc-ribbon domain
     0.0011   18.6   0.5     0.0023   17.5   0.5    1.5  1  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
     0.0029   17.8   0.5       0.63   10.4   0.0    2.4  2  zf-Di19         Drought induced 19 protein (Di19), zinc-bindi
  ------ inclusion threshold ------
      0.018   15.0   0.6       0.03   14.3   0.6    1.3  1  DZR             Double zinc ribbon
      0.033   13.7   3.6       0.07   12.7   3.6    1.5  1  TF_Zn_Ribbon    TFIIB zinc-binding
      0.034   14.1   2.4        3.9    7.5   0.2    2.4  2  Cys_rich_CPXG   Cysteine-rich CPXCG
       0.06   13.3   0.7      0.095   12.6   0.7    1.3  1  Prok-RING_1     Prokaryotic RING finger family 1
      0.062   13.5   1.7        1.6    8.9   0.2    2.4  2  zf-RING_7       C4-type zinc ribbon domain
      0.071   13.2   3.4        1.1    9.3   0.1    2.4  2  zf-CHCC         Zinc-finger domain
       0.08   13.8   0.3        7.7    7.7   0.0    2.7  2  zf-C2H2_4       C2H2-type zinc finger
       0.11   13.0   0.3         11    6.5   0.0    2.5  2  zf-IS66         zinc-finger binding domain of transposase IS6
       0.11   12.5   0.4       0.19   11.7   0.4    1.3  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
        0.2   11.8   0.8        4.7    7.4   0.1    2.5  2  Zn-ribbon_8     Zinc ribbon domain
       0.39   10.9   4.6        1.7    8.8   0.2    2.8  3  UPF0547         Uncharacterised protein family UPF0547
       0.44   11.1   1.4          4    8.1   0.1    2.5  2  zf-C2H2         Zinc finger, C2H2 type
       0.83   10.0   5.3         21    5.5   5.6    2.3  2  zinc_ribbon_9   zinc-ribbon


Domain annotation for each model (and alignments):
>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   1.6     2e-06     0.002       2      21 ..       4      23 ..       4      23 .. 0.98
   2 ?    5.1   0.4     0.023        23       1       8 [.      21      28 ..      21      36 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2e-06
                 DNA_ligase_ZBD  2 CPvCGsavvReegeaiyRCt 21
                                   CP CG+ v+R++ge+++ C+
  gi|119719941|ref|YP_920436.1|  4 CPYCGANVERNPGEVVLTCP 23
                                   *****************997 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.023
                 DNA_ligase_ZBD  1 hCPvCGsa 8 
                                   +CP CG+a
  gi|119719941|ref|YP_920436.1| 21 TCPYCGTA 28
                                   7*****98 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.1   0.00047      0.47       5      11 ..       4      10 ..       1      14 [. 0.56
   2 !    8.5   0.1    0.0014       1.4      18      24 ..      21      27 ..      15      32 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00047
                    zf-ribbon_3  5 CPnCGap 11
                                   CP+CGa+
  gi|119719941|ref|YP_920436.1|  4 CPYCGAN 10
                                   5555554 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0014
                    zf-ribbon_3 18 vCpyCGt 24
                                   +CpyCGt
  gi|119719941|ref|YP_920436.1| 21 TCPYCGT 27
                                   5777776 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.2   0.00087      0.87      14      22 ..       2      10 ..       1      11 [. 0.83
   2 !    9.3   0.2   0.00093      0.92      15      22 ..      21      28 ..      12      29 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00087
                  zinc_ribbon_2 14 kFCpyCGtp 22
                                   + CpyCG++
  gi|119719941|ref|YP_920436.1|  2 TLCPYCGAN 10
                                   57*****97 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00093
                  zinc_ribbon_2 15 FCpyCGtp 22
                                    CpyCGt 
  gi|119719941|ref|YP_920436.1| 21 TCPYCGTA 28
                                   5*****95 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.5   2.4e-06    0.0023       6      30 ..       4      28 ..       2      29 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.4e-06
                  zf-NADH-PPase  6 CgrCGaptepaeggwarvCpaCgle 30
                                   C+ CGa +e+++g+  + Cp Cg+ 
  gi|119719941|ref|YP_920436.1|  4 CPYCGANVERNPGEVVLTCPYCGTA 28
                                   ***********************85 PP

>> zf-Di19  Drought induced 19 protein (Di19), zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1     0.024        24       4      13 ..       3      12 ..       1      14 [. 0.78
   2 !   10.4   0.0   0.00063      0.63       3      15 ..      20      32 ..      19      41 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.024
                        zf-Di19  4 tCPyCgkelt 13
                                    CPyCg +++
  gi|119719941|ref|YP_920436.1|  3 LCPYCGANVE 12
                                   5****98765 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00063
                        zf-Di19  3 ftCPyCgkeltvk 15
                                   +tCPyCg ++tv+
  gi|119719941|ref|YP_920436.1| 20 LTCPYCGTAFTVE 32
                                   59******99986 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.6     3e-05      0.03      14      38 ..       3      29 ..       1      33 [. 0.84

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3e-05
                            DZR 14 fCseCgtklkavaa..edrCpsCgekv 38
                                    C++Cg+++++ +     +Cp Cg++ 
  gi|119719941|ref|YP_920436.1|  3 LCPYCGANVERNPGevVLTCPYCGTAF 29
                                   6*******99888789999****9975 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   3.6     7e-05      0.07       3      27 ..       4      27 ..       2      31 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7e-05
                                   ETTTTCEECHEETSTTCEEESSSSB CS
                   TF_Zn_Ribbon  3 CPnCgstnlveDpergelvCtdCGl 27
                                   CP+Cg  n++++p +  l+C+ CG+
  gi|119719941|ref|YP_920436.1|  4 CPYCGA-NVERNPGEVVLTCPYCGT 27
                                   *****6.69**************96 PP

>> Cys_rich_CPXG  Cysteine-rich CPXCG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.2    0.0088       8.8       3      11 ..       4      12 ..       2      14 .. 0.87
   2 ?    7.5   0.2    0.0039       3.9       2      12 ..      21      31 ..      20      32 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0088
                  Cys_rich_CPXG  3 CPyCgeeie 11
                                   CPyCg+++e
  gi|119719941|ref|YP_920436.1|  4 CPYCGANVE 12
                                   *****9876 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0039
                  Cys_rich_CPXG  2 qCPyCgeeiev 12
                                   +CPyCg  ++v
  gi|119719941|ref|YP_920436.1| 21 TCPYCGTAFTV 31
                                   7*****99876 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.7   9.6e-05     0.095       6      29 ..       3      28 ..       1      31 [. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.6e-05
                    Prok-RING_1  6 kCpvCgkelkee..dDiVvCpeCgtp 29
                                    Cp Cg +++ +  + + +Cp Cgt 
  gi|119719941|ref|YP_920436.1|  3 LCPYCGANVERNpgEVVLTCPYCGTA 28
                                   6*******99876355668******7 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1      0.08        80      26      31 ..       4       9 ..       1       9 [. 0.84
   2 ?    8.9   0.2    0.0016       1.6      21      30 ..      17      26 ..      10      27 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.08
                                   -TTT-- CS
                      zf-RING_7 26 CpeCGR 31
                                   Cp+CG+
  gi|119719941|ref|YP_920436.1|  4 CPYCGA 9 
                                   ****96 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0016
                                   TB-EE-TTT- CS
                      zf-RING_7 21 devvtCpeCG 30
                                   ++v tCp+CG
  gi|119719941|ref|YP_920436.1| 17 EVVLTCPYCG 26
                                   568******9 PP

>> zf-CHCC  Zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.5     0.048        47      30      35 ..       4       9 ..       2      10 .. 0.86
   2 ?    9.3   0.1    0.0011       1.1      29      37 .]      21      29 ..      15      29 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.048
                                   ETTTTE CS
                        zf-CHCC 30 CgYCgl 35
                                   C+YCg 
  gi|119719941|ref|YP_920436.1|  4 CPYCGA 9 
                                   ****95 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0011
                                   EETTTTEEE CS
                        zf-CHCC 29 dCgYCglrF 37
                                   +C+YCg+ F
  gi|119719941|ref|YP_920436.1| 21 TCPYCGTAF 29
                                   8*****988 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1      0.16   1.6e+02       3      10 ..       4      11 ..       2      16 .. 0.80
   2 ?    7.7   0.0    0.0077       7.7       2      11 ..      21      30 ..      20      41 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.16
                      zf-C2H2_4  3 CpiCgksF 10
                                   Cp+Cg++ 
  gi|119719941|ref|YP_920436.1|  4 CPYCGANV 11
                                   ****9875 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0077
                      zf-C2H2_4  2 kCpiCgksFs 11
                                   +Cp+Cg+ F+
  gi|119719941|ref|YP_920436.1| 21 TCPYCGTAFT 30
                                   7********5 PP

>> zf-IS66  zinc-finger binding domain of transposase IS66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1     0.063        62       3      17 ..       3      17 ..       2      19 .. 0.68
   2 ?    6.5   0.0     0.011        11       3      22 ..      21      39 ..      20      53 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.063
                        zf-IS66  3 tCpcCGgllkpiged 17
                                    Cp CG+ + + +++
  gi|119719941|ref|YP_920436.1|  3 LCPYCGANVERNPGE 17
                                   6*****965555554 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.011
                        zf-IS66  3 tCpcCGgllkpigedrvree 22
                                   tCp CG++ +  g++ v e+
  gi|119719941|ref|YP_920436.1| 21 TCPYCGTAFTVEGGE-VGEH 39
                                   7******98888888.7665 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.4   0.00019      0.19      30      55 ..       3      28 ..       2      30 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00019
                 OrfB_Zn_ribbon 30 tCseCgsknkealsgrtfkCpnCgfe 55
                                    C+ Cg+++++++ + +++Cp Cg+ 
  gi|119719941|ref|YP_920436.1|  3 LCPYCGANVERNPGEVVLTCPYCGTA 28
                                   5**********99999*******985 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1    0.0047       4.7      27      38 ..       2      13 ..       1      15 [. 0.86
   2 ?    2.4   0.1      0.17   1.7e+02      28      34 ..      21      27 ..      17      32 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0047
                    Zn-ribbon_8 27 taCPeCgsevrr 38
                                   t CP Cg++v+r
  gi|119719941|ref|YP_920436.1|  2 TLCPYCGANVER 13
                                   45********99 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.17
                    Zn-ribbon_8 28 aCPeCgs 34
                                   +CP Cg 
  gi|119719941|ref|YP_920436.1| 21 TCPYCGT 27
                                   4888876 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1      0.11   1.1e+02      17      21 ..       4       8 ..       1      11 [. 0.82
   2 ?    8.8   0.2    0.0017       1.7      16      24 ..      21      29 ..      19      30 .. 0.87
   3 ?   -2.1   0.1       4.3   4.3e+03       8      16 ..     224     232 ..     224     232 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.11
                        UPF0547 17 CphCG 21
                                   Cp+CG
  gi|119719941|ref|YP_920436.1|  4 CPYCG 8 
                                   99998 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0017
                        UPF0547 16 fCphCGyvF 24
                                    Cp+CG+ F
  gi|119719941|ref|YP_920436.1| 21 TCPYCGTAF 29
                                   6******99 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 4.3
                        UPF0547   8 akvPvaaqf 16 
                                    a++Pv a+f
  gi|119719941|ref|YP_920436.1| 224 AEIPVEAKF 232
                                    68***9997 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1       0.6     6e+02       3       7 ..       4       8 ..       3      14 .. 0.82
   2 ?    8.1   0.1     0.004         4       2      11 ..      21      30 ..      20      33 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.6
                                  ETTTT CS
                        zf-C2H2 3 CpdCg 7
                                  Cp+Cg
  gi|119719941|ref|YP_920436.1| 4 CPYCG 8
                                  ****9 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.004
                                   EETTTTEEES CS
                        zf-C2H2  2 kCpdCgksFk 11
                                   +Cp+Cg  F+
  gi|119719941|ref|YP_920436.1| 21 TCPYCGTAFT 30
                                   8********7 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   1.0      0.23   2.3e+02      23      28 ..       3       8 ..       1      11 [. 0.82
   2 ?    5.5   5.6     0.021        21       8      32 ..       7      30 ..       4      32 .. 0.65

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.23
                  zinc_ribbon_9 23 lCPhCg 28
                                   lCP+Cg
  gi|119719941|ref|YP_920436.1|  3 LCPYCG 8 
                                   7****8 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.021
                  zinc_ribbon_9  8 CdrfVsvspdedsdv..lCPhCgggFV 32
                                   C  +V+       +v  +CP+Cg  F 
  gi|119719941|ref|YP_920436.1|  7 CGANVERN---PGEVvlTCPYCGTAFT 30
                                   55666643...3332258******995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1950.98
//
Query:       gi|119719942|ref|YP_920437.1|  [L=171]
Description: hypothetical protein Tpen_1034 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.087   12.9   0.0       0.12   12.5   0.0    1.2  1  SRA       SET and RING associated domain


Domain annotation for each model (and alignments):
>> SRA  SET and RING associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   6.5e-06      0.12      90     127 ..      72     111 ..      43     115 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.5e-06
                                    ...S-SEEEEEEEEE-TTTTEEEEEEEEEEEEEEEST..T CS
                            SRA  90 e..knekrivFakvkdelgrvaYrFlGvFkldkeksdkek 127
                                    +   ne ++vF +v  +l+ ++Y ++G F   k ++++ +
  gi|119719942|ref|YP_920437.1|  72 AatYNEVQAVFDRVVSKLKTMSYGYTGFFDAVKIEEKELD 111
                                    44478999**********************9998887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1277.83
//
Query:       gi|119719943|ref|YP_920438.1|  [L=325]
Description: hypothetical protein Tpen_1035 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-32  111.8   0.0    5.1e-32  111.3   0.0    1.2  1  Band_7_1         SPFH domain-Band 7 family
    2.7e-23   82.9   0.0    3.4e-23   82.6   0.0    1.1  1  Band_7           SPFH domain / Band 7 family
    1.6e-19   69.6  15.1    7.2e-12   45.2   3.2    2.3  2  UPF0547          Uncharacterised protein family UPF0547
    1.4e-17   63.4  16.8    6.3e-13   48.5   8.6    1.7  2  DZR              Double zinc ribbon
    5.1e-17   61.0  13.4    2.8e-09   36.4   3.6    2.3  2  zinc_ribbon_2    zinc-ribbon domain
    6.8e-15   53.9  11.1    1.4e-07   30.7   1.5    2.3  2  zf-ribbon_3      zinc-ribbon domain
    1.1e-09   38.9   2.8     0.0012   19.6   1.6    2.2  2  zinc_ribbon_15   zinc-ribbon family
     0.0025   17.7   4.6      0.038   14.0   0.2    2.3  2  DUF2116          Uncharacterized protein containing a Zn-ribb
     0.0057   16.7   7.5       0.18   11.8   1.3    2.5  2  HypA             Hydrogenase/urease nickel incorporation, met
  ------ inclusion threshold ------
      0.016   15.2   4.7        1.9    8.6   7.1    2.4  2  zinc-ribbons_6   zinc-ribbons
      0.019   14.6   4.2       0.83    9.4   0.1    2.8  2  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
      0.021   14.7   9.2      0.094   12.7   1.4    2.4  2  Prok-RING_1      Prokaryotic RING finger family 1
      0.033   14.4   1.3      0.033   14.4   1.3    3.2  3  zf-LITAF-like    LITAF-like zinc ribbon domain
      0.036   13.7   9.2       0.74    9.5   0.6    3.5  4  zf_UBZ           Ubiquitin-Binding Zinc Finger
      0.039   13.8  15.7      0.045   13.6   2.3    2.4  2  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
      0.079   12.7   2.8       0.71    9.6   0.2    2.6  2  zf_C2H2_6        Zinc Finger domain
      0.085   13.5   2.1        8.3    7.2   0.2    2.3  2  zinc-ribbon_6    zinc-ribbon domain
       0.11   13.0   5.0        2.8    8.5   3.6    2.2  2  zf-CHY           CHY zinc finger
       0.13   12.5   8.0       0.56   10.5   0.7    2.4  2  Ribosomal_L32p   Ribosomal L32p protein family
       0.14   11.8  15.7          5    6.9   0.0    3.9  3  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
       0.16   12.0   7.6         29    4.7   7.6    2.6  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
       0.16   11.9   0.0       0.16   11.9   0.0    4.2  4  zf-C2HC_2        zinc-finger of a C2HC-type
       0.21   11.7   4.4        4.9    7.3   0.5    2.2  2  DHHC             DHHC palmitoyltransferase
       0.31   11.1   8.9        1.8    8.7   1.4    2.3  2  DUF3330          Domain of unknown function (DUF3330)
       0.36   11.0  17.0        1.7    8.8   1.6    3.6  3  Zn-ribbon_8      Zinc ribbon domain
       0.38   11.0  17.6        6.8    7.0   0.8    4.4  4  zf-RING_7        C4-type zinc ribbon domain
       0.44   10.2   1.6       0.91    9.2   0.1    2.2  2  zf_C2H2_13       Zinc finger domain
        1.4    8.7  12.9        2.6    7.8   1.4    2.5  2  YacG             DNA gyrase inhibitor YacG
        1.5    8.2   3.0        7.7    5.9   3.0    2.0  1  NMD3             NMD3 family
        1.5    8.4  13.3       0.47   10.1   0.4    3.5  4  Sgf11            Sgf11 (transcriptional regulation protein)
        1.5    8.7  11.9       0.51   10.2   1.6    3.0  3  zf-C3HC4_3       Zinc finger, C3HC4 type (RING finger)
        1.6    8.5   7.1         18    5.2   0.1    2.4  2  DUF4187          Domain of unknown function (DUF4187)
        1.9    8.8   9.1         23    5.3   5.9    2.3  2  IBR              IBR domain, a half RING-finger domain
        1.9    8.6  11.3        4.4    7.5   8.4    2.8  1  PknG_rubred      Protein kinase G rubredoxin domain
        6.5    6.6   8.9        2.7    7.8   0.2    3.0  2  A2L_zn_ribbon    A2L zinc ribbon domain
          7    6.8  10.6    1.1e+02    3.1  10.4    2.2  2  zf-MYND          MYND finger
        8.7    6.4  13.1        9.8    6.2   1.0    3.7  4  YhfH             YhfH-like protein
        9.1    6.0  17.1        2.1    8.0   3.0    3.1  3  zf-tcix          Putative treble-clef, zinc-finger, Zn-bindin


Domain annotation for each model (and alignments):
>> Band_7_1  SPFH domain-Band 7 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.3   0.0   1.1e-34   5.1e-32       1     201 [.      16     206 ..      16     216 .. 0.89

  Alignments for each domain:
  == domain 1  score: 111.3 bits;  conditional E-value: 1.1e-34
                       Band_7_1   1 vwrfprydneiknGakLivregqeavfvneGqiaDvfapGtytLttenlPvlstLkgwkyGf.esPfkaevYfvntrqft 79 
                                    vwr+p  d++i  Ga+Liv+e   avf ++G+  Dv +pG++tLtt+nlP+l+++     G+ ++Pfka v fv+t+qf+
  gi|119719943|ref|YP_920438.1|  16 VWRYP--DENITWGAQLIVHEYEVAVFFRDGKAYDVLGPGRHTLTTQNLPLLTRVLSAIAGYpTTPFKATVIFVSTKQFR 93 
                                    8****..888********************************************99999998468*************** PP

                       Band_7_1  80 dlkwGtknpvilrDpefglvrvrafGtyslrvvdpakllreivGtdgefdteeiseqlkslivtrlsdvlaeskipvldl 159
                                     l  G  ++      e +++     G y +rv dp+ +++e+vG +g++++ e++e ++  i +++ + l+  + ++ + 
  gi|119719943|ref|YP_920438.1|  94 GLFGGRSQTT-----ELAPL--MFRGSYWFRVGDPKLFVTEVVGGQGKYTSAEVNEFIRGFINEKVIKHLS--GYSLAEA 164
                                    *955544433.....44444..4459***************************************998886..5677899 PP

                       Band_7_1 160 aakseelaeklkealkeelaeyGlelekleienislpeevek 201
                                     +  e+++ k k  l ee+ ++Glel +l+ e i+  +e + 
  gi|119719943|ref|YP_920438.1| 165 FSSLEQVSFKTKAFLLEEVRRIGLELIDLKFEAIDTTPEYRD 206
                                    999******************************998877655 PP

>> Band_7  SPFH domain / Band 7 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.6   0.0   7.3e-26   3.4e-23       2     168 ..      31     222 ..      30     233 .. 0.93

  Alignments for each domain:
  == domain 1  score: 82.6 bits;  conditional E-value: 7.3e-26
                         Band_7   2 iieegevgvvvrfGklsrvlepG....................lhfilPfgrsvtvvsvrvqtldvsvsltvptkDglpv 61 
                                    i++e ev+v +r Gk ++vl+pG                    ++   Pf  +v++vs+++++  +      +t +  p+
  gi|119719943|ref|YP_920438.1|  31 IVHEYEVAVFFRDGKAYDVLGPGrhtlttqnlplltrvlsaiaGYPTTPFKATVIFVSTKQFRGLFGG--RSQTTELAPL 108
                                    799***********************99999999999999997777999*******************..********** PP

                         Band_7  62 tidvtviyrvpddapklvaav.....eresanldnlirrvlesalrevisemtleellsnreelaeelknelneqlrkyG 136
                                     + +++++rv  d++ +v++v     +++sa+++++ir  +++++  ++s ++l+e +s+ e++  + k+ l e++r++G
  gi|119719943|ref|YP_920438.1| 109 MFRGSYWFRV-GDPKLFVTEVvggqgKYTSAEVNEFIRGFINEKVIKHLSGYSLAEAFSSLEQVSFKTKAFLLEEVRRIG 187
                                    **********.********************************************************************* PP

                         Band_7 137 vevldvritdidpppevaqa...laakqaaeaeaq 168
                                    +e++d++ ++id  pe++++   + +  aa + +q
  gi|119719943|ref|YP_920438.1| 188 LELIDLKFEAIDTTPEYRDRlfwIKQTGAAGYVLQ 222
                                    *******************9777777777766663 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2   3.2   1.5e-14   7.2e-12       1      26 []     273     298 ..     273     298 .. 0.98
   2 !   30.1   4.2   7.6e-10   3.6e-07       1      22 [.     301     322 ..     301     323 .. 0.97

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 1.5e-14
                        UPF0547   1 KvCPeCeakvPvaaqfCphCGyvFqa 26 
                                    K+CP+C ++vP++a fCp+CGy+Fq+
  gi|119719943|ref|YP_920438.1| 273 KTCPQCGRPVPLDALFCPYCGYRFQP 298
                                    9***********************97 PP

  == domain 2  score: 30.1 bits;  conditional E-value: 7.6e-10
                        UPF0547   1 KvCPeCeakvPvaaqfCphCGy 22 
                                    K+CP C ++vP++a  Cp+CG+
  gi|119719943|ref|YP_920438.1| 301 KKCPNCGREVPADALYCPYCGT 322
                                    9********************8 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   1.1   5.2e-09   2.5e-06      27      49 .]     267     293 ..     257     293 .. 0.81
   2 !   48.5   8.6   1.3e-15   6.3e-13       1      49 []     275     321 ..     275     321 .. 0.98

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 5.2e-09
                            DZR  27 a....edrCpsCgekvdpearfCpeCG 49 
                                    a     ++Cp+Cg++v+++a fCp+CG
  gi|119719943|ref|YP_920438.1| 267 AqppaTKTCPQCGRPVPLDALFCPYCG 293
                                    1344599*******************9 PP

  == domain 2  score: 48.5 bits;  conditional E-value: 1.3e-15
                            DZR   1 CpqCgeelppdarfCseCgtklkavaaedrCpsCgekvdpearfCpeCG 49 
                                    CpqCg+++p da fC++Cg + +  +a ++Cp+Cg++v+++a +Cp+CG
  gi|119719943|ref|YP_920438.1| 275 CPQCGRPVPLDALFCPYCGYRFQ--PATKKCPNCGREVPADALYCPYCG 321
                                    **********************8..789********************9 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   2.3   5.6e-10   2.6e-07       2      22 ..     275     295 ..     274     296 .. 0.94
   2 !   36.4   3.6   5.8e-12   2.8e-09       1      23 []     302     324 ..     302     324 .. 0.97

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 5.6e-10
                  zinc_ribbon_2   2 CpnCGaelqdnakFCpyCGtp 22 
                                    Cp+CG++++ +a FCpyCG+ 
  gi|119719943|ref|YP_920438.1| 275 CPQCGRPVPLDALFCPYCGYR 295
                                    *******************85 PP

  == domain 2  score: 36.4 bits;  conditional E-value: 5.8e-12
                  zinc_ribbon_2   1 fCpnCGaelqdnakFCpyCGtpl 23 
                                    +CpnCG+e++ +a +CpyCGt+l
  gi|119719943|ref|YP_920438.1| 302 KCPNCGREVPADALYCPYCGTKL 324
                                    8********************97 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   1.5   2.9e-10   1.4e-07       2      25 ..     272     295 ..     271     296 .. 0.94
   2 !   28.2   2.5   1.7e-09   8.1e-07       2      26 .]     300     324 ..     299     324 .. 0.93

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 2.9e-10
                    zf-ribbon_3   2 tvrCPnCGaplssddnvCpyCGtk 25 
                                    t++CP+CG p+  d+ +CpyCG++
  gi|119719943|ref|YP_920438.1| 272 TKTCPQCGRPVPLDALFCPYCGYR 295
                                    89*******99***********98 PP

  == domain 2  score: 28.2 bits;  conditional E-value: 1.7e-09
                    zf-ribbon_3   2 tvrCPnCGa.plssddnvCpyCGtkl 26 
                                    t++CPnCG  +  +d+  CpyCGtkl
  gi|119719943|ref|YP_920438.1| 300 TKKCPNCGReV-PADALYCPYCGTKL 324
                                    89*******77.************97 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   5.1e-06    0.0024      61      86 .]     268     293 ..     222     293 .. 0.84
   2 !   19.6   1.6   2.5e-06    0.0012      65      86 .]     300     321 ..     295     321 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 5.1e-06
                 zinc_ribbon_15  61 essekkeCknCgkeveeefkyCpkCg 86 
                                    +   +k+C++Cg+ v  +  +Cp+Cg
  gi|119719943|ref|YP_920438.1| 268 QPPATKTCPQCGRPVPLDALFCPYCG 293
                                    333499*******************9 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 2.5e-06
                 zinc_ribbon_15  65 kkeCknCgkeveeefkyCpkCg 86 
                                    +k+C+nCg+ev ++  yCp+Cg
  gi|119719943|ref|YP_920438.1| 300 TKKCPNCGREVPADALYCPYCG 321
                                    689******************9 PP

>> DUF2116  Uncharacterized protein containing a Zn-ribbon (DUF2116)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.2     8e-05     0.038       4      34 ..     273     302 ..     270     302 .. 0.88
   2 ?    6.6   0.6     0.017       7.8       4      20 ..     301     317 ..     298     324 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 8e-05
                        DUF2116   4 kHCivCGkaIpldesfCsekCqeeyekkrkk 34 
                                    k C+ CG ++pld  fC + C  +++ + kk
  gi|119719943|ref|YP_920438.1| 273 KTCPQCGRPVPLDALFC-PYCGYRFQPATKK 302
                                    66***************.6899999988776 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.017
                        DUF2116   4 kHCivCGkaIpldesfC 20 
                                    k C++CG  +p d   C
  gi|119719943|ref|YP_920438.1| 301 KKCPNCGREVPADALYC 317
                                    77************999 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.5    0.0046       2.2      67      94 ..     269     294 ..     265     297 .. 0.85
   2 !   11.8   1.3   0.00039      0.18      67      94 ..     297     322 ..     294     325 .] 0.86

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0046
                                    E--EEEETTTS-EEECHHHHHS-TTTSS CS
                           HypA  67 vpvkvrCreCgkefeleekalrCpkCgs 94 
                                     p++ +C +Cg+ + l+  al Cp Cg 
  gi|119719943|ref|YP_920438.1| 269 PPATKTCPQCGRPVPLD--ALFCPYCGY 294
                                    688899*********99..568****95 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00039
                                    E--EEEETTTS-EEECHHHHHS-TTTSS CS
                           HypA  67 vpvkvrCreCgkefeleekalrCpkCgs 94 
                                    +p++ +C +Cg+e+  +  al Cp Cg+
  gi|119719943|ref|YP_920438.1| 297 QPATKKCPNCGREVPAD--ALYCPYCGT 322
                                    68999*********987..578****97 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   2.6     0.044        21      15      41 ..     271     298 ..     262     303 .. 0.69
   2 ?    8.6   7.1    0.0039       1.9       3      38 ..     275     323 ..     273     325 .] 0.48

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.044
                                    SEEE-TTT--EEEEEE.E-SSS-S---E CS
                 zinc-ribbons_6  15 eqyhCeaCqedlkkea.lCpeCeqelev 41 
                                    ++ +C +C + +   a +Cp C+ + + 
  gi|119719943|ref|YP_920438.1| 271 ATKTCPQCGRPVPLDAlFCPYCGYRFQP 298
                                    5668999999776554279999988774 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0039
                                    -SSS-S--EE-S............SEEE-TTT--EEEEEE.E-SSS-S- CS
                 zinc-ribbons_6   3 CpeCqqelekrg............eqyhCeaCqedlkkea.lCpeCeqe 38 
                                    Cp+C +++  +             ++ +C +C +++   a +Cp C+ +
  gi|119719943|ref|YP_920438.1| 275 CPQCGRPVPLDAlfcpycgyrfqpATKKCPNCGREVPADAlYCPYCGTK 323
                                    7777777665552333333333333355666666554433256666655 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.1    0.0018      0.83       3      26 ..     275     295 ..     274     296 .. 0.88
   2 ?    5.3   0.8     0.033        16       2      26 ..     302     323 ..     302     324 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0018
                                    -SSS--B----SSS----SSS--- CS
                 DNA_RNApol_7kD   3 CgeCgaevslkkgdpiRCkeCGhR 26 
                                    C +Cg +v l   d++ C +CG+R
  gi|119719943|ref|YP_920438.1| 275 CPQCGRPVPL---DALFCPYCGYR 295
                                    999*****99...5679******9 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.033
                                    B-SSS--B----SSS----SSS--- CS
                 DNA_RNApol_7kD   2 iCgeCgaevslkkgdpiRCkeCGhR 26 
                                    +C +Cg ev   + d++ C +CG +
  gi|119719943|ref|YP_920438.1| 302 KCPNCGREV---PADALYCPYCGTK 323
                                    588999998...578899****986 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   1.3      0.02       9.4       5      27 ..     273     293 ..     271     297 .. 0.87
   2 ?   12.7   1.4    0.0002     0.094       4      28 ..     300     322 ..     297     324 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.02
                    Prok-RING_1   5 kkCpvCgkelkeedDiVvCpeCg 27 
                                    k Cp Cg+++  +  +  Cp Cg
  gi|119719943|ref|YP_920438.1| 273 KTCPQCGRPVPLD--ALFCPYCG 293
                                    68******99865..9******9 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.0002
                    Prok-RING_1   4 gkkCpvCgkelkeedDiVvCpeCgt 28 
                                     kkCp Cg+e+  +  +  Cp Cgt
  gi|119719943|ref|YP_920438.1| 300 TKKCPNCGREVPAD--ALYCPYCGT 322
                                    589*******9875..********9 PP

>> zf-LITAF-like  LITAF-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.6      0.61   2.9e+02       5      64 ..     272     280 ..     268     283 .. 0.56
   2 ?   14.4   1.3     7e-05     0.033      43      66 ..     287     310 ..     282     314 .. 0.89
   3 ?    2.7   0.3      0.32   1.5e+02      58      66 ..     316     324 ..     313     325 .] 0.64

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.61
                  zf-LITAF-like   5 qvdCpaCqqrvvTsveyksgkltwllalllclfgcllccliPfcvdslkdvehyCpnCga 64 
                                    + +Cp+C                                                   g+
  gi|119719943|ref|YP_920438.1| 272 TKTCPQC---------------------------------------------------GR 280
                                    4455555...................................................54 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 7e-05
                  zf-LITAF-like  43 cliPfcvdslkdvehyCpnCgall 66 
                                    +++P+c  +++ ++ +CpnCg+ +
  gi|119719943|ref|YP_920438.1| 287 LFCPYCGYRFQPATKKCPNCGREV 310
                                    456******************976 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.32
                  zf-LITAF-like  58 yCpnCgall 66 
                                    yCp Cg++l
  gi|119719943|ref|YP_920438.1| 316 YCPYCGTKL 324
                                    677777665 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.6    0.0016      0.74       2      16 ..     272     286 ..     271     289 .. 0.87
   2 ?    1.1   0.1      0.65   3.1e+02       3      15 ..     287     299 ..     285     302 .. 0.79
   3 ?    7.8   0.1    0.0053       2.5       2      16 ..     300     314 ..     299     316 .. 0.86
   4 ?   -0.7   0.1       2.3   1.1e+03       4      11 ..     316     323 ..     313     325 .] 0.79

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0016
                         zf_UBZ   2 tylCerCgkeipese 16 
                                    t +C++Cg+++p ++
  gi|119719943|ref|YP_920438.1| 272 TKTCPQCGRPVPLDA 286
                                    789*********875 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.65
                         zf_UBZ   3 ylCerCgkeipes 15 
                                     +C+ Cg +++++
  gi|119719943|ref|YP_920438.1| 287 LFCPYCGYRFQPA 299
                                    69*****988765 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0053
                         zf_UBZ   2 tylCerCgkeipese 16 
                                    t  C+ Cg+e+p ++
  gi|119719943|ref|YP_920438.1| 300 TKKCPNCGREVPADA 314
                                    679*********875 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 2.3
                         zf_UBZ   4 lCerCgke 11 
                                     C+ Cg++
  gi|119719943|ref|YP_920438.1| 316 YCPYCGTK 323
                                    6*****87 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   5.8     0.038        18      13      32 ..     274     293 ..     271     295 .. 0.92
   2 ?   13.6   2.3   9.6e-05     0.045      13      33 ..     302     322 ..     300     324 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.038
                        DUF35_N  13 rCpdCGtvqfPPr.avCphCg 32 
                                     Cp CG+  +P    +Cp+Cg
  gi|119719943|ref|YP_920438.1| 274 TCPQCGRP-VPLDaLFCPYCG 293
                                    5*******.69999******8 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 9.6e-05
                        DUF35_N  13 rCpdCGtvqfPPr.avCphCgs 33 
                                    +Cp+CG+  +P+   +Cp+Cg 
  gi|119719943|ref|YP_920438.1| 302 KCPNCGRE-VPADaLYCPYCGT 322
                                    8*******.7**********95 PP

>> zf_C2H2_6  Zinc Finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.2    0.0015      0.71       4      13 ..     288     297 ..     285     302 .. 0.78
   2 ?    2.8   0.3      0.21        99       5       9 ..     317     321 ..     313     325 .] 0.80

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0015
                      zf_C2H2_6   4 VCpYCsLRFs 13 
                                     CpYC+ RF 
  gi|119719943|ref|YP_920438.1| 288 FCPYCGYRFQ 297
                                    6*******95 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.21
                      zf_C2H2_6   5 CpYCs 9  
                                    CpYC+
  gi|119719943|ref|YP_920438.1| 317 CPYCG 321
                                    ****8 PP

>> zinc-ribbon_6  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.1     0.033        16       3      24 ..     274     295 ..     272     302 .. 0.89
   2 ?    7.2   0.2     0.018       8.3       3      26 ..     302     325 .]     300     325 .] 0.95

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.033
                  zinc-ribbon_6   3 eCeqCgqllffenssClkCgaa 24 
                                    +C qCg+++  +   C  Cg +
  gi|119719943|ref|YP_920438.1| 274 TCPQCGRPVPLDALFCPYCGYR 295
                                    6******************976 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.018
                  zinc-ribbon_6   3 eCeqCgqllffenssClkCgaalg 26 
                                    +C +Cg+++  +   C  Cg++l+
  gi|119719943|ref|YP_920438.1| 302 KCPNCGREVPADALYCPYCGTKLA 325
                                    7********************996 PP

>> zf-CHY  CHY zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.2     0.028        13      52      73 ..     270     293 ..     261     295 .. 0.82
   2 ?    8.5   3.6    0.0059       2.8      43      73 ..     288     321 ..     286     323 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.028
                         zf-CHY  52 ekavlCkkCkk..efaeyfCpiCk 73 
                                    +++++C +C++   +++ fCp+C 
  gi|119719943|ref|YP_920438.1| 270 PATKTCPQCGRpvPLDALFCPYCG 293
                                    67889****9977789999****6 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0059
                         zf-CHY  43 lcllCete.qekavlCkkCkk..efaeyfCpiCk 73 
                                     c  C  + q+++++C +C++   +++ +Cp+C 
  gi|119719943|ref|YP_920438.1| 288 FCPYCGYRfQPATKKCPNCGRevPADALYCPYCG 321
                                    577886542899*******9955467778****7 PP

>> Ribosomal_L32p  Ribosomal L32p protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.7    0.0012      0.56      20      47 ..     266     294 ..     262     297 .. 0.86
   2 ?    5.6   1.5     0.041        20      24      47 ..     298     322 ..     295     323 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0012
                                    ------EEEETTTC.CEECTTC-BTTTTB CS
                 Ribosomal_L32p  20 klkapnlvecpncg.elklpHrvcpscGy 47 
                                    ++++p+  +cp+cg  + l    cp+cGy
  gi|119719943|ref|YP_920438.1| 266 AAQPPATKTCPQCGrPVPLDALFCPYCGY 294
                                    78999*********667799999****98 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.041
                                    --EEEETTTC.CEECTTC-BTTTTB CS
                 Ribosomal_L32p  24 pnlvecpncg.elklpHrvcpscGy 47 
                                    p+  +cpncg e+      cp+cG+
  gi|119719943|ref|YP_920438.1| 298 PATKKCPNCGrEVPADALYCPYCGT 322
                                    67789*****999999999999996 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.7      0.14        65       6      12 ..     275     281 ..     273     282 .. 0.67
   2 ?    5.3   6.0     0.033        15       4      31 ..     287     310 ..     285     310 .. 0.90
   3 ?    6.9   0.0     0.011         5       3      12 ..     314     323 ..     312     325 .] 0.81

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.14
                  zf-NADH-PPase   6 CgrCGap 12 
                                    C++CG p
  gi|119719943|ref|YP_920438.1| 275 CPQCGRP 281
                                    6677665 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.033
                  zf-NADH-PPase   4 rFCgrCGaptepaeggwarvCpaCgleh 31 
                                     FC+ CG + +pa       Cp+Cg+e+
  gi|119719943|ref|YP_920438.1| 287 LFCPYCGYRFQPATK----KCPNCGREV 310
                                    6************98....******985 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.011
                  zf-NADH-PPase   3 hrFCgrCGap 12 
                                      +C+ CG++
  gi|119719943|ref|YP_920438.1| 314 ALYCPYCGTK 323
                                    579*****98 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   7.6     0.062        29      31      59 ..     289     313 ..     269     325 .] 0.67

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.062
                 OrfB_Zn_ribbon  31 CseCgsknkealsgrtfkCpnCgfeadrD 59 
                                    C+ Cg++ +    + t kCpnCg e  +D
  gi|119719943|ref|YP_920438.1| 289 CPYCGYRFQ----PATKKCPNCGREVPAD 313
                                    444444444....4777888888777776 PP

>> zf-C2HC_2  zinc-finger of a C2HC-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.6     0.084        40       2      10 ..     272     280 ..     271     281 .. 0.90
   2 ?    2.3   0.8      0.35   1.6e+02       5       9 ..     289     293 ..     287     298 .. 0.85
   3 ?   11.9   0.0   0.00034      0.16       2      17 ..     300     315 ..     299     315 .. 0.85
   4 ?   -1.2   3.0       4.3     2e+03       5       9 ..     317     321 ..     317     321 .. 0.97

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.084
                      zf-C2HC_2   2 lvpCpkCgR 10 
                                    +  Cp CgR
  gi|119719943|ref|YP_920438.1| 272 TKTCPQCGR 280
                                    679*****9 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.35
                      zf-C2HC_2   5 CpkCg 9  
                                    Cp+Cg
  gi|119719943|ref|YP_920438.1| 289 CPYCG 293
                                    ****9 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 0.00034
                      zf-C2HC_2   2 lvpCpkCgRsFnpdrl 17 
                                    + +Cp+CgR   +d+l
  gi|119719943|ref|YP_920438.1| 300 TKKCPNCGREVPADAL 315
                                    689******9888876 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 4.3
                      zf-C2HC_2   5 CpkCg 9  
                                    Cp+Cg
  gi|119719943|ref|YP_920438.1| 317 CPYCG 321
                                    ****9 PP

>> DHHC  DHHC palmitoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.2     0.026        12       4      26 ..     271     293 ..     268     298 .. 0.88
   2 ?    7.3   0.5      0.01       4.9       4      26 ..     299     321 ..     296     324 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.026
                           DHHC   4 elkfCstcniykpprskHcrvCn 26 
                                     +k C+ c +++p  + +c  C+
  gi|119719943|ref|YP_920438.1| 271 ATKTCPQCGRPVPLDALFCPYCG 293
                                    6799******************7 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.01
                           DHHC   4 elkfCstcniykpprskHcrvCn 26 
                                     +k C++c +++p+ + +c  C+
  gi|119719943|ref|YP_920438.1| 299 ATKKCPNCGREVPADALYCPYCG 321
                                    5789******************7 PP

>> DUF3330  Domain of unknown function (DUF3330)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   1.4    0.0038       1.8       6      28 ..     268     290 ..     265     296 .. 0.86
   2 ?    6.7   1.0     0.016       7.6       8      28 ..     298     318 ..     294     323 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0038
                        DUF3330   6 sdstttsccvcckeiPldaaftP 28 
                                    + ++t +c  c + +Plda f P
  gi|119719943|ref|YP_920438.1| 268 QPPATKTCPQCGRPVPLDALFCP 290
                                    557899999************99 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.016
                        DUF3330   8 stttsccvcckeiPldaaftP 28 
                                    ++t  c  c +e+P da + P
  gi|119719943|ref|YP_920438.1| 298 PATKKCPNCGREVPADALYCP 318
                                    67999************9999 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   1.6    0.0037       1.7      22      36 ..     266     282 ..     261     284 .. 0.79
   2 ?    6.5   4.0     0.019       8.8       8      36 ..     289     310 ..     286     312 .. 0.75
   3 ?    3.3   3.3      0.19        91       7      35 ..     302     323 ..     302     325 .] 0.61

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0037
                    Zn-ribbon_8  22 s.daplta.CPeCgsev 36 
                                    + ++p t+ CP+Cg +v
  gi|119719943|ref|YP_920438.1| 266 AaQPPATKtCPQCGRPV 282
                                    447899999*****876 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.019
                    Zn-ribbon_8   8 CeeCghefevlqsisdapltaCPeCgsev 36 
                                    C  Cg +f +         ++CP+Cg ev
  gi|119719943|ref|YP_920438.1| 289 CPYCGYRFQPA-------TKKCPNCGREV 310
                                    88888888744.......345*****876 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.19
                    Zn-ribbon_8   7 rCeeCghefevlqsisdapltaCPeCgse 35 
                                    +C +Cg+e      ++      CP Cg +
  gi|119719943|ref|YP_920438.1| 302 KCPNCGREVP----AD---ALYCPYCGTK 323
                                    6888885444....22...4459999875 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.8     0.014       6.8      25      31 ..     274     280 ..     272     280 .. 0.95
   2 ?    3.9   0.2      0.13        63      25      30 ..     288     293 ..     285     293 .. 0.90
   3 ?    6.1   0.9     0.027        13      25      31 ..     302     308 ..     301     308 .. 0.92
   4 ?    3.9   0.2      0.14        64      25      30 ..     316     321 ..     313     322 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.014
                                    E-TTT-- CS
                      zf-RING_7  25 tCpeCGR 31 
                                    tCp+CGR
  gi|119719943|ref|YP_920438.1| 274 TCPQCGR 280
                                    8*****9 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.13
                                    E-TTT- CS
                      zf-RING_7  25 tCpeCG 30 
                                    +Cp+CG
  gi|119719943|ref|YP_920438.1| 288 FCPYCG 293
                                    8****9 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.027
                                    E-TTT-- CS
                      zf-RING_7  25 tCpeCGR 31 
                                    +Cp+CGR
  gi|119719943|ref|YP_920438.1| 302 KCPNCGR 308
                                    6*****9 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.14
                                    E-TTT- CS
                      zf-RING_7  25 tCpeCG 30 
                                    +Cp+CG
  gi|119719943|ref|YP_920438.1| 316 YCPYCG 321
                                    8****9 PP

>> zf_C2H2_13  Zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.1    0.0019      0.91      20      32 ..     275     287 ..     272     288 .. 0.90
   2 ?   -1.7   0.2       4.9   2.3e+03      20      28 ..     303     311 ..     302     315 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0019
                     zf_C2H2_13  20 CnkCGkPisleai 32 
                                    C +CG+P+ l+a+
  gi|119719943|ref|YP_920438.1| 275 CPQCGRPVPLDAL 287
                                    9*********997 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 4.9
                     zf_C2H2_13  20 CnkCGkPis 28 
                                    C +CG+ + 
  gi|119719943|ref|YP_920438.1| 303 CPNCGREVP 311
                                    999**9665 PP

>> YacG  DNA gyrase inhibitor YacG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   4.3     0.027        13       2      25 ..     274     295 ..     273     298 .. 0.91
   2 ?    7.8   1.4    0.0056       2.6       2      24 ..     302     322 ..     301     324 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.027
                           YacG   2 kCPtCkkevewseenpfrPFCSeR 25 
                                    +CP+C+++v  ++   f P+C  R
  gi|119719943|ref|YP_920438.1| 274 TCPQCGRPVPLDA--LFCPYCGYR 295
                                    6**********99..99****887 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0056
                           YacG   2 kCPtCkkevewseenpfrPFCSe 24 
                                    kCP C++ev  ++   + P+C  
  gi|119719943|ref|YP_920438.1| 302 KCPNCGREVPADA--LYCPYCGT 322
                                    7********9988..99****86 PP

>> NMD3  NMD3 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   3.0     0.016       7.7       1      42 [.     275     321 ..     275     324 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.016
                           NMD3   1 CcrCGkeieelinglCedCllkevdite.....giek.ievevCkeCg 42 
                                    C++CG+++ +l   +C+ C  +  + t+     g e  ++  +C+ Cg
  gi|119719943|ref|YP_920438.1| 275 CPQCGRPV-PLDALFCPYCGYRFQPATKkcpncGREVpADALYCPYCG 321
                                    99999999.475559999988888888733333333334477888887 PP

>> Sgf11  Sgf11 (transcriptional regulation protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.1     0.022        10       6      14 ..     274     282 ..     271     283 .. 0.89
   2 ?   -2.1   0.2       6.4     3e+03       7      11 ..     289     293 ..     287     293 .. 0.90
   3 ?   10.1   0.4     0.001      0.47       6      15 ..     302     311 ..     299     313 .. 0.86
   4 ?    0.1   0.2       1.3   6.1e+02       6      11 ..     316     321 ..     312     325 .] 0.78

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.022
                                    E-TTTSSEE CS
                          Sgf11   6 tCpnCgRqi 14 
                                    tCp CgR++
  gi|119719943|ref|YP_920438.1| 274 TCPQCGRPV 282
                                    8******98 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 6.4
                                    -TTTS CS
                          Sgf11   7 CpnCg 11 
                                    Cp+Cg
  gi|119719943|ref|YP_920438.1| 289 CPYCG 293
                                    ****7 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.001
                                    E-TTTSSEEE CS
                          Sgf11   6 tCpnCgRqia 15 
                                    +CpnCgR++ 
  gi|119719943|ref|YP_920438.1| 302 KCPNCGREVP 311
                                    7*******95 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 1.3
                                    E-TTTS CS
                          Sgf11   6 tCpnCg 11 
                                     Cp+Cg
  gi|119719943|ref|YP_920438.1| 316 YCPYCG 321
                                    7****8 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.2       0.1        49      37      47 ..     272     282 ..     266     284 .. 0.85
   2 ?   10.2   1.6    0.0011      0.51      25      47 ..     288     310 ..     286     313 .. 0.91
   3 ?    0.5   0.2       1.2   5.8e+02      39      46 ..     316     323 ..     312     325 .] 0.75

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.1
                                    T-B-TTT--B- CS
                     zf-C3HC4_3  37 kkkCpiCrrpi 47 
                                    +k+Cp C rp+
  gi|119719943|ref|YP_920438.1| 272 TKTCPQCGRPV 282
                                    689*****998 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0011
                                    E-HHHHHHHHHTT-B-TTT--B- CS
                     zf-C3HC4_3  25 lCeeCaekllkrkkkCpiCrrpi 47 
                                    +C  C  +++  +kkCp C r++
  gi|119719943|ref|YP_920438.1| 288 FCPYCGYRFQPATKKCPNCGREV 310
                                    8********88********9997 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 1.2
                                    B-TTT--B CS
                     zf-C3HC4_3  39 kCpiCrrp 46 
                                     Cp+C ++
  gi|119719943|ref|YP_920438.1| 316 YCPYCGTK 323
                                    58999775 PP

>> DUF4187  Domain of unknown function (DUF4187)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   2.8     0.039        18      27      47 ..     287     304 ..     285     309 .. 0.85
   2 ?    5.2   0.1     0.039        18      27      35 ..     315     323 ..     312     325 .] 0.86

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.039
                        DUF4187  27 lYCfwCgtkYedeedLeenCP 47 
                                    l+C +Cg++++ +++   +CP
  gi|119719943|ref|YP_920438.1| 287 LFCPYCGYRFQPATK---KCP 304
                                    69********98887...776 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.039
                        DUF4187  27 lYCfwCgtk 35 
                                    lYC +Cgtk
  gi|119719943|ref|YP_920438.1| 315 LYCPYCGTK 323
                                    7******97 PP

>> IBR  IBR domain, a half RING-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   5.9     0.048        23      16      48 ..     270     296 ..     263     309 .. 0.65
   2 ?    4.2   2.1      0.11        51      16      46 ..     298     322 ..     296     324 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.048
                            IBR  16 pnlkwCprpdCeaiieksegcksvtCskCgfef 48 
                                    p +k Cp  +C++++  ++      C+ Cg++f
  gi|119719943|ref|YP_920438.1| 270 PATKTCP--QCGRPVPLDAL----FCPYCGYRF 296
                                    66899**..9*****99999....355555554 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.11
                            IBR  16 pnlkwCprpdCeaiieksegcksvtCskCgf 46 
                                    p +k+Cp  +C++ +  ++   +  C+ Cg+
  gi|119719943|ref|YP_920438.1| 298 PATKKCP--NCGREVPADAL--Y--CPYCGT 322
                                    6789***..9**76655555..5..999987 PP

>> PknG_rubred  Protein kinase G rubredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   8.4    0.0092       4.4      55     126 ..     233     296 ..     211     308 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0092
                                    XXXXXXXXETTTTEEEE------TTGGG-CSS--..-GGG-B-TTT--B-S---SS----SEEE-TTT--EEE- CS
                    PknG_rubred  55 rslspvrrlGgGLveiprvveadPleAlltnpvv..pEskRfCwrCGrpvGRsekerkgaseGtCpkCgspysF 126
                                      +sp   +G+G+v ip + +  P++ l ++p    p + ++C +CGrpv           + +Cp+Cg    F
  gi|119719943|ref|YP_920438.1| 233 LGKSPGAAVGAGVVMIPPLFQPPPQQPLPQQPPAaqPPATKTCPQCGRPVPL--------DALFCPYCGY--RF 296
                                    346788899**********************976225689*********953........3457777774..34 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.2    0.0056       2.7       4      32 ..     273     297 ..     271     297 .. 0.87
   2 ?   -0.4   4.1       2.1     1e+03       4      28 ..     301     321 ..     299     323 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0056
                  A2L_zn_ribbon   4 kvCsvCggngilnseqgylvCieCgasfp 32 
                                    k+C  Cg+++ l    + l+C+ Cg+ f+
  gi|119719943|ref|YP_920438.1| 273 KTCPQCGRPVPL----DALFCPYCGYRFQ 297
                                    789999999999....99*******9776 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 2.1
                  A2L_zn_ribbon   4 kvCsvCggngilnseqgylvCieCg 28 
                                    k+C +Cg+++      + l+C+ Cg
  gi|119719943|ref|YP_920438.1| 301 KKCPNCGREVPA----DALYCPYCG 321
                                    577777777655....677777777 PP

>> zf-MYND  MYND finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.9      0.56   2.6e+02       8      17 ..     270     279 ..     264     289 .. 0.75
   2 ?    3.1  10.4      0.23   1.1e+02       1      22 [.     289     317 ..     275     323 .. 0.71

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.56
                                    B-SCE-TTTS CS
                        zf-MYND   8 ealkkCagCk 17 
                                    +a+k C++C 
  gi|119719943|ref|YP_920438.1| 270 PATKTCPQCG 279
                                    67889****4 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.23
                                    -TTT--...B-SCE-TTT.....S-SEES CS
                        zf-MYND   1 CavCgk..aealkkCagC.....ksvfYC 22 
                                    C +Cg   ++a+kkC++C       + YC
  gi|119719943|ref|YP_920438.1| 289 CPYCGYrfQPATKKCPNCgrevpADALYC 317
                                    666666999*********77777455666 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.3     0.021        10      13      21 ..     272     280 ..     270     282 .. 0.87
   2 ?   -1.6   0.1       5.9   2.8e+03      16      21 ..     289     294 ..     288     298 .. 0.82
   3 ?    6.2   1.0     0.021       9.8      13      22 ..     300     309 ..     294     312 .. 0.88
   4 ?    0.4   0.0       1.4   6.8e+02      16      23 ..     317     324 ..     315     325 .] 0.84

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.021
                           YhfH  13 kKkCteCGk 21 
                                    +K+C++CG 
  gi|119719943|ref|YP_920438.1| 272 TKTCPQCGR 280
                                    6*******6 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 5.9
                           YhfH  16 CteCGk 21 
                                    C+ CG 
  gi|119719943|ref|YP_920438.1| 289 CPYCGY 294
                                    9****6 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.021
                           YhfH  13 kKkCteCGke 22 
                                    +KkC++CG e
  gi|119719943|ref|YP_920438.1| 300 TKKCPNCGRE 309
                                    6*******87 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 1.4
                           YhfH  16 CteCGkei 23 
                                    C+ CG ++
  gi|119719943|ref|YP_920438.1| 317 CPYCGTKL 324
                                    *****875 PP

>> zf-tcix  Putative treble-clef, zinc-finger, Zn-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   2.6     0.033        16      11      36 ..     273     296 ..     272     301 .. 0.79
   2 ?    8.0   3.0    0.0045       2.1      11      27 ..     301     317 ..     299     318 .. 0.92
   3 ?    2.0   0.5      0.34   1.6e+02      13      18 ..     317     322 ..     315     323 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.033
                        zf-tcix  11 rkCpkCGtyNGtRglsCkNkaCdqvf 36 
                                    + Cp+CG   +  +l+C  + C + f
  gi|119719943|ref|YP_920438.1| 273 KTCPQCGRPVPLDALFC--PYCGYRF 296
                                    89*****9999999999..5566555 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0045
                        zf-tcix  11 rkCpkCGtyNGtRglsC 27 
                                    +kCp+CG + +  +l C
  gi|119719943|ref|YP_920438.1| 301 KKCPNCGREVPADALYC 317
                                    9*******999999999 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.34
                        zf-tcix  13 CpkCGt 18 
                                    Cp CGt
  gi|119719943|ref|YP_920438.1| 317 CPYCGT 322
                                    *****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       723  (0.0403257); expected 358.6 (0.02)
Passed bias filter:                      610  (0.0340231); expected 358.6 (0.02)
Passed Vit filter:                       128  (0.00713927); expected 17.9 (0.001)
Passed Fwd filter:                        69  (0.00384851); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              38  [number of targets reported over threshold]
# CPU time: 0.66u 0.29s 00:00:00.95 Elapsed: 00:00:00.51
# Mc/sec: 1923.94
//
Query:       gi|119719944|ref|YP_920439.1|  [L=297]
Description: hypothetical protein Tpen_1036 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       234  (0.0130515); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1925.19
//
Query:       gi|119719945|ref|YP_920440.1|  [L=85]
Description: hypothetical protein Tpen_1037 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 600.68
//
Query:       gi|119719946|ref|YP_920441.1|  [L=450]
Description: L-lactate permease-like [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-36  126.2  43.0    2.3e-21   76.1  13.0    2.1  2  Lactate_perm  L-lactate permease
     0.0039   16.8   0.1     0.0087   15.6   0.1    1.6  1  MOZART2       Mitotic-spindle organizing gamma-tubulin ring a


Domain annotation for each model (and alignments):
>> Lactate_perm  L-lactate permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.8  22.5   3.9e-19   3.5e-15      14     245 ..      19     241 ..       6     259 .. 0.82
   2 !   76.1  13.0   2.6e-25   2.3e-21     349     521 ..     269     444 ..     250     445 .. 0.81

  Alignments for each domain:
  == domain 1  score: 55.8 bits;  conditional E-value: 3.9e-19
                   Lactate_perm  14 llalavlklkgykaallslavsviiallvykmpvekvlaavlkgalsgllpialviiaavflyklsvksgafeiirksil 93 
                                     l l vlk+  ++a l+++a+ v+ all  k ++  v  a+ +ga +g++ i l+i+aa+++yk  +  g++  +r+s+ 
  gi|119719946|ref|YP_920441.1|  19 SLVLGVLKKDVVTASLATFATVVAAALLQSKAGA--VFRAAPVGAWTGVQ-ISLLIVAAIYFYKAYESLGYVGRLRESL- 94 
                                    35688999999********999999999888776..56677789999985.99999********************976. PP

                   Lactate_perm  94 sispdrriqvlligfafgaflEGaaGfGtpvAIsaalLvglGfkPlyaaglcLIantapvafGavGiPitagagatklsa 173
                                      ++ + + v  ++  f+ f+E  +G+G+  A++a++L glG   + a+ l +     +v f ++G+P++++ ++t+ +a
  gi|119719946|ref|YP_920441.1|  95 --TSGKGVEVF-LAVYFSGFIESMSGYGVSPAVTAPILAGLGVGAVEATLLPMFGHVWAVPFASLGVPTLVLSQVTGADA 171
                                    ..667888887.6889**************************************************************** PP

                   Lactate_perm 174 leisslvgiilvlislliplllvilldgvkdiketfpavlvsgl..sfaiaqflisnvlGpelpsilgalvslv 245
                                      +++ +++il+ ++l + +l+++ll+g    + +++a++ s+l   fa+a +++++  G  ++ ++ +l++  
  gi|119719946|ref|YP_920441.1| 172 ESLAAFTARILF-APL-VLILALALLVGRARRRAALVALASSALlpLFAVAGTMVAALTG--FAGLVLGLLATQ 241
                                    ********9975.444.4455666777766677888888777763348999999999886..666666666444 PP

  == domain 2  score: 76.1 bits;  conditional E-value: 2.6e-25
                   Lactate_perm 349 lsspgtiillaavls..iavlklsskdalkvlketlkelklpilaiilvlalanlmnvsGlsktlalalae.tGsaftlf 425
                                    l + g++ ++ +++   +av+  + +   ++ +++l   k +++a+il  a+a++++++G    la  +a  +G+a+  +
  gi|119719946|ref|YP_920441.1| 269 LGARGLLWVALTTVAvsLAVQLAHRRFSREAAVSALSMTKRSVVAVILFSAVAEVSKQAGYTVALAEVVAVtAGKAYLPL 348
                                    55555554444444321333333333334455666667788999999999********************989******* PP

                   Lactate_perm 426 spllGalGvfltGSdtvsNllFgslQletaeqiglsevlllaantvGgvvgkmispqsiaiacaavglvgkEsdllrktv 505
                                     p++ +lG+f+tGS t sNll g lQ++ +e  g+++ l+la++++G+ +g  i+p  i +a+++ g    E++++r+ v
  gi|119719946|ref|YP_920441.1| 349 VPVVAVLGAFITGSATNSNLLLGLLQKTFGELAGVDQSLVLALQNAGAGLGSGIAPAKISVAASTTGGKRVEAEVFRRVV 428
                                    *****************************************************************************988 PP

                   Lactate_perm 506 iysliyliivgvvall 521
                                        +++  ++++a+l
  gi|119719946|ref|YP_920441.1| 429 PVIALLVAPLSILAVL 444
                                    7666666667777665 PP

>> MOZART2  Mitotic-spindle organizing gamma-tubulin ring associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   9.7e-07    0.0087      40      74 ..     415     449 ..     410     450 .] 0.91

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 9.7e-07
                        MOZART2  40 aGiviDqevfkiivDLLklnvaPlavfqvLksmca 74 
                                     G  ++ evf+ +v ++ l vaPl+++ vL  m+ 
  gi|119719946|ref|YP_920441.1| 415 GGKRVEAEVFRRVVPVIALLVAPLSILAVLACMAK 449
                                    5778999*************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       794  (0.0442858); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.42
# Mc/sec: 3186.16
//
Query:       gi|119719947|ref|YP_920442.1|  [L=212]
Description: hypothetical protein Tpen_1039 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1290.80
//
Query:       gi|119719948|ref|YP_920443.1|  [L=282]
Description: protoheme IX farnesyltransferase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.8e-48  163.2  27.5    8.8e-48  162.8  27.5    1.1  1  UbiA          UbiA prenyltransferase family
  ------ inclusion threshold ------
       0.22   11.5   2.1       0.84    9.7   2.1    2.0  1  TNFR_16_TM    Tumor necrosis factor receptor member 16 trans-
       0.25   10.8   4.9       0.71    9.4   4.9    1.7  1  E1-E2_ATPase  E1-E2 ATPase
       0.45    9.3   1.5       0.76    8.6   1.5    1.3  1  VSP           Giardia variant-specific surface protein
        4.9    7.1   5.4        2.2    8.2   2.7    1.8  2  Trypan_PARP   Procyclic acidic repetitive protein (PARP)


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.8  27.5   2.5e-51   8.8e-48       2     250 ..      20     268 ..      19     278 .. 0.82

  Alignments for each domain:
  == domain 1  score: 162.8 bits;  conditional E-value: 2.5e-51
                           UbiA   2 lipalvglalaaggspdlllllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivllilgl 81 
                                    l+ + v++ l + g pd+ +l+l+ l ++l +a++ ++N+++D++iD+ m rt+nRPl+++r+s k a++++ + l++gl
  gi|119719948|ref|YP_920443.1|  20 LLVTGVCAYLEGAGKPDPATLVLASLSMFLSIAGTTGFNMVLDADIDSAMFRTRNRPLPARRMSAKDAVLASSAALAAGL 99 
                                    56677889999********************************************************************* PP

                           UbiA  82 lllalllnpltallgllallly.vvYtglrlKrrtllgtvvggiafglppllgwaavtgsl....sllalllalavfllt 156
                                    + + + +np++++ gll++l+   vYt + lKr +++  v+gg+a+g+p+l+gwaa+tg +     ll+ll+a++  l++
  gi|119719948|ref|YP_920443.1| 100 AAG-VAVNPYVFVAGLLGFLIDiAVYT-VLLKRKSPWSVVFGGFAGGMPALGGWAAATGGFgyqgVLLMLLVAVWSSLHI 177
                                    ***.*****************99****.9***************************999996777777777777777777 PP

                           UbiA 157 waialandlrdregDrkagiktlpvvlGrkaaril.lalllavlllallllllalllllylllalllaalallraarlvr 235
                                    w++ ++      e++r+ag+++lp+v+G++a ++  la+++av+l+a+l++ ++l + + +++a++ ++la+++ ++ + 
  gi|119719948|ref|YP_920443.1| 178 WTLSTY----YSEDYRRAGVPMLPAVYGERAGVVAsLAAAVAVFLVAFLAFRAGLISAVGFAVAAVPLVLAVAVLLKGLV 253
                                    777777....55555******************97555555555555556666666666666666666666555555555 PP

                           UbiA 236 rrdakkaakfflfls 250
                                    + + +++a ++++l 
  gi|119719948|ref|YP_920443.1| 254 SGEYREKAYRAFKLV 268
                                    544444444444554 PP

>> TNFR_16_TM  Tumor necrosis factor receptor member 16 trans-membrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   2.1   0.00023      0.84      12      29 ..     209     226 ..     206     228 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00023
                     TNFR_16_TM  12 SILaaVvvgLlaYvifKr 29 
                                    S+ aaV v+L+a+++f+ 
  gi|119719948|ref|YP_920443.1| 209 SLAAAVAVFLVAFLAFRA 226
                                    889*************96 PP

>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   4.9    0.0002      0.71     123     168 ..     206     248 ..     201     256 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0002
                                    HHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHHHHS-TTHHHHHH CS
                   E1-E2_ATPase 123 vpvvlliallvflialllgkslaeallralallvaaiPcaLplavp 168
                                    v+++l++a++vfl+a+l ++     l++a++++vaa+P  L++av 
  gi|119719948|ref|YP_920443.1| 206 VVASLAAAVAVFLVAFLAFR---AGLISAVGFAVAAVPLVLAVAVL 248
                                    46677888888888877666...57****************99985 PP

>> VSP  Giardia variant-specific surface protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   1.5   0.00021      0.76     360     388 ..      91     119 ..      82     123 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00021
                            VSP 360 nksGlstGaiaGisvavvvvvgGlvGflc 388
                                      + l++G  aG++v   v v+Gl+Gfl 
  gi|119719948|ref|YP_920443.1|  91 SSAALAAGLAAGVAVNPYVFVAGLLGFLI 119
                                    456899*********************95 PP

>> Trypan_PARP  Procyclic acidic repetitive protein (PARP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0         2   7.2e+03     108     126 ..      34      52 ..      30      55 .. 0.73
   2 ?    8.2   2.7   0.00062       2.2       4      28 ..     214     238 ..     211     258 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2
                    Trypan_PARP 108 epepgaatlksvalpfaia 126
                                    +p+p +  l s+++ ++ia
  gi|119719948|ref|YP_920443.1|  34 KPDPATLVLASLSMFLSIA 52 
                                    6888888888888888877 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00062
                    Trypan_PARP   4 rslyllaillfsanlfagvgfaaaa 28 
                                     +++l+a l f a l++ vgfa aa
  gi|119719948|ref|YP_920443.1| 214 VAVFLVAFLAFRAGLISAVGFAVAA 238
                                    5789******************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       863  (0.0481343); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.51
# Mc/sec: 1677.25
//
Query:       gi|119719949|ref|YP_920444.1|  [L=154]
Description: NUDIX hydrolase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-16   59.7   0.7    3.4e-16   59.5   0.7    1.1  1  NUDIX     NUDIX domain


Domain annotation for each model (and alignments):
>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.5   0.7   1.9e-20   3.4e-16       5     130 ..       4     123 ..       2     124 .. 0.80

  Alignments for each domain:
  == domain 1  score: 59.5 bits;  conditional E-value: 1.9e-20
                                    EEEEEEEETTSEEEEEEESSSSTTT.EESSEEECBTTSHHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEEEEEEEEEE CS
                          NUDIX   5 avgvvllnekgevLlvrrskkpfpg.WelPgGkvepgEtpeeAArREleEEtGleaellellgrlhylapydgpygdehe 83 
                                    a  ++ll+++ evLl+r  +   +g +  +gGkve+gE+++ AA+RE+ EEtG+e++ l + g l+  a ++    +++ 
  gi|119719949|ref|YP_920444.1|   4 ATLCYLLRGD-EVLLIRKLRGFGAGkYNGVGGKVEEGEDIWRAAMREVLEETGVEVKGLSYRGLLEFYAGGE----EPEI 78 
                                    5678888999.6****9884455556789*************************999999999554444433....3666 PP

                                    EEEEEE.EEECSGCSSTSTTTEEEEEEEEHHHHHHHHTHCTHHHHHHH CS
                          NUDIX  84 ilyvfl.eevegelepndenevsevrwvpleellkeklaaesrkllpw 130
                                    i++vf+ +++ ge +p   +e     w+++ e+  +++++++r +lp+
  gi|119719949|ref|YP_920444.1|  79 IVHVFVsRDFAGEARPS--DEAVPT-WFKVGEIPYDEMWEDDRVWLPR 123
                                    78888889999998886..775555.9******999999999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       259  (0.0144459); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 1083.63
//
Query:       gi|119719950|ref|YP_920445.1|  [L=303]
Description: prenyltransferase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-35  121.5  28.5    4.5e-35  121.2  25.7    2.0  2  UbiA      UbiA prenyltransferase family
  ------ inclusion threshold ------
        8.2    6.4   8.9        5.2    7.0   0.7    3.2  2  PsbN      Photosystem II reaction centre N protein (psbN)


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.9   1.3    0.0016        14      85     114 ..      13      41 ..       3      42 .. 0.86
   2 !  121.2  25.7     5e-39   4.5e-35       3     234 ..      28     264 ..      26     283 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0016
                           UbiA  85 alllnpltallgllalllyvvYtglrlKrr 114
                                     +++ p++++++++++  + +Yt ++l r+
  gi|119719950|ref|YP_920445.1|  13 FIFTRPWSFVMTAISITGAAAYT-YYLARS 41 
                                    47899******************.788875 PP

  == domain 2  score: 121.2 bits;  conditional E-value: 5e-39
                           UbiA   3 ipalvglalaaggspdlllllllllgtllaaaaanalNdyfDreiDadme...rtpnRP..lvsGrispkealifaivll 77 
                                    i+ ++++++    s+d+ll +++llg++l++a+an+lNdy+D   + d+e    t+ RP  + +G++s  +++ f+++l+
  gi|119719950|ref|YP_920445.1|  28 ITGAAAYTYYLARSFDPLLYAATLLGVTLLHASANVLNDYYDTVRGVDVEgapTTRYRPhpIIAGKMSAGQVRNFGLALM 107
                                    56677788888899***************************************6666652277***************** PP

                           UbiA  78 ilgllll...alllnpltallgllalllyvvYtg.lrlKrrtllgtvvggiafglppllgwaa.vtgslsllalllalav 152
                                    + gl+++   al  + +++ll+l +++l++ Y+g   lK+r l g++ +++++g++ +lg ++  tg+lsll++l++++v
  gi|119719950|ref|YP_920445.1| 108 AGGLAFAfalALVRQVVVVLLALTGVVLLFTYSGpPGLKYRAL-GELGVFLSWGVFMWLGTFYvLTGELSLLPVLAGIPV 186
                                    ***99999878888899999999999999****667*******.*******************9**************** PP

                           UbiA 153 flltwaialandlrdregDrkagiktlpvvlGrkaarillalllavlllallllllalllllylllalllaalallraar 232
                                    +ll++a+++an+lrd+e D  +g  tl+vvlGr + + ++a+ ++ +++a    ++al+ll  l l++lla+l l  a+r
  gi|119719950|ref|YP_920445.1| 187 GLLVAAVLTANNLRDIEFDSSRGAVTLAVVLGRSRGLAFYAFEVFSAYAA----TIALVLLGVLPLGSLLALLSLPQAFR 262
                                    *************************************9777666666666....55555555555555555555555444 PP

                           UbiA 233 lv 234
                                    l+
  gi|119719950|ref|YP_920445.1| 263 LC 264
                                    44 PP

>> PsbN  Photosystem II reaction centre N protein (psbN)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   2.1     0.028   2.5e+02      11      25 ..      21      35 ..      19      37 .. 0.85
   2 ?    7.0   0.7   0.00058       5.2       4      31 ..     116     144 ..     113     147 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.028
                           PsbN 11 iaavlvaiTgfsiYt 25
                                   +++  ++iTg + Yt
  gi|119719950|ref|YP_920445.1| 21 FVMTAISITGAAAYT 35
                                   677889********9 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.00058
                           PsbN   4 AtvlsisiaavlvaiTgfs.iYtaFGPPs 31 
                                    A++l+  +++vl+a+Tg+  ++t  GPP 
  gi|119719950|ref|YP_920445.1| 116 ALALVRQVVVVLLALTGVVlLFTYSGPPG 144
                                    677778899********87369999**95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2087.30
//
Query:       gi|119719951|ref|YP_920446.1|  [L=440]
Description: major facilitator transporter [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.9e-39  133.8  50.7    3.2e-29  101.9  20.7    2.1  2  MFS_1          Major Facilitator Superfamily
    5.5e-09   35.4  11.0    2.1e-05   23.6   0.1    2.1  2  MFS_1_like     MFS_1 like family
    5.9e-07   28.7   3.5    5.9e-07   28.7   3.5    2.3  2  Sugar_tr       Sugar (and other) transporter
    1.1e-06   27.3  13.2    0.00054   18.5   3.2    2.1  2  MFS_3          Transmembrane secretion effector
    0.00062   18.9   0.6    0.00062   18.9   0.6    1.9  2  Nuc_H_symport  Nucleoside H+ symporter
  ------ inclusion threshold ------
       0.36   11.2   8.7        1.7    9.0   1.2    3.4  3  DUF3021        Protein of unknown function (DUF3021)
        2.4    6.4   6.8       0.26    9.5   0.1    2.5  4  OATP           Organic Anion Transporter Polypeptide (OATP) f


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.9  20.7   1.3e-32   3.2e-29      15     299 ..      58     333 ..      44     336 .. 0.90
   2 !   45.7  22.0   1.6e-15     4e-12      14     172 ..     259     423 ..     248     432 .. 0.86

  Alignments for each domain:
  == domain 1  score: 101.9 bits;  conditional E-value: 1.3e-32
                          MFS_1  15 lgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll.fasslw.lllvlr 92 
                                    +gp    ++ + lg+sp  i+l+ ++  ++ a++ +++G+lsdr+Gr+rvl++g +l al+ +ll+ + ++ w   +++ 
  gi|119719951|ref|YP_920446.1|  58 AGPYTQ-LYVSRLGASPEDISLVQSATQVANALSRIVGGFLSDRYGRKRVLWVGTFLVALA-YLLMsV-ATDWrSYAIAS 134
                                    445555.567889************************************************.555524.99999****** PP

                          MFS_1  93 vlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg....Wravfyilaivsllafvlf 168
                                    vl G++  ++ pa   + ad +p   rgr+++ll +  +l++ l pl g++l+ ++g     r++f++  + ++  +v  
  gi|119719951|ref|YP_920446.1| 135 VLNGFAL-FYQPALEGIQADSVPLHLRGRMNALLHLVPGLASSLSPLGGAALVNAYGlvggVRVIFFLSFVTGVAIAVA- 212
                                    ******7.*************************************************9999********9999999776. PP

                          MFS_1 169 llllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlglsglllagl 248
                                      ll+ e++ ++r s++       ++ +   ++++ +d +    li+l + f  + ++++l+  y+   lg +   ++++
  gi|119719951|ref|YP_920446.1| 213 -RLLWIEETLEPRGSGVNM----LESYVDA-LRHVSRDVY---TLITLDTLFNLVGAMSFLSNYYMYYYLGVD-KSELAM 282
                                    .***************999....6777777.********4...4555555555888899999999********.899999 PP

                          MFS_1 249 llallalvgailallagrlsdrlgrrrrlllallllllaalglallavtss 299
                                    l +l++lv+++l + agr +d  gr + ++l++l ++l+ l+++l +++ss
  gi|119719951|ref|YP_920446.1| 283 LASLGSLVNLGLLIPAGRAVDTRGRNFSITLGFLMGTLSQLFFVLSPPSSS 333
                                    9*********************************************99954 PP

  == domain 2  score: 45.7 bits;  conditional E-value: 1.6e-15
                          MFS_1  14 ilgpalpl.alaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa...sslwl.. 87 
                                     ++++l+  ++   lg+++se+ +l++l +l+ + + +p+Gr +d  Gr   + lg+l+  l+ l+++++   ss++l  
  gi|119719951|ref|YP_920446.1| 259 GAMSFLSNyYMYYYLGVDKSELAMLASLGSLVNLGLLIPAGRAVDTRGRNFSITLGFLMGTLSQLFFVLSppsSSFTLpa 338
                                    45666777799999*************************************************66666655543333234 PP

                          MFS_1  88 llvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvl 167
                                    l+v+ ++ ++g++++  a  +l ad+++ke rgr ++l++++ +++  lg+ +gg+++s+lg + +f++   + +l+  l
  gi|119719951|ref|YP_920446.1| 339 LIVSTLFGAVGGAFYGLAYSSLRADLVAKEYRGRIYALWGLAPAASWSLGAYIGGWMYSNLGPQTPFVASFMLRVLLTPL 418
                                    99999999999999999999******************************************999999998888888776 PP

                          MFS_1 168 fllll 172
                                    +l l+
  gi|119719951|ref|YP_920446.1| 419 ALTLF 423
                                    66665 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.1   8.3e-09   2.1e-05      19      83 ..      59     122 ..      43     170 .. 0.86
   2 !   13.8   7.1   7.6e-06     0.019     209     383 ..     228     405 ..     175     407 .. 0.70

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 8.3e-09
                     MFS_1_like  19 lPYltiylkskglkaseigiitlilpltsilsppiwgvlaDrfgkrkkvvilslllsavlflsll 83 
                                     PY ++y +  g ++++i ++ ++  + + ls+ + g+l+Dr+g+ k v+ ++++l a+++l + 
  gi|119719951|ref|YP_920446.1|  59 GPYTQLYVSRLGASPEDISLVQSATQVANALSRIVGGFLSDRYGR-KRVLWVGTFLVALAYLLMS 122
                                    59****************************************985.7788888888888888443 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 7.6e-06
                     MFS_1_like 209 lkvtkslqvllnilknpeviifllvali.lgmswgiienFlflYLkelgasntllGslvalgvvaeiplfffaekllekl 287
                                    +++ +s  + l+ +++  + ++ l +l+ l  +++++ n++  Y+  lg  ++ l +l  lg + ++ l++ a + +++ 
  gi|119719951|ref|YP_920446.1| 228 VNMLESYVDALRHVSRDVYTLITLDTLFnLVGAMSFLSNYYMYYY--LGVDKSELAMLASLGSLVNLGLLIPAGRAVDTR 305
                                    333333344444444444444444444313345788999999999..9******************************** PP

                     MFS_1_like 288 Ghvklliiallayil..rfllyaii..enawlvlpievLhgisfgllwaaave.yvskiapksleatgqgllsglyfglG 362
                                    G  + +++++l+ +l   f++++    + +  +l++ +L g+  g++++ a +   ++++ k++++++ +l   +   + 
  gi|119719951|ref|YP_920446.1| 306 GRNFSITLGFLMGTLsqLFFVLSPPssSFTLPALIVSTLFGAVGGAFYGLAYSsLRADLVAKEYRGRIYALWGLA-PAAS 384
                                    **********987652245556555533444578999***********97766155689***********98655.7889 PP

                     MFS_1_like 363 ralGsliGGllwdlksaiflF 383
                                      lG++iGG ++   ++++ F
  gi|119719951|ref|YP_920446.1| 385 WSLGAYIGGWMYSNLGPQTPF 405
                                    99999****999877776666 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   3.5   2.3e-10   5.9e-07      45     191 ..      73     216 ..      49     222 .. 0.87
   2 ?    2.9   3.7     0.016        40     251     390 ..     241     376 ..     226     423 .. 0.68

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 2.3e-10
                                    ..HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHH CS
                       Sugar_tr  45 svlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvP 124
                                      +++l+ s+++v  +++ +++g+l+dr+GRk +l ++++l+  + +l+ +a+    +  ++++ vl G+++  + +l  
  gi|119719951|ref|YP_920446.1|  73 PEDISLVQSATQVANALSRIVGGFLSDRYGRKRVLWVGTFLVALAYLLMSVAT---DWRSYAIASVLNGFALFYQPALEG 149
                                    446899***********************************************...9**************977777766 PP

                                    HHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHH.HTSS-TTHHHHHHHCCHHHHHHHHHHGGGS CS
                       Sugar_tr 125 myisEiApkklRgalvslyqlaitfGilvaaifglgl.nktsnadgwrillglqlvpallllilllfl 191
                                    + ++   p +lRg++  l  l   +   ++   g++l n ++   g r+ ++l++v  +++++++l++
  gi|119719951|ref|YP_920446.1| 150 I-QADSVPLHLRGRMNALLHLVPGLASSLSPLGGAALvNAYGLVGGVRVIFFLSFVTGVAIAVARLLW 216
                                    5.66777************999999999999999988666666899************9999998776 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.016
                                    ...HHHHHHHHHHHHHHTTHHHHHHHTTTHHHHSS-THH..HHHHHHHHHHHHHHHHHHHHHHHHS-SHHHHHHHHHHHH CS
                       Sugar_tr 251 vrqrlligvvlqifqqltGinaimyysptifenlglsks..llvtiivgvvnfvatfvaiflvdrfGRRtllllGaagma 328
                                    v + + + + l+ + +l+G ++ +    +++  lg++ks  ++   + + vn    + a   vd  GR     lG+++++
  gi|119719951|ref|YP_920446.1| 241 VSRDVYTLITLDTLFNLVGAMS-FLSNYYMYYYLGVDKSelAMLASLGSLVNLGLLIPAGRAVDTRGRNFSITLGFLMGT 319
                                    5567888899999999999544.4445578999999999976666666789999999999***************99999 PP

                                    HHHHHHH..HHHHTTSS.....CHHHHHHHHHHHHHHHTTTTHHHHHHHHHHSHTTTHHHHHHH CS
                       Sugar_tr 329 icfvilgivalllvaks..kaasivaivfialfialfalgwgpvpwvlvsElfpqsvRskalai 390
                                    +  +++    l  +++s    a iv++ f a+  a+++l        l ++l  ++ R+  +a+
  gi|119719951|ref|YP_920446.1| 320 LSQLFFV---LSPPSSSftLPALIVSTLFGAVGGAFYGLAY----SSLRADLVAKEYRGRIYAL 376
                                    9999984...3333332233344555555555555555544....4444666666666666655 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   3.2   2.1e-07   0.00054      37     107 ..      66     136 ..      45     264 .. 0.72
   2 !   13.8   3.4   5.5e-06     0.014      45     177 ..     278     410 ..     241     430 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.1e-07
                          MFS_3  37 mtdisasplmvAlvqaaatLPifllsilaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlll 107
                                    ++ + asp  + lvq a+ +   l  i+ G l+D + r++vl ++  l+al+ +l+ v +     +  ++l
  gi|119719951|ref|YP_920446.1|  66 VSRLGASPEDISLVQSATQVANALSRIVGGFLSDRYGRKRVLWVGTFLVALAYLLMSVATDWRSYAIASVL 136
                                    66789************************************999988888877766666655444444333 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 5.5e-06
                          MFS_3  45 lmvAlvqaaatLPifllsilaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllaltlligiGaalndPaW 124
                                       A++   ++L  + l i+aG   D+  r   +  + l+  l+ ++ +++     ++  +l+++tl+ ++G a+   a+
  gi|119719951|ref|YP_920446.1| 278 SELAMLASLGSLVNLGLLIPAGRAVDTRGRNFSITLGFLMGTLSQLFFVLSPPSSSFTLPALIVSTLFGAVGGAFYGLAY 357
                                    567888888999999999*****999987766666666555566666666667888999999****************** PP

                          MFS_3 125 qAsvgelvkrrdvpaAvaLnsvginiaRsvGPAlgGvlvaavGaalafavnal 177
                                    +    +lv+++      aL  +    + s G  +gG + + +G+ + f +  +
  gi|119719951|ref|YP_920446.1| 358 SSLRADLVAKEYRGRIYALWGLAPAASWSLGAYIGGWMYSNLGPQTPFVASFM 410
                                    **********************************************9987644 PP

>> Nuc_H_symport  Nucleoside H+ symporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.6   2.4e-07   0.00062      26     109 ..      63     147 ..      39     155 .. 0.77
   2 ?   -2.0   0.7      0.51   1.3e+03     246     318 ..     281     353 ..     243     381 .. 0.66

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.4e-07
                  Nuc_H_symport  26 fsylsktlfaaaeiglvysslgiaailspilvgiiaDkflsaervlavlhligavvlflaaqvtefeal..flvlLvysl 103
                                     +y+s ++ ++ +i+lv s++ +a  ls i+ g ++D++ + +rvl v  ++ a++ +l +  t+  ++    vl  ++l
  gi|119719951|ref|YP_920446.1|  63 QLYVSRLGASPEDISLVQSATQVANALSRIVGGFLSDRYGR-KRVLWVGTFLVALAYLLMSVATDWRSYaiASVLNGFAL 141
                                    46889999******************************865.89999999999999888888888765510556666888 PP

                  Nuc_H_symport 104 aymPtl 109
                                     y P+l
  gi|119719951|ref|YP_920446.1| 142 FYQPAL 147
                                    899987 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.51
                  Nuc_H_symport 246 sillslsqvaeilfiLtlpfflkrfGikkvlllslvaaalrfalfaygaddepvgvvlllLslivyGvaydff 318
                                    ++l sl+ + ++ +++  ++ +   G    + l+ +  +l   +f+    ++ +++  l++s +   v  +f+
  gi|119719951|ref|YP_920446.1| 281 AMLASLGSLVNLGLLIPAGRAVDTRGRNFSITLGFLMGTLSQLFFVLSPPSSSFTLPALIVSTLFGAVGGAFY 353
                                    4445666666666666666777777777777777777777777777776666666666666666555555555 PP

>> DUF3021  Protein of unknown function (DUF3021)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1     0.052   1.3e+02      58      99 ..      96     137 ..      84     144 .. 0.78
   2 ?    1.9   0.1       0.1   2.6e+02      39      62 ..     197     220 ..     181     225 .. 0.81
   3 ?    9.0   1.2   0.00068       1.7       7     106 ..     310     411 ..     308     428 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.052
                        DUF3021  58 feserlsllkqtlihflvvlllvlllalllgWfplsvigili 99 
                                    f s+r   ++ +++  ++v l++ll+++   W ++++ ++l 
  gi|119719951|ref|YP_920446.1|  96 FLSDRYGRKRVLWVGTFLVALAYLLMSVATDWRSYAIASVLN 137
                                    6677778888889999999*************9997766654 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.1
                        DUF3021  39 kqvllsaliGvlfalaslifeser 62 
                                      ++ls++ Gv +a+a l++  e 
  gi|119719951|ref|YP_920446.1| 197 VIFFLSFVTGVAIAVARLLWIEET 220
                                    568899999999999999997765 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.00068
                        DUF3021   7 giliGiligliislvislfsgettllestavlkqvllsaliGvlfalaslifeserlsllkqtlihflvv...lllvlll 83 
                                    +i++G+l+g++  l++ l  +++++ ++ a++ ++l+ a+ G++++la      +     ++  i++l +    + + l 
  gi|119719951|ref|YP_920446.1| 310 SITLGFLMGTLSQLFFVLSPPSSSF-TLPALIVSTLFGAVGGAFYGLAYSSLRADLVAKEYRGRIYALWGlapAASWSLG 388
                                    799****************999998.999999999999999999888877777777777777779988883334678888 PP

                        DUF3021  84 alllgWfplsvigilivilifii 106
                                    a++ gW+  +++  + +++ f++
  gi|119719951|ref|YP_920446.1| 389 AYIGGWMYSNLGPQTPFVASFML 411
                                    89999*99988877777666644 PP

>> OATP  Organic Anion Transporter Polypeptide (OATP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1    0.0001      0.26      30      85 ..      68     123 ..      43     131 .. 0.86
   2 ?   -2.8   0.2      0.55   1.4e+03     289     320 ..     239     267 ..     230     296 .. 0.68
   3 ?   -3.7   0.0       1.1   2.7e+03     470     505 ..     283     318 ..     277     325 .. 0.71
   4 ?   -0.3   0.1     0.096   2.5e+02     339     380 ..     380     421 ..     372     426 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0001
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           OATP  30 rFklpsstsgliassneignillilfvsYfggrghrPrwigigallmalgslllal 85 
                                    r + + + + l++s+ +++n+l  ++ +++ +r  r r++ +g++l+al++ll+++
  gi|119719951|ref|YP_920446.1|  68 RLGASPEDISLVQSATQVANALSRIVGGFLSDRYGRKRVLWVGTFLVALAYLLMSV 123
                                    55667788999******************************************987 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.55
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           OATP 289 rllknpifllvilssvfeillvaGfitFlpky 320
                                    r ++  +++l++l + f+++++   + Fl+ y
  gi|119719951|ref|YP_920446.1| 239 RHVSRDVYTLITLDTLFNLVGA---MSFLSNY 267
                                    5567788888888876666554...4454443 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 1.1
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           OATP 470 vsflgalgrvpallvilRcVkkedksfalGlqllli 505
                                    ++ lg+l + + l+   R V+ + + f++ l +l+ 
  gi|119719951|ref|YP_920446.1| 283 LASLGSLVNLGLLIPAGRAVDTRGRNFSITLGFLMG 318
                                    556677777777777778888888888887777764 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 0.096
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           OATP 339 vvipgaalGillgGllvkklklsakklaklvlvvsllsllll 380
                                    +   +  lG  +gG++ + l +++  +a ++l v l+ l+l+
  gi|119719951|ref|YP_920446.1| 380 APAASWSLGAYIGGWMYSNLGPQTPFVASFMLRVLLTPLALT 421
                                    55566789*****************99999998888777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.63u 0.27s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 2751.70
//
Query:       gi|119719952|ref|YP_920447.1|  [L=268]
Description: NAD+ synthetase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-67  227.6   0.0    1.5e-67  227.3   0.0    1.1  1  NAD_synthase   NAD synthase
    0.00057   18.8   0.0       0.05   12.4   0.0    2.2  2  tRNA_Me_trans  tRNA methyl transferase


Domain annotation for each model (and alignments):
>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  227.3   0.0   1.7e-71   1.5e-67       5     242 .]      20     261 ..      16     261 .. 0.95

  Alignments for each domain:
  == domain 1  score: 227.3 bits;  conditional E-value: 1.7e-71
                                    HHHHHHHHH.HHCTTSEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTS...EEEE-- CS
                   NAD_synthase   5 lvdflkeyv.kkagakgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgi...evktid 80 
                                    ++  l+ yv ++ag +g v+G+SGGvDS+++  l+ +alg+en  al++Pss ++eed++da +++   g+   +v+t+d
  gi|119719952|ref|YP_920447.1|  20 ITRELRRYVfEEAGKSGGVVGVSGGVDSAVTLLLTARALGPENTYALIMPSSATPEEDLRDAYEVVRIAGLpggNVETVD 99 
                                    5667888884677889*************************************************98776533389**** PP

                                    -HHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHTEEEB---BHHHHTTT-S-TTTTT--SBETTTTS-HHHHH CS
                   NAD_synthase  81 ikpivrafeqelkeakedlakgNlkaRiRmailyaianklnllvlgTgnksElvvGyfTkyGDgaadlapiaellKtevk 160
                                    i+pi++ fe++l + +  + +gNl aR+Rm+il a a + n+lv+gTg+ksEl++GyfTkyGDg++d++pi++l+Kt+v+
  gi|119719952|ref|YP_920447.1| 100 IEPILSRFEESLGPLT-RVERGNLAARVRMCILHARAYRRNSLVIGTGDKSELLLGYFTKYGDGGVDVLPIGDLYKTQVR 178
                                    **************99.9************************************************************** PP

                                    HHHHHTT--HHHHCS--B--SSTT-BHHHHHSS-HHHHHHHHT.HSSSS...HHHHHTTT--HHHHHHHHHHHHHTGGGG CS
                   NAD_synthase 161 eLakelnvPervlkkpPsAdLkpgqtDeeeLgikYdelDeiLk.lvekkkspeeiikekelpaevvekieklvkksehKr 239
                                    +L  +l+ Per+  kp s +L+pg + eeeL ++Y++ D+iL  l++++  p e+   +++ +e ve++ +l ++sehKr
  gi|119719952|ref|YP_920447.1| 179 RLGLHLGLPERIAFKPSSPRLWPGHVAEEELKLTYEVADKILYlLFDRGVDPSEVPGMLGVGRELVERVLELHRRSEHKR 258
                                    *******************************************99*********************************** PP

                                    SSS CS
                   NAD_synthase 240 klp 242
                                    ++p
  gi|119719952|ref|YP_920447.1| 259 RPP 261
                                    998 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   5.6e-06      0.05       4      56 ..      38      83 ..      37     103 .. 0.61
   2 !    4.2   0.0    0.0017        15     165     193 ..     166     196 ..     164     199 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.6e-06
                  tRNA_Me_trans  4 vvalSgGVDSsvaaallkeqg..yevigvflklweeedeegkeccaeedlkdaer 56
                                   vv++SgGVDS+v+++l +++    ++ ++++  ++         + eedl+da +
  gi|119719952|ref|YP_920447.1| 38 VVGVSGGVDSAVTLLLTARALgpENTYALIMPSSA---------TPEEDLRDAYE 83
                                   79***********9988776422333333333322.........23344444444 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0017
                  tRNA_Me_trans 165 lfPlgeltKeevrkiAkeagla..vaekkdS 193
                                    ++P+g+l K++vr++  + gl+  +a k+ S
  gi|119719952|ref|YP_920447.1| 166 VLPIGDLYKTQVRRLGLHLGLPerIAFKPSS 196
                                    68*************9999998667767665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1839.59
//
Query:       gi|119719953|ref|YP_920448.1|  [L=98]
Description: hypothetical protein Tpen_1045 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 649.05
//
Query:       gi|119719954|ref|YP_920449.1|  [L=426]
Description: phosphonopyruvate decarboxylase-related protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.4e-50  170.2   0.0    4.8e-50  169.7   0.0    1.2  1  PhosphMutase   2,3-bisphosphoglycerate-independent phosphogly
    2.9e-31  108.7   0.0    3.5e-31  108.5   0.0    1.0  1  Metalloenzyme  Metalloenzyme superfamily
     0.0017   18.0   0.0      0.002   17.8   0.0    1.2  1  Phosphodiest   Type I phosphodiesterase / nucleotide pyrophos
  ------ inclusion threshold ------
       0.11   12.6   0.0       0.16   12.0   0.0    1.2  1  PglZ           PglZ domain


Domain annotation for each model (and alignments):
>> PhosphMutase  2,3-bisphosphoglycerate-independent phosphoglycerate mutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.7   0.0   1.1e-53   4.8e-50       1     170 []      34     224 ..      34     224 .. 0.96

  Alignments for each domain:
  == domain 1  score: 169.7 bits;  conditional E-value: 1.1e-53
                                    HHTSEEEEEE-----------TCHHHHTT--HHCH---HHHHHHHHTT----TT-.EEEEEEEEEEC..TTCEEETTGGG CS
                   PhosphMutase   1 AkkGetGlldtvpegiapgSdvAnlsilGydpkkyytGRGplEAlgiGlelkpgd.vafRcnlvtvdeedgiiidrragr 79 
                                    A+k+++Gl++tv +g+ap+Sd A++silGydp++ ytGRGp+EA+g+Gle+++g  vafR+n++tvd+e+++iidrr+gr
  gi|119719954|ref|YP_920449.1|  34 ASKSACGLVYTVGRGVAPESDAAVFSILGYDPHTEYTGRGPIEAVGAGLEIREGFeVAFRANFATVDPETRRIIDRRCGR 113
                                    899**************************************************965************************ PP

                                    -..-TTHHHHHHHT-EEE...TTEEEEEEE-STTEEEEEE......--S-B--S--..SSTTS..........------B CS
                   PhosphMutase  80 i.steeakeLikalneel.e.egvevkfypgveyrhllvl......lsdkitdtdpphdkegk..........eikellp 140
                                      s+eea+eL++al++     ++ ++++ ++v++r+++v+      lsd++ +tdp+++k g            ++e+ p
  gi|119719954|ref|YP_920449.1| 114 NlSSEEARELARALDGVDlGvHDGYARVVATVGHRAVVVIgsrsrrLSDNVGNTDPAYEKRGYvsvakpsfepFVAEARP 193
                                    99**************99966899**********************************9999999999999988899999 PP

                                    S..SGGGHHHHHHHHHHHHHHHHHHHHSHHH CS
                   PhosphMutase 141 l.kseeaketaellnelieksqeiLedhpvN 170
                                    l +seea++ta+l+n+++e s ++L+ hpvN
  gi|119719954|ref|YP_920449.1| 194 LdDSEEARRTADLVNAFTELSIRVLRGHPVN 224
                                    98899*************************9 PP

>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.5   0.0   7.8e-35   3.5e-31       2     234 ..       2     405 ..       1     410 [. 0.95

  Alignments for each domain:
  == domain 1  score: 108.5 bits;  conditional E-value: 7.8e-35
                                    EEEEEEETTBB----GGGTTHHHS--HHHHHHHHH.......SEEEEEESSSTT----HHHHHHHH.............. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............. RF
                  Metalloenzyme   2 kvvlvvlDGlGeapadelnaihvAktPtldkLkkeaPerwlikahgtavglpeddmgnsevgHlel.............. 67 
                                    k+v +vlDG++++p+d   +++vA++P ld  + +       +a+g+ +++  +  + s+ + +++              
  gi|119719954|ref|YP_920449.1|   2 KLVYLVLDGVADKPEDGPTSLEVARKPALDGVASK-------SACGLVYTVGRGVAPESDAAVFSIlgydphteytgrgp 74 
                                    67889*****************************9.......8*****************888888888888888***** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                  Metalloenzyme  68 ................................................................................ 67 
                                                                                                                    
  gi|119719954|ref|YP_920449.1|  75 ieavgagleiregfevafranfatvdpetrriidrrcgrnlsseearelaraldgvdlgvhdgyarvvatvghravvvig 154
                                    ******************************************************************************** PP

                                    .......................................................................HHHHTT--- CS
                                    .......................................................................xxxxxxxxx RF
                  Metalloenzyme  68 .......................................................................lrisetvkf 76 
                                                                                                            r  e++ +
  gi|119719954|ref|YP_920449.1| 155 srsrrlsdnvgntdpayekrgyvsvakpsfepfvaearplddseearrtadlvnaftelsirvlrghpvnmARAREGKLP 234
                                    **********************************************************************99999***** PP

                                    --EEEEEE.EE-S---SSHHHHHT--EEEE--SHH....................STT--HHHHHHHHHHHH.CC.-SEE CS
                                    xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx....................xxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Metalloenzyme  77 ahvtffwn.ggrsgyfnpleereeipsdtvitfdl....................qpemkavevaekaldailsgkfdlv 135
                                    a+ +++++ ggr ++++ ++e+++++   v+++ +                     ++ ++ +  e++l+ +  ++ d+v
  gi|119719954|ref|YP_920449.1| 235 ANAILLRDsGGRLPRLQRISEKYGLRFGAVAEMPVeigiarilgmdmasvpppseDKAKDYADRLEATLKLL--ERNDVV 312
                                    ****998538999***************************************77666666667777777777..456*** PP

                                    EEEE-HHHHHHHTT-HHHHHHHHHHHHH.HHHHHHTTS-TTTEEEEEE-SSB--TTTSS........-----EEEEEEST CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Metalloenzyme 136 vvniknaDmvGHtgdleatiaaieaaDe.avkeildaieqvdgilvvtADHgnaedmvkrdkqplTsHtlepVPilivgk 214
                                    +v++k +D+ GH+gdl+++++aiea+D+  ++ +l +i+   + l+vtADH ++ + +         Ht +pVP++++ +
  gi|119719954|ref|YP_920449.1| 313 YVHLKGPDEPGHDGDLKRKVEAIEAIDKyYLAPLLREIDPATTALLVTADHATPYTRKS--------HTDDPVPLALMAP 384
                                    ****************************99***********************999888........************* PP

                                    T----S--S.SHHHHTT-TTE CS
                                    xxxxxxxxx.xxxxxxxxxxx RF
                  Metalloenzyme 215 glapdkvke.gakfrekggLa 234
                                    g++pd v + ++k++++g+L+
  gi|119719954|ref|YP_920449.1| 385 GVTPDGVPRfTEKECSRGSLG 405
                                    *******999*******9997 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   4.5e-07     0.002     156     234 ..     295     365 ..     163     383 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4.5e-07
                                    HHHCHTHSHHHHHCT.SSESEEEEEECCCHHHHHHH-TTSHHHHHHHHHHHH.HHHHHHHHHHHTTGTTTEEEEEEES-- CS
                   Phosphodiest 156 wldaafakvvlekel.ekpdlllvyleetDtvgHkfGpdspevedalrrvDk.aigdLlealderglsaetniilvSDHG 233
                                    + d+ +a    +++l e+ d+++v+l ++D  gH    d +   +a++ +Dk +++ Ll+++d+     +t++++++DH 
  gi|119719954|ref|YP_920449.1| 295 YADRLEA----TLKLlERNDVVYVHLKGPDEPGHDG--DLKRKVEAIEAIDKyYLAPLLREIDPA----TTALLVTADHA 364
                                    3333333....34447******************65..4333457899999945**********9....**********6 PP

                                    - CS
                   Phosphodiest 234 m 234
                                     
  gi|119719954|ref|YP_920449.1| 365 T 365
                                    5 PP

>> PglZ  PglZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   3.6e-05      0.16     103     174 ..     300     370 ..     290     372 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.6e-05
                           PglZ 103 derrellkdkevvyivhnkvDalgdkasteqksfeaveeslk..elkelvkslleengykvlltaDHGfiyqrg 174
                                    ++ ++ll+ ++vvy+ +   D+ g+    + +  ea+ e++    l+ l++++  + ++ +l+taDH + y r+
  gi|119719954|ref|YP_920449.1| 300 EATLKLLERNDVVYVHLKGPDEPGHDGDLK-RKVEAI-EAIDkyYLAPLLREIDPA-TTALLVTADHATPYTRK 370
                                    45566999*****************44433.334444.45554689*******999.**********9988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 3334.99
//
Query:       gi|119719955|ref|YP_920450.1|  [L=271]
Description: 4-vinyl reductase, 4VR [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-05   24.3   0.1    4.3e-05   23.4   0.1    1.5  1  V4R       V4R domain
  ------ inclusion threshold ------
      0.011   15.5   0.0      0.021   14.6   0.0    1.5  1  ACT       ACT domain
      0.011   15.5   0.0      0.017   14.9   0.0    1.3  1  UPF0669   Putative cytokine, C6ORF120
      0.054   13.3   0.7      0.068   13.0   0.1    1.6  2  ACT_5     ACT domain


Domain annotation for each model (and alignments):
>> V4R  V4R domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.1   9.6e-09   4.3e-05       2      61 ..     205     267 ..     204     268 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 9.6e-09
                                    -EEEEEES-S-TT---SS---HHHHHHHHHHHHHHHSSE...EEEEEEE-GGGT-SSEEEEEE CS
                            V4R   2 elsieespelaglpgkeePvCyleaGllagalsellgkr...veveEveCaaeGhdhCeFeve 61 
                                    ++++++  e+++l+g e P+ ++  G lag++s+l g +   v veE +C  +G+++Ce +++
  gi|119719955|ref|YP_920450.1| 205 VVKVYDGTEAKALKGTEVPAEFITKGMLAGLVSGLWGAPygeVWVEEKKCVLRGDEYCETHLK 267
                                    7899999**************************99997622267**************98775 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   4.8e-06     0.021      10      39 ..      34      63 ..      26      81 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.8e-06
                                   STTHHHHHHHHHHHTTSEEEEEEEEEESTT CS
                            ACT 10 rPGlLarvfgaladrgiNidsieqrssedk 39
                                   ++G+L r++ ++ +++++i    ++ s+++
  gi|119719955|ref|YP_920450.1| 34 EVGVLERILEVFRRANVSILTFKVSGSRPG 63
                                   79***********************99997 PP

>> UPF0669  Putative cytokine, C6ORF120
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   3.8e-06     0.017      72     130 ..     153     211 ..     145     230 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.8e-06
                        UPF0669  72 lyvsdstlkpsfdeyelqsvtcgadvvsipahfrrpvgigiyghpshlesefelkvyyd 130
                                    +y s ++ +  fdey    ++  +d + + +++ r  g+g++   s+ e e  +kvy  
  gi|119719955|ref|YP_920450.1| 153 FYSSFQAARRVFDEYIAPKSSKLEDRLLLVEEILRVFGLGVFKVSSYSEREVVVKVYDG 211
                                    5888889999******9999999*********************************854 PP

>> ACT_5  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   1.5e-05     0.068       3      26 ..      35      58 ..      33      99 .. 0.81
   2 ?   -3.2   0.1       1.8   7.9e+03       6      20 ..     182     196 ..     181     198 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.5e-05
                          ACT_5  3 pgvLeRvlrvvrrrgFevkslnms 26
                                    gvLeR+l v+rr  +++ + ++s
  gi|119719955|ref|YP_920450.1| 35 VGVLERILEVFRRANVSILTFKVS 58
                                   59************9999876665 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.8
                          ACT_5   6 LeRvlrvvrrrgFev 20 
                                    +e +lrv+    F+v
  gi|119719955|ref|YP_920450.1| 182 VEEILRVFGLGVFKV 196
                                    677999997777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       262  (0.0146132); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1759.71
//
Query:       gi|119719956|ref|YP_920451.1|  [L=146]
Description: MarR family transcriptional regulator [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.7e-05   24.8   0.6    3.1e-05   24.0   0.6    1.5  1  HTH_9        RNA polymerase III subunit RPC82 helix-turn-heli
    0.00087   19.1   0.2     0.0014   18.5   0.2    1.3  1  TrmB         Sugar-specific transcriptional regulator TrmB
     0.0098   15.8   0.1      0.098   12.6   0.1    2.3  2  MarR_2       MarR family
  ------ inclusion threshold ------
      0.013   15.3   0.2      0.038   13.9   0.2    1.7  1  HTH_5        Bacterial regulatory protein, arsR family
      0.015   15.0   0.0       0.19   11.4   0.0    2.0  2  DUF4423      Domain of unknown function (DUF4423)
      0.016   15.1   0.0      0.027   14.3   0.0    1.5  1  TFIIE_alpha  TFIIE alpha subunit
      0.046   13.5   0.9      0.073   12.9   0.2    1.8  2  HTH_IclR     IclR helix-turn-helix domain
      0.097   12.8   0.9       0.24   11.5   0.9    1.7  1  DprA_WH      DprA winged helix domain


Domain annotation for each model (and alignments):
>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.6   1.4e-08   3.1e-05      11      60 ..      18      68 ..       8      70 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1.4e-08
                                   STTHHHHHHHHH.HHHSSBEHHHHHHHHSSTHHHHHHHHHHHHHTTSEEEE CS
                          HTH_9 11 FGevvakVvetL.lrkgrltlrelvkktkLsldqVkksLvvLiqhrlVqyl 60
                                   +Ge ++kV  +L l++  l+  elvk+t+ sl+qV ++L+ L+ +++V+++
  gi|119719956|ref|YP_920451.1| 18 LGEAASKVLAVLvLSEHPLSQLELVKATGYSLSQVSSALAFLTGLGFVSFV 68
                                   8********99956999*********************************8 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.2     6e-07    0.0014       3      62 ..      15      76 ..      12      80 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 6e-07
                                   HCHHHHHCCCHCHHHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES.STTTEE CS
                           TrmB  3 klGLseyEakvYlaLl.klgpatadeiaeelgvprskvYevLrsLedkGlVerek.grpklY 62
                                    l L e  +kv ++L+ ++ p++  e+ +++g + s+v ++L  L   G+V  ++ gr+klY
  gi|119719956|ref|YP_920451.1| 15 RLELGEAASKVLAVLVlSEHPLSQLELVKATGYSLSQVSSALAFLTGLGFVSFVRsGRKKLY 76
                                   68899999********9***********************************9994557777 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.1   4.4e-05     0.098      10      56 ..      25      70 ..      18      74 .. 0.86
   2 ?    0.4   0.0      0.27   6.1e+02      23      31 ..      85      93 ..      75      94 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.4e-05
                                   HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                         MarR_2 10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                   vLa+L  ++ + l++ el++++g+s s vs +l+ L   G+v  +++
  gi|119719956|ref|YP_920451.1| 25 VLAVLVLSEHP-LSQLELVKATGYSLSQVSSALAFLTGLGFVSFVRS 70
                                   77777777776.9*****************************98876 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.27
                                   EHHHHHHHH CS
                         MarR_2 23 tvgelarrl 31
                                    vge+arr+
  gi|119719956|ref|YP_920451.1| 85 LVGEIARRM 93
                                   599****97 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   1.7e-05     0.038       5      46 ..      25      66 ..      23      66 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.7e-05
                                   HHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_5  5 lkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                   +  +  L+e +l+  el++++g s s vS  L++L  +G+V+
  gi|119719956|ref|YP_920451.1| 25 VLAVLVLSEHPLSQLELVKATGYSLSQVSSALAFLTGLGFVS 66
                                   5567889*********************************96 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   8.4e-05      0.19      37     117 ..      36     113 ..      21     119 .. 0.75
   2 ?    5.5   0.1    0.0056        13      15      58 ..      91     132 ..      77     134 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.4e-05
                        DUF4423  37 adpeelakrlrpkisaeevekalefLlklgllkkded..gkyrqtekslttssevkseavrsyhkqmlelAiealervpk 114
                                     +  el k+++   s ++v++al fL+ lg++   ++  +k+  +ek++t   +   e +r +  q ++  i+ le++p 
  gi|119719956|ref|YP_920451.1|  36 LSQLELVKATG--YSLSQVSSALAFLTGLGFVSFVRSgrKKLYYSEKNIT---DLVGEIARRMLEQDIKPLIRELEKMPE 110
                                    55678899999..9*****************9755552277888888888...777788888888887777777777776 PP

                        DUF4423 115 eeR 117
                                    ++ 
  gi|119719956|ref|YP_920451.1| 111 KRE 113
                                    655 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0056
                        DUF4423  15 feyfssWyypvirellplkdfkadpeelakrlrpkisaeeveka 58 
                                     +++++ + p irel +++++++ ++ l + ++  + ae+ +k+
  gi|119719956|ref|YP_920451.1|  91 RRMLEQDIKPLIRELEKMPEKRERIRLLLDDCN--LAAEKLQKS 132
                                    458899999************************..999999986 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.2e-05     0.027       2      98 ..       8     107 ..       7     114 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.2e-05
                                    HHHHHHHH.CS-HHHHHHHHHHH.CTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEE.TTTEEEEEEEEEEC CS
                    TFIIE_alpha   2 llkevvrk.fygeeavlvldvLl.ekgevteedlakelkidlnelrklLnrLyearlvkykrrrd.eekswykyywriny 78 
                                    ll+ ++ + + ge a +vl vL+ ++  ++  +l k ++  l ++ ++L+ L + ++v+++r+        +k+   +  
  gi|119719956|ref|YP_920451.1|   8 LLARLISRlELGEAASKVLAVLVlSEHPLSQLELVKATGYSLSQVSSALAFLTGLGFVSFVRSGRkKLYYSEKNITDLVG 87 
                                    5555555515689999****996267789*******************************99754233333444444445 PP

                                    CCHCCCHHHHHHHHHHHHHH CS
                    TFIIE_alpha  79 eklvdvvkrkleevvkkLee 98 
                                    e +  ++ + ++ ++++Le+
  gi|119719956|ref|YP_920451.1|  88 EIARRMLEQDIKPLIRELEK 107
                                    55556666666666666665 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   3.3e-05     0.073       8      49 ..      25      66 ..      20      69 .. 0.87
   2 ?   -3.2   0.0       3.4   7.7e+03      23      27 ..      88      92 ..      86      96 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.3e-05
                                   HHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                       HTH_IclR  8 iLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                   +L  l     +l+  el ++tg + S v+  L+ L+ lG+v 
  gi|119719956|ref|YP_920451.1| 25 VLAVLVLSEHPLSQLELVKATGYSLSQVSSALAFLTGLGFVS 66
                                   666666677889999*************************96 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.4
                                   HHHHH CS
                       HTH_IclR 23 elArr 27
                                   e+Arr
  gi|119719956|ref|YP_920451.1| 88 EIARR 92
                                   67765 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.9   0.00011      0.24      12      46 ..      20      56 ..       8      59 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00011
                        DprA_WH 12 dlerrvLaaL..gpePvhvDqLvrrtglpaaevsaaL 46
                                   + + +vLa L  +  P++  +Lv++tg + ++vs+aL
  gi|119719956|ref|YP_920451.1| 20 EAASKVLAVLvlSEHPLSQLELVKATGYSLSQVSSAL 56
                                   667788888777999*********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       709  (0.0395449); expected 358.6 (0.02)
Passed bias filter:                      604  (0.0336884); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 908.65
//
Query:       gi|119719957|ref|YP_920452.1|  [L=191]
Description: hypothetical protein Tpen_1049 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-27   96.2  26.6    1.9e-27   96.1  26.6    1.0  1  DUF998        Protein of unknown function (DUF998)
  ------ inclusion threshold ------
      0.028   14.4   1.7      0.028   14.4   1.7    1.9  1  Borrelia_P13  Borrelia membrane protein P13


Domain annotation for each model (and alignments):
>> DUF998  Protein of unknown function (DUF998)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.1  26.6   2.1e-31   1.9e-27       2     185 .]      14     186 ..       9     186 .. 0.94

  Alignments for each domain:
  == domain 1  score: 96.1 bits;  conditional E-value: 2.1e-31
                         DUF998   2 aaallalavilaaallrpgydplrhaiSeLgaeggpggwlfnaglvllgllvlalavgllraargragragrlllavagl 81 
                                    +a +++ +v++++a  +p +++ +ha+S+Lg+++++++w+fn+gl+++gllv+++++g+l a++++ + ++++ll vag+
  gi|119719957|ref|YP_920452.1|  14 LAFAAFPVVVYFSASSNPWWSLYKHAFSDLGGPRAANPWIFNYGLMAMGLLVVVYSFGVLLASKTKYESFAAGLLFVAGV 93 
                                    455666777*********************************************************************** PP

                         DUF998  82 glvlagvfptdpgggspslsglvHglasavaflalavavlllasaarrrawallrlvggvallllvaalvwllaa....a 157
                                    +l+l+g++p ++          +H+++s++++l+ ++a  +l+      ++ ll+ + +v+++ll+++lv + +     a
  gi|119719957|ref|YP_920452.1|  94 FLFLIGYYPSGTK---------PHTFVSLWFYLQSFIASTALG------IALLLSGRKAVGTALLALGLVPVPLGtlieA 158
                                    *************.........9********************......999999999999999999999888888899* PP

                         DUF998 158 ldgslllGlaerllvlaitawllalals 185
                                    ++g+++++++e +++l i a  ++++l+
  gi|119719957|ref|YP_920452.1| 159 TVGWPSVAILELAGALFIGASAIVATLH 186
                                    ********************99999875 PP

>> Borrelia_P13  Borrelia membrane protein P13
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   1.7   3.1e-06     0.028      21      90 ..     113     183 ..     108     188 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.1e-06
                   Borrelia_P13  21 lslGiGsfvqGdyiGGglll.GfdvlGlililaGvikaldgivkkaeaavisgkvlllaGvltlaasylte 90 
                                    l + + sf+    +G +lll G +++G +l+  G +    g   +a++ + s  +l laG l ++as ++ 
  gi|119719957|ref|YP_920452.1| 113 LWFYLQSFIASTALGIALLLsGRKAVGTALLALGLVPVPLGTLIEATVGWPSVAILELAGALFIGASAIVA 183
                                    4567889********99988689*************9******************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.38s 00:00:00.99 Elapsed: 00:00:00.57
# Mc/sec: 1010.98
//
Query:       gi|119719958|ref|YP_920453.1|  [L=228]
Description: hypothetical protein Tpen_1050 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00071   19.6  12.7    0.00071   19.6  12.7    2.0  2  ECF-ribofla_trS  ECF-type riboflavin transporter, S component
  ------ inclusion threshold ------
        5.4    6.8  19.9        0.2   11.4  12.5    2.3  2  DUF2157          Predicted membrane protein (DUF2157)


Domain annotation for each model (and alignments):
>> ECF-ribofla_trS  ECF-type riboflavin transporter, S component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6  12.7   7.9e-08   0.00071       8     158 ..       2     146 ..       1     148 [. 0.76
   2 ?   -0.4   1.1      0.11   9.8e+02     115     161 ..     166     210 ..     147     221 .. 0.52

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 7.9e-08
                                    HHHHHHHHHHHHHHHH---B-S..SS-B..--TTHHHHHHHHHHSS--STHHHHHHHHHHHHHHHSS-GGGHHHHH.HHH CS
                ECF-ribofla_trS   8 vatailaAlvvvltlfisIplp.anteg..sinlgdavlalaallfGpvvGflvGaiGsalaDllsgYgiwapftl.iik 83 
                                     ++a+ aAl++vl+++    l+ +   g   + ++  v a++a+ f p++G+l +aiG +++D+++   + ++ ++ +  
  gi|119719958|ref|YP_920453.1|   2 SLVALCAALYAVLGYLTYLGLFaPVI-GtvRFWPSVFVPATFAVAFSPLIGGLGAAIGIFISDMAVHGNPLLSLSVgVPA 80 
                                    579************98888885444.514677788999*************************7764444444443777 PP

                                    HHHHHHHHHH--S-S-SSH...HHHHHHHHHHHHHHHHHHHHHHHH..........S-HHHHHHHHHHHHHHHHH CS
                ECF-ribofla_trS  84 gliGlivGliakklkknkengvfkilalvlfaivmvigyviaegllpildiiiysepaekvalqsipaniiqavv 158
                                     ++G+ +  ++++l+++ +        ++++ +v ++++v+a   l   +  i  e  ++++++ + ++++ +vv
  gi|119719958|ref|YP_920453.1|  81 NFLGFYAVGAVYRLARDER-------RVLAGIAVELVATVLALSAL--YYARILDESFVVASAVALAFTVTPMVV 146
                                    7888888888888877777.......67888888888888888888..444444667777778888888887776 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.11
                                    HHHHHHHHHHHHHHH..........S-HHHHHHHHHHHHHHHHHHHH CS
                ECF-ribofla_trS 115 aivmvigyviaegllpildiiiysepaekvalqsipaniiqavvgai 161
                                    ai++v+  + +++++  l + +++ pa+++ ++ + + ++ + ++a+
  gi|119719958|ref|YP_920453.1| 166 AIIGVGVWAYSQFFV--LPTGQAQLPAWAALVWFVWTYLTEIPFIAL 210
                                    333333333333333..334444555666655555555555555555 PP

>> DUF2157  Predicted membrane protein (DUF2157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   3.9      0.18   1.6e+03     108     139 ..      83     114 ..       1     128 [. 0.55
   2 ?   11.4  12.5   2.2e-05       0.2      35     142 ..      99     204 ..      83     208 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.18
                        DUF2157 108 aaialvgqifqlsgdaysllllwalllllmay 139
                                     ++  vg ++ l  d   +l+  a+ l+++++
  gi|119719958|ref|YP_920453.1|  83 LGFYAVGAVYRLARDERRVLAGIAVELVATVL 114
                                    23333444444444444444444444333333 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 2.2e-05
                        DUF2157  35 leallvlGalllglGlilfvAanWqglsrlvkfllllvllllslllgavlwrdrrvpprlgeallllaalllgaaialvg 114
                                    +++l+++++ l+ + ++ + A  ++++  ++ f+++ +++l++ ++ +v+ r++r+  + g   l+l++ ++g++++  +
  gi|119719958|ref|YP_920453.1|  99 RRVLAGIAVELV-ATVLALSALYYARIL-DESFVVASAVALAFTVTPMVVARQSRRIVFAGSTGLMLGSAIIGVGVWAYS 176
                                    567777765554.558888888888888.5566666666666665556777777899999******************** PP

                        DUF2157 115 qifqlsgdaysllllwalllllmayllr 142
                                    q f l +   +l ++ al+ +++ yl++
  gi|119719958|ref|YP_920453.1| 177 QFFVLPTGQAQLPAWAALVWFVWTYLTE 204
                                    ***********************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       648  (0.0361426); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 1411.80
//
Query:       gi|119719959|ref|YP_920454.1|  [L=296]
Description: GHMP kinase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.5e-08   32.2   6.5    1.8e-07   31.3   5.5    2.0  2  GHMP_kinases_N  GHMP kinases N terminal domain
      2e-06   28.1   0.1    5.9e-06   26.6   0.1    1.9  1  GHMP_kinases_C  GHMP kinases C terminal


Domain annotation for each model (and alignments):
>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   5.5     2e-11   1.8e-07       2      62 ..      86     146 ..      85     150 .. 0.84
   2 ?    1.3   0.2     0.046   4.1e+02       8      29 ..     134     155 ..     131     156 .. 0.82

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 2e-11
                                    EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHHHHHHHHHHHHHHHHHHHHHSHHHHHH CS
                 GHMP_kinases_N   2 ivikseiPvgaGLGSSAAlavalvaAllallglsleeaklaleaerlaqggngsggDvaas 62 
                                    ++++  +Pvg GLG S+A a+a+++Al +llgl+l  ++la +a+ + ++ +++ g v+  
  gi|119719959|ref|YP_920454.1|  86 VRVDVSVPVGGGLGTSGASALATALALGKLLGLKLGYMELARVAHVAEVKNRTGLGTVSGL 146
                                    6788899*************************99988999999997777677777655555 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.046
                                    SHTTSSSCHHHHHHHHHHHHHH CS
                 GHMP_kinases_N   8 iPvgaGLGSSAAlavalvaAll 29 
                                    +   +GLG  + l+v++++ +l
  gi|119719959|ref|YP_920454.1| 134 VKNRTGLGTVSGLVVGGAVVVL 155
                                    55679***********998775 PP

>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.1   6.6e-10   5.9e-06      10      83 ..     214     279 ..     195     281 .. 0.79

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 6.6e-10
                 GHMP_kinases_C  10 lellgellnlsqrselkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkdeaeqvaralreef 83 
                                    +e ++e   ++       ++g  +p+++++ ++++elG  +++  +a  G+t f l+  +d++e++ ral+e +
  gi|119719959|ref|YP_920454.1| 214 IEKFAEVSKRFSL-----ETGLATPNVRKAFKLAEELG--AVGAGQAQIGDTAFLLV-YEDKVERASRALSEMG 279
                                    3444444444444.....8999****************..777777777********.************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1996.50
//
Query:       gi|119719960|ref|YP_920455.1|  [L=90]
Description: acylphosphatase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.3e-28   96.5   0.0      1e-27   96.3   0.0    1.0  1  Acylphosphatase  Acylphosphatase


Domain annotation for each model (and alignments):
>> Acylphosphatase  Acylphosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.3   0.0   5.7e-32     1e-27       2      85 .]       4      87 ..       3      87 .. 0.98

  Alignments for each domain:
  == domain 1  score: 96.3 bits;  conditional E-value: 5.7e-32
                Acylphosphatase  2 rllvtGrVQgvgFRkfvrrlAkelglkGyvrNlsdgsVeivaegeeekvekfleelksgppkarvdeveveeleeeeefkdF 83
                                   +++v+G VQgv+FR+ +++ A++lg++G+vrNl+dg+Ve+v+egee +v k++e+ ++gpp arv++v+ve++e+++ef+dF
  gi|119719960|ref|YP_920455.1|  4 HIYVSGLVQGVFFRASMQEVARSLGVNGWVRNLPDGRVEAVLEGEEGAVLKVIEWARRGPPLARVERVDVEWEEYRGEFRDF 85
                                   799******************************************************************************* PP

                Acylphosphatase 84 ei 85
                                    i
  gi|119719960|ref|YP_920455.1| 86 YI 87
                                   76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 637.42
//
Query:       gi|119719961|ref|YP_920456.1|  [L=397]
Description: MoeA domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-33  114.9   0.2    4.2e-33  114.3   0.2    1.2  1  MoeA_N         MoeA N-terminal region (domain I and II)
    1.9e-18   66.4   0.6    2.4e-16   59.7   0.2    2.6  2  MoeA_C         MoeA C-terminal region (domain IV)
    6.4e-17   61.5   0.0      1e-16   60.9   0.0    1.3  1  MoCF_biosynth  Probable molybdopterin binding domain


Domain annotation for each model (and alignments):
>> MoeA_N  MoeA N-terminal region (domain I and II)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.3   0.2     7e-37   4.2e-33      13     154 ..      14     164 ..       3     167 .. 0.88

  Alignments for each domain:
  == domain 1  score: 114.3 bits;  conditional E-value: 7e-37
                                    H-.HH-EEE.EEGGCG-TT-BBSS-EE-SS-BSSS-EESSSEEEEEEBTTB--....................-S---TT CS
                         MoeA_N  13 al.eleeee.vplaaealgrvlaedvvApedvPpfdnSamDGYAvraeagsgaseeep.........saageeperllpg 81 
                                    +l + +++e vp+ +++lgr +ae vv++ ++Pp  +S +DGYAvrae+ + as+  p          + g++++ +lp+
  gi|119719961|ref|YP_920456.1|  14 LLsR-PPAEsVPV-LDSLGRYSAETVVSSFKLPPAPKSVVDGYAVRAEDVEPASPGAPvtlrllegvLRPGSTEGFELPR 91 
                                    4433.44555***.9***************************************9999*********9999999999999 PP

                                    -.EEEE-TTSB--TT--EEEEGGGE.E....EETTE...S--STTTTEE-TTSSB-TTSEEE-TTBB--CCCHHHHH CS
                         MoeA_N  82 g.avrimTGaplPegadaVvpvEdteeeeaketvev...kavkpgenvrraGedikaGevllragtrltpaeiglla 154
                                    g avr++TGa lP gadaVvpvEd+  ee  +   v   + v++ env   Ge++++G  ++r g+r++p+++++l 
  gi|119719961|ref|YP_920456.1|  92 GsAVRVETGALLPVGADAVVPVEDAL-EEDGR---VhlfRRVARYENVSLPGEEYEEGVPIVRVGDRIQPHHLSALV 164
                                    99**********************95.22233...234589999*****************************9985 PP

>> MoeA_C  MoeA C-terminal region (domain IV)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.5   0.0    0.0068        40      49      71 ..      52      74 ..      51      75 .. 0.91
   2 !   59.7   0.2     4e-20   2.4e-16       1      71 [.     321     391 ..     321     392 .. 0.98

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0068
                                   -EEEEE-TT--EE-TT-EEEEEE CS
                         MoeA_C 49 nglivipegtegleaGeeVevil 71
                                   +g++v  e++e +++G+ V   l
  gi|119719961|ref|YP_920456.1| 52 DGYAVRAEDVEPASPGAPVTLRL 74
                                   9******************8766 PP

  == domain 2  score: 59.7 bits;  conditional E-value: 4e-20
                                    EEEESS-EE--SSS-EEEEEEEES-S-EEEEEE-S---TT-GGGCTT--EEEEE-TT--EE-TT-EEEEEE CS
                         MoeA_C   1 karlaedlksdpgrreflRvilteedgeyvaeptgkqgSglLsslaeAnglivipegtegleaGeeVevil 71 
                                    karl+++++ ++g   f Rv++  e+g + aep+  +gSg+L+sl + ng++++peg eg+++GeeVev+l
  gi|119719961|ref|YP_920456.1| 321 KARLTRRITVKAGVVGFARVRVYREGGTLLAEPVMLGGSGALASLLRGNGYVIVPEGLEGYDEGEEVEVHL 391
                                    79*******************************************************************87 PP

>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.9   0.0   1.7e-20     1e-16       2     143 ..     180     308 ..     179     309 .. 0.89

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 1.7e-20
                                    EEEE-HHHHTTSSGBHHHHHH.HHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTSSEEEEESS-SSSTT--HHHHHHH CS
                  MoCF_biosynth   2 vitvGdellsgkieDtngpll.aellkelgvevskytvvpDdeeeikeallaaleeadviittGGtGptpdDvtpealak 80 
                                    ++ vGde++ g++    +++l a++l++lg++v +++v pD +e+++e      +++ ++++ GGt+++  D+t++al+ 
  gi|119719961|ref|YP_920456.1| 180 ILNVGDEIVGGTYFRPFTHFLvASWLRSLGFRVTDVSVAPDSPEAVAEWA--GSRGEWLVVILGGTSMGGHDFTVKALES 257
                                    8999*******99888888873679**********************987..446779********************** PP

                                    HHSEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EETTEEEEE-SSHHHHHHHHHHHHHGGHH CS
                  MoCF_biosynth  81 lfekelegfeeafrrvslkpgkpvgvapgailsravgktiigLPGspkavkealeeillpale 143
                                    l+ +       ++++++l+pgk   +a++a+ +++     ++  G p+a+  +le++l+p l+
  gi|119719961|ref|YP_920456.1| 258 LGPE------YIVHGLALQPGK---TACVAVKGGR---LYLAASGLPVAALSTLEVFLRPLLR 308
                                    ***8......************...7777666654...577*******************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2761.23
//
Query:       gi|119719962|ref|YP_920457.1|  [L=651]
Description: molybdenum cofactor synthesis domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-52  177.3   0.3    3.5e-52  176.3   0.3    1.5  1  PBP_like       PBP superfamily domain
    1.6e-37  128.7   0.4      8e-37  126.4   0.7    2.0  2  MoeA_N         MoeA N-terminal region (domain I and II)
    5.5e-21   74.7   0.0    3.7e-20   72.1   0.0    2.3  3  MoCF_biosynth  Probable molybdopterin binding domain
    1.1e-09   38.4   0.7    5.9e-09   36.0   0.1    2.6  2  MoeA_C         MoeA C-terminal region (domain IV)
  ------ inclusion threshold ------
      0.037   13.7   0.0         12    5.5   0.0    2.6  3  PBP_like_2     PBP superfamily domain


Domain annotation for each model (and alignments):
>> PBP_like  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.3   0.3   9.9e-56   3.5e-52      12     192 ..     440     625 ..     435     626 .. 0.95

  Alignments for each domain:
  == domain 1  score: 176.3 bits;  conditional E-value: 9.9e-56
                                    EEEEEES-HHHHHHHHHTTS-SEEEESS---CCCHHCCCCCEEEEEEEEEEEE-CC-HCHCCCCHCCHHHS--BGGGC-S CS
                       PBP_like  12 rvavanvGsggGlkalrageadiagshlldketeeynapalrkaldgievvlvnlarreqglvvakgnpkkitnwkdlad 91 
                                    +v+v nvGs++Gl+a++ g adiag+hlld+et+eyn+p+++++  + ++vlv++++reqg+v++k+    +++++++ +
  gi|119719962|ref|YP_920457.1| 440 EVRVVNVGSLAGLQAVKSGVADIAGTHLLDPETGEYNVPYVKRLGIR-DAVLVKGYKREQGFVYRKE-VGPVSSFAEVIE 517
                                    589***************************************98777.69*****************.668********* PP

                                    -B-EEEEE-TTSHHHHHHHHHHC-CEECT........E-SSTTSEEESSHHHHHCCHCCETTCCECCCGG-HCCCCCCEC CS
                       PBP_like  92 aplrlvnRetGSGtrdlfdellkkegisk........ssikgyaqearshlavaaaVaagradvgvgieavaeelkgldf 163
                                     ++r+vnR+ GSGtr+l d+ll++e  +k        +++kgy+ e+++h ava  V++g advgv+++ vae+ +gl+f
  gi|119719962|ref|YP_920457.1| 518 GGYRFVNRNPGSGTRVLVDHLLEEEARGKgvdaaelkERLKGYSFEVKTHEAVAYLVSRGVADVGVAVRYVAER-YGLGF 596
                                    **********************98855558888***************************************98.7**** PP

                                    TTCE-EEEEEEEECTCCCSHHHHHHHHHH CS
                       PBP_like 164 vplaeerydlvvrkealddpevqaflefl 192
                                    + la e+ydl+vrke l++ +v++++e+l
  gi|119719962|ref|YP_920457.1| 597 TYLASEEYDLLVRKESLEKSAVKRIIEAL 625
                                    **************************998 PP

>> MoeA_N  MoeA N-terminal region (domain I and II)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.4   0.7   2.2e-40     8e-37      16     157 .]      25     176 ..      10     176 .. 0.86
   2 ?   -1.7   0.0      0.59   2.1e+03      50      63 ..     386     399 ..     384     435 .. 0.69

  Alignments for each domain:
  == domain 1  score: 126.4 bits;  conditional E-value: 2.2e-40
                                    H...-EEEEEGGCG-TT-BBSS-EE-SS-BSSS-EESSSEEEEEEBTTB--...................-S---TT-.E CS
                         MoeA_N  16 l...eeeevplaaealgrvlaedvvApedvPpfdnSamDGYAvraeagsgaseeep........saageeperllpgg.a 83 
                                    l      e+p+ +ea+grvlae+v +p ++Pp++++ +DGYAvr+++  g  e++p        + +ge++  ++ +g +
  gi|119719962|ref|YP_920457.1|  25 LvplGVVELPV-SEAVGRVLAENVFSPLNYPPYTRALVDGYAVRSDDLVGVYEDRPrklrlvgkVSTGETRLVTIGRGeC 103
                                    34435566999.99**************************************************888888888888888* PP

                                    EEE-TTSB--TT--EEEEGGGE.E....EETTE...S--STTTTEE-TTSSB-TTSEEE-TTBB--CCCHHHHHHCT CS
                         MoeA_N  84 vrimTGaplPegadaVvpvEdteeeeaketvev...kavkpgenvrraGedikaGevllragtrltpaeigllasvG 157
                                    v++ TGa++P  adaVvpvE+t++ e  e   v   ++v++genv  aG+d+++Gev++ +gt+ltp   ++la++G
  gi|119719962|ref|YP_920457.1| 104 VEVSTGAVVPYPADAVVPVEYTHQ-EGGE---VtfyRSVARGENVDAAGSDVAEGEVVAWKGTQLTPTLAATLAALG 176
                                    **********************62.2233...234689*************************************98 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.59
                                    SSEEEEEEBTTB-- CS
                         MoeA_N  50 mDGYAvraeagsga 63 
                                    +DG+Av  e+ + a
  gi|119719962|ref|YP_920457.1| 386 VDGFAVIPENLEYA 399
                                    8*****54444443 PP

>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.1   0.0     1e-23   3.7e-20       2     142 ..     190     325 ..     189     327 .. 0.93
   2 ?   -4.1   0.0       3.2   1.1e+04     107     133 ..     357     383 ..     354     384 .. 0.68
   3 ?   -1.2   0.0       0.4   1.5e+03      74     101 ..     566     593 ..     563     608 .. 0.85

  Alignments for each domain:
  == domain 1  score: 72.1 bits;  conditional E-value: 1e-23
                                    EEEE-HHHH.......TTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTSSEEEEESS-SSSTT--H CS
                  MoCF_biosynth   2 vitvGdell.......sgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleeadviittGGtGptpdDvt 74 
                                    ++ +G+el         g+++D+n+ +++++ k +g+e + y   +D+  e++e l++al+e+dv+ t+GGt+++p D++
  gi|119719962|ref|YP_920457.1| 190 IVPTGNELRqpgepleYGQVYDSNSTMVYAYAKLAGAEPKVYPRARDELGEVEEVLHRALDENDVVATIGGTSAGPEDLV 269
                                    7889999999999999****************************************9999******************** PP

                                    HHHHHHHHSEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EETTEEEEE-SSHHHHHHHHHHHHHGGH CS
                  MoCF_biosynth  75 pealaklfekelegfeeafrrvslkpgkpvgvapgailsravgktiigLPGspkavkealeeillpal 142
                                    ++al++l         +++++v+ kpg+p+ va +   +++    ++ LPG+p ++  ++ ++llp++
  gi|119719962|ref|YP_920457.1| 270 YRALSRLDPG------IILHGVREKPGRPLAVALH---GEK---IVFSLPGFPMSCLLTVNLYLLPVI 325
                                    *******885......*************999998...543...699************999998876 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 3.2
                                    GGGGGGE.EETTEEEEE-SSHHHHHHH CS
                  MoCF_biosynth 107 apgailsravgktiigLPGspkavkea 133
                                    +p++  +r+ ++  + LPG ++ v  +
  gi|119719962|ref|YP_920457.1| 357 VPVILAERGGRQAAFPLPGHSGRVSLM 383
                                    566666666455699999999887765 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.4
                                    HHHHHHHHHSEE-HHHHHHHHHHHHHHC CS
                  MoCF_biosynth  74 tpealaklfekelegfeeafrrvslkpg 101
                                    t+ea+a l  + +   ++a+r v+ ++g
  gi|119719962|ref|YP_920457.1| 566 THEAVAYLVSRGVADVGVAVRYVAERYG 593
                                    89*********************99985 PP

>> MoeA_C  MoeA C-terminal region (domain IV)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1      0.78   2.8e+03      54      68 ..     144     158 ..     121     160 .. 0.73
   2 !   36.0   0.1   1.7e-12   5.9e-09       1      70 [.     340     408 ..     340     409 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.78
                                    E-TT--EE-TT-EEE CS
                         MoeA_C  54 ipegtegleaGeeVe 68 
                                    +++ + ++++Ge+V 
  gi|119719962|ref|YP_920457.1| 144 VDAAGSDVAEGEVVA 158
                                    445555677777775 PP

  == domain 2  score: 36.0 bits;  conditional E-value: 1.7e-12
                                    EEEESS-EE--SSS-EEEEEEEES-S-EEEEEE-S---TT-GGGCTT--EEEEE-TT--EE-TT-EEEEE CS
                         MoeA_C   1 karlaedlksdpgrreflRvilteedgeyvaeptgkqgSglLsslaeAnglivipegtegleaGeeVevi 70 
                                    +a++a++l+ ++g r f++vil e +g+  a p+  + Sg++s ++  +g++vipe+ e++ +G e ev 
  gi|119719962|ref|YP_920457.1| 340 RAVIATPLRGEAGIRVFVPVILAERGGRQAAFPL-PGHSGRVSLMVLVDGFAVIPENLEYAPEGSELEVV 408
                                    588999****************************.9*******************************997 PP

>> PBP_like_2  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0         1   3.6e+03      54      82 ..     139     165 ..     121     181 .. 0.67
   2 ?    5.2   0.0    0.0041        15      39      65 ..     440     466 ..     418     480 .. 0.85
   3 ?    5.5   0.0    0.0033        12     133     185 ..     518     572 ..     513     616 .. 0.59

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1
                     PBP_like_2  54 lrngdvdfagsdrplteseiaagwaang.a 82 
                                     r++ vd+agsd +++++ ++a w++++  
  gi|119719962|ref|YP_920457.1| 139 ARGENVDAAGSD-VAEGE-VVA-WKGTQlT 165
                                    455669999999.44444.433.7776643 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0041
                     PBP_like_2  39 kvnyastGSgagikalrngdvdfagsd 65 
                                    +v++  +GS ag++a+++g +d+ag++
  gi|119719962|ref|YP_920457.1| 440 EVRVVNVGSLAGLQAVKSGVADIAGTH 466
                                    38999********************99 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.0033
                     PBP_like_2 133 gpIkvvhrsdgsgttflfstalaeq.....................gpwtasgigasgsegvasavsnngaigy 185
                                    g+ ++v r++gsg t+++ ++l+e+                     +                  v++  a +y
  gi|119719962|ref|YP_920457.1| 518 GGYRFVNRNPGSG-TRVLVDHLLEEeargkgvdaaelkerlkgysfE------------------VKTHEAVAY 572
                                    5678*********.667778887773333333322222222222221..................233333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (651 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 4590.34
//
Query:       gi|119719963|ref|YP_920458.1|  [L=418]
Description: extracellular solute-binding protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.9e-39  134.3   5.0    9.8e-39  133.8   5.0    1.2  1  SBP_bac_8  Bacterial extracellular solute-binding protein
    6.8e-27   95.2   8.8      1e-26   94.6   8.8    1.3  1  SBP_bac_1  Bacterial extracellular solute-binding protein


Domain annotation for each model (and alignments):
>> SBP_bac_8  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.8   5.0   1.1e-42   9.8e-39       1     276 [.      62     357 ..      62     363 .. 0.84

  Alignments for each domain:
  == domain 1  score: 133.8 bits;  conditional E-value: 1.1e-42
                                    HHHHHHHHH-.TEEEEEEE--SSSHHHHHHHHHHTT---SEE.EEE-HHHHHHHHHTTSB--GG.GSTTHHH..-HHHHH CS
                      SBP_bac_8   1 klakefekkt.gvkvnvvtaasndleqklkaalaagtapdidvvwanedalatlaeeglladls.dldnldd..ltdala 76 
                                    +++++f +k+ ++++ +v+++ ++l +k+  a++ g++pd  ++++++d+ ++l+++g+l+d++ ++   ++  +++al+
  gi|119719963|ref|YP_920458.1|  62 AVIDDFRAKNpNYQIDIVNVPFDQLKNKVIQAVPVGEGPD--LFTGPHDWTGELVQAGALVDITdKVSAFKGeyMESALQ 139
                                    589***********************************96..78999*****************7667776677999*** PP

                                    TT--TS.----EEEEEEE-EEEEEHHHHHHS.---BHHHHHHHHHHH..HHH-SEGG---GGGGGGTHH.ETTEE---H. CS
                      SBP_bac_8  77 avgydgklygvPyasetpyvliynkdllekaedpktwdellaaakkl..kgkfglpdpasgwlqaalla.kdgksldddg 153
                                    +v+++gk+yg+P  +  p +li+nk+ll    +pkt+del+++ +++  kg +gl+ +  + ++   ++  +g+++ d +
  gi|119719963|ref|YP_920458.1| 140 GVTLKGKIYGLPESIKLP-ALIVNKKLLA-T-PPKTLDELWSIMDQFkaKGMYGLAYDVQNAYFSSCWFyGLGAYYLDPN 216
                                    ****************98.**********.5.***********9988335888887777663333333332444443333 PP

                                    .......HHH.HHHHHHHHHHHHTT-EE-S..--SSTTTTTSBSEEEE-TTHHHHHH-T.TT...SEEEE.--......S CS
                      SBP_bac_8 154 ......gkdglkealellkklkdngktydtgadavsefanGevaftingswdiaaaqka.gk...klgai.vp......k 216
                                          +++g ++a+++++k++++     +++ ++++f nG++a++ing+w i +++ka g+   +++++ +p      +
  gi|119719963|ref|YP_920458.1| 217 tletalDSPGAVQAFQIIAKFSKYLPPDISYDMMTNLFMNGKAAMAINGPWWIGDLKKAfGEnlaDIEITlIPaidpahP 296
                                    355788999****************7445789*************************99998445566666566665543 PP

                                    --EEEEEEEEEEBTTS-HHHH..HHHHHHHHHTTSHHHHHHHHHH---BS-S-TTTHHHHHH CS
                      SBP_bac_8 217 qgsfaggkglavpknaknedl..aAldFlkwltspenqaalaektgyipvnksaalspevkk 276
                                      +f  ++ + v+kna ++    +A++++ ++t +++ + la+  g +p+ k+a  +p+v+ 
  gi|119719963|ref|YP_920458.1| 297 ARPFMTVEAVFVTKNAAERGVldEAIALAHYITGEASVK-LAKMAGHVPTWKNAMKDPAVSG 357
                                    45*************999966678*********999988.9**************9999875 PP

>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.6   8.8   1.2e-30     1e-26       4     312 ..      54     332 ..      51     335 .. 0.86

  Alignments for each domain:
  == domain 1  score: 94.6 bits;  conditional E-value: 1.2e-30
                                    HHHHHHHHHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHHHHTTSSSCSEEEECGGHHHHHHHTTSBECCHHHHHHTTE CS
                      SBP_bac_1   4 ltegaalqalvakafekehpgikVeiesvgsgslaqkltlaiaaGdgpaDviavdndwiarlakaglllpldpyvkayla 83 
                                      e++al+a++ ++f +++p++++ i+ v++++l++k++ a+  G gp D++++ +dw+++l++ag+l ++++ v a   
  gi|119719963|ref|YP_920458.1|  54 GGEYDALKAVI-DDFRAKNPNYQIDIVNVPFDQLKNKVIQAVPVGEGP-DLFTGPHDWTGELVQAGALVDITDKVSAF-- 129
                                    556889*****.************************************.************************88885.. PP

                                    CTTCCTEEEEHHHHTHHHHCEEE.ES.EEEEE.EEEEEEETTTHHCTTGGGSHBHHHHHHHHHHHHHHCTCTHCCHCCEE CS
                      SBP_bac_1  84 pgvkdaadklsssvlpkildskv.ly.vPlya.argliYNkdlfekagldppwtWdelveaakklkekgkkpiggarggs 160
                                      + +++ ++ + v+      k+ +y +P      +li+Nk+l++    +pp+t del      +k+kg ++       +
  gi|119719963|ref|YP_920458.1| 130 --KGEYMESALQGVTL-----KGkIYgLPESIkLPALIVNKKLLA----TPPKTLDELWSIMDQFKAKGMYG------LA 192
                                    ..56677776666653.....5589******66************....8899*****99888888888888......** PP

                                    HHHHHHHHHHHHHHHHTGGGEECCCT..HHCSHHHHSHHHHHHHHHHHHHHHHHHHTTEEECSSHHHHHHHHHTTSCSEE CS
                      SBP_bac_1 161 asgtayyfalalakslggkvfdkdgg..gldnpegvtaatylvklyavanltkelkgkgaenkdgaaalalfeaGeaama 238
                                    +  +++yf + ++ +lg+++ d +    +ld+p++v+a++ +           + + + +++ + + +++lf +G+aama
  gi|119719963|ref|YP_920458.1| 193 YDVQNAYFSSCWFYGLGAYYLDPNTLetALDSPGAVQAFQIIA----------KFSKYLPPDISYDMMTNLFMNGKAAMA 262
                                    ***********************75444444444444333333..........6668888999999999*********** PP

                                    EEEHHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEE..EEEEEEEEBTTCST...HHHHHHHHHHHTSHH CS
                      SBP_bac_1 239 ivglwaalaamkvapkvafaadkekpkeelgvaplPagkggkpgi..lgayglaipkgskn...peaAkkFldfllspe 312
                                    i+g+w+          ++++++  ++  +++++ +Pa++++ p+     +  + + k++++    ++A ++  ++++++
  gi|119719963|ref|YP_920458.1| 263 INGPWW---------IGDLKKAFGENLADIEITLIPAIDPAHPARpfMTVEAVFVTKNAAErgvLDEAIALAHYITGEA 332
                                    ******.........89999999999999999**************888888999999999777777999999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       808  (0.0450667); expected 358.6 (0.02)
Passed bias filter:                      684  (0.0381505); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 2816.55
//
Query:       gi|119719964|ref|YP_920459.1|  [L=313]
Description: binding-protein-dependent transport systems inner membrane component [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.3e-17   63.3  20.2    2.3e-17   63.3  20.2    2.0  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   4.5      0.43   7.7e+03      29      50 ..      16      34 ..       8      96 .. 0.59
   2 !   63.3  20.2   1.3e-21   2.3e-17       2     174 ..      93     302 ..      92     307 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 0.43
                   BPD_transp_1 29 slPsfv.laillvlvfvilsilg 50
                                    lP +v la++ ++      ++g
  gi|119719964|ref|YP_920459.1| 16 LLPALVvLAMVSFYP----LVFG 34
                                   333333222222221....1122 PP

  == domain 2  score: 63.3 bits;  conditional E-value: 1.3e-21
                   BPD_transp_1   2 illGilaa...lnrnkkldkllrpliivllslPsfvlaillvlvf......................vilsilghlilpv 56 
                                    +l+G+  a   ++ +  ++++ + ++iv++++P ++ ++ ++++                           +  + + ++
  gi|119719964|ref|YP_920459.1|  93 VLVGVAFAfmlNSDKLLWRRFWQAVFIVPWAVPGYISIMAWFFLYqysygyfnqilmnlgleridwlGQRLDTFWPWVSI 172
                                    677888887766777889******************777777555889****************5554444445555555 PP

                   BPD_transp_1  57 iillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG 136
                                     ++ ++ a p+++ ++ aal++lp+dl  aa+++Ga+ wq+fr+vvlP+++pp+    +l+ +  + ++ ++ +l+++++
  gi|119719964|ref|YP_920459.1| 173 NATNVWLAYPFIMTVTLAALQTLPRDLLDAAKVDGAGGWQTFRYVVLPHIKPPLTIATVLTTITTFQQFGVVWLLTGGGP 252
                                    67889****************************************************************99999997777 PP

                   BPD_transp_1 137 ......lgtllleailgydyseis......nggvlalviavlllnlvadi 174
                                          +gt++  + l + y + +      +g+ +a+ i+++ll++ a i
  gi|119719964|ref|YP_920459.1| 253 qifvkaIGTTIYVTDLLMTYGYRTiwqfgdYGYGAAFSIFLALLVVPASI 302
                                    9*999988888888888888888899****66666666666666665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       687  (0.0383178); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 2041.28
//
Query:       gi|119719965|ref|YP_920460.1|  [L=304]
Description: binding-protein-dependent transport systems inner membrane component [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.9e-22   77.7  14.5    8.9e-22   77.7  14.5    1.8  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.2      0.13   2.3e+03     107     120 ..      13      26 ..       5      41 .. 0.51
   2 !   77.7  14.5   4.9e-26   8.9e-22       2     181 ..      98     295 ..      97     299 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.13
                   BPD_transp_1 107 lppiitglilafgg 120
                                    l ++++ l +a+++
  gi|119719965|ref|YP_920460.1|  13 LLVLVAVLSYAIVY 26 
                                    23333333333333 PP

  == domain 2  score: 77.7 bits;  conditional E-value: 4.9e-26
                   BPD_transp_1   2 illGilaa...lnrnkkldkllrpliivllslPsfvlaillvlvf..........vilsilghlilpviillllsaapyv 68 
                                    +l+G +++    ++n+++++ l++   vl s+P +v +i+l+ ++           + ++   +  ++i+++l +a+py 
  gi|119719965|ref|YP_920460.1|  98 VLVGTMSGyafSRYNFPGKRKLLWTLLVLNSIPGLVTFIPLYRLLvfydqtfraiGLPKGTFLGPGGLILVYLAGAIPYS 177
                                    7889999999999***********************9999776666799***9976777777777779************ PP

                   BPD_transp_1  69 rlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG...lgtllleai 145
                                     ++ +++++++p++l e a+++Ga+++qif+k++lP+alp i+t +il+f g++++++l+ +l+s+     l  ++++ +
  gi|119719965|ref|YP_920460.1| 178 SWFLKSFFDTIPRELDEQALVDGATPFQIFWKITLPLALPGIATIAILVFLGAWNEFMLATLLLSNENyytL-PVFITQL 256
                                    ****************************************************************99864211.1122222 PP

                   BPD_transp_1 146 lgydyseis...nggvlalviavlllnlvadilqrlldp 181
                                     +++y++++    + ++a   a +++++++ + q++l  
  gi|119719965|ref|YP_920460.1| 257 RNQQYASTYggiPAFAAASFMASIPVVILFVVSQKYLKS 295
                                    334444444987666666667777788888888888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2154.49
//
Query:       gi|119719966|ref|YP_920461.1|  [L=367]
Description: phosphate ABC transporter, periplasmic phosphate-binding protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.8e-60  204.4   0.1    3.4e-60  204.1   0.1    1.0  1  PBP_like_2  PBP superfamily domain
    1.6e-16   61.2   1.3      4e-16   59.9   1.3    1.6  1  SBP_bac_1   Bacterial extracellular solute-binding protein
    1.3e-09   37.5   0.0    9.9e-09   34.6   0.0    2.1  1  PBP_like    PBP superfamily domain
  ------ inclusion threshold ------
      0.028   14.2   0.1      0.086   12.6   0.1    1.8  1  HCV_NS4a    Hepatitis C virus non-structural protein NS4a


Domain annotation for each model (and alignments):
>> PBP_like_2  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  204.1   0.1   7.6e-64   3.4e-60       3     281 ..      29     334 ..      26     335 .. 0.89

  Alignments for each domain:
  == domain 1  score: 204.1 bits;  conditional E-value: 7.6e-64
                     PBP_like_2   3 aaeatsvgeifgaGsttpapalrkladafekaapgakvnyastGSgagikalrngdvdfagsdrplteseiaagwaang. 81 
                                    +a+  +   ++g+G+t+p p ++++a  f +++pg+k++ya++GSg+gi +++ng vdfagsd pl ++++    aa++ 
  gi|119719966|ref|YP_920461.1|  29 QAQREVL--LKGSGATFPMPQIQAWAYRFTSKHPGIKIEYAGVGSGQGISDFLNGIVDFAGSDVPLNDQQY---SAARSr 103
                                    3334444..9***************999*****************************************77...344447 PP

                     PBP_like_2  82 aggliqvpvaigaialvvnkd.....nplnlsreaLakIfsgkItnWnd........vlglpadgpIkvvhrsdgsgttf 148
                                    +g+  q p+  g++a+v+n++     ++l+l+ e+La+I+ gkI  W+d        +l+lp  + I +v+rsd sgt +
  gi|119719966|ref|YP_920461.1| 104 FGEVYQLPYILGGVAVVYNVPeikgaGNLRLTGEVLADILLGKIAYWDDprirelnpGLNLP-HKEIVLVYRSDASGTNE 182
                                    *******************888*8888888******************************99.***************** PP

                     PBP_like_2 149 lfstalaeq...............gpwt..asgigasgsegvasav.snngaigyvsvaywlavkgysladvtngagkfv 210
                                    +f+++l+ +               +p     +++ga+g++gva+av s+++a gyv++ay +   g+ +a++ n+ g+fv
  gi|119719966|ref|YP_920461.1| 183 VFTKYLSYVspewrktvgagktvqWPLAglGRAVGAKGNPGVAQAVnSTPYALGYVELAYTK---GLGVAAIRNKSGNFV 259
                                    *******997776666666666552222565678899*********9**************9...*************** PP

                     PBP_like_2 211 lptaata...asalkvakias.....nplawslqpveeniadgayPlsrftyiivyqpyayhgnnaalakaFldyllsd 281
                                    lpt+ ++   asal++++ +s     n     l+    n++++ayP+s++t+++v+ p +y++ +a+++  Fl+y++++
  gi|119719966|ref|YP_920461.1| 260 LPTPRSVtiaASALPALDPSSsiagvN----YLEAIFGNPDPDAYPISTPTFLVVKGPKNYDPPKAKALALFLKYIATE 334
                                    *******99999999977766865566....6777999*******************99888888888889****9875 PP

>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.9   1.3   8.8e-20     4e-16       7     313 ..      40     336 ..      36     338 .. 0.85

  Alignments for each domain:
  == domain 1  score: 59.9 bits;  conditional E-value: 8.8e-20
                                    HHHHHHHHHHH....HHHHHTTEEEEEEEECHHHHHH...HHHHHHHTTSSSCSEEEE.CGGHHH.HHHHT.TSBECCHH CS
                      SBP_bac_1   7 gaalqalvaka....fekehpgikVeiesvgsgslaq...kltlaiaaGdgpaDviav.dndwia.rlaka.glllpldp 76 
                                    ga+++ + ++a    f+ +hpgik+e+  vgsg+++    ++++++a++d p       +++  + r+ +  +l+  l+ 
  gi|119719966|ref|YP_920461.1|  40 GATFPMPQIQAwayrFTSKHPGIKIEYAGVGSGQGISdflNGIVDFAGSDVP---LNDqQYSAARsRFGEVyQLPYILGG 116
                                    5666666666666679**********************************88...3333333333788888999999999 PP

                                    HHHHT.TECTTCCTEEEEHHHHTHHHHCEEEESEEEEEEEEEEEETTTHHCTTGGGSHBHHHHHHHHHHHHHHCTCT.HC CS
                      SBP_bac_1  77 yvkay.lapgvkdaadklsssvlpkildskvlyvPlyaargliYNkdlfekagldppwtWdelveaakklkekgkkp.ig 154
                                    +++ y  ++++  + ++l+++vl++il             g+i                Wd++ +   +++ + + + i+
  gi|119719966|ref|YP_920461.1| 117 VAVVYnVPEIKGAGNLRLTGEVLADILL------------GKIA--------------YWDDPRIRELNPGLNLPHKeIV 170
                                    99999445567788999*********99............7777..............9********************* PP

                                    CHCCEEHHHHHHHHHHHHHHHHTGGGEECCCT......................HHCSHHHHS..HHHHHHHHHHHHHHH CS
                      SBP_bac_1 155 garggsasgtayyfalalakslggkvfdkdgg......................gldnpegvt..aatylvklyavanlt 210
                                     +++++asgt+ +f+ +l+ +++  +++k +g                      g+++ + +t  a++y++ +y     t
  gi|119719966|ref|YP_920461.1| 171 LVYRSDASGTNEVFTKYLSYVSP--EWRKTVGagktvqwplaglgravgakgnpGVAQAVNSTpyALGYVELAY-----T 243
                                    ***********************..************************99999999999999***********.....* PP

                                    HHHHTTEEECSSHHHHHHHHHTTSCSEEEEEHHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEEEEEEEEE CS
                      SBP_bac_1 211 kelkgkgaenkdgaaalalfeaGeaamaivglwaalaamkvapkvafaadkekpkeelgvaplPagkggkpgilgaygla 290
                                    k+l+ +   nk+g+++l+   + ++a+  + l  al+  ++  +v++ ++  ++++ +++++            ++ ++ 
  gi|119719966|ref|YP_920461.1| 244 KGLGVAAIRNKSGNFVLPTPRSVTIAA--SALP-ALDPSSSIAGVNYLEAIFGNPDPDAYPI------------STPTFL 308
                                    *****************9776555555..5554.5888889999999999999999999998............777899 PP

                                    EBTTCST...HHH..HHHHHHHHTSHHH CS
                      SBP_bac_1 291 ipkgskn...pea..AkkFldfllspea 313
                                    ++kg kn   p+a     Fl++++++++
  gi|119719966|ref|YP_920461.1| 309 VVKGPKNydpPKAkaLALFLKYIATEGQ 336
                                    9999999997333446668888888876 PP

>> PBP_like  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   0.0   2.2e-12   9.9e-09       3     148 ..      54     236 ..      52     265 .. 0.62

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 2.2e-12
                                    HHHHH-TTCEEEEEES-HHHHHHHHHTTS-SEEEESS---CCCH..........HCCCCCEEEEEEEEEEE..E-CC-HC CS
                       PBP_like   3 elaeknpgvrvavanvGsggGlkalrageadiagshlldketee..........ynapalrkaldgievvl..vnlarre 70 
                                    ++  k+pg+++++a+vGsg+G++ + +g +d ags+++  +++           y++          +++l  v +++  
  gi|119719966|ref|YP_920461.1|  54 RFTSKHPGIKIEYAGVGSGQGISDFLNGIVDFAGSDVPLNDQQYsaarsrfgevYQL----------PYILggVAVVYNV 123
                                    68899*********************************8755432333333333222..........2222232222222 PP

                                    HCCCCHCCHHHS.........................--BGG...GC-S-B-EEEEE-TTSHHHHHHHHHHC-CEECT.. CS
                       PBP_like  71 qglvvakgnpkk.........................itnwk...dladaplrlvnRetGSGtrdlfdellkkegisk.. 120
                                     ++        +                         i+ ++    l+ ++++lv R   SGt  +f++ l+   +s+  
  gi|119719966|ref|YP_920461.1| 124 PEIKG------AgnlrltgevladillgkiaywddprIRELNpglNLPHKEIVLVYRSDASGTNEVFTKYLSY--VSPew 195
                                    22222......12222223334455555555555444433332125599**********************66..45545 PP

                                    ..............E-SSTTSEEESSHHHHHCCHCCETTCCE CS
                       PBP_like 121 ..............ssikgyaqearshlavaaaVaagradvg 148
                                                  + +   a  a+ +  va+aV++++ + g
  gi|119719966|ref|YP_920461.1| 196 rktvgagktvqwplAGLGR-AVGAKGNPGVAQAVNSTPYALG 236
                                    5566666666666544444.4566666666777777776666 PP

>> HCV_NS4a  Hepatitis C virus non-structural protein NS4a
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   1.9e-05     0.086       2      41 ..      11      45 ..      11      55 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.9e-05
                       HCV_NS4a  2 pvvlvGlalAglAiyalttGSvvvvtrwsvnGkgppvvvv 41
                                   +v+lvGlalA++    l++GS    +++ ++G g    ++
  gi|119719966|ref|YP_920461.1| 11 TVLLVGLALAAV----LWIGSQQAQREVLLKGSG-ATFPM 45
                                   79********87....79***9999999999999.33344 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2396.79
//
Query:       gi|119719967|ref|YP_920462.1|  [L=298]
Description: binding-protein-dependent transport systems inner membrane component [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.8e-08   33.7  16.5    2.8e-08   33.7  16.5    2.3  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
       0.46   10.5   1.7        3.3    7.8   0.1    2.4  2  YjbT          Uncharacterised protein family


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   2.0     0.041   3.7e+02     119     174 ..      18      89 ..       4      98 .. 0.40
   2 !   33.7  16.5   3.1e-12   2.8e-08       7     171 ..      90     277 ..      84     288 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.041
                   BPD_transp_1 119 ggllggavlleflgswpG...lgtllleailgydyseis.............nggvlalviavlllnlvadi 174
                                     +++g  v+++   s p     g+ +l+++ +++    s               +++ ++++v+l++l++ +
  gi|119719967|ref|YP_920462.1|  18 LLAVGSMVVVLARESIPVlarEGLAILTSNAWRPSEDPSeelygvavpvlgsLYTAALALALVALFSLSLTV 89 
                                    444444444444333333333333333333333333333444555555533333333333444444444444 PP

  == domain 2  score: 33.7 bits;  conditional E-value: 3.1e-12
                   BPD_transp_1   7 laalnrnkkldkllrpliivllslPsfv.......laillvlvf...........vilsilghlilpviillllsaapyv 68 
                                    ++     ++l+ +l    +v  s+P++v               +            + ++ g +il++ i+l+++++py+
  gi|119719967|ref|YP_920462.1|  90 FVEEVAPRPLRAALEEALNVAASVPTVVyglwglsT-------VvpavrwlgrtlGMEGVSGPSILSASIVLATMITPYA 162
                                    5555566889999999999*********77533331.......223477778999889999******************* PP

                   BPD_transp_1  69 rlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG.......lgtll 141
                                      ++  a +s+p  +vea + lGa+r ++ r ++l ++   ++++l++ fg+++g++++++++ ++              
  gi|119719967|ref|YP_920462.1| 163 AAMMLVAYKSVPLAYVEAVTSLGATRVERAR-IILGMIRGFFAASLLIGFGRAVGETTAVSMVVGNVYnlspnvfE---- 237
                                    ****************************888.********************************553244444332.... PP

                   BPD_transp_1 142 leailgydyseis................nggvlalviavlllnlv 171
                                            y+ +s                 ++++a+++++++ +++
  gi|119719967|ref|YP_920462.1| 238 ------PSYTVTSlianqfgmayyyrylpSALYFAALLLLAVSSIA 277
                                    ......3333333445555556688866433333333333333333 PP

>> YjbT  Uncharacterised protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1     0.035   3.2e+02      10      29 ..     157     178 ..     149     200 .. 0.72
   2 ?    7.8   0.1   0.00037       3.3      14      41 ..     264     291 ..     257     295 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.035
                           YjbT  10 kmkpyfaalmlsv..svlpaya 29 
                                     + py aa+ml    sv  ay 
  gi|119719967|ref|YP_920462.1| 157 MITPYAAAMMLVAykSVPLAYV 178
                                    5689****99964225555665 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00037
                           YjbT  14 yfaal.mlsvsvlpayagplgtadkadlp 41 
                                    yfaal +l+vs + +yag l  a +a lp
  gi|119719967|ref|YP_920462.1| 264 YFAALlLLAVSSIATYAG-LRLASRAGLP 291
                                    999972579********9.7788888888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1951.26
//
Query:       gi|119719968|ref|YP_920463.1|  [L=279]
Description: phosphate ABC transporter, inner membrane subunit PstA [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.3e-16   58.6  10.9    6.3e-16   58.6  10.9    2.2  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   1.7     0.077   1.4e+03     140     140 ..      39      39 ..       2      85 .. 0.43
   2 !   58.6  10.9   3.5e-20   6.3e-16       1     183 [.      86     277 ..      82     279 .] 0.83

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.077
                   BPD_transp_1 140 l 140
                                     
  gi|119719968|ref|YP_920463.1|  39 S 39 
                                    1 PP

  == domain 2  score: 58.6 bits;  conditional E-value: 3.5e-20
                   BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilp.viillllsaapyvrlirraalrsl 79 
                                    g+l+Gi++  +++ +l +l    +++l+ +Ps++l+++++ ++v+  + ++  l  +++ l l  +py+++ ++++l+s+
  gi|119719968|ref|YP_920463.1|  86 GVLTGIYVSEYPRDPLARLAEHASQFLSEVPSVLLGVFVYGAVVV--YTKSPSLLaGALSLSLVVTPYIVVHTKEILSSI 163
                                    677788888*****************************9865444..4554444437888888899************** PP

                   BPD_transp_1  80 pkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG..............lgtllleai 145
                                    p  ++eaa alG+++w+++  v+lP+ l+ i+++l+ a  ++lg+++ ++f++   G                +ll+ ++
  gi|119719968|ref|YP_920463.1| 164 PFAYREAAFALGLPKWKTVLLVLLPMNLRGIASSLLAAYFRALGETAPVLFTA---GaafngfygllgpssTLSLLVWTY 240
                                    *****************************************************...445677877777776555666666 PP

                   BPD_transp_1 146 lgydyseisnggvlalviavlllnlvadilqrlldprv 183
                                     ++++ +++  +++ +++++++++l+a i  r+  + v
  gi|119719968|ref|YP_920463.1| 241 GQSPFENWQ-ELAWGAAFILVAFTLAASIALRVSVREV 277
                                    677777777.7888888888888888888777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1748.40
//
Query:       gi|119719969|ref|YP_920464.1|  [L=257]
Description: ABC transporter related [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.2e-30  104.5   0.0    1.1e-29  103.7   0.0    1.4  1  ABC_tran         ABC transporter
    1.8e-12   47.7   0.0    9.4e-08   32.2   0.0    2.1  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    4.5e-09   36.1   0.0    4.8e-08   32.7   0.0    2.0  1  SMC_N            RecF/RecN/SMC N terminal domain
      3e-05   24.3   0.0    9.7e-05   22.7   0.0    1.9  1  AAA_22           AAA domain
    3.5e-05   24.3   0.2    0.00012   22.5   0.2    1.9  1  AAA_16           AAA ATPase domain
    0.00069   19.4   0.0       0.16   11.7   0.0    2.1  2  AAA_15           AAA ATPase domain
    0.00073   19.2   0.0     0.0015   18.3   0.0    1.5  1  AAA_29           P-loop containing region of AAA domain
     0.0032   17.4   0.0     0.0096   15.8   0.0    1.8  2  RsgA_GTPase      RsgA GTPase
     0.0035   17.1   0.0      0.012   15.4   0.0    1.9  3  PRK              Phosphoribulokinase / Uridine kinase family
      0.005   17.4   0.0      0.009   16.5   0.0    1.3  1  AAA_23           AAA domain
     0.0058   17.1   0.0        0.4   11.1   0.0    2.6  2  AAA              ATPase family associated with various cellul
     0.0085   16.0   0.0      0.029   14.3   0.0    1.7  2  ATPase_2         ATPase domain predominantly from Archaea
  ------ inclusion threshold ------
       0.01   15.6   0.0      0.083   12.6   0.0    2.0  2  AAA_30           AAA domain
      0.011   15.7   0.0      0.016   15.2   0.0    1.3  1  Rad17            Rad17 P-loop domain
      0.014   14.6   0.0      0.025   13.8   0.0    1.5  1  NB-ARC           NB-ARC domain
      0.016   14.5   0.0       0.94    8.7   0.0    2.2  2  Zeta_toxin       Zeta toxin
      0.017   15.6   0.0       0.18   12.3   0.0    2.1  2  AAA_18           AAA domain
      0.027   14.2   0.0      0.056   13.1   0.0    1.7  1  AAA_24           AAA domain
      0.037   14.3   0.0       0.66   10.2   0.0    2.2  1  SbcCD_C          Putative exonuclease SbcCD, C subunit
      0.038   14.2   0.2       0.23   11.6   0.2    2.1  1  AAA_33           AAA domain
      0.055   13.4   0.0       0.12   12.2   0.0    1.5  1  NACHT            NACHT domain
      0.065   12.0   0.0        1.2    7.8   0.0    2.1  2  ABC_ATPase       Predicted ATPase of the ABC class
      0.071   11.9   0.0       0.11   11.3   0.0    1.2  1  Adeno_IVa2       Adenovirus IVa2 protein
      0.097   13.1   0.0       0.22   11.9   0.0    1.6  1  RNA_helicase     RNA helicase
       0.11   11.3   0.0       0.16   10.8   0.0    1.2  1  AAA_PrkA         PrkA AAA domain
       0.12   12.3   0.0       0.27   11.2   0.0    1.6  1  AAA_5            AAA domain (dynein-related subfamily)
       0.13   12.6   0.0       0.26   11.6   0.0    1.5  1  TrkA_N           TrkA-N domain
       0.13   12.3   0.0       0.26   11.3   0.0    1.5  1  AAA_14           AAA domain
       0.15   11.3   0.0       0.41    9.8   0.0    1.6  1  DUF2075          Uncharacterized conserved protein (DUF2075)
       0.15   11.7   0.0       0.29   10.8   0.0    1.4  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.7   0.0   1.8e-32   1.1e-29       3     137 .]      23     177 ..      21     177 .. 0.94

  Alignments for each domain:
  == domain 1  score: 103.7 bits;  conditional E-value: 1.8e-32
                                    EEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--.....SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   3 nvslklkegekvaivGenGaGKStLlkllagllkp.....teGeilldgkdlke.qeleslrkeigvlpqepqlfpeltv 76 
                                    +v++++ +  ++a++G++G+GKStLl+++ +l +       +G+++++g d+ +  + e++ + +g+++q+p+  p+l++
  gi|119719969|ref|YP_920464.1|  23 DVNISVPRRGIYAVMGPSGCGKSTLLRTINRLIELrpearVKGRVEVNGLDVYRdLSPEQVARMVGMVFQTPNPLPHLSI 102
                                    8999***************************99877788899******99999977889999****************** PP

                                    HHH..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    xxx..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  77 ren..............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                    ++n              + d+ + +al++  l +  ++++++ +++LSgGq+qr+++aral+ kp++ll+DEpta
  gi|119719969|ref|YP_920464.1| 103 YDNvalgprlhglargrQLDAIVREALEQAALWDEVKDKLRKPATTLSGGQQQRLCIARALALKPSVLLMDEPTA 177
                                    *************888888888******************9999*****************************97 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0     7e-05     0.042       3      25 ..      35      57 ..      33      84 .. 0.73
   2 !   32.2   0.0   1.6e-10   9.4e-08     226     300 ..     138     208 ..      98     208 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7e-05
                         AAA_21  3 vliGpNgsGKSnLLdaldllarl 25
                                   ++ Gp g+GKS+LL+++  l  l
  gi|119719969|ref|YP_920464.1| 35 AVMGPSGCGKSTLLRTINRLIEL 57
                                   678**************999544 PP

  == domain 2  score: 32.2 bits;  conditional E-value: 1.6e-10
                         AAA_21 226 ngdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSpl 300
                                     +d    pa+ lS G+++ l+++ al+  +   s+ll DEp ++L+P   +++ +l+k+lsr  + vi++TH+p+
  gi|119719969|ref|YP_920464.1| 138 VKDKLRKPATTLSGGQQQRLCIARALALKP---SVLLMDEPTANLDPVNAAKIEDLVKSLSR-EITVIIVTHDPE 208
                                    444555578889******988888888766...*****************************.**********95 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.0     8e-11   4.8e-08      24     201 ..      31     209 ..      21     223 .. 0.78

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 8e-11
                                    SSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCH.CCCCCC--BTTCSSTTEEEEEEEEEETTEE...SSSSSSCEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxx RF
                          SMC_N  24 ksftaivGpNGSGKsnlldAilFvLGersakklrse.klsdlihkskekasvkkaeveitfdnedkk...lkiekeevsi 99 
                                    +++ a++Gp G+GKs ll  i  ++  r    ++ + +++ l  +++ ++++    v ++f+ ++     +  ++  +  
  gi|119719969|ref|YP_920464.1|  31 RGIYAVMGPSGCGKSTLLRTINRLIELRPEARVKGRvEVNGLDVYRDLSPEQVARMVGMVFQTPNPLphlSIYDNVALGP 110
                                    67889*****************99999988788765378888666688888888899****9999884323333333444 PP

                                    EEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-ST.TCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 100 srrvkrkgeseykingkevtkkevsellesagisk.elLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkk 178
                                    + +    g++  +i ++  +++ + + ++++  ++ ++LSgG+++ + +a  +A++   p ++ l+De  a+LD  n +k
  gi|119719969|ref|YP_920464.1| 111 RLHGLARGRQLDAIVREALEQAALWDEVKDKLRKPaTTLSGGQQQRLCIARALALK---P-SVLLMDEPTANLDPVNAAK 186
                                    55556677777777777777777777777665554258*******99999998874...4.5679*************** PP

                                    HHHHHHHHCTTSEEEEE-SSHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 179 vaellkeksknaQfivislreem 201
                                    + +l+k+ s +  +i+++++ e+
  gi|119719969|ref|YP_920464.1| 187 IEDLVKSLSREITVIIVTHDPEQ 209
                                    *******************9876 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   1.6e-07   9.7e-05       5      61 ..      31      88 ..      28     211 .. 0.61

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.6e-07
                         AAA_22  5 agilvvtGesGtGKTtllrrlleqldeeakaee.erpevvfvtlpsstsskdllrell 61
                                   +gi +v+G+sG+GK+tllr++ +  + +++a+   r+ev   ++  + s+++++r++ 
  gi|119719969|ref|YP_920464.1| 31 RGIYAVMGPSGCGKSTLLRTINRLIELRPEARVkGRVEVNGLDVYRDLSPEQVARMVG 88
                                   89********************999877666555333333333333334444444444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.2     2e-07   0.00012      24     120 ..      31     158 ..      18     229 .. 0.58

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 2e-07
                         AAA_16  24 pelvllsGesGvGKsslvrellralekd.............................ggiflrgkcdqlesa........ 66 
                                     ++  + G+sG+GKs+l+r++ r +e +                             g                      
  gi|119719969|ref|YP_920464.1|  31 RGIYAVMGPSGCGKSTLLRTINRLIELRpearvkgrvevngldvyrdlspeqvarmvG-------------Mvfqtpnpl 97 
                                    37899*****************977777656665555554444444444444443332.............033333222 PP

                         AAA_16  67 ........ipysalaqalareellrqlldeaesaeleawrekleealaavpelagaeasrll 120
                                            +++ + +  lar + l ++ +ea + +++ w+e  ++  +++  l+g + +rl+
  gi|119719969|ref|YP_920464.1|  98 phlsiydnVALGPRLHGLARGRQLDAIVREALE-QAALWDEVKDKLRKPATTLSGGQQQRLC 158
                                    222222224445544444444555555555222.3333443333333334445555444444 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.015         9      25      48 ..      33      56 ..      19      81 .. 0.84
   2 !   11.7   0.0   0.00026      0.16     295     366 ..     147     207 ..     118     209 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.015
                         AAA_15 25 ltvliGkNnsGKSsilealdlFln 48
                                   +  + G+ ++GKS++l+ ++ +++
  gi|119719969|ref|YP_920464.1| 33 IYAVMGPSGCGKSTLLRTINRLIE 56
                                   56778999***********98876 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00026
                         AAA_15 295 nknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSp 366
                                    +  + G+q+ l ++  ++          k+ +ll++EP a+L p +   + +l k+l+++    vii TH p
  gi|119719969|ref|YP_920464.1| 147 TTLSGGQQQRLCIARALAL---------KPSVLLMDEPTANLDPVNAAKIEDLVKSLSREIT--VIIVTHDP 207
                                    5555555555555433332.........3578*****************************6..******98 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   2.4e-06    0.0015      16      45 ..      25      54 ..      18      63 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.4e-06
                         AAA_29 16 tieidlkgatlltGpsGsGKSTllDAiqal 45
                                    i++ ++g++ ++GpsG GKSTll  i+ l
  gi|119719969|ref|YP_920464.1| 25 NISVPRRGIYAVMGPSGCGKSTLLRTINRL 54
                                   57888899***************9776655 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.6e-05    0.0096     100     121 ..      32      53 ..       6      66 .. 0.81
   2 ?   -2.2   0.0       5.7   3.4e+03      85     105 ..     182     202 ..     170     204 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.6e-05
                                    SEEEEECSTTSSHHHHHHHHCT CS
                    RsgA_GTPase 100 ktsvlvGqSGvGKStLinallp 121
                                     + +++G+SG GKStL+ +++ 
  gi|119719969|ref|YP_920464.1|  32 GIYAVMGPSGCGKSTLLRTINR 53 
                                    68899***********998875 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5.7
                                    TTHTTHHHHHHHCTTSEEEEE CS
                    RsgA_GTPase  85 ktkegleelkellkdktsvlv 105
                                     + +++e+l + l+ +++v++
  gi|119719969|ref|YP_920464.1| 182 VNAAKIEDLVKSLSREITVII 202
                                    456778888888888888775 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0     2e-05     0.012       2      55 ..      34      85 ..      33      97 .. 0.78
   2 ?   -3.0   0.0       8.2   4.9e+03     154     165 ..     116     127 ..     100     132 .. 0.77
   3 ?   -2.4   0.0       5.4   3.2e+03     113     132 ..     225     244 ..     180     247 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2e-05
                            PRK  2 IgvagsSGaGkttvarklekifgrekvkaaeiegdsflrldraekdleleerkr 55
                                    +v g+SG+Gk+t+ r+++ +++    + a ++g ++++   ++ dl++e+ +r
  gi|119719969|ref|YP_920464.1| 34 YAVMGPSGCGKSTLLRTINRLIE--LRPEARVKGRVEVNGLDVYRDLSPEQVAR 85
                                   5899****************999..55556777877777777777777776655 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 8.2
                            PRK 154 eRGrsleavlds 165
                                    +RGr+l+a++ +
  gi|119719969|ref|YP_920464.1| 116 ARGRQLDAIVRE 127
                                    799999999865 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 5.4
                            PRK 113 lviEGlhalydervaelldl 132
                                    +v EG+++ + ++ +e+ d+
  gi|119719969|ref|YP_920464.1| 225 VVREGVLSSVITSSREYYDI 244
                                    45677777777777777775 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.5e-05     0.009      13      39 ..      18      51 ..       9      55 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.5e-05
                         AAA_23 13 qeidF.......skgltlItGpNGaGKTTildAi 39
                                   +++ F        +g++++ Gp G+GK+T+l+ i
  gi|119719969|ref|YP_920464.1| 18 EQVLFdvnisvpRRGIYAVMGPSGCGKSTLLRTI 51
                                   44444446677899*****************987 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   0.00066       0.4       3      35 ..      36      75 ..      34     107 .. 0.68
   2 ?    3.2   0.0      0.19   1.1e+02      45      66 ..     154     174 ..     122     220 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00066
                                   EESSTTSSHHHHHHHHHHHHTHE.......EEEEETTTCS CS
                            AAA  3 lyGppGtGKTllakavakelgve.......fleisgsell 35
                                   ++Gp G+GK++l + + + ++ +        +e++g ++ 
  gi|119719969|ref|YP_920464.1| 36 VMGPSGCGKSTLLRTINRLIELRpearvkgRVEVNGLDVY 75
                                   78************99888753322233334666666665 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.19
                                    HHHHHHHHHHHTS.TSEEEEEET CS
                            AAA  45 kirelfkeakeka.kpsilfiDE 66 
                                    + r ++++a   a kps+l++DE
  gi|119719969|ref|YP_920464.1| 154 QQRLCIARA--LAlKPSVLLMDE 174
                                    444444444..445699999998 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   4.9e-05     0.029      20      40 ..      31      51 ..      26      64 .. 0.83
   2 ?   -1.4   0.0         3   1.8e+03     104     125 ..     185     206 ..     158     222 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.9e-05
                       ATPase_2 20 neiyfiYGpegsGKtaLlkei 40
                                   + iy + Gp g+GK++Ll+ i
  gi|119719969|ref|YP_920464.1| 31 RGIYAVMGPSGCGKSTLLRTI 51
                                   56999*************976 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3
                       ATPase_2 104 kaielllekikkkgkkiiiiiD 125
                                    ++ie+l ++++++ + ii+  D
  gi|119719969|ref|YP_920464.1| 185 AKIEDLVKSLSREITVIIVTHD 206
                                    3455555555555554444444 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00014     0.083      17      49 ..      30      63 ..      15      70 .. 0.81
   2 ?    0.7   0.1       0.6   3.6e+02      86     127 ..     163     209 ..     107     220 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00014
                         AAA_30 17 gdrvavltGpAGtGKttalkalreaweaa.ggrv 49
                                   ++ + ++ Gp G GK+t+l+++++++e + + rv
  gi|119719969|ref|YP_920464.1| 30 RRGIYAVMGPSGCGKSTLLRTINRLIELRpEARV 63
                                   5568899*****************9997744555 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.6
                         AAA_30  86 lepg.tllivDEagmv....dtkqlaallkaaekagakvilvGDerQ 127
                                    l+ + ++l+ DE        +++++++l+k+++++ + +i+  D++Q
  gi|119719969|ref|YP_920464.1| 163 LALKpSVLLMDEPTANldpvNAAKIEDLVKSLSREITVIIVTHDPEQ 209
                                    33334677777765533444778888888888887777777778887 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   2.6e-05     0.016      45      67 ..      30      53 ..      17     108 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.6e-05
                          Rad17 45 kr.iLLisGPsGCgkstvvkvLsk 67
                                   +r i  + GPsGCgkst ++ + +
  gi|119719969|ref|YP_920464.1| 30 RRgIYAVMGPSGCGKSTLLRTINR 53
                                   4448999***********998766 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.2e-05     0.025      22     110 ..      33     173 ..      24     208 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.2e-05
                                    EEEEEESTTSSHHHHHHHHCCSHCCCCC..CBTEEEEE.......................................... CS
                         NB-ARC  22 vvalvGmgGvGKttlakqilnksdeveg..rFdsvawv.......................................... 57 
                                    + a++G  G+GK+tl++ i++   e++   r  + + v                                          
  gi|119719969|ref|YP_920464.1|  33 IYAVMGPSGCGKSTLLRTINRL-IELRPeaRVKGRVEVngldvyrdlspeqvarmvgmvfqtpnplphlsiydnvalgpr 111
                                    7799***************998.555441345555555777777777777777777777777777777777777777777 PP

                                    ............EEESXXHHHHHHHXXHHHHHCCCTTSSSS-STTSHHHHHHHHCCCTTEEEEEE CS
                         NB-ARC  58 ............vvsktdkseeiletilkeLslseddleekeeveslkrklvrlLltkrfllvlD 110
                                                 v +  ++  +++++  +L +  + + +  +++     + r+L  k ++l++D
  gi|119719969|ref|YP_920464.1| 112 lhglargrqldaIVREALEQAALWDEVKDKLRKP-ATTLSGGQQQ--RLCIARALALKPSVLLMD 173
                                    7777777777777777777777777777777444.3333333333..466677777777777776 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0    0.0016      0.94      18      60 ..      33      81 ..      19     150 .. 0.82
   2 ?    4.0   0.0     0.045        27     107     173 ..     181     245 ..     164     254 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0016
                     Zeta_toxin 18 lillgGqpGAGKselaellkdele.....rqgnvvrldp.DdlRelhPe 60
                                   ++ + G +G+GKs+l++ +++ +e     r ++ v++++ D +R l Pe
  gi|119719969|ref|YP_920464.1| 33 IYAVMGPSGCGKSTLLRTINRLIElrpeaRVKGRVEVNGlDVYRDLSPE 81
                                   6778899***********9998877777777778888754889998887 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.045
                     Zeta_toxin 107 pdvvkklaealkkaGYevevvvvavkkelSrlgvldRyeeevaegRlvpkeehdeafeglresveal 173
                                    p +++k+ + +k+  +e+ v++v+ ++e++ l++++R      +gR+v + +   + +  re  ++l
  gi|119719969|ref|YP_920464.1| 181 PVNAAKIEDLVKSLSREITVIIVTHDPEQA-LRLASRGALL-FKGRVVREGVLSSVITSSREYYDIL 245
                                    5577889999******************98.5677787777.4468888877777777777666655 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0    0.0003      0.18       3      25 ..      36      62 ..      35      91 .. 0.74
   2 ?    1.2   0.0      0.85   5.1e+02      73     114 ..     166     217 ..     110     228 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0003
                         AAA_18  3 ltGtpGvGKttlakeLskrlgf....g 25
                                   ++G++G+GK+tl + ++++ ++     
  gi|119719969|ref|YP_920464.1| 36 VMGPSGCGKSTLLRTINRLIELrpeaR 62
                                   89*************988755455441 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.85
                         AAA_18  73 egknlvidghlaeleseaakdikk..........vvLtaspeelleRlekRg 114
                                    ++++l++d   a+l + +a +i            v++ +++ e + Rl+ Rg
  gi|119719969|ref|YP_920464.1| 166 KPSVLLMDEPTANLDPVNAAKIEDlvkslsreitVIIVTHDPEQALRLASRG 217
                                    5667777777777777777776667777777888666666666666888887 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   9.4e-05     0.056       6      36 ..      35      64 ..      32     163 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.4e-05
                         AAA_24  6 liyGpsgiGKTtlakelgpkplfidtekGlk 36
                                   +++Gpsg GK+tl++++ ++ + +  e+ +k
  gi|119719969|ref|YP_920464.1| 35 AVMGPSGCGKSTLLRTI-NRLIELRPEARVK 64
                                   79***************.9999887777555 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0    0.0011      0.66      22      83 ..     138     186 ..     122     193 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0011
                        SbcCD_C  22 kekelsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiat 83 
                                     + +l++ ++tlSGG++q    l++a ala           +++++++DE  ++lD+ ++a+
  gi|119719969|ref|YP_920464.1| 138 VKDKLRKPATTLSGGQQQR---LCIARALA----L------KPSVLLMDEPTANLDPVNAAK 186
                                    4456999**********65...44443333....2......245566666666666666665 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   0.00039      0.23       4      19 ..      36      51 ..      33     220 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00039
                         AAA_33  4 lvGlpGsGKstlaerl 19
                                   + G++G+GKstl++ +
  gi|119719969|ref|YP_920464.1| 36 VMGPSGCGKSTLLRTI 51
                                   68**********9986 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00021      0.12       4      24 ..      35      55 ..      33      64 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00021
                                   EEEC-TTTCHHHHHHHHHHHH CS
                          NACHT  4 ilqGeaGsGKTtLlqklalaw 24
                                   ++ G++G+GK+tLl+ + +++
  gi|119719969|ref|YP_920464.1| 35 AVMGPSGCGKSTLLRTINRLI 55
                                   689************997765 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0     0.002       1.2     243     266 ..      30      53 ..      26      56 .. 0.90
   2 ?    2.0   0.0      0.12        74     324     351 ..     150     177 ..     141     204 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.002
                                    -SSEEEEEE-TTSSHHHHHHHHHH CS
                     ABC_ATPase 243 pkGvtlIvGggfhGKsTLLeAlek 266
                                    ++G+ +++G+   GKsTLL+ +++
  gi|119719969|ref|YP_920464.1|  30 RRGIYAVMGPSGCGKSTLLRTINR 53 
                                    579*****************9986 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.12
                                    -HHHHHHHHHHHHHHTT-SEEEEEGGGS CS
                     ABC_ATPase 324 SGStsqAanimealeagakllLiDEDts 351
                                    SG   q   i++al ++ ++lL+DE t+
  gi|119719969|ref|YP_920464.1| 150 SGGQQQRLCIARALALKPSVLLMDEPTA 177
                                    899999999****************886 PP

>> Adeno_IVa2  Adenovirus IVa2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00018      0.11      91     119 ..      35      61 ..      18      68 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00018
                     Adeno_IVa2  91 viyGPtGsGksqllrnlissklisPiPet 119
                                     + GP G+Gks llr++  ++li+  Pe+
  gi|119719969|ref|YP_920464.1|  35 AVMGPSGCGKSTLLRTI--NRLIELRPEA 61 
                                    578************97..7888888875 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00037      0.22       3      22 ..      36      55 ..      34      77 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00037
                   RNA_helicase  3 lyGpsgeGKStlakeLakal 22
                                   + Gpsg+GKStl +++ + +
  gi|119719969|ref|YP_920464.1| 36 VMGPSGCGKSTLLRTINRLI 55
                                   78***********9965544 PP

>> AAA_PrkA  PrkA AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00027      0.16      87     116 ..      30      59 ..      25      86 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00027
                       AAA_PrkA  87 rkqilyllGPvggGksslverlkklleaap 116
                                    r+ i  ++GP g Gks+l  ++ +l+e +p
  gi|119719969|ref|YP_920464.1|  30 RRGIYAVMGPSGCGKSTLLRTINRLIELRP 59 
                                    5668889********************987 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00045      0.27       5      24 ..      37      56 ..      35      85 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00045
                                   E--SSSSHHHHHHHGGGGBS CS
                          AAA_5  5 vGppGtgKselaerlaaaln 24
                                    Gp+G+gKs+l + + ++++
  gi|119719969|ref|YP_920464.1| 37 MGPSGCGKSTLLRTINRLIE 56
                                   7***************9994 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00044      0.26      13      57 ..     190     233 ..     188     250 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00044
                                    HHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHH CS
                         TrkA_N  13 laeeLseggkdvvvidkdeerveelreeglevvvgdatdeevLee 57 
                                    l++ Ls++   v+++ +d+e++ +l+ +g+  ++g + +e vL +
  gi|119719969|ref|YP_920464.1| 190 LVKSLSREI-TVIIVTHDPEQALRLASRGALLFKGRVVREGVLSS 233
                                    678888877.5*****************************99976 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00043      0.26       2      23 ..      31      52 ..      30      85 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00043
                         AAA_14  2 rkilvitGaRrvGKTtllkqli 23
                                   r i++++G+  +GK+tll+++ 
  gi|119719969|ref|YP_920464.1| 31 RGIYAVMGPSGCGKSTLLRTIN 52
                                   57999************98874 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00069      0.41       6     142 ..      36     217 ..      31     222 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00069
                        DUF2075   6 VtGvaGtGKtvvllnllael.........................edde.........................eertav 35 
                                    V G +G GK+ +l ++   +                         e  +                         ++ + +
  gi|119719969|ref|YP_920464.1|  36 VMGPSGCGKSTLLRTINRLIelrpearvkgrvevngldvyrdlspE--QvarmvgmvfqtpnplphlsiydnvaLGPRLH 113
                                    6666666666665544444444554444444444444333333330..03333333333334444444444444666677 PP

                        DUF2075  36 ylsvNhplvlvlrealakkeekkkkkeafeklssfinnlsefkkaeekkeepkedvvivDEAhrlltksdqaekqseenq 115
                                     l + ++l +++real++ +   + k++++k+++     ++ +  ++++   k  v+++DE    l+   + +  + e+ 
  gi|119719969|ref|YP_920464.1| 114 GLARGRQLDAIVREALEQAALWDEVKDKLRKPATTLSGGQQQRLCIARALALKPSVLLMDEPTANLD---PVNAAKIEDL 190
                                    7888899999**********99****************9999999****************988888...4444545666 PP

                        DUF2075 116 lkelmkrakvvvalvDegQelntgeig 142
                                    +k+l ++  v+++  D++Q+l+  ++g
  gi|119719969|ref|YP_920464.1| 191 VKSLSREITVIIVTHDPEQALRLASRG 217
                                    666666688************998765 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00049      0.29       3      21 ..      36      54 ..      35      85 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00049
                Viral_helicase1  3 vhGvpGcGKStlirkllrt 21
                                   v G  GcGKStl+r++ r 
  gi|119719969|ref|YP_920464.1| 36 VMGPSGCGKSTLLRTINRL 54
                                   56778*********99888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                       109  (0.00607954); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              30  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 1607.63
//
Query:       gi|119719970|ref|YP_920465.1|  [L=365]
Description: amidohydrolase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00029   20.2   0.0     0.0013   18.2   0.0    1.9  1  Amidohydro_1  Amidohydrolase family
  ------ inclusion threshold ------
      0.012   15.0   0.0      0.028   13.8   0.0    1.6  2  TatD_DNase    TatD related DNase
       0.17   12.1   1.6       0.45   10.7   1.6    1.7  1  YXWGXW        YXWGXW repeat (2 copies)


Domain annotation for each model (and alignments):
>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   2.1e-07    0.0013       2     225 ..      36     243 ..      35     300 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.1e-07
                                    EEE-EEEEEEECETTECSSS.....GHHHHH.............STTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHHH CS
                   Amidohydro_1   2 vlPGlIDaHvHleqsllrga.....tledwl.............vppetaaealesgiktalksGtttvadmgattstgi 63 
                                    v PG+ DaH H  q + +g+        +w+              + et+ae +e ++   l +G+t va +g      +
  gi|119719970|ref|YP_920465.1|  36 VSPGFSDAHAHP-QVVDVGEggrwrNSYEWIegrrlrvneaslrRDAETSAELAEVALLLSLLDGVTLVALTGS-----L 109
                                    89*********6.5555555888876666668*****************************************9.....6 PP

                                    HHHHHHHHTSSSEEEEEEESSEGGSGCCCSHHHH.HHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHHHHHHHHHH CS
                   Amidohydro_1  64 ealleaaeelplglrilggkvsldrgsaetskas.reklkagaaetikgkadgvvkvalapheapafsdeelkealkeak 142
                                    e  +ea+++l + +r ++  +++  g++ + ++s ++k ++      + + dg  + ++  h+   + +++l++  + a+
  gi|119719970|ref|YP_920465.1| 110 EGNIEAVRRLKVAPRTVLLPTVMR-GEGWSLPESiYVKYVKN-----LSMWDGYYSLGFFVHSLRMADRSMLRASKRMAE 183
                                    777777777777788888877776.55544444414455444.....456699999************************ PP

                                    HHTTEEEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEEHHHHHHHHHHHHHHCEEHHHHHH CS
                   Amidohydro_1 143 krdlpvaiHaletkgevedaeaafgetiehgthlevaeslglldeiklilahgvhltpteaellkerlkeagvahcpfsn 222
                                    + ++p+a H++e   e  + ++a               +    d+  +i++h+     +     +++  + +v+hcp+sn
  gi|119719970|ref|YP_920465.1| 184 RLGVPFALHLSEGVDEADELVEALE-------------G----DTRGVIAVHCFEGAEK----CRRH--GLRVVHCPTSN 240
                                    **********775555433333333.............2....3334566666555555....5667..77777777777 PP

                                    HHS CS
                   Amidohydro_1 223 sil 225
                                    ++l
  gi|119719970|ref|YP_920465.1| 241 LYL 243
                                    774 PP

>> TatD_DNase  TatD related DNase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0      0.69   4.1e+03      83      95 ..      44      56 ..      40      87 .. 0.72
   2 ?   13.8   0.0   4.8e-06     0.028     105     162 ..     167     225 ..     161     234 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.69
                                   CCCTSEEEEEEEE CS
                     TatD_DNase 83 vkhskvvaiGeiG 95
                                    +h++vv +Ge G
  gi|119719970|ref|YP_920465.1| 44 HAHPQVVDVGEGG 56
                                   4567777777766 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 4.8e-06
                                    GHHHHHHHHHHHHHHHHHTTEEEEEEEES-HHHHHHHHHHCG.GCCSEEEETT--S-HH CS
                     TatD_DNase 105 tkeaqeevFeeqlrlAkelklplviHlrkaeedlleilkeaa.eakakvvlHsfsgsae 162
                                     + a + ++++  r+A++l+ p  +Hl +  ++  e++++++ +++  + +H+f+g ++
  gi|119719970|ref|YP_920465.1| 167 LRMADRSMLRASKRMAERLGVPFALHLSEGVDEADELVEALEgDTRGVIAVHCFEGAEK 225
                                    5566778999999****************9999999999998555548899*****876 PP

>> YXWGXW  YXWGXW repeat (2 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.6   7.5e-05      0.45       8      24 ..      55      68 ..      54      68 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 7.5e-05
                         YXWGXW  8 pGyWywdggsyvWvpGp 24
                                   +G+W+   +sy W++G+
  gi|119719970|ref|YP_920465.1| 55 GGRWR---NSYEWIEGR 68
                                   6****...*******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.66u 0.34s 00:00:01.00 Elapsed: 00:00:00.56
# Mc/sec: 1955.59
//
Query:       gi|119719971|ref|YP_920466.1|  [L=349]
Description: GMP reductase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   4.1e-116  387.8   1.8   4.9e-116  387.5   1.8    1.0  1  IMPDH            IMP dehydrogenase / GMP reductase domain
    1.4e-08   34.5  10.4    5.7e-06   25.9   9.0    2.1  2  NMO              Nitronate monooxygenase
    8.7e-07   28.3  15.2    5.2e-05   22.4  15.2    3.0  3  FMN_dh           FMN-dependent dehydrogenase
      6e-06   25.9   0.8      0.015   14.8   0.2    2.2  2  His_biosynth     Histidine biosynthesis protein
    0.00025   20.3   2.2    0.00025   20.3   2.2    2.0  2  Glu_synthase     Conserved region in glutamate synthase
     0.0035   16.5   0.0     0.0053   15.9   0.0    1.2  1  Dus              Dihydrouridine synthase (Dus)
  ------ inclusion threshold ------
       0.01   15.1   0.9       0.01   15.1   0.9    2.3  2  ThiG             Thiazole biosynthesis protein ThiG
      0.054   12.9   0.3       0.25   10.7   0.1    2.0  2  G3P_antiterm     Glycerol-3-phosphate responsive antiterminat
      0.058   11.9   0.0       0.31    9.5   0.0    1.8  2  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
       0.18   11.1   2.0        2.9    7.2   0.7    2.2  2  TMP-TENI         Thiamine monophosphate synthase
       0.23   10.6   3.3       0.99    8.6   0.1    2.6  3  NanE             Putative N-acetylmannosamine-6-phosphate epi
       0.25   10.8   0.4       0.78    9.2   0.1    1.8  2  EAL              EAL domain
       0.68    9.1   6.5          2    7.5   0.7    2.9  3  DHO_dh           Dihydroorotate dehydrogenase


Domain annotation for each model (and alignments):
>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  387.5   1.8  3.5e-119  4.9e-116       1     344 [.      14     341 ..      14     342 .. 0.97

  Alignments for each domain:
  == domain 1  score: 387.5 bits;  conditional E-value: 3.5e-119
                                    E--GGGEEEE---B-S-GGGSB--EESSTTEEESSSEEE-SSTTT-SHHHHHHHHHTTSEEEE-SSS-HHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH   1 gltfddvllvpaksevlpkevdlktkltkkiklniPlvsaamdtvtesemAialareGgigvihknlsieeqaeevkkvk 80 
                                    gl+fddvllvp++s+v  +evd++t+ltk++ l+iP++s++mdtvt+ emA +l + Gg+gv+ +n+  ++ +e vkk+ 
  gi|119719971|ref|YP_920466.1|  14 GLSFDDVLLVPKYSDVRIDEVDVSTRLTKNLLLKIPIISSPMDTVTGFEMARKLGELGGLGVLPRNIPLDAVVEYVKKIS 93 
                                    799*******************************************************************9999988887 PP

                                    TSTTSXBXTTSXB-EEEEE-SSTTHHHHHHHHHHTT-SEEEEE-STSSSHHHHHHHHHHHHHTTTSEEEEEEE-SHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH  81 rspnaakdekgrllvgaavgvkedalervkalveagvdvlvvdsahghsekvleavkeikkkveeveviaGnvataegak 160
                                              ++l vg avg  +   erv++ ++ag+ ++v+d+ahghs++vlea ++        ev+aGn++tae+a 
  gi|119719971|ref|YP_920466.1|  94 ---------GENLPVGVAVGPFD--DERVSKALDAGASIIVIDTAHGHSRNVLEATRRYAGMG--AEVMAGNIVTAEAAL 160
                                    .........678**********7..69****************************99988666..799************ PP

                                    HHHHTT-SEEEE-SS-STTBHHHHHCSB---HHHHHHHHHHHHCTCT-EEEEES---SHHHHHHHHHTT-SEEEESCCCT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH 161 aLieagadavkvGiGpGsiCttrvvagvGvpqltAvaevaeaakkagvpviaDGGikysgdivkAlaaGadavmlGslla 240
                                    +Li aga  ++vG+GpG  Cttr+vagvG pql+Ava+va+aa+++gv v+aDGGi++  divkAlaaGadavmlG lla
  gi|119719971|ref|YP_920466.1| 161 DLIGAGAVSLRVGVGPGHACTTREVAGVGYPQLSAVAKVADAARSHGVSVVADGGIEKPADIVKALAAGADAVMLGYLLA 240
                                    ******************************************************************************** PP

                                    TBTTSSSEEEEETTEEEEEEEETTSHHHHHH-SS-TTS-..--SS-SBEEEEEE--B-HHHHHHHHHHHHHHHHHHHT-S CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH 241 gteEspgeviliegrkyKeyrGmgslgamkkgskdryfqkkeklvpeGvegrvpykgsvkevveqlvgglrsgmgylGak 320
                                    g +E+pg+v++  g+ +K+yrGmgs ga + + + ry +   k vpeGveg vp++g+v+ vve lv+gl++gmgy+Ga+
  gi|119719971|ref|YP_920466.1| 241 GSDEAPGHVVVRGGECFKVYRGMGSRGALR-SGSTRYGE--FKRVPEGVEGLVPCRGPVEGVVEFLVNGLKQGMGYVGAR 317
                                    *****************************5.55789974..489************************************ PP

                                    SHHHHHHH-EEEEE-HHHHHHHS- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH 321 tieelkekakfvritaaglkeshv 344
                                    ++eel+ ka+fvr+t+ag++es++
  gi|119719971|ref|YP_920466.1| 318 NLEELRVKAEFVRLTHAGVRESGP 341
                                    **********************86 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0   0.00043      0.59       2      41 ..      38      77 ..      37      94 .. 0.82
   2 !   25.9   9.0   4.1e-09   5.7e-06      76     238 ..      81     252 ..      75     254 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00043
                            NMO  2 slltellkikppvvqpgmggiskarLaaavsnaGgLGvla 41
                                   ++lt+ l  k p++ ++m  +++ ++a    + GgLGvl 
  gi|119719971|ref|YP_920466.1| 38 TRLTKNLLLKIPIISSPMDTVTGFEMARKLGELGGLGVLP 77
                                   678888899*****************************97 PP

  == domain 2  score: 25.9 bits;  conditional E-value: 4.1e-09
                            NMO  76 aadraekykkeleeaalelnieegvrfyrkvevvldekvevvs..fgfglpteevvarlkeagvvliptissvkearkve 153
                                    ++d   +y k+++++ l + + +g  ++++v   ld ++ ++   ++ g  ++ ++a +  ag+ + ++++ +  a ++ 
  gi|119719971|ref|YP_920466.1|  81 PLDAVVEYVKKISGENLPVGVAVGPFDDERVSKALDAGASIIVidTAHGHSRNVLEATRRYAGMGAEVMAGNIVTAEAAL 160
                                    56666677788888888888888888***********8887661155666777777888889998888877776666555 PP

                            NMO 154 a.rGaDalivqGpeaGGhqG.tpevgd..kglfaLvpqvldavd...iPviAaGGiidrrgvaaaLalGAsgvqigtrfL 226
                                       Ga a+ +  + + Gh   t+ev++    +++ v++v+da     + v+A GGi +  ++  aLa+GA +v +g  + 
  gi|119719971|ref|YP_920466.1| 161 DlIGAGAVSLRVGVGPGHACtTREVAGvgYPQLSAVAKVADAARshgVSVVADGGIEKPADIVKALAAGADAVMLGYLLA 240
                                    42577778778788889999889999944445555889999988999*****************************9999 PP

                            NMO 227 ltkesdakdahk 238
                                    + +e++ +++++
  gi|119719971|ref|YP_920466.1| 241 GSDEAPGHVVVR 252
                                    999999998875 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.2   1.6e+03      29      67 ..      16      57 ..      13      70 .. 0.72
   2 !   22.4  15.2   3.8e-08   5.2e-05     232     300 ..     113     236 ..     100     248 .. 0.69
   3 ?    1.7   0.0     0.078   1.1e+02     315     342 ..     296     323 ..     293     328 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.2
                                   GGGGEEE---SS.SS-SS-B--EEETTE.EESSSEEE--B.S CS
                         FMN_dh 29 aferirlrprvl.rdvskvdlsttllGq.klslPvliaPv.g 67
                                   +f+++ l+p++  + + +vd+st+l  +  l++P++ +P+  
  gi|119719971|ref|YP_920466.1| 16 SFDDVLLVPKYSdVRIDEVDVSTRLTKNlLLKIPIISSPMdT 57
                                   578888888876357888999999985525799999999952 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 3.8e-08
                                    HHHHTTESEEEE--GGG.....................................................TSSTT-.--H CS
                         FMN_dh 232 raveaGvdgivvSNHGG.....................................................Rqldga.pat 257
                                    +a++aG+++iv+    G                                                     R++ g+  + 
  gi|119719971|ref|YP_920466.1| 113 KALDAGASIIVIDTAHGhsrnvleatrryagmgaevmagnivtaeaaldligagavslrvgvgpghacttREVAGVgYPQ 192
                                    55555555555555555555555555555555555555555555555555555555555555555666666665542456 PP

                                    HHCHHHHHHHH..S.S-EEEESS--SHHHHHHHHHTT-SEEEES CS
                         FMN_dh 258 idvLpeiveavggr.ievlvDgGirrGsDvlkAlalGAdavllG 300
                                    +++  ++++a++++ + v++DgGi + +D++kAla GAdav+lG
  gi|119719971|ref|YP_920466.1| 193 LSAVAKVADAARSHgVSVVADGGIEKPADIVKALAAGADAVMLG 236
                                    888999999999755****************************9 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.078
                                    HHHHHHHHHHHHHHHHHHHT-SBHHHHH CS
                         FMN_dh 315 vervleilraelertmallGvksvaeld 342
                                    ve v+e l + l++ m  +G+++++el+
  gi|119719971|ref|YP_920466.1| 296 VEGVVEFLVNGLKQGMGYVGARNLEELR 323
                                    7899*********************997 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0   0.00048      0.66      62     115 ..      86     138 ..      79     151 .. 0.87
   2 !   14.8   0.2   1.1e-05     0.015     185     221 ..     201     237 ..     183     244 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00048
                                    HHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHH CS
                   His_biosynth  62 ldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavknpelikel 115
                                     ++v++i  e ++pv v  G  + e+v ++l+aga+ ++i ta  ++ ++++  
  gi|119719971|ref|YP_920466.1|  86 VEYVKKISGE-NLPVGVAVGPFDDERVSKALDAGASIIVIDTAHGHSRNVLEAT 138
                                    6889999999.9******************************998888887765 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 1.1e-05
                                    HHHHHHSSEEEEESS--SHHHHHHHHHTTCSEEEESH CS
                   His_biosynth 185 elaeavkipviasGGvgsledlkelksegvdavivgs 221
                                    + a++  ++v+a GG+++++d+ ++ ++g+dav++g 
  gi|119719971|ref|YP_920466.1| 201 DAARSHGVSVVADGGIEKPADIVKALAAGADAVMLGY 237
                                    3333445566666666666666666666666666655 PP

>> Glu_synthase  Conserved region in glutamate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.4     0.065        90     190     256 ..      82     147 ..      78     175 .. 0.82
   2 !   20.3   2.2   1.8e-07   0.00025     244     303 ..     181     236 ..     157     240 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.065
                                    HHHHHHHHHHH-.TTSEEEEEEE-STTHHHHHHHHHHTT-SEEEEE-TT---SSEEHHHHHHB---HH CS
                   Glu_synthase 190 laqliedLkevn.keakvsvKlvaeagvetiaagvakanadiilidGleGGTGAspkssikhaGlPle 256
                                    l  ++e  k+++ ++ +v+v ++    + + +a   +a+a ii+id  +G    + +  + +aG+  e
  gi|119719971|ref|YP_920466.1|  82 LDAVVEYVKKISgENLPVGVAVGPFDDERVSKA--LDAGASIIVIDTAHGHSRNVLEATRRYAGMGAE 147
                                    567788999999888999999998888877777..9************99988888888888887665 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 1.8e-07
                                    EHHHHHHB---HHHHHHHHHHHHHHTT-GGG-EEEEESS--SHHHHHHHHHHT-SEEE-S CS
                   Glu_synthase 244 pkssikhaGlPlelalaevdqtlkeeglrdrvsliadGglktgadvvkalalGAdavgig 303
                                     +  +  +G P + a+a+v  + ++    + vs+ adGg+  +ad+vkala GAdav +g
  gi|119719971|ref|YP_920466.1| 181 TTREVAGVGYPQLSAVAKVADAARS----HGVSVVADGGIEKPADIVKALAAGADAVMLG 236
                                    4455667899999999988776665....569*************************998 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   3.9e-06    0.0053     169     213 ..     190     236 ..     162     250 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.9e-06
                                    G--CHHHHHHHHH-S...S-EEEESS--SHHHHHHHHHHH--SEEEES CS
                            Dus 169 tadweaIkevkqavs...ipviaNGdIkdaedaqaileetGadgvmig 213
                                      +++a+++v +a +   ++v+a G+I+++ d+ ++l+  Gad+vm g
  gi|119719971|ref|YP_920466.1| 190 YPQLSAVAKVADAARshgVSVVADGGIEKPADIVKALAA-GADAVMLG 236
                                    556778888988888889********************9.******98 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.8     0.051        70     137     228 ..      64     152 ..      56     169 .. 0.70
   2 ?   15.1   0.9   7.5e-06      0.01     174     211 ..     206     243 ..     186     249 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.051
                                    HHHHHHTT-SEBEEBSSSTTS----S-HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSHHHH CS
                           ThiG 137 arrleevGcaavmPlaapiGsglGllnkealkiiieeakvPvivDAGigspsdaaqamelGadavllntavaeakdpvam 216
                                    ar+l e+G   v+P   p+ +       e +k i +  ++Pv v  G    + + +a++ Ga+ ++++ta  ++++  + 
  gi|119719971|ref|YP_920466.1|  64 ARKLGELGGLGVLPRNIPLDAVV-----EYVKKI-SGENLPVGVAVGPFDDERVSKALDAGASIIVIDTAHGHSRNVLEA 137
                                    66666666666666666654432.....223333.344789999999999999999*************99999998776 PP

                                    HH...HHHHHHHHHH CS
                           ThiG 217 Ar...afklaveaGr 228
                                     r    + + v aG 
  gi|119719971|ref|YP_920466.1| 138 TRryaGMGAEVMAGN 152
                                    652213555566665 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 7.5e-06
                                    -SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSS CS
                           ThiG 174 akvPvivDAGigspsdaaqamelGadavllntavaeak 211
                                      v v+ D Gi +p d+++a+  Gadav+l   +a ++
  gi|119719971|ref|YP_920466.1| 206 HGVSVVADGGIEKPADIVKALAAGADAVMLGYLLAGSD 243
                                    4799*************************987777665 PP

>> G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.61   8.4e+02     150     166 ..     107     123 ..      78     128 .. 0.77
   2 ?   10.7   0.1   0.00018      0.25     128     166 ..     197     234 ..     191     237 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.61
                                    SHHHHHHHCTT.SSEEE CS
                   G3P_antiterm 150 tkedveealkaGaiavs 166
                                    + e+v +al+aGa+ + 
  gi|119719971|ref|YP_920466.1| 107 DDERVSKALDAGASIIV 123
                                    56899999999998875 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00018
                                    HHHHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEE CS
                   G3P_antiterm 128 pkvikeikkelkipiiaGGLietkedveealkaGaiavs 166
                                    +kv+++ +++  + ++a G ie+  d+ +al+aGa+av+
  gi|119719971|ref|YP_920466.1| 197 AKVADAARSH-GVSVVADGGIEKPADIVKALAAGADAVM 234
                                    4555555555.99************************97 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       0.2   2.8e+02      84     120 ..     111     147 ..      99     160 .. 0.81
   2 ?    9.5   0.0   0.00023      0.31     156     193 ..     196     234 ..     186     264 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.2
                                    HHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEE CS
                Cys_Met_Meta_PP  84 ilallkaGdeivvsddlYggtqrllkkvlkklgievk 120
                                    + + l aG  i+v d+++g ++++l+ + +  g+ ++
  gi|119719971|ref|YP_920466.1| 111 VSKALDAGASIIVIDTAHGHSRNVLEATRRYAGMGAE 147
                                    6677899***************999988777665554 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00023
                                    HHHHHHHHHHTT-EEEEEGTTTHT.TTS-GGGGT-SEEE CS
                Cys_Met_Meta_PP 156 iekiaklakkagvlvvvDntfasp.llqrplklgaDivv 193
                                    ++k+a++a+++gv vv D  +  p  ++++l+ gaD v+
  gi|119719971|ref|YP_920466.1| 196 VAKVADAARSHGVSVVADGGIEKPaDIVKALAAGADAVM 234
                                    789*********************669*********998 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.074     1e+02      17      64 ..     109     156 ..     106     173 .. 0.83
   2 ?    7.2   0.7    0.0021       2.9     120     176 ..     172     234 ..     155     236 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.074
                       TMP-TENI  17 evveealkggvtlvqlRekeldarellelaeklaalcrkygvpliind 64 
                                    e+v++al++g++++ +   + ++r++le  ++ a + ++  +  i+  
  gi|119719971|ref|YP_920466.1| 109 ERVSKALDAGASIIVIDTAHGHSRNVLEATRRYAGMGAEVMAGNIVTA 156
                                    6899***********************999999888777766666655 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0021
                       TMP-TENI 120 igvGpifpTdtKkda..eplgleglkelaeale...iPvvaiGGi.tlenvaevleagadgva 176
                                    +gvGp ++ +t++ a      l+ ++++a+a++   + vva GGi +++++ ++l+agad v 
  gi|119719971|ref|YP_920466.1| 172 VGVGPGHACTTREVAgvGYPQLSAVAKVADAARshgVSVVADGGIeKPADIVKALAAGADAVM 234
                                    6888888888888875555666677777777778889********45799*********9885 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.18   2.5e+02     134     178 ..      86     130 ..      74     142 .. 0.73
   2 ?   -0.0   0.1      0.31   4.3e+02     144     173 ..     145     173 ..     126     185 .. 0.81
   3 ?    8.6   0.1   0.00072      0.99     141     174 ..     204     237 ..     190     245 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.18
                                    HHHHHHHHHTT--E.EEES---SHHHHHHHHTT--SEEEE-HHHH- CS
                           NanE 134 falvkalseaglkv.iaeGrintPekakkaieiGvdavvvGsaitr 178
                                    +++vk++s ++l v +a G ++  e+  ka++ G+  +v+ +a   
  gi|119719971|ref|YP_920466.1|  86 VEYVKKISGENLPVgVAVGPFDD-ERVSKALDAGASIIVIDTAHGH 130
                                    56788888888876466777764.7778889999999999887655 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.31
                                    T--EEEES---SHHHHHHHHTT--SEEEE- CS
                           NanE 144 glkviaeGrintPekakkaieiGvdavvvG 173
                                    g +v+a G i t e a + i  G++++ vG
  gi|119719971|ref|YP_920466.1| 145 GAEVMA-GNIVTAEAALDLIGAGAVSLRVG 173
                                    555665.99999999999999999999988 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.00072
                                    HHTT--EEEES---SHHHHHHHHTT--SEEEE-H CS
                           NanE 141 seaglkviaeGrintPekakkaieiGvdavvvGs 174
                                     + g+ v+a+G i+ P+   ka+  G+dav++G 
  gi|119719971|ref|YP_920466.1| 204 RSHGVSVVADGGIEKPADIVKALAAGADAVMLGY 237
                                    567999*************************996 PP

>> EAL  EAL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.1   1.5e+03     190     222 ..     131     162 ..     118     169 .. 0.55
   2 ?    9.2   0.1   0.00056      0.78     192     235 ..     194     239 ..     184     241 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.1
                                    HHHHHHHCHHHHCCCT-EEEE-S--SHHHHHHH CS
                            EAL 190 aqalvkalialakelgikvvaegVeteeqleal 222
                                    ++++++a  ++a  +g++v+a  + t e + +l
  gi|119719971|ref|YP_920466.1| 131 SRNVLEATRRYAG-MGAEVMAGNIVTAEAALDL 162
                                    4444444444443.3666666666666555555 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00056
                                    HHHHHCHHHHCCCT-EEEE-.S--SHHHHHHHHHHT-SEE-.STTT CS
                            EAL 192 alvkalialakelgikvvae.gVeteeqlealrelgcdlvQ.Gyll 235
                                    + v+ ++++a++ g+ vva+ g+e +++  ++ ++g+d v  Gyll
  gi|119719971|ref|YP_920466.1| 194 SAVAKVADAARSHGVSVVADgGIEKPADIVKALAAGADAVMlGYLL 239
                                    5678899************946****************87436665 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.12   1.7e+02     233     276 ..      85     128 ..      20     138 .. 0.64
   2 ?    2.1   0.4     0.067        92     250     274 ..     150     174 ..     147     182 .. 0.88
   3 ?    7.5   0.7    0.0015         2     243     273 ..     206     236 ..     179     246 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.12
                                    HHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHH CS
                         DHO_dh 233 virelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytal 276
                                    v+ +++k   +++p+    G +  e +   + aGAs++ + ta 
  gi|119719971|ref|YP_920466.1|  85 VVEYVKKISGENLPVGVAVGPFDDERVSKALDAGASIIVIDTAH 128
                                    44455555566677755556666677778888999999998886 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.067
                                    ESS--SHHHHHHHHHHTECEEEESH CS
                         DHO_dh 250 vGGiesgeDalekieaGAslvqvyt 274
                                     G i ++e al+ i aGA  + v+ 
  gi|119719971|ref|YP_920466.1| 150 AGNIVTAEAALDLIGAGAVSLRVGV 174
                                    588***************9999885 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0015
                                    T.S-EEEESS--SHHHHHHHHHHTECEEEES CS
                         DHO_dh 243 keipiIgvGGiesgeDalekieaGAslvqvy 273
                                    + + +++ GGie   D +  + aGA +v ++
  gi|119719971|ref|YP_920466.1| 206 HGVSVVADGGIEKPADIVKALAAGADAVMLG 236
                                    3499**********************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.70u 0.34s 00:00:01.04 Elapsed: 00:00:00.56
# Mc/sec: 1891.79
//
Query:       gi|119719972|ref|YP_920467.1|  [L=316]
Description: phosphate uptake regulator, PhoU [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.6e-11   43.0   0.5    1.5e-10   41.4   0.0    2.1  2  PhoU            PhoU domain
    2.9e-08   33.5   0.0    8.1e-08   32.0   0.0    1.8  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
     0.0078   16.1   0.0      0.019   14.8   0.0    1.6  1  DUF1508         Domain of unknown function (DUF1508)
  ------ inclusion threshold ------
      0.085   12.8   0.0       0.31   11.0   0.0    1.8  2  RNase_H_2       RNase_H superfamily
      0.088   12.1   0.7       0.15   11.4   0.7    1.3  1  DUF1978         Domain of unknown function (DUF1978)


Domain annotation for each model (and alignments):
>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.4   0.0   4.3e-14   1.5e-10       1      88 [.     143     234 ..     143     235 .. 0.87
   2 ?   -1.7   0.1       1.1   4.1e+03       8      30 ..     292     315 ..     290     316 .] 0.77

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 4.3e-14
                                    HHHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SH....HHHH.HHHHHHHHHHH CS
                           PhoU   1 lrrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplae....dlre.llsllriardl 75 
                                    l+rm  +v++ ++d+ + +eekd  ++r v+erd e+d+++++++r++   l+  ++ ae    + r  ll + +  + l
  gi|119719972|ref|YP_920467.1| 143 LSRMEILVKNDVRDLEDYYEEKDSSYLRSVVERDVELDKFYFLLSRQVALSLKS-SSYAEkigvKSRPlLLPYFNYGKTL 221
                                    689999*****************************************8877755.44444477855541589******** PP

                                    HHHHHHHHHHHHH CS
                           PhoU  76 ERigDhavniaer 88 
                                    ER+gD  v+ia+ 
  gi|119719972|ref|YP_920467.1| 222 ERVGDVLVSIARA 234
                                    ***********96 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.1
                                    HHHHHHHHHHHHHCT.-HHHHHHH CS
                           PhoU   8 veemlddalealeek.dtelarev 30 
                                    v + l+++l++le++ d e+++++
  gi|119719972|ref|YP_920467.1| 292 VGNLLSLSLDMLESRiDLEALEKI 315
                                    677888999999888787887877 PP

>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.0   2.3e-11   8.1e-08       4      45 ..      14      55 ..      11      56 .. 0.92

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 2.3e-11
                                   TTEEEEEE-CCCHHHCCEECTCEEEEEECTTCCCCCCCHHSX CS
                 MazE_antitoxin  4 GnsgavriPkevrfelgireGdevelevdgdkiilrplkslp 45
                                    +s+av++P  + + + +reGd v le+ +++++++p  +++
  gi|119719972|ref|YP_920467.1| 14 KSSLAVTLPSKWLKRHSLREGDVVYLEEREEGLLVAPGLREQ 55
                                   69**********************************988766 PP

>> DUF1508  Domain of unknown function (DUF1508)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   5.2e-06     0.019      15      35 ..     238     258 ..     235     262 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.2e-06
                                    S-EEEEEEEBSSHHHHHHHHH CS
                        DUF1508  15 gevIatsegYsskaaaenGIe 35 
                                    ge Ia+s+ Y+++ a+enGI+
  gi|119719972|ref|YP_920467.1| 238 GESIAKSHLYTARRAVENGIN 258
                                    899*****************7 PP

>> RNase_H_2  RNase_H superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.74   2.7e+03      88      88 ..     152     152 ..     107     189 .. 0.56
   2 ?   11.0   0.0   8.5e-05      0.31     108     145 ..     251     288 ..     236     293 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.74
                      RNase_H_2  88 f 88 
                                    +
  gi|119719972|ref|YP_920467.1| 152 N 152
                                    1 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 8.5e-05
                      RNase_H_2 108 ksvekelgierreedlsGsqavklyqeylrtgdeelle 145
                                     +ve+ +++ r+ +++s s++v+ly++y++t  +++l 
  gi|119719972|ref|YP_920467.1| 251 RAVENGINVFRTGDKASKSSLVNLYSRYFSTTHRQSLV 288
                                    6899**************************99998875 PP

>> DUF1978  Domain of unknown function (DUF1978)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.7   4.1e-05      0.15     148     182 ..     135     169 ..     117     182 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.1e-05
                        DUF1978 148 levdLetalgsiEeeyrevvrdQedywKeeekkel 182
                                     +++Le +l ++E   +++vrd edy+ e+++  l
  gi|119719972|ref|YP_920467.1| 135 STMSLERILSRMEILVKNDVRDLEDYYEEKDSSYL 169
                                    356**************************998764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.51
# Mc/sec: 1851.18
//
Query:       gi|119719973|ref|YP_920468.1|  [L=153]
Description: nuclease [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.5e-11   42.2   0.1    1.1e-10   41.6   0.1    1.3  1  ParBc     ParB-like nuclease domain


Domain annotation for each model (and alignments):
>> ParBc  ParB-like nuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6   0.1   6.4e-15   1.1e-10      11      81 ..      22      91 ..      10      98 .. 0.84

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 6.4e-15
                          ParBc 11 nplqprkd.spekieelvasIkkkGll.qPiivrktrqgryeiiaGerRlrAakrlglkevpvivleiddeea 81
                                    +l+p+ + s+e++eel + + ++G+l +Pi ++     +  i++G++R++A+ rlg+kevpv + + dde+ 
  gi|119719973|ref|YP_920468.1| 22 GSLKPHEEfSEERVEELLRDMLERGVLiKPIAAESR---YGVILDGHHRVEALRRLGVKEVPVALVDYDDERI 91
                                   577899889******************777777666...48899**********************9997765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1084.83
//
Query:       gi|119719974|ref|YP_920469.1|  [L=135]
Description: hypothetical protein Tpen_1067 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       206  (0.0114898); expected 358.6 (0.02)
Passed bias filter:                      197  (0.0109878); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 984.86
//
Query:       gi|119719975|ref|YP_920470.1|  [L=109]
Description: GCN5-related N-acetyltransferase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.5e-16   58.6   0.1    7.2e-16   58.5   0.1    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    4.3e-12   46.3   0.1    5.2e-12   46.0   0.1    1.1  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    7.7e-09   35.6   0.0    8.6e-09   35.4   0.0    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    2.1e-07   31.0   0.0    2.7e-07   30.6   0.0    1.3  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
    5.5e-06   26.3   0.0    6.9e-06   26.0   0.0    1.1  1  FR47             FR47-like protein
    0.00014   21.5   0.0    0.00018   21.2   0.0    1.1  1  Acetyltransf_8   Acetyltransferase (GNAT) domain
     0.0011   19.1   0.0     0.0016   18.5   0.0    1.4  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
     0.0012   18.6   0.0     0.0014   18.3   0.0    1.1  1  PanZ             Acetyltransferase (GNAT) domain, PanZ
     0.0017   19.0   0.0     0.0018   19.0   0.0    1.1  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.028   14.6   0.0      0.032   14.4   0.0    1.2  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
      0.029   13.8   0.3      0.056   12.9   0.3    1.6  1  Acetyltransf_15  Putative acetyl-transferase


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.5   0.1   4.4e-19   7.2e-16      45     117 .]      23      97 ..       7      97 .. 0.85

  Alignments for each domain:
  == domain 1  score: 58.5 bits;  conditional E-value: 4.4e-19
                                    EEEEEEEEEET..TSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETTEHHHHHHHHHTTE CS
                 Acetyltransf_1  45 iGfisllkipd..ekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlaveedndaairlYeklGF 117
                                    ++++ ++ i +  + +++a +e+++V++eyrg+G+G++L+++++e ar+ +++ki ++ +   +a ++ YeklGF
  gi|119719975|ref|YP_920470.1|  23 VAHCYIYLIKNdlHPEPYALLEDVYVDEEYRGRGIGTELVKKAIEVARSMNCYKIIATSRFEREAVHKWYEKLGF 97 
                                    5555444444457889**************************************9887888899**********9 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.0   0.1   3.2e-15   5.2e-12      13      76 .]      21      99 ..       8      99 .. 0.63

  Alignments for each domain:
  == domain 1  score: 46.0 bits;  conditional E-value: 3.2e-15
                                   EEEEEEEEEEES........TCTEEEEE-GGGTTSSHHHHHHH.HTT.....SEEE.EE.EEEETHHHHHH.HHHHTTEEE CS
                 Acetyltransf_7 13 kivGfialslld........aeitrlaVdpeyrgkGiGraLle.aae.....kgii.le.qlelnaekaik.fYeklGFee 76
                                   ++v  ++++l++        a ++ ++Vd+eyrg+GiG++L++ a +      ++  ++ +++ +  +a++ +YeklGF++
  gi|119719975|ref|YP_920470.1| 21 REVAHCYIYLIKndlhpepyALLEDVYVDEEYRGRGIGTELVKkA-IevarsMNCYkIIaTSRFER-EAVHkWYEKLGFKR 99
                                   4555555555555676665444445*****************943.22444433432222222222.56556*******95 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   0.0   5.3e-12   8.6e-09      54     113 ..      43     104 ..      13     107 .. 0.84

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 5.3e-12
                Acetyltransf_10  54 isllfVdpeyrgqGigkaLleaveeeaekdgikl..eltvnaspyavpfYeklGFkavgeeq 113
                                    ++ ++Vd+eyrg+Gig++L+++++e a+ ++  +  +++  +  +  + YeklGFk+ g e+
  gi|119719975|ref|YP_920470.1|  43 LEDVYVDEEYRGRGIGTELVKKAIEVARSMNCYKiiATSRFEREAVHKWYEKLGFKRYGYEF 104
                                    6789**********************9999877655555555567889*********98876 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.0   1.7e-10   2.7e-07      27      71 ..      43      88 ..      14      95 .. 0.83

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 1.7e-10
                Acetyltransf_CG 27 fthTeVpeelrGkGiAkkLvkaalddareegl.kvvptCsyvaayl 71
                                   ++ ++V+ee+rG+Gi+ +Lvk+a++ ar+ +  k+++t  + ++ +
  gi|119719975|ref|YP_920470.1| 43 LEDVYVDEEYRGRGIGTELVKKAIEVARSMNCyKIIATSRFEREAV 88
                                   6789************************988659999998877665 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   4.2e-09   6.9e-06      20      80 ..      39     100 ..      28     106 .. 0.88

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 4.2e-09
                                    TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHH.S-S-EEEEEETT-HHHHHHHHHHT-EEE CS
                           FR47  20 dggelgalqvlpehrrrGlgsrlvkalakeiae.rgktvllvvvasNtpsirlyeklGfeki 80 
                                    ++  l  ++v++e r+rG g+ lvk+ ++  +  + +++++  + + ++  + yeklGf+ +
  gi|119719975|ref|YP_920470.1|  39 PYALLEDVYVDEEYRGRGIGTELVKKAIEVARSmNCYKIIATSRFEREAVHKWYEKLGFKRY 100
                                    5688999*******************999888889999*********************987 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   1.1e-07   0.00018      48     140 ..      15     100 ..       3     104 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.1e-07
                                    EEEETTEEEEEEEEEEGGGCGGGGCS---TT-EEEEEEESSHHHCTTTCHHHHHHHHHHHHHCCTT--EEEE--BTT-HH CS
                 Acetyltransf_8  48 iglldgepvgyfeiYwakedelaeyydaepgdrGiHlligeaeargkglttallralvhylfadprtrrvvvEPdvrNer 127
                                    i  +dg++v+   iY +k+d      + ep+ +  ++ +  +e+rg+g++t+l+++ ++ + +   + ++++  + + e+
  gi|119719975|ref|YP_920470.1|  15 ISIVDGREVAHCYIYLIKND-----LHPEPYALLEDVYVD-EEYRGRGIGTELVKKAIEVARSM-NCYKIIATSRFEREA 87 
                                    77899999999999999999.....688999999999995.799**************987665.9************** PP

                                    HHHHHHHTT-EEE CS
                 Acetyltransf_8 128 airllekaGfeke 140
                                    +++ +ek+Gf++ 
  gi|119719975|ref|YP_920470.1|  88 VHKWYEKLGFKRY 100
                                    **********986 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   9.9e-07    0.0016      72     125 ..      39      97 ..      15     104 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 9.9e-07
                                    EEEEEEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--.....SSHHHHHTTT- CS
                 Acetyltransf_9  72 kaagvtgVavapehrgrgvlskLlaraleemreegqplsllfP.....ssipiYrrfGy 125
                                    ++a + +V v+ e+rgrg+ ++L+++a+e +r+++   ++ +      +  + Y+++G+
  gi|119719975|ref|YP_920470.1|  39 PYALLEDVYVDEEYRGRGIGTELVKKAIEVARSMNCYKIIATSrfereAVHKWYEKLGF 97 
                                    678999**************************987665555555332222356666665 PP

>> PanZ  Acetyltransferase (GNAT) domain, PanZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   8.7e-07    0.0014      61     122 ..      40      99 ..      31     105 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 8.7e-07
                           PanZ  61 eaelsdlcVRevTRrRGVgsyLleearrqaPevkswvlaeedvkeldlavlqaflealgfaa 122
                                    +a l+d+ V e+ R RG+g  L+++a + a +++++++  +     ++++++++ e+lgf++
  gi|119719975|ref|YP_920470.1|  40 YALLEDVYVDEEYRGRGIGTELVKKAIEVARSMNCYKIIATS--RFEREAVHKWYEKLGFKR 99 
                                    6889********************************999877..567889999999999975 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   1.1e-06    0.0018      85     138 .]      46      98 ..      10      98 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.1e-06
                 Acetyltransf_3  85 ymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGfe 138
                                     +++++++g+G++te v+ ++e+a + ++  +++a+   e ea  + +eklGf+
  gi|119719975|ref|YP_920470.1|  46 VYVDEEYRGRGIGTELVKKAIEVA-RSMNCYKIIATSRFEREAVHKWYEKLGFK 98 
                                    567899******************.999999**********************7 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0     2e-05     0.032      81     138 ..      45     101 ..      17     107 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2e-05
                 Acetyltransf_4  81 svylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhkalGFelvg 138
                                     vy++ +  + +g+g el++  ++v++ +n  ++ a    ++e+  + +++lGF+  g
  gi|119719975|ref|YP_920470.1|  45 DVYVD-EEYRGRGIGTELVKKAIEVARSMNCYKIIATSRFEREAVHKWYEKLGFKRYG 101
                                    69**6.78******************99999999999988999999********9776 PP

>> Acetyltransf_15  Putative acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.3   3.4e-05     0.056      77     106 ..      45      76 ..      23     103 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.4e-05
                Acetyltransf_15  77 tlyvsekyrgkGlakklLeeslkelk..knYk 106
                                    ++yv+e+yrg+G+  +l++++++  +  + Yk
  gi|119719975|ref|YP_920470.1|  45 DVYVDEEYRGRGIGTELVKKAIEVARsmNCYK 76 
                                    69******************987543225555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 741.42
//
Query:       gi|119719976|ref|YP_920471.1|  [L=340]
Description: phosphate uptake regulator, PhoU [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.9e-21   75.3   3.2    4.2e-14   52.8   0.2    2.5  2  PhoU            PhoU domain
    1.4e-10   40.8   0.2    3.9e-10   39.4   0.2    1.8  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an


Domain annotation for each model (and alignments):
>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.8   0.2   4.7e-18   4.2e-14       1      88 [.     147     239 ..     147     240 .. 0.91
   2 !   22.9   0.4     1e-08     9e-05       2      88 ..     254     332 ..     253     333 .. 0.84

  Alignments for each domain:
  == domain 1  score: 52.8 bits;  conditional E-value: 4.7e-18
                                    HHHHHHHHHHHHHHHHHHHHCT-HHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SH....HHHHHHHHHHHHHHH CS
                           PhoU   1 lrrmaeiveemlddalealeekdtela.revierddeidrlekeiersllealakrqplae....dlrellsllriardl 75 
                                    + +m + v  ml+d+  al  +d+e +  e+++rdd +d+l+    r+l  al  +  l+e    +++e+l   ++ +++
  gi|119719976|ref|YP_920471.1| 147 ITKMRDAVTGMLEDVKAALGGGDVEKIaSEIVSRDDIVDKLYLYGLRQLHAALRGYVGLEEiglrKVEEVLPHGMVLKNI 226
                                    578********************86666********************999997777777788899999999******** PP

                                    HHHHHHHHHHHHH CS
                           PhoU  76 ERigDhavniaer 88 
                                    ERi+Dha++ia+ 
  gi|119719976|ref|YP_920471.1| 227 ERIADHAASIAQA 239
                                    ***********86 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 1e-08
                                    HHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHHHHH CS
                           PhoU   2 rrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlERigDh 81 
                                    + +++ v+e +  ++ ++ ++d+ +a++++  d ++++l k++er+++ +la+r p+     e+l+++ ++ ++ Ri D+
  gi|119719976|ref|YP_920471.1| 254 STLSDKVSEFFTASVHVFLDRDKTTANRLL--DVDAEKL-KALERKVFDELARRIPE-----EILAVRLMVGSYRRIFDY 325
                                    568999********************9995..6666666.66777777777776664.....57889************* PP

                                    HHHHHHH CS
                           PhoU  82 avniaer 88 
                                    +++i e 
  gi|119719976|ref|YP_920471.1| 326 STDILEA 332
                                    ****986 PP

>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.4   0.2   4.3e-14   3.9e-10       2      43 ..      16      58 ..      15      61 .. 0.91

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 4.3e-14
                                   EETTEEEEEE-CCCHHHCCEECTCEEEEEECTT.CCCCCCCHH CS
                 MazE_antitoxin  2 kvGnsgavriPkevrfelgireGdevelevdgd.kiilrplks 43
                                   ++G++ +v+iPke++++l i +G+ ++l+ ++d +i ++p  +
  gi|119719976|ref|YP_920471.1| 16 TGGSTFIVSIPKEWAEKLSIGKGSLLVLSLENDgSIRIVPSLK 58
                                   89*******************************9999888655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2327.30
//
Query:       gi|119719977|ref|YP_920472.1|  [L=142]
Description: NADH-quinone oxidoreductase, B subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-30  105.9   0.2    1.5e-30  105.7   0.2    1.0  1  Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit


Domain annotation for each model (and alignments):
>> Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.7   0.2   8.5e-35   1.5e-30       1     130 [.      22     132 ..      22     133 .. 0.94

  Alignments for each domain:
  == domain 1  score: 105.7 bits;  conditional E-value: 8.5e-35
                                    -SHHHHHHT-TTTTHHHHHHTEEEEEETTT-S--HHHHHHTHTTTSEEEEEESBE...EEEHHHHHHHHGGGSSEEEEES CS
                    Oxidored_q6   1 CtGcsisllaleedlldllelielryhetlladskeeeieakekeadvlvveGavtrkpkealellkelaekakaviavG 80 
                                    C+Gc+i++ a+ ++ +dl     +r++ +l+ +++         +advlvv+G+vtr++++al++++++ +++++v+a+G
  gi|119719977|ref|YP_920472.1|  22 CNGCDIEFVAALTPRFDL-----ERLGVQLVPSPR---------HADVLVVTGPVTRASADALKTIYDQVPEPRIVVAFG 87 
                                    ********999999****.....************.........************************************ PP

                                    HHHHH-TGGGSTT-TEE-HHHHHHHC.S-E.EEE-SSS--HHHHHHHHHH CS
                    Oxidored_q6  81 tCAafGGipaaannpsvgeevgellevvpvdinipGCPphpeailetlla 130
                                    tCA++GG++  +n    +   g++++v+pvd++ipGCPp+pe +l++l+ 
  gi|119719977|ref|YP_920472.1|  88 TCACSGGVF--SN-CYNV--LGGADKVLPVDVKIPGCPPKPESLLHALSR 132
                                    *********..55.2223..579**********************99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1028.21
//
Query:       gi|119719978|ref|YP_920473.1|  [L=537]
Description: NADH-ubiquinone oxidoreductase, chain 49kDa [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.7e-73  244.9   0.1    4.3e-49  167.0   0.1    2.9  3  Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd s
    8.8e-23   81.2   0.0    3.1e-22   79.5   0.0    1.9  2  Complex1_30kDa  Respiratory-chain NADH dehydrogenase, 30 Kd s
    9.1e-15   54.5   3.2    1.2e-13   50.9   0.1    2.8  3  NiFeSe_Hases    Nickel-dependent hydrogenase


Domain annotation for each model (and alignments):
>> Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0     0.076   4.5e+02      25      48 ..     174     197 ..     163     231 .. 0.88
   2 !  167.0   0.1   7.2e-53   4.3e-49       3     163 ..     268     428 ..     267     436 .. 0.97
   3 !   73.9   0.0   1.8e-24   1.1e-20     198     271 .]     438     511 ..     434     511 .. 0.98

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.076
                                    HHSSSSS-TTBESSBBSS---TTH CS
                 Complex1_49kDa  25 vtGaRltasyiriGGvarDlpegl 48 
                                    v G R+ ++++riG v+r +++ +
  gi|119719978|ref|YP_920473.1| 174 VDGERIVKAFVRIGFVHRGIEKAA 197
                                    569************999998865 PP

  == domain 2  score: 167.0 bits;  conditional E-value: 7.2e-53
                                    T-HHHHHHHHHHHHHHHHHHHHHHSSSSS-TTBESSBBSS---TTHHHHHHHHHHHHHHHHHHHHHHHHSSSSHHHHHSS CS
                 Complex1_49kDa   3 GaltvflyafreRekildlleevtGaRltasyiriGGvarDlpegllekikeflkelekkldeleklltknrifkkRtkg 82 
                                    G  t+f++++  Re i+dllee++G+R+++s++ iGGv+rD+p+ ll++++e ++++++++++l + l+  + +++Rtkg
  gi|119719978|ref|YP_920473.1| 268 GFETMFMWVWGLRETIMDLLEEISGNRVHKSFVTIGGVRRDVPDALLRRVSERVETFRREFESLLESLSYSEEIISRTKG 347
                                    889************************************************************999999999999***** PP

                                    SS-BSHHHHHHHTT-SSSSGGGT-TTTHHHHSS-SSGGGS-------SSBSHHHHHHHHHHHHHHHHHHHHHHHHT--.S CS
                 Complex1_49kDa  83 vgvlskeealelgltGpvlRasGvkyDlRkaepYeaYdeldfdvpvgeegDvydRylvrveEmrqSlkIieqaleklpeg 162
                                    +g +s ++a +++++Gpv Ra+G ++D+R+ epY aY e++f+vp+++egDvy+ + vrv+E+ +S++Ii+q++ek+p+g
  gi|119719978|ref|YP_920473.1| 348 IGRYSLDDARKYCAVGPVRRAAGDPFDVRRIEPYGAYPEVEFEVPTSNEGDVYNLIRVRVKEVVESASIIQQLVEKMPSG 427
                                    ******************************************************************************98 PP

                                    - CS
                 Complex1_49kDa 163 p 163
                                    +
  gi|119719978|ref|YP_920473.1| 428 N 428
                                    6 PP

  == domain 3  score: 73.9 bits;  conditional E-value: 1.8e-24
                                    ---SEEEEEEEEETTEEEEEEEEEESSSS-SEEEEE-HHHHTTTTHHHHTTTS-SGGGTHHHHTT---HHHHH- CS
                 Complex1_49kDa 198 kvpkgevyaavEapkGelgvylvsdgsskpyrlkirapsfvnlqaleellkgellaDvvailgsldivlgevDR 271
                                    +vp+ge+y+++Eap+Gel +y+ ++++++pyr+k+r+p+ +n+q  +++l+g++l+D+++++ s+d++++++DR
  gi|119719978|ref|YP_920473.1| 438 TVPEGEAYSRIEAPRGELFYYVKANNTHNPYRVKVRTPTLANIQLAAKILEGQTLSDFPVVVTSIDPCFSCMDR 511
                                    58***********************************************************************9 PP

>> Complex1_30kDa  Respiratory-chain NADH dehydrogenase, 30 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.5   0.0   5.2e-26   3.1e-22       1     118 [.      10     124 ..      10     128 .. 0.90
   2 ?   -2.2   0.0         1   6.1e+03      38      61 ..     452     475 ..     443     493 .. 0.60

  Alignments for each domain:
  == domain 1  score: 79.5 bits;  conditional E-value: 5.2e-26
                                    EE--HHHHHHHHHHHHH...TT--EEEEEEEEETTSSSEEEEEEEE--S-.-EEEEEE....-S-BEE--TTT-STHHHH CS
                 Complex1_30kDa   1 lvvepedllevakflkdeeelgfdvlsdltavDekeerfevvyhllsleknerirvkvevdeeepevpSvtdlfpgadwy 80 
                                    ++v+pe ++e+++ l     +g+ +l+ +tavD  ++++e++yh+      ++++vk+  ++ +p++pS+++++pgad+y
  gi|119719978|ref|YP_920473.1|  10 VQVPPEGIREAVRRLVA---EGYAHLTAITAVDL-QDSIELIYHFDGGGGYRHVSVKL--PRANPTLPSIAQVVPGADYY 83 
                                    5799************9...89***********7.69*********665558899999..99****************** PP

                                    HHHHHHHSHHBCTTSSTSS-SSSSTTS...SS-TTSTTS-- CS
                 Complex1_30kDa  81 EREayDmfGivfeghpdlrrillpedf...eghPLRkdfpl 118
                                    E+E++D+fG++f++  + rr++lpe +      PL kd++ 
  gi|119719978|ref|YP_920473.1|  84 EKEVRDLFGVNFQDGAEKRRFILPECYppdAPPPLLKDVDP 124
                                    ***********************99985443349***9975 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1
                                    SEEEEEEEE--S-...-EEEEEE... CS
                 Complex1_30kDa  38 rfevvyhllslekn..erirvkvevd 61 
                                    r e++y++   +++   r++v++  +
  gi|119719978|ref|YP_920473.1| 452 RGELFYYVKANNTHnpYRVKVRT--P 475
                                    66788888855333134444444..3 PP

>> NiFeSe_Hases  Nickel-dependent hydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.9   0.1     2e-17   1.2e-13       1      69 [.     191     259 ..     191     261 .. 0.98
   2 !    3.0   0.0    0.0063        38     392     444 ..     416     464 ..     405     474 .. 0.73
   3 ?   -1.7   0.8      0.17     1e+03     492     502 ..     498     508 ..     494     509 .. 0.90

  Alignments for each domain:
  == domain 1  score: 50.9 bits;  conditional E-value: 2e-17
                                    --HHHHTTTS-GGGHHHHHHTT-SSSTTHHHHHHHHHHHHHHT----HHHHHHHHHHHHHHHHHHHHHH CS
                   NiFeSe_Hases   1 RGlElilkgrdprdawalvqRiCGVCttvHalasvravedAlgikipknarlirnliaaalllhdhivh 69 
                                    RG+E+  + r      +lv+RiCG+C t+Ha++ v+ave+ l++++p+ a ++r+l+a  + +h+h ++
  gi|119719978|ref|YP_920473.1| 191 RGIEKAAESRSFFRDIFLVERICGICSTSHAWCFVEAVERLLNMEVPRRAAYLRTLVAELERIHSHALW 259
                                    9**********99999**************************************************987 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.0063
                                    HHHHHHHHHHTTB---B--TT-SGGGS-SEEEEEEEEEETTEEEEEEEEEETT CS
                   NiFeSe_Hases 392 wldelvenikkgdtetaneekldkkevpkeakGvglveapRGaLsHwikikdg 444
                                     +++lve++ +g+    +       +vp+  + +  +eapRG L  ++k +++
  gi|119719978|ref|YP_920473.1| 416 IIQQLVEKMPSGNPVPPKPF---MGTVPE-GEAYSRIEAPRGELFYYVKANNT 464
                                    56677777777643333333...445666.89999*************98875 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.17
                                    HHHHT--BHHH CS
                   NiFeSe_Hases 492 tihSfDPClAC 502
                                    ++ S DPC +C
  gi|119719978|ref|YP_920473.1| 498 VVTSIDPCFSC 508
                                    689******** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (537 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 3721.14
//
Query:       gi|119719979|ref|YP_920474.1|  [L=233]
Description: 4Fe-4S ferredoxin iron-sulfur binding domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-14   53.6   9.1    5.3e-07   29.2   0.5    2.2  2  Fer4      4Fe-4S binding domain
    1.1e-09   38.2   6.5    1.7e-09   37.6   6.5    1.3  1  Fer4_10   4Fe-4S dicluster domain
    1.3e-09   38.4   7.5    2.6e-09   37.5   7.5    1.5  1  Fer4_7    4Fe-4S dicluster domain
    3.8e-09   37.3   6.2    0.00013   22.9   0.5    2.2  2  Fer4_16   4Fe-4S double cluster binding domain
    5.4e-09   36.1   4.8    9.3e-09   35.3   4.8    1.4  1  Fer4_9    4Fe-4S dicluster domain
    6.7e-08   32.3  11.9    2.2e-05   24.3   1.9    2.2  2  Fer4_6    4Fe-4S binding domain
    9.2e-08   32.1   9.3    0.00018   21.6   1.3    2.0  2  Fer4_21   4Fe-4S dicluster domain
    3.3e-07   30.0  11.0    0.00022   21.1   1.4    2.3  2  Fer4_2    4Fe-4S binding domain
      1e-05   26.0   7.5    3.4e-05   24.3   7.5    1.8  1  Fer4_17   4Fe-4S dicluster domain
    6.2e-05   23.4   8.8    0.00023   21.5   9.1    1.7  2  Fer4_8    4Fe-4S dicluster domain
    0.00031   21.5  18.0      0.013   16.4   4.4    2.3  2  Fer4_3    4Fe-4S binding domain
    0.00049   20.8   8.2      0.019   15.7   8.2    2.3  1  Fer4_15   4Fe-4S single cluster domain
     0.0019   18.6  11.7      0.068   13.7   3.2    2.2  2  Fer4_4    4Fe-4S binding domain
     0.0034   18.2   5.0       0.82   10.6   0.5    2.2  2  Fer4_22   4Fe-4S dicluster domain
     0.0047   17.4   9.8       0.46   11.0   1.3    2.4  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
  ------ inclusion threshold ------
        1.1    9.5   9.0        1.1    9.5   1.5    2.2  2  Fer4_18   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.5   4.8e-10   5.3e-07       3      24 .]      42      63 ..      40      63 .. 0.93
   2 !   28.5   2.7     8e-10   8.9e-07       3      24 .]      84     105 ..      82     105 .. 0.90

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 4.8e-10
                                   EETTTSSS-THHHHHSTTTEEE CS
                           Fer4  3 ideekCigCGaCvevCPvgAIt 24
                                    d +kC gC +C+  CP gAIt
  gi|119719979|ref|YP_920474.1| 42 LDRDKCLGCSLCARSCPSGAIT 63
                                   699******************7 PP

  == domain 2  score: 28.5 bits;  conditional E-value: 8e-10
                                    EETTTSSS-THHHHHSTTTEEE CS
                           Fer4   3 ideekCigCGaCvevCPvgAIt 24 
                                    +++  Ci+CG C+evCP  AI+
  gi|119719979|ref|YP_920474.1|  84 FNYYQCIYCGVCAEVCPGRAIS 105
                                    78889***************95 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6   6.5   1.5e-12   1.7e-09       3      56 .]      41     100 ..      39     100 .. 0.92

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 1.5e-12
                        Fer4_10   3 vidddtCirCgkCvkaCPadl......tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                     +d+d+C++C  C ++CP+ +       ++++ g++ e +  + ++++C+ cg C+e+CP
  gi|119719979|ref|YP_920474.1|  41 LLDRDKCLGCSLCARSCPSGAitmvpgGKKVVGGKEVERKIPSFNYYQCIYCGVCAEVCP 100
                                    5799***************99****9977888888899999999***************9 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.5   7.5   2.3e-12   2.6e-09       1      50 [.      46     101 ..      46     103 .. 0.81

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 2.3e-12
                         Fer4_7   1 rCigCgaCvaaCpvkaieldeeenek......gtekveidpekClgCgaCvavCPt 50 
                                    +C gC  C++ Cp++ai++ +  ++       +++ + +++ +C++Cg+C++vCP 
  gi|119719979|ref|YP_920474.1|  46 KCLGCSLCARSCPSGAITMVPGGKKVvggkevERKIPSFNYYQCIYCGVCAEVCPG 101
                                    7******************9854443444433557779999**************5 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.7   5.9e-06    0.0066       1      20 [.      46      65 ..      46      82 .. 0.86
   2 !   22.9   0.5   1.1e-07   0.00013       1      26 [.      88     113 ..      88     125 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 5.9e-06
                        Fer4_16  1 rCgtCgkCaevCPtnaikek 20
                                   +C +C  Ca +CP++ai++ 
  gi|119719979|ref|YP_920474.1| 46 KCLGCSLCARSCPSGAITMV 65
                                   5****************975 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 1.1e-07
                        Fer4_16   1 rCgtCgkCaevCPtnaikekkekeie 26 
                                    +C+ Cg CaevCP +ai++ k++ +e
  gi|119719979|ref|YP_920474.1|  88 QCIYCGVCAEVCPGRAISMVKKQPVE 113
                                    6*****************99777665 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   4.8   8.3e-12   9.3e-09       1      51 []      46     104 ..      41     104 .. 0.94

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 8.3e-12
                         Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase........eaCigCgaCveaCpkgai 51 
                                    kC gC  C ++Cp+g++++  +++k+   ++ e         +Ci Cg C+e+Cp  ai
  gi|119719979|ref|YP_920474.1|  46 KCLGCSLCARSCPSGAITMVPGGKKVVGGKEVErkipsfnyYQCIYCGVCAEVCPGRAI 104
                                    7**********************99999887779*******99************9876 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   1.9     2e-08   2.2e-05       5      24 .]      43      62 ..      42      62 .. 0.98
   2 !   13.1   2.7   6.9e-05     0.078       1      23 [.      81     103 ..      81     104 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 2e-08
                         Fer4_6  5 dpdkCigCgdCvrvCPegai 24
                                   d+dkC+gC  C+r CP gai
  gi|119719979|ref|YP_920474.1| 43 DRDKCLGCSLCARSCPSGAI 62
                                   9*****************98 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 6.9e-05
                         Fer4_6   1 vveidpdkCigCgdCvrvCPega 23 
                                    ++ +++  Ci Cg C+ vCP  a
  gi|119719979|ref|YP_920474.1|  81 IPSFNYYQCIYCGVCAEVCPGRA 103
                                    57899999************555 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   1.3   1.6e-07   0.00018      37      59 .]      43      64 ..      36      64 .. 0.88
   2 !   14.1   1.7   3.5e-05     0.039       7      25 ..      88     106 ..      82     118 .. 0.61

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.6e-07
                        Fer4_21 37 vedeCvGCnlCssvCPvedciem 59
                                     d+C GC lC+  CP +++i+m
  gi|119719979|ref|YP_920474.1| 43 DRDKCLGCSLCARSCP-SGAITM 64
                                   479*************.6***98 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 3.5e-05
                        Fer4_21   7 kCigCgkCliaCedtshqa 25 
                                    +Ci Cg C+ +C+  ++  
  gi|119719979|ref|YP_920474.1|  88 QCIYCGVCAEVCPGRAISM 106
                                    5666666666666544444 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   1.4     2e-07   0.00022       3      21 ..      40      58 ..      38      59 .. 0.91
   2 !   13.6   2.6   4.9e-05     0.055       3      21 ..      82     100 ..      80     100 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2e-07
                         Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                                   +  d+d+C+gC+ C  +CP
  gi|119719979|ref|YP_920474.1| 40 PLLDRDKCLGCSLCARSCP 58
                                   789**************** PP

  == domain 2  score: 13.6 bits;  conditional E-value: 4.9e-05
                         Fer4_2   3 vvvdtdrCigCgaCvsaCP 21 
                                    + ++   Ci Cg C  +CP
  gi|119719979|ref|YP_920474.1|  82 PSFNYYQCIYCGVCAEVCP 100
                                    5678888***********9 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   7.5   3.1e-08   3.4e-05       1      58 [.      46     101 ..      46     103 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 3.1e-08
                        Fer4_17   1 rCiqCgyClpeCpsyeaydne.pkkllraaklglleeaekeekaslCieCgeCerkCPq 58 
                                    +C +C+ C+++Cps++++     kk++     +++e+ + + +  +Ci Cg C+++CP 
  gi|119719979|ref|YP_920474.1|  46 KCLGCSLCARSCPSGAITMVPgGKKVVGG---KEVERKIPSFNYYQCIYCGVCAEVCPG 101
                                    6****************776425566666...6788888899****************5 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   9.1   2.1e-07   0.00023       3      62 ..      45     100 ..      43     103 .. 0.74
   2 !   12.2   2.1   0.00017      0.19       3      16 ..      87     100 ..      85     120 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2.1e-07
                         Fer4_8   3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCp 62 
                                    +kC +C++C  +Cp+   t     ++  + +e v+++       + ++C  cg C+evCp
  gi|119719979|ref|YP_920474.1|  45 DKCLGCSLCARSCPSGAITMVPGGKKVVGGKE-VERKIP---SFNYYQCIYCGVCAEVCP 100
                                    69************999997444444444444.333222...4679*************9 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00017
                         Fer4_8   3 ekCieCgaCqsaCp 16 
                                    ++Ci Cg C + Cp
  gi|119719979|ref|YP_920474.1|  87 YQCIYCGVCAEVCP 100
                                    46888888888887 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   4.4   1.1e-05     0.013       1      15 []      47      61 ..      47      61 .. 0.98
   2 !   10.9   5.7   0.00066      0.74       1      15 []      89     103 ..      89     103 .. 0.95

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.1e-05
                         Fer4_3  1 CtgCgaCvevCPvgA 15
                                   C+gC++C ++CP+gA
  gi|119719979|ref|YP_920474.1| 47 CLGCSLCARSCPSGA 61
                                   **************9 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00066
                         Fer4_3   1 CtgCgaCvevCPvgA 15 
                                    C+ Cg C evCP +A
  gi|119719979|ref|YP_920474.1|  89 CIYCGVCAEVCPGRA 103
                                    9***********987 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   8.2   1.7e-05     0.019       3      65 ..      42     105 ..      41     106 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.7e-05
                        Fer4_15   3 vDrdaCigcglCvaea.pevfeldedglasvllddgeiaegevpddeeeaaqeAaraCPvdAIr 65 
                                    +Drd+C gc lC++ + +  +++   g+++v +++ e++   ++  +       a++CP+ AI+
  gi|119719979|ref|YP_920474.1|  42 LDRDKCLGCSLCARSCpSGAITMVPGGKKVVGGKEVERKIPSFNYYQCIYCGVCAEVCPGRAIS 105
                                    8***************5579*********999999998888**********************7 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   3.2   6.1e-05     0.068       2      17 .]      45      60 ..      44      60 .. 0.93
   2 !    9.7   1.3    0.0012       1.4       4      15 ..      89     100 ..      80     111 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.1e-05
                         Fer4_4  2 erCigCgsCvaaCPqg 17
                                   ++C+gC  C ++CP+g
  gi|119719979|ref|YP_920474.1| 45 DKCLGCSLCARSCPSG 60
                                   89************86 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0012
                         Fer4_4   4 CigCgsCvaaCP 15 
                                    Ci Cg+C  +CP
  gi|119719979|ref|YP_920474.1|  89 CIYCGVCAEVCP 100
                                    999********* PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.4    0.0015       1.7      78      94 ..      43      59 ..      29      62 .. 0.80
   2 !   10.6   0.5   0.00073      0.82      77      94 ..      84     101 ..      71     111 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0015
                        Fer4_22 78 gesgCvGCgRCieacpv 94
                                   ++ +C GC  C ++cp+
  gi|119719979|ref|YP_920474.1| 43 DRDKCLGCSLCARSCPS 59
                                   67788888888888886 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00073
                        Fer4_22  77 fgesgCvGCgRCieacpv 94 
                                    f+ ++C+ Cg C e+cp 
  gi|119719979|ref|YP_920474.1|  84 FNYYQCIYCGVCAEVCPG 101
                                    566677777777777764 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   1.3   0.00041      0.46       2      18 ..      43      59 ..      42      62 .. 0.94
   2 !   10.6   1.7   0.00058      0.65       5      17 ..      88     100 ..      85     101 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00041
                        Fer4_13  2 DrdtCiacgaCvelaPd 18
                                   Drd+C +c +C+  +P 
  gi|119719979|ref|YP_920474.1| 43 DRDKCLGCSLCARSCPS 59
                                   9**************95 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00058
                        Fer4_13   5 tCiacgaCvelaP 17 
                                    +Ci cg+C+e++P
  gi|119719979|ref|YP_920474.1|  88 QCIYCGVCAEVCP 100
                                    8***********9 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   1.1     0.041        46      59      74 ..      45      60 ..      40      71 .. 0.86
   2 ?    9.5   1.5   0.00099       1.1      58      79 ..      86     108 ..      69     121 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.041
                        Fer4_18 59 gdcidcescvkvcPtg 74
                                    +c+ c+ c + cP g
  gi|119719979|ref|YP_920474.1| 45 DKCLGCSLCARSCPSG 60
                                   5799999999999986 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00099
                        Fer4_18  58 agdcidcescvkvcPt.gidirk 79 
                                      +ci c++c +vcP   i + k
  gi|119719979|ref|YP_920474.1|  86 YYQCIYCGVCAEVCPGrAISMVK 108
                                    468***********951455555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1594.96
//
Query:       gi|119719980|ref|YP_920475.1|  [L=322]
Description: respiratory-chain NADH dehydrogenase, subunit 1 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-71  240.2  16.1    3.6e-71  239.9  16.1    1.0  1  NADHdh    NADH dehydrogenase


Domain annotation for each model (and alignments):
>> NADHdh  NADH dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  239.9  16.1     2e-75   3.6e-71       9     297 ..      15     314 ..       7     316 .. 0.95

  Alignments for each domain:
  == domain 1  score: 239.9 bits;  conditional E-value: 2e-75
                                    HHHHHHH.HHHHHHHHHHHHHTTS--S-SSTTTTTTHHHHHHHHHCCS-----TTS-HHHHHHHHHHHHHHHHCTTTTS- CS
                         NADHdh   9 vlllvva.lltlleRkvlAriqdRlGPnrvGplGllqplaDalKlllKediipkkadkllfllapvlalilallafaviP 87 
                                    ++++++   + +leRkv+Ariq+R+GP ++Gp+Gllqp++D++KlllKe+i+p  +d + f +ap+la+++ ++ ++v+P
  gi|119719980|ref|YP_920475.1|  15 LFTVAMGfWFEYLERKVTARIQRRVGPLYAGPHGLLQPVYDFFKLLLKEEIVPGWTDVFTFRVAPILAVTIPVFGMCVLP 94 
                                    34445556899********************************************************************* PP

                                    SSS..SSS--TTHHHHHHHHHHHCHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-SS-HHHHHHC CS
                         NADHdh  88 fge..vladlnvglllilalsslgvygillaGwasnskYallGalRsaaqmisyEvalglsllavvllagslslseivea 165
                                    +++   l  ++ ++ l++ l++lgv+ + l G++  s+Y+ +G  R ++q+ +yE +++lsl + +l a+++s++ i ++
  gi|119719980|ref|YP_920475.1|  95 VAStkGLLSFEGDFALVFLLLALGVLTLSLTGYSVLSPYTAIGVGRLLVQYSMYEGVFLLSLASAALQAKTMSFEGILAY 174
                                    **5569999999******************************************************************** PP

                                    CCTT-C.CCCHHHHHHHHHHHHHHCCTCTTBTTTTSTTSSSSCCCTT-HCHHHHHHHHHHHHHHHHHHHHHHHHCT.SS- CS
                         NADHdh 166 qeeiwf.illqllafiifliallaetnraPFDlpeaesELvaGfhtEYsgmkfalfflaeyanmvlvsalavllFlgGwl 244
                                    qe++ f  l+q++++ + l+alla++++ PFDlp a++E+vaG++tE sg  +a++ l e ++mv   al+v++FlgG l
  gi|119719980|ref|YP_920475.1| 175 QESHGFlGLYQPVSLAAALVALLAKLEKRPFDLPHAKQEVVAGWMTELSGRGLAFMRLYEDLSMVWGIALIVVVFLGGPL 254
                                    *9996668899*******************************************************************99 PP

                                    HCCS.......HHHHHHHHHHHHHHHHHHHHHC----TCHHHHHHHCCTCHHHHHHHHHH CS
                         NADHdh 245 lpfs.......gllwfllKvllllflfiwiratlpRlRydqlmklgwkvllplalanlll 297
                                    +p         g+ wf+lK l++ + +i++ at  R+R+  l ++ wk + pl l+ l++
  gi|119719980|ref|YP_920475.1| 255 GPGYkelgalaGFAWFALKSLIVALAVILVSATTSRVRVYGLAEVFWKRVYPLVLLQLVV 314
                                    9977999**************************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2176.98
//
Query:       gi|119719981|ref|YP_920476.1|  [L=146]
Description: hypothetical protein Tpen_1074 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
       0.41   10.8   0.1       0.41   10.8   0.1    3.5  4  Internalin_N  Bacterial adhesion/invasion protein N terminal
       0.47    9.2   1.5       0.56    9.0   1.5    1.1  1  VSP           Giardia variant-specific surface protein
       0.83    9.4  13.2       0.54   10.0  11.4    1.7  1  DUF975        Protein of unknown function (DUF975)
       0.97    9.2  18.8        1.6    8.4  18.8    1.5  1  Oxidored_q3   NADH-ubiquinone/plastoquinone oxidoreductase ch
        2.3    8.4  13.0       0.29   11.3   6.2    2.4  3  DUF872        Eukaryotic protein of unknown function (DUF872)
        4.2    6.6   6.5        5.2    6.3   6.5    1.3  1  DUF3810       Protein of unknown function (DUF3810)


Domain annotation for each model (and alignments):
>> Internalin_N  Bacterial adhesion/invasion protein N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   1.8      0.45   1.3e+03      20      34 ..      34      48 ..      21      59 .. 0.57
   2 ?   10.8   0.1   0.00014      0.41      15      42 ..      61      87 ..      54      91 .. 0.86
   3 ?   -0.6   0.3       0.5   1.5e+03       9      22 ..      91     104 ..      84     108 .. 0.69
   4 ?   -0.1   0.2      0.33   9.7e+02      15      26 ..     124     135 ..     112     141 .. 0.65

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.45
                                   XXXXXXXXXXXXXGS CS
                   Internalin_N 20 sllvltsnGekvqAe 34
                                   ++lv +s+G  v A 
  gi|119719981|ref|YP_920476.1| 34 TVLVAMSIGLLVGAT 48
                                   355566666544443 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00014
                                   XXXXXXXXXXXXXXXXXXGSXS-SSSEE CS
                   Internalin_N 15 lvLllsllvltsnGekvqAeasitpPaP 42
                                   lv llsl++++ ++e+++A+ si+  a+
  gi|119719981|ref|YP_920476.1| 61 LVALLSLWLIVTEKEEARAD-SIYVVAA 87
                                   6779****************.9997665 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.5
                                    XXXXXXXXXXXXXX CS
                   Internalin_N   9 klltvtlvLllsll 22 
                                    +l+tv+ ++ll+++
  gi|119719981|ref|YP_920476.1|  91 VLITVAFAVLLAFA 104
                                    56777777777765 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 0.33
                                    XXXXXXXXXXXX CS
                   Internalin_N  15 lvLllsllvlts 26 
                                    l L+l+l+ +ts
  gi|119719981|ref|YP_920476.1| 124 LLLTLLLVSVTS 135
                                    445555555544 PP

>> VSP  Giardia variant-specific surface protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   1.5   0.00019      0.56     362     395 ..      41      73 ..      22      75 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00019
                            VSP 362 sGlstGaiaGisvavvvvvgGlvGflcwwficrG 395
                                     Gl  Ga aGi va+v   g lv +l  w+i   
  gi|119719981|ref|YP_920476.1|  41 IGLLVGATAGILVATV-FAGALVALLSLWLIVTE 73 
                                    5999*********986.5799*********9765 PP

>> DUF975  Protein of unknown function (DUF975)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0  11.4   0.00018      0.54      78     175 ..      20     115 ..       1     127 [. 0.77

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00018
                         DUF975  78 rkekvelkeslasfkeknfiklLvllllkelflllwsliallglliiiislslallsseieenlvvvllvlliilllivl 157
                                    + ++v+l+ +l s+   + + ++ + ll++    +++  ++ g l+++ sl l+ ++++ e      ++v +++ +li++
  gi|119719981|ref|YP_920476.1|  20 S-KRVSLSLLLLSL--GTVLVAMSIGLLVGATAGILVATVFAGALVALLSLWLI-VTEKEEARADSIYVVAAVFFVLITV 95 
                                    3.567777777777..9999999999*******999999999*********997.7777777777777788888888888 PP

                         DUF975 158 ilaiive..yayslveyilv 175
                                    ++a++ +  y++s+v+ il 
  gi|119719981|ref|YP_920476.1|  96 AFAVLLAfaYRLSPVPVILR 115
                                    88888887799999999996 PP

>> Oxidored_q3  NADH-ubiquinone/plastoquinone oxidoreductase chain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4  18.8   0.00054       1.6       3      95 ..      15     106 ..      10     140 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00054
                                    HHHHH-SBHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHIIIIIHHHHHHHHHHHSSTTS----TTCHHHHHHHHHHH CS
                    Oxidored_q3   3 llvitsknpvysalfLilsfvgvaglfillgaeFlallqilvYvGAilvlflFvimllesaeeeepeslsrslalaalli 82 
                                    +++++sk++  s l L l +v+va+ + ll     ++l   v++GA + l+   +  + ++ee+++ s+   +a++ +li
  gi|119719981|ref|YP_920476.1|  15 VGALYSKRVSLSLLLLSLGTVLVAMSIGLLVGATAGILVATVFAGALVALLSLWLIVT-EKEEARADSIYVVAAVFFVLI 93 
                                    688999*********************************************9999996.556666667777777777888 PP

                                    HHHHHHHHTT--. CS
                    Oxidored_q3  83 gllllalllllll 95 
                                     +++++ll++++ 
  gi|119719981|ref|YP_920476.1|  94 TVAFAVLLAFAYR 106
                                    8888888877755 PP

>> DUF872  Eukaryotic protein of unknown function (DUF872)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   6.2   9.7e-05      0.29      44      87 ..      21      64 ..      17      72 .. 0.86
   2 ?    1.6   1.8       0.1     3e+02      53      92 ..      56      97 ..      48     108 .. 0.60
   3 ?    0.3   0.5      0.25   7.5e+02      45      63 ..      84     102 ..      67     131 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 9.7e-05
                         DUF872 44 kvvlaallLlllGlvLlllgvvilvepseGvssavflvlGlllf 87
                                   k v ++llLl lG+vL+++++ +lv+ ++G   a  ++  l+++
  gi|119719981|ref|YP_920476.1| 21 KRVSLSLLLLSLGTVLVAMSIGLLVGATAGILVATVFAGALVAL 64
                                   78999*************************98887776666655 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.1
                         DUF872 53 lllGlvLlllgvvilvep.seGvssavflvlG.lllfiPGvY 92
                                   ++ G+++ ll++++ v+   e     +++v+  + ++i  ++
  gi|119719981|ref|YP_920476.1| 56 VFAGALVALLSLWLIVTEkEEARADSIYVVAAvFFVLITVAF 97
                                   566777778888776665255666677755541444554444 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.25
                         DUF872  45 vvlaallLlllGlvLlllg 63 
                                    vv+a +++l++ +  +ll+
  gi|119719981|ref|YP_920476.1|  84 VVAAVFFVLITVAFAVLLA 102
                                    4444444444333333333 PP

>> DUF3810  Protein of unknown function (DUF3810)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   6.5    0.0018       5.2      23      87 ..      47     110 ..      13     136 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0018
                        DUF3810  23 SvgellivllillvilylvlaiklkkrkkkkkrllkvllrvllvllvvyflftllwglnYyrepl 87 
                                    + + +l++ +++ ++++l+  + l   +k+++r+ ++++ ++++++++ + f +l ++ Y  +p+
  gi|119719981|ref|YP_920476.1|  47 ATAGILVATVFAGALVALLSLW-LIVTEKEEARADSIYVVAAVFFVLITVAFAVLLAFAYRLSPV 110
                                    3334444444444444444444.444667778899999999999999999999999999987776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1320  (0.0736237); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.33s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 939.38
//
Query:       gi|119719982|ref|YP_920477.1|  [L=99]
Description: NADH-ubiquinone oxidoreductase, chain 4L [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      5e-05   22.9   3.3    7.7e-05   22.3   3.3    1.3  1  Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase cha
  ------ inclusion threshold ------
       0.09   12.7   0.4       0.13   12.2   0.3    1.3  2  DUF2678      Protein of unknown function (DUF2678)
       0.11   12.2   0.1       0.15   11.8   0.1    1.2  1  GlutR_N      Glutamyl-tRNAGlu reductase, N-terminal domain
       0.17   11.7   1.0       0.17   11.7   1.0    3.0  3  UL73_N       Cytomegalovirus glycoprotein N terminal


Domain annotation for each model (and alignments):
>> Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase chain 4L
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   3.3   1.7e-08   7.7e-05       3      99 ..       8      90 ..       6      98 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.7e-08
                                   HHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHHHHHHHHC.............TTSCGGHHHHHHHHHHHHHHHHH CS
                    Oxidored_q2  3 llliallfliGlygvllrrnllkvliglelisnavnlllvlagvftegtlvitnpatefadplpqalvLtaivigaaetavg 84
                                   l + +ll++ G+  v ++rnl+kv +gl+ + ++  l+l +a  ++               p +  + L++ + ga+e++  
  gi|119719982|ref|YP_920477.1|  8 LGVGGLLVIAGATSVAATRNLVKVAMGLQAMILGSLLILSTAVGSS-------------PTPSVDPVLLVVAAAGASEVVS- 75
                                   56789************************************99988.............6666666777777777777655. PP

                                   HHHHHHHHHHSSS-B CS
                    Oxidored_q2 85 Lallvrlyreygtdd 99
                                   +++l+ ++  ++t+d
  gi|119719982|ref|YP_920477.1| 76 ISVLYLAWSRHRTID 90
                                   455555555566655 PP

>> DUF2678  Protein of unknown function (DUF2678)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.94   4.2e+03      29      39 ..       5      15 ..       3      24 .. 0.57
   2 ?   12.2   0.3   2.8e-05      0.13      25      90 ..      24      92 ..       8      97 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.94
                        DUF2678 29 iinlvvgglts 39
                                   i+ l vggl  
  gi|119719982|ref|YP_920477.1|  5 IVLLGVGGLLV 15
                                   55566666533 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 2.8e-05
                        DUF2678 25 ardriinlvvg....gltsllvlvtvvssfvfpslppkplniffavcillisssvivlifwyrqgdlepk 90
                                   a  +++++++g     l sll+l t v s   ps++p  l +  a    ++s+sv+  + w r   ++p+
  gi|119719982|ref|YP_920477.1| 24 ATRNLVKVAMGlqamILGSLLILSTAVGSSPTPSVDPVLLVVAAAGASEVVSISVLY-LAWSRHRTIDPH 92
                                   445566666663322477999999999999999999999988888888888877765.579999999885 PP

>> GlutR_N  Glutamyl-tRNAGlu reductase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   3.4e-05      0.15      84     107 ..      22      45 ..      15      49 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.4e-05
                        GlutR_N  84 eeavrHlfrVasGLdSlvlGEdqI 107
                                     +a r l++Va GL+ ++lG   I
  gi|119719982|ref|YP_920477.1|  22 VAATRNLVKVAMGLQAMILGSLLI 45 
                                    5799****************7665 PP

>> UL73_N  Cytomegalovirus glycoprotein N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.4     0.073   3.3e+02       2      11 ..      12      21 ..      12      25 .. 0.73
   2 ?   11.7   1.0   3.7e-05      0.17       2      13 ..      42      53 ..      42      57 .. 0.89
   3 ?   -2.6   1.1       1.1   4.9e+03       3      10 ..      62      68 ..      61      71 .. 0.45

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.073
                         UL73_N  2 GLLVLSVaag 11
                                   GLLV+  a++
  gi|119719982|ref|YP_920477.1| 12 GLLVIAGATS 21
                                   8999966654 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 3.7e-05
                         UL73_N  2 GLLVLSVaagSS 13
                                   +LL+LS a+gSS
  gi|119719982|ref|YP_920477.1| 42 SLLILSTAVGSS 53
                                   79*********7 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1.1
                         UL73_N  3 LLVLSVaa 10
                                   LLV   aa
  gi|119719982|ref|YP_920477.1| 62 LLVVA-AA 68
                                   45543.34 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 730.38
//
Query:       gi|119719983|ref|YP_920478.1|  [L=553]
Description: proton-translocating NADH-quinone oxidoreductase, chain L [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.7e-75  252.2  19.7    5.7e-75  252.2  19.7    1.8  2  Proton_antipo_M  Proton-conducting membrane transporter
    8.9e-12   44.9   0.2    5.8e-11   42.3   0.2    2.5  1  Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), 


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   1.5      0.67     6e+03      38      68 ..      67      97 ..      62     109 .. 0.54
   2 !  252.2  19.7   6.4e-79   5.7e-75       2     286 ..     112     390 ..     111     399 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 0.67
                Proton_antipo_M 38 lflltllgsliLLlgilllynltgtlefeel 68
                                   l++++ lg li L+++ ++ + +g +    l
  gi|119719983|ref|YP_920478.1| 67 LAVVNVLGFLITLYSVGYMSGEAGYVRYYSL 97
                                   4556666666666666666666654433333 PP

  == domain 2  score: 252.2 bits;  conditional E-value: 6.4e-79
                Proton_antipo_M   2 ndLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskalelglnslel 81 
                                    +dL+llyl++Elv++++ lLi++w +kp++ +A+lk+f +t++g++ LLl+++ + ++tgt+ ++ ++    l  n   +
  gi|119719983|ref|YP_920478.1| 112 EDLVLLYLFWELVGVCSALLIAYWWEKPEARRAGLKAFTVTRVGDVGLLLALATVIQATGTTRIPGVIAS--LSGNAQLA 189
                                    69****************************************************************9999..44444455 PP

                Proton_antipo_M  82 llllllllvgllvKsaqvplhlWlpdayveaPtpvsall.Aatlvkagvlllirlllllavssneisqlllilaiismll 160
                                    l +  lllv+++ Ksaq+pl +Wlpda +e+Pt+vsal+ Aat+vkagv+ll+r+ +ll+ +++ +  l++ l++ ++ll
  gi|119719983|ref|YP_920478.1| 190 LTVCSLLLVAAVGKSAQFPLFVWLPDA-MEGPTSVSALIhAATMVKAGVYLLARFYPLLQ-VAPGLGELVVYLSVFTALL 267
                                    55556788999****************.********************************.******************* PP

                Proton_antipo_M 161 gslvalaqtdiKrllAySsishlGymlialavatqygveaaiihllthalfkallFllagsviyerektrdirayggLak 240
                                     +l+al  +d+K++lAyS+i+hl++m++a+++    ++ aa+ hll+h++fkallFl+ag +i+e+ ktr++++++gL+ 
  gi|119719983|ref|YP_920478.1| 268 SALAALGASDLKKVLAYSTINHLALMFLAIGA---GALGAAMYHLLAHSMFKALLFLCAGLIIHET-KTRSLDKLEGLWD 343
                                    ********************************...6779********************9999988.9***********9 PP

                Proton_antipo_M 241 .kmPilalvllvlllslaGlPptagFlskfliLeaavavslillvla 286
                                        ++a+++lv++lslaGlPp+ gF+ k ++L+++ ++ +  +vla
  gi|119719983|ref|YP_920478.1| 344 aGLKFTAVAFLVGALSLAGLPPLPGFFTKEAVLASLESAIHGEAVLA 390
                                    6789*****************************99988777666666 PP

>> Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   0.2   6.5e-15   5.8e-11      15      57 ..      56      98 ..      48      99 .. 0.93

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 6.5e-15
                Proton_antipo_N 15 gfllDklsalmllvvtfvsllvhlYSigYMaddegyqRFfayl 57
                                   g + D +s lml+vv ++++l+ lYS+gYM+++ gy R+++++
  gi|119719983|ref|YP_920478.1| 56 GAYGDWISRLMLAVVNVLGFLITLYSVGYMSGEAGYVRYYSLI 98
                                   56779***********************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (553 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 3685.58
//
Query:       gi|119719984|ref|YP_920479.1|  [L=430]
Description: NADH dehydrogenase (quinone) [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-55  186.8  20.4      5e-55  186.8  20.4    1.7  2  Proton_antipo_M  Proton-conducting membrane transporter
    0.00076   18.9   4.7    0.00076   18.9   4.7    2.1  2  NADHdeh_related  NADH dehydrogenase I, subunit N related prot
  ------ inclusion threshold ------
        4.4    7.3   7.3        8.7    6.3   0.1    4.2  4  COX8             Cytochrome oxidase c subunit VIII


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.2       0.3   1.8e+03     247     267 ..      37      57 ..      29      71 .. 0.51
   2 !  186.8  20.4   8.4e-59     5e-55       3     289 ..     101     372 ..     100     376 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.3
                Proton_antipo_M 247 lvllvlllslaGlPptagFls 267
                                    +v+l ll    G P++ag+++
  gi|119719984|ref|YP_920479.1|  37 AVMLALLYISLGNPGLAGYVG 57 
                                    333333333346666655544 PP

  == domain 2  score: 186.8 bits;  conditional E-value: 8.4e-59
                Proton_antipo_M   3 dLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskalelglnslell 82 
                                    dLl l++++E ++++++ L ++ +++ +s+eA++k+++l  ++sl+ L gi+l y  tg+l++e  +ka          l
  gi|119719984|ref|YP_920479.1| 101 DLLRLFVAWETISVCILALTAFHRDR-ESAEAAVKYIMLCGVASLLALAGIALSYLETGSLSVESFAKA---------SL 170
                                    9*********************9777.******************************************.........99 PP

                Proton_antipo_M  83 lllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirlllllavssneisqlllilaiismllgs 162
                                    ++ +l++vg+ + +a++plh+Wlpda++ aP   sa l++++ +a++ll+ rl+     s++++  ll +la++++llg+
  gi|119719984|ref|YP_920479.1| 171 AAKMLVVVGFGAEAAVFPLHFWLPDAHMVAPSTASAVLSGITIEAAGLLVYRLVG----SEPILLRLLSVLAVAGALLGN 246
                                    99*************************************************7654....789****************** PP

                Proton_antipo_M 163 lvalaqtdiKrllAySsishlGymlialavatqygveaaiihllthalfkallFllagsviyerektrdirayggLakkm 242
                                    + a +q+d+KrllAySs++ +Gy++++l  +++ + +aa++h+  h+++ka+lF+l+ +v  +   +r +++++g     
  gi|119719984|ref|YP_920479.1| 247 FSAYRQVDVKRLLAYSSVANVGYIFLGLTSGNATARTAAYLHVAGHGFLKAALFILS-GVLLADFGSRRLDKLQGSLSGS 325
                                    *********************************************************.56677779*********9999* PP

                Proton_antipo_M 243 PilalvllvlllslaGlPptagFlskfliLeaavavslillvlavva 289
                                     +l++vl+v++l+l+G P+ + F+s+++i+ ++ + sl+l++la++a
  gi|119719984|ref|YP_920479.1| 326 KVLKAVLVVAALGLTGAPLALTFWSELYIIVGVAQSSLLLALLALTA 372
                                    ************************************99999988544 PP

>> NADHdeh_related  NADH dehydrogenase I, subunit N related protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   4.7   1.3e-07   0.00076      87     196 ..      98     205 ..      75     233 .. 0.79
   2 ?   -1.4   1.0       0.2   1.2e+03     114     178 ..     278     341 ..     220     374 .. 0.59

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.3e-07
                NADHdeh_related  87 vtgdvfnftlflaliGianiGivaavkkefvleaafnyGlvaliatlplfggaalilastGtlsifelaklagdvlliak 166
                                    + gd++   +    i +  + + a  ++++  eaa +y +++ +a+l  ++g al   +tG ls+  +ak +     +ak
  gi|119719984|ref|YP_920479.1|  98 LLGDLLRLFVAWETISVCILALTAFHRDRESAEAAVKYIMLCGVASLLALAGIALSYLETGSLSVESFAKASL----AAK 173
                                    556666544444467778888889999**************************************88887665....7** PP

                NADHdeh_related 167 lllvlGvvGetGvaP..fyaakaeifrapgap 196
                                    +l+v+G   e+ v P  f+   a ++  + a 
  gi|119719984|ref|YP_920479.1| 174 MLVVVGFGAEAAVFPlhFWLPDAHMVAPSTAS 205
                                    *************9955566667666655555 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.2
                NADHdeh_related 114 kefvleaafnyGlvaliatlplfggaalilastGtlsifelaklagdvlliaklllvlGvvGetG 178
                                    +  + +aa+ +          lf  ++++la  G   +  l++   +   + k++lv+  +G tG
  gi|119719984|ref|YP_920479.1| 278 NATARTAAYLHVAGHGFLKAALFILSGVLLADFGSRRLDKLQGSLSGSK-VLKAVLVVAALGLTG 341
                                    4444555554433222333456666677888888888877777755533.334455555555555 PP

>> COX8  Cytochrome oxidase c subunit VIII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.6     0.048   2.9e+02      16      31 ..     106     121 ..     102     122 .. 0.86
   2 ?   -1.4   0.1      0.37   2.2e+03      23      38 ..     141     156 ..     133     157 .. 0.81
   3 ?   -1.5   0.0       0.4   2.4e+03      24      42 ..     234     252 ..     232     252 .. 0.87
   4 ?    6.3   0.1    0.0014       8.7      15      33 ..     406     424 ..     393     425 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.048
                                    HHHHHHHHHHHHHHHH CS
                           COX8  16 aiglsvffvtfLlPaG 31 
                                    ++++ +++v++L++ +
  gi|119719984|ref|YP_920479.1| 106 FVAWETISVCILALTA 121
                                    899*********9876 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.37
                                    HHHHHHHHHHHHHTHH CS
                           COX8  23 fvtfLlPaGWvLsHLe 38 
                                    ++++L++aG  Ls Le
  gi|119719984|ref|YP_920479.1| 141 VASLLALAGIALSYLE 156
                                    5689999999999887 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.4
                                    HHHHHHHHHHHHTHHHHHT CS
                           COX8  24 vtfLlPaGWvLsHLesYKk 42 
                                    +++L+ aG  L +   Y++
  gi|119719984|ref|YP_920479.1| 234 LSVLAVAGALLGNFSAYRQ 252
                                    689999**99999999985 PP

  == domain 4  score: 6.3 bits;  conditional E-value: 0.0014
                                    HHHHHHHHHHHHHHHHHHH CS
                           COX8  15 qaiglsvffvtfLlPaGWv 33 
                                    +++gl+++++++L++ GW+
  gi|119719984|ref|YP_920479.1| 406 SIVGLVALSASLLVLYGWI 424
                                    689***************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2916.36
//
Query:       gi|119719985|ref|YP_920480.1|  [L=120]
Description: NADH dehydrogenase subunit A [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.5e-08   33.5   0.0    4.6e-08   33.1   0.0    1.2  1  Oxidored_q4  NADH-ubiquinone/plastoquinone oxidoreductase, ch


Domain annotation for each model (and alignments):
>> Oxidored_q4  NADH-ubiquinone/plastoquinone oxidoreductase, chain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.0   2.6e-12   4.6e-08       3      85 ..      20     105 ..       7     112 .. 0.82

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 2.6e-12
                                    HHHHHHCHSS-----HHHHS-SSSS--SS---.--HHCHHHHHHHHHHHHHHHHHHHHHHHHSST.....HHHHHHHHHH CS
                    Oxidored_q4   3 lllllsallgpkkpnkeklspYEcGfepvgearlrfsvkfylvallFliFDvevvflfpwavslkel...glfgliemll 79 
                                    l+++l+ +l +  + k k++ YE+G  p gea+++++ ++y + ll+l  +  ++fl+ +  + +e+   +++ l++++l
  gi|119719985|ref|YP_920480.1|  20 LVVVLALILVKGPEGKFKRKRYEAGNPPSGEAKTQLPYQYYGYLLLYLTVEPLLAFLYLYPGVPREQalpSFLVLLSAFL 99 
                                    45666666664446666******************************************999888884444555777788 PP

                                    HHHHHH CS
                    Oxidored_q4  80 Fllill 85 
                                    Fl+ l+
  gi|119719985|ref|YP_920480.1| 100 FLAPLV 105
                                    877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       722  (0.04027); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.21s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 998.60
//
Query:       gi|119719986|ref|YP_920481.1|  [L=171]
Description: NADH-quinone oxidoreductase, B subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-21   76.8   0.0    1.7e-21   76.4   0.0    1.1  1  Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit


Domain annotation for each model (and alignments):
>> Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.4   0.0   9.4e-26   1.7e-21       3     130 ..      51     158 ..      50     159 .. 0.89

  Alignments for each domain:
  == domain 1  score: 76.4 bits;  conditional E-value: 9.4e-26
                                    HHHHHHT-TTTTHHHHHHTEEEEEETTT-S--HHHHHHTHTTTSEEEEEESBE...EEEHHHHHHHHGGGSSEEEEESHH CS
                    Oxidored_q6   3 GcsisllaleedlldllelielryhetlladskeeeieakekeadvlvveGavtrkpkealellkelaekakaviavGtC 82 
                                    +c  +++a++ + +d+     +r++    ++++         + +++v+eG++t+k+ ea ++++++++ +k+via+G+C
  gi|119719986|ref|YP_920481.1|  51 CCGAEFAATSAPRFDA-----ERFGFLPFNSPR---------QTNLMVIEGTLTKKMGEAAKIVYDQMPWPKFVIAMGAC 116
                                    4999999999999999.....999999999999.........99************************************ PP

                                    HHH-TGGGSTT-TEE-HHHHHHHC.S-E.EEE-SSS--HHHHHHHHHH CS
                    Oxidored_q6  83 AafGGipaaannpsvgeevgellevvpvdinipGCPphpeailetlla 130
                                    A++GG++  +n+++ +    + ++ +pv+++ipGCPp+pea+++++ +
  gi|119719986|ref|YP_920481.1| 117 AIDGGLF--YNSYNIV----RPKDILPVEYFIPGCPPRPEAVAQAIIM 158
                                    *******..7744334....456779******************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       268  (0.0149478); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1368.09
//
Query:       gi|119719987|ref|YP_920482.1|  [L=161]
Description: NADH dehydrogenase (ubiquinone), 30 kDa subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.3e-34  117.0   0.0    9.1e-34  116.7   0.0    1.1  1  Complex1_30kDa  Respiratory-chain NADH dehydrogenase, 30 Kd s


Domain annotation for each model (and alignments):
>> Complex1_30kDa  Respiratory-chain NADH dehydrogenase, 30 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.7   0.0   5.1e-38   9.1e-34       5     119 ..      36     152 ..      32     155 .. 0.89

  Alignments for each domain:
  == domain 1  score: 116.7 bits;  conditional E-value: 5.1e-38
                                    HHHHHHHHHHHHH...TT--EEEEEEEEETT.SSSEEEEEEEE--...S-.-EEEEEE....-S-BEE--TTT-STHHHH CS
                 Complex1_30kDa   5 pedllevakflkdeeelgfdvlsdltavDek.eerfevvyhllsl...eknerirvkvevdeeepevpSvtdlfpgadwy 80 
                                    p +++eva+++ +    gfd+l++++++D++ ++ +evvyh +s+   +++    v+v++++e+p+ pS+ d++p+a ++
  gi|119719987|ref|YP_920482.1|  36 PGKVREVAAAAVE---AGFDHLASVEGIDWPsKGVIEVVYHAESYepeKRRFLFEVRVQLPREKPVTPSLFDVWPNALFM 112
                                    6688899999888...9**************999***********76333344458888899****************** PP

                                    HHHHHHHSHHBCTTSSTSS-SSSSTTSSS-.TTSTTS--- CS
                 Complex1_30kDa  81 EREayDmfGivfeghpdlrrillpedfegh.PLRkdfpls 119
                                    ERE+++m+G+ feghp+lrr+llp ++eg  PLRkdf++ 
  gi|119719987|ref|YP_920482.1| 113 ERETWEMLGVIFEGHPELRRLLLPPGWEGPpPLRKDFKVV 152
                                    ***************************99889*****975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1235.61
//
Query:       gi|119719988|ref|YP_920483.1|  [L=404]
Description: NADH dehydrogenase subunit D [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-90  302.2   0.0    3.6e-90  301.8   0.0    1.2  1  Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd s
  ------ inclusion threshold ------
       0.13   11.8   0.0       0.22   11.0   0.0    1.3  1  RhgB_N          Rhamnogalacturonan lyase B, N-terminal


Domain annotation for each model (and alignments):
>> Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  301.8   0.0     4e-94   3.6e-90       4     271 .]     138     404 .]     136     404 .] 0.97

  Alignments for each domain:
  == domain 1  score: 301.8 bits;  conditional E-value: 4e-94
                                    -HHHHHHHHHHHHHHHHHHHHHHSSSSS-TTBESSBBSS---TTHHHHHHHHHHHHHHHHHHHHHHHHSSSSHHHHHSSS CS
                 Complex1_49kDa   4 altvflyafreRekildlleevtGaRltasyiriGGvarDlpegllekikeflkelekkldeleklltknrifkkRtkgv 83 
                                    + t+f++af +Re +l+l ee+tGaRlt++y  +GGv+rDlp+g+ ek++++++++e++l+++ +++ +n+ +++R +gv
  gi|119719988|ref|YP_920483.1| 138 HSTMFMWAFGDREVWLQLAEELTGARLTHTYSVPGGVRRDLPQGFGEKFEKAARYMERRLQDYMRIFLENPQVVARYEGV 217
                                    68****************************************************************************** PP

                                    S-BSHHHHHHHTT-SSSSGGGT-TTTHHHHSS-SSGGGS-------SSBSHHHHHHHHHHHHHHHHHHHHHHHHT--.S- CS
                 Complex1_49kDa  84 gvlskeealelgltGpvlRasGvkyDlRkaepYeaYdeldfdvpvgeegDvydRylvrveEmrqSlkIieqaleklpegp 163
                                    gvl+k+ea +lg++Gp+lRasGvkyD R a++Y aY++l+f+vp++eegD+++R+lvrveE++qS++Ii+q+l+k+p+gp
  gi|119719988|ref|YP_920483.1| 218 GVLKKSEASRLGVVGPNLRASGVKYDARLADDYGAYKDLEFEVPTREEGDCMARMLVRVEEIKQSISIIRQVLRKMPDGP 297
                                    ******************************************************************************** PP

                                    SB---TTTS---GGGGGT-HHHHHHHHHHHHS-----SEEEEEEEEETTEEEEEEEEEESSSS-SEEEEE-HHHHTTTTH CS
                 Complex1_49kDa 164 vlaedkkvalpkkeevkksmealihhfklvtegfkvpkgevyaavEapkGelgvylvsdgsskpyrlkirapsfvnlqal 243
                                    +l+e+    lp+k++    +++   +f  +   +k+p+ge++a+ E ++Ge+ ++++ dgs kpyrl++ +psf n+  +
  gi|119719988|ref|YP_920483.1| 298 ILSEKYLKLLPPKTRER-VLQEGRVKFPALFASLKLPAGEAVARAEMGHGEIFYHITGDGSAKPYRLRVVTPSFRNVILF 376
                                    *****999999977654.45555569****************************************************** PP

                                    HHHTTTS-SGGGTHHHHTT---HHHHH- CS
                 Complex1_49kDa 244 eellkgellaDvvailgsldivlgevDR 271
                                    ++l+ g++++D++ai+gsld++ +e+DR
  gi|119719988|ref|YP_920483.1| 377 RYLAPGHRFMDFPAIYGSLDYFPPEADR 404
                                    ***************************9 PP

>> RhgB_N  Rhamnogalacturonan lyase B, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   2.5e-05      0.22      78     117 ..      11      50 ..       2      72 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 2.5e-05
                         RhgB_N  78 hylvvrsgentiYlatyitaepsvgelRfiaRlkksllpn 117
                                      l+ r+g++++Y      + ps g +Rfi+Rl+ +++ +
  gi|119719988|ref|YP_920483.1|  11 SRLLLREGDESVYELFIGPQHPSSGHMRFIVRLQGDVIVS 50 
                                    56789********88888****************998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2641.30
//
Query:       gi|119719989|ref|YP_920484.1|  [L=337]
Description: respiratory-chain NADH dehydrogenase, subunit 1 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.5e-83  278.1  19.2      1e-82  277.8  19.2    1.0  1  NADHdh    NADH dehydrogenase


Domain annotation for each model (and alignments):
>> NADHdh  NADH dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  277.8  19.2   5.8e-87     1e-82       9     297 ..      27     327 ..      20     329 .. 0.93

  Alignments for each domain:
  == domain 1  score: 277.8 bits;  conditional E-value: 5.8e-87
                                    HHHHHHHHHHHHHHHHHHHHTTS--S-SSTTT..TTTHHHHHHHHHCCS-----TTS-HHHHHHHHHHHHHHHHCTTTTS CS
                         NADHdh   9 vlllvvalltlleRkvlAriqdRlGPnrvGpl..GllqplaDalKlllKediipkkadkllfllapvlalilallafavi 86 
                                    ++l v+++++++eRk++Ar+q+R+GP +v  +  G+lq+laD+ +++++e i+p++adk+ ++lap+lal+la++ fa+i
  gi|119719989|ref|YP_920484.1|  27 TALAVLLIVIWAERKIAARVQMRVGPLYVTRHfgGVLQMLADGTRYMFQEFIVPETADKVPYMLAPALALTLAIAPFALI 106
                                    3444555**********************97667********************************************** PP

                                    -SSSSSS--..TTHHHHHHHHHHHCHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-SS-HHHHHH CS
                         NADHdh  87 Pfgevladl..nvglllilalsslgvygillaGwasnskYallGalRsaaqmisyEvalglsllavvllagslslseive 164
                                    P ++ +a++   ++l  +la+++ +++ +ll+Gw+sn+k+++ Ga+R+a ++++yEv+l+ls+l++++l+gs++l+eiv 
  gi|119719989|ref|YP_920484.1| 107 PSAPGFAPVksPYSLPALLAILASTPLSVLLMGWSSNNKFSIQGAVREAFMTLAYEVPLFLSALSMAILYGSMDLEEIVG 186
                                    *998555552266******************************************************************* PP

                                    CCCTT-C...CCCHHHHHHHHHHHHHHCCTCTTBTTTTSTTSSSSCCCTT-HCHHHHHHHHHHHHHHHHHHHHHHHHCT. CS
                         NADHdh 165 aqeeiwf...illqllafiifliallaetnraPFDlpeaesELvaGfhtEYsgmkfalfflaeyanmvlvsalavllFlg 241
                                     q    f   +ll+++a+++f++a++++ +r PFD++e+e+E+vaG+++EY+g+ f++ +   y++++++s+l +llFl 
  gi|119719989|ref|YP_920484.1| 187 RQ----FlpgALLNPVAAFTFFVAMVMSSGRLPFDIVEGEQEIVAGPYVEYTGIVFGIGMGLAYLKLYALSLLYSLLFLS 262
                                    99....33558899****************************************************************** PP

                                    SS-HCCS..........HHHHHHHHHHHHHHHHHHHHHC----TCHHHHHHHCCTCHHHHHHHHHH CS
                         NADHdh 242 Gwllpfs..........gllwfllKvllllflfiwiratlpRlRydqlmklgwkvllplalanlll 297
                                    Gw++ ++            +w+++K+++l+++++++r+++ R+R+dq+++ gw v l la++++ll
  gi|119719989|ref|YP_920484.1| 263 GWEP-LPralysvypglAGVWLFAKAFTLMLFVVFLRSVYGRYRLDQALRAGWRVYLVLAVVSILL 327
                                    **85.55588999999999********************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2335.36
//
Query:       gi|119719990|ref|YP_920485.1|  [L=156]
Description: NADH dehydrogenase subunit I [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.4e-16   60.8  27.1    2.2e-09   37.7  10.6    2.2  3  Fer4_7      4Fe-4S dicluster domain
    2.7e-16   58.6  13.3    5.7e-08   32.2   3.2    2.4  2  Fer4        4Fe-4S binding domain
    1.1e-09   39.1   4.7    0.00015   22.6   0.9    2.2  2  Fer4_16     4Fe-4S double cluster binding domain
    1.1e-09   38.3   6.4    1.6e-09   37.7   6.4    1.2  1  Fer4_21     4Fe-4S dicluster domain
    1.4e-09   37.6  15.6      8e-06   25.7   3.2    2.7  3  Fer4_6      4Fe-4S binding domain
    1.6e-09   37.8   8.9    2.4e-09   37.2   8.9    1.3  1  Fer4_9      4Fe-4S dicluster domain
    2.5e-09   37.1   7.6    3.8e-09   36.5   7.6    1.4  1  Fer4_10     4Fe-4S dicluster domain
    1.2e-08   34.5  11.7    4.3e-05   23.4   1.0    2.6  3  Fer4_2      4Fe-4S binding domain
    6.3e-08   32.5  12.2    0.00067   20.0   1.8    2.2  2  Fer4_4      4Fe-4S binding domain
    1.2e-05   25.8   9.1     0.0085   16.6   2.0    2.2  3  Fer4_17     4Fe-4S dicluster domain
    5.8e-05   23.5   9.8      0.068   13.6   0.7    2.1  2  Fer4_8      4Fe-4S dicluster domain
    0.00089   19.7  11.6       0.17   12.5   1.1    2.4  2  Fer4_13     4Fe-4S single cluster domain of Ferredoxin I
     0.0012   19.6   3.5       0.35   11.7   0.2    2.3  2  Fer4_15     4Fe-4S single cluster domain
     0.0015   19.3  16.0       0.04   14.9   2.5    2.3  2  Fer4_3      4Fe-4S binding domain
     0.0084   16.3   9.3       0.12   12.6   9.3    2.1  1  Fer4_18     4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.029   14.5   2.4      0.081   13.1   2.6    1.6  2  ETF_QO      Electron transfer flavoprotein-ubiquinone oxidore
       0.22   12.4  12.8        1.2   10.1   3.6    2.2  2  Fer4_22     4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   1.9   5.2e-07   0.00055      31      52 .]      47      68 ..      28      68 .. 0.78
   2 !   37.7  10.6   2.1e-12   2.2e-09       1      52 []      53     103 ..      53     103 .. 0.88
   3 !   25.5   0.6   1.4e-08   1.5e-05       1      24 [.      88     111 ..      88     126 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 5.2e-07
                         Fer4_7 31 veidpekClgCgaCvavCPtga 52
                                   +++ pekC++Cg C+  CP+ga
  gi|119719990|ref|YP_920485.1| 47 IKYYPEKCIQCGLCAMICPAGA 68
                                   57789**************997 PP

  == domain 2  score: 37.7 bits;  conditional E-value: 2.1e-12
                         Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                    +Ci+Cg C+  Cp++a+++  ++ ek + ++ +++++C++Cg Cv+ CP +a
  gi|119719990|ref|YP_920485.1|  53 KCIQCGLCAMICPAGAMKMYVKKGEK-KGRPGVNYQRCIFCGFCVDICPQDA 103
                                    7*****************97654444.4789999***************987 PP

  == domain 3  score: 25.5 bits;  conditional E-value: 1.4e-08
                         Fer4_7   1 rCigCgaCvaaCpvkaieldeeen 24 
                                    rCi Cg+Cv+ Cp++a+e++++++
  gi|119719990|ref|YP_920485.1|  88 RCIFCGFCVDICPQDALEMTKVHD 111
                                    8******************99865 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   3.2   5.4e-11   5.7e-08       2      23 ..      48      69 ..      47      70 .. 0.91
   2 !   31.8   2.5   7.5e-11   7.9e-08       3      24 .]      84     105 ..      82     105 .. 0.92

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 5.4e-11
                                   EEETTTSSS-THHHHHSTTTEE CS
                           Fer4  2 videekCigCGaCvevCPvgAI 23
                                   ++ +ekCi CG+C+++CP gA 
  gi|119719990|ref|YP_920485.1| 48 KYYPEKCIQCGLCAMICPAGAM 69
                                   6789****************97 PP

  == domain 2  score: 31.8 bits;  conditional E-value: 7.5e-11
                                    EETTTSSS-THHHHHSTTTEEE CS
                           Fer4   3 ideekCigCGaCvevCPvgAIt 24 
                                    +++ +Ci+CG Cv++CP +A++
  gi|119719990|ref|YP_920485.1|  84 VNYQRCIFCGFCVDICPQDALE 105
                                    8999****************85 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.9   1.4e-07   0.00015       1      21 [.      53      73 ..      53      87 .. 0.81
   2 !   18.3   0.2   3.1e-06    0.0033       1      21 [.      88     108 ..      88     133 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.4e-07
                        Fer4_16  1 rCgtCgkCaevCPtnaikekk 21
                                   +C++Cg Ca++CP++a+k+  
  gi|119719990|ref|YP_920485.1| 53 KCIQCGLCAMICPAGAMKMYV 73
                                   6****************9883 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 3.1e-06
                        Fer4_16   1 rCgtCgkCaevCPtnaikekk 21 
                                    rC+ Cg C+++CP++a++++k
  gi|119719990|ref|YP_920485.1|  88 RCIFCGFCVDICPQDALEMTK 108
                                    6****************9984 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.7   6.4   1.5e-12   1.6e-09       5      59 .]      51     106 ..      47     106 .. 0.83

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 1.5e-12
                        Fer4_21   5 edkCigCgkCliaCedtshqai..eidaktvlkvvedeCvGCnlCssvCPvedciem 59 
                                    ++kCi+Cg+C++ C+ ++++    ++++k +  v  ++C+ C  C+++CP +d++em
  gi|119719990|ref|YP_920485.1|  51 PEKCIQCGLCAMICPAGAMKMYvkKGEKKGRPGVNYQRCIFCGFCVDICP-QDALEM 106
                                    689*************99998733333444557789**************.799998 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   3.2   7.6e-09     8e-06       6      23 ..      51      68 ..      47      69 .. 0.94
   2 !   19.1   2.4   9.6e-07     0.001       3      24 .]      83     104 ..      81     104 .. 0.89
   3 ?   -1.7   0.0       3.4   3.6e+03       1       8 [.     144     151 ..     144     151 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 7.6e-09
                         Fer4_6  6 pdkCigCgdCvrvCPega 23
                                   p+kCi+Cg C+++CP+ga
  gi|119719990|ref|YP_920485.1| 51 PEKCIQCGLCAMICPAGA 68
                                   79**************98 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 9.6e-07
                         Fer4_6   3 eidpdkCigCgdCvrvCPegai 24 
                                     +++++Ci Cg Cv++CP +a+
  gi|119719990|ref|YP_920485.1|  83 GVNYQRCIFCGFCVDICPQDAL 104
                                    689***************8875 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 3.4
                         Fer4_6   1 vveidpdk 8  
                                    ++++d+++
  gi|119719990|ref|YP_920485.1| 144 KPVFDEER 151
                                    69***985 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.2   8.9   2.3e-12   2.4e-09       1      50 [.      53     103 ..      53     104 .. 0.86

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 2.3e-12
                         Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase.eaCigCgaCveaCpkga 50 
                                    kC++Cg C   Cpag++++  ++++ + r   + ++Ci+Cg Cv++Cp++a
  gi|119719990|ref|YP_920485.1|  53 KCIQCGLCAMICPAGAMKMYVKKGEKKGRPGVNyQRCIFCGFCVDICPQDA 103
                                    7****************8888888877765433699*************97 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   7.6   3.6e-12   3.8e-09       2      56 .]      47     100 ..      46     110 .. 0.80

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 3.6e-12
                        Fer4_10   2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                    +++ +++Ci+Cg C   CPa   ++ + ++ +++++  +++++C++cg Cv++CP
  gi|119719990|ref|YP_920485.1|  47 IKYYPEKCIQCGLCAMICPA-GAMKMYVKKGEKKGRPGVNYQRCIFCGFCVDICP 100
                                    567789**************.33333334444445555599*************9 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   1.0     4e-08   4.3e-05       3      22 .]      47      66 ..      45      66 .. 0.92
   2 !   17.1   2.1   4.1e-06    0.0043       2      22 .]      81     101 ..      80     101 .. 0.92
   3 ?   -2.8   0.0       8.6   9.1e+03       3       9 ..     145     151 ..     144     151 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 4e-08
                         Fer4_2  3 vvvdtdrCigCgaCvsaCPa 22
                                   +++ +++Ci+Cg C   CPa
  gi|119719990|ref|YP_920485.1| 47 IKYYPEKCIQCGLCAMICPA 66
                                   7899***************8 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 4.1e-06
                         Fer4_2   2 pvvvdtdrCigCgaCvsaCPa 22 
                                    ++ v+ +rCi Cg Cv+ CP+
  gi|119719990|ref|YP_920485.1|  81 RPGVNYQRCIFCGFCVDICPQ 101
                                    6789****************6 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 8.6
                         Fer4_2   3 vvvdtdr 9  
                                    +v+d++r
  gi|119719990|ref|YP_920485.1| 145 PVFDEER 151
                                    8999986 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   1.8   6.4e-07   0.00067       1      17 []      51      67 ..      51      71 .. 0.92
   2 !   17.8   3.1   3.2e-06    0.0034       1      16 [.      86     101 ..      86     103 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 6.4e-07
                         Fer4_4  1 qerCigCgsCvaaCPqg 17
                                   +e+Ci+Cg C  +CP g
  gi|119719990|ref|YP_920485.1| 51 PEKCIQCGLCAMICPAG 67
                                   69*************75 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 3.2e-06
                         Fer4_4   1 qerCigCgsCvaaCPq 16 
                                    ++rCi Cg Cv++CPq
  gi|119719990|ref|YP_920485.1|  86 YQRCIFCGFCVDICPQ 101
                                    58*************8 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   2.0   8.1e-06    0.0085      40      59 ..      48      67 ..      20      69 .. 0.79
   2 !   13.5   0.8   7.7e-05     0.081      41      59 ..      84     102 ..      67     104 .. 0.66
   3 !   11.8   0.9   0.00026      0.28       1      15 [.      88     102 ..      88     132 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 8.1e-06
                        Fer4_17 40 eekaslCieCgeCerkCPqg 59
                                   + + ++Ci+Cg+C++ CP+g
  gi|119719990|ref|YP_920485.1| 48 KYYPEKCIQCGLCAMICPAG 67
                                   457799************86 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 7.7e-05
                        Fer4_17  41 ekaslCieCgeCerkCPqg 59 
                                     + ++Ci Cg C+  CPq+
  gi|119719990|ref|YP_920485.1|  84 VNYQRCIFCGFCVDICPQD 102
                                    3778899999999999986 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 0.00026
                        Fer4_17   1 rCiqCgyClpeCpsy 15 
                                    rCi Cg+C++ Cp+ 
  gi|119719990|ref|YP_920485.1|  88 RCIFCGFCVDICPQD 102
                                    699999999999974 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3  12.0   8.2e-05     0.087       3      62 ..      52     100 ..      50     100 .. 0.72
   2 !   13.6   0.7   6.4e-05     0.068       3      17 ..      87     106 ..      85     142 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.2e-05
                         Fer4_8   3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCp 62 
                                    ekCi+Cg+C   Cp+   +    + ++ge+++   +  v     + ++C  cg C++ Cp
  gi|119719990|ref|YP_920485.1|  52 EKCIQCGLCAMICPAGAMK---MYVKKGEKKG---RPGV-----NYQRCIFCGFCVDICP 100
                                    69************65554...3444444444...2223.....3688***********9 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 6.4e-05
                         Fer4_8   3 ekCieCgaCqsaCp.....v 17 
                                    ++Ci Cg+C + Cp     +
  gi|119719990|ref|YP_920485.1|  87 QRCIFCGFCVDICPqdaleM 106
                                    68***********9664441 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   3.5   0.00022      0.24       4      18 ..      52      66 ..      51      67 .. 0.92
   2 !   12.5   1.1   0.00016      0.17       1      18 [.      84     101 ..      84     107 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00022
                        Fer4_13  4 dtCiacgaCvelaPd 18
                                   ++Ci cg+C++++P 
  gi|119719990|ref|YP_920485.1| 52 EKCIQCGLCAMICPA 66
                                   79************5 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00016
                        Fer4_13   1 VDrdtCiacgaCvelaPd 18 
                                    V+ ++Ci cg Cv+++P+
  gi|119719990|ref|YP_920485.1|  84 VNYQRCIFCGFCVDICPQ 101
                                    78899************5 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.3    0.0024       2.5       6      20 ..      52      66 ..      47      77 .. 0.89
   2 !   11.7   0.2   0.00033      0.35       3      20 ..      84     101 ..      83     125 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0024
                        Fer4_15  6 daCigcglCvaeape 20
                                   ++Ci cglC+  +p 
  gi|119719990|ref|YP_920485.1| 52 EKCIQCGLCAMICPA 66
                                   79***********85 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00033
                        Fer4_15   3 vDrdaCigcglCvaeape 20 
                                    v+ ++Ci cg Cv+ +p+
  gi|119719990|ref|YP_920485.1|  84 VNYQRCIFCGFCVDICPQ 101
                                    5678************74 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   5.9    0.0012       1.3       1      15 []      54      68 ..      54      68 .. 0.97
   2 !   14.9   2.5   3.8e-05      0.04       1      15 []      89     103 ..      89     103 .. 0.97

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0012
                         Fer4_3  1 CtgCgaCvevCPvgA 15
                                   C++Cg+C   CP gA
  gi|119719990|ref|YP_920485.1| 54 CIQCGLCAMICPAGA 68
                                   ************998 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 3.8e-05
                         Fer4_3   1 CtgCgaCvevCPvgA 15 
                                    C+ Cg Cv+ CP +A
  gi|119719990|ref|YP_920485.1|  89 CIFCGFCVDICPQDA 103
                                    ************998 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   9.3   0.00011      0.12      60      97 ..      53     101 ..      46     109 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00011
                        Fer4_18  60 dcidcescvkvcPtg...idirkG.......lql.eciscllcidacdk 97 
                                    +ci+c+ c  +cP g   + ++kG       + +  ci c+ c+d c +
  gi|119719990|ref|YP_920485.1|  53 KCIQCGLCAMICPAGamkMYVKKGekkgrpgVNYqRCIFCGFCVDICPQ 101
                                    7************86333556665111111155426***********65 PP

>> ETF_QO  Electron transfer flavoprotein-ubiquinone oxidoreductase, 4Fe-4S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1       1.1   1.2e+03      69      82 ..      48      61 ..      34      63 .. 0.74
   2 ?   13.1   2.6   7.7e-05     0.081      45      88 ..      59     102 ..      48     110 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.1
                                   EE-CCC--S--HHH CS
                         ETF_QO 69 qinaqnCvhCktCd 82
                                   +   + C+ C  C 
  gi|119719990|ref|YP_920485.1| 48 KYYPEKCIQCGLCA 61
                                   556789****9996 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 7.7e-05
                                    THHHH-TTS-EEEEETTTTSSEEEEE-CCC--S--HHHHH-TT- CS
                         ETF_QO  45 peqryCPagvyeivedeeakekklqinaqnCvhCktCdikdpsq 88 
                                     ++ +CPag  ++  ++ +k+ +  +n q C+ C  C    p++
  gi|119719990|ref|YP_920485.1|  59 LCAMICPAGAMKMYVKKGEKKGRPGVNYQRCIFCGFCVDICPQD 102
                                    57789*******9999988999*************995555555 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   3.6    0.0011       1.2       1      16 [.      53      68 ..      53      84 .. 0.81
   2 ?    8.6   1.6    0.0031       3.3      76      94 ..      83     101 ..      67     103 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0011
                        Fer4_22  1 rClsCgaCtlvCptCs 16
                                   +C++Cg C+++Cp+  
  gi|119719990|ref|YP_920485.1| 53 KCIQCGLCAMICPAGA 68
                                   7************865 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0031
                        Fer4_22  76 kfgesgCvGCgRCieacpv 94 
                                     ++ + C+ Cg C++ cp+
  gi|119719990|ref|YP_920485.1|  83 GVNYQRCIFCGFCVDICPQ 101
                                    4578899999999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 1016.69
//
Query:       gi|119719991|ref|YP_920486.1|  [L=161]
Description: NADH-plastoquinone oxidoreductase subunit 6 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.3e-09   35.9  17.4    5.3e-09   35.9  17.4    1.4  2  Oxidored_q3  NADH-ubiquinone/plastoquinone oxidoreductase cha
  ------ inclusion threshold ------
        6.1    6.1  12.6       0.73    9.2   8.6    1.6  2  TssN         Type VI secretion system, TssN
        8.5    6.8   6.7        1.3    9.5   0.1    2.3  2  DUF2663      Protein of unknown function (DUF2663)


Domain annotation for each model (and alignments):
>> Oxidored_q3  NADH-ubiquinone/plastoquinone oxidoreductase chain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.4       1.3     8e+03      18      22 ..       6      10 ..       2      18 .. 0.40
   2 !   35.9  17.4   8.9e-13   5.3e-09       2     137 ..      20     150 ..      19     155 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.3
                                   HHHHH CS
                    Oxidored_q3 18 Lilsf 22
                                   L+ ++
  gi|119719991|ref|YP_920486.1|  6 LVYVL 10
                                   22222 PP

  == domain 2  score: 35.9 bits;  conditional E-value: 8.9e-13
                                    HHHHHH-SBHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHIIIIIHHHHHHHHHHHSSTTS----TTCHHHHHHHHHH CS
                    Oxidored_q3   2 allvitsknpvysalfLilsfvgvaglfillgaeFlallqilvYvGAilvlflFvimllesaeeeepeslsrslalaall 81 
                                    +ll++  k  +y+a+ L ++ ++va l+ llg +++a+++ lvYvGA + +++  + ++ +       +++r++ +a++l
  gi|119719991|ref|YP_920486.1|  20 SLLAVKVKEDFYAAVLLGFVGLSVASLIALLGFTYVAVFHALVYVGATVLFVIMGVIFIGR-----GLGYERRMLAAGVL 94 
                                    6788888999**************************************9999999999744.....45666666666555 PP

                                    HHHHHHHHHTT--......--------TT-HHHHHHHHTT.TTHHHHHHHHHHHHHH CS
                    Oxidored_q3  82 igllllalllllllessssavdaqvadvsnieaigsllft.kyllpfelasllLLva 137
                                    ++++   l++++ l+ss++  +++ +   +++++++++++ +  l+f++ +l LL++
  gi|119719991|ref|YP_920486.1|  95 TSVFAGSLFYYA-LQSSAASGSPAPRVGVDLQQLSQAVLQnQVALVFLVFALALLLV 150
                                    554444444444.4434444466677788*******999978889999988887765 PP

>> TssN  Type VI secretion system, TssN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   8.6   0.00012      0.73       8      77 ..       5      78 ..       1     110 [. 0.71
   2 ?   -2.4   0.1      0.41   2.5e+03      32      45 ..     136     148 ..     123     154 .. 0.43

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00012
                           TssN  8 pllavilllilsliakknkllkkkkliiyiLlaglvla...lpgllgf.lknefvpygyillqilylllGilhl 77
                                   +l+ v++++++ + ++  +++ k  ++  +Ll  + l+   l++llgf     f+   y+ +++l++++G++++
  gi|119719991|ref|YP_920486.1|  5 LLVYVLISCAVAVASSLLAVKVKEDFYAAVLLGFVGLSvasLIALLGFtYVAVFHALVYVGATVLFVIMGVIFI 78
                                   3444444444444444455556667788888777665511166777776566788999**************98 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.41
                           TssN  32 kliiyiLlaglvla 45 
                                     ++++ L+++l l 
  gi|119719991|ref|YP_920486.1| 136 VALVF-LVFALALL 148
                                    22222.22222222 PP

>> DUF2663  Protein of unknown function (DUF2663)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   3.2      0.53   3.2e+03      46      67 ..      20      41 ..       1      79 [. 0.53
   2 ?    9.5   0.1   0.00021       1.3      15      69 ..      84     149 ..      83     155 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.53
                        DUF2663 46 sllsallessvlllllllvall 67
                                   sll++ ++++++  +ll ++ l
  gi|119719991|ref|YP_920486.1| 20 SLLAVKVKEDFYAAVLLGFVGL 41
                                   4444444444444444433332 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00021
                        DUF2663  15 lekrllllsllallvlllfliyvlik...........ssslssllsallessvlllllllvallyv 69 
                                    +e+r+l+  +l+ +++  +++y l+               l++l +a+l+++v l++l+++++l++
  gi|119719991|ref|YP_920486.1|  84 YERRMLAAGVLTSVFAGSLFYYALQSsaasgspaprvGVDLQQLSQAVLQNQVALVFLVFALALLL 149
                                    78999999999999999999999888999999988877788****************999887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1211  (0.0675442); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 1046.24
//
Query:       gi|119719992|ref|YP_920487.1|  [L=101]
Description: NADH-ubiquinone oxidoreductase, chain 4L [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.6e-13   49.5   8.4    3.2e-13   49.2   8.4    1.1  1  Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase cha


Domain annotation for each model (and alignments):
>> Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase chain 4L
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.2   8.4   1.8e-17   3.2e-13       2     103 ..       8      96 ..       7      99 .. 0.96

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 1.8e-17
                                    HHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHHHHHHHHC.............TTSCGGHHHHHHHHHHHHHH CS
                    Oxidored_q2   2 lllliallfliGlygvllrrnllkvliglelisnavnlllvlagvftegtlvitnpatefadplpqalvLtaivigaaet 81 
                                    +l+ +a+lf+iG++g +++r+++kv+i+le++ n+v l+l++++++              + +++ +l L+ai+++  e+
  gi|119719992|ref|YP_920487.1|   8 YLAASAALFGIGALGAVVSRSVVKVMISLEIMFNGVLLALLTLASMG-------------NPLVGYTLSLFAIALSSVEV 74 
                                    7899*****************************************99.............9999**************** PP

                                    HHHHHHHHHHHHHSSS-BCCG- CS
                    Oxidored_q2  82 avgLallvrlyreygtddvqel 103
                                     +++++++ lyr ++++dv e+
  gi|119719992|ref|YP_920487.1|  75 GLLVSVFILLYRRTRSLDVYEI 96 
                                    ******************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       726  (0.0404931); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.32u 0.25s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 822.25
//
Query:       gi|119719993|ref|YP_920488.1|  [L=500]
Description: proton-translocating NADH-quinone oxidoreductase, chain M [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.6e-61  206.6  26.8    4.6e-61  206.6  26.8    1.9  2  Proton_antipo_M  Proton-conducting membrane transporter
     0.0058   16.7   0.3     0.0058   16.7   0.3    2.6  2  Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), 


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   1.0      0.43   3.9e+03      56      61 ..      47      52 ..       6      94 .. 0.50
   2 !  206.6  26.8   5.1e-65   4.6e-61       1     280 [.     137     415 ..     137     433 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.43
                Proton_antipo_M 56 lynltg 61
                                   ly  +g
  gi|119719993|ref|YP_920488.1| 47 LYLTNG 52
                                   233333 PP

  == domain 2  score: 206.6 bits;  conditional E-value: 5.1e-65
                Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskalelglnsle 80 
                                    +++++ +y++lEl+l+p++lLi+++++  ++l+ ++ +++ t +g l++L+g l + +  g  +f +  k + lgl++  
  gi|119719993|ref|YP_920488.1| 137 STNIIEFYVFLELTLIPSFLLIAFYGYG-ERLKIAIMYLIWTHVGALLFLIGALTVGSKVG-FDFVDPEKGFLLGLGEGV 214
                                    6899*********************999.99999**********************99999.9999999999******** PP

                Proton_antipo_M  81 lllllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirllllla.vssneisqlllilaiisml 159
                                     +l++ l++vgl vK+a++ lh+Wlp a+ eaPtp+sall+  l  +g+ +++r++ +l+ +   ++s +l++ a+++m+
  gi|119719993|ref|YP_920488.1| 215 GVLAFWLMVVGLSVKLAAAGLHMWLPYAHAEAPTPISALLSPNLIGLGGAMMFRVVYVLFpKTFAAASPVLMAWALVTMI 294
                                    ****************************************999***********9999888999999************* PP

                Proton_antipo_M 160 lgslvalaqtdiKrllAySsishlGymlialavatqygveaaiihllthalfkallFllagsviyerektrdirayggLa 239
                                    +g+l+al+q+d KrllAySsis++Gy+l++la   +ygv++ ++h ++ha+ ka lF++ag +i   +  rdi+++ggLa
  gi|119719993|ref|YP_920488.1| 295 YGGLMALSQSDFKRLLAYSSISQMGYLLLGLASVDVYGVAGTFLHYMVHAFGKAILFAVAGILIATYHGLRDITRMGGLA 374
                                    ******************************************************************************** PP

                Proton_antipo_M 240 kkmPilalvllvlllslaGlPptagFlskfliLeaavavsl 280
                                     kmP +a + l++++ ++G+Ppt+g +s+ liL +ava  l
  gi|119719993|ref|YP_920488.1| 375 SKMPYTASLALIGFMHITGIPPTLGIWSEYLILRGAVAHAL 415
                                    **********************************9998765 PP

>> Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.3   6.4e-07    0.0058      13      47 ..      69     103 ..      59     125 .. 0.85
   2 ?   -2.5   0.5      0.62   5.5e+03      23      36 ..     170     183 ..     169     185 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6.4e-07
                Proton_antipo_N  13 eigfllDklsalmllvvtfvsllvhlYSigYMadd 47 
                                    ++++ +D++  l+++ v + ++++ lYS+ YM++ 
  gi|119719993|ref|YP_920488.1|  69 TFSLVMDPMVFLVAFSVAVTTSVIALYSSPYMEHR 103
                                    58999***************************984 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.62
                Proton_antipo_N  23 almllvvtfvsllv 36 
                                    a+m l+ t v++l 
  gi|119719993|ref|YP_920488.1| 170 AIMYLIWTHVGALL 183
                                    7999****999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (500 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       747  (0.0416643); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.39
# Mc/sec: 3850.55
//
Query:       gi|119719994|ref|YP_920489.1|  [L=691]
Description: proton-translocating NADH-quinone oxidoreductase, chain L [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-55  188.4  27.9    2.4e-52  177.9  26.9    3.7  4  Proton_antipo_M  Proton-conducting membrane transporter
    2.7e-10   40.2   4.5    2.7e-10   40.2   4.5    3.1  3  Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), 


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   2.5      0.33     3e+03     133     184 ..      16      70 ..       4     101 .. 0.55
   2 ?   -2.6   0.3      0.27   2.5e+03       6      50 ..      85     126 ..      81     127 .. 0.56
   3 !   18.0   0.0   1.5e-07    0.0013       1      30 [.     129     158 ..     129     163 .. 0.92
   4 !  177.9  26.9   2.7e-56   2.4e-52      30     293 .]     177     459 ..     173     459 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.33
                Proton_antipo_M 133 irlllllavssneisqlllilaiismllgslvalaqt.diKr..llAySsishlG 184
                                    +  +ll   +s+ +++ + il+i+   l+s+ a a++ + K+   l y  ++ lG
  gi|119719994|ref|YP_920489.1|  16 TLAVLLANRYSWRVKSAISILSILVSALTSTYAAAEFlSSKEpiHLQYTWVGSLG 70 
                                    3333445577888888888888776666666665543144542234455555555 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.27
                Proton_antipo_M   6 llylglElvllplylLiglwkkkpksleAslklflltllgsliLL 50 
                                    +l++++ ++l+++y    + + + +  e    lf+++++gs++LL
  gi|119719994|ref|YP_920489.1|  85 ALVVSWLCFLIAVYS---YEYMRGEVGETRYWLFFTFFVGSMMLL 126
                                    445555555554443...333334446666778888888888887 PP

  == domain 3  score: 18.0 bits;  conditional E-value: 1.5e-07
                Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpk 30 
                                    +++L++l++g+E+++l++y Lig w+++++
  gi|119719994|ref|YP_920489.1| 129 SDNLVSLFVGWEGTGLASYALIGHWFTDEE 158
                                    79************************9976 PP

  == domain 4  score: 177.9 bits;  conditional E-value: 2.7e-56
                Proton_antipo_M  30 ksleAslklflltllgsliLLlgilllynltgtlefeelskal..elglnslelllllllllvgllvKsaqvplhlWlpd 107
                                    + ++++l +++ t+lg++ +++gi+ l++l gt+ ++++++a   +  ++   l + l ll++g+l+Ksaq+p+h Wl+ 
  gi|119719994|ref|YP_920489.1| 177 EPSHSGLRAIVFTRLGDVGMVVGIATLHTLLGTTLIPAVAQASwaSELFARGVLPAFLWLLFLGALAKSAQFPFHEWLVT 256
                                    567899***********************************9887677777777788899******************** PP

                Proton_antipo_M 108 ayveaPtpvsall.Aatlvkagvlllirllllla.........vssneisql...llilaiismllgslvalaqtdiKrl 174
                                    a + +Pt+vsal+ Aat+vkagv+  +r+ ++l            s  ++ +   l++l++ ++++ +++a++ +++K +
  gi|119719994|ref|YP_920489.1| 257 A-MTGPTSVSALIhAATMVKAGVYFALRFAPILVaaylalepvGGSAVVQGFlggLALLGAFTAFMMATMAVVSRELKLV 335
                                    *.***************************999874443333322234455553335799999****************** PP

                Proton_antipo_M 175 lAySsishlGymlialav.....atqygveaaiihllthalfkallFllagsviyerektrdirayggLakkmPilalvl 249
                                    lA+S+ s+lGym++++a+     + + g+ a + hl++ha+fka+lFl+ag+vi++  ++r i+++ggL+k mP++a+++
  gi|119719994|ref|YP_920489.1| 336 LAFSTASQLGYMFLGVAAgtlaaGAVGGLYAGFSHLMSHAVFKASLFLAAGAVIHAV-HSRFIDDMGGLSKDMPLTAAAF 414
                                    ***************9994333334567888999*******************9987.9********************* PP

                Proton_antipo_M 250 lvlllslaGlPptagFlskfliLeaavavslillvla.vvasvlt 293
                                    l+++lslaG+Pp+agF+ k++++ a+++++l l +++ vv+++lt
  gi|119719994|ref|YP_920489.1| 415 LLAALSLAGVPPFAGFWTKDEVIHASIEAGLALPATLaVVTAALT 459
                                    *******************************99999989999887 PP

>> Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   4.5     3e-14   2.7e-10       3      56 ..      64     115 ..      61     119 .. 0.83
   2 ?   -2.1   0.1      0.47   4.2e+03      15      37 ..     247     269 ..     233     270 .. 0.68
   3 ?   -1.4   0.4      0.28   2.5e+03      21      33 ..     317     329 ..     313     347 .. 0.77

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 3e-14
                Proton_antipo_N   3 tWlsvgglsieigfllDklsalmllvvtfvsllvhlYSigYMaddegyqRFfay 56 
                                    tW  vg+l +++g+++D+ls lm+lvv+++ +l+ +YS +YM+++ g +R+  +
  gi|119719994|ref|YP_920489.1|  64 TW--VGSLGVTVGVFFDGLSTLMALVVSWLCFLIAVYSYEYMRGEVGETRYWLF 115
                                    44..68899**********************************98665555443 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.47
                Proton_antipo_N  15 gfllDklsalmllvvtfvsllvh 37 
                                    +f + +  ++ ++  t vs+l+h
  gi|119719994|ref|YP_920489.1| 247 QFPFHEWLVTAMTGPTSVSALIH 269
                                    55555566777777899999999 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.28
                Proton_antipo_N  21 lsalmllvvtfvs 33 
                                    ++a m+++  +vs
  gi|119719994|ref|YP_920489.1| 317 FTAFMMATMAVVS 329
                                    7999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (691 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 4662.39
//
Query:       gi|119719995|ref|YP_920490.1|  [L=456]
Description: NADH dehydrogenase (quinone) [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-39  135.6  16.2    3.8e-39  134.7  16.2    1.5  1  Proton_antipo_M  Proton-conducting membrane transporter


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.7  16.2   2.1e-43   3.8e-39       6     292 ..     119     405 ..     114     406 .. 0.86

  Alignments for each domain:
  == domain 1  score: 134.7 bits;  conditional E-value: 2.1e-43
                Proton_antipo_M   6 llylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskalelglnslelllll 85 
                                    ll +++ lv+ ++y  i+l ++k  s++ + k+ l++l++s++LL ++ l   ++ +l+++ ++ a     +   + l+l
  gi|119719995|ref|YP_920490.1| 119 LLLVSWVLVSAASYASIALPRDK-YSASGASKYGLMSLASSMLLLTALGLASFNSPSLSLPSVVPA-----GREVAALAL 192
                                    6789999*************888.566666699999999998888888777777779*******99.....555566666 PP

                Proton_antipo_M  86 llllvgllvKsaqvplhlWlpday.veaPtpvsallAatlvkagv.lllirllllla.vssneisqlllilaiismllgs 162
                                     + ++++ +K++++p+h Wlpd y v  P pvs+     l+k +v l++ +++ +la  + +e+  ++ ++a+++m +g+
  gi|119719995|ref|YP_920490.1| 193 AFTVASVGFKAGAFPFHAWLPDTYgVSDPYPVSIVA-P-LSKGAVlLAFYKVSAILApEARQEWLWIVGLIALLTMTYGN 270
                                    67788899****************55669***9765.5.555555055667777777899******************** PP

                Proton_antipo_M 163 lvalaqtdiKrllAySsishlGymlialav.atqy....gveaaiihllthalfkallFllagsviyerektrdiraygg 237
                                    + al q+  + llAySsi+h Gy+l+++a+ ++q+    ++ +++++l ++++ k +lFlla  +  ++     +++++g
  gi|119719995|ref|YP_920490.1| 271 ITALLQRGFQGLLAYSSIAHAGYLLVGVAAlSSQQaaptALYGLVLQLAAYSFAKTGLFLLARLARAREGPPVALDDLRG 350
                                    ****************************997555411114567788999*************99999999********** PP

                Proton_antipo_M 238 LakkmPilalvllvlllslaGlPptagFlskfliLeaavavslillvlavvasvl 292
                                    L++++  la+  ++l+lsl+G+Pp+agF++k+ i+ aav   ++l ++a++ +++
  gi|119719995|ref|YP_920490.1| 351 LSTVDKPLAASATILVLSLMGMPPLAGFWGKLFIFLAAVGPAPWLTAVALINTGI 405
                                    ****9999**************************************999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (456 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      186  (0.0103743); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 2823.57
//
Query:       gi|119719996|ref|YP_920491.1|  [L=425]
Description: glutamate--ammonia ligase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-73  247.4   0.0    3.3e-73  246.6   0.0    1.4  1  Gln-synt_C    Glutamine synthetase, catalytic domain
    3.9e-05   23.3   0.0    8.5e-05   22.2   0.0    1.5  1  Gln-synt_N    Glutamine synthetase, beta-Grasp domain
  ------ inclusion threshold ------
      0.023   13.9   0.0      0.037   13.3   0.0    1.2  1  RE_XcyI       XcyI restriction endonuclease
       0.12   12.2   0.0       0.29   11.0   0.0    1.6  1  Gln-synt_N_2  Glutamine synthetase N-terminal domain


Domain annotation for each model (and alignments):
>> Gln-synt_C  Glutamine synthetase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  246.6   0.0   7.5e-77   3.3e-73       3     345 .]     102     422 ..     100     422 .. 0.91

  Alignments for each domain:
  == domain 1  score: 246.6 bits;  conditional E-value: 7.5e-77
                                    -HHHHHHHHHHHHHHTTCEEEEEEEEEEEEESEECCCESSEEEEEEE.TB...B.TSS-TTBHCCCCCTCCHHHHHHHHH CS
                     Gln-synt_C   3 dPRsvlkralarlaeeGltvvvgpElEFflfdkeedkeasksllevdseekgrpaekggyfsvapvdeaedlrreiveal 82 
                                     PR++lk+ +a   e+ ++v++g+ElEF+l ++                   +p ++ggy+ v+p +++ ++++eiv+ +
  gi|119719996|ref|YP_920491.1| 102 YPRNLLKKWEA---ESRYKVLLGAELEFYLARDY------------------KPVDNGGYMYVSPYSTVYPVIAEIVTKA 160
                                    69999999886...56699***********8844..................45678*********************** PP

                                    HHTT--EECCEEECCCTEEEEEE--EECHHHHHHHHHHHHHHHHHHHHTT-EEE-SSSSSTTS---BEEEEEEEEECTTE CS
                     Gln-synt_C  83 ealgieveashhEvatgQvEinlkfadalkaaDnvvtfKrvvkevArkhgltatFmpKplegdnGsgmHvhlSlwdkdgk 162
                                    e++g+ ++a+hhEv++gQ+E+   + ++l+  D +v++K+++ e A+++gl+atFmpKp++g +G+g+Hvh+S+    ++
  gi|119719996|ref|YP_920491.1| 161 EEAGLALKAAHHEVGPGQYEVLPTPMSPLALSDAIVFLKKLIWEAASARGLQATFMPKPFNGLPGNGLHVHISVH-DGDR 239
                                    ***************************************************************************.3447 PP

                                    ESSB-TTSGGGB-HHHHHHHHHHHHHHHHHHHHHS-SCCHHHHCSSSTTSSSBEEEESS-TTCSEEEE-.TSGGCSTEEE CS
                     Gln-synt_C 163 nlfadeddeyalselarhfigGllkhakaltaltaptvnSYkRlvpgyeaPvalawgarNRsallRipa.skekakrvEl 241
                                    n++++++   +l+e +r++igGll++   l ++t+pt+nSYkRlvpg+eaP++l+wg  NRs+++R+p+  ++ +  vE+
  gi|119719996|ref|YP_920491.1| 240 NVLFEDG---ELTEEGRSVIGGLLAYTVPLILFTNPTINSYKRLVPGFEAPIYLTWGRGNRSTMIRVPMgLRGASGVVEY 316
                                    7777776...5**********************************************************77999999*** PP

                                    ECEBTTS-HHHHHHHHHHHHHHHHHTT--------S-SSSS-TTTHTSS-B--SSHHHHHHHHHCS.HHHCCSS-HHHHH CS
                     Gln-synt_C 242 RlpdasaNPYLalAallaAgldGienklepgepvekdlyelspeerkgieelPasleeAlealeed.ellkevlgeevie 320
                                    Rlpd+s N YL   a+l ++ +G++++++pg++++ +++ ++      ++++P +l eAle+  e+   + e   +++++
  gi|119719996|ref|YP_920491.1| 317 RLPDSSGNVYLKALAVLYSAERGLRERVDPGPECRVNAFLADG-----YPRIPGTLGEALEKSLESiGKAPE--LRDLLS 389
                                    **************************************98877.....678*********986666355555..467888 PP

                                    HHHHHHHHCHHHH........HCT--HHHHHHH CS
                     Gln-synt_C 321 aylalkraEleel........eeevsdwelery 345
                                    +  +l + E++++         +ev++we++ry
  gi|119719996|ref|YP_920491.1| 390 KVAELEKGEWRRYleeagspeASEVTEWEVKRY 422
                                    999999999999988888887888888888887 PP

>> Gln-synt_N  Glutamine synthetase, beta-Grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   1.9e-08   8.5e-05       2      66 ..      18      79 ..      17      94 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.9e-08
                                   --EEEEEEE-SSS-EEEEEEEHHHHHHHTTTT-EEEETTSSTTT------EEEEEEEGGGEEE-S CS
                     Gln-synt_N  2 vkfvdlqFtDikgklkhvtipadelsedaleegvsFDGSsiegfaeieeSDmlLkPdlstavidP 66
                                   vkf ++ F D+ g l+   ++ ++   d +  g+ +D+ s+ gf ++e+SD  L Pdlst+ +  
  gi|119719996|ref|YP_920491.1| 18 VKFFEVVFQDLGGVLRGRVLKPEKP--DDVARGFRIDAFST-GFSGVEDSDATLLPDLSTLRVYE 79
                                   8999************999996666..88889*********.******************98765 PP

>> RE_XcyI  XcyI restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   8.2e-06     0.037      35      85 ..     242     292 ..     228     303 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.2e-06
                        RE_XcyI  35 yvkasalqklatfGlrgevlfavPslieenPkligyyrlllGfsqkelyrg 85 
                                    + +  +l + ++  + g + ++vP ++ +nP++ +y rl+ Gf +  + + 
  gi|119719996|ref|YP_920491.1| 242 LFEDGELTEEGRSVIGGLLAYTVPLILFTNPTINSYKRLVPGFEAPIYLTW 292
                                    55566677777777888899***********************99887665 PP

>> Gln-synt_N_2  Glutamine synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   6.5e-05      0.29       5      34 ..       8      37 ..       4      44 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6.5e-05
                                   ......------EEEEEEE-TTS-EEEEEE CS
                   Gln-synt_N_2  5 avveqleekqveLieflyvdlaGvtrGkal 34
                                   +  +ql+ k v++ e ++ dl+Gv rG++l
  gi|119719996|ref|YP_920491.1|  8 RAFKQLRDKGVKFFEVVFQDLGGVLRGRVL 37
                                   677899**********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2941.64
//
Query:       gi|119719997|ref|YP_920492.1|  [L=247]
Description: hypothetical protein Tpen_1090 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-44  150.9   0.0    2.8e-44  150.5   0.0    1.2  1  SIS_2     SIS domain
    9.4e-09   35.1   0.0    0.00099   18.8   0.0    2.1  2  DUF2529   Domain of unknown function (DUF2529)
    1.9e-05   24.5   0.3    0.00079   19.3   0.0    2.3  2  SIS       SIS domain


Domain annotation for each model (and alignments):
>> SIS_2  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.5   0.0   4.6e-48   2.8e-44       1     138 []       8     143 ..       8     143 .. 0.99

  Alignments for each domain:
  == domain 1  score: 150.5 bits;  conditional E-value: 4.6e-48
                                    HHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHHHTT--EEEEESGGGHHHHHHTSSSTT-BTTEEEE--GGGSSSSST..T CS
                          SIS_2   1 qYlaevteilerivetqaeaiekaaeliadslenggkvlvfGsGhSaalaeelaaragglaeferialpalalhtdaeat 80 
                                    ++++ v  i +ri  +++ ++eka+e++a++l++gg ++vfG+GhS+++a+e+++raggl+ ++++++ ++  +++a  +
  gi|119719997|ref|YP_920492.1|   8 EFYRGVVGIFDRILREEKLNLEKASEVLAHTLKSGGFIYVFGTGHSMLMAMEVFYRAGGLVRVYPLLDLSVSGFNGA--L 85 
                                    58889999*******************************************************************99..* PP

                                    HHHHHTT-TTHHHHHHHHTT--TT-EEEEE-SS--SHHHHHHHHHHHHHT-EEEEEE- CS
                          SIS_2  81 kssalerdegyakqilrlvrlkpgDvLlviSnsGnnavvveaaeaakergmkviAlts 138
                                    ks+++er++gyak++l+++++kp+  L+++SnsG+nav+ve+a +a++rg+kviA+ts
  gi|119719997|ref|YP_920492.1|  86 KSTYMERLPGYAKALLDSTPIKPNSSLIIVSNSGKNAVPVEMAVEARNRGVKVIAITS 143
                                    *********************************************************8 PP

>> DUF2529  Domain of unknown function (DUF2529)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.7e-07   0.00099      10      63 ..      14      67 ..       9      79 .. 0.85
   2 !   14.5   0.0   3.4e-06      0.02      61     162 ..      91     205 ..      81     211 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.7e-07
                                   HHHHHHH.HCCHHHHHHHHHHHHHHHHTT--EEEEE-GGGGGGHHHHHCSTT-- CS
                        DUF2529 10 tGllkriqekeeesiedaarlLaqavigdgkvyikgfgeleaveaealegkekl 63
                                    G++ ri  +e  ++e+a  +La ++ + g +y+ g+g    ++ e+++ +  l
  gi|119719997|ref|YP_920492.1| 14 VGIFDRILREEKLNLEKASEVLAHTLKSGGFIYVFGTGHSMLMAMEVFYRAGGL 67
                                   7***********************************998777777777666655 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 3.4e-06
                                    T--TTEEE.--TT----TT-EEEEEES-S--HHHHHHHHHHHHHT--EEEEESS---T...........TGGGSSS-EE- CS
                        DUF2529  61 eklpsvkk.leeekeltetDrvllfsresndkealklakkleekgievvavsskvkeeda.........lteladvfidl 130
                                    e+lp  +k l ++  +++    +++s++ +++  +++a +++++g++v+a++s + +++          l e+adv id+
  gi|119719997|ref|YP_920492.1|  91 ERLPGYAKaLLDSTPIKPNSSLIIVSNSGKNAVPVEMAVEARNRGVKVIAITSVEYSRKVppsnplgkrLYEVADVVIDN 170
                                    5555544404444478888889999999999999*******************9998887889999************** PP

                                    ---S-..SEE-TTS-EE---.HHHHHHHHHHHHHH CS
                        DUF2529 131 klkkg..lvptedgeriglP.sliaalyvYyalkl 162
                                    k+++g  ++  e  e+ + P s+i+++++ + l  
  gi|119719997|ref|YP_920492.1| 171 KVPEGdaILKIEGCEQKVAPvSTIVCSFILQLLVA 205
                                    **986659999999999999568999999988765 PP

>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1     0.016        97       8      25 ..      45      62 ..      39      64 .. 0.89
   2 !   19.3   0.0   1.3e-07   0.00079      49      90 ..     104     145 ..      88     148 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.016
                                   EEEEESHHHHHHHHHHHH CS
                            SIS  8 iyvlGaGtsyaiakelal 25
                                   iyv+G+G s  +a+e+ +
  gi|119719997|ref|YP_920492.1| 45 IYVFGTGHSMLMAMEVFY 62
                                   9*************9876 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 1.3e-07
                                    GG-STTCEEEEEESSSHHHHHHHHHHHHHHTTSEEEEEESST CS
                            SIS  49 alideddlvilisfsgetkdlvaaaelakergakiiaITdsk 90 
                                     +i+++  +i++s sg ++  v+ a +a++rg+k+iaIT+ +
  gi|119719997|ref|YP_920492.1| 104 TPIKPNSSLIIVSNSGKNAVPVEMAVEARNRGVKVIAITSVE 145
                                    5799999********************************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1934.30
//
Query:       gi|119719998|ref|YP_920493.1|  [L=90]
Description: phosphotransferase system, phosphocarrier protein HPr [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-29  102.3   0.3    1.3e-29  102.2   0.3    1.0  1  PTS-HPr   PTS HPr component phosphorylation site
  ------ inclusion threshold ------
      0.036   14.3   0.1      0.049   13.9   0.1    1.4  1  FeoA      FeoA domain


Domain annotation for each model (and alignments):
>> PTS-HPr  PTS HPr component phosphorylation site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.2   0.3   1.5e-33   1.3e-29       4      81 ..       5      82 ..       2      83 .. 0.97

  Alignments for each domain:
  == domain 1  score: 102.2 bits;  conditional E-value: 1.5e-33
                                   EEEEESTCCCSHHHHHHHHHHHTTSSSEEEEEE....EETTSHHHHHHCTCSTT-EEEEEEESTTHHHHHHHHHHHHC CS
                        PTS-HPr  4 kvtiknekGlhaRpAamlvqaasefksevtlekkdkpvnaksilglmsLgvkkGeevtvsaeGedeeealealaelle 81
                                   kv++ n++GlhaRpAa++vq+a++fks++t++k dk+++ k+il+l++Lgv  G+e+++ aeG+deeea+++l +ll+
  gi|119719998|ref|YP_920493.1|  5 KVKVSNRSGLHARPAAVFVQTARKFKSRITVRKLDKAADSKNILQLLALGVDMGDEIEIVAEGPDEEEAIAELGKLLT 82
                                   89*******************************99****************************************997 PP

>> FeoA  FeoA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   5.5e-06     0.049      11      46 ..      32      68 ..      19      78 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.5e-06
                                   EEEEEEE-T.T.SSHHHHHHHHT--TT-EEEEEEE-T CS
                           FeoA 11 rgeiarisd.edpellrrLremGlvpGarievvarap 46
                                   r +++++++ +d +   +L+++G+  G +ie+va++p
  gi|119719998|ref|YP_920493.1| 32 RITVRKLDKaADSKNILQLLALGVDMGDEIEIVAEGP 68
                                   6788888878899999*****************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 650.49
//
Query:       gi|119719999|ref|YP_920494.1|  [L=566]
Description: phosphoenolpyruvate-protein phosphotransferase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.4e-79  265.6   0.0    6.3e-79  265.1   0.0    1.2  1  PEP-utilizers_C  PEP-utilising enzyme, TIM barrel domain
    2.5e-14   53.5   0.5    2.5e-14   53.5   0.5    2.3  3  PEP-utilisers_N  PEP-utilising enzyme, N-terminal
    1.1e-10   41.0   0.1    9.6e-10   38.1   0.1    2.6  3  PEP-utilizers    PEP-utilising enzyme, mobile domain
    3.6e-05   23.0   0.0      7e-05   22.1   0.0    1.4  1  HpcH_HpaI        HpcH/HpaI aldolase/citrate lyase family


Domain annotation for each model (and alignments):
>> PEP-utilizers_C  PEP-utilising enzyme, TIM barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  265.1   0.0   1.4e-82   6.3e-79      11     293 ..     246     528 ..     237     529 .. 0.96

  Alignments for each domain:
  == domain 1  score: 265.1 bits;  conditional E-value: 1.4e-82
                                    CCCHCCCXBCEEEEEESSCHHHHHHHHCTXSSEEEEEHHHHCTTSCCHHHHHHHHHHHHHHHHHTTTSEEEEEXXXSSCC CS
                PEP-utilizers_C  11 lavtkdgkkikvlaNidtpedaekalengaeGiGLlRtEflfmareelpteeeqaeaykkvleamngrpvvvRtlDiggd 90 
                                    + vt dg++++vl N++  e++++a   g  GiGL+R+Ef +m r+e+p eee++  +kk le + grp++vR  Diggd
  gi|119719999|ref|YP_920494.1| 246 EPVTLDGRRVDVLCNAGGLEEVRAAPGYGCGGIGLFRIEFAYMVRQEAPGEEELYGLFKKSLEVLGGRPLTVRAPDIGGD 325
                                    56899*************************************************************************** PP

                                    GGSGGCHHHH.XSXGGGSSXTHHHHCCS.HHHHHHHHHHHHHHCCCCEEEEEESSXXSHHHHHHHHHHHHHHHHHHHHCT CS
                PEP-utilizers_C  91 kelpelkeepeevNPmlGfRgirlglse.pelfetqlrAllrasaagkleimlPmvasveeleeakkiieevkeelekeg 169
                                    k ++ l e+p+e+NP lG+Rg rl l++ ++l++  lrA lra+++g l++m+Pmv++vee+ee  + +++++eel++eg
  gi|119719999|ref|YP_920494.1| 326 KPVNFL-ELPKEANPQLGLRGTRLLLEYrDKLLRPLLRAALRAAVHGDLRLMFPMVSTVEEVEELSEEVRRAEEELRSEG 404
                                    ******.********************96789***********************************************7 PP

                                    CTXXTTXEEEEEEXSHHHHHTHHHHCTT..SSEEEEXHHHHHHHHHTXXCCCHCHHHHSXTTTCHHCCCHHHHHHHHHHC CS
                PEP-utilizers_C 170 vkkkkkvkvGiMiEvpsaalladklake..vdFfSiGtNDLtQytlavdRdneevaklydplepavlrlikevikaaeek 247
                                     + +   ++G+M+Evpsaall ++l+++   +F+S+GtNDLtQy+la+dR +++v k+yd+l+pavlrli++ +++    
  gi|119719999|ref|YP_920494.1| 405 FEAR-VPRLGVMVEVPSAALLSRELVEKggLSFVSFGTNDLTQYVLAADRGSAHVGKVYDELNPAVLRLIAYAVDKLGG- 482
                                    6655.569*******************9999*******************************************99765. PP

                                    CXEEEEESCCCCSCCCHHHHHHCTXSEEEEXGGGHHHHHHHHHCTT CS
                PEP-utilizers_C 248 glkvgiCGelagdpsavellvglGldelSmsaasvpaaraalaqve 293
                                    +++v +CGe+a+   av+ l+glG++ lS+ +  v ++++++++++
  gi|119719999|ref|YP_920494.1| 483 RAEVEVCGEMASRTLAVPALLGLGVQGLSVAPVFVGRVKYVVRRID 528
                                    489***************************************9986 PP

>> PEP-utilisers_N  PEP-utilising enzyme, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.5   0.5   5.5e-18   2.5e-14       5     109 ..       2     108 ..       1     114 [. 0.85
   2 ?   -2.3   0.0       1.1   4.9e+03      31      49 ..     384     402 ..     377     417 .. 0.68
   3 ?   -1.7   0.1      0.69   3.1e+03       7      40 ..     508     543 ..     506     554 .. 0.59

  Alignments for each domain:
  == domain 1  score: 53.5 bits;  conditional E-value: 5.5e-18
                                    EE-SEEEEEEE.........---.-----G.GGHHHHHHHHHHHHHHHHHHHHHHHHHH.T-HHHHHHHHHHHHHHT-HH CS
                PEP-utilisers_N   5 aspGiaiGkav.........eveveeeeveaedveaelerleeAlekvreelealaeka.lgeeeaaifeahlmlleDpe 74 
                                    +s+G+a G+++              +ee +  dve elerl +A   vre+le+l++ + +  +e++i++a+l++le  +
  gi|119719999|ref|YP_920494.1|   2 VSQGVARGRLLvvravdvlgL----VEERRVGDVEGELERLSRAGSLVRERLEELKRVLpA--AEREIVDAQLLMLE--S 73 
                                    89*********9999965431....33446689**********************855554..4589*********8..6 PP

                                    HHHHHHHHHHHHT--HHHHHHHHHHHHHHHHHHTT CS
                PEP-utilisers_N  75 lleeveerIregglnaeaAveevveefaaqfeald 109
                                    l++e+ e+++++ l+ae+Av++v e++a+++++ +
  gi|119719999|ref|YP_920494.1|  74 LVAEAGELVKSSSLSAEYAVKSVYEKYAEMLKSGS 108
                                    ******************************99855 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.1
                                    HHHHHHHHHHHHHHHHHHH CS
                PEP-utilisers_N  31 aelerleeAlekvreelea 49 
                                    +e+e l e +++++eel++
  gi|119719999|ref|YP_920494.1| 384 EEVEELSEEVRRAEEELRS 402
                                    5666666666666666655 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.69
                                    -SEEEEEEE..---.-----G.GGHHHHHHHHHHHH CS
                PEP-utilisers_N   7 pGiaiGkav..eveveeeeveaedveaelerleeAl 40 
                                    +G+ +++++  +v++ +++++ e++ +e++ + e  
  gi|119719999|ref|YP_920494.1| 508 QGLSVAPVFvgRVKYVVRRIDLEEASREVREVVESA 543
                                    677778888764445555555555555555444443 PP

>> PEP-utilizers  PEP-utilising enzyme, mobile domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.1   2.1e-13   9.6e-10       4      73 .]     140     211 ..     137     211 .. 0.91
   2 ?   -1.6   0.0      0.52   2.3e+03      59      71 ..     240     253 ..     234     254 .. 0.82
   3 ?   -2.1   0.0      0.74   3.3e+03      42      54 ..     494     506 ..     492     510 .. 0.85

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 2.1e-13
                                    S-EEEEES---HHHHTTS-..GEEEEEES--TTHHHHHHHHHHTT--EEE--SSHH.HH--TEEEEEETTTT CS
                  PEP-utilizers   4 egvILvaeetspsdiagld..kaaGivterGGmtSHaAivArelgiPaVvgvgeatielkegdlitvDgstG 73 
                                    +g I vaee++p ++ +     +aG+vt +GG t H++i+Ar  g+P  +  +  +  +++gd++++D+ +G
  gi|119719999|ref|YP_920494.1| 140 SGRIAVAEELDPIQFLEAAeeGLAGLVTRKGGLTAHVSILARLKGVPYMISGELDLGLVRDGDEAVLDCVNG 211
                                    5789************99889**************************977777777699999*******988 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.52
                                    HH--T.EEEEEETT CS
                  PEP-utilizers  59 elkeg.dlitvDgs 71 
                                    + +eg + +t+Dg+
  gi|119719999|ref|YP_920494.1| 240 SKEEGlEPVTLDGR 253
                                    5688999******7 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.74
                                    HHHTT--EEE--S CS
                  PEP-utilizers  42 ArelgiPaVvgvg 54 
                                    +r+l +Pa++g+g
  gi|119719999|ref|YP_920494.1| 494 SRTLAVPALLGLG 506
                                    799******9987 PP

>> HpcH_HpaI  HpcH/HpaI aldolase/citrate lyase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   1.6e-08     7e-05      86     156 ..     373     446 ..     356     471 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.6e-08
                                    SEEEESS--SHHHHHHHHHHTSHTTTS---...HCCC-EEEEEE-SHHHHHTHHHHHTSTTEEEEEE-HHHHHH CS
                      HpcH_HpaI  86 qvvlvPkvetaeealevvsalrepekgirg...anketrllaqiEsaegvknaeeIaavegldgvflGaeDlsa 156
                                      +++P+v t ee++e+ + +r++e++ r+   ++   rl + +E   + +  +e ++  gl  v +G++Dl+ 
  gi|119719999|ref|YP_920494.1| 373 LRLMFPMVSTVEEVEELSEEVRRAEEELRSegfEARVPRLGVMVEVPSAALLSRELVEKGGLSFVSFGTNDLTQ 446
                                    569***************************777556667788888888888899*****************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (566 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.45
# Mc/sec: 3770.96
//
Query:       gi|119720000|ref|YP_920495.1|  [L=385]
Description: N-acetylglucosamine-6-phosphate deacetylase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-25   90.3   0.5    2.1e-25   89.8   0.5    1.2  1  Amidohydro_1  Amidohydrolase family
    7.6e-12   45.4   3.4    5.3e-05   22.9   0.0    2.8  2  Amidohydro_3  Amidohydrolase family


Domain annotation for each model (and alignments):
>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.8   0.5   2.4e-29   2.1e-25       1     344 []      48     382 ..      48     382 .. 0.82

  Alignments for each domain:
  == domain 1  score: 89.8 bits;  conditional E-value: 2.4e-29
                                    EEEE-EEEEEEECETTECSSSGHHHHHSTTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTH.....HHHHHHHHHHT... CS
                   Amidohydro_1   1 ivlPGlIDaHvHleqsllrgatledwlvppetaaealesgiktalksGtttvadmgattst.....giealleaaee... 72 
                                    +v PG+ID+H+H+++++          +  e +ae +  +   + ++G+t ++++  ++++     + + ++ a+++   
  gi|119720000|ref|YP_920495.1|  48 YVAPGFIDTHIHGYGGV----------DVTEASAEEILEMSGGLAEHGVTGFLASTVAAPHerllqACSNVAAASSRwsp 117
                                    589**********9996..........88889999999999999999999999999988767777733333333333466 PP

                                    ....SSSEEEEEEESSEGGS....GCCCSHHHHHHHHHHHHHHHHHHCTTTCEE.EEEEECGTCCSHHHHHHHHHHHHHH CS
                   Amidohydro_1  73 ....lplglrilggkvsldr....gsaetskasreklkagaaetikgkadgvvk.valapheapafsdeelkealkeakk 143
                                         +lg++++g+++++++     ++  +k s ++l++++       ++g+v  v++ap+   a+  e ++ea+     
  gi|119720000|ref|YP_920495.1| 118 skgaRILGVHLEGPYLNPKMkgamNEQYFRKPSLRELDEYV-----SASRGLVRqVTVAPEVEGAL--EFIEEAS----- 185
                                    6677789*******999999998866677888888898887.....67788888888888855555..3666666..... PP

                                    HTTEEEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCC.............HHTTTHCCEEEHCTCEEEHHHHHHHHHHH CS
                   Amidohydro_1 144 rdlpvaiHaletkgevedaeaafgetiehgthlevaes.............lglldeiklilahgvhltpteaellkerl 210
                                        +++++++t++++e+a++a   ++  + h  + +              l   d+   ++++ vhl+p++++l+ + +
  gi|119720000|ref|YP_920495.1| 186 -RRGITVSVGHTDATYEQALRAVEAGARKANHIFNQMRgfhhrepgtamalLLDTDVFVEMIVDFVHLHPATVRLVYRLA 264
                                    .67788899**************************99999999999999988888889999******************9 PP

                                    HHHCEEHHHHHHHH.....SEHHHHHHHHHHHHTSCEEEEEE.CTTSSCCGGHHHHHHHHHHHHHHCCTTTTHCHCHHHH CS
                   Amidohydro_1 211 keagvahcpfsnsi.....lrsgrealrkaldeGvkvglgtD.gaasgnslnlleelrlalklqrgllyedeegglslke 284
                                       + +++ ++ +       +  +  lr +++eGv      D ga +g++l++ + +r+++           ++g   +e
  gi|119720000|ref|YP_920495.1| 265 GPLRTVLITDAVRAaglpdGEYTLGGLRIVVKEGVSR--LADsGALAGSTLTMDRAVRNMT-----------KVGANTLE 331
                                    9999997777777777666555555666667776443..445358********888*****...........999***** PP

                                    HHHHHTHHHHH...HTT-TTTSSSS-TTSB--EEEECCCTCGGGTTTCTSEEEEEEEETTEEE CS
                   Amidohydro_1 285 alrmaTingAk...alglddkvGsievGkdADlvvvdldilaafvglkkdgnvkkvivkGklv 344
                                    al+ma++ +Ak   alg+ ++vG + +G+ AD+vv+            +  +vkk+i++G++v
  gi|119720000|ref|YP_920495.1| 332 ALTMASYTPAKsvgALGR-ERVGLLRPGYAADMVVL-----------DERLEVKKTIIAGEVV 382
                                    **********94444677.6****************...........999**********997 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   5.9e-09   5.3e-05       1      40 [.      40      78 ..      40     119 .. 0.65
   2 !   22.0   1.1   1.1e-08    0.0001     410     473 .]     329     383 ..     178     383 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 5.9e-09
                   Amidohydro_3  1 eviDakGrlvlPGFvDsHtHlagggvnlrllrlpdarvts 40
                                   +v+Da+  +v+PGF+D H+H +gg v++++++ ++   +s
  gi|119720000|ref|YP_920495.1| 40 RVVDAERYYVAPGFIDTHIHGYGG-VDVTEASAEEILEMS 78
                                   69******************5554.677766666644443 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 1.1e-08
                   Amidohydro_3 410 leealalyTrgpAkalgledrk..GtLevGadADlvvldadpldvdppelaearvrltvvdGrvvy 473
                                      eal + + +pAk +g+  r   G L++G+ AD vvld ++l+v+          +t+++G+vvy
  gi|119720000|ref|YP_920495.1| 329 TLEALTMASYTPAKSVGALGRErvGLLRPGYAADMVVLD-ERLEVK----------KTIIAGEVVY 383
                                    67999999*9***99888774445**************8.555555..........6788888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2624.12
//
Query:       gi|119720001|ref|YP_920496.1|  [L=609]
Description: glutamine amidotransferase, class-II [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-36  123.6   0.0    3.3e-23   82.0   0.0    2.4  2  SIS       SIS domain
    2.6e-15   56.8   0.0    6.3e-15   55.5   0.0    1.6  1  GATase_6  Glutamine amidotransferase domain
    8.5e-12   45.1   0.0    1.9e-11   44.0   0.0    1.6  1  GATase_7  Glutamine amidotransferase domain
  ------ inclusion threshold ------
      0.032   14.3   2.9       0.86    9.7   0.4    3.0  3  DUF1707   Domain of unknown function (DUF1707)
      0.056   13.5   3.0      0.072   13.1   0.1    2.6  4  SIS_2     SIS domain


Domain annotation for each model (and alignments):
>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.0   0.0   9.2e-27   3.3e-23       4     130 ..     287     413 ..     284     414 .. 0.95
   2 !   39.4   0.0   1.4e-13   4.9e-10       9     126 ..     466     588 ..     458     589 .. 0.85

  Alignments for each domain:
  == domain 1  score: 82.0 bits;  conditional E-value: 9.2e-27
                                    TSSEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHHTTSEE CS
                            SIS   4 kakriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelakergaki 83 
                                     a+++y+++ Gts ++++ +++++ e+ g++ +v++a+e+   +l +i ++ lv++is+sget d++ ++ +ak rga+i
  gi|119720001|ref|YP_920496.1| 287 GADNVYIIANGTSLHAGMVASYYFSELVGVNPVVVSAAEFPLYYLENIGPGSLVLAISQSGETGDVLSSLYEAKLRGATI 366
                                    5889********************99999999999******9************************************** PP

                                    EEEESSTTSHHHHHSSEEEEEEEECHCSSSHCHHHHHHHHHHHHHHH CS
                            SIS  84 iaITdskgsplareadlalyinaepetlvastksltaqlaaldalav 130
                                    ++IT+  gs lar + l l i+a+pe  v++tk++t++l++l+++a+
  gi|119720001|ref|YP_920496.1| 367 LGITNYVGSRLARLSNLYLPIAAGPELAVPATKTFTSTLLLLYLVAL 413
                                    ***************888888888888***************99886 PP

  == domain 2  score: 39.4 bits;  conditional E-value: 1.4e-13
                                    EEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEE.SSSHHHHHHHHHH.HHHHTTSEEEEE CS
                            SIS   9 yvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilis.fsgetkdlvaaae.lakergakiiaI 86 
                                    yv+ +G  y++a+e+alkl+e +++++e+++a+e+khg+  l++++  v+++      +++ +  +   a e gak++a+
  gi|119720001|ref|YP_920496.1| 466 YVVSRGLTYPLALEGALKLKEASYFHAEGVEAGEFKHGPFVLVEKGFGVVFVVpVEKVSAEATYPLVgMALEAGAKVVAV 545
                                    8999******************************************9999999666667777777777*********999 PP

                                    ESSTTSHHHHHSSEEEEEEEECHC...SSSHCHHHHHHHHHHH CS
                            SIS  87 Tdskgsplareadlalyinaepet...lvastksltaqlaald 126
                                        + +l + +    ++ a+p +   l++++ ++++ql+a+ 
  gi|119720001|ref|YP_920496.1| 546 GFAGDQSLEALSEKGAAVVAAPPAerhLAPIVLAVPLQLLAYR 588
                                    888888888888666666666666666*************996 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.5   0.0   1.8e-18   6.3e-15      11     111 ..      66     175 ..      35     195 .. 0.85

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 1.8e-18
                       GATase_6  11 edevalaHvRlaivglaeeegaqPfpsedgrlllvhNGeiynykelreelpalkglafrsrsDtevllall.....eelG 85 
                                    +++val+H+R a++g ++ e a+P +   +rl++v  G+i+ny+el++++    g+++ srsD ev++++l     e  G
  gi|119720001|ref|YP_920496.1|  66 QGSVALGHTRYATHGRPTAENAHPHVDCGRRLAVVGDGSISNYEELKDKVLL-NGHRLTSRSDFEVVAHVLeeafrE--G 142
                                    456**************77777*****************************9.******************666541..1 PP

                       GATase_6  86 ......eevl.erlrGmfafaiwdkrentlila 111
                                          + vl e+l+G fa+a+ d++++ +  a
  gi|119720001|ref|YP_920496.1| 143 rapealPGVLsEKLQGFFAVAFLDASTGSIYAA 175
                                    555777888889************988887665 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.0   0.0   5.2e-15   1.9e-11       9      94 ..      83     176 ..      73     199 .. 0.86

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 5.2e-15
                       GATase_7   9 seagaQPmvssedgrlvivfnGeiyNykelreeLeakghrfrtksDtevllallea........ewgeeal.erlnGmfA 79 
                                    ++++a P v + ++rl++v +G i Ny+el+++   +ghr +++sD ev++++le+        e +  +l e+l+G fA
  gi|119720001|ref|YP_920496.1|  83 TAENAHPHV-DCGRRLAVVGDGSISNYEELKDKVLLNGHRLTSRSDFEVVAHVLEEafregrapEALPGVLsEKLQGFFA 161
                                    567788999.68999**********************************************9998899988689****** PP

                       GATase_7  80 faiwdeeekrlllaR 94 
                                    +a +d++++++++a 
  gi|119720001|ref|YP_920496.1| 162 VAFLDASTGSIYAAT 176
                                    **********99985 PP

>> DUF1707  Domain of unknown function (DUF1707)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1     0.026        93       9      23 ..     129     143 ..     123     144 .. 0.86
   2 ?   -2.9   0.0       2.1   7.4e+03      31      43 ..     167     179 ..     165     181 .. 0.74
   3 ?    9.7   0.4   0.00024      0.86      14      40 ..     412     438 ..     409     445 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.026
                        DUF1707   9 eravelLrealaeGr 23 
                                    e ++++L ea+ eGr
  gi|119720001|ref|YP_920496.1| 129 EVVAHVLEEAFREGR 143
                                    7799**********9 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.1
                        DUF1707  31 eRleaalaArtrg 43 
                                      ++ ++aA+t  
  gi|119720001|ref|YP_920496.1| 167 ASTGSIYAATTGP 179
                                    567899****965 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.00024
                        DUF1707  14 lLrealaeGrLtldEfdeRleaalaAr 40 
                                    +Lr+  +eGr++ d++   l+a+++A 
  gi|119720001|ref|YP_920496.1| 412 ALRASRQEGRIDEDTLNSKLAAVAEAA 438
                                    799999*****************9874 PP

>> SIS_2  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   0.0       4.1   1.5e+04     109     120 ..       7      18 ..       4      29 .. 0.80
   2 ?    0.4   0.0      0.17   5.9e+02      17      67 ..     274     320 ..     258     326 .. 0.55
   3 ?   13.1   0.1     2e-05     0.072      98     137 ..     331     370 ..     277     371 .. 0.70
   4 ?   -4.1   0.2       4.1   1.5e+04     126     136 ..     535     545 ..     531     546 .. 0.67

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 4.1
                                    EE-SS--SHHHH CS
                          SIS_2 109 viSnsGnnavvv 120
                                     +S sG n v++
  gi|119720001|ref|YP_920496.1|   7 AVSRSGGNVVPL 18 
                                    689999998875 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.17
                                    SHHHHHHHHHHHHHHHHTT--EEEEESGGGHHHHHHTSSSTT-BTTEEEE- CS
                          SIS_2  17 qaeaiekaaeliadslenggkvlvfGsGhSaalaeelaaragglaeferia 67 
                                    q++ ++ aa+l++        v++  +G S  + + + + +  l+++++++
  gi|119720001|ref|YP_920496.1| 274 QKKYLQLAARLVTG----ADNVYIIANGTSLHAGMVASYYFSELVGVNPVV 320
                                    45555555555443....345666666655555555555555555555554 PP

  == domain 3  score: 13.1 bits;  conditional E-value: 2e-05
                                    HTT--TT-EEEEE-SS--SHHHHHHHHHHHHHT-EEEEEE CS
                          SIS_2  98 lvrlkpgDvLlviSnsGnnavvveaaeaakergmkviAlt 137
                                    l ++ pg + l iS+sG+   v+  + +ak rg+++ ++t
  gi|119720001|ref|YP_920496.1| 331 LENIGPGSLVLAISQSGETGDVLSSLYEAKLRGATILGIT 370
                                    34579**********************************9 PP

  == domain 4  score: -4.1 bits;  conditional E-value: 4.1
                                    HHHHT-EEEEE CS
                          SIS_2 126 akergmkviAl 136
                                    a e g+kv+A+
  gi|119720001|ref|YP_920496.1| 535 ALEAGAKVVAV 545
                                    55677788776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (609 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.63u 0.32s 00:00:00.95 Elapsed: 00:00:00.51
# Mc/sec: 3567.68
//
Query:       gi|119720002|ref|YP_920497.1|  [L=415]
Description: hypothetical protein Tpen_1095 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.1e-10   38.9   0.0    5.3e-05   22.1   0.0    3.0  3  Ceramidase_alk  Neutral/alkaline non-lysosomal ceramidase, N-
  ------ inclusion threshold ------
        0.2   11.9   0.0       0.46   10.8   0.0    1.5  1  Gate            Nucleoside recognition


Domain annotation for each model (and alignments):
>> Ceramidase_alk  Neutral/alkaline non-lysosomal ceramidase, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   5.9e-09   5.3e-05      12     106 ..      16     103 ..       4     125 .. 0.82
   2 !   10.7   0.0   1.6e-05      0.15     169     217 ..     153     199 ..     148     202 .. 0.87
   3 !    2.3   0.0    0.0056        50     420     450 ..     326     356 ..     310     362 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 5.9e-09
                                    --SEEEEEESS--SS-EEEEESS--EEEEEEEEESSS--EEEEEEESSS---HHHHHHHHHHHHHHSTTT-SGGGEEEEE CS
                 Ceramidase_alk  12 GpvaevnlmGYakleqkasGlhqRlysraFivadaekkkrvvfvsldaamvsqavrlevlkkLkakygdlYteenvalsg 91 
                                     p a  +l+GY + + ++ G h  + +r  +++    +  v+ v+ld+  v++ + + v +  +++        +v++s+
  gi|119720002|ref|YP_920497.1|  16 SPPAGHELAGYIARQGRSLGAHDDVEARCMLIDW---QPAVLLVNLDLLGVDSGIVETVHRVAERE----VGAVEVVVSA 88 
                                    478999************************9988...789********998877766665554444....5778****** PP

                                    --BSBEE----SSHH CS
                 Ceramidase_alk  92 tHtHsgpggylqyll 106
                                    tHtHs+p+  +++ l
  gi|119720002|ref|YP_920497.1|  89 THTHSAPATLFTNPL 103
                                    ********9988765 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 1.6e-05
                                    -TT-TTS---EEEEEEEEE...T-EEEEEEE----B-SS-TT--SBB-H CS
                 Ceramidase_alk 169 rakYksnvdkemtlLkledasdkkeiGvlnwfavHgtslnntntlisgD 217
                                    r+   ++vd+e  ++ +++  + ++ G l  +avH+t l  +n lis D
  gi|119720002|ref|YP_920497.1| 153 REDPGRKVDDEALVVVFKR--GLQTAGYLLNYAVHPTVLGPDNLLISKD 199
                                    55556789*********99..4478**********************98 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.0056
                                    EEEEEEEEETTEEEEE-SSEE-HHHHHHHHH CS
                 Ceramidase_alk 420 ivdvqilriGqlvivavpgEvttmaGrRlre 450
                                     v++++lriG+l ++ +p+E+    + Rl++
  gi|119720002|ref|YP_920497.1| 326 EVELRVLRIGSLRLLFAPFELHSDFSLRLKR 356
                                    68999***************98888888775 PP

>> Gate  Nucleoside recognition
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   5.1e-05      0.46      30      59 ..     200     227 ..     194     253 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 5.1e-05
                           Gate  30 llepvfaplgqeldwkatvslltgfaakev 59 
                                    l++pv++ lg    wka v+l+++ aa  v
  gi|119720002|ref|YP_920497.1| 200 LVDPVLRYLG--AAWKAGVGLFLNGAAANV 227
                                    799*******..***********9996554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2898.90
//
Query:       gi|119720003|ref|YP_920498.1|  [L=370]
Description: oxidoreductase domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-18   67.8   0.0    2.1e-18   67.3   0.0    1.3  1  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f
    8.1e-09   35.5   0.0    1.4e-08   34.7   0.0    1.4  1  GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta 
  ------ inclusion threshold ------
      0.022   15.4   0.0      0.043   14.4   0.0    1.6  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
      0.023   14.4   0.0       0.67    9.6   0.0    2.3  1  ox_reductase_C  Putative oxidoreductase C terminal domain


Domain annotation for each model (and alignments):
>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.3   0.0   4.7e-22   2.1e-18       1     118 [.       3     128 ..       3     130 .. 0.92

  Alignments for each domain:
  == domain 1  score: 67.3 bits;  conditional E-value: 4.7e-22
                                    EEEEEETTSHHHHHHHHHHHHTTTTE........EEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S-G CS
                   GFO_IDH_MocA   1 lrvaiiGaGkigskhlrplnesqrle........evvalldpdaeraeavaesfgveaysdleelladpeidavivatpn 72 
                                    +rv++iG+G+ +s ++ +l    r          e+  ++++ ++ aea+a+++g+e ++  e  +  ++ d+v +a+pn
  gi|119720003|ref|YP_920498.1|   3 IRVGLIGSGWSASAQAFSLSSLGRVVrrsgfpevELRVVFSRTPAHAEALARQYGFEKWTTSESEFFGEDLDVVGIASPN 82 
                                    69*********88887666666555577788999*****************************99999************ PP

                                    GGHHHHHHHHHHTT-EEEEESSS-SSHHHHHHHHHHHHHHTS-EEE CS
                   GFO_IDH_MocA  73 gtheelakaaleagkhvllEKPlattveeakelvelaekkgklvsv 118
                                    +th+ +a++ale+g +v+lEKP+a++ +ea+e+ ++ ++ g+ v+v
  gi|119720003|ref|YP_920498.1|  83 NTHYPYALRALERGFNVVLEKPVAFNAREAEEIERYSRRVGRSVAV 128
                                    ***********************************99999998876 PP

>> GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.0   3.2e-12   1.4e-08       2     104 ..     143     258 ..     142     268 .. 0.76

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 3.2e-12
                                    HHHHTTTTSSEEEEEE.EEECBEEECHHHHCCGGSH.HCSTSHHHHTCHHHHHHHHHHHTSEEEEEE.....EEE.SEEE CS
                 GFO_IDH_MocA_C   2 elIengklGevvsvdv.wtldtragaeakkrwkrrk.kksgGvlgdlgiHdiDllqwLfGqppsvva.....algrmrqn 74 
                                     l+  g+lG+++ + +   + ++a++++++ w+ ++ + +gGv+ d+g+H +Dl  + +G   ++v+     +       
  gi|119720003|ref|YP_920498.1| 143 DLVVRGELGDFLEFRGvIAHAKHAYKDTPFEWRMDRsVAGGGVFADIGVHVLDLSEYVTGGRVRRVFgkvytLV------ 216
                                    67788**************************************************************6543322...... PP

                                    SCTCCSCSEEE...............EEEEEEEETTEEEEEEEEC CS
                 GFO_IDH_MocA_C  75 aeaaededaav...............msvlnlekgsgevitlesg 104
                                       +e+ d a+               ++++ ++ gs+e++  ++g
  gi|119720003|ref|YP_920498.1| 217 ---GERVDPATglkrrvdtedigfavLEYEAGAVGSVEASKVSPG 258
                                    ...333333333333555778555555666666666665555555 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   9.5e-06     0.043       1      71 [.       4      82 ..       4     101 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 9.5e-06
                                   EEEEETTSHHHHHHHHHHHHTTS.......-GGCEEEEEESSCCCHHHHHHHHC.-EEECECHHHHHHH-SEEEE-S-H CS
                  F420_oxidored  1 kigiiGaGnmgealasgllaaga.......qpheivvansrnpekaeelaeelg.vkvtavdneeaaeeadvvvlavkp 71
                                   ++g+iG+G  ++a a  l++ g+       ++ e++v+ sr+p  ae+la+++g  k t+++ e   e+ dvv +a + 
  gi|119720003|ref|YP_920498.1|  4 RVGLIGSGWSASAQAFSLSSLGRvvrrsgfPEVELRVVFSRTPAHAEALARQYGfEKWTTSESEFFGEDLDVVGIASPN 82
                                   578888888887766666666655555555999*********************7677776777777799999888775 PP

>> ox_reductase_C  Putative oxidoreductase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00015      0.67      25     140 ..     161     270 ..     151     272 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00015
                 ox_reductase_C  25 aryvsayehaakkawweksisaGpvv.eqathfcdlsryfgGd.vd..ldtvkaksvewyekaGklskipvdeskipede 100
                                    a+ + ay+ +  +   ++s+ +G v  + + h+ dls y +G  v      v +   e  ++a  l          +   
  gi|119720003|ref|YP_920498.1| 161 AHAKHAYKDTPFEWRMDRSVAGGGVFaDIGVHVLDLSEYVTGGrVRrvFGKVYTLVGERVDPATGL----------KRRV 230
                                    556667766655444567888777752668999999999866413311112222222333333333..........2222 PP

                 ox_reductase_C 101 riprltsaswkyksGavGslehavalqGtkystelevlad 140
                                        +  a   y+ GavGs+e + +  G++ ++ +ev+ d
  gi|119720003|ref|YP_920498.1| 231 DTEDIGFAVLEYEAGAVGSVEASKVSPGFEEQMRVEVYGD 270
                                    2334567888999999999999999999999999998877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 2318.91
//
Query:       gi|119720004|ref|YP_920499.1|  [L=167]
Description: PTS system sorbose subfamily IIB component [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.4e-39  134.9   0.0    2.9e-39  134.6   0.0    1.0  1  PTSIIB_sorb  PTS system sorbose subfamily IIB component


Domain annotation for each model (and alignments):
>> PTSIIB_sorb  PTS system sorbose subfamily IIB component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.6   0.0   1.6e-43   2.9e-39       3     145 ..       8     150 ..       7     153 .. 0.96

  Alignments for each domain:
  == domain 1  score: 134.6 bits;  conditional E-value: 1.6e-43
                                    EEEEETTGCGTTHHHHHHCCCTTSEEEEE-HHHHC-HHHHHHHHCCS-TTSEEEEE-HHHHHHHHHCB-.TTEEEEEEES CS
                    PTSIIB_sorb   3 lvRiDdRLiHGqVataWtkelkanriivvdDevakdelqkellkmaapsgvkvsilsvekaievlkkakvekekvlllvk 82 
                                    ++RiDdR+iHGqV+ aWtk+++an i vv+D++a ++  k+l  m ap+g++v++l+ve+a+++ ++   ++++vl+l++
  gi|119720004|ref|YP_920499.1|   8 FIRIDDRFIHGQVTAAWTKKFEANAIWVVNDKIAGNPALKQLQIMLAPPGISVEVLKVEEAAAKARN-VGNNTRVLMLFE 86 
                                    79*****************************************************************.4467******** PP

                                    SHHHHHHHHHT.T---SEEEEEEB---TTSEESSSSBEE-HHHHHHHHHHHHC--EEEE-SSTT CS
                    PTSIIB_sorb  83 npedalklveg.gvkikevnvGnmakkegkkqvsksvslteeeiealkelaekgveveiqkvps 145
                                    np d+l+++e+ gvk++ +  G+m +++g+ +v k++ + +ee +al +l ++g++v++q++p+
  gi|119720004|ref|YP_920499.1|  87 NPIDVLAFIEKsGVKVDWILAGQMGYRAGRVKVEKTFDVGPEEHKALLRLLDMGIKVYYQQLPD 150
                                    *******9975389*************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1154.37
//
Query:       gi|119720005|ref|YP_920500.1|  [L=129]
Description: PTS system fructose subfamily IIA component [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.1e-12   45.4   0.3      1e-11   45.1   0.3    1.2  1  EIIA-man  PTS system fructose IIA component


Domain annotation for each model (and alignments):
>> EIIA-man  PTS system fructose IIA component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.1   0.3   5.8e-16     1e-11      16     105 ..       3      88 ..       1      96 [. 0.76

  Alignments for each domain:
  == domain 1  score: 45.1 bits;  conditional E-value: 5.8e-16
                                    HHHHCCHSSS-SCEE.EEEC-TTS-CCCHHHHHHHHHCTS--TTEEEEEESSCCCHHHHHHHHCCTTSTTEEEEEC--CH CS
                       EIIA-man  16 elleelagedqekvi.avggtpdesigtlaekikeaieevdsedevlvLvDlggatpfneaaleleekeelevitgvnlP 94 
                                    e++ +++g  +++v+  v + ++es+++  ek++  +     + + +vL Dl+g+tp+++a ++l+e +  +vitg+n++
  gi|119720005|ref|YP_920500.1|   3 EAVAMILGVSVKEVTdCVELLEGESFENYYEKLASRV-----DGDTIVLADLFGGTPSKAALMLLQESKVKAVITGFNMA 77 
                                    6777777774444432566666666666666666655.....46789********************************* PP

                                    HHHHHHHHHCH CS
                       EIIA-man  95 lveeavaaras 105
                                    +v+++++ +++
  gi|119720005|ref|YP_920500.1|  78 MVIQLLSSQDE 88 
                                    *****997644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 963.71
//
Query:       gi|119720006|ref|YP_920501.1|  [L=294]
Description: hypothetical protein Tpen_1099 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.064   12.4   0.0       0.24   10.5   0.0    1.8  2  N_Asn_amidohyd  Protein N-terminal asparagine amidohydrolase


Domain annotation for each model (and alignments):
>> N_Asn_amidohyd  Protein N-terminal asparagine amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   1.3e-05      0.24       9      47 ..       3      41 ..       1      54 [. 0.92
   2 ?   -0.8   0.0     0.037   6.7e+02     178     209 ..      61      92 ..      48      94 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 1.3e-05
                 N_Asn_amidohyd  9 kgllYvaQrElAvvapadksvsivgsddattCvivvlrh 47
                                   k++l +  rElA ++ +d + s+v s+  t C  vv+++
  gi|119720006|ref|YP_920501.1|  3 KRVLDLSGRELAKISAKDFKSSVVSSEGRTICAEVVVQS 41
                                   67888899****************************985 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.037
                 N_Asn_amidohyd 178 kklldiYdakkeelkigPfkykplrkvdlwle 209
                                      ll++Yd+ + +++  P +y  + + +++l+
  gi|119720006|ref|YP_920501.1|  61 MVLLNMYDVFNPRVEGVPEEYASISDLSEFLQ 92 
                                    3689*****************99999888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 2074.14
//
Query:       gi|119720007|ref|YP_920502.1|  [L=534]
Description: PTS system mannose/fructose/sorbose family IID component [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-78  262.8   5.2    2.6e-78  262.8   5.2    2.1  2  EIID-AGA  PTS system mannose/fructose/sorbose family IID comp
    2.5e-58  197.2  24.6    2.5e-58  197.2  24.6    2.3  2  EII-Sor   PTS system sorbose-specific iic component


Domain annotation for each model (and alignments):
>> EIID-AGA  PTS system mannose/fructose/sorbose family IID component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   2.4      0.28   2.5e+03     108     160 ..     176     228 ..     173     259 .. 0.82
   2 !  262.8   5.2   2.9e-82   2.6e-78       3     265 .]     276     533 ..     274     533 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.28
                       EIID-AGA 108 DslfwgtlrpilaaiaaslAlqgnilGpilflvvfnvvrlalryyllelGYkl 160
                                    D+l ++ + p ++ +   +A++g +l ++ + ++++++    +++++ lG+ l
  gi|119720007|ref|YP_920502.1| 176 DALQVVQIGPFTVRFWDAMAVAGAVLPALGAAILMKLMISRRNVMFFVLGFAL 228
                                    77777778888888888899999999999998888888888888888888765 PP

  == domain 2  score: 262.8 bits;  conditional E-value: 2.9e-82
                       EIID-AGA   3 tkkdlnkvflrslflqasfnyermqalgflysmlpalkklYkkdkedlkealkrhleffNtepqlatfilGitlalEeek 82 
                                    t kd+++ f  s+f+q+s+nyerm+++gf++ ml + kkl  kd+e+lk+ ++ h ef+Ntep+l++ i G++++lEe+ 
  gi|119720007|ref|YP_920502.1| 276 TTKDFIRWFGVSWFIQSSWNYERMMGTGFAHGMLEIEKKLR-KDPEELKSWMRLHNEFYNTEPHLHNAIYGMVISLEEQG 354
                                    7899999999*******************************.6************************************* PP

                       EIID-AGA  83 angeideeainavKvglmGPlAGiGDslfwgtlrpilaaiaaslAlqgnilGpilflvvfnvvrlalryyllelGYklGt 162
                                    a    d+++i++vK++lmGP+AG+GDs++w+t+ pi++ ++asl  qgnilGp+++l+++  v++a++yy+l +GYk G 
  gi|119720007|ref|YP_920502.1| 355 A----DQDTIRGVKTALMGPFAGLGDSIMWFTILPIAFLLGASLGAQGNILGPVIALLIWIPVSWAVKYYTLVYGYKYGL 430
                                    *....9************************************************************************** PP

                       EIID-AGA 163 kaieklsesgllqkltkaasilGlfvvGaliaswvkistplkissget.tvslqdildkilpgllpllltllvywllkkk 241
                                    ++ e l+ +++l+ +++++  + + +vG+++a++v+ +tp+++++    +++lq +ld+++p+llpll+tl  ywl+k k
  gi|119720007|ref|YP_920502.1| 431 SLAEILK-GEVLKIFREGIAAFAMAMVGGIAATYVRATTPIVLAQYAGhAIKLQPVLDQLMPSLLPLLFTLYAYWLIKVK 509
                                    ****999.669*****************************9987544337****************************** PP

                       EIID-AGA 242 kvspikiilllvvigivgsllgil 265
                                    + s+ k++++l++ +++++llg+l
  gi|119720007|ref|YP_920502.1| 510 GYSYGKAVVILFLTAFILALLGVL 533
                                    **********************86 PP

>> EII-Sor  PTS system sorbose-specific iic component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.2  24.6   2.8e-62   2.5e-58       3     230 ..       8     246 ..       6     251 .. 0.95
   2 ?   -3.6   4.0      0.66     6e+03      98     117 ..     453     473 ..     366     533 .. 0.62

  Alignments for each domain:
  == domain 1  score: 197.2 bits;  conditional E-value: 2.8e-62
                        EII-Sor   3 qailiglvaflaglds.llgeltlerPlvagllvGlilGdlqtGlivGatlqlvylGvvtiGgavppdaalagiigtala 81 
                                    ++ l+gl+af++gld+ +++ l ++rP+vag+l+G+ilGd+ tGl+vG  l++v+ G++tiGg + p+aa+++i+++++a
  gi|119720007|ref|YP_920502.1|   8 EVGLLGLLAFIFGLDYiWVTPLGIWRPVVAGTLTGIILGDPLTGLLVGSLLEFVFAGLFTIGGGTVPEAASGTIASVVVA 87 
                                    5679************99999*********************************************************** PP

                        EII-Sor  82 ilsgasaeaavalavpvallgqllttlvrtinsvfvhkadkaaekgnlkkierlhlllplllglllrfipvfl...alyf 158
                                    +++g ++eaav la+pva+l++ l+++vr +++vf+h+ad+ +e+gn+ +i ++++l+ ++ + l+r+ip++l   al++
  gi|119720007|ref|YP_920502.1|  88 VTTGLKPEAAVPLAIPVAVLTMNLEIVVRSFDAVFTHWADREIERGNYGAIPLINILG-AVPWGLSRAIPIWLfagALAI 166
                                    **********************************************************.*************988899** PP

                        EII-Sor 159 gaeavqallnai......pew..llkgLsvaGglLpavGfAmllkvmlkkkllpffllGFvlaaylklnliavaiigvai 230
                                    + +av+a+++a+      p +  ++++++vaG++Lpa+G A+l+k+m++++ ++ff+lGF+laaylkl+l+a+a+++  i
  gi|119720007|ref|YP_920502.1| 167 NPQAVKAAIDALqvvqigPFTvrFWDAMAVAGAVLPALGAAILMKLMISRRNVMFFVLGFALAAYLKLSLLAIALVAGSI 246
                                    **********99777777333569****************************************************9554 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 0.66
                        EII-Sor  98 vallgqllttlvr.tinsvfv 117
                                    +a++g +  t vr t+ +v++
  gi|119720007|ref|YP_920502.1| 453 MAMVGGIAATYVRaTTPIVLA 473
                                    222222222222212223333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (534 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       868  (0.0484132); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 3521.04
//
Query:       gi|119720008|ref|YP_920503.1|  [L=228]
Description: HAD family hydrolase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-29  103.4   0.0    2.9e-18   66.6   0.0    2.0  2  Hydrolase_3      haloacid dehalogenase-like hydrolase
    3.5e-11   43.1   0.0    6.3e-10   39.0   0.0    2.0  1  S6PP             Sucrose-6F-phosphate phosphohydrolase
    9.1e-05   21.7   0.0       0.29   10.2   0.0    2.1  2  Trehalose_PPase  Trehalose-phosphatase
    0.00092   19.7   0.1      0.052   13.9   0.1    2.7  1  HAD              haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.048   13.2   0.0      0.086   12.3   0.0    1.3  1  DUF2608          Protein of unknown function (DUF2608)


Domain annotation for each model (and alignments):
>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.0   3.3e-12   1.2e-08       1      67 [.       7      75 ..       7      84 .. 0.89
   2 !   66.6   0.0     8e-22   2.9e-18     145     255 .]     107     218 ..      98     218 .. 0.89

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 3.3e-12
                                   EEEEIIIIIS-TTS---HHHHHHHHHHHHT.TSEEEEE-SS-HHHHHHHHHHCCCCSEEEEGGGTEE.E CS
                    Hydrolase_3  1 ialDlDGTLlnsdkkisektkeaikklkek.gikvviATGRslravlpvleelgldlpvialNGali.d 67
                                   +++D DGTL  ++ +++++  e +++lk+k  +k+viAT+R+l+++++++ +l l  ++i   G+++  
  gi|119720008|ref|YP_920503.1|  7 VVSDYDGTLAEENREVEPRVLEKLEELKAKyPFKFVIATARPLEDISRFVGKLWLVDALILEVGSVVaL 75
                                   689*************************96379*********************999999999999954 PP

  == domain 2  score: 66.6 bits;  conditional E-value: 8e-22
                                    EEEES-HHHHHHHHHHHHHHCTTTE..EEEEESTTEEEEEETT-SHHHHHHHHHHHCT--GGGEEEEESSGGGHHHHHHS CS
                    Hydrolase_3 145 ililkdkekldelekelksklnkll..titssskgyleimpkgvsKgtalkklakelnisleeviafGDgeNDieMLeaa 222
                                    +l++ d+e+l+ +e   ++kl+  +  +  + +   + +mp+g++Kg +l++l+k  ++s ++++++GD+  D+++++++
  gi|119720008|ref|YP_920503.1| 107 VLYYVDEEELQVAERVAREKLGA-FgyDLAKVGSRTYAFMPRGIDKGVGLERLLKLTGWSDAMIVSIGDSRTDLPLFQKS 185
                                    56667777777776666666654.347899999999******************************************** PP

                                    SEEEEETTS-HHHHHHSSEEE--GGGTHHHHHH CS
                    Hydrolase_3 223 glgvAmgnaseevkkaAdyvtksnnedGVakal 255
                                    ++ vA+gna +evk++Ad v++ +  d V++++
  gi|119720008|ref|YP_920503.1| 186 KVKVAVGNAAREVKEKADIVCEEKYGDCVVRVI 218
                                    **************************9999987 PP

>> S6PP  Sucrose-6F-phosphate phosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   0.0   1.8e-13   6.3e-10       4     215 ..       6     199 ..       4     210 .. 0.84

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 1.8e-13
                                    EEEE-TBTTTB.S-HHHHHH.HHHHHH.GGGGGEEEEEE-SS-HHHHHHHHHHHT----SEEEETTTTEEEE..TTEE-H CS
                           S6PP   4 llvsdLDntlvdgdnealar.lnelleaeerkdvllvfaTGRsldsakellkeknllkPdvlitsvGteiyygeelvpdk 82 
                                    ++vsd D+tl ++++e   r l++l e + +  +++v+aT+R l++ ++ + +  l+  d+li +vG+ ++  e      
  gi|119720008|ref|YP_920503.1|   6 IVVSDYDGTLAEENREVEPRvLEKLEELKAKYPFKFVIATARPLEDISRFVGKLWLV--DALILEVGSVVALPEA----- 78 
                                    79*********6655555551555555888999*******************99998..9**********99333..... PP

                                    HHHHHHHTT--HHHHHHHHHT-TTEEE--GGG-BTTBEEEEE-TTS-THHHHHHHHHHHTTTS-EEEEEETTTEEEEEET CS
                           S6PP  83 aweeildekwdrqavvealaklpeLtlQpeeeqrehKvSyfvdkekaaevlkeleqlLekreldvkviyssgkdlDvlPk 162
                                       e++ + w +++++++l++       p  +++  +v y+vd+e+++   +  +++L + + d   + s   ++  +P+
  gi|119720008|ref|YP_920503.1|  79 --LEVIFKPWGWDRLRAVLRES-----VPAVNEG--RVLYYVDEEELQVAERVAREKLGAFGYDLAKVGSRTYAF--MPR 147
                                    ..36788999999999999863.....2444555..9**********9966666889999999999998877775..9** PP

                                    T-SHHHHHHHHHHHHT--GGGEEEEE-SGGGHHHHTSSSEEEE-TT--HHHHH CS
                           S6PP 163 raskgeAlryLakkleleleqilvcGdsgnDeellignvlgVvVgnaqeellq 215
                                    + +kg  l+ L+k  +     i+  Gds  D  l++++   V Vgna +e ++
  gi|119720008|ref|YP_920503.1| 148 GIDKGVGLERLLKLTGWSDAMIVSIGDSRTDLPLFQKSKVKVAVGNAARE-VK 199
                                    *************************************************9.43 PP

>> Trehalose_PPase  Trehalose-phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0   8.2e-05      0.29       3      55 ..      10      57 ..       8      63 .. 0.88
   2 !    9.6   0.0   0.00012      0.44     159     203 ..     146     187 ..     112     208 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 8.2e-05
                                   ETBTTTB---SSGGG--B-TTHHHHHHHHHTTS-..EEEE-SS-HHHHHHHH- CS
                Trehalose_PPase  3 DydGTlspivedpdaavpssellslLkkLasdpknvvaivSGrslkeeellvk 55
                                   DydGTl +  +      + +++l+ L++L ++++   +i ++r l++ +++v+
  gi|119720008|ref|YP_920503.1| 10 DYDGTLAEENR-----EVEPRVLEKLEELKAKYPFKFVIATARPLEDISRFVG 57
                                   ******99988.....99**************************999888743 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00012
                                    -S---HHHHHHHHHHTS--------EEEEEE-SSTTHHHHTTS-T CS
                Trehalose_PPase 159 pqgvsKGkaverlleslgsadseddfvlciGDdrtDedmFsvlrk 203
                                    p+g  KG  +erll+  g +   d +++ iGD rtD   F+  + 
  gi|119720008|ref|YP_920503.1| 146 PRGIDKGVGLERLLKLTGWS---DAMIVSIGDSRTDLPLFQKSKV 187
                                    99999*************99...*************988877655 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.1   1.4e-05     0.052       2     188 .]       8     183 ..       7     183 .. 0.44

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.4e-05
                            HAD   2 lfDfDgTLldgdsle......lllrfllrrgaprlwralreklllalfrellrldraglaelleallaglseelaaeler 75 
                                    ++D+DgTL  ++           l+  l+ + p  +  + +++l+++ r  ++l   ++  l+     +l+e+l+  ++ 
  gi|119720008|ref|YP_920503.1|   8 VSDYDGTLAEENREVeprvleK-LE-ELKAKYPFKFVIATARPLEDISRFVGKLWLVDALILEVGSVVALPEALEVIFKP 85 
                                    6777777777743333432211.11.111111111222223344444444444444444444444444444444444444 PP

                            HAD  76 fvaevirpklldpgalellaahra.......aGdrvvvvSgglrplvepll.aelgadevlatelevdd.rltgelgleg 146
                                    ++              ++l+a+++       +G  ++ v     +++e+++ ++lg     + +l++++ r  +   ++ 
  gi|119720008|ref|YP_920503.1|  86 WG-------------WDRLRAVLResvpavnEGRVLYYVDEEELQVAERVArEKLG---AFGYDLAKVGsRTYAF--MPR 147
                                    44.............22222222200000002223333333333444444444444...2222223333355555..999 PP

                            HAD 147 kpvrgegkvaalrewlaaegegidleevvayGDspsDlpllr 188
                                    ++ +g      l++ l+ +g+ ++   +v +GDs++Dlpl++
  gi|119720008|ref|YP_920503.1| 148 GIDKG----VGLERLLKLTGWSDAM--IVSIGDSRTDLPLFQ 183
                                    99999....9999977777766666..************986 PP

>> DUF2608  Protein of unknown function (DUF2608)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.4e-05     0.086     158     193 ..     144     179 ..     141     188 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.4e-05
                        DUF2608 158 lftsglnKGeaLlklLdkigrepksviFiDDkkknl 193
                                    ++  g++KG  L +lL+ +g++   ++ i D++  l
  gi|119720008|ref|YP_920503.1| 144 FMPRGIDKGVGLERLLKLTGWSDAMIVSIGDSRTDL 179
                                    8999***************************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1577.02
//
Query:       gi|119720009|ref|YP_920504.1|  [L=250]
Description: phosphoribosyltransferase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.9e-15   56.1   0.1      8e-15   54.7   0.0    1.7  2  Pribosyltran  Phosphoribosyl transferase domain
     0.0067   15.9   0.2      0.025   14.0   0.0    1.9  2  UPRTase       Uracil phosphoribosyltransferase
  ------ inclusion threshold ------
      0.029   14.7   0.0      0.055   13.7   0.0    1.6  1  DUF1400       Alpha/beta hydrolase of unknown function (DUF14
      0.091   12.9   0.2       0.19   11.8   0.2    1.5  1  Resolvase     Resolvase, N terminal domain
      0.093   12.2   0.0       0.15   11.5   0.0    1.3  1  PRTase_2      Phosphoribosyl transferase


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       1.8   6.6e+03     103     116 ..      28      41 ..      14      45 .. 0.75
   2 !   54.7   0.0   2.2e-18     8e-15      19     137 ..     107     233 ..      95     242 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.8
                                    HHHHHHHHHCC-BS CS
                   Pribosyltran 103 llaalelLkekgpe 116
                                    l+++ ++L+e+++e
  gi|119720009|ref|YP_920504.1|  28 LQEVYRALREEKVE 41 
                                    56677777777766 PP

  == domain 2  score: 54.7 bits;  conditional E-value: 2.2e-18
                                    TEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE................EE----TTSEE CS
                   Pribosyltran  19 aaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdes........rlledpagkkV 90 
                                     a+++ ++++  dvv++ a  G+p+a+  a +L+++la+ r+++ +p+ +  +a  +   +          + + +g +V
  gi|119720009|ref|YP_920504.1| 107 VASAYPTFFRGVDVVLTAAVNGIPLASFAAWALDARLAVARRERESPSMKYLTAYLFQRDPpsvvplyvPSSLLERGARV 186
                                    56666779999********************************9999998888866655559******9999999***** PP

                                    EEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-HHHHHHHHHH- CS
                   Pribosyltran  91 liVDDildtGgTllaalelLkekgpeevriavlvdkpateeevdkna 137
                                    liVDD+l tG+Tl+a l l+ e+++e v++ +lv  ++ ++ v   +
  gi|119720009|ref|YP_920504.1| 187 LIVDDLLRTGRTLKALLSLIDEADAEPVGVLALVSLSEAWKSVLTRD 233
                                    **********************************9888888776655 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1      0.28   9.9e+02     142     184 ..      67     108 ..      58     111 .. 0.76
   2 !   14.0   0.0     7e-06     0.025     115     178 ..     175     238 ..     151     246 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.28
                        UPRTase 142 qlLkergvgeekIlvlsvlaseegvkrlaeefpkvkvvtaavD 184
                                      Lk+rg   ++Il  ++ + e+gv ++a+   +v+v  aav 
  gi|119720009|ref|YP_920504.1|  67 VALKRRGL-LREILSKKISMDENGVVNVAQLAYDVEVLSAAVA 108
                                    45666665.4678888888889999999999999999999885 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 7e-06
                        UPRTase 115 LPkki..aertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvlaseegvkrlaeefpkvkv 178
                                    +P+++  +  +vl++D ++ TG+++ a ++l+ e  ++ e + vl++++ +e+ k+++++  ++ v
  gi|119720009|ref|YP_920504.1| 175 VPSSLleRGARVLIVDDLLRTGRTLKALLSLIDE--ADAEPVGVLALVSLSEAWKSVLTRDIQTMV 238
                                    56666556678***********************..66789*******999999999887665555 PP

>> DUF1400  Alpha/beta hydrolase of unknown function (DUF1400)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.5e-05     0.055      13      67 ..      39      93 ..      10     109 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.5e-05
                        DUF1400 13 ersisvedLekfaktgevsseLatylkllskeqreelreaLqaeiklspvllsql 67
                                   + ++s ++L+++a   +++++L+++  l++ + r  lre+L ++i ++++ + ++
  gi|119720009|ref|YP_920504.1| 39 KVEVSPSELSRYAAGHSLPPSLKAVHILVALKRRGLLREILSKKISMDENGVVNV 93
                                   4457778***************************************998766554 PP

>> Resolvase  Resolvase, N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   5.2e-05      0.19      62     101 ..     182     220 ..     177     244 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.2e-05
                                    T-EE..EEEESSCCCC-S...S-HHHHHHHHHTT-EEEESS CS
                      Resolvase  62 egkg.dvlvvekldRLaRsvrdlltlleelrekgvslvsld 101
                                    +  g +vl+v +l R +R+++ ll+l++e ++  v +  l 
  gi|119720009|ref|YP_920504.1| 182 R--GaRVLIVDDLLRTGRTLKALLSLIDEADAEPVGVLALV 220
                                    4..4379************************9999887765 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   4.3e-05      0.15     116     164 ..     178     225 ..     170     243 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.3e-05
                       PRTase_2 116 ellaaakelvLvDDEistGktalnliralqeklprkryvvvslvdwrse 164
                                    +ll++ +++++vDD + tG+t+ +l++ + e+  ++ + v++lv ++++
  gi|119720009|ref|YP_920504.1| 178 SLLERGARVLIVDDLLRTGRTLKALLSLIDEA-DAEPVGVLALVSLSEA 225
                                    67888999*************99999877665.4566666677666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1729.58
//
Query:       gi|119720010|ref|YP_920505.1|  [L=251]
Description: hypothetical protein Tpen_1103 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
        3.6    7.9  11.3       0.61   10.4   6.2    2.3  2  DUF2754          Protein of unknown function (DUF2754)


Domain annotation for each model (and alignments):
>> DUF2754  Protein of unknown function (DUF2754)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.2      0.25   4.4e+03      16      28 ..     118     130 ..     104     136 .. 0.64
   2 ?   10.4   6.2   3.4e-05      0.61      13      57 ..     147     194 ..     143     197 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.25
                        DUF2754  16 valGlifilnGvv 28 
                                    ++lG i +l G+v
  gi|119720010|ref|YP_920505.1| 118 ISLGSIVLLLGIV 130
                                    4566676666665 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 3.4e-05
                        DUF2754  13 yyavalGlifilnG.vvGllGfeakGwqtyavGlv..twvisfwiaGl 57 
                                     y+v  Gl + + G +vGl   +ak w ty vG+v  +++  +w aG 
  gi|119720010|ref|YP_920505.1| 147 VYSVYTGLALAVLGlLVGLAVGNAKTWATYIVGVVltSFISGLWGAGT 194
                                    58899999876555279**999***********874245666898885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       839  (0.0467957); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 1701.49
//
Query:       gi|119720011|ref|YP_920506.1|  [L=274]
Description: cobalt transport protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-21   77.0  14.9    2.2e-21   76.5  14.9    1.1  1  CbiQ      Cobalt transport protein


Domain annotation for each model (and alignments):
>> CbiQ  Cobalt transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.5  14.9   1.2e-25   2.2e-21       7     210 ..      20     236 ..      14     242 .. 0.87

  Alignments for each domain:
  == domain 1  score: 76.5 bits;  conditional E-value: 1.2e-25
                                    S-HHHHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHTTS---.HHHHHHHCCCHCHHHHHHHHHHE............ CS
                           CbiQ   7 rldprvkliwlfllllalvlapnlvtlliiiallllllllvilp.rvlaqalilpllflllgllillf............ 73 
                                     l+p vk ++ ++++l + l+  + ++  +  +++l++l v +p rv   +l+  l+  l  +++l +            
  gi|119720011|ref|YP_920506.1|  20 GLSPLVKIVVPLSFSLDVLLVKDVPSAAALTLAVFLVVLAVKVPlRVVKGFLV--LIASLSAFIVLSLtlftslpgrvlf 97 
                                    578999*********************77777777777777777777666666..3444444444433667899999999 PP

                                    .........EECTTEEE...E-TTHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHHHHCCCSS--HHHHHHHHHHHHHHH CS
                           CbiQ  74 ..qlittegefvfagggqisitseGllrglllalRiltllslllllalTTppeeltsslerlgvPlelalillLayRfif 151
                                      +l +++ e  + +++ i +t+e l r+ +++lRil+++++++l+++T +  +++ +l+ l+ Pl +a++++L +R i 
  gi|119720011|ref|YP_920506.1|  98 eyTLLSVKAEKGVLAWR-IVVTDEALSRSFFFVLRILAMILTATLFVATVSDRDVVRALRGLRLPLGVAVAASLFFRGIS 176
                                    99777777777888888.88************************************************************ PP

                                    HHHHHHHHHHHHHHHTTTTS...SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS-S CS
                           CbiQ 152 lLleevqrikqAqklRlgds.klgirrslrslgkliaalflralkraervalAmeaRGYt 210
                                    ++l+ +++i++A+++R++d+ k+++ r+   +  ++++l+   + r+ +v lA+e++G +
  gi|119720011|ref|YP_920506.1| 177 MFLDDFRVIREAMMARGVDFeKTSLYRRFFLYVNALIPLISLMVSRSYEVSLALESKGLS 236
                                    *********************************************************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      196  (0.010932); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1972.97
//
Query:       gi|119720012|ref|YP_920507.1|  [L=541]
Description: ABC transporter related [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      1e-57  194.5   0.0    9.5e-30  103.9   0.0    2.3  2  ABC_tran      ABC transporter
    5.5e-14   52.7   1.6     0.0043   16.9   0.0    4.1  4  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    3.6e-09   36.4   0.3      0.012   15.0   0.0    3.6  3  SMC_N         RecF/RecN/SMC N terminal domain
    1.9e-07   31.8   0.2     0.0011   19.5   0.0    2.3  2  AAA_23        AAA domain
      4e-07   29.8   2.8      0.013   15.0   0.4    3.5  2  AAA_25        AAA domain
    4.7e-07   30.3   2.6      0.012   16.0   0.2    2.7  2  AAA_16        AAA ATPase domain
    1.4e-06   27.9   1.1      0.035   13.8   0.1    2.3  2  AAA_29        P-loop containing region of AAA domain
      1e-05   25.8   4.1       0.14   12.4   0.4    4.1  2  AAA_22        AAA domain
    1.9e-05   24.1   0.0      0.025   14.0   0.0    2.5  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
    2.5e-05   24.1   1.0      0.087   12.5   0.0    2.9  2  AAA_30        AAA domain
    5.7e-05   23.5   1.3      0.011   16.2   0.1    3.3  2  AAA           ATPase family associated with various cellular 
    9.6e-05   22.4   0.4      0.082   12.8   0.1    2.7  2  NACHT         NACHT domain
    0.00011   22.4   0.4       0.18   11.9   0.2    2.6  2  AAA_33        AAA domain
    0.00019   20.9   0.1        0.2   10.9   0.0    2.4  2  DnaB_C        DnaB-like helicase C terminal domain
    0.00019   21.4   0.7       0.68    9.8   0.1    3.2  3  NTPase_1      NTPase
    0.00021   20.6   0.5       0.41    9.8   0.0    2.5  2  NB-ARC        NB-ARC domain
    0.00021   21.9   3.7       0.25   11.9   0.1    3.4  3  AAA_18        AAA domain
     0.0003   20.7   1.2       0.72    9.7   0.1    2.7  2  RsgA_GTPase   RsgA GTPase
    0.00087   19.3   1.2       0.24   11.4   0.1    2.3  2  TsaE          Threonylcarbamoyl adenosine biosynthesis protei
     0.0015   17.9   1.9       0.42    9.9   0.1    2.9  3  ATPase        KaiC
     0.0015   18.3   0.6       0.42   10.3   0.0    2.4  2  AAA_24        AAA domain
      0.003   17.8   0.1       0.87    9.9   0.1    3.2  2  SbcCD_C       Putative exonuclease SbcCD, C subunit
     0.0047   16.7   0.4      0.023   14.4   0.0    2.2  2  RuvB_N        Holliday junction DNA helicase RuvB P-loop doma
      0.005   16.6   0.0       0.13   12.0   0.0    2.1  2  AAA_15        AAA ATPase domain
     0.0053   16.4   2.4       0.48   10.0   0.2    2.5  2  cobW          CobW/HypB/UreG, nucleotide-binding domain
     0.0061   16.2   0.4       0.51    9.9   0.0    2.4  2  SRP54         SRP54-type protein, GTPase domain
  ------ inclusion threshold ------
       0.01   15.9   0.9       0.37   10.8   0.1    2.7  2  AAA_5         AAA domain (dynein-related subfamily)
       0.01   14.9   1.7        2.2    7.3   0.1    2.4  2  T2SSE         Type II/IV secretion system protein
      0.015   15.2   1.0          2    8.3   0.1    2.7  2  MobB          Molybdopterin guanine dinucleotide synthesis pr
      0.015   15.0   4.1        2.7    7.7   0.1    3.7  4  IstB_IS21     IstB-like ATP binding protein
       0.02   14.9   1.2          6    6.9   0.1    2.8  2  AAA_14        AAA domain
      0.025   14.5   0.2          4    7.3   0.0    2.4  2  ATPase_2      ATPase domain predominantly from Archaea
      0.034   14.0   0.5        4.6    7.1   0.1    2.4  2  APS_kinase    Adenylylsulphate kinase
       0.04   13.3   0.1        3.3    7.1   0.0    3.3  4  TniB          Bacterial TniB protein
      0.052   12.2   0.2       0.18   10.4   0.0    1.9  3  AAA_13        AAA domain
      0.056   13.2   0.4         15    5.3   0.0    2.7  2  ATP_bind_1    Conserved hypothetical ATP binding protein
      0.056   12.9   1.0       0.77    9.2   0.1    2.6  3  PhoH          PhoH-like protein
      0.057   12.9   1.1        5.1    6.5   0.1    2.7  3  RecA          recA bacterial DNA recombination protein
      0.062   13.0   0.4        3.2    7.4   0.1    2.4  2  PRK           Phosphoribulokinase / Uridine kinase family
      0.073   12.8   0.9       0.87    9.3   0.0    2.5  2  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
      0.087   13.1   3.3        1.4    9.1   0.1    2.5  2  AAA_28        AAA domain
      0.093   12.8   1.5        9.3    6.4   0.0    2.8  2  MMR_HSR1      50S ribosome-binding GTPase
      0.098   12.3   0.7        2.7    7.6   0.0    2.8  3  ATP-synt_ab   ATP synthase alpha/beta family, nucleotide-bind
       0.11   12.9   0.3        2.8    8.4   0.0    2.5  2  RNA_helicase  RNA helicase
       0.12   11.2   0.2       0.19   10.6   0.2    1.2  1  DUF463        YcjX-like family, DUF463
       0.18   11.1   0.3       0.35   10.2   0.0    1.6  1  Gtr1_RagA     Gtr1/RagA G protein conserved region
        0.2   10.8   0.2         17    4.5   0.0    2.3  2  PIF1          PIF1-like helicase
       0.21   11.5   0.1         18    5.2   0.0    2.2  2  Rad17         Rad17 P-loop domain
       0.48   10.7   4.3         16    5.8   0.3    3.2  3  AAA_19        AAA domain
        1.1    9.3   3.1         21    5.1   0.2    2.5  2  DUF87         Helicase HerA, central domain
        2.1    8.4   5.8       0.66   10.0   0.3    2.9  3  BCA_ABC_TP_C  Branched-chain amino acid ATP-binding cassette 


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.5   0.0   1.5e-27   5.3e-25       1     137 []      21     173 ..      21     173 .. 0.89
   2 !  103.9   0.0   2.7e-32   9.5e-30       1     136 [.     310     455 ..     310     456 .. 0.91

  Alignments for each domain:
  == domain 1  score: 88.5 bits;  conditional E-value: 1.5e-27
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--.....SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSB CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp.....teGeilldgkdlkeqeleslrkeigvlpqepqlfpelt 75 
                                    l+ v+l +++ge +ai+G +GaGK+tL+  ++g   +      +G++++ g ++ +++ ++  +++gv++++p+++  + 
  gi|119720012|ref|YP_920507.1|  21 LNGVNLGVEKGEFLAITGLSGAGKTTLVLSILGIIPQrlpgeFSGKVKVLGLSTLSTDVTIIAQRVGVVFEDPEIQFVMG 100
                                    789******************************99888888889*******99999****************77665554 PP

                                    .HHHH..........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    .xxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  76 .vren..........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                     v+++            +e  e+ l  l+l++l +  ++++ps+LSgG+kqrva+a a++k+p+ll+lDEpt+
  gi|119720012|ref|YP_920507.1| 101 tVEDEvalsleamglPPEEVRERTLWALELVGLGAGFLQRNPSQLSGGEKQRVAIASAVAKEPELLILDEPTS 173
                                    277779999999999555556777777777777779999999*****************************96 PP

  == domain 2  score: 103.9 bits;  conditional E-value: 2.7e-32
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS..--S-TTSBHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxx RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe..pqlfpeltvre 78 
                                    l+nv+l+l+ ge+va++G+nG+GK+tL+k++agl++pt+G++l++g+d+++  + +l++ +g++ q+  +qlf ++ v+e
  gi|119720012|ref|YP_920507.1| 310 LDNVTLTLYSGELVALMGPNGSGKTTLAKVIAGLVRPTSGRVLVRGRDVSSYGRLELSSIVGYVYQNpqHQLFCQS-VYE 388
                                    79*****************************************************************545555555.888 PP

                                    H.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    x.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  79 n.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                    +             e ++ +++al+ ++l+++++++       LS+G+k+r+ala + + +p++l++DEpt
  gi|119720012|ref|YP_920507.1| 389 EvafglrlrgagegEVRKAVDEALRLFNLEGKAEEHP----FFLSKGEKRRLALASVYALNPSVLIVDEPT 455
                                    88********987777777999999999999666666....*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.3      0.46   1.6e+02       2      21 ..      34      53 ..      33      72 .. 0.82
   2 !   13.5   0.0   0.00014     0.048     232     287 ..     140     192 ..     136     201 .. 0.81
   3 !   16.5   0.0   1.6e-05    0.0057       2      24 ..     323     345 ..     322     383 .. 0.76
   4 !   16.9   0.0   1.2e-05    0.0043     225     301 ..     416     489 ..     384     491 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.46
                         AAA_21  2 nvliGpNgsGKSnLLdaldl 21
                                    +++G  g+GK++L   + +
  gi|119720012|ref|YP_920507.1| 34 LAITGLSGAGKTTLVLSILG 53
                                   689**********9766654 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00014
                         AAA_21 232 lparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr 287
                                    +++++lS G k+  a+++a++  +    ll++DEp + L+P+  ++++  +++l+r
  gi|119720012|ref|YP_920507.1| 140 RNPSQLSGGEKQRVAIASAVAKEP---ELLILDEPTSDLDPAGKEEVVSAIESLRR 192
                                    68899********99999999988...9*************766666655555555 PP

  == domain 3  score: 16.5 bits;  conditional E-value: 1.6e-05
                         AAA_21   2 nvliGpNgsGKSnLLdaldllar 24 
                                     +l GpNgsGK++L + + +l r
  gi|119720012|ref|YP_920507.1| 323 VALMGPNGSGKTTLAKVIAGLVR 345
                                    6899**************99944 PP

  == domain 4  score: 16.9 bits;  conditional E-value: 1.2e-05
                         AAA_21 225 engdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSpll 301
                                      ++  e  ++ lS G kr lal++ ++  +   s+l++DEp +g + ++ + l+  l++l+++g  v++ THS  l
  gi|119720012|ref|YP_920507.1| 416 NLEGKAEEHPFFLSKGEKRRLALASVYALNP---SVLIVDEPTTGQDRAFSEYLFSTLRRLAEEGKAVVAITHSVDL 489
                                    4455556666668*******66666666666...9***********************999999**********765 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1     0.097        34      25      45 ..      32      52 ..      19      63 .. 0.86
   2 !   15.0   0.0   3.5e-05     0.012     134     199 ..     142     203 ..      69     221 .. 0.81
   3 !   13.2   0.0   0.00013     0.045      22     153 ..     318     444 ..     305     501 .. 0.58

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.097
                                   SEEEEEESTTSSHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 25 sftaivGpNGSGKsnlldAil 45
                                   +f ai+G  G+GK+ l+ +il
  gi|119720012|ref|YP_920507.1| 32 EFLAITGLSGAGKTTLVLSIL 52
                                   699*************99984 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 3.5e-05
                                    TTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 134 kelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislre 199
                                    +++LSgGek+ va+a  +A    k   l +lDe  + LD +  ++v++ +++ + +  + ++ +++
  gi|119720012|ref|YP_920507.1| 142 PSQLSGGEKQRVAIASAVA----KEPELLILDEPTSDLDPAGKEEVVSAIESLRRQLDVTIVMVEQ 203
                                    449*******999986644....555699*************************999988887766 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 0.00013
                                    TTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--...BTTCSSTTEEEEEEEEEETTEE..SSSSSSC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxx..xxxxxxx RF
                          SMC_N  22 fsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk...skekasvkkaeveitfdnedkk..lkiekee 96 
                                    +s ++ a++GpNGSGK+ l   i    G      +r ++ + l+     s+ ++   +  v  +++n++++   +   ee
  gi|119720012|ref|YP_920507.1| 318 YSGELVALMGPNGSGKTTLAKVI---AG-----LVRPTSGRVLVRGrdvSSYGRLELSSIVGYVYQNPQHQlfCQSVYEE 389
                                    4567889************9999...33.....35666666666665544556666677777788888888332233344 PP

                                    EEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  97 vsisrrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAi 153
                                    v    r+   ge e+   +   +   + +l  +a+ ++  LS Gek  +ala + A+
  gi|119720012|ref|YP_920507.1| 390 VAFGLRLRGAGEGEV--RKAVDEALRLFNLEGKAEEHPFFLSKGEKRRLALASVYAL 444
                                    444444444444332..2222222233333333333344788888887777766655 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0    0.0024      0.83      22      45 ..      34      57 ..      21     116 .. 0.72
   2 !   19.5   0.0   3.2e-06    0.0011       6      39 ..     306     340 ..     305     343 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0024
                         AAA_23 22 tlItGpNGaGKTTildAiklaLyg 45
                                    +ItG  GaGKTT++  i  +   
  gi|119720012|ref|YP_920507.1| 34 LAITGLSGAGKTTLVLSILGIIPQ 57
                                   58************9777666555 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 3.2e-06
                         AAA_23   6 nfrsfrdqeidF.skgltlItGpNGaGKTTildAi 39 
                                    ++r ++++++ + s  l+++ GpNG+GKTT+   i
  gi|119720012|ref|YP_920507.1| 306 GIRALDNVTLTLySGELVALMGPNGSGKTTLAKVI 340
                                    79999*******8889**************98766 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.4   3.8e-05     0.013      31     187 ..      29     202 ..      20     205 .. 0.64
   2 !   11.6   0.1   0.00042      0.15      32      53 ..     319     340 ..     310     353 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.8e-05
                         AAA_25  31 pagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEds.edelrrRlravgeal............ 97 
                                     +ge+ +++G +g+GKttl+l++   + +    +g++ + ++kVl +s+  +    +++R+  v+e+             
  gi|119720012|ref|YP_920507.1|  29 EKGEFLAITGLSGAGKTTLVLSILGIIPQRL--PGEF-SGKVKVLGLSTLSTdVTIIAQRVGVVFEDPeiqfvmgtvede 105
                                    789********************99999755..5766.566777766654442446778888888777777788666666 PP

                         AAA_25  98 ..............rddarllvldlagveslpLfakdrggtlltadvdaleaaieevegvrlvviDplsr.alggdensn 162
                                                   + ++l +l l+g      f +++ ++l  ++ ++++ a   +++++l+++D  ++ + +++++  
  gi|119720012|ref|YP_920507.1| 106 valsleamglppeeVRERTLWALELVGL--GAGFLQRNPSQLSGGEKQRVAIASAVAKEPELLILDEPTSdLDPAGKE-- 181
                                    6666666666655433444444444443..222333344444333322222222222459999999655524444444.. PP

                         AAA_25 163 sdvgalvealeriarrtgaavllvh 187
                                        ++v+a+e+++r++++++++v 
  gi|119720012|ref|YP_920507.1| 182 ----EVVSAIESLRRQLDVTIVMVE 202
                                    ....789999999999999998885 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00042
                         AAA_25  32 agelallaGapgtGKttlaldl 53 
                                     gel++l+G+ g+GKttla  +
  gi|119720012|ref|YP_920507.1| 319 SGELVALMGPNGSGKTTLAKVI 340
                                    699***************9655 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.2   0.00013     0.045      25      61 ..      32      64 ..      18     195 .. 0.86
   2 !   16.0   0.2   3.4e-05     0.012      23      63 ..     319     360 ..     307     492 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 0.00013
                         AAA_16 25 elvllsGesGvGKsslvrellralekdggiflrgkcd 61
                                   e + ++G sG GK++lv ++l  + ++    l g++ 
  gi|119720012|ref|YP_920507.1| 32 EFLAITGLSGAGKTTLVLSILGIIPQR----LPGEFS 64
                                   7899****************9988888....666554 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 3.4e-05
                         AAA_16  23 rpelvllsGesGvGKsslvrellralekdggif.lrgkcdql 63 
                                    ++elv l G+ G+GK++l++ ++  ++ + g + +rg+ +++
  gi|119720012|ref|YP_920507.1| 319 SGELVALMGPNGSGKTTLAKVIAGLVRPTSGRVlVRGRDVSS 360
                                    3489******************97777775555588877777 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.1   0.00025     0.086      15      39 ..      24      48 ..      18      56 .. 0.78
   2 !   13.8   0.1    0.0001     0.035      14      40 ..     312     338 ..     308     351 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00025
                         AAA_29 15 htieidlkgatlltGpsGsGKSTll 39
                                     + ++  ++  +tG sG+GK+Tl+
  gi|119720012|ref|YP_920507.1| 24 VNLGVEKGEFLAITGLSGAGKTTLV 48
                                   556666444999************8 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 0.0001
                         AAA_29  14 ghtieidlkgatlltGpsGsGKSTllD 40 
                                    + t+++   + + l+Gp+GsGK+Tl  
  gi|119720012|ref|YP_920507.1| 312 NVTLTLYSGELVALMGPNGSGKTTLAK 338
                                    5566666445999***********965 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.4   0.00039      0.14       4      30 ..      30      56 ..      28     211 .. 0.62
   2 !   10.6   0.2    0.0014      0.51       6      25 ..     321     340 ..     317     491 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00039
                         AAA_22  4 tagilvvtGesGtGKTtllrrlleqld 30
                                   +  +l++tG sG+GKTtl+  +l   +
  gi|119720012|ref|YP_920507.1| 30 KGEFLAITGLSGAGKTTLVLSILGIIP 56
                                   5679**************988776655 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0014
                         AAA_22   6 gilvvtGesGtGKTtllrrl 25 
                                     +++++G+ G+GKTtl++ +
  gi|119720012|ref|YP_920507.1| 321 ELVALMGPNGSGKTTLAKVI 340
                                    57899***********9865 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0    0.0073       2.6      25      76 ..      34      85 ..      19      94 .. 0.85
   2 !   14.0   0.0   7.1e-05     0.025      24      63 ..     322     361 ..     305     386 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0073
                   Mg_chelatase 25 lllvGppGsGKtmlakrlpsllpplseeealevakiasvagkkeeekllkrr 76
                                   l ++G +G+GKt l   + +++p+    e     k+  +++ +++ +++++r
  gi|119720012|ref|YP_920507.1| 34 LAITGLSGAGKTTLVLSILGIIPQRLPGEFSGKVKVLGLSTLSTDVTIIAQR 85
                                   6789********************9999999888888888877777776665 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 7.1e-05
                   Mg_chelatase  24 nlllvGppGsGKtmlakrlpsllpplseeealevakiasv 63 
                                     + l+Gp GsGKt lak +++l+ p s +  +  + ++s 
  gi|119720012|ref|YP_920507.1| 322 LVALMGPNGSGKTTLAKVIAGLVRPTSGRVLVRGRDVSSY 361
                                    5779*******************99988777776666665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.2    0.0025      0.88      19      53 ..      32      73 ..      24     194 .. 0.81
   2 !   12.5   0.0   0.00025     0.087      14      50 ..     317     352 ..     310     364 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0025
                         AAA_30 19 rvavltGpAGtGKttalkalreaweaa.g......grviglA 53
                                    + ++tG  G+GKtt++ ++  ++ ++         +v+gl+
  gi|119720012|ref|YP_920507.1| 32 EFLAITGLSGAGKTTLVLSILGIIPQRlPgefsgkVKVLGLS 73
                                   4889************99998888777534777555555555 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00025
                         AAA_30  14 ltsgdrvavltGpAGtGKttalkalreaweaaggrvi 50 
                                    l sg+ +++l Gp G+GKtt+ k+++ +++   grv+
  gi|119720012|ref|YP_920507.1| 317 LYSGE-LVALMGPNGSGKTTLAKVIAGLVRPTSGRVL 352
                                    55665.999*****************99998866775 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1      0.16        57       3      21 ..      36      54 ..      34      92 .. 0.81
   2 !   16.2   0.1     3e-05     0.011       2      23 ..     324     345 ..     323     495 .. 0.69

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.16
                                   EESSTTSSHHHHHHHHHHH CS
                            AAA  3 lyGppGtGKTllakavake 21
                                   ++G  G GKT+l+ ++   
  gi|119720012|ref|YP_920507.1| 36 ITGLSGAGKTTLVLSILGI 54
                                   68999********999876 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 3e-05
                                    EEESSTTSSHHHHHHHHHHHHT CS
                            AAA   2 llyGppGtGKTllakavakelg 23 
                                     l+Gp G GKT+lak +a  + 
  gi|119720012|ref|YP_920507.1| 324 ALMGPNGSGKTTLAKVIAGLVR 345
                                    699***************9863 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0     0.015       5.1       3      21 ..      34      52 ..      32      64 .. 0.86
   2 !   12.8   0.1   0.00023     0.082       2      21 ..     322     341 ..     321     348 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.015
                                   EEEEC-TTTCHHHHHHHHH CS
                          NACHT  3 vilqGeaGsGKTtLlqkla 21
                                   ++++G +G GKTtL+ ++ 
  gi|119720012|ref|YP_920507.1| 34 LAITGLSGAGKTTLVLSIL 52
                                   689***********98886 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00023
                                    CEEEEC-TTTCHHHHHHHHH CS
                          NACHT   2 lvilqGeaGsGKTtLlqkla 21 
                                    lv+l G++GsGKTtL++ +a
  gi|119720012|ref|YP_920507.1| 322 LVALMGPNGSGKTTLAKVIA 341
                                    799*************9998 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0      0.01       3.6       4      18 ..      36      50 ..      34     125 .. 0.91
   2 !   11.9   0.2   0.00052      0.18       1      19 [.     322     340 ..     322     358 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.01
                         AAA_33  4 lvGlpGsGKstlaer 18
                                   + Gl+G+GK+tl+ +
  gi|119720012|ref|YP_920507.1| 36 ITGLSGAGKTTLVLS 50
                                   57*********9865 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00052
                         AAA_33   1 lvllvGlpGsGKstlaerl 19 
                                    lv l G++GsGK+tla+ +
  gi|119720012|ref|YP_920507.1| 322 LVALMGPNGSGKTTLAKVI 340
                                    7899************865 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0    0.0068       2.4       8      41 ..      20      53 ..      16      86 .. 0.85
   2 !   10.9   0.0   0.00058       0.2       5      43 ..     306     344 ..     303     359 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0068
                                   HHHHHCTSBXTTXEEEEEEXTTSSHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         DnaB_C  8 dLDkltsGlqkgdliiiAarpsmGktalalniae 41
                                    L+ +  G++kg+++ i + ++ Gkt+l+l+i  
  gi|119720012|ref|YP_920507.1| 20 ALNGVNLGVEKGEFLAITGLSGAGKTTLVLSILG 53
                                   6778889***********************9975 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00058
                                    STHHHHHHCTSBXTTXEEEEEEXTTSSHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         DnaB_C   5 gfkdLDkltsGlqkgdliiiAarpsmGktalalniaena 43 
                                    g + LD++t  l +g+l+ + +  + Gkt+la  ia  +
  gi|119720012|ref|YP_920507.1| 306 GIRALDNVTLTLYSGELVALMGPNGSGKTTLAKVIAGLV 344
                                    7889****************************9999654 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.1    0.0019      0.68       2      23 ..      34      55 ..      33      67 .. 0.89
   2 !    7.6   0.1    0.0093       3.3       2      24 ..     323     345 ..     322     356 .. 0.84
   3 ?   -0.4   0.0       2.7   9.5e+02      95     137 ..     445     490 ..     425     506 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0019
                                   EEEE--TTSSHHHHHHHHHHHH CS
                       NTPase_1  2 vfiTGppGvGKtTlvkkvlell 23
                                   ++iTG +G GKtTlv  +l  +
  gi|119720012|ref|YP_920507.1| 34 LAITGLSGAGKTTLVLSILGII 55
                                   579************9998765 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0093
                                    EEEE--TTSSHHHHHHHHHHHH. CS
                       NTPase_1   2 vfiTGppGvGKtTlvkkvlellk 24 
                                    v++ Gp G+GKtTl k ++ l++
  gi|119720012|ref|YP_920507.1| 323 VALMGPNGSGKTTLAKVIAGLVR 345
                                    6789**********999987765 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 2.7
                                    HH-EEEE--..-STTGGG-HHHHHHHHHHHTTTSEEEEE--SS-.- CS
                       NTPase_1  95 eadviviDE..iGkmElkskkfkeaveevLksekpvlavihrrk.d 137
                                    ++ v+++DE   G+   +s+ + ++++++ +++k v+a+ h  +  
  gi|119720012|ref|YP_920507.1| 445 NPSVLIVDEptTGQDRAFSEYLFSTLRRLAEEGKAVVAITHSVDlA 490
                                    5678888886668888899999999999999999999999987544 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0032       1.1      21      43 ..      32      54 ..      26     119 .. 0.75
   2 !    9.8   0.0    0.0012      0.41      22      40 ..     322     340 ..     309     346 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0032
                                   EEEEEEESTTSSHHHHHHHHCCS CS
                         NB-ARC 21 lvvalvGmgGvGKttlakqilnk 43
                                    ++a+ G  G GKttl+ +il  
  gi|119720012|ref|YP_920507.1| 32 EFLAITGLSGAGKTTLVLSILGI 54
                                   489**************999865 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0012
                                    EEEEEESTTSSHHHHHHHH CS
                         NB-ARC  22 vvalvGmgGvGKttlakqi 40 
                                    +val+G  G+GKttlak i
  gi|119720012|ref|YP_920507.1| 322 LVALMGPNGSGKTTLAKVI 340
                                    799*************977 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.2     0.024       8.5       2      15 ..      35      48 ..      34      66 .. 0.92
   2 ?    2.2   0.0      0.72   2.5e+02      31     112 ..     159     238 ..     137     248 .. 0.61
   3 !   11.9   0.1   0.00072      0.25       1      19 [.     323     341 ..     323     369 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.024
                         AAA_18  2 lltGtpGvGKttla 15
                                   ++tG +G+GKttl 
  gi|119720012|ref|YP_920507.1| 35 AITGLSGAGKTTLV 48
                                   59**********95 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.72
                         AAA_18  31 vakenglllevdpealdeskrldedkldklldaleenss...aleegknlvidghlaeleseaakdikk......vvLta 101
                                    vake +ll+ ++p   ++ + + ++ + ++++ l+++ +    + e+++ +i  +                    v L+ 
  gi|119720012|ref|YP_920507.1| 159 VAKEPELLILDEPT--SDLDPAGKEEVVSAIESLRRQLDvtiVMVEQEPDIIYRFADRV---------VvlekgrVALEG 227
                                    55555555555555..5555555555555555555554433333333333333333322.........23455569**** PP

                         AAA_18 102 speelleRlek 112
                                     p el+ R+e+
  gi|119720012|ref|YP_920507.1| 228 TPRELYHRMEE 238
                                    ********997 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 0.00072
                         AAA_18   1 IlltGtpGvGKttlakeLs 19 
                                    ++l+G+ G+GKttlak ++
  gi|119720012|ref|YP_920507.1| 323 VALMGPNGSGKTTLAKVIA 341
                                    689*************986 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.1    0.0037       1.3      99     122 ..      31      54 ..      22      93 .. 0.83
   2 !    9.7   0.1    0.0021      0.72      97     121 ..     318     342 ..     298     363 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0037
                                    TSEEEEECSTTSSHHHHHHHHCTT CS
                    RsgA_GTPase  99 dktsvlvGqSGvGKStLinallpe 122
                                    +++ ++ G SG+GK+tL+ ++l+ 
  gi|119720012|ref|YP_920507.1|  31 GEFLAITGLSGAGKTTLVLSILGI 54 
                                    578899************988875 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0021
                                    CTTSEEEEECSTTSSHHHHHHHHCT CS
                    RsgA_GTPase  97 lkdktsvlvGqSGvGKStLinallp 121
                                     ++++++l+G+ G GK+tL +++++
  gi|119720012|ref|YP_920507.1| 318 YSGELVALMGPNGSGKTTLAKVIAG 342
                                    35599***************99987 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.2     0.025       8.7      18      39 ..      30      51 ..      19      57 .. 0.79
   2 !   11.4   0.1   0.00069      0.24      18      40 ..     317     341 ..     307     351 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.025
                                   HTEEEEEEESTTSSHHHHHHHH CS
                           TsaE 18 lgdvilLeGdLGaGKTtlvrgl 39
                                    g++++++G  GaGKTtlv ++
  gi|119720012|ref|YP_920507.1| 30 KGEFLAITGLSGAGKTTLVLSI 51
                                   3678999***********9776 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00069
                                    H..TEEEEEEESTTSSHHHHHHHHH CS
                           TsaE  18 l..gdvilLeGdLGaGKTtlvrgla 40 
                                    l  g++++L G+ G+GKTtl++ +a
  gi|119720012|ref|YP_920507.1| 317 LysGELVALMGPNGSGKTTLAKVIA 341
                                    134789****************987 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.2      0.02       7.2      15      37 ..      27      49 ..      21      52 .. 0.89
   2 ?   -1.4   0.0       3.5   1.2e+03     142     166 ..     181     206 ..     174     234 .. 0.81
   3 !    9.9   0.1    0.0012      0.42       2      37 ..     304     338 ..     303     343 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.02
                         ATPase 15 GipegrvvlitGepGtGKtifal 37
                                   G+ +g+   itG +G+GKt+++l
  gi|119720012|ref|YP_920507.1| 27 GVEKGEFLAITGLSGAGKTTLVL 49
                                   888999*************9976 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.5
                         ATPase 142 eilrqlvrvl.kklgvTailvsekss 166
                                    e++   ++ l ++l+vT ++v++ ++
  gi|119720012|ref|YP_920507.1| 181 EEVVSAIESLrRQLDVTIVMVEQEPD 206
                                    56777888898999999999999765 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.0012
                         ATPase   2 ktgIeglDeilkgGipegrvvlitGepGtGKtifal 37 
                                    + gI  lD+++   +++g+ v ++G  G+GKt++a+
  gi|119720012|ref|YP_920507.1| 304 PGGIRALDNVT-LTLYSGELVALMGPNGSGKTTLAK 338
                                    5699*****97.89*******************986 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1      0.03        11       5      22 ..      34      51 ..      31      61 .. 0.87
   2 !   10.3   0.0    0.0012      0.42       5      22 ..     323     340 ..     320     362 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.03
                         AAA_24  5 iliyGpsgiGKTtlakel 22
                                   ++i+G sg+GKTtl++++
  gi|119720012|ref|YP_920507.1| 34 LAITGLSGAGKTTLVLSI 51
                                   589***********9876 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0012
                         AAA_24   5 iliyGpsgiGKTtlakel 22 
                                    ++++Gp+g+GKTtlak +
  gi|119720012|ref|YP_920507.1| 323 VALMGPNGSGKTTLAKVI 340
                                    689************976 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.1    0.0025      0.87      26      88 ..     138     187 ..     132     189 .. 0.75
   2 ?    3.4   0.0      0.26        91      48      89 ..     436     471 ..     428     472 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0025
                        SbcCD_C  26 lsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllell 88 
                                    l+r+ ++lSGGekq    +a+a    +++ +       ++l++LDE  s lD+   +++++++
  gi|119720012|ref|YP_920507.1| 138 LQRNPSQLSGGEKQR---VAIA----SAVAK------EPELLILDEPTSDLDPAGKEEVVSAI 187
                                    567788999999954...3344....33444......4899***********99988888776 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.26
                        SbcCD_C  48 aalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                    +ala++y        ++++++ DE   + D  +++ l+++l+
  gi|119720012|ref|YP_920507.1| 436 LALASVYAL------NPSVLIVDEPTTGQDRAFSEYLFSTLR 471
                                    567777777......47899******************9987 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1       5.1   1.8e+03      36      51 ..      34      49 ..      27      57 .. 0.81
   2 !   14.4   0.0   6.7e-05     0.023      36      76 ..     323     359 ..     317     369 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 5.1
                         RuvB_N 36 vllyGpPGlGkttlak 51
                                   + ++G  G Gkttl  
  gi|119720012|ref|YP_920507.1| 34 LAITGLSGAGKTTLVL 49
                                   5678999******975 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 6.7e-05
                         RuvB_N  36 vllyGpPGlGkttlakiiakelgvklkitsgPvlekagdla 76 
                                    v l+Gp G Gkttlak+ia      ++ tsg vl + +d++
  gi|119720012|ref|YP_920507.1| 323 VALMGPNGSGKTTLAKVIAG----LVRPTSGRVLVRGRDVS 359
                                    789***************95....57899999999998876 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   0.00037      0.13      12      44 ..     308     341 ..     308     357 .. 0.86
   2 ?    2.3   0.0      0.32   1.1e+02     324     366 ..     446     487 ..     435     490 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00037
                         AAA_15  12 Rslkdveidlsee.ltvliGkNnsGKSsileald 44 
                                    R+l++v++ l +  l  l G+N+sGK+++++++ 
  gi|119720012|ref|YP_920507.1| 308 RALDNVTLTLYSGeLVALMGPNGSGKTTLAKVIA 341
                                    677787777777679****************995 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.32
                         AAA_15 324 nvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSp 366
                                    + +l+++EP + +   + + l+ +l++la+++k  v+  THS 
  gi|119720012|ref|YP_920507.1| 446 PSVLIVDEPTTGQDRAFSEYLFSTLRRLAEEGK-AVVAITHSV 487
                                    678999999999999999**************9.9******95 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.2    0.0014      0.48       3      21 ..      34      52 ..      32      85 .. 0.87
   2 ?    5.8   0.1     0.026       9.3       3      18 ..     323     338 ..     321     352 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0014
                                   EEEEESTTCCHHHHHHHHH CS
                           cobW  3 tvltGflGsGKTtLlnhll 21
                                   + +tG  G+GKTtL+ ++l
  gi|119720012|ref|YP_920507.1| 34 LAITGLSGAGKTTLVLSIL 52
                                   579************9988 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.026
                                    EEEEESTTCCHHHHHH CS
                           cobW   3 tvltGflGsGKTtLln 18 
                                    + l G+ GsGKTtL +
  gi|119720012|ref|YP_920507.1| 323 VALMGPNGSGKTTLAK 338
                                    5689*********966 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1      0.11        38       4      18 ..      34      48 ..      32      57 .. 0.85
   2 !    9.9   0.0    0.0014      0.51       4      38 ..     323     357 ..     321     365 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.11
                                   EEEEESTTSSHHHHH CS
                          SRP54  4 illvGlqGaGKTttl 18
                                   +++ Gl GaGKTt +
  gi|119720012|ref|YP_920507.1| 34 LAITGLSGAGKTTLV 48
                                   6789*********86 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0014
                                    EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                          SRP54   4 illvGlqGaGKTttlaKLaallkkegkkvllvaaD 38 
                                    ++l+G++G+GKTt +  +a l++    +vl+   D
  gi|119720012|ref|YP_920507.1| 323 VALMGPNGSGKTTLAKVIAGLVRPTSGRVLVRGRD 357
                                    789*********98887887777777777666555 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1      0.36   1.3e+02       4      25 ..      36      57 ..      34      62 .. 0.85
   2 ?   10.8   0.1    0.0011      0.37       2      23 ..     323     344 ..     322     361 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.36
                                   EE--SSSSHHHHHHHGGGGBS- CS
                          AAA_5  4 LvGppGtgKselaerlaaalnr 25
                                   + G +G gK++l+ +++  + +
  gi|119720012|ref|YP_920507.1| 36 ITGLSGAGKTTLVLSILGIIPQ 57
                                   6899*********999988855 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0011
                                    EEEE--SSSSHHHHHHHGGGGB CS
                          AAA_5   2 vlLvGppGtgKselaerlaaal 23 
                                    v L Gp G+gK++la+ +a ++
  gi|119720012|ref|YP_920507.1| 323 VALMGPNGSGKTTLAKVIAGLV 344
                                    569***************9988 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.1     0.012       4.2     129     156 ..      31      58 ..      20      62 .. 0.84
   2 ?    7.3   0.1    0.0062       2.2     131     160 ..     322     351 ..     307     354 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.012
                          T2SSE 129 rglilvsGgTgsGKttllyallkeinks 156
                                       + ++G  g GKttl+ ++l +i+++
  gi|119720012|ref|YP_920507.1|  31 GEFLAITGLSGAGKTTLVLSILGIIPQR 58 
                                    456679*****************99875 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0062
                          T2SSE 131 lilvsGgTgsGKttllyallkeinksderi 160
                                    l+ + G+ gsGKttl+ ++   +  ++ r+
  gi|119720012|ref|YP_920507.1| 322 LVALMGPNGSGKTTLAKVIAGLVRPTSGRV 351
                                    55678************9999988876666 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1    0.0058         2       2      23 ..      34      55 ..      33      59 .. 0.85
   2 ?    4.8   0.1     0.071        25       2      19 ..     323     340 ..     322     352 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0058
                           MobB  2 lgivgksgsGKTtLleklipel 23
                                   l+i+g sg+GKTtL+  ++ ++
  gi|119720012|ref|YP_920507.1| 34 LAITGLSGAGKTTLVLSILGII 55
                                   789***********99887665 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.071
                           MobB   2 lgivgksgsGKTtLlekl 19 
                                    ++++g +gsGKTtL + +
  gi|119720012|ref|YP_920507.1| 323 VALMGPNGSGKTTLAKVI 340
                                    68999********97644 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.2     0.074        26      44      66 ..      28      50 ..      20      54 .. 0.88
   2 ?   -0.4   0.0       2.3   8.2e+02     100     135 ..     154     188 ..     146     203 .. 0.71
   3 ?    7.7   0.1    0.0077       2.7      47      68 ..     320     341 ..     306     349 .. 0.87
   4 ?    0.5   0.0       1.2   4.3e+02     106     146 ..     443     482 ..     430     498 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.074
                      IstB_IS21 44 iekkenivllGpsGvGKshlaia 66
                                   +ek e ++++G sG+GK+ l  +
  gi|119720012|ref|YP_920507.1| 28 VEKGEFLAITGLSGAGKTTLVLS 50
                                   678899************99876 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 2.3
                      IstB_IS21 100 aralkrllkvdllilDdlgllpldqaeaellfevie 135
                                    a a +   +++llilD+  + +ld a +e++   ie
  gi|119720012|ref|YP_920507.1| 154 AIASAVAKEPELLILDEP-TSDLDPAGKEEVVSAIE 188
                                    44555667789*****96.56777777777766665 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0077
                      IstB_IS21  47 kenivllGpsGvGKshlaialg 68 
                                     e ++l+Gp G GK+ la  ++
  gi|119720012|ref|YP_920507.1| 320 GELVALMGPNGSGKTTLAKVIA 341
                                    57799*************8775 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 1.2
                      IstB_IS21 106 llkvdllilDdlgllpldqaeaellfeviekryerrsiiit 146
                                     l++++li+D+  +   d+a +e+lf  + +  e    +++
  gi|119720012|ref|YP_920507.1| 443 ALNPSVLIVDEPTT-GQDRAFSEYLFSTLRRLAEEGKAVVA 482
                                    456799****9765.56999999999999988776554443 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1     0.035        12       3      22 ..      32      51 ..      30      57 .. 0.87
   2 ?    6.9   0.1     0.017         6       3      23 ..     321     341 ..     319     365 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.035
                         AAA_14  3 kilvitGaRrvGKTtllkql 22
                                   + l+itG+  +GKTtl+  +
  gi|119720012|ref|YP_920507.1| 32 EFLAITGLSGAGKTTLVLSI 51
                                   6799************9876 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.017
                         AAA_14   3 kilvitGaRrvGKTtllkqli 23 
                                    ++++++G+  +GKTtl+k ++
  gi|119720012|ref|YP_920507.1| 321 ELVALMGPNGSGKTTLAKVIA 341
                                    6799************87665 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1     0.071        25      18      40 ..      29      51 ..      21      56 .. 0.87
   2 ?    7.3   0.0     0.011         4      22      41 ..     322     341 ..     308     352 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.071
                       ATPase_2 18 epneiyfiYGpegsGKtaLlkei 40
                                   e+ e++ i+G  g GKt+L+  i
  gi|119720012|ref|YP_920507.1| 29 EKGEFLAITGLSGAGKTTLVLSI 51
                                   5678999************9877 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.011
                       ATPase_2  22 iyfiYGpegsGKtaLlkeii 41 
                                     + + Gp gsGKt+L k i+
  gi|119720012|ref|YP_920507.1| 322 LVALMGPNGSGKTTLAKVIA 341
                                    56678***********9987 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.1     0.013       4.6       3      20 ..      32      49 ..      30      57 .. 0.83
   2 ?    4.7   0.0      0.07        25       4      23 ..     322     341 ..     319     366 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.013
                                   EEEEEESSTTSSHHHHHH CS
                     APS_kinase  3 vvvwltGlsgsGKstian 20
                                     + +tGlsg+GK+t+  
  gi|119720012|ref|YP_920507.1| 32 EFLAITGLSGAGKTTLVL 49
                                   56789**********965 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.07
                                    EEEEESSTTSSHHHHHHHHH CS
                     APS_kinase   4 vvwltGlsgsGKstianale 23 
                                     v l G  gsGK+t+a+ ++
  gi|119720012|ref|YP_920507.1| 322 LVALMGPNGSGKTTLAKVIA 341
                                    67899***********9876 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1       3.9   1.4e+03      38      52 ..      34      48 ..      29      53 .. 0.87
   2 ?    7.1   0.0    0.0094       3.3     106     160 ..     149     201 ..     114     208 .. 0.79
   3 ?   -0.4   0.0       1.8   6.4e+02      38      53 ..     323     338 ..     320     348 .. 0.85
   4 ?    0.6   0.0      0.91   3.2e+02     106     151 ..     432     475 ..     418     487 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 3.9
                           TniB 38 lllvGdsnnGKtmiv 52
                                   l + G s  GKt++v
  gi|119720012|ref|YP_920507.1| 34 LAITGLSGAGKTTLV 48
                                   7899*********98 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0094
                           TniB 106 kleqqvlrllrelkvrvLiiDEihnllagsarkqreflnalksLgnelkipivlv 160
                                    ++++ +++   + ++++Li+DE  + l      ++e++ a+ sL ++l+++iv+v
  gi|119720012|ref|YP_920507.1| 149 EKQRVAIASAVAKEPELLILDEPTSDL--DPAGKEEVVSAIESLRRQLDVTIVMV 201
                                    5555556666667899******99999..788899******************98 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.8
                           TniB  38 lllvGdsnnGKtmive 53 
                                    + l+G+   GKt++++
  gi|119720012|ref|YP_920507.1| 323 VALMGPNGSGKTTLAK 338
                                    5799*********987 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 0.91
                           TniB 106 kleqqvlrllrelkvrvLiiDEihnllagsarkqreflnalksLgn 151
                                    ++++ +l+   +l++ vLi+DE        +   + ++ +l++L +
  gi|119720012|ref|YP_920507.1| 432 EKRRLALASVYALNPSVLIVDEPTTGQ--DRAFSEYLFSTLRRLAE 475
                                    667777777888888999999864333..22223344555666555 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       4.2   1.5e+03      23      33 ..      38      48 ..      35      66 .. 0.82
   2 ?   10.4   0.0   0.00051      0.18      23      40 ..     327     344 ..     323     356 .. 0.87
   3 ?   -3.7   0.0       9.5   3.3e+03     527     572 ..     446     488 ..     440     491 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 4.2
                         AAA_13 23 GwNGaGKTtLS 33
                                   G  GaGKTtL 
  gi|119720012|ref|YP_920507.1| 38 GLSGAGKTTLV 48
                                   778******95 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00051
                         AAA_13  23 GwNGaGKTtLSrllrsle 40 
                                    G NG+GKTtL+++++ l 
  gi|119720012|ref|YP_920507.1| 327 GPNGSGKTTLAKVIAGLV 344
                                    99************9984 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 9.5
                         AAA_13 527 dkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnle 572
                                      + ++D P    D  ++ + fs ++  +   ++ k +   TH+++
  gi|119720012|ref|YP_920507.1| 446 PSVLIVDEPTTGQDRAFSEYLFSTLRRLA---EEGKAVVAITHSVD 488
                                    67899999999999999999999999998...89999999999987 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.042        15       1      22 [.      36      57 ..      36      60 .. 0.87
   2 ?    5.2   0.1     0.046        16       2      16 ..     326     340 ..     325     352 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.042
                     ATP_bind_1  1 vvGpaGsGKttfvgalseilel 22
                                   ++G  G+GKtt+v ++  i+++
  gi|119720012|ref|YP_920507.1| 36 ITGLSGAGKTTLVLSILGIIPQ 57
                                   689**********999888876 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.046
                     ATP_bind_1   2 vGpaGsGKttfvgal 16 
                                    +Gp GsGKtt+ + +
  gi|119720012|ref|YP_920507.1| 326 MGPNGSGKTTLAKVI 340
                                    8*********98766 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.2      0.89   3.1e+02      18      37 ..      30      49 ..      24      53 .. 0.83
   2 ?    9.2   0.1    0.0022      0.77      17      40 ..     318     341 ..     309     354 .. 0.85
   3 ?   -2.1   0.0       6.2   2.2e+03     118     152 ..     444     482 ..     442     494 .. 0.65

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.89
                                   H-SEEEEE--TTSSTTHHHH CS
                           PhoH 18 kndivfaiGpaGtGKtylav 37
                                   k +++ ++G +G+GKt l +
  gi|119720012|ref|YP_920507.1| 30 KGEFLAITGLSGAGKTTLVL 49
                                   5678899*********9976 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0022
                                    HH-SEEEEE--TTSSTTHHHHHHH CS
                           PhoH  17 kkndivfaiGpaGtGKtylavala 40 
                                     + ++v  +Gp G+GKt la ++a
  gi|119720012|ref|YP_920507.1| 318 YSGELVALMGPNGSGKTTLAKVIA 341
                                    46789***************8776 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 6.2
                                    B-SEEEEE-SG...GG.--HHHHHHHHTTB-TT-EEEEE CS
                           PhoH 118 lndafvilDEA...Qn.ttkeqmkmfltRlGenskvvvt 152
                                    ln +++i+DE    Q+ + +e +   l Rl e+ k+vv+
  gi|119720012|ref|YP_920507.1| 444 LNPSVLIVDEPttgQDrAFSEYLFSTLRRLAEEGKAVVA 482
                                    677888888852223312344455677888888888875 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1     0.088        31      49      75 ..      27      53 ..      17      62 .. 0.87
   2 ?   -1.9   0.0       5.3   1.9e+03     188     202 ..      81      95 ..      71      98 .. 0.82
   3 ?    6.5   0.1     0.015       5.1      50      74 ..     317     340 ..     289     352 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.088
                                   SEETTSEEEEEESTTSSHHHHHHHHHH CS
                           RecA 49 GlpkGriieiyGpessGkttlalhaia 75
                                   G+ kG  + i G   +Gkttl l+++ 
  gi|119720012|ref|YP_920507.1| 27 GVEKGEFLAITGLSGAGKTTLVLSILG 53
                                   899********************9875 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 5.3
                                    E-------------- CS
                           RecA 188 qirekiGvmfgnpet 202
                                     i +++Gv+f +pe+
  gi|119720012|ref|YP_920507.1|  81 IIAQRVGVVFEDPEI 95 
                                    57889********96 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.015
                                    EETTSEEEEEESTTSSHHHHHHHHH CS
                           RecA  50 lpkGriieiyGpessGkttlalhai 74 
                                    l  G ++ + Gp+ sGkttla   i
  gi|119720012|ref|YP_920507.1| 317 LYSGELVALMGPNGSGKTTLAKV-I 340
                                    66899***************954.3 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1    0.0091       3.2       2      24 ..      34      56 ..      33      81 .. 0.83
   2 ?    3.3   0.0      0.17        59       2      24 ..     323     345 ..     322     366 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0091
                            PRK  2 IgvagsSGaGkttvarklekifg 24
                                   ++++g SGaGktt+   +  i+ 
  gi|119720012|ref|YP_920507.1| 34 LAITGLSGAGKTTLVLSILGIIP 56
                                   69***********9988877665 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.17
                            PRK   2 IgvagsSGaGkttvarklekifg 24 
                                    +++ g+ G+Gktt+a+ +  +++
  gi|119720012|ref|YP_920507.1| 323 VALMGPNGSGKTTLAKVIAGLVR 345
                                    7899**********999876655 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1      0.94   3.3e+02       6      20 ..      36      50 ..      33      55 .. 0.82
   2 ?    9.3   0.0    0.0025      0.87       4      23 ..     323     342 ..     321     345 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.94
                      PduV-EutP  6 liGkvgsGKttLtqa 20
                                   + G +g+GKttL  +
  gi|119720012|ref|YP_920507.1| 36 ITGLSGAGKTTLVLS 50
                                   56999*******765 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0025
                      PduV-EutP   4 illiGkvgsGKttLtqalkg 23 
                                    + l+G+ gsGKttL++ + g
  gi|119720012|ref|YP_920507.1| 323 VALMGPNGSGKTTLAKVIAG 342
                                    679************99876 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.9      0.18        65       3      16 ..      35      48 ..      33      53 .. 0.89
   2 ?    9.1   0.1     0.004       1.4       2      20 ..     323     341 ..     322     358 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.18
                         AAA_28  3 vitGgestGKTtll 16
                                   +itG +++GKTtl+
  gi|119720012|ref|YP_920507.1| 35 AITGLSGAGKTTLV 48
                                   79**********97 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.004
                         AAA_28   2 ivitGgestGKTtlleaLa 20 
                                    ++++G+ ++GKTtl++ +a
  gi|119720012|ref|YP_920507.1| 323 VALMGPNGSGKTTLAKVIA 341
                                    89************99777 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0     0.026       9.3       2      21 ..      34      53 ..      33      97 .. 0.84
   2 ?    4.5   0.1       0.1        36       2      22 ..     323     343 ..     322     376 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.026
                                   EEEEESTTSSHHHHHHHHHT CS
                       MMR_HSR1  2 vaivGrpNvGKStLinaltg 21
                                    ai G + +GK+tL+ +++g
  gi|119720012|ref|YP_920507.1| 34 LAITGLSGAGKTTLVLSILG 53
                                   589***********999887 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.1
                                    EEEEESTTSSHHHHHHHHHTS CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltge 22 
                                    va++G   +GK+tL + + g 
  gi|119720012|ref|YP_920507.1| 323 VALMGPNGSGKTTLAKVIAGL 343
                                    89************9999874 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1      0.73   2.6e+02      12      35 ..      29      52 ..      24      59 .. 0.86
   2 ?    7.6   0.0    0.0078       2.7       1      35 [.     306     341 ..     306     355 .. 0.88
   3 ?   -0.5   0.0       2.3   8.1e+02     133     155 ..     458     480 ..     450     495 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.73
                                   BTT-EEEEEESTTSSHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxx RF
                    ATP-synt_ab 12 vqGqrtlipgafgvGktvisqsls 35
                                    +G+ ++i g +g Gkt+++ s++
  gi|119720012|ref|YP_920507.1| 29 EKGEFLAITGLSGAGKTTLVLSIL 52
                                   6899999***********997775 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0078
                                    SSHHHHHH.S-EBTT-EEEEEESTTSSHHHHHHHHH CS
                                    xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    ATP-synt_ab   1 GirvlDal.fpivqGqrtlipgafgvGktvisqsls 35 
                                    Gir+lD + +++  G+ ++++g +g Gkt++++ ++
  gi|119720012|ref|YP_920507.1| 306 GIRALDNVtLTLYSGELVALMGPNGSGKTTLAKVIA 341
                                    899**9752799*******************98886 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 2.3
                                    EGGGSBTTHHHHHHHHHTTSEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxx RF
                    ATP-synt_ab 133 adqgypaylgaklaslyERagka 155
                                     d+++  yl+++l +l E    +
  gi|119720012|ref|YP_920507.1| 458 QDRAFSEYLFSTLRRLAEEGKAV 480
                                    6899************9975544 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1      0.88   3.1e+02       3      19 ..      36      52 ..      34      74 .. 0.80
   2 ?    8.4   0.0    0.0079       2.8       2      19 ..     324     341 ..     323     362 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.88
                   RNA_helicase  3 lyGpsgeGKStlakeLa 19
                                   ++G sg GK+tl+ ++ 
  gi|119720012|ref|YP_920507.1| 36 ITGLSGAGKTTLVLSIL 52
                                   8999*******997755 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0079
                   RNA_helicase   2 wlyGpsgeGKStlakeLa 19 
                                     l Gp+g GK+tlak +a
  gi|119720012|ref|YP_920507.1| 324 ALMGPNGSGKTTLAKVIA 341
                                    689************965 PP

>> DUF463  YcjX-like family, DUF463
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.2   0.00055      0.19       3      21 ..      34      52 ..      33      62 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00055
                         DUF463  3 lavTGLsraGKtvfitsLv 21
                                   la+TGLs+aGKt+++ s+ 
  gi|119720012|ref|YP_920507.1| 34 LAITGLSGAGKTTLVLSIL 52
                                   89************99875 PP

>> Gtr1_RagA  Gtr1/RagA G protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0     0.001      0.35       2      27 ..     323     348 ..     322     363 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.001
                      Gtr1_RagA   2 vLLmGksgsGKtsmrsiiFdnylard 27 
                                    v LmG++gsGKt++ ++i   + ++ 
  gi|119720012|ref|YP_920507.1| 323 VALMGPNGSGKTTLAKVIAGLVRPTS 348
                                    569**************976666665 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1      0.08        28      20      48 ..      29      57 ..      19      75 .. 0.88
   2 ?    4.5   0.0     0.047        17      20      55 ..     318     353 ..     308     357 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.08
                                   HCTS-EEEEESTTSSCHHHHHHHHHHCHC CS
                           PIF1 20 ekgklfFvtGsgGtgKtflwkallkklrs 48
                                   ekg+++ +tG +G+gKt l   +l ++ +
  gi|119720012|ref|YP_920507.1| 29 EKGEFLAITGLSGAGKTTLVLSILGIIPQ 57
                                   7999****************999999876 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.047
                                    HCTS-EEEEESTTSSCHHHHHHHHHHCHCTCCCEEE CS
                           PIF1  20 ekgklfFvtGsgGtgKtflwkallkklrsegkivla 55 
                                     +g+l+ + G  G+gKt l k +   +r++   vl+
  gi|119720012|ref|YP_920507.1| 318 YSGELVALMGPNGSGKTTLAKVIAGLVRPTSGRVLV 353
                                    57889999********************99888875 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0      0.13        44      39      62 ..      25      48 ..      18      58 .. 0.78
   2 ?    5.2   0.0     0.051        18      42      66 ..     317     341 ..     307     348 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.13
                          Rad17 39 vLesrkkriLLisGPsGCgkstvv 62
                                    L  +k + L i+G sG gk+t v
  gi|119720012|ref|YP_920507.1| 25 NLGVEKGEFLAITGLSGAGKTTLV 48
                                   566677789*************76 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.051
                          Rad17  42 srkkriLLisGPsGCgkstvvkvLs 66 
                                        +++ + GP G gk+t  kv++
  gi|119720012|ref|YP_920507.1| 317 LYSGELVALMGPNGSGKTTLAKVIA 341
                                    5555688899**********99987 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.2      0.13        45      10      33 ..      31      54 ..      24      70 .. 0.85
   2 ?   -0.6   0.0       4.4   1.5e+03     101     128 ..     161     190 ..     105     211 .. 0.76
   3 ?    5.8   0.3     0.046        16      10      32 ..     320     342 ..     313     353 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.13
                         AAA_19 10 ekvllvtaGpGtGKTrvlkhival 33
                                    + l++t+  G GKT+++  i+ +
  gi|119720012|ref|YP_920507.1| 31 GEFLAITGLSGAGKTTLVLSILGI 54
                                   567899**********99988765 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 4.4
                         AAA_19 101 qeeellivDE.fqdvd.elqyrLlkallge 128
                                    +e elli DE ++d+d     ++++a+   
  gi|119720012|ref|YP_920507.1| 161 KEPELLILDEpTSDLDpAGKEEVVSAIESL 190
                                    334499999977999988888888888754 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.046
                         AAA_19  10 ekvllvtaGpGtGKTrvlkhiva 32 
                                     ++++++++ G+GKT++ k i  
  gi|119720012|ref|YP_920507.1| 320 GELVALMGPNGSGKTTLAKVIAG 342
                                    57899**********98776654 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.2      0.15        52      26      44 ..      34      52 ..      28      57 .. 0.92
   2 ?    5.1   0.2      0.06        21      26      44 ..     323     341 ..     309     353 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.15
                          DUF87 26 lAilgsTGsGKSntvavLl 44
                                   lAi g +G+GK+++v ++l
  gi|119720012|ref|YP_920507.1| 34 LAITGLSGAGKTTLVLSIL 52
                                   79*************9987 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.06
                          DUF87  26 lAilgsTGsGKSntvavLl 44 
                                    +A +g  GsGK+++++v+ 
  gi|119720012|ref|YP_920507.1| 323 VALMGPNGSGKTTLAKVIA 341
                                    6889999**********85 PP

>> BCA_ABC_TP_C  Branched-chain amino acid ATP-binding cassette transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.5       6.6   2.3e+03       7      12 ..     116     121 ..     116     122 .. 0.86
   2 ?   -0.7   0.0         4   1.4e+03       5      10 ..     226     231 ..     222     232 .. 0.83
   3 ?   10.0   0.3    0.0019      0.66       1      17 [.     504     520 ..     504     522 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 6.6
                   BCA_ABC_TP_C   7 tPaEvr 12 
                                    +P+Evr
  gi|119720012|ref|YP_920507.1| 116 PPEEVR 121
                                    6****9 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 4
                   BCA_ABC_TP_C   5 eGtPaE 10 
                                    eGtP E
  gi|119720012|ref|YP_920507.1| 226 EGTPRE 231
                                    9***98 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.0019
                   BCA_ABC_TP_C   1 rvIAeGtPaEvrndPrV 17 
                                    r+ A+G P+ v +dP V
  gi|119720012|ref|YP_920507.1| 504 RIVADGEPDSVLADPGV 520
                                    799************88 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (541 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                       115  (0.00641419); expected 17.9 (0.001)
Passed Fwd filter:                        52  (0.00290033); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              51  [number of targets reported over threshold]
# CPU time: 0.72u 0.32s 00:00:01.04 Elapsed: 00:00:00.50
# Mc/sec: 3279.07
//
Query:       gi|119720013|ref|YP_920508.1|  [L=179]
Description: glutamine amidotransferase class-I [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.7e-06   26.5   0.0      5e-05   23.2   0.0    2.0  1  GATase         Glutamine amidotransferase class-I
     0.0033   17.3   0.1        1.1    9.1   0.0    2.1  2  SNO            SNO glutamine amidotransferase family
  ------ inclusion threshold ------
      0.091   12.3   0.0       0.11   12.1   0.0    1.2  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
       0.11   12.3   0.3       0.35   10.6   0.1    1.9  3  Peptidase_C26  Peptidase C26


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   1.1e-08     5e-05      40     176 ..      44     170 ..      15     176 .. 0.70

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1.1e-08
                                    HHSTSEEEEEEESSCTT.TTTHHHHHHHHCTSTS-EEEETHHHHHHHHHTTTEEEEEECEEEEEEEEEEEETTTCGGTTT CS
                         GATase  40 lknpdgilvsgGpgspg.vegkieaikearenkiPiLGICLGmQllaiefgrkvvkekekehhggtmrlgddetallygl 118
                                     + +d++++sg   +   +   ++  +++ e + P+LGIC G+Ql+ + f   +  +        + ++          +
  gi|119720013|ref|YP_920508.1|  44 VERYDKVVISGTALKDFdYLRYVDRFSWVKEFEGPVLGICAGLQLVSLVFRVGLRDKL--VIGVREVEVVR--------E 113
                                    5678999999876554458888999999999999**************9976555443..44444444444........2 PP

                                    TSEEEEEEEEEEEEESG.CHHHTTEEEEEEEETTEEEEEEEEETTTEEEESSBTTSTTS CS
                         GATase 119 knevierhrHryevnpk.elepaglevtakseddeelmeiiekknpfvgvQFHPEstst 176
                                    ++  ++     y v+ k    ++ +ev+++se +  ++ +  k++ ++++ FHPE+  +
  gi|119720013|ref|YP_920508.1| 114 NRLAKTGKLKAYFVTSKlPAPSSAVEVLGVSEGE--NVFFKVKDREVYALAFHPEVYNE 170
                                    2455555666666666533345669999999554..55555555569********9765 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0   0.00024       1.1      60     103 ..      68     113 ..      48     119 .. 0.77
   2 !    6.2   0.0    0.0018       8.2     142     175 ..     136     171 ..     122     176 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00024
                                    HHHHHHTT.--EEEETHHHHHHCCEETTB..SS-SS--CCEEEETT CS
                            SNO  60 llefvknsekvvlGtCaGlillskelene..lvktlellkvkvkrn 103
                                     +  vk+ e +vlG CaGl l+s        +   +++ +v+v r+
  gi|119720013|ref|YP_920508.1|  68 RFSWVKEFEGPVLGICAGLQLVSLVFRVGlrDKLVIGVREVEVVRE 113
                                    4667999999********9888765444322777788888888774 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0018
                                    TTCEEEEECTTEEEEEE..ETTEEEESS-GGGSTTH CS
                            SNO 142 eavkvlyeldgeivvak..qkkilatsfhPelaedd 175
                                     av+vl   +ge v  k   +++ a++fhPe+ +++
  gi|119720013|ref|YP_920508.1| 136 SAVEVLGVSEGENVFFKvkDREVYALAFHPEVYNEE 171
                                    4678888888855554431669*********98775 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.4e-05      0.11      39      88 ..      45      89 ..       4     120 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.4e-05
                       GATase_3 39 edadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmL 88
                                   e +d v++ G+   ++d  +lr  +   ++ke+   +gpvlgiC+Glq+ 
  gi|119720013|ref|YP_920508.1| 45 ERYDKVVISGT--ALKDFDYLRYVDRFSWVKEF---EGPVLGICAGLQLV 89
                                   55777777776..46677777777777777775...79**********86 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0      0.99   4.4e+03      55      68 ..      43      56 ..      38      67 .. 0.80
   2 ?   10.6   0.1   7.8e-05      0.35     106     124 ..      77      95 ..      71     130 .. 0.79
   3 ?   -1.9   0.0      0.51   2.3e+03     201     216 .]     153     166 ..     132     166 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.99
                  Peptidase_C26 55 ildkldgllltGgq 68
                                   ++++ d+++++G +
  gi|119720013|ref|YP_920508.1| 43 VVERYDKVVISGTA 56
                                   68899999999976 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 7.8e-05
                  Peptidase_C26 106 vPilgiCrGlqllnvalGG 124
                                     P+lgiC Glql+  ++  
  gi|119720013|ref|YP_920508.1|  77 GPVLGICAGLQLVSLVFRV 95 
                                    6***********9877654 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.51
                  Peptidase_C26 201 seeakafvlgvQwHPE 216
                                    ++  +  v+++ +HPE
  gi|119720013|ref|YP_920508.1| 153 VK--DREVYALAFHPE 166
                                    33..345899999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 1431.72
//
Query:       gi|119720014|ref|YP_920509.1|  [L=229]
Description: putative ATP binding protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-74  250.3   0.1    1.6e-74  250.1   0.1    1.0  1  Diphthami_syn_2  Diphthamide synthase
  ------ inclusion threshold ------
       0.17   11.3   0.0       0.25   10.8   0.0    1.3  1  QueC             Queuosine biosynthesis protein QueC


Domain annotation for each model (and alignments):
>> Diphthami_syn_2  Diphthamide synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  250.1   0.1   1.8e-78   1.6e-74       1     218 [.       1     221 [.       1     222 [. 0.95

  Alignments for each domain:
  == domain 1  score: 250.1 bits;  conditional E-value: 1.8e-78
                Diphthami_syn_2   1 mkvavlysGGkDsilaLykalkesevesLvsvisenkesymfhvvnvhlvellaesvGiplikletaGeeekevedLkg. 79 
                                    m+ avl+sGGkDs la+++a++++ev  Lv+v+s n+esymfhv+n+hl+el+ae++G+pl+k e +G +e+  edL+  
  gi|119720014|ref|YP_920509.1|   1 MRLAVLFSGGKDSHLAMFRAMRHHEVACLVTVESRNPESYMFHVPNIHLTELQAEAIGLPLVKVESEGRKEE-LEDLRRa 79 
                                    899****************************************************************99875.4555550 PP

                Diphthami_syn_2  80 ...tlkkldveavviGaieseyqksriervCrelGlksvaPLWkkdpeelleeiveekfevivvavkaegldeslLGrri 156
                                        +++  ve+vv+Gai s yq +r++rvCrel l  + PLW +d  e+  e +e++feviv +v  + ld slLGrr+
  gi|119720014|ref|YP_920509.1|  80 lelAVERYAVEGVVTGAIRSTYQSTRVQRVCRELDLWCFNPLWLEDEYEVYRELLENGFEVIVSGVFSYPLDASLLGRRV 159
                                    000567778*********************************************************************** PP

                Diphthami_syn_2 157 dkklidelkklsekygidkagegGeaetlvlDaPlfkkrlevkelekkwderrgyldierak 218
                                    d  l++el kl e+yg+  agegGe et vlDaP+++kr+ v e+ek +++  g++ ++ra+
  gi|119720014|ref|YP_920509.1| 160 DWGLVEELGKLKERYGVSMAGEGGELETTVLDAPFYRKRVVVLEAEKVYSNYSGVYRVKRAR 221
                                    ************************************************************97 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   2.8e-05      0.25       4      31 ..       5      32 ..       2      63 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 2.8e-05
                                   EE--SSHHHHHHHHHHHHH-SEEEEEEE CS
                           QueC  4 vllSGGlDSttvlalakkegkevealtf 31
                                   vl+SGG DS  +++ a+++ +  +++t+
  gi|119720014|ref|YP_920509.1|  5 VLFSGGKDSHLAMFRAMRHHEVACLVTV 32
                                   89***************99777666766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1423.50
//
Query:       gi|119720015|ref|YP_920510.1|  [L=342]
Description: hypothetical protein Tpen_1108 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.011   15.3   0.0      0.017   14.6   0.0    1.3  1  Pribosyltran  Phosphoribosyl transferase domain
      0.017   14.6   0.0      0.025   14.0   0.0    1.2  1  UPRTase       Uracil phosphoribosyltransferase
       0.21   11.7   0.4       0.46   10.6   0.4    1.5  1  SAM_Exu       Exuperantia SAM-like domain


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   2.9e-06     0.017      57     116 ..     130     185 ..      79     212 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.9e-06
                                    -EEEEEE-TTT--EE........EE----TTSEEEEE-SEESSSHHHHHHHH.HHHCC-BS CS
                   Pribosyltran  57 yvrkvkyrpdgseeaargssdesrlledpagkkVliVDDildtGgTllaale.lLkekgpe 116
                                    +v ++++++ g ++++ +     +  + ++g+  l+V D ++tG Tl+a+++  Lk ++ +
  gi|119720015|ref|YP_920510.1| 130 FVKITSHSQHGEGNVTFS-----SVGAFTKGSDTLVVADTVATGATLEATVNfTLKIAEIK 185
                                    444444444444444433.....478999**********************9777776666 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   4.2e-06     0.025      65     176 ..      97     213 ..      80     223 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.2e-06
                        UPRTase  65 deekialVpilRa..GegmeealrellpearvghlglqreeetlepveyynkLPkkiaertvlllDpviaTGgsaaaaiq 142
                                     +e++++  +lR+  G  ++eal ++  + r g +++  + ++ e    ++ + +  + +  l++  ++aTG+++ a ++
  gi|119720015|ref|YP_920510.1|  97 GSEELMFLHVLRGspGYMLHEALAKAGARLREGFVKITSHSQHGEGNVTFSSVGAFTKGSDTLVVADTVATGATLEATVN 176
                                    56788999999987799999***********************************99888888898999*******9998 PP

                        UPRTase 143 lLker....gvgeekIlvlsvlaseegvkrlaeefpkv 176
                                      ++     g++ ++I+v   + +eeg++rla+  +kv
  gi|119720015|ref|YP_920510.1| 177 FTLKIaeikGINLRRIIVYGFI-AEEGLRRLASLAEKV 213
                                    5433223348888899888877.5899*9999887776 PP

>> SAM_Exu  Exuperantia SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.4   7.6e-05      0.46      13      50 ..     298     334 ..     295     339 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 7.6e-05
                        SAM_Exu  13 keRvravklRrlLAEngidyesLkeiweekkkeGlekl 50 
                                    + R +  +lR +LAE g   + L+e++  k+ +Gle++
  gi|119720015|ref|YP_920510.1| 298 RSRAKLEELRSILAERGWYPDWLEEVYR-KRVDGLERA 334
                                    46777789*******************7.578898875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       274  (0.0152825); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 2284.09
//
Query:       gi|119720016|ref|YP_920511.1|  [L=426]
Description: major facilitator transporter [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.3e-48  165.7  29.5      4e-40  137.8  19.8    2.0  2  MFS_1       Major Facilitator Superfamily
    4.5e-05   22.5  22.8     0.0042   16.0   9.2    2.3  2  Sugar_tr    Sugar (and other) transporter
    0.00014   20.8  10.1     0.0062   15.4   5.6    2.8  2  MFS_1_like  MFS_1 like family
    0.00021   19.8  10.2     0.0029   16.0   1.6    2.7  3  OATP        Organic Anion Transporter Polypeptide (OATP) fami


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.8  19.8     9e-44     4e-40       5     291 ..      17     305 ..      12     311 .. 0.79
   2 !   37.2   6.1   3.5e-13   1.6e-09      64     163 ..     290     403 ..     285     414 .. 0.82

  Alignments for each domain:
  == domain 1  score: 137.8 bits;  conditional E-value: 9e-44
                          MFS_1   5 aflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll.fas 83 
                                    + ++ ++r+i+++++p  +++++ +s s++gl+++l  l+aa++ +++G+l dr++r+ +  l++l+++++ +++  + s
  gi|119720016|ref|YP_920511.1|  17 LTIHQADRFIVSAVAP-QVMDEFKVSYSQLGLVFSLTVLVAAFLYPVWGYLYDRYSRKLLAGLAALIWGFT-TIFNaL-S 93 
                                    5677888999999999.788***********************************9999************.333324.7 PP

                          MFS_1  84 slw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllgglla.sslgWravfyilaivs 161
                                      +  +++ r+ +G+   a+ p++++l+ad+f +  rg+a+gll+a+  lGai+g +l+  ++ + l+Wr +f+i ++++
  gi|119720016|ref|YP_920511.1|  94 RTFsEFFATRLATGID-DAAPPGIYSLVADYFDPYSRGKALGLLNATGPLGAIIGTILSLSIVaAGLSWRNAFFITGPIG 172
                                    7777***********7.7******************************************99989999************ PP

                          MFS_1 162 llafvlfllllpeepperkrkspkeee...kgtgpaplvpawkallkdpvlw.illialllfffgfsglltllplylqev 237
                                    +  + l   ++++++++r+ ++p+ +    +   +a+l++ + ++l ++ l  ++l ++ ++f  ++++++++ +y+ + 
  gi|119720016|ref|YP_920511.1| 173 VAIGAL--TFFLVKDVPRGVSEPELKDvltEDIYRAKLSD-LPKVLENKSLVlLYLQGFWGVF-PWNAITFWFVTYMEKE 248
                                    ***998..66655555555555544445888889999999.8888888877435666666665.9999************ PP

                          MFS_1 238 lgls..glllaglllallalvgailallagrlsdr....lgrrrrlllallllllaalgl 291
                                    +gls  + ++++  ++l+ ++++++ ++ag + d     ++r r++l a+++++ a+l++
  gi|119720016|ref|YP_920511.1| 249 RGLSpdT-VMVV--MSLSLIAMVAGNIVAGIIGDWlfkkTKRGRAILGAVVVFFSAVLIY 305
                                    ****853.5555..6666666666666666666663111554444444444444444443 PP

  == domain 2  score: 37.2 bits;  conditional E-value: 3.5e-13
                          MFS_1  64 vlllglllfalglllllfa..sslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpll 140
                                     +l ++++f++++l+ l a  + ++  ++++ vl+++   +++p+++a+i+d++ +e r++a+g+l  + +lG++  p l
  gi|119720016|ref|YP_920511.1| 290 AILGAVVVFFSAVLIYL-AirAESTeEFILFTVLTAFEIPMAAPNVVAAITDVTEPELRSSATGYLRFFENLGSATSPFL 368
                                    44455555555523333.346777779***************************************************** PP

                          MFS_1 141 ggllasslg............Wravfyilaivsll 163
                                     g+la+s g            W ++f+++a+++++
  gi|119720016|ref|YP_920511.1| 369 TGVLAESMGlgeaillvsvytWLLCFVFFAVLAAI 403
                                    *****999998888888887777778888888776 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   5.6   1.4e-05     0.063      44     191 ..      41     182 ..       6     188 .. 0.80
   2 !   16.0   9.2   9.4e-07    0.0042      25     188 ..     236     396 ..     214     404 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.4e-05
                                    ...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHH CS
                       Sugar_tr  44 ssvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlv 123
                                    s +++gl++s+++++a++   + g+l dr++Rk     aa++    ++ +a++    ++  +++ R+ +Gi   +  ++ 
  gi|119720016|ref|YP_920511.1|  41 SYSQLGLVFSLTVLVAAFLYPVWGYLYDRYSRKLLAGLAALIWGFTTIFNALSR---TFSEFFATRLATGIDDAAPPGIY 117
                                    667999*********9999999999******99888888888888888888888...9*************999999999 PP

                                    HHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGGGS CS
                       Sugar_tr 124 PmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllilllfl 191
                                    ++ ++ + p + Rg+  +l +    +G ++++i+ l +   +    wr  ++++  + +++ +l +fl
  gi|119720016|ref|YP_920511.1| 118 SLVADYFDPYS-RGKALGLLNATGPLGAIIGTILSLSIVAAGL--SWRNAFFITGPIGVAIGALTFFL 182
                                    98777776665.6666667777778999999999999944444..49999999999998887777775 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 9.4e-07
                                    HHHHHHTSTT--SHH.HHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-T CS
                       Sugar_tr  25 llkfaknfglsksks.skeessvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsve 103
                                     + f++  +++k+++ s ++  v ++l++ ++++G i+ ++++ +l ++  R  ++l a+v+f+ + ++  a+  ++s+e
  gi|119720016|ref|YP_920511.1| 236 AITFWFVTYMEKERGlSPDTVMVVMSLSLIAMVAGNIVAGIIGDWLFKKTKRGRAILGAVVVFFSAVLIYLAIR-AESTE 314
                                    44455555555544412333677888999999999999999999999999999999888888875555555555.77999 PP

                                    GGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHH CS
                       Sugar_tr 104 vlivgRvlvGigvGlasvlvPmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpall 183
                                     +i+  vl+ + + +a   v   i  ++ ++lR+  +++  ++  +G   + +++ +l+++ +       + l +v + l
  gi|119720016|ref|YP_920511.1| 315 EFILFTVLTAFEIPMAAPNVVAAITDVTEPELRSSATGYLRFFENLGSATSPFLTGVLAESMG---LGEAILLVSVYTWL 391
                                    999999999999999999999999999999999999999999999999888888888888877...33333333333333 PP

                                    HHHHG CS
                       Sugar_tr 184 llill 188
                                    l++++
  gi|119720016|ref|YP_920511.1| 392 LCFVF 396
                                    33333 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   5.6   1.4e-06    0.0062     112     326 ..       7     326 ..       4     354 .. 0.85
   2 !    5.9   0.1    0.0011         5      30      83 ..     345     398 ..     341     420 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.4e-06
                     MFS_1_like 112 wilfllvvlasfflaailvlldaatlkelgedrkdyGrqrlfGsvGyaifaf...itGilidhysvnllp.ysallyvla 187
                                    w+++l+ + + ++ +a  +++ a++ + + e++  y++  l  s+   ++af   + G+l d ys++ll  + al+  ++
  gi|119720016|ref|YP_920511.1|   7 WFVVLFFFTFLTIHQADRFIVSAVAPQVMDEFKVSYSQLGLVFSLTVLVAAFlypVWGYLYDRYSRKLLAgLAALIWGFT 86 
                                    77777888888899999**********************999999999887722257**********9886555555555 PP

                     MFS_1_like 188 allvisllvvlilnetekesklkvtksl.................................................... 215
                                     ++ + +  ++ +  t+ ++ ++ ++ +                                                    
  gi|119720016|ref|YP_920511.1|  87 TIFNALSRTFSEFFATRLATGIDDAAPPgiyslvadyfdpysrgkalgllnatgplgaiigtilslsivaaglswrnaff 166
                                    5555555555666666666666666655**************************************************** PP

                     MFS_1_like 216 ..........................................qvllnilknpeviifllvalilgmswgiienFlflYL. 252
                                                                              ++l ++l+n++++++ l  +   + w++i  ++  Y+ 
  gi|119720016|ref|YP_920511.1| 167 itgpigvaigaltfflvkdvprgvsepelkdvltediyraklSDLPKVLENKSLVLLYLQGFWGVFPWNAITFWFVTYMe 246
                                    ******************************************99***********************************9 PP

                     MFS_1_like 253 kelgasn....tllGslvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaii..enawlvlpievLhgis 326
                                    ke g s      +++  ++  v+++i+  +++ +l++k+   + ++ a+++++   l+y +i  e++   +++ vL ++ 
  gi|119720016|ref|YP_920511.1| 247 KERGLSPdtvmVVMSLSLIAMVAGNIVAGIIGDWLFKKTKRGRAILGAVVVFFSAVLIYLAIraESTEEFILFTVLTAFE 326
                                    999*996222256788888889999**************99999999988887777666666587777777777777765 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0011
                     MFS_1_like  30 glkaseigiitlilpltsilsppiwgvlaDrfgkrkkvvilslllsavlflsll 83 
                                    +l  s  g +     l s  sp ++gvla+ +g  ++++++s+  ++++f+ + 
  gi|119720016|ref|YP_920511.1| 345 ELRSSATGYLRFFENLGSATSPFLTGVLAESMGLGEAILLVSVYTWLLCFVFFA 398
                                    777888888888888999999999999999999999999888877776666222 PP

>> OATP  Organic Anion Transporter Polypeptide (OATP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.9   0.00011      0.47       1      92 [.       7      99 ..       7     151 .. 0.87
   2 !   16.0   1.6   6.4e-07    0.0029     288     381 ..     212     305 ..     191     322 .. 0.78
   3 ?   -2.2   0.0      0.21   9.3e+02     465     522 ..     317     374 ..     309     378 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00011
                                   xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           OATP  1 vflvllsllglvq.amvsgyfkstittiEkrFklpsstsgliassneignillilfvsYfggrghrPrwigigallmalgsl 81
                                   +f+vl+ +  l+   +   +++ +  ++  +Fk + s+ gl+ s+  + +++l  + +Y+ +r  r  + g++al+ ++ ++
  gi|119720016|ref|YP_920511.1|  7 WFVVLFFFTFLTIhQADRFIVSAVAPQVMDEFKVSYSQLGLVFSLTVLVAAFLYPVWGYLYDRYSRKLLAGLAALIWGFTTI 88
                                   566666666555536666677778899******************************************************* PP

                                   xxxxxxxxxxx RF
                           OATP 82 llalPhfisgk 92
                                     al   +s+ 
  gi|119720016|ref|YP_920511.1| 89 FNALSRTFSEF 99
                                   99999888764 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 6.4e-07
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                           OATP 288 krllknpifllvilssvfeillvaGfitFlpkylEtqFslsaseAnlltGvvvipgaalGillgGllvkk.lklsakkla 366
                                     ++l+n+ ++l+ l++   ++ ++++  +   y+E++ +ls+ +  +++ +++++++++G +++G++    +k + ++ a
  gi|119720016|ref|YP_920511.1| 212 PKVLENKSLVLLYLQGFWGVFPWNAITFWFVTYMEKERGLSPDTVMVVM-SLSLIAMVAGNIVAGIIGDWlFKKTKRGRA 290
                                    4689****************************************99998.668889999999999887752344444455 PP

                                    xxxxxxxxxxxxxxx RF
                           OATP 367 klvlvvsllslllll 381
                                     l +vv ++s++l+ 
  gi|119720016|ref|YP_920511.1| 291 ILGAVVVFFSAVLIY 305
                                    555555555544443 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.21
                                    xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           OATP 465 illflvsflgalgrvpall.vilRcVkkedksfalGlqlllirllgliPgPiifGaiiD 522
                                    il+++++++    + p+++ +i  + ++e +s a G   ++ +l g   +P + G++ +
  gi|119720016|ref|YP_920511.1| 317 ILFTVLTAFEIPMAAPNVVaAITDVTEPELRSSATGYLRFFENL-GSATSPFLTGVLAE 374
                                    34444455555555666662444556789999999987777666.88888888887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1039  (0.0579508); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.67u 0.28s 00:00:00.95 Elapsed: 00:00:00.45
# Mc/sec: 2855.69
//
Query:       gi|119720017|ref|YP_920512.1|  [L=517]
Description: glycoside hydrolase family protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-61  207.8   0.0    9.1e-47  159.5   0.0    2.5  2  Glyco_hydro_1  Glycosyl hydrolase family 1
    5.1e-06   26.1   0.0    3.5e-05   23.4   0.0    2.0  2  Cellulase      Cellulase (glycosyl hydrolase family 5)


Domain annotation for each model (and alignments):
>> Glyco_hydro_1  Glycosyl hydrolase family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.7   0.0   3.4e-16     3e-12       5      91 ..       2      94 ..       1     106 [. 0.78
   2 !  159.5   0.0     1e-50   9.1e-47      91     449 ..     122     497 ..     117     500 .. 0.80

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 3.4e-16
                                   S-TT-EEEEE--HHHHH--TTSTT---BHHH..HHHHH....GGGSTTS---SSTT-HHHHHHHHHHHHHHTT-SEEEEE-- CS
                  Glyco_hydro_1  5 fpedFlwgaataayqiEGawnedGkgesiwD..tftet....pgkvlegsngdvacdsYhrykeDvallkelgvkayrfSis 80
                                   fp+ Flwg++ a +q E +  ++     + D  ++ +     ++ +++g+  + ++d++h ++eD +l k lg++ayr+ + 
  gi|119720017|ref|YP_920512.1|  2 FPKSFLWGVSLAGFQFEMGDPAGEALDPNTDwyVWVHDeyniREGIVSGDLPEKGIDYWHLFREDHSLAKSLGLNAYRLNVE 83
                                   9****************8877665555554422555551111455667777889**************************** PP

                                   HHHHSTTSTT- CS
                  Glyco_hydro_1 81 WpRilPkGege 91
                                   W+R++P+++ +
  gi|119720017|ref|YP_920512.1| 84 WSRVFPEPTFS 94
                                   ******99544 PP

  == domain 2  score: 159.5 bits;  conditional E-value: 1e-50
                                    ---HHHHHHHHHHHHHHHHTT-EEEEEEESS--BHHHHH..H........-..GGG-SHHHHHHHHHHHHHHHHHTTT-- CS
                  Glyco_hydro_1  91 einekGlayYerLidelleagieplvTlyHwdlPqaLqd..e........G..gwenrsiidafkeyaevvfkrfgdkvk 158
                                      n+k +++Y+++++ l e+g   ++ l H+ lP +++d  +        G  g+++ +   +f ++a++v + fgd v+
  gi|119720017|ref|YP_920512.1| 122 IANKKAVQHYREVVEDLREKGFYVILNLVHFTLPTWIHDplTaratnakkGplGYADPRFPVEFAKFAAYVAASFGDLVD 201
                                    5699*********************************9753233333333466888899999****************** PP

                                    EEEEEE-HHHHHHHHHTS..S-STT-S-TTTHHHHHHHHHHHHHHHH.........HHHHHHHTTT-EEEEEEEEEEEEE CS
                  Glyco_hydro_1 159 lwlTfnEpnvvallgylt..gefaPgkkdleaayeaaHnlllahara.........vklykevaqkgkigivlnlslaep 227
                                    +w TfnEp vv+  g+l   g+f+Pg  ++ a  +a+ n+  ah  a         vk+y + a+++++gi++n+   +p
  gi|119720017|ref|YP_920512.1| 202 AWSTFNEPSVVTESGFLKrrGKFPPGIFNFDAYKRAMINIAQAHLLAyiaikkfdrVKAYSDSAESASVGIIHNMIPFHP 281
                                    ****************85449*****777776666666666666544111111112555566669*************** PP

                                    SSSSHHHH.HHHHHHHHHHTHHHHHHHHHSS--HHHHHHHGGG..S----HHHHHHHTT--SEEEEEEEEEEEEEE--.. CS
                  Glyco_hydro_1 228 lseseedk.eaaeraleflngwfldpvvkGdYpeemkellrergalpeiteedkellkgkadflglnyYtsrlvknke.. 304
                                    l++s++++  a+  + +++n w+ + +v+G   ++     +e         e  e+ k   d++g+nyY++++vk k   
  gi|119720017|ref|YP_920512.1| 282 LDPSRKRDrDASMVTHHLHNSWIPNSLVNGWIDRDFDL-KQEP-------SEVFEKYKSRLDWMGINYYSRSVVKGKVnl 353
                                    ****999989999*****************87766543.2332.......34556778999*************998733 PP

                                    ....-STT---SSGGGGG-...........SBSS-B-SSSS-B-HHHHHHHHHHHHHTS----EEEEE----EE-BSSSH CS
                  Glyco_hydro_1 305 .seeaslskteekkleeev...........dpslpktdigwiiepeglrkllellkkeYqklpiyiteNGlgakdeieeg 372
                                      + + + +     +  +                p+td gw+++peg+ +++++   +Y+ +p+++teNG+++       
  gi|119720017|ref|YP_920512.1| 354 lRPVIPFPAFP---VLVKGygfecapnsqsLAGRPTTDFGWEVYPEGIVEVVKMA-MQYN-VPLLVTENGVADAR----- 423
                                    31222222211...1111123444555443455799**************99865.8999.**********9766..... PP

                                    HH--HHHHHHHHHHHHHHHHHH.HTT--EEEEEEE-SB----GGGTTSEE--SEEEETTTTTEEEE-HHHHHHHHHHH CS
                  Glyco_hydro_1 373 kveDdkRidYlkehlnevkkai.edgvdlkgYvawsllDnfewaegyskrfGlvyvdrnetleRtpkkSakwykevie 449
                                       D+ R ++l+ hl+ +++a+ +  + lkgY+ w+l+Dn+ewa g+++rfGl+ vd  ++++R ++ Sa  ++ +++
  gi|119720017|ref|YP_920512.1| 424 ---DELRPHFLALHLKLLEDALeSREISLKGYLHWALTDNYEWADGFRMRFGLFEVD-LSSKRRVKRPSADLFARIVS 497
                                    ...99*****************8899*******************************.99************999987 PP

>> Cellulase  Cellulase (glycosyl hydrolase family 5)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   3.9e-09   3.5e-05      27     135 ..      67     213 ..      58     226 .. 0.79
   2 ?   -0.3   0.0     0.063   5.7e+02     224     251 ..     397     424 ..     388     438 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 3.9e-09
                                    HHHHHHHT-SEEEEEEECTGGTTSSTTT............................GCTHHHHHHHHHHHHHHHHTT-EE CS
                      Cellulase  27 idevkdagfntvRlpvswgelvenapdy............................kvdenslerveevvkyakenglyv 78 
                                    ++++k+ g n+ Rl+v w + + ++p++                              ++++++ + evv+   e+g+yv
  gi|119720017|ref|YP_920512.1|  67 HSLAKSLGLNAYRLNVEWSRVF-PEPTFsvevgveeedgvktgididdsdlekldsIANKKAVQHYREVVEDLREKGFYV 145
                                    5678899999999999998888.3555545555555554566665555555544444555******************** PP

                                    EEEEESS..TTTCSSSSTTTTHHHHHHH.............HHHHHHHHHHHHTTTTTTEEEESSSS--STT CS
                      Cellulase  79 ildiHse..egwltkadgnssedtaeef.............fkklwtqiAerykkndevvifelmNEPhgnn 135
                                    il++ +   ++w   +d+ +  +t  ++             f+k+ + +A+ +   d v ++ ++NEP  ++
  gi|119720017|ref|YP_920512.1| 146 ILNLVHFtlPTW--IHDPLTARATNAKKgplgyadprfpveFAKFAAYVAASF--GDLVDAWSTFNEPSVVT 213
                                    ***877669999..899999999988888999999999***************..6677799******8755 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.063
                                    HHHHHHHHHHHTTSEEEEEEEESSTTSS CS
                      Cellulase 224 rledaakylvekgipviigEfGgsnadg 251
                                     + ++ k +++ ++p++++E G+ +a +
  gi|119720017|ref|YP_920512.1| 397 GIVEVVKMAMQYNVPLLVTENGVADARD 424
                                    5567789999************987654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (517 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 3687.14
//
Query:       gi|119720018|ref|YP_920513.1|  [L=303]
Description: hypothetical protein Tpen_1111 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.3e-05   21.9   0.0    0.00015   21.3   0.0    1.4  1  HTH_24         Winged helix-turn-helix DNA-binding
     0.0087   16.0   0.2      0.022   14.7   0.0    1.7  2  HTH_11         HTH domain
  ------ inclusion threshold ------
       0.02   14.8   0.0      0.034   14.0   0.0    1.4  1  MarR_2         MarR family
      0.068   13.0   0.0       0.13   12.1   0.0    1.4  1  HTH_AsnC-type  AsnC-type helix-turn-helix domain
      0.078   13.0   0.0       0.13   12.3   0.0    1.3  1  DUF4366        Domain of unknown function (DUF4366)


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   4.1e-08   0.00015      27      48 .]     267     288 ..     244     288 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 4.1e-08
                         HTH_24  27 lglSpstvnrrlkrLeeeGlIk 48 
                                    + l+p+t++rr++rLe+ G++k
  gi|119720018|ref|YP_920513.1| 267 VSLPPTTLWRRIRRLEKLGYVK 288
                                    789*****************97 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       2.5     9e+03       6      23 ..     228     242 ..     227     243 .. 0.70
   2 !   14.7   0.0   6.1e-06     0.022      30      52 ..     272     295 ..     262     297 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.5
                         HTH_11   6 lelLleargpisgeeLAe 23 
                                    l lLl+arg   g eL e
  gi|119720018|ref|YP_920513.1| 228 LALLLKARG---GRELGE 242
                                    788999998...666655 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 6.1e-06
                         HTH_11  30 rtvrrdIkaLeelg.vpIesepgr 52 
                                    +t +r+I++Le+lg v+Ie+++gr
  gi|119720018|ref|YP_920513.1| 272 TTLWRRIRRLEKLGyVKIEKKAGR 295
                                    79*******************997 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   9.6e-06     0.034      18      59 ..     255     293 ..     227     296 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 9.6e-06
                                    TTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSS CS
                         MarR_2  18 pgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeD 59 
                                    +g+   ++++  +  l++ ++ r+++rL++ G+v  ++   +
  gi|119720018|ref|YP_920513.1| 255 GGG-AFQSDIGLYVSLPPTTLWRRIRRLEKLGYVKIEKK--A 293
                                    333.699***************************88754..4 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   3.6e-05      0.13      22      42 .]     262     282 ..     258     282 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.6e-05
                  HTH_AsnC-type  22 eLAervGlSestvlrRvrrLe 42 
                                    +++  v l ++t +rR+rrLe
  gi|119720018|ref|YP_920513.1| 262 DIGLYVSLPPTTLWRRIRRLE 282
                                    6777799*************8 PP

>> DUF4366  Domain of unknown function (DUF4366)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   3.6e-05      0.13      79     142 ..     172     233 ..     162     237 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.6e-05
                        DUF4366  79 ctekcaagkvntdcpveepepekeaepeepeeepekksnnglllvvlavaligggaayyfkvlk 142
                                      +  +  +vn + p  +p+p+++ +  +p++ +++ s + +  + +av++++g+a+++  +lk
  gi|119720018|ref|YP_920513.1| 172 PPQTSQPSRVNASQPASQPQPTPSPQ--QPAPAKTTPSGMPIEPLYIAVLGAAGAAVVLALLLK 233
                                    44555677888888888887777744..455555555446666677777777778877776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       751  (0.0418874); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2135.65
//
Query:       gi|119720019|ref|YP_920514.1|  [L=338]
Description: galactose-1-phosphate uridylyltransferase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-19   70.3   0.0      8e-19   68.8   0.0    1.7  1  GalP_UDP_transf  Galactose-1-phosphate uridyl transferase, N-
    8.6e-16   58.1   0.0    1.3e-15   57.6   0.0    1.2  1  GalP_UDP_tr_C    Galactose-1-phosphate uridyl transferase, C-
     0.0055   17.4   0.0      0.014   16.1   0.0    1.7  1  HIT              HIT domain
     0.0082   15.5   0.0       0.11   11.8   0.0    2.2  1  DUF4931          Domain of unknown function (DUF4931)
  ------ inclusion threshold ------
      0.014   15.9   0.0      0.023   15.2   0.0    1.3  1  DcpS_C           Scavenger mRNA decapping enzyme C-term bindi
       0.11   11.3   0.1       0.18   10.6   0.0    1.4  2  DUF4921          Domain of unknown function (DUF4921)


Domain annotation for each model (and alignments):
>> GalP_UDP_transf  Galactose-1-phosphate uridyl transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.8   0.0   2.7e-22     8e-19      11     184 .]       5     155 ..       1     155 [. 0.90

  Alignments for each domain:
  == domain 1  score: 68.8 bits;  conditional E-value: 2.7e-22
                GalP_UDP_transf  11 ashrrfnpltgewvlvsphrtkrpwqgqqekiskdtlpekDklkcyLcPgnsrangefnpky.kstfvftndFpalseds 89 
                                     +++r np++g wv+vs+ r++rpw     ++        +  kc++cPg +++       y  ++ v  n+Fpal++d+
  gi|119720019|ref|YP_920514.1|   5 YNELRWNPVLGCWVIVSSSRARRPW----RRV--------E--KCPFCPGSEET------GYgWDVLVLDNKFPALRRDA 64 
                                    4677*********************....333........4..7*****98765......3556789***********99 PP

                GalP_UDP_transf  90 nyikteaiaknilfkaepayGrceviifsskheltladlspkdikavvaaWqektaelkakeypkcvlifENkGaamgvs 169
                                       +     + +l+ +++ayG  +v++  ++he+ l +++ +++ + ++   + t+e ++ e++++vl f NkG+ +gvs
  gi|119720019|ref|YP_920514.1|  65 RVSRS----SRDLYVVREAYGAAKVVVETPEHEGDLDSIPFENLVKYLESLGRVTEEECRDERVAYVLPFRNKGEVIGVS 140
                                    88887....446*******************************************99999******************** PP

                GalP_UDP_transf 170 nphPHgqiwaeehlp 184
                                    ++hPH+q++  +++p
  gi|119720019|ref|YP_920514.1| 141 LTHPHSQVYVLPFVP 155
                                    *********999988 PP

>> GalP_UDP_tr_C  Galactose-1-phosphate uridyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.6   0.0   4.2e-19   1.3e-15      10     122 ..     169     280 ..     161     315 .. 0.89

  Alignments for each domain:
  == domain 1  score: 57.6 bits;  conditional E-value: 4.2e-19
                                    HHH.SS-HHHHHHHHHHHH-TTEEEE-SSEEEE--TT--STT-EEEEESS--SSGGG--HHHHHHHHHHHHHHHHHHHHH CS
                  GalP_UDP_tr_C  10 agsngsillhdyvqmelaekervvelkdsflavvpylakWPfevlllrkaevkslaeladeekedlaailkklarkydnl 89 
                                    +++ g  l+   +++e +e  r+v ++++fl+  p++a+WP+e  + +k++v sl+ l+  e+  la +l+  +  y+ l
  gi|119720019|ref|YP_920514.1| 169 REKRGGCLFCHVLELEAEEGARTVYENEHFLVFLPFFAMWPYELHVYPKRHVGSLNTLSSDERVSLADALRVTVAAYNSL 248
                                    34448889999999****************************************************************** PP

                                    CTS---EEEEEE---SCCCTTTT--EEEEE--B CS
                  GalP_UDP_tr_C  90 fetsfeysmGlhqaplnaeednswlHaHfevpl 122
                                    f  s +y m +hq+p   e +   lH+ f++ +
  gi|119720019|ref|YP_920514.1| 249 FGFSLPYIMVFHQSPCRDEGS-LHLHVEFYPVH 280
                                    ***************986654.33788888877 PP

>> HIT  HIT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   4.6e-06     0.014       3      64 ..     186     247 ..     184     274 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.6e-06
                                    CC-CCEEEE-SSEEEEE-SS-SSSSEEEEEESSTGCSGGGCCHHHHHHHHHHHHHHHHHHHT CS
                            HIT   3 eipstvvyeddlvlafldidpkapghlLvipkkhlselhdlteeelakllsavkkvakalqk 64 
                                    e+ ++ vye++++l+fl  ++++p  l v pk+h+  l+ l+ +e+  l  a +  ++a + 
  gi|119720019|ref|YP_920514.1| 186 EEGARTVYENEHFLVFLPFFAMWPYELHVYPKRHVGSLNTLSSDERVSLADALRVTVAAYNS 247
                                    677899************************************99998888887777766665 PP

>> DUF4931  Domain of unknown function (DUF4931)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   3.5e-05      0.11      53     119 ..      83     149 ..      26     156 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.5e-05
                        DUF4931  53 qtvlietdeceedistyseehlrellrfgvkhwlelekseeyksvllfknhGPlsGGsikhahmqiv 119
                                      v++et e e+d+ +   e l + l+   +   e  ++e+   vl f+n G + G s+ h+h q+ 
  gi|119720019|ref|YP_920514.1|  83 AKVVVETPEHEGDLDSIPFENLVKYLESLGRVTEEECRDERVAYVLPFRNKGEVIGVSLTHPHSQVY 149
                                    458899999999999888888777776433333444466788899********************85 PP

>> DcpS_C  Scavenger mRNA decapping enzyme C-term binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   7.8e-06     0.023      10      99 ..     185     274 ..     174     286 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 7.8e-06
                                    TSS-B-EEEE-SSEEEEE-SS-SSSEEEEEEESS---SGGG--TTTTTHHHHHHHHHHHHHHHTT-T-EEEEE--SCCCT CS
                         DcpS_C  10 gkepervvyedekfvvlkDikpkaklhllvipkrdikslrdLtkehlpllkemrekakkvieekynevdaeelrvgvhyq 89 
                                     +e +r vye+e+f+v+    +  ++ l v pkr++ sl+ L++++   l++  ++  ++ ++ +  + +    + +h  
  gi|119720019|ref|YP_920514.1| 185 AEEGARTVYENEHFLVFLPFFAMWPYELHVYPKRHVGSLNTLSSDERVSLADALRVTVAAYNSLF--GFSLPYIMVFHQS 262
                                    3457788************************************9999999999999999999988..4788889999999 PP

                                    -..-S-S--EEE CS
                         DcpS_C  90 P..svyhlHlHv 99 
                                    P      lHlHv
  gi|119720019|ref|YP_920514.1| 263 PcrDEGSLHLHV 274
                                    978777899998 PP

>> DUF4921  Domain of unknown function (DUF4921)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.2       1.2   3.6e+03      10      31 ..      11      32 ..       9      35 .. 0.73
   2 ?   10.6   0.0   6.1e-05      0.18     217     335 ..     120     244 ..      72     251 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.2
                        DUF4921 10 nPftGtevWtvpgrgnrPlsek 31
                                   nP+ G  v   ++r++rP ++ 
  gi|119720019|ref|YP_920514.1| 11 NPVLGCWVIVSSSRARRPWRRV 32
                                   7888888888888888887654 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 6.1e-05
                        DUF4921 217 rnryvrYvavfqnWLkpaGasfdhlhkqlvaiDergvqaeaeiarlre.....nPnlynelavdyaakhnlviaendhav 291
                                    r++ v Yv  f+n  +  G s+ h h q+  +  +  + + e+a++re        l+ ++    a +    + en+h +
  gi|119720019|ref|YP_920514.1| 120 RDERVAYVLPFRNKGEVIGVSLTHPHSQVYVLPFVPPRVSREMAMAREfrekrGGCLFCHVLELEAEEGARTVYENEHFL 199
                                    56789************************9999888777777776664211113569999988888889999******** PP

                        DUF4921 292 afagfGhryp.tlevysksatkePweqseeevravsdlvhalhaa 335
                                    +f  f   +p  l+vy k ++ +  + s++e+ +++d +  + aa
  gi|119720019|ref|YP_920514.1| 200 VFLPFFAMWPyELHVYPKRHVGSLNTLSSDERVSLADALRVTVAA 244
                                    *********956***********999*****99999988766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.57u 0.35s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 1980.83
//
Query:       gi|119720020|ref|YP_920515.1|  [L=100]
Description: hypothetical protein Tpen_1113 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-05   24.2  13.9    0.00044   20.9  13.3    2.0  1  Phage_holin_4_2  Mycobacterial 4 TMS phage holin, superfamily
  ------ inclusion threshold ------
       0.72   10.1  17.8        0.1   12.9   3.5    1.9  1  TctB             Tripartite tricarboxylate transporter TctB f
        3.9    7.3   0.0        3.9    7.3   0.0    2.5  3  Phage_holin_2_4  Bacteriophage holin family, superfamily II-l


Domain annotation for each model (and alignments):
>> Phage_holin_4_2  Mycobacterial 4 TMS phage holin, superfamily IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9  13.3   7.3e-08   0.00044       1      81 [.       1      92 [.       1      95 [. 0.77

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 7.3e-08
                Phage_holin_4_2  1 mrfllrllvnalallvaalllpgvev.as....fltallaalvlgllnalvkpilkllslpltiltl......Glftlvina 71
                                   m+fl+ ++v+++a+++a +l+pg +  +s    fltal+ al++ + ++l  p+ +ll++ + +  l      G ++  + a
  gi|119720020|ref|YP_920515.1|  1 MNFLVGWIVSGIAVWLALKLFPGKQKaESipgaFLTALIGALIFWVFKVLHIPFGTLLAILVWLYALrkiqgvGWLGAAVLA 82
                                   89*******************9954323345559999999***999999999999999876655555667766777777777 PP

                Phage_holin_4_2 72 lmlllaaalv 81
                                   ++++l++al+
  gi|119720020|ref|YP_920515.1| 83 VLVYLINALF 92
                                   7777776665 PP

>> TctB  Tripartite tricarboxylate transporter TctB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   3.5   1.7e-05       0.1      86     134 ..       4      54 ..       1      55 [. 0.72

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.7e-05
                           TctB  86 plGfilatalflllll.g...reerkwlkalilavvlallvyllFtklLgvpL 134
                                     +G+i++ ++++l+l  +   ++ ++++ a+++a++ al+ +++F k+L++p+
  gi|119720020|ref|YP_920515.1|   4 LVGWIVSGIAVWLALKlFpgkQKAESIPGAFLTALIGALI-FWVF-KVLHIPF 54 
                                    47*******6664444545666667777777777777766.89**.8999997 PP

>> Phage_holin_2_4  Bacteriophage holin family, superfamily II-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.2       1.2   7.1e+03      26      31 ..       5      10 ..       3      17 .. 0.56
   2 ?    7.3   0.0   0.00066       3.9      41      54 ..      35      48 ..      21      50 .. 0.85
   3 ?    2.2   1.2     0.025   1.5e+02      26      47 ..      73      94 ..      54      97 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.2
                Phage_holin_2_4 26 aGflas 31
                                   +G++ s
  gi|119720020|ref|YP_920515.1|  5 VGWIVS 10
                                   455554 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.00066
                Phage_holin_2_4 41 avAliGlLvnWyYk 54
                                   + AliG+L+ W +k
  gi|119720020|ref|YP_920515.1| 35 LTALIGALIFWVFK 48
                                   579********998 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.025
                Phage_holin_2_4 26 aGflasselialvGlavAliGl 47
                                   +G+l ++ l+ lv l+ Al Gl
  gi|119720020|ref|YP_920515.1| 73 VGWLGAAVLAVLVYLINALFGL 94
                                   5777777777777777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       945  (0.0527079); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 713.45
//
Query:       gi|119720021|ref|YP_920516.1|  [L=382]
Description: GHMP kinase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.4e-17   61.8   0.1    5.4e-17   61.8   0.1    2.4  3  GHMP_kinases_N   GHMP kinases N terminal domain
    9.9e-10   38.7   0.3      3e-09   37.1   0.1    1.9  2  GHMP_kinases_C   GHMP kinases C terminal
    1.3e-09   37.5   0.0    2.3e-09   36.6   0.0    1.4  1  GalKase_gal_bdg  Galactokinase galactose-binding signature
  ------ inclusion threshold ------
       0.38   10.7   1.1         14    5.7   0.3    2.4  2  DUF4574          Ubiquinol-cytochrome-c reductase complex ass


Domain annotation for each model (and alignments):
>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.49   2.2e+03      23      36 ..      85      98 ..      83     102 .. 0.87
   2 !   61.8   0.1   1.2e-20   5.4e-17       2      66 .]     104     171 ..     103     171 .. 0.93
   3 ?   -3.4   0.9       2.6   1.2e+04      11      17 ..     336     342 ..     332     342 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.49
                                   HHHHHHHHHTTEHH CS
                 GHMP_kinases_N 23 alvaAllallglsl 36
                                   a+v+A+ ++lg++l
  gi|119720021|ref|YP_920516.1| 85 AVVRAVEEYLGKPL 98
                                   89********9887 PP

  == domain 2  score: 61.8 bits;  conditional E-value: 1.2e-20
                                    EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHH..HH.HHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
                 GHMP_kinases_N   2 ivikseiPvgaGLGSSAAlavalvaAllallglsl..ee.aklaleaerlaqggngsggDvaasvyGg 66 
                                     v++se+Pvg+GL+SSAAl v+ ++A+ ++++l l  +e a+la++ae+ ++g  ++  D++as+yGg
  gi|119720021|ref|YP_920516.1| 104 AVVRSEVPVGSGLSSSAALEVSFLKAIDYYFNLGLgkKElAELAFQAENRIAGIPCGRLDQYASAYGG 171
                                    689*****************************99985337********99999**************8 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 2.6
                                    TSSSCHH CS
                 GHMP_kinases_N  11 gaGLGSS 17 
                                    gaG+G+S
  gi|119720021|ref|YP_920516.1| 336 GAGMGGS 342
                                    99***98 PP

>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.3   5.9e+03      11      40 ..     213     236 ..     205     238 .. 0.65
   2 !   37.1   0.1   6.7e-13     3e-09      21      84 ..     303     364 ..     291     365 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.3
                 GHMP_kinases_C  11 ellgellnlsqrselkavvgilppeleell 40 
                                    e+++++l+       + + +++pp l++ll
  gi|119720021|ref|YP_920516.1| 213 EEINRGLRA------LMEDPSVPPGLKRLL 236
                                    455555553......445788888888876 PP

  == domain 2  score: 37.1 bits;  conditional E-value: 6.7e-13
                 GHMP_kinases_C  21 qrselkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkdeaeqvaralreefe 84 
                                    +++ l++ ++++ pele++ +a+++ Gal+ak+sGaG G+++ al+ +  e e v +alre ++
  gi|119720021|ref|YP_920516.1| 303 HEL-LRDLYEVSLPELERIRDAMLRSGALAAKISGAGMGGSLLALT-EGGEEEVVGSALREGGK 364
                                    444.4557999**********************************9.66666666666677665 PP

>> GalKase_gal_bdg  Galactokinase galactose-binding signature
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.0   5.2e-13   2.3e-09      12      45 ..       6      39 ..       2      41 .. 0.94

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 5.2e-13
                                   EEEEEEEEEEEE--S-TTTT-EEEEEEEEEEEEE CS
                GalKase_gal_bdg 12 fvasAPGRvnLiGEHtDYngGfVlpmAieqdiyi 45
                                   f asAPGRv+++  H DY g  V p+Ai++++y+
  gi|119720021|ref|YP_920516.1|  6 FTASAPGRVDFLNTHQDYKGLPVVPVAINLRTYV 39
                                   889*****************************98 PP

>> DUF4574  Ubiquinol-cytochrome-c reductase complex assembly factor 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.017        75      45      81 ..     255     291 ..     241     294 .. 0.73
   2 ?    5.7   0.3    0.0031        14      16      34 ..     335     353 ..     323     364 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.017
                        DUF4574  45 qdpqrrdeaakkkaLvlatLqeAaatqenvawRknwt 81 
                                        r dea +k+ L+   +q ++     +  Rk w+
  gi|119720021|ref|YP_920516.1| 255 PYLDRLDEASRKRILFTLLMQASTSRAVGILRRKGWK 291
                                    556789**99998888877777777777888888885 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0031
                        DUF4574  16 aGaGlGsaLfvLvtPgeer 34 
                                    +GaG+G  L++L++ gee 
  gi|119720021|ref|YP_920516.1| 335 SGAGMGGSLLALTEGGEEE 353
                                    79**************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 2354.46
//
Query:       gi|119720022|ref|YP_920517.1|  [L=127]
Description: hypothetical protein Tpen_1116 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-22   79.9   0.0    1.6e-22   79.6   0.0    1.1  1  DUF498    Protein of unknown function (DUF498/DUF598)


Domain annotation for each model (and alignments):
>> DUF498  Protein of unknown function (DUF498/DUF598)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.6   0.0   8.8e-27   1.6e-22       1     109 []      16     124 ..      16     124 .. 0.97

  Alignments for each domain:
  == domain 1  score: 79.6 bits;  conditional E-value: 8.8e-27
                                    EEEEESSEEEETTEEESSEEEE-SSSE.EE-THCSTTCEECHHHHHHCT..T..SEEEEE-TTS.-----HHHHHHHHCC CS
                         DUF498   1 idaygeggfelngvkysgsllvlpeea.fawdvakaedlteeslellellepkpellilGtGkr.qlplspevrealnel 78 
                                    iday++g + ++g+ y+++++++p+++  +w+  ++++l+ e+++ +  l  +++ +++GtG +  ++++ ev+e ++++
  gi|119720022|ref|YP_920517.1|  16 IDAYKFGRLVVGGRAYERDVIITPSGVvPNWWRLEGHRLQLEDVKKY--LGLDVDAVVVGTGYHgFMRVDSEVVESFRRM 93 
                                    89*************************99999666************..78899************************** PP

                                    TSEEEEE-HHHHHHHHHHHHHHT--EEEEEE CS
                         DUF498  79 gigvevmdtraAartyNllaaegrrVaaaLi 109
                                    g +v v++t+ A+++yN l+a grrV+a+L+
  gi|119720022|ref|YP_920517.1|  94 GREVYVLETGRAVEKYNELVARGRRVLAMLH 124
                                    *****************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 926.28
//
Query:       gi|119720023|ref|YP_920518.1|  [L=675]
Description: TPR repeat-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00021   21.5   3.3    0.00076   19.7   1.2    3.1  3  TPR_12    Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.012   15.6   3.1       0.13   12.4   0.9    3.1  2  TPR_2     Tetratricopeptide repeat
      0.018   15.7   3.5       0.13   13.0   1.8    3.2  2  TPR_16    Tetratricopeptide repeat
       0.04   13.8   3.0      0.095   12.6   1.6    2.5  2  TPR_10    Tetratricopeptide repeat
      0.048   13.8   3.3       0.08   13.1   0.9    2.7  2  TPR_9     Tetratricopeptide repeat
       0.11   12.5   0.1         14    5.7   0.0    2.4  2  AAA_5     AAA domain (dynein-related subfamily)
       0.21   11.8   0.8       0.69   10.2   0.0    2.3  3  ANAPC3    Anaphase-promoting complex, cyclosome, subunit 3
       0.43   10.9   2.5        1.3    9.5   0.3    3.1  3  TPR_8     Tetratricopeptide repeat
        2.7    9.0   5.3        8.6    7.5   1.3    4.0  3  TPR_14    Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.9   3.7e+03      29      60 ..     293     322 ..     291     323 .. 0.77
   2 ?   -2.1   0.0       2.6   5.1e+03      45      66 ..     472     492 ..     468     498 .. 0.71
   3 !   19.7   1.2   3.8e-07   0.00076      40      77 .]     550     587 ..     516     587 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.9
                         TPR_12  29 aleiarrllGpdhpltattlrnLgrlyralgr 60 
                                    a+eia++   p +p  + +   +  l+r++g+
  gi|119720023|ref|YP_920518.1| 293 AREIAEKC--PGNPSCVDAASLYLALCRQAGK 322
                                    78999999..6677788888888888888887 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.6
                         TPR_12  45 attlrnLgrlyralgryeeAle 66 
                                     +tl+ Lg l r++ r   Al+
  gi|119720023|ref|YP_920518.1| 472 GSTLHRLGVLERYA-RSSGALA 492
                                    57888888888776.7776666 PP

  == domain 3  score: 19.7 bits;  conditional E-value: 3.8e-07
                         TPR_12  40 dhpltattlrnLgrlyralgryeeAlelleealaiaek 77 
                                      p+ta++l   g ++++l+ry eA+++l ++la++e+
  gi|119720023|ref|YP_920518.1| 550 GLPETARSLALRGFALLQLERYGEAESALARVLAMYEE 587
                                    3689********************************96 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.9   6.6e-05      0.13       2      32 ..     556     586 ..     555     588 .. 0.90
   2 ?    1.7   0.1      0.17   3.5e+02       7      26 ..     602     621 ..     599     626 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.6e-05
                          TPR_2   2 ealynlGlayyklgdyeeAleafekAleldP 32 
                                    + l  +G a+++l +y eA+ a+ ++l+ ++
  gi|119720023|ref|YP_920518.1| 556 RSLALRGFALLQLERYGEAESALARVLAMYE 586
                                    67889**********************9886 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.17
                          TPR_2   7 lGlayyklgdyeeAleafek 26 
                                    l +a++k+g+ e+Al  +e 
  gi|119720023|ref|YP_920518.1| 602 LSEAWLKKGEREKALSELEG 621
                                    67899*********998875 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   1.8   6.3e-05      0.13      31      63 ..     552     584 ..     545     589 .. 0.84
   2 ?   11.2   2.8   0.00023      0.46       6      40 ..     564     597 ..     559     622 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.3e-05
                         TPR_16  31 PdaaeAllllgdaalrqgrlaeAaalyraalra 63 
                                    P++a++l l+g a+l++ r+ eA+ ++++ l+ 
  gi|119720023|ref|YP_920518.1| 552 PETARSLALRGFALLQLERYGEAESALARVLAM 584
                                    99**********************777666655 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00023
                         TPR_16   6 aalragdyddAaaaleaalkrdpssPdaaeAllll 40 
                                    a+l++ +y +A+ al ++l+++ +s  +a+Al+++
  gi|119720023|ref|YP_920518.1| 564 ALLQLERYGEAESALARVLAMYEESG-RADALFFS 597
                                    799*******************6665.89888874 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   1.6   4.8e-05     0.095       1      34 [.     554     587 ..     554     588 .. 0.95
   2 ?   -3.8   0.0       6.7   1.3e+04       8      26 ..     602     620 ..     601     621 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.8e-05
                         TPR_10   1 tAsslnNLanalrqrgrydeAealleealairrr 34 
                                    tA+sl   + al q+ ry eAe  l ++la++++
  gi|119720023|ref|YP_920518.1| 554 TARSLALRGFALLQLERYGEAESALARVLAMYEE 587
                                    89999999************************98 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 6.7
                         TPR_10   8 LanalrqrgrydeAealle 26 
                                    L+ a  + g++++A+  le
  gi|119720023|ref|YP_920518.1| 602 LSEAWLKKGEREKALSELE 620
                                    5666777899999987665 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       1.6   3.3e+03      15      44 ..     452     480 ..     448     502 .. 0.64
   2 ?   13.1   0.9     4e-05      0.08      25      68 ..     551     594 ..     537     595 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.6
                          TPR_9  15 lavverllllaPddpeerrdRGlllaqlGc 44 
                                    l+++e + +l P +++  + RG  l++lG 
  gi|119720023|ref|YP_920518.1| 452 LQALEAVAILRPGTVSGFL-RGSTLHRLGV 480
                                    5566666666666655433.5666666554 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 4e-05
                          TPR_9  25 aPddpeerrdRGlllaqlGclsaAladLeaylalapdapdaeai 68 
                                     P++++ +  RG++l ql+++ +A  +L + la+ ++   a+a+
  gi|119720023|ref|YP_920518.1| 551 LPETARSLALRGFALLQLERYGEAESALARVLAMYEESGRADAL 594
                                    5899999999**************************99988875 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.019        38       2      24 ..     196     221 ..     195     228 .. 0.82
   2 ?    5.7   0.0     0.007        14       3      98 ..     427     521 ..     426     531 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.019
                                    EEEE--SSSSHHHHHHHGGGGB...S CS
                          AAA_5   2 vlLvGppGtgKselaerlaaal...n 24 
                                    v L+G+ G+g+ +la  la++l   +
  gi|119720023|ref|YP_920518.1| 196 VALKGKAGSGRHSLAYLLASRLleeG 221
                                    679****************9986433 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.007
                                    EEE--SSSSHHHHHHHGGGGB.S--EEEEE--TT--HHHHH--B--.........--------.G-SEEEEESGGG--HH CS
                          AAA_5   3 lLvGppGtgKselaerlaaal.nreveyvqltrdtteedlkgrreikngttslvdsplvraar.egeilvlDEveraese 80 
                                    l+ G pG g+     +l +++ +++++     + +++ ++ g ++   g t ++ ++l r ar +g+++v +E+ +++ +
  gi|119720023|ref|YP_920518.1| 427 LVSGVPGAGRVLAYTSLNSLTeEASLQALEAVAILRPGTVSGFLR---GSTLHRLGVLERYARsSGALAVSEELAHLSAS 503
                                    566888888888888888888877777777777777777777777...899999*********99*************** PP

                                    HHHHHHHHHHSSEEE..- CS
                          AAA_5  81 vlnsLlslleerrlllee 98 
                                    +l++L +  ee r+ll +
  gi|119720023|ref|YP_920518.1| 504 ILERLAPHGEEYRVLLGS 521
                                    *****9888887777665 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       8.1   1.6e+04      62      79 ..      23      42 ..      22      43 .. 0.75
   2 ?   -2.8   0.0         4     8e+03       5      16 ..     207     218 ..     195     225 .. 0.58
   3 ?   10.2   0.0   0.00034      0.69      29      80 ..     526     579 ..     502     581 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 8.1
                                   HHHHHHHT..T-HHHHHHHH CS
                         ANAPC3 62 fAqcllkL..kkyeeAiaaL 79
                                   +Aq ll+   k++e+ +++L
  gi|119720023|ref|YP_920518.1| 23 LAQILLDCgkKHWEDVESVL 42
                                   58889999777788877766 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4
                                    HHHHHHHHHHHH CS
                         ANAPC3   5 yknAiflaerll 16 
                                    +  A++la+rll
  gi|119720023|ref|YP_920518.1| 207 HSLAYLLASRLL 218
                                    333444444444 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.00034
                                    HHHHHHHTT-HHHHHHHHHCT.SHH.HC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                         ANAPC3  29 lAlclylngqykrAyellrka.kln.skslgcrylfAqcllkLkkyeeAiaaLe 80 
                                    lA++ + +g  + +++ l++  +l  +++ +++ l + +ll+L++y eA++aL 
  gi|119720023|ref|YP_920518.1| 526 LAEVRLGRGLPELCLYTLKRReELGlPETARSLALRGFALLQLERYGEAESALA 579
                                    5777777788888999999986554145559999999***************96 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       4.4   8.7e+03       6      17 ..      22      33 ..      21      34 .. 0.86
   2 ?    9.5   0.3   0.00063       1.3       1      31 [.     555     585 ..     555     588 .. 0.91
   3 ?   -1.9   0.1       2.7   5.4e+03      12      29 ..     607     624 ..     601     625 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 4.4
                                   HHHHHHHHTT-H CS
                          TPR_8  6 nlgsiylklgdy 17
                                   +l++i+l+ g++
  gi|119720023|ref|YP_920518.1| 22 RLAQILLDCGKK 33
                                   79******9987 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00063
                                    CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                          TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleld 31 
                                    a+++ + g ++l+l++y eA++++ ++l + 
  gi|119720023|ref|YP_920518.1| 555 ARSLALRGFALLQLERYGEAESALARVLAMY 585
                                    78999*******************9999876 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 2.7
                                    HHTT-HHHHHHHHHHHHH CS
                          TPR_8  12 lklgdyeeAkeyyekale 29 
                                    lk+g+ e+A + +e  ++
  gi|119720023|ref|YP_920518.1| 607 LKKGEREKALSELEGLVK 624
                                    578999999888876665 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       6.1   1.2e+04      23      35 ..     292     304 ..     291     318 .. 0.69
   2 ?    7.5   1.3    0.0043       8.6       3      36 ..     557     590 ..     555     600 .. 0.83
   3 ?   -1.0   0.0       2.3   4.6e+03       2      24 ..     604     626 ..     602     628 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 6.1
                         TPR_14  23 llrralalaPdda 35 
                                    l+r++ +++P+++
  gi|119720023|ref|YP_920518.1| 292 LAREIAEKCPGNP 304
                                    7788889999886 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0043
                         TPR_14   3 allalaeallalGdpdeAiallrralalaPddae 36 
                                     l++++ all+l+++ eA+ +l r+la + ++ +
  gi|119720023|ref|YP_920518.1| 557 SLALRGFALLQLERYGEAESALARVLAMYEESGR 590
                                    5788999*******************98877644 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 2.3
                         TPR_14   2 eallalaeallalGdpdeAiall 24 
                                    ea+l+ +e + al ++++ ++ll
  gi|119720023|ref|YP_920518.1| 604 EAWLKKGEREKALSELEGLVKLL 626
                                    78888888888888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (675 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.48
# Mc/sec: 4207.94
//
Query:       gi|119720024|ref|YP_920519.1|  [L=347]
Description: metallophosphoesterase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-15   57.3   0.0    7.1e-08   32.8   0.0    2.2  2  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    4.9e-10   40.2   0.2      3e-07   31.1   0.1    2.1  2  Metallophos    Calcineurin-like phosphoesterase
  ------ inclusion threshold ------
       0.66   10.5   2.6        2.4    8.7   2.0    2.0  2  TcpE           TcpE family


Domain annotation for each model (and alignments):
>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.0   1.2e-11   7.1e-08       3     103 ..      24     150 ..      23     171 .. 0.65
   2 !   22.3   0.0   2.1e-08   0.00012     120     158 ..     280     321 ..     269     325 .. 0.79

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 1.2e-11
                  Metallophos_2   3 laiiSDlH..............snldaleavlealkevgvdaiihaGDl.eeeep..........evleellela.pvla 56 
                                    ++++SD+H              +  + le vle    + + +++++GD+ e  +           ++l+ l +l   ++ 
  gi|119720024|ref|YP_920519.1|  24 VLVFSDVHfglrfngrelslheELAEFLESVLEGG--EHPRLVVLLGDIfELWSAslrdvfsdafDSLRLLSRLDsTIVF 101
                                    799************77744433333333334442..457********6532222233333332245555555559**** PP

                  Metallophos_2  57 VrGNnDeevveedvlreaaelgtdl...peeaelelagekvlliHgdpl.g 103
                                    V+GN+D   v  +++ e+ + g+ +   pe   l+++g+kvll+Hg++l g
  gi|119720024|ref|YP_920519.1| 102 VPGNHD--RVTTRLHLESLRGGGGFviaPEIVLLDIDGKKVLLFHGHQLdG 150
                                    ******..444444444444444445999******************8762 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 2.1e-08
                  Metallophos_2 120 dvvvcGHtHvpevekeggvlvvnPGsvgeprdgdpe...tya 158
                                    d+vv+GHtHvpe  +egg+l++n Gs  +   +  +   ty+
  gi|119720024|ref|YP_920519.1| 280 DLVVFGHTHVPEYLAEGGRLILNTGSWVRSNSSTGVdnkTYV 321
                                    69************************9887433333444655 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.1     5e-11     3e-07       3     145 ..      24     162 ..      23     188 .. 0.63
   2 !    7.2   0.0    0.0011       6.6     191     204 .]     277     290 ..     256     290 .. 0.85

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 5e-11
                                    EEEEESBTB.....TTCCTHHHHHHHHHHHHHHH.TTESEEEEESTSSSSS......HHHHHHHHHHHHHHHHTSEEEEE CS
                    Metallophos   3 ilvigDlHl.....algggqlddllkllddllre.ekpdlvllaGDlvdrg......dlekellellaalvkypipvyll 70 
                                    +lv++D+H+      ++   +++l+++l+ +l+  e p lv+l+GD+++        +  ++  + l+ l +++  ++++
  gi|119720024|ref|YP_920519.1|  24 VLVFSDVHFglrfnGRELSLHEELAEFLESVLEGgEHPRLVVLLGDIFELWsaslrdV-FSDAFDSLRLLSRLDSTIVFV 102
                                    89*********999666666666666666663334899********999988866642.22233333444444679**** PP

                                    C-TTS..CHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTE.EEEEEEESECEEETHHHHHHHHHHHSCHHHH CS
                    Metallophos  71 lGNHe..gfeeellnkygylgifsepwrsdaevfnnlplaslgsgs.lkvlllhGgspellvsldklgslnleleape 145
                                    +GNH+  +       +   +        + ++ f + p ++l +    kvll hG+      +ld l   ++ l   +
  gi|119720024|ref|YP_920519.1| 103 PGNHDrvT------TRLHLES------LRGGGGFVIAPEIVLLDIDgKKVLLFHGH------QLDGLFLAVKGLWKLQ 162
                                    *****441......3322222......22266666666666555555699999999......5555555555544444 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0011
                                    TTESEEEEESSSSE CS
                    Metallophos 191 ygvdlvisGHtHvy 204
                                    +++dlv++GHtHv+
  gi|119720024|ref|YP_920519.1| 277 GKLDLVVFGHTHVP 290
                                    579*********86 PP

>> TcpE  TcpE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.45   2.7e+03      73      83 ..     133     143 ..     122     149 .. 0.79
   2 ?    8.7   2.0   0.00041       2.4       5      66 ..     158     222 ..     156     242 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.45
                           TcpE  73 lepdgKkllef 83 
                                    l++dgKk+l f
  gi|119720024|ref|YP_920519.1| 133 LDIDGKKVLLF 143
                                    799*****988 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00041
                           TcpE   5 ilkapkkiqkikd..fsLpfpislsqiivfvlvlvlllllaslipv.ikgvlpflllyivipvvl 66 
                                    ++k    ++ + +  +sLp p++  + +v++ +++ll++l + +++ ++ +++  +l+++ p+v+
  gi|119720024|ref|YP_920519.1| 158 LWKLQSYVYIFSEslMSLPGPLEWVFAAVAATTVLLLMVLIQATSLlMEAAIALSALILLSPMVI 222
                                    6777888888888899*****************99999997777775444443335666666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2470.77
//
Query:       gi|119720025|ref|YP_920520.1|  [L=275]
Description: cation diffusion facilitator family transporter [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.4e-32  110.7  10.7      9e-32  110.4  10.7    1.1  1  Cation_efflux    Cation efflux family
      1e-18   67.2   4.1    1.9e-18   66.4   4.1    1.4  1  ZT_dimer         Dimerisation domain of Zinc Transporter
  ------ inclusion threshold ------
      0.021   15.1   1.1      0.039   14.3   1.1    1.4  1  AMP-binding_C_2  AMP-binding enzyme C-terminal domain
       0.14   12.3   0.4       0.14   12.3   0.4    2.3  3  TetR_C_35        Bacterial Tetracyclin repressor,  C-terminal


Domain annotation for each model (and alignments):
>> Cation_efflux  Cation efflux family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.4  10.7     2e-35     9e-32       3     199 .]       8     194 ..       6     194 .. 0.98

  Alignments for each domain:
  == domain 1  score: 110.4 bits;  conditional E-value: 2e-35
                  Cation_efflux   3 lsllanlilalvelivglltnSlalladafhslsdlvsllllllalklsrkppderfpfGygrlevlgalvsgllllgla 82 
                                    l +la+l++++++l+v++lt S+a + + + s++d++++ l+ll+++lsrkppde++ +G+g++e l++ + gl+     
  gi|119720025|ref|YP_920520.1|   8 LTFLAVLGITVAKLAVYALTSSMAAFTEFVDSVTDIATSALALLSVRLSRKPPDEDHHYGHGKAEALAGYTIGLFAGTSL 87 
                                    6799**************************************************************************** PP

                  Cation_efflux  83 vfllleaiqklikegereihaglalvvalvslvvnlalllilrragrklrsaalkaaalhvlgDaltslgvlvsalvill 162
                                    ++++ e +++++ eg  +   +la+ +a++ ++v   l+  ++ + r+ +s al+a+a++ +gD+l +lgvl ++  ++l
  gi|119720025|ref|YP_920520.1|  88 AYVVAELVKRVL-EGYIVRSDPLAVQIAAAIVAVDSGLAGVNYLGYRASKSVALRANAVNYMGDSLRALGVLTAITTAWL 166
                                    ************.***************************************************************7776 PP

                  Cation_efflux 163 fnlksgplaDpvaslligliilysalkllkeslseLl 199
                                             Dp+++ +++ i+++  ++ll+es s+L+
  gi|119720025|ref|YP_920520.1| 167 ---------DPFVTAVLASILAVEVFHLLRESTSILM 194
                                    .........**************************97 PP

>> ZT_dimer  Dimerisation domain of Zinc Transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.4   4.1   4.2e-22   1.9e-18       2      79 .]     198     275 .]     196     275 .] 0.97

  Alignments for each domain:
  == domain 1  score: 66.4 bits;  conditional E-value: 4.2e-22
                                    ...HHHHHHHHHTT-SS-EEEEEEEEE-S----EEEEEEEE-TTS-HHHHHHHHHHHHHHHHHH-TT--EEEEEEEE. CS
                       ZT_dimer   2 deeeeeeireiiksvpgvkgvhdlrtrksGskifvdlhievdgdlsvkeaHeiadevekrikeefpgvadvliHvePe 79 
                                    +ee  ++i e ++ v++v++v ++r+r+sG+++ vd+ + v+g  +++eaH+ adevekr+k+++    dvl+HveP+
  gi|119720025|ref|YP_920520.1| 198 SEELTRRIAESLRGVEEVEEVRKIRVRHSGTHYQVDVVVAVKGGKTIEEAHRAADEVEKRVKAALGAEVDVLVHVEPC 275
                                    57889999999*99***************************************************************7 PP

>> AMP-binding_C_2  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   1.1   8.6e-06     0.039       8      75 ..     204     269 ..     202     274 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8.6e-06
                                    HHHHHHHT-TTEEEEEEEEEEEETTEEEEEEEEEE-TT----HHHHHHHHHHHHHHHHHHHSS--EEE CS
                AMP-binding_C_2   8 qieevlkeieevepeYqivvtregelDelevkvEvkegfsdelkelealekkiakklksklgvsvkve 75 
                                     i e l+ +eeve+  +i v+++g+  ++ v v vk g   +++e ++ +++++k++k++lg +v+v 
  gi|119720025|ref|YP_920520.1| 204 RIAESLRGVEEVEEVRKIRVRHSGTHYQVDVVVAVKGGK--TIEEAHRAADEVEKRVKAALGAEVDVL 269
                                    58899*******************************974..577889999999999999999888874 PP

>> TetR_C_35  Bacterial Tetracyclin repressor,  C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1      0.87   3.9e+03      62      62 ..      37      37 ..       6      74 .. 0.53
   2 ?   -2.1   0.1      0.96   4.3e+03      74      98 ..      92     116 ..      84     120 .. 0.46
   3 ?   12.3   0.4   3.2e-05      0.14       9      68 ..     156     215 ..     151     225 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.87
                      TetR_C_35 62 w 62
                                    
  gi|119720025|ref|YP_920520.1| 37 V 37
                                   2 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.96
                      TetR_C_35  74 adavvRlalShvvlPpedpeetaad 98 
                                    a+ v R+   ++v     + ++aa+
  gi|119720025|ref|YP_920520.1|  92 AELVKRVLEGYIVRSDPLAVQIAAA 116
                                    4444444444444444444444443 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 3.2e-05
                      TetR_C_35   9 avrafleeaaadpLvravltgeakedLlpllTtdseplleaAsarlaevlaeswpqldea 68 
                                    +v + +++a  dp v avl++    +   ll      l+++As++l++++aes   ++e 
  gi|119720025|ref|YP_920520.1| 156 GVLTAITTAWLDPFVTAVLASILAVEVFHLLRESTSILMDEASEELTRRIAESLRGVEEV 215
                                    56678899999**********************9999***************99888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       776  (0.0432818); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1850.73
//
Query:       gi|119720026|ref|YP_920521.1|  [L=383]
Description: hypothetical protein Tpen_1120 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0018   18.2   2.4     0.0052   16.7   2.4    1.7  1  Apolipoprotein   Apolipoprotein A1/A4/E domain
     0.0029   17.7   6.3     0.0029   17.7   6.3    2.4  2  Tropomyosin_1    Tropomyosin like
     0.0046   17.0   5.2      0.042   13.9   1.9    2.6  2  DUF1664          Protein of unknown function (DUF1664)
      0.006   16.8   4.2      0.006   16.8   4.2    3.5  3  ABC_tran_CTD     ABC transporter C-terminal domain
  ------ inclusion threshold ------
      0.011   15.6   4.1      0.011   15.6   4.1    1.7  1  PhaP_Bmeg        Polyhydroxyalkanoic acid inclusion protein (
      0.034   14.0   9.5       0.56   10.0   0.6    2.9  2  CdvA             CdvA-like coiled-coil domain
      0.036   13.8   0.0      0.054   13.2   0.0    1.3  1  PRiA4_ORF3       Plasmid pRiA4b ORF-3-like protein
      0.047   13.2   1.8      0.091   12.2   1.8    1.4  1  MIF4G_like_2     MIF4G like
       0.11   12.4   0.3        1.3    9.0   0.1    2.7  2  TPR_10           Tetratricopeptide repeat
       0.15   12.6   3.8       0.53   10.8   3.8    2.0  1  DUF2408          Protein of unknown function (DUF2408)
       0.19   11.6   2.6        0.8    9.6   0.1    2.2  2  CK2S             Casein Kinase 2 substrate
       0.49   10.6  11.8       0.49   10.6   4.6    2.8  2  TMF_TATA_bd      TATA element modulatory factor 1 TATA bindin
       0.59   10.2  14.5        7.2    6.7   8.8    2.7  2  DHR10            Designed helical repeat protein 10 domain
        0.6   10.2   8.8        0.1   12.7   1.2    2.3  2  MnmE_helical     MnmE helical domain
       0.62   10.1  10.5        3.5    7.7   2.4    2.8  3  ApoLp-III        Apolipophorin-III precursor (apoLp-III)
       0.82    8.5   5.4       0.44    9.4   2.3    1.8  2  Fmp27_WPPW       RNA pol II promoter Fmp27 protein domain
        1.1    9.3  14.3      0.047   13.7   3.6    2.9  4  Laminin_II       Laminin Domain II
        1.2    9.2   5.2       0.99    9.5   1.1    2.3  2  Cob_adeno_trans  Cobalamin adenosyltransferase
        1.7    8.9  13.7       0.66   10.2   8.9    2.6  2  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
        1.9    8.7  12.5       0.55   10.4   4.5    2.4  2  ATG16            Autophagy protein 16 (ATG16)
          4    8.1   8.2        3.8    8.2   2.0    2.8  2  SlyX             SlyX
        4.7    7.6   5.9         19    5.6   4.1    2.9  2  KxDL             Uncharacterized conserved protein
        5.4    6.5  18.5        3.8    7.0   6.4    2.5  2  PspA_IM30        PspA/IM30 family
        8.7    5.1  16.7        1.2    8.0  10.2    2.2  2  Spc7             Spc7 kinetochore protein


Domain annotation for each model (and alignments):
>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   2.4   6.9e-06    0.0052       8      66 ..     273     333 ..     255     338 .. 0.59

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6.9e-06
                                    CHHHHHCCHHHCHHCHHH..HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHCCCH CS
                 Apolipoprotein   8 elkayaeeleeqlaplaq..elrdrlskeleelrarlraeleevrarlepyrdevqeqlgq 66 
                                    +l++++eelee l++ a+   + +  +ke +++ ++l++el+ev ++l +  + v+++++ 
  gi|119720026|ref|YP_920521.1| 273 NLTERLEELEEELNETAAkiAAGNVSAKEVKKAGKQLEKELKEVEKKLNEVFSRVENKIAT 333
                                    4555556666666666553334444455666666666666666666666655555555555 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.6       1.9   1.4e+03      74      96 ..     154     176 ..     123     207 .. 0.58
   2 !   17.7   6.3   3.9e-06    0.0029      85     138 ..     274     327 ..     266     332 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.9
                  Tropomyosin_1  74 nnealtrkiqlLEeeleesdkkL 96 
                                    + e l+ +++lL e l + +++L
  gi|119720026|ref|YP_920521.1| 154 QLEVLENRVDLLLEVLGKVNTSL 176
                                    44444555555544444444333 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 3.9e-06
                  Tropomyosin_1  85 LEeeleesdkkLkettekLretdvkaeelERkvkaLeqerdewekkyeeleeky 138
                                    L e lee +++L+et  k+   +v a e+ ++ k+Le+e +e ekk++e+ ++ 
  gi|119720026|ref|YP_920521.1| 274 LTERLEELEEELNETAAKIAAGNVSAKEVKKAGKQLEKELKEVEKKLNEVFSRV 327
                                    7799*******************************************9987665 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1     0.091        68      53     108 ..     140     195 ..     135     209 .. 0.86
   2 !   13.9   1.9   5.7e-05     0.042      48     117 ..     258     327 ..     252     338 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.091
                        DUF1664  53 vseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvke 108
                                    v +s+a  +  L+ +++ +++++d   e+  +++  + +v++ +s ++e    ++e
  gi|119720026|ref|YP_920521.1| 140 VNASIAINRTALTLQLEVLENRVDLLLEVLGKVNTSLYNVSGAISLLQEAKLLLEE 195
                                    77899999********************************9999988876555555 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 5.7e-05
                        DUF1664  48 kqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskl 117
                                      +++ + +++  k +L++r+++++++l+e+++ +++ +   +ev++  +++++++++v++  +++ s++
  gi|119720026|ref|YP_920521.1| 258 PLINHTKIKVKGLKGNLTERLEELEEELNETAAKIAAGNVSAKEVKKAGKQLEKELKEVEKKLNEVFSRV 327
                                    556777788999999***************9999988887777777777777777777665444333332 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1       1.2     9e+02      42      52 ..     106     116 ..      80     134 .. 0.67
   2 ?    0.9   0.6      0.72   5.4e+02      10      59 ..     155     202 ..     149     204 .. 0.68
   3 !   16.8   4.2   8.1e-06     0.006      12      63 ..     273     326 ..     266     339 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.2
                   ABC_tran_CTD  42 klaelsaelee 52 
                                    ++ el++el+e
  gi|119720026|ref|YP_920521.1| 106 QVLELQEELAE 116
                                    44455555443 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.72
                   ABC_tran_CTD  10 leeleaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeLee 59 
                                    le le++ + L e + ++++ l + +       l+e+   lee+ea+Le+
  gi|119720026|ref|YP_920521.1| 155 LEVLENRVDLLLEVLGKVNTSLYNVS--GAISLLQEAKLLLEEAEAKLEA 202
                                    56666666666666666666666665..3346678888888999998885 PP

  == domain 3  score: 16.8 bits;  conditional E-value: 8.1e-06
                   ABC_tran_CTD  12 eleaeIeaLEeeiaeleaeladpelysdp..eklaelsaeleeleaeLeelyer 63 
                                    +l +++e+LEee+ e  a++a+ ++ +++  ++ ++l +el+e+e++L+e ++r
  gi|119720026|ref|YP_920521.1| 273 NLTERLEELEEELNETAAKIAAGNVSAKEvkKAGKQLEKELKEVEKKLNEVFSR 326
                                    5889********************9977765558999999**********9998 PP

>> PhaP_Bmeg  Polyhydroxyalkanoic acid inclusion protein (PhaP_Bmeg)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   4.1   1.5e-05     0.011      45     111 ..     270     334 ..     263     339 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.5e-05
                      PhaP_Bmeg  45 lvkeltkalselekeskqltaeledqlqktvenlrskaGnkvednieEwtdkleevsakleklalsp 111
                                    l  +lt+ l+ele+e  ++ a++    ++  +++ +kaG ++e +++E   kl+ev  ++e+   ++
  gi|119720026|ref|YP_920521.1| 270 LKGNLTERLEELEEELNETAAKIAAGNVSA-KEV-KKAGKQLEKELKEVEKKLNEVFSRVENKIATK 334
                                    55679******************6544443.334.788********************998765555 PP

>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.6   0.00075      0.56      31      65 ..     260     294 ..     250     300 .. 0.86
   2 ?    7.5   2.8    0.0046       3.4      13      50 ..     295     332 ..     292     339 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00075
                           CdvA  31 lkklkekakelkeklkkrlkeledqikslekalan 65 
                                    ++  k k k lk +l++rl+ele+++++++  +a+
  gi|119720026|ref|YP_920521.1| 260 INHTKIKVKGLKGNLTERLEELEEELNETAAKIAA 294
                                    567788999*******************9988876 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0046
                           CdvA  13 gdipkstyeeikekleealkklkekakelkeklkkrlk 50 
                                    g+++++++++  ++le++lk++++k +e+ ++++++++
  gi|119720026|ref|YP_920521.1| 295 GNVSAKEVKKAGKQLEKELKEVEKKLNEVFSRVENKIA 332
                                    55666666666666777777777777766666666665 PP

>> PRiA4_ORF3  Plasmid pRiA4b ORF-3-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   7.3e-05     0.054      59     131 ..     301     375 ..     203     380 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.3e-05
                     PRiA4_ORF3  59 eeeedeeeeeevldeskvklddvlkekgkkltyeYDfgdsWeheielekvledkeear..yprclagegacppED 131
                                    e +++ ++ e+ l+e + kl++v+++ ++k+  +     +W+hei++e   +  ++++  +p +++ge +   E+
  gi|119720026|ref|YP_920521.1| 301 EVKKAGKQLEKELKEVEKKLNEVFSRVENKIATKAKEKGGWKHEIKVEVKEKHGQGPQpwTPSVTQGESEEEHEE 375
                                    445566677788889999******************************999998887789*******98877665 PP

>> MIF4G_like_2  MIF4G like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.8   0.00012     0.091     159     248 ..     266     362 ..     245     367 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00012
                   MIF4G_like_2 159 kvnkrvkkvrqeleelkkkeeeekak....eeed.keeeeeleraeekleaaqkeqkelflivferlveilses...lee 230
                                    kv++   ++ ++leel+++ +e++ak    +  + ke +++ +++e++l++++k+ +e+f++v++++++ ++e    + e
  gi|119720026|ref|YP_920521.1| 266 KVKGLKGNLTERLEELEEELNETAAKiaagNV-SaKEVKKAGKQLEKELKEVEKKLNEVFSRVENKIATKAKEKggwKHE 344
                                    55555556778888888887777555644333.25888899999****************************99998777 PP

                   MIF4G_like_2 231 letsgseentevieewkk 248
                                     +++ +e++ + +++w+ 
  gi|119720026|ref|YP_920521.1| 345 IKVEVKEKHGQGPQPWTP 362
                                    777777777666777765 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1    0.0018       1.3      14      37 ..      86     109 ..      80     113 .. 0.92
   2 ?   -0.3   0.0       1.5   1.1e+03       8      28 ..     169     189 ..     166     196 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0018
                         TPR_10  14 qrgrydeAealleealairrrllG 37 
                                    + g+y+eA  ++++a++++ ++l+
  gi|119720026|ref|YP_920521.1|  86 NAGNYTEAKIYAIKAINTYGQVLE 109
                                    67*****************99996 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.5
                         TPR_10   8 LanalrqrgrydeAealleea 28 
                                    L+ + +++++  +A  ll+ea
  gi|119720026|ref|YP_920521.1| 169 LGKVNTSLYNVSGAISLLQEA 189
                                    677777888888888888887 PP

>> DUF2408  Protein of unknown function (DUF2408)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   3.8   0.00071      0.53      11      72 ..     274     331 ..     259     352 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00071
                        DUF2408  11 iyekLvsirrsLlslaakskaeeakeseevkeelkelkeeLkkieskrdeegkFkseegkev 72 
                                    + e+L ++  +L ++aak +a  + +++evk+  k+l++eLk++e+k +e   F   e+ ++
  gi|119720026|ref|YP_920521.1| 274 LTERLEELEEELNETAAKIAAG-NVSAKEVKKAGKQLEKELKEVEKKLNE--VFSRVEN-KI 331
                                    5788889999999999998886.667778999999999999999999998..6644343.32 PP

>> CK2S  Casein Kinase 2 substrate
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.3       0.3   2.3e+02      67     148 ..     161     236 ..     148     248 .. 0.74
   2 ?    9.6   0.1    0.0011       0.8      31     123 ..     272     365 ..     270     366 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.3
                           CK2S  67 aleevlakLrekleelqkvrdsleklvrdalqlyeekadklslkeliersavtPsladmlewlqdiermyrseyllkksl 146
                                     ++ +l+ L ++ ++l++v  +++ l++++l l e +a+      l  ++ + P la+ l   ++i    ++e+++ +  
  gi|119720026|ref|YP_920521.1| 161 RVDLLLEVLGKVNTSLYNVSGAISLLQEAKLLLEEAEAK------LEAGNITVPELAKTLAVVKKILGLVNAELHRASLA 234
                                    466667777777777777777777666666655555544......88888889999999999999999999999998887 PP

                           CK2S 147 ls 148
                                    l 
  gi|119720026|ref|YP_920521.1| 235 LT 236
                                    76 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0011
                           CK2S  31 snlaeqlqalqnvklygtplrdfpdlqerLrekqlealeevlakLreklee.lqkvrdsleklvrdalqlyeekadklsl 109
                                    +nl e+l+ l++  ++++   + +++  + ++k  ++le++l++ ++kl+e +  v ++++ + +++   + e + +++ 
  gi|119720026|ref|YP_920521.1| 272 GNLTERLEELEEELNETAAKIAAGNVSAKEVKKAGKQLEKELKEVEKKLNEvFSRVENKIATKAKEKGGWKHEIKVEVKE 351
                                    69***************99999999999********************98757899999999998888888888888999 PP

                           CK2S 110 keliersavtPsla 123
                                    k ++  ++ tPs++
  gi|119720026|ref|YP_920521.1| 352 KHGQGPQPWTPSVT 365
                                    99999999999997 PP

>> TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.7      0.14     1e+02      62      90 ..     144     172 ..     105     176 .. 0.71
   2 ?   10.6   4.6   0.00065      0.49      12      83 ..     251     323 ..     246     331 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.14
                    TMF_TATA_bd  62 lkkeleelekeleelqeryetlLellGek 90 
                                     + + + l+ +le l++r + lLe+lG+ 
  gi|119720026|ref|YP_920521.1| 144 IAINRTALTLQLEVLENRVDLLLEVLGKV 172
                                    4445667888*****************86 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00065
                    TMF_TATA_bd  12 qlverlsseirrlEgElaslkeel.erleaerdeareeivklmkeneelkelkkeleelekeleelqeryetl 83 
                                    +l  ++s  i +  + ++ lk +l erle+  +e++e  +k+ + n + ke kk  ++lekel+e++++++++
  gi|119720026|ref|YP_920521.1| 251 TLPLNMSPLINHTKIKVKGLKGNLtERLEELEEELNETAAKIAAGNVSAKEVKKAGKQLEKELKEVEKKLNEV 323
                                    566788889999999999999887368999999999999******************************9875 PP

>> DHR10  Designed helical repeat protein 10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.3     0.015        11      48      97 ..     182     231 ..     151     240 .. 0.79
   2 ?    6.7   8.8    0.0097       7.2      50      97 ..     276     323 ..     273     338 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.015
                          DHR10  48 elakleeakkklkelrdaleekeielrelerkeerlqrqlenaeeklerl 97 
                                     +  l+eak  l+e++++le  +i++ el ++ + +++ l   + +l r+
  gi|119720026|ref|YP_920521.1| 182 AISLLQEAKLLLEEAEAKLEAGNITVPELAKTLAVVKKILGLVNAELHRA 231
                                    45567899999999999999999999999999999999999998888887 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0097
                          DHR10  50 akleeakkklkelrdaleekeielrelerkeerlqrqlenaeeklerl 97 
                                    ++lee +++l+e+ ++++  +  ++e+++  ++l++ l+  e+kl+ +
  gi|119720026|ref|YP_920521.1| 276 ERLEELEEELNETAAKIAAGNVSAKEVKKAGKQLEKELKEVEKKLNEV 323
                                    566666777777777777777777777777777777777666666654 PP

>> MnmE_helical  MnmE helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.7      0.42   3.1e+02     121     194 ..     155     226 ..     132     228 .. 0.69
   2 ?   12.7   1.2   0.00014       0.1      19      87 ..     263     329 ..     260     336 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.42
                                    xxxxxxxxxx.xx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   MnmE_helical 121 ieeLeeaike.le.leeieeeplltnaRhkealekalealeeakealeaglpldlvaedLrealeaLgeItGevvt 194
                                    +e Le+++   le l+++++ +l   +  +++l++a+  leea+ +leag    +   +L ++l  +++I+G v+ 
  gi|119720026|ref|YP_920521.1| 155 LEVLENRVDLlLEvLGKVNT-SLYNVSGAISLLQEAKLLLEEAEAKLEAGN---ITVPELAKTLAVVKKILGLVNA 226
                                    66666666543333344333.555556678899999999999999999885...7778888888888888887665 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00014
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   MnmE_helical  19 akaalrqleGelskkikelrekllellaeleaaiDFpeedleelseeelaekleelkeelekllatakr 87 
                                     k+ ++ l+G+l ++++el+e+l e+ a++ a  + + +++++  + +l+++l+e++++l+++ +++++
  gi|119720026|ref|YP_920521.1| 263 TKIKVKGLKGNLTERLEELEEELNETAAKIAAG-NVSAKEVKKAGK-QLEKELKEVEKKLNEVFSRVEN 329
                                    5788999***********************997.444557665544.6**************9999886 PP

>> ApoLp-III  Apolipophorin-III precursor (apoLp-III)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1         4     3e+03      44      84 ..     171     213 ..     156     221 .. 0.60
   2 ?    7.1   0.3    0.0071       5.3      40      78 ..     258     296 ..     245     301 .. 0.83
   3 ?    7.7   2.4    0.0047       3.5      47      77 ..     300     330 ..     296     338 .. 0.64

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 4
                      ApoLp-III  44 slqeelkkksdeleealkevkkkieetadklse...enPevkkk 84 
                                    +++ +l + s+ + ++l+e+k  +ee+ +kl++     Pe++k 
  gi|119720026|ref|YP_920521.1| 171 KVNTSLYNVSG-AISLLQEAKLLLEEAEAKLEAgniTVPELAKT 213
                                    55555555443.33567777777777777777755555665555 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0071
                      ApoLp-III  40 qvikslqeelkkksdeleealkevkkkieetadklseen 78 
                                     +i+ ++ ++k   ++l+e l+e+ ++++eta+k+ + n
  gi|119720026|ref|YP_920521.1| 258 PLINHTKIKVKGLKGNLTERLEELEEELNETAAKIAAGN 296
                                    567788889999999*******************98755 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0047
                      ApoLp-III  47 eelkkksdeleealkevkkkieetadklsee 77 
                                     e+kk+  +le+ lkev kk++e++  ++++
  gi|119720026|ref|YP_920521.1| 300 KEVKKAGKQLEKELKEVEKKLNEVFSRVENK 330
                                    4677777777777777777777776666553 PP

>> Fmp27_WPPW  RNA pol II promoter Fmp27 protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.55   4.1e+02     170     241 ..     152     229 ..     141     252 .. 0.73
   2 ?    9.4   2.3   0.00058      0.44     176     244 ..     274     338 ..     265     377 .. 0.67

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.55
                     Fmp27_WPPW 170 rvqkelleeRleeleeqiekleekleelelkseke......deelkeeieelekeikelkeklefletlledlkesee 241
                                    ++q e+le+R++ l e + k++++l +++   +         ee ++++e+ + ++ el + l +++++l  ++++ +
  gi|119720026|ref|YP_920521.1| 152 TLQLEVLENRVDLLLEVLGKVNTSLYNVSGAISLLqeakllLEEAEAKLEAGNITVPELAKTLAVVKKILGLVNAELH 229
                                    689999999999999999999999887765554322234666777777777777777888888888877776666655 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00058
                     Fmp27_WPPW 176 leeRleeleeqiekleekleelelksekedeelkeeieelekeikelkeklefletlledlkeseesse 244
                                    l eRleelee+++++  k+   + + ++    +k+  ++leke+ke+++kl+ + + +e+  +++++++
  gi|119720026|ref|YP_920521.1| 274 LTERLEELEEELNETAAKIAAGNVSAKE----VKKAGKQLEKELKEVEKKLNEVFSRVENKIATKAKEK 338
                                    5688888888888888888776666655....8888888888888888888766655555444444333 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       3.9   2.9e+03      19      55 ..      16      52 ..      12      58 .. 0.71
   2 ?    0.7   0.3      0.63   4.7e+02      60      93 ..     154     184 ..      98     208 .. 0.55
   3 ?    1.6   0.7      0.34   2.5e+02      18      80 ..     154     219 ..     140     239 .. 0.68
   4 ?   13.7   3.6   6.3e-05     0.047      11      84 ..     263     329 ..     256     351 .. 0.62

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 3.9
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                     Laminin_II 19 laplsqnlentkeklseinrsveetnekvkdankair 55
                                   lapl+  l  t  +++ + +++++ +++v+  n++i 
  gi|119720026|ref|YP_920521.1| 16 LAPLQIALAGTDTSAEILVSNAKRLQQLVHYRNTVIS 52
                                   6677777777777777777777777777777776664 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.63
                                    XXXXX--TTTTTGGGHHHHHHHHHH...HHHHHH CS
                     Laminin_II  60 svkkLeklapqLldklkelkqleeassslsdnis 93 
                                    +   Le+ ++ Ll+ l ++++   +   +s  is
  gi|119720026|ref|YP_920521.1| 154 QLEVLENRVDLLLEVLGKVNTSLYN---VSGAIS 184
                                    3445666667777766666666666...333333 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.34
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXX--TTTTTGGGHHHHHH CS
                     Laminin_II  18 qlaplsqnlentkeklseinrsveetnekvk...dankairdArrsvkkLeklapqLldklkelkq 80 
                                    ql+ l+++++ + e l ++n+s+ ++   ++   +a+  +++A+ +    + ++p+L + l  +k+
  gi|119720026|ref|YP_920521.1| 154 QLEVLENRVDLLLEVLGKVNTSLYNVSGAISllqEAKLLLEEAEAKLEAGNITVPELAKTLAVVKK 219
                                    556677777777777777777777776655533255555566666666666777777777766665 PP

  == domain 4  score: 13.7 bits;  conditional E-value: 6.3e-05
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH CS
                     Laminin_II  11 takevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleea 84 
                                    t  +v+  + +l ++le+++e+l+e +++++  n  +k+ +ka ++ +++ k++ek++++++++++       +
  gi|119720026|ref|YP_920521.1| 263 TKIKVKGLKGNLTERLEELEEELNETAAKIAAGNVSAKEVKKAGKQLEKELKEVEKKLNEVFSRVE-------N 329
                                    455555555666666666666666666666666666666666666666666666666666666654.......3 PP

>> Cob_adeno_trans  Cobalamin adenosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.2      0.45   3.4e+02      49      97 ..     154     202 ..     101     247 .. 0.53
   2 ?    9.5   1.1    0.0013      0.99      50     105 ..     271     323 ..     243     339 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.45
                                    T.......THHHHHHHHHHHHHHHHHHHHHHT.-BTCCG-S--HHHHHHHHHHHHH CS
                Cob_adeno_trans  49 e.......eeelkeaLeeiqneLfdlgaelatpekkkekkkiteeeveelekeide 97 
                                    +        + l e+L ++ ++L ++  +++     +e+k +     ee e+++++
  gi|119720026|ref|YP_920521.1| 154 QlevlenrVDLLLEVLGKVNTSLYNVSGAISLL---QEAKLLL----EEAEAKLEA 202
                                    133333333344555566666666666666533...1111111....222222222 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0013
                                    THHHHHHHHHHHHHHHHHHHHHHT.-BTCCG-S--HHHHHHHHHHHHHHHHHS--E CS
                Cob_adeno_trans  50 eeelkeaLeeiqneLfdlgaelatpekkkekkkiteeeveelekeideleaelppl 105
                                    + +l+e+Lee+++eL +  a++a+   ++++k+++++  ++leke++e+e++l+++
  gi|119720026|ref|YP_920521.1| 271 KGNLTERLEELEEELNETAAKIAAG--NVSAKEVKKA-GKQLEKELKEVEKKLNEV 323
                                    77899*****************954..6677778866.789999999999999865 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1       1.3   9.7e+02      54      77 ..     178     204 ..     147     235 .. 0.57
   2 ?   10.2   8.9   0.00089      0.66      40     101 ..     273     331 ..     261     336 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 1.3
                                    HHHHHCCCCCCTT...S-TCCCCCCCH CS
                   Seryl_tRNA_N  54 elskeIgkakkkk...edaeeliaevk 77 
                                    ++s +I+ + ++k   e+ae+ ++ ++
  gi|119720026|ref|YP_920521.1| 178 NVSGAISLLQEAKlllEEAEAKLEAGN 204
                                    455555555555555555555554433 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00089
                                    HHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   Seryl_tRNA_N  40 elqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaelekll 101
                                    +l  +leel +e Ne +++I+        a+e+++ +k+l +elk++e++l+e+ +++e+++
  gi|119720026|ref|YP_920521.1| 273 NLTERLEELEEELNETAAKIAAGNV---SAKEVKKAGKQLEKELKEVEKKLNEVFSRVENKI 331
                                    567899**************99886...5899*********************988888776 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   1.1      0.17   1.3e+02      81     181 ..     105     204 ..      81     207 .. 0.83
   2 ?   10.4   4.5   0.00074      0.55      99     154 ..     273     321 ..     267     329 .. 0.59

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.17
                          ATG16  81 qklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDEl 160
                                     ++++l+eelae y  + +l+  + e  +   kl  ++ + + +  +l+ + ++le +++ + e l   ++ + ++  ++
  gi|119720026|ref|YP_920521.1| 105 GQVLELQEELAEEYDIHFKLEGEIEEGYANATKLGVNA-SIAINRTALTLQLEVLENRVDLLLEVLGKVNTSLYNVSGAI 183
                                    67889999999999999999999988888777776655.45555678999999999999999999999999999999999 PP

                          ATG16 161 saLqlqlnqaEeklrklekEN 181
                                    s Lq +   +Ee+  kle+ N
  gi|119720026|ref|YP_920521.1| 184 SLLQEAKLLLEEAEAKLEAGN 204
                                    999999999999999999877 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00074
                          ATG16  99 elaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvq 154
                                            l+e l++lee+l+e ++++a+ + + ++++++ k++e+el+e ek ++
  gi|119720026|ref|YP_920521.1| 273 N-------LTERLEELEEELNETAAKIAAGNVSAKEVKKAGKQLEKELKEVEKKLN 321
                                    4.......555566666666666666666666666666666666666666555443 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.5      0.27     2e+02       4      55 ..     154     205 ..     151     214 .. 0.87
   2 ?    8.2   2.0     0.005       3.8       2      51 ..     275     324 ..     274     337 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.27
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXX CS
                           SlyX   4 rleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkeleessg 55 
                                    +le LE ++  + +++ + n  +++    i+ lq+   ll+e  ++le+ + 
  gi|119720026|ref|YP_920521.1| 154 QLEVLENRVDLLLEVLGKVNTSLYNVSGAISLLQEAKLLLEEAEAKLEAGNI 205
                                    588899999999999999****************999999999888887765 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.005
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXX CS
                           SlyX   2 eerleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkele 51 
                                     erleeLE++l  +   i + n    e  +  ++l+++l++++++l+e+ 
  gi|119720026|ref|YP_920521.1| 275 TERLEELEEELNETAAKIAAGNVSAKEVKKAGKQLEKELKEVEKKLNEVF 324
                                    79********************************************8875 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       2.4   1.8e+03      37      72 ..     187     222 ..     158     231 .. 0.73
   2 ?    5.6   4.1     0.026        19      24      71 ..     277     327 ..     255     338 .. 0.52

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 2.4
                           KxDL  37 alsqerlaklrarfkqgtkllkevkkdLesifkkir 72 
                                    ++++  l++++a+++ g  ++ e+ k L  ++k + 
  gi|119720026|ref|YP_920521.1| 187 QEAKLLLEEAEAKLEAGNITVPELAKTLAVVKKILG 222
                                    555555777777777777777777777776666554 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.026
                           KxDL  24 rlnkknreLlelnalsqe...rlaklrarfkqgtkllkevkkdLesifkki 71 
                                    rl++ ++eL e  a+  +     +++++  kq  k lkev k L+ +f+++
  gi|119720026|ref|YP_920521.1| 277 RLEELEEELNETAAKIAAgnvSAKEVKKAGKQLEKELKEVEKKLNEVFSRV 327
                                    334444444444333322111334444444444444555555555555555 PP

>> PspA_IM30  PspA/IM30 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   3.5     0.016        12      41     123 ..     109     202 ..     101     241 .. 0.73
   2 ?    7.0   6.4    0.0051       3.8      91     149 ..     276     334 ..     266     340 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.016
                      PspA_IM30  41 karqalaqviarqkqlerkleeqkeqakklekkAkaALtkg...........eeeLArealaeikslekqaealetqlaq 109
                                    +++++la+    + +le ++ee  + a kl ++A  A ++            + +L  e+l +  +   ++ +   +l++
  gi|119720026|ref|YP_920521.1| 109 ELQEELAEEYDIHFKLEGEIEEGYANATKLGVNASIAINRTaltlqlevlenRVDLLLEVLGKVNTSLYNVSGAISLLQE 188
                                    7899**********************************999455555555544455555555555555555555555555 PP

                      PspA_IM30 110 qrsaveqlrkqlea 123
                                    ++   e+++++lea
  gi|119720026|ref|YP_920521.1| 189 AKLLLEEAEAKLEA 202
                                    55555555555554 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0051
                      PspA_IM30  91 aeikslekqaealetqlaqqrsaveqlrkqlealetkieelkakkellkarekaakaqe 149
                                    +++++le+++++  ++ a  + ++++++k+ ++le+ ++e+++k +++ +r +   a +
  gi|119720026|ref|YP_920521.1| 276 ERLEELEEELNETAAKIAAGNVSAKEVKKAGKQLEKELKEVEKKLNEVFSRVENKIATK 334
                                    67777888888888888888888888888888888888888888888888877666554 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.3      0.27     2e+02     200     241 ..     185     226 ..     139     242 .. 0.59
   2 ?    8.0  10.2    0.0016       1.2     198     269 ..     275     346 ..     248     354 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.27
                           Spc7 200 eLeelreelaelkaeieekkkelaelqeqleeleekieelke 241
                                     L+e++  l+e++a++e+ +  + el + l+ +++ +  +++
  gi|119720026|ref|YP_920521.1| 185 LLQEAKLLLEEAEAKLEAGNITVPELAKTLAVVKKILGLVNA 226
                                    355666666666666666666555555555555555544444 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0016
                           Spc7 198 keeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevs 269
                                     e+Leel eel+e  a+i++ +   +e+++  ++le++++e++++ +e+ ++++++  ++ ++kg  ++e++
  gi|119720026|ref|YP_920521.1| 275 TERLEELEEELNETAAKIAAGNVSAKEVKKAGKQLEKELKEVEKKLNEVFSRVENKIATKAKEKGGWKHEIK 346
                                    567888888888888888888888888888888888888888888888888888777777777766666664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2189  (0.122093); expected 358.6 (0.02)
Passed bias filter:                     1037  (0.0578393); expected 358.6 (0.02)
Passed Vit filter:                       205  (0.011434); expected 17.9 (0.001)
Passed Fwd filter:                        32  (0.00178482); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.77u 0.32s 00:00:01.09 Elapsed: 00:00:00.48
# Mc/sec: 2416.01
//
Query:       gi|119720027|ref|YP_920522.1|  [L=812]
Description: molybdopterin oxidoreductase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-53  181.5   0.0    4.9e-53  180.6   0.0    1.4  1  Molybdopterin    Molybdopterin oxidoreductase
    8.4e-17   61.2   0.1      3e-16   59.4   0.0    2.0  2  Molydop_binding  Molydopterin dinucleotide binding domain
    9.1e-07   28.8   0.1    1.6e-06   28.0   0.1    1.4  1  Molybdop_Fe4S4   Molybdopterin oxidoreductase Fe4S4 domain
  ------ inclusion threshold ------
       0.08   13.1   0.0       0.25   11.6   0.0    1.8  1  CDC48_N          Cell division protein 48 (CDC48), N-terminal


Domain annotation for each model (and alignments):
>> Molybdopterin  Molybdopterin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.6   0.0   1.1e-56   4.9e-53       1     430 [.      96     573 ..      96     575 .. 0.83

  Alignments for each domain:
  == domain 1  score: 180.6 bits;  conditional E-value: 1.1e-56
                                    B--S-EEECTTTTTSEEEE--HHHHHHHHHHHHHHHHHHCSGGGEEEEEBTSSCSHHHHH....HHHHHHHHTT-EEE-B CS
                  Molybdopterin   1 RlkyPmvRkqargeGkFvrvsWdeAleliaaslkytikkygpdrvagfssgplmsmesla....slkkllsllggknlsf 76 
                                    Rlk+P++R+++rgeGkF++v Wd+Al++ia +lk++i kygp++v++++  ++  ++ +     +l +       ++ ++
  gi|119720027|ref|YP_920522.1|  96 RLKKPLKRVGERGEGKFQEVDWDTALNEIATKLKEIISKYGPESVVFTYH-DFY-AWHMPliafTLGTPNHVQHASCCHN 173
                                    9*********************************************7443.444.3333300001222222223333444 PP

                                    EECCGGGTTHHHHCHHCCCCCTTTS-SS-CC..GGGG-SEEEEESS-HHHHSHHHHHHHHHHHHTTC-EEEEECSSB-HC CS
                  Molybdopterin  77 ydwyadlppasaqqtigsdsrsnyessnple..dlensdliilwGsNvreerpilnarirkaalkkkakvivigpryael 154
                                     ++ya+         ++ +    +      +  d e +++++ +G  +   + ++  + +++a+++++k++ ++pr  + 
  gi|119720027|ref|YP_920522.1| 174 ASTYARM--------LVLGAGGPPT-----VdpDYERARYVVFVGRVLCAAMGMV--QRLQKARESGVKLVFVDPRMGNA 238
                                    4444443........2222122222.....23499***********988888888..5667789989***********98 PP

                                    GGGCSEEEEEHTTTHHHHHHHHHHHHHHCCCCTCHHHHHHEECHHHCCCCCCCEECCS...................... CS
                  Molybdopterin 155 lkfadewlaikpgtdaalalamghvilqelkvdkeflrkytygkeetdmpllvtleee...................... 212
                                    +  + ew++i pgtdaa++l+m hvil+e ++d++fl+kyt+++   +   + ++e+                       
  gi|119720027|ref|YP_920522.1| 239 AMAEGEWVPILPGTDAAFLLSMIHVILSEKLYDESFLKKYTNATFLIKPDGSPLTEKDlgregsdyvvydadakdflsyk 318
                                    889******************************************************9********************** PP

                                    ....................................HHHHHHCCHHHHHHHHHHHHHHTSSEEEEECHHHHTSTTHHHHH CS
                  Molybdopterin 213 ....................................tgkkkevvariarelarnaaktagksmiivGaglnhrqdgdaiy 256
                                                                        ++k+++v+a+++r+ ar++a+++g   +  G+   + ++ +++y
  gi|119720027|ref|YP_920522.1| 319 ksknpalewegdvagfhvktaflllkerasqyapeqAEKICGVPADTIRRIAREFANARG--VVEDGWWSAKNANDSDAY 396
                                    ************************************************************..7777************** PP

                                    HHHHHHHHHCTHCSSTTCEEEEESSCTTHHHCHHHHTCCTTCCCCCCCTTHHHHHCCCTTTCSTSS--ECGGCHHHHHHT CS
                  Molybdopterin 257 ravinLallvgnvgqpgGgwahlnGqlilagaaekvgalpvllsvkslkeekikfaaeqpgnlgnfprnlfversnllks 336
                                    ra+++L++lvg +++ gG + +l + ++ +  a  ++++ ++ +  +l+  + k ++ q+   + +    +  ++   k 
  gi|119720027|ref|YP_920522.1| 397 RAALTLNALVGSIETAGGLYIKLGS-KMPPS-ATATAEKVTTITGGTLPGIRAKRIDTQKYPAVPHVFDAVLDAALEGKP 474
                                    ********************99874.44444.666666655556666666333333333333333344455556666677 PP

                                    TSSSEEEEESH.HHHHSTTSCCCHCHHHCSSEEEEEESCSSHHHHTSSEEEEBE-CCGSEEEEE-TTSEEEE...EEESS CS
                  Molybdopterin 337 sgkkvlyllgnnpevdhadenevekalekldlvvvldgrltstalyaDiiLPaatwyEkedlytndegrfqh...lkqav 413
                                      +k+l+++g +p++++ ++ +++kal+ ++lvvv+d+  ++++ yaD++LP+  ++E+e+l+   + ++      ++a 
  gi|119720027|ref|YP_920522.1| 475 YPVKALFIVGAEPFTRDVNTEKLKKALKAMELVVVIDVVPNDSVDYADYVLPDNIFLEREELTDVKFTPHAAiqlSHKAL 554
                                    89***********************************************************9988887776666899999 PP

                                    S-S..TT-BEHHHHHHHHH CS
                  Molybdopterin 414 spp..geaksdwkIlkaLa 430
                                    +pp   +a++ ++I+ ++ 
  gi|119720027|ref|YP_920522.1| 555 DPPpgIDARNGFWIMMEIL 573
                                    9875569*******99986 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       2.1   9.3e+03      77      83 ..     381     395 ..     371     409 .. 0.54
   2 !   59.4   0.0   6.6e-20     3e-16       1     110 [.     685     804 ..     685     805 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.1
                                    ESSHCC......... CS
                Molydop_binding  77 pfgwwe........a 83 
                                    + gww+        a
  gi|119720027|ref|YP_920522.1| 381 EDGWWSaknandsdA 395
                                    456666444333333 PP

  == domain 2  score: 59.4 bits;  conditional E-value: 6.6e-20
                                    EEEEEE-BTTBSTTTTTCGCCHHHHCSSS-EEEEEHHHHHHHT--TT-EEEEEETTE..EEEEEEEEESSB-TTEEEEES CS
                Molydop_binding   1 lrLitgrsldqlhsqtrtrpvlrlakpepevveinpedAaalGikdGdlVevesrrG..svevrakvtervrpGvvfmpf 78 
                                    ++L++gr +  +   + t+++  l +  + +v++np+dA++lGikdGdl+e+e      ++++r+kvt+rvr+Gv+f+++
  gi|119720027|ref|YP_920522.1| 685 FYLVSGRDQFVTAHAVWTKNIIHLVD--R-RVWMNPNDAKRLGIKDGDLIELEGLDNhyKARARVKVTNRVREGVLFVYS 761
                                    56777777666666666666655555..3.7**********************987755888888*************** PP

                                    SHCC................S-GHCTS--SCSTTT--CSTT-E CS
                Molydop_binding  79 gwwe...........agekggnaNaltddatdplsgtpefksv 110
                                     ++             +++g n N+ t + ++pl g+  ++s+
  gi|119720027|ref|YP_920522.1| 762 RAGGrfsrlitgeyeVMKEGINPNMFTLSWLEPLNGSTGLNST 804
                                    ************************************9988875 PP

>> Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.1   3.6e-10   1.6e-06       7      54 ..      47      92 ..      41      93 .. 0.90

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 3.6e-10
                                   E-SSBTT--EEEEEEETTEEEEEEE-TTSTTTTT---HHHHTCHHCCC CS
                 Molybdop_Fe4S4  7 aCpyCgvgCglevhvkdgkivkvegdpdhpvnegrlCvKGrtllervy 54
                                    C++C  gCg++++ +++ +v+ve++ +hp  +  lC++ +++l+  +
  gi|119720027|ref|YP_920522.1| 47 MCSMCAAGCGILLVKEGNGTVYVEPNLEHP--QPGLCARAASALQLWN 92
                                   7*****************************..669******9998766 PP

>> CDC48_N  Cell division protein 48 (CDC48), N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   5.5e-05      0.25      15      41 ..     711     738 ..     706     750 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.5e-05
                                    TEEEE-HHHHHHHTS-TTSEEEEEC.CC CS
                        CDC48_N  15 givridpedmeelglepgdvveieg.kr 41 
                                     +v ++p+d ++lg++ gd +e+eg ++
  gi|119720027|ref|YP_920522.1| 711 RRVWMNPNDAKRLGIKDGDLIELEGlDN 738
                                    5799********************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (812 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.73u 0.32s 00:00:01.05 Elapsed: 00:00:00.49
# Mc/sec: 4965.39
//
Query:       gi|119720028|ref|YP_920523.1|  [L=187]
Description: 4Fe-4S ferredoxin iron-sulfur binding domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-21   75.2   8.1    3.6e-21   75.2   8.1    1.9  2  Fer4_11   4Fe-4S dicluster domain
    1.6e-17   62.8  31.3      9e-08   31.9   1.5    4.5  4  Fer4_6    4Fe-4S binding domain
    1.2e-15   57.9  27.9    7.1e-10   39.3   8.2    3.1  3  Fer4_7    4Fe-4S dicluster domain
    6.1e-15   54.3  37.6    2.5e-08   33.4   2.4    5.3  6  Fer4      4Fe-4S binding domain
    8.3e-13   47.6  32.4    6.7e-06   25.9   1.6    4.7  4  Fer4_2    4Fe-4S binding domain
    3.3e-11   43.1  30.8    1.7e-05   24.9   9.2    4.2  3  Fer4_10   4Fe-4S dicluster domain
    5.9e-10   39.2  25.8      1e-05   25.6   8.6    3.4  4  Fer4_9    4Fe-4S dicluster domain
    5.4e-08   33.2  23.1    6.5e-06   26.5   5.6    3.2  2  Fer4_8    4Fe-4S dicluster domain
    7.7e-08   32.3  34.6     0.0016   18.8   2.9    4.6  4  Fer4_4    4Fe-4S binding domain
    5.9e-06   26.9  45.8      0.035   15.1   7.6    4.3  4  Fer4_3    4Fe-4S binding domain
    9.3e-05   22.5  33.6      0.013   15.6  12.4    3.8  3  Fer4_21   4Fe-4S dicluster domain
    0.00011   23.0  27.0       0.26   12.3   0.9    4.2  5  Fer4_16   4Fe-4S double cluster binding domain
    0.00035   21.0  26.6      0.071   13.7   4.6    3.9  4  Fer4_17   4Fe-4S dicluster domain
    0.00042   21.0  14.9      0.032   15.0   0.7    3.8  4  Fer4_15   4Fe-4S single cluster domain
      0.002   18.3   4.9      0.002   18.3   4.9    3.4  3  Fer4_18   4Fe-4S dicluster domain
  ------ inclusion threshold ------
       0.16   12.8   1.4       0.16   12.8   1.4    3.9  4  Fer4_22   4Fe-4S dicluster domain
       0.42   10.7   0.1       0.42   10.7   0.1    4.0  4  Fer4_19   Divergent 4Fe-4S mono-cluster


Domain annotation for each model (and alignments):
>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.2       1.2   1.2e+03      13      29 ..      15      32 ..       5      46 .. 0.61
   2 !   75.2   8.1   3.4e-24   3.6e-21       8      99 ..      60     151 ..      54     152 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.2
                        Fer4_11 13 CleppCvasapse...aivk 29
                                   C   +C+a++++    + +k
  gi|119720028|ref|YP_920523.1| 15 C--GACIAACNAAnyrSTTK 32
                                   3..35666666543334444 PP

  == domain 2  score: 75.2 bits;  conditional E-value: 3.4e-24
                        Fer4_11   8 eqCrhCleppCvasapseaivkdeetGaVlldektkkeevrevveacPykivrkneetgkvekC..dmcldrveaGllpa 85 
                                     qC+hC+++pCva++p++a + d+ +G+V ++++ +  +++ +++acPy +   + + g  ekC  + c +rv+aGl+p+
  gi|119720028|ref|YP_920523.1|  60 VQCQHCENAPCVAVCPTGASYIDR-DGLVKINPDLCI-GCKYCMTACPYGMRWLDPDFGLPEKCmgETCQSRVKAGLMPV 137
                                    69*********************9.***********7.**************************4447************ PP

                        Fer4_11  86 cvescptgalnfgd 99 
                                    cv++cp+ga+ fgd
  gi|119720028|ref|YP_920523.1| 138 CVTVCPAGARAFGD 151
                                    ************98 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   2.0   1.4e-08   1.5e-05       4      21 ..       7      24 ..       6      27 .. 0.91
   2 !   13.8   3.8   4.4e-05     0.047       9      23 ..      62      78 ..      59      79 .. 0.92
   3 !   31.9   1.5   8.5e-11     9e-08       2      23 ..      87     108 ..      86     108 .. 0.94
   4 !    8.9   1.7    0.0016       1.7      15      23 ..     138     146 ..     135     146 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 1.4e-08
                         Fer4_6  4 idpdkCigCgdCvrvCPe 21
                                   +d+++CigCg+C+++C +
  gi|119720028|ref|YP_920523.1|  7 WDQSRCIGCGACIAACNA 24
                                   9***************76 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 4.4e-05
                         Fer4_6  9 CigCgd..CvrvCPega 23
                                   C +C++  Cv+vCP+ga
  gi|119720028|ref|YP_920523.1| 62 CQHCENapCVAVCPTGA 78
                                   9***8889*******98 PP

  == domain 3  score: 31.9 bits;  conditional E-value: 8.5e-11
                         Fer4_6   2 veidpdkCigCgdCvrvCPega 23 
                                    v i+pd+CigC  C+++CP+g+
  gi|119720028|ref|YP_920523.1|  87 VKINPDLCIGCKYCMTACPYGM 108
                                    78*****************985 PP

  == domain 4  score: 8.9 bits;  conditional E-value: 0.0016
                         Fer4_6  15 CvrvCPega 23 
                                    Cv+vCP+ga
  gi|119720028|ref|YP_920523.1| 138 CVTVCPAGA 146
                                    *******98 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.3   8.2   6.7e-13   7.1e-10       1      52 []      11      78 ..      11      78 .. 0.79
   2 !   19.3   2.9   1.2e-06    0.0013      32      51 ..      88     107 ..      82     108 .. 0.78
   3 !   21.4  12.3   2.7e-07   0.00028       2      52 .]      94     146 ..      93     146 .. 0.69

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 6.7e-13
                         Fer4_7  1 rCigCgaCvaaCpvkaieldeeenek..............gtekveidpekClgCga..CvavCPtga 52
                                   rCigCgaC aaC +   + + ++n+                +ek++i   +C++C++  CvavCPtga
  gi|119720028|ref|YP_920523.1| 11 RCIGCGACIAACNAANYRSTTKDNPTwggvqtnikrivfdLKEKPYILLVQCQHCENapCVAVCPTGA 78
                                   8************88888877766667666555544444433888999999*****99********98 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 1.2e-06
                         Fer4_7  32 eidpekClgCgaCvavCPtg 51 
                                    +i+p+ C+gC+ C+++CP+g
  gi|119720028|ref|YP_920523.1|  88 KINPDLCIGCKYCMTACPYG 107
                                    67888888888888888887 PP

  == domain 3  score: 21.4 bits;  conditional E-value: 2.7e-07
                         Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClg..Cg.........aCvavCPtga 52 
                                    CigC++C+ aCp++ + ld++          + pekC+g  C+         +Cv+vCP+ga
  gi|119720028|ref|YP_920523.1|  94 CIGCKYCMTACPYGMRWLDPDF---------GLPEKCMGetCQsrvkaglmpVCVTVCPAGA 146
                                    ************9999999884.........3556665433322222222228*******97 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   2.7   1.4e-08   1.5e-05       3      18 ..       7      22 ..       5      22 .. 0.95
   2 ?   -2.1   0.2       3.7     4e+03      11      16 ..      62      67 ..      60      68 .. 0.55
   3 !    9.6   1.4   0.00077      0.81      14      22 ..      70      78 ..      69      80 .. 0.95
   4 !   33.4   2.4   2.3e-11   2.5e-08       1      22 [.      87     108 ..      87     110 .. 0.93
   5 ?   -0.7   0.0       1.4   1.5e+03       5      10 ..     118     123 ..     117     123 .. 0.86
   6 !    9.0   1.7    0.0012       1.3      14      22 ..     138     146 ..     137     148 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.4e-08
                                   EETTTSSS-THHHHHS CS
                           Fer4  3 ideekCigCGaCvevC 18
                                   +d+++CigCGaC+ +C
  gi|119720028|ref|YP_920523.1|  7 WDQSRCIGCGACIAAC 22
                                   8*************** PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.7
                                   -THHHH CS
                           Fer4 11 CGaCve 16
                                   C  C++
  gi|119720028|ref|YP_920523.1| 62 CQHCEN 67
                                   555654 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00077
                                   HHHHSTTTE CS
                           Fer4 14 CvevCPvgA 22
                                   Cv vCP+gA
  gi|119720028|ref|YP_920523.1| 70 CVAVCPTGA 78
                                   ********9 PP

  == domain 4  score: 33.4 bits;  conditional E-value: 2.3e-11
                                    EEEETTTSSS-THHHHHSTTTE CS
                           Fer4   1 vvideekCigCGaCvevCPvgA 22 
                                    v+i++++CigC++C+ +CP+g 
  gi|119720028|ref|YP_920523.1|  87 VKINPDLCIGCKYCMTACPYGM 108
                                    68*****************995 PP

  == domain 5  score: -0.7 bits;  conditional E-value: 1.4
                                    TTTSSS CS
                           Fer4   5 eekCig 10 
                                    +ekC+g
  gi|119720028|ref|YP_920523.1| 118 PEKCMG 123
                                    79**97 PP

  == domain 6  score: 9.0 bits;  conditional E-value: 0.0012
                                    HHHHSTTTE CS
                           Fer4  14 CvevCPvgA 22 
                                    Cv vCP gA
  gi|119720028|ref|YP_920523.1| 138 CVTVCPAGA 146
                                    ********9 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   2.0   4.4e-07   0.00046       5      22 .]       7      24 ..       4      24 .. 0.89
   2 !    9.9   2.9   0.00076       0.8      10      22 .]      62      76 ..      53      76 .. 0.83
   3 !   25.9   1.6   6.4e-09   6.7e-06       3      22 .]      87     106 ..      85     106 .. 0.93
   4 !    8.6   3.2     0.002       2.1       7      22 .]     118     144 ..     109     144 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 4.4e-07
                         Fer4_2  5 vdtdrCigCgaCvsaCPa 22
                                    d  rCigCgaC+ aC a
  gi|119720028|ref|YP_920523.1|  7 WDQSRCIGCGACIAACNA 24
                                   6899************65 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00076
                         Fer4_2 10 CigCg..aCvsaCPa 22
                                   C +C+  +Cv +CP+
  gi|119720028|ref|YP_920523.1| 62 CQHCEnaPCVAVCPT 76
                                   8899888*******7 PP

  == domain 3  score: 25.9 bits;  conditional E-value: 6.4e-09
                         Fer4_2   3 vvvdtdrCigCgaCvsaCPa 22 
                                    v++++d CigC+ C +aCP+
  gi|119720028|ref|YP_920523.1|  87 VKINPDLCIGCKYCMTACPY 106
                                    789****************5 PP

  == domain 4  score: 8.6 bits;  conditional E-value: 0.002
                         Fer4_2   7 tdrCig..Cg.........aCvsaCPa 22 
                                    +++C+g  C           Cv++CPa
  gi|119720028|ref|YP_920523.1| 118 PEKCMGetCQsrvkaglmpVCVTVCPA 144
                                    6799999995556677999*******8 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8  14.4     1e-05     0.011       5      56 .]       8      75 ..       5      75 .. 0.81
   2 !   10.1   2.9   0.00065      0.69       6      21 ..      59      76 ..      54      85 .. 0.75
   3 !   24.9   9.2   1.6e-08   1.7e-05       2      56 .]      87     143 ..      86     165 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1e-05
                        Fer4_10  5 dddtCirCgkCvkaCPadl................tsvgakgeaseeeavrkkvekCtgcg..aCveaCP 56
                                   d+++Ci+Cg+C +aC  ++                +++ ++   + +e+  + + +C++c+   Cv++CP
  gi|119720028|ref|YP_920523.1|  8 DQSRCIGCGACIAAC--NAanyrsttkdnptwggvQTNIKRIVFDLKEKPYILLVQCQHCEnaPCVAVCP 75
                                   789************..6678**********997644444444455667777999*****7669*****9 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00065
                        Fer4_10  6 ddtCirCg..kCvkaCPa 21
                                     +C +C+   Cv++CP+
  gi|119720028|ref|YP_920523.1| 59 LVQCQHCEnaPCVAVCPT 76
                                   568999998889999999 PP

  == domain 3  score: 24.9 bits;  conditional E-value: 1.6e-08
                        Fer4_10   2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtg........cg...aCveaCP 56 
                                    v+i++d Ci+C+ C++aCP+              +++ + +ekC+g         g    Cv +CP
  gi|119720028|ref|YP_920523.1|  87 VKINPDLCIGCKYCMTACPY---------GMRWLDPDFGLPEKCMGetcqsrvkAGlmpVCVTVCP 143
                                    789*****************.........5555678888899999888444444125569*****9 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   3.2     3e-05     0.032      33      48 ..       9      24 ..       3      27 .. 0.73
   2 !   25.6   8.6   9.5e-09     1e-05       1      50 [.      11      78 ..      11      81 .. 0.75
   3 !   16.6   9.5   6.2e-06    0.0065       2      50 ..      94     146 ..      93     147 .. 0.83
   4 ?    4.0   1.9     0.054        57       8      16 ..     138     146 ..     120     158 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3e-05
                         Fer4_9 33 eeaCigCgaCveaCpk 48
                                   +++CigCgaC++aC+ 
  gi|119720028|ref|YP_920523.1|  9 QSRCIGCGACIAACNA 24
                                   5678888888888864 PP

  == domain 2  score: 25.6 bits;  conditional E-value: 9.5e-09
                         Fer4_9  1 kCtgCgaCveaCpagvv.vedaaerkarlraase...............eaCigCga..CveaCpkga 50
                                   +C+gCgaC++aC+a  + +  + + ++   +++                 +C +C+   Cv++Cp+ga
  gi|119720028|ref|YP_920523.1| 11 RCIGCGACIAACNAANYrSTTKDNPTWGGVQTNIkrivfdlkekpyillVQCQHCENapCVAVCPTGA 78
                                   6***********666552334444444444444467777788888****99**************986 PP

  == domain 3  score: 16.6 bits;  conditional E-value: 6.2e-06
                         Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaC..igCga.........CveaCpkga 50 
                                    C+gC++C++aCp+g+   d   +  +        C   +C++         Cv +Cp ga
  gi|119720028|ref|YP_920523.1|  94 CIGCKYCMTACPYGMRWLDPDFGLPEK-------CmgETCQSrvkaglmpvCVTVCPAGA 146
                                    **************9987777777663.......62235999999************985 PP

  == domain 4  score: 4.0 bits;  conditional E-value: 0.054
                         Fer4_9   8 CveaCpagv 16 
                                    Cv++Cpag+
  gi|119720028|ref|YP_920523.1| 138 CVTVCPAGA 146
                                    555555544 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   5.6   6.1e-09   6.5e-06       2      64 ..       9      77 ..       8      78 .. 0.69
   2 !    9.5   9.5    0.0013       1.3       5      34 ..      94     123 ..      91     173 .. 0.72

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 6.1e-09
                         Fer4_8  2 lekCieCgaCqsaCpvlrrtk.khlldargeaae...dvqeeqvleeeealwsCttcga..CtevCpvg 64
                                    ++Ci+CgaC +aC +++ +     + + g+++    + + + +++ +  l +C++c++  C+ vCp+g
  gi|119720028|ref|YP_920523.1|  9 QSRCIGCGACIAACNAANYRStTKDNPTWGGVQTnikRIVFDLKEKPYILLVQCQHCENapCVAVCPTG 77
                                   589***********866666633333333333334664444444444899*****************87 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0013
                         Fer4_8   5 CieCgaCqsaCpvlrrtkkhlldargeaae 34 
                                    Ci+C +C++aCp   r+ +  +  +++ ++
  gi|119720028|ref|YP_920523.1|  94 CIGCKYCMTACPYGMRWLDPDFGLPEKCMG 123
                                    ************998887444433333343 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   2.9   1.5e-06    0.0016       1      14 [.       9      22 ..       9      29 .. 0.92
   2 !   10.6   1.8   0.00066      0.69       4      17 .]      62      77 ..      52      77 .. 0.89
   3 !   17.2   2.6   4.8e-06     0.005       1      17 []      91     107 ..      91     107 .. 0.92
   4 ?    2.6   4.4      0.23   2.4e+02       8      17 .]     136     145 ..     118     147 .. 0.66

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.5e-06
                         Fer4_4  1 qerCigCgsCvaaC 14
                                   q+rCigCg+C+aaC
  gi|119720028|ref|YP_920523.1|  9 QSRCIGCGACIAAC 22
                                   68************ PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00066
                         Fer4_4  4 CigCgs..CvaaCPqg 17
                                   C++C    Cva+CP+g
  gi|119720028|ref|YP_920523.1| 62 CQHCENapCVAVCPTG 77
                                   *****789******86 PP

  == domain 3  score: 17.2 bits;  conditional E-value: 4.8e-06
                         Fer4_4   1 qerCigCgsCvaaCPqg 17 
                                    ++ CigC+ C+ aCP+g
  gi|119720028|ref|YP_920523.1|  91 PDLCIGCKYCMTACPYG 107
                                    589************86 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.23
                         Fer4_4   8 gsCvaaCPqg 17 
                                    ++Cv +CP g
  gi|119720028|ref|YP_920523.1| 136 PVCVTVCPAG 145
                                    35******75 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   6.2    0.0027       2.9       1      11 [.      12      22 ..      12      22 .. 0.99
   2 !   15.1   7.6   3.3e-05     0.035       1      15 []      62      78 ..      62      78 .. 0.92
   3 !   13.6   4.6   9.6e-05       0.1       1      14 [.      94     107 ..      94     107 .. 0.96
   4 !    7.8   3.6    0.0069       7.3       4      15 .]     126     146 ..     121     146 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0027
                         Fer4_3  1 CtgCgaCvevC 11
                                   C+gCgaC  +C
  gi|119720028|ref|YP_920523.1| 12 CIGCGACIAAC 22
                                   *********** PP

  == domain 2  score: 15.1 bits;  conditional E-value: 3.3e-05
                         Fer4_3  1 CtgCg..aCvevCPvgA 15
                                   C++C+  +Cv vCP+gA
  gi|119720028|ref|YP_920523.1| 62 CQHCEnaPCVAVCPTGA 78
                                   ****8778********9 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 9.6e-05
                         Fer4_3   1 CtgCgaCvevCPvg 14 
                                    C+gC  C+ +CP+g
  gi|119720028|ref|YP_920523.1|  94 CIGCKYCMTACPYG 107
                                    ****99******98 PP

  == domain 4  score: 7.8 bits;  conditional E-value: 0.0069
                         Fer4_3   4 Cg.........aCvevCPvgA 15 
                                    C+          Cv vCP gA
  gi|119720028|ref|YP_920523.1| 126 CQsrvkaglmpVCVTVCPAGA 146
                                    766666555545******998 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4  13.4   0.00012      0.13       4      53 ..       8      76 ..       5      81 .. 0.70
   2 !   15.6  12.4   1.3e-05     0.013       7      52 ..      61     105 ..      56     109 .. 0.82
   3 ?   -0.2   3.2       1.1   1.1e+03      46      53 ..     137     144 ..     117     147 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00012
                        Fer4_21  4 dedkCigCgkCliaCedtshqai...............eidaktvl........kvvedeCvGCnl..CssvCPv 53
                                   d+++CigCg C+ aC+ + +                  +      +         ++  +C  C+   C++vCP+
  gi|119720028|ref|YP_920523.1|  8 DQSRCIGCGACIAACNAANYRSTtkdnptwggvqtnikR------IvfdlkekpYILLVQCQHCENapCVAVCPT 76
                                   899*************99999995555555544433330......03444444255678999997555******6 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 1.3e-05
                        Fer4_21   7 kCigCgk..CliaCedtshqaieidaktvlkvvedeCvGCnlCssvCP 52 
                                    +C +C++  C+ +C++ +     id +  +k+  d C+GC+ C++ CP
  gi|119720028|ref|YP_920523.1|  61 QCQHCENapCVAVCPT-GAS--YIDRDGLVKINPDLCIGCKYCMTACP 105
                                    6888975559*****4.444..556778999***************** PP

  == domain 3  score: -0.2 bits;  conditional E-value: 1.1
                        Fer4_21  46 lCssvCPv 53 
                                    +C++vCP 
  gi|119720028|ref|YP_920523.1| 137 VCVTVCPA 144
                                    6999**94 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.9   0.00024      0.26       1      19 [.      11      29 ..      11      48 .. 0.83
   2 !   10.4   1.4   0.00093      0.98       1      16 [.      61      78 ..      61      92 .. 0.83
   3 !    9.5   5.0    0.0018       1.9       2      15 ..      94     107 ..      93     132 .. 0.87
   4 ?    2.9   1.4       0.2   2.2e+02      59      66 ..     137     144 ..     119     145 .. 0.74
   5 ?    5.2   0.3     0.039        41       8      16 ..     138     146 ..     135     175 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00024
                        Fer4_16  1 rCgtCgkCaevCPtnaike 19
                                   rC++Cg+C+ +C ++  ++
  gi|119720028|ref|YP_920523.1| 11 RCIGCGACIAACNAANYRS 29
                                   6***********8876655 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00093
                        Fer4_16  1 rCgtCgk..CaevCPtna 16
                                   +C+ C++  C+ vCPt+a
  gi|119720028|ref|YP_920523.1| 61 QCQHCENapCVAVCPTGA 78
                                   59***9999*******99 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.0018
                        Fer4_16   2 CgtCgkCaevCPtn 15 
                                    C++C+ C+ +CP +
  gi|119720028|ref|YP_920523.1|  94 CIGCKYCMTACPYG 107
                                    99999999999986 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.2
                        Fer4_16  59 iCqdvCPa 66 
                                    +C++vCPa
  gi|119720028|ref|YP_920523.1| 137 VCVTVCPA 144
                                    68888886 PP

  == domain 5  score: 5.2 bits;  conditional E-value: 0.039
                        Fer4_16   8 CaevCPtna 16 
                                    C+ vCP++a
  gi|119720028|ref|YP_920523.1| 138 CVTVCPAGA 146
                                    888888877 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1  10.6   0.00043      0.45       1      59 [.      11      77 ..      11      79 .. 0.65
   2 ?    5.9   2.6     0.018        19       1      18 [.      61      80 ..      61      92 .. 0.82
   3 !   13.7   4.6   6.7e-05     0.071       2      17 ..      94     109 ..      93     135 .. 0.78
   4 ?    1.7   0.2      0.35   3.7e+02       8      15 ..     138     145 ..     126     174 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00043
                        Fer4_17  1 rCiqCgyClpeCpsyea...ydnepkkllraaklg.lleeaeke..ekaslCieCge..CerkCPqg 59
                                   rCi+Cg+C+++C   +    ++++p     +++++ ++ + +++      +C +C++  C+++CP g
  gi|119720028|ref|YP_920523.1| 11 RCIGCGACIAACNAANYrstTKDNPTWGGVQTNIKrIVFDLKEKpyILLVQCQHCENapCVAVCPTG 77
                                   7***********97555233445566555555553133333334224779*****8777******86 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.018
                        Fer4_17  1 rCiqCgy..ClpeCpsyeay 18
                                   +C++C+   C+++Cp+++ y
  gi|119720028|ref|YP_920523.1| 61 QCQHCENapCVAVCPTGASY 80
                                   599999778******87765 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 6.7e-05
                        Fer4_17   2 CiqCgyClpeCpsyea 17 
                                    Ci+C+yC+ +Cp++++
  gi|119720028|ref|YP_920523.1|  94 CIGCKYCMTACPYGMR 109
                                    9999999999999876 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.35
                        Fer4_17   8 ClpeCpsy 15 
                                    C+ +Cp +
  gi|119720028|ref|YP_920523.1| 138 CVTVCPAG 145
                                    66666654 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.7     3e-05     0.032       4      19 ..       8      23 ..       6      35 .. 0.89
   2 ?   -0.1   0.7       1.6   1.7e+03      13      20 ..      69      76 ..      60      86 .. 0.62
   3 !   13.7   0.3   7.4e-05     0.078       1      19 [.      87     105 ..      87     116 .. 0.92
   4 ?   -0.5   0.0       2.1   2.2e+03      13      20 ..     137     144 ..     133     164 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3e-05
                        Fer4_15  4 DrdaCigcglCvaeap 19
                                   D+++Cigcg+C+a++ 
  gi|119720028|ref|YP_920523.1|  8 DQSRCIGCGACIAACN 23
                                   99***********995 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.6
                        Fer4_15 13 lCvaeape 20
                                    Cva++p+
  gi|119720028|ref|YP_920523.1| 69 PCVAVCPT 76
                                   57777764 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 7.4e-05
                        Fer4_15   1 VvvDrdaCigcglCvaeap 19 
                                    V+++ d+Cigc  C++++p
  gi|119720028|ref|YP_920523.1|  87 VKINPDLCIGCKYCMTACP 105
                                    8999**************8 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 2.1
                        Fer4_15  13 lCvaeape 20 
                                    +Cv+++p 
  gi|119720028|ref|YP_920523.1| 137 VCVTVCPA 144
                                    78888864 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   3.4    0.0026       2.7      82      97 ..       9      24 ..       7      33 .. 0.87
   2 !   18.3   4.9   1.9e-06     0.002      59     103 ..      60     112 ..      36     120 .. 0.77
   3 ?    1.9   1.0      0.23   2.4e+02      66      74 ..     137     145 ..     124     149 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0026
                        Fer4_18 82 qleciscllcidacdk 97
                                   q  ci c+ ci ac+ 
  gi|119720028|ref|YP_920523.1|  9 QSRCIGCGACIAACNA 24
                                   779***********96 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 1.9e-06
                        Fer4_18  59 gdcidces..cvkvcPtgidi..rkGl.qle...ciscllcidacdkvmeklg 103
                                     +c +ce   cv+vcPtg     r+Gl +++   ci c  c+ ac   m  l+
  gi|119720028|ref|YP_920523.1|  60 VQCQHCENapCVAVCPTGASYidRDGLvKINpdlCIGCKYCMTACPYGMRWLD 112
                                    5799998556*******96533499983454556***********98887665 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.23
                        Fer4_18  66 scvkvcPtg 74 
                                    +cv+vcP g
  gi|119720028|ref|YP_920523.1| 137 VCVTVCPAG 145
                                    799999987 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.4   0.00015      0.16      78      94 ..       8      24 ..       2      26 .. 0.84
   2 ?    1.4   2.8      0.54   5.7e+02       1      17 [.      61      79 ..      61      88 .. 0.78
   3 ?    9.1   1.6    0.0022       2.3      78      95 ..      90     107 ..      82     108 .. 0.82
   4 ?   -0.7   0.0       2.5   2.7e+03       8      15 ..     138     145 ..     135     175 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00015
                        Fer4_22 78 gesgCvGCgRCieacpv 94
                                   ++s C+GCg Ci+ac++
  gi|119720028|ref|YP_920523.1|  8 DQSRCIGCGACIAACNA 24
                                   7899***********86 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.54
                        Fer4_22  1 rClsCga..CtlvCptCsC 17
                                   +C +C +  C +vCpt   
  gi|119720028|ref|YP_920523.1| 61 QCQHCENapCVAVCPTGAS 79
                                   699997555******9765 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0022
                        Fer4_22  78 gesgCvGCgRCieacpvk 95 
                                    +   C+GC  C++acp +
  gi|119720028|ref|YP_920523.1|  90 NPDLCIGCKYCMTACPYG 107
                                    6678***********975 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 2.5
                        Fer4_22   8 CtlvCptC 15 
                                    C +vCp+ 
  gi|119720028|ref|YP_920523.1| 138 CVTVCPAG 145
                                    88888864 PP

>> Fer4_19  Divergent 4Fe-4S mono-cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.8      0.34   3.6e+02      10      23 ..       7      20 ..       3      32 .. 0.87
   2 ?   10.7   0.1    0.0004      0.42      27      58 ..      47      78 ..      40      84 .. 0.91
   3 ?    4.9   0.6     0.026        27       8      24 ..      87     103 ..      80     114 .. 0.87
   4 ?    0.0   0.1      0.88   9.3e+02      51      58 ..     139     146 ..     134     149 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.34
                        Fer4_19 10 dnrelCihsgnCvk 23
                                   ++++ Ci+ g C+ 
  gi|119720028|ref|YP_920523.1|  7 WDQSRCIGCGACIA 20
                                   8999********86 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0004
                        Fer4_19 27 evFdpkrkpwikpdeasteeiievverCPSGA 58
                                    vFd+k+kp+i   + +  e    v+ CP GA
  gi|119720028|ref|YP_920523.1| 47 IVFDLKEKPYILLVQCQHCENAPCVAVCPTGA 78
                                   59*****************************9 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.026
                        Fer4_19   8 iednrelCihsgnCvkg 24 
                                    +  n++lCi+ + C++ 
  gi|119720028|ref|YP_920523.1|  87 VKINPDLCIGCKYCMTA 103
                                    788***********975 PP

  == domain 4  score: 0.0 bits;  conditional E-value: 0.88
                        Fer4_19  51 verCPSGA 58 
                                    v  CP GA
  gi|119720028|ref|YP_920523.1| 139 VTVCPAGA 146
                                    789****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1146.98
//
Query:       gi|119720029|ref|YP_920524.1|  [L=292]
Description: polysulphide reductase, NrfD [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-21   76.5  31.5    3.3e-21   76.2  31.5    1.1  1  NrfD      Polysulphide reductase, NrfD
    3.5e-15   56.7  30.0      5e-15   56.2  30.0    1.1  1  NrfD_2    Polysulfide reductase


Domain annotation for each model (and alignments):
>> NrfD  Polysulphide reductase, NrfD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.2  31.5   3.7e-25   3.3e-21      10     309 ..       6     286 ..       1     289 [. 0.81

  Alignments for each domain:
  == domain 1  score: 76.2 bits;  conditional E-value: 3.7e-25
                           NrfD  10 vWglliav.ylFligisAgalilaillklfkkkegkslkliirtgallaalavlagllilvldlgrperflklll....y 84 
                                    vW  +i++ +l++ gi+ + ++  +l+kl k +e++  k++  ++++   + ++++l+++v dl rp  +  +++    +
  gi|119720029|ref|YP_920524.1|   6 VWNPVIIGlFLWFAGIAGMGSVAYALMKLGKVEEKT--KEL--SCVVF--ASIVLALVFVVADLSRPLNMPLAIIrsvlS 79 
                                    78888887799999**99977777777777666553..466..44442..444445899999999998765555522224 PP

                           NrfD  85 ynf.....sSimswgvlllslyivvlvlyllvifekdlaakglpalgilaklislaervakilaiialilavllgsytgf 159
                                      f     +S+m++g+ lls+ +++++l ll    ++  akg      l+k++       k++ +++ ++   + +y gf
  gi|119720029|ref|YP_920524.1|  80 GTFfyklsTSWMTIGISLLSILLLLALLVLL----RETVAKG------LQKIVDA-----KWYLVLTGFVGFMVVIYSGF 144
                                    444444456**********998888887763....4778888......5666555.....5999999999********** PP

                           NrfD 160 llsavlsrplwnspllpvlFlasaiasGlavlllasllaarfekesedagllkklellvilteagllvilfvglalegge 239
                                    l++     p+wn+ l+pvl + sa   ++avl ++   + +     e +++l+k +l+v + ea++l+ l+    ++g+e
  gi|119720029|ref|YP_920524.1| 145 LIADAPGVPFWNNSLIPVLWILSASICAIAVLKIL---VHK----PEVSNFLTKSGLAVDIAEAVALASLLNVSLYSGVE 217
                                    *********************99999999775444...444....578999****************9988777788899 PP

                           NrfD 240 kiealeaalsggfltvlFwlgvvllglaiplllslavprlrenvavvviasilalvgvlllrfllliagq 309
                                    +++  ++al +g l+  Fwl vvl+g+a+p++l +++ r +e+++  ++a++ alvg l+lr+l+l ag+
  gi|119720029|ref|YP_920524.1| 218 AARRSAEALVAGELAAAFWLLVVLVGVAVPMVLGFMLLR-KEDRRLALLAAACALVGALALRILVLQAGI 286
                                    999999999999**********************99999.99999999********************98 PP

>> NrfD_2  Polysulfide reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.2  30.0   5.5e-19     5e-15      20     256 ..      16     285 ..       3     289 .. 0.77

  Alignments for each domain:
  == domain 1  score: 56.2 bits;  conditional E-value: 5.5e-19
                         NrfD_2  20 vhflllalaGGtafliavlGlrdeaaarslaflalifivldllllivelgarvrfsh..vwllls...fepisviwlGaa 94 
                                    + f  +a +G  a+ +  lG  +e+ ++ l+ + ++ ivl l++++++l++++ +    +  +ls   f  +s+ w+   
  gi|119720029|ref|YP_920524.1|  16 LWFAGIAGMGSVAYALMKLGKVEEK-TKELSCVVFASIVLALVFVVADLSRPLNMPLaiIRSVLSgtfFYKLSTSWMTIG 94 
                                    4567789999999999999977666.578999*****************9998764311333443455788999998766 PP

                         NrfD_2  95 vlalsalgllllll........glgparewaGvlvlvsav...vlaytGvllaanaarplw.dhlllaiflasalllala 162
                                       ls l ll ll+        gl  +     +lvl+  v   v+ y+G+l+a     p+w + l++++++ sa + a+a
  gi|119720029|ref|YP_920524.1|  95 ISLLSILLLLALLVllretvakGLQKIVDAKWYLVLTGFVgfmVVIYSGFLIADAPGVPFWnNSLIPVLWILSASICAIA 174
                                    6566666665554412222222333444444456776666888**********999*****889**************** PP

                         NrfD_2 163 llvllrnaeeaapglqvi..........alielvlvvlyp.valaknavdaalafelalafwGfvll.Gval.lyleafl 229
                                    +l +l  + e++  l +           al++l  v ly  v  a+ +++a +a+ela afw  v+l Gva+ + l  +l
  gi|119720029|ref|YP_920524.1| 175 VLKILVHKPEVSNFLTKSglavdiaeavALASLLNVSLYSgVEAARRSAEALVAGELAAAFWLLVVLvGVAVpMVLGFML 254
                                    ******99999999998877788888889999999999974788999***************998764898865555444 PP

                         NrfD_2 230 ....arraaalaallvlaGafllrsfiveaG 256
                                        +rr a laa+++l Ga+ lr  +++aG
  gi|119720029|ref|YP_920524.1| 255 lrkeDRRLALLAAACALVGALALRILVLQAG 285
                                    33336899******************99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1068  (0.0595683); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 1976.28
//
Query:       gi|119720030|ref|YP_920525.1|  [L=114]
Description: putative succinate dehydrogenase cytochrome b subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.6e-11   42.8   5.4    5.8e-11   42.5   5.4    1.1  1  Sdh_cyt         Succinate dehydrogenase/Fumarate reductase tr
    0.00081   19.5   5.9     0.0011   19.1   5.9    1.1  1  Fumarate_red_D  Fumarate reductase subunit D
  ------ inclusion threshold ------
      0.043   13.9   4.3      0.062   13.4   4.3    1.3  1  Fumarate_red_C  Fumarate reductase subunit C


Domain annotation for each model (and alignments):
>> Sdh_cyt  Succinate dehydrogenase/Fumarate reductase transmembrane subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.5   5.4   9.7e-15   5.8e-11      19     120 ..       6     105 ..       2     107 .. 0.80

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 9.7e-15
                        Sdh_cyt  19 gawlsilhritGvallv.glllllvwlllalslsspesfarvvallaspiklilllllllallyHllnGiRhllwDlglg 97 
                                    + +++ l+ +tG++l++ ++ +++ + l + s+++  ++++v a l++p  ++ +l+l++++ yH+l G+ ++l+   + 
  gi|119720030|ref|YP_920525.1|   6 SGVAWFLQAVTGAVLALaVSAHIVRVHL-LGSAHGIPTYEEVLAALKNPLVMLGELVLAFSATYHALYGLHMVLVES-KL 83 
                                    5689*************99999998755.67789999**************************************95.33 PP

                        Sdh_cyt  98 lelesarksalavlalavalvlv 120
                                    l++e++ ++ l +l++a+a+++v
  gi|119720030|ref|YP_920525.1|  84 LSEEKS-RKVLTALGIALATWIV 105
                                    443333.4445555555555554 PP

>> Fumarate_red_D  Fumarate reductase subunit D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   5.9   1.8e-07    0.0011       8     113 ..       7     110 ..       3     111 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.8e-07
                 Fumarate_red_D   8 pifwlLFgaGGmvaAlvlpvlililglllplGlldsdalsyekvlafaqswigklvllvviilplwhalhrihhglhdlk 87 
                                     ++w L ++ G v Al + + i+ + ll  +        +ye+vla +++++++l  lv+ + +++hal  +h++l + k
  gi|119720030|ref|YP_920525.1|   7 GVAWFLQAVTGAVLALAVSAHIVRVHLLGSAHG----IPTYEEVLAALKNPLVMLGELVLAFSATYHALYGLHMVLVESK 82 
                                    589**************9999999888754433....359**************************************99 PP

                 Fumarate_red_D  88 ihvkkaaklif..YglAallsvvalill 113
                                    + ++++++ ++   g+A+++ +va+ +l
  gi|119720030|ref|YP_920525.1|  83 LLSEEKSRKVLtaLGIALATWIVAFNVL 110
                                    9877665544325899998888887665 PP

>> Fumarate_red_C  Fumarate reductase subunit C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   4.3     1e-05     0.062      33     117 ..      19     108 ..       7     114 .] 0.57

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1e-05
                 Fumarate_red_C  33 lvalfalvlllgllaLa..qgeaayeafleflqnPlvlllniiaLaaallhavTwfelaPkavkivvkg...eklpeevi 107
                                    ++al++   ++ ++ L   +g  +ye+ l++l+nPlv+l ++++  +a++ha    +++    k++ ++   + l++  i
  gi|119720030|ref|YP_920525.1|  19 VLALAVSAHIVRVHLLGsaHGIPTYEEVLAALKNPLVMLGELVLAFSATYHALYGLHMVLVESKLLSEEksrKVLTALGI 98 
                                    222232233333333334488899***************************98766666555555444411122222233 PP

                 Fumarate_red_C 108 vkalwaalvv 117
                                      a+w+++  
  gi|119720030|ref|YP_920525.1|  99 ALATWIVAFN 108
                                    3333333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 772.93
//
Query:       gi|119720031|ref|YP_920526.1|  [L=127]
Description: succinate dehydrogenase cytochrome b-556 subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      7e-09   35.8   7.4    8.5e-09   35.5   7.4    1.1  1  Sdh_cyt         Succinate dehydrogenase/Fumarate reductase tr
     0.0027   17.8   3.9     0.0043   17.1   3.9    1.4  1  Fumarate_red_C  Fumarate reductase subunit C
  ------ inclusion threshold ------
        1.3    9.5   3.6       0.89   10.0   1.4    1.7  2  DUF4231         Protein of unknown function (DUF4231)
        7.9    6.7  10.7        2.8    8.1   1.2    2.7  3  VMA21           VMA21-like domain


Domain annotation for each model (and alignments):
>> Sdh_cyt  Succinate dehydrogenase/Fumarate reductase transmembrane subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   7.4   1.9e-12   8.5e-09      18     119 ..      19     117 ..       3     121 .. 0.74

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 1.9e-12
                        Sdh_cyt  18 lgawlsilhritGvallvglllllvwlllalslsspesfarvvallas.piklilllllllallyHllnGiRhllwDlgl 96 
                                    l+ + + l r++G++l++ ++l++++ + +++++++e+++ +  +++s p  l+ l+l+ ++++ H++ G ++ ++  g+
  gi|119720031|ref|YP_920526.1|  19 LEHVSFSLRRLSGIVLAL-YFLVHMVDI-STVVLGKEVYDSFLKVFTSpPAVLVDLFLWGVLVV-HGVLGAYSAVVESGF 95 
                                    667788999*********.777776666.555789*************7888888555555555.************999 PP

                        Sdh_cyt  97 glelesarksalavlalavalvl 119
                                     le+++ +  a+++la++v++ +
  gi|119720031|ref|YP_920526.1|  96 LLEKRR-QLLAASWLAIVVLFAV 117
                                    884322.3455666666555443 PP

>> Fumarate_red_C  Fumarate reductase subunit C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   3.9   9.5e-07    0.0043      21      84 ..      21      84 ..       5     126 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 9.5e-07
                 Fumarate_red_C 21 YrfYmlrEatavlvalfalvlllgllaLaqgeaayeafleflqnPlvlllniiaLaaallhavT 84
                                   ++ + lr ++ +++al+ lv ++ + ++  g++ y++fl++ ++P ++l+++ +  ++++h v 
  gi|119720031|ref|YP_920526.1| 21 HVSFSLRRLSGIVLALYFLVHMVDISTVVLGKEVYDSFLKVFTSPPAVLVDLFLWGVLVVHGVL 84
                                   56799***********************************************999999999862 PP

>> DUF4231  Protein of unknown function (DUF4231)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.46     2e+03      21      32 ..      28      39 ..       7      64 .. 0.60
   2 ?   10.0   1.4    0.0002      0.89      22      63 ..      79     126 ..      71     127 .] 0.89

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.46
                        DUF4231 21 rlitivlgallp 32
                                   rl  ivl+ ++ 
  gi|119720031|ref|YP_920526.1| 28 RLSGIVLALYFL 39
                                   344444444333 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0002
                        DUF4231  22 litivlgallpilvs......sklgagvsvlkiltallsalvailaal 63 
                                    ++  vlga+++++ s      + +   +s+l+i+++++  +++i++a+
  gi|119720031|ref|YP_920526.1|  79 VVHGVLGAYSAVVESgfllekRRQLLAASWLAIVVLFAVGAAVIVNAF 126
                                    566799***************889999******************997 PP

>> VMA21  VMA21-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1      0.91   4.1e+03      55      62 ..      33      40 ..      31      52 .. 0.67
   2 ?    5.0   0.9    0.0058        26      48      61 ..      76      89 ..      74      91 .. 0.86
   3 ?    8.1   1.2   0.00062       2.8      27      64 .]      89     126 ..      88     126 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.91
                          VMA21 55 vlasYiiv 62
                                   vla+Y +v
  gi|119720031|ref|YP_920526.1| 33 VLALYFLV 40
                                   55555444 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0058
                          VMA21 48 AVivvnlvlasYii 61
                                    V+vv+ vl++Y  
  gi|119720031|ref|YP_920526.1| 76 GVLVVHGVLGAYSA 89
                                   69**********75 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.00062
                          VMA21  27 llfegvfglsnssatlysgvlAVivvnlvlasYiivAf 64 
                                     ++e+ f l+++ + l +  lA++v+ +v a+ i+ Af
  gi|119720031|ref|YP_920526.1|  89 AVVESGFLLEKRRQLLAASWLAIVVLFAVGAAVIVNAF 126
                                    5788999**********************999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       756  (0.0421663); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 887.28
//
Query:       gi|119720032|ref|YP_920527.1|  [L=219]
Description: succinate dehydrogenase and fumarate reductase iron-sulfur protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.3e-30  102.8   0.0    1.3e-29  102.3   0.0    1.2  1  Fer2_3    2Fe-2S iron-sulfur cluster binding domain
    5.5e-10   39.5   0.5    5.5e-10   39.5   0.5    2.0  2  Fer4_8    4Fe-4S dicluster domain
    3.1e-06   27.2   1.9    3.1e-06   27.2   1.9    2.2  2  Fer4_10   4Fe-4S dicluster domain
    9.5e-06   25.5   0.5    9.5e-06   25.5   0.5    2.1  1  Fer2      2Fe-2S iron-sulfur cluster binding domain
    2.3e-05   24.8  10.8    0.00079   19.9   3.9    2.4  3  Fer4_17   4Fe-4S dicluster domain
    0.00036   20.8   0.4    0.00036   20.8   0.4    2.8  2  Fer4_4    4Fe-4S binding domain
    0.00043   20.8   2.9    0.00043   20.8   2.9    2.4  2  Fer4_7    4Fe-4S dicluster domain
    0.00045   20.3   7.1     0.0067   16.6   5.1    2.9  3  Fer4_9    4Fe-4S dicluster domain
     0.0036   17.3   1.7     0.0036   17.3   1.7    3.2  3  Fer4_2    4Fe-4S binding domain
  ------ inclusion threshold ------
      0.018   14.8   5.0      0.018   14.8   5.0    3.3  3  Fer4      4Fe-4S binding domain
      0.046   13.9   1.2      0.046   13.9   1.2    2.6  3  Fer4_21   4Fe-4S dicluster domain
      0.079   12.7   3.0          4    7.3   0.9    2.3  2  Fer4_20   Dihydroprymidine dehydrogenase domain II, 4Fe-4S cl
      0.085   13.8   7.3       0.14   13.1   4.7    2.4  2  Fer4_16   4Fe-4S double cluster binding domain


Domain annotation for each model (and alignments):
>> Fer2_3  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.3   0.0   9.7e-33   1.3e-29       2     108 ..       5     108 ..       4     109 .. 0.94

  Alignments for each domain:
  == domain 1  score: 102.3 bits;  conditional E-value: 9.7e-33
                         Fer2_3   2 lkvkRfdprrdrgkqkvqeyeveaeeedtvldaLlkikeevdptlafrasCregiCGscavainGkptlaCtatikdlak 81 
                                    l v+R+++    +++ +  yev+++++++vldaL+k+  e+dptl+f++ C++g+CG+c+++inG ++laC ++i ++a+
  gi|119720032|ref|YP_920527.1|   5 LVVRRYKQ--GWREAEYRAYEVDVDPDTSVLDALEKVSLEQDPTLTFEHACHHGVCGACGMVINGVERLACVTRIGEVAR 82 
                                    56899999..445899**************************************************************97 PP

                         Fer2_3  82 qkseieleplpkfpvirDLvvDideml 108
                                        + +epl++f+v+ DL vD+++m+
  gi|119720032|ref|YP_920527.1|  83 GG-VVVVEPLRGFRVVSDLAVDKSRMF 108
                                    65.8********************997 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   1.0       5.6   7.7e+03       8      11 ..      58      61 ..      50      75 .. 0.74
   2 !   39.5   0.5     4e-13   5.5e-10       2      64 ..     131     197 ..     130     198 .. 0.68

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 5.6
                         Fer4_8  8 CgaC 11
                                   CgaC
  gi|119720032|ref|YP_920527.1| 58 CGAC 61
                                   4444 PP

  == domain 2  score: 39.5 bits;  conditional E-value: 4e-13
                         Fer4_8   2 lekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvlee.....eealwsCttcgaCtevCpvg 64 
                                    l++C+eCg C saCp+++++ + l  +   a ++  +++++       ++++w+C++  +C+++Cpvg
  gi|119720032|ref|YP_920527.1| 131 LFDCVECGVCYSACPIANTFPEYLG-PSVIALAYRSSKDGKVPavldsRRGVWACHAAFECSVRCPVG 197
                                    789************8888644333.2222233233333322245555789***************97 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.3      0.85   1.2e+03      45      51 ..      53      61 ..      37      75 .. 0.71
   2 !   27.2   1.9   2.2e-09   3.1e-06       8      56 .]     133     195 ..     126     195 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.85
                        Fer4_10 45 Ctg..cgaC 51
                                   C++  cgaC
  gi|119720032|ref|YP_920527.1| 53 CHHgvCGAC 61
                                   444445555 PP

  == domain 2  score: 27.2 bits;  conditional E-value: 2.2e-09
                        Fer4_10   8 tCirCgkCvkaCPadl..............tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                     C++Cg C +aCP  +               ++++ g+       r +v++C++ ++C   CP
  gi|119720032|ref|YP_920527.1| 133 DCVECGVCYSACPIANtfpeylgpsvialaYRSSKDGKVPAVLDSRRGVWACHAAFECSVRCP 195
                                    7*************88************9988888888899999999***************9 PP

>> Fer2  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.5   6.9e-09   9.5e-06       8      77 ..      22      77 ..      17      78 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 6.9e-09
                                   EEEEEETTTHBHHHHHH.....HTTTTTSTTSSSSSSSSTTEEEEEESCECTTSSSSTHHHHHTTEEEEGGGSEE CS
                           Fer2  8 vevevadgettlldaae.....enggidipysCggggCgtClvevlegevqsdetelegeeldegklrlaCqtiv 77
                                   +ev+v+++++ +lda+e     +++ + ++++C++g Cg+C   ++            g e      rlaC+t++
  gi|119720032|ref|YP_920527.1| 22 YEVDVDPDTS-VLDALEkvsleQDPTLTFEHACHHGVCGACGMVIN------------GVE------RLACVTRI 77
                                   6899966666.******999966899****************9888............787......79**9985 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.6       6.4   8.8e+03      49      52 ..      58      61 ..      50      66 .. 0.61
   2 !   16.1   0.6   8.7e-06     0.012      32      57 ..     120     145 ..     101     148 .. 0.73
   3 !   19.9   3.9   5.7e-07   0.00079       2      60 ..     134     198 ..     133     199 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 6.4
                        Fer4_17 49 CgeC 52
                                   Cg C
  gi|119720032|ref|YP_920527.1| 58 CGAC 61
                                   4444 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 8.7e-06
                        Fer4_17  32 glleeaekeekaslCieCgeCerkCP 57 
                                    ++++++ + ek  +C+eCg C ++CP
  gi|119720032|ref|YP_920527.1| 120 ERVDGVVELEKLFDCVECGVCYSACP 145
                                    445555555899*************9 PP

  == domain 3  score: 19.9 bits;  conditional E-value: 5.7e-07
                        Fer4_17   2 CiqCgyClpeCpsyeaydne..pkkllraakl...glleeaeke.ekaslCieCgeCerkCPqgl 60 
                                    C +Cg C  +Cp  +  +++  p  ++ a+++   g++ ++ ++ + +  C+   eC+ +CP g+
  gi|119720032|ref|YP_920527.1| 134 CVECGVCYSACPIANTFPEYlgPSVIALAYRSskdGKVPAVLDSrRGVWACHAAFECSVRCPVGF 198
                                    ****************9997557777777766455555556555479***************876 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.4   2.6e-07   0.00036       4      15 ..     134     145 ..     128     163 .. 0.91
   2 ?   -2.2   1.5       6.4   8.8e+03      14      14 ..     190     190 ..     182     197 .. 0.47

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.6e-07
                         Fer4_4   4 CigCgsCvaaCP 15 
                                    C++Cg+C++aCP
  gi|119720032|ref|YP_920527.1| 134 CVECGVCYSACP 145
                                    ***********9 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 6.4
                         Fer4_4  14 C 14 
                                    C
  gi|119720032|ref|YP_920527.1| 190 C 190
                                    2 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1      0.57   7.8e+02      38      44 ..      53      61 ..      11      75 .. 0.70
   2 !   20.8   2.9   3.1e-07   0.00043       2      51 ..     134     197 ..     133     198 .. 0.64

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.57
                         Fer4_7 38 Clg..CgaC 44
                                   C +  CgaC
  gi|119720032|ref|YP_920527.1| 53 CHHgvCGAC 61
                                   333445555 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 3.1e-07
                         Fer4_7   2 CigCgaCvaaCpvkaie..........ldeeenekgtekveidpek....ClgCgaCvavCPtg 51 
                                    C++Cg C +aCp               l ++++++g+  +++d+++    C    +C  +CP+g
  gi|119720032|ref|YP_920527.1| 134 CVECGVCYSACPIANTFpeylgpsviaLAYRSSKDGKVPAVLDSRRgvwaCHAAFECSVRCPVG 197
                                    ***********855555122222222255688888876677776653222555556******98 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1      0.28   3.8e+02      34      42 ..      51      61 ..       8      76 .. 0.73
   2 !   15.4   1.4   1.1e-05     0.015      33      47 ..     130     145 ..      99     149 .. 0.74
   3 !   16.6   5.1   4.9e-06    0.0067       1      49 [.     133     197 ..     133     198 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.28
                         Fer4_9 34 eaCig..CgaC 42
                                    aC++  CgaC
  gi|119720032|ref|YP_920527.1| 51 HACHHgvCGAC 61
                                   56766668877 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1.1e-05
                         Fer4_9  33 e.eaCigCgaCveaCp 47 
                                    +  +C++Cg C+ aCp
  gi|119720032|ref|YP_920527.1| 130 KlFDCVECGVCYSACP 145
                                    1467***********9 PP

  == domain 3  score: 16.6 bits;  conditional E-value: 4.9e-06
                         Fer4_9   1 kCtgCgaCveaCpagvv.vedaaerkarlraase...............eaCigCgaCveaCpkg 49 
                                    +C++Cg C +aCp   +  e  ++  ++l  +s                +aC+   +C  +Cp g
  gi|119720032|ref|YP_920527.1| 133 DCVECGVCYSACPIANTfPEYLGPSVIALAYRSSkdgkvpavldsrrgvWACHAAFECSVRCPVG 197
                                    5***********86555155555555555554449999*************************86 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   1.8       1.4     2e+03      13      16 ..      58      61 ..      52      75 .. 0.67
   2 !   17.3   1.7   2.6e-06    0.0036      10      21 ..     134     145 ..     126     145 .. 0.94
   3 ?   -2.2   1.3       4.2   5.8e+03      16      21 ..     190     195 ..     182     196 .. 0.64

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.4
                         Fer4_2 13 CgaC 16
                                   CgaC
  gi|119720032|ref|YP_920527.1| 58 CGAC 61
                                   4444 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 2.6e-06
                         Fer4_2  10 CigCgaCvsaCP 21 
                                    C++Cg C+saCP
  gi|119720032|ref|YP_920527.1| 134 CVECGVCYSACP 145
                                    ***********9 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 4.2
                         Fer4_2  16 Cvsa.CP 21 
                                    C s+ CP
  gi|119720032|ref|YP_920527.1| 190 C-SVrCP 195
                                    7.55588 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   1.6      0.77   1.1e+03      11      15 ..      58      62 ..      57      64 .. 0.74
   2 ?   14.8   5.0   1.3e-05     0.018       7      19 ..     133     145 ..     132     147 .. 0.92
   3 ?    1.9   0.3      0.16   2.2e+02      14      21 ..     190     197 ..     189     198 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.77
                                   -THHH CS
                           Fer4 11 CGaCv 15
                                   CGaC 
  gi|119720032|ref|YP_920527.1| 58 CGACG 62
                                   99995 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 1.3e-05
                                    TSSS-THHHHHST CS
                           Fer4   7 kCigCGaCvevCP 19 
                                    +C+ CG C+++CP
  gi|119720032|ref|YP_920527.1| 133 DCVECGVCYSACP 145
                                    5************ PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.16
                                    HHHHSTTT CS
                           Fer4  14 CvevCPvg 21 
                                    C   CPvg
  gi|119720032|ref|YP_920527.1| 190 CSVRCPVG 197
                                    9999**98 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.2       3.8   5.2e+03      11      14 ..      58      61 ..      39      67 .. 0.66
   2 ?   13.9   1.2   3.3e-05     0.046      40      55 ..     133     148 ..     121     150 .. 0.82
   3 ?    1.4   0.2      0.26   3.6e+02      41      53 ..     184     196 ..     171     199 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.8
                        Fer4_21 11 CgkC 14
                                   Cg C
  gi|119720032|ref|YP_920527.1| 58 CGAC 61
                                   3333 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 3.3e-05
                        Fer4_21  40 eCvGCnlCssvCPved 55 
                                    +Cv C +C+s CP+ +
  gi|119720032|ref|YP_920527.1| 133 DCVECGVCYSACPIAN 148
                                    7999999999999865 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.26
                        Fer4_21  41 CvGCnlCssvCPv 53 
                                    C +   Cs  CPv
  gi|119720032|ref|YP_920527.1| 184 CHAAFECSVRCPV 196
                                    7777789999*98 PP

>> Fer4_20  Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.9    0.0029         4      24      46 ..     134     154 ..     125     165 .. 0.90
   2 ?    5.2   0.0     0.012        17      26      52 ..     183     210 ..     159     216 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0029
                                    ----TT-HHHHCSTT---HHHHH CS
                        Fer4_20  24 ClqCkkapcvkgCPveidipefi 46 
                                    C++C    c ++CP+ ++ pe++
  gi|119720032|ref|YP_920527.1| 134 CVEC--GVCYSACPIANTFPEYL 154
                                    9999..78*************97 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.012
                                    --TT-H.HHHCSTT---HHHHHHHHHTT CS
                        Fer4_20  26 qCkkap.cvkgCPveidipefikkiaeg 52 
                                     C+ a  c+  CPv  +  e i k+++g
  gi|119720032|ref|YP_920527.1| 183 ACHAAFeCSVRCPVGFKPGETIMKVRRG 210
                                    5886544**********99999999876 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0         1   1.4e+03      53      62 ..      52      63 ..      16      64 .. 0.61
   2 ?   13.1   4.7    0.0001      0.14       2      66 ..     134     196 ..     133     197 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1
                        Fer4_16 53 ai..tgCdiCqd 62
                                   a+    C++C +
  gi|119720032|ref|YP_920527.1| 52 AChhGVCGACGM 63
                                   444456777755 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.0001
                        Fer4_16   2 CgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCPa 66 
                                    C++Cg C ++CP +    +  +   +    +y+  ++ +++    ++   +a++    C   CP+
  gi|119720032|ref|YP_920527.1| 134 CVECGVCYSACPIANTFPE--YLGPSVIALAYRSSKDGKVPAVLDSRRGVWACHAAFECSVRCPV 196
                                    ************9776555..45555556666666666666666666667999999999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1652.36
//
Query:       gi|119720033|ref|YP_920528.1|  [L=384]
Description: FAD dependent oxidoreductase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.3e-55  187.7   0.5    5.2e-55  187.4   0.5    1.0  1  DAO             FAD dependent oxidoreductase
    4.7e-11   42.5   0.0    7.2e-11   41.9   0.0    1.3  1  FAD_binding_3   FAD binding domain
    9.7e-08   31.5   2.7     0.0013   17.9   2.1    2.2  2  FAD_binding_2   FAD binding domain
    2.6e-07   30.2   0.5      2e-06   27.3   0.5    2.0  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    1.8e-05   24.3   2.3    0.00029   20.3   2.3    2.1  1  FAD_oxidored    FAD dependent oxidoreductase
    2.1e-05   24.6   3.8    5.2e-05   23.4   2.5    2.2  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    0.00012   22.6   2.4    0.00083   19.9   1.1    2.8  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
     0.0016   17.4   1.6        0.9    8.3   0.0    2.1  2  Trp_halogenase  Tryptophan halogenase
      0.007   15.1   0.5      0.033   12.9   0.5    1.9  2  HI0933_like     HI0933-like protein
  ------ inclusion threshold ------
      0.013   14.7   0.6      0.024   13.9   0.6    1.4  1  Thi4            Thi4 family
      0.016   14.3   1.2      0.027   13.6   1.0    1.4  2  GIDA            Glucose inhibited division protein A
      0.016   15.6   0.0      0.036   14.5   0.0    1.6  1  NAD_binding_7   Putative NAD(P)-binding
      0.023   14.0   0.1      0.043   13.1   0.1    1.4  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
      0.028   14.3   0.6      0.054   13.4   0.6    1.5  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
      0.074   12.1   1.0       0.19   10.8   0.5    1.8  2  Lycopene_cycl   Lycopene cyclase protein
       0.13   11.4   0.0        3.5    6.7   0.1    2.1  2  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
       0.15   11.8   0.6       0.29   10.9   0.6    1.5  1  FAD_binding_4   FAD binding domain
        1.1    8.8   3.5       0.38   10.4   0.5    1.8  2  ApbA            Ketopantoate reductase PanE/ApbA


Domain annotation for each model (and alignments):
>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.4   0.5   5.2e-58   5.2e-55       1     342 [.       4     337 ..       4     354 .. 0.85

  Alignments for each domain:
  == domain 1  score: 187.4 bits;  conditional E-value: 5.2e-58
                                    EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTHHHHHHHHHHHHHHHHHHHHHSST CS
                            DAO   1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsglrylpeaselarlslealeelreleeelgid 78 
                                    +vv+iGGG++G++ Ay+La rg  Vtlle+g  +gsg+Sgr+ gllhsg+ry ++     ++++e++ e   l +  ++ 
  gi|119720033|ref|YP_920528.1|   4 KVVVIGGGVTGAALAYDLALRGlrVTLLERG-SIGSGTSGRTHGLLHSGCRYVADV----EVARECYSENVVLRRI-AP- 76 
                                    59*****************************.8888***************99965....9999999999999988.76. PP

                                    TSEEEEEEEEEESSHHHHHHHHHHHHHHHHTTTTEEEEEHHHHHHHSTT.STTTSEEEEETTEEEEEHHHHHHHHHHHHH CS
                            DAO  79 idyrrtGllslaadeeelealdkllallleagldaelldaeevrelepa.lpgllgalfypdtgqvdpakltaalaraae 157
                                    + ++++G +++a de++le+ d  l++++eag++++ +++ee+++lep+  p+l++a+++pd g++dp k++ ++++ a+
  gi|119720033|ref|YP_920528.1|  77 FLFEKNGGIFVAVDESDLEYKDFFLKKCEEAGIPVKEVSREEALKLEPNlNPDLKAAVLVPD-GTFDPLKVILSFLASAK 155
                                    99***********9999**99999999999*****99***********9766**********.***************** PP

                                    HTT-EEEESECEEEEEEEETCEEEEE.....EECTEEEE...EEEEEEE--GGGHHHHHTTCTTTSEEEEEEEEEEEEEE CS
                            DAO 158 alGveilegtevtgleeedgkvwgve.....rttpgend...aadavVnaaGawsdllgllkeldlpispvrgqvlvlkp 229
                                    ++G++i+ + ev+g++ e+g v+ v+           ++   +ad  Vna+Gaw++++++l  ld+p++p  g +++l+ 
  gi|119720033|ref|YP_920528.1| 156 QRGADIRPYNEVVGFRVEGGEVKAVKvrdkvS----LREyelEADFFVNATGAWAKKVARLAGLDVPVKPSPGVMVALDG 231
                                    ***************99999999998753321....2213345688**********8844445689************76 PP

                                    CCTHSTGSGCSEEEEE.EEETTTTEEEEEETTSEEEEEESSEEETTCSSTSCSHHHHHHHHHHHHHHSGG..GCGEEEEE CS
                            DAO 230 lseklvspaailpvpe.tdddgrgvyvtprkdgrvlvGgtadeesgdddpevdeedidellealrklfPq..lgdvlrkw 306
                                    +          + v+   + +g+g +++  + g+ ++G+t    +++d +e++ e+++ ll++ r+l P   + +v+  +
  gi|119720033|ref|YP_920528.1| 232 RVG--------FRVFNrLNKPGDGDIIVHHR-GTSVIGTTSWVVEDPDKVEAPREHVELLLRRGRELAPVtsKLRVKAVY 302
                                    555........34444489999999999997.99999**99555556669********************6557788999 PP

                                    EEEEEETTSSEEEEEEETEEEEEEEEECTTTHHHHH CS
                            DAO 307 aGlrplpdglpligetpgvkglylatGhsghGltla 342
                                    +  rpl+  lp      +v++ +    hs+ G  ++
  gi|119720033|ref|YP_920528.1| 303 VSSRPLVGSLPAGTG-REVSRSFAIIDHSREGAGNM 337
                                    *****9888887555.45777888778877776554 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9   0.0   7.2e-14   7.2e-11       3     175 ..       4     216 ..       2     264 .. 0.84

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 7.2e-14
                                    EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSS.S--EEEHHHHHHHHHTT-HHHHHHHSEECCCCEEEEEEE.. CS
                  FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlp.radglnqrtmellrqlGledrilaegapnelmgealyne.. 79 
                                    +V+++G+G +G+ la  L+ +G rv+l+e+ s  + ++ r +gl     +   ++ +++++++e ++   ++ +l ++  
  gi|119720033|ref|YP_920528.1|   4 KVVVIGGGVTGAALAYDLALRGLRVTLLERGSIGSGTSgRTHGLLHSGCRYVADVEVARECYSENVVLRRIAPFLFEKng 83 
                                    79*******************************999999***************************99999988877779 PP

                                    ..............................CCCC......CEEEEEHHCHHCST-CEE--HHHHHHHHHHHHHHHTEEET CS
                  FAD_binding_3  80 ..............................lsdt......pkaradlelesspervtvypqteleriLvehaeerglqvr 123
                                                                  +s+       p+ + dl++    ++ t  p + ++  L+++ ++rg+++r
  gi|119720033|ref|YP_920528.1|  84 gifvavdesdleykdfflkkceeagipvkeVSREealklePNLNPDLKAAVLVPDGTFDPLKVILSFLASA-KQRGADIR 162
                                    *******9999999999888887777755522223444445555555555666666666666666666665.******** PP

                                    CSEEEECCEECCCCCCCE.EEECCTTEEEEEEEEEEEE--GTT-H.HHHHHTGG CS
                  FAD_binding_3 124 fktevesleqdeegvtae.vrdketgeeetvrakYlvGaDGgrSt.vrktlgie 175
                                      +ev++++ ++ +v+a+ vrdk + +e++++a++ v a G++ + v++ +g++
  gi|119720033|ref|YP_920528.1| 163 PYNEVVGFRVEGGEVKAVkVRDKVSLREYELEADFFVNATGAWAKkVARLAGLD 216
                                    ***************995388*********************986255555665 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   2.1   1.3e-06    0.0013       2      43 ..       5      46 ..       4      50 .. 0.87
   2 !   12.1   0.0   7.5e-05     0.075     143     208 ..     146     210 ..     128     235 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.3e-06
                                   EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S CS
                  FAD_binding_2  2 viViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqG 43
                                   v+ViG+G+ G a A+ +a +Gl+v+++e ++  +g++    G
  gi|119720033|ref|YP_920528.1|  5 VVVIGGGVTGAALAYDLALRGLRVTLLERGSIGSGTSGRTHG 46
                                   9****************************9987777765555 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 7.5e-05
                                    HHHHHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----GG.... CS
                  FAD_binding_2 143 llarlvesarkagvdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfgrallk 208
                                    ++  +++sa+++g d+++  e++ + ve+g+v  + v+++ s re +++a+  v atg++ + ++ 
  gi|119720033|ref|YP_920528.1| 146 VILSFLASAKQRGADIRPYNEVVGFRVEGGEVKAVKVRDKVSLREYELEADFFVNATGAWAK-KVA 210
                                    6677999*****************************************************96.333 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.5     2e-09     2e-06       1     118 [.       3     214 ..       3     234 .. 0.86

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 2e-09
                                    CSEEEE--SHHHHHHHHHHHHHTS-EEEEE....TTHCHHHCSHHHHCHHHHHHHHHHHHH................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxx................... RF
                    Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlve....legtclnggcllskallgvaedaeias................... 57 
                                    k+vvviGgG+ G a+a +la  g++vtl+e      gt    + ll++ ++ va+ +  ++                   
  gi|119720033|ref|YP_920528.1|   3 KKVVVIGGGVTGAALAYDLALRGLRVTLLErgsiGSGTSGRTHGLLHSGCRYVADVEVAREcysenvvlrriapflfekn 82 
                                    58***************************87775222222333444555555555554444778888999********** PP

                                    .....................................................................HHHHCHHHHCC CS
                                    .....................................................................xxxxxxxxxxx RF
                    Pyr_redox_2  58 .....................................................................evvkklnqgie 68 
                                                                                                            k+ +++i+
  gi|119720033|ref|YP_920528.1|  83 ggifvavdesdleykdfflkkceeagipvkevsreealklepnlnpdlkaavlvpdgtfdplkvilsflASAKQRGADIR 162
                                    ********************************************************************977788999999 PP

                                    CCHCCTCEEEEESC.EEEEETEEECTCEEEEEESEEEE---EEE-BC.TCTT CS
                                    xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx RF
                    Pyr_redox_2  69 lllgeevvkidpgk.kkvklekkkegdeekiaydklvlAtGssprdl.gipG 118
                                     ++++ +++++ g+ k vk+++k++  e ++++d  v AtG+++++   + G
  gi|119720033|ref|YP_920528.1| 163 PYNEVVGFRVEGGEvKAVKVRDKVSLREYELEADFFVNATGAWAKKVaRLAG 214
                                    99998899999888899999999999999*************9998755555 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   2.3   2.9e-07   0.00029       2     145 ..       5     204 ..       4     219 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.9e-07
                   FAD_oxidored   2 vvVvGGgpaGvaAAiaAaraGakvlLveergvlGGll..tsglvatdignkaee...........qvvtgiareflerlr 68 
                                    vvV+GGg+ G a A+  a +G +v L+e+     G++  t gl+ + +  + ++            v ++ia  ++e++ 
  gi|119720033|ref|YP_920528.1|   5 VVVIGGGVTGAALAYDLALRGLRVTLLERGSIGSGTSgrTHGLLHSGCR-YVADvevarecysenVVLRRIAPFLFEKNG 83 
                                    9***************************999855655334444444444.222243333344443233333333333332 PP

                   FAD_oxidored  69 qrgga......rlkkrskwn...............................................tfepevakavlee 95 
                                               +       +                                               tf+p  +   + +
  gi|119720033|ref|YP_920528.1|  84 ----GifvavdE-------SdleykdfflkkceeagipvkevsreealklepnlnpdlkaavlvpdgTFDPLKVILSFLA 152
                                    ....12232221.......02222233344455666667777788888899999999**************999999999 PP

                   FAD_oxidored  96 mlaeagvtvllntrlvevekegkriesvtveske.g.rktirAkvfiDATgd 145
                                      ++ g ++    ++v+ ++eg+++++v+v++k    +++++A++f+ ATg 
  gi|119720033|ref|YP_920528.1| 153 SAKQRGADIRPYNEVVGFRVEGGEVKAVKVRDKVsLrEYELEADFFVNATGA 204
                                    99********************9*******99985479************95 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   2.5   5.2e-08   5.2e-05       1      37 [.       7      41 ..       7      62 .. 0.80
   2 ?   -0.9   0.0         2   1.9e+03      28      41 ..     338     355 ..     321     375 .. 0.70

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 5.2e-08
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-E CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraas 37
                                   ++G+G++G+++Ay La +g++v+lle+++  +G  +s
  gi|119720033|ref|YP_920528.1|  7 VIGGGVTGAALAYDLALRGLRVTLLERGSIGSG--TS 41
                                   8**************************965444..33 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2
                                    SSSSSGGG-EECE....T CS
                  NAD_binding_8  28 rdrlGGraasyev....p 41 
                                    ++ +GG+ +++++     
  gi|119720033|ref|YP_920528.1| 338 ASVIGGKFTTARLmaekT 355
                                    456788877777655442 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   1.1   8.4e-07   0.00083       1      31 [.       4      34 ..       4      37 .. 0.96
   2 ?    0.2   0.0       1.1   1.1e+03      50      80 ..     154     184 ..     149     186 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 8.4e-07
                                   EEEEECSSHHHHHHHHHHHHTTSEEEEEESS CS
                      Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvvers 31
                                   kvvv+GgG++g  lA  la  g +Vt++er+
  gi|119720033|ref|YP_920528.1|  4 KVVVIGGGVTGAALAYDLALRGLRVTLLERG 34
                                   79***************************97 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.1
                                    HHHTTEEEECSEEEEEEEEETTSEEEEEEET CS
                      Pyr_redox  50 lekngievllntkveeiegsedgvesvklkd 80 
                                     +++g +++  ++v+ ++ ++ +v++vk++d
  gi|119720033|ref|YP_920528.1| 154 AKQRGADIRPYNEVVGFRVEGGEVKAVKVRD 184
                                    67789999999999999999988999*9986 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   1.0    0.0014       1.4       1      42 [.       4      42 ..       4      51 .. 0.80
   2 !    8.3   0.0   0.00091       0.9     158     210 ..     148     205 ..      89     215 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0014
                                   EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS---SS- CS
                 Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlveseeigtvgvG 42
                                   k+v++GGG  G   A  la  +   l+vtl+e   ig    G
  gi|119720033|ref|YP_920528.1|  4 KVVVIGGGVTGAALAYDLALRG---LRVTLLERGSIGSGTSG 42
                                   79*********65555555444...********999976655 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00091
                                    HHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETT.....S-EEE-SEEEE-SGGG CS
                 Trp_halogenase 158 kfLrrvaearGvtrvegkvvevqldedgrveslrled.....greveadlfiDcsGfr 210
                                        + a++rG +++  + v     e g+v+++++ d     + e+ead+f+ ++G  
  gi|119720033|ref|YP_920528.1| 148 LSFLASAKQRGADIRPYNEVVGFRVEGGEVKAVKVRDkvslrEYELEADFFVNATGAW 205
                                    4556778999999887665555555689*********999999*************75 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.5   3.3e-05     0.033       2      32 ..       4      34 ..       3      40 .. 0.93
   2 ?   -0.9   0.0      0.51   5.1e+02     111     164 ..     146     204 ..     142     208 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.3e-05
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SS CS
                    HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVllleka 32
                                   +v+viGgG  G   A  +a rg rV+lle++
  gi|119720033|ref|YP_920528.1|  4 KVVVIGGGVTGAALAYDLALRGLRVTLLERG 34
                                   89***************************97 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.51
                                    HHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE......TTEEEEESEEEE---- CS
                    HI0933_like 111 ivdallkelkeagvklrletevksvekeedgkfrvkt.k....seeeleadklvlAtGG 164
                                    ++  +l+ +k++g ++r  +ev +++ e +++  vk+ +     e elead  v AtG 
  gi|119720033|ref|YP_920528.1| 146 VILSFLASAKQRGADIRPYNEVVGFRVEGGEVKAVKVrDkvslREYELEADFFVNATGA 204
                                    66778889999**************9999999999984345555667788888888775 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.6   2.4e-05     0.024      18      58 ..       3      41 ..       1      59 [. 0.87

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.4e-05
                                   EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTT CS
                           Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailersvspGGGaw 58
                                     vv++G+G +G + ay la + +l+v++ler  s+G G+ 
  gi|119720033|ref|YP_920528.1|  3 KKVVVIGGGVTGAALAYDLALR-GLRVTLLERG-SIGSGTS 41
                                   579*******************.********85.7777765 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   1.0   2.7e-05     0.027       1      28 [.       4      31 ..       4      53 .. 0.82
   2 ?   -3.4   0.0         4     4e+03     132     154 ..     186     208 ..     165     218 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.7e-05
                                   CEEEE-SSHHHHHHHHHHHHTT--EEEE CS
                           GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi 28
                                   +v+ViGgG  G + A+ +a +G++v+L+
  gi|119720033|ref|YP_920528.1|  4 KVVVIGGGVTGAALAYDLALRGLRVTLL 31
                                   69*************************9 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 4
                                    EETTS-EEEECEEEE--TT-BT- CS
                           GIDA 132 vtedgetikakavviatGtflkg 154
                                    v  ++ +++a+ +v atG++ k 
  gi|119720033|ref|YP_920528.1| 186 VSLREYELEADFFVNATGAWAKK 208
                                    23334456667999999997665 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   3.7e-05     0.036       7      96 ..       2     118 ..       1     122 [. 0.73

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.7e-05
                  NAD_binding_7   7 gkkvlvvGgGevAarkvrklleagakvtvvapev...keele...............elvklaeeelekd.......... 58 
                                    +kkv+v+GgG  +a  ++ l+  g +vt++   +                         v++a+e+++++          
  gi|119720033|ref|YP_920528.1|   2 TKKVVVIGGGVTGAALAYDLALRGLRVTLLERGSigsG---TsgrthgllhsgcryvADVEVARECYSENvvlrriapfl 78 
                                    589**************************988864430...144555666667666655778888887776777766666 PP

                  NAD_binding_7  59 legadlviaatddrelner..iaeaakarrilvnvadkpe 96 
                                    +e+   +++a+d+ +l+ +    +++++++i+v  + ++e
  gi|119720033|ref|YP_920528.1|  79 FEKNGGIFVAVDESDLEYKdfFLKKCEEAGIPVKEVSREE 118
                                    555556666665555544434999********99998876 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   4.3e-05     0.043     165     197 ..       3      35 ..       1      44 [. 0.81

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.3e-05
                    Pyr_redox_3 165 qkvvViGgknSavDaAlelvrkgaeVtvvtrgs 197
                                    +kvvViGg+ +++  A++l+ +g +Vt++ rgs
  gi|119720033|ref|YP_920528.1|   3 KKVVVIGGGVTGAALAYDLALRGLRVTLLERGS 35 
                                    788999999999999999999999999988876 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.6   5.5e-05     0.054       1      30 [.       4      33 ..       4      45 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.5e-05
                                   EEEEE--SCCHHHHHHHHHHTT-EEEEE-S CS
                        3HCDH_N  1 kvaviGaGtmGagiaavfasagleVvlvdi 30
                                   kv viG G+ Ga +a+ +a +gl+V+l+++
  gi|119720033|ref|YP_920528.1|  4 KVVVIGGGVTGAALAYDLALRGLRVTLLER 33
                                   699************************986 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.5   0.00019      0.19       2      33 ..       5      34 ..       4      41 .. 0.94
   2 ?   -1.9   0.0       1.3   1.3e+03     218     240 ..      97     119 ..      92     122 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00019
                  Lycopene_cycl  2 vvviGaGpAglslAarlteakpglkvvlieas 33
                                   vvviG+G  g +lA  l  a  gl+v+l+e +
  gi|119720033|ref|YP_920528.1|  5 VVVIGGGVTGAALAYDL--ALRGLRVTLLERG 34
                                   8****************..**********976 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.3
                  Lycopene_cycl 218 kkrlaaylralglkvkevveeEq 240
                                    k    +++++ g+ vkev +eE 
  gi|119720033|ref|YP_920528.1|  97 KDFFLKKCEEAGIPVKEVSREEA 119
                                    5556788999***********95 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1    0.0035       3.5     192     213 ..       3      24 ..       1      35 [. 0.85
   2 ?    2.4   0.0     0.068        67     292     339 ..     156     203 ..     148     205 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0035
                    K_oxygenase 192 kriaVvGsGqSaaeifedllrr 213
                                    k+++V+G+G ++a +++dl+ r
  gi|119720033|ref|YP_920528.1|   3 KKVVVIGGGVTGAALAYDLALR 24 
                                    89****************9866 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.068
                    K_oxygenase 292 eerlrllpnrevesaeaegkgeveltlrneesgeeetlevdavvlATG 339
                                    ++ + ++p+ ev + + eg +   +++r++ s +e +le+d  v ATG
  gi|119720033|ref|YP_920528.1| 156 QRGADIRPYNEVVGFRVEGGEVKAVKVRDKVSLREYELEADFFVNATG 203
                                    45589999**********9878889**********************9 PP

>> FAD_binding_4  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.6   0.00029      0.29      63     127 ..       3      59 ..       1      64 [. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00029
                                    TTEEEEETTSBHHHHHHHHHHHTTECSSGGGTTCGSBHHHTTTTT-EETTEEGG--HHGTEEEEE CS
                  FAD_binding_4  63 egtatveaGvtlgdlvealaakglllglepgsgipgtvGGaiatnagGygsekyGlirdnvlgle 127
                                    ++++++++Gvt+++l+  la +gl +      +++g++G+ ++++++G   +       +v  +e
  gi|119720033|ref|YP_920528.1|   3 KKVVVIGGGVTGAALAYDLALRGLRVT----LLERGSIGSGTSGRTHGLLHSGC----RYVADVE 59 
                                    789********************9998....6799*************776655....5555555 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.5   0.00038      0.38       1      31 [.       5      35 ..       5      72 .. 0.84
   2 ?   -3.2   0.1       5.8   5.8e+03       5      18 ..     333     346 ..     333     349 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00038
                                   EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH CS
                           ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr 31
                                   ++++G G  G  la+ La  g  vtl+ r+ 
  gi|119720033|ref|YP_920528.1|  5 VVVIGGGVTGAALAYDLALRGLRVTLLERGS 35
                                   689************************9987 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 5.8
                                    S-SHHHHHHHHHHH CS
                           ApbA   5 GaGaiGsllaakLa 18 
                                    GaG + s++++k +
  gi|119720033|ref|YP_920528.1| 333 GAGNMASVIGGKFT 346
                                    9*********9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2441.91
//
Query:       gi|119720034|ref|YP_920529.1|  [L=523]
Description: glycerol kinase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-72  243.4   0.0    3.2e-72  243.0   0.0    1.2  1  FGGY_N    FGGY family of carbohydrate kinases, N-terminal dom
    5.4e-59  199.3   0.1    1.6e-56  191.2   0.1    2.2  2  FGGY_C    FGGY family of carbohydrate kinases, C-terminal dom


Domain annotation for each model (and alignments):
>> FGGY_N  FGGY family of carbohydrate kinases, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  243.0   0.0   3.6e-76   3.2e-72       1     245 []       4     268 ..       4     268 .. 0.96

  Alignments for each domain:
  == domain 1  score: 243.0 bits;  conditional E-value: 3.6e-76
                                    EEEEEEEESSEEEEEEEETTS-EE..EEEEEE--EB-SSTT--EE-HHHHHHHHHHHHHHHHHHCT.-GCCEEEEEEEE- CS
                         FGGY_N   1 lilglDcGttstkaivldekgkvv..asaqaelelsspkegwaeqdpeeiwqalaeairkvleqagisekqikaIgisgq 78 
                                    l+l++D+Gtt+t+a+++d +g+ v  + +++e+++++p++gw+e++p eiw+++ e+ir +++++++++ +i+aIg+++q
  gi|119720034|ref|YP_920529.1|   4 LVLVIDQGTTGTRAAIFDPEGRPVpgGWSYREHTQIYPRPGWVEHNPLEIWEKTLECIRDAVRRSKVDPGEIAAIGVTNQ 83 
                                    589***************999988445789************************************************** PP

                                    SS-EEEEETTT.EESSEEE-TT--TTHHHHHHHHHTTCHCCHHHHHSS-SSTTSHHHHHHHHHHHSCCHHCCHC....EE CS
                         FGGY_N  79 reglvllDknd.kpLynailwkdrrtaeiveklkeegnekklyektglvlstgftlsklkWlkenepevfekie....kf 153
                                    re++v++D ++ +pLynai+w+drrta+i +klke  + ++++ektgl+ +++f++sk++Wl+en+++ +ek++     f
  gi|119720034|ref|YP_920529.1|  84 RETVVVWDVRTgNPLYNAIVWQDRRTAPITDKLKE-ERLEEIREKTGLIPDPYFSGSKIQWLLENVEGLREKVArreaVF 162
                                    **********99**********************9.68899********************************999999* PP

                                    EEHHHHHHHHHCT............--EEEHHHHCTTTSEETTTTEE-HHHHHHT.T--GGGS-EEE-TC..CEEEEEEC CS
                         FGGY_N 154 lliddyLiwrLtg............qfvtdvtnasesmlfnikklewdeellail.gipeelLPklvess..eiigelkp 218
                                    ++id+++iw Lt             ++vtd++nas++mlfnik lewd+ell+++ gipe+ LP  ++ss  ei+g++ p
  gi|119720034|ref|YP_920529.1| 163 GTIDSWIIWNLTRgsrevltpekggAHVTDYSNASRTMLFNIKRLEWDPELLEAMgGIPEDSLPTPRPSSdpEIYGYTGP 242
                                    ************99**************************************99846**********998678******* PP

                                    CCCCCTT.S-EEEEEEEEEHHHHHHHH CS
                         FGGY_N 219 elaaklGlkegvpvvggggDqqaaalG 245
                                    el+  +   + + v+g +gDqqaa++G
  gi|119720034|ref|YP_920529.1| 243 ELNGIFN-GKSIAVAGDAGDQQAALFG 268
                                    *****96.78****************9 PP

>> FGGY_C  FGGY family of carbohydrate kinases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.0   0.0   0.00098       8.8      46     119 ..     136     209 ..     125     217 .. 0.79
   2 !  191.2   0.1   1.8e-60   1.6e-56       2     197 ..     278     467 ..     277     468 .. 0.96

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.00098
                         FGGY_C  46 vagslvawlldnl.glreeirdageveeslaelaaaeavadaggvvfvpafsglrapywdpdargtitglssstt 119
                                    + gs ++wll+n  glre++++ + v+++++++   ++   + + v+ p+  g + + + +++r +++++++ ++
  gi|119720034|ref|YP_920529.1| 136 FSGSKIQWLLENVeGLREKVARREAVFGTIDSWIIWNLTRGS-REVLTPEKGGAHVTDYSNASRTMLFNIKRLEW 209
                                    67999*********************9999966555555555.66677888888888888888888888877665 PP

  == domain 2  score: 191.2 bits;  conditional E-value: 1.8e-60
                         FGGY_C   2 kvslGTssflll.vgtkpvisehglltpva..gedgkpeyalegsiavagslvawlldnlglreeirdageveeslaela 78 
                                    k+++GT+ f+l+ +g +   s  gllt+v    ++g+ +yalegsi+++g++++wl+d l+l   i+ + e+ ++la   
  gi|119720034|ref|YP_920529.1| 278 KCTYGTGNFILMnTGGEIRYSRSGLLTTVFysLSKGRATYALEGSIFITGAAIQWLRDGLKL---IEVSPEI-DPLA--- 350
                                    8***********77777779*********966445899*********************999...9999999.****... PP

                         FGGY_C  79 aaeavadaggvvfvpafsglrapywdpdargtitglsssttlahiarAaleavalqlrailealekdsgkpldrlavdGG 158
                                      e++ d+gg++fvpaf+gl apywdp arg i+g++++tt  h+arA+le++a+ +r+++ea+++d g +++ l +dGG
  gi|119720034|ref|YP_920529.1| 351 --ESADDTGGLYFVPAFTGLGAPYWDPYARGLIIGITRGTTRKHLARAVLESIAYLTRDVVEAMQADAGYAVRILKADGG 428
                                    ..9***************************************************************************** PP

                         FGGY_C 159 gskndllmqllAdilgvpVerpktaeatalGaAilAava 197
                                    ++++d+l+q++Adilgv+V+rp  +e+talGaA+lA++a
  gi|119720034|ref|YP_920529.1| 429 AARSDFLLQFQADILGVDVVRPLVRETTALGAAYLAGLA 467
                                    *************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (523 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 3730.91
//
Query:       gi|119720035|ref|YP_920530.1|  [L=137]
Description: thioredoxin [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.9e-25   87.0   0.0    9.1e-25   86.6   0.0    1.1  1  Thioredoxin    Thioredoxin
    1.7e-06   28.3   0.0     0.0042   17.4   0.0    2.1  2  Thioredoxin_8  Thioredoxin-like
    8.6e-06   26.2   0.1      9e-05   22.9   0.1    2.0  1  Thioredoxin_2  Thioredoxin-like domain
     0.0001   21.8   0.0    0.00013   21.5   0.0    1.1  1  OST3_OST6      OST3 / OST6 family, transporter family
    0.00024   20.8   0.0    0.00033   20.4   0.0    1.2  1  Thioredoxin_9  Thioredoxin
     0.0012   18.9   0.0     0.0018   18.2   0.0    1.3  1  Thioredoxin_3  Thioredoxin domain
     0.0022   17.7   0.0     0.0027   17.4   0.0    1.1  1  Redoxin        Redoxin
  ------ inclusion threshold ------
      0.016   15.4   0.0      0.023   14.9   0.0    1.3  1  Thioredoxin_7  Thioredoxin-like
      0.018   14.9   0.0      0.027   14.4   0.0    1.2  1  AhpC-TSA       AhpC/TSA family
      0.034   13.9   0.0      0.045   13.5   0.0    1.2  1  KaiB           KaiB domain
      0.044   13.4   0.1       0.23   11.1   0.0    2.1  2  DUF953         Eukaryotic protein of unknown function (DUF953
      0.073   12.9   0.0      0.088   12.6   0.0    1.1  1  TraF           F plasmid transfer operon protein


Domain annotation for each model (and alignments):
>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.6   0.0   6.1e-28   9.1e-25       9      93 ..      38     121 ..      33     128 .. 0.94

  Alignments for each domain:
  == domain 1  score: 86.6 bits;  conditional E-value: 6.1e-28
                                    HHHHHHTTTSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEETTEEEEEE CS
                    Thioredoxin   9 nFeeevakekklvlveFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklfkngkevkky 88 
                                    +F+++++k  k  l +F+A+wCg+C+  +P +e+la +++++v ++kv+vden+dla +y+v +iPt+++fk gke k++
  gi|119720035|ref|YP_920530.1|  38 TFNDALSK-CKVALADFWAEWCGPCRLTEPIFEELAAKYAGRVAFLKVNVDENPDLAVQYDVMSIPTMIVFKGGKEFKRF 116
                                    79999999.9********************************************************************99 PP

                                    ESS-H CS
                    Thioredoxin  89 egare 93 
                                     g ++
  gi|119720035|ref|YP_920530.1| 117 IGYSP 121
                                    99765 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   2.8e-06    0.0042       3      46 ..      48      89 ..      45      91 .. 0.92
   2 !   11.4   0.1    0.0002       0.3      66      91 ..      84     109 ..      81     113 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.8e-06
                                   EEEEEE--SSSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-SS- CS
                  Thioredoxin_8  3 vvlLyfgaswcppckaftpklkelyeklkkkkkveivyvsldkk 46
                                   v l  f+a+wc pc+   p   el  k+    +v ++ v++d++
  gi|119720035|ref|YP_920530.1| 48 VALADFWAEWCGPCRLTEPIFEELAAKYA--GRVAFLKVNVDEN 89
                                   66778***********************9..9**********86 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.0002
                                    E-TT-HHHHTT-S--TT-SEEEEE-T CS
                  Thioredoxin_8  66 fddkkrnklkkkynvkaiPtlvvldk 91 
                                    ++ +++  l+ +y+v++iPt++v + 
  gi|119720035|ref|YP_920530.1|  84 VNVDENPDLAVQYDVMSIPTMIVFKG 109
                                    555677799*************9875 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.1     6e-08     9e-05       6     101 ..      47     121 ..      42     128 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 6e-08
                  Thioredoxin_2   6 kpvlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtPtiv 85 
                                    k  l++f++++C+ C++ +  ++el     +     +   + +  v+++ +++             la +y+v + Pt++
  gi|119720035|ref|YP_920530.1|  47 KVALADFWAEWCGPCRLTEPIFEEL---AAK-----YAGRVAFLKVNVDENPD-------------LAVQYDVMSIPTMI 105
                                    77899************99999999...333.....55556666666666555.............68**********77 PP

                  Thioredoxin_2  86 fldgkeivarlpGyvp 101
                                    ++ g +++ r  Gy p
  gi|119720035|ref|YP_920530.1| 106 VFKGGKEFKRFIGYSP 121
                                    666666999*999976 PP

>> OST3_OST6  OST3 / OST6 family, transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   8.5e-08   0.00013      46     109 ..      58     114 ..      51     130 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 8.5e-08
                      OST3_OST6  46 CelCrefepefelvakswrkdekskskklfFakvdfdegkdvFqklglnsaPhlllfppkkgpk 109
                                    C +Cr  ep fe +a  +          + F kv++de++d+  ++ + s+P +++f+  k+ k
  gi|119720035|ref|YP_920530.1|  58 CGPCRLTEPIFEELAAKYAGR-------VAFLKVNVDENPDLAVQYDVMSIPTMIVFKGGKEFK 114
                                    9**************999888.......9****************************9966544 PP

>> Thioredoxin_9  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   2.2e-07   0.00033      50     114 ..      55     116 ..      44     127 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.2e-07
                                    -TT-HHHHHHHHHHHHHH.HH-TTEEEEEE-HHHHHHHTTTTTT-SS--SSEEEEE-TT--EEEEE CS
                  Thioredoxin_9  50 edwCgDaavnvPvlakia.elnpnievkillrdenlelmdqyltngaraiPtliildeegeelgvw 114
                                    ++wCg ++ + P+++++a +++ ++ +  +  den++l  qy      +iPt+i+++ +g+e+  +
  gi|119720035|ref|YP_920530.1|  55 AEWCGPCRLTEPIFEELAaKYAGRVAFLKVNVDENPDLAVQYD---VMSIPTMIVFK-GGKEFKRF 116
                                    68*************997589999******************5...59*******95.44444444 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.2e-06    0.0018      10      55 ..      58     106 ..      45     113 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.2e-06
                                    STTCHHHHHHHHHHCHCC.T.CECEEECCTTHHHH.HHCT-SSSSEEEC CS
                  Thioredoxin_3  10 CakCpklekavkeaaaek.g.ikaevekvtdfeei.ekygVmsvPalvi 55 
                                    C  C+ +e +++e+aa+  g + +  ++v +++++  +y Vms+P++++
  gi|119720035|ref|YP_920530.1|  58 CGPCRLTEPIFEELAAKYaGrVAFLKVNVDENPDLaVQYDVMSIPTMIV 106
                                    999***************545666667779****************976 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   1.8e-06    0.0027      29     102 ..      47     128 ..      37     135 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.8e-06
                                    SEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHH...HHHHHHH.......TT-TSEEEE-TTSHHH CS
                        Redoxin  29 kkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndaf...vkefwgk.......eglkfpvlsDgsaaft 98 
                                    k+++  f++  +c++C+   p +e+la+++ ++ v ++ v++d+++    ++++++         g+ f++++  s  ++
  gi|119720035|ref|YP_920530.1|  47 KVALADFWAE-WCGPCRLTEPIFEELAAKY-AGRVAFLKVNVDENPDlavQYDVMSIptmivfkGGKEFKRFIGYSPLLA 124
                                    5667789*99.******************5.556********99998777555554444444445555666665555555 PP

                                    HHTT CS
                        Redoxin  99 kalG 102
                                    ++l+
  gi|119720035|ref|YP_920530.1| 125 RQLD 128
                                    5555 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   1.5e-05     0.023      18      81 ..      47     107 ..      36     109 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.5e-05
                                    --EEEEE--TT-HHHHHHHHHHHH-HHHHH.HHHT-EEEEESS--S-GGG.-TT---SSEEEEE CS
                  Thioredoxin_7  18 kpvlvffgaswcftCqalerdflsdeevkaalaekfvllrvdvterdanileldeqgvPvvafl 81 
                                    k  l +f a+wc++C+  e  f++    ++ +a+++++l+v+v+e+ +  +++d   +P+ +++
  gi|119720035|ref|YP_920530.1|  47 KVALADFWAEWCGPCRLTEPIFEEL--AAK-YAGRVAFLKVNVDENPDLAVQYDVMSIPTMIVF 107
                                    55688999**********9999877..666.************888874457776669999988 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.8e-05     0.027      26      77 ..      47      96 ..      35     116 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.8e-05
                                   SEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHH CS
                       AhpC-TSA 26 kpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfi 77
                                   k+++  f+++ wc +C+   p +++l+ +++   v  + v+vd+  +++ + 
  gi|119720035|ref|YP_920530.1| 47 KVALADFWAE-WCGPCRLTEPIFEELAAKYA-GRVAFLKVNVDENPDLAVQY 96
                                   6777789***.*******************9.56999999999887766555 PP

>> KaiB  KaiB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0     3e-05     0.045      29      58 ..      79     107 ..      64     131 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3e-05
                                    TEEEEEEETTTSHCHHCCTCEESCCCCCCC CS
                           KaiB  29 qyeLqvvdvleqPelaeedrlvatPaLikl 58 
                                       L+ v+v e+P+la ++ ++ +P++i  
  gi|119720035|ref|YP_920530.1|  79 VAFLK-VNVDENPDLAVQYDVMSIPTMIVF 107
                                    44444.69******************9955 PP

>> DUF953  Eukaryotic protein of unknown function (DUF953)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.9   2.8e+03      32      44 ..      22      34 ..       8      50 .. 0.65
   2 ?   11.1   0.0   0.00016      0.23      36      98 ..      56     109 ..      52     117 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.9
                                   TTS-BSSHHHHHH CS
                         DUF953 32 teGesWCPdCvka 44
                                   t G + CP+   a
  gi|119720035|ref|YP_920530.1| 22 TAGSARCPYERWA 34
                                   7788888875444 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00016
                                    BSSHHHHHHHHHHHHHHHH-SS-EEEEEEE---HHHHT-TTSHHHH..TS---SSSEEEEETS CS
                         DUF953  36 sWCPdCvkaepvieealkeapedvklvrvdvGdrevWkdpanpfRkdpklkltgvPtLlrwkg 98 
                                     WC  C   ep+ ee   + +  v +++v+v + +   d a++      + ++ +Pt++ +kg
  gi|119720035|ref|YP_920530.1|  56 EWCGPCRLTEPIFEELAAKYAGRVAFLKVNVDENP---DLAVQ------YDVMSIPTMIVFKG 109
                                    5******************************8876...33333......34455666666665 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   5.9e-05     0.088     130     211 ..      47     119 ..      40     128 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.9e-05
                           TraF 130 eygLlfFyrgkcpyceaqapilqafadky..glevraVsvdgrplpelpnarvdkgqaarlgvkrtPalvlvdpksqkvv 207
                                    +++L  F ++ c+ c+   pi +++a ky    + + V+vd++p+  l+          ++ v ++P++++++  ++   
  gi|119720035|ref|YP_920530.1|  47 KVALADFWAEWCGPCRLTEPIFEELAAKYagRVAFLKVNVDENPD--LAV---------QYDVMSIPTMIVFKGGKEFKR 115
                                    56788899999******************5556667899999988..777.........999999999999988765555 PP

                           TraF 208 pvaa 211
                                     +++
  gi|119720035|ref|YP_920530.1| 116 FIGY 119
                                    6665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.40u 0.30s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 945.60
//
Query:       gi|119720036|ref|YP_920531.1|  [L=421]
Description: ATPase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-06   28.0   0.0    3.3e-06   27.1   0.0    1.4  1  AAA_14    AAA domain
    0.00088   19.6   0.1        2.7    8.3   0.0    2.8  2  AAA_22    AAA domain
  ------ inclusion threshold ------
      0.015   15.1   0.0      0.024   14.4   0.0    1.3  1  AAA_24    AAA domain


Domain annotation for each model (and alignments):
>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0   5.6e-10   3.3e-06       4     110 ..      24     122 ..      21     145 .. 0.72

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 5.6e-10
                         AAA_14   4 ilvitGaRrvGKTtllkqlikell...vkkesilyinldderdkkladpekllelileklkeekktylflDEiqevp.ew 79 
                                     +++ G R+vGK+++++++ k      v +e  ++++ ++ ++++++      +++ eklk  +++ ++ DE q++p e+
  gi|119720036|ref|YP_920531.1|  24 WVLVYGRRKVGKSYFIRNFTKWDSyyfVGREGEIFVDSERISYEAFR------RELAEKLK--HNETVVVDEFQRLPsEF 95 
                                    5899***************8765566899999999999998887666......44666653..4567*********8359 PP

                         AAA_14  80 ekalkslvdegknldvivtGSnskllskeia 110
                                    +++l sl  +g   ++++  S+ + ls+ei 
  gi|119720036|ref|YP_920531.1|  96 SDMLHSLGTRG---RLVAV-SSTLWLSREIL 122
                                    99999999988...44444.44555555443 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0   0.00057       3.4       7      29 ..      24      46 ..      17      59 .. 0.87
   2 !    8.3   0.0   0.00045       2.7      79     111 ..      66     101 ..      55     115 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00057
                         AAA_22  7 ilvvtGesGtGKTtllrrlleql 29
                                    ++v+G   +GK++ +r++++++
  gi|119720036|ref|YP_920531.1| 24 WVLVYGRRKVGKSYFIRNFTKWD 46
                                   579******************97 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00045
                         AAA_22  79 lealeqalrarav.ielliiDEaqhlrs...eealee 111
                                    +ea+++ l ++ +  e +++DE+q+l +    ++l  
  gi|119720036|ref|YP_920531.1|  66 YEAFRRELAEKLKhNETVVVDEFQRL-PsefSDMLHS 101
                                    35666666666666677*********.7344444444 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0     4e-06     0.024       4      77 ..      24      91 ..      21     100 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4e-06
                         AAA_24  4 kiliyGpsgiGKTtlakel..gpkplfidtekGlksldadkfpdieswedfldevvelaaeladyktlviDtidel 77
                                    +l+yG  ++GK+++++++   ++  f+  e+      +d  ++i s+e+f+ e   la++l++ +t+v+D  + l
  gi|119720036|ref|YP_920531.1| 24 WVLVYGRRKVGKSYFIRNFtkWDSYYFVGREGEI---FVDS-ERI-SYEAFRRE---LAEKLKHNETVVVDEFQRL 91
                                   589****************998999999999933...3333.333.79999876...677888889****987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       705  (0.0393218); expected 358.6 (0.02)
Passed bias filter:                      616  (0.0343577); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 2662.07
//
Query:       gi|119720037|ref|YP_920532.1|  [L=129]
Description: HEPN domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-32  112.2   1.3    1.6e-32  112.1   1.3    1.0  1  HEPN          HEPN domain
  ------ inclusion threshold ------
       0.03   14.4   0.0      0.034   14.3   0.0    1.1  1  RC-P840_PscD  Photosystem P840 reaction centre protein PscD
      0.047   14.1   2.2          2    8.9   1.3    2.3  2  DUF1771       Domain of unknown function (DUF1771)
       0.16   12.3   0.0       0.36   11.2   0.0    1.6  2  DUF1548       Domain of Unknown Function (DUF1548)


Domain annotation for each model (and alignments):
>> HEPN  HEPN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.1   1.3   3.7e-36   1.6e-32       2     117 ..       6     126 ..       5     127 .. 0.96

  Alignments for each domain:
  == domain 1  score: 112.1 bits;  conditional E-value: 3.7e-36
                                    HHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHTT--.SSCCHHHHHHCCHHHT....-HHHHHHHHHH CS
                           HEPN   2 eewlrrAeedleaAellleegdydlacfhaqqaaekalKAlllkkggeppkthdlreLleelkkelke.seelreeleeL 80 
                                    + w+r+Ae+dle+A+++l ++d+d+a+f++qqaaekalKAlll+ g+   ++h+l++L+e +k el+   ++++ +l+eL
  gi|119720037|ref|YP_920532.1|   6 SLWFRQAERDLEKARNDLVTHDWDSAAFWSQQAAEKALKALLLSRGRV-YRGHSLLALAETAKSELGLsVDDIIGDLREL 84 
                                    68*********************************************7.***********999888888*********** PP

                                    HCCCHHCCCTSS--S.....--HHHHHHHHHHHHHHHHHHHH CS
                           HEPN  81 ekayiesrYpdakee.....yteedaeealkdaeevlelvee 117
                                    + +y+ srYp+a++      y+e  a+e++++a++v+e+v++
  gi|119720037|ref|YP_920532.1|  85 TVHYTISRYPNAANAfpyelYDEAKARELVERARRVVEWVRR 126
                                    **************9************************986 PP

>> RC-P840_PscD  Photosystem P840 reaction centre protein PscD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   7.5e-06     0.034      18     118 ..      29     129 .]      11     129 .] 0.87

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7.5e-06
                   RC-P840_PscD  18 sksgpwsgnavhkaekyfitsakrdrsgklqleispasgrrklsptkeliekliegeielfvlttqpdiaidlkkkvldn 97 
                                      ++ ws +a+ ka+k ++ s  r  +g+  l ++ ++     ++  ++i  l e  ++ + ++  p+ a  ++ ++ d+
  gi|119720037|ref|YP_920532.1|  29 DSAAFWSQQAAEKALKALLLSRGRVYRGHSLLALAETAKSELGLSVDDIIGDLRELTVH-YTISRYPNAANAFPYELYDE 107
                                    46899************************999999988888888999*******99998.567999************97 PP

                   RC-P840_PscD  98 .enryvidfdkrgvkwtmrdip 118
                                     + r +++  +r v w  r++p
  gi|119720037|ref|YP_920532.1| 108 aKARELVERARRVVEWVRRHLP 129
                                    36799************99987 PP

>> DUF1771  Domain of unknown function (DUF1771)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   1.3   0.00045         2       5      47 ..       2      44 ..       1      67 [. 0.92
   2 ?    4.2   0.0     0.013        57      26      44 ..     102     120 ..      93     126 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00045
                        DUF1771  5 RaeAdeharkrnelfekAaeAyrrGdgaaAkelseqGkehgek 47
                                   R+eA +  r+  + +ekA++     d  +A++ s+q+ e   k
  gi|119720037|ref|YP_920532.1|  2 REEASLWFRQAERDLEKARNDLVTHDWDSAAFWSQQAAEKALK 44
                                   9***********************************9876555 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.013
                        DUF1771  26 yrrGdgaaAkelseqGkeh 44 
                                    y+  d a+A+el+e++++ 
  gi|119720037|ref|YP_920532.1| 102 YELYDEAKARELVERARRV 120
                                    5556899*********986 PP

>> DUF1548  Domain of Unknown Function (DUF1548)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.79   3.5e+03      63      93 ..      18      49 ..       8      53 .. 0.64
   2 ?   11.2   0.0   7.9e-05      0.36       7      50 ..      57     100 ..      54     122 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.79
                        DUF1548 63 asvseLveyile.qilessqelkaalsnylle 93
                                   ++ ++Lv +  + ++  s+q  ++al+  ll+
  gi|119720037|ref|YP_920532.1| 18 KARNDLVTHDWDsAAFWSQQAAEKALKALLLS 49
                                   55667776654415566777777777777765 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 7.9e-05
                        DUF1548   7 HeitglKhlyGeeLGLivdnlakildaltlrltsrlilkkkekY 50 
                                    H + +l ++  +eLGL vd++   l +lt++ t +++++  + +
  gi|119720037|ref|YP_920532.1|  57 HSLLALAETAKSELGLSVDDIIGDLRELTVHYTISRYPNAANAF 100
                                    88889999999**********999*********99999987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       660  (0.0368119); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 878.38
//
Query:       gi|119720038|ref|YP_920533.1|  [L=114]
Description: DNA polymerase beta subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-10   41.5   0.0    1.9e-10   40.9   0.0    1.3  1  NTP_transf_2    Nucleotidyltransferase domain
    7.9e-07   29.1   0.0    1.1e-06   28.6   0.0    1.2  1  Polbeta         Polymerase beta, Nucleotidyltransferase
  ------ inclusion threshold ------
      0.043   13.6   0.3       0.28   11.0   0.3    2.0  1  DUF294          Putative nucleotidyltransferase DUF294
      0.071   12.9   0.0      0.083   12.7   0.0    1.1  1  MdcG            Phosphoribosyl-dephospho-CoA transferase MdcG
       0.14   11.9   0.0        0.2   11.4   0.0    1.2  1  DNA_pol3_delta  DNA polymerase III, delta subunit


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   0.0   5.2e-14   1.9e-10      14      86 ..      36      99 ..      25     109 .. 0.80

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 5.2e-14
                                   TSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEECEEECCCCTEEE CS
                   NTP_transf_2 14 vakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevdlvtrekledpllvk 86
                                    + ++l+GS+arG++l++SD+Dl++v++         egl++l + + f e  l  evdl++ ++ e+ +  +
  gi|119720038|ref|YP_920533.1| 36 LVGAYLVGSRARGDYLETSDVDLVLVVEGV-------EGLNALQRLELFKEV-LEPEVDLLVLSPEEW-REGR 99
                                   6789**************************.......777888888888877.888*****9999994.4433 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0   3.1e-10   1.1e-06      12      70 ..      35      91 ..      25      97 .. 0.83

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 3.1e-10
                                   HHHSTTEEEEEE-S------EEEEEEEESS---HHHHHHHHHHHHHH.SSSEEEEEETT CS
                        Polbeta 12 eielaylFGSrakgkareeSDiDlavllkekldleeelelaaelediklgkkvDlvdln 70
                                   ++  ayl GSra+g++ e SD+Dl ++++   +  + l+  + ++++ l+ +vDl++l+
  gi|119720038|ref|YP_920533.1| 35 KLVGAYLVGSRARGDYLETSDVDLVLVVEGV-EGLNALQRLELFKEV-LEPEVDLLVLS 91
                                   67789**************************.566667777778888.78899999987 PP

>> DUF294  Putative nucleotidyltransferase DUF294
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.3   7.9e-05      0.28      53      87 ..      40      74 ..       9     110 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 7.9e-05
                         DUF294 53 lvmGSeGReEqtlktDqDnalvledeeeeaareyf 87
                                   + +GS +R++ +  +D D  lv+e  e+ +a +++
  gi|119720038|ref|YP_920533.1| 40 YLVGSRARGDYLETSDVDLVLVVEGVEGLNALQRL 74
                                   568********************994444444444 PP

>> MdcG  Phosphoribosyl-dephospho-CoA transferase MdcG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.3e-05     0.083     106     179 ..      31      99 ..       3     112 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.3e-05
                           MdcG 106 glawgvyGSlgwqlatglpylhesSDLDLlirvasalqlarlldllaaleaa.avrlDgeielpsggavalrEla 179
                                    g  ++++G       +  +yl e+SD+DL++ v+  + l++l + l+ +++  ++ +D+ +  p+    ++rE  
  gi|119720038|ref|YP_920533.1|  31 GRGFKLVGAYLVGSRARGDYL-ETSDVDLVLVVEGVEGLNAL-QRLELFKEVlEPEVDLLVLSPE----EWREGR 99 
                                    556666666666666666777.68*********999987665.55677777736*******9999....777755 PP

>> DNA_pol3_delta  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   5.5e-05       0.2      78     119 ..      69     111 ..      54     113 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.5e-05
                                    THHHHHHHHTTT--SSEEEEEEES.S--HHHH.HHHHHTTTEE CS
                 DNA_pol3_delta  78 kllkeLeeylsnlpedtlLiliapkklderkk.lvklLkkkat 119
                                    + l++Le + + l +++ L++ +p++ +e ++ +v +Lkk+a+
  gi|119720038|ref|YP_920533.1|  69 NALQRLELFKEVLEPEVDLLVLSPEEWREGRSaWVETLKKEAV 111
                                    7899********************888888888*******996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 797.98
//
Query:       gi|119720039|ref|YP_920534.1|  [L=237]
Description: hydrolase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.2e-09   35.8   0.0    1.2e-08   35.3   0.0    1.2  1  HAD_2            Haloacid dehalogenase-like hydrolase
      3e-06   27.7   0.1    3.9e-05   24.0   0.1    2.1  1  Hydrolase        haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.014   15.5   0.0      0.027   14.5   0.0    1.5  1  Hydrolase_like   HAD-hyrolase-like
      0.049   13.2   0.0       0.37   10.3   0.0    2.0  2  Acid_phosphat_B  HAD superfamily, subfamily IIIB (Acid phosph
      0.063   13.4   0.0         15    5.8   0.0    2.4  2  Hydrolase_6      Haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.0   3.3e-12   1.2e-08       3     178 .]      16     206 ..      15     206 .. 0.86

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 3.3e-12
                          HAD_2   3 FDlDgTlldteeliiqafnelleey.....glselseeelrkliglslrellrklgeseeeee...........kieell 66 
                                    FD+DgTlld+ +++ ++++ ll         l+ ++++ +r+ + l+ r ++++ +     ee           +++e+ 
  gi|119720039|ref|YP_920534.1|  16 FDVDGTLLDSYTYMRDVLQILLLYIgvpagMLEMVTDDVYRSWYDLEKRGVFDYGKMHLFLEEfarkyavpvryDVKEFQ 95 
                                    9******************9998777777544578899999***************999999999999999888888888 PP

                          HAD_2  67 rkyneekkkkevkpydgvkelLeeLkeagyklgivTsk..sreaveekleqlgiesyFdvivtsedvekkKPdpevieka 144
                                    +   e   k   +py  + +lL eLk++g  +  v+ +     + ++ +e+    ++Fd+i++  +   +    e ++++
  gi|119720039|ref|YP_920534.1|  96 DLLLEARVK-GSEPYRCAVKLLSELKKRGKIVVSVSGGdgVPGMKRRRIEEGVPVKLFDKILVVPEDAPS--RVEALNAV 172
                                    888888888.***************888877766776623456788888888888******877655555..39****** PP

                          HAD_2 145 leklklkkeeviyvGDsptDieaakkagikviav 178
                                     e++++++eev+ v D p+    a  ag k+++v
  gi|119720039|ref|YP_920534.1| 173 REEFGVSNEEVLHVDDRPQHAAEAYSAGFKAMVV 206
                                    ****************************999876 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.1   1.1e-08   3.9e-05       1     206 [.      11     196 ..      11     200 .. 0.71

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1.1e-08
                                    SSEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHH.HHHH.HHHHHETTTEHHHHTHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx.xxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase   1 iktvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakar.sgal.tgfatfigrgayaigkpewlt 78 
                                    +k++ fD+dGTL+++    +dv++ +               +   + a   ++ + ++  ++  ++ rg++  gk  ++ 
  gi|119720039|ref|YP_920534.1|  11 VKVFSFDVDGTLLDSYTYMRDVLQIL--------------LLYIGVPAGMLEMvTDDVyRSWYDLEKRGVFDYGKMHLFL 76 
                                    68999*********************..............3333453333333555555888889999999999999888 PP

                                    HHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHH.TT. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx. RF
                      Hydrolase  79 aldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanq.lG. 156
                                    ++       a+ ++   +     +++  + a ++ ++   ++  a++++ +Lk++g  vv ++g++  + ++  +   G 
  gi|119720039|ref|YP_920534.1|  77 EE------FARKYAVPVRYDVKEFQDLLLEARVKGSE---PYRCAVKLLSELKKRGKIVVSVSGGDGVPGMKRRRIeEGv 147
                                    88......55555555555555555434445555554...6**************888*****99887777444443675 PP

                                    .GGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHH CS
                                    .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase 157 .ddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgvnDaaal 206
                                      + fd ++ + +++ +    e+++a+ +e++++ eev++V+D++  aa +
  gi|119720039|ref|YP_920534.1| 148 pVKLFDKILVVPEDAPS--RVEALNAVREEFGVSNEEVLHVDDRPQHAAEA 196
                                    55555555555555544..5599********************99876655 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   7.6e-06     0.027       9      55 ..     168     213 ..     163     230 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 7.6e-06
                                    HHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESSSSS-T CS
                 Hydrolase_like   9 mydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVltGvtrp 55 
                                    ++ + +e++g+  eevl + Dr  +  a A  aG k + V+tG ++p
  gi|119720039|ref|YP_920534.1| 168 ALNAVREEFGVSNEEVLHVDDR-PQHAAEAYSAGFKAMVVKTGFYDP 213
                                    567889999*************.677999****************98 PP

>> Acid_phosphat_B  HAD superfamily, subfamily IIIB (Acid phosphatase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0    0.0001      0.37      72      92 ..      10      30 ..       3      35 .. 0.84
   2 ?    0.2   0.0      0.13   4.6e+02     113     140 ..     104     131 ..      83     133 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0001
                                   SEEEEEE--BTTTEEHHHHHH CS
                Acid_phosphat_B 72 kkdavvfDiDeTvLsnspYqk 92
                                   + +++ fD+D T+L+++ Y +
  gi|119720039|ref|YP_920534.1| 10 EVKVFSFDVDGTLLDSYTYMR 30
                                   47899**************65 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.13
                                    TGGCCECCHHHHHHHHHHTTEEEEEEEE CS
                Acid_phosphat_B 113 geakaipgalelikkvverGvkiffvsg 140
                                    + +++ + a++l+ ++++rG  ++ vsg
  gi|119720039|ref|YP_920534.1| 104 KGSEPYRCAVKLLSELKKRGKIVVSVSG 131
                                    344677779***********99999987 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.007        25       1      22 [.      14      35 ..      14      40 .. 0.83
   2 ?    5.8   0.0    0.0041        15      11      39 ..     104     132 ..      95     151 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.007
                                   EEEESTTTSEETTEE-TTHHHH CS
                    Hydrolase_6  1 flfDidGvLwrgdkaipgaaea 22
                                   f fD+dG+L++ ++ +  + ++
  gi|119720039|ref|YP_920534.1| 14 FSFDVDGTLLDSYTYMRDVLQI 35
                                   569********99988877665 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0041
                                    ETTEE-TTHHHHHHHHHHTT-EEEEEE-- CS
                    Hydrolase_6  11 rgdkaipgaaealnalraagkpvvllTNn 39 
                                    +g++++  a+++l  l+++gk vv ++ +
  gi|119720039|ref|YP_920534.1| 104 KGSEPYRCAVKLLSELKKRGKIVVSVSGG 132
                                    78999*****************9999866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1660.82
//
Query:       gi|119720040|ref|YP_920535.1|  [L=288]
Description: protein of unknown function DUF340, membrane [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.1e-40  136.8  14.6    6.1e-40  136.8  14.6    1.8  2  Lys_export       Lysine exporter LysO
  ------ inclusion threshold ------
       0.15   10.9   0.1        1.9    7.3   0.4    2.1  2  Chlorophyllase2  Chlorophyllase enzyme


Domain annotation for each model (and alignments):
>> Lys_export  Lysine exporter LysO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   1.3      0.14   1.2e+03       3      74 ..      12      79 ..      10      88 .. 0.56
   2 !  136.8  14.6   6.8e-44   6.1e-40       2     189 ..     101     284 ..      99     285 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.14
                     Lys_export  3 aliaGillGllllleaelleeelseylLylLlflvGislgss.kelleklkklnlkllllplatilgsllggl 74
                                   +++a +++G +l+l+     + + ++   +L+  +    +ss  e l+   +l   ll+l+++++   +lg+l
  gi|119720040|ref|YP_920535.1| 12 VFVASVVVGRALRLSL---PKAFFDVSVGVLVWAISAWAASSgLEALKY--SLAQTLLFLAAIVCYVVVLGAL 79
                                   6777777777666654...556666667777777766666664443333..4555555555444444444443 PP

  == domain 2  score: 136.8 bits;  conditional E-value: 6.8e-44
                     Lys_export   2 laliaGillGllllleaelleeelseylLylLlflvGislgsskelleklkklnlkllllplatilgsllggllaalllg 81 
                                    +++++G++ Gl+   +   + +e+  +l ++ ++  G++++s  + +++l++ ++ +l   ++t+++++l+gl +a llg
  gi|119720040|ref|YP_920535.1| 101 ALIAVGWASGLSA-GWLRPYLSEALPVLVLAVIAATGLTMHSALS-VASLRRGGVVALKAVAVTLASAVLAGLTVAALLG 178
                                    5667888888843.3445677788888888888999****99988.566799**************************** PP

                     Lys_export  82 lslkeslavasGfGwYSLsgilitelkgaelGtiallanllREllalllipllakrfgklaaisvaGatsmDttLPiitk 161
                                    ls + +l+v++G+GwYS++g ++++++g+e G +a+l+n+lRE+l++ l+p++ ++  +++ais++Gat+mD tLP+++ 
  gi|119720040|ref|YP_920535.1| 179 LSPHYALSVTLGLGWYSFAGSFVAQFLGPEQGFTAFLVNILREQLTFALVPVISRF--RVSAISLGGATTMDNTLPVYAY 256
                                    *****************************************************996..6679****************** PP

                     Lys_export 162 ssgkevvvlaivhGvilsllvPilvslf 189
                                    ++g ++vv +ivhG++l++lvP+l +l+
  gi|119720040|ref|YP_920535.1| 257 VYGDDAVVPSIVHGFLLTFLVPFLEALV 284
                                    ***********************97765 PP

>> Chlorophyllase2  Chlorophyllase enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.4   0.00021       1.9      70     127 ..     113     182 ..     108     189 .. 0.75
   2 ?    0.7   0.0     0.023     2e+02      71     108 ..     213     250 ..     208     256 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00021
                Chlorophyllase2  70 lnWlakgLesvlpeevepdlsklalsgHS........rGgktaf.alalgkaktsl...kfsaligvdPv 127
                                    + Wl  +L+++lp  v + +  ++l+ HS        rGg +a+ a+a+  a++ l   +++al+g+ P 
  gi|119720040|ref|YP_920535.1| 113 AGWLRPYLSEALPVLVLAVIAATGLTMHSalsvaslrRGGVVALkAVAVTLASAVLaglTVAALLGLSPH 182
                                    57***********999999999999999966666666798887523455555533345599999999996 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.023
                Chlorophyllase2  71 nWlakgLesvlpeevepdlsklalsgHSrGgktafala 108
                                      l + L+++l+  ++p +s++ +s+ S Gg t ++ +
  gi|119720040|ref|YP_920535.1| 213 AFLVNILREQLTFALVPVISRFRVSAISLGGATTMDNT 250
                                    5678889999*********************9988755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       750  (0.0418317); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2127.43
//
Query:       gi|119720041|ref|YP_920536.1|  [L=364]
Description: major facilitator transporter [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.8e-12   45.2  47.6      7e-10   38.3  37.5    2.1  2  MFS_1       Major Facilitator Superfamily
    5.1e-05   22.3   9.2    0.00072   18.5   0.9    2.2  2  MFS_1_like  MFS_1 like family
  ------ inclusion threshold ------
        2.4    6.9  12.5       0.87    8.4   8.2    2.2  2  Sugar_tr    Sugar (and other) transporter


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.3  37.5   1.2e-13     7e-10       5     322 ..      10     292 ..       6     304 .. 0.79
   2 !   14.7   6.3   1.8e-06     0.011      70     172 ..     257     351 ..     249     363 .. 0.82

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 1.2e-13
                          MFS_1   5 aflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll.fas 83 
                                     f ++l  s+ +p+l  +++ +lg++++e+gl++++ ++++++++l+ ++l+ r+G  +++ll+l+++a g ++ll  ++
  gi|119720041|ref|YP_920536.1|  10 SFSMSLLQSLMIPVLV-LYMLQLGYTEAEVGLVTGTASAVYIAGALLSSVLAGRLGDSKTILLSLASMATG-YALLsAST 87 
                                    5667777788888888.66699*************************************************.44442348 PP

                          MFS_1  84 slw.lllvlrv.lqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivs 161
                                    +l+ +ll++ v l G+  g+++pa+  l++    k      ++ +s ++s G++ g+ll   l+ +l  ra++ ++ + s
  gi|119720041|ref|YP_920536.1|  88 GLYaILLASGVvLLGF--GVFWPAVENLVSSSGGK------VSAFSFSWSSGSLAGMLLVYPLS-LLDPRALYAAFSASS 158
                                    8887777777635555..57*********998777......999999************99999.99************* PP

                          MFS_1 162 llafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlgls 241
                                    ll+++    + + e+++r+r +  +             +++l + +  w +l+++++     sgl t+ p+ l+e+ gl+
  gi|119720041|ref|YP_920536.1| 159 LLLAL---SVRRGEERARARATFGDV------------LSSLYSLRASW-VLCVAYSL--SSSGLITFYPV-LVERAGLP 219
                                    ***88...888888888888877666............56666666333.45555555..7899*******.5******* PP

                          MFS_1 242 glllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvliGfglgfvfpsl 321
                                      ++++  lal+ ++    a+++++  d l++ +   + +++   ++l+  l+++ ++++l+l +++++G g+g++++++
  gi|119720041|ref|YP_920536.1| 220 -RFMLS--LALFLMILSRTAVFFAY--DALPA-PLKRVEIAAP--VLLASSLIPFVDNPFLHLPLSLIAGAGQGVIYGIA 291
                                    .67777..77777777666777777..66443.4444555444..44555555566669999999999******998876 PP

                          MFS_1 322 l 322
                                    l
  gi|119720041|ref|YP_920536.1| 292 L 292
                                    5 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 1.8e-06
                          MFS_1  70 llfalglllllfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg 149
                                    +l+a++ l+++ + + +l+l l +++G+g+g+++ +++  + +  ++ +   +++l+ +++++G+ lgpll++ll +++g
  gi|119720041|ref|YP_920536.1| 257 VLLASS-LIPF-VDNPFLHLPLSLIAGAGQGVIYGIALEGVFKSGSD-RVHNYTALFESFIGAGYSLGPLLAALLGEYAG 333
                                    666777.7777.477679************99999999888888888.9999**************************** PP

                          MFS_1 150 Wravfyilaivsllafvlfllll 172
                                     + +     ++sl a++      
  gi|119720041|ref|YP_920536.1| 334 LQPLLSTSLLASLAALL-----A 351
                                    99998888888888833.....3 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.9   1.2e-07   0.00072      16      71 ..      18      73 ..       4     100 .. 0.82
   2 !    8.4   1.6   0.00015      0.87     184     371 ..     149     326 ..     120     337 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.2e-07
                     MFS_1_like 16 gsllPYltiylkskglkaseigiitlilpltsilsppiwgvlaDrfgkrkkvvils 71
                                   + ++P l +y+ + g++ +e+g++t  + ++ i+++++ +vla r+g  k++++  
  gi|119720041|ref|YP_920536.1| 18 SLMIPVLVLYMLQLGYTEAEVGLVTGTASAVYIAGALLSSVLAGRLGDSKTILLSL 73
                                   6688**********************************************976432 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00015
                     MFS_1_like 184 yvlaallvisllvvlilnetekesklkvtkslqvllnilknpeviifllvalilgmswgiienFlflYLkelgasntllG 263
                                    +++aa+   sll++l++  +e       t + +vl  + + +  ++++++  +   s++ + +F+ +  +  g ++++l+
  gi|119720041|ref|YP_920536.1| 149 ALYAAFSASSLLLALSVRRGEERARARAT-FGDVLSSLYSLRASWVLCVAYSL---SSSGLITFYPVLVERAGLPRFMLS 224
                                    57888888888888888888777776666.34555555555555555555443...4555568999999*********** PP

                     MFS_1_like 264 slvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaiienawlvlpievLhgisfgllwaaaveyvskiap 343
                                     +++l  ++   +ff    l   l  v+  i+a ++ +   +l+ +++n+ l lp+ ++ g+  g+++++a e v k  +
  gi|119720041|ref|YP_920536.1| 225 LALFLMILSRTAVFFAYDALPAPLKRVE--IAAPVLLAS--SLIPFVDNPFLHLPLSLIAGAGQGVIYGIALEGVFKSGS 300
                                    ********************88775555..555555544..678999*****************************9999 PP

                     MFS_1_like 344 ksleatgqgllsglyfglGralGsliGG 371
                                    +++   + +l++++ +g+G  lG l++ 
  gi|119720041|ref|YP_920536.1| 301 DRVH-NYTALFESF-IGAGYSLGPLLAA 326
                                    8886.688999998.7888888887764 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   8.2   0.00014      0.87      46     116 ..      36     105 ..      27     164 .. 0.87
   2 ?   -0.5   0.1     0.072   4.3e+02      46      88 ..     305     347 ..     286     352 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00014
                                    .HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHH CS
                       Sugar_tr  46 vlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigv 116
                                      +gl+++ ++++ i+G+l+++ l+ r+G  k++l + + +  g +l  a++g     +l+ g vl+G+gv
  gi|119720041|ref|YP_920536.1|  36 AEVGLVTGTASAVYIAGALLSSVLAGRLGDSKTILLSLASMATGYALLSASTGL-YAILLASGVVLLGFGV 105
                                    5689************************************************55.4445555688888887 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.072
                                    .HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHH CS
                       Sugar_tr  46 vlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvi 88 
                                     ++ l+ s+  +G  +G l+a llg++ G ++ l ++ + +++
  gi|119720041|ref|YP_920536.1| 305 NYTALFESFIGAGYSLGPLLAALLGEYAGLQPLLSTSLLASLA 347
                                    56788889999999****************9988887766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      196  (0.010932); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2363.53
//
Query:       gi|119720042|ref|YP_920537.1|  [L=334]
Description: ABC transporter related [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.3e-29  100.8   0.0    1.5e-28  100.0   0.0    1.4  1  ABC_tran      ABC transporter
    8.1e-15   55.4   0.3    4.7e-09   36.5   0.0    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    2.5e-08   34.5   0.0    5.7e-08   33.4   0.0    1.7  1  DUF4162       Domain of unknown function (DUF4162)
    9.5e-05   22.1   0.3    0.00019   21.1   0.3    1.4  1  AAA_29        P-loop containing region of AAA domain
    0.00097   18.9   0.0        1.5    8.5   0.0    2.1  2  AAA_15        AAA ATPase domain
     0.0013   18.2   0.0       0.52    9.7   0.0    2.2  2  SMC_N         RecF/RecN/SMC N terminal domain
     0.0022   17.9   0.0     0.0037   17.2   0.0    1.3  1  Rad17         Rad17 P-loop domain
      0.004   17.5   0.1       0.01   16.3   0.1    1.8  1  AAA_16        AAA ATPase domain
     0.0065   16.2   0.0        1.3    8.7   0.0    2.3  2  IstB_IS21     IstB-like ATP binding protein
     0.0077   15.2   0.3      0.027   13.5   0.1    1.9  2  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
     0.0086   16.6   0.0      0.012   16.1   0.0    1.3  1  AAA_23        AAA domain
  ------ inclusion threshold ------
       0.01   16.1   0.0       0.11   12.8   0.0    2.3  1  AAA_22        AAA domain
      0.012   16.1   0.0      0.064   13.7   0.0    2.3  1  AAA           ATPase family associated with various cellular 
      0.029   14.0   0.5       0.69    9.5   0.1    2.7  3  AAA_27        AAA domain
      0.034   14.1   0.0       0.11   12.4   0.0    1.8  2  RsgA_GTPase   RsgA GTPase
      0.046   13.8   0.1       0.12   12.5   0.1    1.6  1  DUF87         Helicase HerA, central domain
      0.073   13.1   0.1        1.1    9.3   0.0    2.2  2  AAA_5         AAA domain (dynein-related subfamily)
      0.089   12.5   0.2       0.42   10.3   0.1    2.1  1  AAA_30        AAA domain
      0.091   12.6   0.0       0.17   11.7   0.0    1.4  1  MukB          MukB N-terminal
       0.11   11.9   0.0       0.22   10.9   0.0    1.4  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
       0.12   12.9   0.0       0.28   11.8   0.0    1.7  1  AAA_18        AAA domain
       0.14   12.0   0.2       0.97    9.3   0.0    2.1  2  NACHT         NACHT domain
       0.15   10.9   0.1       0.31    9.9   0.0    1.5  2  AAA_PrkA      PrkA AAA domain
       0.16   10.6   0.0        1.1    7.8   0.0    1.9  2  AAA_13        AAA domain
       0.18   12.2   0.0        0.3   11.5   0.0    1.5  1  RNA_helicase  RNA helicase


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.0   0.0   2.1e-31   1.5e-28       1     136 [.      32     176 ..      32     177 .. 0.96

  Alignments for each domain:
  == domain 1  score: 100.0 bits;  conditional E-value: 2.1e-31
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltvren 79 
                                    lk vsl+  +ge+++i+G+nGaGKStL+k+la ll p++G  ++ g d+ + e+ ++rk igv     + +f++lt ren
  gi|119720042|ref|YP_920537.1|  32 LKGVSLTAVKGEVLGILGPNGAGKSTLVKILATLLLPDSGYARIMGFDVVS-ERDEVRKLIGVSLSVeKGFFYKLTGREN 110
                                    789**********************************************99.89999999998665559*********** PP

                                    .............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    .............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 .............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                 + +e+++++l+ +gl+  +d+      +++S G+k r+++arall++p++l+lDEpt
  gi|119720042|ref|YP_920537.1| 111 lkyfgmlygldgkALEERVNEVLRDVGLQPYADKLY----EEMSLGMKARLSIARALLTDPPVLILDEPT 176
                                    ************9999**************999999....*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   5.2e-06    0.0037       3      22 ..      46      65 ..      44      98 .. 0.85
   2 !   36.5   0.0   6.6e-12   4.7e-09     235     299 ..     147     209 ..     125     212 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5.2e-06
                         AAA_21  3 vliGpNgsGKSnLLdaldll 22
                                   ++ GpNg+GKS+L ++l  l
  gi|119720042|ref|YP_920537.1| 46 GILGPNGAGKSTLVKILATL 65
                                   799**************877 PP

  == domain 2  score: 36.5 bits;  conditional E-value: 6.6e-12
                         AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTHSp 299
                                     e+S G+k  l ++ all ++   ++l++DEp +gL+P   rr+  ll ++++++g  v++tTH+ 
  gi|119720042|ref|YP_920537.1| 147 EEMSLGMKARLSIARALLTDP---PVLILDEPTLGLDPVSARRIRSLLtSLAHSKGKTVLVTTHNM 209
                                    589*******99999999999...**************999999988855555589********96 PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.0   7.9e-11   5.7e-08       3      80 ..     233     326 ..     232     327 .. 0.76

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 7.9e-11
                                    HHHHHTTS-SSEEE.EE......--.-----..---EEE..E-TT..S-EEEEE-..-.-----------.----EEEEE CS
                        DUF4162   3 leeiKrsygknrie.ve......ad.aeelleepgveev..eeeg..gelelkle..d.eeaanellkal.tsgveirsF 66 
                                    ++ +K++ +   +  ++       + +  l+++pgve+    ++g  +++++ ++  + eea +++l++l ++g+++rs+
  gi|119720042|ref|YP_920537.1| 233 VDSLKKRVADSVFLeIRiaglagLQvQNVLRNVPGVEVRtaHRKGlgDKVVVSVPvaHaEEAFERVLHELrSAGLKVRSI 312
                                    78888888888777788877655224777778899777743444476666666555577***********88******** PP

                                    EEE---HHHHHHHH CS
                        DUF4162  67 eeeePsLndIFiek 80 
                                    + +ePsL+d+Fi++
  gi|119720042|ref|YP_920537.1| 313 SIVEPSLEDVFIKL 326
                                    ************96 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.3   2.6e-07   0.00019      22      50 ..      41      70 ..      31      74 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2.6e-07
                         AAA_29 22 kg.atlltGpsGsGKSTllDAiqalLvpak 50
                                   kg +  + Gp+G+GKSTl+  +++lL+p++
  gi|119720042|ref|YP_920537.1| 41 KGeVLGILGPNGAGKSTLVKILATLLLPDS 70
                                   4556779*********************87 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0021       1.5      28      48 ..      47      67 ..      36     105 .. 0.85
   2 !    8.4   0.0    0.0021       1.5     323     365 ..     166     208 ..     147     210 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0021
                         AAA_15 28 liGkNnsGKSsilealdlFln 48
                                   + G+N++GKS+++++l  +l 
  gi|119720042|ref|YP_920537.1| 47 ILGPNGAGKSTLVKILATLLL 67
                                   78**************88775 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0021
                         AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                    ++ +l+++EP + L p   + +  ll +la ++ + v++tTH+
  gi|119720042|ref|YP_920537.1| 166 DPPVLILDEPTLGLDPVSARRIRSLLTSLAHSKGKTVLVTTHN 208
                                    456899************************************8 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0   0.00073      0.52      23      42 ..      41      60 ..      24      70 .. 0.82
   2 !    6.4   0.0    0.0076       5.5     136     201 ..     148     209 ..     106     225 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00073
                                   TSSEEEEEESTTSSHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 23 sksftaivGpNGSGKsnlld 42
                                   + ++  i+GpNG+GKs l+ 
  gi|119720042|ref|YP_920537.1| 41 KGEVLGILGPNGAGKSTLVK 60
                                   556778**********9986 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0076
                                    CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHH..HHCTTSEEEEE-SSHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxx RF
                          SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellk..eksknaQfivislreem 201
                                    ++S G k+     L +A       p+ +lDe    LD    +++ +ll   ++sk   ++v++++  m
  gi|119720042|ref|YP_920537.1| 148 EMSLGMKAR----LSIARALLTDPPVLILDEPTLGLDPVSARRIRSLLTslAHSKGKTVLVTTHN--M 209
                                    555555553....334455567789***********************94445666778888775..3 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   5.2e-06    0.0037      33      69 ..      30      66 ..      22      74 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 5.2e-06
                          Rad17 33 ewlkadvLesrkkriLLisGPsGCgkstvvkvLskel 69
                                   e+lk  +L   k ++L i GP G gkst vk+L+  l
  gi|119720042|ref|YP_920537.1| 30 EALKGVSLTAVKGEVLGILGPNGAGKSTLVKILATLL 66
                                   6899999****99********************9766 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   1.4e-05      0.01      20     125 ..      40     193 ..      25     262 .. 0.60

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.4e-05
                         AAA_16  20 rsgrpelvllsGesGvGKsslvrellralekd.............................ggiflrgkcdqlesaipys 70 
                                     +g  e++ + G+ G GKs+lv+ l++ l  d                             +g+f + + +++   + y 
  gi|119720042|ref|YP_920537.1|  40 VKG--EVLGILGPNGAGKSTLVKILATLLLPDsgyarimgfdvvserdevrkligvslsveKGFFYKLTGREN---LKYF 114
                                    444..78889*****************9999944444444433333333333333333332222222222222...4444 PP

                         AAA_16  71 alaqalareellrqlldeaesaeleawrekleeala........................avpelagaeasrllellkr 125
                                      +  l+ + l + +++ +++  l+++++kl e+++                        ++  l++ +a+r++ ll++
  gi|119720042|ref|YP_920537.1| 115 GMLYGLDGKALEERVNEVLRDVGLQPYADKLYEEMSlgmkarlsiaralltdppvlildePTLGLDPVSARRIRSLLTS 193
                                    4333333333333333335556666666666666665555555555555554444444443333444444444444444 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0    0.0019       1.3      30      68 ..      24      63 ..       9      72 .. 0.81
   2 ?    5.1   0.0     0.023        16     102     149 ..     160     209 ..     142     219 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0019
                      IstB_IS21 30 ldkrkvkeLatlsfiekk.enivllGpsGvGKshlaialg 68
                                   +++++v++L + s ++ k e + +lGp G+GKs l   l+
  gi|119720042|ref|YP_920537.1| 24 VEETRVEALKGVSLTAVKgEVLGILGPNGAGKSTLVKILA 63
                                   67889999999999985516777**********9987665 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.023
                      IstB_IS21 102 alkrllkvdllilDd..lgllpldqaeaellfeviekryerrsiiitsnl 149
                                    a + l+ + +lilD+  lgl p++    + l+  +++  +++ ++ t n+
  gi|119720042|ref|YP_920537.1| 160 ARALLTDPPVLILDEptLGLDPVSARRIRSLLTSLAHSKGKTVLVTTHNM 209
                                    444577889*****97789***************9999998877666665 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.1   3.8e-05     0.027      17      55 ..      30      68 ..      12      86 .. 0.79
   2 ?   -1.2   0.0       1.1   7.7e+02      37      68 ..     286     318 ..     271     321 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.8e-05
                                   HHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHC CS
                           MeaB 17 ellerllakaGraqvvGltGvPGaGkstlvealglelrr 55
                                   e l+ ++ +a + +v+G+ G  GaGkstlv+ l++ l  
  gi|119720042|ref|YP_920537.1| 30 EALKGVSLTAVKGEVLGILGPNGAGKSTLVKILATLLLP 68
                                   45777788889999*****************99988764 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.1
                                    -TTSSHHHHHHHHHHHHHCTT--EEEEE.E--- CS
                           MeaB  37 vPGaGkstlvealglelrrrGkrvavla.vDPs 68 
                                    vP a    + e++  elr++G +v  ++ v+Ps
  gi|119720042|ref|YP_920537.1| 286 VPVAHAEEAFERVLHELRSAGLKVRSISiVEPS 318
                                    566666667899999999***999766515665 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.7e-05     0.012      23      43 ..      46      66 ..      34     113 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.7e-05
                         AAA_23 23 lItGpNGaGKTTildAiklaL 43
                                    I GpNGaGK+T++  +   L
  gi|119720042|ref|YP_920537.1| 46 GILGPNGAGKSTLVKILATLL 66
                                   69***********99887766 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00015      0.11       9     131 ..      46     207 ..      40     212 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00015
                         AAA_22   9 vvtGesGtGKTtllrrlleqldeeakaee..................................erpevvfvtlpsst.ss 53 
                                     + G+ G+GK+tl++ l+  l  ++  ++                                  e+ +++ +    ++  +
  gi|119720042|ref|YP_920537.1|  46 GILGPNGAGKSTLVKILATLLLPDSGYARimgfdvvserdevrkligvslsvekgffykltgrENLKYFGMLYGLDGkAL 125
                                    588***************99976666665889999998875555555555555555555544333333322222222234 PP

                         AAA_22  54 kdllrellralglelkaerlsseellealeqalrarav...ielliiDEaqh.lrseealeeLrsllnl.srkgvqliLv 128
                                    ++  +e+lr++gl+  a  l +e  l + ++ + ara    +++li+DE    l  +   + +rsll   ++++ + +Lv
  gi|119720042|ref|YP_920537.1| 126 EERVNEVLRDVGLQPYADKLYEEMSLGMKARLSIARALltdPPVLILDEPTLgL-DPVSARRIRSLLTSlAHSKGKTVLV 204
                                    444555555555555553333333335555555555557899999999988888.6666666666665555777777777 PP

                         AAA_22 129 Gtp 131
                                     t+
  gi|119720042|ref|YP_920537.1| 205 TTH 207
                                    766 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   8.9e-05     0.064       3      66 ..      47     174 ..      45     224 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8.9e-05
                                    EESSTTSSHHHHHHHHHHHH..THEEEEEETTTCSSS........................................... CS
                            AAA   3 lyGppGtGKTllakavakel..gvefleisgsellsk........................................... 37 
                                    + Gp G GK++l+k +a+ l  ++ + +i g +++s+                                           
  gi|119720042|ref|YP_920537.1|  47 ILGPNGAGKSTLVKILATLLlpDSGYARIMGFDVVSErdevrkligvslsvekgffykltgrenlkyfgmlygldgkale 126
                                    57*****************8665667777777777555667776666666666666666666666677777777777777 PP

                                    ..................STTHHHHHHHHHHHHHHHTS.TSEEEEEET CS
                            AAA  38 ..................yvgesekkirelfkeakeka.kpsilfiDE 66 
                                                      + +e++  +++ ++ a++   +p +l++DE
  gi|119720042|ref|YP_920537.1| 127 ervnevlrdvglqpyadkLYEEMSLGMKARLSIARALLtDPPVLILDE 174
                                    777777777777777777677777777777777776666677777777 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1   0.00096      0.69      31      50 ..      47      66 ..      33      68 .. 0.83
   2 ?    1.2   0.0      0.33   2.4e+02     105     139 ..     100     134 ..      80     139 .. 0.80
   3 ?   -1.1   0.0       1.6   1.2e+03      68     114 ..     256     302 ..     252     307 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00096
                         AAA_27 31 iyGpNEAGKstalrAisdll 50
                                   i+GpN AGKst+++ +  ll
  gi|119720042|ref|YP_920537.1| 47 ILGPNGAGKSTLVKILATLL 66
                                   89**********99888876 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.33
                         AAA_27 105 evlaallggldretFealFgLdherLreGGealle 139
                                      + +l+g  + + F  l+gLd ++L+e  +++l+
  gi|119720042|ref|YP_920537.1| 100 GFFYKLTGRENLKYFGMLYGLDGKALEERVNEVLR 134
                                    55666777777889************998888876 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1.6
                         AAA_27  68 LrigavleeadgeelefaRrkgrkktlldaddqalpeevlaallggl 114
                                    L+++ vl++  g e++ a rkg  ++++ +   a +ee+++++l++l
  gi|119720042|ref|YP_920537.1| 256 LQVQNVLRNVPGVEVRTAHRKGLGDKVVVSVPVAHAEEAFERVLHEL 302
                                    89999999999999999999999999999999999999999988876 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00015      0.11      95     120 ..      38      63 ..       7      74 .. 0.83
   2 ?   -2.5   0.0       5.7   4.1e+03      61      85 ..     291     315 ..     282     330 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00015
                                    HHCTTSEEEEECSTTSSHHHHHHHHC CS
                    RsgA_GTPase  95 ellkdktsvlvGqSGvGKStLinall 120
                                    +++k+++  ++G+ G+GKStL++ l+
  gi|119720042|ref|YP_920537.1|  38 TAVKGEVLGILGPNGAGKSTLVKILA 63 
                                    467889999*************9886 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 5.7
                                    HHHHHHHHHHHHHHTTSEEEE--TT CS
                    RsgA_GTPase  61 eeeeleelkeelealgyevllvsak 85 
                                     ee++e++ +el+++g++v  +s  
  gi|119720042|ref|YP_920537.1| 291 AEEAFERVLHELRSAGLKVRSISIV 315
                                    4555777778888888887777665 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   0.00017      0.12      26      60 ..      45      80 ..      40     100 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00017
                          DUF87 26 lAilgsTGsGKSntvavLleellekkga.tililDp 60
                                   l+ilg  G+GKS++v++L   ll + g+ +i  +D+
  gi|119720042|ref|YP_920537.1| 45 LGILGPNGAGKSTLVKILATLLLPDSGYaRIMGFDV 80
                                   69****************999996444346666665 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0    0.0015       1.1       4      25 ..      47      70 ..      45      91 .. 0.81
   2 ?    1.3   0.0      0.45   3.2e+02      52      85 ..     201     244 ..     185     250 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0015
                                   EE--SSSSHHHHHHHGGGGB..S- CS
                          AAA_5  4 LvGppGtgKselaerlaaal..nr 25
                                   ++Gp G gKs+l++ la +l   +
  gi|119720042|ref|YP_920537.1| 47 ILGPNGAGKSTLVKILATLLlpDS 70
                                   68***************9997544 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.45
                                    .....--------..........G-SEEEEESGGG--HHHHHHH CS
                          AAA_5  52 tslvdsplvraar..........egeilvlDEveraesevlnsL 85 
                                    t+lv    + +a+          eg+il +D v+ +++ v++s+
  gi|119720042|ref|YP_920537.1| 201 TVLVTTHNMFEAEiicdrvaiisEGRILAVDSVDSLKKRVADSV 244
                                    444444444444466666667779**********9999999886 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00058      0.42      17      45 ..      41      69 ..      33     208 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00058
                         AAA_30 17 gdrvavltGpAGtGKttalkalreaweaa 45
                                   +  v  + Gp G+GK+t++k l+ ++  +
  gi|119720042|ref|YP_920537.1| 41 KGEVLGILGPNGAGKSTLVKILATLLLPD 69
                                   34588999************998765444 PP

>> MukB  MukB N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00024      0.17      28      56 ..      44      72 ..      38     110 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00024
                                   HHHHHS--SHHHHHHHHHHHHHHS--TTT CS
                           MukB 28 vttlsGgnGaGksttmaafvtaliPdlsl 56
                                   v  + G nGaGkst +  + t l+Pd   
  gi|119720042|ref|YP_920537.1| 44 VLGILGPNGAGKSTLVKILATLLLPDSGY 72
                                   5567799*******************764 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0    0.0003      0.22      13      48 ..      33      68 ..      25      88 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0003
                   Mg_chelatase 13 raleiaaaGgHnlllvGppGsGKtmlakrlpsllpp 48
                                   + + ++a  g  l ++Gp G+GK+ l k l++ll p
  gi|119720042|ref|YP_920537.1| 33 KGVSLTAVKGEVLGILGPNGAGKSTLVKILATLLLP 68
                                   556677777778889***************998744 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00038      0.28       3      22 ..      47      66 ..      45     114 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00038
                         AAA_18  3 ltGtpGvGKttlakeLskrl 22
                                   + G+ G+GK+tl k L+ +l
  gi|119720042|ref|YP_920537.1| 47 ILGPNGAGKSTLVKILATLL 66
                                   89**************8875 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0    0.0014      0.97       3      24 ..      45      66 ..      43      80 .. 0.87
   2 ?    0.4   0.0      0.76   5.4e+02      57     127 ..     132     206 ..     120     239 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0014
                                   EEEEC-TTTCHHHHHHHHHHHH CS
                          NACHT  3 vilqGeaGsGKTtLlqklalaw 24
                                   + + G++G GK+tL++ la+++
  gi|119720042|ref|YP_920537.1| 45 LGILGPNGAGKSTLVKILATLL 66
                                   5689************999876 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.76
                                    HHCCCCTS--SSS-C.....CHHHHCCSCCCEE.....EEEE-STT-SS-TCH.........HHHHHCTTTTT--EEEEE CS
                          NACHT  57 llfsqlpepaapvse.....vwavllelperlL.....lilDglDelvtdlgqkekqpvrtlLselirkkllpeaslllt 126
                                    +l++++++p a+        +++ +l++++ lL     lilD      +      ++++r lL++l      ++ ++l+t
  gi|119720042|ref|YP_920537.1| 132 VLRDVGLQPYADKLYeemslGMKARLSIARALLtdppvLILDEPTLGLDPV---SARRIRSLLTSLAHS---KGKTVLVT 205
                                    555555555444433456667777777777777888878887433222222...235566666655554...55666666 PP

                                    E CS
                          NACHT 127 v 127
                                    +
  gi|119720042|ref|YP_920537.1| 206 T 206
                                    5 PP

>> AAA_PrkA  PrkA AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00043      0.31      86     112 ..      40      66 ..       5      84 .. 0.83
   2 ?   -3.4   0.0       4.8   3.4e+03     290     316 ..     207     233 ..     193     251 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00043
                       AAA_PrkA  86 erkqilyllGPvggGksslverlkkll 112
                                    ++ ++l +lGP g+Gks+lv+ l +ll
  gi|119720042|ref|YP_920537.1|  40 VKGEVLGILGPNGAGKSTLVKILATLL 66 
                                    566899***************998877 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 4.8
                       AAA_PrkA 290 ksnkknealldrivvvkvPyclrvsee 316
                                    ++  + e + dr+ ++     l v+  
  gi|119720042|ref|YP_920537.1| 207 HNMFEAEIICDRVAIISEGRILAVDSV 233
                                    444567888888888877777777654 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0    0.0016       1.1      21      39 ..      47      65 ..      44      75 .. 0.89
   2 ?    0.3   0.0       0.3   2.1e+02     525     571 ..     165     209 ..     156     211 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0016
                         AAA_13 21 iYGwNGaGKTtLSrllrsl 39
                                   i G NGaGK+tL ++l+ l
  gi|119720042|ref|YP_920537.1| 47 ILGPNGAGKSTLVKILATL 65
                                   679*************987 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.3
                         AAA_13 525 gkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnl 571
                                    +   + ++D P   LD  s   + sl+ s +  ++k k +++ THn+
  gi|119720042|ref|YP_920537.1| 165 TDPPVLILDEPTLGLDPVSARRIRSLLTSLA--HSKGKTVLVTTHNM 209
                                    56789999**********************9..8999*********6 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00042       0.3       3      26 ..      47      70 ..      45     141 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00042
                   RNA_helicase  3 lyGpsgeGKStlakeLakallkkl 26
                                   + Gp+g GKStl+k La+ ll ++
  gi|119720042|ref|YP_920537.1| 47 ILGPNGAGKSTLVKILATLLLPDS 70
                                   68**************99988554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      609  (0.0339673); expected 358.6 (0.02)
Passed Vit filter:                       101  (0.00563333); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 2199.38
//
Query:       gi|119720043|ref|YP_920538.1|  [L=260]
Description: ABC-2 type transporter [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-09   37.6   6.0    1.5e-09   37.6   6.0    1.6  2  ABC2_membrane  ABC-2 type transporter


Domain annotation for each model (and alignments):
>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0      0.38   6.9e+03      53      60 ..      35      42 ..      15      55 .. 0.56
   2 !   37.6   6.0   8.2e-14   1.5e-09      91     208 ..      93     216 ..      77     217 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 0.38
                  ABC2_membrane 53 pgllffsv 60
                                   p++++ ++
  gi|119720043|ref|YP_920538.1| 35 PYFVYALL 42
                                   22222222 PP

  == domain 2  score: 37.6 bits;  conditional E-value: 8.2e-14
                  ABC2_membrane  91 yslsayvlakvlvelpvsllqalifllivyflvgldls......rfflflllllltalaasslgllisalapsfedasql 164
                                     s+  ++la v+++lp+ +l++l+  + +++++ l+        + + +++llll +l +++++ l++  +  ++  s +
  gi|119720043|ref|YP_920538.1|  93 LSPGGVLLALVVSYLPRYILETLLKAVAFLPVLALEEGpadallHLLAAYALLLLGLLPLLGISTLVAGATLLVHEESPV 172
                                    3777799*****************9999999987777676665555888888888899999******************* PP

                  ABC2_membrane 165 aslvllpllllsGffipidsmpkwlqwiaylnPltyavealrsn 208
                                       v+ + lllsG+++p++ +p+w+++++ l P+ty+ve+ r+ 
  gi|119720043|ref|YP_920538.1| 173 LEWVTPLVLLLSGAVYPVSVLPGWMRALSALIPVTYVVELSRAL 216
                                    ****************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1880.72
//
Query:       gi|119720044|ref|YP_920539.1|  [L=247]
Description: putative ABC-2 type transport system permease protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1607.08
//
Query:       gi|119720045|ref|YP_920540.1|  [L=463]
Description: ferredoxin-dependent glutamate synthase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.3e-24   86.2   2.6    6.1e-24   84.8   1.9    2.0  2  Glu_synthase  Conserved region in glutamate synthase
    2.6e-19   69.5   3.5    3.1e-13   49.5   1.9    2.2  2  FMN_dh        FMN-dependent dehydrogenase
    0.00039   19.9   2.0     0.0006   19.3   2.0    1.2  1  NMO           Nitronate monooxygenase


Domain annotation for each model (and alignments):
>> Glu_synthase  Conserved region in glutamate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.8   1.9     1e-27   6.1e-24     136     309 ..     224     402 ..     215     407 .. 0.80
   2 ?   -2.6   0.0      0.37   2.2e+03     343     367 ..     407     431 ..     403     432 .. 0.85

  Alignments for each domain:
  == domain 1  score: 84.8 bits;  conditional E-value: 1e-27
                                    SEEEEE---TTSTTS--EE-.....GGG--HHHHHHHTS-TT--EE--SS-T.T-SSHHHHHHHHHHHHHH-TTSEEEEE CS
                   Glu_synthase 136 kaleikiaQGakpgeGgqlp.....geKvseeiakiRkikpgvdliSPaphh.diysiedlaqliedLkevnkeakvsvK 209
                                     a+eik++QGakpg Gg ++     + Kv e+   +   ++  ++          y  + l  +i+ +k+  ++akv +K
  gi|119720045|ref|YP_920540.1| 224 VAFEIKVGQGAKPGLGGVIKmrkeeAVKVKEKYHFLEDPAEARTAWVERYSApGTYTADILRGMIRLMKTSYPRAKVWIK 303
                                    379**************9972222255677777777776666666544433313455555667777777777******** PP

                                    EE-STTHHHHHHHHHHTT-SEEEEE-TT---SSEEHHHHHHB---HHHHHHHHHHHHHHTT-GGG-EEEEESS--SHHHH CS
                   Glu_synthase 210 lvaeagvetiaagvakanadiilidGleGGTGAspkssikhaGlPlelalaevdqtlkeeglrdrvsliadGglktgadv 289
                                    ++  + v  +     + +ad++ idG eGGTG +p + +k+ G P++++la++ ++ +  g+ dr+sl  +G+l  ga +
  gi|119720045|ref|YP_920540.1| 304 VGPFRDVLEVVKVSYEEGADAVIIDGKEGGTGMAPSVAMKELGYPTVVGLAKIRKA-RLMGVDDRMSLLLAGRLFNGAHI 382
                                    **9877655555599*************************************9876.77899****************** PP

                                    HHHHHHT-SEEE-SHHHHHH CS
                   Glu_synthase 290 vkalalGAdavgigtaalia 309
                                    vka alGA a+++g+  ++a
  gi|119720045|ref|YP_920540.1| 383 VKARALGATAIYVGRPFIVA 402
                                    ***************99988 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.37
                                    -HHHHHHHHHHHHHHHHHHHHHHT- CS
                   Glu_synthase 343 kaervvnyikalaeevrellaalgi 367
                                    ++  v n+i+a++ e ++++ alg+
  gi|119720045|ref|YP_920540.1| 407 DEAGVRNFIEATRVETQMIVSALGK 431
                                    567899************9999985 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   7.1e-08   0.00042      44      96 ..     106     157 ..      95     162 .. 0.91
   2 !   49.5   1.9   5.2e-17   3.1e-13     259     346 ..     351     442 ..     311     444 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 7.1e-08
                                    SS-B--EEETTEEESSSEEE--BSTGGGTSTTHHHHHHHHHHHHTS-EEEETT CS
                         FMN_dh  44 skvdlsttllGqklslPvliaPvglaklahpdgelalaraaakagipfvlstv 96 
                                    ++v+l+t++ G k+s+P++++ +g + +a  +  l +araaak gip++++++
  gi|119720045|ref|YP_920540.1| 106 TDVNLETSIGGLKSSMPLVVGTMGSTDIAS-RYSLVIARAAAKEGIPYGIGEN 157
                                    57899***********************97.88999************99865 PP

  == domain 2  score: 49.5 bits;  conditional E-value: 5.2e-17
                                    HCHHHHHHHH......SS-EEEESS--SHHHHHHHHHTT-SEEEESHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                         FMN_dh 259 dvLpeiveav....ggrievlvDgGirrGsDvlkAlalGAdavllGRpflyglaagGeeGvervleilraelertmallG 334
                                      L +i++a     ++r+ +l+ g   +G++++kA alGA+a+ +GRpf+++++++ e+Gv++ +e  r e++     lG
  gi|119720045|ref|YP_920540.1| 351 VGLAKIRKARlmgvDDRMSLLLAGRLFNGAHIVKARALGATAIYVGRPFIVAAMVKDEAGVRNFIEATRVETQMIVSALG 430
                                    44566655532222679*************************************************************** PP

                                    -SBHHHHHCGGE CS
                         FMN_dh 335 vksvaeldrsll 346
                                      s+ +++++ +
  gi|119720045|ref|YP_920540.1| 431 KYSIGDVSPEDV 442
                                    *******99866 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   2.0     1e-07    0.0006     150     234 ..     315     408 ..     302     437 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1e-07
                            NMO 150 rkvearGaDalivqGpeaG.GhqGtpevgd..kglfaLvpqvldavd......iPviAaGGiidrrgvaaaLalGAsgvq 220
                                    ++  + GaDa+i++G+e+G G+ +++++++    ++  ++++++a        + ++ aG ++++  +  a alGA +++
  gi|119720045|ref|YP_920540.1| 315 KVSYEEGADAVIIDGKEGGtGMAPSVAMKElgYPTVVGLAKIRKARLmgvddrMSLLLAGRLFNGAHIVKARALGATAIY 394
                                    666789************99999977777744334444566777755666699*************************** PP

                            NMO 221 igtrfLltkesdak 234
                                    +g  f+++   + +
  gi|119720045|ref|YP_920540.1| 395 VGRPFIVAAMVKDE 408
                                    ******98644433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 3193.48
//
Query:       gi|119720046|ref|YP_920541.1|  [L=364]
Description: asparagine synthetase A [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-50  171.5   0.0    2.7e-50  171.2   0.0    1.0  1  tRNA-synt_2     tRNA synthetases class II (D, K and N)
  ------ inclusion threshold ------
      0.084   12.3   0.0       0.14   11.6   0.0    1.2  1  BAR_3_WASP_bdg  WASP-binding domain of Sorting nexin protein


Domain annotation for each model (and alignments):
>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.2   0.0     3e-54   2.7e-50       6     313 ..      45     357 ..      41     358 .. 0.89

  Alignments for each domain:
  == domain 1  score: 171.2 bits;  conditional E-value: 3e-54
                                    HHTHHHHCCSHHHHHHHHHHHHHHHHHHHHHHHTT-EE----SEESS-..-SSSS--EEEEETTT.TEEE-E-S-SHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    tRNA-synt_2   6 lknryldlrtekvskvlrlrstvtkavrkyleengfieietPiLsksd..teegarlFkvksrekekeffaLtqspqlyl 83 
                                     ++ +   r++k+  v+r+++++++a+r+yl+++gf+e  +Pi+   +  +  ga++ +v    +  e+     s  ly+
  gi|119720046|ref|YP_920541.1|  45 TRYSWKWARESKYATVFRIQASILRAIREYLDSHGFTEALPPIIGPVTdpGIRGAKQVTVDFYGH--EY-KVMSSAILYK 121
                                    567777889***********************************988634667889888844444..44.599******* PP

                                    HHHHHCTHSEEEEEEEEE--S--B...TTB-S-CEEEEEEEEET-SCHHHHHHHHHHHHHHHHHHHHCSCCCCCHTTTTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    tRNA-synt_2  84 ellivagidrvfqiaraFRaEdsr...tdrhlaEFtqieaemsfieeedimqvleelikslvkevlessakdiefvirrn 160
                                    +++++  +++v+ ++++ R E  +   t rhl EF q+++e+   + ed m+++e+l+ ++++ v e +  d+e+  r+ 
  gi|119720046|ref|YP_920541.1| 122 QYMAAV-LGKVYFVSPNIRLEPNDsifTGRHLVEFFQVDIEILDGTLEDAMSLAEGLFMHVARYVEEVHGADLEKLGRT- 199
                                    ***999.**************88867799************************************66666666666555. PP

                                    SEE-SSS-EEEEHHHHHHHHHTS......-SS--HHHHHHHHHHS--SEEEEEEEBGGGSTTCBBBSTTSTTBBSEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    tRNA-synt_2 161 skdlkkpfkrltykeaieklnei......gkdldkaderalvkkeknepvfvtdfPaelkpFyarkeeddkkltesyDll 234
                                      + ++pf r+t++ea+e +n        + ++  + e++l   ++++p+f++ +P+  + Fy+r++ +++   + +D+l
  gi|119720046|ref|YP_920541.1| 200 LPEYRTPFARYTHAEAVELVNRLgcrnprNTEILWECEKVLSA-HHTSPLFIYGYPKGSRGFYNREDPERPGYLRDFDML 278
                                    5699***************998877777766677777888877.999********************************* PP

                                    ET.TE.EEEEEEEB--SHHHHHHHHHHCCHHSSSGGGGHHHHHHHH.CT--SEEEEEEEHHHHHHHHCT-SSGGGCSSS- CS
                                    xx.xx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    tRNA-synt_2 235 in.gv.ElvgGslRiedpeeleeklkskgldeeaeekfswyleale.yGapphgGlglGldRlvmlllgsesIrdviaFP 311
                                    ++ g+ E ++G  R+ +p +  +++k+ g d   ++k++w+le+l+ +   +++G+g+G++Rl+ +++g++ + +  ++P
  gi|119720046|ref|YP_920541.1| 279 YPeGFgEAISGGEREYEPAKVIARIKESGED---PKKYKWFLEMLRdFYPLKTAGFGIGVERLTRYICGLRAVWESRPYP 355
                                    *9788**************************...*********97527999***************************** PP

                                    XX CS
                                    xx RF
                    tRNA-synt_2 312 kl 313
                                    k+
  gi|119720046|ref|YP_920541.1| 356 KV 357
                                    96 PP

>> BAR_3_WASP_bdg  WASP-binding domain of Sorting nexin protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   1.5e-05      0.14      87     141 ..     151     205 ..     147     216 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.5e-05
                 BAR_3_WASP_bdg  87 alsqafevdeqvassaLnealaatgktYeeigevfaeqpkkDleflletleeYkG 141
                                     l + f+vd +  + +L++a++ +   + +++ +++e    Dle+l  tl eY+ 
  gi|119720046|ref|YP_920541.1| 151 HLVEFFQVDIEILDGTLEDAMSLAEGLFMHVARYVEEVHGADLEKLGRTLPEYRT 205
                                    67889************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2558.49
//
Query:       gi|119720047|ref|YP_920542.1|  [L=183]
Description: flavin reductase domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.8e-27   94.0   0.0    1.1e-26   93.8   0.0    1.0  1  Flavin_Reduct  Flavin reductase like domain


Domain annotation for each model (and alignments):
>> Flavin_Reduct  Flavin reductase like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.8   0.0     6e-31   1.1e-26       4     139 ..      19     154 ..      15     171 .. 0.94

  Alignments for each domain:
  == domain 1  score: 93.8 bits;  conditional E-value: 6e-31
                                    S-EE-EEEEE.EETTEEEEEEESSEEEEETTTTEEEEEEETTSHHHHHHHHHSEEEEEEEBCCGHHHHHHTCS...SCCC CS
                  Flavin_Reduct   4 vaqpvavvttsvpptsplgatlssftslsldPplvafslrlpsstadalkeagefvinllsesqealadafsqksgprtd 83 
                                    ++  va++++ +++++p+ +++ + t++s +Pplva++++++++t++ +k++g+f++n + +    ++++ ++ sg r++
  gi|119720047|ref|YP_920542.1|  19 HPKLVALIVSVDASGRPNFMPAAWLTPVSVKPPLVAVAVAPERYTYSLVKSSGVFTVNPVDAGMLRVVEEAGSVSG-RDV 97 
                                    57789*****999************************************************************9**.*** PP

                                    CCCCCCCCEEECT.CCCSEEETTCSEEEEEEEEEEECCTTEEEEEEEEEEEEESTTE CS
                  Flavin_Reduct  84 dksifagltwees.ptgapallgalasleCqvvgsvelgdhelfigeVvavkvgdda 139
                                    dk +  g+   ++ ++gap+++gala leC++  ++++gdh +++geV a++ + da
  gi|119720047|ref|YP_920542.1|  98 DKASSLGVRFLPAlRVGAPCIEGALACLECRLWAEYPAGDHSILVGEVQAARARRDA 154
                                    **887799999999*************************************999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       237  (0.0132188); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 1169.84
//
Query:       gi|119720048|ref|YP_920543.1|  [L=76]
Description: hypothetical protein Tpen_1142 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.14   12.3   3.8       0.17   12.1   3.8    1.1  1  CENP-Q    CENP-Q, a CENPA-CAD centromere complex subunit


Domain annotation for each model (and alignments):
>> CENP-Q  CENP-Q, a CENPA-CAD centromere complex subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   3.8   9.5e-06      0.17      29      78 ..      20      69 ..      16      72 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.5e-06
                         CENP-Q 29 klldekaaleaqLspelhslelLeaeiekeeralerdyeaLreLeknaka 78
                                   ++l++   +ea L  +l+++e+  a ++ + + le+d+e  reLe+ ++ 
  gi|119720048|ref|YP_920543.1| 20 STLRRDGLYEARLVEALDAVEEFLASVRSAPARLEEDEELARELEEDVEE 69
                                   577778889*************************************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       819  (0.0456802); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 552.96
//
Query:       gi|119720049|ref|YP_920544.1|  [L=477]
Description: hypothetical protein Tpen_1143 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (477 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.37
# Mc/sec: 3836.24
//
Query:       gi|119720050|ref|YP_920545.1|  [L=265]
Description: putative circadian clock protein, KaiC [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.4e-52  177.6   0.0    2.8e-52  177.4   0.0    1.0  1  ATPase     KaiC
    1.6e-08   34.4   1.8    4.9e-08   32.8   0.2    2.0  2  AAA_25     AAA domain
    2.3e-05   24.3   0.1    5.3e-05   23.1   0.1    1.5  1  MEDS       MEDS: MEthanogen/methylotroph, DcmR Sensory domain
    8.4e-05   22.2   0.1    0.00013   21.5   0.1    1.3  1  RecA       recA bacterial DNA recombination protein
    9.9e-05   21.7   0.1    0.00016   21.0   0.1    1.5  1  Rad51      Rad51
     0.0043   16.8   0.0     0.0086   15.8   0.0    1.5  1  AAA_24     AAA domain
     0.0083   15.9   0.1       0.02   14.7   0.1    1.7  1  IstB_IS21  IstB-like ATP binding protein
  ------ inclusion threshold ------
      0.012   15.0   0.2      0.044   13.1   0.1    2.1  2  DnaB_C     DnaB-like helicase C terminal domain
       0.03   14.7   0.0      0.058   13.8   0.0    1.6  1  AAA        ATPase family associated with various cellular act
      0.059   13.6   0.0       0.13   12.6   0.0    1.6  1  AAA_22     AAA domain
      0.083   12.1   0.1      0.083   12.1   0.1    1.7  2  NB-ARC     NB-ARC domain
       0.11   11.0   0.0       0.49    9.0   0.0    2.0  2  GvpD       GvpD gas vesicle protein
       0.12   11.9   0.5        1.7    8.2   0.5    2.1  1  SRP54      SRP54-type protein, GTPase domain
       0.16   12.6   0.0       0.41   11.3   0.0    1.7  1  DUF643     Protein of unknown function (DUF643)


Domain annotation for each model (and alignments):
>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  177.4   0.0   2.2e-55   2.8e-52       2     227 ..       7     232 ..       6     236 .. 0.96

  Alignments for each domain:
  == domain 1  score: 177.4 bits;  conditional E-value: 2.2e-55
                         ATPase   2 ktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekleeeg 81 
                                    +tg+ glD++l gG+peg  v ++G pGtGKti +l+F++ g++  ge  ++vt+ee+ e++ ++a+++G+d+e  +++g
  gi|119720050|ref|YP_920545.1|   7 STGVAGLDKLLAGGVPEGFFVALVGMPGTGKTIACLHFVWAGLKA-GESAIYVTTEESRESIVRQAAQFGMDFEGAQKSG 85 
                                    7*****************************************888.********************************** PP

                         ATPase  82 klaiidasesaeesaeekdkedleelieelaeaikeika..krvviDsitglayeekeavaReilrqlvrvlkklgvTai 159
                                    +l+iida + ++e++   ++ ++ee+++++ ea k+++   +r+viDs +++     + +aRe   +++r+l+k+g T  
  gi|119720050|ref|YP_920545.1|  86 RLIIIDALMREKEDEWMMRELAVEEMLSRVIEAKKRLGRsaRRLVIDSMSAF-WLRAPVKAREDSYTVKRILNKWGFTIY 164
                                    **********999888799*****************98766***********.*************************** PP

                         ATPase 160 lvsekssseeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIte.egikvl 227
                                     +s+   + ++a g g+e+ ++dg+i+ +++ +++ l+R++++ kmR+t+h+ + ++++I + eg + +
  gi|119720050|ref|YP_920545.1| 165 ATSQYAITTGSAFGWGIEH-VADGIIHFKRRVVDGVLTRYIIVEKMRQTPHDLRAWEIQIRDkEGLTLV 232
                                    *******************.******************************************9998765 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.2   3.8e-11   4.9e-08      22     172 ..      13     159 ..       2     185 .. 0.75
   2 ?    0.8   0.1      0.24   3.1e+02      79     136 ..     206     255 ..     182     261 .. 0.64

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 3.8e-11
                         AAA_25  22 rrwlvkgllpagelallaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgeal... 97 
                                    +++l+ g +p+g +++l+G pgtGKt ++l+ + a +  G+             +yv +E+s++ + r +++ g ++   
  gi|119720050|ref|YP_920545.1|  13 LDKLLAGGVPEGFFVALVGMPGTGKTIACLHFVWAGLkAGE-----------SAIYVTTEESRESIVRQAAQFGMDFega 81 
                                    677888888**********************9999885555...........78*******************9777776 PP

                         AAA_25  98 rddarllvld.lagv.eslpLfakdrggtlltadvdaleaaieeveg.vrlvviDplsralgg....densnsdvgalve 170
                                    +  +rl ++d l+++ e+  ++    ++ ++++ + ++++a ++  + +r +viD++s+++        +++  v+++++
  gi|119720050|ref|YP_920545.1|  82 QKSGRLIIIDaLMREkEDEWMM----RELAVEEMLSRVIEAKKRLGRsARRLVIDSMSAFWLRapvkAREDSYTVKRILN 157
                                    8899999988223333332222....23335555555555555544389**********998744333333333688877 PP

                         AAA_25 171 al 172
                                    ++
  gi|119720050|ref|YP_920545.1| 158 KW 159
                                    77 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.24
                         AAA_25  79 aEdsedelrrRlravgealrddarllvldlagveslpLfakdrggtlltadvdaleaa 136
                                     E  + +++  lra+  ++rd+++l+++        pL+    +++l + + +++ ++
  gi|119720050|ref|YP_920545.1| 206 VEKMR-QTPHDLRAWEIQIRDKEGLTLVR-------PLARRLEDESLPEKVARRIKER 255
                                    56666.67778999999999999999986.......3333333444444444444444 PP

>> MEDS  MEDS: MEthanogen/methylotroph, DcmR Sensory domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.1   4.1e-08   5.3e-05      18     105 ..      42     130 ..      38     145 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 4.1e-08
                           MEDS  18 vpfikaglargekvlyvasastldelrealrkagldvdaalesgqleildaeetylrgggfdp...ermlealrralaka 94 
                                    + f+ agl++ge  +yv+++++++ + ++ ++ g+d + a++sg+l i+da    +r+ + ++   e ++e++ +++ +a
  gi|119720050|ref|YP_920545.1|  42 LHFVWAGLKAGESAIYVTTEESRESIVRQAAQFGMDFEGAQKSGRLIIIDAL---MREKEDEWmmrELAVEEMLSRVIEA 118
                                    57999********************************************965...5555555555577777777777777 PP

                           MEDS  95 l.adgyaglrvi 105
                                      + g +  r++
  gi|119720050|ref|YP_920545.1| 119 KkRLGRSARRLV 130
                                    633366555555 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.1     1e-07   0.00013      33     106 ..       5      79 ..       1      85 [. 0.87

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1e-07
                                    EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEESS----H..HHHHHTT--GG CS
                           RecA  33 tissGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaqkkggvaafidaehaldp..kyakklGvdid 106
                                     +s+G  +ld  l  GG+p+G  + + G   +Gkt  +lh +    k+g  a ++ +e + ++  + a+++G+d +
  gi|119720050|ref|YP_920545.1|   5 RLSTGVAGLDKLLA-GGVPEGFFVALVGMPGTGKTIACLHFVWAGLKAGESAIYVTTEESRESivRQAAQFGMDFE 79 
                                    689*******9987.*******************************************998752245677777765 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.1   1.3e-07   0.00016      17     100 ..       4      79 ..       1     148 [. 0.82

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.3e-07
                                    -EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEESSS---GGGGHHHHHHTT CS
                          Rad51  17 lqlttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavyidtegtfrperlveiaeryk 96 
                                     +l+tG   lD+lL GG++ g    ++G  ++Gkt  c  + v + l      + + a+y+ te +   e +v+ a +++
  gi|119720050|ref|YP_920545.1|   4 RRLSTGVAGLDKLLAGGVPEGFFVALVGMPGTGKTIACLHF-VWAGLK-----AGESAIYVTTEESR--ESIVRQAAQFG 75 
                                    579********************************999886.455554.....33568889888763..55777777787 PP

                                    --HH CS
                          Rad51  97 ldke 100
                                    +d e
  gi|119720050|ref|YP_920545.1|  76 MDFE 79 
                                    7755 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   6.7e-06    0.0086       5      78 ..      27     138 ..      24     154 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6.7e-06
                         AAA_24   5 iliyGpsgiGKTtlakel.......gpkplfidtekGlksldadkfpdie.............................. 47 
                                    ++++G +g+GKT  ++++       g++++++ te++  s+     +                                 
  gi|119720050|ref|YP_920545.1|  27 VALVGMPGTGKTIACLHFvwaglkaGESAIYVTTEESRESIVRQAAQF-Gmdfegaqksgrliiidalmrekedewmmre 105
                                    689*****************************9999887776666543.2477788888888888888888887777777 PP

                         AAA_24  48 .swedfldevvel.aaeladyktlviDtidele 78 
                                     ++e++l+ v e  ++  +  + lviD+ + ++
  gi|119720050|ref|YP_920545.1| 106 lAVEEMLSRVIEAkKRLGRSARRLVIDSMSAFW 138
                                    777777777777678888999999999999987 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   1.5e-05      0.02      50     121 ..      27      97 ..      21     126 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.5e-05
                      IstB_IS21  50 ivllGpsGvGKshlaialgveavraglsvlfvrvedLveelkrarrdgklaralkrllkv.dllilDdlgllp 121
                                    ++l+G +G+GK+     +  ++ +ag s ++v++e+  e++ r+    ++    +  +k+ +l+i+D l  ++
  gi|119720050|ref|YP_920545.1|  27 VALVGMPGTGKTIACLHFVWAGLKAGESAIYVTTEESRESIVRQ--AAQFGMDFEGAQKSgRLIIIDALMREK 97 
                                    789**********99********************998887654..455666666666665888888776555 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   3.4e-05     0.044       2      67 ..       6      71 ..       5     141 .. 0.80
   2 ?   -1.3   0.0      0.89   1.1e+03      89     124 ..     206     239 ..     181     247 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.4e-05
                                   BXSSTHHHHHHCT.SBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHHHHH CS
                                   xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         DnaB_C  2 lstgfkdLDklts.GlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeqlvqRl 67
                                   lstg + LDkl+  G+ +g ++ + + p++Gkt  +l+++ +  + +  + +++  e s+e++v++ 
  gi|119720050|ref|YP_920545.1|  6 LSTGVAGLDKLLAgGVPEGFFVALVGMPGTGKTIACLHFVWAGLK-AGESAIYVTTEESRESIVRQA 71
                                   6899*****98751688888999***************9986654.455677778888888888664 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.89
                                    HHHHHHHHHHHHHSEEEEEEXSSXCHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         DnaB_C  89 weklteaieelseaklfiddtpaltvseirskarrl 124
                                    +ek+ ++ ++l+  ++ i d+ +lt+  +r  arrl
  gi|119720050|ref|YP_920545.1| 206 VEKMRQTPHDLRAWEIQIRDKEGLTL--VRPLARRL 239
                                    45666667778888888888887765..44555555 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.6e-05     0.058       2      92 ..      28     114 ..      27     147 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.6e-05
                                    EEESSTTSSHHHHHHHHHHH...HTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCC CS
                            AAA   2 llyGppGtGKTllakavake...lgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgse 78 
                                     l+G pGtGKT+++   +     +g + + +   e + + +  +++++ + f+ a+++     ++iD   al++++ ++e
  gi|119720050|ref|YP_920545.1|  28 ALVGMPGTGKTIACLHFVWAglkAGESAIYVTTEESR-ESIVRQAAQFGMDFEGAQKSG--RLIIID---ALMREK-EDE 100
                                    69**********9987777654446777888888888.556667778888888888776..666665...555555.444 PP

                                    CHHHHHHHHHHHHH CS
                            AAA  79 seeeervvnqLlte 92 
                                       +e +v+++l+ 
  gi|119720050|ref|YP_920545.1| 101 WMMRELAVEEMLSR 114
                                    45555555555554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   9.8e-05      0.13       7     100 ..      26     134 ..      23     163 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.8e-05
                         AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.sskdllrellralglelka............... 70 
                                    +++++G +GtGKT  +  ++    ++      + + ++vt  +s  s    + ++  +++  +k+               
  gi|119720050|ref|YP_920545.1|  26 FVALVGMPGTGKTIACLHFVWAGLKA------GESAIYVTTEESReSIVRQAAQFGMDFEGAQKSgrliiidalmreked 99 
                                    6799***********99998765443......666666666666644444455555555555555666666666666666 PP

                         AAA_22  71 ....erlsseellealeqalrarav.ielliiDEa 100
                                        ++l  ee+l+++ +a ++ ++  + l+iD +
  gi|119720050|ref|YP_920545.1| 100 ewmmRELAVEEMLSRVIEAKKRLGRsARRLVIDSM 134
                                    88888888888888888888888888888888866 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   6.5e-05     0.083      10      35 ..      14      39 ..      10      45 .. 0.88
   2 ?   -2.6   0.2       1.9   2.4e+03      72     104 ..      89     120 ..      86     122 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.5e-05
                                   HHHHCTTTSCSEEEEEEESTTSSHHH CS
                         NB-ARC 10 ekLlekdelqslvvalvGmgGvGKtt 35
                                   +kLl  + ++ ++valvGm+G GKt+
  gi|119720050|ref|YP_920545.1| 14 DKLLAGGVPEGFFVALVGMPGTGKTI 39
                                   57777888999*************96 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.9
                                    XHHHHHCCCTTSSSS-STTSHHHHHHHHCCCTT CS
                         NB-ARC  72 ilkeLslseddleekeeveslkrklvrlLltkr 104
                                    i+  L ++++d   + e    +++l r+++ k+
  gi|119720050|ref|YP_920545.1|  89 IIDALMREKEDEWMMRELA-VEEMLSRVIEAKK 120
                                    5666777777766777666.8888888888775 PP

>> GvpD  GvpD gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.23   2.9e+02     239     263 ..       5      29 ..       2      30 .. 0.87
   2 ?    9.0   0.0   0.00038      0.49      15      97 ..      29     114 ..      23     219 .. 0.54

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.23
                           GvpD 239 kfsvglrdldkllseGtdrGsvvil 263
                                    ++s+g+  ldkll++G+  G  v l
  gi|119720050|ref|YP_920545.1|   5 RLSTGVAGLDKLLAGGVPEGFFVAL 29 
                                    789**************99988876 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00038
                           GvpD  15 ikGaPGtGktlftlrgl.dvlrresdvlyvstrvddetvseay......fsgeaeldktalldllkdpleldldvdvPie 87 
                                    + G PGtGkt+  l+++   l+  +  +yv+t    e++          f+g  +  +     ++ d+l  + + +  + 
  gi|119720050|ref|YP_920545.1|  29 LVGMPGTGKTIACLHFVwAGLKAGESAIYVTTEESRESIVRQAaqfgmdFEGAQKSGRL----IIIDALMREKEDEWMMR 104
                                    569************983579999999***99887777654332433333333332232....23345555555555555 PP

                           GvpD  88 kldlesllef 97 
                                    +l +e +l+ 
  gi|119720050|ref|YP_920545.1| 105 ELAVEEMLSR 114
                                    5555555554 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.5    0.0013       1.7       4      56 ..      27      79 ..      25     137 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0013
                                   EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTT CS
                          SRP54  4 illvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklg 56
                                   ++lvG+ G+GKT ++        k g++++ v++   R + v Q ++++   +
  gi|119720050|ref|YP_920545.1| 27 VALVGMPGTGKTIACLHFVWAGLKAGESAIYVTTEESRESIVRQAAQFGMDFE 79
                                   78999999999999999999999999999999999999999988888776554 PP

>> DUF643  Protein of unknown function (DUF643)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00032      0.41      23     104 ..     150     236 ..     139     245 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00032
                         DUF643  23 yeteqltleqkkqlysavkkiqeykiktGksveeiindiiepekefikdvlkdknlikkykns....knlkvdfsykkGm 98 
                                    y+++++  +    +y + + +   +   G  +e + ++ii+ +++++  vl +  +++k +++    ++ ++++ +k+G+
  gi|119720050|ref|YP_920545.1| 150 YTVKRILNKWGFTIYATSQYAITTGSAFGWGIEHVADGIIHFKRRVVDGVLTRYIIVEKMRQTphdlRAWEIQIRDKEGL 229
                                    66666666666667766666666666667789***************************975422226778888888886 PP

                         DUF643  99 .lekclk 104
                                     l + l 
  gi|119720050|ref|YP_920545.1| 230 tLVRPLA 236
                                    3455555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       725  (0.0404373); expected 358.6 (0.02)
Passed bias filter:                      576  (0.0321267); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 1848.36
//
Query:       gi|119720051|ref|YP_920546.1|  [L=453]
Description: hypothetical protein Tpen_1145 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       283  (0.0157845); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 2942.61
//
Query:       gi|119720052|ref|YP_920547.1|  [L=233]
Description: HAD family hydrolase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.8e-08   33.5   0.0    2.6e-07   31.2   0.0    1.9  1  Hydrolase       haloacid dehalogenase-like hydrolase
    5.3e-08   33.2   0.0    8.5e-08   32.5   0.0    1.4  1  HAD_2           Haloacid dehalogenase-like hydrolase
    7.1e-05   22.8   0.0    0.00013   22.0   0.0    1.3  1  Hydrolase_like  HAD-hyrolase-like
  ------ inclusion threshold ------
      0.018   15.5   0.2      0.034   14.5   0.2    1.6  1  HAD             haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.0   5.7e-11   2.6e-07       2     204 ..      27     201 ..      26     207 .. 0.77

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 5.7e-11
                                    SEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTEHHHHTHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase   2 ktvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakarsgaltgfatfigrgayaigkpewltald 81 
                                    ++v +D+dGT++  e  v  ++ ++            ++ ++++     ++ +  + +        ++  g  +w +   
  gi|119720052|ref|YP_920547.1|  27 RVVSLDLDGTVVSRE-YVDYFWLEL-----------VPRLYARRHGLNLEEAKRLVYSAYD-----EVGPGDMRWYQPS- 88 
                                    678899999999666.788888888...........3444444443444444444444444.....6888888888888. PP

                                    CHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT..GGG CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxx RF
                      Hydrolase  82 ippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlG..ddy 159
                                             +   + g ++ l   +al++        v+++a+ +++sL    i  vl t+ ++e++e ++++    +  
  gi|119720052|ref|YP_920547.1|  89 ---------YWFKRFGIEEWLG--DALREAGRLVR--VYEDARRFLESLPGSLI-AVLSTSASREFVELVMEREPflRGV 154
                                    .........8888899999999..77777777777..*************8888.9************999994459999 PP

                                    ESEEEEHHCES..STTTSHHHHHHHHHHHTSTGGGEEEEESSHH.HHH CS
                                    xxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx RF
                      Hydrolase 160 fdaviasdiet..vakpspegkvaaireLqgkpeevamVGDgvn.Daa 204
                                    f  v++s+ +    +kp pe ++ ++reL+++peev++VGD +  D +
  gi|119720052|ref|YP_920547.1| 155 FRRVFSSSSDYslPGKP-PEFFRIILRELGARPEEVVHVGDDPVhDYE 201
                                    97777777777767777.***********************9876765 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.0   1.9e-11   8.5e-08       4     175 ..      32     210 ..      29     213 .. 0.66

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 1.9e-11
                          HAD_2   4 DlDgTlldteel...iiqafnelleeygls.elseeelrkliglslrel....lrklgeseeeee.kieellrkyneekk 74 
                                    DlDgT + +e +   +++ + +l+++      l++ee ++l+   ++e+    +r +++s++ +   iee+l +   e  
  gi|119720052|ref|YP_920547.1|  32 DLDGTVVSREYVdyfWLELVPRLYAR---RhGLNLEEAKRLVYSAYDEVgpgdMRWYQPSYWFKRfGIEEWLGDALREAG 108
                                    67777776654311133333333332...223455555555444444441111333333333333566666666666666 PP

                          HAD_2  75 kkevkpydgvkelLeeLkeagyklgivTsksreaveekleqlgie.syFdvivtse.dvekk.KPdpeviekaleklklk 151
                                    +  v++y++++ +Le+L    +   + Ts sre ve  +e+  +   +F  + +s+ d + + KP pe ++ +l++l++ 
  gi|119720052|ref|YP_920547.1| 109 R-LVRVYEDARRFLESL-PGSLIAVLSTSASREFVELVMEREPFLrGVFRRVFSSSsDYSLPgKP-PEFFRIILRELGAR 185
                                    7.9**************.5555555677889******9998876538999887765155544698.9************* PP

                          HAD_2 152 keeviyvGDsp.tDieaakkagikv 175
                                    +eev+ vGD p +D e  +kag+++
  gi|119720052|ref|YP_920547.1| 186 PEEVVHVGDDPvHDYENPRKAGLRA 210
                                    **********************987 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   2.8e-08   0.00013       3      48 ..     169     213 ..     168     222 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 2.8e-08
                                    STTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEE CS
                 Hydrolase_like   3 gKPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLV 48 
                                    gKP pe+++ +l++lg+ peev+ +GD++ +D +  ++aG++  L 
  gi|119720052|ref|YP_920547.1| 169 GKP-PEFFRIILRELGARPEEVVHVGDDPVHDYENPRKAGLRAYLL 213
                                    677.589999*******************************99664 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.2   7.7e-06     0.034       3     130 ..      31     153 ..      29     201 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 7.7e-06
                            HAD   3 fDfDgTLldgdslelllrfllrrgaprlwralreklllal...frellrldraglaelleallaglseelaaelerfvae 79 
                                    +D+DgT +  +  ++++  l+ r   r+  +++e+++  +   ++e +  d ++++  ++    g +e l + l+++++ 
  gi|119720052|ref|YP_920547.1|  31 LDLDGTVVSREYVDYFWLELVPRLYARRHGLNLEEAKRLVysaYDEVGPGDMRWYQPSYWFKRFGIEEWLGDALREAGR- 109
                                    6*********999988888999999998777777766666566788888888888888877788888888888888883. PP

                            HAD  80 virpklldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlat 130
                                      + +  +++a+++l+  +      v+ +++ r++ve ++++     +l  
  gi|119720052|ref|YP_920547.1| 110 --LVR-VYEDARRFLE-SLPGSLIAVLSTSASREFVELVMEREP---FLRG 153
                                    ..223.55********.65777788888999*******996433...3444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.62u 0.34s 00:00:00.96 Elapsed: 00:00:00.56
# Mc/sec: 1262.70
//
Query:       gi|119720053|ref|YP_920548.1|  [L=229]
Description: orotidine 5'-phosphate decarboxylase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.5e-17   64.0   0.0    1.9e-17   63.6   0.0    1.1  1  OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS famil


Domain annotation for each model (and alignments):
>> OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.6   0.0   1.1e-21   1.9e-17       1     224 [.      13     218 ..      13     219 .. 0.85

  Alignments for each domain:
  == domain 1  score: 63.6 bits;  conditional E-value: 1.1e-21
                                    SEEEEEE-SSSHHHHH...HHHHHHGGGSSEEEEEHHHHHHHTHH.HHTHHHHHHHHHT..SEEEEEEEE-S-HHHHHHH CS
                      OMPdecase   1 snLclalDvatarell...eladkvgpsivvlKthydlvegwgfegtgaklaalarkhg..flifeDrKfaDIGntvekq 75 
                                    s+L+lalD+ + + ++   +l+  ++p +v +K++++l+ + g       +++l+++ g     ++D+K+aDI+++v++ 
  gi|119720053|ref|YP_920548.1|  13 SRLILALDFVSGDPAVfadRLLAALEPLVVGVKVGLPLALRMG----FRGVCELVERYGsgYYFLADFKLADIPDVVREE 88 
                                    689********9988888899**********************....557778888877778999*************** PP

                                    HHSTCHHHHTTESEEEEEGTGHHHHHHHHHHHHHHTTS.EEEEEESTSSGGHHHHHHHSHHHHHHHHHHHHHHHTTESEE CS
                      OMPdecase  76 atagsarikewadivtvhavaGkasvkalaeaaekwgnrgllilaqmsskgnlmlqekgytqacveaarehkaedfvmGf 155
                                     +     ++++ d  +vh ++    +++++ + + ++   ++ l+ ms++g+  l e    ++++  a++      + G+
  gi|119720053|ref|YP_920548.1|  89 LA---LLSEAGFDGSIVHLFP--MGLEEALSGVRGHD---VFGLVAMSHAGSRLLDE--HFEDLLRYASRLG----IRGV 154
                                    *6...789*************..99999999999996...************99999..6666666666666....66** PP

                                    ECCCHTH....HHHHH..TTCSCEEEHHHTTEEEEECTTCCGGGHHHHHHHTTCSEEEESHHHHTSSSHHHHHHH CS
                      OMPdecase 156 vaqetln....ateed..addfihltpgigleqggdgkgqqyntpekligiagadiiivGRgIlkagdpveeaer 224
                                    va +t++    + + +   +d ++l pg+g+ qg         +p  + +  ga + ivGR+I+ ++d   +aer
  gi|119720053|ref|YP_920548.1| 155 VAPATKPglvaRAR-AflPEDYLILSPGVGA-QG--------AEPGSALR-HGATFEIVGRSITASEDYYGAAER 218
                                    *******9874333.3599999999999997.33........32333333.68*****************99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       206  (0.0114898); expected 358.6 (0.02)
Passed bias filter:                      192  (0.0107089); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.34s 00:00:00.92 Elapsed: 00:00:00.54
# Mc/sec: 1277.26
//
Query:       gi|119720054|ref|YP_920549.1|  [L=173]
Description: orotate phosphoribosyltransferase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.9e-24   83.8   0.3    1.2e-23   83.4   0.3    1.1  1  Pribosyltran     Phosphoribosyl transferase domain
    8.1e-05   22.1   0.0    9.4e-05   21.9   0.0    1.2  1  UPRTase          Uracil phosphoribosyltransferase
    0.00066   19.2   0.4     0.0063   16.0   0.1    2.0  2  PRTase_2         Phosphoribosyl transferase
  ------ inclusion threshold ------
      0.058   13.8   0.4        3.6    8.0   0.1    2.1  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.4   0.3   2.7e-27   1.2e-23       7     132 ..      36     150 ..      31     156 .. 0.95

  Alignments for each domain:
  == domain 1  score: 83.4 bits;  conditional E-value: 2.7e-27
                                    T---EEEEEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE----T CS
                   Pribosyltran   7 enpaildavarlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdesrlledpa 86 
                                    ++p+++++v +++a   ++   + d+v gia gG+p+a++la  L+ pl y r++k+ ++++ +               +
  gi|119720054|ref|YP_920549.1|  36 SHPQAFRRVVEALAAVART--IEFDAVCGIAVGGLPIATALAYTLGKPLIYARREKKAHGTMKQL---------EGDYAR 104
                                    67899999999999999**..********************************************.........6899** PP

                                    TSEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-HHHHHH CS
                   Pribosyltran  87 gkkVliVDDildtGgTllaalelLkekgpeevriavlvdkpateee 132
                                    g+kVl+VDD+ +tGgTll +++lLk++g e+v++ v+vd+ +++ e
  gi|119720054|ref|YP_920549.1| 105 GMKVLLVDDVATTGGTLLDIARLLKSEGLEVVEALVVVDREEGASE 150
                                    ****************************************998765 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   2.1e-08   9.4e-05      62     171 ..      53     153 ..      11     166 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 2.1e-08
                        UPRTase  62 elldeekialVpilRaGegmeealrellpearvghlglqreeetlepveyynkLPkki.aertvlllDpviaTGgsaaaa 140
                                    ++++ + ++++++  +G++++ al   l ++ ++     r+e  ++++  +++L  +  +  +vll+D v  TGg++ ++
  gi|119720054|ref|YP_920549.1|  53 RTIEFDAVCGIAV--GGLPIATALAYTLGKPLIYA----RRE--KKAHGTMKQLEGDYaRGMKVLLVDDVATTGGTLLDI 124
                                    4555566777777..78888887777777665553....333..34568899******89999***************** PP

                        UPRTase 141 iqlLkergvgeekIlvlsvlaseegvkrlae 171
                                     +lLk++g   e +  l v+  eeg++++++
  gi|119720054|ref|YP_920549.1| 125 ARLLKSEGL--EVVEALVVVDREEGASEALR 153
                                    ******988..56888889999999987765 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.022        96      23      72 ..      32      79 ..      24     103 .. 0.67
   2 !   16.0   0.1   1.4e-06    0.0063     111     150 ..      95     134 ..      77     158 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.022
                       PRTase_2 23 khiPvkpstvreagaaLaellaeakkeelpepvlvigfAEtAtaLghgva 72
                                   + +P +p++ r++++aLa+  ++ +    +   + +g    AtaL+ ++ 
  gi|119720054|ref|YP_920549.1| 32 RKLPSHPQAFRRVVEALAAVARTIEF--DAVCGIAVGGLPIATALAYTLG 79
                                   6799**************99884333..2233344555556666665554 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 1.4e-06
                       PRTase_2 111 yaedeellaaakelvLvDDEistGktalnliralqeklpr 150
                                    +++ e   a+  +++LvDD ++tG t+l+++r l+++  +
  gi|119720054|ref|YP_920549.1|  95 MKQLEGDYARGMKVLLVDDVATTGGTLLDIARLLKSEGLE 134
                                    4445566677889*******************99987543 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.011        48      47     101 ..      31      84 ..      11     112 .. 0.65
   2 ?    8.0   0.1   0.00081       3.6       8      46 ..     122     163 ..     118     172 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.011
                Glyco_trans_4_4  47 vprrpspladlaalralrrll.....rqrrerpdvvhahspt.aglaarlarrrrgiplvv 101
                                    ++      + +++++a+rr++      +r   +d v       +++a +la  + g pl++
  gi|119720054|ref|YP_920549.1|  31 LR------KLPSHPQAFRRVVealaaVARTIEFDAVCGIAVGgLPIATALAY-TLGKPLIY 84 
                                    33......34444555555444334323888999999988542666666666.77777776 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00081
                Glyco_trans_4_4   8 aelaraLaarGheVt...vltpapapgapeleedgvrvhrlp 46 
                                     ++ar L  +G eV+   v+++++ +++++l+ +g+r+++l 
  gi|119720054|ref|YP_920549.1| 122 LDIARLLKSEGLEVVealVVVDREEGASEALRSEGLRLRSLT 163
                                    789*********999887889999999***********9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.36s 00:00:00.93 Elapsed: 00:00:00.55
# Mc/sec: 950.61
//
Query:       gi|119720055|ref|YP_920550.1|  [L=358]
Description: ABC transporter related [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.4e-34  117.2   0.0    1.1e-33  116.6   0.0    1.3  1  ABC_tran         ABC transporter
    7.5e-10   39.1   0.5    0.00022   21.2   0.1    2.1  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    3.3e-09   37.4   0.4    1.4e-08   35.4   0.1    2.2  2  OB_MalK          MalK OB fold domain
      2e-07   31.5   0.1    6.9e-07   29.7   0.1    2.0  1  CysA_C_terminal  CysA C-terminal regulatory domain
    0.00028   20.4   0.1       0.14   11.6   0.0    2.2  2  SMC_N            RecF/RecN/SMC N terminal domain
    0.00065   20.1   0.0     0.0017   18.8   0.0    1.8  1  AAA_16           AAA ATPase domain
    0.00068   19.3   0.0     0.0013   18.4   0.0    1.4  1  AAA_29           P-loop containing region of AAA domain
     0.0049   16.8   0.0     0.0085   16.0   0.0    1.3  1  RsgA_GTPase      RsgA GTPase
  ------ inclusion threshold ------
       0.01   16.0   0.5      0.048   13.8   0.5    2.2  1  TOBE_2           TOBE domain
      0.014   15.9   0.0      0.024   15.2   0.0    1.3  1  AAA_23           AAA domain
      0.018   14.8   0.0      0.039   13.7   0.0    1.5  1  AAA_30           AAA domain
      0.028   14.7   0.0      0.094   13.0   0.0    1.8  2  AAA_22           AAA domain
      0.069   13.4   0.0       0.38   11.0   0.0    2.2  3  AAA_28           AAA domain
      0.092   12.7   0.0       0.32   10.9   0.0    1.8  2  NACHT            NACHT domain
       0.12   12.4   0.0        0.4   10.7   0.1    1.8  2  AAA_5            AAA domain (dynein-related subfamily)
       0.14   12.3   0.0       0.28   11.3   0.0    1.7  1  AAA_33           AAA domain
       0.15   12.6   0.0        0.3   11.6   0.0    1.5  1  AAA_18           AAA domain
       0.16   11.5   0.0       0.27   10.8   0.0    1.3  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
       0.17   11.8   0.0       0.28   11.0   0.0    1.2  1  ATPase_2         ATPase domain predominantly from Archaea


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.6   0.0   1.2e-36   1.1e-33       3     136 ..      20     160 ..      18     161 .. 0.90

  Alignments for each domain:
  == domain 1  score: 116.6 bits;  conditional E-value: 1.2e-36
                                    EEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                       ABC_tran   3 nvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren... 79 
                                    nv+l ++ ge  +++G++G+GKStLl+++agl++p+eGe+ + g+ +++     +++ i++++q+  l p++tv++n   
  gi|119720055|ref|YP_920550.1|  20 NVNLRVESGEFFVLLGPSGSGKSTLLRIIAGLEEPDEGEVIIGGRVVND--VDPSERDIAFVFQNYALYPHMTVYDNiaf 97 
                                    9**********************************************99..999************************** PP

                                    ..........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    ..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ..........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                              +  +++ +++s lgl++    ++++ p++LSgG++qrvalara+++kp+++llDEp 
  gi|119720055|ref|YP_920550.1|  98 plrmrkvpkdQIHARVLEVASMLGLTN----HLSKYPYQLSGGEQQRVALARAIVRKPRVFLLDEPL 160
                                    ****99755555555555555555555....556777*****************************7 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.1   2.3e-07   0.00022       1      22 [.      30      51 ..      30      97 .. 0.71
   2 !   16.4   0.0   6.4e-06    0.0061     234     299 ..     130     194 ..      97     198 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 2.3e-07
                         AAA_21  1 lnvliGpNgsGKSnLLdaldll 22
                                   + vl Gp gsGKS+LL+++ +l
  gi|119720055|ref|YP_920550.1| 30 FFVLLGPSGSGKSTLLRIIAGL 51
                                   68*****************999 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 6.4e-06
                         AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrll.ellkelsr.ngaQviltTHSp 299
                                    +++lS G ++  al+ a+ r +   +++l+DEp ++L+ kl  +l  el k+l++  ++  i +TH+ 
  gi|119720055|ref|YP_920550.1| 130 PYQLSGGEQQRVALARAIVRKP---RVFLLDEPLSNLDAKLRVKLRfELRKLLHDeLKTTTIYVTHDQ 194
                                    7999***99999*******988...**************88877776555666665557889999986 PP

>> OB_MalK  MalK OB fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0         6   5.7e+03      34      48 ..      47      63 ..      17      64 .. 0.61
   2 !   35.4   0.1   1.5e-11   1.4e-08       1      53 []     235     280 ..     235     280 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 6
                        OB_MalK 34 l..alklyagkevilGi 48
                                   +   l++ ++ evi+G 
  gi|119720055|ref|YP_920550.1| 47 IiaGLEEPDEGEVIIGG 63
                                   14456677888888885 PP

  == domain 2  score: 35.4 bits;  conditional E-value: 1.5e-11
                        OB_MalK   1 GSPaMNflpatveedgvlvegggvtlplpeeqklalklyagkevilGiRPEhi 53 
                                    G+P+MNflpa+v e+   +  g+  l++  e+   l++ a+ evilGiRP h+
  gi|119720055|ref|YP_920550.1| 235 GTPPMNFLPARVAEKT--LRLGN--LAIRSEE---LEGLAEGEVILGIRPQHL 280
                                    99***********886..55566..5555555...88*************996 PP

>> CysA_C_terminal  CysA C-terminal regulatory domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.1   7.4e-10   6.9e-07       1      43 []     240     282 ..     240     282 .. 0.98

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 7.4e-10
                CysA_C_terminal   1 NlFhGrvedGklriGglalpvPelagadgqevvayVRPhDlei 43 
                                    N++++rv + +lr+G+la+  +el+g +++ev++++RP +le+
  gi|119720055|ref|YP_920550.1| 240 NFLPARVAEKTLRLGNLAIRSEELEGLAEGEVILGIRPQHLEV 282
                                    9****************************************98 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.0    0.0042         4      25      42 ..      29      46 ..      18      51 .. 0.83
   2 !   11.6   0.0   0.00015      0.14     135     212 ..     107     207 ..      61     214 .. 0.60

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0042
                                   SEEEEEESTTSSHHHHHH CS
                                   xxxxxxxxxxxxxxxxxx RF
                          SMC_N 25 sftaivGpNGSGKsnlld 42
                                   +f +++Gp GSGKs ll 
  gi|119720055|ref|YP_920550.1| 29 EFFVLLGPSGSGKSTLLR 46
                                   68899*********9986 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00015
                                    T........................CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHH....HH CS
                                    x........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xx RF
                          SMC_N 135 e........................lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellk....ek 186
                                    +                        +LSgGe++ vala   Ai  v++  ++llDe  ++LD+k + k+   l+     +
  gi|119720055|ref|YP_920550.1| 107 DqiharvlevasmlgltnhlskypyQLSGGEQQRVALAR--AI--VRKPRVFLLDEPLSNLDAKLRVKLRFELRkllhDE 182
                                    05555555555555555555556669******9888764..44..45555789***999999988777765555111033 PP

                                    CTTSEEEEE-SSHHHCCC-SCEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 187 sknaQfivislreemlekadklvgvt 212
                                      ++  i +++++     +   vgv 
  gi|119720055|ref|YP_920550.1| 183 L-KTTTIYVTHDQVEAMTMADRVGVI 207
                                    3.355566666665555555556665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.8e-06    0.0017      10      57 ..      16      61 ..       9     203 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.8e-06
                         AAA_16 10 eqLlsalervrsgrpelvllsGesGvGKsslvrellralekdggiflr 57
                                   +++ ++  rv sg  e  +l G+sG+GKs+l+r ++   e d+g ++ 
  gi|119720055|ref|YP_920550.1| 16 AAVYNVNLRVESG--EFFVLLGPSGSGKSTLLRIIAGLEEPDEGEVII 61
                                   4444444467777..789**************9998544444344433 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.4e-06    0.0013      17      39 ..      23      45 ..      17      51 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.4e-06
                         AAA_29 17 ieidlkgatlltGpsGsGKSTll 39
                                   ++++  ++++l GpsGsGKSTll
  gi|119720055|ref|YP_920550.1| 23 LRVESGEFFVLLGPSGSGKSTLL 45
                                   5566445999************8 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0     9e-06    0.0085      99     124 ..      28      53 ..       8      61 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 9e-06
                                    TSEEEEECSTTSSHHHHHHHHCTT-- CS
                    RsgA_GTPase  99 dktsvlvGqSGvGKStLinallpele 124
                                    +++ vl+G+SG GKStL+  +++ +e
  gi|119720055|ref|YP_920550.1|  28 GEFFVLLGPSGSGKSTLLRIIAGLEE 53 
                                    4899**************99988555 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.5   5.1e-05     0.048       1      66 [.     273     332 ..     273     335 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.1e-05
                         TOBE_2   1 laiRPEklrlaaagganglsGtVedveylGsstryvvelaggqlvvvrqpnadrdsalapGdtVel 66 
                                    l+iRP +l++   g  +gl+ +V+ ve lG+ + ++   +g +  +++ + ++ +++++   +V+l
  gi|119720055|ref|YP_920550.1| 273 LGIRPQHLEV---GE-EGLPVRVVGVERLGTGSILHGVFEGFEV-TAYSEKRE-HAQPELNAEVRL 332
                                    79********...54.8**************9999966666544.44444444.346666666666 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   2.5e-05     0.024      18      39 ..      27      48 ..       9      50 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.5e-05
                         AAA_23 18 skgltlItGpNGaGKTTildAi 39
                                   s  ++++ Gp G+GK+T+l+ i
  gi|119720055|ref|YP_920550.1| 27 SGEFFVLLGPSGSGKSTLLRII 48
                                   55799**************987 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   4.1e-05     0.039      16      50 ..      27      60 ..      20      65 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.1e-05
                         AAA_30 16 sgdrvavltGpAGtGKttalkalreaweaaggrvi 50
                                   sg  + vl Gp G+GK+t+l+ ++ + e ++g+vi
  gi|119720055|ref|YP_920550.1| 27 SG-EFFVLLGPSGSGKSTLLRIIAGLEEPDEGEVI 60
                                   45.4999****************999998866666 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0    0.0001     0.094       4      26 ..      27      49 ..      24      77 .. 0.87
   2 ?   -2.0   0.0       4.1   3.9e+03      84      99 ..     145     158 ..     121     198 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.0001
                         AAA_22  4 tagilvvtGesGtGKTtllrrll 26
                                   +  + v+ G+sG+GK+tllr ++
  gi|119720055|ref|YP_920550.1| 27 SGEFFVLLGPSGSGKSTLLRIIA 49
                                   567899************99665 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.1
                         AAA_22  84 qalraravielliiDE 99 
                                    +a+ ++ +  ++++DE
  gi|119720055|ref|YP_920550.1| 145 RAIVRKPR--VFLLDE 158
                                    33333333..566665 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0    0.0004      0.38       2      20 ..      31      49 ..      30     112 .. 0.85
   2 ?   -1.9   0.0       3.8   3.6e+03     108     142 ..     149     184 ..     128     196 .. 0.59
   3 ?   -1.5   0.0       2.8   2.7e+03      83     107 ..     310     333 ..     308     345 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0004
                         AAA_28  2 ivitGgestGKTtlleaLa 20
                                   +v++G++++GK+tll+ +a
  gi|119720055|ref|YP_920550.1| 31 FVLLGPSGSGKSTLLRIIA 49
                                   79*************9988 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.8
                         AAA_28 108 rydlvfllpp.apeidddgeRre.dleereaiderlr 142
                                    r  +vfll++    + d + R + ++e r+ +++ l+
  gi|119720055|ref|YP_920550.1| 149 RKPRVFLLDEpLSNL-DAKLRVKlRFELRKLLHDELK 184
                                    334466666325555.666665446666666666665 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 2.8
                         AAA_28  83 ldtlaYarayggeaeaeleaaarek 107
                                    ++++aY++ ++ + ++el+a++r k
  gi|119720055|ref|YP_920550.1| 310 FEVTAYSEKREHA-QPELNAEVRLK 333
                                    5678999999999.99999998865 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00033      0.32       4      21 ..      32      49 ..      29      55 .. 0.88
   2 ?   -1.4   0.0       2.1   1.9e+03      84     115 ..     148     181 ..      93     200 .. 0.51

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00033
                                   EEEC-TTTCHHHHHHHHH CS
                          NACHT  4 ilqGeaGsGKTtLlqkla 21
                                   +l G++GsGK+tLl+ +a
  gi|119720055|ref|YP_920550.1| 32 VLLGPSGSGKSTLLRIIA 49
                                   899***********9886 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.1
                                    E.....EEEE-.STT-SS-TCH.........HHHHHCT CS
                          NACHT  84 L.....lilDg.lDelvtdlgqkekqpvrtlLselirk 115
                                    +     ++lD  l  l ++     + ++r  L++l+  
  gi|119720055|ref|YP_920550.1| 148 VrkprvFLLDEpLSNLDAK----LRVKLRFELRKLLHD 181
                                    2333335555323334333....333555555555554 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00042       0.4       3      21 ..      32      50 ..      31      64 .. 0.86
   2 ?   -3.3   0.0       8.9   8.4e+03      61      73 ..     146     158 ..     126     159 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00042
                                   EEE--SSSSHHHHHHHGGG CS
                          AAA_5  3 lLvGppGtgKselaerlaa 21
                                   +L+Gp+G+gKs+l + +a 
  gi|119720055|ref|YP_920550.1| 32 VLLGPSGSGKSTLLRIIAG 50
                                   8*************99886 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 8.9
                                    ----G-SEEEEES CS
                          AAA_5  61 raaregeilvlDE 73 
                                      +r++++++lDE
  gi|119720055|ref|YP_920550.1| 146 AIVRKPRVFLLDE 158
                                    2456899999998 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0    0.0003      0.28       3      19 ..      32      48 ..      30     194 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0003
                         AAA_33  3 llvGlpGsGKstlaerl 19
                                   +l G++GsGKstl++ +
  gi|119720055|ref|YP_920550.1| 32 VLLGPSGSGKSTLLRII 48
                                   688**********9865 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00032       0.3       3      31 ..      33      69 ..      32      96 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00032
                         AAA_18  3 ltGtpGvGKttlakeLskrlgf........gvnlrdv 31
                                   l G++G+GK+tl + ++ +++         g++++dv
  gi|119720055|ref|YP_920550.1| 33 LLGPSGSGKSTLLRIIAGLEEPdegeviigGRVVNDV 69
                                   89************99766433444445555555555 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00028      0.27       3      36 ..      31      69 ..      29      90 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00028
                                   EEEEESTTCCHHHHHHHHH..CT--SS-EEE...EESS- CS
                           cobW  3 tvltGflGsGKTtLlnhll..enraglklav...ivNef 36
                                   +vl G+ GsGK+tLl+ +   e+ ++ ++ +   +vN++
  gi|119720055|ref|YP_920550.1| 31 FVLLGPSGSGKSTLLRIIAglEEPDEGEVIIggrVVNDV 69
                                   6899************99854333333333333345555 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0    0.0003      0.28      17      43 ..      25      51 ..      14      61 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0003
                       ATPase_2 17 repneiyfiYGpegsGKtaLlkeiien 43
                                    e+ e+ ++ Gp gsGK++Ll+ i+  
  gi|119720055|ref|YP_920550.1| 25 VESGEFFVLLGPSGSGKSTLLRIIAGL 51
                                   56788999*************977655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 2151.36
//
Query:       gi|119720056|ref|YP_920551.1|  [L=279]
Description: binding-protein-dependent transport systems inner membrane component [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-11   44.5  13.7    1.4e-11   44.5  13.7    1.9  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   7.0      0.41   7.4e+03      43      71 ..      72     127 ..       6     129 .. 0.56
   2 !   44.5  13.7   7.9e-16   1.4e-11       4     181 ..      95     266 ..      88     273 .. 0.71

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 0.41
                   BPD_transp_1  43 f...........................vilsilghlilpviillllsaapyvrli 71 
                                                                ++l   g   +  ++l+ll+ +p+++li
  gi|119720056|ref|YP_920551.1|  72 RwvlntalvsglvvaanivtsatagyafAFLRFPGKNKIFSALLALLMVPPFITLI 127
                                    04334444444444445555556666667777778888888888888888887765 PP

  == domain 2  score: 44.5 bits;  conditional E-value: 7.9e-16
                   BPD_transp_1   4 lGilaalnrnkkldkllrpliivllslPsfv.laillvlvfvilsilghlilpviillllsaapyvrlirraalrslpkd 82 
                                    +G+  a + ++++++ +     +ll++P+f+ l++  +lv     + g       +++l sa    ++++r++  sl ++
  gi|119720056|ref|YP_920551.1|  95 AGYAFA-FLRFPGKNKIFSALLALLMVPPFItLIPNYILV----VKMGLIDNLFGLAFLGSASVSGIFLMRQYYLSLGRE 169
                                    566666.444455555555555555666666155555533....67777777778888888889999999********** PP

                   BPD_transp_1  83 lveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseisnggvlalv 162
                                    l eaar++Ga++ + f++v+lP+++p + +++i++f g+++ ++ ++ ++ +p   tl +  + ++  s+++   +  ++
  gi|119720056|ref|YP_920551.1| 170 LFEAARLDGAGPLRAFVYVALPLSKPALGALAIYQFLGAWNSFLGPLVFLRSPENYTLPVGLNFAFSRSMWT--EYTPII 247
                                    **************************************************9995444444444444444444..555555 PP

                   BPD_transp_1 163 iavlllnlvadilqrlldp 181
                                    +  ll +l + il+ ll++
  gi|119720056|ref|YP_920551.1| 248 AGSLLASLPTIILYVLLNK 266
                                    5555555555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      182  (0.0101512); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1875.74
//
Query:       gi|119720057|ref|YP_920552.1|  [L=314]
Description: binding-protein-dependent transport systems inner membrane component [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-17   63.6  14.8    1.9e-17   63.6  14.8    1.7  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   1.0       0.3   5.4e+03     155     161 ..      28      34 ..      13      49 .. 0.41
   2 !   63.6  14.8   1.1e-21   1.9e-17       3     175 ..     106     301 ..      87     310 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.3
                   BPD_transp_1 155 nggvlal 161
                                    ++g++ +
  gi|119720057|ref|YP_920552.1|  28 VFGYFSM 34 
                                    1111111 PP

  == domain 2  score: 63.6 bits;  conditional E-value: 1.1e-21
                   BPD_transp_1   3 llGilaa..lnrnkkldkllrpliivllslPsfvlaillvlvf...................vilsilghlilpviilll 61 
                                    ll++++a   n++ ++++++r+ ++++ ++ ++++ ++++++f                    +l++  +l  +++i+++
  gi|119720057|ref|YP_920552.1| 106 LLALVLAvlANQKVRGSHFFRVAYFLPATTCPVIVSLIFIWLFmrdgfvnyfvsavtggfrpDWLNDPLFLLPAIAIVAI 185
                                    677888877789999999*******99999888888888888899*********************************** PP

                   BPD_transp_1  62 lsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG..lgt 139
                                    +++ + +  ++ a+l++lpk+ +eaar++Ga+  ++f ++++P+++p i+  ++l ++g+l  + l+  +++++G   g 
  gi|119720057|ref|YP_920552.1| 186 WGTSAHFSATFLAGLQALPKEVYEAARIDGANALKRFIYITIPLMKPLIVYAVVLGSIGALQMFDLAWVMAGQSGgpGGA 265
                                    ***********************************************************************99999*788 PP

                   BPD_transp_1 140 llleailgydyseis..nggvlalviavlllnlvadil 175
                                      + a+ +y++++ +  +g+++a +++++l+++++   
  gi|119720057|ref|YP_920552.1| 266 GYTVALDIYNTAFLQlrYGYAAAKAVLLFLIVFSL--N 301
                                    88888888888888854444444444444444443..3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 2259.13
//
Query:       gi|119720058|ref|YP_920553.1|  [L=393]
Description: extracellular solute-binding protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    7.7e-36  124.6  15.7    9.3e-36  124.4  15.7    1.1  1  SBP_bac_1   Bacterial extracellular solute-binding protein
    1.3e-33  117.1   5.8    1.6e-33  116.8   5.8    1.1  1  SBP_bac_8   Bacterial extracellular solute-binding protein
      1e-05   25.4   0.0    5.7e-05   23.0   0.0    2.0  1  SBP_bac_11  Bacterial extracellular solute-binding protein
  ------ inclusion threshold ------
      0.064   13.1   0.1       0.17   11.7   0.1    1.8  1  VbhA        Antitoxin VbhA


Domain annotation for each model (and alignments):
>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.4  15.7   2.1e-39   9.3e-36       4     314 ..      11     306 ..       8     307 .. 0.91

  Alignments for each domain:
  == domain 1  score: 124.4 bits;  conditional E-value: 2.1e-39
                                    HHHHHHHHHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHHHHTTSSSCSEEEECGGHHHHHHHTTSBECCHHHHHHTTE CS
                      SBP_bac_1   4 ltegaalqalvakafekehpgikVeiesvgsgslaqkltlaiaaGdgpaDviavdndwiarlakaglllpldpyvkayla 83 
                                    +te++ +q+++ ++f+k++p+i V++e + ++ + +++ +  aaG++p D+++vd++w ++++++g+l p+++ + ++ +
  gi|119720058|ref|YP_920553.1|  11 ETEMKNYQKII-EDFQKANPDIIVKYEVI-TQMFSENILASYAAGAAP-DIFYVDSAWAPTFISKGALYPIGDKLPKDFI 87 
                                    678889*****.*****************.999999**********88.*****************************99 PP

                                    CTTCCTEEEEHHHHTHHHHCE.EE....ES.EEEEE.EEEEEEETTTHHCTTGGG...SHBHHHHHHHHHHHHHHCTCTH CS
                      SBP_bac_1  84 pgvkdaadklsssvlpkilds.kv....ly.vPlya.argliYNkdlfekagldp...pwtWdelveaakklkekgkkpi 153
                                    ++           ++p  l+  k+    +y +P +  +  l+YNk+lf++ag+++    wtWd+l  aak +  k++kp+
  gi|119720058|ref|YP_920553.1|  88 DQ-----------FYPFLLEPfKGpdgkIYgLPKDWsVLSLFYNKKLFAQAGVPEptaDWTWDDLFNAAKTIYQKTGKPG 156
                                    99...........999999999999999*******55******************************************6 PP

                                    CCHCCEEHHHHHHHHHHHHHHHHTGGGEECCCT..HHCSHHHHSHHHHHHHHHHHHHHHHHHHTTEEECSSHHHHHHHHH CS
                      SBP_bac_1 154 ggarggsasgtayyfalalakslggkvfdkdgg..gldnpegvtaatylvklyavanltkelkgkgaenkdgaaalalfe 231
                                     +++   + +  ++    ++++++++ fd+ +    +d+pe  +a+  + +++ ++ ++     ++  n++++    +f 
  gi|119720058|ref|YP_920553.1| 157 LVVHAELNRWVPFL----VSNGAPPPRFDSAADaaYFDKPEVRNAISKMIAKIQEGRKEGYIVLPSDVNAGWNG--EAFG 230
                                    66666555555555....67999999999999998889999999*********777777777777777777777..7899 PP

                                    TTSCSEEEEEHHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEEEEEEEEEEBTTCSTHHHHHHHHHHHTSH CS
                      SBP_bac_1 232 aGeaamaivglwaalaamkvapkvafaadkekpkeelgvaplPagkggkpgilgayglaipkgsknpeaAkkFldfllsp 311
                                    +  aam+i g+w+        p  a+ ++  k++ +++ a+lP+g+ g  +  ++  l++++++ n +aA kFl+++ + 
  gi|119720058|ref|YP_920553.1| 231 KQLAAMTIEGSWM-------IPYLADQFPNFKYGSDWDLAMLPKGPAGRASMAYTVALGVNSKTENLDAALKFLQYVEGI 303
                                    *************.......8***************************9999************************9888 PP

                                    HHH CS
                      SBP_bac_1 312 eaq 314
                                    e+q
  gi|119720058|ref|YP_920553.1| 304 EGQ 306
                                    877 PP

>> SBP_bac_8  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.8   5.8   3.5e-37   1.6e-33       1     274 [.      19     329 ..      19     336 .. 0.75

  Alignments for each domain:
  == domain 1  score: 116.8 bits;  conditional E-value: 3.5e-37
                                    HHHHHHHHH-.TEEEEEEE--SSSHHHHHHHHHHTT---SEE.EEE-HHHHHHHHHTTSB--GG.GS..TTHHH-HH.HH CS
                      SBP_bac_8   1 klakefekkt.gvkvnvvtaasndleqklkaalaagtapdidvvwanedalatlaeeglladls.dl..dnlddltd.al 75 
                                    k++++f+k++ ++ v+++ +  +   +++ a+ aag apd  +++ ++++++t++ +g+l+++  +l  d +d++ +  l
  gi|119720058|ref|YP_920553.1|  19 KIIEDFQKANpDIIVKYEVIT-QMFSENILASYAAGAAPD--IFYVDSAWAPTFISKGALYPIGdKLpkDFIDQFYPfLL 95 
                                    689*********999998885.4667889999*******7..679999***************97443367777766799 PP

                                    HTT--.TS.----EEEEEEE-EEEEEHHHHHHS......---BHHHHHHHHHHHHHH-...SEGG---.GGGGGGTHH.. CS
                      SBP_bac_8  76 aavgy.dgklygvPyasetpyvliynkdlleka.....edpktwdellaaakklkgkf...glpdpas.gwlqaalla.. 143
                                    +++++ dgk+yg+P +++    l+ynk+l+ +a        +twd+l+ aak++ +k+   gl   a+ + +  +l+   
  gi|119720058|ref|YP_920553.1|  96 EPFKGpDGKIYGLPKDWSV-LSLFYNKKLFAQAgvpepTADWTWDDLFNAAKTIYQKTgkpGLVVHAElNRWVPFLVSng 174
                                    999666************7.8***********999877778********9999966663335544443255566666644 PP

                                    .........ETTEE---H..HHH.HHHHHHHHHHHHTT-EE...-S..--SS.TTTTTSBSEEEE-TTHHHHHH...... CS
                      SBP_bac_8 144 .........kdgksldddggkdglkealellkklkdngkty...dtgadavs.efanGevaftingswdiaaaq...... 204
                                             +d +++d+   + ++ ++++++++ ++ g+++   d +a ++  +f ++ +a+ti gsw i  ++      
  gi|119720058|ref|YP_920553.1| 175 appprfdsaADAAYFDKPEVRNAISKMIAKIQEGRKEGYIVlpsDVNAGWNGeAFGKQLAAMTIEGSWMIPYLAdqfpnf 254
                                    44444444333333332222345588888888888888766765223444446*********************666666 PP

                                    -TTTSEEEE.--S--.....EEEEEEEEEEBTTS-HHHHHHHHHHHHHTTSHHHHHHHHHH--.-BS-S-TTTHHHH CS
                      SBP_bac_8 205 kagkklgai.vpkqg.....sfaggkglavpknaknedlaAldFlkwltspenqaalaektgy.ipvnksaalspev 274
                                    k g ++  + +pk g     s+a +  l v+++++n d aAl+Fl+++   e+q+ l+ k+g  +p++k++a++p++
  gi|119720058|ref|YP_920553.1| 255 KYGSDWDLAmLPK-GpagraSMAYTVALGVNSKTENLD-AALKFLQYVEGIEGQKLLVVKMGHtLPSIKALANDPDL 329
                                    6666666553353.222344777777788999999999.7****************999888768*******97764 PP

>> SBP_bac_11  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   1.3e-08   5.7e-05      14     224 ..      18     309 ..       8     314 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 1.3e-08
                                    HHHHHHH.HHHH-..--E.EEEESSHHHHHHHHHHH..-SEEEESSH.HHHHHHHHGGGGG...GG-EEEEEEEEEEEES CS
                     SBP_bac_11  14 relaaaF.eahtg..vkv.evsaggsgklarqiadgarpDvwipassawlellaaaglvqa...esavplassplviavp 86 
                                    + ++++F +a+++  vk+ +++   s +++++ a+ga+pD++  +s aw    +++g++ +   + ++++      ++  
  gi|119720058|ref|YP_920553.1|  18 QKIIEDFqKANPDiiVKYeVITQMFSENILASYAAGAAPDIFYVDS-AWAPTFISKGALYPigdKLPKDFIDQFYPFLLE 96 
                                    6799***555899999994445778********************8.7***************97788888888777776 PP

                                    TT-.........TT---SHHH...HHHSS-..-EEEE--T-TTTTH....H.HHHHGGG--................... CS
                     SBP_bac_11  87 kgn.........pkkikgwad...Llkpgl..klavadPttspsGl....aalalleaaga................... 129
                                    + +         p   k+w       +++l  + +v+ Pt++ + +    aa++++++ g+                   
  gi|119720058|ref|YP_920553.1|  97 PFKgpdgkiyglP---KDWSVlslFYNKKLfaQAGVPEPTADWTWDdlfnAAKTIYQKTGKpglvvhaelnrwvpflvsn 173
                                    6665333342222...444443323334666999*****99999997777777777777777777777777777777777 PP

                                    ........HHHHHHHHHTEEEEESSHHHHHHHHHTTT-SEEEEEHHHHH......HSTTSSEEEE--TTT--........ CS
                     SBP_bac_11 130 ........qellkalekkvvklgessrqlltaveageadagivyeseakaa....engdkleavylpeglnld....... 190
                                            ++ + a ++k    +++++ +++ +++g+ + +iv  s+++a     + g+ l a ++  +++++       
  gi|119720058|ref|YP_920553.1| 174 gappprfdSAADAAYFDKPE-VRNAISKMIAKIQEGRKEGYIVLPSDVNAGwngeAFGKQLAAMTIEGSWMIPyladqfp 252
                                    78888887778888888877.56777999999**************99644556468999999999999998679999** PP

                                    .........................EEEEEEEE-TT--HHHHHHHHHTTSHHHHHHH CS
                     SBP_bac_11 191 .......................pldypaavlkkaakreaAraFlafLrspeaqail 224
                                                             +++++v +k+ +  aA +Fl+++ + e+q++l
  gi|119720058|ref|YP_920553.1| 253 nfkygsdwdlamlpkgpagrasmAYTVALGVNSKTENLDAALKFLQYVEGIEGQKLL 309
                                    *******************99554455555556778889***************987 PP

>> VbhA  Antitoxin VbhA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   3.9e-05      0.17      30      46 ..     369     385 ..     365     386 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.9e-05
                           VbhA  30 yvrGeIdadElvrrvra 46 
                                     vrGeI++dE++r ++ 
  gi|119720058|ref|YP_920553.1| 369 AVRGEITIDEALRLMKD 385
                                    59***********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 2776.81
//
Query:       gi|119720059|ref|YP_920554.1|  [L=353]
Description: glycosidase, PH1107-related [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-56  192.0   0.2    2.5e-27   95.7   0.0    2.0  2  Glyco_hydro_130  beta-1,4-mannooligosaccharide phosphorylase


Domain annotation for each model (and alignments):
>> Glyco_hydro_130  beta-1,4-mannooligosaccharide phosphorylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.7   0.0   1.4e-31   2.5e-27       3     117 ..      30     144 ..      28     153 .. 0.96
   2 !   94.6   0.2   2.9e-31   5.3e-27     210     321 ..     238     349 ..     225     350 .. 0.89

  Alignments for each domain:
  == domain 1  score: 95.7 bits;  conditional E-value: 1.4e-31
                                    ---TT-------TT--SSEEE-TTS-STTEEEEEEEEEEEETTE......EEEEEEEEETTS-E.EEEEEEESSS.SS-E CS
                Glyco_hydro_130   3 rkietidileRvsyitgedvrisnnpvrkpvavFNpavvlvekeLevyaRvvllYrkyvsdiaslrigledlkdG.ikkt 81 
                                    r+  ++d++eR+ yit+  v+++n + r+pvavFNp++ l + ++ +++R+v++Y+ yvs++  +r+g++dl++G i  t
  gi|119720059|ref|YP_920554.1|  30 RRGLEQDVFERLAYITPIRVEVTN-YARRPVAVFNPGAALEGSNVAIFPRMVFDYYWYVSSVGRIRVGVDDLLSGsIPGT 108
                                    666678****************77.******************************************************* PP

                                    E-SS---EE-TTS-B--EEEEEEEEETTEEEEEEE. CS
                Glyco_hydro_130  82 lepeevvlpedkqellgveDPRvvkinskyyltYtg 117
                                    l++++v+ p  ++el g+eDPRv+  +++y ++Ytg
  gi|119720059|ref|YP_920554.1| 109 LKADLVIYPSEEWELRGCEDPRVYGADGNYLVLYTG 144
                                    ***********************************8 PP

  == domain 2  score: 94.6 bits;  conditional E-value: 2.9e-31
                                    GGS...SEEEE-S--EEETTE.EEEEEEEEETTEEEEEEEEEEE-SS-SEEEEBSS-SB-S-SHH.HHSSSSSSBEEEEE CS
                Glyco_hydro_130 210 fenpfelkigwgtppvetkeg.lLvlihgvdteklvYrvgaalldlegkvlartkeyilePeeey.EeyGdrpnvvFpcg 287
                                      + fe k+gw+t+ ++ + g +Lv++hgv  +  vYr+g+a++  eg +l    ey+l+P++   E yGdrp vvF+cg
  gi|119720059|ref|YP_920554.1| 238 VAESFEYKVGWSTNALKLSSGeYLVGWHGVGVD-NVYRNGLAVVSEEGELLEL-SEYLLVPRKSLeEFYGDRPGVVFGCG 315
                                    5577***************999******99876.69************66655.679999987651569*********** PP

                                    EEE-TTEEEEEEEETTTEEEEEEEEHHHHHHHHH CS
                Glyco_hydro_130 288 alveeekvlvyyGaaDtaiglaeisveeildllk 321
                                    +l+ +ek+++++G++D a+g++ +++++ l+ lk
  gi|119720059|ref|YP_920554.1| 316 LLRIKEKLVWVGGVSDYAVGVFAVDMDKALEHLK 349
                                    ***************************9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       185  (0.0103185); expected 358.6 (0.02)
Passed bias filter:                      180  (0.0100396); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 2312.08
//
Query:       gi|119720060|ref|YP_920555.1|  [L=344]
Description: transcriptional regulator, TrmB [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      4e-54  183.3   0.0    5.3e-54  182.9   0.0    1.1  1  Regulator_TrmB  Archaeal transcriptional regulator TrmB
    1.4e-23   82.5   0.3    3.2e-23   81.4   0.3    1.6  1  TrmB            Sugar-specific transcriptional regulator TrmB
    0.00013   21.8   0.9    0.00065   19.5   0.0    2.5  3  MarR_2          MarR family
    0.00018   21.4   0.0    0.00068   19.5   0.0    2.0  1  MarR            MarR family
    0.00027   20.7   0.5    0.00087   19.0   0.0    2.1  2  HTH_IclR        IclR helix-turn-helix domain
    0.00032   20.2   0.1    0.00091   18.7   0.0    1.8  2  HTH_24          Winged helix-turn-helix DNA-binding
     0.0034   17.4   2.4      0.013   15.5   0.0    3.0  4  HTH_20          Helix-turn-helix domain
     0.0048   17.2   0.0      0.013   15.8   0.0    1.7  1  Rrf2            Transcriptional regulator
  ------ inclusion threshold ------
      0.023   14.5   0.0      0.086   12.7   0.0    2.0  1  HTH_5           Bacterial regulatory protein, arsR family
      0.025   14.6   0.0        2.2    8.3   0.0    2.9  3  HTH_29          Winged helix-turn helix


Domain annotation for each model (and alignments):
>> Regulator_TrmB  Archaeal transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  182.9   0.0   2.9e-57   5.3e-54       2     232 ..     119     342 ..     118     343 .. 0.98

  Alignments for each domain:
  == domain 1  score: 182.9 bits;  conditional E-value: 2.9e-57
                                    EEEESSHHHHHHHHHHHHHH-SSEEEEEE-GGGHHHHHHHHHHHHHTT-EEEEEESS----GGGSSSSEEEEEE-S---S CS
                 Regulator_TrmB   2 vwvvksretvierieelIesAenelivslpselLeelreeliaaaergvtVllliypdedleeldleevatevrvrrsga 81 
                                    vw++ ++++  + + + +esA++el+v++ s++L+ + ++l+++   + +++l++y+  ++++ ++ +v++evr+r ++a
  gi|119720060|ref|YP_920555.1| 119 VWTAVGQNAGESLFLSALESARHELLVAGYSKFLRGFLDRLART---DLATCLVLYD--GEDIGSFVNVFDEVRLRPTRA 193
                                    89***************************************777...79********..********************* PP

                                    .EEEEETTTEEEEE-SSS-EEEE--HHHHHHHHHHHHHH........HHH-EEEEEEES-TT-EEES-HHHHHHHHHHHT CS
                 Regulator_TrmB  82 pllvivDrkrgvvaprevlrdkeeeyaiifkekelihvlshyFlttlWktseviktdepvekpitfssirlavedikkll 161
                                    p+++i+D +++v+++    +++ + +a+++++++l++++  y+l++l  +++v+++++ + + +t++++ +a+e+i++ll
  gi|119720060|ref|YP_920555.1| 194 PQMAIPDFSQVVIVSG---WESGQVTAYKVTDDNLMRIFAVYYLDYLRGSGKVVAAKFGQLERRTYHHMTRALEHINALL 270
                                    **************99...************************************************************* PP

                                    .TTS-EEEEEEEEETTT--EEEEEEEEEEEEEETTTTEEEEEEEETTE.EEEEE-TT--SSSEEEEEEEEEE CS
                 Regulator_TrmB 162 raglkveaeveGrdtetgeevtieGrvveatlnstpgvaslvvetedg.evtVGGlgAvlEDieaeeitler 232
                                     ag+k++++v+Gr+++tgee+t++G +v+++ ns++ v +++++ edg ev+VGG gA+lED+ea+eit+e+
  gi|119720060|ref|YP_920555.1| 271 GAGRKPVLTVRGRWVATGEEATVRGVPVRLFENSFRSVGTILLKLEDGrEVSVGGVGAYLEDVEAYEITVEA 342
                                    *********************************************************************975 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.4   0.3   1.8e-26   3.2e-23       2      67 ..      15      81 ..      14      82 .. 0.97

  Alignments for each domain:
  == domain 1  score: 81.4 bits;  conditional E-value: 1.8e-26
                                   H.HCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE--H CS
                           TrmB  2 q.klGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYravdp 67
                                   +  lGL+eyEa++Y+aL+ +g++ta+e+a+++++p+++vY+v++ Le+kGlV +++g+p++++a+dp
  gi|119720060|ref|YP_920555.1| 15 AeSLGLREYEARAYIALVLYGSMTATELAKRSELPQPRVYDVVKALEEKGLVAISEGKPRKFSALDP 81
                                   5589**************************************************************9 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   3.6e-07   0.00065      17      56 ..      34      71 ..      18      75 .. 0.83
   2 ?   -1.1   0.1         1   1.8e+03      36      48 ..      98     110 ..      83     118 .. 0.63
   3 ?   -3.2   0.0       4.6   8.3e+03      12      32 ..     235     256 ..     232     272 .. 0.63

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 3.6e-07
                                   TTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                         MarR_2 17 rpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                    +   +t++ela+r  l++++v  ++k L+++GLv  ++g
  gi|119720060|ref|YP_920555.1| 34 YGS--MTATELAKRSELPQPRVYDVVKALEEKGLVAISEG 71
                                   444..9*****************************87755 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1
                                    HHHHHHHHHHHHT CS
                         MarR_2  36 savsrilkrLvaa 48 
                                    s+++ il+ L++a
  gi|119720060|ref|YP_920555.1|  98 STLNSILRLLESA 110
                                    5556666666666 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 4.6
                                    HHHHCTTTS.EEEHHHHHHHHT CS
                         MarR_2  12 aaLgrrpgr.dltvgelarrlg 32 
                                     +L+ ++       g+l+rr+ 
  gi|119720060|ref|YP_920555.1| 235 DYLRGSGKVvAAKFGQLERRTY 256
                                    5555555533336677777764 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   3.8e-07   0.00068      16      47 ..      35      66 ..      33      70 .. 0.95

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 3.8e-07
                                   TTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                           MarR 16 gplsvseLakklgvskstvtrvldrLekkGli 47
                                   g+++ +eLak++++ ++ v  v+++Le+kGl+
  gi|119720060|ref|YP_920555.1| 35 GSMTATELAKRSELPQPRVYDVVKALEEKGLV 66
                                   89*****************************9 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   4.9e-07   0.00087      18      48 ..      36      66 ..      27      68 .. 0.95
   2 ?   -3.8   0.1       6.8   1.2e+04      36      44 ..     257     265 ..     255     268 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 4.9e-07
                                   S-BHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                       HTH_IclR 18 eltlselArrtglpkStvhRlLqtLvelGyv 48
                                    +t +elA+r+ lp + v+  ++ L+e G+v
  gi|119720060|ref|YP_920555.1| 36 SMTATELAKRSELPQPRVYDVVKALEEKGLV 66
                                   69****************************9 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 6.8
                                    HHHHHHHHH CS
                       HTH_IclR  36 hRlLqtLve 44 
                                    h++++ L++
  gi|119720060|ref|YP_920555.1| 257 HHMTRALEH 265
                                    899999998 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   5.1e-07   0.00091      16      47 ..      35      66 ..      29      67 .. 0.95
   2 ?   -3.7   0.0       5.2   9.2e+03      33      42 ..      99     108 ..      98     110 .. 0.52

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 5.1e-07
                         HTH_24 16 prisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                   ++++ +eLA+r+ l+++ v   +k Lee+Gl+
  gi|119720060|ref|YP_920555.1| 35 GSMTATELAKRSELPQPRVYDVVKALEEKGLV 66
                                   6799**************************98 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 5.2
                         HTH_24  33 tvnrrlkrLe 42 
                                    t+n  l+ Le
  gi|119720060|ref|YP_920555.1|  99 TLNSILRLLE 108
                                    5555555555 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   7.4e-06     0.013      23      55 ..      35      67 ..      25      72 .. 0.91
   2 ?   -3.3   0.0       5.4   9.7e+03      45      53 ..     104     112 ..      98     117 .. 0.62
   3 ?   -1.5   0.0       1.5   2.7e+03      13      32 ..     153     172 ..     150     176 .. 0.81
   4 ?   -1.1   0.1       1.1     2e+03      37      50 ..     258     271 ..     244     273 .. 0.56

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 7.4e-06
                                   TTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                         HTH_20 23 egltaselaerldlskntlsyHLrvLeeagLve 55
                                   + +ta+ela+r +l++  +++ +++Lee gLv 
  gi|119720060|ref|YP_920555.1| 35 GSMTATELAKRSELPQPRVYDVVKALEEKGLVA 67
                                   689****************************96 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 5.4
                                    HHHHHHCTT CS
                         HTH_20  45 LrvLeeagL 53 
                                    Lr Le+a L
  gi|119720060|ref|YP_920555.1| 104 LRLLESASL 112
                                    566666544 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.5
                                    HHHHHHHSTCTTB-HHHHHH CS
                         HTH_20  13 rrilraLaraegltaselae 32 
                                    r++l+ Lar + +t+  l +
  gi|119720060|ref|YP_920555.1| 153 RGFLDRLARTDLATCLVLYD 172
                                    78999999999999987765 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 1.1
                                    -HHHHHHHHHHHHH CS
                         HTH_20  37 skntlsyHLrvLee 50 
                                    +++ +  H+++L  
  gi|119720060|ref|YP_920555.1| 258 HMTRALEHINALLG 271
                                    33445556666655 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   7.2e-06     0.013      21      61 ..      33      72 ..      22      74 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 7.2e-06
                                   STCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT CS
                           Rrf2 21 eeeepvsseeiaerqnispsylekilakLrkaglvksvrGk 61
                                     ++ ++++e+a+r +++++ +  +++ L+++glv   +Gk
  gi|119720060|ref|YP_920555.1| 33 LYGS-MTATELAKRSELPQPRVYDVVKALEEKGLVAISEGK 72
                                   4444.9******************************99997 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.8e-05     0.086      14      45 ..      35      66 ..      29      67 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.8e-05
                                   SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          HTH_5 14 gelcvcelaeelglsqstvShHLkkLreaGLV 45
                                   g+++++ela+  +l+q+ v    k+L+e GLV
  gi|119720060|ref|YP_920555.1| 35 GSMTATELAKRSELPQPRVYDVVKALEEKGLV 66
                                   99*****************************9 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0012       2.2      11      49 ..      35      74 ..      26      83 .. 0.79
   2 ?   -3.0   0.0       4.5     8e+03       7      28 ..     235     255 ..     233     256 .. 0.79
   3 ?    2.8   0.0     0.065   1.2e+02      21      46 ..     269     294 ..     266     299 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0012
                         HTH_29 11 GvstvsqiAkllglsrrtvyrwlkrfeegGlaalld.rrr 49
                                   G +t  ++Ak+  l  + vy+++k+ ee+Gl a+ + ++r
  gi|119720060|ref|YP_920555.1| 35 GSMTATELAKRSELPQPRVYDVVKALEEKGLVAISEgKPR 74
                                   55699999**********************9998664444 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.5
                         HTH_29   7 llaeGvstvsqiAkllglsrrt 28 
                                     + +G +    +Ak+ +l rrt
  gi|119720060|ref|YP_920555.1| 235 DYLRGSG-KVVAAKFGQLERRT 255
                                    5677887.88999999998887 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.065
                         HTH_29  21 llglsrrtvyrwlkrfeegGlaalld 46 
                                    llg  r+ v +++ r++++G++a+ +
  gi|119720060|ref|YP_920555.1| 269 LLGAGRKPVLTVRGRWVATGEEATVR 294
                                    68999*****************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 2168.84
//
Query:       gi|119720061|ref|YP_920556.1|  [L=704]
Description: Kojibiose phosphorylase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   3.3e-101  338.9   0.0     4e-101  338.7   0.0    1.1  1  Glyco_hydro_65m  Glycosyl hydrolase family 65 central catalyt
    5.4e-21   75.3   0.0    8.7e-21   74.6   0.0    1.3  1  Glyco_hydro_65N  Glycosyl hydrolase family 65, N-terminal dom


Domain annotation for each model (and alignments):
>> Glyco_hydro_65m  Glycosyl hydrolase family 65 central catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  338.7   0.0  4.5e-105    4e-101       2     387 .]     284     667 ..     283     667 .. 0.95

  Alignments for each domain:
  == domain 1  score: 338.7 bits;  conditional E-value: 4.5e-105
                Glyco_hydro_65m   2 lalfhllqtlaaadarldvgakGltGegYrGhvfWDtElfvlPlylltepevarnlLeyRynrleaArekAkekglkGAl 81 
                                    ++ fhllq +++   +  ++a+Gl+G gYrGhvfWD++++ lP+yll epe+ar++LeyR + l aAre A ++g +GA 
  gi|119720061|ref|YP_920556.1| 284 FNAFHLLQLYNEGGGEFMLPARGLHGYGYRGHVFWDSDTYSLPFYLLLEPEAARKILEYRCRCLGAAREYASSTGFRGAR 363
                                    789***************************************************************************** PP

                Glyco_hydro_65m  82 yPwesasdGeEesqelh.lnirsgewepdas.eeeiHvnaaiayavvqYveatgDeefleeeglellvetarfWasrael 159
                                    yPwe ++d +E ++    l+   ++   +++ + e H++a++ayav  Y+e+tgDeef+e++gl +++etarfWasr+el
  gi|119720061|ref|YP_920556.1| 364 YPWEGVDDCREATPVEVpLDLEGSRKAFIETgRLEQHITADVAYAVDMYYEYTGDEEFMERCGLRIIFETARFWASRVEL 443
                                    *************976658888887776666599********************************************** PP

                Glyco_hydro_65m 160 dkdkgryeidgviGPdEYeenvdnNaytnliaawnlelalealeeleeea......eklevkeeelekwekvleklylpi 233
                                        g y+i+gviGPdEY+ +vd+  ytn++a++nl l ++  +  +++        + +v+ ee e w +v+ ++ +p 
  gi|119720061|ref|YP_920556.1| 444 GG-DGYYHIRGVIGPDEYHVGVDDSFYTNVMARYNLVLGAKYYALSQSKPgwlrvaVEEGVSREEAEGWLEVAGRVRVPC 522
                                    *8.5**********************************9998887777668988876678999****************9 PP

                Glyco_hydro_65m 234 deelgviaqkdgflelaeldleeykalagdetdlllkaegdkvlesqviKQaDvllllyllkeefseeqikanldfYepr 313
                                    +   g++++++g+++l+ l++++     gd+      a+g +v  + ++KQaDv+ +l+ll+  f+++ ++ n ++Y++r
  gi|119720061|ref|YP_920556.1| 523 EP-GGLCEEFEGYFKLKDLEVSN---CFGDSC-----AKGLDVGSTRLVKQADVVAGLFLLRRFFDRRVLEGNYEYYLRR 593
                                    87.6*******************...777776.....78999999*********************************** PP

                Glyco_hydro_65m 314 tvhdSslSalvhaivaaelgklekalelfkeaariDldaqerstedGiHiaslagtleaivqgfaglrlregel 387
                                    t+h SslS  ++a +aa lg++e+al l+++aa++Dl+++ ++ edG H+a+ ag+++a+  gf gl+ r+g+l
  gi|119720061|ref|YP_920556.1| 594 TTHASSLSLPMYAAMAAYLGRVEEALALLRKAASTDLEDTYGNLEDGFHVAAAAGSWMALLLGFLGLEPRGGKL 667
                                    ********************************************************************999876 PP

>> Glyco_hydro_65N  Glycosyl hydrolase family 65, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.6   0.0   9.7e-25   8.7e-21      12     227 ..      15     234 ..       9     235 .. 0.86

  Alignments for each domain:
  == domain 1  score: 74.6 bits;  conditional E-value: 9.7e-25
                                    HHHHHT-EE-SSEEE----TTTT--...-EEETT-EE-T........TSSS-EE----EEEEEEEEETTEE--GGGSEEE CS
                Glyco_hydro_65N  12 lrEslftlGNGylGtRgafeeeysd..pgtyiaGvYdreiseeanGypeeneelvnlpdwlglrlrvdgeeldldegeil 89 
                                    +  +l+tl+NG l +Rg  e    +   gt++aGvY           p  ++elvnlp  +++ +++dg ++ + +g   
  gi|119720061|ref|YP_920556.1|  15 KIATLTTLSNGFLSVRGDPET--APseYGTLVAGVYSYT--------PIFYRELVNLPRITPVYVELDGVPMLPVQG--- 81 
                                    5679*****************..22225********666........9*********************99777665... PP

                                    EEEEEEETTTTEEEEEEEEE-TTS-EEEEEEEEEE-SSSTTEEEEEEEEEESS--EEEEEEEEEETT--B.......... CS
                Glyco_hydro_65N  90 dyereLdlreGvltrsltwrspagkevrveserfvsladrhlaairlevtplnfsgevevesgldgdvan.......... 159
                                    + e  Ld + G+l+ +  + s+ g e++ es r+++++ + ++a+r+++ + n++g++ ++  ++ d+ n          
  gi|119720061|ref|YP_920556.1|  82 SNEFLLDAEGGTLSYKAILGSSLG-ELEYESLRLTHKKFKGIFALRYRLASRNAEGRLCIKHPIELDTLNvssppevkvk 160
                                    68999**************99987.7********************************************9877766554 PP

                                    ......................EEEEETTSS-EEEEEEEEEEEETTEE--SEE...SEEEEEEEEEE-TT-EEEEEEEEE CS
                Glyco_hydro_65N 160 ....ekhkdprka.........levrtresgitvavaartrveasgeklevee...ekiaqtlsvelkagetvtleKyva 223
                                        e       +         l vrt ++ ++v +a  +r + ++ k        ++++  + v++k+g+ v+ eK+v+
  gi|119720061|ref|YP_920556.1| 161 lykvE-------EvsaegsspsLSVRTADNAYRVLYALIVRGSPAEPKS---YytgKEVGSCYCVDVKPGSVVEGEKVVI 230
                                    43221.......0223455678***************998887766655...1456************************ PP

                                    EEET CS
                Glyco_hydro_65N 224 vats 227
                                    va s
  gi|119720061|ref|YP_920556.1| 231 VALS 234
                                    9977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (704 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       268  (0.0149478); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 4441.48
//
Query:       gi|119720062|ref|YP_920557.1|  [L=226]
Description: HAD family hydrolase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.9e-05   23.3   0.0    8.8e-05   23.0   0.0    1.2  1  HAD        haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.029   14.7   0.0      0.045   14.0   0.0    1.3  1  Hydrolase  haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   9.9e-09   8.8e-05       2     110 ..       8     121 ..       7     169 .. 0.71

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 9.9e-09
                            HAD   2 lfDfDgTLldgdslelllrfllrrgaprlwralreklllalfrellrldraglaelleallagls...eelaaelerfva 78 
                                    ++DfDg ++ +   e+++    +++++ l    +e++++++    + + r++ a+++ ++l+gls   +++++++++f  
  gi|119720062|ref|YP_920557.1|   8 VWDFDGVIVETPHEEAWAA---ACREWGLEGFDHEFYEEYV----SGRPRLEGARNVLSMLGGLSpsqPDFEKRVAEFA- 79 
                                    9**********77777777...8888998888888888888....4445558889999999999833223444444444. PP

                            HAD  79 evirpk..........lldpgalellaahraaGdrvvvvSgg 110
                                    e +++             + +++ +++ +r++G+++v+ S++
  gi|119720062|ref|YP_920557.1|  80 ERKTEIylrlvgegryRVRRDVVNFISYARREGIPQVLASAS 121
                                    33333356666666432445*********************9 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0     5e-06     0.045       4     205 ..       7     182 ..       5     187 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5e-06
                                    EEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHH..HHHHHETTTEHHHHTHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase   4 vvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakarsgal..tgfatfigrgayaigkpewltald 81 
                                    +v+D+dG+++  e  +e++++ a                       + + + +   ++f +     +y  g+p++  a +
  gi|119720062|ref|YP_920557.1|   7 FVWDFDGVIV--ETPHEEAWAAA-----------------------CREWGLEGfdHEFYE-----EYVSGRPRLEGARN 56 
                                    5777777777..44466666666.......................7777444455*****.....********999997 PP

                                    CHHHHHHHHHHHHHHCHHHHHH...TTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHH.HHHHH.TT CS
                                    xxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx.xx RF
                      Hydrolase  82 ippdlgaaigsaqsqgrtvall...qaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetae.raanq.lG 156
                                    + + lg    s  +  + va     + +++  +  +  ++v+ +++ ++ + ++ gi+ vl++ +    +  r     lG
  gi|119720062|ref|YP_920557.1|  57 VLSMLGGLSPSQPDFEKRVAEFaerKTEIYLRLVGEGRYRVRRDVVNFISYARREGIPQVLASASRNVLVVlRKEPSlLG 136
                                    7777777777777776666666444445555566679999*****************99999976665555455555566 PP

                                    GGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase 157 ddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgvnDaaa 205
                                       fda ++++     +++ ++++ + ++     +  + ++D++ +++a
  gi|119720062|ref|YP_920557.1| 137 --LFDADVSGSGRSKDEVLSSALRVVRERWP-AVACNVLFEDSPAGVEA 182
                                    ..66666666666677777666666666662.23334555666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1553.90
//
Query:       gi|119720063|ref|YP_920558.1|  [L=315]
Description: aspartate carbamoyltransferase catalytic subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-42  143.9   0.0    4.9e-42  143.4   0.0    1.2  1  OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl
    1.2e-21   77.4   0.0    1.8e-21   76.9   0.0    1.2  1  OTCace    Aspartate/ornithine carbamoyltransferase, Asp/Orn b


Domain annotation for each model (and alignments):
>> OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.4   0.0   5.5e-46   4.9e-42       1     146 [.      15     153 ..      15     155 .. 0.95

  Alignments for each domain:
  == domain 1  score: 143.4 bits;  conditional E-value: 5.5e-46
                                    S-BSSGGGS-HHHHHHHHHHHHHHHHHHHTTT-STTTTT-EEEEEESS--HHHHHHHHHHHHHTTSEEEEEESTTTSCTT CS
                       OTCace_N   1 rhllsledlskeeieelldlaaelkekvkkekkekllkgktlallFeepStRTrvSfevAakrlGgkvlslseaediqls 80 
                                    r++ls+ d+s++++e+l+ +a++++++++    +  l+g +la+ F+epStRTr+Sf++A+ rlGg+ + l+ +  ++ s
  gi|119720063|ref|YP_920558.1|  15 RDVLSILDFSRSDLEYLFAEADRVRRDPS--AFSGELRGYVLATAFFEPSTRTRLSFQAAMLRLGGSCIDLG-E--LEKS 89 
                                    799**********************9987..89999************************************.3..6789 PP

                                    TGGSTTSSCHHHHHHHHHHHTSEEEEEES..SHHHHHHHHHHHSSEEEEEEETSSB-HHHHHHHHHHH CS
                       OTCace_N  81 svskgrkEsleDtarvlsryvdaiviRhp..gaeeleelakyasvpviNagdgdgeHPtQaLaDllti 146
                                    s++kg  E+++Dt+r+l++y+d+iv+Rh+  ga  ++  a+ a+ pviNagdg+++HPtQa++Dl+ +
  gi|119720063|ref|YP_920558.1|  90 SIAKG--ENFADTVRMLDAYADVIVVRHRleGA--ARFAAEVAEKPVINAGDGKRHHPTQAMLDLYSV 153
                                    99***..**********************8777..88889999**********************987 PP

>> OTCace  Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.9   0.0     2e-25   1.8e-21       2     156 ..     162     311 ..     161     312 .. 0.91

  Alignments for each domain:
  == domain 1  score: 76.9 bits;  conditional E-value: 2e-25
                                    C.EEEEESS.TTSHHHHHHHHHHHHCT-E.EEEES-TTSSH-HHHHHHHHHHHHHHT-EEEEESSCHHHHTT-SEEEE-- CS
                         OTCace   2 glkiafvGd.kknnvanslikllarlgmd.vvlvaPkglepdkevleeakknakksggsititedleeavkgaDvvytdv 79 
                                    gl +  +Gd k+++ a s i +l+ ++   v+l++P  l+  ++v     +   + g  ++  e+++e++ + Dv+y ++
  gi|119720063|ref|YP_920558.1| 162 GLVYGVLGDlKYGRAAASFILGLSLFKPRkVYLISPGLLKAREDVK----EALRERGVGFEEVESPSEVIGELDVLYVTR 237
                                    5667789*******************98879999999999865554....4555679*********************** PP

                                    SSETTCCGGHH...HHHHHHCC.CSB-HHHHHHS-TT-EEEE-S---BTTTB-HHHHTSTTBHHHHHHHHHHHHHHHHHH CS
                         OTCace  80 wvsmgeekere...erlkklkd.yqvteellklakkdaivlHcLPakrgeEvtdeVfdsprsvvfeqaeNrlhtikAllv 155
                                    ++     +er+   ++++k+++ y v+++ll++ak+ +ivlH+LP  r +E++ +V+  p++ +feqa+ ++  ++All 
  gi|119720063|ref|YP_920558.1| 238 IQ-----RERFpdpSEYEKVRGsYVVDSKLLRNAKEGLIVLHPLP--RVDEISFDVDGTPHAKYFEQARLGIPLRMALLK 310
                                    **.....88888889******************************..*******************************97 PP

                                    H CS
                         OTCace 156 l 156
                                    l
  gi|119720063|ref|YP_920558.1| 311 L 311
                                    6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 2070.23
//
Query:       gi|119720064|ref|YP_920559.1|  [L=159]
Description: aspartate carbamoyltransferase regulatory subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.2e-34  116.1   0.2      8e-34  115.8   0.2    1.1  1  PyrI      Aspartate carbamoyltransferase regulatory chain, al
    3.1e-18   65.4   0.2    5.7e-18   64.5   0.2    1.5  1  PyrI_C    Aspartate carbamoyltransferase regulatory chain, me


Domain annotation for each model (and alignments):
>> PyrI  Aspartate carbamoyltransferase regulatory chain, allosteric domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.8   0.2     9e-38     8e-34       2      94 .]       6      97 ..       5      97 .. 0.97

  Alignments for each domain:
  == domain 1  score: 115.8 bits;  conditional E-value: 9e-38
                                   -----SCEEEEEEEETT-HHHHHHHCT--T...TS-EEEEEEEEETTTEEEEEEEEET----HHHHHHHCCC-TT-EEEEEE CS
                           PyrI  2 kvkkienGiViDHIkagkalkvlklLkldklkseekvaiiknvkskklgkKdiikiegkelseeeldklaliapnatiniIk 83
                                    v+ki++G+ViDHI+ag+al+vlk+L+l++ +++ ++a+++nv+s+klg Kdi+k+e+++l+ +e+dk+aliap+atiniI+
  gi|119720064|ref|YP_920559.1|  6 LVRKIREGTVIDHIPAGRALNVLKILGLTG-REGLTIAVVMNVPSRKLGVKDIVKVEKRFLEPSEVDKIALIAPSATINIIR 86
                                   699**************************8.7777*********************************************** PP

                                   TTEEEEEE--. CS
                           PyrI 84 dgevveKkkve 94
                                   d++v++K++ve
  gi|119720064|ref|YP_920559.1| 87 DFQVASKRRVE 97
                                   ********985 PP

>> PyrI_C  Aspartate carbamoyltransferase regulatory chain, metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.5   0.2   6.4e-22   5.7e-18       2      48 .]     102     150 ..     101     150 .. 0.96

  Alignments for each domain:
  == domain 1  score: 64.5 bits;  conditional E-value: 6.4e-22
                                    EESSS--S-TTBGGGT..TS-.-EEEEEETTTTEEEETTT--EEEHHHH CS
                         PyrI_C   2 iegvlkCpNpnCItnn..epveskFkvedkekvklkCkYCekeiseeei 48 
                                    ++g+l+CpNpnC+tn+  epv+++F++++ +++klkC YCe+++se ei
  gi|119720064|ref|YP_920559.1| 102 VTGILRCPNPNCVTNSerEPVTPRFVRVSLSPLKLKCAYCEETLSEAEI 150
                                    89**************888***************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1086.62
//
Query:       gi|119720065|ref|YP_920560.1|  [L=431]
Description: dihydroorotase, multifunctional complex type [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-26   93.4   0.0    2.1e-26   93.0   0.0    1.1  1  Amidohydro_1  Amidohydrolase family
    2.8e-10   40.3   0.6    0.00011   21.9   0.0    2.6  3  Amidohydro_3  Amidohydrolase family


Domain annotation for each model (and alignments):
>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.0   0.0   2.4e-30   2.1e-26       1     344 []      54     406 ..      54     406 .. 0.79

  Alignments for each domain:
  == domain 1  score: 93.0 bits;  conditional E-value: 2.4e-30
                                    EEEE-EEEEEEECETTECSSSGHHHHHSTTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTH......HHHHHHHHHHTSS CS
                   Amidohydro_1   1 ivlPGlIDaHvHleqsllrgatledwlvppetaaealesgiktalksGtttvadmgattst......giealleaaeelp 74 
                                    +vlPG++D+HvH +             +p+++++e  ++g ++a+k+G+t+vadm+++ ++       +e l++a e+  
  gi|119720065|ref|YP_920560.1|  54 LVLPGMVDIHVHMR-------------EPGQEYKEDWRTGSRAAVKGGVTFVADMPNNKPPantcerLAEKLRRAGEKSL 120
                                    59***********9.............******************************98889977777777777777766 PP

                                    SEEEEEEESSEGGSGCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHHHHHHHHHHHHTTEEEEEETS CS
                   Amidohydro_1  75 lglrilggkvsldrgsaetskasreklkagaaetikgkadgvvkvalapheapafsdeelkealkeakkrdlpvaiHale 154
                                    +++ +++g      +s++  +++  +  +             v  +l+p+e ++ s+++ + ++   +k ++p+++Ha +
  gi|119720065|ref|YP_920560.1| 121 VDFAFYAG------FSEN--PEELLRCPEL-----------FVGGKLYPEELFSRSAAYFARLM---AKLGKPLVVHAED 178
                                    77777777......4433..2223333222...........24599**********99999999...899********88 PP

                                    SCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEEHH.......HHHHHHHHHHHHCEE........... CS
                   Amidohydro_1 155 tkgevedaeaafgetiehgthlevaeslglldeiklilahgvhltpt.......eaellkerlkeagva........... 216
                                     + + e +   +     ++ + e  e  g+ + ++l+ + g ++++t         ell     +a+++           
  gi|119720065|ref|YP_920560.1| 179 PSMFRESRGLPHS----YARPPEA-ELSGVRRALRLCGEAGAWVHVThvstgaaVTELL-----SAKLSglkatfdvtph 248
                                    8888765555555....4446666.778999**************66566654322333.....3333333366778888 PP

                                    .HHHHHHHH...............SEHHHHHHHHHHHHTSCEEEEEECT.......TSSCCGGHHHHHHHHHHHHHHCCT CS
                   Amidohydro_1 217 .hcpfsnsi...............lrsgrealrkaldeGvkvglgtDga.......asgnslnlleelrlalklqrglly 273
                                      + +++++                + +r a+  al +G+  +l+tD+a       as + +  + +l lal    +ll 
  gi|119720065|ref|YP_920560.1| 249 hALLTDSLYsttlsriakvnpplrGEADRSAVYSALARGLPDALVTDHAphspeekASEDPPPGFPGLELAL----HLLL 324
                                    633333333777778999999999*******************************99999999999999999....4555 PP

                                    TTTHCHCHHHHHHHHHTHHHHHHTT-TTTSSSS-TTSB--EEEECCCT.............CGGGTTTCTSEEEEEEEET CS
                   Amidohydro_1 274 edeegglslkealrmaTingAkalglddkvGsievGkdADlvvvdldi.............laafvglkkdgnvkkvivk 340
                                    ++  +g  ++ ++++++  +A  lg+  ++G+i+vG dADlvvv+                +++f+g+  + +++ v+v+
  gi|119720065|ref|YP_920560.1| 325 SEVLAGRLPLGVIDLYSSRPASLLGV--EKGAIAVGMDADLVVVKREEwvvrgdemvskarYTPFEGWRLSTKTHAVFVR 402
                                    544555777799**************..9***************7722556677789999******************** PP

                                    TEEE CS
                   Amidohydro_1 341 Gklv 344
                                    G++v
  gi|119720065|ref|YP_920560.1| 403 GRMV 406
                                    *987 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   7.4e-07    0.0067       6      47 ..      51      92 ..      50     104 .. 0.82
   2 ?   -1.8   0.0      0.18   1.6e+03     310     340 ..     221     251 ..     157     301 .. 0.55
   3 !   21.9   0.0   1.2e-08   0.00011     414     462 ..     337     396 ..     333     407 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 7.4e-07
                   Amidohydro_3  6 kGrlvlPGFvDsHtHlagggvnlrllrlpdarvtslegvlta 47
                                   kG lvlPG+vD+H H+ + g+++ + +  ++r+    gv+ +
  gi|119720065|ref|YP_920560.1| 51 KGYLVLPGMVDIHVHMREPGQEYKEDWRTGSRAAVKGGVTFV 92
                                   799*****************9998777777777666666655 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.18
                   Amidohydro_3 310 rlehaegvtesqiervaalqvaagvqpvfnf 340
                                     ++++ +vte   +++  l ++ +v p ++ 
  gi|119720065|ref|YP_920560.1| 221 HVSTGAAVTELLSAKLSGLKATFDVTPHHAL 251
                                    2333333355555555555555555555555 PP

  == domain 3  score: 21.9 bits;  conditional E-value: 1.2e-08
                   Amidohydro_3 414 lalyTrgpAkalgledrkGtLevGadADlvvldadpldvdppelaear.............v 462
                                    ++ly+++pA +lg e+  G ++vG+dADlvv  ++   v  +e++++               
  gi|119720065|ref|YP_920560.1| 337 IDLYSSRPASLLGVEK--GAIAVGMDADLVVVKREEWVVRGDEMVSKArytpfegwrlstkT 396
                                    899*************..***************99888888877776445555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       214  (0.011936); expected 358.6 (0.02)
Passed bias filter:                      203  (0.0113224); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 3180.80
//
Query:       gi|119720066|ref|YP_920561.1|  [L=266]
Description: oxidoreductase FAD/NAD(P)-binding subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      9e-12   44.6   2.2    1.5e-11   43.9   2.2    1.4  1  DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydr
  ------ inclusion threshold ------
      0.011   16.4   0.0      0.028   15.1   0.0    1.7  1  NAD_binding_1    Oxidoreductase NAD-binding domain


Domain annotation for each model (and alignments):
>> DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydroorotate dehydrogenase B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9   2.2   1.7e-15   1.5e-11       1      41 [.     210     244 ..     210     245 .. 0.93

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 1.7e-15
                                    ----SSSSSSS-TTEEEETTCTT.CEEETTTT-CEEECCCB CS
                DHODB_Fe-S_bind   1 eerMaCGvGaClgCvvktkggdggeykrvCkdGPvFdadev 41 
                                    e++++CGvG+C++C+++  g       rvC+dGPvFd++ +
  gi|119720066|ref|YP_920561.1| 210 ERIIKCGVGVCGACALEPLG------LRVCSDGPVFDGETL 244
                                    899***************76......9***********976 PP

>> NAD_binding_1  Oxidoreductase NAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   3.1e-06     0.028       1     107 [.     102     194 ..     102     196 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.1e-06
                                    EEEEGGGGHHHHHHHHHHHHHCTTCSEEEEEEEESSGCGSTTHHHHHHHHHHCTTEEEEEEEESSCTTTSSSEESSHHHH CS
                  NAD_binding_1   1 miagGtGiaPvrsvlraileeakdktkvvlvyGnrteedllyreeleelakklpgrlkvvavvsreeagweggkgrvqda 80 
                                    +++gG G aP++ + +++  +      v+ v G r++e+ l+ e+++++     g+  +va+    e+g+eg kg+  d 
  gi|119720066|ref|YP_920561.1| 102 LVGGGYGAAPLLYLAERLSGA---GATVHAVLGFRSREHALLVEDFRRV----AGE-VWVAT----EDGSEGFKGTAVDL 169
                                    79*********9888888775...789*******************999....443.45555....55556678888777 PP

                                    HHHHHHHHSSTTEEEEEECSHHHHHHH CS
                  NAD_binding_1  81 lleellslkkeethvyvCGppgMikav 107
                                    + + + +   + + vy CG + M++ v
  gi|119720066|ref|YP_920561.1| 170 FERVFPG--GGYDAVYTCGKELMMEKV 194
                                    7444555..9999********999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 2005.28
//
Query:       gi|119720067|ref|YP_920562.1|  [L=299]
Description: dihydroorotate dehydrogenase family protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.1e-50  171.1   0.0    3.6e-50  170.9   0.0    1.0  1  DHO_dh        Dihydroorotate dehydrogenase
    4.4e-06   26.0   0.0      5e-05   22.6   0.0    2.1  1  Dus           Dihydrouridine synthase (Dus)
  ------ inclusion threshold ------
      0.013   14.5   0.0      0.025   13.6   0.0    1.4  1  IMPDH         IMP dehydrogenase / GMP reductase domain
      0.024   13.8   0.1        1.9    7.6   0.2    2.4  2  NanE          Putative N-acetylmannosamine-6-phosphate epimer
       0.05   12.8   1.1       0.54    9.4   0.0    2.3  3  DUF561        Protein of unknown function (DUF561)
       0.12   11.8   0.1        2.4    7.5   0.1    2.2  2  His_biosynth  Histidine biosynthesis protein
       0.75    9.1   5.1       0.86    8.9   2.6    1.9  2  NMO           Nitronate monooxygenase


Domain annotation for each model (and alignments):
>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.9   0.0   1.4e-53   3.6e-50       2     294 ..       4     281 ..       3     282 .. 0.88

  Alignments for each domain:
  == domain 1  score: 170.9 bits;  conditional E-value: 1.4e-53
                                    G-EEETTEEESSSEEE-TTSSTTSSSHHHHH.CTTSSEEEEEEE-SS-B--S-S--EEEETTCTEEEE---S-BS-HHHH CS
                         DHO_dh   2 latkvlglkfknpiglAaGfdkegeeilkll.klgfgaieigsvtpkpqeGnpkPrvfrlkedrsvlNslGlnneGldav 80 
                                    l+++v+gl+++np+++A+G+ + ++ + k   ++g+ga++ ++vt++p+eG p+P v +l  +  ++Ns+Gl+n+G++++
  gi|119720067|ref|YP_920562.1|   4 LSVEVAGLRLRNPVVVASGVLGVSVGLMKRAeDAGAGAVTSKTVTLNPREGYPNPVVYELDYG--LVNSMGLPNPGAEEM 81 
                                    789*******************9999877651667****************************..**************9 PP

                                    HHHHHHHHHHHHCC.CEEEEEEE-TTSS.HHHHHHHHHHHHGGGESEEEEES-SCTCCTS.CCCGCHHHHHHHHHHHHHH CS
                         DHO_dh  81 lekllkrrkeqeekkelginlskakktenavddyvevvrkigpfadilelNvSsPntpgl.rdlqekeelkaillkvvke 159
                                     + l++ r+       +++++s+  +t    d+   +++ ++ f d+lelN S+P+++gl +dl ++++  + +++++k 
  gi|119720067|ref|YP_920562.1|  82 GRILREARRV----LGIPVIASIGAST---PDEALRIAEALEGF-DALELNASCPHVKGLgADLMSDPDAVYGIVSALKS 153
                                    9888777755....469******9998...99999999999877.99***********75389**************998 PP

                                    HHSSEEEEEE-SSSSHHHHHHHHHHHHHHTECEEEE...BSEE--CTTCCGCCCCTTSSEEEEEGGGHHHHHHHHHHHHH CS
                         DHO_dh 160 vskvpvlvKlaPdltdeekkdiadvllelkldgiivtNttvqrlaidlkseknvkanktGGlsGkalkdialkvirelyk 239
                                         v+ Kl+P     + + +a      ++dg  ++N t + + id+ ++k+v     GGlsG+a+ +ia++v++el +
  gi|119720067|ref|YP_920562.1| 154 SG-YRVFLKLSPHGDYLAVARKAY---SAGVDGFTAIN-TAKAMVIDVYARKPVLGGVVGGLSGRAIHPIAVRVVYELHR 228
                                    77.99*******555555555555...55555555555.556666**********99*********************** PP

                                    HTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTCHHHHHHHHHHHH CS
                         DHO_dh 240 rlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfegpkiakkikkeleel 294
                                    ++  e+p+Ig+GG+e    a+e i aGAs+v v+tal ++g  ++ +i  ++e+ 
  gi|119720067|ref|YP_920562.1| 229 EFP-EVPVIGTGGVEGWVEAVELILAGASAVGVGTAL-KRGFEVIGEILGGIERY 281
                                    *98.*********************************.9*********9999876 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   1.9e-08     5e-05      57     214 ..      97     262 ..      83     271 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.9e-08
                                    EEEEE-S-HHHHHHHHHHHHHTT-SCEEEEESSTTEEETTEEEGGGGGGSHHHHHHHHHHHHCCSSS-EEEEEESESS.. CS
                            Dus  57 avQlggsdpallaeaAklvadlgadeIdlNvGCPskkvtrggaGaaLlrkpdlvaqivkavvkaveiPvtvkirigid.. 134
                                    +  +g+s p++++  A+     g d+ +lN+ CP      +g Ga L+ +pd v+ iv+a+++  +  v +k +   d  
  gi|119720067|ref|YP_920562.1|  97 IASIGASTPDEALRIAEAL--EGFDALELNASCPHV----KGLGADLMSDPDAVYGIVSALKSS-GYRVFLKLSPHGDyl 169
                                    5556677777766666654..47***********75....69******************9875.778888888777766 PP

                                    ....TTTC.HHHHHHHHHHCT-SEEEEESS........ECCCTT-C.G--CHHHHHHHHH-S.S-EEEESS--SHHHHHH CS
                            Dus 135 ....deeenalelakiveaaGaqaltvHgR........traqnyeg.tadweaIkevkqavs.ipviaNGdIkdaedaqa 200
                                        +++   ++   +++ a a  + v +R            ++ + ++  + ++e+ ++++ +pvi+ G+++ + +a +
  gi|119720067|ref|YP_920562.1| 170 avarKAYSAGVDGFTAINTAKAMVIDVYARkpvlggvvGGLSGRAIhPIAVRVVYELHREFPeVPVIGTGGVEGWVEAVE 249
                                    666677888888888888888888889999999999875556666689999**********************9977777 PP

                                    HHHHH--SEEEESC CS
                            Dus 201 ileetGadgvmigr 214
                                     +   Ga +v +g 
  gi|119720067|ref|YP_920562.1| 250 LILA-GASAVGVGT 262
                                    6665.787777775 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   9.6e-06     0.025     195     250 ..     219     275 ..     210     293 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.6e-06
                                    HHHHHHHHHCTC.T-EEEEES---SHHHHHHHHHTT-SEEEESCCCTTBTTSSSEEE CS
                                    xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          IMPDH 195 Avaevaeaakka.gvpviaDGGikysgdivkAlaaGadavmlGsllagteEspgevi 250
                                    Av  v+e  +++ +vpvi  GG++   + v  + aGa+av +G  l +  E  ge++
  gi|119720067|ref|YP_920562.1| 219 AVRVVYELHREFpEVPVIGTGGVEGWVEAVELILAGASAVGVGTALKRGFEVIGEIL 275
                                    78888898888879********************************99999999876 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0      0.01        27      24      61 ..      85     122 ..      78     181 .. 0.85
   2 ?    7.6   0.2   0.00076       1.9     144     183 ..     232     271 ..     206     279 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.01
                                    HHHHHTT--S-EEEE-B---TTS---BS-SHHHHHHHH CS
                           NanE  24 ikaikavvdlPiiGivkrdlpdsevritatlkdideLa 61 
                                    +++ ++v  +P+i  +    pd  +ri+  l+  d+L 
  gi|119720067|ref|YP_920562.1|  85 LREARRVLGIPVIASIGASTPDEALRIAEALEGFDALE 122
                                    67889999************************999874 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00076
                                    T--EEEES---SHHHHHHHHTT--SEEEE-HHHH-HHHHH CS
                           NanE 144 glkviaeGrintPekakkaieiGvdavvvGsaitrleeia 183
                                    ++ vi  G ++   +a + i  G+ av vG+a+ r  e++
  gi|119720067|ref|YP_920562.1| 232 EVPVIGTGGVEGWVEAVELILAGASAVGVGTALKRGFEVI 271
                                    56799999999999*********************99886 PP

>> DUF561  Protein of unknown function (DUF561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0     0.052   1.3e+02     186     212 ..      14      40 ..       6      55 .. 0.80
   2 ?   -4.0   0.0       2.6   6.7e+03     185     197 ..      92     104 ..      89     112 .. 0.75
   3 ?    9.4   0.0   0.00021      0.54     177     219 ..     222     266 ..     212     281 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.052
                         DUF561 186 slPvicasGlsdvtvplalslgasGiG 212
                                    + Pv+ asG+  v+v l   +  +G G
  gi|119720067|ref|YP_920562.1|  14 RNPVVVASGVLGVSVGLMKRAEDAGAG 40 
                                    56***********99998887777777 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 2.6
                         DUF561 185 vslPvicasGlsd 197
                                    + +Pvi++ G s+
  gi|119720067|ref|YP_920562.1|  92 LGIPVIASIGAST 104
                                    5689999988764 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.00021
                         DUF561 177 styeiskkv.slPvicasGlsdvtvplal.slgasGiGigsavsk 219
                                     +ye+ ++  ++Pvi + G+      + l  +gas +G+g a+++
  gi|119720067|ref|YP_920562.1| 222 VVYELHREFpEVPVIGTGGVEGWVEAVELiLAGASAVGVGTALKR 266
                                    57888777548**********98888765268*********9987 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.054   1.4e+02     183     209 ..      85     111 ..      79     121 .. 0.80
   2 ?    7.5   0.1   0.00095       2.4      62     115 ..     220     274 ..     208     280 .. 0.69

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.054
                                    HHHHHHHHSSEEEEESS--SHHHHHHH CS
                   His_biosynth 183 tkelaeavkipviasGGvgsledlkel 209
                                    ++e ++ + ipvias G++++++  ++
  gi|119720067|ref|YP_920562.1|  85 LREARRVLGIPVIASIGASTPDEALRI 111
                                    678888899**********99886555 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00095
                                    HHHHHHHHHH-S.SEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHH CS
                   His_biosynth  62 ldlveeiaeevf.ipvqvGGGIrsledveelleagadkviigtaavknpelikel 115
                                      +v e+ +e+  +pv   GG+    ++ el+ aga+ v +gta  +  e+i e+
  gi|119720067|ref|YP_920562.1| 220 VRVVYELHREFPeVPVIGTGGVEGWVEAVELILAGASAVGVGTALKRGFEVIGEI 274
                                    5566666666544677777777777777777777777777777777666666665 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.17   4.2e+02     173     201 ..      73     101 ..      70     107 .. 0.82
   2 ?    8.9   2.6   0.00034      0.86     164     225 ..     204     264 ..     173     266 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.17
                            NMO 173 tpevgdkglfaLvpqvldavdiPviAaGG 201
                                     p++g ++  +++ +++ ++ iPviA  G
  gi|119720067|ref|YP_920562.1|  73 LPNPGAEEMGRILREARRVLGIPVIASIG 101
                                    566777888899999***********755 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00034
                            NMO 164 GpeaGGhqGtpevgdkglfaLvpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqigtrf 225
                                    G+  GG  G +++       + +  ++  ++Pvi +GG+    +    + +GAs+v +gt++
  gi|119720067|ref|YP_920562.1| 204 GGVVGGLSG-RAIHPIAVRVVYELHREFPEVPVIGTGGVEGWVEAVELILAGASAVGVGTAL 264
                                    566677777.55543445555566667778*********877666666778*********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1936.52
//
Query:       gi|119720068|ref|YP_920563.1|  [L=217]
Description: metal dependent phosphohydrolase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-17   62.9   1.5    3.2e-17   62.9   1.5    1.8  2  HD        HD domain
     0.0032   17.4   0.0     0.0065   16.4   0.0    1.4  1  DUF4202   Domain of unknown function (DUF4202)


Domain annotation for each model (and alignments):
>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.9   1.5   3.6e-21   3.2e-17       3     121 ..      30     133 ..      28     134 .. 0.93
   2 ?   -1.1   0.0      0.23     2e+03      62      93 ..     174     203 ..     155     211 .. 0.62

  Alignments for each domain:
  == domain 1  score: 62.9 bits;  conditional E-value: 3.6e-21
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHHHHH...HH CS
                             HD   3 eHsleVaklarrlaedlgeeedrellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrlgld...le 79 
                                     H  +V++la r+a++lg   d e+l +aa+lHD++   + +         +  ++H+ +ga+i+re++kr g++   +e
  gi|119720068|ref|YP_920563.1|  30 SHVERVYRLAMRIARELGAGVDLEVLGAAAILHDVARSMEDE---------GLVEDHAREGARIAREILKRVGFPedkIE 100
                                    7**************************************553.........44578****************999***** PP

                                    HHHHHHHTTCCHHHHHHHHHHHHCCTSCHHHHHHHHHHHHHH CS
                             HD  80 dvaklirehheswegkkrprglaerqlslearivklaDrlaa 121
                                     va  i++h+ +           +r+ s+ea+i+++aDrl+a
  gi|119720068|ref|YP_920563.1| 101 RVAYCIEAHRYRGG---------GRPSSIEAQILQDADRLDA 133
                                    *************7.........67***************98 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.23
                                    HHHHHHHHHHHHHHHHHHHHHHHHHTTCCHHH CS
                             HD  62 vgaeilrevekrlgldledvaklirehheswe 93 
                                    +++e+l +v+  l  ++e + ++++  h+ +e
  gi|119720068|ref|YP_920563.1| 174 HFYEKLLKVKDTL--NTEPARRIAEGRHRFME 203
                                    4444444444444..36777777777777665 PP

>> DUF4202  Domain of unknown function (DUF4202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   7.2e-07    0.0065      83     133 ..      76     131 ..      74     135 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 7.2e-07
                        DUF4202  83 elkkrqAelaaelleeagydeeeiervaalvrkeelk.....rdeetqlLEDvacL 133
                                    ++++  A++a+e+l+++g++e++ierva  ++ ++ +     +  e+q+L D+  L
  gi|119720068|ref|YP_920563.1|  76 DHAREGARIAREILKRVGFPEDKIERVAYCIEAHRYRgggrpSSIEAQILQDADRL 131
                                    577889*****************************9955444378******99755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1508.07
//
Query:       gi|119720069|ref|YP_920564.1|  [L=555]
Description: CTP synthetase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   8.8e-112  372.7   0.0   1.1e-111  372.4   0.0    1.1  1  CTP_synth_N    CTP synthase N-terminus
    6.9e-44  149.9   0.0    1.1e-43  149.2   0.0    1.3  1  GATase         Glutamine amidotransferase class-I
    6.9e-11   42.3   0.0    2.9e-10   40.3   0.0    2.0  2  Peptidase_C26  Peptidase C26
    4.7e-05   23.4   0.0     0.0001   22.4   0.0    1.5  1  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain


Domain annotation for each model (and alignments):
>> CTP_synth_N  CTP synthase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  372.4   0.0  2.5e-115  1.1e-111       1     265 []       4     281 ..       4     281 .. 0.98

  Alignments for each domain:
  == domain 1  score: 372.4 bits;  conditional E-value: 2.5e-115
                                    EEEEEEE--STTTTHHHHHHHHHHHHHCTT--EEEEEEE-SSSSSSTT--CCCC--EEE-TT........-.....-EEE CS
                    CTP_synth_N   1 kyilvtGGvvSglGkGiiaaslgallksrglkvtlikiDPYlnvdagtlsplehGEvfvldd........G.....aetD 67 
                                    +y++vtGGvvSglGkG +aas+g+l++ rg+kv +ikiDPYlnvd+gtl+p+ehGEvfv+++        G     ae+D
  gi|119720069|ref|YP_920564.1|   4 RYVFVTGGVVSGLGKGAVAASIGKLMQLRGFKVDMIKIDPYLNVDPGTLNPVEHGEVFVCEEvwefepapGyrftiAEID 83 
                                    7*************************************************************888888873555669*** PP

                                    THHHHHHHHHT----GGGEEEHHHHHHHHHHHHHTTTTTT----CCCHHHHHHHHHHHHHH.HCT-SEEEEEE-S-TTSG CS
                    CTP_synth_N  68 lDlGnYeRfldikltkennittGkiyksviekerrGdylGktvqviphvtdeikeriekvakkveadvviveigGtvgdi 147
                                     D+G+YeRfld++++ +nnit+G++y svi ker G+ylG+t+qviphvt+eik+ri++va+++++dv++ve+gGtvgdi
  gi|119720069|ref|YP_920564.1|  84 QDFGTYERFLDVNMHPSNNITSGQVYLSVILKERMGEYLGRTIQVIPHVTEEIKRRIRAVAERSRPDVLVVEVGGTVGDI 163
                                    **************************************************************99**************** PP

                                    GGHHHHHHHHHHHHHH-TTTEEEEEEEE--B-TTTSSB-HHHHHHHHHHHHHHT---SEEEEEESS---HHHHHHHHHHC CS
                    CTP_synth_N 148 eslpfleairqlklelgkenvllihvtlvpvlkaagelktkptqhsvkelrslGiqpdiivcrsekeleeevkekialfc 227
                                    e++pfleairq++le+    ++l+hvtlvp+l++ g+lktkptqhsvkel+s+G+qpd+++ rs+++l+e++++kial++
  gi|119720069|ref|YP_920564.1| 164 EAMPFLEAIRQFRLEYPPGYTALVHVTLVPYLSSLGQLKTKPTQHSVKELQSMGLQPDVVIGRSDRPLPEDIRRKIALYS 243
                                    ******************************************************************************** PP

                                    T--GGGEEEEE--S-GGGHHHHHHHCTHHHHHHHHTT- CS
                    CTP_synth_N 228 nvekeavisvkdvesiyevpllleeqglaelileklkl 265
                                    +v+ eav+s +d+es+y +p++leeqgl +++++ l+l
  gi|119720069|ref|YP_920564.1| 244 SVPLEAVFSDPDLESVYLLPVVLEEQGLGDYLCRVLRL 281
                                    **********************************9986 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.2   0.0   2.5e-47   1.1e-43       2     190 .]     318     545 ..     317     545 .. 0.89

  Alignments for each domain:
  == domain 1  score: 149.2 bits;  conditional E-value: 2.5e-47
                                    EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHH..HH...THHSTSEEEEEEESSCTTTTTHHHHHHHHCTSTS-EEE CS
                         GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeei..le...llknpdgilvsgGpgspgvegkieaikearenkiPiLG 76 
                                    + D+y s++e+l ha+++lg+kv+ + i+a++ e+  ++    l++ +gil+ +G+gs+gveg+i+a+++a++ ++P+LG
  gi|119720069|ref|YP_920564.1| 318 IQDSYISINEALSHAGAHLGAKVKRLYIEAEDIEEnpEKvreVLDSSHGILLTPGFGSRGVEGMIQAARYALDTGKPFLG 397
                                    68***************************9776663422543499*********************************** PP

                                    ETHHHHHHHHHTTT...................EEE....EEECEEEEEEEEEEEETTT........CGGTTTTSEEEEE CS
                         GATase  77 ICLGmQllaiefgr...................kvv....kekekehhggtmrlgddet........allyglknevier 125
                                    IC+G Qll+ +f r                   +vv    ++k    +ggtmrlg+++          ++y++ + ++er
  gi|119720069|ref|YP_920564.1| 398 ICFGAQLLFVAFMRyrvglagahsteidpetphPVVdllpEQKGVAFKGGTMRLGAHPVkvvpgtrlFEAYKS-ELIYER 476
                                    **************999999888887777777755589998888************999*****966666666.8899** PP

                                    EEEEEEEESG...CHHHTTEEEEEEEETTEEEEEEEEETT.T.EEEESSBTTSTTSTTHHHHHHHHHHHH CS
                         GATase 126 hrHryevnpk...elepaglevtakseddeelmeiiekkn.p.fvgvQFHPEststpegpellfnflika 190
                                    +rHry +np+     e +gl+v+ ++ ++ +++  ie      +vgvQFHPE++s+p +p+++  +++ka
  gi|119720069|ref|YP_920564.1| 477 FRHRYHINPAyreLAERHGLVVSSTDPSG-RIINSIEVAGdAwIVGVQFHPEFKSRPARPSPVYLEFLKA 545
                                    *********9*98789999*******998.6777777777689*********************999985 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.37   1.7e+03      46      66 ..     351     371 ..     347     385 .. 0.84
   2 !   40.3   0.0   6.4e-14   2.9e-10      98     216 .]     385     527 ..     379     527 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.37
                  Peptidase_C26  46 eedeedvkaildkldgllltG 66 
                                    ee++e+v+++ld+ +g+llt 
  gi|119720069|ref|YP_920564.1| 351 EENPEKVREVLDSSHGILLTP 371
                                    67899**************94 PP

  == domain 2  score: 40.3 bits;  conditional E-value: 6.4e-14
                  Peptidase_C26  98 iraalergvPilgiCrGlqllnval.......GGtlyqdieeqsgltdhrehe..............q....saashavk 152
                                     r al+ g+P lgiC G qll va+        G   ++i+   ++      +              +       +h vk
  gi|119720069|ref|YP_920564.1| 385 ARYALDTGKPFLGICFGAQLLFVAFmryrvglAGAHSTEIDP--ETP-----HpvvdllpeqkgvafKggtmRLGAHPVK 457
                                    57899****************999632222114555555553..222.....12344455656665515556888***** PP

                  Peptidase_C26 153 vekgsllaellgseeievnslHhqaike....lae..elrveAvae.DgviEaieseeakafvlgvQwHPE 216
                                    v++g+ l e+++se i     H+  i+     lae  +l v+++++   +i  ie+   +a+++gvQ+HPE
  gi|119720069|ref|YP_920564.1| 458 VVPGTRLFEAYKSELIYERFRHRYHINPayreLAErhGLVVSSTDPsGRIINSIEVAG-DAWIVGVQFHPE 527
                                    ************9999999999999886666666522799******55589******9.77*********9 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   2.3e-08    0.0001       8     120 ..      14     444 ..       7     450 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 2.3e-08
                                    TTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH................................. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................. RF
                           CbiA   8 GGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep................................. 54 
                                    +G GK  +aa+++++++ rg++V +++ Dp  n +    g+ n +e                                  
  gi|119720069|ref|YP_920564.1|  14 SGLGKGAVAASIGKLMQLRGFKVDMIKIDPYLNVDP---GTLNPVEHgevfvceevwefepapgyrftiaeidqdfgtye 90 
                                    89*****************************99999...88888888999****************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                           CbiA  55 ................................................................................ 54 
                                                                                                                    
  gi|119720069|ref|YP_920564.1|  91 rfldvnmhpsnnitsgqvylsvilkermgeylgrtiqviphvteeikrriravaersrpdvlvvevggtvgdieampfle 170
                                    **********************************9999999999999999999999999999999999999999999999 PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                           CbiA  55 ................................................................................ 54 
                                                                                                                    
  gi|119720069|ref|YP_920564.1| 171 airqfrleyppgytalvhvtlvpylsslgqlktkptqhsvkelqsmglqpdvvigrsdrplpedirrkialyssvpleav 250
                                    99999999999999999999999999999999999999999999999999999999999999999999999999999999 PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                           CbiA  55 ................................................................................ 54 
                                                                                                                    
  gi|119720069|ref|YP_920564.1| 251 fsdpdlesvyllpvvleeqglgdylcrvlrldgrldaarfeewrrvaerfvkyseevvvampgkytmiqdsyisineals 330
                                    99999999999999999999999999999999999999999999999999999999999999999999999999999999 PP

                                    ..............................................CCHCCCHHH.HHHCHCHHHH........EEEEEE CS
                                    ..............................................xxxxxxxxx.xxxxxxxxxx......xxxxxxxx RF
                           CbiA  55 ..............................................dlkrllell.ealgkkkall......lkiagvvl 81 
                                                                                  +++ +++ +  al+++k+ +       ++++v +
  gi|119720069|ref|YP_920564.1| 331 hagahlgakvkrlyieaedieenpekvrevldsshgilltpgfgsrGVEGMIQAArYALDTGKP-FlgicfgAQLLFVAF 409
                                    9999999999999999999999999999999999999999999888555555555223333333.347788888888888 PP

                                    EEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           CbiA  82 nrvdgeneetllkealeelkqrygvpvlgviprdeavae 120
                                     r++  +   +++  ++ +    + pv++++p+ ++va+
  gi|119720069|ref|YP_920564.1| 410 MRYRVGL-AGAHSTEIDPET---PHPVVDLLPEQKGVAF 444
                                    8888884.566777788876...8999999999888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (555 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 3731.77
//
Query:       gi|119720070|ref|YP_920565.1|  [L=714]
Description: hypothetical protein Tpen_1164 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-11   43.3   0.0    4.6e-11   42.6   0.0    1.3  1  TAL_FSA         Transaldolase/Fructose-6-phosphate aldolase
  ------ inclusion threshold ------
       0.19   12.2   0.5       0.95    9.9   0.1    2.2  2  ParD_antitoxin  Bacterial antitoxin of ParD toxin-antitoxin t


Domain annotation for each model (and alignments):
>> TAL_FSA  Transaldolase/Fructose-6-phosphate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.6   0.0   5.1e-15   4.6e-11      18     151 ..     222     393 ..     211     441 .. 0.83

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 5.1e-15
                                    T---EEE--HHHHHH..TTS.-HHHHHHHHHHH........................................H-S-EEE CS
                        TAL_FSA  18 kgiqgvTtNPsliekaikykalydeaieeikkeg....kkvkeaydkLavedileal.dll...........gadgrvsl 81 
                                     g+  v tNP l ++a k  + + ea ee  +++    + +++  d+La++  l al +++            +dg++s 
  gi|119720070|ref|YP_920565.1| 222 LGFVQVSTNPVLAAEAYKDDPGLWEAFEEYLRRHpelvERAESDPDELAMAATLIALwPNMevfrpvahlldFKDGMISY 301
                                    5677899***********77777777777776655555555555666665544333313336678888888999****** PP

                                    E-S-...-SHHHHHHHHHHHHTT-T.......................TEEEEEESS.HHHHHHHHHHHHTT--EEEEEE CS
                        TAL_FSA  82 EVdarlsddteatieeArrlialye.....................renvlIKiPat.eeGikAikeLkkeGinvnvTli 139
                                    + +++++d++e+++++A ++++l e                     r+n++ K+++  e+ i++ + L++ Gi +n T  
  gi|119720070|ref|YP_920565.1| 302 QLNPNVADSVEGSVRDALKIYRLSEeyfekydeyllwgwpstmergRPNIVFKVAGSsEAAIEITRMLESMGIGTNNTVT 381
                                    *******************************************************886889******************* PP

                                    -SHHHHHHHHHH CS
                        TAL_FSA 140 Fsleqalaaaea 151
                                    F + q ++ + a
  gi|119720070|ref|YP_920565.1| 382 FAVSQEVQLILA 393
                                    *****9998877 PP

>> ParD_antitoxin  Bacterial antitoxin of ParD toxin-antitoxin type II system and RHH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   0.00011      0.95      25      55 ..     425     455 ..     404     466 .. 0.76
   2 ?   -0.9   0.1      0.25   2.3e+03      29      58 ..     624     653 ..     608     655 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00011
                                    S-SSHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                 ParD_antitoxin  25 rYgsaseviraaLrLLeeretklkaLreaLe 55 
                                    r   a+e i++aLr Le+ e +l+ L   L 
  gi|119720070|ref|YP_920565.1| 425 REVKAAELIKTALRQLENPEEELARLARELG 455
                                    55679******************99966553 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.25
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                 ParD_antitoxin  29 aseviraaLrLLeeretklkaLreaLeege 58 
                                    a  v+r a r +ee   k++  r+a e  e
  gi|119720070|ref|YP_920565.1| 624 ANAVLRGAPREVEELLVKMEDFRKAYELTE 653
                                    6779**************999999987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (714 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.77u 0.32s 00:00:01.09 Elapsed: 00:00:00.56
# Mc/sec: 3855.91
//
Query:       gi|119720071|ref|YP_920566.1|  [L=363]
Description: ABC transporter related [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-32  111.3   0.0    7.5e-32  110.7   0.0    1.3  1  ABC_tran         ABC transporter
    6.6e-12   46.1   0.0    1.9e-11   44.6   0.0    1.9  1  OB_MalK          MalK OB fold domain
    1.2e-06   28.5   0.0       0.02   14.7   0.0    2.2  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    2.5e-05   24.3   0.0    8.5e-05   22.7   0.0    2.0  1  TOBE_2           TOBE domain
    0.00016   21.7   0.0    0.00022   21.2   0.0    1.2  1  Rad17            Rad17 P-loop domain
     0.0027   17.2   0.1       0.11   11.9   0.0    2.2  2  SMC_N            RecF/RecN/SMC N terminal domain
     0.0027   18.0   0.3      0.006   16.9   0.3    1.8  1  AAA_22           AAA domain
     0.0033   17.8   0.1     0.0052   17.2   0.1    1.5  1  AAA_16           AAA ATPase domain
  ------ inclusion threshold ------
      0.022   15.2   0.1      0.062   13.7   0.0    1.8  2  AAA              ATPase family associated with various cellul
      0.031   14.8   0.2       0.14   12.7   0.1    2.2  1  CysA_C_terminal  CysA C-terminal regulatory domain
      0.038   14.2   0.0       0.18   12.1   0.0    2.1  2  AAA_28           AAA domain
      0.048   13.6   0.0        0.1   12.5   0.0    1.5  1  RsgA_GTPase      RsgA GTPase
      0.059   13.7   0.0       0.14   12.5   0.0    1.6  1  TOBE             TOBE domain
      0.093   12.4   0.0       0.27   10.9   0.0    1.7  2  AAA_30           AAA domain
      0.093   12.6   0.0       0.16   11.9   0.0    1.3  1  ATPase_2         ATPase domain predominantly from Archaea
      0.099   13.0   0.1       0.42   11.0   0.0    1.9  2  AAA_19           AAA domain
       0.16   12.0   0.1       0.42   10.6   0.0    1.7  2  AAA_5            AAA domain (dynein-related subfamily)
       0.17   11.1   0.0       0.24   10.5   0.0    1.1  1  G-alpha          G-protein alpha subunit
        0.2   11.5   0.0       0.65    9.8   0.0    1.8  2  AAA_29           P-loop containing region of AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.7   0.0   7.9e-35   7.5e-32       2     136 ..      20     161 ..      19     162 .. 0.96

  Alignments for each domain:
  == domain 1  score: 110.7 bits;  conditional E-value: 7.9e-35
                                    EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                       ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                    ++vs++ k ge ++++G++G+GK+t l+++agl++p+eGei + ++ +++  l+  ++ +++++q+  l p+++v++n  
  gi|119720071|ref|YP_920566.1|  20 DRVSFEAKDGEFLVLLGPSGCGKTTTLRMIAGLETPDEGEIYIGDRLVND--LPPKDRDVAMVFQNYALYPHMKVYDNia 97 
                                    78***************************************888888888..**************************** PP

                                    ...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                               e d+++ ++++ l+++el d+      ++LSgGq+qrval ral+++p+++l+DEp 
  gi|119720071|ref|YP_920566.1|  98 fplrirklpadEIDRRVREVAKLLRIEELLDRYP----RQLSGGQQQRVALGRALVRQPQVFLMDEPL 161
                                    ****************************999998....*****************************7 PP

>> OB_MalK  MalK OB fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.6   0.0     2e-14   1.9e-11       1      53 []     235     290 ..     235     290 .. 0.93

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 2e-14
                        OB_MalK   1 GSPaMNflpatveedg..vlvegggvtlplpeeq.klalklyagkevilGiRPEhi 53 
                                    G PaMNf++a  + ++  v+++ g  +++lp+++ ++  k+ +  evi+GiRPEhi
  gi|119720071|ref|YP_920566.1| 235 GAPAMNFVDASAKVEDdtVVLDTGIYRIRLPKDAsEVLIKQGVPSEVIFGIRPEHI 290
                                    99********9876666899**************888******************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   0.00015      0.14       1      49 [.      31      70 ..      31      97 .. 0.67
   2 !   14.7   0.0   2.1e-05      0.02     211     298 ..     108     193 ..      86     197 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00015
                         AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipsll 49
                                   + vl Gp g+GK++ L+ + +l         +t++++ +   +   + l
  gi|119720071|ref|YP_920566.1| 31 FLVLLGPSGCGKTTTLRMIAGL---------ETPDEGEIYIGDRLVNDL 70
                                   579****************999.........344444444444444444 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 2.1e-05
                         AAA_21 211 svderlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ng 289
                                    ++++r  ++   +l  +   ++ +r+lS G+++  al  al r++    ++l DEp ++L+ kl       lk+l+r  g
  gi|119720071|ref|YP_920566.1| 108 DEIDRRVREVAKLLRIEELLDRYPRQLSGGQQQRVALGRALVRQP---QVFLMDEPLSNLDAKLRVYMRAELKRLQReLG 184
                                    333333333666666667778899**********9********99...9*************999999988888888899 PP

                         AAA_21 290 aQviltTHS 298
                                    +  i +TH+
  gi|119720071|ref|YP_920566.1| 185 ITTIYVTHD 193
                                    999****98 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0     9e-08   8.5e-05       2      76 .]     284     354 ..     283     354 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 9e-08
                         TOBE_2   2 aiRPEklrlaaagganglsGtVedveylGsstryvvelaggqlvvvrqpnadrdsalapGdtVelswdpddavvl 76 
                                    +iRPE++++++++  ++++++V  +e lGs+t +  + ++   ++ ++ +++      pG+++ ++++ + a+v+
  gi|119720071|ref|YP_920566.1| 284 GIRPEHITVSKQEFPGSFAAEVFVTEPLGSETIIDFKHGDA--ILKAKYPGHF--EASPGEKIYIGFQLQYAHVF 354
                                    8********5333258****************977666666..4455555554..788************99998 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   2.3e-07   0.00022      38     112 ..      22      96 ..       6     159 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 2.3e-07
                          Rad17  38 dvLesrkkriLLisGPsGCgkstvvkvLskelgiklrewlnp.vslkepdnqksdfkgltekesrflsqiesfkel 112
                                     + e +  + L++ GPsGCgk+t++++++   +++  e   +  ++++ + +  d+  +++    + + ++++ ++
  gi|119720071|ref|YP_920566.1|  22 VSFEAKDGEFLVLLGPSGCGKTTTLRMIAGLETPDEGEIYIGdRLVNDLPPKDRDVAMVFQNY-ALYPHMKVYDNI 96 
                                    5677787889******************98888777665444044455555666665444444.477777777765 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.058        55      24      41 ..      29      46 ..      10      51 .. 0.80
   2 !   11.9   0.0   0.00012      0.11     119     213 ..     113     206 ..      66     213 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.058
                                   SSEEEEEESTTSSHHHHH CS
                                   xxxxxxxxxxxxxxxxxx RF
                          SMC_N 24 ksftaivGpNGSGKsnll 41
                                    +f +++Gp G+GK+  l
  gi|119720071|ref|YP_920566.1| 29 GEFLVLLGPSGCGKTTTL 46
                                   57999*********9765 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00012
                                    -HHHHHHHHHCTT-...STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE CS
                                    xxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 119 tkkevsellesagi...skelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivi 195
                                    + +ev++ll+ +++   ++ +LSgG+++ val        v++  ++l+De  ++LD+k +  +   lk+ + +  +  i
  gi|119720071|ref|YP_920566.1| 113 RVREVAKLLRIEELldrYPRQLSGGQQQRVALGRA----LVRQPQVFLMDEPLSNLDAKLRVYMRAELKRLQRELGITTI 188
                                    456666666665552224569******98887543....34566689*****************9999999999777666 PP

                                    -SSHHHCCC-SCEEEEEE CS
                                    xxxxxxxxxxxxxxxxxx RF
                          SMC_N 196 slreemlekadklvgvtk 213
                                     +++++ e +    +v  
  gi|119720071|ref|YP_920566.1| 189 YVTHDQAEAMTMADRVAV 206
                                    666666666655555544 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.3   6.3e-06     0.006       4      27 ..      28      51 ..      25     198 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6.3e-06
                         AAA_22  4 tagilvvtGesGtGKTtllrrlle 27
                                   +  +lv+ G+sG+GKTt+lr+++ 
  gi|119720071|ref|YP_920566.1| 28 DGEFLVLLGPSGCGKTTTLRMIAG 51
                                   6789****************9875 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   5.6e-06    0.0052      22      46 ..      27      51 ..      18     183 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 5.6e-06
                         AAA_16 22 grpelvllsGesGvGKsslvrellr 46
                                    ++e ++l G+sG+GK++ +r+++ 
  gi|119720071|ref|YP_920566.1| 27 KDGEFLVLLGPSGCGKTTTLRMIAG 51
                                   45589****************9984 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   6.6e-05     0.062       2      20 ..      33      51 ..      32      68 .. 0.92
   2 ?   -2.1   0.0       5.1   4.9e+03      56      66 ..     148     159 ..     108     191 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.6e-05
                                   EEESSTTSSHHHHHHHHHH CS
                            AAA  2 llyGppGtGKTllakavak 20
                                   +l Gp G+GKT++ + +a 
  gi|119720071|ref|YP_920566.1| 33 VLLGPSGCGKTTTLRMIAG 51
                                   799*************995 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 5.1
                                    TS.TSEEEEEET CS
                            AAA  56 ka.kpsilfiDE 66 
                                       +p ++++DE
  gi|119720071|ref|YP_920566.1| 148 LVrQPQVFLMDE 159
                                    223467777776 PP

>> CysA_C_terminal  CysA C-terminal regulatory domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   0.00015      0.14       5      43 .]     246     292 ..     245     292 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00015
                CysA_C_terminal   5 GrvedGklriGg..lalpvPelaga......dgqevvayVRPhDlei 43 
                                    ++ved +++++   +++ +P++a          +ev+ ++RP+++++
  gi|119720071|ref|YP_920566.1| 246 AKVEDDTVVLDTgiYRIRLPKDASEvlikqgVPSEVIFGIRPEHITV 292
                                    5788888888555599999944444577744459***********87 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00019      0.18       3      22 ..      33      52 ..      31      77 .. 0.86
   2 ?   -1.2   0.0       2.2   2.1e+03     130     155 ..     165     190 ..     125     201 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00019
                         AAA_28  3 vitGgestGKTtlleaLaar 22
                                   v++G++++GKTt+l+ +a  
  gi|119720071|ref|YP_920566.1| 33 VLLGPSGCGKTTTLRMIAGL 52
                                   99************999854 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.2
                         AAA_28 130 dleereaiderlrealrelgipviiv 155
                                    d + r  + + l+ + relgi  i v
  gi|119720071|ref|YP_920566.1| 165 DAKLRVYMRAELKRLQRELGITTIYV 190
                                    44556666677777777777777766 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00011       0.1      91     123 ..      20      53 ..       8      63 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                                    HHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT- CS
                    RsgA_GTPase  91 eelkellkd.ktsvlvGqSGvGKStLinallpel 123
                                    ++++ + kd ++ vl+G+SG GK+t + ++++ +
  gi|119720071|ref|YP_920566.1|  20 DRVSFEAKDgEFLVLLGPSGCGKTTTLRMIAGLE 53 
                                    566666666699*************999998754 PP

>> TOBE  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00015      0.14       5      57 ..     299     346 ..     296     349 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00015
                           TOBE   5 NqlpgtVvvveplgseveVrvdlgggatLtArvtrrsaeeLgLapGeeVfali 57 
                                    + + ++V v eplgse+ ++   g+   L A+ ++   ++    pGe++++ +
  gi|119720071|ref|YP_920566.1| 299 GSFAAEVFVTEPLGSETIIDFKHGDAI-LKAKYPGHFEAS----PGEKIYIGF 346
                                    789************************.*****7666666....*****9866 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00028      0.27      18      42 ..      29      53 ..      22      77 .. 0.84
   2 ?   -2.9   0.0       4.9   4.6e+03      40      66 ..     178     204 ..     171     220 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00028
                         AAA_30 18 drvavltGpAGtGKttalkalreaw 42
                                     + vl Gp G GKtt+l+ ++ + 
  gi|119720071|ref|YP_920566.1| 29 GEFLVLLGPSGCGKTTTLRMIAGLE 53
                                   35889**************998765 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.9
                         AAA_30  40 eaweaaggrviglAptgkaAkvLaeel 66 
                                    ++ ++ g + i +++ ++ A ++a+ +
  gi|119720071|ref|YP_920566.1| 178 RLQRELGITTIYVTHDQAEAMTMADRV 204
                                    444444666666666666666665554 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00017      0.16      18      54 ..      27      62 ..      21      83 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00017
                       ATPase_2 18 epneiyfiYGpegsGKtaLlkeiienledkdkyviyy 54
                                   +  e++++ Gp g+GKt+ l+ i+      d+  iy+
  gi|119720071|ref|YP_920566.1| 27 KDGEFLVLLGPSGCGKTTTLRMIAGLE-TPDEGEIYI 62
                                   567899**************9876554.445566665 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00044      0.42       9      31 ..      28      50 ..      20      58 .. 0.83
   2 ?   -1.0   0.1       2.1     2e+03      44      89 ..     186     232 ..     168     257 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00044
                         AAA_19  9 kekvllvtaGpGtGKTrvlkhiv 31
                                     + l+++++ G+GKT++l++i 
  gi|119720071|ref|YP_920566.1| 28 DGEFLVLLGPSGCGKTTTLRMIA 50
                                   56789999***********9875 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.1
                         AAA_19  44 eillvaftgrAakelrerlaalgae.atTiHrlalldfddllteale 89 
                                    + + v+  +  a+ +++r+a++++  ++ +   a+l f + +t  ++
  gi|119720071|ref|YP_920566.1| 186 TTIYVTHDQAEAMTMADRVAVMNEGkIMQLADPAELYFRPANTFVAG 232
                                    45566666667777777776655434444444444444444444444 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00044      0.42       2      22 ..      32      52 ..      31      66 .. 0.85
   2 ?   -3.0   0.0       7.1   6.7e+03      72     102 ..     108     139 ..     107     168 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00044
                                   EEEE--SSSSHHHHHHHGGGG CS
                          AAA_5  2 vlLvGppGtgKselaerlaaa 22
                                   ++L+Gp+G+gK++  + +a +
  gi|119720071|ref|YP_920566.1| 32 LVLLGPSGCGKTTTLRMIAGL 52
                                   68***********99988865 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 7.1
                                    ESGGG--HHHHHHH..HHHHHSSEEE..-SSSE CS
                          AAA_5  72 DEveraesevlnsL..lslleerrllleeggel 102
                                    DE++r  +ev++ L    ll++  ++  +gg++
  gi|119720071|ref|YP_920566.1| 108 DEIDRRVREVAKLLriEELLDRYPRQ-LSGGQQ 139
                                    56666666665544213445544444.333333 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00025      0.24      26      49 ..      32      55 ..      16      75 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00025
                                   EEEEESTTSSHHHHHHHHHHHCS- CS
                        G-alpha 26 llllGqseSGKsTilkqlkllykk 49
                                   l+llG s++GK+T+l+ +  l+++
  gi|119720071|ref|YP_920566.1| 32 LVLLGPSGCGKTTTLRMIAGLETP 55
                                   89**************99887766 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00069      0.65      16      39 ..      23      46 ..      17      59 .. 0.74
   2 ?   -2.1   0.0       3.6   3.4e+03      16      41 ..     220     244 ..     202     248 .. 0.53

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00069
                         AAA_29 16 tieidlkg.atlltGpsGsGKSTll 39
                                   ++e +  g + +l GpsG GK+T l
  gi|119720071|ref|YP_920566.1| 23 SFEAKD-GeFLVLLGPSGCGKTTTL 46
                                   445553.358999**********87 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.6
                         AAA_29  16 tieidlkgatlltGpsGsGKSTllDA 41 
                                    ++ +++++ t+++G +G+    ++DA
  gi|119720071|ref|YP_920566.1| 220 ELYFRPAN-TFVAGFIGAPAMNFVDA 244
                                    44455554.88888777655555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 2172.32
//
Query:       gi|119720072|ref|YP_920567.1|  [L=120]
Description: hypothetical protein Tpen_1166 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 856.88
//
Query:       gi|119720073|ref|YP_920568.1|  [L=233]
Description: glycerophosphoryl diester phosphodiesterase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.7e-40  138.8   0.0    8.1e-40  137.2   0.0    1.7  1  GDPD        Glycerophosphoryl diester phosphodiesterase famil
    0.00024   21.5   0.5    0.00046   20.6   0.5    1.4  1  GDPD_2      Glycerophosphoryl diester phosphodiesterase famil
  ------ inclusion threshold ------
      0.023   14.0   0.0      0.032   13.5   0.0    1.3  1  ThiG        Thiazole biosynthesis protein ThiG
       0.03   13.3   0.0      0.045   12.8   0.0    1.3  1  FMN_dh      FMN-dependent dehydrogenase
      0.035   14.1   0.0       0.47   10.4   0.0    2.5  3  ADH_zinc_N  Zinc-binding dehydrogenase


Domain annotation for each model (and alignments):
>> GDPD  Glycerophosphoryl diester phosphodiesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.2   0.0   2.3e-43   8.1e-40       1     257 [.      11     221 ..      11     223 .. 0.91

  Alignments for each domain:
  == domain 1  score: 137.2 bits;  conditional E-value: 2.3e-43
                                    TTTTTTTSSTTSHHHHHHHHHTT-SEEEEEEEE-TTS-EEE-SSSBSTTTCSCCCH.BGGGS-HHHHHTSTECCTTCCCC CS
                           GDPD   1 HRGasgnlpEnTlesfakAaelGadyiEfDvqlTkDgvpVvlHDfnldrttdvagrldvkdltleelkrldkiakenkaq 80 
                                    HRGa +  pEnTl+sf kA+e Ga  iEfDv+lT+Dgv Vv HD+ l+r+ +v+g  +v++ t++el   + ++      
  gi|119720073|ref|YP_920568.1|  11 HRGAAALEPENTLPSFLKAYECGATGIEFDVRLTRDGV-VVAHDDELERVAGVKG--RVSEKTYSELLGVR-VGG----- 81 
                                    *************************************8.5679************..**************.433..... PP

                                    SCCCSSGCCB...BHHHHHHHHHHCCSEEEEEEECCCCCCCHHHHHHTCHHHCCCCCSCHHTT..STTCSCEEEESTHHH CS
                           GDPD  81 lsenrvrlefpfptleevlkkpqnvglnieikipmlseakeeeelqivkeilksvdeilkkvlkkadkrkvifssfnpdi 160
                                        r     ++ptl evl+  ++  l+++i++++  +  e        + l+ vd+ l             ++sf p++
  gi|119720073|ref|YP_920568.1|  82 ----RA----RIPTLREVLSL-AKGRLSVDIELKVVGAEAEVVD---SLRELRMVDDAL-------------VTSFVPEA 136
                                    ....33....67********8.***********99877666666...445555555555.............56****** PP

                                    HHHHHHTCTCTEEEEEEHHHHHHC-E.EECHCCCCCCCTCCCCHHCCCHCCCEB.CHHHHHHHTT-EEEEBSB-THSHHH CS
                           GDPD 161 lkllrekqpklpllflteggteaeadssleraakfakadallgevsavaeglgdpdlVkraksrglvvhvytvnnedeee 240
                                    l++++e++p++ +  l+e+ +  +        a++++a+all++ +a+++      lV+r+k+rg +v ++tv+++  e 
  gi|119720073|ref|YP_920568.1| 137 LRRVKELAPEVSVGVLLEEWDDEYLE-----IAEKLGAEALLPYYEALSRD-----LVERIKKRGFKVITWTVDDP--EV 204
                                    ******************99999998.....99*****************9.....********************..** PP

                                    HHHHHCCC-SEEEES-H CS
                           GDPD 241 mkrlleagvdgvitDfp 257
                                      rl ++g+dgvitD+p
  gi|119720073|ref|YP_920568.1| 205 AERLYRLGIDGVITDDP 221
                                    ***************98 PP

>> GDPD_2  Glycerophosphoryl diester phosphodiesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.5   1.3e-07   0.00046       2      29 ..     194     221 ..     193     221 .. 0.94

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.3e-07
                         GDPD_2   2 vrfWttddeavwrelvgaGVdgInTDdl 29 
                                    v  Wt+dd+ v   l ++G dg++TDd+
  gi|119720073|ref|YP_920568.1| 194 VITWTVDDPEVAERLYRLGIDGVITDDP 221
                                    668************************8 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   9.1e-06     0.032     103     148 ..     170     216 ..     133     219 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.1e-06
                                    TTTEB-HHHHHHH.HHHHHHTT-EEEEEE-S-HHHHHHHHHTT-SEB CS
                           ThiG 103 ktLlPdvvetlka.aeiLvkeGFevlpYvsdDlvlarrleevGcaav 148
                                    + LlP    + +   e + k GF+v++++ dD+ +a+rl  +G+  v
  gi|119720073|ref|YP_920568.1| 170 EALLPYYEALSRDlVERIKKRGFKVITWTVDDPEVAERLYRLGIDGV 216
                                    56667666665432688999*********************998776 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.3e-05     0.045     116     153 ..     171     208 ..     134     218 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.3e-05
                                    EE-CSSHHHHHHHHHHHHHCTESEEEEESSTSS---BH CS
                         FMN_dh 116 lyvpkdrelteellkraeaagykalvltvDtpvlgkRe 153
                                      +p  ++l+++l++r+++ g+k++  tvD p   +R 
  gi|119720073|ref|YP_920568.1| 171 ALLPYYEALSRDLVERIKKRGFKVITWTVDDPEVAERL 208
                                    556677899*********************99888775 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.59   2.1e+03      64      77 ..     106     119 ..      73     144 .. 0.64
   2 ?   10.4   0.0   0.00013      0.47      23      74 ..     157     207 ..     151     211 .. 0.70
   3 ?    3.7   0.0     0.015        56      12      41 ..     189     219 ..     188     232 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.59
                                    ESSCSHHHHHHHHH CS
                     ADH_zinc_N  64 ecvGsgatleaalk 77 
                                     +vG++a + ++l+
  gi|119720073|ref|YP_920568.1| 106 KVVGAEAEVVDSLR 119
                                    34443333333333 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00013
                                    SHHHHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHHHH CS
                     ADH_zinc_N  23 seeklelakklGadevinykeadlverikeltggegvdvvfecvGsgatlea 74 
                                    ++e le+a+klGa++++ y e  l+ ++ e  +++g++v+  +v ++++ e+
  gi|119720073|ref|YP_920568.1| 157 DDEYLEIAEKLGAEALLPYYE-ALSRDLVERIKKRGFKVITWTVDDPEVAER 207
                                    56789**************44.455555555555667777766666666555 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.015
                                    HTT-EEEE.EESSHHHHHHHHHTTESEEEET CS
                     ADH_zinc_N  12 alGaevia.vdsseeklelakklGadeviny 41 
                                      G++vi+ ++ ++e +e + +lG d vi+ 
  gi|119720073|ref|YP_920568.1| 189 KRGFKVITwTVDDPEVAERLYRLGIDGVITD 219
                                    5799999999*******************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1571.22
//
Query:       gi|119720074|ref|YP_920569.1|  [L=634]
Description: transglutaminase domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.2e-22   78.0   0.1    1.3e-21   77.1   0.1    1.5  1  Transglut_core  Transglutaminase-like superfamily


Domain annotation for each model (and alignments):
>> Transglut_core  Transglutaminase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.1   0.1   7.4e-26   1.3e-21       3     112 .]     271     379 ..     269     379 .. 0.92

  Alignments for each domain:
  == domain 1  score: 77.1 bits;  conditional E-value: 7.4e-26
                 Transglut_core   3 laeeltagakdplekakaiyewvrknveys...aprrtpgsrdaeavletgkGncedfaslfvallRalGipaRvvtgyl 79 
                                    +a++l +g ++  + a +i+++v++  +y+   ++ r++ s  a ++l +++G c +fa l+va++Ra+G+paRvv g++
  gi|119720074|ref|YP_920569.1| 271 VARRLSSGVSTVRQLASRIADYVSSTLRYNdalRSIRDSWSLGALWALHAKQGMCLQFARLYVAIARAAGLPARVVEGLV 350
                                    789999999999******************8776777777777************************************* PP

                 Transglut_core  80 sgeeekeqsvasedaHawvevylegygWvplDp 112
                                     ++      ++s++ Ha++e+yl+gygWvp++p
  gi|119720074|ref|YP_920569.1| 351 VTPPG----GSSSYLHAYAEFYLPGYGWVPVEP 379
                                    *8853....899999****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (634 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.65u 0.28s 00:00:00.93 Elapsed: 00:00:00.49
# Mc/sec: 3884.57
//
Query:       gi|119720075|ref|YP_920570.1|  [L=315]
Description: NAD-dependent epimerase/dehydratase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-57  194.5   0.0    2.8e-57  194.0   0.0    1.3  1  Epimerase        NAD dependent epimerase/dehydratase family
    9.6e-52  176.4   0.0    4.3e-51  174.3   0.0    1.8  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    7.5e-27   94.0   0.0    1.3e-26   93.3   0.0    1.3  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    2.4e-21   76.1   0.0    1.8e-20   73.3   0.0    1.9  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    3.1e-16   59.8   0.0    7.5e-16   58.5   0.0    1.6  2  NAD_binding_10   NAD(P)H-binding
    7.4e-15   54.8   0.0    9.3e-15   54.5   0.0    1.1  1  RmlD_sub_bind    RmlD substrate binding domain
    1.5e-11   44.0   0.1    2.2e-06   27.0   0.0    2.4  2  NAD_binding_4    Male sterility protein
    7.9e-11   41.8   0.5    3.5e-09   36.4   0.5    2.7  1  adh_short        short chain dehydrogenase
    2.1e-08   34.0   0.1    6.1e-08   32.5   0.1    1.8  1  NmrA             NmrA-like family
    3.8e-05   23.7   0.2    9.5e-05   22.4   0.1    1.6  2  KR               KR domain
    4.1e-05   23.3   0.0     0.0029   17.2   0.0    2.3  2  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
     0.0093   16.2   0.1       0.02   15.2   0.1    1.6  1  TrkA_N           TrkA-N domain
  ------ inclusion threshold ------
      0.021   14.9   0.2       0.12   12.4   0.0    2.2  3  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
      0.025   15.2   0.1      0.079   13.5   0.0    1.9  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
      0.067   13.5   0.1       0.16   12.2   0.1    1.7  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
      0.097   12.8   0.0        0.2   11.8   0.0    1.6  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
        0.1   12.7   0.0       0.16   12.1   0.0    1.3  1  Ldh_1_N          lactate/malate dehydrogenase, NAD binding do
        0.2   11.5   0.0       0.34   10.8   0.0    1.3  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  194.0   0.0   2.8e-60   2.8e-57       1     241 []       7     238 ..       7     238 .. 0.95

  Alignments for each domain:
  == domain 1  score: 194.0 bits;  conditional E-value: 2.8e-60
                                    EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC...EEEE--TT-HHHHHHHHHHHT-SEEEE--S---H CS
                      Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl...elveldltdrsalerlfkeeqpdavihlAavggv 77 
                                    +lVtG++GfiGs+lv++l ++gyev++ld+lss+s ++++  l   e+v++d++ r+++e++++  ++dav+h+Aa  ++
  gi|119720075|ref|YP_920570.1|   7 VLVTGGAGFIGSHLVERLVARGYEVVVLDNLSSGSLENLRSVLgdvEFVRGDVRSREDVEKALR--GVDAVFHFAA--NP 82 
                                    79*****************************88887777766699*******************..9*******77..66 PP

                                    HHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHHHH CS
                      Epimerase  78 aassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklveaya 157
                                    ++++ dp + +e+n+  t n+lea+r+ gv  ++f+sSs+vYG+ ++ p+ e+   gplkp s Y+a+Kla e l+ +y+
  gi|119720075|ref|YP_920570.1|  83 EVRVGDPREHFEHNVFATFNVLEAMRRLGVSDIVFASSSTVYGDAEKLPTPEDY--GPLKPISVYGASKLACEALISSYT 160
                                    66679**************************************99998877777..8*********************** PP

                                    HHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHTT-STTEE CS
                      Epimerase 158 aqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvlehvdagdkgei 237
                                    +++g++ ++lr+ n++Gpr      ++v+  ++rk+ e+   + +lgdgt++  ++++eD++ea ll+ e+  +g+  e+
  gi|119720075|ref|YP_920570.1| 161 HTFGFKGVALRYANVVGPR----ATRGVVKDFVRKLRENPRVLEILGDGTQRKSYVWIEDAVEATLLAWER--TGEGFEA 234
                                    *******************....9**************9999*****************************..777788* PP

                                    EEES CS
                      Epimerase 238 yniG 241
                                    yn+G
  gi|119720075|ref|YP_920570.1| 235 YNVG 238
                                    ***9 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  174.3   0.0   4.3e-54   4.3e-51       1     330 [.       8     305 ..       8     307 .. 0.86

  Alignments for each domain:
  == domain 1  score: 174.3 bits;  conditional E-value: 4.3e-54
                                    EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEE CS
                  GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevy 80 
                                    L+TG+aGfiGs+l+e+L+++gyev++++++ss  ++++++++         +++++++gD++ ++ +e++l+ v  d+v+
  gi|119720075|ref|YP_920570.1|   8 LVTGGAGFIGSHLVERLVARGYEVVVLDNLSSG-SLENLRSVL--------GDVEFVRGDVRSREDVEKALRGV--DAVF 76 
                                    9************************99988764.555555554........5689******************9..9*** PP

                                    E--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TT.S-----SHHHHHHHH CS
                  GDP_Man_Dehyd  81 nLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEt.tpfyPrsPYaaaKly 159
                                    ++AA   V+v   +P + +e nv +t+++Lea+r+lg++    +++aS+s+vYG++++ p  E+  p++P s Y+a+Kl+
  gi|119720075|ref|YP_920570.1|  77 HFAANPEVRV--GDPREHFEHNVFATFNVLEAMRRLGVS---DIVFASSSTVYGDAEKLPTPEDyGPLKPISVYGASKLA 151
                                    *****99987..8************************96...6889**************988768************** PP

                                    HHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHHHHHHHHHC CS
                  GDP_Man_Dehyd 160 adwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkDyveamwlmlqq 239
                                    ++ ++ +y +++g+  v  ++ n  +pr         + ++v +  ++ +   +lG++ +++++ +++D vea  l+ ++
  gi|119720075|ref|YP_920570.1| 152 CEALISSYTHTFGFKGVALRYANVVGPRA----TRGVVKDFVRKLRENPRVLEILGDGTQRKSYVWIEDAVEATLLAWER 227
                                    ****************************4....2334556666666666666668*******************999987 PP

                                    ..SS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB--B-THHHHHHH CS
                  GDP_Man_Dehyd 240 ..dkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdlllgdaskakeeL 317
                                      +  e y++++ +  +vre++++ + ++g + +            + +g     v   +   g+v+++  d+ k+k +L
  gi|119720075|ref|YP_920570.1| 228 tgEGFEAYNVGSEDAITVREVADIVVSAMGLSNVEY----------RFTG----GVMGGRGWVGDVKNMHLDIGKLK-KL 292
                                    4344599*****************999999853321..........1222....23344455699***********9.9* PP

                                    ----SS-HHHHHH CS
                  GDP_Man_Dehyd 318 gWkpkvsfeelvr 330
                                    gW+p+++ ++ vr
  gi|119720075|ref|YP_920570.1| 293 GWSPRYTSRDAVR 305
                                    *****99988776 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.3   0.0   1.3e-29   1.3e-26       1     229 [.       8     225 ..       8     234 .. 0.89

  Alignments for each domain:
  == domain 1  score: 93.3 bits;  conditional E-value: 1.3e-29
                      3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslvdva 80 
                                    +vtGgaGF+G++lv++Lv ++   ev vlD   s +l +  s ++  +++ gDv++ +++e+al+gvd+v+h a+  +v+
  gi|119720075|ref|YP_920570.1|   8 LVTGGAGFIGSHLVERLVARG--YEVVVLDNLSSGSLENLRSVLGDVEFVRGDVRSREDVEKALRGVDAVFHFAANPEVR 85 
                                    69*******************..6************988888999999*************************9999999 PP

                      3Beta_HSD  81 gkltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKalaEklvlka 160
                                      + ++   + nv  T nvlea ++ gv  +v+ Ss  v g+   +e++     e + + ++ ++y  sK   E+l+ + 
  gi|119720075|ref|YP_920570.1|  86 VGDPRE-HFEHNVFATFNVLEAMRRLGVSDIVFASSSTVYGD---AEKLP--TPEDYGPLKPISVYGASKLACEALISSY 159
                                    877776.7899*******************************...77777..3455678899**************9887 PP

                      3Beta_HSD 161 NgrtlknggrlyTcaLRpagiyGegdkl..lvpllkqlaklglalfkigdeevlsdrvYvgNvawahilAa 229
                                              +  +aLR a + G++ ++  ++ ++++l  +   l  +gd  + +++v+ +  + a +lA 
  gi|119720075|ref|YP_920570.1| 160 TH---TF--GFKGVALRYANVVGPRATRgvVKDFVRKLRENPRVLEILGDGTQRKSYVWIEDAVEATLLAW 225
                                    77...33..4899***********988632566888888888888899*******************9996 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.3   0.0   1.8e-23   1.8e-20       1     260 [.       7     264 ..       7     274 .. 0.82

  Alignments for each domain:
  == domain 1  score: 73.3 bits;  conditional E-value: 1.8e-23
                                    EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T-SE CS
                Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkvdv 80 
                                    vlvtG++G iGs+lv++++++  + ++l + +  +l ++++ l     +  ++     v gdvr +e +ekal+  +vd+
  gi|119720075|ref|YP_920570.1|   7 VLVTGGAGFIGSHLVERLVARGYEVVVLDNLSSGSLENLRSVLG----D--VE----FVRGDVRSREDVEKALR--GVDA 74 
                                    8**********************999999999999999999882....3..33....347**************..**** PP

                                    EEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEE.......GGG........SS--SHHHHHHHHH CS
                Polysacc_synt_2  81 vfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliSt.......DKA........vnPtnvmGatKrla 145
                                    vfh AA  +V +    p e ++ Nv++t nv+ea  + gv+++v+ S+        K          +P++v+Ga+K+++
  gi|119720075|ref|YP_920570.1|  75 VFHFAANPEVRVG--DPREHFEHNVFATFNVLEAMRRLGVSDIVFASSstvygdaEKLptpedygpLKPISVYGASKLAC 152
                                    *******999986..699***************************997334432223233333333789*********** PP

                                    HHHHHHGGG--SSS--EEEEEEE-EETTGTTS..SHHHHHHHHHTT.SSEEES.-TT-EEEEE-HHHHHHHHHHHHHH.- CS
                Polysacc_synt_2 146 ekllqalakeseekktkfvvvRfGNVlgSrGS..viplFkkqikeg.gpvtvT.dpemtRyfmtieeavqLvlqalal.a 220
                                    e l+ ++ ++      k v+ R+ NV+g r    v+  F ++++e+   + +  d +  + ++ ie+av+  l a ++ +
  gi|119720075|ref|YP_920570.1| 153 EALISSYTHTF---GFKGVALRYANVVGPRATrgVVKDFVRKLRENpRVLEILgDGTQRKSYVWIEDAVEATLLAWERtG 229
                                    *****999988...78999********9775333999999999998567777615555567999*******999987515 PP

                                    -SS-EEEE--.-EEEHHHHHHHH..........SSSS-EE CS
                Polysacc_synt_2 221 kggeifvldmGepvkivdlakalielsgleekkeedieik 260
                                    +g e + +   ++++++++a  +++ +gl++     +e +
  gi|119720075|ref|YP_920570.1| 230 EGFEAYNVGSEDAITVREVADIVVSAMGLSN-----VEYR 264
                                    666999888889***********99999754.....3444 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.5   0.0   7.6e-19   7.5e-16       1     108 [.      11     130 ..      11     171 .. 0.76
   2 ?   -2.4   0.0       3.7   3.7e+03     167     180 ..     242     255 ..     228     262 .. 0.66

  Alignments for each domain:
  == domain 1  score: 58.5 bits;  conditional E-value: 7.6e-19
                                    TTTSHHHHHHHHHHHHC-T-EEEEEETT..HHHCHHHHCT.TTCEEEE--TT-CCHHHHHHTT-SEEEES---TCC.... CS
                 NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRn..peklaeleae.eglevvegdvtdvedlaealkgadaVvsalggggk.... 73 
                                    G+ G +G++lv++l+arg +ev++l  n  + +l++l++    +e v gdv + ed+++al+g+daV+  +++ +     
  gi|119720075|ref|YP_920570.1|  11 GGAGFIGSHLVERLVARG-YEVVVL-DNlsSGSLENLRSVlGDVEFVRGDVRSREDVEKALRGVDAVFHFAANPEVrvgd 88 
                                    99***************5.**9776.55225577788766699************************9888666655664 PP

                                    .HHHH........HHHHHHHHHHCT--EEEEEEETTTTSGCGCH CS
                 NAD_binding_10  74 .deeg........aknivdaakeagvkRfvlvsaigvgdevpge 108
                                     +           + n+++a+++ gv+ +v+ s+  v+ ++++ 
  gi|119720075|ref|YP_920570.1|  89 pR--EhfehnvfaTFNVLEAMRRLGVSDIVFASSSTVYGDAEKL 130
                                    42..244666799************************9754432 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.7
                                    EEEHHHHHHHHHHH CS
                 NAD_binding_10 167 sisradVAdvlvav 180
                                     i+ + VAd +v++
  gi|119720075|ref|YP_920570.1| 242 AITVREVADIVVSA 255
                                    45556666665554 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.5   0.0   9.3e-18   9.3e-15       2     233 ..       6     258 ..       5     266 .. 0.85

  Alignments for each domain:
  == domain 1  score: 54.5 bits;  conditional E-value: 9.3e-18
                                    EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT..................T--TTSHHHHHHHHHHH--SEEEE------ CS
                  RmlD_sub_bind   2 kilvtGanGqlGseLakqlaeeglevlaltre..................eldltdaeavaellkeakpdvvvnaAAyta 63 
                                    ++lvtG+ G +Gs+L+++l ++g+ev+ l++                   + d++ +e v+++l+    d+v + AA  +
  gi|119720075|ref|YP_920570.1|   6 RVLVTGGAGFIGSHLVERLVARGYEVVVLDNLssgslenlrsvlgdvefvRGDVRSREDVEKALRG--VDAVFHFAANPE 83 
                                    79***************************77779*******************************9..789*******99 PP

                                    HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT-E.EEEEEEGGGS-S-TTS-B-TT.S----SSHHHHHHHHHHHHHHHH-S CS
                  RmlD_sub_bind  64 vDkaEseeeaayavnaeavealAeaaaavgal.LihvStDyVFdGekkrpYeed.detsPlnvYGrtKlaGEqavlaagk 141
                                    v     ++++ ++ n+ a+ ++ ea ++ g+  +++ S+  V+  ++k p  ed  + +P++vYG++Kla E  + ++ +
  gi|119720075|ref|YP_920570.1|  84 VRVG--DPREHFEHNVFATFNVLEAMRRLGVSdIVFASSSTVYGDAEKLPTPEDyGPLKPISVYGASKLACEALISSYTH 161
                                    9885..68899999****************96599********877777755442689******************9665 PP

                                    ....SEEEEEE-SEESS.SSS-HHHHHHHHH.HH-SEEEEESS..-EE--EEHHHHHHHHHHHHHHCHH.GGG-EEEE-- CS
                  RmlD_sub_bind 142 ....kalivRtswvyge.kgknfvktmlrla.kereelkvvaD..qlgsPTsardlAevllqllekaaeekelagvyHla 213
                                        k + +R + v g    +  vk ++r++ ++   l++  D  q  s  + +d  e++l + e+  e    ++ y ++
  gi|119720075|ref|YP_920570.1| 162 tfgfKGVALRYANVVGPrATRGVVKDFVRKLrENPRVLEILGDgtQRKSYVWIEDAVEATLLAWERTGE---GFEAYNVG 238
                                    22336799*******8757899***99999835556789999955666666778888888777777775...78999999 PP

                                    -BS-EEHHHHHHHHHHHHCH CS
                  RmlD_sub_bind 214 negetswlefArailkeaga 233
                                    +e++++  e+A+ +++++g 
  gi|119720075|ref|YP_920570.1| 239 SEDAITVREVADIVVSAMGL 258
                                    99999999999999988776 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   1.3e-05     0.013       1      27 [.       9      33 ..       9      41 .. 0.86
   2 !   27.0   0.0   2.2e-09   2.2e-06      60     216 ..      43     186 ..      33     218 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.3e-05
                                   EE-TTSHHHHHHHHHHHHHS-.TEEEE CS
                  NAD_binding_4  1 lTGaTGFLGkvLlekLLrttpevkiyl 27
                                   +TG+ GF+G++L+e+L+ +  e  +++
  gi|119720075|ref|YP_920570.1|  9 VTGGAGFIGSHLVERLVARGYE--VVV 33
                                   7****************98774..444 PP

  == domain 2  score: 27.0 bits;  conditional E-value: 2.2e-09
                                    TTEEEEE--TTSGGGG-.-HHHHHHHHHH--EEEE--SS-S..STTSSEEHHHHHHHHHHHHHHHTSSS--.-EEEEEEG CS
                  NAD_binding_4  60 erikvveGDlseprlGL.seedlqelaeevdviihsaAtvnf.depykellrvNveGtrevlelakklkklkvllhvSTa 137
                                    e+++ v GD++  r  + s ed+++  + vd+++h aA+ ++ +++ +e ++ Nv +t +vle  ++l     +++ S++
  gi|119720075|ref|YP_920570.1|  43 ENLRSVLGDVEFVRGDVrSREDVEKALRGVDAVFHFAANPEVrVGDPREHFEHNVFATFNVLEAMRRLGVS-DIVFASSS 121
                                    55666666666666555256899999************98872469999***************9999888.99*****9 PP

                                    GGTTS-TTT--SSS-H......HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE-.-SSST--- CS
                  NAD_binding_4 138 yvngeregeveekvyeegekeekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitg.esktGwin 216
                                    +v+g+ e+               l + e     +    Y  sK + E l+ ++ +  g++ v +R  +++g + + G+++
  gi|119720075|ref|YP_920570.1| 122 TVYGDAEK---------------LPTPEDYGPLKPISVYGASKLACEALISSYTHTFGFKGVALRYANVVGpRATRGVVK 186
                                    9*999994...............56778888888899********************************99555556655 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.5   3.5e-12   3.5e-09       3     173 ..       7     169 ..       5     191 .. 0.78

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 3.5e-12
                                    EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEEE CS
                      adh_short   3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldvLv 82 
                                    vlvtG+++ IG  ++++l+++G++vvv+d+ ++     +++l++   ++ ++++Dv++re+ve++++ +       d++ 
  gi|119720075|ref|YP_920570.1|   7 VLVTGGAGFIGSHLVERLVARGYEVVVLDNLSSGS---LENLRSVLGDVEFVRGDVRSREDVEKALRGV-------DAVF 76 
                                    8**************************99877666...4444444445*************99987765.......9999 PP

                                    E---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGG..G...TS.......B-TTBHHHH CS
                      adh_short  83 nNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSva..g...kv.......pvagvaaYs 150
                                    + A+        e+   + ++ +e N++++f++ +a    m +    +Iv+ sS +  g   k        p++  ++Y+
  gi|119720075|ref|YP_920570.1|  77 HFAAN------PEVRVGDPREHFEHNVFATFNVLEA----MRRLGVSDIVFASSSTvyGdaeKLptpedygPLKPISVYG 146
                                    99998......799999**************98766....5566899*****9964223211332222222345589*** PP

                                    HHHHHHHHHHHHHHHHHGGGTEE CS
                      adh_short 151 AsKaavagltrslakelaptgir 173
                                    AsK a ++l++s  + +  +g+ 
  gi|119720075|ref|YP_920570.1| 147 ASKLACEALISSYTHTFGFKGVA 169
                                    **********9999998888876 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.1   6.1e-11   6.1e-08       1      99 [.       7     117 ..       7     265 .. 0.80

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 6.1e-11
                                    EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHS.T.TEEEES-TT-HHHHHHHHTT-SEEEE---GG... CS
                           NmrA   1 IlviGaTGrqGksvvrallkaghkvralvRdtkselakslkea.G.velvkgdlddkeslvealkgvdvvfsvtgfy... 75 
                                    +lv+G++G +G+++v+ l+++g++v +l  +++s  +++l +  G ve+v gd+ ++e +++al+gvd+vf   +     
  gi|119720075|ref|YP_920570.1|   7 VLVTGGAGFIGSHLVERLVARGYEVVVL-DNLSSGSLENLRSVlGdVEFVRGDVRSREDVEKALRGVDAVFHFAANPevr 85 
                                    79***********************776.688888888888743449************************987733455 PP

                                    ........S-HHHHHHHHHHHHHHHS-SEEEE CS
                           NmrA  76 ........skeiedgkklvdAakeaGvkhfiy 99 
                                            + ++    ++ +A  + Gv  +++
  gi|119720075|ref|YP_920570.1|  86 vgdprehfEHNVFATFNVLEAMRRLGVSDIVF 117
                                    66665555555555556666666666666666 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.1   9.6e-08   9.5e-05       3      77 ..       7      74 ..       6      81 .. 0.90
   2 ?   -3.5   0.0       8.1   8.1e+03     132     143 ..     115     126 ..      97     130 .. 0.56

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 9.6e-08
                                   EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHH CS
                             KR  3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeika 77
                                   +l+tGG+G +G +l++ l+++g + +vl   s       +  +++l++   +ve+v+ Dv ++++ve++l+ ++a
  gi|119720075|ref|YP_920570.1|  7 VLVTGGAGFIGSHLVERLVARGYEVVVLDNLS-------SGSLENLRSVLGDVEFVRGDVRSREDVEKALRGVDA 74
                                   69**********************99997766.......457999****9*******************998875 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 8.1
                                    EEEEEHHHHH-- CS
                             KR 132 vlfSSiagllgs 143
                                    ++f+S ++++g 
  gi|119720075|ref|YP_920570.1| 115 IVFASSSTVYGD 126
                                    345555555554 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.9e-06    0.0029       6      66 ..      16      75 ..      11      80 .. 0.87
   2 ?    3.8   0.0     0.036        36     139     172 ..     143     179 ..     135     225 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.9e-06
                                   HHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSE.EEE--TTSHHHHHHHHHHHHHH CS
                   adh_short_C2  6 IGraiAkalaeeGaevvltdlneeakkrveelaeelgae.vlecDVtdeeqvealveevvek 66
                                   IG +++++l ++G+evv+ d   ++  ++e+l + lg   +++ DV+++e+ve++ + v + 
  gi|119720075|ref|YP_920570.1| 16 IGSHLVERLVARGYEVVVLDNLSSG--SLENLRSVLGDVeFVRGDVRSREDVEKALRGVDAV 75
                                   9*******************99998..78888888885549*************99887765 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.036
                                    THHHHHHHHHHHHHHHHHHHHGGGTEE...EEEEEE- CS
                   adh_short_C2 139 naygaaKaalealtrylAvelgpkgiR...vNavspg 172
                                    ++yga+K a+eal+ +  + +g kg+     N+v p 
  gi|119720075|ref|YP_920570.1| 143 SVYGASKLACEALISSYTHTFGFKGVAlryANVVGPR 179
                                    69******************99999842234666654 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1     2e-05      0.02       5      58 ..      12      68 ..       8     116 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2e-05
                                   S-SHHHHHHHHHHHH.TTEEEEEEESSH.HHHHHHHHTT..SEEEES-TTSHHHHHHT CS
                         TrkA_N  5 GlGrvGrslaeeLse.ggkdvvvidkde.erveelreeg..levvvgdatdeevLeea 58
                                   G+G +G++l+e+L + g+ +vvv d+     +e+lr     +e+v gd+ ++e +e+a
  gi|119720075|ref|YP_920570.1| 12 GAGFIGSHLVERLVArGY-EVVVLDNLSsGSLENLRSVLgdVEFVRGDVRSREDVEKA 68
                                   89*************777.5*****987355999998888999*********999998 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00012      0.12      14      90 ..       6      86 ..       2     100 .. 0.83
   2 ?   -0.5   0.0       1.2   1.2e+03      56      84 ..      93     121 ..      85     123 .. 0.74
   3 ?   -3.1   0.0       7.5   7.5e+03      74      84 ..     247     257 ..     234     261 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00012
                                   EEEEE.S-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-...EEEEGCGHHHHHHT-SEEEE-SSSSS-SB CS
                   Shikimate_DH 14 kvlli.GaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeei...ealkleelkellaeadvvisataseepil 90
                                   +vl+  GaG +++ +++ L+a+g++ vv  N +    ++l++ l+++e+    +++ e+++++l+ +d v+   a +e+ +
  gi|119720075|ref|YP_920570.1|  6 RVLVTgGAGFIGSHLVERLVARGYEVVVLDNLSSGSLENLRSVLGDVEFvrgDVRSREDVEKALRGVDAVFHFAANPEVRV 86
                                   5666637******************99999*999999999999988877333578889*************9888887766 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.2
                                    HT.ET-EEEEGCGHHHHHHT-SEEEE-SS CS
                   Shikimate_DH  56 lkgeeiealkleelkellaeadvvisata 84 
                                    ++++ + + ++ e +++l  +d+v+++ +
  gi|119720075|ref|YP_920570.1|  93 FEHNVFATFNVLEAMRRLGVSDIVFASSS 121
                                    55555566677778889999*****9976 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 7.5
                                    HT-SEEEE-SS CS
                   Shikimate_DH  74 aeadvvisata 84 
                                    + ad+v+sa +
  gi|119720075|ref|YP_920570.1| 247 EVADIVVSAMG 257
                                    56899999876 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0     8e-05     0.079       6      66 ..      12      76 ..       6      84 .. 0.90
   2 ?   -2.2   0.0       6.4   6.4e+03      54      71 ..     241     258 ..     218     262 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8e-05
                                   TTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC........-EEECECHHHHHHH-SEEE CS
                  F420_oxidored  6 GaGnmgealasgllaagaqpheivvansrnpekaeelaeelg........vkvtavdneeaaeeadvvv 66
                                   GaG +g+ l+++l+a+g   +e+vv  + +  ++e l++ lg        v+  + d e+a++  d v+
  gi|119720075|ref|YP_920570.1| 12 GAGFIGSHLVERLVARG---YEVVVLDNLSSGSLENLRSVLGdvefvrgdVRSRE-DVEKALRGVDAVF 76
                                   9****************...******999*******9999999999998888888.8888999888887 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 6.4
                                    CHHHHHHH-SEEEE-S-H CS
                  F420_oxidored  54 dneeaaeeadvvvlavkp 71 
                                    d+ ++ e ad+vv a+  
  gi|119720075|ref|YP_920570.1| 241 DAITVREVADIVVSAMGL 258
                                    355555678888877655 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00016      0.16       3      77 ..       9      79 ..       7      85 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00016
                                   EE--.SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-S CS
                Sacchrp_dh_NADP  3 iiGa.GsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnls 77
                                   + G+ G++G+ ++e l++++ +  e++v d   ++  + + +    ++e++  d+  +e+ ++++l++ d+v + +
  gi|119720075|ref|YP_920570.1|  9 VTGGaGFIGSHLVERLVARG-Y--EVVVLDNLSSGSLENLRS-VLGDVEFVRGDVRSRED-VEKALRGVDAVFHFA 79
                                   55555*************98.5..79**99988886666655.5778*************.9*******9998766 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0    0.0002       0.2       6      61 ..      12      77 ..      10     130 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0002
                                   --SHHHHHHHHHHHHTT-EEEEE-.SSHHHHHHHHHTT.........EEE-SSHHHHHHHCSEEEE CS
                  NAD_binding_2  6 GlGvMGsnmalnllkagykvavyn.rtkekveelvaeg.........akaaesieelvasldvvit 61
                                   G G +Gs+++++l+++gy+v+v + +++ ++e+l +           ++  e++e++++++d+v+ 
  gi|119720075|ref|YP_920570.1| 12 GAGFIGSHLVERLVARGYEVVVLDnLSSGSLENLRSVLgdvefvrgdVRSREDVEKALRGVDAVFH 77
                                   899********************9455555555544324557777777777777777777777775 PP

>> Ldh_1_N  lactate/malate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00016      0.16       1      82 [.       5      84 ..       5     118 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00016
                                   EEEEEETTTSHHHHHHHHHHHHTTSSSEEEEE-SSHHHHHHHHHHHHHCHCCSTS-EEEEESSGGGGTTESEEEE--S-SS- CS
                        Ldh_1_N  1 vkvavvGaaGgiGqslalllankkladelaLlDiakekleGvaldlshistflsvkvkvsekeeealkdadvvvitagvprk 82
                                   v+v v+G aG+iG++l   l+++++   ++L ++ +  le     l ++++    +v+++e+ e+al+++d v   a+ p  
  gi|119720075|ref|YP_920570.1|  5 VRVLVTGGAGFIGSHLVERLVARGYEV-VVLDNLSSGSLENLRSVLGDVEFVR-GDVRSREDVEKALRGVDAVFHFAANPEV 84
                                   589********************9977.6666666667777777777777666.7888888999999999999988888764 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00034      0.34       6      44 ..      12      51 ..       6      84 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00034
                                   --SCCHHHHHHHHHHTT-EEEEE-S.-HHHHHHHHHHHHH CS
                        3HCDH_N  6 GaGtmGagiaavfasagleVvlvdi.seealekalekiek 44
                                   GaG +G+ + + ++++g+eVv++d  s+ +le+ ++ + +
  gi|119720075|ref|YP_920570.1| 12 GAGFIGSHLVERLVARGYEVVVLDNlSSGSLENLRSVLGD 51
                                   89*********************98566666666665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 2090.94
//
Query:       gi|119720076|ref|YP_920571.1|  [L=140]
Description: hypothetical protein Tpen_1170 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.2e-06   26.7   0.0    6.4e-06   26.1   0.0    1.3  1  Thioredoxin    Thioredoxin
    0.00039   20.8   0.1    0.00069   20.0   0.1    1.4  1  Thioredoxin_2  Thioredoxin-like domain
  ------ inclusion threshold ------
      0.025   14.9   0.1       0.53   10.6   0.1    2.0  2  Thioredoxin_8  Thioredoxin-like
      0.049   13.3   0.0       0.14   11.9   0.0    1.7  1  SET_assoc      Histone lysine methyltransferase SET associate
      0.081   13.1   0.0       0.14   12.4   0.0    1.3  1  Thioredoxin_4  Thioredoxin
       0.21   11.4   0.0       0.24   11.2   0.0    1.1  1  TraF           F plasmid transfer operon protein


Domain annotation for each model (and alignments):
>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   2.2e-09   6.4e-06      17      95 ..      34     124 ..      27     132 .. 0.70

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 2.2e-09
                                    TSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTT.TSEEEEEE.......TTTSHHHHHHTT-SSSSEEEEE..ETTE..E CS
                    Thioredoxin  17 ekklvlveFyApwCghCkalaPeleklaeelkd.kvklakvd.......vdenedlakkyevegiPtlklf..kngk..e 84 
                                    ++   +v F  + Cg C++++ ++ kl +el++ +++++ +d        ++ + l + ++v+  Ptl+++  +ngk  +
  gi|119720076|ref|YP_920571.1|  34 ADGFYVVYFSNTMCGACRKFNETWFKLTKELSGaTFVVVLCDwfarscrSETAKRLFEIFDVHVSPTLVFLvrENGKitR 113
                                    57789***************************99666666662221111344556667799******9987224555444 PP

                                    EEEEESS-HHH CS
                    Thioredoxin  85 vkkyegareke 95 
                                    + k eg+ ++e
  gi|119720076|ref|YP_920571.1| 114 MYKHEGTITAE 124
                                    44555655555 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.1   2.3e-07   0.00069       8     108 ..      38     129 ..      34     130 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.3e-07
                  Thioredoxin_2   8 vlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtPtivfl 87 
                                     +v+f+ + C+ C+k++++ ++l   t        k+ + + +v + c+    ++ +  e+ + l + ++v+  Pt+vfl
  gi|119720076|ref|YP_920571.1|  38 YVVYFSNTMCGACRKFNETWFKL---T--------KELSGATFVVVLCDWFA-RSCRS-ETAKRLFEIFDVHVSPTLVFL 104
                                    5899*******************...4........44466799999999998.68888.999999999********9987 PP

                  Thioredoxin_2  88 dgk....eivarlpGyvpaeeleal 108
                                      +    ++ ++ +G ++ae ++a+
  gi|119720076|ref|YP_920571.1| 105 VREngkiTRMYKHEGTITAEGFLAV 129
                                    55556598889999******99986 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00018      0.53       4      39 ..      38      72 ..      36      75 .. 0.83
   2 ?    2.1   0.0     0.081   2.4e+02      61      95 .]      76     111 ..      73     111 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00018
                                   EEEEE--SSSHHHHHHHHHHHHHHHHHHHTTSEEEE CS
                  Thioredoxin_8  4 vlLyfgaswcppckaftpklkelyeklkkkkkveiv 39
                                   +++yf+++ c  c++f+++  +l ++l+ +  +++v
  gi|119720076|ref|YP_920571.1| 38 YVVYFSNTMCGACRKFNETWFKLTKELS-GATFVVV 72
                                   689****************999999987.5555554 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.081
                                    SEE.EE-TT-HHHHTT-S--TT-SEEEEE-.TT-BE CS
                  Thioredoxin_8  61 wlsvpfddkkrnklkkkynvkaiPtlvvld.kngev 95 
                                    w +    ++  + l + ++v   Ptlv l   ng++
  gi|119720076|ref|YP_920571.1|  76 WFARSCRSETAKRLFEIFDVHVSPTLVFLVrENGKI 111
                                    5555566677788999999999***99876588876 PP

>> SET_assoc  Histone lysine methyltransferase SET associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   4.6e-05      0.14      27      54 ..      28      55 ..      26      61 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.6e-05
                      SET_assoc 27 eriledktGyYivFndskeAerCfraed 54
                                   e+i  d +G+Y+v  ++  +  C + ++
  gi|119720076|ref|YP_920571.1| 28 EKIPLDADGFYVVYFSNTMCGACRKFNE 55
                                   67889******************88765 PP

>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   4.5e-05      0.14      17      41 ..      39      63 ..      33      72 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.5e-05
                                   EEEEE-TT-HHHHHHHHHHHHHHHH CS
                  Thioredoxin_4 17 vieyedlrCphCakfeeevekllee 41
                                   v+ +++  C  C+kf+e+ +kl +e
  gi|119720076|ref|YP_920571.1| 39 VVYFSNTMCGACRKFNETWFKLTKE 63
                                   8899*****************9987 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0     8e-05      0.24     131     207 ..      37     112 ..      28     135 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 8e-05
                           TraF 131 ygLlfFyrgkcpyceaqapilqafadkyglevraVsvdgrplpelpnarvdkgqaarlgvkrtPalvlvdpksqkvv 207
                                    +  ++F +  c++c+++ ++  +++++   ++ +V + + + ++  + +  k   + + v+  P+lv+  ++++k++
  gi|119720076|ref|YP_920571.1|  37 FYVVYFSNTMCGACRKFNETWFKLTKELSGATFVVVLCDWFARSCRS-ETAKRLFEIFDVHVSPTLVFLVRENGKIT 112
                                    56789***********************8888888888888877665.8999999***********99999888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1028.60
//
Query:       gi|119720077|ref|YP_920572.1|  [L=257]
Description: hypothetical protein Tpen_1171 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1664.52
//
Query:       gi|119720078|ref|YP_920573.1|  [L=243]
Description: ABC transporter related [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-27   96.6   0.0    2.4e-27   96.1   0.0    1.2  1  ABC_tran      ABC transporter
    4.3e-11   43.2   1.0    0.00022   21.2   0.0    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    0.00081   19.9   0.2      0.002   18.7   0.1    1.5  2  AAA_23        AAA domain
     0.0012   18.3   0.1     0.0025   17.2   0.0    1.5  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
  ------ inclusion threshold ------
      0.014   15.1   0.1       0.11   12.1   0.1    2.0  2  SRP54         SRP54-type protein, GTPase domain
      0.014   15.1   0.1      0.023   14.4   0.1    1.6  1  AAA_30        AAA domain
      0.019   14.7   0.1        2.3    7.9   0.0    2.1  2  IstB_IS21     IstB-like ATP binding protein
      0.021   14.6   0.0      0.043   13.6   0.0    1.5  1  AAA_29        P-loop containing region of AAA domain
      0.027   13.9   0.2        4.1    6.8   0.1    2.1  2  SMC_N         RecF/RecN/SMC N terminal domain
      0.064   12.8   0.1       0.12   11.9   0.1    1.4  1  AAA_27        AAA domain
       0.12   12.0   0.0       0.41   10.3   0.0    1.6  2  AAA_15        AAA ATPase domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.1   0.0   1.5e-30   2.4e-27       1     136 [.      19     160 ..      19     161 .. 0.95

  Alignments for each domain:
  == domain 1  score: 96.1 bits;  conditional E-value: 1.5e-30
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren. 79 
                                    l+ vs+ ++ege+ +++G+nGaGK+t +++lagll pt+G++l+ gk   +   ++l++ + +lp+++   ++lt +e  
  gi|119720078|ref|YP_920573.1|  19 LRGVSFAVEEGEVFGLIGPNGAGKTTTFRILAGLLPPTSGKVLVLGKAPGS---PELKRVVTYLPEDAGTYRNLTGYEFl 95 
                                    678******************************************999988...99*******************9999* PP

                                    ........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    ........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                             +++e+e+al+    +    ++++++++ +S+G+k+r+++aral+ kp+l +lDEpt
  gi|119720078|ref|YP_920573.1|  96 rmvselyfGRSREAEEALELGVKIASLGEKIHEKMKGYSKGMKRRIQVARALMVKPRLAILDEPT 160
                                    ******99999999999998777777999999********************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.3   1.8e-07   0.00029       2      23 ..      32      53 ..      31      74 .. 0.87
   2 !   21.2   0.0   1.3e-07   0.00022     237     300 ..     133     194 ..      87     197 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.8e-07
                         AAA_21  2 nvliGpNgsGKSnLLdaldlla 23
                                    +liGpNg+GK++ +++l +l 
  gi|119720078|ref|YP_920573.1| 32 FGLIGPNGAGKTTTFRILAGLL 53
                                   68****************9994 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 1.3e-07
                         AAA_21 237 lSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSpl 300
                                     S G+kr + ++ al   +   +l ++DEp  gL+    +++ +l+ke +r +g+ ++l++H+ l
  gi|119720078|ref|YP_920573.1| 133 YSKGMKRRIQVARALMVKP---RLAILDEPTVGLDVVHAKEIRTLIKEFAReHGSTILLSSHNML 194
                                    4999999988888888766...**************777777777766666677********976 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   1.2e-06     0.002       6      39 ..      15      49 ..      11      55 .. 0.79
   2 ?   -2.4   0.0       3.5   5.7e+03     101     126 ..     106     131 ..      82     153 .. 0.63

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.2e-06
                         AAA_23  6 nfrsfrdqeidF.skgltlItGpNGaGKTTildAi 39
                                   nf+ +r++++   +  ++ ++GpNGaGKTT ++ +
  gi|119720078|ref|YP_920573.1| 15 NFQALRGVSFAVeEGEVFGLIGPNGAGKTTTFRIL 49
                                   6666677777776668**************99876 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.5
                         AAA_23 101 gkttkkaklelleideleqfisellg 126
                                    +++  +a + +++i+ l ++i e+++
  gi|119720078|ref|YP_920573.1| 106 SREAEEALELGVKIASLGEKIHEKMK 131
                                    44444445555555555555555444 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   1.5e-06    0.0025       2      51 ..       9      58 ..       8      64 .. 0.93
   2 ?   -3.1   0.0       2.7   4.3e+03      99     112 ..     200     213 ..     182     230 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.5e-06
                   Mg_chelatase  2 lkdvkGqeeakraleiaaaGgHnlllvGppGsGKtmlakrlpsllpplse 51
                                   l++v G+ +a r +  a+  g  + l+Gp G+GKt   + l++llpp s 
  gi|119720078|ref|YP_920573.1|  9 LTKVFGNFQALRGVSFAVEEGEVFGLIGPNGAGKTTTFRILAGLLPPTSG 58
                                   7899******************************************9875 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.7
                   Mg_chelatase  99 pGeislahnGvLfL 112
                                     Ge++   +Gv++L
  gi|119720078|ref|YP_920573.1| 200 CGEVAIIDRGVVLL 213
                                    57777777777776 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   6.7e-05      0.11       4      34 ..      32      62 ..      30      65 .. 0.81
   2 ?    0.4   0.0      0.27   4.3e+02     157     181 ..     104     128 ..      86     141 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.7e-05
                                   EEEEESTTSSHHHHHHHHHHHHHHTTS-EEE CS
                          SRP54  4 illvGlqGaGKTttlaKLaallkkegkkvll 34
                                   + l+G++GaGKTtt   La ll     kvl+
  gi|119720078|ref|YP_920573.1| 32 FGLIGPNGAGKTTTFRILAGLLPPTSGKVLV 62
                                   5689************999988777666655 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.27
                                    THHHHHHHHHTS-EEEEE-SSSTTG CS
                          SRP54 157 GaalsiaaelklPikfigvGekied 181
                                    G    ++++l+l +k+ ++Geki++
  gi|119720078|ref|YP_920573.1| 104 GRSREAEEALELGVKIASLGEKIHE 128
                                    555567889999**********965 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   1.4e-05     0.023      14      52 ..      25      63 ..      16     191 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.4e-05
                         AAA_30 14 ltsgdrvavltGpAGtGKttalkalreaweaaggrvigl 52
                                   + ++  v  l Gp G+GKtt+ + l+ ++    g+v++l
  gi|119720078|ref|YP_920573.1| 25 AVEEGEVFGLIGPNGAGKTTTFRILAGLLPPTSGKVLVL 63
                                   445556999*****************9999886666654 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0014       2.3      35      61 ..      16      43 ..       9      50 .. 0.89
   2 ?    4.7   0.0     0.013        22      98     169 ..     140     207 ..     116     211 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0014
                      IstB_IS21 35 vkeLatlsf.iekkenivllGpsGvGKs 61
                                   +++L++ sf +e+ e + l+Gp G+GK+
  gi|119720078|ref|YP_920573.1| 16 FQALRGVSFaVEEGEVFGLIGPNGAGKT 43
                                   789999999778899999*********9 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.013
                      IstB_IS21  98 klaralkrllkvdllilDdlgllpldqaeaellfeviek.ryerrsiiitsnlpfaewdevlgdatlatAilD 169
                                    +++ a + ++k++l ilD+   + ld  +a+++  +i++ + e+ s+i+ s  ++ e ++v g+     Ai+D
  gi|119720078|ref|YP_920573.1| 140 RIQVARALMVKPRLAILDEPT-VGLDVVHAKEIRTLIKEfAREHGSTILLSSHNMLEVEDVCGE----VAIID 207
                                    444455567899******953.455666666666666552679999999999999999888884....45555 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.6e-05     0.043      10      40 ..      17      47 ..      12      60 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.6e-05
                         AAA_29 10 gtfdghtieidlkgatlltGpsGsGKSTllD 40
                                   + ++g ++ +++ +++ l+Gp+G+GK+T + 
  gi|119720078|ref|YP_920573.1| 17 QALRGVSFAVEEGEVFGLIGPNGAGKTTTFR 47
                                   45556667777555999***********874 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1    0.0025       4.1      25      40 ..      30      45 ..      10      59 .. 0.72
   2 ?    5.3   0.0    0.0074        12     161     211 ..     153     203 ..     140     211 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0025
                                   SEEEEEESTTSSHHHH CS
                                   xxxxxxxxxxxxxxxx RF
                          SMC_N 25 sftaivGpNGSGKsnl 40
                                   ++  ++GpNG+GK+  
  gi|119720078|ref|YP_920573.1| 30 EVFGLIGPNGAGKTTT 45
                                   355799*******975 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0074
                                    EEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 161 lyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadklvgv 211
                                    l +lDe    LD  + k++ +l+ke   +    +   +++mle  d +  v
  gi|119720078|ref|YP_920573.1| 153 LAILDEPTVGLDVVHAKEIRTLIKEFAREHGSTILLSSHNMLEVEDVCGEV 203
                                    789*********************988886666666667787777766655 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   7.5e-05      0.12      10      50 ..      12      53 ..       5      54 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.5e-05
                         AAA_27 10 ryGkftd.rsldfsaeeadlhliyGpNEAGKstalrAisdll 50
                                    +G+f+  r ++f  ee ++  ++GpN AGK+t++r +  ll
  gi|119720078|ref|YP_920573.1| 12 VFGNFQAlRGVSFAVEEGEVFGLIGPNGAGKTTTFRILAGLL 53
                                   589998636799999888888899**********99887765 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00025      0.41      10      44 ..      15      50 ..      13      60 .. 0.84
   2 ?   -1.9   0.0       1.3   2.1e+03     325     365 ..     152     192 ..     124     193 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00025
                         AAA_15 10 NFRslkdveidlsee.ltvliGkNnsGKSsileald 44
                                   NF +l+ v+  ++e  +  liG+N++GK++  ++l 
  gi|119720078|ref|YP_920573.1| 15 NFQALRGVSFAVEEGeVFGLIGPNGAGKTTTFRILA 50
                                   8888888887777777889***********999885 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.3
                         AAA_15 325 villiEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                     + +++EP + L   + k++  l+ke a+++   +++++H+
  gi|119720078|ref|YP_920573.1| 152 RLAILDEPTVGLDVVHAKEIRTLIKEFAREHGSTILLSSHN 192
                                    56678888888888888899999999999998889999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 1610.90
//
Query:       gi|119720079|ref|YP_920574.1|  [L=437]
Description: ABC-2 type transporter [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-25   89.1  10.4    3.9e-25   88.7  10.4    1.1  1  ABC2_membrane_3  ABC-2 family transporter protein
    4.3e-16   59.0  18.3    6.7e-16   58.4  18.3    1.3  1  ABC2_membrane_2  ABC-2 family transporter protein
    6.6e-08   32.2  23.1    5.8e-07   29.1  17.9    3.0  2  ABC2_membrane    ABC-2 type transporter
    1.9e-07   31.2   3.3    1.9e-07   31.2   3.3    3.0  3  ABC2_membrane_4  ABC-2 family transporter protein
    1.8e-05   24.4   4.3    1.8e-05   24.4   4.3    2.7  3  ABC2_membrane_5  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.7  10.4   1.1e-28   3.9e-25       3     333 ..      24     409 ..      20     417 .. 0.75

  Alignments for each domain:
  == domain 1  score: 88.7 bits;  conditional E-value: 1.1e-28
                ABC2_membrane_3   3 fliitlllPiilvlllglifsnsve.ddentpi.avvdednsslsqqlvealea.spsve.lvyevdseeeakkalkngd 78 
                                    f+i+ l+lP+i +++  + ++++v  ++e  ++ av+d+d++ +s+++ve+l +  + ve    ++ + e+a +a   ++
  gi|119720079|ref|YP_920574.1|  24 FVISALILPVIGLAV-SIPMKAAVQqAVEGAKVvAVIDLDRTAYSREFVEWLRSkLSVVElPADYAGNVEKAAEAASAKG 102
                                    677788888888886.455577777655555556********************44556699999999************ PP

                ABC2_membrane_3  79 idgilvipkgfskdllkgesatvtvli..nssnlnss...kailnalns.llqqlnasalv...........lqseatst 141
                                    ++ ilv++kgf ++l+  ++a+v v++  ++ ++++    ++++  +++  l++++ + ++            ++e+ + 
  gi|119720079|ref|YP_920574.1| 103 ASVILVLDKGFGESLSARRRAEVRVISvvDEIYFLAGvesSSVQRLVDDfALSKIL-EGTGiapgvvrrpvnFSEETYVK 181
                                    ***************97777777666666777776667777777778874444433.33334555555555444445555 PP

                ABC2_membrane_3 142 saninvestqleeelsnvasflvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllql 221
                                    ++ + +   +      ++   lv++i++ ++++++++ a+s + E+e +++e +l+ +v+ ++++lsk+ g+f+v+l+ +
  gi|119720079|ref|YP_920574.1| 182 AKGVALPYPPAALAGISMSVMLVPMIVLSMAMVVMQMSATSAAVENEEKTLETLLTLPVTSTEILLSKLAGMFIVSLVGS 261
                                    555555555545555555556888******************************************************** PP

                ABC2_membrane_3 222 ll.illlafgl.........................gipfgnlglllllfllfglayialgyllsslfknsetaqilifi 275
                                    +l +++l++ l                         ++  g++ ll   ++l +l ++a+g ++++l+k+ + a++l+++
  gi|119720079|ref|YP_920574.1| 262 ALeVIGLVLYLqtfawamtgpsaaegllgsagglsqFVGTGDVALLAASLVLSLLFSAAIGVMVGALSKDVRIASTLMSP 341
                                    9844446444455899****************988888888999999********************************* PP

                ABC2_membrane_3 276 vil.llsgffgglfp.ledlpsalkwifsiiPffapglgllrli.tgdplwe.......illsliila 333
                                    + + +l+  +++ f     l  +lk++++++P ++p ++  ++i   +p+         + lsl++++
  gi|119720079|ref|YP_920574.1| 342 IAMlVLIPGYIVAFApSRFLGVYLKTLLYVVPVTQPVVMSRDIIgARVPPEAplyllasLTLSLAVMY 409
                                    *9922333344444323335599********************9533344333332222333333333 PP

>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.4  18.3   1.9e-19   6.7e-16       2     238 ..       5     373 ..       4     420 .. 0.76

  Alignments for each domain:
  == domain 1  score: 58.4 bits;  conditional E-value: 1.9e-19
                ABC2_membrane_2   2 aiakkEfrdlvrsrrfllltvllpli.............................dvalaylkdlgsslqseakaikeat 52 
                                    ++++kE++d++r++r+++ +v+ +li                             d        + +  ++e+++   + 
  gi|119720079|ref|YP_920574.1|   5 VLVAKEVKDTLRDPRIIIPFVISALIlpviglavsipmkaavqqavegakvvaviD-------LDRTAYSREFVEWLRSK 77 
                                    6899**********************999999999999988888888844444440.......44444444444444444 PP

                ABC2_membrane_2  53 laleyveaasasdeaedtdqdlkv........................................................ 76 
                                    l++  + a+ a  + ++      +                                                        
  gi|119720079|ref|YP_920574.1|  78 LSVVELPADYAGNVEKAAE----Aasakgasvilvldkgfgeslsarrraevrvisvvdeiyflagvesssvqrlvddfa 153
                                    4443333333322222222....1333355566666677777777777777899************************** PP

                ABC2_membrane_2  77 .................................................vstimavlipviaalfgadaiagEkergTlk 107
                                                                                     ++ ++ + ++++ + ++a++ a E e++Tl+
  gi|119720079|ref|YP_920574.1| 154 lskilegtgiapgvvrrpvnfseetyvkakgvalpyppaalagismsvmLVPMIVLSMAMVVMQMSATSAAVENEEKTLE 233
                                    ******************************************999887755566677888899***************** PP

                ABC2_membrane_2 108 llLskPvsRdeillgKfigglaiglaiavallatvll.................alaiilalgivlaledllllvvasvl 170
                                     lL++Pv+  eill+K+ g+++++l++  + +++++l                  l+   +l+  + ++d+ ll+++ vl
  gi|119720079|ref|YP_920574.1| 234 TLLTLPVTSTEILLSKLAGMFIVSLVGSALEVIGLVLylqtfawamtgpsaaegLLGSAGGLSQFVGTGDVALLAASLVL 313
                                    **************************999999998889**************9555555566666667777777777777 PP

                ABC2_membrane_2 171 llllvvflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavpqeindflsllsp 238
                                    +ll  + +a+g+++ +++++ r a +l  + +++l+++ +++++   + ++g +       +l+++ p
  gi|119720079|ref|YP_920574.1| 314 SLL--FSAAIGVMVGALSKDVRIASTL-MSPIAMLVLIPGYIVAFAPSRFLGVYL-----KTLLYVVP 373
                                    777..67************66666665.578888888888888776776666666.....44444444 PP

>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.4   0.0    0.0061        22       3      41 ..       3      39 ..       1      59 [. 0.81
   2 !   29.1  17.9   1.6e-10   5.8e-07      51     208 ..     203     384 ..     184     386 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0061
                  ABC2_membrane  3 ikallkreflqrwrdpslgllwrliqplllalvfgtvfg 41
                                   i++l+ +e++  +rdp ++   +++   l++ v+g++ +
  gi|119720079|ref|YP_920574.1|  3 IRVLVAKEVKDTLRDPRII--IPFVISALILPVIGLAVS 39
                                   799*************555..699999999999999887 PP

  == domain 2  score: 29.1 bits;  conditional E-value: 1.6e-10
                  ABC2_membrane  51 nrpgllffsvlflafsaltsvapvferergvlerelvsplyslsayvlakvlvelpvsllqalifll.ivyflvgldls. 128
                                      p+++  +++ ++   ++++++ +e e+++le +l+ p+ +  +++l+k++++++vsl+ +++ ++ +v++l  + +  
  gi|119720079|ref|YP_920574.1| 203 LVPMIVLSMAMVVM--QMSATSAAVENEEKTLETLLTLPV-TSTEILLSKLAGMFIVSLVGSALEVIgLVLYLQTFAWAm 279
                                    34667777777777..7777779*****************.**********************99999999987777766 PP

                  ABC2_membrane 129 .................rf......flflllllltalaasslgllisalapsfedasqlaslvllpllllsGf..fipid 183
                                                     +f      +l+ + l+l++l++ ++g++++al+++++ as+l+s + ++ l+ + +  f p  
  gi|119720079|ref|YP_920574.1| 280 tgpsaaegllgsagglsQFvgtgdvALLAASLVLSLLFSAAIGVMVGALSKDVRIASTLMSPIAMLVLIPGYIvaFAPSR 359
                                    6888888888887777733667788999999*****************************99999999977761144555 PP

                  ABC2_membrane 184 smpkwlqwiaylnPltyavealrsn 208
                                     + ++l+ + y+ P+t  v + r +
  gi|119720079|ref|YP_920574.1| 360 FLGVYLKTLLYVVPVTQPVVMSRDI 384
                                    5567************999888876 PP

>> ABC2_membrane_4  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1      0.44   1.6e+03      13      33 ..      19      39 ..      15      57 .. 0.70
   2 !   31.2   3.3   5.2e-11   1.9e-07      54     121 ..     205     272 ..     189     291 .. 0.80
   3 ?   -0.2   6.1      0.24   8.6e+02     103     170 ..     308     375 ..     303     381 .. 0.59

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.44
                ABC2_membrane_4 13 kivwllvlaallvpllallyf 33
                                   +i++ +v++al++p+++l+++
  gi|119720079|ref|YP_920574.1| 19 RIIIPFVISALILPVIGLAVS 39
                                   567777788888888877764 PP

  == domain 2  score: 31.2 bits;  conditional E-value: 5.2e-11
                ABC2_membrane_4  54 ftlllllplilgiiasylifrEeqndtlknLltiPvsrtklllaKlivllllsvllmlvtflitvlfa 121
                                     +++l + +++  +++++   E++++tl  Llt+Pv++t++ll+Kl+ ++++s++ + + ++  vl  
  gi|119720079|ref|YP_920574.1| 205 PMIVLSMAMVVMQMSATSAAVENEEKTLETLLTLPVTSTEILLSKLAGMFIVSLVGSALEVIGLVLYL 272
                                    335566667777799***************************************99988887776653 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.24
                ABC2_membrane_4 103 lllsvllmlvtflitvlfallsgfvgfsvklvlellkkclelgllvffavlpiialvllkksyvlpli 170
                                    +   vl +l++++i v+++ ls  v++ ++l+  + + +l+ g +v+fa +  + + l +  yv+p++
  gi|119720079|ref|YP_920574.1| 308 AASLVLSLLFSAAIGVMVGALSKDVRIASTLMSPIAMLVLIPGYIVAFAPSRFLGVYLKTLLYVVPVT 375
                                    33445556666677777788888777766666666555566666666555544444444446777775 PP

>> ABC2_membrane_5  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1      0.64   2.3e+03     117     136 ..      22      41 ..      12      49 .. 0.62
   2 !   24.4   4.3     5e-09   1.8e-05      24     102 ..     195     269 ..     185     291 .. 0.74
   3 ?   -0.8   5.5      0.25   9.1e+02      90     147 ..     311     368 ..     304     420 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.64
                ABC2_membrane_5 117 llsiliglvialiflaivlP 136
                                    + +++ +l++ +i la+++P
  gi|119720079|ref|YP_920574.1|  22 IPFVISALILPVIGLAVSIP 41 
                                    44445555555555555555 PP

  == domain 2  score: 24.4 bits;  conditional E-value: 5e-09
                ABC2_membrane_5  24 laiiiliflndsvllifsilslvisiililttlsyDekskwnkylltLPvtrkeiVksKYlfvlililiailitlllli 102
                                    ++i+++++l   v +i++ +++v+ +++  t+ + +  +k+   lltLPvt  ei  sK  +++i++l+++ + ++ l+
  gi|119720079|ref|YP_920574.1| 195 AGISMSVML---VPMIVLSMAMVV-MQMSATSAAVENEEKTLETLLTLPVTSTEILLSKLAGMFIVSLVGSALEVIGLV 269
                                    444455443...223333333333.4446789999********************************999988766654 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.25
                ABC2_membrane_5  90 iliailitlllliiavlikgnvtisevllsiliglvialiflaivlPlyfkfgvekgr 147
                                     ++++l++++++++++ +++ v i ++l+s +++lv++  +++ + P  f+  + k+ 
  gi|119720079|ref|YP_920574.1| 311 LVLSLLFSAAIGVMVGALSKDVRIASTLMSPIAMLVLIPGYIVAFAPSRFLGVYLKTL 368
                                    4556667777777777788888888888888888888877777777777766666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (437 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       756  (0.0421663); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2827.12
//
Query:       gi|119720080|ref|YP_920575.1|  [L=502]
Description: extracellular solute-binding protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.3e-25   88.8  12.0    1.2e-24   87.9  12.0    1.3  1  SBP_bac_1    Bacterial extracellular solute-binding protein
  ------ inclusion threshold ------
       0.03   14.5   0.0        0.2   11.8   0.0    2.1  2  Speriolin_C  Speriolin C-terminus
      0.097   12.7   0.1       0.18   11.8   0.1    1.4  1  DUF1043      Protein of unknown function (DUF1043)
       0.21   11.7   0.9        2.2    8.4   0.0    2.8  3  SepRS_C      O-phosphoseryl-tRNA synthetase C-terminal domain


Domain annotation for each model (and alignments):
>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.9  12.0   2.6e-28   1.2e-24      25     311 ..     115     408 ..     104     412 .. 0.87

  Alignments for each domain:
  == domain 1  score: 87.9 bits;  conditional E-value: 2.6e-28
                                    EEEE..EEEECHHHHHHHHHHHHHTTSSSCSEEEECGGHHHHHHHTTSBECCHHHHHHTTECTTCCTEEEEHHHHTHHHH CS
                      SBP_bac_1  25 ikVe..iesvgsgslaqkltlaiaaGdgpaDviavdndwiarlakaglllpldpyvkaylapgvkdaadklsssvlpkil 102
                                    +kVe  + + ++ +++ k+ la+++G+gp  ++++++ w a la++g+ +pld+yvk+y+  ++ d    l+ssv++   
  gi|119720080|ref|YP_920575.1| 115 VKVEgdFSTASWTDYRKKVFLALEGGTGP-CIFQMEHVWSAVLAENGWIIPLDDYVKKYWNWTYYDIIPGLWSSVTY--- 190
                                    5666446677*******************.*********************************************86... PP

                                    CEEE.ES.EEEEE.EEEEEEETTTHH.....CTTGGG........SHBHHHHHHHHHHHHHHCTCT..HCCHCCEEHHHH CS
                      SBP_bac_1 103 dskv.ly.vPlya.argliYNkdlfe.....kagldp........pwtWdelveaakklkekgkkp..iggarggsasgt 164
                                      k+ ++ +P+++ ar++++Nk l++     ++++++        ++t ++ + +ak++++kg     +g+ ++ +a+ +
  gi|119720080|ref|YP_920575.1| 191 --KGkIWgIPQDTeARPIYFNKLLLKklgwtDEQINAlpekirrgEFTLQDMLMVAKEAVDKGVVApgYGIWHRPTAGPD 268
                                    ..4567******77************66666666666***************************8866666666666666 PP

                                    HHHHHHHHHHHHTGGGEECCCTHHCSHHHHS...HHHHHHHHHHHHHHHHHHHTTEEECSSHHHHHHHHHTTSCSEEEEE CS
                      SBP_bac_1 165 ayyfalalakslggkvfdkdgggldnpegvt...aatylvklyavanltkelkgkgaenkdgaaalalfeaGeaamaivg 241
                                    + +    +++ +ggk++d+  g+l+++  v+    + ++ +++    + k  ++k ++   ++++ + + aG++ +++ g
  gi|119720080|ref|YP_920575.1| 269 WPI----VYLAFGGKLYDETSGKLVADMKVWkkvFDWFYAASM---QKYKVITDKMTSLDWNRDVHPTIVAGKVLFWMGG 341
                                    666....5699***********999999999995555555555...445666666666666788999999******8888 PP

                                    HHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEE..EEEEEEEEBTTCSTHHHHHHHHHHHTSH CS
                      SBP_bac_1 242 lwaalaamkvapkvafaadkekpkeelgvaplPagkggkpgi..lgayglaipkgsknpeaAkkFldfllsp 311
                                    +w      k  + + f+ + +k+ e++g+a  Pag++g  +      + + i+k+ k+pe A+  +++++ p
  gi|119720080|ref|YP_920575.1| 342 TWH-----KGQWVGSFNLSESKFWEMFGFALYPAGEPGLKPVtlSQPQAYFISKTCKYPEIAFLIITLATDP 408
                                    887.....899999************************99999999999**************999998876 PP

>> Speriolin_C  Speriolin C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       0.3   1.3e+03      43      70 ..      38      65 ..      31      72 .. 0.79
   2 ?   11.8   0.0   4.4e-05       0.2      54      82 ..     304     332 ..     288     337 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.3
                    Speriolin_C 43 pltrkldeekrkaltkryeslmerLkkl 70
                                   p ++ + ++++++l+k +es+ ++L+++
  gi|119720080|ref|YP_920575.1| 38 PAEEVVPKSQYEQLQKELESVKAQLQQM 65
                                   6667788889999999999999999886 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 4.4e-05
                    Speriolin_C  54 kaltkryeslmerLkklgynkkvHpelve 82 
                                    +a +++y+ +++++++l++n++vHp++v+
  gi|119720080|ref|YP_920575.1| 304 AASMQKYKVITDKMTSLDWNRDVHPTIVA 332
                                    56689********************9875 PP

>> DUF1043  Protein of unknown function (DUF1043)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   3.9e-05      0.18       2      50 ..      16      65 ..      15      74 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.9e-05
                        DUF1043  2 liglvvGiiiGalilrltnsklkkqkkl.ekelekakaeleeqkqeledH 50
                                   +++l+vG+  G++i   t +k+  ++ + + + e+ ++ele  k++l++ 
  gi|119720080|ref|YP_920575.1| 16 VVVLLVGLLAGYFIGVSTAPKAPAEEVVpKSQYEQLQKELESVKAQLQQM 65
                                   68999********9999999987666653667888888888888888765 PP

>> SepRS_C  O-phosphoseryl-tRNA synthetase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.18   8.1e+02      10      20 ..     108     118 ..     107     132 .. 0.84
   2 ?    8.4   0.0    0.0005       2.2       4      17 ..     188     202 ..     188     205 .. 0.90
   3 ?   -3.0   0.3       1.9   8.4e+03      17      24 ..     293     300 ..     291     301 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.18
                                    EEEEES-TTTC CS
                        SepRS_C  10 IlGvPdtekwk 20 
                                    ++GvP t k++
  gi|119720080|ref|YP_920575.1| 108 VVGVPATVKVE 118
                                    89***998876 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0005
                                    EEETTEEEEEE.S-T CS
                        SepRS_C   4 yVYdGnIlGvP.dte 17 
                                    + Y+G+I G+P dte
  gi|119720080|ref|YP_920575.1| 188 VTYKGKIWGIPqDTE 202
                                    68*********9987 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 1.9
                                    TTTCCHHH CS
                        SepRS_C  17 ekwkeare 24 
                                    + wk++++
  gi|119720080|ref|YP_920575.1| 293 KVWKKVFD 300
                                    67****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (502 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1303  (0.0726756); expected 358.6 (0.02)
Passed bias filter:                     1104  (0.0615762); expected 358.6 (0.02)
Passed Vit filter:                       155  (0.00864521); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.69u 0.35s 00:00:01.04 Elapsed: 00:00:00.48
# Mc/sec: 3157.20
//
Query:       gi|119720081|ref|YP_920576.1|  [L=304]
Description: binding-protein-dependent transport systems inner membrane component [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-15   56.7  19.3    2.5e-15   56.7  19.3    2.1  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    2.4   0.9    0.0062   1.1e+02      25     178 ..      14      37 ..       2      84 .. 0.63
   2 !   56.7  19.3   1.4e-19   2.5e-15       2     176 ..      86     288 ..      85     292 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.0062
                   BPD_transp_1  25 ivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlP 104
                                     +l+ lP  ++++l++                                                                
  gi|119720081|ref|YP_920576.1|  14 MALFLLPAAAIIVLFL---------------------------------------------------------------- 29 
                                    3333333333333333................................................................ PP

                   BPD_transp_1 105 nalppiitglilafggllggavlleflgswpGlgtllleailgydyseisnggvlalviavlllnlvadilqrl 178
                                                                                                      v+  + ++
  gi|119720081|ref|YP_920576.1|  30 ------------------------------------------------------------------VVPSVLTI 37 
                                    ..................................................................33322222 PP

  == domain 2  score: 56.7 bits;  conditional E-value: 1.4e-19
                   BPD_transp_1   2 illGilaa...lnrnkkldkllrpliivllslPsfvlaillvlvf....................vilsilghlilpvii 58 
                                    +++G+l+a   ++ +  l  ++r   ++++ lPs+++a+++ ++f                         +++++  + i
  gi|119720081|ref|YP_920576.1|  86 VGVGLLLAllsTHVHDALGTFMRAAWYLPRVLPSVIWAFVMMWIFspmdtgflnsllksaglspvP--WTFKYYWPFLYI 163
                                    678888888888************************************************998433..347788888*** PP

                   BPD_transp_1  59 llllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlg 138
                                    +  +    + ++i+++a++s+p+dl+ aa+++Gas  +i+r+++lP+++  i+  ++++  +ll  +  +++++ ++G g
  gi|119720081|ref|YP_920576.1| 164 VNGFIGCSLGMVIFSSAIKSIPQDLIVAAKVDGASGLTIVRRIILPLIKWHIAFVVAYQTLSLLASFEYILLTL-DGGPG 242
                                    ************************************************************99988776666666.55566 PP

                   BPD_transp_1 139 tllleailgydyseis........nggvlalviavlllnlvadilq 176
                                    +  +e+ + + y+++         +g+++++v ++l++ lv+ +++
  gi|119720081|ref|YP_920576.1| 243 YYSTEVMILQAYHLAFgqylaamrYGYAAVFVTILLVIGLVLSVVY 288
                                    666666666666666666******9999999999999999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       871  (0.0485805); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2169.51
//
Query:       gi|119720082|ref|YP_920577.1|  [L=278]
Description: binding-protein-dependent transport systems inner membrane component [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.6e-11   43.2  20.6    3.6e-11   43.2  20.6    2.4  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
       0.16   12.4   1.7       0.96    9.9   0.1    2.3  2  FLILHELTA     Hypothetical protein FLILHELTA


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   7.7       1.3   1.2e+04      23      61 ..      11      89 ..       2      97 .. 0.51
   2 !   43.2  20.6     4e-15   3.6e-11       3     174 ..      92     262 ..      85     270 .. 0.82

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 1.3
                   BPD_transp_1 23 liivllslPsfvlaillvlvf........................................vilsilghlilpviilll 61
                                   +  ++  +P + l++ll l+f                                        ++++ l  l  ++i++l+
  gi|119720082|ref|YP_920577.1| 11 IALAVAVIPLVPLVLLLALAFsesqvdirgftlrnfdflrngvlfaedpvysklypnvytvAFNTFLLALGNMLIVVLI 89
                                   5555666666666666666666666666666666666666666666666655555554444222222222222233333 PP

  == domain 2  score: 43.2 bits;  conditional E-value: 4e-15
                   BPD_transp_1   3 llGilaa...lnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalrsl 79 
                                    ++    +    ++++k++ +l++ + v+ ++P  vl+i l+++++ + +l ++ l+v+++ +   +p+ +++ +++ +s+
  gi|119720082|ref|YP_920577.1|  92 MA----GyiiSRYSFKGRSALLGSFLVIHGVPASVLLIALYYMLKSM-GLLNTLLGVVLVKVAVDLPLGVWVLKGFYDSI 166
                                    34....3555599****************************996666.66778999999999999*************** PP

                   BPD_transp_1  80 pkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG..lgtllleailgydyseisngg 157
                                    p d + a++++G sr   f++v+lP+++p i++  +++f + +g++++++++++++     +ll+++++g +   ++ ++
  gi|119720082|ref|YP_920577.1| 167 PWDIEIASLVDGSSRLGAFFRVMLPLVKPGIFAVGLFSFLSGWGEYIFVYTFIQSSTnwTFSLLIRSLIGEMGGINL-AL 245
                                    *****************************************************998666666666666666666555.55 PP

                   BPD_transp_1 158 vlalviavlllnlvadi 174
                                    ++al i++l+ ++v+++
  gi|119720082|ref|YP_920577.1| 246 IAALSIIYLIPVIVIFV 262
                                    55555544444444443 PP

>> FLILHELTA  Hypothetical protein FLILHELTA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.2     0.054   4.8e+02      36      48 ..      16      28 ..       6      47 .. 0.76
   2 ?    9.9   0.1   0.00011      0.96      24      52 ..     108     136 ..      96     164 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.054
                      FLILHELTA 36 AivPllglfalfh 48
                                   A++Pl+ l+ l+ 
  gi|119720082|ref|YP_920577.1| 16 AVIPLVPLVLLLA 28
                                   9999999988875 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00011
                      FLILHELTA  24 hvtsFLiLHElTAivPllglfalfhyldl 52 
                                     + sFL++H + A v l++l ++++++ l
  gi|119720082|ref|YP_920577.1| 108 LLGSFLVIHGVPASVLLIALYYMLKSMGL 136
                                    5679********************99764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       696  (0.0388198); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 1881.69
//
Query:       gi|119720083|ref|YP_920578.1|  [L=356]
Description: ABC transporter related [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.9e-34  118.5   0.0    4.4e-34  117.9   0.0    1.3  1  ABC_tran     ABC transporter
    3.4e-07   30.3   0.4      9e-07   29.0   0.1    1.9  1  TOBE_2       TOBE domain
    7.9e-07   29.2   0.0     0.0035   17.2   0.0    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    0.00013   21.5   0.5      0.016   14.7   0.0    2.4  2  SMC_N        RecF/RecN/SMC N terminal domain
     0.0021   18.9   0.0     0.0063   17.3   0.0    1.9  1  OB_MalK      MalK OB fold domain
     0.0039   17.1   0.0     0.0054   16.7   0.0    1.3  1  Rad17        Rad17 P-loop domain
     0.0055   17.0   0.1      0.028   14.7   0.0    2.3  1  TOBE         TOBE domain
  ------ inclusion threshold ------
      0.016   15.6   0.6      0.085   13.3   0.6    2.1  1  AAA          ATPase family associated with various cellular a
      0.017   14.8   0.0       0.35   10.6   0.1    2.3  2  AAA_29       P-loop containing region of AAA domain
      0.025   14.9   0.2      0.044   14.0   0.2    1.7  1  AAA_22       AAA domain
      0.042   14.2   0.0       0.13   12.7   0.0    1.7  2  AAA_16       AAA ATPase domain
      0.049   13.2   0.1       0.47   10.0   0.1    2.2  2  AAA_25       AAA domain
      0.069   13.1   0.0       0.16   11.9   0.0    1.5  1  RsgA_GTPase  RsgA GTPase
      0.089   12.8   0.0       0.17   11.9   0.0    1.5  1  AAA_14       AAA domain
      0.099   12.4   0.0        0.2   11.3   0.0    1.4  1  AAA_30       AAA domain
       0.11   12.8   0.0       0.23   11.8   0.0    1.4  1  AAA_19       AAA domain
       0.13   12.2   0.0       0.18   11.7   0.0    1.3  1  ATPase_2     ATPase domain predominantly from Archaea
       0.15   11.8   0.0       0.22   11.3   0.0    1.3  1  AAA_11       AAA domain
       0.22   11.2   0.5       0.77    9.4   0.1    1.9  2  SRP54        SRP54-type protein, GTPase domain
       0.24   11.1   0.0       0.44   10.2   0.0    1.4  2  AAA_15       AAA ATPase domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.9   0.0   4.9e-37   4.4e-34       1     136 [.      20     162 ..      20     163 .. 0.97

  Alignments for each domain:
  == domain 1  score: 117.9 bits;  conditional E-value: 4.9e-37
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren. 79 
                                    +kn++l+++  e ++++G++G+GK+t l ++ag +kpt+G i +d++ +++  le  ++++g+++q   l p++tv+en 
  gi|119720083|ref|YP_920578.1|  20 VKNLNLTINDKEFMVLLGPSGCGKTTTLLMIAGVYKPTSGYIYFDDRIVND--LEPKDRNVGMVFQSYALYPHMTVYENi 97 
                                    58*******************************************999999..*************************** PP

                                    ............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    ............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                e d+++++++s l++++l d+      ++LSgGq+qrvalara++k+p+++l+DEp 
  gi|119720083|ref|YP_920578.1|  98 afplklkklpkgEIDRRVKEVASMLRIDNLLDRYP----RQLSGGQQQRVALARAIAKQPDIFLMDEPL 162
                                    *****************************999998....*****************************7 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.1     1e-09     9e-07       2      75 ..     282     347 ..     281     348 .. 0.91

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 1e-09
                         TOBE_2   2 aiRPEklrlaaagganglsGtVedveylGsstryvvelaggqlvvvrqpnadrdsalapGdtVelswdpddavv 75 
                                    ++RPE++++       g    V +ve+lG + + +v+ ++g+l++v  p+++    l++G +V ++++ ++++v
  gi|119720083|ref|YP_920578.1| 282 MVRPEDVKV---VE--GQGFLVYSVEWLGREALAHVRAPDGTLLRVLLPPES---KLTIGAEVSVTFNYAKVHV 347
                                    79*******...43..334469******************************...9************999997 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0   0.00059      0.53       1      71 [.      32      93 ..      32      99 .. 0.72
   2 !   17.2   0.0   3.9e-06    0.0035     228     298 ..     126     194 ..      99     200 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00059
                         AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvr 71
                                   ++vl Gp g+GK++ L  + ++          +++++ +   + i + l ++d +  ++f+ + +  ++++
  gi|119720083|ref|YP_920578.1| 32 FMVLLGPSGCGKTTTLLMIAGVY---------KPTSGYIYFDDRIVNDLEPKDRNVGMVFQSYALYPHMTV 93
                                   79**************9998884.........566666666666666666666666666666655555555 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 3.9e-06
                         AAA_21 228 dgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHS 298
                                    +  ++ +r+lS G+++  al+ a++ ++   +++l DEp ++L+ k+  ++   lk+l+r  g+  i +TH+
  gi|119720083|ref|YP_920578.1| 126 NLLDRYPRQLSGGQQQRVALARAIAKQP---DIFLMDEPLSNLDAKIRVEVRAELKRLQReLGITTIYVTHD 194
                                    45567899********999999999999...*********************999999999**********8 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1     0.019        17      23      39 ..      29      45 ..      11      53 .. 0.81
   2 !   14.7   0.0   1.8e-05     0.016     121     204 ..     116     198 ..      71     214 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.019
                                   TSSEEEEEESTTSSHHH CS
                                   xxxxxxxxxxxxxxxxx RF
                          SMC_N 23 sksftaivGpNGSGKsn 39
                                   +k+f +++Gp G+GK+ 
  gi|119720083|ref|YP_920578.1| 29 DKEFMVLLGPSGCGKTT 45
                                   688************96 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 1.8e-05
                                    HHHHHHHHCTT-...STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-S CS
                                    xxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 121 kevsellesagi...skelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivisl 197
                                    kev+++l+  ++   ++ +LSgG+++ vala  +A    k+  ++l+De  ++LD+k + +v   lk+ + +  +  i +
  gi|119720083|ref|YP_920578.1| 116 KEVASMLRIDNLldrYPRQLSGGQQQRVALARAIA----KQPDIFLMDEPLSNLDAKIRVEVRAELKRLQRELGITTIYV 191
                                    4555555544442224569*******999887655....445699*****************999999998865555544 PP

                                    SHHHCCC CS
                                    xxxxxxx RF
                          SMC_N 198 reemlek 204
                                    ++++ e 
  gi|119720083|ref|YP_920578.1| 192 THDQAEA 198
                                    4444443 PP

>> OB_MalK  MalK OB fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   7.1e-06    0.0063       1      52 [.     236     287 ..     236     288 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 7.1e-06
                        OB_MalK   1 GSPaMNflpatveedg..vlvegggvtlplpeeqklalklyagkevilGiRPEh 52 
                                    GSPa N+++a v+e g  +++e  g +++lp +   a+  + + +vi+ +RPE+
  gi|119720083|ref|YP_920578.1| 236 GSPAANLVDADVVEAGgeYYLEMLGSRFKLPSDL--AAIVKGESRVIFMVRPED 287
                                    9************9999*8888888899999987..8899999**********9 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0     6e-06    0.0054      38      68 ..      23      53 ..      11     137 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6e-06
                          Rad17 38 dvLesrkkriLLisGPsGCgkstvvkvLske 68
                                     L  + k+ +++ GPsGCgk+t++ +++  
  gi|119720083|ref|YP_920578.1| 23 LNLTINDKEFMVLLGPSGCGKTTTLLMIAGV 53
                                   5566677889999***********9888765 PP

>> TOBE  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   3.1e-05     0.028      11      64 .]     298     347 ..     297     347 .. 0.96

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.1e-05
                           TOBE  11 VvvveplgseveVrvdlgggatLtArvtrrsaeeLgLapGeeVfalikaakvhl 64 
                                    V+ ve lg e++ +v++++g+ L + ++++s       +G eV ++++ akvh+
  gi|119720083|ref|YP_920578.1| 298 VYSVEWLGREALAHVRAPDGTLLRVLLPPESKLT----IGAEVSVTFNYAKVHV 347
                                    8899************************999888....***************7 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.6   9.5e-05     0.085       1      23 [.      33      55 ..      33     184 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.5e-05
                                   EEEESSTTSSHHHHHHHHHHHHT CS
                            AAA  1 vllyGppGtGKTllakavakelg 23
                                   ++l Gp G+GKT++   +a   +
  gi|119720083|ref|YP_920578.1| 33 MVLLGPSGCGKTTTLLMIAGVYK 55
                                   789************99998764 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00039      0.35      16      39 ..      24      47 ..      16      58 .. 0.83
   2 ?    1.4   0.0      0.29   2.6e+02       3      41 ..     204     245 ..     202     248 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00039
                         AAA_29 16 tieidlkgatlltGpsGsGKSTll 39
                                    ++i+ k++++l GpsG GK+T l
  gi|119720083|ref|YP_920578.1| 24 NLTINDKEFMVLLGPSGCGKTTTL 47
                                   5677777899***********965 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.29
                         AAA_29   3 rlqlvNWgtfdghtieidlkg...atlltGpsGsGKSTllDA 41 
                                    r+ ++N g +++   + dl +   +t+++G +Gs    l+DA
  gi|119720083|ref|YP_920578.1| 204 RIAVMNEGVLQQVGTPDDLYNrpaNTFVAGFIGSPAANLVDA 245
                                    78889999998865555554445789*******999999998 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.2   4.9e-05     0.044       4      26 ..      29      51 ..      26     199 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.9e-05
                         AAA_22  4 tagilvvtGesGtGKTtllrrll 26
                                   ++ ++v+ G+sG+GKTt+l +++
  gi|119720083|ref|YP_920578.1| 29 DKEFMVLLGPSGCGKTTTLLMIA 51
                                   6789**************98765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00014      0.13      23      45 ..      29      51 ..      18      84 .. 0.81
   2 ?   -1.6   0.0       3.5   3.2e+03      72     106 ..     145     178 ..     120     222 .. 0.50

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00014
                         AAA_16 23 rpelvllsGesGvGKsslvrell 45
                                   + e ++l G+sG+GK++ + +++
  gi|119720083|ref|YP_920578.1| 29 DKEFMVLLGPSGCGKTTTLLMIA 51
                                   55889************997776 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.5
                         AAA_16  72 laqalareellrqlldeaesaeleawrekleeala 106
                                    la+a+a+ +    l de+ s++ +  r + +++l+
  gi|119720083|ref|YP_920578.1| 145 LARAIAK-QPDIFLMDEPLSNLDAKIRVEVRAELK 178
                                    4444433.222233333233333333333333332 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00052      0.47      30      54 ..      27      51 ..      20      59 .. 0.87
   2 ?    0.2   0.0      0.53   4.8e+02     169     188 ..     174     193 ..     160     197 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00052
                         AAA_25 30 lpagelallaGapgtGKttlaldla 54
                                   +  +e+ +l G++g+GKtt +l +a
  gi|119720083|ref|YP_920578.1| 27 INDKEFMVLLGPSGCGKTTTLLMIA 51
                                   677899*************998766 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.53
                         AAA_25 169 vealeriarrtgaavllvhH 188
                                     + l+r++r++g++++ v H
  gi|119720083|ref|YP_920578.1| 174 RAELKRLQRELGITTIYVTH 193
                                    57899*************99 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00018      0.16      89     120 ..      19      51 ..       6      63 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00018
                                    THHHHHHHCTT.SEEEEECSTTSSHHHHHHHHC CS
                    RsgA_GTPase  89 gleelkellkd.ktsvlvGqSGvGKStLinall 120
                                    ++++l+  ++d +++vl+G+SG GK+t + +++
  gi|119720083|ref|YP_920578.1|  19 AVKNLNLTINDkEFMVLLGPSGCGKTTTLLMIA 51 
                                    56777888888799************9776665 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00019      0.17       3      40 ..      31      65 ..      29      94 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00019
                         AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesilyinldd 40
                                   + +v+ G+  +GKTt l  ++  +  + + ++y  +dd
  gi|119720083|ref|YP_920578.1| 31 EFMVLLGPSGCGKTTTLLMIAGVYK-PTSGYIY--FDD 65
                                   6789*************99997766.5455555..555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00023       0.2      15      44 ..      27      56 ..      19      67 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00023
                         AAA_30 15 tsgdrvavltGpAGtGKttalkalreawea 44
                                    +++ ++vl Gp G GKtt+l  ++ +++ 
  gi|119720083|ref|YP_920578.1| 27 INDKEFMVLLGPSGCGKTTTLLMIAGVYKP 56
                                   455679***************999988875 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00026      0.23      10      35 ..      30      55 ..      23      62 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00026
                         AAA_19 10 ekvllvtaGpGtGKTrvlkhivallv 35
                                   ++ ++++++ G+GKT++l +i  +++
  gi|119720083|ref|YP_920578.1| 30 KEFMVLLGPSGCGKTTTLLMIAGVYK 55
                                   67899*************99987776 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0    0.0002      0.18      18      56 ..      28      65 ..      17     126 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0002
                       ATPase_2 18 epneiyfiYGpegsGKtaLlkeiienledkdkyviyyia 56
                                   + +e++++ Gp g+GKt+ l  i+   +  +   iy+++
  gi|119720083|ref|YP_920578.1| 28 NDKEFMVLLGPSGCGKTTTLLMIAGVYKPTSG-YIYFDD 65
                                   448999************99999888766554.455444 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00025      0.22      10      43 ..      23      75 ..      17     210 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00025
                         AAA_11 10 iksalseseitliqGPPGtgKTktivellsqll...................s 43
                                   ++ +++ +e+ ++ GP G+gKT+t++ +  +                      
  gi|119720083|ref|YP_920578.1| 23 LNLTINDKEFMVLLGPSGCGKTTTLLMIAGVYKptsgyiyfddrivndlepkD 75
                                   5667888999****************998887655555555555555544440 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.1   0.00086      0.77       3      26 ..      32      55 ..      30      62 .. 0.86
   2 ?   -0.8   0.0       1.1   9.6e+02      93     149 ..     137     193 ..     135     200 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00086
                                   EEEEEESTTSSHHHHHHHHHHHHH CS
                          SRP54  3 villvGlqGaGKTttlaKLaallk 26
                                    ++l+G+ G GKTttl  +a ++k
  gi|119720083|ref|YP_920578.1| 32 FMVLLGPSGCGKTTTLLMIAGVYK 55
                                   6799************99998887 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.1
                                    -SSTTHHHHHHHHHHHHHHHSSSEEEEEEETTBHTHHHHHHHHHHHHSSCSEEEEES CS
                          SRP54  93 GrlqndkelmeelkkikkvvkpdevllvldattgqeavkqakaFkeavgitgviltk 149
                                    G +q+  +l + ++k  ++   de l  lda +  e+ ++ k+ ++++git++ +t 
  gi|119720083|ref|YP_920578.1| 137 GGQQQRVALARAIAKQPDIFLMDEPLSNLDAKIRVEVRAELKRLQRELGITTIYVTH 193
                                    667777788888888888888888888899999999999999999999999998885 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00049      0.44      18      70 ..      24      73 ..      19      98 .. 0.77
   2 ?   -3.2   0.0         6   5.4e+03     320     332 ..     149     161 ..     139     194 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00049
                         AAA_15 18 eidlsee.ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifen 70
                                    + ++++ ++vl G+ ++GK++ l ++    + +    + +i++++  +++ e 
  gi|119720083|ref|YP_920578.1| 24 NLTINDKeFMVLLGPSGCGKTTTLLMIAGVYKPT----SGYIYFDDRIVNDLEP 73
                                   45555555****************9997777766....5566666666665555 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 6
                         AAA_15 320 keeknvilliEEP 332
                                    + ++++i+l++EP
  gi|119720083|ref|YP_920578.1| 149 IAKQPDIFLMDEP 161
                                    4567788888888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2274.62
//
Query:       gi|119720084|ref|YP_920579.1|  [L=200]
Description: metal dependent phosphohydrolase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-15   57.6   0.0    2.4e-15   56.8   0.0    1.4  1  HD_3      HD domain
    1.9e-12   47.4   0.0    6.5e-12   45.6   0.0    1.7  1  HD_2      HD containing hydrolase-like enzyme
    1.5e-05   25.2   1.3    6.1e-05   23.2   1.1    2.1  2  HD        HD domain
  ------ inclusion threshold ------
      0.051   13.1   0.1       0.18   11.3   0.1    1.8  2  HDOD      HDOD domain


Domain annotation for each model (and alignments):
>> HD_3  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.8   0.0   5.4e-19   2.4e-15       3     130 ..       8     134 ..       6     165 .. 0.81

  Alignments for each domain:
  == domain 1  score: 56.8 bits;  conditional E-value: 5.4e-19
                           HD_3   3 kLKfqkRqgwlqtg..rvreesvaeHmwrvalmalllseelk...ekvdiarvikmfLiHDlvEiltgDiispde.lake 76 
                                    +L++ +R+gw+  g     +e+va+H++ +al+a+ +++ +     +++ ++v+ m+++HD++E++tgD++ +++ l++e
  gi|119720084|ref|YP_920579.1|   8 SLRHLPRTGWVLRGvpASIAETVADHSFLTALVAIDVARRARergFELELEKVLAMSILHDVAEAVTGDVVRYVKqLDEE 87 
                                    59*********999333458*****************9999833347*************************99435555 PP

                           HD_3  77 ekeeeekeaaerilkllpeelaeellalweEFeeretkeakfakdlDklepllq 130
                                       + e    e+ l+ l  +    ++al+ E  + e++ea ++k+ D l +++ 
  gi|119720084|ref|YP_920579.1|  88 LFGKAE----EEALRSLGLG---AYSALLAELRRLESPEALVVKASDDLATIIE 134
                                    544444....4445555555...7999**********************99986 PP

>> HD_2  HD containing hydrolase-like enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   0.0   1.4e-15   6.5e-12      21     178 ..      25     172 ..      17     176 .. 0.84

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 1.4e-15
                           HD_2  21 treenvaeHslevaliahalalienkkfggkldaerlallalyHDasEiitGDlptpvKyanpeireaykevEeeaeekl 100
                                    +  e+va+Hs+ +al+a  +a  ++++ g +l++e++++++++HD++E++tGD+   vK  ++e+   + + Eeea ++l
  gi|119720084|ref|YP_920579.1|  25 SIAETVADHSFLTALVAIDVARRARER-GFELELEKVLAMSILHDVAEAVTGDVVRYVKQLDEEL---FGKAEEEALRSL 100
                                    5689****************9988888.78************************99999999876...778888887777 PP

                           HD_2 101 lelLpeelreeyeella.deeaeeeekklvkaaDklsalikcleelkagnkeFeeakkeieeklkelelpevdyFleef 178
                                              +y+ lla  ++ e+ e  +vka D l ++i+  + l++g    ee+ +++ ++++el+  + + F +++
  gi|119720084|ref|YP_920579.1| 101 GLG-------AYSALLAeLRRLESPEALVVKASDDLATIIEGSRLLRQGYAGVEEILDNVCRHVEELSARARREFGDSL 172
                                    654.......455555334555667889*********************999999999999999999888877776665 PP

>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   1.1   1.4e-08   6.1e-05       2     121 ..      31     131 ..      30     132 .. 0.68
   2 ?   -2.0   0.0       0.9     4e+03      67      68 ..     164     165 ..     137     189 .. 0.53

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1.4e-08
                                    HHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHHHHHH CS
                             HD   2 leHsleVaklarrlaedlge...eedrellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrlgldl 78 
                                    ++Hs+ +a +a   a++  e   e + e++l++ +lHD+++ ++gd                   ++ ++++ + l    
  gi|119720084|ref|YP_920579.1|  31 ADHSFLTALVAIDVARRARErgfELELEKVLAMSILHDVAEAVTGD------------------VVRYVKQLDEEL---- 88 
                                    78999999999999999988999********************998..................222333333333.... PP

                                    HHHHHHHHTTCCHHHHHHHHH...HHHCCTSCHHHHHHHHHHHHHH CS
                             HD  79 edvaklirehheswegkkrpr...glaerqlslearivklaDrlaa 121
                                      + k+ +e ++s    ++++   ++  r  s+ea++vk+ D la+
  gi|119720084|ref|YP_920579.1|  89 --FGKAEEEALRSLG-LGAYSallAELRRLESPEALVVKASDDLAT 131
                                    ..3444444433332.222222344445566888888888888875 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.9
                                    HH CS
                             HD  67 lr 68 
                                    +r
  gi|119720084|ref|YP_920579.1| 164 AR 165
                                    22 PP

>> HDOD  HDOD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1     4e-05      0.18      92     139 ..      27      78 ..      18     102 .. 0.78
   2 ?    0.2   0.0     0.099   4.4e+02      91     122 ..      91     122 ..      71     125 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4e-05
                                    HHHHHHHHHHHHHHHHHHHHHTT-S-.H...HHHHHHHHTTTHHHHHHHHHS CS
                           HDOD  92 lkklwehslavAlvarelaeelgled.p...eeaflaGLLhdiGklvllsll 139
                                    ++++++hs+ +Alva  +a++++ +  +   e+++   +Lhd+ + v  +++
  gi|119720084|ref|YP_920579.1|  27 AETVADHSFLTALVAIDVARRARERGfElelEKVLAMSILHDVAEAVTGDVV 78 
                                    67899*****************877643567************999875544 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.099
                                    -HHHHHHHHHHHHHHHHHHHHHTT-S-HHHHH CS
                           HDOD  91 dlkklwehslavAlvarelaeelgledpeeaf 122
                                    ++++ + +sl  ++++  lae  +le+pe ++
  gi|119720084|ref|YP_920579.1|  91 KAEEEALRSLGLGAYSALLAELRRLESPEALV 122
                                    55566678999999999999999999988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1358.77
//
Query:       gi|119720085|ref|YP_920580.1|  [L=299]
Description: UbiA prenyltransferase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-25   90.1  19.9    1.9e-25   89.6  19.9    1.3  1  UbiA      UbiA prenyltransferase family


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.6  19.9   1.1e-29   1.9e-25       9     226 ..      35     263 ..      14     277 .. 0.80

  Alignments for each domain:
  == domain 1  score: 89.6 bits;  conditional E-value: 1.1e-29
                           UbiA   9 lalaaggspdlllllllllgtllaaaaanalNdyfDreiDadme.......rtpnRPlvsGrispkealifaivllilgl 81 
                                    ++++  + +d+ +++  l+g+ l+ a+++++NdyfD+ ++ d +         ++  lv G    k +++++++ +++  
  gi|119720085|ref|YP_920580.1|  35 ILASKSPGFDAVMAVYGLAGGGLIEAWTHLVNDYFDFVHGVDLPgvsgttvY-RKHLLVEGYPRAKLLRLLVVLAGVVL- 112
                                    56666777889999999***************************99996531.44557787766444444444444443. PP

                           UbiA  82 lll...alllnpltallgllalllyvvYt.g.lrlKrrtllgtvvggiafglppllgwaa.vtgslsllalllalavfll 155
                                    l++   a+   p++++l++++l+l+++Yt + + +K+r l g+v + + + l+ + + ++ +tgs+s+ +ll++l+ +ll
  gi|119720085|ref|YP_920580.1| 113 LMAfvaAAVGRPYAVALAAAGLFLGYAYTgPpFTFKYRAL-GHVNLLAGWWLVNTPALYYmATGSFSAKPLLVSLPGILL 191
                                    33346457777*******************89********.99999999988777777777******************* PP

                           UbiA 156 twaialandlrdregDrkagiktlpvvlGrkaarillalllavllla.llllllalllllylllalllaala 226
                                    ++a+++  ++rd+e Dr+ag++tl v+lG+k +ril+a+++a +++a l+l ll++ + l++ll+l+l++ a
  gi|119720085|ref|YP_920580.1| 192 VIAVLMGDNIRDLEVDRRAGVRTLEVILGKKPSRILFAVYVASAYAAqLALSLLLGAGMLLPLLSLPLLPSA 263
                                    ***********************************8777777777777666666666666666666655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1902.34
//
Query:       gi|119720086|ref|YP_920581.1|  [L=418]
Description: radical SAM domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.6e-22   79.5   0.0    6.7e-22   78.6   0.0    1.4  1  Radical_SAM  Radical SAM superfamily
    2.1e-09   37.8   0.2    4.4e-09   36.7   0.2    1.6  1  SPASM        Iron-sulfur cluster-binding domain
    9.6e-07   29.1   0.0    2.1e-06   28.1   0.0    1.5  1  Fer4_12      4Fe-4S single cluster domain
    3.9e-06   27.0   0.0    6.5e-06   26.3   0.0    1.4  1  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.6   0.0   1.5e-25   6.7e-22       2     166 ..      69     225 ..      68     226 .. 0.94

  Alignments for each domain:
  == domain 1  score: 78.6 bits;  conditional E-value: 1.5e-25
                                    EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHH.HHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelk.aekgvkevilgggepllypdfvellerlaklavpgiri 80 
                                    +vt +CnlrC +C+ +     ++++ +l++e  ++ +++l  +++  ++++++ggepl+++d+ el+++++ l   g+ +
  gi|119720086|ref|YP_920581.1|  69 EVTAACNLRCAHCHASA---GRPYPGELDTEGAKRVIESLTtVKD-FRTLVFTGGEPLVRKDIWELTRHAVDL---GFGV 141
                                    7999************8...8*******************95555.***************************...**** PP

                                    EEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  81 tvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdrivglpGendee 159
                                    ++ tng+l++e +++++++lgv   +++l++  +  v+++++  ++ +   ++++++l + g+  v ++i+  +  n +e
  gi|119720086|ref|YP_920581.1| 142 VFATNGVLVSESVAAEMRRLGVLGAAVSLDSSRPL-VHDKLRgVPGAWRGAVRGIKNLLKEGLY-VQVNITANR-LNVDE 218
                                    ***********************************.888888899*****************99.999999988.88888 PP

                                    HHHHHHH CS
                                    xxxxxxx RF
                    Radical_SAM 160 leellel 166
                                    +e++++l
  gi|119720086|ref|YP_920581.1| 219 IEDVVRL 225
                                    9998876 PP

>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.2   9.9e-13   4.4e-09       1      67 [.     306     364 ..     306     365 .. 0.88

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 9.9e-13
                          SPASM   1 CfapsrslfInsdGdVvpCcvdkktyveelklGnireesleeIwnseeyqefrkskkfplielCrnC 67 
                                    C a + +++++++Gd  pC +       +++ Gn+ +++  e+w+++ ++++r+  +++l+e+Cr+C
  gi|119720086|ref|YP_920581.1| 306 CIAARGMFYVKPNGDAWPCAFI------PVSGGNVARQPAIEVWEGDLFKAIRN--RENLEEPCRSC 364
                                    7788999************333......7************************4..6667788***9 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   4.7e-10   2.1e-06      13     100 ..      72     154 ..      66     170 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 4.7e-10
                        Fer4_12  13 sgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesi.egltllGGEPllpenaeallelvkevkeekpekdiwly 91 
                                    + Cnl+C+ C++ + + +  g+  ++e ++++ie+l   ++ + l+++GGEPl+   ++++ el ++    ++ ++++++
  gi|119720086|ref|YP_920581.1|  72 AACNLRCAHCHASAGR-PYPGE-LDTEGAKRVIESLTTVKDfRTLVFTGGEPLV---RKDIWELTRHAVDLGF-GVVFAT 145
                                    67*********55554.44444.45556667777777655549***********...9***************.69**** PP

                        Fer4_12  92 tgytleels 100
                                    +g+   e  
  gi|119720086|ref|YP_920581.1| 146 NGVLVSESV 154
                                    **9887765 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   1.5e-09   6.5e-06       4      94 ..      70     152 ..      67     171 .. 0.75

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 1.5e-09
                        Fer4_14   4 rlsgCnlsCkgCdnketwkselgkpqteelleqilk.dlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekk 82 
                                     ++ Cnl C  C  ++  +   g+ +te    ++++  ++ +++  + lv+tGGePL     k++ +l ++ ++ +  + 
  gi|119720086|ref|YP_920581.1|  70 VTAACNLRCAHCHASA-GRPYPGELDTEGAK-RVIEsLTTVKDF--RTLVFTGGEPLV---RKDIWELTRHAVDLG--FG 140
                                    4899*********877.55555555555554.555413355555..66*********5...599*******99999..9* PP

                        Fer4_14  83 iwletngtleie 94 
                                    + + tng+l  e
  gi|119720086|ref|YP_920581.1| 141 VVFATNGVLVSE 152
                                    *******99854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2703.14
//
Query:       gi|119720087|ref|YP_920582.1|  [L=460]
Description: hypothetical protein Tpen_1181 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.035   13.8   0.1      0.076   12.8   0.1    1.5  1  DUF3104   Protein of unknown function (DUF3104)


Domain annotation for each model (and alignments):
>> DUF3104  Protein of unknown function (DUF3104)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   4.2e-06     0.076      31      61 ..     356     386 ..     350     393 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.2e-06
                        DUF3104  31 iihvvggardPsiptLFqvadiDtGvvkvvn 61 
                                    +i  v+ + +P+ ++    +d+DtG+vk++ 
  gi|119720087|ref|YP_920582.1| 356 VIARVSVSYNPNQMSYTSSVDVDTGIVKWIH 386
                                    899999***********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (460 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 3557.70
//
Query:       gi|119720088|ref|YP_920583.1|  [L=143]
Description: hypothetical protein Tpen_1182 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-11   43.2   0.0    4.2e-11   42.8   0.0    1.2  1  Polbeta   Polymerase beta, Nucleotidyltransferase


Domain annotation for each model (and alignments):
>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.8   0.0   2.4e-15   4.2e-11       2      90 ..      28     119 ..      27     121 .. 0.87

  Alignments for each domain:
  == domain 1  score: 42.8 bits;  conditional E-value: 2.4e-15
                                    STTTTHHHHHHHHSTTEEEEEE-S------EEEEEEEESS-....--HHHHHHHHHHHHHH..SSSEEEEEETTTS-HHH CS
                        Polbeta   2 kikeilekekeielaylFGSrakgkareeSDiDlavllkek....ldleeelelaaeledi.klgkkvDlvdlneappll 76 
                                    +i ++l +++e+ +a+++G + + ++ +  DiD+av+l  k    +++ +  +l + l+++ k+   +D++ l+ app +
  gi|119720088|ref|YP_920583.1|  28 RIAQLLMDRPEVLIAVVHGGFISSDIFR--DIDIAVYLGHKlpfmDTVFYVDRLRDRLQEAlKIDIALDVQLLDYAPPAF 105
                                    5899***********************9..***********655555555666666666669999999************ PP

                                    HHHHHHS-EEEES- CS
                        Polbeta  77 lyeilkegkllysk 90 
                                     y+il++g++++++
  gi|119720088|ref|YP_920583.1| 106 TYRILSSGQIIVER 119
                                    ***********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 897.96
//
Query:       gi|119720089|ref|YP_920584.1|  [L=57]
Description: hypothetical protein Tpen_1183 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.8e-07   29.2   0.1      7e-07   29.1   0.1    1.1  1  DUF86     Protein of unknown function DUF86


Domain annotation for each model (and alignments):
>> DUF86  Protein of unknown function DUF86
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.1   3.9e-11     7e-07      76     116 ..       4      45 ..       1      53 [. 0.82

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 3.9e-11
                                    HHHHHHHHCCHHHHHT-CCCTTHHHHHHHHHH.TCHHHHHHH CS
                          DUF86  76 eepwrkmiglRNrLvHgYlgidpeivwsiike.nlpdleefl 116
                                    + +++k++ lRN++vH+Y+ id+ ++ + +k    + ++ef+
  gi|119720089|ref|YP_920584.1|   4 AMKMAKLASLRNIIVHRYWAIDDARILNEAKGsGTKAVREFI 45 
                                    67899*********************9988874556666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 404.97
//
Query:       gi|119720090|ref|YP_920585.1|  [L=324]
Description: hypothetical protein Tpen_1184 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2147.01
//
Query:       gi|119720091|ref|YP_920586.1|  [L=213]
Description: multiple antibiotic resistance (MarC)-related proteins [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-42  145.0  10.0    2.2e-42  144.8  10.0    1.1  1  MarC      MarC family integral membrane protein


Domain annotation for each model (and alignments):
>> MarC  MarC family integral membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.8  10.0   1.2e-46   2.2e-42       2     202 ..      23     210 ..      22     211 .. 0.95

  Alignments for each domain:
  == domain 1  score: 144.8 bits;  conditional E-value: 1.2e-46
                           MarC   2 kaiikafvsLlaiinplgnvpvflslleevskeerkrialkasilallillvfllfGelilklfgisidalkiaGgillf 81 
                                    k+++ +f++L+++++ +gn+p+f sl++ +  eer +i  k + +a ++l++f++fG  ++++ g+s   +kiaGg+ll+
  gi|119720091|ref|YP_920586.1|  23 KELWDTFLMLFIVVDSIGNIPIFYSLTSGMGREERIKIFEKSVAVASALLVFFAVFGYPFFQYYGVSFTDFKIAGGLLLL 102
                                    68999*************************************************************************** PP

                           MarC  82 liaidmlkakqkkekkkkseeeeseekdeiavvPLAlPliaGPgaittvlvlaseassivekvavvlaillaalitllil 161
                                    +ia++ ++++ ++         e+ ++++ avvP+A+Pl+aGPgai +v+ l s +      + ++++i+l +l ++lil
  gi|119720091|ref|YP_920586.1| 103 IIALQGVFGRVEA---------EALRSEDLAVVPMATPLLAGPGAIYMVMYLNSVYGL----LPTLVSIALNTLASYLIL 169
                                    **********994.........44567899*********************9998877....7999************** PP

                           MarC 162 llsslilrllgktginaleRlmGllLvalavqlivdGikei 202
                                      s+++l++ gk+ i +l+R++ llL++lav li  Gi e+
  gi|119720091|ref|YP_920586.1| 170 TKSNVLLEKAGKNTILVLSRIFSLLLAVLAVSLIRSGIYEA 210
                                    **************************************886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1560.03
//
Query:       gi|119720092|ref|YP_920587.1|  [L=582]
Description: hypothetical protein Tpen_1186 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.11   12.7   0.0       0.28   11.5   0.0    1.6  1  AAA_22    AAA domain


Domain annotation for each model (and alignments):
>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   1.6e-05      0.28       8      29 ..     290     311 ..     284     319 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 1.6e-05
                         AAA_22   8 lvvtGesGtGKTtllrrlleql 29 
                                    l+++Ge+GtGKT+  + +   +
  gi|119720092|ref|YP_920587.1| 290 LALFGEPGTGKTFATKDFILGN 311
                                    799***********99987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (582 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.23s 00:00:00.79 Elapsed: 00:00:00.40
# Mc/sec: 4329.66
//
Query:       gi|119720093|ref|YP_920588.1|  [L=149]
Description: PilT domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.9e-13   49.4   0.2    1.4e-12   48.2   0.2    1.5  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.2   0.2   7.8e-17   1.4e-12       1     121 [.       4     139 ..       4     140 .. 0.85

  Alignments for each domain:
  == domain 1  score: 48.2 bits;  conditional E-value: 7.8e-17
                                    EEE-HHHHHHHH....TTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHS........SCHCHHHHHHH...HHHHHHH CS
                            PIN   1 ivlDTsvliall....rgeekaeaarklleeleelvtsalvlaEllyvlar........rkskrekaael...velllll 65 
                                    ++lD+s++++ +     +e+ ++ + k+l++ ++l +sa  + E+l vl +        r++ ++++ ++   + +ll l
  gi|119720093|ref|YP_920588.1|   4 VYLDSSAVVKRYvlepGSEVVSRVYYKALNGESTLSFSAWNIGEVLGVLDKyyrrgwlsREDYEKARFQFlgeTIRLLKL 83 
                                    69*******99977888888888888888888************************998444444444431114555569 PP

                                    HTSEEEEBCHHHHHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHHHHH CS
                            PIN  66 salkilpidaeiaeeaaeialkygllpnDaliaAtAkehgikliatfDedfrrvak 121
                                    + lki+p+ ++++ e ++i +ky +  +Dal ++ Ak+ g++ ++t De+++++a+
  gi|119720093|ref|YP_920588.1|  84 RLLKIVPVRTKLLIETWRIVEKYHVYEADALQLVSAKYVGAEEFYTGDEQLHKIAA 139
                                    9****************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1145.51
//
Query:       gi|119720094|ref|YP_920589.1|  [L=88]
Description: hypothetical protein Tpen_1188 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.061   13.4   0.0      0.086   12.9   0.0    1.4  1  ClpB_D2-small  C-terminal, D2-small domain, of ClpB protein
        0.1   13.0   0.1       0.42   11.1   0.1    1.9  1  CcdA           Post-segregation antitoxin CcdA


Domain annotation for each model (and alignments):
>> ClpB_D2-small  C-terminal, D2-small domain, of ClpB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   9.6e-06     0.086      45      74 ..      24      53 ..       2      62 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.6e-06
                                   TTTBTCCHHHHHHHHTHHHHHHHHHTTSSS CS
                  ClpB_D2-small 45 peyGARpLrriiqreiedplaeeilsgelk 74
                                   +e G R L r+i++ +e +++++++ ++l+
  gi|119720094|ref|YP_920589.1| 24 SERGLRALSRAIEEALEEEVSDVLVVKALE 53
                                   56788******************9988776 PP

>> CcdA  Post-segregation antitoxin CcdA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   4.7e-05      0.42       1      36 [.       3      44 ..       3      55 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.7e-05
                           CcdA  1 KkavnlsldsdllaqAralgiN......lSatleeaLaeevk 36
                                   K+++++++ds+l ++ ++   +      lS+++eeaL+eev 
  gi|119720094|ref|YP_920589.1|  3 KVKTSITVDSELWEEFKSRVGSerglraLSRAIEEALEEEVS 44
                                   7899***********99876544555559*********9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 682.95
//
Query:       gi|119720095|ref|YP_920590.1|  [L=227]
Description: hypothetical protein Tpen_1189 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1620.09
//
Query:       gi|119720096|ref|YP_920591.1|  [L=203]
Description: hypothetical protein Tpen_1190 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1517.71
//
Query:       gi|119720097|ref|YP_920592.1|  [L=385]
Description: hypothetical protein Tpen_1191 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.1e-119  399.3   0.0   1.2e-119  399.1   0.0    1.0  1  DUF763    Protein of unknown function (DUF763)
  ------ inclusion threshold ------
       0.13   12.7   3.5       0.54   10.6   3.5    2.1  1  HTH_31    Helix-turn-helix domain
        6.6    7.4   6.6    2.6e+02    2.3   6.6    3.0  1  ABATE     Putative stress-induced transcription regulator


Domain annotation for each model (and alignments):
>> DUF763  Protein of unknown function (DUF763)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  399.1   0.0  2.1e-123  1.2e-119       1     312 []       4     339 ..       4     339 .. 0.96

  Alignments for each domain:
  == domain 1  score: 399.1 bits;  conditional E-value: 2.1e-123
                         DUF763   1 GiadLpLhegkvPewllermkkLskaiveliveeygkeellerlsdPlwFqslgnvlGmdWdsSGsTtvvlgalkealks 80 
                                    G+a+LpLh+g+vP+wl++rm++L++++ve+iveeyg++ llerl+dP++Fq+++n++GmdWdsSGsTtv++++lk++l++
  gi|119720097|ref|YP_920592.1|   4 GVAELPLHDGSVPRWLIARMERLAGILVEMIVEEYGTRGLLERLADPVYFQAINNIIGMDWDSSGSTTVTTAVLKKVLEE 83 
                                    89****************************************************************************** PP

                         DUF763  81 eelgilvaGGkGkksrktpeeleklaeklgldeeklvkasrlvakvdnaalqdgyqlYlhalivsekgkwaviqQGmnee 160
                                    +elg++ +GGkG++srk pee++ +aek+gld + lv++s lvakvd+aalq gyqlY+ha++++e+g+wav+qQGm+ +
  gi|119720097|ref|YP_920592.1|  84 RELGVKACGGKGSSSRKAPEEIRLHAEKYGLDPSGLVSTSYLVAKVDSAALQAGYQLYHHAFFFDEEGRWAVVQQGMKPS 163
                                    ******************************************************************************** PP

                         DUF763 161 erlARRYhwlseelesfveephsgiagekkeeevlnlvskeseearkaildlvkekpekllkelkelkallkgekkl... 237
                                    +r+ARRYhw+se++ +++ ephsgi+g  +e  +ln+v++e+ e r++++dlv e++++l++ ++e+ ++l+g + l   
  gi|119720097|ref|YP_920592.1| 164 TRTARRYHWFSERVGDVTVEPHSGIHG-FREPFALNTVAAEAGEFRRLVVDLVGEGASRLERLVSEALRVLEGYSPLvsy 242
                                    ***************************.99999***************************************99999999 PP

                         DUF763 238 .............klpakhev........lekvlekayelqpedfeellllkgvGpktlraLalvaeliygekasfkDPv 296
                                                 +      +         +++l++++ + +e+f+++l +k vGp+++raLalvael+y++++s++DPv
  gi|119720097|ref|YP_920592.1| 243 apysaekarslreR------MrrlgkpslSREALASLAGRGVESFRDILAAKAVGPSAIRALALVAELVYETPPSWRDPV 316
                                    98887776655441......1445666669************************************************** PP

                         DUF763 297 .......kysfavGgKdgvPypv 312
                                           k+++avGgKdgvP+pv
  gi|119720097|ref|YP_920592.1| 317 thqvdpfKFAYAVGGKDGVPFPV 339
                                    **********************8 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   3.5   9.1e-05      0.54       7      51 ..     251     299 ..     247     305 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 9.1e-05
                         HTH_31   7 ralRera......GLsqeevAerlgvsestlsrlEqGrrgrpspavleala 51 
                                    r lRer        Ls+e++A ++g  +   +++  ++   + p++++ala
  gi|119720097|ref|YP_920592.1| 251 RSLRERMrrlgkpSLSREALASLAGRGVESFRDILAAKA--VGPSAIRALA 299
                                    56666666679999*************************..7999999998 PP

>> ABATE  Putative stress-induced transcription regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   6.6     0.044   2.6e+02      49      92 ..     235     311 ..     155     321 .. 0.67

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.044
                                    .............HHHHHHHHHHHHHHT...HHHH................................HHHHHHHHHS--- CS
                          ABATE  49 a..........elararaLRealralla...aaaag.......................dpppaaalaalnallaaappa 92 
                                                 + ar+LRe++r+l     +   +                        p +  ala++ +l+ ++pp+
  gi|119720097|ref|YP_920592.1| 235 GysplvsyapySAEKARSLRERMRRLGKpslS---RealaslagrgvesfrdilaakavGPSAIRALALVAELVYETPPS 311
                                    04444445566558999999999999984431...223333333455555544444433344444555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2774.16
//
Query:       gi|119720098|ref|YP_920593.1|  [L=139]
Description: hypothetical protein Tpen_1192 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-21   75.2  17.3    5.8e-21   75.1  17.3    1.0  1  EamA      EamA-like transporter family
    0.00032   20.3   7.0    0.00037   20.1   7.0    1.0  1  SLC35F    Solute carrier family 35
  ------ inclusion threshold ------
      0.087   12.9   4.1       0.15   12.1   4.1    1.6  1  TMEM234   Putative transmembrane family 234
        1.8    6.7  13.0        2.1    6.5  13.0    1.1  1  DUF2070   Predicted membrane protein (DUF2070)
        5.9    7.1   8.2       0.36   11.0   0.7    2.4  2  Pox_A14   Poxvirus virion envelope protein A14


Domain annotation for each model (and alignments):
>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.1  17.3   1.6e-24   5.8e-21       3     136 ..       4     138 ..       2     139 .] 0.93

  Alignments for each domain:
  == domain 1  score: 75.1 bits;  conditional E-value: 1.6e-24
                           EamA   3 gillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegkl..aklslkdwllllllgllgtvlafl 80 
                                    + llall a+f a++++++ki+l++v+++t+t++r+++  ++ + ++l ++g+   + ++ ++ l++ll g +++ + ++
  gi|119720098|ref|YP_920593.1|   4 WFLLALLDAFFAALATIFAKIGLQNVDSITATALRSVVMMLFAVGMMLAFRGTGfvSTITSREALYILLSG-IAGGASWV 82 
                                    5699*********************************9999998888777777779*******99999988.5888899* PP

                           EamA  81 lffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                    l+f al+k++ + +sl+   + +f+++lsvl+l+e lt+k++++++l+l++++++ 
  gi|119720098|ref|YP_920593.1|  83 LYFLALQKGETTPVSLVDKSSLAFVVLLSVLILHEELTVKKIIAVGLVLAAIYILA 138
                                    ****************************************************9975 PP

>> SLC35F  Solute carrier family 35
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   7.0     1e-07   0.00037      23     142 ..      15     136 ..       4     139 .] 0.73

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1e-07
                         SLC35F  23 altskylaek...kinaPvlqtflnyvllalvy.tgillfrrgaeklleilkrkwykylllalvdveanylv.vkayqyt 97 
                                    a +++ +a+    +++  +  t l  v+++l   + +l+fr g+  +++ +  +   y+ll+ +   a +++   a q  
  gi|119720098|ref|YP_920593.1|  15 AALATIFAKIglqNVDS-ITATALRSVVMMLFAvGMMLAFR-GT-GFVSTITSREALYILLSGIAGGASWVLyFLALQKG 91 
                                    44444444442103333.34455655655555505555566.55.59999***********99999998876379***** PP

                         SLC35F  98 sltsvqlldcfaipvvlvlswlflkvryrlvkiigvvvcilGvvl 142
                                    + t v+l+d  +++ v++ls l+l+    + kii+v + ++ + +
  gi|119720098|ref|YP_920593.1|  92 ETTPVSLVDKSSLAFVVLLSVLILHEELTVKKIIAVGLVLAAIYI 136
                                    ************************************988887765 PP

>> TMEM234  Putative transmembrane family 234
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   4.1   4.2e-05      0.15      57     115 ..      79     137 ..       9     138 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.2e-05
                        TMEM234  57 gS.vlfflllgkadlslavpiaNs.lafvfTvltelllgekvlkkktvlgmllvvvgialc 115
                                    +S vl+fl+l+k + + ++ +  s lafv  vl + l+  + l+ k+++ ++lv+++i+++
  gi|119720098|ref|YP_920593.1|  79 ASwVLYFLALQKGETTPVSLVDKSsLAFV--VLLSVLILHEELTVKKIIAVGLVLAAIYIL 137
                                    44499*********998888865415554..556655555556677788999999999985 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5  13.0   0.00058       2.1      72     182 ..       5     124 ..       1     138 [. 0.64

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.00058
                        DUF2070  72 lflalltelivviisllaillsall........qalvllalvlslalvfalrllvlvavsdesllkavlpaliqpllail 143
                                    ++lall ++++++ +++a +    +         ++v++ ++  + +++a+r   +v++  +++  ++l++ i   ++++
  gi|119720098|ref|YP_920593.1|   5 FLLALLDAFFAALATIFAKIGLQNVdsitatalRSVVMMLFA--VGMMLAFRGTGFVSTITSREALYILLSGIAGGASWV 82 
                                    555555555555555555554444444445434555555555..55899999999999999999999************* PP

                        DUF2070 144 llvlyfspesflllll...lslifalavylfivvvdrplkrn 182
                                    l++l +++  + ++ l   +sl+f++++ ++i   +  +k++
  gi|119720098|ref|YP_920593.1|  83 LYFLALQKGETTPVSLvdkSSLAFVVLLSVLILHEELTVKKI 124
                                    999995555555555411245566655555555555555554 PP

>> Pox_A14  Poxvirus virion envelope protein A14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.7    0.0001      0.36      23      58 ..      16      51 ..       7      60 .. 0.91
   2 ?   -0.4   1.6      0.36   1.3e+03      64      64 ..     114     114 ..      60     139 .] 0.60

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0001
                        Pox_A14 23 ilacifafvdfskststtdkawralsivsFilgivi 58
                                   +la ifa + +  + s t +a+r++ ++ F +g+++
  gi|119720098|ref|YP_920593.1| 16 ALATIFAKIGLQNVDSITATALRSVVMMLFAVGMML 51
                                   689******************************987 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.36
                        Pox_A14  64 l 64 
                                    +
  gi|119720098|ref|YP_920593.1| 114 I 114
                                    1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       800  (0.0446204); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 970.85
//
Query:       gi|119720099|ref|YP_920594.1|  [L=252]
Description: threonyl/alanyl tRNA synthetase, SAD [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.3e-12   45.7   0.0    4.3e-12   45.3   0.0    1.1  1  tRNA-synt_2c  tRNA synthetases class II (A)
    5.9e-07   29.5   0.2    1.2e-06   28.5   0.2    1.5  1  tRNA_SAD      Threonyl and Alanyl tRNA synthetase second addi


Domain annotation for each model (and alignments):
>> tRNA-synt_2c  tRNA synthetases class II (A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   0.0   4.8e-16   4.3e-12     478     551 ..      36     109 ..      24     110 .. 0.94

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 4.8e-16
                                    EEEEEETTEEEESEEXXXXSSSSCSXXXEEEEESSEEEEESEEEEETTEEEEEXSS.XSXXXTTSEEEEEEXHH CS
                   tRNA-synt_2c 478 eveegeevgvvLdrTpfYaesGGqigDeGliekegaefrvkdvqkakgvvlhkgkleegklkvgdkvkaevdee 551
                                    e+ +g++++v LdrT f + +GGq +DeG i +  + f+vk++ + +g + h g++e g+l+vgd+v++e+++e
  gi|119720099|ref|YP_920594.1|  36 ELLKGSKAYVELDRTIFHPLGGGQPSDEGSIVSPRGAFAVKKAIRDRGRIRHWGRIEAGSLEVGDTVRCELNWE 109
                                    678999****************************************************************9986 PP

>> tRNA_SAD  Threonyl and Alanyl tRNA synthetase second additional domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.2   1.4e-10   1.2e-06       2      34 ..     207     239 ..     206     245 .. 0.88

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 1.4e-10
                                    EEEEETT.EEEEESS---SBGGGC-SEEEECCE CS
                       tRNA_SAD   2 rvvsiGdisvelCgGtHvpnTgeIgafkilsee 34 
                                    rvv+i  +   +C GtHv+nT+e+g +k+l  e
  gi|119720099|ref|YP_920594.1| 207 RVVEIPGVNAMPCTGTHVSNTREVGRIKVLGVE 239
                                    9****558*********************9554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       269  (0.0150036); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1829.08
//
Query:       gi|119720100|ref|YP_920595.1|  [L=256]
Description: methyltransferase type 11 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.9e-22   78.0   0.0    3.6e-21   75.7   0.0    2.0  2  Methyltransf_25  Methyltransferase domain
    4.1e-19   69.0   0.1    7.8e-18   64.9   0.0    2.3  2  Methyltransf_11  Methyltransferase domain
    1.3e-15   57.5   0.0      2e-15   56.9   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
      7e-14   52.0   0.0      1e-13   51.5   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    1.6e-12   47.3   0.1    4.5e-12   45.8   0.0    1.7  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    2.5e-12   47.4   0.0    1.8e-11   44.6   0.0    2.1  2  Methyltransf_12  Methyltransferase domain
    5.2e-09   36.0   0.0    9.3e-09   35.2   0.0    1.3  1  NodS             Nodulation protein S (NodS)
    8.6e-05   22.0   0.0    0.00012   21.6   0.0    1.2  1  TehB             Tellurite resistance protein TehB
    9.7e-05   22.0   0.0    0.00016   21.3   0.0    1.3  1  MTS              Methyltransferase small domain
    0.00013   21.4   0.0    0.00021   20.7   0.0    1.3  1  CMAS             Mycolic acid cyclopropane synthetase
    0.00017   21.4   0.0    0.00026   20.8   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
     0.0009   18.4   0.0     0.0013   17.9   0.0    1.1  1  RrnaAD           Ribosomal RNA adenine dimethylase
     0.0012   17.8   0.0     0.0017   17.4   0.0    1.2  1  Methyltransf_9   Protein of unknown function (DUF1698)
      0.002   17.6   0.0     0.0041   16.6   0.0    1.5  1  Methyltransf_4   Putative methyltransferase
      0.003   16.9   0.0     0.0047   16.2   0.0    1.3  1  Methyltransf_2   O-methyltransferase domain
     0.0034   17.1   0.0      0.005   16.5   0.0    1.2  1  TPMT             Thiopurine S-methyltransferase (TPMT)
     0.0041   17.0   0.0     0.0075   16.2   0.0    1.3  1  Methyltransf_18  Methyltransferase domain
     0.0069   15.8   0.0     0.0094   15.4   0.0    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
     0.0073   16.6   0.0      0.014   15.7   0.0    1.5  1  AdoMet_MTase     Predicted AdoMet-dependent methyltransferase
  ------ inclusion threshold ------
       0.01   16.0   0.0      0.014   15.5   0.0    1.5  1  FtsJ             FtsJ-like methyltransferase
      0.021   14.0   0.1        2.3    7.4   0.0    2.6  2  N2227            N2227-like protein
      0.021   14.8   0.0       0.03   14.3   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
      0.051   13.2   0.0      0.064   12.8   0.0    1.3  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
      0.067   12.8   0.0       0.11   12.0   0.0    1.4  1  MetW             Methionine biosynthesis protein MetW
       0.11   12.2   0.0       0.13   12.0   0.0    1.2  1  MethyltransfD12  D12 class N6 adenine-specific DNA methyltran


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.7   0.0     5e-24   3.6e-21       1      96 [.      42     135 ..      42     135 .. 0.95
   2 ?   -0.5   0.0         3   2.1e+03      74      95 ..     210     224 ..     168     226 .. 0.55

  Alignments for each domain:
  == domain 1  score: 75.7 bits;  conditional E-value: 5e-24
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEEST.GGG.SS CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssga.lhh.ls 78 
                                    vLd+GcGtG +t++l +r+  ++ +gvDis++mle ar++a+e   nvef+  da++l f++ +fD+ +++++ +++ ++
  gi|119720100|ref|YP_920595.1|  42 VLDVGCGTGLHTIELGRRG--YRAVGVDISQNMLEVARSKARE-MTNVEFILSDATKLGFNS-EFDAAIAMYGvVSYfVD 117
                                    9*****************5..********************64.46**************97.9*********9999889 PP

                                    HHHHHHHHHHHHHHEEEE CS
                Methyltransf_25  79 dedlekalkeiarvLkpg 96 
                                    de l  +l+ ++r++kpg
  gi|119720100|ref|YP_920595.1| 118 DESLLGFLRSVRRAIKPG 135
                                    999**************8 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 3
                                    GGGSSHHHHHHHHHHHHHHEEE CS
                Methyltransf_25  74 lhhlsdedlekalkeiarvLkp 95 
                                    l ++       +l+ei  vL++
  gi|119720100|ref|YP_920595.1| 210 LRLF-------TLREIVHVLRE 224
                                    3333.......35556666655 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.9   0.0   1.1e-20   7.8e-18       1      96 []      43     140 ..      43     140 .. 0.93
   2 ?    1.8   0.0      0.52   3.7e+02      73      93 ..     206     227 ..     165     230 .. 0.82

  Alignments for each domain:
  == domain 1  score: 64.9 bits;  conditional E-value: 1.1e-20
                                    EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES.-CCC-...CC CS
                Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvsse.vlhhv...ed 76 
                                    LdvGcGtG+++ +l +rg+r vgvD+s++ml++a++ka+e  + vef+ +da+kl f++  fD+ ++   v+ ++   e 
  gi|119720100|ref|YP_920595.1|  43 LDVGCGTGLHTIELGRRGYRAVGVDISQNMLEVARSKAREMTN-VEFILSDATKLGFNS-EFDAAIAMYgVVSYFvddES 120
                                    8***************************************995.*************99.99998887767777789889 PP

                                    HHHHHHHHHHHEEEEEEEEE CS
                Methyltransf_11  77 pekalkeiaRvLkpgGllvi 96 
                                    +  +l+ ++R  kpg ++v+
  gi|119720100|ref|YP_920595.1| 121 LLGFLRSVRRAIKPGSVFVF 140
                                    999*************9987 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.52
                                    C-.CCHHHHHHHHHHHEEEEEE CS
                Methyltransf_11  73 hv.edpekalkeiaRvLkpgGl 93 
                                    h  + +  +l+ei+ vL+  G+
  gi|119720100|ref|YP_920595.1| 206 HSlKLRLFTLREIVHVLRESGF 227
                                    44366667899******99985 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.9   0.0   2.8e-18     2e-15       6     114 ..      41     145 ..      39     189 .. 0.81

  Alignments for each domain:
  == domain 1  score: 56.9 bits;  conditional E-value: 2.8e-18
                Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsn.evl 84 
                                    +vlD+GCGtG  t+el ++   + + vG+Dis++++e+Ar++a+  + +nveF  +d+++l   ++ + fD  ++  +v+
  gi|119720100|ref|YP_920595.1|  41 SVLDVGCGTGLHTIELGRR---GYRAVGVDISQNMLEVARSKAR--EMTNVEFILSDATKLG--FN-SEFDAAIAMyGVV 112
                                    79***************55...5679***************877..9***************..88.99***88874555 PP

                Methyltransf_31  85 ...naladpdkileeiervlkpggilliedprl 114
                                        +  ++  +l+++ r++kpg++++ ++ +l
  gi|119720100|ref|YP_920595.1| 113 syfVDDESLLGFLRSVRRAIKPGSVFVFDTWSL 145
                                    33355555556666*************998883 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.5   0.0   1.4e-16     1e-13      11     164 ..      25     231 ..      14     232 .. 0.80

  Alignments for each domain:
  == domain 1  score: 51.5 bits;  conditional E-value: 1.4e-16
                Methyltransf_23  11 dklerllpk..lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae.kakkaqkdqfdeqeaae..pqgkfdl 85 
                                    d+ler++    l + ++vLd+GcGtG  + +l ++g+  +gvD+s ++ e a+ ka+ + ++ f  ++a++   +  fd 
  gi|119720100|ref|YP_920595.1|  25 DFLERVFRDysLIPVKSVLDVGCGTGLHTIELGRRGYRAVGVDISQNMLEVARsKAREMTNVEFILSDATKlgFNSEFDA 104
                                    678888843468999***********99999*******************99887788888888666666655566**** PP

                Methyltransf_23  86 Ivlrevleh..vpd..ppellrqiatllkpgGylllseplasl.............................kedrllld 132
                                    ++++++  +  v+d  +   lr++++ +kpg ++++ ++  sl                              ++ ++ld
  gi|119720100|ref|YP_920595.1| 105 AIAMYGVVSyfVDDesLLGFLRSVRRAIKPGSVFVFDTW--SLvgvlekrvyyetpfssfrksgsqlaikeeNWRVDFLD 182
                                    999997655225555699********************9..5667999999**********9999999988657777777 PP

                Methyltransf_23 133 ........wlylvpag......rhi...sffsarslkelleeaGlevve 164
                                            w  l+ a       +h+   ++f+ r++ + l+e+G+e+v+
  gi|119720100|ref|YP_920595.1| 183 qvayaeiqWSILDLAKgeidvfKHSlklRLFTLREIVHVLRESGFELVK 231
                                    7777777754443333334344444445******************996 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   0.0   6.3e-15   4.5e-12      49     168 ..      40     157 ..      25     187 .. 0.77
   2 ?   -1.3   0.0       1.6   1.1e+03      33      61 ..     174     203 ..     167     217 .. 0.77

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 6.3e-15
                                    TEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEES-GGG CS
                Ubie_methyltran  49 akvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvtvsfGlrn 128
                                    ++vlDv +Gtg  +++l +   + ++ v++Di++nmL+v++ k++e   +n+ef+ ++a +L f+   fD     +G+  
  gi|119720100|ref|YP_920595.1|  40 KSVLDVGCGTGLHTIELGR---RGYRAVGVDISQNMLEVARSKAREM--TNVEFILSDATKLGFNS-EFDAAIAMYGVVS 113
                                    689************9975...456889***************9985..69*************86.5999999999864 PP

                                    .-S-HHH...HHHHHHHHEEEEEEEEEEEE----SHHHHHHHHH CS
                Ubie_methyltran 129 .vtDklk...aLkeayrvlkpGGrlvvlefskvelpllsqayel 168
                                     + D +     L++++r +kpG  +v    s v +   ++ ye+
  gi|119720100|ref|YP_920595.1| 114 yFVDDESllgFLRSVRRAIKPGSVFVFDTWSLVGVLEKRVYYET 157
                                    266655412268*********98877666666666555555554 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.6
                                    HHHHH.HHHHH--S--TTEEEEES-TT-HH CS
                Ubie_methyltran  33 rlWkk.fveklvavkrgakvlDvagGtgDl 61 
                                    + W+  f+ ++       ++lD+a G  D+
  gi|119720100|ref|YP_920595.1| 174 ENWRVdFLDQVAYAEIQWSILDLAKGEIDV 203
                                    468875777777777777999999998886 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.6   0.0   2.6e-14   1.8e-11       1      98 [.      43     137 ..      43     138 .. 0.88
   2 ?    0.4   0.0       1.5   1.1e+03      74      97 ..     202     226 ..     168     227 .. 0.84

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 2.6e-14
                Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvas.nvlhhl 79 
                                    L++GcGtG  + +l ++  + + +gvDis++++     + a+ +++  +nve+   d+ +l  +s fD+ +a  +v++++
  gi|119720100|ref|YP_920595.1|  43 LDVGCGTGLHTIELGRR--GYRAVGVDISQNML-----EVARSKAREMTNVEFILSDATKLGFNSEFDAAIAMyGVVSYF 115
                                    8****************..**************.....55555555566999999999999999*****88555****** PP

                Methyltransf_12  80 ...kdirevldnirklLkpgGr 98 
                                       + +  +l+++r+++kpg +
  gi|119720100|ref|YP_920595.1| 116 vddESLLGFLRSVRRAIKPGSV 137
                                    *988899************976 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.5
                Methyltransf_12  74 nvlhhlkdir.evldnirklLkpgG 97 
                                    +v+ h  ++r ++l++i ++L+  G
  gi|119720100|ref|YP_920595.1| 202 DVFKHSLKLRlFTLREIVHVLRESG 226
                                    6888886666699999999999877 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.0   1.3e-11   9.3e-09      44     145 ..      39     141 ..      30     144 .. 0.93

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 1.3e-11
                           NodS  44 iadalevGcaaGalterlapyckrltvvdvveeaiararervkesshiswivsdvqqfstdekfdliv.vaevlyyiedv 122
                                    + ++l+vGc +G  t +l     r   vd+ ++ ++ ar + +e++++ +i sd +++  + +fd  + +  v+ y  d 
  gi|119720100|ref|YP_920595.1|  39 VKSVLDVGCGTGLHTIELGRRGYRAVGVDISQNMLEVARSKAREMTNVEFILSDATKLGFNSEFDAAIaMYGVVSYFVDD 118
                                    789**************************************************************865156899999999 PP

                           NodS 123 aelraavrnlvsllapdgqlvfG 145
                                    + l + +r + + ++p+  +vf 
  gi|119720100|ref|YP_920595.1| 119 ESLLGFLRSVRRAIKPGSVFVFD 141
                                    99*******************95 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   1.6e-07   0.00012      31     128 ..      38     136 ..       2     160 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.6e-07
                                    S-E.EEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG----S-EEEEEE..ESSGGG CS
                           TehB  31 pgk.vldlgcgqgrnslylsllgydvtawdknensiafleeikekenlknistalydineaklderydfils..tvvlmf 107
                                    p k vld+gcg g  ++ l   gy    +d  +n ++ + + k +e ++n++  l d  ++ ++ ++d  ++   vv  f
  gi|119720100|ref|YP_920595.1|  38 PVKsVLDVGCGTGLHTIELGRRGYRAVGVDISQNMLE-VARSKARE-MTNVEFILSDATKLGFNSEFDAAIAmyGVVSYF 115
                                    44438*************************9988775.55666666.555999***************87652279**** PP

                                    S-GGGHHHHHHHHHHTEEEEE CS
                           TehB 108 leaeripsiienmqectkvgg 128
                                    ++ e++   ++ +++  k+g 
  gi|119720100|ref|YP_920595.1| 116 VDDESLLGFLRSVRRAIKPGS 136
                                    **************9999996 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   2.3e-07   0.00016      30     101 ..      34     105 ..      14     107 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2.3e-07
                                    C...TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEE CS
                            MTS  30 e...lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkfdli 101
                                          ++vlD+GcG+G+ +++l ++  +   + vd++ + le+a+  +++   +ve++ sd+++   + +fd+ 
  gi|119720100|ref|YP_920595.1|  34 YsliPVKSVLDVGCGTGLHTIELGRRGYR--AVGVDISQNMLEVARSKAREMT-NVEFILSDATKLGFNSEFDAA 105
                                    35555578*****************9888..79*************9887655.79******9998888888875 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   2.9e-07   0.00021      52     166 ..      28     142 ..      20     155 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.9e-07
                                    HHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG..-----S CS
                           CMAS  52 dlileklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyed..ldekvd 129
                                    +++++  +l p + +Ld+GcG G  +++  +r + + vg+ +S++  ++a+ +  e+    +ve  l+d     ++ ++d
  gi|119720100|ref|YP_920595.1|  28 ERVFRDYSLIPVKSVLDVGCGTGLHTIELGRR-GYRAVGVDISQNMLEVARSKAREMT---NVEFILSDATKlgFNSEFD 103
                                    56677778889999**************9999.******************9998887...5666666665512677999 PP

                                    EEEEE.S-GGGT.SGGGHHHHHHHHHHHS-TT-EEEEEE CS
                           CMAS 130 rvvsv.gafehv.gkenydtffkklkkllkedGllllht 166
                                    + +++ g++  +   e++  f + + +++k++ +++  t
  gi|119720100|ref|YP_920595.1| 104 AAIAMyGVVSYFvDDESLLGFLRSVRRAIKPGSVFVFDT 142
                                    755432777765377889999999999999999888766 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   3.6e-07   0.00026      71     137 ..      36      98 ..      18     109 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 3.6e-07
                                    --TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGG.TT CS
                           PCMT  71 lkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrk.Gy 137
                                    l ++++vL+vG+G+G +t  l    ++  r+v+++ ++++ e a+ + +  +++nv ++ +D +k G+
  gi|119720100|ref|YP_920595.1|  36 LIPVKSVLDVGCGTGLHTIEL---GRRGYRAVGVDISQNMLEVARSKAR--EMTNVEFILSDATKlGF 98 
                                    78999************9755...5677899***********9998655..67899999999764266 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.8e-06    0.0013      20      93 ..      28     101 ..      23     119 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.8e-06
                                    HHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTTTCCCEEEE-S-CCGHHHHHH CS
                         RrnaAD  20 neIldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkklskdeklkvvhqDflkfetpee 93 
                                    +++++   l + + vl++g G+G+ T eL  r    v + + ++++++ + k ++ ++++ +  D+ k  + +e
  gi|119720100|ref|YP_920595.1|  28 ERVFRDYSLIPVKSVLDVGCGTGLHTIELGRRGYRAVGVDISQNMLEVARSKAREMTNVEFILSDATKLGFNSE 101
                                    56677777888899****************************************************99988875 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   2.3e-06    0.0017     105     224 ..      28     147 ..      20     166 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.3e-06
                                    HHHGGGS.--TT-EEEEET-TTSHHHHHHHHCT-SEEEEE---HHHHHHHHHHHCCTTTTSSEEEE---GGGS-T---EE CS
                 Methyltransf_9 105 drvlphlsdlkgrtildvGcgnGyhlwrmvgegaklvvGidPselfliqfeavrkllgedqrahllplgieqlpeleafd 184
                                    +rv +  s +  +++ldvGcg+G h    +g+    +vG+d s+  l   ++  +    ++ ++ l     +l   + fd
  gi|119720100|ref|YP_920595.1|  28 ERVFRDYSLIPVKSVLDVGCGTGLHTIE-LGRRGYRAVGVDISQNMLEVARSKARE--MTNVEFIL-SDATKLGFNSEFD 103
                                    5777778888899************997.68888999*****99988655443333..34455555.4566777788888 PP

                                    EEEEE.S-G.GG..-S-HHHHHHHHHCTEEEEEEEEEEEE-BSS CS
                 Methyltransf_9 185 tvfsm.Gvl.yh..rrsPldhllqlkdqlvkgGelvletlvieG 224
                                    +  +m Gv+ y    +s l  l+ ++ +++ g  +v++t  + G
  gi|119720100|ref|YP_920595.1| 104 AAIAMyGVVsYFvdDESLLGFLRSVRRAIKPGSVFVFDTWSLVG 147
                                    87777666533322567888888888888888888888766655 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   5.7e-06    0.0041       4      63 ..      41      96 ..      39     108 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.7e-06
                                   EEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCCH CS
                 Methyltransf_4  4 vvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgdalkv 63
                                    vl++GcG G ++++l  +      +G++i++++++ +  + +a+e++N++ + +da+k+
  gi|119720100|ref|YP_920595.1| 41 SVLDVGCGTGLHTIELGRRG--YRAVGVDISQNMLEVA--RSKAREMTNVEFILSDATKL 96
                                   689**************985..789*********9965..5667789**********764 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   6.6e-06    0.0047      51     164 ..      27     139 ..       4     152 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 6.6e-06
                                    HHHHHHSS-GGG-SEEEEET-TTSHHHHHHHHH-TT-EEEEEE-HH.HHHHHHHHS-----TTEEEEES-TTTS---.-- CS
                 Methyltransf_2  51 akkvleafdleglkslvDvGGGtGalakaivsayPtikvivfDlpe.VveaAkehlsageeervefvgGdffkdslP.ea 128
                                     ++v++ + l ++ks++DvG GtG    +  +   + +++  D+++   e A+++  a e ++vef+  d  k     e 
  gi|119720100|ref|YP_920595.1|  27 LERVFRDYSLIPVKSVLDVGCGTGLHTIELGRR--GYRAVGVDISQnMLEVARSK--AREMTNVEFILSDATKLGFNsEF 102
                                    4789999*****************988888775..67888889986266778877..9999*********9987776666 PP

                                    SE.EEEES.SGGGS-HHHHHHHHHHHHHH--TT-EEEE CS
                 Methyltransf_2 129 Da.illkr.vlhDwsdekcvklLkrvkkalpagGkviv 164
                                    Da i +   v +  +de+   +L+ v++a+++g  v v
  gi|119720100|ref|YP_920595.1| 103 DAaIAMYGvVSYFVDDESLLGFLRSVRRAIKPG-SVFV 139
                                    752445551556678889999*********985.5555 PP

>> TPMT  Thiopurine S-methyltransferase (TPMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0     7e-06     0.005      26      84 ..      27      85 ..      19     117 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 7e-06
                                   HHHHHHT.T-S--EEEEEET-TT-HHHHHH-BTTEEEEEE-S-HHHHHHHHHHHTTSGG CS
                           TPMT 26 lkkfldalkakaglrvlvPlCGkaldlvwlAeqgrevvGvelselAvekffeeanlepk 84
                                   l + + + ++ + ++vl  +CG +l  + l  +g++ vGv++s++ +e + ++a ++ +
  gi|119720100|ref|YP_920595.1| 27 LERVFRDYSLIPVKSVLDVGCGTGLHTIELGRRGYRAVGVDISQNMLEVARSKAREMTN 85
                                   5666667777888899999**************************99987666665444 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0     1e-05    0.0075      11      84 ..      36     103 ..      28     114 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1e-05
                Methyltransf_18  11 lvekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGleklkeeevd 84 
                                    l++  ++v+D+G+  g+ +i+l ++g   +++ +Di+++ le a++++++    +++e++lsd  +   ++e+d
  gi|119720100|ref|YP_920595.1|  36 LIP-VKSVLDVGCGTGLHTIELGRRGY--RAVGVDISQNMLEVARSKAREM---TNVEFILSDATKLGFNSEFD 103
                                    555.6789**************98886..6*****************9985...57999999987765566655 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.3e-05    0.0094     161     205 ..      38      81 ..      23     141 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.3e-05
                           PrmA 161 egeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNae 205
                                    + ++vlDvG+G+G+ +i   + g  ++v+vDi +  ++va++ a+
  gi|119720100|ref|YP_920595.1|  38 PVKSVLDVGCGTGLHTIELGRRGY-RAVGVDISQNMLEVARSKAR 81 
                                    4579************99888886.678************98764 PP

>> AdoMet_MTase  Predicted AdoMet-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0     2e-05     0.014      57      91 ..      37      71 ..      14      89 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2e-05
                   AdoMet_MTase 57 eketsfvdvgcgngllvyvlaaegykgygidlrkr 91
                                      +s  dvgcg gl    l   gy+  g+d+ + 
  gi|119720100|ref|YP_920595.1| 37 IPVKSVLDVGCGTGLHTIELGRRGYRAVGVDISQN 71
                                   4568999************************9765 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.0   1.9e-05     0.014      12      76 ..      30      99 ..      27     248 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.9e-05
                                   HHHHHT-S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEES.SSS........HHHTTEEEECS-CCCSSHH CS
                           FtsJ 12 idekfklfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDl.qpm........aplpgvttiqgditdpeti 76
                                   +   ++l+ p+k v+D+g+++G  +  l +r g   + v+vD+ q+m        + + +v++i  d t+    
  gi|119720100|ref|YP_920595.1| 30 VFRDYSLI-PVKSVLDVGCGTGLHTIELGRR-G--YRAVGVDIsQNMlevarskaREMTNVEFILSDATKLGFN 99
                                   56677755.999*******************.5..79******8888999998665669*****9999886555 PP

>> N2227  N2227-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0    0.0032       2.3      60      92 ..      41      73 ..      24      78 .. 0.85
   2 ?    4.5   0.0     0.023        16     146     200 ..      85     139 ..      74     237 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0032
                                   EEEEET-TT-HHHHHHHHTT-EEEEEE--HHHH CS
                          N2227 60 kilvPGaGlGrlavelatkgyqvegnEfsyfml 92
                                   ++l  G+G+G  ++el + gy++ g+++s  ml
  gi|119720100|ref|YP_920595.1| 41 SVLDVGCGTGLHTIELGRRGYRAVGVDISQNML 73
                                   56777*************************998 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.023
                                    -EEEEES-HHHHH--SSHTT-EEEEEEE.....S-TTSSS-HHHHHHHHHHHEEEEEEEE CS
                          N2227 146 nlsmaagdflevykeeeaaesydvvvtc.....fFiDtaeNvleYletiekvlkpgglwi 200
                                    n++  + d +++  ++    ++d+ + +     +F+D  e +l +l+++ +  kpg++++
  gi|119720100|ref|YP_920595.1|  85 NVEFILSDATKLGFNS----EFDAAIAMygvvsYFVDD-ESLLGFLRSVRRAIKPGSVFV 139
                                    4444444444444433....44443322233349**95.789**************9665 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   4.2e-05      0.03      12      75 ..      26      84 ..      17     100 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.2e-05
                Methyltransf_32 12 lvakllkelakesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklg 75
                                   ++++++++  +  + ++v+DvG+G g  +  l       +++ vg+d+++++ e a+  a+++ 
  gi|119720100|ref|YP_920595.1| 26 FLERVFRD-YSLIPVKSVLDVGCGTGLHTIELGR----RGYRAVGVDISQNMLEVARSKAREMT 84
                                   55566666.35556789*********99999999....59******************999987 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   8.9e-05     0.064       2      60 ..      40      95 ..      39     173 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.9e-05
                Methyltransf_15  2 rvilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfe 60
                                   + +lD+ +G+G  +i++ + + + ++++i+++ l++a   a+      ++ ++l d ++
  gi|119720100|ref|YP_920595.1| 40 KSVLDVGCGTGLHTIELGRRGYRAVGVDISQNMLEVARSKAREM---TNVEFILSDATK 95
                                   579*****************99***************9999876...778888887776 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00016      0.11      12     106 ..      38     132 ..      29     146 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00016
                           MetW  12 kpgsrvldlGcGdGellellkeekqvdgrGleldeeg..vaecvakGlsviqgdldkdlenfedksfdyvvlsqtlqatr 89 
                                    +    vld+GcG G     l  +++ ++ G++++++   va++ a+ ++ ++  l +  +   +++fd ++    + +  
  gi|119720100|ref|YP_920595.1|  38 PV-KSVLDVGCGTGLHTIEL-GRRGYRAVGVDISQNMleVARSKAREMTNVEFILSDATKLGFNSEFDAAIAMYGVVSYF 115
                                    44.459********665555.6799******9999862266677777776666666666666666777777666666655 PP

                           MetW  90 npkevldellrigrrai 106
                                      +e l   lr  rrai
  gi|119720100|ref|YP_920595.1| 116 VDDESLLGFLRSVRRAI 132
                                    55555556666666655 PP

>> MethyltransfD12  D12 class N6 adenine-specific DNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00018      0.13      21      85 ..      39     105 ..      23     187 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00018
                                    -SEEEETT-TTSCCHHCS...SSCEEEEES-HHHHHHHHHHCCH..SHHHHHHHHH.TCTTGGC.TS CS
                MethyltransfD12  21 gktfvepFaGggaVffeakkqgkkvlinDinedlinlykalikn..nveelikelekllekeelene 85 
                                    +k + ++ +G+g  ++e+ ++g++++  Di +    +++ + ++  nve ++++++kl +++e++  
  gi|119720100|ref|YP_920595.1|  39 VKSVLDVGCGTGLHTIELGRRGYRAVGVDISQNMLEVARSKAREmtNVEFILSDATKLGFNSEFDAA 105
                                    46788999*******************************999989*************999998655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              25  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1539.15
//
Query:       gi|119720101|ref|YP_920596.1|  [L=270]
Description: LmbE family protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.2e-30  104.1   0.0    1.2e-29  103.6   0.0    1.3  1  PIG-L           GlcNAc-PI de-N-acetylase
     0.0052   16.8   0.1      0.009   16.0   0.1    1.4  1  Glyco_transf_4  Glycosyltransferase Family 4


Domain annotation for each model (and alignments):
>> PIG-L  GlcNAc-PI de-N-acetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.6   0.0   1.4e-33   1.2e-29       1     130 [.      45     171 ..      45     172 .. 0.95

  Alignments for each domain:
  == domain 1  score: 103.6 bits;  conditional E-value: 1.4e-33
                                    EEEESSTTHHHHHHHHHHHHHHHTT-EEEEEECE--TT---STTTTHH-HHHHHHHHHHHHHHHHCTE..EEEEECCCBT CS
                          PIG-L   1 llvlAHpDDellfaggtiaklvaagvevkivcltaGdagsplatleekeelaeiRekEaraaakhlgvadedvffldfpD 80 
                                    l+v +HpDD +++aggt+a+l+++g++v++++lt+G++g+++   + + elaeiR+kE ++aa+++gv  e+v++l++pD
  gi|119720101|ref|YP_920596.1|  45 LCVGPHPDDCEYGAGGTLAYLARSGKRVVYLILTDGSKGTTSPGVDPR-ELAEIRRKEQEEAARIIGV--EKVIWLGYPD 121
                                    789************************************877777766.*******************..********** PP

                                    T-STTS-CHHHHHHHHHHHHHH--SEEEEE-TTTT..H-HHHHHHHHHHHHH CS
                          PIG-L  81 gslesydedellddlaklieryrPdvvltldpegd..dhpDHtavasaavaa 130
                                    ++l +  + e+++ + ++i++ rPdvv+ +dp      hpDH++ + +a++a
  gi|119720101|ref|YP_920596.1| 122 TELPY--TPEARNSVIRVIREERPDVVFSPDPWLLyeAHPDHRVGGLLAAEA 171
                                    *****..************************9988889******99999887 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1     1e-06     0.009      14      88 ..      64     158 ..      60     198 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1e-06
                 Glyco_transf_4  14 aLarrGheVtvv..........tpgddgpleeev..................elvvrvprvplpllkrllrslaflrrlr 65 
                                    +Lar G +V+ +          +pg        v                  + +v+ + +   ++  l++++ ++ ++ 
  gi|119720101|ref|YP_920596.1|  64 YLARSGKRVVYLiltdgskgttSPG--------VdprelaeirrkeqeeaarIIGVEKVIWLGYPDTELPYTPEARNSVI 135
                                    7888888887777755544444444........33344444588888888777777777777788888999999****** PP

                 Glyco_transf_4  66 rllkrekpDvvHahspaalgaal 88 
                                    r++++e+pDvv + +p+ l+ a+
  gi|119720101|ref|YP_920596.1| 136 RVIREERPDVVFSPDPWLLYEAH 158
                                    ***********999888776554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1821.07
//
Query:       gi|119720102|ref|YP_920597.1|  [L=455]
Description: amino acid permease-associated region [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-51  176.2  29.7    1.2e-51  175.9  29.7    1.1  1  AA_permease_2  Amino acid permease
    5.8e-29  101.0  30.3    1.2e-28  100.0  30.3    1.4  1  AA_permease    Amino acid permease
  ------ inclusion threshold ------
       0.13   12.0   0.0       0.25   11.1   0.0    1.4  1  RVP_2          Retroviral aspartyl protease


Domain annotation for each model (and alignments):
>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.9  29.7   2.1e-55   1.2e-51       8     398 ..      15     412 ..      10     440 .. 0.86

  Alignments for each domain:
  == domain 1  score: 175.9 bits;  conditional E-value: 2.1e-55
                  AA_permease_2   8 alvigsv.igsgifvkn..laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkkvaflsawfn 84 
                                    a+++g + +g+gi+++   +aa++gpa+ l + +a++ + l  +l yaEls+a p  gG  v++ +afg+++af+++w++
  gi|119720102|ref|YP_920597.1|  15 AFSFGYAdVGAGIYMTLglVAAYAGPATPLAFAVASVSY-LFTALSYAELSAAYPEAGGGMVFADRAFGRLAAFIAGWSL 93 
                                    56777777899999999989999****************.89********999*************************** PP

                  AA_permease_2  85 wfayvpvlasilsvaasyllnalgpdlqgntwltyliaiaililvalinirgikesakiqnilgilkillpliiliilgl 164
                                    +++yv++ ++ + + ++yl +++ p l + + ++  +a++++ +++++ni+gi+esa + + l++l i ++ +i+  +g+
  gi|119720102|ref|YP_920597.1|  94 LLDYVVTGSIFALSTTGYLGHLF-PLL-KRDEFFGPVAALLVFFLVVLNILGIRESAAFSSALVLLDIAGLSVIMG-IGY 170
                                    ********88889999***9976.766.455688999*******************************98877777.888 PP

                  AA_permease_2 165 itvdgggfsslstetdtffpn.gwpgvllgllivlwsfdGfesaanvseevkk..kdvpkaifigllivlvlyllvniaf 241
                                    +t  +  f+     + +   n  w++++ g + ++ s+ G+e++++ +ee ++  +++p+a  ++ ++v+++ ll++ ++
  gi|119720102|ref|YP_920597.1| 171 LTSFKPFFD-----KVNLGVNpDWQSFMYGSTLAMASYLGIEVISQTAEETRRagATIPRAVKLVSVVVIFFALLFSTLA 245
                                    886555665.....4444444489999999999*****************9987779*********************** PP

                  AA_permease_2 242 lgvvpddeianlsnlgsvaalffeavg.gkvvaiivvilialsllgaintavigssrvlealardgvlPrffakvn.kfg 319
                                    +g v+++ +a ++   ++aa+++e +  g+v+a  v+++++ ++  a nt ++g+sr+++a++r+g+lPr++   + +f+
  gi|119720102|ref|YP_920597.1| 246 VGTVGWEVLAASQK--DPAAVVAEHLPyGSVLALWVSVIGMTVCYAATNTGIVGVSRMVYAMGREGMLPRWLTELHgRFK 323
                                    *********99887..67999999998578************************************************** PP

                  AA_permease_2 320 spiraiiltaivslillllfllassaaynfllsvsslgliisyllliigalilrkkrphlkrpgk............... 384
                                    +p+rai+++a+++l+l+  + +     + + ++++++g+++sy+++ +++l lr+k ph+ rp+k               
  gi|119720102|ref|YP_920597.1| 324 TPYRAIVVFAVIQLLLA--Y-V---GHLGLAADLYNFGALLSYMVVNLSVLALRVKDPHRYRPYKvpgnvplrvggrkvy 397
                                    *************5543..3.2...3699*********************************888677777777777655 PP

                  AA_permease_2 385 .ilvaiigalfllfl 398
                                     +l a +g+l++l +
  gi|119720102|ref|YP_920597.1| 398 vPLGAVLGFLTNLAM 412
                                    333444445555554 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.0  30.3   1.9e-32   1.2e-28      11     422 ..      23     409 ..      20     446 .. 0.80

  Alignments for each domain:
  == domain 1  score: 100.0 bits;  conditional E-value: 1.9e-32
                    AA_permease  11 iGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviGlnylfswitvl 90 
                                    +G+g+++ lg v++ aGp ++ la+++a v +++++ls +e++ ++p++gg  ++a r  g+ ++f  G+++l+ ++++ 
  gi|119720102|ref|YP_920597.1|  23 VGAGIYMTLGLVAAYAGP-ATPLAFAVASVSYLFTALSYAELSAAYPEAGGGMVFADRAFGRLAAFIAGWSLLLDYVVTG 101
                                    69****************.999*************************************************777666665 PP

                    AA_permease  91 aleltaasiliqfwelvtdlpkawvt...gavflvvlliinlvgvkvygeaefilalikiiaiiafiivgiillaggkpn 167
                                     +       +++ +  ++ l   + +   +a+++++l+++n++g++ +++++   al+++ ++   +i+gi +l++ kp 
  gi|119720102|ref|YP_920597.1| 102 SIFALSTTGYLGHL--FPLLKRDEFFgpvAALLVFFLVVLNILGIRESAAFS--SALVLLDIAGLSVIMGIGYLTSFKPF 177
                                    55444444445555..566665555566799999999999999999999944..45555555566677778899999876 PP

                    AA_permease 168 kgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiagEvkdPeksiPkailqvviritifY 247
                                     +      + n++     + p+         ++f+++   ++ ++ Gie +  +a+E++    +iP+a++ v + +++f 
  gi|119720102|ref|YP_920597.1| 178 FD------KVNLG-----VNPD--------WQSFMYGSTLAMASYLGIEVISQTAEETRRAGATIPRAVKLVSVVVIFFA 238
                                    66......66666.....6788........99************************************************ PP

                    AA_permease 248 vlsllligllvprndlgllndsasaaspfvifikesgvsvlaplinaviltaalssansslysasRvlyslakdglaP.k 326
                                    +l++ l++ +v++  l   ++        v++ +    svla  + ++  t ++ + n +++  sR++y++ ++g++P +
  gi|119720102|ref|YP_920597.1| 239 LLFSTLAVGTVGWEVLAASQKDP----AAVVAEHLPYGSVLALWVSVIGMTVCYAATNTGIVGVSRMVYAMGREGMLPrW 314
                                    ***************77777444....55788888888999999999999****************************55 PP

                    AA_permease 327 vlkkvskrgvPlraillsmiisllalllaslnlaapivfnfllaisaliglivwlliilsylrfRkalkyqgrsieelgf 406
                                      + +++ + P+rai+++++i ll+  +  l laa+     +l ++++++l+v+ l      r+R+ +   +  + ++g 
  gi|119720102|ref|YP_920597.1| 315 LTELHGRFKTPYRAIVVFAVIQLLLAYVGHLGLAADLYNFGALLSYMVVNLSVLALRVKDPHRYRPYKVPGNVPL-RVGG 393
                                    55678899******************9999999966666667777788888777777666666666533333322.4444 PP

                    AA_permease 407 kaallplgvilvlaal 422
                                    +  ++plg++l+++ +
  gi|119720102|ref|YP_920597.1| 394 RKVYVPLGAVLGFLTN 409
                                    4444444444444444 PP

>> RVP_2  Retroviral aspartyl protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   4.2e-05      0.25      90     123 ..     147     180 ..     136     186 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.2e-05
                          RVP_2  90 giefladlilLdlkdlDviLgmdWLsknkanidc 123
                                    +  f + l+lLd+  l vi+g+ +L+++k   d 
  gi|119720102|ref|YP_920597.1| 147 SAAFSSALVLLDIAGLSVIMGIGYLTSFKPFFDK 180
                                    568999**********************987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (455 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 3292.98
//
Query:       gi|119720103|ref|YP_920598.1|  [L=247]
Description: MscS mechanosensitive ion channel [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.8e-26   92.3   0.0      4e-26   91.9   0.0    1.1  1  MS_channel  Mechanosensitive ion channel


Domain annotation for each model (and alignments):
>> MS_channel  Mechanosensitive ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.9   0.0   2.2e-30     4e-26       7     200 ..      56     243 ..      52     246 .. 0.91

  Alignments for each domain:
  == domain 1  score: 91.9 bits;  conditional E-value: 2.2e-30
                                    HHHHHHHHHHHHTTT--SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESSSEEEEEEEE-SSEEEE CS
                     MS_channel   7 liivvgilivlsllgvnvsallavlGalglalglalkdlisnlvaGiillfekpfkiGDlveigdieGtVediglrttki 86 
                                    +i+vvg+l+ l+ll+  + ++l+  ++lg+ + l+lkd++ +++a  +l + kpf++GD++++gd  G+V+d++ + t +
  gi|119720103|ref|YP_920598.1|  56 TIYVVGLLVSLELLNLRLETVLVFTALLGALVILGLKDVLPSIFARQFLEMYKPFRVGDWIRVGDTCGRVIDVNDLYTVV 135
                                    699***************************************************************************** PP

                                    EETTSEEEEEEHHHHHTS-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-TTB-TTS-EEEEEEEE-SS CS
                     MS_channel  87 rtfdgrivtiPnsslvtsnieNlsresgtrrikvsigvtyssdvkklekvleelkealkekpevlkdkellvvldefgds 166
                                     t + + ++iPns l+++ + Nl+   ++  ++v++    s+    l+++l+++k a++e+ + +  +e++ ++  ++ +
  gi|119720103|ref|YP_920598.1| 136 FTSSHEKLYIPNSRLLQERVYNLTA-GTGFYVDVDFAASPSEG---LDQLLRKVKGAIEEEAKEEGLEEPEIFVVGLEPD 211
                                    *************************.67777777776666666...9999999999999998888888888888888888 PP

                                    SEEEEEEEEEET...TTHHHHHHHHHHHHHHHHH CS
                     MS_channel 167 slnfevrvfvktvvpeeylsvqseinlrikkile 200
                                    ++ ++vrv v +  p+++ +v+s + +r+ k+++
  gi|119720103|ref|YP_920598.1| 212 AVYLRVRVRVLN--PQRKDEVRSRLLRRVYKAVR 243
                                    888888888888..88************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       745  (0.0415528); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1570.63
//
Query:       gi|119720104|ref|YP_920599.1|  [L=214]
Description: TrkA domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.6e-29  100.5   1.9    1.1e-28   99.8   0.6    1.8  2  TrkA_N           TrkA-N domain
    8.9e-15   54.3   2.6    2.4e-14   52.9   1.5    2.2  2  TrkA_C           TrkA-C domain
    1.1e-05   25.8   1.8    1.3e-05   25.6   0.6    1.7  2  NAD_binding_7    Putative NAD(P)-binding
    5.6e-05   23.6   0.8    5.6e-05   23.6   0.8    2.3  2  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
    0.00015   21.7   1.1    0.00025   21.0   0.1    1.9  2  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
    0.00026   20.4   0.1    0.00031   20.1   0.1    1.3  1  FAD_binding_3    FAD binding domain
    0.00032   20.4   0.7    0.00078   19.1   0.3    1.7  2  DAO              FAD dependent oxidoreductase
    0.00053   20.5   0.3     0.0027   18.2   0.1    2.2  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    0.00095   19.4   0.2     0.0023   18.1   0.2    1.7  1  NAD_binding_8    NAD(P)-binding Rossmann-like domain
    0.00099   18.7   1.2     0.0044   16.6   0.5    2.1  2  NmrA             NmrA-like family
     0.0011   18.2   0.3     0.0018   17.6   0.3    1.5  1  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
     0.0018   18.2   1.9      0.066   13.1   0.6    2.3  2  NAD_binding_10   NAD(P)H-binding
     0.0032   17.4   0.0     0.0055   16.7   0.0    1.5  1  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
     0.0066   16.1   0.3      0.013   15.1   0.3    1.6  1  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
     0.0089   14.8   0.1      0.012   14.3   0.1    1.2  1  HI0933_like      HI0933-like protein
       0.01   15.9   0.1       0.02   15.0   0.1    1.5  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
  ------ inclusion threshold ------
       0.01   16.1   0.5      0.022   15.0   0.5    1.7  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
      0.011   14.8   0.2       0.02   14.0   0.2    1.3  1  FAD_binding_2    FAD binding domain
      0.048   13.5   0.3       0.46   10.4   0.0    2.4  3  LpxI_N           LpxI N-terminal domain
       0.05   13.8   0.2       0.19   11.9   0.0    2.0  2  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
      0.051   14.1   1.1       0.41   11.1   0.2    2.4  2  CoA_binding_2    CoA binding domain
      0.059   13.4   5.3       0.23   11.4   0.5    2.6  3  ADH_zinc_N       Zinc-binding dehydrogenase
      0.067   13.3   0.0       0.11   12.5   0.0    1.3  1  NUC202           NUC202 domain


Domain annotation for each model (and alignments):
>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.8   0.6   1.4e-31   1.1e-28       1     115 [.       3     118 ..       3     119 .. 0.97
   2 ?   -0.8   0.0       2.2   1.7e+03      15      36 ..     163     184 ..     158     198 .. 0.63

  Alignments for each domain:
  == domain 1  score: 99.8 bits;  conditional E-value: 1.4e-31
                                    EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTT.SEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHHHH CS
                         TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeg.levvvgdatdeevLeeagiekadaviaatgddeanila 79 
                                    +++iG GrvG+s+ae +s++g++vvv++k+e+++ el+    ++v++gda +  +Leeag++kad++ a+ g+d  ni +
  gi|119720104|ref|YP_920599.1|   3 VAVIGGGRVGYSIAEFFSKRGDRVVVVEKNEKVCGELAGSLdVTVYCGDARSIRLLEEAGVNKADVLFAVSGSDSLNIRV 82 
                                    68*****************7778***************888899************************************ PP

                                    HHHHHHHTSSSEEEEEESSGGGHHHHHHHTTSEEEE CS
                         TrkA_N  80 vllakelnpkkkiiaraqdpehaellkklgadvvis 115
                                    + +ak+ ++ +++++r++++e++e++ + gad+vi 
  gi|119720104|ref|YP_920599.1|  83 ASVAKKRFGVPRVVVRVNHAENKEKAAQSGADEVIC 118
                                    **********************************95 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.2
                                    HHHHH.TTEEEEEEESSHHHHHH CS
                         TrkA_N  15 eeLse.ggkdvvvidkdeervee 36 
                                    +eL e g  +vv++ +d + ve 
  gi|119720104|ref|YP_920599.1| 163 RELVEkGL-KVVAVVRDGSLVEA 184
                                    44555233.47777776666655 PP

>> TrkA_C  TrkA-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       1.7   1.3e+03      49      56 ..      22      29 ..      11      37 .. 0.67
   2 !   52.9   1.5   3.1e-17   2.4e-14       1      66 [.     146     209 ..     146     213 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.7
                                   TT-EEEEE CS
                         TrkA_C 49 eGDvllvv 56
                                    GD+++vv
  gi|119720104|ref|YP_920599.1| 22 RGDRVVVV 29
                                   46666665 PP

  == domain 2  score: 52.9 bits;  conditional E-value: 3.1e-17
                                    CEEEEEE--GGGTTSBHHHHTHHHHS-EEEEEE-T-EEES--TT-B--TT-EEEEEEEHHHHHHHH CS
                         TrkA_C   1 lvevtvpagsplvGktlkelnlrargvlvvairRggeliipsgdtvLeeGDvllvvgspsdlaelr 66 
                                    +ve++v ++sp +Gk+l+e  l ++g  vva++R+g l+ +++d+vLe++D+l+++g  ++++e r
  gi|119720104|ref|YP_920599.1| 146 VVEIRVLPDSPAIGKPLRE--LVEKGLKVVAVVRDGSLVEAGEDLVLEADDRLVLAGREEAINETR 209
                                    79*****************..*****************************************9987 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.6   1.6e-08   1.3e-05      10      85 ..       3      89 ..       2     110 .. 0.73
   2 ?   -2.4   0.0       8.4   6.5e+03      26      39 ..     165     178 ..     162     207 .. 0.57

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.6e-08
                  NAD_binding_7 10 vlvvGgGevAarkvrklleagakvtvvapev..keeleelvkla.....eeel....ekdlegadlviaatddrelneriae 80
                                   v v+GgG+v+++ ++ + + g +v+vv ++   + el + ++++      + +    e+ +++ad+++a+   ++ln r+a 
  gi|119720104|ref|YP_920599.1|  3 VAVIGGGRVGYSIAEFFSKRGDRVVVVEKNEkvCGELAGSLDVTvycgdARSIrlleEAGVNKADVLFAVSGSDSLNIRVAS 84
                                   68*************************998555666666666542222122223344566********************** PP

                  NAD_binding_7 81 aakar 85
                                    ak+r
  gi|119720104|ref|YP_920599.1| 85 VAKKR 89
                                   99863 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 8.4
                  NAD_binding_7  26 lleagakvtvvape 39 
                                    l+e+g kv+ v  +
  gi|119720104|ref|YP_920599.1| 165 LVEKGLKVVAVVRD 178
                                    55555555544433 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.8   7.2e-08   5.6e-05       2      35 ..       3      36 ..       3      47 .. 0.92
   2 ?   -0.9   0.0       3.2   2.5e+03       3      23 ..      71      92 ..      70     115 .. 0.70

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 7.2e-08
                                   EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                      Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                   v+v+GgG +g   A+++++ g++V vve ++k++
  gi|119720104|ref|YP_920599.1|  3 VAVIGGGRVGYSIAEFFSKRGDRVVVVEKNEKVC 36
                                   79*****************************998 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 3.2
                                   EEECSSHHHHHHHHHHHH.TTS CS
                      Pyr_redox  3 vvvGgGyiglElAgalae.lgk 23
                                   +v G++ +++ +A+++++ +g 
  gi|119720104|ref|YP_920599.1| 71 AVSGSDSLNIRVASVAKKrFGV 92
                                   5778888888899888664663 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.1   3.2e-07   0.00025       2      38 ..       3      39 ..       2      66 .. 0.90
   2 ?   -2.2   0.0       4.2   3.3e+03      19      47 ..     166     194 ..     162     211 .. 0.64

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 3.2e-07
                                   EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHH CS
                        3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseealeka 38
                                   vaviG G +G +ia+ f ++g +Vv+v+ +e+   + 
  gi|119720104|ref|YP_920599.1|  3 VAVIGGGRVGYSIAEFFSKRGDRVVVVEKNEKVCGEL 39
                                   9*****************************9987665 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 4.2
                                    HHTT-EEEEE-S-HHHHHHHHHHHHHHHH CS
                        3HCDH_N  19 asagleVvlvdiseealekalekieksle 47 
                                    +++gl+Vv v ++ + +e++++ + +  +
  gi|119720104|ref|YP_920599.1| 166 VEKGLKVVAVVRDGSLVEAGEDLVLEADD 194
                                    56677777777776666666665555444 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.1     4e-07   0.00031       4      60 ..       3      65 ..       1     123 [. 0.83

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 4e-07
                                   EEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSS......S--EEEHHHHHHHHHTT-HH CS
                  FAD_binding_3  4 VlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlp......radglnqrtmellrqlGled 60
                                   V+++G+G +G + a + s++G rvv+vek ++   +            + r+++ll+++G+ +
  gi|119720104|ref|YP_920599.1|  3 VAVIGGGRVGYSIAEFFSKRGDRVVVVEKNEKVCGELagsldvTVYCGDARSIRLLEEAGVNK 65
                                   99***************************9998776622222222234678888888888865 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.3     1e-06   0.00078       2      33 ..       3      36 ..       3      43 .. 0.91
   2 ?   -1.0   0.0       1.3     1e+03     234     264 ..     153     182 ..      77     212 .. 0.60

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1e-06
                                   EEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                            DAO  2 vviiGGGiiGlstAyeLarrg..Vtllekgdiag 33
                                   v++iGGG +G s+A + ++rg  V+++ek++ ++
  gi|119720104|ref|YP_920599.1|  3 VAVIGGGRVGYSIAEFFSKRGdrVVVVEKNEKVC 36
                                   89******************99*******97665 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.3
                                    STGSGCSEEEEEEEETTTTEEEEEETTSEEE CS
                            DAO 234 lvspaailpvpetdddgrgvyvtprkdgrvl 264
                                    ++spa + p++e ++ g  v ++ r dg+++
  gi|119720104|ref|YP_920599.1| 153 PDSPAIGKPLRELVEKGLKVVAVVR-DGSLV 182
                                    3345555555555555555555555.34443 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   3.5e-06    0.0027       2      50 ..       3      47 ..       2      73 .. 0.81
   2 ?   -0.3   0.0       2.1   1.6e+03      20      39 ..      60      78 ..      52     119 .. 0.45

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.5e-06
                                   EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EE CS
                  F420_oxidored  2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkv 50
                                   +++iG+G++g ++a+ ++++g     +vv+ ++n++   ela +l v+v
  gi|119720104|ref|YP_920599.1|  3 VAVIGGGRVGYSIAEFFSKRG---DRVVVV-EKNEKVCGELAGSLDVTV 47
                                   79*******************...****88.*****9999999998554 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 2.1
                                   HTTS-GGCEEEEEESSCCCH CS
                  F420_oxidored 20 aagaqpheivvansrnpeka 39
                                   +ag+++ ++++a s   +++
  gi|119720104|ref|YP_920599.1| 60 EAGVNKADVLFAVSG-SDSL 78
                                   566666666666333.2222 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.2     3e-06    0.0023       1      36 [.       5      40 ..       5      57 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 3e-06
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG- CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraa 36
                                   ++G+G  G ++A + +k+g +v+++ek+++++G +a
  gi|119720104|ref|YP_920599.1|  5 VIGGGRVGYSIAEFFSKRGDRVVVVEKNEKVCGELA 40
                                   8******************************99765 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.5   5.7e-06    0.0044       1      98 [.       3      96 ..       3     113 .. 0.78
   2 ?   -0.3   0.0      0.85   6.6e+02      16      32 ..     163     179 ..     157     193 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.7e-06
                                   EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEE.ES-TT-HHHHHHH.HTT-SEEEE---GGS-HHH CS
                           NmrA  1 IlviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelv.kgdlddkeslvea.lkgvdvvfsvtgfyskeie 80
                                   ++viG+ Gr G s+++++ k+g +v ++  + ++++  +l+ +  ++v +gd+ +  +l+ea ++++dv f+v g  s+ ++
  gi|119720104|ref|YP_920599.1|  3 VAVIGG-GRVGYSIAEFFSKRGDRVVVV--EKNEKVCGELAGSLDVTVyCGDARSIRLLEEAgVNKADVLFAVSG--SDSLN 79
                                   678887.***************988665..5566778888877666666***********9989***********..66666 PP

                                   HHHHHHHHHHHHS-SEEE CS
                           NmrA 81 dgkklvdAakeaGvkhfi 98
                                   + ++ v A k+ Gv++++
  gi|119720104|ref|YP_920599.1| 80 IRVASV-AKKRFGVPRVV 96
                                   655444.45667788877 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.85
                                    HHHHHHT-EEEEEES-S CS
                           NmrA  16 rallkaghkvralvRdt 32 
                                    r l+++g kv a+vRd 
  gi|119720104|ref|YP_920599.1| 163 RELVEKGLKVVAVVRDG 179
                                    67889999*******96 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.3   2.3e-06    0.0018     145     178 ..       3      36 ..       2     118 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.3e-06
                                    EEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 145 ivvvGgGyiGvElAaalaklgkevtlveardrll 178
                                    ++v+GgG +G  +A +++k g++v++ve +++++
  gi|119720104|ref|YP_920599.1|   3 VAVIGGGRVGYSIAEFFSKRGDRVVVVEKNEKVC 36 
                                    6899999999999999999999999999888887 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.6   8.5e-05     0.066       3      95 ..       8      97 ..       7     135 .. 0.82
   2 ?    4.3   0.0     0.041        32      11      33 ..     162     183 ..     157     198 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.5e-05
                                   TSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCCHHHHHHHHHHH CS
                 NAD_binding_10  3 tGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsalggggkdeegaknivda 84
                                    G+vG  +++   +rg  +v+++  n++   el+ +  ++v  gd+ +   l+ea  +   V++a++g+++     ++++ +
  gi|119720104|ref|YP_920599.1|  8 GGRVGYSIAEFFSKRG-DRVVVVEKNEKVCGELAGSLDVTVYCGDARSIRLLEEAGVNKADVLFAVSGSDSL---NIRVASV 85
                                   59*************6.788888778888899**99*******************98888899999888764...5555555 PP

                                   HHH.CT--EEEE CS
                 NAD_binding_10 85 ake.agvkRfvl 95
                                   ak+  gv R+v+
  gi|119720104|ref|YP_920599.1| 86 AKKrFGVPRVVV 97
                                   544279999887 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.041
                                    HHHHHHC-T-EEEEEETTHHHCH CS
                 NAD_binding_10  11 vkellargghevtalvRnpekla 33 
                                    ++el+++ g++v+a+vR+ + ++
  gi|119720104|ref|YP_920599.1| 162 LRELVEK-GLKVVAVVRDGSLVE 183
                                    479****.5********987665 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   7.1e-06    0.0055       2      42 ..       3      43 ..       2      92 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 7.1e-06
                                   EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHHS CS
                 NAD_Gly3P_dh_N  2 iavlGaGswGtalAkvlaenghevrlwvreeelieeineeh 42
                                   +av+G+G  G ++A  ++++g +v++  ++e+++ e+  + 
  gi|119720104|ref|YP_920599.1|  3 VAVIGGGRVGYSIAEFFSKRGDRVVVVEKNEKVCGELAGSL 43
                                   8******************************9998887655 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.3   1.7e-05     0.013       1      39 [.       1      39 [.       1      56 [. 0.90

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.7e-05
                                   SEEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHH CS
                 UDPG_MGDP_dh_N  1 mkisviGlGYvGlvtaavlaeighevigvDideekvdkl 39
                                   m ++viG G vG   a  ++++g  v++v ++e+   +l
  gi|119720104|ref|YP_920599.1|  1 MFVAVIGGGRVGYSIAEFFSKRGDRVVVVEKNEKVCGEL 39
                                   5699****************************9866655 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.1   1.6e-05     0.012       3      36 ..       3      36 ..       1      53 [. 0.92

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.6e-05
                                   EEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                    HI0933_like  3 viviGgGaAGlmaAisaakrgkrVlllekakklg 36
                                   v+viGgG  G   A+  +krg rV+++ek++k+ 
  gi|119720104|ref|YP_920599.1|  3 VAVIGGGRVGYSIAEFFSKRGDRVVVVEKNEKVC 36
                                   89****************************9986 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   2.5e-05      0.02      15      96 ..       3      86 ..       2     124 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.5e-05
                                   EEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-..EEEEGCGHHHH.HHT-SEEEE-SSSSS-SB-HH CS
                   Shikimate_DH 15 vlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeei..ealkleelkel.laeadvvisataseepileke 93
                                   v +iG G+++  +a+ ++++g + vvv+  + +   ela +l+ + +   a+++  l+e+ +++adv+++  +s +  ++ +
  gi|119720104|ref|YP_920599.1|  3 VAVIGGGRVGYSIAEFFSKRGDR-VVVVEKNEKVCGELAGSLDVTVYcgDARSIRLLEEAgVNKADVLFAVSGSDSLNIRVA 83
                                   789***********999977766.****************9955533224666666665449********999999888877 PP

                                   HHH CS
                   Shikimate_DH 94 eve 96
                                   +v 
  gi|119720104|ref|YP_920599.1| 84 SVA 86
                                   776 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.5   2.8e-05     0.022       1      72 [.       3      68 ..       3     113 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.8e-05
                                   EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHH.HTTSSE CS
                Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaal.lkegdl 72
                                   v +iG+G+vG ++ae  ++++d   +++v++++++ + +la    + +++ +  da  ++  L+++ ++++d+
  gi|119720104|ref|YP_920599.1|  3 VAVIGGGRVGYSIAEFFSKRGD---RVVVVEKNEKVCGELA---GSLDVTVYCGDARSIRL-LEEAgVNKADV 68
                                   689******************9...7**********99998...56666666666666665.55554555555 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.2   2.6e-05      0.02       2      39 ..       3      40 ..       3      46 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.6e-05
                                   EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGG CS
                  FAD_binding_2  2 viViGsGlAGLaAAleaaeaGlkvavvekeqefggata 39
                                   v ViG+G  G++ A   +++G +v+vvek +++ g++a
  gi|119720104|ref|YP_920599.1|  3 VAVIGGGRVGYSIAEFFSKRGDRVVVVEKNEKVCGELA 40
                                   78****************************99887766 PP

>> LpxI_N  LpxI N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00059      0.46       7      68 ..       7      65 ..       3      71 .. 0.84
   2 ?    0.2   0.0      0.84   6.5e+02       6      43 ..      73     111 ..      68     128 .. 0.71
   3 ?   -2.4   0.0       5.2     4e+03      17      30 ..     163     176 ..     159     189 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00059
                         LpxI_N  7 GsGrlPllvaeaakaagrevvvvalegeadeelekivdevaevsvgqlgklikaLkregvte 68
                                   G+Gr    +ae   ++g +vvvv  ++++  el+   d  ++v  g+    i++L+++gv++
  gi|119720104|ref|YP_920599.1|  7 GGGRVGYSIAEFFSKRGDRVVVVEKNEKVCGELAGSLD--VTVYCGDAR-SIRLLEEAGVNK 65
                                   99*******************************99766..667777764.467888888776 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.84
                         LpxI_N   6 AGsGrlPllvaeaaka.agrevvvvalegeadeelekiv 43 
                                     Gs +l + va  ak+  g + vvv ++++ ++e ++++
  gi|119720104|ref|YP_920599.1|  73 SGSDSLNIRVASVAKKrFGVPRVVVRVNHAENKEKAAQS 111
                                    577778888999888856888888888876666655544 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 5.2
                         LpxI_N  17 eaakaagrevvvva 30 
                                    +++ ++g +vv+v 
  gi|119720104|ref|YP_920599.1| 163 RELVEKGLKVVAVV 176
                                    45666677776665 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00025      0.19       2      41 ..       3      42 ..       2      72 .. 0.87
   2 ?   -2.2   0.0       5.2     4e+03      17      66 ..     164     179 ..     157     194 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00025
                                   EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHT CS
                  NAD_binding_2  2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvae 41
                                   +++iG G  G ++a+ + k+g +v+v++ +++ + el+ +
  gi|119720104|ref|YP_920599.1|  3 VAVIGGGRVGYSIAEFFSKRGDRVVVVEKNEKVCGELAGS 42
                                   79****************************9999988765 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5.2
                                    HHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSH CS
                  NAD_binding_2  17 nllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkag 66 
                                    +l+++g kv+++ r+                                  g
  gi|119720104|ref|YP_920599.1| 164 ELVEKGLKVVAVVRD----------------------------------G 179
                                    444455554444443..................................3 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   0.00053      0.41       3     100 ..       3      88 ..       2     113 .. 0.78
   2 ?    0.9   0.0      0.81   6.3e+02      19      35 ..     161     177 ..     144     205 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00053
                                    EEEET--S-TTSHHHHHHHHHHHHT--EEEESSS-SEETTEES----T....T--EEEE-S-HHHHGGGHHHHHHH--SE CS
                  CoA_binding_2   3 iaVvGasdnpgkfgykvlryllehglpvvpVnpkeeeilgekvyaslaedpepvdlvdvftppeatpeivkealalgaka 82 
                                    +aV+G     g+ gy +++++ ++g +vv+V  k e+++g     +la   + +d v+v+   ++   +++ea+  +a +
  gi|119720104|ref|YP_920599.1|   3 VAVIG----GGRVGYSIAEFFSKRGDRVVVV-EKNEKVCG-----ELA---GSLD-VTVYCGDARSIRLLEEAGVNKADV 68 
                                    67888....79**************777777.67788888.....455...3344.788888899999999998888888 PP

                                    EEE-TT..---HHHHHHHHH CS
                  CoA_binding_2  83 vwlqpg..sedeeaaelaee 100
                                    +   +g  s +  +a++a++
  gi|119720104|ref|YP_920599.1|  69 LFAVSGsdSLNIRVASVAKK 88 
                                    88888866566666666665 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.81
                                    HHHHHHHHT--EEEESS CS
                  CoA_binding_2  19 vlryllehglpvvpVnp 35 
                                     lr l+e+gl+vv+V  
  gi|119720104|ref|YP_920599.1| 161 PLRELVEKGLKVVAVVR 177
                                    46667777777777744 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.3     0.039        31      14      73 ..      23      79 ..      11      89 .. 0.72
   2 ?   11.4   0.5   0.00029      0.23       9      67 ..      85     143 ..      80     152 .. 0.73
   3 ?   -1.9   0.0       3.9     3e+03      14      25 ..     169     180 ..     158     208 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.039
                                   T-EEEEEESSHHHH.HHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHHH CS
                     ADH_zinc_N 14 Gaeviavdsseekl.elakklGadevinykeadlverikeltggegvdvvfecvGsgatle 73
                                   G +v++v  +e+ + ela +l ++++        + r+ e  g +++dv f ++G  ++l+
  gi|119720104|ref|YP_920599.1| 23 GDRVVVVEKNEKVCgELAGSLDVTVYCGD---ARSIRLLEEAGVNKADVLFAVSG-SDSLN 79
                                   55888888888744688888988888888...5677788888899**********.55544 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00029
                                    HHH.HTT-.EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSC CS
                     ADH_zinc_N   9 lAk.alGa.eviavdsseeklelakklGadevinykeadlverikeltggegvdvvfecvG 67 
                                    +Ak  +G+ +v++ +  +e+ e+a++ Gadevi  +e   +  +++ t + ++ v f + G
  gi|119720104|ref|YP_920599.1|  85 VAKkRFGVpRVVVRVNHAENKEKAAQSGADEVICLDE-VAELFVRAVT-EVDYRVLFKHGG 143
                                    566689*******88999999************8855.3333344444.445666666655 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 3.9
                                    T-EEEEEESSHH CS
                     ADH_zinc_N  14 Gaeviavdssee 25 
                                    G +v+av+++ +
  gi|119720104|ref|YP_920599.1| 169 GLKVVAVVRDGS 180
                                    567777776655 PP

>> NUC202  NUC202 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00015      0.11      18      43 ..      34      59 ..      21      69 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00015
                         NUC202 18 ltCGasegsLqvsafsseaLltaLls 43
                                   ++CG  +gsL+v  ++++a  + Ll 
  gi|119720104|ref|YP_920599.1| 34 KVCGELAGSLDVTVYCGDARSIRLLE 59
                                   57*****************9998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 1589.87
//
Query:       gi|119720105|ref|YP_920600.1|  [L=423]
Description: geranylgeranyl reductase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.4e-17   62.4   0.7      5e-16   58.9   0.7    2.2  1  FAD_binding_3   FAD binding domain
    9.1e-13   48.0   1.1    2.2e-07   30.3   0.5    2.4  2  Lycopene_cycl   Lycopene cyclase protein
      1e-10   41.3   0.9    1.7e-10   40.6   0.9    1.4  1  FAD_binding_2   FAD binding domain
    1.7e-10   40.7   0.1    2.3e-10   40.2   0.1    1.2  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    8.3e-09   35.3   5.7      2e-08   34.0   5.7    1.6  1  FAD_oxidored    FAD dependent oxidoreductase
      1e-08   34.9   0.6    2.9e-05   23.5   0.3    2.1  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    3.2e-08   32.7   1.1    2.9e-06   26.3   0.6    2.3  2  HI0933_like     HI0933-like protein
    3.8e-08   33.3   8.6    0.00017   21.3   3.2    2.8  3  DAO             FAD dependent oxidoreductase
    1.1e-06   28.8   0.8      2e-05   24.7   0.7    2.8  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    1.3e-06   27.5   0.4      0.024   13.5   0.2    3.1  3  Trp_halogenase  Tryptophan halogenase
    2.5e-06   26.8   4.8    1.5e-05   24.2   4.8    1.9  1  GIDA            Glucose inhibited division protein A
      1e-05   26.0   0.5    0.00024   21.6   0.2    2.5  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    0.00062   19.2   4.1       0.01   15.1   0.1    2.9  3  Amino_oxidase   Flavin containing amine oxidoreductase
     0.0023   17.2   0.5     0.0035   16.6   0.5    1.2  1  Thi4            Thi4 family
  ------ inclusion threshold ------
      0.021   14.8   1.4        0.2   11.7   1.4    2.2  1  NAD_binding_9   FAD-NAD(P)-binding
      0.028   13.7   0.3      0.043   13.1   0.3    1.3  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
      0.096   12.8   0.3       0.38   10.8   0.1    2.0  2  Fer2_4          2Fe-2S iron-sulfur cluster binding domain
        0.1   12.4   0.2       0.16   11.8   0.2    1.3  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
       0.11   11.5   0.0       0.18   10.8   0.0    1.2  1  SE              Squalene epoxidase
       0.19   11.5   1.3         10    5.9   0.4    2.4  2  DUF348          G5-linked-Ubiquitin-like domain


Domain annotation for each model (and alignments):
>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.9   0.7   5.6e-19     5e-16       3     337 ..       3     332 ..       1     336 [. 0.74

  Alignments for each domain:
  == domain 1  score: 58.9 bits;  conditional E-value: 5.6e-19
                                    EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS--EEEHHHHHHHHHTT-HHHHHHHSEECCCCEEEEEEECCC CS
                  FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpradglnqrtmellrqlGledrilaegapnelmgealynelsd 82 
                                    d ++VG+GpaG ++a   ++aG +vv++ek +++ ++  ++g++  t ++lr+lG ++ ++     n   g++l  +   
  gi|119720105|ref|YP_920600.1|   3 DLVVVGGGPAGSSAAIAAARAGLSVVVLEKGERNRDKYCGGGISVLTQNSLRELGAAEALETFE--NYAEGHVLVLP--- 77 
                                    678******************************************************9998888..55556777777... PP

                                    CCEEEEEHHCHHCST-CEE--HHHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEEEEEE-- CS
                  FAD_binding_3  83 tpkaradlelesspervtvypqteleriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetvrakYlvGaD 162
                                        ++ ++    +  + ++  + ++  L+e ae+ g++v+++ e  s++ d+++v  + r   +ge   v+ +Y v a 
  gi|119720105|ref|YP_920600.1|  78 --GEKVLVD-AIPGLGYGLVRRSVFDAKLRELAESYGATVKHGFEASSITVDGDKVVVRSR---KGEV--VEGRYAVVAT 149
                                    ..3344455.567777888899999*****************************9644433...4555..9********* PP

                                    GTT-HHHHHHTGGEEEEEEEEEEEEEEEEEEC-SCCCTTCCEEEEECCTTEE............EEEECCETEEEEEEEE CS
                  FAD_binding_3 163 GgrStvrktlgiefegeetvyeagvldvlfdadlsdiveplvlilsaesrgv............mviPlentlerfyvqv 230
                                    G+     ++lg++   +e++   +  ++ ++ ++s+ ve   + ++  ++ +             v P +n   ++ v +
  gi|119720105|ref|YP_920600.1| 150 GAGNFPERALGFPPLRPENL--GHCWGTEAEYPVSAEVER--WRHEYGFTPIflmfgfvtygymWVFPKRN---HMNVGM 222
                                    *************6556656..677777777777755555..33333333333444556666657889888...333444 PP

                                    ECCE-GGGSCCCHHHHHHHHHHH..HHHTT..SSCEEEEEEEEEEEEEEEEESSSEETTEEE-GGGTEEE-STTSHHHHH CS
                  FAD_binding_3 231 earaekeersekfteeevkarlr..eivge..ktldveieevsawtvaqrvaekyrkgrvflaGDAaHihpPtgGqGlNt 306
                                     ++  ++ r  +   e  ++ l+  + +g+  +  + ++++    + + r ++  ++ rv+laGDAa  + P +G G+  
  gi|119720105|ref|YP_920600.1| 223 GTTLAESARYGRLHLEGFARGLElaRRMGIlsEPGRLRVDRSWLIPGKPRAVTYSQERRVLLAGDAAGFVHPLTGEGISG 302
                                    4444444444444444444433300333330033333444444444555555555555********************** PP

                                    HHHHHHHHHHHHHHHHTTSS-GGGGHHHHHH CS
                  FAD_binding_3 307 aiqDavnLawkLaavlkGeAkeelLdtYeee 337
                                    a++     a    ++l  + ++ lL+ Ye++
  gi|119720105|ref|YP_920600.1| 303 AVRSGRLAAETVKQALD-KEDPGLLKEYEAK 332
                                    ************99999.99********975 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.5   2.5e-10   2.2e-07       1     145 [.       3     155 ..       3     179 .. 0.72
   2 !   15.8   0.0   6.3e-06    0.0057     255     299 ..     279     329 ..     266     397 .. 0.79

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 2.5e-10
                  Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlieaspsl..lfpnnyvWsdefedlga......leecvehsWsgtivylddg 72 
                                    D+vv+G+GpAg s A     a++gl+vv++e ++     + +    +  ++ l +      le   e   +g+++ l+ g
  gi|119720105|ref|YP_920600.1|   3 DLVVVGGGPAGSSAAIAA--ARAGLSVVVLEKGERNrdKYCGGGISVLTQNSLRElgaaeaLET-FENYAEGHVLVLP-G 78 
                                    9************99888..************99761112222233333433333332442333.3333455555555.5 PP

                  Lycopene_cycl  73 kkillg....raYgrvsskrlkeellerlvengvkllea.kvesveeeeageslvvleggrkirarlvvdarglaslk 145
                                    +k+l++    + Yg v+++ + ++l e   + g++  ++  + s++ + + +++v    g+ +++r +v+a+g+++ +
  gi|119720105|ref|YP_920600.1|  79 EKVLVDaipgLGYGLVRRSVFDAKLRELAESYGATVKHGfEASSITVDGD-KVVVRSRKGEVVEGRYAVVATGAGNFP 155
                                    5566666788**************98877788888777636788888888.9999******************76654 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 6.3e-06
                  Lycopene_cycl 255 eqkvlaiGaaaglvhPaTGYsvarslaeapllasaiaaalres......sl 299
                                    e +vl +G aag vhP TG  +  +++  +l a+ + +al+++      + 
  gi|119720105|ref|YP_920600.1| 279 ERRVLLAGDAAGFVHPLTGEGISGAVRSGRLAAETVKQALDKEdpgllkEY 329
                                    345999***********************************9865555422 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   0.9   1.9e-13   1.7e-10       1      65 [.       3      65 ..       3      79 .. 0.87

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 1.9e-13
                                   SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S-EE-TT..SSGGSTC.CHHHHH CS
                  FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqGgidavlspeqkkagikdspelh 65
                                   D++V+G+G AG +AA++aa+aGl+v+v+ek+++      +++Ggi ++ ++  +++g  + +e  
  gi|119720105|ref|YP_920600.1|  3 DLVVVGGGPAGSSAAIAAARAGLSVVVLEKGER--NRDKYCGGGISVLTQNSLRELGAAEALETF 65
                                   89******************************8..6778**********8888888886665555 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.1   2.6e-13   2.3e-10       1     112 [.       2     154 ..       2     176 .. 0.85

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 2.6e-13
                                    CSEEEE--SHHHHHHHHHHHHHTS-EEEEE.....TTHCHHHCSHHHHCHHHHHHHHHHHHH.................. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxx.................. RF
                    Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlve.....legtclnggcllskallgvaedaeias.................. 57 
                                    +d+vv+GgGpAG +aa+ +a+ag+ v+++e     ++++c +g  +l++  l+  ++ae ++                  
  gi|119720105|ref|YP_920600.1|   2 YDLVVVGGGPAGSSAAIAAARAGLSVVVLEkgernRDKYCGGGISVLTQNSLRELGAAEALEtfenyaeghvlvlpgekv 81 
                                    689**************************8888878888888888887776666666666667889************** PP

                                    .......................HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE- CS
                                    .......................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  58 .......................evvkklnqgielllgeevvkidpgkkkvklekkkegdeekiaydklvlAtGsspr 112
                                                           e  +++++ ++   +  + +i  +  kv+++     ++e ++  + v+AtG+ ++
  gi|119720105|ref|YP_920600.1|  82 lvdaipglgyglvrrsvfdaklrELAESYGATVKHGFE--ASSITVDGDKVVVRS---RKGEVVEGRYAVVATGAGNF 154
                                    *******************9999888899999998888..666666666788844...56889***********9665 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   5.7   2.2e-11     2e-08       1     147 [.       3     153 ..       3     158 .. 0.67

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 2.2e-11
                   FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLve.....ergvlGGlltsglvatdignkaeeqvvtgiareflerlrqrgga.. 73 
                                    D+vVvGGgpaG  AAiaAaraG +v+++e     +++++GG  +    +++ +  a+e        e +e+ ++ g+   
  gi|119720105|ref|YP_920600.1|   3 DLVVVGGGPAGSSAAIAAARAGLSVVVLEkgernRDKYCGGGISVLTQNSLRELGAAE-----AL-ETFENYAE-GHVlv 75 
                                    99***************************55444456677766655555555433222.....22.22222222.22222 PP

                   FAD_oxidored  74 .rlkkrskwn.........tfepevakavleemlaeagvtvllntrlvevekegkriesvtveskegrktirAkvfiDAT 143
                                     +  ++   +          +  +v+ a l e+ + +g tv ++ ++++++++g   ++v+v+ +++++++++++ + AT
  gi|119720105|ref|YP_920600.1|  76 lPG-EKVL-VdaipglgygLVRRSVFDAKLRELAESYGATVKHGFEASSITVDG---DKVVVR-SRKGEVVEGRYAVVAT 149
                                    211.1111.123445556688899999999999999999999999999999987...678884.5678899999999999 PP

                   FAD_oxidored 144 gdGd 147
                                    g G 
  gi|119720105|ref|YP_920600.1| 150 GAGN 153
                                    9886 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.3   3.2e-08   2.9e-05       1      31 [.       5      34 ..       5      38 .. 0.94
   2 !    9.4   0.0   0.00061      0.55      87     140 ..     103     157 ..      93     162 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 3.2e-08
                    Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgn 31
                                   +++G+GPaG +aai++ +agl ++++lEkg+
  gi|119720105|ref|YP_920600.1|  5 VVVGGGPAGSSAAIAAARAGL-SVVVLEKGE 34
                                   79*******************.7******96 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00061
                    Pyr_redox_3  87 lrevaksfelpiklfeeVesvkkedegfevetske.tyeAkkviiAtGefdkPnk 140
                                    lre+a+s+   +k   e  s++ ++++ +v+++k+ ++e ++ ++AtG  ++P++
  gi|119720105|ref|YP_920600.1| 103 LRELAESYGATVKHGFEASSITVDGDKVVVRSRKGeVVEGRYAVVATGAGNFPER 157
                                    899*******************************8699**********9888865 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.6   3.2e-09   2.9e-06       2      45 ..       3      44 ..       2      61 .. 0.86
   2 ?    4.6   0.0     0.012        11     116     169 ..     104     156 ..      96     160 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 3.2e-09
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHHHCGGG CS
                    HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklgrKilisGgG 45
                                   d++v+GgG+AG  aAi+aa++g +V++lek+++   K    GgG
  gi|119720105|ref|YP_920600.1|  3 DLVVVGGGPAGSSAAIAAARAGLSVVVLEKGERNRDKY--CGGG 44
                                   89*****************************9988875..3444 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.012
                                    HHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----SS-GG CS
                    HI0933_like 116 lkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGlSiPk 169
                                     + +++ g +++   e +s++ + d+ + v+ +++e +e ++ v+AtG   +P+
  gi|119720105|ref|YP_920600.1| 104 RELAESYGATVKHGFEASSITVDGDK-VVVRSRKGEVVEGRYAVVATGAGNFPE 156
                                    344566899999999*****999998.8888889**************998885 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   3.2   1.9e-07   0.00017       1      30 [.       3      34 ..       3      75 .. 0.90
   2 !   14.4   0.1   2.3e-05     0.021     150     219 ..     101     166 ..      89     313 .. 0.69
   3 ?   -1.9   0.0       2.2   1.9e+03     279     299 ..     382     402 ..     359     411 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.9e-07
                                   EEEEECTSHHHHHHHHHHHHTT..EEEEESSS CS
                            DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgd 30
                                   d+v++GGG +G+s+A ++ar+g  V++lekg+
  gi|119720105|ref|YP_920600.1|  3 DLVVVGGGPAGSSAAIAAARAGlsVVVLEKGE 34
                                   89****************************94 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 2.3e-05
                                    HHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHHHH.HTT...CTTTSEEEE CS
                            DAO 150 aalaraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsdll.gll...keldlpisp 219
                                    a l++ ae+ G+++  g e+ ++  + g+ + v   ++ ge+++ ++ V+a+Ga+   + +++   +    p++p
  gi|119720105|ref|YP_920600.1| 101 AKLRELAESYGATVKHGFEASSITVD-GDKVVV--RSRkGEVVEGRYAVVATGAG--NFpERAlgfP----PLRP 166
                                    678999*****************664.443445..44448886669*******99..3543332233....4454 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 2.2
                                    SCSHHHHHHHHHHHHHHSGGG CS
                            DAO 279 evdeedidellealrklfPql 299
                                    ++d  + ++l+e+l k+fP+l
  gi|119720105|ref|YP_920600.1| 382 RADRSASRRLYEYLLKHFPEL 402
                                    567788899999999999995 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.7   2.2e-08     2e-05       1      30 [.       6      35 ..       6      37 .. 0.97
   2 ?    0.4   0.0      0.87   7.8e+02      35      57 ..     317     339 ..     297     346 .. 0.76

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 2.2e-08
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSS CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdr 30
                                   +vG+G +G++aA ++a+ag++v++lek++r
  gi|119720105|ref|YP_920600.1|  6 VVGGGPAGSSAAIAAARAGLSVVVLEKGER 35
                                   8**************************986 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.87
                                    G-EECETTCEECTS---EEETTH CS
                  NAD_binding_8  35 aasyevpgvrvdygahifhgsgy 57 
                                    a ++e+pg   +y a +++++g+
  gi|119720105|ref|YP_920600.1| 317 ALDKEDPGLLKEYEAKWWADFGE 339
                                    45566688888999999999875 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.2   2.7e-05     0.024       2      37 ..       4      36 ..       3      66 .. 0.79
   2 ?    4.0   0.0     0.021        19     153     209 ..      96     151 ..      85     160 .. 0.81
   3 !    6.5   0.0    0.0035       3.1     316     367 ..     280     333 ..     253     340 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.7e-05
                                   EEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS- CS
                 Trp_halogenase  2 ivivGGGtaGwlaAaalakalkgklevtlveseeig 37
                                   +v+vGGG+aG+ aA+a a+a+   l+v ++e+ e  
  gi|119720105|ref|YP_920600.1|  4 LVVVGGGPAGSSAAIAAARAG---LSVVVLEKGERN 36
                                   79******************9...999999997655 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.021
                                    HHHHHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-SEEEE-SGG CS
                 Trp_halogenase 153 aalyakfLrrvaearGvtrvegkvvevqldedgrveslrledgreveadlfiDcsGf 209
                                    ++ ++  Lr+ ae+ G t+ +g  ++  +  dg+   +r  +g++ve++ ++ ++G 
  gi|119720105|ref|YP_920600.1|  96 RSVFDAKLRELAESYGATVKHGFEASS-ITVDGDKVVVRSRKGEVVEGRYAVVATGA 151
                                    5679999************99976444.44444444699999**********99995 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.0035
                                    TTEEE-CCCTEE--CCCS-HHHHHHH....HHHHHHHT--BTT--HHHHHHHHHHH CS
                 Trp_halogenase 316 knvvalGlasgfvePlestsihliqa....alrrLlallpdksdepaaiaefnrev 367
                                    + v++ G+a+gfv Pl + +i  + +    a++++ + l ++  +p +++e++++ 
  gi|119720105|ref|YP_920600.1| 280 RRVLLAGDAAGFVHPLTGEGISGAVRsgrlAAETVKQALDKE--DPGLLKEYEAKW 333
                                    568889***************999886666777777766655..788889988765 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   4.8   1.7e-08   1.5e-05       1     150 [.       3     151 ..       3     156 .. 0.67

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 1.7e-08
                                    CEEEE-SSHHHHHHHHHHHHTT--EEEE.......ES-GGGTT--SSSSEEE-TTHHHHHHHHHHHT.-SHHHHHHHHEE CS
                           GIDA   1 dviViGgGhAGceAAlaaarlGakvlLi.......thkldtiaelsCnpsiggiakgllvrEidalg.gliikaadkagi 72 
                                    d++V+GgG AG+ AA+aaar+G++v+ +        +  +  +++  ++s++ +++++  +  ++   g +  +  ++ +
  gi|119720105|ref|YP_920600.1|   3 DLVVVGGGPAGSSAAIAAARAGLSVVVLekgernrDKYCGGGISVLTQNSLRELGAAEALETFENYAeGHVLVLPGEKVL 82 
                                    689************************98886554333333334556788887777777776666553444444333333 PP

                                    EEEEESTTS-CCC-EEEEEE-HHHHHHHHHHHHHTSTTEEEEES.-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT CS
                           GIDA  73 qfrilNrskGpavralraqvdrelyskevteklenepnleiiee.eveeliveekkvkgvvtedgetikakavviatGt 150
                                     ++       p  ++    v r+ + ++++e  e+    ++ ++ e++++ v ++   +v+ ++ge+++ +  v+atG+
  gi|119720105|ref|YP_920600.1|  83 -VDAI-----PGLGYG--LVRRSVFDAKLRELAES-YGATVKHGfEASSITV-DGDKVVVRSRKGEVVEGRYAVVATGA 151
                                    .3443.....555555..67777777777776666.6667766635666655.66666788888888888888888886 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.2   2.7e-07   0.00024       2      54 ..       4      57 ..       3      65 .. 0.96
   2 ?    1.9   0.0      0.37   3.3e+02      46      78 ..     103     132 ..      96     137 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 2.7e-07
                                   EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS.TTSSHHHHHHHHHHHHHTT CS
                      Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll.rllDeeaskilqeklekng 54
                                   +vvvGgG  g  +A a+a+ g +V v+e +++ + ++++  +s ++q++l+++g
  gi|119720105|ref|YP_920600.1|  4 LVVVGGGPAGSSAAIAAARAGLSVVVLEKGERNRdKYCGGGISVLTQNSLRELG 57
                                   79*************************************************998 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.37
                                    HHHHHHHTTEEEECSEEEEEEEEETTSEEEEEE CS
                      Pyr_redox  46 lqeklekngievllntkveeiegsedgvesvkl 78 
                                    l+e  e  g +v ++ ++ +i+ ++d+   v++
  gi|119720105|ref|YP_920600.1| 103 LRELAESYGATVKHGFEASSITVDGDK---VVV 132
                                    455566669*****************9...444 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.64   5.7e+02       5      25 ..      15      35 ..      11      37 .. 0.86
   2 !   15.1   0.1   1.2e-05      0.01     205     267 ..      75     157 ..      34     177 .. 0.72
   3 ?    4.1   0.0     0.026        23     417     451 ..     277     314 ..     261     315 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.64
                                   HHHHHHHHTTEEEEEEESSSS CS
                  Amino_oxidase  5 aaArqLlsaGfdVtvlEardr 25
                                   +aA   ++aG++V+vlE  +r
  gi|119720105|ref|YP_920600.1| 15 SAAIAAARAGLSVVVLEKGER 35
                                   7888889**********9987 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 1.2e-05
                                    E....................TTHTHHHHHHHHHTTTTEEEETSEEEEEEEEETTCEEEEETTSTEEEESEEEE-S-HHH CS
                  Amino_oxidase 205 p....................rgGlsqlpealaeelrgldirlntrVkeikregdgvtvtledgevveaDaVvvTvplgv 264
                                    +                    r  +++  + lae + g +++ + + ++i+ +gd+v v+ + gevve+++ vv++  g+
  gi|119720105|ref|YP_920600.1|  75 VlpgekvlvdaipglgyglvrRSVFDAKLRELAE-SYGATVKHGFEASSITVDGDKVVVRSRKGEVVEGRYAVVATGAGN 153
                                    4455555555555554444444445666778888.999***************************************999 PP

                                    HH.S CS
                  Amino_oxidase 265 lk.a 267
                                       +
  gi|119720105|ref|YP_920600.1| 154 FPeR 157
                                    8753 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.026
                                    HCSTTEEE.SGGGCTTT..TTS.HHHHHHHHHHHHHHH CS
                  Amino_oxidase 417 egdprlffAGehtsrey..pgt.vegAilSGlraAari 451
                                     +  r+ +AG++    +  +g  + gA++SG+ aA+ +
  gi|119720105|ref|YP_920600.1| 277 SQERRVLLAGDAAGFVHplTGEgISGAVRSGRLAAETV 314
                                    577899999998543331134459***********976 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.5   3.9e-06    0.0035      19      49 ..       3      32 ..       1      50 [. 0.85

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3.9e-06
                                   EEEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
                           Thi4 19 DvvivGaGssGLtaayylakkpdlkvailer 49
                                   D+v+vG+G++G +aa   a++ +l v++le+
  gi|119720105|ref|YP_920600.1|  3 DLVVVGGGPAGSSAAIAAARA-GLSVVVLEK 32
                                   99**************99999.*******97 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.4   0.00022       0.2       1     155 [.       5     151 ..       5     152 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00022
                  NAD_binding_9   1 aivGaGprGlavlerLlarakkkspleitlfdpsepgagrvwrtdqseelllNvpasemslftddpptfaeWlrerga.. 78 
                                    ++vG+Gp+G +++ + ++       l++ + ++ e   +  +     + l  N + +e+ + +   +tf+++++++    
  gi|119720105|ref|YP_920600.1|   5 VVVGGGPAGSSAAIAAARA-----GLSVVVLEKGERN-RDKYCGGGISVLTQN-SLRELGAAE-ALETFENYAEGHVLvl 76 
                                    6899999999999887776.....6999999998888.566666655555445.455555543.3599*******99876 PP

                  NAD_binding_9  79 ..lee.....aeeldpddfvpRalyGrYlrdlfeellarlpegvtvevhraevvdleeradgqavlladgaslaadaVvL 151
                                      + +     +++l ++  v+R+++ + lr+l+e+  a+++       h  e+ +++ ++d++ v+ ++g+ ++ ++ v+
  gi|119720105|ref|YP_920600.1|  77 pgE-KvlvdaIPGL-GYGLVRRSVFDAKLRELAESYGATVK-------HGFEASSITVDGDKVVVRSRKGEVVEGRYAVV 147
                                    541.2343334443.66777777777777777777776664.......556***************************** PP

                  NAD_binding_9 152 AlGh 155
                                    A+G 
  gi|119720105|ref|YP_920600.1| 148 ATGA 151
                                    **95 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.3   4.8e-05     0.043      31      64 ..       4      37 ..       2      65 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.8e-05
                                   EEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHH CS
                    AlaDh_PNT_C 31 vlviGgGvaGlqAiatakglgakVtvlDvrparl 64
                                    +v+GgG aG +A+ +a++ g +V+vl++ ++ +
  gi|119720105|ref|YP_920600.1|  4 LVVVGGGPAGSSAAIAAARAGLSVVVLEKGERNR 37
                                   59*************************9876655 PP

>> Fer2_4  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00042      0.38      15      49 ..      10      44 ..       9      46 .. 0.95
   2 ?   -1.8   0.0       3.6   3.3e+03       5      16 ..     122     133 ..     119     142 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00042
                         Fer2_4 15 vpeGdtvasAllangvdvprsckygrprgelcagg 49
                                   +p+G++ a A++++g +v+ + k +r+r+++c gg
  gi|119720105|ref|YP_920600.1| 10 GPAGSSAAIAAARAGLSVVVLEKGERNRDKYCGGG 44
                                   799*****************************987 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.6
                         Fer2_4   5 tltfDGkevtvp 16 
                                    ++t+DG +v v+
  gi|119720105|ref|YP_920600.1| 122 SITVDGDKVVVR 133
                                    688888888764 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   0.00018      0.16       3      36 ..       5      38 ..       3      67 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00018
                                   EEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHH CS
                        3HCDH_N  3 aviGaGtmGagiaavfasagleVvlvdiseeale 36
                                    v+G G  G++ a ++a+agl+Vv+++  e+  +
  gi|119720105|ref|YP_920600.1|  5 VVVGGGPAGSSAAIAAARAGLSVVVLEKGERNRD 38
                                   69***********************998766554 PP

>> SE  Squalene epoxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00021      0.18     126     178 ..     276     328 ..     262     336 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00021
                             SE 126 knekkGlillGDalnmRHPltggGmtvalnDivllskllkpledlsdeekvle 178
                                     ++++ ++l GDa    HPltg G+  a++   l ++++k+  d +d   + e
  gi|119720105|ref|YP_920600.1| 276 YSQERRVLLAGDAAGFVHPLTGEGISGAVRSGRLAAETVKQALDKEDPGLLKE 328
                                    45678899********************9999999999999877777665555 PP

>> DUF348  G5-linked-Ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.4     0.012        10       3      19 ..     123     139 ..     122     141 .. 0.87
   2 ?    4.1   0.0     0.042        38      13      25 ..     308     320 ..     300     324 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.012
                                    EEETTEEEEE----SSH CS
                         DUF348   3 ltvDGktvtvrTaadTV 19 
                                    +tvDG +v+vr+ ++ V
  gi|119720105|ref|YP_920600.1| 123 ITVDGDKVVVRSRKGEV 139
                                    9**********988765 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.042
                                    ----SSHHHHHHH CS
                         DUF348  13 rTaadTVgdlLee 25 
                                    r aa TV+++L++
  gi|119720105|ref|YP_920600.1| 308 RLAAETVKQALDK 320
                                    679********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.43
# Mc/sec: 2933.33
//
Query:       gi|119720106|ref|YP_920601.1|  [L=229]
Description: hypothetical protein Tpen_1200 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0036   17.3   0.0     0.0078   16.3   0.0    1.5  1  Ntox22    Bacterial toxin 22


Domain annotation for each model (and alignments):
>> Ntox22  Bacterial toxin 22
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   4.3e-07    0.0078      69     100 ..     122     153 ..     107     160 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.3e-07
                         Ntox22  69 agdgnqafvsiptnlgvnvigavthayggata 100
                                     g+g++af si  + gvnv+  ++ ay gat 
  gi|119720106|ref|YP_920601.1| 122 EGEGKEAFYSIEVPEGVNVFYFLAGAYEGATQ 153
                                    699**************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       255  (0.0142228); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1677.21
//
Query:       gi|119720107|ref|YP_920602.1|  [L=241]
Description: hypothetical protein Tpen_1201 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-05   24.1   0.0     0.0023   17.8   0.0    2.1  2  RsgA_GTPase    RsgA GTPase
    3.8e-05   23.2   0.0    6.7e-05   22.4   0.0    1.4  1  HTH_47         winged helix-turn-helix
     0.0096   16.3   0.0      0.015   15.7   0.0    1.4  1  AAA_16         AAA ATPase domain
  ------ inclusion threshold ------
      0.013   15.0   0.0      0.028   13.9   0.0    1.6  1  Sigma70_r4     Sigma-70, region 4
      0.021   14.0   0.0       0.03   13.5   0.0    1.2  1  DUF815         Protein of unknown function (DUF815)
      0.024   15.1   0.0      0.044   14.3   0.0    1.6  1  ABC_tran       ABC transporter
      0.035   13.9   0.0      0.064   13.1   0.0    1.4  1  HTH_IclR       IclR helix-turn-helix domain
      0.036   13.8   0.0       0.07   12.9   0.0    1.4  1  AAA_29         P-loop containing region of AAA domain
      0.038   13.9   0.0      0.081   12.8   0.0    1.5  1  TrmB           Sugar-specific transcriptional regulator TrmB
      0.039   14.1   0.0      0.059   13.5   0.0    1.5  1  AAA_33         AAA domain
      0.087   13.1   0.0       0.13   12.5   0.0    1.3  1  AAA_28         AAA domain
      0.089   12.5   0.0       0.17   11.6   0.0    1.4  1  Sigma70_r4_2   Sigma-70, region 4
      0.091   12.9   0.0       0.22   11.6   0.0    1.6  2  MMR_HSR1       50S ribosome-binding GTPase
      0.092   12.2   0.0       0.16   11.4   0.0    1.4  1  HTH_Tnp_ISL3   Helix-turn-helix domain of transposase family 
      0.092   12.4   0.0       0.26   11.0   0.0    1.6  2  Guanylate_kin  Guanylate kinase
      0.096   12.5   0.0       0.26   11.1   0.0    1.7  2  DUF742         Protein of unknown function (DUF742)
       0.16   12.4   0.0       0.23   11.9   0.0    1.4  1  AAA            ATPase family associated with various cellular
       0.17   12.4   0.0       0.21   12.1   0.0    1.4  1  AAA_18         AAA domain
       0.17   11.1   0.0       0.31   10.3   0.0    1.4  1  Zeta_toxin     Zeta toxin


Domain annotation for each model (and alignments):
>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   2.5e-06    0.0023     100     129 ..       5      34 ..       2      40 .. 0.89
   2 ?    4.1   0.0     0.041        38      22      96 ..      76     148 ..      70     153 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.5e-06
                                    SEEEEECSTTSSHHHHHHHHCTT-----S- CS
                    RsgA_GTPase 100 ktsvlvGqSGvGKStLinallpelelktge 129
                                    k++v++G  G GKS+Li+al pel+++  e
  gi|119720107|ref|YP_920602.1|   5 KLVVFAGAKGSGKSSLIKALFPELDVRFDE 34 
                                    689********************9998766 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.041
                                    EEESTTTT--HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHH CS
                    RsgA_GTPase  22 vvslkepelslnlldrfLvlaeekgiepvivlnKiDlleeeeeleelkeelealgyevllvsaktkegleelkel 96 
                                    +v+ +++ ++  l  ++Lv++e+++ +  +v  K+D    ++ + +lk    + g+e+++ s+k+  ++eel+ +
  gi|119720107|ref|YP_920602.1|  76 LVADASQPFQRALEPKALVVVENAERKC-LVAAKADSPYGDT-VARLKGFAGERGFEFFAASVKDPGSIEELRLW 148
                                    3444457888899999*****9999765.6679****99999.9*************************999866 PP

>> HTH_47  winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   7.1e-08   6.7e-05      35      77 ..     191     233 ..     181     234 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 7.1e-08
                                    HHHHHHHH-EEEEEHHHHHHHHT--HHHHHHHHHHHHHTT-EE CS
                         HTH_47  35 allwvLnlaDGkrsLldiAeriglpfdrvaaiaraLaeaglla 77 
                                    + l v  l+DGkr+L +iA ++g +  +v+ ia++L ++g +a
  gi|119720107|ref|YP_920602.1| 191 EELAVFELCDGKRGLAEIARITGKSYGEVKRIADSLMTKGFIA 233
                                    568999********************************99885 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.6e-05     0.015      26      55 ..       6      48 ..       2     140 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.6e-05
                         AAA_16 26 lvllsGesGvGKsslvrellralekd.............ggif 55
                                   lv++ G++G+GKssl+++l+ +l  +             gg++
  gi|119720107|ref|YP_920602.1|  6 LVVFAGAKGSGKSSLIKALFPELDVRfdepsyyrdyplsGGVV 48
                                   7999****************88876666666666666663333 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0     3e-05     0.028       4      43 ..     187     225 ..     186     229 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3e-05
                                    HS-HHHHHHHHHHHTTT--HHHHHHHHTS-HHHHHHHHHH CS
                     Sigma70_r4   4 sLpererevlelrfgeglTleEIgerlgiSrerVrqiekr 43 
                                     L+e+e  v+el+ g+   l+EI+++ g S + V++i   
  gi|119720107|ref|YP_920602.1| 187 ALSEEELAVFELCDGKR-GLAEIARITGKSYGEVKRIADS 225
                                    69************766.7*****************9765 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   3.2e-05      0.03      56      77 ..       7      28 ..       4      32 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.2e-05
                         DUF815 56 vLLwGarGtGKSslvkallney 77
                                   v++ Ga+G+GKSsl+kal+ e+
  gi|119720107|ref|YP_920602.1|  7 VVFAGAKGSGKSSLIKALFPEL 28
                                   6789*************98765 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   4.7e-05     0.044      12      36 ..       5      29 ..       1      87 [. 0.90

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.7e-05
                                   SEEEEEESTTSSHHHHHHHHTTSS- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran 12 ekvaivGenGaGKStLlkllagllk 36
                                   ++v++ G  G+GKS+L+k+l  +l+
  gi|119720107|ref|YP_920602.1|  5 KLVVFAGAKGSGKSSLIKALFPELD 29
                                   67999**************987665 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   6.8e-05     0.064      11      48 ..     195     232 ..     193     233 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.8e-05
                                    T-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                       HTH_IclR  11 alaeapqeltlselArrtglpkStvhRlLqtLvelGyv 48 
                                     ++ +++  +l+e+Ar tg +   v R+  +L+  G++
  gi|119720107|ref|YP_920602.1| 195 VFELCDGKRGLAEIARITGKSYGEVKRIADSLMTKGFI 232
                                    6667777789**************************97 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   7.4e-05      0.07      25      42 ..       7      24 ..       2      34 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.4e-05
                         AAA_29 25 tlltGpsGsGKSTllDAi 42
                                   ++++G+ GsGKS+l+ A+
  gi|119720107|ref|YP_920602.1|  7 VVFAGAKGSGKSSLIKAL 24
                                   5789***********775 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   8.6e-05     0.081      13      53 ..     195     233 ..     187     239 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.6e-05
                                    HCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEE CS
                           TrmB  13 vYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVe 53 
                                    v+   l+ g+    eia+++g ++  v ++  sL+ kG++ 
  gi|119720107|ref|YP_920602.1| 195 VFE--LCDGKRGLAEIARITGKSYGEVKRIADSLMTKGFIA 233
                                    555..68899999**************************96 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   6.3e-05     0.059       1      34 [.       6      38 ..       6     113 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.3e-05
                         AAA_33  1 lvllvGlpGsGKstlaerllkklgavllssdtlr 34
                                   lv++ G++GsGKs l++ l  +l  v+ ++++++
  gi|119720107|ref|YP_920602.1|  6 LVVFAGAKGSGKSSLIKALFPEL-DVRFDEPSYY 38
                                   89****************99444.5666666654 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00014      0.13       2      20 ..       7      25 ..       6      60 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00014
                         AAA_28  2 ivitGgestGKTtlleaLa 20
                                   +v+ G+ ++GK++l++aL 
  gi|119720107|ref|YP_920602.1|  7 VVFAGAKGSGKSSLIKALF 25
                                   8****************97 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00018      0.17      10      45 ..     187     221 ..     185     222 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00018
                                    TS-HHHHHHHHHHHTS---HHHHHHHHT--HHHHHH CS
                   Sigma70_r4_2  10 eLperqreifllryleglsykEIAellgisegtVks 45 
                                    +L+e++ ++f+l++      +EIA+++g s g Vk+
  gi|119720107|ref|YP_920602.1| 187 ALSEEELAVFELCD-GKRGLAEIARITGKSYGEVKR 221
                                    79999999****86.9999**************996 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00023      0.22       2      22 ..       7      27 ..       6      42 .. 0.87
   2 ?   -2.0   0.0         4   3.8e+03      64      87 ..      59      85 ..      30     108 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00023
                                   EEEEESTTSSHHHHHHHHHTS CS
                       MMR_HSR1  2 vaivGrpNvGKStLinaltge 22
                                   v+++G   +GKS+Li+al+ e
  gi|119720107|ref|YP_920602.1|  7 VVFAGAKGSGKSSLIKALFPE 27
                                   799***************865 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4
                                   HHHHHHHHHHHCTSEEEEEEETT...T CS
                       MMR_HSR1 64 kglgkaflaleeadlillvvdas...e 87
                                    ++  +++   + ++ +lv das   +
  gi|119720107|ref|YP_920602.1| 59 LDVVSTIAGRWRISVGVLVADASqpfQ 85
                                   455555555555667777777663332 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00017      0.16      20      51 ..     195     226 ..     191     227 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00017
                   HTH_Tnp_ISL3  20 ilelllesrsvkavArqlgvSwtTVwrildry 51 
                                    ++el+   r  +++Ar++g S   V+ri d++
  gi|119720107|ref|YP_920602.1| 195 VFELCDGKRGLAEIARITGKSYGEVKRIADSL 226
                                    44555555999*****************9975 PP

>> Guanylate_kin  Guanylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00027      0.26       3      30 ..       5      32 ..       3      37 .. 0.90
   2 ?   -1.9   0.0       2.5   2.3e+03      67      83 ..     204     220 ..     196     230 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00027
                                   SEEEEESTTTSSHHHHHHHHHHHSTTTE CS
                  Guanylate_kin  3 rpvvlvgpsgaGksslkkaLlselpekf 30
                                   ++vv  g++g Gkssl+kaL+ el  +f
  gi|119720107|ref|YP_920602.1|  5 KLVVFAGAKGSGKSSLIKALFPELDVRF 32
                                   789******************9998887 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.5
                                    TEEEEEEETTEEEEEEH CS
                  Guanylate_kin  67 eflEaaefsgnlygtsv 83 
                                     + E a+ +g++yg+++
  gi|119720107|ref|YP_920602.1| 204 GLAEIARITGKSYGEVK 220
                                    56799999999999976 PP

>> DUF742  Protein of unknown function (DUF742)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       3.4   3.2e+03      29      32 ..      76      79 ..      52     113 .. 0.62
   2 ?   11.1   0.0   0.00027      0.26      34      86 ..     181     233 ..     165     240 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3.4
                         DUF742 29 vvae 32
                                   +va 
  gi|119720107|ref|YP_920602.1| 76 LVAD 79
                                   3333 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00027
                         DUF742  34 gapeaarlqpehrailrLcreplsVaelaAelklPvgvvrvLlsdLldagllt 86 
                                    +ap + +l++e+ a+ +Lc  ++  ae+a  +    g v+ +  +L+++g ++
  gi|119720107|ref|YP_920602.1| 181 KAPGKGALSEEELAVFELCDGKRGLAEIARITGKSYGEVKRIADSLMTKGFIA 233
                                    35667899*********************999999999998888888888876 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00024      0.23       1      26 [.       7      32 ..       7     105 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00024
                                   EEEESSTTSSHHHHHHHHHHHHTHEE CS
                            AAA  1 vllyGppGtGKTllakavakelgvef 26
                                   v++ G +G GK++l+ka+  el+v+f
  gi|119720107|ref|YP_920602.1|  7 VVFAGAKGSGKSSLIKALFPELDVRF 32
                                   6799*****************99886 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00022      0.21       1      41 [.       7      62 ..       7     163 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00022
                         AAA_18  1 IlltGtpGvGKttlakeLskrlgf...............gvnlrdvakenglllev 41
                                   ++ +G+ G+GK++l k+L  +l +               gv++r+va  +++l+ v
  gi|119720107|ref|YP_920602.1|  7 VVFAGAKGSGKSSLIKALFPELDVrfdepsyyrdyplsgGVVVREVAGRHESLDVV 62
                                   6789**************77775566777777888888877777777666666555 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00033      0.31      17      40 ..       5      28 ..       4      41 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00033
                     Zeta_toxin 17 klillgGqpGAGKselaellkdel 40
                                   kl++ +G+ G+GKs+l+++l  el
  gi|119720107|ref|YP_920602.1|  5 KLVVFAGAKGSGKSSLIKALFPEL 28
                                   6899*************9987666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 1705.92
//
Query:       gi|119720108|ref|YP_920603.1|  [L=403]
Description: saccharopine dehydrogenase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-10   40.9   0.0    3.3e-10   40.3   0.0    1.3  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
  ------ inclusion threshold ------
      0.021   15.1   0.0      0.039   14.2   0.0    1.5  1  TrkA_N           TrkA-N domain
      0.049   14.3   0.0      0.081   13.6   0.0    1.3  1  PglD_N           PglD N-terminal domain
       0.06   12.7   0.3      0.095   12.0   0.3    1.3  1  ThiF             ThiF family
       0.13   11.8   0.1       0.24   11.0   0.1    1.4  1  DAO              FAD dependent oxidoreductase
       0.14   11.7   0.1       0.28   10.8   0.1    1.5  1  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
       0.19   11.3   0.0       0.34   10.5   0.0    1.5  1  ApbA             Ketopantoate reductase PanE/ApbA


Domain annotation for each model (and alignments):
>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   0.0   1.3e-13   3.3e-10       1     129 [.       3     134 ..       3     135 .. 0.94

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 1.3e-13
                                    EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-SSGG CS
                Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnlsppi 80 
                                    ++++G+G+vG+ va+l a+ +  d e+ + d++ e++++ ++      +  +  da   e+ L+a ++++d++vn +p +
  gi|119720108|ref|YP_920603.1|   3 IVVVGCGAVGSLVARLAAKWKVAD-EVLCLDKDVERAKRYLDYPEPLGIPVERADALAAEE-LKAKVAGYDFLVNSLPTF 80 
                                    89*****************98765.****************9999999*************.****************** PP

                                    .........GHHHHHHHHHHHT-EEEE.SS-BCGCCSCHCCSHHHHHTHHHHHHCTSEE CS
                Sacchrp_dh_NADP  81 .........ssldvlkaCietgvhyvd.tsiskeertnyalreavlklkekakeagvta 129
                                             ++ +++  ++++g +y d +++       ++ r ++l++ ++++eag  a
  gi|119720108|ref|YP_920603.1|  81 vkvdkaerlLNPQLMSVALKAGLNYADlACY-----GGKRRRAEQLSFSKAFSEAGLLA 134
                                    99999999999****************7777.....9999999**********999887 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.5e-05     0.039       1      38 [.       3      42 ..       3      74 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.5e-05
                                   EEEES-SHHHHHHHHHHHH.TT.EEEEEEESSHHHHHHHH CS
                         TrkA_N  1 iiiiGlGrvGrslaeeLse.gg.kdvvvidkdeerveelr 38
                                   i+++G+G vG+ +a+   + +  ++v+  dkd er++++ 
  gi|119720108|ref|YP_920603.1|  3 IVVVGCGAVGSLVARLAAKwKVaDEVLCLDKDVERAKRYL 42
                                   89*************9999665967**********99874 PP

>> PglD_N  PglD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   3.2e-05     0.081       1      58 [.       2      62 ..       2      69 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.2e-05
                         PglD_N  1 kivIiGaGGhgkvvadiieangeyeiigflDdnkk..tevegypv.lgkaiellkslseee 58
                                   kiv++G+G  g  va+++ + +  +++ +lD++ +  +   +yp  lg ++e ++ l +ee
  gi|119720108|ref|YP_920603.1|  2 KIVVVGCGAVGSLVARLAAKWKVADEVLCLDKDVEraKRYLDYPEpLGIPVERADALAAEE 62
                                   79*****************************987522344455541344555555555555 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.3   3.7e-05     0.095      19      43 ..       1      25 [.       1      35 [. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.7e-05
                                   SEEEEE--SHHHHHHHHHHHHHTTT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ThiF 19 skvllvGaGglGsellknLalsGvg 43
                                   +k+++vG+G++Gs ++++ a++ v 
  gi|119720108|ref|YP_920603.1|  1 MKIVVVGCGAVGSLVARLAAKWKVA 25
                                   599**************99998774 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   9.2e-05      0.24       1      29 [.       2      34 ..       2      40 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 9.2e-05
                                   EEEEECTSHHHHHHHHHHHHTT....EEEEESS CS
                            DAO  1 dvviiGGGiiGlstAyeLarrg....Vtllekg 29
                                   ++v++G G +G+ +A+ +a+ +    V+ l+k+
  gi|119720108|ref|YP_920603.1|  2 KIVVVGCGAVGSLVARLAAKWKvadeVLCLDKD 34
                                   59****************998777899999998 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00011      0.28       1      36 [.       1      38 [.       1      43 [. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00011
                                   SEEEEE--STTHHHHHHHHHHCT..SEEEEE-S-HHHH CS
                 UDPG_MGDP_dh_N  1 mkisviGlGYvGlvtaavlaeig..hevigvDideekv 36
                                   mki+v+G G vG   a + a+     ev+++D+d e+ 
  gi|119720108|ref|YP_920603.1|  1 MKIVVVGCGAVGSLVARLAAKWKvaDEVLCLDKDVERA 38
                                   89************9999998765589*******9875 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00013      0.34       1      33 [.       3      35 ..       3      92 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00013
                                   EEEES-SHHHHHHHHHHHH.HTHCEEEE-SCHHH CS
                           ApbA  1 iailGaGaiGsllaakLak.agadvtlilrsrrl 33
                                   i+++G+Ga+Gsl+a   ak + ad +l+l ++ +
  gi|119720108|ref|YP_920603.1|  3 IVVVGCGAVGSLVARLAAKwKVADEVLCLDKD-V 35
                                   89***********9887887777755555555.4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.54u 0.23s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2807.42
//
Query:       gi|119720109|ref|YP_920604.1|  [L=465]
Description: citrate transporter [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-35  122.4  24.8      2e-35  122.4  24.8    2.2  2  CitMHS    Citrate transporter
    9.1e-08   31.8  17.7    9.5e-08   31.8  17.2    1.3  1  ArsB      Arsenical pump membrane protein
  ------ inclusion threshold ------
          8    7.0   9.6        9.2    6.8   1.5    3.7  4  DUF2583   Protein of unknown function (DUF2583)


Domain annotation for each model (and alignments):
>> CitMHS  Citrate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   2.6      0.07   4.2e+02      73     108 ..      15      52 ..       3      55 .. 0.76
   2 !  122.4  24.8   3.4e-39     2e-35       9     296 ..      58     402 ..      45     409 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.07
                                    x.xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx RF
                         CitMHS  73 d.llvllvlltallsafvsndgv.vlimipivlslakr 108
                                      l+++ +l+tal s+++ + +  vl +++ ++++++ 
  gi|119720109|ref|YP_920604.1|  15 VlLVLVAGLVTALASSLLGLEAQqVLALTAFLMTIYAT 52 
                                    44666688888888888877666799999999998875 PP

  == domain 2  score: 122.4 bits;  conditional E-value: 3.4e-39
                                    xxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                         CitMHS   9 lrldvvallvlvll...vltieealsgiaspiillllgamiigaaleetGlfdrlaakllrlaggkrd.llvllvlltal 84 
                                     rl+++ l v +l+   vl+ e  +++   ++i++l+++m+i+++lee  +f+++a+ ++r++g + +  ++++v+l+++
  gi|119720109|ref|YP_920604.1|  58 YRLPFAFLGVSALFllgVLDVEYFVEHSHLDVIAFLIAMMTIVGYLEEDRFFEFIAQEIVRRVGVNFRaTFLVVVFLSGF 137
                                    56777777777777889999999********************************************************* PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..............xxxxxxxxx RF
                         CitMHS  85 lsafvsndgvvlimipivlslakrlkklppllliplalaaniggaltpiGtpttraa..............arpglslpn 150
                                    l+++v+ ++ +l+m+++vl+l  +++ +p+ l+i+ ++a nig+a+tp G+p  + +              a p   l  
  gi|119720109|ref|YP_920604.1| 138 LAPLVDEVTSILVMLSVVLPLSGKIGVDPLPLVIASIFATNIGSAMTPLGNPVGVLVafesgltfsdflarAAPVSALSL 217
                                    ************************8888888*********************5555588888777766655444444444 PP

                                    xxxxxxxxxxx.....................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         CitMHS 151 llllalllvgl.....................................lplvllfmfgvalalpvnapkvkkqkaiieai 193
                                    +++ a+l+ ++                                     ++++++++++v+  ++         k+ + + 
  gi|119720109|ref|YP_920604.1| 218 VVAAAILMHLFrgyieegnalasqrftdgwsvaslerrtlyrdasvfsATILFIAAHHVLEEALGLP------KNSLLLA 291
                                    4445554443366666666666666666666666666666666666557777777555555444332......2222222 PP

                                    xxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....x.xxxxxxxxxxxxxx RF
                         CitMHS 194 arsllpvatillla.........ykkveWsvlllfaGvfllvgaleqtGilealadllga....g.gplvalalvlglia 259
                                    a+  l+va++++l+           kveW++l++f  +f  vgale+tG++e l+++lg+    g g ++   ++++ ++
  gi|119720109|ref|YP_920604.1| 292 AP--LMVAGLIMLLdpsrgfhalETKVEWPTLVFFLLLFASVGALEKTGVVEVLSKSLGSlsasGvGAFM--GAFTLSSS 367
                                    22..3345555444********999*********************************888753233333..67799999 PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         CitMHS 260 llsafisnvavaalmapialgmapalgllspsplala 296
                                    l+saf++nv ++a++  ++ ++ ++ g ++ +p+++ 
  gi|119720109|ref|YP_920604.1| 368 LMSAFMDNVIAVAILSRVVHELGAQ-G-FHTEPFWWL 402
                                    9**********99999999886654.6.777777775 PP

>> ArsB  Arsenical pump membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8  17.2   1.6e-11   9.5e-08      56     421 ..      90     462 ..      40     464 .. 0.82

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 1.6e-11
                           ArsB  56 laf.vaiilislildnigffewaalhmakaakgygvrmfvyvsllgaivaalfandgaaliltpivlamvralhfneklv 134
                                    +af +a++ i   l++  ffe+ a  + +         f+ v +l   +a l+ +  + l++  +vl +   + ++    
  gi|119720109|ref|YP_920604.1|  90 IAFlIAMMTIVGYLEEDRFFEFIAQEIVRRVGVNFRATFLVVVFLSGFLAPLVDEVTSILVMLSVVLPLSGKIGVDP--- 166
                                    34425677788889999*********998875555557889999999********************9999988764... PP

                           ArsB 135 fpfiiasgfiadttslpfvvsnlvnivsadyfhitfidyasrmvvpylfsllasiivlylffrksipkrydltevk.... 210
                                    +p++ias f ++  s    + n v ++ a    +tf d+ +r      +sl+ +  +l  +fr  i +   l+  +    
  gi|119720109|ref|YP_920604.1| 167 LPLVIASIFATNIGSAMTPLGNPVGVLVAFESGLTFSDFLARAAPVSALSLVVAAAILMHLFRGYIEEGNALASQRftdg 246
                                    8*****************************************99889999999999999999*****9999987762222 PP

                           ArsB 211 kpveaikdqnmfr.lswyilglllig..yfaseffsipvs..vvagsiaiifliaa.qkspavhtkkvvkeapwaivffs 284
                                      v +++ + ++r  s +   +l+i   ++  e + +p +  ++a  + +  li   + s   h+ +   +  w  ++f 
  gi|119720109|ref|YP_920604.1| 247 WSVASLERRTLYRdASVFSATILFIAahHVLEEALGLPKNslLLAAPLMVAGLIMLlDPSRGFHALET--KVEWPTLVFF 324
                                    47999999****94467777888886224568999999752245666666666554145666666554..4556666666 PP

                           ArsB 285 igmyvvvygvrnagltdvlsdviqaaadqglfagtigmgfiaailssimnnlptvmidalaiagtdthgmmrealiyanv 364
                                    + ++  v  + ++g+ +vls  + + +  g+ a    + + ++++s+ m+n+ +v i +  +    ++g+  e + +  +
  gi|119720109|ref|YP_920604.1| 325 LLLFASVGALEKTGVVEVLSKSLGSLSASGVGAFMGAFTLSSSLMSAFMDNVIAVAILSRVVHELGAQGFHTEPFWWLTL 404
                                    779999****************998777777666666677899************************************* PP

                           ArsB 365 igsdlgpkitpigslatllwlhvlshk.gmkiswgtyfktgiiltiptllitlvglyi 421
                                      +    +++pigs a ++ l vl ++ g    +  +++ g+ +t  tl + +  +y+
  gi|119720109|ref|YP_920604.1| 405 FSAVYAGNLSPIGSTANIVALSVLEKRlGRSAGFKEWLRVGLPVTAATLALGFAAVYL 462
                                    ************************876488888999*************999988886 PP

>> DUF2583  Protein of unknown function (DUF2583)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   1.5    0.0015       9.2      18      57 ..      16      56 ..      11      60 .. 0.89
   2 ?   -3.1   0.0       1.8   1.1e+04      18      42 ..      93     117 ..      88     129 .. 0.74
   3 ?    0.5   0.0      0.14   8.4e+02       4      22 ..     285     303 ..     284     329 .. 0.85
   4 ?    2.0   0.1     0.047   2.8e+02      31      81 ..     357     407 ..     338     412 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0015
                        DUF2583 18 lllmvaslaysvlnqlpelelpellaeaa.llgifiGallW 57
                                   ll++va+l+ ++++ l  le  ++la +a l++i+   llW
  gi|119720109|ref|YP_920604.1| 16 LLVLVAGLVTALASSLLGLEAQQVLALTAfLMTIYATLLLW 56
                                   7899*******************998654389********* PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.8
                        DUF2583  18 lllmvaslaysvlnqlpelelpell 42 
                                    l++m++ ++y    +++e+   e++
  gi|119720109|ref|YP_920604.1|  93 LIAMMTIVGYLEEDRFFEFIAQEIV 117
                                    6778888888877777777666665 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.14
                        DUF2583   4 kkalllGnvlmglGlllmv 22 
                                    k++lll   lm+ Gl++++
  gi|119720109|ref|YP_920604.1| 285 KNSLLLAAPLMVAGLIMLL 303
                                    788999999******9987 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.047
                        DUF2583  31 nqlpelelpellaeaallgifiGallWlaGarvgGrekvadrywWlrhydk 81 
                                    + + ++ l+  l++a +  +   a+l  +  ++g +   ++ +wWl  + +
  gi|119720109|ref|YP_920604.1| 357 AFMGAFTLSSSLMSAFMDNVIAVAILSRVVHELGAQGFHTEPFWWLTLFSA 407
                                    556677788888888888888889999999999999999999***998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (465 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 3194.14
//
Query:       gi|119720110|ref|YP_920605.1|  [L=135]
Description: hypothetical protein Tpen_1204 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.012   14.2   1.6      0.021   13.4   1.6    1.3  1  FUSC      Fusaric acid resistance protein family
      0.048   11.9   6.9      0.052   11.8   6.9    1.0  1  DUF2070   Predicted membrane protein (DUF2070)
      0.099   12.7   1.8       0.13   12.4   0.0    2.1  2  DUF4235   Protein of unknown function (DUF4235)
       0.13   12.6   0.1       0.27   11.6   0.1    1.5  1  PsbR      Photosystem II 10 kDa polypeptide PsbR
       0.15   10.5   1.9       0.15   10.5   1.1    1.4  1  GerA      Bacillus/Clostridium GerA spore germination protein


Domain annotation for each model (and alignments):
>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   1.6     6e-06     0.021      47      86 ..      82     121 ..      79     124 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6e-06
                           FUSC  47 sKslyRllGTllGaaaavllvalfvqapllfllalalWig 86 
                                    +K+ +R++G ++ +aa+vll++++v   ll+l +lal+i 
  gi|119720110|ref|YP_920605.1|  82 EKGNFRMAGLTALVAASVLLIPATVAGVLLLLGGLALYIS 121
                                    89***********************************986 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   6.9   1.4e-05     0.052      66     174 ..      21     124 ..       8     135 .] 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.4e-05
                        DUF2070  66 ltykrslflalltelivviisllaillsall.qalvllalvlslalvfalrllvlvavsdesllkavlpaliqpllaill 144
                                    l ++  +++a++  ++++i +++ ++  + + ++ ++ ++++s a++fa+  l  +a  ++s++    +a ++ l+a+ +
  gi|119720110|ref|YP_920605.1|  21 LSVRIGILVAVVYGIFWAIKLFFEYIHGLQFlSRPFVEYMAFS-AVSFAVAALTSYANERYSEKGNFRMAGLTALVAASV 99 
                                    6777789*******************99999999999999999.9******************************99999 PP

                        DUF2070 145 lvlyfspesfllllllslifalavylfivv 174
                                    l++      + ++ +l+l+ +la+y+   +
  gi|119720110|ref|YP_920605.1| 100 LLIP-----ATVAGVLLLLGGLALYISAEI 124
                                    9999.....444555555555555543333 PP

>> DUF4235  Protein of unknown function (DUF4235)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       1.2   4.4e+03      42      56 ..      22      36 ..      19      39 .. 0.66
   2 ?   12.4   0.0   3.6e-05      0.13      40      74 ..      53      87 ..      50      90 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.2
                        DUF4235 42 slrevllfAaisGav 56
                                   s+r  +l A++ G+ 
  gi|119720110|ref|YP_920605.1| 22 SVRIGILVAVVYGIF 36
                                   556667778877765 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 3.6e-05
                        DUF4235 40 dvslrevllfAaisGavlavvrvaadRgtargver 74
                                   +++++e ++f a+s av+a+++ a +R + +g  r
  gi|119720110|ref|YP_920605.1| 53 SRPFVEYMAFSAVSFAVAALTSYANERYSEKGNFR 87
                                   57899**********************99998666 PP

>> PsbR  Photosystem II 10 kDa polypeptide PsbR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   7.5e-05      0.27      54      94 ..      75     115 ..      69     119 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.5e-05
                           PsbR  54 ytkdewsesGdvyvgGttglliwavllagllagGallvynt 94 
                                    y+++ +se G+  ++G t+l++ +vll+   ++G+ll++  
  gi|119720110|ref|YP_920605.1|  75 YANERYSEKGNFRMAGLTALVAASVLLIPATVAGVLLLLGG 115
                                    999*********************************98765 PP

>> GerA  Bacillus/Clostridium GerA spore germination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.1   4.2e-05      0.15     376     428 ..      65     117 ..      57     128 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 4.2e-05
                           GerA 376 ivvAltaiasFaipsyelslairllrflllilaallglyGivlglllllihla 428
                                    +  A++a++s+a  +y+ +  +r+  +  l++a++l +   v+g+llll  la
  gi|119720110|ref|YP_920605.1|  65 VSFAVAALTSYANERYSEKGNFRMAGLTALVAASVLLIPATVAGVLLLLGGLA 117
                                    5679*******************************************998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       728  (0.0406046); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 920.39
//
Query:       gi|119720111|ref|YP_920606.1|  [L=240]
Description: ABC transporter related [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.8e-19   68.5   0.0    1.1e-18   68.0   0.0    1.2  1  ABC_tran  ABC transporter
    1.4e-10   41.5   1.1    2.9e-05   24.1   0.0    2.2  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
      1e-05   25.1   0.0      0.021   14.3   0.0    2.3  2  SMC_N     RecF/RecN/SMC N terminal domain
    0.00029   21.3   0.0     0.0059   17.0   0.0    2.2  1  AAA       ATPase family associated with various cellular acti
  ------ inclusion threshold ------
      0.051   13.3   0.0      0.089   12.5   0.0    1.4  1  AAA_24    AAA domain
       0.11   12.2   0.0       0.17   11.5   0.0    1.3  1  AAA_15    AAA ATPase domain
       0.11   12.9   0.0       0.18   12.3   0.0    1.2  1  AAA_23    AAA domain
       0.21   11.3   0.1       0.41   10.4   0.1    1.4  1  AAA_29    P-loop containing region of AAA domain
       0.25   10.5   0.0       0.42    9.8   0.0    1.3  1  NB-ARC    NB-ARC domain
       0.32   10.9   1.4       0.81    9.6   0.1    2.2  3  NACHT     NACHT domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.0   0.0   6.3e-22   1.1e-18       1     134 [.      19     164 ..      19     167 .. 0.83

  Alignments for each domain:
  == domain 1  score: 68.0 bits;  conditional E-value: 6.3e-22
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTT..SS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllag..llkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvr 77 
                                    l+ v+l++ +g +v+++G+nG+GK++L+  ++g  l++ +eGei+ldg+ +++ +++e++++ +  ++q p    +l v 
  gi|119720111|ref|YP_920606.1|  19 LRGVDLEVPPGVIVGLIGPNGSGKTSLAYSIMGhpLYRVEEGEITLDGEVINHlKTEERASRGLFLVFQSPPEIGGLPVS 98 
                                    6789****************************9444777**************9999*************7777777555 PP

                                    HH...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEES CS
                                    xx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  78 en...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDE 134
                                                   +e ++ +++++gl e  +   ++  + +SgG+k+r +  +all kpk+l++DE
  gi|119720111|ref|YP_920606.1|  99 VFlrevlarrgveVGEEALSMYMREVGLGE--EYLSRYVHEGFSGGEKRRFEFLQALLFKPKILIVDE 164
                                    446677887776444444888888888887..333333459**************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.5   6.4e-06     0.012       2      17 ..      32      47 ..      31      60 .. 0.88
   2 !   24.1   0.0   1.6e-08   2.9e-05     237     302 ..     139     201 ..     132     202 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6.4e-06
                         AAA_21  2 nvliGpNgsGKSnLLd 17
                                    +liGpNgsGK++L +
  gi|119720111|ref|YP_920606.1| 32 VGLIGPNGSGKTSLAY 47
                                   68***********965 PP

  == domain 2  score: 24.1 bits;  conditional E-value: 1.6e-08
                         AAA_21 237 lSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSplll 302
                                    +S G kr + +l all  +   ++l++DE+++gL+ + +++l + ++el++ ga v+  +H+pl l
  gi|119720111|ref|YP_920606.1| 139 FSGGEKRRFEFLQALLFKP---KILIVDELDSGLDLEGVKSLTGKVRELAESGAGVLYISHNPLAL 201
                                    699**************99...9********************999999999***********865 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   1.1e-05     0.021      27      48 ..      32      50 ..      19      86 .. 0.87
   2 !    8.9   0.0   0.00052      0.93     138     200 ..     140     199 ..     101     217 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.1e-05
                                   EEEEESTTSSHHHHHHHHHHHC CS
                                   xxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 27 taivGpNGSGKsnlldAilFvL 48
                                     ++GpNGSGK++l  +i   +
  gi|119720111|ref|YP_920606.1| 32 VGLIGPNGSGKTSLAYSI---M 50
                                   4689***********999...4 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00052
                                    -HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                          SMC_N 138 SgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislree 200
                                    SgGek      +l A+  +kp+ + ++De+d+ LD + vk +   ++e  ++ a ++ is++  
  gi|119720111|ref|YP_920606.1| 140 SGGEKRR--FEFLQAL-LFKPK-ILIVDELDSGLDLEGVKSLTGKVRELAESgAGVLYISHNPL 199
                                    6666653..2333333.25555.5689********************99887788999998765 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   3.3e-06    0.0059       3      69 ..      34     167 ..      32     187 .. 0.63

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.3e-06
                                    EESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSS............................................. CS
                            AAA   3 lyGppGtGKTllakavakelgvefleisgsellsk............................................. 37 
                                    l+Gp G GKT+la +++ +   ++++++  e++ +                                             
  gi|119720111|ref|YP_920606.1|  34 LIGPNGSGKTSLAYSIMGH---PLYRVEEGEITLDgevinhlkteerasrglflvfqsppeigglpvsvflrevlarrgv 110
                                    89***************99...4444444444422234444444444555666666666666666777777777777777 PP

                                    .......................STTHHHHHH.HHHHHHHHHTS.TSEEEEEETGGG CS
                            AAA  38 .......................yvgesekki.relfkeakeka.kpsilfiDEida 69 
                                                           yv e+ +   +  f+ +++   kp+il++DE+d+
  gi|119720111|ref|YP_920606.1| 111 evgeealsmymrevglgeeylsrYVHEGFSGGeKRRFEFLQALLfKPKILIVDELDS 167
                                    777777777777666655555554444333220223333333347889999999997 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     5e-05     0.089       5      28 ..      32      55 ..      29      76 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5e-05
                         AAA_24  5 iliyGpsgiGKTtlakelgpkplf 28
                                   + ++Gp+g+GKT+la+++  +pl+
  gi|119720111|ref|YP_920606.1| 32 VGLIGPNGSGKTSLAYSIMGHPLY 55
                                   779**************9888886 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   9.6e-05      0.17      28      43 ..      34      49 ..      20      78 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9.6e-05
                         AAA_15 28 liGkNnsGKSsileal 43
                                   liG+N+sGK+s+++ +
  gi|119720111|ref|YP_920606.1| 34 LIGPNGSGKTSLAYSI 49
                                   9***********9987 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   9.8e-05      0.18      21      37 ..      31      47 ..      11      51 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9.8e-05
                         AAA_23 21 ltlItGpNGaGKTTild 37
                                   ++ ++GpNG+GKT++  
  gi|119720111|ref|YP_920606.1| 31 IVGLIGPNGSGKTSLAY 47
                                   45689*********975 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00023      0.41      23      38 ..      30      45 ..      12      50 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00023
                         AAA_29 23 gatlltGpsGsGKSTl 38
                                    ++ l+Gp+GsGK++l
  gi|119720111|ref|YP_920606.1| 30 VIVGLIGPNGSGKTSL 45
                                   37779********998 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00023      0.42      21      42 ..      30      51 ..      16      57 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00023
                                   EEEEEEESTTSSHHHHHHHHCC CS
                         NB-ARC 21 lvvalvGmgGvGKttlakqiln 42
                                   ++v+l G  G+GKt la +i+ 
  gi|119720111|ref|YP_920606.1| 30 VIVGLIGPNGSGKTSLAYSIMG 51
                                   79***************99975 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1   0.00045      0.81       4      21 ..      33      50 ..      30      52 .. 0.88
   2 ?   -2.4   0.0       2.2   3.9e+03      84      92 ..     154     167 ..     144     208 .. 0.74
   3 ?   -0.7   0.0      0.67   1.2e+03      74      89 ..     200     215 ..     174     224 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00045
                                   EEEC-TTTCHHHHHHHHH CS
                          NACHT  4 ilqGeaGsGKTtLlqkla 21
                                    l G++GsGKT L+ +++
  gi|119720111|ref|YP_920606.1| 33 GLIGPNGSGKTSLAYSIM 50
                                   589***********9997 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.2
                                    E.....EEEE-STT CS
                          NACHT  84 L.....lilDglDe 92 
                                    L     li+D lD 
  gi|119720111|ref|YP_920606.1| 154 LfkpkiLIVDELDS 167
                                    33333388888885 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.67
                                    HHHCCSCCCEEEEEE- CS
                          NACHT  74 avllelperlLlilDg 89 
                                    a+++ +p+r++ ++Dg
  gi|119720111|ref|YP_920606.1| 200 ALRTLRPHRIVVLVDG 215
                                    5678899999999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1608.46
//
Query:       gi|119720112|ref|YP_920607.1|  [L=470]
Description: FeS assembly protein SufB [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-65  220.6   0.1    2.5e-65  220.2   0.1    1.2  1  UPF0051   Uncharacterized protein family (UPF0051)


Domain annotation for each model (and alignments):
>> UPF0051  Uncharacterized protein family (UPF0051)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  220.2   0.1   1.4e-69   2.5e-65       2     218 .]     214     439 ..     213     439 .. 0.97

  Alignments for each domain:
  == domain 1  score: 220.2 bits;  conditional E-value: 1.4e-69
                        UPF0051   2 qfertlivveegaevtiieey.........agcgvveifvgenAklkyvkvqnwsedavnlstkraeegrdaklelttvs 72 
                                    q+e+t++v++eg+ v++ie           +++g+ve+++++++++k+++ qnws++ vn+++kra +++ a +e++++s
  gi|119720112|ref|YP_920607.1| 214 QMEHTIVVADEGSFVHFIEGCaapmfkkysFHNGMVEVYAHKGSHVKFTTAQNWSKNLVNFNNKRALVEEGAVVEWVEGS 293
                                    899***************666666666667777*********************************99************ PP

                        UPF0051  73 lggkltrkepsvelkgegaeaelnglylakgkqhldtrtkvdhngpntssrilskgvlkdearavfrgkikvrkgaqktd 152
                                    +g+k+++ +ps+ l+g +a+++++ ++lakg    d + kv h +p tss+++sk++++d+++av+rg +kv++ga ++ 
  gi|119720112|ref|YP_920607.1| 294 IGSKVSYVYPSAILRGANARVSITNITLAKGPVWKDGGAKVYHLAPSTSSEVVSKSISADGGTAVYRGLVKVARGARGST 373
                                    ******************************************************************************** PP

                        UPF0051 153 ahqenrnLllsdkaradtiPeleidaddvkasHgAtvGkideeqlfYLmsRGlseeeArrlivrgf 218
                                    a +++++L+l++k++a t P+ e+d++d ++ H+At+G+++ee+lfYL++RGlse eArrl+v g+
  gi|119720112|ref|YP_920607.1| 374 AAVKCDSLILDKKSKALTYPRNEVDEEDSTVVHEATTGRLSEEALFYLKTRGLSESEARRLVVLGY 439
                                    ***************************************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (470 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.49
# Mc/sec: 2870.59
//
Query:       gi|119720113|ref|YP_920608.1|  [L=364]
Description: SufBD protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.4e-29  101.4   0.0    6.8e-29  101.1   0.0    1.1  1  UPF0051   Uncharacterized protein family (UPF0051)


Domain annotation for each model (and alignments):
>> UPF0051  Uncharacterized protein family (UPF0051)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.1   0.0   3.8e-33   6.8e-29      26     216 ..     140     330 ..     109     332 .. 0.88

  Alignments for each domain:
  == domain 1  score: 101.1 bits;  conditional E-value: 3.8e-33
                        UPF0051  26 gvveifvgenAklkyvkvqnwsedavnlstkraeegrdaklelttvslggkltrkepsvelkgegaeaelnglylakgkq 105
                                      +++ v+e+++ ++  +   s+++       a++g+ ++l+   v ++g+  ++++++ l+g g++++ + l+++ ++ 
  gi|119720113|ref|YP_920608.1| 140 LSLNVSVEEGSRSRLEVILFDSGSSATALMAVARLGEGSALQESVVAVSGRALYADLKASLRGGGSSLDSSILAVSPREA 219
                                    4567888888888887777666655555556689999******************************************* PP

                        UPF0051 106 hldtrtkvdhngpntssrilskgvlkdearavfrgkikvrkgaqktdahqenrnLllsdkaradtiPeleidaddvk.as 184
                                    h+ ++t v  + p++s+ i   g+++d +    +g +k+ +g+ +++++ ++r + l++ +++++ P lei+ dd++ a+
  gi|119720113|ref|YP_920608.1| 220 HASLNTDVAVESPRSSALIRLVGASAD-GFLAHKGAVKIVRGSVNARGRLSSRLIPLTPSSKVYASPTLEIESDDAEeAQ 298
                                    **************************7.88************************************************** PP

                        UPF0051 185 HgAtvGkideeqlfYLmsRGlseeeArrlivr 216
                                    H A+ + +d + +fYL+sRG++e+eA rl ++
  gi|119720113|ref|YP_920608.1| 299 HSASQSPVDPQRIFYLRSRGFTEQEALRLALK 330
                                    **************************999776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       246  (0.0137208); expected 358.6 (0.02)
Passed bias filter:                      217  (0.0121033); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2614.14
//
Query:       gi|119720114|ref|YP_920609.1|  [L=320]
Description: sugar binding protein of ABC transporter [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.2e-44  149.9   0.0    1.1e-43  149.7   0.0    1.1  1  Peripla_BP_4  Periplasmic binding protein domain
    2.5e-08   33.7   0.0    3.5e-08   33.2   0.0    1.1  1  Peripla_BP_1  Periplasmic binding proteins and sugar binding 
    1.9e-05   24.5   0.1    6.4e-05   22.8   0.1    1.7  1  Peripla_BP_6  Periplasmic binding protein


Domain annotation for each model (and alignments):
>> Peripla_BP_4  Periplasmic binding protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.7   0.0   1.9e-47   1.1e-43       7     255 ..      35     286 ..      28     289 .. 0.95

  Alignments for each domain:
  == domain 1  score: 149.7 bits;  conditional E-value: 1.9e-47
                                    -SSTCHHHHHHHHHHHHHHHTTCEEEEEECSTT-HHHHHHHHHHHHHTT-SEEEE--SSHHHHHHHHHHHHHTT-EEEEE CS
                   Peripla_BP_4   7 dksnpffsaaregleeaakelgaevtvvgdaendaaeQvaqiedaiakgvdgiivapvdstalapalkkakaaGIpVvaf 86 
                                     + +p++ ++ +g ++aa+ l+++v++ g+++ ++++ v+ +++aia+++ gii++ +d +al +   +a a+GIp++a+
  gi|119720114|ref|YP_920609.1|  35 GPADPWWAPVIKGSQDAARLLNVKVVYSGPEKFSIQALVDLLNSAIAAKPQGIILTITDYKALDEPARRAIAQGIPIIAV 114
                                    56788*************************************************************************** PP

                                    STT....GCTTT-CEEEEEC-HHHHHHHHHHHHHHHCTTH.EEEEEETSCCCHHHHHHHHHHHHHHHHH.-TTCEECCEE CS
                   Peripla_BP_4  87 dsd....dapsgerlayvgfdneaaGelqaeylaeklggkkgkvvilaGspgdpnaeeriegfrkvlke.ypgikivaev 161
                                    + +    +++  ++l+yvg+++++aG+ +a+yl++k  +  + vvi   + g+   e r++g+++++++ ypg  + +  
  gi|119720114|ref|YP_920609.1| 115 NVPdprpPNERIPYLSYVGQNEYDAGYYLAKYLVDKGYKP-KRVVIGIHEVGHIGLETRAKGITDAITQaYPGTPVEK-- 191
                                    ****99999999999***********************98.*************************999899999988.. PP

                                    ESTTTCHHHHHHHHHHHHHTTT.ECEEEESSCCHHHCHHHHHHHTTTTSTEEEEEES-HHHHHHHHHTTSSEEEEE--HH CS
                   Peripla_BP_4 162 aganwdaekaqqalealltanp.ldgilaandgmaegalealeaaglagkvvvtgqDatpealeaikdGtidatvaqdpy 240
                                      + +d++ka +   ++lta+p  d+i++ +  +a +al+ l++  l+gkv + ++D ++  l+ai++G +da+v+q+py
  gi|119720114|ref|YP_920609.1| 192 LDITTDPTKAAEVFKSYLTAHPdTDVIFTLGPLGAHPALQVLREMKLTGKVHLLTVDIDNVILKAIEAGELDAAVSQQPY 271
                                    45679**************9966********************************************************* PP

                                    HHHHHHHHHHHHHHT CS
                   Peripla_BP_4 241 elgyaavelavallk 255
                                    ++g   v +++ ++k
  gi|119720114|ref|YP_920609.1| 272 AQGFLPVVFMYLYVK 286
                                    ***********9987 PP

>> Peripla_BP_1  Periplasmic binding proteins and sugar binding domain of LacI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   0.0   5.9e-12   3.5e-08      12     199 ..      37     233 ..      33     259 .. 0.78

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 5.9e-12
                                    TSHHHHHHHHHHHHHHHHHTEEEEEEE-SSHHHHHHHHHHHH...HTT-SEEEEE-S-GG.HHHHHHHHHH.T-EEEEES CS
                   Peripla_BP_1  12 dePffldlvkgitkaakehgvdvlllaageeedlakaidllk...akgidgliiatsdts.fdditakaes.gipviale 86 
                                     +P+++ ++kg + aa+ ++v+v+   ++e+  +++ +dll+   a ++ g+i++  d +  d+  + a + gip+ia++
  gi|119720114|ref|YP_920609.1|  37 ADPWWAPVIKGSQDAARLLNVKVVY-SGPEKFSIQALVDLLNsaiAAKPQGIILTITDYKaLDEPARRAIAqGIPIIAVN 115
                                    68*****************999865.556665666555555422278********555554888777777779******9 PP

                                    S--B-T..TTS-...EEEE-HHHHHHHHHHHHHHHHHHHT.GEEEEEE-TTSHHHHHHHHHHHHHHHT..T-GGGEEEEE CS
                   Peripla_BP_1  87 daidap..dgvP...cvipddtqageestqkLiaeghkrp.iallegpesaltakervqGflaalaea..Glevkdvhva 158
                                         p  + +P    v  +++ ag+   ++L+ +g+k   +++   +  + + + r++G  +a+ +a  G +v++ ++ 
  gi|119720114|ref|YP_920609.1| 116 VPDPRPpnERIPylsYVGQNEYDAGYYLAKYLVDKGYKPKrVVIGIHEVGHIGLETRAKGITDAITQAypGTPVEKLDI- 194
                                    885555996666221455679****************977677777777888*************99944557776666. PP

                                    -SSSSHHHHHHHHHHHHTT-TT-SEEE-SSHHHHHHHHHHH CS
                   Peripla_BP_1 159 lgsndiedaaealnelleshPeidaivaindeaalGavlal 199
                                      + d ++aae  ++ l  hP+ d+i +     a  a ++l
  gi|119720114|ref|YP_920609.1| 195 --TTDPTKAAEVFKSYLTAHPDTDVIFTLGPLGAHPALQVL 233
                                    ..568999******************987666666555555 PP

>> Peripla_BP_6  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.1   1.1e-08   6.4e-05      89     250 ..     104     272 ..      35     279 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.1e-08
                                    HHHHT-EEEE...SS-HHCCTTSTTEEESS--HHHHHHHHHHHHHHH.TTSCEEEEEEES.SHHHHHHHH.HHHHHHHCC CS
                   Peripla_BP_6  89 lakdgvpvig...pagltgekcspyvfslgpsysaqasalveylake.lggkkvalvyad.yafgregia.alkaaakaa 162
                                    + ++g+p+i    p    +++  py  ++g++ ++ +  l++yl+++ ++ k+v++  +     g e++a ++++a+++a
  gi|119720114|ref|YP_920609.1| 104 AIAQGIPIIAvnvPDPRPPNERIPYLSYVGQNEYDAGYYLAKYLVDKgYKPKRVVIGIHEvGHIGLETRAkGITDAITQA 183
                                    345799999954332444789************************96345667766556658888888664888888766 PP

                                    .TEEEEEEEEE-TTHHHHHHHHHHHHTTT-SE.EEEESSHHHHHHHHHHHHHTT-SSSCEEEECCC-CHHHHHHHHHHHH CS
                   Peripla_BP_6 163 .Ggevvgeepvplgttdfsaqvlqikaagada.vllagtgadlaallkaaaeaGldakrillvswsgseedlkalggeaa 240
                                      g+ v+  +++++ t  +++      a++d+ v+++ ++  +  +l+ ++e  l++k + l++ ++++  lka++++ +
  gi|119720114|ref|YP_920609.1| 184 yPGTPVEKLDITTDPTKAAEVFKSYLTAHPDTdVIFTLGPLGAHPALQVLREMKLTGK-VHLLTVDIDNVILKAIEAGEL 262
                                    4788889*************************************************97.******************999 PP

                                    TTEEEEESCS CS
                   Peripla_BP_6 241 egvlavtpyf 250
                                    + +++ +py+
  gi|119720114|ref|YP_920609.1| 263 DAAVSQQPYA 272
                                    9999998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2129.59
//
Query:       gi|119720115|ref|YP_920610.1|  [L=328]
Description: inner-membrane translocator [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.7e-45  153.8  38.6    7.8e-45  153.1  38.6    1.3  1  BPD_transp_2  Branched-chain amino acid transport system / pe


Domain annotation for each model (and alignments):
>> BPD_transp_2  Branched-chain amino acid transport system / permease component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.1  38.6   4.3e-49   7.8e-45       4     267 ..      49     313 ..      46     314 .. 0.89

  Alignments for each domain:
  == domain 1  score: 153.1 bits;  conditional E-value: 4.3e-49
                   BPD_transp_2   4 nlltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsllllallvallvgaavglllgllvlrlkvd 83 
                                    ++ltla+ l+ ++lG+a+++ i+G++nl++++++al  + +a++++++    lla +v+l+++  +g+l+g+ +++++++
  gi|119720115|ref|YP_920610.1|  49 SILTLAGELGVVSLGVAFLM-ITGEFNLSVSSVYALVPMGVAIMANMGVD-MLLASVVMLALAYGIGVLVGYVTIKTGIP 126
                                    699*****************.****************9999999999998.99*************************** PP

                   BPD_transp_2  84 eliitllllsvlvgltlllltgitsgvkgqs.svkellgf.agallsflsavivllalllvlavllllrrtrfGralrav 161
                                    ++i++l+++ +l+g++l     it+g      + ++l+   +g     +    ++++++l++++ ++l  t++G++ +av
  gi|119720115|ref|YP_920610.1| 127 SFITSLGMMMFLRGILL----AITGGFPVRLeHDHWLMYAlNGPVGEQGLRTSAAWLVALTALLAFILDWTPYGNWTYAV 202
                                    *****************....233322222202222222212222233333444999*********************** PP

                   BPD_transp_2 162 geneeaaralGinvkrvklltfvisgalAglaGallalllgsippnigvglgfnaiaavvlGga......gsllgtviGa 235
                                    g ++++ar lG++v++vkll f +s++lAglaG++   ++++++p  g+gl+++ai+++vlGg+      gs+ gt++Ga
  gi|119720115|ref|YP_920610.1| 203 GASPNTARELGVSVTKVKLLNFGLSSLLAGLAGLMALSRFKVVDPTLGQGLELEAITSAVLGGClltggyGSITGTFLGA 282
                                    ******************************************************************************** PP

                   BPD_transp_2 236 liigvvksllltllgiptelarvllgallilv 267
                                    ++i++    +l l  +p  ++++++g++li++
  gi|119720115|ref|YP_920610.1| 283 FLIAMTRV-GLVLAKAPAYWYSAFIGVILIVA 313
                                    ********.999999***************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       964  (0.0537676); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2139.74
//
Query:       gi|119720116|ref|YP_920611.1|  [L=259]
Description: ABC transporter related [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.6e-30  104.0   0.0    1.1e-29  103.6   0.0    1.2  1  ABC_tran     ABC transporter
    3.5e-09   36.9   0.3    0.00086   19.2   0.0    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    8.8e-06   25.3   0.2     0.0002   20.9   0.2    2.0  1  SMC_N        RecF/RecN/SMC N terminal domain
    0.00032   20.5   0.1     0.0015   18.3   0.1    1.8  1  AAA_30       AAA domain
    0.00032   19.6   1.0       0.12   11.2   0.2    2.9  2  ABC_ATPase   Predicted ATPase of the ABC class
    0.00056   19.0   0.1      0.001   18.1   0.1    1.4  1  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
    0.00072   19.3   0.1       0.31   10.8   0.0    2.2  2  IstB_IS21    IstB-like ATP binding protein
     0.0017   18.1   0.0     0.0033   17.1   0.0    1.4  1  AAA_29       P-loop containing region of AAA domain
     0.0061   17.1   0.0       0.01   16.4   0.0    1.3  1  AAA_23       AAA domain
  ------ inclusion threshold ------
      0.058   13.8   0.1       0.07   13.5   0.1    1.4  1  AAA_16       AAA ATPase domain
      0.064   13.2   0.0       0.13   12.1   0.0    1.5  1  RsgA_GTPase  RsgA GTPase
      0.071   12.5   0.0         13    5.1   0.0    2.3  2  TniB         Bacterial TniB protein
      0.073   13.0   0.0       0.14   12.0   0.0    1.5  1  NACHT        NACHT domain
      0.097   12.7   0.0       0.22   11.5   0.0    1.6  1  TsaE         Threonylcarbamoyl adenosine biosynthesis protein
       0.11   12.6   0.1       0.15   12.1   0.0    1.6  1  MMR_HSR1     50S ribosome-binding GTPase
       0.11   12.0   0.0       0.19   11.3   0.0    1.3  1  AAA_27       AAA domain
       0.16   11.1   0.0       0.28   10.3   0.0    1.3  1  DUF815       Protein of unknown function (DUF815)
       0.27   10.9   0.0       0.38   10.4   0.0    1.2  1  AAA_15       AAA ATPase domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.6   0.0   1.1e-32   1.1e-29       1     137 []      21     176 ..      21     176 .. 0.94

  Alignments for each domain:
  == domain 1  score: 103.6 bits;  conditional E-value: 1.1e-32
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvren 79 
                                    l+ v++++ + e+v++vG+nGaGKStL+k++ag ++p++G++ ++g+++   ++ e   + i+++ q+  l + l++ +n
  gi|119720116|ref|YP_920611.1|  21 LRGVDFHVGRAEVVGLVGDNGAGKSTLVKIIAGVYQPDAGQMFFEGQPVVFrHPSEARARGIEIVYQHLALIDLLSIDRN 100
                                    6789********************************************99878999999********************* PP

                                    ....................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    ....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ....................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                                         +++e+  +l+ +gl     +  +++ ++LSgG++q va+ ra+  k+kll+lDEpta
  gi|119720116|ref|YP_920611.1| 101 iflgreptkrigpiaildkaRMEREAWSILQDIGLRR--IRSPSERVAKLSGGERQSVAIGRAMHFKAKLLILDEPTA 176
                                    *****************99999999*********999..44444667*****************************97 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   8.6e-07   0.00086       2      31 ..      34      61 ..      33      87 .. 0.76
   2 !   15.7   0.0   9.9e-06    0.0098     236     299 ..     147     207 ..     137     210 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 8.6e-07
                         AAA_21  2 nvliGpNgsGKSnLLdaldllarldrdveg 31
                                    +l+G+Ng+GKS+L +++ ++ +  +d+ +
  gi|119720116|ref|YP_920611.1| 34 VGLVGDNGAGKSTLVKIIAGVYQ--PDAGQ 61
                                   68****************98874..44444 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 9.9e-06
                         AAA_21 236 elSdGtkrllalltallralkkgsllliDEpEngLHPkllrrll.ellkelsrngaQviltTHSp 299
                                    +lS G ++  a+  a++  +   +ll++DEp + L  + +rr+l  +l+ +++ g+ vi+ +H+ 
  gi|119720116|ref|YP_920611.1| 147 KLSGGERQSVAIGRAMHFKA---KLLILDEPTAALSVRETRRVLdHVLEVKKQ-GVSVIIISHNI 207
                                    56777777777777777766...99*******************666677766.*********95 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.2     2e-07    0.0002      26     211 ..      33     220 ..      24     227 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2e-07
                                    EEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEE.SSSSSSCEEEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
                          SMC_N  26 ftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkk.lkiekeevsisrrvk 104
                                    +  +vG NG+GKs l+  i  v   ++  ++   + + ++++  + +++    +ei++++     l   + ++ + r+  
  gi|119720116|ref|YP_920611.1|  33 VVGLVGDNGAGKSTLVKIIAGVYQPDAG-QMF-FEGQPVVFR--HPSEARARGIEIVYQHLALIdLLSIDRNIFLGREPT 108
                                    56789**************999987777.443.356778887..344445556888887777663333344455555555 PP

                                    TTSEEEEEETTEEE-HHHHHHHHHCTT-STT........CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 105 rkgeseykingkevtkkevsellesagiske........lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknv 176
                                    +     ++i +k   ++e  ++l++ g+ +          LSgGe++ va+    A+    +a l +lDe  aaL  +++
  gi|119720116|ref|YP_920611.1| 109 KRIG-PIAILDKARMEREAWSILQDIGLRRIrspservaKLSGGERQSVAIGR--AM--HFKAKLLILDEPTAALSVRET 183
                                    5555.4555666666677888999999988788999999*******9766653..44..4467799*************9 PP

                                    HHHHHHHHHHCTT.SEEEEE-SSHHHCCC-.SCEEEE CS
                                    xxxxxxxxxxxxx.xxxxxxxxxxxxxxxx.xxxxxx RF
                          SMC_N 177 kkvaellkekskn.aQfivislreemleka.dklvgv 211
                                    ++v + + e +k+ + +i+is++  ++ ++ d++v +
  gi|119720116|ref|YP_920611.1| 184 RRVLDHVLEVKKQgVSVIIISHNIYHVYEVsDRIVAL 220
                                    999887766666659*******976554442777665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   1.5e-06    0.0015      16     120 ..      29     201 ..      23     205 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.5e-06
                         AAA_30  16 sgdrvavltGpAGtGKttalkalreaweaa.g......grviglAptgkaAkvLa......................... 63 
                                    +++ v+ l+G  G+GK+t++k ++ +++ + g      ++v+   p+++ A+ ++                         
  gi|119720116|ref|YP_920611.1|  29 GRAEVVGLVGDNGAGKSTLVKIIAGVYQPDaGqmffegQPVVFRHPSEARARGIEivyqhlalidllsidrniflgrept 108
                                    5567999*********************99679****9999999********9999999999999999999998888888 PP

                         AAA_30  64 ......................eelgi.....eastiakllkrlk.....grarlepgtllivDEagmv.dtkqlaallk 110
                                                          +++g+     +++++akl    +     gra   +++lli DE   + + ++++++l+
  gi|119720116|ref|YP_920611.1| 109 krigpiaildkarmereawsilQDIGLrrirsPSERVAKLSGGERqsvaiGRAMHFKAKLLILDEPTAAlSVRETRRVLD 188
                                    8888888888887777777777455544445599999999988889999965556667*******765559999999988 PP

                         AAA_30 111 aaek...agakvi 120
                                    ++ +   +g++vi
  gi|119720116|ref|YP_920611.1| 189 HVLEvkkQGVSVI 201
                                    7654111456665 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.022        21     246     270 ..      33      56 ..      22      70 .. 0.85
   2 !   11.2   0.2   0.00012      0.12     324     412 ..     149     221 ..     140     235 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.022
                                    EEEEEE-TTSSHHHHHHHHHHCCSE CS
                     ABC_ATPase 246 vtlIvGggfhGKsTLLeAlekGvyn 270
                                    v+ +vG +  GKsTL++ + +Gvy+
  gi|119720116|ref|YP_920611.1|  33 VVGLVGDNGAGKSTLVKII-AGVYQ 56 
                                    66789***********966.68886 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00012
                                    -HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HHHHHHS-GGG--B--HHHCHHHHHHHH--EEEEEESS-GCCTT CS
                     ABC_ATPase 324 SGStsqAanimealeagakllLiDEDtsAtNlmirDermqelvskekepitplvdrvrelykklgvstilvvggsgdyld 403
                                    SG   q+++i +a++ +akll++DE t+A                     + ++d v e+ kk gvs+i+++  + +  +
  gi|119720116|ref|YP_920611.1| 149 SGGERQSVAIGRAMHFKAKLLILDEPTAALSVRET---------------RRVLDHVLEV-KKQGVSVIIISHNIYHVYE 212
                                    89999999999999999999999999999543222...............2345666666.6777777777777777777 PP

                                    T-SEEEEEE CS
                     ABC_ATPase 404 vAdtvilme 412
                                    v+d++++++
  gi|119720116|ref|YP_920611.1| 213 VSDRIVALD 221
                                    777777776 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1     1e-06     0.001      19      49 ..      21      51 ..      13      63 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1e-06
                                   HHHHGGG-S-SEEEEEEE-TTSSHHHHHHHH CS
                           MeaB 19 lerllakaGraqvvGltGvPGaGkstlveal 49
                                   l+ +  + Gra+vvGl G  GaGkstlv+ +
  gi|119720116|ref|YP_920611.1| 21 LRGVDFHVGRAEVVGLVGDNGAGKSTLVKII 51
                                   66677789*******************9865 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   0.00031      0.31      34     115 ..      17      98 ..       8     134 .. 0.75
   2 !    6.7   0.0    0.0053       5.3     106     149 ..     163     206 ..     143     219 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00031
                      IstB_IS21  34 kvkeLatlsf.iekkenivllGpsGvGKshlaialgveavraglsvlfvrvedLveelkrarrdgklaralkrllkvdll 112
                                    +v++L++ +f + ++e + l+G  G+GKs l   ++     +  +++f   + ++++ + ar+ g ++   ++l+ +dll
  gi|119720116|ref|YP_920611.1|  17 RVEALRGVDFhVGRAEVVGLVGDNGAGKSTLVKIIAGVYQPDAGQMFFEGQPVVFRHPSEARARG-IEIVYQHLALIDLL 95 
                                    5789999998689999999***********99888766666666667776777777766666665.56666666667777 PP

                      IstB_IS21 113 ilD 115
                                     +D
  gi|119720116|ref|YP_920611.1|  96 SID 98 
                                    666 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0053
                      IstB_IS21 106 llkvdllilDdlgllpldqaeaellfeviekryerrsiiitsnl 149
                                      k++llilD+       ++ +++l +v+e + +  s+ii s  
  gi|119720116|ref|YP_920611.1| 163 HFKAKLLILDEPTAALSVRETRRVLDHVLEVKKQGVSVIIISHN 206
                                    46889******9999888999999******99999999998765 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   3.3e-06    0.0033      15      46 ..      24      55 ..      19      65 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.3e-06
                         AAA_29 15 htieidlkgatlltGpsGsGKSTllDAiqalL 46
                                    ++++ +++++ l+G++G+GKSTl+  i+ + 
  gi|119720116|ref|YP_920611.1| 24 VDFHVGRAEVVGLVGDNGAGKSTLVKIIAGVY 55
                                   566777777888************96666555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0     1e-05      0.01      15      39 ..      24      51 ..      11      61 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1e-05
                         AAA_23 15 idF...skgltlItGpNGaGKTTildAi 39
                                   +dF      ++ ++G+NGaGK+T++  i
  gi|119720116|ref|YP_920611.1| 24 VDFhvgRAEVVGLVGDNGAGKSTLVKII 51
                                   566555668999************9877 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1     7e-05      0.07      22      64 ..      29      74 ..      15     203 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7e-05
                         AAA_16 22 grpelvllsGesGvGKsslvrellralekd.ggiflrgkcdql..e 64
                                   gr e+v l+G+ G GKs+lv+ ++  ++ d g  f++g+ + +  +
  gi|119720116|ref|YP_920611.1| 29 GRAEVVGLVGDNGAGKSTLVKIIAGVYQPDaGQMFFEGQPVVFrhP 74
                                   5669999*************99998777774466688877777441 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00014      0.13      99     121 ..      31      53 ..      14      63 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00014
                                    TSEEEEECSTTSSHHHHHHHHCT CS
                    RsgA_GTPase  99 dktsvlvGqSGvGKStLinallp 121
                                     +++ lvG  G+GKStL++ +++
  gi|119720116|ref|YP_920611.1|  31 AEVVGLVGDNGAGKSTLVKIIAG 53 
                                    47888*************99987 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.013        13      34      66 ..      30      62 ..      17      84 .. 0.74
   2 ?    5.1   0.1     0.014        13      93     144 ..     137     188 ..     114     203 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.013
                           TniB 34 rmpnlllvGdsnnGKtmivekFarlhppekded 66
                                   r + + lvGd   GK+++v+  a  ++p+  + 
  gi|119720116|ref|YP_920611.1| 30 RAEVVGLVGDNGAGKSTLVKIIAGVYQPDAGQM 62
                                   6667789************98887777766554 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.014
                           TniB  93 algaplkararvskleqqvlrl..lrelkvrvLiiDEihnllagsarkqrefln 144
                                    +++ p +  a++s  e+q +++    ++k+++Li+DE   +l  s+r+ r++l 
  gi|119720116|ref|YP_920611.1| 137 RIRSPSERVAKLSGGERQSVAIgrAMHFKAKLLILDEPTAAL--SVRETRRVLD 188
                                    5555555555555444554444004467899******99999..6666666665 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00014      0.14       2      47 ..      33      80 ..      32     104 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00014
                                   CEEEEC-TTTCHHHHHHHHHHHHC..TS-SCCCC-SEEEEEETTTTTT CS
                          NACHT  2 lvilqGeaGsGKTtLlqklalawa..egklpqgafklvFflslrelsr 47
                                   +v l G++G GK+tL++ +a   +  +g+ + +  ++vF +++ ++ r
  gi|119720116|ref|YP_920611.1| 33 VVGLVGDNGAGKSTLVKIIAGVYQpdAGQMFFEGQPVVFRHPSEARAR 80
                                   67799***********98875443113333333357777777666665 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00023      0.22      19      40 ..      31      52 ..       7      59 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00023
                                   TEEEEEEESTTSSHHHHHHHHH CS
                           TsaE 19 gdvilLeGdLGaGKTtlvrgla 40
                                   ++v+ L Gd GaGK+tlv+ +a
  gi|119720116|ref|YP_920611.1| 31 AEVVGLVGDNGAGKSTLVKIIA 52
                                   56799**************987 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00015      0.15       2      39 ..      34      77 ..      33     213 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00015
                                   EEEEESTTSSHHHHHHHHHT.....S.TEEESSSTTSSSSEEEE CS
                       MMR_HSR1  2 vaivGrpNvGKStLinaltg.....e.kaivsdkpgtTrdineg 39
                                   v++vG   +GKStL++ + g     + +   + +p + r++ e+
  gi|119720116|ref|YP_920611.1| 34 VGLVGDNGAGKSTLVKIIAGvyqpdAgQMFFEGQPVVFRHPSEA 77
                                   89*************99988444331233444555555555444 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00019      0.19       9      45 ..      13      50 ..       9      55 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00019
                         AAA_27  9 eryGkftd.rsldfsaeeadlhliyGpNEAGKstalrA 45
                                   +r+G+++  r +df+ ++a++  ++G N AGKst+++ 
  gi|119720116|ref|YP_920611.1| 13 KRFGRVEAlRGVDFHVGRAEVVGLVGDNGAGKSTLVKI 50
                                   79999987468***********************9875 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00028      0.28      53      78 ..      31      56 ..      24      63 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00028
                         DUF815 53 annvLLwGarGtGKSslvkallneya 78
                                   a+ v L+G+ G+GKS+lvk +   y+
  gi|119720116|ref|YP_920611.1| 31 AEVVGLVGDNGAGKSTLVKIIAGVYQ 56
                                   667789*************9987776 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00039      0.38      26      44 ..      34      52 ..      24      95 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00039
                         AAA_15 26 tvliGkNnsGKSsileald 44
                                     l+G N++GKS++++++ 
  gi|119720116|ref|YP_920611.1| 34 VGLVGDNGAGKSTLVKIIA 52
                                   569*************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 1788.35
//
Query:       gi|119720117|ref|YP_920612.1|  [L=447]
Description: monomethylamine methyltransferase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-69  235.4   0.0    1.3e-69  235.2   0.0    1.0  1  MtmB      Monomethylamine methyltransferase MtmB


Domain annotation for each model (and alignments):
>> MtmB  Monomethylamine methyltransferase MtmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  235.2   0.0   7.3e-74   1.3e-69       9     444 ..      10     442 ..       7     447 .] 0.94

  Alignments for each domain:
  == domain 1  score: 235.2 bits;  conditional E-value: 7.3e-74
                           MtmB   9 rakkGekveedewdyveipqkaeelkekydikfenefiPededladrlfqaGlelLvetGvycidtervikvteeeileg 88 
                                    ra+kGe ve++++d + + ++ +el+++y ++f+       edla+ +f+aG+ l vetG+y +d  rv ++teee++e+
  gi|119720117|ref|YP_920612.1|  10 RARKGEYVEQKRFDLERVSRRVAELEKEYGVSFDPSSPAPSEDLAKPVFEAGFTLAVETGLYVVDESRVARFTEEEVREA 89 
                                    899*******************************88777789************************************** PP

                           MtmB  89 ikkapkklelGegkdaveleerksndskkPiiqgGPtGapvsedvfleviqsyaqeplvdtivsGvletvegkeaktksP 168
                                    +++ap++l++G+gkd   l++r   d+    + gG  G+pv  + f +   sya  p vd++ +G ++ v g++    +P
  gi|119720117|ref|YP_920612.1|  90 LRNAPRELRVGRGKDERVLRARGPGDRV--FVFGGLAGTPVPLEFFEASAASYAAVPRVDALDHGSIQAVAGEAVRGYAP 167
                                    **********************999875..799*********************************************** PP

                           MtmB 169 feikatlaearlvkeatslagrpglalkGpetplsaagrlaadlaeglresdshevsqLnelkidvealnliagykangd 248
                                     e  a ++ea  v++a + +grpg+ + G+e ++s+ g l+a   ++l e d++    Lnelk+d+ +l++     a+g 
  gi|119720117|ref|YP_920612.1| 168 SEALAGIEEAEGVRRALRAVGRPGMHVLGAESSVSSVGSLSALSLGLLGEGDAQLLPVLNELKTDYGQLTKAYVGLARGL 247
                                    **********************************************************************9999999998 PP

                           MtmB 249 vilveqmPifGGyaggieetaivdvattlasfvltdasfhldGpihirwgstttretlqiaahaaaaidantdlllanqy 328
                                    +      P+ GGya g  + aiv va+tl + v  +a + l  p+hi   +t+t e +++ + +  a ++++ l      
  gi|119720117|ref|YP_920612.1| 248 IGAALVDPVVGGYARGPAGSAIVSVAETLLALVAYEAGYFLVHPVHILRKATSTLECMWVESVVGLA-NRYMGLPVVADI 326
                                    8888889*******************************************************99998.89********** PP

                           MtmB 329 ytlaGpctemclletaaqaiadtasGrellsGvaaakGvvkdkttGlearlmgevaiaaaglevs..evneildklvsky 406
                                    ++  G +t   l+e+aa +    asG ++l G+  a G+ + +  G+e+ +++ +a  +a+ +vs   +     +l+ ky
  gi|119720117|ref|YP_920612.1| 327 WPANGGGTREYLYEAAANTFVAVASGLNVL-GPVPANGT-QPNGGGFESWFVASLADLVAEKKVSvgAAWSAALELYEKY 404
                                    ****************************98.89999996.56689************9999877622566777799**** PP

                           MtmB 407 eknyakaPaGkrfqeCydvktvePtdeyldvydkalkk 444
                                     ++ +++  Gk+f e yd+k+++P+ e+ +   ++l++
  gi|119720117|ref|YP_920612.1| 405 ADKLSSPNPGKPFWELYDLKSLKPSAEWEKTVWEVLRE 442
                                    ***************************97765555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.22s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 3229.36
//
Query:       gi|119720118|ref|YP_920613.1|  [L=224]
Description: methionine synthase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      6e-28   97.3   2.5      6e-28   97.3   2.5    1.6  2  B12-binding    B12 binding domain
    8.6e-16   58.2   0.1    2.2e-15   56.8   0.1    1.7  1  B12-binding_2  B12 binding domain


Domain annotation for each model (and alignments):
>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0      0.85   7.6e+03      40      55 ..      21      37 ..      12      39 .. 0.63
   2 !   97.3   2.5   6.7e-32     6e-28       2     120 ..      94     206 ..      93     207 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.85
                    B12-binding 40 n.edivaairaekpdvv 55
                                   + e++v+++ +   dvv
  gi|119720118|ref|YP_920613.1| 21 TvERLVSEALEAGCDVV 37
                                   34677777777777766 PP

  == domain 2  score: 97.3 bits;  conditional E-value: 6.7e-32
                    B12-binding   2 kvllatvggdlhplGlavlaaalrdagfeVqllganvenedivaairaekpdvvglSalltsqleavkelvel..lkrir 79 
                                    +v+++tv gd+h++G++++a +lr +gfeV++lg++v++e++v+a+++  ++vvg+Sallt+++ ++++++++  +++ r
  gi|119720118|ref|YP_920613.1|  94 RVVIGTVRGDIHDIGKNLVATMLRVNGFEVVDLGVDVPPERFVEAVEKYGAEVVGMSALLTTTMLEMRNVIDAlkAAGLR 173
                                    89***********************************************************************99999** PP

                    B12-binding  80 prvkvvvGGahpsldpeetleaklgiddvvvgegedaleal 120
                                    ++vkv+vGGa+++   ++   + +g +d    +g+da++a+
  gi|119720118|ref|YP_920613.1| 174 DKVKVIVGGAPVTEEIAR---E-IG-AD---AYGRDAVDAV 206
                                    **********95555555...6.**.66...69*9999886 PP

>> B12-binding_2  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.8   0.1   2.5e-19   2.2e-15       3      72 ..       8      77 ..       6      79 .. 0.95

  Alignments for each domain:
  == domain 1  score: 56.8 bits;  conditional E-value: 2.5e-19
                  B12-binding_2  3 erlhwaivhgdkegieelidealaqgsaavdvlndvllpamkeVGdlfgagelflpqvllsaevmkkava 72
                                    ++ + + ++d   +e+l+ eal++g ++v+v++++l ++m eVG +f++ge+flp+++ ++++++++++
  gi|119720118|ref|YP_920613.1|  8 AEISRRLADLDAGTVERLVSEALEAGCDVVEVVEEGLRKGMVEVGVRFERGEYFLPELVEAGDIFNSVME 77
                                   57889999********************************************************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1714.59
//
Query:       gi|119720119|ref|YP_920614.1|  [L=93]
Description: hypothetical protein Tpen_1213 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 769.12
//
Query:       gi|119720120|ref|YP_920615.1|  [L=144]
Description: hypothetical protein Tpen_1214 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.6e-07   29.7  14.6      1e-06   29.1  14.6    1.3  1  Arch_flagellin  Archaebacterial flagellin
     0.0019   19.1   4.5     0.0019   19.1   4.5    2.0  2  Pilin_N         Archaeal Type IV pilin, N-terminal
  ------ inclusion threshold ------
      0.013   15.8   1.9      0.023   15.0   1.8    1.5  1  PapD_C          Pili assembly chaperone PapD, C-terminal doma
      0.031   14.1   0.1      0.074   12.9   0.1    1.7  1  RRM_9           RNA recognition motif
       0.54   10.6   9.2       0.99    9.7   9.2    1.5  1  MacB_PCD        MacB-like periplasmic core domain


Domain annotation for each model (and alignments):
>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1  14.6   2.8e-10     1e-06       8     164 .]      12     140 ..       5     140 .. 0.80

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 2.8e-10
                                    HHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHT--EEEEEEEEEE-SSSSSEEEEEEE--TTS--EEGGG CS
                 Arch_flagellin   8 lIvfIAmVlVAAvaagvlinta.gflqqkaqstgeesteqvssgleitgdvgdsatngtineitiyvklnaGsspidlnk 86 
                                      ++I+  ++AAv+a+++i+   g+l+q+a      st+q++++++i  + +    ng  +++t yv+ n G  ++++n 
  gi|119720120|ref|YP_920615.1|  12 TLLLIVIAVAAAVLAYIWITGYqGTLTQQA------STTQLQERIAIEAVSY----NG--TTLTAYVR-NVG--DVKVNI 76 
                                    457899999********9986525666655......688*********9999....22..3389****.***..567777 PP

                                    -EEEEEESS--EE--E..................T-EE-TT-EEEEEEE--TTT---TT-EEEEEEE-SSS--EEEEE CS
                 Arch_flagellin  87 ttisvtddgqetlltadefgivvisdtdgsltngdevlekgekvelevnvneddgitagdevsvevvpenGasttief 164
                                    tti v++            +i++ ++++ +l     v+++g++ +++  v     +tag++++vevv+++G ++++ f
  gi|119720120|ref|YP_920615.1|  77 TTIYVFNGS---------GTIINSNNNNYQLATP-VVISPGQVSTVTTSV----TLTAGNTYTVEVVTKYGTKASYVF 140
                                    777766666.........4677777777777777.************999....5******************99865 PP

>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   4.5   5.2e-07    0.0019       1      50 [.       4      59 ..       4     101 .. 0.56
   2 ?   -0.6   0.1      0.71   2.5e+03      21      47 ..     107     133 ..      98     142 .. 0.49

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 5.2e-07
                        Pilin_N  1 eAVSpViGviLmvaitvIlaAviaaf.vlgl.asneekapqasievk.....idssa 50
                                   ++VSpVi  +L+++i v +aAv+a + ++g+    +++a  ++++++     +++++
  gi|119720120|ref|YP_920615.1|  4 RGVSPVIATLLLIVIAV-AAAVLAYIwITGYqGTLTQQASTTQLQERiaieaVSYNG 59
                                   69*********999876.677777652777754555555556665553322222222 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.71
                        Pilin_N  21 Aviaafvlglasneekapqasievkid 47 
                                    + ++++ +++  ++ ++  +++ +k++
  gi|119720120|ref|YP_920615.1| 107 GQVSTVTTSVTLTAGNTYTVEVVTKYG 133
                                    444444444433344444444444444 PP

>> PapD_C  Pili assembly chaperone PapD, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   1.8   6.4e-06     0.023       5      60 ..      78     134 ..      74     137 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 6.4e-06
                                    SSS-EEEEEEEEEETTEEEEEEE.EEE-TTEEEEETT--S--TT-EEEEEEE-TTS- CS
                         PapD_C   5 tPYyvtfsslevkgggkslalea.gmvaPfssatfakkaapaagatvsftvINDyGg 60 
                                    t Y ++ s+  +++++++++l++ ++++P++  t++++ + +ag+t +++v+  yG 
  gi|119720120|ref|YP_920615.1|  78 TIYVFNGSGTIINSNNNNYQLATpVVISPGQVSTVTTSVTLTAGNTYTVEVVTKYGT 134
                                    5677888888899999****9999*******************************95 PP

>> RRM_9  RNA recognition motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   2.1e-05     0.074      20      49 ..      44      73 ..      27      85 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.1e-05
                          RRM_9 20 isRktrvalqnasveggvlvgyVktkkdae 49
                                    + + r+a++ +s++g +l++yV++  d++
  gi|119720120|ref|YP_920615.1| 44 TQLQERIAIEAVSYNGTTLTAYVRNVGDVK 73
                                   55678*******************988875 PP

>> MacB_PCD  MacB-like periplasmic core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   9.2   0.00028      0.99       3      71 ..      11     101 ..       9     143 .. 0.48

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00028
                       MacB_PCD   3 ltvLGiaiGvaaviaivslgeglqasvlsqisdlgnlv.tvtpgk.gsges............................. 51 
                                     t+L i+i+vaa ++  ++++g q ++++q s   +l  ++ + + +++++                             
  gi|119720120|ref|YP_920615.1|  11 ATLLLIVIAVAAAVLAYIWITGYQGTLTQQASTT-QLQeRIAIEAvSYNGTtltayvrnvgdvkvnittiyvfngsgtii 89 
                                    699**************************99944.333256666552222222222222222222222222222222221 PP

                       MacB_PCD  52 .lsdpdvealrrevpveavap 71 
                                      + ++          + ++p
  gi|119720120|ref|YP_920615.1|  90 nSNNNN---------YQLATP 101
                                    111111.........111222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1337  (0.0745719); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1008.41
//
Query:       gi|119720121|ref|YP_920616.1|  [L=275]
Description: UDP-glucose/GDP-mannose dehydrogenase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-08   34.1   0.0    3.7e-08   33.4   0.0    1.3  1  UDPG_MGDP_dh     UDP-glucose/GDP-mannose dehydrogenase family
    0.00041   19.7   0.0    0.00065   19.1   0.0    1.3  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
     0.0029   17.2   0.1        3.1    7.4   0.0    3.0  3  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
  ------ inclusion threshold ------
      0.015   15.5   0.0      0.044   14.1   0.0    1.8  1  TrkA_N           TrkA-N domain
       0.24   11.6   0.0       0.77    9.9   0.0    1.9  2  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
       0.39   11.1   7.4        1.2    9.6   7.4    1.8  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain


Domain annotation for each model (and alignments):
>> UDPG_MGDP_dh  UDP-glucose/GDP-mannose dehydrogenase family, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.0   1.2e-11   3.7e-08       3      92 ..     154     239 ..     152     241 .. 0.83

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 1.2e-11
                   UDPG_MGDP_dh   3 AEliKlaaNaflatkIsfiNelanlcealgidveeVieavgldpr.igpkf.lkpglGvGGsclpkDvkaLvalaeelgl 80 
                                     E++Kl + +++a++I+ + el++++ ++g+d++ V+e ++  ++ +g++  + p+  +GG+cl   ++ L ++  +   
  gi|119720121|ref|YP_920616.1| 154 LEIAKLWETVYRAVMIASWQELHRVAARYGADIRVVAEFIAEVHEvLGDRPvYFPDY-IGGHCLIPNTEILNKAYPS--- 229
                                    599***********************************9998877688877366776.******9999999876644... PP

                   UDPG_MGDP_dh  81 eaelleavrevN 92 
                                      +l+e v e+N
  gi|119720121|ref|YP_920616.1| 230 --KLFEFVLESN 239
                                    ..4555555555 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   2.2e-07   0.00065      38     124 ..       3      80 ..       1      84 [. 0.82

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 2.2e-07
                                    EEEEES-SHHHHHHHHHHH.HTT-EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SEEEE-S--STTTTTSBSHHHHHC CS
                   2-Hacid_dh_C  38 tvGiiGlGrIGqavakrlk.afgmkviaydrskkkeeeeeelgvelvsleellaesDivslhlpltpetrhlinaeelak 116
                                    +v ++GlG++G+av ++l+ + +m+v++yd  ++k         +++ le++ a  D++ +++p tp   + +++   +k
  gi|119720121|ref|YP_920616.1|   3 RVLVVGLGEVGSAVYEVLRdSGRMEVYGYDLDPSK---------TVHRLEDVPAPLDYLHVAIPFTPRFVDAVKSY-AEK 72 
                                    799****************77789********883.........34579999999999999999999877777654.477 PP

                                    STTTEEEE CS
                   2-Hacid_dh_C 117 mkkgaili 124
                                    +k+ a+++
  gi|119720121|ref|YP_920616.1|  73 LKPRAVFV 80 
                                    77777776 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0     0.001       3.1       2      35 ..       3      37 ..       2      49 .. 0.88
   2 !    5.7   0.0    0.0033        10     103     129 ..      62      90 ..      44      98 .. 0.77
   3 ?    0.3   0.0      0.15   4.6e+02     134     157 ..     136     155 ..     122     169 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.001
                                   EEEEE--STTHHHHHHHHHHCT.SEEEEE-S-HHH CS
                 UDPG_MGDP_dh_N  2 kisviGlGYvGlvtaavlaeig.hevigvDideek 35
                                   ++ v+GlG vG     vl   g +ev g D d +k
  gi|119720121|ref|YP_920616.1|  3 RVLVVGLGEVGSAVYEVLRDSGrMEVYGYDLDPSK 37
                                   799*******************99********876 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0033
                                    HHHHHHHHHHC..EEEEEE-S---TTHHH CS
                 UDPG_MGDP_dh_N 103 aarsiaealkk..gkvvvvkSTvpvgtae 129
                                     +++++++++k   + v v STv++gt++
  gi|119720121|ref|YP_920616.1|  62 FVDAVKSYAEKlkPRAVFVHSTVAPGTTR 90 
                                    5667777777766788999********97 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.15
                                    HHHHHHCSS-TTCEEEEE------ CS
                 UDPG_MGDP_dh_N 134 kileeaskkkgvdfdvvsnPEflr 157
                                    + le    + g +++++s+PE l+
  gi|119720121|ref|YP_920616.1| 136 RHLE----AAGFKVKLASSPESLE 155
                                    2222....236899*******886 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.5e-05     0.044       1      38 [.       4      43 ..       4      54 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.5e-05
                                   EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHH.HHHHH CS
                         TrkA_N  1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeer.veelr 38
                                   ++++GlG+vG++++e L++ g ++v++ d d+++ v++l+
  gi|119720121|ref|YP_920616.1|  4 VLVVGLGEVGSAVYEVLRDsGRMEVYGYDLDPSKtVHRLE 43
                                   68*****************77788******9976466655 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00026      0.77       3      42 ..       5      45 ..       3      99 .. 0.73
   2 ?   -3.1   0.0       2.6   7.9e+03      17      29 ..     137     149 ..     132     189 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00026
                                   EEE--SHHHHHHHHHHHHTT.-EEEEE-SSHHHHHHHHHTT CS
                  NAD_binding_2  3 gfiGlGvMGsnmalnllkag.ykvavynrtkekveelvaeg 42
                                    ++GlG+ Gs   + l ++g ++v++y+++++k+ + +++ 
  gi|119720121|ref|YP_920616.1|  5 LVVGLGEVGSAVYEVLRDSGrMEVYGYDLDPSKTVHRLEDV 45
                                   589*************8766389*********998877665 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.6
                                    HHHHTT-EEEEE- CS
                  NAD_binding_2  17 nllkagykvavyn 29 
                                    +l++ag+kv +  
  gi|119720121|ref|YP_920616.1| 137 HLEAAGFKVKLAS 149
                                    5566666665443 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   7.4   0.00039       1.2      41     105 ..      38     123 ..      19     204 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00039
                Glyco_trans_4_4  41 rvhrlp.vprrps.....pladlaalralrrllrqrrerpdvvhahsptaglaarlarrrrgiplvvtl..........h 104
                                    +vhrl  vp+  +      + +++++ a++++   ++ +p  v +hs  a++  rl+   +++p+ +t+          h
  gi|119720121|ref|YP_920616.1|  38 TVHRLEdVPAPLDylhvaIPFTPRFVDAVKSYA--EKLKPRAVFVHSTVAPGTTRLLHGEARLPVAYTPvrgkhpnlkkH 115
                                    567774355444322222555677777778887..**********************9899********55553333331 PP

                Glyco_trans_4_4 105 .......g 105
                                            
  gi|119720121|ref|YP_920616.1| 116 llfwpkwV 123
                                    33333330 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 1997.93
//
Query:       gi|119720122|ref|YP_920617.1|  [L=88]
Description: hypothetical protein Tpen_1216 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.13   11.9   1.8       0.22   11.1   1.8    1.5  1  Saf_2TM   SAVED-fused 2TM effector domain
        2.6    7.8   4.9          2    8.1   0.3    2.3  2  FeoB_C    Ferrous iron transport protein B C terminus


Domain annotation for each model (and alignments):
>> Saf_2TM  SAVED-fused 2TM effector domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.8   2.5e-05      0.22      19      85 ..       4      73 ..       1      83 [. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.5e-05
                        Saf_2TM 19 rsaelllftigvalllailgt..dwalkialklaggslevsfssse.ipeivlaiilvigvllivvGavl 85
                                   r++++ll+  g+al++  ++   + al++  +  gg+  ++fss    + +++  +++++v++++++ +l
  gi|119720122|ref|YP_920617.1|  4 RKIAALLLASGAALIVLVFVLavQAALSYQKPQIGGDAGAAFSSMLsEVLYLFGKAVFLFVAILAASHLL 73
                                   788899999***9999999987788898888888*********988788888889999999999888655 PP

>> FeoB_C  Ferrous iron transport protein B C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.6     0.026   2.3e+02       3      21 ..      16      34 ..       7      46 .. 0.70
   2 ?    8.1   0.3   0.00023         2       4      21 ..      53      70 ..      52      83 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.026
                         FeoB_C  3 slYllgilvallvalllkk 21
                                   +l++l +++a+ +al  +k
  gi|119720122|ref|YP_920617.1| 16 ALIVLVFVLAVQAALSYQK 34
                                   5677777777777766655 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00023
                         FeoB_C  4 lYllgilvallvalllkk 21
                                   lYl+g +v+l+va+l+ +
  gi|119720122|ref|YP_920617.1| 53 LYLFGKAVFLFVAILAAS 70
                                   9*************9955 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       726  (0.0404931); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 646.90
//
Query:       gi|119720123|ref|YP_920618.1|  [L=251]
Description: hypothetical protein Tpen_1217 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-33  116.8   0.1    1.7e-33  116.6   0.1    1.0  1  DUF72         Protein of unknown function DUF72
  ------ inclusion threshold ------
      0.083   12.3   0.0       0.11   11.9   0.0    1.3  1  AP_endonuc_2  Xylose isomerase-like TIM barrel


Domain annotation for each model (and alignments):
>> DUF72  Protein of unknown function DUF72
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.6   0.1   1.9e-37   1.7e-33      13     215 ..      17     242 ..      14     245 .. 0.81

  Alignments for each domain:
  == domain 1  score: 116.6 bits;  conditional E-value: 1.9e-37
                                    HHCCT-SEEEE-HHCCSSS-HHHHHHHHCTS-TT-EEEEE--CCCCC.......S..................G-.SCHH CS
                          DUF72  13 yYarhfntVEinstFYalpspetvakwaaqtpedFrFavKapraith.......e............r.....ne.daee 67 
                                     Y + f++VE++ tFY +p+pe++ak ++++pe+F+F++Ka++a+th       +            r        ++ e
  gi|119720123|ref|YP_920618.1|  17 KYYSMFSAVELQETFYNPPDPEKLAKLRREAPEGFVFTMKAWQAVTHpldsptwKrarvkpgkeladRygflrPTkEVFE 96 
                                    6999*******************************************665555515555555555441445431224667 PP

                                    HHHHHHHH.CHHHCT-EEEEEEE--TT--S.HHHHHHHHHHTTTS-....SEEEE--BGGGH....HHHHHHHHTT-E.E CS
                          DUF72  68 alerflesalepLgeklgpllfQlppsfkfdeenlerLeaflaalp....llavEvRhrswf....ellellrehgva.v 138
                                    a+e   ++  ++Lg +l  +++Q ppsf+ + enl++  +f++ ++    ll +E R + w+    ++ e++ +   + +
  gi|119720123|ref|YP_920618.1|  97 AWELTARA-AKALGARL--VVLQTPPSFDASDENLRNAVEFFSSVEtgdfLLGWEPRGD-WLrkpeRIAEVVGRFSRVvH 172
                                    77777764.88898888..9********99877999999999988889955******96.87798559999999877769 PP

                                    EEE--SSC--------SSTEEEEEE--S...HHTTB----HHHHHHHHHHHHHHHTCSSEEEEEE-SBCCCHHHHHHHHH CS
                          DUF72 139 vldepkkpklpledvttadfvyvRlhgr...eeryayrYseeelaewaerikawaaegrevyvffnndaegqaplnaraL 215
                                    v+d      ++ ++v+ ++++y+Rlhg    e +y+yrY++e+l  + + +  + a  +evyv+fnn +   ++++a ++
  gi|119720123|ref|YP_920618.1| 173 VVD-----PFRSKPVVERPTAYFRLHGIgpgEVNYRYRYTDEDLSTLCSIVSGLGA--EEVYVMFNNVY---MAQDASRF 242
                                    999.....355688888999********996589*******************988..79*******65...45555555 PP

>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   1.2e-05      0.11      65     112 ..      91     163 ..      23     176 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.2e-05
                                    HHHHHHHHHHHHHHHHHHTBSEEEEEBCC...........................GBCTTTSGHHHHHHHHHHH CS
                   AP_endonuc_2  65 reesvdalkraielaaaLGapllvlhpGt...........................agagpkgseeeawerlaes 112
                                     +e ++a++ ++++a+aLGa+l+vl+  t                            g+ p+g++    er+ae+
  gi|119720123|ref|YP_920618.1|  91 TKEVFEAWELTARAAKALGARLVVLQ--TppsfdasdenlrnaveffssvetgdflLGWEPRGDWLRKPERIAEV 163
                                    456699********************..55577777777777777777766666665555555555666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1863.96
//
Query:       gi|119720124|ref|YP_920619.1|  [L=372]
Description: peptidase M48, Ste24p [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-37  128.8   0.6    9.3e-37  126.7   0.0    2.1  2  Peptidase_M48  Peptidase family M48
     0.0028   16.9   0.0     0.0045   16.2   0.0    1.5  1  Peptidase_M56  BlaR1 peptidase M56


Domain annotation for each model (and alignments):
>> Peptidase_M48  Peptidase family M48
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.3      0.17   1.5e+03      82     127 ..      75     121 ..      73     127 .. 0.73
   2 !  126.7   0.0     1e-40   9.3e-37       4     195 ..     140     365 ..     138     366 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.17
                                    HHHHHHHHHHHHHHHHHHHHTT-SH.HHHHTT--S---HHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M48  82 vslivsllasillllglallisrae.edaagafldalavliglliil 127
                                    +s +++++a +l ++gl++l+ +   ++   ++l +la++++l++ l
  gi|119720124|ref|YP_920619.1|  75 RSSMIATMAGVLGGFGLVALGVSSLlGAELTGQLLSLAIVFALVPSL 121
                                    56788999999999999888766641566777888888888888766 PP

  == domain 2  score: 126.7 bits;  conditional E-value: 1e-40
                                    SSHHHHHHHHHHHHTT-..-EEEEEEE-GGGT-EEEEESSS-E.EEEEEHHHH-SSB-HHHHHHHHHHHHHHHHTTHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M48   4 eaelkevveelakeaglpkpltkvyvvnspkrNAFalgggknk.rivltdgLlkqllseeelaaVlGHElGHikhrhsvv 82 
                                    ++ l+++v+++a++ag+ kp++ v   ++++ NAFa+       ++++t+g++ +l + eel+aV+GHElGH+kh++++v
  gi|119720124|ref|YP_920619.1| 140 DPVLQDIVNRVAQRAGM-KPPKAVIATRMREPNAFAYSSPLFGsYVAVTEGMM-RLAKGEELEAVIGHELGHHKHKDNTV 217
                                    6789*************.88888999999999*****8777677*********.************************** PP

                                    HHHHHHHHHHHHHHHHHH..HTT-SHHHHHTT--S---HHHHHHHHHHTT..............HHHHHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..............xxxxxxxxxxxxxxxx RF
                  Peptidase_M48  83 slivsllasillllglal..lisraeedaagafldalavliglliillfl..............alSRkrEyqADeagve 146
                                    +li++l++s++++lg++l  ++ + ++++  + +++ +   g+l +l+ +              alSR rE +AD +g+ 
  gi|119720124|ref|YP_920619.1| 218 MLIFGLIPSVVYFLGRFLayMGFFSSGARYDGDGERRGGGGGFLLVLVGIalmavsviiqlavlALSRLREHYADVHGAM 297
                                    ***************8761145566666666666666666666666666688889999********************** PP

                                    TTT.HHHHHHHHHHHHHHTT--S---HHHH....................HHS-SS--HHHHHHHHHH- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................xxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M48 147 llkrakdlvraliklakdlerqdvsaslrs....................ellstHPplleRiqalkel 195
                                    +++ ++++++al++l + + + +v++   +                    ell+tHPp+++Ri+ l++l
  gi|119720124|ref|YP_920619.1| 298 VTS-PDAMISALASLDSYYGSREVAKRRVEdsklkmffiyalaeplvsleELLATHPPIEKRIAFLEAL 365
                                    ***.*****************999999888899********************************9976 PP

>> Peptidase_M56  BlaR1 peptidase M56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0     5e-07    0.0045     144     227 ..     144     230 ..      10     234 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5e-07
                  Peptidase_M56 144 keaLkeakeemqlkrnikirlsssidsPavlgllkp....rIvlPadflkklsdeeleyillHElaHlkrkDllvnllva 219
                                    +++++   ++ +  +++k +++  +  P  +++  p    ++ + + +++  ++eele ++ HEl H k+kD  v l++ 
  gi|119720124|ref|YP_920619.1| 144 QDIVNRVAQRAG-MKPPKAVIATRMREPNAFAYSSPlfgsYVAVTEGMMRLAKGEELEAVIGHELGHHKHKDNTVMLIFG 222
                                    344555555555.57788888888888988887665333368888888888999*******************9999987 PP

                  Peptidase_M56 220 vlqclfwf 227
                                    ++  +++f
  gi|119720124|ref|YP_920619.1| 223 LIPSVVYF 230
                                    77666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       687  (0.0383178); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2411.87
//
Query:       gi|119720125|ref|YP_920620.1|  [L=68]
Description: hypothetical protein Tpen_1219 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.041   13.5   0.1      0.047   13.4   0.1    1.0  1  DSHCT     DSHCT (NUC185) domain


Domain annotation for each model (and alignments):
>> DSHCT  DSHCT (NUC185) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   2.6e-06     0.047     106     158 ..      11      63 ..       6      65 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.6e-06
                          DSHCT 106 faellektdldeGdiVRllrrleellrqlakaakvigneeLkkkaeeaielik 158
                                    +a++l+   l+e  ++ +l  +ee+l  ++ a++v ++e+L++k++e +e ++
  gi|119720125|ref|YP_920620.1|  11 LASTLRRDGLYEARLIDALDAIEEFLASVRGAPQVKEDEKLARKLREGVEVLR 63 
                                    45566667899999999999***************************998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 516.65
//
Query:       gi|119720126|ref|YP_920621.1|  [L=458]
Description: hypothetical protein Tpen_1220 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (458 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.20s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 3514.79
//
Query:       gi|119720127|ref|YP_920622.1|  [L=395]
Description: zinc finger, RanBP2-type [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.1e-05   22.8   0.8    5.9e-05   22.3   0.8    1.2  1  zf-RanBP       Zn-finger in Ran binding protein and others
    0.00058   19.5   3.8    0.00095   18.8   3.8    1.3  1  zinc_ribbon_2  zinc-ribbon domain
     0.0011   19.0   1.4     0.0019   18.2   1.4    1.3  1  DZR            Double zinc ribbon
     0.0058   16.0   5.7      0.011   15.2   5.7    1.4  1  zf-ribbon_3    zinc-ribbon domain
  ------ inclusion threshold ------
      0.012   15.5   0.2      0.037   13.9   0.2    1.9  1  MarR_2         MarR family
      0.055   13.5   0.0       0.14   12.2   0.0    1.6  1  Thioredoxin_3  Thioredoxin domain
      0.076   13.4   0.0       0.14   12.5   0.0    1.3  1  ArsD           Arsenical resistance operon trans-acting repre
      0.082   12.7   1.1       0.18   11.6   1.1    1.5  1  MNHE           Na+/H+ ion antiporter subunit
       0.11   12.4   0.0       0.18   11.7   0.0    1.3  1  MarR           MarR family
        0.2   11.8   0.2       0.44   10.7   0.0    1.6  2  DUF1525        Protein of unknown function (DUF1525)
       0.66    9.9   7.3        1.4    8.9   7.3    1.5  1  DUF35_N        Rubredoxin-like zinc ribbon domain (DUF35_N)


Domain annotation for each model (and alignments):
>> zf-RanBP  Zn-finger in Ran binding protein and others
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.8   3.6e-08   5.9e-05       2      29 ..     276     303 ..     275     304 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 3.6e-08
                                    SSSEE-SSS--EEESSSSB-TTT--BTS CS
                       zf-RanBP   2 egdWdCskClvqNfawstkCvaCqapkp 29 
                                     g W C++C++ N++ + +C aC++ +p
  gi|119720127|ref|YP_920622.1| 276 IGGWVCPSCGALNPPGNATCRACGSTRP 303
                                    578***********************98 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   3.8   5.8e-07   0.00095       2      21 ..     281     300 ..     280     301 .. 0.95

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 5.8e-07
                  zinc_ribbon_2   2 CpnCGaelqdnakFCpyCGt 21 
                                    Cp+CGa +++++  C  CG+
  gi|119720127|ref|YP_920622.1| 281 CPSCGALNPPGNATCRACGS 300
                                    *******************6 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   1.4   1.2e-06    0.0019       1      21 [.     281     301 ..     281     308 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.2e-06
                            DZR   1 CpqCgeelppdarfCseCgtk 21 
                                    Cp+Cg+ +pp++ +C +Cg++
  gi|119720127|ref|YP_920622.1| 281 CPSCGALNPPGNATCRACGST 301
                                    *******************86 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   5.7   6.5e-06     0.011       5      24 ..     281     300 ..     280     301 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 6.5e-06
                    zf-ribbon_3   5 CPnCGa.plssddnvCpyCGt 24 
                                    CP+CGa +  ++  +C  CG+
  gi|119720127|ref|YP_920622.1| 281 CPSCGAlN-PPGNATCRACGS 300
                                    ******99.***********6 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   2.2e-05     0.037       2      51 ..     309     357 ..     307     394 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.2e-05
                                    T--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSE CS
                         MarR_2   2 gltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLv 51 
                                    gl p + ++L  L+  +g+  t g+l  rlg++k+ v  +l+ L a+ L+
  gi|119720127|ref|YP_920622.1| 309 GLGPVHVDILRILYSMGGE-ATHGALLSRLGYEKPQVVDALRALFARKLI 357
                                    88899************97.7**************************999 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   8.5e-05      0.14      39      64 ..      64      89 ..      57     100 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.5e-05
                                   HHHHHHCT-SSSSEEECTTCEEEESS CS
                  Thioredoxin_3 39 feeiekygVmsvPalvidgkvvvsGk 64
                                    +e   +gV + P +v+d++vv++G+
  gi|119720127|ref|YP_920622.1| 64 ADEAVFRGVKALPCVVVDDQVVIEGR 89
                                   5666679******************8 PP

>> ArsD  Arsenical resistance operon trans-acting repressor ArsD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   8.4e-05      0.14      68      90 ..      70      92 ..      63     105 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.4e-05
                           ArsD 68 kgaeaLPlvlvdgeivktgrYpt 90
                                   +g++aLP v+vd+++v +grY  
  gi|119720127|ref|YP_920622.1| 70 RGVKALPCVVVDDQVVIEGRYVF 92
                                   5999*****************75 PP

>> MNHE  Na+/H+ ion antiporter subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.1   0.00011      0.18      18      89 ..     109     192 ..      97     196 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00011
                           MNHE  18 lllGlllallvalllrrll.............lplrrv..llrllayllvflweivkanldVakrvlrpklpirpgivkv 82 
                                    l++++  allva +l + +             l    v  ll++ + ++v ++++++a l+  +rv+ + l+++pg v v
  gi|119720127|ref|YP_920622.1| 109 LAFAASSALLVATVLGSTYaavrlfpgapgglLA---VlaLLAASVAFAVAFYNVYVAALRGLVRVFLGALSVDPGRVGV 185
                                    4556666666666664444444444555544222...144444555566789***************999********** PP

                           MNHE  83 plrlksd 89 
                                    pl+ +++
  gi|119720127|ref|YP_920622.1| 186 PLDFEKP 192
                                    **99876 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00011      0.18       4      47 ..     313     357 ..     310     358 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00011
                                    HHHHHHHHHHHSTT.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                           MarR   4 tqfviLrilyeqgp.lsvseLakklgvskstvtrvldrLekkGli 47 
                                    ++++iLrily++g+ ++   L ++lg +k+ v  +l++L  + li
  gi|119720127|ref|YP_920622.1| 313 VHVDILRILYSMGGeATHGALLSRLGYEKPQVVDALRALFARKLI 357
                                    6889**********99999*******************9877766 PP

>> DUF1525  Protein of unknown function (DUF1525)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00027      0.44      75      98 ..      66      89 ..      55     102 .. 0.83
   2 ?   -3.8   0.1       8.7   1.4e+04      26      40 ..     256     270 ..     250     273 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00027
                        DUF1525 75 dawqlgikkiPAVvvdrraVvYGe 98
                                   +a+  g+k +P Vvvd++ V+ G 
  gi|119720127|ref|YP_920622.1| 66 EAVFRGVKALPCVVVDDQVVIEGR 89
                                   67888***************9886 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 8.7
                        DUF1525  26 Daverleeelsaelp 40 
                                     ++++l+++l a l 
  gi|119720127|ref|YP_920622.1| 256 EHSHELARSLKASLE 270
                                    444455555555444 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   7.3   0.00083       1.4      14      34 ..     281     301 ..     280     303 .. 0.94

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00083
                        DUF35_N  14 CpdCGtvqfPPr.avCphCgsd 34 
                                    Cp+CG++  PP  a C+ Cgs+
  gi|119720127|ref|YP_920622.1| 281 CPSCGALN-PPGnATCRACGST 301
                                    *******9.***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       742  (0.0413855); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2735.89
//
Query:       gi|119720128|ref|YP_920623.1|  [L=319]
Description: ABC transporter related [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.7e-28   97.5   0.0    2.9e-27   95.9   0.0    1.7  2  ABC_tran  ABC transporter
    2.3e-11   44.2   0.2    7.7e-11   42.6   0.0    1.8  2  DUF4162   Domain of unknown function (DUF4162)
    6.5e-08   32.7   0.0     0.0069   16.2   0.0    2.4  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    1.8e-05   24.3   0.2    0.00014   21.5   0.1    2.1  2  KdpD      Osmosensitive K+ channel His kinase sensor domain
     0.0045   17.5   0.1     0.0088   16.6   0.1    1.5  1  AAA_23    AAA domain
     0.0051   16.0   0.1      0.018   14.3   0.1    1.8  1  NB-ARC    NB-ARC domain
     0.0064   16.9   0.5       0.26   11.7   0.4    2.8  2  AAA       ATPase family associated with various cellular acti
     0.0087   15.5   0.0        3.1    7.2   0.1    2.8  3  SMC_N     RecF/RecN/SMC N terminal domain
  ------ inclusion threshold ------
      0.014   15.1   0.1      0.056   13.1   0.0    2.0  2  SRP54     SRP54-type protein, GTPase domain
      0.024   14.3   0.1      0.051   13.3   0.1    1.5  1  AAA_29    P-loop containing region of AAA domain
      0.037   13.8   0.1       0.12   12.1   0.1    1.9  1  AAA_30    AAA domain
      0.096   12.0   0.0       0.17   11.2   0.0    1.4  1  HEM4      Uroporphyrinogen-III synthase HemD


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.9   0.0   1.9e-30   2.9e-27       2     137 .]      23     166 ..      22     166 .. 0.91
   2 ?   -1.0   0.0       1.5   2.2e+03      82     124 ..     242     284 ..     179     296 .. 0.65

  Alignments for each domain:
  == domain 1  score: 95.9 bits;  conditional E-value: 1.9e-30
                                    EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                       ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                    + ++l+++ege+ +++G+nG+GK+t l ++a  +kpt+G+i + g ++++ +  ++rk +g+ +qep+     t +e   
  gi|119720128|ref|YP_920623.1|  23 DGLNLDIYEGEIFGLLGPNGSGKTTTLLTIATVYKPTSGDIYVHGYSVSR-QGDIVRKYVGIAFQEPKALWVDTPYELll 101
                                    789**********************************************9.99*************55555555788899 PP

                                    ...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                               e+++ +++++++l+l e +++      ++LSgG ++++++a++l+++pk+ ++DEpta
  gi|119720128|ref|YP_920623.1| 102 wharvvgysssEARAVVKEVMEQLNLWEHRKKQF----YQLSGGTRKKLEIAKVLIQRPKVAIFDEPTA 166
                                    999****87655555599********99888888....*****************************97 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.5
                                    HTCHHHHHHHSTTGGTTCBGESTTS.GGS-HHHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx RF
                       ABC_tran  82 deeiekalsklglkelkdtvvkssp.ssLSgGqkqrvalarall 124
                                    +e++ k+ls+l+ +  + tv ++s   +L  G+ +  +++++l+
  gi|119720128|ref|YP_920623.1| 242 EENVRKLLSELEGVS-NYTVTDHSLrIHLNRGEERAAEIVELLA 284
                                    444556666666555.4444433334667777777777666665 PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       3.5   5.2e+03      28      61 ..     156     188 ..     129     192 .. 0.49
   2 !   42.6   0.0   5.2e-14   7.7e-11       1      77 [.     219     304 ..     219     307 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 3.5
                                    ---EEEE-TTS-EEEEE-------------.---- CS
                        DUF4162  28 pgveeveeeggelelkledeeaanellkal.tsgv 61 
                                    p+v + +e +  +++ + +++a  ++++ l ++g+
  gi|119720128|ref|YP_920623.1| 156 PKVAIFDEPT--AQVDVLTKHALWDIIRGLrDEGT 188
                                    3333333332..55666666777777777744554 PP

  == domain 2  score: 42.6 bits;  conditional E-value: 5.2e-14
                                    E-HHHHHTTS.-SSEEEEE.....-------...---EEEE-TTS-EEEEE--.-----------.----EEEEEEEE-- CS
                        DUF4162   1 GtleeiKrsy.gknrieve.....adaeellee.pgveeveeeggelelkled.eeaanellkal.tsgveirsFeeeeP 71 
                                    Gt++e+K+   +++ ie++     +++ +ll+e +gv+  + ++++l+++l+  ee a e+ + l +sgv++r++ ++eP
  gi|119720128|ref|YP_920623.1| 219 GTVSELKDMVpAGDVIEISfegpeENVRKLLSElEGVSNYTVTDHSLRIHLNRgEERAAEIVELLaSSGVKVRKLMVHEP 298
                                    9*********9999999**9866544555555536699999999********99***********88************* PP

                                    -HHHHH CS
                        DUF4162  72 sLndIF 77 
                                    +L+d+F
  gi|119720128|ref|YP_920623.1| 299 TLDDVF 304
                                    ****** PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.1   2.1e-05     0.031       2      20 ..      35      53 ..      34      78 .. 0.85
   2 !   16.2   0.0   4.6e-06    0.0069     234     298 ..     135     196 ..     115     199 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.1e-05
                         AAA_21  2 nvliGpNgsGKSnLLdald 20
                                    +l GpNgsGK++ L ++ 
  gi|119720128|ref|YP_920623.1| 35 FGLLGPNGSGKTTTLLTIA 53
                                   689**********999885 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 4.6e-06
                         AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHS 298
                                    +++lS Gt++ l ++  l++++   ++ ++DEp +  +    + l+++++ l+++g+ vi++T +
  gi|119720128|ref|YP_920623.1| 135 FYQLSGGTRKKLEIAKVLIQRP---KVAIFDEPTAQVDVLTKHALWDIIRGLRDEGTTVIVATND 196
                                    89*****************999...99**********************999999********76 PP

>> KdpD  Osmosensitive K+ channel His kinase sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0       0.3   4.4e+02      13      37 ..      41      65 ..      34      91 .. 0.79
   2 !   21.5   0.1   9.1e-08   0.00014      36     123 ..     106     195 ..     103     207 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.3
                           KdpD 13 pGvGktyamLeeaqelkeegvdvvi 37
                                   +G Gkt ++L+ a+  k +  d+ +
  gi|119720128|ref|YP_920623.1| 41 NGSGKTTTLLTIATVYKPTSGDIYV 65
                                   699********99998888888776 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 9.1e-08
                           KdpD  36 viglvethgrketeallegleviprke...veykgkeleeldldailarkpevvlvDelahtnapgsrhekryqdveelL 112
                                    v+g+ +++ r+ +++++e+l++ ++++   ++ +g + ++l++ ++l ++p+v++ De   + ++   ++  ++ ++ l 
  gi|119720128|ref|YP_920623.1| 106 VVGYSSSEARAVVKEVMEQLNLWEHRKkqfYQLSGGTRKKLEIAKVLIQRPKVAIFDEPTAQ-VDVLTKHALWDIIRGLR 184
                                    89******************99976552225668999*********************7665.577888899******** PP

                           KdpD 113 eagidVittvn 123
                                    ++g  Vi + n
  gi|119720128|ref|YP_920623.1| 185 DEGTTVIVATN 195
                                    *****998766 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   5.9e-06    0.0088       3      36 ..       8      49 ..       6      85 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.9e-06
                         AAA_23  3 kienf.rsf......rdqeidF.skgltlItGpNGaGKTTil 36
                                   ki+nf ++f      ++ ++d  +  ++ + GpNG+GKTT l
  gi|119720128|ref|YP_920623.1|  8 KISNFvKKFgdtvavDGLNLDIyEGEIFGLLGPNGSGKTTTL 49
                                   66776566644444444555558889**************87 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.1   1.2e-05     0.018      22     141 ..      34     197 ..      25     213 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.2e-05
                                    EEEEEESTTSSHHHHHHHHCCSHCCCCC.CBTEEEEE...................................EEESXX.H CS
                         NB-ARC  22 vvalvGmgGvGKttlakqilnksdeveg.rFdsvawv...................................vvsktd.k 64 
                                    + +l G  G+GKtt +  i   ++ + g  +     v                                   vv+ ++ +
  gi|119720128|ref|YP_920623.1|  34 IFGLLGPNGSGKTTTLLTIATVYKPTSGdIYVHGYSVsrqgdivrkyvgiafqepkalwvdtpyelllwharVVGYSSsE 113
                                    78999*******99998888888888884454445559999999****************************99876515 PP

                                    HHHHHHXXHHHHHCCCTTSSSS-STTS...HHHHHHHHCCCTTEEEEEE......EE-SHHH.H.....HHHHCHTTSEE CS
                         NB-ARC  65 seeiletilkeLslseddleekeeves...lkrklvrlLltkrfllvlD......DVweeed.wdkigvvlparenrlrv 134
                                     + ++++++++L+l e+  +++ +      +k ++ ++L+++  + ++D      DV +++  w  i   l   +++  v
  gi|119720128|ref|YP_920623.1| 114 ARAVVKEVMEQLNLWEHRKKQFYQLSGgtrKKLEIAKVLIQRPKVAIFDeptaqvDVLTKHAlW-DIIRGLR--DEGTTV 190
                                    6789*********99999999988777888999****************888888899998867.4444554..678888 PP

                                    EEEESBC CS
                         NB-ARC 135 llTTRde 141
                                    ++ T d+
  gi|119720128|ref|YP_920623.1| 191 IVATNDM 197
                                    8888765 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.4   0.00018      0.26       3      93 ..      37     125 ..      35     212 .. 0.43
   2 ?   -2.2   0.0       3.4   5.1e+03      84      99 ..     243     258 ..     237     275 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00018
                                    EESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH...TTCCC CS
                            AAA   3 lyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr...sgses 79 
                                    l Gp G GKT++   +a+  + +   i ++      v+ + + +r+++  a ++  p+ l++D  ++l        g +s
  gi|119720128|ref|YP_920623.1|  37 LLGPNGSGKTTTLLTIATVYKPTSGDIYVHGYS---VSRQGDIVRKYVGIAFQE--PKALWVDTPYELLLWHarvVGYSS 111
                                    78***************9986442222222222...223333333333333322..333333333333222222322233 PP

                                    HHHHHHHHHHHHHH CS
                            AAA  80 eeeervvnqLltel 93 
                                    +e++ vv++ +++l
  gi|119720128|ref|YP_920623.1| 112 SEARAVVKEVMEQL 125
                                    33333333333333 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.4
                                    HHHHHHHHHHHHTTTS CS
                            AAA  84 rvvnqLlteldgvkkk 99 
                                    + v +Ll+el+gv+++
  gi|119720128|ref|YP_920623.1| 243 ENVRKLLSELEGVSNY 258
                                    5678899999999875 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.1    0.0021       3.1      27      42 ..      35      50 ..       9      62 .. 0.85
   2 ?    4.3   0.0     0.016        24     136     203 ..     137     199 ..      65     215 .. 0.74
   3 ?    0.3   0.0      0.25   3.8e+02      99     135 ..     255     291 ..     228     310 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0021
                                   EEEEESTTSSHHHHHH CS
                                   xxxxxxxxxxxxxxxx RF
                          SMC_N 27 taivGpNGSGKsnlld 42
                                     ++GpNGSGK+  l 
  gi|119720128|ref|YP_920623.1| 35 FGLLGPNGSGKTTTLL 50
                                   5689*******98665 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.016
                                    CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemle 203
                                    +LSgG ++ + +a ++    +++  + ++De  a+ D    +++ ++++  +++   ++++ +++m+e
  gi|119720128|ref|YP_920623.1| 137 QLSGGTRKKLEIAKVL----IQRPKVAIFDEPTAQVDVLTKHALWDIIRGLRDEGTTVIVA-TNDMFE 199
                                    7999998877777664....444557799********************999774444443.455555 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.25
                                    EEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  99 isrrvkrkgeseykingkevtkkevsellesagiske 135
                                    +s   +++ + ++++n+ e + +e+ ell+s+g++  
  gi|119720128|ref|YP_920623.1| 255 VSNYTVTDHSLRIHLNRGEERAAEIVELLASSGVKVR 291
                                    566667777888999***************9998866 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   3.7e-05     0.056       6      32 ..      37      63 ..      33      76 .. 0.80
   2 ?   -2.0   0.0       1.5   2.3e+03      45      78 ..     122     155 ..     120     162 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.7e-05
                                   EEESTTSSHHHHHHHHHHHHHHTTS-E CS
                          SRP54  6 lvGlqGaGKTttlaKLaallkkegkkv 32
                                   l+G++G+GKTttl  +a ++k    ++
  gi|119720128|ref|YP_920623.1| 37 LLGPNGSGKTTTLLTIATVYKPTSGDI 63
                                   89****************999776555 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.5
                                    HHHHHHHHHHTTEEEEE.SSTTSCHHHHHHHHHHH CS
                          SRP54  45 veQLktlaeklgvpvik.kkeeadpaavakeavek 78 
                                    +eQL+ + ++ + ++++ +  +++  ++ak  +++
  gi|119720128|ref|YP_920623.1| 122 MEQLNLWEHRKK-QFYQlSGGTRKKLEIAKVLIQR 155
                                    799999999998.8888555555777777777666 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   3.4e-05     0.051      17      49 ..      27      59 ..      21      64 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.4e-05
                         AAA_29 17 ieidlkgatlltGpsGsGKSTllDAiqalLvpa 49
                                   ++i + +++ l Gp+GsGK+T l  i+++  p+
  gi|119720128|ref|YP_920623.1| 27 LDIYEGEIFGLLGPNGSGKTTTLLTIATVYKPT 59
                                   56654448889**********998888887665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   7.7e-05      0.12      21      47 ..      35      78 ..      29     197 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.7e-05
                         AAA_30 21 avltGpAGtGKttalkalreaweaa.g................g 47
                                     l Gp G+GKtt+l +++ +++   g                +
  gi|119720128|ref|YP_920623.1| 35 FGLLGPNGSGKTTTLLTIATVYKPTsGdiyvhgysvsrqgdivR 78
                                   5688******************9985554444444444444442 PP

>> HEM4  Uroporphyrinogen-III synthase HemD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00011      0.17      93     150 ..     235     297 ..     219     315 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                                    --SEE-..SSSHHHHGGGS-.....---EEE......EEE-SS.S--HHHHHHHHHTTEEEEEE-SEE CS
                           HEM4  93 rvdlvpseegtaegLaeelae....slagkr......vlllrgeiarddlaegLeergaevdevevYe 150
                                    ++++ ++ e+++++L++el+                 + l rge++ ++++e L++ g++v+++ v e
  gi|119720128|ref|YP_920623.1| 235 EISFEGP-EENVRKLLSELEGvsnyT----VtdhslrIHLNRGEERAAEIVELLASSGVKVRKLMVHE 297
                                    5677787.9999********865542....2234566999**********************998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       695  (0.038764); expected 358.6 (0.02)
Passed bias filter:                      657  (0.0366445); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2024.14
//
Query:       gi|119720129|ref|YP_920624.1|  [L=260]
Description: ABC-2 type transporter [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0068   16.4  14.3     0.0088   16.0  13.0    1.9  1  ABC2_membrane_4  ABC-2 family transporter protein
  ------ inclusion threshold ------
      0.031   13.4  23.8      0.041   13.0  23.8    1.3  1  ABC2_membrane_3  ABC-2 family transporter protein
       0.36   10.1  16.5      0.088   12.1  13.5    1.6  1  ABC2_membrane_2  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane_4  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0  13.0   1.5e-06    0.0088      10     156 ..      13     157 ..       8     201 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.5e-06
                ABC2_membrane_4  10 krskivwllvlaallvpllall.yfnllgk.tgldp..aefyslsvfgftlllllplilgiiasylifrEeqndtlknLl 85 
                                    kr+ ++ ++ +a + ++++++  ++n++ + +g+ +    +y++  + f+++  + + + +  +y + +E++++++ +Ll
  gi|119720129|ref|YP_920624.1|  13 KRRTVFVVMRVAWFALQVTVFGlAMNAIVRfRGVVAqgIDYYHF--YLFGVYASMLFSISVSKAYDVAEEFEEGMIEYLL 90 
                                    77777777666666666543221334333325544300345555..456689999************************* PP

                ABC2_membrane_4  86 tiPvsrtklllaKlivllllsvllmlvtflitvlfallsgfvgfsvklvlellkkclelgllvffavlpii 156
                                     +P++r+ l l+  i   l ++l++l  ++  v++ ll  + ++  + +l+ll  ++  + ++ f++++++
  gi|119720129|ref|YP_920624.1|  91 SLPMKRKILSLGRSIGGGLSAFLFTLPMYA--VVVLLLGVYDPV--AVLLSLLSALVFAVGVTGFVISVVL 157
                                    *****************9999999987554..444334444444..3344444444444444444444433 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0  23.8   6.9e-06     0.041     158     320 ..      53     218 ..      26     250 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.9e-06
                ABC2_membrane_3 158 nvasflvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllill...lafglgip 234
                                     +  +l+g+++ +l++i++s  a+ ++eE e +++e +l+ ++++  + l++ +g +l ++l++l + +   l++g  ++
  gi|119720129|ref|YP_920624.1|  53 YYHFYLFGVYASMLFSISVS-KAYDVAEEFEEGMIEYLLSLPMKRKILSLGRSIGGGLSAFLFTLPMYAvvvLLLG-VYD 130
                                    34445666777777777777.7889****************************************99884334777.333 PP

                ABC2_membrane_3 235 fgnlglllllfllfglayialgyllsslfknsetaqil...ifivilllsgffgglfpledlpsalkwifsiiPffapgl 311
                                       ++l ll  l+f+  ++ ++  +    k+s+ + i+   + ++i+ ls +f++ +++ +++    +++ ++P +++ +
  gi|119720129|ref|YP_920624.1| 131 PVAVLLSLLSALVFAVGVTGFVISVVLSLKSSDYTDIFfgvLDALIIRLSTVFYPAVVVAKIAP-YYYAALVNPVSHFVD 209
                                    3355555555555555555555555555556655544411133444446666666666776666.789************ PP

                ABC2_membrane_3 312 gllrlitgd 320
                                    +l +  + +
  gi|119720129|ref|YP_920624.1| 210 LLRTFFFFE 218
                                    *98887433 PP

>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1  13.5   1.5e-05     0.088      97     185 ..      77     158 ..      51     250 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.5e-05
                ABC2_membrane_2  97 iagEkergTlkllLskPvsRdeillgKfigglaigla.iavallatvllalaiilalgivlaledllllvvasvlllllv 175
                                    +a+E e+g ++ lLs+P+ R+ + lg  igg +++ + ++ ++ ++vll       + + + +  l ll +++ ++++  
  gi|119720129|ref|YP_920624.1|  77 VAEEFEEGMIEYLLSLPMKRKILSLGRSIGGGLSAFLfTLPMYAVVVLL------LGVYDPVAVLLSLLSALVFAVGV-- 148
                                    899*******************************666444444444333......33333333333333333333344.. PP

                ABC2_membrane_2 176 vflalglllS 185
                                    + + ++++lS
  gi|119720129|ref|YP_920624.1| 149 TGFVISVVLS 158
                                    2233344443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       883  (0.0492498); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1671.15
//
Query:       gi|119720130|ref|YP_920625.1|  [L=260]
Description: ABC-2 type transporter [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-15   57.7  14.4      1e-15   57.7  14.4    1.4  2  ABC2_membrane    ABC-2 type transporter
    1.4e-07   31.1  16.3    1.4e-07   31.1  16.3    1.6  2  ABC2_membrane_2  ABC-2 family transporter protein
    4.4e-06   26.0  19.0    5.6e-06   25.7  19.0    1.1  1  ABC2_membrane_3  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.7  14.4   1.7e-19     1e-15       6     208 ..      14     222 ..      11     224 .. 0.90
   2 ?   -3.2   0.1      0.79   4.7e+03      21      31 ..     238     248 ..     225     255 .. 0.45

  Alignments for each domain:
  == domain 1  score: 57.7 bits;  conditional E-value: 1.7e-19
                  ABC2_membrane   6 llkreflqrwrdpslgllwrliqplllalvfgtvfgnlgnsedglnr.....pgllffsvlflafsaltsvapvfererg 80 
                                    +  r++ ++w+ ++ +  +++++ l  +l+f ++f n+ n++ + ++      g+l+ s++  a +++    + +e++r+
  gi|119720130|ref|YP_920625.1|  14 IALRDLDRFWKYKFWL-GAQVAMNLADILIFAVIFNNIVNRQYIPDYvkflaTGVLALSTFASA-FSIGRE-VGIEIRRE 90 
                                    6679999999999777.99*****************8765555555578888888888888888.444444.79999*** PP

                  ABC2_membrane  81 vlerelvsplyslsayvlakvlvelpvsllqalifllivyflvgldls.rfflflllllltalaasslgllisalapsfe 159
                                    +   +l+ p+ s+ a v++++l+  +++l+  + f++++ ++vg +     +l+l +  +++  +ssl+++is+ +++f 
  gi|119720130|ref|YP_920625.1|  91 FTHYLLSIPV-SREALVFGRILSGTLRGLIYQASFIVLAALIVGTPTAlGAVLVLSTSAMLSASMSSLAIAISTSTRDFN 169
                                    **********.***********************************986569**************************** PP

                  ABC2_membrane 160 dasqlaslvllpllllsGffipidsm....pkwlqwiaylnPltyavealrsn 208
                                      +++ sl +++l+++s +f+p + +    p+ + ++ +l+P++ a +++r++
  gi|119720130|ref|YP_920625.1| 170 LQATFRSLTYYVLFFFSNVFYPEEILkqrfPGAVVFLIKLSPVSLAADVYRWA 222
                                    ***********************99998889999***************9987 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 0.79
                  ABC2_membrane  21 gllwrliqpll 31 
                                    +l+w l++ +l
  gi|119720130|ref|YP_920625.1| 238 LLAWTLVTLVL 248
                                    22222222222 PP

>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1      0.21   1.2e+03     155     173 ..      56      74 ..      29      90 .. 0.50
   2 !   31.1  16.3   2.4e-11   1.4e-07     109     285 ..      95     255 ..      92     256 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.21
                ABC2_membrane_2 155 vlaledllllvvasvllll 173
                                     +++ ++l + v+++ +++
  gi|119720130|ref|YP_920625.1|  56 IPDYVKFLATGVLALSTFA 74 
                                    3333333333333333333 PP

  == domain 2  score: 31.1 bits;  conditional E-value: 2.4e-11
                ABC2_membrane_2 109 lLskPvsRdeillgKfigglaigla.iavallatvllalaiilalgivlaledllllvvasvlllllvvflalglllSsv 187
                                    lLs PvsR ++++g +++g + gl+  a  ++ + l       ++g+++al+++l+l  +++l++    + +l++++S+ 
  gi|119720130|ref|YP_920625.1|  95 LLSIPVSREALVFGRILSGTLRGLIyQASFIVLAAL-------IVGTPTALGAVLVLSTSAMLSAS---MSSLAIAISTS 164
                                    9*********************88886665555544.......48*****************9999...89********* PP

                ABC2_membrane_2 188 arssreaaalalglfvvlailvpivlyg...vaellagpavpqeindflsllsptsayntllneilagsdlnalgstatn 264
                                    +r+++ +a+     + vl+++++++ y+   + + + g++v      fl  lsp s    ++++ +      +++  +  
  gi|119720130|ref|YP_920625.1| 165 TRDFNLQATFRSLTYYVLFFFSNVF-YPeeiLKQRFPGAVV------FLIKLSPVSLAADVYRWAFGYN---TSINVFHE 234
                                    *********9999998885555555.553656666777777......9999999999888888887666...3589999* PP

                ABC2_membrane_2 265 llilllllavllvlgyvlFkr 285
                                    +++ll++++v lvl+  l+ r
  gi|119720130|ref|YP_920625.1| 235 YALLLAWTLVTLVLASALYLR 255
                                    ***************999987 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7  19.0   9.4e-10   5.6e-06     140     343 ..      40     249 ..      24     251 .. 0.78

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 9.4e-10
                ABC2_membrane_3 140 stsaninvestqleeelsnvasflvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyll 219
                                    +  + + ++++ + ++ ++++ fl++ +l+++ f +a++i +++  E ++   + +l+ +vs+ ++++++il+  l +l+
  gi|119720130|ref|YP_920625.1|  40 ILIFAVIFNNIVNRQYIPDYVKFLATGVLALSTFASAFSIGREVGIEIRREFTHYLLSIPVSREALVFGRILSGTLRGLI 119
                                    555666777777888999*************************************************************9 PP

                ABC2_membrane_3 220 qlllilll...afglgipfgnlglllllfllfglayialgyllsslfknsetaqil..ifivilllsgffgglfp....l 290
                                      + +++l   ++g   + + lg++l+l+   +l++++ ++++   +++ +   ++   +++  +l++f+ +++p     
  gi|119720130|ref|YP_920625.1| 120 YQASFIVLaalIVG---TPTALGAVLVLSTSAMLSASMSSLAIAISTSTRDFNLQAtfRSLTYYVLFFFSNVFYPeeilK 196
                                    86655554322777...666888888777777777766666666655554443333113444447777777778877644 PP

                ABC2_membrane_3 291 edlpsalkwifsiiPffapglgllrlitgd.plweillsliilalfavvyllla 343
                                    + +p+a+  +  + P +  +++      g+ + ++++  +++l++ ++v+l+la
  gi|119720130|ref|YP_920625.1| 197 QRFPGAVVFLIKLSPVSLAADVYRWAF-GYnTSINVFHEYALLLAWTLVTLVLA 249
                                    558899***************996665.444789******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       739  (0.0412181); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 1638.58
//
Query:       gi|119720131|ref|YP_920626.1|  [L=823]
Description: peptidase M1, membrane alanine aminopeptidase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-49  168.5   0.1    2.1e-49  168.0   0.1    1.2  1  Peptidase_M1    Peptidase family M1 domain
    1.2e-28   99.3  12.7    3.1e-10   40.3   0.8    4.0  4  HEAT_2          HEAT repeats
    9.3e-18   65.1   0.0    1.5e-17   64.4   0.0    1.3  1  Peptidase_M1_N  Peptidase M1 N-terminal domain
    1.2e-07   31.7  22.1      0.025   15.2   0.4    6.9  6  HEAT_PBS        PBS lyase HEAT-like repeat
     0.0011   19.1   1.0        5.1    7.6   0.0    5.5  6  HEAT            HEAT repeat
     0.0029   16.1   0.0      0.057   11.8   0.0    2.2  2  Vitellogenin_N  Lipoprotein amino terminal region
     0.0086   16.5   5.3      0.018   15.4   5.3    1.5  1  DUF4200         Domain of unknown function (DUF4200)
  ------ inclusion threshold ------
      0.024   14.2   0.2       0.34   10.4   0.1    2.5  3  ERAP1_C         ERAP1-like C-terminal domain
      0.028   14.5   0.7        9.8    6.3   0.1    3.5  3  UPF0147         Uncharacterised protein family (UPF0147)
      0.047   14.1   3.7       0.17   12.3   3.7    2.0  1  Latarcin        Latarcin precursor
      0.049   13.5   0.6       0.12   12.3   0.3    1.8  2  FTA4            Kinetochore complex Fta4 of Sim4 subunit, or 
      0.071   13.6   0.0       0.19   12.2   0.0    1.7  1  DUF3458         Domain of unknown function (DUF3458) Ig-like 
       0.25    9.9   0.2        7.5    5.0   0.2    2.1  3  Adaptin_N       Adaptin N terminal region
        0.4   10.5   4.0       0.78    9.6   4.0    1.5  1  DivIC           Septum formation initiator
       0.68   10.4   3.7        2.1    8.8   3.7    1.9  1  DUF4140         N-terminal domain of unknown function (DUF414


Domain annotation for each model (and alignments):
>> Peptidase_M1  Peptidase family M1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.0   0.1   1.8e-52   2.1e-49       3     218 .]     232     439 ..     230     439 .. 0.90

  Alignments for each domain:
  == domain 1  score: 168.0 bits;  conditional E-value: 1.8e-52
                                    HHHHHHHHHHHHHHHTS--SSSEEEEEEESSTTSSEEEETTEEEEEGGGC-SSTTTS-HHHHHHHHHHHHHHHHHHHBTT CS
                   Peptidase_M1   3 levtkkllefleeyfkvpYplpkldlvalpdfsagAMEnwglityreelllvdpenssesdkrsvaeviaHElaHqWfGn 82 
                                    +  tk++++f+ee ++v+Yp+pk+ +v++++f ag+MEn +++++++++l  +    +++   + + ++ HElaHqWfG+
  gi|119720131|ref|YP_920626.1| 232 FSQTKEMVRFFEEFTGVKYPYPKYAQVCVDEFVAGGMENASVTILTSATLHDE----KAHADFRSEPLVSHELAHQWFGD 307
                                    567999***************************************99988766....33344577899************ PP

                                    TEEESSGGGGHHHHHHHHHHHHHHHHHHSCCCHCHHHHHHHCHHHHHHHHTSTTHHHSSGG-GSHHHHHHTSSHHHHHHH CS
                   Peptidase_M1  83 lVtmkwWddlwLnEGfatyleylildklepewevseqllleeveealsedaldeshpitqevekpseidevFdsiaYeKG 162
                                    lVt++ W++lwLnE+fat +e+l+  +  +e e+  +l + ++ +   ++  + ++pi +++ k   +devFd+++Y KG
  gi|119720131|ref|YP_920626.1| 308 LVTCRDWSHLWLNESFATLMEALWRRRELGEEEFVYDL-IGMLDS-YLSEYGKYARPIVTRLYKY--PDEVFDAHSYPKG 383
                                    ***************************99999977777.555555.5556778899998777755..9************ PP

                                    HHHHHHHHHHCTHHHHHHHHHHHHHHCTTEEE-HHHHHHHHHHCCCSCHHTHHHHH CS
                   Peptidase_M1 163 asllrmlekllgeevFqkglksYlkefkyknaetedlwdaleealnkdisevmdtw 218
                                    a +l  l +++gee F++g+k+Yl++ + +na t+dl +aleea++  ++++++++
  gi|119720131|ref|YP_920626.1| 384 ALVLWTLMNIVGEEAFRRGVKKYLESRREDNAVTDDLRRALEEASGARLDWFFEQY 439
                                    *****************************************************987 PP

>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1       3.2   3.8e+03      45      74 ..     397     427 ..     389     432 .. 0.73
   2 !   38.5   0.1   9.3e-13   1.1e-09       2      72 ..     535     607 ..     534     611 .. 0.93
   3 !   40.3   0.8   2.6e-13   3.1e-10      13      88 .]     611     689 ..     609     689 .. 0.89
   4 !   27.1   0.2   3.5e-09   4.2e-06       2      86 ..     698     782 ..     696     787 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 3.2
                         HEAT_2  45 pavRraaaeaLg.aigdpealpaLkellddd 74 
                                    +a Rr + ++L  +  d+++ + L+++l + 
  gi|119720131|ref|YP_920626.1| 397 EAFRRGVKKYLEsRREDNAVTDDLRRALEEA 427
                                    5678888888861445788889999988765 PP

  == domain 2  score: 38.5 bits;  conditional E-value: 9.3e-13
                         HEAT_2   2 daLlqalendpdpevrraairaLgrignpealpaLvell..ededpavRraaaeaLgaigdpealpaLkelld 72 
                                    + Ll++++++p  + r aa+r+L+++++p+a++ L  ll  ede +  R ++a a+g ig ++al+aL+e+ld
  gi|119720131|ref|YP_920626.1| 535 EELLSIVKHCPYLYPRVAAVRELAKKASPTAVEELKGLLlsEDEFWGLRSEVASAIGSIGGQAALNALLEALD 607
                                    789999999999999**********************99888899*************************997 PP

  == domain 3  score: 40.3 bits;  conditional E-value: 2.6e-13
                         HEAT_2  13 dpevrraairaLgrignpealpaLvelleded..pavRraaaeaLgaigdpealpaLkellddddd.dvvReaAaeaLa 88 
                                    +p+vrra++raLg ++++ + + L ++l+de+   +vR++aa ++++ g  e  +aLke+l+ +++  v+ ++A+eaLa
  gi|119720131|ref|YP_920626.1| 611 HPKVRRAIVRALGGYREKAVAERLSKVLKDESesYYVRAEAALSIAKTGFREYSDALKEALNVPSHnHVIAASALEALA 689
                                    79**************************88553279****************************984677777888885 PP

  == domain 4  score: 27.1 bits;  conditional E-value: 3.5e-09
                         HEAT_2   2 daLlqalendpdpevrraairaLgri.gnpealpaLvellededpavRraaaeaLgaigdpealpaLkellddddddvvR 80 
                                    d+L ++++ +    +rraai +Lg +  ++++l +L    ++ +p+v   ++ a  ++ +p++lp+L++l + d++ +v 
  gi|119720131|ref|YP_920626.1| 698 DLLEKYASPSTPMPLRRAAIASLGYLpPSQRVLSLLEYSSRSRHPHVKLSVISACTRLLSPRVLPILERL-QGDTSGRVA 776
                                    77888887788888**********9835789999999999****************************95.566666666 PP

                         HEAT_2  81 eaAaea 86 
                                    ++A  a
  gi|119720131|ref|YP_920626.1| 777 RSARDA 782
                                    666544 PP

>> Peptidase_M1_N  Peptidase M1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.4   0.0   1.2e-20   1.5e-17       8     186 .]      33     196 ..      26     196 .. 0.88

  Alignments for each domain:
  == domain 1  score: 64.4 bits;  conditional E-value: 1.2e-20
                                    EEEEETTTTEEEEEEEEEEEESS-ECEEEEEESSEEEECEEEEECTTCTCEEEEEEEECTTTTCEEEEECCEEETTCEEE CS
                 Peptidase_M1_N   8 dlkidlkektfkGsvtitlqlkeatseivldakdlkiksvslsaevksesvkidfkieqkdeelltiklkeslqqtskyt 87 
                                    ++++d++++t++G +  +l+++++++ +v++a d+ki      +ev  ++ k+    +++d+  l++  +  + + ++++
  gi|119720131|ref|YP_920626.1|  33 EVDVDFESRTLRGVCVNRLKVTAPAERVVFHAVDMKI------EEVLVNGRKAA---YTYDGRELSVGVEG-VGAGGEVE 102
                                    5789999******************************......77777787776...55667777777776.667***** PP

                                    EEEEEEEE-BSSSSEEEEEEEEETSCEEEEEEEE-TTTTGGGTS-B--STTSEBEEEEEEEEETTSEEEESSECCCEEEE CS
                 Peptidase_M1_N  88 LeieyegelndklaGlykstYtdkgekkvvvvTqfeatdARsafPCfDePsvKAtftisikapkeetalSnmpeeesekl 167
                                    + + y + ++ k  + +    + +g+k ++v Tq +++d R+++P +D+P+ KA+ ++ +++pk  ++++n+    +e+l
  gi|119720131|ref|YP_920626.1| 103 VYVRYAT-VEPKAGAWFV---PVDGGKPYMVYTQGQPEDTRYWLPTYDYPNRKAKVSLAVTVPKGIVVVANGVLVGREEL 178
                                    *****99.6666555555...34999*************************************************9**** PP

                                    TTCEEEEEEEEEESBEGGG CS
                 Peptidase_M1_N 168 engqkiteFeqtpkmstYL 186
                                    ++ ++ + F    +++tYL
  gi|119720131|ref|YP_920626.1| 179 GD-KERWSFRLDSRIPTYL 196
                                    96.55899**********8 PP

>> HEAT_PBS  PBS lyase HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1      0.33   3.9e+02       2      25 ..     550     573 ..     549     575 .. 0.90
   2 !   15.2   0.4   2.1e-05     0.025       2      26 ..     583     607 ..     582     608 .. 0.95
   3 !   14.2   0.2   4.6e-05     0.055       1      27 []     614     640 ..     614     640 .. 0.98
   4 !    7.2   0.1    0.0079       9.4       1      26 [.     647     672 ..     647     672 .. 0.97
   5 ?   -0.7   0.5       2.8   3.3e+03       3      22 ..     682     701 ..     680     704 .. 0.60
   6 ?    3.9   0.1     0.091   1.1e+02       1      16 [.     712     728 ..     712     738 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.33
                                    HHHHHHHHHHCTSGGGHHHHHHHC CS
                       HEAT_PBS   2 RraAakaLgqlgdeeaipaLleaL 25 
                                    R aA++ L++  ++ a++ L+ +L
  gi|119720131|ref|YP_920626.1| 550 RVAAVRELAKKASPTAVEELKGLL 573
                                    99****************998666 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 2.1e-05
                                    HHHHHHHHHHCTSGGGHHHHHHHCT CS
                       HEAT_PBS   2 RraAakaLgqlgdeeaipaLleaLq 26 
                                    R + a a+g +g ++a+ aLleaL+
  gi|119720131|ref|YP_920626.1| 583 RSEVASAIGSIGGQAALNALLEALD 607
                                    999*********************8 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 4.6e-05
                                    HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
                       HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLqd 27 
                                    vRra ++aLg  + ++++++L ++L+d
  gi|119720131|ref|YP_920626.1| 614 VRRAIVRALGGYREKAVAERLSKVLKD 640
                                    9************************98 PP

  == domain 4  score: 7.2 bits;  conditional E-value: 0.0079
                                    HHHHHHHHHHHCTSGGGHHHHHHHCT CS
                       HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLq 26 
                                    vR++Aa ++++ g  e+ +aL+eaL+
  gi|119720131|ref|YP_920626.1| 647 VRAEAALSIAKTGFREYSDALKEALN 672
                                    9***********************95 PP

  == domain 5  score: -0.7 bits;  conditional E-value: 2.8
                                    HHHHHHHHHCTSGGGHHHHH CS
                       HEAT_PBS   3 raAakaLgqlgdeeaipaLl 22 
                                    ++A++aL+ l  +e++++L 
  gi|119720131|ref|YP_920626.1| 682 ASALEALAMLLGDEVLDLLE 701
                                    34555555554478888776 PP

  == domain 6  score: 3.9 bits;  conditional E-value: 0.091
                                    HHHHHHHHHHHCTS.GG CS
                       HEAT_PBS   1 vRraAakaLgqlgd.ee 16 
                                    +RraA+ +Lg l   ++
  gi|119720131|ref|YP_920626.1| 712 LRRAAIASLGYLPPsQR 728
                                    5*********9977444 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0       0.3   3.6e+02       9      27 ..     575     593 ..     572     596 .. 0.87
   2 !    7.6   0.0    0.0043       5.1       2      25 ..     599     623 ..     598     625 .. 0.89
   3 ?    1.3   0.0      0.46   5.5e+02       9      25 ..     638     656 ..     632     657 .. 0.77
   4 ?   -2.2   0.0       6.2   7.4e+03      17      25 ..     713     721 ..     710     723 .. 0.84
   5 ?    0.1   0.0       1.1   1.3e+03       8      28 ..     736     756 ..     729     757 .. 0.77
   6 ?   -1.4   0.0       3.4   4.1e+03       1      18 [.     760     778 ..     760     779 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.3
                                    HT-SSHHHHHHHHHHHHHH CS
                           HEAT   9 lsDpspeVReaAakaLgal 27 
                                     +D+ +  R+ +a a+g +
  gi|119720131|ref|YP_920626.1| 575 SEDEFWGLRSEVASAIGSI 593
                                    48***************98 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0043
                                    HHHHHHHH.T-SSHHHHHHHHHHHH CS
                           HEAT   2 lPlllkll.sDpspeVReaAakaLg 25 
                                    l++ll++l +  +p+VR+a ++aLg
  gi|119720131|ref|YP_920626.1| 599 LNALLEALdKVRHPKVRRAIVRALG 623
                                    688999997779************9 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.46
                                    HT-..SSHHHHHHHHHHHH CS
                           HEAT   9 lsD..pspeVReaAakaLg 25 
                                    l+D  +s  VR+ Aa++++
  gi|119720131|ref|YP_920626.1| 638 LKDesESYYVRAEAALSIA 656
                                    555559999******9986 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 6.2
                                    HHHHHHHHH CS
                           HEAT  17 ReaAakaLg 25 
                                    R+aA+ +Lg
  gi|119720131|ref|YP_920626.1| 713 RRAAIASLG 721
                                    99****999 PP

  == domain 5  score: 0.1 bits;  conditional E-value: 1.1
                                    HHT-SSHHHHHHHHHHHHHHH CS
                           HEAT   8 llsDpspeVReaAakaLgala 28 
                                      ++ +p+V  +++ a+++l+
  gi|119720131|ref|YP_920626.1| 736 SSRSRHPHVKLSVISACTRLL 756
                                    358899***********9987 PP

  == domain 6  score: -1.4 bits;  conditional E-value: 3.4
                                    HHHHHHHHHT-SSHHH.HH CS
                           HEAT   1 llPlllkllsDpspeV.Re 18 
                                    +lP+l +l  D+s +V R+
  gi|119720131|ref|YP_920626.1| 760 VLPILERLQGDTSGRVaRS 778
                                    589988877***9999554 PP

>> Vitellogenin_N  Lipoprotein amino terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   4.8e-05     0.057     517     615 ..     589     681 ..     547     683 .. 0.87
   2 ?    4.0   0.0     0.011        14     493     557 ..     661     725 ..     655     729 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.8e-05
                                    HHHHHT-GGGHHHHHTTSS----S-HHHHHHHHHTTTTGGGT-HHHHHHHHHHHHH-TTS-HHHHHHHHHHHHHT---HH CS
                 Vitellogenin_N 517 aLgNlGhpeilkvlepylegkeevstfvRlaavlaLrnlakkaprkvrsvllriyentaekpevRvaAvlalmetkPsaa 596
                                    a+g +G ++ l+ l + l  ++    +vR a+v aL       ++ v + l ++++++ e + vR+ A+l + +t    +
  gi|119720131|ref|YP_920626.1| 589 AIGSIGGQAALNALLEAL--DKVRHPKVRRAIVRALG---GYREKAVAERLSKVLKDESESYYVRAEAALSIAKTG-FRE 662
                                    8999999***********..77777789*********...999999****************************94.444 PP

                                    HHHHHHHHHTT-S-HHHHH CS
                 Vitellogenin_N 597 llqriaestnkdpskqVaa 615
                                       ++ e +n  + ++V a
  gi|119720131|ref|YP_920626.1| 663 YSDALKEALNVPSHNHVIA 681
                                    4677777777776677766 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.011
                                    HHHHHHHHHHHHTT-HH..HHHHHHHHHHHHT-GGGHHHHHTTSS----S-HHHHHHHHHTTTTGGG CS
                 Vitellogenin_N 493 pylaqklkeavekgdse..kiqvylkaLgNlGhpeilkvlepylegkeevstfvRlaavlaLrnlak 557
                                    +++++ lkea++  + +   +  +l aL+ l  +e+l+ le+y+  + +++  +R aa+++L +l  
  gi|119720131|ref|YP_920626.1| 661 REYSDALKEALNVPSHNhvIAASALEALAMLLGDEVLDLLEKYA--SPSTPMPLRRAAIASLGYLPP 725
                                    5677888888887433323666799******99***********..88889999********99876 PP

>> DUF4200  Domain of unknown function (DUF4200)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   5.3   1.5e-05     0.018      62     108 ..     776     822 ..     767     822 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.5e-05
                        DUF4200  62 aralkkaeeerklkkekeaeikklkaeietlkseiekleekleeykk 108
                                    ar  + a+e+ k++ e+ +e +klk+e+++l++e ++l e++e+++k
  gi|119720131|ref|YP_920626.1| 776 ARSARDAAEQIKKHMERGEEYRKLKEELDKLREEERRLSERVERLEK 822
                                    677899*************************************9975 PP

>> ERAP1_C  ERAP1-like C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00029      0.34     123     264 ..     578     671 ..     532     716 .. 0.47
   2 ?    1.4   0.0      0.16   1.9e+02     166     222 ..     681     737 ..     644     754 .. 0.64
   3 ?   -1.1   0.0      0.91   1.1e+03      62     107 ..     763     807 ..     754     813 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00029
                                    HHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHCSTT-S-HHHHHHHHHHHHHHS-HHHHHHHHHHHHC-SSHHHHHHHH CS
                        ERAP1_C 123 ldaqlrslllsaacaagdpevveearklfkawlegddlippdlrwavycalaanggeaewdallerykdtsapsekeaal 202
                                      +                                       lr+ v +a+ + gg+a ++alle   +   p  ++a++
  gi|119720131|ref|YP_920626.1| 578 EFWG--------------------------------------LRSEVASAIGSIGGQAALNALLEALDKVRHPKVRRAIV 619
                                    3444......................................55555555544456666666666653333455566666 PP

                                    HHHCC-S-HHHHHHHHHHCTTT..S-GGGHHHHHHHH.HSTTHHHHHHHHHHHCHCCHHHHT CS
                        ERAP1_C 203 ralaatpdpellerllnfvlesdevrnqdlrallaglannpegrellwefvkenwdalakrw 264
                                    ral+  +++++ er l  vl +de  + ++ra        +++  ++   ++e+ dal++ +
  gi|119720131|ref|YP_920626.1| 620 RALGGYREKAVAER-LSKVL-KDESESYYVRA--------EAALSIAKTGFREYSDALKEAL 671
                                    66666666666666.55554.22221111111........1122222233333333333333 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.16
                                    HHHHHHHHHHHS-HHHHHHHHHHHHC-SS.HHHHHHHHHHHCC-S-HHHHHHHHHHCT CS
                        ERAP1_C 166 rwavycalaanggeaewdallerykdtsa.psekeaalralaatpdpellerllnfvl 222
                                      +++ ala   g++ +  lle+y ++s+    ++aa+++l++ p ++ +  ll++++
  gi|119720131|ref|YP_920626.1| 681 AASALEALAMLLGDE-VLDLLEKYASPSTpMPLRRAAIASLGYLPPSQRVLSLLEYSS 737
                                    444445554442444.445668888888745779999999999999999999999885 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.91
                                    GGG.GGGG--SHHHHHHHHHHHHHHHHHHTTSTTHHHHHHHHHHHH CS
                        ERAP1_C  62 lllgylanEtdylvwsqalsqlatlksllsadplyaalkaflrkll 107
                                    +l+ + +++t+  v ++a + ++++k+++++ ++y++lk+ l+kl 
  gi|119720131|ref|YP_920626.1| 763 ILERL-QGDTSGRVARSARDAAEQIKKHMERGEEYRKLKEELDKLR 807
                                    56667.6888889999999999999999987788999999888875 PP

>> UPF0147  Uncharacterised protein family (UPF0147)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.6   1.9e+03       8      32 ..     403     427 ..     396     431 .. 0.83
   2 ?    6.3   0.1    0.0082       9.8      27      53 ..     629     655 ..     598     689 .. 0.90
   3 ?    4.2   0.0     0.038        46       8      44 ..     760     798 ..     756     802 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.6
                                    HHHHHHHHHT-TTS-HHHHHHHHHH CS
                        UPF0147   8 vielLeeiiedtsvPrniRraakea 32 
                                    v ++Le+  ed++v    Rra +ea
  gi|119720131|ref|YP_920626.1| 403 VKKYLESRREDNAVTDDLRRALEEA 427
                                    6678999999***********9997 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0082
                                    HHHHHHHHHHT-TTS-HHHHHHHHHHH CS
                        UPF0147  27 raakeakekLkdekeslavraataisi 53 
                                     +a+   + Lkde+es+ vra  a+si
  gi|119720131|ref|YP_920626.1| 629 AVAERLSKVLKDESESYYVRAEAALSI 655
                                    57889999**************99997 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.038
                                    HHHHHHHHHT-TT..S-HHHHHHHHHHHHHHT-TTS-HH CS
                        UPF0147   8 vielLeeiiedts..vPrniRraakeakekLkdekesla 44 
                                    v+ +Le++  dts  v r+ R aa+++k++++  +e  +
  gi|119720131|ref|YP_920626.1| 760 VLPILERLQGDTSgrVARSARDAAEQIKKHMERGEEYRK 798
                                    678999999999767***************999887655 PP

>> Latarcin  Latarcin precursor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   3.7   0.00014      0.17      16      49 ..     789     822 ..     778     823 .] 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00014
                       Latarcin  16 elergainrklmemvnnlRkvqgRLeemvenlrk 49 
                                      erg+ +rkl e +++lR+ + RL e ve l+k
  gi|119720131|ref|YP_920626.1| 789 HMERGEEYRKLKEELDKLREEERRLSERVERLEK 822
                                    56788899************************98 PP

>> FTA4  Kinetochore complex Fta4 of Sim4 subunit, or CENP-50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0         2   2.4e+03     133     163 ..     534     564 ..     532     578 .. 0.88
   2 ?   12.3   0.3   9.9e-05      0.12     111     155 ..     757     822 ..     624     823 .] 0.73

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2
                           FTA4 133 rarLielserrqqlqarlarlrklkallepf 163
                                    +++L+++ ++  +l+ r+a  r+l ++ +p+
  gi|119720131|ref|YP_920626.1| 534 VEELLSIVKHCPYLYPRVAAVRELAKKASPT 564
                                    578999999999*************999987 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 9.9e-05
                           FTA4 111 e......................veekeaeeepleallerYaelrarLielserrqqlqarlarlrk 155
                                    +                       +++e+ ++ +e   e+Y +l+++L +l+e+ ++l +r++rl+k
  gi|119720131|ref|YP_920626.1| 757 SprvlpilerlqgdtsgrvarsaRDAAEQIKKHMER-GEEYRKLKEELDKLREEERRLSERVERLEK 822
                                    055555555555555555555543334444445555.79**************************86 PP

>> DUF3458  Domain of unknown function (DUF3458) Ig-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00016      0.19       1      74 [.     444     510 ..     444     529 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00016
                                    S--EEEEEEEEETTTTEEEEEEEEE---BSSBSS-----EEEEEEEEETTS-BECEEEEEEE-SSEEEEEEC-- CS
                        DUF3458   1 GtPevtvsesydeaaktytltlsQktpptagqkekkplviPiklalldekGeelelekvlelteaeqsftfenv 74 
                                    G P ++vs ++ e+++ ++l++sQ+      +++   + +P+++++l+e  +e    +++ ++e++  f+f+  
  gi|119720131|ref|YP_920626.1| 444 GHPALSVSYKWVEKEGVLELRVSQTQG----DDSLPRYRVPLEVEFLGEGFRER---RTVWVEERQSVFSFRLP 510
                                    89**********************984....55568899*******98755554...47888888888888633 PP

>> Adaptin_N  Adaptin N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.019        23     414     453 ..     597     635 ..     594     640 .. 0.84
   2 ?    5.0   0.2    0.0063       7.5     115     179 ..     630     691 ..     626     714 .. 0.72
   3 ?   -0.3   0.1      0.25   2.9e+02      84     128 ..     667     709 ..     660     766 .. 0.66

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.019
                                    TCHHHHCCTCCGXXSHHHHHHHHHHHHHTTTTXTT...HH CS
                      Adaptin_N 414 eiiekLaellekieseearaaaiWllGeygelvsntesas 453
                                     +++ L+e+l+k++++++r+a++  lG y e++   e++s
  gi|119720131|ref|YP_920626.1| 597 AALNALLEALDKVRHPKVRRAIVRALGGYREKAVA-ERLS 635
                                    57899*************************99885.4444 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0063
                                    HHHHHHHHHT-SSH..HHHHHHHHHHHHC.CCCCHHCCCCCHHHHHHHCT..T-SSHHHHHHHHHHHHHH CS
                      Adaptin_N 115 lapaikkllkdrsp..yvrkkAalailkl.ykkdpdllrkqlveeikell..sdkdpgvvlaAvalleei 179
                                    +a+ + k+lkd+s   yvr +Aal+i+k  ++ ++d+l++        +l   ++++ + ++A+ +l  +
  gi|119720131|ref|YP_920626.1| 630 VAERLSKVLKDESEsyYVRAEAALSIAKTgFREYSDALKE--------ALnvPSHNHVIAASALEALAML 691
                                    6788999999988889**********99745666666544........3333667777777777776666 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.25
                                    HHHHCC..SSSHHHHHHHHHHHCCC--CCCHHHHHHHHHHHHT-SSH CS
                      Adaptin_N  84 lqkDlk..dpnqlirglALrvLssirvpelaedlapaikkllkdrsp 128
                                    l+ +l+  + n +i ++AL +L+++  +e+++     ++k ++ ++p
  gi|119720131|ref|YP_920626.1| 667 LKEALNvpSHNHVIAASALEALAMLLGDEVLD----LLEKYASPSTP 709
                                    66666666889999999999999987666554....44555555555 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   4.0   0.00065      0.78      16      51 ..     786     821 ..     783     823 .] 0.86

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00065
                                    XXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-X CS
                          DivIC  16 llaykqlkqeiaalqaelaklkaeneeLeaevkdLk 51 
                                    + + ++  +e+ +l++el+kl++e+++L ++v++L+
  gi|119720131|ref|YP_920626.1| 786 IKKHMERGEEYRKLKEELDKLREEERRLSERVERLE 821
                                    56667788999***********************95 PP

>> DUF4140  N-terminal domain of unknown function (DUF4140)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   3.7    0.0018       2.1      65      94 ..     785     823 .]     770     823 .] 0.76

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0018
                        DUF4140  65 e.........elkalraeleeledelaaledelaaaear 94 
                                    +         e+++l++el++l++e ++l+++ +++e+r
  gi|119720131|ref|YP_920626.1| 785 QikkhmergeEYRKLKEELDKLREEERRLSERVERLEKR 823
                                    23444666646*************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (823 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1129  (0.0629706); expected 358.6 (0.02)
Passed bias filter:                      870  (0.0485247); expected 358.6 (0.02)
Passed Vit filter:                       140  (0.00780858); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.84u 0.31s 00:00:01.14 Elapsed: 00:00:00.46
# Mc/sec: 5357.40
//
Query:       gi|119720132|ref|YP_920627.1|  [L=93]
Description: hypothetical protein Tpen_1226 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0011   18.0   0.0     0.0012   17.8   0.0    1.0  1  LMBR1            LMBR1-like membrane protein
     0.0086   16.1   5.8      0.013   15.6   5.8    1.3  1  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
  ------ inclusion threshold ------
      0.018   14.7   0.2       0.02   14.5   0.2    1.1  1  DUF4131          Domain of unknown function (DUF4131)
      0.025   14.6   0.1      0.029   14.5   0.1    1.1  1  DUF2614          Zinc-ribbon containing domain


Domain annotation for each model (and alignments):
>> LMBR1  LMBR1-like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   2.7e-07    0.0012     129     211 ..       8      87 ..       2      93 .] 0.69

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.7e-07
                          LMBR1 129 iyllllvivlglliyvliil.qklsllsiksllpilislantwGlvllilllGyGlvel.Prslwreiksdldeelkkly 206
                                     ++l l+ v+++l+y ++++ +++++l   +l+      a + G++ ++  +Gy l+ + P + + ei+++++eelk+l+
  gi|119720132|ref|YP_920627.1|   8 GWALALISVVVILLYGWLVFfTSWDVL---VLKLT--GFAAVAGVFGILAWIGYTLATTpPPKPIEEIEKEIEEELKRLE 82 
                                    566666666666666555521444444...55555..555556****************86677788************7 PP

                          LMBR1 207 feaak 211
                                     e ++
  gi|119720132|ref|YP_920627.1|  83 QESQQ 87 
                                    77655 PP

>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   5.8   2.9e-06     0.013      34     108 ..       7      73 ..       2      82 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.9e-06
                Phage_holin_3_6  34 gsgagllgaagvlallalllllval.alalaalwlaalivaavllvlagvlalvglkklkkakplpertieelked 108
                                    +  a++l+  +v++l+++l+++    +l+l       l  +a+++ + g+la++g+  +     +p + iee+++ 
  gi|119720132|ref|YP_920627.1|   7 VGWALALISVVVILLYGWLVFFTSWdVLVL------KLTGFAAVAGVFGILAWIGYTLATT---PPPKPIEEIEKE 73 
                                    444455555555555555555555555555......4555788888889999999996665...355666766665 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.2   4.5e-06      0.02       6      59 ..       9      67 ..       5      92 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.5e-06
                        DUF4131  6 alvllalllllllllllllrr......rprrrvllllllllllallgfalrapqpnandl 59
                                   ++++l++++++ll+ +l++         +   ++++++++ +la++g++l +  p++ ++
  gi|119720132|ref|YP_920627.1|  9 WALALISVVVILLYGWLVFFTswdvlvLKLTGFAAVAGVFGILAWIGYTLATTPPPK-PI 67
                                   444444444444444444433467777666667777888888888777776655544.33 PP

>> DUF2614  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   6.4e-06     0.029       9      61 ..       6      57 ..       2      74 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.4e-06
                        DUF2614  9 irtfalllvfiglivmyigllfkeselllvlflllGlllvlastvvyfwiGll 61
                                   +  +al l+ + +i++y  l+f +s  +  ++ l G+ +v   + +  wiG +
  gi|119720132|ref|YP_920627.1|  6 LVGWALALISVVVILLYGWLVFFTSWDV-LVLKLTGFAAVAGVFGILAWIGYT 57
                                   5679*************99877665444.456789****************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2027  (0.113057); expected 358.6 (0.02)
Passed bias filter:                     1122  (0.0625802); expected 358.6 (0.02)
Passed Vit filter:                       114  (0.00635841); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.31s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 652.27
//
Query:       gi|119720133|ref|YP_920628.1|  [L=443]
Description: ribulose bisophosphate carboxylase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-96  322.7   0.0    2.4e-96  322.5   0.0    1.1  1  RuBisCO_large    Ribulose bisphosphate carboxylase large chai
    1.3e-42  144.8   0.0    2.5e-42  143.9   0.0    1.5  1  RuBisCO_large_N  Ribulose bisphosphate carboxylase large chai
     0.0059   16.3   0.0       0.02   14.6   0.0    1.7  2  4HFCP_synth      4-HFC-P synthase
  ------ inclusion threshold ------
      0.031   14.0   0.1       0.28   10.9   0.0    2.1  2  Glyco_trans_4_3  Glycosyl transferase family 4 group


Domain annotation for each model (and alignments):
>> RuBisCO_large  Ribulose bisphosphate carboxylase large chain, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  322.5   0.0  5.4e-100   2.4e-96       1     299 []     141     437 ..     141     437 .. 0.98

  Alignments for each domain:
  == domain 1  score: 322.5 bits;  conditional E-value: 5.4e-100
                                    .HHHHHHHH...T--EEEEE-SSSS---HHHHHHHHHHHHTT-.SEEE--TT-SSBTTB-HHHHHHHHHHHHHHHHHHHS CS
                  RuBisCO_large   1 giaverevlnkegrpilGtiiKPklGLspknyarvvyelllgglDfiKdDEnlnsqpfarlkdrieavaeaikraqdetG 80 
                                    g+++ r +l+  grpi+Gt+ KPk+G sp+++++++ye+l gg+Df+KdDEnl+ + ++r+++r++a+++ai+ra++etG
  gi|119720133|ref|YP_920628.1| 141 GVEGVRGKLKIWGRPIIGTVPKPKVGYSPEEVEKLAYEILVGGMDFVKDDENLAGPSYCRFEERAKAIMKAIDRAEKETG 220
                                    57888999************************************************************************ PP

                                    S--EEEEE---SSHHHHHHHHHHHHHHHGGEEEEEHHHH-HHHHHHHHHHSTTS..EEEEE-TTTHHHHST--SEE-HHH CS
                  RuBisCO_large  81 ekklyalnitaddleemlrraefvketggeivlvdvlviGfaaitslrkafrknelllHlHraghgaltrqskhGisfrv 160
                                    e+k + +nita d++em+rr  +v+e+g + v+vdv+ +G++++t++r  + + +l++H Hra h+a+tr++ hG+s++ 
  gi|119720133|ref|YP_920628.1| 221 ERKAWLANITA-DVREMERRLKLVAELGNTHVMVDVVIAGWSSLTYVRDLAADYKLAIHGHRAFHAAFTRNPYHGVSMFT 299
                                    **********5.67****************************************************************** PP

                                    HHHHHHHHT-SEEE---TTSSSBS--GG......GHHHHHHHHSSEEE-SS-EEE-TT----EEEEESS--TTTHHHHHH CS
                  RuBisCO_large 161 lakllRLlGvdhlhtgtvgvgklegdesvvkgfkdtlrekmleedeaegiffeqdlaslkavlpvasgGihagqlpelle 240
                                    lakl R++Gvd+lh+gt +vgkle ++  v  +   lre++ + d ++g +++q++ ++k+++pv sgG+h g+lp++++
  gi|119720133|ref|YP_920628.1| 300 LAKLYRIIGVDQLHVGTPEVGKLEAKAVDVIRMARLLREQTYKPDIEDGLHMQQPFPGIKPAFPVSSGGLHPGTLPAVIK 379
                                    *************************9988888888********************************************* PP

                                    HHS---SEEE-HHHHHTSTT-HHHHHHHHHHHHHHHHHT--HHHHHTT-HHHHHHHHHX CS
                  RuBisCO_large 241 nlgesdvilqaGGGilgHpdgaaaGakalrqaleaaveGadleeyAkehkeLarAlesw 299
                                    ++g  d+++q+GGG++gHpdg+ aGa+a rqa+ea +eG++l+eyAk+h+eLarAle+w
  gi|119720133|ref|YP_920628.1| 380 AMGV-DTVIQVGGGVVGHPDGPRAGAAAARQAVEAYLEGVPLQEYAKTHRELARALEKW 437
                                    ****.*****************************************************9 PP

>> RuBisCO_large_N  Ribulose bisphosphate carboxylase large chain, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.9   0.0   5.5e-46   2.5e-42       2     120 .]      11     131 ..      10     131 .. 0.97

  Alignments for each domain:
  == domain 1  score: 143.9 bits;  conditional E-value: 5.5e-46
                RuBisCO_large_N   2 yvdedyepk.etdllaafrvePaegvsveeaaaavAaeSStgtwtevsttkd.ellkklkakvyeieeveeekelvkiAY 79 
                                    +v ++y p+ ++d++++frv+P+eg+++e+aa+ vAaeSS+gtwt++++++d +++++lk+k+y++e + ++++++++AY
  gi|119720133|ref|YP_920628.1|  11 FVVKSYLPDpDKDVIVTFRVTPSEGFTIEDAAGGVAAESSVGTWTTLYQWYDkSRIDRLKGKAYYMESLGDGSYILRVAY 90 
                                    67789999989***************************************99789************************* PP

                RuBisCO_large_N  80 plelFeegsipqllssiaGnifgmkavkalrleDirlPkay 120
                                    p+elFeeg++p++l+s+aGnifgm++v++lr+eDi+lP+a+
  gi|119720133|ref|YP_920628.1|  91 PVELFEEGNMPAFLASVAGNIFGMRRVRSLRVEDIYLPEAF 131
                                    **************************************986 PP

>> 4HFCP_synth  4-HFC-P synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   4.5e-06      0.02      62     160 ..     167     265 ..     160     280 .. 0.86
   2 ?   -1.7   0.0      0.43   1.9e+03      18      43 ..     308     333 ..     300     342 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.5e-06
                                    S-HHHHHHHHHHHHHTT-SEEE.....EEE-S--SHHHHHHHHHHHHHHHHHH-TTSEEEEEEETTGGGTT---GGG.HH CS
                    4HFCP_synth  62 ekpgtvslaalgaaaagvdyvK.....vGlaglkkeeealealkavvkavkeedkekkvvavlyaDaervasvsple.ll 135
                                    ++p+ v + a+++ + g+d+vK      G   ++ ee+a   +ka+ +a ke++++k++ a + aD +      ++e  l
  gi|119720133|ref|YP_920628.1| 167 YSPEEVEKLAYEILVGGMDFVKddenlAGPSYCRFEERAKAIMKAIDRAEKETGERKAWLANITADVR------EMErRL 240
                                    67889999999***********6666667888999********************************8......444499 PP

                                    HHHHHHT-SEEEEE-SS-SS--HHH CS
                    4HFCP_synth 136 elaaeagaagvmlDTadKdgkslld 160
                                    +l+ae g + vm+D ++   +sl+ 
  gi|119720133|ref|YP_920628.1| 241 KLVAELGNTHVMVDVVIAGWSSLTY 265
                                    99************88776666665 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.43
                                    T-SEEEE--GGG-TT----HHHHHHH CS
                    4HFCP_synth  18 gadiiDvKnPaeGsLGalfpevirei 43 
                                    g+d + v  P+ G L a + +vir +
  gi|119720133|ref|YP_920628.1| 308 GVDQLHVGTPEVGKLEAKAVDVIRMA 333
                                    78888899999999999999999865 PP

>> Glyco_trans_4_3  Glycosyl transferase family 4 group
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   6.3e-05      0.28      28      95 ..     216     280 ..     200     306 .. 0.83
   2 ?    0.2   0.0      0.11   5.1e+02      48      68 ..     325     345 ..     310     348 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 6.3e-05
                Glyco_trans_4_3  28 ereatpeahpyvreleaavlrgeavaraaeeLkkeGfvPDvivaHsgwGetlflkdvfPdarlllYfe 95 
                                    e+e t e + +++++ a v++ e+ +++++eL +  ++ Dv++a  gw + ++++d+  d +l +   
  gi|119720133|ref|YP_920628.1| 216 EKE-TGERKAWLANITADVREMERRLKLVAELGNTHVMVDVVIA--GWSSLTYVRDLAADYKLAIHGH 280
                                    333.448889*********************************8..9*********988887776655 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.11
                Glyco_trans_4_3  48 rgeavaraaeeLkkeGfvPDv 68 
                                    ++  v+r+a+ L+++ ++PD+
  gi|119720133|ref|YP_920628.1| 325 KAVDVIRMARLLREQTYKPDI 345
                                    567899**************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (443 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 2693.55
//
Query:       gi|119720134|ref|YP_920629.1|  [L=515]
Description: radical SAM domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.3e-19   69.5   0.0    3.6e-18   66.5   0.0    2.2  2  Radical_SAM  Radical SAM superfamily
     0.0013   18.7   0.0      0.053   13.6   0.0    2.3  2  B12-binding  B12 binding domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0     0.095   8.5e+02      97     143 ..      69     143 ..      53     151 .. 0.64
   2 !   66.5   0.0     4e-22   3.6e-18       1     167 []     220     405 ..     220     405 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.095
                                    HHHTT-SEEEEEEBSSSHH...........................HHHHHHTCTSHHHHHHH..HHHHHHHTTSE CS
                                    xxxxxxxxxxxxxxxxxxx...........................xxxxxxxxxxxxxxxxx..xxxxxxxxxxx RF
                    Radical_SAM  97 llelgvdrvslgleaadde...........................kvlklmnrghtfeevle..aleklreagik 143
                                    l e+g++   ++ +++d+                            + ++++nr  +f +++e  a++k++e+g+k
  gi|119720134|ref|YP_920629.1|  69 LQEAGFNAAIVDPDHLDKHldtmkvllvghhdyfaygppssewwviTGREPVNR-RSFRRLMEspAVRKAKEKGVK 143
                                    555555555555555555555555555555555555777777777777777754.778888875568888888888 PP

  == domain 2  score: 66.5 bits;  conditional E-value: 4e-22
                                    EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS.....TTHHHHHHHHHHTC. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxx. RF
                    Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggeplly.....pdfvellerlakla. 74 
                                    v+++rgC+++C+fC+++      ++ r++++e++++ev+ + ++ g ++v+l++ ++lly     ++  e +++l+++  
  gi|119720134|ref|YP_920629.1| 220 VEIMRGCPRGCRFCSVT-----LRPLRFMPIEKVVAEVRVN-VRAGLRNVLLHSEDVLLYgadgvKPRPEPVLKLHAEVl 293
                                    689**************.....6******************.9**********************555566666666555 PP

                                    ......CCTEEEEEEECSSCHG.....HHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHTCTSHH........HHHHHHH CS
                                    ......xxxxxxxxxxxxxxxx.....xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxx RF
                    Radical_SAM  75 ......vpgiritvetngtlpd.....eeklerllelg.vdrvslgleaaddekvlklmnrghtf........eevleal 134
                                          v++ + ++++  +  d      + +e l e+  +  v++g+e+++ +   + +++ + +        e v++a+
  gi|119720134|ref|YP_920629.1| 294 keapgsVAWSHASLSAVKYAEDnyrlvSRLMEMLSERQeILGVEVGIETGSAR-LAREVMPAKALpyraeewvEVVKDAF 372
                                    5789999999999999999999*7776555555555559**************.55555444444577766667777777 PP

                                    HHHHHTTSETEEEEEEEBTTTSHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM 135 eklreagikrvvdrivglpGendeeleellell 167
                                     +++++++ +  + i+glpGe+ +++++++el+
  gi|119720134|ref|YP_920629.1| 373 AIMHDNRVVPAATLILGLPGETPDDVVKTAELV 405
                                    7777777777********************986 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.014   1.3e+02      12      37 ..      57      82 ..      54      98 .. 0.86
   2 !   13.6   0.0   5.9e-06     0.053      66     120 ..     123     181 ..     114     182 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.014
                    B12-binding 12 lhplGlavlaaalrdagfeVqllgan 37
                                   + p+Gl+ + a l++agf+  +++ +
  gi|119720134|ref|YP_920629.1| 57 VAPYGLRKIEAKLQEAGFNAAIVDPD 82
                                   5799****************999876 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 5.9e-06
                    B12-binding  66 eavkelvel...lkrirprvkvvvGGahpsldpeetleak.lgiddvvvgegedaleal 120
                                    + +++l+e    +k++ ++vk+++GG+++    +e+ ++k  g+d vv gege  + +l
  gi|119720134|ref|YP_920629.1| 123 RSFRRLMESpavRKAKEKGVKIIAGGPAAWQWLWELESWKkWGVDTVVDGEGEGVVVDL 181
                                    567888888888999999********986555555555569************988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (515 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      561  (0.0312901); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 3358.27
//
Query:       gi|119720135|ref|YP_920630.1|  [L=95]
Description: hypothetical protein Tpen_1229 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       256  (0.0142785); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.29s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 662.54
//
Query:       gi|119720136|ref|YP_920631.1|  [L=177]
Description: flavin reductase domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.4e-25   87.8   0.0    8.4e-25   87.6   0.0    1.0  1  Flavin_Reduct  Flavin reductase like domain


Domain annotation for each model (and alignments):
>> Flavin_Reduct  Flavin reductase like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.6   0.0   4.7e-29   8.4e-25       4     154 ..      12     171 ..       9     172 .. 0.90

  Alignments for each domain:
  == domain 1  score: 87.6 bits;  conditional E-value: 4.7e-29
                                    S-EE-EEEEE.EETTEEEEEEESSEEEEETTTTEEEEEEETTSHHHHHHHHHSEEEEEEEBCCGHHHHHHTCS...SCCC CS
                  Flavin_Reduct   4 vaqpvavvttsvpptsplgatlssftslsldPplvafslrlpsstadalkeagefvinllsesqealadafsqksgprtd 83 
                                    +++p +++ + + +++++ + +s++t+++ +Pplv+++++ +s t++ +++ gef++n+++ s  +     +++sg r++
  gi|119720136|ref|YP_920631.1|  12 HPRPAYIIGSGRVGEKANFMAASWVTPVAEEPPLVGVAIDVESLTHELIERYGEFTVNVVPTSMLDKLYYAGSRSG-RDE 90 
                                    699*******999*****************************************************8888888899.*** PP

                                    CCCCCCCCEEECTCCCSEEETTCSEEEEEEEEEEECCTTEEEEEEEEEEEEESTTECTT...........BEECCCCCEE CS
                  Flavin_Reduct  84 dksifagltweesptgapallgalasleCqvvgsvelgdhelfigeVvavkvgddadee...........pLlywrrrya 152
                                    dk +  +   +e ++ ap+++ga++++eC v+g++++ d + f g+Vv + v++   +e           pL  w r + 
  gi|119720136|ref|YP_920631.1|  91 DKASSIPHRKGE-KVSAPVVEGAVGVVECVVHGKLRAEDVTFFAGRVVYAAVDERFFNErsgwlfkeidlPLHNWGRGFY 169
                                    **5555666666.79************************************99995555788888888888888888887 PP

                                    EE CS
                  Flavin_Reduct 153 gl 154
                                    g+
  gi|119720136|ref|YP_920631.1| 170 GV 171
                                    76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       250  (0.0139439); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1395.04
//
Query:       gi|119720137|ref|YP_920632.1|  [L=347]
Description: 3-dehydroquinate synthase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.2e-65  219.2   0.1    9.4e-65  218.8   0.1    1.1  1  Fe-ADH_2      Iron-containing alcohol dehydrogenase
    1.5e-29  103.0   2.7    6.4e-29  100.9   2.7    1.7  1  Fe-ADH        Iron-containing alcohol dehydrogenase
    1.4e-09   37.6   0.1    8.2e-06   25.2   0.0    2.7  2  DHQ_synthase  3-dehydroquinate synthase


Domain annotation for each model (and alignments):
>> Fe-ADH_2  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  218.8   0.1   1.6e-68   9.4e-65       2     250 .]      11     267 ..      10     267 .. 0.91

  Alignments for each domain:
  == domain 1  score: 218.8 bits;  conditional E-value: 1.6e-68
                       Fe-ADH_2   2 igegaleklgellkelelkkvllvadentkkaagekveeslkeagikvevveeveeeadleeveklvealreketdlvva 81 
                                    +++gal+ l+e+l+el+ +k ++v+d+++++++g+ ve +l+  +++v  +e +++++++e ++   +a+r  e+ +v +
  gi|119720137|ref|YP_920632.1|  11 VERGALQFLPEVLRELGCSKTVVVTDSGVWSVVGSVVEGALRGLAYEVVYIE-AADNSNVERAR---SAARRVEACAVAG 86 
                                    789*********************************************8775.55555555555...5555556889*** PP

                       Fe-ADH_2  82 vGgGtiiDiakyvsaklnvpyvsvpTaaSvDGfaspgaslvvd.gkkrtvakaaaPlaviaDldvlaeAPrrllasGvGD 160
                                    +GgG+ +D+aky+++ +++p+vsvpTa+S+DGfasp ++l+   g+  ++  ++ P+av++Dl v+++APrrllasGvGD
  gi|119720137|ref|YP_920632.1|  87 LGGGRPVDVAKYAAFMEGLPFVSVPTAISHDGFASPIVALKDPeGNPLSI-FTRPPAAVLVDLAVVSRAPRRLLASGVGD 165
                                    *****************************************988*****9.899************************** PP

                       Fe-ADH_2 161 llgkytaladwklan........evseplaklsaamvqeaaeklve.dkke..tealeellealalsgigisrpaSGsEH 229
                                    ++gk+t++ad +la+        ev+  +a+++a+mv ++++++++  ++   + a + ll ++a++++g+srp+SGsEH
  gi|119720137|ref|YP_920632.1| 166 IVGKVTSVADARLAQrltgeevpEVALRMAETAARMVLDEVDEIASwTERGvgVLAQAGLLAGMAMAVAGSSRPCSGSEH 245
                                    ***************8888877777889****************99533332377778899999**************** PP

                       Fe-ADH_2 230 liSHaldmlal.kqalHGeqVG 250
                                    l+SH ld+  + k+ lHGeqVG
  gi|119720137|ref|YP_920632.1| 246 LFSHSLDKYVPwKKSLHGEQVG 267
                                    *********9999********9 PP

>> Fe-ADH  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.9   2.7   1.1e-32   6.4e-29       1     327 [.       6     319 ..       6     331 .. 0.76

  Alignments for each domain:
  == domain 1  score: 100.9 bits;  conditional E-value: 1.1e-32
                                    -SEEEEETTGGGGHHHHHTTT-..EEEEEEEHHHH.HH.THHHHHHHHHCTT-EEE.E.EEE-S---HHHHHHHHTTS-T CS
                         Fe-ADH   1 Ptrivfgkgaleelgellkklgakralivtdkgslkksglldkvlesleeagievt.vfdgvepnptleeveeaaalare 79 
                                    P+r+v ++gal+ l+e l++lg+++ ++vtd+g++   +++  v+e     g++++ v+ +     + ++ve+a ++ar 
  gi|119720137|ref|YP_920632.1|   6 PKRVVVERGALQFLPEVLRELGCSKTVVVTDSGVW---SVVGSVVEGA-LRGLAYEvVYIE---AADNSNVERARSAARR 78 
                                    89*********************************...6676666655.588888845544...4677788899999999 PP

                                    T.--EEEEEESHHHHHHHHHHHHHTT..................--EEEEESS-S-S-TT-SEEEEE.-TTSEEEEE-.. CS
                         Fe-ADH  80 egadvviavGGGsviDtAKaialllanpevedylgegkakkkkalpliaiPTtaGtGsevtplavitdeeegeklsifdp 159
                                     +a +v ++GGG ++D+AK++a++ +                  lp++ +PT  + +  ++p+  +  + eg  lsif  
  gi|119720137|ref|YP_920632.1|  79 VEACAVAGLGGGRPVDVAKYAAFMEG------------------LPFVSVPTAISHDGFASPIVALK-DPEGNPLSIF-- 137
                                    9999**********************..................***********************.55569*****.. PP

                                    SS--SEEEEEHHHHHHS-HHHHHHHHHHHHHHHHHHHHHHT---TTS........SB--HHHHHHHHHHHHHHHHHHHHH CS
                         Fe-ADH 160 ellPdlaivDpeltltlPkrvtaatglDalahalEayvskkanplsd........alaleairliaknleravadgedle 231
                                    +  P++++vD +++  +P+r++a++++D++ ++     ++ a+ l+         ++a+ a+r++++ ++++     +  
  gi|119720137|ref|YP_920632.1| 138 TRPPAAVLVDLAVVSRAPRRLLASGVGDIVGKVTSVADARLAQRLTGeevpevalRMAETAARMVLDEVDEIASW--TER 215
                                    889***************************999999888888887773333222234444444444444443332..558 PP

                                    HHHHHHHHHHHHHHHHHSS---.....HHHHHHHHHHC.CGGG...GGS-HHH...HHHHHH..........HHHHHHT. CS
                         Fe-ADH 232 areqmllastlaglafsnaglg.....avHalahalgalfgip...hglanai...llpavlrfnaeaaperlaqlaral 300
                                        +++a +lag+a++ ag +       H ++h+l +++      hg+ +++   +  +   fn +  ++ la++    
  gi|119720137|ref|YP_920632.1| 216 GVGVLAQAGLLAGMAMAVAGSSrpcsgSEHLFSHSLDKYVPWKkslHGEQVGVgaiIASYLHGFNWRVIRDALAKVGAPT 295
                                    888999*************9999888899999999999545435567776654443566666888877778888877775 PP

                                    ......T--HHHHHHHHHHHHHTT--- CS
                         Fe-ADH 301 ggesdeeaaeeliealrellkelglpt 327
                                    +    e     + +a+r+llk+  l +
  gi|119720137|ref|YP_920632.1| 296 TV---EGLGVTGEDAVRALLKARELRK 319
                                    43...3444444444444444444443 PP

>> DHQ_synthase  3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   1.4e-09   8.2e-06      33     159 ..      83     206 ..      63     216 .. 0.83
   2 !    9.5   0.0   8.4e-05       0.5     183     241 ..     245     296 ..     232     317 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 1.4e-09
                                    EEEEEESHHHHHHHHHHHHHBTT--EEEEEE-SHHHHHTTTSSSEEEEEETTEEEEEEEE-.--SEEEEEGGGGGGS-HH CS
                   DHQ_synthase  33 llialGGGvvgDlaGfvAatylRGvrfvqvPttllaqvDssvGgKtainlplgKNliGafa.qPkavlidlevLktLper 111
                                    ++  lGGG   D+a ++A  ++ G+ fv vPt++    D      +a+  p+g N +  f+  P avl+dl+v++  p+r
  gi|119720137|ref|YP_920632.1|  83 AVAGLGGGRPVDVAKYAA--FMEGLPFVSVPTAIS--HDGFASPIVALKDPEG-NPLSIFTrPPAAVLVDLAVVSRAPRR 157
                                    5778************87..9***********984..4666667899999988.777777615789************** PP

                                    HHHHHHHHHH.HHHHHT-HHHHHHHHHHHHHHHCTTTHHHHHHHHHHHH CS
                   DHQ_synthase 112 elraGlaEvi.Kyalikdeelfelleenaeallkeeeeealeeliarsi 159
                                     l++G+++++ K++ ++d++l ++l+ ++   ++ + +e++++++   +
  gi|119720137|ref|YP_920632.1| 158 LLASGVGDIVgKVTSVADARLAQRLTGEEVPEVALRMAETAARMVLDEV 206
                                    ********9989*************999988888777777777776665 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 8.4e-05
                                    HHHHHHHHHHHTTTTS-HHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHTT---S CS
                   DHQ_synthase 183 HtigHaiEallgyekllHGeaVaiGmvlaaelseklgllkkeeverllkllkklglpvs 241
                                    H ++H +++ +  +k lHGe V +G ++a +l            + +++ l+k+g p++
  gi|119720137|ref|YP_920632.1| 245 HLFSHSLDKYVPWKKSLHGEQVGVGAIIASYLHGFN-------WRVIRDALAKVGAPTT 296
                                    99************************9998876222.......3345555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2527.48
//
Query:       gi|119720138|ref|YP_920633.1|  [L=286]
Description: Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      1e-36  126.7   0.0    1.1e-36  126.5   0.0    1.0  1  CN_hydrolase  Carbon-nitrogen hydrolase
  ------ inclusion threshold ------
       0.17   11.4   0.1       0.26   10.8   0.1    1.2  1  Angiomotin_C  Angiomotin C terminal


Domain annotation for each model (and alignments):
>> CN_hydrolase  Carbon-nitrogen hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.5   0.0   1.3e-40   1.1e-36       1     260 [.      17     257 ..      17     258 .. 0.92

  Alignments for each domain:
  == domain 1  score: 126.5 bits;  conditional E-value: 1.3e-40
                                    EEEEEEBB-STTHHHHHHHHHHHHHHHHHHTTESEEEEETTT...TTBSSSHHHHHHHHBHSSSHHHHHHHHHHHHHTEE CS
                   CN_hydrolase   1 rvAvvQlpqkaadleanlqklleliaeAarkgadLivlPElf...itgykeeahfleaAeaglgetlallaalarkngia 77 
                                    rvA+ Ql+  + ++ +nl+k+l+l++     +a L v+PE+    ++g+  ++ +   Ae ++ge++ ++ + + + g+a
  gi|119720138|ref|YP_920633.1|  17 RVALHQLAV-SGEKRENLEKALRLLEL---GDAYLHVFPEYLmgvDPGGPTRDYVWRVAEPIDGEFASRIVEKTGELGVA 92 
                                    799999999.89***************...9*********96222456688888889999******************** PP

                                    EEEEEEEEECCTTEEEEEEEEEEEETTSEEEEEEE-SS--EECTTSCECCGHHTSCS-SSS-EEEETTEEEEEEEGGGGG CS
                   CN_hydrolase  78 vvigliereltngklqayntavlldldgklvgkyrKlhLfpgeprpptaverelfepgdgipvfdtpvgkiGaaiCyeig 157
                                    +v++++ r  +++ +  yn+avl  ++gk+ + yrK+hLf    +  +++e+++f+pg +  v+d+++ ++G+a+C + +
  gi|119720138|ref|YP_920633.1|  93 AVFTMFLR--EGPGV--YNAAVLA-EEGKVKAVYRKIHLF----DAYGYRESSVFSPGREPVVADLKGLRLGIAVCFDLR 163
                                    ********..9****..**99876.788889********9....479**********99766779*************** PP

                                    SHHHHHHHHHTT-SEEEEBH.GCCCTCHHHHHHHHHHHHHHHHHHTSEEEEEEBEEEHCETTEEEE--EEEE-TTS-EEE CS
                   CN_hydrolase 158 fpellralalkgaeilvnlserapvpksmgppqwellgraralengcfviaanqvggyeqlilwpvghSaiidpdGrila 237
                                    fpel r + l+gae+ v    +a++ +    +qw +l+ ara en  +++a+nqvg       ++ ghS ++ p G +l+
  gi|119720138|ref|YP_920633.1| 164 FPELFRSMFLRGAEVFVV--PSAWYRGPYKVEQWKALTAARAHENTSYLVAVNQVGE------SFTGHSLVATPLGHLLV 235
                                    ******************..77***********************************......***************** PP

                                    ECCSSSTEEEEEEEEHHHHHHHH CS
                   CN_hydrolase 238 glgeeeegvliaeidladvratr 260
                                    +lge e+  + +++d ++++++r
  gi|119720138|ref|YP_920633.1| 236 DLGEGER-SIAVDLDEGELASAR 257
                                    ******8.777888877777766 PP

>> Angiomotin_C  Angiomotin C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   2.9e-05      0.26       9      30 ..      17      38 ..      13      44 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 2.9e-05
                   Angiomotin_C  9 qqaLaqlqaaceKREqlekrlr 30
                                   + aL+ql  + eKRE+lek lr
  gi|119720138|ref|YP_920633.1| 17 RVALHQLAVSGEKRENLEKALR 38
                                   679****************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2036.73
//
Query:       gi|119720139|ref|YP_920634.1|  [L=237]
Description: hydrolase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.6e-15   55.1   0.0    1.6e-14   54.4   0.0    1.4  2  HAD_2           Haloacid dehalogenase-like hydrolase
      8e-12   45.9   0.0    2.8e-11   44.1   0.0    1.8  1  Hydrolase       haloacid dehalogenase-like hydrolase
    5.6e-10   39.2   0.0    1.5e-09   37.8   0.0    1.7  1  Hydrolase_like  HAD-hyrolase-like
  ------ inclusion threshold ------
      0.028   14.5   0.0        4.1    7.6   0.0    2.7  2  Hydrolase_6     Haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       1.6   7.3e+03       3      27 ..       6      29 ..       6      43 .. 0.62
   2 !   54.4   0.0   3.7e-18   1.6e-14      80     175 ..     100     199 ..      63     202 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.6
                          HAD_2  3 FDlDgTlldteeliiqafnelleey 27
                                   FD+ gTll  e   ++a+++++ee 
  gi|119720139|ref|YP_920634.1|  6 FDVWGTLLRIE-PFYEAAARAMEEL 29
                                   66667776433.3455555555554 PP

  == domain 2  score: 54.4 bits;  conditional E-value: 3.7e-18
                          HAD_2  80 pydgvkelLeeLkeagyklgivTsk...sreaveekleqlgiesyFdvivtsedvekkKPdpeviekaleklklkkeevi 156
                                    +++g  e++e L+e+gy+l+++++       +++  l++ g+ ++F v v +++v++ KPdp  ++++l+ +++ +e v+
  gi|119720139|ref|YP_920634.1| 100 LIPGSLETVERLHEEGYSLAVASNViywPGYVTRVLLDRAGFSRFFRVQVYADEVGRLKPDPGFFAELLRLTGAPREGVV 179
                                    689*********************954456799999******************************************** PP

                          HAD_2 157 yvGDsp.tDieaakkagikv 175
                                     vGDsp  D+ +a +ag+  
  gi|119720139|ref|YP_920634.1| 180 HVGDSPqEDLAGALAAGVAG 199
                                    *****************975 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1   0.0   6.3e-15   2.8e-11       1     210 []       1     196 [.       1     196 [. 0.78

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 6.3e-15
                                    SSEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTEHHHHTHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase   1 iktvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakarsgaltgfatfigrgayaigkpewltal 80 
                                    +++v fD+ GTL++ ep  e + +                     +  + +a+   ++g+++++g  ++    p  +   
  gi|119720139|ref|YP_920634.1|   1 MRLVSFDVWGTLLRIEPFYEAAARAM---------------EELGILGFREALDLLVKGYREVKGARRLGAIDPGDVIGS 65 
                                    67899***********9999988888...............333566777777888899999888773333333333333 PP

                                    HCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEH..HHHH.HHHHHTT. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxx.xxxxxxx. RF
                      Hydrolase  81 dippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnp..etae.raanqlG. 156
                                     +   lg+    +     +v+l  ara   + ++d   + p+  e+v++L++ g+ ++++++       +   +++++G 
  gi|119720139|ref|YP_920634.1|  66 SVAVALGSSGAGL--TKGDVFLAFARAANRVSVSDL--LIPGSLETVERLHEEGYSLAVASNVIYwpGYVTrVLLDRAGf 141
                                    2344444444444..445555555599999999999..***********************9877665555266666**9 PP

                                    GGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHH.HHHHHHHTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                      Hydrolase 157 ddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgvn.DaaalaaAg 210
                                     ++f + + +d+++  kp+p  + +++r  +++ e v++VGD++  D+a++ aAg
  gi|119720139|ref|YP_920634.1| 142 SRFFRVQVYADEVGRLKPDPGFFAELLRLTGAPREGVVHVGDSPQeDLAGALAAG 196
                                    9999***************************99999***************9998 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   0.0   3.3e-13   1.5e-09       4      53 ..     158     207 ..     156     224 .. 0.94

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 3.3e-13
                                    TTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESSSSS CS
                 Hydrolase_like   4 KPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVltGvt 53 
                                    KP p+++ + l+ +g+++e v+ +GD++  D+agA +aG+ +vLV  G  
  gi|119720139|ref|YP_920634.1| 158 KPDPGFFAELLRLTGAPREGVVHVGDSPQEDLAGALAAGVAGVLVDGGRG 207
                                    9********************************************99975 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0   0.00091       4.1       2      27 ..       5      30 ..       4      39 .. 0.90
   2 ?    3.9   0.0     0.013        57      15      38 ..     100     123 ..      94     135 .. 0.93

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00091
                                   EEESTTTSEETTEE-TTHHHHHHHHH CS
                    Hydrolase_6  2 lfDidGvLwrgdkaipgaaealnalr 27
                                    fD++G+L+r +  ++ aa+a++ l 
  gi|119720139|ref|YP_920634.1|  5 SFDVWGTLLRIEPFYEAAARAMEELG 30
                                   59*******************99875 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.013
                                    E-TTHHHHHHHHHHTT-EEEEEE- CS
                    Hydrolase_6  15 aipgaaealnalraagkpvvllTN 38 
                                    +ipg+ e++++l+++g+ +++ +N
  gi|119720139|ref|YP_920634.1| 100 LIPGSLETVERLHEEGYSLAVASN 123
                                    79******************9999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1768.68
//
Query:       gi|119720140|ref|YP_920635.1|  [L=166]
Description: hypothetical protein Tpen_1234 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.8e-07   30.3   0.0    1.1e-06   29.2   0.0    1.6  2  Methyltransf_11  Methyltransferase domain
     0.0047   17.6   0.0     0.0097   16.6   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
  ------ inclusion threshold ------
      0.037   13.9   0.0      0.064   13.1   0.0    1.3  1  Methyltransf_8   Hypothetical methyltransferase
       0.19   11.1   0.0       0.26   10.6   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.0   2.4e-10   1.1e-06      48      96 .]      66     114 ..      44     114 .. 0.92
   2 ?   -2.8   0.0       2.4   1.1e+04       4      25 ..     127     149 ..     126     154 .. 0.65

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 2.4e-10
                                    TTEECCCTSS-TT-EEEEEEES-CCC-CCHHHHHHHHHHHEEEEEEEEE CS
                Methyltransf_11  48 vvadaeklpfednsfDlvvssevlhhvedpekalkeiaRvLkpgGllvi 96 
                                    v a+a +lpf+++s+ l +++ +++  +++e +lke+ RvL  gG+lvi
  gi|119720140|ref|YP_920635.1|  66 VYAEALRLPFREGSVGLLLCFACIERADELEGFLKEACRVLGAGGRLVI 114
                                    5577889****************************************96 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.4
                                    T-TTSHHHHHHHHTT.SEEEEEE CS
                Methyltransf_11   4 GcGtGrlaealakrg.arvvgvD 25 
                                    G+G G     +ak + +++ ++D
  gi|119720140|ref|YP_920635.1| 127 GSGEGWPPGLFAKVAaKHLSCMD 149
                                    77777777777766555555555 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   2.2e-06    0.0097      51      97 .]      66     110 ..      54     110 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.2e-06
                                    EESBCCGBSSSTTTEEEEEEESTGGGSSHHHHHHHHHHHHHHEEEEE CS
                Methyltransf_25  51 vqgdaedlpfedgsfDlvvssgalhhlsdedlekalkeiarvLkpgG 97 
                                    v ++a +lpf +gs+ l +++ +++    ++le +lke++rvL  gG
  gi|119720140|ref|YP_920635.1|  66 VYAEALRLPFREGSVGLLLCFACIERA--DELEGFLKEACRVLGAGG 110
                                    6678899*************8778864..589***********9998 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.4e-05     0.064     114     159 ..      71     117 ..      61     129 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.4e-05
                                    TS-S--TT-EEEEEEES--.-SS-HHHHHHHHHHHEEEEEEEEEEEE CS
                 Methyltransf_8 114 akvPledesvdvavfclsl.mgtnladflkeanrvlkvGGllkvaev 159
                                     ++P  ++sv + ++   +  +++l+ flkea rvl  GG l +  +
  gi|119720140|ref|YP_920635.1|  71 LRLPFREGSVGLLLCFACIeRADELEGFLKEACRVLGAGGRLVIGGL 117
                                    589999999998766444424678******************99765 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   5.8e-05      0.26     103     151 ..      66     114 ..      61     127 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 5.8e-05
                                    EE--TTT-TTS-T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEE CS
                Ubie_methyltran 103 lqanaeeLpfeddsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvv 151
                                    + a+a +Lpf ++s  ++     +    + +  Lkea rvl +GGrlv+
  gi|119720140|ref|YP_920635.1|  66 VYAEALRLPFREGSVGLLLCFACIERADELEGFLKEACRVLGAGGRLVI 114
                                    678999*********988665566666666778*************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1186.82
//
Query:       gi|119720141|ref|YP_920636.1|  [L=434]
Description: radical SAM domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      3e-15   56.5   0.1    6.2e-15   55.5   0.1    1.5  1  SPASM        Iron-sulfur cluster-binding domain
    9.4e-10   39.1   0.0    2.4e-09   37.8   0.0    1.6  1  Radical_SAM  Radical SAM superfamily
    0.00055   20.1   0.0     0.0013   18.8   0.0    1.6  1  Fer4_14      4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.043   14.1   0.0       0.12   12.7   0.0    1.7  1  Fer4_12      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.5   0.1   1.4e-18   6.2e-15       1      68 []     317     397 ..     317     397 .. 0.82

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 1.4e-18
                          SPASM   1 C.fapsrslfInsdGdVvpCcvd...........kktyveelklGnireesleeIwnseeyqefr..kskkfplielCrn 66 
                                    C ++ s+++++ ++GdVvpC +d           + + v+++++Gn ++e+l eIw+s++y++fr  ++k  ++ ++C +
  gi|119720141|ref|YP_920636.1| 317 CpYIDSNYAVVLWNGDVVPC-MDlaythplytnmHYKLVRRVVFGNASREPLGEIWESPRYRAFReaRRKLSDNVPWCGD 395
                                    766778999***********.44566777777675566666************************874556667899*** PP

                          SPASM  67 Cp 68 
                                    Cp
  gi|119720141|ref|YP_920636.1| 396 CP 397
                                    *7 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   0.0   5.3e-13   2.4e-09       1     138 [.      18     151 ..      18     169 .. 0.88

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 5.3e-13
                                    EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiri 80 
                                    v++t+ Cnl C+ C r++   r+g   ++++    ++v+e++ +   +  + g gepll+p f e ++ +++   +   i
  gi|119720141|ref|YP_920636.1|  18 VEPTNECNLSCVMCVRRT--WRGGAFGFMDLGLYRRLVDEGSGKL-RRLALYGFGEPLLHPGFPEMVRYAREVLGDSAYI 94 
                                    6799*************9..79*******************8333.999*********************999999**** PP

                                    EEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  81 tvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklr 138
                                      +tngtl ++  +++   +g+d v+++++a+  +  l +++ g    +vl +l+ ++
  gi|119720141|ref|YP_920636.1|  95 LTVTNGTLMSPARAAEVFGAGIDEVAFSVDAPELD-LLSRIRVGVQSYDVLGNLRSAA 151
                                    ***********************************.9999985555555556666555 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   2.9e-07    0.0013       5      93 ..      21     104 ..      19     124 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.9e-07
                        Fer4_14   5 lsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltG.GePLhyenkkellklvkrlkeey.pekk 82 
                                    ++ CnlsC++C +++ w+  +    +  l  + + d      k + l l G GePL++   + + ++v++ +e    +  
  gi|119720141|ref|YP_920636.1|  21 TNECNLSCVMCVRRT-WRGGAFGFMDLGLYRRLV-DEGSG--KLRRLALYGfGEPLLH---PGFPEMVRYAREVLgDSAY 93 
                                    689*********999.*99999999999997777.33333..3356**********99...6666666666665544599 PP

                        Fer4_14  83 iwletngtlei 93 
                                    i   tngtl+ 
  gi|119720141|ref|YP_920636.1|  94 ILTVTNGTLMS 104
                                    *******9984 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.6e-05      0.12      13      95 ..      22     102 ..      20     127 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.6e-05
                        Fer4_12  13 sgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllG.GEPllpenaeallelvkevkeekp..ekdiw 89 
                                    + CnlsC  C+ + tw+  +   ++  l ++++++    + + l l G GEPll    + + e+v++ +e         +
  gi|119720141|ref|YP_920636.1|  22 NECNLSCVMCV-RRTWRGGAFGFMDLGLYRRLVDEG-SGKLRRLALYGfGEPLL---HPGFPEMVRYAREVLGdsAYILT 96 
                                    58*********.99*****999***********997.788899999999*****...66666777666666552113444 PP

                        Fer4_12  90 lytgyt 95 
                                    +++g+ 
  gi|119720141|ref|YP_920636.1|  97 VTNGTL 102
                                    555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 3161.11
//
Query:       gi|119720142|ref|YP_920637.1|  [L=133]
Description: CopG family transcriptional regulator [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-20   72.3   0.1    4.2e-20   71.7   0.1    1.3  1  NikR_C    NikR C terminal nickel binding domain
    2.6e-07   30.3   0.7    4.8e-07   29.5   0.7    1.5  1  RHH_1     Ribbon-helix-helix protein, copG family
    1.9e-05   24.4   0.1    4.2e-05   23.3   0.1    1.6  1  RHH_5     CopG-like RHH_1 or ribbon-helix-helix domain, RHH_5
    6.3e-05   22.9   0.3    0.00012   22.0   0.3    1.4  1  RHH_3     Ribbon-helix-helix domain


Domain annotation for each model (and alignments):
>> NikR_C  NikR C terminal nickel binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.7   0.1   9.5e-24   4.2e-20       1      76 [.      51     125 ..      51     126 .. 0.97

  Alignments for each domain:
  == domain 1  score: 71.7 bits;  conditional E-value: 9.5e-24
                                    EEEEEEEEETTSTTHHHHHHHHHHHHSSEEEEEEEEEESSSEEEEEEEEEE-HHHHHHHHHHHHTSTTEEEEEEEE CS
                         NikR_C   1 vGvitivydhhqrelserltdiqheyhdliisslhvhldhdncLevivlkGeaeeikelaeklralkgVkhvkltl 76 
                                    +G+i+++ydh++ e    +td qh+y  +i +slh+hl++d cLev+ ++Ge+ ++k+l+ +lr+++gV +v+++l
  gi|119720142|ref|YP_920637.1|  51 AGAIIVLYDHSRGETVYGVTDAQHDY-PEISASLHMHLSEDLCLEVLGVRGEGGRLKNLISALRGVSGVITVQYSL 125
                                    69***********************9.789*******************************************987 PP

>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.7   1.1e-10   4.8e-07       1      37 [.       3      40 ..       3      42 .. 0.96

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 1.1e-10
                                   EEEEEEEHHHHHHHHHHHHHHT.SSHHHHHHHHHHHHH CS
                          RHH_1  1 rvsirldeellerLdelarrrg.rSrSelIReAlreyl 37
                                   r+s+++++e++++L+ela+r++ ++rS l+ +A+++y 
  gi|119720142|ref|YP_920637.1|  3 RISLTVPDEVYKALEELAERTRiSNRSRLVSDAIMAYA 40
                                   8*********************************9996 PP

>> RHH_5  CopG-like RHH_1 or ribbon-helix-helix domain, RHH_5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.1   9.3e-09   4.2e-05       2      23 ..       2      23 ..       1      30 [. 0.91

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 9.3e-09
                          RHH_5  2 kRvnvtLPeelleeLeewAdee 23
                                    R+++t+P+e++++Lee+A+ +
  gi|119720142|ref|YP_920637.1|  2 RRISLTVPDEVYKALEELAERT 23
                                   7******************986 PP

>> RHH_3  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.3   2.6e-08   0.00012       3      37 ..       2      37 ..       2      40 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 2.6e-08
                          RHH_3  3 trttvsidpelaekLkaLSekTrI.prSklldeAie 37
                                   +r++ ++++e ++ L++L e+TrI +rS+l+  Ai 
  gi|119720142|ref|YP_920637.1|  2 RRISLTVPDEVYKALEELAERTRIsNRSRLVSDAIM 37
                                   58999*******************88****999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 936.93
//
Query:       gi|119720143|ref|YP_920638.1|  [L=160]
Description: YbaK/prolyl-tRNA synthetase associated region [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.9e-30  104.4   0.1    4.8e-30  104.2   0.1    1.1  1  tRNA_edit  Aminoacyl-tRNA editing domain
  ------ inclusion threshold ------
      0.026   14.9   0.2       0.11   12.9   0.2    2.1  1  DUF4350    Domain of unknown function (DUF4350)


Domain annotation for each model (and alignments):
>> tRNA_edit  Aminoacyl-tRNA editing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.2   0.1   5.4e-34   4.8e-30       4     121 ..      29     145 ..      26     147 .. 0.97

  Alignments for each domain:
  == domain 1  score: 104.2 bits;  conditional E-value: 5.4e-34
                      tRNA_edit   4 tktieelaaalgvdpsaiaKtlvlkdkkgelvlvllpgdreldlkklakllgakklrlaseeelrellgvepGgvgPlgl 83 
                                    ++t+ e+ + lgv  ++iaKt+v+k++ ge+vlv++++d ++d  +la+llg ++lrla  ee+ e +g+epGgv+P+g+
  gi|119720143|ref|YP_920638.1|  29 AATSLEASESLGVGLDRIAKTVVFKSDGGETVLVVVRADLKVDQSRLARLLGYRRLRLARREEVVEETGYEPGGVPPVGH 108
                                    68999**************************************************************************9 PP

                      tRNA_edit  84 kaagvpvllDeslkeyptvvvgagengatlelspedlr 121
                                      ++++v++D++l++  +v++g+g++ ++++l+  +l+
  gi|119720143|ref|YP_920638.1| 109 -RKRLKVYVDSRLLDAGEVYAGGGDERHLVRLDLRELV 145
                                    .8*******************************99987 PP

>> DUF4350  Domain of unknown function (DUF4350)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   1.3e-05      0.11      12      58 ..      31      81 ..       2      84 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.3e-05
                        DUF4350 12 elLeaq...Gvevrrvrkp.fdalegedgtllvvapdlrlteeelaallew 58
                                   + Lea+   Gv ++r+ k+  ++ +g++++l+vv  dl  ++ +la+ll +
  gi|119720143|ref|YP_920638.1| 31 TSLEASeslGVGLDRIAKTvVFKSDGGETVLVVVRADLKVDQSRLARLLGY 81
                                   44555444577777777764667788**********************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 1182.08
//
Query:       gi|119720144|ref|YP_920639.1|  [L=246]
Description: hypothetical protein Tpen_1238 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-05   24.5   0.1    2.1e-05   24.1   0.1    1.3  1  Glyco_hydro_16  Glycosyl hydrolases family 16
     0.0052   16.9   0.1      0.017   15.3   0.1    1.8  2  Laminin_G_3     Concanavalin A-like lectin/glucanases superfa
  ------ inclusion threshold ------
      0.096   13.3   0.0       0.17   12.5   0.0    1.5  1  Laminin_G_2     Laminin G domain


Domain annotation for each model (and alignments):
>> Glyco_hydro_16  Glycosyl hydrolases family 16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.1   3.6e-09   2.1e-05     105     142 ..     161     198 ..     148     241 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 3.6e-09
                                    SS-TTTS-EEEEEEEETTEEEEEETTEEEEEEESSHHH CS
                 Glyco_hydro_16 105 wfdptedfHtYaieWtpdkikfyVDgkpvrtltkkeae 142
                                    ++   +++H Y +eW  ++++fyVDg++  +l +k  e
  gi|119720144|ref|YP_920639.1| 161 QHLDLTQWHVYRVEWGASEVRFYVDGVLAARLPNKGYE 198
                                    5566789**********************999988654 PP

>> Laminin_G_3  Concanavalin A-like lectin/glucanases superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.73   4.4e+03     125     140 ..     107     122 ..      93     123 .. 0.73
   2 !   15.3   0.1   2.8e-06     0.017      75     121 ..     161     206 ..     152     223 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.73
                    Laminin_G_3 125 dpggddpfdGlidevr 140
                                    +++g +pf+G  ++vr
  gi|119720144|ref|YP_920639.1| 107 QSRGPYPFQGFFAQVR 122
                                    3367999**9999998 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 2.8e-06
                    Laminin_G_3  75 asvpageWtHvavtydggtlrlYvNGvevgsatltggllsatsgplv 121
                                    + + + +W+   v + ++++r+Yv+Gv++++ +++g  ++a  ++++
  gi|119720144|ref|YP_920639.1| 161 QHLDLTQWHVYRVEWGASEVRFYVDGVLAARLPNKGYESRA-RADIW 206
                                    567789*************************9999986653.34444 PP

>> Laminin_G_2  Laminin G domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.8e-05      0.17      46      81 ..     157     194 ..     129     238 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.8e-05
                                    S..SSS-ESSSSEEEEEEECTTEEEEEECTS--CCCE- CS
                    Laminin_G_2  46 s..gkklndgewHsveverkgknltlsvDggetseane 81 
                                    +   ++l+  +wH+ +ve+  +++++ vDg   ++  +
  gi|119720144|ref|YP_920639.1| 157 KpsMQHLDLTQWHVYRVEWGASEVRFYVDGVLAARLPN 194
                                    144788999*********************97766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1774.18
//
Query:       gi|119720145|ref|YP_920640.1|  [L=279]
Description: hypothetical protein Tpen_1239 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.038   13.6   0.0        0.1   12.3   0.0    1.7  1  GntR      Bacterial regulatory proteins, gntR family
      0.076   13.0   0.0       0.15   12.1   0.0    1.4  1  HTH_45    Winged helix-turn-helix
       0.18   10.2   0.0       0.26    9.6   0.0    1.1  1  DUF505    Protein of unknown function (DUF505)
          2    8.3  16.9       0.12   12.2   5.6    2.3  3  VIT1      VIT family


Domain annotation for each model (and alignments):
>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.3e-05       0.1      34      59 ..      43      68 ..      30      69 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.3e-05
                                   HTS-HHHHHHHHHHHHHTTSEEEETT CS
                           GntR 34 fgVsrttvReALrrLeaeglverrqg 59
                                    g +   +R+AL++L+ eglv+ ++g
  gi|119720145|ref|YP_920640.1| 43 VGLDPAEIRKALSELSGEGLVVCKDG 68
                                   56667779**************9998 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   3.3e-05      0.15      30      72 ..      44      86 ..      41      90 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.3e-05
                         HTH_45 30 nLsykllnkYLdmLvekglikkskekYvlTekGlelleklkel 72
                                    L+   ++k L+ L  +gl+  +++  +lTe Gl++ e+ ++l
  gi|119720145|ref|YP_920640.1| 44 GLDPAEIRKALSELSGEGLVVCKDGVLELTEAGLKISEDWRNL 86
                                   5666778999**************************9998876 PP

>> DUF505  Protein of unknown function (DUF505)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   5.8e-05      0.26     488     532 ..      37      80 ..      29      86 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 5.8e-05
                         DUF505 488 elveevdeleeeevrealeklearglvevlpdgnvvlTeaGelik 532
                                    el+ + ++l+  e+r+al++l   glv v +dg+++lTeaG +i 
  gi|119720145|ref|YP_920640.1|  37 ELYGNEVGLDPAEIRKALSELSGEGLV-VCKDGVLELTEAGLKIS 80 
                                    677777899999*************99.679**********9986 PP

>> VIT1  VIT family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   3.8     0.048   2.2e+02       4     181 ..      96     146 ..      20     162 .. 0.65
   2 ?    1.1   3.6     0.067     3e+02       4      46 ..      96     137 ..      93     183 .. 0.74
   3 ?   12.2   5.6   2.7e-05      0.12     133     214 ..     196     276 ..     151     277 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.048
                           VIT1   4 avlGanDGLvspfalvaGlsaaslgssktvllaGlaellAGaiSMgiGeYlsvkserdlekaerkreeeeleedpeegea 83 
                                    +v G+ DG v+ +  v+    a+l ssk+ ++a l                                             
  gi|119720145|ref|YP_920640.1|  96 VVAGLTDGTVTGLITVISSHLAGL-SSKLTVFASLL-------------------------------------------- 130
                                    445555555555555555444454.44444444444............................................ PP

                           VIT1  84 eelaeilearglseelaqevaaellknpdallelmlreelgpsaseelasplkaAlssalsfliGgliPllpylfvesvg 163
                                                                                                                    
  gi|119720145|ref|YP_920640.1|   - --------------------------------------------------------------------------------   -
                                    ................................................................................ PP

                           VIT1 164 lalvvsiavtllalllfG 181
                                       ++s+avt +  +++G
  gi|119720145|ref|YP_920640.1| 131 --ALTSVAVTNFSSFFLG 146
                                    ..4444444555555554 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.067
                           VIT1   4 avlGanDGLvspfalvaGlsaaslgssktvllaGlaellAGai 46 
                                    +v G+ DG v+ +  v+    a+l ssk+ ++a l  l + a+
  gi|119720145|ref|YP_920640.1|  96 VVAGLTDGTVTGLITVISSHLAGL-SSKLTVFASLLALTSVAV 137
                                    678888888888888888888887.778888888777776665 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 2.7e-05
                           VIT1 133 splkaAlssalsfliGgliPllpylfvesvglalvvsiavtllalllfGavkalltgssklvsalrmlliGalAaaaayl 212
                                      + +A+ s+++ l  g++P++ yl ++     l++siav+++a+l++   ++ + ++   +   ++ll+ +l  +++ l
  gi|119720145|ref|YP_920640.1| 196 ANVLSAALSGVATLAAGFVPIALYLALP-PPFNLLASIAVVSAAILALAKYRSSAARTHFKRTLAETLLVILLVVLVSLL 274
                                    34569999******************99.788899999*********999999999999999999999999998888888 PP

                           VIT1 213 ig 214
                                    +g
  gi|119720145|ref|YP_920640.1| 275 LG 276
                                    76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       825  (0.0460148); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1885.26
//
Query:       gi|119720146|ref|YP_920641.1|  [L=290]
Description: uridine phosphorylase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.9e-40  137.0   2.1    8.1e-40  136.5   2.1    1.1  1  PNP_UDP_1        Phosphorylase superfamily
  ------ inclusion threshold ------
      0.066   11.8   0.2       0.11   11.0   0.2    1.3  1  P22_CoatProtein  P22 coat protein - gene protein 5
       0.07   13.2   0.2       0.32   11.0   0.1    2.1  3  bact-PGI_C       Bacterial phospho-glucose isomerase C-termin


Domain annotation for each model (and alignments):
>> PNP_UDP_1  Phosphorylase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.5   2.1   1.4e-43   8.1e-40       3     232 ..      43     267 ..      41     269 .. 0.91

  Alignments for each domain:
  == domain 1  score: 136.5 bits;  conditional E-value: 1.4e-43
                                    EEEESSHHHHHHHHHHEEEEEEEEEE.TTEEEEEEEETTEEEEEEE--SSHHHHHHHHHHHHHHHC--SEEEEEEEEEES CS
                      PNP_UDP_1   3 aiivgspgevellaespleetpfgregrgfkfvtGtlkgkpvvivstGiGkpnaavvaeirllkefgvkaiiriGtaGgl 82 
                                    +++ g+p++v+ +++   +e ++  ++r++ ++tG++kg++v+++stGiG p aa +a+ +ll  + + ++ir+Gt G++
  gi|119720146|ref|YP_920641.1|  43 VLLPGDPERVPYISSF-WDEYREVARHREYVTHTGRYKGVEVSATSTGIGGPAAA-IAVEELLRVG-ASTFIRVGTTGAI 119
                                    8999************.**************************************.********66.************* PP

                                    STTT-TT-EEEEEEEEESSSCCGCCTHHCCTCCCCTTSSEE--HHHHHHHHHCHHTTTTTEEEEEEEEESESS-CH.... CS
                      PNP_UDP_1  83 npdlkvGDvvipddainfdgrsplygpkeegqyfpdsydapadpelrallkeaaealgikvhrGvvatadgfyaet.... 158
                                    +p + vGDv+i   a+++dg+++        qy++++y+a a+ e +++l eaae  g+++h+Gvva++d+fy  +    
  gi|119720146|ref|YP_920641.1| 120 QPFIDVGDVIIVAGAVRLDGTTK--------QYVRAEYPAIAHFEVVEALIEAAESVGARYHVGVVASTDSFYTGQarpg 191
                                    ***********************........************************************************* PP

                                    .........HHHHHHHHHTC-CEEESSHHHHHHHHHHTT--EE.EEEEEEETTTBETTCTCH.HCCCHHHHHHHHHHHHH CS
                      PNP_UDP_1 159 .........eaelrllrrlgadaveMEtaavaqlArelgipfa.airvvsdlaaggadaeatheeveefaqeaaknaaal 228
                                             ++ +  l+r g+   eME++ +++l++ +g++ + +++vv++++++        e ve+++ eaa ++a  
  gi|119720146|ref|YP_920641.1| 192 fkgyeqswmKDLIPDLQRAGVLSFEMEASTILTLSSIYGARGGaVLAVVANRVKD--------ELVENAGVEAAVRTANE 263
                                    99888776666666***************************99455555666555........77777777777776666 PP

                                    HHHH CS
                      PNP_UDP_1 229 llal 232
                                    + ++
  gi|119720146|ref|YP_920641.1| 264 AVKI 267
                                    6555 PP

>> P22_CoatProtein  P22 coat protein - gene protein 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.2   1.9e-05      0.11     248     301 ..     109     166 ..      81     187 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 1.9e-05
                                    S-EEEEBS--TS..--TT-EEEEEEEEEETTTTT-EE....EEEEEEEEEE..ESSSS CS
                P22_CoatProtein 248 rtatvtlsattgatlkaGDvlsiagvkainqvtKqal....sqlatFtvvadaataat 301
                                     +  v  +++ ++++  GDv+ +ag   +   tKq      ++ a F vv++   aa 
  gi|119720146|ref|YP_920641.1| 109 TFIRVGTTGAIQPFIDVGDVIIVAGAVRLDGTTKQYVraeyPAIAHFEVVEALIEAAE 166
                                    5666667777777**********************888888*********86544444 PP

>> bact-PGI_C  Bacterial phospho-glucose isomerase C-terminal SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0      0.95   5.7e+03     138     148 ..      48      58 ..      43      75 .. 0.76
   2 ?   -1.7   0.0      0.44   2.6e+03      42      62 ..     142     163 ..     127     185 .. 0.64
   3 ?   11.0   0.1   5.3e-05      0.32      21      53 ..     233     264 ..     217     280 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.95
                                    --S-TTTTHHH CS
                     bact-PGI_C 138 DPtpvpaIdel 148
                                    DP++vp+I+ +
  gi|119720146|ref|YP_920641.1|  48 DPERVPYISSF 58 
                                    78888887654 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.44
                                    ----B---.SSHHHHHHHTT..S CS
                     bact-PGI_C  42 Kipafagvlpeanhneivgl..e 62 
                                    K+ + a++ p  +h e+v    e
  gi|119720146|ref|YP_920641.1| 142 KQYVRAEY-PAIAHFEVVEAliE 163
                                    55555554.88888887754333 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 5.3e-05
                                    -..TT-THHHHHHHHHHHHTT----B---.SSH CS
                     bact-PGI_C  21 gssellevaArRfknqlnenAKipafagvlpea 53 
                                    g +++l+v+A+R+k++l enA + a + +  ea
  gi|119720146|ref|YP_920641.1| 233 G-GAVLAVVANRVKDELVENAGVEAAVRTANEA 264
                                    3.7899****************99999887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1863.42
//
Query:       gi|119720147|ref|YP_920642.1|  [L=147]
Description: RpiB/LacA/LacB family sugar-phosphate isomerase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    7.9e-37  126.4   0.0    8.4e-37  126.3   0.0    1.0  1  LacAB_rpiB  Ribose/Galactose Isomerase


Domain annotation for each model (and alignments):
>> LacAB_rpiB  Ribose/Galactose Isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.3   0.0   4.7e-41   8.4e-37       2     126 ..       4     128 ..       3     143 .. 0.90

  Alignments for each domain:
  == domain 1  score: 126.3 bits;  conditional E-value: 4.7e-41
                                    EEEE-GCGHHHHHHHHHHHHHTTTEEEEECESS.SS---HHHHHHHHHHHHHTTSSSEEEEEESSSHHHHHHHHTSTT-- CS
                     LacAB_rpiB   2 aigsDhagfelkekikeyLkekghevidvgtes.eesvdYpdfakkvaeavasgeadlgiliCgtGiGmsiaaNkvkgir 80 
                                    a+g+D++ +++   ++e+Lk++ghev+ vg     + + +p++a +vae+vasg++d gi++C tG G+siaaNkvkg+r
  gi|119720147|ref|YP_920642.1|   4 AFGADDN-YSIARFVVEELKRRGHEVVLVGSPLtGKPYPWPKVAVEVAELVASGKVDTGIVMCYTGTGVSIAANKVKGVR 82 
                                    6677765.899999******99********5555669******************************************* PP

                                    EEE-SSHHHHHHHHHTT--SEEEEETTTS-HHHHHHHHHHHHHS-- CS
                     LacAB_rpiB  81 aalchdeesAklarehnnanvlalGarvigeelakeivkaFletef 126
                                    aalc+d++ A+ ar  n+anvlal+ar+++ee+akei++++++ e 
  gi|119720147|ref|YP_920642.1|  83 AALCTDAKNARGARLWNDANVLALSARLLSEEVAKEILDEWFSVEK 128
                                    ******************************************9776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.30s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 984.94
//
Query:       gi|119720148|ref|YP_920643.1|  [L=202]
Description: hypothetical protein Tpen_1242 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1409.99
//
Query:       gi|119720149|ref|YP_920644.1|  [L=165]
Description: hypothetical protein Tpen_1243 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 1083.03
//
Query:       gi|119720150|ref|YP_920645.1|  [L=232]
Description: hypothetical protein Tpen_1244 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       192  (0.0107089); expected 358.6 (0.02)
Passed bias filter:                      160  (0.00892409); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1622.62
//
Query:       gi|119720151|ref|YP_920646.1|  [L=716]
Description: extracellular solute-binding protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.9e-55  187.0   8.7    2.2e-43  148.7   0.9    2.3  2  SBP_bac_5  Bacterial extracellular solute-binding proteins, f
  ------ inclusion threshold ------
      0.025   14.8   0.8      0.046   13.9   0.1    1.8  2  DUF1120    Protein of unknown function (DUF1120)
      0.062   14.2   0.0       0.15   12.9   0.0    1.6  1  DUF4065    Protein of unknown function (DUF4065)


Domain annotation for each model (and alignments):
>> SBP_bac_5  Bacterial extracellular solute-binding proteins, family 5 Middle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.7   0.9   3.7e-47   2.2e-43     150     370 ..      48     266 ..      44     271 .. 0.92
   2 !   42.3   1.6   7.8e-15   4.7e-11       2     146 ..     488     704 ..     487     713 .. 0.91

  Alignments for each domain:
  == domain 1  score: 148.7 bits;  conditional E-value: 3.7e-47
                                    SSSSEEEEEE-.SHHHHHHHHHTTSSSEEESTTCCTHCHHHHHTTEEE......EEEEEEEEEEEEEETTTSTGGGSHHH CS
                      SBP_bac_5 150 pkldriefkvipdsdaraaalqsGeiddvaepppsdieqlkeakglkv......lyespgggvtylafNtkkppfddkrv 223
                                    p  ++i + +++d+ +r+++ ++G   d+a ++p+ ++ + ++   +       + ++p+++++y+++N  k+p++ ++v
  gi|119720151|ref|YP_920646.1|  48 PFHKQILYVIVNDEGTRINMYKTGVF-DIAAVTPARWPDVNNTRVGNFtlhlvrRPDKPQLTIQYIGLNPMKEPLNIPEV 126
                                    566899*****9999999999*****.88899*99***99777766668889999************************* PP

                                    HHHHHHHS-HHHHHHHCTTTSSEEESSSSTTTSTTCCSCHCCCSHHSHHHHHHHHHHHTT-BCSSTSCEETCEEEEEEEE CS
                      SBP_bac_5 224 RqAlsyAiDreeivkavlegyatpansllppsspgadeeykpaykaydpekAkklLkeaGykdgdggglrekklkltlll 303
                                    RqAl+yA +++ i+k+v++g++++ ++++p +++g+ e   ++ ++yd++kA++++ +   k+ d g++     ++t+++
  gi|119720151|ref|YP_920646.1| 127 RQALAYATPYDVILKQVFGGLYVRLYTIIPKGMSGYTEFGINK-YEYDMAKAQQIISQLKAKGFDPGKY-----VITIIY 200
                                    ************************************8766655.58*********99988888887777.....8***** PP

                                    ETTSHHHHHHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHCTTESEEEEEEECTTSTTHHHHHHHH CS
                      SBP_bac_5 304 asgspaekaiaeliqqqlkkiGikvevktvdwaatylervkdgdfdmillgwgadypdpdnflnpfl 370
                                    + g++a+++ia+l+qq++ ++G+kv+v++++w  +yl+ v+  +++++llgw +dy+dpd++l+pf 
  gi|119720151|ref|YP_920646.1| 201 NEGNTARQQIATLLQQSWSQLGFKVTVESYSW-PKYLDLVDHFQYQVMLLGWIPDYFDPDDYLMPFV 266
                                    ********************************.*******************************995 PP

  == domain 2  score: 42.3 bits;  conditional E-value: 7.8e-15
                                    EEESSEEEEEEEETTTTEEEEEE-TT-B....-TTSS.B-SHHHHHHHHHHHHTGGGHCTTHHHHHC............. CS
                      SBP_bac_5   2 vvpaLAeswwevsdDgktytfkLRkgvk....FsDGt.pltAeDvvfsferlldpdtasgyasllee............. 63 
                                    ++p L  + w  s+D + + f  R +vk    + + t p+tA D  fs+ r+++ + ++g++++++              
  gi|119720151|ref|YP_920646.1| 488 PIPELSVA-WAFSKDMTDLYFVMRGNVKaydpWNNKTyPITAVDALFSIWRAVRLNLPGGPQWMIDSyidvnassvltes 566
                                    67888889.799***************99777777757***************************99************* PP

                                    ...........................TCTEEEEEEEETTEEEEEESSETTT.TTTHCHHHHHHHGC............. CS
                      SBP_bac_5  64 ...........................dqdikkveavddytvrftlkkpnal.fltllaavpasiak............. 102
                                                                 d  +   +   +v+f+l  p+ + + ++++ v + i+              
  gi|119720151|ref|YP_920646.1| 567 eldsiaksqglvtvykgksaevhslkeLLDFFGYSGPTAGVVKFKLRFPYVPiLQIFVTGVGSIIPMqyalgdkyqaala 646
                                    *************************99999999999999**********77536666666666666589999999***** PP

                                    ..............CHTCTCTTTTTGTTTSE-BSSSEEEEEEETTTEEEEEE-TTSTT CS
                      SBP_bac_5 103 ..............kaaekeddkdkdtnekpvgtGPYklkefkpgqkivlernpdYwg 146
                                                  +   ++d+++k   +kpv+tGPY ++++k +++i l+ np+Yw+
  gi|119720151|ref|YP_920646.1| 647 dsnngrnpaawakyVGVGDTDATFKLLSTKPVSTGPYYVADYKEDSYILLKYNPYYWN 704
                                    ***********99999999**************************************3 PP

>> DUF1120  Protein of unknown function (DUF1120)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.1       1.9   1.1e+04      27      43 ..     208     224 ..     205     226 .. 0.85
   2 ?   13.9   0.1   7.7e-06     0.046      12      57 ..     320     368 ..     309     405 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.9
                        DUF1120  27 ksvsaLsptklnqlGtk 43 
                                    +++++L  ++  qlG k
  gi|119720151|ref|YP_920646.1| 208 QQIATLLQQSWSQLGFK 224
                                    57899999*******87 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 7.7e-06
                        DUF1120  12 CtPvlsgGGvvdyGtksvsaLsptklnqlGt...kditltitCeaatki 57 
                                      P+++ G vvd+ t + +  +p +++ lGt   kd++l+  C+aa +i
  gi|119720151|ref|YP_920646.1| 320 NKPIITVGYVVDWDTTKSNWAEPVNMVTLGTgglKDVALSALCKAAQRI 368
                                    57***************************87666***********9886 PP

>> DUF4065  Protein of unknown function (DUF4065)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.5e-05      0.15       5      51 ..     383     433 ..     382     447 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.5e-05
                        DUF4065   5 lYfadflhlkrtgkpitglkyiawkyGPVvp....evydeikelgskpiee 51 
                                    +Yf  +  +   g++itg++y  w +G ++p    + yd ++e  ++p  +
  gi|119720151|ref|YP_920646.1| 383 IYFNKQATMLILGQQITGENYGSWVHGMYYPlatfARYDLVWEDPNAPVVD 433
                                    788889999999********************9999999999998888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (716 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.47
# Mc/sec: 4533.85
//
Query:       gi|119720152|ref|YP_920647.1|  [L=352]
Description: binding-protein-dependent transport systems inner membrane component [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      1e-38  132.9  19.9      1e-38  132.9  19.9    1.7  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.14   2.5e+03     112     131 ..      13      32 ..       7      48 .. 0.58
   2 !  132.9  19.9   5.8e-43     1e-38       1     185 []     115     352 .]     115     352 .] 0.99

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.14
                   BPD_transp_1 112 tglilafggllggavllefl 131
                                    t+l+ ++g+ll  +++++ +
  gi|119720152|ref|YP_920647.1|  13 TFLPSVLGALLITYLIAYVI 32 
                                    44444444444444444443 PP

  == domain 2  score: 132.9 bits;  conditional E-value: 5.8e-43
                   BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf..................................... 43 
                                    gi+lGilaa ++ +++d ++r++  +++s+P fvl  +l+l+f                                     
  gi|119720152|ref|YP_920647.1| 115 GIPLGILAAAKKDSFVDFFVRVFALFGSSMPAFVLYYFLILAFyvyvrasllagvpslspacaasldsvrnavpllgyvv 194
                                    89****************************************************************************** PP

                   BPD_transp_1  44 ..................vilsilghlilpviillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPn 105
                                                      v++  +  ++lp+++l+lls ++++r++r++ l++l++d + +ara+G++  + +++++l+n
  gi|119720152|ref|YP_920647.1| 195 wavgqvpmfgglmcgdlgVVSATFVRMWLPGLALGLLSGGFIARIVRNSLLDALSSDAILFARARGLTSGR-IWRHALKN 273
                                    *****************99999999**********************************************.******** PP

                   BPD_transp_1 106 alppiitglilafggllggavlleflgswpGlgtllleailgydyseisnggvlalviavlllnlvadilqrlldprvrk 185
                                    a+ pi+t l+l+f+gll+gav++e++++ pG+g+ + + i   +++ i+ +g++++ ++++++nl++d++++l+dprvr+
  gi|119720152|ref|YP_920647.1| 274 AFAPIVTILGLNFAGLLTGAVIAETVFNIPGMGLYMYQGITRLNFPIII-AGTFIFSVIYIVMNLLVDLVYALIDPRVRY 352
                                    ***********************************************99.****************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 2274.48
//
Query:       gi|119720153|ref|YP_920648.1|  [L=371]
Description: binding-protein-dependent transport systems inner membrane component [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.4e-28   97.5  10.8    7.4e-28   97.5  10.8    1.9  2  BPD_transp_1  Binding-protein-dependent transport system inne
     0.0001   22.2   0.1     0.0001   22.2   0.1    2.9  3  OppC_N        N-terminal TM domain of oligopeptide transport 
  ------ inclusion threshold ------
       0.52    9.0   1.2        1.8    7.2   1.2    1.9  1  DUF2207       Predicted membrane protein (DUF2207)
        1.1    9.4  19.6       0.55   10.4   0.2    3.4  3  DUF5518       Family of unknown function (DUF5518)


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.3      0.69   3.1e+03      46      65 ..      49      69 ..      39      74 .. 0.53
   2 !   97.5  10.8   1.7e-31   7.4e-28       1     185 []     143     359 ..     143     359 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.69
                   BPD_transp_1 46 lsilghlilp.viillllsaa 65
                                   +s++g + l+ v ++l+l ++
  gi|119720153|ref|YP_920648.1| 49 SSKIGLTGLAlVTVTLFLAIF 69
                                   456666666633333333333 PP

  == domain 2  score: 97.5 bits;  conditional E-value: 1.7e-31
                   BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf..........................vilsilg.hli 53 
                                    g++lG++++ ++++ +d++++++++++l++P ++lai + l +                             ++      
  gi|119720153|ref|YP_920648.1| 143 GVVLGLVSG-YFGGAVDEAIMRFTDMMLAFPGLILAIAFSLTLrlslrdfmmsnpaftglvasmfaldpR--DAPNlANL 219
                                    89*******.************************99999988899*********************9651..34441333 PP

                   BPD_transp_1  54 lp.viillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflg 132
                                    l+  ++l+l+ ++py+r++r ++l + +++++eaaralG+s++++++++vlPn+++p++  + + f+ +   +++l+flg
  gi|119720153|ref|YP_920648.1| 220 LSvFLALILVWWPPYARVVRGSVLTVKEQGFIEAARALGLSTRKVLFRHVLPNIMSPLLVMVTFDFATATLSSAALSFLG 299
                                    44479999************************************************************************ PP

                   BPD_transp_1 133 swpG.....lgtllleailgydyseis..nggvlalviavlllnlvadilqrlldprvrk 185
                                     +p      lg+ + +a + ++  ++   + +  al+++ l  nlv d+l +++dp++r+
  gi|119720153|ref|YP_920648.1| 300 LGPQppvpdLGLIISQAGQFFPERSWWivVEAGTALLLISLGWNLVGDALRDVFDPKTRR 359
                                    7776777777766666666666665559999999***********************985 PP

>> OppC_N  N-terminal TM domain of oligopeptide transport permease C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.1   2.2e-08    0.0001       7      42 ..      44      85 ..      40      97 .. 0.81
   2 ?   -1.7   1.2      0.65   2.9e+03      17      31 ..     126     140 ..     123     153 .. 0.70
   3 ?   -3.0   0.2       1.6   7.4e+03      23      33 ..     223     228 ..     219     236 .. 0.44

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 2.2e-08
                         OppC_N  7 wrrFkrNklAvvglvilllllliaifaPlia..Pydp....q 42
                                   ++ F + k+ + gl+++ + l++aif+P+ia  Pyd     +
  gi|119720153|ref|YP_920648.1| 44 LYVFSSSKIGLTGLALVTVTLFLAIFGPFIAwePYDVypvlS 85
                                   67899**************************88887555443 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.65
                         OppC_N  17 vvglvilllllliai 31 
                                     ++lv+ +++++ ++
  gi|119720153|ref|YP_920648.1| 126 RISLVMSVIIVVTSA 140
                                    578888888887653 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 1.6
                         OppC_N  23 lllllliaifa 33 
                                    +     +a++ 
  gi|119720153|ref|YP_920648.1| 223 F-----LALIL 228
                                    2.....22222 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   1.2   0.00041       1.8     351     409 ..      12     146 ..       5     261 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00041
                        DUF2207 351 kkfkkalkkwksavkk.....kergyfdkkgkkklkklsalglgliilglilillallllvll................. 408
                                    +++ +a++++++ +       +++++ ++k + + +++s +gl ++ l+++ ++la+++ +++                 
  gi|119720153|ref|YP_920648.1|  12 SRLIDAYARLRDRLSPgwlekNKSKLVETKLSLYVFSSSKIGLTGLALVTVTLFLAIFGPFIAwepydvypvlsnpdlag 91 
                                    56666677777766666666566677777766666666666666666666666655555554499999999999999999 PP

                        DUF2207 409 ......................................................l 409
                                                                                          l
  gi|119720153|ref|YP_920648.1|  92 klphppclgnceglppagtdqygrdvlslvirgfrislvmsviivvtsavlgvvL 146
                                    9999999999999999999999999999998876665444222222222222220 PP

>> DUF5518  Family of unknown function (DUF5518)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.7      0.32   1.4e+03      84     101 ..      56      67 ..      38      75 .. 0.43
   2 ?    6.5   7.0     0.002       8.9      83     117 ..     123     156 ..     114     157 .. 0.77
   3 ?   10.4   0.2   0.00012      0.55       4      73 ..     170     238 ..     167     267 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.32
                        DUF5518  84 gfvallvalllvvllllv 101
                                    g++++ v+l+l      +
  gi|119720153|ref|YP_920648.1|  56 GLALVTVTLFL------A 67 
                                    11111111111......1 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.002
                        DUF5518  83 agfvallvalllvvllllvvllvilgaiGGaiGgl 117
                                     gf ++lv+++++ ++ ++vl+v+lg++ G++Gg+
  gi|119720153|ref|YP_920648.1| 123 RGFRISLVMSVII-VVTSAVLGVVLGLVSGYFGGA 156
                                    5666666666666.899999999999999999986 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00012
                        DUF5518   4 aliGavvaivlslllglllpsvgsllgllvgGlvaGylaggdskdgavaGalaGligaipvlvlllvlll 73 
                                    a+ G ++ai++sl l+ l+    ++  + ++Glva  +a + +++  +a +l+ +++ i v +   + ++
  gi|119720153|ref|YP_920648.1| 170 AFPGLILAIAFSLTLR-LSLRDFMMSNPAFTGLVASMFALDPRDAPNLANLLSVFLALILVWWPPYARVV 238
                                    789*************.99999999999***********9999999999998888888888887666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       660  (0.0368119); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2490.51
//
Query:       gi|119720154|ref|YP_920649.1|  [L=332]
Description: oligopeptide/dipeptide ABC transporter, ATPase subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-26   93.3   0.0    2.4e-26   92.9   0.0    1.2  1  ABC_tran      ABC transporter
    2.1e-20   73.0   0.1    3.7e-20   72.2   0.1    1.4  1  oligo_HPY     Oligopeptide/dipeptide transporter, C-terminal 
    2.1e-08   34.3   0.2    0.00013   21.9   0.0    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
     0.0031   17.8   0.9      0.081   13.2   0.9    2.1  1  AAA_22        AAA domain
     0.0041   16.6   0.0        1.5    8.2   0.0    2.2  2  SMC_N         RecF/RecN/SMC N terminal domain
     0.0067   16.1   0.0      0.012   15.3   0.0    1.3  1  AAA_29        P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.017   15.2   0.0      0.036   14.2   0.0    1.5  1  DUF87         Helicase HerA, central domain
      0.019   14.7   0.1        0.5   10.1   0.0    2.2  2  IstB_IS21     IstB-like ATP binding protein
      0.035   14.5   0.2      0.095   13.1   0.2    1.8  1  AAA_16        AAA ATPase domain
       0.12   12.0   0.1        2.6    7.6   0.1    2.3  2  AAA_25        AAA domain
       0.13   12.3   0.0        0.2   11.7   0.0    1.3  1  TsaE          Threonylcarbamoyl adenosine biosynthesis protei
       0.17   11.4   0.0       0.28   10.7   0.0    1.3  1  AAA_7         P-loop containing dynein motor region
       0.17   11.2   0.0        1.1    8.6   0.0    1.9  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
       0.21   10.4   0.1       0.58    8.9   0.1    1.7  1  ABC_ATPase    Predicted ATPase of the ABC class
       0.32   10.7   0.0        9.1    5.9   0.0    2.0  2  AAA_15        AAA ATPase domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.9   0.0     2e-29   2.4e-26       4     136 ..      32     192 ..      29     193 .. 0.86

  Alignments for each domain:
  == domain 1  score: 92.9 bits;  conditional E-value: 2e-29
                                    EEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--....SEEEEEETTCEGGG.........B-HHHCCHCEEEE-SS..- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxx..x RF
                       ABC_tran   4 vslklkegekvaivGenGaGKStLlkllagllkp....teGeilldgkdlke.........qeleslrkeigvlpqe..p 68 
                                      l+++ege va+vGe+G+GKS + k+l+gl +p    ++G++l++ +d +          + +e+   ei++++q+  +
  gi|119720154|ref|YP_920649.1|  32 AYLDVYEGESVALVGETGSGKSVFTKALTGLIDPpgriESGSVLFRRRDGRVvdllklspeEVREIRGDEISYVFQDpsS 111
                                    5689******************************999999999888777666677889998999999**********999 PP

                                    -S-TTSBHHHH..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEES CS
                                    xxxxxxxxxxx..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  69 qlfpeltvren..............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDE 134
                                     l+p +t++++              ++ +e+  +l+ + +++ ++ +vk+ p++LSgG++qrv++a a+++kp+ll++DE
  gi|119720154|ref|YP_920649.1| 112 ALDPLYTAGDHiaetitehrgvpkgDALREAVSLLRDVMIPN-PEVRVKNYPHELSGGMRQRVVIATAIANKPRLLIADE 190
                                    9*********9**99999888855545555555666666665.667778888**************************** PP

                                    TT CS
                                    xx RF
                       ABC_tran 135 pt 136
                                    pt
  gi|119720154|ref|YP_920649.1| 191 PT 192
                                    *9 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.2   0.1   3.1e-23   3.7e-20       2      65 .]     245     308 ..     244     308 .. 0.98

  Alignments for each domain:
  == domain 1  score: 72.2 bits;  conditional E-value: 3.1e-23
                      oligo_HPY   2 ErgpssklfdeplHPYTkaLlrsvprldrekdklekikgeapslerldeGCpFapRCpfaleeC 65 
                                    E++++ ++f++p+HPYT++Llrsvp + ++ ++le+i+g++p+l +++ GCpFapRCpfa+e C
  gi|119720154|ref|YP_920649.1| 245 ETADVYTVFESPAHPYTQLLLRSVPNPLKKIERLESIPGTVPNLIDMKPGCPFAPRCPFAMEVC 308
                                    8999**********************************************************99 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.1    0.0003      0.36       3      25 ..      43      65 ..      41     111 .. 0.73
   2 !   21.9   0.0   1.1e-07   0.00013     233     302 ..     161     228 ..     126     229 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0003
                         AAA_21  3 vliGpNgsGKSnLLdaldllarl 25
                                   +l+G  gsGKS + +al +l + 
  gi|119720154|ref|YP_920649.1| 43 ALVGETGSGKSVFTKALTGLIDP 65
                                   89***************999763 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 1.1e-07
                         AAA_21 233 parelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSplll 302
                                     ++elS G+++   ++ta++  +k+ +ll+ DEp ++L+  +++ +l+llk+l++  g  ++l TH+  ++
  gi|119720154|ref|YP_920649.1| 161 YPHELSGGMRQRVVIATAIA--NKP-RLLIADEPTTNLDVTVQAQILDLLKDLRSkYGMSLLLITHNLGVV 228
                                    57899****99855555555..554.************************999999***********8876 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.9   6.8e-05     0.081       6     128 ..      40     221 ..      36     227 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.8e-05
                         AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaee.......erpevvfvtlpsstsskdllrellralglelka........ 70 
                                     +++++Ge+G+GK++  + l+   d    +e        ++ +vv     s+++ ++++ +  + + ++ ++        
  gi|119720154|ref|YP_920649.1|  40 ESVALVGETGSGKSVFTKALTGLIDPPGRIESgsvlfrrRDGRVVDLLKLSPEEVREIRGDEISYVFQDPSSaldplyta 119
                                    5789****************999876555555888887644444422223333355553333222222222225555555 PP

                         AAA_22  71 .........................................erlsseell.ealeqalrarav.ielliiDEaqh.lr.. 104
                                                                             ++++++  + +++  a   +   ++lli DE    l+  
  gi|119720154|ref|YP_920649.1| 120 gdhiaetitehrgvpkgdalreavsllrdvmipnpevrvknYPHELSGGMrQRVVIATAIA-NkPRLLIADEPTTnLDvt 198
                                    5555555555555666667888888888888777666655544444444413333333333.257888888877778775 PP

                         AAA_22 105 .seealeeLrsllnlsrkgvqliLv 128
                                     ++++l  L++l    ++g++l+L+
  gi|119720154|ref|YP_920649.1| 199 vQAQILDLLKDLRS--KYGMSLLLI 221
                                    55777777788877..888888777 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.0    0.0043       5.2      26      44 ..      41      59 ..      30      63 .. 0.86
   2 !    8.2   0.0    0.0013       1.5     136     212 ..     164     239 ..      87     245 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0043
                                   EEEEEESTTSSHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxx RF
                          SMC_N 26 ftaivGpNGSGKsnlldAi 44
                                     a+vG+ GSGKs ++ A+
  gi|119720154|ref|YP_920649.1| 41 SVALVGETGSGKSVFTKAL 59
                                   5789**********99998 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0013
                                    CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC-.SCEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxx.xxxxxxx RF
                          SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQfivislreemleka.dklvgvt 212
                                    +LSgG ++ v +a    +  +++  l + De   +LD +  +++ +llk  +++  + ++ i+++ +++++  d+++ ++
  gi|119720154|ref|YP_920649.1| 164 ELSGGMRQRVVIA----TAIANKPRLLIADEPTTNLDVTVQAQILDLLKDLRSKygMSLLLITHNLGVVAETaDRVYVMY 239
                                    7888887765555....444455668999********************877775689999***9988765537666554 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0     1e-05     0.012      21      51 ..      38      68 ..      26      71 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1e-05
                         AAA_29 21 lkg.atlltGpsGsGKSTllDAiqalLvpakk 51
                                   + g ++ l+G++GsGKS +  A++ l+ p+ +
  gi|119720154|ref|YP_920649.1| 38 E-GeSVALVGETGSGKSVFTKALTGLIDPPGR 68
                                   3.34899*****************99999875 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0     3e-05     0.036      13      43 ..      31      59 ..      22      66 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3e-05
                          DUF87 13 pvyldlnklvtrHlAilgsTGsGKSntvavL 43
                                   ++yld+ +   +++A +g+TGsGKS +++ L
  gi|119720154|ref|YP_920649.1| 31 DAYLDVYE--GESVALVGETGSGKSVFTKAL 59
                                   57888844..499**************9988 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00042       0.5      46      68 ..      38      60 ..      12      89 .. 0.89
   2 ?    2.4   0.0     0.093   1.1e+02     106     151 ..     180     227 ..     165     232 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00042
                      IstB_IS21 46 kkenivllGpsGvGKshlaialg 68
                                   + e+++l+G +G GKs ++ al 
  gi|119720154|ref|YP_920649.1| 38 EGESVALVGETGSGKSVFTKALT 60
                                   6799****************995 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.093
                      IstB_IS21 106 llkvdllilDdlgl..lpldqaeaellfeviekryerrsiiitsnlpf 151
                                      k++lli D+  +      qa+  +l++ + ++y+ + ++it nl +
  gi|119720154|ref|YP_920649.1| 180 ANKPRLLIADEPTTnlDVTVQAQILDLLKDLRSKYGMSLLLITHNLGV 227
                                    56889*****965410334466667778888899*99999***99865 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.2   7.9e-05     0.095      10      51 ..      27      66 ..      23     221 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.9e-05
                         AAA_16 10 eqLlsalervrsgrpelvllsGesGvGKsslvrellralekd 51
                                   +++++a+ +v +g  e+v l+Ge G+GKs   ++l   +   
  gi|119720154|ref|YP_920649.1| 27 HAVTDAYLDVYEG--ESVALVGETGSGKSVFTKALTGLIDPP 66
                                   6677777778777..89*************999998666655 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.1    0.0022       2.6      32      51 ..      38      57 ..      28      63 .. 0.88
   2 ?    1.7   0.0      0.14   1.6e+02     165     188 ..     199     223 ..     181     224 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0022
                         AAA_25 32 agelallaGapgtGKttlal 51
                                   +ge ++l+G +g+GK++++ 
  gi|119720154|ref|YP_920649.1| 38 EGESVALVGETGSGKSVFTK 57
                                   799**************985 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.14
                         AAA_25 165 v.galvealeriarrtgaavllvhH 188
                                    v +++++ l++++ ++g  +ll+ H
  gi|119720154|ref|YP_920649.1| 199 VqAQILDLLKDLRSKYGMSLLLITH 223
                                    46899999****************9 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00017       0.2      19      44 ..      39      64 ..      21     102 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00017
                                   TEEEEEEESTTSSHHHHHHHHHHHTT CS
                           TsaE 19 gdvilLeGdLGaGKTtlvrglakalg 44
                                   g+ ++L G+ G+GK++++++l   ++
  gi|119720154|ref|YP_920649.1| 39 GESVALVGETGSGKSVFTKALTGLID 64
                                   667****************9976655 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00023      0.28      32      54 ..      38      60 ..      28      75 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00023
                          AAA_7 32 nkkpvllvGptGtGKtviikdll 54
                                   ++ +v lvG+tG+GK+v +k l+
  gi|119720154|ref|YP_920649.1| 38 EGESVALVGETGSGKSVFTKALT 60
                                   67899*************99876 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0    0.0009       1.1      24      49 ..      41      66 ..      24      74 .. 0.86
   2 ?   -0.1   0.0      0.43   5.1e+02     177     200 ..     157     180 ..     150     185 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0009
                   Mg_chelatase 24 nlllvGppGsGKtmlakrlpsllppl 49
                                   ++ lvG  GsGK++  k+l++l+ p 
  gi|119720154|ref|YP_920649.1| 41 SVALVGETGSGKSVFTKALTGLIDPP 66
                                   7889*****************98765 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.43
                   Mg_chelatase 177 eierYlsklsgplldRidlqvevk 200
                                    ++++Y + lsg +  R+ +  ++ 
  gi|119720154|ref|YP_920649.1| 157 RVKNYPHELSGGMRQRVVIATAIA 180
                                    6899*************9988875 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.1   0.00049      0.58     375     412 ..     202     239 ..     159     261 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00049
                                    -HHHCHHHHHHHH--EEEEEESS-GCCTTT-SEEEEEE CS
                     ABC_ATPase 375 plvdrvrelykklgvstilvvggsgdyldvAdtvilme 412
                                     ++d++++l++k+g+s++l++  +g   + Ad+v +m 
  gi|119720154|ref|YP_920649.1| 202 QILDLLKDLRSKYGMSLLLITHNLGVVAETADRVYVMY 239
                                    36899*****************************9996 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0    0.0076       9.1      26      48 ..      42      64 ..      29     106 .. 0.83
   2 ?    3.0   0.0     0.056        67     301     366 ..     169     225 ..     132     228 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0076
                         AAA_15 26 tvliGkNnsGKSsilealdlFln 48
                                     l+G+ +sGKS +++al  +++
  gi|119720154|ref|YP_920649.1| 42 VALVGETGSGKSVFTKALTGLID 64
                                   689**************976665 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.056
                         AAA_15 301 vqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSp 366
                                    +++ +++++ i+         +k+ +l+ +EP ++L    q ++ +llk+l ++  + +++ TH+ 
  gi|119720154|ref|YP_920649.1| 169 MRQRVVIATAIA---------NKPRLLIADEPTTNLDVTVQAQILDLLKDLRSKYGMSLLLITHNL 225
                                    555555555444.........456669************************999999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2224.84
//
Query:       gi|119720155|ref|YP_920650.1|  [L=320]
Description: oligopeptide/dipeptide ABC transporter, ATPase subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.2e-33  114.8   0.0    5.7e-33  114.3   0.0    1.2  1  ABC_tran      ABC transporter
    6.4e-21   74.6   0.5    1.1e-20   73.9   0.5    1.4  1  oligo_HPY     Oligopeptide/dipeptide transporter, C-terminal 
    1.2e-08   35.2   1.4    5.8e-07   29.6   0.3    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    2.5e-05   23.8   0.4    0.00015   21.3   0.4    2.1  1  SMC_N         RecF/RecN/SMC N terminal domain
    0.00071   19.9   0.1      0.002   18.4   0.1    1.7  1  AAA_22        AAA domain
     0.0085   15.8   0.0      0.015   15.0   0.0    1.3  1  AAA_29        P-loop containing region of AAA domain
       0.01   16.3   0.2      0.014   15.7   0.2    1.4  1  AAA_16        AAA ATPase domain
  ------ inclusion threshold ------
      0.036   14.5   0.0       0.38   11.2   0.0    2.0  2  AAA           ATPase family associated with various cellular 
      0.041   14.1   0.0       0.89    9.8   0.0    2.2  1  SbcCD_C       Putative exonuclease SbcCD, C subunit
      0.048   13.5   0.1      0.076   12.9   0.1    1.2  1  RsgA_GTPase   RsgA GTPase
       0.19   11.1   0.0       0.44    9.9   0.0    1.6  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
       0.19   11.4   0.0        0.3   10.8   0.0    1.4  1  IstB_IS21     IstB-like ATP binding protein
       0.21   11.6   0.1       0.49   10.4   0.1    1.7  1  AAA_5         AAA domain (dynein-related subfamily)
       0.28    9.8   0.5       0.44    9.1   0.1    1.4  2  AAA_13        AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.3   0.0   4.4e-36   5.7e-33       2     137 .]      28     178 ..      27     178 .. 0.91

  Alignments for each domain:
  == domain 1  score: 114.3 bits;  conditional E-value: 4.4e-36
                                    EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG...B-HHHCCHCEEEE-SS..--S-TTSBH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxx..xxxxxxxxx RF
                       ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke...qeleslrkeigvlpqe..pqlfpeltv 76 
                                    + vs++++ege++++vGe+G+GKStL +++++ll+pt G++ ++g+d+     ++l+++r++ ++++q+  ++l+p++t+
  gi|119720155|ref|YP_920650.1|  28 DGVSFEIREGETLGLVGESGCGKSTLGRVVIRLLEPTGGKVFFKGQDVAAlkgEKLKQFRRQAQIVFQDpnTSLNPRMTI 107
                                    78**********************************************99999****************9999******* PP

                                    HHH..........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    xxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  77 ren..........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                     e             d+  + + ++l+ ++l  +++++ p++LSgGqkqrva+ rall +p++++lDEpt+
  gi|119720155|ref|YP_920650.1| 108 LEIlseplyehniPVDDPEDFITKQLESVGLGREHLYRYPHELSGGQKQRVAILRALLLNPSFVVLDEPTS 178
                                    ***9*9999888744444555556666666777999999******************************96 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.9   0.5   8.5e-24   1.1e-20       1      65 []     229     296 ..     229     296 .. 0.97

  Alignments for each domain:
  == domain 1  score: 73.9 bits;  conditional E-value: 8.5e-24
                      oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekd...klekikgeapslerldeGCpFapRCpfaleeC 65 
                                    vE gps+++f++plHPYTk Ll++vp +d++     k   i+ge+ps+ + + GC+F+pRCp+a+e+C
  gi|119720155|ref|YP_920650.1| 229 VELGPSDAVFENPLHPYTKFLLSAVPVPDPKYArarKRLAIPGEPPSPINVPPGCRFHPRCPYATEKC 296
                                    8*****************************9998888889**************************** PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.022        28       3      19 ..      41      57 ..      40      74 .. 0.81
   2 !   29.6   0.3   4.5e-10   5.8e-07     179     300 ..     102     211 ..      78     214 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.022
                         AAA_21  3 vliGpNgsGKSnLLdal 19
                                   +l+G  g+GKS+L +  
  gi|119720155|ref|YP_920650.1| 41 GLVGESGCGKSTLGRVV 57
                                   69***********8876 PP

  == domain 2  score: 29.6 bits;  conditional E-value: 4.5e-10
                         AAA_21 179 akekrllqrlvrslklveielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkkg 258
                                    +++ ++l+ l+ +l + +i+++d ++++ ++ ++  + re             + ++elS G+k+  a+l all  +   
  gi|119720155|ref|YP_920650.1| 102 NPRMTILEILSEPLYEHNIPVDDPEDFITKQLESVGLGRE----------HLYRYPHELSGGQKQRVAILRALLLNP--- 168
                                    5666677777777777777777777777777777777666..........556778999*******99999999999... PP

                         AAA_21 259 sllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSpl 300
                                    s++++DEp ++L+ ++++ +l +lk+ ++ ++   ++ +H+  
  gi|119720155|ref|YP_920650.1| 169 SFVVLDEPTSSLDVSVQAQILNMLKDFQAqRKLSYLFISHDIG 211
                                    ************************9999988899999999965 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.4   1.1e-07   0.00015      29     212 ..      42     223 ..       5     229 .. 0.67

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.1e-07
                                    EEESTTSSHHHHHHHHHHHCTT.TTTT.TTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEEETT. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                          SMC_N  29 ivGpNGSGKsnlldAilFvLGersakk.lrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrrvkrk. 106
                                    +vG+ G+GKs l   +  +L  +  k  ++ +++ +l  + k k++  +a  +i+f++++ +    +++++i   +++  
  gi|119720155|ref|YP_920650.1|  42 LVGESGCGKSTLGRVVIRLLEPTGGKVfFKGQDVAALKGE-KLKQFRRQA--QIVFQDPNTS---LNPRMTILEILSEPl 115
                                    6777777777777777777765555431444455444433.444444444..4566676666...333333333222220 PP

                                    SEEEEEETTEEE-HHHHHHHHHCTT-STT.......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 107 geseykingkevtkkevsellesagiske.......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkv 179
                                     e ++ +++    +  ++++les+g+ +e       +LSgG+k+ va+  l A+   +  ++++lDe  + LD +  +++
  gi|119720155|ref|YP_920650.1| 116 YEHNIPVDD---PEDFITKQLESVGLGREhlyryphELSGGQKQRVAI--LRALL-LN-PSFVVLDEPTSSLDVSVQAQI 188
                                    112222222...2344666777777776677777779******97664..44543.34.47******************* PP

                                    HHHHH..HHCTTSEEEEE-SSHHHCCC-SCEEEEE CS
                                    xxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 180 aellk..eksknaQfivislreemlekadklvgvt 212
                                     ++lk  +++ +  ++ is++ ++++ +++ + v+
  gi|119720155|ref|YP_920650.1| 189 LNMLKdfQAQRKLSYLFISHDIGVVKYMSQRIAVM 223
                                    *****6666667999**********9998888776 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   1.5e-06     0.002      10     128 ..      42     206 ..      34     216 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.5e-06
                         AAA_22  10 vtGesGtGKTtllrrlleqldeeakaee...................erpevvfvtlpsstsskdllrellralglelka 70 
                                    ++GesG+GK+tl r + + l+    ++                    + ++++ +  + +++s + +  +l++l ++l +
  gi|119720155|ref|YP_920650.1|  42 LVGESGCGKSTLGRVVIRLLE----PTGgkvffkgqdvaalkgeklkQFRRQAQIVFQDPNTSLNPRMTILEILSEPLYE 117
                                    89*****************94....3335688999999999988877555556777777777788888888888888888 PP

                         AAA_22  71 ..................erlsseell.ealeqalrarav...............ielliiDEaqh.lr...seealeeL 112
                                                             l  e+l+++ ++ +                ++++++DE    l+   ++++l+ L
  gi|119720155|ref|YP_920650.1| 118 hnipvddpedfitkqlesV-----GLGrEHLYRYPHELSGgqkqrvailralllnPSFVVLDEPTSsLDvsvQAQILNML 192
                                    9999999999999655553.....333344444444444344447777777788999******9999999655******* PP

                         AAA_22 113 rsllnlsrkgvqliLv 128
                                    ++++   + +++ +++
  gi|119720155|ref|YP_920650.1| 193 KDFQA--QRKLSYLFI 206
                                    *9999..888887776 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.2e-05     0.015      13      49 ..      28      64 ..      25      71 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.2e-05
                         AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDAiqalLvpa 49
                                   dg ++ei++ ++  l+G+sG GKSTl   ++ lL p+
  gi|119720155|ref|YP_920650.1| 28 DGVSFEIREGETLGLVGESGCGKSTLGRVVIRLLEPT 64
                                   77889998666778***********976666666665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.2   1.1e-05     0.014      24      60 ..      37      74 ..      30     206 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.1e-05
                         AAA_16 24 pelvllsGesGvGKsslvrellralekdggif.lrgkc 60
                                   +e + l+GesG+GKs+l r + r le +gg + ++g+ 
  gi|119720155|ref|YP_920650.1| 37 GETLGLVGESGCGKSTLGRVVIRLLEPTGGKVfFKGQD 74
                                   367889****************9999886444244433 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0    0.0003      0.38       3      52 ..      42      96 ..      40     111 .. 0.67
   2 ?    1.2   0.0      0.37   4.7e+02      59     109 ..     168     207 ..     129     221 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0003
                                   EESSTTSSHHHHHHHHHHHH.....THEEEEEETTTCSSSSTTHHHHHHHHHHHH CS
                            AAA  3 lyGppGtGKTllakavakel.....gvefleisgsellskyvgesekkirelfke 52
                                   l+G  G+GK++l + v++ l     +v f   +++ l  + +++  ++ + +f++
  gi|119720155|ref|YP_920650.1| 42 LVGESGCGKSTLGRVVIRLLeptggKVFFKGQDVAALKGEKLKQFRRQAQIVFQD 96
                                   89****************9955544344444444444444444666666666655 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.37
                                    SEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEE CS
                            AAA  59 psilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigat 109
                                    ps +++DE  +    +          v++q+l++l++++ + +k+  + ++
  gi|119720155|ref|YP_920650.1| 168 PSFVVLDEPTSSLDVS----------VQAQILNMLKDFQAQ-RKLSYLFIS 207
                                    5555555555554444..........999999999999985.446555555 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0    0.0007      0.89      63      89 ..     167     193 ..     128     194 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0007
                        SbcCD_C  63 alrlvfLDEAFsklDeesiatllelle 89 
                                    ++++v+LDE  s+lD   +a++l++l+
  gi|119720155|ref|YP_920650.1| 167 NPSFVVLDEPTSSLDVSVQAQILNMLK 193
                                    4789*******************9987 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   5.9e-05     0.076      85     117 ..      22      55 ..       9      68 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.9e-05
                                    TTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHH CS
                    RsgA_GTPase  85 ktkegleelkellkd.ktsvlvGqSGvGKStLin 117
                                    kt ++++ ++ ++++ +t  lvG+SG GKStL  
  gi|119720155|ref|YP_920650.1|  22 KTVKAVDGVSFEIREgETLGLVGESGCGKSTLGR 55 
                                    4567778888888887999************965 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00035      0.44      25      84 ..      40     100 ..      30     107 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00035
                   Mg_chelatase  25 lllvGppGsGKtmlakrlpsllpplseeealevakiasvag.kkeeekllkrrpfraphhs 84 
                                    l lvG +G+GK+ l + +  ll p   +  ++ + +a+++g k ++ +  ++  f++p  s
  gi|119720155|ref|YP_920650.1|  40 LGLVGESGCGKSTLGRVVIRLLEPTGGKVFFKGQDVAALKGeKLKQFRRQAQIVFQDPNTS 100
                                    6699************************999999999999944444555666677777665 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00023       0.3      24      80 ..      13      70 ..       1     108 [. 0.78

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00023
                      IstB_IS21 24 fraarsldkrkvkeLatlsf.iekkenivllGpsGvGKshlaialgveavraglsvlf 80
                                   + + r++  ++vk++ + sf i++ e + l+G sG GKs l   + +    +g +v+f
  gi|119720155|ref|YP_920650.1| 13 YFKVRGSFSKTVKAVDGVSFeIREGETLGLVGESGCGKSTLGRVVIRLLEPTGGKVFF 70
                                   5567788899999******99999***************9987665555556666666 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00038      0.49       4      24 ..      42      65 ..      39      99 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00038
                                   EE--SSSSHHHHHHHGGGGB...S CS
                          AAA_5  4 LvGppGtgKselaerlaaal...n 24
                                   LvG++G+gKs+l + + ++l   +
  gi|119720155|ref|YP_920650.1| 42 LVGESGCGKSTLGRVVIRLLeptG 65
                                   9************99999986653 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       1.8   2.3e+03      23      38 ..      44      59 ..      44      85 .. 0.76
   2 ?    9.1   0.1   0.00034      0.44     527     580 ..     168     219 ..     161     232 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.8
                         AAA_13 23 GwNGaGKTtLSrllrs 38
                                   G  G GK+tL r+   
  gi|119720155|ref|YP_920650.1| 44 GESGCGKSTLGRVVIR 59
                                   66799*****997544 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00034
                         AAA_13 527 dkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleffkevkkn 580
                                       vv+D P SSLD  ++  + +++k+    + k + lfi+ H +   k+++++
  gi|119720155|ref|YP_920650.1| 168 PSFVVLDEPTSSLDVSVQAQILNMLKDFQ-AQRKLSYLFIS-HDIGVVKYMSQR 219
                                    567************************97.799999***97.888888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 2135.37
//
Query:       gi|119720156|ref|YP_920651.1|  [L=608]
Description: nucleotidyl transferase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-13   51.1   0.1    2.7e-12   47.3   0.0    2.4  2  NTP_transf_3     MobA-like NTP transferase domain
    7.5e-12   45.4   0.0    5.7e-10   39.2   0.0    2.2  2  NTP_transferase  Nucleotidyl transferase


Domain annotation for each model (and alignments):
>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.3   0.0   3.1e-16   2.7e-12       1     124 [.       3     131 ..       3     167 .. 0.84
   2 ?    1.1   0.0     0.049   4.4e+02      62      84 ..     177     199 ..     150     222 .. 0.80

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 3.1e-16
                                    EEEEEESS-TTTT...T..THHHHCC.CCCCHHHHHHHHHCTT.-CEEEEECSH...CHHHHHHTTCTS-EEE-TTSS-S CS
                   NTP_transf_3   1 aviLAGGrSsRmg...g..dKallpl.ggkpllervldalraagvdevvvvggd...eevlaalarlgvrvvededpgkg 71 
                                    +vi A+G++sR+    +  +K l++l  g p+++ +l+++ a++ ++vvvv+++   + ++++la+l   v++d + g g
  gi|119720156|ref|YP_920651.1|   3 VVIVAAGEASRLRpysEemPKTLMELrPGLPIIDFILKRVMALSPRKVVVVTRRtwkDILASHLAGLAEVVTVDLEGGFG 82 
                                    69**********7553258*******99***************99*******997744456677877777778888899* PP

                                    HHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESS CS
                   NTP_transf_3  72 plaslaaalraaadadavlvlacDmPlltpelverllaaaaasgadvvvptye 124
                                     l+s+++al ++   d +l+l+ D+++ ++e++ rl+++a  + + +v++ ++
  gi|119720156|ref|YP_920651.1|  83 NLYSVYTALTRV--GDEFLILMSDHIF-EEEVLMRLAEHAS-KASFTVCLDRN 131
                                    **********98..7**********99.**********986.44445555554 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.049
                                    EEE-TTSS-SHHHHHHHHHHHH. CS
                   NTP_transf_3  62 vvededpgkgplaslaaalraaa 84 
                                    ++e+   +kgp+as+a  lr aa
  gi|119720156|ref|YP_920651.1| 177 FIEEVIRQKGPGASIADVLRFAA 199
                                    566666789**********9865 PP

>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   0.0   6.3e-14   5.7e-10       3     142 ..       4     133 ..       2     152 .. 0.86
   2 !    4.1   0.0    0.0034        30     202     246 ..     189     232 ..     164     234 .. 0.84

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 6.3e-14
                                    EEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEEEESS CS
                NTP_transferase   3 vILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlialepe 82 
                                    vI a G+ +RL+P + +++k l+    + ++i++ l+r+++ + ++++vv+ +  + +++++l+  ++      +++  e
  gi|119720156|ref|YP_920651.1|   4 VIVAAGEASRLRPYSEEMPKTLMELRPGLPIIDFILKRVMALSPRKVVVVTRRTWKDILASHLAGLAE-----VVTVDLE 78 
                                    9***************************************************************8874.....3344444 PP

                                    --.BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEES CS
                NTP_transferase  83 gk.gtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpv 142
                                    g  g   +v+ a++ ++de+     l+L +Dh++++++   ++++++ka+  tv++   p 
  gi|119720156|ref|YP_920651.1|  79 GGfGNLYSVYTALTRVGDEF-----LILMSDHIFEEEVLMRLAEHASKAS-FTVCLDRNPS 133
                                    44588899999999999887.....9**********88888888888877.5777666655 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0034
                                    CHHHHHHHHHHHTTEEEEEECSTTEE-EEEXSSHHHHHHHHHHHH CS
                NTP_transferase 202 deitdilpkaleegkvalaflfkdaeyWsDvGtldslleanekla 246
                                     +i+d+l+ a ++g++  +++ ++   W+D+ t+++l++a + ++
  gi|119720156|ref|YP_920651.1| 189 ASIADVLRFAASKGEEVDYVDVTGL-LWKDIDTPEDLVKARKLVE 232
                                    5789999999999999999999997.7************988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (608 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.27s 00:00:00.91 Elapsed: 00:00:00.49
# Mc/sec: 3768.89
//
Query:       gi|119720157|ref|YP_920652.1|  [L=410]
Description: hypothetical protein Tpen_1251 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00015   22.5   0.3    0.00015   22.5   0.3    2.1  2  CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase


Domain annotation for each model (and alignments):
>> CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.3   8.2e-09   0.00015       1      51 [.     214     263 ..     214     276 .. 0.72
   2 ?   -2.3   0.6      0.46   8.2e+03      34      34 ..     354     354 ..     298     383 .. 0.57

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 8.2e-09
                                    S-HHHHHHHHHHHHHHHHHGGGS-H..HHHHHHHHHHHHHTTHHHHHHHHT CS
                CDP-OH_P_transf   1 nlPnaiTllrlllsvlailllltyyplvlailllliasltDalDGklARrl 51 
                                    ++Pn +Tll  ll+++ ++++     l la++   + +++D++DGklAR +
  gi|119720157|ref|YP_920652.1| 214 VTPNRVTLLVDLLAFMVAFFI-LQASLPLALVAAYLVGVLDGVDGKLARVR 263
                                    58******8877777777555.333355666666677888*********87 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.46
                                    H CS
                CDP-OH_P_transf  34 l 34 
                                    l
  gi|119720157|ref|YP_920652.1| 354 L 354
                                    1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2642.93
//
Query:       gi|119720158|ref|YP_920653.1|  [L=147]
Description: DNA polymerase beta subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-12   47.6   0.0    1.6e-12   47.3   0.0    1.1  1  Polbeta       Polymerase beta, Nucleotidyltransferase
    2.1e-05   24.7   0.1    2.8e-05   24.3   0.1    1.2  1  NTP_transf_2  Nucleotidyltransferase domain


Domain annotation for each model (and alignments):
>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.3   0.0   1.8e-16   1.6e-12       2      90 ..      25     113 ..      24     116 .. 0.89

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 1.8e-16
                                    STTTTHHHHHHHHSTTEEEEEE-S------EEEEEEEESS---HHHHHHHHHHHHHH....SSSEEEEEETTTS-HHHHH CS
                        Polbeta   2 kikeilekekeielaylFGSrakgkareeSDiDlavllkekldleeelelaaeledi...klgkkvDlvdlneappllly 78 
                                    k++++le ++e++la++FGS+++g + +  D+Dlav+l ++ dl+e +e+++ l ++   ++g  +D+v+ln a   ll+
  gi|119720158|ref|YP_920653.1|  25 KVRKVLEPREEVALALIFGSFVRGGFAR--DVDLAVYLARSVDLYEAAEYSELLGRVlerETGLPFDVVVLNVAGEGLLA 102
                                    899************************9..***********9999988888888888888999*********999***** PP

                                    HHHHS-EEEES- CS
                        Polbeta  79 eilkegkllysk 90 
                                    ++++  k+l  +
  gi|119720158|ref|YP_920653.1| 103 RAMRGEKVL-VR 113
                                    ****55555.44 PP

>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.1   3.2e-09   2.8e-05       3      76 ..      25      93 ..      23     115 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 3.2e-09
                                   HHHHHHHHHTTTSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEECE CS
                   NTP_transf_2  3 klleelkelepvakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevdlvtr 76
                                   k+++ l+ +e va + +fGS++rG +    D+Dl+v+l ++v+    +e +e+      +le+ +gl+ d+v+ 
  gi|119720158|ref|YP_920653.1| 25 KVRKVLEPREEVALALIFGSFVRGGFA--RDVDLAVYLARSVD---LYEAAEYSELLGRVLERETGLPFDVVVL 93
                                   67888888888**************99..69**********99...688999999999999999******9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1072.98
//
Query:       gi|119720159|ref|YP_920654.1|  [L=142]
Description: hypothetical protein Tpen_1253 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-12   47.4   0.0    1.8e-12   47.1   0.0    1.2  1  DUF86     Protein of unknown function DUF86
  ------ inclusion threshold ------
       0.11   12.8   0.3        0.6   10.5   0.1    2.3  2  PqqD      Coenzyme PQQ synthesis protein D (PqqD)
       0.17   11.6   0.1       0.61    9.9   0.1    1.9  2  DnaB_2    Replication initiation and membrane attachment


Domain annotation for each model (and alignments):
>> DUF86  Protein of unknown function DUF86
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.1   0.0   3.1e-16   1.8e-12      25     118 ..      40     135 ..      12     136 .. 0.90

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 3.1e-16
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHTT----SSC.HHHHHHHTTSS-HHHHHHHHHHHCCHHHHHT-CCCTTHHHHHH CS
                          DUF86  25 leydavernlqvigEaaidiakhlakklgikkpgdy.ifeilaekgviaeepeepwrkmiglRNrLvHgYlgidpeivws 103
                                     +  a+ +++ +++E +  ia +la+  g   +g+  ++++la++g+ ++   e++ ++++lRN LvH+Y+++++e++ +
  gi|119720159|ref|YP_920654.1|  40 ADAFALRYAVIQVVEGLAVIASRLAELRGTVVEGYVeAMSFLARAGIVDPAVGEELVRLARLRNLLVHRYWEVSDEKILE 119
                                    5667899999*************9999999999999******************************************** PP

                                    HHHH.TCHHHHHHHHH CS
                          DUF86 104 iike.nlpdleefles 118
                                     +++  ++ +ee+++s
  gi|119720159|ref|YP_920654.1| 120 EARKsGVKTVEEAVKS 135
                                    9999778999988887 PP

>> PqqD  Coenzyme PQQ synthesis protein D (PqqD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1    0.0001       0.6      22      46 ..      27      50 ..      17      68 .. 0.83
   2 ?   -0.2   0.0      0.21   1.3e+03      55      55 ..     122     122 ..      96     141 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0001
                                   HHHH-SSSS-HHHHHHHHHHHCT-- CS
                           PqqD 22 iWklldgersveeivaalaeeydvd 46
                                   +++l+ + r v+++++a+a +y v 
  gi|119720159|ref|YP_920654.1| 27 VLRLCAE-RGVRDLADAFALRYAVI 50
                                   89***99.99************876 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.21
                                    H CS
                           PqqD  55 l 55 
                                    +
  gi|119720159|ref|YP_920654.1| 122 R 122
                                    1 PP

>> DnaB_2  Replication initiation and membrane attachment
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       0.5     3e+03      55      68 ..      27      40 ..      11      48 .. 0.61
   2 ?    9.9   0.1    0.0001      0.61      53      71 ..     115     133 ..     107     135 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.5
                                   HHHHHHHHT---XX CS
                         DnaB_2 55 ilknWaekgikTve 68
                                   +l+  ae+g++ ++
  gi|119720159|ref|YP_920654.1| 27 VLRLCAERGVRDLA 40
                                   33334455555555 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0001
                                    HHHHHHHHHHT---XXXXX CS
                         DnaB_2  53 ekilknWaekgikTveqae 71 
                                    ekil++  ++g+kTve+a 
  gi|119720159|ref|YP_920654.1| 115 EKILEEARKSGVKTVEEAV 133
                                    89***************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1056.97
//
Query:       gi|119720160|ref|YP_920655.1|  [L=384]
Description: radical SAM domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.7e-18   65.4   0.0    2.3e-17   63.9   0.0    1.8  2  Radical_SAM  Radical SAM superfamily
    6.7e-08   32.9   0.0    1.3e-07   31.9   0.0    1.4  1  Fer4_12      4Fe-4S single cluster domain
     0.0028   17.8   0.0      0.006   16.7   0.0    1.5  1  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.9   0.0   3.9e-21   2.3e-17       2     166 ..     156     325 ..     155     326 .. 0.82
   2 ?   -2.0   0.0      0.67     4e+03     109     144 ..     337     371 ..     327     380 .. 0.71

  Alignments for each domain:
  == domain 1  score: 63.9 bits;  conditional E-value: 3.9e-21
                                    EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS....TTHHHHHHHHHHTCCCT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxx RF
                    Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggeplly....pdfvellerlaklavpg 77 
                                    v++ +Cn++C fC++++    ++ + s+s++  +ee+ e++ +++v  v ++gg+p  +      f+++l+++a+   + 
  gi|119720160|ref|YP_920655.1| 156 VFYGACNHNCAFCQNWF---YRRNAVSRSPRVSVEELLEAALDPRVTCVCFFGGDPAPQvlhaLAFTRELLERARG--RI 230
                                    57889************...7*******************87777**************87776666666666666..7* PP

                                    EEEEEEECSSCHG...HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET.....EEEEE CS
                                    xxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxx RF
                    Radical_SAM  78 iritvetngtlpd...eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikr.....vvdri 149
                                    +r++ e+ng+      ++++e+ l+ g  +v ++l+a+++  + + +  g +   +l++  + +ea  +r      +  +
  gi|119720160|ref|YP_920655.1| 231 MRVCWESNGHFSPkilPRVIEASLRSG-GTVKFDLKAWSPG-IYRAL-TGVEQGSLLDNAGRVAEAAKERpevplFTAST 307
                                    ***********7466666666666666.*************.77777.7789999999999999998888999**77777 PP

                                    EEBTTTSH.HHHHHHHHH CS
                                    xxxxxxxx.xxxxxxxxx RF
                    Radical_SAM 150 vglpGend.eeleellel 166
                                    +++pG+ d ee+++++++
  gi|119720160|ref|YP_920655.1| 308 LLVPGYVDeEEVRAIARF 325
                                    777777762666666666 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.67
                                    EBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSET CS
                                    xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM 109 leaaddekvlklmn.rghtfeevlealeklreagikr 144
                                    l a++++  ++++  ++ ++ +  ea + +re g+ r
  gi|119720160|ref|YP_920655.1| 337 LLAFHPD--HRMLDlPPTSRRHAEEAARVAREEGLLR 371
                                    5566666..4455557777888888888888888775 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.0   2.2e-11   1.3e-07       5      96 ..     150     242 ..     145     255 .. 0.75

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 2.2e-11
                        Fer4_12   5 G.vrlslfvsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpena..eallelvkevke 81 
                                    G v l++f + Cn++C++C n   ++   ++  ++   ee++e + +++++ + ++GG+P  +         el+++ + 
  gi|119720160|ref|YP_920655.1| 150 GyVNLAVFYGACNHNCAFCQNWFYRRNAVSRS-PRVSVEELLEAALDPRVTCVCFFGGDPAPQVLHalAFTRELLERARG 228
                                    556789************99766665555544.5666677777777**************87322223556788888888 PP

                        Fer4_12  82 ekpekdiwlytgytl 96 
                                    + +  ++w+++g   
  gi|119720160|ref|YP_920655.1| 229 RIM-RVCWESNGHFS 242
                                    888.69*****9765 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0     1e-06     0.006       2      92 ..     157     242 ..     155     253 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1e-06
                        Fer4_14   2 fvrlsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkel...lklvkrlkeey 78 
                                    f   + Cn++C +C n   ++ ++   + +  +e+ l+ + + ++    + + GG+P  ++  ++l    +l++r + ++
  gi|119720160|ref|YP_920655.1| 157 FY--GACNHNCAFCQNWF-YRRNAVSRSPRVSVEELLEAALDPRV--TCVCFFGGDPA-PQVLHALaftRELLERARGRI 230
                                    44..89********9655.44444444444444455544446666..679*******8.544444311145555555555 PP

                        Fer4_14  79 pekkiwletngtle 92 
                                      +++  e+ng + 
  gi|119720160|ref|YP_920655.1| 231 --MRVCWESNGHFS 242
                                    ..999999999775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 2436.95
//
Query:       gi|119720161|ref|YP_920656.1|  [L=276]
Description: binding-protein-dependent transport systems inner membrane component [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-14   53.5  18.4    2.5e-14   53.5  18.4    1.8  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.9     0.034   6.2e+02     136     174 ..      36      80 ..       5      86 .. 0.49
   2 !   53.5  18.4   1.4e-18   2.5e-14       2     183 ..      79     268 ..      78     270 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.034
                   BPD_transp_1 136 Glgtllleailgydyseis......nggvlalviavlllnlvadi 174
                                    ++gt++l++ ++ d+ +          +++ ++++vl+  ++a +
  gi|119720161|ref|YP_920656.1|  36 AMGTPVLQPPSQPDFGNVVaalekfSSTIALTGLIVLPAAFAATL 80 
                                    366666666666666655566556544455555555555555544 PP

  == domain 2  score: 53.5 bits;  conditional E-value: 1.4e-18
                   BPD_transp_1   2 illGilaa...lnrnkkldkllrpliivllslPsfvlaillvlvf.....vilsilghlilpviillllsaapyvrlirr 73 
                                    +llG+l+a   + +++k+ ++l ++i ++ ++P+ +++++lv v+     +    l+++  +++++ll++++p+++l++ 
  gi|119720161|ref|YP_920656.1|  79 TLLGSLSAfaiRLYGGKVADWLPVVIALTTYIPYQAIIVPLVSVIrqvevATGIPLYDTSQGLFLVLLVYYTPMATLLMF 158
                                    6899999999**************************************98555568899999****************** PP

                   BPD_transp_1  74 aalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydysei 153
                                     + +++p++ +ea++++Ga+  +i+++v+lP++ p ++++li+ +++++++ ++++ ++   G   +++  i +y  +++
  gi|119720161|ref|YP_920656.1| 159 IFSNAMPREPIEASLVDGAGLPTIYWRVALPLLGPGFVSTLIFLLINMWNNLFIPLSMT--RGYEKFVTLKIFSYVGQAG 236
                                    ***********************************************************..6688888888888888888 PP

                   BPD_transp_1 154 s..nggvlalviavlllnlvadilqrlldprv 183
                                    +  n +++a++i  l+ ++v+ ++ +++ + +
  gi|119720161|ref|YP_920656.1| 237 TiyNEMFAAALIGSLPPLVVFLFMSKYFIRGM 268
                                    8999***********************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      193  (0.0107647); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1901.01
//
Query:       gi|119720162|ref|YP_920657.1|  [L=291]
Description: binding-protein-dependent transport systems inner membrane component [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.4e-13   50.2  20.7    2.4e-13   50.2  20.7    1.9  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.9     0.092   1.6e+03      37      58 ..      17      38 ..      11      60 .. 0.63
   2 !   50.2  20.7   1.3e-17   2.4e-13       1     172 [.      82     273 ..      82     283 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.092
                   BPD_transp_1 37 illvlvfvilsilghlilpvii 58
                                   +llv+v+vi  ++g+ ++  ++
  gi|119720162|ref|YP_920657.1| 17 PLLVFVAVIYYGVGWNFWLSLT 38
                                   3333333444666666665544 PP

  == domain 2  score: 50.2 bits;  conditional E-value: 1.3e-17
                   BPD_transp_1   1 gillGilaa....lnrnkkldkllrpliivllslPsfvlaillvlvf.................vilsilghlilpviil 59 
                                    g++lG+++a      r++kl+ +l+ ++i ++++P ++ ++++ ++f                 v + +  +++++++++
  gi|119720162|ref|YP_920657.1|  82 GNVLGLVIAssifQLRSSKLRSVLTSYFIYPMAVPLVASGVIWRWLFdsvkgfnavlaplgfprVEWLSGNNAFWSLVLV 161
                                    789999999999999*****************************999***************99555566679999**** PP

                   BPD_transp_1  60 lllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgt 139
                                    +l+ + ++v l++ aa++++p + +eaa+++Ga   ++++k+v+P+++  +i g++++  ++l  + l++ ++  +++++
  gi|119720162|ref|YP_920657.1| 162 SLWVYSGFVALMYLAAFYNVPASAIEAALVDGADMLTVMVKIVIPASKLGLILGVVFSTLFALQMFDLPYSVLYINPFTS 241
                                    *************************************************************************6666444 PP

                   BPD_transp_1 140 llleailgydyseis...nggvlalviavlllnlva 172
                                    +l+    +y y+  +   + +++a+ i++++l++++
  gi|119720162|ref|YP_920657.1| 242 TLV----MYLYNKFAymvFNLSAAACIFLIALSASI 273
                                    443....33333222322345555555555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 2050.80
//
Query:       gi|119720163|ref|YP_920658.1|  [L=467]
Description: extracellular solute-binding protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.8e-19   70.9   1.2    2.5e-19   70.4   1.2    1.2  1  SBP_bac_1   Bacterial extracellular solute-binding protein
    5.1e-13   49.5   0.5    7.5e-13   48.9   0.4    1.3  1  SBP_bac_8   Bacterial extracellular solute-binding protein
  ------ inclusion threshold ------
      0.089   12.5   0.1        8.6    6.0   0.0    2.5  2  SBP_bac_11  Bacterial extracellular solute-binding protein


Domain annotation for each model (and alignments):
>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.4   1.2   4.2e-23   2.5e-19      14     315 .]      58     357 ..      50     357 .. 0.85

  Alignments for each domain:
  == domain 1  score: 70.4 bits;  conditional E-value: 4.2e-23
                                    HHHH....HHHHHTTEEEEEEEECHHHHHH...HHHHHHHTTSSSCSEEEE..CGGHHHHHHHT....TSBECCHHHHHH CS
                      SBP_bac_1  14 vaka....fekehpgikVeiesvgsgslaq...kltlaiaaGdgpaDviav..dndwiarlaka....glllpldpyvka 80 
                                    +++a    f+k ++g+ Ve + v++g++ +   ++++ i+aG++p + ++v  ++  i+ +  a    + + +l+++ ++
  gi|119720163|ref|YP_920658.1|  58 AIDAlignFTK-NTGVAVEKTAVPGGAGVNakyAIIALIMAGKPP-EAFQVhcGPEMISYFMAAphgkDDFVDLTSVGQE 135
                                    44555555***.*******************************66.999999*999999888888999999999888888 PP

                                    TTECTTCCTEEEEHHHHTHHHHCE.EE.ES.EEEE.E.EEEEEEETTTHHCTTGGGSHBHHHHHHHHHHHHHHCTCTHCC CS
                      SBP_bac_1  81 ylapgvkdaadklsssvlpkilds.kv.ly.vPly.a.argliYNkdlfekagldppwtWdelveaakklkekgkkpigg 155
                                       + ++           p+   +  + ly +P++ + a++++ Nk++++k+g++pp+t del +a+ klk++g     +
  gi|119720163|ref|YP_920658.1| 136 IGLTATP-----------PGQVCMlSGrLYtLPVNlHrANLIFMNKQVLDKYGVKPPTTIDELNAACSKLKAAGVPC-LV 203
                                    7776655...........3333333559***********************************************86.** PP

                                    HCCEEHHHHHHHHHHHHHHHHTGGGEECCCT..HHCSHHHHSHHHHHHHHHHHHHHHHHHHTTEEECSSHHHHHHHHHTT CS
                      SBP_bac_1 156 arggsasgtayyfalalakslggkvfdkdgg..gldnpegvtaatylvklyavanltkelkgkgaenkdgaaalalfeaG 233
                                    ++g+++ + + ++ + +++++g++ f k ++     n++  t at++   y       + ++++    d+++a++ + +G
  gi|119720163|ref|YP_920658.1| 204 QAGADQFTVLHLWEQIFLAVAGPDKFIKFMYgtLDPNDPSITQATQIFLGY------VDTFPPDWMALDWTSAVDRVVKG 277
                                    **************************9999966444444444555555555......3667******************* PP

                                    SCSEEEEEHHHHHHHHCEEEEECHHCHHHHTTS.TEEEECEEBETTTTSEEEEEEEEEEBTTCSTHHHHHHHHHHHTSHH CS
                      SBP_bac_1 234 eaamaivglwaalaamkvapkvafaadkekpke.elgvaplPagkggkpgilgayglaipkgsknpeaAkkFldfllspe 312
                                      a+ ++g wa+    +v+p+v++ +++   ++ ++ vap+P++ g  ++  + + +a+pkg ++ +   +F +f++s +
  gi|119720163|ref|YP_920658.1| 278 MGAFHVDGDWAVGLIYNVYPNVKMCPIDAITPDcNIIVAPFPGTQGIYNM--VIDAVAVPKGPAQ-DLGVQFAKFFASRD 354
                                    **********************9966555544449999999*99999998..9999999999888.99999*******99 PP

                                    HHH CS
                      SBP_bac_1 313 aqa 315
                                    +q+
  gi|119720163|ref|YP_920658.1| 355 GQK 357
                                    996 PP

>> SBP_bac_8  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.9   0.4   1.3e-16   7.5e-13       3     255 ..      63     359 ..      61     384 .. 0.73

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 1.3e-16
                                    HHHHHHH-TEEEEEEE-.-SSSHHHH..HHHHHHTT---SEE.EEE-HHHHHHHHH....TTSB--GGGSTTHHH-HHHH CS
                      SBP_bac_8   3 akefekktgvkvnvvta.asndleqk..lkaalaagtapdidvvwanedalatlae....eglladlsdldnlddltdal 75 
                                    +  f+k tgv v+ + + +++++++k  + a + ag+ p++++v    + ++ + +    ++ ++dl+++ +  +lt++ 
  gi|119720163|ref|YP_920658.1|  63 IGNFTKNTGVAVEKTAVpGGAGVNAKyaIIALIMAGKPPEAFQVHCGPEMISYFMAaphgKDDFVDLTSVGQEIGLTATP 142
                                    667******999988776556666663378**********7777776788888888798788888999774444443433 PP

                                    HTT..--TS.----EEEEEEE-EEEEEHHHHHHS...---BHHHHHHHHHHHHHH-....SEGG---G......GGGGGT CS
                      SBP_bac_8  76 aav..gydgklygvPyasetpyvliynkdlleka..edpktwdellaaakklkgkf....glpdpasg......wlqaal 141
                                     ++  ++ g ly +P++  +  ++++nk +l+k   ++p+t+del+aa+ klk +        + a++      w q++l
  gi|119720163|ref|YP_920658.1| 143 PGQvcMLSGRLYTLPVNLHRANLIFMNKQVLDKYgvKPPTTIDELNAACSKLKAAGvpclV-QAGADQftvlhlWEQIFL 221
                                    33355999************************94666***************744445531.233333455666666666 PP

                                    HHETTEE---H.........HHH.HHHHHHHHHHHHTT-..EE-.S..--SSTTTTTSBSEEEE-TTHHHHHH-TTTSEE CS
                      SBP_bac_8 142 lakdgksldddg.......gkdglkealellkklkdngk..tyd.tgadavsefanGevaftingswdiaaaqkagkklg 211
                                       +g ++  +        +++ + +a +++  ++d     ++  ++++av+ + +G+ af + g+w++  + +  ++++
  gi|119720163|ref|YP_920658.1| 222 AV-AGPDKFIKFmygtldpNDPSITQATQIFLGYVDTFPpdWMAlDWTSAVDRVVKGMGAFHVDGDWAVGLIYNVYPNVK 300
                                    66.444443322455555556777888888888888875557765899*************************8888888 PP

                                    EE--................S--.EEEEEEEEEEBTTS-HHHHHHHHHHHHHTTSHHHHHH CS
                      SBP_bac_8 212 aivp................kqg.sfaggkglavpknaknedlaAldFlkwltspenqaal 255
                                    + ++                 qg +   ++ +avpk+ +++dl  ++F+k+++s ++q+ +
  gi|119720163|ref|YP_920658.1| 301 MCPIdaitpdcniivapfpgTQGiYNMVIDAVAVPKG-PAQDL-GVQFAKFFASRDGQKIF 359
                                    8764444446655555454445533333345666665.66665.9*************976 PP

>> SBP_bac_11  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0    0.0056        33      10      38 ..      56      84 ..      51     106 .. 0.77
   2 ?    6.0   0.0    0.0014       8.6     185     224 ..     319     359 ..     170     360 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0056
                                   HHHHHHHHHHHHHHH---EEEEESSHHHH CS
                     SBP_bac_11 10 aaalrelaaaFeahtgvkvevsaggsgkl 38
                                   ++a+++l+ +F+++tgv ve +a++ g+ 
  gi|119720163|ref|YP_920658.1| 56 RFAIDALIGNFTKNTGVAVEKTAVPGGAG 84
                                   689****************9999888654 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0014
                                    TTT--....EEEEEEEE-TT--HHHHHHHHHTTSHHHHHHH CS
                     SBP_bac_11 185 eglnl.dpldypaavlkkaakreaAraFlafLrspeaqail 224
                                    +g++    +++ a+ + k++ +     F++f +s+++q+i+
  gi|119720163|ref|YP_920658.1| 319 PGTQGiYNMVIDAVAVPKGPAQDLGVQFAKFFASRDGQKIF 359
                                    44433335777777777788999*****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (467 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 3169.04
//
Query:       gi|119720164|ref|YP_920659.1|  [L=224]
Description: formate dehydrogenase family accessory protein FdhD [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.4e-45  155.1   0.1    2.5e-37  128.8   0.1    2.0  2  FdhD-NarQ  FdhD/NarQ family
  ------ inclusion threshold ------
      0.019   14.8   0.1        5.5    7.0   0.0    2.5  2  GCV_T_C    Glycine cleavage T-protein C-terminal barrel domai


Domain annotation for each model (and alignments):
>> FdhD-NarQ  FdhD/NarQ family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   1.7e-09   1.6e-05       1      39 [.      21      59 ..      21      81 .. 0.88
   2 !  128.8   0.1   2.8e-41   2.5e-37     105     236 ..      90     221 ..      65     222 .. 0.95

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 1.7e-09
                                   E--EEEEEEETTEEEEEEEE-SSSHHHHHHHHHHHCTS- CS
                      FdhD-NarQ  1 veEepltivvngrelatlmatpadleelalGfllsegli 39
                                   v+E++++++vng+ l++l ++p+++eelalGfl + g+ 
  gi|119720164|ref|YP_920659.1| 21 VVERAYAVYVNGSRLVSLSCSPGMEEELALGFLAGLGFS 59
                                   68*******************************987765 PP

  == domain 2  score: 128.8 bits;  conditional E-value: 2.8e-41
                                    -EEGGGHHHHHHHHHTS-SHHHHHS--EEEEEEE.TTEEEEEEEESSHHHHHHHHHHHHHT.TSS-SSSEEEESS-B-HH CS
                      FdhD-NarQ 105 klsaeallrlmdalrekqelfketggvHaaalfdadgellavreDvGRHnAlDkviGaallegldlsdkilvvsgRlsse 184
                                    k+ ae ++r++++l e  e f++tg++H+a  f++ ge++ ++eDv+RH A+Dk +G a+++gldl +  + v+ Rl+  
  gi|119720164|ref|YP_920659.1|  90 KFPAEVVVRAVERLAELGEGFRATGALHGALCFTPGGEVVGFVEDVSRHCAVDKCLGLAVKRGLDLGSLGFAVTCRLTGS 169
                                    788999************************************************************************** PP

                                    HHHHHHHHT-SEEEESS-B-HHHHHHHHHHT-EEEEEEETTEEEEEE-GGGE CS
                      FdhD-NarQ 185 mvqKaaragipvlvsvsaptslavelAeeagltlvgfvrgkrfnvYtgaeRi 236
                                    +v K + a +p+++s++a+t  +v  Ae+ g+tlvgf+rg+rfnvYt ++Ri
  gi|119720164|ref|YP_920659.1| 170 VVEKFVSASVPLVASKAAVTLQGVLAAERGGVTLVGFARGGRFNVYTYPKRI 221
                                    ***************************************************9 PP

>> GCV_T_C  Glycine cleavage T-protein C-terminal barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0    0.0017        16      14      72 ..      21      76 ..      12      85 .. 0.76
   2 ?    7.0   0.0   0.00062       5.5      15      48 ..     115     149 ..     106     180 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0017
                        GCV_T_C 14 llrggepilrdgevvGhvTSgaysptlgksialAyvkaelaklgtevevevrgkrvpae 72
                                   +++  ++++ +g    ++ S   sp ++  +al+++++    +   + v v g rv+++
  gi|119720164|ref|YP_920659.1| 21 VVERAYAVYVNGS---RLVSLSCSPGMEEELALGFLAGLGFSPSRGYSVSVEGGRVEVR 76
                                   5567777777774...4789999**************6555567777777777777764 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.00062
                        GCV_T_C  15 lrggepil.rdgevvGhvTSgaysptlgksialAy 48 
                                    + +g+  +  +gevvG+v  +    +++k ++lA+
  gi|119720164|ref|YP_920659.1| 115 ALHGALCFtPGGEVVGFVEDVSRHCAVDKCLGLAV 149
                                    45666666369**********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       265  (0.0147805); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1460.28
//
Query:       gi|119720165|ref|YP_920660.1|  [L=336]
Description: hypothetical protein Tpen_1259 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       279  (0.0155614); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 2284.61
//
Query:       gi|119720166|ref|YP_920661.1|  [L=274]
Description: hypothetical protein Tpen_1260 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-07   30.8   0.1    4.1e-07   29.4   0.1    1.7  1  HTH_24          Winged helix-turn-helix DNA-binding
    1.7e-07   31.0   0.2      5e-07   29.5   0.2    1.8  1  MarR_2          MarR family
    7.1e-06   26.0   1.4    1.6e-05   24.9   0.1    2.2  2  HTH_20          Helix-turn-helix domain
    2.6e-05   23.9   0.2    2.6e-05   23.9   0.2    2.2  2  HTH_IclR        IclR helix-turn-helix domain
    0.00011   21.9   1.0    0.00028   20.6   1.0    1.7  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    0.00029   21.3   0.0    0.00055   20.4   0.0    1.3  1  HTH_27          Winged helix DNA-binding domain
    0.00056   19.8   0.0     0.0011   18.8   0.0    1.5  1  MarR            MarR family
     0.0017   18.5   0.0     0.0046   17.1   0.0    1.7  1  HTH_34          Winged helix DNA-binding domain
     0.0023   17.8   0.1     0.0053   16.7   0.1    1.5  1  HTH_11          HTH domain
  ------ inclusion threshold ------
      0.033   14.4   0.0      0.083   13.1   0.0    1.6  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.049   13.5   0.0       0.11   12.3   0.0    1.5  1  TrmB            Sugar-specific transcriptional regulator TrmB
      0.057   13.8   0.1       0.19   12.1   0.0    1.9  2  Rrf2            Transcriptional regulator


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.1   2.8e-10   4.1e-07       5      48 .]     216     260 ..     216     260 .. 0.90

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 2.8e-10
                         HTH_24   5 drkILelLqk.nprisqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                    d +IL  L++  +r   +e+ e+lg++++t++rr++rLe++G+++
  gi|119720166|ref|YP_920661.1| 216 DEAILDFLRRsGGRAYLKEIREALGIPSTTLLRRVRRLEKAGYLR 260
                                    66899999996666999**************************86 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.2   3.4e-10     5e-07      10      57 ..     219     265 ..     216     268 .. 0.93

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 3.4e-10
                                    HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESS CS
                         MarR_2  10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgp 57 
                                    +L +L+r++gr    +e+ ++lg++  ++ r+++rL++aG+++ ++ p
  gi|119720166|ref|YP_920661.1| 219 ILDFLRRSGGR-AYLKEIREALGIPSTTLLRRVRRLEKAGYLRLEKTP 265
                                    89********8.7*****************************999765 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1       1.9   2.9e+03      24      48 ..       4      28 ..       2      29 .. 0.74
   2 !   24.9   0.1   1.1e-08   1.6e-05      15      58 ..     219     263 ..     217     265 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.9
                                   TB-HHHHHHHHTS-HHHHHHHHHHH CS
                         HTH_20 24 gltaselaerldlskntlsyHLrvL 48
                                   g+ta +l ++l  ++  l + L+vL
  gi|119720166|ref|YP_920661.1|  4 GVTAFALLALLAATQLALAQPLEVL 28
                                   7888888888887777777777776 PP

  == domain 2  score: 24.9 bits;  conditional E-value: 1.1e-08
                                    HHHHH.STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                         HTH_20  15 ilraL.araegltaselaerldlskntlsyHLrvLeeagLvevvr 58 
                                    il+ L ++++ + ++e+ e+l+++ +tl +++r Le+ag++++++
  gi|119720166|ref|YP_920661.1| 219 ILDFLrRSGGRAYLKEIREALGIPSTTLLRRVRRLEKAGYLRLEK 263
                                    8888888899999*****************************987 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   1.0       1.7   2.5e+03       5      16 ..       7      18 ..       6      23 .. 0.79
   2 !   23.9   0.2   1.8e-08   2.6e-05       7      50 ..     218     261 ..     218     263 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.7
                                   HHHHHCT-CTTB CS
                       HTH_IclR  5 alaiLdalaeap 16
                                   a+a+L +la+++
  gi|119720166|ref|YP_920661.1|  7 AFALLALLAATQ 18
                                   789999999875 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 1.8e-08
                                    HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                       HTH_IclR   7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50 
                                    aiLd+l++ +++  l+e+ +++g+p +t  R ++ L++ Gy++ 
  gi|119720166|ref|YP_920661.1| 218 AILDFLRRSGGRAYLKEIREALGIPSTTLLRRVRRLEKAGYLRL 261
                                    69****************************************97 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   1.0   1.9e-07   0.00028       5      42 .]     216     254 ..     214     254 .. 0.97

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.9e-07
                  HTH_AsnC-type   5 DrkILeaLqed.aRisyaeLAervGlSestvlrRvrrLe 42 
                                    D +IL+ L++  +R+  +e+ e++G+  +t lrRvrrLe
  gi|119720166|ref|YP_920661.1| 216 DEAILDFLRRSgGRAYLKEIREALGIPSTTLLRRVRRLE 254
                                    899***********************************8 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   3.7e-07   0.00055       7      49 ..     218     260 ..     214     267 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 3.7e-07
                         HTH_27   7 lvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLve 49 
                                    ++L  +r+ ++r+ l++++++l + +++    +++L+++G++ 
  gi|119720166|ref|YP_920661.1| 218 AILDFLRRSGGRAYLKEIREALGIPSTTLLRRVRRLEKAGYLR 260
                                    689999************************************3 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   7.7e-07    0.0011       8      51 ..     219     263 ..     218     266 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 7.7e-07
                                    HHHHHHHSTT.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                           MarR   8 iLrilyeqgp.lsvseLakklgvskstvtrvldrLekkGlieRsk 51 
                                    iL  l+++g+ ++++e+ ++lg+ ++t+ r ++rLek+G+++ +k
  gi|119720166|ref|YP_920661.1| 219 ILDFLRRSGGrAYLKEIREALGIPSTTLLRRVRRLEKAGYLRLEK 263
                                    666778888779****************************98665 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   3.1e-06    0.0046       6      49 ..     220     264 ..     218     267 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.1e-06
                         HTH_34   6 lsyLas.vdeadfvelkealeatdgnLsvhlkkLekagYievdke 49 
                                    l +L     +a  +e++eal++ +  L   ++ LekagY+  +k+
  gi|119720166|ref|YP_920661.1| 220 LDFLRRsGGRAYLKEIREALGIPSTTLLRRVRRLEKAGYLRLEKT 264
                                    5555554678999****************************9996 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   3.5e-06    0.0053       4      53 ..     218     267 ..     216     268 .. 0.95

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.5e-06
                         HTH_11   4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg.vpIesepgrG 53 
                                    +il +L+++ g    +e+ e L++  +t  r++++Le++g +++e++pg G
  gi|119720166|ref|YP_920661.1| 218 AILDFLRRSGGRAYLKEIREALGIPSTTLLRRVRRLEKAGyLRLEKTPG-G 267
                                    799*************************************99*****99.6 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   5.5e-05     0.083      11      57 ..     217     264 ..     216     266 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.5e-05
                                    HHHHHHHH.HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT CS
                 Fe_dep_repress  11 etIYtlse.ekkvvktkdlaerLnvspssVsemlkkLekdGyveyeky 57 
                                    e+I++    +++ +  k++ e+L++   +    +++Lek+Gy+  ek 
  gi|119720166|ref|YP_920661.1| 217 EAILDFLRrSGGRAYLKEIREALGIPSTTLLRRVRRLEKAGYLRLEKT 264
                                    57777777788889999**************************99885 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   7.6e-05      0.11      22      56 ..     229     263 ..     219     268 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.6e-05
                                    CCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                           TrmB  22 patadeiaeelgvprskvYevLrsLedkGlVerek 56 
                                    +a  +ei e+lg+p ++  + +r+Le++G+ + ek
  gi|119720166|ref|YP_920661.1| 229 RAYLKEIREALGIPSTTLLRRVRRLEKAGYLRLEK 263
                                    56678************************987765 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       3.6   5.3e+03      58      71 ..     205     217 ..     204     224 .. 0.79
   2 ?   12.1   0.0   0.00013      0.19      20      61 ..     225     265 ..     217     273 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 3.6
                                    ETTT-TCEEESSHC CS
                           Rrf2  58 vrGkgGGyrLakpp 71 
                                    +rG  GG++L ++ 
  gi|119720166|ref|YP_920661.1| 205 RRGE-GGVVLEEDE 217
                                    6888.999998765 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00013
                                    SSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT CS
                           Rrf2  20 eeeeepvsseeiaerqnispsylekilakLrkaglvksvrGk 61 
                                    +++++ + ++ei e  +i+ + l + +++L+kag+++ ++ +
  gi|119720166|ref|YP_920661.1| 225 RSGGR-AYLKEIREALGIPSTTLLRRVRRLEKAGYLRLEKTP 265
                                    44444.789**************************9987766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2078.29
//
Query:       gi|119720167|ref|YP_920662.1|  [L=95]
Description: Alba, DNA/RNA-binding protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.3e-10   38.5   0.1      1e-09   38.1   0.1    1.2  1  Alba      Alba


Domain annotation for each model (and alignments):
>> Alba  Alba
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.1   5.7e-14     1e-09       4      66 ..       7      66 ..       4      67 .. 0.91

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 5.7e-14
                                   EE-STS-HHHHHHHHHHHHTHTTESEEEEEEETTHHHHHHHHHHHHHHHTCTT.EEEEEEEEE CS
                           Alba  4 yVsskspimsyvkralklLsnkkeeeVvlkatGraIskAvsvaeilkrrfgkglyqvnvltss 66
                                    V+  +p + y ++++++L +k+++ Vv+ a+Gr+IskAv v e ++r  g +++ + ++ ++
  gi|119720167|ref|YP_920662.1|  7 LVGE-KPESAYTLELMTML-GKGAPRVVVRAVGRNISKAVYVTEGVRRLTG-DKIAYGKIRIY 66
                                   5777.9999**********.****************************997.66999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 688.90
//
Query:       gi|119720168|ref|YP_920663.1|  [L=410]
Description: AAA family ATPase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.9e-26   90.8   0.0      1e-25   90.3   0.0    1.3  1  AAA_14    AAA domain
    1.1e-08   35.2   0.0    3.9e-08   33.5   0.0    2.0  3  DUF4143   Domain of unknown function (DUF4143)
     0.0011   19.0   0.0     0.0017   18.4   0.0    1.3  1  ATPase_2  ATPase domain predominantly from Archaea
     0.0015   18.8   0.0       0.17   12.1   0.0    2.9  3  AAA_22    AAA domain
  ------ inclusion threshold ------
      0.049   14.0   0.0       0.11   12.9   0.0    1.6  1  AAA_16    AAA ATPase domain


Domain annotation for each model (and alignments):
>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.3   0.0   2.9e-29     1e-25       3     130 ..      34     158 ..      32     159 .. 0.94

  Alignments for each domain:
  == domain 1  score: 90.3 bits;  conditional E-value: 2.9e-29
                         AAA_14   3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqevpeweka 82 
                                     i++++G+Rr+GKT+++ + +++ l++  + ly+ ld++++++l+   ++ e+++e+++e ++  l++DE+q  ++w + 
  gi|119720168|ref|YP_920663.1|  34 DIVAVVGPRRSGKTFVMLRSVERDLAEGLQALYVPLDEPSLRRLDAR-RFAEMVREEYRE-GRVRLYMDEVQDWEDWDSK 111
                                    689*******************999999*************987754.7999****9766.9999*************** PP

                         AAA_14  83 lkslvdegknldvivtGSnskllskeiatslagrvaeielyplsfaEf 130
                                    l+ l+d + +++++vtGS+s l s+ei ++l+gr+ +  + p+sf+E+
  gi|119720168|ref|YP_920663.1| 112 LRWLHDVK-DFQLYVTGSSSALQSSEIPSRLRGRYVSRLVLPFSFREV 158
                                    ******99.9*************************************7 PP

>> DUF4143  Domain of unknown function (DUF4143)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       2.7   9.7e+03      21      46 ..      99     126 ..      75     136 .. 0.70
   2 !   33.5   0.0   1.1e-11   3.9e-08       2     120 ..     211     357 ..     210     359 .. 0.89
   3 ?   -2.9   0.0         2   7.3e+03      80     103 ..     374     393 ..     368     394 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.7
                                    xxxxxxxxx..xxxxxxxxxxxxxxxxx RF
                        DUF4143  21 verlppwse..spnskkrlrkspKlyfv 46 
                                    +++++ w++  s+++   ++k + ly++
  gi|119720168|ref|YP_920663.1|  99 MDEVQDWEDwdSKLRWLHDVKDFQLYVT 126
                                    4566777667677777777888888775 PP

  == domain 2  score: 33.5 bits;  conditional E-value: 1.1e-11
                                    xxxxxxxxxxxxxxxxx............................................xxxxxxxxxxxxxxxxxxx RF
                        DUF4143   2 rDirklagvrdpeelrk............................................glverlppwsespnskkrl 37 
                                    rDi + ++vr+pe+l                                              +lv+ ++++     ++ r 
  gi|119720168|ref|YP_920663.1| 211 RDIVERHRVREPEALLElayvvlssyaspvtwrslarslkglgvevdaktaasyveymrqaFLVFVVKRF--AYSERLRA 288
                                    899999999999999999999999999999999999999999999999999999999999**********..88888899 PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        DUF4143  38 rkspKlyfvDtGLlvallgldkeelledsenkGallEnlVaqeLlkysekegaklyyyrdkngaEvDfvielkggkivpi 117
                                    r+  K+y+vD+++  a l+ +       + ++G+ +En+V+ eL++    +g ++ yy +++g+EvDf  + +gg + ++
  gi|119720168|ref|YP_920663.1| 289 RSPRKVYVVDPAV--ASLFER-------PLDLGRRAENVVLVELVR----RGCEPGYYVTSRGREVDFAAK-CGGSLRLV 354
                                    9*********966..544444.......4569**************....8*********99********8.8*9***** PP

                                    xxx RF
                        DUF4143 118 EvK 120
                                    Ev 
  gi|119720168|ref|YP_920663.1| 355 EVC 357
                                    *97 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 2
                                    xxxxxxxxxxxxxxxxxxxxxxxx RF
                        DUF4143  80 eLlkysekegaklyyyrdkngaEv 103
                                    eL+     ++a+l  + d++++Ev
  gi|119720168|ref|YP_920663.1| 374 ELRL----REAELVSWDDEDEREV 393
                                    4444....6899999*99999998 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   4.6e-07    0.0017      17      77 ..      30      94 ..      24     136 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 4.6e-07
                       ATPase_2 17 repneiyfiYGpegsGKtaLlkeiienledkdkyviyyi....alreesiskldefieeeeekkk 77
                                   re+ +i+ + Gp++sGKt ++ +++e+ +  + + +y+     +lr+ +  ++ e+++ee+ + +
  gi|119720168|ref|YP_920663.1| 30 RESPDIVAVVGPRRSGKTFVMLRSVERDLAEGLQALYVPldepSLRRLDARRFAEMVREEYREGR 94
                                   78899***********************9999888876322224444444444444446665555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   4.8e-05      0.17       4      65 ..      32      91 ..      30      96 .. 0.71
   2 !    5.8   0.0    0.0043        15      67     132 ..      68     130 ..      56     134 .. 0.72
   3 ?   -0.3   0.0      0.33   1.2e+03      44      85 ..     230     271 ..     204     300 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.8e-05
                         AAA_22  4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst..sskdllrellralg 65
                                   +  i++v+G+  +GKT+++ r +e++ +e      ++ +v  + ps+   + + +++++ +++ 
  gi|119720168|ref|YP_920663.1| 32 SPDIVAVVGPRRSGKTFVMLRSVERDLAE----GLQALYVPLDEPSLRrlDARRFAEMVREEYR 91
                                   56799*******************99654....3455555555555557777777777666665 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0043
                         AAA_22  67 elka...erlsseellealeqalraravielliiDEaqhlrseealeeLrsllnlsrkgvqliLvGtpe 132
                                    +l++   +rl+ +++ e++++  r+ +v   l  DE+q    e+  ++Lr l++   k++ql + G  +
  gi|119720168|ref|YP_920663.1|  68 PLDEpslRRLDARRFAEMVREEYREGRV--RLYMDEVQDW--EDWDSKLRWLHD--VKDFQLYVTGSSS 130
                                    4444344477777777778888777777..9*********..788888888899..9999998888764 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.33
                         AAA_22  44 fvtlpsst...sskdllrellralglelkaerlsseellealeqa 85 
                                    +v l+s     ++++l+r l   lg+e +a  ++   ++e+++qa
  gi|119720168|ref|YP_920663.1| 230 YVVLSSYAspvTWRSLARSLK-GLGVEVDA--KTAASYVEYMRQA 271
                                    555555554458888877664.45555555..4555555555554 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0     3e-05      0.11      22     101 ..      31     112 ..      25     174 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3e-05
                         AAA_16  22 grpelvllsGesGvGKsslv.rellralekdggiflrgkcdql....esaipysalaqalareellrqlldeaesaelea 96 
                                     +p +v ++G++ +GK+ ++ r++ r l +    +l+   d+       a++++  ++   re+ +r   de   +++e+
  gi|119720168|ref|YP_920663.1|  31 ESPDIVAVVGPRRSGKTFVMlRSVERDLAEG-LQALYVPLDEPslrrLDARRFAEMVREEYREGRVRLYMDE--VQDWED 107
                                    56799**************967777666655.3333333333311211112223333333344444444444..445777 PP

                         AAA_16  97 wrekl 101
                                    w+ kl
  gi|119720168|ref|YP_920663.1| 108 WDSKL 112
                                    77665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2747.63
//
Query:       gi|119720169|ref|YP_920664.1|  [L=253]
Description: CRISPR-associated protein APE2256 family [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.1e-42  144.2   0.0    3.2e-42  143.6   0.0    1.3  1  Cas_APE2256  CRISPR-associated protein (Cas_APE2256)
  ------ inclusion threshold ------
      0.011   15.4   0.0      0.015   15.0   0.0    1.2  1  Cas_NE0113   CRISPR-associated protein NE0113 (Cas_NE0113)


Domain annotation for each model (and alignments):
>> Cas_APE2256  CRISPR-associated protein (Cas_APE2256)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.6   0.0   3.6e-46   3.2e-42       2     136 .]      63     191 ..      62     191 .. 0.97

  Alignments for each domain:
  == domain 1  score: 143.6 bits;  conditional E-value: 3.6e-46
                    Cas_APE2256   2 kasAElnallkllekkkkeqkeelvllssdTaaGklvaeilkeyleeegaevevveieklsdlgreeFreglrnLvekla 81 
                                     +sAElna++ +le ++     +++ll+sd++a++l+a++lkeyl e+g+evev++   ++dlgr+ F +gl nL+++l+
  gi|119720169|ref|YP_920664.1|  63 GVSAELNAMWPYLEAGRVA---AAYLLASDSGASTLCASVLKEYLGEHGVEVEVER---VADLGRD-FDKGLYNLLDALS 135
                                    68***************98...69***********************999999966...*******.************* PP

                    Cas_APE2256  82 revknkkregekvlinaTgGfKpeiavltlvall.ladevyYihEsfsevvelPkl 136
                                    r+v+ ++r+g++v++naTgGfKpe+av++++a+l +a++vyYihE+++evvelP+l
  gi|119720169|ref|YP_920664.1| 136 RAVEGYRRRGYAVYVNATGGFKPETAVVYAAASLfGASRVYYIHETMGEVVELPTL 191
                                    **********************************9*******************86 PP

>> Cas_NE0113  CRISPR-associated protein NE0113 (Cas_NE0113)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   1.6e-06     0.015      78     133 ..     127     179 ..      83     197 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.6e-06
                     Cas_NE0113  78 neallqlivrlvrelrenegerlhlsiaGGRKtmsillalaaqLygreqDrlyHvl 133
                                       ll+++ r v+ +r   g++++++  GG K  ++++  aa+L+g  + r+y+++
  gi|119720169|ref|YP_920664.1| 127 LYNLLDALSRAVEGYRRR-GYAVYVNATGGFKPETAVVYAAASLFG--ASRVYYIH 179
                                    46799999**********.9**************************..*******6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1730.32
//
Query:       gi|119720170|ref|YP_920665.1|  [L=235]
Description: hypothetical protein Tpen_1264 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1661.79
//
Query:       gi|119720171|ref|YP_920666.1|  [L=464]
Description: phosphoenolpyruvate carboxylase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   1.5e-103  347.0   0.0   1.6e-103  346.8   0.0    1.0  1  PEPcase_2  Phosphoenolpyruvate carboxylase
    1.2e-07   30.2   0.1    2.3e-07   29.3   0.0    1.4  2  PEPcase    Phosphoenolpyruvate carboxylase
  ------ inclusion threshold ------
      0.014   14.6   0.0      0.031   13.4   0.0    1.5  2  HpcH_HpaI  HpcH/HpaI aldolase/citrate lyase family


Domain annotation for each model (and alignments):
>> PEPcase_2  Phosphoenolpyruvate carboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  346.8   0.0  2.7e-107  1.6e-103       2     470 ..       4     446 ..       3     464 .] 0.91

  Alignments for each domain:
  == domain 1  score: 346.8 bits;  conditional E-value: 2.7e-107
                                    -SEEEE--ST-.......SS--B-TTTHHHHHHHHHSS----EEEEE-SSB---TTHHHHHHHHHHC..TT--TTTSSEE CS
                      PEPcase_2   2 prtmsTQHPDnakvPefaeeevisgedEveEAykalselgvdEvMwDfEGKevdehvvrkllseyeeffkekvlGedvfl 81 
                                    pr+m+TQHPD        ++ ++ +++EveEA++ ++ +g+dEvM D+EGK +++ ++++++ ++ e   ++++Ge +++
  gi|119720171|ref|YP_920666.1|   4 PRLMCTQHPD--------STVKVPVQEEVEEAVRSFLVYGCDEVMSDYEGKLTPYAQPKEIVVKAGE--LGVPVGEGFYV 73 
                                    9*********........9************************************************..*********** PP

                                    EEE---TTTS-HHHHHHHHHHHHHHHHH.HHHHH.SS-S-SEEEESS--SHHHHHHHHHHHHHHHH.........HHHHH CS
                      PEPcase_2  82 tlRvPnpkvEkaerkvlaetlesipnsydlaekfeetkpifevilPmttsaeelievakyyekvvagkeeleladlkvke 161
                                    t+R Pnp++E+ +r  la+ +++++n y +++ +  ++++ +v+lPmt+sae++  v++ + +  +         +  +e
  gi|119720171|ref|YP_920666.1|  74 TVRAPNPRLEDFDRVDLALEAAVLANYYSYKR-L-GVQAVRWVVLPMTDSAETVRLVQRLLARKTR---------VLCEE 142
                                    ****************************5555.5.6***************************999.........89999 PP

                                    -SS---TTSSEEEEEE-SHHHHHTHHHHHHHHH...HHT..--SEEEEEEESHHHHHHH-HHHHHHHHHHHHHHHHHHHH CS
                      PEPcase_2 162 lvgelkpesievIPLiEdkesllnideiveeyv...kek..klkelRvflarSDpAlnyGlisavllvkvAlselyklee 236
                                    + ++++  + +++PL+Ed++sll+++ei++++    +e   ++  lRvfl++SD+Al+ G+i+++l+  +Al e +k +e
  gi|119720171|ref|YP_920666.1| 143 VGQPCE--QAQLVPLLEDVDSLLRVREILRDLHsalAELgsDPGVLRVFLGKSDSALKAGHIASALSLLYALGESAKAGE 220
                                    999988..7789*******************9965533367999************************************ PP

                                    HHT-EEEEEEE-BSSGGGT---TTGHHHH.HHHTTT-SEEEE-HHHHHTTHHHHHHHHHHHHHHGGG-------HHHHHH CS
                      PEPcase_2 237 elgvkiyPilGvGslpfRGhlspenveev.leeYagvkTfTvQSafkYdyeeeevkeairkineaevkkprelseeeeel 315
                                    elg+++ PilG Gs+pfRG++++ ++  v ++ Y+g+ T+TvQSa++Yd + +e++e+ +k+   +  +p          
  gi|119720171|ref|YP_920666.1| 221 ELGLEVKPILGGGSPPFRGGVNNPRLVGVeVQRYRGYSTVTVQSAVRYDASFSEYQEVRSKLLGGAGGEPGDAGGR---- 296
                                    *********************988777666**********************************999999988877.... PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHTTS---S-B----------EEE--H....E---HHHHHHHHHHTT--GGGTTH CS
                      PEPcase_2 316 llevieklseaYqekiekladvinevaklipkrRaRklhiglfgYsReieev....elPRAIsftgalYsiGlPpellgi 391
                                    + e+++ +++ Y++  +k+ d++ne a+ +p +R+R +++   +Y R +e      + PRAI +t+a+Ys+G+Pp+ l++
  gi|119720171|ref|YP_920666.1| 297 VAELARLAASMYRSLASKYLDFVNEYARSVPTTRDRVSWR---EYGRALELEdklfSAPRAIVYTAAWYSLGVPPTFLDA 373
                                    689999********************************99...9***98876778899********************** PP

                                    HHHHHHHHHHH.HHHHHHSTTHHHHHHHHHTT--SSTTTTTS-HHHHHHHHHHHHHHHHHTT--HHHHHHH-HHHHHHHH CS
                      PEPcase_2 392 ssllelaeeel.evllevykalkedlaeaarylnleksklkldeetvkkikedleiveeildlkyeeeeheeltsellka 470
                                      +le++  +  + +l  ++ l+e+++ +a+++ ++ +  +l+ee vkk++e+l+++         ++e+ e +++l ++
  gi|119720171|ref|YP_920666.1| 374 DFVLEAYRGDFlDEVLGYLPGLEEEWRYDAQFYLPRLAGERLGEELVKKVDEALDAMGL-------RPEPLEPYEKLART 446
                                    *****9996544*****************************************998765.......45555555555544 PP

>> PEPcase  Phosphoenolpyruvate carboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.0   3.9e-11   2.3e-07     359     496 ..     104     241 ..      87     252 .. 0.86
   2 ?   -3.5   0.1      0.33     2e+03     565     594 ..     298     327 ..     296     329 .. 0.85

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 3.9e-11
                                    -...TTSEEEEEEET--SHHHHHHHH.HHHHHTT-..-......S---EEEEE-SHHHHHHHHHHHHHHHHSHHHHHHTT CS
                        PEPcase 359 eefgkeiietyviSmaeeasdvLevl.lLakeaglldkaega..aelrvvPLfEtvedLknapevleellslplyrelvk 435
                                    +++g ++++  v+ m+++a+ v  v  lLa+++ +l ++ g+  ++ ++vPL+E v+ L +  e+l++l s  +    + 
  gi|119720171|ref|YP_920666.1| 104 KRLGVQAVRWVVLPMTDSAETVRLVQrLLARKTRVLCEEVGQpcEQAQLVPLLEDVDSLLRVREILRDLHSALA---ELG 180
                                    67999*****************77753899***9999988888899**********************987644...344 PP

                                    T...EEEEEE-HHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHT-EEEEEE-SSTGGGS-HH CS
                        PEPcase 436 ksgelqevMlGYSDSnKdaGfltsnWelykaqealvkvaeeagvklrlFHGrGGsvgRGGg 496
                                    +   +  v lG SDS+  aG ++s+ +l  a  + +k  ee g++++   G G    RGG 
  gi|119720171|ref|YP_920666.1| 181 SDPGVLRVFLGKSDSALKAGHIASALSLLYALGESAKAGEELGLEVKPILGGGSPPFRGGV 241
                                    4456899*************************************99998887777778875 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 0.33
                                    HHHHHHHHHHHHHHHTT-SSHHHHHHHHS- CS
                        PEPcase 565 eelsevsreaYrklvyeepdfveyFreaTP 594
                                    +el++ + + Yr+l  +  dfv+ ++++ P
  gi|119720171|ref|YP_920666.1| 298 AELARLAASMYRSLASKYLDFVNEYARSVP 327
                                    6899999********999999988877776 PP

>> HpcH_HpaI  HpcH/HpaI aldolase/citrate lyase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0      0.54   3.2e+03      13      30 ..      27      44 ..      22      46 .. 0.84
   2 ?   13.4   0.0   5.3e-06     0.031      85     162 ..     111     203 ..      92     226 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.54
                                   HHHHHCTC--SEEEEESS CS
                      HpcH_HpaI 13 laekaaiagaDsvliDlE 30
                                    ++ + ++g D+v+ D E
  gi|119720171|ref|YP_920666.1| 27 AVRSFLVYGCDEVMSDYE 44
                                   57788999******9987 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 5.3e-06
                                    SSEEEESS--SHHHHHHHHHHTSHTTT....S---HCCC-EEEEEE-SHHHHHTHHHHH.TST..........TEEEEEE CS
                      HpcH_HpaI  85 aqvvlvPkvetaeealevvsalrepek....girganketrllaqiEsaegvknaeeIa.ave..........gldgvfl 149
                                    +  v++P++++ae ++ v+++l++ ++    ++++  ++ +l+  +E  + ++ ++eI+ ++           g+  vfl
  gi|119720171|ref|YP_920666.1| 111 VRWVVLPMTDSAETVRLVQRLLARKTRvlceEVGQPCEQAQLVPLLEDVDSLLRVREILrDLHsalaelgsdpGVLRVFL 190
                                    44589***************99998852221555578889999999*************97778899************* PP

                                    -HHHHHHHTT-TT CS
                      HpcH_HpaI 150 GaeDlsadlgtkr 162
                                    G++D + + g+  
  gi|119720171|ref|YP_920666.1| 191 GKSDSALKAGHIA 203
                                    ****887777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (464 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 3079.17
//
Query:       gi|119720172|ref|YP_920667.1|  [L=558]
Description: hypothetical protein Tpen_1266 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
        8.1    5.4  15.5         17    4.4  15.5    1.4  1  ABC2_membrane_3  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4  15.5   0.00094        17     211     293 ..      28     121 ..       5     152 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.00094
                ABC2_membrane_3 211 lgdflvyllqlllilllafgl.....gipfgnlglllllfl.....lfglayialgyllsslfknsetaqilifivilll 280
                                    +++++v++  ++l+l+l fg+     ++ +++l++lll++l     l++l++++++++l s+ ++s++  ++++++   +
  gi|119720172|ref|YP_920667.1|  28 IWLVAVAVAASALALALTFGRraglaFLAVYSLLYLLLVLLavplpLYALLVAVFTAFLLSAATRSRAFLAAMLALAA-F 106
                                    699999999999999999999998886777777776644443344489999999999999999999887777777777.4 PP

                ABC2_membrane_3 281 sgffggl..fpledl 293
                                    +++f++l  ++l + 
  gi|119720172|ref|YP_920667.1| 107 LVVFLALqgYFLASW 121
                                    444444434444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (558 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       829  (0.0462379); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.26s 00:00:00.87 Elapsed: 00:00:00.43
# Mc/sec: 3927.86
//
Query:       gi|119720173|ref|YP_920668.1|  [L=342]
Description: ATPase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.4e-16   58.4   0.0    2.5e-15   57.0   0.0    1.7  2  ATPase_2     ATPase domain predominantly from Archaea
    5.1e-08   33.0   0.0     0.0031   17.6   0.0    2.3  2  AAA_14       AAA domain
    4.4e-07   30.4   2.3    1.1e-06   29.1   2.3    1.8  1  AAA_16       AAA ATPase domain
     0.0097   16.2   0.0       0.48   10.7   0.0    2.4  2  AAA_22       AAA domain
  ------ inclusion threshold ------
      0.045   13.5   0.0        0.1   12.4   0.0    1.5  1  tRNA_bind_4  tRNA-binding domain
      0.059   12.9   0.0       0.12   12.0   0.0    1.5  1  GerE         Bacterial regulatory proteins, luxR family
      0.077   12.7   0.0       0.17   11.6   0.0    1.6  1  HTH_33       Winged helix-turn helix


Domain annotation for each model (and alignments):
>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.0   0.0   9.8e-19   2.5e-15       1     231 [.      15     241 ..      15     243 .. 0.76
   2 ?   -2.5   0.0       1.6     4e+03      73      99 ..     292     318 ..     280     326 .. 0.75

  Alignments for each domain:
  == domain 1  score: 57.0 bits;  conditional E-value: 9.8e-19
                       ATPase_2   1 FfdRekelkeleeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefie..eeeekkkl 78 
                                    +fdRe+el+el + ++r+   +  + G +++GKt++l+ ++ +      + +y++a   ++ + l++ ++   +e+  +l
  gi|119720173|ref|YP_920668.1|  15 LFDRERELEELHRAVDRGLPLVA-LLGVRRVGKTSVLRTFLGEV-----NGLYVDARGLVRRADLETRVAdaLSESLGRL 88 
                                    59***************887766.56***************999.....5588888777777777666443322222333 PP

                       ATPase_2  79 ekal....giavpkaeleeilk..eksklvfkaielllekikkkgkkiiiiiDelqklidlglngaellvkeLlnliesl 152
                                    ++ l    g  v  +++    +   + ++   +++ ll +i k+g + +  +De+q+ +      +++l + L++ +++ 
  gi|119720173|ref|YP_920668.1|  89 RRFLegvrGVSVAGFSV----EvrWRGRD-SVSLAGLLSEIDKRGERFVFALDEVQQSK---PPVSAELRSVLAYGYDN- 159
                                    33333322444444444....13234444.678999***********************...23345666666666666. PP

                       ATPase_2 153 tkekhlcvviclsSeglfie...rvyneselegrhky.ilvddldketalnflkegfkeleel.skedfeeiyryvGGkP 227
                                       +++++v+++s+ g++++   + + +s+l+gr  y ++v+ +  + +++fl++gf+e   + +   +ee++ +++G++
  gi|119720173|ref|YP_920668.1| 160 --LENVTFVVVGSEVGMLRDflaLEDPSSPLYGRYAYeVHVERFSEDLSREFLERGFREEGVEpPPGVVEEAVGFFDGIV 237
                                    ..57899**********9998878999********************************955536666799999999998 PP

                       ATPase_2 228 kalv 231
                                    + lv
  gi|119720173|ref|YP_920668.1| 238 GWLV 241
                                    8776 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.6
                       ATPase_2  73 eekkklekalgiavpkaeleeilkeks 99 
                                    e+++++++ +g a+pka+l +i+++  
  gi|119720173|ref|YP_920668.1| 292 EVRRYVDERFGVALPKATLSRIIEKLE 318
                                    667788888888999999888877433 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   2.5e-05     0.063       4      26 ..      35      57 ..      33      90 .. 0.81
   2 !   17.6   0.0   1.2e-06    0.0031      56     118 ..     121     193 ..     104     205 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.5e-05
                         AAA_14  4 ilvitGaRrvGKTtllkqlikel 26
                                   ++++ G+RrvGKT +l++++ e 
  gi|119720173|ref|YP_920668.1| 35 LVALLGVRRVGKTSVLRTFLGEV 57
                                   5889*************998664 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 1.2e-06
                         AAA_14  56 ileklkeekktylflDEiqev.....pewekalkslvdegknldvivtGSnskllskeia.....tslagrva 118
                                    + e  k+ ++ ++ lDE+q++      e++++l + +d+ +n+ ++v GS  ++l   +a     + l gr+a
  gi|119720173|ref|YP_920668.1| 121 LSEIDKRGERFVFALDEVQQSkppvsAELRSVLAYGYDNLENVTFVVVGSEVGMLRDFLAledpsSPLYGRYA 193
                                    44443445677889*******888889999********99*************99654433333366666665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   2.3   4.5e-10   1.1e-06       2     149 ..      15     143 ..      14     168 .. 0.64

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 4.5e-10
                         AAA_16   2 lvGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareel 81 
                                    l+ Re+ele+L++a++r      +lv l G + vGK+s++r++l     +    ++g +++           + l r+  
  gi|119720173|ref|YP_920668.1|  15 LFDRERELEELHRAVDRGL----PLVALLGVRRVGKTSVLRTFLG----E----VNGLYVDA----------RGLVRRAD 72 
                                    778************9776....9********************5....4....55555555..........33334444 PP

                         AAA_16  82 lrqlldeaesaeleawrekleeala.avpelagaea......srllellkrllallsrderplvlvlDdlqwade 149
                                    l+   ++a s +l++ r++le++ + +v+  + + +       +l+ ll+++    +r+er +v+ lD++q+ ++
  gi|119720173|ref|YP_920668.1|  73 LETRVADALSESLGRLRRFLEGVRGvSVAGFSVEVRwrgrdsVSLAGLLSEID---KRGER-FVFALDEVQQSKP 143
                                    44444444444888888888887665333333333344333244444444444...44344.*********8877 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   0.00019      0.48       8     131 ..      36     171 ..      29     177 .. 0.81
   2 ?    2.9   0.0     0.046   1.2e+02      37      85 ..     267     320 ..     253     329 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00019
                         AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka................. 70 
                                    +++ G   +GKT +lr++l +              ++v++ ++  ++dl ++++ al ++l +                 
  gi|119720173|ref|YP_920668.1|  36 VALLGVRRVGKTSVLRTFLGEV-----------NGLYVDARGLVRRADLETRVADALSESLGRlrrflegvrgvsvagfs 104
                                    67889999************75...........678888888888888888888888888888888888888889999** PP

                         AAA_22  71 ....erlsseellealeqalraravielliiDEaqhlrseealeeLrsllnl...srkgvqliLvGtp 131
                                         r++ +  l+ l   +++r+ + ++ +DE+q   ++ +  eLrs l     +  +v++++vG +
  gi|119720173|ref|YP_920668.1| 105 vevrWRGRDSVSLAGLLSEIDKRGERFVFALDEVQQS-KPPVSAELRSVLAYgydNLENVTFVVVGSE 171
                                    **9744444444466666667766669**********.999999999998777888999***999975 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.046
                         AAA_22  37 e......erpevvfvtlpsst.sskdllrellralglelkaerlsseellealeqa 85 
                                    e      +r + v+  +++++ s+++++r + + +g+ l +  +++++++e+le+ 
  gi|119720173|ref|YP_920668.1| 267 EelgklsPRERMVLRAVAEGCrSWSEVRRYVDERFGVALPK--ATLSRIIEKLEKL 320
                                    2346677666666666677777*****************99..9999998888776 PP

>> tRNA_bind_4  tRNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0     4e-05       0.1      67     140 ..      66     141 ..      55     148 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4e-05
                                    SSS-HHHHHHHHHHHHHHHCCC..CCS--EEEEEEEEEEEEEE-SS--HH---TTECEEEEETTEEEEEEES--HH CS
                    tRNA_bind_4  67 ryvRahdallrlkkplaeklGk..kyriGvRgikveeyeieiesekelkaekipeveeveveegkitlelkdvdes 140
                                      vR  d   r+  +l+e lG+  ++  GvRg++v  +++e++   + +       +e++++ ++++  l +v++s
  gi|119720173|ref|YP_920668.1|  66 GLVRRADLETRVADALSESLGRlrRFLEGVRGVSVAGFSVEVRWRGRDSVSLAGLLSEIDKRGERFVFALDEVQQS 141
                                    5677788888999********7335667**************9986665666667778888888888888887765 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   4.6e-05      0.12       3      21 ..     272     290 ..     270     291 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.6e-05
                                    S-HHHHHHHHHHCTTS-HH CS
                           GerE   3 LskRErevLrllaeGksnk 21 
                                    Ls+REr vLr +aeG  ++
  gi|119720173|ref|YP_920668.1| 272 LSPRERMVLRAVAEGCRSW 290
                                    9**************7765 PP

>> HTH_33  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   6.6e-05      0.17       4      32 ..     287     315 ..     284     318 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.6e-05
                         HTH_33   4 rWtlarlaqlieerfgvsysvsgvyrlLk 32 
                                    + + +++++++ erfgv + +++++r+  
  gi|119720173|ref|YP_920668.1| 287 CRSWSEVRRYVDERFGVALPKATLSRIIE 315
                                    556689*******************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2646.78
//
Query:       gi|119720174|ref|YP_920669.1|  [L=323]
Description: PP-loop domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-18   67.3   0.0    5.7e-18   65.3   0.0    1.9  1  ATP_bind_3     PP-loop family
     0.0054   15.6   0.2      0.019   13.7   0.2    1.9  2  tRNA_Me_trans  tRNA methyl transferase
     0.0081   15.7   0.9     0.0081   15.7   0.9    3.1  3  RecR           RecR protein
  ------ inclusion threshold ------
       0.11   12.1   0.0       0.14   11.8   0.0    1.1  1  Asn_synthase   Asparagine synthase
       0.15   11.5   0.0          1    8.8   0.0    2.0  2  QueC           Queuosine biosynthesis protein QueC
       0.32   10.7   0.2       0.32   10.7   0.2    3.3  3  zf-RRN7        Zinc-finger of RNA-polymerase I-specific TFIIB
       0.38   11.1   2.1         18    5.7   0.1    3.0  3  C1_2           C1 domain
       0.68   10.1   0.0       0.68   10.1   0.0    2.8  3  C5HCH          NSD Cys-His rich domain
        1.4    8.9  14.6        1.1    9.1   0.2    4.2  4  zf-HIT         HIT zinc finger
        5.3    7.0  10.2         21    5.2   0.1    3.6  3  Nudix_N_2      Nudix N-terminal
          9    6.3   6.4         73    3.4   0.0    3.6  4  zf-C4_ClpX     ClpX C4-type zinc finger


Domain annotation for each model (and alignments):
>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.3   0.0   3.5e-21   5.7e-18       2     166 ..      52     226 ..      51     233 .. 0.81

  Alignments for each domain:
  == domain 1  score: 65.3 bits;  conditional E-value: 3.5e-21
                                    EEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE--HHHCTTSTCCCHHH CS
                     ATP_bind_3   2 vlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckklnikleiekvdvakkkgknleeaAR 81 
                                    vl+AvSgG+DS a+l +lak +  lg++l+a+hvd g+   s++ +++v+elc +l++++ + +++  +  g +l e AR
  gi|119720174|ref|YP_920669.1|  52 VLAAVSGGADSAAMLGVLAKASVALGFRLAAVHVDLGIEGFSEASRRAVEELCGSLGVPFAVVSLP--EVAGVGLPELAR 129
                                    799**************************************************************9..556999999999 PP

                                    HHHHHH...........HHHCHHCCT.CEEE---BHHHHHHHHHHHHCCT--CCHHH-S-SEEEETT..CCEE-CCCT-- CS
                     ATP_bind_3  82 elRYev...........lkealkkegievlllAhhadDqaEtfllrlargsglaglagikeaseias..irlvRPlLkvs 148
                                    ++R  v           ++ a+ + g++v++l+hhadD +  ++ ++  ++ + +la + +++e ++  +  vRPl++v+
  gi|119720174|ref|YP_920669.1| 130 RARRPVcsvcgavkrylVNVAAAEAGADVVALGHHADDLLAYAVKNFLFQRLP-ELAKLGPKTESTGglVGRVRPLYEVY 208
                                    99975422222211111445678899*************99988877664444.5555555554444237789******* PP

                                    HHHHHHHHHHTT---B-- CS
                     ATP_bind_3 149 keeleeylkekkikwveD 166
                                    k+e + y++ +++++ e 
  gi|119720174|ref|YP_920669.1| 209 KSEASLYARLSGLPFTEE 226
                                    *********999999885 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.2   1.2e-05     0.019       2     126 ..      51     165 ..      50     180 .. 0.68
   2 ?   -3.2   0.0       1.7   2.8e+03     159     179 ..     297     317 ..     291     321 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.2e-05
                  tRNA_Me_trans   2 kvvvalSgGVDSsvaaallkeqgyevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdfekeykekvfee 81 
                                    +v++a+SgG DS+  + +l+++     g+ l+ ++   + g e  +e+  + +e+ +  lg+p+ vv++ +     v   
  gi|119720174|ref|YP_920669.1|  51 RVLAAVSGGADSAAMLGVLAKASVA-LGFRLAAVHV--DLGIEGFSEASRRAVEELCGSLGVPFAVVSLPE-----VAGV 122
                                    799**********999999987654.4555555544..566677999999*****************9864.....4444 PP

                  tRNA_Me_trans  82 fleeyeeGrTPnPdvlCNkeiKfgallekakeelgadalatGHYa 126
                                     l e+++      + +C   +K   l++ a +e+gad +a GH a
  gi|119720174|ref|YP_920669.1| 123 GLPELARRARRPVCSVCG-AVKRY-LVNVAAAEAGADVVALGHHA 165
                                    444444432222344553.45533.44444444666666666665 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.7
                  tRNA_Me_trans 159 ealekllfPlgeltKeevrki 179
                                     +l+ l  P+g++ +e+vr+ 
  gi|119720174|ref|YP_920669.1| 297 LTLKALGRPMGDVAREKVREA 317
                                    56788888**********986 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1      0.35   5.8e+02      18      23 ..       4       9 ..       3      13 .. 0.79
   2 ?    0.9   0.1       0.2   3.3e+02      19      24 ..     136     141 ..     131     144 .. 0.60
   3 !   15.7   0.9     5e-06    0.0081      17      35 ..     278     296 ..     277     298 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.35
                                   E-TTT- CS
                           RecR 18 hCsrCg 23
                                   +Cs+Cg
  gi|119720174|ref|YP_920669.1|  4 RCSVCG 9 
                                   599997 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.2
                                    -TTT-- CS
                           RecR  19 CsrCgn 24 
                                    Cs+Cg 
  gi|119720174|ref|YP_920669.1| 136 CSVCGA 141
                                    666654 PP

  == domain 3  score: 15.7 bits;  conditional E-value: 5e-06
                                    EE-TTT--EESSSS-CCCC CS
                           RecR  17 rhCsrCgnlteedlCaICs 35 
                                    r C++Cg  +e +lC++C+
  gi|119720174|ref|YP_920669.1| 278 RACRVCGAPSEGELCSFCR 296
                                    57****************7 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   8.7e-05      0.14      20     133 ..      52     170 ..      43     228 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.7e-05
                   Asn_synthase  20 vGalLSGGlDSSliaalaarqsk...splktFsigfeekgsdea..kyakevaehlgtehtelvlteeellda.lpdviy 93 
                                    v a  SGG DS++   ++a+ s     +l ++++++  +g++ea  ++ +e++  lg++   + l   e++ + lp++++
  gi|119720174|ref|YP_920669.1|  52 VLAAVSGGADSAAMLGVLAKASValgFRLAAVHVDLGIEGFSEAsrRAVEELCGSLGVPFAVVSLP--EVAGVgLPELAR 129
                                    67889*************99988888778888888855777776226899*********5444444..455555****** PP

                   Asn_synthase  94 hleepfadrsaiplyllsrla.krkgvkvvLsGeGaDElfg 133
                                       +p+++     + +l + a  + g  vv  G+ aD l +
  gi|119720174|ref|YP_920669.1| 130 RARRPVCSVCGAVKRYLVNVAaAEAGADVVALGHHADDLLA 170
                                    9999999998888877777775799999**99999999874 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00064         1       2      64 ..      52     119 ..      51     133 .. 0.76
   2 ?    0.3   0.0      0.25   4.1e+02     109     187 ..     151     233 ..     145     256 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00064
                                    EEEE--SSHHHHHHHHHHHHH....-SEEEEEEEESS-T..TSHHHHHHHHHHHHT--.-EEEEE-GGG CS
                           QueC   2 avvllSGGlDSttvlalakke....gkevealtfdYgqr..hkkeleaakkiakelgveehkildldll 64 
                                    ++  +SGG DS+++l +  k+    g +++a+++d g     ++  +a+++++ +lgv    +++l  +
  gi|119720174|ref|YP_920669.1|  52 VLAAVSGGADSAAMLGVLAKAsvalGFRLAAVHVDLGIEgfSEASRRAVEELCGSLGV-PFAVVSLPEV 119
                                    56789*******998655443122258999*****99997777788899999999999.8888887755 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.25
                                    HHHHT-SEEEE---S-STT--GGGSHHHHHHHHHHHHHH.....HTS--EEE-TTTT--HHHHHHHHHHTTHHHHH-B-S CS
                           QueC 109 aealgaeaiiiGvneedfsgYPDcrdefvkalnkalnlg.....edkkieieaPlidlsKaeivklgkelgvpleetlsC 183
                                    a + ga+ +++G ++ d  +Y   ++  ++ l ++++lg     ++  +  + Pl+++ K+e    +   g+p+ e    
  gi|119720174|ref|YP_920669.1| 151 AAEAGADVVALGHHADDLLAYA-VKNFLFQRLPELAKLGpktesTGGLVGRVRPLYEVYKSEASLYARLSGLPFTEERCP 229
                                    6778899999999999999995.344445778888888877654444566678999999999888888888888887777 PP

                                    TTS. CS
                           QueC 184 Yege 187
                                    Y+++
  gi|119720174|ref|YP_920669.1| 230 YSPN 233
                                    7775 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1      0.14   2.3e+02       6      12 ..       4      10 ..       2      19 .. 0.83
   2 ?   10.7   0.2   0.00019      0.32       3      15 ..     132     145 ..     130     147 .. 0.84
   3 ?   -0.2   0.5      0.51   8.3e+02       6      12 ..     279     285 ..     277     290 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.14
                        zf-RRN7  6 pCgvCgc 12
                                   +C vCg 
  gi|119720174|ref|YP_920669.1|  4 RCSVCGE 10
                                   7****96 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00019
                        zf-RRN7   3 kgppCgvCgc.rsf 15 
                                    ++p+C vCg+ +++
  gi|119720174|ref|YP_920669.1| 132 RRPVCSVCGAvKRY 145
                                    89********6565 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.51
                        zf-RRN7   6 pCgvCgc 12 
                                    +C vCg+
  gi|119720174|ref|YP_920669.1| 279 ACRVCGA 285
                                    699**97 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.076   1.2e+02      20      28 ..       4      13 ..       1      20 [. 0.75
   2 ?   -0.3   0.1      0.88   1.4e+03      20      25 ..     135     140 ..     128     145 .. 0.80
   3 ?    5.7   0.1     0.011        18      18      42 ..     277     299 ..     266     301 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.076
                           C1_2 20 nCsaCgrk.i 28
                                   +Cs+Cg++ +
  gi|119720174|ref|YP_920669.1|  4 RCSVCGEPaV 13
                                   7*****9844 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.88
                           C1_2  20 nCsaCg 25 
                                     Cs+Cg
  gi|119720174|ref|YP_920669.1| 135 VCSVCG 140
                                    699998 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.011
                           C1_2  18 sfnCsaCgrkidgffYsCseCdfsl 42 
                                     + C++Cg +++g+   Cs C+ +l
  gi|119720174|ref|YP_920669.1| 277 PRACRVCGAPSEGE--LCSFCRLTL 299
                                    578*******9998..798898776 PP

>> C5HCH  NSD Cys-His rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00042      0.68       3      32 ..       4      33 ..       2      41 .. 0.89
   2 ?   -2.8   0.1       4.6   7.6e+03       4       9 ..     136     141 ..     134     142 .. 0.78
   3 ?    2.6   1.9     0.091   1.5e+02       3      18 ..     279     295 ..     278     298 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00042
                          C5HCH  3 qCsvCgkaatsfCefCPssFCkeHekGalv 32
                                   +CsvCg++a+++ e+  +  C  H +G + 
  gi|119720174|ref|YP_920669.1|  4 RCSVCGEPAVARVEYARKWLCGAHFAGYVE 33
                                   7***********************999765 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.6
                          C5HCH   4 CsvCgk 9  
                                    CsvCg+
  gi|119720174|ref|YP_920669.1| 136 CSVCGA 141
                                    899975 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.091
                          C5HCH   3 qCsvCgkaat.sfCefC 18 
                                     C vCg+++    C fC
  gi|119720174|ref|YP_920669.1| 279 ACRVCGAPSEgELCSFC 295
                                    5*****99863679999 PP

>> zf-HIT  HIT zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.2     0.021        34       3      12 ..       3      12 ..       1      13 [. 0.82
   2 ?    9.1   0.2    0.0007       1.1       1      14 [.     132     145 ..     132     146 .. 0.92
   3 ?    2.5   0.3     0.086   1.4e+02       3      12 ..     278     287 ..     276     289 .. 0.79
   4 ?    0.5   0.3      0.34   5.6e+02       3       9 ..     290     296 ..     288     300 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.021
                                   -B-TTT-SB- CS
                         zf-HIT  3 klCgvCgfpa 12
                                     C+vCg+pa
  gi|119720174|ref|YP_920669.1|  3 ARCSVCGEPA 12
                                   57*****986 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0007
                                    ---B-TTT-SB-SE CS
                         zf-HIT   1 prklCgvCgfpakY 14 
                                    +r++C+vCg+ ++Y
  gi|119720174|ref|YP_920669.1| 132 RRPVCSVCGAVKRY 145
                                    699*******9999 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.086
                                    -B-TTT-SB- CS
                         zf-HIT   3 klCgvCgfpa 12 
                                      C vCg+p+
  gi|119720174|ref|YP_920669.1| 278 RACRVCGAPS 287
                                    56*****986 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 0.34
                                    -B-TTT- CS
                         zf-HIT   3 klCgvCg 9  
                                    +lC++C 
  gi|119720174|ref|YP_920669.1| 290 ELCSFCR 296
                                    79****6 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1     0.013        21       3      14 ..       5      16 ..       5      19 .. 0.88
   2 ?    4.2   1.1     0.025        41      22      31 ..     133     142 ..     129     143 .. 0.86
   3 ?    1.6   0.2      0.17   2.7e+02       3      10 ..     280     287 ..     278     291 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.013
                                   -TTT--B-EEE- CS
                      Nudix_N_2  3 CsqCGtpvelri 14
                                   Cs CG+p   r+
  gi|119720174|ref|YP_920669.1|  5 CSVCGEPAVARV 16
                                   *******98887 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.025
                                    EEEETTTTEE CS
                      Nudix_N_2  22 RlvCpaCgti 31 
                                    R vC+ Cg++
  gi|119720174|ref|YP_920669.1| 133 RPVCSVCGAV 142
                                    89******98 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.17
                                    -TTT--B- CS
                      Nudix_N_2   3 CsqCGtpv 10 
                                    C+ CG+p 
  gi|119720174|ref|YP_920669.1| 280 CRVCGAPS 287
                                    99999985 PP

>> zf-C4_ClpX  ClpX C4-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.045        73       2       9 ..       4      11 ..       3      14 .. 0.87
   2 ?    1.2   0.0      0.22   3.5e+02       2       8 ..     135     141 ..     134     150 .. 0.87
   3 ?   -1.9   0.1         2   3.2e+03       2      10 ..     279     287 ..     278     288 .. 0.79
   4 ?    2.7   0.2     0.072   1.2e+02       3       7 ..     292     296 ..     290     300 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.045
                     zf-C4_ClpX  2 rCSFCgks 9 
                                   rCS Cg +
  gi|119720174|ref|YP_920669.1|  4 RCSVCGEP 11
                                   8*****87 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.22
                     zf-C4_ClpX   2 rCSFCgk 8  
                                     CS Cg 
  gi|119720174|ref|YP_920669.1| 135 VCSVCGA 141
                                    6****96 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 2
                     zf-C4_ClpX   2 rCSFCgkse 10 
                                     C  Cg + 
  gi|119720174|ref|YP_920669.1| 279 ACRVCGAPS 287
                                    6999**875 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.072
                     zf-C4_ClpX   3 CSFCg 7  
                                    CSFC 
  gi|119720174|ref|YP_920669.1| 292 CSFCR 296
                                    ****7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 2153.41
//
Query:       gi|119720175|ref|YP_920670.1|  [L=1113]
Description: glycoside hydrolase family protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-07   30.2   0.0    4.3e-07   29.5   0.0    1.2  1  Glyco_hydro_57  Glycosyl hydrolase family 57
     0.0043   17.6   3.5       0.76   10.4   0.6    3.3  2  VCBS            Repeat domain in Vibrio, Colwellia, Bradyrhiz


Domain annotation for each model (and alignments):
>> Glyco_hydro_57  Glycosyl hydrolase family 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.0   4.8e-11   4.3e-07      96     278 ..     292     477 ..     253     521 .. 0.75

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 4.8e-11
                                    HHHHHHHHHHHHHHHHHHT.TT-HHHHHHHHHHCTSEEEEEE-TT-B-GGG-S-HHHHHHHHHHHHHHHHHHHSS--SBE CS
                 Glyco_hydro_57  96 avlfnlaisgplleqiqkwlnkevlelfrelqesgqvElltspyyHpllpllpdsedieaqvkkarelyeeyfgqePrgf 175
                                     + + +++sg+l  ++  w ++ +   +r+l+ +g   +++ + ++ +++++ d    +    +++ + e +fg++P + 
  gi|119720175|ref|YP_920670.1| 292 RIPVCVHMSGTLAASYVWW-DPSIVAHLRSLAAKGLACIVGGTWAEYITAYFYD-NFNDPSFYLGKLYAEALFGYTPLTA 369
                                    356899**********999.********************************99.88889999***************** PP

                                    E-GGG-B--S..HHHHHHHTT--EEEE-C------------TTS-EE-TTS......-EEEE--CHH-TTTSGGG-.... CS
                 Glyco_hydro_57 176 wlpElavspe..ileilaelGfeylftdelaeiledkskespyrpyllkngg.....iavffRdreLsddigFryseqyp 248
                                    w pE+++++e   +++   + +  ++ d+  +  +++ + spy p + + ++     ++vff+d e+ +++  + ++   
  gi|119720175|ref|YP_920670.1| 370 WIPERTWDDErtGIAYTVSKHYYAVILDGNTHHDDWSPNTSPYKPHQYDPSKtggreLYVFFIDWEMQQLLLANTDGGLN 449
                                    *********95533444557788888999555555555559999876654445579********9998776555453333 PP

                                    ........TTSB..........-TT---TT CS
                 Glyco_hydro_57 249 leavddfinwlkkvkkaksevvtialdgEn 278
                                        ++ + w  +    ++ ++++a d E+
  gi|119720175|ref|YP_920670.1| 450 I-NLRRKLAWAATN-ADQQMLFLYADDWEK 477
                                    3.455555565532.226666666666666 PP

>> VCBS  Repeat domain in Vibrio, Colwellia, Bradyrhizobium and Shewanella
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.0   0.1     0.002        18      43      60 ..     680     697 ..     664     698 .. 0.81
   2 !   10.4   0.6   8.4e-05      0.76      37      60 ..     779     803 ..     745     804 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.002
                           VCBS  43 gtgvavgDlDgDGdlDll 60 
                                    g++  vgD+D DG+++ +
  gi|119720175|ref|YP_920670.1| 680 GASYLVGDFDWDGRPEAV 697
                                    455679*********987 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 8.4e-05
                           VCBS  37 lgg.sgggtgvavgDlDgDGdlDll 60 
                                    +++ +g  + +a+ D+DgDG++D++
  gi|119720175|ref|YP_920670.1| 779 SDAeGGVVVKLAAPDMDGDGRPDFY 803
                                    23323334468999*********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.73u 0.31s 00:00:01.04 Elapsed: 00:00:00.53
# Mc/sec: 6322.75
//
Query:       gi|119720176|ref|YP_920671.1|  [L=418]
Description: hypothetical protein Tpen_1270 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-13   50.9  20.6      5e-09   36.3   7.5    3.4  3  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
    1.6e-10   41.0  28.6    6.9e-06   26.2   1.1    3.9  3  Big_3_5          Bacterial Ig-like domain (group 3)
     0.0001   22.2   1.0     0.0011   19.0   0.5    2.4  2  CarbopepD_reg_2  CarboxypepD_reg-like domain
    0.00022   20.3   1.7     0.0003   19.9   1.7    1.1  1  IFT57            Intra-flagellar transport protein 57
    0.00031   20.5   2.1    0.00052   19.8   2.1    1.2  1  DUF745           Protein of unknown function (DUF745)
      0.002   18.2   0.2      0.017   15.3   0.1    2.3  2  MG4              Macroglobulin domain MG4
     0.0074   16.6   1.6       0.95    9.8   0.1    3.7  4  AglB_L1          Archaeal glycosylation protein B long periph
     0.0092   16.0   8.1     0.0092   16.0   8.1    3.8  4  Big_1            Bacterial Ig-like domain (group 1)
  ------ inclusion threshold ------
      0.041   13.9   0.1       0.24   11.5   0.1    2.2  2  CooC_C           CS1-pili formation C-terminal
      0.047   13.0   0.5      0.085   12.1   0.5    1.3  1  HemX             HemX, putative uroporphyrinogen-III C-methyl
       0.07   13.3   8.2        0.1   12.8   8.2    1.2  1  ATG16            Autophagy protein 16 (ATG16)
      0.077   11.9   5.4       0.11   11.3   5.4    1.1  1  Spc7             Spc7 kinetochore protein
       0.11   11.2   0.0       0.16   10.7   0.0    1.1  1  Sortilin-Vps10   Sortilin, neurotensin receptor 3,
       0.15   11.6   0.0       0.19   11.3   0.0    1.1  1  Exonuc_VII_L     Exonuclease VII, large subunit
       0.16   11.9   5.7       0.25   11.3   5.7    1.2  1  YscO             Type III secretion protein YscO
       0.24   11.8   3.9       0.36   11.2   3.9    1.1  1  DUF4200          Domain of unknown function (DUF4200)
       0.26   11.7   3.9       0.38   11.2   3.9    1.1  1  Fez1             Fez1
       0.37   10.9   3.6       0.63   10.2   3.6    1.2  1  Med9             RNA polymerase II transcription mediator com
       0.38   10.6   2.3       0.62    9.9   2.3    1.2  1  DUF1068          Protein of unknown function (DUF1068)
        0.4    9.7   2.7       0.57    9.2   2.7    1.1  1  Atg14            Vacuolar sorting 38 and autophagy-related su
       0.46   10.8   3.3       0.39   11.0   1.3    1.9  2  Cytomega_UL20A   Cytomegalovirus UL20A protein
       0.54   10.3   9.5        1.1    9.2   9.5    1.5  1  TMF_DNA_bd       TATA element modulatory factor 1 DNA binding
       0.57   10.3   6.6       0.85    9.7   6.6    1.1  1  ADIP             Afadin- and alpha -actinin-Binding
       0.64    9.7   8.6       0.95    9.1   8.6    1.1  1  Lebercilin       Ciliary protein causing Leber congenital ama
       0.65   10.1   3.5        5.2    7.2   0.6    2.2  2  TolA_bind_tri    TolA binding protein trimerisation
       0.68    9.3   4.9       0.97    8.7   4.9    1.1  1  GAS              Growth-arrest specific micro-tubule binding
       0.78    9.3   4.1        1.1    8.8   4.1    1.1  1  HAUS-augmin3     HAUS augmin-like complex subunit 3
        1.7    8.8   5.2        2.7    8.2   5.2    1.2  1  Cnn_1N           Centrosomin N-terminal motif 1
        5.8    7.3   9.3         13    6.2   8.7    1.8  1  CCDC-167         Coiled-coil domain-containing protein 167
        6.3    7.1   8.8         10    6.3   8.8    1.3  1  JIP_LZII         JNK-interacting protein  leucine zipper II


Domain annotation for each model (and alignments):
>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   7.5   8.3e-12     5e-09       1      81 [.      31     108 ..      31     109 .. 0.82
   2 !   17.0   0.8   8.8e-06    0.0052      16      78 ..     149     217 ..     138     220 .. 0.73
   3 ?    5.6   0.3     0.031        19       3      64 ..     231     295 ..     229     314 .. 0.66

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 8.3e-12
                CarboxypepD_reg   1 tisGrVtdasgapiagatVtvtnadtgtvastttdadGafrlrglpp....gtysvtvsapGyatatreevtltagqttt 76 
                                    t+ G+V+ ++g p aga+Vtv+  ++g++ast+td++G+++++ l+      t +vt+s  Gya +++     + ++ ++
  gi|119720176|ref|YP_920671.1|  31 TVWGYVKMPDGSPAAGASVTVS--AGGASASTVTDSTGKYKVD-LTVsstpVTVTVTASLGGYAGSAS----ASGEGVVR 103
                                    799*******************..8*****************8.544464477777779999999886....35555667 PP

                CarboxypepD_reg  77 lditL 81 
                                    +d++L
  gi|119720176|ref|YP_920671.1| 104 VDVVL 108
                                    77777 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 8.8e-06
                CarboxypepD_reg  16 gatVtvtn.adtgtvastttdadGafrlrglpp..gtysvtvsapG...yatatreevtltagqtttld 78 
                                     ++V+v + +++  + s+ t++dG+f++r   +  g  s+ + +pG   y ++t++ vt+ a+++t l 
  gi|119720176|ref|YP_920671.1| 149 AVKVVVVApNGSRYEVSVSTGSDGSFTVRIPLTsrGAWSIYAAFPGsdeYSPSTSQVVTVVAKEKTFLS 217
                                    45555554246667999***********9444479*******777622256777788999998888765 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.031
                CarboxypepD_reg   3 sGrVtda.sgapiagatVtvtnadtgt.vastttdadGafrlrglpp..gtysvtvsapGyatatr 64 
                                    sG+   a sg ++ ++ V++ n +t +   ++  + dG+f+ +  ++  g++ v++ + G   +++
  gi|119720176|ref|YP_920671.1| 231 SGSLAPApSG-AVVEVYVSIDNGSTWArLLNAPVGGDGSFSANLSTAvyGRILVKAVFRGTFDYAQ 295
                                    5555554244.56678888887555432599**********87555599******97777544443 PP

>> Big_3_5  Bacterial Ig-like domain (group 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7  13.0      0.12        72       5      79 ..      25      99 ..      14     107 .. 0.50
   2 !   26.2   1.1   1.1e-08   6.9e-06      33      87 ..     158     211 ..     135     214 .. 0.76
   3 !   19.6   0.7   1.3e-06   0.00075      13      88 ..     227     308 ..     217     310 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.12
                                   ETTSEEEEEEE--CCCC.TTS--EEEEEETTEE-SS-EE--TTS..EEEEEEE-SS-EEEEEEEEEE-TTS---S--E CS
                        Big_3_5  5 tagqtvtltatVtaasg.gtptGtVtftdggttlgtavllsanG..tAtltvsalaaGthsitAtYsGdanyaastss 79
                                   +a+ +vt+   V+  +g +++  +Vt+  gg++  t v+ s +G  ++ ltvs++ + t ++tA+  G a  a+++ +
  gi|119720176|ref|YP_920671.1| 25 SAQVPVTVWGYVKMPDGsPAAGASVTVSAGGASAST-VTDS-TGkyKVDLTVSST-PVTVTVTASLGGYAGSASASGE 99
                                   334444444455544442344446666666666533.3333.4422333344444.3466666666666666555555 PP

  == domain 2  score: 26.2 bits;  conditional E-value: 1.1e-08
                                    TTEE-SS-EE--TTSEEEEEEE-SS-EEEEEEEEEE-TTS---S--EEEEEEEES CS
                        Big_3_5  33 ggttlgtavllsanGtAtltvsalaaGthsitAtYsGdanyaastssavtvtVtk 87 
                                    +g  +   v + ++G+ t+ +++++ G+ si A + G++ y++sts+ vtv V+k
  gi|119720176|ref|YP_920671.1| 158 NGSRYEVSVSTGSDGSFTVRIPLTSRGAWSIYAAFPGSDEYSPSTSQVVTV-VAK 211
                                    66666666666779********************************98855.444 PP

  == domain 3  score: 19.6 bits;  conditional E-value: 1.3e-06
                                    EEE--CCCCTTS--.EEEEEE...TTEE-SS..-EE--TTSEEEEEEE-SS-EEEEEEEEEE-TTS---S--EEEEEEEE CS
                        Big_3_5  13 tatVtaasggtptG.tVtftd...ggttlgt..avllsanGtAtltvsalaaGthsitAtYsGdanyaastssavtvtVt 86 
                                     ++V+++ +++p+G  V++++   +g t +   ++++ ++G+ ++++s+   G   ++A++ G+ +ya+s +++v+v+V+
  gi|119720176|ref|YP_920671.1| 227 IVQVSGSLAPAPSGaVVEVYVsidNGSTWARllNAPVGGDGSFSANLSTAVYGRILVKAVFRGTFDYAQSETAPVAVEVS 306
                                    5778888888899933456655544433322225566789***************************************8 PP

                                    S- CS
                        Big_3_5  87 ka 88 
                                    ++
  gi|119720176|ref|YP_920671.1| 307 SP 308
                                    75 PP

>> CarbopepD_reg_2  CarboxypepD_reg-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.5   1.8e-06    0.0011       3      56 ..      34      91 ..      32     109 .. 0.73
   2 ?    1.1   0.0      0.65   3.9e+02      13      39 ..     149     177 ..     138     219 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.8e-06
                CarbopepD_reg_2  3 GtVvdketkeplpgatVyv..kgtkkgtvTdenGnFelk...nlpagkytLvvsyvGyk 56
                                   G V+   ++ p +ga+V+v   g ++ tvTd+ G+++++   + ++ ++t+++s  Gy 
  gi|119720176|ref|YP_920671.1| 34 GYVKMP-DGSPAAGASVTVsaGGASASTVTDSTGKYKVDltvSSTPVTVTVTASLGGYA 91
                                   666654.468999987777326689************9852233345677777777876 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.65
                CarbopepD_reg_2  13 plpgatVyvkgt..kkgtvTdenGnFelk 39 
                                    ++ ++ V  +g+  ++ ++T ++G+F+++
  gi|119720176|ref|YP_920671.1| 149 AVKVVVVAPNGSryEVSVSTGSDGSFTVR 177
                                    55555555555522467789999999986 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   1.7     5e-07    0.0003     255     323 ..     314     382 ..     310     386 .. 0.95

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 5e-07
                          IFT57 255 sktlekiesrEkylnsqleellqeyreaqeelsevkekykqlsegvseltrelaeiseelekvkqemee 323
                                    +++ e++++rEk ln+ le l +e  e+++  +e+k +++  +++v++++r l++++ el  +  e+e+
  gi|119720176|ref|YP_920671.1| 314 TQENERLKAREKALNETLERLSAEVGELRRLSDELKSSLSSCNATVEARERALENLERELALLRGELEK 382
                                    7889********************************************************999998876 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   2.1   8.7e-07   0.00052     101     177 ..     319     395 ..     306     398 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 8.7e-07
                         DUF745 101 qaqqqlealkallkaakenlenaeqvaagaqqelaektqlleaAkkRveeLkkqlkearkdlektkkaAykAacAAq 177
                                      ++  +al+++l+  ++++ ++++++++ +++l++ ++ +ea ++ +e+L+++l+  r +lekt+  Ay A  AA+
  gi|119720176|ref|YP_920671.1| 319 RLKAREKALNETLERLSAEVGELRRLSDELKSSLSSCNATVEARERALENLERELALLRGELEKTRLLAYAAVPAAA 395
                                    56677799************************************9***************************99996 PP

>> MG4  Macroglobulin domain MG4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   2.8e-05     0.017      15      77 ..      29      85 ..      26     100 .. 0.73
   2 ?   -0.0   0.0       1.7     1e+03      29      61 ..     144     177 ..     137     212 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.8e-05
                            MG4 15 PfsikVlvkdpdgspaknvpVkiealkseteekeslttdedGtakfsintpedaksltitvkt 77
                                   P ++  +vk pdgspa++  V+++a +     + s  t  d t k  ++++ +++ +t+tv+ 
  gi|119720176|ref|YP_920671.1| 29 PVTVWGYVKMPDGSPAAGASVTVSA-G-----GASASTVTDSTGKYKVDLTVSSTPVTVTVTA 85
                                   6677778******************.5.....3444455556666666667777777777765 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1.7
                            MG4  29 paknvpVkiealk.seteekeslttdedGtakfs 61 
                                    pa +  Vk+ ++  +++ ++ s+ t +dG   + 
  gi|119720176|ref|YP_920671.1| 144 PAMQAAVKVVVVApNGSRYEVSVSTGSDGSFTVR 177
                                    5555555555533335666666677777754444 PP

>> AglB_L1  Archaeal glycosylation protein B long peripheral domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1       1.4   8.4e+02      59      82 ..      59      82 ..      40      99 .. 0.70
   2 !    9.8   0.1    0.0016      0.95       3      52 ..     137     184 ..     135     219 .. 0.73
   3 ?    1.2   0.0      0.76   4.6e+02       5      46 ..     231     273 ..     228     286 .. 0.82
   4 ?    1.1   0.0      0.85   5.1e+02       9      36 ..     270     299 ..     266     302 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 1.4
                                   SSSSEESS-EEEEETTEEEEE--- CS
                        AglB_L1 59 nssveaagpYevtagnvtaeveVp 82
                                   ++ +  +g+Y+v    +++ v+V+
  gi|119720176|ref|YP_920671.1| 59 STVTDSTGKYKVDLTVSSTPVTVT 82
                                   334456777777776666666555 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0016
                                    EEEEEBSSSSEEEEEEEEE-TTS-EEEEEEEEE.-BTTEEEEEE---SS. CS
                        AglB_L1   3 titGsaeagatvtasveletnqgrtftYrqeaeadedGefeltvPYsteg 52 
                                     ++G+ ++  ++ ++v +   +g   +Y+ ++ +++dG+f++++P    g
  gi|119720176|ref|YP_920671.1| 137 LVQGRLSPAMQAAVKVVVVAPNG--SRYEVSVSTGSDGSFTVRIPLTSRG 184
                                    56777777766666666666544..689999999***********87776 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.76
                                    EEE.BSSSSEEEEEEEEE-TTS-EEEEEEEEE.-BTTEEEEEE CS
                        AglB_L1   5 tGs.aeagatvtasveletnqgrtftYrqeaeadedGefeltv 46 
                                    +Gs a+a+  ++++v +++++g t+    +a ++ dG+f+  +
  gi|119720176|ref|YP_920671.1| 231 SGSlAPAPSGAVVEVYVSIDNGSTWARLLNAPVGGDGSFSANL 273
                                    56524556889999999999999999999999*******9766 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.85
                                    SSS..SEEEEEEEEE-TTS-EEEEEEEEE. CS
                        AglB_L1   9 eag..atvtasveletnqgrtftYrqeaea 36 
                                    +a+  + v+ ++ ++     tf+Y q+ +a
  gi|119720176|ref|YP_920671.1| 270 SANlsTAVYGRILVKAVFRGTFDYAQSETA 299
                                    45555889999999999999******9876 PP

>> Big_1  Bacterial Ig-like domain (group 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   8.1   1.5e-05    0.0092      13      64 .]      36      85 ..      23      85 .. 0.86
   2 ?    6.4   0.1     0.015       9.2      24      53 ..     150     179 ..     145     190 .. 0.84
   3 ?   -1.7   0.3       5.1     3e+03      24      50 ..     204     230 ..     199     233 .. 0.69
   4 ?    0.1   0.0       1.3     8e+02      25      64 .]     244     285 ..     241     285 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.5e-05
                          Big_1 13 vkDangnpvagatVtfsvsggalsassgtTdanGkatvtlt.stkagtvtvtA 64
                                   vk  +g p aga+Vt+s+ g++   +s++Td+ Gk+ v lt s+++ tvtvtA
  gi|119720176|ref|YP_920671.1| 36 VKMPDGSPAAGASVTVSAGGAS---ASTVTDSTGKYKVDLTvSSTPVTVTVTA 85
                                   666789***********99955...599************9899999999998 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.015
                          Big_1  24 atVtfsvsggalsassgtTdanGkatvtlt 53 
                                    ++V + +++g+  + s+ T+++G +tv + 
  gi|119720176|ref|YP_920671.1| 150 VKVVVVAPNGSRYEVSVSTGSDGSFTVRIP 179
                                    6899999999999*************9875 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 5.1
                          Big_1  24 atVtfsvsggalsassgtTdanGkatv 50 
                                    + Vt+ +   + ++ s+++ a G+++v
  gi|119720176|ref|YP_920671.1| 204 QVVTVVAKEKTFLSVSARSPAPGIVQV 230
                                    556666666666688888888888777 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 1.3
                          Big_1  25 tVtfsvsggals..assgtTdanGkatvtltstkagtvtvtA 64 
                                    +V +s+++g++     ++  + +G ++++l+  + g   v+A
  gi|119720176|ref|YP_920671.1| 244 EVYVSIDNGSTWarLLNAPVGGDGSFSANLSTAVYGRILVKA 285
                                    688888887777687888888999999999999888776665 PP

>> CooC_C  CS1-pili formation C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1    0.0004      0.24       8      64 ..      21      81 ..      19     107 .. 0.81
   2 ?   -1.5   0.0       4.5   2.7e+03      42      55 ..     164     178 ..     138     182 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0004
                         CooC_C  8 vlevsvkktvtviGrlvdedgqplanakil....nhagvavteedGvFtlevdakapsltv 64
                                   ++++s++  vtv G ++ +dg+p a+a++     + ++ +vt++ G ++++++  ++  tv
  gi|119720176|ref|YP_920671.1| 21 TRNASAQVPVTVWGYVKMPDGSPAAGASVTvsagGASASTVTDSTGKYKVDLTVSSTPVTV 81
                                   678899999******************9863333556689999******998776665555 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 4.5
                         CooC_C  42 vavte.edGvFtlev 55 
                                    v+v+  +dG Ft+ +
  gi|119720176|ref|YP_920671.1| 164 VSVSTgSDGSFTVRI 178
                                    445545688888866 PP

>> HemX  HemX, putative uroporphyrinogen-III C-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.5   0.00014     0.085      34     112 ..     314     389 ..     300     391 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00014
                           HemX  34 taevaelqqqlaaleqqlaqveaekeqkqeleerlqqlaeklealekeleqlqkqleelqqqlskvsgaerkdWlLaeA 112
                                    t+e+++l+ + +al+++l++   + ++  el +  ++l+++l++ ++++e+ +++le+l+++l+ + g+ +k++lLa A
  gi|119720176|ref|YP_920671.1| 314 TQENERLKAREKALNETLER---LSAEVGELRRLSDELKSSLSSCNATVEARERALENLERELALLRGELEKTRLLAYA 389
                                    45556666666666666666...55556666777777888899999999999999999999999999999999999866 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   8.2   0.00017       0.1     123     180 ..     315     372 ..     302     382 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00017
                          ATG16 123 erlaeleaeraaletklkdreeelrekeklvqdlqDElsaLqlqlnqaEeklrklekE 180
                                    ++ ++l+a+ +al++ l+++ +e+ e+++l ++l+  ls+ + +++ +E +l++le+E
  gi|119720176|ref|YP_920671.1| 315 QENERLKAREKALNETLERLSAEVGELRRLSDELKSSLSSCNATVEARERALENLERE 372
                                    67789999999******************************************99998 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   5.4   0.00019      0.11     165     239 ..     313     383 ..     304     390 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00019
                           Spc7 165 ldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieel 239
                                    l++  ++l++++++l+e+le+l +++ el  +      el+++l++++a++e++++ l++l+++l+ l+ ++e++
  gi|119720176|ref|YP_920671.1| 313 LTQENERLKAREKALNETLERLSAEVGELRRLS----DELKSSLSSCNATVEARERALENLERELALLRGELEKT 383
                                    556666777777777777777777666655543....35677777777777777777777777777777666654 PP

>> Sortilin-Vps10  Sortilin, neurotensin receptor 3,
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00027      0.16     353     395 ..     221     261 ..     204     264 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00027
                                    --TTSTT-EEEEEEEESSHHSS.S-EEEEESSSSSS-EEEESS CS
                 Sortilin-Vps10 353 SspsApGlimgvGnvGkslksyeeadtfiSrDaGltWkevlkg 395
                                     sp ApG++   G++    +     ++++S D G tW + l+ 
  gi|119720176|ref|YP_920671.1| 221 RSP-APGIVQVSGSLAPAPSGA-VVEVYVSIDNGSTWARLLNA 261
                                    356.***************996.9*************998875 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00032      0.19     165     250 ..     292     377 ..     230     409 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00032
                   Exonuc_VII_L 165 eekkqrleklasrlkspee.llerkrqrldeleerleralkkqlkkkrerleelkerlkekleekkerlkklkerlelle 243
                                    + ++++   +a +++sp+e ll+++++rl+  e+ l++ + ++l+++  +l++l+++lk++l++ +++++++++ le+le
  gi|119720176|ref|YP_920671.1| 292 DYAQSETAPVAVEVSSPRElLLTQENERLKAREKALNE-TLERLSAEVGELRRLSDELKSSLSSCNATVEARERALENLE 370
                                    55555556666666777774566667777777777777.66677777777777777776555555555555544444333 PP

                   Exonuc_VII_L 244 ekkerle 250
                                    ++   l+
  gi|119720176|ref|YP_920671.1| 371 RELALLR 377
                                    3333333 PP

>> YscO  Type III secretion protein YscO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   5.7   0.00042      0.25      63     122 ..     326     385 ..     302     397 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00042
                                    --HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           YscO  63 vllkelekvkqqvalLrekeaelekqveeakqqleaerealrqarkelqearraveKfae 122
                                    +l + le++ ++v+ Lr  + el++ +   ++++ea ++al+++++el+  r ++eK   
  gi|119720176|ref|YP_920671.1| 326 ALNETLERLSAEVGELRRLSDELKSSLSSCNATVEARERALENLERELALLRGELEKTRL 385
                                    45688***********************************************99999654 PP

>> DUF4200  Domain of unknown function (DUF4200)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   3.9   0.00061      0.36      24      92 ..     315     383 ..     304     387 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00061
                        DUF4200  24 rleealkqreeelekkeqeleedllkfdkflkendakraralkkaeeerklkkekeaeikklkaeietl 92 
                                    + +e+lk re++l+++ ++l  ++ ++ +   e ++  +  +  +e  +++ ++ e+e++ l+ e+e+ 
  gi|119720176|ref|YP_920671.1| 315 QENERLKAREKALNETLERLSAEVGELRRLSDELKSSLSSCNATVEARERALENLERELALLRGELEKT 383
                                    567899*********************************************************999975 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   3.9   0.00063      0.38      72     148 ..     314     384 ..     295     389 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00063
                           Fez1  72 enelqrkkseaellrekvekleeelkelreelselsleeeeaalesdeakaqrqeaeeleelkreverlraeLkeer 148
                                     +e +r k++++ l+e++e+l++e+ elr+ ls+  +++ ++++++ ea+     +++le+l+re++ lr+eL++ r
  gi|119720176|ref|YP_920671.1| 314 TQENERLKAREKALNETLERLSAEVGELRR-LSDELKSSLSSCNATVEAR-----ERALENLERELALLRGELEKTR 384
                                    678899999999****************99.5553433333333333322.....3578899999999999998866 PP

>> Med9  RNA polymerase II transcription mediator complex subunit 9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   3.6    0.0011      0.63      14      75 ..     324     382 ..     314     385 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0011
                           Med9  14 ekdpnlsskdletktgelrhkLkkarelirelpgidrsveeqeaeieeleeqlakKrelLkk 75 
                                    ek+ n + + l++++gelr   ++ ++ +++    + +ve +e+ +e+le +la  r  L+k
  gi|119720176|ref|YP_920671.1| 324 EKALNETLERLSAEVGELRRLSDELKSSLSS---CNATVEARERALENLERELALLRGELEK 382
                                    6777888999*********9999****9999...9*******************99987776 PP

>> DUF1068  Protein of unknown function (DUF1068)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   2.3     0.001      0.62      90     146 ..     317     373 ..     298     382 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.001
                        DUF1068  90 seelklreaeaeekqkradvalleakklasqYqkeAdKCnsgmetcEeaREkaeaal 146
                                    +e lk re+  +e+ +r  + + e ++l+ + +     Cn+++e  E a E  e +l
  gi|119720176|ref|YP_920671.1| 317 NERLKAREKALNETLERLSAEVGELRRLSDELKSSLSSCNATVEARERALENLEREL 373
                                    5789***************************************99888888877766 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   2.7   0.00095      0.57      51     120 ..     313     382 ..     294     390 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00095
                          Atg14  51 gkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklkkRrsdles 120
                                     ++e+e+l++++k +++ le+l +++ +lr+   elk +ls+ ++ +e++ + l+ l ++l+  r +le+
  gi|119720176|ref|YP_920671.1| 313 LTQENERLKAREKALNETLERLSAEVGELRRLSDELKSSLSSCNATVEARERALENLERELALLRGELEK 382
                                    4455677888888888888888888888888888888888888888888888888888888777777654 PP

>> Cytomega_UL20A  Cytomegalovirus UL20A protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   1.3   0.00065      0.39       3      76 ..       4      73 ..       1      84 [. 0.79
   2 ?   -2.0   0.0       7.3   4.4e+03      36      47 ..     165     176 ..     148     206 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00065
                 Cytomega_UL20A  3 rrlwilsllavtltvalaapsqkskrsvtveqpststnsdgnttpsknvtlsqggsttdgdedysggdydvlit 76
                                   rr++ l lla  l+va aa  + s   v v         dg  +    vt+s gg+++    d s g y v +t
  gi|119720176|ref|YP_920671.1|  4 RRVYALVLLA--LAVAYAATRNASA-QVPVTVWGYVKMPDGSPAAGASVTVSAGGASASTVTD-STGKYKVDLT 73
                                   7777777776..7899998877664.4666667788899****************99988877.6678887665 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 7.3
                 Cytomega_UL20A  36 ststnsdgnttp 47 
                                    s st sdg  t 
  gi|119720176|ref|YP_920671.1| 165 SVSTGSDGSFTV 176
                                    667777776654 PP

>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   9.5    0.0019       1.1      17      67 ..     313     370 ..     312     383 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0019
                     TMF_DNA_bd  17 LmeEGekLskkelklnntikkLrkknkelekeikelk.......kkleklekeleele 67 
                                    L +E e+L++ e +ln+t+ +L +++ el    +elk         +e  e+ le+le
  gi|119720176|ref|YP_920671.1| 313 LTQENERLKAREKALNETLERLSAEVGELRRLSDELKsslsscnATVEARERALENLE 370
                                    789***************************9999999444444444455555555555 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   6.6    0.0014      0.85      54     122 ..     316     384 ..     309     389 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0014
                           ADIP  54 qreslnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrlk 122
                                    ++e l+++ + l+ ++erl++++  l + + +l++ l++ +a+    e++l++le+ l  ++ el++++
  gi|119720176|ref|YP_920671.1| 316 ENERLKAREKALNETLERLSAEVGELRRLSDELKSSLSSCNATVEARERALENLERELALLRGELEKTR 384
                                    455566666666666666666666666666666666666666666666666666666666666666665 PP

>> Lebercilin  Ciliary protein causing Leber congenital amaurosis disease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   8.6    0.0016      0.95      83     155 ..     317     381 ..     304     387 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0016
                     Lebercilin  83 erelekklkekeaellrlkdklkklkkLsedknLaereeLqkkLeeleakleekeekikeLerkleleeksfr 155
                                    +++l+ + k  ++ l+rl+ ++ +l++Ls        +eL++ L++ +a++e++e+ +++Ler+l l+  + +
  gi|119720176|ref|YP_920671.1| 317 NERLKAREKALNETLERLSAEVGELRRLS--------DELKSSLSSCNATVEARERALENLERELALLRGELE 381
                                    33344445555555666666666666665........9****************************9987765 PP

>> TolA_bind_tri  TolA binding protein trimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.2      0.13        80      23      48 ..     327     352 ..     313     364 .. 0.76
   2 ?    7.2   0.6    0.0088       5.2      25      43 ..     364     382 ..     361     385 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.13
                  TolA_bind_tri  23 lqqqlealqqelreLRGqiEelqyql 48 
                                    l + le+l++e+ eLR   +el+  l
  gi|119720176|ref|YP_920671.1| 327 LNETLERLSAEVGELRRLSDELKSSL 352
                                    66778889999999987777776655 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0088
                  TolA_bind_tri  25 qqlealqqelreLRGqiEe 43 
                                    + le+l++el+ LRG++E+
  gi|119720176|ref|YP_920671.1| 364 RALENLERELALLRGELEK 382
                                    5699**************7 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   4.9    0.0016      0.97      46     117 ..     314     382 ..     303     384 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0016
                            GAS  46 ekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrfek 117
                                    ++e + ++++ k l+e+L+++ +ev eLr+     ++ k+sl + +a ++  e+ l++l+ e   l+ ++ek
  gi|119720176|ref|YP_920671.1| 314 TQENERLKAREKALNETLERLSAEVGELRRLS---DELKSSLSSCNATVEARERALENLERELALLRGELEK 382
                                    67888899999999999999999999999864...5567799999999999999999999999888877766 PP

>> HAUS-augmin3  HAUS augmin-like complex subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   4.1    0.0018       1.1      63     132 ..     314     383 ..     302     395 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0018
                   HAUS-augmin3  63 qedvellevileeeeesleaLeqelqeLqkekalklkrlnkLqvqaaslqqelrkleeeekeakkklkea 132
                                    ++++e l++  ++++e+le L +e+ eL++  + + + l+  ++++ ++++ l++le+e    +++l+++
  gi|119720176|ref|YP_920671.1| 314 TQENERLKAREKALNETLERLSAEVGELRRLSDELKSSLSSCNATVEARERALENLERELALLRGELEKT 383
                                    467778889999999********************************************99999999986 PP

>> Cnn_1N  Centrosomin N-terminal motif 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   5.2    0.0045       2.7      12      72 ..     313     372 ..     312     373 .. 0.95

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0045
                         Cnn_1N  12 LkKENFdLKLriyfLeerleklseeqkeellkenielkveveslqkelkekkkllreaeka 72 
                                    L+ EN  LK r + L+e le+ls  ++ el +   elk  + s   +++++++ l+++e++
  gi|119720176|ref|YP_920671.1| 313 LTQENERLKAREKALNETLERLSA-EVGELRRLSDELKSSLSSCNATVEARERALENLERE 372
                                    789*********************.9999***************************99987 PP

>> CCDC-167  Coiled-coil domain-containing protein 167
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   8.7     0.022        13       7      74 ..     318     389 ..     313     395 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.022
                       CCDC-167   7 dkleeklascrerLeaverrl.rkeelseeeResleeEeaslkeq...leenekeLksLrkeNrksmllsva 74 
                                    ++l  + ++++e Le++  ++ + ++ls+e + sl    a+++ +   le+ e+eL+ Lr+e  k++ll+ a
  gi|119720176|ref|YP_920671.1| 318 ERLKAREKALNETLERLSAEVgELRRLSDELKSSLSSCNATVEAReraLENLERELALLRGELEKTRLLAYA 389
                                    5666666777778888877764679999999***997777776433339*******************9976 PP

>> JIP_LZII  JNK-interacting protein  leucine zipper II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   8.8     0.018        10      10      70 ..     313     373 ..     310     374 .. 0.97

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.018
                       JIP_LZII  10 LikENteLletknaLnvvkddLIarvdeLtsereiLreEleslqkakerlesrikelEeel 70 
                                    L +EN++L++   aLn   + L a+v eL    + L++ l+s++++ e+ e  +++lE el
  gi|119720176|ref|YP_920671.1| 313 LTQENERLKAREKALNETLERLSAEVGELRRLSDELKSSLSSCNATVEARERALENLEREL 373
                                    679*******************************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1376  (0.0767472); expected 358.6 (0.02)
Passed bias filter:                      986  (0.0549947); expected 358.6 (0.02)
Passed Vit filter:                       227  (0.0126611); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              30  [number of targets reported over threshold]
# CPU time: 0.72u 0.31s 00:00:01.03 Elapsed: 00:00:00.46
# Mc/sec: 2714.78
//
Query:       gi|119720177|ref|YP_920672.1|  [L=272]
Description: beta-lactamase domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.7e-13   49.1   0.8    1.5e-12   47.9   0.8    1.7  1  Lactamase_B    Metallo-beta-lactamase superfamily
    2.2e-10   40.4   0.0    3.4e-10   39.8   0.0    1.4  1  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.025   14.5   0.0      0.043   13.7   0.0    1.3  1  Lactamase_B_3  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.9   0.8   2.5e-16   1.5e-12       8      67 ..      63     120 ..      61     194 .. 0.84

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 2.5e-16
                                    EEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTH CS
                    Lactamase_B   8 syliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglvea 67 
                                    s+++e +g  +L+D+G ++         a+lg+++ ++dav+++H+H+DH+Ggl+ ++ +
  gi|119720177|ref|YP_920672.1|  63 SVYVEAGGARLLFDAGPEPGVLERN--AARLGVDLSRIDAVVVSHGHYDHVGGLRLFAGR 120
                                    899***************9998875..79**************************99876 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.8   0.0   5.7e-14   3.4e-10       2      65 ..      72     129 ..      71     160 .. 0.80

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 5.7e-14
                                    EEEES--TT..HHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHH CS
                  Lactamase_B_2   2 riLiDagpd..lrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkg 65 
                                    r+L+Dagp+  +++  + a+    l  +l++idaV+++h+HyDH+ gl  ++    + l++y+p+g
  gi|119720177|ref|YP_920672.1|  72 RLLFDAGPEpgVLER-NAAR----LGVDLSRIDAVVVSHGHYDHVGGLRLFAG---RGLRVYVPAG 129
                                    89*******665555.3333....67899****************99777766...4599999976 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   7.2e-06     0.043       9      50 ..      63     111 ..      60     130 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.2e-06
                  Lactamase_B_3   9 sflletagarilvDPf.......kanlgyeppa......eeaDlvlisqaledHa 50 
                                    s+ +e +gar+l D +       +      + a       ++D+v++s+++ dH 
  gi|119720177|ref|YP_920672.1|  63 SVYVEAGGARLLFDAGpepgvleR------NAArlgvdlSRIDAVVVSHGHYDHV 111
                                    6789999*******9944444432......3335555669**************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1829.22
//
Query:       gi|119720178|ref|YP_920673.1|  [L=454]
Description: CRISPR-associated DxTHG family protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.9e-16   59.0   0.0    1.6e-14   54.3   0.0    2.0  2  Cas_DxTHG  CRISPR-associated (Cas) DxTHG family


Domain annotation for each model (and alignments):
>> Cas_DxTHG  CRISPR-associated (Cas) DxTHG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.3   0.0   8.7e-19   1.6e-14       1     149 [.       6     213 ..       6     242 .. 0.78
   2 !    2.7   0.0    0.0042        75     346     359 .]     374     407 ..     329     407 .. 0.62

  Alignments for each domain:
  == domain 1  score: 54.3 bits;  conditional E-value: 8.7e-19
                      Cas_DxTHG   1 vlisflGt.gnykevkYelkeeeeeeketsfvqeallell.aekedpdkvvilltdtlad.................kea 61 
                                    +l++++G+  ++++++Yel    + e+ +sf++  +l  + ++ +++++ ++l+ ++l+d                    
  gi|119720178|ref|YP_920673.1|   6 LLLATWGNpAQWNTARYELG---G-ESDESFTSLGILCRHlSKSGCEARALVLVLESLLDakldkepdgkrpgyaylY-- 79 
                                    599*****999*******43...3.567888888887666799*****************888776666655555552.. PP

                      Cas_DxTHG  62 eek.................eeaak.lkeeleelle......iekvdveiipgggte..............ee.lweife 102
                                      +                  ea + l++ +e l +         v ve++p +g++              +  l+    
  gi|119720178|ref|YP_920673.1|  80 --ErreelarlrglllegryGEAVEgLRSVVEGLAKsagagcSGGVAVEVLPAIGSFgggvrfagdvrnfhSFaLLAAAR 157
                                    ..055557778888888888556666999998776689999777888**************9998887666555666777 PP

                      Cas_DxTHG 103 kllekleendeiilDiThGfrylPvla.........llalaylrnvknltikgi.yY 149
                                    ++l+  +  ++i++D+ThG++++P++a         l++la  r+v   +++++ +Y
  gi|119720178|ref|YP_920673.1| 158 EVLRGGPAPSKIVVDLTHGVNFMPTYAyevareaasLSLLAGSRSVE-MEVYNSdPY 213
                                    777777777************************77777777777776.778888444 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.0042
                      Cas_DxTHG 346 k....................lsniRNdiaHaGl 359
                                                          +++R +iaHaGl
  gi|119720178|ref|YP_920673.1| 374 LiaqelsqveagrfeeaayprKPDKRIMIAHAGL 407
                                    03333333334456666777789**********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 3070.10
//
Query:       gi|119720179|ref|YP_920674.1|  [L=318]
Description: ABC transporter related [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.6e-22   78.3   0.0    1.1e-21   77.8   0.0    1.3  1  ABC_tran  ABC transporter
    4.2e-10   39.9   0.4    5.4e-07   29.7   0.0    2.1  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
  ------ inclusion threshold ------
      0.034   14.0   0.1         12    5.8   0.1    2.4  2  MobB      Molybdopterin guanine dinucleotide synthesis protei
      0.085   13.6   0.0       0.19   12.4   0.0    1.7  1  DUF4162   Domain of unknown function (DUF4162)
       0.12   12.6   0.0        0.2   11.8   0.0    1.7  1  AAA_33    AAA domain
       0.14   12.6   0.1       0.24   11.9   0.1    1.3  1  AAA_23    AAA domain
       0.15   11.6   1.0       0.33   10.5   1.0    1.5  1  SRP54     SRP54-type protein, GTPase domain
       0.15   11.4   0.1        7.9    5.8   0.0    2.2  2  SMC_N     RecF/RecN/SMC N terminal domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.8   0.0   4.9e-25   1.1e-21       1     136 [.      32     175 ..      32     176 .. 0.94

  Alignments for each domain:
  == domain 1  score: 77.8 bits;  conditional E-value: 4.9e-25
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren. 79 
                                    l++vs+++++ge+v++vG nGaGK+t +++  g l p++G++ +dg +++e ++ ++++++g++p+ p + +e+++ +  
  gi|119720179|ref|YP_920674.1|  32 LEDVSFSVRNGEVVGFVGLNGAGKTTTIRITVGVLPPDAGDVFIDGYSVSE-DKVEASARVGWVPELPIFESEYRALDYf 110
                                    689************************************************.8888999***************988889 PP

                                    ............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    ............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                e+++   ++ +++g+ e +++++    +++S+G+k+r ala +l+++p+ +l+DE  
  gi|119720179|ref|YP_920674.1| 111 aylagyygysegEARRLGRELFERVGIGEAANKRL----EEFSQGMKKRFALAVSLINDPPNFLFDEVL 175
                                    ********887555555899***************....****************************75 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.4    0.0013       2.9       2      18 ..      45      61 ..      44      88 .. 0.84
   2 !   29.7   0.0   2.4e-10   5.4e-07     235     298 ..     146     206 ..     138     211 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0013
                         AAA_21  2 nvliGpNgsGKSnLLda 18
                                    +++G Ng+GK++ +++
  gi|119720179|ref|YP_920674.1| 45 VGFVGLNGAGKTTTIRI 61
                                   579**********9997 PP

  == domain 2  score: 29.7 bits;  conditional E-value: 2.4e-10
                         AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHS 298
                                     e+S+G+k+ +al+++l+ +++    +l+DE+ ngL+P+ ++ + +l+ e ++ g  v++++H 
  gi|119720179|ref|YP_920674.1| 146 EEFSQGMKKRFALAVSLINDPPN---FLFDEVLNGLDPQGIAFFRGLVQEFRKAGKAVLFSSHI 206
                                    689******************66...************8888888888888888889******5 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.1    0.0052        12       1      22 [.      44      65 ..      44      71 .. 0.85
   2 ?    5.7   0.0    0.0058        13      18      40 ..     281     303 ..     280     306 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0052
                           MobB  1 vlgivgksgsGKTtLleklipe 22
                                   v+g+vg +g+GKTt +   + +
  gi|119720179|ref|YP_920674.1| 44 VVGFVGLNGAGKTTTIRITVGV 65
                                   689***********99776655 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0058
                           MobB  18 klipelkarglrvgtiKhahhgf 40 
                                     l++el a g+rv+ +K +++++
  gi|119720179|ref|YP_920674.1| 281 SLVAELVAAGYRVAEVKRSEKSL 303
                                    699**************998765 PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   8.7e-05      0.19       3      81 .]     231     311 ..     230     311 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.7e-05
                                    HHHHHTTS-SSEEE.EE.-------..--.-EEEE-TTS-EEEEE--.-----------.----EEEEEEEE---HHHHH CS
                        DUF4162   3 leeiKrsygknrie.ve.adaeelleepg.veeveeeggelelkled.eeaanellkal.tsgveirsFeeeePsLndIF 77 
                                     +ei+r+  ++ ++ v+   ++ ++++ +   e e++g+   l +++ + ++++l ++l ++g+++ +++  e sL++ F
  gi|119720179|ref|YP_920674.1| 231 MDEIRRRASGELLVsVSpL-DDGAASIAAkYGEPEKRGN--ALAVKGfSGDPSSLVAELvAAGYRVAEVKRSEKSLEEFF 307
                                    6899999866666657753.4444444442333355555..56666667899999999988******************* PP

                                    HHHH CS
                        DUF4162  78 iekv 81 
                                     e+v
  gi|119720179|ref|YP_920674.1| 308 FELV 311
                                    9987 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   8.9e-05       0.2       1      25 [.      44      72 ..      44     218 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.9e-05
                         AAA_33  1 lvllvGlpGsGKstlaerllkklg....a 25
                                   +v +vGl+G+GK+t ++  +  l+     
  gi|119720179|ref|YP_920674.1| 44 VVGFVGLNGAGKTTTIRITVGVLPpdagD 72
                                   6889**********998777666655553 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00011      0.24      15      36 ..      35      59 ..      22      62 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                         AAA_23 15 idF...skgltlItGpNGaGKTTil 36
                                   + F   +  ++ ++G NGaGKTT +
  gi|119720179|ref|YP_920674.1| 35 VSFsvrNGEVVGFVGLNGAGKTTTI 59
                                   555556668999***********87 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.0   0.00015      0.33       3      18 ..      44      59 ..      42      63 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00015
                                   EEEEEESTTSSHHHHH CS
                          SRP54  3 villvGlqGaGKTttl 18
                                   v+ +vGl+GaGKTtt+
  gi|119720179|ref|YP_920674.1| 44 VVGFVGLNGAGKTTTI 59
                                   6779***********8 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.1     0.019        43      11      39 ..      24      57 ..      16      65 .. 0.63
   2 ?    5.8   0.0    0.0035       7.9     149     190 ..     156     197 ..     124     223 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.019
                                   TTEECEEEEEETT.....SSEEEEEESTTSSHHH CS
                                   xxxxxxxxxxxxx.....xxxxxxxxxxxxxxxx RF
                          SMC_N 11 ksyagktvilpfs.....ksftaivGpNGSGKsn 39
                                   ks+ + +v  ++s      ++   vG NG+GK+ 
  gi|119720179|ref|YP_920674.1| 24 KSFGKARVLEDVSfsvrnGEVVGFVGLNGAGKTT 57
                                   6666555554443111112355679*******96 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0035
                                    HHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 149 LlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskna 190
                                    + +A+  ++  p +l+De+   LD + ++ +  l++e +k  
  gi|119720179|ref|YP_920674.1| 156 FALAVSLINDPPNFLFDEVLNGLDPQGIAFFRGLVQEFRKAG 197
                                    45677789999****************999999999888764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 2019.58
//
Query:       gi|119720180|ref|YP_920675.1|  [L=485]
Description: hypothetical protein Tpen_1274 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.8e-16   58.0  19.6    2.4e-15   56.6  19.6    1.7  1  ABC2_membrane_2  ABC-2 family transporter protein
     0.0001   21.6  15.3    0.00018   20.8  15.3    1.3  1  ABC2_membrane_3  ABC-2 family transporter protein
     0.0012   18.4   4.5     0.0026   17.4   4.5    1.4  1  ABC2_membrane_5  ABC-2 family transporter protein
     0.0058   16.6   8.3     0.0058   16.6   8.3    2.4  2  ABC2_membrane_4  ABC-2 family transporter protein
  ------ inclusion threshold ------
        5.2    6.8   6.0         13    5.6   6.0    1.6  1  SPC25            Microsomal signal peptidase 25 kDa subunit (


Domain annotation for each model (and alignments):
>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.6  19.6   6.6e-19   2.4e-15      76     287 ..     110     482 ..       5     483 .. 0.71

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 6.6e-19
                ABC2_membrane_2  76 v............................................................................... 76 
                                    +                                                                               
  gi|119720180|ref|YP_920675.1| 110 Rfkaelrrgstnasvnleirvanrygsslswssgircfpadmhtslgigfgstfnktwlavgeviplegggyrlavavap 189
                                    05555555555555555555555555555555555555556666666666666666666666666666666666666666 PP

                ABC2_membrane_2  77 ................................................................................ 76 
                                                                                                                    
  gi|119720180|ref|YP_920675.1| 190 pdcnysevagsklyytvynetpgrlayagelgasgvgvfdlkaagsgkalyleletrrgrvrldtpvslagssalkgwiv 269
                                    66666666666666666666666666666666666666666666777777777777777777777777777777777777 PP

                ABC2_membrane_2  77 .....vstimavlipviaalfgadaiagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvllalaiila 151
                                         +s  +a+l p+  +l++++++a+ +  g l++ L++Pv+R ++ l+ f +g+++    a  llat  + l+i+ a
  gi|119720180|ref|YP_920675.1| 270 aamlvSSNVLAFLYPIAVMLTAYNLVAKPRSTGALEFVLARPVTRLQLFLSRFAAGALA--SAASPLLATAAMHLVISWA 347
                                    777778999********************************************999887..378889999999******* PP

                ABC2_membrane_2 152 lgivlaledllllvvasvlllllvvflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavpqeind 231
                                    +g +++led  ll++ + +++l  ++ ++++ +++ a+  ++ ++la+++++v+ +l+  +++++a +  g   p+   +
  gi|119720180|ref|YP_920675.1| 348 VGSPPPLEDSALLAAGIAASML--AYYSVFYSIAASAK-GKSYLLLAVVVYIVFTVLWAPIAFAIAVAVRGTPDPA-AVQ 423
                                    **********************..89************.8999*********************988887555544.455 PP

                ABC2_membrane_2 232 flsllsptsayntllneilagsdlna...lgstatnllilllllavllvlgyvlFkrkD 287
                                       +++p +a++++++++    ++ a    ++ a  +++  ++ + +lv ++ +F+++ 
  gi|119720180|ref|YP_920675.1| 424 QAYYFNPSVAFQAATEALHLKYGQAAvqaALKPAYVAAAAAAWVLLPLVAAWLAFRKAN 482
                                    55699************9988877778866677777788999*************9975 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8  15.3     5e-08   0.00018     163     342 ..     278     469 ..     262     478 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 5e-08
                ABC2_membrane_3 163 lvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllill...l....afglgipf 235
                                    ++++++ i++++ta+++   +++ ++++++e+ l  +v++lq++ls++ + +l+++ + ll+++   l    a+g   p 
  gi|119720180|ref|YP_920675.1| 278 VLAFLYPIAVMLTAYNL---VAKPRSTGALEFVLARPVTRLQLFLSRFAAGALASAASPLLATAamhLviswAVG--SPP 352
                                    33445555555555533...48************************************99999865533455555..666 PP

                ABC2_membrane_3 236 g..nlglllllfllfglayialgyllsslfknsetaqilifivil.....llsgffgglfpledlp.salkwifsiiPff 307
                                       ++ ll   +   +lay +++y + +  k  +   +++++ i+      +++f +++ +  +++  a++++ +++P++
  gi|119720180|ref|YP_920675.1| 353 PleDSALLAAGIAASMLAYYSVFYSIAASAKGKSYLLLAVVVYIVftvlwAPIAFAIAVAVRGTPDpAAVQQAYYFNPSV 432
                                    66678888899999************99988775544333333331111224444444444333324779********** PP

                ABC2_membrane_3 308 apglgllrli..tgdplweillsliilalfavvylll 342
                                    a+  +   l   +g+  ++ +l  ++ a+ a++++ll
  gi|119720180|ref|YP_920675.1| 433 AFQAATEALHlkYGQAAVQAALKPAYVAAAAAAWVLL 469
                                    *****99998777778888776666666666666665 PP

>> ABC2_membrane_5  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   4.5   7.2e-07    0.0026      31     162 ..     274     400 ..     262     421 .. 0.65

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 7.2e-07
                ABC2_membrane_5  31 flndsvllifsilslvisiililttlsyDekskwnkylltLPvtrkeiVksKYlfvlililiailitlllli.iavlikg 109
                                    + +++vl +  +++++++  ++ +++++ +  +   ++l  Pvtr ++  s++  +++ ++++ l+ ++++  +++   g
  gi|119720180|ref|YP_920675.1| 274 V-SSNVLAF--LYPIAVML-TAYNLVAKPRSTGALEFVLARPVTRLQLFLSRFAAGALASAASPLLATAAMHlVISWAVG 349
                                    2.2333332..33433333.466899**********************************99999988887513444444 PP

                ABC2_membrane_5 110 n.vtisevllsiliglvialiflaivlPlyfkfgvekgrivliiiifgiifllv 162
                                    +   ++++ l ++ + + +l+++++++ +    +   g+ +l++++++ i++ v
  gi|119720180|ref|YP_920675.1| 350 SpPPLEDSALLAAGIAASMLAYYSVFYSIAASAK---GKSYLLLAVVVYIVFTV 400
                                    4366666666666666666666666666665555...55444444444333322 PP

>> ABC2_membrane_4  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1      0.21   7.6e+02      17      40 ..      18      41 ..      13      57 .. 0.74
   2 !   16.6   8.3   1.6e-06    0.0058      50     177 ..     273     400 ..     256     415 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.21
                ABC2_membrane_4 17 llvlaallvpllallyfnllgktg 40
                                   l++laal+++  a+ y+++++ tg
  gi|119720180|ref|YP_920675.1| 18 LVLLAALVAVGAAVGYMAYAQMTG 41
                                   567788888888888998888776 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 1.6e-06
                ABC2_membrane_4  50 svfgftlllllplilgiiasylifrEeqndtlknLltiPvsrtklllaKlivllllsvllmlvtflitvlf.allsgfvg 128
                                     v+++ l +l+p+ + + a  l+ + ++ + l   l +Pv+r +l+l+ +++ +l s++  l++++++ l+ ++ +g+++
  gi|119720180|ref|YP_920675.1| 273 LVSSNVLAFLYPIAVMLTAYNLVAKPRSTGALEFVLARPVTRLQLFLSRFAAGALASAASPLLATAAMHLViSWAVGSPP 352
                                    355666779999999999****************************************9999888777765488888865 PP

                ABC2_membrane_4 129 .fsvklvlellkkclelgllvffavlpiialvllkksy.vlpliltlvyti 177
                                     ++ +++l +        +l ++ v   ia ++  ksy +l++++ +v+t+
  gi|119720180|ref|YP_920675.1| 353 pLEDSALLAAGI---AASMLAYYSVFYSIAASAKGKSYlLLAVVVYIVFTV 400
                                    488776544433...333333333444445555555554556666666654 PP

>> SPC25  Microsomal signal peptidase 25 kDa subunit (SPC25)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   6.0    0.0035        13      30      73 ..     360     402 ..     356     415 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0035
                          SPC25  30 LalGylavaiaavaflydykveFeeskpvlaiavvlYfilsgil 73 
                                    La G++a+++a ++ +y+   +  + k++l++avv+Y++++++ 
  gi|119720180|ref|YP_920675.1| 360 LAAGIAASMLAYYSVFYSIAAS-AKGKSYLLLAVVVYIVFTVLW 402
                                    7889999999999999999865.899*************98775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (485 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       839  (0.0467957); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.49
# Mc/sec: 2990.25
//
Query:       gi|119720181|ref|YP_920676.1|  [L=117]
Description: hypothetical protein Tpen_1275 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-12   46.0   1.1    5.3e-12   45.6   1.1    1.3  1  DUF3883   Domain of unknown function (DUF3883)
  ------ inclusion threshold ------
      0.063   13.7   0.3       0.08   13.4   0.3    1.2  1  DUF4550   Domain of unknown function (DUF4550)


Domain annotation for each model (and alignments):
>> DUF3883  Domain of unknown function (DUF3883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   1.1   5.9e-16   5.3e-12      22      90 ..      12      79 ..       1      96 [. 0.82

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 5.9e-16
                        DUF3883 22 nedve.dglgYDiesvdkedgeerfIEVKttakgkkdfelsrnElefaqekgdkYwlyrVfnagkepkvk 90
                                    ++v+ +++gYDies d ++g++r+IEVK +  +   ++l++nE+    +++++ wly+V++ + e++v 
  gi|119720181|ref|YP_920676.1| 12 AQNVSsEKKGYDIESKD-REGNTRYIEVKKRDLKYGFVFLTHNEFMNFLRNENS-WLYIVYKENGETRVI 79
                                   33333399*********.89************99**********9888766654.7*****997777665 PP

>> DUF4550  Domain of unknown function (DUF4550)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.3   8.9e-06      0.08      30      93 ..      48     114 ..      33     116 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.9e-06
                        DUF4550  30 vfleseskvvkpweeddklwiswth...tieinvtkellkkllehkiklklwdtkdkvsskarfdrp 93 
                                    vfl+++  +    +e+  l+i++++   t  i++++e++ k  + ++k ++   k+  +++ar +r 
  gi|119720181|ref|YP_920676.1|  48 VFLTHNEFMNFLRNENSWLYIVYKEngeTRVIEISREKVLKHAKPELKWRVSLRKEVTGRRARNQRQ 114
                                    555554444445557777888888622246799******************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 790.60
//
Query:       gi|119720182|ref|YP_920677.1|  [L=177]
Description: hypothetical protein Tpen_1276 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-10   39.5   2.9    5.4e-06   26.3   0.1    2.3  2  TMF_DNA_bd       TATA element modulatory factor 1 DNA binding
    1.3e-08   34.9   1.3    0.00015   21.8   0.4    2.4  2  DUF1664          Protein of unknown function (DUF1664)
    5.2e-08   33.0   4.6    0.00044   20.4   3.5    2.4  2  XhlA             Haemolysin XhlA
    1.1e-07   32.0   0.7       0.03   14.6   0.1    3.3  2  ABC_tran_CTD     ABC transporter C-terminal domain
    1.1e-07   32.0   3.0    2.7e-06   27.6   1.2    2.6  2  BLOC1_2          Biogenesis of lysosome-related organelles co
    1.4e-07   31.1   0.2    6.6e-07   28.9   0.1    1.8  2  DUF3450          Protein of unknown function (DUF3450)
    1.4e-07   31.7   0.8     0.0042   17.4   0.3    3.0  3  FlaC_arch        Flagella accessory protein C (FlaC)
    3.3e-07   30.7   1.9    3.7e-07   30.6   1.9    1.1  1  ATG16            Autophagy protein 16 (ATG16)
    3.3e-07   30.0   3.2      0.013   15.2   0.6    3.1  3  DivIC            Septum formation initiator
    6.8e-07   29.1   2.5      0.011   15.4   0.2    3.0  3  DUF4988          Domain of unknown function
    1.2e-06   28.4   0.6       0.21   11.5   0.1    3.1  3  Prefoldin_2      Prefoldin subunit
    1.6e-06   28.1   0.2      0.047   13.8   0.0    3.0  4  bZIP_1           bZIP transcription factor
    1.8e-06   28.4   0.9    6.3e-06   26.6   0.9    1.9  1  DUF16            Protein of unknown function DUF16
    1.9e-06   27.0   0.6    2.5e-06   26.6   0.6    1.2  1  Spc7             Spc7 kinetochore protein
    2.6e-06   25.9   0.2    1.3e-05   23.7   0.2    1.8  2  EzrA             Septation ring formation regulator, EzrA
    3.7e-06   27.1   0.9     0.0012   19.1   0.2    3.0  3  Lzipper-MIP1     Leucine-zipper of ternary complex factor MIP
    3.9e-06   27.4   0.7    0.00053   20.6   0.2    2.6  2  SlyX             SlyX
    4.5e-06   26.3   0.6    0.00045   19.7   0.6    2.5  1  FliD_C           Flagellar hook-associated protein 2 C-termin
    4.9e-06   26.6   1.8    1.6e-05   24.9   1.8    1.7  1  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
    5.9e-06   26.4   0.0    0.00059   19.9   0.0    2.1  2  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
    9.3e-06   25.6   0.5      0.015   15.3   0.1    2.1  2  BRE1             BRE1 E3 ubiquitin ligase
      1e-05   25.4   0.0    1.4e-05   25.0   0.0    1.2  1  Laminin_I        Laminin Domain I
    1.2e-05   24.8   2.0    2.1e-05   24.0   2.0    1.4  1  DUF3552          Domain of unknown function (DUF3552)
    1.3e-05   25.1   0.3      7e-05   22.7   0.1    1.8  2  KASH_CCD         Coiled-coil region of CCDC155 or KASH
    1.7e-05   25.2   6.6       0.18   12.3   4.4    3.1  2  DUF4140          N-terminal domain of unknown function (DUF41
    1.8e-05   25.1   0.8      0.003   18.0   0.5    2.7  2  NPV_P10          Nucleopolyhedrovirus P10 protein
    2.3e-05   24.7   0.3    5.5e-05   23.5   0.3    1.8  1  Snapin_Pallidin  Snapin/Pallidin
    2.5e-05   23.2   2.7    0.00038   19.3   0.5    2.0  2  Tektin           Tektin family
    2.8e-05   24.1   3.8      0.064   13.1   1.3    2.1  2  Spc29            Spindle Pole Component 29
    2.8e-05   23.8   0.4      0.001   18.7   0.3    2.2  1  DUF4795          Domain of unknown function (DUF4795)
    3.1e-05   24.1   0.4      0.019   15.0   0.1    2.1  2  ADIP             Afadin- and alpha -actinin-Binding
    3.7e-05   24.0   3.0       0.34   11.3   0.1    3.5  3  Csm1_N           Csm1 N-terminal domain
    4.1e-05   23.8   2.8    0.00016   21.8   2.8    1.9  1  Tropomyosin_1    Tropomyosin like
      5e-05   23.5   0.2    8.4e-05   22.8   0.2    1.4  1  Fib_alpha        Fibrinogen alpha/beta chain family
    5.2e-05   23.4   0.4     0.0002   21.5   0.2    1.8  1  Nup54            Nucleoporin complex subunit 54
    5.8e-05   23.1   0.1       0.38   10.9   0.1    3.2  2  MbeD_MobD        MbeD/MobD like
    6.4e-05   23.2   1.1       0.13   12.5   0.0    2.2  2  DUF5082          Domain of unknown function (DUF5082)
    6.4e-05   23.2   2.1        0.2   12.0   0.2    2.9  2  CLZ              C-terminal leucine zipper domain of cyclic n
    6.9e-05   22.5   0.1      0.031   13.8   0.0    2.1  2  MscS_porin       Mechanosensitive ion channel porin domain
    8.7e-05   22.3  15.1      0.034   14.0   0.9    3.9  3  HSBP1            Heat shock factor binding protein 1
    0.00011   21.1   0.3    0.00059   18.6   0.3    1.8  1  AAA_13           AAA domain
    0.00011   22.1   1.3      0.073   13.0   0.2    2.9  3  Prefoldin        Prefoldin subunit
    0.00011   22.3   0.0      0.062   13.6   0.0    2.5  2  DUF948           Bacterial protein of unknown function (DUF94
    0.00015   21.8   0.1        5.7    7.1   0.2    3.4  3  bZIP_2           Basic region leucine zipper
    0.00017   21.0   0.2     0.0021   17.5   0.2    2.0  1  GAS              Growth-arrest specific micro-tubule binding
    0.00018   21.6   0.3    0.00055   20.0   0.3    1.8  1  Laminin_II       Laminin Domain II
    0.00018   20.5   0.1    0.00028   19.9   0.1    1.3  1  DUF812           Protein of unknown function (DUF812)
    0.00019   19.9   0.5    0.00067   18.1   0.4    1.7  2  Gp58             gp58-like protein
    0.00019   22.0   1.6     0.0067   17.0   1.1    2.1  1  APG6_N           Apg6 coiled-coil region
     0.0002   20.8   0.1    0.00026   20.4   0.1    1.3  1  DUF4407          Domain of unknown function (DUF4407)
     0.0002   21.7   0.4       0.19   12.2   0.1    2.5  2  ZapB             Cell division protein ZapB
    0.00021   20.5   1.5    0.00031   19.9   1.5    1.4  1  Atg14            Vacuolar sorting 38 and autophagy-related su
    0.00022   21.3   3.0      0.026   14.6   0.4    2.7  3  DUF2730          Protein of unknown function (DUF2730)
    0.00022   21.4   6.6     0.0035   17.5   1.4    2.1  2  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
    0.00023   21.0   0.1       0.46   10.2   0.0    2.0  2  TACC_C           Transforming acidic coiled-coil-containing p
    0.00023   21.2   0.6        1.3    9.2   0.0    3.4  3  DUF2802          Protein of unknown function (DUF2802)
    0.00025   19.1   1.2    0.00028   18.9   1.2    1.0  1  Myosin_tail_1    Myosin tail
    0.00025   21.3   0.3      0.015   15.5   0.1    2.1  2  Jnk-SapK_ap_N    JNK_SAPK-associated protein-1
    0.00026   21.0   4.6       0.13   12.3   0.6    3.2  2  Prefoldin_3      Prefoldin subunit
    0.00026   21.4   0.5    0.00094   19.6   0.5    1.8  1  DUF4200          Domain of unknown function (DUF4200)
     0.0003   20.9   0.2     0.0011   19.1   0.1    1.9  2  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
    0.00038   20.3   5.9      0.013   15.3   5.9    2.7  1  DUF2721          Protein of unknown function (DUF2721)
    0.00039   20.6   2.1    0.00092   19.4   1.9    2.1  1  Uds1             Up-regulated During Septation
    0.00039   19.8   1.8     0.0015   17.8   1.8    1.8  1  LegC3_N          LegC3 N-terminal coiled-coil domain
    0.00046   19.9   1.2       0.19   11.3   0.1    1.7  2  Filament         Intermediate filament protein
    0.00051   19.5   0.2       0.92    8.9   0.0    2.5  3  DUF4618          Domain of unknown function (DUF4618)
    0.00052   20.1   2.3      0.013   15.6   2.3    2.5  2  DHR10            Designed helical repeat protein 10 domain
    0.00056   19.3   0.4      0.041   13.3   0.0    2.3  2  Helo_like_N      Fungal N-terminal domain of STAND proteins
    0.00056   20.6   0.1       0.05   14.3   0.0    2.0  2  DUF4472          Domain of unknown function (DUF4472)
    0.00058   20.0   3.2          2    8.6   0.2    3.3  4  DUF3782          Protein of unknown function (DUF3782)
    0.00066   19.5   0.0      0.096   12.5   0.0    2.2  2  Bacillus_HBL     Bacillus haemolytic enterotoxin (HBL)
    0.00067   20.1   0.2     0.0095   16.4   0.1    2.2  2  Spectrin         Spectrin repeat
    0.00074   18.6   3.4        1.5    8.1   0.0    4.4  6  MRF_C1           Myelin gene regulatory factor -C-terminal do
    0.00075   19.9   3.1       0.11   12.9   0.2    2.3  2  HrpB7            Bacterial type III secretion protein (HrpB7)
    0.00076   17.1   0.6    0.00088   16.9   0.6    1.1  1  DUF3584          Protein of unknown function (DUF3584)
    0.00078   18.8   0.0        0.4    9.9   0.0    2.1  2  HemX             HemX, putative uroporphyrinogen-III C-methyl
     0.0008   19.1   1.4     0.0033   17.1   1.5    2.0  1  Lebercilin       Ciliary protein causing Leber congenital ama
    0.00083   18.8   4.4     0.0029   17.0   4.4    1.7  1  Tropomyosin      Tropomyosin
    0.00091   18.7   3.3       0.13   11.6   0.6    2.1  2  Cluap1           Clusterin-associated protein-1
    0.00096   19.4   0.9      0.042   14.1   0.3    2.4  2  KLRAQ            Predicted coiled-coil domain-containing prot
     0.0011   19.0   0.5       0.87    9.7   0.1    2.8  3  DivIVA           DivIVA protein
     0.0012   18.7   3.3      0.066   13.1   0.3    2.5  2  DASH_Spc19       Spc19
     0.0013   18.6   3.7     0.0039   17.1   3.7    1.9  1  Transcrip_act    Transcriptional activator
     0.0013   17.0   1.3     0.0014   16.9   1.3    1.0  1  HOOK             HOOK protein
     0.0013   17.6   1.8     0.0087   15.0   0.6    2.0  2  Fmp27_WPPW       RNA pol II promoter Fmp27 protein domain
     0.0015   17.5   0.0     0.0019   17.1   0.0    1.2  1  FemAB            FemAB family
     0.0016   18.1   0.3      0.004   16.8   0.3    1.7  1  PI3K_P85_iSH2    Phosphatidylinositol 3-kinase regulatory sub
     0.0016   17.8   0.2        0.1   11.9   0.1    2.1  2  DUF4763          Domain of unknown function (DUF4763)
     0.0017   17.7   0.0     0.0022   17.3   0.0    1.1  1  TMPIT            TMPIT-like protein
     0.0018   17.9   0.2     0.0021   17.7   0.2    1.1  1  Exonuc_VII_L     Exonuclease VII, large subunit
     0.0019   17.9   0.2        1.4    8.5   0.0    2.2  2  GrpE             GrpE
      0.002   16.7   3.2     0.0024   16.5   3.2    1.1  1  CCDC154          Coiled-coil domain-containing protein 154
     0.0021   18.4   1.3        2.8    8.4   0.2    3.2  2  DUF4094          Domain of unknown function (DUF4094)
     0.0021   18.3   0.0     0.0041   17.3   0.0    1.5  1  FliJ             Flagellar FliJ protein
     0.0021   18.0   0.6       0.38   10.7   0.6    2.5  1  Ax_dynein_light  Axonemal dynein light chain
     0.0022   17.7   0.4        3.7    7.4   0.1    3.2  3  DASH_Dam1        DASH complex subunit Dam1
     0.0022   17.1   2.7     0.0028   16.8   2.7    1.1  1  AIP3             Actin interacting protein 3
     0.0024   16.3   0.3     0.0036   15.8   0.3    1.2  1  MAD              Mitotic checkpoint protein
     0.0026   17.1   0.8      0.044   13.1   0.1    2.0  2  FmiP_Thoc5       Fms-interacting protein/Thoc5
     0.0029   18.3   0.1       0.26   12.1   0.1    2.7  2  Occludin_ELL     Occludin homology domain
     0.0033   15.3   0.6     0.0038   15.1   0.6    1.1  1  Nup88            Nuclear pore component
     0.0038   15.5   0.2     0.0043   15.3   0.2    1.1  1  FPP              Filament-like plant protein, long coiled-coi
     0.0039   16.8   2.4      0.068   12.8   1.0    2.5  2  Snf7             Snf7
      0.004   16.1   3.8     0.0047   15.9   3.8    1.1  1  CALCOCO1         Calcium binding and coiled-coil domain (CALC
     0.0042   16.8   0.6       0.29   10.8   0.3    2.1  2  SHE3             SWI5-dependent HO expression protein 3
     0.0049   16.9   0.1      0.099   12.7   0.1    2.2  2  DUF730           Protein of unknown function (DUF730)
     0.0055   16.9   0.5        1.1    9.6   0.5    2.7  1  Spc24            Spc24 subunit of Ndc80
     0.0055   16.1   5.5       0.72    9.1   0.1    2.3  2  CorA             CorA-like Mg2+ transporter protein
     0.0058   16.8   0.4      0.037   14.2   0.4    2.1  1  TMF_TATA_bd      TATA element modulatory factor 1 TATA bindin
     0.0065   16.0   0.2      0.008   15.7   0.2    1.2  1  HMMR_N           Hyaluronan mediated motility receptor N-term
     0.0067   16.7   1.2      0.013   15.7   1.2    1.6  1  CENP-Q           CENP-Q, a CENPA-CAD centromere complex subun
     0.0072   15.9   0.1        1.1    8.8   0.0    2.1  2  PspA_IM30        PspA/IM30 family
     0.0076   14.7   0.5       0.79    8.0   0.4    2.1  2  Hemagglutinin    Haemagglutinin
     0.0077   16.3   1.4      0.024   14.6   1.4    1.9  1  Sipho_Gp157      Siphovirus Gp157
     0.0077   16.1   3.1       0.35   10.7   2.2    3.0  2  CdvA             CdvA-like coiled-coil domain
     0.0079   15.9   0.9      0.047   13.4   0.4    2.3  2  RPW8             Arabidopsis broad-spectrum mildew resistance
     0.0082   15.8   3.5       0.08   12.6   0.0    3.2  3  Vac_Fusion       Chordopoxvirus multifunctional envelope prot
     0.0083   15.7   0.1      0.024   14.2   0.1    1.7  2  HAUS-augmin3     HAUS augmin-like complex subunit 3
     0.0087   16.0   0.0       0.56   10.2   0.0    2.5  1  FlxA             FlxA-like protein
     0.0088   14.7   1.0       0.97    8.0   0.1    1.9  2  FapA             Flagellar Assembly Protein A
     0.0088   15.2   0.2       0.29   10.2   0.0    2.0  2  RmuC             RmuC family
     0.0091   15.6   1.5        1.3    8.5   0.3    2.2  2  Vps5             Vps5 C terminal like
     0.0091   16.1   0.4        1.8    8.7   0.1    2.2  2  COG2             COG (conserved oligomeric Golgi) complex com
     0.0091   15.2   3.1       0.21   10.7   3.1    2.4  1  phiKZ_IP         phiKZ-like phage internal head proteins
     0.0093   16.0   2.5      0.016   15.3   2.5    1.5  1  DUF1640          Protein of unknown function (DUF1640)
     0.0097   15.6   3.1        1.4    8.6   1.1    2.9  2  Phage_tail_NK    Sf6-type phage tail needle knob or tip of so
     0.0098   15.4   2.3       0.21   11.1   2.3    2.4  1  DegS             Sensor protein DegS
     0.0099   15.7   2.6       0.48   10.2   2.3    2.5  2  DUF1465          Protein of unknown function (DUF1465)
  ------ inclusion threshold ------
       0.01   16.4   9.7        1.1    9.9   0.6    4.3  3  MerR-DNA-bind    MerR, DNA binding
      0.011   15.5   2.3       0.16   11.7   1.5    2.4  2  DUF4201          Domain of unknown function (DUF4201)
      0.011   15.0   0.2       0.31   10.2   0.1    2.0  3  Taxilin          Myosin-like coiled-coil protein
      0.011   14.3   0.7      0.014   13.9   0.7    1.2  1  FUSC             Fusaric acid resistance protein family
      0.011   16.1   0.9       0.32   11.3   0.2    2.4  3  DUF641           Plant protein of unknown function (DUF641)
      0.012   16.0   1.4       0.47   10.8   0.9    2.3  2  Syntaxin_2       Syntaxin-like protein
      0.013   15.8  15.4       0.14   12.4   3.9    2.9  2  DUF4164          Domain of unknown function (DUF4164)
      0.013   15.6   0.7      0.013   15.6   0.7    1.5  1  UPF0242          Uncharacterised protein family (UPF0242) N-t
      0.013   15.4   1.7        0.7    9.8   0.4    2.3  2  YscO             Type III secretion protein YscO
      0.013   15.1   0.4      0.032   13.9   0.3    1.7  2  Syntaxin         Syntaxin
      0.014   15.7   6.9       0.44   10.9   3.0    3.3  2  CCDC-167         Coiled-coil domain-containing protein 167
      0.018   15.2   0.3        5.2    7.1   0.0    2.8  3  DUF2959          Protein of unknown function (DUF2959)
      0.018   13.4   0.5      0.027   12.9   0.5    1.3  1  Sec3_C           Exocyst complex component Sec3
      0.019   14.8   0.1       0.23   11.2   0.1    2.4  1  DASH_Spc34       DASH complex subunit Spc34
      0.019   15.2   0.5       0.66   10.3   0.2    2.5  2  KxDL             Uncharacterized conserved protein
      0.019   14.8   1.5       0.56   10.0   1.5    2.4  1  DUF241           Arabidopsis protein of unknown function
      0.019   14.8   0.4       0.35   10.7   0.2    2.1  2  Phage_GP20       Phage minor structural protein GP20
      0.019   15.1   2.7       0.15   12.2   1.0    2.4  3  JIP_LZII         JNK-interacting protein  leucine zipper II
       0.02   15.0   1.3       0.36   10.9   0.3    2.5  2  TolA_bind_tri    TolA binding protein trimerisation
      0.021   14.4   0.3      0.068   12.7   0.2    1.7  2  Allexi_40kDa     Allexivirus 40kDa protein
      0.022   13.7   1.0        1.1    8.1   0.1    2.2  2  DUF677           Protein of unknown function (DUF677)
      0.023   14.7   0.3       0.47   10.4   0.1    2.3  2  DUF4446          Protein of unknown function (DUF4446)
      0.024   14.7   0.2         18    5.5   0.1    3.1  4  Vps51            Vps51/Vps67
      0.026   14.6   0.1       0.99    9.5   0.1    2.6  1  TssO             Type VI secretion system, TssO
      0.026   14.6   0.1       0.12   12.5   0.1    2.0  1  Mod_r            Modifier of rudimentary (Mod(r)) protein
      0.026   15.4   1.9       0.11   13.4   0.6    2.5  1  PRKG1_interact   cGMP-dependent protein kinase interacting do
      0.029   14.5   0.1        3.5    7.8   0.1    2.7  3  Swi5             Swi5
      0.029   14.2   0.1      0.041   13.7   0.1    1.4  1  DUF724           Protein of unknown function (DUF724)
      0.029   14.4   3.4        1.4    9.0   0.9    3.0  2  Phasin           Poly(hydroxyalcanoate) granule associated pr
      0.033   14.0   0.3       0.63    9.9   0.1    2.5  2  Dynactin_p22     Dynactin subunit p22
      0.034   13.6   0.3      0.041   13.3   0.3    1.1  1  Rab5-bind        Rabaptin-like protein
      0.035   12.4   1.8      0.038   12.3   1.8    1.1  1  DUF390           Protein of unknown function (DUF390)
      0.036   14.7   0.1        1.2    9.8   0.1    2.4  1  YabA             Initiation control protein YabA
      0.038   14.4   1.2         19    5.7   1.2    3.3  1  HHH_8            Helix-hairpin-helix domain
      0.038   14.4   0.8       0.59   10.6   0.8    2.3  1  Enkurin          Calmodulin-binding
      0.039   13.6   0.6        0.3   10.7   0.2    2.0  2  TPD52            Tumour protein D52 family
      0.041   14.0   3.8       0.43   10.7   1.2    2.7  3  Med9             RNA polymerase II transcription mediator com
      0.043   14.3   3.7       0.17   12.3   2.2    2.6  1  Cep57_MT_bd      Centrosome microtubule-binding domain of Cep
      0.043   14.4   0.1       0.71   10.5   0.0    2.1  2  HIP1_clath_bdg   Clathrin-binding domain of Huntingtin-intera
      0.044   13.9   1.2       0.94    9.7   1.3    2.5  1  Cnn_1N           Centrosomin N-terminal motif 1
      0.046   11.6   0.0      0.058   11.3   0.0    1.1  1  V_ATPase_I       V-type ATPase 116kDa subunit family
      0.047   13.2   0.2       0.31   10.6   0.1    2.2  2  Fzo_mitofusin    fzo-like conserved region
      0.048   14.2   2.7       0.86   10.2   0.4    2.4  2  Syntaxin-6_N     Syntaxin 6, N-terminal
      0.048   13.3   3.9        1.4    8.6   2.0    2.7  2  Med4             Vitamin-D-receptor interacting Mediator subu
      0.049   13.5   0.1        7.6    6.3   0.1    2.1  2  SKA1             Spindle and kinetochore-associated protein 1
      0.051   11.8   0.2      0.076   11.2   0.1    1.3  1  COG6             Conserved oligomeric complex COG6
      0.053   13.0   0.4       0.11   11.9   0.4    1.6  1  HBM              Helical bimodular sensor domain
      0.053   13.4   0.2       0.14   12.1   0.2    1.6  1  Wtap             WTAP/Mum2p family
      0.055   12.6   1.8       0.83    8.7   0.4    1.8  2  APG17            Autophagy protein Apg17
      0.063   13.1   0.2        1.2    9.0   0.1    2.1  2  Nsp1_C           Nsp1-like C-terminal region
      0.063   13.7   0.2       0.92   10.0   0.0    2.1  2  UPF0449          Uncharacterised protein family UPF0449
      0.064   12.6   2.7       0.11   11.8   2.1    1.7  2  TraF_2           F plasmid transfer operon, TraF, protein
      0.064   13.4   0.8       0.62   10.2   0.2    2.0  2  DUF4337          Domain of unknown function (DUF4337)
      0.066   12.3   0.2      0.097   11.7   0.2    1.3  1  TelA             Toxic anion resistance protein (TelA)
      0.066   12.6   0.1        3.2    7.1   0.0    2.4  3  DUF1202          Protein of unknown function (DUF1202)
      0.067   13.1   0.0       0.28   11.0   0.0    1.7  1  Sec34            Sec34-like family
      0.068   12.3   0.1      0.086   12.0   0.1    1.3  1  DUF4686          Domain of unknown function (DUF4686)
      0.071   13.1   0.5       0.52   10.3   0.3    2.1  2  MIP-T3_C         Microtubule-binding protein MIP-T3 C-termina
      0.073   12.0   1.2      0.083   11.8   1.2    1.2  1  Vps53_N          Vps53-like, N-terminal
      0.074   12.0   0.1      0.097   11.6   0.1    1.2  1  IFT57            Intra-flagellar transport protein 57
      0.074   13.0   0.3       0.32   11.0   0.1    1.9  2  Noelin-1         Neurogenesis glycoprotein
      0.074   12.9   0.7        3.1    7.7   0.2    2.8  2  TRAF_BIRC3_bd    TNF receptor-associated factor BIRC3 binding
      0.077   12.5   0.0       0.12   11.9   0.0    1.4  1  DUF2884          Protein of unknown function (DUF2884)
       0.08   12.5   0.1       0.11   12.1   0.1    1.2  1  TMCO5            TMCO5 family
      0.081   12.8   0.8        9.2    6.2   0.2    3.0  2  Matrilin_ccoil   Trimeric coiled-coil oligomerisation domain 
      0.086   11.1   6.9       0.14   10.4   4.3    1.8  2  Cast             RIM-binding protein of the cytomatrix active
      0.086   12.8   3.7        1.3    9.0   0.4    3.1  2  Tnp_22_trimer    L1 transposable element trimerization domain
      0.088   12.5   0.2       0.16   11.6   0.2    1.5  1  YkyA             Putative cell-wall binding lipoprotein
      0.089   13.3   0.0       0.35   11.3   0.0    1.9  1  T3SSipB          Type III cell invasion protein SipB
      0.089   13.0   0.4       0.71   10.0   0.3    2.4  1  CREPT            Cell-cycle alteration and expression-elevate
      0.095   12.8   6.2        2.7    8.1   0.1    3.7  3  DUF465           Protein of unknown function (DUF465)
        0.1   11.2   0.0       0.12   11.0   0.0    1.1  1  DHC_N1           Dynein heavy chain, N-terminal region 1
        0.1   12.0   0.3       0.66    9.3   0.1    2.1  2  CASP_C           CASP C terminal
       0.11   12.0   0.1       0.17   11.3   0.1    1.3  1  Mce4_CUP1        Cholesterol uptake porter CUP1 of Mce4, puta
       0.11   12.4   1.0        1.8    8.4   1.0    2.1  1  FTA4             Kinetochore complex Fta4 of Sim4 subunit, or
       0.12   11.0   0.5       0.15   10.7   0.5    1.2  1  DUF4455          Domain of unknown function (DUF4455)
       0.12   12.4   1.3       0.79    9.9   0.7    2.2  2  TRPM_tetra       Tetramerisation domain of TRPM
       0.13   12.3   1.9        7.8    6.6   0.3    2.8  3  DUF2205          Short coiled-coil protein
       0.14   11.4   0.0       0.21   10.8   0.0    1.4  1  DUF3535          Domain of unknown function (DUF3535)
       0.14   10.7   0.9       0.15   10.6   0.9    1.1  1  Macoilin         Macoilin family
       0.16   12.0   0.7        2.4    8.2   0.2    2.8  2  U62_UL91         Functional domain of U62 and UL91 proteins
       0.16   12.0   7.2         11    6.1   0.4    3.4  3  PspB             Phage shock protein B
       0.17   11.8   0.4        7.3    6.5   0.1    2.0  2  EMP24_GP25L      emp24/gp25L/p24 family/GOLD
       0.18   11.3   4.8         16    4.9   3.7    3.2  1  BRI3BP           Negative regulator of p53/TP53
       0.19   12.2   2.0         12    6.3   0.5    2.9  2  DUF1690          Protein of Unknown function (DUF1690)
       0.19   11.0   1.0       0.62    9.4   1.0    1.7  1  FAM76            FAM76 protein
       0.19   11.3   0.0       0.48   10.0   0.0    1.7  1  Phage_GPO        Phage capsid scaffolding protein (GPO) serin
        0.2   11.5   0.8        2.9    7.7   0.1    2.1  2  DUF4515          Domain of unknown function (DUF4515)
       0.21   11.9   9.5        4.4    7.7   6.1    3.1  2  HalX             HalX domain
       0.21   12.2   7.5       0.91   10.2   1.0    3.2  3  GTP-bdg_M        GTP-binding GTPase Middle Region
       0.24   10.8   1.9       0.32   10.4   1.0    1.5  1  Phlebovirus_NSM  Phlebovirus nonstructural protein NS-M
       0.24   10.8   6.2        9.8    5.6   2.1    3.1  2  DUF4349          Domain of unknown function (DUF4349)
       0.27   11.5   8.7        1.8    8.9   0.4    3.8  4  Val_tRNA-synt_C  Valyl tRNA synthetase tRNA binding arm
        0.3   10.9   3.1        4.9    6.9   3.1    2.3  1  Glyco_H_20C_C    Glycoside Hydrolase 20C C-terminal domain
       0.37   11.1   5.5         10    6.4   1.1    3.1  2  Osmo_CC          Osmosensory transporter coiled coil
       0.42   10.9   2.9        3.1    8.1   2.9    2.3  1  Ntox28           Bacterial toxin 28
       0.81    9.8   5.6        2.1    8.5   0.5    3.0  3  DUF1003          Protein of unknown function (DUF1003)
       0.85   10.0   3.6        3.2    8.2   0.7    2.5  3  MutS_IV          MutS family domain IV
        2.4    8.5   7.0         17    5.7   3.9    3.1  2  DUF3618          Protein of unknown function (DUF3618)
        4.3    6.1  14.3        2.8    6.8   1.0    3.2  4  DUF3375          Protein of unknown function (DUF3375)
        4.3    6.9   8.0         17    5.0   0.4    3.7  3  YvrJ             YvrJ protein family


Domain annotation for each model (and alignments):
>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.1   6.9e-08   5.4e-06      13      72 ..      60     119 ..      50     121 .. 0.95
   2 !   20.2   0.5   5.7e-06   0.00044      31      72 ..     106     147 ..     104     149 .. 0.93

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 6.9e-08
                     TMF_DNA_bd  13 qIaqLmeEGekLskkelklnntikkLrkknkelekeikelkkkleklekeleeleerlke 72 
                                     I+ L+ E+e L+     l + +++L    +el k i++l +++++l+k +++l +r ++
  gi|119720182|ref|YP_920677.1|  60 DIEGLRRELEGLERDVASLAERVSRLEGAYAELSKRIDSLGERISDLDKRIDSLDKRIDG 119
                                    69****************************************************999775 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 5.7e-06
                     TMF_DNA_bd  31 lnntikkLrkknkelekeikelkkkleklekeleeleerlke 72 
                                    l + i++L+k +  l+k i++l+k++e+l+k +++l +rl+ 
  gi|119720182|ref|YP_920677.1| 106 LDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDSLDKRLDH 147
                                    6789***********************************985 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   0.00063     0.049      77     121 ..      49      93 ..      31      95 .. 0.81
   2 !   21.8   0.4   1.9e-06   0.00015      62     121 ..      90     149 ..      87     152 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00063
                        DUF1664  77 eqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                    ++++  ++++++++ +r++l+ +++dv s+ e v+ le+  ++++
  gi|119720182|ref|YP_920677.1|  49 DVEKHWEATRRDIEGLRRELEGLERDVASLAERVSRLEGAYAELS 93 
                                    345566899*****************************9888776 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 1.9e-06
                        DUF1664  62 rhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                     +Ls+rid++++++ +  + + ++++ ++ + + ++++++ +es+++ + +l+++l++i 
  gi|119720182|ref|YP_920677.1|  90 AELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDSLDKRLDHIA 149
                                    689*****************************************************9996 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   0.00076     0.059       4      46 ..      66     108 ..      63     110 .. 0.92
   2 !   20.4   3.5   5.7e-06   0.00044       2      45 ..     106     149 ..     105     169 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00076
                           XhlA   4 erlerietkldnleervdkleekaaeaeekiknleedlkkles 46 
                                     +le +e+++ +l erv++le   ae  ++i++l e++++l +
  gi|119720182|ref|YP_920677.1|  66 RELEGLERDVASLAERVSRLEGAYAELSKRIDSLGERISDLDK 108
                                    578999*********************************9975 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 5.7e-06
                           XhlA   2 ikerlerietkldnleervdkleekaaeaeekiknleedlkkle 45 
                                    +++r+  +++++d l++r+d l+++ +  +++i++l ++l+ + 
  gi|119720182|ref|YP_920677.1| 106 LDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDSLDKRLDHIA 149
                                    67899999999999999999999999999999999999999886 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.2   0.00045     0.035       9      58 ..      60     111 ..      51     116 .. 0.52
   2 !   14.6   0.1   0.00038      0.03       8      28 ..     122     142 ..      88     165 .. 0.53

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 0.00045
                   ABC_tran_CTD   9 eleeleaeIeaLEeeiaeleaeladpely.sdp.eklaelsaeleeleaeLe 58 
                                     +e l +e+e LE + a+l ++++  e   +   +++  l +++ +l++ ++
  gi|119720182|ref|YP_920677.1|  60 DIEGLRRELEGLERDVASLAERVSRLEGAyAELsKRIDSLGERISDLDKRID 111
                                    5555555555555555555555555442211112555555555555555554 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 0.00038
                   ABC_tran_CTD   8 releeleaeIeaLEeeiaele 28 
                                    ++++ l+++Ie+L+++i +l+
  gi|119720182|ref|YP_920677.1| 122 KRIDSLDKRIESLDKRIDSLD 142
                                    222233333333333333333 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0    0.0058      0.45      55      94 ..      56      95 ..      37      97 .. 0.75
   2 !   27.6   1.2   3.5e-08   2.7e-06      11      95 ..      64     145 ..      55     152 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0058
                        BLOC1_2 55 ekyeelqpylqqidqiekqvteLeeavseLDeyskeLEak 94
                                   ++   ++ + ++++ +e++v++L e vs+L+    eL ++
  gi|119720182|ref|YP_920677.1| 56 ATRRDIEGLRRELEGLERDVASLAERVSRLEGAYAELSKR 95
                                   3444777788888889999999999999998888888766 PP

  == domain 2  score: 27.6 bits;  conditional E-value: 3.5e-08
                        BLOC1_2  11 leaeleatvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyske 90 
                                    l+ ele+   d+  L +   + +  y++l+++++sl + +++l++    ++++ ++id ++k++++L + ++ LD+ + +
  gi|119720182|ref|YP_920677.1|  64 LRRELEGLERDVASLAERVSRLEGAYAELSKRIDSLGERISDLDK---RIDSLDKRIDGLDKRIDSLDKRIESLDKRIDS 140
                                    678999999999999999999999999999999999999999999...88888899999999999999999999999999 PP

                        BLOC1_2  91 LEakf 95 
                                    L +++
  gi|119720182|ref|YP_920677.1| 141 LDKRL 145
                                    98775 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1      0.34        27      48      91 ..      49      92 ..      38      95 .. 0.64
   2 !   28.9   0.1   8.4e-09   6.6e-07      17     103 ..      74     160 ..      68     166 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.34
                        DUF3450 48 ellaeyralkeeleslevyneqlerlvasqeqeiasleeqieei 91
                                   ++++  +a ++ +e l+ + e ler vas+ +++++le   +e+
  gi|119720182|ref|YP_920677.1| 49 DVEKHWEATRRDIEGLRRELEGLERDVASLAERVSRLEGAYAEL 92
                                   55555666666666777777777777777776666666655554 PP

  == domain 2  score: 28.9 bits;  conditional E-value: 8.4e-09
                        DUF3450  17 tldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeier 96 
                                    +++++ +  ++   a a+ +k+id+l +  ++l +++ +l ++++ l++  + l++ ++s++++i+sl+++++ i +i+ 
  gi|119720182|ref|YP_920677.1|  74 DVASLAERVSRLEGAYAELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDSLDKRLDHIAKISY 153
                                    66777788888888999*************************************************************98 PP

                        DUF3450  97 elvplle 103
                                     l+   +
  gi|119720182|ref|YP_920677.1| 154 TLTASVL 160
                                    8876655 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0     0.013      0.98       5      40 ..      50      85 ..      48      94 .. 0.85
   2 !   11.1   0.0    0.0053      0.41       3      40 ..      69     106 ..      68     108 .. 0.94
   3 !   17.4   0.3   5.4e-05    0.0042       1      30 [.     109     138 ..      95     159 .. 0.52

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.013
                      FlaC_arch  5 lEnklsklsteletvkkeneelsksveelkenVkdl 40
                                   +E+  + +   +e +++e+e l+ +v  l e+V +l
  gi|119720182|ref|YP_920677.1| 50 VEKHWEATRRDIEGLRRELEGLERDVASLAERVSRL 85
                                   677777888899*********************988 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0053
                      FlaC_arch   3 delEnklsklsteletvkkeneelsksveelkenVkdl 40 
                                    + lE ++ +l  +++ ++    elsk ++ l e++ dl
  gi|119720182|ref|YP_920677.1|  69 EGLERDVASLAERVSRLEGAYAELSKRIDSLGERISDL 106
                                    569*******************************9987 PP

  == domain 3  score: 17.4 bits;  conditional E-value: 5.4e-05
                      FlaC_arch   1 ridelEnklsklsteletvkkeneelsksv 30 
                                    rid+l+++++ l+ +++++ k +e+l k +
  gi|119720182|ref|YP_920677.1| 109 RIDSLDKRIDGLDKRIDSLDKRIESLDKRI 138
                                    333333333333333333333333333333 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   1.9   4.7e-09   3.7e-07      70     169 ..      48     147 ..      10     157 .. 0.87

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 4.7e-09
                          ATG16  70 skqsakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrek 149
                                     + +++ +++   +  lr el+ l +  + la+r+ +l+ + ++l +++ +  er+ +l +++ +l ++++ +++++  +
  gi|119720182|ref|YP_920677.1|  48 HDVEKHWEATRRDIEGLRRELEGLERDVASLAERVSRLEGAYAELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSL 127
                                    4567778888999999**************************************************************** PP

                          ATG16 150 eklvqdlqDElsaLqlqlnq 169
                                    +k ++ l   +++L  +l +
  gi|119720182|ref|YP_920677.1| 128 DKRIESLDKRIDSLDKRLDH 147
                                    *****999988888777766 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0     0.036       2.8      22      50 ..      57      85 ..      39      88 .. 0.73
   2 !   11.2   0.1     0.003      0.23      23      59 ..      79     115 ..      77     117 .. 0.70
   3 !   15.2   0.6   0.00017     0.013      19      60 ..     110     151 ..     108     152 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.036
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHCC- CS
                          DivIC 22 lkqeiaalqaelaklkaeneeLeaevkdL 50
                                   ++++i+ l +el+ l  + ++L+++v++L
  gi|119720182|ref|YP_920677.1| 57 TRRDIEGLRRELEGLERDVASLAERVSRL 85
                                   56677777777777777777777777776 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.003
                                    HHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXXXX CS
                          DivIC  23 kqeiaalqaelaklkaeneeLeaevkdLksdedyiee 59 
                                     + + +l+  +a+l++++++L ++++dL +  d +++
  gi|119720182|ref|YP_920677.1|  79 AERVSRLEGAYAELSKRIDSLGERISDLDKRIDSLDK 115
                                    5667777888888888888888888888666666655 PP

  == domain 3  score: 15.2 bits;  conditional E-value: 0.00017
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXXXXX CS
                          DivIC  19 ykqlkqeiaalqaelaklkaeneeLeaevkdLksdedyieer 60 
                                    + +l++ i+ l + +++l +++e+L+++++ L +  d i+++
  gi|119720182|ref|YP_920677.1| 110 IDSLDKRIDGLDKRIDSLDKRIESLDKRIDSLDKRLDHIAKI 151
                                    6688999999**********************8888888775 PP

>> DUF4988  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.1    0.0034      0.27       1      47 [.      71     118 ..      64     119 .. 0.75
   2 !   10.6   0.1    0.0041      0.32       2      29 ..     100     127 ..      99     127 .. 0.91
   3 !   15.4   0.2   0.00014     0.011       1      33 [.     120     152 ..     120     162 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0034
                        DUF4988   1 leddvndlkdrvaaleeqvkelndniealkkll.eegkviteveensd 47 
                                    le dv +l +rv+ le ++ el + i++l++ + +  k i +++++ d
  gi|119720182|ref|YP_920677.1|  71 LERDVASLAERVSRLEGAYAELSKRIDSLGERIsDLDKRIDSLDKRID 118
                                    577888888888888888888888888886533366677777666665 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0041
                        DUF4988   2 eddvndlkdrvaaleeqvkelndnieal 29 
                                     ++++dl++r+ +l+++++ l++ i++l
  gi|119720182|ref|YP_920677.1| 100 GERISDLDKRIDSLDKRIDGLDKRIDSL 127
                                    5799******************999987 PP

  == domain 3  score: 15.4 bits;  conditional E-value: 0.00014
                        DUF4988   1 leddvndlkdrvaaleeqvkelndniealkkll 33 
                                    l++++++l++r+++l++++++l++ ++ ++k+ 
  gi|119720182|ref|YP_920677.1| 120 LDKRIDSLDKRIESLDKRIDSLDKRLDHIAKIS 152
                                    6789**********************9999885 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0      0.25        20      57      96 ..      47      86 ..      41      92 .. 0.61
   2 ?    9.6   0.0     0.011      0.88      66      98 ..      84     116 ..      76     123 .. 0.60
   3 !   11.5   0.1    0.0027      0.21      68      95 ..     121     148 ..     120     157 .. 0.56

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.25
                                   EE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    Prefoldin_2 57 kqdkeevkeeLeerketlekeiktlekqleklekeleelk 96
                                   k+d+e+  e    ++e l  e++ le+   +l ++++ l+
  gi|119720182|ref|YP_920677.1| 47 KHDVEKHWEATRRDIEGLRRELEGLERDVASLAERVSRLE 86
                                   5555555566666666666666666666666666666555 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.011
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    Prefoldin_2  66 eLeerketlekeiktlekqleklekeleelkee 98 
                                    +Le   ++l+k+i++l +++++l k+++ l + 
  gi|119720182|ref|YP_920677.1|  84 RLEGAYAELSKRIDSLGERISDLDKRIDSLDKR 116
                                    566666666666666666666666666655544 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.0027
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    Prefoldin_2  68 eerketlekeiktlekqleklekeleel 95 
                                    ++r+++l+k+i++l k++++l k+l+ +
  gi|119720182|ref|YP_920677.1| 121 DKRIDSLDKRIESLDKRIDSLDKRLDHI 148
                                    5555555555555555555555555443 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0       3.2   2.5e+02      44      61 ..      63      80 ..      58      83 .. 0.73
   2 !   12.5   0.0    0.0015      0.12      28      61 ..      75     108 ..      71     115 .. 0.86
   3 !   13.8   0.0   0.00061     0.047      28      61 ..     103     136 ..     100     150 .. 0.63
   4 ?    9.8   0.0     0.011      0.85      26      59 ..     122     155 ..     121     159 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 3.2
                                   HHHHHHHHHHHHHHHHHH CS
                         bZIP_1 44 sLkseleelkkevekLks 61
                                    L+ ele l+ +v++L +
  gi|119720182|ref|YP_920677.1| 63 GLRRELEGLERDVASLAE 80
                                   688888888888887754 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.0015
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         bZIP_1  28 ieeLerrvkaLekeNksLkseleelkkevekLks 61 
                                    ++ L++rv+ Le+  ++L++++++l + ++ L +
  gi|119720182|ref|YP_920677.1|  75 VASLAERVSRLEGAYAELSKRIDSLGERISDLDK 108
                                    6789999999999999999999999999988865 PP

  == domain 3  score: 13.8 bits;  conditional E-value: 0.00061
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         bZIP_1  28 ieeLerrvkaLekeNksLkseleelkkevekLks 61 
                                    i+ L +r + L+k    L +++++l k +e+L +
  gi|119720182|ref|YP_920677.1| 103 ISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDK 136
                                    5666666666666666666666666666666543 PP

  == domain 4  score: 9.8 bits;  conditional E-value: 0.011
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         bZIP_1  26 aeieeLerrvkaLekeNksLkseleelkkevekL 59 
                                    ++i+ L +r + L+k   sL ++l+ ++k +++L
  gi|119720182|ref|YP_920677.1| 122 KRIDSLDKRIESLDKRIDSLDKRLDHIAKISYTL 155
                                    6899999******************999999887 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.9     8e-08   6.3e-06      37     103 ..      76     142 ..      12     150 .. 0.66

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 8e-08
                                    HHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHHHHHHHHHHC CS
                          DUF16  37 kkieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetleliletLqkinkRlDsie 103
                                      + ++v+ l+   ++l + ++ +ge+i++l ++++  +++++ +d+ ++++ + +++++kR+Ds++
  gi|119720182|ref|YP_920677.1|  76 ASLAERVSRLEGAYAELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDSLD 142
                                    3444455555555555555555555555555555555555555555555555555555555555443 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.6   3.2e-08   2.5e-06     142     241 ..      62     157 ..      48     166 .. 0.78

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 3.2e-08
                           Spc7 142 egleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkke 221
                                    egl+++legle+d + L+++ + l+ ++ el+++ ++l e++ +l ++ ++   +  +++  l +++++l++ ie++ k+
  gi|119720182|ref|YP_920677.1|  62 EGLRRELEGLERDVASLAERVSRLEGAYAELSKRIDSLGERISDLDKRIDS---L-DKRIDGLDKRIDSLDKRIESLDKR 137
                                    677888888888888888888888888888888888888888888885554...3.347999999999999999999999 PP

                           Spc7 222 laelqeqleeleekieelke 241
                                    +++l ++l+++++   +l++
  gi|119720182|ref|YP_920677.1| 138 IDSLDKRLDHIAKISYTLTA 157
                                    99999999988877766665 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.2   1.6e-07   1.3e-05     345     430 ..      60     145 ..      31     147 .. 0.85
   2 ?    5.4   0.1     0.055       4.3     305     342 ..     121     159 ..     118     165 .. 0.67

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.6e-07
                                    THHHHHHHHHHHHHHHHHHHHHHS-SS---STTGGGTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           EzrA 345 klrelekelkelekdyeeleekleekkvaYSelqeeleeleekleeieekqeeileslkslrkdEkrAreqldeikkelk 424
                                     +++l +el+ le+d+ +l e+++  + aY el++++++l e++++++++ +++++ +++l k      ++++ ++k++ 
  gi|119720182|ref|YP_920677.1|  60 DIEGLRRELEGLERDVASLAERVSRLEGAYAELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRID 139
                                    4667889*******************************************************999999999999999988 PP

                                    HHHHHS CS
                           EzrA 425 eikrki 430
                                    ++ +++
  gi|119720182|ref|YP_920677.1| 140 SLDKRL 145
                                    877665 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.055
                                    TTTSSSSSHHHHT--HHHHTTGGG-TTTS-.GGGSSTTT CS
                           EzrA 305 eknlkelkeklehlekqnkelkeeldrlkq.sYeLseee 342
                                    +k++++l +++e l+k ++ l + ld++ + sY+L+ + 
  gi|119720182|ref|YP_920677.1| 121 DKRIDSLDKRIESLDKRIDSLDKRLDHIAKiSYTLTASV 159
                                    566777777777777777777777777755477777665 PP

>> Lzipper-MIP1  Leucine-zipper of ternary complex factor MIP1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.2   1.6e-05    0.0012      14      78 ..      20      86 ..      19      91 .. 0.83
   2 ?    2.5   0.0       2.3   1.8e+02      53      79 ..      89     115 ..      83     119 .. 0.82
   3 ?    3.2   0.0       1.4   1.1e+02       5      34 ..     130     159 ..     126     172 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.6e-05
                   Lzipper-MIP1 14 eqLqerLqeeeklrraLekal....ssssdgsllslstllpkkakellkeiallEeevvkLEqkllsLy 78
                                   ++L e L  e ++r aL +a+    ++++     +    +++ ++ l++e++ lE +v+ L ++++ L+
  gi|119720182|ref|YP_920677.1| 20 KRLAELLVSEPDVRLALINAVirdvATKH--DVEKHWEATRRDIEGLRRELEGLERDVASLAERVSRLE 86
                                   589999***************98643333..3344444589***********************99986 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 2.3
                   Lzipper-MIP1  53 akellkeiallEeevvkLEqkllsLyr 79 
                                     +el k i  l e ++ L ++++sL  
  gi|119720182|ref|YP_920677.1|  89 YAELSKRIDSLGERISDLDKRIDSLDK 115
                                    578889999999999999999999976 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 1.4
                   Lzipper-MIP1   5 krssLeqeveqLqerLqeeeklrraLekal 34 
                                    +  sL + +  L +rL++  k+   L   +
  gi|119720182|ref|YP_920677.1| 130 RIESLDKRIDSLDKRLDHIAKISYTLTASV 159
                                    5578999*********99888888887555 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.1      0.27        22      33      54 ..      61      82 ..      54      92 .. 0.55
   2 !   20.6   0.2   6.7e-06   0.00053       3      54 ..      80     131 ..      78     157 .. 0.65

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.27
                                   HHHHHHHHHHHHHT-XXXXXXX CS
                           SlyX 33 idrlqrqlrllaerlkeleess 54
                                   i+ l+r+l+ l++ +++l+e+ 
  gi|119720182|ref|YP_920677.1| 61 IEGLRRELEGLERDVASLAERV 82
                                   5555555555555555554443 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 6.7e-06
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXX CS
                           SlyX   3 erleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkeleess 54 
                                    er+ +LE  +a + + i++L + + + +++id l ++++ l +r+ +l+++ 
  gi|119720182|ref|YP_920677.1|  80 ERVSRLEGAYAELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRI 131
                                    6666666666666666666666666666666666666666666666555443 PP

>> FliD_C  Flagellar hook-associated protein 2 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.6   5.7e-06   0.00045     172     224 ..      91     145 ..      36     157 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 5.7e-06
                                    SHHHHHHHHHHHHH..STT.SHHHHHHHHXXXXHHHHHHHHHHHHHCHHHHHHHH CS
                         FliD_C 172 glatrlenllksyv..kssngtlqtasknltkqikdldkkiedldkrletleerl 224
                                    +l +r+++l + ++  + + ++l+++++ l+k+i++ldk+ie+ldkr+++l +rl
  gi|119720182|ref|YP_920677.1|  91 ELSKRIDSLGERISdlDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDSLDKRL 145
                                    3444555554444422233345556666666666666666666666666666666 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   1.8   2.1e-07   1.6e-05       8     100 ..      50     142 ..      42     152 .. 0.37

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 2.1e-07
                 CENP-F_leu_zip   8 vlekLKeserkadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLek 87 
                                    v++ + +++r+ + L+   e+Ler++  + e  ++++    +  + + +l e i  l ++   l   ++ l +  ++L+k
  gi|119720182|ref|YP_920677.1|  50 VEKHWEATRRDIEGLRRELEGLERDVASLAERVSRLEGAYAELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDK 129
                                    33333333333333333333333333333333333333322222233333333333333333333333333333333333 PP

                 CENP-F_leu_zip  88 elqkkqervseLe 100
                                     ++   +r+++L+
  gi|119720182|ref|YP_920677.1| 130 RIESLDKRIDSLD 142
                                    3333333333333 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0       0.3        24      81     105 ..      62      86 ..      34      92 .. 0.79
   2 !   19.9   0.0   7.5e-06   0.00059      34     101 ..      90     159 ..      84     171 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.3
                   Baculo_PEP_C  81 dtlrneLtnlnsiltnLlssvtNin 105
                                    + lr eL++l+ ++++L+  v  ++
  gi|119720182|ref|YP_920677.1|  62 EGLRRELEGLERDVASLAERVSRLE 86 
                                    5689999999999999998887665 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 7.5e-06
                   Baculo_PEP_C  34 aqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq...dtlrneLtnlnsiltnLlssv 101
                                    a+l++ +d++ +++++l++++ sl + +d  ld+ ++ L++ + +l    d+l+++L+ + +i  +L++sv
  gi|119720182|ref|YP_920677.1|  90 AELSKRIDSLGERISDLDKRIDSLDKRID-GLDKRIDSLDKRIESLDkriDSLDKRLDHIAKISYTLTASV 159
                                    78999999999999999999999666665.79999999999999999999999999999999999999988 PP

>> BRE1  BRE1 E3 ubiquitin ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   0.00019     0.015       8      94 ..      50     136 ..      48     137 .. 0.78
   2 !   15.3   0.1    0.0002     0.015       5      70 ..      82     147 ..      78     158 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 0.00019
                           BRE1   8 lekafeelseqlskkvkeltileekklrleaekakadqkyfaamrskdalenelkkLnkllsKsselieqLkelekefvr 87 
                                    +ek +e++++ ++ +  el+ le  ++ l    ++ +  y ++ + +d+l   +  L k ++   + i+ L  +  ++ +
  gi|119720182|ref|YP_920677.1|  50 VEKHWEATRRDIEGLRRELEGLERDVASLAERVSRLEGAYAELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDK 129
                                    67888888888888888888888888888888888888888888888888888888888888888888888877777777 PP

                           BRE1  88 klkelek 94 
                                    ++++l+k
  gi|119720182|ref|YP_920677.1| 130 RIESLDK 136
                                    7777765 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 0.0002
                           BRE1   5 LvklekafeelseqlskkvkeltileekklrleaekakadqkyfaamrskdalenelkkLnkllsK 70 
                                    + +le a+ els+ ++++ + +++l +++  l++ ++  d+ + ++++ +++l++ +  L k l+ 
  gi|119720182|ref|YP_920677.1|  82 VSRLEGAYAELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDSLDKRLDH 147
                                    578999*************************************************99999887765 PP

>> Laminin_I  Laminin Domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   1.7e-07   1.4e-05      32     111 ..      51     132 ..      33     156 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.7e-07
                      Laminin_I  32 lskesakkskieilekelesLaqeteeLqkkatqvlakaqkvnaesertlnnakeLaekikkladnikeilekvatlne. 110
                                    ++  +a+ ++ie+l +ele+L+ ++ +L++++ +      ++ ++++   +++++L++ i  l++ i  + +++  l++ 
  gi|119720182|ref|YP_920677.1|  51 EKHWEATRRDIEGLRRELEGLERDVASLAERVSRLEGAYAELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKr 130
                                    566788999***********************************************************999999999984 PP

                      Laminin_I 111 .n 111
                                     +
  gi|119720182|ref|YP_920677.1| 131 iE 132
                                    43 PP

>> DUF3552  Domain of unknown function (DUF3552)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   2.0   2.7e-07   2.1e-05      62     147 ..      64     152 ..      31     162 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 2.7e-07
                        DUF3552  62 ihklreelekelkerrnelqrle...kRllqkeetLdrkeeslekkeesleekekelkqkeqsleekeeeleelveeqrq 138
                                    +++  e le+++ +  + ++rle     l ++ ++L ++ ++l+k+ +sl ++ + l+++ +sl+++ e+l++ + + ++
  gi|119720182|ref|YP_920677.1|  64 LRRELEGLERDVASLAERVSRLEgayAELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDSLDK 143
                                    333344457777776666666663336899************************************************** PP

                        DUF3552 139 eLerisgLt 147
                                    +L +i++++
  gi|119720182|ref|YP_920677.1| 144 RLDHIAKIS 152
                                    ******987 PP

>> KASH_CCD  Coiled-coil region of CCDC155 or KASH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1       5.8   4.5e+02     109     139 ..       6      36 ..       4      69 .. 0.78
   2 !   22.7   0.1   8.9e-07     7e-05      64     144 ..      63     143 ..      48     158 .. 0.61

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 5.8
                       KASH_CCD 109 eenikllaekdelkkklkeLlkekaeLkkql 139
                                    e + kl  e  +++k+l+eLl ++ +++  l
  gi|119720182|ref|YP_920677.1|   6 EYIVKLFEEDPKSRKRLAELLVSEPDVRLAL 36 
                                    5577899999999999999999988877665 PP

  == domain 2  score: 22.7 bits;  conditional E-value: 8.9e-07
                       KASH_CCD  64 lleeEleelkalvkeleEkrarlkaqnkqlekenqsLiakiesLqeenikllaekdelkkklkeLlkekaeLkkqlhele 143
                                     l  Ele l + v +l E+  rl+    +l k  +sL ++i +L+ ++  l   +d l k++  L k +++L k++++l+
  gi|119720182|ref|YP_920677.1|  63 GLRRELEGLERDVASLAERVSRLEGAYAELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDSLD 142
                                    45556666666666666666666666666666666666666666666666666666666666666666666666655554 PP

                       KASH_CCD 144 e 144
                                    +
  gi|119720182|ref|YP_920677.1| 143 K 143
                                    4 PP

>> DUF4140  N-terminal domain of unknown function (DUF4140)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   4.4    0.0023      0.18      47      84 ..      39     120 ..      31     134 .. 0.65
   2 ?    9.3   0.3     0.019       1.5      67      96 ..     117     146 ..     114     150 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0023
                        DUF4140  47 atildvqvervpnreaeee............................................elkalraeleeledela 82 
                                    a+i dv+++++ ++  e++                                            +++ l++++++l ++++
  gi|119720182|ref|YP_920677.1|  39 AVIRDVATKHDVEKHWEATrrdieglrreleglerdvaslaervsrlegayaelskridslgeRISDLDKRIDSLDKRID 118
                                    78888888888888888888878888888888888888888888888874444444444444224444444444444444 PP

                        DUF4140  83 al 84 
                                     l
  gi|119720182|ref|YP_920677.1| 119 GL 120
                                    44 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.019
                        DUF4140  67 lkalraeleeledelaaledelaaaearla 96 
                                    ++ l++++++l ++++ l+++++++++rl+
  gi|119720182|ref|YP_920677.1| 117 IDGLDKRIDSLDKRIESLDKRIDSLDKRLD 146
                                    678999999999999999999999999986 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0      0.54        42      29      60 ..      53      84 ..      28      91 .. 0.71
   2 !   18.0   0.5   3.8e-05     0.003      12      64 ..     102     151 ..      87     165 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.54
                        NPV_P10 29 dvqenlpdvtelnekLdaqsaqLaeletkven 60
                                   + ++  +d++ l  +L+++   +a+l + v+ 
  gi|119720182|ref|YP_920677.1| 53 HWEATRRDIEGLRRELEGLERDVASLAERVSR 84
                                   34556678888999999999999999999986 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 3.8e-05
                        NPV_P10  12 dikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdi 64 
                                     i+++d+++d+l++++d +++ +     l ++++++ + +++l++ +++I +i
  gi|119720182|ref|YP_920677.1| 102 RISDLDKRIDSLDKRIDGLDKRIDS---LDKRIESLDKRIDSLDKRLDHIAKI 151
                                    5899999**********99997666...7788888888888888888777765 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.3     7e-07   5.5e-05      11      89 ..      71     148 ..      62     149 .. 0.93

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 7e-07
                Snapin_Pallidin  11 lepkldeldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqklkkRaekL 89 
                                    le ++  l e+++ l+    eL++++d+l e++ +l +  + ++ ++++   k++ ++ kr++sl +r+ +l kR++++
  gi|119720182|ref|YP_920677.1|  71 LERDVASLAERVSRLEGAYAELSKRIDSLGERISDLDKRID-SLDKRIDGLDKRIDSLDKRIESLDKRIDSLDKRLDHI 148
                                    67889999****************************99999.77899*****************************997 PP

>> Tektin  Tektin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.1      0.19        15      60     350 ..      62      92 ..      38      98 .. 0.42
   2 !   19.3   0.5   4.8e-06   0.00038      47      97 ..      98     149 ..      94     156 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.19
                         Tektin  60 eeLekeleelkeeieaLeeekrrlekalealeeplhiaqeclelRekRqgidlvhDevekeLlkEveliegvqellkrtl 139
                                    e                                                                               
  gi|119720182|ref|YP_920677.1|  62 E------------------------------------------------------------------------------- 62 
                                    2............................................................................... PP

                         Tektin 140 eqaeeqlrllraakhkLekdlsdKkeAleiDeeclslkntsanisykpgaerlpetsstpeeWekftkdnieraekerqa 219
                                                                                                                    
  gi|119720182|ref|YP_920677.1|   - --------------------------------------------------------------------------------   -
                                    ................................................................................ PP

                         Tektin 220 sakLreaidsilkqtandlraqaeavnealrkrieetedaknkleeqlkkvleeiaeleknieeLekairdkeaplklaq 299
                                                                                                                    
  gi|119720182|ref|YP_920677.1|   - --------------------------------------------------------------------------------   -
                                    ................................................................................ PP

                         Tektin 300 tRlenRtqRpnvElcrDeaqyrLveEvkeleetieaLkeklaeaeaslkaL 350
                                                         +L +E++ le+++++L e+++  e ++ +L
  gi|119720182|ref|YP_920677.1|  63 ---------------------GLRRELEGLERDVASLAERVSRLEGAYAEL 92 
                                    .....................233333333333333333333333333333 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 4.8e-06
                         Tektin  47 rLeeRiediefwkeeLekeleelkeeieaLeeekrrlekalealeeplh.ia 97 
                                    +L+eRi+d+++  + L+k ++ l++ i++L +  + l+k +++l++ l+ ia
  gi|119720182|ref|YP_920677.1|  98 SLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDSLDKRLDhIA 149
                                    79*******************************************9998444 PP

>> Spc29  Spindle Pole Component 29
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0    0.0014      0.11     112     164 ..      40      92 ..      30     100 .. 0.85
   2 !   13.1   1.3   0.00082     0.064     112     167 ..      96     151 ..      88     161 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0014
                          Spc29 112 iyssvkkivelekklddqkleIkeLkreleqqrtvnseLqekvaeleeevkrl 164
                                    + ++v +  ++ek  +  +  I+ L+rele  +     L e+v +le    +l
  gi|119720182|ref|YP_920677.1|  40 VIRDVATKHDVEKHWEATRRDIEGLRRELEGLERDVASLAERVSRLEGAYAEL 92 
                                    5567777799*********************99999***********877555 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00082
                          Spc29 112 iyssvkkivelekklddqkleIkeLkreleqqrtvnseLqekvaeleeevkrlaal 167
                                    i s  ++i +l+k +d+   +I  L + ++     ++ L ++++ l+++++++a +
  gi|119720182|ref|YP_920677.1|  96 IDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDSLDKRLDHIAKI 151
                                    33333344446666666666666666666666666666666666666666666555 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.3   1.3e-05     0.001       8      56 ..      92     143 ..      28     155 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.3e-05
                        DUF4795   8 l...lkklqeaieklqeelekleekvkelekrledkekklealkkqieelek 56 
                                    l   ++ l e i++l++++++l+++   l+kr+  ++k +e+l k i+ l+k
  gi|119720182|ref|YP_920677.1|  92 LskrIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDSLDK 143
                                    1333666667777777777777777777777777777777777777776665 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   0.00061     0.047      43     107 ..      35      99 ..      31     105 .. 0.93
   2 !   15.0   0.1   0.00024     0.019      57     121 ..      77     141 ..      77     160 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00061
                           ADIP  43 sLlqardrdleqreslnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktl 107
                                    +L+ a  rd +++  +++  +  + +ie l+ + e l++ +++l+ +++ ++ + ++l k++ +l
  gi|119720182|ref|YP_920677.1|  35 ALINAVIRDVATKHDVEKHWEATRRDIEGLRRELEGLERDVASLAERVSRLEGAYAELSKRIDSL 99 
                                    7999999*****************************************************99887 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 0.00024
                           ADIP  57 slnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrl 121
                                    sl+e++++le  ++ l+++i++l ++ ++l+++++++ ++   l k++ +l++ + ++   +  l
  gi|119720182|ref|YP_920677.1|  77 SLAERVSRLEGAYAELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDSL 141
                                    57899999999999999999999999999999999999999999999999998887776655544 PP

>> Csm1_N  Csm1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0      0.14        11      37      60 ..      62      85 ..      50      92 .. 0.58
   2 ?    8.3   0.0     0.038         3      32      63 ..      92     123 ..      90     128 .. 0.78
   3 !   11.3   0.1    0.0043      0.34      37      64 ..     118     145 ..     113     153 .. 0.62

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.14
                         Csm1_N 37 etkdqeiesLkeqlaeleekvkel 60
                                   e   +e+e L++ +a+l e+v++l
  gi|119720182|ref|YP_920677.1| 62 EGLRRELEGLERDVASLAERVSRL 85
                                   333455555555555555555555 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.038
                         Csm1_N  32 LsqkletkdqeiesLkeqlaeleekvkeleer 63 
                                    Ls+++++  ++i+ L +++++l+++++ l++r
  gi|119720182|ref|YP_920677.1|  92 LSKRIDSLGERISDLDKRIDSLDKRIDGLDKR 123
                                    66777778888999999999999998888877 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.0043
                         Csm1_N  37 etkdqeiesLkeqlaeleekvkeleerr 64 
                                    +  d++i sL +++++l++++++l++r 
  gi|119720182|ref|YP_920677.1| 118 DGLDKRIDSLDKRIESLDKRIDSLDKRL 145
                                    5556666666666666666666666654 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   2.8   2.1e-06   0.00016      49     134 ..      59     148 ..      37     154 .. 0.62

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 2.1e-06
                  Tropomyosin_1  49 eevekleeklkeakekaeesekkktnne....altrkiqlLEeeleesdkkLkettekLretdvkaeelERkvkaLeqer 124
                                     ++e l  +l+  ++ + + +++ +  e    +l+++i+ L e + + dk++ +  +++   d++ + l++++++L+++ 
  gi|119720182|ref|YP_920677.1|  59 RDIEGLRRELEGLERDVASLAERVSRLEgayaELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRI 138
                                    34444444444333333333333333333333777777777777777777777777777777777777777777777777 PP

                  Tropomyosin_1 125 dewekkyeel 134
                                    d  +k+++++
  gi|119720182|ref|YP_920677.1| 139 DSLDKRLDHI 148
                                    7777777765 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.2   1.1e-06   8.4e-05      28     126 ..      52     146 ..      44     156 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.1e-06
                                    CCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHH CS
                      Fib_alpha  28 kyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvL 107
                                    k+ + +++d+e l++ele +++   +  e v++++  ++e  k  +     + +  ++l+++i  l+++id   ++i  L
  gi|119720182|ref|YP_920677.1|  52 KHWEATRRDIEGLRRELEGLERDVASLAERVSRLEGAYAELSKRIDS----LGERISDLDKRIDSLDKRIDGLDKRIDSL 127
                                    566778999****************************9999999984....66666777777778888888888888888 PP

                                    HHHHHHHHHHHHHHHHHHH CS
                      Fib_alpha 108 qnvlesneqkiqkLeqdid 126
                                     + +es++++i  L +  d
  gi|119720182|ref|YP_920677.1| 128 DKRIESLDKRIDSLDKRLD 146
                                    8888888888888877654 PP

>> Nup54  Nucleoporin complex subunit 54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.2   2.5e-06    0.0002      43     125 ..      66     147 ..      47     159 .. 0.71

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2.5e-06
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SS---SSHHHHHHHHHHHHHH CS
                          Nup54  43 kevaqhrerlkeisdrleeleqkhqletsvrlekakkrhvelshRllrllrkleilrsrgyaldaeEeelrarletleaq 122
                                    +e++ ++  + ++++r++ le    +e+s+r++ +  r   l +R+ +l ++++ l +r  +ld+  e+l +r+++l+++
  gi|119720182|ref|YP_920677.1|  66 RELEGLERDVASLAERVSRLE-GAYAELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDSLDKR 144
                                    456666667777777777777.7777777777777777777777777777777777777777777777777777777777 PP

                                    HS- CS
                          Nup54 123 lnd 125
                                    l++
  gi|119720182|ref|YP_920677.1| 145 LDH 147
                                    774 PP

>> MbeD_MobD  MbeD/MobD like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.1    0.0048      0.38      35      68 ..      52      85 ..      47      87 .. 0.90
   2 ?    7.4   0.0     0.058       4.6      44      65 ..     103     124 ..      86     150 .. 0.51

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0048
                      MbeD_MobD 35 rmfeltqrenaaLseqvtgLsqQVesLseqvrRl 68
                                   +  e t+r+   L+   +gL + V sL+e+v+Rl
  gi|119720182|ref|YP_920677.1| 52 KHWEATRRDIEGLRRELEGLERDVASLAERVSRL 85
                                   66789999999**********************9 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.058
                      MbeD_MobD  44 naaLseqvtgLsqQVesLseqv 65 
                                     + L ++++ L + ++ L +++
  gi|119720182|ref|YP_920677.1| 103 ISDLDKRIDSLDKRIDGLDKRI 124
                                    3333333333333333333332 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0    0.0017      0.13       4      52 ..      60     108 ..      57     112 .. 0.88
   2 !   10.3   0.4     0.008      0.63      84     116 ..     111     143 ..     104     152 .. 0.43

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.0017
                        DUF5082   4 kisklqaqiaelrseiaaleekIerLkeaktklsdekeslkqkkkklek 52 
                                     i+ l+++ + l+ ++a+l e ++rL+ a+ +ls+   sl + +++l k
  gi|119720182|ref|YP_920677.1|  60 DIEGLRRELEGLERDVASLAERVSRLEGAYAELSKRIDSLGERISDLDK 108
                                    688899999999***********************99999999999876 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.008
                        DUF5082  84 dkldelidaieeEIerLenqiseaqgvldtlqs 116
                                    d ld+ id +++ I  L + i+++ + +d+l++
  gi|119720182|ref|YP_920677.1| 111 DSLDKRIDGLDKRIDSLDKRIESLDKRIDSLDK 143
                                    333333444444444444444444444444443 PP

>> CLZ  C-terminal leucine zipper domain of cyclic nucleotide-gated channels
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.2    0.0063      0.49      23      70 ..      58     108 ..      48     109 .. 0.74
   2 !   12.0   0.2    0.0026       0.2      27      59 ..     111     143 ..      95     158 .. 0.52

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0063
                            CLZ  23 gaeqkeleekverLessLeaLqtrlarLlaeyessqrk...LkqRitkLEk 70 
                                    + + + l + +e Le  + +L  r+ rL + y +  ++   L +Ri++L+k
  gi|119720182|ref|YP_920677.1|  58 RRDIEGLRRELEGLERDVASLAERVSRLEGAYAELSKRidsLGERISDLDK 108
                                    45667788899999*************998887776652225678888876 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.0026
                            CLZ  27 keleekverLessLeaLqtrlarLlaeyessqr 59 
                                    ++l+++++ L++++++L++r++ L +  +s ++
  gi|119720182|ref|YP_920677.1| 111 DSLDKRIDGLDKRIDSLDKRIESLDKRIDSLDK 143
                                    333444444444444444444444443333333 PP

>> MscS_porin  Mechanosensitive ion channel porin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0     0.017       1.3      79     139 ..      46     106 ..      16     109 .. 0.88
   2 !   13.8   0.0   0.00039     0.031     164     207 ..     102     145 ..      97     152 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.017
                     MscS_porin  79 sleeLeqrllqtssqlqelqeqlaqlnsqlvelqtrperaqqqltearqrlqeirnrLnst 139
                                    +  + e+ +++t  + + l+++l  l+ ++++l  r +r+  + +e ++r++ +  r++++
  gi|119720182|ref|YP_920677.1|  46 TKHDVEKHWEATRRDIEGLRRELEGLERDVASLAERVSRLEGAYAELSKRIDSLGERISDL 106
                                    566789999******************************************9998887665 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 0.00039
                     MscS_porin 164 qieeleqellsnnnrqeLlklqrdllklriqqleqelqaLqell 207
                                    +i+ l++   s ++r++ l ++ d l +ri+ l+++++ L ++l
  gi|119720182|ref|YP_920677.1| 102 RISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDSLDKRL 145
                                    56666667777777777777777777777777777777666554 PP

>> HSBP1  Heat shock factor binding protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.9   0.00043     0.034      23      46 ..      90     113 ..      82     115 .. 0.85
   2 !   10.8   3.0    0.0044      0.34      26      46 ..     114     134 ..     111     136 .. 0.87
   3 ?    7.8   0.9     0.036       2.8      27      45 ..     129     147 ..     129     151 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 0.00043
                          HSBP1  23 dqilsriDdMssriDdLEksiadl 46 
                                     ++ +riD +++ri dL+k i++l
  gi|119720182|ref|YP_920677.1|  90 AELSKRIDSLGERISDLDKRIDSL 113
                                    57889****************987 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0044
                          HSBP1  26 lsriDdMssriDdLEksiadl 46 
                                     +riD + +riD+L+k i++l
  gi|119720182|ref|YP_920677.1| 114 DKRIDGLDKRIDSLDKRIESL 134
                                    58****************987 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.036
                          HSBP1  27 sriDdMssriDdLEksiad 45 
                                    +ri+ + +riD+L+k ++ 
  gi|119720182|ref|YP_920677.1| 129 KRIESLDKRIDSLDKRLDH 147
                                    5999999******998875 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.3   7.6e-06   0.00059     390     470 ..      73     148 ..      37     160 .. 0.52

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 7.6e-06
                         AAA_13 390 eekeeakkklelhlveeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeeinkeLka 469
                                    ++++++++ +      +le ++ e+ k +++l + i++l+k+++   +++  l+++i  L k++++  + ++ + k L +
  gi|119720182|ref|YP_920677.1|  73 RDVASLAERVS-----RLEGAYAELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDSLDKRLDH 147
                                    33333333333.....3333444444555555555555555555555555555555555555555555555555555554 PP

                         AAA_13 470 f 470
                                    +
  gi|119720182|ref|YP_920677.1| 148 I 148
                                    4 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0      0.95        74      80     117 ..      55      92 ..      42      95 .. 0.62
   2 ?    5.7   0.1      0.16        13       7      23 ..      91     107 ..      64     118 .. 0.49
   3 !   13.0   0.2   0.00094     0.073      79     111 ..     117     149 ..     112     159 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.95
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Prefoldin  80 ellkkkleelekqlekleeeleklkdqittleanlaql 117
                                    e   + +e l++ le le +++ l++++  le + a+l
  gi|119720182|ref|YP_920677.1|  55 EATRRDIEGLRRELEGLERDVASLAERVSRLEGAYAEL 92 
                                    55556677777777777777777777777666665555 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.16
                                    HHHHHHHHHHHHHHHHH CS
                      Prefoldin   7 slqaelaqlkeaieele 23 
                                    +l +++++l e+i++l+
  gi|119720182|ref|YP_920677.1|  91 ELSKRIDSLGERISDLD 107
                                    22222222222222222 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 0.00094
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Prefoldin  79 iellkkkleelekqlekleeeleklkdqittle 111
                                    i+ l+k++++l+k +e+l + ++ l ++++ + 
  gi|119720182|ref|YP_920677.1| 117 IDGLDKRIDSLDKRIESLDKRIDSLDKRLDHIA 149
                                    566777777777777777777777777776665 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   0.00079     0.062      14      87 ..      40     113 ..      34     115 .. 0.83
   2 !   12.7   0.0    0.0015      0.12      23      84 ..      91     155 ..      88     166 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00079
                         DUF948  14 viflivvllklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvsel 87 
                                    vi  + +   ++k  +++++ ie+l+++++++ ++v+ l + v +l     e ++++d+l e + dl + + +l
  gi|119720182|ref|YP_920677.1|  40 VIRDVATKHDVEKHWEATRRDIEGLRRELEGLERDVASLAERVSRLEGAYAELSKRIDSLGERISDLDKRIDSL 113
                                    55555666677899999999999999999999999999999999988888888999999999999999999887 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.0015
                         DUF948  23 klkktldeaaatieelekqvdpilkevedllakvnelledvne...klekvdplteavadlgesv 84 
                                    +l+k +d++ ++i +l k++d++ k +++l + +  l + +++   +++++d+  +++a+++ ++
  gi|119720182|ref|YP_920677.1|  91 ELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESldkRIDSLDKRLDHIAKISYTL 155
                                    68888999999999999999999888888888888766666654448999999999999998765 PP

>> bZIP_2  Basic region leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.2     0.073       5.7      22      52 ..      56      86 ..      52      88 .. 0.89
   2 ?    5.1   0.0      0.31        24      28      53 ..      90     115 ..      88     116 .. 0.86
   3 ?    6.4   0.0      0.12       9.1      26      52 ..     116     142 ..     108     144 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.073
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         bZIP_2 22 kkkakeeeleervkeLeeeNaqLrqkveqLe 52
                                     +   e+l ++++ Le++ a L ++v+ Le
  gi|119720182|ref|YP_920677.1| 56 ATRRDIEGLRRELEGLERDVASLAERVSRLE 86
                                   578889999999999********99999997 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.31
                                    HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         bZIP_2  28 eeleervkeLeeeNaqLrqkveqLek 53 
                                    +el +r+ +L e+++ L +++++L k
  gi|119720182|ref|YP_920677.1|  90 AELSKRIDSLGERISDLDKRIDSLDK 115
                                    78999999999999999999999875 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.12
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         bZIP_2  26 keeeleervkeLeeeNaqLrqkveqLe 52 
                                    +  +l +r+ +L ++++ L +++++L 
  gi|119720182|ref|YP_920677.1| 116 RIDGLDKRIDSLDKRIESLDKRIDSLD 142
                                    445666777777777777777777665 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.2   2.7e-05    0.0021      45     131 ..      50     133 ..      40     148 .. 0.64

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.7e-05
                            GAS  45 nekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrfekvekerde 124
                                     ek+ +++  + + l+ +L+ +e++v+ L +++ + e    ++++l +r+ +l + ++dl    ++l +r++ + k +d 
  gi|119720182|ref|YP_920677.1|  50 VEKHWEATRRDIEGLRRELEGLERDVASLAERVSRLEG---AYAELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDS 126
                                    56777777777777777777777777777776665544...555555666666666666666666666666666666666 PP

                            GAS 125 lykkfea 131
                                    l k+ e+
  gi|119720182|ref|YP_920677.1| 127 LDKRIES 133
                                    6665554 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.3   7.1e-06   0.00055      14      95 ..      56     134 ..      37     159 .. 0.57

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 7.1e-06
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH...HHHHHH CS
                     Laminin_II  14 evleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeassslsdnis 93 
                                    ++ +++++l  +le ++ ++ ++++ v + +    +++k i++ ++ +++L+k ++ L +++  l+++ +    l + i+
  gi|119720182|ref|YP_920677.1|  56 ATRRDIEGLRRELEGLERDVASLAERVSRLEGAYAELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDS---LDKRIE 132
                                    44555555555555555555555555555555555555555555555555555555555555555554444...333333 PP

                                    HH CS
                     Laminin_II  94 ei 95 
                                     +
  gi|119720182|ref|YP_920677.1| 133 SL 134
                                    33 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.1   3.5e-06   0.00028     316     416 ..      45     149 ..       5     154 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 3.5e-06
                         DUF812 316 kkaeteeelkkkreeeleelqeqieeleskieeleeeikklessikqveeeleeekeeneelekevklkkktlellpd.. 393
                                    +++++ e   ++  +++e l++++e le+++++l+e +++le    ++++ ++ + e  + l k ++   k ++ l++  
  gi|119720182|ref|YP_920677.1|  45 ATKHDVEKHWEATRRDIEGLRRELEGLERDVASLAERVSRLEGAYAELSKRIDSLGERISDLDKRIDSLDKRIDGLDKri 124
                                    34445555556667799**************************************************9999999995444 PP

                         DUF812 394 ..aeeniekLqalveasaqrlvela 416
                                       ++ ie L + +++  +rl ++a
  gi|119720182|ref|YP_920677.1| 125 dsLDKRIESLDKRIDSLDKRLDHIA 149
                                    4467788888888888888887776 PP

>> Gp58  gp58-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0       2.1   1.7e+02     139     181 ..      28      68 ..      11      78 .. 0.60
   2 !   18.1   0.4   8.5e-06   0.00067     265     348 ..      78     166 ..      60     176 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 2.1
                           Gp58 139 edtdkklalinetieGirreyqdadrelsssyqagieGlkatl 181
                                    ++ d +lalin+ i  +  +  d++++  ++ +  ieGl+ +l
  gi|119720182|ref|YP_920677.1|  28 SEPDVRLALINAVIRDVATK-HDVEKHWEAT-RRDIEGLRREL 68 
                                    46666777777777666554.3555555444.44566665554 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 8.5e-06
                           Gp58 265 isqeiknregavsrvqqdldsyqrrlqdaeknyssLtqtvkGlqstvsdpnskles...rvtqLadlieq..kvtrgdve 339
                                    +  +++  ega + +++ +ds+  r+ d +k   sL + + Gl++++ + ++++es   r+  L + ++   k++     
  gi|119720182|ref|YP_920677.1|  78 LAERVSRLEGAYAELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESldkRIDSLDKRLDHiaKISYTLTA 157
                                    56789999****************************************99999987555788888777743366666666 PP

                           Gp58 340 siirqsgds 348
                                    s+++    s
  gi|119720182|ref|YP_920677.1| 158 SVLATLAAS 166
                                    666654444 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   1.1   8.6e-05    0.0067      44     122 ..      53     134 ..       7     140 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 8.6e-05
                         APG6_N  44 k...qdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynelqlelleleeeld 120
                                    +   ++ ++e l++ele le++ ++l e   +le + +el + + +l e  ++l++  +   ++   l+    +l+++ +
  gi|119720182|ref|YP_920677.1|  53 HweaTRRDIEGLRRELEGLERDVASLAERVSRLEGAYAELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIE 132
                                    14446778888999999999999999999999999999999999999988888888766555555555555555555555 PP

                         APG6_N 121 sl 122
                                    sl
  gi|119720182|ref|YP_920677.1| 133 SL 134
                                    55 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.1   3.3e-06   0.00026     130     230 ..      56     149 ..      20     173 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 3.3e-06
                        DUF4407 130 altaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaqldaaqaelaelkakld.a 208
                                    a + +++ l+++++ l++ ++++ +r+++l+ +++ el+       +++   g++    ++ +d ++++++ l++++d  
  gi|119720182|ref|YP_920677.1|  56 ATRRDIEGLRRELEGLERDVASLAERVSRLEGAYA-ELS-------KRIDSLGERISDLDKRIDSLDKRIDGLDKRIDsL 127
                                    24455555555555666666666666665555555.333.......3455668888889999999999999999998888 PP

                        DUF4407 209 tarlaalraelaeleaeraker 230
                                    ++r+++l++++++l++++++++
  gi|119720182|ref|YP_920677.1| 128 DKRIESLDKRIDSLDKRLDHIA 149
                                    8888888888888888877655 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.1    0.0025      0.19      19      64 ..      60     105 ..      49     113 .. 0.62
   2 ?    7.5   0.1     0.073       5.7       9      45 ..     106     142 ..     101     150 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0025
                           ZapB  19 titlLqmeieeLkeeneelkeenreleeeneqlkeereawqerlkk 64 
                                     i+ L+ e+e L++++++l+e+  +le    +l +   ++ er++ 
  gi|119720182|ref|YP_920677.1|  60 DIEGLRRELEGLERDVASLAERVSRLEGAYAELSKRIDSLGERISD 105
                                    5777777777777777777777777775555555444444444444 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.073
                           ZapB   9 LEskiqkaidtitlLqmeieeLkeeneelkeenrele 45 
                                    L ++i+++  +i+ L ++i+ L ++ e+l ++++ l 
  gi|119720182|ref|YP_920677.1| 106 LDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDSLD 142
                                    5555555555666666666666655555555555444 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   1.5     4e-06   0.00031      21     111 ..      58     145 ..      37     171 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 4e-06
                          Atg14  21 perlyelrerlaklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieek 100
                                    +++++ lr +l  l  + +sl ++++  leg +   +l+++i+++ +++++l ++i +l +r+  l +++++l+k+ie  
  gi|119720182|ref|YP_920677.1|  58 RRDIEGLRRELEGLERDVASLAERVS-RLEGAY--AELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESL 134
                                    56788888888888888888888888.556666..688889999999999999999999999999999999999998888 PP

                          Atg14 101 kkklaklsdkl 111
                                     k++ +l++ l
  gi|119720182|ref|YP_920677.1| 135 DKRIDSLDKRL 145
                                    88888888776 PP

>> DUF2730  Protein of unknown function (DUF2730)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1      0.11       8.6      32      92 ..      19      81 ..       1      92 [. 0.64
   2 ?    6.5   0.1      0.11       8.8      49      90 ..      61     100 ..      47     106 .. 0.66
   3 !   14.6   0.4   0.00033     0.026      35      93 ..      96     152 ..      84     161 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.11
                        DUF2730 32 redleklaekveendkrlteletkvenLPtakdlek....Lkllladlrgelkaleaevrqlshq 92
                                   r+ l++l   v+e d rl+ +++ + ++ t++d+ek     + ++++lr el+ le++v++l+ +
  gi|119720182|ref|YP_920677.1| 19 RKRLAEL--LVSEPDVRLALINAVIRDVATKHDVEKhweaTRRDIEGLRRELEGLERDVASLAER 81
                                   6666666..68888888888888888888888876421113455555555666666666665544 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.11
                        DUF2730  49 lteletkvenLPtakdlekLkllladlrgelkaleaevrqls 90 
                                    ++ l  ++e L  ++d+++L   ++ l+g   +l++++++l 
  gi|119720182|ref|YP_920677.1|  61 IEGLRRELEGL--ERDVASLAERVSRLEGAYAELSKRIDSLG 100
                                    44455555555..57888888888888888888888888774 PP

  == domain 3  score: 14.6 bits;  conditional E-value: 0.00033
                        DUF2730  35 leklaekveendkrlteletkvenLPtakdlekLkllladlrgelkaleaevrqlshqv 93 
                                    + +l e +++ dkr+++l+ +++ L   k +++L++ ++ l+ +++ l+++++++++ +
  gi|119720182|ref|YP_920677.1|  96 IDSLGERISDLDKRIDSLDKRIDGLD--KRIDSLDKRIESLDKRIDSLDKRLDHIAKIS 152
                                    56788999999************996..55779*****************999999876 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.3   0.00086     0.067      26      99 ..      42     119 ..      32     124 .. 0.86
   2 !   17.5   1.4   4.5e-05    0.0035      11     101 ..      61     149 ..      57     152 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00086
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT....S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH CS
                   Seryl_tRNA_N  26 advdelleldekrrelqveleelqaerNelskeIgkakkkk....edaeeliaevkelkeelkaleaelkeleaelek 99 
                                     dv++  ++++++++++ ++e l++e   l + ++++ ++        +el +++++l+e++++l+++ + l+++++ 
  gi|119720182|ref|YP_920677.1|  42 RDVATKHDVEKHWEATRRDIEGLRRELEGLERDVASLAERVsrleGAYAELSKRIDSLGERISDLDKRIDSLDKRIDG 119
                                    577777889999**********************99998878887778999999999********9999999999875 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 4.5e-05
                                    HHHHHHHHCCCT.CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHH CS
                   Seryl_tRNA_N  11 peavkeklkkRg.edkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleae 89 
                                    +e +++ l+  + + +++ +++  l+ +  el +++++l ++   l k I ++ k+   ++ l +++++l ++++ l+++
  gi|119720182|ref|YP_920677.1|  61 IEGLRRELEGLErDVASLAERVSRLEGAYAELSKRIDSLGERISDLDKRIDSLDKR---IDGLDKRIDSLDKRIESLDKR 137
                                    55555555543324556777888899999999999999999999999999999875...899999999999999999999 PP

                                    HHHHHHHHHHHH CS
                   Seryl_tRNA_N  90 lkeleaelekll 101
                                     + l+++l++++
  gi|119720182|ref|YP_920677.1| 138 IDSLDKRLDHIA 149
                                    999999998875 PP

>> TACC_C  Transforming acidic coiled-coil-containing protein (TACC), C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0    0.0084      0.66      91     138 ..      47      94 ..       6      99 .. 0.79
   2 !   10.2   0.0    0.0059      0.46      83     135 ..      95     147 ..      91     154 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0084
                         TACC_C  91 fsdlfkryekqkevlegykkneeslkkcaeeylarvkkeeqRYqaLka 138
                                      d+ k +e  +  +eg+++  e l + +  + +rv + e  Y +L +
  gi|119720182|ref|YP_920677.1|  47 KHDVEKHWEATRRDIEGLRRELEGLERDVASLAERVSRLEGAYAELSK 94 
                                    469999**********************************99998865 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0059
                         TACC_C  83 dlnsveksfsdlfkryekqkevlegykkneeslkkcaeeylarvkkeeqRYqa 135
                                     + s+   +sdl kr++ + + ++g+ k  +sl k +e + +r+   ++R ++
  gi|119720182|ref|YP_920677.1|  95 RIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDSLDKRLDH 147
                                    56677788999999999999999999999999999999999999999999876 PP

>> DUF2802  Protein of unknown function (DUF2802)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1      0.69        54       2      24 ..      64      86 ..      63      99 .. 0.74
   2 ?    5.9   0.0      0.17        14       3      22 ..     100     119 ..      91     127 .. 0.63
   3 ?    9.2   0.0     0.017       1.3       2      26 ..     120     144 ..     119     167 .. 0.66

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.69
                        DUF2802  2 mgqrlaelekrlkqleerleele 24
                                   ++++l+ le+++ +l+er++ le
  gi|119720182|ref|YP_920677.1| 64 LRRELEGLERDVASLAERVSRLE 86
                                   56788888888888888888775 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.17
                        DUF2802   3 gqrlaelekrlkqleerlee 22 
                                    g+r+++l+kr+++l++r++ 
  gi|119720182|ref|YP_920677.1| 100 GERISDLDKRIDSLDKRIDG 119
                                    56666666666666666554 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.017
                        DUF2802   2 mgqrlaelekrlkqleerleeleqq 26 
                                    +++r+++l+kr+++l++r+++l ++
  gi|119720182|ref|YP_920677.1| 120 LDKRIDSLDKRIESLDKRIDSLDKR 144
                                    6677777777777777777776332 PP

>> Myosin_tail_1  Myosin tail
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   1.2   3.5e-06   0.00028     477     573 ..      53     150 ..      20     161 .. 0.62

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 3.5e-06
                  Myosin_tail_1 477 lqeetrqkLa.lssrlrqleeeknalkeqleeeeeakknvekqlstlqaqlsdlkkkleeeasavealeeakkrlqrele 555
                                      e tr+ ++ l   l  le + ++l e++   e a  +++k++ +l  ++sdl k+++   + ++ l+     l + +e
  gi|119720182|ref|YP_920677.1|  53 HWEATRRDIEgLRRELEGLERDVASLAERVSRLEGAYAELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIE 132
                                    33445444442444466666666666666666666666666666666666666666666666666666666666666666 PP

                  Myosin_tail_1 556 altqrleekaaaydklek 573
                                    +l +r+++  +  d++ k
  gi|119720182|ref|YP_920677.1| 133 SLDKRIDSLDKRLDHIAK 150
                                    666666666665555555 PP

>> Jnk-SapK_ap_N  JNK_SAPK-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   0.00019     0.015      81     143 ..      48     106 ..      19     117 .. 0.85
   2 ?    7.3   0.0     0.066       5.1      89     134 ..     101     146 ..      97     162 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 0.00019
                  Jnk-SapK_ap_N  81 eeiedqweeerkelqekveqleeenrelelkaknaadqlsrleekeaelkkeysklheretel 143
                                    + +e++we  r++++    +le  +r +     ++a+++srle   ael+k+ ++l er ++l
  gi|119720182|ref|YP_920677.1|  48 HDVEKHWEATRRDIEGLRRELEGLERDVA----SLAERVSRLEGAYAELSKRIDSLGERISDL 106
                                    56899999999888887777777777777....999***************999999998876 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.066
                  Jnk-SapK_ap_N  89 eerkelqekveqleeenrelelkaknaadqlsrleekeaelkkeys 134
                                    e+ ++l++++ +l+++++ l+++++++++++++l ++ ++l k+ +
  gi|119720182|ref|YP_920677.1| 101 ERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDSLDKRLD 146
                                    5567788888888888888888888888888888887777766655 PP

>> Prefoldin_3  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.5     0.064         5      72      98 ..      91     117 ..      50     118 .. 0.77
   2 !   12.3   0.6    0.0016      0.13      70      98 ..     117     145 ..     115     146 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.064
                    Prefoldin_3  72 lisrRiDYVkqniktlekrleaaenkl 98 
                                     +s+RiD   + i+ l+kr+++ ++++
  gi|119720182|ref|YP_920677.1|  91 ELSKRIDSLGERISDLDKRIDSLDKRI 117
                                    589999999999999999999988875 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.0016
                    Prefoldin_3  70 vdlisrRiDYVkqniktlekrleaaenkl 98 
                                    +d +++RiD   + i++l+kr+++ +++l
  gi|119720182|ref|YP_920677.1| 117 IDGLDKRIDSLDKRIESLDKRIDSLDKRL 145
                                    57799********************9998 PP

>> DUF4200  Domain of unknown function (DUF4200)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.5   1.2e-05   0.00094      16     104 ..      55     146 ..      44     157 .. 0.53

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.2e-05
                        DUF4200  16 eakkeeiq...rleealkqreeelekkeqeleedllkfdkflkendakraralkkaeeerklkkekeaeikklkaeietl 92 
                                    ea + +i+   r  e l++  + l ++ ++le  ++++ k + +  ++ ++  k++++  k+++  ++ i  l + ie l
  gi|119720182|ref|YP_920677.1|  55 EATRRDIEglrRELEGLERDVASLAERVSRLEGAYAELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESL 134
                                    33333333221444444455555555555555555555555555555555556666666666666666666666666666 PP

                        DUF4200  93 kseiekleekle 104
                                     ++i+ l+++l+
  gi|119720182|ref|YP_920677.1| 135 DKRIDSLDKRLD 146
                                    666666655555 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.1   1.4e-05    0.0011      54     129 .]      56     134 ..      45     134 .. 0.81
   2 ?    2.0   0.0       2.6     2e+02     100     117 ..     126     143 ..     122     148 .. 0.62

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.4e-05
                     TPR_MLP1_2  54 edvkelqalreelnelkaeiaelkaea...esakaeleeseesweeqkeelekelselekriedlneqNklLhdQlEsl 129
                                    ++ ++++ lr el+ l+ ++a+l +++   e a ael++   s+ e+ + l+k++++l kri+ l++  + L +++Esl
  gi|119720182|ref|YP_920677.1|  56 ATRRDIEGLRRELEGLERDVASLAERVsrlEGAYAELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESL 134
                                    345689999****999999999988761115567889999999************************999999999985 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 2.6
                     TPR_MLP1_2 100 elekelselekriedlne 117
                                    +l+k++++l kri+ l++
  gi|119720182|ref|YP_920677.1| 126 SLDKRIESLDKRIDSLDK 143
                                    466666666666666654 PP

>> DUF2721  Protein of unknown function (DUF2721)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   5.9   0.00017     0.013      18      86 ..     106     171 ..      24     176 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 0.00017
                        DUF2721  18 ltnRlariadrirqLedeleelaeeeeedeelakeiknlrrRarlirrailllvlsallvvlvvlllfl 86 
                                    l  R+ ++ +ri  L +++++l+++    e+l+k+i++l++R+  i +   +l++s+l++++++++l++
  gi|119720182|ref|YP_920677.1| 106 LDKRIDSLDKRIDGLDKRIDSLDKRI---ESLDKRIDSLDKRLDHIAKISYTLTASVLATLAASIILLA 171
                                    56788888889999999999776663...579999***********************99998888765 PP

>> Uds1  Up-regulated During Septation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   1.9   1.2e-05   0.00092      21     124 ..      59     149 ..      48     162 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.2e-05
                           Uds1  21 eeVeelkkelkaLeerlealrkkLaletklrdaarsLsrlyssskksakssaarsnskssreslakaeeelaeserkvde 100
                                     ++e l++el+ Le+ + +l ++    ++l  a  +Ls++  +s+ ++         ++ ++  +  ++ ++ +++++d 
  gi|119720182|ref|YP_920677.1|  59 RDIEGLRRELEGLERDVASLAER---VSRLEGAYAELSKRI-DSLGER--------ISDLDKRIDSLDKRIDGLDKRIDS 126
                                    689********************...9**************.777772........223335667777777777777777 PP

                           Uds1 101 laselekleeraaevrrrLLeHtA 124
                                    l + +e+l++r  ++++rL  H+A
  gi|119720182|ref|YP_920677.1| 127 LDKRIESLDKRIDSLDKRL-DHIA 149
                                    7777777777777777774.5555 PP

>> LegC3_N  LegC3 N-terminal coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   1.8   1.9e-05    0.0015      98     212 ..      49     153 ..      36     167 .. 0.49

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.9e-05
                                    HHHHHHTTHHHHHHHHHHHHHHHHHHHHTT--..-------------------------SHHHHHHHHHHHHHHHHHHHH CS
                        LegC3_N  98 kLtreleaikaekseyerellllelklerlle..sqtkvevtqhsqpvvkkllsssshsatierlelslqdleekirsll 175
                                    ++ ++ ea +  ++ + rel  le+ +++l e  s+ +    +               s+ i++l   ++dl+++i sl 
  gi|119720182|ref|YP_920677.1|  49 DVEKHWEATRRDIEGLRRELEGLERDVASLAErvSRLEGAYAEL--------------SKRIDSLGERISDLDKRIDSLD 114
                                    55555555555555555555555554444444112222233344..............4455555555555555555555 PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH..HHHHH CS
                        LegC3_N 176 erevnikkeLkeleerakeRekrrekRekRlQ..ArlgY 212
                                    +r+   +k+++ l++r ++  kr ++  kRl   A++ Y
  gi|119720182|ref|YP_920677.1| 115 KRIDGLDKRIDSLDKRIESLDKRIDSLDKRLDhiAKISY 153
                                    555555555555555555555555555555533355555 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.1    0.0062      0.48     209     254 ..      52      97 ..      34     105 .. 0.70
   2 !   11.3   0.1    0.0025      0.19     198     254 ..      90     146 ..      88     159 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0062
                                    XXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Filament 209 ealrsakeeitelrrqiqsleieleslkkqkasleaqlaeleerle 254
                                    ++ ++++++i+ lrr+++ le +++sl +  + le + ael +r++
  gi|119720182|ref|YP_920677.1|  52 KHWEATRRDIEGLRRELEGLERDVASLAERVSRLEGAYAELSKRID 97 
                                    4456677777777777777777777777777777777777777654 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.0025
                                    XXXXXXXXXXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Filament 198 eelqeaaeknsealrsakeeitelrrqiqsleieleslkkqkasleaqlaeleerle 254
                                    +el++ +++ +e ++   + i  l ++i+ l   ++sl k  +sl +++  l++rl+
  gi|119720182|ref|YP_920677.1|  90 AELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDSLDKRLD 146
                                    566666666666666666666666666666666666666666666666666666655 PP

>> DUF4618  Domain of unknown function (DUF4618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0     0.012      0.92     180     223 ..      39      82 ..      10      92 .. 0.79
   2 ?    5.5   0.0      0.12       9.7      70     220 ..      90     121 ..      79     130 .. 0.47
   3 ?    7.8   0.0     0.025         2      77     221 ..     111     143 ..      93     155 .. 0.52

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.012
                        DUF4618 180 aLlqktlenqvlkkeiekfrefieeleeeipeLkaeveqLqaqa 223
                                    a+ +++  +++++k+ e  r+ ie l+ e++ L+++v  L++++
  gi|119720182|ref|YP_920677.1|  39 AVIRDVATKHDVEKHWEATRRDIEGLRRELEGLERDVASLAERV 82 
                                    66677777888888888888899999999998888888887665 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.12
                        DUF4618  70 aeLqeweekeekklekLeqqleqlnakvqklqeelnvLstYkDkeYpvkavqIanlvrqlqqlkdsqqdeldeleelike 149
                                    aeL +  + + +++++L++ ++ l++++                                                    
  gi|119720182|ref|YP_920677.1|  90 AELSKRIDSLGERISDLDKRIDSLDKRI---------------------------------------------------- 117
                                    4444444444444444444444444444.................................................... PP

                        DUF4618 150 vleklskkiqkkkekllkslaektlkatqeaLlqktlenqvlkkeiekfrefieeleeeipeLkaeveqLq 220
                                                                                                       + L 
  gi|119720182|ref|YP_920677.1| 118 -------------------------------------------------------------------DGLD 121
                                    ...................................................................4333 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.025
                        DUF4618  77 ekeekklekLeqqleqlnakvqklqeelnvLstYkDkeYpvkavqIanlvrqlqqlkdsqqdeldeleelikevleklsk 156
                                    +                                                                               
  gi|119720182|ref|YP_920677.1| 111 D------------------------------------------------------------------------------- 111
                                    3............................................................................... PP

                        DUF4618 157 kiqkkkekllkslaektlkatqeaLlqktlenqvlkkeiekfrefieeleeeipeLkaeveqLqa 221
                                                                     +l k i+   + i+ l ++i+ L + ++ L +
  gi|119720182|ref|YP_920677.1| 112 ---------------------------------SLDKRIDGLDKRIDSLDKRIESLDKRIDSLDK 143
                                    .................................33444444444444444444444444444444 PP

>> DHR10  Designed helical repeat protein 10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   2.3   0.00016     0.013      32     103 ..      58     133 ..      31     147 .. 0.71
   2 ?    5.6   0.0      0.21        16      10      30 ..     123     143 ..     116     157 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 0.00016
                          DHR10  32 ekdlrsciklleeieaelakleeakkklk....elrdaleekeielrelerkeerlqrqlenaeeklerlreqaee 103
                                     +d++ + + le +e+++a+l e  ++l+    el++++++++++ ++l+++++ l ++++   ++++ l ++ e 
  gi|119720182|ref|YP_920677.1|  58 RRDIEGLRRELEGLERDVASLAERVSRLEgayaELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIES 133
                                    5677778888888888888888877777522225666677778888888888888888888888888888777664 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.21
                          DHR10  10 elaelErkarelqakidalqv 30 
                                     +++l++++  l ++id+l++
  gi|119720182|ref|YP_920677.1| 123 RIDSLDKRIESLDKRIDSLDK 143
                                    466666666666666666654 PP

>> Helo_like_N  Fungal N-terminal domain of STAND proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   0.00052     0.041      11      94 ..      34     116 ..      32     123 .. 0.88
   2 ?    6.3   0.2     0.071       5.5      35      75 ..     107     146 ..      91     169 .. 0.50

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00052
                    Helo_like_N  11 lalvtfalqssksLyetvksfrsrdktvreLkeeleaLeevLesLeevavaeeeselalLklpllrCgkaCkefeqvikk 90 
                                    lal+++ ++ + + +++ k++  +++++  L++ele Le+ + sL+e +v++ e   a L++ ++  g+  +++++ i +
  gi|119720182|ref|YP_920677.1|  34 LALINAVIRDVATKHDVEKHWEATRRDIEGLRRELEGLERDVASLAE-RVSRLEGAYAELSKRIDSLGERISDLDKRIDS 112
                                    578888888888999999999**************************.77799999999*99999999999999999988 PP

                    Helo_like_N  91 cskk 94 
                                    + k+
  gi|119720182|ref|YP_920677.1| 113 LDKR 116
                                    7776 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.071
                    Helo_like_N  35 dktvreLkeeleaLeevLesLeevavaeeeselalLklpll 75 
                                    dk++  L + ++ L + ++sL + ++++ ++ + +L++ l+
  gi|119720182|ref|YP_920677.1| 107 DKRIDSLDKRIDGLDKRIDSLDK-RIESLDKRIDSLDKRLD 146
                                    34444444444444444444444.33333344444433333 PP

>> DUF4472  Domain of unknown function (DUF4472)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0    0.0071      0.55      43      97 ..      46     100 ..      33     108 .. 0.85
   2 !   14.3   0.0   0.00064      0.05      24     101 ..      69     146 ..      61     157 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0071
                        DUF4472  43 rvlelelerekaaeeiqslrerlaeleeekkeleeeyvvlkknyqalekefekek 97 
                                    + +++e + e  +++i+ lr++l++le++  +l+e+++ l+ +y +l+k  ++  
  gi|119720182|ref|YP_920677.1|  46 TKHDVEKHWEATRRDIEGLRRELEGLERDVASLAERVSRLEGAYAELSKRIDSLG 100
                                    5567888999999************************************988765 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 0.00064
                        DUF4472  24 eqheaekfelknkvlalenrvlelelerekaaeeiqslrerlaeleeekkeleeeyvvlkknyqalekefekekkkqq 101
                                    e +e++   l  +v +le    el+ + + + e i++l++r + l++  + l ++  +l+k++ +l k  ++  k+ +
  gi|119720182|ref|YP_920677.1|  69 EGLERDVASLAERVSRLEGAYAELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDSLDKRLD 146
                                    678889999999*************************************************99999999998887765 PP

>> DUF3782  Protein of unknown function (DUF3782)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.3     0.098       7.7       6      37 ..      50      81 ..      45      84 .. 0.89
   2 ?    8.5   0.1     0.029       2.3       2      37 ..      67     102 ..      66     105 .. 0.91
   3 ?    6.9   0.1     0.087       6.8       6      37 ..      85     116 ..      80     124 .. 0.53
   4 ?    8.6   0.2     0.026         2       3      37 ..     110     144 ..     101     150 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.098
                        DUF3782  6 leeeeeetkedleelekeieklertigaLGaR 37
                                   +e++ e+t++d+e l++e+e ler +++L+ R
  gi|119720182|ref|YP_920677.1| 50 VEKHWEATRRDIEGLRRELEGLERDVASLAER 81
                                   4556789***********************99 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.029
                        DUF3782   2 elekleeeeeetkedleelekeieklertigaLGaR 37 
                                    ele le++ +++ e++ +le + ++l+++i++LG R
  gi|119720182|ref|YP_920677.1|  67 ELEGLERDVASLAERVSRLEGAYAELSKRIDSLGER 102
                                    5677888899999*********************99 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.087
                        DUF3782   6 leeeeeetkedleelekeieklertigaLGaR 37 
                                    le   +e++++++ l ++i+ l+++i++L +R
  gi|119720182|ref|YP_920677.1|  85 LEGAYAELSKRIDSLGERISDLDKRIDSLDKR 116
                                    45555555555555555555555555555444 PP

  == domain 4  score: 8.6 bits;  conditional E-value: 0.026
                        DUF3782   3 lekleeeeeetkedleelekeieklertigaLGaR 37 
                                    + +l+++   ++++++ l+k+ie+l+++i++L +R
  gi|119720182|ref|YP_920677.1| 110 IDSLDKRIDGLDKRIDSLDKRIESLDKRIDSLDKR 144
                                    44455555666667777777777777777766655 PP

>> Bacillus_HBL  Bacillus haemolytic enterotoxin (HBL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0    0.0022      0.18     114     175 ..      50     111 ..      38     112 .. 0.91
   2 !   12.5   0.0    0.0012     0.096     105     175 ..      66     139 ..      62     147 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0022
                   Bacillus_HBL 114 iqqnqkevkqlikeLkklklklakdsknFktdvdeltsilagdsgvisqlqneiedlqgkik 175
                                    + +  ++++++i+ L++  + l+ d++++ + v+ l+  +a  s+ i+ l ++i+dl++ i 
  gi|119720182|ref|YP_920677.1|  50 VEKHWEATRRDIEGLRRELEGLERDVASLAERVSRLEGAYAELSKRIDSLGERISDLDKRID 111
                                    666678889999999999999*************************************9985 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.0012
                   Bacillus_HBL 105 ellekLqeeiqqnqkevkql...ikeLkklklklakdsknFktdvdeltsilagdsgvisqlqneiedlqgkik 175
                                      le L++++ +  + v +l    +eL+k  ++l +  +++++ +d l++ + g ++ i+ l ++ie+l++ i 
  gi|119720182|ref|YP_920677.1|  66 RELEGLERDVASLAERVSRLegaYAELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRID 139
                                    56666777777666666554111556666667777888888888888888888888888888888888888775 PP

>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   0.00012    0.0095      34      98 ..      59     126 ..      33     133 .. 0.66
   2 ?    3.0   0.0       1.8   1.4e+02      37      65 ..     125     153 ..     122     162 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 0.00012
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHTTHTTHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Spectrin  34 eevqallkkhkaleaelaaqqervkaln....elaeklldeghsaseeieerleelnerWeeLkelaae 98 
                                     +++ l +++++le+++a+  erv +l+    el++++ d+ ++   ++ +r++ l++r + L +++++
  gi|119720182|ref|YP_920677.1|  59 RDIEGLRRELEGLERDVASLAERVSRLEgayaELSKRI-DSLGERISDLDKRIDSLDKRIDGLDKRIDS 126
                                    356777779999*************9996664333333.555666677777777777777777776665 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 1.8
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Spectrin  37 qallkkhkaleaelaaqqervkalnelae 65 
                                     +l k+ + l + +++ ++r++++ +++ 
  gi|119720182|ref|YP_920677.1| 125 DSLDKRIESLDKRIDSLDKRLDHIAKISY 153
                                    56677777777777777777777776655 PP

>> MRF_C1  Myelin gene regulatory factor -C-terminal domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0     0.019       1.5      14      35 ..      87     108 ..      87     109 .. 0.90
   2 ?    2.5   0.1         1        80      24      34 ..     111     121 ..     108     123 .. 0.85
   3 ?    3.7   0.2      0.43        34      24      34 ..     118     128 ..     112     130 .. 0.78
   4 ?    3.5   0.2      0.52        41      24      34 ..     125     135 ..     120     137 .. 0.78
   5 ?    2.1   0.1       1.3     1e+02      25      34 ..     133     142 ..     130     144 .. 0.85
   6 ?    1.0   0.1         3   2.3e+02      24      34 ..     139     149 ..     136     151 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.019
                         MRF_C1  14 gAVkeLcklTgnLEtrIeelEk 35 
                                    gA  eL+k  ++L +rI++l k
  gi|119720182|ref|YP_920677.1|  87 GAYAELSKRIDSLGERISDLDK 108
                                    6778***************975 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 1
                         MRF_C1  24 gnLEtrIeelE 34 
                                    ++L++rI+ l 
  gi|119720182|ref|YP_920677.1| 111 DSLDKRIDGLD 121
                                    79*****9886 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.43
                         MRF_C1  24 gnLEtrIeelE 34 
                                    ++L++rI+ l 
  gi|119720182|ref|YP_920677.1| 118 DGLDKRIDSLD 128
                                    78999999886 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.52
                         MRF_C1  24 gnLEtrIeelE 34 
                                    ++L++rIe l 
  gi|119720182|ref|YP_920677.1| 125 DSLDKRIESLD 135
                                    78999999886 PP

  == domain 5  score: 2.1 bits;  conditional E-value: 1.3
                         MRF_C1  25 nLEtrIeelE 34 
                                    +L++rI+ l 
  gi|119720182|ref|YP_920677.1| 133 SLDKRIDSLD 142
                                    79*****986 PP

  == domain 6  score: 1.0 bits;  conditional E-value: 3
                         MRF_C1  24 gnLEtrIeelE 34 
                                    ++L++r++++ 
  gi|119720182|ref|YP_920677.1| 139 DSLDKRLDHIA 149
                                    789****9975 PP

>> HrpB7  Bacterial type III secretion protein (HrpB7)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.3     0.024       1.9      85     132 ..      51      98 ..      35     100 .. 0.61
   2 !   12.9   0.2    0.0014      0.11      81     132 ..      96     147 ..      88     152 .. 0.51

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.024
                          HrpB7  85 egrvraaeaelaaarqaldaaedavaatarkiaRndaqidacrerier 132
                                    e + +a  + ++ +r +l+  e+ va  a++++R++++     +ri+ 
  gi|119720182|ref|YP_920677.1|  51 EKHWEATRRDIEGLRRELEGLERDVASLAERVSRLEGAYAELSKRIDS 98 
                                    555555556666666666666666666666666666665555555554 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.0014
                          HrpB7  81 rdvlegrvraaeaelaaarqaldaaedavaatarkiaRndaqidacrerier 132
                                    +d l +r+  +++++  + +++d   +++   +++i ++d +id  ++r++ 
  gi|119720182|ref|YP_920677.1|  96 IDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDSLDKRLDH 147
                                    3444555555555555555555555555555555555555555555555554 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.6   1.1e-05   0.00088     251     355 ..      55     143 ..      27     159 .. 0.45

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.1e-05
                        DUF3584 251 qeefeqleslelrLsllkgelkadeerlaekqeevqeakaelkqqlrtledelkeaidelnqelsaakaklaakeselea 330
                                    ++   ++e+l  +L +l++++ +  er+++   + +e ++               +id l +++s++++ ++   ++++ 
  gi|119720182|ref|YP_920677.1|  55 EATRRDIEGLRRELEGLERDVASLAERVSRLEGAYAELSK---------------RIDSLGERISDLDKRIDSLDKRIDG 119
                                    3333333344444444444333333333333333333333...............3333333333333333333333333 PP

                        DUF3584 331 leeqkkkyedadieklkadldqlps 355
                                    l+++ +  +d++ie+l +  d l++
  gi|119720182|ref|YP_920677.1| 120 LDKRIDS-LDKRIESLDKRIDSLDK 143
                                    3333332.23333333333333333 PP

>> HemX  HemX, putative uroporphyrinogen-III C-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0     0.025       1.9      59     102 ..      45      88 ..      20      96 .. 0.88
   2 !    9.9   0.0    0.0051       0.4      47      99 ..      96     148 ..      88     162 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.025
                           HemX  59 eqkqeleerlqqlaeklealekeleqlqkqleelqqqlskvsga 102
                                    ++k+++e++ +++  ++e l++ele l++++++l++++s+++ga
  gi|119720182|ref|YP_920677.1|  45 ATKHDVEKHWEATRRDIEGLRRELEGLERDVASLAERVSRLEGA 88 
                                    577889999999*****************************998 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0051
                           HemX  47 leqqlaqveaekeqkqeleerlqqlaeklealekeleqlqkqleelqqqlskv 99 
                                    +++  ++++ ++++ + l +r++ l++++++l k++e+l+k++++l ++l ++
  gi|119720182|ref|YP_920677.1|  96 IDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDSLDKRLDHI 148
                                    33333444557777777778888888888888888888888888888877766 PP

>> Lebercilin  Ciliary protein causing Leber congenital amaurosis disease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   1.5   4.2e-05    0.0033      19     109 ..      53     143 ..      44     150 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.2e-05
                     Lebercilin  19 elaelqskleelrkEnklLkrlqkrqekaLskyedteaeLpqllarhneEvrvlrerlRksqekerelekklkekeaell 98 
                                      +  ++ +e lr+E++ L+r     +++ s++e++ aeL++ +++  e +  l +r+  + ++ + l+k++ + +++++
  gi|119720182|ref|YP_920677.1|  53 HWEATRRDIEGLRRELEGLERDVASLAERVSRLEGAYAELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIE 132
                                    55677889999999999999999999999999999999999999999999999999999999999999999999999999 PP

                     Lebercilin  99 rlkdklkklkk 109
                                    +l++ ++ l+k
  gi|119720182|ref|YP_920677.1| 133 SLDKRIDSLDK 143
                                    99999999887 PP

>> Tropomyosin  Tropomyosin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   4.4   3.8e-05    0.0029      16     227 ..      53     145 ..      42     155 .. 0.39

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.8e-05
                    Tropomyosin  16 rlekakkkleeaekkaekaeaEvaalnrriqlleeelerteerleealekLeeaekaadeserarKvlEnrelkdeekle 95 
                                    + e++ + +e  +++ e  e +va+l  r++ le    + ++r+++  e+++++ k+ d  ++ +  l +r  + + ++e
  gi|119720182|ref|YP_920677.1|  53 HWEATRRDIEGLRRELEGLERDVASLAERVSRLEGAYAELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIE 132
                                    33333333333333333333333333333333333333333333333333333333333333333333333333333333 PP

                    Tropomyosin  96 eleaqlkeakeiaeeadrkyeEvarklvvvesdLeraeeraeaaeskiveLeeeLkvvgnnlksLevseekaseredeye 175
                                    +l                                                                              
  gi|119720182|ref|YP_920677.1| 133 SL------------------------------------------------------------------------------ 134
                                    33.............................................................................. PP

                    Tropomyosin 176 eeirtLeekLkeaeeRaeeAErsvqkLekevdrledeleaekekykaiseeL 227
                                                                              ++++++++ L
  gi|119720182|ref|YP_920677.1| 135 -----------------------------------------DKRIDSLDKRL 145
                                    .........................................33333333333 PP

>> Cluap1  Clusterin-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.1    0.0055      0.43     138     219 ..      21      99 ..       9     101 .. 0.82
   2 !   11.6   0.6    0.0017      0.13     168     222 ..      97     151 ..      89     153 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0055
                         Cluap1 138 sLydlLekevelreartkalsrqleleeiekalkeaikkvkeelektkkalenlesdeanLeakiekkkqeleraqkrLq 217
                                    +L +lL  e ++r a  +a+ r++ +   ++ ++++ +++++++e ++++le le+d a+L++++ + +  +   +kr++
  gi|119720182|ref|YP_920677.1|  21 RLAELLVSEPDVRLALINAVIRDVAT---KHDVEKHWEATRRDIEGLRRELEGLERDVASLAERVSRLEGAYAELSKRID 97 
                                    56666666666666666666665554...457888999999*******************************99999999 PP

                         Cluap1 218 sl 219
                                    sl
  gi|119720182|ref|YP_920677.1|  98 SL 99 
                                    88 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.0017
                         Cluap1 168 kalkeaikkvkeelektkkalenlesdeanLeakiekkkqeleraqkrLqslqsv 222
                                     +l e+i++++++++++ k+++ l++  ++L+++ie   + ++   krL+++ ++
  gi|119720182|ref|YP_920677.1|  97 DSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDSLDKRLDHIAKI 151
                                    4677889999999999999999999999999999999999999999999988765 PP

>> KLRAQ  Predicted coiled-coil domain-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.1      0.66        51      18      75 ..      37      94 ..      33     102 .. 0.84
   2 !   14.1   0.3   0.00053     0.042      28      70 ..     103     145 ..      72     163 .. 0.51

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.66
                          KLRAQ 18 kkavleEqskeaslkeelkekeqslrkseqEvdsLtFrNkqLekrvellqeeleveek 75
                                     av+ + + +++++++       +   + E++ L+     L+ rv+ l    ++ +k
  gi|119720182|ref|YP_920677.1| 37 INAVIRDVATKHDVEKHWEATRRDIEGLRRELEGLERDVASLAERVSRLEGAYAELSK 94
                                   5799999999999999999999999999999999999999999999999876666555 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 0.00053
                          KLRAQ  28 easlkeelkekeqslrkseqEvdsLtFrNkqLekrvellqeel 70 
                                     ++l + + + ++ +   ++ +dsL+ r + L kr+++l + l
  gi|119720182|ref|YP_920677.1| 103 ISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDSLDKRL 145
                                    2333333333333333333333333333333333333333333 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0      0.18        14      22      67 ..      49      94 ..      45     103 .. 0.64
   2 ?    3.5   0.0      0.88        69      34      64 ..      89     119 ..      83     124 .. 0.70
   3 ?    9.7   0.1     0.011      0.87      28      71 ..     118     161 ..     111     166 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.18
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCTXXXXXXXXXXXXX CS
                         DivIVA 22 eVdeFLdqvakdyeallkeneelkekvkeleeklkeykeleetLkk 67
                                   +V++  +   +d+e l +e e l++ v+ l e++++ + +  +L+k
  gi|119720182|ref|YP_920677.1| 49 DVEKHWEATRRDIEGLRRELEGLERDVASLAERVSRLEGAYAELSK 94
                                   5666666666677777777777777777777777666655555554 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.88
                                    HHHHHHHHHHHHHHHHCCCCTXXXXXXXXXX CS
                         DivIVA  34 yeallkeneelkekvkeleeklkeykeleet 64 
                                    y +l k+ ++l e++++l++++++ +++ + 
  gi|119720182|ref|YP_920677.1|  89 YAELSKRIDSLGERISDLDKRIDSLDKRIDG 119
                                    6777777777888888888877777766555 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.011
                                    HHHHHHHHHHHHHHHHHHHHHHCCCCTXXXXXXXXXXXXXXXXX CS
                         DivIVA  28 dqvakdyeallkeneelkekvkeleeklkeykeleetLkktlvv 71 
                                    d + k + +l k+ e+l ++++ l+++l++ +++  tL  ++++
  gi|119720182|ref|YP_920677.1| 118 DGLDKRIDSLDKRIESLDKRIDSLDKRLDHIAKISYTLTASVLA 161
                                    566678899999***************************99987 PP

>> DASH_Spc19  Spc19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.4      0.14        11      49      99 ..      49      98 ..      25     109 .. 0.59
   2 !   13.1   0.3   0.00084     0.066      64      99 ..     112     147 ..      99     159 .. 0.58

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.14
                                   THHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     DASH_Spc19 49 dleaakaslaeeiePqieellekaekeleklerreetLkaklelqegrlsn 99
                                   d+e++ ++ + +ie  ++  le +e+ +++l++r + L+  ++ +++r+++
  gi|119720182|ref|YP_920677.1| 49 DVEKHWEATRRDIEG-LRRELEGLERDVASLAERVSRLEGAYAELSKRIDS 98
                                   444444444444442.34445555555555555555555555555555554 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00084
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     DASH_Spc19  64 qieellekaekeleklerreetLkaklelqegrlsn 99 
                                    ++++ ++ ++k +++l++r e+L ++++ +++rl++
  gi|119720182|ref|YP_920677.1| 112 SLDKRIDGLDKRIDSLDKRIESLDKRIDSLDKRLDH 147
                                    334445555555555555555555555555555554 PP

>> Transcrip_act  Transcriptional activator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   3.7     5e-05    0.0039      18     104 ..      51     140 ..      37     153 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5e-05
                  Transcrip_act  18 kedeevsrsalsafkakeeeierkklevrekveaqLgrveeetkrLaeire...eLealadPlrkevavvrkkidavnre 94 
                                    ++  e++r ++  ++   e +er    + e+v+   g   e +kr+ ++ e   +L+   d l k ++ + k+id++++ 
  gi|119720182|ref|YP_920677.1|  51 EKHWEATRRDIEGLRRELEGLERDVASLAERVSRLEGAYAELSKRIDSLGErisDLDKRIDSLDKRIDGLDKRIDSLDKR 130
                                    4466899****************************9********98877662225677789******************* PP

                  Transcrip_act  95 lkplgqscqk 104
                                    + +l + +  
  gi|119720182|ref|YP_920677.1| 131 IESLDKRIDS 140
                                    ***9987765 PP

>> HOOK  HOOK protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   1.3   1.8e-05    0.0014     173     282 ..      39     150 ..       6     157 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.8e-05
                           HOOK 173 elkeaqeekdelaQrcheldkqlsllqeEknaLlaenkklqerlsele..ngeesgtiqltskkylelqkqleqlqeelf 250
                                     +  +++ k +++   + + + +  l  E + L  +  +l er+s+le    e s+ i+  +++ ++l k++++l   + 
  gi|119720182|ref|YP_920677.1|  39 AVIRDVATKHDVEKHWEATRRDIEGLRRELEGLERDVASLAERVSRLEgaYAELSKRIDSLGERISDLDKRIDSLDKRID 118
                                    44455666666666666666777777777777777777777777777754345556667777777777777777777777 PP

                           HOOK 251 rlEtarddyrlkceelekevlelqqrneelts 282
                                     l++  d +  ++e l+k +  l +r +++++
  gi|119720182|ref|YP_920677.1| 119 GLDKRIDSLDKRIESLDKRIDSLDKRLDHIAK 150
                                    77777777777777777777777777666555 PP

>> Fmp27_WPPW  RNA pol II promoter Fmp27 protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1      0.41        32     179     239 ..      33      95 ..      19      99 .. 0.70
   2 !   15.0   0.6   0.00011    0.0087     175     233 ..      98     152 ..      90     163 .. 0.56

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.41
                     Fmp27_WPPW 179 Rleeleeqiekle..ekleelelksekedeelkeeieelekeikelkeklefletlledlkes 239
                                    Rl+ +++ i+++   +++e++ + ++++ e l++e+e le+++++l e+++ le ++ +l+++
  gi|119720182|ref|YP_920677.1|  33 RLALINAVIRDVAtkHDVEKHWEATRRDIEGLRRELEGLERDVASLAERVSRLEGAYAELSKR 95 
                                    555555555544400344444444445478899999999999999999999999999888876 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 0.00011
                     Fmp27_WPPW 175 lleeRleeleeqiekleekleelelksekedeelkeeieelekeikelkeklefletll 233
                                     l eR+++l+++i++l+++++ l+++  +    l+++ie+l k i++l+++l+++ ++ 
  gi|119720182|ref|YP_920677.1|  98 SLGERISDLDKRIDSLDKRIDGLDKRIDS----LDKRIESLDKRIDSLDKRLDHIAKIS 152
                                    23445555555555555555555555555....66666666666666666666666555 PP

>> FemAB  FemAB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   2.5e-05    0.0019     236     303 ..      88     157 ..      74     171 .. 0.60

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.5e-05
                          FemAB 236 Aelnlaeylkelqekleklekklakleekleknpe..kkkkkklkelekqlaslekelkeaeefiekdge 303
                                    A+++l++++++l e++++l+k+++ l++++   ++  ++  k+++ l+k ++sl+k+l+ + +++ +  +
  gi|119720182|ref|YP_920677.1|  88 AYAELSKRIDSLGERISDLDKRIDSLDKRIDGLDKriDSLDKRIESLDKRIDSLDKRLDHIAKISYTLTA 157
                                    6677777777777777777777777777666666566666666666666666666666666665444443 PP

>> PI3K_P85_iSH2  Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.3   5.1e-05     0.004      80     151 ..      65     136 ..       7     151 .. 0.55

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.1e-05
                  PI3K_P85_iSH2  80 ehEieklqenleqlksrlkelhsskekLeedlkqqkeeereleReinalkpellqLqkrkdkylewLktkgv 151
                                    ++E e l+  ++ l +r++ l+ + ++L++ + +  e+   l+++i +l   +  L kr d + ++++  + 
  gi|119720182|ref|YP_920677.1|  65 RRELEGLERDVASLAERVSRLEGAYAELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDK 136
                                    555555555555555555555555555555555555555555555555555555555555444433333332 PP

>> DUF4763  Domain of unknown function (DUF4763)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0       0.4        31     118     155 ..      49      86 ..      44      94 .. 0.88
   2 !   11.9   0.1    0.0013       0.1     112     156 ..      99     143 ..      90     151 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.4
                        DUF4763 118 elqqhlkasrkslkelreslcqekkrlrklqkrlneld 155
                                    ++++h +a+r +++ lr++l  + + +++l++r  +l+
  gi|119720182|ref|YP_920677.1|  49 DVEKHWEATRRDIEGLRRELEGLERDVASLAERVSRLE 86 
                                    678999999999******99999999999999988775 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.0013
                        DUF4763 112 Lrqqlaelqqhlkasrkslkelreslcqekkrlrklqkrlnelds 156
                                    L  ++++l ++  + +k +  l++++ ++ kr+++l kr++ ld+
  gi|119720182|ref|YP_920677.1|  99 LGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDSLDK 143
                                    556788888888888888888888888888888888888888875 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   2.8e-05    0.0022       3      87 ..      67     150 ..      65     170 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.8e-05
                          TMPIT   3 eweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvl 82 
                                    e+e le+++ +l e+ ++++   +elsk ++++ ++i+   kr+ +l+++++ l+k+++ + ++++e+l++++++ +k l
  gi|119720182|ref|YP_920677.1|  67 ELEGLERDVASLAERVSRLEGAYAELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRID-SLDKRIESLDKRIDSLDKRL 145
                                    66677777777777777777777777777777777777777777777777777777764.55556666666666655555 PP

                          TMPIT  83 keves 87 
                                    + +++
  gi|119720182|ref|YP_920677.1| 146 DHIAK 150
                                    54433 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.2   2.7e-05    0.0021     160     250 ..      57     149 ..      17     169 .. 0.42

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.7e-05
                   Exonuc_VII_L 160 ikrlleekkqrleklasrlkspeellerkrqrldeleerleralkkqlkkkrerleelkerlk...ekleekkerlkklk 236
                                    ++r +e  +++le l+++++s  e+++r + ++ el++r+++ l ++++   +r+++l +r+    +++++ ++r+++l 
  gi|119720182|ref|YP_920677.1|  57 TRRDIEGLRRELEGLERDVASLAERVSRLEGAYAELSKRIDS-LGERISDLDKRIDSLDKRIDgldKRIDSLDKRIESLD 135
                                    222222222333333333333333333333333333333333.3333333333333333333223333333333333333 PP

                   Exonuc_VII_L 237 erlelleekkerle 250
                                    +r+++l+++ ++++
  gi|119720182|ref|YP_920677.1| 136 KRIDSLDKRLDHIA 149
                                    33333333333322 PP

>> GrpE  GrpE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0     0.026         2       5      51 ..      52      98 ..      46     107 .. 0.87
   2 ?    8.5   0.0     0.018       1.4       8      50 ..     104     146 ..      97     160 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.026
                                   ..CTTTHHHHCCCCCCTTCHHHCTTSCCCCCCTTTTTTTTHHHHHHH CS
                           GrpE  5 eeeeeeedeeeeleeeleelekevkelkekllrllaefenlrkrtek 51
                                   ++ e+++ ++e l++ele le+ v++l e++ rl+  + +l kr + 
  gi|119720182|ref|YP_920677.1| 52 KHWEATRRDIEGLRRELEGLERDVASLAERVSRLEGAYAELSKRIDS 98
                                   566788899999*****************************999865 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.018
                                    TTTHHHHCCCCCCTTCHHHCTTSCCCCCCTTTTTTTTHHHHHH CS
                           GrpE   8 eeeedeeeeleeeleelekevkelkekllrllaefenlrkrte 50 
                                     ++++++++l+++++ l+k++++l ++++ l + ++ l kr++
  gi|119720182|ref|YP_920677.1| 104 SDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDSLDKRLD 146
                                    4566667777777777777777777777777777776666654 PP

>> CCDC154  Coiled-coil domain-containing protein 154
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   3.2     3e-05    0.0024     323     432 ..      45     149 ..       9     153 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3e-05
                        CCDC154 323 avqlatdlarrEtesalellqEKsqaleesvaelatqlkDLsDhvlalsWrldLqeqtLslklseakeewekaerrslek 402
                                    a++ + ++ +  t++++e l+    +le++va la+++  L+     ls r+d     L+ ++s++ + ++  ++r+ ++
  gi|119720182|ref|YP_920677.1|  45 ATKHDVEKHWEATRRDIEGLRRELEGLERDVASLAERVSRLEGAYAELSKRID----SLGERISDLDKRIDSLDKRI-DG 119
                                    4567888888999999999999999***********************99998....46899999999999887775.89 PP

                        CCDC154 403 lvqwekeveahLrevqekvdslkrqieavs 432
                                    l ++     + ++ + +++dsl + ++ ++
  gi|119720182|ref|YP_920677.1| 120 LDKRIDSLDKRIESLDKRIDSLDKRLDHIA 149
                                    988899999999999999999999998775 PP

>> DUF4094  Domain of unknown function (DUF4094)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.2     0.036       2.8      53      79 ..      94     121 ..      38     130 .. 0.75
   2 ?    7.4   0.1     0.074       5.8      62      82 ..     125     145 ..     120     150 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.036
                        DUF4094  53 rskdilg.evskthkaiqtLdktissLe 79 
                                    +  d lg ++s+  k i +Ldk+i+ L 
  gi|119720182|ref|YP_920677.1|  94 KRIDSLGeRISDLDKRIDSLDKRIDGLD 121
                                    3457777788888888888888887665 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.074
                        DUF4094  62 skthkaiqtLdktissLemeL 82 
                                    +   k i++Ldk+i+sL   L
  gi|119720182|ref|YP_920677.1| 125 DSLDKRIESLDKRIDSLDKRL 145
                                    555688999999999998877 PP

>> FliJ  Flagellar FliJ protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   5.2e-05    0.0041       4      80 ..      65     136 ..      62     152 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5.2e-05
                           FliJ   4 areLaeaqrelqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqvekare 80 
                                    +reL+  +r +++  e++ +le  ++e++k++ + +     +++  + + i++ld++i+ + + ++ + k++e   +
  gi|119720182|ref|YP_920677.1|  65 RRELEGLERDVASLAERVSRLEGAYAELSKRIDSLG-----ERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDK 136
                                    68999999****************************.....999999999999999999999999999999997665 PP

>> Ax_dynein_light  Axonemal dynein light chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.6    0.0048      0.38     121     151 ..     103     133 ..      41     148 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0048
                Ax_dynein_light 121 kselekkikeLeeekeelekqvaelkaklea 151
                                     s+l+k+i +L+++ + l k++ +l++++e+
  gi|119720182|ref|YP_920677.1| 103 ISDLDKRIDSLDKRIDGLDKRIDSLDKRIES 133
                                    2233333333333333333333333333333 PP

>> DASH_Dam1  DASH complex subunit Dam1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0      0.38        30       6      24 ..      90     108 ..      64     115 .. 0.62
   2 ?    7.3   0.1     0.053       4.1       2      35 ..     100     133 ..      92     134 .. 0.81
   3 ?    7.4   0.1     0.047       3.7       3      29 ..     129     155 ..     127     160 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.38
                      DASH_Dam1   6 aeLaDsletLdknledLqq 24 
                                    aeL++ ++ L ++++dL++
  gi|119720182|ref|YP_920677.1|  90 AELSKRIDSLGERISDLDK 108
                                    4555555555555555544 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.053
                      DASH_Dam1   2 epafaeLaDsletLdknledLqqihesLsdfNeS 35 
                                     +++++L + ++ Ldk+++ L++  +sL++  eS
  gi|119720182|ref|YP_920677.1| 100 GERISDLDKRIDSLDKRIDGLDKRIDSLDKRIES 133
                                    5778899999999999999999888888877666 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.047
                      DASH_Dam1   3 pafaeLaDsletLdknledLqqihesL 29 
                                    +++++L + ++ Ldk+l+++ +i+ +L
  gi|119720182|ref|YP_920677.1| 129 KRIESLDKRIDSLDKRLDHIAKISYTL 155
                                    68999*****************99877 PP

>> AIP3  Actin interacting protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   2.7   3.6e-05    0.0028     129     252 ..      29     150 ..       7     156 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.6e-05
                                    .......XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXHHHHHHHHHHHHHHHHHHHHHHHH CS
                           AIP3 129 elkaqlkevqslrrdLavlrqlysefkseikeslselrekakkvkeaslastkkssnrayiekgkkkLseesdklvtkvd 208
                                    e + +l+ ++++ rd+a+   ++++  + ++  ++ lr++++ ++  ++as    +  + +e + ++Ls++ d+l +++ 
  gi|119720182|ref|YP_920677.1|  29 EPDVRLALINAVIRDVATKHDVEKH-WEATRRDIEGLRRELEGLE-RDVAS--LAERVSRLEGAYAELSKRIDSLGERIS 104
                                    5556666777777888776666554.4667888999999999998.55534..44455669999**************** PP

                                    HHHHHHHHH..HHHHHHHXXXXXHHHHHHHHHHHHHHHHHHHHHHH CS
                           AIP3 209 dLqDlvedl..rkDVvqRgvrpskkqlesvakeikkakkelkklee 252
                                    dL+  +++l  r D +++++    k +es+ k i+++ k+l+++ +
  gi|119720182|ref|YP_920677.1| 105 DLDKRIDSLdkRIDGLDKRIDSLDKRIESLDKRIDSLDKRLDHIAK 150
                                    *******9977889*************************9998765 PP

>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.3   4.5e-05    0.0036     279     369 ..      55     145 ..      31     161 .. 0.52

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.5e-05
                            MAD 279 ealsrkieqLqqeeivlkeeksslesslkqlekaqreleqelaqllkkiedlkkkrkehkelkrRLQrrvllltkErdll 358
                                    ea +r ie L +e   l+  + sl++++++le a +el +++++l ++i dl k+ +  ++ ++ L +r+  l k ++ l
  gi|119720182|ref|YP_920677.1|  55 EATRRDIEGLRRELEGLERDVASLAERVSRLEGAYAELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESL 134
                                    33344444444444444444444444455555555555555555545555555544444444444444444444444444 PP

                            MAD 359 railesyDkel 369
                                     + ++s Dk l
  gi|119720182|ref|YP_920677.1| 135 DKRIDSLDKRL 145
                                    44444444443 PP

>> FmiP_Thoc5  Fms-interacting protein/Thoc5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1      0.56        44      98     153 ..      27      82 ..       8      97 .. 0.70
   2 !   13.1   0.1   0.00057     0.044      99     154 ..      90     146 ..      80     163 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.56
                     FmiP_Thoc5  98 ewEleqRkelaeqlkeleekkkkleqeieekkkfLssLppkLkslkkatkplqeal 153
                                      E + R  l +++    + k  +e+  e  ++ ++ L  +L+ l++ ++ l e +
  gi|119720182|ref|YP_920677.1|  27 VSEPDVRLALINAVIRDVATKHDVEKHWEATRRDIEGLRRELEGLERDVASLAERV 82 
                                    55666666666666666677777788888888888888888888888777777665 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00057
                     FmiP_Thoc5  99 wEleqRke.laeqlkeleekkkkleqeieekkkfLssLppkLkslkkatkplqealg 154
                                     El +R++ l e +++l ++  +l + i    k+++sL ++++sl k +  l + l+
  gi|119720182|ref|YP_920677.1|  90 AELSKRIDsLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDSLDKRLD 146
                                    577777642677788888888888888888888888888888888888888887775 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0     0.056       4.3      23      49 ..      88     114 ..      45     118 .. 0.53
   2 !   12.1   0.1    0.0033      0.26      24      88 ..      89     144 ..      87     153 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.056
                   Occludin_ELL  23 eYkelhaeleevskkfseLerelkelk 49 
                                     Y el ++++++ +++s+L++++++l+
  gi|119720182|ref|YP_920677.1|  88 AYAELSKRIDSLGERISDLDKRIDSLD 114
                                    345555555555555555555555444 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.0033
                   Occludin_ELL  24 YkelhaeleevskkfseLerelkelkegskeykkieeeilqeykklkkdpeyqekkkrceyLkek 88 
                                    Y el ++++++ +++s+L++++++l+++ +  +k+++++ ++ ++l          kr++ L ++
  gi|119720182|ref|YP_920677.1|  89 YAELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLD---------KRIDSLDKR 144
                                    88888999999999999999888888887777777776555555553.........344444444 PP

>> Nup88  Nuclear pore component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.6   4.9e-05    0.0038     550     657 ..      44     147 ..      18     161 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.9e-05
                          Nup88 550 elvreeiekrvkllkkqkeqqleelqsleeerkslseraeklAekyeeikdkQeklvrrvkkvlkrlnsklpvlseaere 629
                                       ++++ek+ ++ +   e   +el+ le +  sl er+ +l   y e +++ ++l +r++++ kr+ s    +      
  gi|119720182|ref|YP_920677.1|  44 VATKHDVEKHWEATRRDIEGLRRELEGLERDVASLAERVSRLEGAYAELSKRIDSLGERISDLDKRIDSLDKRIDG---- 119
                                    5667889999999999999999**************************************9998777665544433.... PP

                          Nup88 630 mkkelekikeklkslknalkqvkkkldk 657
                                    + k + +++++++sl+++++ + k+ld 
  gi|119720182|ref|YP_920677.1| 120 LDKRIDSLDKRIESLDKRIDSLDKRLDH 147
                                    4455666666666666666666655554 PP

>> FPP  Filament-like plant protein, long coiled-coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.2   5.5e-05    0.0043     702     792 ..      45     135 ..      13     154 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.5e-05
                            FPP 702 sekenlevelksatenleslkaqlqesEqllaelkseLeslkeskslaetqlkcmkesyesletrateleaelnelkqki 781
                                    ++k+++e + +    ++e l   l+  E+ +a+l + +++l+ +   + + +++  e  ++l+ r   l++ +  l ++i
  gi|119720182|ref|YP_920677.1|  45 ATKHDVEKHWEATRRDIEGLRRELEGLERDVASLAERVSRLEGAYAELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRI 124
                                    56778888888888888888888888888888888888888888888888888888888888888888888888888888 PP

                            FPP 782 eaLeveLeeek 792
                                    ++L++ +e+  
  gi|119720182|ref|YP_920677.1| 125 DSLDKRIESLD 135
                                    88877766544 PP

>> Snf7  Snf7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0       0.2        16      10      36 ..      89     115 ..      80     119 .. 0.53
   2 !   12.8   1.0   0.00087     0.068       3      36 ..     110     143 ..     102     161 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.2
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                           Snf7  10 erkldkkqeslekkikkleaelkklak 36 
                                      +l+k+++sl ++i++l++ +  l k
  gi|119720182|ref|YP_920677.1|  89 YAELSKRIDSLGERISDLDKRIDSLDK 115
                                    555555555555555555555544433 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00087
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                           Snf7   3 irsLrkaerkldkkqeslekkikkleaelkklak 36 
                                    i sL k ++ ldk+++sl+k+i+ l++ +  l k
  gi|119720182|ref|YP_920677.1| 110 IDSLDKRIDGLDKRIDSLDKRIESLDKRIDSLDK 143
                                    6677888888888888888888888777766554 PP

>> CALCOCO1  Calcium binding and coiled-coil domain (CALCOCO1) like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   3.8     6e-05    0.0047      52     157 ..      45     143 ..      19     155 .. 0.55

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 6e-05
                       CALCOCO1  52 aanrqrekekeeykrdreeldrerkelesrveelkeelkesrekveeleekqkelerlseelaeeksalleakeeseari 131
                                    a+++++ek  e  +rd e l r       ++e l+++++++ e v +le  + el++  ++l e+ s l +  +   +ri
  gi|119720182|ref|YP_920677.1|  45 ATKHDVEKHWEATRRDIEGLRR-------ELEGLERDVASLAERVSRLEGAYAELSKRIDSLGERISDLDKRIDSLDKRI 117
                                    4445555554444444444444.......444555555555555555555555555555555555555555555555555 PP

                       CALCOCO1 132 rELEeDiktltqralekEteLeRlke 157
                                      L++ i +l +r    + +++ l +
  gi|119720182|ref|YP_920677.1| 118 DGLDKRIDSLDKRIESLDKRIDSLDK 143
                                    55555555555554444444443333 PP

>> SHE3  SWI5-dependent HO expression protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0     0.075       5.8      54      97 ..      68     111 ..      41     115 .. 0.56
   2 !   10.8   0.3    0.0037      0.29      67     117 ..     102     153 ..     100     162 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.075
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           SHE3  54 NdnLsslLkRKerrlkdlekelselkesveelklekkqlkkrle 97 
                                     + L   +     r+  le  ++el++++++l ++   l+kr++
  gi|119720182|ref|YP_920677.1|  68 LEGLERDVASLAERVSRLEGAYAELSKRIDSLGERISDLDKRID 111
                                    33333333333445555666666666666666666666655554 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0037
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH.HHHH CS
                           SHE3  67 rlkdlekelselkesveelklekkqlkkrlenssaseteleeelerl.kvqY 117
                                    r+ dl+k + +l ++++ l ++ + l+kr+e++ ++  +l ++l+++ k++Y
  gi|119720182|ref|YP_920677.1| 102 RISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDSLDKRLDHIaKISY 153
                                    7777777777777777777777777777777777777777777766534555 PP

>> DUF730  Protein of unknown function (DUF730)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0      0.21        16      77     120 ..      58     101 ..      42     104 .. 0.86
   2 !   12.7   0.1    0.0013     0.099      69     120 ..      92     143 ..      88     145 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.21
                         DUF730  77 keektemkkdleaakkrvesqaekiflmekkfetlekkyeslnk 120
                                    + +   ++++le  ++ v s ae++  +e  +  l k+ +sl +
  gi|119720182|ref|YP_920677.1|  58 RRDIEGLRRELEGLERDVASLAERVSRLEGAYAELSKRIDSLGE 101
                                    5566778999999************************9999865 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.0013
                         DUF730  69 lcdefdkikeektemkkdleaakkrvesqaekiflmekkfetlekkyeslnk 120
                                    l   +d + e   ++ k +++ +kr+++  ++i  ++k++e+l+k+ +sl k
  gi|119720182|ref|YP_920677.1|  92 LSKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDSLDK 143
                                    566789999999************************************9987 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.5     0.014       1.1      23      34 ..     113     124 ..      44     167 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.014
                          Spc24  23 leselaelkeel 34 
                                    l ++ + l +++
  gi|119720182|ref|YP_920677.1| 113 LDKRIDGLDKRI 124
                                    222222222222 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.1    0.0092      0.72     172     226 ..      39      93 ..      19      95 .. 0.85
   2 ?    7.8   2.1     0.023       1.8     115     147 ..     112     145 ..      92     170 .. 0.48

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0092
                           CorA 172 evlkrllakaddkllddedkeylrdlldelerllemlealrerleslqdtyssll 226
                                    +v+ ++ +k+d +++ ++ ++ ++ l+ ele l++++ +l+er+++l  +y+ l+
  gi|119720182|ref|YP_920677.1|  39 AVIRDVATKHDVEKHWEATRRDIEGLRRELEGLERDVASLAERVSRLEGAYAELS 93 
                                    5666666778888888888889****************************99775 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.023
                           CorA 115 lldeivdrlfellekleeeldeledel.edstkk 147
                                     ld+ +d l++ ++ l+++++ l++++ + +++ 
  gi|119720182|ref|YP_920677.1| 112 SLDKRIDGLDKRIDSLDKRIESLDKRIdSLDKRL 145
                                    2333333333333333333333333332222222 PP

>> TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.4   0.00048     0.037      14      82 ..      61     126 ..      48     151 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 0.00048
                    TMF_TATA_bd  14 verlsseirrlEgElaslkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqeryet 82 
                                    +e l  e+  lE ++asl e+++rle    e+++ i +l    e+ ++l+k++++l k+++ l++r ++
  gi|119720182|ref|YP_920677.1|  61 IEGLRRELEGLERDVASLAERVSRLEGAYAELSKRIDSLG---ERISDLDKRIDSLDKRIDGLDKRIDS 126
                                    6778888888999999999999999998888888888887...44455555555555555555555443 PP

>> HMMR_N  Hyaluronan mediated motility receptor N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.2    0.0001     0.008     179     277 ..      49     144 ..      12     161 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 0.0001
                         HMMR_N 179 evsvkQedmeaklqvtqknLeeskakvaqLkeklvslekekieekseteklleyieelsnvseqlekykldiaqleellk 258
                                     v    e +  +++ + ++Le     va L e+ + le   +e  + ++ l e i+ l + +++l    ++i+ l   ++
  gi|119720182|ref|YP_920677.1|  49 DVEKHWEATRRDIEGLRRELEGLERDVASLAERVSRLEGAYAELSKRIDSLGERISDLDKRIDSL---DKRIDGLDKRID 125
                                    44444455556666667777777777777777777777776666666666666666666666666...555555555555 PP

                         HMMR_N 259 ekndeiesLkssLeekeqe 277
                                    + ++ iesL + ++  ++ 
  gi|119720182|ref|YP_920677.1| 126 SLDKRIESLDKRIDSLDKR 144
                                    5555555555544443333 PP

>> CENP-Q  CENP-Q, a CENPA-CAD centromere complex subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   1.2   0.00017     0.013      18     110 ..      45     137 ..      16     161 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 0.00017
                         CENP-Q  18 dggkekeldfeklldekaaleaqLspelhslelLeaeiekeeralerdyeaLreLeknakaearerkeklkkehvllqes 97 
                                    + ++++e++ e++ + +  l+++L+ +++ ++ L + ++++e a+++  + + +L + ++++ ++ +   k+   l ++ 
  gi|119720182|ref|YP_920677.1|  45 ATKHDVEKHWEATRRDIEGLRRELEGLERDVASLAERVSRLEGAYAELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRI 124
                                    56899999999999999999999999999999999999999999999999999999999999999888778877777776 PP

                         CENP-Q  98 dseelslleassd 110
                                    ds +++ +++ + 
  gi|119720182|ref|YP_920677.1| 125 DSLDKRIESLDKR 137
                                    6666666555554 PP

>> PspA_IM30  PspA/IM30 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.2      0.07       5.5      29     131 ..      58      92 ..      12      99 .. 0.55
   2 ?    8.8   0.0     0.014       1.1      88     142 ..      91     145 ..      86     161 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.07
                      PspA_IM30  29 eqairdmqselakarqalaqviarqkqlerkleeqkeqakklekkAkaALtkgeeeLArealaeikslekqaealetqla 108
                                    ++                                                                    ++e+l+ +l+
  gi|119720182|ref|YP_920677.1|  58 RR--------------------------------------------------------------------DIEGLRRELE 69 
                                    22....................................................................3333333333 PP

                      PspA_IM30 109 qqrsaveqlrkqlealetkieel 131
                                     ++  v+ l + +++le  ++el
  gi|119720182|ref|YP_920677.1|  70 GLERDVASLAERVSRLEGAYAEL 92 
                                    33444444444444444333333 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.014
                      PspA_IM30  88 ealaeikslekqaealetqlaqqrsaveqlrkqlealetkieelkakkellkare 142
                                    e+ ++i sl + + +l++  + + + ++ l k ++ l+++ie l + ++ l  r+
  gi|119720182|ref|YP_920677.1|  91 ELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDSLDKRL 145
                                    6667889999999999999999999999999999999999999998888887776 PP

>> Hemagglutinin  Haemagglutinin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0     0.014       1.1     365     415 ..      60     113 ..      38     125 .. 0.57
   2 ?    8.0   0.4      0.01      0.79     384     421 ..     110     149 ..     106     169 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.014
                                    XHHHHHHHHHHHHHHHHHHHHHTTT...EEEBXSSXXTTTTHHHHHHHHHHHHH CS
                  Hemagglutinin 365 dkkstqeainkitkkvnsliekenk...qleavgkelnelekrieeldkkvddg 415
                                    d +  ++ ++++ ++v sl e+  +    +  ++k ++ l +ri +ldk++d +
  gi|119720182|ref|YP_920677.1|  60 DIEGLRRELEGLERDVASLAERVSRlegAYAELSKRIDSLGERISDLDKRIDSL 113
                                    555555555666666666665543211145556666666666666666666632 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.01
                                    HHHTTTEEEBXSSXXTTTTHHHHHHHHHHH..HHHHHHHH CS
                  Hemagglutinin 384 iekenkqleavgkelnelekrieeldkkvd..dgfldvit 421
                                    i+   k+++ + k ++ l+krie ldk++d  d +ld i+
  gi|119720182|ref|YP_920677.1| 110 IDSLDKRIDGLDKRIDSLDKRIESLDKRIDslDKRLDHIA 149
                                    5556667777777777777777777777775555666543 PP

>> Sipho_Gp157  Siphovirus Gp157
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   1.4   0.00031     0.024      32      85 ..      85     138 ..      17     165 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 0.00031
                    Sipho_Gp157  32 LesleeeieeKaeniakviknleaeaeaikeeekrLaerkkslenkaenLKeyl 85 
                                    Le+   e+ ++++  +  i+ l+ +++ ++++++ L++r  sl++++e+L +++
  gi|119720182|ref|YP_920677.1|  85 LEGAYAELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRI 138
                                    333334444444444444444444444444444444444444444444444433 PP

>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0       4.9   3.8e+02      95     117 ..      55      77 ..      17      85 .. 0.74
   2 !   10.7   2.2    0.0045      0.35       8      63 ..      91     145 ..      61     157 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 4.9
                           CdvA  95 leekeeikklleklskleleeee 117
                                    ++ +++i+ l ++l+ le +  +
  gi|119720182|ref|YP_920677.1|  55 EATRRDIEGLRRELEGLERDVAS 77 
                                    45556666666666666655544 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0045
                           CdvA   8 eLvsegdipkstyeeikekleealkklkekakelkeklkkrlkeledqikslekal 63 
                                    eL+++ d   ++ +++ +++++ l+k  +  ++ ++ l+kr+++l++ i+sl+k l
  gi|119720182|ref|YP_920677.1|  91 ELSKRIDSLGERISDLDKRIDS-LDKRIDGLDKRIDSLDKRIESLDKRIDSLDKRL 145
                                    6677777777777777777765.444445555556778888888888888888876 PP

>> RPW8  Arabidopsis broad-spectrum mildew resistance protein RPW8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0       6.1   4.8e+02      48      69 ..      58      79 ..      34      94 .. 0.62
   2 !   13.4   0.4    0.0006     0.047      34      74 ..      93     133 ..      70     154 .. 0.59

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 6.1
                           RPW8 48 vkeieklnkeldrpreeieeLk 69
                                   + +ie l+ el+  + ++ +L 
  gi|119720182|ref|YP_920677.1| 58 RRDIEGLRRELEGLERDVASLA 79
                                   3445555555544444444444 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.0006
                           RPW8  34 lkrLestleritPvvkeieklnkeldrpreeieeLkklLek 74 
                                    +kr++s  eri+ + k+i++l k++d  ++ i++L k++e+
  gi|119720182|ref|YP_920677.1|  93 SKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIES 133
                                    34444444555555555555555555555555555555543 PP

>> Vac_Fusion  Chordopoxvirus multifunctional envelope protein A27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1       4.5   3.5e+02      33      44 ..      50      61 ..      40      70 .. 0.83
   2 !   12.6   0.0     0.001      0.08       2      52 ..      75     125 ..      74     127 .. 0.95
   3 ?    2.9   0.1       1.1        83       6      33 ..     121     148 ..     116     164 .. 0.60

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 4.5
                                   HH-XXXXXXXXX CS
                     Vac_Fusion 33 lEnHleTlRkam 44
                                   +E+H e  R+ +
  gi|119720182|ref|YP_920677.1| 50 VEKHWEATRRDI 61
                                   799999999875 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.001
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-XXXXXXXXXXXXXXXXX CS
                     Vac_Fusion   2 lkdleerllvlekdfqlvikcckrvnealkRlEnHleTlRkamlaLakKID 52 
                                    + +l er+ +le  + ++ k+    +e+++ l +  + l k +  L k+ID
  gi|119720182|ref|YP_920677.1|  75 VASLAERVSRLEGAYAELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRID 125
                                    67899**************************************99***999 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 1.1
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Vac_Fusion   6 eerllvlekdfqlvikcckrvnealkRl 33 
                                     +r+ +l k  + + k+    +++l+ +
  gi|119720182|ref|YP_920677.1| 121 DKRIDSLDKRIESLDKRIDSLDKRLDHI 148
                                    5566666666666666666666655554 PP

>> HAUS-augmin3  HAUS augmin-like complex subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.1   0.00031     0.024      64     137 ..      45     118 ..      26     141 .. 0.83
   2 ?    3.0   0.0      0.81        63      75     122 ..      98     145 ..      91     162 .. 0.57

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 0.00031
                   HAUS-augmin3  64 edvellevileeeeesleaLeqelqeLqkekalklkrlnkLqvqaaslqqelrkleeeekeakkklkeaqeelr 137
                                     + + +e+  e+ + ++e L++el+ L++  a++ +r ++L+ + a+l+++  +l e+ +   k++  +++ + 
  gi|119720182|ref|YP_920677.1|  45 ATKHDVEKHWEATRRDIEGLRRELEGLERDVASLAERVSRLEGAYAELSKRIDSLGERISDLDKRIDSLDKRID 118
                                    5677888899********************************************99998888888777776654 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.81
                   HAUS-augmin3  75 eeeesleaLeqelqeLqkekalklkrlnkLqvqaaslqqelrkleeee 122
                                     ++e + +L + ++ L k  + + kr + L+  + sl ++  +l+++ 
  gi|119720182|ref|YP_920677.1|  98 SLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDSLDKRL 145
                                    445555555555555555555555555555555555555555554443 PP

>> FlxA  FlxA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0    0.0071      0.56      27      61 ..     104     134 ..      52     158 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0071
                           FlxA  27 knlqkqLkelses.deltkeekkkqqqliqaQIqql 61 
                                    ++l k +++l +  d l+     k+++ + + I++l
  gi|119720182|ref|YP_920677.1| 104 SDLDKRIDSLDKRiDGLD-----KRIDSLDKRIESL 134
                                    333333333322221111.....2222222222222 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.1     0.012      0.97     333     408 ..      48     117 ..      35     122 .. 0.60
   2 ?    7.9   0.3     0.013         1     339     376 ..     110     144 ..     105     167 .. 0.50

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.012
                           FapA 333 pelkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeel 408
                                    +++ +  ++ ++++e l++ele l++++++l + ++     s+ +  +++l +   +l e++++l++++++l++++
  gi|119720182|ref|YP_920677.1|  48 HDVEKHWEATRRDIEGLRRELEGLERDVASLAE-RV-----SRLEGAYAELSKRIDSLGERISDLDKRIDSLDKRI 117
                                    445555566677777777777777777666666.22.....23445555555555555555555555555555554 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.013
                           FapA 339 lkeleeeleeleeeleklkkkikklpklkaekqlesek 376
                                    ++ l++++  l ++++ l+k+i++l+k ++  +   ++
  gi|119720182|ref|YP_920677.1| 110 IDSLDKRIDGLDKRIDSLDKRIESLDK-RI--DSLDKR 144
                                    455555555555555555555555544.22..112223 PP

>> RmuC  RmuC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0     0.052       4.1     213     279 ..      39     104 ..      24     109 .. 0.76
   2 !   10.2   0.0    0.0036      0.29     223     281 ..      91     148 ..      88     162 .. 0.60

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.052
                           RmuC 213 rtvamlwrqeaqeknaeeiaellgelydkfekfgedleklgkklekaqksydkavkklegnilrkae 279
                                     +++ + +++++ek+ e   + ++ l  ++e+++ d+ +l +++++++ +y +  +k+ +++ +++ 
  gi|119720182|ref|YP_920677.1|  39 AVIRDVATKHDVEKHWEATRRDIEGLRRELEGLERDVASLAERVSRLEGAYAE-LSKRIDSLGERIS 104
                                    45677888889999999999999999999999999999999999999999999.5555555555554 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0036
                           RmuC 223 aqeknaeeiaellgelydkfekfgedleklgkklekaqksydkavkklegnilrkaekl 281
                                    +++k+ + + e++++l +++ ++ ++++ l k+++++ k +++  +k+ +++ ++++ +
  gi|119720182|ref|YP_920677.1|  91 ELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIES-LDKRIDSLDKRLDHI 148
                                    4455555555666666666666666666666666666666666.555555555555555 PP

>> Vps5  Vps5 C terminal like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1     0.067       5.2      24      73 ..      52     101 ..      35     113 .. 0.70
   2 ?    8.5   0.3     0.017       1.3      30      67 ..     121     158 ..     101     169 .. 0.53

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.067
                           Vps5  24 ewFedkkqeldslesqLkkLykaiellvsqrkelasataelakslesLas 73 
                                    +  e  +  ++ l  +L  L++ + +l +  + l  a ael+k ++sL++
  gi|119720182|ref|YP_920677.1|  52 KHWEATRRDIEGLRRELEGLERDVASLAERVSRLEGAYAELSKRIDSLGE 101
                                    44555666777777777777777777777777777777777777777764 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.017
                           Vps5  30 kqeldslesqLkkLykaiellvsqrkelasataelaks 67 
                                     +++dsl++++ +L k i++l++    +a++   l++s
  gi|119720182|ref|YP_920677.1| 121 DKRIDSLDKRIESLDKRIDSLDKRLDHIAKISYTLTAS 158
                                    34555666666666666666665555555555554332 PP

>> COG2  COG (conserved oligomeric Golgi) complex component, COG2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.1     0.023       1.8      74     121 ..      50      98 ..      23     110 .. 0.58
   2 ?    7.2   0.1     0.064         5      59     107 ..      98     146 ..      89     166 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.023
                           COG2  74 vesplaaarkkvesvreklsereeeveskleeakeleekr.ellklllk 121
                                    ve+  +a+r+++e +r++l+  e++v s  e  ++le +  el k++ +
  gi|119720182|ref|YP_920677.1|  50 VEKHWEATRRDIEGLRRELEGLERDVASLAERVSRLEGAYaELSKRIDS 98 
                                    4444455555555555555555555555555555555444333344444 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.064
                           COG2  59 slSghLvglqeeleevesplaaarkkvesvreklsereeeveskleeak 107
                                    sl+++  +l+++++ +++ +  + k+++s+ + ++   ++++s  +   
  gi|119720182|ref|YP_920677.1|  98 SLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDSLDKRLD 146
                                    4566666666666666666666666666666666666666665544444 PP

>> phiKZ_IP  phiKZ-like phage internal head proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   3.1    0.0027      0.21      19     107 ..      55     143 ..      32     156 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0027
                       phiKZ_IP  19 esldkel.gaektstalEsydatarvkleaiavsle....dlkeklkeagkkakelikkiietlkdaavritsgierlsk 93 
                                    e +++++ g++++ ++lE    +  +  e +  +le    +l++++ ++g+++ +l k+ i+ l   ++ +   i++l+k
  gi|119720182|ref|YP_920677.1|  55 EATRRDIeGLRRELEGLER---DVASLAERVS-RLEgayaELSKRIDSLGERISDLDKR-IDSLDKRIDGLDKRIDSLDK 129
                                    4555555555555544442...2222222222.22222226677777777766665444.45556666666666666666 PP

                       phiKZ_IP  94 ridkLeerlkslkk 107
                                    ri+ L++r+ sl+k
  gi|119720182|ref|YP_920677.1| 130 RIESLDKRIDSLDK 143
                                    66666666666644 PP

>> DUF1640  Protein of unknown function (DUF1640)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   2.5    0.0002     0.016      37     173 ..      39     174 ..       8     176 .. 0.54

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 0.0002
                        DUF1640  37 kvakslvskselekseylqkaalselrkevqisersefaalrseteklqreleklkqkLreeidklkadirldlnleKgr 116
                                     v +++++k ++ek+    + +++ lr e++ +er ++a+l +   +l+    +l +++ +  +++      dl+++   
  gi|119720182|ref|YP_920677.1|  39 AVIRDVATKHDVEKHWEATRRDIEGLRRELEGLER-DVASLAERVSRLEGAYAELSKRIDSLGERIS-----DLDKRIDS 112
                                    55666666666666666666677777777666665.4555555555555555555554444333322.....34444444 PP

                        DUF1640 117 ireelakleakiqelnnk...idrevsalrteiE.svKld.vikyliglvvgilavglavvR 173
                                           l+++i+ l+++   +d+ + +l + ++  +K+  ++  ++   ++ ++++la++R
  gi|119720182|ref|YP_920677.1| 113 LDKRIDGLDKRIDSLDKRiesLDKRIDSLDKRLDhIAKISyTLTASVLATLAASIILLAIIR 174
                                    44444444444444444433334555555555553334331233333444555556666666 PP

>> Phage_tail_NK  Sf6-type phage tail needle knob or tip of some Caudovirales
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0      0.27        21       2      29 ..      72      99 ..      71     102 .. 0.94
   2 ?    8.6   1.1     0.017       1.4       5      31 ..     103     129 ..     100     172 .. 0.61

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.27
                                   XXXXXXXXXXXXXXXXXXXXXXXHHHHH CS
                  Phage_tail_NK  2 esdissldtrvqslesqvsdhetridal 29
                                   e d++sl  rv  le   ++   rid+l
  gi|119720182|ref|YP_920677.1| 72 ERDVASLAERVSRLEGAYAELSKRIDSL 99
                                   789***********************98 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.017
                                    XXXXXXXXXXXXXXXXXXXXHHHHHHH CS
                  Phage_tail_NK   5 issldtrvqslesqvsdhetridaley 31 
                                    is ld r++sl+ ++   + rid+l+ 
  gi|119720182|ref|YP_920677.1| 103 ISDLDKRIDSLDKRIDGLDKRIDSLDK 129
                                    566666666666666666666666653 PP

>> DegS  Sensor protein DegS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   2.3    0.0027      0.21      14     117 ..      46     148 ..      35     153 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0027
                           DegS  14 skeeifeIaEsarkeverlkkeleelkeevsevikevdklekkerkarkrLaeVskdFkkyseeeikeaYeeakelqvel 93 
                                     k+++ +  E++r+++e l++ele l+++v+++ ++v +le  + +  kr      + ++  +++i +  ++ + l  ++
  gi|119720182|ref|YP_920677.1|  46 TKHDVEKHWEATRRDIEGLRRELEGLERDVASLAERVSRLEGAYAELSKRIDSLGERISDL-DKRIDSLDKRIDGLDKRI 124
                                    47778888899***************************99998888888877777666554.456666666666666666 PP

                           DegS  94 allrekEkqlrerRdelerrLkkl 117
                                      l ++ ++l +r d+l++rL ++
  gi|119720182|ref|YP_920677.1| 125 DSLDKRIESLDKRIDSLDKRLDHI 148
                                    666666666666666666666665 PP

>> DUF1465  Protein of unknown function (DUF1465)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.3     0.022       1.7      92     129 ..      72     110 ..      40     113 .. 0.71
   2 !   10.2   2.3    0.0062      0.48      95     136 ..      90     131 ..      55     165 .. 0.54

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.022
                                    -...-----------HHHHHHHHHHHHHHHHHHHHHHHH CS
                        DUF1465  92 aae.asdaeavaeLpeelqeLierserLyervrrLdrel 129
                                    + + as ae v++L+ + +eL +r ++L er+  Ld+++
  gi|119720182|ref|YP_920677.1|  72 ERDvASLAERVSRLEGAYAELSKRIDSLGERISDLDKRI 110
                                    333467777888888888888888888888888888876 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0062
                                    -----------HHHHHHHHHHHHHHHHHHHHHHHHHT-SSXX CS
                        DUF1465  95 asdaeavaeLpeelqeLierserLyervrrLdrelreeaeaa 136
                                    a+ ++ +++L e++ +L +r ++L +r+  Ld+++    ++ 
  gi|119720182|ref|YP_920677.1|  90 AELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRI 131
                                    333333333333333333333333333333333333333333 PP

>> MerR-DNA-bind  MerR, DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   1.2       1.7   1.3e+02      43      61 ..      56      74 ..      33      95 .. 0.60
   2 ?    7.3   0.6     0.089         7      41      57 ..     106     122 ..      80     130 .. 0.62
   3 ?    9.9   0.6     0.014       1.1      42      63 ..     121     142 ..     112     157 .. 0.58

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 1.7
                                   HHHHHHHHHHHHHHHHHHH CS
                  MerR-DNA-bind 43 rklaeleeriaeLqalrae 61
                                   + + ++e  ++eL+ l+++
  gi|119720182|ref|YP_920677.1| 56 ATRRDIEGLRRELEGLERD 74
                                   4444444444444444433 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.089
                                    HHHHHHHHHHHHHHHHH CS
                  MerR-DNA-bind  41 larklaeleeriaeLqa 57 
                                    l++++++l++ri+ L++
  gi|119720182|ref|YP_920677.1| 106 LDKRIDSLDKRIDGLDK 122
                                    34455555555555544 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.014
                                    HHHHHHHHHHHHHHHHHHHHHH CS
                  MerR-DNA-bind  42 arklaeleeriaeLqalraeLa 63 
                                    ++++++l++ri+ L++  + L+
  gi|119720182|ref|YP_920677.1| 121 DKRIDSLDKRIESLDKRIDSLD 142
                                    5555555555555555444444 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0     0.068       5.3     143     176 ..      50      83 ..      44      84 .. 0.84
   2 ?   11.7   1.5     0.002      0.16      45     129 ..      62     146 ..      57     158 .. 0.54

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.068
                        DUF4201 143 LlkDYdktkekveekrksvkkLrrkvkilemrlk 176
                                    + k  + t  ++e +r +++ L+r v +l++r++
  gi|119720182|ref|YP_920677.1|  50 VEKHWEATRRDIEGLRRELEGLERDVASLAERVS 83 
                                    5566788999999999999999999999999986 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.002
                        DUF4201  45 eqlqienqalnkkIeernkeLkrlkkkttktvhalthlkeklhmleselselkkelkekeerlaklrkelykvklerdkl 124
                                    e l++e + l+  +++  + ++rl   ++  ++++  l e+ + l++    l k+++ +++r+++l+k+++++ ++ d l
  gi|119720182|ref|YP_920677.1|  62 EGLRRELEGLERDVASLAERVSRLEGAYAELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDSL 141
                                    44555555555555555555555555555555555555555555555555555555555555555555555555555555 PP

                        DUF4201 125 rkqne 129
                                    +k+ +
  gi|119720182|ref|YP_920677.1| 142 DKRLD 146
                                    55544 PP

>> Taxilin  Myosin-like coiled-coil protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0       2.9   2.2e+02      57      80 ..      53      76 ..      19      91 .. 0.57
   2 ?    4.9   0.0      0.16        12     249     303 ..      50     104 ..      44     108 .. 0.82
   3 ?   10.2   0.1    0.0039      0.31      11      57 ..     101     147 ..      90     163 .. 0.50

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 2.9
                        Taxilin 57 qlqaelskaalaksKLekLcRelq 80
                                   + +a +++   ++  Le L R++ 
  gi|119720182|ref|YP_920677.1| 53 HWEATRRDIEGLRRELEGLERDVA 76
                                   233333344444444555544443 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.16
                        Taxilin 249 mtkktkklEketnlwkskfektnkallemaeertekkkeieklkkkiqkLeklcr 303
                                    + k+ +   ++ + +++  e  ++ ++++ae   + +  +++l k+i++L + + 
  gi|119720182|ref|YP_920677.1|  50 VEKHWEATRRDIEGLRRELEGLERDVASLAERVSRLEGAYAELSKRIDSLGERIS 104
                                    5677777788888899999999999999999999999999999999999976555 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.0039
                        Taxilin  11 sklespeekleaLvkkyaelleerkrlqkqlkklkkkleqlqkekeq 57 
                                    +++++ +++++ L k++  l +   +l+k +  l+k+ + l k+ ++
  gi|119720182|ref|YP_920677.1| 101 ERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDSLDKRLDH 147
                                    33344444444444444444444444444444444444444444443 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.7   0.00018     0.014     255     361 ..      35     165 ..      17     174 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00018
                           FUSC 255 e.laallaelaaleaaaaaealeaalaalrarlralrraleadadtaalllarlaellaelaqllaslraleaaiaa... 330
                                    + + a+++++a+      +++ e++++a r++++ lrr+le      a l++r+  l +++a+l + +++l ++i++   
  gi|119720182|ref|YP_920677.1|  35 AlINAVIRDVAT------KHDVEKHWEATRRDIEGLRRELEGLERDVASLAERVSRLEGAYAELSKRIDSLGERISDldk 108
                                    335555555555......56666666666666666666666666666666666666666666666666666666666666 PP

                           FUSC 331 ..........................arraerlarhrdhlaallnglraalaillag 361
                                                              ++r   l  + dh a + ++l a + + la+
  gi|119720182|ref|YP_920677.1| 109 ridsldkridgldkridsldkrieslDKRIDSLDKRLDHIAKISYTLTASVLATLAA 165
                                    666666666666666666666666666666666666666666666665544433333 PP

>> DUF641  Plant protein of unknown function (DUF641)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.1       1.2        90      93     128 .]      46      81 ..      38      81 .. 0.85
   2 ?    4.2   0.1      0.64        50       6      28 ..      71      93 ..      67      96 .. 0.87
   3 ?   11.3   0.2    0.0041      0.32      51     119 ..      80     149 ..      75     156 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 1.2
                         DUF641  93 tvkkleaelkakdseieeLkekLeeaeksnkklekr 128
                                    t +++e++ +a + +ie L+++Le +e+   +l +r
  gi|119720182|ref|YP_920677.1|  46 TKHDVEKHWEATRRDIEGLRRELEGLERDVASLAER 81 
                                    556789999999************999988887765 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.64
                         DUF641  6 leallaklFaavSalkaAYvqLQ 28
                                   le  +a+l + vS l+ AY++L 
  gi|119720182|ref|YP_920677.1| 71 LERDVASLAERVSRLEGAYAELS 93
                                   5778999*************995 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.0041
                         DUF641  51 kklselkrlyrkkqkkkas.eaeeseleaeiqeqrsllktyeitvkkleaelkakdseieeLkekLeeae 119
                                    +++s+l   y + +k  +s  ++ s l+++i+ + + ++ +++++++l++ +++ d+ i++L ++L+++ 
  gi|119720182|ref|YP_920677.1|  80 ERVSRLEGAYAELSKRIDSlGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDSLDKRLDHIA 149
                                    5778888888887776666448888889999999999999999999999999999999999999888776 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0       1.5   1.2e+02      29      58 ..      55      84 ..      33      90 .. 0.55
   2 ?   10.8   0.9     0.006      0.47       2      61 ..      93     150 ..      90     163 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 1.5
                     Syntaxin_2 29 eelreklhelieeinelikktnellkklsq 58
                                   e +r+ ++ l+ e+  l +++ +l +++s+
  gi|119720182|ref|YP_920677.1| 55 EATRRDIEGLRRELEGLERDVASLAERVSR 84
                                   444555555555555555555555555554 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.006
                     Syntaxin_2   2 ssnlqkinsnvstleklvkqLgtkkdteelreklhelieeinelikktnellkklsqldn 61 
                                    s+ + ++ + +s l+k +++L ++ d   l++++++l ++i  l k++ +l k+l+++++
  gi|119720182|ref|YP_920677.1|  93 SKRIDSLGERISDLDKRIDSLDKRID--GLDKRIDSLDKRIESLDKRIDSLDKRLDHIAK 150
                                    67777777888888888888877744..77788888888888888888888888887765 PP

>> DUF4164  Domain of unknown function (DUF4164)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   3.9    0.0018      0.14      24      86 ..      44     106 ..      33     109 .. 0.88
   2 ?    9.7   3.3     0.013      0.99      12      56 ..     105     146 ..     103     152 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0018
                        DUF4164  24 vdrrleaerkrdeleaeiealgedrsRLaeeLdqaearaarleevnrEvsrrLkaaietirav 86 
                                    v  + + e++ ++ +++ie l+++ + L+ +  +   r +rle + +E+s+r++++ e i ++
  gi|119720182|ref|YP_920677.1|  44 VATKHDVEKHWEATRRDIEGLRRELEGLERDVASLAERVSRLEGAYAELSKRIDSLGERISDL 106
                                    556777777889999999*****************************************9875 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.013
                        DUF4164  12 rLeaaldsLEkavdrrleaerkrdeleaeiealgedrsRLaeeLd 56 
                                    +L++ +dsL+k++d     ++  d+l+++ie l++    L+++Ld
  gi|119720182|ref|YP_920677.1| 105 DLDKRIDSLDKRIDG---LDKRIDSLDKRIESLDKRIDSLDKRLD 146
                                    567777777766653...344446666666666666666666666 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.7   0.00017     0.013      83     170 ..      53     146 ..       9     155 .. 0.54

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 0.00017
                        UPF0242  83 glktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelkle...leeqLaekqellqeyqetie 159
                                    + +  +  +e l+ e e L++ +++  e + rl+   ++L+++     e +++l +    l+++++   ++++ + + ie
  gi|119720182|ref|YP_920677.1|  53 HWEATRRDIEGLRRELEGLERDVASLAERVSRLEGAYAELSKRIDSLGERISDLDKRidsLDKRIDGLDKRIDSLDKRIE 132
                                    23344446666666666666666666666666666666666666665554443333200033344444444444444444 PP

                        UPF0242 160 eqrs...vlekrqd 170
                                    ++ +   +l+kr d
  gi|119720182|ref|YP_920677.1| 133 SLDKridSLDKRLD 146
                                    33221113444444 PP

>> YscO  Type III secretion protein YscO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.4    0.0089       0.7      65      96 ..      65      96 ..      16     112 .. 0.73
   2 ?    6.0   0.0      0.14        11      68     122 ..      96     150 ..      92     162 .. 0.57

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0089
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           YscO 65 lkelekvkqqvalLrekeaelekqveeakqql 96
                                   ++ele + + va+L e++ +le + +e+ ++ 
  gi|119720182|ref|YP_920677.1| 65 RRELEGLERDVASLAERVSRLEGAYAELSKRI 96
                                   45555555556666666665555555555544 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.14
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           YscO  68 lekvkqqvalLrekeaelekqveeakqqleaerealrqarkelqearraveKfae 122
                                    ++ + ++++ L ++  +l k+++ ++++ +   ++ +++ k +    + ++ +a+
  gi|119720182|ref|YP_920677.1|  96 IDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDSLDKRLDHIAK 150
                                    5555556666666666666666666555555555555555555555555555555 PP

>> Syntaxin  Syntaxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0       0.5        39      43      77 ..      46      80 ..      36      90 .. 0.73
   2 ?   13.9   0.3   0.00041     0.032       7      78 ..      60     130 ..      52     165 .. 0.57

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.5
                       Syntaxin 43 lkkrmesdikeikkraesvkarLeaLdksnkenek 77
                                   +k+++e++ ++ ++  e ++++Le L++++++  +
  gi|119720182|ref|YP_920677.1| 46 TKHDVEKHWEATRRDIEGLRRELEGLERDVASLAE 80
                                   68888888888888888888888888887776554 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 0.00041
                       Syntaxin   7 eveeikkeiekleeevkklkkqneesktstraksvklkkrmesdikeikkraesvkarLeaLdksnkenekk 78 
                                    ++e +++e+e le++v++l +  +++  +  + s++  + + + i++  kr +s+ +r++ Ldk++++  k+
  gi|119720182|ref|YP_920677.1|  60 DIEGLRRELEGLERDVASLAERVSRLEGAYAELSKR-IDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKR 130
                                    555666666666666666666666666666555553.23344555555555555555555555555544432 PP

>> CCDC-167  Coiled-coil domain-containing protein 167
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1       2.7   2.1e+02       4      24 ..      66      86 ..      48      91 .. 0.76
   2 ?   10.9   3.0    0.0056      0.44       4      60 ..      94     147 ..      91     150 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 2.7
                       CCDC-167  4 seIdkleeklascrerLeave 24
                                   +e+++le  +as+ er+ ++e
  gi|119720182|ref|YP_920677.1| 66 RELEGLERDVASLAERVSRLE 86
                                   577777777777777777666 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0056
                       CCDC-167   4 seIdkleeklascrerLeaverrlrkeelseeeResleeEeaslkeqleenekeLks 60 
                                    + Id+l e+++++ +r++++++r+ +     ++ +sl +  +sl +++++ +k+L +
  gi|119720182|ref|YP_920677.1|  94 KRIDSLGERISDLDKRIDSLDKRIDGLD---KRIDSLDKRIESLDKRIDSLDKRLDH 147
                                    6799999999999999999999998754...44579999999999999999999976 PP

>> DUF2959  Protein of unknown function (DUF2959)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0      0.57        45     152     177 ..      58      83 ..      18      86 .. 0.85
   2 ?    7.1   0.0     0.067       5.2      43      81 ..      76     114 ..      42     121 .. 0.59
   3 ?    4.8   0.0      0.36        28      52      87 ..     120     155 ..     113     163 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.57
                        DUF2959 152 aqaiaalkgelselekdvsklikeme 177
                                     ++i++l+ el+ le+dv++l +++ 
  gi|119720182|ref|YP_920677.1|  58 RRDIEGLRRELEGLERDVASLAERVS 83 
                                    479*****************998765 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.067
                        DUF2959  43 avvefdggeLekeyeklnkeyeesekaaeevrerieave 81 
                                    a ++ + + Le +y +l+k+ ++  ++ +++ +ri++++
  gi|119720182|ref|YP_920677.1|  76 ASLAERVSRLEGAYAELSKRIDSLGERISDLDKRIDSLD 114
                                    233334566777777777777777777777777777665 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.36
                        DUF2959  52 Lekeyeklnkeyeesekaaeevrerieaveevaeal 87 
                                    L+k+ ++l+k+ e+ +k+ +++ +r++++ +++  l
  gi|119720182|ref|YP_920677.1| 120 LDKRIDSLDKRIESLDKRIDSLDKRLDHIAKISYTL 155
                                    677788888888888888888888888888887665 PP

>> Sec3_C  Exocyst complex component Sec3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.5   0.00034     0.027      18      70 ..      89     141 ..      61     155 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00034
                         Sec3_C  18 eaanikrllesdkkveelkkdidkalkecdeldalltlysveLstlsedieyI 70 
                                     a+  kr+ ++ +++++l k+id+  k +d ld+++++ ++ +++l + i+  
  gi|119720182|ref|YP_920677.1|  89 YAELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDSL 141
                                    44444555555555555555555555555555555555555555555555544 PP

>> DASH_Spc34  DASH complex subunit Spc34
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1     0.003      0.23     154     224 ..      31     126 ..       4     159 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.003
                     DASH_Spc34 154 dfdvelllkvleelltkyplleake.........................kieelreeYeelseeieeleaeiaeQkkqL 208
                                    d+ + l+  v++++ tk  ++++ e                         ++++l+  Y+els+ i++l ++i++ +k++
  gi|119720182|ref|YP_920677.1|  31 DVRLALINAVIRDVATKHDVEKHWEatrrdieglrreleglerdvaslaeRVSRLEGAYAELSKRIDSLGERISDLDKRI 110
                                    45555555666666666666665555666555555555555555555555777888888888888888888888888777 PP

                     DASH_Spc34 209 eaqnknesesssedds 224
                                    ++ +k+ +  ++  ds
  gi|119720182|ref|YP_920677.1| 111 DSLDKRIDGLDKRIDS 126
                                    7776665555544443 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0       1.2        97      40      79 ..      51      83 ..      44      91 .. 0.52
   2 ?   10.3   0.2    0.0084      0.66      23      78 ..      83     138 ..      79     140 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 1.2
                           KxDL 40 qerlaklrarfkqgtkllkevkkdLesifkkirslkakla 79
                                   +++ + +r       +++  ++++Le + + + sl ++++
  gi|119720182|ref|YP_920677.1| 51 EKHWEATR-------RDIEGLRRELEGLERDVASLAERVS 83
                                   33444444.......4555555555555555555554443 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0084
                           KxDL  23 grlnkknreLlelnalsqerlaklrarfkqgtkllkevkkdLesifkkirslkakl 78 
                                     rl+   +eL++ ++ + er ++l +r+ +  k +  + k ++s+ k+i+sl +++
  gi|119720182|ref|YP_920677.1|  83 SRLEGAYAELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRI 138
                                    56777778888888888888888889988888888999999999999998888776 PP

>> DUF241  Arabidopsis protein of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   1.5    0.0072      0.56     177     220 ..     103     148 ..       3     151 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0072
                         DUF241 177 lekvdaalesllssskkek..vqsalkrleeleecieelEeglekv 220
                                    ++++d+ + sl ++ +  +  ++s+ kr+e+l++ i++l++ l+++
  gi|119720182|ref|YP_920677.1| 103 ISDLDKRIDSLDKRIDGLDkrIDSLDKRIESLDKRIDSLDKRLDHI 148
                                    3445555555555544444567777777777777777777777766 PP

>> Phage_GP20  Phage minor structural protein GP20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0       1.5   1.2e+02      30      67 ..      57      91 ..      37      99 .. 0.55
   2 ?   10.7   0.2    0.0045      0.35      25      69 ..     101     142 ..      88     162 .. 0.45

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 1.5
                     Phage_GP20 30 lkeqlkdrdkqLedLkkkakdneeLqkqieelqaknkk 67
                                      +++    +Le+L+    d+++L + +  l+ ++++
  gi|119720182|ref|YP_920677.1| 57 TRRDIEGLRRELEGLE---RDVASLAERVSRLEGAYAE 91
                                   3444444444444443...3466666666666655555 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0045
                     Phage_GP20  25 eerdtlkeqlkdrdkqLedLkkkakdneeLqkqieelqaknkkak 69 
                                    e   +l ++++  dk +++L k     ++L k ie+l + ++  +
  gi|119720182|ref|YP_920677.1| 101 ERISDLDKRIDSLDKRIDGLDKR---IDSLDKRIESLDKRIDSLD 142
                                    23333333333333333333322...3333333333333333322 PP

>> JIP_LZII  JNK-interacting protein  leucine zipper II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1      0.21        16      42      67 ..      61      86 ..      45     101 .. 0.76
   2 ?   12.2   1.0     0.002      0.15       2      68 ..      63     129 ..      62     132 .. 0.96
   3 ?    8.7   0.3     0.024       1.9      31      70 ..     106     145 ..     103     150 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.21
                       JIP_LZII 42 reiLreEleslqkakerlesrikelE 67
                                    e Lr Ele l+   ++l +r++ lE
  gi|119720182|ref|YP_920677.1| 61 IEGLRRELEGLERDVASLAERVSRLE 86
                                   56677777777777777777777776 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.002
                       JIP_LZII   2 GmgkevenLikENteLletknaLnvvkddLIarvdeLtsereiLreEleslqkakerlesrikelEe 68 
                                    G+++e+e L ++ + L e    L+ +  +L +r+d L ++ + L + ++sl k  + l +ri  l++
  gi|119720182|ref|YP_920677.1|  63 GLRRELEGLERDVASLAERVSRLEGAYAELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDK 129
                                    899***********************************************************99987 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.024
                       JIP_LZII  31 LIarvdeLtsereiLreEleslqkakerlesrikelEeel 70 
                                    L +r+d L ++ + L + ++sl k  e+l +ri  l++ l
  gi|119720182|ref|YP_920677.1| 106 LDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDSLDKRL 145
                                    5567777777777777777777777777777777766654 PP

>> TolA_bind_tri  TolA binding protein trimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1       0.1       7.8      21      66 ..      48      96 ..      31     101 .. 0.74
   2 ?   10.9   0.3    0.0046      0.36       1      65 [.      77     141 ..      77     152 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.1
                  TolA_bind_tri 21 lelqqqlealqqelreLRGqiEelqyqleqleerQrdl...YldlDerl 66
                                   +++ +  ea ++++  LR ++E l+ ++ +l er   l   Y +l +r+
  gi|119720182|ref|YP_920677.1| 48 HDVEKHWEATRRDIEGLRRELEGLERDVASLAERVSRLegaYAELSKRI 96
                                   6777788999999999999999999999999998655433366665555 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0046
                  TolA_bind_tri   1 sledrvarLErilearsqlllelqqqlealqqelreLRGqiEelqyqleqleerQrdlYldlDer 65 
                                    sl +rv+rLE + +  s+ +  l +++++l + +++L   i+ l  ++++l +r   l + +D++
  gi|119720182|ref|YP_920677.1|  77 SLAERVSRLEGAYAELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDSL 141
                                    68899999999999999777777777777777777777777777777777777766665555554 PP

>> Allexi_40kDa  Allexivirus 40kDa protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0     0.041       3.2      83     139 ..      57     115 ..      32     127 .. 0.57
   2 ?   12.7   0.2   0.00087     0.068      75     143 ..      77     147 ..      60     165 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.041
                   Allexi_40kDa  83 lrdalrtltklldklksvekklelsaeta..sdskllkklesietsleelhakldelss 139
                                     r +++ l+++l+ l+++  +l ++ ++      +l k+++s+ +++ +l +++d l +
  gi|119720182|ref|YP_920677.1|  57 TRRDIEGLRRELEGLERDVASLAERVSRLegAYAELSKRIDSLGERISDLDKRIDSLDK 115
                                    45555555555555555555544444433113345556666666666666666665543 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00087
                   Allexi_40kDa  75 sqttlLselrdalrtltklldklksvekklelsaetasds..kllkklesietsleelhakldelsssets 143
                                    s +  +s+l  a  +l+k +d+l +  + l +++++ +++   l k+++s+++++e+l +++d l +  ++
  gi|119720182|ref|YP_920677.1|  77 SLAERVSRLEGAYAELSKRIDSLGERISDLDKRIDSLDKRidGLDKRIDSLDKRIESLDKRIDSLDKRLDH 147
                                    55667788888888888888888888887777777665542246788999999999999998888776665 PP

>> DUF677  Protein of unknown function (DUF677)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.1     0.014       1.1     246     319 ..      48     125 ..      32     133 .. 0.50
   2 ?    5.4   0.1     0.094       7.4     157     198 ..     129     171 ..     118     175 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.014
                         DUF677 246 ssmekgievakkdvenisilverleseiksilktv...efAvekeene.aavklaleeikkkvekltekieevgeeaa 319
                                    +++ek  e+  +d+e ++ ++e le  + s+ + v   e A  + ++   +    +++++k ++ l + i  ++++++
  gi|119720182|ref|YP_920677.1|  48 HDVEKHWEATRRDIEGLRRELEGLERDVASLAERVsrlEGAYAELSKRiDSLGERISDLDKRIDSLDKRIDGLDKRID 125
                                    556666666666666666666666666666666551112232222221023333444444555555555544444444 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.094
                         DUF677 157 llleklrktkkkldkklrniktkraisnvvfvaaf.vaVlvlS 198
                                    + +e l k+   ldk+l  i + +   ++  +a+  +++++l 
  gi|119720182|ref|YP_920677.1| 129 KRIESLDKRIDSLDKRLDHIAKISYTLTASVLATLaASIILLA 171
                                    4577888888888888888877665444444444404444444 PP

>> DUF4446  Protein of unknown function (DUF4446)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0      0.44        34      39      77 ..      46      84 ..      33     103 .. 0.65
   2 ?   10.4   0.1     0.006      0.47      23      76 ..      81     139 ..      75     171 .. 0.63

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.44
                        DUF4446 39 dgksleellkekleeveelkeeseelekeieeleeklkk 77
                                   +++++e++ + + +++e l++e e le+++++l e++++
  gi|119720182|ref|YP_920677.1| 46 TKHDVEKHWEATRRDIEGLRRELEGLERDVASLAERVSR 84
                                   556666666666667777777777666666666666543 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.006
                        DUF4446  23 klkklkkkykklmk.....gkdgksleellkekleeveelkeeseelekeieeleeklk 76 
                                    ++++l+  y +l k     g++ ++l++ + +  ++++ l+++ ++l+k+ie+l+++++
  gi|119720182|ref|YP_920677.1|  81 RVSRLEGAYAELSKridslGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRID 139
                                    56666666666665333334455556666666666666666666666666666665544 PP

>> Vps51  Vps51/Vps67
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0       3.3   2.6e+02      58      84 ..      59      85 ..      56      94 .. 0.79
   2 ?    4.0   0.0      0.68        53      57      85 ..      79     107 ..      73     116 .. 0.72
   3 ?    4.8   0.0      0.36        29      58      83 ..     101     126 ..      91     130 .. 0.63
   4 ?    5.5   0.1      0.23        18      58      85 ..     122     149 ..     115     151 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 3.3
                          Vps51 58 dtIrkmksemdkldqklselkqaiski 84
                                    +I+ +++e++ l+  + +l +++s++
  gi|119720182|ref|YP_920677.1| 59 RDIEGLRRELEGLERDVASLAERVSRL 85
                                   578888888888888888888887765 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.68
                          Vps51  57 sdtIrkmksemdkldqklselkqaiskia 85 
                                    ++ ++++++   +l++++++l+++is+++
  gi|119720182|ref|YP_920677.1|  79 AERVSRLEGAYAELSKRIDSLGERISDLD 107
                                    66777777777777777777777777654 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.36
                          Vps51  58 dtIrkmksemdkldqklselkqaisk 83 
                                    + I+++ + +d+ld++++ l+++i++
  gi|119720182|ref|YP_920677.1| 101 ERISDLDKRIDSLDKRIDGLDKRIDS 126
                                    45666666666666666666666665 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.23
                          Vps51  58 dtIrkmksemdkldqklselkqaiskia 85 
                                    + I ++ + +++ld+++++l++++++ia
  gi|119720182|ref|YP_920677.1| 122 KRIDSLDKRIESLDKRIDSLDKRLDHIA 149
                                    5677888888888888888888888876 PP

>> TssO  Type VI secretion system, TssO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1     0.013      0.99      52      97 ..     105     130 ..      65     156 .. 0.49

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.013
                           TssO  52 kfeekqkelkkkvdsiykkIdsLkpevnavfleneIkkdlndiknt 97 
                                    +++++ + l k +d ++k+IdsL                     + 
  gi|119720182|ref|YP_920677.1| 105 DLDKRIDSLDKRIDGLDKRIDSL--------------------DKR 130
                                    22222222222222222222222....................222 PP

>> Mod_r  Modifier of rudimentary (Mod(r)) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1    0.0015      0.12       6      84 ..      66     145 ..      15     167 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.0015
                          Mod_r   6 eeLqelledeeklealvktl.pevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqel 84 
                                     eL+ l  d   l ++v+ l     +l ++ ++l + + +l ++  sl ++++ l +++ +  + +++l k+ + + ++l
  gi|119720182|ref|YP_920677.1|  66 RELEGLERDVASLAERVSRLeGAYAELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDSLDKRL 145
                                    34444444444444444444333444444444444444444444444444444444444444444555555555555555 PP

>> PRKG1_interact  cGMP-dependent protein kinase interacting domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.6    0.0014      0.11       4      78 ..      52     126 ..      49     160 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.0014
                 PRKG1_interact   4 kLYeeekeenerLkreLeelekelselkseleklkqqrqesvskrssllelekrerrslerkiseleeel....kelee 78 
                                    k +e+ +++ e L+reLe le+++++l +++++l+       ++ s+ ++   +  + l+++i  l++ +    k ++ 
  gi|119720182|ref|YP_920677.1|  52 KHWEATRRDIEGLRRELEGLERDVASLAERVSRLEGAY----AELSKRIDSLGERISDLDKRIDSLDKRIdgldKRIDS 126
                                    668999***************************99663....3333333333444444444444444433223323333 PP

>> Swi5  Swi5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0      0.59        46       3      45 ..      59     101 ..      57     102 .. 0.78
   2 ?    4.5   0.0      0.48        38       4      43 ..      74     113 ..      71     123 .. 0.56
   3 ?    7.8   0.1     0.045       3.5      22      43 ..     120     141 ..      92     163 .. 0.52

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.59
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHH CS
                           Swi5   3 aeikeleeqleelekelaelkeelkekkdpeetvkrhIklLhe 45 
                                    ++i+ l+++le le ++a+l e+    + + +++++ I+ L e
  gi|119720182|ref|YP_920677.1|  59 RDIEGLRRELEGLERDVASLAERVSRLEGAYAELSKRIDSLGE 101
                                    5678888888888888888888888888888888888888765 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.48
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHH CS
                           Swi5   4 eikeleeqleelekelaelkeelkekkdpeetvkrhIklL 43 
                                    ++++l e++++le ++ael+++ ++  +    +++ I+ L
  gi|119720182|ref|YP_920677.1|  74 DVASLAERVSRLEGAYAELSKRIDSLGERISDLDKRIDSL 113
                                    5666666666666666666666555444444444444444 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.045
                                    HHHHHHHHH.HHHHHHHHHHHH CS
                           Swi5  22 lkeelkekkdpeetvkrhIklL 43 
                                    l+++ ++ ++  e +++ I+ L
  gi|119720182|ref|YP_920677.1| 120 LDKRIDSLDKRIESLDKRIDSL 141
                                    3333333333333333333333 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   0.00053     0.041     107     181 ..      64     138 ..      39     163 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00053
                         DUF724 107 lleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaekleeeledveqeF 181
                                    l++e+++le++++  +++ ++le   +el+k+i  l ++   l ++ ++ dk+i  l +  ++l++++e+  ++ 
  gi|119720182|ref|YP_920677.1|  64 LRRELEGLERDVASLAERVSRLEGAYAELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRI 138
                                    455555555555555555555555555555555555555555554555555555555555555444444444433 PP

>> Phasin  Poly(hydroxyalcanoate) granule associated protein (phasin)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1      0.64        50     103     125 ..      57      79 ..      41      93 .. 0.78
   2 ?    9.0   0.9     0.017       1.4      64     125 ..      90     149 ..      84     150 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.64
                         Phasin 103 sredveaLsarvdeLtkelekla 125
                                    +r+d+e L+++++ L++ +++la
  gi|119720182|ref|YP_920677.1|  57 TRRDIEGLRRELEGLERDVASLA 79 
                                    67777777777777777766654 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.017
                         Phasin  64 esvkskveevkekaeeqwdklekafdervakaLsrlgvpsredveaLsarvdeLtkelekla 125
                                     +++++++++ e++++  ++++  +d+r+    +r++    + +e+L +r+d+L k+l+++a
  gi|119720182|ref|YP_920677.1|  90 AELSKRIDSLGERISDLDKRID-SLDKRIDGLDKRIDSL-DKRIESLDKRIDSLDKRLDHIA 149
                                    5667777888888866666665.5789998888888855.4569999999999999998865 PP

>> Dynactin_p22  Dynactin subunit p22
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0      0.96        75     114     147 ..      73     106 ..      55     110 .. 0.75
   2 ?    9.9   0.1    0.0081      0.63       2      42 ..     103     146 ..      95     166 .. 0.60

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.96
                   Dynactin_p22 114 kdvpelkekLekLsqihlkqqeeveelseevkkl 147
                                    +dv +l+e++++L+  + + ++++++l e++++l
  gi|119720182|ref|YP_920677.1|  73 RDVASLAERVSRLEGAYAELSKRIDSLGERISDL 106
                                    4677777777777777777777777777777776 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0081
                   Dynactin_p22   2 ldaLEeriaeLEkrvlGeekekeked...esiidsLakvqkkls 42 
                                    ++ L++ri++L kr+ G +k  ++ d   es+ +++  ++k+l+
  gi|119720182|ref|YP_920677.1| 103 ISDLDKRIDSLDKRIDGLDKRIDSLDkriESLDKRIDSLDKRLD 146
                                    56677777777777777777766655222233333333333332 PP

>> Rab5-bind  Rabaptin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.3   0.00053     0.041     193     293 ..      55     152 ..      22     158 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00053
                      Rab5-bind 193 etlqleierlkeelasisslkveleeikvekeslekslaektrqldklqtikselEeqlkelekekaaveqlvleeknka 272
                                    e+   +ie l+ el+ ++   + l e       le + ae ++ +d+l +++s+l++++  l+k    +++ +    ++ 
  gi|119720182|ref|YP_920677.1|  55 EATRRDIEGLRRELEGLERDVASLAE---RVSRLEGAYAELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRI 131
                                    34456888888888875444433332...223456666777777777777777777777777776666777776666677 PP

                      Rab5-bind 273 qrLqtELDvseqvqrDFvkLs 293
                                    ++L + +D  ++      k+s
  gi|119720182|ref|YP_920677.1| 132 ESLDKRIDSLDKRLDHIAKIS 152
                                    766666666555444444555 PP

>> DUF390  Protein of unknown function (DUF390)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.8   0.00049     0.038     610     684 ..      62     134 ..      15     140 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00049
                         DUF390 610 eqarrnlegirakraaleqrvaelearekeldarersggaavgesdlvarlaaaehsvaelqraldssageveal 684
                                    e  rr+leg+  + a+l +rv+ le    el  r  s g  +  sdl  r+ + ++ +  l++ +ds    +e+l
  gi|119720182|ref|YP_920677.1|  62 EGLRRELEGLERDVASLAERVSRLEGAYAELSKRIDSLGERI--SDLDKRIDSLDKRIDGLDKRIDSLDKRIESL 134
                                    6789*********************************99987..67889****************9988888876 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1     0.016       1.2      18      56 ..      90     128 ..      45     160 .. 0.53

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.016
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXX CS
                           YabA  18 eelleeleelkeelaelleenaeLeleneklrerleeee 56 
                                    +el++++++l e++++l ++ ++L    + l +r+++ +
  gi|119720182|ref|YP_920677.1|  90 AELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLD 128
                                    333333333333333333333333333333333332222 PP

>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   1.2      0.25        19      57      57 ..     122     122 ..      65     164 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.25
                                    H CS
                          HHH_8  57 k 57 
                                    k
  gi|119720182|ref|YP_920677.1| 122 K 122
                                    3 PP

>> Enkurin  Calmodulin-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.8    0.0075      0.59      39      96 ..      69     122 ..      37     145 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0075
                        Enkurin  39 seeerqellegLkkkweelnkeyqslpllidtlskrqrKeklEkeLkqlEkdikllek 96 
                                    +  er+  + +L ++ ++l+  y +l+ +id+l++r   ++l+k+++ l+k i  l+k
  gi|119720182|ref|YP_920677.1|  69 EGLERD--VASLAERVSRLEGAYAELSKRIDSLGER--ISDLDKRIDSLDKRIDGLDK 122
                                    333443..4578888888888999999999988765..45677777777776665544 PP

>> TPD52  Tumour protein D52 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.2    0.0039       0.3      11      65 ..      42      97 ..      35     108 .. 0.88
   2 ?    1.1   0.0       3.3   2.6e+02      32      65 ..     113     146 ..     101     158 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0039
                          TPD52 11 edaaesvsasep.tlteeereeLkseLakleeeivtLrqvLaakekhlaelkrklG 65
                                    d+a+++++++  + t  + e L++eL  le ++++L + ++  e  +ael ++ +
  gi|119720182|ref|YP_920677.1| 42 RDVATKHDVEKHwEATRRDIEGLRRELEGLERDVASLAERVSRLEGAYAELSKRID 97
                                   57788888888889999999*******************************98865 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 3.3
                          TPD52  32 LkseLakleeeivtLrqvLaakekhlaelkrklG 65 
                                    L + +  l++ i +L + + + +k++  l ++l+
  gi|119720182|ref|YP_920677.1| 113 LDKRIDGLDKRIDSLDKRIESLDKRIDSLDKRLD 146
                                    5555566677777777777777777777777765 PP

>> Med9  RNA polymerase II transcription mediator complex subunit 9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0       2.2   1.7e+02      46      70 ..      48      72 ..       7      82 .. 0.73
   2 ?    4.1   0.2      0.64        50      43      77 ..      66     100 ..      37     110 .. 0.66
   3 ?   10.7   1.2    0.0055      0.43      30      73 ..      98     145 ..      82     152 .. 0.52

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 2.2
                           Med9 46 pgidrsveeqeaeieeleeqlakKr 70
                                   +++++  e   + ie l+ +l+  +
  gi|119720182|ref|YP_920677.1| 48 HDVEKHWEATRRDIEGLRRELEGLE 72
                                   4588888888888888888887655 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.64
                           Med9  43 relpgidrsveeqeaeieeleeqlakKrelLkkyk 77 
                                    rel+g++r v++  +++  le   a   + + +++
  gi|119720182|ref|YP_920677.1|  66 RELEGLERDVASLAERVSRLEGAYAELSKRIDSLG 100
                                    45555555555555555555555555555555555 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.0055
                           Med9  30 elrhkLkkarelirelpg....idrsveeqeaeieeleeqlakKrelL 73 
                                    +l  +++   + i++l+     +d+ +++ +++ie+l+++++   + L
  gi|119720182|ref|YP_920677.1|  98 SLGERISDLDKRIDSLDKridgLDKRIDSLDKRIESLDKRIDSLDKRL 145
                                    333333333333333322333366666666666666666666655554 PP

>> Cep57_MT_bd  Centrosome microtubule-binding domain of Cep57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   2.2    0.0022      0.17      12      75 ..      77     142 ..      60     144 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0022
                    Cep57_MT_bd  12 aLaevlkeLedEfehlklelqelaaqynaldpslgkrkRkd..LaeeleelvkrlEaKadqIykLy 75 
                                    +Lae +  Le   ++l+++ + l +++ +ld+++++  +++  L ++++ l kr+E+ ++ I +L 
  gi|119720182|ref|YP_920677.1|  77 SLAERVSRLEGAYAELSKRIDSLGERISDLDKRIDSLDKRIdgLDKRIDSLDKRIESLDKRIDSLD 142
                                    7999999************************99955444322499999999999999999999886 PP

>> HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interacting protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0     0.009      0.71      40      93 ..      47     100 ..      42     106 .. 0.89
   2 ?    1.9   0.0       4.5   3.5e+02      50      88 ..     120     158 ..     103     166 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.009
                 HIP1_clath_bdg  40 keeaerkleeqkeelekLkreleakraelarlkssLesseqsgeqlssqlaaLq 93 
                                    k++ e++ e  +  +e L+rele  + ++a+l + +++ e + ++ls+++++L 
  gi|119720182|ref|YP_920677.1|  47 KHDVEKHWEATRRDIEGLRRELEGLERDVASLAERVSRLEGAYAELSKRIDSLG 100
                                    55667778889999***********************************99985 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 4.5
                 HIP1_clath_bdg  50 qkeelekLkreleakraelarlkssLesseqsgeqlssq 88 
                                      + +++L + +e+  +++++l + L++ ++ + +l+++
  gi|119720182|ref|YP_920677.1| 120 LDKRIDSLDKRIESLDKRIDSLDKRLDHIAKISYTLTAS 158
                                    456788888888888888888888888888877776654 PP

>> Cnn_1N  Centrosomin N-terminal motif 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   1.3     0.012      0.94      12      72 ..      64     130 ..      46     151 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.012
                         Cnn_1N  12 LkKENFdLKLriyfLeerleklse......eqkeellkenielkveveslqkelkekkkllreaeka 72 
                                    L++E  +L   ++ L er+ +l+       + +++l +   +l  ++ sl k ++ ++k+++++ k+
  gi|119720182|ref|YP_920677.1|  64 LRRELEGLERDVASLAERVSRLEGayaelsKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKR 130
                                    3333333333334444444444446666666777777777777777777777777777777776665 PP

>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00074     0.058      13     104 ..      49     150 ..      37     167 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00074
                     V_ATPase_I  13 Dlnedvnafqrkfvkevrrcdemerklrfleeeieklekavikeeea..........eesleapeekeldeleeelekle 82 
                                    D++++ +a  r+     r ++ +er +  l e +++le a ++ ++            +++ ++ +k++d l++++++l+
  gi|119720182|ref|YP_920677.1|  49 DVEKHWEATRRDIEGLRRELEGLERDVASLAERVSRLEGAYAELSKRidslgerisdLDKRIDSLDKRIDGLDKRIDSLD 128
                                    55555555555555555556667777777777777666666655555666444444333333333444444444444444 PP

                     V_ATPase_I  83 eelkelnenleklkkelnelve 104
                                    +++++l++  ++l k+l ++ +
  gi|119720182|ref|YP_920677.1| 129 KRIESLDKRIDSLDKRLDHIAK 150
                                    4444444444444444444443 PP

>> Fzo_mitofusin  fzo-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0      0.29        23     110     134 ..      85     109 ..      39     115 .. 0.56
   2 ?   10.6   0.1    0.0039      0.31      98     155 ..      84     148 ..      71     157 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.29
                  Fzo_mitofusin 110 vdetekeleeeikelekeiekleev 134
                                     + + +el+++i++l ++i+ l++ 
  gi|119720182|ref|YP_920677.1|  85 LEGAYAELSKRIDSLGERISDLDKR 109
                                    2333455555555555555555554 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0039
                  Fzo_mitofusin  98 elsstfarlcqqvdete...keleeeikelekeiekle....evqkkakllrnkaslleseLekf 155
                                    +l+ ++a+l++++d      ++l+++i++l+k+i+ l+    ++ k+ + l ++  +l+++L++ 
  gi|119720182|ref|YP_920677.1|  84 RLEGAYAELSKRIDSLGeriSDLDKRIDSLDKRIDGLDkridSLDKRIESLDKRIDSLDKRLDHI 148
                                    56777777777777543111577888888888886554111145667777888888888888765 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.4     0.011      0.86      16      67 ..      60     113 ..      32     118 .. 0.77
   2 ?    9.9   0.7     0.013       1.1      15      65 ..      83     139 ..      78     157 .. 0.43

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.011
                   Syntaxin-6_N  16 kaeslyrrwerlledtss..stseeldetrteLrkalrsiewdledLeetvriv 67 
                                     +e+l r+ e l +d  s  ++ + l+ +  eL k ++s+ + ++dL++ ++ +
  gi|119720182|ref|YP_920677.1|  60 DIEGLRRELEGLERDVASlaERVSRLEGAYAELSKRIDSLGERISDLDKRIDSL 113
                                    45666666666666666655588999999*******************999765 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.013
                   Syntaxin-6_N  15 nkaeslyrrwe.rlledtss.s....tseeldetrteLrkalrsiewdledLeetvr 65 
                                    +++e+ y++ + r+ ++++  s    + ++ld+  + L k ++s+++ +e L++ ++
  gi|119720182|ref|YP_920677.1|  83 SRLEGAYAELSkRIDSLGERiSdldkRIDSLDKRIDGLDKRIDSLDKRIESLDKRID 139
                                    455555555532333333322122333333333333344444444444444443333 PP

>> Med4  Vitamin-D-receptor interacting Mediator subunit 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0      0.82        64      24      57 ..      54      87 ..      45      98 .. 0.80
   2 ?    8.6   2.0     0.018       1.4      17      52 ..     116     145 ..      76     159 .. 0.57

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.82
                           Med4 24 hqknearilqLraeveslDekikeivksLkeyek 57
                                   +++ + +i+ Lr e e l++ + ++++ + ++e 
  gi|119720182|ref|YP_920677.1| 54 WEATRRDIEGLRRELEGLERDVASLAERVSRLEG 87
                                   3556788****************99999988775 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.018
                           Med4  17 slkeleehqknearilqLraeveslDekikeivksL 52 
                                     ++         +ri++L++++eslD+ i ++ k L
  gi|119720182|ref|YP_920677.1| 116 RID------GLDKRIDSLDKRIESLDKRIDSLDKRL 145
                                    222......223444444444444444444444444 PP

>> SKA1  Spindle and kinetochore-associated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0      0.26        20       5      61 ..      41      97 ..      38     102 .. 0.84
   2 ?    6.3   0.1     0.096       7.6      15      64 ..     114     163 ..     101     169 .. 0.62

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.26
                                   XXX................XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                           SKA1  5 lrelvslrainqdpallkedlskieaevsaleellnklkkelqeeeeaikklkkeie 61
                                   +r++   ++++++ ++++ d++ ++ e++ le+ +++l +++ + e a  +l k i+
  gi|119720182|ref|YP_920677.1| 41 IRDVATKHDVEKHWEATRRDIEGLRRELEGLERDVASLAERVSRLEGAYAELSKRID 97
                                   666667778888889999************************999988888887776 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.096
                                    .........XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                           SKA1  15 nqdpallkedlskieaevsaleellnklkkelqeeeeaikklkkeieasl 64 
                                    ++  + l + +  +++ +++l + +++l k+l++ +++  +l++ + a+l
  gi|119720182|ref|YP_920677.1| 114 DKRIDGLDKRIDSLDKRIESLDKRIDSLDKRLDHIAKISYTLTASVLATL 163
                                    44444456667777777777777777777777777777777766666655 PP

>> COG6  Conserved oligomeric complex COG6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00098     0.076      38     101 ..      88     151 ..      59     167 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00098
                           COG6  38 efqpvaeqLkriesdveklnelcdemkkklssakeetsdlleeaeeLkeekkklelkqkllkaf 101
                                    ++ ++ ++++++++++++l++ +d++ k+++   ++ ++l + +e+L ++ ++l+++ + + ++
  gi|119720182|ref|YP_920677.1|  88 AYAELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDSLDKRLDHIAKI 151
                                    6788999999999999999999999999999999999999999999999999998887776655 PP

>> HBM  Helical bimodular sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.4    0.0014      0.11      25     122 ..      30     124 ..      17     157 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0014
                                    HHHHHHHHHHHHTTT-HHHHHHHHHHHHHHHHHHHHHHH--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            HBM  25 kdLRiaRlqyelsngdataaavqkkldelkaqlqklkakfkspenvrlLqeqlalvqeyrksfnelraayesrnaaRqel 104
                                     d+R+a ++  + ++ at+ +v+k+ + +++  + l+++++  e  r++++ ++ v++++ +++el + ++s  +  + l
  gi|119720182|ref|YP_920677.1|  30 PDVRLALIN-AVIRDVATKHDVEKHWEATRRDIEGLRRELEGLE--RDVASLAERVSRLEGAYAELSKRIDSLGERISDL 106
                                    566666555.4667888999999999999999999999999876..89999999************************** PP

                                    HHHHHHHHHHHHHHHHHH CS
                            HBM 105 dsaaeraleaideleaev 122
                                    d++ ++++++id+l++++
  gi|119720182|ref|YP_920677.1| 107 DKRIDSLDKRIDGLDKRI 124
                                    *************99987 PP

>> Wtap  WTAP/Mum2p family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2    0.0018      0.14      89     152 ..      76     141 ..      49     145 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0018
                           Wtap  89 krLmakcrvLeqENeELgkvlee..grvakLeselalqkkfveelkkaleeleelleeleeevevl 152
                                     +L +++ +Le   +EL k +++  +r++ L +++  ++k ++ l k+   l++ +e+l++ ++ l
  gi|119720182|ref|YP_920677.1|  76 ASLAERVSRLEGAYAELSKRIDSlgERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDSL 141
                                    458889999999999998888875578888888888888888888888888888888888877766 PP

>> APG17  Autophagy protein Apg17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0      0.52        41     226     279 ..      33      96 ..       7     104 .. 0.50
   2 ?    8.7   0.4     0.011      0.83     121     178 ..     103     161 ..      96     172 .. 0.60

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.52
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHH..........HHHHHHHHHHHHHHHHHHHHHHHHH CS
                          APG17 226 reelleVlekDaaeledVvkelqerleem..........ekakkllsekkeeiekllsalkkal 279
                                    r  l++ + +D a  +dV k+ +++ +++          e++ ++l e+ +++e ++++l+k +
  gi|119720182|ref|YP_920677.1|  33 RLALINAVIRDVATKHDVEKHWEATRRDIeglrreleglERDVASLAERVSRLEGAYAELSKRI 96 
                                    5566666666666666666666666666644433333334444444444444444444433333 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.011
                                    TTHHHHHHHHH...HHHHHHHHHHHHTTHH..HHHHHHHHHHH-------STCCHHHHHHH CS
                          APG17 121 veelkealkes...idelqaaqkkldssllefdtdlrelkkelsksksksessslipellk 178
                                    +++l ++++++   id l++  ++ld++++++d+++++l+k+l+  +  + s++l+ ++l+
  gi|119720182|ref|YP_920677.1| 103 ISDLDKRIDSLdkrIDGLDKRIDSLDKRIESLDKRIDSLDKRLD--HIAKISYTLTASVLA 161
                                    55566666444555777777777777777777777777777773..223345555555554 PP

>> Nsp1_C  Nsp1-like C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0      0.53        41      67     101 ..      55      89 ..       8      98 .. 0.57
   2 ?    9.0   0.1     0.015       1.2      51     105 ..      88     142 ..      61     158 .. 0.50

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.53
                         Nsp1_C  67 leaeqeqnkidqeLeyiesqqdeLeslLdnyEkel 101
                                    ++++++ + + +eLe +e++   L + + ++E   
  gi|119720182|ref|YP_920677.1|  55 EATRRDIEGLRRELEGLERDVASLAERVSRLEGAY 89 
                                    23333344444555555555555555555555555 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.015
                         Nsp1_C  51 vLvengekIskLysevleaeqeqnkidqeLeyiesqqdeLeslLdnyEkeleell 105
                                    +  e +++I +L + + + ++    +d++++ + +  d L++ ++++ k++++l 
  gi|119720182|ref|YP_920677.1|  88 AYAELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDSLD 142
                                    4444444444444444444444444444444444444444444444444444443 PP

>> UPF0449  Uncharacterised protein family UPF0449
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0     0.012      0.92      37     100 ..      48     111 ..      27     112 .. 0.77
   2 ?    1.9   0.0       3.9     3e+02      58      97 ..     118     157 ..     110     160 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.012
                        UPF0449  37 dsveedkkassseeedleaeveelYeqvrtylelnerLeeakeeLkqkceeLktageeLeeeie 100
                                    ++ve++ +a+ +  e l+ e e+l + v ++ e   rLe a  eL ++ + L    ++L++ i+
  gi|119720182|ref|YP_920677.1|  48 HDVEKHWEATRRDIEGLRRELEGLERDVASLAERVSRLEGAYAELSKRIDSLGERISDLDKRID 111
                                    23445666666677888999***********************************999999885 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 3.9
                        UPF0449  58 eelYeqvrtylelnerLeeakeeLkqkceeLktageeLee 97 
                                    ++l +++ ++ +  e L +  ++L ++++++ +++ +L+ 
  gi|119720182|ref|YP_920677.1| 118 DGLDKRIDSLDKRIESLDKRIDSLDKRLDHIAKISYTLTA 157
                                    4444444444455556666666677777777666666665 PP

>> TraF_2  F plasmid transfer operon, TraF, protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0       3.2   2.5e+02      39      78 ..      60     106 ..      31     109 .. 0.61
   2 ?   11.8   2.1    0.0014      0.11      31      88 ..     104     157 ..      76     169 .. 0.66

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 3.2
                         TraF_2  39 kiDdlsdildgleaavnaasad.......etqvdeaaddlnalLedl 78 
                                    +i+ l  +l+gle++v++++++        +++++++d l + ++dl
  gi|119720182|ref|YP_920677.1|  60 DIEGLRRELEGLERDVASLAERvsrlegaYAELSKRIDSLGERISDL 106
                                    34455555555555555555543333222333555555555555555 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.0014
                         TraF_2  31 gdvdnlvDkiDdlsdildgleaavnaasadetq.vdeaaddlnalLedlggdgylkasa 88 
                                    +   +l  +iD+l++++dgl++ +++++++  + +d+++d l++ L+ +++  y +++a
  gi|119720182|ref|YP_920677.1| 104 S---DLDKRIDSLDKRIDGLDKRIDSLDKRI-EsLDKRIDSLDKRLDHIAKISY-TLTA 157
                                    3...344455666666666667776766653.3499999999999999998774.3333 PP

>> DUF4337  Domain of unknown function (DUF4337)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1       1.4   1.1e+02      69     111 ..      44      86 ..      19     100 .. 0.58
   2 ?   10.2   0.2    0.0079      0.62      70     133 ..     101     172 ..      80     176 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 1.4
                        DUF4337  69 eelaaavdkkiakykkkiarykkekkeikkkAkeleaerdean 111
                                     +++ +v+k+ ++++++i+  ++e + ++++  +l +++ +++
  gi|119720182|ref|YP_920677.1|  44 VATKHDVEKHWEATRRDIEGLRRELEGLERDVASLAERVSRLE 86 
                                    4445555555555555555555555555554444444444333 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0079
                        DUF4337  70 elaaavdkkiakykkkiarykkekkeikkkAkeleaerdeaneasdk........fdlasalLqiaIvlaai 133
                                    e  ++ dk+i+++ k+i+  +k+ + + k+ ++l+++ d ++++ d+         +   a L  +I+l ai
  gi|119720182|ref|YP_920677.1| 101 ERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDSLDKRLDHiakisytlTASVLATLAASIILLAI 172
                                    555678999999999999999999999999999999999999999998888865333344567788888887 PP

>> TelA  Toxic anion resistance protein (TelA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2    0.0012     0.097     105     188 ..      64     141 ..      38     164 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0012
                           TelA 105 LekgqdellkdnaaLdqlyeknleyfkeLekyiaaGekkleeldekllpeleakaeasgdpedaqalrdleealdrleqr 184
                                    L+++ + l +d+a+L +   ++  ++ eL+k i    +++ +ld++ +  l+++ +  g ++++  l++    ++ l++r
  gi|119720182|ref|YP_920677.1|  64 LRRELEGLERDVASLAERVSRLEGAYAELSKRIDSLGERISDLDKR-IDSLDKRID--GLDKRIDSLDK---RIESLDKR 137
                                    3444444555555555555555555555555554333335555533.455555544..33333222222...44444444 PP

                           TelA 185 vqDL 188
                                    ++ L
  gi|119720182|ref|YP_920677.1| 138 IDSL 141
                                    4333 PP

>> DUF1202  Protein of unknown function (DUF1202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0       2.8   2.2e+02     141     169 ..      49      77 ..      42      82 .. 0.88
   2 ?    6.2   0.0     0.074       5.8     136     175 ..      79     118 ..      71     123 .. 0.89
   3 ?    7.1   0.0     0.041       3.2     137     176 ..     101     140 ..      96     152 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 2.8
                        DUF1202 141 qleaalraqkasipalekelkaldkkivv 169
                                    ++e  ++a +  i +l +el+ l+++++ 
  gi|119720182|ref|YP_920677.1|  49 DVEKHWEATRRDIEGLRRELEGLERDVAS 77 
                                    68999******************999875 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.074
                        DUF1202 136 nyrfsqleaalraqkasipalekelkaldkkivvakkead 175
                                      r s+le a+    + i +l ++++ ldk+i   +k  d
  gi|119720182|ref|YP_920677.1|  79 AERVSRLEGAYAELSKRIDSLGERISDLDKRIDSLDKRID 118
                                    56999***************************99888877 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.041
                        DUF1202 137 yrfsqleaalraqkasipalekelkaldkkivvakkeada 176
                                     r+s+l+  +++  + i +l+k++++ldk+i   +k  d+
  gi|119720182|ref|YP_920677.1| 101 ERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDS 140
                                    5777777777888888888888888888888877777665 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0    0.0036      0.28       8      70 ..      85     147 ..      78     162 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0036
                          Sec34   8 keeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLky 70 
                                     e  + el +++d++ e +++l ++ +s +++   l+++ ++l +  ++l++  ++++++L++
  gi|119720182|ref|YP_920677.1|  85 LEGAYAELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDSLDKRLDH 147
                                    556678888888888899999999999999999999999999998888888888888888876 PP

>> DUF4686  Domain of unknown function (DUF4686)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1    0.0011     0.086     184     261 ..      64     145 ..      16     156 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0011
                        DUF4686 184 LdqnveeLqqqvrslrdkeaqlertnsqqqlriqqqeaqlkklenekrksdehl....ksnqeLsekLsslqqekealqe 259
                                    L ++ e L + v sl ++ ++le + ++++ ri+    +++ l++ +   d+++    k    L +++ sl +  ++l +
  gi|119720182|ref|YP_920677.1|  64 LRRELEGLERDVASLAERVSRLEGAYAELSKRIDSLGERISDLDKRIDSLDKRIdgldKRIDSLDKRIESLDKRIDSLDK 143
                                    55555666666666666666666666666666666666666666666555555555555555555555555555555555 PP

                        DUF4686 260 el 261
                                    +l
  gi|119720182|ref|YP_920677.1| 144 RL 145
                                    44 PP

>> MIP-T3_C  Microtubule-binding protein MIP-T3 C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.3    0.0066      0.52      71     150 ..      52     127 ..      47     138 .. 0.63
   2 ?    6.0   0.4      0.14        11      52      85 ..     103     136 ..      90     154 .. 0.49

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0066
                       MIP-T3_C  71 klldfiqdDidsMqrELemWrseyrqqaeelaeerrateealeplkaqlaeleeaIkdqkekisnvrakilkNeakiqkl 150
                                    k  ++   Di+ + rELe       + a    e  +  e+a  +l +++  l e I+d  ++i+ + ++i   +++i+ l
  gi|119720182|ref|YP_920677.1|  52 KHWEATRRDIEGLRRELEGLERDVASLA----ERVSRLEGAYAELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSL 127
                                    5567777888888888887655444444....444445666666777777777777777777766666665555555544 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.14
                       MIP-T3_C  52 iekLresiQkltksvnPLgklldfiqdDidsMqr 85 
                                    i++L + i +l k +  L k +d     i+s+ +
  gi|119720182|ref|YP_920677.1| 103 ISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDK 136
                                    4444444444444444444444444444444333 PP

>> Vps53_N  Vps53-like, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   1.2    0.0011     0.083      20     105 ..      68     149 ..      32     174 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0011
                        Vps53_N  20 lanidelikklqeeikklddeiksvvraqanvgekgkealeeaqkaieelfqkikeikdkaekseemvkeitrdIkqLDi 99 
                                    l++++  +++l e +++l+   +++ +   + ge+    +++++k i +l + i  + ++ ++ ++ ++ + + I  LD 
  gi|119720182|ref|YP_920677.1|  68 LEGLERDVASLAERVSRLEGAYAELSKRIDSLGER----ISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDSLDK 143
                                    66777777888888999999999888888888888....88999999999999999999999999999999999888875 PP

                        Vps53_N 100 AKknlt 105
                                       +++
  gi|119720182|ref|YP_920677.1| 144 RLDHIA 149
                                    444433 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1    0.0012     0.097     281     356 ..      56     132 ..      41     157 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0012
                          IFT57 281 eaqeelsevkekykqlsegvseltrelaeiseelekvkqemeergssmtDg.splvkikkaltklkkEikqmdvrig 356
                                    ++++ ++ ++++++ l++ v +l +  ++++  + ++++++++ g++++D  + + ++ k ++ l k i ++d ri 
  gi|119720182|ref|YP_920677.1|  56 ATRRDIEGLRRELEGLERDVASLAERVSRLEGAYAELSKRIDSLGERISDLdKRIDSLDKRIDGLDKRIDSLDKRIE 132
                                    34444555555555555555555555555555555555555555555555423344555555555555555555553 PP

>> Noelin-1  Neurogenesis glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0       1.2        90      46      87 ..      73     114 ..      51     118 .. 0.52
   2 ?   11.0   0.1     0.004      0.32      36      86 ..      98     148 ..      88     160 .. 0.54

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 1.2
                       Noelin-1  46 ekvqnlsqsievldlRtsrdlqyvrktetllktlesklkvve 87 
                                      v+ l++ +  l+   ++  + + +  + +++l++++++++
  gi|119720182|ref|YP_920677.1|  73 RDVASLAERVSRLEGAYAELSKRIDSLGERISDLDKRIDSLD 114
                                    444444444444444333333444444444444444444433 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.004
                       Noelin-1  36 arsrqlrqllekvqnlsqsievldlRtsrdlqyvrktetllktlesklkvv 86 
                                    +  +++ +l +++  l + i+ ld+R  +  + +++ ++ +++l+++l+++
  gi|119720182|ref|YP_920677.1|  98 SLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDSLDKRLDHI 148
                                    333445555555555555555555555554455555555555555555554 PP

>> TRAF_BIRC3_bd  TNF receptor-associated factor BIRC3 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1       0.6        47      35      57 ..      55      77 ..      42      87 .. 0.53
   2 ?    7.7   0.2      0.04       3.1       7      61 ..      76     130 ..      71     146 .. 0.60

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.6
                  TRAF_BIRC3_bd 35 eaverqrrldqekieaLekKvrq 57
                                   ea +r  +  ++  e+Le+ v++
  gi|119720182|ref|YP_920677.1| 55 EATRRDIEGLRRELEGLERDVAS 77
                                   34444444444444444444444 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.04
                  TRAF_BIRC3_bd   7 saLetkvatFEnIVsVLnrEverssttieaverqrrldqekieaLekKvrqLert 61 
                                    + L ++v   E+  + L++ +++    i ++ +      + i++L+k++ +L + 
  gi|119720182|ref|YP_920677.1|  76 ASLAERVSRLEGAYAELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKR 130
                                    5566666666666666677777766666666555444444566666666655443 PP

>> DUF2884  Protein of unknown function (DUF2884)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0    0.0015      0.12     157     223 ..      78     142 ..      46     149 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0015
                        DUF2884 157 lgsemlesegdnleafeqrmeklgekieeeveeqakalekkaealCeslkeldaleqqLqkkipeLk 223
                                    l + +   eg+  +++++r+++lge+i  +++++ ++l+k+ + l +++++ld+  + L k+i +L 
  gi|119720182|ref|YP_920677.1|  78 LAERVSRLEGA-YAELSKRIDSLGERIS-DLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDSLD 142
                                    55666666777.7999999999999995.79999999999999999999999999999999999886 PP

>> TMCO5  TMCO5 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1    0.0014      0.11      47     139 ..      49     143 ..      30     157 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0014
                          TMCO5  47 lereedeeenfsenekedalkeLeletaklekkneiLlkevveLqkkisrkeskqddlek..etlkqkleelkvklqkse 124
                                      ++ +e ++  ++   ++l  Le + a l ++   L    +eL k+i+ + ++ +dl+k   +l++  ++l  +++ ++
  gi|119720182|ref|YP_920677.1|  49 DVEKHWEATRRDIEGLRRELEGLERDVASLAERVSRLEGAYAELSKRIDSLGERISDLDKriDSLDKRIDGLDKRIDSLD 128
                                    33444555555555555566668888666666666666666666666666665555666655556667777777777777 PP

                          TMCO5 125 escaeqekelakvee 139
                                    +  ++ +k + ++ +
  gi|119720182|ref|YP_920677.1| 129 KRIESLDKRIDSLDK 143
                                    666666666665554 PP

>> Matrilin_ccoil  Trimeric coiled-coil oligomerisation domain of matrilin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1      0.29        22      23      44 ..      95     116 ..      67     124 .. 0.71
   2 ?    6.2   0.2      0.12       9.2      24      45 .]     117     138 ..     108     145 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.29
                                    HHHHHHHHHHHHHHHHHHHHHH CS
                 Matrilin_ccoil  23 eiqaLtqkLeavtkRlealEnk 44 
                                    +i++L ++ ++  kR+  l+ +
  gi|119720182|ref|YP_920677.1|  95 RIDSLGERISDLDKRIDSLDKR 116
                                    4555555555555555555544 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.12
                                    HHHHHHHHHHHHHHHHHHHHHH CS
                 Matrilin_ccoil  24 iqaLtqkLeavtkRlealEnkl 45 
                                    i+ L ++ ++  kR+e l+ ++
  gi|119720182|ref|YP_920677.1| 117 IDGLDKRIDSLDKRIESLDKRI 138
                                    5556666666666666666654 PP

>> Cast  RIM-binding protein of the cytomatrix active zone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.6     0.078       6.1     466     515 ..      57     106 ..      23     113 .. 0.44
   2 ?   10.4   4.3    0.0017      0.14     373     441 ..      94     163 ..      71     168 .. 0.69

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.078
                           Cast 466 rleeleslkkenkelkeklsalqaeltekesslldlkekasslassglkk 515
                                     + ++e l++e++ l+  + +l ++++  e +  +l ++  sl +++   
  gi|119720182|ref|YP_920677.1|  57 TRRDIEGLRRELEGLERDVASLAERVSRLEGAYAELSKRIDSLGERISDL 106
                                    22333333333333333333333333333333333333333333333222 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0017
                           Cast 373 eekstlageirdlkdmldvkeRkvnvlqkkienLqeqlrdkdkqlaelkervkslqtDssn.tDtALatl 441
                                    +   +l + i+dl + +d  ++++  l k+i++L   +   dk +++l +r+  + + s + t + Latl
  gi|119720182|ref|YP_920677.1|  94 KRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDSLDKRLDHIAKISYTlTASVLATL 163
                                    3344455668888888888888888888888888888888888888888888888777654377778887 PP

>> Tnp_22_trimer  L1 transposable element trimerization domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.4     0.017       1.3       1      30 [.      95     124 ..      95     131 .. 0.84
   2 ?    6.8   0.4     0.082       6.4       1      34 [.     109     142 ..     109     149 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.017
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                  Tnp_22_trimer   1 RidelEERvSaaEDeieeidrevKereKrk 30 
                                    Rid l ER+S     i+ +d+     +Kr+
  gi|119720182|ref|YP_920677.1|  95 RIDSLGERISDLDKRIDSLDKRIDGLDKRI 124
                                    9***********999999999887777777 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.082
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                  Tnp_22_trimer   1 RidelEERvSaaEDeieeidrevKereKrkkile 34 
                                    Rid l  R+ +    i+ +d+     +Kr+  l+
  gi|119720182|ref|YP_920677.1| 109 RIDSLDKRIDGLDKRIDSLDKRIESLDKRIDSLD 142
                                    8999999999999999999999999899886665 PP

>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2     0.002      0.16      17      93 ..      72     147 ..      49     163 .. 0.51

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.002
                           YkyA  17 EkefeeqqekLtelekkeqelyeeiielg..mdefdkikklsdealenveeReellekekesieeakeefekikeeiee 93 
                                    E+++++ +e  ++le    el ++i +lg  ++++dk  +  d+ ++ +++R + l+k    ie+  + ++++++ +++
  gi|119720182|ref|YP_920677.1|  72 ERDVASLAERVSRLEGAYAELSKRIDSLGerISDLDKRIDSLDKRIDGLDKRIDSLDK---RIESLDKRIDSLDKRLDH 147
                                    4455555555555555555555555444411233444444444444444444444444...333333333333333333 PP

>> T3SSipB  Type III cell invasion protein SipB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0    0.0045      0.35      41      93 ..      89     141 ..      46     156 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0045
                                    T----STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT- CS
                        T3SSipB  41 asklSdelqtalseakgatddleaaiekadqaksaadaatkkvdeaqkrlkeL 93 
                                      +lS+ +  + +  +++ + ++   +++d +++ +d ++k+++   kr+++L
  gi|119720182|ref|YP_920677.1|  89 YAELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDSL 141
                                    44566666666666666666666666666666666666666666666666666 PP

>> CREPT  Cell-cycle alteration and expression-elevated protein in tumour
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.3    0.0091      0.71      55     123 ..      73     141 ..      15     158 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0091
                          CREPT  55 ealellaeYnkrLeaeleeRkklakmledfleaqkellakaeekleelkeklekvksvrkelkshiqsL 123
                                      ++ lae ++rLe    e +k    l + ++ + ++++  +++++ l ++++ +++  ++l+++i+sL
  gi|119720182|ref|YP_920677.1|  73 RDVASLAERVSRLEGAYAELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDSL 141
                                    444555555666665555555555566666666666666666666666666666666666666666665 PP

>> DUF465  Protein of unknown function (DUF465)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.1     0.034       2.7       3      32 ..      84     113 ..      82     116 .. 0.86
   2 ?    3.7   0.2      0.82        64      10      26 ..     105     121 ..     104     127 .. 0.67
   3 ?    4.9   0.6      0.33        26      11      32 ..     120     141 ..     117     149 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.034
                                    HHHHHHHHHHHHHHHHHTT-.S-HHHHHHH CS
                         DUF465   3 kLeeeHeeLdkeIhalearpvtddleierL 32 
                                    +Le  ++eL k+I+ l +r ++ d +i  L
  gi|119720182|ref|YP_920677.1|  84 RLEGAYAELSKRIDSLGERISDLDKRIDSL 113
                                    78999**************99888887665 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.82
                                    HHHHHHHHHHTT-.S-H CS
                         DUF465  10 eLdkeIhalearpvtdd 26 
                                    +Ldk+I+ l +r    d
  gi|119720182|ref|YP_920677.1| 105 DLDKRIDSLDKRIDGLD 121
                                    68888888888765444 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.33
                                    HHHHHHHHHTT-.S-HHHHHHH CS
                         DUF465  11 LdkeIhalearpvtddleierL 32 
                                    Ldk+I+ l +r +  d +i  L
  gi|119720182|ref|YP_920677.1| 120 LDKRIDSLDKRIESLDKRIDSL 141
                                    7777777777777666666554 PP

>> DHC_N1  Dynein heavy chain, N-terminal region 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0    0.0015      0.12     233     317 ..      77     151 ..      32     163 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0015
                         DHC_N1 233 etieqfsklekvggtkgkelegqieeileefeeaveklks..ksydvLdvsaeefeadfkeFkerikdlerrlqaiinqa 310
                                    + +           +++++leg   e+ ++++++ e++++  k++d Ld +  + ++ +++ ++ri++l++r+ + ++++
  gi|119720182|ref|YP_920677.1|  77 SLA-----------ERVSRLEGAYAELSKRIDSLGERISDldKRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDS-LDKR 144
                                    333...........4455566666666666666666665411346666666666666666666666666666654.3555 PP

                         DHC_N1 311 fedassl 317
                                    ++++ ++
  gi|119720182|ref|YP_920677.1| 145 LDHIAKI 151
                                    5555555 PP

>> CASP_C  CASP C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1    0.0085      0.66     102     135 ..      49      82 ..      45     105 .. 0.89
   2 ?   -0.4   0.0       7.5   5.9e+02      98     117 ..     115     134 ..      97     145 .. 0.48

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0085
                         CASP_C 102 eLEeelrkqeetvsslraeiaslqkDNlkLYEkv 135
                                    ++E++ + +++ ++ lr+e++ l++D  +L E+v
  gi|119720182|ref|YP_920677.1|  49 DVEKHWEATRRDIEGLRRELEGLERDVASLAERV 82 
                                    789******************************8 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 7.5
                         CASP_C  98 krnaeLEeelrkqeetvssl 117
                                    kr+  L++ +++  + ++sl
  gi|119720182|ref|YP_920677.1| 115 KRIDGLDKRIDSLDKRIESL 134
                                    23333333333333333333 PP

>> Mce4_CUP1  Cholesterol uptake porter CUP1 of Mce4, putative
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1    0.0021      0.17      26      92 ..      92     158 ..      74     171 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0021
                      Mce4_CUP1  26 LeGrGerlGesltdlnevLdelNprlpqlredireladladvYadaapdlldaLdnavttsrTiveq 92 
                                    L+ r + lGe ++dl++ +d l++r++ l + i +l +  +  ++  + l + Ld++++ s T+++ 
  gi|119720182|ref|YP_920677.1|  92 LSKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDSLDKRLDHIAKISYTLTAS 158
                                    5667789**************************************************9999999864 PP

>> FTA4  Kinetochore complex Fta4 of Sim4 subunit, or CENP-50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   1.0     0.024       1.8     115     166 ..      47      98 ..       4     162 .. 0.53

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.024
                           FTA4 115 keaeeepleallerYaelrarLielserrqqlqarlarlrklkallepflgs 166
                                    k+  e+  ea++++ + lr +L  l++    l++r++rl+   a+l++  +s
  gi|119720182|ref|YP_920677.1|  47 KHDVEKHWEATRRDIEGLRRELEGLERDVASLAERVSRLEGAYAELSKRIDS 98 
                                    3333334455555555555555555555555555555555555544443333 PP

>> DUF4455  Domain of unknown function (DUF4455)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.5    0.0019      0.15      13     100 ..      62     151 ..      18     172 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0019
                        DUF4455  13 asleeelasiseeveplileageellkklsesdeeieklfkkledde...dlekltiqelqelwdkVaeeslkrkswIke 89 
                                    + l +el+ ++++v + ++e + +l+ + +e  ++i++l +++ d +   d ++  i+ l +  d + ++++   + I+ 
  gi|119720182|ref|YP_920677.1|  62 EGLRRELEGLERDVAS-LAERVSRLEGAYAELSKRIDSLGERISDLDkriDSLDKRIDGLDKRIDSLDKRIESLDKRIDS 140
                                    4455555555555543.455555566665665555555555543333111556666777777777777777777777777 PP

                        DUF4455  90 ldetLeklEke 100
                                    ld++L+ ++k 
  gi|119720182|ref|YP_920677.1| 141 LDKRLDHIAKI 151
                                    77777666654 PP

>> TRPM_tetra  Tetramerisation domain of TRPM
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0         2   1.5e+02      19      42 ..      90     113 ..      75     122 .. 0.55
   2 ?    9.9   0.7      0.01      0.79       2      54 ..     108     161 ..     107     163 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 2
                     TRPM_tetra  19 eevneKenlikaSLqsldfrLgkL 42 
                                     e++++  +  + +++ld r+  L
  gi|119720182|ref|YP_920677.1|  90 AELSKRIDSLGERISDLDKRIDSL 113
                                    455555555555555555555444 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.01
                     TRPM_tetra   2 eRIrvttERvEnmsmkveevneKenlikaSLqsldfrLgkLedls.altvdtLk 54 
                                    +RI     R++ +  +++ ++++  +  + + sld rL ++  +s  lt++ L+
  gi|119720182|ref|YP_920677.1| 108 KRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDSLDKRLDHIAKISyTLTASVLA 161
                                    5666667788888899*************************9998446777776 PP

>> DUF2205  Short coiled-coil protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1      0.28        22      10      42 ..      68      99 ..      45     103 .. 0.80
   2 ?    6.6   0.3       0.1       7.8      17      49 ..      88     120 ..      76     134 .. 0.62
   3 ?    5.2   0.3      0.27        21      21      40 ..     120     139 ..      97     151 .. 0.55

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.28
                        DUF2205 10 veklerearerLqqqakeLqssLqaLaervdeV 42
                                   +e ler+  + L +++  L     +L++r+d+ 
  gi|119720182|ref|YP_920677.1| 68 LEGLERDV-ASLAERVSRLEGAYAELSKRIDSL 99
                                   44444443.67999****************985 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.1
                        DUF2205  17 arerLqqqakeLqssLqaLaervdeVkeehdKL 49 
                                    a ++L++++++L +   +L +r+d+  +  d L
  gi|119720182|ref|YP_920677.1|  88 AYAELSKRIDSLGERISDLDKRIDSLDKRIDGL 120
                                    446677777777777777777777665554444 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.27
                        DUF2205  21 LqqqakeLqssLqaLaervd 40 
                                    L++++++L +  ++L +r+d
  gi|119720182|ref|YP_920677.1| 120 LDKRIDSLDKRIESLDKRID 139
                                    34444444444444444444 PP

>> DUF3535  Domain of unknown function (DUF3535)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0    0.0026      0.21     234     303 ..     103     170 ..      57     173 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0026
                        DUF3535 234 aftleqaeklvttdyekllkslslkqkllaekqLeerrrrlqaaieeakeeqealhvrvqaalAgAlval 303
                                    + +l++  +  ++ ++ l k++ +  k+++  +L++r  +l + ++++++   +l+ +v+a+lA+ ++ l
  gi|119720182|ref|YP_920677.1| 103 ISDLDKRIDSLDKRIDGLDKRIDSLDKRIE--SLDKRIDSLDKRLDHIAKISYTLTASVLATLAASIILL 170
                                    555666666677788999999999999999..***********************************987 PP

>> Macoilin  Macoilin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.9    0.0019      0.15     396     477 ..      66     147 ..      12     160 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0019
                       Macoilin 396 dalvrLeadikkLkaeLqasrqteqelrskissltseerslkselqqlkkendllqtklhelvsakqkdkqtlqqlekrL 475
                                     +l+ Le d++ L   ++       el ++i+sl ++   l + +++l k  d l +++++l +      + + +l+krL
  gi|119720182|ref|YP_920677.1|  66 RELEGLERDVASLAERVSRLEGAYAELSKRIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDSLDKRL 145
                                    3488899999999999999999999*********99999999999*****9****9999999998888888999999999 PP

                       Macoilin 476 ke 477
                                    ++
  gi|119720182|ref|YP_920677.1| 146 DH 147
                                    76 PP

>> U62_UL91  Functional domain of U62 and UL91 proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0       6.1   4.8e+02       5      49 ..      34      78 ..      32      86 .. 0.71
   2 ?    8.2   0.2     0.031       2.4      25      56 ..     117     148 ..      88     163 .. 0.65

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 6.1
                       U62_UL91  5 LaelkddfeacetkeDlFkiiDklsknfnFlveqvEslPRRvdsa 49
                                   La ++      +tk D+ k  +   ++++ l  + E l R v s 
  gi|119720182|ref|YP_920677.1| 34 LALINAVIRDVATKHDVEKHWEATRRDIEGLRRELEGLERDVASL 78
                                   667788888899999998877766666666666666666666555 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.031
                       U62_UL91  25 iDklsknfnFlveqvEslPRRvdsaAilFdnL 56 
                                    iD l k ++ l + +Esl +R+ds     d++
  gi|119720182|ref|YP_920677.1| 117 IDGLDKRIDSLDKRIESLDKRIDSLDKRLDHI 148
                                    44555555555555555555555544444443 PP

>> PspB  Phage shock protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.3      0.53        42      40      61 ..      65      86 ..      46      92 .. 0.85
   2 ?    4.5   0.1      0.45        36      41      65 ..      94     118 ..      89     122 .. 0.77
   3 ?    6.1   0.4      0.14        11      41      65 ..     122     146 ..     115     150 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.53
                           PspB 40 ekrLeellekAekleeRietLE 61
                                   +++Le l ++   l+eR++ LE
  gi|119720182|ref|YP_920677.1| 65 RRELEGLERDVASLAERVSRLE 86
                                   689*****************99 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.45
                           PspB  41 krLeellekAekleeRietLEriLd 65 
                                    kr+++l e+ + l++Ri++L + +d
  gi|119720182|ref|YP_920677.1|  94 KRIDSLGERISDLDKRIDSLDKRID 118
                                    6788888888888888888877555 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.14
                           PspB  41 krLeellekAekleeRietLEriLd 65 
                                    kr+++l ++ e l++Ri++L + Ld
  gi|119720182|ref|YP_920677.1| 122 KRIDSLDKRIESLDKRIDSLDKRLD 146
                                    6778888888888888888888777 PP

>> EMP24_GP25L  emp24/gp25L/p24 family/GOLD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0       0.6        47     103     151 ..      51      99 ..      28     104 .. 0.59
   2 ?    6.5   0.1     0.093       7.3     109     168 ..     113     172 ..      97     175 .. 0.57

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.6
                    EMP24_GP25L 103 dykdsakkekletleselkkleekldsikreqkylrereerlrdtnest 151
                                    +++ +a+  ++e l +el+ le+ + s+ + +  l+   ++l + + s+
  gi|119720182|ref|YP_920677.1|  51 EKHWEATRRDIEGLRRELEGLERDVASLAERVSRLEGAYAELSKRIDSL 99 
                                    3445555666666666666666666666666666666666666666555 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.093
                    EMP24_GP25L 109 kkekletleselkkleekldsikreqkylrereerlrdtnestnsrvvwwsilqllvlvl 168
                                     ++ ++ l ++++ l+++++s+ + +++l +r +   +++  ++  v+    +++++l++
  gi|119720182|ref|YP_920677.1| 113 LDKRIDGLDKRIDSLDKRIESLDKRIDSLDKRLDHIAKISYTLTASVLATLAASIILLAI 172
                                    245555666666666666666666666666666666666666666666666666666655 PP

>> BRI3BP  Negative regulator of p53/TP53
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   3.7      0.21        16     161     172 ..     120     131 ..      50     151 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.21
                         BRI3BP 161 leakvrsLerqv 172
                                    l+++++sL++++
  gi|119720182|ref|YP_920677.1| 120 LDKRIDSLDKRI 131
                                    333333333333 PP

>> DUF1690  Protein of Unknown function (DUF1690)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.1       0.7        55      70     107 ..      46      82 ..      13      94 .. 0.65
   2 ?    6.3   0.5      0.16        12      75      98 ..     114     137 ..      78     161 .. 0.47

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.7
                        DUF1690  70 adakdelsskalnekieeLrkkleefkkkeeeklpeev 107
                                    ++++ e++ +a +++ie Lr+ le +++ +   l e v
  gi|119720182|ref|YP_920677.1|  46 TKHDVEKHWEATRRDIEGLRRELEGLERDVA-SLAERV 82 
                                    3346677788889999999999998776665.555544 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.16
                        DUF1690  75 elsskalnekieeLrkkleefkkk 98 
                                     +  + l++ i++L k++e ++k+
  gi|119720182|ref|YP_920677.1| 114 DKRIDGLDKRIDSLDKRIESLDKR 137
                                    222223333333333333333332 PP

>> FAM76  FAM76 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   1.0    0.0079      0.62     220     260 ..      95     135 ..      44     159 .. 0.46

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0079
                          FAM76 220 avtqLkeeiaslkkqleqkdqellekdkkitelkaelleke 260
                                     +  L e+i  l k++++ d+ +   dk i +l    ++ +
  gi|119720182|ref|YP_920677.1|  95 RIDSLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLD 135
                                    23333333333333333333333333333333322222222 PP

>> Phage_GPO  Phage capsid scaffolding protein (GPO) serine peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0    0.0061      0.48     190     248 ..      76     138 ..       5     155 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0061
                      Phage_GPO 190 ksddarfadveeavelvAeevkelsekveall....aleaelaalkkeveklkaeleaLkekL 248
                                    +s  +r++ +e a  ++ +++ +l e++++l     +l++++  l+k++++l++++e+L +++
  gi|119720182|ref|YP_920677.1|  76 ASLAERVSRLEGAYAELSKRIDSLGERISDLDkridSLDKRIDGLDKRIDSLDKRIESLDKRI 138
                                    333344444444444444444444444442211111333334444444444444444444444 PP

>> DUF4515  Domain of unknown function (DUF4515)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.1     0.037       2.9     147     193 ..      43      89 ..      37      99 .. 0.86
   2 ?    2.5   0.1       1.4   1.1e+02      82     106 ..     119     143 ..      89     156 .. 0.51

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.037
                        DUF4515 147 klaAkkalseftrsvkreNqeLrkeLlqliketkkLekekskLeeqk 193
                                    ++a k  ++ ++++ +r+ + Lr+eL  l +++ +L+++ s+Le   
  gi|119720182|ref|YP_920677.1|  43 DVATKHDVEKHWEATRRDIEGLRRELEGLERDVASLAERVSRLEGAY 89 
                                    566778889999*******************************9765 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 1.4
                        DUF4515  82 qqerkiqtLeeekekvqaetaeklr 106
                                      +++i+ L +  e++ +  +++++
  gi|119720182|ref|YP_920677.1| 119 GLDKRIDSLDKRIESLDKRIDSLDK 143
                                    2333333333333333333333333 PP

>> HalX  HalX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   6.1     0.056       4.4       2      60 ..      58     112 ..      57     130 .. 0.80
   2 ?    3.9   0.2      0.88        69      40      60 ..     127     147 ..     120     152 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.056
                           HalX   2 rseYdeelqelfaLasKravLeaekseaeLadseeYqeLearleelraqldetldeldd 60 
                                    r+  +   +el++L++ +a L   +s   L+   +Y+eL  r+++l ++++++  ++d+
  gi|119720182|ref|YP_920677.1|  58 RRDIEGLRRELEGLERDVASLAERVSR--LEG--AYAELSKRIDSLGERISDLDKRIDS 112
                                    667777889999999999999887664..544..9999999999999999998888766 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.88
                           HalX  40 Learleelraqldetldeldd 60 
                                    L  r+e+l  ++d +  +ld+
  gi|119720182|ref|YP_920677.1| 127 LDKRIESLDKRIDSLDKRLDH 147
                                    566666666666666555544 PP

>> GTP-bdg_M  GTP-binding GTPase Middle Region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.3       1.7   1.3e+02      47      72 ..      50      75 ..      21      81 .. 0.80
   2 ?   10.2   1.0     0.012      0.91      13      75 ..      75     134 ..      74     137 .. 0.78
   3 ?    4.6   0.1      0.63        49      49      71 ..     129     151 ..     125     158 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 1.7
                                   XHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      GTP-bdg_M 47 leldrrlireriaklkkeLekvkkkr 72
                                   +e +    r+ i+ l++eLe +++  
  gi|119720182|ref|YP_920677.1| 50 VEKHWEATRRDIEGLRRELEGLERDV 75
                                   55556667888999999999998865 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.012
                                    HHHHHHHHHHHCXXXXXXXXX..X..XXXXXXXXXHHHHH..HHHHHHHHHHHHHHHHHHHHH.. CS
                      GTP-bdg_M  13 lAqlkyllprLeglgkelsrqgGgigtrGpGetkleldrr..lireriaklkkeLekvkkkrelq 75 
                                    +A l  + +rLeg+++els+      +   Ge   +ld+r   +++ri+ l k++++++k+ e +
  gi|119720182|ref|YP_920677.1|  75 VASLAERVSRLEGAYAELSKR-----IDSLGERISDLDKRidSLDKRIDGLDKRIDSLDKRIESL 134
                                    578888899999999999998.....5567777777776633699***********999987765 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.63
                                    HHHHHHHHHHHHHHHHHHHHHHH CS
                      GTP-bdg_M  49 ldrrlireriaklkkeLekvkkk 71 
                                     +   +++ri++l k+L++++k 
  gi|119720182|ref|YP_920677.1| 129 KRIESLDKRIDSLDKRLDHIAKI 151
                                    45567889999999999999886 PP

>> Phlebovirus_NSM  Phlebovirus nonstructural protein NS-M
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   1.0     0.004      0.32     183     262 ..      91     167 ..      65     169 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.004
                Phlebovirus_NSM 183 elqkkRndikrgqekrdakklveesmArvkdlkeelkiltdelsqikseiqilrkkikdfetvvpAllsvAllsllvspi 262
                                    el+k R d   g++  d +k+++ ++ r+ +l ++   l   ++ + + i +l k+      +   l +  +l++l+++i
  gi|119720182|ref|YP_920677.1|  91 ELSK-RID-SLGERISDLDKRIDSLDKRIDGLDKRIDSLDKRIESLDKRIDSLDKRLDHIAKISYTL-TASVLATLAASI 167
                                    4555.555.589********************************************99999998776.566778888877 PP

>> DUF4349  Domain of unknown function (DUF4349)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.3      0.19        15     122     147 ..      58      83 ..      21      85 .. 0.78
   2 ?    5.6   2.1      0.13       9.8     124     147 ..     102     125 ..      79     173 .. 0.62

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.19
                        DUF4349 122 ereLsevqaeieslegqlryLdnqva 147
                                     r+++  + e+e le+  ++L+++v+
  gi|119720182|ref|YP_920677.1|  58 RRDIEGLRRELEGLERDVASLAERVS 83 
                                    45666677777777777777777775 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.13
                        DUF4349 124 eLsevqaeieslegqlryLdnqva 147
                                    ++s+  ++i+sl +++  Ld++++
  gi|119720182|ref|YP_920677.1| 102 RISDLDKRIDSLDKRIDGLDKRID 125
                                    444444444444444444444444 PP

>> Val_tRNA-synt_C  Valyl tRNA synthetase tRNA binding arm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1       1.4   1.1e+02       8      28 ..      63      83 ..      49      87 .. 0.78
   2 ?    5.2   0.3      0.34        26       9      26 ..     106     123 ..      77     126 .. 0.58
   3 ?    8.9   0.4     0.023       1.8       1      27 [.     105     131 ..     105     139 .. 0.70
   4 ?    8.0   0.2     0.045       3.5       2      27 ..     120     145 ..     119     150 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 1.4
                Val_tRNA-synt_C  8 RLeKeLaklekeiervqkKLa 28
                                    L +eL+ le ++++++++ +
  gi|119720182|ref|YP_920677.1| 63 GLRRELEGLERDVASLAERVS 83
                                   477888888888888888766 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.34
                Val_tRNA-synt_C   9 LeKeLaklekeiervqkK 26 
                                    L+K+++ l+k i++++k+
  gi|119720182|ref|YP_920677.1| 106 LDKRIDSLDKRIDGLDKR 123
                                    445555555555555554 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.023
                Val_tRNA-synt_C   1 DvekeraRLeKeLaklekeiervqkKL 27 
                                    D++k ++ L+K+++ l+k i++++k++
  gi|119720182|ref|YP_920677.1| 105 DLDKRIDSLDKRIDGLDKRIDSLDKRI 131
                                    677777777777777777777777776 PP

  == domain 4  score: 8.0 bits;  conditional E-value: 0.045
                Val_tRNA-synt_C   2 vekeraRLeKeLaklekeiervqkKL 27 
                                    ++k ++ L+K+++ l+k i++++k+L
  gi|119720182|ref|YP_920677.1| 120 LDKRIDSLDKRIESLDKRIDSLDKRL 145
                                    56778889999999999999999988 PP

>> Glyco_H_20C_C  Glycoside Hydrolase 20C C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   3.1     0.063       4.9     142     171 ..     112     140 ..      17     152 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.063
                  Glyco_H_20C_C 142 vldiRlGGllaRlesaeeRLeaYlegkier 171
                                     ld R+ Gl +R++s  +R+e+ l+ +i++
  gi|119720182|ref|YP_920677.1| 112 SLDKRIDGLDKRIDSLDKRIES-LDKRIDS 140
                                    4677777777777777777765.4445544 PP

>> Osmo_CC  Osmosensory transporter coiled coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.2      0.15        12      11      34 ..      93     116 ..      83     123 .. 0.61
   2 ?    6.4   1.1      0.13        10      17      38 ..     120     141 ..     111     150 .. 0.55

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.15
                                    XXXXTHHHHHHHHHHHHHHHHHHH CS
                        Osmo_CC  11 qehYdnIEqkvedideeIaaLeek 34 
                                    + + d+  +++ d+d+ I  L ++
  gi|119720182|ref|YP_920677.1|  93 SKRIDSLGERISDLDKRIDSLDKR 116
                                    444455556677777777777665 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.13
                                    HHHHHHHHHHHHHHHHHHHHHH CS
                        Osmo_CC  17 IEqkvedideeIaaLeekRqrL 38 
                                      ++++ +d+ I+ L ++ ++L
  gi|119720182|ref|YP_920677.1| 120 LDKRIDSLDKRIESLDKRIDSL 141
                                    4455555555555555543333 PP

>> Ntox28  Bacterial toxin 28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   2.9      0.04       3.1      16      97 ..      44     129 ..      31     154 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.04
                         Ntox28  16 iinseltendysaarRelqG...evvarkPD.GtpydHvkeltdaqkGLenvrralekelenppdsdteRevLerklkea 91 
                                    +  ++  e++++a+rR+++G   e      D  +  + v  l+ a+  L+++++ l +++ ++ + +   ++ ++ l++ 
  gi|119720182|ref|YP_920677.1|  44 VATKHDVEKHWEATRRDIEGlrrELEGLERDvASLAERVSRLEGAYAELSKRIDSLGERISDLDKRIDSLDKRIDGLDKR 123
                                    46788899999999999998444333333341455678899999999999999999888777766665555555555555 PP

                         Ntox28  92 vleLdr 97 
                                    ++ Ld+
  gi|119720182|ref|YP_920677.1| 124 IDSLDK 129
                                    555554 PP

>> DUF1003  Protein of unknown function (DUF1003)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.2         2   1.6e+02      74     102 ..      52      80 ..      39     109 .. 0.78
   2 ?    1.2   0.0       5.1     4e+02      71      99 ..     120     147 ..     100     152 .. 0.57
   3 ?    8.5   0.5     0.027       2.1      29      58 ..     143     172 ..     138     176 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 2
                        DUF1003  74 qvnlkaeaeiekLtrevaalrealgevat 102
                                    +  + ++++ie L re++ l+ ++ + a+
  gi|119720182|ref|YP_920677.1|  52 KHWEATRRDIEGLRRELEGLERDVASLAE 80 
                                    44566778888888888888887776665 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 5.1
                        DUF1003  71 edrqvnlkaeaeiekLtrevaalrealge 99 
                                    +d +++    + ie L +++++l ++l +
  gi|119720182|ref|YP_920677.1| 120 LDKRIDSLD-KRIESLDKRIDSLDKRLDH 147
                                    344443333.3667777777776666655 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.027
                        DUF1003  29 kpfDpypFillnlvlslqaalaaplIllsq 58 
                                    k+ D    i ++l  s++a laa +Ill+ 
  gi|119720182|ref|YP_920677.1| 143 KRLDHIAKISYTLTASVLATLAASIILLAI 172
                                    67788888999*****************85 PP

>> MutS_IV  MutS family domain IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1       4.9   3.8e+02       6      26 ..      61      81 ..      55      87 .. 0.58
   2 ?    0.8   0.1       8.1   6.4e+02       4      23 ..      94     113 ..      78     119 .. 0.62
   3 ?    8.2   0.7      0.04       3.2       3      48 ..     107     155 ..     105     162 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 4.9
                                   HHHHHHHHHHHHHHHHHHHCC CS
                        MutS_IV  6 Ldelrdrleelekeleeleek 26
                                   +  lr+ le+le++ ++l+e+
  gi|119720182|ref|YP_920677.1| 61 IEGLRRELEGLERDVASLAER 81
                                   344555566666655555555 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 8.1
                                    HHHHHHHHHHHHHHHHHHHH CS
                        MutS_IV   4 eeLdelrdrleelekeleel 23 
                                    +++d l +r+++l k++++l
  gi|119720182|ref|YP_920677.1|  94 KRIDSLGERISDLDKRIDSL 113
                                    34555555555555555555 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.04
                                    SHHHHHHHHHHHHHHHHHHHHHCCCCC.CCT-TTBE..ECCCSSSEEEE CS
                        MutS_IV   3 deeLdelrdrleelekeleeleekere.klgikslk..veynkvlGyyl 48 
                                    d+++d l +r+++l k++++l ++ ++ + +i+sl+  +++++++ y l
  gi|119720182|ref|YP_920677.1| 107 DKRIDSLDKRIDGLDKRIDSLDKRIESlDKRIDSLDkrLDHIAKISYTL 155
                                    8899999999999999999999999888999999877788888888877 PP

>> DUF3618  Protein of unknown function (DUF3618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   3.9      0.22        17       8      30 ..      58      83 ..      54      83 .. 0.79
   2 ?    1.9   0.0       3.5   2.7e+02      16      28 ..      90     102 ..      86     104 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.22
                        DUF3618  8 erdIertRaeL...aeTvdeLaarad 30
                                   +rdIe  R+eL    ++v +La+r++
  gi|119720182|ref|YP_920677.1| 58 RRDIEGLRRELeglERDVASLAERVS 83
                                   89999999986322799*****9996 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 3.5
                        DUF3618  16 aeLaeTvdeLaar 28 
                                    aeL+  +d+L++r
  gi|119720182|ref|YP_920677.1|  90 AELSKRIDSLGER 102
                                    79**********9 PP

>> DUF3375  Protein of unknown function (DUF3375)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   1.5       1.4   1.1e+02     127     167 ..      43      81 ..      31      99 .. 0.70
   2 ?    5.1   0.6      0.11       8.9     134     159 ..      90     115 ..      75     120 .. 0.67
   3 ?    6.8   1.0     0.036       2.8     134     158 ..     104     128 ..      94     129 .. 0.74
   4 ?    6.4   1.1     0.048       3.7     138     159 ..     122     143 ..     120     158 .. 0.68

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 1.4
                        DUF3375 127 qlaeetepDpeeRlaeLeaeiaeidaeidrlrageveeldd 167
                                    ++  +t+ D+e++ ++ +++i+ +++e++ l+++   + ++
  gi|119720182|ref|YP_920677.1|  43 DV--ATKHDVEKHWEATRRDIEGLRRELEGLERDVASLAER 81 
                                    44..4678888888888888888888888888766655554 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.11
                        DUF3375 134 pDpeeRlaeLeaeiaeidaeidrlra 159
                                    +  ++R+ +L ++i  +d++id l++
  gi|119720182|ref|YP_920677.1|  90 AELSKRIDSLGERISDLDKRIDSLDK 115
                                    55677888888888888888887765 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.036
                        DUF3375 134 pDpeeRlaeLeaeiaeidaeidrlr 158
                                     D ++R+ +L+++i+ +d++id l+
  gi|119720182|ref|YP_920677.1| 104 SDLDKRIDSLDKRIDGLDKRIDSLD 128
                                    4677788888888888888887775 PP

  == domain 4  score: 6.4 bits;  conditional E-value: 0.048
                        DUF3375 138 eRlaeLeaeiaeidaeidrlra 159
                                    +R+ +L+++i+ +d++id l++
  gi|119720182|ref|YP_920677.1| 122 KRIDSLDKRIESLDKRIDSLDK 143
                                    6777777777777777776664 PP

>> YvrJ  YvrJ protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1      0.84        66      21      34 ..      94     107 ..      83     109 .. 0.78
   2 ?    3.3   0.1      0.77        60      20      35 ..     107     122 ..     106     123 .. 0.87
   3 ?    5.0   0.4      0.22        17      21      35 ..     122     136 ..     120     144 .. 0.68

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.84
                           YvrJ  21 kkLdeLtksIeeLs 34 
                                    k++d+L + I +L 
  gi|119720182|ref|YP_920677.1|  94 KRIDSLGERISDLD 107
                                    78888888888886 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.77
                           YvrJ  20 EkkLdeLtksIeeLse 35 
                                     k++d+L k I+ L +
  gi|119720182|ref|YP_920677.1| 107 DKRIDSLDKRIDGLDK 122
                                    79*********99975 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.22
                           YvrJ  21 kkLdeLtksIeeLse 35 
                                    k++d+L k Ie L +
  gi|119720182|ref|YP_920677.1| 122 KRIDSLDKRIESLDK 136
                                    677777777777754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1156  (0.0644765); expected 358.6 (0.02)
Passed bias filter:                      922  (0.0514251); expected 358.6 (0.02)
Passed Vit filter:                       323  (0.0180155); expected 17.9 (0.001)
Passed Fwd filter:                       231  (0.0128842); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):             229  [number of targets reported over threshold]
# CPU time: 1.62u 0.37s 00:00:01.99 Elapsed: 00:00:00.61
# Mc/sec: 877.87
//
Query:       gi|119720183|ref|YP_920678.1|  [L=145]
Description: DNA polymerase beta subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      9e-14   51.3   0.0    1.5e-13   50.6   0.0    1.4  1  Polbeta       Polymerase beta, Nucleotidyltransferase
    2.7e-05   24.4   0.1    5.4e-05   23.4   0.0    1.5  1  NTP_transf_2  Nucleotidyltransferase domain
  ------ inclusion threshold ------
      0.053   13.3   0.3        1.2    9.0   0.0    2.3  2  DUF2997       Protein of unknown function (DUF2997)


Domain annotation for each model (and alignments):
>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.6   0.0   2.5e-17   1.5e-13       1      92 [.      19     105 ..      19     106 .. 0.94

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 2.5e-17
                                    -STTTTHHHHHHHHSTTEEEEEE-S------EEEEEEEESS---HHHHHHHHHHHHHH.SSSEEEEEETTTS-HHHHHHH CS
                        Polbeta   1 ekikeilekekeielaylFGSrakgkareeSDiDlavllkekldleeelelaaelediklgkkvDlvdlneapplllyei 80 
                                    e +k+++ek++++++a+lFGS ++ +  +  DiD+av  + +  lee le  aele+  lg  vD+v l +app ++ ++
  gi|119720183|ref|YP_920678.1|  19 ETLKKYFEKRSDVAVAVLFGSALRRRKVR--DIDIAVHADWS--LEELLEATAELEKE-LGTPVDIVPLPNAPPQVRLKA 93 
                                    689********************888776..********999..**************.9******************** PP

                                    HHS-EEEES-SH CS
                        Polbeta  81 lkegkllyskde 92 
                                    l+eg  +  k++
  gi|119720183|ref|YP_920678.1|  94 LAEGLPITVKNH 105
                                    ****99998886 PP

>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   9.1e-09   5.4e-05       2      80 ..      19      86 ..      18     109 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 9.1e-09
                                   HHHHHHHHHHTTTSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEECEEECC CS
                   NTP_transf_2  2 kklleelkelepvakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevdlvtrekle 80
                                   ++l++ +++++ va +vlfGS+ r    k  DiD++v+ +++          e+l e   +le+ lg +vd+v+    +
  gi|119720183|ref|YP_920678.1| 19 ETLKKYFEKRSDVAVAVLFGSALRRR--KVRDIDIAVHADWSL---------EELLEATAELEKELGTPVDIVPLPNAP 86
                                   679999**9999**********9976..669***********4.........5677777777777777****9544443 PP

>> DUF2997  Protein of unknown function (DUF2997)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0    0.0002       1.2      24      43 ..      63      82 ..      63      85 .. 0.84
   2 ?    2.1   0.1     0.028   1.7e+02      26      41 ..     108     123 ..     106     125 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0002
                        DUF2997 24 leataalEqaLGkvesrelt 43
                                   leata+lE++LG+ ++  ++
  gi|119720183|ref|YP_920678.1| 63 LEATAELEKELGTPVDIVPL 82
                                   69**********99886655 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.028
                        DUF2997  26 ataalEqaLGkvesre 41 
                                    +t+ l++a+G++ + e
  gi|119720183|ref|YP_920678.1| 108 YTELLKEAIGETRDME 123
                                    9**********98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       912  (0.0508673); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 953.93
//
Query:       gi|119720184|ref|YP_920679.1|  [L=327]
Description: hypothetical protein Tpen_1278 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.062   13.2   0.0      0.099   12.5   0.0    1.3  1  PLDc_2    PLD-like domain


Domain annotation for each model (and alignments):
>> PLDc_2  PLD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.5e-06     0.099      70     120 ..     266     312 ..     240     321 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.5e-06
                         PLDc_2  70 vevrvfetllgslHaKlylidgktvivGSsNltkrgldlnlElnvviedke 120
                                    ++v++   +++ lHa +y  +g+ v++ S+Nlt  +l +  E++vv+++++
  gi|119720184|ref|YP_920679.1| 266 LDVEF---TEKPLHANIYASEGE-VLLSSANLTGDSLYRSVEFGVVVKSSP 312
                                    44443...23679*****99886.6789*******************9974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 2044.55
//
Query:       gi|119720185|ref|YP_920680.1|  [L=252]
Description: queuine tRNA-ribosyltransferase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-14   53.4   3.2    8.3e-14   51.7   2.9    2.0  1  DUF5591   Domain of unknown function (DUF5591)


Domain annotation for each model (and alignments):
>> DUF5591  Domain of unknown function (DUF5591)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.7   2.9   4.6e-18   8.3e-14       2      73 ..      46     124 ..      45     207 .. 0.70

  Alignments for each domain:
  == domain 1  score: 51.7 bits;  conditional E-value: 4.6e-18
                                    -HHHHHHHHH---S..SSEEEEEE--SSSSGGGSHHHHHHHHHS---......SEEEEE-SS-.EEEGG....GTT--- CS
                        DUF5591   2 krfrervlerYeppeekkvlvLlPcsakkPyseskshrkfaeaikkrka...kvheviltsPlGvvPre....leevYP 73 
                                    + + + + e Y+pp ekkvl+  Pcs  kPy+es+s++++ +++++  +    +h+v ++ P+G vP e    +ee Y 
  gi|119720185|ref|YP_920680.1|  46 VGWLKFIAESYTPPPEKKVLLFYPCSTVKPYHESRSYKALYKTLESLGEkrrLIHVVAVSEPFGAVPEEyfyeWEEWYD 124
                                    56888899*******************************99966655422339**************962222566653 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 1891.43
//
Query:       gi|119720186|ref|YP_920681.1|  [L=162]
Description: hypothetical protein Tpen_1280 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.079   12.3   1.5      0.082   12.3   0.8    1.3  1  ThrE      Putative threonine/serine exporter


Domain annotation for each model (and alignments):
>> ThrE  Putative threonine/serine exporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.8   4.6e-06     0.082     130     178 ..      51      99 ..      35     114 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.6e-06
                           ThrE 130 widflvaflagllggllrlllakrglnsfvleavaaflasllallavsl 178
                                    + ++lv++l++ll+++lr++  k gl++ +++a  a+  ++ a++a++ 
  gi|119720186|ref|YP_920681.1|  51 LREVLVILLLALLAYALRRVAGKLGLPPSASNAPVAAASAVRAAAALHN 99 
                                    6899*****************************9999999999888873 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1051.07
//
Query:       gi|119720187|ref|YP_920682.1|  [L=31]
Description: hypothetical protein Tpen_1281 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (31 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       270  (0.0150594); expected 358.6 (0.02)
Passed bias filter:                      165  (0.00920297); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.24s 00:00:00.56 Elapsed: 00:00:00.40
# Mc/sec: 230.44
//
Query:       gi|119720188|ref|YP_920683.1|  [L=109]
Description: hypothetical protein Tpen_1282 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       267  (0.0148921); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 794.87
//
Query:       gi|119720189|ref|YP_920684.1|  [L=115]
Description: hypothetical protein Tpen_1283 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       246  (0.0137208); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 823.01
//
Query:       gi|119720190|ref|YP_920685.1|  [L=870]
Description: ankyrin [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   1.8e-185  594.2  27.8    3.9e-10   39.7   0.0   24.6 25  Ank             Ankyrin repeat
   3.8e-181  585.4  23.3    8.8e-15   54.9   0.0   22.5 23  Ank_4           Ankyrin repeats (many copies)
   1.5e-175  570.3  23.5    5.1e-20   71.9   0.1   13.9 15  Ank_2           Ankyrin repeats (3 copies)
   2.9e-165  534.1  43.0    4.8e-17   61.8   0.3   18.1 18  Ank_5           Ankyrin repeats (many copies)
   2.7e-153  479.0  27.2    2.1e-08   33.8   0.0   25.5 25  Ank_3           Ankyrin repeat
    0.00046   20.1   0.0         52    3.8   0.0    7.4 10  GATase_7        Glutamine amidotransferase domain
  ------ inclusion threshold ------
       0.02   15.2   0.6         73    3.7   0.0    5.9  8  HTH_18          Helix-turn-helix domain
      0.079   12.7   2.5    2.2e+02    1.7   0.0    6.6  7  MOZART1         Mitotic-spindle organizing gamma-tubulin ring
        0.1   12.3   0.0         90    2.6   0.0    4.7  7  Shigella_OspC   Shigella flexneri OspC protein
       0.35   10.1   2.2        5.4    6.2   0.2    3.4  4  Amidohydro_1    Amidohydrolase family
        4.5    7.7  14.8    2.4e+02    2.2   0.1    8.0  9  Arm-DNA-bind_3  Arm DNA-binding domain


Domain annotation for each model (and alignments):
>> Ank  Ankyrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.033        53       9      29 ..      18      39 ..      15      41 .. 0.81
   2 !   21.5   0.1   1.4e-07   0.00023       5      32 .]      47      75 ..      44      75 .. 0.92
   3 !   27.3   0.0     2e-09   3.2e-06       2      31 ..      89     119 ..      88     120 .. 0.94
   4 !   32.7   0.3   3.8e-11   6.2e-08       2      31 ..     122     152 ..     121     153 .. 0.93
   5 !   30.9   0.0   1.4e-10   2.3e-07       2      31 ..     155     185 ..     154     186 .. 0.95
   6 !   29.0   0.0   5.8e-10   9.5e-07       1      32 []     187     217 ..     187     217 .. 0.92
   7 !   34.6   0.0     1e-11   1.6e-08       2      31 ..     219     249 ..     218     250 .. 0.95
   8 !   30.2   0.0   2.4e-10   3.9e-07       2      31 ..     252     280 ..     251     281 .. 0.94
   9 !   35.8   0.0   4.2e-12   6.8e-09       2      32 .]     283     314 ..     282     314 .. 0.97
  10 !   13.6   0.1   4.3e-05      0.07       1      28 [.     315     353 ..     315     356 .. 0.83
  11 !   10.1   0.0   0.00054      0.88       3      31 ..     360     389 ..     358     390 .. 0.80
  12 !   39.7   0.0   2.4e-13   3.9e-10       1      32 []     391     423 ..     391     423 .. 0.96
  13 !   31.5   0.0   9.4e-11   1.5e-07       2      29 ..     425     453 ..     424     455 .. 0.96
  14 ?    5.4   0.0     0.017        27       2      27 ..     458     499 ..     457     501 .. 0.68
  15 !   13.6   0.0   4.4e-05     0.072       6      32 .]     503     530 ..     503     530 .. 0.95
  16 !   32.8   0.0   3.6e-11   5.9e-08       1      32 []     531     563 ..     531     563 .. 0.96
  17 !   25.6   0.0   6.8e-09   1.1e-05       2      29 ..     565     593 ..     564     596 .. 0.95
  18 !   12.4   0.0   0.00011      0.17       5      31 ..     595     622 ..     594     623 .. 0.81
  19 !   16.5   0.0   5.3e-06    0.0087       3      31 ..     626     655 ..     625     656 .. 0.88
  20 !   27.4   0.0   1.9e-09   3.1e-06       1      32 []     657     689 ..     657     689 .. 0.96
  21 !   29.6   0.4   3.7e-10     6e-07       4      31 ..     693     721 ..     691     722 .. 0.94
  22 !   28.8   0.2     7e-10   1.1e-06       1      31 [.     723     764 ..     723     765 .. 0.80
  23 !   29.0   0.0     6e-10   9.8e-07       3      31 ..     768     800 ..     767     801 .. 0.89
  24 !   22.7   0.0   5.8e-08   9.4e-05       2      31 ..     803     837 ..     802     838 .. 0.83
  25 ?   -2.0   0.0       3.6   5.9e+03       2      13 ..     840     851 ..     839     859 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.033
                                   HHHHTTHHHHHHHH.TTTSTTC CS
                            Ank  9 AatngkkriiklLL.hGAnlna 29
                                   A++ g++  +k+LL  G ++na
  gi|119720190|ref|YP_920685.1| 18 AVCSGDAKRVKALLeGGVDPNA 39
                                   67678899******557****8 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 1.4e-07
                                   HHHHHHHHTTHHHHHHHH.TTTSTTCBTT CS
                            Ank  5 PLHlAatngkkriiklLL.hGAnlnaldn 32
                                   PLH+Aa +g+++ ++lLL +GA++n +d+
  gi|119720190|ref|YP_920685.1| 47 PLHCAAIFGHAEAARLLLeRGADPNVKDK 75
                                   ******9***********99******995 PP

  == domain 3  score: 27.3 bits;  conditional E-value: 2e-09
                                    SBBHHHHHHHHTTHHHHHHHH.TTTSTTCBT CS
                            Ank   2 GnTPLHlAatngkkriiklLL.hGAnlnald 31 
                                    G+TPLH+Aa +g+  +++ LL +GA++na+d
  gi|119720190|ref|YP_920685.1|  89 GRTPLHWAAVYGHFVVAEVLLdRGADPNATD 119
                                    9********99**********779*****99 PP

  == domain 4  score: 32.7 bits;  conditional E-value: 3.8e-11
                                    SBBHHHHHHHHTTHHHHHHHH.TTTSTTCBT CS
                            Ank   2 GnTPLHlAatngkkriiklLL.hGAnlnald 31 
                                    GnTPLHlAa  g ++i++lLL +GA++na++
  gi|119720190|ref|YP_920685.1| 122 GNTPLHLAALLGFADIARLLLdRGADVNAKN 152
                                    9********999999******779*****99 PP

  == domain 5  score: 30.9 bits;  conditional E-value: 1.4e-10
                                    SBBHHHHHHHHTTHHHHHHHH.TTTSTTCBT CS
                            Ank   2 GnTPLHlAatngkkriiklLL.hGAnlnald 31 
                                    G TPLH+Aa  g+++++klLL +GA++ a+d
  gi|119720190|ref|YP_920685.1| 155 GKTPLHYAAEQGSAEVAKLLLeRGADPGATD 185
                                    99*******************99****9998 PP

  == domain 6  score: 29.0 bits;  conditional E-value: 5.8e-10
                                    TSBBHHHHHH.HHTTHHHHHHHH.TTTSTTCBTT CS
                            Ank   1 dGnTPLHlAa.tngkkriiklLL.hGAnlnaldn 32 
                                    +GnTPLHlA+ ++    + klLL +GA++na++n
  gi|119720190|ref|YP_920685.1| 187 YGNTPLHLAVrSIE---VSKLLLeRGADVNARNN 217
                                    7********97777...99****99*******98 PP

  == domain 7  score: 34.6 bits;  conditional E-value: 1e-11
                                    SBBHHHHHHHHTTHHHHHHHH.TTTSTTCBT CS
                            Ank   2 GnTPLHlAatngkkriiklLL.hGAnlnald 31 
                                    G+TPLH+Aa++g+++++k+LL +GA++ a+d
  gi|119720190|ref|YP_920685.1| 219 GRTPLHRAAMEGSAEVVKFLLeRGADPCAVD 249
                                    9********************99******99 PP

  == domain 8  score: 30.2 bits;  conditional E-value: 2.4e-10
                                    SBBHHHHHHHHTTHHHHHHHH.TTTSTTCBT CS
                            Ank   2 GnTPLHlAatngkkriiklLL.hGAnlnald 31 
                                    GnTPLHl a +++ +++klLL +GA++na++
  gi|119720190|ref|YP_920685.1| 252 GNTPLHL-A-FKNMEVAKLLLeKGADPNAKN 280
                                    9******.9.8999*******99******99 PP

  == domain 9  score: 35.8 bits;  conditional E-value: 4.2e-12
                                    SBBHHHHHHHHTTHHHHHHHH.TTTSTTCBTT CS
                            Ank   2 GnTPLHlAatngkkriiklLL.hGAnlnaldn 32 
                                    G+TPLH Aa  gk+++++lLL hGA+++a+dn
  gi|119720190|ref|YP_920685.1| 283 GMTPLHFAAGLGKVEVVELLLeHGADVDAKDN 314
                                    9********99********************8 PP

  == domain 10  score: 13.6 bits;  conditional E-value: 4.3e-05
                                    TSBBHHHHHHHHTT..........HHHHHHHH.TTTSTT CS
                            Ank   1 dGnTPLHlAatngk..........kriiklLL.hGAnln 28 
                                    dG TPL +Aa++ +          + ++ lLL +GA++ 
  gi|119720190|ref|YP_920685.1| 315 DGLTPLAYAAHRQDmyiradaltaLKVVGLLLeRGADPS 353
                                    8********96666677777788888******99***96 PP

  == domain 11  score: 10.1 bits;  conditional E-value: 0.00054
                                    BBHHHHHH...HHTTHHHHHHHH.TTTSTTCBT CS
                            Ank   3 nTPLHlAa...tngkkriiklLL.hGAnlnald 31 
                                    +T LH Aa   + +   +++lLL +G + na+d
  gi|119720190|ref|YP_920685.1| 360 YTLLHKAAfwcYAK---VVRLLLeKGLDANAKD 389
                                    9****999665555...******9997777776 PP

  == domain 12  score: 39.7 bits;  conditional E-value: 2.4e-13
                                    TSBBHHHHHHHHTTHHHHHHHH.TTTSTTCBTT CS
                            Ank   1 dGnTPLHlAatngkkriiklLL.hGAnlnaldn 32 
                                    +G+TPLH+Aa +g +++++lLL hGA++na+++
  gi|119720190|ref|YP_920685.1| 391 YGRTPLHWAAERGCPEVVELLLeHGADPNARND 423
                                    69*****************************95 PP

  == domain 13  score: 31.5 bits;  conditional E-value: 9.4e-11
                                    SBBHHHHHHHHTTHHHHHHHH.TTTSTTC CS
                            Ank   2 GnTPLHlAatngkkriiklLL.hGAnlna 29 
                                    G+TPLHlAat ++++ +klLL hGA++na
  gi|119720190|ref|YP_920685.1| 425 GMTPLHLAATVKDTEAAKLLLeHGADPNA 453
                                    9***************************9 PP

  == domain 14  score: 5.4 bits;  conditional E-value: 0.017
                                    SBBHHHHHH.............HHTT..HHHHHHHH.TTTST CS
                            Ank   2 GnTPLHlAa.............tngk..kriiklLL.hGAnl 27 
                                    G TPL + +             t+ +  ++ i+lLL hGA++
  gi|119720190|ref|YP_920685.1| 458 GSTPLAIISsffcyddnitdwlTGEHkaLEFIRLLLeHGAEP 499
                                    667777644677555555555544447899**********97 PP

  == domain 15  score: 13.6 bits;  conditional E-value: 4.4e-05
                                    HHHHHHHTTHHHHHHHH.TTTSTTCBTT CS
                            Ank   6 LHlAatngkkriiklLL.hGAnlnaldn 32 
                                    LH A+++g ++++k LL  G n+n +dn
  gi|119720190|ref|YP_920685.1| 503 LHAAVRCGRPECVKKLLeWGVNPNTRDN 530
                                    9****************66*******97 PP

  == domain 16  score: 32.8 bits;  conditional E-value: 3.6e-11
                                    TSBBHHHHHHHHTTHHHHHHHH.TTTSTTCBTT CS
                            Ank   1 dGnTPLHlAatngkkriiklLL.hGAnlnaldn 32 
                                    dGnT LH Aa+ng++++i+ LL +GA++na+++
  gi|119720190|ref|YP_920685.1| 531 DGNTLLHAAAWNGDVEVIEILLeRGADINARNK 563
                                    9*********************99*******95 PP

  == domain 17  score: 25.6 bits;  conditional E-value: 6.8e-09
                                    SBBHHHHHHHHTTHHHHHHHH.TTTSTTC CS
                            Ank   2 GnTPLHlAatngkkriiklLL.hGAnlna 29 
                                    G TPLH+Aa +g+ + +klLL +GA++na
  gi|119720190|ref|YP_920685.1| 565 GETPLHVAAERGNFEAVKLLLeRGAEVNA 593
                                    99*******************99*****9 PP

  == domain 18  score: 12.4 bits;  conditional E-value: 0.00011
                                    HHHHHH...HHTTHHHHHHHH.TTTSTTCBT CS
                            Ank   5 PLHlAa...tngkkriiklLL.hGAnlnald 31 
                                    +L +Aa   + +   +  lLL +GA++na+d
  gi|119720190|ref|YP_920685.1| 595 ALCYAArscRWD---VFTLLLeRGADINARD 622
                                    677888444555...******99*******9 PP

  == domain 19  score: 16.5 bits;  conditional E-value: 5.3e-06
                                    BBHHHHHH...HHTTHHHHHHHH.TTTSTTCBT CS
                            Ank   3 nTPLHlAa...tngkkriiklLL.hGAnlnald 31 
                                    +TPLH Aa     g   i+++L+ +GA++na++
  gi|119720190|ref|YP_920685.1| 626 RTPLHGAAgcrDAG---IARFLIeRGADINART 655
                                    6****999777777...******99******98 PP

  == domain 20  score: 27.4 bits;  conditional E-value: 1.9e-09
                                    TSBBHHHHHHHHTTHHHHHHHH.TTTSTTCBTT CS
                            Ank   1 dGnTPLHlAatngkkriiklLL.hGAnlnaldn 32 
                                    dG TPLH A + g+++ ++lLL hGA+++a+++
  gi|119720190|ref|YP_920685.1| 657 DGETPLHKATSSGNVEAVRLLLeHGADVDARND 689
                                    8*******9999******************995 PP

  == domain 21  score: 29.6 bits;  conditional E-value: 3.7e-10
                                    BHHHHHHHHTTHHHHHHHH.TTTSTTCBT CS
                            Ank   4 TPLHlAatngkkriiklLL.hGAnlnald 31 
                                    TPLH Aa +g+++i++lLL hGA+ na++
  gi|119720190|ref|YP_920685.1| 693 TPLHHAAARGHLEIVRLLLkHGADSNARN 721
                                    9***99999******************98 PP

  == domain 22  score: 28.8 bits;  conditional E-value: 7e-10
                                    TSBBHHHHHH.....HHTT......HHHHHHHH.TTTSTTCBT CS
                            Ank   1 dGnTPLHlAa.....tngk......kriiklLL.hGAnlnald 31 
                                    +G TPLH+ a     +  k      +ri++lLL hGA++na+d
  gi|119720190|ref|YP_920685.1| 723 HGETPLHYVAehadmC-SKnawdncLRIAELLLiHGADVNARD 764
                                    69******77777742.22577779******999********9 PP

  == domain 23  score: 29.0 bits;  conditional E-value: 6e-10
                                    BBHHHHHH...HHTTHHHHHHHH.TTTSTTCBT CS
                            Ank   3 nTPLHlAa...tngkkriiklLL.hGAnlnald 31 
                                     TPLH+A+   ++ +++++++LL hGA++na+d
  gi|119720190|ref|YP_920685.1| 768 QTPLHIAVffgSREHLEVARWLLeHGADPNARD 800
                                    5*******7666666*****************9 PP

  == domain 24  score: 22.7 bits;  conditional E-value: 5.8e-08
                                    SBBHHHHHH.......HHTTHHHHHHHH.TTTSTTCBT CS
                            Ank   2 GnTPLHlAa.......tngkkriiklLL.hGAnlnald 31 
                                    GnTPLH+ +       +    + i+lLL hGA++ +++
  gi|119720190|ref|YP_920685.1| 803 GNTPLHYVIehsfwreR---REAIELLLeHGADPSIRN 837
                                    9******6677785554...55************9998 PP

  == domain 25  score: -2.0 bits;  conditional E-value: 3.6
                                    SBBHHHHHHHHT CS
                            Ank   2 GnTPLHlAatng 13 
                                    G +PL lA+  g
  gi|119720190|ref|YP_920685.1| 840 GLSPLQLAVIKG 851
                                    889****99444 PP

>> Ank_4  Ankyrin repeats (many copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.95   1.5e+03       5      29 ..      15      39 ..      12      43 .. 0.83
   2 !   21.3   0.0   1.8e-07   0.00029       2      33 ..      45      75 ..      44      81 .. 0.89
   3 !   42.3   0.0   4.7e-14   7.7e-11       1      54 [.      89     141 ..      89     141 .. 0.95
   4 !   35.3   0.0   7.2e-12   1.2e-08      15      55 .]     136     175 ..     135     175 .. 0.96
   5 !   24.5   0.0   1.8e-08   2.9e-05       8      44 ..     162     197 ..     162     198 .. 0.93
   6 !   39.3   0.0     4e-13   6.5e-10      18      55 .]     203     239 ..     198     239 .. 0.94
   7 !   25.0   0.0   1.3e-08   2.1e-05      10      44 ..     228     261 ..     227     262 .. 0.90
   8 !   43.0   0.0   2.9e-14   4.8e-11      11      55 .]     260     303 ..     258     303 .. 0.96
   9 !   26.1   0.0   5.7e-09   9.4e-06      12      46 ..     294     327 ..     291     336 .. 0.91
  10 !   16.0   0.0   8.4e-06     0.014      14      55 .]     339     379 ..     330     379 .. 0.94
  11 !   36.4   0.0   3.3e-12   5.4e-09       2      46 ..     360     403 ..     359     403 .. 0.97
  12 !   54.9   0.0   5.4e-18   8.8e-15       2      55 .]     393     445 ..     393     445 .. 0.98
  13 !    9.6   0.0   0.00083       1.4      14      39 ..     438     462 ..     436     464 .. 0.83
  14 !   12.9   0.0   8.1e-05      0.13      12      55 .]     484     519 ..     481     519 .. 0.85
  15 !   37.0   0.1   2.2e-12   3.5e-09       5      55 .]     503     552 ..     500     552 .. 0.96
  16 !   43.9   0.0   1.5e-14   2.4e-11      14      55 .]     545     585 ..     544     585 .. 0.97
  17 !   20.4   0.1   3.6e-07   0.00058       3      43 ..     594     633 ..     592     638 .. 0.92
  18 !   38.3   0.0   8.5e-13   1.4e-09      17      55 .]     641     678 ..     632     678 .. 0.96
  19 !   51.0   0.1   8.8e-17   1.4e-13      11      55 .]     668     711 ..     665     711 .. 0.97
  20 !   40.7   0.2   1.5e-13   2.4e-10       3      45 ..     693     734 ..     693     737 .. 0.95
  21 !   29.6   0.1   4.4e-10   7.2e-07      11      47 ..     744     779 ..     734     781 .. 0.89
  22 !   33.1   0.0   3.5e-11   5.8e-08      12      46 ..     781     814 ..     779     819 .. 0.91
  23 !   24.0   0.0   2.5e-08   4.1e-05      15      54 ..     821     859 ..     817     859 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.95
                          Ank_4  5 LhyaaisgrlelvrlLlekgadina 29
                                   L++a+ sg+ + v+ Lle g+d+na
  gi|119720190|ref|YP_920685.1| 15 LFRAVCSGDAKRVKALLEGGVDPNA 39
                                   5666667888889*****9***997 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 1.8e-07
                          Ank_4  2 ltaLhyaaisgrlelvrlLlekgadinaqdnr 33
                                   l +Lh aai+g+ e++rlLle+gad+n   ++
  gi|119720190|ref|YP_920685.1| 45 LAPLHCAAIFGHAEAARLLLERGADPNVK-DK 75
                                   679************************97.54 PP

  == domain 3  score: 42.3 bits;  conditional E-value: 4.7e-14
                          Ank_4   1 eltaLhyaaisgrlelvrlLlekgadinaqdnrsGetalhiAakrgnveilklL 54 
                                    ++t+Lh+aa +g++ +++ Ll++gad+na+ +++G+t+lh Aa+ g+ +i++lL
  gi|119720190|ref|YP_920685.1|  89 GRTPLHWAAVYGHFVVAEVLLDRGADPNAT-DEEGNTPLHLAALLGFADIARLL 141
                                    589***************************.************99999999887 PP

  == domain 4  score: 35.3 bits;  conditional E-value: 7.2e-12
                          Ank_4  15 elvrlLlekgadinaqdnrsGetalhiAakrgnveilklLl 55 
                                    +++rlLl++gad+na  n+sG t+lh+Aa  g+ e++klLl
  gi|119720190|ref|YP_920685.1| 136 DIARLLLDRGADVNAK-NSSGKTPLHYAAEQGSAEVAKLLL 175
                                    579************9.***********************8 PP

  == domain 5  score: 24.5 bits;  conditional E-value: 1.8e-08
                          Ank_4   8 aaisgrlelvrlLlekgadinaqdnrsGetalhiAak 44 
                                    aa++g  e+++lLle+gad+ a+ + +G+t+lh A++
  gi|119720190|ref|YP_920685.1| 162 AAEQGSAEVAKLLLERGADPGAT-DTYGNTPLHLAVR 197
                                    6788999****************.***********96 PP

  == domain 6  score: 39.3 bits;  conditional E-value: 4e-13
                          Ank_4  18 rlLlekgadinaqdnrsGetalhiAakrgnveilklLl 55 
                                    +lLle+gad+na+ n++G+t+lh+Aa+ g+ e++k+Ll
  gi|119720190|ref|YP_920685.1| 203 KLLLERGADVNAR-NNEGRTPLHRAAMEGSAEVVKFLL 239
                                    89***********.***********************8 PP

  == domain 7  score: 25.0 bits;  conditional E-value: 1.3e-08
                          Ank_4  10 isgrlelvrlLlekgadinaqdnrsGetalhiAak 44 
                                    ++g  e+v++Lle+gad++a+ ++ G+t+lh A k
  gi|119720190|ref|YP_920685.1| 228 MEGSAEVVKFLLERGADPCAV-DAFGNTPLHLAFK 261
                                    567779***************.**********976 PP

  == domain 8  score: 43.0 bits;  conditional E-value: 2.9e-14
                          Ank_4  11 sgrlelvrlLlekgadinaqdnrsGetalhiAakrgnveilklLl 55 
                                    + ++e+++lLlekgad+na  n+sG+t+lh+Aa  g+ve+++lLl
  gi|119720190|ref|YP_920685.1| 260 FKNMEVAKLLLEKGADPNAK-NSSGMTPLHFAAGLGKVEVVELLL 303
                                    679****************9.***********************8 PP

  == domain 9  score: 26.1 bits;  conditional E-value: 5.7e-09
                          Ank_4  12 grlelvrlLlekgadinaqdnrsGetalhiAakrg 46 
                                    g++e+v+lLle+gad++a  +++G+t+l +Aa r 
  gi|119720190|ref|YP_920685.1| 294 GKVEVVELLLEHGADVDAK-DNDGLTPLAYAAHRQ 327
                                    789***************9.999********9886 PP

  == domain 10  score: 16.0 bits;  conditional E-value: 8.4e-06
                          Ank_4  14 lelvrlLlekgadinaqdnrsGetalhiAakrgnveilklLl 55 
                                    l++v lLle+gad+     ++  t+lh+Aa + + ++++lLl
  gi|119720190|ref|YP_920685.1| 339 LKVVGLLLERGADPSLI-GSDSYTLLHKAAFWCYAKVVRLLL 379
                                    78999***********8.999*******************98 PP

  == domain 11  score: 36.4 bits;  conditional E-value: 3.3e-12
                          Ank_4   2 ltaLhyaaisgrlelvrlLlekgadinaqdnrsGetalhiAakrg 46 
                                    +t+Lh+aa  +  ++vrlLlekg d na  +++G+t+lh Aa rg
  gi|119720190|ref|YP_920685.1| 360 YTLLHKAAFWCYAKVVRLLLEKGLDANAK-DEYGRTPLHWAAERG 403
                                    589*************************9.************997 PP

  == domain 12  score: 54.9 bits;  conditional E-value: 5.4e-18
                          Ank_4   2 ltaLhyaaisgrlelvrlLlekgadinaqdnrsGetalhiAakrgnveilklLl 55 
                                    +t+Lh+aa+ g+ e+v+lLle+gad+na+ n+sG+t+lh Aa   + e++klLl
  gi|119720190|ref|YP_920685.1| 393 RTPLHWAAERGCPEVVELLLEHGADPNAR-NDSGMTPLHLAATVKDTEAAKLLL 445
                                    69***************************.**********************98 PP

  == domain 13  score: 9.6 bits;  conditional E-value: 0.00083
                          Ank_4  14 lelvrlLlekgadinaqdnrsGetal 39 
                                    +e+++lLle+gad+na     G t+l
  gi|119720190|ref|YP_920685.1| 438 TEAAKLLLEHGADPNAE-EYGGSTPL 462
                                    799************94.66677776 PP

  == domain 14  score: 12.9 bits;  conditional E-value: 8.1e-05
                          Ank_4  12 grlelvrlLlekgadinaqdnrsGetalhiAakrgnveilklLl 55 
                                      le +rlLle+ga++           lh A++ g++e++k Ll
  gi|119720190|ref|YP_920685.1| 484 KALEFIRLLLEHGAEPGN--------GLHAAVRCGRPECVKKLL 519
                                    568899********9433........39*************997 PP

  == domain 15  score: 37.0 bits;  conditional E-value: 2.2e-12
                          Ank_4   5 LhyaaisgrlelvrlLlekgadinaqdnrsGetalhiAakrgnveilklLl 55 
                                    Lh+a+  gr e+v+ Lle g+++n + +++G+t+lh Aa++g+ve+++ Ll
  gi|119720190|ref|YP_920685.1| 503 LHAAVRCGRPECVKKLLEWGVNPNTR-DNDGNTLLHAAAWNGDVEVIEILL 552
                                    8999999*******************.999*****************9997 PP

  == domain 16  score: 43.9 bits;  conditional E-value: 1.5e-14
                          Ank_4  14 lelvrlLlekgadinaqdnrsGetalhiAakrgnveilklLl 55 
                                    +e++++Lle+gadina+ n+ Get+lh Aa rgn+e++klLl
  gi|119720190|ref|YP_920685.1| 545 VEVIEILLERGADINAR-NKFGETPLHVAAERGNFEAVKLLL 585
                                    799**************.***********************8 PP

  == domain 17  score: 20.4 bits;  conditional E-value: 3.6e-07
                          Ank_4   3 taLhyaaisgrlelvrlLlekgadinaqdnrsGetalhiAa 43 
                                    +aL yaa s+r ++  lLle+gadina+ +  ++t+lh Aa
  gi|119720190|ref|YP_920685.1| 594 DALCYAARSCRWDVFTLLLERGADINAR-DWFDRTPLHGAA 633
                                    689*************************.999******665 PP

  == domain 18  score: 38.3 bits;  conditional E-value: 8.5e-13
                          Ank_4  17 vrlLlekgadinaqdnrsGetalhiAakrgnveilklLl 55 
                                    +r+L+e+gadina+  ++Get+lh+A + gnve+++lLl
  gi|119720190|ref|YP_920685.1| 641 ARFLIERGADINAR-TKDGETPLHKATSSGNVEAVRLLL 678
                                    89************.***********************8 PP

  == domain 19  score: 51.0 bits;  conditional E-value: 8.8e-17
                          Ank_4  11 sgrlelvrlLlekgadinaqdnrsGetalhiAakrgnveilklLl 55 
                                    sg++e+vrlLle+gad++a+ n+ G t+lh+Aa rg++ei++lLl
  gi|119720190|ref|YP_920685.1| 668 SGNVEAVRLLLEHGADVDAR-NDFGGTPLHHAAARGHLEIVRLLL 711
                                    89******************.***********************8 PP

  == domain 20  score: 40.7 bits;  conditional E-value: 1.5e-13
                          Ank_4   3 taLhyaaisgrlelvrlLlekgadinaqdnrsGetalhiAakr 45 
                                    t+Lh+aa+ g+le+vrlLl +gad na+ n+ Get+lh++a +
  gi|119720190|ref|YP_920685.1| 693 TPLHHAAARGHLEIVRLLLKHGADSNAR-NSHGETPLHYVAEH 734
                                    79**************************.***********987 PP

  == domain 21  score: 29.6 bits;  conditional E-value: 4.4e-10
                          Ank_4  11 sgrlelvrlLlekgadinaqdnrsGetalhiAakrgn 47 
                                    +++l++++lLl +gad+na+ +++++t+lhiA+ +g+
  gi|119720190|ref|YP_920685.1| 744 DNCLRIAELLLIHGADVNAR-DSRDQTPLHIAVFFGS 779
                                    799*****************.999***********97 PP

  == domain 22  score: 33.1 bits;  conditional E-value: 3.5e-11
                          Ank_4  12 grlelvrlLlekgadinaqdnrsGetalhiAakrg 46 
                                    ++le++r+Lle+gad+na+ + +G+t+lh+++ ++
  gi|119720190|ref|YP_920685.1| 781 EHLEVARWLLEHGADPNAR-DWEGNTPLHYVIEHS 814
                                    79*****************.666********9886 PP

  == domain 23  score: 24.0 bits;  conditional E-value: 2.5e-08
                          Ank_4  15 elvrlLlekgadinaqdnrsGetalhiAakrgnveilklL 54 
                                    e+++lLle+gad+  + n++G+++l+ A+ +g+ +++ lL
  gi|119720190|ref|YP_920685.1| 821 EAIELLLEHGADPSIR-NSEGLSPLQLAVIKGDTDAFALL 859
                                    7899************.*****************998776 PP

>> Ank_2  Ankyrin repeats (3 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.3   0.0   6.3e-20     1e-16       1      83 []      15     119 ..      15     119 .. 0.84
   2 !   23.7   0.0   3.3e-08   5.4e-05      50      83 .]     119     152 ..     117     152 .. 0.93
   3 !   71.1   0.1   5.3e-23   8.6e-20       1      83 []     126     216 ..     126     216 .. 0.91
   4 !   52.9   0.0   2.6e-17   4.2e-14      25      83 .]     218     280 ..     215     280 .. 0.88
   5 !   35.7   0.0     6e-12   9.8e-09      25      80 ..     282     353 ..     278     355 .. 0.80
   6 !   28.5   0.0     1e-09   1.7e-06      25      83 .]     315     389 ..     312     389 .. 0.77
   7 !   56.1   0.0   2.6e-18   4.3e-15      11      83 .]     340     422 ..     329     422 .. 0.87
   8 !   71.9   0.1   3.1e-23   5.1e-20       1      81 [.     363     453 ..     363     455 .. 0.88
   9 !   24.4   0.0   2.1e-08   3.4e-05      24      57 ..     423     462 ..     418     485 .. 0.59
  10 !   53.5   0.0   1.6e-17   2.6e-14       8      83 .]     484     562 ..     478     562 .. 0.89
  11 !   44.5   0.0   1.1e-14   1.8e-11      24      83 .]     563     622 ..     560     622 .. 0.90
  12 !   58.2   0.0   5.8e-19   9.5e-16       1      83 []     596     688 ..     596     688 .. 0.86
  13 !   47.1   0.8   1.6e-15   2.6e-12      23      83 .]     687     764 ..     684     764 .. 0.82
  14 !   37.8   0.0   1.4e-12   2.2e-09      26      83 .]     724     800 ..     722     800 .. 0.80
  15 !   22.3   0.0   9.2e-08   0.00015      25      73 ..     802     860 ..     798     866 .. 0.82

  Alignments for each domain:
  == domain 1  score: 61.3 bits;  conditional E-value: 6.3e-20
                          Ank_2   1 LhlAakngnlelvklLl.egadpn.k..ngktaLhyAakngnleivklLleh..............ad....ndgrtpLh 58 
                                    L+ A+ +g+ + vk Ll  g+dpn     g+ +Lh+Aa+ g+ e+++lLle               +     ++grtpLh
  gi|119720190|ref|YP_920685.1|  15 LFRAVCSGDAKRVKALLeGGVDPNaAgpAGLAPLHCAAIFGHAEAARLLLERgadpnvkdkitwdvLSselgRKGRTPLH 94 
                                    67899999899******999****8357**********************955455555566644411456688****** PP

                          Ank_2  59 yAarsghleivklLlekgadinlkd 83 
                                    +Aa +gh+ ++++Ll++gad+n++d
  gi|119720190|ref|YP_920685.1|  95 WAAVYGHFVVAEVLLDRGADPNATD 119
                                    **********************997 PP

  == domain 2  score: 23.7 bits;  conditional E-value: 3.3e-08
                          Ank_2  50 dndgrtpLhyAarsghleivklLlekgadinlkd 83 
                                    d++g+tpLh+Aa  g  +i++lLl++gad+n+k+
  gi|119720190|ref|YP_920685.1| 119 DEEGNTPLHLAALLGFADIARLLLDRGADVNAKN 152
                                    578*********99*****************996 PP

  == domain 3  score: 71.1 bits;  conditional E-value: 5.3e-23
                          Ank_2   1 LhlAakngnlelvklLl.egadpn..k.ngktaLhyAakngnleivklLleh......adndgrtpLhyAarsghleivk 70 
                                    LhlAa+ g  ++ +lLl  gad+n  +  gkt+LhyAa++g+ e++klLle       +d +g+tpLh+A+r  ++e+ k
  gi|119720190|ref|YP_920685.1| 126 LHLAALLGFADIARLLLdRGADVNakNsSGKTPLHYAAEQGSAEVAKLLLERgadpgaTDTYGNTPLHLAVR--SIEVSK 203
                                    8*****99779*************8537**********************967667766799*********7..56**** PP

                          Ank_2  71 lLlekgadinlkd 83 
                                    lLle+gad+n+++
  gi|119720190|ref|YP_920685.1| 204 LLLERGADVNARN 216
                                    **********986 PP

  == domain 4  score: 52.9 bits;  conditional E-value: 2.6e-17
                          Ank_2  25 ngktaLhyAakngnleivklLleh......adndgrtpLhyAarsghleivklLlekgadinlkd 83 
                                    +g+t+Lh Aa++g+ e+vk+Lle       +d  g+tpLh+A  ++  e++klLlekgad+n+k+
  gi|119720190|ref|YP_920685.1| 218 EGRTPLHRAAMEGSAEVVKFLLERgadpcaVDAFGNTPLHLAF-KN-MEVAKLLLEKGADPNAKN 280
                                    79********************967567777799********7.34.5**************986 PP

  == domain 5  score: 35.7 bits;  conditional E-value: 6e-12
                          Ank_2  25 ngktaLhyAakngnleivklLleh...ad...ndgrtpLhyAarsg..........hleivklLlekgadin 80 
                                     g+t+Lh+Aa  g++e+v+lLleh   +d   ndg tpL yAa  +           l++v lLle+gad+ 
  gi|119720190|ref|YP_920685.1| 282 SGMTPLHFAAGLGKVEVVELLLEHgadVDakdNDGLTPLAYAAHRQdmyiradaltALKVVGLLLERGADPS 353
                                    69*********************997733556***********66456666666667888889999999975 PP

  == domain 6  score: 28.5 bits;  conditional E-value: 1e-09
                          Ank_2  25 ngktaLhyAakngnle..........ivklLleh.ad.....ndgrtpLhyAarsghleivklLlekgadinlkd 83 
                                    +g+t+L yAa++++            +v lLle  ad     +d +t Lh Aa++ + ++v+lLlekg d n+kd
  gi|119720190|ref|YP_920685.1| 315 DGLTPLAYAAHRQDMYiradaltalkVVGLLLERgADpsligSDSYTLLHKAAFWCYAKVVRLLLEKGLDANAKD 389
                                    79*********973333333333333477777768555566699****************************998 PP

  == domain 7  score: 56.1 bits;  conditional E-value: 2.6e-18
                          Ank_2  11 elvklLl.egadpn...kngktaLhyAakngnleivklLleh......adndgrtpLhyAarsghleivklLlekgadin 80 
                                    ++v lLl  gadp+   ++  t Lh Aa   + ++v+lLle+       d++grtpLh+Aa+ g +e+v+lLle+gad+n
  gi|119720190|ref|YP_920685.1| 340 KVVGLLLeRGADPSligSDSYTLLHKAAFWCYAKVVRLLLEKgldanaKDEYGRTPLHWAAERGCPEVVELLLEHGADPN 419
                                    589999999***99864499*********9999********88774444499**************************** PP

                          Ank_2  81 lkd 83 
                                    +++
  gi|119720190|ref|YP_920685.1| 420 ARN 422
                                    986 PP

  == domain 8  score: 71.9 bits;  conditional E-value: 3.1e-23
                          Ank_2   1 LhlAak.ngnlelvklLl.egadpn..k.ngktaLhyAakngnleivklLleh......adndgrtpLhyAarsghleiv 69 
                                    Lh Aa   +  ++v+lLl +g d+n  +  g+t+Lh+Aa++g+ e+v+lLleh       +++g+tpLh+Aa  + +e++
  gi|119720190|ref|YP_920685.1| 363 LHKAAFwCY-AKVVRLLLeKGLDANakDeYGRTPLHWAAERGCPEVVELLLEHgadpnaRNDSGMTPLHLAATVKDTEAA 441
                                    789999523.45*******9999998538***********************99776644499*********9999**** PP

                          Ank_2  70 klLlekgadinl 81 
                                    klLle+gad+n+
  gi|119720190|ref|YP_920685.1| 442 KLLLEHGADPNA 453
                                    **********97 PP

  == domain 9  score: 24.4 bits;  conditional E-value: 2.1e-08
                          Ank_2  24 kngktaLhyAakngnleivklLleh.ad.....ndgrtpL 57 
                                    + g+t+Lh+Aa   ++e++klLleh ad     + g tpL
  gi|119720190|ref|YP_920685.1| 423 DSGMTPLHLAATVKDTEAAKLLLEHgADpnaeeYGGSTPL 462
                                    2566777766666666777777776633323355566777 PP

  == domain 10  score: 53.5 bits;  conditional E-value: 1.6e-17
                          Ank_2   8 gnlelvklLl.egadpnkngktaLhyAakngnleivklLle...h...adndgrtpLhyAarsghleivklLlekgadin 80 
                                    ++le+++lLl +ga+p+    + Lh+A++ g  e+vk Lle   +    dndg+t Lh+Aa++g  e++++Lle+gadin
  gi|119720190|ref|YP_920685.1| 484 KALEFIRLLLeHGAEPG----NGLHAAVRCGRPECVKKLLEwgvNpntRDNDGNTLLHAAAWNGDVEVIEILLERGADIN 559
                                    56789*****999***9....88*****************9765355666****************************** PP

                          Ank_2  81 lkd 83 
                                    +++
  gi|119720190|ref|YP_920685.1| 560 ARN 562
                                    986 PP

  == domain 11  score: 44.5 bits;  conditional E-value: 1.1e-14
                          Ank_2  24 kngktaLhyAakngnleivklLleh.adndgrtpLhyAarsghleivklLlekgadinlkd 83 
                                    k+g+t+Lh+Aa++gn e+vklLle  a+  +  +L yAars + +++ lLle+gadin++d
  gi|119720190|ref|YP_920685.1| 563 KFGETPLHVAAERGNFEAVKLLLERgAEV-NADALCYAARSCRWDVFTLLLERGADINARD 622
                                    489********************987554.346*************************997 PP

  == domain 12  score: 58.2 bits;  conditional E-value: 5.8e-19
                          Ank_2   1 LhlAakngnlelvklLl.egadpn..k.ngktaLhyAakngnleivklLleh...ad...ndgrtpLhyAarsghleivk 70 
                                    L +Aa++   +++ lLl  gad+n  + +++t+Lh Aa   +  i+++L+e    ++   +dg+tpLh A +sg+ e+v+
  gi|119720190|ref|YP_920685.1| 596 LCYAARSCRWDVFTLLLeRGADINarDwFDRTPLHGAAGCRDAGIARFLIERgadINartKDGETPLHKATSSGNVEAVR 675
                                    567888753579************8659*********99998899*****977562255799****************** PP

                          Ank_2  71 lLlekgadinlkd 83 
                                    lLle+gad+++++
  gi|119720190|ref|YP_920685.1| 676 LLLEHGADVDARN 688
                                    *********9875 PP

  == domain 13  score: 47.1 bits;  conditional E-value: 1.6e-15
                          Ank_2  23 n.kngktaLhyAakngnleivklLleh......adndgrtpLhyAars......g....hleivklLlekgadinlkd 83 
                                    + ++g t+Lh+Aa +g+leiv+lLl+h       +++g+tpLhy a++      +     l+i++lLl +gad+n++d
  gi|119720190|ref|YP_920685.1| 687 RnDFGGTPLHHAAARGHLEIVRLLLKHgadsnaRNSHGETPLHYVAEHadmcskNawdnCLRIAELLLIHGADVNARD 764
                                    424899********************99675544488*********997666551555489*******99*****997 PP

  == domain 14  score: 37.8 bits;  conditional E-value: 1.4e-12
                          Ank_2  26 gktaLhyAakn..........gnleivklLleh......adndgrtpLhyAarsg...hleivklLlekgadinlkd 83 
                                    g+t+Lhy a++          ++l i++lLl h       d+  +tpLh+A+++g   hle++++Lle+gad+n++d
  gi|119720190|ref|YP_920685.1| 724 GETPLHYVAEHadmcsknawdNCLRIAELLLIHgadvnaRDSRDQTPLHIAVFFGsreHLEVARWLLEHGADPNARD 800
                                    89********85666665555566689****98867543337799*******9965669***************997 PP

  == domain 15  score: 22.3 bits;  conditional E-value: 9.2e-08
                          Ank_2  25 ngktaLhyAakn....gnleivklLleh......adndgrtpLhyAarsghleivklLl 73 
                                    +g+t+Lhy +++      +e+++lLleh       +++g +pL++A+ +g ++++ lL 
  gi|119720190|ref|YP_920685.1| 802 EGNTPLHYVIEHsfwrERREAIELLLEHgadpsiRNSEGLSPLQLAVIKGDTDAFALLS 860
                                    699********744435779*******99666655599************999998885 PP

>> Ank_5  Ankyrin repeats (many copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.0   1.4e-10   2.3e-07       1      47 [.      30      75 ..      30      81 .. 0.94
   2 !   42.8   0.1   2.8e-14   4.5e-11      14      56 .]      87     129 ..      84     129 .. 0.96
   3 !   61.8   0.3     3e-20   4.8e-17       1      56 []     108     162 ..     108     162 .. 0.99
   4 !   56.6   0.1   1.3e-18   2.1e-15       1      56 []     141     195 ..     141     195 .. 0.99
   5 !   48.7   0.1   3.9e-16   6.4e-13       1      56 []     205     259 ..     205     259 .. 0.99
   6 !   54.9   0.1   4.2e-18   6.8e-15       1      56 []     269     323 ..     269     323 .. 0.99
   7 !   22.8   0.0     5e-08   8.1e-05       1      52 [.     345     395 ..     345     395 .. 0.96
   8 !   47.3   0.1     1e-15   1.7e-12       1      49 [.     378     425 ..     378     425 .. 0.98
   9 !   42.3   0.1   3.9e-14   6.3e-11       1      55 [.     411     464 ..     411     465 .. 0.96
  10 !   25.6   0.1   6.8e-09   1.1e-05       1      51 [.     492     534 ..     492     535 .. 0.87
  11 !   48.2   0.3   5.4e-16   8.9e-13       2      53 ..     519     569 ..     518     569 .. 0.95
  12 !   32.7   0.1   3.9e-11   6.3e-08       7      44 ..     556     593 ..     555     598 .. 0.95
  13 !    6.9   0.0    0.0051       8.3      19      46 ..     595     622 ..     592     623 .. 0.93
  14 !   41.9   0.0   5.3e-14   8.7e-11       1      56 []     611     665 ..     611     665 .. 0.96
  15 !   55.1   0.3   3.8e-18   6.2e-15       1      55 [.     677     730 ..     677     731 .. 0.98
  16 !   22.7   0.1   5.5e-08   8.9e-05      24      56 .]     742     774 ..     742     774 .. 0.98
  17 !   21.6   0.0   1.2e-07   0.00019      28      55 ..     782     809 ..     779     810 .. 0.94
  18 !   35.6   0.0   4.9e-12     8e-09       1      56 []     789     847 ..     789     847 .. 0.84

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 1.4e-10
                          Ank_5  1 LlehgpadvnrldgggntpLhvAakygaadvvrlLlargadlnltds 47
                                   Lle g +d+n+  + g  pLh Aa  g+a+ +rlLl+rgad+n++d+
  gi|119720190|ref|YP_920685.1| 30 LLEGG-VDPNAAGPAGLAPLHCAAIFGHAEAARLLLERGADPNVKDK 75
                                   78888.***************************************97 PP

  == domain 2  score: 42.8 bits;  conditional E-value: 2.8e-14
                          Ank_5  14 gggntpLhvAakygaadvvrlLlargadlnltdsrGltaldlA 56 
                                    ++g tpLh+Aa yg++ v+++Ll+rgad+n+td++G+t+l+lA
  gi|119720190|ref|YP_920685.1|  87 RKGRTPLHWAAVYGHFVVAEVLLDRGADPNATDEEGNTPLHLA 129
                                    6788*************************************98 PP

  == domain 3  score: 61.8 bits;  conditional E-value: 3e-20
                          Ank_5   1 LlehgpadvnrldgggntpLhvAakygaadvvrlLlargadlnltdsrGltaldlA 56 
                                    Ll++g ad+n++d++gntpLh+Aa  g ad++rlLl+rgad n+++s+G+t+l++A
  gi|119720190|ref|YP_920685.1| 108 LLDRG-ADPNATDEEGNTPLHLAALLGFADIARLLLDRGADVNAKNSSGKTPLHYA 162
                                    89***.*************************************************9 PP

  == domain 4  score: 56.6 bits;  conditional E-value: 1.3e-18
                          Ank_5   1 LlehgpadvnrldgggntpLhvAakygaadvvrlLlargadlnltdsrGltaldlA 56 
                                    Ll++g advn+++  g tpLh+Aa++g+a+v++lLl+rgad+++td +G+t+l+lA
  gi|119720190|ref|YP_920685.1| 141 LLDRG-ADVNAKNSSGKTPLHYAAEQGSAEVAKLLLERGADPGATDTYGNTPLHLA 195
                                    89***.************************************************98 PP

  == domain 5  score: 48.7 bits;  conditional E-value: 3.9e-16
                          Ank_5   1 LlehgpadvnrldgggntpLhvAakygaadvvrlLlargadlnltdsrGltaldlA 56 
                                    Lle+g advn+++++g tpLh Aa  g+a+vv++Ll+rgad+ + d+ G+t+l+lA
  gi|119720190|ref|YP_920685.1| 205 LLERG-ADVNARNNEGRTPLHRAAMEGSAEVVKFLLERGADPCAVDAFGNTPLHLA 259
                                    89***.************************************************98 PP

  == domain 6  score: 54.9 bits;  conditional E-value: 4.2e-18
                          Ank_5   1 LlehgpadvnrldgggntpLhvAakygaadvvrlLlargadlnltdsrGltaldlA 56 
                                    Lle+g ad+n+++  g+tpLh+Aa  g  +vv+lLl++gad +++d++Glt+l +A
  gi|119720190|ref|YP_920685.1| 269 LLEKG-ADPNAKNSSGMTPLHFAAGLGKVEVVELLLEHGADVDAKDNDGLTPLAYA 323
                                    899*9.***********************************************998 PP

  == domain 7  score: 22.8 bits;  conditional E-value: 5e-08
                          Ank_5   1 LlehgpadvnrldgggntpLhvAakygaadvvrlLlargadlnltdsrGlta 52 
                                    Lle+g ad+     +++t Lh Aa   +a vvrlLl+ g+d+n++d++G+t+
  gi|119720190|ref|YP_920685.1| 345 LLERG-ADPSLIGSDSYTLLHKAAFWCYAKVVRLLLEKGLDANAKDEYGRTP 395
                                    899*9.99999999999********99************************8 PP

  == domain 8  score: 47.3 bits;  conditional E-value: 1e-15
                          Ank_5   1 LlehgpadvnrldgggntpLhvAakygaadvvrlLlargadlnltdsrG 49 
                                    Lle+g  d n++d++g tpLh+Aa++g+++vv+lLl++gad+n+++++G
  gi|119720190|ref|YP_920685.1| 378 LLEKG-LDANAKDEYGRTPLHWAAERGCPEVVELLLEHGADPNARNDSG 425
                                    89999.****************************************987 PP

  == domain 9  score: 42.3 bits;  conditional E-value: 3.9e-14
                          Ank_5   1 LlehgpadvnrldgggntpLhvAakygaadvvrlLlargadlnltdsrGltaldl 55 
                                    Llehg ad+n+++  g+tpLh+Aa     + ++lLl++gad+n+ +  G+t+l +
  gi|119720190|ref|YP_920685.1| 411 LLEHG-ADPNARNDSGMTPLHLAATVKDTEAAKLLLEHGADPNAEEYGGSTPLAI 464
                                    8****.****************************************999***965 PP

  == domain 10  score: 25.6 bits;  conditional E-value: 6.8e-09
                          Ank_5   1 LlehgpadvnrldgggntpLhvAakygaadvvrlLlargadlnltdsrGlt 51 
                                    Llehg     ++ g   + Lh A+++g++++v++Ll+ g+++n++d++G+t
  gi|119720190|ref|YP_920685.1| 492 LLEHG-----AEPG---NGLHAAVRCGRPECVKKLLEWGVNPNTRDNDGNT 534
                                    56666.....4333...99******************************99 PP

  == domain 11  score: 48.2 bits;  conditional E-value: 5.4e-16
                          Ank_5   2 lehgpadvnrldgggntpLhvAakygaadvvrlLlargadlnltdsrGltal 53 
                                    le g +++n++d++gnt Lh Aa++g  +v+++Ll+rgad+n++++ G+t+l
  gi|119720190|ref|YP_920685.1| 519 LEWG-VNPNTRDNDGNTLLHAAAWNGDVEVIEILLERGADINARNKFGETPL 569
                                    5556.9*********************************************8 PP

  == domain 12  score: 32.7 bits;  conditional E-value: 3.9e-11
                          Ank_5   7 advnrldgggntpLhvAakygaadvvrlLlargadlnl 44 
                                    ad+n+++++g+tpLhvAa++g+++ v+lLl+rga  n+
  gi|119720190|ref|YP_920685.1| 556 ADINARNKFGETPLHVAAERGNFEAVKLLLERGAEVNA 593
                                    89*******************************99986 PP

  == domain 13  score: 6.9 bits;  conditional E-value: 0.0051
                          Ank_5  19 pLhvAakygaadvvrlLlargadlnltd 46 
                                    +L++Aa+  ++dv+ lLl+rgad+n++d
  gi|119720190|ref|YP_920685.1| 595 ALCYAARSCRWDVFTLLLERGADINARD 622
                                    799999999*****************98 PP

  == domain 14  score: 41.9 bits;  conditional E-value: 5.3e-14
                          Ank_5   1 LlehgpadvnrldgggntpLhvAakygaadvvrlLlargadlnltdsrGltaldlA 56 
                                    Lle+g ad+n++d +  tpLh Aa ++ a ++r+L++rgad+n+++++G+t+l+ A
  gi|119720190|ref|YP_920685.1| 611 LLERG-ADINARDWFDRTPLHGAAGCRDAGIARFLIERGADINARTKDGETPLHKA 665
                                    89***.99999999999************************************976 PP

  == domain 15  score: 55.1 bits;  conditional E-value: 3.8e-18
                          Ank_5   1 LlehgpadvnrldgggntpLhvAakygaadvvrlLlargadlnltdsrGltaldl 55 
                                    Llehg adv++++ +g tpLh+Aa +g++++vrlLl++gad n+++s+G+t+l++
  gi|119720190|ref|YP_920685.1| 677 LLEHG-ADVDARNDFGGTPLHHAAARGHLEIVRLLLKHGADSNARNSHGETPLHY 730
                                    8****.***********************************************98 PP

  == domain 16  score: 22.7 bits;  conditional E-value: 5.5e-08
                          Ank_5  24 akygaadvvrlLlargadlnltdsrGltaldlA 56 
                                    a+ +++++++lLl +gad n++dsr +t+l++A
  gi|119720190|ref|YP_920685.1| 742 AWDNCLRIAELLLIHGADVNARDSRDQTPLHIA 774
                                    799*****************************9 PP

  == domain 17  score: 21.6 bits;  conditional E-value: 1.2e-07
                          Ank_5  28 aadvvrlLlargadlnltdsrGltaldl 55 
                                    +++v+r+Ll++gad+n++d +G+t+l++
  gi|119720190|ref|YP_920685.1| 782 HLEVARWLLEHGADPNARDWEGNTPLHY 809
                                    89************************98 PP

  == domain 18  score: 35.6 bits;  conditional E-value: 4.9e-12
                          Ank_5   1 LlehgpadvnrldgggntpLhvAakygaa....dvvrlLlargadlnltdsrGltaldlA 56 
                                    Llehg ad+n++d +gntpLh+ +++  +    + ++lLl++gad+ +++s+Gl++l+lA
  gi|119720190|ref|YP_920685.1| 789 LLEHG-ADPNARDWEGNTPLHYVIEHSFWrerrEAIELLLEHGADPSIRNSEGLSPLQLA 847
                                    8****.****************997765511115555555******************99 PP

>> Ank_3  Ankyrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0   0.00054      0.89       6      31 .]      15      39 ..      15      39 .. 0.94
   2 !   20.2   0.1   3.4e-07   0.00055       2      31 .]      44      72 ..      43      72 .. 0.93
   3 !   27.2   0.0   1.8e-09   2.9e-06       2      31 .]      89     117 ..      88     117 .. 0.96
   4 !   26.8   0.1   2.4e-09     4e-06       1      31 []     121     150 ..     121     150 .. 0.96
   5 !   23.8   0.0   2.3e-08   3.8e-05       2      29 ..     155     181 ..     154     183 .. 0.94
   6 !   18.7   0.0     1e-06    0.0017       1      31 []     187     214 ..     187     214 .. 0.94
   7 !   27.2   0.0   1.7e-09   2.8e-06       1      29 [.     218     245 ..     218     247 .. 0.95
   8 !   12.6   0.0    0.0001      0.17       2      31 .]     252     278 ..     251     278 .. 0.90
   9 !   26.7   0.0   2.5e-09   4.1e-06       2      31 .]     283     311 ..     282     311 .. 0.95
  10 ?    5.0   0.0     0.029        47       1      30 [.     315     353 ..     315     354 .. 0.81
  11 !   11.5   0.0   0.00023      0.37       3      31 .]     360     387 ..     358     387 .. 0.94
  12 !   33.8   0.0   1.3e-11   2.1e-08       1      31 []     391     420 ..     391     420 .. 0.97
  13 !   22.6   0.0   5.6e-08   9.1e-05       2      31 .]     425     453 ..     424     453 .. 0.96
  14 ?    0.5   0.0      0.83   1.4e+03      16      29 ..     487     499 ..     482     500 .. 0.79
  15 !   14.8   0.0   1.8e-05      0.03       6      30 ..     503     526 ..     501     527 .. 0.96
  16 !   21.2   0.1   1.5e-07   0.00025       1      31 []     531     560 ..     531     560 .. 0.97
  17 !   28.4   0.0   7.3e-10   1.2e-06       2      31 .]     565     593 ..     564     593 .. 0.96
  18 !   10.4   0.1    0.0005      0.81       8      31 .]     598     620 ..     595     620 .. 0.92
  19 !   14.4   0.0   2.6e-05     0.043       3      31 .]     626     653 ..     624     653 .. 0.94
  20 !   27.4   0.0   1.6e-09   2.5e-06       1      31 []     657     686 ..     657     686 .. 0.96
  21 !   26.2   0.1   3.8e-09   6.2e-06       2      31 .]     691     719 ..     690     719 .. 0.93
  22 !   14.4   0.1   2.6e-05     0.043       1      31 []     723     762 ..     723     762 .. 0.77
  23 !   23.0   0.0   4.2e-08   6.8e-05       3      31 .]     768     798 ..     766     798 .. 0.89
  24 !   17.4   0.0   2.8e-06    0.0046       1      30 [.     802     834 ..     802     835 .. 0.88
  25 ?    3.9   0.0     0.067   1.1e+02       1      22 [.     839     859 ..     839     862 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00054
                          Ank_3  6 LhlAarsgnleivkfLlenkgadvna 31
                                   L++A+ sg+ ++vk+Lle  g+d+na
  gi|119720190|ref|YP_920685.1| 15 LFRAVCSGDAKRVKALLE-GGVDPNA 39
                                   7899**************.9****96 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 3.4e-07
                          Ank_3  2 GetpLhlAarsgnleivkfLlenkgadvna 31
                                   G  pLh+Aa +g+ e +++Lle +gad+n+
  gi|119720190|ref|YP_920685.1| 44 GLAPLHCAAIFGHAEAARLLLE-RGADPNV 72
                                   667*******************.*****95 PP

  == domain 3  score: 27.2 bits;  conditional E-value: 1.8e-09
                          Ank_3   2 GetpLhlAarsgnleivkfLlenkgadvna 31 
                                    G+tpLh+Aa +g++ +++ Ll+ +gad+na
  gi|119720190|ref|YP_920685.1|  89 GRTPLHWAAVYGHFVVAEVLLD-RGADPNA 117
                                    9*********************.*****96 PP

  == domain 4  score: 26.8 bits;  conditional E-value: 2.4e-09
                          Ank_3   1 nGetpLhlAarsgnleivkfLlenkgadvna 31 
                                    +G+tpLhlAa+ g  +i+++Ll+ +gadvna
  gi|119720190|ref|YP_920685.1| 121 EGNTPLHLAALLGFADIARLLLD-RGADVNA 150
                                    69*********************.*****96 PP

  == domain 5  score: 23.8 bits;  conditional E-value: 2.3e-08
                          Ank_3   2 GetpLhlAarsgnleivkfLlenkgadv 29 
                                    G tpLh+Aa++g+ e++k+Lle +gad+
  gi|119720190|ref|YP_920685.1| 155 GKTPLHYAAEQGSAEVAKLLLE-RGADP 181
                                    89********************.9***8 PP

  == domain 6  score: 18.7 bits;  conditional E-value: 1e-06
                          Ank_3   1 nGetpLhlAarsgnleivkfLlenkgadvna 31 
                                    +G+tpLhlA+rs+ ++  k+Lle +gadvna
  gi|119720190|ref|YP_920685.1| 187 YGNTPLHLAVRSIEVS--KLLLE-RGADVNA 214
                                    7*************96..9****.9****96 PP

  == domain 7  score: 27.2 bits;  conditional E-value: 1.7e-09
                          Ank_3   1 nGetpLhlAarsgnleivkfLlenkgadv 29 
                                    +G+tpLh+Aa+ g+ e+vkfLle +gad+
  gi|119720190|ref|YP_920685.1| 218 EGRTPLHRAAMEGSAEVVKFLLE-RGADP 245
                                    69*********************.9***8 PP

  == domain 8  score: 12.6 bits;  conditional E-value: 0.0001
                          Ank_3   2 GetpLhlAarsgnleivkfLlenkgadvna 31 
                                    G+tpLh  + + n e++k+Lle kgad+na
  gi|119720190|ref|YP_920685.1| 252 GNTPLH--LAFKNMEVAKLLLE-KGADPNA 278
                                    9*****..77889999******.9****96 PP

  == domain 9  score: 26.7 bits;  conditional E-value: 2.5e-09
                          Ank_3   2 GetpLhlAarsgnleivkfLlenkgadvna 31 
                                    G+tpLh+Aa  g++e+v++Lle +gadv+a
  gi|119720190|ref|YP_920685.1| 283 GMTPLHFAAGLGKVEVVELLLE-HGADVDA 311
                                    99********************.9***985 PP

  == domain 10  score: 5.0 bits;  conditional E-value: 0.029
                          Ank_3   1 nGetpLhlAarsgnl..........eivkfLlenkgadvn 30 
                                    +G tpL +Aa+ ++           ++v +Lle +gad+ 
  gi|119720190|ref|YP_920685.1| 315 DGLTPLAYAAHRQDMyiradaltalKVVGLLLE-RGADPS 353
                                    6999*****999999988876654446999999.999985 PP

  == domain 11  score: 11.5 bits;  conditional E-value: 0.00023
                          Ank_3   3 etpLhlAarsgnleivkfLlenkgadvna 31 
                                    +t+Lh Aa  +  ++v++Lle kg d na
  gi|119720190|ref|YP_920685.1| 360 YTLLHKAAFWCYAKVVRLLLE-KGLDANA 387
                                    8********************.9***996 PP

  == domain 12  score: 33.8 bits;  conditional E-value: 1.3e-11
                          Ank_3   1 nGetpLhlAarsgnleivkfLlenkgadvna 31 
                                    +G+tpLh+Aa+ g++e+v++Lle +gad+na
  gi|119720190|ref|YP_920685.1| 391 YGRTPLHWAAERGCPEVVELLLE-HGADPNA 420
                                    79*********************.9****96 PP

  == domain 13  score: 22.6 bits;  conditional E-value: 5.6e-08
                          Ank_3   2 GetpLhlAarsgnleivkfLlenkgadvna 31 
                                    G+tpLhlAa   ++e +k+Lle +gad+na
  gi|119720190|ref|YP_920685.1| 425 GMTPLHLAATVKDTEAAKLLLE-HGADPNA 453
                                    99********************.9****96 PP

  == domain 14  score: 0.5 bits;  conditional E-value: 0.83
                          Ank_3  16 eivkfLlenkgadv 29 
                                    e +++Lle +ga++
  gi|119720190|ref|YP_920685.1| 487 EFIRLLLE-HGAEP 499
                                    679*****.89976 PP

  == domain 15  score: 14.8 bits;  conditional E-value: 1.8e-05
                          Ank_3   6 LhlAarsgnleivkfLlenkgadvn 30 
                                    Lh A+r+g++e vk Lle +g+++n
  gi|119720190|ref|YP_920685.1| 503 LHAAVRCGRPECVKKLLE-WGVNPN 526
                                    9*****************.9****9 PP

  == domain 16  score: 21.2 bits;  conditional E-value: 1.5e-07
                          Ank_3   1 nGetpLhlAarsgnleivkfLlenkgadvna 31 
                                    +G+t+Lh Aa +g++e+++ Lle +gad+na
  gi|119720190|ref|YP_920685.1| 531 DGNTLLHAAAWNGDVEVIEILLE-RGADINA 560
                                    69*********************.*****96 PP

  == domain 17  score: 28.4 bits;  conditional E-value: 7.3e-10
                          Ank_3   2 GetpLhlAarsgnleivkfLlenkgadvna 31 
                                    GetpLh+Aa+ gn+e vk+Lle +ga+vna
  gi|119720190|ref|YP_920685.1| 565 GETPLHVAAERGNFEAVKLLLE-RGAEVNA 593
                                    9*********************.9****96 PP

  == domain 18  score: 10.4 bits;  conditional E-value: 0.0005
                          Ank_3   8 lAarsgnleivkfLlenkgadvna 31 
                                    +Aars++ ++  +Lle +gad+na
  gi|119720190|ref|YP_920685.1| 598 YAARSCRWDVFTLLLE-RGADINA 620
                                    8***************.*****96 PP

  == domain 19  score: 14.4 bits;  conditional E-value: 2.6e-05
                          Ank_3   3 etpLhlAarsgnleivkfLlenkgadvna 31 
                                    +tpLh Aa + +  i++fL+e +gad+na
  gi|119720190|ref|YP_920685.1| 626 RTPLHGAAGCRDAGIARFLIE-RGADINA 653
                                    8********************.*****96 PP

  == domain 20  score: 27.4 bits;  conditional E-value: 1.6e-09
                          Ank_3   1 nGetpLhlAarsgnleivkfLlenkgadvna 31 
                                    +GetpLh A +sgn+e v++Lle +gadv+a
  gi|119720190|ref|YP_920685.1| 657 DGETPLHKATSSGNVEAVRLLLE-HGADVDA 686
                                    69*********************.9***985 PP

  == domain 21  score: 26.2 bits;  conditional E-value: 3.8e-09
                          Ank_3   2 GetpLhlAarsgnleivkfLlenkgadvna 31 
                                    G tpLh+Aa  g+leiv++Ll+ +gad na
  gi|119720190|ref|YP_920685.1| 691 GGTPLHHAAARGHLEIVRLLLK-HGADSNA 719
                                    78********************.9***885 PP

  == domain 22  score: 14.4 bits;  conditional E-value: 2.6e-05
                          Ank_3   1 nGetpLhlAarsgnl........e..ivkfLlenkgadvna 31 
                                    +GetpLh++a++++         +  i+++Ll  +gadvna
  gi|119720190|ref|YP_920685.1| 723 HGETPLHYVAEHADMcsknawdnClrIAELLLI-HGADVNA 762
                                    79*************888777652424555555.9****96 PP

  == domain 23  score: 23.0 bits;  conditional E-value: 4.2e-08
                          Ank_3   3 etpLhlAarsgnle...ivkfLlenkgadvna 31 
                                    +tpLh+A+ +g+ e   ++++Lle +gad+na
  gi|119720190|ref|YP_920685.1| 768 QTPLHIAVFFGSREhleVARWLLE-HGADPNA 798
                                    8************65448******.9****96 PP

  == domain 24  score: 17.4 bits;  conditional E-value: 2.8e-06
                          Ank_3   1 nGetpLhlAarsgnl....eivkfLlenkgadvn 30 
                                    +G+tpLh+++++       e +++Lle +gad+ 
  gi|119720190|ref|YP_920685.1| 802 EGNTPLHYVIEHSFWrerrEAIELLLE-HGADPS 834
                                    69*************866557******.9***97 PP

  == domain 25  score: 3.9 bits;  conditional E-value: 0.067
                          Ank_3   1 nGetpLhlAarsgnleivkfLl 22 
                                    +G +pL lA+  g+++ + +Ll
  gi|119720190|ref|YP_920685.1| 839 EGLSPLQLAVIKGDTD-AFALL 859
                                    599***********99.66666 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.39   6.3e+02      91     109 ..     148     166 ..     124     173 .. 0.81
   2 ?   -3.6   0.0       6.2     1e+04      93     107 ..     183     197 ..     183     200 .. 0.84
   3 ?   -0.6   0.0      0.73   1.2e+03      92     107 ..     246     261 ..     213     267 .. 0.81
   4 ?    0.8   0.0      0.27   4.4e+02      93     121 ..     311     339 ..     305     341 .. 0.83
   5 ?    0.3   0.0      0.38   6.2e+02      93     108 ..     387     402 ..     383     407 .. 0.89
   6 ?   -3.2   0.0       4.5   7.3e+03      93     107 ..     420     434 ..     419     439 .. 0.84
   7 ?    3.8   0.0     0.032        52      91     109 ..     558     576 ..     537     582 .. 0.84
   8 ?   -2.2   0.0       2.2   3.6e+03      93     109 ..     686     702 ..     682     707 .. 0.84
   9 ?    0.8   0.0      0.26   4.3e+02      93     108 ..     719     734 ..     712     739 .. 0.86
  10 ?   -2.2   0.0       2.3   3.7e+03      93     107 ..     798     812 ..     797     816 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.39
                       GATase_7  91 llaRDrlGikPLyygedkg 109
                                    + a++  G++PL+y+ ++g
  gi|119720190|ref|YP_920685.1| 148 VNAKNSSGKTPLHYAAEQG 166
                                    6689999*******99975 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 6.2
                       GATase_7  93 aRDrlGikPLyyged 107
                                    a D++G +PL+++ +
  gi|119720190|ref|YP_920685.1| 183 ATDTYGNTPLHLAVR 197
                                    6799******98865 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.73
                       GATase_7  92 laRDrlGikPLyyged 107
                                    +a D +G +PL+++ +
  gi|119720190|ref|YP_920685.1| 246 CAVDAFGNTPLHLAFK 261
                                    6889999999998877 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 0.27
                       GATase_7  93 aRDrlGikPLyygedkgdallfaSelkal 121
                                    a+D+ G +PL y+ +++d ++ a  l al
  gi|119720190|ref|YP_920685.1| 311 AKDNDGLTPLAYAAHRQDMYIRADALTAL 339
                                    78999**********98777777777776 PP

  == domain 5  score: 0.3 bits;  conditional E-value: 0.38
                       GATase_7  93 aRDrlGikPLyygedk 108
                                    a+D++G +PL+++ ++
  gi|119720190|ref|YP_920685.1| 387 AKDEYGRTPLHWAAER 402
                                    89**********9876 PP

  == domain 6  score: -3.2 bits;  conditional E-value: 4.5
                       GATase_7  93 aRDrlGikPLyyged 107
                                    aR+  G++PL+++ +
  gi|119720190|ref|YP_920685.1| 420 ARNDSGMTPLHLAAT 434
                                    89999*****98865 PP

  == domain 7  score: 3.8 bits;  conditional E-value: 0.032
                       GATase_7  91 llaRDrlGikPLyygedkg 109
                                    + aR+++G++PL+++ ++g
  gi|119720190|ref|YP_920685.1| 558 INARNKFGETPLHVAAERG 576
                                    679***********99976 PP

  == domain 8  score: -2.2 bits;  conditional E-value: 2.2
                       GATase_7  93 aRDrlGikPLyygedkg 109
                                    aR+ +G +PL+ + ++g
  gi|119720190|ref|YP_920685.1| 686 ARNDFGGTPLHHAAARG 702
                                    89********9988764 PP

  == domain 9  score: 0.8 bits;  conditional E-value: 0.26
                       GATase_7  93 aRDrlGikPLyygedk 108
                                    aR+  G++PL+y+ ++
  gi|119720190|ref|YP_920685.1| 719 ARNSHGETPLHYVAEH 734
                                    8***********9875 PP

  == domain 10  score: -2.2 bits;  conditional E-value: 2.3
                       GATase_7  93 aRDrlGikPLyyged 107
                                    aRD  G +PL+y+ +
  gi|119720190|ref|YP_920685.1| 798 ARDWEGNTPLHYVIE 812
                                    89*********9876 PP

>> HTH_18  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       2.1   3.5e+03      19      42 ..     120     143 ..     117     151 .. 0.63
   2 ?   -1.0   0.0       1.4   2.2e+03      18      44 ..     152     178 ..     148     184 .. 0.83
   3 ?   -3.7   0.0       9.6   1.6e+04      20      38 ..     315     333 ..     312     340 .. 0.74
   4 ?    2.8   0.0     0.088   1.4e+02      12      47 ..     383     418 ..     379     422 .. 0.84
   5 ?    3.7   0.0     0.045        73      19      48 ..     423     452 ..     419     456 .. 0.86
   6 ?   -1.7   0.0       2.3   3.7e+03      18      46 ..     562     589 ..     560     599 .. 0.72
   7 ?   -1.4   0.0       1.8   2.9e+03      20      48 ..     690     718 ..     687     733 .. 0.67
   8 ?   -3.5   0.0       8.1   1.3e+04      18      38 ..     800     820 ..     799     831 .. 0.66

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.1
                                    HTSS-HHHHHHHHHHHHHHHHHHS CS
                         HTH_18  19 vlgltpkeylrrlRlerArrlLle 42 
                                    + g tp +++  l +  + rlLl+
  gi|119720190|ref|YP_920685.1| 120 EEGNTPLHLAALLGFADIARLLLD 143
                                    556666666666666666666665 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.4
                                    HHTSS-HHHHHHHHHHHHHHHHHHSSS CS
                         HTH_18  18 rvlgltpkeylrrlRlerArrlLlent 44 
                                    +  g+tp +y+ +    ++ +lLle+ 
  gi|119720190|ref|YP_920685.1| 152 NSSGKTPLHYAAEQGSAEVAKLLLERG 178
                                    56899********99999999999854 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 9.6
                                    TSS-HHHHHHHHHHHHHHH CS
                         HTH_18  20 lgltpkeylrrlRlerArr 38 
                                     gltp +y+ ++   ++r+
  gi|119720190|ref|YP_920685.1| 315 DGLTPLAYAAHRQDMYIRA 333
                                    6899999999887666665 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.088
                                    HHHHHHHHTSS-HHHHHHHHHHHHHHHHHHSSS--- CS
                         HTH_18  12 LqrlfkrvlgltpkeylrrlRlerArrlLlentgls 47 
                                    L +  k+++g tp +++ ++   ++ +lLle+ +++
  gi|119720190|ref|YP_920685.1| 383 LDANAKDEYGRTPLHWAAERGCPEVVELLLEHGADP 418
                                    6666799**********************9966655 PP

  == domain 5  score: 3.7 bits;  conditional E-value: 0.045
                                    HTSS-HHHHHHHHHHHHHHHHHHSSS---H CS
                         HTH_18  19 vlgltpkeylrrlRlerArrlLlentglsv 48 
                                      g+tp +++ +++  +A +lLle+ +++ 
  gi|119720190|ref|YP_920685.1| 423 DSGMTPLHLAATVKDTEAAKLLLEHGADPN 452
                                    58*********************9777665 PP

  == domain 6  score: -1.7 bits;  conditional E-value: 2.3
                                    HHTSS-HHHHHHHHHHHHHHHHHHSSS-- CS
                         HTH_18  18 rvlgltpkeylrrlRlerArrlLlentgl 46 
                                    + +g tp +++ ++   +A +lLle  g 
  gi|119720190|ref|YP_920685.1| 562 NKFGETPLHVAAERGNFEAVKLLLE-RGA 589
                                    5688888888888888888888886.444 PP

  == domain 7  score: -1.4 bits;  conditional E-value: 1.8
                                    TSS-HHHHHHHHHHHHHHHHHHSSS---H CS
                         HTH_18  20 lgltpkeylrrlRlerArrlLlentglsv 48 
                                    +g tp +++ ++   ++ rlLl++ ++s 
  gi|119720190|ref|YP_920685.1| 690 FGGTPLHHAAARGHLEIVRLLLKHGADSN 718
                                    66677777777777777777776555554 PP

  == domain 8  score: -3.5 bits;  conditional E-value: 8.1
                                    HHTSS-HHHHHHHHHHHHHHH CS
                         HTH_18  18 rvlgltpkeylrrlRlerArr 38 
                                    ++ g tp +y+ ++ + r rr
  gi|119720190|ref|YP_920685.1| 800 DWEGNTPLHYVIEHSFWRERR 820
                                    567788888887766555444 PP

>> MOZART1  Mitotic-spindle organizing gamma-tubulin ring associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0       0.2   3.3e+02      28      38 ..      29      39 ..      27      39 .. 0.90
   2 ?   -2.1   0.0       2.2   3.6e+03      29      38 ..     269     278 ..     263     278 .. 0.89
   3 ?   -2.3   0.0       2.5     4e+03      23      37 ..     339     353 ..     337     355 .. 0.76
   4 ?   -2.6   0.0       3.1     5e+03      29      38 ..     411     420 ..     410     420 .. 0.91
   5 ?   -2.8   0.0       3.6   5.9e+03      29      38 ..     444     453 ..     444     453 .. 0.92
   6 ?    1.7   0.0      0.13   2.2e+02      28      37 ..     517     526 ..     514     527 .. 0.85
   7 ?    1.7   0.0      0.14   2.3e+02      19      38 ..     779     798 ..     779     798 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.2
                        MOZART1 28 kLienGVnPea 38
                                   +L+e GV+P+a
  gi|119720190|ref|YP_920685.1| 29 ALLEGGVDPNA 39
                                   69*******87 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.2
                        MOZART1  29 LienGVnPea 38 
                                    L+e+G +P+a
  gi|119720190|ref|YP_920685.1| 269 LLEKGADPNA 278
                                    99******87 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2.5
                        MOZART1  23 LsicvkLienGVnPe 37 
                                    L++   L+e+G +P 
  gi|119720190|ref|YP_920685.1| 339 LKVVGLLLERGADPS 353
                                    5666669******96 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 3.1
                        MOZART1  29 LienGVnPea 38 
                                    L+e+G +P+a
  gi|119720190|ref|YP_920685.1| 411 LLEHGADPNA 420
                                    89******87 PP

  == domain 5  score: -2.8 bits;  conditional E-value: 3.6
                        MOZART1  29 LienGVnPea 38 
                                    L+e+G +P+a
  gi|119720190|ref|YP_920685.1| 444 LLEHGADPNA 453
                                    89******87 PP

  == domain 6  score: 1.7 bits;  conditional E-value: 0.13
                        MOZART1  28 kLienGVnPe 37 
                                    kL+e GVnP+
  gi|119720190|ref|YP_920685.1| 517 KLLEWGVNPN 526
                                    7********7 PP

  == domain 7  score: 1.7 bits;  conditional E-value: 0.14
                        MOZART1  19 DretLsicvkLienGVnPea 38 
                                    +re L++   L+e+G +P+a
  gi|119720190|ref|YP_920685.1| 779 SREHLEVARWLLEHGADPNA 798
                                    689999999*********87 PP

>> Shigella_OspC  Shigella flexneri OspC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.51   8.3e+02     252     286 ..     148     179 ..     137     184 .. 0.83
   2 ?   -1.2   0.0      0.79   1.3e+03     258     286 ..     215     243 ..     198     245 .. 0.83
   3 ?   -2.8   0.0       2.5     4e+03     258     290 ..     279     311 ..     263     312 .. 0.85
   4 ?   -2.0   0.0       1.4   2.4e+03     258     286 ..     421     449 ..     399     453 .. 0.86
   5 ?    2.6   0.0     0.055        90     258     289 ..     528     559 ..     519     591 .. 0.88
   6 ?    1.7   0.0      0.11   1.7e+02     251     291 ..     650     687 ..     628     688 .. 0.81
   7 ?   -4.0   0.0       5.6   9.2e+03     267     290 ..     696     719 ..     691     720 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.51
                  Shigella_OspC 252 vnkkfkkvnsgdtmldnaikskdakmidlllkyga 286
                                    vn    k  sg t l  a  +  a++ +lll  ga
  gi|119720190|ref|YP_920685.1| 148 VNA---KNSSGKTPLHYAAEQGSAEVAKLLLERGA 179
                                    443...5789**********************998 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.79
                  Shigella_OspC 258 kvnsgdtmldnaikskdakmidlllkyga 286
                                    + n g t l  a     a+++++ll  ga
  gi|119720190|ref|YP_920685.1| 215 RNNEGRTPLHRAAMEGSAEVVKFLLERGA 243
                                    57899999***9999***********998 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 2.5
                  Shigella_OspC 258 kvnsgdtmldnaikskdakmidlllkygaildk 290
                                    k  sg t l  a    + ++++lll +ga +d 
  gi|119720190|ref|YP_920685.1| 279 KNSSGMTPLHFAAGLGKVEVVELLLEHGADVDA 311
                                    667899999999999999**********98876 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 1.4
                  Shigella_OspC 258 kvnsgdtmldnaikskdakmidlllkyga 286
                                    + +sg t l  a   kd++  +lll +ga
  gi|119720190|ref|YP_920685.1| 421 RNDSGMTPLHLAATVKDTEAAKLLLEHGA 449
                                    4679999999999*************998 PP

  == domain 5  score: 2.6 bits;  conditional E-value: 0.055
                  Shigella_OspC 258 kvnsgdtmldnaikskdakmidlllkygaild 289
                                    + n g+t+l  a    d ++i++ll  ga ++
  gi|119720190|ref|YP_920685.1| 528 RDNDGNTLLHAAAWNGDVEVIEILLERGADIN 559
                                    56899999999999999999999999999765 PP

  == domain 6  score: 1.7 bits;  conditional E-value: 0.11
                  Shigella_OspC 251 dvnkkfkkvnsgdtmldnaikskdakmidlllkygaildkk 291
                                    d+n    +++ g+t l +a  s + + + lll +ga +d +
  gi|119720190|ref|YP_920685.1| 650 DINA---RTKDGETPLHKATSSGNVEAVRLLLEHGADVDAR 687
                                    5665...5678*************************98865 PP

  == domain 7  score: -4.0 bits;  conditional E-value: 5.6
                  Shigella_OspC 267 dnaikskdakmidlllkygaildk 290
                                      a    + +++ lllk+ga ++ 
  gi|119720190|ref|YP_920685.1| 696 HHAAARGHLEIVRLLLKHGADSNA 719
                                    556666677999*******98765 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.3   2.2e+03     173     201 ..     284     312 ..     269     358 .. 0.80
   2 ?   -0.1   0.0      0.28   4.5e+02     160     200 ..     385     423 ..     377     456 .. 0.69
   3 ?   -0.2   0.0       0.3     5e+02     154     199 ..     553     592 ..     536     619 .. 0.84
   4 ?    6.2   0.2    0.0033       5.4     153     239 ..     678     793 ..     670     795 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.3
                                    ETTTTSTCCHHTTTHCCEEEHCTCEEEHH CS
                   Amidohydro_1 173 gthlevaeslglldeiklilahgvhltpt 201
                                    +t+l++a +lg  +++ l+l+hg  ++++
  gi|119720190|ref|YP_920685.1| 284 MTPLHFAAGLGKVEVVELLLEHGADVDAK 312
                                    78999999999999999999999877744 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.28
                                    HHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEE...H CS
                   Amidohydro_1 160 edaeaafgetiehgthlevaeslglldeiklilahgvhlt...p 200
                                    ++a++++g      t+l++a + g ++++ l+l+hg  +    +
  gi|119720190|ref|YP_920685.1| 385 ANAKDEYG-----RTPLHWAAERGCPEVVELLLEHGADPNarnD 423
                                    56777777.....6799999999999999999999988775332 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.3
                                    SSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEE CS
                   Amidohydro_1 154 etkgevedaeaafgetiehgthlevaeslglldeiklilahgvhlt 199
                                    e  +++ +a+++fg     +t+l+va + g ++ +kl+l++g  + 
  gi|119720190|ref|YP_920685.1| 553 ERGADI-NARNKFG-----ETPLHVAAERGNFEAVKLLLERGAEVN 592
                                    555666.8999999.....55999*****************98776 PP

  == domain 4  score: 6.2 bits;  conditional E-value: 0.0033
                                    TSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEE......HHHHHHHHHHHHHHCEE...HHHHHHH CS
                   Amidohydro_1 153 letkgevedaeaafgetiehgthlevaeslglldeiklilahgvhlt......pteaellkerlkeagva...hcpfsns 223
                                    le+ ++v da+++fg     gt+l+ a   g+l++++l+l+hg           t + +++e++++++ +   +c +  +
  gi|119720190|ref|YP_920685.1| 678 LEHGADV-DARNDFG-----GTPLHHAAARGHLEIVRLLLKHGADSNarnshgETPLHYVAEHADMCSKNawdNCLRIAE 751
                                    6788888.999****.....889999999***************999765554449999999999998778885555444 PP

                                    H..........................SEHHHHHHHHHHHHT CS
                   Amidohydro_1 224 i..........................lrsgrealrkaldeG 239
                                                               +r+++e +r++l+ G
  gi|119720190|ref|YP_920685.1| 752 LllihgadvnardsrdqtplhiavffgSREHLEVARWLLEHG 793
                                    445555555555777777777777777777777777777766 PP

>> Arm-DNA-bind_3  Arm DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1      0.15   2.4e+02      54      70 ..      24      40 ..      22      43 .. 0.91
   2 ?    1.5   0.0      0.24   3.9e+02      53      70 ..      56      73 ..      44      76 .. 0.82
   3 ?   -2.3   0.0       3.8   6.1e+03      59      71 ..     107     119 ..     105     121 .. 0.79
   4 ?   -2.2   0.1       3.4   5.5e+03      54      69 ..     168     183 ..     162     185 .. 0.85
   5 ?    2.0   0.0      0.17   2.7e+02      46      70 ..     255     279 ..     231     282 .. 0.83
   6 ?    1.8   0.0      0.19   3.2e+02      46      70 ..     430     454 ..     420     456 .. 0.81
   7 ?   -0.3   0.0      0.91   1.5e+03      40      69 ..     691     719 ..     672     722 .. 0.83
   8 ?   -0.5   0.0         1   1.7e+03      51      70 ..     780     799 ..     779     801 .. 0.85
   9 ?   -0.6   0.1       1.1   1.8e+03      51      69 ..     817     835 ..     817     839 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.15
                 Arm-DNA-bind_3 54 arelraliaqGiDPaee 70
                                   a++++al++ G+DP+++
  gi|119720190|ref|YP_920685.1| 24 AKRVKALLEGGVDPNAA 40
                                   89************985 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.24
                 Arm-DNA-bind_3 53 karelraliaqGiDPaee 70
                                    a+++r l+++G DP+ +
  gi|119720190|ref|YP_920685.1| 56 HAEAARLLLERGADPNVK 73
                                   6999***********875 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 3.8
                 Arm-DNA-bind_3  59 aliaqGiDPaeek 71 
                                    +l+++G DP++  
  gi|119720190|ref|YP_920685.1| 107 VLLDRGADPNATD 119
                                    6799*****9875 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 3.4
                 Arm-DNA-bind_3  54 arelraliaqGiDPae 69 
                                    a+ ++ l+++G DP +
  gi|119720190|ref|YP_920685.1| 168 AEVAKLLLERGADPGA 183
                                    77889999******76 PP

  == domain 5  score: 2.0 bits;  conditional E-value: 0.17
                 Arm-DNA-bind_3  46 slaeARkkarelraliaqGiDPaee 70 
                                     l  A k  + ++ l+++G DP+++
  gi|119720190|ref|YP_920685.1| 255 PLHLAFKNMEVAKLLLEKGADPNAK 279
                                    47779999999***********975 PP

  == domain 6  score: 1.8 bits;  conditional E-value: 0.19
                 Arm-DNA-bind_3  46 slaeARkkarelraliaqGiDPaee 70 
                                     la+  k  ++++ l+++G DP++e
  gi|119720190|ref|YP_920685.1| 430 HLAATVKDTEAAKLLLEHGADPNAE 454
                                    56666677889999*********98 PP

  == domain 7  score: -0.3 bits;  conditional E-value: 0.91
                 Arm-DNA-bind_3  40 GrypavslaeARkkarelraliaqGiDPae 69 
                                    G  p +  a+AR   + +r l+++G D ++
  gi|119720190|ref|YP_920685.1| 691 GGTP-LHHAAARGHLEIVRLLLKHGADSNA 719
                                    6667.78899***************99765 PP

  == domain 8  score: -0.5 bits;  conditional E-value: 1
                 Arm-DNA-bind_3  51 RkkarelraliaqGiDPaee 70 
                                    R+  + +r l+++G DP+++
  gi|119720190|ref|YP_920685.1| 780 REHLEVARWLLEHGADPNAR 799
                                    77788899999******975 PP

  == domain 9  score: -0.6 bits;  conditional E-value: 1.1
                 Arm-DNA-bind_3  51 RkkarelraliaqGiDPae 69 
                                    R++++++  l+++G DP+ 
  gi|119720190|ref|YP_920685.1| 817 RERREAIELLLEHGADPSI 835
                                    7888999999999****85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (870 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       196  (0.010932); expected 358.6 (0.02)
Passed bias filter:                      187  (0.01043); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.72u 0.28s 00:00:01.00 Elapsed: 00:00:00.45
# Mc/sec: 5868.43
//
Query:       gi|119720191|ref|YP_920686.1|  [L=671]
Description: hypothetical protein Tpen_1285 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.2e-69  233.8   2.5    3.9e-69  233.0   2.5    1.4  1  Thermopsin  Thermopsin
  ------ inclusion threshold ------
       0.23   11.3   0.0        2.4    8.1   0.0    2.2  2  S4_2        S4 domain
          8    6.5   6.4         16    5.5   6.4    1.5  1  Titin_Z     Titin Z


Domain annotation for each model (and alignments):
>> Thermopsin  Thermopsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  233.0   2.5   6.6e-73   3.9e-69      12     260 .]     123     381 ..     107     381 .. 0.93

  Alignments for each domain:
  == domain 1  score: 233.0 bits;  conditional E-value: 6.6e-73
                     Thermopsin  12 epaPmGiadyGiknnsgkltpysyntssvlGevnisslsaynsssn..spesaslQLNvvlevvt.ggktysywvQnVv. 87 
                                       P+G+a+y+         ++++nts+vlG +n+s++sa+++ss+  +++++slQLN+v+ev+  gg++++ywvQn+v 
  gi|119720191|ref|YP_920686.1| 123 YGLPAGLASYP---------DVAVNTSMVLGFFNVSAASAKSYSSRaaEADAWSLQLNAVVEVSLaGGRKQYYWVQNMVg 193
                                    33577777776.........99**********************99888888************99************** PP

                     Thermopsin  88 .......sfnttekq..ltfidNiWNftspsanlsnsaisGnGtvyasskgefYyayateylelslPltlkLvinvslts 158
                                           + n+tek+  +++++NiWN t++ + ls+++isG+G+vy ++++e+Yya+ ++y++++lPl+  Lv+++ ++s
  gi|119720191|ref|YP_920686.1| 194 giegtrsYENKTEKAimYQVWNNIWNNTGRLSLLSDERISGCGGVY-RDRDEYYYACVYTYSPCDLPLAGFLVVRA-YAS 271
                                    *****98667777767899***************************.****************************9.888 PP

                     Thermopsin 159 ngvpevsFgYsid.......ggvvtYDnvtinstgkasa.eilvngssltpsgllyDaeLvlgGpgngekttfnslnatl 230
                                    ng+ +v+FgY+++       +++++YDnvti+++ +a    i+ ++s+l+++gl++++eLv++G++++e++tf++l+a+l
  gi|119720191|ref|YP_920686.1| 272 NGAVHVDFGYVTAqsgdyrpAIITWYDNVTIRTNPPAVGaGIVATSSYLNGRGLPLNVELVFCGFCCSEHATFSELEARL 351
                                    9999*******98*******9***********999887779*************************************** PP

                     Thermopsin 231 sLyYlngtnyqpvknaydfGsdTaEtaenv 260
                                    +L+Y++g  ++p++n+y+fG++T+Eta+nv
  gi|119720191|ref|YP_920686.1| 352 TLAYWRGGGWAPFPNLYSFGVSTNETATNV 381
                                    *****************************8 PP

>> S4_2  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0       0.1   6.1e+02      34      54 ..     499     519 ..     487     529 .. 0.76
   2 ?    8.1   0.0   0.00039       2.4      33      61 ..     569     597 ..     564     600 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.1
                           S4_2  34 eVkvNGevetrRgkKlraGdv 54 
                                     V+vNG  +tr    l aG  
  gi|119720191|ref|YP_920686.1| 499 PVTVNGTRTTRYAGWLDAGSS 519
                                    59*******997666666655 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00039
                           S4_2  33 geVkvNGevetrRgkKlraGdvVeidget 61 
                                      V+vNGe ++r  + l +G ++e++ e 
  gi|119720191|ref|YP_920686.1| 569 YPVLVNGERTERYSRYLAPGTQLEVKAEP 597
                                    57**********************98775 PP

>> Titin_Z  Titin Z
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   6.4    0.0028        16      11      26 ..     639     654 ..     637     658 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0028
                        Titin_Z  11 aAVAtVVaAvDkarvr 26 
                                    aAVAtV +Av+ ar r
  gi|119720191|ref|YP_920686.1| 639 AAVATVLVAVAVARRR 654
                                    6*************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (671 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       676  (0.0377043); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.46
# Mc/sec: 4376.06
//
Query:       gi|119720192|ref|YP_920687.1|  [L=128]
Description: hypothetical protein Tpen_1286 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 857.59
//
Query:       gi|119720193|ref|YP_920688.1|  [L=237]
Description: CRISPR-associated Csm3 family protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.5e-24   84.6   0.0    1.8e-23   83.7   0.0    1.4  1  RAMPs     RAMP superfamily


Domain annotation for each model (and alignments):
>> RAMPs  RAMP superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.7   0.0   9.8e-28   1.8e-23       2     213 .]      19     208 ..      18     208 .. 0.91

  Alignments for each domain:
  == domain 1  score: 83.7 bits;  conditional E-value: 9.8e-28
                                    EEESS-EE----...................---S----HHHHHHHHHHHHHHHHH.HHHTT-HHHHH.H.......... CS
                          RAMPs   2 letltPlhiGdg.....kisdekeespefrdkgglPyIPGSSlkGalRsalekllgsekkekkdeysrkkekqrvkkgd. 75 
                                    le ltPl++G+g     +++   e + ++     +PyIPGSSlkG++Rs++e++++ e++   d  + ++  q+++ g+ 
  gi|119720193|ref|YP_920688.1|  19 LENLTPLRVGAGreaqlGSPVDLEPLRVRLGDRSVPYIPGSSLKGVFRSLAEAIARAEGHVIHDPWDFEAAEQEARDGKy 98 
                                    7889************9999999999******************************999999999999998888888889 PP

                                    .HHHHHH--S...SS--SEEEEE.......................EEEEEEEEEEEEEEEEE--SSS-EEEEEE...-T CS
                          RAMPs  76 .leeaiFGneeeskiagrvffeDarpvkipgqileeskqikstpspklsgselrelldhsterrtrvaidrktktngkkk 154
                                     l++ iFG++     a+ v++ Da+p  +p                             ++  +t+v i+r ++ +++  
  gi|119720193|ref|YP_920688.1|  99 cLICGIFGST---RLASHVRIYDAYPKGTP-----------------------------TLFMKTGVGINRDFRGAHP-- 144
                                    9*********...*************9876.............................999****************.. PP

                                    T-EEEEEEEESS...................HHHHHHHHHHHHHH.HHH---STTTTBTTT-EE CS
                          RAMPs 155 gglftleaipae.....rikfsgrirlenlsdeelgallklLdlldlhflglGggkplGfGsve 213
                                    ++l+t++ ++++        +  +  + +  de  + l  +Ld l + ++++G++k++G+G+++
  gi|119720193|ref|YP_920688.1| 145 NILYTERQVEPGhrwsfMMDIVNIRVYPEPGDERGRILRRVLDMLAEGMVQVGARKTVGYGLLR 208
                                    999**********77665555555567777899999999999999****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       244  (0.0136092); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1745.29
//
Query:       gi|119720194|ref|YP_920689.1|  [L=307]
Description: CRISPR-associated Csm3 family protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-29  102.9   0.0    3.2e-29  102.5   0.0    1.2  1  RAMPs     RAMP superfamily
     0.0051   16.3   0.0     0.0063   16.0   0.0    1.2  1  Cas_Cmr3  CRISPR-associated protein (Cas_Cmr3)


Domain annotation for each model (and alignments):
>> RAMPs  RAMP superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.5   0.0   3.5e-33   3.2e-29       2     213 .]      22     239 ..      21     239 .. 0.87

  Alignments for each domain:
  == domain 1  score: 102.5 bits;  conditional E-value: 3.5e-33
                                    EEESS-EE----...................---S----HHHHHHHHHHHHHHHHH.HHHTT-HHHHH.H.......... CS
                          RAMPs   2 letltPlhiGdg.....kisdekeespefrdkgglPyIPGSSlkGalRsalekllgsekkekkdeysrkkekqrvkkgd. 75 
                                    l + +Pl++G+g     +++    ++ ++     +PyIPGSSlkG++Rs    l++ ++   ++ +s + + +++   + 
  gi|119720194|ref|YP_920689.1|  22 LVAESPLRVGAGreaplGSPVDLSVLRVRLGGKSVPYIPGSSLKGVFRSFSQSLAVAKGLSVCSGLSGETCMDYEDPSLg 101
                                    6789********************************************99996666444444444444333333333335 PP

                                    .............................HHHHHH--S...SS--SEEEEE.......................EEEEEE CS
                          RAMPs  76 .............................leeaiFGneeeskiagrvffeDarpvkipgqileeskqikstpspklsgse 126
                                                                 l +++FG +   ++ g v+f+Da+pv+ +g                     
  gi|119720194|ref|YP_920689.1| 102 gekllsylqglmreghsleavrlfhekacLMCKVFGAP---SFSGHVEFSDAYPVDEKGG-------------------- 158
                                    55666668888888999999999999999*********...***************8765.................... PP

                                    EEEEEEEEEEE--SSS-EEEEEE...-TT-EEEEEEEESS..............HHHHHHHHHHHHHH.HHH---STTTT CS
                          RAMPs 127 lrelldhsterrtrvaidrktktngkkkgglftleaipaerikfsgrirlenlsdeelgallklLdlldlhflglGggkp 206
                                       ++d+st +rt++ai+r+t+ + +   +l+++e+++++ ++f+++ r +nl++ +lg+l ++++ +++ ++++Gg k+
  gi|119720194|ref|YP_920689.1| 159 ---VVDVSTGVRTGIAINRRTGAVYE--RALYQVEYVEPG-ARFRFEARTTNLPNYALGLLSAVIRMMNEGWVRVGGFKT 232
                                    ...689********************..************.*************************************** PP

                                    BTTT-EE CS
                          RAMPs 207 lGfGsve 213
                                    +GfG v+
  gi|119720194|ref|YP_920689.1| 233 RGFGEVR 239
                                    ****875 PP

>> Cas_Cmr3  CRISPR-associated protein (Cas_Cmr3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   7.1e-07    0.0063     174     211 ..     164     201 ..     104     234 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 7.1e-07
                       Cas_Cmr3 174 keeRigialdpetrtaeegalyqteglrlkedvrlall 211
                                    +  R+gia++++t ++ e alyq+e++++  ++r+ ++
  gi|119720194|ref|YP_920689.1| 164 TGVRTGIAINRRTGAVYERALYQVEYVEPGARFRFEAR 201
                                    568**************************966555443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 2023.34
//
Query:       gi|119720195|ref|YP_920690.1|  [L=332]
Description: hypothetical protein Tpen_1289 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.6e-06   26.5   0.0    8.3e-06   26.0   0.0    1.2  1  RAMPs     RAMP superfamily


Domain annotation for each model (and alignments):
>> RAMPs  RAMP superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   4.6e-10   8.3e-06       6      99 ..      36     189 ..      32     234 .. 0.74

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 4.6e-10
                                    S-EE----............................................---S----HHHHHHHHHHHHH....... CS
                          RAMPs   6 tPlhiGdg..............................kisdekeespefrdkgglPyIPGSSlkGalRsale....... 48 
                                    + lh+G+g                               ++  + ++ +    gg+ ++PGSS+kG +Rs le       
  gi|119720195|ref|YP_920690.1|  36 SYLHVGSGvqrvsvpveevrssasrartrreledlvarLSGKIELDYAQPVYAGGRLVVPGSSVKGNVRSRLElsfkpkn 115
                                    56888888888888888888888888888888888886666677788899999********************5555555 PP

                                    ..................HHHH.HHHTT-HHHHH.H..........................................HH CS
                          RAMPs  49 ..................kllgsekkekkdeysrkkekqrvkkgd.................................le 77 
                                                      k                         +                                 l+
  gi|119720195|ref|YP_920690.1| 116 gvarsclirategpvappK-------------------------KgeqgwrhfrvweaslsypgreaceysedspevcLL 170
                                    4444444444444333330.........................1444444445555555555555555566666666** PP

                                    HHHH--S...SS--SEEEEE.. CS
                          RAMPs  78 eaiFGneeeskiagrvffeDar 99 
                                    + iFG +   +  g v f+D +
  gi|119720195|ref|YP_920690.1| 171 CDIFGTA---GLQGLVYFGDLV 189
                                    *******...*********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 2104.38
//
Query:       gi|119720196|ref|YP_920691.1|  [L=914]
Description: metal dependent phosphohydrolase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-07   32.0   3.9    1.2e-07   32.0   3.9    2.6  3  HD        HD domain
  ------ inclusion threshold ------
       0.01   15.3   0.1      0.024   14.1   0.1    1.6  1  HDOD      HDOD domain
      0.049   13.8   0.4       0.23   11.6   0.2    2.2  2  HD_6      HD domain
      0.086   11.8   0.0       0.15   11.0   0.0    1.3  1  DUF3435   Protein of unknown function (DUF3435)


Domain annotation for each model (and alignments):
>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   3.9   2.6e-11   1.2e-07       3     120 ..     169     269 ..     167     274 .. 0.83
   2 ?   -1.1   0.0      0.48   2.2e+03      51      78 ..     320     349 ..     309     390 .. 0.77
   3 ?   -3.2   0.0       2.1   9.3e+03       7      26 ..     421     438 ..     419     447 .. 0.69

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 2.6e-11
                                    HHHHHHHHHHHHHHHHHHH.....HHHHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHHHHH CS
                             HD   3 eHsleVaklarrlaedlge.....eedrellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrlgld 77 
                                     H l++  la  la + g+     + +  ++++aaLlHDiGk + ++              H++++a+i++ ++k     
  gi|119720196|ref|YP_920691.1| 169 AHLLMTSALAWALAYESGKteeerRREAAVARVAALLHDIGKAVDPE-------------RHAEESARIAEYLLKGIV-G 234
                                    689999999999998888899989899999**************886.............7******99999988773.3 PP

                                    ...HHHHHHHHHTTCCHHHHHHHHHHHHCCTSCHHHHHHHHHHHHH CS
                             HD  78 ...ledvaklirehheswegkkrprglaerqlslearivklaDrla 120
                                       l  v+  +rehh ++              s+ +r++++aDrla
  gi|119720196|ref|YP_920691.1| 235 devLARVVGEVREHHAREG-----------YVSRADRLASAADRLA 269
                                    3676666666666666665...........8999999999999997 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.48
                                    HHCTCCHHHHHHHHHHHHHHHHHHHHH..H CS
                             HD  51 eefekflaHekvgaeilrevekrlgld..l 78 
                                    e++e fl+ ++++ae +r++ek +g++  +
  gi|119720196|ref|YP_920691.1| 320 ELTELFLERAEEAAENVRKEEKEEGVKglT 349
                                    446778889999999999999999876551 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 2.1
                                    HHHHHHHHHHHHHHHHHHHH CS
                             HD   7 eVaklarrlaedlgeeedre 26 
                                    +V++lar+  e+l   e   
  gi|119720196|ref|YP_920691.1| 421 RVWELARKVKEELP--EPLR 438
                                    78999999999987..3333 PP

>> HDOD  HDOD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   5.3e-06     0.024      89     153 ..     161     231 ..     151     254 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.3e-06
                                    SS-HHHHHHHHHHHHHHHHHHHHHTT-S-H......HHHHHHHHTTTHHHHHHHHHSHHHHHHHHHHHHHH CS
                           HDOD  89 gadlkklwehslavAlvarelaeelgledp......eeaflaGLLhdiGklvllsllpeeleellekvaee 153
                                    g + ++l++h l ++++a +la e g++++      + a +a+LLhdiGk v  +++ ee ++++e+  ++
  gi|119720196|ref|YP_920691.1| 161 GYNTSSLAAHLLMTSALAWALAYESGKTEEerrreaAVARVAALLHDIGKAVDPERHAEESARIAEYLLKG 231
                                    567789999*************9996666435544467889**********99999999999988876555 PP

>> HD_6  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2     5e-05      0.23      13      68 ..     164     213 ..     156     272 .. 0.72
   2 ?   -2.6   0.0       1.1   5.1e+03      12      41 ..     777     815 ..     769     833 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5e-05
                                    EEEHHHHHHHHHHHHHHHHHHTS-HHHHHC.TS-HHHHHHHHHHHHHCCCGGGSSH CS
                           HD_6  13 whpLvaHllDvaavaealldkwlsllarllrgleeealrrllaflaalHDlGKasp 68 
                                    + +L+aHll + a a+al  ++ +     + + e+++  +++ + a lHD+GKa +
  gi|119720196|ref|YP_920691.1| 164 TSSLAAHLLMTSALAWALAYESGK-----T-EEERRREAAVARVAALLHDIGKAVD 213
                                    678999999999999999876652.....2.3344566677888899******964 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.1
                                    .EEEHHHHHHHHHHHHHHHHHHTS-H.........HHHH CS
                           HD_6  12 awhpLvaHllDvaavaealldkwlsl.........larl 41 
                                    aw  L  H+l v a +++  d + +          la++
  gi|119720196|ref|YP_920691.1| 777 AWARLFSHVLGVPARGAWCEDSSFKAhaeafgkayLASR 815
                                    399999999999999998888887774555444443333 PP

>> DUF3435  Protein of unknown function (DUF3435)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   3.3e-05      0.15     314     373 ..     815     873 ..     793     882 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.3e-05
                        DUF3435 314 akgtelyeelekakrelrnerqrlrrelkkkireeFkeeqpvidierqlsGkaldeevke 373
                                    +++  ++ee+e+a+++l+  r+ + +  ++   + + +eq+ i + rql  +al ee  e
  gi|119720196|ref|YP_920691.1| 815 RAEG-EDEEVERARKRLAALRRVALDTWREVSGSAYWREQAYIYVLRQLESEALGEETSE 873
                                    3333.589**********************************************999554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (914 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.74u 0.29s 00:00:01.03 Elapsed: 00:00:00.47
# Mc/sec: 5895.15
//
Query:       gi|119720197|ref|YP_920692.1|  [L=222]
Description: hypothetical protein Tpen_1291 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-08   34.1   0.0    4.1e-08   33.5   0.0    1.3  1  RAMPs     RAMP superfamily


Domain annotation for each model (and alignments):
>> RAMPs  RAMP superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.0   2.3e-12   4.1e-08      27     111 ..      38     126 ..      28     187 .. 0.77

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 2.3e-12
                                    .---S----HHHHHHHHHHHHHHHHH.HHHTT-HHHHH.H................HHHHHH--S....SS--SEEEEE. CS
                          RAMPs  27 dkgglPyIPGSSlkGalRsalekllgsekkekkdeysrkkekqrvkkgd.......leeaiFGne.eeskiagrvffeDa 98 
                                    d + + y+PGS++kG+lRsa+ +++g  +   + e + +k    v+k          ++ +FG + ++   a++v ++D+
  gi|119720197|ref|YP_920692.1|  38 DGTYEYYVPGSTVKGVLRSAASRVAGAYGFTSCGEVDPEK----VRKAHeamggpcDVCTLFGYPyPSVEGASKVYVSDF 113
                                    678999********************55555555555533....2222245556779*********************** PP

                                    ............. CS
                          RAMPs  99 rpvkipgqilees 111
                                    +pv  p+++++ +
  gi|119720197|ref|YP_920692.1| 114 SPVGRPAPVIVAR 126
                                    ****998877654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       254  (0.014167); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1757.72
//
Query:       gi|119720198|ref|YP_920693.1|  [L=324]
Description: hypothetical protein Tpen_1292 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-05   23.7   0.2      0.004   17.2   0.2    2.2  1  RAMPs     RAMP superfamily


Domain annotation for each model (and alignments):
>> RAMPs  RAMP superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.2   2.2e-07     0.004      30     211 ..      27     208 ..      15     210 .. 0.56

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.2e-07
                                    -S----HHHHHHHHHHHHHHHHH.HHHTT-HHHHH.H.............................HHHHHH........ CS
                          RAMPs  30 glPyIPGSSlkGalRsalekllgsekkekkdeysrkkekqrvkkgd....................leeaiF........ 81 
                                     l yIPGS+l+Ga+  al+++ +       d+++r++e   v+                       +e+ +         
  gi|119720198|ref|YP_920693.1|  27 PLGYIPGSTLRGAILDALRAEGVLS----LDDLRREAESPSVLSSPayplvggkralpaspfaaycRECGVVydfapvya 102
                                    566****************887733....344444444433333312233333333333333333333333322222222 PP

                                    ..--S...SS--SEEEEE................................EEEEEEEEEEEEEEEEE--SSS-EEEEEE. CS
                          RAMPs  82 ..GneeeskiagrvffeDarpvkipgqileeskqikstpsp.........klsgselrelldhsterrtrvaidrktktn 150
                                      G+   ++i+  v    +   +                 +           +g   +e  + +t r+t v + ++ +  
  gi|119720198|ref|YP_920693.1| 103 rqGKL--ESIKCPVGRDHTLKPA-----------------YpgivvykrvAEGGVVVAEKAPIRTFRSTSVGVSKRRGAF 163
                                    22222..3333333333333333.................1344444454677777777777777777777777765443 PP

                                    ..-TT-EEEEEEEESS..............HHHHHHHHHHHHHH.HHH---STTTTBTTT- CS
                          RAMPs 151 gkkkgglftleaipaerikfsgrirlenlsdeelgallklLdlldlhflglGggkplGfGs 211
                                      ++g+lf +ea+ ++               e   ++ + +dl+    + +G g ++GfG+
  gi|119720198|ref|YP_920693.1| 164 --ERGMLFDYEAVAEG--------------TEFWAYVWAPFDLPGRLEVTVGRGASRGFGW 208
                                    ..35888888888888..............8888888888888888888888888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 2188.50
//
Query:       gi|119720199|ref|YP_920694.1|  [L=288]
Description: hypothetical protein Tpen_1293 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-16   59.8   0.0      6e-16   59.1   0.0    1.3  1  RAMPs     RAMP superfamily


Domain annotation for each model (and alignments):
>> RAMPs  RAMP superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.1   0.0   3.3e-20     6e-16       2     213 .]      19     247 ..      18     247 .. 0.82

  Alignments for each domain:
  == domain 1  score: 59.1 bits;  conditional E-value: 3.3e-20
                                    EEESS-EE----..............---S----HHHHHHHHHHHHHHHHH............................. CS
                          RAMPs   2 letltPlhiGdgkisdekeespefrdkgglPyIPGSSlkGalRsalekllg............................. 52 
                                    +e+  Plh+G+    +e++++ + r ++g+  +PGS++kGa+Rs +ekl+                              
  gi|119720199|ref|YP_920694.1|  19 FEARGPLHVGGR---REGNVLYALRLPDGRLLVPGSTWKGAFRSIAEKLAPsipatgpeklalelaaagergrdaylekl 95 
                                    68999*******...********************************777777777666666666666666666666666 PP

                                    .........................HHHTT-HHHHH.H...........HHHHHH--S...SS--SEEEEE......... CS
                          RAMPs  53 ........................sekkekkdeysrkkekqrvkkgd..leeaiFGneeeskiagrvffeDarpvkipgq 106
                                                            +e++++++  ++  e  +++ ++   + ++FGn+    +ag ++f D++       
  gi|119720199|ref|YP_920694.1|  96 rgdfeaalkgaatrfdpadvkrvvGELGLDREAGIDAREALEQYLEYycPVGKLFGNR---VRAGSLKFADSV------- 165
                                    6666666666666666666666664444444444444444444444477*********...**********95....... PP

                                    ..............EEEEEEEEEEEEEEEEE--SSS-EEEEEE...-TT-EEEEEEEESS...............HHHHH CS
                          RAMPs 107 ileeskqikstpspklsgselrelldhsterrtrvaidrktktngkkkgglftleaipae.rikfsgrirlenlsdeelg 185
                                                            +   t r+++v idrkt+t+++  g l+ +ea  ++   k+      ++    + +
  gi|119720199|ref|YP_920694.1| 166 ------------------------VEAPTFRKPGVGIDRKTGTVKE--GVLYFVEAGDPGaPVKLLMVGEVDERGSAASR 219
                                    ........................6788******************..************99999999999999999999 PP

                                    HHHHHHHHH.HHH---STTTTBTTT-EE CS
                          RAMPs 186 allklLdlldlhflglGggkplGfGsve 213
                                    +l   L  +++  + +Gg+k+ G+G++e
  gi|119720199|ref|YP_920694.1| 220 LLASTLLYVKELGVAVGGKKSTGMGLLE 247
                                    999999999****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       227  (0.0126611); expected 358.6 (0.02)
Passed bias filter:                      202  (0.0112667); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 2025.63
//
Query:       gi|119720200|ref|YP_920695.1|  [L=147]
Description: hypothetical protein Tpen_1294 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.12   12.2   0.0       0.22   11.3   0.0    1.4  1  DUF1450   Protein of unknown function (DUF1450)


Domain annotation for each model (and alignments):
>> DUF1450  Protein of unknown function (DUF1450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   1.2e-05      0.22      47      68 ..     104     125 ..     101     128 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.2e-05
                        DUF1450  47 pfAlVnGeivaaetpeelleki 68 
                                     +A VnG+iv+ae pe  le++
  gi|119720200|ref|YP_920695.1| 104 TYAKVNGSIVEAEIPETPLEEL 125
                                    79**************988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       244  (0.0136092); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1158.63
//
Query:       gi|119720201|ref|YP_920696.1|  [L=191]
Description: hypothetical protein Tpen_1295 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1373.00
//
Query:       gi|119720202|ref|YP_920697.1|  [L=515]
Description: hypothetical protein Tpen_1296 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0023   18.1   0.0        2.3    8.3   0.0    2.6  2  Cu-oxidase    Multicopper oxidase
  ------ inclusion threshold ------
       0.12   12.7   0.0        4.5    7.6   0.0    2.8  3  DUF4177       Domain of unknown function (DUF4177)
       0.17   11.9   0.4       0.84    9.7   0.0    2.3  3  P_proprotein  Proprotein convertase P-domain
       0.19   10.6   0.0       0.82    8.6   0.0    1.8  2  RAG2          Recombination activating protein 2


Domain annotation for each model (and alignments):
>> Cu-oxidase  Multicopper oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.0    0.0014       6.2      34      65 ..      44      74 ..      25      92 .. 0.67
   2 !    8.3   0.0   0.00051       2.3      34     100 ..     120     185 ..      99     196 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0014
                                   T--SEEEETTBSS.......CTTTTSGGGEEE CS
                     Cu-oxidase 34 pvpdavlingkggfnatladkdgaslatltve 65
                                     pdavl+ng  + n+tl+ k+  ++ tl+  
  gi|119720202|ref|YP_920697.1| 44 YGPDAVLVNGSARGNCTLTVKA-PATLTLDAS 74
                                   459**************98854.333344433 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00051
                                    T--SEEEETTBSS.......CTTTTSGGGE.EEEETTEEEEEEEESSS-BEEEEETSB-EEEEEETCE CS
                     Cu-oxidase  34 pvpdavlingkggfnatladkdgaslatlt.vepgktyrlriinvsaddslnfsIeGHkltVvevDgv 100
                                      p a++ing++  natl+  ++a la+++  +pg + +  +in+s  +    +I+G   tV+e+ + 
  gi|119720202|ref|YP_920697.1| 120 RGPGALVINGTSYGNATLTLSVPALLAINAsPQPGWKLKTLLINGSRAQPGVARIAGD--TVIEAFFA 185
                                    34889*************999888887765169*************************..****8555 PP

>> DUF4177  Domain of unknown function (DUF4177)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0     0.001       4.5      30      64 ..      71     110 ..      61     111 .. 0.82
   2 ?    1.5   0.0     0.082   3.7e+02      30      52 ..     147     168 ..     143     175 .. 0.75
   3 ?   -2.4   0.0       1.4   6.1e+03      37      45 ..     230     242 ..     223     261 .. 0.60

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.001
                        DUF4177  30 lnelAkeGWrlvsii.....pvkesrgvgaaesilliFeR 64 
                                    l++ A +GWrl++ +     +  + + v +++ i++ FeR
  gi|119720202|ref|YP_920697.1|  71 LDASAPKGWRLKALLvngspALPGATRVSGNTTIEAFFER 110
                                    8999*********998888644488888888888888888 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.082
                        DUF4177  30 lnelAkeGWrlvsiipvkesrgv 52 
                                    +n+  + GW+l++ + +++sr++
  gi|119720202|ref|YP_920697.1| 147 INASPQPGWKLKTLL-INGSRAQ 168
                                    7777788******88.5666665 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.4
                        DUF4177  37 GWrlvsii....p 45 
                                     Wrl++ +    p
  gi|119720202|ref|YP_920697.1| 230 SWRLKALLvngsP 242
                                    5999997754443 PP

>> P_proprotein  Proprotein convertase P-domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       2.4   1.1e+04       9      27 ..      60      78 ..      53      82 .. 0.56
   2 ?    9.7   0.0   0.00019      0.84      46      85 ..     306     348 ..     301     349 .. 0.88
   3 ?   -1.8   0.1      0.73   3.3e+03      50      67 ..     377     393 ..     365     395 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2.4
                                   EEEESSGGGEEEEEE-TTS CS
                   P_proprotein  9 nithtrrgdlritLvsPsG 27
                                   ++t++  + l+++  +P+G
  gi|119720202|ref|YP_920697.1| 60 TLTVKAPATLTLDASAPKG 78
                                   4455555555555566665 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00019
                                    EEEEEEESTTTTS---EEEEEEEEE...SSTT--EEEEEEEEE CS
                   P_proprotein  46 ldwtfmsthlwgeraeGeWkLevkd...seeedtgtlkswkLr 85 
                                    l++t   +h w+ +++G+W+L   d   + ++dt  +  w+L+
  gi|119720202|ref|YP_920697.1| 306 LNETCEAVHYWNASVAGRWTLLHGDaslEVANDTVLVAGWSLK 348
                                    5778889**************9999998889999999999986 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.73
                                    EEESTTTTS---EEEEEE CS
                   P_proprotein  50 fmsthlwgeraeGeWkLe 67 
                                    f+s   w  + +G W++e
  gi|119720202|ref|YP_920697.1| 377 FQSG-SWRYKGNGVWEIE 393
                                    5555.6888899999987 PP

>> RAG2  Recombination activating protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.14   6.4e+02     172     199 ..      67      94 ..      54     112 .. 0.78
   2 ?    8.6   0.0   0.00018      0.82     163     219 ..     210     266 ..     206     292 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.14
                                    BBTTTTB--S-EEEEEEEEESSEEEEEE CS
                           RAG2 172 hslannsrpprlyrlkvdlllGspvvsc 199
                                     +l+ ++ +p+ +rlk  l+ Gsp++  
  gi|119720202|ref|YP_920697.1|  67 ATLTLDASAPKGWRLKALLVNGSPALPG 94 
                                    57788899999*************9864 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00018
                                    TTEEEEE--BBTTTTB--S-EEEEEEEEESSEEEEEEEEESSS---BS--EEE-SSS CS
                           RAG2 163 ndtvyllGGhslannsrpprlyrlkvdlllGspvvsctvleeglsvssaivtqtgse 219
                                    ndt+ l GG  l+ n+ +pr +rlk  l+ Gsp+   +v  +g +   a + q++ +
  gi|119720202|ref|YP_920697.1| 210 NDTLLLRGGALLSINASTPRSWRLKALLVNGSPTSPGEVRVSGNTTIEAFFEQVKVK 266
                                    89*******************************988888777766666766666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (515 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 3400.15
//
Query:       gi|119720203|ref|YP_920698.1|  [L=557]
Description: glycoside hydrolase family protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      4e-19   69.2   0.0    1.3e-18   67.5   0.0    1.9  1  Glyco_hydro_20  Glycosyl hydrolase family 20, catalytic domai
  ------ inclusion threshold ------
      0.031   14.1   0.1        1.1    9.1   0.1    2.6  2  MEDS            MEDS: MEthanogen/methylotroph, DcmR Sensory d


Domain annotation for each model (and alignments):
>> Glyco_hydro_20  Glycosyl hydrolase family 20, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.5   0.0   1.4e-22   1.3e-18       1     273 [.      99     361 ..      99     407 .. 0.84

  Alignments for each domain:
  == domain 1  score: 67.5 bits;  conditional E-value: 1.4e-22
                 Glyco_hydro_20   1 fkyRGlmlDvaRh.flsveeikrliDamaaaKlNvlHwHltDdqgwrleikkyPeLtekgakreskeseeelsgfYtked 79 
                                    f++RG++lDvaR    +vee+krl+  + + K N l   + D   w    ++yP+   +ga+r            Yt ++
  gi|119720203|ref|YP_920698.1|  99 FEFRGFHLDVARGgVATVEELKRLLRWLFLLKYNYLAVYVEDLFPW----DRYPD---IGARRG----------RYTGKE 161
                                    99**********736789************************9877....79**7...578777..........6***** PP

                 Glyco_hydro_20  80 ireiveYAaergieVipEidmPgHaraalkaypelvtkekaeqsveqsvqvevkesvlnptneetyeflekvldevaelf 159
                                     re+veY+ + g+eV p +++ gH++++l  +p + +          s + +++e+ l+++ +e+ +f e++l+e +e  
  gi|119720203|ref|YP_920698.1| 162 WREVVEYGGRLGVEVFPSLELAGHMENILS-LPGYRRF---------SEWHRPEEGCLDVGDPEARRFAEELLEEALEKT 231
                                    **************************9765.5665554.........3456788899*********************** PP

                 Glyco_hydro_20 160 pseyvHiGGDEvkkkqwkkspeiqalikeeglksveelqsyfvkrvekilkekgkkligWdeilekgk.a.......... 228
                                    +s+y+HiGGDE+++    +s        +    ++ +l +   +r+ +  +e+gk++++W ++l++              
  gi|119720203|ref|YP_920698.1| 232 KSRYIHIGGDETWAMGRGRS--LD----RTLRFEWPRLYAEHHSRLLRLARERGKTPLIWGDMLAGMYlReterdlwrpi 305
                                    ***********976665555..33....333356889999999**********************998526788999998 PP

                 Glyco_hydro_20 229 .sklakknttvqsWrele......keaaeklakkgydvilspad....alYlDfgq 273
                                      + a ++++v  W+  +      k++++ + ++gy+ i++p      ++Y Df  
  gi|119720203|ref|YP_920698.1| 306 lENPAWREAVVANWDYSPgtveyfKQKIRLFKERGYEQIVCPGLwnwdRYYPDFDA 361
                                    87777788999999987688888888899999999999999864333366666654 PP

>> MEDS  MEDS: MEthanogen/methylotroph, DcmR Sensory domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1   0.00012       1.1      68     126 ..     204     260 ..     190     268 .. 0.76
   2 ?    2.1   0.0     0.017   1.5e+02      78     106 ..     357     385 ..     326     393 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00012
                           MEDS  68 aeetylrgggfdpermlealrralakaladgyaglrvigemtwalrspaereelleyEa 126
                                     ee  l+ g  ++ r+ e+l +++ +    + + +++ g+ twa+ +++++++ l++E+
  gi|119720203|ref|YP_920698.1| 204 PEEGCLDVGDPEARRFAEELLEEALEK--TKSRYIHIGGDETWAMGRGRSLDRTLRFEW 260
                                    555566666666655555555555554..45577***********************97 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.017
                           MEDS  78 fdpermlealrralakaladgyaglrvig 106
                                     d +++l++++++l++a+++g +g+ v++
  gi|119720203|ref|YP_920698.1| 357 PDFDAALANVKSFLQAAREEGVKGFMVTA 385
                                    56788999999999999999999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (557 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 3511.25
//
Query:       gi|119720204|ref|YP_920699.1|  [L=597]
Description: hypothetical protein Tpen_1298 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.011   16.2   0.2         38    4.8   0.0    3.9  5  Lyase_8_C        Polysaccharide lyase family 8, C-terminal be
      0.039   13.7   7.3          3    7.6   0.2    3.7  3  T2SS-T3SS_pil_N  Pilus formation protein N terminal region
      0.098   12.6   0.0         12    5.9   0.0    2.9  3  DUF3113          Protein of unknown function (DUF3113)


Domain annotation for each model (and alignments):
>> Lyase_8_C  Polysaccharide lyase family 8, C-terminal beta-sandwich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0    0.0064        38      20      62 ..      17      60 ..      12      65 .. 0.87
   2 ?    4.5   0.0    0.0085        51      23      58 ..      99     132 ..      85     133 .. 0.83
   3 ?    1.5   0.0     0.073   4.3e+02      13      57 ..     166     207 ..     165     218 .. 0.68
   4 ?   -3.5   0.0       2.6   1.6e+04      34      49 ..     327     343 ..     322     355 .. 0.70
   5 ?   -2.7   0.0       1.5   8.9e+03      31      45 ..     361     378 ..     337     379 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0064
                                   EEEEESSSEEEEECTCTEEESSSEEEEEE.EETTEEEEEEEBTT CS
                      Lyase_8_C 20 vaavfwkagtvtlknlsltvdkpasvlvk.keggsltvsvsDPt 62
                                   va+ f++a+  +   l+l v +p+ ++v+    g++t+ vs Pt
  gi|119720204|ref|YP_920699.1| 17 VAYLFFAAQRPSGATLTLRVHGPGGLVVNgSAYGNATLRVSVPT 60
                                   7889999988887799999**********988888999888887 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0085
                                    EESSSEEEEECTCTEEESSSEEEEEE.EETTEEEEEE CS
                      Lyase_8_C  23 vfwkagtvtlknlsltvdkpasvlvk.keggsltvsv 58 
                                    +f++++  t    +l+v +p+++lv+ +  g++t+++
  gi|119720204|ref|YP_920699.1|  99 AFFEEERYT---VTLKVRGPGALLVNgTAFGNATLTI 132
                                    688996666...79************99999888886 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.073
                                    EETTTTEEEEEESSSEEEEECTCTEEESSSEEEEEE.EETTEEEEE CS
                      Lyase_8_C  13 rhaelglvaavfwkagtvtlknlsltvdkpasvlvk.keggsltvs 57 
                                    r  ++ ++ a+f ++ ++t    +l v +p++++++ ++ g++t++
  gi|119720204|ref|YP_920699.1| 166 RVSGNTTIEAIFGRS-EAT---VTLRVRGPGALVINgTSYGNATLT 207
                                    556666666666666.333...479999999999998666665554 PP

  == domain 4  score: -3.5 bits;  conditional E-value: 2.6
                                    TCTEEESSSEEEEEE.E CS
                      Lyase_8_C  34 nlsltvdkpasvlvk.k 49 
                                    + +l v  pa++ vk k
  gi|119720204|ref|YP_920699.1| 327 GVKLYVENPAAIPVKvK 343
                                    55677888888877765 PP

  == domain 5  score: -2.7 bits;  conditional E-value: 1.5
                                    EEC...TCTEEESSSEEE CS
                      Lyase_8_C  31 tlk...nlsltvdkpasv 45 
                                    tl+   n+s+ +d+++++
  gi|119720204|ref|YP_920699.1| 361 TLEfprNASIVLDAKCIY 378
                                    333446888888888876 PP

>> T2SS-T3SS_pil_N  Pilus formation protein N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1     0.019   1.1e+02      32      56 ..      32      56 ..      27      68 .. 0.85
   2 ?    5.2   0.3    0.0029        17      33      58 ..     109     134 ..     107     140 .. 0.88
   3 ?    7.6   0.2    0.0005         3      18      56 ..     170     208 ..     162     211 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.019
                T2SS-T3SS_pil_N 32 advtvlsprevlltGksvGtTnliv 56
                                   +  +v+ p+ +++ G ++G ++l v
  gi|119720204|ref|YP_920699.1| 32 LTLRVHGPGGLVVNGSAYGNATLRV 56
                                   5678999***************998 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0029
                T2SS-T3SS_pil_N  33 dvtvlsprevlltGksvGtTnlivwd 58 
                                      +v+ p+ +l+ G ++G ++l++ +
  gi|119720204|ref|YP_920699.1| 109 TLKVRGPGALLVNGTAFGNATLTIHG 134
                                    568999****************9865 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0005
                T2SS-T3SS_pil_N  18 pepvervavgnpkiadvtvlsprevlltGksvGtTnliv 56 
                                    + ++e ++   ++ +  +v+ p+ +++ G s+G ++l++
  gi|119720204|ref|YP_920699.1| 170 NTTIEAIFGRSEATVTLRVRGPGALVINGTSYGNATLTL 208
                                    56788899999999**********************986 PP

>> DUF3113  Protein of unknown function (DUF3113)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0    0.0021        12       4      21 ..      47      64 ..      44      67 .. 0.90
   2 ?   -3.3   0.0       1.5   9.1e+03       5      17 ..     200     212 ..     199     213 .. 0.86
   3 ?    3.3   0.0     0.014        82       5      24 ..     388     407 ..     386     409 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0021
                        DUF3113  4 qaYinasvDiRiPteves 21
                                    aY na++ + +Pt ve 
  gi|119720204|ref|YP_920699.1| 47 SAYGNATLRVSVPTAVEV 64
                                   59**************96 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.5
                        DUF3113   5 aYinasvDiRiPt 17 
                                    +Y na++ +++P 
  gi|119720204|ref|YP_920699.1| 200 SYGNATLTLKVPA 212
                                    589****999995 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.014
                        DUF3113   5 aYinasvDiRiPtevesvny 24 
                                    aY+na+    iP  ve   +
  gi|119720204|ref|YP_920699.1| 388 AYVNATCYRWIPGLVETFRF 407
                                    9***************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (597 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 4098.28
//
Query:       gi|119720205|ref|YP_920700.1|  [L=145]
Description: hypothetical protein Tpen_1299 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       160  (0.00892409); expected 358.6 (0.02)
Passed bias filter:                      142  (0.00792013); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1001.64
//
Query:       gi|119720206|ref|YP_920701.1|  [L=127]
Description: HEPN domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.6e-20   71.6   1.8    6.2e-20   71.5   1.8    1.0  1  HEPN      HEPN domain


Domain annotation for each model (and alignments):
>> HEPN  HEPN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.5   1.8   3.5e-24   6.2e-20       1     114 [.       6     123 ..       6     127 .] 0.92

  Alignments for each domain:
  == domain 1  score: 71.5 bits;  conditional E-value: 3.5e-24
                                    HHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHTT--.SSCCHHHHHHCCHHHT...-HHHHHHH... CS
                           HEPN   1 aeewlrrAeedleaAellleegdydlacfhaqqaaekalKAlllkkggeppkthdlreLleelkkelkeseelreel... 77 
                                    ae + rrA  +l++A +l++eg+ydla+f  +q + ++l + ll ++g++p+th+lr+L++el + +++  el e +   
  gi|119720206|ref|YP_920701.1|   6 AEVLRRRAHAFLRNALRLIDEGEYDLAAFSLEQYCRLILEYKLLVLKGSYPRTHSLRRLIRELGEAEPSVLELVENVgnl 85 
                                    57899**************************************************************9966666666666 PP

                                    ...HHHHCCCHHCCCTSS--S--HHHHHHHHHHHHHHHHH CS
                           HEPN  78 ...eeLekayiesrYpdakeeyteedaeealkdaeevlel 114
                                        +Le+ay  srY ++++  +e +++++ +++ ev++ 
  gi|119720206|ref|YP_920701.1|  86 hyvARLEEAYLASRYFPTAY--EEAEVRDLARFVAEVFRR 123
                                    777****************9..9*********99999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 874.74
//
Query:       gi|119720207|ref|YP_920702.1|  [L=103]
Description: DNA polymerase beta subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-11   44.0   0.0    2.4e-11   43.7   0.0    1.1  1  NTP_transf_2    Nucleotidyltransferase domain
      8e-07   29.1   0.0      1e-06   28.8   0.0    1.2  1  Polbeta         Polymerase beta, Nucleotidyltransferase
    0.00039   20.6   0.0    0.00045   20.4   0.0    1.1  1  DNA_pol_B_palm  DNA polymerase beta palm
  ------ inclusion threshold ------
      0.078   12.8   0.0      0.086   12.6   0.0    1.2  1  DUF294          Putative nucleotidyltransferase DUF294


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.7   0.0   5.4e-15   2.4e-11       4      85 ..      19      93 ..      16     101 .. 0.81

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 5.4e-15
                                   HHHHHHHHTT.TSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEECEEECCCCTE CS
                   NTP_transf_2  4 lleelkelep.vakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevdlvtrekledpll 84
                                   l +e+ +++   a+v++fGS++rG+++  SDiD+lvv+++        +++++l+ + +   e  ++e ++   e++e++++
  gi|119720207|ref|YP_920702.1| 19 LVKEVARRFDpEARVFVFGSAVRGDYTAASDIDVLVVTSAV-------DRKYDLMVEVYRSTE-APVELHVASPEQFEKWYK 92
                                   67788888888******************************.......667777777777777.788888887777776665 PP

                                   E CS
                   NTP_transf_2 85 v 85
                                   +
  gi|119720207|ref|YP_920702.1| 93 R 93
                                   5 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.0   2.2e-10     1e-06      14      53 ..      31      71 ..      20      88 .. 0.75

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 2.2e-10
                                   HSTTEEEEEE-S------EEEEEEEESS-.--HHHHHHHHH CS
                        Polbeta 14 elaylFGSrakgkareeSDiDlavllkek.ldleeelelaa 53
                                   + +++FGS ++g+++  SDiD+ v+++   ++++  +e++ 
  gi|119720207|ref|YP_920702.1| 31 ARVFVFGSAVRGDYTAASDIDVLVVTSAVdRKYDLMVEVYR 71
                                   5699**********************999544444555544 PP

>> DNA_pol_B_palm  DNA polymerase beta palm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0     1e-07   0.00045       8      56 ..      14      63 ..      11      89 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1e-07
                                   HHHHHHHHHHHHHH-TT-EEEE-HHHHTT-SE.ESSEEEEEEBTTBSTTS CS
                 DNA_pol_B_palm  8 ealealvkkaakeldpevevivcGSYRRgaes.sGDvDvlitkkdakses 56
                                   +a++ lvk+ a+++dpe++v v GS  Rg  + + D+Dvl+  + ++++ 
  gi|119720207|ref|YP_920702.1| 14 RAVAGLVKEVARRFDPEARVFVFGSAVRGDYTaASDIDVLVVTSAVDRKY 63
                                   678889*******************9999755278******998887754 PP

>> DUF294  Putative nucleotidyltransferase DUF294
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.9e-05     0.086      38      77 ..      18      58 ..       9      95 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.9e-05
                         DUF294 38 laeeelgkp.pvpfallvmGSeGReEqtlktDqDnalvled 77
                                    +++e++++ + +  ++v+GS+ R++ t ++D D   v + 
  gi|119720207|ref|YP_920702.1| 18 GLVKEVARRfDPEARVFVFGSAVRGDYTAASDIDVLVVTSA 58
                                   44455555447778899*****************9999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 808.99
//
Query:       gi|119720208|ref|YP_920703.1|  [L=75]
Description: hypothetical protein Tpen_1302 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.088   12.7   0.2      0.092   12.7   0.2    1.4  1  DUF3437   Domain of unknown function (DUF3437)


Domain annotation for each model (and alignments):
>> DUF3437  Domain of unknown function (DUF3437)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   5.1e-06     0.092      44      69 ..      44      69 ..       4      74 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.1e-06
                        DUF3437 44 rktvkktlseFkrthqDtWeedkkkF 69
                                   +  ++k+l+eF  t+++tW++ ++++
  gi|119720208|ref|YP_920703.1| 44 GVDAEKALEEFEETRSETWRTLEEEY 69
                                   56799**************8876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 528.42
//
Query:       gi|119720209|ref|YP_920704.1|  [L=395]
Description: major facilitator transporter [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.3e-26   90.6  41.8    2.7e-22   79.2  32.9    2.0  2  MFS_1           Major Facilitator Superfamily
    0.00021   20.3   5.9    0.00021   20.3   5.9    2.1  2  MFS_1_like      MFS_1 like family
  ------ inclusion threshold ------
       0.63   10.2   3.6          1    9.5   0.4    2.4  2  Acetyltransf_6  Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.2  32.9   4.6e-26   2.7e-22       1     328 [.      12     327 ..      12     328 .. 0.79
   2 !   22.3  22.1   8.8e-09   5.2e-05       5     177 ..     213     389 ..     206     395 .] 0.77

  Alignments for each domain:
  == domain 1  score: 79.2 bits;  conditional E-value: 4.6e-26
                          MFS_1   1 lllaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll 80 
                                    l++++f+++++ s+++p++   +a++lg+s s +g++++ y+  a+++ +++G l d++ +r  ++ +l+l  l++++l 
  gi|119720209|ref|YP_920704.1|  12 LYIVVFITMIDHSTISPIVA-QYAKSLGASDSLAGIIVASYSMSALISLPVVGLLLDKV-SRAGVVQSLILADLAVVYLY 89 
                                    5799****************.899***********************************.88888888888888844444 PP

                          MFS_1  81 .fasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyila 158
                                     + + ++  llv+r+l G+  +alfp+++a+++d++++ +   ++ l+ + ++  +++g ll+  ++ ++g+r+vfy+l 
  gi|119720209|ref|YP_920704.1|  90 tL-PRSPtELLVVRALHGAVDSALFPGILAVFRDMVTR-RLETGFTLYWVVTGTPIAIGSLLARTVVLHYGFRGVFYALI 167
                                    36.999999*****************************.***************************************** PP

                          MFS_1 159 ivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsg...lltllplylq 235
                                    ++++ +++   + +  +++ r+  + + +            w+  + +  l  l++a +++ + ++g   ++  + + l 
  gi|119720209|ref|YP_920704.1| 168 PLYVAGLI---ASIEISRRYREALARRAL------------WEGPRDPVALGTLVAAYVSAYILYTGigtVVGSMSISLT 232
                                    ******88...888888888888888888............666666665543333333333333333334444444358 PP

                          MFS_1 236 evlgls....glllaglllallalvgail..allagrls.drlgrrrrlllallllllaalglallavtssavllllvlv 308
                                      lgl+    +  +++    ++++  + l  + +++r + + +++  +l+   ++l+ +al++ ll v+ +++   l+++
  gi|119720209|ref|YP_920704.1| 233 RGLGLPreaaA-AEVA--WWAFQATLFSLlvMAFTARHVvREVSK--ALWALAIGLSGVALSMGLLLVSIESLSRTLSSL 307
                                    888888*9963.5555..333333322221255555555144555..777777777777777777777778999999*** PP

                          MFS_1 309 liGfglgfvfpsllalasdl 328
                                    ++G++lg+v p++  ++sd 
  gi|119720209|ref|YP_920704.1| 308 FFGVALGTVLPASSKIVSDT 327
                                    ************99999986 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 8.8e-09
                          MFS_1   5 aflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrf......Grrrvlllglllfalg.ll 77 
                                    a + +++++++  ++++ l++ lg+   ++   ++  a+ a ++sl++++++ r+       + + l +gl + al+ +l
  gi|119720209|ref|YP_920704.1| 213 AYILYTGIGTVVGSMSISLTRGLGLPREAAAAEVAWWAFQATLFSLLVMAFTARHvvrevsKALWALAIGLSGVALSmGL 292
                                    55677888888888888999999988888888888888888888888888888875665433444666666666666333 PP

                          MFS_1  78 lllfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyil 157
                                    ll+ ++ +    ++ ++ G++ g+++pa+  +++d   k  rgra +lls++f  G+i g+++++ l++ +   ++ y+ 
  gi|119720209|ref|YP_920704.1| 293 LLV-SIESLSRTLSSLFFGVALGTVLPASSKIVSDTHYK-YRGRASALLSVSFLTGVITGAVASSRLLETAHGLYTNYLP 370
                                    333.34444478889999*****************9999.****************************888889999999 PP

                          MFS_1 158 aivsllafvlfllllpeepp 177
                                    a++++ +++l +l+ +++++
  gi|119720209|ref|YP_920704.1| 371 AAAGASLGLLLVLY-VASRR 389
                                    99999999964444.33333 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   5.9   3.5e-08   0.00021     227     378 ..       9     158 ..       7     165 .. 0.88
   2 ?   -3.3   2.1       0.5     3e+03     291     330 ..     245     284 ..     237     316 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 3.5e-08
                     MFS_1_like 227 viifllvalilgmswgiienFlflYLkelgasntllGslvalgvvaeiplfffaeklleklGhvklliiallayilrfll 306
                                    +i + +v++i  + ++ i   +  Y k+lgas +l+G++va   ++ ++ + +   ll+k++   ++   +la  +   l
  gi|119720209|ref|YP_920704.1|   9 YISLYIVVFITMIDHSTISPIVAQYAKSLGASDSLAGIIVASYSMSALISLPVVGLLLDKVSRAGVVQSLILADLAVVYL 88 
                                    57789999************************************************************9999999999** PP

                     MFS_1_like 307 yaiienawlvlpievLhgisfgllwaaaveyvskiapksleatgqgllsglyfglGralGsliGGllwdlks 378
                                    y + +++  +l++ +Lhg+   +l+  +  + +++++++le+ g  l+  +  g   a+Gsl++  +  +++
  gi|119720209|ref|YP_920704.1|  89 YTLPRSPTELLVVRALHGAVDSALFPGILAVFRDMVTRRLET-GFTLYWVV-TGTPIAIGSLLARTVVLHYG 158
                                    ***************************************997.55666554.67777888877755555555 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 0.5
                     MFS_1_like 291 klliiallayilrfllyaiienawlvlpievLhgisfgll 330
                                    ++  +a+ a+ + +l++a++   +++ +  +L ++++gl 
  gi|119720209|ref|YP_920704.1| 245 EVAWWAFQATLFSLLVMAFTARHVVREVSKALWALAIGLS 284
                                    5566777777788888888877777777777777777765 PP

>> Acetyltransf_6  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.2       0.1   6.2e+02      39      92 ..     102     152 ..      96     190 .. 0.63
   2 ?    9.5   0.4   0.00017         1      71     120 ..     337     386 ..     325     392 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.1
                 Acetyltransf_6  39 raqwarrpdvfadpltraflrdllaalaargalrlyvlrldgrpvAvalglrsg 92 
                                    ra++++  d +  p   a +rd++ +  + g   ly++   g+p+A+  +l   
  gi|119720209|ref|YP_920704.1| 102 RALHGAV-DSALFPGILAVFRDMVTRRLETG-FTLYWVVT-GTPIAIGSLLART 152
                                    5555566.44444888999999999986544.45555544.4444444333333 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00017
                 Acetyltransf_6  71 lrlyvlrldgrpvAvalglrsgdrlyywlggydpelaklspgllllweli 120
                                    + l+v  l g + ++++  r  ++++ +++ y p++a+ s+glll+++++
  gi|119720209|ref|YP_920704.1| 337 ALLSVSFLTGVITGAVASSRLLETAHGLYTNYLPAAAGASLGLLLVLYVA 386
                                    5567777788899999999999***********************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2621.51
//
Query:       gi|119720210|ref|YP_920705.1|  [L=87]
Description: hypothetical protein Tpen_1304 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 566.47
//
Query:       gi|119720211|ref|YP_920706.1|  [L=696]
Description: hypothetical protein Tpen_1305 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.019   15.0   6.8       0.11   12.7   0.3    4.1  3  TPR_2     Tetratricopeptide repeat
      0.071   13.4   7.4       0.32   11.3   0.5    4.0  3  TPR_12    Tetratricopeptide repeat
       0.14   12.4   0.2       0.75   10.0   0.0    2.2  3  DUF4240   Protein of unknown function (DUF4240)


Domain annotation for each model (and alignments):
>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.3   1.8e-05      0.11       3      33 ..     378     408 ..     376     409 .. 0.92
   2 ?    3.5   0.2     0.016        93       6      29 ..     429     452 ..     426     456 .. 0.87
   3 ?   -2.9   0.1       1.8   1.1e+04       8      14 ..     569     575 ..     563     578 .. 0.43

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.8e-05
                          TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                    ++ n ++a+++ g++e A+e+++kA +l P+
  gi|119720211|ref|YP_920706.1| 378 LHLNAARAARAIGRLESAEEHLRKAEALLPR 408
                                    68999********************999985 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.016
                          TPR_2   6 nlGlayyklgdyeeAleafekAle 29 
                                    ++G+++++l+++ eA  +f+++ e
  gi|119720211|ref|YP_920706.1| 429 ERGMVAMYLKRLGEAWGYFRRVAE 452
                                    69*************999998876 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1.8
                          TPR_2   8 Glayykl 14 
                                    + ++y+l
  gi|119720211|ref|YP_920706.1| 569 ASLLYAL 575
                                    2333333 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.2     0.025   1.5e+02      22      73 ..     269     317 ..     266     321 .. 0.73
   2 ?   11.3   0.5   5.4e-05      0.32      48      75 ..     379     406 ..     358     408 .. 0.86
   3 ?   -0.5   0.0      0.26   1.5e+03       8      29 ..     429     450 ..     421     454 .. 0.69

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.025
                         TPR_12  22 AlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeala 73 
                                    A+ ll++ale +++   +   l+  +l   + ++  +gr++ A el   ala
  gi|119720211|ref|YP_920706.1| 269 ARGLLDRALEEVEKG--GSGSLVRHALGVAASTL-TSGRWDLANELAPLALA 317
                                    788899999999543..44547888888888886.99999999887655555 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 5.4e-05
                         TPR_12  48 lrnLgrlyralgryeeAlelleealaia 75 
                                      n +r+ ra gr+e A+e+l++a a++
  gi|119720211|ref|YP_920706.1| 379 HLNAARAARAIGRLESAEEHLRKAEALL 406
                                    578999999*************999986 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.26
                         TPR_12   8 nlaavlrrlgrydeAlelleka 29 
                                    ++++v ++l+r+ eA  +++++
  gi|119720211|ref|YP_920706.1| 429 ERGMVAMYLKRLGEAWGYFRRV 450
                                    6777888888887777776665 PP

>> DUF4240  Protein of unknown function (DUF4240)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       0.5     3e+03      55      84 ..     239     268 ..     235     279 .. 0.84
   2 ?   10.0   0.0   0.00013      0.75      61     120 ..     477     537 ..     454     543 .. 0.79
   3 ?   -4.0   0.0       2.6   1.6e+04      64      91 ..     619     646 ..     607     662 .. 0.67

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.5
                        DUF4240  55 ytwdlwaaaylinggcsddgFlyfrawlia 84 
                                      ++l  a++l+++   ++ F+ +r  l+a
  gi|119720211|ref|YP_920706.1| 239 SGEELESALHLMDEASATWYFASARIYLVA 268
                                    566777888999999999999999999997 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00013
                        DUF4240  61 aaa.yling..gcsddgFlyfrawliaqGrevyeevladpdsLaelpavedeeeelefeelly 120
                                    a    +++   g +++gF++  + l+a G+e+ e++++  d L+e+   +  ++  ++e + +
  gi|119720211|ref|YP_920706.1| 477 ALRvGVMEAllGGDEEGFWEHAGRLVALGEEYEERCVEGHDPLCEMLGPR--YALAHAEAVAV 537
                                    4444566655566899*****************************98888..66666666655 PP

  == domain 3  score: -4.0 bits;  conditional E-value: 2.6
                        DUF4240  64 ylinggcsddgFlyfrawliaqGr.evye 91 
                                    ++++gg++  +Fl + + l++ G+ e+ +
  gi|119720211|ref|YP_920706.1| 619 EMLRGGYTRHQFLAV-CVLVGCGElEAAK 646
                                    567778888888765.7888888634444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (696 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 4462.87
//
Query:       gi|119720212|ref|YP_920707.1|  [L=91]
Description: hypothetical protein Tpen_1306 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       213  (0.0118802); expected 358.6 (0.02)
Passed bias filter:                      177  (0.00987227); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.42
# Mc/sec: 658.20
//
Query:       gi|119720213|ref|YP_920708.1|  [L=80]
Description: paREP6 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0019   17.9   0.6     0.0065   16.1   0.6    2.2  1  UPF0175   Uncharacterised protein family (UPF0175)


Domain annotation for each model (and alignments):
>> UPF0175  Uncharacterised protein family (UPF0175)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.6   3.6e-07    0.0065      22      61 ..      40      78 ..       7      80 .] 0.85

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.6e-07
                        UPF0175 22 ialAvklYeegrlSlgkAaelaglsrveflelLarrgipl 61
                                     +A+klY e+   +   +++ag++  ef+elL++  ip+
  gi|119720213|ref|YP_920708.1| 40 VRAALKLYVEKG-DIRLTSRIAGMNIDEFRELLRKARIPV 78
                                   567888885543.3345689******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       788  (0.0439511); expected 358.6 (0.02)
Passed bias filter:                      600  (0.0334653); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 560.87
//
Query:       gi|119720214|ref|YP_920709.1|  [L=192]
Description: PaREP8 domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-22   80.0   2.6      2e-22   79.3   2.6    1.4  1  PaREP1    Archaeal PaREP1/PaREP8 family
  ------ inclusion threshold ------
      0.011   15.8   0.1      0.051   13.7   0.1    2.2  1  DUF1707   Domain of unknown function (DUF1707)
      0.035   12.5   0.0      0.039   12.4   0.0    1.2  1  DUF3141   Protein of unknown function (DUF3141)
      0.066   12.9   0.0       0.23   11.1   0.0    1.8  2  TMP_2     Prophage tail length tape measure protein
      0.094   12.7   0.0       0.15   12.0   0.0    1.4  1  DUF2019   Domain of unknown function (DUF2019)


Domain annotation for each model (and alignments):
>> PaREP1  Archaeal PaREP1/PaREP8 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.3   2.6   5.5e-26     2e-22       2     114 ..      66     170 ..      65     171 .. 0.97

  Alignments for each domain:
  == domain 1  score: 79.3 bits;  conditional E-value: 5.5e-26
                         PaREP1   2 rleeaekeleeAeellekGdlrqAaeKaykAvkalvkalaeknnlklleeaeekerwstkellkavaklleelgdkevvd 81 
                                    + e+ ek++ eA+el ++Gd+rqA+eK+++Av+al+k++a++       +     +wst++l ++v++ + + ++k ++d
  gi|119720214|ref|YP_920709.1|  66 YRELFEKYYAEALELKRRGDARQAGEKLWGAVTALIKLYAAE-------KGVFVAHWSTGKLDRFVTSNVGKEHRKLFRD 138
                                    6899**************************************.......78889************************** PP

                         PaREP1  82 lwklAldLHeyqfheaklelsdveskeeavkdl 114
                                    l+++A +LHe+ f+e++l+++  e++  ++ dl
  gi|119720214|ref|YP_920709.1| 139 LIDKAHRLHEN-FYEGSLDPETLEERWAEALDL 170
                                    ***********.***************999998 PP

>> DUF1707  Domain of unknown function (DUF1707)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   1.4e-05     0.051      12      37 ..     143     168 ..     141     169 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.4e-05
                        DUF1707  12 velLrealaeGrLtldEfdeRleaal 37 
                                    +++L+e + eG L+ ++++eR ++al
  gi|119720214|ref|YP_920709.1| 143 AHRLHENFYEGSLDPETLEERWAEAL 168
                                    689******************99997 PP

>> DUF3141  Protein of unknown function (DUF3141)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.1e-05     0.039     337     393 ..     109     165 ..      68     190 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.1e-05
                        DUF3141 337 ivyllhesiGhLgifvsgkvarkeheelvsaldlidvLppGlyeaeiedkkeeeeek 393
                                     v++ h s+G L  fv ++v++++ + +   +d  + L   +ye +++ ++ ee  +
  gi|119720214|ref|YP_920709.1| 109 GVFVAHWSTGKLDRFVTSNVGKEHRKLFRDLIDKAHRLHENFYEGSLDPETLEERWA 165
                                    599******************88888888999************9999887766544 PP

>> TMP_2  Prophage tail length tape measure protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   6.5e-05      0.23     146     187 ..      23      64 ..      15      75 .. 0.86
   2 ?   -0.9   0.0       0.3   1.1e+03     136     195 ..     111     170 ..      85     176 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 6.5e-05
                          TMP_2 146 ggeqlervakaaaelekatGqsvdetakelaklakdPvkaae 187
                                    +ge+l++  ++++e+++a G  vd+++++la+++ dP   +e
  gi|119720214|ref|YP_920709.1|  23 AGERLGEGEAVVKEVAEAAGWGVDDVVEDLARIGVDPSGRVE 64 
                                    5677778888999************************86655 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.3
                          TMP_2 136 laalastGkiggeqlervakaaaelekatGqsvdetakelaklakdPvkaaeklneqlhf 195
                                      a  stGk  +  +++v k  ++l + +  ++  + +++ + + dP    e  +e l +
  gi|119720214|ref|YP_920709.1| 111 FVAHWSTGKLDRFVTSNVGKEHRKLFRDLIDKAHRLHENFYEGSLDPETLEERWAEALDL 170
                                    444455666666666666666666666666666666666666666665555555555555 PP

>> DUF2019  Domain of unknown function (DUF2019)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   4.1e-05      0.15      22      74 ..      62     113 ..      47     131 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.1e-05
                                    -HHHHHHHHHHHHHHHHHHHHSTT-GGGGGGGGGGSS-HHHHHHHHHTTTTT- CS
                        DUF2019  22 eiakynrlfakmkevsaELkrrdGDqRraLlsLyehpnvqvRlkAAkatLAva 74 
                                     +++y  lf+k  + + ELkrr GD R+a  +L+      ++l AA++ + va
  gi|119720214|ref|YP_920709.1|  62 RVERYRELFEKYYAEALELKRR-GDARQAGEKLWGAVTALIKLYAAEKGVFVA 113
                                    5789****************87.**************999****999877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1217.52
//
Query:       gi|119720215|ref|YP_920710.1|  [L=278]
Description: hypothetical protein Tpen_1310 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.6e-15   55.0   0.0    1.6e-14   54.3   0.0    1.4  1  CRISPR_Cas6  CRISPR-associated endoribonuclease Cas6


Domain annotation for each model (and alignments):
>> CRISPR_Cas6  CRISPR-associated endoribonuclease Cas6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.3   0.0     9e-19   1.6e-14       1      85 [.     144     261 ..     144     262 .. 0.77

  Alignments for each domain:
  == domain 1  score: 54.3 bits;  conditional E-value: 9e-19
                                    EEEEEEE-EE......TEEESS--HHHHHHHHHHHHHHHTSS......................EECHHHHHH....... CS
                    CRISPR_Cas6   1 lrfltPtrfk......krkgllpsprlvfssllrrwnalaglkgk...................ptveeeleg....... 48 
                                    +rf+tPt+f       ++k+l+p+p ++++ l+ + ++l+g+++                    p               
  gi|119720215|ref|YP_920710.1| 144 VRFHTPTYFNplsgdkEYKVLYPDPVHMLAGLVATAHRLTGASLPkpeelastvyvagldvktpP-------Mepskpap 216
                                    79************9999999*********************97766555544444444433321.......03334444 PP

                                    .EEEEEEEE...--....HHHECCCHHHHHHHH-SSSTGGGTTT- CS
                    CRISPR_Cas6  49 .GfvGevky...sg....eleelekllrfaeylgvGkktafGlGk 85 
                                     GfvG+vk+   ++    +l+ +++ll+++e++++G ++++G+G 
  gi|119720215|ref|YP_920710.1| 217 nGFVGWVKLkarKNapsdKLSLVHGLLKLGELTNIGGNRSAGYGV 261
                                    5********7651155668888888*******************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       158  (0.00881254); expected 358.6 (0.02)
Passed bias filter:                      131  (0.0073066); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1835.46
//
Query:       gi|119720216|ref|YP_920711.1|  [L=78]
Description: hypothetical protein Tpen_1311 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    7.1e-26   90.8   0.0    7.8e-26   90.7   0.0    1.0  1  ThiP_synth  Thiamine-phosphate synthase


Domain annotation for each model (and alignments):
>> ThiP_synth  Thiamine-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.7   0.0   4.3e-30   7.8e-26       2      73 ..       4      75 ..       3      77 .. 0.97

  Alignments for each domain:
  == domain 1  score: 90.7 bits;  conditional E-value: 4.3e-30
                                   HHHHHHHHHCC--.GCC--TT-B-EEEE-ST--SGGGEEEETT-EEE-TSSEEE-S-EEETS-CHHHHHHHH CS
                     ThiP_synth  2 leralelleeeeefakliPevgsNiayalpdAksieDvaavpGRIvrvkgrvkvvgepefgasshvarvlla 73
                                   l ra+ +le ++e++ liPev+sNi+yalp+++++ Dva+v+GRI++v+gr+k+ + p+fgas h+ar++++
  gi|119720216|ref|YP_920711.1|  4 LVRAVGMLEGCPELSMLIPEVRSNIVYALPNPRTVRDVAGVEGRITVVNGRPKASSYPRFGASWHMARLIVE 75
                                   679******************************************************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       194  (0.0108205); expected 358.6 (0.02)
Passed bias filter:                      184  (0.0102627); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 595.20
//
Query:       gi|119720217|ref|YP_920712.1|  [L=105]
Description: hypothetical protein Tpen_1312, partial [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.7e-12   46.2   0.0    4.1e-12   46.0   0.0    1.1  1  ThiP_synth  Thiamine-phosphate synthase


Domain annotation for each model (and alignments):
>> ThiP_synth  Thiamine-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.0   0.0   2.3e-16   4.1e-12      85     164 ..       1      89 [.       1      90 [. 0.89

  Alignments for each domain:
  == domain 1  score: 46.0 bits;  conditional E-value: 2.3e-16
                                    EEEE--HHHH....HHHCCTTSEEEE--CCCS-CCC....T-HHHHHHHHHHHCC.S-ECEEEE--BCTB--EEEEEESS CS
                     ThiP_synth  85 inirydekil....ealeelglkvvefdreeepeev....gstmewgvaeaieel.evpdviydeGgvGkEpmiyvlgkd 155
                                    +n+r+ e+++    + + e+gl+v  +dr  ep +v    g++ +w+v+  +e++ ++p ++++  + GkEp +++lg++
  gi|119720217|ref|YP_920712.1|   1 MNLRFGEEVKgflyAYAGEKGLEVGFIDRGGEPGGVarveGASTPWKVKYLVENYgGIPGIVVEGEAPGKEPLLVILGRS 80 
                                    67888877762222567899***************99******************99*********************** PP

                                    HHHHHHHHH CS
                     ThiP_synth 156 aeevvekvl 164
                                    a ev+e ++
  gi|119720217|ref|YP_920712.1|  81 AAEVAEMAV 89 
                                    ******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       234  (0.0130515); expected 358.6 (0.02)
Passed bias filter:                      202  (0.0112667); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 812.05
//
Query:       gi|119720218|ref|YP_920713.1|  [L=89]
Description: ABC-type sulfate/molybdate transport systems ATPase component-like [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.024   14.5   0.2      0.027   14.4   0.2    1.1  1  Transglut_core3  Transglutaminase-like superfamily


Domain annotation for each model (and alignments):
>> Transglut_core3  Transglutaminase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.2   1.5e-06     0.027       8      76 ..      12      82 ..       5      84 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.5e-06
                Transglut_core3  8 rlrlarlglarlrarlreaprgarpasaeearrlgravraaarllpgrskCLpralal..alllrrrgipa 76
                                   r+ ++ l+   +++  ++++  +r ++a+   ++ ++vr+++  + + s C+++++++  ++++rr gi+a
  gi|119720218|ref|YP_920713.1| 12 RASARALATPGILLLDEPSSCIDRESRARLRGEVMKIVRSVNVATLLVSHCVEDSVVAdaVVFMRRGGIAA 82
                                   4444444444443333444444455566666899**********************964378899999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       249  (0.0138881); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 661.67
//
Query:       gi|119720219|ref|YP_920714.1|  [L=112]
Description: quinolinate phosphoribosyl transferase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.7e-14   51.5   0.0    1.1e-13   51.3   0.0    1.0  1  QRPTase_C       Quinolinate phosphoribosyl transferase, C-ter
     0.0016   17.8   1.1      0.046   13.1   1.1    2.0  1  TMP-TENI        Thiamine monophosphate synthase
  ------ inclusion threshold ------
      0.019   14.4   0.0      0.022   14.2   0.0    1.2  1  Aldolase        KDPG and KHG aldolase
      0.027   13.9   0.1      0.038   13.4   0.1    1.2  1  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
      0.099   13.3   0.0       0.17   12.6   0.0    1.4  1  Multi_Drug_Res  Small Multidrug Resistance protein
       0.12   12.7   0.0       0.19   12.0   0.0    1.4  1  HTH_Tnp_1       Transposase


Domain annotation for each model (and alignments):
>> QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.3   0.0   3.7e-17   1.1e-13      65     166 ..       7     106 ..       1     108 [. 0.91

  Alignments for each domain:
  == domain 1  score: 51.3 bits;  conditional E-value: 3.7e-17
                                    SHHHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHHT-SEEEEES--HHHHHHHHHHHHHHSTTSEEEEESS--TTTHHHH CS
                      QRPTase_C  65 siveavksvreavdkevkievevesleeleevleaeadiimLDnfsveelkkaveelkeknkrvlievSGgvtlenveey 144
                                    +++ av+++ + v+  + + vev +lee+ e+lea+a   ++D + + +l+  v ++k+  ++ ++ +SGgvt env++y
  gi|119720219|ref|YP_920714.1|   7 GVEGAVERLVARVGYRA-VGVEVVTLEEALEALEAGARYARFDGVGPATLNGWVRVVKAGFPEARVGASGGVTAENVADY 85 
                                    5889999999***9996.************************************************************** PP

                                    HCTT-SEEEECHHCHTB----E CS
                      QRPTase_C 145 aksgvdvisvgalthsvkalDi 166
                                    a+ gvdv+ ++ +  ++ +lD+
  gi|119720219|ref|YP_920714.1|  86 ARAGVDVVVTS-APFRALPLDF 106
                                    ******98655.5556677776 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   1.1   1.5e-05     0.046      96     176 ..      21      94 ..       7      97 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.5e-05
                       TMP-TENI  96 dliiGlSvhsleeaeeaealgadYigvGpifpTdtKkdaeplgleglkelaeale.....iPvvaiGGitlenvaevlea 170
                                    +  +G+ v +leea+ea ++ga Y  +  +            g ++l+ +++ ++       v a GG+t+enva+ ++a
  gi|119720219|ref|YP_920714.1|  21 YRAVGVEVVTLEEALEALEAGARYARFDGV------------GPATLNGWVRVVKagfpeARVGASGGVTAENVADYARA 88 
                                    566777777777777777777777776666............4444444444444444578999**************** PP

                       TMP-TENI 171 gadgva 176
                                    g+d v 
  gi|119720219|ref|YP_920714.1|  89 GVDVVV 94 
                                    **9875 PP

>> Aldolase  KDPG and KHG aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   7.5e-06     0.022     108     175 ..      28      95 ..      10     102 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.5e-06
                                    ESSHHHHHHHHHTT--EEEE...TTTTTTTHHHHHHHHCTTTTT-EEEEBSS--TTTHHHHHTSTTBS-EE CS
                       Aldolase 108 vstpseimlaldlGlkrlkl...fPaeasGGvkalkalagpfaqvrfiPtGGispanvrdylalpsvlvvg 175
                                    v t  e  +al+ G +  ++    Pa  +G v+++ka    f++ r+   GG++ +nv dy +++  +vv+
  gi|119720219|ref|YP_920714.1|  28 VVTLEEALEALEAGARYARFdgvGPATLNGWVRVVKA---GFPEARVGASGGVTAENVADYARAGVDVVVT 95 
                                    4566777888888877776633359999998877775...7999999999999999999999988766664 PP

>> Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   1.3e-05     0.038     165     194 ..      67      96 ..      53      99 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.3e-05
                                    ---EEEEESS--TTTCHHHHHHT--EEEES CS
                 Ribul_P_3_epim 165 ldlkievDGGvkldnieqiaeagadvlVag 194
                                     + ++ + GGv+++n++  a+ag+dv+V++
  gi|119720219|ref|YP_920714.1|  67 PEARVGASGGVTAENVADYARAGVDVVVTS 96 
                                    45789999******************9975 PP

>> Multi_Drug_Res  Small Multidrug Resistance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   5.6e-05      0.17      38      69 ..      23      54 ..       6      62 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.6e-05
                                   HHHHHHHHHHHHH-------HHHHHHHHHHHH CS
                 Multi_Drug_Res 38 gygisfllLskalkslpvsvAYavwsGiGtvl 69
                                   ++g+ ++ L  al+ l+++  Ya + G+G + 
  gi|119720219|ref|YP_920714.1| 23 AVGVEVVTLEEALEALEAGARYARFDGVGPAT 54
                                   68999************************875 PP

>> HTH_Tnp_1  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   6.5e-05      0.19      16      50 ..      31      65 ..      27      86 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.5e-05
                      HTH_Tnp_1 16 VreslepgksvsevArrhgvspnqLykWrrqyreg 50
                                   ++e+le+    ++ Ar  gv p++L  W+r +++g
  gi|119720219|ref|YP_920714.1| 31 LEEALEALEAGARYARFDGVGPATLNGWVRVVKAG 65
                                   579999999999******************98865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 831.61
//
Query:       gi|119720220|ref|YP_920715.1|  [L=371]
Description: hypothetical protein Tpen_1315 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      7e-09   35.6   0.4    0.00014   21.4   0.0    2.2  2  Cas_Cmr3  CRISPR-associated protein (Cas_Cmr3)


Domain annotation for each model (and alignments):
>> Cas_Cmr3  CRISPR-associated protein (Cas_Cmr3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.1   3.9e-06     0.069       3      42 ..       9      51 ..       7      58 .. 0.82
   2 !   21.4   0.0   7.8e-09   0.00014     133     212 ..     107     196 ..      68     305 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.9e-06
                       Cas_Cmr3  3 lePlDplffrdgrpFe...dgeearaasllfPlPsTlaGavrt 42
                                   + P+D++ fr+   F+   +g+++ a ++  PlPsTlaG++ +
  gi|119720220|ref|YP_920715.1|  9 VYPVDRVRFRRTGAFDpyaSGPATHASTMHYPLPSTLAGLLAS 51
                                   5699999999987666332777777**************9987 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 7.8e-09
                       Cas_Cmr3 133 prpkkkpkplpaylsleglskwLrgelpesselvkeed........lltkeeRigialdpetrtaeegalyqteglrlk. 203
                                      ++++p+ l+ayl  + l+ +L+g ++  sel+++            ++e R+g+ l+++ + a+eg+ly++  l lk 
  gi|119720220|ref|YP_920715.1| 107 ALRRAVPEALEAYL--DALEAYLEGSASRGSELLEKAGralrgayaEAKPEWRMGVGLERAVKVAREGYLYSAAELDLKa 184
                                    45666777777776..68999**********9999766999999999********************************6 PP

                       Cas_Cmr3 204 ...edvrlallv 212
                                        d ++a+ +
  gi|119720220|ref|YP_920715.1| 185 algADAAVAAEI 196
                                    633333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 2383.86
//
Query:       gi|119720221|ref|YP_920716.1|  [L=978]
Description: hypothetical protein Tpen_1316 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-27   96.2   0.0      3e-27   95.0   0.0    1.6  1  DUF3692       CRISPR-associated protein
  ------ inclusion threshold ------
       0.65   10.4   2.8       0.79   10.1   1.1    1.9  2  Rubrerythrin  Rubrerythrin


Domain annotation for each model (and alignments):
>> DUF3692  CRISPR-associated protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.0   0.0   3.4e-31     3e-27       2     110 ..     205     340 ..     204     341 .. 0.88

  Alignments for each domain:
  == domain 1  score: 95.0 bits;  conditional E-value: 3.4e-31
                                    EEEEEEESHHHHHS-SSHHHHHHHHHHHHHHHHHHHHHHHHHT-GGGEEES--TT-HHHHHHTS-............... CS
                        DUF3692   2 lvvsigpVqefIaaaRktrDlWagSyllSylawkaikelvekyGpdvliyPslrgnplvdawlle............... 66 
                                    +vv+ ++Vqe+I++aRk+ DlWa+S++ S ++w++++++ve +Gpdv+++Pslrgn++++awll                
  gi|119720221|ref|YP_920716.1| 205 VVVDYAGVQEYISKARKALDLWASSWVASLVTWATVQPFVELLGPDVVVTPSLRGNWFYAAWLLGrlrgtgaygaareaa 284
                                    899*************************************************************9888888888888888 PP

                                    ....--GGGGGSB---SEEEEEEE.TT..THHHHHHH......HHHHHHHHHHHHH CS
                        DUF3692  67 ....kleeeletalipnrfvlilpkee..eaeelaee......veealkeawkeia 110
                                         ++  ++++++p r+vl+lp+     +++l +e      +e++++eaw++++
  gi|119720221|ref|YP_920716.1| 285 rlayGYSGFPRHPIMPTRAVLFLPEVPgaLEDALRDEaslrgfIERKASEAWSKAV 340
                                    88777777****************8775422244444777888*********9875 PP

>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   1.1   8.8e-05      0.79      43     122 ..     563     642 ..     549     647 .. 0.91
   2 ?   -1.7   0.0      0.38   3.4e+03       7      31 ..     886     910 ..     883     920 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 8.8e-05
                                    HHHHHHHHHHHHHCSTTHH..B.SSBBS-------TTGGHHHHHHHHHHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHH CS
                   Rubrerythrin  43 reHakilnklleklepele.levkekvreyaeakpkflttaknLeeaiegayaeeeemyrfyeelaekegneeakklfkk 121
                                    ++H++ ++k+l  +++++e  +++   r y  a  ++ + a  L  a+ ++ a e+e  + ++++++  g+ ea++ +++
  gi|119720221|ref|YP_920716.1| 563 ERHREAVAKVLAGFQWDHEyYSRRLARRAYRRAGREVALVALRLL-AALIEAATEQEYRERFAKALDALGDGEARREIEE 641
                                    58*****************999999999999999********999.8899999999999*********999999987776 PP

                                    H CS
                   Rubrerythrin 122 l 122
                                    l
  gi|119720221|ref|YP_920716.1| 642 L 642
                                    6 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.38
                                    HHHHHHHHHHHHHHHHCHHTT-HHH CS
                   Rubrerythrin   7 iagEssarrlYkelaekakegypqi 31 
                                    ++gE s   +Y +++ +++e  + +
  gi|119720221|ref|YP_920716.1| 886 LRGEVSSSLFYDFFSWRFDELVERL 910
                                    689***********99998544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (978 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.68u 0.28s 00:00:00.96 Elapsed: 00:00:00.44
# Mc/sec: 6727.88
//
Query:       gi|119720222|ref|YP_920717.1|  [L=295]
Description: CRISPR-associated RAMP Cmr6 family protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.8e-09   37.9   0.3    1.3e-08   35.2   0.3    2.1  1  RAMPs        RAMP superfamily
  ------ inclusion threshold ------
      0.026   15.2   0.6      0.067   13.9   0.5    1.7  1  CRISPR_Cas6  CRISPR-associated endoribonuclease Cas6
        0.1   13.2   0.1       0.18   12.3   0.1    1.4  1  Cas_Cas6     CRISPR associated protein Cas6


Domain annotation for each model (and alignments):
>> RAMPs  RAMP superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.3   2.2e-12   1.3e-08      26     213 .]      99     260 ..      85     260 .. 0.69

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 2.2e-12
                                    ..---S----HHHHHHHHHHHHHHHHH.HHHTT-HHHHH.H.........HHHHHH--S...SS--SEEEEE........ CS
                          RAMPs  26 rdkgglPyIPGSSlkGalRsalekllgsekkekkdeysrkkekqrvkkgdleeaiFGneeeskiagrvffeDarpvkipg 105
                                    +++ +lP+IPGSS+kGa+R  +e+  ++                       ++ +FG   +s++ag + f Da+pv+   
  gi|119720222|ref|YP_920717.1|  99 DHVLDLPFIPGSSVKGAVRAVAERASRD----------------------DADVLFGRGGDSGWAGLLLFFDAYPVEAGD 156
                                    567789*************999988762......................789***99999**************99865 PP

                                    ...............EEEEEEEEEEEEEEEEE--SSS-EEEEEE....-TT-EEE.EEEEESS................. CS
                          RAMPs 106 qileeskqikstpspklsgselrelldhsterrtrvaidrktktngk.kkgglft.leaipae.........rikfsgri 174
                                    + l e+            ++   + ++++  +r++  ++       +   g+ f+ + a++++         r+      
  gi|119720222|ref|YP_920717.1| 157 RLL-EP------------DIVTPHYSRGGRPVRFEYEVEPVPVAHVSiAPGAVFRfVVAVEPGggvlheevdRALANICG 223
                                    443.33............33333444444444444444443333333433555555666666666666666666677777 PP

                                    ......HHHHHHHHHHHHHH.HHH---STTTTBTTT-EE CS
                          RAMPs 175 rlenlsdeelgallklLdlldlhflglGggkplGfGsve 213
                                    rl  +      +ll lL+     + g+G++++ G+G++e
  gi|119720222|ref|YP_920717.1| 224 RLGVQGGGPASLLLGLLEYA--LASGVGARTSQGYGRFE 260
                                    77777777777777777777..88888888888888875 PP

>> CRISPR_Cas6  CRISPR-associated endoribonuclease Cas6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.5   1.1e-05     0.067      51      85 ..     222     258 ..     173     259 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.1e-05
                                    EEEEEE--..HHHECCCHHHHHHHH-SSSTGGGTTT- CS
                    CRISPR_Cas6  51 vGevkysg..eleelekllrfaeylgvGkktafGlGk 85 
                                    +G++  +g  + + l +ll++a ++gvG +t+ G+G+
  gi|119720222|ref|YP_920717.1| 222 CGRLGVQGggPASLLLGLLEYALASGVGARTSQGYGR 258
                                    55555544457777899*******************7 PP

>> Cas_Cas6  CRISPR associated protein Cas6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1     3e-05      0.18     124     146 .]     239     261 ..     237     261 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3e-05
                                    HHHHHHHC-SCS-CCCT-S-EEE CS
                       Cas_Cas6 124 llklaydaGlGeknsqGFGmvev 146
                                    ll++a+  G+G+++sqG+G +ev
  gi|119720222|ref|YP_920717.1| 239 LLEYALASGVGARTSQGYGRFEV 261
                                    899****************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1938.04
//
Query:       gi|119720223|ref|YP_920718.1|  [L=587]
Description: hypothetical protein Tpen_1318 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.039   14.0   0.1        5.4    7.0   0.0    2.3  2  RAMPs     RAMP superfamily


Domain annotation for each model (and alignments):
>> RAMPs  RAMP superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0    0.0003       5.4      37      84 ..      55     107 ..      48     165 .. 0.78
   2 ?    4.7   0.1    0.0015        27     185     212 ..     265     292 ..     201     293 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0003
                                    HHHHHHHHHHHHHHHH.HHHTT-HHHHH.H........................HHHHHH--S CS
                          RAMPs  37 SSlkGalRsalekllgsekkekkdeysrkkekqrvkkgd...............leeaiFGne 84 
                                     S+kG lR++ +++++s     +        +q + +g+               l+eaiFG  
  gi|119720223|ref|YP_920718.1|  55 RSVKGLLRWLTRAVVASFV--PD--------DQLASHGYaavecfpncgsskpgLVEAIFGTV 107
                                    59**********9999432..22........22233444555556666666666888888865 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0015
                                    HHHHHHHHHH.HHH---STTTTBTTT-E CS
                          RAMPs 185 gallklLdlldlhflglGggkplGfGsv 212
                                    + l++lL    l  +g+G  +++GfG++
  gi|119720223|ref|YP_920718.1| 265 KRLEELLLVYGLLLFGIGKASSRGFGRF 292
                                    33344444445779************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (587 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 4011.06
//
Query:       gi|119720224|ref|YP_920719.1|  [L=165]
Description: CRISPR-associated Cmr5 family protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-05   24.6   0.0    3.8e-05   24.0   0.0    1.3  1  Cas_Cmr5  CRISPR-associated protein (Cas_Cmr5)


Domain annotation for each model (and alignments):
>> Cas_Cmr5  CRISPR-associated protein (Cas_Cmr5)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   2.1e-09   3.8e-05      12      94 ..      17      91 ..       9     110 .. 0.69

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 2.1e-09
                                   HHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHHHHHCTSS...STTTCHHHHHH CS
                       Cas_Cmr5 12 kvkelkekskkkekkykslvkklPalIltnGLgqalAfllskgkkkkedahkkllehlaewlkkeksaskkkkgendllkel 93
                                   +v++l +  +   ++++ +v+++P l+  +GL++alAf+lsk       + + +l++ ++ +++      + + ++++l+ l
  gi|119720224|ref|YP_920719.1| 17 AVRDLCGGAEGCGESFQRRVEDFPGLVSAAGLVPALAFYLSKV------EDYGVLRDFYSLFSSG--SLPRDARREKMLEDL 90
                                   5555555556677899**************************6......5555666666666666..444444445555555 PP

                                   H CS
                       Cas_Cmr5 94 l 94
                                   +
  gi|119720224|ref|YP_920719.1| 91 R 91
                                   4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1216.28
//
Query:       gi|119720225|ref|YP_920720.1|  [L=336]
Description: CRISPR-associated RAMP Cmr4 family protein family protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-16   61.0   0.0    2.3e-16   60.5   0.0    1.2  1  RAMPs     RAMP superfamily


Domain annotation for each model (and alignments):
>> RAMPs  RAMP superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.5   0.0   1.3e-20   2.3e-16       5     212 ..      28     329 ..      25     330 .. 0.94

  Alignments for each domain:
  == domain 1  score: 60.5 bits;  conditional E-value: 1.3e-20
                                    SS-EE----..............---S----HHHHHHHHHHHHHHHHH.HHHTT-HHHHH.H.........HHHHHH--S CS
                          RAMPs   5 ltPlhiGdgkisdekeespefrdkgglPyIPGSSlkGalRsalekllgsekkekkdeysrkkekqrvkkgdleeaiFGne 84 
                                     tP+h G+g ++   +++p++rd+ g+P ++GSS+kGal+  l++ +g                        ++  FG+e
  gi|119720225|ref|YP_920720.1|  28 YTPVHAGSG-RGYGFVDLPVQRDSLGYPEVWGSSVKGALKGFLLRSVGV----------------------EAKGFFGSE 84 
                                    59*******.******************************887777772......................677899*** PP

                                    .....SS--SEEEEE................................................................. CS
                          RAMPs  85 ..eeskiagrvffeDarpvkipgqileeskqikstpsp.......................................... 120
                                      e+   +g   +   +++++p+++++++ ++++tp+                                           
  gi|119720225|ref|YP_920720.1|  85 peESPTVPGLAVVTGLSLLAVPVPSVRRGIVYVTTPYLasrvagyvdvvkrlrgfegveslafpleafekalvevveags 164
                                    *999**************************************************************************** PP

                                    ...........................................................EEEEEEEEEEEEEEEEE--SS CS
                          RAMPs 121 ...........................................................klsgselrelldhsterrtrv 141
                                                                                               +l++   r ++++ + + +r+
  gi|119720225|ref|YP_920720.1| 165 slgegeaaaskgvavdgavyvsgsrvrvsrelefpgglddalrslnvlysykkvfgnlvVLPDGVGRSVVNGALQVVYRN 244
                                    ******************************************************************************** PP

                                    S-EEEEEE...-TT-EEEEEEEESS...............................HHHHHHHHHHHHHH.HHH---STT CS
                          RAMPs 142 aidrktktngkkkgglftleaipae.................rikfsgrirlenlsdeelgallklLdlldlhflglGgg 204
                                    ++ + tkt++   g+l+++e++p +                  ++    + + +l +++ g+l  +L ++ + +l +Gg+
  gi|119720225|ref|YP_920720.1| 245 RLSDATKTVER--GALWSEEYLPYGsllvgavmvkdfeklrgLLEAGRYEAQLRLYESAWGKLRSILGAM-NGYLVVGGK 321
                                    **********9..**********************88887766666666777777788888888888888.********* PP

                                    TTBTTT-E CS
                          RAMPs 205 kplGfGsv 212
                                    +++G+G +
  gi|119720225|ref|YP_920720.1| 322 ETVGKGVL 329
                                    ******87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2351.35
//
Query:       gi|119720226|ref|YP_920721.1|  [L=327]
Description: CRISPR-associated Cas1 family protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-27   96.0   0.0    3.9e-27   95.1   0.0    1.4  1  Cas_Cas1  CRISPR associated protein Cas1


Domain annotation for each model (and alignments):
>> Cas_Cas1  CRISPR associated protein Cas1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.1   0.0   2.2e-31   3.9e-27      11     255 ..      13     254 ..       4     277 .. 0.84

  Alignments for each domain:
  == domain 1  score: 95.1 bits;  conditional E-value: 2.2e-31
                                    EEETTEEEEEESSEEEEEEECCCEEEEEEEST.EEEEHHHHHHHHHTT-EEEEE-TTS-EEEEEEESSSSTHHHHHHHHH CS
                       Cas_Cas1  11 rkkgerlvvekegeekkeiplediesivifge.vslstkalrllaekgipvvflsengkylgrlepeesgnvelrraQyr 89 
                                    ++++++ vv k g+++ e  l+d++ ++++g+ +++s+++   la +gip+++l  +g++   l p  ++  ++r  Qy 
  gi|119720226|ref|YP_920721.1|  13 TVSSRSTVVIKSGNRVFERALRDVDAVLVVGSgIKISSSLPPVLALHGIPLSILA-KGHVAVLLNPVGTKYNNYRALQYT 91 
                                    556666677777778**************************************97.6899999999999999******** PP

                                    HHHSHHHHHHHHHHHHHHHHHHHHHHHHHCCHHCTTHHHHCHCHHHHHHHHHHHH-HSHHHHHHHHHHHHHHHHHHHHHH CS
                       Cas_Cas1  90 aaddeekrlelakkivagklenqrkvlrrlkrdreeeeleeaieeleelleklekaesleeLrgiEGeaakaYfeafdkl 169
                                    + +++  +l++a + ++++++ +++++r+   + +   l e  +         + a+  + +r  E++a+++ ++++ kl
  gi|119720226|ref|YP_920721.1|  92 LPKNK--ALAIALEYLKSRVRGMASIIRNRGGRLPA--LPEPPDPAL----YEDPARLESDIRSWEAAASNTLWDEVFKL 163
                                    97665..5*******************999999943..333333221....2244555678******************* PP

                                    CS........CGGS-SS-SSSS-SSHHHHHHHHHHHHHHHHHHHHHHTSS--TT--SSS--TTSS-HHHHHHHHHHHHHH CS
                       Cas_Cas1 170 lk........eefefegRsrrppkDpvNalLsfgYtllysevlsaieavgLdPyiGfLHedrpgrpsLalDLmEefRpll 241
                                    l+        e++ f gR+  ++ Dp+N  +s +Y++ly+  ++a+ a+gLdP++GfLH+++++   La+D +E f+p l
  gi|119720226|ref|YP_920721.1| 164 LDpsaarelrERYGFAGRKP-GHPDPLNKAISAMYAVLYTLSTKALVAAGLDPTYGFLHRTQYSV-PLAFDYAEAFKP-L 240
                                    *9999999977999999965.457***********************************999975.6***********.7 PP

                                    CHHHHHHHHHTTSS CS
                       Cas_Cas1 242 vDrlvlslinkrql 255
                                    + +++l l+n++ l
  gi|119720226|ref|YP_920721.1| 241 AVEAALDLVNEEGL 254
                                    7788999*999866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.21s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 2485.19
//
Query:       gi|119720227|ref|YP_920722.1|  [L=93]
Description: CRISPR-associated Cas2 family protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.3e-15   55.7   0.0    5.2e-15   55.4   0.0    1.1  1  CRISPR_Cas2     CRISPR associated protein Cas2
  ------ inclusion threshold ------
      0.019   15.0   0.1      0.026   14.6   0.1    1.2  1  Cas_Cas2CT1978  CRISPR-associated protein (Cas_Cas2CT1978)
        0.1   12.7   0.0       0.87    9.7   0.0    1.9  2  DUF72           Protein of unknown function DUF72


Domain annotation for each model (and alignments):
>> CRISPR_Cas2  CRISPR associated protein Cas2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.4   0.0   8.6e-19   5.2e-15       1      75 [.       1      73 [.       1      74 [. 0.97

  Alignments for each domain:
  == domain 1  score: 55.4 bits;  conditional E-value: 8.6e-19
                                   EEEEEEEECHCHHHHHHHHHHHHHHTTEEEEETTEEEEEESHHHHHHHHHHHHHHSHTTTCEEEEEEEETCHHHT CS
                    CRISPR_Cas2  1 mlvlvvYDikedrkrrrkvakilkkyGfqrvQySVFegelseaqleklkkrlkkiidpeedsiriykltekqfek 75
                                   m v+v+YDi +d+ rr +++++l++ G+ rv  SV+ g  + + +e +++r k+i+++  ds+ ++ ++e+ +++
  gi|119720227|ref|YP_920722.1|  1 MIVIVAYDI-SDEDRRGRLRRYLRRLGLARVNRSVYAGPGTATTAELVAERAKEIVEEG-DSVFVIVVREDEYQR 73
                                   899******.***********************************************98.9*****9**999976 PP

>> Cas_Cas2CT1978  CRISPR-associated protein (Cas_Cas2CT1978)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   4.4e-06     0.026       1      62 [.       1      68 [.       1      85 [. 0.78

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.4e-06
                                   EEEEEEES--HH.HHHHHHHHS.....EEEETTEEEEEE-HHHHHHHHHHHHHH-TSSEEEEEEE-SS CS
                 Cas_Cas2CT1978  1 mvVivleavpar.lRGeLtrwl.....lEvragVyvgrvsarVreklwerveekieegsavmvysann 62
                                   m+Viv+ +++++  RG+L r l       v+ +Vy g  +a  +e + er +e +eeg  v v   ++
  gi|119720227|ref|YP_920722.1|  1 MIVIVAYDISDEdRRGRLRRYLrrlglARVNRSVYAGPGTATTAELVAERAKEIVEEGDSVFVIVVRE 68
                                   9999999998752789999986332226899************************9999887765544 PP

>> DUF72  Protein of unknown function DUF72
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00015      0.87       7      42 ..      13      49 ..       7      55 .. 0.82
   2 ?    4.9   0.0    0.0042        25     179     205 ..      44      70 ..      40      76 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00015
                                   CCC.HHHHHCCT-SEEEE-HHCCSSS-HHHHHHHHCT CS
                          DUF72  7 kke.rLeyYarhfntVEinstFYalpspetvakwaaq 42
                                   +++ rL+ Y r++ +  +n++ Ya p ++t a+ +a+
  gi|119720227|ref|YP_920722.1| 13 DRRgRLRRYLRRLGLARVNRSVYAGPGTATTAELVAE 49
                                   4555********************9999988877665 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0042
                                    HHHHHHHHHHHHTCSSEEEEEE-SBCC CS
                          DUF72 179 laewaerikawaaegrevyvffnndae 205
                                     + +aer+k++ +eg++v+v++  ++e
  gi|119720227|ref|YP_920722.1|  44 AELVAERAKEIVEEGDSVFVIVVREDE 70 
                                    56789****************988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 691.43
//
Query:       gi|119720228|ref|YP_920723.1|  [L=701]
Description: DEAD/DEAH box helicase domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-06   26.9   0.0    0.00014   21.7   0.0    2.5  2  DEAD      DEAD/DEAH box helicase
  ------ inclusion threshold ------
      0.023   14.7   0.0        0.3   11.1   0.0    2.3  2  ResIII    Type III restriction enzyme, res subunit


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   1.5e-08   0.00014       1      86 [.      30     111 ..      30     125 .. 0.84
   2 ?    2.6   0.0     0.012     1e+02     126     173 ..     248     289 ..     190     293 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.5e-08
                                    -HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTT.STSEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                           DEAD   1 tdiQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkky.idlrvl 79 
                                    t+ Q e+  ++ +  dvl+ a+TGsGKTl  l+     +   +g++ p  + + P   L +++++++ + +++ ++ r l
  gi|119720228|ref|YP_920723.1|  30 TEFQVEVSRELGKRSDVLLVAPTGSGKTLTLLLSPG--L---DGEDFPGFVALYPNNVLLQNQMETVASALSEaLGARPL 104
                                    577899999999999**************9877555..3...6999999************9999999988876777777 PP

                                    EEETTSS CS
                                    xxxxxxx RF
                           DEAD  80 liiggva 86 
                                      +gg++
  gi|119720228|ref|YP_920723.1| 105 EGFGGDS 111
                                    7777765 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.012
                                    EEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSEEEEEESSBSHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD 126 VlDEadrlldqgfsdfinrilnqlpqitcdgklqrqvivlSATlpkdv 173
                                     +DE + +      d ++++++ +   ++d++l   v++ SAT+ +d+
  gi|119720228|ref|YP_920723.1| 248 FVDEFHLYGPY-EVDALHAVISMF---KSDTNLP--VVFSSATPADDI 289
                                    57889888887.666677777777...5555655..*******99664 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   3.3e-05       0.3      23      43 ..      42      62 ..      26     100 .. 0.70
   2 ?    0.9   0.0     0.044     4e+02      47     146 ..     165     257 ..     157     287 .. 0.47

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.3e-05
                                   TTSEEEEEESTTSTHHHHHHH CS
                         ResIII 23 rdkrglikmaTGtGKTlvaak 43
                                   ++  +l++++TG+GKTl+++ 
  gi|119720228|ref|YP_920723.1| 42 KRSDVLLVAPTGSGKTLTLLL 62
                                   56689************9864 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.044
                                    HH-S.....-EEEEESSH..HHHHHHHHHGGGGTGG....GEEEESSS-B--...........-SEEEEEHHHHHHTH.. CS
                         ResIII  47 rllkkgkeekflflvprk..slleqtleefkkflseaykeigkkvsgdkkka....kekdstnkkilvttiqsldadsee 120
                                    +l++kg+  +++f  p +   ++  ++++f+++ ++ ++       g+ ++a     ++ +t +++ +++iq ++++   
  gi|119720228|ref|YP_920723.1| 165 KLSRKGGLYHVVFATPDTylLIYTGAYRDFEDVGKTVHNLLVSLAAGKDERAledaLRSTKTATRFELSKIQGVKERV-- 242
                                    555555555666666655334455555666666666554433333333333333333444555555555555444443.. PP

                                    ......HHHTTT-SEEEEETGGGTTS CS
                         ResIII 121 eeeeseellrdrfdviiiDEaHrlga 146
                                                   +++DE H +g 
  gi|119720228|ref|YP_920723.1| 243 -----------LVHPVFVDEFHLYGP 257
                                    ...........222456666665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (701 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 4722.11
//
Query:       gi|119720229|ref|YP_920724.1|  [L=226]
Description: hypothetical protein Tpen_1324 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1566.13
//
Query:       gi|119720230|ref|YP_920725.1|  [L=374]
Description: hypothetical protein Tpen_1325 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.9e-07   28.7   0.1    1.6e-05   24.0   0.0    2.1  2  Csc2             Csc2 Crispr
  ------ inclusion threshold ------
      0.019   13.9   0.0      0.034   13.1   0.0    1.3  1  DDE_Tnp_ISAZ013  Rhodopirellula transposase DDE domain
      0.033   14.6   0.8         12    6.4   0.1    2.4  2  Phage_holin_6_1  Bacteriophage holin of superfamily 6 (Holin_


Domain annotation for each model (and alignments):
>> Csc2  Csc2 Crispr
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    2.7   0.0    0.0086        51       8      59 ..      31      88 ..      27     106 .. 0.75
   2 !   24.0   0.0   2.6e-09   1.6e-05      97     217 ..     151     273 ..     141     343 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.0086
                           Csc2  8 lpkgkyvhlvllRetqsfpifqtdge....lnkarvqaGiedkeki..sRlvmfKRKq 59
                                   +pk++ +++v l ++  + +++t+g     + + + ++G  +   i  ++l+ + R+q
  gi|119720230|ref|YP_920725.1| 31 FPKAHRIEVVFLVRAANYLLLRTEGAgtinMTTLEYSGGAMEVPVIqpQKLMAVTRRQ 88
                                   789999*****999***********988666666777776665555223555556665 PP

  == domain 2  score: 24.0 bits;  conditional E-value: 2.6e-09
                           Csc2  97 kcpDcilYGfAigdsg.........sekskvvtddAfsllayeesveeftlnavfetGtmsekgeassalnesdhikPev 167
                                     cp c ++G A+ ++            k++v  d Af+   +++ ++  t n v  +G +s +g    al ++ h+ P++
  gi|119720230|ref|YP_920725.1| 151 FCPHCTIFGAALTEQHnekfgglsiGIKTRVRFDPAFA---TQRRITPETHNKVT-EGHLSMTG---QALFSEVHVEPGT 223
                                    599********99988777778877789*********7...56778889999999.58887766...5899********* PP

                           Csc2 168 tFpdvvtlkDvtedellYvlgnilrtrrYGAqesRtGkvknellgivfsd 217
                                    +F     l D te el+  l  +   r  G ++   G+v+ e+lg+  ++
  gi|119720230|ref|YP_920725.1| 224 VFIGRAELVDLTEPELVATLYSLATLRELGGRSGIYGTVRVEILGVKAGK 273
                                    **********************************************8775 PP

>> DDE_Tnp_ISAZ013  Rhodopirellula transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   5.8e-06     0.034      19      86 ..     273     340 ..     268     347 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.8e-06
                DDE_Tnp_ISAZ013  19 rwttkslrklaeeLkeqghkvsaetvaelLkelgyslqsnrKtkegkkhpdrdaqFekinekvkeaqe 86 
                                    ++++ ++++la+e   +g++  ++ ++e L++lg++   n+K  +  +h+d +  F+ + ++  ++ e
  gi|119720230|ref|YP_920725.1| 273 KYASTTAYDLAAENAGKGYEEVKKNLKERLEKLGFTPVDNSKLLAAVDHKDPNGLFKDLWRSSIDFAE 340
                                    8999*****************************************************99887777665 PP

>> Phage_holin_6_1  Bacteriophage holin of superfamily 6 (Holin_LLH)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1     0.002        12      44      92 ..     272     319 ..     260     321 .. 0.73
   2 ?    6.3   0.1    0.0021        13      43      70 ..     338     365 ..     334     373 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.002
                Phage_holin_6_1  44 aknaVkaveqvake.dakgeeKkeeAleklkellkekgi.sitddeleglI 92 
                                     k a++ ++++a e ++kg    ee++++lke+l+++g+  +++++l +++
  gi|119720230|ref|YP_920725.1| 272 GKYASTTAYDLAAEnAGKG---YEEVKKNLKERLEKLGFtPVDNSKLLAAV 319
                                    5667778888887733333...689**************777777777666 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0021
                Phage_holin_6_1  43 iaknaVkaveqvakedakgeeKkeeAle 70 
                                     a++ Vk+ve+++ ++ kg  Kk+  ++
  gi|119720230|ref|YP_920725.1| 338 FAEKMVKWVEELKGGGQKGSGKKSRSKK 365
                                    48999******************98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.22s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 2811.36
//
Query:       gi|119720231|ref|YP_920726.1|  [L=158]
Description: hypothetical protein Tpen_1326 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
     0.0029   17.2   0.0     0.0039   16.8   0.0    1.2  1  PCIF1_WW    Phosphorylated CTD interacting factor 1 WW domain
  ------ inclusion threshold ------
      0.055   14.0   0.0      0.092   13.3   0.0    1.4  1  YdaT_toxin  Putative bacterial toxin ydaT


Domain annotation for each model (and alignments):
>> PCIF1_WW  Phosphorylated CTD interacting factor 1 WW domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   4.3e-07    0.0039      56     114 ..      80     140 ..      61     153 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4.3e-07
                       PCIF1_WW  56 gvsfecfAsPlncyfeqycsafpdtDayFGsvGsffdf....kpasgsfeanPPfveevlera 114
                                    +v  ecfAs l+  +++++ a +d+    Gs+ +++++     ++  ++  +PP+ve++l+++
  gi|119720231|ref|YP_920726.1|  80 RVARECFASLLEGLLRKFVEASKDI--SVGSRIELMNIvvssIAEMAMHRSFPPYVEQFLSEV 140
                                    6899****************99665..67****99987444234448999********99886 PP

>> YdaT_toxin  Putative bacterial toxin ydaT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0     1e-05     0.092      28      74 ..      63     109 ..      57     123 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1e-05
                     YdaT_toxin  28 eLtPail.avLPleyrarllnvdsfmsrlavlekeiseakvavllgap 74 
                                    eL+P i  a +P e r+r+   ++f s+l  l + + ea   + +g+ 
  gi|119720231|ref|YP_920726.1|  63 ELIPEIArAHIPDELRSRV-ARECFASLLEGLLRKFVEASKDISVGSR 109
                                    78999863779********.********************99999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1126.68
//
Query:       gi|119720232|ref|YP_920727.1|  [L=616]
Description: hypothetical protein Tpen_1327 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (616 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.59u 0.25s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 4040.63
//
Query:       gi|119720233|ref|YP_920728.1|  [L=195]
Description: ABC transporter related [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.3e-18   65.9   0.0    7.6e-18   65.4   0.0    1.2  1  ABC_tran      ABC transporter
    7.2e-09   35.9   0.0    0.00073   19.4   0.0    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    0.00016   21.3   0.0    0.00027   20.6   0.0    1.3  1  AAA_29        P-loop containing region of AAA domain
    0.00028   21.3   0.0    0.00034   21.0   0.0    1.3  1  AAA_16        AAA ATPase domain
     0.0025   18.1   0.0      0.003   17.8   0.0    1.3  1  AAA_22        AAA domain
     0.0033   17.9   0.1     0.0052   17.3   0.1    1.2  1  AAA_23        AAA domain
     0.0038   17.4   0.0     0.0054   16.9   0.0    1.5  1  AAA_33        AAA domain
     0.0081   16.4   0.0      0.014   15.6   0.0    1.5  1  AAA_28        AAA domain
  ------ inclusion threshold ------
      0.011   15.6   0.0      0.022   14.7   0.0    1.4  1  RsgA_GTPase   RsgA GTPase
      0.019   14.3   0.0      0.031   13.7   0.0    1.3  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
       0.02   14.5   0.0      0.027   14.1   0.0    1.2  1  AAA_25        AAA domain
      0.021   15.4   0.0      0.032   14.8   0.0    1.3  1  AAA_18        AAA domain
      0.023   14.4   0.0      0.023   14.4   0.0    1.1  1  AAA_15        AAA ATPase domain
      0.024   14.4   0.0      0.034   13.9   0.0    1.2  1  AAA_24        AAA domain
      0.026   14.6   0.0      0.038   14.0   0.0    1.3  1  AAA_14        AAA domain
       0.03   14.2   0.0      0.038   13.9   0.0    1.2  1  ATPase_2      ATPase domain predominantly from Archaea
      0.032   14.6   0.0      0.062   13.7   0.0    1.5  1  AAA           ATPase family associated with various cellular 
      0.056   13.1   0.1      0.091   12.4   0.1    1.3  1  SRP54         SRP54-type protein, GTPase domain
      0.067   13.1   0.0       0.12   12.3   0.0    1.4  1  NACHT         NACHT domain
      0.075   12.5   0.0       0.12   11.9   0.0    1.3  1  AAA_7         P-loop containing dynein motor region
       0.09   13.2   0.0       0.13   12.6   0.0    1.3  1  RNA_helicase  RNA helicase
       0.12   12.4   0.0       0.19   11.7   0.0    1.3  1  TsaE          Threonylcarbamoyl adenosine biosynthesis protei
       0.13   12.2   0.0       0.22   11.5   0.0    1.4  1  AAA_5         AAA domain (dynein-related subfamily)
       0.16   12.2   0.0       0.27   11.5   0.0    1.4  1  SbcCD_C       Putative exonuclease SbcCD, C subunit
       0.18   11.7   0.0        0.3   11.0   0.0    1.4  1  NTPase_1      NTPase
       0.25   10.5   0.0       0.48    9.6   0.0    1.4  1  NB-ARC        NB-ARC domain
       0.27   11.6   0.0       0.41   11.0   0.0    1.2  1  zf-UBP        Zn-finger in ubiquitin-hydrolases and other pro


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.4   0.0   1.1e-20   7.6e-18       2     136 ..      17     150 ..      16     151 .. 0.82

  Alignments for each domain:
  == domain 1  score: 65.4 bits;  conditional E-value: 1.1e-20
                                    EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                       ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                    k ++l++++g+ +a++G+nG GK+tLlk+l+ ll+p eG +ll+g+  ++      r++i +l++   +  ++t+++   
  gi|119720233|ref|YP_920728.1|  17 KALNLQFERGSAIAFFGPNGVGKTTLLKTLSTLLEPLEGYVLLNGEAAEK-----RRQRIFYLTELIDVPLRVTAKQYvd 91 
                                    6799*************************************999877655.....9**********99999998877744 PP

                                    HHHTC..HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTS..SEEEEESTT CS
                                    xxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxx RF
                       ABC_tran  80 esdee..iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkp..kllllDEpt 136
                                    +  +     + +++l+   l+  + + +  +LS G+++r +la+al+ +p  +l++lD+p+
  gi|119720233|ref|YP_920728.1|  92 A--VSgfYPDSIDSLEALRLAGVPPNVKLGKLSMGMRRRAQLAAALAVAPyvELMCLDDPF 150
                                    2..33554444555555555555555567******************998556899***96 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   1.1e-06   0.00073       3      23 ..      30      50 ..      29      85 .. 0.86
   2 !   14.6   0.0   3.3e-05     0.022     232     283 ..     116     166 ..     113     176 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.1e-06
                         AAA_21  3 vliGpNgsGKSnLLdaldlla 23
                                   ++ GpNg+GK++LL++l+ l 
  gi|119720233|ref|YP_920728.1| 30 AFFGPNGVGKTTLLKTLSTLL 50
                                   689**************9885 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 3.3e-05
                         AAA_21 232 lparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellk 283
                                    + + +lS+G++r + l++al+ a+    l ++D+p  g + +  +r+le +k
  gi|119720233|ref|YP_920728.1| 116 VKLGKLSMGMRRRAQLAAALAVAPYV-ELMCLDDPFVGVDAQSSSRILEHFK 166
                                    567899*******************9.**************99999998776 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0     4e-07   0.00027      17      55 ..      21      60 ..      15      66 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 4e-07
                         AAA_29 17 ieidlkgatlltGpsGsGKSTllDAiqalLvpak.kvrfN 55
                                   +++++ +a+ + Gp+G+GK+Tll  +++lL p +  v  N
  gi|119720233|ref|YP_920728.1| 21 LQFERGSAIAFFGPNGVGKTTLLKTLSTLLEPLEgYVLLN 60
                                   5677555999********************9977556555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   5.1e-07   0.00034      23      76 ..      25      81 ..      13     174 .. 0.70

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 5.1e-07
                         AAA_16 23 rpelvllsGesGvGKsslvrellralekdggif.lrgkcdqlesa.ipysa.laqal 76
                                   r++++ + G+ GvGK++l+++l + le  +g++ l+g++ + +++ i y++ l+++ 
  gi|119720233|ref|YP_920728.1| 25 RGSAIAFFGPNGVGKTTLLKTLSTLLEPLEGYVlLNGEAAEKRRQrIFYLTeLIDVP 81
                                   3479999****************9888889999888888877444244444455444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   4.5e-06     0.003       5      30 ..      26      51 ..      22     148 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4.5e-06
                         AAA_22  5 agilvvtGesGtGKTtllrrlleqld 30
                                    + ++ +G+ G+GKTtll++l   l+
  gi|119720233|ref|YP_920728.1| 26 GSAIAFFGPNGVGKTTLLKTLSTLLE 51
                                   67899****************99884 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   7.8e-06    0.0052      14      40 ..      20      47 ..      10      50 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 7.8e-06
                         AAA_23 14 eidFskg.ltlItGpNGaGKTTildAik 40
                                   +++F++g   +++GpNG GKTT+l  + 
  gi|119720233|ref|YP_920728.1| 20 NLQFERGsAIAFFGPNGVGKTTLLKTLS 47
                                   66776642679************98765 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   8.1e-06    0.0054       3      36 ..      30      67 ..      29     184 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 8.1e-06
                         AAA_33  3 llvGlpGsGKstlaerl...lkklg.avllssdtlrrr 36
                                    + G++G+GK+tl++ l   l++l  +vll+  ++ +r
  gi|119720233|ref|YP_920728.1| 30 AFFGPNGVGKTTLLKTLstlLEPLEgYVLLNGEAAEKR 67
                                   689************99555666669999999886554 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   2.2e-05     0.014       2      31 ..      29      64 ..      28      78 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.2e-05
                         AAA_28  2 ivitGgestGKTtlleaLaar.....gypvv.pEaa 31
                                   i+++G+ + GKTtll+ L+       gy+ +  Eaa
  gi|119720233|ref|YP_920728.1| 29 IAFFGPNGVGKTTLLKTLSTLlepleGYVLLnGEAA 64
                                   99****************965556678877766766 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   3.3e-05     0.022      98     121 ..      24      48 ..       7      60 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.3e-05
                                    TT.SEEEEECSTTSSHHHHHHHHCT CS
                    RsgA_GTPase  98 kd.ktsvlvGqSGvGKStLinallp 121
                                    +  + +++ G+ GvGK+tL+++l  
  gi|119720233|ref|YP_920728.1|  24 ERgSAIAFFGPNGVGKTTLLKTLST 48 
                                    4448899**************9975 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   4.7e-05     0.031      13      51 ..      17      55 ..       7      72 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.7e-05
                   Mg_chelatase 13 raleiaaaGgHnlllvGppGsGKtmlakrlpsllpplse 51
                                   +al++    g  + ++Gp G GKt l k l++ll pl+ 
  gi|119720233|ref|YP_920728.1| 17 KALNLQFERGSAIAFFGPNGVGKTTLLKTLSTLLEPLEG 55
                                   56666666677899********************99975 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0     4e-05     0.027      31     148 ..      24     146 ..      11     161 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4e-05
                         AAA_25  31 pagelallaGapgtGKttla..ldlalavatGkpwlg.pvapeqgkVlyvsaEdsedelrrRlravgeal.....rddar 102
                                     +g+ ++++G+ g+GKttl+  l+  l+ ++G  +l  + a +++  +++ +E     lr  +++   a+     +  + 
  gi|119720233|ref|YP_920728.1|  24 ERGSAIAFFGPNGVGKTTLLktLSTLLEPLEGYVLLNgEAAEKRRQRIFYLTELIDVPLRVTAKQYVDAVsgfypDSIDS 103
                                    6899***************7224444555577766667777788888888888877666666666666667778777888 PP

                         AAA_25 103 llvldlagv.eslpLfakdrggtlltadvdaleaaieevegvrlvvi 148
                                    l +l lagv  ++ L ++  g+ ++++    l+aa+  ++ v+l ++
  gi|119720233|ref|YP_920728.1| 104 LEALRLAGVpPNVKLGKLSMGMRRRAQ----LAAALAVAPYVELMCL 146
                                    888888888888888777666655433....4444444344555555 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   4.8e-05     0.032       1      22 [.      29      50 ..      29      81 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.8e-05
                         AAA_18  1 IlltGtpGvGKttlakeLskrl 22
                                   I+  G+ GvGKttl k Ls +l
  gi|119720233|ref|YP_920728.1| 29 IAFFGPNGVGKTTLLKTLSTLL 50
                                   7889**************9986 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   3.4e-05     0.023      25      80 ..      28      79 ..      16     170 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.4e-05
                         AAA_15 25 ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifeniseskdikId 80
                                      + G+N++GK+++l+ l  +l+      + ++ ++ e  e+ +++ +  +  Id
  gi|119720233|ref|YP_920728.1| 28 AIAFFGPNGVGKTTLLKTLSTLLEPL----EGYVLLNGEAAEKRRQRIFYLTELID 79
                                   67899*****************9987....56666666666666555555555555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0     5e-05     0.034       4      27 ..      28      49 ..      25      71 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5e-05
                         AAA_24  4 kiliyGpsgiGKTtlakelgpkpl 27
                                    i+ +Gp+g+GKTtl+k+l  ++l
  gi|119720233|ref|YP_920728.1| 28 AIAFFGPNGVGKTTLLKTL--STL 49
                                   58899*************9..333 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   5.8e-05     0.038       4      49 ..      28      72 ..      25      91 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.8e-05
                         AAA_14  4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladp 49
                                   +++  G+  vGKTtllk+l  +ll + e ++ +n +  ++++++ +
  gi|119720233|ref|YP_920728.1| 28 AIAFFGPNGVGKTTLLKTLS-TLLEPLEGYVLLNGEAAEKRRQRIF 72
                                   67788***********9997.5555889999999999999887766 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   5.8e-05     0.038      18      52 ..      24      58 ..      17     101 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.8e-05
                       ATPase_2 18 epneiyfiYGpegsGKtaLlkeiienledkdkyvi 52
                                   e+ + +  +Gp g+GKt+Llk + + le ++ yv+
  gi|119720233|ref|YP_920728.1| 24 ERGSAIAFFGPNGVGKTTLLKTLSTLLEPLEGYVL 58
                                   556667789*************9999988777765 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   9.3e-05     0.062       2      22 ..      30      50 ..      29      91 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 9.3e-05
                                   EEESSTTSSHHHHHHHHHHHH CS
                            AAA  2 llyGppGtGKTllakavakel 22
                                    ++Gp G+GKT+l k + + l
  gi|119720233|ref|YP_920728.1| 30 AFFGPNGVGKTTLLKTLSTLL 50
                                   689************998765 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00014     0.091       3      26 ..      28      51 ..      26      62 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00014
                                   EEEEEESTTSSHHHHHHHHHHHHH CS
                          SRP54  3 villvGlqGaGKTttlaKLaallk 26
                                    i+++G++G+GKTt l  L+ ll+
  gi|119720233|ref|YP_920728.1| 28 AIAFFGPNGVGKTTLLKTLSTLLE 51
                                   689*************99998876 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00017      0.12       3      24 ..      29      50 ..      27      55 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00017
                                   EEEEC-TTTCHHHHHHHHHHHH CS
                          NACHT  3 vilqGeaGsGKTtLlqklalaw 24
                                   ++  G++G+GKTtLl+ l +++
  gi|119720233|ref|YP_920728.1| 29 IAFFGPNGVGKTTLLKTLSTLL 50
                                   5667*************99876 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00018      0.12      26      58 ..      19      51 ..      12      68 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00018
                          AAA_7 26 lelllknkkpvllvGptGtGKtviikdllkkld 58
                                   l+l ++++  + + Gp G+GKt+++k+l + l+
  gi|119720233|ref|YP_920728.1| 19 LNLQFERGSAIAFFGPNGVGKTTLLKTLSTLLE 51
                                   6778899999***************99876665 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0    0.0002      0.13       1      22 [.      29      50 ..      29      74 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0002
                   RNA_helicase  1 iwlyGpsgeGKStlakeLakal 22
                                   i ++Gp+g+GK+tl k+L++ l
  gi|119720233|ref|YP_920728.1| 29 IAFFGPNGVGKTTLLKTLSTLL 50
                                   5799*************87655 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00029      0.19       8      41 ..      17      48 ..      11      56 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00029
                                   HHHHHHHHHCHTEEEEEEESTTSSHHHHHHHHHH CS
                           TsaE  8 ealgkklakalgdvilLeGdLGaGKTtlvrglak 41
                                   +al  ++ +  g++i++ G+ G+GKTtl + l  
  gi|119720233|ref|YP_920728.1| 17 KALNLQFER--GSAIAFFGPNGVGKTTLLKTLST 48
                                   444444444..889****************9876 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00032      0.22       5      24 ..      32      52 ..      28     102 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00032
                                   E--SSSSHHHHHHHGGGGB.S CS
                          AAA_5  5 vGppGtgKselaerlaaal.n 24
                                    Gp G+gK++l + l+ +l  
  gi|119720233|ref|YP_920728.1| 32 FGPNGVGKTTLLKTLSTLLeP 52
                                   6****************9952 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0    0.0004      0.27      60      89 ..     137     166 ..     119     167 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0004
                        SbcCD_C  60 repalrlvfLDEAFsklDeesiatllelle 89 
                                      p ++l+ LD+ F ++D++s++++le ++
  gi|119720233|ref|YP_920728.1| 137 VAPYVELMCLDDPFVGVDAQSSSRILEHFK 166
                                    357799*******************99876 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00046       0.3       5      24 ..      32      51 ..      28      75 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00046
                                   E--TTSSHHHHHHHHHHHH. CS
                       NTPase_1  5 TGppGvGKtTlvkkvlellk 24
                                    Gp GvGKtTl+k ++ ll+
  gi|119720233|ref|YP_920728.1| 32 FGPNGVGKTTLLKTLSTLLE 51
                                   59***********9999986 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00072      0.48      17      39 ..      24      45 ..      12      55 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00072
                                   TSCSEEEEEEESTTSSHHHHHHH CS
                         NB-ARC 17 elqslvvalvGmgGvGKttlakq 39
                                   e +   +a+ G  GvGKttl+k 
  gi|119720233|ref|YP_920728.1| 24 ERG-SAIAFFGPNGVGKTTLLKT 45
                                   555.57999***********986 PP

>> zf-UBP  Zn-finger in ubiquitin-hydrolases and other protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00062      0.41      13      47 ..     144     178 ..     139     180 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00062
                                    EETTT--EEE-TTTT-HHHHHHHHH---EEEETTT CS
                         zf-UBP  13 lCLkCghvgCgrksnghalkHyeetrHplavdlst 47 
                                    +CL++ +vg   +s++ +l+H++ +++ l+v  +t
  gi|119720233|ref|YP_920728.1| 144 MCLDDPFVGVDAQSSSRILEHFKRDNYVLVVASRT 178
                                    7*****************************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                       107  (0.00596798); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              27  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1373.11
//
Query:       gi|119720234|ref|YP_920729.1|  [L=142]
Description: hypothetical protein Tpen_1329 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.37   11.2  10.4      0.076   13.4   1.4    2.2  2  PhoR      Phosphate regulon sensor protein PhoR
        8.2    6.8   8.5       0.71   10.2   1.7    2.2  2  KASH      Nuclear envelope localisation domain


Domain annotation for each model (and alignments):
>> PhoR  Phosphate regulon sensor protein PhoR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   1.4   8.5e-06     0.076       6      53 ..      24      71 ..      19      86 .. 0.80
   2 ?    2.9   2.1     0.016   1.4e+02      10      45 ..     102     137 ..      94     139 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.5e-06
                           PhoR  6 llrlallllaallvgllvgalaallllalllllawhlyqllrLsrWLr 53
                                    ++l+llllaa lvg+l+g ++    +a ++l ++ + +++ + + L 
  gi|119720234|ref|YP_920729.1| 24 SRLLVLLLLAASLVGVLTGCYSCIANVAEIVLAFFAYAYVHEVAQFLF 71
                                   456777777777****************99999999999999888775 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.016
                           PhoR  10 allllaallvgllvgalaallllalllllawhlyql 45 
                                      ++++ +l  +++g ++a+ l++lll l+  l++l
  gi|119720234|ref|YP_920729.1| 102 CGIVAPGVLGAAALGSFPAFGLVVLLLTLITLLRYL 137
                                    345566667778889998888888888888888776 PP

>> KASH  Nuclear envelope localisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.7   7.9e-05      0.71      11      36 ..      22      47 ..      17      57 .. 0.88
   2 ?    0.2   0.7       0.1     9e+02      13      22 ..     124     133 ..     117     140 .. 0.51

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 7.9e-05
                           KASH 11 pLqllLllllllalLvplseedesCs 36
                                   +L  lL+llll+a+Lv++    +sC 
  gi|119720234|ref|YP_920729.1| 22 WLSRLLVLLLLAASLVGVLTGCYSCI 47
                                   57779*************99999994 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.1
                           KASH  13 qllLllllll 22 
                                     +lLl l+ l
  gi|119720234|ref|YP_920729.1| 124 VVLLLTLITL 133
                                    3333333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       687  (0.0383178); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 954.96
//
Query:       gi|119720235|ref|YP_920730.1|  [L=388]
Description: hypothetical protein Tpen_1330 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       702  (0.0391544); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2926.55
//
Query:       gi|119720236|ref|YP_920731.1|  [L=153]
Description: hypothetical protein Tpen_1331 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.014   15.8   1.8      0.022   15.2   1.8    1.3  1  DUF2569        Protein of unknown function (DUF2569)
      0.054   12.3   0.2       0.06   12.1   0.2    1.0  1  O-antigen_lig  O-antigen ligase like membrane protein


Domain annotation for each model (and alignments):
>> DUF2569  Protein of unknown function (DUF2569)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   1.8   2.4e-06     0.022       4     101 ..      17     105 ..      14     118 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.4e-06
                        DUF2569   4 igGwLllpligLilsllsialelidalkalfsleewstlknleslltlllileiitnialvafsilllvlffkrrksf.. 81 
                                    i+GwL++++i+ i+ ++ + + +     +l++  + + +++           + i+++a++a s l++     +rk+   
  gi|119720236|ref|YP_920731.1|  17 INGWLWAIAITAIVVAANMHAGFSAD--PLVKRYQAAGYTEY--------SATPILFAATFATSALAITKARDKRKVYyl 86 
                                    9******9999999888877777766..88877777777444........456777778888888888888888887777 PP

                        DUF2569  82 .Pklyiifllanlvlalidal 101
                                     P+l i++ ++ + l+++  l
  gi|119720236|ref|YP_920731.1|  87 aPALAIAITIIAIGLVTA--L 105
                                    798888886665555443..3 PP

>> O-antigen_lig  O-antigen ligase like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   6.7e-06      0.06      66     154 ..      20     113 ..       2     130 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.7e-06
                  O-antigen_lig  66 Yllllaiylilhllnvlnlkslgdlvtelkyivkliy.....livlllalvlifkkkkelkiekeklikvlliasliysv 140
                                    +l ++ai+ i+  +n+   +s ++lv+ ++    + y     l+ +++a   + ++k ++k +  +l  +l+ia++i+++
  gi|119720236|ref|YP_920731.1|  20 WLWAIAITAIVVAANMHAGFSADPLVKRYQAAGYTEYsatpiLFAATFATSALAITKARDKRKVYYLAPALAIAITIIAI 99 
                                    56789999999999**************99877666622221222223322233335555555599************** PP

                  O-antigen_lig 141 lilislitgtslkt 154
                                     ++++li++ s ++
  gi|119720236|ref|YP_920731.1| 100 GLVTALIIDRSAQS 113
                                    ********999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       911  (0.0508115); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1219.57
//
Query:       gi|119720237|ref|YP_920732.1|  [L=305]
Description: ABC-type transport system involved in multi-copper enzyme maturation permease component-like [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-35  122.1  21.3    3.7e-35  121.6  21.3    1.2  1  ABC2_membrane_2  ABC-2 family transporter protein
    0.00012   22.1  10.0    0.00012   22.1  10.0    2.3  2  ABC2_membrane_4  ABC-2 family transporter protein
    0.00012   21.7   3.2    0.00012   21.7   3.2    2.4  3  ABC2_membrane_5  ABC-2 family transporter protein
    0.00032   19.9  14.0    0.00032   19.9  14.0    2.0  2  ABC2_membrane_3  ABC-2 family transporter protein
  ------ inclusion threshold ------
       0.42   10.5   9.2       0.52   10.2   1.2    2.9  3  TRIQK            Triple QxxK/R motif-containing protein famil


Domain annotation for each model (and alignments):
>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.6  21.3     1e-38   3.7e-35       2     283 ..       7     299 ..       6     303 .. 0.83

  Alignments for each domain:
  == domain 1  score: 121.6 bits;  conditional E-value: 1e-38
                ABC2_membrane_2   2 aiakkEfrdlvrsrrfllltvllplidvalaylkdlgsslqseakaikeatlaleyveaasasdeaedtdqdlkvvstim 81 
                                    +ia+kEf+d+v srrf++++++++l+ +    ++ + s+   + ++++++ l +  +  +                 +++
  gi|119720237|ref|YP_920732.1|   7 VIARKEFADTVSSRRFWIVVAVFLLV-FLFNTVSVYLSFRAGQIPQERDLFLEIGRG--IV----------------ASL 67 
                                    7*************************.999999999999999999999998887544..33................499 PP

                ABC2_membrane_2  82 avlipviaalfgadaiagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvll..alaiilalgivlale 159
                                     v+ p++++++g+ ai+gE+ergTl+l LskPv+Rd ++ gK++++la   +++v  +a++l+  a ai+ +  ++  + 
  gi|119720237|ref|YP_920732.1|  68 EVAAPLLGIALGFSAISGERERGTLRLILSKPVYRDVVVSGKVLASLAC--ITLVVSGASLLAvlASAIQGVAVMPDHIV 145
                                    **********************************************999..66666677744422334555555555555 PP

                ABC2_membrane_2 160 dllllvvasvlllllvvflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavp............q 227
                                     l +++++++l++l  ++ a++ll S+++r+s+ +++l+l+++v++ai+ p ++ ++a+lla+p +p             
  gi|119720237|ref|YP_920732.1| 146 RLAIFIALATLYAL--TYYAFSLLASILSRKSSHSLLLSLAVWVFFAIALPAASIAIASLLAEPPPPtttglaewlsrvI 223
                                    55555555555555..9*********************************************99999*********9998 PP

                ABC2_membrane_2 228 eindflsllsptsayntllneilagsdlna....................lgstatnllilllllavllvlgyvlF 283
                                    + +++l+++sp  +y  l  +++    + +                        ++ l++l l+ +  +  +y +F
  gi|119720237|ref|YP_920732.1| 224 QTSLTLQYFSPNLHYASLGYQLFGIRITFTakgnvvevteyigkidpvrlVVTQWADLALLALYSLMAILASYIAF 299
                                    8888999999988887777666666655556888888888888899888888889999999999988888888777 PP

>> ABC2_membrane_4  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1  10.0   3.2e-08   0.00012      14     178 ..      21     192 ..      11     193 .. 0.65
   2 ?   -0.0   0.0      0.21   7.5e+02      56      75 ..     282     301 ..     245     305 .] 0.66

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 3.2e-08
                ABC2_membrane_4  14 ivwllvlaallvpllallyfn.llgktgl.dpaefysl..svfgftlllllplilgiiasylifrEeqndtlknLltiPv 89 
                                     +w++v++ llv l+ ++ ++  +++ ++ ++  +++     +  +l +  pl+ + ++   i+ E++ +tl+ +l  Pv
  gi|119720237|ref|YP_920732.1|  21 RFWIVVAVFLLVFLFNTVSVYlSFRAGQIpQERDLFLEigRGIVASLEVAAPLLGIALGFSAISGERERGTLRLILSKPV 100
                                    45555555444444333322202222222022333332113444444456666666689999****************** PP

                ABC2_membrane_4  90 srtklllaKlivllllsvllmlvtflitvlfallsgfvgfsvklvl..ellkkclelgllvffavlpiialvl.lkksyv 166
                                     r  ++ +K+++ l  + l++  + l++vl++ + g +++  + v   +++   ++++l+ ++++l + +l+     s +
  gi|119720237|ref|YP_920732.1| 101 YRDVVVSGKVLASLACITLVVSGASLLAVLASAIQGVAVMPDHIVRlaIFIALATLYALTYYAFSLLASILSRkSSHSLL 180
                                    **********998888888888889999*********9999876541044444445555555556666777774555679 PP

                ABC2_membrane_4 167 lpliltlvytia 178
                                    l+l++ ++++ia
  gi|119720237|ref|YP_920732.1| 181 LSLAVWVFFAIA 192
                                    999999999875 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.21
                ABC2_membrane_4  56 lllllplilgiiasylifrE 75 
                                    +ll l  +++i+asy+ f  
  gi|119720237|ref|YP_920732.1| 282 ALLALYSLMAILASYIAFVN 301
                                    34555566666667666554 PP

>> ABC2_membrane_5  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.3     0.077   2.8e+02     180     200 ..      23      42 ..       3      49 .. 0.48
   2 !   21.7   3.2   3.3e-08   0.00012      42     161 ..      69     193 ..      55     229 .. 0.74
   3 ?   -3.1   0.2       1.3   4.8e+03     187     199 ..     285     297 ..     272     301 .. 0.50

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.077
                ABC2_membrane_5 180 yilliillviillliivSyfi 200
                                    +i++ ++l +++l+  vS+ +
  gi|119720237|ref|YP_920732.1|  23 WIVVAVFL-LVFLFNTVSVYL 42 
                                    22222222.222333333333 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 3.3e-08
                ABC2_membrane_5  42 ilslvisiililttlsyDekskwnkylltLPvtrkeiVksKYlfvlililiailitlllliiavlikgnvtisevllsil 121
                                    ++++++ i l ++++s ++  ++ +++l+ Pv r  +V+ K l +l +i++++   +ll+++a+ i+g   + + +  ++
  gi|119720237|ref|YP_920732.1|  69 VAAPLLGIALGFSAISGERERGTLRLILSKPVYRDVVVSGKVLASLACITLVVSGASLLAVLASAIQGVAVMPDHIVRLA 148
                                    567788889999*************************************9999999999999999999977777777777 PP

                ABC2_membrane_5 122 iglvialiflaivlPlyf....kfgvekgri.vliiiifgiifll 161
                                    i++++a+++   ++ + +    +   +   + +++++++++++ l
  gi|119720237|ref|YP_920732.1| 149 IFIALATLYALTYYAFSLlasiLSRKSSHSLlLSLAVWVFFAIAL 193
                                    777777666555555554000044433333323333443333333 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 1.3
                ABC2_membrane_5 187 lviillliivSyf 199
                                    ++ +l+ i++Sy+
  gi|119720237|ref|YP_920732.1| 285 ALYSLMAILASYI 297
                                    2233333333333 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.6      0.32   1.1e+03       6      22 ..      23      39 ..      19      53 .. 0.55
   2 !   19.9  14.0     9e-08   0.00032     172     302 ..      73     220 ..      56     300 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.32
                ABC2_membrane_3  6 itlllPiilvlllglif 22
                                   ++++ +++lv+l++++ 
  gi|119720237|ref|YP_920732.1| 23 WIVVAVFLLVFLFNTVS 39
                                   44555555555555443 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 9e-08
                ABC2_membrane_3 172 ifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilll.afgl......gipfg..nlglll 242
                                    ++ +a+ + ++i  E+e++++ l+l+ +v +   + +k+l+++++  l++  + ll ++++       +p     l +++
  gi|119720237|ref|YP_920732.1|  73 LLGIALGF-SAISGERERGTLRLILSKPVYRDVVVSGKVLASLACITLVVSGASLLaVLASaiqgvaVMPDHivRLAIFI 151
                                    44444433.37999********************************9999888776666666787855555577888888 PP

                ABC2_membrane_3 243 llfllfglayialgyllsslfknsetaqilifivilllsgffgglfp......ledlp....salkwifs 302
                                     l  l++l+y a+++l s l+++s+   +l ++v++ ++++ ++  +      l  +p    ++l+ ++s
  gi|119720237|ref|YP_920732.1| 152 ALATLYALTYYAFSLLASILSRKSSHSLLLSLAVWV-FFAIALPAASiaiaslLAEPPppttTGLAEWLS 220
                                    ************************999999999988.555555554422222344444667733333333 PP

>> TRIQK  Triple QxxK/R motif-containing protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1    0.0084        30      52      73 ..      22      44 ..       9      48 .. 0.76
   2 ?   10.2   1.2   0.00015      0.52      47      74 ..     133     165 ..     129     169 .. 0.78
   3 ?   -2.3   0.1       1.2   4.2e+03      62      69 ..     283     290 ..     268     298 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0084
                          TRIQK 52 llvlvailvlllalYal.fflnl 73
                                   ++++va+++l++ + ++ ++l++
  gi|119720237|ref|YP_920732.1| 22 FWIVVAVFLLVFLFNTVsVYLSF 44
                                   79*****9999987665355555 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00015
                          TRIQK  47 gikevllv.....lvailvlllalYalfflnls 74 
                                    +i+ v+ +      +ai++ l++lYal ++ +s
  gi|119720237|ref|YP_920732.1| 133 AIQGVAVMpdhivRLAIFIALATLYALTYYAFS 165
                                    555555555554478****************98 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 1.2
                          TRIQK  62 llalYalf 69 
                                    llalY+l+
  gi|119720237|ref|YP_920732.1| 283 LLALYSLM 290
                                    67788777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       990  (0.0552178); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2073.03
//
Query:       gi|119720238|ref|YP_920733.1|  [L=315]
Description: ABC transporter related [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.7e-29  101.0   0.0    1.3e-28  100.2   0.0    1.4  1  ABC_tran  ABC transporter
    4.3e-09   36.6   3.5    0.00049   20.0   1.4    2.2  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    0.00036   21.1   0.1    0.00073   20.1   0.1    1.4  1  AAA_23    AAA domain
     0.0026   17.5   0.3     0.0069   16.1   0.1    1.7  2  AAA_29    P-loop containing region of AAA domain
      0.005   16.8   0.0      0.013   15.5   0.0    1.6  2  ATPase_2  ATPase domain predominantly from Archaea
     0.0079   16.5   0.2       0.24   11.7   0.2    2.7  2  AAA_22    AAA domain
  ------ inclusion threshold ------
      0.024   15.0   0.7       0.07   13.5   0.0    2.0  2  AAA_16    AAA ATPase domain
       0.03   14.5   0.0        1.8    8.7   0.0    2.6  2  AAA_33    AAA domain
       0.04   14.0   0.3        9.6    6.2   0.0    2.8  2  AAA_14    AAA domain
      0.044   13.2   0.0       0.28   10.6   0.0    2.1  2  SMC_N     RecF/RecN/SMC N terminal domain
      0.057   12.3   0.0       0.11   11.2   0.0    1.4  1  DLIC      Dynein light intermediate chain (DLIC)
        0.1   12.4   0.0       0.15   11.8   0.0    1.3  1  CLP1_P    mRNA cleavage and polyadenylation factor CLP1 P-loo
       0.11   12.2   0.2        8.3    6.1   0.0    2.6  2  AAA_30    AAA domain
       0.12   11.4   0.6       0.53    9.3   0.0    2.3  3  T2SSE     Type II/IV secretion system protein
       0.14   11.6   0.0       0.25   10.8   0.0    1.4  1  RecA      recA bacterial DNA recombination protein
       0.14   11.8   0.1       0.78    9.4   0.1    2.1  3  AAA_24    AAA domain
       0.16   10.6   0.4       0.31    9.6   0.4    1.3  1  AAA_13    AAA domain
       0.18   11.7   0.6          1    9.3   0.1    2.4  2  MobB      Molybdopterin guanine dinucleotide synthesis protei


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.2   0.0   1.3e-31   1.3e-28       1     136 [.      24     167 ..      24     168 .. 0.97

  Alignments for each domain:
  == domain 1  score: 100.2 bits;  conditional E-value: 1.3e-31
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren. 79 
                                    l++vsl + +g++ +i+G+nG+GK+tL+++l+gl  pt G+ ++ g d+ + +  s+rk++g lp+   l +++t+ +n 
  gi|119720238|ref|YP_920733.1|  24 LDEVSLRVPAGSIFGIFGPNGSGKTTLISILLGLILPTRGSARVLGYDVVK-QSLSVRKRVGLLPEAFGLYEHMTALDNl 102
                                    789**********************************************99.78899*********************** PP

                                    ............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    ............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                e ++++ ++l+ +gl++++  +v    s++S G+ qr+ la++l+k+p+l++lDEpt
  gi|119720238|ref|YP_920733.1| 103 vffglldevpkgEVEKRAREVLELVGLSNKAGAKV----STFSRGMIQRLGLAQVLMKDPDLVILDEPT 167
                                    **********9999999************999999....*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   1.4   4.9e-07   0.00049       2      22 ..      37      57 ..      36      79 .. 0.85
   2 !   16.9   0.0   4.4e-06    0.0044     199     297 ..     137     197 ..      75     202 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 4.9e-07
                         AAA_21  2 nvliGpNgsGKSnLLdaldll 22
                                    ++ GpNgsGK++L+ +l +l
  gi|119720238|ref|YP_920733.1| 37 FGIFGPNGSGKTTLISILLGL 57
                                   689***************988 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 4.4e-06
                         AAA_21 199 lsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHP...kll 275
                                    +s                                    +S G+ + l+l+  l  ++   +l+++DEp  gL+P   +ll
  gi|119720238|ref|YP_920733.1| 137 VS-----------------------------------TFSRGMIQRLGLAQVLMKDP---DLVILDEPTMGLDPdgiELL 178
                                    33...................................34999999999999999999...9*************666666 PP

                         AAA_21 276 rrllellkelsrngaQviltTH 297
                                    + l+     l+++g  ++++TH
  gi|119720238|ref|YP_920733.1| 179 KILV---LGLRERGKTIMISTH 197
                                    6666...333335788999999 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.1   7.4e-07   0.00073      21      37 ..      36      52 ..      23      62 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 7.4e-07
                         AAA_23 21 ltlItGpNGaGKTTild 37
                                   ++ I+GpNG+GKTT++ 
  gi|119720238|ref|YP_920733.1| 36 IFGIFGPNGSGKTTLIS 52
                                   899************95 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1     7e-06    0.0069      17      49 ..      29      61 ..      22      66 .. 0.74
   2 ?   -2.4   0.0       4.2   4.2e+03      24      39 ..     179     194 ..     164     198 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 7e-06
                         AAA_29 17 ieidlkg.atlltGpsGsGKSTllDAiqalLvpa 49
                                   +++  +g ++ + Gp+GsGK+Tl+  +  l++p+
  gi|119720238|ref|YP_920733.1| 29 LRVP-AGsIFGIFGPNGSGKTTLISILLGLILPT 61
                                   5555.4558889************7777777765 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.2
                         AAA_29  24 atlltGpsGsGKSTll 39 
                                     +l+ G  + GK+ ++
  gi|119720238|ref|YP_920733.1| 179 KILVLGLRERGKTIMI 194
                                    4688899999998665 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.3e-05     0.013       3      38 ..      16      52 ..      14      60 .. 0.84
   2 ?   -3.7   0.0       9.3   9.3e+03      24      38 ..     181     195 ..     180     200 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.3e-05
                       ATPase_2  3 dRekelkeleeilerepn.eiyfiYGpegsGKtaLlk 38
                                   dR  e+k l e+  r p+ +i  i+Gp gsGKt+L+ 
  gi|119720238|ref|YP_920733.1| 16 DRGSEVKALDEVSLRVPAgSIFGIFGPNGSGKTTLIS 52
                                   99999****99987777616666************96 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 9.3
                       ATPase_2  24 fiYGpegsGKtaLlk 38 
                                    ++ G +  GKt ++ 
  gi|119720238|ref|YP_920733.1| 181 LVLGLRERGKTIMIS 195
                                    688999999998875 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.2   0.00024      0.24       9      99 ..      38     165 ..      33     199 .. 0.60
   2 ?   -1.7   0.0       3.3   3.3e+03     105     117 ..     246     258 ..     220     272 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00024
                         AAA_22   9 vvtGesGtGKTtllrrlleqldeeakaee................................erpevv...fvtlpsstss 53 
                                     ++G+ G+GKTtl+  ll         ++                                 +   v   + +   +++ 
  gi|119720238|ref|YP_920733.1|  38 GIFGPNGSGKTTLISILLGLILPTRGSARvlgydvvkqslsvrkrvgllpeafglyehmtaLDNL-VffgLLDEVPKGEV 116
                                    59************988877643333333566666666666666666666666666555432222.22344444444456 PP

                         AAA_22  54 kdllrellralglelkaerlsseell.ealeqalrarav...ielliiDE 99 
                                    ++ +re+l+ +gl++ka +++ + +   ++++   a+     + l+i+DE
  gi|119720238|ref|YP_920733.1| 117 EKRAREVLELVGLSNKA-GAKVSTFSrGMIQRLGLAQVLmkdPDLVILDE 165
                                    66666666666666666.55555555444455444444466667777777 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.3
                         AAA_22 105 seealeeLrslln 117
                                    se++leeLrsl +
  gi|119720238|ref|YP_920733.1| 246 SERLLEELRSLPE 258
                                    4666777777765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0     7e-05      0.07       5      51 ..      17      61 ..      14     165 .. 0.79
   2 ?   -0.3   0.1       1.2   1.2e+03      80     106 ..     229     254 ..     170     291 .. 0.47

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7e-05
                         AAA_16  5 ReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekd 51
                                   R+ e+++L ++  rv +g  ++  + G+ G+GK++l+  ll  +  +
  gi|119720238|ref|YP_920733.1| 17 RGSEVKALDEVSLRVPAG--SIFGIFGPNGSGKTTLISILLGLILPT 61
                                   888999999998899999..7999*************9888655555 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.2
                         AAA_16  80 ellrqlldeaesaeleawrekleeala 106
                                    el ++  ++  +  + +++e+l+e+l+
  gi|119720238|ref|YP_920733.1| 229 ELAEKQYSA-YAVRRTDYSERLLEELR 254
                                    222222222.33333444444444444 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0    0.0018       1.8       5      20 ..      40      55 ..      37     122 .. 0.79
   2 ?    3.2   0.0     0.092        91      13      99 ..     138     292 ..     123     305 .. 0.54

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0018
                         AAA_33  5 vGlpGsGKstlaerll 20
                                    G++GsGK+tl+  ll
  gi|119720238|ref|YP_920733.1| 40 FGPNGSGKTTLISILL 55
                                   6**********98773 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.092
                         AAA_33  13 stlaerllkklg.avllssdt........................................................... 32 
                                    st++++++++lg a++l +d                                                            
  gi|119720238|ref|YP_920733.1| 138 STFSRGMIQRLGlAQVLMKDPdlvildeptmgldpdgiellkilvlglrergktimisthllhevgnicthaaiirkgkv 217
                                    67777777777775555555445555555566666666666666666666666666666655555555555554333333 PP

                         AAA_33  33 ....lrrrlfg.tdqqsktdytr.vldrlyqilnelarkalsagrnvildat......nlsrrerarflklarrlgvpv 99 
                                            l++ t +  +++y+  +  r+ +  ++l+++ +s    +++  +      ++++++ ++++++a+++g++v
  gi|119720238|ref|YP_920733.1| 218 laqgS---LEEvTRELAEKQYSAyAVRRTDYS-ERLLEELRSLPEVIVTGHGgntirvLAKNDRVSALIEVAEKHGAAV 292
                                    32220...111211111222333133333333.4666665555555555333344554555666677777777777665 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0    0.0097       9.6       4      22 ..      36      54 ..      33     113 .. 0.83
   2 ?    4.8   0.1     0.027        26       5      25 ..     180     200 ..     178     233 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0097
                         AAA_14  4 ilvitGaRrvGKTtllkql 22
                                   i  i G+  +GKTtl+  l
  gi|119720238|ref|YP_920733.1| 36 IFGIFGPNGSGKTTLISIL 54
                                   7889***********9766 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.027
                         AAA_14   5 lvitGaRrvGKTtllkqlike 25 
                                    +++ G+R  GKT ++ + + +
  gi|119720238|ref|YP_920733.1| 180 ILVLGLRERGKTIMISTHLLH 200
                                    5799*********99776544 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00028      0.28      25      42 ..      35      52 ..      19      60 .. 0.77
   2 ?   -0.4   0.0      0.63   6.3e+02     155     196 ..     154     195 ..     117     203 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00028
                                   SEEEEEESTTSSHHHHHH CS
                                   xxxxxxxxxxxxxxxxxx RF
                          SMC_N 25 sftaivGpNGSGKsnlld 42
                                   s+  i GpNGSGK+ l+ 
  gi|119720238|ref|YP_920733.1| 35 SIFGIFGPNGSGKTTLIS 52
                                   46679*********9985 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.63
                                    CCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 155 kvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivis 196
                                     +k   l++lDe  + LD   ++ +  l+   +++   i+is
  gi|119720238|ref|YP_920733.1| 154 LMKDPDLVILDEPTMGLDPDGIELLKILVLGLRERGKTIMIS 195
                                    455556899*********999999888887777777777766 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00012      0.11      19      56 ..      28      65 ..      18      79 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00012
                           DLIC 19 ssklPsgksvlvlGedgsGkttliaklqGveeekkGrG 56
                                   s ++P+g    ++G +gsGkttli+ l G+  + +G+ 
  gi|119720238|ref|YP_920733.1| 28 SLRVPAGSIFGIFGPNGSGKTTLISILLGLILPTRGSA 65
                                   55789999999*****************9988888865 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00015      0.15       1      46 [.      41      86 ..      41     123 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00015
                         CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvGqseispPgtisla 46
                                   Gp+ sGK+Tl+ +Ll  +l    +  ++  Dv ++++s+   ++l 
  gi|119720238|ref|YP_920733.1| 41 GPNGSGKTTLISILLGLILPTRGSARVLGYDVVKQSLSVRKRVGLL 86
                                   899***************99999999********999998888875 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0    0.0083       8.3      22      39 ..      38      55 ..      29      86 .. 0.81
   2 ?    3.5   0.0     0.051        51      62     101 ..     129     174 ..     112     255 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0083
                         AAA_30 22 vltGpAGtGKttalkalr 39
                                    + Gp G+GKtt+++ l 
  gi|119720238|ref|YP_920733.1| 38 GIFGPNGSGKTTLISILL 55
                                   578**********99875 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.051
                         AAA_30  62 Laeelgieastiak.llkrlk.grarlepgtllivDEagmv....d 101
                                    L++++g++ st  + +++rl+ +++ +++ +l+i DE  m     +
  gi|119720238|ref|YP_920733.1| 129 LSNKAGAKVSTFSRgMIQRLGlAQVLMKDPDLVILDEPTMGldpdG 174
                                    456777777777762344444765667777*******999733333 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00053      0.53     131     154 ..      36      59 ..      10      97 .. 0.83
   2 ?   -1.9   0.0       1.3   1.3e+03     189     207 ..     147     165 ..     127     165 .. 0.76
   3 ?   -1.2   0.1      0.86   8.5e+02     185     205 ..     242     262 ..     178     272 .. 0.54

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00053
                          T2SSE 131 lilvsGgTgsGKttllyallkein 154
                                    ++ + G+ gsGKttl+ +ll  i 
  gi|119720238|ref|YP_920733.1|  36 IFGIFGPNGSGKTTLISILLGLIL 59 
                                    55578**************99874 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.3
                          T2SSE 189 adllraaLRlrPDrimvGE 207
                                    + +l ++L ++PD +++ E
  gi|119720238|ref|YP_920733.1| 147 RLGLAQVLMKDPDLVILDE 165
                                    5568899999****99865 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.86
                          T2SSE 185 kvtfadllraaLRlrPDrimv 205
                                    + ++++ l + LR  P +i+ 
  gi|119720238|ref|YP_920733.1| 242 RTDYSERLLEELRSLPEVIVT 262
                                    234444444445555555544 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00025      0.25      50      70 ..      31      51 ..      17      66 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00025
                                   EETTSEEEEEESTTSSHHHHH CS
                           RecA 50 lpkGriieiyGpessGkttla 70
                                   +p G i  i+Gp+ sGkttl 
  gi|119720238|ref|YP_920733.1| 31 VPAGSIFGIFGPNGSGKTTLI 51
                                   79*****************85 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.1   0.00078      0.78       6      22 ..      38      54 ..      34      81 .. 0.81
   2 ?   -1.5   0.0       1.7   1.7e+03       4      21 ..     179     196 ..     178     205 .. 0.87
   3 ?   -2.8   0.0       4.4   4.3e+03     117     130 ..     249     264 ..     223     267 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00078
                         AAA_24  6 liyGpsgiGKTtlakel 22
                                    i+Gp+g+GKTtl++ l
  gi|119720238|ref|YP_920733.1| 38 GIFGPNGSGKTTLISIL 54
                                   69***********9877 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.7
                         AAA_24   4 kiliyGpsgiGKTtlake 21 
                                    kil+ G  + GKT ++++
  gi|119720238|ref|YP_920733.1| 179 KILVLGLRERGKTIMIST 196
                                    8999*********99876 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 4.4
                         AAA_24 117 klqelrk..nvifiah 130
                                     l+elr    vi+++h
  gi|119720238|ref|YP_920733.1| 249 LLEELRSlpEVIVTGH 264
                                    3666666667888887 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.4   0.00031      0.31      21      36 ..      39      54 ..      34      64 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00031
                         AAA_13 21 iYGwNGaGKTtLSrll 36
                                   i+G NG+GKTtL ++l
  gi|119720238|ref|YP_920733.1| 39 IFGPNGSGKTTLISIL 54
                                   9***********8776 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1     0.001         1       1      22 [.      36      57 ..      36      68 .. 0.86
   2 ?   -0.8   0.1       1.3   1.3e+03       3      18 ..     181     196 ..     179     214 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.001
                           MobB  1 vlgivgksgsGKTtLleklipe 22
                                   ++gi g +gsGKTtL++ l+  
  gi|119720238|ref|YP_920733.1| 36 IFGIFGPNGSGKTTLISILLGL 57
                                   689*************999865 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.3
                           MobB   3 givgksgsGKTtLlek 18 
                                     + g  + GKT +++ 
  gi|119720238|ref|YP_920733.1| 181 LVLGLRERGKTIMIST 196
                                    56789999***99864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 2022.02
//
Query:       gi|119720239|ref|YP_920734.1|  [L=596]
Description: membrane protein-like [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-29  101.7   1.7    1.9e-09   37.7   0.1    4.6  4  NPCBM_assoc      NPCBM-associated, NEW3 domain of alpha-galac
    1.7e-14   53.8   4.4    8.9e-11   41.9   0.0    5.4  6  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
    7.4e-08   32.6   0.1       0.44   10.8   0.1    4.6  4  FixG_C           IG-like fold at C-terminal of FixG, putative
    0.00028   21.1  11.2       0.39   11.1   1.5    4.5  4  DUF11            Domain of unknown function DUF11
    0.00035   20.5   0.3       0.45   10.5   0.0    3.4  3  CarbopepD_reg_2  CarboxypepD_reg-like domain
    0.00039   20.6   2.6       0.12   12.6   0.4    4.1  4  CARDB            CARDB
     0.0055   16.8   0.0         19    5.3   0.0    4.7  6  DUF916           Bacterial protein of unknown function (DUF91
     0.0077   16.1   0.0       0.03   14.2   0.0    2.0  2  DUF1416          Protein of unknown function (DUF1416)
     0.0085   16.2   0.2      0.098   12.8   0.2    2.8  3  fn3_6            Fibronectin type-III domain
  ------ inclusion threshold ------
       0.01   15.7   0.1        1.9    8.3   0.0    2.7  3  DUF4832          Domain of unknown function (DUF4832)
      0.013   15.9   0.0        4.9    7.7   0.0    4.6  6  MG2              MG2 domain
       0.11   12.8   0.2       0.61   10.4   0.0    2.3  3  DUF4352          Domain of unknown function (DUF4352)


Domain annotation for each model (and alignments):
>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   5.1e-08   7.6e-05      21      75 ..     155     211 ..     140     213 .. 0.83
   2 !   29.7   0.0   3.8e-10   5.7e-07       2      75 ..     244     322 ..     243     325 .. 0.85
   3 !    7.2   0.0     0.004         6      21      67 ..     379     428 ..     359     439 .. 0.72
   4 !   37.7   0.1   1.3e-12   1.9e-09       1      75 [.     469     543 ..     469     544 .. 0.96

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 5.1e-08
                    NPCBM_assoc  21 atnvslslslPeGWtvvevspasaa....slapGetveatvkVtppagaaaGdyevtak 75 
                                     + v ls+s+P+GWt   +    ++     l pG+t++ ++ +++p +a  G y++t+ 
  gi|119720239|ref|YP_920734.1| 155 EETVTLSASAPSGWT-AGFYLGDLEvksiVLSPGQTLKLDLVLKVPYNAS-GRYNITVD 211
                                    4789***********.66666555556789********************.9****986 PP

  == domain 2  score: 29.7 bits;  conditional E-value: 3.8e-10
                    NPCBM_assoc   2 epGetvtlt.ltvtndgtaaatnvslslslPeGWt...vvevspasaa..slapGetveatvkVtppagaaaGdyevtak 75 
                                    +pG+tv+l+ l++tn+  + +++v + l lP+ W+     ++s++++   sl pGe+v+a+v +++p++aa+G y+v ++
  gi|119720239|ref|YP_920734.1| 244 SPGSTVSLDgLEITNKLPDRTSGVVF-LLLPSRWSgsiLDSTSGNNLYklSLNPGESVKAKVVLQIPDTAAPGNYTVGVV 322
                                    67888887658888888888887766.669*****8887888888888999*************************9776 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.004
                    NPCBM_assoc  21 atnvslslsl.PeG..Wtvvevspasaa..slapGetveatvkVtppagaaa 67 
                                    + ++ ++  + P+G  W+++   ++ ++   l++Ge+ + +v V++p  a++
  gi|119720239|ref|YP_920734.1| 379 VVELVVK--GlPPGysWRIEDLNGNVISklYLKAGESRQLKVVVSVPLLAEP 428
                                    4444443..33665559999999999998889***************88876 PP

  == domain 4  score: 37.7 bits;  conditional E-value: 1.3e-12
                    NPCBM_assoc   1 vepGetvtltltvtndgtaaatnvslslsl.PeGWtvvevspasaaslapGetveatvkVtppagaaaGdyevtak 75 
                                    v+ G++ t++l v+n+g +++tnv++++s  P+G + v++sp+ + sl++ e + +tv+V + ++  aGdy +t+k
  gi|119720239|ref|YP_920734.1| 469 VTSGSSATFQLGVKNTGYSSLTNVRIEVSNvPRGLR-VNISPEVVLSLKAQENANFTVTVYAEPDVSAGDYYITLK 543
                                    578*************************977*****.************************************985 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9   0.0     6e-14   8.9e-11       2      73 ..      42     110 ..      41     122 .. 0.89
   2 ?    2.5   0.0      0.12   1.7e+02      49      81 ..     157     196 ..     151     197 .. 0.81
   3 ?    4.9   0.1     0.021        31      47      72 ..     203     227 ..     198     238 .. 0.82
   4 ?   -0.0   0.0      0.73   1.1e+03      46      65 ..     313     332 ..     307     349 .. 0.73
   5 ?   -0.5   0.2         1   1.5e+03      50      70 ..     477     495 ..     450     526 .. 0.61
   6 ?   -1.7   0.1       2.5   3.7e+03      32      32 ..     507     507 ..     481     543 .. 0.57

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 6e-14
                CarboxypepD_reg   2 isGrVtdasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatreevtltagq 73 
                                    ++G V+d+ gapi+ +++ ++ +d++ va+++t  +G+f+   l+pgty+    + Gy+  t++ ++++ g+
  gi|119720239|ref|YP_920734.1|  42 VHGVVVDPRGAPISDVSILIFGEDNTLVARVKTSMTGDFWAL-LAPGTYKASLIKVGYEAKTIS-FSIS-GD 110
                                    89**************************************75.*******************95.8887.44 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.12
                CarboxypepD_reg  49 tysvtvsapGyatatr.......eevtltagqtttlditL 81 
                                    t ++ +sap   ta +       ++++l++gqt  ld++L
  gi|119720239|ref|YP_920734.1| 157 TVTLSASAPSGWTAGFylgdlevKSIVLSPGQTLKLDLVL 196
                                    6677788888887777788888889************998 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.021
                CarboxypepD_reg  47 pgtysvtvsapGyatatreevtltag 72 
                                     g+y++tv   Gy  ++r  +t++ +
  gi|119720239|ref|YP_920734.1| 203 SGRYNITVDVLGYTLQRR-VITVDIE 227
                                    49************9996.6888765 PP

  == domain 4  score: -0.0 bits;  conditional E-value: 0.73
                CarboxypepD_reg  46 ppgtysvtvsapGyatatre 65 
                                    +pg+y+v v + G +++  +
  gi|119720239|ref|YP_920734.1| 313 APGNYTVGVVFRGVDPYFES 332
                                    46*****9999999988763 PP

  == domain 5  score: -0.5 bits;  conditional E-value: 1
                CarboxypepD_reg  50 ysvtvsapGyatatreevtlt 70 
                                    +++ v  +Gy + t   v+++
  gi|119720239|ref|YP_920734.1| 477 FQLGVKNTGYSSLTN--VRIE 495
                                    444445555555553..3333 PP

  == domain 6  score: -1.7 bits;  conditional E-value: 2.5
                CarboxypepD_reg  32 t 32 
                                     
  gi|119720239|ref|YP_920734.1| 507 I 507
                                    1 PP

>> FixG_C  IG-like fold at C-terminal of FixG, putative oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0022       3.3      42     102 ..     151     213 ..     145     237 .. 0.77
   2 ?    2.9   0.0     0.079   1.2e+02      68      94 ..     291     317 ..     278     332 .. 0.82
   3 ?    4.9   0.0     0.019        28      47      93 ..     378     429 ..     365     445 .. 0.69
   4 !   10.8   0.1   0.00029      0.44      35      91 ..     477     535 ..     462     562 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0022
                                    -SSS-EEEEEEEES-S....S-EE.E.S--EEEE-TT-EEEEEEEEEE-GGG-SSSEEEEEEEEE CS
                         FixG_C  42 ktekprrytlsveglp....glelagraekeitvapgekrkvpvfvrvpaealkkkstpitfkvt 102
                                    k +++ ++tls++       g+ l + + k+i + pg+++k+ ++++vp +a  +++ +it+ v 
  gi|119720239|ref|YP_920734.1| 151 KGSREETVTLSASAPSgwtaGFYLGDLEVKSIVLSPGQTLKLDLVLKVPYNA--SGRYNITVDVL 213
                                    6778889999999655343444443344699*******************99..77788888874 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.079
                                    EEEE-TT-EEEEEEEEEE-GGG-SSSE CS
                         FixG_C  68 eitvapgekrkvpvfvrvpaealkkks 94 
                                    ++++ pge++k +v++++p  a++   
  gi|119720239|ref|YP_920734.1| 291 KLSLNPGESVKAKVVLQIPDTAAPGNY 317
                                    57899**************99966544 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.019
                                    EEEEEEEES-S.S-EE......E.S--EEEE-TT-EEEEEEEEEE-GGG-SSS CS
                         FixG_C  47 rrytlsveglp.glel.....agraekeitvapgekrkvpvfvrvpaealkkk 93 
                                      ++l v+glp g ++     +g+  +++ +++ge+r+++v+v+vp  a +++
  gi|119720239|ref|YP_920734.1| 378 GVVELVVKGLPpGYSWriedlNGNVISKLYLKAGESRQLKVVVSVPLLA-EPS 429
                                    566777888544666655555334468899***************9765.444 PP

  == domain 4  score: 10.8 bits;  conditional E-value: 0.00029
                                    EEEEEEE-SSS-EE.EEEEEES-S.S-EE.E.S--EEEE-TT-EEEEEEEEEE-GGG-S CS
                         FixG_C  35 YtlkilNktekprr.ytlsveglp.glelagraekeitvapgekrkvpvfvrvpaealk 91 
                                    ++l + N+  +  + ++++v++ p gl+++  +e  ++++++e+ +++v+v ++++ ++
  gi|119720239|ref|YP_920734.1| 477 FQLGVKNTGYSSLTnVRIEVSNVPrGLRVNISPEVVLSLKAQENANFTVTVYAEPDVSA 535
                                    55666666666555599****9767****8899********************998733 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0         2   3.1e+03      62      82 ..     182     202 ..     126     210 .. 0.63
   2 ?    5.4   0.2     0.015        23      27      85 ..     248     315 ..     234     320 .. 0.65
   3 !    8.2   0.0    0.0021       3.1      11      79 ..     359     423 ..     346     430 .. 0.78
   4 !   11.1   1.5   0.00026      0.39       9      83 ..     468     534 ..     437     541 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 2
                          DUF11  62 gsLeagesatlsftvrvtrta 82 
                                      L +g++++l + ++v+  a
  gi|119720239|ref|YP_920734.1| 182 IVLSPGQTLKLDLVLKVPYNA 202
                                    235777777777777776555 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.015
                          DUF11  27 pasangvvvtDtlPaglayvsvsas..........qgtasaltsv....gsLeagesatlsftvrvtrtaasg 85 
                                    ++s+ g+ +t  lP  +++v +             + ++           sL++ges + ++ ++ + taa g
  gi|119720239|ref|YP_920734.1| 248 TVSLDGLEITNKLPDRTSGVVFLLLpsrwsgsildSTSG-----NnlykLSLNPGESVKAKVVLQIPDTAAPG 315
                                    455566666666666666655554445554333322233.....24444699************999999876 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0021
                          DUF11  11 rpGdtvtytltvtNtgpasa.ngvvvtDtlPaglayvsvsasqgtasaltsvgsLeagesatlsftvrvt 79 
                                     +G   ++ +t++N g  +   ++vv+  lP+g +          +++ ++   L+ages++l++ v+v+
  gi|119720239|ref|YP_920734.1| 359 YAGRSASFLVTTRNIGEGDGvVELVVKG-LPPGYSWRIEDLN---GNVISK-LYLKAGESRQLKVVVSVP 423
                                    5788999*********988768888888.8999987666666...222222.579***********9986 PP

  == domain 4  score: 11.1 bits;  conditional E-value: 0.00026
                          DUF11   9 evrpGdtvtytltvtNtgpasangvvvt.DtlPaglayvsvsasqgtasaltsvgsLeagesatlsftvrvtrtaa 83 
                                    ev++G   t+ l v+Ntg +s+++v+++   +P gl+ v  s           v sL+a e a +++tv + +  +
  gi|119720239|ref|YP_920734.1| 468 EVTSGSSATFQLGVKNTGYSSLTNVRIEvSNVPRGLR-VNISPE--------VVLSLKAQENANFTVTVYAEPDVS 534
                                    799*********************9987345788888.555555........458899999999999998887665 PP

>> CarbopepD_reg_2  CarboxypepD_reg-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0    0.0003      0.45       1      68 [.      42     111 ..      42     126 .. 0.80
   2 !    5.9   0.0    0.0083        12      41      66 ..     201     226 ..     197     241 .. 0.81
   3 ?   -1.3   0.1       1.5   2.2e+03      42      59 ..     473     490 ..     454     514 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0003
                CarbopepD_reg_2   1 isGtVvdketkeplpgatVyvkgtk....kgtvTdenGnFelknlpagkytLvvsyvGyktqekkvtvskek 68 
                                    ++G Vvd   + p+  +++++ g      + + T + G F    l +g+y+     vGy+ ++++ ++s++ 
  gi|119720239|ref|YP_920734.1|  42 VHGVVVDPR-GAPISDVSILIFGEDntlvARVKTSMTGDFWA-LLAPGTYKASLIKVGYEAKTISFSISGDR 111
                                    679999976.69*********775412335677*******98.5999***99999**********9998773 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0083
                CarbopepD_reg_2  41 lpagkytLvvsyvGyktqekkvtvsk 66 
                                      +g+y ++v ++Gy+ q + +tv+ 
  gi|119720239|ref|YP_920734.1| 201 NASGRYNITVDVLGYTLQRRVITVDI 226
                                    5689***************9999964 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.5
                CarbopepD_reg_2  42 pagkytLvvsyvGyktqe 59 
                                     + +++L v+  Gy + +
  gi|119720239|ref|YP_920734.1| 473 SSATFQLGVKNTGYSSLT 490
                                    344566777777777743 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       1.3   1.9e+03      37      83 ..     167     211 ..     140     213 .. 0.74
   2 ?    3.8   0.0     0.046        68      56      83 ..     293     322 ..     278     329 .. 0.84
   3 ?   -0.9   0.0       1.3   1.9e+03      13      34 ..     356     377 ..     347     384 .. 0.85
   4 !   12.6   0.4   8.1e-05      0.12      14      82 ..     468     542 ..     457     548 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.3
                                    EEEEEEEETTEEEEEEEESEE-CTEEEEEEEEEE-S.-S-CEEEEEEE CS
                          CARDB  37 atkvalyldgelvgtvtvpsLaagesttvsftwtte.ategevtltvv 83 
                                     +++ +yl + +v+++    L++g++ + ++  +++  ++g + +tv 
  gi|119720239|ref|YP_920734.1| 167 GWTAGFYLGDLEVKSI---VLSPGQTLKLDLVLKVPyNASGRYNITVD 211
                                    5666677766665533...37888888888887777667788877775 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.046
                                    EE-CTEEEEEEEEEE-S..-S-CEEEEEEE CS
                          CARDB  56 sLaagesttvsftwtte..ategevtltvv 83 
                                    sL++ges++ ++  +++  a++g++t+ vv
  gi|119720239|ref|YP_920734.1| 293 SLNPGESVKAKVVLQIPdtAAPGNYTVGVV 322
                                    8**************9999999****9886 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1.3
                                    SEEETTSEEEEEEEEEE-SSS- CS
                          CARDB  13 seafvgeentitvtvkNqGtaa 34 
                                     ++++g++ ++ vt +N G+++
  gi|119720239|ref|YP_920734.1| 356 LNTYAGRSASFLVTTRNIGEGD 377
                                    57899999***********986 PP

  == domain 4  score: 12.6 bits;  conditional E-value: 8.1e-05
                                    EEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE....EEEEESEE-CTEEEEEEEEEE-S..-S-CEEEEEE CS
                          CARDB  14 eafvgeentitvtvkNqGtaasgatkvalyldgelv....gtvtvpsLaagesttvsftwtte..ategevtltv 82 
                                    e++ g++ t+++ vkN+G  + +++++++           +   v sL+a+e+++ ++t+ +e   ++g++++t+
  gi|119720239|ref|YP_920734.1| 468 EVTSGSSATFQLGVKNTGYSSLTNVRIEVSNVPRGLrvniSPEVVLSLKAQENANFTVTVYAEpdVSAGDYYITL 542
                                    678999************99888887777543333233445555699*******99999999999999***9987 PP

>> DUF916  Bacterial protein of unknown function (DUF916)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.17   2.5e+02      90     119 ..     151     180 ..     119     181 .. 0.73
   2 ?   -3.0   0.0       4.9   7.3e+03       8      37 ..     229     258 ..     223     260 .. 0.69
   3 ?    5.3   0.0     0.013        19      85     118 ..     290     323 ..     279     324 .. 0.86
   4 ?   -0.8   0.0       1.1   1.6e+03      85     104 ..     404     423 ..     393     428 .. 0.82
   5 ?    2.0   0.0      0.13     2e+02      17      42 ..     463     488 ..     455     499 .. 0.77
   6 ?   -2.3   0.0         3   4.4e+03      86     103 ..     510     527 ..     503     538 .. 0.55

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.17
                         DUF916  90 pakesktvklkikmPkeefdGvilGGiyve 119
                                    +   ++tv+l+ ++P+ ++ G +lG ++v+
  gi|119720239|ref|YP_920734.1| 151 KGSREETVTLSASAPSGWTAGFYLGDLEVK 180
                                    33456678888899***********99986 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.9
                         DUF916   8 penqidkkksYFdLkvkpgqeqele.vkikN 37 
                                     + q  ++ +Y  +k+ pg++ +l  ++i+N
  gi|119720239|ref|YP_920734.1| 229 RDPQLVTS-TYLSVKASPGSTVSLDgLEITN 258
                                    55566555.9999999999998885366666 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.013
                         DUF916  85 keitlpakesktvklkikmPkeefdGvilGGiyv 118
                                     +++l+++es+++k+ +++P+++  G +  G+ +
  gi|119720239|ref|YP_920734.1| 290 YKLSLNPGESVKAKVVLQIPDTAAPGNYTVGVVF 323
                                    5789********************9998888766 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 1.1
                         DUF916  85 keitlpakesktvklkikmP 104
                                    +++ l+a+es+++k+ +++P
  gi|119720239|ref|YP_920734.1| 404 SKLYLKAGESRQLKVVVSVP 423
                                    67889999999999999988 PP

  == domain 5  score: 2.0 bits;  conditional E-value: 0.13
                         DUF916  17 sYFdLkvkpgqeqelevkikNssdke 42 
                                    + F L+v+ g++ ++++ +kN+  ++
  gi|119720239|ref|YP_920734.1| 463 QNFYLEVTSGSSATFQLGVKNTGYSS 488
                                    5699*****************97544 PP

  == domain 6  score: -2.3 bits;  conditional E-value: 3
                         DUF916  86 eitlpakesktvklkikm 103
                                    e+ l  k ++++++++++
  gi|119720239|ref|YP_920734.1| 510 EVVLSLKAQENANFTVTV 527
                                    444444444444444443 PP

>> DUF1416  Protein of unknown function (DUF1416)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0     2e-05      0.03      19      73 ..      39      94 ..      30     114 .. 0.86
   2 ?   -3.2   0.0       5.5   8.3e+03      63      74 ..     312     323 ..     311     326 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2e-05
                        DUF1416 19 eaviqGkvtr.dgepvggayvRLLdssgeFtaevvtsaeGefrFfaapGeWtvRal 73
                                    + + G+v++  g+p++   + +  +++  +a v ts +G+f    apG+++   +
  gi|119720239|ref|YP_920734.1| 39 SVNVHGVVVDpRGAPISDVSILIFGEDNTLVARVKTSMTGDFWALLAPGTYKASLI 94
                                   56689****99*******9999****************************987544 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 5.5
                        DUF1416  63 aapGeWtvRala 74 
                                    aapG++tv ++ 
  gi|119720239|ref|YP_920734.1| 312 AAPGNYTVGVVF 323
                                    89*****98765 PP

>> fn3_6  Fibronectin type-III domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0         3   4.5e+03      34      70 ..      88     128 ..      70     137 .. 0.67
   2 ?   -2.1   0.0         3   4.5e+03      43      73 ..     389     424 ..     359     449 .. 0.62
   3 !   12.8   0.2   6.6e-05     0.098      14      73 ..     470     531 ..     457     542 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3
                          fn3_6  34 tYkakve....apegvkvtVePseLefsekgekksftvtvt 70 
                                    tYka++     + + ++ +++ ++L+++  + + +++++v+
  gi|119720239|ref|YP_920734.1|  88 TYKASLIkvgyEAKTISFSISGDRLHVELGEITLDYSLSVS 128
                                    66666653333346666667777777665555666666655 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3
                          fn3_6  43 egvkvtVeP......seLefsekgekksftvtvtakk 73 
                                    +g++ ++e       s+L ++ +ge+++ +v v++  
  gi|119720239|ref|YP_920734.1| 389 PGYSWRIEDlngnviSKLYLK-AGESRQLKVVVSVPL 424
                                    444444444445555667777.788888888777655 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 6.6e-05
                          fn3_6  14 elkgtvtvtRtvtnVgsse.atYkakve.apegvkvtVePse.Lefsekgekksftvtvtakk 73 
                                    ++ +++t++  v+n g s+ ++ +++v+  p+g++v+++P++ L+++ ++e+++ftvtv a+ 
  gi|119720239|ref|YP_920734.1| 470 TSGSSATFQLGVKNTGYSSlTNVRIEVSnVPRGLRVNISPEVvLSLK-AQENANFTVTVYAEP 531
                                    4577888888889988875355667765367*********9725665.**********98875 PP

>> DUF4832  Domain of unknown function (DUF4832)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0         2     3e+03     168     194 ..     184     209 ..     136     213 .. 0.57
   2 ?    4.2   0.0     0.023        35     168     196 ..     294     322 ..     283     333 .. 0.88
   3 ?    8.3   0.0    0.0013       1.9     109     195 ..     460     542 ..     453     554 .. 0.66

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2
                        DUF4832 168 wlpgttttitiklklpselakGkykvy 194
                                    + pg+t ++++ lk+p   a+G y++ 
  gi|119720239|ref|YP_920734.1| 184 LSPGQTLKLDLVLKVP-YNASGRYNIT 209
                                    3456666666666666.3345666655 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.023
                        DUF4832 168 wlpgttttitiklklpselakGkykvyLn 196
                                    + pg++++ ++ l++p++ a G+y+v++ 
  gi|119720239|ref|YP_920734.1| 294 LNPGESVKAKVVLQIPDTAAPGNYTVGVV 322
                                    679999999999**************975 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0013
                        DUF4832 109 lessslskkvkaggtlsleltlkNeGfAalynerkvelvlrdeegeekyklkldadprkwlpgttttitiklklpselak 188
                                     +  ++  +v++g++++++l +kN+G+++l n r +e+  + +  +++    + + + +++ +++ ++t+++  + ++++
  gi|119720239|ref|YP_920734.1| 460 YTTQNFYLEVTSGSSATFQLGVKNTGYSSLTNVR-IEVSNVPRGLRVN---ISPEVVLSLKAQENANFTVTVYAEPDVSA 535
                                    5566667778899****************99855.4444444444332...24444445555555666666666667777 PP

                        DUF4832 189 GkykvyL 195
                                    G+y + L
  gi|119720239|ref|YP_920734.1| 536 GDYYITL 542
                                    7776666 PP

>> MG2  MG2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       5.3   7.8e+03      11      33 ..      33      56 ..      26      75 .. 0.73
   2 ?    0.4   0.0      0.62   9.2e+02      35      74 ..     126     167 ..     115     172 .. 0.78
   3 ?   -1.3   0.0         2     3e+03      13      26 ..     186     200 ..     183     257 .. 0.55
   4 ?    7.7   0.0    0.0033       4.9      42      80 ..     283     321 ..     243     334 .. 0.78
   5 ?   -2.7   0.0       5.5   8.3e+03      39      62 ..     394     417 ..     391     429 .. 0.68
   6 ?   -0.4   0.0       1.1   1.6e+03      53      84 ..     515     544 ..     505     562 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 5.3
                                   E-TT-E.EEEEEEEESTTCSB--- CS
                            MG2 11 YrPget.Vslkallrdetlqglak 33
                                   ++++ t V++ +++ d+++ ++ +
  gi|119720239|ref|YP_920734.1| 33 LTAQSTsVNVHGVVVDPRGAPISD 56
                                   555555588899999988888877 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.62
                                    EEEEEEE-TTSSEEEEEEE..EE-CTTEEEEEEE--TT--SE CS
                            MG2  35 plkltirdpdgkevkelpl..atdetggaesefalpeaaklG 74 
                                    ++++++rd +    ++l++  +  e+g+ e +++l+++a+ G
  gi|119720239|ref|YP_920734.1| 126 SVSVELRDVRASCLSTLRIpvVLAEKGSREETVTLSASAPSG 167
                                    5677777777775555444449999************99988 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 2
                                    TT-EEEEEEEEES.T CS
                            MG2  13 PgetVslkallrd.e 26 
                                    Pg+t++l  +l++  
  gi|119720239|ref|YP_920734.1| 186 PGQTLKLDLVLKVpY 200
                                    666666666665531 PP

  == domain 4  score: 7.7 bits;  conditional E-value: 0.0033
                                    -TTSSEEEEEEEEE-CTTEEEEEEE--TT--SEEEEEEE CS
                            MG2  42 dpdgkevkelplatdetggaesefalpeaaklGeysvel 80 
                                    +++g++ ++l+l+  e+  a++ +++p++a  G+y+v +
  gi|119720239|ref|YP_920734.1| 283 STSGNNLYKLSLNPGESVKAKVVLQIPDTAAPGNYTVGV 321
                                    567788888998888888899999999999999999987 PP

  == domain 5  score: -2.7 bits;  conditional E-value: 5.5
                                    EEE-TTSSEEEEEEEEE-CTTEEE CS
                            MG2  39 tirdpdgkevkelplatdetggae 62 
                                    +i+d +g+++++l l++ e+   +
  gi|119720239|ref|YP_920734.1| 394 RIEDLNGNVISKLYLKAGESRQLK 417
                                    577888888888877777665544 PP

  == domain 6  score: -0.4 bits;  conditional E-value: 1.1
                                    EEE-CTTEEEEEEE--TT--SEEEEEEEEECS CS
                            MG2  53 latdetggaesefalpeaaklGeysvelsads 84 
                                    l+++e+  + +++    + + G+y ++l  ++
  gi|119720239|ref|YP_920734.1| 515 LKAQENANFTVTVYAEPDVSAGDYYITL--KP 544
                                    566777778888888999999****999..22 PP

>> DUF4352  Domain of unknown function (DUF4352)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       4.7     7e+03      89     113 ..     184     209 ..     178     214 .. 0.83
   2 ?   10.4   0.0   0.00041      0.61      78     109 ..     283     314 ..     276     325 .. 0.82
   3 ?   -2.8   0.0         5   7.4e+03      43      55 ..     478     490 ..     456     492 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 4.7
                                    E-TT-EEEEEEEEEESTT-CG.EEEE CS
                        DUF4352  89 lnpGkkvtGklvFdvpkgkkk.leLe 113
                                    l+pG++ + +lv  vp ++++ + ++
  gi|119720239|ref|YP_920734.1| 184 LSPGQTLKLDLVLKVPYNASGrYNIT 209
                                    88999999999999999999777665 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00041
                                    CCCTTB--EEEE-TT-EEEEEEEEEESTT-CG CS
                        DUF4352  78 sskaddlflgtlnpGkkvtGklvFdvpkgkkk 109
                                    s ++++l + +lnpG++v++k+v ++p  + +
  gi|119720239|ref|YP_920734.1| 283 STSGNNLYKLSLNPGESVKAKVVLQIPDTAAP 314
                                    5566679999*****************98876 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 5
                                    EEEEEE-SSS-EE CS
                        DUF4352  43 dvtvkNkgkealt 55 
                                    ++ vkN+g+++lt
  gi|119720239|ref|YP_920734.1| 478 QLGVKNTGYSSLT 490
                                    4567888877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (596 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.44
# Mc/sec: 4036.23
//
Query:       gi|119720240|ref|YP_920735.1|  [L=135]
Description: hypothetical protein Tpen_1335 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.8e-07   30.0   6.6      7e-07   29.2   6.6    1.5  1  PaREP1          Archaeal PaREP1/PaREP8 family
      5e-05   23.5   0.1    7.8e-05   22.9   0.1    1.3  1  DUF5618         Domain of unknown function (DUF5618)
  ------ inclusion threshold ------
      0.093   12.4   0.0       0.13   11.9   0.0    1.2  1  MRP-S34         Mitochondrial 28S ribosomal protein S34
      0.099   13.1   0.1       0.19   12.2   0.1    1.6  1  Telomere_reg-2  Telomere length regulation protein


Domain annotation for each model (and alignments):
>> PaREP1  Archaeal PaREP1/PaREP8 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   6.6   1.6e-10     7e-07       4     114 ..      11     126 ..       8     127 .. 0.65

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 1.6e-10
                         PaREP1   4 eeaekeleeAeellekG.......dlrqAaeKaykAvkalvkalaeknnlklleeaeekerwstkellkavaklleelgd 76 
                                    eeae +l+ A+e  ekG        +r +aeKa++Av+ +  al+ ++  ++   +  + ++++++ l+++a    e+ +
  gi|119720240|ref|YP_920735.1|  11 EEAENLLRVALEEFEKGvkegsdeAIRDSAEKAWRAVAKAADALLLAKGFSE---ENIETHRQKRLALEELAAKDPEVAR 87 
                                    66666666666666666333333379*****************999955444...2222222333333333333334444 PP

                         PaREP1  77 kevvd.lwklAldLHeyqfheaklelsdveskeeavkdl 114
                                    +++ d +++  ++LH+  f++++++ls+ +++ e+++++
  gi|119720240|ref|YP_920735.1|  88 QGFKDrFMAREYTLHVRCFYDGEYTLSSLREELEKARQF 126
                                    5555514456799**********************9986 PP

>> DUF5618  Domain of unknown function (DUF5618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.1   1.7e-08   7.8e-05      31     122 ..      33     131 ..       2     132 .. 0.68

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.7e-08
                                    HHHHHHHHHHHHHHHHHHHHHHH---S.....SS-.--HHHHHHHHHCC-HHHHHH.....HHHHHHHHIIIICCT---B CS
                        DUF5618  31 kkyvkeAggtAYsgvLlaldellgkkglek..kkrpksvetYkealkkldkkllke.....fnsaydvLhlagyydGiks 103
                                       ++  ++ A+ +v  a d+ll  kg ++   +++++     e+l+ +d ++ ++     f+   ++Lh+   ydG ++
  gi|119720240|ref|YP_920735.1|  33 DEAIRDSAEKAWRAVAKAADALLLAKGFSEenIETHRQKRLALEELAAKDPEVARQgfkdrFMAREYTLHVRCFYDGEYT 112
                                    4679999********************7653322233333345666667766654332223999999************* PP

                                    HHHHHHHHHHHHHHHHHHH CS
                        DUF5618 104 akvvkeglkaaeklikkie 122
                                     +  +e+l++a ++++ ++
  gi|119720240|ref|YP_920735.1| 113 LSSLREELEKARQFVEDVK 131
                                    ***************9997 PP

>> MRP-S34  Mitochondrial 28S ribosomal protein S34
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.9e-05      0.13      53     101 ..      18      66 ..       6      82 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.9e-05
                        MRP-S34  53 kawgektfrGknegkvkeisktnkadwrLvpkheeeeflekakpkepek 101
                                    ++  e+  +G++eg  + i+++ ++ wr v k  ++ +l+k  ++e+ +
  gi|119720240|ref|YP_920735.1|  18 RVALEEFEKGVKEGSDEAIRDSAEKAWRAVAKAADALLLAKGFSEENIE 66 
                                    67889999*************************9999998655555444 PP

>> Telomere_reg-2  Telomere length regulation protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   4.2e-05      0.19      50      99 ..      54     105 ..       3     107 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.2e-05
                 Telomere_reg-2  50 ltledkfdienfeelrln..alvallvatpekvaeylteeffsnqyslqqRi 99 
                                    l l + f++en+e+ r++  al +l++++pe + + + ++f++++y+l  R+
  gi|119720240|ref|YP_920735.1|  54 LLLAKGFSEENIETHRQKrlALEELAAKDPEVARQGFKDRFMAREYTLHVRC 105
                                    3467889*******999855788*************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       728  (0.0406046); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 892.53
//
Query:       gi|119720241|ref|YP_920736.1|  [L=120]
Description: DNA polymerase beta subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.7e-10   40.0   0.8    5.4e-10   39.4   0.8    1.3  1  NTP_transf_2    Nucleotidyltransferase domain
    0.00069   19.6   0.0     0.0011   19.0   0.0    1.4  1  Polbeta         Polymerase beta, Nucleotidyltransferase
     0.0083   16.3   0.3      0.063   13.5   0.3    2.0  1  DNA_pol_B_palm  DNA polymerase beta palm


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.4   0.8     9e-14   5.4e-10       2      65 ..      23      83 ..      22     109 .. 0.80

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 9e-14
                                   HHHHHHHHHHTTTSEEEEEHHHHCTTSCTT.SSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEE CS
                   NTP_transf_2  2 kklleelkelepvakvvlfGSyarGtalkg.SDiDllvvlpeevsrekkeegleklaeiikflee 65
                                   +++ +el e++ + +v++ GS arG++ +g SD+D+lvv+++evs+     ++++l    ++++e
  gi|119720241|ref|YP_920736.1| 23 ERVVDELVERYRPLEVIVAGSLARGEFVRGlSDVDILVVVEREVSD----SERFALRSVGDVDVE 83
                                   68899999***********************************986....444444444444444 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   1.8e-07    0.0011       5      53 ..      28      76 ..      25     119 .. 0.61

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.8e-07
                                   TTHHHHHHHHSTTEEEEEE-S----.--EEEEEEEESS---HHHHHHHHH CS
                        Polbeta  5 eilekekeielaylFGSrakgkare.eSDiDlavllkekldleeelelaa 53
                                   e++e++     +++ GS a+g++ +  SD+D+ v+++++ + +e++ l +
  gi|119720241|ref|YP_920736.1| 28 ELVERY-RPLEVIVAGSLARGEFVRgLSDVDILVVVEREVSDSERFALRS 76
                                   566777.66667888******987559************55555554433 PP

>> DNA_pol_B_palm  DNA polymerase beta palm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.3   1.1e-05     0.063      12      56 ..      24      69 ..      15     109 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.1e-05
                                   HHHHHHHHHH-TT-EEEE-HHHHTT-SEES..SEEEEEEBTTBSTTS CS
                 DNA_pol_B_palm 12 alvkkaakeldpevevivcGSYRRgaessG..DvDvlitkkdakses 56
                                   ++v + +++  + +eviv+GS  Rg+   G  DvD+l+  +++ s+s
  gi|119720241|ref|YP_920736.1| 24 RVVDELVERY-RPLEVIVAGSLARGEFVRGlsDVDILVVVEREVSDS 69
                                   4444444444.4489**********9888888******998887754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 797.79
//
Query:       gi|119720242|ref|YP_920737.1|  [L=69]
Description: hypothetical protein Tpen_1337 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0054   16.6   0.5        6.3    6.7   0.0    2.9  2  HSBP1     Heat shock factor binding protein 1


Domain annotation for each model (and alignments):
>> HSBP1  Heat shock factor binding protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.0   0.00035       6.3      24      37 ..      20      33 ..      16      36 .. 0.86
   2 !    6.1   0.2   0.00055       9.8      34      46 ..      53      65 ..      41      69 .] 0.77

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.00035
                          HSBP1 24 qilsriDdMssriD 37
                                   ++  r+D+++ r+D
  gi|119720242|ref|YP_920737.1| 20 ELKRRMDELGGRVD 33
                                   5668*********9 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.00055
                          HSBP1 34 sriDdLEksiadl 46
                                   + ++dLEk ia+l
  gi|119720242|ref|YP_920737.1| 53 KAVEDLEKVIASL 65
                                   5689999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       708  (0.0394891); expected 358.6 (0.02)
Passed bias filter:                      592  (0.0330191); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 486.12
//
Query:       gi|119720243|ref|YP_920738.1|  [L=535]
Description: hypothetical protein Tpen_1338 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.5e-08   34.6   0.0    7.3e-07   29.1   0.0    2.4  1  Cas_DxTHG  CRISPR-associated (Cas) DxTHG family


Domain annotation for each model (and alignments):
>> Cas_DxTHG  CRISPR-associated (Cas) DxTHG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0     4e-11   7.3e-07       2     359 .]       6     502 ..       5     502 .. 0.55

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 4e-11
                      Cas_DxTHG   2 lisflGt.gnykevkYe.................lkeeeeeeketsfvqeallellaekedpdkvvilltdtlad..... 58 
                                    +++++G  gn+ + +Y+                     ++ +   s ++++  + l+e + +  vv+ + d+l+      
  gi|119720243|ref|YP_920738.1|   6 VVATWGFpGNWLKERYSaavppanvdkwhrlsewS--IGGYVEAHSPTPVEA-KALSEMGFDVGVVVYALDSLSAvprls 82 
                                    89********************9999999999641..333333333333333.33456678899********999*8876 PP

                      Cas_DxTHG  59 ....keaeekeeaak.lkeeleelle...................................iekvdveiipgggte.... 94 
                                               ++++ l eel+++                                     + kv+ +++pg g +    
  gi|119720243|ref|YP_920738.1|  83 vpsdD------DVRGkLVEELNKYVDgwlnkdpegygevrgraekvaglfvsgyfgevgfpLDKVSTVVLPGTGVYalgp 156
                                    44331......34444555552222233333333333344444445556677888888889999999************* PP

                      Cas_DxTHG  95 ..............eelweifekllekleen..deiilDiThGfrylPvla.......llalaylrnvknltikgiyYga 151
                                                  +  + +  +lle+++    d +++D ThG++ylP++a       +  ++ + + +++ ++ +    
  gi|119720243|ref|YP_920738.1| 157 gskgkryvfrgspqNAAVAMELDLLERVDAFkpDAVVFDSTHGINYLPIVAkrvvervA-RVYSALEGRKVCVATV---- 231
                                    ***9988888888544777888*****999889******************99999953.4444444444444444.... PP

                      Cas_DxTHG 152 fkeeeedPil............dlteflelsdwltaverflktgdaeklaellrekkekkkeklkklkklkeklkkelee 219
                                       ++ +P              d++ f   +   + +e++l + d e+++ l       k ek k+  +lke l+ke+ e
  gi|119720243|ref|YP_920738.1| 232 ---QSDTPAGglaglelgvmvvDVKVFSASP--REVLEELLPHFDSEPYRMLK------KDEKVKPPDSLKE-LRKEFGE 299
                                    ...3356666777777777777777777777..33333333333666666666......2223333334443.5556666 PP

                      Cas_DxTHG 220 fskalelirp.lellekaekleke...................iveklkeeleei.esleeeesakplel.......... 268
                                    +++   l ++ +el    + l+ +                   +       le++   l+         +          
  gi|119720243|ref|YP_920738.1| 300 LKEVKPLAKAlVELA--GYGLTLYlcskvrelaggdfssmagrL-------LERVrGALY---------Erdvasggevr 361
                                    666666666433333..222222222222333333222222222.......222211111.........02222233334 PP

                      Cas_DxTHG 269 ...................lldeikkklekf..lkkq....ikwclekgliqqaltllreliislllegedilnkkkrre 323
                                                       +l ++  +l+++  +  q    ++ +le g+      l + l+      g ++++ k+r +
  gi|119720243|ref|YP_920738.1| 362 vehvyafsdsvpgvleavyVLGRVVPRLAELcgVDEQgfmgVDRLLEVGRSLGLTRLGERLL------GYEVSDVKRRVS 435
                                    44444444455555555555555555555555533334555555566655555555555555......666666666644 PP

                      Cas_DxTHG 324 ei...................eeelknlskvekksseekeek...............................lsniRNd 353
                                     +                                                                         + RN+
  gi|119720243|ref|YP_920738.1| 436 AArdagielegrvvpyaavydA-------------------VegllrkegvgdsvrreavekfkeilgrgvkcDVDARNF 496
                                    4444433333333333222220...................033333334444444444444444444444445777788 PP

                      Cas_DxTHG 354 iaHaGl 359
                                    +aHaGl
  gi|119720243|ref|YP_920738.1| 497 YAHAGL 502
                                    888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (535 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 3436.14
//
Query:       gi|119720244|ref|YP_920739.1|  [L=59]
Description: hypothetical protein Tpen_1339 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.069   13.7   0.1       0.12   12.9   0.1    1.4  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   6.6e-06      0.12      80     107 ..       2      29 ..       1      33 [. 0.91

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.6e-06
                                    HHHHHHHHHHSBHHHHHHHHHHHHHT-E CS
                            PIN  80 eaaeialkygllpnDaliaAtAkehgik 107
                                    +a+e+++++++ + D++ +AtA++ +++
  gi|119720244|ref|YP_920739.1|   2 RAGELKKRLRIALPDCYTIATAQALDAT 29 
                                    799********************98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 440.89
//
Query:       gi|119720245|ref|YP_920740.1|  [L=80]
Description: AbrB family transcriptional regulator [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-10   41.2   0.6    2.8e-10   39.9   0.2    1.8  2  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an


Domain annotation for each model (and alignments):
>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   0.2   1.6e-14   2.8e-10       2      42 ..       6      46 ..       5      48 .. 0.95
   2 ?   -0.6   0.0     0.077   1.4e+03      15      23 ..      61      69 ..      49      73 .. 0.57

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 1.6e-14
                                   EETTEEEEEE-CCCHHHCCEECTCEEEEEECTTCCCCCCCH CS
                 MazE_antitoxin  2 kvGnsgavriPkevrfelgireGdevelevdgdkiilrplk 42
                                   +v ++g v +Pk +r+++gi+eGdev  ev g+ i+l+pl+
  gi|119720245|ref|YP_920740.1|  6 RVRRKGVVILPKKLREAAGISEGDEVYAEVAGGAIVLKPLR 46
                                   6889***********************************97 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.077
                                   CHHHCCEEC CS
                 MazE_antitoxin 15 vrfelgire 23
                                   +r+e +++e
  gi|119720245|ref|YP_920740.1| 61 LREEYELEE 69
                                   345555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 520.07
//
Query:       gi|119720246|ref|YP_920741.1|  [L=146]
Description: hypothetical protein Tpen_1341 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
        0.1   12.5   0.0       0.17   11.8   0.0    1.3  1  RNaseH_like  Ribonuclease H-like
       0.33   11.1   4.8       0.58   10.3   2.5    2.4  2  ELK          ELK domain


Domain annotation for each model (and alignments):
>> RNaseH_like  Ribonuclease H-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   1.9e-05      0.17     110     144 ..       7      41 ..       4      42 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.9e-05
                    RNaseH_like 110 kelikevvgmvegsgfeakiKPesfaAssvAdryt 144
                                    +e ++ev+g ++  gf++ + Pe faA   Ad yt
  gi|119720246|ref|YP_920741.1|   7 EERVREVCGELRRRGFDCDVSPEEFAAYMEADTYT 41 
                                    5779****************************998 PP

>> ELK  ELK domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.15   1.3e+03      11      16 ..     118     123 ..     118     123 .. 0.87
   2 ?   10.3   2.5   6.4e-05      0.58       5      13 ..     136     144 ..     135     144 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.15
                            ELK  11 sGyLss 16 
                                    +GyLs+
  gi|119720246|ref|YP_920741.1| 118 AGYLSD 123
                                    6***97 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 6.4e-05
                            ELK   5 qLLrKYsGy 13 
                                    +LLrKYsGy
  gi|119720246|ref|YP_920741.1| 136 RLLRKYSGY 144
                                    7*******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1040.51
//
Query:       gi|119720247|ref|YP_920742.1|  [L=278]
Description: CRISPR-associated protein APE2256 family [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.8e-43  147.1   0.0    4.3e-43  146.5   0.0    1.3  1  Cas_APE2256  CRISPR-associated protein (Cas_APE2256)


Domain annotation for each model (and alignments):
>> Cas_APE2256  CRISPR-associated protein (Cas_APE2256)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.5   0.0   2.4e-47   4.3e-43       1     136 []      70     217 ..      70     217 .. 0.96

  Alignments for each domain:
  == domain 1  score: 146.5 bits;  conditional E-value: 2.4e-47
                    Cas_APE2256   1 kkasAElnallkllekkkkeqke...elvllssdTaaGklvaeilkeylee......egaevevveieklsdlgree..F 69 
                                    ++asAElnall +le++k + ++   el+++s+dT++G ++a+++++y +e       ga+v+v+e++kl+++g++   F
  gi|119720247|ref|YP_920742.1|  70 REASAELNALLGFLERRKGSLAGadvELMFYSTDTGTGYFCARLVERYARErlrgalGGARVQVQEPVKLKKFGWGYeyF 149
                                    589***************99988999******************************999***************76666* PP

                    Cas_APE2256  70 reglrnLveklarevknkkregekvlinaTgGfKpeiavltlvall.ladevyYihEsfsevvelPkl 136
                                    +e+l ++v+k+ar + nkkr+g++v++naT+GfK+e+a+ltlv+ll +ad+v+Y+hE++++v+elP l
  gi|119720247|ref|YP_920742.1| 150 HEALLDMVDKAARLMANKKRSGYRVYVNATAGFKVEAAYLTLVSLLvGADSVFYVHEATRDVIELPVL 217
                                    ******************************************************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2061.05
//
Query:       gi|119720248|ref|YP_920743.1|  [L=321]
Description: chromosome segregation ATPases-like [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-14   53.2  14.7    1.6e-05   25.4   0.3    4.3  4  SlyX             SlyX
    3.4e-10   40.4   1.8     0.0024   18.3   0.7    3.4  3  DUF16            Protein of unknown function DUF16
    5.9e-09   36.3   0.9    0.00012   22.2   0.1    2.7  2  Fib_alpha        Fibrinogen alpha/beta chain family
    9.7e-09   35.1  15.3    9.1e-05   22.4   0.6    4.0  3  TMF_DNA_bd       TATA element modulatory factor 1 DNA binding
    3.7e-08   33.3  11.0    2.2e-06   27.6   4.2    2.8  3  BRE1             BRE1 E3 ubiquitin ligase
    7.5e-08   32.6   6.1      0.029   14.7   0.1    3.7  3  BLOC1_2          Biogenesis of lysosome-related organelles co
      2e-07   30.1   6.3    3.2e-07   29.4   6.3    1.3  1  AAA_13           AAA domain
    9.1e-07   27.5   7.2    1.2e-06   27.1   7.2    1.1  1  Cast             RIM-binding protein of the cytomatrix active
    3.5e-06   27.2  12.9     0.0055   16.8   2.1    3.1  4  ADIP             Afadin- and alpha -actinin-Binding
    1.4e-05   24.5  18.4       0.11   12.1   0.1    5.2  6  Trimer_CC        Trimerisation motif
    1.8e-05   24.9   8.4       0.36   11.0   1.1    3.3  3  CEP209_CC5       Coiled-coil region of centrosome protein CE2
    3.6e-05   23.3   9.6       0.29   10.8   0.1    5.3  5  Vac_Fusion       Chordopoxvirus multifunctional envelope prot
    5.4e-05   21.6   6.3    6.8e-05   21.2   6.3    1.1  1  HOOK             HOOK protein
    7.5e-05   23.0   0.9        4.4    7.8   0.0    4.3  4  FlaC_arch        Flagella accessory protein C (FlaC)
    0.00012   21.1  17.8      0.049   12.5   0.4    2.1  2  Spc7             Spc7 kinetochore protein
    0.00013   21.4   6.7    0.00021   20.7   6.7    1.2  1  ALIX_LYPXL_bnd   ALIX V-shaped domain binding to HIV
    0.00013   22.1   6.5     0.0024   18.0   2.4    2.2  2  UPF0242          Uncharacterised protein family (UPF0242) N-t
    0.00014   21.3   8.4       0.12   11.7   2.0    2.2  2  GAS              Growth-arrest specific micro-tubule binding
    0.00015   20.8  11.1     0.0047   15.9   8.1    2.0  2  DUF812           Protein of unknown function (DUF812)
    0.00027   21.0   5.5       0.12   12.4   3.3    2.9  2  DUF1664          Protein of unknown function (DUF1664)
    0.00028   21.0  13.2      0.062   13.5   2.0    4.3  6  XhlA             Haemolysin XhlA
    0.00037   20.6   0.6        0.2   11.7   0.4    2.8  2  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
    0.00059   20.1  16.9      0.074   13.3   6.5    3.8  3  FliJ             Flagellar FliJ protein
    0.00067   17.7   1.4    0.00086   17.3   1.4    1.0  1  Herpes_U30       Herpes virus tegument protein U30
    0.00084   19.6  22.1      0.036   14.3  13.5    2.4  2  ATG16            Autophagy protein 16 (ATG16)
     0.0012   18.0  11.8      0.025   13.7   0.6    2.1  2  Atg14            Vacuolar sorting 38 and autophagy-related su
     0.0017   18.7  38.8       0.75   10.2  14.9    3.3  2  HrpB7            Bacterial type III secretion protein (HrpB7)
     0.0018   17.6   3.8       0.12   11.6   2.3    2.2  2  FmiP_Thoc5       Fms-interacting protein/Thoc5
     0.0025   18.1  15.6      0.025   14.8   9.1    2.3  2  Jnk-SapK_ap_N    JNK_SAPK-associated protein-1
     0.0041   16.4   0.7     0.0063   15.7   0.7    1.3  1  Taxilin          Myosin-like coiled-coil protein
     0.0044   17.1   4.0        2.7    8.1   0.1    3.3  3  DUF2730          Protein of unknown function (DUF2730)
     0.0047   16.7   0.5       0.62    9.7   0.1    2.9  3  LXG              LXG domain of WXG superfamily
     0.0059   16.8   5.5       0.55   10.5   0.0    3.2  3  Spc24            Spc24 subunit of Ndc80
     0.0062   14.9   0.2     0.0079   14.5   0.2    1.1  1  Gp58             gp58-like protein
     0.0063   16.8   5.7      0.015   15.5   0.8    3.0  3  KxDL             Uncharacterized conserved protein
     0.0065   15.8   4.7      0.022   14.0   3.7    1.9  2  TMPIT            TMPIT-like protein
      0.007   15.8   5.1      0.048   13.1   5.2    2.4  1  DUF4618          Domain of unknown function (DUF4618)
      0.007   16.0  14.8      0.028   14.1  14.8    1.9  1  Lebercilin       Ciliary protein causing Leber congenital ama
  ------ inclusion threshold ------
      0.011   15.2   5.4        1.2    8.5   2.1    2.5  2  Helo_like_N      Fungal N-terminal domain of STAND proteins
      0.011   16.1   3.2        2.5    8.5   0.2    3.4  4  Flagellin_C      Bacterial flagellin C-terminal helical regio
      0.011   14.9   4.8      0.014   14.5   4.8    1.1  1  DUF4686          Domain of unknown function (DUF4686)
      0.011   15.8  12.9        4.9    7.3   1.0    5.2  6  TolA_bind_tri    TolA binding protein trimerisation
      0.012   15.7   4.9       0.99    9.6   0.0    3.8  3  MbeD_MobD        MbeD/MobD like
      0.013   15.5  18.2       0.26   11.2   0.5    3.8  4  Wtap             WTAP/Mum2p family
      0.013   15.1   6.4       0.12   12.0   4.0    2.5  2  PTRF_SDPR        PTRF/SDPR family
      0.014   15.0   5.6        1.5    8.4   4.2    2.8  2  DUF4795          Domain of unknown function (DUF4795)
      0.015   15.3  10.7        2.4    8.1   0.2    3.7  5  Prefoldin_2      Prefoldin subunit
      0.015   14.7   5.7       0.95    8.8   5.2    2.2  2  Not3             Not1 N-terminal domain, CCR4-Not complex com
      0.017   14.5  11.0       0.21   10.9   2.0    2.7  2  HemX             HemX, putative uroporphyrinogen-III C-methyl
      0.019   15.3  17.2       0.69   10.3   3.3    4.5  4  Sbi-IV           C3 binding domain 4 of IgG-bind protein SBI
       0.02   14.3   1.0       0.58    9.5   0.2    2.7  3  DUF5305          Family of unknown function (DUF5305)
      0.021   14.9   9.8       0.21   11.7   6.1    2.3  2  Mod_r            Modifier of rudimentary (Mod(r)) protein
      0.024   14.2   3.4      0.039   13.5   3.4    1.3  1  TMCO5            TMCO5 family
      0.025   14.4  14.0          1    9.3   0.5    5.3  5  PKcGMP_CC        Coiled-coil N-terminus of cGMP-dependent pro
      0.033   14.9   6.6        1.1   10.0   1.4    3.5  2  Sulfatase_C      C-terminal region of aryl-sulfatase
      0.035   11.7  17.0      0.048   11.2  17.0    1.1  1  DUF3584          Protein of unknown function (DUF3584)
      0.038   14.3  14.3        2.4    8.5   8.9    4.2  3  DUF5082          Domain of unknown function (DUF5082)
      0.038   14.3  10.7        7.3    7.0   1.0    3.6  3  CC2-LZ           Leucine zipper of domain CC2 of NEMO, NF-kap
      0.044   13.7   6.2       0.33   10.9   4.4    2.7  2  NCD2             NAB conserved region 2 (NCD2)
      0.047   13.5   2.3        1.8    8.4   0.4    2.4  2  Nsp1_C           Nsp1-like C-terminal region
      0.047   13.9   7.2        1.4    9.1   1.8    3.2  3  COG5             Golgi transport complex subunit 5
      0.048   13.7  13.7       0.98    9.4   7.0    2.2  2  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
      0.048   13.5  12.6        0.3   10.9   8.6    2.3  2  DUF724           Protein of unknown function (DUF724)
      0.049   13.9   0.5        1.7    8.9   0.3    2.7  3  DUF3130          Protein of unknown function (DUF3130
      0.051   12.2   5.4       0.51    8.9   5.4    2.1  1  FapA             Flagellar Assembly Protein A
      0.053   13.6  19.5        3.5    7.8   1.6    5.9  6  Exonuc_VII_S     Exonuclease VII small subunit
      0.061   11.5   7.9       0.88    7.7   4.7    2.0  2  EzrA             Septation ring formation regulator, EzrA
      0.072   12.4  18.0        3.9    6.7  18.0    2.1  1  DUF4407          Domain of unknown function (DUF4407)
      0.076   12.8   3.8       0.54   10.1   0.5    2.5  2  Spc29            Spindle Pole Component 29
      0.079   12.8  28.8       0.11   12.3  16.2    2.2  2  ERM              Ezrin/radixin/moesin family
       0.08   13.3   3.6         50    4.4   0.1    4.1  4  ANAPC16          Anaphase-promoting complex, subunit 16
      0.082   13.2   1.7         43    4.5   0.8    3.3  3  DUF948           Bacterial protein of unknown function (DUF94
      0.086   12.2   5.8        1.3    8.3   0.7    2.0  2  FAM76            FAM76 protein
      0.095   11.1  10.6       0.61    8.5  10.9    1.9  1  BicD             Microtubule-associated protein Bicaudal-D
       0.12   10.7  11.9       0.27    9.5  11.9    1.4  1  MAD              Mitotic checkpoint protein
       0.14   11.6   9.1       0.22   11.0   5.5    2.0  2  Leu_zip          Leucine zipper
       0.14   10.8  14.2        3.2    6.4   2.3    3.0  1  Tektin           Tektin family
       0.15   11.9  12.2       0.51   10.1   8.2    2.1  1  KASH_CCD         Coiled-coil region of CCDC155 or KASH
       0.16   12.4  12.8       0.86   10.0   8.0    2.1  2  Fez1             Fez1
       0.16   12.3   0.3       0.97    9.7   0.0    2.2  1  DUF5071          Domain of unknown function (DUF5071)
       0.16   11.5  14.9       0.38   10.3   9.7    2.2  2  Filament         Intermediate filament protein
       0.19   11.3   0.5        6.7    6.4   0.1    2.6  3  DUF2674          Protein of unknown function (DUF2674)
        0.2   11.5  13.7       0.57   10.0   3.3    3.1  3  DUF1465          Protein of unknown function (DUF1465)
       0.21   11.6  26.7       0.19   11.8   8.9    2.9  3  DHR10            Designed helical repeat protein 10 domain
       0.22   10.8  16.3       0.59    9.4   2.2    3.1  3  DUF3450          Protein of unknown function (DUF3450)
       0.23   11.7  12.2    2.6e+02    1.9   0.1    4.4  2  DUF3782          Protein of unknown function (DUF3782)
       0.24   11.3   2.1        1.8    8.4   0.8    2.4  2  Sec8_exocyst     Sec8 exocyst complex component specific doma
       0.28   11.3   9.7       0.39   10.8   7.7    2.2  2  Cob_adeno_trans  Cobalamin adenosyltransferase
       0.28   10.8  11.6        1.8    8.1   8.6    2.5  2  Phage_GPO        Phage capsid scaffolding protein (GPO) serin
       0.29   10.9   0.5        4.6    7.0   0.8    2.1  2  Bacillus_HBL     Bacillus haemolytic enterotoxin (HBL)
        0.3   10.3   3.6       0.66    9.2   3.0    1.7  2  DUF2130          Uncharacterized protein conserved in bacteri
        0.3   10.6   9.0       0.44   10.1   5.4    2.3  2  Paralemmin       Paralemmin
        0.3   11.0   3.6        8.9    6.3   1.1    2.9  3  MIP-T3_C         Microtubule-binding protein MIP-T3 C-termina
       0.31   11.4  13.8         15    6.0   1.2    4.3  4  Csm1_N           Csm1 N-terminal domain
       0.37   10.6   8.4       0.78    9.5   5.4    2.1  2  TACC_C           Transforming acidic coiled-coil-containing p
       0.39   10.8   6.2         13    5.9   0.3    3.4  3  Med9             RNA polymerase II transcription mediator com
       0.39    8.9   8.7        0.2    9.9   0.1    2.5  2  Fusion_gly       Fusion glycoprotein F0
        0.4    9.7   2.5       0.67    8.9   1.4    1.8  2  DUF3818          Domain of unknown function in PX-proteins (D
       0.42   10.1  33.3         10    5.6  24.4    2.6  2  PspA_IM30        PspA/IM30 family
       0.46   11.5  22.6        3.4    8.7   4.4    4.1  5  DUF1484          Protein of unknown function (DUF1484)
       0.57   10.0   5.5         12    5.7   1.6    3.0  2  Dynactin_p22     Dynactin subunit p22
       0.58   10.2   2.5        6.6    6.8   0.1    2.5  2  DUF1043          Protein of unknown function (DUF1043)
        0.6    9.9   5.3          4    7.3   1.8    2.4  2  DUF2570          Protein of unknown function (DUF2570)
       0.61   10.1  11.4        1.4    9.0   1.2    3.1  3  LidA_Long_CC     LidA long coiled-coil domain
       0.61    8.9   5.2       0.94    8.3   5.2    1.3  1  LMBR1            LMBR1-like membrane protein
       0.75    9.9  17.1          7    6.8   1.5    4.0  4  ABC_tran_Xtn     ABC transporter
       0.75   10.2  15.1       0.73   10.2   9.0    2.6  2  DUF4200          Domain of unknown function (DUF4200)
       0.78    9.4  12.9        3.1    7.4  12.9    1.8  1  TMP_2            Prophage tail length tape measure protein
       0.81    9.3   2.8         21    4.7   0.0    2.7  2  Phage_tail_NK    Sf6-type phage tail needle knob or tip of so
       0.84    9.7  25.3          2    8.5  16.9    2.5  2  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
       0.86    9.8   6.1        4.4    7.5   1.5    2.9  2  PHM7_cyt         Cytosolic domain of 10TM putative phosphate 
       0.91    8.2   6.7        1.4    7.6   6.7    1.3  1  Herpes_UL17      Herpesvirus UL17 protein
          1    8.2   5.9        1.2    8.0   5.2    1.4  1  FemAB            FemAB family
          1    9.7  25.2    1.8e+04   -9.9  25.2    4.0  0  ABC_tran_CTD     ABC transporter C-terminal domain
          1   10.2   5.9         54    4.7   0.1    3.7  4  EF-hand_11       EF-hand domain
        1.1    9.6  11.4        3.9    7.8   1.4    2.3  2  DUF641           Plant protein of unknown function (DUF641)
        1.2    9.4   8.4       0.66   10.2   4.2    2.1  2  zf-C4H2          Zinc finger-containing protein
        1.3    9.0  10.6        1.5    8.8   3.4    2.5  2  Rootletin        Ciliary rootlet component, centrosome cohesi
        1.4    9.2  18.2        3.6    7.9  10.2    3.1  3  Troponin         Troponin
        1.5    9.3  13.5         25    5.3   2.1    4.3  4  CLZ              C-terminal leucine zipper domain of cyclic n
        1.6    9.5   7.8       0.98   10.1   1.6    2.8  2  CDH1_2_SANT_HL1  CDH1/2 SANT-Helical linker 1
        1.9    8.0  13.4        4.2    6.9   9.7    2.5  2  HAUS-augmin3     HAUS augmin-like complex subunit 3
          2    7.3   6.7        9.2    5.1   3.6    2.2  2  Vps53_N          Vps53-like, N-terminal
        2.1    8.8  29.3       0.27   11.7  11.3    3.8  3  BTAD             Bacterial transcriptional activator domain
        2.2    8.4  29.7         13    6.0   3.6    3.5  3  CENP-Q           CENP-Q, a CENPA-CAD centromere complex subun
        2.6    8.3  20.0        5.1    7.3   1.3    3.3  3  TMF_TATA_bd      TATA element modulatory factor 1 TATA bindin
        2.9    6.3  22.8        5.3    5.4  22.8    1.3  1  FUSC             Fusaric acid resistance protein family
        3.2    8.4   8.1         10    6.8   1.1    2.7  3  BST2             Bone marrow stromal antigen 2
        3.3    7.4   5.1         42    3.8   5.1    2.5  1  UBN_AB           Ubinuclein conserved middle domain
        3.5    8.1  14.9         15    6.1   5.0    2.3  2  T3SSipB          Type III cell invasion protein SipB
        3.7    7.7   9.5        7.3    6.7   0.2    4.2  3  DUF5632          Family of unknown function (DUF5632)
        3.7    8.1  24.7         11    6.5   3.1    3.0  3  APG6_N           Apg6 coiled-coil region
        3.9    8.2   4.9         96    3.7   1.5    3.3  4  YabA             Initiation control protein YabA
        5.1    7.3   6.5         10    6.3   6.5    1.5  1  MutS_III         MutS domain III
        5.2    7.0  12.1    1.7e+02    2.1   9.7    3.6  2  Prefoldin        Prefoldin subunit
        5.2    7.2  10.0        7.3    6.7   6.7    2.2  2  CREPT            Cell-cycle alteration and expression-elevate
        5.2    7.6  18.5        7.4    7.1   0.7    2.4  3  FlgN             FlgN protein
        5.3    7.6  17.8         32    5.1   1.1    3.5  3  ZapB             Cell division protein ZapB
        5.9    7.4  20.7        5.9    7.3   4.4    4.6  5  DUF2218          Uncharacterized protein conserved in bacteri
        6.5    6.1  11.1         28    4.1  11.1    2.1  1  CAP_N            Adenylate cyclase associated (CAP) N termina
        6.6    7.1  23.6        3.2    8.1   0.5    4.2  3  TPR_12           Tetratricopeptide repeat
        6.7    6.7   7.0         10    6.2   0.6    3.3  3  P4Ha_N           Prolyl 4-Hydroxylase alpha-subunit, N-termin
        7.5    6.1  11.0          6    6.4   0.4    2.3  2  HAUS6_N          HAUS augmin-like complex subunit 6 N-terminu
        7.9    6.1  10.2        7.3    6.2   8.1    1.9  2  YkyA             Putative cell-wall binding lipoprotein
        8.4    5.7  26.6         15    4.8  20.2    2.2  1  Tropomyosin      Tropomyosin


Domain annotation for each model (and alignments):
>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.2      0.39        48       7      46 ..      31      70 ..      28      77 .. 0.55
   2 !   12.7   0.5    0.0012      0.15       2      54 ..      54     106 ..      51     110 .. 0.56
   3 !   22.0   0.7   1.5e-06   0.00018       2      42 ..     110     150 ..     109     155 .. 0.93
   4 !   25.4   0.3   1.3e-07   1.6e-05       2      53 ..     152     203 ..     151     211 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.39
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                           SlyX  7 eLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaer 46
                                   +L  +l  + +++e+L ++ a+ +++++rl++ ++ l e 
  gi|119720248|ref|YP_920743.1| 31 DLRAELKGLREAVERLVEAHARAEERLSRLEAAVAGLGEA 70
                                   4444444455566666666666666666666666655555 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.0012
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXX CS
                           SlyX   2 eerleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkeleess 54 
                                    eerl +LE  +a + +++ + ++++a+ +  ++r  + +++l+  ++ l+e++
  gi|119720248|ref|YP_920743.1|  54 EERLSRLEAAVAGLGEAVSRHSEAIARLEVAVARHDEAVARLEAAVARLAEAQ 106
                                    56666666666666666655555555555555555555555555555555554 PP

  == domain 3  score: 22.0 bits;  conditional E-value: 1.5e-06
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           SlyX   2 eerleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrl 42 
                                    eerl +LE+ +a q + i +L ++v ++ + i+rl++ +++
  gi|119720248|ref|YP_920743.1| 110 EERLARLEEAVARQSESIAKLEAAVSKHSEVIARLEAAVAK 150
                                    89**********************************98875 PP

  == domain 4  score: 25.4 bits;  conditional E-value: 1.3e-07
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXX CS
                           SlyX   2 eerleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkelees 53 
                                    +e + +LE  +a +++ i +L +++a++++ i+rl++ +r la ++  l+e+
  gi|119720248|ref|YP_920743.1| 152 DETIARLEKAVAKHDESIARLEKAIARHDEAIARLEEAVRGLAAQVGRLSEA 203
                                    5889******************************************999886 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   0.00091      0.11      38     103 ..      52     117 ..      29     118 .. 0.92
   2 !   18.3   0.7   1.9e-05    0.0024      31      83 ..     108     160 ..     100     162 .. 0.88
   3 !   15.5   0.1   0.00015     0.019      33      78 ..     152     197 ..     144     214 .. 0.52

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00091
                                    HHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHHHHHHHHHHC CS
                          DUF16  38 kieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetleliletLqkinkRlDsie 103
                                    + e++++ l+  ++ l ++v++  e i +l+v +   +e++ +++ ++  ++e+ +k ++Rl ++e
  gi|119720248|ref|YP_920743.1|  52 RAEERLSRLEAAVAGLGEAVSRHSEAIARLEVAVARHDEAVARLEAAVARLAEAQAKSEERLARLE 117
                                    57899999999999*******************************999999999999999999987 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 1.9e-05
                                    .BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH....... CS
                          DUF16  31 snkqrLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvde 83 
                                      ++rL ++e+ v+ + e+i+kle +v+k  e i +l++ + + +e + ++++
  gi|119720248|ref|YP_920743.1| 108 KSEERLARLEEAVARQSESIAKLEAAVSKHSEVIARLEAAVAKHDETIARLEK 160
                                    56899************************************999999887665 PP

  == domain 3  score: 15.5 bits;  conditional E-value: 0.00015
                                    HHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.. CS
                          DUF16  33 kqrLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeel 78 
                                    ++ + ++e+ v+k++e+i++le+++ + +e i +l++ +    +++
  gi|119720248|ref|YP_920743.1| 152 DETIARLEKAVAKHDESIARLEKAIARHDEAIARLEEAVRGLAAQV 197
                                    3344445555555555555555555555555555555554444444 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.1     1e-06   0.00012      26     128 ..      46     151 ..      41     154 .. 0.87
   2 !   12.6   0.1   0.00095      0.12      87     128 ..     152     193 ..     149     197 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1e-06
                                    CCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHCCCHHHHHHHCCHH CS
                      Fib_alpha  26 llkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvik...ksskeleeeilrlketidaqes 102
                                    l + +   +++l++le  ++ + +  +  +e + +++  ++++ +  +  + ++    + + + ee+ +rl+e + +q +
  gi|119720248|ref|YP_920743.1|  46 LVEAHARAEERLSRLEAAVAGLGEAVSRHSEAIARLEVAVARHDEAVARLEAAVArlaEAQAKSEERLARLEEAVARQSE 125
                                    6778888999****************************9999999988876665511156677899************** PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Fib_alpha 103 nirvLqnvlesneqkiqkLeqdidqk 128
                                    +i +L   +++ ++ i++Le ++++ 
  gi|119720248|ref|YP_920743.1| 126 SIAKLEAAVSKHSEVIARLEAAVAKH 151
                                    *********************99876 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00095
                                    HHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Fib_alpha  87 eeeilrlketidaqesnirvLqnvlesneqkiqkLeqdidqk 128
                                    +e i+rl++ + ++ ++i  L + + + ++ i++Le+++  +
  gi|119720248|ref|YP_920743.1| 152 DETIARLEKAVAKHDESIARLEKAIARHDEAIARLEEAVRGL 193
                                    5789*********************************99765 PP

>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.3     0.054       6.6      38      68 ..      32      62 ..      29      67 .. 0.80
   2 !    9.8   2.0    0.0062      0.76      30      63 ..      87     120 ..      66     131 .. 0.48
   3 !   22.4   0.6   7.3e-07   9.1e-05      24      70 ..     144     190 ..     142     194 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.054
                     TMF_DNA_bd 38 Lrkknkelekeikelkkkleklekeleelee 68
                                   Lr+++k l + +++l +  ++ e+ l++le+
  gi|119720248|ref|YP_920743.1| 32 LRAELKGLREAVERLVEAHARAEERLSRLEA 62
                                   8888888888888888888888888888886 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0062
                     TMF_DNA_bd  30 klnntikkLrkknkelekeikelkkkleklekel 63 
                                    ++ +++ +L + ++ l + +++ +++l++le+ +
  gi|119720248|ref|YP_920743.1|  87 RHDEAVARLEAAVARLAEAQAKSEERLARLEEAV 120
                                    3444444444444444444444444444444444 PP

  == domain 3  score: 22.4 bits;  conditional E-value: 7.3e-07
                     TMF_DNA_bd  24 LskkelklnntikkLrkknkelekeikelkkkleklekeleeleerl 70 
                                    L++   k+ +ti +L k +++++++i++l+k +++ ++ +++lee  
  gi|119720248|ref|YP_920743.1| 144 LEAAVAKHDETIARLEKAVAKHDESIARLEKAIARHDEAIARLEEAV 190
                                    777889*************************************9865 PP

>> BRE1  BRE1 E3 ubiquitin ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.1     0.016       1.9       5      39 ..      29      63 ..      28      67 .. 0.93
   2 ?   -0.1   0.0       7.9   9.8e+02      12      36 ..      78     102 ..      67     113 .. 0.44
   3 !   27.6   4.2   1.8e-08   2.2e-06       5      89 ..     113     197 ..     109     203 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.016
                           BRE1  5 Lvklekafeelseqlskkvkeltileekklrleae 39
                                   L++l ++ + l+e+++ +v+ +++ ee+++rlea 
  gi|119720248|ref|YP_920743.1| 29 LEDLRAELKGLREAVERLVEAHARAEERLSRLEAA 63
                                   78999***************************985 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 7.9
                           BRE1  12 feelseqlskkvkeltileekklrl 36 
                                    +  l+ ++    + +++le  ++rl
  gi|119720248|ref|YP_920743.1|  78 IARLEVAVARHDEAVARLEAAVARL 102
                                    3333333333333333333333333 PP

  == domain 3  score: 27.6 bits;  conditional E-value: 1.8e-08
                           BRE1   5 LvklekafeelseqlskkvkeltileekklrleaekakadqkyfaamrskdalenelkkLnkllsKsselieqLkeleke 84 
                                    L +le+a   +se++ k+ + ++ + e ++rlea  ak d+ +  ++++  + +  + +L k +++  e i++L+e+ + 
  gi|119720248|ref|YP_920743.1| 113 LARLEEAVARQSESIAKLEAAVSKHSEVIARLEAAVAKHDETIARLEKAVAKHDESIARLEKAIARHDEAIARLEEAVRG 192
                                    899************************************************************************97666 PP

                           BRE1  85 fvrkl 89 
                                    + +++
  gi|119720248|ref|YP_920743.1| 193 LAAQV 197
                                    66555 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   0.00023     0.029      11      94 ..      32     112 ..      29     114 .. 0.90
   2 !   11.1   2.4    0.0031      0.38      34      92 ..     111     173 ..     100     175 .. 0.45
   3 ?    8.5   0.1     0.019       2.4      69      95 ..     164     190 ..     160     204 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 0.00023
                        BLOC1_2  11 leaeleatvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyske 90 
                                    l+ael++ +e ++ L + + +a+e+   l+ ++a+l + +++ +e   +++ +   + + ++ v++Le+av++L e   +
  gi|119720248|ref|YP_920743.1|  32 LRAELKGLREAVERLVEAHARAEERLSRLEAAVAGLGEAVSRHSE---AIARLEVAVARHDEAVARLEAAVARLAEAQAK 108
                                    6899*********************************99998888...99999999999***************988776 PP

                        BLOC1_2  91 LEak 94 
                                     E++
  gi|119720248|ref|YP_920743.1| 109 SEER 112
                                    6655 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0031
                        BLOC1_2  34 ekykklkdvaaslekkleklne....kyeelqpylqqidqiekqvteLeeavseLDeyskeLE 92 
                                    e+ + l++++a  ++++ kl++     +e ++ +   + + ++++++Le+av++ De + +LE
  gi|119720248|ref|YP_920743.1| 111 ERLARLEEAVARQSESIAKLEAavskHSEVIARLEAAVAKHDETIARLEKAVAKHDESIARLE 173
                                    344444444444444444333311002233333444455555555666666666666666665 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.019
                        BLOC1_2  69 qiekqvteLeeavseLDeyskeLEakf 95 
                                    + ++++++Le+a+++ De + +LE+ +
  gi|119720248|ref|YP_920743.1| 164 KHDESIARLEKAIARHDEAIARLEEAV 190
                                    446666666666666666666666543 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   6.3   2.6e-09   3.2e-07     335     469 ..      34     178 ..      13     205 .. 0.63

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 2.6e-09
                         AAA_13 335 eqLkglqraleaKrkepfk........svelesvkakiesikklvaeineliakhNekvanleeekeeakkklelhl..v 404
                                    ++Lkgl++a+e+ ++  ++        ++ +  + + +++ ++++a+++  +a+h e va+le+++++++++  +++  +
  gi|119720248|ref|YP_920743.1|  34 AELKGLREAVERLVEAHARaeerlsrlEAAVAGLGEAVSRHSEAIARLEVAVARHDEAVARLEAAVARLAEAQAKSEerL 113
                                    33333333333333222221000000122333444444577777777888888888888888877777777666665446 PP

                         AAA_13 405 eeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeeinkeLka 469
                                    ++le+++ +  + ++kle+a++k  + ++  ea+++k +e i+ Lek + ++ ++++ ++k +++
  gi|119720248|ref|YP_920743.1| 114 ARLEEAVARQSESIAKLEAAVSKHSEVIARLEAAVAKHDETIARLEKAVAKHDESIARLEKAIAR 178
                                    77777777777777777777777777777777777777777777777777777777777777665 PP

>> Cast  RIM-binding protein of the cytomatrix active zone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   7.2   9.8e-09   1.2e-06     469     619 ..      28     171 ..       3     206 .. 0.80

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 9.8e-09
                           Cast 469 eleslkkenkelkeklsalqaeltekesslldlkekasslassglkkdsklksleiavekkkeecskleaqlkkaqeaee 548
                                     le+l+ e+k l+e ++ l +  +  e+ l+ l+     l +++ ++   +  le+av +++e + +lea   +  ea++
  gi|119720248|ref|YP_920743.1|  28 GLEDLRAELKGLREAVERLVEAHARAEERLSRLEAAVAGLGEAVSRHSEAIARLEVAVARHDEAVARLEAAVARLAEAQA 107
                                    589*******************************9999999999999999*******************99877655443 PP

                           Cast 549 aeranpeitdriklLekevarkkeessksqaeveRLleiLrevenekndkdkkiaelesltlrqvkeqkkn 619
                                             +r+  Le+ var+ e  +k +a v +  e++   e    + d+ ia le+ + ++ ++ + +
  gi|119720248|ref|YP_920743.1| 108 ------KSEERLARLEEAVARQSESIAKLEAAVSKHSEVIARLEAAVAKHDETIARLEKAVAKHDESIA-R 171
                                    ......34579999********************************************99865543222.2 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.8   0.00018     0.022      56     130 ..      30     104 ..       8     107 .. 0.89
   2 !   16.8   2.1   4.4e-05    0.0055      62     126 ..      71     135 ..      67     142 .. 0.90
   3 !   14.1   6.9    0.0003     0.037      52     127 ..     103     178 ..      98     185 .. 0.91
   4 !   12.3   0.6    0.0011      0.13      62     122 ..     141     201 ..     133     205 .. 0.49

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 0.00018
                           ADIP  56 eslnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrlknalqqikt 130
                                    e l ++++ l+   erl  ++ r +++l++le  +a + ++      ++++le ++ +  e ++rl+ a+++++ 
  gi|119720248|ref|YP_920743.1|  30 EDLRAELKGLREAVERLVEAHARAEERLSRLEAAVAGLGEAVSRHSEAIARLEVAVARHDEAVARLEAAVARLAE 104
                                    677788899999999*********************999999999999******************999998765 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 4.4e-05
                           ADIP  62 irkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrlknalq 126
                                    +++ +  i+rl+ ++ r ++ +++le  +a + +++++ e +l++le+++ +++e++++l+ a+ 
  gi|119720248|ref|YP_920743.1|  71 VSRHSEAIARLEVAVARHDEAVARLEAAVARLAEAQAKSEERLARLEEAVARQSESIAKLEAAVS 135
                                    667778899***************************************************99886 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 0.0003
                           ADIP  52 leqreslnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrlknalqq 127
                                    +e++ +++e++ +le   +r++ +i +l++ +++    +a ++a+ ++   ++++le+++ +  e+++rl++a+++
  gi|119720248|ref|YP_920743.1| 103 AEAQAKSEERLARLEEAVARQSESIAKLEAAVSKHSEVIARLEAAVAKHDETIARLEKAVAKHDESIARLEKAIAR 178
                                    678899999************************9999999******************************999986 PP

  == domain 4  score: 12.3 bits;  conditional E-value: 0.0011
                           ADIP  62 irkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrlk 122
                                    i +lea  ++   +i rl++ +++ +  +a ++++ +    ++++le+++++++ ++ rl 
  gi|119720248|ref|YP_920743.1| 141 IARLEAAVAKHDETIARLEKAVAKHDESIARLEKAIARHDEAIARLEEAVRGLAAQVGRLS 201
                                    4445555555555555555555555555555555555555555555555555555554444 PP

>> Trimer_CC  Trimerisation motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1       1.8   2.2e+02      25      49 ..      54      64 ..      35      66 .. 0.65
   2 ?    3.2   0.7      0.54        67      19      46 ..      55      82 ..      44      87 .. 0.61
   3 ?    6.9   0.9     0.036       4.5      16      49 ..      66      99 ..      56     102 .. 0.86
   4 !    9.6   2.8    0.0052      0.65      18      50 ..      89     121 ..      84     123 .. 0.90
   5 ?    8.0   5.1     0.017       2.1       4      50 ..     103     149 ..     100     179 .. 0.92
   6 !   12.1   0.1   0.00087      0.11      17      36 ..     179     198 ..     168     203 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 1.8
                                   HHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Trimer_CC 25 EEelrkLqatVQelQkRLDrLEetv 49
                                   E              +RL rLE +v
  gi|119720248|ref|YP_920743.1| 54 E--------------ERLSRLEAAV 64
                                   3..............4555555554 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.54
                                   XX--HHHHHHHHHHHHHHHHHHHHHHHH CS
                      Trimer_CC 19 davSRLEEelrkLqatVQelQkRLDrLE 46
                                   + +SRLE  +  L   V  + + + rLE
  gi|119720248|ref|YP_920743.1| 55 ERLSRLEAAVAGLGEAVSRHSEAIARLE 82
                                   4556666666666666666655555555 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.036
                                   XXXXX--HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Trimer_CC 16 pssdavSRLEEelrkLqatVQelQkRLDrLEetv 49
                                      +avSR  E + +L   V  + + + rLE +v
  gi|119720248|ref|YP_920743.1| 66 GLGEAVSRHSEAIARLEVAVARHDEAVARLEAAV 99
                                   5579***************************988 PP

  == domain 4  score: 9.6 bits;  conditional E-value: 0.0052
                                    XXX--HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Trimer_CC  18 sdavSRLEEelrkLqatVQelQkRLDrLEetvq 50 
                                     +av RLE  + +L     +  +RL rLEe+v 
  gi|119720248|ref|YP_920743.1|  89 DEAVARLEAAVARLAEAQAKSEERLARLEEAVA 121
                                    69************9999999**********96 PP

  == domain 5  score: 8.0 bits;  conditional E-value: 0.017
                                    XXXXXXXXXXXXXXXXX--HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Trimer_CC   4 srrratpeasgtpssdavSRLEEelrkLqatVQelQkRLDrLEetvq 50 
                                    ++ +a++e + +  ++av R  E + kL a V ++ + + rLE +v 
  gi|119720248|ref|YP_920743.1| 103 AEAQAKSEERLARLEEAVARQSESIAKLEAAVSKHSEVIARLEAAVA 149
                                    566788888889999****************************9985 PP

  == domain 6  score: 12.1 bits;  conditional E-value: 0.00087
                                    XXXX--HHHHHHHHHHHHHH CS
                      Trimer_CC  17 ssdavSRLEEelrkLqatVQ 36 
                                      +a+ RLEE +r L a V 
  gi|119720248|ref|YP_920743.1| 179 HDEAIARLEEAVRGLAAQVG 198
                                    579*************9986 PP

>> CEP209_CC5  Coiled-coil region of centrosome protein CE290
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   1.1    0.0029      0.36      38     115 ..      27     109 ..      13     122 .. 0.77
   2 ?    7.1   0.1     0.048       5.9      72     107 ..     115     150 ..     112     156 .. 0.83
   3 !    9.5   0.1    0.0086       1.1      72     104 ..     157     189 ..     156     196 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0029
                     CEP209_CC5  38 kgLeelistlkdakga.qkvleWhkkiee..lrlqel..klkreltkqkeeikylknlieeqertisklEeeivqlnkvh 112
                                     gLe+l + lk  + a ++++e h++ ee  +rl+     l  +++++ e i  l+  ++++++++++lE  + +l +++
  gi|119720248|ref|YP_920743.1|  27 LGLEDLRAELKGLREAvERLVEAHARAEErlSRLEAAvaGLGEAVSRHSEAIARLEVAVARHDEAVARLEAAVARLAEAQ 106
                                    6999*******9887725699999998874446655411456799*************************9998887765 PP

                     CEP209_CC5 113 eer 115
                                       
  gi|119720248|ref|YP_920743.1| 107 AKS 109
                                    433 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.048
                     CEP209_CC5  72 klkreltkqkeeikylknlieeqertisklEeeivq 107
                                    +l+ ++ +q e i  l+  ++++ + i++lE  + +
  gi|119720248|ref|YP_920743.1| 115 RLEEAVARQSESIAKLEAAVSKHSEVIARLEAAVAK 150
                                    667788999999999999999999999999987655 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.0086
                     CEP209_CC5  72 klkreltkqkeeikylknlieeqertisklEee 104
                                    +l++++ k+ e i  l++ i++++++i++lEe 
  gi|119720248|ref|YP_920743.1| 157 RLEKAVAKHDESIARLEKAIARHDEAIARLEEA 189
                                    7889999************************96 PP

>> Vac_Fusion  Chordopoxvirus multifunctional envelope protein A27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.1    0.0024      0.29       5      34 ..      53      82 ..      49      94 .. 0.89
   2 ?    4.7   0.1      0.19        24       9      35 ..      92     118 ..      84     121 .. 0.89
   3 ?    6.5   0.9      0.05       6.2       4      40 ..     115     155 ..     110     162 .. 0.78
   4 ?    3.3   0.1      0.49        61      19      35 ..     158     174 ..     148     177 .. 0.73
   5 ?    4.6   0.3       0.2        24      13      34 ..     166     187 ..     156     193 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0024
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Vac_Fusion  5 leerllvlekdfqlvikcckrvnealkRlE 34
                                    eerl +le  +  + +  +r++ea+ RlE
  gi|119720248|ref|YP_920743.1| 53 AEERLSRLEAAVAGLGEAVSRHSEAIARLE 82
                                   589**************************9 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.19
                                    HHHHHHHHHHHHHHHHHHHHHHHHHH- CS
                     Vac_Fusion   9 llvlekdfqlvikcckrvnealkRlEn 35 
                                    + +le  +  +++ + +++e+l RlE 
  gi|119720248|ref|YP_920743.1|  92 VARLEAAVARLAEAQAKSEERLARLEE 118
                                    678999999999*************95 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.05
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH....-XXXXX CS
                     Vac_Fusion   4 dleerllvlekdfqlvikcckrvnealkRlE....nHleTl 40 
                                    +lee + +  ++  +++   ++++e++ RlE    +H eT+
  gi|119720248|ref|YP_920743.1| 115 RLEEAVARQSESIAKLEAAVSKHSEVIARLEaavaKHDETI 155
                                    566666666677778888999*********97777799998 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.49
                                    HHHHHHHHHHHHHHHH- CS
                     Vac_Fusion  19 vikcckrvnealkRlEn 35 
                                    ++k   +++e++ RlE+
  gi|119720248|ref|YP_920743.1| 158 LEKAVAKHDESIARLEK 174
                                    55667788888888887 PP

  == domain 5  score: 4.6 bits;  conditional E-value: 0.2
                                    HHHHHHHHHHHHHHHHHHHHHH CS
                     Vac_Fusion  13 ekdfqlvikcckrvnealkRlE 34 
                                     ++   ++k   r++ea+ RlE
  gi|119720248|ref|YP_920743.1| 166 DESIARLEKAIARHDEAIARLE 187
                                    3444455666677777777777 PP

>> HOOK  HOOK protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   6.3   5.5e-07   6.8e-05     402     578 ..      30     201 ..       4     215 .. 0.67

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 5.5e-07
                           HOOK 402 erllaerdaLketneELkcaqlqqke.lsqad....alaskssssgen.laaellpaevreklirLqhENKmLklkqegs 475
                                    e l ae   L+e++e L  a++ ++e ls+ +     l +  s+++e  +  e+  a   e + rL++   +L ++q +s
  gi|119720248|ref|YP_920743.1|  30 EDLRAELKGLREAVERLVEAHARAEErLSRLEaavaGLGEAVSRHSEAiARLEVAVARHDEAVARLEAAVARLAEAQAKS 109
                                    66888999999999999988887766555544222222222233333304457888888899999999999998888777 PP

                           HOOK 476 eeekltelqelledanrrkneLetenrlanqrileLeaqveelqkalqeqgskaedssllkkkleehleklkevqeelqk 555
                                     ee+l++l+e    + +++ +Le    ++ + i  Lea v            + e+ + l+k++ +h e + ++++ +++
  gi|119720248|ref|YP_920743.1| 110 -EERLARLEEAVARQSESIAKLEAAVSKHSEVIARLEAAVA----------KHDETIARLEKAVAKHDESIARLEKAIAR 178
                                    .8999999999999999999999999999999999999872..........23333344555555555555555555555 PP

                           HOOK 556 kkeqleelepklssnkqkieele 578
                                      e +  le++++  + ++  l 
  gi|119720248|ref|YP_920743.1| 179 HDEAIARLEEAVRGLAAQVGRLS 201
                                    55555555555544444444444 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0       2.6   3.2e+02      16      33 ..      29      46 ..      26      49 .. 0.70
   2 ?    1.7   0.0       2.7   3.4e+02       6      37 ..      54      85 ..      52     105 .. 0.82
   3 ?    6.5   0.1     0.087        11       1      38 [.     112     149 ..     112     153 .. 0.91
   4 ?    7.8   0.0     0.036       4.4       3      40 ..     156     193 ..     154     196 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 2.6
                      FlaC_arch 16 letvkkeneelsksveel 33
                                   le +++e++ l++ ve+l
  gi|119720248|ref|YP_920743.1| 29 LEDLRAELKGLREAVERL 46
                                   566777777777777776 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 2.7
                      FlaC_arch  6 EnklsklsteletvkkeneelsksveelkenV 37
                                   E++ls+l+  ++ + +  +  s+ + +l+  V
  gi|119720248|ref|YP_920743.1| 54 EERLSRLEAAVAGLGEAVSRHSEAIARLEVAV 85
                                   78889999999888888888888888887666 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.087
                      FlaC_arch   1 ridelEnklsklsteletvkkeneelsksveelkenVk 38 
                                    r+  lE+ + + s +++ +++  ++ s+ + +l+  V 
  gi|119720248|ref|YP_920743.1| 112 RLARLEEAVARQSESIAKLEAAVSKHSEVIARLEAAVA 149
                                    67789***************************998884 PP

  == domain 4  score: 7.8 bits;  conditional E-value: 0.036
                      FlaC_arch   3 delEnklsklsteletvkkeneelsksveelkenVkdl 40 
                                      lE+ + k++ +++ ++k +    + + +l+e V+ l
  gi|119720248|ref|YP_920743.1| 156 ARLEKAVAKHDESIARLEKAIARHDEAIARLEEAVRGL 193
                                    679*******************************9865 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.4   0.00039     0.049     199     257 ..      27      85 ..       3      91 .. 0.86
   2 !   12.1  11.8   0.00052     0.065     163     258 ..      93     184 ..      85     211 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00039
                           Spc7 199 eeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervl 257
                                      Le lr el+ l + +e++ + +a+ +e+l +le++++ l e  s++ e+ia+ e  +
  gi|119720248|ref|YP_920743.1|  27 LGLEDLRAELKGLREAVERLVEAHARAEERLSRLEAAVAGLGEAVSRHSEAIARLEVAV 85 
                                    569**************************************************988665 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00052
                           Spc7 163 eeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeq 242
                                    + l++++ +l e +a+ ee+l++l+ea++     ++e++++l  +++++++ i+++++ +a+  e +++le+++++ +e+
  gi|119720248|ref|YP_920743.1|  93 ARLEAAVARLAEAQAKSEERLARLEEAVAR----QSESIAKLEAAVSKHSEVIARLEAAVAKHDETIARLEKAVAKHDES 168
                                    344555555555555555555555554433....5556666666666666666666666666666666666666666666 PP

                           Spc7 243 kseleeeiaeaervle 258
                                    +++le++ia++++ + 
  gi|119720248|ref|YP_920743.1| 169 IARLEKAIARHDEAIA 184
                                    6666666665554443 PP

>> ALIX_LYPXL_bnd  ALIX V-shaped domain binding to HIV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   6.7   1.7e-06   0.00021      76     229 ..      31     194 ..      28     208 .. 0.64

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.7e-06
                 ALIX_LYPXL_bnd  76 elraelqkyreileeAsesDkivrqklqenkedlelLsgpeeeleaalpssssaaasesveeqirklrsllekldelkae 155
                                     lrael+ +re++e  +e+ +  +++l   +++++ L+   +   +a+   + a      +e++++l+ ++++l e +a+
  gi|119720248|ref|YP_920743.1|  31 DLRAELKGLREAVERLVEAHARAEERLSRLEAAVAGLGEAVSRHSEAIARLEVA--VARHDEAVARLEAAVARLAEAQAK 108
                                    689999999999999999999999999999999999977777777777744333..358999****************** PP

                 ALIX_LYPXL_bnd 156 reqllkdlkekaendDitpklltekkr............diaanefealfeeelekydplqeqleqslakqeellkeiqe 223
                                     e++l +l+e++++++ + + l+++ +              + +e  a +e+++ k+d+ +++le+++a+ +e +++++e
  gi|119720248|ref|YP_920743.1| 109 SEERLARLEEAVARQSESIAKLEAAVSkhseviarleaaVAKHDETIARLEKAVAKHDESIARLEKAIARHDEAIARLEE 188
                                    ********999888833222233333333333443332211111222234444555555555555555555555555555 PP

                 ALIX_LYPXL_bnd 224 aneefe 229
                                    a++ ++
  gi|119720248|ref|YP_920743.1| 189 AVRGLA 194
                                    555444 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   2.4     2e-05    0.0024      79     179 ..      45     148 ..      27     152 .. 0.80
   2 ?    6.8   0.1     0.054       6.6      79     125 ..     150     196 ..     146     205 .. 0.65

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2e-05
                        UPF0242  79 eldeglktkeealeelqeeeeeLkeeldakeeelerlk...eenqqLqekleaiaedfeelkleleeqLaekqellqeyq 155
                                     l e ++  ee l  l++    L e ++  +e+++rl+    +  +   +lea+++  +e + ++ee+La+ +e +    
  gi|119720248|ref|YP_920743.1|  45 RLVEAHARAEERLSRLEAAVAGLGEAVSRHSEAIARLEvavARHDEAVARLEAAVARLAEAQAKSEERLARLEEAVARQS 124
                                    22366677777777777777777777999999999998333344466779****************************** PP

                        UPF0242 156 etieeqrsvlekrqdqieqLeskV 179
                                    e+i ++ + + k  + i++Le+ V
  gi|119720248|ref|YP_920743.1| 125 ESIAKLEAAVSKHSEVIARLEAAV 148
                                    *********************988 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.054
                        UPF0242  79 eldeglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqek 125
                                    + de ++  e+a+ +  e   +L++ ++  +e+++rl+e    L  +
  gi|119720248|ref|YP_920743.1| 150 KHDETIARLEKAVAKHDESIARLEKAIARHDEAIARLEEAVRGLAAQ 196
                                    55666677777777777777777777777777777777666666555 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   2.0     0.001      0.12      29     102 ..      37     110 ..      30     131 .. 0.84
   2 !   10.8   4.4    0.0018      0.22      56     136 ..     113     193 ..     107     202 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.001
                            GAS  29 kslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelk 102
                                    k l+e +e+l +  +r+e +ls +++    l e + +  e +++L+ +++++++  ++l+++ arl e++ + +
  gi|119720248|ref|YP_920743.1|  37 KGLREAVERLVEAHARAEERLSRLEAAVAGLGEAVSRHSEAIARLEVAVARHDEAVARLEAAVARLAEAQAKSE 110
                                    7899**********************************************************999998765543 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0018
                            GAS  56 nkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrfekvekerdelykkfeaaiqe 135
                                      rl+e + ++ e +++L++++ ++++  ++l+++ a+  e+   l++   +h+    r+ek+ +  de  ++ e+a++ 
  gi|119720248|ref|YP_920743.1| 113 LARLEEAVARQSESIAKLEAAVSKHSEVIARLEAAVAKHDETIARLEKAVAKHDESIARLEKAIARHDEAIARLEEAVRG 192
                                    56777777777777777777777777777777777777777777777777777777777777777777777777777665 PP

                            GAS 136 v 136
                                    +
  gi|119720248|ref|YP_920743.1| 193 L 193
                                    5 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   1.4    0.0025      0.31     330     416 ..      34     117 ..      29     120 .. 0.77
   2 !   15.9   8.1   3.8e-05    0.0047     317     416 ..      98     201 ..      87     204 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0025
                         DUF812 330 eeleelqeqieeleskieeleeeikklessikqveeeleeekeeneelekevklkkktlellpdaeeniekLqalveasa 409
                                    +el+ l+e +e+l +  ++ ee +++le+ +  + e++ ++ e  ++le  v+ +  +++ l   e+ +++L ++  +s+
  gi|119720248|ref|YP_920743.1|  34 AELKGLREAVERLVEAHARAEERLSRLEAAVAGLGEAVSRHSEAIARLEVAVARHDEAVARL---EAAVARLAEAQAKSE 110
                                    58888888888888888888888888888888888888888888888888888888888888...555666666666666 PP

                         DUF812 410 qrlvela 416
                                    +rl  l+
  gi|119720248|ref|YP_920743.1| 111 ERLARLE 117
                                    6666665 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 3.8e-05
                         DUF812 317 kaeteeelkkkreeeleelqeqieeleskieeleeeikklessikqveeeleeekeeneelekevklkkktlellpd... 393
                                    ++    e+++k ee l+ l+e + + +++i++le+ ++k ++ i ++e ++ +++e+ ++lek v+++   ++ l++   
  gi|119720248|ref|YP_920743.1|  98 AVARLAEAQAKSEERLARLEEAVARQSESIAKLEAAVSKHSEVIARLEAAVAKHDETIARLEKAVAKHDESIARLEKaia 177
                                    56677888999999999999999999999999999999999999999999999999999999999998888887766455 PP

                         DUF812 394 .aeeniekLqalveasaqrlvela 416
                                      +e i++L+++v   a+++  l+
  gi|119720248|ref|YP_920743.1| 178 rHDEAIARLEEAVRGLAAQVGRLS 201
                                    568899999999888888777665 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.1     0.031       3.9      57     122 ..      39     104 ..      29     106 .. 0.57
   2 !   12.4   3.3   0.00096      0.12      70     119 ..     115     164 ..      89     204 .. 0.47

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.031
                        DUF1664  57 laatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleriee 122
                                    l+++ ++L +  +r +++l   +++ + + e v++ +e +++++  v   +eav  le+ ++r+ e
  gi|119720248|ref|YP_920743.1|  39 LREAVERLVEAHARAEERLSRLEAAVAGLGEAVSRHSEAIARLEVAVARHDEAVARLEAAVARLAE 104
                                    444444555555555666666666666666666666666666666666666666666666666655 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00096
                        DUF1664  70 rvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskler 119
                                    r+++ +  q+e ++++++ v++ +e +++++  v + +e++  le+ +++
  gi|119720248|ref|YP_920743.1| 115 RLEEAVARQSESIAKLEAAVSKHSEVIARLEAAVAKHDETIARLEKAVAK 164
                                    44444444444444444444444444444444444444444444433322 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1       1.3   1.6e+02       6      38 ..      29      61 ..      28      71 .. 0.80
   2 ?    7.2   1.2     0.046       5.7       6      46 ..      78     118 ..      53     134 .. 0.71
   3 ?    7.0   0.4     0.054       6.6       3      37 ..     110     144 ..     108     150 .. 0.85
   4 ?    8.5   0.4     0.018       2.3       4      40 ..     125     161 ..     123     164 .. 0.87
   5 !   13.5   2.0    0.0005     0.062       4      42 ..     139     177 ..     136     183 .. 0.93
   6 !   12.1   1.5    0.0014      0.17       3      42 ..     152     191 ..     150     197 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 1.3
                           XhlA  6 lerietkldnleervdkleekaaeaeekiknle 38
                                   le + ++l+ l e v++l e  a+aee++  le
  gi|119720248|ref|YP_920743.1| 29 LEDLRAELKGLREAVERLVEAHARAEERLSRLE 61
                                   566677899999999999999999999887765 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.046
                           XhlA   6 lerietkldnleervdkleekaaeaeekiknleedlkkles 46 
                                    ++r+e  +  ++e v +le   a+  e     ee+l++le+
  gi|119720248|ref|YP_920743.1|  78 IARLEVAVARHDEAVARLEAAVARLAEAQAKSEERLARLEE 118
                                    56666666666666666666555555555555566666554 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.054
                           XhlA   3 kerlerietkldnleervdkleekaaeaeekiknl 37 
                                    +erl+r+e+ +   +e + kle   +++ e i  l
  gi|119720248|ref|YP_920743.1| 110 EERLARLEEAVARQSESIAKLEAAVSKHSEVIARL 144
                                    799******************99999988766655 PP

  == domain 4  score: 8.5 bits;  conditional E-value: 0.018
                           XhlA   4 erlerietkldnleervdkleekaaeaeekiknleed 40 
                                    e ++++e+ + +++e + +le   a+++e i  le+ 
  gi|119720248|ref|YP_920743.1| 125 ESIAKLEAAVSKHSEVIARLEAAVAKHDETIARLEKA 161
                                    7899999999999999999999999999999988876 PP

  == domain 5  score: 13.5 bits;  conditional E-value: 0.0005
                           XhlA   4 erlerietkldnleervdkleekaaeaeekiknleedlk 42 
                                    e ++r+e+ + +++e++ +le+  a+++e+i  le+ ++
  gi|119720248|ref|YP_920743.1| 139 EVIARLEAAVAKHDETIARLEKAVAKHDESIARLEKAIA 177
                                    789*******************************99987 PP

  == domain 6  score: 12.1 bits;  conditional E-value: 0.0014
                           XhlA   3 kerlerietkldnleervdkleekaaeaeekiknleedlk 42 
                                    +e ++r+e+ + +++e + +le+  a+++e i  lee + 
  gi|119720248|ref|YP_920743.1| 152 DETIARLEKAVAKHDESIARLEKAIARHDEAIARLEEAVR 191
                                    589*****************************99998765 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1     0.045       5.5      47     105 ..      57     131 ..      27     137 .. 0.48
   2 !   11.7   0.4    0.0016       0.2      28     103 ..     123     199 ..      90     214 .. 0.49

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.045
                   Baculo_PEP_C  47 Lnalsedlksllaeldt.............rldtlltnLtdalnalq...dtlrneLtnlnsiltnLlssvtNin 105
                                    L+ l++++  l +++++             r d+++++L++a+++l+    + +++L  l+  ++    s++ ++
  gi|119720248|ref|YP_920743.1|  57 LSRLEAAVAGLGEAVSRhseaiarlevavaRHDEAVARLEAAVARLAeaqAKSEERLARLEEAVARQSESIAKLE 131
                                    333333333333333333333333444444556666666666666664433445556666666665555555555 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.0016
                   Baculo_PEP_C  28 qnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq...dtlrneLtnlnsiltnLlssvtN 103
                                    q+ +i a+l++++ +  +++  l++++ +   e  +rl++++++ ++++++l+      ++++  l+  +  L+++v+ 
  gi|119720248|ref|YP_920743.1| 123 QSESI-AKLEAAVSKHSEVIARLEAAVAK-HDETIARLEKAVAKHDESIARLEkaiARHDEAIARLEEAVRGLAAQVGR 199
                                    33333.44444444444444444444333.3333334555555555555555422222233444444444444444444 PP

>> FliJ  Flagellar FliJ protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   7.2    0.0096       1.2       7     104 ..      36     128 ..      28     131 .. 0.69
   2 !   13.3   6.5    0.0006     0.074       2      80 ..      90     167 ..      89     171 .. 0.76
   3 ?    5.2   0.2      0.19        24      54      75 ..     169     190 ..     165     203 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0096
                           FliJ   7 Laeaqrelqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqvekareewqear 86 
                                    L+  + ++++  e  ++ e+ +++++   +g +     ++    ++ i++l+ a+a++ +++a++e++v +  e+  + +
  gi|119720248|ref|YP_920743.1|  36 LKGLREAVERLVEAHARAEERLSRLEAAVAGLG-----EAVSRHSEAIARLEVAVARHDEAVARLEAAVARLAEAQAKSE 110
                                    344444444444444444444444444444444.....888889999999999999999999999999999999999999 PP

                           FliJ  87 qerkklekLkerekkeeq 104
                                     ++  le   +r+ +  +
  gi|119720248|ref|YP_920743.1| 111 ERLARLEEAVARQSESIA 128
                                    999999988888877655 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.0006
                           FliJ   2 eaareLaeaqrelqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqvekare 80 
                                    ea  +L++a ++l++a++k ee    ++e   ++s++  +   a+  + ++ i++l+ a+a++ +++a++ek+v k  e
  gi|119720248|ref|YP_920743.1|  90 EAVARLEAAVARLAEAQAKSEERLARLEEAVARQSESI-AKLEAAVSKHSEVIARLEAAVAKHDETIARLEKAVAKHDE 167
                                    66677777777777777777777777777777777776.333466788899*********************9988665 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.19
                           FliJ  54 isaldeaiaqqkqelaqaekqv 75 
                                    i++l++aia++ +++a++e++v
  gi|119720248|ref|YP_920743.1| 169 IARLEKAIARHDEAIARLEEAV 190
                                    5566666666666666666655 PP

>> Herpes_U30  Herpes virus tegument protein U30
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   1.4     7e-06   0.00086     662     812 ..      31     177 ..      18     191 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 7e-06
                     Herpes_U30 662 lyssvaeelqkavnkflketetlledilrltrlaaklcrtrlnydeetgtvrvpvaegdkivrvdlkafketvkelqell 741
                                     +++ ++ l +av+++++   +  e  +rl  + a+l ++  +++e+  +++v va  d+ v   l+a ++ ++e q + 
  gi|119720248|ref|YP_920743.1|  31 DLRAELKGLREAVERLVEAHARAEERLSRLEAAVAGLGEAVSRHSEAIARLEVAVARHDEAV-ARLEAAVARLAEAQAKS 109
                                    567888999***********************************************555544.4666666666666**** PP

                     Herpes_U30 742 realvtlseslkelqtlyrqllv.ilseseelanhalkidlsepdleelketllkalkrlaslaselansvs 812
                                    +e l++l+e+ +    ++++l   ++++se +a+       +  +  e+ ++l+ka+++  + ++ l++ ++
  gi|119720248|ref|YP_920743.1| 110 EERLARLEEAVARQSESIAKLEAaVSKHSEVIARLE----AAVAKHDETIARLEKAVAKHDESIARLEKAIA 177
                                    ********************9998888888888744....56678889999999999999999999988775 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   3.2    0.0063      0.78     111     178 ..      29      96 ..       2      98 .. 0.59
   2 !   14.3  13.5   0.00029     0.036      17     135 ..      92     200 ..      84     205 .. 0.47

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0063
                          ATG16 111 lqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDElsaLqlqlnqaEeklrkle 178
                                    l++l+++lk  +e++++l + +a+ e++l+++e++++++ ++v    ++++ L++++   +e+  +le
  gi|119720248|ref|YP_920743.1|  29 LEDLRAELKGLREAVERLVEAHARAEERLSRLEAAVAGLGEAVSRHSEAIARLEVAVARHDEAVARLE 96 
                                    56666666666666666666666666666666666666666666666666666666666666655555 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 0.00029
                          ATG16  17 faeliqaynrLldrtsaleaenaklekaaasakssksskksakekeasasqsnskqsakiqsleqklaqlreelaelyks 96 
                                     a l +a  rL++ +++ e++ a+le+a a++++     + ak ++a      sk s+ i+ le+++a++ e  a l k+
  gi|119720248|ref|YP_920743.1|  92 VARLEAAVARLAEAQAKSEERLARLEEAVARQSE-----SIAKLEAA-----VSKHSEVIARLEAAVAKHDETIARLEKA 161
                                    3334444445555555555555555444333332.....12222222.....2223455555555555555555555555 PP

                          ATG16  97 rgelaqrllelneelqkleeklkedeerlaeleaeraal 135
                                     +++ +++ +l++++++ +e + + ee+++ l a++ +l
  gi|119720248|ref|YP_920743.1| 162 VAKHDESIARLEKAIARHDEAIARLEEAVRGLAAQVGRL 200
                                    555555555555555555555555555555555555555 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.6    0.0002     0.025      30     134 ..       8     111 ..       3     113 .. 0.83
   2 ?    7.2  10.0     0.018       2.3      23     120 ..      94     192 ..      86     204 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.0002
                          Atg14  30 rlaklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsd 109
                                    ++ +l+ e e+++  +  +l  ++    l++++k +++++e+l   +a+ +erl++l++ +  l +++   ++ +a+l  
  gi|119720248|ref|YP_920743.1|   8 EMLRLLREDEEFRYAVVGLLGLED----LRAELKGLREAVERLVEAHARAEERLSRLEAAVAGLGEAVSRHSEAIARLEV 83 
                                    566788888888888888888888....**************************************************** PP

                          Atg14 110 klk...kRrsdleslqneleerrkkqia 134
                                    +++   +  ++le++  +l+e+++k+ +
  gi|119720248|ref|YP_920743.1|  84 AVArhdEAVARLEAAVARLAEAQAKSEE 111
                                    **95554455666777777777776655 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.018
                          Atg14  23 rlyelrerlaklksekeslkkkiekalegke.eaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekk 101
                                    rl+    rla  ++++e+   ++e+a+++++ +  +le+++ ++++ + +l + +a+  e +++l++ + + +++i+   
  gi|119720248|ref|YP_920743.1|  94 RLEAAVARLAEAQAKSEERLARLEEAVARQSeSIAKLEAAVSKHSEVIARLEAAVAKHDETIARLEKAVAKHDESIARLE 173
                                    66777777888888888888888888877775667778888888888888888888888888888888888888888888 PP

                          Atg14 102 kklaklsdklkkRrsdles 120
                                    k +a++++++++  +  + 
  gi|119720248|ref|YP_920743.1| 174 KAIARHDEAIARLEEAVRG 192
                                    8888888888766665554 PP

>> HrpB7  Bacterial type III secretion protein (HrpB7)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2  14.9    0.0061      0.75      78     146 ..      40     108 ..      32     112 .. 0.88
   2 ?    7.5   4.6     0.041       5.1      96     140 ..     156     200 ..     154     205 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0061
                          HrpB7  78 rayrdvlegrvraaeaelaaarqaldaaedavaatarkiaRndaqidacrerierlrraaeraredaad 146
                                    r  ++ l + ++ ae++l ++++a++   +av++  ++iaR++ ++ + +e ++rl++a  r +e+ a 
  gi|119720248|ref|YP_920743.1|  40 REAVERLVEAHARAEERLSRLEAAVAGLGEAVSRHSEAIARLEVAVARHDEAVARLEAAVARLAEAQAK 108
                                    55677899999***************************************************9997654 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.041
                          HrpB7  96 aaarqaldaaedavaatarkiaRndaqidacrerierlrraaera 140
                                    a++++a+++  + +a+ +++iaR d +i + +e ++ l+++  r 
  gi|119720248|ref|YP_920743.1| 156 ARLEKAVAKHDESIARLEKAIARHDEAIARLEEAVRGLAAQVGRL 200
                                    556666666666666666666666666666666666555555554 PP

>> FmiP_Thoc5  Fms-interacting protein/Thoc5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.067       8.2     106     154 ..      31      79 ..      30      95 .. 0.82
   2 !   11.6   2.3   0.00098      0.12      44     154 ..      95     205 ..      91     213 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.067
                     FmiP_Thoc5 106 elaeqlkeleekkkkleqeieekkkfLssLppkLkslkkatkplqealg 154
                                    +l ++lk l e ++ l ++ +  +++Ls+L+ +++ l +a++   ea+ 
  gi|119720248|ref|YP_920743.1|  31 DLRAELKGLREAVERLVEAHARAEERLSRLEAAVAGLGEAVSRHSEAIA 79 
                                    67899***********************************999988884 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00098
                     FmiP_Thoc5  44 lekEikkcldFkskdeeieLvpeeeFyeeapeeiskpedtkkeadehelmlaRLewEleqRke....laeqlkeleekkk 119
                                    le ++ +  + + k ee  L  +ee  +++ e+i+k e      ++h++ +aRLe    +  e    l++++ +  e+  
  gi|119720248|ref|YP_920743.1|  95 LEAAVARLAEAQAKSEE-RLARLEEAVARQSESIAKLEA---AVSKHSEVIARLEAAVAKHDEtiarLEKAVAKHDESIA 170
                                    67778888888899999.999999999999999955533...567**********9988766511114455556667777 PP

                     FmiP_Thoc5 120 kleqeieekkkfLssLppkLkslkkatkplqealg 154
                                     le++i+ + + + +L+++++ l++++  l ea+g
  gi|119720248|ref|YP_920743.1| 171 RLEKAIARHDEAIARLEEAVRGLAAQVGRLSEAIG 205
                                    78888888888888888888888888888887776 PP

>> Jnk-SapK_ap_N  JNK_SAPK-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   4.2    0.0022      0.27      52     138 ..      29     111 ..      26     112 .. 0.87
   2 !   14.8   9.1    0.0002     0.025      47     151 ..      80     190 ..      67     194 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0022
                  Jnk-SapK_ap_N  52 leelreeleqLeteyerekelrkraeeeleeiedqweeerkelqekveqleeenrelelkaknaadqlsrleekeaelkk 131
                                    le+lr+el+ L++  er  e++ raee+l ++e ++ +    l e+v++  e + +le+ +   ++ ++rle   a l +
  gi|119720248|ref|YP_920743.1|  29 LEDLRAELKGLREAVERLVEAHARAEERLSRLEAAVAG----LGEAVSRHSEAIARLEVAVARHDEAVARLEAAVARLAE 104
                                    799****************************9998865....77899999999999999999999999999999988877 PP

                  Jnk-SapK_ap_N 132 eysklhe 138
                                     ++k +e
  gi|119720248|ref|YP_920743.1| 105 AQAKSEE 111
                                    7666555 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 0.0002
                  Jnk-SapK_ap_N  47 eeeaeleelreeleqLeteyerekelrkraeeeleeiedqweeerk...elqekveqleeenrelelkaknaadqlsrle 123
                                    + e+ + +  e++ +Le    r +e++ ++ee+l ++e+++ ++ +   +l+++v++  e + +le+ + + ++ ++rle
  gi|119720248|ref|YP_920743.1|  80 RLEVAVARHDEAVARLEAAVARLAEAQAKSEERLARLEEAVARQSEsiaKLEAAVSKHSEVIARLEAAVAKHDETIARLE 159
                                    456778888999***************************9988776233689999999********************** PP

                  Jnk-SapK_ap_N 124 ekeaelkkeysklhe...retellkklkelv 151
                                    +  a+  ++ ++l++   r+ e + +l e v
  gi|119720248|ref|YP_920743.1| 160 KAVAKHDESIARLEKaiaRHDEAIARLEEAV 190
                                    *999999999999989999999999999877 PP

>> Taxilin  Myosin-like coiled-coil protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.7   5.1e-05    0.0063     130     260 ..      33     176 ..      27     204 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 5.1e-05
                        Taxilin 130 reenaelteKlkslieqyelreehf...........ekllktkel..elqlaeaKlqqadallkeeqekkkrekeyllke 196
                                    r e + l+e  + l+e     ee++           e + ++ e    l++a a++++a a l+++  + ++ +    ++
  gi|119720248|ref|YP_920743.1|  33 RAELKGLREAVERLVEAHARAEERLsrleaavaglgEAVSRHSEAiaRLEVAVARHDEAVARLEAAVARLAEAQAKSEER 112
                                    45555578888888888888888888888888888866666666422445556677777666666666665555555577 PP

                        Taxilin 197 akeltkkvkalketekelkeqlnlYaeKfeefqdtLakSnelFatFkkEmekmtkktkklEket 260
                                    +  l++ v   +e  ++l++ ++ ++e    ++ + ak +e++a+  k + k  +++ +lEk+ 
  gi|119720248|ref|YP_920743.1| 113 LARLEEAVARQSESIAKLEAAVSKHSEVIARLEAAVAKHDETIARLEKAVAKHDESIARLEKAI 176
                                    7777777777777777777777777777777777777777777777777777777777777764 PP

>> DUF2730  Protein of unknown function (DUF2730)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.1     0.022       2.7      32      88 ..      40     101 ..      32     108 .. 0.68
   2 ?    2.2   0.1       1.6     2e+02      37      58 ..     101     122 ..      91     150 .. 0.55
   3 ?    7.7   0.4     0.031       3.8      28      96 ..     133     200 ..     124     204 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.022
                        DUF2730  32 redleklaekveendkrlteletkvenLPtakd.....lekLkllladlrgelkaleaevrq 88 
                                    re +e+l+e  ++ ++rl++le+ v+ L  a+      +++L++ +a  +  +  lea v++
  gi|119720248|ref|YP_920743.1|  40 REAVERLVEAHARAEERLSRLEAAVAGLGEAVSrhseaIARLEVAVARHDEAVARLEAAVAR 101
                                    788999*********************98765311111444555554444444444444444 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 1.6
                        DUF2730  37 klaekveendkrlteletkven 58 
                                    +lae  ++ ++rl++le  v+ 
  gi|119720248|ref|YP_920743.1| 101 RLAEAQAKSEERLARLEEAVAR 122
                                    4555555555555555555543 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.031
                        DUF2730  28 kYakredl.eklaekveendkrlteletkvenLPtakdlekLkllladlrgelkaleaevrqlshqvdLL 96 
                                       k +++ ++l+  v+++d+ +++le  v++    + +++L++ +a  +  +  le+ vr l+ qv+ L
  gi|119720248|ref|YP_920743.1| 133 AVSKHSEViARLEAAVAKHDETIARLEKAVAK--HDESIARLEKAIARHDEAIARLEEAVRGLAAQVGRL 200
                                    55566664256778888999999999998887..577889999999999988999999998888888766 PP

>> LXG  LXG domain of WXG superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0       2.1   2.6e+02       6      37 ..      37      68 ..      32      75 .. 0.83
   2 ?    5.8   0.2     0.079       9.8     144     199 ..      99     154 ..      91     157 .. 0.88
   3 !    9.7   0.1     0.005      0.62     103     196 ..     115     207 ..     109     211 .. 0.65

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 2.1
                            LXG  6 aelieaieqlkseleelkeqleqlkkaiqklv 37
                                   + l ea+e+l ++ ++ +e l++l++a+ +l 
  gi|119720248|ref|YP_920743.1| 37 KGLREAVERLVEAHARAEERLSRLEAAVAGLG 68
                                   56789999999999999999999999998865 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.079
                            LXG 144 kdslqkakkkvqetiekledfdqeqksalanlesdlkalktyvseLeemtskgkis 199
                                    ++ l++a+ k +e +  le++ + q+++ a+le+ +++ +  +++Le+++ k + +
  gi|119720248|ref|YP_920743.1|  99 VARLAEAQAKSEERLARLEEAVARQSESIAKLEAAVSKHSEVIARLEAAVAKHDET 154
                                    677899999**************************************999988765 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.005
                            LXG 103 elenglkkakevteelkdeinkilasvsdivslpelddsevkdslqkakkkvqetiekledfdqeqksalanlesdlkal 182
                                     le ++ + +e+++ l+ ++ k  ++v   ++    + +e ++ l+ka  k +e i  le++ + +++a a le+ ++ l
  gi|119720248|ref|YP_920743.1| 115 RLEEAVARQSESIAKLEAAVSK-HSEVIARLEAAVAKHDETIARLEKAVAKHDESIARLEKAIARHDEAIARLEEAVRGL 193
                                    4555555666666666666666.333333345555666777777888888888888888888888888888888888888 PP

                            LXG 183 ktyvseLeemtskg 196
                                    ++ v +L+e++++g
  gi|119720248|ref|YP_920743.1| 194 AAQVGRLSEAIGFG 207
                                    88888877777765 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1       4.2   5.3e+02      22      46 ..      31      55 ..      28      83 .. 0.45
   2 ?    4.2   3.2      0.39        49      11      49 ..      90     135 ..      80     159 .. 0.56
   3 !   10.5   0.0    0.0045      0.55       2      75 ..     151     234 ..     150     264 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 4.2
                          Spc24 22 sleselaelkeeleeleeeseekes 46
                                   +l++el+ l+e +e l e   + e+
  gi|119720248|ref|YP_920743.1| 31 DLRAELKGLREAVERLVEAHARAEE 55
                                   3444444444444433333333121 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.39
                          Spc24  11 kelsdleselesleselaelkeeleeleeeseekeser.......v 49 
                                    +++  le+++ +l + +a+ +e+l+ lee   ++++++       +
  gi|119720248|ref|YP_920743.1|  90 EAVARLEAAVARLAEAQAKSEERLARLEEAVARQSESIakleaavS 135
                                    5666777777777777777777777777766662222223333331 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.0045
                          Spc24   2 ldnekfriakelsdleselesleselaelkeeleeleeesee...keser...........ve.detllklklYrsLGie 66 
                                    +d++  r+ k++ + ++++ +le+  a+  e ++ lee       +   +           ++  + ++   lYr+LG+e
  gi|119720248|ref|YP_920743.1| 151 HDETIARLEKAVAKHDESIARLEKAIARHDEAIARLEEAVRGlaaQ---VgrlseaigfglEDvAALMVPGWLYRHLGVE 227
                                    5677778888888888888888888888888888888877664430...23445556788544444456679******** PP

                          Spc24  67 lekdvnkvl 75 
                                    +e    + +
  gi|119720248|ref|YP_920743.1| 228 VELG--RGV 234
                                    9876..333 PP

>> Gp58  gp58-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.2   6.4e-05    0.0079     145     315 ..      36     201 ..      28     215 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.4e-05
                           Gp58 145 lalinetieGirreyqdadrelsssyqagieGlkatlasdklglkaeiqasaqgLsqkyddeirkLsakitttssGttea 224
                                    l  ++e++e + + +  a+ e+ s+ +a++ Gl + +   + +  a ++++      ++d+ + +L+a ++++++   ++
  gi|119720248|ref|YP_920743.1|  36 LKGLREAVERLVEAHARAE-ERLSRLEAAVAGLGEAVSRHS-EAIARLEVA----VARHDEAVARLEAAVARLAEAQAKS 109
                                    5556666666666666665.556789999999999998888.334444444....5799**************9965555 PP

                           Gp58 225 ye..skLddlraeftrsnqGmrvele...skisGlqstqqstakqisqeiknregavsrvqqdldsyqrrlqdaeknyss 299
                                     e  ++L++ +a  ++s      +le   sk s + +  +++  + +  i   e av++ + +++ + + +   ++  + 
  gi|119720248|ref|YP_920743.1| 110 EErlARLEEAVARQSESIA----KLEaavSKHSEVIARLEAAVAKHDETIARLEKAVAKHDESIARLEKAIARHDEAIAR 185
                                    4322455555555555554....5551115555666667788889999******************************** PP

                           Gp58 300 LtqtvkGlqstvsdpn 315
                                    L+++v+Gl ++v   +
  gi|119720248|ref|YP_920743.1| 186 LEEAVRGLAAQVGRLS 201
                                    *********9997655 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0       6.8   8.4e+02      26      51 ..      40      65 ..      33      77 .. 0.76
   2 !   15.5   0.8   0.00013     0.015      12      80 ..      82     150 ..      77     152 .. 0.88
   3 ?    2.4   0.1       1.5   1.9e+02      27      54 ..     153     180 ..     138     203 .. 0.47

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 6.8
                           KxDL 26 nkknreLlelnalsqerlaklrarfk 51
                                    +  ++L e  a ++erl++l+a ++
  gi|119720248|ref|YP_920743.1| 40 REAVERLVEAHARAEERLSRLEAAVA 65
                                   55567888888999999998887665 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 0.00013
                           KxDL  12 deilalQaqtsgrlnkknreLlelnalsqerlaklrarfkqgtkllkevkkdLesifkkirslkaklak 80 
                                    + ++a   + ++rl++  ++L e +a+s+erla+l++ ++++ + + ++ +   +  + i +l+a +ak
  gi|119720248|ref|YP_920743.1|  82 EVAVARHDEAVARLEAAVARLAEAQAKSEERLARLEEAVARQSESIAKLEAAVSKHSEVIARLEAAVAK 150
                                    55666778899***********************************99999999999999999888776 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 1.5
                           KxDL  27 kknreLlelnalsqerlaklrarfkqgt 54 
                                    ++ ++L++  a+ +e  a+l++ ++++ 
  gi|119720248|ref|YP_920743.1| 153 ETIARLEKAVAKHDESIARLEKAIARHD 180
                                    2223333333333333333333333333 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.65        80       3      82 ..      35      92 ..      29     104 .. 0.43
   2 !   14.0   3.7   0.00018     0.022       3      92 ..      91     179 ..      89     191 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.65
                          TMPIT  3 eweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvl 82
                                   e++ l++ +++l e++ + +++l +l++    + ++++++++ + +l+ ++ + +++                      +
  gi|119720248|ref|YP_920743.1| 35 ELKGLREAVERLVEAHARAEERLSRLEAAVAGLGEAVSRHSEAIARLEVAVARHDEA----------------------V 92
                                   333344444444444444444444444444444444444444444444444333333......................2 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 0.00018
                          TMPIT   3 eweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvl 82 
                                     +++le  + +l e++ + +++l++l++   + s++i+k +  +++ ++ + +l+++v ++++e++++l++ +++ ++++
  gi|119720248|ref|YP_920743.1|  91 AVARLEAAVARLAEAQAKSEERLARLEEAVARQSESIAKLEAAVSKHSEVIARLEAAV-AKHDETIARLEKAVAKHDESI 169
                                    67899999999*******************************************9997.688999999999999999999 PP

                          TMPIT  83 kevesllpkk 92 
                                    +++e+ + ++
  gi|119720248|ref|YP_920743.1| 170 ARLEKAIARH 179
                                    9999887665 PP

>> DUF4618  Domain of unknown function (DUF4618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   5.2   0.00039     0.048      64     222 ..      38     203 ..      29     211 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00039
                        DUF4618  64 qleqakaeLqeweekeekklekLeqqleqlnakvqklqeelnvLstYkDkeYpvkavqIanlvrqlqqlkdsqqdeldel 143
                                     l +a + L e + + e++l++Le  +  l + v   +e +  L+    ++       +a l   +  l++ q +  + l
  gi|119720248|ref|YP_920743.1|  38 GLREAVERLVEAHARAEERLSRLEAAVAGLGEAVSRHSEAIARLEVAVARH----DEAVARLEAAVARLAEAQAKSEERL 113
                                    566777778888888888888888888888888888888888776544332....2234555555555555555555544 PP

                        DUF4618 144 eelikev......leklskkiqkkkekllk...slae..ktlkatqeaLlqktlenqvlkkeiekfrefieeleeeipeL 212
                                     +l ++v      ++kl++ + k++e + +   ++a+  +t+++ ++a+ ++  + ++l+k i+++ e i +lee +  L
  gi|119720248|ref|YP_920743.1| 114 ARLEEAVarqsesIAKLEAAVSKHSEVIARleaAVAKhdETIARLEKAVAKHDESIARLEKAIARHDEAIARLEEAVRGL 193
                                    4444333111111678888888887765432113443224677788999999999999********************** PP

                        DUF4618 213 kaeveqLqaq 222
                                     a+v +L++ 
  gi|119720248|ref|YP_920743.1| 194 AAQVGRLSEA 203
                                    ****999875 PP

>> Lebercilin  Ciliary protein causing Leber congenital amaurosis disease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1  14.8   0.00023     0.028      20     182 ..      29     200 ..      28     204 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 0.00023
                     Lebercilin  20 laelqskleelrkEnklLkrlqkrqekaLskyedteaeLpqllarhneEvrvlrerlRksqekerelekklkekeaellr 99 
                                    l++l+ +l+ lr+  + L + + r e++Ls++e + a L + ++rh+e +  l   + ++ e++ +le  + +  ++  +
  gi|119720248|ref|YP_920743.1|  29 LEDLRAELKGLREAVERLVEAHARAEERLSRLEAAVAGLGEAVSRHSEAIARLEVAVARHDEAVARLEAAVARLAEAQAK 108
                                    6799999999999999999****************************************************999999999 PP

                     Lebercilin 100 lkdklkklkk.Lsed.knLaereeLqkk....LeeleakleekeekikeLerkleleeksfrr...qlaaekkktkeaqe 170
                                     ++ l +l++ ++++  + a  e   +k    +++lea + + +e+i +Le+ +   ++s +r    +a+  + +  ++e
  gi|119720248|ref|YP_920743.1| 109 SEERLARLEEaVARQsESIAKLEAAVSKhsevIARLEAAVAKHDETIARLEKAVAKHDESIARlekAIARHDEAIARLEE 188
                                    999*****99544331234444444444677799********************99998876611134444555555556 PP

                     Lebercilin 171 evkalqeeierl 182
                                     v+ l +++ rl
  gi|119720248|ref|YP_920743.1| 189 AVRGLAAQVGRL 200
                                    666666666555 PP

>> Helo_like_N  Fungal N-terminal domain of STAND proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.1     0.019       2.3      38      90 ..      29      80 ..      27      94 .. 0.85
   2 ?    8.5   2.1    0.0096       1.2       8      91 ..      97     179 ..      90     196 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.019
                    Helo_like_N 38 vreLkeeleaLeevLesLeevavaeeeselalLklpllrCgkaCkefeqvikk 90
                                   + +L++el+ L+e +e L e a a++e+ l+ L+  +   g+a +   ++i++
  gi|119720248|ref|YP_920743.1| 29 LEDLRAELKGLREAVERLVE-AHARAEERLSRLEAAVAGLGEAVSRHSEAIAR 80
                                   579*****************.6699999******9998888877777777765 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0096
                    Helo_like_N   8 sgvlalvtfalqssksLyetvksfrsrdktvreLkeeleaLeevLesLeevavaeeeselalLklpllrCgkaCkefeqv 87 
                                    ++v  l+++ ++s   L +  +    +++++ +L++ +++ +ev+  Le  ava++++++a L++ + + ++    +e++
  gi|119720248|ref|YP_920743.1|  97 AAVARLAEAQAKSEERLARLEEAVARQSESIAKLEAAVSKHSEVIARLEA-AVAKHDETIARLEKAVAKHDESIARLEKA 175
                                    78889999999999999999999999***********************9.77899999*****9999988888888888 PP

                    Helo_like_N  88 ikkc 91 
                                    i++ 
  gi|119720248|ref|YP_920743.1| 176 IARH 179
                                    8765 PP

>> Flagellin_C  Bacterial flagellin C-terminal helical region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.2      0.02       2.5       5      49 ..      54      98 ..      50     116 .. 0.87
   2 ?    3.3   0.5      0.85   1.1e+02      23      62 ..      93     131 ..      86     161 .. 0.60
   3 ?    3.6   0.2      0.69        86       2      48 ..     128     174 ..     113     177 .. 0.82
   4 ?    4.4   0.0      0.38        47       5      48 ..     159     202 ..     155     211 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.02
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHCHHCCH CS
                    Flagellin_C  5 deaitdldkvrselGavqnRlesaitnlkaqsenlkaaesrledv 49
                                   +e ++ l+++ + lG + +R ++ai++l+ ++   ++a+ rle +
  gi|119720248|ref|YP_920743.1| 54 EERLSRLEAAVAGLGEAVSRHSEAIARLEVAVARHDEAVARLEAA 98
                                   67788999999*********************9999999999864 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.85
                                    HHHHHHHHHHHHHHCHHHHHHCHHCCHHHHHHHHHHHHHH CS
                    Flagellin_C  23 nRlesaitnlkaqsenlkaaesrledvDpaeestrvtklq 62 
                                    +Rle a+++l  ++   +++  rle++ +a  s  ++kl+
  gi|119720248|ref|YP_920743.1|  93 ARLEAAVARLAEAQAKSEERLARLEEA-VARQSESIAKLE 131
                                    455555666655555555555555554.333333333333 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.69
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHCHHCC CS
                    Flagellin_C   2 divdeaitdldkvrselGavqnRlesaitnlkaqsenlkaaesrled 48 
                                    ++++ a+++ ++v + l a+ ++ +++i++l++++   ++++ rle+
  gi|119720248|ref|YP_920743.1| 128 AKLEAAVSKHSEVIARLEAAVAKHDETIARLEKAVAKHDESIARLEK 174
                                    56777888888888888888888888888888888888888888886 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.38
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHCHHCC CS
                    Flagellin_C   5 deaitdldkvrselGavqnRlesaitnlkaqsenlkaaesrled 48 
                                    ++a+ + d+  + l  + +R ++ai++l+ ++  l+a+++rl +
  gi|119720248|ref|YP_920743.1| 159 EKAVAKHDESIARLEKAIARHDEAIARLEEAVRGLAAQVGRLSE 202
                                    56666666666666677777777777777777777777777654 PP

>> DUF4686  Domain of unknown function (DUF4686)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   4.8   0.00012     0.014     154     318 ..      30     197 ..       8     204 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 0.00012
                        DUF4686 154 kqLeekikeaseneaklkqqlqeeqqkrklLdqnveeLqqqvrslrdkeaqlertnsqqqlriqqqeaqlkklenekrks 233
                                    + L+ + k ++e  ++l +       +   L+  v  L + v    +  a+le ++++    +   ea + +l + + ks
  gi|119720248|ref|YP_920743.1|  30 EDLRAELKGLREAVERLVEAHARAEERLSRLEAAVAGLGEAVSRHSEAIARLEVAVARHDEAVARLEAAVARLAEAQAKS 109
                                    6677788888888888877777777777789999999999999999999******************************* PP

                        DUF4686 234 dehlksnqeLsekLsslqqekealqeelqqvLkqldahvrkynekq...ehhkaklrrvkelllkeveqrderikqLene 310
                                    +e+l   +e   + s++    ea   ++++v+  l+a v k++e     e+  ak  +   +l k++ ++de i +Le+ 
  gi|119720248|ref|YP_920743.1| 110 EERLARLEEAVARQSESIAKLEAAVSKHSEVIARLEAAVAKHDETIarlEKAVAKHDESIARLEKAIARHDEAIARLEEA 189
                                    ****7777777888999999***********************9751114455788888899*****************9 PP

                        DUF4686 311 iailksqs 318
                                    ++ l  q 
  gi|119720248|ref|YP_920743.1| 190 VRGLAAQV 197
                                    99887775 PP

>> TolA_bind_tri  TolA binding protein trimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.6      0.45        56      27      54 ..      29      56 ..      26      60 .. 0.87
   2 ?    0.5   0.1       5.4   6.7e+02       3      14 ..      54      65 ..      52      81 .. 0.84
   3 ?    0.1   0.0       6.9   8.6e+02       4      30 ..      76     102 ..      73     107 .. 0.74
   4 ?    7.3   1.0      0.04       4.9       2      41 ..     109     148 ..     108     161 .. 0.78
   5 ?    5.3   0.1      0.17        21       3      37 ..     152     186 ..     150     190 .. 0.75
   6 ?    7.1   0.1     0.045       5.6       3      37 ..     166     200 ..     164     204 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.45
                  TolA_bind_tri 27 lealqqelreLRGqiEelqyqleqleer 54
                                   le+l++el+ LR  +E+l     ++eer
  gi|119720248|ref|YP_920743.1| 29 LEDLRAELKGLREAVERLVEAHARAEER 56
                                   89***************98888888887 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 5.4
                  TolA_bind_tri  3 edrvarLErile 14
                                   e+r++rLE +++
  gi|119720248|ref|YP_920743.1| 54 EERLSRLEAAVA 65
                                   899999999876 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 6.9
                  TolA_bind_tri   4 drvarLErilearsqlllelqqqleal 30 
                                    + +arLE +++ ++++  +l   + +l
  gi|119720248|ref|YP_920743.1|  76 EAIARLEVAVARHDEAVARLEAAVARL 102
                                    568888888888888887777666655 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.04
                  TolA_bind_tri   2 ledrvarLErilearsqlllelqqqlealqqelreLRGqi 41 
                                     e+r+arLE++++ +s+++ +l   +++ ++ +++L   +
  gi|119720248|ref|YP_920743.1| 109 SEERLARLEEAVARQSESIAKLEAAVSKHSEVIARLEAAV 148
                                    589**********999999999998888887777776555 PP

  == domain 5  score: 5.3 bits;  conditional E-value: 0.17
                  TolA_bind_tri   3 edrvarLErilearsqlllelqqqlealqqelreL 37 
                                    ++ +arLE++++++++++ +l + + +  + +++L
  gi|119720248|ref|YP_920743.1| 152 DETIARLEKAVAKHDESIARLEKAIARHDEAIARL 186
                                    56788899999999888888888877766666665 PP

  == domain 6  score: 7.1 bits;  conditional E-value: 0.045
                  TolA_bind_tri   3 edrvarLErilearsqlllelqqqlealqqelreL 37 
                                    ++ +arLE++++ +++++ +l + +  l +++ +L
  gi|119720248|ref|YP_920743.1| 166 DESIARLEKAIARHDEAIARLEEAVRGLAAQVGRL 200
                                    6889***********************99999988 PP

>> MbeD_MobD  MbeD/MobD like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.5      0.37        45      20      68 ..      54     102 ..      31     116 .. 0.62
   2 ?    1.4   0.5       2.9   3.6e+02      46      69 ..     115     138 ..      96     174 .. 0.61
   3 ?    9.6   0.0     0.008      0.99      29      64 ..     168     203 ..     156     205 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.37
                      MbeD_MobD  20 eqrlqeWesafaelqrmfeltqrenaaLseqvtgLsqQVesLseqvrRl 68 
                                    e rl+  e a a l + ++  +   a L+  v +    V +L   v+Rl
  gi|119720248|ref|YP_920743.1|  54 EERLSRLEAAVAGLGEAVSRHSEAIARLEVAVARHDEAVARLEAAVARL 102
                                    3455555555555555555555555555555655556666666666555 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 2.9
                      MbeD_MobD  46 aLseqvtgLsqQVesLseqvrRls 69 
                                     L+e v + s  + +L   v++ s
  gi|119720248|ref|YP_920743.1| 115 RLEEAVARQSESIAKLEAAVSKHS 138
                                    444444444444444444444333 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.008
                      MbeD_MobD  29 afaelqrmfeltqrenaaLseqvtgLsqQVesLseq 64 
                                    + a l + +       a L+e v gL+ QV +Lse 
  gi|119720248|ref|YP_920743.1| 168 SIARLEKAIARHDEAIARLEEAVRGLAAQVGRLSEA 203
                                    556666666666777789****************97 PP

>> Wtap  WTAP/Mum2p family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.5      0.23        29     114     154 ..      29      69 ..       9      71 .. 0.83
   2 ?    6.2   0.9     0.074       9.2      94     147 ..      56     111 ..      55     113 .. 0.84
   3 ?    9.8   2.5    0.0059      0.72     108     156 .]     107     155 ..     103     155 .. 0.92
   4 ?   11.2   0.5    0.0021      0.26     112     155 ..     153     196 ..     146     197 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.23
                           Wtap 114 vakLeselalqkkfveelkkaleeleelleeleeevevlqs 154
                                    ++ L  el+ +++ ve+l +a++++ee l+ le+ v +l +
  gi|119720248|ref|YP_920743.1|  29 LEDLRAELKGLREAVERLVEAHARAEERLSRLEAAVAGLGE 69 
                                    678999***************************99988876 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.074
                           Wtap  94 kcrvLeqENeELgkvle..egrvakLeselalqkkfveelkkaleeleelleelee 147
                                    ++ +Le   + Lg++++  ++ +a+Le  +a +++ v++l+ a ++l e  ++ ee
  gi|119720248|ref|YP_920743.1|  56 RLSRLEAAVAGLGEAVSrhSEAIARLEVAVARHDEAVARLEAAVARLAEAQAKSEE 111
                                    77789999999999877225679***********************9999888776 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.0059
                           Wtap 108 vleegrvakLeselalqkkfveelkkaleeleelleeleeevevlqstl 156
                                    + +e+r+a+Le+ +a q + +++l+ a ++  e+++ le+ v ++ +t+
  gi|119720248|ref|YP_920743.1| 107 AKSEERLARLEEAVARQSESIAKLEAAVSKHSEVIARLEAAVAKHDETI 155
                                    56899***********************************999998876 PP

  == domain 4  score: 11.2 bits;  conditional E-value: 0.0021
                           Wtap 112 grvakLeselalqkkfveelkkaleeleelleeleeevevlqst 155
                                    + +a+Le+ +a++++ +++l+ka ++ +e ++ lee v +l  +
  gi|119720248|ref|YP_920743.1| 153 ETIARLEKAVAKHDESIARLEKAIARHDEAIARLEEAVRGLAAQ 196
                                    579**********************************9999877 PP

>> PTRF_SDPR  PTRF/SDPR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.81     1e+02      13      50 ..      38      75 ..      32      87 .. 0.83
   2 ?   12.0   4.0   0.00096      0.12      13      94 ..      94     175 ..      90     186 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.81
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      PTRF_SDPR 13 kvvgivdsvqesqkrlEerqaelenavksiqgdllkLa 50
                                    + ++v+ + e+  r Eer + le av ++   +++ +
  gi|119720248|ref|YP_920743.1| 38 GLREAVERLVEAHARAEERLSRLEAAVAGLGEAVSRHS 75
                                   5678899999999**************99988887766 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00096
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      PTRF_SDPR  13 kvvgivdsvqesqkrlEerqaelenavksiqgdllkLakshssTsntvnklleksrkvsvnvkevrerlekqavqvkklE 92 
                                    ++ ++v  + e+q + Eer a le+av      ++kL  + s+ s+ + +l   + k   ++  + + + k+   + +lE
  gi|119720248|ref|YP_920743.1|  94 RLEAAVARLAEAQAKSEERLARLEEAVARQSESIAKLEAAVSKHSEVIARLEAAVAKHDETIARLEKAVAKHDESIARLE 173
                                    6778899999*******************9999**********************************************9 PP

                                    HH CS
                      PTRF_SDPR  93 an 94 
                                    + 
  gi|119720248|ref|YP_920743.1| 174 KA 175
                                    74 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0      0.69        85      18      52 ..      31      65 ..      22      83 .. 0.59
   2 ?    8.4   4.2     0.012       1.5       6      57 ..     124     175 ..      49     203 .. 0.47

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.69
                        DUF4795 18 klqeelekleekvkelekrledkekklealkkqie 52
                                   +l +el+ l e+v++l + +++ e+ l  l+ ++ 
  gi|119720248|ref|YP_920743.1| 31 DLRAELKGLREAVERLVEAHARAEERLSRLEAAVA 65
                                   45555555555555555555555555555554443 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.012
                        DUF4795   6 aellkklqeaieklqeelekleekvkelekrledkekklealkkqieelekv 57 
                                    +e + kl++a++k +e +++le +v++ +++++++ek +  + ++i +lek+
  gi|119720248|ref|YP_920743.1| 124 SESIAKLEAAVSKHSEVIARLEAAVAKHDETIARLEKAVAKHDESIARLEKA 175
                                    2222333333333333333333333333333333333333333333333222 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1      0.23        28      38      93 ..      10      65 ..       5      76 .. 0.78
   2 ?    4.8   0.5      0.22        27      61      99 ..      82     120 ..      77     127 .. 0.78
   3 ?    5.6   0.9      0.12        15      60      99 ..      95     134 ..      92     138 .. 0.81
   4 ?    8.1   0.2      0.02       2.4      60      99 ..     137     176 ..     133     179 .. 0.90
   5 ?    8.0   0.3     0.022       2.7      60     102 ..     151     193 ..     148     197 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.23
                                   HHHS-TT--EEEEETTEEEEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    Prefoldin_2 38 lelldedtkvyklvGdvlvkqdkeevkeeLeerketlekeiktlekqleklekele 93
                                   l ll ed++  + v ++l ++d+   ++ L e  e+l +  ++ e++l++le+ ++
  gi|119720248|ref|YP_920743.1| 10 LRLLREDEEFRYAVVGLLGLEDLRAELKGLREAVERLVEAHARAEERLSRLEAAVA 65
                                   77888888888888888888888888888888888888888888888888887665 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.22
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    Prefoldin_2  61 eevkeeLeerketlekeiktlekqleklekeleelkeel 99 
                                    e + ++ +e  ++le+ +++l + + k e++l+ l+e +
  gi|119720248|ref|YP_920743.1|  82 EVAVARHDEAVARLEAAVARLAEAQAKSEERLARLEEAV 120
                                    667777888888888888888888888888888888876 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.12
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    Prefoldin_2  60 keevkeeLeerketlekeiktlekqleklekeleelkeel 99 
                                    +e + ++L e +++ e+++++le+   +  + +++l++ +
  gi|119720248|ref|YP_920743.1|  95 LEAAVARLAEAQAKSEERLARLEEAVARQSESIAKLEAAV 134
                                    5777888999999999999999999888888888888765 PP

  == domain 4  score: 8.1 bits;  conditional E-value: 0.02
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    Prefoldin_2  60 keevkeeLeerketlekeiktlekqleklekeleelkeel 99 
                                      ev+++Le+  ++ ++ i++lek   k+ + ++ l++ +
  gi|119720248|ref|YP_920743.1| 137 HSEVIARLEAAVAKHDETIARLEKAVAKHDESIARLEKAI 176
                                    67999***************************99999987 PP

  == domain 5  score: 8.0 bits;  conditional E-value: 0.022
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC CS
                    Prefoldin_2  60 keevkeeLeerketlekeiktlekqleklekeleelkeelqkk 102
                                     +e++++Le+  ++ ++ i++lek + ++ + ++ l+e ++ +
  gi|119720248|ref|YP_920743.1| 151 HDETIARLEKAVAKHDESIARLEKAIARHDEAIARLEEAVRGL 193
                                    6889999999999999999999999999999999999988765 PP

>> Not3  Not1 N-terminal domain, CCR4-Not complex component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.6     0.034       4.2     133     211 ..      44     125 ..      27     132 .. 0.53
   2 ?    8.8   5.2    0.0077      0.95     114     190 ..     116     194 ..      69     205 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.034
                           Not3 133 deLneqvekleaeieklsskkkkkkk..skekarveeleklierhkfhieklelllrlleneelep.eevekikedieyy 209
                                    + L e   + e+ + +l+++     +  s++++ +++le  + rh   +++le  +  l + + ++ e++++++e++   
  gi|119720248|ref|YP_920743.1|  44 ERLVEAHARAEERLSRLEAAVAGLGEavSRHSEAIARLEVAVARHDEAVARLEAAVARLAEAQAKSeERLARLEEAVARQ 123
                                    34444444444444444333322211123334467777777777777777777655444444443337777777776654 PP

                           Not3 210 ve 211
                                     e
  gi|119720248|ref|YP_920743.1| 124 SE 125
                                    44 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0077
                           Not3 114 ldpkekekeearewlkdaideLneqvekleaeieklsskkkkkkk..skekarveeleklierhkfhieklelllrlle 190
                                    l+++  +++e ++ l+ a+++ +e + +lea + k  ++  + +k  +k+++++++lek i rh   i++le+ +r l 
  gi|119720248|ref|YP_920743.1| 116 LEEAVARQSESIAKLEAAVSKHSEVIARLEAAVAKHDETIARLEKavAKHDESIARLEKAIARHDEAIARLEEAVRGLA 194
                                    2333334444444444444444444444444444444443222222344445788888888888888888888887765 PP

>> HemX  HemX, putative uroporphyrinogen-III C-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   6.2      0.02       2.4      18     101 ..      67     146 ..      23     150 .. 0.72
   2 ?   10.9   2.0    0.0017      0.21      32     101 ..     129     195 ..     119     205 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.02
                           HemX  18 vgaglyylgqqqvqeltaevaelqqqlaaleqqlaqveaekeqkqeleerlqqlaeklealekeleqlqkqleelqqqls 97 
                                    +g ++  +++   ++l+  va++++++a le+++a+   ++e ++++eerl+ l+e+++++++++++l++++++ ++ ++
  gi|119720248|ref|YP_920743.1|  67 LGEAVSRHSEAI-ARLEVAVARHDEAVARLEAAVAR---LAEAQAKSEERLARLEEAVARQSESIAKLEAAVSKHSEVIA 142
                                    343444444333.24455557777788888887777...66667777777777777777777777777777777777776 PP

                           HemX  98 kvsg 101
                                    ++++
  gi|119720248|ref|YP_920743.1| 143 RLEA 146
                                    6665 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0017
                           HemX  32 eltaevaelqqqlaaleqqlaqveaekeqkqeleerlqqlaeklealekeleqlqkqleelqqqlskvsg 101
                                    +l+a v+++++ +a le+++a+   ++e+ ++le+++++ +e++++lek+++  ++++++l++++  + +
  gi|119720248|ref|YP_920743.1| 129 KLEAAVSKHSEVIARLEAAVAK---HDETIARLEKAVAKHDESIARLEKAIARHDEAIARLEEAVRGLAA 195
                                    3444555666666666666666...777777777777777777777777777777777777777766554 PP

>> Sbi-IV  C3 binding domain 4 of IgG-bind protein SBI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   3.3    0.0056      0.69       3      39 ..      81     117 ..      79     137 .. 0.90
   2 ?    0.1   0.1       8.4     1e+03       3      26 ..     116     139 ..     115     144 .. 0.84
   3 ?    3.9   0.6      0.58        72       4      26 ..     145     167 ..     140     170 .. 0.73
   4 ?    8.1   0.2     0.028       3.5       3      22 ..     172     191 ..     170     197 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0056
                         Sbi-IV   3 iekaivrhdervksandaisklnekdsienrrlaqre 39 
                                    +e a+ rhde v   + a+++l e  +  + rla+ e
  gi|119720248|ref|YP_920743.1|  81 LEVAVARHDEAVARLEAAVARLAEAQAKSEERLARLE 117
                                    689******************************9876 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 8.4
                         Sbi-IV   3 iekaivrhdervksandaisklne 26 
                                    +e a+ r  e +   + a+sk  e
  gi|119720248|ref|YP_920743.1| 116 LEEAVARQSESIAKLEAAVSKHSE 139
                                    588999999999999999999766 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.58
                         Sbi-IV   4 ekaivrhdervksandaisklne 26 
                                    e a+ +hde +   + a++k +e
  gi|119720248|ref|YP_920743.1| 145 EAAVAKHDETIARLEKAVAKHDE 167
                                    77778888888777777777665 PP

  == domain 4  score: 8.1 bits;  conditional E-value: 0.028
                         Sbi-IV   3 iekaivrhdervksandais 22 
                                    +ekai rhde +   ++a+ 
  gi|119720248|ref|YP_920743.1| 172 LEKAIARHDEAIARLEEAVR 191
                                    79********9988888876 PP

>> DUF5305  Family of unknown function (DUF5305)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0         6   7.4e+02     142     166 ..      72      96 ..      60     104 .. 0.68
   2 ?    9.5   0.2    0.0047      0.58     140     179 ..     133     172 ..     112     174 .. 0.85
   3 ?    5.9   0.1     0.061       7.6     138     167 ..     159     188 ..     155     194 .. 0.67

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 6
                        DUF5305 142 skaekyelelekilkeYdewIvkgs 166
                                    s ++++ ++le++  ++de +++++
  gi|119720248|ref|YP_920743.1|  72 SRHSEAIARLEVAVARHDEAVARLE 96 
                                    4456666777777777777666665 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0047
                        DUF5305 140 tsskaekyelelekilkeYdewIvkgslppdlgdekviev 179
                                    + sk+++  ++le +  ++de I+++++ ++ +de++ ++
  gi|119720248|ref|YP_920743.1| 133 AVSKHSEVIARLEAAVAKHDETIARLEKAVAKHDESIARL 172
                                    5688899999999999999999999999999999988876 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.061
                        DUF5305 138 iftsskaekyelelekilkeYdewIvkgsl 167
                                     ++  k+++  ++lek++ ++de I+++++
  gi|119720248|ref|YP_920743.1| 159 EKAVAKHDESIARLEKAIARHDEAIARLEE 188
                                    455566777777777777777777777665 PP

>> Mod_r  Modifier of rudimentary (Mod(r)) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1      0.19        24       8      64 ..       9      65 ..       5      88 .. 0.73
   2 ?   11.7   6.1    0.0017      0.21      28     117 ..      85     175 ..      64     191 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.19
                          Mod_r  8 Lqelledeeklealvktlpevkqlkeekeellaeneslaeknlslepeleelrselq 64
                                   + +ll ++e ++  v  l  +++l++e++ l+++ e+l e+    e++l  l + ++
  gi|119720248|ref|YP_920743.1|  9 MLRLLREDEEFRYAVVGLLGLEDLRAELKGLREAVERLVEAHARAEERLSRLEAAVA 65
                                   556777777777777777778889999999999999998888888888877766654 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.0017
                          Mod_r  28 vkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqeldell.qkfspdallarLqtavae 106
                                    v + +e+   l+a+  +lae++ ++e++l  l + ++ + e++++le+++ +  +   +l       d + arL++ava+
  gi|119720248|ref|YP_920743.1|  85 VARHDEAVARLEAAVARLAEAQAKSEERLARLEEAVARQSESIAKLEAAVSKHSEVIARLEaAVAKHDETIARLEKAVAK 164
                                    56667888999****************999999999999999888888777766666555544456678999******** PP

                          Mod_r 107 aeeeSealaee 117
                                     +e   +l++ 
  gi|119720248|ref|YP_920743.1| 165 HDESIARLEKA 175
                                    99987776665 PP

>> TMCO5  TMCO5 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   3.4   0.00031     0.039       7     150 ..      31     175 ..      29     201 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00031
                          TMCO5   7 dlekdlqrldeaNqslLrkiqekeetiqslereitkldsllereed..eeenfsenekedalkeLeletaklekkneiLl 84 
                                    dl  +l+ l ea + l +    +ee  ++le  ++ l ++  r+ +    ++++  ++++a   Le   a+l +  +   
  gi|119720248|ref|YP_920743.1|  31 DLRAELKGLREAVERLVEAHARAEERLSRLEAAVAGLGEAVSRHSEaiARLEVAVARHDEAVARLEAAVARLAEAQAKSE 110
                                    56677778888888888888888888888888888887666554441234566667777788888888888887777777 PP

                          TMCO5  85 kevveLqkkisrkeskqddlek..etlkqkleelkvklqkseescaeqekelakveedyqsvaqlCkd 150
                                    + ++ L++ + r+++   +le   ++ ++  ++l++ + k +e  a+ ek +ak  e   s+a+l k 
  gi|119720248|ref|YP_920743.1| 111 ERLARLEEAVARQSESIAKLEAavSKHSEVIARLEAAVAKHDETIARLEKAVAKHDE---SIARLEKA 175
                                    777777777777776666666633444555666666666667777777777776666...55555444 PP

>> PKcGMP_CC  Coiled-coil N-terminus of cGMP-dependent protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0       1.8   2.3e+02       8      27 ..      76      95 ..      71      97 .. 0.87
   2 ?    4.8   0.5      0.21        26       7      27 ..     110     130 ..     106     137 .. 0.89
   3 ?    3.5   0.1      0.53        66       8      27 ..     139     158 ..     133     161 .. 0.85
   4 ?    9.3   0.5    0.0081         1       3      27 ..     162     186 ..     160     188 .. 0.88
   5 ?   -0.4   0.0       8.7   1.1e+03       7      13 ..     305     311 ..     303     313 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 1.8
                      PKcGMP_CC  8 ERIRELEkrlaekdeEIqEL 27
                                   E I+ LE ++a+ de ++ L
  gi|119720248|ref|YP_920743.1| 76 EAIARLEVAVARHDEAVARL 95
                                   66999**********99876 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.21
                      PKcGMP_CC   7 DERIRELEkrlaekdeEIqEL 27 
                                    +ER + LE+++a++ e I+ L
  gi|119720248|ref|YP_920743.1| 110 EERLARLEEAVARQSESIAKL 130
                                    89****************988 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.53
                      PKcGMP_CC   8 ERIRELEkrlaekdeEIqEL 27 
                                    E I+ LE+++a+ de I+ L
  gi|119720248|ref|YP_920743.1| 139 EVIARLEAAVAKHDETIARL 158
                                    66899**********99977 PP

  == domain 4  score: 9.3 bits;  conditional E-value: 0.0081
                      PKcGMP_CC   3 lllKDERIRELEkrlaekdeEIqEL 27 
                                    + + DE I+ LEk++a+ de I+ L
  gi|119720248|ref|YP_920743.1| 162 VAKHDESIARLEKAIARHDEAIARL 186
                                    5667******************977 PP

  == domain 5  score: -0.4 bits;  conditional E-value: 8.7
                      PKcGMP_CC   7 DERIREL 13 
                                    DER REL
  gi|119720248|ref|YP_920743.1| 305 DERAREL 311
                                    9*****9 PP

>> Sulfatase_C  C-terminal region of aryl-sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.2      0.38        47      74     106 ..      72     104 ..      65     124 .. 0.65
   2 ?   10.0   1.4    0.0089       1.1      69     105 ..     130     166 ..     119     204 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.38
                                    CCHHHHHHHHHHHHHHHCCC------TCCHHCH CS
                    Sulfatase_C  74 peykevlkeikkaveehkktlkpvpnqlakgel 106
                                    ++++e++++++ av++h++ ++  ++ +a++ +
  gi|119720248|ref|YP_920743.1|  72 SRHSEAIARLEVAVARHDEAVARLEAAVARLAE 104
                                    566777777777777777777766666665533 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0089
                                    TTSTTCCHHHHHHHHHHHHHHHCCC------TCCHHC CS
                    Sulfatase_C  69 lsaespeykevlkeikkaveehkktlkpvpnqlakge 105
                                    l+a+ ++++ev++++++av++h++t++  ++ +ak +
  gi|119720248|ref|YP_920743.1| 130 LEAAVSKHSEVIARLEAAVAKHDETIARLEKAVAKHD 166
                                    5666688889999999999999999888888877764 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2  17.0   0.00039     0.048     603     759 ..      31     180 ..      27     205 .. 0.48

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00039
                        DUF3584 603 eLrerlqaleealqsaeakqkqaeeelkqlnaeleeakravaeaatalknardtlerlqnekesekdklekaiaerkqqa 682
                                     Lr++l+ l ea++   + +++aee+l+ l+a++  + +av+++ +a+   +  + r  ++  +++ ++   +ae++++ 
  gi|119720248|ref|YP_920743.1|  31 DLRAELKGLREAVERLVEAHARAEERLSRLEAAVAGLGEAVSRHSEAIARLEVAVARHDEAVARLEAAVA-RLAEAQAKS 109
                                    5666666666666666666666666666666666666666666666665555555555444444444443.345555555 PP

                        DUF3584 683 eeqlqkldaqlkqleeqqkaaleelkedlseerlekkakwqevvgeldeqlaelkkaieaartqakarlkeleeayk 759
                                    ee+l  l+++     e     +++l+  +s+++ e  a +++ v++ de +a+l+ka++++ ++ ++ l++     +
  gi|119720248|ref|YP_920743.1| 110 EERLARLEEAVARQSES----IAKLEAAVSKHS-EVIARLEAAVAKHDETIARLEKAVAKHDESIAR-LEKAIARHD 180
                                    55555555544333332....333333333333.444555555666666666665555544333222.222222222 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1      0.52        64      13      44 ..      30      61 ..      28      69 .. 0.85
   2 ?    8.5   8.9     0.019       2.4       6     118 ..      58     176 ..      54     178 .. 0.83
   3 ?    7.2   0.5     0.046       5.7       9      43 ..     166     200 ..     155     205 .. 0.62

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.52
                        DUF5082 13 aelrseiaaleekIerLkeaktklsdekeslk 44
                                   ++lr+e+++l e +erL ea  + ++  ++l+
  gi|119720248|ref|YP_920743.1| 30 EDLRAELKGLREAVERLVEAHARAEERLSRLE 61
                                   6899**************99988888777766 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.019
                        DUF5082   6 sklqaqiaelrseiaaleekIerLkeaktklsdekeslkqkkkklekplnsse....sWkGkeennydgirs..nlessy 79 
                                    s+l+a++a l + ++  +e I+rL+ a  + +++ ++l+++   l++  ++se     +    + + ++i+      s+ 
  gi|119720248|ref|YP_920743.1|  58 SRLEAAVAGLGEAVSRHSEAIARLEVAVARHDEAVARLEAAVARLAEAQAKSEerlaRLEEAVARQSESIAKleAAVSKH 137
                                    78999999999999999********8888888888888888888888888888655555555555555555566888899 PP

                        DUF5082  80 qtyvdkldelidaieeEIerLenqiseaqgvldtlqsql 118
                                    ++++ +l++++++ +e I rLe+ + ++  ++++l++++
  gi|119720248|ref|YP_920743.1| 138 SEVIARLEAAVAKHDETIARLEKAVAKHDESIARLEKAI 176
                                    99********************************99988 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.046
                        DUF5082   9 qaqiaelrseiaaleekIerLkeaktklsdekesl 43 
                                     + ia l++ ia  +e I+rL+ea + l ++  +l
  gi|119720248|ref|YP_920743.1| 166 DESIARLEKAIARHDEAIARLEEAVRGLAAQVGRL 200
                                    44566666777777777777777666666655555 PP

>> CC2-LZ  Leucine zipper of domain CC2 of NEMO, NF-kappa-B essential modulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1      0.25        31      13      56 ..      40      83 ..      30      89 .. 0.80
   2 ?    5.2   2.9      0.22        27      18      53 ..      94     129 ..      82     153 .. 0.56
   3 ?    7.0   1.0     0.059       7.3      16      60 ..     148     196 ..     131     198 .. 0.65

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.25
                         CC2-LZ 13 keeieeLkaqlqaaeealaakqeeidelkeeikkkeeeletisv 56
                                   +e +e+L ++   aee l++ +  +  l e +++++e +  ++v
  gi|119720248|ref|YP_920743.1| 40 REAVERLVEAHARAEERLSRLEAAVAGLGEAVSRHSEAIARLEV 83
                                   78899999999999999999999999999999999997774443 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.22
                         CC2-LZ  18 eLkaqlqaaeealaakqeeidelkeeikkkeeelet 53 
                                    +L+a++    ea a+++e++ +l+e +++++e + +
  gi|119720248|ref|YP_920743.1|  94 RLEAAVARLAEAQAKSEERLARLEEAVARQSESIAK 129
                                    555555555555555555555555555555553322 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.059
                         CC2-LZ  16 ieeLkaqlqaaeealaakqeeidelkeeikkkee...ele.tisvlkaQ 60 
                                    + +  + +   e+a+a+++e i +l++ i++++e    le  +  l aQ
  gi|119720248|ref|YP_920743.1| 148 VAKHDETIARLEKAVAKHDESIARLEKAIARHDEaiaRLEeAVRGLAAQ 196
                                    4444455666677888888888888888888887555555567777776 PP

>> NCD2  NAB conserved region 2 (NCD2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0       4.2   5.2e+02       5      42 ..      41      78 ..      33      88 .. 0.60
   2 ?   10.9   4.4    0.0027      0.33       4     113 ..      89     199 ..      82     202 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 4.2
                           NCD2  5 eqvekvaesaerlvkslpklepkllklkkklakeveei 42
                                   e+ve+++e+  r  ++l++le+  + l   ++++ e+i
  gi|119720248|ref|YP_920743.1| 41 EAVERLVEAHARAEERLSRLEAAVAGLGEAVSRHSEAI 78
                                   45666666666666666666665555555555555554 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0027
                           NCD2   4 eeqvekvaesaerlvkslpklepkllklkkklakeveeilemseedprreeeirkysaiYGRfd.skRkeekqLtlhevt 82 
                                    +e+v+++++++ rl++  +k+e++l++l+  +a++ e+i +++ + +++ e i +  a   + d +  + ek+++ h+ +
  gi|119720248|ref|YP_920743.1|  89 DEAVARLEAAVARLAEAQAKSEERLARLEEAVARQSESIAKLEAAVSKHSEVIARLEAAVAKHDeTIARLEKAVAKHDES 168
                                    688999*******************************************9999998877777762678999999999999 PP

                           NCD2  83 vneaaaqlCkkdpaLltrRdeLFsLaRqvvr 113
                                    +      + ++d+a+    + +  La qv r
  gi|119720248|ref|YP_920743.1| 169 IARLEKAIARHDEAIARLEEAVRGLAAQVGR 199
                                    9888888888888776666667777777766 PP

>> Nsp1_C  Nsp1-like C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.4     0.015       1.8      52     109 ..      71     128 ..      34     135 .. 0.84
   2 ?    7.8   0.4     0.022       2.7      21      94 ..     117     190 ..     113     205 .. 0.47

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.015
                         Nsp1_C  52 LvengekIskLysevleaeqeqnkidqeLeyiesqqdeLeslLdnyEkeleellskle 109
                                    + + +e I++L  +v + +++ ++++     +++ q   e+ L+++E+ + +++++++
  gi|119720248|ref|YP_920743.1|  71 VSRHSEAIARLEVAVARHDEAVARLEAAVARLAEAQAKSEERLARLEEAVARQSESIA 128
                                    5567899*******************************************99997765 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.022
                         Nsp1_C  21 delinkWtteLeeqekeFeeqakkvneWDrvLvengekIskLysevleaeqeqnkidqeLeyiesqqdeLeslL 94 
                                    +e + + ++++ + e   ++ ++ ++  + ++ +  e I++L ++v + +++ +++++ +    +    Le+ +
  gi|119720248|ref|YP_920743.1| 117 EEAVARQSESIAKLEAAVSKHSEVIARLEAAVAKHDETIARLEKAVAKHDESIARLEKAIARHDEAIARLEEAV 190
                                    44444444444444444444444444444444444444444444444444444444444444444444444443 PP

>> COG5  Golgi transport complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1      0.86   1.1e+02      78     111 ..      54      87 ..      28     102 .. 0.56
   2 ?    9.1   1.8     0.011       1.4      65     117 ..     104     156 ..      87     163 .. 0.79
   3 ?    9.0   3.2     0.012       1.5      33     109 ..     111     190 ..     104     206 .. 0.62

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.86
                                    XXXXXXXXXXXXXXX-TTHHHHHHHHHHHHHHHH CS
                           COG5  78 ksslesLsasyerlkskvlepyeeaeklqsalkr 111
                                    +++l++L+a++  l + v++  e +  l+ a +r
  gi|119720248|ref|YP_920743.1|  54 EERLSRLEAAVAGLGEAVSRHSEAIARLEVAVAR 87 
                                    3445555555555555555555555555555444 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.011
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXX-TTHHHHHHHHHHHHHHHHHHHHHH CS
                           COG5  65 skskslssvlselksslesLsasyerlkskvlepyeeaeklqsalkrlhqtld 117
                                    + +++ ++ l  l++ +++ s+s+ +l+  v++  e +  l++a ++  +t  
  gi|119720248|ref|YP_920743.1| 104 EAQAKSEERLARLEEAVARQSESIAKLEAAVSKHSEVIARLEAAVAKHDETIA 156
                                    44555556999*****************************9999998777765 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.012
                                    XXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXX-TTHHHHHHHHHHHHHH CS
                           COG5  33 tplkrlnydiqeldkrlrql..itsnhleLlehlskskslss.vlselksslesLsasyerlkskvlepyeeaeklqsal 109
                                     +l+rl++++    + + +l   +s+h+e++++l+    + + +   l++ +++  +s+ rl++ + +  e +  l++a 
  gi|119720248|ref|YP_920743.1| 111 ERLARLEEAVARQSESIAKLeaAVSKHSEVIARLEAAVAKHDeTIARLEKAVAKHDESIARLEKAIARHDEAIARLEEAV 190
                                    55566666665555555543225666777777776665555557777777777777777777777777666666666665 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   5.1      0.03       3.8      45     131 ..      27     113 ..       2     118 .. 0.83
   2 ?    9.4   7.0    0.0079      0.98      25     131 ..      98     193 ..      86     202 .. 0.49

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.03
                 CENP-F_leu_zip  45 leaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelqkkqervseLeslnsslenlleekEqekvqmkees 124
                                    l  E+ +ae+++l+e +e+l e   + e  L+ l      L + +    e +  Le +     + + ++E+  +++ e++
  gi|119720248|ref|YP_920743.1|  27 LGLEDLRAELKGLREAVERLVEAHARAEERLSRLEAAVAGLGEAVSRHSEAIARLEVAVARHDEAVARLEAAVARLAEAQ 106
                                    6789999****************************************************************999999998 PP

                 CENP-F_leu_zip 125 kaaveeL 131
                                     ++ e L
  gi|119720248|ref|YP_920743.1| 107 AKSEERL 113
                                    8887776 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0079
                 CENP-F_leu_zip  25 kvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelqkkqervseLeslns 104
                                     v +L      see + +              l+e + + +e+  +le+ +++ ++    Le  + k  e++  Le++  
  gi|119720248|ref|YP_920743.1|  98 AVARLAEAQAKSEERLAR--------------LEEAVARQSESIAKLEAAVSKHSEVIARLEAAVAKHDETIARLEKAVA 163
                                    444444444444444444..............555555555555555555555555555555555555555555555555 PP

                 CENP-F_leu_zip 105 slenlleekEqekvqmke...eskaaveeL 131
                                    +  + + ++E+  ++  e   + ++av  L
  gi|119720248|ref|YP_920743.1| 164 KHDESIARLEKAIARHDEaiaRLEEAVRGL 193
                                    555555555555444443111234444444 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   3.5     0.021       2.7     104     178 ..      57     131 ..      15     135 .. 0.54
   2 ?   10.9   8.6    0.0024       0.3      99     184 ..     101     193 ..      92     202 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.021
                         DUF724 104 qtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaekleeeledve 178
                                     ++l+ +  +l + ++ ++++ ++le  ++  ++++++le   a+l e + ++++++arl+  +++ +e++ + e
  gi|119720248|ref|YP_920743.1|  57 LSRLEAAVAGLGEAVSRHSEAIARLEVAVARHDEAVARLEAAVARLAEAQAKSEERLARLEEAVARQSESIAKLE 131
                                    233333334444444444444444555555555555555555555556666666666666666666655555544 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0024
                         DUF724  99 slkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallk.......ekkeaadkeiarlkseaekle 171
                                     l + q+k +e++ +le+ ++ ++++ +kle+ +++ ++ i++le   a          +   ++d++iarl++  ++ +
  gi|119720248|ref|YP_920743.1| 101 RLAEAQAKSEERLARLEEAVARQSESIAKLEAAVSKHSEVIARLEAAVAKHDetiarleKAVAKHDESIARLEKAIARHD 180
                                    56677888888888888888888888888888888888888877765543336666665777778888999999998888 PP

                         DUF724 172 eeledveqeFeav 184
                                    e++ + e+ ++ +
  gi|119720248|ref|YP_920743.1| 181 EAIARLEEAVRGL 193
                                    8888888777665 PP

>> DUF3130  Protein of unknown function (DUF3130
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0       3.9   4.8e+02      42      76 ..      29      63 ..      27      74 .. 0.88
   2 ?    0.9   0.0       4.5   5.6e+02      49      84 ..      57      92 ..      47      98 .. 0.86
   3 ?    8.9   0.3     0.014       1.7      38      85 ..     123     170 ..     100     176 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 3.9
                        DUF3130 42 indlrsaLielvdavekvqsvvkkDaerlkklgaa 76
                                   ++dlr+ L  l +ave + ++  +  erl +l+aa
  gi|119720248|ref|YP_920743.1| 29 LEDLRAELKGLREAVERLVEAHARAEERLSRLEAA 63
                                   5799*************999999999999998877 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 4.5
                        DUF3130 49 LielvdavekvqsvvkkDaerlkklgaafikkDkel 84
                                   L+ l  av  + ++v +  e + +l++a +++D+ +
  gi|119720248|ref|YP_920743.1| 57 LSRLEAAVAGLGEAVSRHSEAIARLEVAVARHDEAV 92
                                   7788889999999999999*********99999876 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.014
                        DUF3130  38 kansindlrsaLielvdavekvqsvvkkDaerlkklgaafikkDkele 85 
                                    +++si +l +a+++  +++  ++ +v k  e + +l++a +k+D+ + 
  gi|119720248|ref|YP_920743.1| 123 QSESIAKLEAAVSKHSEVIARLEAAVAKHDETIARLEKAVAKHDESIA 170
                                    6899****************************************9865 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   5.4    0.0041      0.51     333     408 ..     107     183 ..      22     204 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0041
                           FapA 333 pelkeklkeleeeleeleeeleklkkkikklpklka.ekqlesekkeqlkklletkeklkeeleeleeelkelkeel 408
                                     +  e+l++lee + +  e++ kl+++++k ++  a  ++  +++ e++++l+++  k+ e+++ le+ +++ +e +
  gi|119720248|ref|YP_920743.1| 107 AKSEERLARLEEAVARQSESIAKLEAAVSKHSEVIArLEAAVAKHDETIARLEKAVAKHDESIARLEKAIARHDEAI 183
                                    22233335555555555555555555544444433323334444444444444444444444444444444444444 PP

>> Exonuc_VII_S  Exonuclease VII small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.3      0.72        89       4      34 ..      49      79 ..      47      87 .. 0.72
   2 ?    4.4   0.4      0.31        39       3      15 ..      90     102 ..      74     107 .. 0.76
   3 ?    4.2   4.1      0.37        45       3      39 ..      90     126 ..      88     133 .. 0.78
   4 ?    5.0   1.3       0.2        25       2      31 ..     110     139 ..     110     146 .. 0.80
   5 ?    7.8   1.6     0.028       3.5       2      46 ..     145     189 ..     144     191 .. 0.83
   6 ?    4.8   0.1      0.23        29       3      17 ..     181     195 ..     179     204 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.72
                   Exonuc_VII_S  4 alaeLeeIvekLEsgelsLeeslklyeeGvk 34
                                   a a+ ee +++LE     L e++    e+++
  gi|119720248|ref|YP_920743.1| 49 AHARAEERLSRLEAAVAGLGEAVSRHSEAIA 79
                                   6677777777777777777777777777776 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.31
                   Exonuc_VII_S   3 ealaeLeeIvekL 15 
                                    ea+a+Le+ v++L
  gi|119720248|ref|YP_920743.1|  90 EAVARLEAAVARL 102
                                    7788888888777 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.37
                   Exonuc_VII_S   3 ealaeLeeIvekLEsgelsLeeslklyeeGvkLlkeC 39 
                                    ea+a+Le+ v++L + +   ee l+  ee+v+   e 
  gi|119720248|ref|YP_920743.1|  90 EAVARLEAAVARLAEAQAKSEERLARLEEAVARQSES 126
                                    8999999999999999999999999988888765555 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.2
                   Exonuc_VII_S   2 EealaeLeeIvekLEsgelsLeeslklyee 31 
                                    Ee la+Lee v++ ++    Le ++ +  e
  gi|119720248|ref|YP_920743.1| 110 EERLARLEEAVARQSESIAKLEAAVSKHSE 139
                                    899********9977777788888877666 PP

  == domain 5  score: 7.8 bits;  conditional E-value: 0.028
                   Exonuc_VII_S   2 EealaeLeeIvekLEsgelsLeeslklyeeGvkLlkeCekkLdea 46 
                                    E+a+a+ +e +++LE+     +es++  e++++   e+ ++L+ea
  gi|119720248|ref|YP_920743.1| 145 EAAVAKHDETIARLEKAVAKHDESIARLEKAIARHDEAIARLEEA 189
                                    778888888999999999999999999999998888888888887 PP

  == domain 6  score: 4.8 bits;  conditional E-value: 0.23
                   Exonuc_VII_S   3 ealaeLeeIvekLEs 17 
                                    ea+a+Lee v+ L  
  gi|119720248|ref|YP_920743.1| 181 EAIARLEEAVRGLAA 195
                                    9*********98865 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1     0.097        12     347     413 ..      30      94 ..      26     109 .. 0.71
   2 ?    7.7   4.7    0.0071      0.88     342     426 ..     109     193 ..     101     201 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.097
                                    HHHHHHHHHHHHHHHHHHHHHS-SS---STTGGGTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           EzrA 347 relekelkelekdyeeleekleekkvaYSelqeeleeleekleeieekqeeileslkslrkdEkrAr 413
                                    ++l +elk l++ +e+l+e+++  +   S+l+  +  l e +++ +e   +++ +    r dE+ Ar
  gi|119720248|ref|YP_920743.1|  30 EDLRAELKGLREAVERLVEAHARAEERLSRLEAAVAGLGEAVSRHSEAIARLEVA--VARHDEAVAR 94 
                                    5677788888888888888888888888888888888888888777777766544..4466666666 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0071
                                    TSTTHHHHHHHHHHHHHHHHHHHHHHS-SS---STTGGGTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           EzrA 342 eleklrelekelkelekdyeeleekleekkvaYSelqeeleeleekleeieekqeeileslkslrkdEkrAreqldeikk 421
                                      e+l  le+ + + ++++ +le ++++++ +  +l+  + + +e+++++e+ + + +es++ l+k  +r  e ++++++
  gi|119720248|ref|YP_920743.1| 109 SEERLARLEEAVARQSESIAKLEAAVSKHSEVIARLEAAVAKHDETIARLEKAVAKHDESIARLEKAIARHDEAIARLEE 188
                                    44666677777777777777777777777777777777777777777777777777777777777777777777777776 PP

                                    HHHHH CS
                           EzrA 422 elkei 426
                                     ++ +
  gi|119720248|ref|YP_920743.1| 189 AVRGL 193
                                    66655 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7  18.0     0.032       3.9     131     250 ..      53     147 ..      13     202 .. 0.40

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.032
                        DUF4407 131 ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaqldaaqaelaelkakld.at 209
                                    ++++l++lea +a l ++++  ++++++l+ +++++ +                            a+l+++ a+l  a+
  gi|119720248|ref|YP_920743.1|  53 AEERLSRLEAAVAGLGEAVSRHSEAIARLEVAVARHDEA--------------------------VARLEAAVARLAeAQ 106
                                    333333333333333333333333333333333333222..........................111111111111122 PP

                        DUF4407 210 arlaalraelaeleaerakeraasqaaaaaddGllarleal 250
                                    a+ +++ a+l+e+ a++++++a+ +aa ++ + ++arlea 
  gi|119720248|ref|YP_920743.1| 107 AKSEERLARLEEAVARQSESIAKLEAAVSKHSEVIARLEAA 147
                                    22222222222222333333333333333333333333332 PP

>> Spc29  Spindle Pole Component 29
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.4       0.4        49     111     162 ..      70     125 ..      37     140 .. 0.76
   2 ?   10.1   0.5    0.0044      0.54     114     165 ..     136     187 ..     113     204 .. 0.63

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.4
                          Spc29 111 siyssvkkivelekklddqkleIkeLkreleqqrtvnseLqekvaeleeev....k 162
                                     + ++ + i +le  +  + + +  L+ ++        +  e++a+lee v    +
  gi|119720248|ref|YP_920743.1|  70 AVSRHSEAIARLEVAVARHDEAVARLEAAVARLAEAQAKSEERLARLEEAVarqsE 125
                                    56677778889999999999999999999999999999999999999999943332 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0044
                          Spc29 114 ssvkkivelekklddqkleIkeLkreleqqrtvnseLqekvaeleeevkrla 165
                                    ++ ++i +le  + ++ ++I  L++++ ++  ++  L + +a+ +e + rl+
  gi|119720248|ref|YP_920743.1| 136 KHSEVIARLEAAVAKHDETIARLEKAVAKHDESIARLEKAIARHDEAIARLE 187
                                    3445555666666666666666666666666666666666666666655554 PP

>> ERM  Ezrin/radixin/moesin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0  17.9      0.29        36      10     100 ..      39     129 ..      28     139 .. 0.47
   2 ?   12.3  16.2   0.00087      0.11      16     109 ..     108     201 ..     101     205 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.29
                            ERM  10 leerLkqlqeeaekaqeaLreseetaelLaekarraeeeaelLeqkaaeaeeeiqrlkesaekeeeekeklerklreael 89 
                                    l+e  ++l e  ++a+e L++ e  +  L e   r  e+  +Le   a+  e+ +rl+ + ++ +e ++k e++l++ e+
  gi|119720248|ref|YP_920743.1|  39 LREAVERLVEAHARAEERLSRLEAAVAGLGEAVSRHSEAIARLEVAVARHDEAVARLEAAVARLAEAQAKSEERLARLEE 118
                                    44444455555555566666666666666666665555555555555554444444444444444444444444444444 PP

                            ERM  90 eaarleeeser 100
                                     +ar  e   +
  gi|119720248|ref|YP_920743.1| 119 AVARQSESIAK 129
                                    44444333222 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00087
                            ERM  16 qlqeeaekaqeaLreseetaelLaekarraeeeaelLeqkaaeaeeeiqrlkesaekeeeekeklerklreaeleaarle 95 
                                    + +e  ++ +ea  ++ e + +L+    +  e   +Le+  a+  e i+rl+++ +k +e+ ++le+ +++ ++ +arle
  gi|119720248|ref|YP_920743.1| 108 KSEERLARLEEAVARQSESIAKLEAAVSKHSEVIARLEAAVAKHDETIARLEKAVAKHDESIARLEKAIARHDEAIARLE 187
                                    56777788888888888888888888888888888888888888888888888888888888888888888888888888 PP

                            ERM  96 eeserkeeeaerLk 109
                                    e+++  ++++ rL 
  gi|119720248|ref|YP_920743.1| 188 EAVRGLAAQVGRLS 201
                                    88887777777665 PP

>> ANAPC16  Anaphase-promoting complex, subunit 16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.1      0.47        58      44      69 ..      86     112 ..      55     123 .. 0.74
   2 ?    4.4   0.1       0.4        50      44      58 ..     149     163 ..     134     171 .. 0.80
   3 ?    3.8   0.1      0.61        76      44      58 ..     163     177 ..     160     185 .. 0.80
   4 ?    0.1   0.0       8.6   1.1e+03      44      55 ..     177     188 ..     169     200 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.47
                                    HHHHHHHHHHHH.HHHHHHHHHHTGGG CS
                        ANAPC16  44 vkhdqqvarmek.laglveeleadewr 69 
                                     +hd+ var+e  +a l e     e r
  gi|119720248|ref|YP_920743.1|  86 ARHDEAVARLEAaVARLAEAQAKSEER 112
                                    58********97245555554445555 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.4
                                    HHHHHHHHHHHHHHH CS
                        ANAPC16  44 vkhdqqvarmeklag 58 
                                     khd+ +ar+ek  +
  gi|119720248|ref|YP_920743.1| 149 AKHDETIARLEKAVA 163
                                    59*********9765 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.61
                                    HHHHHHHHHHHHHHH CS
                        ANAPC16  44 vkhdqqvarmeklag 58 
                                     khd+ +ar+ek  +
  gi|119720248|ref|YP_920743.1| 163 AKHDESIARLEKAIA 177
                                    59*********9765 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 8.6
                                    HHHHHHHHHHHH CS
                        ANAPC16  44 vkhdqqvarmek 55 
                                     +hd+ +ar+e 
  gi|119720248|ref|YP_920743.1| 177 ARHDEAIARLEE 188
                                    479******986 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0       1.1   1.3e+02      48      86 ..      35      73 ..      28     105 .. 0.64
   2 ?    4.5   0.8      0.35        43      33      87 ..      90     144 ..      75     160 .. 0.61
   3 ?    3.2   0.0      0.83     1e+02      22      53 ..     170     201 ..     141     215 .. 0.58

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 1.1
                         DUF948 48 evedllakvnelledvneklekvdplteavadlgesvse 86
                                   e+++l + v++l+e   +  e++ +l +ava lge+vs 
  gi|119720248|ref|YP_920743.1| 35 ELKGLREAVERLVEAHARAEERLSRLEAAVAGLGEAVSR 73
                                   444555555555555555666666666666666666653 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.35
                         DUF948  33 atieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvsel 87 
                                    ++++ le  v  + +  ++  +   +l e v +++e++ +l +av + +e ++ l
  gi|119720248|ref|YP_920743.1|  90 EAVARLEAAVARLAEAQAKSEERLARLEEAVARQSESIAKLEAAVSKHSEVIARL 144
                                    4455555555555554444455555555666677777777777777777666665 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.83
                         DUF948  22 lklkktldeaaatieelekqvdpilkevedll 53 
                                     +l+k + +  ++i+ le+ v+++  +v +l 
  gi|119720248|ref|YP_920743.1| 170 ARLEKAIARHDEAIARLEEAVRGLAAQVGRLS 201
                                    34445555555555555555555555554444 PP

>> FAM76  FAM76 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   1.1     0.028       3.4     213     295 ..      63     144 ..      31     148 .. 0.75
   2 ?    8.3   0.7     0.011       1.3     220     264 ..     147     191 ..     127     204 .. 0.56

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.028
                          FAM76 213 nssdhlvavtqLkeeiaslkkqleqkdqellekdkkitelkaellekekelreklkelekeakekieklekkirellkev 292
                                    ++     av++  e ia+l+  ++++d+++   +  ++ l   + ++ +e   +l+e  +  +e+i kle+ +++    +
  gi|119720248|ref|YP_920743.1|  63 AVAGLGEAVSRHSEAIARLEVAVARHDEAVARLEAAVARLAEAQAKS-EERLARLEEAVARQSESIAKLEAAVSKHSEVI 141
                                    55555557788889999999999999999999999999996555554.45567899999999999999999888877777 PP

                          FAM76 293 ael 295
                                    a+l
  gi|119720248|ref|YP_920743.1| 142 ARL 144
                                    766 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.011
                          FAM76 220 avtqLkeeiaslkkqleqkdqellekdkkitelkaellekekelr 264
                                    av++  e+ia+l+k ++++d+++   +k i+       + e+ +r
  gi|119720248|ref|YP_920743.1| 147 AVAKHDETIARLEKAVAKHDESIARLEKAIARHDEAIARLEEAVR 191
                                    445555666666666666666666666666655555555554444 PP

>> BicD  Microtubule-associated protein Bicaudal-D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5  10.9    0.0049      0.61     300     432 ..      35     167 ..      28     205 .. 0.58

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0049
                           BicD 300 alseqkekvnrLte.hlealrklqaskerqaaedkekerdsnedgdeyevdingkevlecklkvaveelaelkeelktlk 378
                                    +l+  +e v+rL e h  a ++l     + a + +  +r+s++ +   ev +  ++   ++l++av+ lae +++ ++  
  gi|119720248|ref|YP_920743.1|  35 ELKGLREAVERLVEaHARAEERLSRLEAAVAGLGEAVSRHSEA-IARLEVAVARHDEAVARLEAAVARLAEAQAKSEERL 113
                                    5555555666655424444455444444444444444444433.356666666666666666666666666666666666 PP

                           BicD 379 akyekleerykeekarlraeiqelkeklrslekaskqdkekiaelekelkklrk 432
                                    a++e+  +r +e  a+l+a + + +e +++le a  +  e ia+lek + k  +
  gi|119720248|ref|YP_920743.1| 114 ARLEEAVARQSESIAKLEAAVSKHSEVIARLEAAVAKHDETIARLEKAVAKHDE 167
                                    666666666666666666666666666666666666666666666666655433 PP

>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5  11.9    0.0022      0.27      84     219 ..      49     189 ..      28     194 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0022
                            MAD  84 nlealnkkekekesklaearevisalknelaelkrqiekqelelsekeseleelqerldllkkklseleqli....qqle 159
                                     ++ ++++++  e+ +a + e  s   + +a+l+  + + + ++ + e  + +l e++   +++l+ le+ +    ++  
  gi|119720248|ref|YP_920743.1|  49 AHARAEERLSRLEAAVAGLGEAVSRHSEAIARLEVAVARHDEAVARLEAAVARLAEAQAKSEERLARLEEAVarqsESIA 128
                                    33333344444556677778888999999999999999999999999999999999999999999999988865555556 PP

                            MAD 160 kkqkelaeaeqrikeLefeiqsqeddslivknsksel.aripelekelerlreenkklnel 219
                                    k +   +++ + i  Le  +++  +  + ++++ ++  ++i++lek ++r+ e +++l+e 
  gi|119720248|ref|YP_920743.1| 129 KLEAAVSKHSEVIARLEAAVAKHDETIARLEKAVAKHdESIARLEKAIARHDEAIARLEEA 189
                                    66666777888899999999999988888888888888*******************9986 PP

>> Leu_zip  Leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1         1   1.2e+02     131     175 ..      39      83 ..      29      93 .. 0.74
   2 ?   11.0   5.5    0.0018      0.22     127     215 ..      91     180 ..      87     197 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 1
                        Leu_zip 131 LkkeierLkeenekLkerlkelEkqatsaleeksklekalkelqk 175
                                    L+  +erL e   + +erl +lE+ +  + e  s+ ++a+++l+ 
  gi|119720248|ref|YP_920743.1|  39 LREAVERLVEAHARAEERLSRLEAAVAGLGEAVSRHSEAIARLEV 83 
                                    778899999999999999999999888777766666666666654 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0018
                        Leu_zip 127 gaeLLkkeierLkeenekLkerlkelEkqatsaleeksklekalkelqkelgek.kdekenskeiskleeklaelkldle 205
                                    +++ L+  ++rL e   k +erl +lE+ + +  e   kle+a+++  + +     ++++++++i++le+ +a+    + 
  gi|119720248|ref|YP_920743.1|  91 AVARLEAAVARLAEAQAKSEERLARLEEAVARQSESIAKLEAAVSKHSEVIARLeAAVAKHDETIARLEKAVAKHDESIA 170
                                    56779999************************************999888777624556689999*****9999887776 PP

                        Leu_zip 206 ktleektasa 215
                                    +  ++ +++ 
  gi|119720248|ref|YP_920743.1| 171 RLEKAIARHD 180
                                    6555554444 PP

>> Tektin  Tektin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   2.3     0.026       3.2     247     292 ..      93     138 ..      81     145 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.026
                         Tektin 247 ealrkrieetedaknkleeqlkkvleeiaeleknieeLekairdke 292
                                    + l+  ++ + +a  k ee l++++e +a++ ++i++Le a+ + +
  gi|119720248|ref|YP_920743.1|  93 ARLEAAVARLAEAQAKSEERLARLEEAVARQSESIAKLEAAVSKHS 138
                                    567888999999***************************9998766 PP

>> KASH_CCD  Coiled-coil region of CCDC155 or KASH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   8.2    0.0041      0.51      64     189 ..      31     156 ..      26     158 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0041
                       KASH_CCD  64 lleeEleelkalvkeleEkrarlkaqnkqlekenqsLiakiesLqeenikllaekdelkkklkeLlkekaeLkkqlhele 143
                                     l  El  l++ v++l E +ar++ + ++le     L + +    e + +l +      + ++ L +  a L +   + e
  gi|119720248|ref|YP_920743.1|  31 DLRAELKGLREAVERLVEAHARAEERLSRLEAAVAGLGEAVSRHSEAIARLEVAVARHDEAVARLEAAVARLAEAQAKSE 110
                                    5788999*****************************************************************99999999 PP

                       KASH_CCD 144 ellaekealleektkqieeLkltieEyssiieeLraeksrLeeqlq 189
                                    e la  e+++  + + i +L++++   s +i  L a + + +e ++
  gi|119720248|ref|YP_920743.1| 111 ERLARLEEAVARQSESIAKLEAAVSKHSEVIARLEAAVAKHDETIA 156
                                    999999999999************************9999888775 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   7.0     0.054       6.6      36     138 ..      32     135 ..      27     148 .. 0.63
   2 ?   10.0   8.0     0.007      0.86      34     142 ..      93     202 ..      82     206 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.054
                           Fez1  36 lkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelselsleeeeaa. 114
                                    l+a+l+ lr+++e+  e+  ++ee+l+  ++ +  + + ++r+++    l+  v + +e +++l  ++++l++ +++++ 
  gi|119720248|ref|YP_920743.1|  32 LRAELKGLREAVERLVEAHARAEERLSRLEAAVAGLGEAVSRHSEAIARLEVAVARHDEAVARLEAAVARLAEAQAKSEe 111
                                    78888888888888888888888888888888888888888888777777777888888888887777765544444332 PP

                           Fez1 115 ..lesdeakaqrqeaeeleelkreve 138
                                      ++ +ea   rq+ e++++l++ v 
  gi|119720248|ref|YP_920743.1| 112 rlARLEEAV-ARQS-ESIAKLEAAVS 135
                                    212222221.2222.33444444333 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.007
                           Fez1  34 valkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelselsleeeea 113
                                      l a +  l ++  ++ee++ +lee++  +++++ ++e+ ++++++    l+  v k +e +++l ++++++ ++ ++ 
  gi|119720248|ref|YP_920743.1|  93 ARLEAAVARLAEAQAKSEERLARLEEAVARQSESIAKLEAAVSKHSEVIARLEAAVAKHDETIARLEKAVAKHDESIARL 172
                                    35778888888888999999*************************99999999999999999999999888855443333 PP

                           Fez1 114 alesdeakaqrqe.....aeeleelkreverlra 142
                                    +    +a a+++e     +e+++ l ++v rl +
  gi|119720248|ref|YP_920743.1| 173 E----KAIARHDEaiarlEEAVRGLAAQVGRLSE 202
                                    2....22222222222334678888888888876 PP

>> DUF5071  Domain of unknown function (DUF5071)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0    0.0079      0.97      64     108 ..      12      56 ..       3      65 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0079
                                    HHSS-HHHHHHHHHHHGGGS-HHHHHHHHHHHHHHHTS--SSHHH CS
                        DUF5071  64 LeknDeewkyfvleflveklpveskkklkeelerlveeptedEke 108
                                    L ++Dee++y v+ +l+ +    + k l+e++erlve+ +++E+ 
  gi|119720248|ref|YP_920743.1|  12 LLREDEEFRYAVVGLLGLEDLRAELKGLREAVERLVEAHARAEER 56 
                                    4689*************9998888889***********9998875 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.6      0.37        46     219     281 ..      37      74 ..      25     104 .. 0.35
   2 ?   10.3   9.7    0.0031      0.38     185     278 ..     101     197 ..      90     203 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.37
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Filament 219 telrrqiqsleieleslkkqkasleaqlaeleerleaeleklqeklseleeelaeireemarq 281
                                    + lr  ++                         rl +++++++e ls+le+++a + e + r+
  gi|119720248|ref|YP_920743.1|  37 KGLREAVE-------------------------RLVEAHARAEERLSRLEAAVAGLGEAVSRH 74 
                                    22222222.........................222222222222222222222222222221 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0031
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHH CS
                       Filament 185 nreeaeewykskleelqeaaeknsealrsakeeitelrrqiqsleieleslkkqkasleaqlaelee...rleaeleklq 261
                                      +ea++  +++l++l+ea++++se++ + +  +++    i +le+ ++++ ++ a le+++a  +e   rle++++++ 
  gi|119720248|ref|YP_920743.1| 101 RLAEAQAKSEERLARLEEAVARQSESIAKLEAAVSKHSEVIARLEAAVAKHDETIARLEKAVAKHDEsiaRLEKAIARHD 180
                                    46788888899************************************************9998665423388999***** PP

                                    HHHHHHHHHHHHHHHHH CS
                       Filament 262 eklseleeelaeireem 278
                                    e++++lee+++ + +++
  gi|119720248|ref|YP_920743.1| 181 EAIARLEEAVRGLAAQV 197
                                    *********99877665 PP

>> DUF2674  Protein of unknown function (DUF2674)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0       1.4   1.8e+02      42      60 ..     141     159 ..     134     161 .. 0.83
   2 ?    3.6   0.1      0.38        47      38      57 ..     151     170 ..     144     172 .. 0.79
   3 ?    6.4   0.1     0.054       6.7      38      60 ..     165     187 ..     160     189 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 1.4
                        DUF2674  42 lcvLEKsieaeDetIenee 60 
                                    +  LE  +  +DetI  +e
  gi|119720248|ref|YP_920743.1| 141 IARLEAAVAKHDETIARLE 159
                                    6679999********9876 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.38
                        DUF2674  38 edaFlcvLEKsieaeDetIe 57 
                                    +d  +  LEK +  +De+I 
  gi|119720248|ref|YP_920743.1| 151 HDETIARLEKAVAKHDESIA 170
                                    56677889999999999985 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.054
                        DUF2674  38 edaFlcvLEKsieaeDetIenee 60 
                                    +d  +  LEK i  +De+I  +e
  gi|119720248|ref|YP_920743.1| 165 HDESIARLEKAIARHDEAIARLE 187
                                    5777889************8765 PP

>> DUF1465  Protein of unknown function (DUF1465)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.3     0.073       9.1      98     143 ..      33      78 ..       5      84 .. 0.77
   2 ?   10.0   3.3    0.0046      0.57      84     152 ..      74     146 ..      68     148 .. 0.76
   3 ?    4.1   0.8      0.31        38      94     152 ..     147     202 ..     130     205 .. 0.53

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.073
                                    --------HHHHHHHHHHHHHHHHHHHHHHHHHT-SSXXXX.XXXX CS
                        DUF1465  98 aeavaeLpeelqeLierserLyervrrLdrelreeaeaaeaaenpv 143
                                      +++ L e+++ L+e+  r  er+ rL++++ +  ea +++++++
  gi|119720248|ref|YP_920743.1|  33 RAELKGLREAVERLVEAHARAEERLSRLEAAVAGLGEAVSRHSEAI 78 
                                    56789999***********************999888876655554 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0046
                                    SS-------...-----------HHHHHHHHHHHHHHHHHHHHHHHHHT-SSXXXX.XXXXXXX...XXXXXX CS
                        DUF1465  84 ekkrvklaaae.asdaeavaeLpeelqeLierserLyervrrLdrelreeaeaaeaaenpvaeq...lerLea 152
                                    + + +++ + + a+++eava+L+++++ L e+  +  er++rL++++ +++e+ ++ e +v+++   ++rLea
  gi|119720248|ref|YP_920743.1|  74 HSEAIARLEVAvARHDEAVARLEAAVARLAEAQAKSEERLARLEEAVARQSESIAKLEAAVSKHsevIARLEA 146
                                    555555545555999***********************************99998877777665111555555 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.31
                                    ..-----------HHHHHHHHHHHHHHHHHHHHHHHHHT-SSXXXX.XXXXXXXXXXXXX CS
                        DUF1465  94 e.asdaeavaeLpeelqeLierserLyervrrLdrelreeaeaaeaaenpvaeqlerLea 152
                                    + a+++e++a+L++++++  e   rL + ++r d+++ + +ea       +a+q+ rL++
  gi|119720248|ref|YP_920743.1| 147 AvAKHDETIARLEKAVAKHDESIARLEKAIARHDEAIARLEEAV----RGLAAQVGRLSE 202
                                    33555566666666666665656666666666666665555554....334555555555 PP

>> DHR10  Designed helical repeat protein 10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   1.5      0.18        22      66      99 ..      29      62 ..      28      74 .. 0.73
   2 ?    4.4   6.1       0.3        38      41      92 ..      77     125 ..      62     132 .. 0.44
   3 ?   11.8   8.9    0.0015      0.19      41     111 ..     116     185 ..     112     192 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.18
                          DHR10 66 leekeielrelerkeerlqrqlenaeeklerlre 99
                                   le++++el+ l    erl    ++aee+l+rl+ 
  gi|119720248|ref|YP_920743.1| 29 LEDLRAELKGLREAVERLVEAHARAEERLSRLEA 62
                                   5667777777777777777777777777777764 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.3
                          DHR10  41 lleeieaelakleeakkklkelrdaleekeielrelerkeerlqrqlenaee 92 
                                    ++  +e+ +a+++ea ++l+++ ++l+e +++++e   + +rl+  +++  e
  gi|119720248|ref|YP_920743.1|  77 AIARLEVAVARHDEAVARLEAAVARLAEAQAKSEE---RLARLEEAVARQSE 125
                                    33344444444444444444444444444443332...22333333333333 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 0.0015
                          DHR10  41 lleeieaelakleeakkklkelrdaleekeielrelerkeerlqrqlenaeeklerlreqaeekreaakar 111
                                    l e ++++ ++  + ++ ++++++ ++ +e+ +++ + +++rl++ ++++ e ++rl++  ++++ea   r
  gi|119720248|ref|YP_920743.1| 116 LEEAVARQSESIAKLEAAVSKHSEVIARLEAAVAKHDETIARLEKAVAKHDESIARLEKAIARHDEAIA-R 185
                                    5567999999999**********************************************9998888764.4 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   2.2    0.0048      0.59      15      92 ..      33     110 ..      21     118 .. 0.90
   2 ?    5.9   4.7     0.055       6.8      30      93 ..     118     181 ..     107     203 .. 0.44
   3 ?    1.2   0.1       1.5   1.9e+02     160     181 ..     225     246 ..     222     258 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0048
                        DUF3450  15 aatldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeie 92 
                                     a+l+ ++++ e+ v+a a+++++ ++l+   + l + + + +e +++lev  ++ ++ va +e+ +a+l e +++ e
  gi|119720248|ref|YP_920743.1|  33 RAELKGLREAVERLVEAHARAEERLSRLEAAVAGLGEAVSRHSEAIARLEVAVARHDEAVARLEAAVARLAEAQAKSE 110
                                    789999****************************************************************99988766 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.055
                        DUF3450  30 aaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeiee 93 
                                    +a a+ ++ i kl+   +++++ + +l++ +++ +   ++le+ va+ +++ia+le+ i++ +e
  gi|119720248|ref|YP_920743.1| 118 EAVARQSESIAKLEAAVSKHSEVIARLEAAVAKHDETIARLEKAVAKHDESIARLEKAIARHDE 181
                                    2223333334444444444444444444444444444444444444444444444444443333 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 1.5
                        DUF3450 160 grtievyqgeleldGeevqvdf 181
                                    g ++e+ +g + +dGeev+vd+
  gi|119720248|ref|YP_920743.1| 225 GVEVELGRGVVRVDGEEVEVDL 246
                                    77899999************97 PP

>> DUF3782  Protein of unknown function (DUF3782)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1       2.1   2.6e+02       3      35 ..      36      68 ..      30      80 .. 0.70
   2 ?    0.8   9.4       4.4   5.5e+02       7      43 ..     166     202 ..      55     230 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 2.1
                        DUF3782  3 lekleeeeeetkedleelekeieklertigaLG 35
                                   l+ l+e  e++ e   + e+++++le +++ LG
  gi|119720248|ref|YP_920743.1| 36 LKGLREAVERLVEAHARAEERLSRLEAAVAGLG 68
                                   555666666666667777777777777777777 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 4.4
                        DUF3782   7 eeeeeetkedleelekeieklertigaLGaRWGlvsE 43 
                                    +e  +++++ + +++++i++le+++  L+a  G +sE
  gi|119720248|ref|YP_920743.1| 166 DESIARLEKAIARHDEAIARLEEAVRGLAAQVGRLSE 202
                                    3334455555555555666666666666666666665 PP

>> Sec8_exocyst  Sec8 exocyst complex component specific domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.8     0.015       1.8      58     128 ..      69     146 ..      57     160 .. 0.71
   2 ?    0.7   0.0       3.6   4.4e+02      99     128 ..     159     188 ..     148     203 .. 0.53

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.015
                   Sec8_exocyst  58 evvnehhqaFns...siasYskilssiqesqekvselK....esleeakkklstkkkeLkelnarsakykevieiLda 128
                                    e+v+ h++a ++   ++a + +++  ++ +  +++e +    e+l+  ++++ ++++++ +l+a  +k++evi  L+a
  gi|119720248|ref|YP_920743.1|  69 EAVSRHSEAIARlevAVARHDEAVARLEAAVARLAEAQakseERLARLEEAVARQSESIAKLEAAVSKHSEVIARLEA 146
                                    555566655543333667777777777766666655441122467777888999*******************99986 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 3.6
                   Sec8_exocyst  99 kkklstkkkeLkelnarsakykevieiLda 128
                                    +k++ ++++++  l++  a+++e i  L++
  gi|119720248|ref|YP_920743.1| 159 EKAVAKHDESIARLEKAIARHDEAIARLEE 188
                                    344445555555555555555555554442 PP

>> Cob_adeno_trans  Cobalamin adenosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   2.0      0.31        38      49     112 ..      46     102 ..      22     125 .. 0.40
   2 ?   10.8   7.7    0.0031      0.39      28     131 ..      84     181 ..      65     215 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.31
                                    T...THHHHHHHHHHHHHHHHHHHHHHT...-BTCCG-S--HHHHHHHHHHHHHHHHHS--EESEEES- CS
                Cob_adeno_trans  49 e...eeelkeaLeeiqneLfdlgaelatp..ekkkekkkiteeeveelekeideleaelpplksfilpg 112
                                        +++++e+L++++  +  lg++++ +  +            +++le ++ + ++ + +l+  +   
  gi|119720248|ref|YP_920743.1|  46 LveaHARAEERLSRLEAAVAGLGEAVSRHseA------------IARLEVAVARHDEAVARLEAAVARL 102
                                    23333444444555555555555554432220............3333333333332222222222211 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0031
                                    HHHHHHHHHHHHHHHHHHCTTTTHHHHHHHHHHHHHHHHHHHHHHT.-BTCCG-S--HHHHHHHHHHHHHHHHHS--EES CS
                Cob_adeno_trans  28 ayGtvDelnsaiglarallaeeeeelkeaLeeiqneLfdlgaelatpekkkekkkiteeeveelekeideleaelpplks 107
                                    a++  De+ + +  a a lae++++ +e+L+++++ + +  +++a    + + +k  +e +++le+++ + ++++ +l++
  gi|119720248|ref|YP_920743.1|  84 AVARHDEAVARLEAAVARLAEAQAKSEERLARLEEAVARQSESIAKL--EAAVSKH-SEVIARLEAAVAKHDETIARLEK 160
                                    68899***********9999999999999999999999999999843..2222222.33367777777777777777765 PP

                                    EEES-SSHHHHHHHHHHHHHHHHH CS
                Cob_adeno_trans 108 filpggspaaaalhvaRtvcRraE 131
                                     +  + +++ a+l+  ++++R  E
  gi|119720248|ref|YP_920743.1| 161 AVAKH-DESIARLE--KAIARHDE 181
                                    55544.44444443..33444444 PP

>> Phage_GPO  Phage capsid scaffolding protein (GPO) serine peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   9.5     0.033         4     163     252 ..      81     166 ..       8     170 .. 0.71
   2 ?    8.1   8.6     0.015       1.8     171     258 ..      89     172 ..      80     205 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.033
                      Phage_GPO 163 lefeeeeeeeegeslferikallskkkksddarfadveeavelvAeevkelsekveallaleaelaalkkeveklkaele 242
                                    le++ ++++e+ ++l + + + l++ ++++++r a +eeav +  e++++l+ +v+   ++++ +a l+++v+k+++ ++
  gi|119720248|ref|YP_920743.1|  81 LEVAVARHDEAVARLEAAVAR-LAEAQAKSEERLARLEEAVARQSESIAKLEAAVS---KHSEVIARLEAAVAKHDETIA 156
                                    444444444554455444444.4555666667777777777777777777777666...555566666666666666666 PP

                      Phage_GPO 243 aLkekLsktd 252
                                    +L++ + k d
  gi|119720248|ref|YP_920743.1| 157 RLEKAVAKHD 166
                                    6666666555 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.015
                      Phage_GPO 171 eeegeslferikallskkkksddarfadveeavelvAeevkelsekveallaleaelaalkkeveklkaeleaLkekLsk 250
                                    +e+ ++l + + + l++ ++++++r a +eeav +  e++++l+ +v+   ++++ +a l+++v+k+++ +++L++ + k
  gi|119720248|ref|YP_920743.1|  89 DEAVARLEAAVAR-LAEAQAKSEERLARLEEAVARQSESIAKLEAAVS---KHSEVIARLEAAVAKHDETIARLEKAVAK 164
                                    4444445444444.5667778888899999998888888888888888...55666666677777777777777777776 PP

                      Phage_GPO 251 tdakekqr 258
                                     d++  + 
  gi|119720248|ref|YP_920743.1| 165 HDESIARL 172
                                    66654444 PP

>> Bacillus_HBL  Bacillus haemolytic enterotoxin (HBL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0      0.25        31      93     175 ..      41     128 ..      33     129 .. 0.77
   2 ?    7.0   0.8     0.037       4.6      97     175 ..     103     184 ..      90     186 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.25
                   Bacillus_HBL  93 eav..dkkdkaellellekLqeeiqqnqkevkqlikeLkklklklakds...knFktdvdeltsilagdsgvisqlqnei 167
                                    eav    ++ a + e+l++L++ +    ++v + ++++ +l++++a  +   + ++++v+ l +  a ++  ++ l++++
  gi|119720248|ref|YP_920743.1|  41 EAVerLVEAHARAEERLSRLEAAVAGLGEAVSRHSEAIARLEVAVARHDeavARLEAAVARLAEAQAKSEERLARLEEAV 120
                                    55533347888999****************************99986541115677788888888888888888888888 PP

                   Bacillus_HBL 168 edlqgkik 175
                                    ++  ++i+
  gi|119720248|ref|YP_920743.1| 121 ARQSESIA 128
                                    88777776 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.037
                   Bacillus_HBL  97 kkdkaellellekLqeeiqqnqkevkqlikeLkklkl...klakdsknFktdvdeltsilagdsgvisqlqneiedlqgk 173
                                    ++++a+  e+l +L+e +  +++++ +l ++++k  +   +l++ +++ +++++ l++ +a  +  i+ l+++i++ +++
  gi|119720248|ref|YP_920743.1| 103 AEAQAKSEERLARLEEAVARQSESIAKLEAAVSKHSEviaRLEAAVAKHDETIARLEKAVAKHDESIARLEKAIARHDEA 182
                                    56777888999999999999999888888888887761114556777788888999999999999999999999999988 PP

                   Bacillus_HBL 174 ik 175
                                    i+
  gi|119720248|ref|YP_920743.1| 183 IA 184
                                    86 PP

>> DUF2130  Uncharacterized protein conserved in bacteria (DUF2130)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.3       1.1   1.4e+02     200     237 ..      79     116 ..      36     137 .. 0.58
   2 ?    9.2   3.0    0.0053      0.66     171     237 ..     114     179 ..      97     204 .. 0.51

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 1.1
                        DUF2130 200 knieaavekfqkaieeidkelekikekleksinkllla 237
                                     ++e av ++++a + ++ ++ + +e+  ks+++l + 
  gi|119720248|ref|YP_920743.1|  79 ARLEVAVARHDEAVARLEAAVARLAEAQAKSEERLARL 116
                                    44555566666666666666555555555555544332 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0053
                        DUF2130 171 kkelenvkekneditefetkkeefkekfrknieaavekfqkaieeidkelekikekleksinkllla 237
                                     + +e v+ ++e i + e     + ++   ++eaav k++++i+ ++k++ k  e++ + ++ + + 
  gi|119720248|ref|YP_920743.1| 114 ARLEEAVARQSESIAKLEA-AVSKHSEVIARLEAAVAKHDETIARLEKAVAKHDESIARLEKAIARH 179
                                    4445555555555555555.33333344455555555555555555555333333333333333222 PP

>> Paralemmin  Paralemmin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.3       1.3   1.5e+02      14      61 ..      53     100 ..      36     111 .. 0.73
   2 ?   10.1   5.4    0.0036      0.44       7      66 ..     109     173 ..     104     194 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 1.3
                     Paralemmin  14 LEesiqrLekeieeLeseesaisakeevlaeklketeksvedlqksll 61 
                                     Ee ++rLe  +  L +  s  s+    l+ ++ +++++v +l+ ++ 
  gi|119720248|ref|YP_920743.1|  53 AEERLSRLEAAVAGLGEAVSRHSEAIARLEVAVARHDEAVARLEAAVA 100
                                    488999999999999999988887777777777777777766665554 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0036
                     Paralemmin   7 deakvrkLEesiqrLekeieeLeseesaisakeevlaeklketeksvedlqksllstdk.....e 66 
                                     e++  +LEe++ r  + i +Le+  s+ s+    l++++ ++++++ +l+k++ ++d+     e
  gi|119720248|ref|YP_920743.1| 109 SEERLARLEEAVARQSESIAKLEAAVSKHSEVIARLEAAVAKHDETIARLEKAVAKHDEsiarlE 173
                                    6889999***********************9999999999*************999988433332 PP

>> MIP-T3_C  Microtubule-binding protein MIP-T3 C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0      0.64        79      95     150 ..      40      95 ..      30      99 .. 0.86
   2 ?    6.3   1.1     0.072       8.9     101     152 ..     109     160 ..      96     162 .. 0.76
   3 ?    2.7   0.1       0.9   1.1e+02     116     150 ..     152     186 ..     144     204 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.64
                       MIP-T3_C  95 rqqaeelaeerrateealeplkaqlaeleeaIkdqkekisnvrakilkNeakiqkl 150
                                    r++ e l e+++  ee l++l+a +a l ea++ + e i  +   + + ++++++l
  gi|119720248|ref|YP_920743.1|  40 REAVERLVEAHARAEERLSRLEAAVAGLGEAVSRHSEAIARLEVAVARHDEAVARL 95 
                                    6677889999999************************9999988888888877766 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.072
                       MIP-T3_C 101 laeerrateealeplkaqlaeleeaIkdqkekisnvrakilkNeakiqkllk 152
                                     +e  +  eea+ +  + +a+le+a++ + e i  + a + k ++ i++l k
  gi|119720248|ref|YP_920743.1| 109 SEERLARLEEAVARQSESIAKLEAAVSKHSEVIARLEAAVAKHDETIARLEK 160
                                    2233344578889999999999999999999999999999999999998866 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.9
                       MIP-T3_C 116 kaqlaeleeaIkdqkekisnvrakilkNeakiqkl 150
                                     + +a le+a++ + e i  + + i + +++i++l
  gi|119720248|ref|YP_920743.1| 152 DETIARLEKAVAKHDESIARLEKAIARHDEAIARL 186
                                    56788888888888888888888888888888776 PP

>> Csm1_N  Csm1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.2       1.1   1.4e+02      40      63 ..      33      56 ..      28      62 .. 0.59
   2 ?    6.0   1.2      0.12        15      33      69 ..      82     118 ..      70     125 .. 0.91
   3 ?    5.5   2.9      0.18        22      33      63 ..     145     175 ..     115     194 .. 0.67
   4 ?    1.5   0.0       3.1   3.8e+02      32      60 ..     172     200 ..     170     203 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 1.1
                         Csm1_N 40 dqeiesLkeqlaeleekvkeleer 63
                                     e++ L+e ++ l e  +++eer
  gi|119720248|ref|YP_920743.1| 33 RAELKGLREAVERLVEAHARAEER 56
                                   446666666666666666666655 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.12
                         Csm1_N  33 sqkletkdqeiesLkeqlaeleekvkeleerrkkqeE 69 
                                    + ++  +d+ + +L++ +a l e  +++eer +  eE
  gi|119720248|ref|YP_920743.1|  82 EVAVARHDEAVARLEAAVARLAEAQAKSEERLARLEE 118
                                    56788999**********************9999888 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.18
                         Csm1_N  33 sqkletkdqeiesLkeqlaeleekvkeleer 63 
                                    + ++ ++d+ i +L++ +a+ +e +++le+ 
  gi|119720248|ref|YP_920743.1| 145 EAAVAKHDETIARLEKAVAKHDESIARLEKA 175
                                    4455555555555555555555555555554 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 3.1
                         Csm1_N  32 LsqkletkdqeiesLkeqlaeleekvkel 60 
                                    L++++  +d+ i +L+e +  l ++v +l
  gi|119720248|ref|YP_920743.1| 172 LEKAIARHDEAIARLEEAVRGLAAQVGRL 200
                                    67778889999999999999999888665 PP

>> TACC_C  Transforming acidic coiled-coil-containing protein (TACC), C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   2.5      0.23        29      65     158 ..      38     127 ..      17     137 .. 0.66
   2 ?    9.5   5.4    0.0063      0.78       3      90 ..     106     192 ..      96     204 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.23
                         TACC_C  65 lakkeiqkvleekeqlladlnsveksfsdlfkryekqkevlegykkneeslkkcaeeylarvkkeeqRYqaLkahaeekL 144
                                      ++ +++++e +  + + l+ +e +++ l + + +  e++  +    e+  +  +e +ar++ +  R  + +a+ ee+L
  gi|119720248|ref|YP_920743.1|  38 GLREAVERLVEAHARAEERLSRLEAAVAGLGEAVSRHSEAIARL----EVAVARHDEAVARLEAAVARLAEAQAKSEERL 113
                                    45566777777777777777777777777777777777777664....45555566677777777778888888888888 PP

                         TACC_C 145 ekAneeiaqvrska 158
                                     + +e +a+ +++ 
  gi|119720248|ref|YP_920743.1| 114 ARLEEAVARQSESI 127
                                    87777777655443 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0063
                         TACC_C   3 qkdldaalekvkeeveekeeeiqelkkkveelkkenqemkkivaefektiaqlieekqkqkelakkeiqkvleekeqlla 82 
                                    q++ ++ l++++e v ++ e i++l++ v++  +  ++++  va+ ++tia+l +   +++ ++ + ++k+++ +++++a
  gi|119720248|ref|YP_920743.1| 106 QAKSEERLARLEEAVARQSESIAKLEAAVSKHSEVIARLEAAVAKHDETIARLEKAV-AKHDESIARLEKAIARHDEAIA 184
                                    677788888999999999999999999999999999999999999999999987776.5555778899999999999999 PP

                         TACC_C  83 dlnsveks 90 
                                     l++  + 
  gi|119720248|ref|YP_920743.1| 185 RLEEAVRG 192
                                    99776554 PP

>> Med9  RNA polymerase II transcription mediator complex subunit 9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1      0.79        98      30      61 ..      31      62 ..      28      99 .. 0.87
   2 ?    5.9   0.3      0.11        13      44      76 ..     112     144 ..      90     148 .. 0.67
   3 ?    3.8   0.1      0.49        61      46      78 ..     156     188 ..     141     190 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.79
                           Med9 30 elrhkLkkarelirelpgidrsveeqeaeiee 61
                                   +lr  Lk  re+++ l +     ee++ ++e+
  gi|119720248|ref|YP_920743.1| 31 DLRAELKGLREAVERLVEAHARAEERLSRLEA 62
                                   68889999999999999988888888888875 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.11
                           Med9  44 elpgidrsveeqeaeieeleeqlakKrelLkky 76 
                                     l  +++ v+ q + i++le  + k  e+++++
  gi|119720248|ref|YP_920743.1| 112 RLARLEEAVARQSESIAKLEAAVSKHSEVIARL 144
                                    344467777777777777777777777777776 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.49
                           Med9  46 pgidrsveeqeaeieeleeqlakKrelLkkykn 78 
                                      +++ v+  ++ i+ le+ +a+  e ++++ +
  gi|119720248|ref|YP_920743.1| 156 ARLEKAVAKHDESIARLEKAIARHDEAIARLEE 188
                                    447888888899999999999999999988876 PP

>> Fusion_gly  Fusion glycoprotein F0
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   5.1         2   2.4e+02     104     145 ..      93     136 ..      33     157 .. 0.59
   2 ?    9.9   0.1    0.0016       0.2     116     157 ..     163     204 ..     154     211 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 2
                                    HHHHHHHH.HHHHH.HHHHHHHHHHHHHHTHHSSEEEECHCCSH CS
                     Fusion_gly 104 AqitAgiA.lakal.knaeeiaklkeslektnkAveklqngvse 145
                                    A   A++A la+a+ k +e  a+l e+++   +++ kl+ +vs+
  gi|119720248|ref|YP_920743.1|  93 ARLEAAVArLAEAQaKSEERLARLEEAVARQSESIAKLEAAVSK 136
                                    23333443344443123344555555555555555555555555 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0016
                                    HHHHHHHHHHHHHHHTHHSSEEEECHCCSHCEEEEETTHHHH CS
                     Fusion_gly 116 lknaeeiaklkeslektnkAveklqngvselvlavnalqdyi 157
                                     k +e ia+l ++++  ++A+  l+++v+ l+  v  l + i
  gi|119720248|ref|YP_920743.1| 163 AKHDESIARLEKAIARHDEAIARLEEAVRGLAAQVGRLSEAI 204
                                    467789*****************************9997765 PP

>> DUF3818  Domain of unknown function in PX-proteins (DUF3818)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       9.1   1.1e+03     105     148 ..      67     110 ..      63     116 .. 0.78
   2 ?    8.9   1.4    0.0054      0.67     105     158 ..     116     169 ..     113     196 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 9.1
                        DUF3818 105 lnedlkelekeikelekkidkseelieklkkfveaseeeqeeir 148
                                    l e ++  ++ i+ le  + +++e +++l++ v    e q + +
  gi|119720248|ref|YP_920743.1|  67 LGEAVSRHSEAIARLEVAVARHDEAVARLEAAVARLAEAQAKSE 110
                                    56677788889999999999999999999999988877766655 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0054
                        DUF3818 105 lnedlkelekeikelekkidkseelieklkkfveaseeeqeeireeseeekldl 158
                                    l+e +  ++++i++le+ ++k++e+i++l++ v + +e+   +++  ++++ ++
  gi|119720248|ref|YP_920743.1| 116 LEEAVARQSESIAKLEAAVSKHSEVIARLEAAVAKHDETIARLEKAVAKHDESI 169
                                    7899999*****************************998887777776666544 PP

>> PspA_IM30  PspA/IM30 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9  27.4      0.28        34      32     147 ..      29     163 ..      27     166 .. 0.76
   2 ?    5.6  24.4     0.083        10      15     141 ..      68     196 ..      65     204 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.28
                      PspA_IM30  32 irdmqselakarqalaqviarqkqlerkleeqkeqak......klekkAkaALtkg..........eeeLArealaeiks 95 
                                    ++d+++el+ +r+a+++++  + ++e++l + ++ ++      ++ ++A a L+ +           e++ + +++  ++
  gi|119720248|ref|YP_920743.1|  29 LEDLRAELKGLREAVERLVEAHARAEERLSRLEAAVAglgeavSRHSEAIARLEVAvarhdeavarLEAAVARLAEAQAK 108
                                    79****************************99998772221114555666666666999988888766777777777788 PP

                      PspA_IM30  96 lekqaealetqlaqqrsaveqlrkqlealetkieelka...kkellkarekaaka 147
                                     e+ +++le+ +a+q +++++l++++++   +i+ l+a   k ++ +ar++ a a
  gi|119720248|ref|YP_920743.1| 109 SEERLARLEEAVARQSESIAKLEAAVSKHSEVIARLEAavaKHDETIARLEKAVA 163
                                    8999999999999999999999999999999888887522256666666666655 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.083
                      PspA_IM30  15 selldkaeDPekileqairdmqselakarqalaqviarqkqlerkleeqkeqakklek...kAkaALtkgeeeLAreala 91 
                                     e+++ + ++   le a+   ++++a+++ a+a++   q ++e++l++ +e +++  +   k +aA +k +e  Ar   a
  gi|119720248|ref|YP_920743.1|  68 GEAVSRHSEAIARLEVAVARHDEAVARLEAAVARLAEAQAKSEERLARLEEAVARQSEsiaKLEAAVSKHSEVIARLE-A 146
                                    567777778888888888888899999999999999999999998888877666544311133566666677777644.4 PP

                      PspA_IM30  92 eikslekqaealetqlaqqrsaveqlrkqlealetkieelkakkellkar 141
                                      +++ +++++le+ +a+  ++++ l+k++++ +  i+ l++ ++ l+a+
  gi|119720248|ref|YP_920743.1| 147 AVAKHDETIARLEKAVAKHDESIARLEKAIARHDEAIARLEEAVRGLAAQ 196
                                    46778899999999999999999999999999999999999888888776 PP

>> DUF1484  Protein of unknown function (DUF1484)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.6      0.37        46      10      48 ..      36      74 ..      33      79 .. 0.86
   2 ?    6.3   2.4      0.16        20       9      44 ..      70     105 ..      67     114 .. 0.82
   3 ?    6.7   3.8      0.12        14       9      46 ..      91     128 ..      81     130 .. 0.84
   4 ?    8.7   4.4     0.028       3.4       9      55 ..     119     164 ..     114     178 .. 0.78
   5 ?    2.9   0.4       1.7   2.1e+02      11      35 ..     163     187 ..     159     205 .. 0.54

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.37
                        DUF1484 10 larlreliaqLaeqlakkdkaaaresAatvaqletvsed 48
                                   l+ lre++ +L e +a+++ +  r +Aa +   e+vs++
  gi|119720248|ref|YP_920743.1| 36 LKGLREAVERLVEAHARAEERLSRLEAAVAGLGEAVSRH 74
                                   566899*********************998888888765 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.16
                        DUF1484   9 alarlreliaqLaeqlakkdkaaaresAatvaqlet 44 
                                    a+ r  e+ia+L    a+ d a+ar +Aa ++  e+
  gi|119720248|ref|YP_920743.1|  70 AVSRHSEAIARLEVAVARHDEAVARLEAAVARLAEA 105
                                    678999999999999999999999999987776554 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.12
                        DUF1484   9 alarlreliaqLaeqlakkdkaaaresAatvaqletvs 46 
                                    a+arl+ ++a+Lae  ak + + ar + a ++q e+++
  gi|119720248|ref|YP_920743.1|  91 AVARLEAAVARLAEAQAKSEERLARLEEAVARQSESIA 128
                                    78899999999999999999999999999999988876 PP

  == domain 4  score: 8.7 bits;  conditional E-value: 0.028
                        DUF1484   9 alarlreliaqLaeqlakkdkaaaresAatvaqletvsediedavee 55 
                                    a+ar+ e ia+L +  +k +   ar +Aa +++ et++  +e+av  
  gi|119720248|ref|YP_920743.1| 119 AVARQSESIAKLEAAVSKHSEVIARLEAAVAKHDETIA-RLEKAVAK 164
                                    899**************************999966655.56776653 PP

  == domain 5  score: 2.9 bits;  conditional E-value: 1.7
                        DUF1484  11 arlreliaqLaeqlakkdkaaares 35 
                                    a+  e ia+L +  a+ d a ar +
  gi|119720248|ref|YP_920743.1| 163 AKHDESIARLEKAIARHDEAIARLE 187
                                    5555566666666666665555432 PP

>> Dynactin_p22  Dynactin subunit p22
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1      0.39        49       6      34 ..      54      81 ..      49      97 .. 0.80
   2 ?    5.7   1.6     0.097        12       6      57 ..     110     161 ..     107     181 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.39
                   Dynactin_p22  6 EeriaeLEkrvlGeekekekedesiidsL 34
                                   Eer+++LE  v G  +  +  +e  i +L
  gi|119720248|ref|YP_920743.1| 54 EERLSRLEAAVAGLGEAVSRHSE-AIARL 81
                                   9************9999888884.44444 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.097
                   Dynactin_p22   6 EeriaeLEkrvlGeekekekedesiidsLakvqkklssavskrek.ikellkk 57 
                                    Eer+a+LE+ v  ++++ +k + + +++  +v ++l++av+k+++ i  l k 
  gi|119720248|ref|YP_920743.1| 110 EERLARLEEAVARQSESIAKLE-AAVSKHSEVIARLEAAVAKHDEtIARLEKA 161
                                    89*********88888877766.888899999999999998887635544444 PP

>> DUF1043  Protein of unknown function (DUF1043)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.5      0.82     1e+02      26      74 ..      88     136 ..      67     145 .. 0.54
   2 ?    6.8   0.1     0.053       6.6      16      78 ..     142     203 ..     138     217 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.82
                        DUF1043  26 qkklekelekakaeleeqkqeledHfaqsaelLetlaedyqkLyqhlak 74 
                                    +++  ++le+a a+l+e +++ e+ +a+  e +++ +e+  kL   ++k
  gi|119720248|ref|YP_920743.1|  88 HDEAVARLEAAVARLAEAQAKSEERLARLEEAVARQSESIAKLEAAVSK 136
                                    3333444444444444444444444444444444444444444444444 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.053
                        DUF1043  16 lrltnsklkkqkklekelekakaeleeqkqeledHfaqsaelLetlaedyqkLyqhlakssee 78 
                                    +rl +++++k++++ ++leka a+++e  + le+ +a+  e +++l+e  + L  ++ + se+
  gi|119720248|ref|YP_920743.1| 142 ARL-EAAVAKHDETIARLEKAVAKHDESIARLEKAIARHDEAIARLEEAVRGLAAQVGRLSEA 203
                                    555.677899999999**********************************9999988777665 PP

>> DUF2570  Protein of unknown function (DUF2570)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.1      0.52        64      11      52 ..      64     105 ..      57     119 .. 0.85
   2 ?    7.3   1.8     0.032         4      17      81 ..     119     183 ..     113     189 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.52
                        DUF2570  11 ilgLgvwlwsqsqkidsLraenkaqaqlieeqqkanqrLteq 52 
                                    + gLg ++   s+ i  L+  ++ +++ +++ ++a  rL+e+
  gi|119720248|ref|YP_920743.1|  64 VAGLGEAVSRHSEAIARLEVAVARHDEAVARLEAAVARLAEA 105
                                    779******************************999999875 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.032
                        DUF2570  17 wlwsqsqkidsLraenkaqaqlieeqqkanqrLteqLeqerqavekqqkianelkakveeekeev 81 
                                    ++  qs+ i +L+a +  + ++i++ ++a  +  e +    +av k  ++   l++++  + e +
  gi|119720248|ref|YP_920743.1| 119 AVARQSESIAKLEAAVSKHSEVIARLEAAVAKHDETIARLEKAVAKHDESIARLEKAIARHDEAI 183
                                    567899999*****999999999999999999999999999999999999999999998888877 PP

>> LidA_Long_CC  LidA long coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1       1.6   1.9e+02      11      49 ..      29      66 ..      28     100 .. 0.69
   2 ?    5.1   0.8      0.17        21       3      37 ..     105     139 ..     103     150 .. 0.81
   3 ?    9.0   1.2     0.011       1.4       2      60 ..     146     203 ..     145     206 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 1.6
                                   HHHHHHHHHHHHHHHHHHHH-S-HHHHHHHHHHHHHHHH CS
                   LidA_Long_CC 11 iaklekkldkqaeeIneliesgsdgkeeearkllhelng 49
                                   +++l+++l+  +e++++l+e++ +++ e  ++l + + g
  gi|119720248|ref|YP_920743.1| 29 LEDLRAELKGLREAVERLVEAHARAE-ERLSRLEAAVAG 66
                                   67888889999999999999944333.334444444444 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.17
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHH-S-HHHH CS
                   LidA_Long_CC   3 kiekieeriaklekkldkqaeeIneliesgsdgke 37 
                                    + +k eer+a+le+ ++ q e I +l  + s++ e
  gi|119720248|ref|YP_920743.1| 105 AQAKSEERLARLEEAVARQSESIAKLEAAVSKHSE 139
                                    66899*********************999776663 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.011
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-S-HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   LidA_Long_CC   2 ekiekieeriaklekkldkqaeeIneliesgsdgkeeearkllhelnglnlqvaglkdm 60 
                                    ++++k +e+ia+lek ++k+ e I +l ++  +++ e   +l + + gl +qv  l+++
  gi|119720248|ref|YP_920743.1| 146 AAVAKHDETIARLEKAVAKHDESIARLEKAIARHD-EAIARLEEAVRGLAAQVGRLSEA 203
                                    578999*********************99966555.66677778899999999988775 PP

>> LMBR1  LMBR1-like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   5.2    0.0076      0.94     196     282 ..      86     178 ..      25     204 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0076
                          LMBR1 196 sdldeelkklyfeaaklntekeeaereledllkevkklrksisesdp.lrkyleeilk......kvPeeiaeklks.... 264
                                    +++de   +l++ +a+l + ++++e++l  l ++v+++++si + +  ++k++e i +      k       +  +    
  gi|119720248|ref|YP_920743.1|  86 ARHDEAVARLEAAVARLAEAQAKSEERLARLEEAVARQSESIAKLEAaVSKHSEVIARleaavaK------HD--Etiar 157
                                    5688889999999*****************************99987666777777663322221......21..11111 PP

                          LMBR1 265 ...nenkteeslaklekqlik 282
                                          k  es+a+lek++ +
  gi|119720248|ref|YP_920743.1| 158 lekAVAKHDESIARLEKAIAR 178
                                    221222233333333333222 PP

>> ABC_tran_Xtn  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.2         1   1.2e+02      24      62 ..      41      79 ..      30      84 .. 0.63
   2 ?    2.6   3.3       1.1   1.4e+02      28      70 ..      80     116 ..      52     119 .. 0.57
   3 ?    5.8   5.3      0.11        14      21      72 ..     108     160 ..     104     168 .. 0.70
   4 ?    6.8   1.5     0.057         7      20      52 ..     149     181 ..     141     203 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 1
                   ABC_tran_Xtn 24 erleqqqkayekqqkeikkleefIerfrakakkakqaqs 62
                                   e+ e+  +a+++ ++++ +le+ ++ +++  ++++ a +
  gi|119720248|ref|YP_920743.1| 41 EAVERLVEAHARAEERLSRLEAAVAGLGEAVSRHSEAIA 79
                                   455666666666677777777766666665566666555 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 1.1
                   ABC_tran_Xtn  28 qqqkayekqqkeikkleefIerfrakakkakqaqsrekaLekl 70 
                                    + + a +++ + +++le+ ++r+++     +qa+s   +L +l
  gi|119720248|ref|YP_920743.1|  80 RLEVAVARHDEAVARLEAAVARLAE-----AQAKSE-ERLARL 116
                                    4444444555555555555555554.....222222.333333 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.11
                   ABC_tran_Xtn  21 ekeerleqqqkayekqqkeikkleefIerfra.kakkakqaqsrekaLeklek 72 
                                    + eerl++ ++a ++q + i+kle+ + + ++  a+  +++      + +lek
  gi|119720248|ref|YP_920743.1| 108 KSEERLARLEEAVARQSESIAKLEAAVSKHSEvIARLEAAVAKHDETIARLEK 160
                                    67999999999999999999999999999886234444445555555555554 PP

  == domain 4  score: 6.8 bits;  conditional E-value: 0.057
                   ABC_tran_Xtn  20 eekeerleqqqkayekqqkeikkleefIerfra 52 
                                    ++ +e  ++ +ka +k+ + i++le+ I+r  +
  gi|119720248|ref|YP_920743.1| 149 AKHDETIARLEKAVAKHDESIARLEKAIARHDE 181
                                    556677778888888888888888888888765 PP

>> DUF4200  Domain of unknown function (DUF4200)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0  10.8       2.2   2.7e+02      18     107 ..      74     159 ..      29     160 .. 0.67
   2 ?   10.2   9.0    0.0059      0.73       7      92 ..     112     200 ..      97     205 .. 0.53

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 2.2
                        DUF4200  18 kkeeiqrleealkqreeelekkeqeleedllkfdkflkendakraralkkaeeerklkkekeaeikklkaeietlkseie 97 
                                      e i+rle a+++++e++    ++le  ++++ +   + +++ ar ++ ++++++ + + ea + k  + i++l++  +
  gi|119720248|ref|YP_920743.1|  74 HSEAIARLEVAVARHDEAV----ARLEAAVARLAEAQAKSEERLARLEEAVARQSESIAKLEAAVSKHSEVIARLEAAVA 149
                                    3444444444444444444....345566666667777777777777777777777777777777777777777777777 PP

                        DUF4200  98 kleekleeyk 107
                                    k +e++++++
  gi|119720248|ref|YP_920743.1| 150 KHDETIARLE 159
                                    7777777665 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0059
                        DUF4200   7 emfevqealeakkeeiqrleealkqreeelekke...qeleedllkfdkflkendakraralkkaeeerklkkekeaeik 83 
                                     + +++ea++++ e i++le a++++ e + + e   ++  e++++++k + ++d+  ar +k +++  +++ + e+ ++
  gi|119720248|ref|YP_920743.1| 112 RLARLEEAVARQSESIAKLEAAVSKHSEVIARLEaavAKHDETIARLEKAVAKHDESIARLEKAIARHDEAIARLEEAVR 191
                                    34455555555555555555555555555444442224445555555555555555555555555555555555555555 PP

                        DUF4200  84 klkaeietl 92 
                                     l a++ +l
  gi|119720248|ref|YP_920743.1| 192 GLAAQVGRL 200
                                    555555554 PP

>> TMP_2  Prophage tail length tape measure protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4  12.9     0.025       3.1      83     201 ..      46     163 ..      32     204 .. 0.56

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.025
                          TMP_2  83 lalAyykgakearefnkaliltGnaaGlTasqLeamaesiaeaggtqaaaaealaalastGkiggeqlervakaaaelek 162
                                    l+ A++++++ +++++ a+ ++G+a+   ++ ++++  ++a+  + +a+  +a+a la++ + ++e+l+r+ +a+a+ ++
  gi|119720248|ref|YP_920743.1|  46 LVEAHARAEERLSRLEAAVAGLGEAVSRHSEAIARLEVAVARHDEAVARLEAAVARLAEAQAKSEERLARLEEAVARQSE 125
                                    45555555555555555555555555555555555555555555555555555555555555555555555555555444 PP

                          TMP_2 163 atGqsvdetakelaklakdPvkaaeklneqlhfLtaaqy 201
                                        ++++++++ +++ +    a++k +e++  L++a+ 
  gi|119720248|ref|YP_920743.1| 126 -SIAKLEAAVSKHSEVIARLEAAVAKHDETIARLEKAVA 163
                                    .34445555555555555555555555555555544443 PP

>> Phage_tail_NK  Sf6-type phage tail needle knob or tip of some Caudovirales
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0      0.17        21       2      40 ..      54      92 ..      53     105 .. 0.87
   2 ?    3.2   0.1      0.47        58       3      38 ..     146     181 ..     144     192 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.17
                                   XXXXXXXXXXXXXXXXXXXXXXXHHHHHHHHTS--EEEE CS
                  Phage_tail_NK  2 esdissldtrvqslesqvsdhetridaleyattrkksev 40
                                   e  +s l++ v  l   vs h   i  le a +r+   v
  gi|119720248|ref|YP_920743.1| 54 EERLSRLEAAVAGLGEAVSRHSEAIARLEVAVARHDEAV 92
                                   5668999**************************988766 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.47
                                    XXXXXXXXXXXXXXXXXXXXXXHHHHHHHHTS--EE CS
                  Phage_tail_NK   3 sdissldtrvqslesqvsdhetridaleyattrkks 38 
                                    + ++  d  +  le  v+ h+  i  le a +r+  
  gi|119720248|ref|YP_920743.1| 146 AAVAKHDETIARLEKAVAKHDESIARLEKAIARHDE 181
                                    566777889999999**********9*999999765 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.8      0.21        27      60      92 ..      30      62 ..      28      78 .. 0.62
   2 ?    8.5  16.9     0.016         2       3     112 ..      92     197 ..      90     203 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.21
                     TPR_MLP1_2 60 qalreelnelkaeiaelkaeaesakaeleesee 92
                                   ++lr+el+ l++ ++ l ++  +a++ l++ e+
  gi|119720248|ref|YP_920743.1| 30 EDLRAELKGLREAVERLVEAHARAEERLSRLEA 62
                                   455566666666666665555555555555554 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.016
                     TPR_MLP1_2   3 lksleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaes 82 
                                    +++le+ +++l e ++++e++l+ l+e +  q+e+ ++ +      + kh+e +  l+a+ ++++e+ a+++++ a+ ++
  gi|119720248|ref|YP_920743.1|  92 VARLEAAVARLAEAQAKSEERLARLEEAVARQSESIAKLEA----AVSKHSEVIARLEAAVAKHDETIARLEKAVAKHDE 167
                                    57899999999999999999999999999999999998888....99********************************* PP

                     TPR_MLP1_2  83 akaeleeseesweeqkeelekelselekri 112
                                      a le++ +  +e   +le+ ++ l +++
  gi|119720248|ref|YP_920743.1| 168 SIARLEKAIARHDEAIARLEEAVRGLAAQV 197
                                    *****9999999999999999988777665 PP

>> PHM7_cyt  Cytosolic domain of 10TM putative phosphate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1      0.87   1.1e+02      41      71 ..      78     108 ..      64     124 .. 0.80
   2 ?    7.5   1.5     0.036       4.4      41     111 ..     127     191 ..     115     206 .. 0.68

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.87
                       PHM7_cyt  41 vkkldklveerekavrkleaalskykkngkk 71 
                                    +++l+  v+++++av +leaa +++ + + k
  gi|119720248|ref|YP_920743.1|  78 IARLEVAVARHDEAVARLEAAVARLAEAQAK 108
                                    6678888999999999999999887665544 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.036
                       PHM7_cyt  41 vkkldklveerekavrkleaalskykkngkklpkkrpthklgflglkligkkvdaidyyrekleeldeeie 111
                                    ++kl+  v ++ +++ +leaa +k++++  +l+k   +h  +  +l        ai    e + +l+e ++
  gi|119720248|ref|YP_920743.1| 127 IAKLEAAVSKHSEVIARLEAAVAKHDETIARLEKAVAKHDESIARL------EKAIARHDEAIARLEEAVR 191
                                    7889999999999999999999999999887766555555554432......2355555555555555444 PP

>> Herpes_UL17  Herpesvirus UL17 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   6.7     0.011       1.4     140     246 ..      43     177 ..      29     227 .. 0.54

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.011
                    Herpes_UL17 140 ydeLlpegtrynadaerlralcrqllayt.rlpaalpsaakeaaahleac.............................. 188
                                    +++L++++ r+ ++  rl+a+   l + + r  +a+++  ++ a+h ea                               
  gi|119720248|ref|YP_920743.1|  43 VERLVEAHARAEERLSRLEAAVAGLGEAVsRHSEAIARLEVAVARHDEAVarleaavarlaeaqakseerlarleeavar 122
                                    67788888888888888888888888888777777777777777777777777666666655443333333333333322 PP

                    Herpes_UL17 189 ............apgafdeaaaearlkddfdeilslikraaeavnkraPv...................aavasgllqga 237
                                                +++++                                v                   +ava  + + a
  gi|119720248|ref|YP_920743.1| 123 qsesiakleaavSKHSE--------------------------------ViarleaavakhdetiarleKAVAKHDESIA 170
                                    22222222222222222................................2333331111111112222233333333332 PP

                    Herpes_UL17 238 lasllagrr 246
                                    +  l ++++
  gi|119720248|ref|YP_920743.1| 171 R--LEKAIA 177
                                    2..333333 PP

>> FemAB  FemAB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   5.2    0.0095       1.2     235     304 ..     104     182 ..      91     191 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0095
                          FemAB 235 lAelnlaeylkelqekleklekklakleekleknpe.........kkkkkklkelekqlaslekelkeaeefiekdgee 304
                                     A++  +e+l++l+e  +  ++++akle++++k+ e         +k  + +++lek +a+++++++ +e+ i+ ++e 
  gi|119720248|ref|YP_920743.1| 104 EAQAKSEERLARLEEAVARQSESIAKLEAAVSKHSEviarleaavAKHDETIARLEKAVAKHDESIARLEKAIARHDEA 182
                                    47788899**********************9999999977777777777777777777777777777777777776665 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   [No individual domains that satisfy reporting thresholds (although complete target did)]

>> EF-hand_11  EF-hand domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1         5   6.2e+02       4      23 ..      74      93 ..      57     114 .. 0.81
   2 ?    4.3   0.1      0.58        72       4      23 ..     137     156 ..     133     161 .. 0.88
   3 ?    4.3   0.1      0.58        72       4      23 ..     151     170 ..     148     171 .. 0.84
   4 ?    4.7   0.1      0.44        54       4      26 ..     165     187 ..     161     199 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 5
                                   HHHHHHHHHHHHHHSHHHHH CS
                     EF-hand_11  4 drdilarlqkavashyhaiv 23
                                   + + +arl+ ava h  a++
  gi|119720248|ref|YP_920743.1| 74 HSEAIARLEVAVARHDEAVA 93
                                   56678888888888887765 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.58
                                    HHHHHHHHHHHHHHSHHHHH CS
                     EF-hand_11   4 drdilarlqkavashyhaiv 23 
                                    + +++arl+ ava h  +i+
  gi|119720248|ref|YP_920743.1| 137 HSEVIARLEAAVAKHDETIA 156
                                    789************99997 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.58
                                    HHHHHHHHHHHHHHSHHHHH CS
                     EF-hand_11   4 drdilarlqkavashyhaiv 23 
                                    + + +arl+kava h  +i+
  gi|119720248|ref|YP_920743.1| 151 HDETIARLEKAVAKHDESIA 170
                                    66789**********98875 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.44
                                    HHHHHHHHHHHHHHSHHHHHHHH CS
                     EF-hand_11   4 drdilarlqkavashyhaivqef 26 
                                    + + +arl+ka+a h  ai++  
  gi|119720248|ref|YP_920743.1| 165 HDESIARLEKAIARHDEAIARLE 187
                                    55679************998755 PP

>> DUF641  Plant protein of unknown function (DUF641)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   1.4     0.031       3.9      48     128 .]      34     112 ..      30     112 .. 0.90
   2 ?    6.5   3.5     0.082        10      62     126 ..     122     187 ..     111     191 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.031
                         DUF641  48 seLkklselkrlyrkkqkkkaseaeeseleaeiqeqrsllktyeitvkkleaelkakdseieeLkekLeeaeksnkklek 127
                                    +eLk l e  ++ ++ +     e++ s+lea +  + +++  +  ++ +le  + + d+ + +L++ ++++ +++ k e+
  gi|119720248|ref|YP_920743.1|  34 AELKGLREAVERLVEAHARA--EERLSRLEAAVAGLGEAVSRHSEAIARLEVAVARHDEAVARLEAAVARLAEAQAKSEE 111
                                    68888999999999987755..46999*******************************************9999999998 PP

                         DUF641 128 r 128
                                    r
  gi|119720248|ref|YP_920743.1| 112 R 112
                                    7 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.082
                         DUF641  62 kkqkkkas.eaeeseleaeiqeqrsllktyeitvkkleaelkakdseieeLkekLeeaeksnkkle 126
                                    +++++ a+ ea  s+ +  i ++  +++ ++ t+ +le+ + + d+ i +L++ +++  ++  +le
  gi|119720248|ref|YP_920743.1| 122 RQSESIAKlEAAVSKHSEVIARLEAAVAKHDETIARLEKAVAKHDESIARLEKAIARHDEAIARLE 187
                                    433333222355555556666677788888888888999999999999999988888777766666 PP

>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   2.7      0.56        69      10     105 ..      34     130 ..      25     139 .. 0.69
   2 ?   10.2   4.2    0.0053      0.66       7     108 ..     107     208 ..     101     214 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.56
                        zf-C4H2  10 leleklknklakevealekeekcleeykkelelLeqEkmaHveeLrlIhaDinalEsvikeaeeekekslekakklyeey 89 
                                     el+ l++ + + vea  + e+ l+  ++ +  L +    H+e +  ++  + + ++ + + e +  +  e+  k  e +
  gi|119720248|ref|YP_920743.1|  34 AELKGLREAVERLVEAHARAEERLSRLEAAVAGLGEAVSRHSEAIARLEVAVARHDEAVARLEAAVARLAEAQAKSEERL 113
                                    46777777788888888889999999999999999999999999988887777766666666666666666666666666 PP

                        zf-C4H2  90 kklkeevnelrse.lgl 105
                                    ++l e v +  ++   l
  gi|119720248|ref|YP_920743.1| 114 ARLEEAVARQSESiAKL 130
                                    66666665555443333 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0053
                        zf-C4H2   7 ekt.leleklknklakevealekeekcleeykkelelLeqEkmaHveeLrlIhaDinalEsvikeaeeekekslekakkl 85 
                                    +k+ ++l +l++ +a++ e++ k e  +++ ++ +  Le    +H e +  +++ + + ++ i + e++  ++ e++ +l
  gi|119720248|ref|YP_920743.1| 107 AKSeERLARLEEAVARQSESIAKLEAAVSKHSEVIARLEAAVAKHDETIARLEKAVAKHDESIARLEKAIARHDEAIARL 186
                                    454146899999999999************************************************************** PP

                        zf-C4H2  86 yeeykklkeevnelrselglekl 108
                                     e ++ l  +v +l + +g   l
  gi|119720248|ref|YP_920743.1| 187 EEAVRGLAAQVGRLSEAIGFG-L 208
                                    ************999997765.4 PP

>> Rootletin  Ciliary rootlet component, centrosome cohesion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   2.9      0.33        41      30      97 ..      55     124 ..      39     128 .. 0.63
   2 ?    8.8   3.4     0.012       1.5       3      78 ..     112     188 ..     110     199 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.33
                      Rootletin  30 krcseleqrlle..ktselektkltlll......ssareleeeesadleealakLeeErqrsek.laqvnslLreql 97 
                                    +r s le+ ++   + + +++      +      ++a ++++e  a le a+a+L e + +se+ la++ +    q 
  gi|119720248|ref|YP_920743.1|  55 ERLSRLEAAVAGlgE-AVSRH------SeaiarlEVAVARHDEAVARLEAAVARLAEAQAKSEErLARLEEAVARQS 124
                                    445555555555321.12222......022223477788999999999***********999763666666666665 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.012
                      Rootletin   3 rlqayqeaqqrqaqLvskLqaKvlqYkkrcseleqrllektselektkltlll.ssareleeeesadleealakLee 78 
                                    rl   +ea  rq++ ++kL a v +  + ++ le+ +++++ +  + ++   +  +  ++ e+ +a  +ea+a+Lee
  gi|119720248|ref|YP_920743.1| 112 RLARLEEAVARQSESIAKLEAAVSKHSEVIARLEAAVAKHDETIARLEKAVAKhDESIARLEKAIARHDEAIARLEE 188
                                    8889999999************************9999944443333322222233445566677777888888887 PP

>> Troponin  Troponin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.6       0.5        62      39      74 ..      30      64 ..       8      86 .. 0.61
   2 ?    7.7   3.7     0.033       4.1      46      88 ..      92     134 ..      75     139 .. 0.87
   3 ?    7.9  10.2     0.029       3.6      10      89 ..      95     177 ..      91     201 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.5
                                   X.XXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       Troponin 39 keldglseeqlqelckklheridkleeekydieekv 74
                                   ++l++ + + l+e +++l e  ++ ee   ++e+ v
  gi|119720248|ref|YP_920743.1| 30 EDLRA-ELKGLREAVERLVEAHARAEERLSRLEAAV 64
                                   33444.444455555555555555555444444444 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.033
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       Troponin  46 eeqlqelckklheridkleeekydieekvakkdkeieelkkkv 88 
                                     + l++ + +l+e ++k ee  +++ee va++ + i +l+ +v
  gi|119720248|ref|YP_920743.1|  92 VARLEAAVARLAEAQAKSEERLARLEEAVARQSESIAKLEAAV 134
                                    4899**********************************99887 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.029
                                    HHHHHHHHHTXXXXXXXXXXXXXXXXXXXX.XXX.XX.....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       Troponin  10 lkaaeelkfeqrkkeeerlrvLkerieplkeldglse.....eqlqelckklheridkleeekydieekvakkdkeieel 84 
                                    l+aa    +e++ k eerl+ L+e + + +e +   +      +  e+  +l + ++k +e  +++e  vak+d+ i  l
  gi|119720248|ref|YP_920743.1|  95 LEAAVARLAEAQAKSEERLARLEEAVARQSE-SI-AKleaavSKHSEVIARLEAAVAKHDETIARLEKAVAKHDESIARL 172
                                    5666666789999***********9977763.32.2235566899999999999999999******************99 PP

                                    XXXXX CS
                       Troponin  85 kkkvn 89 
                                    +k++ 
  gi|119720248|ref|YP_920743.1| 173 EKAIA 177
                                    99875 PP

>> CLZ  C-terminal leucine zipper domain of cyclic nucleotide-gated channels
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.3         1   1.3e+02      34      62 ..      30      58 ..      28      64 .. 0.75
   2 ?    5.3   2.1       0.2        25      30      69 ..      82     117 ..      60     132 .. 0.57
   3 ?    1.1   6.8       4.1   5.1e+02      18      57 ..      98     137 ..      94     194 .. 0.76
   4 ?    4.0   0.2      0.51        63      16      50 ..     166     200 ..     152     205 .. 0.62

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 1
                            CLZ 34 erLessLeaLqtrlarLlaeyessqrkLk 62
                                   e L ++L+ L   ++rL++ +  ++++L 
  gi|119720248|ref|YP_920743.1| 30 EDLRAELKGLREAVERLVEAHARAEERLS 58
                                   67788888888888888888888877775 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.2
                            CLZ  30 eekverLessLeaLqtrlarLlaeyessqrkLkqRitkLE 69 
                                    e  v r ++++  L+  +arL     ++q+k ++R+++LE
  gi|119720248|ref|YP_920743.1|  82 EVAVARHDEAVARLEAAVARL----AEAQAKSEERLARLE 117
                                    333444444444444444444....445555555555555 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 4.1
                            CLZ  18 eaakagaeqkeleekverLessLeaLqtrlarLlaeyess 57 
                                    ++a   + q + ee++ rLe+++      +a+L a +++ 
  gi|119720248|ref|YP_920743.1|  98 AVARLAEAQAKSEERLARLEEAVARQSESIAKLEAAVSKH 137
                                    4555567777888888888888877777777777665543 PP

  == domain 4  score: 4.0 bits;  conditional E-value: 0.51
                            CLZ  16 DeeaakagaeqkeleekverLessLeaLqtrlarL 50 
                                    De+ a  ++     +e + rLe+++  L  ++ rL
  gi|119720248|ref|YP_920743.1| 166 DESIARLEKAIARHDEAIARLEEAVRGLAAQVGRL 200
                                    44445555555556666666666666666666666 PP

>> CDH1_2_SANT_HL1  CDH1/2 SANT-Helical linker 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   1.6    0.0079      0.98      17      58 ..      87     129 ..      74     145 .. 0.81
   2 ?    1.8   0.2       3.2   3.9e+02       5      47 ..     152     195 ..     149     204 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0079
                CDH1_2_SANT_HL1  17 kfsaplkrld.aiacdAeLqeKplsdLkklgellkerCeeale 58 
                                    +  +++ rl+ a+a+ Ae q K+++ L +l e + ++ e++ +
  gi|119720248|ref|YP_920743.1|  87 RHDEAVARLEaAVARLAEAQAKSEERLARLEEAVARQSESIAK 129
                                    56678999*9459*********************998877655 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 3.2
                CDH1_2_SANT_HL1   5 daeiRrFvksykkfsaplkrld.aiacdAeLqeKplsdLkklge 47 
                                    d+ i r  k++ k  +++ rl+ aia+  e   + ++ ++ l+ 
  gi|119720248|ref|YP_920743.1| 152 DETIARLEKAVAKHDESIARLEkAIARHDEAIARLEEAVRGLAA 195
                                    67788888999999999999985688887777666666666665 PP

>> HAUS-augmin3  HAUS augmin-like complex subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1      0.73        91      74     110 ..      30      66 ..      21      75 .. 0.72
   2 ?    6.9   9.7     0.034       4.2      63     143 ..      74     155 ..      58     204 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.73
                   HAUS-augmin3  74 eeeeesleaLeqelqeLqkekalklkrlnkLqvqaas 110
                                    e++++ l+ L++ ++ L +  a+ ++rl++L++++a 
  gi|119720248|ref|YP_920743.1|  30 EDLRAELKGLREAVERLVEAHARAEERLSRLEAAVAG 66 
                                    6666777777777777777777777777777777665 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.034
                   HAUS-augmin3  63 q.edvellevileeeeesleaLeqelqeLqkekalklkrlnkLqvqaaslqqelrkleeeekeakkklkeaqeelraena 141
                                    + e+   lev ++  +e++  Le+ +  L + +a  ++rl +L+ ++a +++   kle++ ++ ++++ ++++++++   
  gi|119720248|ref|YP_920743.1|  74 HsEAIARLEVAVARHDEAVARLEAAVARLAEAQAKSEERLARLEEAVARQSESIAKLEAAVSKHSEVIARLEAAVAKHDE 153
                                    33777888999999999999999999999999999999999999999999999888888888888777777666655443 PP

                   HAUS-augmin3 142 et 143
                                     +
  gi|119720248|ref|YP_920743.1| 154 TI 155
                                    32 PP

>> Vps53_N  Vps53-like, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   1.3      0.19        23      19      85 ..      77     139 ..      54     146 .. 0.67
   2 ?    5.1   3.6     0.074       9.2      29     105 ..     122     194 ..     108     204 .. 0.37

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.19
                        Vps53_N  19 slanidelikklqeeikklddeiksvvraqanvgekgkealeeaqkaieelfqkikeikdkaeksee 85 
                                    ++a ++  +++  e + +l++ ++ + +aqa    k++e l+ +++a+ + +++i ++     k  e
  gi|119720248|ref|YP_920743.1|  77 AIARLEVAVARHDEAVARLEAAVARLAEAQA----KSEERLARLEEAVARQSESIAKLEAAVSKHSE 139
                                    4445555556666677777777777777777....55666888888888888888877654444444 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.074
                        Vps53_N  29 klqeeikklddeiksvvraqanvgekgkealeeaqkaieelfqkikeikdkaekseemvkeitrdIkqLDiAKknlt 105
                                    +  e+i kl++ + ++ +  a    + + a+++ +++i +l++ + +  +  ++ e+ +    + I +L+ A + l+
  gi|119720248|ref|YP_920743.1| 122 RQSESIAKLEAAVSKHSEVIA----RLEAAVAKHDETIARLEKAVAKHDESIARLEKAIARHDEAIARLEEAVRGLA 194
                                    444444444444443333222....2222333333333333333333333333333333333333333333333333 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   3.2       1.4   1.7e+02      48      92 ..      30      74 ..      19      77 .. 0.85
   2 ?   11.7  11.3    0.0022      0.27      17      93 ..      76     152 ..      69     154 .. 0.83
   3 ?    4.0   1.2      0.51        63      54      90 ..     155     191 ..     152     198 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 1.4
                                   TTHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHS CS
                           BTAD 48 ewleaererleelrlealealaeaelrlGraeealaelealvaeh 92
                                   e l+ae++ l+e   + +ea+a+ae rl r e+a+a l ++v+ h
  gi|119720248|ref|YP_920743.1| 30 EDLRAELKGLREAVERLVEAHARAEERLSRLEAAVAGLGEAVSRH 74
                                   568889999999999999999999999999999999999988877 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.0022
                                    HHTT-HHHHHHHHHHHHTT--SSTTGGGTTSTTHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                           BTAD  17 laagdpeeaaelleaAlalwrGpaladleagewleaererleelrlealealaeaelrlGraeealaelealvaehP 93 
                                     a  + e a+++ ++A+a  ++ +   +ea+   e +++rlee   +  e++a++e+++ +++e++a+lea+va+h+
  gi|119720248|ref|YP_920743.1|  76 EAIARLEVAVARHDEAVARLEAAVARLAEAQAKSEERLARLEEAVARQSESIAKLEAAVSKHSEVIARLEAAVAKHD 152
                                    3333677777888888888888888888889999****************************************997 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.51
                                    HHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                           BTAD  54 rerleelrlealealaeaelrlGraeealaelealva 90 
                                    ++rle+   +  e++a++e +++r++ea+a+le++v+
  gi|119720248|ref|YP_920743.1| 155 IARLEKAVAKHDESIARLEKAIARHDEAIARLEEAVR 191
                                    5677787788888888888889999999999988875 PP

>> CENP-Q  CENP-Q, a CENPA-CAD centromere complex subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   3.6       0.1        13      42      78 ..      30      66 ..      28      76 .. 0.84
   2 ?    4.6  11.7      0.27        33      29      85 ..      73     130 ..      69     154 .. 0.82
   3 ?    4.7   4.3      0.25        31      34      80 ..     155     194 ..     124     203 .. 0.53

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.1
                         CENP-Q 42 spelhslelLeaeiekeeralerdyeaLreLeknaka 78
                                   + ++  l+ L++ +e++++a +r +e L +Le+ +  
  gi|119720248|ref|YP_920743.1| 30 EDLRAELKGLREAVERLVEAHARAEERLSRLEAAVAG 66
                                   566778899**********************998765 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.27
                         CENP-Q  29 klldekaaleaqLspelhslelLeaeiekeeralerdyeaLreLeknakaeare.rke 85 
                                    + ++++a+le  ++   ++++ Lea + ++ +a ++ +e L++Le+ + ++ ++  k 
  gi|119720248|ref|YP_920743.1|  73 RHSEAIARLEVAVARHDEAVARLEAAVARLAEAQAKSEERLARLEEAVARQSESiAKL 130
                                    56789999****************************************9999985544 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.25
                         CENP-Q  34 kaaleaqLspelhslelLeaeiekeeralerdyeaLreLeknakaea 80 
                                    +a+le+ ++   +s       i ++e+a +r  ea+++Le+ ++ +a
  gi|119720248|ref|YP_920743.1| 155 IARLEKAVAKHDES-------IARLEKAIARHDEAIARLEEAVRGLA 194
                                    23334444444444.......44444444444444444444444443 PP

>> TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.9      0.29        35      48     102 ..       8      65 ..       2      75 .. 0.50
   2 ?    6.5   5.9     0.077       9.5      10      81 ..      74     145 ..      69     148 .. 0.67
   3 ?    7.3   1.3     0.041       5.1      16      69 ..     136     189 ..     133     205 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.29
                    TMF_TATA_bd  48 eivklmkeneelkelkke...leelekeleelqeryetlLellGeksEeveELraDva 102
                                    e+++l++e ee + +      le+l++el+ l+e  e l e     +E+   L+a va
  gi|119720248|ref|YP_920743.1|   8 EMLRLLREDEEFRYAVVGllgLEDLRAELKGLREAVERLVEAHARAEERLSRLEAAVA 65 
                                    4555555555544444321113444445555555555555555555555555555555 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.077
                    TMF_TATA_bd  10 svqlverlsseirrlEgElaslkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqerye 81 
                                    +++ + rl+ ++ r +  +a l+  ++rl++ + + +e +++l + + +++e+ ++le   ++ +e+  r+e
  gi|119720248|ref|YP_920743.1|  74 HSEAIARLEVAVARHDEAVARLEAAVARLAEAQAKSEERLARLEEAVARQSESIAKLEAAVSKHSEVIARLE 145
                                    456677777777777777777777777777777777777777776666666666666666666666666655 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.041
                    TMF_TATA_bd  16 rlsseirrlEgElaslkeelerleaerdeareeivklmkeneelkelkkeleel 69 
                                    + s  i rlE+ +a+  e+++rle+   +  e i++l k   + +e+ ++lee 
  gi|119720248|ref|YP_920743.1| 136 KHSEVIARLEAAVAKHDETIARLEKAVAKHDESIARLEKAIARHDEAIARLEEA 189
                                    556677888888888888888888888888888888876665555555544443 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4  22.8     0.043       5.3     192     356 ..      31     195 ..      24     201 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.043
                           FUSC 192 rlaadilalealrsqaayesprirararalrrllsrmlallallsslarllarlraeeaaavpelaallaelaaleaaaa 271
                                    +l a++ +l ++++ ++  ++r  +r  +l ++ + + +++++ s+   +l+   a++++av+ l+a +a+la+     a
  gi|119720248|ref|YP_920743.1|  31 DLRAELKGLREAVERLVEAHARAEERLSRLEAAVAGLGEAVSRHSEAIARLEVAVARHDEAVARLEAAVARLAE-----A 105
                                    56677778888888888888888888888888888888889998888888888889999998889999999999.....4 PP

                           FUSC 272 aealeaalaalrarlralrrale...adadtaalllarlaellaelaqllaslraleaaiaa..arraerlarhrdhlaa 346
                                    +++ e++la+l++++++++++ +   a+ + + +++arl   +a+  ++ a l++  a   +  ar ++++arh +  a 
  gi|119720248|ref|YP_920743.1| 106 QAKSEERLARLEEAVARQSESIAkleAAVSKHSEVIARLEAAVAKHDETIARLEKAVAKHDEsiARLEKAIARHDEAIAR 185
                                    66677777777777777777766677777788888888888887777766666655444444445677779999999998 PP

                           FUSC 347 llnglraala 356
                                    l  ++r+++a
  gi|119720248|ref|YP_920743.1| 186 LEEAVRGLAA 195
                                    9899998876 PP

>> BST2  Bone marrow stromal antigen 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.8       2.6   3.2e+02      15      84 ..      39     108 ..      28     115 .. 0.64
   2 ?    6.8   1.1     0.083        10      27      90 ..      72     135 ..      62     136 .. 0.89
   3 ?    5.5   4.3       0.2        25      14      88 ..     108     182 ..     104     199 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 2.6
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           BST2  15 crnvtrlLerqLtqaqeslreaeaqaatcnqtvvtLkasLekekaqsqkqqakvqelqgeikkLnqkLqd 84 
                                    +r+  + L +  ++a+e l + ea +a   + v   ++++ + +    ++ + v  l+  +++L++   +
  gi|119720248|ref|YP_920743.1|  39 LREAVERLVEAHARAEERLSRLEAAVAGLGEAVSRHSEAIARLEVAVARHDEAVARLEAAVARLAEAQAK 108
                                    4444444444557788888888888888888887777777666666666666777777777777765544 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.083
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC CS
                           BST2  27 tqaqeslreaeaqaatcnqtvvtLkasLekekaqsqkqqakvqelqgeikkLnqkLqdaeaeve 90 
                                     +  e +++ e  +a  ++ v  L+a+  +    + k ++++  l++ ++++ +++ + ea+v 
  gi|119720248|ref|YP_920743.1|  72 SRHSEAIARLEVAVARHDEAVARLEAAVARLAEAQAKSEERLARLEEAVARQSESIAKLEAAVS 135
                                    5667888899999999999*********99999999999*****************99999875 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.2
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           BST2  14 ecrnvtrlLerqLtqaqeslreaeaqaatcnqtvvtLkasLekekaqsqkqqakvqelqgeikkLnqkLqdaeae 88 
                                    + ++    Le+  ++  es+++ ea ++  ++++  L+a+  k+     + ++ v +  + i++L++ +    ++
  gi|119720248|ref|YP_920743.1| 108 KSEERLARLEEAVARQSESIAKLEAAVSKHSEVIARLEAAVAKHDETIARLEKAVAKHDESIARLEKAIARHDEA 182
                                    555555667777777888888888888888888888888888777777777777777777777777777655544 PP

>> UBN_AB  Ubinuclein conserved middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   5.1      0.34        42       9      79 ..      95     161 ..      30     199 .. 0.62

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.34
                         UBN_AB   9 leesiekLkeaakseeaegkkkfFseelnnllldielqarelstsarsavyshLesvlpcskdtLlkrlkk 79 
                                    le+++  L ea  ++e  +++  ++e ++++  +i++    +  s+ s+v + Le+ +    +t+ ++ k 
  gi|119720248|ref|YP_920743.1|  95 LEAAVARLAEAQAKSE--ERLARLEEAVARQSESIAKLEAAV--SKHSEVIARLEAAVAKHDETIARLEKA 161
                                    4444444444444444..333334555555554444444444..444555555555555555555444444 PP

>> T3SSipB  Type III cell invasion protein SipB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   4.2      0.14        17      47      92 ..      66     111 ..      26     128 .. 0.63
   2 ?    6.1   5.0      0.12        15      33      92 ..     129     188 ..     113     204 .. 0.60

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.14
                                    THHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                        T3SSipB  47 elqtalseakgatddleaaiekadqaksaadaatkkvdeaqkrlke 92 
                                     l +a+s  ++a   le a+++ d+a +  +aa +++ eaq++ +e
  gi|119720248|ref|YP_920743.1|  66 GLGEAVSRHSEAIARLEVAVARHDEAVARLEAAVARLAEAQAKSEE 111
                                    3556777777777777777777777777777777777777774332 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.12
                                    HHHHTTTTT----STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                        T3SSipB  33 mskaqqeaasklSdelqtalseakgatddleaaiekadqaksaadaatkkvdeaqkrlke 92 
                                    + +a++ + s++   l+ a+ + ++    le+a++k d+  +  ++a ++ dea +rl+e
  gi|119720248|ref|YP_920743.1| 129 KLEAAVSKHSEVIARLEAAVAKHDETIARLEKAVAKHDESIARLEKAIARHDEAIARLEE 188
                                    345555555555555555555555555556666666665555555555555555555554 PP

>> DUF5632  Family of unknown function (DUF5632)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.1       1.6     2e+02       5      22 ..      41      58 ..      38      66 .. 0.85
   2 ?    6.7   0.2     0.059       7.3       3      21 ..     109     127 ..     107     151 .. 0.79
   3 ?    2.0   0.1       1.7   2.1e+02       5      36 ..     184     216 ..     163     237 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 1.6
                        DUF5632  5 qrLqRlldavaRqeprLa 22
                                   + ++Rl++a aR e rL+
  gi|119720248|ref|YP_920743.1| 41 EAVERLVEAHARAEERLS 58
                                   5689********999986 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.059
                        DUF5632   3 eeqrLqRlldavaRqeprL 21 
                                    +e+rL Rl +avaRq   +
  gi|119720248|ref|YP_920743.1| 109 SEERLARLEEAVARQSESI 127
                                    789************8643 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 1.7
                        DUF5632   5 qrLqRlldavaRqeprLaWavGe.raDgttllv 36 
                                    +rL+  +  +a q  rL+ a+G   +D   l+v
  gi|119720248|ref|YP_920743.1| 184 ARLEEAVRGLAAQVGRLSEAIGFgLEDVAALMV 216
                                    678888888889999999999852455555555 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   3.1      0.09        11      56     124 ..      29      97 ..       7     100 .. 0.60
   2 ?    3.3  15.7      0.93   1.1e+02      18     126 ..      29     148 ..      26     151 .. 0.70
   3 ?    2.8  13.7       1.3   1.6e+02      37     125 ..     109     196 ..     102     204 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.09
                         APG6_N  56 leklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynelqlelleleeeldslea 124
                                    le+l++e + l e  ++l +++++ e+ l+ le+  + l e   r+ +    l++ +++++e  + lea
  gi|119720248|ref|YP_920743.1|  29 LEDLRAELKGLREAVERLVEAHARAEERLSRLEAAVAGLGEAVSRHSEAIARLEVAVARHDEAVARLEA 97 
                                    555666666666666666666666666666666666666555555555555555555555555555555 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.93
                         APG6_N  18 leqaekerdaYeeflkklkkekkeeek...........qdeeleeleeeleklekeeeelleeLkelekereeleaelaa 86 
                                    le++++e + ++e  ++l + +  +e+             e + +  e +++le + ++  e  ++le++ ++l+++ a+
  gi|119720248|ref|YP_920743.1|  29 LEDLRAELKGLREAVERLVEAHARAEErlsrleaavagLGEAVSRHSEAIARLEVAVARHDEAVARLEAAVARLAEAQAK 108
                                    56677777777777777776666655556666667777666666677777778888888888888888888888888888 PP

                         APG6_N  87 leeelealeeeeerfwreynelqlelleleeeldsleaqy 126
                                     ee l++lee  +r  ++  +l+  ++++ e  + lea++
  gi|119720248|ref|YP_920743.1| 109 SEERLARLEEAVARQSESIAKLEAAVSKHSEVIARLEAAV 148
                                    8888888887777777777777777777777777777665 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 1.3
                         APG6_N  37 kekkeeek...qdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynelqlell 113
                                    +e+    +    +e +++  e+++kle++ ++  e +++le++ ++ ++ +a le+  ++ +e  +r  +    ++   +
  gi|119720248|ref|YP_920743.1| 109 SEE----RlarLEEAVARQSESIAKLEAAVSKHSEVIARLEAAVAKHDETIARLEKAVAKHDESIARLEKAIARHDEAIA 184
                                    222....2344677888888889999999999999999999999999999999998888888887777777777777777 PP

                         APG6_N 114 eleeeldsleaq 125
                                    +lee  + l+aq
  gi|119720248|ref|YP_920743.1| 185 RLEEAVRGLAAQ 196
                                    777777666666 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1       4.8     6e+02      18      40 ..      30      52 ..       3      67 .. 0.59
   2 ?    3.1   1.8       1.2   1.4e+02       9      52 ..      77     120 ..      26     144 .. 0.52
   3 ?    3.7   1.5      0.78        96       8      65 ..     111     168 ..     105     188 .. 0.71
   4 ?    0.3   0.0       8.6   1.1e+03       9      29 ..     182     202 ..     163     217 .. 0.59

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 4.8
                                   HHHHHHHHHHHHHHHHHHHHHHH CS
                           YabA 18 eelleeleelkeelaelleenae 40
                                   e+l +el+ l+e++++l+e +a+
  gi|119720248|ref|YP_920743.1| 30 EDLRAELKGLREAVERLVEAHAR 52
                                   33444444444444444444433 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 1.2
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           YabA   9 kleeleeqleelleeleelkeelaelleenaeLeleneklrerl 52 
                                    ++++le  +++  e +++l++++a+l e  a+ e    +l e +
  gi|119720248|ref|YP_920743.1|  77 AIARLEVAVARHDEAVARLEAAVARLAEAQAKSEERLARLEEAV 120
                                    23333333333333333333333333333333333333333333 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.78
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXX CS
                           YabA   8 dkleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkke 65 
                                    ++l++lee +++ +e++++l++++++  e  a+Le+   k  e++++ ek+ ++++++
  gi|119720248|ref|YP_920743.1| 111 ERLARLEEAVARQSESIAKLEAAVSKHSEVIARLEAAVAKHDETIARLEKAVAKHDES 168
                                    6788999999999999999999999999999999888766666664444444333333 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 8.6
                                    HHHHHHHHHHHHHHHHHHHHH CS
                           YabA   9 kleeleeqleelleeleelke 29 
                                    ++++lee ++ l +++++l e
  gi|119720248|ref|YP_920743.1| 182 AIARLEEAVRGLAAQVGRLSE 202
                                    344555555555555555555 PP

>> MutS_III  MutS domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   6.5     0.082        10      67     176 ..      29     171 ..      13     205 .. 0.37

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.082
                                    HHHHHHHHTT--.-HHHHHHHHHTT---HHHHHH.......HHHHHHHHHTTTTT---SSTHHHHH..HHHHHHHHHHB- CS
                                    xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxx RF
                       MutS_III  67 reelrellrrlp.DleRllsrislgkakardlka.......llealkaleelvallekeklaesee..eslaelleeaid 136
                                     e+lr++l+ l+  +eRl+   +  + +   l++       l ea++++ e +a le   + ++ e  ++l++ + + + 
  gi|119720248|ref|YP_920743.1|  29 LEDLRAELKGLReAVERLVEAHARAEER---LSRleaavagLGEAVSRHSEAIARLEVAVARHD-EavARLEAAVAR-LA 103
                                    3556666665443566666433221111...222111112222222222222222221111111.112111112221.22 PP

                                    SS--SSGGGS--B-T............................HHHHHHHHHHHHHHHHHHTHHHHHH CS
                                    xxxxxxxxxxxxxxx............................xxxxxxxxxxxxxxxxxxxxxxxxx RF
                       MutS_III 137 eeplalekegedlra............................iealeqelfqelleeveealerlrr 176
                                    e + ++e++   l++                            + a+++e +++l + v+++ e + r
  gi|119720248|ref|YP_920743.1| 104 EAQAKSEERLARLEEavarqsesiakleaavskhseviarleaAVAKHDETIARLEKAVAKHDESIAR 171
                                    22222222222222222222222222223222333333333332222244444444444444444444 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   5.0         4   4.9e+02      80     106 ..      93     119 ..      29     146 .. 0.66
   2 ?    2.1   9.7       1.4   1.7e+02       4     117 ..      77     186 ..      75     203 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 4
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Prefoldin  80 ellkkkleelekqlekleeeleklkdq 106
                                    + l+  ++ l +++ k ee l+ l ++
  gi|119720248|ref|YP_920743.1|  93 ARLEAAVARLAEAQAKSEERLARLEEA 119
                                    333333333333333333333333332 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 1.4
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT.-TT-EEEEEEETTEEEEEE--STTEEEEEEETTEEEEEEHHHHHHHHH CS
                      Prefoldin   4 eleslqaelaqlkeaieelektletlktlkkedegkevlvplgaglyvkaevkdtdkvlvdlGagyyveksleeAiellk 83 
                                    ++++l+  +a+ +ea  +le++ ++l + ++  +++e l  l++ +  + e + + ++ v+  +++ + ++   A++  +
  gi|119720248|ref|YP_920743.1|  77 AIARLEVAVARHDEAVARLEAAVARLAEAQA--KSEERLARLEEAVARQSESIAKLEAAVSKHSEVIARLE--AAVAKHD 152
                                    6778888888888888888888888888888..88888888888888888888888888888888888654..4444455 PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Prefoldin  84 kkleelekqlekleeeleklkdqittleanlaql 117
                                    + ++ lek++ k+ e+++ l ++i    +++a+l
  gi|119720248|ref|YP_920743.1| 153 ETIARLEKAVAKHDESIARLEKAIARHDEAIARL 186
                                    6666666666666666666655555544444443 PP

>> CREPT  Cell-cycle alteration and expression-elevated protein in tumour
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   3.1      0.54        67      54     117 ..      68     131 ..      29     135 .. 0.78
   2 ?    6.7   6.7     0.059       7.3      43     115 ..     106     178 ..      90     202 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.54
                          CREPT  54 eealellaeYnkrLeaeleeRkklakmledfleaqkellakaeekleelkeklekvksvrkelk 117
                                     ea++  +e  +rLe  +    +    le+ ++ + e+ ak+ee+l++l+e +++ ++  ++l+
  gi|119720248|ref|YP_920743.1|  68 GEAVSRHSEAIARLEVAVARHDEAVARLEAAVARLAEAQAKSEERLARLEEAVARQSESIAKLE 131
                                    5777777888888888888888888888888888888888999988888888888777766665 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.059
                          CREPT  43 keeaekllkqveealellaeYnkrLeaeleeRkklakmledfleaqkellakaeekleelkeklekvksvrke 115
                                    +++ e+ l   eea++  +e  ++Lea +++ +++   le+ ++ + e++a+ e+ ++++ e +++++++ + 
  gi|119720248|ref|YP_920743.1| 106 QAKSEERLARLEEAVARQSESIAKLEAAVSKHSEVIARLEAAVAKHDETIARLEKAVAKHDESIARLEKAIAR 178
                                    4455566667777788888888888888888888888888888888888888887777777777777665544 PP

>> FlgN  FlgN protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.7      0.06       7.4      48     124 ..       7      81 ..       3      92 .. 0.70
   2 ?    3.8   7.0      0.62        76       5      98 ..      30     118 ..      28     123 .. 0.55
   3 ?    3.3  11.6      0.89   1.1e+02      33     103 ..     109     186 ..      86     205 .. 0.39

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.06
                                    HHHHHHHHHHHHHHHHHHHHTT--SCHHHHHHHHCTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHH CS
                           FlgN  48 qellekleqleqkrakllaelglsaeeatlsellakeedeelkelwqelkelleelkelnelNgrlieqslefnqrl 124
                                     e l+ l++ e+ r +++  lgl++ +a+l+ l +  + e+l e+ ++ +e+l +l ++    g+++ ++ e + rl
  gi|119720248|ref|YP_920743.1|   7 GEMLRLLREDEEFRYAVVGLLGLEDLRAELKGLRE--AVERLVEAHARAEERLSRLEAAVAGLGEAVSRHSEAIARL 81 
                                    56677778888888888888888866666666655..7777777777777777777777777777777776666654 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.62
                                    CHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SCHHHHHHHHCTT CS
                           FlgN   5 eeLielleeelelleeLlelleeEteaLkagdieaLeelleekqellekleqleqkrakllaelglsaeeatlsellake 84 
                                    e+L + l+ ++e++e+L e  ++ +e L++ + +a  +l e      e++++le + a++ ++++    ea + +l++  
  gi|119720248|ref|YP_920743.1|  30 EDLRAELKGLREAVERLVEAHARAEERLSRLE-AAVAGLGEAVSRHSEAIARLEVAVARHDEAVARL--EAAVARLAE-- 104
                                    56667777777888888888888888888776.5555555555555555555555555555555555..333444444.. PP

                                    CCHHHHHHHHHHHH CS
                           FlgN  85 edeelkelwqelke 98 
                                    ++++ +e  ++l+e
  gi|119720248|ref|YP_920743.1| 105 AQAKSEERLARLEE 118
                                    44444443333333 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.89
                                    HTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--..SCHHHHHHHHCT.....TCCHHHHHHHHHHHHHHHHH CS
                           FlgN  33 kagdieaLeelleekqellekleqleqkrakllaelgls..aeeatlsellak.....eedeelkelwqelkelleel 103
                                    +++ +++Lee + +  e ++kle++  k ++++a+l+    + ++t+ +l ++     e+ ++l+++ ++ +e++++l
  gi|119720248|ref|YP_920743.1| 109 SEERLARLEEAVARQSESIAKLEAAVSKHSEVIARLEAAvaKHDETIARLEKAvakhdESIARLEKAIARHDEAIARL 186
                                    333344444444444444444444444444444444444332222222222211112222222222222222222222 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.8       0.3        37      37      65 ..      32      60 ..       4      69 .. 0.71
   2 ?    5.1   1.1      0.26        32      23      52 ..      32      61 ..      26      90 .. 0.58
   3 ?    0.1  12.2       8.9   1.1e+03       6      56 ..      92     152 ..      55     205 .. 0.63

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.3
                           ZapB 37 lkeenreleeeneqlkeereawqerlkkL 65
                                   l  e + l+e +e+l e ++  +erl+ L
  gi|119720248|ref|YP_920743.1| 32 LRAELKGLREAVERLVEAHARAEERLSRL 60
                                   44444445566666666666666666544 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.26
                           ZapB 23 LqmeieeLkeeneelkeenreleeeneqlk 52
                                   L+ e++ L+e +e l e  ++ ee +++l+
  gi|119720248|ref|YP_920743.1| 32 LRAELKGLREAVERLVEAHARAEERLSRLE 61
                                   445555555555555555555544444444 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 8.9
                           ZapB   6 LeqLEskiqkaidtitlLqmeieeLkeeneelkeenrele..........eeneqlkeere 56 
                                      +LE+ +  + +  ++  +++++L+e ++  +e +++le          + +e+  + + 
  gi|119720248|ref|YP_920743.1|  92 VARLEAAVARLAEAQAKSEERLARLEEAVARQSESIAKLEaavskhseviARLEAAVAKHD 152
                                    3344444444444444444444444444444444444444333333333333333334444 PP

>> DUF2218  Uncharacterized protein conserved in bacteria (DUF2218)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.3       5.1   6.3e+02      53      71 ..      47      65 ..      30      79 .. 0.74
   2 ?    0.8   2.6       5.3   6.6e+02      42      81 ..      58      96 ..      41     101 .. 0.62
   3 ?    7.3   4.4     0.048       5.9      35      81 ..      86     131 ..      67     136 .. 0.81
   4 ?    3.3   0.6      0.88   1.1e+02      58      82 ..     136     160 ..     128     164 .. 0.77
   5 ?    5.0   0.5      0.26        32      56      82 ..     162     188 ..     160     191 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 5.1
                                   EEEEESSHHHHHHHHHHHH CS
                        DUF2218 53 lrveaedaeslarlkavva 71
                                   ++++a  +e+l+rl+a+va
  gi|119720248|ref|YP_920743.1| 47 VEAHARAEERLSRLEAAVA 65
                                   4566777788888888876 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 5.3
                                   EEEEEETTEEEEEEEESSHHHHHHHHHHHHHHHHHTSTTS CS
                        DUF2218 42 crleaeddaLtlrveaedaeslarlkavvarhLerfafre 81
                                    rlea+ + L   v   + e++arl+ +varh e +a+ e
  gi|119720248|ref|YP_920743.1| 58 SRLEAAVAGLGEAVSRHS-EAIARLEVAVARHDEAVARLE 96
                                   455555555555554444.777777777777766666554 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.048
                                    EE-SSS-EEEEEETTEEEEEEEESSHHHHHHHHHHHHHHHHHTSTTS CS
                        DUF2218  35 iefprgtcrleaeddaLtlrveaedaeslarlkavvarhLerfafre 81 
                                     + +++++rlea+ ++L ++++a+++e+larl+++var  e +a+ e
  gi|119720248|ref|YP_920743.1|  86 ARHDEAVARLEAAVARL-AEAQAKSEERLARLEEAVARQSESIAKLE 131
                                    44566699999999999.599*****************999999877 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.88
                                    SSHHHHHHHHHHHHHHHHHTSTTSS CS
                        DUF2218  58 edaeslarlkavvarhLerfafree 82 
                                    +  e +arl+a+va+h e++a+ e+
  gi|119720248|ref|YP_920743.1| 136 KHSEVIARLEAAVAKHDETIARLEK 160
                                    4458899*********999999875 PP

  == domain 5  score: 5.0 bits;  conditional E-value: 0.26
                                    EESSHHHHHHHHHHHHHHHHHTSTTSS CS
                        DUF2218  56 eaedaeslarlkavvarhLerfafree 82 
                                     a+ +es+arl++++arh e +a+ ee
  gi|119720248|ref|YP_920743.1| 162 VAKHDESIARLEKAIARHDEAIARLEE 188
                                    58899*************999999876 PP

>> CAP_N  Adenylate cyclase associated (CAP) N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1  11.1      0.23        28       4      89 ..      92     183 ..      54     219 .. 0.56

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.23
                                    XXXXXXXXXXXXXX......................XXXXXXXXXXXXXXXXXXXXXXXSXH.......HHHHHHHHHH. CS
                          CAP_N   4 ikRLEaatsrLEdiais............essssasskasssssaaaaaaaaaakaaaaaaaa......ksveaFdeli. 64 
                                    + RLEaa++rL + +++            +            +s++ a+ +aa ++++    +      ++v+++de i 
  gi|119720248|ref|YP_920743.1|  92 VARLEAAVARLAEAQAKseerlarleeavA-----------RQSESIAKLEAAVSKHS----EviarleAAVAKHDETIa 156
                                    789999999998875544433322222210...........11111111111111111....123345555555555542 PP

                                    ..HHHHHHHHHHHHHH-HHHHHHHHHH CS
                          CAP_N  65 ..sgsvkefvelskkiggevaeqaelv 89 
                                      +++v++  e  + +++ +a + e++
  gi|119720248|ref|YP_920743.1| 157 rlEKAVAKHDESIARLEKAIARHDEAI 183
                                    222233333333333333333333333 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   6.7      0.42        52      16      75 ..      43     102 ..      32     104 .. 0.81
   2 ?    4.6   5.4      0.32        40       3      77 .]     100     174 ..      99     177 .. 0.85
   3 ?    8.1   0.5     0.026       3.2      51      73 ..     169     191 ..     167     195 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.42
                         TPR_12  16 lgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                     +r+ eA +  e+ l + +++  +  +++++   +++rl  a  r++eA+++le a+a++
  gi|119720248|ref|YP_920743.1|  43 VERLVEAHARAEERLSRLEAAVAGLGEAVSRHSEAIARLEVAVARHDEAVARLEAAVARL 102
                                    56677777777777777777766778889999999999999*************999875 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.32
                         TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiaek 77 
                                    a+++   a  + rl r++eA +   ++++  +++  ++++  a+   + +   +   r+e+A++ + e++a++ek
  gi|119720248|ref|YP_920743.1| 100 ARLAEAQAKSEERLARLEEAVARQSESIAKLEAAVSKHSEVIARLEAAVAKHDETIARLEKAVAKHDESIARLEK 174
                                    55565788899999*****************99988888777777777777778889*******99999999885 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.026
                         TPR_12  51 LgrlyralgryeeAlelleeala 73 
                                    ++rl  a  r++eA+++leea++
  gi|119720248|ref|YP_920743.1| 169 IARLEKAIARHDEAIARLEEAVR 191
                                    68888899999999999999987 PP

>> P4Ha_N  Prolyl 4-Hydroxylase alpha-subunit, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0       6.3   7.8e+02      24      49 ..      30      55 ..       9      66 .. 0.74
   2 ?    1.9   0.2       1.7   2.1e+02       4      48 ..      66     110 ..      63     126 .. 0.68
   3 ?    6.2   0.6     0.081        10       1      44 [.     126     169 ..     126     190 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 6.3
                         P4Ha_N 24 eeeekkleklkrfleeleeehesake 49
                                   e+++++l+ l++++e+l e+h +a+e
  gi|119720248|ref|YP_920743.1| 30 EDLRAELKGLREAVERLVEAHARAEE 55
                                   56677777777777777777755444 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 1.7
                         P4Ha_N   4 dlekLlklErelveeLesyieeeekkleklkrfleeleeehesak 48 
                                     l ++++  +e + +Le  + +  + +++l+ ++++l e++ +++
  gi|119720248|ref|YP_920743.1|  66 GLGEAVSRHSEAIARLEVAVARHDEAVARLEAAVARLAEAQAKSE 110
                                    556666667777888888888888888888888888887774422 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.081
                         P4Ha_N   1 SladlekLlklErelveeLesyieeeekkleklkrfleeleeeh 44 
                                    S+a+le++++  +e++ +Le  + +  + +++l++++++ +e  
  gi|119720248|ref|YP_920743.1| 126 SIAKLEAAVSKHSEVIARLEAAVAKHDETIARLEKAVAKHDESI 169
                                    78888889999999999999999999999999988888876655 PP

>> HAUS6_N  HAUS augmin-like complex subunit 6 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   5.7      0.61        75     148     222 ..      70     142 ..      39     153 .. 0.66
   2 ?    6.4   0.4     0.049         6     139     188 ..     152     201 ..     139     205 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.61
                        HAUS6_N 148 lvaahrvslrrflrekaaadrarqkyqenaqllekkerelraeleelqaelkaekeaakkekkeasedaeeekik 222
                                    +v +h+ ++ r+  ++a+ d+a ++++  ++ l++ + + +++l++l++ +   +++++++k+ea  ++ +e+i 
  gi|119720248|ref|YP_920743.1|  70 AVSRHSEAIARLEVAVARHDEAVARLEAAVARLAEAQAKSEERLARLEEAVA--RQSESIAKLEAAVSKHSEVIA 142
                                    5566666666666666666666666666666666666666666666666554..455556666655555555554 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.049
                        HAUS6_N 139 skkaqdlsklvaahrvslrrflrekaaadrarqkyqenaqllekkerelr 188
                                    +++ + l+k+va+h  s+ r+ +++a+ d+a+++++e ++ l+ ++  l 
  gi|119720248|ref|YP_920743.1| 152 DETIARLEKAVAKHDESIARLEKAIARHDEAIARLEEAVRGLAAQVGRLS 201
                                    5566789999***************************9999999988776 PP

>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1       8.3     1e+03      51      73 ..      41      63 ..      29      99 .. 0.62
   2 ?    6.2   8.1     0.059       7.3       6     119 ..      71     181 ..      67     193 .. 0.63

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 8.3
                           YkyA 51 kikklsdealenveeReelleke 73
                                   + ++   ea + +eeR ++le  
  gi|119720248|ref|YP_920743.1| 41 EAVERLVEAHARAEERLSRLEAA 63
                                   44444555555566666655554 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.059
                           YkyA   6 iyealeeavelEkefeeqqekLtelekkeqelyeeiielgmdefdkikklsdealenveeReellekekesieeakeefe 85 
                                    ++ + e ++ lE +++   e   +le+    l e    ++ +++ ++++ ++   e++ + e  ++k  e+i + + ++ 
  gi|119720248|ref|YP_920743.1|  71 VSRHSEAIARLEVAVARHDEAVARLEAAVARLAEAQA-KSEERLARLEEAVARQSESIAKLEAAVSKHSEVIARLEAAVA 149
                                    5566677777777777777777777777777766664.466667777777777777777777777777777777777777 PP

                           YkyA  86 kikeeieeiedeelkkeaeelieameeryeaydk 119
                                    k +e+i  +e+     + +e i  +e+  + +d+
  gi|119720248|ref|YP_920743.1| 150 KHDETIARLEKA--VAKHDESIARLEKAIARHDE 181
                                    777777777433..33333444444444444444 PP

>> Tropomyosin  Tropomyosin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8  20.2      0.12        15      14     124 ..      75     188 ..      67     204 .. 0.66

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.12
                    Tropomyosin  14 eerlekakkkleeaekkaekaeaEvaalnrriqlleeelerteerleealekLeeaekaadeserarKvlEnrelkdeek 93 
                                    +e+ ++++  +++++++ ++ ea va l     + ee l r ee ++++ e + ++e a + + +++  lE   +k +e 
  gi|119720248|ref|YP_920743.1|  75 SEAIARLEVAVARHDEAVARLEAAVARLAEAQAKSEERLARLEEAVARQSESIAKLEAAVSKHSEVIARLEAAVAKHDET 154
                                    56666666677777777778888888888888888888888888888888888888888888888888888888888888 PP

                    Tropomyosin  94 leeleaql...keakeiaeeadrkyeEvarklvv 124
                                    +++le+++   +e++ + e a  + +E+  +l  
  gi|119720248|ref|YP_920743.1| 155 IARLEKAVakhDESIARLEKAIARHDEAIARLEE 188
                                    8888865421134444445555555555444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1722  (0.0960455); expected 358.6 (0.02)
Passed bias filter:                      896  (0.0499749); expected 358.6 (0.02)
Passed Vit filter:                       249  (0.0138881); expected 17.9 (0.001)
Passed Fwd filter:                       168  (0.00937029); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):             145  [number of targets reported over threshold]
# CPU time: 1.81u 0.35s 00:00:02.16 Elapsed: 00:00:00.58
# Mc/sec: 1678.71
//
Query:       gi|119720249|ref|YP_920744.1|  [L=339]
Description: ATPase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.2e-50  169.7   0.1    1.2e-49  169.4   0.1    1.1  1  ATPase_2      ATPase domain predominantly from Archaea
    1.4e-07   32.0   0.0    2.2e-07   31.4   0.0    1.3  1  AAA_16        AAA ATPase domain
      2e-05   24.9   0.0    4.3e-05   23.8   0.0    1.5  1  AAA_22        AAA domain
     0.0016   18.8   0.0     0.0028   18.0   0.0    1.3  1  AAA_19        AAA domain
      0.003   17.9   0.0     0.0055   17.1   0.0    1.4  1  RNA_helicase  RNA helicase
      0.007   15.6   0.0      0.013   14.8   0.0    1.3  1  KAP_NTPase    KAP family P-loop domain
     0.0094   16.4   0.0      0.021   15.2   0.0    1.8  1  AAA           ATPase family associated with various cellular 
  ------ inclusion threshold ------
      0.015   14.5   0.0      0.032   13.4   0.0    1.5  1  NB-ARC        NB-ARC domain
       0.02   14.9   0.0       0.12   12.4   0.0    2.1  1  AAA_14        AAA domain
      0.028   13.8   0.0      0.047   13.1   0.0    1.3  1  TniB          Bacterial TniB protein
       0.03   14.0   0.0      0.048   13.4   0.0    1.4  1  AAA_24        AAA domain
      0.077   12.8   0.0       0.14   11.9   0.0    1.4  1  Bac_DnaA      Bacterial dnaA  protein
      0.091   13.0   0.0       0.17   12.1   0.0    1.4  1  AAA_28        AAA domain
       0.13   12.6   0.1       0.32   11.3   0.1    1.6  1  PBECR2        phage-Barnase-EndoU-ColicinE5/D-RelE like nucle
       0.14   10.9   0.0       0.19   10.4   0.0    1.2  1  RNA12         RNA12 protein
       0.17   11.4   0.0       0.35   10.4   0.0    1.5  1  AAA_7         P-loop containing dynein motor region


Domain annotation for each model (and alignments):
>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.4   0.1   1.1e-52   1.2e-49       1     233 []       7     231 ..       7     231 .. 0.95

  Alignments for each domain:
  == domain 1  score: 169.4 bits;  conditional E-value: 1.1e-52
                       ATPase_2   1 FfdRekelkeleeilerepneiyfiYGpegsGKtaLlkeiienledk.dk..yviyyialreesiskldefieeeeekkk 77 
                                    F++R+ke+++l++++++++++++++YGpeg+GKt+Llke++++ e+  ++    iy++al++es+sk+  +   +++++ 
  gi|119720249|ref|YP_920744.1|   7 FVNRVKEIDSLRSWCSSQRATPIYLYGPEGCGKTRLLKEFVSRFEEFfGEdaIAIYIDALERESLSKAFLS---SKSVRI 83 
                                    9*******************************************6642334599****************9...999999 PP

                       ATPase_2  78 lekalgiavpkaeleeilkeksklvfkaielllekikkkgkk...iiiiiDelqklidlglngaellvkeLlnliesltk 154
                                    ++++l++ v+++++ ++    ++l+++ ++l+ ++++k++ +   i i +D+++k++  gl++ el+vk+L++++++l++
  gi|119720249|ref|YP_920744.1|  84 ATETLLSLVERFSGLAV---GRALAESIVTLVEKALTKRKLEesyILIAVDDVAKAV--GLDQIELYVKWLYEAMWKLYE 158
                                    **************666...99*****************9999**************..********************* PP

                       ATPase_2 155 ekhlcvv..iclsSeglfiervyneselegrhkyilvddldketalnflkegfkel.eel...skedfeeiyryvGGkPk 228
                                    e++ + +   +++Seg +++       l+ rh++ ++  l     +n+ k+gf+el eel   s+ dfe+++r++GG+P+
  gi|119720249|ref|YP_920744.1| 159 EYKPRAInmAVTTSEGESLN-------LVLRHRHSYIALL-----WNLDKRGFEELfEELnppSSIDFETVWRLLGGNPG 226
                                    *****99999**********.......*************.....***********88889**9**************** PP

                       ATPase_2 229 alvel 233
                                    +lvel
  gi|119720249|ref|YP_920744.1| 227 KLVEL 231
                                    **986 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.0     2e-10   2.2e-07       1     145 [.       6     134 ..       6     158 .. 0.78

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 2e-10
                         AAA_16   1 rlvGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalaree 80 
                                    r+v R +e++ L+s  +   s+r   ++l+G+ G+GK++l++e+  ++e+     + +++          ++++al+re+
  gi|119720249|ref|YP_920744.1|   6 RFVNRVKEIDSLRSWCS---SQRATPIYLYGPEGCGKTRLLKEFVSRFEEF----FGEDAIA--------IYIDALERES 70 
                                    57888889988877544...444578*******************877754....3333444........49****9999 PP

                         AAA_16  81 llrqlldeaesaeleawrekleeala..avpelagaeasrllellkrllallsrderplvlvlDdlq 145
                                    l ++ l+    ++++ + e+l++ ++  ++ ++ +a+a+++  l+ ++l + + +e+ +++ +Dd+ 
  gi|119720249|ref|YP_920744.1|  71 LSKAFLSS---KSVRIATETLLSLVErfSGLAVGRALAESIVTLVEKALTKRKLEESYILIAVDDVA 134
                                    99999988...456666666666666666788888888***********777777888******986 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   3.9e-08   4.3e-05       4     102 ..      25     135 ..      22     156 .. 0.61

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 3.9e-08
                         AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee.........erpevvfvtlpsst...sskdllrellralglelka. 70 
                                    +a+ ++++G+ G+GKT+ll++++++++e  + e+         er ++ +  l+s++     ++ll+ + r         
  gi|119720249|ref|YP_920744.1|  25 RATPIYLYGPEGCGKTRLLKEFVSRFEE-FFGEDaiaiyidalERESLSKAFLSSKSvriATETLLSLVER-------Fs 96 
                                    67889*********************53.222223444444443333333333333333333333333333.......13 PP

                         AAA_22  71 ....erlsseellealeqalrarav...ielliiDEaqh 102
                                         r+  e +++++e+al +r+      l+ +D++ +
  gi|119720249|ref|YP_920744.1|  97 glavGRALAESIVTLVEKALTKRKLeesYILIAVDDVAK 135
                                    444445777777788888888888777777888887766 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   2.5e-06    0.0028       9     119 ..      25     142 ..      20     155 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.5e-06
                         AAA_19   9 kekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgaeatTiHrlal......ldfdd 82 
                                    +++++ + ++ G+GKTr+lk+ v+ ++e  g+++  i++ a+ + + ++   + +++  +++T+ +l +      +    
  gi|119720249|ref|YP_920744.1|  25 RATPIYLYGPEGCGKTRLLKEFVSRFEEFFGEDAIAIYIDALERESLSKAFLSSKSVRIATETLLSLVErfsglaV-GRA 103
                                    567899**************************************99999888888889999998888435555431.222 PP

                         AAA_19  83 lltealelleeaeeekklqeee.llivDEfqdvd.elqy 119
                                    l +  ++l+e+a +++kl+e + l+ vD +       q 
  gi|119720249|ref|YP_920744.1| 104 LAESIVTLVEKALTKRKLEESYiLIAVDDVAKAVgLDQI 142
                                    233344555577888999899989999998765445555 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   4.9e-06    0.0055       1      35 [.      29      62 ..      29      74 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.9e-06
                   RNA_helicase  1 iwlyGpsgeGKStlakeLakallkklklkkkdsvy 35
                                   i+lyGp+g+GK++l ke+++++++ ++++    +y
  gi|119720249|ref|YP_920744.1| 29 IYLYGPEGCGKTRLLKEFVSRFEEFFGEDA-IAIY 62
                                   89******************9998885553.5555 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.1e-05     0.013      16      49 ..      22     121 ..      14     206 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.1e-05
                     KAP_NTPase  16 tlatpivvgLygkWGsGKssllnkledelkefa............................................... 48 
                                    ++++ +++ Lyg+ G+GK+ ll+++ +  +ef                                                
  gi|119720249|ref|YP_920744.1|  22 SSQRATPIYLYGPEGCGKTRLLKEFVSRFEEFFgedaiaiyidalereslskaflssksvriatetllslverfsglavg 101
                                    569999**************************544444444444444444444444444444444444444444444444 PP

                     KAP_NTPase  49 ...................k 49 
                                                        
  gi|119720249|ref|YP_920744.1| 102 ralaesivtlvekaltkrkL 121
                                    44444444444444444442 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.9e-05     0.021       1      23 [.      29      51 ..      29     184 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.9e-05
                                   EEEESSTTSSHHHHHHHHHHHHT CS
                            AAA  1 vllyGppGtGKTllakavakelg 23
                                   ++lyGp G+GKT l k  ++ ++
  gi|119720249|ref|YP_920744.1| 29 IYLYGPEGCGKTRLLKEFVSRFE 51
                                   68**************9998853 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.8e-05     0.032      22     123 ..      28     144 ..       8     150 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.8e-05
                                    EEEEEESTTSSHHHHHHHHCCSHCCCCCCBTEEEEE......EEESXXHHHHHHHXXHHHHHCCCTTSSSS-STTS.... CS
                         NB-ARC  22 vvalvGmgGvGKttlakqilnksdevegrFdsvawv......vvsktdkseeiletilkeLslseddleekeeves.... 91 
                                     + l+G  G+GKt l+k+ ++ ++e  g+  + +++      ++sk + s++ ++   + L    +  +  + +      
  gi|119720249|ref|YP_920744.1|  28 PIYLYGPEGCGKTRLLKEFVSRFEEFFGEDAIAIYIdalereSLSKAFLSSKSVRIATETLLSLVERFSGLAVGRAlaes 107
                                    589***********************999889999999999988888776665553333332222222222222223334 PP

                                    HHHHHHHHCCCT.....TEEEEEEEE-SHHHH..... CS
                         NB-ARC  92 lkrklvrlLltk.....rfllvlDDVweeedwdkigv 123
                                    + + + ++L ++       l+  DDV + + +d+i +
  gi|119720249|ref|YP_920744.1| 108 IVTLVEKALTKRkleesYILIAVDDVAKAVGLDQIEL 144
                                    3333333443332222156777999999999998876 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00011      0.12       4      46 ..      28      74 ..      25     189 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00011
                         AAA_14  4 ilvitGaRrvGKTtllkqlikell...vkkesilyin.ldderdkkl 46
                                   ++ + G+  +GKT llk+++++      ++   +yi+ l++e+++k+
  gi|119720249|ref|YP_920744.1| 28 PIYLYGPEGCGKTRLLKEFVSRFEeffGEDAIAIYIDaLERESLSKA 74
                                   68899**************9877787555556677753455555433 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   4.2e-05     0.047      20      61 ..      11      52 ..       3      72 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.2e-05
                           TniB 20 lerLeeLleypkrkrmpnlllvGdsnnGKtmivekFarlhpp 61
                                   ++++++L ++ +++r   ++l+G+  +GKt ++++F ++ ++
  gi|119720249|ref|YP_920744.1| 11 VKEIDSLRSWCSSQRATPIYLYGPEGCGKTRLLKEFVSRFEE 52
                                   678899999***************************987655 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   4.3e-05     0.048       5      29 ..      29      61 ..      25     146 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.3e-05
                         AAA_24  5 iliyGpsgiGKTtlakel........gpkplfi 29
                                   i +yGp+g GKT l+ke+        g++++ i
  gi|119720249|ref|YP_920744.1| 29 IYLYGPEGCGKTRLLKEFvsrfeeffGEDAIAI 61
                                   88****************666666664444444 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00013      0.14      31      60 ..      23      52 ..      11      78 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00013
                                   TT.S--EEEE-SSSSSHHHHHHHHHHHHHH CS
                       Bac_DnaA 31 gkkynPlfiygevGlGktHLlkaignevle 60
                                    ++  P+++yg+ G Gkt Llk    + +e
  gi|119720249|ref|YP_920744.1| 23 SQRATPIYLYGPEGCGKTRLLKEFVSRFEE 52
                                   45789****************987666555 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00015      0.17       2      35 ..      29      62 ..      28      88 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00015
                         AAA_28  2 ivitGgestGKTtlleaLaargypvvpEaareil 35
                                   i++ G+e++GKT ll+++ +r  + + E a  i+
  gi|119720249|ref|YP_920744.1| 29 IYLYGPEGCGKTRLLKEFVSRFEEFFGEDAIAIY 62
                                   89***************99998877755444444 PP

>> PBECR2  phage-Barnase-EndoU-ColicinE5/D-RelE like nuclease2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00028      0.32      39      77 ..     250     294 ..     229     321 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00028
                         PBECR2  39 e....krgre.rylplLaetledPdeIwldeee.skklrrrylkr 77 
                                         k+ r+  ++++++ ++edPd Iw +    +++ +r++l+r
  gi|119720249|ref|YP_920744.1| 250 LvsvaKEVRGrGLVEQVKLIIEDPDNIWHRASVeMGEAERILLRR 294
                                    35554444553589999***********87776323444555554 PP

>> RNA12  RNA12 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00017      0.19       1      39 [.      10      47 ..      10      84 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00017
                          RNA12  1 RkekiedlkewleEnvntFivvkGPrGSGkkeLvldrvl 39
                                   R ++i++l++w + +  t i + GP G Gk+ L+ ++ +
  gi|119720249|ref|YP_920744.1| 10 RVKEIDSLRSWCSSQRATPIYLYGPEGCGKTRLL-KEFV 47
                                   7899***************************998.5444 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00031      0.35      31      58 ..      24      51 ..      10      63 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00031
                          AAA_7 31 knkkpvllvGptGtGKtviikdllkkld 58
                                   ++  p+ l+Gp+G+GKt ++k+++++++
  gi|119720249|ref|YP_920744.1| 24 QRATPIYLYGPEGCGKTRLLKEFVSRFE 51
                                   56789*****************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 2157.00
//
Query:       gi|119720250|ref|YP_920745.1|  [L=56]
Description: hypothetical protein Tpen_1345 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       751  (0.0418874); expected 358.6 (0.02)
Passed bias filter:                      589  (0.0328518); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 420.58
//
Query:       gi|119720251|ref|YP_920746.1|  [L=108]
Description: CopG family transcriptional regulator [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0018   18.1  10.0     0.0048   16.8   4.8    2.9  2  RHH_1     Ribbon-helix-helix protein, copG family
      0.004   17.1   1.6       0.01   15.7   1.6    1.7  1  BAT       GAF and HTH_10 associated domain
  ------ inclusion threshold ------
      0.012   15.6   0.9       0.23   11.5   0.1    2.7  2  RHH_3     Ribbon-helix-helix domain
      0.026   14.6   0.1      0.033   14.2   0.1    1.2  1  Band_7    SPFH domain / Band 7 family
      0.045   14.4   0.2       0.09   13.4   0.2    1.6  1  RHH_6     Ribbon-helix-helix domain
       0.08   12.8   1.6        9.4    6.2   0.1    2.6  4  RHH_5     CopG-like RHH_1 or ribbon-helix-helix domain, RHH_5


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   4.8   1.6e-06    0.0048       1      37 [.       3      42 ..       3      44 .. 0.87
   2 ?    2.8   0.2     0.042   1.2e+02      10      22 ..      64      76 ..      62      80 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.6e-06
                                   EEEEEEEHHHHHHHHHHHHHHTSSH...HHHHHHHHHHHH CS
                          RHH_1  1 rvsirldeellerLdelarrrgrSr...SelIReAlreyl 37
                                   r+++++d++l+erL++ a+++  Sr   S ++++Alr yl
  gi|119720251|ref|YP_920746.1|  3 RLTVSIDDDLAERLRRAAEALYGSRrrvSRVVEDALRSYL 42
                                   89*****************986665555999999999998 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.042
                                   HHHHHHHHHHHHT CS
                          RHH_1 10 llerLdelarrrg 22
                                   ++++L ela++++
  gi|119720251|ref|YP_920746.1| 64 EAKTLSELAAKLR 76
                                   5788888888875 PP

>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   1.6   3.5e-06      0.01      46     107 ..      29      89 ..       2      93 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.5e-06
                            BAT  46 tvdgadpeevrdaaedldavedvrvvseeddgtlleltvsgpslastlaehGgtvrsaeaed 107
                                    +v+++  +++r+ +++l+  e+vr ++  +++tl e+++  + la+ l e G+ +r +++ +
  gi|119720251|ref|YP_920746.1|  29 RVSRVVEDALRSYLASLEIEENVRYLAVKGGETLAEAKT-LSELAAKLRELGVDTRGVRIVR 89 
                                    577788999*****************************7.899*************999865 PP

>> RHH_3  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   7.5e-05      0.23       4      41 ..       3      43 ..       2      46 .. 0.80
   2 ?    1.0   0.1      0.14   4.2e+02      12      21 ..      70      79 ..      66      83 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.5e-05
                          RHH_3  4 rttvsidpelaekLkaLSekT...rIprSklldeAiellLe 41
                                   r tvsid++lae+L+   e++   r ++S+ ++ A+  +L+
  gi|119720251|ref|YP_920746.1|  3 RLTVSIDDDLAERLRRAAEALygsRRRVSRVVEDALRSYLA 43
                                   789************99998766666777777777777776 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.14
                          RHH_3 12 elaekLkaLS 21
                                   ela+kL++L 
  gi|119720251|ref|YP_920746.1| 70 ELAAKLRELG 79
                                   8999999985 PP

>> Band_7  SPFH domain / Band 7 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   1.1e-05     0.033      88     146 ..      25      89 ..       2      98 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.1e-05
                         Band_7  88 nldnlirrvlesalrevisemtleell.....sn.reelaeelknelneqlrkyGvevldvritd 146
                                      ++ ++rv+e+alr++++++++ee +     ++      ++   el+++lr++Gv   +vri +
  gi|119720251|ref|YP_920746.1|  25 GSRRRVSRVVEDALRSYLASLEIEENVrylavKGgETLAEAKTLSELAAKLRELGVDTRGVRIVR 89 
                                    467889*****************9999677663324555678899************99999765 PP

>> RHH_6  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2     3e-05      0.09       3      52 ..       2      50 ..       1      63 [. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3e-05
                          RHH_6  3 vrwnvavspetdqavrafLAsqGggrkGdLSrfieeAVrayllelaveea 52
                                   +r++v++ +++ + +r    +  g r+   Sr +e+A r+yl +l +ee 
  gi|119720251|ref|YP_920746.1|  2 ARLTVSIDDDLAERLRRAAEALYGSRRR-VSRVVEDALRSYLASLEIEEN 50
                                   5788888888888887655444455555.9***************99985 PP

>> RHH_5  CopG-like RHH_1 or ribbon-helix-helix domain, RHH_5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1    0.0031       9.4       2      22 ..       2      22 ..       1      24 [. 0.90
   2 ?   -2.5   0.0       1.6   4.8e+03      35      40 ..      34      39 ..      26      46 .. 0.75
   3 ?   -3.2   0.0       2.7   8.1e+03      28      40 ..      40      52 ..      38      54 .. 0.66
   4 ?    5.3   0.0    0.0061        18      22      42 ..      63      83 ..      60      84 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0031
                          RHH_5  2 kRvnvtLPeelleeLeewAde 22
                                    R +v+  ++l e+L++ A++
  gi|119720251|ref|YP_920746.1|  2 ARLTVSIDDDLAERLRRAAEA 22
                                   59999999***********86 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.6
                          RHH_5 35 vekalr 40
                                   ve+alr
  gi|119720251|ref|YP_920746.1| 34 VEDALR 39
                                   666766 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 2.7
                          RHH_5 28 SnlaafLvekalr 40
                                   S la++ +e+ +r
  gi|119720251|ref|YP_920746.1| 40 SYLASLEIEENVR 52
                                   5567776777666 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.0061
                          RHH_5 22 eegRsvSnlaafLvekalrea 42
                                   +e  ++S laa L e +++++
  gi|119720251|ref|YP_920746.1| 63 AEAKTLSELAAKLRELGVDTR 83
                                   6889*********99999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.38u 0.29s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 793.52
//
Query:       gi|119720252|ref|YP_920747.1|  [L=370]
Description: hypothetical protein Tpen_1347 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.5e-99  333.2   1.0    1.7e-99  333.0   1.0    1.0  1  DUF917      Protein of unknown function (DUF917)
  ------ inclusion threshold ------
      0.095   12.6   0.1       0.54   10.2   0.1    2.1  2  LeuA_dimer  LeuA allosteric (dimerisation) domain


Domain annotation for each model (and alignments):
>> DUF917  Protein of unknown function (DUF917)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  333.0   1.0  1.9e-103   1.7e-99       4     350 .]      11     358 ..       8     358 .. 0.97

  Alignments for each domain:
  == domain 1  score: 333.0 bits;  conditional E-value: 1.9e-103
                                    HHHHHHHHHTTTT-SS-HHHHHHHHTT-SBTT.--EEEE-GGG--SEE..EEEEEEE-HHHHTT-SS-HH.......HHH CS
                         DUF917   4 ealatGaavLGtGGGGspysgylllrqaleeg.ksvrvvsldelpddalvvvvgamGsptvieeklpsgd...elleave 79 
                                    +al+ Ga++LGtGGGGsp+ g   + +al++g + vr+v++ elp++ + v+++ +Gs+++++    + +    l++ave
  gi|119720252|ref|YP_920747.1|  11 RALVLGATILGTGGGGSPSRGLAAILDALRRGlP-VRIVDVGELPEEGFAVTAYNVGSIAPGAAAARERRiadPLRRAVE 89 
                                    7899**************************9977.************************9988776544455599***** PP

                                    HHHHHHT--EEEEE-SSSSCCHHHHHHHHHHHHT-EEESB-SSSS--SSGGGSHHHHTT----SEEEE-SSS-EEEEEE. CS
                         DUF917  80 alekllgrkidavislEiGGlNglvallaaaklglpvvDaDgmGRAfPelqqttfavagisltPlaladekgnvvllkka 159
                                    +lek+lg +++a+++ E+GG+N+++al +aa+lg+p vD+D++GRA Pe++q++  vag++l+P+a ++++g+vv++k++
  gi|119720252|ref|YP_920747.1|  90 ELEKVLGGRVAAIVPNEMGGGNTAAALSLAAELGVPAVDGDLVGRAAPEVHQCSAIVAGVPLCPSAAVTASGDVVVVKEY 169
                                    *******************************************************************************9 PP

                                    ---HHHHHHHHHHCTTTTTEEEEEEEEE-HHHHHH--SBSHHHHHHHHHHHHHTT--...-SHHHHHHHHHH-EEEEEEE CS
                         DUF917 160 qsdkavErllRaalvemgsfagvaaypmtgaelkraavpgtlslalriGravaearea.kdvveailealgggakvlfkG 238
                                    +s + +E ++R++ v  g++a+va+ pm+  e+ ra+v+gt+s+a+r+G+ v +are+ + +v+a ++alg g++ +f+G
  gi|119720252|ref|YP_920747.1| 170 ASIDDYEAVVRHLSVLGGGRAAVADTPMRRGEAARAVVRGTVSRAMRVGEEVLRAREEgRGPVAAATRALG-GWR-VFEG 247
                                    99989***************************************************9988***********.899.**** PP

                                    EE--------------EEEET.......EEEEEEESSSEEEEE..ET-SEETTSEEEEEHHB-SSSSB-TTTT.TS-EEE CS
                         DUF917 239 kivdverrteggfdvgevtiegldedegrelkiefqNEnllaeedgevlatvPDlIsvldaetgepigteelryGlrVtV 318
                                     +  +e+r+eggf +ge++++g++e++gr+l+ +++NE++++++dge++++ PDl s+l +++gep+++ el+ G +V+ 
  gi|119720252|ref|YP_920747.1| 248 VVERYEWRDEGGFLLGEAVVRGTGEYRGRTLRTWIKNEHIMVWVDGEPAVMPPDLFSLL-RDDGEPVTNTELKVGDKVHG 326
                                    ***********************************************************.9******************* PP

                                    EEE---GGGS..SHHHH-S-....-....--- CS
                         DUF917 319 lalpasekwrteeglelvgPkaFGydleykpl 350
                                    +a +a+e wrt+egl+++gP++FG+d++y+p+
  gi|119720252|ref|YP_920747.1| 327 VAAKAPEIWRTPEGLRYFGPRHFGFDYDYVPV 358
                                    ******************************97 PP

>> LeuA_dimer  LeuA allosteric (dimerisation) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.13   1.2e+03      62      94 ..      33      76 ..      22      81 .. 0.69
   2 ?   10.2   0.1     6e-05      0.54      42      68 ..     214     239 ..     188     252 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.13
                                   HHHHHHHHHHHHHT-...........EEEEEEEE--TT-TT--E CS
                     LeuA_dimer 62 dAllnAlrkalgvdi...........kLldYsvhaitegtdaqa 94
                                   +A+l+Alr+ l v i            ++ Y+v +i  g+ a  
  gi|119720252|ref|YP_920747.1| 33 AAILDALRRGLPVRIvdvgelpeegfAVTAYNVGSIAPGAAAAR 76
                                   67788888777663333344455555888888888888877765 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 6e-05
                                    EEEE.TTEEEEEEEE-SSHHHHHHHHH CS
                     LeuA_dimer  42 klevkdgeekeasaeGnGpvdAllnAl 68 
                                    +++v ++e   a+ eG Gpv+A+ +Al
  gi|119720252|ref|YP_920747.1| 214 AMRV-GEEVLRAREEGRGPVAAATRAL 239
                                    3344.677799***************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2819.12
//
Query:       gi|119720253|ref|YP_920748.1|  [L=461]
Description: hypothetical protein Tpen_1348 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0031   17.8   0.0      0.068   13.5   0.0    2.6  2  DUF4177   Domain of unknown function (DUF4177)


Domain annotation for each model (and alignments):
>> DUF4177  Domain of unknown function (DUF4177)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   3.8e-06     0.068      29      64 ..      77     117 ..      73     118 .. 0.87
   2 ?    1.1   0.0     0.028   5.1e+02      53      64 ..     176     187 ..     163     188 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.8e-06
                        DUF4177  29 ilnelAkeGWrlvsii....pvk.esrgvgaaesilliFeR 64 
                                    ++n+ A +GWrl++ +    pv  +   v +++ ++++FeR
  gi|119720253|ref|YP_920748.1|  77 AINASAPKGWRLKTLMvngsPVLpGVAKVYGNTTVEAVFER 117
                                    69************999999555488888888899*****9 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.028
                        DUF4177  53 gaaesilliFeR 64 
                                     +++s+ll+FeR
  gi|119720253|ref|YP_920748.1| 176 SSNSSLLLVFER 187
                                    568999*****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (461 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 3407.47
//
Query:       gi|119720254|ref|YP_920749.1|  [L=280]
Description: xylose isomerase domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.6e-30  105.0   0.5    4.6e-30  104.6   0.5    1.1  1  AP_endonuc_2    Xylose isomerase-like TIM barrel
     0.0014   18.3   0.0     0.0031   17.2   0.0    1.6  1  AP_endonuc_2_N  AP endonuclease family 2 C terminus
  ------ inclusion threshold ------
       0.13   11.7   0.0       0.36   10.2   0.0    1.6  2  ComA            (2R)-phospho-3-sulfolactate synthase (ComA)


Domain annotation for each model (and alignments):
>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.6   0.5   7.7e-34   4.6e-30       2     210 .]      27     236 ..      26     236 .. 0.95

  Alignments for each domain:
  == domain 1  score: 104.6 bits;  conditional E-value: 7.7e-34
                                    HHHHHCT-SEEEEECCTCSHHHHCHHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCSHHHHHHHHHHHHHHHHH CS
                   AP_endonuc_2   2 aaaaeaGfdgvElfgrdlvpvselsdeelrelrkaldelglriaslslftrfgypdederearreesvdalkraielaaa 81 
                                    ++a e Gf gvE+  +   + ++   ++l+e+r+ + e+gl+i ++ l+++f  pd  erea+    v+++ +++  a++
  gi|119720254|ref|YP_920749.1|  27 RRAYEDGFAGVEVLVDHVESRAR---SYLKEVRRFAFEHGLEIYAVALHNNFVRPDPAEREAE----VKRVVEWLNVAYE 99 
                                    678889***************95...8******************************999999....************* PP

                                    HTBSEEEEEBCC................GBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEEEEE--TTTTSSSTCHHHH CS
                   AP_endonuc_2  82 LGapllvlhpGt................agagpkgseeeawerlaeslneladyaekegvklalEtlagsgvelgdeela 145
                                    LGa+++ + +G+                 + +++ se++a+e +++ l +++d ae+ gv ++lE+++g ++    e+++
  gi|119720254|ref|YP_920749.1| 100 LGADVVRVDSGRwgtvksfdelmarrgvEPPLEGYSEDDAVEWVVDCLYRCLDAAEELGVIVGLENHWGLTT-RA-ETML 177
                                    ****************************999****************************************6.55.**** PP

                                    HHHHHHTTTTEEEEEEHHHHHHHTTTHHHHHHHHHGGEEEEEE.EESSTTTTSSTTEESTTSSSS CS
                   AP_endonuc_2 146 rlldavdspnvgvclDtgHlliaeedvddalraladrikhvHikDakgdlgagrdrhvpigeGei 210
                                    +++++v+s+++gv++Dtg+++    d +++l+a+a++  +vH+k ++g   +g+++ + ++ G i
  gi|119720254|ref|YP_920749.1| 178 KIVRRVSSRWFGVVMDTGNFV---HDTYSELEAIAPYAVMVHAKTYFG---GGVWYTLDLDYGRI 236
                                    *********************...56*****************76666...99999999988875 PP

>> AP_endonuc_2_N  AP endonuclease family 2 C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   5.1e-07    0.0031       1      23 [.     232     254 ..     232     271 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 5.1e-07
                 AP_endonuc_2_N   1 dwkdifsaLrqiGYdgplSiEwE 23 
                                    d+ +if +Lr+ G++g++S+E+E
  gi|119720254|ref|YP_920749.1| 232 DYGRIFGMLRRHGFKGWVSLEYE 254
                                    5779******************9 PP

>> ComA  (2R)-phospho-3-sulfolactate synthase (ComA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   6.1e-05      0.36      84     174 ..      22     116 ..      13     128 .. 0.79
   2 ?   -0.7   0.0      0.13   8.1e+02     106     158 ..     169     224 ..     113     229 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 6.1e-05
                                    HHHHHHHHHHCT-SEEEE--SSS---HHHHHHHHHHHC.CTTSEEEEEES-SSH.....HHHTT--CCHHHHHHHHHHHH CS
                           ComA  84 vdeyleeckelgfdviEvsdgtlelpeeeklrliekak.keglkvlpevgkkdg.....elesesdveklieeakrdlea 157
                                    ++eyl+++ e gf  +Ev    +e   +  l+ +++++ ++gl++ + v  +++       e+e +v++++e ++   e 
  gi|119720254|ref|YP_920749.1|  22 LREYLRRAYEDGFAGVEVLVDHVESRARSYLKEVRRFAfEHGLEIYA-VALHNNfvrpdPAEREAEVKRVVEWLNVAYEL 100
                                    679****************9999988888777777765377887654.3333333566678899**************** PP

                                    TECEEEE--TTT--SST CS
                           ComA 158 GaekviiEaresGiteg 174
                                    Ga++v +++   G+ ++
  gi|119720254|ref|YP_920749.1| 101 GADVVRVDSGRWGT-VK 116
                                    ********987787.33 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.13
                                    S---HHHHHHHHHHHCCTTSEEEEEES-SSHHHHTT...--CCHHHHHHHHHHHHT CS
                           ComA 106 lelpeeeklrliekakkeglkvlpevgkkdgelese...sdveklieeakrdleaG 158
                                    l+   e++l+++++++++ + v++ +g   ++  se   + ++ ++ +ak  +  G
  gi|119720254|ref|YP_920749.1| 169 LTTRAETMLKIVRRVSSRWFGVVMDTGNFVHDTYSEleaIAPYAVMVHAKTYFGGG 224
                                    44456777888888888888888777774442233333355555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2010.77
//
Query:       gi|119720255|ref|YP_920750.1|  [L=473]
Description: amidohydrolase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-08   34.5   0.0    2.4e-08   33.9   0.0    1.4  1  Peptidase_M20  Peptidase family M20/M25/M40
    2.7e-07   30.5   0.0      8e-07   28.9   0.0    1.7  1  M20_dimer      Peptidase dimerisation domain


Domain annotation for each model (and alignments):
>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.0   2.7e-12   2.4e-08       4     149 ..      78     315 ..      75     417 .. 0.82

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 2.7e-12
                                    EES-BSS.TTCG.GGSSSTTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTTTHHHHH CS
                                    xxxxxxx.xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M20   4 sHlDvVp.eeet.dgwttpfslteedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggrgGakal 81 
                                    + +D++p   ++   w++p  +  + G  +G+G++ + ++ +aa+ a++a  ++ + + gt+++   p+EE   +G   +
  gi|119720255|ref|YP_920750.1|  78 GEYDALPgLSQKvVPWREPLVPGAP-G--HGCGHNIHGASGMAAALAVKAAMEREG-LGGTVKFFGCPAEENF-SGKVFM 152
                                    6789999433332335555555555.7..***************999987766654.479***********54.999999 PP

                                    HH.HHHTTTCESEEEEEEEESSSBTCHSTETEEEE............................................. CS
                                    xx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................................. RF
                  Peptidase_M20  82 le.gleerekvdavfelhieepgileagklaigvv............................................. 115
                                    +  g++  e+vdav++ h   pg ++a +l+  +                                              
  gi|119720255|ref|YP_920750.1| 153 VRdGVF--EGVDAVLSHH---PGDMNAATLKSSLAvnsarfhfygrashagaspeegrsaldavqlmnigvefmrehlpq 227
                                    998888..69***99777...77777555444444789999999999999999999999999999999999999999999 PP

                                    ........................................................EEEEEEEEEESHEEECCHHHHHHH CS
                                    ........................................................xxxxxxxxxxxxxxxxxxxxxxxx RF
                  Peptidase_M20 116 ........................................................kvevelleggapvtlndsplvkal 139
                                                                                            +veve+leg +    n   l++++
  gi|119720255|ref|YP_920750.1| 228 darvhyvvergggqpnvvpeyarawyyvrapereeveriyswvvdiargaalmtqtRVEVEFLEGVYNLLPN-RVLAELV 306
                                    999999999999999999999999999999999999999999999999999999865888877777766666.7777777 PP

                                    HHHHHHHHTS CS
                                    xxxxxxxxxx RF
                  Peptidase_M20 140 aeaaeelfge 149
                                       ++e+ g+
  gi|119720255|ref|YP_920750.1| 307 VGNMREV-GL 315
                                    7777776.63 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0     9e-11     8e-07       8     102 ..     185     275 ..     179     279 .. 0.88

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 9e-11
                                    EEEEEEE-B-EEGG.-TTTTB-HHH..HHHHHHHCSCTTEEC.....TCCTCCCCCEECCE-CCCCEESSEEEEEEEEEH CS
                      M20_dimer   8 ggkitvkgkagHsg.apgagaNAie..klarllaeledeegdiaeerslprttlnvtgiegGsaknvipdeaeakidiRl 84 
                                    +++ ++ g+a H+g  p+ g++A+   +l+ +  e+  e+ ++          +   + +gG ++nv+p++a+a++ +R 
  gi|119720255|ref|YP_920750.1| 185 SARFHFYGRASHAGaSPEEGRSALDavQLMNIGVEFMREHLPQD-------ARVHYVVERGGGQPNVVPEYARAWYYVRA 257
                                    678899******************99999999999999966654.......788888888888***************** PP

                                    HHHHHHHHHHHHHHHHHT CS
                      M20_dimer  85 lpgedpeevleeieeile 102
                                    +  e++e++   +++i++
  gi|119720255|ref|YP_920750.1| 258 PEREEVERIYSWVVDIAR 275
                                    *******99888887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (473 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 3390.25
//
Query:       gi|119720256|ref|YP_920751.1|  [L=311]
Description: abortive infection protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-05   25.4  15.2    1.3e-05   25.4  15.2    2.9  2  CPBP      CPBP intramembrane metalloprotease


Domain annotation for each model (and alignments):
>> CPBP  CPBP intramembrane metalloprotease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4  15.2   7.4e-10   1.3e-05       8      91 ..     140     238 ..       3     239 .. 0.90
   2 ?   -3.5   0.3      0.79   1.4e+04      41      47 ..     269     275 ..     257     280 .. 0.48

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 7.4e-10
                                    HHHHHHHHHHHHHHHHTTCHHHHHHHH.S-HHHHHHHHHHHHHCSGGG................HHHHHHHHHHHHHHHH CS
                           CPBP   8 fllalllapllEEllfRglllqllqergsstlailissilFglaHlpn................gpsvllaalaGlvlgy 71 
                                    ++ +    +l+EEl++Rg+ ++ll    + + ++l+ +++++l+H+p                  p+ +l+++a   l +
  gi|119720256|ref|YP_920751.1| 140 AVTVNAALALGEELGWRGYAYRLLGGEPG-LKSTLVVGVAWALWHAPAtillgynypesrllglLPYSALLSAATYPLLL 218
                                    4445566678**************99955.99****************77776666666655554455888888888999 PP

                                    HHHHTT-HHHHHHHHHHHHH CS
                           CPBP  72 lylktgsllaaillHallnl 91 
                                    ++  +gs+l+a+ lH+++n+
  gi|119720256|ref|YP_920751.1| 219 ATTASGSVLPAASLHGAMNA 238
                                    9999***************8 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 0.79
                                    HHHHHHH CS
                           CPBP  41 ilissil 47 
                                     +++ +l
  gi|119720256|ref|YP_920751.1| 269 AIVAVAL 275
                                    1222233 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.55
# Mc/sec: 1716.05
//
Query:       gi|119720257|ref|YP_920752.1|  [L=854]
Description: DEAD/DEAH box helicase domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.4e-29  102.3   0.0      2e-28   99.3   0.0    2.0  2  DEAD        DEAD/DEAH box helicase
    2.6e-15   56.7   0.0    7.2e-15   55.3   0.0    1.7  2  Helicase_C  Helicase conserved C-terminal domain
    2.6e-08   34.1   0.0    4.8e-08   33.2   0.0    1.4  1  ResIII      Type III restriction enzyme, res subunit
     0.0041   17.4   0.0       0.01   16.1   0.0    1.6  1  AAA_22      AAA domain
  ------ inclusion threshold ------
      0.012   16.0   0.1      0.033   14.6   0.1    1.8  1  AAA_16      AAA ATPase domain
      0.014   15.7   0.0      0.033   14.5   0.0    1.6  1  AAA_19      AAA domain


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.3   0.0   6.7e-32     2e-28       1     170 [.      78     255 ..      78     260 .. 0.85
   2 ?    0.4   0.0      0.16   4.9e+02      47     105 ..     308     367 ..     295     379 .. 0.77

  Alignments for each domain:
  == domain 1  score: 99.3 bits;  conditional E-value: 6.7e-32
                                    -HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHS....TTSTS-EEEEEESSHHHHHHHHHHHHHHTTT.ST CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx RF
                           DEAD   1 tdiQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyet....kgktgpkalivePtreLaeqtlnnlkkfkky.id 75 
                                    t+iQ   ip il+g++vl+ a+TGsGKT+++++pvl+ ++ +    + ++g  +l+++P+r+L+ +++++l+++    ++
  gi|119720257|ref|YP_920752.1|  78 TPIQVLGIPRILRGENVLLVAPTGSGKTECAFLPVLHFLAAEreagRLEPGVYVLYITPLRALCSDVARRLRSYVRSaLG 157
                                    79**********************************99988799999*****************************7555 PP

                                    ..SEEEEEETTSSHHHHHHHHHTT.CSEEEEEHHHHHHHHHCTS.SH..CTTEEEEEEETHHHHHHTTTHHHHHHHHHHS CS
                                    ..xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx.xx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  76 ..lrvlliiggvaardqlskldng.vdivvgtpgrlddllstgk.ln..lsqvrflVlDEadrlldqgfsdfinrilnql 149
                                      + v  + + + ++++++kl ++ + ++v+tp+ l  +l+t++ ++  l ++r++++DE+++l +++++ ++  +l++l
  gi|119720257|ref|YP_920752.1| 158 dgYLV-GVWHADIKKNEKTKLAEKpPLVLVTTPESLEAILDTKHrFRkhLAKLRWVIVDEVHELAESKRGLHLLVLLERL 236
                                    33233.445566677777788655699*************544434355******************************* PP

                                    HHHCTTSTTTSEEEEEESSBS CS
                                    xxxxxxxxxxxxxxxxxxxxx RF
                           DEAD 150 pqitcdgklqrqvivlSATlp 170
                                    + +    +lq   i++SAT+ 
  gi|119720257|ref|YP_920752.1| 237 KATFGIPRLQ--RILISATVG 255
                                    6655554477..*******86 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.16
                                    S-EEEEEESSHHHHHHHHHHHHHHTTTST.SEEEEEETTSSHHHHHHHHH.TTCSEEEEEH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                           DEAD  47 gpkalivePtreLaeqtlnnlkkfkkyid.lrvlliiggvaardqlskld.ngvdivvgtp 105
                                    g   l+ + tr+ ae+ + +l+k++   d l  +  +g +++r+  +k++ ++v+ vv t 
  gi|119720257|ref|YP_920752.1| 308 GSGYLVFVNTRSEAEELHAELEKRGLG-DiLVHHGSMGASKRREAERKFKdREVKAVVCTR 367
                                    456789999999999999999999997.414444677877777777777526699999986 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       3.7   1.1e+04      40      61 ..     159     180 ..     139     187 .. 0.75
   2 !   55.3   0.0   2.4e-18   7.2e-15      10     107 ..     301     400 ..     293     404 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3.7
                                    TSTEEEESTTSTHHHHHHHHHH CS
                     Helicase_C  40 gikvavlhgelpqnereeileq 61 
                                    g+ v v h+++++ne+ +  e+
  gi|119720257|ref|YP_920752.1| 159 GYLVGVWHADIKKNEKTKLAEK 180
                                    7788899999999999988776 PP

  == domain 2  score: 55.3 bits;  conditional E-value: 2.4e-18
                                    H.HHTTTTSEEEEEESSHHHHHH.HHHHHHHT.TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTES CS
                     Helicase_C  10 l.kleeeggkilifvntidrlek.vklllekk.gikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvn 86 
                                    l +l  +g+  l+fvnt++++e+    l ek+    ++v+hg++ +++r+e+ ++f++ e++ +++t+ +e Gid+ +v+
  gi|119720257|ref|YP_920752.1| 301 LeELMGKGSGYLVFVNTRSEAEElHAEL-EKRgLGDILVHHGSMGASKRREAERKFKDREVKAVVCTRTLELGIDVGSVE 379
                                    33445888999********998654444.4553689******************************************** PP

                                    EEEESSSSSSHHHHHHHHTTS CS
                     Helicase_C  87 lVinfdlprnvtsyiqriGRt 107
                                     V++++ p  ++ + qr+GR+
  gi|119720257|ref|YP_920752.1| 380 RVFQVGSPSLPAYFAQRVGRA 400
                                    ********************8 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   0.0   1.6e-11   4.8e-08      23     148 ..      90     224 ..      58     255 .. 0.75

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 1.6e-11
                                    TTSEEEEEESTTSTHHHHHHHHHHHH-S............-EEEEESSHHHHHHHHHHGGGGTGG...........GEEE CS
                         ResIII  23 rdkrglikmaTGtGKTlvaaklierllkkgkee.......kflflvprkslleqtleefkkflseayke.......igkk 88 
                                    r +++l++++TG+GKT +a+  + ++l +++e         +l + p ++l++   ++++++  +a  +       +   
  gi|119720257|ref|YP_920752.1|  90 RGENVLLVAPTGSGKTECAFLPVLHFLAAEREAgrlepgvYVLYITPLRALCSDVARRLRSYVRSALGDgylvgvwH--- 166
                                    567899********************99988889*****************************99998899555542... PP

                                    ESSS-B--.........-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T CS
                         ResIII  89 vsgdkkka..kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk 148
                                       d kk+  ++ +++   +lvtt +sl a+++++  ++ ++   +   +i+DE+H l+++k
  gi|119720257|ref|YP_920752.1| 167 --ADIKKNekTKLAEKPPLVLVTTPESLEAILDTK--HRFRKHLAKLRWVIVDEVHELAESK 224
                                    ..444444222235777889************443..333333334449*********9975 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   3.5e-06      0.01       8     118 ..      94     236 ..      89     255 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.5e-06
                         AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee.erpevvfvtlpsstsskdllrellralglelka................ 70 
                                    +++++++G+GKT ++   +  + +++  +   +p+v+  +++ +     l+++++r l +   +                
  gi|119720257|ref|YP_920752.1|  94 VLLVAPTGSGKTECAFLPVLHFLAAEREAGrLEPGVYVLYITPLR---ALCSDVARRLRSYVRSalgdgylvgvwhadik 170
                                    689***********9876666544333333566666644444444...444444444444443444457788******** PP

                         AAA_22  71 .................erlsseellealeqalraravielliiDEaqhlr.seealeeLrsllnl 118
                                                      + s+e++l++ ++  ++ a+ + +i+DE++ l  s++ l  L+ l  l
  gi|119720257|ref|YP_920752.1| 171 knektklaekpplvlvtTPESLEAILDTKHRFRKHLAKLRWVIVDEVHELAeSKRGLHLLVLLERL 236
                                    ****************99999999999999999999999***********9866666666555443 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   1.1e-05     0.033      20     164 ..      87     238 ..      66     250 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.1e-05
                         AAA_16  20 rsgrpelvllsGesGvGKsslv....rellralekd......ggiflrgkcdqlesaipy.salaqalareellrqllde 88 
                                    r  r+e+vll+ + G+GK+  +     ++l a+e++      g+++l+ +  +      + s +a+ l r +++r  l +
  gi|119720257|ref|YP_920752.1|  87 RILRGENVLLVAPTGSGKTECAflpvLHFL-AAEREagrlepGVYVLYITPLRA-----LcSDVARRL-R-SYVRSALGD 158
                                    333559**************9985445555.44444688887777766666666.....336689999.7.888888877 PP

                         AAA_16  89 aesaeleawrekleeala....avpelagaea.srllellkrllallsrderplvlvlDdlqwadeaslql.laaLlrll 162
                                        +++ w++ ++++ +    + p+l      ++l + l    ++ ++ ++   +++D+++ + e+ + l l  Ll++l
  gi|119720257|ref|YP_920752.1| 159 --GYLVGVWHADIKKNEKtklaEKPPLVLVTTpESLEAILDTKHRFRKHLAKLRWVIVDEVHELAESKRGLhLLVLLERL 236
                                    ..457999999999998865553333333333755555555555555555556789**********99999888888887 PP

                         AAA_16 163 es 164
                                    ++
  gi|119720257|ref|YP_920752.1| 237 KA 238
                                    65 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.1e-05     0.033       8     121 ..      89     227 ..      84     257 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.1e-05
                         AAA_19   8 lkekvllvtaGpGtGKTrvlkhivallvelggvkp.....eeillvaftgrAakelrerlaalgaeatTiHrlal..... 77 
                                    l+ +++l++a+ G+GKT++    v +++++++++        +l +++ +  ++ ++ rl+++ ++a    +l       
  gi|119720257|ref|YP_920752.1|  89 LRGENVLLVAPTGSGKTECAFLPVLHFLAAEREAGrlepgVYVLYITPLRALCSDVARRLRSYVRSALGDGYLVGvwhad 168
                                    567899***********99666665555555443344446789999****99********99999966655553333333 PP

                         AAA_19  78 ..............ldfddlltealelle..............eaeeekklqeeellivDEfqdvdelqyrL 121
                                                  l                            +++ +k+l +  ++ivDE+ ++ e    L
  gi|119720257|ref|YP_920752.1| 169 ikknektklaekppL-------------VlvttpesleaildtKHRFRKHLAKLRWVIVDEVHELAESKRGL 227
                                    334333333334440.............044444445555556778889996666********998766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (854 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.74u 0.29s 00:00:01.03 Elapsed: 00:00:00.48
# Mc/sec: 5378.16
//
Query:       gi|119720258|ref|YP_920753.1|  [L=277]
Description: hypothetical protein Tpen_1353 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.6e-06   26.6   0.8    8.9e-06   25.9   0.8    1.4  1  HD        HD domain


Domain annotation for each model (and alignments):
>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.8     5e-10   8.9e-06      28      95 ..      74     136 ..      46     178 .. 0.82

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 5e-10
                                    HHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHHHHH..HHHHHHHHHTTCCHHHHH CS
                             HD  28 lllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrlgld..ledvaklirehheswegk 95 
                                    +l aaLlHD+Gk +++ + e++       ++H + +a ++++v+ r g+      va +++ hhe   ++
  gi|119720258|ref|YP_920753.1|  74 VLDAALLHDVGKLTEE-YVERAY------HYHNFASAVVAEDVLARMGVGedRFVVASAVLLHHEARHWE 136
                                    6679**********77.666653......69****************99999999*********998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1880.19
//
Query:       gi|119720259|ref|YP_920754.1|  [L=566]
Description: CRISPR-associated helicase Cas3 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.4e-11   42.9   0.0    8.2e-11   42.0   0.0    1.4  1  DEAD        DEAD/DEAH box helicase
    3.4e-07   30.6   0.0    5.5e-07   29.9   0.0    1.3  1  Helicase_C  Helicase conserved C-terminal domain
     0.0048   16.6   0.1      0.018   14.7   0.1    2.0  1  Get5_C      Get5 C-terminal domain
     0.0095   16.0   0.0      0.016   15.2   0.0    1.3  1  ResIII      Type III restriction enzyme, res subunit
  ------ inclusion threshold ------
      0.058   13.8   0.3       0.26   11.6   0.3    2.3  1  AAA_16      AAA ATPase domain
        0.1   11.3   0.0       0.18   10.5   0.0    1.3  1  SNF2_N      SNF2 family N-terminal domain


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.0   0.0   2.7e-14   8.2e-11      15     170 ..      39     197 ..      27     203 .. 0.72

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 2.7e-14
                                    CEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEE...EEETTSSHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxx RF
                           DEAD  15 gdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvl...liiggvaardql 91 
                                    + v+v+a+TG GKT+a+  p ++  ++  +++    ++  Ptr+La  +l++l++++  ++ ++    l +gg    + +
  gi|119720259|ref|YP_920754.1|  39 RLVVVRAPTGCGKTEAATAPFISDAAK-GSRRWVSLVYALPTRSLASAMLRRLSRSLAAAGAEWTtatLSYGG--LWEAR 115
                                    5799******************99977.67778899999*******************877444420144554..55555 PP

                                    HHHHTTCSEEEEEHHHHHHHH....HCTS...SHCTTE..EEEEEETHHHHHHT.TTHHHHH.HHHHHSHHHCTTSTTTS CS
                                    xxxxxxxxxxxxxxxxxxxxx....xxxx...xxxxxx..xxxxxxxxxxxxxx.xxxxxxx.xxxxxxxxxxxxxxxxx RF
                           DEAD  92 skldngvdivvgtpgrlddll....stgk...lnlsqv..rflVlDEadrlldq.gfsdfin.rilnqlpqitcdgklqr 160
                                      l  + d+ v+t + l++ +    s g+   l   +v  +++VlDE + l+d   + + +  + +++l       +l  
  gi|119720259|ref|YP_920754.1| 116 PYL--EGDVAVTTYDTLLHQFygvvSPGYhllLPAAKVsgSLVVLDETHLLQDAhWYAPSLLpAHVASL------VSLGA 187
                                    556..789******9999977799844433224466665679***********9534444330333333......33445 PP

                                    EEEEEESSBS CS
                                    xxxxxxxxxx RF
                           DEAD 161 qvivlSATlp 170
                                    qv+v+ AT+p
  gi|119720259|ref|YP_920754.1| 188 QVLVVGATVP 197
                                    6888888887 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.0   1.8e-10   5.5e-07       7     109 ..     246     347 ..     242     349 .. 0.80

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 1.8e-10
                                    HHHHHHTTTTSEEEEEESSHH.HHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHH...TTSSS.EEEESGGGTSSST CS
                     Helicase_C   7 lellkleeeggkilifvntid.rlekvklllekkgikvavlhgelpqnereeileqfn...kgesd.vLiatdvaerGid 81 
                                    + ll  e   + +l++vn+++  +e  + l++  g +va lh++l    r ++   f    +   d vL+at+v+e G+d
  gi|119720259|ref|YP_920754.1| 246 CSLL--EGAPRPALVVVNKVEkAVEAYRALRSCLGGSVALLHSRLRGGVRARVEGLFEgdgA-PGDlVLVATQVVEAGLD 322
                                    5554..6777889999999995444368886666***********************76432.3567************* PP

                                    STTESEEEESSSSSSHHHHHHHHTTSSS CS
                     Helicase_C  82 ipkvnlVinfdlprnvtsyiqriGRtgR 109
                                    + +v++++    p  v+s+iqr GR++R
  gi|119720259|ref|YP_920754.1| 323 L-DVRFLVTEVSP--VDSLIQRLGRCAR 347
                                    *.57777766666..899*********9 PP

>> Get5_C  Get5 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   6.1e-06     0.018      21      36 ..     400     415 ..     394     416 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 6.1e-06
                         Get5_C  21 aearavleRLqKGWel 36 
                                    + a +v+eRL+KGWe 
  gi|119720259|ref|YP_920754.1| 400 VYAAEVVERLRKGWER 415
                                    6799**********95 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   5.4e-06     0.016      13     150 ..      28     169 ..       9     196 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.4e-06
                                    HHHT......TTSEEEEEESTTSTHHHHH.HHHHHHH-S.......-EEEEESSHHHHHHHHHHGGGGTGG......GEE CS
                         ResIII  13 enlleklkskrdkrglikmaTGtGKTlva.aklierllkkgkee..kflflvprkslleqtleefkkflseayke..igk 87 
                                    e++  +++ ++++ +++ ++TG+GKT  a a +i   +k  +++    +   p++sl + +l+++++ l  a +e  +  
  gi|119720259|ref|YP_920754.1|  28 EDVWRAVD-EGHRLVVVRAPTGCGKTEAAtAPFISDAAKG-SRRwvSLVYALPTRSLASAMLRRLSRSLAAAGAEwtT-- 103
                                    45555565.8888899***********9977777777664.44435777778*************9999987655541.. PP

                                    EESSS-B--...........-SEEEEEHHHHHHTH............HHHTTT-SEEEEETGGGTTS.TTT CS
                         ResIII  88 kvsgdkkka....kekdstnkkilvttiqsldadseee....eeeseellrdrfdviiiDEaHrlgakksw 150
                                         + +     +++   + ++ vtt+++l  +              + + +  +++ DE H l++ ++w
  gi|119720259|ref|YP_920754.1| 104 ----ATLSYgglwEARPYLEGDVAVTTYDTLLHQFYGVvspgYHLLLPAAKVSGSLVVLDETHLLQD-AHW 169
                                    ....3333333334567777*************9944475444444444444444********9998.544 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.3   8.8e-05      0.26      14     150 ..      29     167 ..      24     360 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.8e-05
                         AAA_16  14 salervrsgrpelvllsGesGvGKsslvrell..ralekdggif..lrgkcdqlesaipysalaqalareellrqlldea 89 
                                    +++++v +g  +lv+++ + G+GK+  +++ +  +a+++++ ++  +++  +++        la+a  r +l r l+++ 
  gi|119720259|ref|YP_920754.1|  29 DVWRAVDEGH-RLVVVRAPTGCGKTEAATAPFisDAAKGSRRWVslVYALPTRS--------LASAMLR-RLSRSLAAA- 97 
                                    6677777776.9*************99977661134444443333444444444........6666644.555555555. PP

                         AAA_16  90 esaeleawrekleeala...avpelagaea.srllellkrllallsrder.........plvlvlDdlqwadea 150
                                         ++w ++ ++  +   a p l+g+ a +    ll ++    s++ +           ++vlD+ + +++a
  gi|119720259|ref|YP_920754.1|  98 ----GAEWTTATLSYGGlweARPYLEGDVAvTTYDTLLHQFYGVVSPGYHlllpaakvsGSLVVLDETHLLQDA 167
                                    ....5556665555444777777777777754444444444466666555666666665678888866644443 PP

>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   6.1e-05      0.18     149     191 ..     119     166 ..     112     190 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 6.1e-05
                                    ---EEEE-HHHHHHHT............TTS-S-S-SEEEES-GGGT-- CS
                                    xxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxx RF
                         SNF2_N 149 dydvvittYdvlsreaelq......kkrsvlkqvewkrvvlDEghtlkn 191
                                    + dv +ttYd+l  +  ++      +   +  +v+   vvlDE h l+ 
  gi|119720259|ref|YP_920754.1| 119 EGDVAVTTYDTLLHQF-YGvvspgyHLLLPAAKVSGSLVVLDETHLLQD 166
                                    679**********555.448999999999999*************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (566 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 3650.94
//
Query:       gi|119720260|ref|YP_920755.1|  [L=471]
Description: hypothetical protein Tpen_1355 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   4.4e-109  365.0   0.0   5.3e-109  364.8   0.0    1.1  1  Cas_Csa4  CRISPR-associated protein (Cas_Csa4)


Domain annotation for each model (and alignments):
>> Cas_Csa4  CRISPR-associated protein (Cas_Csa4)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  364.8   0.0  2.9e-113  5.3e-109       1     355 []     116     470 ..     116     470 .. 0.99

  Alignments for each domain:
  == domain 1  score: 364.8 bits;  conditional E-value: 2.9e-113
                       Cas_Csa4   1 kelytPghseildtlImygivrslaragvvelrvertGerYvievevDvrnknleegLrealeevlsghealgrrkiisd 80 
                                    ++lytPghs+++dtlIm++++r++++a++++lrv++tG++Yv+e++vD+r+  l+++Lr+++eev   h+a+++r     
  gi|119720260|ref|YP_920755.1| 116 PTLYTPGHSPYTDTLIMHALARAAWGARDAALRVRGTGFEYVLETSVDART--LAYELRRTFEEV---HAAFLDR----- 185
                                    68*************************************************..************...*******..... PP

                       Cas_Csa4  81 adisagafisdlqrlnrvy.....relesilnnleklkasvkselskkkqaeargrkkklltvpltLmPsagkyllkslk 155
                                                qrl+r++     r+l+s+l ++e+l+a++++els++++a+a+gr++++lt++l+LmPsagkyl+++l+
  gi|119720260|ref|YP_920755.1| 186 ------------QRLGRLFqdkdvRLLDSAL-DPEGLRAFLEGELSRPGHAGAEGRGFDGLTFKLPLMPSAGKYLHTDLT 252
                                    ............9******************.************************************************ PP

                       Cas_Csa4 156 kk...eekpyrvcklcyalawlGfhYyastikikdGesvvvvtlapseev......slidllalkdlkeklsvlqpalvn 226
                                    +k   e+k+yrvck+c+ala+lG+   as++++++G++v+vvtla+s+e+      +++d+l+++++k++l+vl+p+++n
  gi|119720260|ref|YP_920755.1| 253 RKpkyEAKEYRVCKYCAALAALGL---ASSVYVARGARVLVVTLAFSGEAgydalgGYYDFLQGEEAKDVLGVLGPRVDN 329
                                    ************************...***************************************************** PP

                       Cas_Csa4 227 sreallkalllyllslgalellteskftvlvYalefkvgnnqrirsfrevelsklldfiaelkardfastiklvddllre 306
                                    ++e+ll++l+++ll+++ale+l+++++t++vYa++f++g+++++r+f++ve++++++++++l+++d+as++kl +d+l++
  gi|119720260|ref|YP_920755.1| 330 VPERLLAQLAVALLTRNALEALDHAGATWRVYAVKFDTGRAVQVRGFYDVEVDSVVGAMSSLARVDDASYSKL-RDMLKQ 408
                                    *************************************************************************.****** PP

                       Cas_Csa4 307 ..............dleillrLieal.......lygdlrevysalrvlkkagvrldaelvdalaeilaer 355
                                                  +le+l+rL+e++       lyg++r+vy+a++  +kag      ++++++++++++
  gi|119720260|ref|YP_920755.1| 409 laratgadspragyALEALSRLFEFFetaspdsLYGFARSVYCAYE--GKAG------FHGVVESLVRAW 470
                                    **********************************************..9***......999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (471 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 3245.73
//
Query:       gi|119720261|ref|YP_920756.1|  [L=325]
Description: CRISPR-associated autoregulator DevR family protein protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      6e-76  255.1   0.0    7.2e-76  254.8   0.0    1.1  1  DevR      CRISPR-associated negative auto-regulator DevR/Csa2


Domain annotation for each model (and alignments):
>> DevR  CRISPR-associated negative auto-regulator DevR/Csa2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  254.8   0.0     4e-80   7.2e-76       1     268 [.       6     263 ..       6     264 .. 0.96

  Alignments for each domain:
  == domain 1  score: 254.8 bits;  conditional E-value: 4e-80
                                    EEEEEE-------------------EEEEEE--T..T--EEEEEE-THHHHHHHHHHHHHHHHTS...TTSSBHHHHTT- CS
                           DevR   1 isgrvvvnveaLNmdesvGNytehrkvpvvlkee..ykvrtvpaiSgeslkHayfetlvklaken...nlpvcelckrve 75 
                                    ++gr++vnv++ N++++vGNyt + +v vv++++  y+v++ p+iSg+++kH++++ +v++ ke    ++++c++ckr+ 
  gi|119720261|ref|YP_920756.1|   6 VTGRAIVNVHSANAEGAVGNYTGLSRVFVVKRRGsgYEVVEEPVISGNMVKHWHAVRMVEILKEVgggKARLCDNCKRFI 85 
                                    699***************************9999******************************99999*********** PP

                                    -----TT--EEEBTTSEESS-HHHHHHH-HHHHHH-EEEGGGT..EEE--SEEE--BEE-TTTTTTT------------- CS
                           DevR  76 gdggvikfatekklkekelkvekeiikecvveDvfGfLitekeksvkRkspvkfsyavpveesekavvdaqfharydlle 155
                                    + + +++f+           +e e +k+c++eDv+GfL ++ +  v+R+s vkfs++vpvee +  + +a++h+r+ l+e
  gi|119720261|ref|YP_920756.1|  86 MYRSTMNFN-----------DEFEYVKACAIEDVHGFLQPDAG--VRRESLVKFSFMVPVEELDAGS-TAVTHNRVFLDE 151
                                    *********...........899*****************666..*******************766.*********844 PP

                                    ----------------HHHHHSSEEEEEEEEEGGGTTS-TTS--EE---S-HHHHHHHHHHHHHTHHHHHH--------- CS
                           DevR 156 nrarkkgeeeekqnifqvEehsalYalsfvlDldriGkpevkkskieyvleeeerkkRikaalkallnlLsgsfgakrar 235
                                    +++    +e++++++f++E++s+lY++s+v+Dl+++G+p ++ ++++ vl+ +er+ R+kaal a++++Lsg fga +ar
  gi|119720261|ref|YP_920756.1| 152 RGSV--PREQQAMMVFKREHASGLYGFSAVMDLKYVGRPLADPDNANKVLPLDERRLRAKAALLAMADVLSGRFGAASAR 229
                                    4444..458*********************************************************************** PP

                                    -----EEEEEEEE--SSS------TT.TTHHHHH CS
                           DevR 236 llPvfeveslvaavskkpfpvfpirl.edyveee 268
                                    +lP+++ve+lv+av ++p+p +++++ +dy+ee+
  gi|119720261|ref|YP_920756.1| 230 ALPIVKVEELVCAVGRQPIPSLVHGFySDYAEES 263
                                    ************************999*****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2267.71
//
Query:       gi|119720262|ref|YP_920757.1|  [L=169]
Description: hypothetical protein Tpen_1357 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.06   13.6   0.1       0.17   12.1   0.1    1.8  2  Cas_Csa5  CRISPR-associated protein (Cas_Csa5)


Domain annotation for each model (and alignments):
>> Cas_Csa5  CRISPR-associated protein (Cas_Csa5)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   9.8e-06      0.17       4      41 ..      67     104 ..      64     119 .. 0.86
   2 ?   -1.6   0.0      0.17   3.1e+03      19      26 ..     131     138 ..     113     158 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.8e-06
                       Cas_Csa5   4 sesptlvDRianaLskeavakvlydaqRivqmglerge 41 
                                     ++ +l DR+a   s e  a vly++ R+   +l+r e
  gi|119720262|ref|YP_920757.1|  67 EQNLSLFDRLARCRSVEEFASVLYECVRVKDRVLSRLE 104
                                    57889***********************9888887755 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.17
                       Cas_Csa5  19 keavakvl 26 
                                     eav++v+
  gi|119720262|ref|YP_920757.1| 131 SEAVERVV 138
                                    35555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1315.20
//
Query:       gi|119720263|ref|YP_920758.1|  [L=235]
Description: transcriptional regulator, TrmB [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.3e-08   32.8   0.0    9.4e-07   28.5   0.0    2.5  2  HTH_IclR        IclR helix-turn-helix domain
    5.2e-08   32.7   0.0    2.1e-07   30.7   0.0    2.1  1  MarR_2          MarR family
    5.6e-07   29.3   0.0    9.8e-07   28.6   0.0    1.4  1  HTH_5           Bacterial regulatory protein, arsR family
    1.1e-06   28.4   0.0    2.3e-06   27.4   0.0    1.4  1  MarR            MarR family
      1e-05   25.3   0.0    1.8e-05   24.5   0.0    1.4  1  TrmB            Sugar-specific transcriptional regulator TrmB
    1.5e-05   24.5   0.0    2.5e-05   23.7   0.0    1.4  1  HTH_24          Winged helix-turn-helix DNA-binding
    0.00023   21.1   0.0    0.00057   19.8   0.0    1.7  1  HTH_Crp_2       Crp-like helix-turn-helix domain
    0.00074   19.5   0.0     0.0015   18.5   0.0    1.5  1  HTH_20          Helix-turn-helix domain
     0.0016   18.4   0.1     0.0072   16.3   0.1    2.1  1  HTH_29          Winged helix-turn helix
     0.0078   16.2   0.0      0.012   15.6   0.0    1.3  1  HTH_45          Winged helix-turn-helix
  ------ inclusion threshold ------
      0.014   15.4   0.1      0.033   14.2   0.1    1.7  1  HemN_C          HemN C-terminal domain
      0.025   14.8   0.0      0.074   13.3   0.0    1.9  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.047   13.5   0.0       0.14   12.0   0.0    1.8  1  HTH_23          Homeodomain-like domain
      0.075   13.2   0.0       0.12   12.5   0.0    1.2  1  DUF2250         Uncharacterized protein conserved in archaea 
      0.097   12.5   0.0       0.18   11.6   0.0    1.5  1  HTH_38          Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.19   2.3e+02      11      30 ..     151     170 ..     150     175 .. 0.86
   2 !   28.5   0.0   7.9e-10   9.4e-07       6      51 ..     177     221 ..     176     222 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.19
                                    T-CTTBSS-BHHHHHHHHTS CS
                       HTH_IclR  11 alaeapqeltlselArrtgl 30 
                                    +l+ ++++l+l  l+r +g+
  gi|119720263|ref|YP_920758.1| 151 YLEGQGRALRLPRLSRVLGV 170
                                    588999**********9997 PP

  == domain 2  score: 28.5 bits;  conditional E-value: 7.9e-10
                                    HHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                       HTH_IclR   6 laiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveqd 51 
                                    l++L al++ ++ l+ s+l   +g  +Stv+R+L+ ++e G+v+q 
  gi|119720263|ref|YP_920758.1| 177 LEVLSALEKSGP-LGASDLGGLLGKDRSTVFRYLKRMEEAGLVRQV 221
                                    689999998888.9******************************96 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.0   1.7e-10   2.1e-07       2      56 ..     171     223 ..     170     225 .. 0.95

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 1.7e-10
                                    T--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                         MarR_2   2 gltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56 
                                    g++ a++ vL aL  +++  l +++l   lg ++s+v r lkr+++aGLv++++g
  gi|119720263|ref|YP_920758.1| 171 GVPEAWLEVLSALEKSGP--LGASDLGGLLGKDRSTVFRYLKRMEEAGLVRQVDG 223
                                    777899************..*******************************9876 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0   8.2e-10   9.8e-07       5      46 ..     177     219 ..     174     220 .. 0.97

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 8.2e-10
                                    HHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_5   5 lkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVe 46 
                                    l++L++L++ g+l +++l   lg+ +stv ++Lk+++eaGLV+
  gi|119720263|ref|YP_920758.1| 177 LEVLSALEKsGPLGASDLGGLLGKDRSTVFRYLKRMEEAGLVR 219
                                    79****************************************6 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0     2e-09   2.3e-06       7      48 ..     178     219 ..     174     221 .. 0.95

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 2e-09
                                    HHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                           MarR   7 viLrilyeqgplsvseLakklgvskstvtrvldrLekkGlie 48 
                                    ++L  l+ +gpl  s+L+  lg ++stv r l+r+e++Gl++
  gi|119720263|ref|YP_920758.1| 178 EVLSALEKSGPLGASDLGGLLGKDRSTVFRYLKRMEEAGLVR 219
                                    7999************************************97 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   1.5e-08   1.8e-05      12      58 ..     178     224 ..     164     228 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 1.5e-08
                                    CHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                           TrmB  12 kvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58 
                                    +v  aL k+gp+ a+++   lg +rs+v ++L+++e++GlV+ ++g 
  gi|119720263|ref|YP_920758.1| 178 EVLSALEKSGPLGASDLGGLLGKDRSTVFRYLKRMEEAGLVRQVDGG 224
                                    7899999**********************************998876 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   2.1e-08   2.5e-05       7      48 .]     178     219 ..     177     219 .. 0.96

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 2.1e-08
                         HTH_24   7 kILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                    ++L++L+k + +  ++L   lg  +stv r+lkr+ee+Gl++
  gi|119720263|ref|YP_920758.1| 178 EVLSALEKSGPLGASDLGGLLGKDRSTVFRYLKRMEEAGLVR 219
                                    799*************************************96 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   4.8e-07   0.00057      21      65 ..     188     233 ..     163     234 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 4.8e-07
                                    EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.E.TEEEEES-HHHH CS
                      HTH_Crp_2  21 pltqeelAsmlGltretvsrilseLkreglis.r.grririldleaL 65 
                                    pl   +l+ +lG  r+tv r l++++++gl++   g+  + +dl +L
  gi|119720263|ref|YP_920758.1| 188 PLGASDLGGLLGKDRSTVFRYLKRMEEAGLVRqVdGG-YVATDLGRL 233
                                    566789**************************64355.999999888 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.3e-06    0.0015      14      60 ..     178     224 ..     176     225 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.3e-06
                                    HHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                         HTH_20  14 rilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvreg 60 
                                    ++l+aL   ++l as+l  +l+ +++t+ + L+ +eeagLv++v+ g
  gi|119720263|ref|YP_920758.1| 178 EVLSALEKSGPLGASDLGGLLGKDRSTVFRYLKRMEEAGLVRQVDGG 224
                                    79****************************************99866 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1     6e-06    0.0072      22      42 ..     198     218 ..     196     225 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 6e-06
                         HTH_29  22 lglsrrtvyrwlkrfeegGla 42 
                                    lg +r+tv+r+lkr+ee Gl 
  gi|119720263|ref|YP_920758.1| 198 LGKDRSTVFRYLKRMEEAGLV 218
                                    89*****************75 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0     1e-05     0.012      36      66 ..     205     235 .]     201     235 .] 0.91

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1e-05
                         HTH_45  36 lnkYLdmLvekglikkskekYvlTekGlell 66 
                                    + +YL+ + e gl+++ ++ Yv T+ G+ ll
  gi|119720263|ref|YP_920758.1| 205 VFRYLKRMEEAGLVRQVDGGYVATDLGRLLL 235
                                    569************************9876 PP

>> HemN_C  HemN C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   2.8e-05     0.033      23      66 .]     191     233 ..     178     233 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.8e-05
                         HemN_C  23 laafeqrfgldleellaaaleklqeqGLLeldggrlrltprGrl 66 
                                     +++  + g+d + +++  l++++e+GL+ + +g++++t+ Grl
  gi|119720263|ref|YP_920758.1| 191 ASDLGGLLGKDRSTVFRY-LKRMEEAGLVRQVDGGYVATDLGRL 233
                                    556666778888888888.***********************96 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   6.2e-05     0.074      11      53 ..     178     219 ..     163     224 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.2e-05
                                    HHHHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                 Fe_dep_repress  11 etIYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyve 53 
                                    e ++++ e++++ + +dl   L+   s+V   lk++e++G+v 
  gi|119720263|ref|YP_920758.1| 178 E-VLSALEKSGPLGASDLGGLLGKDRSTVFRYLKRMEEAGLVR 219
                                    4.467788999******************************96 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00012      0.14      26      46 ..     197     217 ..     191     219 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00012
                         HTH_23  26 eLgvsrrTvyrwlkryreeGl 46 
                                    +Lg  r+Tv r+lkr +e Gl
  gi|119720263|ref|YP_920758.1| 197 LLGKDRSTVFRYLKRMEEAGL 217
                                    79*************988887 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0    0.0001      0.12      11      60 ..     177     226 ..     171     231 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.0001
                        DUF2250  11 lkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLlervegkti 60 
                                    l+vl  l+k ++  a  +   l ++++ v ++lk++ee+GL+ +v+g  +
  gi|119720263|ref|YP_920758.1| 177 LEVLSALEKSGPLGASDLGGLLGKDRSTVFRYLKRMEEAGLVRQVDGGYV 226
                                    789999999999999999999***********************998765 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00015      0.18      21      43 ..     189     211 ..     178     212 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00015
                         HTH_38  21 lslreIArrLgrspsTIsRElkR 43 
                                    l+ ++ + +Lg+++sT+ R lkR
  gi|119720263|ref|YP_920758.1| 189 LGASDLGGLLGKDRSTVFRYLKR 211
                                    67788999**************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 1370.95
//
Query:       gi|119720264|ref|YP_920759.1|  [L=242]
Description: hypothetical protein Tpen_1359 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-26   91.5   1.0      4e-26   90.7   1.0    1.4  1  PDDEXK_10        PD-(D/E)XK nuclease superfamily
    4.6e-26   90.8  12.5    9.2e-25   86.6  12.5    2.7  1  DUF3782          Protein of unknown function (DUF3782)
  ------ inclusion threshold ------
      0.021   13.7   5.5      0.029   13.2   5.5    1.1  1  CALCOCO1         Calcium binding and coiled-coil domain (CALC
      0.043   13.8   0.2      0.087   12.8   0.2    1.6  1  Peptidase_S24    Peptidase S24-like
      0.088   12.9   3.4       0.14   12.2   3.4    1.3  1  DHR10            Designed helical repeat protein 10 domain
       0.21   12.0   6.5       0.33   11.4   6.5    1.3  1  DUF4200          Domain of unknown function (DUF4200)
       0.25   10.9   0.2       0.32   10.5   0.2    1.2  1  Exonuc_VII_L     Exonuclease VII, large subunit
       0.99    9.6   6.5        1.8    8.8   6.5    1.4  1  Jnk-SapK_ap_N    JNK_SAPK-associated protein-1
        1.2    9.0  14.7        3.5    7.5  14.7    1.8  1  ARGLU            Arginine and glutamate-rich 1
        3.3    7.7  10.4        1.6    8.7   0.9    3.7  4  Dynein_attach_N  Dynein attachment factor N-terminus


Domain annotation for each model (and alignments):
>> PDDEXK_10  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.7   1.0   2.2e-29     4e-26       2      74 .]     172     239 ..     171     239 .. 0.98

  Alignments for each domain:
  == domain 1  score: 90.7 bits;  conditional E-value: 2.2e-29
                      PDDEXK_10   2 evelDvvvkdgkvilvEiksslkrgDlavikrkkelYekakgvkvdrlivvtpfiddrnpervkavAerlgie 74 
                                    +ve+Dv vkdg++il+E+kss++rgD+av++r++elYek+++vk +rli+v+p++d r    + + A+ lg+e
  gi|119720264|ref|YP_920759.1| 172 MVEVDVAVKDGEHILIEVKSSVSRGDVAVFRRIGELYEKVNRVK-PRLIMVSPYVDPR----ALEDARILGVE 239
                                    79******************************************.*************....*********96 PP

>> DUF3782  Protein of unknown function (DUF3782)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.6  12.5   5.1e-28   9.2e-25       3      78 .]      87     170 ..      35     170 .. 0.94

  Alignments for each domain:
  == domain 1  score: 86.6 bits;  conditional E-value: 5.1e-28
                        DUF3782   3 lekleee.......eeetkedleelekeieklertigaLGaRWGlvsEeafReglkeiLeealgv.kVekwlyyDkeGeV 74 
                                    ++k+ee        e+e+k ++e++++ +++l+r+i+aLGaRWG+ sE+afReg+++++e++lg+ kVe+w+yyD+eGeV
  gi|119720264|ref|YP_920759.1|  87 NRKWEEAykrfeaiEAELKGLREDFNRGFDELRRRIDALGARWGIASESAFREGMRGVIERILGAgKVERWMYYDREGEV 166
                                    55555557777777****************************************************************** PP

                        DUF3782  75 ygyP 78 
                                    yg+P
  gi|119720264|ref|YP_920759.1| 167 YGHP 170
                                    ***9 PP

>> CALCOCO1  Calcium binding and coiled-coil domain (CALCOCO1) like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   5.5   1.6e-05     0.029      44     132 ..      35     123 ..      29     140 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.6e-05
                       CALCOCO1  44 aeLlqaqeaanrqrekekeeykrdreeldrerkelesrveelkeelkesrekveeleekqkelerlseelaeeksallea 123
                                     eL + +e  n+ +e e++++++++++++++ +  e++ ++ +e+ k+ +e+ ++ ee +k  e++++el+  ++   + 
  gi|119720264|ref|YP_920759.1|  35 GELKKLREDFNKLVELENRRWEENSKRWEENWRMWEENSKRWEENNKRWEENNRKWEEAYKRFEAIEAELKGLREDFNRG 114
                                    589999999999999999999999*******99999999******99999**********99999999999888887777 PP

                       CALCOCO1 124 keesearir 132
                                     +e + ri 
  gi|119720264|ref|YP_920759.1| 115 FDELRRRID 123
                                    777777775 PP

>> Peptidase_S24  Peptidase S24-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   4.9e-05     0.087      11      39 ..     179     207 ..     172     227 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.9e-05
                                    XXTTXEEEEECTS---TTSEEEEEETTCE CS
                  Peptidase_S24  11 lldGdlilVdkfsepkrGdivvfrlpgee 39 
                                     +dG+ il++  s++ rGd+ vfr  ge 
  gi|119720264|ref|YP_920759.1| 179 VKDGEHILIEVKSSVSRGDVAVFRRIGEL 207
                                    689*********************98885 PP

>> DHR10  Designed helical repeat protein 10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   3.4   7.7e-05      0.14      28     115 ..      37     125 ..      30     127 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.7e-05
                          DHR10  28 lqvvekdlrscikllee.ieaelakleeakkklkelrdaleekeielrelerkeerlqrqlenaeeklerlreqaeekre 106
                                    l+++ +d++++++l +  +e++ +++ee  +  +e+++++ee++++ +e +rk e   ++ e  e +l  lre+ ++  +
  gi|119720264|ref|YP_920759.1|  37 LKKLREDFNKLVELENRrWEENSKRWEENWRMWEENSKRWEENNKRWEENNRKWEEAYKRFEAIEAELKGLREDFNRGFD 116
                                    6788999******99988********************************************************999999 PP

                          DHR10 107 aakarleel 115
                                    + ++r+++l
  gi|119720264|ref|YP_920759.1| 117 ELRRRIDAL 125
                                    999999887 PP

>> DUF4200  Domain of unknown function (DUF4200)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   6.5   0.00018      0.33      14      89 ..      36     111 ..      30     127 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00018
                        DUF4200  14 aleakkeeiqrleealkqreeelekkeqeleedllkfdkflkendakraralkkaeeerklkkekeaeikklkaei 89 
                                    +l++ +e++++l e+ ++r+ee  k+ +e  +  ++  k  +en+++ ++ ++k ee  k+ +  eae+k l+++ 
  gi|119720264|ref|YP_920759.1|  36 ELKKLREDFNKLVELENRRWEENSKRWEENWRMWEENSKRWEENNKRWEENNRKWEEAYKRFEAIEAELKGLREDF 111
                                    78999*****************************************************************999875 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.2   0.00018      0.32     155     257 ..      39     123 ..       3     148 .. 0.52

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00018
                   Exonuc_VII_L 155 rlekaikrlleekkqrleklasrlkspeellerkrqrldeleerleralkkqlkkkrerleelkerlkekleekkerlkk 234
                                    +l++ +++l+e +++r e+ ++r +++ ++ e++++r +e ++r e+  +++++++ +r+e ++                
  gi|119720264|ref|YP_920759.1|  39 KLREDFNKLVELENRRWEENSKRWEENWRMWEENSKRWEENNKRWEE-NNRKWEEAYKRFEAIE---------------- 101
                                    33333344444444444444444444444444444444444444444.3334444444444444................ PP

                   Exonuc_VII_L 235 lkerle.lleekkerleeleekle 257
                                      ++l+ l e+ ++ ++el ++++
  gi|119720264|ref|YP_920759.1| 102 --AELKgLREDFNRGFDELRRRID 123
                                    ..3333222223333333333333 PP

>> Jnk-SapK_ap_N  JNK_SAPK-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   6.5     0.001       1.8      51     130 ..      36     105 ..      30     128 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.001
                  Jnk-SapK_ap_N  51 eleelreeleqLeteyerekelrkraeeeleeiedqweeerkelqekveqleeenrelelkaknaadqlsrleekeaelk 130
                                    el++lre++++L +  +r+    ++  +++ee    wee+ k  +e  ++ ee+nr+ e       +  +r e  eaelk
  gi|119720264|ref|YP_920759.1|  36 ELKKLREDFNKLVELENRRW---EENSKRWEENWRMWEENSKRWEENNKRWEENNRKWE-------EAYKRFEAIEAELK 105
                                    67788888888877444444...334466667777777777777777777777777777.......55555555555554 PP

>> ARGLU  Arginine and glutamate-rich 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5  14.7    0.0019       3.5      67     121 ..      49     103 ..      32     124 .. 0.49

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0019
                          ARGLU  67 eeekrkeeeerkkreelerileenkrkveeaqrklaEerlaeleekrrlkeerqr 121
                                    e e+r+ ee+ k+ ee+ r+ een+++ ee++++ +E+  +  e+ +r +  +++
  gi|119720264|ref|YP_920759.1|  49 ELENRRWEENSKRWEENWRMWEENSKRWEENNKRWEENNRKWEEAYKRFEAIEAE 103
                                    3333444444444444445555555555555444444433333333333332222 PP

>> Dynein_attach_N  Dynein attachment factor N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1      0.17     3e+02       3      20 ..       3      20 ..       1      23 [. 0.86
   2 ?    8.7   0.9   0.00089       1.6       3      26 ..      37      60 ..      36      63 .. 0.92
   3 ?    1.2   0.5       0.2   3.6e+02       9      28 ..      71      90 ..      66     109 .. 0.73
   4 ?   -1.5   0.0       1.4   2.5e+03      18      31 ..     206     219 ..     203     226 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.17
                Dynein_attach_N  3 fkkLekelqeaiekdeky 20
                                   +++L++el + +++de+ 
  gi|119720264|ref|YP_920759.1|  3 VQALKAELLRLLREDEEF 20
                                   789************986 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00089
                Dynein_attach_N  3 fkkLekelqeaiekdekyqrenda 26
                                   +kkL++++++ +e +++++ en++
  gi|119720264|ref|YP_920759.1| 37 LKKLREDFNKLVELENRRWEENSK 60
                                   69********************97 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.2
                Dynein_attach_N  9 elqeaiekdekyqrendaKl 28
                                   e ++  e+++k++ en+ K 
  gi|119720264|ref|YP_920759.1| 71 ENSKRWEENNKRWEENNRKW 90
                                   55566677788888888775 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 1.4
                Dynein_attach_N  18 ekyqrendaKlrAV 31 
                                    e y+++n +K r +
  gi|119720264|ref|YP_920759.1| 206 ELYEKVNRVKPRLI 219
                                    789*******9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1189  (0.0663171); expected 358.6 (0.02)
Passed bias filter:                      635  (0.0354175); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 1752.65
//
Query:       gi|119720265|ref|YP_920760.1|  [L=277]
Description: hypothetical protein Tpen_1360 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.7e-12   47.8   0.2    4.2e-12   46.5   0.2    1.7  1  CRISPR_Cas6  CRISPR-associated endoribonuclease Cas6
  ------ inclusion threshold ------
      0.018   15.4   0.0      0.045   14.0   0.0    1.7  1  Cas6_N       Cas6 N-terminal domain
      0.041   14.4   0.1      0.097   13.2   0.1    1.6  2  Cas_Cas6     CRISPR associated protein Cas6


Domain annotation for each model (and alignments):
>> CRISPR_Cas6  CRISPR-associated endoribonuclease Cas6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.5   0.2     7e-16   4.2e-12       1      86 []     116     251 ..     116     251 .. 0.68

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 7e-16
                                    EEEEEEE-EE..............TEEESS--HHHHHHHHHHHHHHHTSS.............................. CS
                    CRISPR_Cas6   1 lrfltPtrfk..............krkgllpsprlvfssllrrwnalaglkgk........................... 39 
                                    lrfltPt+                +r++l+p++ l +++l+    a+ g+++                            
  gi|119720265|ref|YP_920760.1| 116 LRFLTPTLVPvpgrgsllkaggprRRYRLVPDLPLALAHLAYD-AAMRGVRLAkatpgrihawalralaeldydarpvta 194
                                    79*****************999988899999999999995555.222222222233333444444433333333444444 PP

                                    .EECHHH.......HHHEEEEEEEE....--..HHHECCCHHHHHHHH-SSSTGGGTTT-E CS
                    CRISPR_Cas6  40 .ptveee.......legGfvGevky....sg..eleelekllrfaeylgvGkktafGlGkv 86 
                                          +       +e GfvG v y    ++  + e++++l++fa  +g+G+++++G+G+v
  gi|119720265|ref|YP_920760.1| 195 lY----TvrdgkpaTERGFVGFVAYelldTKseYAEDFRRLMAFALRFGIGRSRSIGFGHV 251
                                    31....13333443334********88762257**************************98 PP

>> Cas6_N  Cas6 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   7.5e-06     0.045      11      32 ..       2      23 ..       1      74 [. 0.67

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.5e-06
                                   S-EE--SSTTHHHHHHHHTSSG CS
                         Cas6_N 11 rDvilppltSKvskyillslsp 32
                                   rD +lpp+tSKv ++ ++ l  
  gi|119720265|ref|YP_920760.1|  2 RDALLPPFTSKVTRTAFAALWG 23
                                   79************99988654 PP

>> Cas_Cas6  CRISPR associated protein Cas6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.3   7.8e+03      12      43 ..      95     124 ..      85     131 .. 0.54
   2 ?   13.2   0.1   1.6e-05     0.097     122     145 ..     229     252 ..     208     253 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.3
                                    TEEEEEEEEEE----S--TCEE.EEESS-BBE CS
                       Cas_Cas6  12 nnefkveevellkepeitssevvfktlSPivv 43 
                                     +e++v e+++l e++   ++  +++l+P +v
  gi|119720265|ref|YP_920760.1|  95 VAEVEVFEASALREDVP--EKFALRFLTPTLV 124
                                    33334444444444442..3345777777665 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 1.6e-05
                                    HHHHHHHHHC-SCS-CCCT-S-EE CS
                       Cas_Cas6 122 pellklaydaGlGeknsqGFGmve 145
                                    ++l+ +a+  G+G  +s GFG ve
  gi|119720265|ref|YP_920760.1| 229 RRLMAFALRFGIGRSRSIGFGHVE 252
                                    789******************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       172  (0.0095934); expected 358.6 (0.02)
Passed bias filter:                      153  (0.00853366); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1980.34
//
Query:       gi|119720266|ref|YP_920761.1|  [L=919]
Description: hypothetical protein Tpen_1361 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.4e-06   25.5   0.0    2.1e-05   24.3   0.0    1.6  1  Csm1_B    Csm1 subunit domain B


Domain annotation for each model (and alignments):
>> Csm1_B  Csm1 subunit domain B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   1.2e-09   2.1e-05       3      87 ..     283     365 ..     281     369 .. 0.94

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 1.2e-09
                                    SS--HHHHHHHHHHHHHHHHHHHHHHHHHTT--CCCEEEEETTEEEEEEE--HHHHHHHHHHHHHHHHHCCCCTSSS-EE CS
                         Csm1_B   3 skgAlksLrgRSfylellleeivdelleklelsranllYagGGhfylLlpntekvkekleeiekelnewllkefkgkLyl 82 
                                    ++ A + LrgRS+ +el+     + +le ++ + +  l   GG  +++lp +   ++k++ +++ l +w+ ++fkg+L l
  gi|119720266|ref|YP_920761.1| 283 ESAASRVLRGRSLLVELVQFTATRIVLELAGATWSAQLSKEGGAPTFVLPGSF--RDKVDALREILGRWMARQFKGSLWL 360
                                    67899*********************************************997..9**********************99 PP

                                    EEEEE CS
                         Csm1_B  83 alayv 87 
                                     +a+ 
  gi|119720266|ref|YP_920761.1| 361 TVACS 365
                                    99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (919 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.44
# Mc/sec: 6258.78
//
Query:       gi|119720267|ref|YP_920762.1|  [L=368]
Description: CRISPR-associated RAMP Csm5 family protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.021   14.9   0.2      0.055   13.5   0.2    1.7  1  RAMPs     RAMP superfamily


Domain annotation for each model (and alignments):
>> RAMPs  RAMP superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2   3.1e-06     0.055      33      65 ..      97     134 ..       7     195 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.1e-06
                                    ---HHHHHHHHHHHHH.....HHHH.HHHTT-HHHHH. CS
                          RAMPs  33 yIPGSSlkGalRsale.....kllgsekkekkdeysrk 65 
                                     +P+SSlkG lR+al+     ++++++++e+  +++r 
  gi|119720267|ref|YP_920762.1|  97 LVPASSLKGYLRTALLfrllrRVAEERGSEEAAKLLRG 134
                                    49*************99888888888777777666664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2632.92
//
Query:       gi|119720268|ref|YP_920763.1|  [L=332]
Description: hypothetical protein Tpen_1363 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 2235.88
//
Query:       gi|119720269|ref|YP_920764.1|  [L=331]
Description: CRISPR-associated RAMP Csm3 family protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.6e-06   26.8   0.2    2.9e-05   24.2   0.2    2.1  1  RAMPs     RAMP superfamily


Domain annotation for each model (and alignments):
>> RAMPs  RAMP superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.2   1.6e-09   2.9e-05      28     213 .]      59     283 ..      17     283 .. 0.69

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 1.6e-09
                                    ---S----HHHHHHHHHHHHHHHHH.HHHTT-HHHHH.H................................HHHHHH--S CS
                          RAMPs  28 kgglPyIPGSSlkGalRsalekllgsekkekkdeysrkkekqrvkkgd.......................leeaiFGne 84 
                                    + ++P +PGSSlkG +R +le  lg+++   +++    +        +                        ++++FG++
  gi|119720269|ref|YP_920764.1|  59 EVEVPLVPGSSLKGRMRGLLELSLGKRLYTSDERIWLHA--------RilwgtrahpmstdelirdisgrcEVDEVFGSP 130
                                    5678*****************888866654444443322........123555555666666666666667888888888 PP

                                    ...SS--SEEEEE..................................................EEEEEEEEEEEEEEEEE CS
                          RAMPs  85 eeskiagrvffeDarpvkipgqileeskqikstpsp...........................klsgselrelldhster 137
                                       ++   v+   + + +++g+     ++++  ++                             ++       +  ++e+
  gi|119720269|ref|YP_920764.1| 131 -AVGFDQLVEMLARDLASKQGKEEPDDADYEEAGKVarslalnlaltrllvddmtpdkdyvgvLSENGRRILAISDFLEE 209
                                    .4555555555555555555444444444444444455555666666666777777777799844555555556667888 PP

                                    --SSS-EEEEEE...-TT-EEEEEEEESS...................HHHHHHHHHHHHHH.HHH---STTTTBTTT-E CS
                          RAMPs 138 rtrvaidrktktngkkkgglftleaipae.....rikfsgrirlenlsdeelgallklLdlldlhflglGggkplGfGsv 212
                                    + +++idr t  +++      ++  + ++      +++ +    ++  ++ l+++ k L+l+      lG+  ++G+G+v
  gi|119720269|ref|YP_920764.1| 210 KGENRIDRITSAADP-----RQVARVKPGvvfqgALRLLVFDIDKGYVKRNLELVAKGLRLV--EETYLGASGSRGYGRV 282
                                    8999*****999999.....555555555555545555555577789999999999999999..999999999*****99 PP

                                    E CS
                          RAMPs 213 e 213
                                    +
  gi|119720269|ref|YP_920764.1| 283 K 283
                                    6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 2237.38
//
Query:       gi|119720270|ref|YP_920765.1|  [L=139]
Description: hypothetical protein Tpen_1365 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0097   16.4   1.0      0.078   13.5   0.0    2.4  3  FliX      Class II flagellar assembly regulator


Domain annotation for each model (and alignments):
>> FliX  Class II flagellar assembly regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   4.4e-06     0.078      38      82 ..      17      62 ..       4      65 .. 0.88
   2 ?   -2.0   0.1      0.27   4.8e+03     126     135 ..      69      78 ..      67      79 .. 0.85
   3 ?    0.9   0.0     0.034   6.1e+02      71      83 ..     120     132 ..     102     135 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.4e-06
                           FliX 38 aaavsaaaavagvdalLalQevd.edeterrrravrrgetlLDkLd 82
                                   + a++a + +++vda+La Qe   +++t++ rr ++   t+LD L 
  gi|119720270|ref|YP_920765.1| 17 TDALNAGKVLEAVDAILASQELVgKTTTTAYRRIHEVVGTVLDYLT 62
                                   5678888999***********8879999999************985 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.27
                           FliX 126 lRaeVELAKl 135
                                     Ra  ELA++
  gi|119720270|ref|YP_920765.1|  69 ARASLELARA 78 
                                    5999****96 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.034
                           FliX  71 vrrgetlLDkLde 83 
                                    ++rg+ +LD+L  
  gi|119720270|ref|YP_920765.1| 120 AERGRAILDALAV 132
                                    789******9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 992.68
//
Query:       gi|119720271|ref|YP_920766.1|  [L=322]
Description: hypothetical protein Tpen_1366 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-06   27.3   0.0    3.6e-06   27.0   0.0    1.1  1  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
  ------ inclusion threshold ------
       0.01   15.6   0.0      0.011   15.4   0.0    1.1  1  AAA_15    AAA ATPase domain


Domain annotation for each model (and alignments):
>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0     4e-10   3.6e-06     179     301 ..     119     279 ..      93     282 .. 0.88

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 4e-10
                         AAA_21 179 akekrllqrlvrslklveielsdlgegeeliasvderlrer.................................gvvfle 225
                                    ++ ++++++ +r +++ve  ls ++++ +l +svd  l+ r                                 g++  +
  gi|119720271|ref|YP_920766.1| 119 PPTGGIASEAYRLIREVEWLLSGSRDVLKLKESVDTKLLSRaerlveevlgrvaeragvrvedvaplhltvtgeGFIVRD 198
                                    6667788889999999999999999999999999999999999999999999*********************9****** PP

                         AAA_21 226 ngdgqelparelSdGtkrll..alltallralkkgsllliDEpEngLHPkllrrllellkelsr...ngaQviltTHSpl 300
                                    +  g e+++ ++S+ + ++l   l  ++++ +  +++l+++EpE  + P  +   ++ l++l++   ++   ++tTHSp+
  gi|119720271|ref|YP_920766.1| 199 ERLGSEVQVESVSSAVSSALlwELTKLFFSVPAAARFLVVEEPEEAMSPLQQVAYARALERLAKempGDNYAVVTTHSPY 278
                                    *******************98*8888888888888**************88866666666665566689999*******9 PP

                         AAA_21 301 l 301
                                    +
  gi|119720271|ref|YP_920766.1| 279 V 279
                                    7 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.0   1.2e-06     0.011     289     369 .]     202     280 ..     124     280 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.2e-06
                         AAA_15 289 deelplnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnkt..QviitTHSp 366
                                    + e+ ++ ++s v+++ll  l +l+++      +   +l++EEPE    p +q   +++l +la++  +    ++tTHSp
  gi|119720271|ref|YP_920766.1| 202 GSEVQVESVSSAVSSALLWELTKLFFSVP----AAARFLVVEEPEEAMSPLQQVAYARALERLAKEMPGdnYAVVTTHSP 277
                                    66788888999999999999999999999....9999****************************9988889******** PP

                         AAA_15 367 hii 369
                                    +++
  gi|119720271|ref|YP_920766.1| 278 YVA 280
                                    *85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2167.49
//
Query:       gi|119720272|ref|YP_920767.1|  [L=158]
Description: hypothetical protein Tpen_1367 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1066.74
//
Query:       gi|119720273|ref|YP_920768.1|  [L=104]
Description: hypothetical protein Tpen_1368 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 765.69
//
Query:       gi|119720274|ref|YP_920769.1|  [L=181]
Description: hypothetical protein Tpen_1369 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.6e-19   68.0   0.0    7.7e-19   67.8   0.0    1.1  1  LDcluster4       SLOG cluster4 family
  ------ inclusion threshold ------
       0.04   13.2   0.0       0.11   11.7   0.0    1.7  2  LSDAT_prok       SLOG in TRPM, prokaryote
       0.22   11.6   0.0       0.35   11.0   0.0    1.4  1  Lysine_decarbox  Possible lysine decarboxylase


Domain annotation for each model (and alignments):
>> LDcluster4  SLOG cluster4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.8   0.0   1.3e-22   7.7e-19      33     156 ..      38     166 ..      12     167 .. 0.89

  Alignments for each domain:
  == domain 1  score: 67.8 bits;  conditional E-value: 1.3e-22
                     LDcluster4  33 gavlltGgrtGvmeaaskGakeagGltvGilpassekehsnkyvdiiiyTGlglagRnlilvlssdvviaiggrsGTlsE 112
                                    g+ +l Gg  Gvm+ ++++a+++g ++v +lp +   e  ++ + + + TGl+l gR++ lv+ssd++ ++gg++GT+ E
  gi|119720274|ref|YP_920769.1|  38 GVRVLLGGYWGVMRDVAEAARRRGLTVVFFLPVDPPAEVPDDELFVRVDTGLDLRGRSVALVRSSDALAVLGGEVGTVVE 117
                                    67899****************************9999999999999********************************** PP

                     LDcluster4 113 ialaleegkpvivlkgt...dellseiiekkekder..kvivaespkel 156
                                      la+++gkpv vl+gt   ++ l+  + +  +  +   v+++++p+el
  gi|119720274|ref|YP_920769.1| 118 AFLAYSYGKPVAVLRGTglsSDALERAFPRGFDGRGsaPVVYVDTPEEL 166
                                    *****************99866666666666665556788888888876 PP

>> LSDAT_prok  SLOG in TRPM, prokaryote
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.26   1.5e+03     128     151 ..      41      64 ..      29      66 .. 0.68
   2 ?   11.7   0.0   1.8e-05      0.11     129     167 ..     107     145 ..      94     177 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.26
                     LSDAT_prok 128 vlvnGgeitlkdiresvkagrpil 151
                                    vl++G    ++d++e+ +++  ++
  gi|119720274|ref|YP_920769.1|  41 VLLGGYWGVMRDVAEAARRRGLTV 64 
                                    677777777777777766655444 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 1.8e-05
                     LSDAT_prok 129 lvnGgeitlkdiresvkagrpilvvaGsgrladeiaaal 167
                                    +++G+  t+ ++  + + g+p+ v++G+g   d++  a 
  gi|119720274|ref|YP_920769.1| 107 VLGGEVGTVVEAFLAYSYGKPVAVLRGTGLSSDALERAF 145
                                    5688899***************************97665 PP

>> Lysine_decarbox  Possible lysine decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   5.8e-05      0.35      41      72 ..      90     121 ..      48     127 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 5.8e-05
                                    SHHHHHHHHHHHESEEEE-S-SHHHHHHHHHH CS
                Lysine_decarbox  41 dmeeRkealveladafvilPGGiGTleEllei 72 
                                    d+  R  alv+ +da+ +l G +GT+ E++ +
  gi|119720274|ref|YP_920769.1|  90 DLRGRSVALVRSSDALAVLGGEVGTVVEAFLA 121
                                    677899********************999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1381.05
//
Query:       gi|119720275|ref|YP_920770.1|  [L=173]
Description: PaREP8 domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-37  127.8   2.0    1.7e-37  127.8   2.0    1.5  2  PaREP1    Archaeal PaREP1/PaREP8 family
  ------ inclusion threshold ------
      0.039   14.0   0.1      0.093   12.8   0.1    1.7  1  DUF357    Protein of unknown function (DUF357)


Domain annotation for each model (and alignments):
>> PaREP1  Archaeal PaREP1/PaREP8 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.53   4.8e+03      77      89 ..      24      36 ..       9      36 .. 0.55
   2 !  127.8   2.0   1.9e-41   1.7e-37       1     115 []      44     158 ..      44     158 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.53
                         PaREP1 77 kevvdlwklAldL 89
                                     vvd+ ++AldL
  gi|119720275|ref|YP_920770.1| 24 SLVVDALSKALDL 36
                                   4466666666665 PP

  == domain 2  score: 127.8 bits;  conditional E-value: 1.9e-41
                         PaREP1   1 arleeaekeleeAeellekGdlrqAaeKaykAvkalvkalaeknnlklleeaeekerwstkellkavaklleelgdkevv 80 
                                    arle+a k++eeA+e+l kGd++qA+eK+yk +++++kalae +n + le+ +e++rw+t++l +a+++l++ lgd++v+
  gi|119720275|ref|YP_920770.1|  44 ARLELAAKFMEEADEYLGKGDPVQASEKLYKVAEECIKALAEGFNAPTLEKVRERGRWDTWLLGMAATDLSRILGDERVH 123
                                    69****************************************************************************** PP

                         PaREP1  81 dlwklAldLHeyqfheaklelsdveskeeavkdlv 115
                                    ++w++A+++H+++fheak++++dv++++++vk+l+
  gi|119720275|ref|YP_920770.1| 124 LAWSKAYEIHVWGFHEAKYRVEDVAAARPVVKWLL 158
                                    ********************************985 PP

>> DUF357  Protein of unknown function (DUF357)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1     1e-05     0.093      26      54 ..      41      69 ..      26      73 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1e-05
                                   HHHHHHHHHHHHHHHHHHHHHTT-HHHHH CS
                         DUF357 26 aaeevlemaesYleDakyflekgdlvnAl 54
                                   +ae  le+a +++e+a ++l kgd+v+A 
  gi|119720275|ref|YP_920770.1| 41 VAEARLELAAKFMEEADEYLGKGDPVQAS 69
                                   578889********************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1268.62
//
Query:       gi|119720276|ref|YP_920771.1|  [L=270]
Description: hypothetical protein Tpen_1371 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.7e-05   23.5   5.5    0.00016   22.0   5.4    1.8  1  Fer4_8    4Fe-4S dicluster domain
     0.0017   18.9   7.2     0.0022   18.5   4.6    2.2  2  Fer4_7    4Fe-4S dicluster domain
     0.0019   18.7   6.4      0.005   17.3   6.4    1.7  1  Fer4_17   4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.011   15.9   4.7      0.027   14.6   4.7    1.7  1  Fer4_9    4Fe-4S dicluster domain
      0.032   14.3   6.8      0.047   13.8   4.8    2.1  2  Fer4_21   4Fe-4S dicluster domain
       0.47   10.6  11.7          3    8.1   2.2    3.2  3  Fer4_6    4Fe-4S binding domain
       0.81    9.8  13.1       0.96    9.6   1.9    2.5  3  Fer4_10   4Fe-4S dicluster domain
        2.5    9.1   8.0        6.8    7.7   0.3    2.6  2  Fer4_16   4Fe-4S double cluster binding domain


Domain annotation for each model (and alignments):
>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   5.4   7.3e-08   0.00016       4      64 ..      31      83 ..      29      84 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 7.3e-08
                         Fer4_8  4 kCieC.gaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64
                                    Ci C g C ++Cp++ +t++ ll++ g       +e +      +++C+ c +C+ +Cp g
  gi|119720276|ref|YP_920771.1| 31 PCIYCpGICLASCPTYTATGNVLLSPLGYSRF---KEVA------AKNCLKCWRCSFECPLG 83
                                   6****99*********************9666...3333......689************75 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   4.6   9.9e-07    0.0022       2      51 ..      32      83 ..      31      84 .. 0.88
   2 ?    0.4   0.0      0.44     1e+03      24      40 ..     216     232 ..     202     247 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 9.9e-07
                         Fer4_7  2 CigC.gaCvaaCpvkaieldeeenekgtekve.idpekClgCgaCvavCPtg 51
                                   Ci C g C a Cp+++ + +   ++ g  + + + + +Cl C +C  +CP g
  gi|119720276|ref|YP_920771.1| 32 CIYCpGICLASCPTYTATGNVLLSPLGYSRFKeVAAKNCLKCWRCSFECPLG 83
                                   9***88**************98888888777515689*************76 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.44
                         Fer4_7  24 nekgtekveidpekClg 40 
                                    +e+g++ +e+d e+C+ 
  gi|119720276|ref|YP_920771.1| 216 EEAGVKATEVDDESCIK 232
                                    56688889999999986 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   6.4   2.2e-06     0.005       2      60 ..      32      84 ..      31      85 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.2e-06
                        Fer4_17  2 CiqCg.yClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPqgl 60
                                   Ci C   Cl++Cp+y a++n   ++l     ++++e+    +a++C++C +C+ +CP g+
  gi|119720276|ref|YP_920771.1| 32 CIYCPgICLASCPTYTATGNVLLSPLGY---SRFKEV----AAKNCLKCWRCSFECPLGF 84
                                   9999636*************77777776...555564....89**************876 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   4.7   1.2e-05     0.027       2      49 ..      32      83 ..      31      85 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.2e-05
                         Fer4_9  2 CtgC.gaCveaCpagvvvedaaerkarlraase...eaCigCgaCveaCpkg 49
                                   C+ C g C ++Cp+ ++++        + +++e   ++C++C +C   Cp g
  gi|119720276|ref|YP_920771.1| 32 CIYCpGICLASCPTYTATGNVLLSPLGYSRFKEvaaKNCLKCWRCSFECPLG 83
                                   999*668******9999998888888888888888899************76 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   4.8   2.1e-05     0.047       6      53 ..      30      82 ..      26      85 .. 0.75
   2 ?   -0.8   0.0      0.77   1.7e+03       2       9 ..     224     231 ..     208     237 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.1e-05
                        Fer4_21  6 dkCigC.gkCliaCed.tshqai...eidaktvlkvvedeCvGCnlCssvCPv 53
                                   + Ci C g Cl +C++ t++  +    +  ++  +v +++C  C  Cs  CP+
  gi|119720276|ref|YP_920771.1| 30 NPCIYCpGICLASCPTyTATGNVllsPLGYSRFKEVAAKNCLKCWRCSFECPL 82
                                   78****889*****973444455333233456668899**************6 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.77
                        Fer4_21   2 ridedkCi 9  
                                     +d+++Ci
  gi|119720276|ref|YP_920771.1| 224 EVDDESCI 231
                                    34455555 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   2.2    0.0013         3       6      22 ..      29      46 ..      26      50 .. 0.90
   2 ?    5.9   0.7    0.0065        14       7      20 ..      68      81 ..      64      87 .. 0.86
   3 ?    1.1   0.0      0.21   4.7e+02       3      10 ..     224     231 ..     223     245 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0013
                         Fer4_6  6 pdkCigC.gdCvrvCPeg 22
                                   +++Ci C g C + CP++
  gi|119720276|ref|YP_920771.1| 29 KNPCIYCpGICLASCPTY 46
                                   689*************85 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0065
                         Fer4_6  7 dkCigCgdCvrvCP 20
                                    +C+ C +C   CP
  gi|119720276|ref|YP_920771.1| 68 KNCLKCWRCSFECP 81
                                   68***********9 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.21
                         Fer4_6   3 eidpdkCi 10 
                                    e+d+++Ci
  gi|119720276|ref|YP_920771.1| 224 EVDDESCI 231
                                    79*****9 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9  12.3    0.0029       6.6       6      56 .]      29      81 ..      25      81 .. 0.84
   2 ?    9.6   1.9   0.00043      0.96       6      22 ..      67      83 ..      62     105 .. 0.81
   3 ?   -2.0   0.0       1.8     4e+03       4      10 ..     225     231 ..     214     245 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0029
                        Fer4_10  6 ddtCirCg.kCvkaCPadl.tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                   ++ Ci C   C ++CP++  t+++      ++  ++++ ++C +c  C  +CP
  gi|119720276|ref|YP_920771.1| 29 KNPCIYCPgICLASCPTYTaTGNVLLSPLGYSRFKEVAAKNCLKCWRCSFECP 81
                                   578****879*******986777777777777778889**************9 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00043
                        Fer4_10  6 ddtCirCgkCvkaCPad 22
                                   ++ C++C +C   CP  
  gi|119720276|ref|YP_920771.1| 67 AKNCLKCWRCSFECPLG 83
                                   678************84 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.8
                        Fer4_10   4 idddtCi 10 
                                    +dd++Ci
  gi|119720276|ref|YP_920771.1| 225 VDDESCI 231
                                    3444454 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   2.4     0.052   1.2e+02       2      16 ..      32      47 ..      31      53 .. 0.79
   2 ?    7.7   0.3     0.003       6.8       1      15 [.      69      83 ..      60     107 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.052
                        Fer4_16  2 CgtC.gkCaevCPtna 16
                                   C+ C g C+ +CPt  
  gi|119720276|ref|YP_920771.1| 32 CIYCpGICLASCPTYT 47
                                   9999556******965 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.003
                        Fer4_16  1 rCgtCgkCaevCPtn 15
                                   +C +C +C   CP +
  gi|119720276|ref|YP_920771.1| 69 NCLKCWRCSFECPLG 83
                                   477788888888754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2101.77
//
Query:       gi|119720277|ref|YP_920772.1|  [L=465]
Description: alkylglycerone-phosphate synthase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-36  125.2   0.1    2.6e-36  124.4   0.1    1.3  1  FAD_binding_4    FAD binding domain
    1.9e-35  122.7   0.1    2.7e-35  122.2   0.1    1.2  1  FAD-oxidase_C    FAD linked oxidases, C-terminal domain
  ------ inclusion threshold ------
        0.2   12.1   1.4          1    9.8   0.4    2.5  3  Glyco_trans_1_2  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> FAD_binding_4  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.4   0.1   4.3e-40   2.6e-36       1     135 [.      54     188 ..      54     191 .. 0.98

  Alignments for each domain:
  == domain 1  score: 124.4 bits;  conditional E-value: 4.3e-40
                                    EEEEEEESSHHHHHHHHHHHHHCTSCEEEESSSTTEESTTCSCCEEEEEETTS--EEEEETTTTEEEEETTSBHHHHHHH CS
                  FAD_binding_4   1 paavvrpeseeevaaalrlaneaglpvlvrGgGssllgqavatggvvldlsrlnrileideeegtatveaGvtlgdlvea 80 
                                    p av++pes+eevaa++r+ +++g+p+++++gGs+++g+ +++g+vv+d++r+nr+l+++e++ +a++e+Gv l +l+e+
  gi|119720277|ref|YP_920772.1|  54 PLAVAWPESAEEVAAVVRVLARHGVPFVPYAGGSGVIGGTICEGCVVIDVKRMNRVLWFSERDAVAVAESGVLLRKLEEY 133
                                    789**********************************99999********99**************************** PP

                                    HHHHTTECSSGGGTTCGSBHHHTTTTT-EETTEEGG--HHGTEEEEEEEETTSEE CS
                  FAD_binding_4  81 laakglllglepgsgipgtvGGaiatnagGygsekyGlirdnvlglevvladGev 135
                                    l+a+g++l++ p+s+ ++ +GG++at + G+ s+kyG i++ vl le+v++dG++
  gi|119720277|ref|YP_920772.1| 134 LNARGFTLRHIPQSYPEAALGGLVATMSTGQFSTKYGGIEELVLDLEAVMPDGRI 188
                                    *****************************************************98 PP

>> FAD-oxidase_C  FAD linked oxidases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.2   0.1   4.5e-39   2.7e-35       6     249 ..     234     462 ..     229     463 .. 0.92

  Alignments for each domain:
  == domain 1  score: 122.2 bits;  conditional E-value: 4.5e-39
                                    EEEEEEESSHHHHHHHHHHHHHHT---SEEEEE-HHHHHHHHHTS-SSTTS-TTT-EEEEEEEEE-HHHHHHHHHHHHHH CS
                  FAD-oxidase_C   6 avalvafpsfeaavkavreiaqagiipaalelmdkkaldlveatkgakkglpdeeealllvefegddeeeaeeelealve 85 
                                       + afpsfe++++a+re++ +g  pa  +l+dk+ + +   +  +          +ll+ +e  +ee +e++ + ++e
  gi|119720277|ref|YP_920772.1| 234 WMRAYAFPSFEKGLEAMREVMLSGATPAVARLYDKDDSAARFHDARD----------ILLLIVEEAEEELLEAKRR-VIE 302
                                    556779********************************999999999..........5555555555578888888.*** PP

                                    HTTT-EEEEE..........ETGGGGGGGGHHHHHHHHHCTTEEEEEEEEEEEHHHHHHHHHHHHHHHHHHH...EEEEE CS
                  FAD-oxidase_C  86 aileatgaadvlvaqdeaeaealwkaRkaalpylrdallkagvavlseDtsvPvsrladlvrdikalldkyg...levvl 162
                                    +il+ +ga d      e+ +e+++k R +++  l++++   + + ++ +t+  +s+l+++++++k+++++     ++ ++
  gi|119720277|ref|YP_920772.1| 303 RILSRHGAVD----AGEEHVEKWLKTRFDVISELKKLVVPLNLWFETIETAALWSNLPRVYAEFKKRVKSVPgvyAVLAH 378
                                    **********....888888***************************************************9999999** PP

                                    EEEEETTEEEEEEEEEEE..--TT--THHHHHHHHHHHHTT-----------------------THHHHHHHHHHHH-TT CS
                  FAD-oxidase_C 163 fgHagdgnlhlyilfdladeaeeeraeklvdevvdlavelgGsisgEHGvGldkkaylerekgeeglalmrriKaalDPk 242
                                     +H++  ++++y++++ +  a e+ + ++++  v++ +e+g +is++HGvGl +++++ +e g+ +l++++r+K+alDP 
  gi|119720277|ref|YP_920772.1| 379 ASHFYTTGACIYFTLTYD--AREDVYWRMWETAVRVLLENGATISHHHGVGLLRAKWVGEELGD-TLEYLKRVKKALDPG 455
                                    *************99664..7888888899999*****************************98.*************** PP

                                    --BSTT- CS
                  FAD-oxidase_C 243 giLNPgk 249
                                    ++ NPgk
  gi|119720277|ref|YP_920772.1| 456 NLSNPGK 462
                                    ******9 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       2.4   1.4e+04      44      62 ..      58      76 ..      55      76 .. 0.67
   2 ?   -0.4   0.0      0.27   1.6e+03      21      63 ..      95     137 ..      92     143 .. 0.67
   3 ?    9.8   0.4   0.00017         1      22      86 ..     251     313 ..     247     319 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2.4
                Glyco_trans_1_2 44 ilfedleelaekiryllan 62
                                    + e+ ee+a+ +r l ++
  gi|119720277|ref|YP_920772.1| 58 AWPESAEEVAAVVRVLARH 76
                                   5667788888877766554 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.27
                Glyco_trans_1_2  21 cGafaltddaeglee..lftpgkevilfedleelaekiryllanp 63 
                                    c ++++ d  + + +  +f++ ++++ +++   l++k++++l+ +
  gi|119720277|ref|YP_920772.1|  95 CEGCVVID-VKRMNRvlWFSE-RDAVAVAESGVLLRKLEEYLNAR 137
                                    77777777.545555224544.46666677788999999999876 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.00017
                Glyco_trans_1_2  22 Gafaltddaegleelftpgkevilfedleelaekiryllanpeerraiaeaarervlaehtydhr 86 
                                      ++l+ +++++++l+++++++  f+d  +++  i +  + +ee  +  ++ +er+l++h  + +
  gi|119720277|ref|YP_920772.1| 251 REVMLSGATPAVARLYDKDDSAARFHDARDILLLIVE--EAEEELLEAKRRVIERILSRHGAVDA 313
                                    5689***99**********************999998..7899999999***********87765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (465 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 3174.89
//
Query:       gi|119720278|ref|YP_920773.1|  [L=479]
Description: carbohydrate kinase, FGGY [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-27   96.0   0.0    5.8e-27   94.7   0.0    1.6  2  FGGY_C    FGGY family of carbohydrate kinases, C-terminal dom
    5.2e-24   85.2   0.0    7.5e-24   84.6   0.0    1.2  1  FGGY_N    FGGY family of carbohydrate kinases, N-terminal dom


Domain annotation for each model (and alignments):
>> FGGY_C  FGGY family of carbohydrate kinases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.38   3.4e+03      50      69 ..     130     150 ..     129     193 .. 0.72
   2 !   94.7   0.0   6.4e-31   5.8e-27       4     192 ..     244     420 ..     241     425 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.38
                         FGGY_C  50 lvawlldnl.glreeirdage 69 
                                    l++wl dn  glre++++ + 
  gi|119720278|ref|YP_920773.1| 130 LMKWLYDNVpGLREKVERGDA 150
                                    578999998888887766444 PP

  == domain 2  score: 94.7 bits;  conditional E-value: 6.4e-31
                         FGGY_C   4 slGTssflllvgtkpvisehglltpva.gedgkpeyalegsiavagslvawlldnlglreeirdageveeslaelaaaea 82 
                                    + GT+sf+  +++k v + +gl   v  + dg+++y++eg+ ++ g +v+wl++  g+   +++ +e+ esla      +
  gi|119720278|ref|YP_920773.1| 244 VHGTGSFVEESTPKLVVPGEGLVPVVIaSLDGRRFYGAEGFLRASGLVVEWLRSA-GF---FSSYEEM-ESLA------S 312
                                    68**************888888777654888**********************99.88...6665565.6666......5 PP

                         FGGY_C  83 vadaggvvfvpafsglrapywdpdargtitglsssttlahiarAaleavalqlrailealekdsgkpldrlavdGGgskn 162
                                    +a++ + ++vp f glr+p   p ++g+i+gl+ stt+a+++  +  +val +++ l +l+k  g+p ++l+  GG s++
  gi|119720278|ref|YP_920773.1| 313 KAKP-RAIVVPSFRGLRTP-DAPLLKGMILGLDPSTTKADVVAGLAWGVALYVAYLLGKLSKYCGSPREPLWSGGGYSRS 390
                                    5555.789***********.58********************************************************** PP

                         FGGY_C 163 dllmqllAdilgvpVerpktaeatalGaAi 192
                                    ++++q lAd++g++V rp++ e+ + G+  
  gi|119720278|ref|YP_920773.1| 391 NAFLQALADATGLKVARPRDVESSIRGVLK 420
                                    ************************999865 PP

>> FGGY_N  FGGY family of carbohydrate kinases, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.6   0.0   8.4e-28   7.5e-24       1     216 [.       1     214 [.       1     228 [. 0.90

  Alignments for each domain:
  == domain 1  score: 84.6 bits;  conditional E-value: 8.4e-28
                                    EEEEEEEESSEEEEEEEETTS-EEEEEEEE--EB-SSTT--EE-HHHHHHHHHHHHHHHHHHCT.-GCCEEEEEEEE-SS CS
                         FGGY_N   1 lilglDcGttstkaivldekgkvvasaqaelelsspkegwaeqdpeeiwqalaeairkvleqagisekqikaIgisgqre 80 
                                    ++ ++D+Gtt++k +v+d + k ++ +++el  + +  g++eq+ +e+      ++r   ++a   +  ++ Ig s+ r 
  gi|119720278|ref|YP_920773.1|   1 MYGVIDVGTTGVKLAVFDGELKSIHYERVELGYEPAGSGRVEQSSAEMSR----VVRGFARKA--RSLGARRIGLSTYRA 74 
                                    7899*****************************************99755....555555555..555799********* PP

                                    -EEEEETTTEESSEEE-TT--TTHHHHHHHHH.TTCHCCHHHHHSS-SSTTSHHHHHHHHHHHSCCHHCCHC....EEEE CS
                         FGGY_N  81 glvllDkndkpLynailwkdrrtaeiveklke.egnekklyektglvlstgftlsklkWlkenepevfekie....kfll 155
                                    ++v++ k ++pL+n+++w d r  e+ve+l       ++l +    vl + ++++ +kWl +n+p+ +ek+e       +
  gi|119720278|ref|YP_920773.1|  75 SVVAWSKSGEPLTNIVTWIDGRGREVVERLPVwVKLLEALSPSLAKVLRPDTPAVLMKWLYDNVPGLREKVErgdaYLWT 154
                                    ******************************9988899***********************************9*977789 PP

                                    HHHHHHHHHCT--EEEHHHHCTTTSEETTTTEE-HHHHHHTT--GGGS-EEE-TCCEEEEE CS
                         FGGY_N 156 iddyLiwrLtgqfvtdvtnasesmlfnikklewdeellailgipeelLPklvesseiigel 216
                                     d+yL + Ltg +++d t  + ++l+  ++le    ++ il +pe+  P++v s + +ge 
  gi|119720278|ref|YP_920773.1| 155 LDSYLVYLLTGRYASDATSSALTGLVHPRDLEPIGAVFGILSLPEA-APEIVDSVHEFGEF 214
                                    9************************999988877777777777765.48888888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (479 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       260  (0.0145016); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 3300.85
//
Query:       gi|119720279|ref|YP_920774.1|  [L=313]
Description: hypothetical protein Tpen_1374 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.6e-07   29.1   0.1      2e-06   27.3   0.1    1.8  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    2.4e-05   24.5   1.4    9.6e-05   22.5   0.2    2.7  4  NAD_binding_8  NAD(P)-binding Rossmann-like domain
  ------ inclusion threshold ------
      0.026   14.5   0.9         12    5.8   0.1    3.3  3  NAD_binding_9  FAD-NAD(P)-binding
      0.083   12.5   1.9        8.9    5.8   0.1    3.1  3  DAO            FAD dependent oxidoreductase
       0.12   13.0   0.7        1.9    9.1   0.1    2.5  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.1   5.5e-10     2e-06       4     233 ..       1     209 [.       1     210 [. 0.75

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 5.5e-10
                                    EEE--SHHHHHHHHHHHHHTS-EEEEE.TTHCHHHCSHHHHCHHHHHHHHHHHHHHHHHCHHHHCCCCHCCTCEEEEESC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2   4 vviGgGpAGlaaaltlaqagakvtlve.legtclnggcllskallgvaedaeiasevvkklnqgielllgeevvkidpgk 82 
                                    +viG+G  Gla+a  l+  +++v+ v  + g ++ ++  +   ++g++         v++l +g ++++g+ ++++d+g 
  gi|119720279|ref|YP_920774.1|   1 MVIGSGLSGLALADSLRGVEVEVYEVRrEPGGFFARDDYPVDGVRGSE--------LVSRLLAGRKVRTGVAAFRLDEGG 72 
                                    79**************99888888884444455555555544444444........4445555678888888******** PP

                                    EEEEETEEECTCEEEEEESEEEE---EEE-BC...TCTTC.TTBEECCSECHHHHHHCCSS-T....SEEEEES-SHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxx RF
                    Pyr_redox_2  83 kkvklekkkegdeekiaydklvlAtGssprdl...gipGvaenvgklvrtldsaealklkllp....krivvvGgGyiGv 155
                                    + +       +++   a +++vlAtG++ r+    g+ G  + +      +  + a+  +++     +r+++ G     +
  gi|119720279|ref|YP_920774.1|  73 AWFLG-----EEGAFRAEGRVVLATGFRERTAvelGVYGCRPAG-----VFPLTAAWDFANMGysvgDRVLIYGFNHYTL 142
                                    88877.....334445559********99998444555554444.....3444444555555555889************ PP

                                    HHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 156 ElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgngeklevvledgeeidadlvvv 233
                                     lA+ l k+ ++v+++++ + l+          + eal+  Gvev  + +v +++g+++ +e+v +d +e+ +d +v+
  gi|119720279|ref|YP_920774.1| 143 SLASRLVKVCDKVVILYREPSLVH--------SVDEALR-LGVEVE-RGRVRRVEGRDR-VELVKTDSSELRVDALVL 209
                                    **********************93........3444454.5*****.88899******8.99*************997 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.2   2.7e-08   9.6e-05       1      40 [.       2      39 ..       2      79 .. 0.85
   2 ?   -1.8   0.0       1.1   3.8e+03       4      22 ..     110     128 ..     110     135 .. 0.78
   3 ?   -3.4   0.0       3.3   1.2e+04      43      63 ..     255     274 ..     249     278 .. 0.63
   4 ?   -2.5   0.0       1.7   6.2e+03      41      54 ..     281     294 ..     265     301 .. 0.64

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 2.7e-08
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECE CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasyev 40
                                   ++G+GlsGl++A  L+  g++v+++e r+ +GG  a+ ++
  gi|119720279|ref|YP_920774.1|  2 VIGSGLSGLALADSLR--GVEVEVYEVRREPGGFFARDDY 39
                                   8**************9..8**************8877655 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.1
                                    -SHHHHHHHHHHHCCTEEE CS
                  NAD_binding_8   4 aGlsGlvaAylLakagfdv 22 
                                    aG++ l+aA+  a+ g++v
  gi|119720279|ref|YP_920774.1| 110 AGVFPLTAAWDFANMGYSV 128
                                    7888899**9999988854 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 3.3
                                    CEECTS---EEETTHHHHCHH CS
                  NAD_binding_8  43 vrvdygahifhgsgyypnvrr 63 
                                    +rv+ g+ +f g   ++++rr
  gi|119720279|ref|YP_920774.1| 255 RRVEGGVPAFPGY-VSEKHRR 274
                                    7788888888775.3455554 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 1.7
                                    TTCEECTS---EEE CS
                  NAD_binding_8  41 pgvrvdygahifhg 54 
                                     g rv +g +i+++
  gi|119720279|ref|YP_920774.1| 281 RGARVRLGDRIVTT 294
                                    35677777777766 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.018        65       2      16 ..       2      16 ..       1      40 [. 0.80
   2 ?    2.2   0.0     0.045   1.6e+02     119     154 ..      58      93 ..      43      95 .. 0.82
   3 ?    5.8   0.1    0.0035        12     115     151 ..     174     209 ..     158     211 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.018
                  NAD_binding_9  2 ivGaGprGlavlerL 16
                                   ++G G +Gla+++ L
  gi|119720279|ref|YP_920774.1|  2 VIGSGLSGLALADSL 16
                                   8*********99987 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.045
                  NAD_binding_9 119 vhraevvdleeradgqavlladgaslaadaVvLAlG 154
                                     +r+ v + + +++g+++l ++ga  a  +VvLA+G
  gi|119720279|ref|YP_920774.1|  58 KVRTGVAAFRLDEGGAWFLGEEGAFRAEGRVVLATG 93 
                                    56778888888899999999999999999******9 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.0035
                  NAD_binding_9 115 vtvevhraevvdleeradgqavlladgaslaadaVvL 151
                                    + vev r++v ++e r d+++++++d ++l++da+vL
  gi|119720279|ref|YP_920774.1| 174 LGVEVERGRVRRVEGR-DRVELVKTDSSELRVDALVL 209
                                    5689999******977.667999************98 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.1    0.0025       8.9       4      33 ..       2      31 ..       1      35 [. 0.93
   2 ?    1.3   0.1     0.056     2e+02     162     202 ..      58      94 ..      48     113 .. 0.71
   3 ?    3.2   0.0     0.015        54     154     198 ..     169     209 ..     161     265 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0025
                                   EECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                            DAO  4 iiGGGiiGlstAyeLarrg..Vtllekgdiag 33
                                   +iG+G  Gl+ A  L  rg  V ++e ++++g
  gi|119720279|ref|YP_920774.1|  2 VIGSGLSGLALADSL--RGveVEVYEVRREPG 31
                                   9**************..7999*****999998 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.056
                                    EEEESECEEEEEEEETCEEEEEEECTEEEEEEEE...EEE--GG CS
                            DAO 162 eilegtevtgleeedgkvwgverttpgendaada...vVnaaGa 202
                                    ++++g  v +++ ++g++w +     ge+ a++a   vV+a+G 
  gi|119720279|ref|YP_920774.1|  58 KVRTG--VAAFRLDEGGAWFL-----GEEGAFRAegrVVLATGF 94 
                                    55555..55555567889999.....55544577778*****95 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.015
                                    HHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE CS
                            DAO 154 raaealGveilegtevtgleeedgkvwgverttp.gendaadavVn 198
                                    ++a +lGve+ +g +v+++e + ++v  v  +t+  e  ++da+V+
  gi|119720279|ref|YP_920774.1| 169 DEALRLGVEVERG-RVRRVEGR-DRVELV--KTDsSEL-RVDALVL 209
                                    68999********.****9654.466666..5553333.3688886 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1   0.00052       1.9       3      31 ..       1      29 [.       1      33 [. 0.89
   2 ?    1.8   0.0       0.1   3.6e+02       2      43 ..     132     173 ..     131     199 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00052
                                   EEECSSHHHHHHHHHHHHTTSEEEEEESS CS
                      Pyr_redox  3 vvvGgGyiglElAgalaelgkkVtvvers 31
                                   +v+G+G++gl lA  l+    +V+ v r+
  gi|119720279|ref|YP_920774.1|  1 MVIGSGLSGLALADSLRGVEVEVYEVRRE 29
                                   59****************99999877775 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.1
                                    EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHH CS
                      Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeas 43 
                                    v++ G     l lA+ l +  +kV ++ r++ l    De+++
  gi|119720279|ref|YP_920774.1| 132 VLIYGFNHYTLSLASRLVKVCDKVVILYREPSLVHSVDEALR 173
                                    556666666678899999999999999999999988888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       279  (0.0155614); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 2149.79
//
Query:       gi|119720280|ref|YP_920775.1|  [L=461]
Description: FAD dependent oxidoreductase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-47  162.4   0.6    2.8e-47  162.0   0.2    1.4  2  DAO             FAD dependent oxidoreductase
    2.3e-11   43.8   6.3    4.1e-11   43.1   6.3    1.4  1  Fer2_BFD        BFD-like [2Fe-2S] binding domain
    1.7e-10   40.6   0.1    0.00024   20.4   0.0    2.3  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    4.3e-08   33.3   0.0    1.2e-07   31.9   0.0    1.7  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    1.8e-05   25.2   0.3      0.002   18.6   0.1    2.7  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
      5e-05   22.2   0.0    0.00046   19.0   0.0    2.0  2  HI0933_like     HI0933-like protein
    8.6e-05   21.9   0.2    0.00027   20.3   0.2    1.9  1  FAD_binding_3   FAD binding domain
    0.00013   21.3   0.8    0.00017   20.9   0.1    1.6  2  Thi4            Thi4 family
    0.00018   20.5   0.5     0.0072   15.2   0.1    2.1  2  Trp_halogenase  Tryptophan halogenase
    0.00028   20.1   0.1    0.00056   19.1   0.1    1.5  1  FAD_binding_2   FAD binding domain
     0.0006   19.0   0.0     0.0017   17.5   0.0    1.8  2  Lycopene_cycl   Lycopene cyclase protein
     0.0052   16.4   0.0     0.0082   15.7   0.0    1.3  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
     0.0085   16.1   0.2       0.26   11.3   0.0    2.3  2  NAD_binding_9   FAD-NAD(P)-binding
  ------ inclusion threshold ------
      0.012   16.0   0.0      0.024   15.0   0.0    1.4  1  SO_alpha_A3     Sarcosine oxidase A3 domain
      0.027   13.8   0.1       0.05   12.9   0.1    1.5  1  FAD_oxidored    FAD dependent oxidoreductase
      0.034   13.4   0.0          7    5.8   0.0    2.2  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
      0.069   13.4   0.1       0.17   12.1   0.1    1.7  1  TrkA_N          TrkA-N domain
      0.088   12.4   0.1       0.28   10.8   0.0    1.8  2  ApbA            Ketopantoate reductase PanE/ApbA
      0.095   12.0   0.0       0.16   11.2   0.0    1.3  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
       0.14   12.6   0.1       0.29   11.6   0.1    1.5  1  NAD_binding_7   Putative NAD(P)-binding


Domain annotation for each model (and alignments):
>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.0   0.2   3.1e-50   2.8e-47       1     351 [.       3     352 ..       3     353 .. 0.79
   2 ?   -3.1   0.0       4.8   4.3e+03     115     161 ..     393     443 ..     378     447 .. 0.61

  Alignments for each domain:
  == domain 1  score: 162.0 bits;  conditional E-value: 3.1e-50
                                    EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTHHHHHHHHHHHHHHHHHHHHHSST CS
                            DAO   1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsglrylpeaselarlslealeelreleeelgid 78 
                                    dvvi+G+Gi+Gl tAy L+r +  V+++++++++g+g S + ++++h  +  lp  s + r+++e++++l e+++elg  
  gi|119720280|ref|YP_920775.1|   3 DVVIVGSGIVGLMTAYRLSRYKlrVLVVDSNPEPGWGVSKGHAAIVHV-VQ-LPFSSLKSRMAREGNRLLGEVARELG-- 78 
                                    9*****************999999************************.65.88777888******************.. PP

                                    TSEEEEEEEEEESSHHHHHHHHHHHHHH.......HHTTT..TEEEEEHHHHHHHSTT.STTTSEEEEETTEEEEEHHHH CS
                            DAO  79 idyrrtGllslaadeeelealdkllall.......leagl..daelldaeevrelepa.lpgllgalfypdtgqvdpakl 148
                                    + ++rt +l++a++         llal+       l +g   +++l  +  +r+ ep+ +++ lga+ +++ g+vd + l
  gi|119720280|ref|YP_920775.1|  79 VRLERTSTLVVATKL---HH---LLALPlvalylrLNLGKefPVKLRGRGYLRREEPGlTRKALGAVEVYGYGCVDNFDL 152
                                    789********9752...22...22332334444432333224455555668888899766999**************** PP

                                    HHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEE..EEE--GGGHHHH.HTTCTTTSEEEEEEEEE CS
                            DAO 149 taalaraaealGveilegtevtgleeedgkvwgverttp.gendaada..vVnaaGawsdll.gllkeldlpispvrgqv 224
                                    + +l++ a a+Gve+++g++v++ +  +++ ++v  +t+ g++  ++a  +VnaaG+w+d++ + +++    ++  +g  
  gi|119720280|ref|YP_920775.1| 153 LYGLYEFASANGVEFRFGERVVAARVLEDR-VEV--ETDkGNV--YEAgfLVNAAGLWADEVaRFTGDE-ASFELGKGVL 226
                                    ***********************9765444.556..7777987..44555**********883444333.58899***** PP

                                    EEEEECCT.HSTGSGCSEEEEEEEETTTTEEEEEETTSEEEEEESSE.EETTCSSTSCSHHHHHHHHHHHHHHSGGGCG. CS
                            DAO 225 lvlkplse.klvspaailpvpetdddgrgvyvtprkdgrvlvGgtad.eesgdddpevdeedidellealrklfPqlgd. 301
                                    lv+++++   +v+pa + p+  + + g+ v +t   dgr l G++    ++++d+  vdeed++ l+++ + l+ ++   
  gi|119720280|ref|YP_920775.1| 227 LVFDRRHTrRFVAPAYLKPD--PKTKGGAVMFTV--DGRGLWGPNLRpARDKYDV-CVDEEDVEMLYRKFAPLLEGDPGi 301
                                    ***77777355555444444..445556666666..788899**99755555555.******************887442 PP

                                    EEEEEEEEEEE.TTSSEEEEEEETEEEEEEEEECTTTHHHHHHHHHHHHHH CS
                            DAO 302 vlrkwaGlrpl.pdglpligetpgvkglylatGhsghGltlapatGkllae 351
                                     l+++aG+rp  p +++ i  +  ++++++a G +++++t +pa++  ++ 
  gi|119720280|ref|YP_920775.1| 302 PLKAYAGVRPIpPENDFRITYSKSSRRVVHAIGTESPAFTASPAIADRIVS 352
                                    447*******74788******77788********************98875 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 4.8
                                    EEEHHHHHHHSTT.STTTSEEEE.ETTE.EEEEHHHHHHHHHHH.HHHTT- CS
                            DAO 115 lldaeevrelepa.lpgllgalf.ypdt.gqvdpakltaalara.aealGv 161
                                    l+++eevre     ++ l+g +f +  + g+++ a+ +a +ar  ae+lGv
  gi|119720280|ref|YP_920775.1| 393 LVTEEEVREAVRRgSRTLQGVMFrTGACmGTCQGARCIAEVARIvAEELGV 443
                                    677777887775433344454442333356666666666666666666666 PP

>> Fer2_BFD  BFD-like [2Fe-2S] binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.1   6.3   4.5e-14   4.1e-11       1      51 []     387     439 ..     387     439 .. 0.96

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 4.5e-14
                       Fer2_BFD   1 iVCrCegvtegeIrdairraglttveevkrrtkagtg.Cgg..CrpaieeiLae 51 
                                    +VC+C  vte+e+r+a+ r g +t+++v+ rt+a +g C+g  C+ ++++i+ae
  gi|119720280|ref|YP_920775.1| 387 VVCTCSLVTEEEVREAV-RRGSRTLQGVMFRTGACMGtCQGarCIAEVARIVAE 439
                                    6****************.6689*****************************986 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   2.7e-07   0.00024       1      50 [.       2      51 ..       2      94 .. 0.76
   2 !   17.9   0.0   1.6e-06    0.0014     194     255 ..     161     224 ..     156     236 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.7e-07
                                   CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHH.HCHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx RF
                    Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcll.skallgva 50
                                   +dvv++G+G+ Gl +a +l++++++v++v + +  +++g++  + a+++v 
  gi|119720280|ref|YP_920775.1|  2 YDVVIVGSGIVGLMTAYRLSRYKLRVLVV-DSNPEPGWGVSKgHAAIVHVV 51
                                   69***************************.888888888776444555554 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 1.6e-06
                                    HHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S-EEES-HHCS..HCCT-EEEET CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxx RF
                    Pyr_redox_2 194 ekeGvevklgtsvkeidgngeklevvledgeeidadlvvvavGvrpstelle..eklglelder 255
                                     ++Gve+++g++v++++  ++++ev++++g++++a  +v a+G+ ++   +   +++  el ++
  gi|119720280|ref|YP_920775.1| 161 SANGVEFRFGERVVAARVLEDRVEVETDKGNVYEAGFLVNAAGLWADEVARFtgDEASFELGKG 224
                                    679******************************************9998887788888887444 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.0   1.3e-10   1.2e-07       1      33 [.       6      39 ..       6      62 .. 0.86

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 1.3e-10
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSS.G CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlG.G 33
                                   IvG+G+ Gl +Ay+L++++++vl++++++ +G G
  gi|119720280|ref|YP_920775.1|  6 IVGSGIVGLMTAYRLSRYKLRVLVVDSNPEPGwG 39
                                   9******************************952 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.1   2.2e-06     0.002       2      35 ..       4      37 ..       3      50 .. 0.92
   2 ?    3.7   0.0       0.1        92      51      77 ..     161     186 ..     156     190 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.2e-06
                                   EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                      Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                   vv+vG+G +gl+ A  l++++ +V vv+ ++++ 
  gi|119720280|ref|YP_920775.1|  4 VVIVGSGIVGLMTAYRLSRYKLRVLVVDSNPEPG 37
                                   8***************************999886 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.1
                                    HHTTEEEECSEEEEEEEEETTSEEEEE CS
                      Pyr_redox  51 ekngievllntkveeiegsedgvesvk 77 
                                    ++ng+e++++++v++ +  ed ve v+
  gi|119720280|ref|YP_920775.1| 161 SANGVEFRFGERVVAARVLEDRVE-VE 186
                                    789************999888743.44 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   5.2e-07   0.00046       1      36 [.       2      37 ..       2      42 .. 0.95
   2 ?    0.7   0.0      0.18   1.6e+02     115     163 ..     156     203 ..     148     206 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 5.2e-07
                                   -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                    HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllekakklg 36
                                   +dv+++G G  Glm+A ++++ + rVl++++++++g
  gi|119720280|ref|YP_920775.1|  2 YDVVIVGSGIVGLMTAYRLSRYKLRVLVVDSNPEPG 37
                                   59******************************9988 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.18
                                    HHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE--- CS
                    HI0933_like 115 llkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtG 163
                                    l + ++++gv++r  ++v +++  ed+ ++v+t++++ +ea  lv A G
  gi|119720280|ref|YP_920775.1| 156 LYEFASANGVEFRFGERVVAARVLEDR-VEVETDKGNVYEAGFLVNAAG 203
                                    66677899*************998888.*****9999999999998877 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.2     3e-07   0.00027       2      35 ..       2      35 ..       1     284 [. 0.80

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 3e-07
                                   EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
                  FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrst 35
                                   +dV+IVG+G +Glm+a  Ls++  rv++v+   +
  gi|119720280|ref|YP_920775.1|  2 YDVVIVGSGIVGLMTAYRLSRYKLRVLVVDSNPE 35
                                   69****************************8765 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.1   1.9e-07   0.00017      19      67 ..       3      50 ..       1      93 [. 0.87
   2 ?   -3.9   0.1       7.4   6.6e+03      33      59 ..     434     457 ..     429     457 .. 0.61

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.9e-07
                                   EEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTTBSEE CS
                           Thi4 19 DvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGqlfsai 67
                                   DvvivG+G  GL +ay l++  +l+v++++++  pG G+  G     ++
  gi|119720280|ref|YP_920775.1|  3 DVVIVGSGIVGLMTAYRLSRY-KLRVLVVDSNPEPGWGVSKGHAAIVHV 50
                                   9*******************9.****************99987665554 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 7.4
                                    HHHHHHCTTS-EEEEESSSS--TTTTT CS
                           Thi4  33 ayylakkpdlkvailersvspGGGawl 59 
                                    a+++a++  l v + e  +  GGG+wl
  gi|119720280|ref|YP_920775.1| 434 ARIVAEE--LGVGVEELTL-RGGGSWL 457
                                    5555555..5555544444.6888886 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   8.1e-06    0.0072       1      51 [.       3      52 ..       3      59 .. 0.86
   2 ?    3.6   0.1     0.028        25     160     209 ..     156     204 ..     137     212 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 8.1e-06
                                   EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS---SS..-EE--THHHH CS
                 Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlveseeigtvgv..Geatipsirk 51
                                   ++vivG G+ G ++A  l+++    l+v++v+s+  +  gv  G a+i ++++
  gi|119720280|ref|YP_920775.1|  3 DVVIVGSGIVGLMTAYRLSRYK---LRVLVVDSNPEPGWGVskGHAAIVHVVQ 52
                                   69*******************9...9********9999998556677777666 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.028
                                    HHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-SEEEE-SGG CS
                 Trp_halogenase 160 LrrvaearGvtrvegkvvevqldedgrveslrledgreveadlfiDcsGf 209
                                    L ++a a+Gv+ + g+ v +    ++rve +++++g+++ea + + + G 
  gi|119720280|ref|YP_920775.1| 156 LYEFASANGVEFRFGERVVAARVLEDRVE-VETDKGNVYEAGFLVNAAGL 204
                                    7789*********9998766666688986.999**************995 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.1   6.3e-07   0.00056       1      33 [.       3      35 ..       3      49 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 6.3e-07
                                   SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSG CS
                  FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqe 33
                                   Dv+++GsG+ GL+ A+++++  l+v+vv+  +e
  gi|119720280|ref|YP_920775.1|  3 DVVIVGSGIVGLMTAYRLSRYKLRVLVVDSNPE 35
                                   9***************************98876 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.9e-06    0.0017       1      39 [.       3      39 ..       3      44 .. 0.94
   2 ?   -3.3   0.0         4   3.6e+03     110     144 ..     174     207 ..     142     227 .. 0.65

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.9e-06
                  Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieaspsllfp 39
                                   Dvv++G+G  gl  A rl  ++++l+v+++++ p++ ++
  gi|119720280|ref|YP_920775.1|  3 DVVIVGSGIVGLMTAYRL--SRYKLRVLVVDSNPEPGWG 39
                                   9*****************..************9998775 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4
                  Lycopene_cycl 110 esveeeeageslvvleggrkirarlvvdarglasl 144
                                     +++  e+ ++ v ++ g+  +a + v a gl + 
  gi|119720280|ref|YP_920775.1| 174 VAARVLED-RVEVETDKGNVYEAGFLVNAAGLWAD 207
                                    33333333.55777777888888888888886554 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   9.1e-06    0.0082       3      35 ..       4      36 ..       2      76 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 9.1e-06
                                   EEEE--STTHHHHHHHHHHCTSEEEEE-S-HHH CS
                 UDPG_MGDP_dh_N  3 isviGlGYvGlvtaavlaeighevigvDideek 35
                                   ++++G+G vGl+ta  l++    v++vD + e 
  gi|119720280|ref|YP_920775.1|  4 VVIVGSGIVGLMTAYRLSRYKLRVLVVDSNPEP 36
                                   89***************************9875 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   0.00029      0.26       1      39 [.       5      38 ..       5      59 .. 0.82
   2 ?    2.5   0.0      0.14   1.3e+02     120     154 ..     169     203 ..     156     204 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00029
                  NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsep.gag 39
                                   +ivG G+ Gl+++ rL + +     l++ ++d ++  g  
  gi|119720280|ref|YP_920775.1|  5 VIVGSGIVGLMTAYRLSRYK-----LRVLVVDSNPEpG-W 38
                                   7****************995.....********76546.3 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.14
                  NAD_binding_9 120 hraevvdleeradgqavlladgaslaadaVvLAlG 154
                                    + ++vv+ +  +d+++v +++g+ ++a  +v A G
  gi|119720280|ref|YP_920775.1| 169 FGERVVAARVLEDRVEVETDKGNVYEAGFLVNAAG 203
                                    3789***********************99998887 PP

>> SO_alpha_A3  Sarcosine oxidase A3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   2.7e-05     0.024      12      66 ..     394     448 ..     385     452 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.7e-05
                    SO_alpha_A3  12 vtvkdielavregfesiehvKRYttlgmgtdQgklsavnaaaivaeltgkevaev 66 
                                    vt++++++avr g + ++ v   t++ mgt Qg     + a+ivae+ g  v+e+
  gi|119720280|ref|YP_920775.1| 394 VTEEEVREAVRRGSRTLQGVMFRTGACMGTCQGARCIAEVARIVAEELGVGVEEL 448
                                    99*******************9************99999********99888776 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   5.6e-05      0.05       1      39 [.       3      41 ..       3      95 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.6e-05
                   FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGllt 39
                                   Dvv+vG+g+ G++ A+   r   +vl+v+ ++  G  ++
  gi|119720280|ref|YP_920775.1|  3 DVVIVGSGIVGLMTAYRLSRYKLRVLVVDSNPEPGWGVS 41
                                   9******************************99985444 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0      0.01       9.3       1      29 [.       5      32 ..       5      37 .. 0.92
   2 ?    5.8   0.0    0.0078         7      89     135 ..     158     205 ..     150     220 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.01
                    Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEk 29
                                   +I+G G  Gl +a+ l + +l ++l+++ 
  gi|119720280|ref|YP_920775.1|  5 VIVGSGIVGLMTAYRLSRYKL-RVLVVDS 32
                                   7********************.799*997 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0078
                    Pyr_redox_3  89 evaksfelpiklfeeVesvkkedegfevetske.tyeAkkviiAtGef 135
                                    e a+ + ++ +  e+V +    ++  evet+k+ +yeA +++ A+G +
  gi|119720280|ref|YP_920775.1| 158 EFASANGVEFRFGERVVAARVLEDRVEVETDKGnVYEAGFLVNAAGLW 205
                                    56777888889999999999999*********879***********76 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00019      0.17       1      32 [.       4      35 ..       4      53 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00019
                                   EEEES-SHHHHHHHHHHHHTTEEEEEEESSHH CS
                         TrkA_N  1 iiiiGlGrvGrslaeeLseggkdvvvidkdee 32
                                   ++i+G G vG   a +Ls+++ +v+v+d+++e
  gi|119720280|ref|YP_920775.1|  4 VVIVGSGIVGLMTAYRLSRYKLRVLVVDSNPE 35
                                   79*****************7756*******98 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00031      0.28       1      30 [.       4      33 ..       4      40 .. 0.90
   2 ?   -2.7   0.0       4.5     4e+03     107     126 ..     395     415 ..     388     419 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00031
                                   EEEES-SHHHHHHHHHHHHHTHCEEEE-SC CS
                           ApbA  1 iailGaGaiGsllaakLakagadvtlilrs 30
                                   ++i+G+G +G + a++L++ +  v +++ +
  gi|119720280|ref|YP_920775.1|  4 VVIVGSGIVGLMTAYRLSRYKLRVLVVDSN 33
                                   68*****************99999988766 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.5
                                    HHHHHTTTSTTS.EEEEEEEE CS
                           ApbA 107 heeelrealpkp.rvlggvtt 126
                                    +eee+rea+++  r l+gv +
  gi|119720280|ref|YP_920775.1| 395 TEEEVREAVRRGsRTLQGVMF 415
                                    689999999885599999976 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00018      0.16      31      77 ..       4      50 ..       2      89 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00018
                                   EEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEE CS
                    AlaDh_PNT_C 31 vlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvev 77
                                   v+++G G++Gl  +   ++ + +V v+D +p+    +++ +a +v+v
  gi|119720280|ref|YP_920775.1|  4 VVIVGSGIVGLMTAYRLSRYKLRVLVVDSNPEPGWGVSKGHAAIVHV 50
                                   9*****************************99877777766666666 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00032      0.29      10      40 ..       4      34 ..       2      96 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00032
                  NAD_binding_7 10 vlvvGgGevAarkvrklleagakvtvvapev 40
                                   v++vG G v++  +++l +++ +v vv+ + 
  gi|119720280|ref|YP_920775.1|  4 VVIVGSGIVGLMTAYRLSRYKLRVLVVDSNP 34
                                   89*************************9883 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (461 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2866.65
//
Query:       gi|119720281|ref|YP_920776.1|  [L=273]
Description: competence damage-inducible protein A [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.1e-39  133.5   0.0    5.4e-39  133.1   0.0    1.1  1  MoCF_biosynth  Probable molybdopterin binding domain


Domain annotation for each model (and alignments):
>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.1   0.0     3e-43   5.4e-39       2     143 ..      14     178 ..      13     179 .. 0.96

  Alignments for each domain:
  == domain 1  score: 133.1 bits;  conditional E-value: 3e-43
                                    EEEE-HHHHTTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTSSEEEEESS-SSSTT--HHHHHHHH CS
                  MoCF_biosynth   2 vitvGdellsgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleeadviittGGtGptpdDvtpealakl 81 
                                    +++vG+ell g++++tn+++la++l+ lg+ v+++ vvpD eeei+ a+++al +adv+++tGG+GptpdDvt  alak+
  gi|119720281|ref|YP_920776.1|  14 ILSVGNELLIGRVVNTNAAWLAQRLTLLGYAVRRIVVVPDVEEEIAGAFRDALGSADVVVSTGGLGPTPDDVTNFALAKA 93 
                                    89**************************************************9999************************ PP

                                    HSEE-HHHHHHHHHHHHHHCC........................TTSHGGGGGGE.EETTE.EEEE-SSHHHHHHHHHH CS
                  MoCF_biosynth  82 fekelegfeeafrrvslkpgk........................pvgvapgailsravgkt.iigLPGspkavkealee 136
                                    +++++e ++ea+r+v+ k+ +                        pvg+apg+ ++++  ++ +++LPG+p+++++++ e
  gi|119720281|ref|YP_920776.1|  94 LGRPAEVNAEALRMVEEKYARrgypmtperekmavmprgarplpnPVGTAPGILVEEG--SKiVVCLPGVPSEMEAIFLE 171
                                    *******************99*******************************999875..55488*************** PP

                                    HHHGGHH CS
                  MoCF_biosynth 137 illpale 143
                                     ++p l+
  gi|119720281|ref|YP_920776.1| 172 HVEPLLR 178
                                    **99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       222  (0.0123822); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1861.23
//
Query:       gi|119720282|ref|YP_920777.1|  [L=269]
Description: hypothetical protein Tpen_1377 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      0.002   17.5   5.0      0.047   13.1   5.4    2.2  2  zf-ribbon_3      zinc-ribbon domain
     0.0023   18.0   2.0       0.13   12.4   0.1    2.4  2  zf-ACC           Acetyl-coA carboxylase zinc finger domain
     0.0041   17.0   0.1     0.0079   16.1   0.1    1.4  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
     0.0049   16.5   2.1     0.0098   15.5   2.1    1.5  1  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
     0.0095   15.6   0.4      0.018   14.7   0.4    1.5  1  DUF4131          Domain of unknown function (DUF4131)
  ------ inclusion threshold ------
      0.011   15.8   1.1      0.019   15.0   1.1    1.3  1  DZR              Double zinc ribbon
      0.011   15.2   2.6      0.017   14.7   2.6    1.2  1  DUF1700          Protein of unknown function (DUF1700)
      0.031   14.2   0.1      0.053   13.5   0.1    1.4  1  PriA_CRR         PriA DNA helicase Cys-rich region (CRR) doma
      0.034   13.7   0.9      0.047   13.2   0.9    1.1  1  Peptidase_A22B   Signal peptide peptidase
      0.036   13.7   0.1      0.037   13.6   0.1    1.2  1  Wzy_C            O-Antigen ligase
      0.057   13.2   4.7        1.9    8.3   4.7    2.2  1  zinc_ribbon_2    zinc-ribbon domain
      0.067   13.1   2.4        2.1    8.3   2.5    2.3  2  zinc_ribbon_4    zinc-ribbon domain
      0.072   12.6   1.5       0.14   11.7   1.5    1.4  1  TF_Zn_Ribbon     TFIIB zinc-binding
       0.14   12.6   0.2       0.23   11.9   0.2    1.4  1  Lar_restr_allev  Restriction alleviation protein Lar
       0.18   11.5   3.6       0.25   10.9   3.6    1.2  1  ABC_membrane     ABC transporter transmembrane region
       0.23   11.5   2.5       0.58   10.2   2.5    1.8  1  DNA_ligase_ZBD   NAD-dependent DNA ligase C4 zinc finger doma
        1.8    8.6   6.4        3.6    7.7   6.4    1.5  1  Ac76             Orf76 (Ac76)


Domain annotation for each model (and alignments):
>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   5.4   4.4e-05     0.047       2      24 ..     225     251 ..     225     253 .. 0.83
   2 !    8.4   0.2    0.0014       1.4       2      11 ..     243     253 ..     242     258 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.4e-05
                    zf-ribbon_3   2 tvrCPnCGapl....ssddnvCpyCGt 24 
                                    tv+CP CGapl    + + ++C yCG+
  gi|119720282|ref|YP_920777.1| 225 TVKCPVCGAPLklpeTGRETKCSYCGA 251
                                    79*******873344489********6 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0014
                    zf-ribbon_3   2 tvrCPnCGa.p 11 
                                    +++C++CGa +
  gi|119720282|ref|YP_920777.1| 243 ETKCSYCGAtV 253
                                    67899999866 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.2     0.028        30       2      11 ..     226     235 ..     226     236 .. 0.86
   2 !   12.4   0.1   0.00012      0.13       2      16 ..     244     258 ..     244     262 .. 0.94

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.028
                         zf-ACC   2 tKCpsCgeml 11 
                                    +KCp Cg+ l
  gi|119720282|ref|YP_920777.1| 226 VKCPVCGAPL 235
                                    7******976 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00012
                         zf-ACC   2 tKCpsCgemlykkeL 16 
                                    tKC  Cg+++y++++
  gi|119720282|ref|YP_920777.1| 244 TKCSYCGATVYAEDV 258
                                    8************97 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   7.5e-06    0.0079      30      57 ..     227     255 ..     224     262 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 7.5e-06
                 OrfB_Zn_ribbon  30 tCseCgsknkealsgrtfkCpnCgfe.ad 57 
                                    +C++Cg+ +k + +gr+ kC+ Cg++ + 
  gi|119720282|ref|YP_920777.1| 227 KCPVCGAPLKLPETGRETKCSYCGATvYA 255
                                    8***********************98444 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   2.1   9.3e-06    0.0098       6      32 .]     228     254 ..     228     254 .. 0.98

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 9.3e-06
                  zf-NADH-PPase   6 CgrCGaptepaeggwarvCpaCglehY 32 
                                    C+ CGap ++ e g+   C+ Cg+ +Y
  gi|119720282|ref|YP_920777.1| 228 CPVCGAPLKLPETGRETKCSYCGATVY 254
                                    ************************998 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.4   1.7e-05     0.018       6      49 ..      10      49 ..       6      91 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.7e-05
                        DUF4131  6 alvllalllllllllllllrrrprrrvllllllllllallgfal 49
                                   ++ l++l++llll+ ++l+    ++ v+++lll+l+l ++++++
  gi|119720282|ref|YP_920777.1| 10 PASLVGLIVLLLLAVVFLW----NPLVAMILLLILFLYSVFVVI 49
                                   5667777777777777775....666666666666666665544 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   1.1   1.8e-05     0.019      15      40 ..     228     255 ..     225     258 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.8e-05
                            DZR  15 CseCgtklkavaa..edrCpsCgekvdp 40 
                                    C+ Cg++lk +++  e++C+ Cg+ v +
  gi|119720282|ref|YP_920777.1| 228 CPVCGAPLKLPETgrETKCSYCGATVYA 255
                                    *******98666688********98765 PP

>> DUF1700  Protein of unknown function (DUF1700)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   2.6   1.6e-05     0.017      81     138 ..      12      69 ..       3      73 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.6e-05
                        DUF1700  81 ailavigLsllnlilvlipliviislvlsllvvalallvsplvllvksllkgfeelsl 138
                                    +++  i L+ll ++++  pl+++i+l++ +l  +++++v+ ++l  + +l+   e+ +
  gi|119720282|ref|YP_920777.1|  12 SLVGLIVLLLLAVVFLWNPLVAMILLLILFLYSVFVVIVAKVALKEERILEKLKEMDA 69 
                                    567788999************************************9999998888765 PP

>> PriA_CRR  PriA DNA helicase Cys-rich region (CRR) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1     5e-05     0.053       1      25 [.     228     252 ..     228     253 .. 0.97

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5e-05
                       PriA_CRR   1 CpnCdvsltyHksrnrLrCHyCgyt 25 
                                    Cp C ++l++   +++ +C yCg+t
  gi|119720282|ref|YP_920777.1| 228 CPVCGAPLKLPETGRETKCSYCGAT 252
                                    ***********************97 PP

>> Peptidase_A22B  Signal peptide peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.9   4.5e-05     0.047     121     174 ..      18     112 ..      12     121 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.5e-05
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...................................... CS
                 Peptidase_A22B 121 ailviellrlpslkvgalLLvglflYDifwVFgtdvmvevAk...................................... 162
                                    ++l+++++ l +  v+++LL+ lflY +f V + +v ++  +                                      
  gi|119720282|ref|YP_920777.1|  18 VLLLLAVVFLWNPLVAMILLLILFLYSVFVVIVAKVALKEERileklkemdasmperpeavlldpdevvvlrghaglcsa 97 
                                    45678899999999*******************98887766666667777777777777777777777777777777777 PP

                                    ...XXXXXXXXXXXX CS
                 Peptidase_A22B 163 ...eldiPillklPq 174
                                        +++P+ l+lP+
  gi|119720282|ref|YP_920777.1|  98 egqAQEFPLTLVLPK 112
                                    777777777777776 PP

>> Wzy_C  O-Antigen ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   3.5e-05     0.037      15      68 ..       9      57 ..       7     184 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.5e-05
                          Wzy_C 15 sRsgiigllvalivlliifykrripfllllgilvgvilliilfvlstnletlkn 68
                                   s ++++gl+v+l++++++++++++     ++il+++++l+ +fv+     +lk 
  gi|119720282|ref|YP_920777.1|  9 SPASLVGLIVLLLLAVVFLWNPLV-----AMILLLILFLYSVFVVIVAKVALKE 57
                                   567899999999999999999999.....7777777777777776555555554 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   4.7    0.0018       1.9       1      21 [.     227     251 ..     227     253 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0018
                  zinc_ribbon_2   1 fCpnCGaelq.dnakF...CpyCGt 21 
                                    +Cp CGa+l+ ++      C+yCG+
  gi|119720282|ref|YP_920777.1| 227 KCPVCGAPLKlPETGRetkCSYCGA 251
                                    7*******97565555677*****8 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.4     0.076        81      25      33 ..     225     233 ..     221     235 .. 0.84
   2 ?    8.3   2.5     0.002       2.1       5      34 ..     228     252 ..     225     253 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.076
                  zinc_ribbon_4  25 kvrCskCgh 33 
                                     v+C+ Cg+
  gi|119720282|ref|YP_920777.1| 225 TVKCPVCGA 233
                                    589999985 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.002
                  zinc_ribbon_4   5 CpsCkakyeiddeklpakgvkvrCskCghv 34 
                                    Cp C+a     + klp++g++ +Cs Cg++
  gi|119720282|ref|YP_920777.1| 228 CPVCGA-----PLKLPETGRETKCSYCGAT 252
                                    555555.....5688889*********975 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.5   0.00013      0.14       2      27 ..     227     251 ..     226     259 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00013
                                    EETTTTCEECHEETSTTCEEESSSSB CS
                   TF_Zn_Ribbon   2 kCPnCgstnlveDpergelvCtdCGl 27 
                                    kCP+Cg + l +++   e+ C+ CG+
  gi|119720282|ref|YP_920777.1| 227 KCPVCGAP-LKLPETGRETKCSYCGA 251
                                    9*****98.79999999*******97 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   0.00022      0.23       5      47 ..     227     258 ..     225     268 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00022
                Lar_restr_allev   5 pCPfCggravlersqrvvaeigqcvyCadCgastpwfkiaede 47 
                                     CP Cg + +l +++r ++       C  Cga    + +aed+
  gi|119720282|ref|YP_920777.1| 227 KCPVCGAPLKLPETGRETK-------CSYCGA----TVYAEDV 258
                                    6***************998.......555577....5555555 PP

>> ABC_membrane  ABC transporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   3.6   0.00024      0.25     127     165 ..      16      54 ..       9      66 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00024
                                    HHHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   ABC_membrane 127 ltfvgglivmfylgwkltlvllailpliilvsaviakil 165
                                    l+++ +l+v+f+ ++ ++++ll il+l+ ++ +++ak+ 
  gi|119720282|ref|YP_920777.1|  16 LIVLLLLAVVFLWNPLVAMILLLILFLYSVFVVIVAKVA 54 
                                    678999******************************975 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   2.5   0.00055      0.58       1      20 [.     227     246 ..     227     256 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00055
                 DNA_ligase_ZBD   1 hCPvCGsavvReegeaiyRC 20 
                                    +CPvCG+++  +e +  + C
  gi|119720282|ref|YP_920777.1| 227 KCPVCGAPLKLPETGRETKC 246
                                    6*******988887776666 PP

>> Ac76  Orf76 (Ac76)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   6.4    0.0034       3.6       5      56 ..      14      65 ..      11      71 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0034
                           Ac76  5 lllialivlafildkneklsellltllllfvlFiillnvyyikteStpadly 56
                                   + li+l++la+++  n  +  +ll +l l+ +F++++  +  k+e   ++l+
  gi|119720282|ref|YP_920777.1| 14 VGLIVLLLLAVVFLWNPLVAMILLLILFLYSVFVVIVAKVALKEERILEKLK 65
                                   5688999999999999999999999999********9998888887666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1149  (0.0640861); expected 358.6 (0.02)
Passed bias filter:                      778  (0.0433934); expected 358.6 (0.02)
Passed Vit filter:                       139  (0.0077528); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 1685.87
//
Query:       gi|119720283|ref|YP_920778.1|  [L=136]
Description: hypothetical protein Tpen_1378 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00011   22.7   0.5    0.00015   22.2   0.5    1.3  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.5   8.6e-09   0.00015      29     119 ..      22     116 ..       2     119 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 8.6e-09
                                    SEEEEEHHHHHHHHHHHHS.....SCHCHHHHHHHHHHHHH.HHTSEEEEBCHHHHHHHHHHHHHHHSBHHHHHHHHHHH CS
                            PIN  29 eelvtsalvlaEllyvlar.....rkskrekaaelvellll.lsalkilpidaeiaeeaaeialkygllpnDaliaAtAk 102
                                    e  vt +l+l+E l+ + +     ++ +re aa+  ++l    +++k l+  ++  + ++eialk +l+++Da  + +A 
  gi|119720283|ref|YP_920778.1|  22 ELGVTLDLALYESLNSVWKeykllGRIDRETAANYADVLAKvFEGIKSLS-IKGSERDVLEIALKENLTVYDASYLYLAM 100
                                    557999*************9999988888888888888888899999999.888999999******************** PP

                                    HHT-EEE.ESSTHHHHH CS
                            PIN 103 ehgikliatfDedfrrv 119
                                    + g +l+ t D+++r+ 
  gi|119720283|ref|YP_920778.1| 101 RDGRTLV-TDDRKLRDK 116
                                    *******.*****9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 941.57
//
Query:       gi|119720284|ref|YP_920779.1|  [L=75]
Description: hypothetical protein Tpen_1379 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0043   16.7   0.5      0.022   14.4   0.2    2.1  2  GntR             Bacterial regulatory proteins, gntR family
     0.0097   15.5   0.7      0.014   14.9   0.0    1.6  2  LEM              LEM domain
  ------ inclusion threshold ------
      0.073   13.1   0.0      0.097   12.7   0.0    1.3  1  tRNA_NucTran2_2  tRNA nucleotidyltransferase domain 2 putativ


Domain annotation for each model (and alignments):
>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.2   3.7e-06     0.022      22      48 ..       8      36 ..       3      45 .. 0.78
   2 !    5.9   0.5    0.0016       9.7       5      32 ..      29      54 ..      28      58 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.7e-06
                                   SB---H.HHHHHHHTS-HHH.HHHHHHHH CS
                           GntR 22 dkLPse.reLaaefgVsrtt.vReALrrL 48
                                   +k+P+e +eL++++gV+  + +ReAL r 
  gi|119720284|ref|YP_920779.1|  8 AKIPRElKELMDKYGVKPGPvIREALERE 36
                                   67887659*********97626****985 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0016
                                   HHHHHHHHHHTTSS-TTSB---HHHHHH CS
                           GntR  5 vyerLredIlsgelrpGdkLPsereLaa 32
                                   + e+L+++I++  l+  +kL   reL++
  gi|119720284|ref|YP_920779.1| 29 IREALEREIRRRILEEAEKL--ARELSK 54
                                   67999999999999999999..788876 PP

>> LEM  LEM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   2.4e-06     0.014       9      25 ..      13      29 ..      12      31 .. 0.92
   2 ?   -3.1   0.1         1   6.1e+03       9      15 ..      47      53 ..      46      54 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.4e-06
                            LEM  9 eLreeLkkyGvspGPIt 25
                                   eL+e + kyGv+pGP+ 
  gi|119720284|ref|YP_920779.1| 13 ELKELMDKYGVKPGPVI 29
                                   9**************96 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1
                            LEM  9 eLreeLk 15
                                    L +eL 
  gi|119720284|ref|YP_920779.1| 47 KLARELS 53
                                   5777776 PP

>> tRNA_NucTran2_2  tRNA nucleotidyltransferase domain 2 putative
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.6e-05     0.097     108     135 ..      15      43 ..       9      56 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.6e-05
                tRNA_NucTran2_2 108 kdLlealgvkpGpwlgeiLk.eleqavve 135
                                    k+L+ ++gvkpGp + e+L+ e+ ++++e
  gi|119720284|ref|YP_920779.1|  15 KELMDKYGVKPGPVIREALErEIRRRILE 43 
                                    79*****************8346666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1216  (0.0678231); expected 358.6 (0.02)
Passed bias filter:                      784  (0.043728); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 561.99
//
Query:       gi|119720285|ref|YP_920780.1|  [L=246]
Description: hypothetical protein Tpen_1380 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        0.1   11.6   0.0       0.13   11.2   0.0    1.1  1  RE_AccI   AccI restriction endonuclease


Domain annotation for each model (and alignments):
>> RE_AccI  AccI restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   7.2e-06      0.13     137     203 ..       4      71 ..       1      89 [. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.2e-06
                        RE_AccI 137 evrssaflidryeeamq.artekfvqialelkdkilaefsellnhparqayielleaitadtlsvldf 203
                                    ev  s++++ +  + ++ + t k  + al +  +il  ++   + p rq+ +++l++i ++ l    f
  gi|119720285|ref|YP_920780.1|   4 EVEESSYIVAKLLNCLKeVYTFKELEEALGVSSQILWRYTTFTQFPERQTARKILDGIREKRLLERAF 71 
                                    8899999999998887626799************************************9998866665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1820.66
//
Query:       gi|119720286|ref|YP_920781.1|  [L=345]
Description: AAA ATPase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-53  182.2   0.0    1.8e-53  181.9   0.0    1.1  1  ATPase_2         ATPase domain predominantly from Archaea
    6.9e-06   26.5   1.7    1.8e-05   25.2   0.3    2.3  2  AAA_16           AAA ATPase domain
    3.8e-05   24.1   0.0    6.5e-05   23.4   0.0    1.3  1  AAA              ATPase family associated with various cellul
    8.4e-05   22.9   0.0    0.00016   21.9   0.0    1.5  1  AAA_22           AAA domain
    0.00063   19.5   0.1     0.0011   18.8   0.1    1.3  1  AAA_30           AAA domain
     0.0007   19.6   0.0     0.0021   18.1   0.0    1.7  1  AAA_14           AAA domain
    0.00075   18.7   0.0     0.0011   18.2   0.0    1.2  1  NB-ARC           NB-ARC domain
  ------ inclusion threshold ------
      0.015   15.2   0.0      0.025   14.5   0.0    1.4  1  NACHT            NACHT domain
      0.016   14.7   0.0      0.025   14.1   0.0    1.2  1  AAA_7            P-loop containing dynein motor region
      0.017   15.2   0.0      0.033   14.2   0.0    1.5  1  AAA_5            AAA domain (dynein-related subfamily)
       0.02   14.8   0.1      0.059   13.3   0.0    1.9  1  MobB             Molybdopterin guanine dinucleotide synthesis
      0.051   13.3   0.0      0.076   12.8   0.0    1.3  1  ATP_bind_1       Conserved hypothetical ATP binding protein
      0.054   13.7   0.0       0.16   12.2   0.0    1.9  1  AAA_28           AAA domain
      0.071   13.5   0.0       0.12   12.8   0.0    1.4  1  RNA_helicase     RNA helicase
      0.082   12.6   0.0       0.15   11.7   0.0    1.3  1  Sigma54_activat  Sigma-54 interaction domain
      0.082   12.8   0.0       0.16   11.9   0.0    1.5  1  NTPase_1         NTPase
      0.094   12.5   0.0       0.16   11.8   0.0    1.3  1  Bac_DnaA         Bacterial dnaA  protein
       0.11   12.2   0.0        0.2   11.4   0.0    1.4  1  AAA_24           AAA domain
       0.13   11.8   0.0       0.24   11.0   0.0    1.4  1  cobW             CobW/HypB/UreG, nucleotide-binding domain


Domain annotation for each model (and alignments):
>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.9   0.0   1.9e-56   1.8e-53       1     233 []      18     226 ..      18     226 .. 0.96

  Alignments for each domain:
  == domain 1  score: 181.9 bits;  conditional E-value: 1.9e-56
                       ATPase_2   1 FfdRekelkeleeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklek 80 
                                    F+dR+++l+++e+++er+++ ++++YGpeg+GKtaL+++++e l+++++ v+y+++  +++ +k+ ++    e++k++  
  gi|119720286|ref|YP_920781.1|  18 FADRDEALRQVERVAERGTRFPVVVYGPEGCGKTALFRQAVEILKSHGYGVVYVNPAASVKDEKVVST----EDVKEIVG 93 
                                    99*****************************************************************9....88888888 PP

                       ATPase_2  81 algiavpkaeleeilkeksklvfkaielllekikkkgkkiiiiiDelqklidlglngaellvkeLlnliesltkekhlcv 160
                                    a+   ++ a++        +l++ka+el+ + ++ k +++++i+De+++++  g ++ae +vk+Ll++ie+++++++ +v
  gi|119720286|ref|YP_920781.1|  94 ATVGLLEPAAA--------TLAEKAFELVSRLLSVK-RRVAVILDEVFQAV--GPERAEVYVKALLDAIEYPSARYESFV 162
                                    88888888888........899*********99999.66************..*************************** PP

                       ATPase_2 161 viclsSeglfiervyneselegrhkyilvddldketalnflkegfkeleel...skedfeeiyryvGGkPkalvel 233
                                    +i++sSeg ++        ++ rh+++++++l     +n+++egfkel+++   +  df+ ++r++GG+P++l++l
  gi|119720286|ref|YP_920781.1| 163 AIIGSSEGTTRA-------RVARHSWATIRVL-----WNMAREGFKELYDQipgPGLDFDSAWRLTGGNPRYLAML 226
                                    ************.......*************.....***************999******************976 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.3   1.9e-08   1.8e-05       2      63 ..      18      76 ..      17     165 .. 0.64
   2 ?   -2.8   0.0       7.5   7.1e+03      93     105 ..     263     275 ..     241     296 .. 0.53

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 1.9e-08
                         AAA_16  2 lvGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdql 63
                                   +  R+e l+q++++ er  +     v+++G+ G+GK++l r++ + l+ +g  +++ +   +
  gi|119720286|ref|YP_920781.1| 18 FADRDEALRQVERVAERGTR---FPVVVYGPEGCGKTALFRQAVEILKSHGYGVVYVNPAAS 76
                                   66799999999998886544...4688*****************888888655554444433 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 7.5
                         AAA_16  93 eleawrekleeal 105
                                    e+ +++++l+e l
  gi|119720286|ref|YP_920781.1| 263 EAVEDPDRLLEYL 275
                                    2333333333333 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   6.9e-08   6.5e-05       1     107 [.      40     165 ..      40     177 .. 0.64

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 6.9e-08
                                    EEEESSTTSSHHHHHHHHHHHHTHE.........EEEEETTTCSSS...........STTHHHHHHHHHHHHHHHTS... CS
                            AAA   1 vllyGppGtGKTllakavakelgve.........fleisgsellsk...........yvgesekkirelfkeakeka... 57 
                                    v++yGp G+GKT+l ++ ++ l+++                  +++           +vg++   ++   +++ eka   
  gi|119720286|ref|YP_920781.1|  40 VVVYGPEGCGKTALFRQAVEILKSHgygvvyvnpA------ASVKDekvvstedvkeIVGATVGLLEPAAATLAEKAfel 113
                                    689******************97555554434442......333112344456666644444444444444433333444 PP

                                    ........TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEE CS
                            AAA  58 ........kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivig 107
                                            + + +++DE+ + ++ +       +e  v++Ll +++  + + + ++ i+
  gi|119720286|ref|YP_920781.1| 114 vsrllsvkRRVAVILDEVFQAVGPE------RAEVYVKALLDAIEYPSARYESFVAII 165
                                    466678844599*****97666655......59999*******999988855555554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   1.7e-07   0.00016       8     100 ..      40     131 ..      33     167 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.7e-07
                         AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.....sskdllrellralglelka.erlsseellea 81 
                                    +vv+G+ G+GKT l r+ +e l+ +      + +vv+v++++s       s++  +e++ a+   l+  +    e  +e+
  gi|119720286|ref|YP_920781.1|  40 VVVYGPEGCGKTALFRQAVEILKSH------GYGVVYVNPAASVkdekvVSTEDVKEIVGATVGLLEPaAATLAEKAFEL 113
                                    79********************776......99******99999765553333334444333333333455566777799 PP

                         AAA_22  82 leqalraravielliiDEa 100
                                    + + l+ +++ +++i+DE+
  gi|119720286|ref|YP_920781.1| 114 VSRLLSVKRR-VAVILDEV 131
                                    9999999999.9*****96 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   1.1e-06    0.0011      11      97 ..      29     131 ..      22     150 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.1e-06
                         AAA_30  11 ealltsgdrv.avltGpAGtGKttalkalreaweaaggrviglAptgkaAkv..La.........eelgi...eastiak 75 
                                    e++++ g r+ +v+ Gp G GKt + ++++e+++++g+ v+ + p + + ++  ++         + +g+   +a+t+a+
  gi|119720286|ref|YP_920781.1|  29 ERVAERGTRFpVVVYGPEGCGKTALFRQAVEILKSHGYGVVYVNPAASVKDEkvVStedvkeivgATVGLlepAAATLAE 108
                                    556666655525778**************************999988776653233332222222122224445555555 PP

                         AAA_30  76 llkrlk.grarlepgtllivDEa 97 
                                       +l  +  +++++  +i DE+
  gi|119720286|ref|YP_920781.1| 109 KAFELVsRLLSVKRRVAVILDEV 131
                                    54444465556677777778875 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   2.2e-06    0.0021       4     106 ..      39     173 ..      36     187 .. 0.62

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.2e-06
                         AAA_14   4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderd.....................kkladpekllelileklke 62 
                                    ++v+ G+  +GKT l +q ++ l  +   ++y+n     +                     +                 +
  gi|119720286|ref|YP_920781.1|  39 PVVVYGPEGCGKTALFRQAVEILKSHGYGVVYVNPAASVKdekvvstedvkeivgatvgllE-----------------P 101
                                    799***************99766667778888874443222233333333333443333320.................1 PP

                         AAA_14  63 ...................ekktylflDEiqev...pewekalkslvd.......egknldvivtGSnsklls 106
                                                       +++  ++lDE+ ++   +++e ++k l+d       ++ +  v + GS+ +   
  gi|119720286|ref|YP_920781.1| 102 aaatlaekafelvsrllsvKRRVAVILDEVFQAvgpERAEVYVKALLDaieypsaRY-ESFVAIIGSSEGTTR 173
                                    222233333333444666689999******888788566667777777654443244.568888999887665 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.2e-06    0.0011      20     116 ..      37     135 ..      22     148 .. 0.65

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.2e-06
                                    SEEEEEEESTTSSHHHHHHHHCCSHCCCCCCBTEEEEE..........EEESXXHHHHHHHXXHHHHHCCCTTSSSS-ST CS
                         NB-ARC  20 slvvalvGmgGvGKttlakqilnksdevegrFdsvawv..........vvsktdkseeiletilkeLslseddleekeev 89 
                                    ++ v ++G  G+GKt l++q+++      + + +v++v          vvs +d  +ei+ + +  L+ + + l ek   
  gi|119720286|ref|YP_920781.1|  37 RFPVVVYGPEGCGKTALFRQAVEI--LKSHGY-GVVYVnpaasvkdekVVSTEDV-KEIVGATVGLLEPAAATLAEK--- 109
                                    46799*****************98..445556.6677756666655544444333.333333333444443333333... PP

                                    TSHHHHHHHHCCCT.TEEEEEEEE-SHH CS
                         NB-ARC  90 eslkrklvrlLltk.rfllvlDDVweee 116
                                      + + + rlL  k r+ ++lD V++ +
  gi|119720286|ref|YP_920781.1| 110 --AFELVSRLLSVKrRVAVILDEVFQAV 135
                                    ..34556778887778999*****9975 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   2.7e-05     0.025       2      90 ..      39     131 ..      38     183 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.7e-05
                                    CEEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-.....-HCHHHCCCCTS--SSS-C.......C CS
                          NACHT   2 lvilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgna..rsladllfsqlpepaapvse.......v 72 
                                    +v++ G+ G+GKT+L ++ ++ +++       + +v++ + +++++++ +    +++++ +    ++ +  +        
  gi|119720286|ref|YP_920781.1|  39 PVVVYGPEGCGKTALFRQAVEILKSHG-----YGVVYVNPAASVKDEKVVstEDVKEIVGATVGLLEPAAATlaekafeL 113
                                    589***************999998877.....457888888888887766765555555555444433333344566667 PP

                                    HHHHCCSCCCEEEEEE-S CS
                          NACHT  73 wavllelperlLlilDgl 90 
                                    ++ ll++++r+  ilD +
  gi|119720286|ref|YP_920781.1| 114 VSRLLSVKRRVAVILDEV 131
                                    777777777777887755 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.7e-05     0.025      33      77 ..      37      81 ..      32      87 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.7e-05
                          AAA_7 33 kkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanq 77
                                   + pv+++Gp+G+GKt++ ++ ++ l++  y ++ +n  a+ + ++
  gi|119720286|ref|YP_920781.1| 37 RFPVVVYGPEGCGKTALFRQAVEILKSHGYGVVYVNPAASVKDEK 81
                                   679***************************999999888776655 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   3.5e-05     0.033       2      77 ..      40     134 ..      39     157 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.5e-05
                                    EEEE--SSSSHHHHHHHGGGGB...S--EEEEE--TT--HHHHH--B--.............--------.......... CS
                          AAA_5   2 vlLvGppGtgKselaerlaaal...nreveyvqltrdtteedlkgrreik....ngttslvdsplvraar.......... 64 
                                    v++ Gp G+gK+ l ++  + l   +  v+yv+  ++ + e+++   ++k         l++ +++ a +          
  gi|119720286|ref|YP_920781.1|  40 VVVYGPEGCGKTALFRQAVEILkshGYGVVYVNPAASVKDEKVVSTEDVKeivgATVGLLEPAAATLAEKafelvsrlls 119
                                    8999******************9999999999999999999998888887664433333444444433336666666667 PP

                                    ..G-SEEEEESGGG- CS
                          AAA_5  65 ..egeilvlDEvera 77 
                                      +   ++lDEv++a
  gi|119720286|ref|YP_920781.1| 120 vkRRVAVILDEVFQA 134
                                    644444556777665 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   6.2e-05     0.059       3      36 ..      41      74 ..      39     166 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.2e-05
                           MobB  3 givgksgsGKTtLleklipelkarglrvgtiKha 36
                                    + g +g+GKT+L  + +++lk++g+ v ++  a
  gi|119720286|ref|YP_920781.1| 41 VVYGPEGCGKTALFRQAVEILKSHGYGVVYVNPA 74
                                   567999********************99888655 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   8.1e-05     0.076       1      37 [.      42      76 ..      42     127 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.1e-05
                     ATP_bind_1  1 vvGpaGsGKttfvgalseilelrgrsvavvNLDPAae 37
                                   v Gp G GKt + ++ +eil++ g+ v +vN  PAa+
  gi|119720286|ref|YP_920781.1| 42 VYGPEGCGKTALFRQAVEILKSHGYGVVYVN--PAAS 76
                                   78*********************99999999..6665 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00017      0.16       2      44 ..      40      87 ..      39     118 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00017
                         AAA_28  2 ivitGgestGKTtll....eaLaargypvv.pEaareileeklakged 44
                                   +v+ G+e++GKT l     e L+++gy vv   +a  + +ek  ++ed
  gi|119720286|ref|YP_920781.1| 40 VVVYGPEGCGKTALFrqavEILKSHGYGVVyVNPAASVKDEKVVSTED 87
                                   89***********98655577889999988777777777777666665 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00013      0.12       1      36 [.      40      71 ..      40      92 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00013
                   RNA_helicase  1 iwlyGpsgeGKStlakeLakallkklklkkkdsvys 36
                                   +++yGp+g+GK+ l ++ a ++lk+      + vy+
  gi|119720286|ref|YP_920781.1| 40 VVVYGPEGCGKTALFRQ-AVEILKSH---GYGVVYV 71
                                   689**************.77777554...3333444 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00016      0.15      10      61 ..      23      76 ..      17      93 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00016
                                   HHHHHHHHHCTSS..S-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS CS
                Sigma54_activat 10 elleqikkvaktd..lsvlitGesGtGKellaraiheaskrkekpfvavncaai 61
                                   e+l+q+++va+     +v++ G  G+GK+ l r+  e  k +   +v vn aa 
  gi|119720286|ref|YP_920781.1| 23 EALRQVERVAERGtrFPVVVYGPEGCGKTALFRQAVEILKSHGYGVVYVNPAAS 76
                                   6788999999755449******************99999999999999999976 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00017      0.16       2      30 ..      40      68 ..      39      91 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00017
                                   EEEE--TTSSHHHHHHHHHHHH...GGGE CS
                       NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvkv 30
                                   v++ Gp G GKt l+++++e lks+g+ v
  gi|119720286|ref|YP_920781.1| 40 VVVYGPEGCGKTALFRQAVEILKSHGYGV 68
                                   6788*********************9976 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00016      0.16      10      70 ..      10      71 ..       7      90 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00016
                                   ----TTTHHHH..HHHHHHHHSTTT..S--EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEE CS
                       Bac_DnaA 10 FviGasnrlAl..aaalkvaeapgk.kynPlfiygevGlGktHLlkaignevlenapelrvvYl 70
                                   F  G s r+A   +a ++v   +++ +  P+++yg+ G Gkt L++ +   ++  ++   vvY+
  gi|119720286|ref|YP_920781.1| 10 FARGVSVRFADrdEALRQVERVAERgTRFPVVVYGPEGCGKTALFRQAVEILK--SHGYGVVYV 71
                                   66677777774224666777776665668***************986544333..345556666 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00021       0.2       5      51 ..      40      87 ..      37     135 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00021
                         AAA_24  5 iliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdie.....swed 51
                                   +++yGp+g GKT l +++    + i   +G+  ++++   +++     s ed
  gi|119720286|ref|YP_920781.1| 40 VVVYGPEGCGKTALFRQA----VEILKSHGYGVVYVNPAASVKdekvvSTED 87
                                   79*************999....666666666666666665555444444444 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00025      0.24       3      89 ..      40     130 ..      38     179 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00025
                                    EEEEESTTCCHHHHHHHHHCT--SS-EEEE.ESS-SSCHCCCCCCHCCCT..EEEETTTTE...CCHCTT-HHHHHHHHH CS
                           cobW   3 tvltGflGsGKTtLlnhllenraglklavi.vNefgevsiDaellretgve.ivelenGci...Cctlredllkeleale 77 
                                    +v+ G+ G GKT+L ++ +e  ++  + v+ vN       D++++++++v+ iv  + G +     tl+e++ + +++l+
  gi|119720286|ref|YP_920781.1|  40 VVVYGPEGCGKTALFRQAVEILKSHGYGVVyVNPAA-SVKDEKVVSTEDVKeIVGATVGLLepaAATLAEKAFELVSRLL 118
                                    5899***************87777777777255555.6778888888866557777666543224556777777777777 PP

                                    HHHTT-SEEEEE CS
                           cobW  78 ereerldviliE 89 
                                    + ++r+ vil E
  gi|119720286|ref|YP_920781.1| 119 SVKRRVAVILDE 130
                                    777777777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                       102  (0.00568911); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2295.94
//
Query:       gi|119720287|ref|YP_920782.1|  [L=305]
Description: spermine synthase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-48  163.3   0.0    5.1e-48  163.0   0.0    1.1  1  Spermine_synth   Spermine/spermidine synthase domain
    1.6e-09   38.2   0.0    3.5e-09   37.2   0.0    1.6  1  Methyltransf_11  Methyltransferase domain
    2.3e-09   37.9   0.0    4.6e-09   36.9   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    1.2e-06   28.3   0.0    2.5e-06   27.3   0.0    1.5  1  Spermine_synt_N  Spermidine synthase tetramerisation domain
    5.6e-06   27.0   0.0    1.1e-05   26.1   0.0    1.5  1  Methyltransf_12  Methyltransferase domain
    0.00017   21.4   0.0    0.00058   19.7   0.0    1.7  1  Methyltransf_23  Methyltransferase domain
  ------ inclusion threshold ------
       0.04   13.2   0.1      0.057   12.7   0.1    1.3  1  Methyltransf_2   O-methyltransferase domain
      0.055   14.5   0.0       0.15   13.1   0.0    1.7  1  Methyltransf_24  Methyltransferase domain
      0.057   13.0   0.0      0.085   12.4   0.0    1.2  1  MTS              Methyltransferase small domain
       0.11   11.7   0.0       0.18   11.0   0.0    1.3  1  DUF43            Branched-chain polyamine synthase A C-termin
       0.11   12.4   0.0        0.2   11.5   0.0    1.4  1  Methyltransf_30  S-adenosyl-L-methionine-dependent methyltran


Domain annotation for each model (and alignments):
>> Spermine_synth  Spermine/spermidine synthase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.0   0.0   3.1e-51   5.1e-48       2     179 ..      85     263 ..      84     271 .. 0.93

  Alignments for each domain:
  == domain 1  score: 163.0 bits;  conditional E-value: 3.1e-51
                                    HHHHHHHHHHHHCCSSST-EEEEESSTTSHHHHHHTTSTT-SEEEEEES-HHHHHHHHHHSHHHHTTCGGCTTEEEEEST CS
                 Spermine_synth   2 faykemiahvplmlhknpkevLiiGGgDGgvlrevvkhntvekitlvdiDqkvidfskkflpslaisafndarvklvlgd 81 
                                     +y+e+++h ++ +h+ p++vL++GGg G +lrev+kh tv+k+++vdiD  v++fskk l++++ ++f+d+rv++v+ d
  gi|119720287|ref|YP_920782.1|  85 YMYHELLVHPAMAAHPAPERVLVLGGGEGATLREVLKHGTVKKAVMVDIDPVVVEFSKKRLGHMHLGSFDDPRVEVVIAD 164
                                    68****************************************************************************** PP

                                    CHHHHCTCSS.-EEEEEEECCSTTCS.SCG.CSSHHHHHHHHHTEEEEEEEEEEEEETTTCHHHHHHHHHHHHTTSSCEE CS
                 Spermine_synth  82 gfkflkayek.kfdvvivdsldpvgp.aen.lFskeffdllkkvlkedGviilqaekpelekelvinvdksgkqvfalqv 158
                                    g  ++++     fdvvi+d++dp    +++ l+s e f  +k++lk+dGv+ +qa +  +  e  ++v++s+k+ fa  v
  gi|119720287|ref|YP_920782.1| 165 GKDYVRQAPSgYFDVVIMDLTDPYASeIAKpLYSPEAFAEVKRILKPDGVVATQAGSSYFYPEEYRSVLESVKKSFA-HV 243
                                    **********************875414558**************************9999****************.** PP

                                    EEEEEETTTSCSCEEEEEEEE CS
                 Spermine_synth 159 epsavlvPtylsgminfvves 179
                                    + +++ vP++  ++ nf+v+s
  gi|119720287|ref|YP_920782.1| 244 SEYWFWVPSFGVNV-NFIVAS 263
                                    *********98775.555555 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.2   0.0   2.1e-12   3.5e-09       1      95 [.     106     216 ..     106     217 .. 0.90

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 2.1e-12
                                    EEET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-......EEEETTEECCC.T.SS-TT-EEEEEEES- CS
                Methyltransf_11   1 LdvGcGtGrlaealakrg..arvvgvDlskemlklakekaseegl......kvefvvadaek.l.pfednsfDlvvssev 70 
                                    L +G G G+ ++++ k+g  ++ v vD+++ +++ +k++    +l      +ve+v ad ++ + + ++++fD+v++  +
  gi|119720287|ref|YP_920782.1| 106 LVLGGGEGATLREVLKHGtvKKAVMVDIDPVVVEFSKKRLGHMHLgsfddpRVEVVIADGKDyVrQAPSGYFDVVIMDLT 185
                                    5689*********************************************************96478************97 PP

                                    CCC-....C..CHHHHHHHHHHHEEEEEEEE CS
                Methyltransf_11  71 lhhv....e..dpekalkeiaRvLkpgGllv 95 
                                      +     +     +a++e++R+Lkp+G+++
  gi|119720287|ref|YP_920782.1| 186 DPYAseiaKplYSPEAFAEVKRILKPDGVVA 216
                                    666643341558899*************975 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   0.0   2.8e-12   4.6e-09       1      97 []     105     213 ..     105     213 .. 0.81

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 2.8e-12
                                    EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT......TEEEEESBCCGB..SSSTTTEEEEEE.. CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl......nvefvqgdaedl..pfedgsfDlvvs.. 70 
                                    vL lG G+G ++++++k++  +k ++vDi++  +e  ++r+ + +l      +ve+v +d +d+  + ++g fD+v++  
  gi|119720287|ref|YP_920782.1| 105 VLVLGGGEGATLREVLKHGTVKKAVMVDIDPVVVEFSKKRLGHMHLgsfddpRVEVVIADGKDYvrQAPSGYFDVVIMdl 184
                                    899***************768********************99444445566*********997334799********44 PP

                                    ..ESTGGGSSHHHHHHHHHHHHHHEEEEE CS
                Methyltransf_25  71 ..sgalhhlsdedlekalkeiarvLkpgG 97 
                                       +a ++ ++   ++a++e++r+Lkp+G
  gi|119720287|ref|YP_920782.1| 185 tdPYASEIAKPLYSPEAFAEVKRILKPDG 213
                                    3322223344445689************9 PP

>> Spermine_synt_N  Spermidine synthase tetramerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   1.5e-09   2.5e-06      11      53 .]      39      81 ..      30      81 .. 0.93

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 1.5e-09
                                   EEEEEEEEEEEEEEEESSSEEEEEEETTTEEEEEETTEEEEET CS
                Spermine_synt_N 11 lalelkVekvLyeekSeyQdieifesktfGkvLvLDgvvqltE 53
                                   l+l +kV+kv   ekS+yQ++ + e + fG+ L LD  +q tE
  gi|119720287|ref|YP_920782.1| 39 LRLLFKVSKVYALEKSPYQEVVLAELEGFGRALLLDKFIQSTE 81
                                   678899***9999****************************98 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   6.8e-09   1.1e-05       1      98 [.     106     214 ..     106     215 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 6.8e-09
                Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg.....ssfDlvvasnv 75 
                                    L +G+G G++lr++l++   ++ + vDi+p ++e  k++l + +  +++  ++e+  ++ +d       ++fD+v++  +
  gi|119720287|ref|YP_920782.1| 106 LVLGGGEGATLREVLKHGTVKKAVMVDIDPVVVEFSKKRLGHMHLGSFDDPRVEVVIADGKDYVrqapsGYFDVVIMDLT 185
                                    569**********************************************99999988654444499999*******9877 PP

                Methyltransf_12  76 lhhl......kdirevldnirklLkpgGr 98 
                                      +           e+++++++ Lkp+G+
  gi|119720287|ref|YP_920782.1| 186 DPYAseiakpLYSPEAFAEVKRILKPDGV 214
                                    77776666544556899999999999997 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   3.5e-07   0.00058      14     116 ..      93     216 ..      81     248 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 3.5e-07
                Methyltransf_23  14 erllpklraggrvLdiGcGtGillevlrengf..svtgvDlspeaveiae................kakkaqkdqfdeqe 75 
                                    + +++  +a+ rvL +G G+G +l++  ++g+  + ++vD++p+ ve  +                +             
  gi|119720287|ref|YP_920782.1|  93 HPAMAAHPAPERVLVLGGGEGATLREVLKHGTvkKAVMVDIDPVVVEFSKkrlghmhlgsfddprvE------------- 159
                                    4555668999*****************9998778**********99987764444444443333331............. PP

                Methyltransf_23  76 aae............pqgkfdlIvlr....evlehvp..dppellrqiatllkpgGyll 116
                                      +            p+g+fd++++     +  e  +  + pe+++ ++++lkp+G++ 
  gi|119720287|ref|YP_920782.1| 160 --VviadgkdyvrqaPSGYFDVVIMDltdpYASEIAKplYSPEAFAEVKRILKPDGVVA 216
                                    ..1444444444555899*****985112122333333457799999999999999875 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   3.5e-05     0.057      66     144 ..     105     188 ..      76     209 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.5e-05
                                    EEEET-TTSHHHHHHHHH-TT-EEEEEE-.HHHHHHHHHHS.---....--TTEEEEES-TTTS-----SEEEEESSGGG CS
                 Methyltransf_2  66 lvDvGGGtGalakaivsayPtikvivfDl.peVveaAkehl.sag....eeervefvgGdffkdslPeaDaillkrvlhD 139
                                    ++ +GGG Ga+++++ ++    k+++ D+ p Vve  k++l +++     ++rve+v  d   d + +a    +  v+ D
  gi|119720287|ref|YP_920782.1| 105 VLVLGGGEGATLREVLKHGTVKKAVMVDIdPVVVEFSKKRLgHMHlgsfDDPRVEVVIADGK-DYVRQAPSGYFDVVIMD 183
                                    5569***************999*******778888888876432211225677777766655.66666666666666666 PP

                                    S-HHH CS
                 Methyltransf_2 140 wsdek 144
                                     +d  
  gi|119720287|ref|YP_920782.1| 184 LTDPY 188
                                    66655 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   9.3e-05      0.15      16     101 ..     118     215 ..     107     217 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.3e-05
                Methyltransf_24  16 ralrrngagrlvavdhdpgaeeaaalare........aglddrvrlikadseealaslaagsiDllfiDgghaaeavled 87 
                                    + l++    + v+vd dp    + ++ ++        +  d rv+++ ad ++++++  +g +D++++D    ++++++ 
  gi|119720287|ref|YP_920782.1| 118 EVLKHGTVKKAVMVDIDP---VVVEFSKKrlghmhlgSFDDPRVEVVIADGKDYVRQAPSGYFDVVIMDLTDPYASEIAK 194
                                    445555558889999999...7788888777777765555668***************************8888654433 PP

                Methyltransf_24  88 .......leallprlapggvv 101
                                           +  + ++l+p+gvv
  gi|119720287|ref|YP_920782.1| 195 plyspeaFAEVKRILKPDGVV 215
                                    222222368888888888887 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   5.2e-05     0.085      31     148 ..     101     228 ..      89     247 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.2e-05
                                    TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC......EEEEE-STTT...TSTTS-EEEE CS
                            MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle......vevvasdvle...eveekkfdli 101
                                    + ++vl lG G G+   +++k+    + ++vd+d   +e++k+ l + +l       vevv  d+ +   +++ + fd++
  gi|119720287|ref|YP_920782.1| 101 APERVLVLGGGEGATLREVLKHGTVKKAVMVDIDPVVVEFSKKRLGHMHLGsfddprVEVVIADGKDyvrQAPSGYFDVV 180
                                    5567999*****************99******************99988877778998888877655111556789**** PP

                                    EE-..--STTTCHCHHHHHHHHHHHHHHHEEEEEEEEEEEETTSCHHHH CS
                            MTS 102 vsN..PPfhagkatelavaeeliaeAkeaLkegGeLliVanrklgyesl 148
                                    ++    P+ ++ a +     e +ae k++Lk++G     a +   y++ 
  gi|119720287|ref|YP_920782.1| 181 IMDltDPYASEIA-KPLYSPEAFAEVKRILKPDGVVATQAGSSYFYPEE 228
                                    9864468888888.77778888899999999999887776666666655 PP

>> DUF43  Branched-chain polyamine synthase A C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00011      0.18      47     119 ..     104     183 ..     101     194 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00011
                                    EEEEES-TT-HHHHHHHH.T--SEEEEE-S-HHHHHHHHHHHHHHT-.....-.EEEE---TTS---TTTSS-BSEEEE- CS
                          DUF43  47 eilvlGdDDLtslalaLt.glpkkvvvvDiDeRlikfiervakelgl.....k.ieaivyDlrkplpeelkekFdvfitD 119
                                    ++lvlG  +  +l   L  g  kk v+vDiD+ +++f ++   ++ l     + +e+++ D ++ + ++ +  Fdv+i D
  gi|119720287|ref|YP_920782.1| 104 RVLVLGGGEGATLREVLKhGTVKKAVMVDIDPVVVEFSKKRLGHMHLgsfddPrVEVVIADGKDYVRQAPSGYFDVVIMD 183
                                    69999988888888888526889***************998766544334432699999999999999999999999855 PP

>> Methyltransf_30  S-adenosyl-L-methionine-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00012       0.2      30      90 ..     155     219 ..     134     225 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00012
                                    TEEEEEEES-HHHHHHHC-.T-EEEEEE...-SS-TTTSGGGCSHHHHHHHHHHEEEEEEEEES- CS
                Methyltransf_30  30 evtlklligdarealkeld.ekadawFl...DgFsPaknPelwseellkelarllkkkgtlatys 90 
                                    + +++++i d ++ + + +  ++d++ +   D+++ + +  l+s+e ++e++r+lk+ g++at +
  gi|119720287|ref|YP_920782.1| 155 DPRVEVVIADGKDYVRQAPsGYFDVVIMdltDPYASEIAKPLYSPEAFAEVKRILKPDGVVATQA 219
                                    56789999********9999899999872225677777889*********************966 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2072.92
//
Query:       gi|119720288|ref|YP_920783.1|  [L=92]
Description: hypothetical protein Tpen_1383 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0063   16.6   0.0     0.0063   16.6   0.0    1.4  1  PgaD             PgaD-like protein
  ------ inclusion threshold ------
       0.01   15.5   0.1       0.01   15.5   0.1    1.1  1  DUF4131          Domain of unknown function (DUF4131)
      0.021   14.9   0.0      0.023   14.8   0.0    1.0  1  Peptidase_S49_N  Peptidase family S49 N-terminal
      0.029   14.7   3.9      0.036   14.4   3.9    1.0  1  Troponin         Troponin
       0.03   14.7   2.0      0.047   14.1   2.0    1.5  1  BatA             Aerotolerance regulator N-terminal
      0.037   14.1   0.6       0.05   13.7   0.6    1.1  1  PspB             Phage shock protein B
       0.04   14.0   0.0      0.049   13.7   0.0    1.1  1  TssO             Type VI secretion system, TssO
      0.045   13.8   0.0      0.046   13.7   0.0    1.0  1  Halogen_Hydrol   5-bromo-4-chloroindolyl phosphate hydrolysis
      0.097   12.4   0.0       0.11   12.2   0.0    1.1  1  DUF3328          Domain of unknown function (DUF3328)
       0.12   11.1   0.0       0.14   10.9   0.0    1.0  1  BatD             Oxygen tolerance
       0.15   11.7   0.0       0.19   11.4   0.0    1.0  1  tRNA_anti-like   tRNA_anti-like
       0.19   12.0   2.0       0.42   10.9   2.0    1.6  1  XhlA             Haemolysin XhlA
       0.19   11.4   0.1       0.24   11.1   0.1    1.2  1  Afaf             Acrosome formation-associated factor
       0.32   11.1   6.2       0.49   10.6   6.2    1.4  1  DUF5326          Family of unknown function (DUF5326)


Domain annotation for each model (and alignments):
>> PgaD  PgaD-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   4.9e-06    0.0063      16      49 ..      31      64 ..      27      86 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4.9e-06
                           PgaD 16 ldsilTllaWagwiyLfvpllvllawllglelfe 49
                                   l++++Tll+W++ i Lf  +l +la+ ++   +e
  gi|119720288|ref|YP_920783.1| 31 LSMLVTLLFWVLLIALFAAILYYLARRASEPHQE 64
                                   789*******************988744433333 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.1   8.2e-06      0.01       4      63 ..      19      69 ..      12      92 .] 0.51

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 8.2e-06
                        DUF4131  4 plalvllalllllllllllllrrrprrrvllllllllllallgfalrapqpnandlsqll 63
                                    +++  l+++++l +l  ll        +++ll++l++++l+++a ra +p+++  s  l
  gi|119720288|ref|YP_920783.1| 19 APWYPGLGFAGALSMLVTLL--------FWVLLIALFAAILYYLARRASEPHQE-SSVSL 69
                                   33333333333333333333........46666666666666666666666654.44333 PP

>> Peptidase_S49_N  Peptidase family S49 N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   1.8e-05     0.023      10      61 ..      34      87 ..      27      92 .] 0.79

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.8e-05
                Peptidase_S49_N 10 laklvtlvvailvvvvlivalaakkk..kekgelevtkLneeykelkeeleeal 61
                                   l+ l+ +v++i+++ ++++ la++++  +++ +++++++++e+ke+ke+le+  
  gi|119720288|ref|YP_920783.1| 34 LVTLLFWVLLIALFAAILYYLARRASepHQESSVSLERIENELKEIKERLERIE 87
                                   45566677778887788888888877789999******************9764 PP

>> Troponin  Troponin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   3.9   2.8e-05     0.036      30      68 ..      53      91 ..      50      92 .] 0.95

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.8e-05
                                   XXXXXXXXXX.XXX.XXXXXXXXXXXXXXXXXXXXXXXX CS
                       Troponin 30 vLkerieplkeldglseeqlqelckklheridkleeeky 68
                                   +L+ r  ++++++++s e +++  k+++er++++eeek 
  gi|119720288|ref|YP_920783.1| 53 YLARRASEPHQESSVSLERIENELKEIKERLERIEEEKR 91
                                   899**********************************97 PP

>> BatA  Aerotolerance regulator N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   2.0   3.7e-05     0.047       8      50 ..      37      78 ..      13      88 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.7e-05
                           BatA  8 llLlallllplpiillyllkrrpqevvfsslrlleevekdeea 50
                                   ll+++ll++    il+yl +r  ++ + ss+ l  ++e++ + 
  gi|119720288|ref|YP_920783.1| 37 LLFWVLLIALFAAILYYLARRASEPHQESSVSLE-RIENELKE 78
                                   5668888777767777777777777799998764.56655555 PP

>> PspB  Phage shock protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.6   3.9e-05      0.05       5      62 ..      33      88 ..      29      88 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.9e-05
                           PspB  5 lavpliifvlfVapiWLiLHYrskkkrskglsaedekrLeellekAekleeRietLEr 62
                                   ++v l   vl++a+   iL+Y  ++   ++  +e   +Le++ ++ ++++eR+e +E+
  gi|119720288|ref|YP_920783.1| 33 MLVTLLFWVLLIALFAAILYYLARRA--SEPHQESSVSLERIENELKEIKERLERIEE 88
                                   566777889999**********9965..555789999****************99995 PP

>> TssO  Type VI secretion system, TssO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   3.8e-05     0.049      12      65 ..      34      87 ..      31      92 .] 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.8e-05
                           TssO 12 yflllFlvtvlllflivffffkssplqekeillkelerkkkfeekqkelkkkvd 65
                                   +++llF v+++ lf ++ ++  +     +++    ler+++++++ ke  + ++
  gi|119720288|ref|YP_920783.1| 34 LVTLLFWVLLIALFAAILYYLARRASEPHQESSVSLERIENELKEIKERLERIE 87
                                   789***************999977777777779999999999999888766666 PP

>> Halogen_Hydrol  5-bromo-4-chloroindolyl phosphate hydrolysis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   3.6e-05     0.046      16      83 ..      30      89 ..      13      92 .] 0.71

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.6e-05
                 Halogen_Hydrol 16 lvsffllgfsffla.lliailggilvyvasrknkkkkhlkksglsrkelkyiretlkeakekikrleka 83
                                    +s++   ++++++ llia++++il+y+a r        ++++ s  +l+ i++ lke ke ++r+e++
  gi|119720288|ref|YP_920783.1| 30 ALSML---VTLLFWvLLIALFAAILYYLARR------ASEPHQESSVSLERIENELKEIKERLERIEEE 89
                                   23333...23333324566788888888877......666788899999999**************986 PP

>> DUF3328  Domain of unknown function (DUF3328)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0     9e-05      0.11      13      66 ..      34      83 ..      23      91 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9e-05
                        DUF3328 13 llllvlllllllllllilssllsssekkaakkkspsspspaldaieyelkqfk..l 66
                                   l+ l++++ll+ l+ +il +l+ + ++      +++++s +l++ie elk++k  l
  gi|119720288|ref|YP_920783.1| 34 LVTLLFWVLLIALFAAILYYLARRASE------PHQESSVSLERIENELKEIKerL 83
                                   344444444444444444444444444......44569999999999999988432 PP

>> BatD  Oxygen tolerance
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00011      0.14     426     475 ..      35      86 ..      20      90 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00011
                           BatD 426 f..lfwlllllplllfvvllllwrkrrrenadvaaskkkkanklarkrlkeA 475
                                    +  lfw+ll+++++++++ l+ +  +  +++ v+  + +   k  ++rl+++
  gi|119720288|ref|YP_920783.1|  35 VtlLFWVLLIALFAAILYYLARRASEPHQESSVSLERIENELKEIKERLERI 86 
                                    2458999999999888433333334444444445555555556666666665 PP

>> tRNA_anti-like  tRNA_anti-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00015      0.19       3      56 ..      32      85 ..      29      91 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00015
                                   ..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX---HHHHHTS-........ CS
                 tRNA_anti-like  3 amlkkilviilivilllfvialvaqaaesardkekaekedadatlaeakakpea 56
                                   +ml  +l+++l+++l++++ ++ a  a+   + +++  e+ + +l+e+k   e+
  gi|119720288|ref|YP_920783.1| 32 SMLVTLLFWVLLIALFAAILYYLARRASEPHQESSVSLERIENELKEIKERLER 85
                                   578899**************9999998999999999999999999999987666 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   2.0   0.00033      0.42       5      28 ..      68      91 ..      65      92 .] 0.89

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00033
                           XhlA  5 rlerietkldnleervdkleekaa 28
                                    lerie++l++++er++++ee ++
  gi|119720288|ref|YP_920783.1| 68 SLERIENELKEIKERLERIEEEKR 91
                                   699****************99875 PP

>> Afaf  Acrosome formation-associated factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00019      0.24     136     169 ..      34      68 ..      29      82 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00019
                           Afaf 136 LltLlLfviLLalcsatlyklkklsyk.elesqys 169
                                    L+tLl++v+L+al +a+ly l +  ++ + es  s
  gi|119720288|ref|YP_920783.1|  34 LVTLLFWVLLIALFAAILYYLARRASEpHQESSVS 68 
                                    8899999*************988666645555544 PP

>> DUF5326  Family of unknown function (DUF5326)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   6.2   0.00038      0.49      30      64 ..      28      62 ..      11      69 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00038
                        DUF5326 30 asvvgvligllfkvLvlvalvggliyvvrkftsss 64
                                   a  +++l++llf vL+++ + + l y+ r+ ++  
  gi|119720288|ref|YP_920783.1| 28 AGALSMLVTLLFWVLLIALFAAILYYLARRASEPH 62
                                   56799***********9999999999999988743 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2266  (0.126387); expected 358.6 (0.02)
Passed bias filter:                     1363  (0.0760221); expected 358.6 (0.02)
Passed Vit filter:                       190  (0.0105974); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 687.88
//
Query:       gi|119720289|ref|YP_920784.1|  [L=618]
Description: ferredoxin [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      5e-85  284.7   0.0    1.3e-84  283.3   0.0    1.6  2  RACo_C_ter   C-terminal domain of RACo the ASKHA domain
    1.9e-51  174.0   0.0    1.2e-50  171.4   0.0    2.1  2  Raco_middle  RACo middle region
    1.3e-13   50.6   0.0    2.8e-13   49.5   0.0    1.5  1  RACo_linker  RACo linker region
    1.2e-10   41.2   0.1    2.2e-10   40.3   0.1    1.5  1  Fer2         2Fe-2S iron-sulfur cluster binding domain
  ------ inclusion threshold ------
      0.059   13.4   0.1       0.18   11.9   0.1    1.8  1  Fer2_4       2Fe-2S iron-sulfur cluster binding domain
      0.096   13.0   0.1      0.096   13.0   0.1    4.0  5  TOBE         TOBE domain


Domain annotation for each model (and alignments):
>> RACo_C_ter  C-terminal domain of RACo the ASKHA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1       1.1   3.3e+03      32      50 ..     314     332 ..     313     334 .. 0.90
   2 !  283.3   0.0   4.3e-88   1.3e-84       3     251 ..     362     610 ..     360     615 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.1
                                    CCCTTTSTTBE-SSTTEEE CS
                     RACo_C_ter  32 AlEGaeikcGmrAapgAIe 50 
                                    AlE    + G  A pgA+ 
  gi|119720289|ref|YP_920784.1| 314 ALEVRAADLGLEAGPGAVA 332
                                    8999999**********96 PP

  == domain 2  score: 283.3 bits;  conditional E-value: 4.3e-88
                                    EEEEEESSSEEEEEE-SS-EEEEEEE--SCCCTTTSTTBE-SSTTEEEEEEEEGGGSSEEEEECTSS--SEEEHHHHHHH CS
                     RACo_C_ter   3 slliDiGTNaEivlgnkdellaasaaaGPAlEGaeikcGmrAapgAIedveidpetlevelkvigdekakGicGsGiidl 82 
                                    ++l+D+GTN E+v+g++d+ l++sa++GPA+EG +i++Gm+A +gAI++v++ ++  eve++++g+++++GicGs++idl
  gi|119720289|ref|YP_920784.1| 362 AMLVDVGTNTEVVVGSGDRFLSGSAPSGPAFEGMQITFGMKAVSGAIDRVRVGEDG-EVEYTTVGGARPRGICGSAMIDL 440
                                    699*************************************************9998.*********************** PP

                                    HHHHHHTTSB-TTS-B-GGG-TTTEEEETTCEEEEEE-GGGSSS.S-EEEEHHHHHHHHHHHHHHHHHHHHHHHHTT--G CS
                     RACo_C_ter  83 iaelleagiidkkgklnkelkserireeeetleyvlakaeetet.kdivitekDieelikakaAiyagiktLleevglev 161
                                    +ael++ag++d +g+++++++++r+r+ e+++e+v+a+a+et++ +div+tekD+e+++ akaA+ ++++tL++  g++ 
  gi|119720289|ref|YP_920784.1| 441 VAELYRAGLLDARGRFRRDASTRRLRRGERGMEFVVAWAKETSIgRDIVFTEKDVEQVLLAKAAVSSAARTLMKMRGFKA 520
                                    ********************************************99********************************** PP

                                    GG--EEEEESSGGGCEEHHHHHHHTSS-SS-GGGEEEECSHHHHHHHHHHCBHHHHHHHHHHHHHEEE--TTSSSHHHHH CS
                     RACo_C_ter 162 ediekvylAGafGsyidaekAitiGllPdlelekvvqvGNtslagAreallseealeeleeiarkityielateeeFqee 241
                                    e++e+v++AG+fGs +++e+A++iGllP ++ ekv ++GNt++ gA  al+seeal+el+ei +k++ +e+a+++e++ e
  gi|119720289|ref|YP_920784.1| 521 EELEEVVVAGSFGSSLNVENALEIGLLPPVPPEKVWFAGNTAVGGAVLALVSEEALSELDEILSKVEFVEFAASPEWKAE 600
                                    ******************************************************************************** PP

                                    HHHHSSSS-S CS
                     RACo_C_ter 242 yvaalflpht 251
                                    ++++lf+p  
  gi|119720289|ref|YP_920784.1| 601 FMNSLFIPYR 610
                                    *******975 PP

>> Raco_middle  RACo middle region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.4   0.0   3.9e-54   1.2e-50       1     162 [.     196     357 ..     196     358 .. 0.99
   2 ?   -0.6   0.0      0.32   9.4e+02      64      91 ..     503     530 ..     488     532 .. 0.83

  Alignments for each domain:
  == domain 1  score: 171.4 bits;  conditional E-value: 3.9e-54
                    Raco_middle   1 yGlavDiGtTtvvaaLvdletgkelaeasalNpQikyGeDvlsRiayakeeeegleklqkavveeinelieelleeagie 80 
                                    y++avD+Gt+++va+Lvd ++g ++a+  a NpQ +yGeD+++R+ +a++++++l+ l++++ve +n l+++l ++ g++
  gi|119720289|ref|YP_920784.1| 196 YAVAVDLGTSKLVAHLVDASRGVVVAKGFAENPQLAYGEDIMTRMDFASRSPGNLDLLRRVLVEGVNGLVARLRSSLGVR 275
                                    89****************************************************************************** PP

                    Raco_middle  81 keeiyevvvagNttMlhlllgldpkslakapyvpvvseavelkakelglkinpeakvyvlpnvssyvGgDivagilasgl 160
                                    ++e+y+ ++agNt+M+h+llgld+++la+apyv+v+++a e++a++lgl++ p a+++v+p ++++vGgD+va++la+gl
  gi|119720289|ref|YP_920784.1| 276 ADEVYAFAFAGNTAMQHFLLGLDVSQLARAPYVAVTRRALEVRAADLGLEAGPGAVALVFPVIGGFVGGDAVADVLATGL 355
                                    ******************************************************************************** PP

                    Raco_middle 161 hk 162
                                    h+
  gi|119720289|ref|YP_920784.1| 356 HR 357
                                    *8 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.32
                    Raco_middle  64 eeinelieelleeagiekeeiyevvvag 91 
                                    ++++++ ++l++  g+++ee++evvvag
  gi|119720289|ref|YP_920784.1| 503 AAVSSAARTLMKMRGFKAEELEEVVVAG 530
                                    4577888999999*************98 PP

>> RACo_linker  RACo linker region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.5   0.0   9.2e-17   2.8e-13       3      81 ..     110     189 ..     108     192 .. 0.94

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 9.2e-17
                    RACo_linker   3 erdieldPavkkvyveleePtledpsgDleRLkeaLekqwd.leid.lsvLrkLpevLrkgnwkVtvalhedeeiiavep 80 
                                    +r++++ P+++ v ++l++P+l+d ++D eRL e L + ++ +e + l vLr Lp+v r++ w   v+ ++++ ++ vep
  gi|119720289|ref|YP_920784.1| 110 ARPVRVAPPLRRVSLSLTPPSLSDWRSDEERLAEGLGRVLGgFEPPgLDVLRSLPRVARESSWSLEVVAWRGR-VLSVEP 188
                                    68999***********************************7677666***********************999.****** PP

                    RACo_linker  81 g 81 
                                    g
  gi|119720289|ref|YP_920784.1| 189 G 189
                                    9 PP

>> Fer2  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   0.1   7.5e-14   2.2e-10       3      77 ..       6      83 ..       4      84 .. 0.82

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 7.5e-14
                                   TTTEEEEEEEETTTHBHHHHHHHTTTTTSTTSSSSSS.SSTTEEEEEESCE...CTT...SSSSTHHHHHTTEEEEGGGSEE CS
                           Fer2  3 idgkevevevadgettlldaaeenggidipysCgggg.CgtClvevlegev...qsd...etelegeeldegklrlaCqtiv 77
                                   +++ + +vev+ g t ll+a+ +  g+ +   Cgg g Cg C+v v+ g+    +     e+ l g +l +g++ laCq++v
  gi|119720289|ref|YP_920784.1|  6 VEPYGARVEVESGAT-LLEALARS-GVRVASVCGGRGfCGKCRVLVTGGSSalsP-PsrsESMLLGGDLGSGYR-LACQARV 83
                                   566778899999999.99999999.**********999***********998652.146777777777888766.*****98 PP

>> Fer2_4  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   5.9e-05      0.18      10      38 ..      10      38 ..       3      54 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.9e-05
                         Fer2_4 10 GkevtvpeGdtvasAllangvdvprscky 38
                                   G +v+v+ G t+++Al++ gv+v   c  
  gi|119720289|ref|YP_920784.1| 10 GARVEVESGATLLEALARSGVRVASVCGG 38
                                   899********************999987 PP

>> TOBE  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1      0.69   2.1e+03      11      25 ..       3      17 ..       3      25 .. 0.83
   2 ?    2.7   0.0     0.051   1.5e+02      30      55 ..      84     105 ..      70     106 .. 0.80
   3 ?   13.0   0.1   3.2e-05     0.096       6      37 ..     178     211 ..     177     217 .. 0.92
   4 ?   -3.3   0.1         4   1.2e+04      42      55 ..     319     332 ..     316     334 .. 0.74
   5 ?   -3.5   0.0       4.6   1.4e+04      29      45 ..     564     579 ..     562     580 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.69
                           TOBE 11 VvvveplgseveVrv 25
                                   Vv+vep g++veV+ 
  gi|119720289|ref|YP_920784.1|  3 VVRVEPYGARVEVES 17
                                   899999999988875 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.051
                           TOBE  30 gatLtArvtrrsaeeLgLapGeeVfa 55 
                                    + ++++ v+++s+e+    pGe+V a
  gi|119720289|ref|YP_920784.1|  84 HGDVAVYVPEESRES----PGERVAA 105
                                    4578999********....****976 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 3.2e-05
                           TOBE   6 qlpgtVvvveplg...seveVrvdlgggatLtArv 37 
                                    +++g+V+ vep+g   +++ V vdlg  + L+A++
  gi|119720289|ref|YP_920784.1| 178 AWRGRVLSVEPGGsgrGTYAVAVDLGTSK-LVAHL 211
                                    59***************************.***97 PP

  == domain 4  score: -3.3 bits;  conditional E-value: 4
                           TOBE  42 aeeLgLapGeeVfa 55 
                                    a++LgL++G  ++a
  gi|119720289|ref|YP_920784.1| 319 AADLGLEAGPGAVA 332
                                    78999999965555 PP

  == domain 5  score: -3.5 bits;  conditional E-value: 4.6
                           TOBE  29 ggatLtArvtrrsaeeL 45 
                                    gga + A v++++  eL
  gi|119720289|ref|YP_920784.1| 564 GGA-VLALVSEEALSEL 579
                                    677.8999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (618 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.40
# Mc/sec: 4689.64
//
Query:       gi|119720290|ref|YP_920785.1|  [L=405]
Description: major facilitator transporter [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-24   85.7  62.4    4.5e-15   55.4  28.4    2.1  2  MFS_1     Major Facilitator Superfamily
     0.0025   16.7  20.4       0.12   11.2   3.4    2.3  2  Sugar_tr  Sugar (and other) transporter


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.4  28.4   5.1e-19   4.5e-15      13     216 ..      24     225 ..      14     242 .. 0.79
   2 !   32.5  31.5   4.8e-12   4.3e-08      16     170 ..     229     393 ..     204     403 .. 0.79

  Alignments for each domain:
  == domain 1  score: 55.4 bits;  conditional E-value: 5.1e-19
                          MFS_1  13 silgpalpl.alaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll..fa..sslw. 86 
                                    ++ ++++ + a + d       +g+++++y l  a+++l++G++sd  Gr+r+l++g+++ ++g+l l+  fa  ss++ 
  gi|119720290|ref|YP_920785.1|  24 GANTFLVAMlASGGDVA-----AGFVMAAYPLMEAIGALLAGSWSDFAGRKRTLIAGYVARSAGMLSLAavFAlsSSSPg 98 
                                    44444444323444444.....9*****************************************5555558768777777 PP

                          MFS_1  87 lllvlrv......lqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaiv 160
                                     l+++ +      + G+++++++ +++++++d++   +rg+++g +   + +++  g+llg+ll+s l    +++++a++
  gi|119720290|ref|YP_920785.1|  99 SLVFAALeaalngVVGFTTALILVSSLSMATDLTETGNRGLGMGGFEFVNLASYGAGYLLGSLLYSVLPGYPAYLAVALL 178
                                    7777777888899****************************************************9999999******** PP

                          MFS_1 161 sllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillial 216
                                    ++la  +f+++l e++p+ + ++   +       + +p  +al+  p +w++l+++
  gi|119720290|ref|YP_920785.1| 179 TALATPVFAAFLEETRPPVPLVRRGLL-------SSLP-RSALVLLP-VWVALTTI 225
                                    ******999999999999998866444.......3333.33333333.23222222 PP

  == domain 2  score: 32.5 bits;  conditional E-value: 4.8e-12
                          MFS_1  16 gpalplalaedlg......ispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll...fa..ss 84 
                                    g+ +p  + ++lg      i ++ igll+ +  ++ + +++++Grlsd +Gr +v+ lgl++ +++ l ++   +a    
  gi|119720290|ref|YP_920785.1| 229 GIYAPRVIHDHLGavhgpaIGKAGIGLLFLGALVLLGSGAVFFGRLSDSWGRVKVFRLGLAGGLAA-LSAMsvlLAlgVD 307
                                    3333335555566666677788889*****************************************.3333244345555 PP

                          MFS_1  85 lwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivslla 164
                                    +   +++ +   + ++a+ p+++al+ d ++ + rgr++g++s+  +lG+ lg +l+gl +s+l +  +  +  ++++  
  gi|119720290|ref|YP_920785.1| 308 ILRAAAAVAPLMFLTSAVGPTILALVGDQASTDARGRVMGVYSVVLGLGMGLGSILAGLASSALPYNRPLALSLVALAAY 387
                                    5546666666777779************************************************9999888888888888 PP

                          MFS_1 165 fvlfll 170
                                     v +l+
  gi|119720290|ref|YP_920785.1| 388 SVAALA 393
                                    774333 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   9.1   1.4e-05      0.12      46     194 ..      39     193 ..      16     195 .. 0.77
   2 !   11.2   3.4   1.3e-05      0.12     257     400 ..     212     358 ..     200     391 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 1.4e-05
                                    .HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTT..SS-TGGGGG......HHHHHHHHH CS
                       Sugar_tr  46 vlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgk..nsvevlivg......RvlvGigvG 117
                                    v  g++++++ + ++iG+l+ag ++d+ GRk +l+++ v  ++g +  aa  +   +s   l+++        +vG+   
  gi|119720290|ref|YP_920785.1|  39 VAAGFVMAAYPLMEAIGALLAGSWSDFAGRKRTLIAGYVARSAGMLSLAAVFALssSSPGSLVFAaleaalNGVVGFTTA 118
                                    66799*********************************999999877766665555444444444466667888888888 PP

                                    HHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGGGS--- CS
                       Sugar_tr 118 lasvlvPmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllilllflPES 194
                                    l+ v +   +  ++ +  Rg  ++ +++   +    ++ +g  l  +    g++  l+++l+ al+  ++  fl+E+
  gi|119720290|ref|YP_920785.1| 119 LILVSSLSMATDLTETGNRGLGMGGFEFVNLASYGAGYLLGSLLYSVLP--GYPAYLAVALLTALATPVFAAFLEET 193
                                    8888888888888888888887777777666665556666655555555..67778888888888888888888887 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 1.3e-05
                                    HHHHHHHHHHHTTHHHHHHHTTTHHH.HSS-THH.........HHHHHHHHHHHHHHHHHHHHHHHHS-SHHHHHHHHHH CS
                       Sugar_tr 257 igvvlqifqqltGinaimyysptife.nlglsks.........llvtiivgvvnfvatfvaiflvdrfGRRtllllGaag 326
                                      v+l ++  lt+i  i +y+p++++  lg             ll+ + ++ +   a+f++  l+d +GR +++ lG+ag
  gi|119720290|ref|YP_920785.1| 212 ALVLLPVWVALTTIIGIGIYAPRVIHdHLGAVHGpaigkagigLLFLGALVLLGSGAVFFG-RLSDSWGRVKVFRLGLAG 290
                                    5688999999999999999999866516888777855555444444444444444444555.89**************** PP

                                    HHHHHHHHH..HHHHTTSS...CHHHHHHHHHHHHHHHTTTTHHHHHHHHHHSHTTTHHHHHHHHHHHHHHHHH CS
                       Sugar_tr 327 maicfvilgivalllvakskaasivaivfialfialfalgwgpvpwvlvsElfpqsvRskalaiavavnwlanf 400
                                    +++++  ++   +l+v+       +a v+    +++ +  +gp++  lv + ++++ R+ ++ +  +v  l   
  gi|119720290|ref|YP_920785.1| 291 GLAALSAMSVLLALGVDI---LRAAAAVAP---LMFLTSAVGPTILALVGDQASTDARGRVMGVYSVVLGLGMG 358
                                    ********9444444444...344444444...44456689999999**************9987776655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       633  (0.0353059); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2584.11
//
Query:       gi|119720291|ref|YP_920786.1|  [L=284]
Description: methyltransferase type 12 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-09   38.6   0.1      2e-09   38.0   0.1    1.3  1  Methyltransf_25  Methyltransferase domain
    6.6e-06   26.0   0.0    8.9e-06   25.6   0.0    1.1  1  Methyltransf_31  Methyltransferase domain
     0.0051   16.4   0.0     0.0079   15.8   0.0    1.2  1  MTS              Methyltransferase small domain
  ------ inclusion threshold ------
       0.01   15.7   0.0      0.014   15.3   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
      0.023   14.0   0.0       0.03   13.7   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
      0.031   15.0   0.0      0.045   14.5   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
      0.035   13.4   0.0      0.054   12.8   0.0    1.2  1  GidB             rRNA small subunit methyltransferase G
       0.11   12.4   0.0       0.14   12.0   0.0    1.2  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
       0.23   11.2   0.0       0.33   10.7   0.0    1.2  1  Methyltransf_16  Lysine methyltransferase


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   0.1   9.9e-13     2e-09       1      97 []      60     162 ..      60     162 .. 0.93

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 9.9e-13
                                    EEEET-TTSHHHHHHHCTS...T.SSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEEEST. CS
                Methyltransf_25   1 vLdlGcGtGrltlalakrl...g.kakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvssga. 73 
                                    v+d++ G G    alak++   g + +++ vD+  e+le ar+  e+ +l   +e ++ da++l+   ++fD+ ++ g  
  gi|119720291|ref|YP_920786.1|  60 VVDVCSGAGLGGVALAKAFterGlEVELVLVDLRREALELARRFSEA-ELgsPAETYVLDARELHALGRRFDVALVYGLt 138
                                    89****************9976599****************998765.3456************************9999 PP

                                    GGGSSHHHHHHHHHHHHHHEEEEE CS
                Methyltransf_25  74 lhhlsdedlekalkeiarvLkpgG 97 
                                      h++  d++++++ ia+ L ++G
  gi|119720291|ref|YP_920786.1| 139 TPHFDAFDAARVYSSIAESLADDG 162
                                    99******************9998 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   4.5e-09   8.9e-06       4     113 ..      57     170 ..      55     202 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 4.5e-09
                Methyltransf_31   4 glrvlDlGCGtGeltfelae...elgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlils 80 
                                     l+v+D+ +G+G  + +la+   e g + e+v++D   ea+elAr  ++    + +e  + d+ el   l  ++fD+ l 
  gi|119720291|ref|YP_920786.1|  57 RLSVVDVCSGAGLGGVALAKaftERGLEVELVLVDLRREALELARRFSEAELGSPAETYVLDARELHA-LG-RRFDVALV 134
                                    5789***************98877777999****************766666668**********995.45.9****999 PP

                Methyltransf_31  81 nevl...naladpdkileeiervlkpggilliedpr 113
                                     ++     +  d + ++ +i + l ++g+ll+e+ +
  gi|119720291|ref|YP_920786.1| 135 YGLTtphFDAFDAARVYSSIAESLADDGVLLVEEND 170
                                    88888999999*********************9876 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0     4e-06    0.0079      32      89 ..      57     119 ..      46     135 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4e-06
                                    CSEEEEET-TTSHHHHHHHHHTT....C.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-ST CS
                            MTS  32 sgkvlDlGcGaGvlgaalakesp....eaevtlvdvdarAlesakenleankle.vevvasdv 89 
                                    + +v+D+++GaG+ g+alak+      e+e++lvd   +Ale+a++  ea+  + +e++  d+
  gi|119720291|ref|YP_920786.1|  57 RLSVVDVCSGAGLGGVALAKAFTerglEVELVLVDLRREALELARRFSEAELGSpAETYVLDA 119
                                    4569********999999987651212567999************988887766666666665 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.0   6.8e-06     0.014      21     122 ..      55     171 ..      30     212 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 6.8e-06
                Methyltransf_23  21 raggrvLdiGcGtGi....llevlrengf..svtgvDlspeaveiae...kakkaqkdqfdeqeaae...pqgkfdlIvl 88 
                                    +++ +v+d+  G G     l++ + e+g   ++++vDl++ea e+a+   +a    +  ++  +a+e     ++fd++  
  gi|119720291|ref|YP_920786.1|  55 KRRLSVVDVCSGAGLggvaLAKAFTERGLevELVLVDLRREALELARrfsEAELGSPAETYVLDARElhaLGRRFDVALV 134
                                    6677899998888865556799999999877899***********9866633333333333334444332666****999 PP

                Methyltransf_23  89 revl.ehvp..dppellrqiatllkpgGylllsepla 122
                                      ++  h++  d +++ ++ia+ l+++G+ll++e ++
  gi|119720291|ref|YP_920786.1| 135 YGLTtPHFDafDAARVYSSIAESLADDGVLLVEENDR 171
                                    886516999999********************99776 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.5e-05      0.03      44     126 ..      53     137 ..      42     186 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.5e-05
                                    -S--TTEEEEES-TT-HHHHHHHHHHHHHH...EEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEE CS
                Ubie_methyltran  44 avkrgakvlDvagGtgDlafklsdsvgekg...kvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvv 120
                                    a+kr  +v+Dv++G+g   ++l+++  e+g   ++v++D+  + L+ +++  + e  +  e  + +a eL      fDv 
  gi|119720291|ref|YP_920786.1|  53 AGKRRLSVVDVCSGAGLGGVALAKAFTERGlevELVLVDLRREALELARRFSEAELGSPAETYVLDARELHALGRRFDVA 132
                                    5688889***********************99999*************99888777777777777888888888888865 PP

                                    EEES-G CS
                Ubie_methyltran 121 tvsfGl 126
                                       +Gl
  gi|119720291|ref|YP_920786.1| 133 L-VYGL 137
                                    4.4666 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   2.2e-05     0.045       5      99 .]      65     164 ..      61     164 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.2e-05
                Methyltransf_12   5 cGtGsllrallekl....pdieytgvDispsaiedakeklakrennn.nnnvelealdlldldggssfDlvvas.nvlhh 78 
                                    +G G    al++++     ++e++ vD+ ++a+   ++++++ e  + ++ + l+a++l+ l  g  fD+ ++   +  h
  gi|119720291|ref|YP_920786.1|  65 SGAGLGGVALAKAFtergLEVELVLVDLRREAL-ELARRFSEAELGSpAETYVLDARELHAL--GRRFDVALVYgLTTPH 141
                                    5556556666666666679**************.5555666655555055555555554433..35****9998455567 PP

                Methyltransf_12  79 l..kdirevldnirklLkpgGrl 99 
                                    +   d ++v ++i++ L+++G+l
  gi|119720291|ref|YP_920786.1| 142 FdaFDAARVYSSIAESLADDGVL 164
                                    7899999**************87 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.7e-05     0.054      49      74 ..      56      82 ..      47      97 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.7e-05
                                   C-..EEEETSTTTTTHHHHHHH-TTSE CS
                           GidB 49 rd.kviDvGsGaGlPGipLaiarpelk 74
                                   r  +v+Dv sGaGl G+ La a+ e  
  gi|119720291|ref|YP_920786.1| 56 RRlSVVDVCSGAGLGGVALAKAFTERG 82
                                   3326****************9988765 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0     7e-05      0.14       5      62 ..      65     124 ..      61     159 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7e-05
                                    E--SCCHHHHHHHHHHTT-EE..EEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCC CS
                        3HCDH_N   5 iGaGtmGagiaavfasagleV..vlvdiseealekalekieksleklvekgklkeeevea 62 
                                     GaG+ G  +a++f ++gleV  vlvd ++eale a++  e++l + +e   l++ e +a
  gi|119720291|ref|YP_920786.1|  65 SGAGLGGVALAKAFTERGLEVelVLVDLRREALELARRFSEAELGSPAETYVLDARELHA 124
                                    59*****************993345799*********99999998888877777666655 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00016      0.33      40      83 ..      50      98 ..      31     121 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00016
                Methyltransf_16 40 lganelsklsvlELGsGtGlvGlavael....lpeakviltDlee.lle 83
                                   +g +  ++lsv+++ sG+Gl G+a+a++      e++++l Dl   +le
  gi|119720291|ref|YP_920786.1| 50 TGIAGKRRLSVVDVCSGAGLGGVALAKAfterGLEVELVLVDLRReALE 98
                                   556677899******************9764225566677776543555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 2148.79
//
Query:       gi|119720292|ref|YP_920787.1|  [L=275]
Description: alpha/beta hydrolase fold [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.1e-71  239.4   0.0    3.6e-71  239.2   0.0    1.0  1  Hydrolase_4    Serine aminopeptidase, S33
    1.1e-16   61.3   0.2    6.2e-11   42.4   0.6    2.1  2  Abhydrolase_1  alpha/beta hydrolase fold
    4.2e-13   50.4   0.6      5e-13   50.2   0.6    1.1  1  Abhydrolase_6  Alpha/beta hydrolase family
    1.8e-10   40.6   1.4    6.2e-07   29.1   0.0    2.1  2  Peptidase_S9   Prolyl oligopeptidase family
      1e-05   25.5   0.6    0.00068   19.5   0.0    2.2  2  Abhydrolase_2  Phospholipase/Carboxylesterase
    0.00012   20.9   0.4      0.022   13.5   0.0    2.4  3  AXE1           Acetyl xylan esterase (AXE1)
    0.00041   20.0   0.0       0.01   15.4   0.0    2.2  2  DLH            Dienelactone hydrolase family
     0.0027   17.4   0.0     0.0077   15.9   0.0    1.9  1  FSH1           Serine hydrolase (FSH1)
     0.0038   17.0   0.9        3.9    7.2   1.6    3.1  2  Abhydrolase_5  Alpha/beta hydrolase family
      0.004   16.9   0.0     0.0053   16.5   0.0    1.2  1  PGAP1          PGAP1-like protein
  ------ inclusion threshold ------
      0.019   14.8   0.4      0.061   13.2   0.4    1.8  1  Lipase_3       Lipase (class 3)
      0.059   13.0   0.0        8.2    5.9   0.0    2.1  2  Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
       0.11   12.4   0.1       0.26   11.1   0.1    1.6  1  Abhydrolase_3  alpha/beta hydrolase fold


Domain annotation for each model (and alignments):
>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  239.2   0.0   2.6e-74   3.6e-71       2     239 .]      26     259 ..      25     259 .. 0.99

  Alignments for each domain:
  == domain 1  score: 239.2 bits;  conditional E-value: 2.6e-74
                    Hydrolase_4   2 epkavvvlvHGlaehsgryaelaeaLaaqGfavyalDhrGhGrsegkrghvpsfddyvdDlaafvekvkeehpelplfll 81 
                                    epkavvv +HG+aehsgrya++++ L  +G+a y++D rGhG s+ +rg+v+sfd++v+D  af++ v++ h +++ f+l
  gi|119720292|ref|YP_920787.1|  26 EPKAVVVGIHGFAEHSGRYAHVGDFLSSRGYALYMYDLRGHGLSKWERGYVDSFDQFVEDSVAFYRLVVSGHAGKKGFVL 105
                                    89****************************************************************************** PP

                    Hydrolase_4  82 GhSmGGliallyllrypdkvaglilsaPalkikaklkappllklllkllgkllpklqvsnnlkadslsrdpevvaayead 161
                                    GhSmGG+ia+l + r   +v+gl+ s++al+++    + +  +lll+ll+ + p+ + + +++ d lsrd++v ++y ad
  gi|119720292|ref|YP_920787.1| 106 GHSMGGVIAVLTVYRLGGEVSGLVTSGAALEVN----VGAGTRLLLRLLSAVNPRGRAKLPVNVDCLSRDKAVAESYVAD 181
                                    *********************************....7789*************************************** PP

                    Hydrolase_4 162 plvhgkitvrlllelldamkrleeraakitlPllllhGeaDkvvdpeasrelyerlgskdktlklypglyHellnEpd 239
                                     lv +++t rll+e+ ++++++++ aak+t+P ll+hGe+D +v+p+asr+l++ l+s+dktl+++pg+ He++nE d
  gi|119720292|ref|YP_920787.1| 182 NLVFKDPTYRLLAEFGRGVSEAWKAAAKVTVPALLMHGEEDCLVPPSASRKLFQVLPSSDKTLEVFPGMKHEIFNEVD 259
                                    ****************************************************************************76 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.4   0.6   4.5e-14   6.2e-11       2     158 ..      30     184 ..      29     188 .. 0.77
   2 !   17.8   0.0   1.5e-06     0.002     175     253 ..     170     255 ..     142     259 .. 0.78

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 4.5e-14
                                    EEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHH..HH.HHHCTTSSEEEE CS
                  Abhydrolase_1   2 vlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddld..ri.ldalgddkltlv 78 
                                    v+v +hG+++ s+ +a   +++ L+ +g+ ++++DlrG+g S+     ++  +  + v+d++   r+ +  +  +k  ++
  gi|119720292|ref|YP_920787.1|  30 VVVGIHGFAEHSGRYAH--VGDFLSSRGYALYMYDLRGHGLSKWERGYVD-SFDQF-VEDSVAfyRLvVSGHAGKKGFVL 105
                                    6899*************..***********************88888765.45443.555555544448888888888** PP

                                    EETHHHHHHHHHHHHHGGGEEEEEEESECSSCCHHHHHHHHHHHHHHCHHCHHHHHHHHHHHHHHHHCCSCHHHHHHHHH CS
                  Abhydrolase_1  79 GhSmGGmialayaaeyperVkalvllgaidpaaslieaqrqqaksfpdffdgyaadcarnpagplladelaaleqrhrlv 158
                                    GhSmGG ia     +    V++lv+ ga +     +   r  +  +   + + +a+  +n+++++ ++ +a + + ++lv
  gi|119720292|ref|YP_920787.1| 106 GHSMGGVIAVLTVYRLGGEVSGLVTSGA-ALEVNVGAGTRLLLRLLSAVNPRGRAKLPVNVDCLSRDKAVAESYVADNLV 184
                                    ****************************.555555555555566666666666666667777776666666666666665 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 1.5e-06
                                    HHHCHHHHHHHHHHHHHHHHCCHHHHHHHHHC.....THHHHSEEEEEEETTCSSSCHHHHHHHHHCHTS..EEEEEEET CS
                  Abhydrolase_1 175 sdnasslatgalksieqwpttdsaklllrlre.....lknvlaptlvisgtsDplvppkaledlaqllpk..krlvvisd 247
                                    +d a+  +++a++ +   pt+   + ++r  +       +v++p+l+++g++D lvpp+a+++l q lp+  k+l+v+++
  gi|119720292|ref|YP_920787.1| 170 RDKAVAESYVADNLVFKDPTYRLLAEFGRGVSeawkaAAKVTVPALLMHGEEDCLVPPSASRKLFQVLPSsdKTLEVFPG 249
                                    5555555555555555555555555566655578888888999************************99999******** PP

                                    CSSSHH CS
                  Abhydrolase_1 248 agHlaf 253
                                      H +f
  gi|119720292|ref|YP_920787.1| 250 MKHEIF 255
                                    ***998 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.2   0.6   3.6e-16     5e-13       1     210 [.      31     255 ..      31     270 .. 0.55

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 3.6e-16
                                    EEEE--GC.....GCHHHHHHHHCCT.CEEEEE--TTSTS-GGCS.....--HHH.CHHHHHHHCCTT....TTSEEEEE CS
                  Abhydrolase_6   1 vlllHGagssassWlvapLaallaag.vhvlapDlpGhGrsdppp.....ldled.ladlaalldelaa..gggpvvlvG 71 
                                    v+ +HG+  +++ ++  ++  +l+++ ++ +++Dl+GhG   +++     ++++  ++d +a+ + +++   g++ +++G
  gi|119720292|ref|YP_920787.1|  31 VVGIHGFAEHSGRYA--HVGDFLSSRgYALYMYDLRGHG--LSKWergyvDSFDQfVEDSVAFYRLVVSghAGKKGFVLG 106
                                    7889**888888886..6644444444888*********..444442222333333344466666665564455559*** PP

                                    ETCHHHHHHHHHHCC.......EEEEES-..----TTT....S----TTHHHHHHTT-C.CCCH....CCH.S-HSCCCC CS
                  Abhydrolase_6  72 HSlGGalalaaapla.....lvvgvlldppptalpagl....laaalelllallallrl.lawl....sre.plprlfla 136
                                    HS+GG++a +           v+g++ ++   a+   +     + +l+ll a++++ r+ l       sr+ +++++++a
  gi|119720292|ref|YP_920787.1| 107 HSMGGVIAVL---TVyrlggEVSGLVTSG---AALEVNvgagTRLLLRLLSAVNPRGRAkLPVNvdclSRDkAVAESYVA 180
                                    **********...3333367767755555...333333233444444444444444444322222233333455557777 PP

                                    HHHCCCCHCHCCCGHHHHCCHHCHTTCCHHTT-TTGCEEE.CTT-CHHHHCHHCCCH....STTEEETCE...SSS.-HH CS
                  Abhydrolase_6 137 dedadaawrarlarlaallaglgllpaaawadlpvpllvl.ggeDplvprllerlla....qagarlpvvlpgaGH.lph 210
                                    d+   +   ++++ la +  g+ +  + a a ++vp l++ g+eD lvp+ + r l     + +++l +v+pg  H   +
  gi|119720292|ref|YP_920787.1| 181 DNL--VFKDPTYRLLAEFGRGVSEA-WKAAAKVTVPALLMhGEEDCLVPPSASRKLFqvlpSSDKTL-EVFPGMKHeI-F 255
                                    555..33333333333333333322.33555555555555379999888777766666776788888.9999998843.3 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   1.3   0.00041      0.56       7      81 ..      48     117 ..      43     123 .. 0.89
   2 !   29.1   0.0   4.5e-10   6.2e-07     135     208 ..     205     274 ..     186     275 .] 0.89

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00041
                                    HHHHHCCT-EEEEE--TTSSTTHCHHHHTTSGGGGHHHHHHHHHHHHHHHHTTS--GGGEEEEEETHHHHHHHHH CS
                   Peptidase_S9   7 lqlladrGyvvvvanirGsggyGeafhdagkrklgqnefdDfiaaaealakegyvdserlaitGgSyGGyltgaa 81 
                                      +l++rGy+  + ++rG g    ++++ g+ +  ++ ++D +a  + +++ +    ++ ++ G+S GG+ +  +
  gi|119720292|ref|YP_920787.1|  48 GDFLSSRGYALYMYDLRGHG--LSKWER-GYVDSFDQFVEDSVAFYRLVVSGHAG--KKGFVLGHSMGGVIAVLT 117
                                    56899*************99..578998.*********************99976..99**********987765 PP

  == domain 2  score: 29.1 bits;  conditional E-value: 4.5e-10
                                    -CGGG-----EEEEEEETT-SSS-THHHHHHHHHHH--S-SEEEEEETTS-SSTTSSHHHHHHHHHHHHHHHHH CS
                   Peptidase_S9 135 spldnvkaypplLlihGlaDdrvppaealklvaaLqkkgknvlllifpdegHgvgkprakveelarllaFlkea 208
                                    + +++  +++p Ll+hG++D  vpp+ + kl++ L + +k+  l +fp+ +H + ++ +k + l++l+++l+++
  gi|119720292|ref|YP_920787.1| 205 KAAAK--VTVPALLMHGEEDCLVPPSASRKLFQVLPSSDKT--LEVFPGMKHEIFNEVDKEKVLEKLAEWLDKH 274
                                    44445..99****************************9997..569*************************997 PP

>> Abhydrolase_2  Phospholipase/Carboxylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.5     0.031        43     108     140 ..     103     135 ..      91     141 .. 0.87
   2 !   19.5   0.0   4.9e-07   0.00068     149     204 ..     206     257 ..     199     275 .] 0.77

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.031
                                    EEEEETHHHHHHHHHHHT-SS--SEEEEES--- CS
                  Abhydrolase_2 108 iigGFSqGaalalylaltlpkklggivafsgal 140
                                    ++ G S+G+++a+ +++ l  +++g v  + al
  gi|119720292|ref|YP_920787.1| 103 FVLGHSMGGVIAVLTVYRLGGEVSGLVTSGAAL 135
                                    789**********************99877665 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 4.9e-07
                                    TS-GGGGG-EEEEEEETT-SSS-HHHHHHHHHHHHTTS-GEEEEEETT--SS--HH CS
                  Abhydrolase_2 149 satavtkklpilqiHgeeDpvvplalgkaakevlkkllkkvelksyeglaHsidee 204
                                    +a +vt  +p l++HgeeD +vp + + ++ +vl ++ k  +l++++g++H+i +e
  gi|119720292|ref|YP_920787.1| 206 AAAKVT--VPALLMHGEEDCLVPPSASRKLFQVLPSSDK--TLEVFPGMKHEIFNE 257
                                    344555..9***************************988..9**********9765 PP

>> AXE1  Acetyl xylan esterase (AXE1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.1   0.2    0.0056       7.7      80     124 ..      25      70 ..      15      97 .. 0.80
   2 ?   -2.7   0.0       1.3   1.8e+03     177     189 ..     103     115 ..      85     118 .. 0.86
   3 !   13.5   0.0   1.6e-05     0.022     254     312 ..     206     265 ..     201     273 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0056
                                    SSSEEEEEEEE-TT--GGGHHHHHHH.HHTT-EEEEEE-TTTS..S CS
                           AXE1  80 eeklPavvefhGYegsrgeihdllny.aaaGyavvvmdvRGqgges 124
                                     e+  +vv  hG+ +++g  +    + ++ Gya  + d RG g ++
  gi|119720292|ref|YP_920787.1|  25 GEPKAVVVGIHGFAEHSGRYAHVGDFlSSRGYALYMYDLRGHGLSK 70 
                                    45677899********99999988872568***********99443 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.3
                                    EEEEETHHHHHHH CS
                           AXE1 177 avlGasqGGalal 189
                                    +vlG+s GG +a+
  gi|119720292|ref|YP_920787.1| 103 FVLGHSMGGVIAV 115
                                    68999***99997 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 1.6e-05
                                    HHCC--S-EEEEEETT-SSS-HHHHHHHHHH--SS.EEEEEETT-STTTTHHHHHHHHHH CS
                           AXE1 254 lAkrvkaevllsvgLeDevcpPstvfaaynklete.keikvyeefahealkafqedkklk 312
                                     A++v +++ll+ g eD + pPs    ++  l ++ k+++v++ ++he  ++  ++k+l+
  gi|119720292|ref|YP_920787.1| 206 AAAKVTVPALLMHGEEDCLVPPSASRKLFQVLPSSdKTLEVFPGMKHEIFNEVDKEKVLE 265
                                    58999*************************996544**************9998887765 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.081   1.1e+02      82     119 ..      83     121 ..      64     131 .. 0.70
   2 !   15.4   0.0   7.5e-06      0.01     129     195 ..     196     260 ..     187     274 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.081
                            DLH  82 lkaavaylksvpe.vstkkvgvvGfCmGGalalllaaev 119
                                    ++++va+++ v +    kk  v G  mGG +a+l   + 
  gi|119720292|ref|YP_920787.1|  83 VEDSVAFYRLVVSgHAGKKGFVLGHSMGGVIAVLTVYRL 121
                                    46777777765440455677799*********9876655 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 7.5e-06
                            DLH 129 YGlspekeleeaakikapilalfgeeDefipadevekleealkaanvdlelkvYpgagHaFandsre 195
                                    +G  +++  ++aak+ +p l ++geeD  +p ++  kl + l  +     l+v+pg +H  +n+ ++
  gi|119720292|ref|YP_920787.1| 196 FGRGVSEAWKAAAKVTVPALLMHGEEDCLVPPSASRKLFQVLPSSD--KTLEVFPGMKHEIFNEVDK 260
                                    5777888999********************************6655..56778******88776554 PP

>> FSH1  Serine hydrolase (FSH1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   5.6e-06    0.0077     156     198 ..     206     249 ..      71     259 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.6e-06
                           FSH1 156 eedkiqtptLhvlGelDtvvdeerseaLaeafkns.skvlkHpg 198
                                       k+++p L ++Ge+D +v+++ s++L ++  +s +++  +pg
  gi|119720292|ref|YP_920787.1| 206 AAAKVTVPALLMHGEEDCLVPPSASRKLFQVLPSSdKTLEVFPG 249
                                    46789*************************99998666666666 PP

>> Abhydrolase_5  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   1.6    0.0028       3.9      58      85 ..     101     129 ..      34     134 .. 0.83
   2 ?    4.8   0.0     0.015        21      98     144 ..     209     256 ..     197     266 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0028
                  Abhydrolase_5  58 kfvvgGhslGGvvasrfaaeee.kiegvv 85 
                                    k +v Ghs+GGv+a   + + + ++ g+v
  gi|119720292|ref|YP_920787.1| 101 KGFVLGHSMGGVIAVLTVYRLGgEVSGLV 129
                                    445679*******9877665533666665 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.015
                  Abhydrolase_5  98 elskkvlsivgteDgvlnvkslekakkflpkdtkvvsi.eGgnhagfG 144
                                    + ++++l + g+eD +++ +  +k  + lp   k +++  G  h  f 
  gi|119720292|ref|YP_920787.1| 209 KVTVPALLMHGEEDCLVPPSASRKLFQVLPSSDKTLEVfPGMKHEIFN 256
                                    56778999*********************9866655542788888776 PP

>> PGAP1  PGAP1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   3.8e-06    0.0053      94     148 ..     103     154 ..      67     196 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.8e-06
                          PGAP1  94 iliGHSmGGivaraaltlknyikqsvntiltlasPhalpplsfdkdilklyervn 148
                                    +++GHSmGG++a  +lt  +   ++v+ ++t ++ ++  + +  + +l+l ++vn
  gi|119720292|ref|YP_920787.1| 103 FVLGHSMGGVIA--VLTVYR-LGGEVSGLVTSGAALEVNVGAGTRLLLRLLSAVN 154
                                    799*********..445445.4788999999988877777666666666666655 PP

>> Lipase_3  Lipase (class 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.4   4.4e-05     0.061      38      86 ..      74     121 ..      49     126 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.4e-05
                                    HHHHHHHS-HHHHHHHHHHHHHHHTT-EEEEEEEETHHHHHHHHHHHHH CS
                       Lipase_3  38 gfleayeeslreqvlkelkrllekypeysivvtGHSLGgalAlLaaldl 86 
                                    g+++++  ++ e+  +  + +++ +   +  v GHS+Gg +A+L+ + l
  gi|119720292|ref|YP_920787.1|  74 GYVDSFD-QFVEDSVAFYRLVVSGHAGKKGFVLGHSMGGVIAVLTVYRL 121
                                    5555555.4444444444556666667777899***********99876 PP

>> Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1     0.011        15      53      72 ..      51      70 ..      14      91 .. 0.75
   2 ?    5.9   0.0    0.0059       8.2     222     262 ..     205     246 ..     166     252 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.011
                                   HHHTT-EEEEEE-TTSTTS- CS
                  Peptidase_S15 53 fvarGYavVvqdvrGtggSe 72
                                   + +rGYa  ++d rG+g S+
  gi|119720292|ref|YP_920787.1| 51 LSSRGYALYMYDLRGHGLSK 70
                                   668**************996 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0059
                                    HHHCT--S-EEEEEECCSSTTC.CHHHHHHHHHCCTT-EEEE CS
                  Peptidase_S15 222 edadkvkapvllvgGwnDwnvk.ngaiklyealkapgvklil 262
                                    ++a+kv++p+ll++G  D  v   ++ kl++ l++ ++ l +
  gi|119720292|ref|YP_920787.1| 205 KAAAKVTVPALLMHGEEDCLVPpSASRKLFQVLPSSDKTLEV 246
                                    4569**************999999999****99998875544 PP

>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00019      0.26      45     100 ..      79     133 ..      77     256 .. 0.50

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00019
                                    TTHHHHHHHHHHHHHHHTHHHHTETTCEEEEEEETHHHHHHHHHHHHHHHTT---....E CS
                  Abhydrolase_3  45 fPaavedalaalrwlaeqawelgadpsrivlaGdSaGGnlaaavalrardegepk....v 100
                                    f + ved++a +r +++      +  ++ +++G S GG +a  ++ r+  e +       
  gi|119720292|ref|YP_920787.1|  79 FDQFVEDSVAFYRLVVSG-----HAGKKGFVLGHSMGGVIAVLTVYRLGGEVSGLvtsgA 133
                                    667799999999999998.....677889**************99999887422233331 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1942.18
//
Query:       gi|119720293|ref|YP_920788.1|  [L=444]
Description: peptidase S8/S53 subtilisin kexin sedolisin [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.7e-53  179.7  12.7      1e-52  179.3  12.7    1.1  1  Peptidase_S8  Subtilase family


Domain annotation for each model (and alignments):
>> Peptidase_S8  Subtilase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.3  12.7   5.8e-57     1e-52       1     298 []     160     429 ..     160     429 .. 0.88

  Alignments for each domain:
  == domain 1  score: 179.3 bits;  conditional E-value: 5.8e-57
                                    -TT-EEEEECS-B-TT-TTTGGGEEE..EEEE---TTSG.GGEETT-SS-TT-SC-SSS....HHHHHHHHHH-B..SSS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Peptidase_S8   1 gkgvlvavlDtGvdpshpdlsvttdgerklvdvideegagfngadsettstnwarddngnsieHGthvAGiaaanapeeg 80 
                                    g+gv+vavlDtG+d++hp+l+       k+v+  ++    ++ ++++ t+ ++ +d ng    HGthvAG++a    +  
  gi|119720293|ref|YP_920788.1| 160 GRGVVVAVLDTGIDYTHPELK------GKVVWCANT----VGVKTYTGTKLSNCADRNG----HGTHVAGTIASA-INGV 224
                                    89*******************......689988888....5566666666677777777....**********99.8888 PP

                                    SSB-SSTTSEEEEEE-SSTTSB-HH..HHHHHHHHHHHHCT-S..........EEEE-EESCETTCHHCHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Peptidase_S8  81 ekngvapgakilsvkvldtsggsmetgteliraieeaaedkvd..........vinmslgestslpktgrsiealainra 150
                                    ++ gvap++++++vkvl++ g+     ++++++i+ a++ ++d          +++mslg+s++ +  ++     a+++a
  gi|119720293|ref|YP_920788.1| 225 GNAGVAPNVTLYAVKVLNDAGSGTY--SDIAEGIIIAVK-GPDgvagtsddakILSMSLGGSSDSQVLYD-----AVKWA 296
                                    999**************77776543..9*******9999.666677**************6666555555.....999** PP

                                    H.CCT-EEEEE--SS-T-HHEEE-TTCEECTTTSTTCEEEEEESTTSSB-TT--B-TT.......-EEEE-S-CCCCCCC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Peptidase_S8 151 vnkkgvlvviSaGNngktgsslqagspvgtpstsknvitvgayttegkiapfSsrGpssdgklkpdivapGgnivstwsr 230
                                      ++g ++v++aGN+g +g+  +++ +v +p+ + +vi+v+a+++++++ ++Ss Gp++      d++apG+n++st+++
  gi|119720293|ref|YP_920788.1| 297 Y-SNGAVLVAAAGNSG-DGD--PTTDNVAYPARYSEVIAVAAVDSNANVPTWSSDGPEV------DVAAPGVNVYSTYKN 366
                                    *.99************.666..8**********************************98......6************** PP

                                    CCHHHTTTHHEEEE-SHHHCHHHHHHHHHHHHH.HHTT....--HHHHHHHHHCCS-EE......SSSSSSTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Peptidase_S8 231 qsnnsaglssyqsmsGTSmAsPnaagaaAllls.alpk....ltpetvraallntAqdlgkadniesfaqGaG 298
                                     +        y + sGTSmA+P++++ +Al++  +l +    ltp +v ++l +tA+d++ +  + +   G+G
  gi|119720293|ref|YP_920788.1| 367 GG--------YATLSGTSMATPHVSATVALIQAlRLAAgkqpLTPSQVYDVLTKTAKDINSP--GFDVFTGYG 429
                                    **........***********************6666699*****************99555..666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (444 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2970.27
//
Query:       gi|119720294|ref|YP_920789.1|  [L=77]
Description: hypothetical protein Tpen_1389 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       828  (0.0461822); expected 358.6 (0.02)
Passed bias filter:                      584  (0.0325729); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 530.09
//
Query:       gi|119720295|ref|YP_920790.1|  [L=135]
Description: PilT domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-12   47.3   0.1    3.1e-12   47.1   0.1    1.0  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.1   0.1   1.7e-16   3.1e-12       2     121 ..       3     124 ..       2     125 .. 0.94

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 1.7e-16
                                    EE-HHHHHHHHTTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHS.....SCHCHHHHHHHHHHHHHHHTSEEEE.BCH CS
                            PIN   2 vlDTsvliallrgeekaeaarklleeleelvtsalvlaEllyvlar.....rkskrekaaelvelllllsalkilp.ida 75 
                                    v+D+s+l a++ +e++ + +++ l      v+ + v+ E+++ + +     ++ + e+a++l+++l  + +++i     a
  gi|119720295|ref|YP_920790.1|   3 VVDASALAAFVLKEPGWKSLAEYL---VGAVSVDMVVKEVANAVWKacrvrGYVGVEEARRLLRVLKSMIGVNIELrPEA 79 
                                    89***************8888888...5699999***************************************9877999 PP

                                    HHHHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHHHHH CS
                            PIN  76 eiaeeaaeialkygllpnDaliaAtAkehgikliatfDedfrrvak 121
                                    + ++ a eia ++g++++Dal +A+A e+g +l+ t De+  rva+
  gi|119720295|ref|YP_920790.1|  80 DYLDAAFEIAVEHGVTVYDALYLALAVEEGEPLL-TLDERQLRVAG 124
                                    999*******************************.******99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 992.60
//
Query:       gi|119720296|ref|YP_920791.1|  [L=295]
Description: beta-lactamase domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-13   51.5   0.1    2.1e-13   50.7   0.1    1.5  1  Lactamase_B    Metallo-beta-lactamase superfamily
    2.5e-11   43.5   0.0    5.2e-11   42.4   0.0    1.5  2  Lactamase_B_2  Beta-lactamase superfamily domain
     0.0036   16.7   0.0     0.0062   16.0   0.0    1.3  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.012   15.8   0.4      0.033   14.4   0.0    1.9  2  DUF1945        Domain of unknown function (DUF1945)
        0.1   12.5   0.0       0.19   11.6   0.0    1.5  2  Lactamase_B_3  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.7   0.1   5.9e-17   2.1e-13      13      98 ..      41     131 ..      29     226 .. 0.81

  Alignments for each domain:
  == domain 1  score: 50.7 bits;  conditional E-value: 5.9e-17
                                    ETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHHHHHHH CS
                    Lactamase_B  13 gdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmeeaddaas 92 
                                    g +  +L+DtG s++  ++     +l+l +++vdav+l+H H+DH+Ggl+ l e++++++++ + +  ++ +   ++   
  gi|119720296|ref|YP_920791.1|  41 GSKYRVLFDTGRSGRVLLEN--ASSLRLSLEEVDAVVLSHRHYDHAGGLPALLEKAGFKPVVAHPDVVKPSYADSGGFKR 118
                                    55778*************96..7**********************************************99999987766 PP

                                    HCCHH.......T CS
                    Lactamase_B  93 rkgll.......l 98 
                                    +  +l        
  gi|119720296|ref|YP_920791.1| 119 FSVALpakaweeV 131
                                    6544433333330 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.4   0.0   1.5e-14   5.2e-11       2      98 ..      45     139 ..      44     154 .. 0.73
   2 ?   -2.8   0.0         1   3.8e+03      69      98 ..     234     262 ..     212     287 .. 0.56

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 1.5e-14
                                    EEEES--TTHHHHHTCGGS--S.SS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHH.HCCTTCGHHHC CS
                  Lactamase_B_2   2 riLiDagpdlrqqalralqPve.lrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvla.vleanfvylal 79 
                                    r+L+D+g + r   l   ++++ lr +l+++daV+l+h HyDH  gl+ l e ++   p++a+++v +   ++++ +  +
  gi|119720296|ref|YP_920791.1|  45 RVLFDTGRSGRVL-L---ENASsLRLSLEEVDAVVLSHRHYDHAGGLPALLEKAGF-KPVVAHPDVVKpSYADSGGFKRF 119
                                    9********5544.2...223447899*************************5442.46999988765356666666666 PP

                                    HTT.TTEEEEEE-TTSEEEE CS
                  Lactamase_B_2  80 eee.pavnvheldwgesfel 98 
                                     ++ pa +++e++ g ++ l
  gi|119720296|ref|YP_920791.1| 120 SVAlPAKAWEEVAGGSELVL 139
                                    66666777777776666655 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1
                                    HCCTTCGHHHCHTTTTEEEEEE-TTSEEEE CS
                  Lactamase_B_2  69 vleanfvylaleeepavnvheldwgesfel 98 
                                      +++  + ++e    + v+e+++g+ + l
  gi|119720296|ref|YP_920791.1| 234 ATAEEVERVVSELS-SLGVEEIHAGHCTGL 262
                                    44444444444444.455555555554444 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.7e-06    0.0062       7      59 ..      44      94 ..      36     104 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.7e-06
                  Lactamase_B_6  7 vkiLlDvGwdeskvslesalkelekviptvdliLLshatlehlGayallyakf 59
                                    ++L D G ++  v l +  + l+  +++vd+++Lsh   +h G+++ l+ k+
  gi|119720296|ref|YP_920791.1| 44 YRVLFDTGRSGR-VLL-ENASSLRLSLEEVDAVVLSHRHYDHAGGLPALLEKA 94
                                   699*******97.545.466789999*********************998775 PP

>> DUF1945  Domain of unknown function (DUF1945)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1         2   7.3e+03      10      26 ..      28      46 ..      24      52 .. 0.58
   2 ?   14.4   0.0   9.3e-06     0.033      14      36 ..     156     178 ..     151     182 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2
                                   SSEEEEE..EEETTEEEEE CS
                        DUF1945 10 dkfLvyr..LyddqhsLkv 26
                                     f vy    ydd    +v
  gi|119720296|ref|YP_920791.1| 28 HGFSVYLslSYDDGSKYRV 46
                                   5566663213777655555 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 9.3e-06
                                    EEEEEETTEEEEEEEE-SSS-EE CS
                        DUF1945  14 vyrLyddqhsLkvfhnLsGeevv 36 
                                    v r+yd+ +++k f+ LsG evv
  gi|119720296|ref|YP_920791.1| 156 VERIYDNSYAVKGFYTLSGGEVV 178
                                    77********************9 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   5.3e-05      0.19      34      50 ..      62      84 ..      10     137 .. 0.75
   2 ?   -3.0   0.0       1.7     6e+03      82     114 ..     227     259 ..     205     268 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.3e-05
                  Lactamase_B_3 34 a......eeaDlvlisqaledHa 50
                                          ee+D+v++s+++ dHa
  gi|119720296|ref|YP_920791.1| 62 SslrlslEEVDAVVLSHRHYDHA 84
                                   14444449**************7 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.7
                  Lactamase_B_3  82 atshdavggsergenngflleqdgltiyhlGhl 114
                                     + h a+  +e+ e ++  l++ g++ +h Gh+
  gi|119720296|ref|YP_920791.1| 227 GGLHLAGATAEEVERVVSELSSLGVEEIHAGHC 259
                                    444444444444444444444455555666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 2049.56
//
Query:       gi|119720297|ref|YP_920792.1|  [L=133]
Description: hypothetical protein Tpen_1392 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        1.2    9.7  13.1         31    5.1  11.4    2.6  2  DUF202    Domain of unknown function (DUF202)


Domain annotation for each model (and alignments):
>> DUF202  Domain of unknown function (DUF202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0    0.0052        93      40      58 ..      21      39 ..       5      45 .. 0.77
   2 ?    5.1  11.4    0.0018        31       9      57 ..      51      93 ..      51     122 .. 0.59

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.0052
                         DUF202 40 gkilglilivlgiltllvg 58
                                     il+++++  gi++l+++
  gi|119720297|ref|YP_920792.1| 21 VTILAYLYLFSGIFVLGMV 39
                                   3899999*******99875 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0018
                         DUF202  9 TfLaWlRtslalialglall.....rffltgepsalgkilglilivlgiltllv 57
                                   TfLaWl  ++al+a+g++++     +++l           +++   l++l++lv
  gi|119720297|ref|YP_920792.1| 51 TFLAWLLYGVALMATGVGFMygmkwAWWL-----------AVVNQSLSALIMLV 93
                                   9******************9333222333...........33222222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       841  (0.0469072); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 957.19
//
Query:       gi|119720298|ref|YP_920793.1|  [L=394]
Description: hypothetical protein Tpen_1393 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-18   66.6   0.0    3.7e-18   66.1   0.0    1.2  1  NurA      NurA domain
  ------ inclusion threshold ------
       0.19   11.3   0.0       0.34   10.4   0.0    1.4  1  Get5_bdg  Binding domain to Get4 on Get5, Golgi to ER traffic


Domain annotation for each model (and alignments):
>> NurA  NurA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.1   0.0   4.1e-22   3.7e-18       5     241 ..      37     357 ..      33     358 .. 0.88

  Alignments for each domain:
  == domain 1  score: 66.1 bits;  conditional E-value: 4.1e-22
                                    EEEEEEEEEEETTCEEEEEEEEEEECCEEECCCEEEECEBTCCHHEEEEE.....HHHHHHHHHHHHHHHHHHHCGGCCS CS
                           NurA   5 AvDGSngvvrlsggilyilsayavvgggkerleealslasvdsispsdel.....errirllmetlElklgallleekge 79 
                                    +vDGSn v  ++ g ++++ ++a +  + +rl   +  ++ +++ +  ++     e+r  l+m +lEl+  a +l + g+
  gi|119720298|ref|YP_920793.1|  37 FVDGSNVVD-ERRGAYVAVFSVASIVLDSGRLRPVSHGSRHPLVAR--IVpkgfgEQRANLYMSILELL-SAARLVRSGV 112
                                    7****9887.777777777777777777788888878888777652..2245666**************.********** PP

                                    CEEEEECSHHCCCH.................................................................. CS
                           NurA  80 dllllDGsligslv.................................................................. 93 
                                    ++++lDGs + + +                                                                  
  gi|119720298|ref|YP_920793.1| 113 EAVFLDGSYVSEMMvvfgyprdvyeeaqglvdreaaesyageaaglveealgsegvkgaaklfegvsglawrlytrlggg 192
                                    ******************************************************************************** PP

                                    ........HHHHHHHHHHHHHHHHHHHHHTT-....TTCEEEEESS-SCTCCHCCC......S--HHHHCCHHCCHCH-- CS
                           NurA  94 ........efdelheeleyeeylyslsrllea....glnlvgvaKsfrskellnllletlligesisDiallgallrkpg 161
                                              d  ++  e + yl +l++ll a    g++l +vaK+  + +l+++     ++g +++D++ll++  r+  
  gi|119720298|ref|YP_920793.1| 193 vggvekrvLLDYSYVFAEVAVYLEALRSLLTAgresGVPLFWVAKDADTDQLAEKE----GVGGWLNDVTLLDYAWRRLE 268
                                    ********888888888888888888888888888*********************....***************99944 PP

                                    -STTS-HHHHTT.........-HCCHHHHHH-.EEEEEEESSTTTTEEEEEHHHHHHCCHHHHHHHHHH..TTB-SSSBC CS
                           NurA 162 ytspllkilrek.........pllrealidke.iyfaYvrlegggsilrleipaevstakdedvlsllasqrlsisGYpr 231
                                     +  +l++++            l  e++ + + +++aY +l   g++l + +p  v+ +++ + l +l    ++++GYp+
  gi|119720298|ref|YP_920793.1| 269 GVYTVLEGREFGrpkpcaapgKLVEELFAKWRrYRVAYFKLRLHGPVLQMTFPGYVGEDEAREALATLS-SLAESRGYPK 347
                                    4444566666668899999974444555555569999*99999************99999999999999.9********* PP

                                    CHHHHHHHHC CS
                           NurA 232 pLalAhelak 241
                                    pL ++h++a+
  gi|119720298|ref|YP_920793.1| 348 PLSYVHNMAV 357
                                    *******996 PP

>> Get5_bdg  Binding domain to Get4 on Get5, Golgi to ER traffic protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   3.8e-05      0.34      12      41 ..     333     362 ..     332     364 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 3.8e-05
                       Get5_bdg  12 LatlnepvlskdYkkPLkevksLGVaLppL 41 
                                    Latl+  + s+ Y kPL+ v++++V  p L
  gi|119720298|ref|YP_920793.1| 333 LATLSSLAESRGYPKPLSYVHNMAVLNPEL 362
                                    99**********************977766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2636.80
//
Query:       gi|119720299|ref|YP_920794.1|  [L=559]
Description: hypothetical protein Tpen_1394 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-33  116.2   0.0      4e-33  115.4   0.0    1.5  1  DUF87            Helicase HerA, central domain
    0.00031   19.5   0.0    0.00068   18.4   0.0    1.5  2  DUF853           Bacterial protein of unknown function (DUF85
  ------ inclusion threshold ------
      0.037   13.9   0.0      0.062   13.2   0.0    1.2  1  Glucosamine_iso  Glucosamine-6-phosphate isomerases/6-phospho
      0.039   12.9   0.0        0.3   10.0   0.0    2.0  2  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
      0.059   12.7   0.0        2.5    7.4   0.0    2.3  2  FtsK_SpoIIIE     FtsK/SpoIIIE family
      0.088   12.6   0.0         11    5.8   0.0    2.2  2  DEAD             DEAD/DEAH box helicase


Domain annotation for each model (and alignments):
>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.4   0.0   1.3e-36     4e-33       1     182 [.     123     308 ..     123     378 .. 0.86

  Alignments for each domain:
  == domain 1  score: 115.4 bits;  conditional E-value: 1.3e-36
                          DUF87   1 ieiGrllsgsevpvyldlnklvtrHlAilgsTGsGKSntvavLleelle.kkgatililDpHGEYgkalekllsekvkvi 79 
                                    i iGrl ++ ev+  l l+ l++rH+A+l++TG+GKSn vav+l e+le ++ ++++++D H+EY+++   +  ++v+v+
  gi|119720299|ref|YP_920794.1| 123 IAIGRLSQNPEVRYTLSLDMLCSRHFAVLAMTGAGKSNAVAVILGEILEkFPYSRVVVVDTHNEYVPLA--EKFDRVRVL 200
                                    579**********************************************9999****************..777889999 PP

                          DUF87  80 tpspsa..........kdkelkinpwsldpeelldlleeddkpaaavqrsvleealdqakakeekeklssdepvekllee 149
                                    +p+             k  +l++++w l  ee++ ll   d++ a++q  +l+ al++++ + +++ + +d+p+++ +ee
  gi|119720299|ref|YP_920794.1| 201 SPAGRIarlvearygvKPSPLEVPIWTLGLEEIAGLLRL-DPTRATKQVMYLRGALQEVR-RARYKYAGADDPIYFRAEE 278
                                    99755599******9************************.8888888************9.59***************** PP

                          DUF87 150 lkkekeelrklknqaiarlldkledllrkggsf 182
                                    l     +l+ l++++++r+ ++l+dl +k +  
  gi|119720299|ref|YP_920794.1| 279 LL---GYLEGLQKSSRQRYDRSLDDLVLKLEML 308
                                    **...6666666666666666666665554433 PP

>> DUF853  Bacterial protein of unknown function (DUF853)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0      0.73   2.2e+03      16      41 ..     139     165 ..     129     180 .. 0.73
   2 !   18.4   0.0   2.3e-07   0.00068     276     362 ..     412     492 ..     374     503 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.73
                         DUF853  16 alkl.anrhGliaGatGtGktvtLqvl 41 
                                    +l++   rh  +   tG+Gk  ++ v+
  gi|119720299|ref|YP_920794.1| 139 SLDMlCSRHFAVLAMTGAGKSNAVAVI 165
                                    44442689999999******9877654 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 2.3e-07
                         DUF853 276 allekveqvvrLirskGvGvyfvtqnPldlPdtvLaqLGnrvqhalraftpkdqkavkaaadtfranpefdveeaiteLg 355
                                       e +e++ +  r  G+G+  v+q P +l +t Laq G+ +  alr   p+dq+ +  + + +      ++ e ++ L 
  gi|119720299|ref|YP_920794.1| 412 PAREILEKIAKEGRKFGIGLGVVSQRPRELSQTLLAQCGTLI--ALRTANPRDQEYILGSMEDVM----REMVEGLSGLV 485
                                    4567789999999***************************98..9*********99876655433....3678999999* PP

                         DUF853 356 vGealvs 362
                                    +Geal+s
  gi|119720299|ref|YP_920794.1| 486 TGEALIS 492
                                    ****998 PP

>> Glucosamine_iso  Glucosamine-6-phosphate isomerases/6-phosphogluconolactonase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.1e-05     0.062     167     217 ..     129     178 ..     120     187 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.1e-05
                                    STSSS-EEEE-HHHHTTCSEEEEEEESHHHHHHHHHHHTT..TTTSGGGGH CS
                Glucosamine_iso 167 pkpppeRitlTlpvlnsarevlflvaGeeKaealeevlsgedpeelPaalv 217
                                     ++p+ R tl+l +l s +  ++ ++G++K++a++ +l  e  e+ P ++v
  gi|119720299|ref|YP_920794.1| 129 SQNPEVRYTLSLDMLCSRHFAVLAMTGAGKSNAVAVILG-EILEKFPYSRV 178
                                    578999********************************8.55688899887 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0    0.0001       0.3      15      56 ..     145     188 ..     141     202 .. 0.90
   2 ?    0.1   0.0     0.095   2.8e+02     261     318 ..     417     466 ..     414     483 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0001
                  TrwB_AAD_bind  15 tqhilivGttGsGKtqalekllrairarg..draivlDltGafv 56 
                                     +h++++  tG+GK++a+  +l +i ++    r++v+D++ ++v
  gi|119720299|ref|YP_920794.1| 145 SRHFAVLAMTGAGKSNAVAVILGEILEKFpySRVVVVDTHNEYV 188
                                    5899***********************97669*******99887 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.095
                  TrwB_AAD_bind 261 lksllaegRkfGgavvlglqsiaqlrevYGedaaqsilslvntklilrvsdaetAeel 318
                                    l+++++egRkfG+     l  ++q      ++ +q++l  ++t + lr+++ +  e++
  gi|119720299|ref|YP_920794.1| 417 LEKIAKEGRKFGIG----LGVVSQR----PRELSQTLLAQCGTLIALRTANPRDQEYI 466
                                    56666677777754....3333332....24567899999999999998877766655 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.02        59      38      60 ..     145     166 ..     113     211 .. 0.81
   2 ?    7.4   0.0   0.00083       2.5     168     212 ..     419     463 ..     397     482 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.02
                                    S-.SEEEE--TTSSHHHHHHHHH CS
                   FtsK_SpoIIIE  38 mashllvaGatgsGKStalntLi 60 
                                    +  h  v+  tg GKS+a+ +++
  gi|119720299|ref|YP_920794.1| 145 S-RHFAVLAMTGAGKSNAVAVIL 166
                                    3.59999999********98876 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.00083
                                    ........-----------B-----EEEEEEC-HHHHHHHHHHH. CS
                   FtsK_SpoIIIE 168 sLsnqgpsygvhvlvtagrelekrpslvvivderieLrlaapkds 212
                                    +++++g ++g+ + v ++r  e  ++l+++ + +i+Lr a p+d+
  gi|119720299|ref|YP_920794.1| 419 KIAKEGRKFGIGLGVVSQRPRELSQTLLAQCGTLIALRTANPRDQ 463
                                    68999*******999999999***********************5 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0    0.0036        11      14      53 ..     145     181 ..     137     193 .. 0.76
   2 ?    4.4   0.0    0.0097        29     121     151 ..     392     422 ..     361     431 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0036
                                    TCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  14 ggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkaliv 53 
                                     +++ v a TG+GK+ a ++ + +i+   ++ +  ++++v
  gi|119720299|ref|YP_920794.1| 145 SRHFAVLAMTGAGKSNAVAVILGEIL---EKFPYSRVVVV 181
                                    5677899**********998888777...35666666665 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0097
                                    TEEEEEEETHHHHHHTTTHHHHHHHHHHSHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD 121 qvrflVlDEadrlldqgfsdfinrilnqlpq 151
                                    q ++lV+ Ea+++  qg+    ++il+++++
  gi|119720299|ref|YP_920794.1| 392 QPTLLVVEEAHNYAPQGRWSPAREILEKIAK 422
                                    6689**************9999999999954 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (559 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.40
# Mc/sec: 4154.44
//
Query:       gi|119720300|ref|YP_920795.1|  [L=296]
Description: pyridoxal-5'-phosphate-dependent enzyme, beta subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-61  207.6   0.1    3.2e-61  207.3   0.1    1.0  1  PALP            Pyridoxal-phosphate dependent enzyme
  ------ inclusion threshold ------
       0.16   12.4   0.6        2.4    8.6   0.1    2.4  2  GHMP_kinases_C  GHMP kinases C terminal


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  207.3   0.1   3.6e-65   3.2e-61       4     279 ..       9     274 ..       6     282 .. 0.94

  Alignments for each domain:
  == domain 1  score: 207.3 bits;  conditional E-value: 3.6e-65
                                    CSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTT...TTTSEEEEEBSSHHHHHHHHHHHHHT-E CS
                           PALP   4 gigpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllarlkeg...tgaktvveassGNhgralAaaaallGlk 80 
                                     +g+TP+++l+       +++++KlE++nptgS+KdR a+y+l ++ e+   +++   veassGN++++lA+a+ l+G+k
  gi|119720300|ref|YP_920795.1|   9 LVGKTPVLELDVPP----GKVYVKLEYTNPTGSHKDRIAVYMLRSAVEEgvlRPGGSFVEASSGNTAVSLAWAGVLAGFK 84 
                                    57999999998754....67*************************88888****************************** PP

                                    EEEEEETTS-HHHHHHHHHTT-EEEEE....CCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHH.HHTHHHHHHHHTT CS
                           PALP  81 vtivvpadaspekvallrllGaevvev....ggdydeavaaaaelaaegegaylvsqfdnptvieg.ygtiglEileqlg 155
                                     +i+ +++ s++k+ ll  +Gaev++v     gd+d+ v+aa+++a+e +g  +++q++n++++ + y+t+g+E+l+q+g
  gi|119720300|ref|YP_920795.1|  85 PIIFAEDTISKGKLGLLLGMGAEVHLVprkpWGDPDHYVNAAKRFAEE-NGLPFLNQYGNEANWRAhYETTGPELLSQTG 163
                                    ***************************8887788**************.******************************7 PP

                                    TTEEEEEEE-SSSHHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTCCS..S.SS..B.SSS.CCSTCSCGTTCCHHHHSE CS
                           PALP 156 gkpdavvvpvGgGgliaGiaaglkerrpdvrvigvepegsdalarslragrrvtvpvsdtiadglavgspselafelldr 235
                                      +da+v+++G+Gg++ Gi+++lker p+ rv+gv p+gs+  ++ l              ++gla     ++  e + r
  gi|119720300|ref|YP_920795.1| 164 -GVDAFVMGIGTGGTVIGIGKYLKERVPEARVVGVVPKGSPIAGGRL-----------GDNIEGLAST-FVPELYERHGR 230
                                    .**********************************************...........9999999999.88888999999 PP

                                    EEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHH.HHHHH CS
                           PALP 236 lvdeivtvsdeealeamrllarregivvepssaaalaal.klrea 279
                                     vd + +vs ++al+ ++ l  r+g++++ps++a+++++ +l+++
  gi|119720300|ref|YP_920795.1| 231 VVDSVEEVSLADALSSLKDLL-RAGVLAGPSTGASFHVArRLASR 274
                                    9********************.*****************555444 PP

>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.1   0.00026       2.4      41      69 ..     157     185 ..     157     196 .. 0.84
   2 ?    1.5   0.0     0.044   3.9e+02      40      57 ..     247     264 ..     227     265 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00026
                 GHMP_kinases_C  41 ealselGalgaklsGaGgGptvfalfkdk 69 
                                    e+ls+ G   a++ G G G+tv++++k  
  gi|119720300|ref|YP_920795.1| 157 ELLSQTGGVDAFVMGIGTGGTVIGIGKYL 185
                                    578999999****************9544 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.044
                 GHMP_kinases_C  40 lealselGalgaklsGaG 57 
                                    l+ l+++G+l++  +Ga+
  gi|119720300|ref|YP_920795.1| 247 LKDLLRAGVLAGPSTGAS 264
                                    455669**********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1973.69
//
Query:       gi|119720301|ref|YP_920796.1|  [L=150]
Description: HEPN domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-19   69.1   0.1    4.2e-19   68.8   0.1    1.1  1  HEPN      HEPN domain
     0.0096   16.0   0.2      0.028   14.5   0.1    1.9  2  MIT       MIT (microtubule interacting and transport) domain


Domain annotation for each model (and alignments):
>> HEPN  HEPN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.8   0.1   4.7e-23   4.2e-19       2     117 ..       8     134 ..       7     135 .. 0.95

  Alignments for each domain:
  == domain 1  score: 68.8 bits;  conditional E-value: 4.7e-23
                                    HHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHTT--.SSCCHHHHHHCCHHHT........-HHHHHH CS
                           HEPN   2 eewlrrAeedleaAellleegdydlacfhaqqaaekalKAlllkkggeppkthdlreLleelkkelke.....seelree 76 
                                    + ++++A e  ++A ++le g y +++  +q+ +e++lKA+l   g+eppk hd+   l++ +   ++      +el+ +
  gi|119720301|ref|YP_920796.1|   8 RSHINQALEIVRQATEALEGGNYPYVVRQCQETVELLLKAALRIVGIEPPKWHDVGPVLRRERARFPAwfqerVDELASI 87 
                                    67899*******************************************************99999999988899999999 PP

                                    HHHHHCCCHHCCCTSS--S......--HHHHHHHHHHHHHHHHHHHH CS
                           HEPN  77 leeLekayiesrYpdakee......yteedaeealkdaeevlelvee 117
                                     + L+k +  + Y+d +++      yt+ dae+al+da+  lelv++
  gi|119720301|ref|YP_920796.1|  88 SRSLRKEREAAMYGDEESGlppeelYTRMDAEKALRDAKITLELVRQ 134
                                    9**************************************99999875 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   3.2e-06     0.028       1      37 [.      11      47 ..      11      51 .. 0.91
   2 ?   -1.9   0.0      0.41   3.7e+03      25      31 ..     134     140 ..     120     142 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.2e-06
                            MIT  1 ldkAlelvkkAveeDnagnyeeAlelYkealelLlqa 37
                                   +++Ale+v++A+e+ + gny+  ++  +e +elLl+a
  gi|119720301|ref|YP_920796.1| 11 INQALEIVRQATEALEGGNYPYVVRQCQETVELLLKA 47
                                   689******************9999999999999887 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.41
                            MIT  25 elYkeal 31 
                                    +lY+ea 
  gi|119720301|ref|YP_920796.1| 134 QLYEEAA 140
                                    3444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1135.90
//
Query:       gi|119720302|ref|YP_920797.1|  [L=171]
Description: DNA polymerase beta subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.7e-09   37.2   0.3      4e-09   36.6   0.3    1.4  1  NTP_transf_2  Nucleotidyltransferase domain
    2.7e-06   27.4   0.0    3.7e-06   26.9   0.0    1.2  1  Polbeta       Polymerase beta, Nucleotidyltransferase
  ------ inclusion threshold ------
      0.032   14.0   0.0      0.074   12.9   0.0    1.5  2  DUF294        Putative nucleotidyltransferase DUF294
      0.098   12.5   0.0        0.3   10.9   0.0    1.7  2  DUF3368       Domain of unknown function (DUF3368)


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.3     9e-13     4e-09       4      74 ..      19      86 ..      16     122 .. 0.69

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 9e-13
                                   HHHHHHHHTT..TSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHH....HHHEHHHHHHHHCCCEEECTTEEEEEE CS
                   NTP_transf_2  4 lleelkelep..vakvvlfGSyarGtalkgSDiDllvvlpeevsre....kkeegleklaeiikfleellglevdlv 74
                                   lle+l +l++   +++v++GS+arG  +++SD+Dllvv+++  +      +          ++ +++e+ +l   l+
  gi|119720302|ref|YP_920797.1| 19 LLESLLRLYGgsLVSLVVYGSVARGSPRRDSDLDLLVVFEDLPKSRvervR---------LFERAEDEVQPLLDELM 86
                                   7899999999999****************************9774344441.........33333333333333333 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0   8.3e-10   3.7e-06      13      52 ..      31      71 ..      20      88 .. 0.78

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 8.3e-10
                                   HHSTTEEEEEE-S------EEEEEEEESS-.--HHHHHHHH CS
                        Polbeta 13 ielaylFGSrakgkareeSDiDlavllkek.ldleeelela 52
                                   +  ++++GS+a+g  r++SD+Dl v++++  ++  e+++l 
  gi|119720302|ref|YP_920797.1| 31 LVSLVVYGSVARGSPRRDSDLDLLVVFEDLpKSRVERVRLF 71
                                   56689***********************9974444444444 PP

>> DUF294  Putative nucleotidyltransferase DUF294
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.7e-05     0.074      50     100 ..      32      84 ..      14      94 .. 0.86
   2 ?   -2.1   0.0      0.68     3e+03      85     102 ..     126     143 ..     110     155 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.7e-05
                         DUF294  50 fallvmGSeGReEqtlktDqDnalvled..eeeeaareyfaelaervneaLaa 100
                                    ++l+v GS +R+     +D D   v+ed  +++ +  + f++  ++v   L++
  gi|119720302|ref|YP_920797.1|  32 VSLVVYGSVARGSPRRDSDLDLLVVFEDlpKSRVERVRLFERAEDEVQPLLDE 84 
                                    5799************************9877778888888888888776665 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.68
                         DUF294  85 eyfaelaervneaLaalG 102
                                      f+ + ++++e+L +lG
  gi|119720302|ref|YP_920797.1| 126 GFFEGVLRALSERLRRLG 143
                                    445556666666666666 PP

>> DUF3368  Domain of unknown function (DUF3368)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   6.7e-05       0.3      18      35 ..      76      93 ..      75      95 .. 0.93
   2 ?   -2.7   0.0       1.2   5.4e+03      20      27 ..     135     142 ..     129     150 .. 0.48

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 6.7e-05
                        DUF3368 18 psvkplldaLiqaGfris 35
                                   ++v+plld+L ++G+++s
  gi|119720302|ref|YP_920797.1| 76 DEVQPLLDELMEKGYYVS 93
                                   679*************99 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.2
                        DUF3368  20 vkplldaL 27 
                                    + + l +L
  gi|119720302|ref|YP_920797.1| 135 LSERLRRL 142
                                    33444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1296.50
//
Query:       gi|119720303|ref|YP_920798.1|  [L=278]
Description: ABC-2 type transporter [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.5e-11   42.3  16.7    9.5e-11   41.5  16.7    1.3  1  ABC2_membrane    ABC-2 type transporter
    1.8e-08   33.9  12.7    1.8e-08   33.9  12.7    1.6  2  ABC2_membrane_3  ABC-2 family transporter protein
  ------ inclusion threshold ------
        2.9    7.1  14.6        1.9    7.7  12.9    1.3  1  ABC2_membrane_2  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5  16.7   1.6e-14   9.5e-11      35     207 ..      69     229 ..      19     230 .. 0.79

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 1.6e-14
                  ABC2_membrane  35 vfgtvfgnlgnsedglnr......pgllffsvlflafsaltsvapvferergvlerelvsplyslsayvlakvlvelpvs 108
                                    v+                      ++ ++++ l+ +     ++ + +e++ g+le +l ++     a+++++ l++ ++s
  gi|119720303|ref|YP_920798.1|  69 VLN--------------TlfwgmiLWDVVGAGLWSF-----GMTIRREQQTGTLEFLLITNA--NRAVLFSRSLYSRLIS 127
                                    233..............2443333555566666666.....5556799************99..88999*******9999 PP

                  ABC2_membrane 109 llqalifll.ivyflvgldls..rfflflllllltalaasslgllisalapsfedasqlaslvllpllllsGffipidsm 185
                                    l ++++++  i+  ++g+++     + ++++l++ ++a++++gll +a +  f++++ l+s++ +++l l+G+f+p++++
  gi|119720303|ref|YP_920798.1| 128 LPLSILYTYaIFTAIFGVNVLllEPLHAVAALFVGLVASMGFGLLYGAAVFRFKNVGPLTSILQFVFLGLCGVFFPVTAL 207
                                    9999999998999999****87777******************************************************* PP

                  ABC2_membrane 186 pkwlqwiaylnPltyavealrs 207
                                    p+ l+  ayl+P+ty+ ++lr+
  gi|119720303|ref|YP_920798.1| 208 PEPLRIPAYLLPFTYTGDLLRH 229
                                    999*************999985 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   2.4      0.54   3.2e+03     198     238 ..      25      64 ..      20      94 .. 0.64
   2 !   33.9  12.7   3.1e-12   1.8e-08     179     344 ..      90     259 ..      67     260 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.54
                ABC2_membrane_3 198 sgvsplqywlskilgdflvyllqlllill.lafglgipfgnl 238
                                    +g++++  + +++++d +    +l+l+++ +++   +p + +
  gi|119720303|ref|YP_920798.1|  25 AGLKNYFRYAAWLVSDIVTTPAWLILLIVpILLF--LPKERW 64 
                                    6677777777777777777777777777666665..444433 PP

  == domain 2  score: 33.9 bits;  conditional E-value: 3.1e-12
                ABC2_membrane_3 179 iavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllill.l...afglgipfg..nlglllllfllfglay 252
                                    + + i +E +++++e++l++   + + ++s+ l + l++l  ++l+++ +   +fg  +++   + + ++  +++++ a+
  gi|119720303|ref|YP_920798.1|  90 FGMTIRREQQTGTLEFLLIT-NANRAVLFSRSLYSRLISLPLSILYTYaIftaIFG--VNVLllEPLHAVAALFVGLVAS 166
                                    456788999***********.9999*******************998754466777..444433777799********** PP

                ABC2_membrane_3 253 ialgyllsslfknsetaqilifivilllsgffgglfpledlpsalkwifsiiPffapglgllrlitgd.plweillslii 331
                                      +g+l ++++ + +++  l++i+ ++++g++g++fp+ +lp++l++ ++++Pf++ g++l   + g+ +l +++l +i+
  gi|119720303|ref|YP_920798.1| 167 MGFGLLYGAAVFRFKNVGPLTSILQFVFLGLCGVFFPVTALPEPLRIPAYLLPFTYTGDLLRHHAAGTeTLLPVGLEWIV 246
                                    *****************************************************************99999********** PP

                ABC2_membrane_3 332 lalfavvylllal 344
                                     ++++++yl++++
  gi|119720303|ref|YP_920798.1| 247 FLAETAAYLVAGF 259
                                    *********9875 PP

>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7  12.9   0.00032       1.9      89     280 ..      85     259 ..      67     273 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00032
                ABC2_membrane_2  89 aalfgada.iagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvllalaiilalgivlaledllllvva 167
                                    a l ++ + i +E   gTl++lL + + R+ +    + ++l++   + +++l t+ +  +    + +vl le l  ++++
  gi|119720303|ref|YP_920798.1|  85 AGLWSFGMtIRREQQTGTLEFLLITNANRAVLFSRSLYSRLIS---LPLSILYTYAI--FTAIFGVNVLLLEPLHAVAAL 159
                                    666666654899*****************98888888888888...99999999766..444455567777888888888 PP

                ABC2_membrane_2 168 svlllllvvflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavpqeindflsllsptsayntlln 247
                                    +v l++    +++gll  + +  +++   l  +l +v++ l +++  +v++l+ +  +p        +l p+ +   ll+
  gi|119720303|ref|YP_920798.1| 160 FVGLVA---SMGFGLLYGAAVFRFKNVGPLTSILQFVFLGLCGVFF-PVTALPEPLRIP-------AYLLPFTYTGDLLR 228
                                    888888...3677777765444488888888888888877777665.788887777764.......55555555555555 PP

                ABC2_membrane_2 248 eilagsdlnalgstatnllilllllavllvlgy 280
                                       ag++  +l++ +   +++l+ +a++lv g+
  gi|119720303|ref|YP_920798.1| 229 HHAAGTE--TLLPVGLEWIVFLAETAAYLVAGF 259
                                    5555553..456666666777777777777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      213  (0.0118802); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1840.77
//
Query:       gi|119720304|ref|YP_920799.1|  [L=278]
Description: ABC-2 type transporter [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-11   43.9  18.8    1.7e-11   43.9  18.8    1.5  2  ABC2_membrane    ABC-2 type transporter
    8.6e-11   41.5  15.4    8.6e-11   41.5  15.4    1.6  1  ABC2_membrane_3  ABC-2 family transporter protein
    4.8e-07   29.8   5.1    7.2e-07   29.2   5.1    1.3  1  ABC2_membrane_6  ABC-2 family transporter protein
  ------ inclusion threshold ------
      0.018   14.4   4.0      0.036   13.4   4.0    1.4  1  CCB1             Cofactor assembly of complex C subunit B
        1.9    7.2   9.4      0.035   12.9   2.5    1.5  2  DUF2254          Predicted membrane protein (DUF2254)


Domain annotation for each model (and alignments):
>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9  18.8   4.8e-15   1.7e-11      22     208 ..      26     230 ..       8     232 .. 0.81
   2 ?   -3.2   0.1       1.3   4.5e+03     108     121 ..     241     254 ..     236     260 .. 0.47

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 4.8e-15
                  ABC2_membrane  22 llwrliqplllalvfgtvfgnlg...nsedgl.nr...............pgllffsvlflafsaltsvapvferergvl 82 
                                    ++ +l++ +++ + +g ++ ++g      ++l n+                g+l+ s + +    +ts+++  e+ +g++
  gi|119720304|ref|YP_920799.1|  26 YVGSLLMVVFMPFALGGLYIGVGlalAGPGALgNFqgntgvsnpvlyftlGGVLMVSSMIMI--ENTSSIIREEQLMGTF 103
                                    36777888888888888888865544233333222556777888977775555555555555..7777767777778889 PP

                  ABC2_membrane  83 erelvsplyslsayvlakvlvelpvsllqalifllivyflvgldls...rfflflllllltalaasslgllisalapsfe 159
                                    e ++ +p  s+ a  + ++l++ ++s+l+ ++ + iv +  g++      ++l++l++l+ +l + +lgl+++al++ f+
  gi|119720304|ref|YP_920799.1| 104 ELHYLTPN-STVALWMLHALASSLLSVLIFALDVSIVALS-GFRGVsaaDWLLAFLVVLVGLLPLAGLGLVVAALTVRFK 181
                                    99999999.9999999999999999999999988888887.8888765566999************************** PP

                  ABC2_membrane 160 dasqlaslvllpllllsGffipidsmpkwlqwiaylnPltyavealrsn 208
                                     +  +++ +  +  +lsGf++p++  p++++  a l+P ++a e+lr  
  gi|119720304|ref|YP_920799.1| 182 EVYAVSQTINAFVAMLSGFYYPLEVFPRVVRVAAALLPTSHASEILREL 230
                                    **********************************************986 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.3
                  ABC2_membrane 108 sllqalifllivyf 121
                                     + +a++fll v++
  gi|119720304|ref|YP_920799.1| 241 HFRIAAMFLLAVLY 254
                                    44444444443322 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5  15.4   2.4e-14   8.6e-11     156     341 ..      67     256 ..      56     258 .. 0.87

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 2.4e-14
                ABC2_membrane_3 156 lsnvasflvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlll.illlafgl..g 232
                                    ++ v +f +g +l+++++i++ ++++ i eE   ++ el ++++ s+ ++w+ + l++ l+++l+++l + ++a++   g
  gi|119720304|ref|YP_920799.1|  67 SNPVLYFTLGGVLMVSSMIMIENTSSIIREEQLMGTFELHYLTPNSTVALWMLHALASSLLSVLIFALdVSIVALSGfrG 146
                                    5668899999************999777777777********************************87433433333348 PP

                ABC2_membrane_3 233 ipfgnlglllllfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlpsalkwifsiiPffapglg 312
                                    ++  +++l++l++l+++l ++ lg+++ +l+ + ++++++   ++ +  +++g+ +ple +p  +++++ ++P+++ ++ 
  gi|119720304|ref|YP_920799.1| 147 VSAADWLLAFLVVLVGLLPLAGLGLVVAALTVRFKEVYAVSQTINAFVAMLSGFYYPLEVFPRVVRVAAALLPTSHASEI 226
                                    ****************************************9****9888888888999999******************* PP

                ABC2_membrane_3 313 llrlitgd.plweillsliilalfavvyll 341
                                    l  l  g+ + ++i   +++++l+av+yl 
  gi|119720304|ref|YP_920799.1| 227 LRELFGGTgQEVPIHFRIAAMFLLAVLYLY 256
                                    ****95553345699*************85 PP

>> ABC2_membrane_6  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   5.1     2e-10   7.2e-07      31     218 ..      71     262 ..      57     271 .. 0.82

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 2e-10
                ABC2_membrane_6  31 lllglflilqglaavffapalsrigesvrdGsldflLlkPinlllqillkrlnlrrvgrllvgiilliyavkkldiklta 110
                                    l+ +l  +l    ++++++ +s i e+   G++++  l P ++ +  +l+ l++  +  l++++ + i a+++    + a
  gi|119720304|ref|YP_920799.1|  71 LYFTLGGVLMVSSMIMIENTSSIIREEQLMGTFELHYLTPNSTVALWMLHALASSLLSVLIFALDVSIVALSGFRG-VSA 149
                                    55556666666677777778888999999***********************************999999999864.568 PP

                ABC2_membrane_6 111 akillliislilglliltslffilgslsfwfvkseeiieilegl...leaakyPltiyplilrklltfiiPvaflsyvPa 187
                                    a+ ll+ ++++ gll l +l +++++l+  f++++++++ ++++   l+   yPl ++p ++r    + +P +  s +  
  gi|119720304|ref|YP_920799.1| 150 ADWLLAFLVVLVGLLPLAGLGLVVAALTVRFKEVYAVSQTINAFvamLSGFYYPLEVFPRVVRVAAAL-LPTSHASEILR 228
                                    8999999999****************************99999955566667***********99988.99988888877 PP

                ABC2_membrane_6 188 eivlgklsi...vfalvlqlilalvllvlskliw 218
                                    e + g  +     f ++ +++la+++l + ++++
  gi|119720304|ref|YP_920799.1| 229 ELFGGTGQEvpiHFRIAAMFLLAVLYLYAGRTVY 262
                                    7765543333457777777777777777766665 PP

>> CCB1  Cofactor assembly of complex C subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   4.0     1e-05     0.036      70     124 ..     144     202 ..     139     217 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1e-05
                           CCB1  70 feGlvapslflAifLtllaalgllclaLVlsilvpelgn....lflllvllsPlAgvfY 124
                                    f+G+ a+++ lA++++l+ +l l+ l+LV++ l+ ++++       + + ++ l+g++Y
  gi|119720304|ref|YP_920799.1| 144 FRGVSAADWLLAFLVVLVGLLPLAGLGLVVAALTVRFKEvyavSQTINAFVAMLSGFYY 202
                                    99***************************999988777622112334456677889988 PP

>> DUF2254  Predicted membrane protein (DUF2254)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   2.5   9.7e-06     0.035      10      72 ..      72     142 ..      66     146 .. 0.76
   2 ?   -3.9   0.7       1.3   4.5e+03       6      29 ..     153     176 ..     152     199 .. 0.46

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.7e-06
                        DUF2254  10 livllavllalllllldealslsldleel.ke........gaeaaralLstiagsmltvagfvfSitvvalq 72 
                                     ++l++vl++  +++++++ s  ++ e+l  +        ++  a  +L ++a+s+l+v  f++ + +val+
  gi|119720304|ref|YP_920799.1|  72 YFTLGGVLMVSSMIMIENT-SSIIREEQLmGTfelhyltpNSTVALWMLHALASSLLSVLIFALDVSIVALS 142
                                    3456677777777788544.444444444233788999999*****************************97 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 1.3
                        DUF2254   6 fipllivllavllalllllldeal 29 
                                    ++++l+vl+++l  + l l+ +al
  gi|119720304|ref|YP_920799.1| 153 LLAFLVVLVGLLPLAGLGLVVAAL 176
                                    555555555554333333332222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.56
# Mc/sec: 1504.59
//
Query:       gi|119720305|ref|YP_920800.1|  [L=334]
Description: daunorubicin resistance ABC transporter ATPase subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-28   98.5   0.0    8.2e-28   97.6   0.0    1.4  1  ABC_tran  ABC transporter
    5.8e-15   55.9   3.3    3.2e-10   40.3   0.1    2.1  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    3.8e-08   33.9   0.0    8.7e-08   32.8   0.0    1.7  1  DUF4162   Domain of unknown function (DUF4162)
    9.7e-06   25.6   0.0    1.5e-05   25.0   0.0    1.3  1  Rad17     Rad17 P-loop domain
    0.00033   20.3   0.0    0.00081   19.1   0.0    1.6  1  AAA_29    P-loop containing region of AAA domain
     0.0011   18.8   0.0        1.3    8.7   0.0    2.1  2  AAA_15    AAA ATPase domain
     0.0075   16.8   3.0      0.047   14.2   3.0    2.0  1  AAA_23    AAA domain
  ------ inclusion threshold ------
      0.025   15.0   0.0      0.058   13.8   0.0    1.5  1  AAA_16    AAA ATPase domain
      0.041   13.7   0.0      0.073   12.9   0.0    1.4  1  MukB      MukB N-terminal
      0.051   14.0   0.2       0.44   11.0   0.2    2.4  1  AAA       ATPase family associated with various cellular acti
      0.086   13.4   0.1       0.37   11.3   0.0    1.9  2  AAA_18    AAA domain
       0.16   11.4   0.1         16    4.8   0.0    2.1  2  SMC_N     RecF/RecN/SMC N terminal domain
        0.3   10.8   0.5        1.8    8.2   0.1    2.0  2  AAA_24    AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.6   0.0     6e-31   8.2e-28       1     136 [.      34     178 ..      34     179 .. 0.94

  Alignments for each domain:
  == domain 1  score: 97.6 bits;  conditional E-value: 6e-31
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren. 79 
                                    l+ vs+++++ge+ +++G+nGaGK+t +k+l+ ll p++Ge +++g ++ e+++++ ++    l  +  +  +lt ren 
  gi|119720305|ref|YP_920800.1|  34 LQGVSFEIRPGEIFGLLGPNGAGKTTTIKILSTLLLPDSGEAWVNGYSVLEEPRKVRESIGVSLYSDRGFYWKLTGRENl 113
                                    689************************************************666666555556777888999999***** PP

                                    ............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    ............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                +++++ie++l+ l+l++++d+ v    +++S G+k+++ +arall +p++l+lDEpt
  gi|119720305|ref|YP_920800.1| 114 eyfarlyhlergYARRRIEELLKLLDLEKDADRLV----EEYSTGMKSKLNIARALLHDPPVLFLDEPT 178
                                    ***********999*********************....*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.7   4.1e-06    0.0056       2      22 ..      47      67 ..      46      88 .. 0.84
   2 !   40.3   0.1   2.4e-13   3.2e-10     195     299 ..     133     210 ..      71     214 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.1e-06
                         AAA_21  2 nvliGpNgsGKSnLLdaldll 22
                                    +l GpNg+GK++ +++l+ l
  gi|119720305|ref|YP_920800.1| 47 FGLLGPNGAGKTTTIKILSTL 67
                                   689***************987 PP

  == domain 2  score: 40.3 bits;  conditional E-value: 2.4e-13
                         AAA_21 195 veielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkl 274
                                                              + +l+ +++ ++ + e S G+k+ l ++ all ++   ++l++DEp  gL+P  
  gi|119720305|ref|YP_920800.1| 133 E------------------------LLKLLDLEKDADRLVEEYSTGMKSKLNIARALLHDP---PVLFLDEPTIGLDPNS 185
                                    2........................444455566777778889****************99...**************** PP

                         AAA_21 275 lrrllellkelsrngaQviltTHSp 299
                                     r++ e++ el++ g  ++ltTH+ 
  gi|119720305|ref|YP_920800.1| 186 ARKVREVVLELKKSGKTILLTTHNM 210
                                    ********999999*********96 PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.0   6.3e-11   8.7e-08       1      78 [.     232     324 ..     232     327 .. 0.77

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 6.3e-11
                                    E-HHHHHTTS.-SSEEEEE.....--.-----..---EEE.....E-TT....S-EEEEE-------------.----EE CS
                        DUF4162   1 GtleeiKrsy.gknrieve.....ad.aeelleepgveev.....eeeg....gelelkledeeaanellkal.tsgvei 63 
                                    G+++e+K+++ gk+ +eve     ++  e++++++gv        +  g    g+l++  e++ + +e+l+a+ +sg+++
  gi|119720305|ref|YP_920800.1| 232 GSPRELKSRIsGKQVVEVEvagrpEEvREKVKSVQGVLATslsagS--GnpyaGTLRVVYEGDGVLREVLSAVlDSGAKL 309
                                    99********8888888**985432234444455665555554332..1456688******************88***** PP

                                    EEEEEE---HHHHHH CS
                        DUF4162  64 rsFeeeePsLndIFi 78 
                                     s++ +eP+L+d+F 
  gi|119720305|ref|YP_920800.1| 310 LSVRTVEPTLEDVFA 324
                                    **************5 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   1.1e-08   1.5e-05      34      98 ..      33      98 ..      17     165 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.1e-08
                          Rad17 34 wlkadvLesrkkriLLisGPsGCgkstvvkvLskelgikl.rewlnpvslkepdnqksdfkgltek 98
                                   +l+  + e r+ +i  + GP G gk+t++k+Ls  l ++  + w+n+ s+ e + ++ +  g+   
  gi|119720305|ref|YP_920800.1| 33 ALQGVSFEIRPGEIFGLLGPNGAGKTTTIKILSTLLLPDSgEAWVNGYSVLEEPRKVRESIGVSLY 98
                                   6788889999999*********************999876266******99999999888776655 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   5.9e-07   0.00081      13      50 ..      35      72 ..      32      81 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 5.9e-07
                         AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                   +g ++ei++ +++ l Gp+G+GK+T +  +++lL+p++
  gi|119720305|ref|YP_920800.1| 35 QGVSFEIRPGEIFGLLGPNGAGKTTTIKILSTLLLPDS 72
                                   56789999999999**********************98 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0013       1.8      27      47 ..      48      68 ..      34      98 .. 0.86
   2 !    8.7   0.0   0.00093       1.3     324     365 ..     169     209 ..     139     211 .. 0.93

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0013
                         AAA_15 27 vliGkNnsGKSsilealdlFl 47
                                    l G+N++GK++ +++l  +l
  gi|119720305|ref|YP_920800.1| 48 GLLGPNGAGKTTTIKILSTLL 68
                                   578**************9887 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00093
                         AAA_15 324 nvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                    + +l+++EP + L p+  + + +  +el +++k  +++tTH+
  gi|119720305|ref|YP_920800.1| 169 PPVLFLDEPTIGLDPNSARKVREVVLELKKSGK-TILLTTHN 209
                                    5689****************************9.9******8 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   3.0   3.4e-05     0.047      13      44 ..      37      69 ..      30     160 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.4e-05
                         AAA_23 13 qeidFsk.gltlItGpNGaGKTTildAiklaLy 44
                                   ++++  +  ++ + GpNGaGKTT +  +   L 
  gi|119720305|ref|YP_920800.1| 37 VSFEIRPgEIFGLLGPNGAGKTTTIKILSTLLL 69
                                   55555553599*************998887775 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.2e-05     0.058       3     143 ..      25     176 ..      23     177 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.2e-05
                         AAA_16   3 vGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekd......ggiflrgkcdqlesa..ipy...sa 71 
                                     G+++e+ +L+ +   +r g  e+  l G+ G GK++ ++ l + l  d      +g+ + ++ ++ +++  +++     
  gi|119720305|ref|YP_920800.1|  25 RGKRREVVALQGVSFEIRPG--EIFGLLGPNGAGKTTTIKILSTLLLPDsgeawvNGYSVLEEPRKVRESigVSLysdRG 102
                                    67777777777766666666..7999*****************9999998766654444666666664442322245333 PP

                         AAA_16  72 laqalareellrqlldeaesaeleawrekleeala..avpelagaeasrllellkrll..allsrderplvlvlDd 143
                                    +   l+ +e l+  ++     e++++r+++ee l+  +  ++a+ + +     +k+ l  a++   ++p vl+lD+
  gi|119720305|ref|YP_920800.1| 103 FYWKLTGRENLEYFARL-YHLERGYARRRIEELLKllDLEKDADRLVEEYSTGMKSKLniARAL-LHDPPVLFLDE 176
                                    44444444555555544.5558888888888888855444444444466666666666422222.24578999886 PP

>> MukB  MukB N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   5.3e-05     0.073      30      54 ..      48      72 ..      38     112 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.3e-05
                                   HHHS--SHHHHHHHHHHHHHHS--T CS
                           MukB 30 tlsGgnGaGksttmaafvtaliPdl 54
                                    l G nGaGk+tt+  + t l+Pd 
  gi|119720305|ref|YP_920800.1| 48 GLLGPNGAGKTTTIKILSTLLLPDS 72
                                   5889********************6 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.2   0.00032      0.44       3      23 ..      49      71 ..      47     193 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00032
                                   EESSTTSSHHHHHHHHHHHH..T CS
                            AAA  3 lyGppGtGKTllakavakel..g 23
                                   l Gp G GKT+++k + + l  +
  gi|119720305|ref|YP_920800.1| 49 LLGPNGAGKTTTIKILSTLLlpD 71
                                   78************999886441 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00027      0.37       3      44 ..      49      87 ..      48      98 .. 0.76
   2 ?   -1.1   0.0       1.9   2.6e+03      74     114 ..     200     245 ..     173     261 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00027
                         AAA_18  3 ltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpe 44
                                   l G+ G+GKtt  k Ls +l      +  a+ ng++  ++p 
  gi|119720305|ref|YP_920800.1| 49 LLGPNGAGKTTTIKILSTLL---LPDSGEAWVNGYSVLEEPR 87
                                   78**************9996...6666666666666666555 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.9
                         AAA_18  74 gknlvidghlaeleseaakdikk......vvLtaspeelleRlekRg 114
                                    gk++++  h     ++ + d++       ++   sp el+ R++   
  gi|119720305|ref|YP_920800.1| 200 GKTILLTTHNMFEADM-LADRVAiinkgrIIAVGSPRELKSRISGKQ 245
                                    4555555444322222.222222244466666667777777777665 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.016        22      28      42 ..      48      62 ..      35      70 .. 0.81
   2 ?    4.8   0.0     0.012        16     156     203 ..     166     212 ..     137     227 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.016
                                   EEEESTTSSHHHHHH CS
                                   xxxxxxxxxxxxxxx RF
                          SMC_N 28 aivGpNGSGKsnlld 42
                                    ++GpNG+GK+  + 
  gi|119720305|ref|YP_920800.1| 48 GLLGPNGAGKTTTIK 62
                                   589*******98765 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.012
                                    CS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 156 vkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemle 203
                                     +  p+ +lDe    LD +  +kv e++ e +k+   i  + ++ m+e
  gi|119720305|ref|YP_920800.1| 166 LHDPPVLFLDEPTIGLDPNSARKVREVVLELKKSGKTILLTTHN-MFE 212
                                    56679999************************998888877654.443 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.1    0.0013       1.8       6      25 ..      48      66 ..      45      74 .. 0.81
   2 ?    0.3   0.0      0.36     5e+02     109     133 ..     187     211 ..     184     227 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0013
                         AAA_24  6 liyGpsgiGKTtlakelgpk 25
                                    + Gp+g+GKTt++k l  +
  gi|119720305|ref|YP_920800.1| 48 GLLGPNGAGKTTTIKIL-ST 66
                                   589***********988.43 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.36
                         AAA_24 109 eefrrllkklqelrknvifiahekt 133
                                    +++r+++  l++ +k++ ++ h   
  gi|119720305|ref|YP_920800.1| 187 RKVREVVLELKKSGKTILLTTHNMF 211
                                    6889999999999999999999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2137.99
//
Query:       gi|119720306|ref|YP_920801.1|  [L=141]
Description: PadR-like family transcriptional regulator [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    9.1e-20   70.4   0.1    1.3e-19   69.9   0.1    1.2  1  PadR       Transcriptional regulator PadR-like family
    8.8e-06   25.7   0.0    2.1e-05   24.5   0.0    1.6  1  HTH_20     Helix-turn-helix domain
    0.00048   19.9   0.0        1.4    8.9   0.1    2.6  2  HTH_5      Bacterial regulatory protein, arsR family
     0.0015   18.4   3.1     0.0021   18.0   1.1    2.2  2  HTH_12     Ribonuclease R winged-helix domain
     0.0017   18.2   0.4     0.0072   16.2   0.1    2.2  2  TrmB       Sugar-specific transcriptional regulator TrmB
     0.0038   17.9   0.0     0.0057   17.3   0.0    1.3  1  RTP        Replication terminator protein
     0.0064   14.9   0.0     0.0084   14.5   0.0    1.1  1  DUF505     Protein of unknown function (DUF505)
  ------ inclusion threshold ------
      0.012   15.3   0.0      0.025   14.3   0.0    1.4  1  AphA_like  Putative AphA-like transcriptional regulator
       0.04   13.8   0.3      0.067   13.1   0.3    1.3  1  DUF3116    Protein of unknown function (DUF3116)
      0.044   13.6   0.0      0.071   13.0   0.0    1.5  1  HxlR       HxlR-like helix-turn-helix
      0.046   13.5   0.0      0.062   13.1   0.0    1.3  1  DUF4364    Domain of unknown function (DUF4364)
      0.051   14.1   0.1       0.19   12.3   0.0    1.9  2  HTH_27     Winged helix DNA-binding domain
      0.054   13.5   0.3       0.15   12.1   0.0    1.8  2  HTH_45     Winged helix-turn-helix
      0.069   13.1   0.0       0.24   11.3   0.0    1.9  1  MarR       MarR family
      0.077   13.0   0.0       0.22   11.5   0.0    1.8  1  BLACT_WH   Beta-lactamase associated winged helix domain
      0.096   12.8   0.3        3.7    7.7   0.0    2.4  2  Mrr_N      Mrr N-terminal domain
       0.11   12.4   0.1       0.29   11.0   0.0    1.7  2  DUF1495    Winged helix DNA-binding domain (DUF1495)


Domain annotation for each model (and alignments):
>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.9   0.1   1.2e-22   1.3e-19       1      74 [.      13      81 ..      13      82 .. 0.96

  Alignments for each domain:
  == domain 1  score: 69.9 bits;  conditional E-value: 1.2e-22
                                   HHHHHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHHH CS
                           PadR  1 iLalleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrela 74
                                   +L+ll+++p+ G+eii+e+ee + g++++s+G +Yp+L+ Le+eglv +e+e     + rk+Y lT++Gr el+
  gi|119720306|ref|YP_920801.1| 13 VLSLLRKRPMSGVEIIEEIEEITLGFWRPSPGAVYPTLRALEEEGLVRREEE-----GWRKVYYLTEKGRMELE 81
                                   89**********************************************9977.....58************998 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0     2e-08   2.1e-05       9      61 .]       7      66 ..       3      66 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 2e-08
                                   -HHHHHHHHHHSTCTTB-HHHHHHHHT........S-HHHHHHHHHHHHHCTTEEEECTEE CS
                         HTH_20  9 hPvRrrilraLaraegltaselaerld........lskntlsyHLrvLeeagLvevvregr 61
                                   +P R ++l++L r+++++  e+ e+++         s+  ++  Lr+Lee gLv++++eg+
  gi|119720306|ref|YP_920801.1|  7 NPLRIMVLSLL-RKRPMSGVEIIEEIEeitlgfwrPSPGAVYPTLRALEEEGLVRREEEGW 66
                                   7**********.**************55556666367777*******************98 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.1    0.0013       1.4       1      25 [.       7      31 ..       7      33 .. 0.90
   2 !    8.4   0.0    0.0019         2      28      46 ..      42      60 ..      40      61 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0013
                                   SHHHHHHHHHHTTSSEEHHHHHHHH CS
                          HTH_5  1 dptRlkILklLaegelcvcelaeel 25
                                   +p R+ +L+lL++++++  e+ ee+
  gi|119720306|ref|YP_920801.1|  7 NPLRIMVLSLLRKRPMSGVEIIEEI 31
                                   699*************999998886 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0019
                                   -HHHHHHHHHHHHHTTSEE CS
                          HTH_5 28 sqstvShHLkkLreaGLVe 46
                                   s+++v   L++L+e+GLV+
  gi|119720306|ref|YP_920801.1| 42 SPGAVYPTLRALEEEGLVR 60
                                   78899999**********6 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   1.1     2e-06    0.0021       2      66 .]      12      80 ..      11      80 .. 0.79
   2 ?   -1.2   0.0       1.9     2e+03      13      24 ..     119     131 ..     115     134 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2e-06
                         HTH_12  2 eILkilaesdkpigakeiaeeLkkr..gy.digeravRyrLrkleergltrrvgya...greltEkGleeL 66
                                   ++L++l +  +p++  ei ee++++  g    +  av   Lr+lee+gl+rr   +      ltEkG  eL
  gi|119720306|ref|YP_920801.1| 12 MVLSLLRK--RPMSGVEIIEEIEEItlGFwRPSPGAVYPTLRALEEEGLVRREEEGwrkVYYLTEKGRMEL 80
                                   66777754..79999999999999966542457789*99**************9994434469****8876 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.9
                         HTH_12  13 piga.keiaeeLk 24 
                                     +++ ++iae+L+
  gi|119720306|ref|YP_920801.1| 119 QVSRiERIAEDLR 131
                                    5555468999997 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   6.8e-06    0.0072      38      64 ..      45      72 ..      14      75 .. 0.84
   2 ?   -2.5   0.0       4.5   4.8e+03      37      41 ..     118     122 ..     106     133 .. 0.53

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 6.8e-06
                                   CHHHHHHHHHHCTSEEEESST.TTEEEE CS
                           TrmB 38 kvYevLrsLedkGlVerekgr.pklYra 64
                                    vY +Lr Le+ GlV+re++  +k+Y  
  gi|119720306|ref|YP_920801.1| 45 AVYPTLRALEEEGLVRREEEGwRKVYYL 72
                                   69*****************987888865 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.5
                                    HCHHH CS
                           TrmB  37 skvYe 41 
                                     +v +
  gi|119720306|ref|YP_920801.1| 118 EQVSR 122
                                    33333 PP

>> RTP  Replication terminator protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   5.4e-06    0.0057      10      67 ..       9      65 ..       4      96 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5.4e-06
                                   HHHHHHHHHHTT-EBCTCHHHHHHHHHTTTT.----HHHHHHHHHHHHHTTSEEEEEEE CS
                            RTP 10 lklylitlvekkklyglklldelkkeFkelg.ykPnhseiyralhelvedgilkrrkel 67
                                   l++ ++ l+ k+++ g+++++e+ +   +lg ++P++  +y +l+ l e+g+++r++e 
  gi|119720306|ref|YP_920801.1|  9 LRIMVLSLLRKRPMSGVEIIEEIEEI--TLGfWRPSPGAVYPTLRALEEEGLVRREEEG 65
                                   6788999***************9764..56669********************998764 PP

>> DUF505  Protein of unknown function (DUF505)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0     8e-06    0.0084     345     404 ..      26      83 ..      17      90 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 8e-06
                         DUF505 345 eiakkfeeakdlekWyednfdlreaLysLesfeLieseveekgkevyvlTeyGekvledq 404
                                    ei+++ ee+     W  +   +   L  Le  +L+++e ee  ++vy+lTe+G+  le++
  gi|119720306|ref|YP_920801.1|  26 EIIEEIEEITLG-FWRPSPGAVYPTLRALEEEGLVRRE-EEGWRKVYYLTEKGRMELEKL 83 
                                    555555555444.588888888899************9.4566***********988865 PP

>> AphA_like  Putative AphA-like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   2.4e-05     0.025       8      94 ..       5      88 ..       2     106 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.4e-05
                      AphA_like  8 pkeavrLvvLGlieraplryselagavrhlvsriagPsldLlgsslellreeGLveavdGeGmednalLaiteaGrrelqaL 89
                                   +++ +r++vL l+++ p+   e+ + +  +    + Ps   ++ +l  l eeGLv     eG  +     +te+Gr el++L
  gi|119720306|ref|YP_920801.1|  5 ARNPLRIMVLSLLRKRPMSGVEIIEEIEEITLGFWRPSPGAVYPTLRALEEEGLVRRE-EEGWRKVYY--LTEKGRMELEKL 83
                                   78999**************************************************986.788876655..59*******999 PP

                      AphA_like 90 ltanl 94
                                     a  
  gi|119720306|ref|YP_920801.1| 84 GLASQ 88
                                   66655 PP

>> DUF3116  Protein of unknown function (DUF3116)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.3   6.4e-05     0.067      51      83 ..      53      83 ..      45      85 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.4e-05
                        DUF3116 51 LElkgyilRkeekannkkrYelTekGellykel 83
                                   LE++g + R+ee    +k Y+lTekG + +++l
  gi|119720306|ref|YP_920801.1| 53 LEEEGLVRREEE--GWRKVYYLTEKGRMELEKL 83
                                   999999999999..79**********9988877 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   6.7e-05     0.071      39      71 ..      49      78 ..      11      85 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.7e-05
                                   HHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGG CS
                           HxlR 39 rLreLeqdglierevypevPpkveYsltekGrs 71
                                   +Lr+Le++gl+ re+    + +  Y ltekGr 
  gi|119720306|ref|YP_920801.1| 49 TLRALEEEGLVRREE---EGWRKVYYLTEKGRM 78
                                   7************85...56777899*****94 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   5.9e-05     0.062      39      73 ..      49      83 ..      45     107 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.9e-05
                        DUF4364 39 alseLvesglieeeekenktlykiTekGketlelf 73
                                   +l  L+e+gl++ ee+  +++y +TekG+  le +
  gi|119720306|ref|YP_920801.1| 49 TLRALEEEGLVRREEEGWRKVYYLTEKGRMELEKL 83
                                   6889*************************988765 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       4.4   4.7e+03       6      24 ..      11      31 ..       7      36 .. 0.61
   2 ?   12.3   0.0   0.00018      0.19      38      68 .]      49      76 ..      39      76 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 4.4
                         HTH_27  6 alvLhlir.hrrrrkkl.adl 24
                                   ++vL l+r +++ ++++ +++
  gi|119720306|ref|YP_920801.1| 11 IMVLSLLRkRPMSGVEIiEEI 31
                                   677777775555555555555 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00018
                         HTH_27 38 slkkLtekGLvertgdeadrrekrvrlTdkG 68
                                    l++L+e GLv   + e+++ +k + lT+kG
  gi|119720306|ref|YP_920801.1| 49 TLRALEEEGLV---RREEEGWRKVYYLTEKG 76
                                   69*********...66688999********9 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       6.9   7.3e+03      62      71 ..      24      33 ..      23      35 .. 0.54
   2 ?   12.1   0.0   0.00014      0.15      40      69 ..      50      83 ..      46      88 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 6.9
                         HTH_45 62 Glelleklke 71
                                   G e++e+++e
  gi|119720306|ref|YP_920801.1| 24 GVEIIEEIEE 33
                                   5555555555 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00014
                         HTH_45 40 LdmLvekgli....kkskekYvlTekGlellekl 69
                                   L  L e+gl+    +   + Y+lTekG+  lekl
  gi|119720306|ref|YP_920801.1| 50 LRALEEEGLVrreeEGWRKVYYLTEKGRMELEKL 83
                                   77899*****7653335689********999987 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00023      0.24      30      50 ..      42      62 ..      39      64 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00023
                                   -HHHHHHHHHHHHHTTSEEEE CS
                           MarR 30 skstvtrvldrLekkGlieRs 50
                                   s+++v  +l++Le++Gl++R+
  gi|119720306|ref|YP_920801.1| 42 SPGAVYPTLRALEEEGLVRRE 62
                                   6889999*************8 PP

>> BLACT_WH  Beta-lactamase associated winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00021      0.22      25      47 .]      46      66 ..      38      66 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00021
                       BLACT_WH 25 vlahLeKLeeeGkVkregdkgkW 47
                                   v+ +L+ LeeeG+V+re+  + W
  gi|119720306|ref|YP_920801.1| 46 VYPTLRALEEEGLVRREE--EGW 66
                                   6668999**********9..477 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0035       3.7      60      86 ..      52      81 ..      48      82 .. 0.86
   2 ?    2.9   0.0      0.11   1.2e+02      22      40 ..     104     122 ..     100     137 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0035
                          Mrr_N 60 yLkkagllespk...rgvwkiTekGrevlk 86
                                    L ++gl+ +++   r v+ +TekGr  l+
  gi|119720306|ref|YP_920801.1| 52 ALEEEGLVRREEegwRKVYYLTEKGRMELE 81
                                   58899999999988999*********8765 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.11
                          Mrr_N  22 eirervaerfglseeerae 40 
                                    e  ++va+r gls+e++++
  gi|119720306|ref|YP_920801.1| 104 EYLREVASRDGLSDEQVSR 122
                                    66799**********9876 PP

>> DUF1495  Winged helix DNA-binding domain (DUF1495)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       2.7   2.8e+03       3      24 ..       2      23 ..       1      35 [. 0.64
   2 ?   11.0   0.0   0.00028      0.29      53      85 ..      47      78 ..      43      83 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2.7
                        DUF1495  3 rslnkSkvRkkvllyLysiype 24
                                   +s  +  +R  vl  L +   +
  gi|119720306|ref|YP_920801.1|  2 ASFARNPLRIMVLSLLRKRPMS 23
                                   6777778888888888755443 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00028
                        DUF1495 53 ynsessLielGLveeeeeseglklYklteeGie 85
                                   y + ++L e GLv+ +ee+   k+Y lte+G+ 
  gi|119720306|ref|YP_920801.1| 47 YPTLRALEEEGLVR-REEEGWRKVYYLTEKGRM 78
                                   666678999****5.45555567********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 895.13
//
Query:       gi|119720307|ref|YP_920802.1|  [L=522]
Description: hypothetical protein Tpen_1402 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-09   38.1   0.8       0.45   10.8   0.0    4.5  4  CARDB        CARDB
  ------ inclusion threshold ------
      0.021   15.1  11.9      0.046   14.0   1.0    4.8  5  NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosi


Domain annotation for each model (and alignments):
>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.011     1e+02      47      84 ..      90     127 ..      76     138 .. 0.82
   2 !   10.7   0.0   5.3e-05      0.48       8      72 ..     163     233 ..     160     263 .. 0.84
   3 !    8.2   0.0   0.00032       2.9      13      78 ..     276     345 ..     268     356 .. 0.83
   4 !   10.8   0.0     5e-05      0.45       7      84 ..     382     462 ..     377     467 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.011
                                    EEEEEEEESEE-CTEEEEEEEEEE-S-S-CEEEEEEEE CS
                          CARDB  47 elvgtvtvpsLaagesttvsftwtteategevtltvvv 84 
                                     ++g+v+v s  +g+ +t +ft  t+   +e tl+v+v
  gi|119720307|ref|YP_920802.1|  90 VSAGSVDVGSWRPGTVKTARFTLNTSSLGSECTLRVSV 127
                                    4559999******************9777788899987 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 5.3e-05
                                    EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEEEEEEE......SEE-CTEEEEEEEEEE-S CS
                          CARDB   8 ntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelvgtvtv......psLaagesttvsftwtte 72 
                                    + + p+ ++  + n + + v+N+G  a ++++v +   g++  +++v        L++ge + v ++++++
  gi|119720307|ref|YP_920802.1| 163 VGVRPQMVYSSTVNPVLLVVENSGRTALRQVEVYVAPQGSVLLNASVptvfelGDLKPGERRVVPLSVVPQ 233
                                    5678999999*************************99999994444444455599*****99999999887 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.00032
                                    SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE....EEEEESEE-CTEEEEEEEEEE-S-S-CEE CS
                          CARDB  13 seafvgeentitvtvkNqGtaasgatkvalyldgelv....gtvtvpsLaagesttvsftwtteategev 78 
                                      +++g+++++++ v N G  a +  ++ l + ++      +   v  L +ges++v +t+ ++at++++
  gi|119720307|ref|YP_920802.1| 276 PVLVAGQASNVSLRVVNAGGVAVKGLSLVLGVQKSPLsvspSFLVVGDLGPGESRSVPVTVLVPATASSS 345
                                    5678999*************************99998778777778**************9999555444 PP

  == domain 4  score: 10.8 bits;  conditional E-value: 5e-05
                                    .EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE....EEEEESEE-CTEEEEEEEEEE-S-S-CEEEEEE CS
                          CARDB   7 tntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelv....gtvtvpsLaagesttvsftwtteategevtltv 82 
                                    ++ + p++++vg+++ + v++   Gt   +a++v+ y+++ l     + +++ +L+++  ttv f++ +  +eg  ++++
  gi|119720307|ref|YP_920802.1| 382 SVDVVPQSPEVGSNVIFAVSLVDDGTFPVYAVNVSAYASRGLSplrsTYAYLGQLNPQVLTTVPFSFRAV-EEGMQEVRF 460
                                    567899***********************************99998778899*****************8.9**999999 PP

                                    EE CS
                          CARDB  83 vv 84 
                                    vv
  gi|119720307|ref|YP_920802.1| 461 VV 462
                                    98 PP

>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0      0.85   7.7e+03       6      27 ..     107     128 ..     103     129 .. 0.81
   2 ?    3.4   0.3      0.01        91      10      61 ..     179     232 ..     174     244 .. 0.75
   3 ?   14.0   1.0   5.2e-06     0.046       3      69 ..     280     346 ..     278     356 .. 0.85
   4 ?   -2.2   0.0      0.55     5e+03       9      32 ..     368     391 ..     365     393 .. 0.86
   5 ?    1.4   0.0     0.042   3.7e+02       4      28 ..     393     417 ..     390     422 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.85
                    NPCBM_assoc   6 tvtltltvtndgtaaatnvsls 27 
                                    t ++tl  ++ g++ + +vs+s
  gi|119720307|ref|YP_920802.1| 107 TARFTLNTSSLGSECTLRVSVS 128
                                    5678888899999988888886 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.01
                    NPCBM_assoc  10 tltvtndgtaaatnvslslslPeGWt.vvevspasaa..slapGetveatvkVtp 61 
                                     l+v n+g++a+++v++ + +P+G     ++ p+ ++  +l+pGe+  + + V p
  gi|119720307|ref|YP_920802.1| 179 LLVVENSGRTALRQVEVYV-APQGSVlLNASVPTVFElgDLKPGERRVVPLSVVP 232
                                    58999***********976.68887654455555555668888888877777766 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 5.2e-06
                    NPCBM_assoc   3 pGetvtltltvtndgtaaatnvslslslPeGWtvvevspasaa..slapGetveatvkVtppagaaaGd 69 
                                    +G+  ++ l v+n g+ a++++sl l + +     +vsp  +   +l pGe+ ++ v+V +pa+a  ++
  gi|119720307|ref|YP_920802.1| 280 AGQASNVSLRVVNAGGVAVKGLSLVLGVQKSPL--SVSPSFLVvgDLGPGESRSVPVTVLVPATASSSE 346
                                    89************************9966555..7777777777********************9765 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 0.55
                    NPCBM_assoc   9 ltltvtndgtaaatnvslslslPe 32 
                                    +t++v++  + ++t+v +  + Pe
  gi|119720307|ref|YP_920802.1| 368 FTFYVAQRSSVSITSVDVVPQSPE 391
                                    789999999999999999988886 PP

  == domain 5  score: 1.4 bits;  conditional E-value: 0.042
                    NPCBM_assoc   4 Getvtltltvtndgtaaatnvslsl 28 
                                    G+ v + +++++dgt ++ +v++s+
  gi|119720307|ref|YP_920802.1| 393 GSNVIFAVSLVDDGTFPVYAVNVSA 417
                                    8899999***************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (522 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.51
# Mc/sec: 3071.58
//
Query:       gi|119720308|ref|YP_920803.1|  [L=393]
Description: hypothetical protein Tpen_1403 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.6e-15   55.8   4.7    1.5e-14   54.8   4.7    1.5  1  MacB_PCD        MacB-like periplasmic core domain
    1.2e-10   41.7   4.6    1.2e-10   41.7   4.6    3.4  3  FtsX            FtsX-like permease family
     0.0024   17.6   0.0      0.048   13.4   0.0    2.2  2  Formyl_trans_N  Formyl transferase


Domain annotation for each model (and alignments):
>> MacB_PCD  MacB-like periplasmic core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.8   4.7   2.5e-18   1.5e-14       4     193 ..      24     238 ..      21     256 .. 0.70

  Alignments for each domain:
  == domain 1  score: 54.8 bits;  conditional E-value: 2.5e-18
                       MacB_PCD   4 tvLGiaiGvaaviaivslgeglqasvlsqisdl..gnlvtvtpgkgsgeslsdpdvealrrevp.veavapvv...tvrg 77 
                                    + LG++i+v a+++ +++ge++q+++ +q+++   ++ v v    g  ++l+d+d+  ++ ++p v+ +  v+    v +
  gi|119720308|ref|YP_920803.1|  24 AALGVMIAVLALSLALGVGESFQKAFVEQLQSTiaADSVFVIG--G-YAGLTDADIAYFK-SIPgVKDAQGVLmasGVVY 99 
                                    78***************************99666644333333..3.3568999995454.5899999999877773345 PP

                       MacB_PCD  78 ggsgeeevtvvgvdpdyfk....vfgl.kl.aeGrffteadlrggpnvvvigeelaerlf......pvGdtirl...... 139
                                    ++sge+ v++v+vdp+++     v ++ k  aeG      + + +  +v+++++l+++         vG+++ +      
  gi|119720308|ref|YP_920803.1| 100 TESGEKPVNIVAVDPSFLPrylgVSDMrKAvAEG------ETEPRGLGVLVSYSLWRDQEtgrkllDVGSVLNVrvggrn 173
                                    55557779******97776644466664333445......33335556********99446666778*****9999**99 PP

                       MacB_PCD 140 kpftVvGvledppgsgsalgdda...vylp....lttl..qrrs....itvrlkdgadleaaaaele 193
                                    +++ VvG le++++s+s+++d++   +y++    +t l           +v +++ + l+++ + ++
  gi|119720308|ref|YP_920803.1| 174 VQVFVVGLLEQTSSSMSMGHDFQvatIYMDpdafFTYLgrT--RnypvAIVLVENLDALDSITENIR 238
                                    9999*****88534444444444445999668864443321..133556666666666666666665 PP

>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.7     0.012        73      26      56 ..      28      58 ..      24      98 .. 0.84
   2 ?    1.5   1.4     0.071   4.2e+02      24      49 ..     261     286 ..     249     293 .. 0.74
   3 !   41.7   4.6   2.1e-14   1.2e-10       2      95 ..     296     385 ..     295     386 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.012
                           FtsX 26 llitlvalviGlglgllaaqllsdvllssvf 56
                                   ++i+++al ++lg+g  + +++   l+s   
  gi|119720308|ref|YP_920803.1| 28 VMIAVLALSLALGVGESFQKAFVEQLQSTIA 58
                                   7999**********99999998888877644 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.071
                           FtsX  24 eillitlvalviGlglgllaaqllsd 49 
                                     ++l  ++al++++g g+ a++++ +
  gi|119720308|ref|YP_920803.1| 261 VGALQLFIALISAVGMGVTALWIFDS 286
                                    45677889999999999999998755 PP

  == domain 3  score: 41.7 bits;  conditional E-value: 2.1e-14
                           FtsX   2 reigilralGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllssvfsselkisidlitvliiivlllllal 81 
                                    +eigil+alG++++++l ++l+e+++++lv++++G    llaa ++s+v+  s f++++ + + + t  ++++l l   +
  gi|119720308|ref|YP_920803.1| 296 KEIGILKALGYTSGDILAVFLLETVIVSLVGAAAG----LLAALASSSVVKISAFGIQIGVALTPHTAGLAVLLPLAANV 371
                                    8********************************99....66666677778888889************************ PP

                           FtsX  82 lagllsiskilkke 95 
                                    la+++++++ +  +
  gi|119720308|ref|YP_920803.1| 372 LAAFIPARRGASLN 385
                                    *******9977666 PP

>> Formyl_trans_N  Formyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.031   1.9e+02       7      52 ..      38      83 ..      33      95 .. 0.85
   2 !   13.4   0.0   8.1e-06     0.048     101     136 ..     106     144 ..     102     158 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.031
                                   ESESSHHHHHHHHHHHHTTSECEEEEEEESCTTEHCHHHHHHCCHC CS
                 Formyl_trans_N  7 isgtgsnlqalldalkkgsleadvvlvvsnkdkaaglekaeaasip 52
                                   + g g+ +q+   ++ ++++ ad v+v++  +++ ++  a  +sip
  gi|119720308|ref|YP_920803.1| 38 ALGVGESFQKAFVEQLQSTIAADSVFVIGGYAGLTDADIAYFKSIP 83
                                   5588999****999**************999988888877777776 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 8.1e-06
                                    TTSEEEEESSSTTTTBSS-HHHHHHHTTSSE...EEEEE CS
                 Formyl_trans_N 101 rlkilniHpSLLPrfkGaaaiqraleaGdke...tGvti 136
                                    +++i+ + pS+LPr+ G++ +++a+ +G++e    Gv +
  gi|119720308|ref|YP_920803.1| 106 PVNIVAVDPSFLPRYLGVSDMRKAVAEGETEprgLGVLV 144
                                    677999***********************9975555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       692  (0.0385967); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2788.29
//
Query:       gi|119720309|ref|YP_920804.1|  [L=243]
Description: ABC transporter related [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.6e-30  104.4   0.0    8.4e-30  104.1   0.0    1.1  1  ABC_tran     ABC transporter
    2.6e-07   30.8   0.2      0.012   15.5   0.0    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    0.00029   21.1   0.4     0.0034   17.6   0.4    2.1  1  AAA_22       AAA domain
     0.0021   17.7   0.1       0.29   10.7   0.1    2.3  2  AAA_25       AAA domain
     0.0023   18.4   0.5      0.004   17.5   0.5    1.6  1  AAA_16       AAA ATPase domain
     0.0025   17.5   0.1     0.0046   16.7   0.1    1.4  1  AAA_29       P-loop containing region of AAA domain
     0.0044   16.5   0.0        1.5    8.2   0.0    2.1  2  SMC_N        RecF/RecN/SMC N terminal domain
     0.0047   16.4   0.2        0.2   11.1   0.1    2.2  2  TniB         Bacterial TniB protein
  ------ inclusion threshold ------
      0.018   15.2   0.3      0.052   13.7   0.3    1.8  1  AAA_33       AAA domain
      0.025   14.3   0.0      0.052   13.3   0.0    1.5  1  AAA_30       AAA domain
      0.027   15.0   0.0      0.043   14.3   0.0    1.2  1  AAA_23       AAA domain
       0.04   13.5   0.0      0.078   12.6   0.0    1.5  2  cobW         CobW/HypB/UreG, nucleotide-binding domain
      0.049   13.5   0.1       0.17   11.8   0.0    1.8  2  NTPase_1     NTPase
      0.097   12.9   0.1        1.6    9.0   0.1    2.2  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
       0.17   11.8   0.1        0.3   11.0   0.1    1.4  1  RsgA_GTPase  RsgA GTPase
       0.18   10.5   0.0       0.26   10.0   0.0    1.1  1  RNA12        RNA12 protein


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.1   0.0   7.5e-33   8.4e-30       1     136 [.      24     173 ..      24     174 .. 0.87

  Alignments for each domain:
  == domain 1  score: 104.1 bits;  conditional E-value: 7.5e-33
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.....B-HHHCCHCEEEE-SS--S-TTSB CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.....qeleslrkeigvlpqepqlfpelt 75 
                                    l+ v+l++ +ge  a+vG++G+GK+tLl l+ gl + t G+i +dg ++++     +     ++ +g+++q   l p+l+
  gi|119720309|ref|YP_920804.1|  24 LRGVTLEVGRGEFFAVVGPSGSGKTTLLHLVGGLDRATRGRIVVDGVEISSlrrdaELSAYRNRTVGFVFQLFYLVPRLR 103
                                    6789***********************************************999844445556789************** PP

                                    HHHH..........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    xxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  76 vren..........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                    v en           ++e+   al+ l+l++  ++ +++ p++LSgG++qrva+ara++ kp++ll+DEpt
  gi|119720309|ref|YP_920804.1| 104 VLENvelplvkrgvPREERRRMALEALRLVG-VEHLAHKYPTQLSGGEQQRVAIARAIVGKPRVLLADEPT 173
                                    **************55555555566666666.333445666*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.1   4.1e-05     0.046       1      23 [.      36      58 ..      36      87 .. 0.77
   2 !   15.5   0.0     1e-05     0.012     236     302 ..     145     209 ..     109     210 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.1e-05
                         AAA_21  1 lnvliGpNgsGKSnLLdaldlla 23
                                   + +++Gp gsGK++LL +  +l 
  gi|119720309|ref|YP_920804.1| 36 FFAVVGPSGSGKTTLLHLVGGLD 58
                                   6799************9888873 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1e-05
                         AAA_21 236 elSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSplll 302
                                    +lS G ++  a++ a+    +k+++ll DEp  +L+ +  + ++e +++l+r  g+ ++++TH+ +l+
  gi|119720309|ref|YP_920804.1| 145 QLSGGEQQRVAIARAIV---GKPRVLLADEPTGNLDASSSEVVMETFRRLNReLGVTIVMVTHNLELI 209
                                    55666665544444444...556************************888888***********9996 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.4   3.1e-06    0.0034       6     128 ..      35     202 ..      30     209 .. 0.63

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.1e-06
                         AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaee...........................................erpev 42 
                                     + +v+G+sG+GKTtll  +   +   a   +                                           e++e+
  gi|119720309|ref|YP_920804.1|  35 EFFAVVGPSGSGKTTLLHLVGGLDR--AT--RgrivvdgveisslrrdaelsayrnrtvgfvfqlfylvprlrvlENVEL 110
                                    6889*************99988863..22..2346788888888888888888777777777777777754444444444 PP

                         AAA_22  43 vfvtlpsst.sskdllrellralglelka.....erlsseellealeqalraravielliiDEaqh.lr...seealeeL 112
                                     +v+  ++  +++ ++ e lr +g+e+ a     +    e+ + a+++a+  + +  +l+ DE    l+   se ++e++
  gi|119720309|ref|YP_920804.1| 111 PLVKRGVPReERRRMALEALRLVGVEHLAhkyptQLSGGEQQRVAIARAIVGKPR--VLLADEPTGnLDassSEVVMETF 188
                                    4555555555666666666666666666655444444444444444444444444..88888877668776447777777 PP

                         AAA_22 113 rsllnlsrkgvqliLv 128
                                    r+l    + gv++++v
  gi|119720309|ref|YP_920804.1| 189 RRLNR--ELGVTIVMV 202
                                    66666..555555554 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.1   0.00026      0.29      31      50 ..      32      51 ..      16      64 .. 0.90
   2 ?    4.8   0.0     0.017        19     162     188 ..     178     204 ..     167     205 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00026
                         AAA_25 31 pagelallaGapgtGKttla 50
                                    +ge+ +++G++g+GKttl+
  gi|119720309|ref|YP_920804.1| 32 GRGEFFAVVGPSGSGKTTLL 51
                                   689***************97 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.017
                         AAA_25 162 nsdvgalvealeriarrtgaavllvhH 188
                                    +s  + ++e ++r+ r++g+++++v H
  gi|119720309|ref|YP_920804.1| 178 ASSSEVVMETFRRLNRELGVTIVMVTH 204
                                    4445778999****************9 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.5   3.6e-06     0.004      22      57 ..      32      68 ..      21     206 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.6e-06
                         AAA_16 22 grpelvllsGesGvGKsslvrellralekd..ggiflr 57
                                   gr+e   ++G+sG+GK++l+  +   l ++  g i++ 
  gi|119720309|ref|YP_920804.1| 32 GRGEFFAVVGPSGSGKTTLLHLVG-GLDRAtrGRIVVD 68
                                   777999**************8886.3444422234444 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   4.1e-06    0.0046      14      39 ..      26      51 ..      21      54 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.1e-06
                         AAA_29 14 ghtieidlkgatlltGpsGsGKSTll 39
                                   g t+e+ + +++ ++GpsGsGK+Tll
  gi|119720309|ref|YP_920804.1| 26 GVTLEVGRGEFFAVVGPSGSGKTTLL 51
                                   56788886669**************8 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0013       1.5      25      41 ..      35      51 ..      25      55 .. 0.86
   2 !    6.5   0.0    0.0046       5.1     135     205 ..     144     212 ..      69     222 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0013
                                   SEEEEEESTTSSHHHHH CS
                                   xxxxxxxxxxxxxxxxx RF
                          SMC_N 25 sftaivGpNGSGKsnll 41
                                   +f a+vGp GSGK+ ll
  gi|119720309|ref|YP_920804.1| 35 EFFAVVGPSGSGKTTLL 51
                                   6899**********987 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0046
                                    TCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxx RF
                          SMC_N 135 elLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQfivislreemleka 205
                                    ++LSgGe++ va+a    i   kp+ + l De   +LD++  + v e +++ + +  + +++++++ e++ ++
  gi|119720309|ref|YP_920804.1| 144 TQLSGGEQQRVAIARA--IVG-KPR-VLLADEPTGNLDASSSEVVMETFRRLNRElgVTIVMVTHNLELIWNC 212
                                    48******99988753..432.343.5577*******************998888334445556666666555 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.045        50      37      52 ..      36      51 ..      27      55 .. 0.84
   2 !   11.1   0.1   0.00018       0.2     108     160 ..     150     202 ..     103     210 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.045
                           TniB 37 nlllvGdsnnGKtmiv 52
                                      +vG+s  GKt+++
  gi|119720309|ref|YP_920804.1| 36 FFAVVGPSGSGKTTLL 51
                                   5689**********97 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00018
                           TniB 108 eqqvlrllrel..kvrvLiiDEihnllagsarkqreflnalksLgnelkipivlv 160
                                    eqq +++ r++  k+rvL+ DE    l   a++ + ++++ ++L++el ++iv+v
  gi|119720309|ref|YP_920804.1| 150 EQQRVAIARAIvgKPRVLLADEPTGNL--DASSSEVVMETFRRLNRELGVTIVMV 202
                                    444444444443389*******99999..6677899*****************98 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.3   4.7e-05     0.052       4      20 ..      39      57 ..      37     220 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.7e-05
                         AAA_33  4 lvGlpGsGKstlaerl..l 20
                                   +vG++GsGK+tl++ +  l
  gi|119720309|ref|YP_920804.1| 39 VVGPSGSGKTTLLHLVggL 57
                                   79**********9866443 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   4.6e-05     0.052      19      50 ..      35      66 ..      27      78 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.6e-05
                         AAA_30 19 rvavltGpAGtGKttalkalreaweaaggrvi 50
                                    + +++Gp G+GKtt+l  +  + +a  gr++
  gi|119720309|ref|YP_920804.1| 35 EFFAVVGPSGSGKTTLLHLVGGLDRATRGRIV 66
                                   47789*************99999998865655 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   3.9e-05     0.043      12      36 ..      26      51 ..      22      54 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.9e-05
                         AAA_23 12 dqeidFsk.gltlItGpNGaGKTTil 36
                                   +++++ ++  +++++Gp G+GKTT+l
  gi|119720309|ref|YP_920804.1| 26 GVTLEVGRgEFFAVVGPSGSGKTTLL 51
                                   566777552589*************8 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0     7e-05     0.078       4      44 ..      38      80 ..      35      95 .. 0.67
   2 ?   -2.7   0.0       3.4   3.8e+03      89     102 ..     171     184 ..     148     207 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7e-05
                                   EEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SSCHCCCC CS
                           cobW  4 vltGflGsGKTtLlnhll..enraglklavivNefgevsiDae 44
                                    ++G+ GsGKTtLl  +   +++   ++ v   e++++  Dae
  gi|119720309|ref|YP_920804.1| 38 AVVGPSGSGKTTLLHLVGglDRATRGRIVVDGVEISSLRRDAE 80
                                   689**********986655333333344333346666666665 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.4
                                    EECTTTTHHHH.HTT CS
                           cobW  89 EttGlaePapv.aft 102
                                    E tG++++  + +  
  gi|119720309|ref|YP_920804.1| 171 EPTGNLDASSSeV-V 184
                                    6677666666631.2 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00015      0.17       3      48 ..      38      85 ..      36      91 .. 0.78
   2 ?   -0.9   0.0       1.2   1.3e+03      94     123 ..     162     192 ..     120     229 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00015
                                   EEE--TTSSHHHHHHHH..HHHH...GGGEEEEEEEEE-------EEE CS
                       NTPase_1  3 fiTGppGvGKtTlvkkv..lellkssgvkvgGfyteevreggrrigFk 48
                                   ++ Gp+G+GKtTl++ v  l+   +  + v+G+  +  r++ + ++++
  gi|119720309|ref|YP_920804.1| 38 AVVGPSGSGKTTLLHLVggLDRATRGRIVVDGVEISSLRRDAELSAYR 85
                                   688************994445566667889999999999887777665 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.2
                                    HHH-EEEE--.-STTGGG-HHHHHHHHHHHT CS
                       NTPase_1  94 seadviviDE.iGkmElkskkfkeaveevLk 123
                                     ++ v++ DE  G++  +s ++  +  + L+
  gi|119720309|ref|YP_920804.1| 162 GKPRVLLADEpTGNLDASSSEVVMETFRRLN 192
                                    5555555555445555554444333333333 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1    0.0014       1.6      32      89 ..     145     189 ..     120     190 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0014
                        SbcCD_C  32 tlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                    +lSGGe+q    +a+a     ++        ++r+++ DE  ++lD+ s++ ++e+++
  gi|119720309|ref|YP_920804.1| 145 QLSGGEQQR---VAIA----RAIVG------KPRVLLADEPTGNLDASSSEVVMETFR 189
                                    566666632...2222....22222......4899999****************9997 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00027       0.3      98     120 ..      33      55 ..      20      68 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00027
                                    TTSEEEEECSTTSSHHHHHHHHC CS
                    RsgA_GTPase  98 kdktsvlvGqSGvGKStLinall 120
                                    ++++ ++vG+SG GK+tL+  + 
  gi|119720309|ref|YP_920804.1|  33 RGEFFAVVGPSGSGKTTLLHLVG 55 
                                    5678899***********97554 PP

>> RNA12  RNA12 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00023      0.26      19      72 ..      36      91 ..      28     100 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00023
                          RNA12 19 FivvkGPrGSGkkeLv.ldrvlkdrkk.vlvidCdelvkarndaelisaaAsqlGY 72
                                   F  v GP GSGk+ L+ l   l + ++  +v+d  e+ + r dael +   + +G+
  gi|119720309|ref|YP_920804.1| 36 FFAVVGPSGSGKTTLLhLVGGLDRATRgRIVVDGVEISSLRRDAELSAYRNRTVGF 91
                                   88899*********982233354444489**************9998877777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1547.00
//
Query:       gi|119720310|ref|YP_920805.1|  [L=110]
Description: hypothetical protein Tpen_1405 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       257  (0.0143343); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 725.51
//
Query:       gi|119720311|ref|YP_920806.1|  [L=156]
Description: hypothetical protein Tpen_1406 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.011   16.0  12.2      0.011   16.0  12.2    2.3  2  DUF2127    Predicted membrane protein (DUF2127)


Domain annotation for each model (and alignments):
>> DUF2127  Predicted membrane protein (DUF2127)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.5    0.0042        76       3      28 ..      28      53 ..      26      64 .. 0.83
   2 ?   16.0  12.2   6.3e-07     0.011      70     136 ..      74     139 ..      70     142 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.0042
                        DUF2127  3 rliallklvkglllllaglallflls 28
                                    ++a+l ++ g+ll+l+gl+ +++ +
  gi|119720311|ref|YP_920806.1| 28 TILAVLNMLGGALLVLLGLIFVAVGP 53
                                   6899**************99888766 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 6.3e-07
                        DUF2127  70 valallaYallklieavgLwrekrWaeylavvstaifiplEiyelvrkvsvlkiallliNlaivvyl 136
                                    ++++l++ +++ li ++gLw +k Wa +++v+  ++ +   +  ++   + ++++ ll+  ++++y+
  gi|119720311|ref|YP_920806.1|  74 LGALLIVMGAVSLIVGWGLWTGKGWAWWVTVIFEVLGLLSGLLSAAA-GDPFSVVGLLVSAIVLWYM 139
                                    5789***************************9888877777776554.4566666666666677776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       821  (0.0457917); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1052.79
//
Query:       gi|119720312|ref|YP_920807.1|  [L=76]
Description: hypothetical protein Tpen_1407 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 531.28
//
Query:       gi|119720313|ref|YP_920808.1|  [L=1170]
Description: formate dehydrogenase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-42  144.9   0.0    3.6e-41  141.5   0.0    2.6  1  Molybdopterin    Molybdopterin oxidoreductase
    2.6e-13   49.7   0.0    5.1e-13   48.8   0.0    1.5  1  Molybdop_Fe4S4   Molybdopterin oxidoreductase Fe4S4 domain
    1.9e-12   47.2   0.0    4.5e-12   46.0   0.0    1.6  1  Molydop_binding  Molydopterin dinucleotide binding domain
    0.00054   19.7   0.1     0.0014   18.4   0.1    1.8  1  TAT_signal       TAT (twin-arginine translocation) pathway si
      0.004   17.1   0.2      0.036   14.0   0.0    2.6  3  MazE_antitoxin   Antidote-toxin recognition MazE, bacterial a
  ------ inclusion threshold ------
      0.016   14.7   0.1      0.026   13.9   0.1    1.2  1  AAA-ATPase_like  Predicted AAA-ATPase


Domain annotation for each model (and alignments):
>> Molybdopterin  Molybdopterin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.5   0.0   1.2e-44   3.6e-41       1     429 [.     110     660 ..     110     663 .. 0.78

  Alignments for each domain:
  == domain 1  score: 141.5 bits;  conditional E-value: 1.2e-44
                                    B--S-EEEC.....................TTTTTSEEEE--HHHHHHHHHHHHHHHHHHCSGGGEEEEEBTSSCSHHHH CS
                  Molybdopterin   1 RlkyPmvRk.....................qargeGkFvrvsWdeAleliaaslkytikkygpdrvagfssgplmsmesl 59 
                                    R+++Pm+R+                      ++   ++++vsWdeA+ +ia+++ ++  +  +      s  p +    +
  gi|119720313|ref|YP_920808.1| 110 RVTQPMIRTgpkpppeeilsakswdelvalVKKYPPQWKPVSWDEAFRFIASRVAKILNEWRS-----SSGAPKQPDGYY 184
                                    99****************************5555889*******************9988666.....333344445555 PP

                                    HHHHHH.HHHTT-EEE-BEECCGGGTTHHHHCHHCCCCCTTTS-SS-CC................GGGG-SEEEEESS-H CS
                  Molybdopterin  60 aslkkl.lsllggknlsfydwyadlppasaqqtigsdsrsnyessnple................dlensdliilwGsNv 122
                                    ++++k  ++l+g++++ ++  y   ++a+   t + ds++  + s++++                d++ +d+++ ++s +
  gi|119720313|ref|YP_920808.1| 185 YVGSKVpIQLIGSSIMVNEAGYLTTKLAEFLGTTNVDSQYRKCHSSTVSslaltygwgaetatieDVALADVVLFFSS-P 263
                                    55555435555555555555555555555444444444444444444445555555555555555******9999977.9 PP

                                    HHHSHHHHHHHHHHHHTTC-EEEEECSSB-HCGGGCSEEEEEHTTTHHHHHHHHHHHHHHCCCCTCHHHHHHEECHHHCC CS
                  Molybdopterin 123 reerpilnarirkaalkkkakvivigpryaellkfadewlaikpgtdaalalamghvilqelkvdkeflrkytygkeetd 202
                                    +e +p+   +++k  +++++ +i ++pry+ ++   d+w++ + gtd a++l++ h+   e     ++l+  +  +    
  gi|119720313|ref|YP_920808.1| 264 AEAHPLSFQYFLKGKKERGTIFITFDPRYSRTAMASDLWVPFRSGTDTAIFLYILHYAFFERDPPIDSLDAFKALR---- 339
                                    *******888888888888************9999**********************9998877555555444433.... PP

                                    CCCCCEECCS..............HHHHHHCCHHHHHHHHHHHHHH.......TSSEEEEECHHHHTSTTHH.HHHHHHH CS
                  Molybdopterin 203 mpllvtleee..............tgkkkevvariarelarnaakt.......agksmiivGaglnhrqdgd.aiyravi 260
                                    +   vt ++               ++ +++v+++  r +ar + ++       +++  + + +g++++++ + +i+ra++
  gi|119720313|ref|YP_920808.1| 340 SRWNVTDDDLadfkelikeydaetVSRITGVPVDMLRTVARIYVENsgvatnhKKHGVVQWAMGMTQHTNATiNIIRAAA 419
                                    33333333334444555666777688889999999999888765441111111567799*********99873689**** PP

                                    HHHHHCTHCSSTTCEEEEESSCTTHHHCH.HHHTCCTTCCCCCCCTT................................. CS
                  Molybdopterin 261 nLallvgnvgqpgGgwahlnGqlilagaa.ekvgalpvllsvkslke................................. 306
                                     + ll+gnvg pgGg   ++G  +++g   ++ g l+ l+ ++ +++                                 
  gi|119720313|ref|YP_920808.1| 420 IMQLLLGNVGFPGGGAHPFRGHSNVQGVTdVQGGGLGALPGYHASPSstfyvrlyqdwklqgmpdawnwvvpewarktft 499
                                    *********************88888854268888888888888888888888888888888888888888888888888 PP

                                    ...........................................HHHHHCCCTTTCSTSS--ECGGCHHHHHHTTSSSEEE CS
                  Molybdopterin 307 ...........................................ekikfaaeqpgnlgnfprnlfversnllkssgkkvly 343
                                                                               + + +++   g++    +++f    + + ++++++ +
  gi|119720313|ref|YP_920808.1| 500 tttpdkgsadltkilqvytfygwrrfellwgffcgtvpeddpvNGTVVCDFPFGTGST--EITFP---RRVLNGEIRAAF 574
                                    8888999999999999999*******************88887444444444444433..33333...3334499***** PP

                                    EESH.HHHHSTTSCCCHCHHHCSSEEEEEESCSSHHHHTSSEEEEBE-CCGSEEEEE-TTSEEEEEEESSS-STT-BEHH CS
                  Molybdopterin 344 llgnnpevdhadenevekalekldlvvvldgrltstalyaDiiLPaatwyEkedlytndegrfqhlkqavsppgeaksdw 423
                                    + g+np v+ ++++ +  al kldl+vv+d++ t+ta++aD++LPa+++ E e++ tn+++ +q + +a +p+ge+++d+
  gi|119720313|ref|YP_920808.1| 575 IFGENPAVTNPNAKVIWAALSKLDLLVVSDIFETETAWFADVLLPASSFAEVEGTKTNGNRVIQWTYAALNPRGESRPDY 654
                                    ******************************************************************************** PP

                                    HHHHHH CS
                  Molybdopterin 424 kIlkaL 429
                                    +I+ +L
  gi|119720313|ref|YP_920808.1| 655 WIITKL 660
                                    ***988 PP

>> Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.8   0.0   1.7e-16   5.1e-13       4      54 ..      56     106 ..      53     107 .. 0.93

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 1.7e-16
                                    EEEE-SSBTT--EEEEEEETTEEEEEEE-TTSTTTTT---HHHHTCHHCCC CS
                 Molybdop_Fe4S4   4 vktaCpyCgvgCglevhvkdgkivkvegdpdhpvnegrlCvKGrtllervy 54 
                                    ++ +CpyC++gC+++ ++ +++i ++eg pd+ +n+g lC+KG+++ e v 
  gi|119720313|ref|YP_920808.1|  56 TPVICPYCSMGCSIDFYTFGDQILWTEGSPDSYINFGALCPKGKAAFELVE 106
                                    6779*****************************************999886 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.0   0.0   1.5e-15   4.5e-12       2      68 ..    1042    1109 ..    1041    1115 .. 0.95

  Alignments for each domain:
  == domain 1  score: 46.0 bits;  conditional E-value: 1.5e-15
                                     EEEEE-BTTBSTTTTTCGCCHHHHCSSS.-EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESS CS
                Molydop_binding    2 rLitgrsldqlhsqtrtrpvlrlakpep.evveinpedAaalGikdGdlVevesrrGsvevrakvter 68  
                                     + +t r  +++hs+ +tr+++ la+ +p ++v++  e A++lG++ Gd Ve+ ++rGs+++ra vte+
  gi|119720313|ref|YP_920808.1| 1042 VITTNRLTEHWHSGSMTRRTPLLAELDPePFVYVPRELARKLGVNSGDYVEIITARGSIKMRAYVTEG 1109
                                     57999************************************************************995 PP

>> TAT_signal  TAT (twin-arginine translocation) pathway signal sequence
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   4.8e-07    0.0014       2      22 ..       5      23 ..       4      27 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 4.8e-07
                     TAT_signal  2 lSRRdFLKgsAAaaAAaalgg 22
                                   ++RR+FLK  +Aa AA al+ 
  gi|119720313|ref|YP_920808.1|  5 IDRRSFLK--LAAIAASALAL 23
                                   89******..55555555553 PP

>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       2.8   8.4e+03      19      31 ..     684     696 ..     682     699 .. 0.76
   2 !   14.0   0.0   1.2e-05     0.036      10      39 ..    1074    1103 ..    1072    1109 .. 0.87
   3 ?   -1.0   0.0       0.6   1.8e+03      21      43 ..    1143    1166 ..    1137    1168 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.8
                                    CCEECTCEEEEEE CS
                 MazE_antitoxin  19 lgireGdevelev 31 
                                      +r+G +v+l  
  gi|119720313|ref|YP_920808.1| 684 VKVRKGGRVVLLY 696
                                    5689999999876 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 1.2e-05
                                     EE-CCCHHHCCEECTCEEEEEECTTCCCCC CS
                 MazE_antitoxin   10 riPkevrfelgireGdevelevdgdkiilr 39  
                                       P+e++++lg++ Gd ve+++  ++i  r
  gi|119720313|ref|YP_920808.1| 1074 YVPRELARKLGVNSGDYVEIITARGSIKMR 1103
                                     57*******************999888765 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.6
                                     EEC..TCEEEEEECTTCCCCCCCHH CS
                 MazE_antitoxin   21 ire..Gdevelevdgdkiilrplks 43  
                                     i++  Gd v+ +++  k ++ ++++
  gi|119720313|ref|YP_920808.1| 1143 ISPdvGDVVTTIQET-KAWIGKIRK 1166
                                     666658888888876.999999876 PP

>> AAA-ATPase_like  Predicted AAA-ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   8.8e-06     0.026     222     262 ..     940     980 ..     937     987 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8.8e-06
                AAA-ATPase_like 222 teeeveellkeeleelalkeatveelieelkewYdgYsFae 262
                                    t e+++++lk+++e++ +++  v+++i+elk wY gYsF+ 
  gi|119720313|ref|YP_920808.1| 940 TYEQMRATLKKYYEQTGNMRDAVNKTIQELKGWYPGYSFTW 980
                                    678899************99*******************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.72u 0.31s 00:00:01.03 Elapsed: 00:00:00.49
# Mc/sec: 7117.54
//
Query:       gi|119720314|ref|YP_920809.1|  [L=286]
Description: 4Fe-4S ferredoxin iron-sulfur binding domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-22   78.8  10.4    2.6e-22   78.8  10.4    1.9  2  Fer4_11   4Fe-4S dicluster domain
      1e-13   51.6  24.7    3.3e-07   30.8   5.7    3.6  4  Fer4_7    4Fe-4S dicluster domain
    2.4e-12   46.1  40.4    8.2e-07   28.6   3.2    5.3  6  Fer4      4Fe-4S binding domain
    4.4e-11   42.7  28.7    4.1e-06   26.8  10.6    3.4  3  Fer4_10   4Fe-4S dicluster domain
    5.8e-11   42.4  24.7    1.8e-05   24.8   8.3    3.1  3  Fer4_9    4Fe-4S dicluster domain
    2.1e-08   33.9  40.1    0.00023   21.1   3.0    5.0  5  Fer4_6    4Fe-4S binding domain
    4.2e-08   32.8  37.4    0.00015   21.7   2.6    4.5  4  Fer4_2    4Fe-4S binding domain
    1.5e-07   31.4  26.1    3.7e-05   23.8  10.2    3.3  3  Fer4_21   4Fe-4S dicluster domain
    2.3e-06   28.0  24.1    7.9e-05   23.0   3.9    3.6  2  Fer4_8    4Fe-4S dicluster domain
    3.9e-06   27.4  41.1       0.12   13.3   2.8    4.3  4  Fer4_3    4Fe-4S binding domain
    4.4e-05   24.3  25.8          1   10.3   2.9    4.8  5  Fer4_16   4Fe-4S double cluster binding domain
     0.0002   21.6  37.8     0.0019   18.6   3.5    4.5  4  Fer4_4    4Fe-4S binding domain
     0.0074   17.0  24.1       0.12   13.2   1.7    4.2  3  Fer4_15   4Fe-4S single cluster domain
  ------ inclusion threshold ------
       0.02   15.1   1.9       0.02   15.1   1.9    3.8  4  Fer4_18   4Fe-4S dicluster domain
      0.029   14.9   0.8      0.029   14.9   0.8    4.1  3  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
        1.2    9.7  31.3         14    6.3   3.9    4.3  4  Fer4_17   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.2      0.98   1.1e+03      36      54 ..      15      32 ..      10      46 .. 0.60
   2 !   78.8  10.4   2.3e-25   2.6e-22       4      99 ..      89     181 ..      86     182 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.98
                        Fer4_11 36 Vlldektkkeevrevveac 54
                                   Vl+d +++  ++r+++ ac
  gi|119720314|ref|YP_920809.1| 15 VLVDLDKCI-GCRACQVAC 32
                                   555555554.555555555 PP

  == domain 2  score: 78.8 bits;  conditional E-value: 2.3e-25
                        Fer4_11   4 lflpeqCrhCleppCvasapseaivkdeetGaVlldektkkeevrevveacPykivrkneetgkvekCdmcldrveaGll 83 
                                    + lp qC+hC ++pC +++p++ai   + +GaV++ ++++  ++  + +acP++++r+ ++ gk  kC++c+dr+++G++
  gi|119720314|ref|YP_920809.1|  89 VPLPFQCMHCATAPCSRACPVGAIKVTP-EGAVVISKEECI-GCGFCETACPFRVPRRGSD-GKYYKCTFCVDRIQNGRA 165
                                    56899****************9998888.9**********7.***************9766.5699************** PP

                        Fer4_11  84 pacvescptgalnfgd 99 
                                    pacve+cptg+ +fg+
  gi|119720314|ref|YP_920809.1| 166 PACVEACPTGVFTFGK 181
                                    *************996 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   5.7   2.9e-10   3.3e-07       1      52 []      21     111 ..      21     111 .. 0.61
   2 !   24.9  14.4     2e-08   2.3e-05       1      51 [.      94     140 ..      94     141 .. 0.91
   3 !   19.4  13.3     1e-06    0.0012       2      52 .]     127     176 ..     126     176 .. 0.83
   4 !   10.4   2.4   0.00068      0.76       2      21 ..     153     181 ..     151     199 .. 0.63

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 2.9e-10
                         Fer4_7   1 rCigCgaCvaaC..........................pvkaieldeeenek.....................gtekvei 33 
                                    +CigC+aC++aC                                                              +e+v++
  gi|119720314|ref|YP_920809.1|  21 KCIGCRACQVACkdwnsrqaekttfsptftnppdltanD------------WkvvfyyegkskkalltpagevVFEQVDV 88 
                                    7***********666666665555555555555555442............03333333333335555554442244455 PP

                         Fer4_7  34 d..pekClgCga..CvavCPtga 52 
                                    +  p +C++C    C ++CP+ga
  gi|119720314|ref|YP_920809.1|  89 VplPFQCMHCATapCSRACPVGA 111
                                    412679****9999*******98 PP

  == domain 2  score: 24.9 bits;  conditional E-value: 2e-08
                         Fer4_7   1 rCigCg..aCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtg 51 
                                    +C++C    C +aCpv+ai++++e        v+i+ e+C+gCg C+++CP+ 
  gi|119720314|ref|YP_920809.1|  94 QCMHCAtaPCSRACPVGAIKVTPE------GAVVISKEECIGCGFCETACPFR 140
                                    6****6669************997......579******************86 PP

  == domain 3  score: 19.4 bits;  conditional E-value: 1e-06
                         Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgC.........gaCvavCPtga 52 
                                    CigCg+C+ aCp ++ +   +          +++ kC++C          aCv++CPtg+
  gi|119720314|ref|YP_920809.1| 127 CIGCGFCETACPFRVPRRGSD----------GKYYKCTFCvdriqngraPACVEACPTGV 176
                                    ************999998765..........57789999977777765557*******96 PP

  == domain 4  score: 10.4 bits;  conditional E-value: 0.00068
                         Fer4_7   2 CigC......g...aCvaaCpvkaielde 21 
                                    C+ C      g   aCv+aCp++++++ +
  gi|119720314|ref|YP_920809.1| 153 CTFCvdriqnGrapACVEACPTGVFTFGK 181
                                    55553333331333788888888777765 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   4.1   8.9e-07   0.00099       2      18 ..      16      32 ..      15      33 .. 0.93
   2 ?   -2.4   0.2       4.5     5e+03      11      15 ..      95      99 ..      94     101 .. 0.55
   3 !   10.9   0.7   0.00027      0.31      14      24 .]     103     113 ..     102     113 .. 0.95
   4 !   28.6   3.2   7.3e-10   8.2e-07       1      22 [.     120     141 ..     120     143 .. 0.91
   5 ?   -0.7   0.2       1.3   1.5e+03       7      11 ..     152     156 ..     150     157 .. 0.86
   6 !   11.9   0.7   0.00014      0.15      13      23 ..     167     177 ..     167     178 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 8.9e-07
                                   EEETTTSSS-THHHHHS CS
                           Fer4  2 videekCigCGaCvevC 18
                                    +d +kCigC aC  +C
  gi|119720314|ref|YP_920809.1| 16 LVDLDKCIGCRACQVAC 32
                                   59*************** PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.5
                                   -THHH CS
                           Fer4 11 CGaCv 15
                                   C+ C+
  gi|119720314|ref|YP_920809.1| 95 CMHCA 99
                                   55555 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00027
                                    HHHHSTTTEEE CS
                           Fer4  14 CvevCPvgAIt 24 
                                    C  +CPvgAI+
  gi|119720314|ref|YP_920809.1| 103 CSRACPVGAIK 113
                                    9*********6 PP

  == domain 4  score: 28.6 bits;  conditional E-value: 7.3e-10
                                    EEEETTTSSS-THHHHHSTTTE CS
                           Fer4   1 vvideekCigCGaCvevCPvgA 22 
                                    vvi +e CigCG C+ +CP+ +
  gi|119720314|ref|YP_920809.1| 120 VVISKEECIGCGFCETACPFRV 141
                                    6899***************976 PP

  == domain 5  score: -0.7 bits;  conditional E-value: 1.3
                                    TSSS- CS
                           Fer4   7 kCigC 11 
                                    kC++C
  gi|119720314|ref|YP_920809.1| 152 KCTFC 156
                                    89999 PP

  == domain 6  score: 11.9 bits;  conditional E-value: 0.00014
                                    HHHHHSTTTEE CS
                           Fer4  13 aCvevCPvgAI 23 
                                    aCve+CP+g+ 
  gi|119720314|ref|YP_920809.1| 167 ACVEACPTGVF 177
                                    7*******986 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.3   2.7e-06     0.003       2      23 ..      15      35 ..      14      60 .. 0.80
   2 !   15.8  15.5   9.8e-06     0.011       7      56 .]      93     138 ..      88     138 .. 0.86
   3 !   26.8  10.6   3.6e-09   4.1e-06       2      56 .]     120     173 ..     119     173 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.7e-06
                        Fer4_10  2 vvidddtCirCgkCvkaCPadl 23
                                   v +d d+Ci+C++C+ aC  d+
  gi|119720314|ref|YP_920809.1| 15 VLVDLDKCIGCRACQVAC-KDW 35
                                   57899*************.434 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 9.8e-06
                        Fer4_10   7 dtCirCg..kCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                     +C++C+   C +aCP+      +  + ++e+av +  e+C+gcg C  aCP
  gi|119720314|ref|YP_920809.1|  93 FQCMHCAtaPCSRACPV------GAIKVTPEGAVVISKEECIGCGFCETACP 138
                                    68****9999*******......555666777777888*************9 PP

  == domain 3  score: 26.8 bits;  conditional E-value: 3.6e-09
                        Fer4_10   2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgc......g...aCveaCP 56 
                                    vvi ++ Ci+Cg C +aCP+          + +    ++k++kCt+c      g   aCveaCP
  gi|119720314|ref|YP_920809.1| 120 VVISKEECIGCGFCETACPF----------RVPRRGSDGKYYKCTFCvdriqnGrapACVEACP 173
                                    7999**************99..........888888999999****98777772567******9 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   9.2   2.9e-07   0.00032       1      51 []      21     112 ..      21     112 .. 0.84
   2 !   22.3  10.8   9.4e-08   0.00011       1      47 [.      94     138 ..      94     141 .. 0.90
   3 !   24.8   8.3   1.6e-08   1.8e-05       1      49 [.     126     175 ..     126     177 .. 0.94

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.9e-07
                         Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase........................................eaCigCg 40 
                                    kC+gC+aC+ aC+ +  ++ +++++                                                 +C++C 
  gi|119720314|ref|YP_920809.1|  21 KCIGCRACQVACKDWNSRQAEKTTFSPTFTN-PpdltandwkvvfyyegkskkalltpagevvfeqvdvvplpFQCMHCA 99 
                                    7***********7777766666666554333.2467778888888888999999*******************9****** PP

                         Fer4_9  41 a..CveaCpkgai 51 
                                    +  C  aCp gai
  gi|119720314|ref|YP_920809.1| 100 TapCSRACPVGAI 112
                                    **********987 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 9.4e-08
                         Fer4_9   1 kCtgCga..CveaCpagvvvedaaerkarlraaseeaCigCgaCveaCp 47 
                                    +C+ C +  C +aCp g+++    +  +  ++    +CigCg C+ aCp
  gi|119720314|ref|YP_920809.1|  94 QCMHCATapCSRACPVGAIKVTPEGAVVISKE----ECIGCGFCETACP 138
                                    6****8778************99999999876....5***********9 PP

  == domain 3  score: 24.8 bits;  conditional E-value: 1.6e-08
                         Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCga.........CveaCpkg 49 
                                    +C+gCg C++aCp+ v ++ + +++ +        C++C +         CveaCp+g
  gi|119720314|ref|YP_920809.1| 126 ECIGCGFCETACPFRVPRRGSDGKYYK--------CTFCVDriqngrapaCVEACPTG 175
                                    5******************99999977........9********************98 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   1.9   3.6e-07   0.00041       2      20 ..      15      33 ..      14      40 .. 0.90
   2 !    6.7   5.7     0.007       7.9       9      24 .]      95     112 ..      94     112 .. 0.82
   3 !   21.1   3.0     2e-07   0.00023       2      22 ..     120     140 ..     119     142 .. 0.88
   4 ?   -3.0   0.3       8.6   9.6e+03      12      16 ..     153     157 ..     152     158 .. 0.76
   5 !    7.7   1.1    0.0036         4      14      23 ..     167     176 ..     165     177 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 3.6e-07
                         Fer4_6  2 veidpdkCigCgdCvrvCP 20
                                   v +d dkCigC++C ++C 
  gi|119720314|ref|YP_920809.1| 15 VLVDLDKCIGCRACQVACK 33
                                   6799**************6 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.007
                         Fer4_6   9 CigCgd..CvrvCPegai 24 
                                    C +C    C r+CP gai
  gi|119720314|ref|YP_920809.1|  95 CMHCATapCSRACPVGAI 112
                                    788855589********8 PP

  == domain 3  score: 21.1 bits;  conditional E-value: 2e-07
                         Fer4_6   2 veidpdkCigCgdCvrvCPeg 22 
                                    v+i ++ CigCg C+++CP+ 
  gi|119720314|ref|YP_920809.1| 120 VVISKEECIGCGFCETACPFR 140
                                    7888999************85 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 8.6
                         Fer4_6  12 CgdCv 16 
                                    C  Cv
  gi|119720314|ref|YP_920809.1| 153 CTFCV 157
                                    88898 PP

  == domain 5  score: 7.7 bits;  conditional E-value: 0.0036
                         Fer4_6  14 dCvrvCPega 23 
                                    +Cv +CP+g+
  gi|119720314|ref|YP_920809.1| 167 ACVEACPTGV 176
                                    5*******98 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   2.6   1.3e-07   0.00015       2      20 ..      14      32 ..      13      33 .. 0.91
   2 !    6.5   4.7    0.0091        10      10      21 ..      95     108 ..      88     109 .. 0.88
   3 !   20.7   1.7   2.7e-07   0.00031       3      21 ..     120     138 ..     118     139 .. 0.86
   4 ?    1.5   5.2      0.34   3.9e+02      15      22 .]     167     174 ..     150     174 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.3e-07
                         Fer4_2  2 pvvvdtdrCigCgaCvsaC 20
                                   +v vd d+CigC+aC+ aC
  gi|119720314|ref|YP_920809.1| 14 AVLVDLDKCIGCRACQVAC 32
                                   5789*************** PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0091
                         Fer4_2  10 CigCg..aCvsaCP 21 
                                    C++C   +C  aCP
  gi|119720314|ref|YP_920809.1|  95 CMHCAtaPCSRACP 108
                                    ****667******* PP

  == domain 3  score: 20.7 bits;  conditional E-value: 2.7e-07
                         Fer4_2   3 vvvdtdrCigCgaCvsaCP 21 
                                    vv+  + CigCg C +aCP
  gi|119720314|ref|YP_920809.1| 120 VVISKEECIGCGFCETACP 138
                                    6677888************ PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.34
                         Fer4_2  15 aCvsaCPa 22 
                                    aCv aCP+
  gi|119720314|ref|YP_920809.1| 167 ACVEACPT 174
                                    8******7 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.5     2e-06    0.0022       3      23 ..      17      38 ..      15      49 .. 0.82
   2 !   23.8  10.2   3.3e-08   3.7e-05       7      53 ..      94     139 ..      92     141 .. 0.91
   3 ?    0.1   0.1       0.8     9e+02      47      53 ..     168     174 ..     164     179 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2e-06
                        Fer4_21  3 idedkCigCgkCliaCed.tsh 23
                                   +d dkCigC  C +aC+d +s 
  gi|119720314|ref|YP_920809.1| 17 VDLDKCIGCRACQVACKDwNSR 38
                                   7889*************93444 PP

  == domain 2  score: 23.8 bits;  conditional E-value: 3.3e-08
                        Fer4_21   7 kCigCgk..CliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPv 53 
                                    +C++C    C  aC+   + ai+++++  + + ++eC+GC  C + CP 
  gi|119720314|ref|YP_920809.1|  94 QCMHCATapCSRACP---VGAIKVTPEGAVVISKEECIGCGFCETACPF 139
                                    799997555******...89****************************5 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.8
                        Fer4_21  47 CssvCPv 53 
                                    C++ CP+
  gi|119720314|ref|YP_920809.1| 168 CVEACPT 174
                                    8888885 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   3.9   7.1e-08   7.9e-05       2      64 ..      19     110 ..      18     111 .. 0.61
   2 ?    5.1  12.3     0.028        32       3      17 ..     125     139 ..     123     176 .. 0.72

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 7.1e-08
                         Fer4_8   2 lekCieCgaCqsaC..............p.................vlrrtk.khlldargeaaedvqeeqvleeeealw 49 
                                    l+kCi+C aCq aC              p                  ++ +  k ll++ ge+   +q + v       +
  gi|119720314|ref|YP_920809.1|  19 LDKCIGCRACQVACkdwnsrqaekttfsPtftnppdltandwkvvfYYEGKSkKALLTPAGEVVF-EQVDVV----PLPF 93 
                                    79************555554444444441444455554444443333333333455555555444.444444....679* PP

                         Fer4_8  50 sCttcga..CtevCpvg 64 
                                    +C++c    C+++Cpvg
  gi|119720314|ref|YP_920809.1|  94 QCMHCATapCSRACPVG 110
                                    *****9999******97 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.028
                         Fer4_8   3 ekCieCgaCqsaCpv 17 
                                    e+Ci+Cg+C++aCp+
  gi|119720314|ref|YP_920809.1| 125 EECIGCGFCETACPF 139
                                    68***********94 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   3.5    0.0018         2       1      11 [.      22      32 ..      22      36 .. 0.95
   2 !   11.8   7.5   0.00035      0.39       1      15 []      95     111 ..      95     111 .. 0.90
   3 !   11.3   3.7    0.0005      0.57       1      13 [.     127     139 ..     127     141 .. 0.93
   4 !   13.3   2.8   0.00011      0.12       1      14 [.     153     175 ..     153     176 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0018
                         Fer4_3  1 CtgCgaCvevC 11
                                   C+gC+aC ++C
  gi|119720314|ref|YP_920809.1| 22 CIGCRACQVAC 32
                                   *********** PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00035
                         Fer4_3   1 CtgCg..aCvevCPvgA 15 
                                    C++C   +C ++CPvgA
  gi|119720314|ref|YP_920809.1|  95 CMHCAtaPCSRACPVGA 111
                                    ****7668********9 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.0005
                         Fer4_3   1 CtgCgaCvevCPv 13 
                                    C+gCg C+ +CP 
  gi|119720314|ref|YP_920809.1| 127 CIGCGFCETACPF 139
                                    ************6 PP

  == domain 4  score: 13.3 bits;  conditional E-value: 0.00011
                         Fer4_3   1 CtgCg.........aCvevCPvg 14 
                                    Ct C          aCve+CP+g
  gi|119720314|ref|YP_920809.1| 153 CTFCVdriqngrapACVEACPTG 175
                                    999*56788899999******98 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.6    0.0043       4.9       2      12 ..      22      32 ..      14      51 .. 0.73
   2 !    9.8   2.8    0.0014       1.5       2      27 ..      95     122 ..      94     126 .. 0.80
   3 !   10.3   2.9   0.00093         1      51      66 ..     124     139 ..     117     140 .. 0.83
   4 ?   -1.8   0.1       5.6   6.3e+03      53      62 ..     149     158 ..     141     159 .. 0.67
   5 !    9.8   0.0    0.0013       1.5       7      25 ..     167     185 ..     163     207 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0043
                        Fer4_16  2 CgtCgkCaevC 12
                                   C++C++C  +C
  gi|119720314|ref|YP_920809.1| 22 CIGCRACQVAC 32
                                   55555555555 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0014
                        Fer4_16   2 CgtCgk..CaevCPtnaikekkekeiea 27 
                                    C  C    C  +CP++aik + e  + +
  gi|119720314|ref|YP_920809.1|  95 CMHCATapCSRACPVGAIKVTPEGAVVI 122
                                    99998888***********987766655 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00093
                        Fer4_16  51 qeaitgCdiCqdvCPa 66 
                                    +e+++gC+ C+++CP+
  gi|119720314|ref|YP_920809.1| 124 KEECIGCGFCETACPF 139
                                    5789999999999998 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 5.6
                        Fer4_16  53 aitgCdiCqd 62 
                                    +++ C  C+d
  gi|119720314|ref|YP_920809.1| 149 KYYKCTFCVD 158
                                    5566777765 PP

  == domain 5  score: 9.8 bits;  conditional E-value: 0.0013
                        Fer4_16   7 kCaevCPtnaikekkekei 25 
                                    +C+e+CPt++++  k+  i
  gi|119720314|ref|YP_920809.1| 167 ACVEACPTGVFTFGKAGDI 185
                                    7**********98844443 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   2.5   1.9e-05     0.021       2      16 ..      20      34 ..      19      40 .. 0.91
   2 ?    3.2   4.2      0.14   1.6e+02       4      17 .]      95     110 ..      93     110 .. 0.92
   3 !   18.6   3.5   1.7e-06    0.0019       1      17 []     124     140 ..     124     142 .. 0.92
   4 ?    5.6   0.3     0.024        27       8      17 .]     166     175 ..     163     176 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.9e-05
                         Fer4_4  2 erCigCgsCvaaCPq 16
                                   ++CigC++C  aC++
  gi|119720314|ref|YP_920809.1| 20 DKCIGCRACQVACKD 34
                                   99***********85 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.14
                         Fer4_4   4 CigCgs..CvaaCPqg 17 
                                    C +C    C +aCP+g
  gi|119720314|ref|YP_920809.1|  95 CMHCATapCSRACPVG 110
                                    99***99*******86 PP

  == domain 3  score: 18.6 bits;  conditional E-value: 1.7e-06
                         Fer4_4   1 qerCigCgsCvaaCPqg 17 
                                    +e CigCg C+ aCP++
  gi|119720314|ref|YP_920809.1| 124 KEECIGCGFCETACPFR 140
                                    689************85 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.024
                         Fer4_4   8 gsCvaaCPqg 17 
                                    ++Cv aCP+g
  gi|119720314|ref|YP_920809.1| 166 PACVEACPTG 175
                                    58******86 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   1.7    0.0001      0.12       1      20 [.      15      34 ..      15      43 .. 0.92
   2 ?    3.9   1.9     0.079        89      57      66 .]     105     114 ..      93     114 .. 0.89
   3 !    9.3   5.5    0.0017       1.9       1      30 [.     120     150 ..     120     195 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.0001
                        Fer4_15  1 VvvDrdaCigcglCvaeape 20
                                   V vD d+Cigc +C  ++++
  gi|119720314|ref|YP_920809.1| 15 VLVDLDKCIGCRACQVACKD 34
                                   78***************986 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.079
                        Fer4_15  57 raCPvdAIrv 66 
                                    raCPv+AI v
  gi|119720314|ref|YP_920809.1| 105 RACPVGAIKV 114
                                    8*******87 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0017
                        Fer4_15   1 VvvDrdaCigcglCvaeapevfelde.dgla 30 
                                    Vv+ +++Cigcg C +++p ++   + dg+ 
  gi|119720314|ref|YP_920809.1| 120 VVISKEECIGCGFCETACPFRVPRRGsDGKY 150
                                    78999*************9888777745553 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.9      0.11   1.3e+02      84      97 ..      21      34 ..      17      45 .. 0.80
   2 ?   -1.4   1.3       2.4   2.7e+03      60      74 ..      94     110 ..      91     116 .. 0.69
   3 ?   15.1   1.9   1.8e-05      0.02      57      94 ..     123     159 ..     111     165 .. 0.84
   4 ?    1.8   0.2      0.24   2.7e+02      66      75 ..     167     176 ..     163     183 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.11
                        Fer4_18 84 eciscllcidacdk 97
                                   +ci c  c  ac++
  gi|119720314|ref|YP_920809.1| 21 KCIGCRACQVACKD 34
                                   69999999999976 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.4
                        Fer4_18  60 dcidces..cvkvcPtg 74 
                                    +c++c +  c + cP+g
  gi|119720314|ref|YP_920809.1|  94 QCMHCATapCSRACPVG 110
                                    47777544477888876 PP

  == domain 3  score: 15.1 bits;  conditional E-value: 1.8e-05
                        Fer4_18  57 gagdcidcescvkvcPtgidirkGlqleciscllcida 94 
                                    ++ +ci c++c + cP  +  r G   +  +c+ c+d 
  gi|119720314|ref|YP_920809.1| 123 SKEECIGCGFCETACPFRVP-RRGSDGKYYKCTFCVDR 159
                                    6789***************7.77888888888889886 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.24
                        Fer4_18  66 scvkvcPtgi 75 
                                    +cv+ cPtg+
  gi|119720314|ref|YP_920809.1| 167 ACVEACPTGV 176
                                    79*****997 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.8   2.6e-05     0.029       1      24 [.      17      40 ..      17      55 .. 0.85
   2 ?    1.7   2.2      0.34   3.8e+02      49      58 .]     105     114 ..      63     114 .. 0.86
   3 ?    6.9   9.2    0.0084       9.4       3      54 ..     124     175 ..     122     183 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.6e-05
                        Fer4_13  1 VDrdtCiacgaCvelaPdvFeedd 24
                                   VD d+Ci+c aC  ++ d   ++ 
  gi|119720314|ref|YP_920809.1| 17 VDLDKCIGCRACQVACKDWNSRQA 40
                                   89**************98766655 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.34
                        Fer4_13  49 daCPvesIgv 58 
                                     aCPv +I+v
  gi|119720314|ref|YP_920809.1| 105 RACPVGAIKV 114
                                    4899999987 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0084
                        Fer4_13   3 rdtCiacgaCvelaPdvFeeddeggasvvaeqptseeekadaeeAadaCPve 54 
                                    +++Ci+cg C  ++P    +   +g+++     ++  +  +a + ++aCP+ 
  gi|119720314|ref|YP_920809.1| 124 KEECIGCGFCETACPFRVPRRGSDGKYYKCTFCVDRIQNGRAPACVEACPTG 175
                                    79*************9999999999999988888888888888888999985 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   3.9     0.013        14      44      56 ..      20      32 ..      11      35 .. 0.84
   2 ?    2.2  14.2      0.24   2.7e+02       1      58 [.      21     109 ..      21     111 .. 0.64
   3 ?    2.7  13.4      0.16   1.8e+02      43      59 ..     124     140 ..      94     142 .. 0.61
   4 ?    4.5  10.1     0.044        50       2      15 ..     127     140 ..     126     196 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.013
                        Fer4_17 44 slCieCgeCerkC 56
                                   ++Ci+C+ C+ +C
  gi|119720314|ref|YP_920809.1| 20 DKCIGCRACQVAC 32
                                   6899999999988 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.24
                        Fer4_17   1 rCiqCgyClpeCpsyea...........ydnepkkllraakl................glleeaeke.........ekas 44 
                                    +Ci+C++C  +C   +              n p+ +++++k+                g       e         +   
  gi|119720314|ref|YP_920809.1|  21 KCIGCRACQVACKDWNSrqaekttfsptFTNPPDLTANDWKVvfyyegkskkalltpaG-------EvvfeqvdvvPLPF 93 
                                    6************7555233344444444456777777777788877655544444331.......0444444455899* PP

                        Fer4_17  45 lCieCge..CerkCPq 58 
                                    +C++C    C+r+CP 
  gi|119720314|ref|YP_920809.1|  94 QCMHCATapCSRACPV 109
                                    *****8555*****96 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.16
                        Fer4_17  43 aslCieCgeCerkCPqg 59 
                                     ++Ci+Cg Ce++CP  
  gi|119720314|ref|YP_920809.1| 124 KEECIGCGFCETACPFR 140
                                    46899999999999976 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.044
                        Fer4_17   2 CiqCgyClpeCpsy 15 
                                    Ci+Cg+C+ +Cp+ 
  gi|119720314|ref|YP_920809.1| 127 CIGCGFCETACPFR 140
                                    67777777767653 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1825.62
//
Query:       gi|119720315|ref|YP_920810.1|  [L=240]
Description: formate dehydrogenase, cytochrome b556 subunit (formate dehydrogenase gamma subunit) [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-13   50.4   9.6    2.2e-13   50.2   9.6    1.0  1  Ni_hydr_CYTB  Prokaryotic cytochrome b561


Domain annotation for each model (and alignments):
>> Ni_hydr_CYTB  Prokaryotic cytochrome b561
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.2   9.6   1.2e-17   2.2e-13       3     181 ..      11     214 ..       9     215 .. 0.84

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 1.2e-17
                                    ---TTHHHHHHHHHHHHHHHHHHHHHS------S-GGG-..................HHHHHHHHHHHHHHHHHHHHHHH CS
                   Ni_hydr_CYTB   3 slvarllHWlnallvvllllsgllianlhprlywgdsgk..................aralHklaGlvllalllfrllwl 64 
                                    s+  r+ H  n  ++ +l ++gl  + l+ +++++ +++                  +r lH+++G+++ +ll+++ ++l
  gi|119720315|ref|YP_920810.1|  11 SKSYRIAHTHNLHFIAILSVTGLTVMALEYFSWLAYVVGlpfapllgvdpvtagvqiFRVLHRIFGVAWGGLLVVYGCYL 90 
                                    5678*****************************999999***************9999999******************* PP

                                    .........------------STTTSSSSS----------------TT.....THHHHHHHHHHHHHHHHHHHTHHHHHH CS
                   Ni_hydr_CYTB  65 .........kkakkpspriifrqikrdltlllrgrkpeagknnplqkl.....vhlllyvllvvliltGlllsfaatagf 130
                                                kkp +++ +++   + + ll ++ pe   + +  +      +++ll v +++l+++G+ l+      +
  gi|119720315|ref|YP_920810.1|  91 fcsgkarvfDPLKKPLRDQLKEASSLAKHYLLGKPIPEEVLEKMERHNvfvsyLAILLGVGFALLAVSGVGLML--RYAL 168
                                    ****9666666666666666666666666666666666666666666699999999999999999999999965..2335 PP

                                    HH...HTS-THHHHHHH.HHHHHHH.HHHHHHHHHHHHHHH---XXXXXXXX CS
                   Ni_hydr_CYTB 131 plllddkggaqlarelHellaaall.afvvlHiaaallhgpvkkdtlrrMit 181
                                    +l   + + a+++ +lH  l++++  +fv+ H++aa+    +   +l +M++
  gi|119720315|ref|YP_920810.1| 169 GL---TAQQAAILLFLH-DLGFGITvLFVLFHLFAAFHPSNRP--LLDAMFG 214
                                    55...************.66666655***********999876..9999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1898.77
//
Query:       gi|119720316|ref|YP_920811.1|  [L=209]
Description: hypothetical protein Tpen_1411 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-06   28.3   0.7    1.8e-06   28.1   0.7    1.1  1  FdhE             Protein involved in formate dehydrogenase fo
     0.0024   18.2   4.6        8.3    7.0   0.1    3.4  3  zf-H2C2_2        Zinc-finger double domain
     0.0032   17.4  10.4     0.0093   15.9   2.8    2.9  3  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
  ------ inclusion threshold ------
      0.015   15.2   6.8      0.027   14.4   1.0    2.8  3  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.025   14.9   0.8      0.075   13.4   0.1    2.0  2  DUF3268          zinc-finger-containing domain
      0.033   14.5   2.8        7.6    6.9   0.0    3.2  3  zinc_ribbon_9    zinc-ribbon
      0.039   13.3   4.9        0.8    9.1   0.2    3.1  4  zf-TFIIB         Transcription factor zinc-finger
      0.043   13.7   5.1        3.6    7.6   0.1    3.8  3  Nudix_N_2        Nudix N-terminal
      0.049   13.2   8.4        3.4    7.3   4.0    3.2  3  TF_Zn_Ribbon     TFIIB zinc-binding
      0.064   13.3   5.6       0.13   12.3   3.3    2.4  2  CpXC             CpXC protein
      0.068   13.2   4.8       0.83    9.7   3.1    2.4  2  Elf1             Transcription elongation factor Elf1 like
      0.089   12.2  10.2          6    6.4   0.4    3.7  3  zf-ribbon_3      zinc-ribbon domain
        0.1   12.6   7.4       0.93    9.5   4.0    3.1  2  HypA             Hydrogenase/urease nickel incorporation, met
        0.2   11.3   1.4       0.93    9.2   0.0    2.4  3  DUF2225          Uncharacterized protein conserved in bacteri
       0.21   12.0  10.2       0.44   10.9   0.5    2.8  3  Lar_restr_allev  Restriction alleviation protein Lar
       0.34   11.5   4.3        1.9    9.1   0.6    2.7  3  Trm112p          Trm112p-like protein
       0.77    9.8   8.4       0.24   11.4   1.2    2.5  2  Ogr_Delta        Ogr/Delta-like zinc finger
       0.86    9.7   8.5         16    5.6   7.7    2.7  1  DZR              Double zinc ribbon
       0.92    9.3   8.7       0.67    9.8   0.5    3.3  3  zf-HYPF          HypF finger
        1.9    8.4   6.6         39    4.2   0.2    3.5  3  TFIIS_C          Transcription factor S-II (TFIIS)
        2.1    8.4   8.5         14    5.8   0.2    3.6  4  Rubredoxin       Rubredoxin
        2.5    8.3   6.9        6.7    6.9   2.5    2.7  3  zf-Mss51         Zinc-finger of mitochondrial splicing suppre
        2.5    8.3  13.0         15    5.8   1.2    3.8  3  Zn-ribbon_8      Zinc ribbon domain
        4.9    6.9  10.3         21    4.9   0.6    3.4  3  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
        6.6    6.6  12.6         22    4.9   1.6    3.8  3  zinc_ribbon_2    zinc-ribbon domain
        8.4    7.1   8.1         65    4.3   0.8    3.6  3  zf-C2H2          Zinc finger, C2H2 type


Domain annotation for each model (and alignments):
>> FdhE  Protein involved in formate dehydrogenase formation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.7   2.6e-09   1.8e-06     107     241 ..      37     170 ..      12     178 .. 0.81

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 2.6e-09
                                    HHHHHH--HHHHHHHHHHHHTT-GGGS-GGGHHHHHHHHHHHHHHHHHT--TTSSS-.-TT-SS-TTT---EEEEEEE-- CS
                           FdhE 107 lerlrkadaeelealadallageleavdaakavfvaaAlqvvwtklaaaldakalaelaeekglCPvCgsaPvasvvrig 186
                                    ++rl k   ++ e+ ++  +a++ e v++a+a+ v   l+ +++k+++al+   +++ +     CPvCg aP+  +++ +
  gi|119720316|ref|YP_920811.1|  37 VRRLPKPVLRSFEEPLAGNVANRDEVVREAEALGVGEELSDYVVKRVTALEFGWVKPRG---LKCPVCGQAPSLVLLEEE 113
                                    55555554455555555556677788999999999999999999999999999997755...47********99999887 PP

                                    --..---EEEEEETTT--EEE--TTS-TTT---SS-EEE------C-EEEEEETTTT CS
                           FdhE 187 ge..aeglRylhCslCeteWhvvRvkCsnCeetkelaylsledekaavkAesCdeCh 241
                                     +   ++ R  +  +C  e ++ R +C +C+++ + ++    +++ + k ++C +C 
  gi|119720316|ref|YP_920811.1| 114 PSvgFAKQRAKARCICGYEREFERFTCPSCGSAGRQNFEVYVSRRTHAKLFVCRNCG 170
                                    641135678888889************************999999999********6 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1     0.059        41      14      22 ..      93     103 ..      91     104 .. 0.74
   2 ?    7.0   0.1     0.012       8.3      14      23 ..     136     146 ..     132     149 .. 0.77
   3 ?    6.7   0.1     0.015        10      13      24 ..     162     173 ..     157     175 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.059
                      zf-H2C2_2  14 p..yeCplCdk 22 
                                    p  ++Cp+C+ 
  gi|119720316|ref|YP_920811.1|  93 PrgLKCPVCGQ 103
                                    4458*****86 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.012
                      zf-H2C2_2  14 p.yeCplCdka 23 
                                    + ++Cp+C+ a
  gi|119720316|ref|YP_920811.1| 136 ErFTCPSCGSA 146
                                    449*****976 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.015
                      zf-H2C2_2  13 kpyeCplCdkaF 24 
                                    k + C  C++aF
  gi|119720316|ref|YP_920811.1| 162 KLFVCRNCGYAF 173
                                    5699*******9 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1       8.1   5.6e+03       4      12 ..      17      25 ..      16      27 .. 0.77
   2 ?    5.8   0.1     0.019        13      16      28 ..      93     106 ..      85     128 .. 0.78
   3 !   15.9   2.8   1.3e-05    0.0093      18      45 ..     137     171 ..     133     172 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 8.1
                  Zn_Tnp_IS1595  4 eearalLea 12
                                   ee++++L +
  gi|119720316|ref|YP_920811.1| 17 EECKQALRE 25
                                   789998876 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.019
                  Zn_Tnp_IS1595  16 pngfvCPhCgsr.k 28 
                                    p g  CP Cg + +
  gi|119720316|ref|YP_920811.1|  93 PRGLKCPVCGQApS 106
                                    45689*****8755 PP

  == domain 3  score: 15.9 bits;  conditional E-value: 1.3e-05
                  Zn_Tnp_IS1595  18 gfvCPhCgsr.....kayrikt..rglfqCkeCrk 45 
                                    +f+CP Cgs+     ++y  ++  ++lf C+ C++
  gi|119720316|ref|YP_920811.1| 137 RFTCPSCGSAgrqnfEVYVSRRthAKLFVCRNCGY 171
                                    79********99888888777789*********97 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1      0.26   1.8e+02      45      53 ..      94     102 ..      90     105 .. 0.65
   2 ?    2.0   1.1       0.3   2.1e+02      30      53 ..      97     130 ..      94     137 .. 0.61
   3 ?   14.4   1.0   3.9e-05     0.027      30      55 ..     139     172 ..     136     174 .. 0.94

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.26
                 OrfB_Zn_ribbon  45 rtfkCpnCg 53 
                                    r +kCp Cg
  gi|119720316|ref|YP_920811.1|  94 RGLKCPVCG 102
                                    666666666 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.3
                 OrfB_Zn_ribbon  30 tCseCgsknke...........alsgrtfkCpnCg 53 
                                    +C++Cg+  +            a+++ + +C  Cg
  gi|119720316|ref|YP_920811.1|  97 KCPVCGQAPSLvlleeepsvgfAKQRAKARCI-CG 130
                                    68999886555444445555555555555555.55 PP

  == domain 3  score: 14.4 bits;  conditional E-value: 3.9e-05
                 OrfB_Zn_ribbon  30 tCseCgsknke........alsgrtfkCpnCgfe 55 
                                    tC+ Cgs +++        + + ++f+C+nCg+ 
  gi|119720316|ref|YP_920811.1| 139 TCPSCGSAGRQnfevyvsrRTHAKLFVCRNCGYA 172
                                    8****************999999*********86 PP

>> DUF3268  zinc-finger-containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       2.9     2e+03       4      14 ..      97     107 ..      94     127 .. 0.82
   2 ?   13.4   0.1   0.00011     0.075       4      37 ..     139     170 ..     136     187 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 2.9
                        DUF3268   4 rCpyCGekvil 14 
                                    +Cp CG++  l
  gi|119720316|ref|YP_920811.1|  97 KCPVCGQAPSL 107
                                    79999987554 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00011
                        DUF3268   4 rCpyCGekvilvsaseiYkerskgkllylCpkCd 37 
                                    +Cp CG++   +++ e+Y +r++++ l++C++C+
  gi|119720316|ref|YP_920811.1| 139 TCPSCGSA--GRQNFEVYVSRRTHAKLFVCRNCG 170
                                    7*****86..68999******************8 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1       1.3   9.1e+02      22      29 ..      97     103 ..      90     104 .. 0.78
   2 ?    5.4   0.1     0.031        22      23      29 ..     139     145 ..     131     147 .. 0.77
   3 ?    6.9   0.0     0.011       7.6      12      33 ..     153     175 ..     150     176 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.3
                  zinc_ribbon_9  22 vlCPhCgg 29 
                                    + CP Cg+
  gi|119720316|ref|YP_920811.1|  97 K-CPVCGQ 103
                                    4.****96 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.031
                  zinc_ribbon_9  23 lCPhCgg 29 
                                    +CP+Cg+
  gi|119720316|ref|YP_920811.1| 139 TCPSCGS 145
                                    7****98 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.011
                  zinc_ribbon_9  12 Vsvspdedsdv.lCPhCgggFVE 33 
                                    V vs+++++   +C +Cg  F+E
  gi|119720316|ref|YP_920811.1| 153 VYVSRRTHAKLfVCRNCGYAFLE 175
                                    7777777777557*********9 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0         4   2.7e+03       5      13 ..      19      27 ..      18      34 .. 0.71
   2 ?    5.0   0.2     0.022        15       1      10 [.      97     106 ..      97     114 .. 0.78
   3 ?    9.1   0.2    0.0012       0.8       2      26 ..     140     170 ..     139     175 .. 0.91
   4 ?   -3.3   0.0       8.4   5.8e+03       9      18 ..     181     190 ..     179     191 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 4
                       zf-TFIIB  5 Cqdeleese 13
                                   C+++l+e+ 
  gi|119720316|ref|YP_920811.1| 19 CKQALREVY 27
                                   999999875 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.022
                       zf-TFIIB   1 kCPkCqdele 10 
                                    kCP+C++++ 
  gi|119720316|ref|YP_920811.1|  97 KCPVCGQAPS 106
                                    8****98764 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0012
                       zf-TFIIB   2 CPkCqdele......eserggveidyCpqCr 26 
                                    CP+C+++ +       s+r + ++++C +C+
  gi|119720316|ref|YP_920811.1| 140 CPSCGSAGRqnfevyVSRRTHAKLFVCRNCG 170
                                    ******9999998988999***********7 PP

  == domain 4  score: -3.3 bits;  conditional E-value: 8.4
                       zf-TFIIB   9 leeserggve 18 
                                    l ese++gv+
  gi|119720316|ref|YP_920811.1| 181 LSESELQGVH 190
                                    6789999987 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1      0.17   1.1e+02       3      12 ..      98     107 ..      98     114 .. 0.74
   2 ?    7.6   0.1    0.0052       3.6      20      29 ..     135     144 ..     132     146 .. 0.86
   3 ?    3.1   0.1      0.13        90      24      30 ..     165     171 ..     164     174 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.17
                                    -TTT--B-EE CS
                      Nudix_N_2   3 CsqCGtpvel 12 
                                    C+ CG++ +l
  gi|119720316|ref|YP_920811.1|  98 CPVCGQAPSL 107
                                    9999998655 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0052
                                    S-EEEETTTT CS
                      Nudix_N_2  20 reRlvCpaCg 29 
                                     eR++Cp+Cg
  gi|119720316|ref|YP_920811.1| 135 FERFTCPSCG 144
                                    58*******9 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.13
                                    EETTTTE CS
                      Nudix_N_2  24 vCpaCgt 30 
                                    vC +Cg+
  gi|119720316|ref|YP_920811.1| 165 VCRNCGY 171
                                    8999987 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1      0.01       7.2       2      11 ..      97     107 ..      96     115 .. 0.73
   2 ?    5.5   0.7     0.018        12      20      27 ..     138     145 ..     128     150 .. 0.77
   3 ?    7.3   4.0     0.005       3.4       1      27 [.     138     171 ..     138     176 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.01
                                    EETTTTCEE.C CS
                   TF_Zn_Ribbon   2 kCPnCgstn.l 11 
                                    kCP+Cg    l
  gi|119720316|ref|YP_920811.1|  97 KCPVCGQAPsL 107
                                    9*****85445 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.018
                                    EEESSSSB CS
                   TF_Zn_Ribbon  20 lvCtdCGl 27 
                                    ++C++CG+
  gi|119720316|ref|YP_920811.1| 138 FTCPSCGS 145
                                    67777775 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.005
                                    EEETTTTCEE.C.....HEETSTTCE.EESSSSB CS
                   TF_Zn_Ribbon   1 ykCPnCgstn.l.....veDpergel.vCtdCGl 27 
                                    ++CP Cgs   +     v    ++ l vC +CG+
  gi|119720316|ref|YP_920811.1| 138 FTCPSCGSAGrQnfevyVSRRTHAKLfVCRNCGY 171
                                    68******7756889997777777777*****96 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   3.3   0.00019      0.13       1      63 [.      96     163 ..      96     168 .. 0.73
   2 ?    0.5   0.1      0.86     6e+02      37      47 ..     163     173 ..     158     177 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00019
                           CpXC   1 ltCpaCgkefea...eiwtsidadedpelkekl..ldgslfeatCpkCgatakleapllyhdpekell 63 
                                    l+Cp Cg+  +    e ++s+  +++   +  +   + ++ ++tCp+Cg  ++ ++++ + ++++  l
  gi|119720316|ref|YP_920811.1|  96 LKCPVCGQAPSLvllEEEPSVGFAKQRAKARCIcgYEREFERFTCPSCGSAGRQNFEVYVSRRTHAKL 163
                                    578888877664111445677777777777777555789******************99988877655 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.86
                           CpXC  37 eatCpkCgata 47 
                                     ++C +Cg+ +
  gi|119720316|ref|YP_920811.1| 163 LFVCRNCGYAF 173
                                    689****9976 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.4      0.18   1.2e+02      22      48 ..      96     127 ..      91     136 .. 0.55
   2 ?    9.7   3.1    0.0012      0.83      20      55 ..     136     173 ..     120     184 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.18
                           Elf1  22 FdCpfCnheksvevkldkkek......iaevsC 48 
                                     +Cp+C++  s+   l+++ +      +a+++C
  gi|119720316|ref|YP_920811.1|  96 LKCPVCGQAPSLVL-LEEEPSvgfakqRAKARC 127
                                    68999998866532.222222233333566666 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0012
                           Elf1  20 tkFdCpfCnhe..ksvevkldkkekiaevsCkvCgesf 55 
                                    ++F+Cp C++   +  ev ++++++     C++Cg  f
  gi|119720316|ref|YP_920811.1| 136 ERFTCPSCGSAgrQNFEVYVSRRTHAKLFVCRNCGYAF 173
                                    68******99632679999****99*********9754 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.2    0.0088       6.1       4      11 ..      97     105 ..      91     107 .. 0.85
   2 ?    6.4   0.4    0.0087         6       4      10 ..     139     145 ..     137     147 .. 0.74
   3 ?    4.1   0.4     0.047        32      18      24 ..     165     171 ..     165     173 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0088
                    zf-ribbon_3   4 rCPnCGa.p 11 
                                    +CP CG+ p
  gi|119720316|ref|YP_920811.1|  97 KCPVCGQaP 105
                                    799999866 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0087
                    zf-ribbon_3   4 rCPnCGa 10 
                                    +CP+CG+
  gi|119720316|ref|YP_920811.1| 139 TCPSCGS 145
                                    5777775 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.047
                    zf-ribbon_3  18 vCpyCGt 24 
                                    vC +CG+
  gi|119720316|ref|YP_920811.1| 165 VCRNCGY 171
                                    7*****8 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   4.0    0.0014      0.93      64      96 ..     118     147 ..      55     159 .. 0.88
   2 ?    1.3   0.1      0.47   3.3e+02      70      80 ..     163     173 ..     152     183 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0014
                                    EEEE--EEEETTTS-EEECHHHHHS-TTTSSS- CS
                           HypA  64 ieevpvkvrCreCgkefeleekalrCpkCgsad 96 
                                    + ++++k+rC  Cg+e e e  +++Cp+Cgsa+
  gi|119720316|ref|YP_920811.1| 118 FAKQRAKARCI-CGYEREFE--RFTCPSCGSAG 147
                                    67889999**5.**999987..479*****986 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.47
                                    EEEETTTS-EE CS
                           HypA  70 kvrCreCgkef 80 
                                     + Cr+Cg+ f
  gi|119720316|ref|YP_920811.1| 163 LFVCRNCGYAF 173
                                    46788888765 PP

>> DUF2225  Uncharacterized protein conserved in bacteria (DUF2225)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.2         1   7.2e+02       6      13 ..      96     103 ..      93     107 .. 0.82
   2 ?   -1.0   0.1       1.7   1.2e+03      50      60 ..     139     149 ..     133     164 .. 0.62
   3 ?    9.2   0.0    0.0014      0.93      48      83 ..     163     198 ..     149     206 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1
                        DUF2225   6 ieCPvCee 13 
                                    ++CPvC +
  gi|119720316|ref|YP_920811.1|  96 LKCPVCGQ 103
                                    68****75 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.7
                        DUF2225  50 vCpkCgYaalk 60 
                                    +Cp+Cg a  +
  gi|119720316|ref|YP_920811.1| 139 TCPSCGSAGRQ 149
                                    57777744443 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0014
                        DUF2225  48 vvvCpkCgYaalkkdfeklskeekeklkekiskkwk 83 
                                    + vC +CgYa+l+   + ls+ e + ++++i+  +k
  gi|119720316|ref|YP_920811.1| 163 LFVCRNCGYAFLEIPRNGLSESELQGVHASIRLVLK 198
                                    68***********99999999999999888876666 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       9.8   6.7e+03       9      23 ..      13      27 ..      12      30 .. 0.70
   2 ?    4.8   5.2     0.052        36       5      35 ..      97     144 ..      95     145 .. 0.74
   3 ?   10.9   0.5   0.00064      0.44       5      36 ..     139     171 ..     136     188 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 9.8
                Lar_restr_allev  9 Cggravlersqrvva 23
                                   Cgg ++ +++ r v+
  gi|119720316|ref|YP_920811.1| 13 CGGSEECKQALREVY 27
                                   888888777666655 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.052
                Lar_restr_allev   5 pCPfCggravlersqrvvaeigq..................cvyCadCg 35 
                                     CP Cg+++ l+  +  ++ +g+                   ++C  Cg
  gi|119720316|ref|YP_920811.1|  97 KCPVCGQAPSLVLLEEEPS-VGFakqrakarcicgyerefeRFTCPSCG 144
                                    6********9887666665.44456788888888888888877887777 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00064
                Lar_restr_allev   5 pCPfCggravlersqrvvaeigq.cvyCadCga 36 
                                     CP Cg+++   ++ +v+       + C +Cg+
  gi|119720316|ref|YP_920811.1| 139 TCPSCGSAGRQNFEVYVSRRTHAkLFVCRNCGY 171
                                    5*******9888887777654447********9 PP

>> Trm112p  Trm112p-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       6.4   4.4e+03      16      16 ..      51      51 ..      16      87 .. 0.48
   2 ?    9.1   0.6    0.0028       1.9       8      61 ..      96     145 ..      95     146 .. 0.91
   3 ?    2.8   0.1      0.27   1.8e+02      54      63 ..     164     173 ..     154     174 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 6.4
                                   C CS
                        Trm112p 16 p 16
                                   p
  gi|119720316|ref|YP_920811.1| 51 P 51
                                   1 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0028
                                    -B-TTTHH..C--HHHHHHHHH.TT---.S-SS----SCHHTTEECCCCEEEETTTTE CS
                        Trm112p   8 LaCpackg..pLdwealvevaa.lglne.lpkekpedyellleldieegeLvCpncgr 61 
                                    L+Cp+c +   L   +l+e++  +g+++  +k+++ +      +++e + ++Cp+cg 
  gi|119720316|ref|YP_920811.1|  96 LKCPVCGQapSL---VLLEEEPsVGFAKqRAKARCICG-----YEREFERFTCPSCGS 145
                                    89*******999...99****99999998889988877.....79***********96 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.27
                                    EEETTTTEEE CS
                        Trm112p  54 LvCpncgraY 63 
                                    +vC+ncg a+
  gi|119720316|ref|YP_920811.1| 164 FVCRNCGYAF 173
                                    79*****998 PP

>> Ogr_Delta  Ogr/Delta-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   1.0      0.31   2.2e+02       1       7 [.      97     103 ..      97     106 .. 0.86
   2 ?   11.4   1.2   0.00034      0.24       1      37 [.     139     173 ..     139     175 .. 0.96

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.31
                      Ogr_Delta   1 rCPhCga 7  
                                    +CP Cg+
  gi|119720316|ref|YP_920811.1|  97 KCPVCGQ 103
                                    6*****7 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00034
                      Ogr_Delta   1 rCPhCgapaaartsrnlskdvreryyqCsnfeCgatf 37 
                                    +CP Cg++ +     + s+ +    ++C+n  Cg+ f
  gi|119720316|ref|YP_920811.1| 139 TCPSCGSAGRQNFEVYVSRRTHAKLFVCRN--CGYAF 173
                                    6*****************************..**988 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   7.7     0.023        16      15      49 .]      98     170 ..      91     177 .. 0.51

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.023
                            DZR  15 CseCgtklkavaa..........................edrCpsCgekvdpearf............CpeCG 49 
                                    C+ Cg++++ v                              +CpsCg++  +++++            C +CG
  gi|119720316|ref|YP_920811.1|  98 CPVCGQAPSLVLLeeepsvgfakqrakarcicgyerefeRFTCPSCGSAGRQNFEVyvsrrthaklfvCRNCG 170
                                    6666666332222334446666666644444444444444445555554444444444444444444444444 PP

>> zf-HYPF  HypF finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.2      0.64   4.4e+02      24      28 ..      98     102 ..      95     108 .. 0.78
   2 ?    2.1   0.2      0.25   1.7e+02      23      28 ..     139     144 ..     135     146 .. 0.83
   3 ?    9.8   0.5   0.00096      0.67      14      28 ..     156     170 ..     148     173 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.64
                                    -TTTS CS
                        zf-HYPF  24 CtnCG 28 
                                    C+ CG
  gi|119720316|ref|YP_920811.1|  98 CPVCG 102
                                    ****9 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.25
                                    --TTTS CS
                        zf-HYPF  23 sCtnCG 28 
                                    +C++CG
  gi|119720316|ref|YP_920811.1| 139 TCPSCG 144
                                    799999 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.00096
                                    STTTT-TT---TTTS CS
                        zf-HYPF  14 dRRfhaqfisCtnCG 28 
                                    +RR ha    C nCG
  gi|119720316|ref|YP_920811.1| 156 SRRTHAKLFVCRNCG 170
                                    7*************9 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1      0.22   1.5e+02       2       8 ..      97     103 ..      96     107 .. 0.86
   2 ?    3.6   0.2     0.089        62       1       8 [.     138     145 ..     138     150 .. 0.83
   3 ?    4.2   0.2     0.057        39      28      38 ..     163     173 ..     160     174 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.22
                        TFIIS_C   2 kCpkCgs 8  
                                    kCp Cg+
  gi|119720316|ref|YP_920811.1|  97 KCPVCGQ 103
                                    8****97 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.089
                        TFIIS_C   1 akCpkCgs 8  
                                    ++Cp+Cgs
  gi|119720316|ref|YP_920811.1| 138 FTCPSCGS 145
                                    58999997 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.057
                        TFIIS_C  28 fykCtkCghrW 38 
                                     ++C +Cg+ +
  gi|119720316|ref|YP_920811.1| 163 LFVCRNCGYAF 173
                                    589****9976 PP

>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.4      0.16   1.1e+02      32      41 ..      93     102 ..      92     106 .. 0.76
   2 ?   -2.1   0.1         6   4.1e+03       3      10 ..     126     132 ..     124     138 .. 0.78
   3 ?    5.8   0.2     0.021        14      34      47 .]     137     151 ..     131     151 .. 0.76
   4 ?    3.1   0.0      0.14        99       2      11 ..     164     173 ..     163     187 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.16
                                    -TT-BBTTTB CS
                     Rubredoxin  32 PddWvCPdCg 41 
                                    P   +CP+Cg
  gi|119720316|ref|YP_920811.1|  93 PRGLKCPVCG 102
                                    5667899998 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 6
                                    EETTT-BE CS
                     Rubredoxin   3 eCkvCgyv 10 
                                    +C +Cgy+
  gi|119720316|ref|YP_920811.1| 126 RC-ICGYE 132
                                    67.89995 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.021
                                    T-BBTTTB-B.GGGE CS
                     Rubredoxin  34 dWvCPdCgve.keqF 47 
                                     ++CP+Cg   +++F
  gi|119720316|ref|YP_920811.1| 137 RFTCPSCGSAgRQNF 151
                                    699****75436666 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.14
                                    EEETTT-BEE CS
                     Rubredoxin   2 yeCkvCgyvY 11 
                                    + C+ Cgy +
  gi|119720316|ref|YP_920811.1| 164 FVCRNCGYAF 173
                                    68******87 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.58     4e+02      17      23 ..      96     102 ..      92     109 .. 0.79
   2 ?    6.9   2.5    0.0097       6.7       1      24 [.      97     145 ..      97     162 .. 0.87
   3 ?    2.6   0.2      0.21   1.5e+02      16      25 ..     163     172 ..     149     174 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.58
                       zf-Mss51  17 feCpdCG 23 
                                    ++Cp CG
  gi|119720316|ref|YP_920811.1|  96 LKCPVCG 102
                                    6799998 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0097
                       zf-Mss51   1 lCPvpkhkqt.........................apkhvdfeCpdCGi 24 
                                    +CPv+ +  +                         +++  +f+Cp CG 
  gi|119720316|ref|YP_920811.1|  97 KCPVCGQAPSlvlleeepsvgfakqrakarcicgyEREFERFTCPSCGS 145
                                    5999987777999999999999999999999999999999********6 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.21
                       zf-Mss51  16 dfeCpdCGip 25 
                                     f C +CG+ 
  gi|119720316|ref|YP_920811.1| 163 LFVCRNCGYA 172
                                    599*****96 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1     0.055        38      28      34 ..      97     103 ..      87     107 .. 0.79
   2 ?    5.8   1.2     0.022        15      28      36 ..     139     147 ..     126     151 .. 0.73
   3 ?    4.5   0.3     0.054        37       6      16 ..     164     174 ..     163     186 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.055
                    Zn-ribbon_8  28 aCPeCgs 34 
                                    +CP Cg+
  gi|119720316|ref|YP_920811.1|  97 KCPVCGQ 103
                                    6****98 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.022
                    Zn-ribbon_8  28 aCPeCgsev 36 
                                    +CP+Cgs+ 
  gi|119720316|ref|YP_920811.1| 139 TCPSCGSAG 147
                                    5*****965 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.054
                    Zn-ribbon_8   6 YrCeeCghefe 16 
                                    + C++Cg  f 
  gi|119720316|ref|YP_920811.1| 164 FVCRNCGYAFL 174
                                    79*****9985 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.6     0.031        21       3      11 ..      94     102 ..      92     103 .. 0.89
   2 ?    3.3   0.2     0.095        65       3      12 ..     136     145 ..     134     152 .. 0.72
   3 ?    3.9   0.3     0.065        45      21      28 ..     163     170 ..     163     170 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.031
                        zf-RRN7   3 kgppCgvCg 11 
                                    +g  C+vCg
  gi|119720316|ref|YP_920811.1|  94 RGLKCPVCG 102
                                    7999****9 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.095
                        zf-RRN7   3 kgppCgvCgc 12 
                                     ++ C+ Cg+
  gi|119720316|ref|YP_920811.1| 136 ERFTCPSCGS 145
                                    6778888887 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.065
                        zf-RRN7  21 fyyCrrCh 28 
                                    +++Cr+C+
  gi|119720316|ref|YP_920811.1| 163 LFVCRNCG 170
                                    59*****8 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.4      0.12        86       1       6 [.      97     102 ..      97     104 .. 0.63
   2 ?    4.9   1.6     0.032        22      13      21 ..     136     145 ..     129     147 .. 0.66
   3 ?    4.4   0.2     0.049        33      16      21 ..     166     171 ..     161     173 .. 0.67

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.12
                  zinc_ribbon_2   1 fCpnCG 6  
                                    +Cp CG
  gi|119720316|ref|YP_920811.1|  97 KCPVCG 102
                                    566666 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.032
                  zinc_ribbon_2  13 akF.CpyCGt 21 
                                    ++F Cp CG+
  gi|119720316|ref|YP_920811.1| 136 ERFtCPSCGS 145
                                    5666888875 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.049
                  zinc_ribbon_2  16 CpyCGt 21 
                                    C +CG+
  gi|119720316|ref|YP_920811.1| 166 CRNCGY 171
                                    555555 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1      0.31   2.1e+02       2       8 ..      97     103 ..      96     104 .. 0.85
   2 ?    2.8   0.1      0.28   1.9e+02       1       8 [.     138     145 ..     138     161 .. 0.78
   3 ?    4.3   0.8     0.094        65       1      10 [.     164     173 ..     164     173 .. 0.94

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.31
                                    EETTTTE CS
                        zf-C2H2   2 kCpdCgk 8  
                                    kCp+Cg+
  gi|119720316|ref|YP_920811.1|  97 KCPVCGQ 103
                                    8****96 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.28
                                    EEETTTTE CS
                        zf-C2H2   1 ykCpdCgk 8  
                                    ++Cp Cg 
  gi|119720316|ref|YP_920811.1| 138 FTCPSCGS 145
                                    89****94 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.094
                                    EEETTTTEEE CS
                        zf-C2H2   1 ykCpdCgksF 10 
                                    ++C  Cg+ F
  gi|119720316|ref|YP_920811.1| 164 FVCRNCGYAF 173
                                    89*****998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       701  (0.0390987); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        37  (0.0020637); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1409.40
//
Query:       gi|119720317|ref|YP_920812.1|  [L=182]
Description: 4Fe-4S ferredoxin iron-sulfur binding domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      8e-13   47.9  27.7    2.9e-06   27.1   1.9    4.2  4  Fer4_6    4Fe-4S binding domain
    4.8e-12   45.8  49.5    1.5e-06   28.2  13.1    2.8  3  Fer4_9    4Fe-4S dicluster domain
    2.6e-11   43.5  11.8    2.6e-11   43.5  11.8    1.6  1  Fer4_11   4Fe-4S dicluster domain
    1.1e-09   38.8  25.2    1.5e-05   25.5  12.5    3.7  4  Fer4_7    4Fe-4S dicluster domain
    1.5e-08   34.3  30.9    5.9e-05   22.9   3.2    4.2  4  Fer4_2    4Fe-4S binding domain
    1.2e-07   31.8  21.0    5.7e-05   23.2   7.5    3.4  3  Fer4_21   4Fe-4S dicluster domain
    1.2e-06   28.5  25.9    0.00039   20.5  12.2    3.3  4  Fer4_10   4Fe-4S dicluster domain
    1.9e-06   27.4  12.8    5.2e-06   26.0   3.6    5.0  6  Fer4      4Fe-4S binding domain
    1.8e-05   24.9  30.0    0.00056   20.2   2.0    4.4  4  Fer4_4    4Fe-4S binding domain
    0.00014   22.6  40.0      0.013   16.4   5.7    4.4  4  Fer4_3    4Fe-4S binding domain
  ------ inclusion threshold ------
      0.018   16.0   3.4      0.018   16.0   3.4    4.1  4  Fer4_16   4Fe-4S double cluster binding domain
      0.064   13.8   3.1      0.064   13.8   3.1    4.1  5  Fer4_17   4Fe-4S dicluster domain
       0.24   12.1  16.0          1   10.1   9.3    3.3  2  Fer4_15   4Fe-4S single cluster domain
        3.4    8.2  29.6        6.8    7.2  20.6    3.5  3  Fer4_8    4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.5   1.2e-05     0.016       5      20 ..      25      40 ..      21      46 .. 0.85
   2 !   13.8   1.8   3.7e-05     0.047       5      24 .]      64      86 ..      60      86 .. 0.84
   3 !   27.1   1.9   2.3e-09   2.9e-06       2      20 ..      95     113 ..      94     119 .. 0.89
   4 !    7.7   2.5     0.003       3.9       9      21 ..     129     144 ..     128     150 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.2e-05
                         Fer4_6  5 dpdkCigCgdCvrvCP 20
                                   d+ +C gC+ C+++C 
  gi|119720317|ref|YP_920812.1| 25 DYLRCSGCRLCEVACS 40
                                   6779***********6 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 3.7e-05
                         Fer4_6  5 d.pdkCigCgd..CvrvCPegai 24
                                   d p +C +C+d  Cv++C + a+
  gi|119720317|ref|YP_920812.1| 64 DvPHLCAQCRDypCVKACRYSAL 86
                                   55889****999******99886 PP

  == domain 3  score: 27.1 bits;  conditional E-value: 2.3e-09
                         Fer4_6   2 veidpdkCigCgdCvrvCP 20 
                                    v +d +kC+gCgdCvr+CP
  gi|119720317|ref|YP_920812.1|  95 VLVDGEKCTGCGDCVRACP 113
                                    568999************* PP

  == domain 4  score: 7.7 bits;  conditional E-value: 0.003
                         Fer4_6   9 CigC.gd..CvrvCPe 21 
                                    C+ C g+  Cv++C e
  gi|119720317|ref|YP_920812.1| 129 CDLCgGEpeCVKACHE 144
                                    ****555*******97 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   8.5   5.8e-06    0.0074       1      50 [.      28      85 ..      28      86 .. 0.79
   2 !   28.2  13.1   1.2e-09   1.5e-06       2      49 ..      69     115 ..      68     117 .. 0.91
   3 !   26.5  11.9   4.1e-09   5.2e-06       1      48 [.     101     144 ..     101     147 .. 0.95

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 5.8e-06
                         Fer4_9  1 kCtgCgaCveaC..pagvvvedaaerkarlraase....eaCigCga..CveaCpkga 50
                                   +C gC+ C+ aC  +++ +v  +a r++  + +        C +C++  Cv+aC   a
  gi|119720317|ref|YP_920812.1| 28 RCSGCRLCEVACslKHEGTVWPEASRIRVFEFFPGvdvpHLCAQCRDypCVKACRYSA 85
                                   5***********77566666666666666655544899999*************9765 PP

  == domain 2  score: 28.2 bits;  conditional E-value: 1.2e-09
                         Fer4_9   2 CtgCga..CveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkg 49 
                                    C++C+   Cv+aC + + + d++++ + ++ +   +C+gCg+Cv aCp +
  gi|119720317|ref|YP_920812.1|  69 CAQCRDypCVKACRYSALRVDESTGAVLVDGE---KCTGCGDCVRACPGK 115
                                    ****9778********************9774...8************87 PP

  == domain 3  score: 26.5 bits;  conditional E-value: 4.1e-09
                         Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCga...CveaCpk 48 
                                    kCtgCg Cv+aCp +v++ +  +rka +       C  Cg    Cv+aC +
  gi|119720317|ref|YP_920812.1| 101 KCTGCGDCVRACPGKVMRLHPETRKAIV-------CDLCGGepeCVKACHE 144
                                    7**************************9.......*****9999*****86 PP

>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.5  11.8   2.1e-14   2.6e-11       6      91 ..      65     143 ..      62     149 .. 0.95

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 2.1e-14
                        Fer4_11   6 lpeqCrhCleppCvasapseaivkdeetGaVlldektkkeevrevveacPykivrkneetgkvekCdmcldrveaGllpa 85 
                                    +p+ C +C + pCv+++  +a+  de+tGaVl+d +++  ++ ++v+acP k++r   et k+  Cd+c      G +p 
  gi|119720317|ref|YP_920812.1|  65 VPHLCAQCRDYPCVKACRYSALRVDESTGAVLVDGEKCT-GCGDCVRACPGKVMRLHPETRKAIVCDLC------GGEPE 137
                                    6999**********************************8.*****************************......67788 PP

                        Fer4_11  86 cvescp 91 
                                    cv++c 
  gi|119720317|ref|YP_920812.1| 138 CVKACH 143
                                    999985 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   9.8   1.9e-05     0.025       1      51 [.      28      84 ..      28      85 .. 0.75
   2 !   25.5  12.5   1.2e-08   1.5e-05       2      50 ..      69     114 ..      68     116 .. 0.91
   3 !   19.2  12.7   1.1e-06    0.0013       1      48 [.     101     142 ..     101     143 .. 0.88
   4 ?    5.5   0.7     0.021        27       2      16 ..     129     146 ..     128     172 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.9e-05
                         Fer4_7  1 rCigCgaCvaaCp..vkaieldeeenekgt..ekveidpekClgCga..CvavCPtg 51
                                   rC gC+ C++aC+  ++   ++e+++ + +     + +p  C +C+   Cv++C + 
  gi|119720317|ref|YP_920812.1| 28 RCSGCRLCEVACSlkHEGTVWPEASRIRVFefFPGVDVPHLCAQCRDypCVKACRYS 84
                                   8***********8656666677776666442132344699******999*****876 PP

  == domain 2  score: 25.5 bits;  conditional E-value: 1.2e-08
                         Fer4_7   2 CigCg..aCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPt 50 
                                    C +C+   Cv+aC ++a+++de+     t  v +d ekC+gCg Cv++CP 
  gi|119720317|ref|YP_920812.1|  69 CAQCRdyPCVKACRYSALRVDES-----TGAVLVDGEKCTGCGDCVRACPG 114
                                    999*9889**************8.....56899*****************5 PP

  == domain 3  score: 19.2 bits;  conditional E-value: 1.1e-06
                         Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavC 48 
                                    +C+gCg Cv+aCp k+++l++e++       +i+ + C g  +Cv++C
  gi|119720317|ref|YP_920812.1| 101 KCTGCGDCVRACPGKVMRLHPETR------KAIVCDLCGGEPECVKAC 142
                                    7*******************9854......367889999999999999 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.021
                         Fer4_7   2 CigCg...aCvaaCpvka 16 
                                    C  Cg    Cv+aC    
  gi|119720317|ref|YP_920812.1| 129 CDLCGgepECVKACHEAG 146
                                    888888889*****7433 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   1.4   2.3e-05      0.03       5      20 ..      24      39 ..      19      40 .. 0.84
   2 !    9.1   2.2    0.0012       1.5       9      20 ..      68      81 ..      61      83 .. 0.84
   3 !   22.9   3.2   4.6e-08   5.9e-05       3      21 ..      95     113 ..      93     113 .. 0.92
   4 ?    4.8   1.9     0.027        35      10      20 ..     129     142 ..     122     144 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.3e-05
                         Fer4_2  5 vdtdrCigCgaCvsaC 20
                                    d  rC gC+ C  aC
  gi|119720317|ref|YP_920812.1| 24 RDYLRCSGCRLCEVAC 39
                                   5778************ PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0012
                         Fer4_2  9 rCigCg..aCvsaC 20
                                    C +C+  +Cv+aC
  gi|119720317|ref|YP_920812.1| 68 LCAQCRdyPCVKAC 81
                                   7****999****** PP

  == domain 3  score: 22.9 bits;  conditional E-value: 4.6e-08
                         Fer4_2   3 vvvdtdrCigCgaCvsaCP 21 
                                    v vd ++C+gCg Cv aCP
  gi|119720317|ref|YP_920812.1|  95 VLVDGEKCTGCGDCVRACP 113
                                    78999*************9 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.027
                         Fer4_2  10 CigCg...aCvsaC 20 
                                    C  Cg    Cv+aC
  gi|119720317|ref|YP_920812.1| 129 CDLCGgepECVKAC 142
                                    999*9999****** PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.7    0.0016         2      40      52 ..      28      40 ..      21      46 .. 0.80
   2 !   23.2   7.5   4.4e-08   5.7e-05       7      52 ..      68     113 ..      65     119 .. 0.84
   3 !    8.4   0.4    0.0018       2.3       8      32 ..     132     156 ..     122     166 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0016
                        Fer4_21 40 eCvGCnlCssvCP 52
                                   +C GC lC   C 
  gi|119720317|ref|YP_920812.1| 28 RCSGCRLCEVACS 40
                                   5888888888885 PP

  == domain 2  score: 23.2 bits;  conditional E-value: 4.4e-08
                        Fer4_21   7 kCigCgk..CliaCedtshqaieidaktvlkvv.edeCvGCnlCssvCP 52 
                                     C +C    C++aC+   + a+++d++t + +v  ++C+GC  C+  CP
  gi|119720317|ref|YP_920812.1|  68 LCAQCRDypCVKACR---YSALRVDESTGAVLVdGEKCTGCGDCVRACP 113
                                    699998555******...89*****99987765379************* PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0018
                        Fer4_21   8 CigCgkCliaCedtshqaieidakt 32 
                                    C g  +C++aC++++ +a+++ + t
  gi|119720317|ref|YP_920812.1| 132 CGGEPECVKACHEAGFDALRVVPYT 156
                                    444458*************987765 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.1   0.00057      0.72       4      22 ..      24      40 ..      21      59 .. 0.79
   2 !   20.5  12.2   3.1e-07   0.00039       6      56 .]      66     113 ..      61     113 .. 0.92
   3 !   18.4  13.2   1.4e-06    0.0017       2      55 ..      95     142 ..      94     143 .. 0.76
   4 ?    5.5   2.0     0.015        19       9      19 ..     129     142 ..     123     171 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00057
                        Fer4_10  4 idddtCirCgkCvkaCPad 22
                                   +d  +C +C+ C  aC  +
  gi|119720317|ref|YP_920812.1| 24 RDYLRCSGCRLCEVAC--S 40
                                   67789*********99..3 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 3.1e-07
                        Fer4_10   6 ddtCirCg..kCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                    +  C +C+   CvkaC     +++a   ++  +av ++ ekCtgcg Cv+aCP
  gi|119720317|ref|YP_920812.1|  66 PHLCAQCRdyPCVKAC-----RYSALRVDESTGAVLVDGEKCTGCGDCVRACP 113
                                    568*****999*****.....7899999999999999***************9 PP

  == domain 3  score: 18.4 bits;  conditional E-value: 1.4e-06
                        Fer4_10   2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcg...aCveaC 55 
                                    v +d ++C++Cg+Cv+aCP          + ++  ++  k   C+ cg   +Cv+aC
  gi|119720317|ref|YP_920812.1|  95 VLVDGEKCTGCGDCVRACPG---------KVMRLHPETRKAIVCDLCGgepECVKAC 142
                                    567999*************9.........4444444444566688887777****** PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.015
                        Fer4_10   9 CirCg...kCvkaC 19 
                                    C  Cg   +CvkaC
  gi|119720317|ref|YP_920812.1| 129 CDLCGgepECVKAC 142
                                    55555555777777 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   1.8   3.9e-05      0.05       4      18 ..      25      39 ..      22      40 .. 0.91
   2 ?   -2.9   0.1       5.6   7.2e+03      11      14 ..      69      72 ..      67      74 .. 0.62
   3 ?    3.9   0.1     0.041        53      14      23 ..      77      86 ..      76      87 .. 0.89
   4 !   26.0   3.6   4.1e-09   5.2e-06       3      20 ..      97     114 ..      95     118 .. 0.87
   5 ?   -2.0   1.1         3   3.8e+03       8      12 ..     129     133 ..     127     134 .. 0.73
   6 ?   -0.7   1.9       1.1   1.4e+03      14      18 ..     138     142 ..     137     142 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.9e-05
                                   ETTTSSS-THHHHHS CS
                           Fer4  4 deekCigCGaCvevC 18
                                   d+ +C gC +C+ +C
  gi|119720317|ref|YP_920812.1| 25 DYLRCSGCRLCEVAC 39
                                   8889*********** PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.6
                                   -THH CS
                           Fer4 11 CGaC 14
                                   C +C
  gi|119720317|ref|YP_920812.1| 69 CAQC 72
                                   6666 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.041
                                   HHHHSTTTEE CS
                           Fer4 14 CvevCPvgAI 23
                                   Cv++C + A+
  gi|119720317|ref|YP_920812.1| 77 CVKACRYSAL 86
                                   *****99987 PP

  == domain 4  score: 26.0 bits;  conditional E-value: 4.1e-09
                                    EETTTSSS-THHHHHSTT CS
                           Fer4   3 ideekCigCGaCvevCPv 20 
                                    +d ekC+gCG Cv +CP 
  gi|119720317|ref|YP_920812.1|  97 VDGEKCTGCGDCVRACPG 114
                                    899**************6 PP

  == domain 5  score: -2.0 bits;  conditional E-value: 3
                                    SSS-T CS
                           Fer4   8 CigCG 12 
                                    C  CG
  gi|119720317|ref|YP_920812.1| 129 CDLCG 133
                                    77777 PP

  == domain 6  score: -0.7 bits;  conditional E-value: 1.1
                                    HHHHS CS
                           Fer4  14 CvevC 18 
                                    Cv++C
  gi|119720317|ref|YP_920812.1| 138 CVKAC 142
                                    ***** PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   1.8   0.00014      0.17       3      15 ..      28      40 ..      26      46 .. 0.92
   2 ?    3.4   3.3      0.11   1.4e+02       3      15 ..      68      82 ..      66      84 .. 0.81
   3 !   20.2   2.0   4.4e-07   0.00056       2      15 ..     100     113 ..      99     124 .. 0.92
   4 ?    5.4   0.9     0.025        32       4      15 ..     132     143 ..     125     155 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00014
                         Fer4_4  3 rCigCgsCvaaCP 15
                                   rC gC+ C+ aC+
  gi|119720317|ref|YP_920812.1| 28 RCSGCRLCEVACS 40
                                   8***********7 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.11
                         Fer4_4  3 rCigCgs..CvaaCP 15
                                    C +C+   Cv aC 
  gi|119720317|ref|YP_920812.1| 68 LCAQCRDypCVKACR 82
                                   699999888999996 PP

  == domain 3  score: 20.2 bits;  conditional E-value: 4.4e-07
                         Fer4_4   2 erCigCgsCvaaCP 15 
                                    e+C+gCg Cv+aCP
  gi|119720317|ref|YP_920812.1| 100 EKCTGCGDCVRACP 113
                                    79************ PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.025
                         Fer4_4   4 CigCgsCvaaCP 15 
                                    C g + Cv aC 
  gi|119720317|ref|YP_920812.1| 132 CGGEPECVKACH 143
                                    445668*****6 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   4.0    0.0067       8.6       1      11 [.      29      39 ..      29      42 .. 0.94
   2 !    8.1   3.2    0.0045       5.7       1      15 []      69      85 ..      67      85 .. 0.79
   3 !   16.4   5.7     1e-05     0.013       1      14 [.     102     115 ..     102     116 .. 0.94
   4 !    8.9   3.5    0.0025       3.2       1      11 [.     129     142 ..     129     146 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0067
                         Fer4_3  1 CtgCgaCvevC 11
                                   C gC++C+++C
  gi|119720317|ref|YP_920812.1| 29 CSGCRLCEVAC 39
                                   99********* PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0045
                         Fer4_3  1 CtgCg..aCvevCPvgA 15
                                   C +C+  +Cv++C++ A
  gi|119720317|ref|YP_920812.1| 69 CAQCRdyPCVKACRYSA 85
                                   66785569*****9876 PP

  == domain 3  score: 16.4 bits;  conditional E-value: 1e-05
                         Fer4_3   1 CtgCgaCvevCPvg 14 
                                    CtgCg Cv++CP +
  gi|119720317|ref|YP_920812.1| 102 CTGCGDCVRACPGK 115
                                    ************86 PP

  == domain 4  score: 8.9 bits;  conditional E-value: 0.0025
                         Fer4_3   1 CtgCg...aCvevC 11 
                                    C+ Cg    Cv++C
  gi|119720317|ref|YP_920812.1| 129 CDLCGgepECVKAC 142
                                    ****99999***** PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   1.1     0.019        24       1      12 [.      28      39 ..      23      43 .. 0.66
   2 ?    8.2   0.7    0.0038       4.9       2      20 ..      69      89 ..      68      96 .. 0.88
   3 ?   16.0   3.4   1.4e-05     0.018       1      22 [.     101     122 ..     101     130 .. 0.83
   4 ?   -1.0   2.5       2.8   3.6e+03       2      14 ..     132     144 ..     128     151 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.019
                        Fer4_16  1 rCgtCgkCaevC 12
                                   rC +C+ C  +C
  gi|119720317|ref|YP_920812.1| 28 RCSGCRLCEVAC 39
                                   466666666666 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0038
                        Fer4_16  2 CgtCgk..CaevCPtnaikek 20
                                   C +C+   C+++C  +a++ +
  gi|119720317|ref|YP_920812.1| 69 CAQCRDypCVKACRYSALRVD 89
                                   *****999*********9987 PP

  == domain 3  score: 16.0 bits;  conditional E-value: 1.4e-05
                        Fer4_16   1 rCgtCgkCaevCPtnaikekke 22 
                                    +C++Cg C+ +CP ++++   e
  gi|119720317|ref|YP_920812.1| 101 KCTGCGDCVRACPGKVMRLHPE 122
                                    5***************997743 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 2.8
                        Fer4_16   2 CgtCgkCaevCPt 14 
                                    Cg+  +C+++C +
  gi|119720317|ref|YP_920812.1| 132 CGGEPECVKACHE 144
                                    4444579999976 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.4    0.0004      0.51      45      57 ..      28      40 ..      10      44 .. 0.84
   2 ?    3.8   2.9     0.067        86       2      16 ..      69      85 ..      68     100 .. 0.81
   3 ?   13.8   3.1     5e-05     0.064      44      59 ..     100     115 ..      94     117 .. 0.87
   4 ?    1.3   1.5      0.42   5.3e+02      42      57 ..     128     143 ..     117     148 .. 0.67
   5 ?    0.7   1.6      0.61   7.8e+02       2      14 ..     129     144 ..     128     174 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0004
                        Fer4_17 45 lCieCgeCerkCP 57
                                   +C++C++Ce +C 
  gi|119720317|ref|YP_920812.1| 28 RCSGCRLCEVACS 40
                                   7999999998885 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.067
                        Fer4_17  2 CiqCgy..ClpeCpsye 16
                                   C+qC+   C+++C + +
  gi|119720317|ref|YP_920812.1| 69 CAQCRDypCVKACRYSA 85
                                   9****779*****8755 PP

  == domain 3  score: 13.8 bits;  conditional E-value: 5e-05
                        Fer4_17  44 slCieCgeCerkCPqg 59 
                                    ++C++Cg C+r+CP +
  gi|119720317|ref|YP_920812.1| 100 EKCTGCGDCVRACPGK 115
                                    5899999999999976 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.42
                        Fer4_17  42 kaslCieCgeCerkCP 57 
                                    +++lC +  eC+++C 
  gi|119720317|ref|YP_920812.1| 128 VCDLCGGEPECVKACH 143
                                    5666666667777774 PP

  == domain 5  score: 0.7 bits;  conditional E-value: 0.61
                        Fer4_17   2 CiqCgy...ClpeCps 14 
                                    C  Cg    C+++C  
  gi|119720317|ref|YP_920812.1| 129 CDLCGGepeCVKACHE 144
                                    6666644457777764 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.5      0.08     1e+02       4      18 ..      25      39 ..      22      51 .. 0.85
   2 ?   10.1   9.3    0.0008         1       1      20 [.      95     114 ..      95     149 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.08
                        Fer4_15  4 DrdaCigcglCvaea 18
                                   D  +C gc lC  ++
  gi|119720317|ref|YP_920812.1| 25 DYLRCSGCRLCEVAC 39
                                   6679*******8887 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0008
                        Fer4_15   1 VvvDrdaCigcglCvaeape 20 
                                    V vD ++C+gcg Cv+++p 
  gi|119720317|ref|YP_920812.1|  95 VLVDGEKCTGCGDCVRACPG 114
                                    789***************85 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2  20.6    0.0053       6.8       3      64 ..      27     115 ..      25     116 .. 0.69
   2 ?    2.8  13.5      0.13   1.6e+02       3      63 ..     100     114 ..      98     146 .. 0.70
   3 ?    0.4   1.6      0.74   9.5e+02       7      16 ..     131     143 ..     125     172 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0053
                         Fer4_8   3 ekCieCgaCqsaCpvlrrtk.khlldargeaae............................dvqeeqvlee.......ee 46 
                                     +C +C +C+ aC  l++++  ++  +r ++ e                            +                  
  gi|119720317|ref|YP_920812.1|  27 LRCSGCRLCEVACS-LKHEGtVWPEASRIRVFEffpgvdvphlcaqcrdypcvkacrysalR--------VdestgavLV 97 
                                    68***********4.55544477777777777777777777777777777666655544331........0334444445 PP

                         Fer4_8  47 alwsCttcgaCtevCpvg 64 
                                      ++Ct+cg C+++Cp +
  gi|119720317|ref|YP_920812.1|  98 DGEKCTGCGDCVRACPGK 115
                                    569*************76 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.13
                         Fer4_8   3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpv 63 
                                    ekC++Cg C  aCp                                               
  gi|119720317|ref|YP_920812.1| 100 EKCTGCGDCVRACP----------------------------------------------G 114
                                    45666666666665..............................................3 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.74
                         Fer4_8   7 eCg...aCqsaCp 16 
                                     Cg    C +aC+
  gi|119720317|ref|YP_920812.1| 131 LCGgepECVKACH 143
                                    3333335556665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 1082.89
//
Query:       gi|119720318|ref|YP_920813.1|  [L=625]
Description: aldehyde ferredoxin oxidoreductase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-74  250.9   0.0    3.3e-74  250.2   0.0    1.2  1  AFOR_C    Aldehyde ferredoxin oxidoreductase, domains 2 & 3
    1.7e-59  201.0   0.1    2.9e-59  200.3   0.1    1.4  1  AFOR_N    Aldehyde ferredoxin oxidoreductase, N-terminal doma


Domain annotation for each model (and alignments):
>> AFOR_C  Aldehyde ferredoxin oxidoreductase, domains 2 & 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  250.2   0.0   3.7e-78   3.3e-74      19     382 .]     250     608 ..     238     608 .. 0.90

  Alignments for each domain:
  == domain 1  score: 250.2 bits;  conditional E-value: 3.7e-78
                                    HHHHH-G.GGHHHHHHHTT---BTTTTBS--TTGGGGSHHHHHHHTEEEE.E.-TT-SS--EEEEE.......ET.EE-- CS
                         AFOR_C  19 elrkyGT.aelvnianetgalptknfqegtfekaekisgealeekylvkneg.CfsCpiaCgrevkveegkk.vk.vegp 94 
                                     +++ GT ++ +++a  t+  p++n+qe+   + ++++ +++e  + vk+    ++Cp  C +  + ++gk  +  ++gp
  gi|119720318|ref|YP_920813.1| 250 LWKHWGTsSGGYEVASLTSSEPVRNWQEEWH-DSRSMGVQNYEA-HWVKRYWgDYGCPQTCMKISRLRSGKFsGAtTDGP 327
                                    5788888455677999999*********864.467788899999.66776545999**************996669**** PP

                                    -HHHHHHHTGGGT---HHHHHHHHHHHHHHTB-HHHHHHHHHHHHHHHHTTSS-HHHHTS----TT-THHHHHHHHHHHT CS
                         AFOR_C  95 eyetlaalGsnlgiddleailklnelcdelGlDtisaGntiafamelyekGllkkedtdglelefgdaeallellekiAk 174
                                    +ye  a+lG+nlg++++ a ++l+ l+delGl  i++Gn+++fa elyekG+l++ed+ g+el++gdaea+ +l+ +iA+
  gi|119720318|ref|YP_920813.1| 328 DYELQAYLGPNLGVFEPRANVYLSSLADELGLCGIQTGNVLGFAAELYEKGVLTREDL-GFELKWGDAEAFARLMSMIAR 406
                                    **********************************************************.********************* PP

                                    T-TTHHHHTT-HHHHHHCTT......-GGG--EETTEE--SS-GGG-HH..HHHHHHH-TTSS-SGGG-THHHHS---TT CS
                         AFOR_C 175 regigdllAeGvkrlaeklg......aeelamhvkGlelpaydprgakg..malaYatsnrGacHlraylialeekvdpl 246
                                    regigd lAeG+ r+a klg        ++a+hvkG+ + a+ +r  k   +a +Ya+  +G++H +        +vd+ 
  gi|119720318|ref|YP_920813.1| 407 REGIGDCLAEGTARAALKLGklkgvdLSKYAVHVKGVGVGAHGARSGKDfpQAFTYAVGVQGGDHTSPPR----LPVDR- 481
                                    ********************9888888******************7665559*************99322....33333. PP

                                    --HHHHHHHHHHHHHHHHHHHHT--GGGG-HHH......HHHHHHHHHT----HHHHHHH.HHHHHHHHHHHHHHHT--. CS
                         AFOR_C 247 etegkaelvkwfqdltalvdslglCkftseaeerldlelyakllsavtGidvteeellka.GeRiynleRlfnlreGlt. 324
                                              w + + a+ ds+++C f+       + +l  ++l a+tG+d+t+e  +++ G+Ri++l+R++ l  G + 
  gi|119720318|ref|YP_920813.1| 482 ---------QWGEFTSAFEDSAVICSFNV------HGDLPFQFLRAITGWDITRETWMRVhGRRIITLQRVLLLLGGPDl 546
                                    .........37777788888********9......567899***************99977****************999 PP

                                    ....HHHS---HHHHHS---SSTTTT---...-HHHHHHHHHHHHT--TTS---HHHHHHCT- CS
                         AFOR_C 325 ....rkddtlperlleeplkegpakgkvl.edeleemldeyYelrGWdetGvPtketlkrLgL 382
                                        r+dd+ p+r++ epl++gp kg+ + ++e+e  ++ey+   GWd+ G+Pt+etl++LgL
  gi|119720318|ref|YP_920813.1| 547 ywdpRRDDDNPPRFY-EPLPSGPFKGRSVsREEVESQKREYFGYLGWDSLGIPTEETLRELGL 608
                                    9998899999****9.9***********98888*****************************8 PP

>> AFOR_N  Aldehyde ferredoxin oxidoreductase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.3   0.1   3.2e-63   2.9e-59       1     197 [.       8     221 ..       8     222 .. 0.93

  Alignments for each domain:
  == domain 1  score: 200.3 bits;  conditional E-value: 3.2e-63
                                    SEEEEEETTTTEEEEEE--HHHHHHH-SCHHHHHHHHHHHS..-.TTS-TTSTTS-EEEEE-TTTTSSSTTB-EEEEEEE CS
                         AFOR_N   1 gkilrvdLstgkieveelpeelaekylGgrglaakllldev..p.pgvdplspenplvfatGpltgtpapgsgrlvvvak 77 
                                    g++l+vdLs+gk +v el+e++a +++Ggrglaa+ll++e+  + ++vdpl+pen l++ tGpltg+ +p   +l++  k
  gi|119720318|ref|YP_920813.1|   8 GRLLEVDLSRGKHRVVELEEDVAFNFIGGRGLAAYLLWRELgdRwEEVDPLGPENMLLVLTGPLTGY-YP-GVKLCISGK 85 
                                    689************************************986535899******************9.77.689****** PP

                                    -TTTSSEEEEEEETCHHHHHHHCT-SEEEEES--SS-EEEEEETTEEEEEE-TTTTTS-HHHHHHHHHH....HHTS... CS
                         AFOR_N  78 sPltgtlgesnaGgrfgaelkraGydaivieGkaekpvylvieddkveiedaedlwgldtyettealke....elgd... 150
                                    sP+++++  s + ++++ el+ aGyd+iv++G++++pvyl++e ++vei++ae+lwgl+  et ++l++    +      
  gi|119720318|ref|YP_920813.1|  86 SPQSNGVVGSVVSSEVAVELRAAGYDGIVVKGASKDPVYLYVEGENVEIRSAEHLWGLGGTETYRRLSRelwgD--Lkrr 163
                                    ******************************************************************99966652..0446 PP

                                    ...........EEEEE-HHHHTT-TTB-E.EETTEEE-SSSHHHHHHHTTEEEEEEE- CS
                         AFOR_N 151 ...........kvaviGpaGenlvrfAsisvddgraagrgGlGavmgsKnlkaivvrg 197
                                               + ++iGpaGen+vr A+++ + ++aag gG GavmgsK lkai+v+g
  gi|119720318|ref|YP_920813.1| 164 llaregltkepSFIYIGPAGENRVRTAAVMAKLSHAAGYGGYGAVMGSKMLKAIAVKG 221
                                    77777788877888***************7789999********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (625 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.26s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 3970.06
//
Query:       gi|119720319|ref|YP_920814.1|  [L=163]
Description: PaREP8 domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-24   85.6   3.9      3e-24   85.2   3.9    1.2  1  PaREP1    Archaeal PaREP1/PaREP8 family
     0.0011   19.0   4.1     0.0014   18.7   1.8    2.1  2  HEPN      HEPN domain
     0.0029   17.8   0.0      0.004   17.4   0.0    1.2  1  DUF5618   Domain of unknown function (DUF5618)


Domain annotation for each model (and alignments):
>> PaREP1  Archaeal PaREP1/PaREP8 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.2   3.9     5e-28     3e-24       3     115 .]      48     150 ..      46     150 .. 0.96

  Alignments for each domain:
  == domain 1  score: 85.2 bits;  conditional E-value: 5e-28
                         PaREP1   3 leeaekeleeAeellekGdlrqAaeKaykAvkalvkalaeknnlklleeaeekerwstkellkavaklleelgdkevvdl 82 
                                    +e+++++le A++ l kGd+rqAaeK++ Av+ +vka+a +        +e+k+  s+++l+++ + l+++lg ++v+d+
  gi|119720319|ref|YP_920814.1|  48 IEASKELLEGARKELGKGDVRQAAEKVWVAVALAVKAYAYA--------KEGKRLASHGDLWRYKEVLVSDLG-EWVRDS 118
                                    7899999**********************************........99**********************.****** PP

                         PaREP1  83 wklAldLHeyqfheaklelsdveskeeavkdlv 115
                                    w+ A ++H++ f+e++++ +dve   +++++lv
  gi|119720319|ref|YP_920814.1| 119 WAYASSMHTC-FYEGWCTEKDVEVGISRAERLV 150
                                    **********.************9999999886 PP

>> HEPN  HEPN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       2.1   1.2e+04       5      18 ..      12      25 ..      10      32 .. 0.55
   2 !   18.7   1.8   2.4e-07    0.0014       1     114 [.      44     152 ..      44     156 .. 0.72

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 2.1
                                   HHHHHHHHHHHHHH CS
                           HEPN  5 lrrAeedleaAell 18
                                   ++rA++  e   ++
  gi|119720319|ref|YP_920814.1| 12 VERARREAERLGVS 25
                                   45555555554444 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 2.4e-07
                                    HHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHTT--.SSCCHHHHHHCCHHHT...-HHHHHHHHHH CS
                           HEPN   1 aeewlrrAeedleaAellleegdydlacfhaqqaaekalKAlllkkggeppkthdlreLleelkkelkeseelreeleeL 80 
                                    ae++++ ++e le A++ l +gd + a+ ++  a+ +a+KA+ ++k+g+  +  +  +L+++ + +  +  e+ ++    
  gi|119720319|ref|YP_920814.1|  44 AEAFIEASKELLEGARKELGKGDVRQAAEKVWVAVALAVKAYAYAKEGK--RLASHGDLWRYKEVLVSDLGEWVRDSWA- 120
                                    68999****************************************9997..4444445555444444334455555433. PP

                                    HCCCHHCCCTSS--S.--HHHHHHHHHHHHHHHHH CS
                           HEPN  81 ekayiesrYpdakee.yteedaeealkdaeevlel 114
                                       y  s    ++e+ +te+d+e  +++ae+++  
  gi|119720319|ref|YP_920814.1| 121 ---YASSMHTCFYEGwCTEKDVEVGISRAERLVGE 152
                                    ...33333333444446899999999999988765 PP

>> DUF5618  Domain of unknown function (DUF5618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   6.7e-07     0.004       5     121 ..      43     153 ..      39     155 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 6.7e-07
                                    HHHHHHHHHHHHHHHHS-EETTEE--HHHHHHHHHHHHHHHHHHHHHHH---S...SS-.--HHHHHHHHHCC-HHHHHH CS
                        DUF5618   5 eakrylenAkeiLsekakkedklYkdkkyvkeAggtAYsgvLlaldellgkkglekkkrpksvetYkealkkldkkllke 84 
                                    +a  ++e +ke+L e a+ke +    k  v++A++  + +v la+ ++   k+ ++   + ++  Yke l +  ++ +++
  gi|119720319|ref|YP_920814.1|  43 KAEAFIEASKELL-EGARKELG----KGDVRQAAEKVWVAVALAVKAYAYAKEGKRLASHGDLWRYKEVLVSDLGEWVRD 117
                                    688899*******.99***965....789***************************9999************99*****9 PP

                                    HHHHHHHHIIIICCT---BHHHHHHHHHHHHHHHHHH CS
                        DUF5618  85 fnsaydvLhlagyydGiksakvvkeglkaaeklikki 121
                                         +++h +  y+G  + k v+ g+++ae+l+  +
  gi|119720319|ref|YP_920814.1| 118 SWAYASSMHTC-FYEGWCTEKDVEVGISRAERLVGEL 153
                                    88777888876.79**9999999*********99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1147.37
//
Query:       gi|119720320|ref|YP_920815.1|  [L=119]
Description: DNA polymerase beta subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.2e-08   34.1   0.0    2.7e-08   33.8   0.0    1.1  1  Polbeta       Polymerase beta, Nucleotidyltransferase
    2.9e-07   30.7   0.0    4.6e-07   30.1   0.0    1.3  1  NTP_transf_2  Nucleotidyltransferase domain
     0.0005   19.9   0.0    0.00076   19.3   0.0    1.3  1  DUF294        Putative nucleotidyltransferase DUF294


Domain annotation for each model (and alignments):
>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.0   4.6e-12   2.7e-08      16      72 ..      36      90 ..      26     109 .. 0.78

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 4.6e-12
                                   TTEEEEEE-S------EEEEEEEESS---HHHHHHHHHHHHHH..SSSEEEEEETTTS CS
                        Polbeta 16 aylFGSrakgkareeSDiDlavllkekldleeelelaaeledi.klgkkvDlvdlnea 72
                                   ++lFGSra+g+   +SD+Dlav+++e+ d+   l l + l ++   g  vD+v+l++ 
  gi|119720320|ref|YP_920815.1| 36 LILFGSRARGDEMLSSDYDLAVVVEEEVDV---LGLTETLVKMrPRGLPVDVVVLQKE 90
                                   78*************************544...5555555555455899*****9955 PP

>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.0   7.6e-11   4.6e-07       6      81 ..      25      92 ..      20     106 .. 0.81

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 7.6e-11
                                   HHHHHHTTTSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEECEEECCC CS
                   NTP_transf_2  6 eelkelepvakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevdlvtrekled 81
                                   +++ +  + + ++lfGS+arG+    SD Dl+vv++eev+        + l e   +  + +gl+vd+v+ +k e 
  gi|119720320|ref|YP_920815.1| 25 RIVGFFGGRVTLILFGSRARGDEMLSSDYDLAVVVEEEVD-------VLGLTETLVKMRP-RGLPVDVVVLQKEEL 92
                                   56666677999*************9*************55.......5778888888888.899999997777664 PP

>> DUF294  Putative nucleotidyltransferase DUF294
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.3e-07   0.00076      47      77 ..      31      61 ..      13      76 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.3e-07
                         DUF294 47 pvpfallvmGSeGReEqtlktDqDnalvled 77
                                     +++l+ +GS +R++ +l++D D a v+e+
  gi|119720320|ref|YP_920815.1| 31 GGRVTLILFGSRARGDEMLSSDYDLAVVVEE 61
                                   56789***********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       261  (0.0145574); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 785.31
//
Query:       gi|119720321|ref|YP_920816.1|  [L=212]
Description: hypothetical protein Tpen_1416 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1376.92
//
Query:       gi|119720322|ref|YP_920817.1|  [L=406]
Description: aminotransferase, class I and II [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-53  182.7   0.0    1.2e-53  182.5   0.0    1.0  1  Aminotran_1_2  Aminotransferase class I and II


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  182.5   0.0   6.9e-58   1.2e-53       4     363 .]      40     390 ..      37     390 .. 0.93

  Alignments for each domain:
  == domain 1  score: 182.5 bits;  conditional E-value: 6.9e-58
                                    EESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHH CS
                  Aminotran_1_2   4 inLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliea 83 
                                    + +g++++++     ++ ev++a +     g ++ +y+p+ glpel+eala +l++++++++k++ +v v++Ga+a+  a
  gi|119720322|ref|YP_920817.1|  40 VSFGIGQPDFS----PPGEVLEALRT---VGAEALKYTPPLGLPELREALAGYLSEKYGVDVKPS-EVAVTPGATAAVFA 111
                                    6799*******....*********76...88999*******************************.************** PP

                                    HHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT-- CS
                  Aminotran_1_2  84 lifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGt 163
                                       ll +    +++v dp +++y++++r +gg vv+     ee+f+  +e++   l e         v +++ p+NPtG+
  gi|119720322|ref|YP_920817.1| 112 SLVLL-VRGRARVVVQDPGFPMYDDVARFAGGRVVYAYSGIEESFEWSAESIAGRLGE-------GGVAVLNFPNNPTGS 183
                                    *****.899999*********************666665778***************8.......235799********* PP

                                    B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHH..HGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHH CS
                  Aminotran_1_2 164 vatleeleklldlakkynlllfvDeaYagfvfgsldavat..ranveeepnllivgslsKafGlaGeRvGyilgnaavvs 241
                                    +a++  le+l  la ++++++++De+Y++fv++ + ++++  ++++ e+   + vgs+sK +GlaG+R+Gy+++  ++v+
  gi|119720322|ref|YP_920817.1| 184 LAPRGLLEELGGLAARKGFYVVSDEVYEDFVYEGS-HESVlqVPELRER--SVYVGSFSKTWGLAGLRLGYVVAPRRLVE 260
                                    ********************************965.3443336666665..57*************************** PP

                                    HHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS.TEEEECCSCSSEEEEEETHH... CS
                  Aminotran_1_2 242 qlrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLael.glkvlasqsgmflltdlsae... 315
                                     l+ ++ +++   +s++q a++ al++ l    +++   +++ +rr+ l +eL +  g++ + + ++++++ +++ +   
  gi|119720322|ref|YP_920817.1| 261 RLEAVAVNVYGspPSPAQLAALRALDHGLG---WFSGVLSEYRRRRDALLEELSKVeGVELYRPRGAFYVYPRVRGLlkr 337
                                    ***********9***************997...********************999************************ PP

                                    ....CHHHHHHHHHHTCTEEEEEGGGGTS...TTEEEEECTTS-HHHHHHHHHHH CS
                  Aminotran_1_2 316 ....takelskkLleevgvyvtpgtsftv...pgrlRitvAglteeeleelveal 363
                                        +  el+++Ll+  gv+v+pg  +     ++++R+++ +l+ e ++e v+++
  gi|119720322|ref|YP_920817.1| 338 lgvgSSRELAESLLQA-GVVVLPGDAYSGragREHVRLSY-ALPVESIREGVRRI 390
                                    ****************.*******9999999*99******.********999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 2594.09
//
Query:       gi|119720323|ref|YP_920818.1|  [L=231]
Description: hypothetical protein Tpen_1418 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.4e-09   36.2   9.0    3.3e-07   30.5   1.8    2.2  2  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
     0.0047   17.2   0.4       0.14   12.4   0.2    2.4  2  Big_6            Bacterial Ig domain
     0.0063   16.8   1.1      0.015   15.6   0.8    1.8  2  Invasin_D3       Invasin, domain 3
     0.0064   16.6   2.8     0.0064   16.6   2.8    2.2  2  Big_3_5          Bacterial Ig-like domain (group 3)
  ------ inclusion threshold ------
      0.017   15.1   0.5        0.1   12.6   0.1    2.2  2  Big_1            Bacterial Ig-like domain (group 1)
      0.028   14.3   0.0      0.078   12.8   0.0    1.7  1  DUF824           Salmonella repeat of unknown function (DUF82


Domain annotation for each model (and alignments):
>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.8   0.00025      0.73       6      75 ..      26      95 ..      23     100 .. 0.82
   2 !   30.5   1.8   1.1e-10   3.3e-07       3      81 ..     104     178 ..     102     179 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00025
                CarboxypepD_reg  6 VtdasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtv.sapGyatatreevtltagqtt 75
                                   ++  +g+ +aga V+v+ + +g v++ t ++   f+++++  g  +v+v s +G      ++vt+ ++ t 
  gi|119720323|ref|YP_920818.1| 26 IVAYDGTSLAGALVRVS-TLDGRVYEFTLNPAAPFTVKDVVKGVLRVEVvSWKGVPVNYEKTVTVYENSTL 95
                                   66679************.6899*************************995556665555677888776665 PP

  == domain 2  score: 30.5 bits;  conditional E-value: 1.1e-10
                CarboxypepD_reg   3 sGrVtdasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatreevtltagqtttlditL 81 
                                    +  V+ a g++++ga Vt+++ ++ tv +   +++G ++   lp+gty+v v + G   +     ++++ ++++++++L
  gi|119720323|ref|YP_920818.1| 104 TVAVKGARGQALPGALVTISR-GGVTVEEGSAGSSGIYST-LLPAGTYEVAVAYGGRSARVE--AVVEPSRESRVEAAL 178
                                    6679999*************4.6668999**********5.6**********9988777774..688999999998887 PP

>> Big_6  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.066     2e+02      13      36 ..      30      48 ..      18      63 .. 0.68
   2 !   12.4   0.2   4.8e-05      0.14      18      53 ..     111     145 ..      98     155 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.066
                          Big_6 13 dgttltGkaeagatVtvkdadgtv 36
                                   d     G+  aga V+v++ dg+v
  gi|119720323|ref|YP_920818.1| 30 D-----GTSLAGALVRVSTLDGRV 48
                                   4.....555567888887777776 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 4.8e-05
                          Big_6  18 tGkaeagatVtvkdadgtvlgtgtadadGeFsvtle 53 
                                     G+a +ga Vt++  +g ++ +g a+++G +s  l+
  gi|119720323|ref|YP_920818.1| 111 RGQALPGALVTIS-RGGVTVEEGSAGSSGIYSTLLP 145
                                    69**********9.599999***********97775 PP

>> Invasin_D3  Invasin, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.2   3.7e+03      53      53 ..      60      60 ..      23      92 .. 0.53
   2 !   15.6   0.8     5e-06     0.015      23      88 ..     102     163 ..      85     169 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.2
                     Invasin_D3 53 a 53
                                   +
  gi|119720323|ref|YP_920818.1| 60 T 60
                                   2 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 5e-06
                     Invasin_D3  23 tltvtlkDangnpvsgltvtfsttsag.tlsavtdngdGtytatLtattagtatitptvnGvaiaat 88 
                                     ltv +k a g+++ g+ vt+s    g t+++ +  ++G+y++ L    agt+ + + ++G ++  +
  gi|119720323|ref|YP_920818.1| 102 RLTVAVKGARGQALPGALVTISR--GGvTVEEGSAGSSGIYSTLL---PAGTYEVAVAYGGRSARVE 163
                                    69********************4..4569999999999*******...7889999999999444443 PP

>> Big_3_5  Bacterial Ig-like domain (group 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1      0.24   7.3e+02      15      37 ..      72      96 ..      56     102 .. 0.69
   2 !   16.6   2.8   2.2e-06    0.0064      11      71 ..     102     159 ..      92     176 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.24
                                   E--CCCC..TTS--EEEEEETTEE- CS
                        Big_3_5 15 tVtaasg..gtptGtVtftdggttl 37
                                   +V + +g   +   tVt+++++t +
  gi|119720323|ref|YP_920818.1| 72 EVVSWKGvpVNYEKTVTVYENSTLV 96
                                   4444444434567899999999866 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 2.2e-06
                                    EEEEE--CCCCTT.S--EEEEEETTEE-SS-EE--TTSEEEEEEE-SS-EEEEEEEEEE-TT CS
                        Big_3_5  11 tltatVtaasggt.ptGtVtftdggttlgtavllsanGtAtltvsalaaGthsitAtYsGda 71 
                                     lt+ V++a g++ p   Vt+  gg+t+ + ++    G+  +  ++l+aGt+++ + Y G +
  gi|119720323|ref|YP_920818.1| 102 RLTVAVKGARGQAlPGALVTISRGGVTVEEGSA----GSSGIYSTLLPAGTYEVAVAYGGRS 159
                                    699******997647889**********99874....5566667899*************86 PP

>> Big_1  Bacterial Ig-like domain (group 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.31   9.4e+02      17      35 ..      30      48 ..      23      77 .. 0.72
   2 ?   12.6   0.1   3.4e-05       0.1       8      52 ..     102     144 ..     101     153 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.31
                          Big_1 17 ngnpvagatVtfsvsggal 35
                                   +g+ +aga V +s+ +g +
  gi|119720323|ref|YP_920818.1| 30 DGTSLAGALVRVSTLDGRV 48
                                   5888999999888866655 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 3.4e-05
                          Big_1   8 tltatvkDangnpvagatVtfsvsggalsassgtTdanGkatvtl 52 
                                    +lt+ vk a g++++ga Vt+s  g ++   +g  +++G++++ l
  gi|119720323|ref|YP_920818.1| 102 RLTVAVKGARGQALPGALVTISRGGVTV--EEGSAGSSGIYSTLL 144
                                    58*******************9666444..577778888887765 PP

>> DUF824  Salmonella repeat of unknown function (DUF824)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.6e-05     0.078      17      39 ..     103     125 ..     102     126 .. 0.96

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.6e-05
                         DUF824  17 ltitvkDasGnPvpnapftltRg 39 
                                    lt+ vk a G+++p a +t++Rg
  gi|119720323|ref|YP_920818.1| 103 LTVAVKGARGQALPGALVTISRG 125
                                    8*********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1679.19
//
Query:       gi|119720324|ref|YP_920819.1|  [L=246]
Description: ABC transporter related [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-24   87.3   0.0    1.7e-24   86.9   0.0    1.2  1  ABC_tran  ABC transporter
    7.3e-13   49.0   0.1    2.9e-07   30.6   0.0    2.1  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
     0.0044   16.8   0.1      0.015   15.0   0.0    1.7  2  AAA_30    AAA domain
     0.0088   16.6   0.0      0.014   15.9   0.0    1.2  1  AAA_23    AAA domain
     0.0099   16.3   0.0      0.022   15.1   0.0    1.7  1  AAA_16    AAA ATPase domain
  ------ inclusion threshold ------
       0.01   15.5   0.0      0.018   14.8   0.0    1.3  1  AAA_29    P-loop containing region of AAA domain
      0.016   15.5   0.0      0.053   13.8   0.0    1.9  1  AAA_22    AAA domain
      0.032   13.8   0.0      0.067   12.8   0.0    1.4  1  AAA_27    AAA domain
      0.067   13.5   0.1       0.25   11.7   0.1    1.8  2  AAA_19    AAA domain
      0.088   12.4   0.0       0.14   11.8   0.0    1.3  1  SRP54     SRP54-type protein, GTPase domain
      0.089   12.6   0.1       0.15   11.9   0.1    1.2  1  MukB      MukB N-terminal
       0.12   12.9   0.0       0.31   11.5   0.0    1.9  1  AAA       ATPase family associated with various cellular acti


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.9   0.0   1.1e-27   1.7e-24       2     136 ..      22     164 ..      21     165 .. 0.95

  Alignments for each domain:
  == domain 1  score: 86.9 bits;  conditional E-value: 1.1e-27
                                    EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                       ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                    + +s+ +++ge++a++G+nGaGK+t lk++ gll+p++G++ + g+++ + e++++ +  g++p++p  f+ l+v e   
  gi|119720324|ref|YP_920819.1|  22 EGLSFAVRPGEIYALLGPNGAGKTTTLKCVVGLLRPDAGDVVVCGHSVLR-ERREVLRCTGYVPENPVGFDYLRVSEFld 100
                                    679***********************************************.666667789******************** PP

                                    ...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                 +e++e+++s +gl++ +d  +     +LS G  q+v ++++ll +p++l++DEp+
  gi|119720324|ref|YP_920819.1| 101 fvgalrriprdVLSERAERYISMFGLEQYRDAFM----GELSRGTVQKVLVVASLLHEPRVLVMDEPM 164
                                    ********99999999***************999....*****************************7 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   2.9e-06    0.0044       2      24 ..      34      56 ..      33      92 .. 0.87
   2 !   30.6   0.0     2e-10   2.9e-07     234     297 ..     134     194 ..      85     200 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.9e-06
                         AAA_21  2 nvliGpNgsGKSnLLdaldllar 24
                                    +l GpNg+GK++ L++  +l r
  gi|119720324|ref|YP_920819.1| 34 YALLGPNGAGKTTTLKCVVGLLR 56
                                   689***************99975 PP

  == domain 2  score: 30.6 bits;  conditional E-value: 2e-10
                         AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                    + elS Gt +   ++++ll  +   ++l+ DEp +g++P+ +++l + l++l+ +ga v+l++H
  gi|119720324|ref|YP_920819.1| 134 MGELSRGTVQKVLVVASLLHEP---RVLVMDEPMSGMDPESQKTLKDELRRLAGRGAAVLLSSH 194
                                    6799***************999...*************************************** PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   9.9e-06     0.015      18      53 ..      31      66 ..      19      81 .. 0.87
   2 ?   -1.2   0.0      0.92   1.4e+03      85     121 ..     151     191 ..     114     194 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 9.9e-06
                         AAA_30 18 drvavltGpAGtGKttalkalreaweaaggrviglA 53
                                     + +l Gp G+GKtt+lk ++ +++ + g+v+++ 
  gi|119720324|ref|YP_920819.1| 31 GEIYALLGPNGAGKTTTLKCVVGLLRPDAGDVVVCG 66
                                   5578999******************99988998876 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.92
                         AAA_30  85 rlepgtllivDE..agmv..dtkqlaallkaaekagakvil 121
                                     l++ ++l+ DE  +gm   ++k+l++ l++++ +ga v+l
  gi|119720324|ref|YP_920819.1| 151 LLHEPRVLVMDEpmSGMDpeSQKTLKDELRRLAGRGAAVLL 191
                                    34455888888853334355566666666666666777665 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   9.4e-06     0.014      21      39 ..      33      51 ..      21      57 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 9.4e-06
                         AAA_23 21 ltlItGpNGaGKTTildAi 39
                                   ++++ GpNGaGKTT l ++
  gi|119720324|ref|YP_920819.1| 33 IYALLGPNGAGKTTTLKCV 51
                                   7899***********9986 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.5e-05     0.022      23     143 ..      29     162 ..      15     205 .. 0.53

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.5e-05
                         AAA_16  23 rp.elvllsGesGvGKsslvrellralekd...................ggiflrgkcdqlesaipysalaqalareell 82 
                                    rp e+  l G+ G GK++ ++++   l+ d                   +    +g   +++ +  y+ + + l++ + l
  gi|119720324|ref|YP_920819.1|  29 RPgEIYALLGPNGAGKTTTLKCVVGLLRPDagdvvvcghsvlrerrevlR---CTGYVPENPVGFDYLRVSEFLDFVGAL 105
                                    3348999*****************98888887666665555555543330...222222222223444444444444444 PP

                         AAA_16  83 rqllde..........aesaeleawrekleealaavpelagaeasrllellkrllallsrderplvlvlDd 143
                                    r + ++          +    le++r+++ ++l+             + ++++ l+ +s  ++p vlv+D+
  gi|119720324|ref|YP_920819.1| 106 RRIPRDvlseraeryiSMF-GLEQYRDAFMGELS-------------RGTVQKVLVVASLLHEPRVLVMDE 162
                                    4444442211333333333.44444444444444.............444444444444444445555443 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   1.2e-05     0.018      16      49 ..      25      58 ..      20      63 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.2e-05
                         AAA_29 16 tieidlkgatlltGpsGsGKSTllDAiqalLvpa 49
                                   ++ +++ +++ l Gp+G+GK+T l  +  lL p+
  gi|119720324|ref|YP_920819.1| 25 SFAVRPGEIYALLGPNGAGKTTTLKCVVGLLRPD 58
                                   5667777799*************99999998886 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.5e-05     0.053       6      56 ..      32      90 ..      28     191 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.5e-05
                         AAA_22  6 gilvvtGesGtGKTtllrrlleqldeeakaee..........erpevvfvtlpsstsskdl 56
                                    i ++ G+ G+GKTt+l+ ++  l  +++a +          er+ev+++t  +++++  +
  gi|119720324|ref|YP_920819.1| 32 EIYALLGPNGAGKTTTLKCVVGLL--RPDAGDvvvcghsvlrERREVLRCTGYVPENPVGF 90
                                   68899**************99998..45555577777777777777776666666655555 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   4.5e-05     0.067      13      50 ..      18      55 ..      11      56 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.5e-05
                         AAA_27 13 kftdrsldfsaeeadlhliyGpNEAGKstalrAisdll 50
                                   k + + l+f     ++  ++GpN AGK+t+l+ +  ll
  gi|119720324|ref|YP_920819.1| 18 KAAVEGLSFAVRPGEIYALLGPNGAGKTTTLKCVVGLL 55
                                   555677999999999999**************998776 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00017      0.25       9      35 ..      30      56 ..      25      68 .. 0.85
   2 ?   -1.0   0.0       1.3   1.9e+03      99     123 ..     151     177 ..     127     191 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00017
                         AAA_19  9 kekvllvtaGpGtGKTrvlkhivallv 35
                                   + ++ +++++ G GKT++lk++v ll 
  gi|119720324|ref|YP_920819.1| 30 PGEIYALLGPNGAGKTTTLKCVVGLLR 56
                                   5678899***************98875 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.3
                         AAA_19  99 klqeeellivDE.fqdvd.elqyrLlk 123
                                     l+e  +l+ DE ++ +d e q++L +
  gi|119720324|ref|YP_920819.1| 151 LLHEPRVLVMDEpMSGMDpESQKTLKD 177
                                    454555999999778888666666643 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   9.3e-05      0.14       3      33 ..      33      63 ..      31      72 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9.3e-05
                                   EEEEEESTTSSHHHHHHHHHHHHHHTTS-EE CS
                          SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvl 33
                                   +++l+G++GaGKTttl  +  ll+ ++ +v+
  gi|119720324|ref|YP_920819.1| 33 IYALLGPNGAGKTTTLKCVVGLLRPDAGDVV 63
                                   6789***********9877766666655555 PP

>> MukB  MukB N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   9.9e-05      0.15      29      54 ..      34      59 ..      30      64 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.9e-05
                                   HHHHS--SHHHHHHHHHHHHHHS--T CS
                           MukB 29 ttlsGgnGaGksttmaafvtaliPdl 54
                                    +l G nGaGk+tt+ ++v  l Pd 
  gi|119720324|ref|YP_920819.1| 34 YALLGPNGAGKTTTLKCVVGLLRPDA 59
                                   5899********************96 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0    0.0002      0.31       3      23 ..      36      56 ..      34     209 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0002
                                   EESSTTSSHHHHHHHHHHHHT CS
                            AAA  3 lyGppGtGKTllakavakelg 23
                                   l Gp G GKT++ k v+  l 
  gi|119720324|ref|YP_920819.1| 36 LLGPNGAGKTTTLKCVVGLLR 56
                                   89*************998774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 1812.56
//
Query:       gi|119720325|ref|YP_920820.1|  [L=524]
Description: hypothetical protein Tpen_1420 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (524 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       882  (0.049194); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 3264.37
//
Query:       gi|119720326|ref|YP_920821.1|  [L=228]
Description: hypothetical protein Tpen_1421 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.46
# Mc/sec: 1499.12
//
Query:       gi|119720327|ref|YP_920822.1|  [L=123]
Description: DNA polymerase beta subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      3e-22   78.5   0.0    3.8e-22   78.2   0.0    1.1  1  Polbeta       Polymerase beta, Nucleotidyltransferase
    3.6e-09   36.8   0.3    6.4e-09   36.0   0.2    1.5  2  NTP_transf_2  Nucleotidyltransferase domain
     0.0052   16.4   0.0     0.0061   16.2   0.0    1.2  1  RlaP          RNA repair pathway DNA polymerase beta family


Domain annotation for each model (and alignments):
>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.2   0.0   6.4e-26   3.8e-22       1      92 [.       8      97 ..       8      98 .. 0.98

  Alignments for each domain:
  == domain 1  score: 78.2 bits;  conditional E-value: 6.4e-26
                                   -STTTTHHHHHHHHSTTEEEEEE-S------EEEEEEEESS---HHHHHHHHHHHHHH.SSSEEEEEETTTS-HHHHHHHHH CS
                        Polbeta  1 ekikeilekekeielaylFGSrakgkareeSDiDlavllkekldleeelelaaelediklgkkvDlvdlneapplllyeilk 82
                                   e+++ ++ek+ ++ +aylFGSra+g  re+SD+D+av++ ++ ++ +e++l+++ e++ +g kvD+v l++ap+++ y +l+
  gi|119720327|ref|YP_920822.1|  8 EELRPVFEKH-GVLFAYLFGSRARGLERENSDWDFAVYFGREVTVVDEARLEDDPEKA-TGLKVDVVALDNAPLDFVYVVLR 87
                                   678999****.***********************************************.99********************* PP

                                   S-EEEES-SH CS
                        Polbeta 83 egkllyskde 92
                                   +g  +ys+de
  gi|119720327|ref|YP_920822.1| 88 DGVPVYSRDE 97
                                   *********8 PP

>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.2   1.1e-12   6.4e-09      11      75 ..      16      81 ..       5     109 .. 0.75
   2 ?   -1.1   0.0      0.39   2.3e+03      48      66 ..      94     112 ..      82     117 .. 0.67

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 1.1e-12
                                   HTTTSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEE........C CS
                   NTP_transf_2 11 lepvakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevdlv........t 75
                                   +++v  ++lfGS+arG+ +++SD D++v++ +e       ++  + a+ ++  e+ +gl+vd+v        +
  gi|119720327|ref|YP_920822.1| 16 KHGVLFAYLFGSRARGLERENSDWDFAVYFGRE-------VTVVDEARLEDDPEKATGLKVDVValdnapldF 81
                                   4558899**************************.......5567788888888888899****9664444330 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.39
                                    HHHEHHHHHHHHCCCEEEC CS
                   NTP_transf_2  48 kkeegleklaeiikfleel 66 
                                     ++e+l+k +ei+  le+l
  gi|119720327|ref|YP_920822.1|  94 SRDERLRKSWEIEAYLEYL 112
                                    3456777778888777775 PP

>> RlaP  RNA repair pathway DNA polymerase beta family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0     1e-06    0.0061       8      43 ..       9      42 ..       4      75 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1e-06
                           RlaP  8 eLeeieeeeevkilyacesGSrawGfpspdsDyDvr 43
                                   eL+++ e+  + +l+a + GSra G++ ++sD D  
  gi|119720327|ref|YP_920822.1|  9 ELRPVFEK--HGVLFAYLFGSRARGLERENSDWDFA 42
                                   55555555..69**********************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 776.05
//
Query:       gi|119720328|ref|YP_920823.1|  [L=228]
Description: formylmethanofuran dehydrogenase, subunit E region [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-35  122.3   0.0    1.8e-35  121.8   0.0    1.2  1  FmdE          FmdE, Molybdenum formylmethanofuran dehydrogena
    5.3e-08   32.7   1.5    5.8e-08   32.5   0.3    1.7  2  zf-dskA_traR  Prokaryotic dksA/traR C4-type zinc finger
  ------ inclusion threshold ------
        0.3   10.5   0.1        0.3   10.5   0.1    2.5  4  zf-ribbon_3   zinc-ribbon domain


Domain annotation for each model (and alignments):
>> FmdE  FmdE, Molybdenum formylmethanofuran dehydrogenase operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.8   0.0     3e-39   1.8e-35       1     128 [.      13     154 ..      13     157 .. 0.96

  Alignments for each domain:
  == domain 1  score: 121.8 bits;  conditional E-value: 3e-39
                                    HHSS--CHHHHHHHHHHHHHHCC....-TT.....SSSEEEEES-STCHHHHHHHHCS--TTTTSEEE--SS-SEEEEEE CS
                           FmdE   1 fHGHlCpglvlGyrmakaalkelgpkeeeg.....deelvaivetdsCldDAiqvltgctlGkgnlivmdygkkaltfkk 75 
                                    fHGH+Cp+lvlG+r++++a ++lg++e+ g     +eelvaive ++C++D++qv+tgct+G+++li+ d+gk alt+ +
  gi|119720328|ref|YP_920823.1|  13 FHGHVCPYLVLGLRASEIAFEKLGVRERPGvsetlGEELVAIVEANNCFADGVQVATGCTFGNNALIYLDTGKTALTLFR 92 
                                    9************************99999************************************************** PP

                                    TTT-EEEEEEE-.........CCTHHHHHHHCCT--GGGS-HHHHHHHHHHHHHHHHHS.HH CS
                           FmdE  76 rktgkavrlklk.........eelpelreklakgkakeekeeeeleeeleeaikkilnapee 128
                                    r+++++vr+++          ++++el++k++ +   ++++ eel ++ ee++ ++l++pe+
  gi|119720328|ref|YP_920823.1|  93 RGEKRGVRVYVVpekveslypPRASELWRKVVVEGRGTREDAEELDKLFEELGLRMLELPES 154
                                    ********************************99995555999*****************86 PP

>> zf-dskA_traR  Prokaryotic dksA/traR C4-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.1   6.7e+03      12      22 ..      29      41 ..      29      43 .. 0.71
   2 !   32.5   0.3   9.7e-12   5.8e-08       1      32 [.     171     204 ..     171     205 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.1
                   zf-dskA_traR 12 pIpeaRlral..P 22
                                   +I++++l ++  P
  gi|119720328|ref|YP_920823.1| 29 EIAFEKLGVRerP 41
                                   6899998887445 PP

  == domain 2  score: 32.5 bits;  conditional E-value: 9.7e-12
                   zf-dskA_traR   1 giygs..CeeCGEpIpeaRlralPgarlCveCqe 32 
                                    +i+++  C++CGE +  +R + ++g++lC +C++
  gi|119720328|ref|YP_920823.1| 171 PIFETvkCSKCGELVWKPRAVYVDGKPLCASCAG 204
                                    6788899*************************97 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.2       1.1   6.5e+03      18      21 ..      17      20 ..      17      20 .. 0.66
   2 ?   -3.6   0.1       1.4   8.6e+03      16      19 ..      57      60 ..      56      61 .. 0.74
   3 ?   10.5   0.1     5e-05       0.3       1      14 [.     174     188 ..     174     191 .. 0.77
   4 ?   -0.7   0.2      0.18   1.1e+03      15      22 ..     195     202 ..     194     203 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.1
                    zf-ribbon_3 18 vCpy 21
                                   vCpy
  gi|119720328|ref|YP_920823.1| 17 VCPY 20
                                   5876 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1.4
                    zf-ribbon_3 16 dnvC 19
                                   +n+C
  gi|119720328|ref|YP_920823.1| 57 ANNC 60
                                   7888 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 5e-05
                    zf-ribbon_3   1 stvrCPnCGa.plss 14 
                                    +tv+C++CG+ + ++
  gi|119720328|ref|YP_920823.1| 174 ETVKCSKCGElVWKP 188
                                    699******966565 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 0.18
                    zf-ribbon_3  15 ddnvCpyC 22 
                                    + + C++C
  gi|119720328|ref|YP_920823.1| 195 GKPLCASC 202
                                    5678**99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1592.45
//
Query:       gi|119720329|ref|YP_920824.1|  [L=374]
Description: periplasmic binding protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-23   83.6   0.0    2.3e-23   83.0   0.0    1.2  1  Peripla_BP_2  Periplasmic binding protein


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.0   0.0   1.3e-27   2.3e-23       1     234 [.      57     303 ..      57     305 .. 0.92

  Alignments for each domain:
  == domain 1  score: 83.0 bits;  conditional E-value: 1.3e-27
                                    EEE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT.............TS-BSBESSSB-HHHHHHH--SEEEE-GGG CS
                   Peripla_BP_2   1 iaslspsvteillalGatdkvvgvdtttsdpldadklee...........aivevgadgeidvEklaalkPDlvilskgl 69 
                                    +++++p+  +++  lGa d vvgv+ + ++++   ++ +           +i   g ++ ++ E +  +kPDlvi+s  +
  gi|119720329|ref|YP_920824.1|  57 VVAIGPGALRLVSYLGAVDLVVGVEDAEKTWSVVGRDYAmvyseffrklpTIGPGGPRSPPNPELIRSVKPDLVIMSRVY 136
                                    79999999999999*********999999999887777788999999999999999999********************* PP

                                    ....GGGHHHHHHHS-EEE----TTS....HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT.-EEEEEEE CS
                   Peripla_BP_2  70 .gltdedeellksgiptvivessntg....eslkeqiralgellgledeaeklvaeidsklaaaksaidsekpkpvlvfg 144
                                     +l d d   +++g+p+v+v+++ +g    +++k+ i+ lg++lg+e++a++l + +ds + ++ s+++   +k + v +
  gi|119720329|ref|YP_920824.1| 137 vELYDPDRLSQEVGAPVVVVDYGIAGylnaSEFKRAITLLGKILGKEERARELCSYVDSLVSDLASRAKGVEKKSIYVGA 216
                                    ***********************988****************************************************** PP

                                    ETTE..EEEE-TTSTTTHHHHTS--EESTTT--STT-EEE-HHHHHHH--SEEEEEEHHHHT-S--HHHHT-S.HHHHTS CS
                   Peripla_BP_2 145 gadeggyvvagsnsyigdlldalgieniaaeskkseyeeisaEqilasdpdvifvsgraeadnktgleflken.pllael 223
                                     +++g+  ++g+++ + +l  +  + ++++++ k +++++++E il+++p ++f++ +   + + +l+++ ++   + +l
  gi|119720329|ref|YP_920824.1| 217 VSYKGAQPFTGTQGKFPPLQLIGTGSIADETG-KVGFINVDFEFILKRQPAYVFIDLN---NLNNVLDDFNKDkSKYCAL 292
                                    ******************98855555555555.*************************...666666666666599**** PP

                                    HHHHTT-EEEE CS
                   Peripla_BP_2 224 pAvkngrVyal 234
                                    +A++ grVya+
  gi|119720329|ref|YP_920824.1| 293 EAFRAGRVYAI 303
                                    *********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 2366.00
//
Query:       gi|119720330|ref|YP_920825.1|  [L=345]
Description: transport system permease protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.9e-80  268.9  38.8    5.9e-80  268.6  38.8    1.1  1  FecCD     FecCD transport family
     0.0021   17.6  17.9     0.0021   17.6  17.9    2.1  1  ABC-3     ABC 3 transport family


Domain annotation for each model (and alignments):
>> FecCD  FecCD transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  268.6  38.8   6.6e-84   5.9e-80       2     312 .]      22     338 ..      16     338 .. 0.96

  Alignments for each domain:
  == domain 1  score: 268.6 bits;  conditional E-value: 6.6e-84
                          FecCD   2 lllllllslllgavkispsevfeallgkadsleaeivlelrlprvlaallvGaaLavaGallQtvtrNpLadPsilGiss 81 
                                    ++++l ls+l g+v ++p++v+++l++   s++a ivl lr  r+++allvGa+L+ aGal Q+ +rNp+a+P +lGis+
  gi|119720330|ref|YP_920825.1|  22 VAAALPLSILSGTV-YKPWDVLRLLQE--GSSDAGIVLALRARRAFVALLVGALLGGAGALTQASFRNPMASPFTLGISQ 98 
                                    45677788899999.6889****9886..788889********************************************* PP

                          FecCD  82 gaalgavlallll.........lgslslfalplaaflgallalllvlllarkrkgasplkliLaGiavsallsaltslll 152
                                    ++alg+++al+++         l+ +    ++l+af++a++ +++vl+l+ +++g +p  l+L+ ia+s++ +a+  l++
  gi|119720330|ref|YP_920825.1|  99 ASALGVAVALVTGiggtggawvLTFSRPTLIALFAFAFAVVQVFVVLALS-WKAGLDPRALVLSSIAISFVYQAALYLMQ 177
                                    *******************999888888999*******************.***************************** PP

                          FecCD 153 lll.neealesilfwllGslsgaswskvllllvllllllllllllarkldllalgdetAkslGvnvervrllllllvall 231
                                    +l+ ne +l++++fw++G+l++a ws++ +l++ + +ll+++++++++ldll++gde+A+s Gv+++ +rl+++l++al 
  gi|119720330|ref|YP_920825.1| 178 YLVlNEVQLATVIFWTFGDLGRAGWSELGVLAAGASALLPVYVAFHKDLDLLSFGDELAASSGVSPRATRLVVTLVAALG 257
                                    **99**************************************************************************** PP

                          FecCD 232 tavavalvGpigFvGLivPhiarllvgadhrkllplsallGallllladllarlllsptelpvgivtaliGapffiylll 311
                                    +a+a+a+vG+++F++L+ Ph+arl+vg +hr+l+p+s+l+G+llll++d ++r +lsp+ lpvgiv++liGap++++lll
  gi|119720330|ref|YP_920825.1| 258 AALATAFVGILAFLCLVSPHLARLFVGGRHRYLVPASMLTGSLLLLVSDAASRSVLSPVVLPVGIVLSLIGAPVLVALLL 337
                                    ******************************************************************************98 PP

                          FecCD 312 r 312
                                    r
  gi|119720330|ref|YP_920825.1| 338 R 338
                                    7 PP

>> ABC-3  ABC 3 transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6  17.9   2.3e-07    0.0021      31     206 ..      89     282 ..      61     315 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.3e-07
                          ABC-3  31 qsllgdalsHaalpGvalayllgvn...............lllgailvgliaavalellkrktklked..taigivlsvf 93 
                                    +s +  ++s a+  Gva+a++ g+                ++l a++++++  +++ +l+ k+ l+    ++  i +s++
  gi|119720330|ref|YP_920825.1|  89 ASPFTLGISQASALGVAVALVTGIGgtggawvltfsrptlIALFAFAFAVVQVFVVLALSWKAGLDPRalVLSSIAISFV 168
                                    45566667777777777777766666667777776699655555666666666666666666655544114557888888 PP

                          ABC-3  94 lalglvlvslikkskvdldsyL...fGniltisqedliliaiieavvllllllfwkelllitfdeelAkveglsvkllkl 170
                                       +l l+++    +v+l+  +   fG++      +l ++a+ +  +l + + f k+l l++f  elA+++g+s+++ +l
  gi|119720330|ref|YP_920825.1| 169 YQAALYLMQYLVLNEVQLATVIfwtFGDLGRAGWSELGVLAAGASALLPVYVAFHKDLDLLSFGDELAASSGVSPRATRL 248
                                    88899999988888888887763337****************************************************** PP

                          ABC-3 171 lllalialavvvalqavGviLvialliiPaatArrl 206
                                    + +++ al  ++a  +vG++     l+ P   Ar++
  gi|119720330|ref|YP_920825.1| 249 VVTLVAALGAALATAFVGILAFLC-LVSPHL-ARLF 282
                                    ******************875554.556644.4444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2606.81
//
Query:       gi|119720331|ref|YP_920826.1|  [L=254]
Description: ABC transporter related [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-31  109.7   0.0      2e-31  109.3   0.0    1.1  1  ABC_tran      ABC transporter
    5.2e-13   49.5   0.3    5.1e-07   29.8   0.1    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    4.4e-06   27.3   0.0    5.4e-06   27.0   0.0    1.2  1  AAA_23        AAA domain
    1.3e-05   24.8   0.0    2.4e-05   24.0   0.0    1.4  1  AAA_29        P-loop containing region of AAA domain
    2.8e-05   23.7   0.0     0.0012   18.3   0.0    2.1  2  SMC_N         RecF/RecN/SMC N terminal domain
    3.2e-05   24.2   0.1    0.00036   20.8   0.1    2.1  1  AAA_22        AAA domain
    4.1e-05   23.5   0.0    0.00045   20.0   0.0    1.9  2  AAA_15        AAA ATPase domain
    7.5e-05   23.2   0.3     0.0003   21.2   0.3    1.9  1  AAA_16        AAA ATPase domain
     0.0024   16.7   0.3      0.014   14.2   0.0    2.1  2  ABC_ATPase    Predicted ATPase of the ABC class
     0.0086   15.7   0.0      0.014   15.0   0.0    1.3  1  AAA_27        AAA domain
  ------ inclusion threshold ------
      0.011   15.9   1.9        1.4    9.1   0.1    2.9  3  HTH_28        Helix-turn-helix domain
      0.016   15.0   0.1      0.051   13.3   0.0    1.8  2  AAA_30        AAA domain
      0.019   15.5   0.0      0.035   14.6   0.0    1.5  1  AAA_18        AAA domain
      0.035   14.5   0.0       0.13   12.7   0.0    1.9  1  AAA           ATPase family associated with various cellular 
      0.038   13.4   0.0      0.083   12.3   0.0    1.5  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.045   13.6   0.0      0.073   13.0   0.0    1.3  1  ATPase_2      ATPase domain predominantly from Archaea
      0.051   13.3   0.1          3    7.6   0.0    3.0  2  Sigma70_r4_2  Sigma-70, region 4
      0.054   13.4   0.0      0.094   12.6   0.0    1.4  1  NACHT         NACHT domain
      0.092   12.5   0.0       0.24   11.1   0.0    1.6  2  PRK           Phosphoribulokinase / Uridine kinase family
        0.1   12.6   0.0        1.2    9.1   0.0    2.5  3  AAA_5         AAA domain (dynein-related subfamily)
       0.12   12.7   0.1       0.43   10.8   0.0    1.8  2  AAA_28        AAA domain
       0.12   12.0   0.0       0.28   10.7   0.0    1.6  2  cobW          CobW/HypB/UreG, nucleotide-binding domain
       0.15   12.1   0.0       0.38   10.8   0.0    1.7  2  AAA_14        AAA domain
       0.16   12.1   0.1       0.22   11.7   0.1    1.6  1  AAA_33        AAA domain
       0.17   11.0   0.0        0.3   10.2   0.0    1.3  1  NB-ARC        NB-ARC domain
       0.18   12.1   0.0        1.6    9.0   0.0    2.1  2  AAA_19        AAA domain
       0.26    8.8   0.0       0.33    8.4   0.0    1.1  1  DUF3584       Protein of unknown function (DUF3584)
       0.29    9.7   0.0       0.52    8.9   0.0    1.3  1  AAA_13        AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.3   0.0   3.1e-34     2e-31       2     137 .]      20     166 ..      19     166 .. 0.93

  Alignments for each domain:
  == domain 1  score: 109.3 bits;  conditional E-value: 3.1e-34
                                    EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                       ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                      vs+++++ge++ i+G+nG+GK+tLl+++ g l+p  G + ldg+++   e+++  + ig+ pq   +++ +tv +   
  gi|119720331|ref|YP_920826.1|  20 GGVSFDVERGEILSIIGPNGSGKTTLLRAIDGILRPRLGAVYLDGREIAGMERREIARIIGYSPQRVDVQSYVTVLDFvl 99 
                                    579***************************************************************************** PP

                                    .............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    .............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 .............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                                  + +++ +al+ ++ ++l+++++     +LSgG+ +rv++aral+ +p++lllDEpt+
  gi|119720331|ref|YP_920826.1| 100 tgrrpyaswdyseSDYRKAVEALRAVNASHLAARRL----DQLSGGEFRRVVIARALAGEPDVLLLDEPTN 166
                                    ********9966444444777888888888888888....******************************8 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.1     8e-10   5.1e-07       4      47 ..      34      76 ..      31      87 .. 0.66
   2 !   18.1   0.0   2.8e-06    0.0018     248     294 ..     146     193 ..      97     199 .. 0.76

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 8e-10
                         AAA_21  4 liGpNgsGKSnLLdaldllarldrdvegltdelsggggirkips 47
                                   +iGpNgsGK++LL+a+d++ r  r +    d +   g++r  + 
  gi|119720331|ref|YP_920826.1| 34 IIGPNGSGKTTLLRAIDGILRP-RLGAVYLDGREIAGMERREIA 76
                                   9******************884.333333333333445555555 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 2.8e-06
                         AAA_21 248 ltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQvil 294
                                    +++  ++++++++ll+DEp n L+Pk + ++l  +++l++ +g+ v++
  gi|119720331|ref|YP_920826.1| 146 VVIARALAGEPDVLLLDEPTNDLDPKHQVEILSAIRRLASgRGVAVVM 193
                                    44555556666*****************99999996666547777766 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.0   8.5e-09   5.4e-06       7      43 ..      16      53 ..      12     128 .. 0.82

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 8.5e-09
                         AAA_23  7 frsfrdqeidFsk.gltlItGpNGaGKTTildAiklaL 43
                                   f+ ++++++d ++  +  I+GpNG+GKTT+l+Ai  +L
  gi|119720331|ref|YP_920826.1| 16 FKALGGVSFDVERgEILSIIGPNGSGKTTLLRAIDGIL 53
                                   667788888887735888****************8777 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   3.8e-08   2.4e-05      14      49 ..      21      56 ..      13      61 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 3.8e-08
                         AAA_29 14 ghtieidlkgatlltGpsGsGKSTllDAiqalLvpa 49
                                   g ++++++ ++  ++Gp+GsGK+Tll Ai  +L p+
  gi|119720331|ref|YP_920826.1| 21 GVSFDVERGEILSIIGPNGSGKTTLLRAIDGILRPR 56
                                   467788866699*****************9999886 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.9e-06    0.0012       9      45 ..      15      50 ..       9      57 .. 0.78
   2 ?    3.6   0.0     0.058        37     136     192 ..     137     189 ..      58     214 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.9e-06
                                   SETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  9 nFksyagktvilpfsksftaivGpNGSGKsnlldAil 45
                                   +Fk + g + +++  + + +i+GpNGSGK+ ll Ai 
  gi|119720331|ref|YP_920826.1| 15 DFKALGGVSFDVERGE-ILSIIGPNGSGKTTLLRAID 50
                                   6777765555555544.889***************95 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.058
                                    CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQf 192
                                    +LSgGe   v +a  +A        + llDe    LD k+  ++ + +++  +   +
  gi|119720331|ref|YP_920826.1| 137 QLSGGEFRRVVIARALA----GEPDVLLLDEPTNDLDPKHQVEILSAIRRLASGRGV 189
                                    78888876665555544....33346799**********999999999987765444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.1   5.7e-07   0.00036       4     128 ..      28     194 ..      26     198 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 5.7e-07
                         AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdl.lrellralglelka............ 70 
                                    +  il ++G+ G+GKTtllr +   l         rp++  v+l + +  + + +re++r++g +  +            
  gi|119720331|ref|YP_920826.1|  28 RGEILSIIGPNGSGKTTLLRAIDGIL---------RPRLGAVYLDGRE-IAGMeRREIARIIGYSPQRvdvqsyvtvldf 97 
                                    567999*******************9.........8888888888877.6666688888888877777888888888888 PP

                         AAA_22  71 .................................erlsseell.ealeqalrarav...ielliiDEaqh.lr...seeal 109
                                                                     +  ++++l    +++ + ara    + +l++DE  + l+   + e+l
  gi|119720331|ref|YP_920826.1|  98 vltgrrpyaswdysesdyrkavealravnashlAARRLDQLSgGEFRRVVIARALagePDVLLLDEPTNdLDpkhQVEIL 177
                                    888888889999999998888888866666666555555555556666665555599999******99999876559999 PP

                         AAA_22 110 eeLrsllnlsrkgvqliLv 128
                                    + +r+l+     gv+++++
  gi|119720331|ref|YP_920826.1| 178 SAIRRLAS--GRGVAVVMC 194
                                    99999998..999998875 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0     7e-07   0.00045      19      48 ..      24      54 ..      15      78 .. 0.78
   2 ?    1.3   0.0      0.36   2.3e+02     323     356 ..     155     188 ..     145     198 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 7e-07
                         AAA_15 19 idlsee.ltvliGkNnsGKSsilealdlFln 48
                                    d++   +  +iG+N+sGK+++l+a+d +l 
  gi|119720331|ref|YP_920826.1| 24 FDVERGeILSIIGPNGSGKTTLLRAIDGILR 54
                                   4444445899****************97765 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.36
                         AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnk 356
                                    ++++ll++EP + L p++q ++  ++++la+   
  gi|119720331|ref|YP_920826.1| 155 EPDVLLLDEPTNDLDPKHQVEILSAIRRLASGRG 188
                                    6899***********************9998665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.3   4.6e-07    0.0003      23      64 ..      28      72 ..      21     212 .. 0.46

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 4.6e-07
                         AAA_16 23 rpelvllsGesGvGKsslvrellralekd.ggiflrgkcdql..e 64
                                   r+e++ ++G+ G+GK++l+r++   l+ + g+++l g+      +
  gi|119720331|ref|YP_920826.1| 28 RGEILSIIGPNGSGKTTLLRAIDGILRPRlGAVYLDGREIAGmeR 72
                                   4489*******************8888775444455554444221 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   2.2e-05     0.014     242     279 ..      26      67 ..       9     113 .. 0.77
   2 ?    0.4   0.0      0.33   2.1e+02     376     413 ..     176     213 ..     135     233 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.2e-05
                                    E-SS.EEEEEE-TTSSHHHHHHHHHHCCSEE...-TTSS-TT CS
                     ABC_ATPase 242 ipkG.vtlIvGggfhGKsTLLeAlekGvynh...vpgDGRef 279
                                    + +G +  I+G++  GK+TLL+A++    ++   v  DGRe+
  gi|119720331|ref|YP_920826.1|  26 VERGeILSIIGPNGSGKTTLLRAIDGILRPRlgaVYLDGREI 67 
                                    6788899*****************854333311145577775 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.33
                                    HHHCHHHHHHHH--EEEEEESS-GCCTTT-SEEEEEET CS
                     ABC_ATPase 376 lvdrvrelykklgvstilvvggsgdyldvAdtvilmee 413
                                    +++ +r+l +  gv +++    + +  + +d++++m++
  gi|119720331|ref|YP_920826.1| 176 ILSAIRRLASGRGVAVVMCLHDLTHAYRYSDKILAMKD 213
                                    34566777777788888888777777788888888876 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   2.2e-05     0.014      11      49 ..      13      52 ..       8      54 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.2e-05
                         AAA_27 11 yGkftdr.sldfsaeeadlhliyGpNEAGKstalrAisdl 49
                                   yG f+    ++f+ e+ ++  i+GpN +GK+t+lrAi  +
  gi|119720331|ref|YP_920826.1| 13 YGDFKALgGVSFDVERGEILSIIGPNGSGKTTLLRAIDGI 52
                                   788877546899999999999***************9865 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1    0.0022       1.4      11      30 ..      68      87 ..      65      88 .. 0.91
   2 ?   -2.5   0.0       9.4     6e+03       1      13 [.     143     155 ..     143     156 .. 0.78
   3 ?    5.2   0.1     0.037        24       4      25 ..     178     199 ..     177     202 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0022
                         HTH_28 11 aGhsvreaArelgisrrtvy 30
                                   aG+ +re+Ar+ g s+++v 
  gi|119720331|ref|YP_920826.1| 68 AGMERREIARIIGYSPQRVD 87
                                   7999*************995 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 9.4
                         HTH_28   1 qRleiikllaaGh 13 
                                    +R+ +i +++aG+
  gi|119720331|ref|YP_920826.1| 143 FRRVVIARALAGE 155
                                    6888899999887 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.037
                         HTH_28   4 eiikllaaGhsvreaArelgis 25 
                                     +i++la+G+ v+ +++++ ++
  gi|119720331|ref|YP_920826.1| 178 SAIRRLASGRGVAVVMCLHDLT 199
                                    69****************9987 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   7.9e-05     0.051      20      46 ..      31      58 ..      25      94 .. 0.76
   2 ?   -1.5   0.0       2.8   1.8e+03      67      67 ..     140     140 ..     111     200 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.9e-05
                         AAA_30 20 vavltGpAGtGKttalkalreaweaa.g 46
                                   +  + Gp G+GKtt+l+a+  +++ + g
  gi|119720331|ref|YP_920826.1| 31 ILSIIGPNGSGKTTLLRAIDGILRPRlG 58
                                   66789**************999887655 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.8
                         AAA_30  67 g 67 
                                    g
  gi|119720331|ref|YP_920826.1| 140 G 140
                                    1 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   5.5e-05     0.035       3     109 ..      34     203 ..      33     209 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.5e-05
                         AAA_18   3 ltGtpGvGKttlakeL....skrlgf................................gvnlrdvakenglllevdpeal 46 
                                    + G+ G+GKttl +++    + rlg                                 +++l +v++ ++++ ++d    
  gi|119720331|ref|YP_920826.1|  34 IIGPNGSGKTTLLRAIdgilRPRLGAvyldgreiagmerreiariigyspqrvdvqsyVTVLDFVLTGRRPYASWDYS-E 112
                                    78**************88885555224666666666688888899999999777777666666667777777776666.5 PP

                         AAA_18  47 deskrldedkldklldaleenss................aleegknlvidghlaeleseaakdikk............vv 98 
                                    +++++++e  ++++ + l + +                   +e+++l++d   ++l +  +++i              vv
  gi|119720331|ref|YP_920826.1| 113 SDYRKAVEALRAVNASHLAARRLdqlsggefrrvviaraLAGEPDVLLLDEPTNDLDPKHQVEILSairrlasgrgvaVV 192
                                    56666666666666666655444777777777777777766777777777777666666666655566666666666666 PP

                         AAA_18  99 LtaspeelleR 109
                                    + +++ +++ R
  gi|119720331|ref|YP_920826.1| 193 MCLHDLTHAYR 203
                                    66666555555 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0    0.0002      0.13       3      35 ..      34      68 ..      32     166 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0002
                                   EESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCS CS
                            AAA  3 lyGppGtGKTllakavakelg..vefleisgsell 35
                                   ++Gp G GKT+l +a+   l      + ++g e+ 
  gi|119720331|ref|YP_920826.1| 34 IIGPNGSGKTTLLRAIDGILRprLGAVYLDGREIA 68
                                   78*************98887522223555555555 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00013     0.083      25      64 ..      32      71 ..      27      93 .. 0.82
   2 ?   -2.9   0.0       5.5   3.5e+03      10     113 ..     143     162 ..     122     181 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                   Mg_chelatase 25 lllvGppGsGKtmlakrlpsllpplseeealevakiasva 64
                                   l ++Gp GsGKt l +++ ++l p   +  l+ ++ia + 
  gi|119720331|ref|YP_920826.1| 32 LSIIGPNGSGKTTLLRAIDGILRPRLGAVYLDGREIAGME 71
                                   5589******************988777777777766655 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.5
                   Mg_chelatase  10 eakraleiaaaGgHnlllvGppGsGKtmlakrlpsllpplseeealevakiasvagkkeeekllkrrpfraphhsaskaa 89 
                                      + ++  a aG+ ++ll+                                                             
  gi|119720331|ref|YP_920826.1| 143 FRRVVIARALAGEPDVLLL------------------------------------------------------------- 161
                                    4444444445555554444............................................................. PP

                   Mg_chelatase  90 lvGggskpkpGeislahnGvLfLD 113
                                                           D
  gi|119720331|ref|YP_920826.1| 162 -----------------------D 162
                                    .......................3 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00011     0.073      18      40 ..      27      49 ..      23      66 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00011
                       ATPase_2 18 epneiyfiYGpegsGKtaLlkei 40
                                   e+ ei+ i Gp gsGKt+Ll+ i
  gi|119720331|ref|YP_920826.1| 27 ERGEILSIIGPNGSGKTTLLRAI 49
                                   6789999*************976 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0    0.0047         3      23      44 ..      66      87 ..      64      89 .. 0.87
   2 ?    2.1   0.0      0.24   1.5e+02       3      30 ..     175     201 ..     173     201 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0047
                                   HTS---HHHHHHHHT--HHHHH CS
                   Sigma70_r4_2 23 yleglsykEIAellgisegtVk 44
                                   ++ g+  +EIA+++g s++ V+
  gi|119720331|ref|YP_920826.1| 66 EIAGMERREIARIIGYSPQRVD 87
                                   67899************99987 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.24
                                    HHHHHHTTS-HHHHHHHHHHHTS---HH CS
                   Sigma70_r4_2   3 alrealaeLperqreifllryleglsyk 30 
                                    +++ a+++L   +  +++++ l++l+++
  gi|119720331|ref|YP_920826.1| 175 EILSAIRRLASGRGVAVVMC-LHDLTHA 201
                                    799****************5.9999986 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00015     0.094       3      20 ..      32      49 ..      30      55 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00015
                                   EEEEC-TTTCHHHHHHHH CS
                          NACHT  3 vilqGeaGsGKTtLlqkl 20
                                   + + G++GsGKTtLl+ +
  gi|119720331|ref|YP_920826.1| 32 LSIIGPNGSGKTTLLRAI 49
                                   5699***********987 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00037      0.24       1      42 [.      31      71 ..      31      78 .. 0.85
   2 ?   -2.3   0.0       4.7     3e+03     136     164 ..     168     196 ..     167     206 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00037
                            PRK  1 vIgvagsSGaGkttvarklekifgrekvkaaeiegdsflrld 42
                                   ++++ g+ G+Gktt+ r+++ i++   + a++ +g ++  ++
  gi|119720331|ref|YP_920826.1| 31 ILSIIGPNGSGKTTLLRAIDGILR-PRLGAVYLDGREIAGME 71
                                   6799*******************9.88888888877776665 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4.7
                            PRK 136 vdisidlelarklqRDiaeRGrsleavld 164
                                    +d+++++e+   + R  + RG  +  +l+
  gi|119720331|ref|YP_920826.1| 168 LDPKHQVEILSAIRRLASGRGVAVVMCLH 196
                                    68888888888888888888877766654 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0    0.0019       1.2       4      24 ..      34      54 ..      31      94 .. 0.78
   2 ?   -0.8   0.0       2.1   1.4e+03      52      73 ..     141     163 ..     117     183 .. 0.68
   3 ?   -0.4   0.0       1.7   1.1e+03      40      69 ..     197     226 ..     175     244 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0019
                                   EE--SSSSHHHHHHHGGGGBS CS
                          AAA_5  4 LvGppGtgKselaerlaaaln 24
                                   ++Gp G+gK++l + +   l+
  gi|119720331|ref|YP_920826.1| 34 IIGPNGSGKTTLLRAIDGILR 54
                                   79************9988874 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.1
                                    .....--------.G-SEEEEES CS
                          AAA_5  52 tslvdsplvraar.egeilvlDE 73 
                                     +++  ++ ra   e+++l+lDE
  gi|119720331|ref|YP_920826.1| 141 GEFRRVVIARALAgEPDVLLLDE 163
                                    45555566666557999999998 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.7
                                    HHH--B--.........--------G-SEE CS
                          AAA_5  40 dlkgrreikngttslvdsplvraaregeil 69 
                                    dl+  ++++++  +++d++++  +r  +++
  gi|119720331|ref|YP_920826.1| 197 DLTHAYRYSDKILAMKDGSVYAFGRPEDVM 226
                                    788888999999999999999777765554 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00067      0.43       4      19 ..      34      49 ..      32      70 .. 0.88
   2 ?   -1.3   0.0       3.6   2.3e+03      32      79 ..     116     162 ..     100     167 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00067
                         AAA_28  4 itGgestGKTtlleaL 19
                                   i+G+ ++GKTtll+a+
  gi|119720331|ref|YP_920826.1| 34 IIGPNGSGKTTLLRAI 49
                                   9************997 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 3.6
                         AAA_28  32 reileeklakgedalpwvedllafaervleeqleeeaaaaankvlfcD 79 
                                    r+ +e + a +  +l++ ++l ++  +  +  + + a a +++vl++D
  gi|119720331|ref|YP_920826.1| 116 RKAVEALRAVNASHLAA-RRLDQLSGGEFRRVVIARALAGEPDVLLLD 162
                                    44444444555555554.355555444333333344555666666666 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00044      0.28       3      20 ..      32      49 ..      30      56 .. 0.88
   2 ?   -2.9   0.0       6.6   4.2e+03     110     122 ..      86      98 ..      83     148 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00044
                                   EEEEESTTCCHHHHHHHH CS
                           cobW  3 tvltGflGsGKTtLlnhl 20
                                   + + G+ GsGKTtLl+++
  gi|119720331|ref|YP_920826.1| 32 LSIIGPNGSGKTTLLRAI 49
                                   5689***********975 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 6.6
                                    CCECEEEEEEETT CS
                           cobW 110 ltldavvavvDak 122
                                    + +++ v+v+D  
  gi|119720331|ref|YP_920826.1|  86 VDVQSYVTVLDFV 98 
                                    6677777777762 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0    0.0006      0.38       3      22 ..      30      49 ..      28      98 .. 0.70
   2 ?   -2.3   0.0       6.5   4.2e+03      60      74 ..     152     165 ..     121     185 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0006
                         AAA_14  3 kilvitGaRrvGKTtllkql 22
                                   +il i G+  +GKTtll+ +
  gi|119720331|ref|YP_920826.1| 30 EILSIIGPNGSGKTTLLRAI 49
                                   7999************9866 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 6.5
                         AAA_14  60 lkeekktylflDEiq 74 
                                    l + +  +l+lDE  
  gi|119720331|ref|YP_920826.1| 152 LAG-EPDVLLLDEPT 165
                                    334.67788888865 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00034      0.22       4      18 ..      34      48 ..      31     192 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00034
                         AAA_33  4 lvGlpGsGKstlaer 18
                                   ++G++GsGK+tl++ 
  gi|119720331|ref|YP_920826.1| 34 IIGPNGSGKTTLLRA 48
                                   79**********986 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00047       0.3      21      40 ..      30      49 ..      23      51 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00047
                                   EEEEEEESTTSSHHHHHHHH CS
                         NB-ARC 21 lvvalvGmgGvGKttlakqi 40
                                    ++++ G  G+GKttl++ i
  gi|119720331|ref|YP_920826.1| 30 EILSIIGPNGSGKTTLLRAI 49
                                   599*************9876 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0    0.0025       1.6      11      30 ..      30      49 ..      23      62 .. 0.84
   2 ?    0.6   0.0         1   6.6e+02     102     126 ..     155     181 ..     113     192 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0025
                         AAA_19 11 kvllvtaGpGtGKTrvlkhi 30
                                   ++l ++++ G+GKT++l++i
  gi|119720331|ref|YP_920826.1| 30 EILSIIGPNGSGKTTLLRAI 49
                                   6788************9987 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1
                         AAA_19 102 eeellivDE.fqdvd.elqyrLlkall 126
                                    e ++l+ DE + d+d + q+++l+a+ 
  gi|119720331|ref|YP_920826.1| 155 EPDVLLLDEpTNDLDpKHQVEILSAIR 181
                                    344899999668999999999999986 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0   0.00052      0.33      21      37 ..      33      49 ..      19      50 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00052
                        DUF3584 21 nieGtNaaGKTtLlrLi 37
                                    i G N++GKTtLlr i
  gi|119720331|ref|YP_920826.1| 33 SIIGPNGSGKTTLLRAI 49
                                   689************76 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0   0.00082      0.52      21      39 ..      34      52 ..      29      65 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00082
                         AAA_13 21 iYGwNGaGKTtLSrllrsl 39
                                   i G NG+GKTtL r+++ +
  gi|119720331|ref|YP_920826.1| 34 IIGPNGSGKTTLLRAIDGI 52
                                   679**********999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                       109  (0.00607954); expected 17.9 (0.001)
Passed Fwd filter:                        28  (0.00156172); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              28  [number of targets reported over threshold]
# CPU time: 0.69u 0.40s 00:00:01.08 Elapsed: 00:00:00.57
# Mc/sec: 1343.92
//
Query:       gi|119720332|ref|YP_920827.1|  [L=802]
Description: plasma-membrane proton-efflux P-type ATPase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-45  155.4   3.9    1.1e-45  155.4   3.9    2.4  4  E1-E2_ATPase     E1-E2 ATPase
    7.2e-29  101.6   0.1    1.3e-28  100.7   0.1    1.5  1  Hydrolase        haloacid dehalogenase-like hydrolase
    3.8e-16   58.5   0.1      1e-15   57.2   0.0    1.8  2  Cation_ATPase_N  Cation transporter/ATPase, N-terminus
    1.6e-07   31.3   0.1    1.9e-06   27.8   0.1    2.2  2  Hydrolase_3      haloacid dehalogenase-like hydrolase
     0.0051   16.9   0.0      0.012   15.7   0.0    1.6  1  Cation_ATPase    Cation transport ATPase (P-type)
  ------ inclusion threshold ------
      0.063   13.7   0.2        2.5    8.5   0.0    2.9  2  HAD              haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.4   3.9   3.6e-49   1.1e-45       6     181 .]     120     294 ..     115     294 .. 0.98
   2 ?   -3.7   0.0       2.4   7.1e+03      51      70 ..     480     499 ..     474     507 .. 0.66
   3 ?   -4.1   0.5       3.3   9.9e+03     112     139 ..     608     635 ..     595     651 .. 0.62
   4 ?   -3.9   0.2       2.9   8.6e+03     124     132 ..     752     760 ..     738     778 .. 0.49

  Alignments for each domain:
  == domain 1  score: 155.4 bits;  conditional E-value: 3.6e-49
                                    EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-SEEE-TTTS---S-EE-G-TTEE-TT-EEEE-EEEEEE CS
                   E1-E2_ATPase   6 takvirdgteeeidakelvpGDivllkagdrvpaDgrivegsaevdesaLTGEslpvekekgdmvfsGtvvvsgeakavV 85 
                                    ++kv+rdg++++ +a+e+vpGD+v l  gd vpaD++iv+g+  vd+saLTGEslpv+ ++ d +++G+vvv+geak+ V
  gi|119720332|ref|YP_920827.1| 120 RVKVLRDGSWTTREAREIVPGDVVMLGLGDLVPADVKIVSGELLVDQSALTGESLPVSLKESDVAYAGSVVVRGEAKCLV 199
                                    689***************************************************************************** PP

                                    EE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHHHHS-TTHHH CS
                   E1-E2_ATPase  86 tatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgkslaeallralallvaaiPcaLpl 165
                                    ++tg +t++g+ a+lv+ a + +++ ++++  +++++  v+++++l+++++al++g +l  + ++a  +l++a+P aLp+
  gi|119720332|ref|YP_920827.1| 200 VNTGVNTYFGRTAELVKIA-KPRSHQEEIILAVTRYMLYVGVAALLATAAYALVRGMDLLSIAVFADIFLMGAVPVALPA 278
                                    *******************.899999****************************************************** PP

                                    HHHHHHHHHHHHHHHT CS
                   E1-E2_ATPase 166 avplalalgarrlakk 181
                                    +++++ a+ga +lak+
  gi|119720332|ref|YP_920827.1| 279 VLTIVQAVGALELAKE 294
                                    **************95 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 2.4
                                    E-TTTS---S-EE-G-TTEE CS
                   E1-E2_ATPase  51 desaLTGEslpvekekgdmv 70 
                                    +  +LTG+++++ +e   ++
  gi|119720332|ref|YP_920827.1| 480 KPMMLTGDNVAIAREVARQA 499
                                    55689999999988544443 PP

  == domain 3  score: -4.1 bits;  conditional E-value: 3.3
                                    HHHHHHHHHHHHHHHHHHHHHHHHS-ST CS
                   E1-E2_ATPase 112 qkkldklgkvlvpvvlliallvfliall 139
                                    q+ l+ +++ +v+vv +i++l++ +++l
  gi|119720332|ref|YP_920827.1| 608 QRLLSWVVNKVVKVVQFIGMLALGFFWL 635
                                    5555556666565555555544444333 PP

  == domain 4  score: -3.9 bits;  conditional E-value: 2.9
                                    HHHHHHHHH CS
                   E1-E2_ATPase 124 pvvlliall 132
                                    +++++ a++
  gi|119720332|ref|YP_920827.1| 752 TIAVFTAMA 760
                                    222222222 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.7   0.1   4.4e-32   1.3e-28       1     209 [.     310     567 ..     310     568 .. 0.84

  Alignments for each domain:
  == domain 1  score: 100.7 bits;  conditional E-value: 4.4e-32
                                    SSEEEEESBTTTBCHHHHHHHHHHHH.....CHHHHHHHHHH..HHCHHHHHHHHHHHHHHHHHHHHHHETTTE...... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...... RF
                      Hydrolase   1 iktvvfDkdGTLttgepsvedvivsa.....alalaaaletg..sehpigkalvaaakarsgaltgfatfigrg...... 67 
                                    i++v++Dk+GT+t+ + sv+ v++ +     ++al aal+ +   +  i  a++ +a  r+  l+ +++           
  gi|119720332|ref|YP_920827.1| 310 IDVVCLDKTGTITQNKLSVVGVVPLRgygedDVALVAALASSeeGKDIIDSAVIGYARSRGLRLEAYRR----Vsftpfd 385
                                    799**************************************9865555556667777777444444444....0223344 PP

                                    .................HHHHTHHHHHHHH..HCHHHHHHHHHHHHHHCHHHHHH.........TTHHHHHHHHHHTHHB CS
                                    .................xxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxx RF
                      Hydrolase  68 .................ayaigkpewltal..dippdlgaaigsaqsqgrtvall.........qaralavftiadplkv 119
                                                     ++ +g p+ + +l    p + ++a +++ ++g  v  +             ++++++adp  v
  gi|119720332|ref|YP_920827.1| 386 pslkrseavvehdgarfKAVKGAPQVVLELcnGAPREAEEALEELSRRGYRVLAVarspdndldTLTPVGLLALADP--V 463
                                    555555666666679999*******99999999999999999999999999999999998877766***********..* PP

                                    HTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT....GGGE.SEEEEHHCES.........STTTSHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxx.xxxxxxxxxx.........xxxxxxxxxxxxxxx RF
                      Hydrolase 120 kpeaaeavasLkaagievvlltgdnpetaeraanqlG....ddyf.daviasdiet.........vakpspegkvaaire 185
                                    +p+ + ++++Lk+ gi+  +ltgdn + a+++a+q+        f +++  s +e+         +a++ pe+k +++r 
  gi|119720332|ref|YP_920827.1| 464 RPDSKALIEELKSLGIKPMMLTGDNVAIAREVARQASigdrVVSFaEFKRLSRDEKlrlvdtydgFAEVYPEDKYEIVRL 543
                                    ***********************************8888983344455555555556777779***************** PP

                                    HTSTGGGEEEEESSHHHHHHHHHT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase 186 LqgkpeevamVGDgvnDaaalaaA 209
                                    Lq+k++ v m GDgvnDa+al++A
  gi|119720332|ref|YP_920827.1| 544 LQEKGHMVGMTGDGVNDAPALKQA 567
                                    **********************99 PP

>> Cation_ATPase_N  Cation transporter/ATPase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.2   0.0   3.4e-19     1e-15       2      69 .]      11      76 ..      10      76 .. 0.97
   2 ?   -3.6   0.1       3.1   9.4e+03      52      63 ..     709     720 ..     709     722 .. 0.80

  Alignments for each domain:
  == domain 1  score: 57.2 bits;  conditional E-value: 3.4e-19
                Cation_ATPase_N  2 halsleevlekLetdlenGLtqaeaaerlkkyGpNelkekkkkslwvkllkqftnplvilLlvaalvs 69
                                   ++l++ee+++ Le  +++GL+++ea++rl+kyG Ne+  +kk+s +v +l+ ++ p+++lL+ a ++s
  gi|119720332|ref|YP_920827.1| 11 AKLPVEEAFRILE-ASPSGLSEEEARRRLEKYGYNEV-VEKKRSPVVEFLSRYWGPMPWLLELAIVLS 76
                                   689*********9.9**********************.***************************998 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 3.1
                Cation_ATPase_N  52 kqftnplvilLl 63 
                                    kq+++++++lL+
  gi|119720332|ref|YP_920827.1| 709 KQLRSFTLLLLV 720
                                    689999999986 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.11   3.3e+02      16      59 ..     463     506 ..     456     509 .. 0.84
   2 !   27.8   0.1   6.5e-10   1.9e-06     199     255 .]     544     600 ..     517     600 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.11
                                    --HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEEE CS
                    Hydrolase_3  16 isektkeaikklkekgikvviATGRslravlpvleelgldlpvi 59 
                                    + + +k+ i++lk+ gik +  TG ++  +++v+++  +   v+
  gi|119720332|ref|YP_920827.1| 463 VRPDSKALIEELKSLGIKPMMLTGDNVAIAREVARQASIGDRVV 506
                                    56788999****************99999999999888776665 PP

  == domain 2  score: 27.8 bits;  conditional E-value: 6.5e-10
                                    CT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE--GGGTHHHHHH CS
                    Hydrolase_3 199 lnisleeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtksnnedGVakal 255
                                    l+ +  +v   GDg ND + L++a++g+A+ na++ +k+ A+ v +     G++ka+
  gi|119720332|ref|YP_920827.1| 544 LQEKGHMVGMTGDGVNDAPALKQAEMGIAVSNATDVAKASASVVLTEEGLKGIVKAI 600
                                    55566677788**********************************999999999987 PP

>> Cation_ATPase  Cation transport ATPase (P-type)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   3.9e-06     0.012      44      89 ..     374     417 ..     317     419 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.9e-06
                  Cation_ATPase  44 eetkkvqeipFnssrKrmsvvlklepekkvrlyvKGApeiilkrCt 89 
                                    e + +v   pF+ s Kr   v++   ++     vKGAp+++l+ C+
  gi|119720332|ref|YP_920827.1| 374 EAYRRVSFTPFDPSLKRSEAVVEH--DGARFKAVKGAPQVVLELCN 417
                                    348999*****************5..699999*************6 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.13   3.9e+02      24      66 ..      24      66 ..       3      81 .. 0.74
   2 ?    8.5   0.0   0.00083       2.5      87     188 .]     464     565 ..     449     565 .. 0.67

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.13
                            HAD 24 rrgaprlwralreklllalfrellrldraglaelleallagls 66
                                   ++++    +++r++l+++ ++e  + +r+ + e+l++++++++
  gi|119720332|ref|YP_920827.1| 24 ASPSGLSEEEARRRLEKYGYNEVVEKKRSPVVEFLSRYWGPMP 66
                                   3333334788888899999********************9997 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00083
                            HAD  87 dpgalellaahraaGdrvvvvSgglrplvepllaelg.adevlat.elevdd...........rltgelglegkpvrgeg 153
                                    +p+ ++l+++ ++ G++  +++g +  ++++++++    d+v++  e++  +            ++g +++++ + ++  
  gi|119720332|ref|YP_920827.1| 464 RPDSKALIEELKSLGIKPMMLTGDNVAIAREVARQASiGDRVVSFaEFK--RlsrdeklrlvdTYDGFAEVYPEDKYE-- 539
                                    589999999999*********************9777445554433222..122444665555566664444433333.. PP

                            HAD 154 kvaalrewlaaegegidleevvay.GDspsDlpllr 188
                                        + + l+++g+      +v   GD+++D p+l+
  gi|119720332|ref|YP_920827.1| 540 ----IVRLLQEKGH------MVGMtGDGVNDAPALK 565
                                    ....3333555664......5555699999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (802 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       855  (0.0476881); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.88u 0.37s 00:00:01.25 Elapsed: 00:00:00.58
# Mc/sec: 4189.99
//
Query:       gi|119720333|ref|YP_920828.1|  [L=440]
Description: cytochrome c biogenesis protein, transmembrane region [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.5e-08   33.9   0.2    1.5e-06   28.6   0.2    2.2  1  Thioredoxin_2  Thioredoxin-like domain
    4.2e-07   29.9   0.0    7.1e-07   29.2   0.0    1.3  1  Thioredoxin    Thioredoxin
    0.00026   21.0   0.0    0.00042   20.3   0.0    1.3  1  Thioredoxin_3  Thioredoxin domain
     0.0012   18.8  15.6       0.11   12.4   5.1    2.3  2  DsbD           Cytochrome C biogenesis protein transmembrane 
     0.0099   15.7   0.1     0.0099   15.7   0.1    2.2  2  VirB8          VirB8 protein
  ------ inclusion threshold ------
       0.22   11.3   0.0       0.38   10.5   0.0    1.3  1  TraF           F plasmid transfer operon protein


Domain annotation for each model (and alignments):
>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.2   5.1e-10   1.5e-06       3     103 ..     108     189 ..     106     195 .. 0.75

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 5.1e-10
                  Thioredoxin_2   3 gngkpvlvvftdpdCpyCkklkkelkel.ddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgt 81 
                                    ++g  v+++f++p+Cp C+k++     l ++  v         ++ +++v++   +             e  +kygv++t
  gi|119720333|ref|YP_920828.1| 108 SSGGAVAIMFSSPTCPVCEKMEPYWAALaSRGGVL--------AVRFYVVRLGEGTA------------EAFYKYGVTST 167
                                    568899*****************888884222222........34455555544444............56999****** PP

                  Thioredoxin_2  82 Pt.ivfldgkeivarlpGyvpae 103
                                    Pt i+fldg+ ++ar++G  p  
  gi|119720333|ref|YP_920828.1| 168 PTyILFLDGR-VAARYVGEFPGP 189
                                    **666*****.*******98765 PP

>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.0   2.4e-10   7.1e-07      14      93 ..     107     187 ..      97     197 .. 0.84

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 2.4e-10
                                    HTTTSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTT.TSEEEEEETTTSH.HHHHHTT-SSSSEEEEEETTEEEEEEESS CS
                    Thioredoxin  14 vakekklvlveFyApwCghCkalaPeleklaeelkd.kvklakvdvdene.dlakkyevegiPtlklfkngkevkkyega 91 
                                    v++    v + F +p C+ C +++P +++la++     v+++ v   e + +   ky+v++ Pt +lf +g+ +++y+g+
  gi|119720333|ref|YP_920828.1| 107 VSS-GGAVAIMFSSPTCPVCEKMEPYWAALASRGGVlAVRFYVVRLGEGTaEAFYKYGVTSTPTYILFLDGRVAARYVGE 185
                                    444.67899**********************9988789999999988865155689**********************98 PP

                                    -H CS
                    Thioredoxin  92 re 93 
                                     +
  gi|119720333|ref|YP_920828.1| 186 FP 187
                                    66 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   1.4e-07   0.00042       6      60 ..     118     179 ..     112     196 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.4e-07
                                    ESSSSTTCHHHHHHHHHHCHCCTCEC....EEECCTTHHHH.HHCT-SSSSEE..ECTTCEE CS
                  Thioredoxin_3   6 lgpgCakCpklekavkeaaaekgika....evekvtdfeei.ekygVmsvPal..vidgkvv 60 
                                     +p+C+ C+k+e  ++++a + g+ a     v   + + e   kygV+s+P+   ++dg+v 
  gi|119720333|ref|YP_920828.1| 118 SSPTCPVCEKMEPYWAALASRGGVLAvrfyVVRLGEGTAEAfYKYGVTSTPTYilFLDGRVA 179
                                    3899*******************8887885455558788878*********97568999985 PP

>> DsbD  Cytochrome C biogenesis protein transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   5.1   3.5e-05      0.11       2      78 ..     243     316 ..     242     327 .. 0.78
   2 !   11.9   2.8   5.3e-05      0.16     128     213 .]     349     436 ..     339     436 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.5e-05
                           DsbD   2 flaGllsflsPCilpliPaylsyisgvsvedvktekkkvkvllkallFvlGlslvfvslglsaaflgqllkdvkevi 78 
                                    f aG+l+ +sPC lpl+ a  +  + v+    +       ++  +   +l l l f++l+ + + + ++l+ ++ ++
  gi|119720333|ref|YP_920828.1| 243 FFAGVLAAFSPCTLPLLIAHAAASARVGARASRMA---GGCFAASASSILALGLLFALLSKALSVAHAVLTSFTAIL 316
                                    89***************999887776666555443...256888888888999999999999998888887776655 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 5.3e-05
                           DsbD 128 tFalgwsPCigP.vlasvlalaask.eslakgallllvyvlGlaipfllvglllellkkklkslkkyskaveiaggvllv 205
                                    +F++ +  C  P vl+  la+++++ e+ ++++ l l y+lG + ++ l+   ++++   ++      + v+ ++g+ll+
  gi|119720333|ref|YP_920828.1| 349 LFGFLSVQCNLPlVLGPFLAVVGTSmEDFSEALYLALGYSLGTSSVLALALSGSGKVASLFERALYREDLVNRLSGLLLI 428
                                    58899999999967999999998762667777778888*****99999987777777777777777789*********** PP

                           DsbD 206 llGvllll 213
                                     +G lll+
  gi|119720333|ref|YP_920828.1| 429 AAGTLLLF 436
                                    ****9985 PP

>> VirB8  VirB8 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   3.3e-06    0.0099       3      54 ..      48      99 ..      46     131 .. 0.92
   2 ?   -2.6   2.1       1.4   4.1e+03      12      40 ..     266     293 ..     261     323 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.3e-06
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXX CS
                          VirB8  3 rqfwderigsarvqarnwrlvafvslliavlavgavvlllplktvePyvvev 54
                                    + w+   +s ++++r  + + ++++++++++++a+++  +++  ePy+  +
  gi|119720333|ref|YP_920828.1| 48 MKTWKLSLNSPAKSRRLGWRALVAMVALSAVLSVALLYARSQRPAEPYLLAS 99
                                   5678888999**************************************9875 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.4
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          VirB8  12 sarvqarnwrlvafvslliavlavgavvl 40 
                                    sarv ar  r++ +++++ ++ +++a+ l
  gi|119720333|ref|YP_920828.1| 266 SARVGARASRMA-GGCFAASASSILALGL 293
                                    566666655555.6666666655555433 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00013      0.38     134     199 ..     115     173 ..     105     185 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00013
                           TraF 134 lfFyrgkcpyceaqapilqafadkyg.levra..VsvdgrplpelpnarvdkgqaarlgvkrtPalvlv 199
                                    ++F +++cp+ce++ p   a+a + g l+vr+  V + ++  +             ++gv++tP+ +l+
  gi|119720333|ref|YP_920828.1| 115 IMFSSPTCPVCEKMEPYWAALASRGGvLAVRFyvVRLGEGTAE----------AFYKYGVTSTPTYILF 173
                                    89********************998723444310222222222..........2335777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 2622.66
//
Query:       gi|119720334|ref|YP_920829.1|  [L=124]
Description: hypothetical protein Tpen_1429 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.2e-25   87.2   0.1    6.8e-25   86.8   0.1    1.2  1  PDDEXK_10    PD-(D/E)XK nuclease superfamily
    5.5e-15   55.3   0.4    8.6e-15   54.7   0.4    1.3  1  DUF3782      Protein of unknown function (DUF3782)
     0.0054   16.9   0.2     0.0073   16.5   0.2    1.2  1  DUF4143      Domain of unknown function (DUF4143)
  ------ inclusion threshold ------
       0.01   15.6   0.0      0.014   15.2   0.0    1.2  1  TraO         Conjugative transposon protein TraO
      0.018   15.3   0.2      0.028   14.7   0.2    1.3  1  UPF0102      Uncharacterised protein family UPF0102
      0.072   13.1   0.0      0.084   12.9   0.0    1.2  1  DUF3883      Domain of unknown function (DUF3883)
        0.1   13.1   0.0       0.15   12.6   0.0    1.2  1  Herpes_HEPA  Herpesvirus DNA helicase/primase complex associa
       0.14   11.8   0.0       0.18   11.3   0.0    1.2  1  AHJR-like    REase_AHJR-like


Domain annotation for each model (and alignments):
>> PDDEXK_10  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.8   0.1   3.1e-28   6.8e-25       1      73 [.      49     116 ..      49     117 .. 0.98

  Alignments for each domain:
  == domain 1  score: 86.8 bits;  conditional E-value: 3.1e-28
                      PDDEXK_10   1 sevelDvvvkdgkvilvEiksslkrgDlavikrkkelYekakgvkvdrlivvtpfiddrnpervkavAerlgi 73 
                                    seve+D+vv+d+++ilvE+ks+++rgD+a+++r++ lYek+ gvk +rl++v++fid++    ++++A +lg+
  gi|119720334|ref|YP_920829.1|  49 SEVEVDLVVRDREHILVEVKSRVSRGDVAELYRVGLLYEKLYGVK-PRLVLVGGFIDTD----AWETAGALGV 116
                                    79*******************************************.*************....********98 PP

>> DUF3782  Protein of unknown function (DUF3782)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.7   0.4   3.8e-18   8.6e-15      34      77 ..       3      47 ..       1      48 [. 0.96

  Alignments for each domain:
  == domain 1  score: 54.7 bits;  conditional E-value: 3.8e-18
                        DUF3782 34 LGaRWGlvsEeafReglkeiLeealgv.kVekwlyyDkeGeVygy 77
                                   +++R+G+++E+afRe++k+++ee+lg+  V+++++yD+eG Vyg+
  gi|119720334|ref|YP_920829.1|  3 VSHRFGVLTESAFREAMKYVVEEVLGAgAVRRVTMYDEEGLVYGH 47
                                   689*****************************************9 PP

>> DUF4143  Domain of unknown function (DUF4143)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.2   3.2e-06    0.0073      71     121 ..      21      69 ..       5      70 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.2e-06
                                    xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        DUF4143  71 allEnlVaqeLlky.sekegaklyyyrdkngaEvDfvielkggkivpiEvKs 121
                                    +++E +  +  +++ + +++  l y + k++ EvD+v++  +++ +++EvKs
  gi|119720334|ref|YP_920829.1|  21 YVVEEVLGAGAVRRvTMYDEEGLVYGH-KSEVEVDLVVR--DREHILVEVKS 69 
                                    555555555555555444344444444.369*******7..56788*****9 PP

>> TraO  Conjugative transposon protein TraO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   6.2e-06     0.014     111     151 ..      35      75 ..      23      84 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 6.2e-06
                           TraO 111 atllnkdafiyGgavtlelelyLsdrvvllvnlrervlfgs 151
                                     t+ +++  +yG + ++e++l + dr  +lv+++ rv  g 
  gi|119720334|ref|YP_920829.1|  35 VTMYDEEGLVYGHKSEVEVDLVVRDREHILVEVKSRVSRGD 75 
                                    48999*******************************98775 PP

>> UPF0102  Uncharacterised protein family UPF0102
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.2   1.2e-05     0.028      26      47 ..      51      73 ..      40      83 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.2e-05
                                   EEEEEEE.TTEEEEEEEEE-... CS
                        UPF0102 26 gEiDiia.tevlvfvEVKtRsse 47
                                    E+D+++ +++ + vEVK+R s+
  gi|119720334|ref|YP_920829.1| 51 VEVDLVVrDREHILVEVKSRVSR 73
                                   7*******889*********543 PP

>> DUF3883  Domain of unknown function (DUF3883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   3.7e-05     0.084       5      60 ..      18      79 ..      14     110 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.7e-05
                        DUF3883  5 vlealkekekeeg.vewvnedvedglgYDiesvd.....kedgeerfIEVKttakgkkdfel 60
                                   +++++ e++   g v++v  ++e+gl Y  +s        +d e +++EVK+++++ +  el
  gi|119720334|ref|YP_920829.1| 18 AMKYVVEEVLGAGaVRRVTMYDEEGLVYGHKSEVevdlvVRDREHILVEVKSRVSRGDVAEL 79
                                   68888888888888999999999999999999855667766889*********976665555 PP

>> Herpes_HEPA  Herpesvirus DNA helicase/primase complex associated protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   6.5e-05      0.15      11      80 ..      41     113 ..      32     121 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.5e-05
                    Herpes_HEPA  11 velvlageq.vtvrvllpkafdlLvtndesksnlallaffr..alhekvfgekevlapiflyigPelnpeged 80 
                                      lv ++++ v+v +++ +  ++Lv  +   s + + +++r   l+ek++g k  l+ +  +i  ++++ + +
  gi|119720334|ref|YP_920829.1|  41 EGLVYGHKSeVEVDLVVRDREHILVEVKSRVSRGDVAELYRvgLLYEKLYGVKPRLVLVGGFIDTDAWETAGA 113
                                    5677777778********99********************9555*******9999999999998888887765 PP

>> AHJR-like  REase_AHJR-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   8.1e-05      0.18      46      75 ..      54      82 ..      49     101 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8.1e-05
                      AHJR-like 46 DliarkdeeaviiEvksrrssaseqyLqel 75
                                   Dl + +d e++ +Evksr s+  + +L ++
  gi|119720334|ref|YP_920829.1| 54 DL-VVRDREHILVEVKSRVSRGDVAELYRV 82
                                   55.557899***********9998888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 942.42
//
Query:       gi|119720335|ref|YP_920830.1|  [L=156]
Description: redoxin domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-38  131.1   0.0    2.2e-38  130.9   0.0    1.0  1  AhpC-TSA       AhpC/TSA family
    1.1e-25   90.0   0.0    1.3e-25   89.8   0.0    1.0  1  Redoxin        Redoxin
    0.00046   20.5   0.0    0.00058   20.1   0.0    1.3  1  Thioredoxin_8  Thioredoxin-like
     0.0019   18.3   0.0     0.0046   17.1   0.0    1.5  2  AhpC-TSA_2     AhpC/TSA antioxidant enzyme
  ------ inclusion threshold ------
       0.14   11.6   0.0       0.18   11.3   0.0    1.1  1  DUF899         Bacterial protein of unknown function (DUF899)


Domain annotation for each model (and alignments):
>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.9   0.0   6.3e-42   2.2e-38       1     123 [.       8     129 ..       8     130 .. 0.98

  Alignments for each domain:
  == domain 1  score: 130.9 bits;  conditional E-value: 6.3e-42
                                    TTSB----EEESTTCEEEECHHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHHHH- CS
                       AhpC-TSA   1 vgdkapdfelknadgetvslsdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfieke 80 
                                    vg++apdfe++ + g+ ++ls ++g+ vvlff+pk+++p+C +el+++++lyeefk +g+ev+gvs+d++ +++kf++++
  gi|119720335|ref|YP_920830.1|   8 VGEQAPDFEAEST-GGVFRLSSLRGRRVVLFFFPKAFTPGCSRELSEFSELYEEFKRLGAEVVGVSADKVNTLRKFAKRY 86 
                                    79********977.69**************************************************************** PP

                                    H.SSEEEE-TTSHHHHHTT-EETTTTECSCEEEEE-TTSBEEE CS
                       AhpC-TSA  81 slnfpllsDeegkvakaygvlkeekglalratfvidkegkiry 123
                                    +  f+l+sD++ +va +ygv+    ++a r tfvid++g++r+
  gi|119720335|ref|YP_920830.1|  87 NAAFNLVSDPSLEVAGKYGVVGRSGKTAERVTFVIDEQGVVRA 129
                                    *********************999*****************97 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.8   0.0   3.6e-29   1.3e-25       2     130 ..       8     130 ..       7     147 .. 0.93

  Alignments for each domain:
  == domain 1  score: 89.8 bits;  conditional E-value: 3.6e-29
                                    TTSBB---ECCEETTCEEEEEHHHHTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHHHHHHHH CS
                        Redoxin   2 agdkaPdftlplaatdgnsvslsefkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndafvkefwg 81 
                                    +g++aPdf+   a + g  + ls+++g++vv++f+p af+P Cs+e+ ++ +l+e++k  g +vv+v+ad+ +  ++f++
  gi|119720335|ref|YP_920830.1|   8 VGEQAPDFE---AESTGGVFRLSSLRGRRVVLFFFPKAFTPGCSRELSEFSELYEEFKRLGAEVVGVSADKVNTLRKFAK 84 
                                    799******...569***************************************************************** PP

                                    HTT-TSEEEE-TTSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEEEEE CS
                        Redoxin  82 keglkfpvlsDgsaaftkalGlrleedaseglrtpryavidedgkvvyl 130
                                    +++  f ++sD+s +++ ++G+  +   ++  + + ++vide+g+v+++
  gi|119720335|ref|YP_920830.1|  85 RYNAAFNLVSDPSLEVAGKYGVVGR--SGK-TAERVTFVIDEQGVVRAV 130
                                    *********************7744..334.499************976 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   1.6e-07   0.00058       2      57 ..      33      86 ..      31     127 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.6e-07
                                   SEEEEEE--SSSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-SS-HHHHHHHGGGS CS
                  Thioredoxin_8  2 kvvlLyfgaswcppckaftpklkelyeklkkkkkveivyvsldkkeeefekylkkn 57
                                   +vvl++f + + p c + +++ +elye++k + + e+v vs dk  +  +k+ k  
  gi|119720335|ref|YP_920830.1| 33 RVVLFFFPKAFTPGCSRELSEFSELYEEFK-RLGAEVVGVSADKV-NTLRKFAKRY 86
                                   7999999**********************9.8***********84.5555544444 PP

>> AhpC-TSA_2  AhpC/TSA antioxidant enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.3e-06    0.0046       3      55 ..      55     108 ..      53     124 .. 0.86
   2 ?   -1.8   0.0      0.95   3.4e+03      96     108 ..     118     130 ..     109     134 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.3e-06
                     AhpC-TSA_2   3 srdkpeldaagvklvaigigdp.sakkFvkltgfpfelyvDpsaklyqalglkr 55 
                                    s++ +e+++ g ++v+++ +++  ++kF+k+ +  f+l+ Dps ++  + g+  
  gi|119720335|ref|YP_920830.1|  55 SELYEEFKRLGAEVVGVSADKVnTLRKFAKRYNAAFNLVSDPSLEVAGKYGVVG 108
                                    677899****************66*******************99988888765 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.95
                     AhpC-TSA_2  96 tflfdkqgelvye 108
                                    tf++d+qg ++  
  gi|119720335|ref|YP_920830.1| 118 TFVIDEQGVVRAV 130
                                    8999999977655 PP

>> DUF899  Bacterial protein of unknown function (DUF899)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0     5e-05      0.18      85     185 ..      44     141 ..      33     151 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5e-05
                         DUF899  85 CpgCslladhvdgalahLeardvtlavvsraplekleaykrrmGwtlpwvssaesdfnrdfnvsleeeqaseelpglsvf 164
                                     pgCs  ++++ +  ++++  +  ++ vs   ++ l ++ +r    +++vs+ + ++  +++v  + +   + +    +f
  gi|119720335|ref|YP_920830.1|  44 TPGCSRELSEFSELYEEFKRLGAEVVGVSADKVNTLRKFAKRYNAAFNLVSDPSLEVAGKYGVVGRSG---KTAER-VTF 119
                                    589********999************************************************988776...33334.445 PP

                         DUF899 165 lrdd.grvfhtYstyaRgleel 185
                                    + d+ g v+      +R+ ++ 
  gi|119720335|ref|YP_920830.1| 120 VIDEqGVVRAVLRDLPRAEDHP 141
                                    5555488888777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1177.68
//
Query:       gi|119720336|ref|YP_920831.1|  [L=452]
Description: phosphotransferase domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00084   19.0   0.3     0.0038   17.0   0.1    2.3  2  PHP_C     PHP-associated
     0.0031   17.8   0.0     0.0039   17.5   0.0    1.3  1  PHP       PHP domain


Domain annotation for each model (and alignments):
>> PHP_C  PHP-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   4.2e-07    0.0038      13      56 .]     289     338 ..     283     338 .. 0.81
   2 ?   -3.1   0.0       0.8   7.2e+03      43      52 ..     436     445 ..     430     446 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.2e-07
                          PHP_C  13 klglpgtgGSDAHrl......eeVGrayTefeepiatpdelleairegrt 56 
                                     +++ ++gGSDAHr+      + +G+  T++ ++  ++de+l+++r gr+
  gi|119720336|ref|YP_920831.1| 289 GRDVVAVGGSDAHRVareegiPRLGEPTTVVYMERLSEDEFLKSLRLGRV 338
                                    588999*******8622222257********8888899********9996 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.8
                          PHP_C  43 tpdelleair 52 
                                    ++d++++ai 
  gi|119720336|ref|YP_920831.1| 436 SEDAVVRAIA 445
                                    6899***995 PP

>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   4.3e-07    0.0039       1      65 [.     144     201 ..     144     330 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.3e-07
                                    EEEE--CCC--.S-H..HHHHHHHHHCT-SEEEEEEEEBTTHHHHHHHHHHHHTTTTSEEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            PHP   1 dlHvHteyslldgalsieelvkkakelglkaiaiTDhgnlfgyvefykaakkkykagikpiiGle 65 
                                    dlHvH+  s  d+++   el++ a  +gl+ + +TDh+ +  + e  + a        ++  G+e
  gi|119720336|ref|YP_920831.1| 144 DLHVHSVHSDGDASV--AELARIASGKGLDFVVLTDHNTVSHVAECLSTA---G--PARVFPGME 201
                                    89*******887888..*********************999777666666...3..234444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (452 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       261  (0.0145574); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 3496.49
//
Query:       gi|119720337|ref|YP_920832.1|  [L=85]
Description: hypothetical protein Tpen_1432 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.4e-09   35.8   0.0    8.8e-09   35.5   0.0    1.0  1  HEPN      HEPN domain
  ------ inclusion threshold ------
      0.035   14.4   0.3      0.044   14.0   0.3    1.3  1  DUF4129   Domain of unknown function (DUF4129)


Domain annotation for each model (and alignments):
>> HEPN  HEPN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.0   9.8e-13   8.8e-09      50     116 ..       7      77 ..       2      79 .. 0.93

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 9.8e-13
                                    .SSCCHHHHHHCCHHHT.........-HHHHHHHHHHHCCCHHCCCTSS--S--HHHHHHHHHHHHHHHHHHH CS
                           HEPN  50 ppkthdlreLleelkkelke......seelreeleeLekayiesrYpdakeeyteedaeealkdaeevlelve 116
                                     p+ hd+reLl  + k++ +       +++r+el+ L + y+ +rY+  ++  +++dae ++  ++ +++l+e
  gi|119720337|ref|YP_920832.1|   7 MPRIHDIRELLAIIYKYTRDsrvdelMRRFRRELRDLVEGYVVARYGSIDY--SRDDAEVCIGLMRDLWRLIE 77 
                                    69***************99999999999999999*****************..*************9999877 PP

>> DUF4129  Domain of unknown function (DUF4129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.3   4.9e-06     0.044      24      65 ..      31      66 ..      14      70 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.9e-06
                        DUF4129 24 EyarrvriapspaaalaalaelfeearYGgrpasaeeyrrlv 65
                                   E+ rr       +++l++l+e +  arYG    s+++++++ 
  gi|119720337|ref|YP_920832.1| 31 ELMRRF------RRELRDLVEGYVVARYGSIDYSRDDAEVCI 66
                                   444444......569***********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 556.04
//
Query:       gi|119720338|ref|YP_920833.1|  [L=133]
Description: DNA polymerase beta subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-08   34.4   0.0    2.7e-08   34.0   0.0    1.4  1  NTP_transf_2  Nucleotidyltransferase domain
    1.7e-07   31.2   0.0    2.1e-07   30.9   0.0    1.2  1  Polbeta       Polymerase beta, Nucleotidyltransferase
  ------ inclusion threshold ------
       0.14   12.1   0.3       0.25   11.3   0.3    1.4  1  S1-like       S1-like


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   0.0   4.5e-12   2.7e-08       5      66 ..      32      89 ..      15     114 .. 0.83

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 4.5e-12
                                   HHHHHHHTT.TSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEEC CS
                   NTP_transf_2  5 leelkelep.vakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleel 66
                                    +++ ++++ + +++ fGS + G+++  SD+D++vv++e        ++ e   +i ++le++
  gi|119720338|ref|YP_920833.1| 32 VKRVLSEYGvDDEIFFFGSIVDGKYTAASDVDIAVVVREVPR-----NRSEIAGKIVEELEKI 89
                                   5666777778*****************************965.....6666666666666664 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.0   3.6e-11   2.1e-07      15      58 ..      44      89 ..      31     110 .. 0.82

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 3.6e-11
                                   STTEEEEEE-S------EEEEEEEESS-..--HHHHHHHHHHHHHH CS
                        Polbeta 15 laylFGSrakgkareeSDiDlavllkek..ldleeelelaaeledi 58
                                    ++ FGS+++gk++  SD+D+av+++e   ++ e   ++ +ele+i
  gi|119720338|ref|YP_920833.1| 44 EIFFFGSIVDGKYTAASDVDIAVVVREVprNRSEIAGKIVEELEKI 89
                                   5899************************877777788999999988 PP

>> S1-like  S1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.3   4.1e-05      0.25       7      35 ..      31      58 ..      28      69 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.1e-05
                        S1-like  7 vVTklqdtfGfvDeevfFqrsvvkGrlpk 35
                                   vV ++  ++G vD+e+fF  s v G+   
  gi|119720338|ref|YP_920833.1| 31 VVKRVLSEYG-VDDEIFFFGSIVDGKYTA 58
                                   68889999*9.8***********998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 964.87
//
Query:       gi|119720339|ref|YP_920834.1|  [L=109]
Description: hypothetical protein Tpen_1434 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-06   27.6   0.0    3.1e-06   27.3   0.0    1.1  1  HEPN      HEPN domain


Domain annotation for each model (and alignments):
>> HEPN  HEPN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   1.7e-10   3.1e-06      31     110 ..       4      93 ..       1     100 [. 0.83

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 1.7e-10
                                    HHHHHHHHHHHHHHHTT--.SSCCH....HHHHHCCHHHT....-HHHHHHHHHHHCCCHHCCCTSS--S......--HH CS
                           HEPN  31 aqqaaekalKAlllkkggeppkthd....lreLleelkkelke.seelreeleeLekayiesrYpdakee......ytee 99 
                                    aq a+e ++KA+++     p + hd    l++Ll+ +    +    el+++++ L +    + Y++ + +      yt+ 
  gi|119720339|ref|YP_920834.1|   4 AQLAVENYAKAVIAYFRV-PSWSHDpsgeLLSLLGSIPADAQReAAELADIAKTLAPEHGRATYGEPERGllpwevYTRS 82 
                                    89**********998888.69999833333445554444444379*********************************** PP

                                    HHHHHHHHHHH CS
                           HEPN 100 daeealkdaee 110
                                    dae+al+ a++
  gi|119720339|ref|YP_920834.1|  83 DAERALELARA 93 
                                    *******9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       268  (0.0149478); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 795.44
//
Query:       gi|119720340|ref|YP_920835.1|  [L=111]
Description: hypothetical protein Tpen_1435 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0004   20.7   1.6    0.00063   20.1   1.6    1.3  1  CcdA           Post-segregation antitoxin CcdA
     0.0084   16.1   0.8      0.023   14.7   0.8    1.7  1  RHH_3          Ribbon-helix-helix domain
  ------ inclusion threshold ------
      0.032   14.2   4.9      0.032   14.2   4.9    2.5  2  RHH_1          Ribbon-helix-helix protein, copG family
      0.061   12.1   0.1      0.072   11.9   0.1    1.0  1  ALMT           Aluminium activated malate transporter
       0.13   11.8   0.0       0.16   11.5   0.0    1.1  1  Imm70          Immunity protein 70
       0.27   12.0   9.4       0.38   11.5   9.4    1.3  1  PSK_trans_fac  Rv0623-like transcription factor


Domain annotation for each model (and alignments):
>> CcdA  Post-segregation antitoxin CcdA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   1.6   2.1e-07   0.00063       7      49 ..      46      87 ..      41     100 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.1e-07
                           CcdA  7 sldsdllaqAralgiNlSatleeaLaeevkeekaerwkeenre 49
                                    + ++l ++A +lgi +S++l +aL+eevk++k e+ + +  e
  gi|119720340|ref|YP_920835.1| 46 KVRRELKEEAERLGIRISEVLRRALEEEVKRRKLEELE-KRLE 87
                                   57789************************988877633.3333 PP

>> RHH_3  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.8   7.7e-06     0.023      15      38 ..      49      72 ..      40      72 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 7.7e-06
                          RHH_3 15 ekLkaLSekTrIprSklldeAiel 38
                                    +Lk+  e+++I++S+ l+ A+e+
  gi|119720340|ref|YP_920835.1| 49 RELKEEAERLGIRISEVLRRALEE 72
                                   68********************95 PP

>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   4.9   1.1e-05     0.032       4      39 .]      41      76 ..      41      76 .. 0.93
   2 ?    1.7   0.7     0.088   2.6e+02       8      22 ..      80      94 ..      79     104 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.1e-05
                                   EEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHH CS
                          RHH_1  4 irldeellerLdelarrrgrSrSelIReAlreyler 39
                                   +++++++ ++L e a+r+g   Se++R+Al+e ++r
  gi|119720340|ref|YP_920835.1| 41 VTVSAKVRRELKEEAERLGIRISEVLRRALEEEVKR 76
                                   678889999***********************9986 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.088
                                   HHHHHHHHHHHHHHT CS
                          RHH_1  8 eellerLdelarrrg 22
                                   eel +rL++++ +++
  gi|119720340|ref|YP_920835.1| 80 EELEKRLEAMRGALE 94
                                   789999999998877 PP

>> ALMT  Aluminium activated malate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   2.4e-05     0.072     287     340 ..      43      96 ..      27     100 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.4e-05
                           ALMT 287 apeelrkkfkeelqrvslesakvlrelaesvkkmkklskveellkevkvaaeeL 340
                                    ++ ++r+++kee +r+++ +++vlr   e+  k++kl++ e+ l+ ++ a+e++
  gi|119720340|ref|YP_920835.1|  43 VSAKVRRELKEEAERLGIRISEVLRRALEEEVKRRKLEELEKRLEAMRGALERI 96 
                                    57789*******************9988888889999999**********9987 PP

>> Imm70  Immunity protein 70
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   5.4e-05      0.16      28      80 ..      54     106 ..      42     111 .] 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.4e-05
                          Imm70  28 ekeawGskfPtllnelydgelsvddlekaeaeLkeirkelkklppekviwdid 80 
                                    e e  G++   +l    ++e++  +le++e+ L+++r  l+   +e v+  i 
  gi|119720340|ref|YP_920835.1|  54 EAERLGIRISEVLRRALEEEVKRRKLEELEKRLEAMRGALERIDVERVVRGIR 106
                                    67889999999*************************************98775 PP

>> PSK_trans_fac  Rv0623-like transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   9.4   0.00013      0.38       8      61 ..      45      98 ..      43     111 .] 0.77

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00013
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--HHHHHHHHHHHHHT CS
                  PSK_trans_fac  8 peverlareLarltgeskteAvrrAleerlerlrreraepllerllallrraaa 61
                                   ++v+r  +e a++ g  + e+ rrAlee+ +r++ e+ e++le ++  l+r++ 
  gi|119720340|ref|YP_920835.1| 45 AKVRRELKEEAERLGIRISEVLRRALEEEVKRRKLEELEKRLEAMRGALERIDV 98
                                   6789999999**********************9866666666666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1332  (0.074293); expected 358.6 (0.02)
Passed bias filter:                      723  (0.0403257); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 748.89
//
Query:       gi|119720341|ref|YP_920836.1|  [L=133]
Description: hypothetical protein Tpen_1436 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-07   31.8   0.2    2.1e-07   31.5   0.2    1.3  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.2   1.2e-11   2.1e-07      35     121 ..      31     121 ..       6     122 .. 0.92

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 1.2e-11
                                    HHHHHHHHHHHHS.....SCHCHHHHHHHHHHHHH.HHTSEEEEBCHHHHHHHHHHHHHHHSBHHHHHHHHHHHHHT-EE CS
                            PIN  35 alvlaEllyvlar.....rkskrekaaelvellll.lsalkilpidaeiaeeaaeialkygllpnDaliaAtAkehgikl 108
                                     l+++E+++ l +     ++ + e+a +lve++ +  + +++l+  ++  +e++e a+k+gl+++Da  +++A+++g++l
  gi|119720341|ref|YP_920836.1|  31 WLTVYEVVNALWKeallaGSISVEEASNLVEVFAEtVKLVEVLS-PHPYEAEILETAAKLGLTAYDASYVVLAIRNGLSL 109
                                    5899**************99***************999999999.999999999************************** PP

                                    E.ESSTHHHHHHH CS
                            PIN 109 iatfDedfrrvak 121
                                    + t D+ +r+ ak
  gi|119720341|ref|YP_920836.1| 110 V-TEDRVLREKAK 121
                                    *.****9999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 847.30
//
Query:       gi|119720342|ref|YP_920837.1|  [L=181]
Description: hypothetical protein Tpen_1437 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00062   20.0   0.0      0.001   19.2   0.0    1.3  1  DUF948        Bacterial protein of unknown function (DUF948)
  ------ inclusion threshold ------
      0.045   14.2   0.0      0.088   13.2   0.0    1.4  1  FlaC_arch     Flagella accessory protein C (FlaC)
      0.046   13.8   0.0      0.096   12.8   0.0    1.6  1  Prefoldin_3   Prefoldin subunit
      0.048   13.8   0.0      0.076   13.2   0.0    1.4  1  PAH           Paired amphipathic helix repeat
      0.089   11.8   0.0       0.13   11.3   0.0    1.3  1  Filo_VP35     Filoviridae VP35
      0.096   12.5   0.0       0.18   11.6   0.0    1.5  1  DASH_Dam1     DASH complex subunit Dam1
       0.15   12.0   0.5       0.66   10.0   0.5    2.1  1  Sugarporin_N  Maltoporin periplasmic N-terminal extension


Domain annotation for each model (and alignments):
>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   4.1e-07     0.001       5      54 ..      16      65 ..      14      77 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 4.1e-07
                         DUF948  5 IaAiAFvvLviflivvllklkktldeaaatieelekqvdpilkevedlla 54
                                   ++A A+++Lv+++ + +  ++k l+ +++++ +le+++d+i++ v+ l++
  gi|119720342|ref|YP_920837.1| 16 LVATAIAILVVYIERRIAYVEKRLSGLESRLGGLESRLDEITRSVNSLVD 65
                                   589*******************************************9986 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   3.4e-05     0.088       1      35 [.      31      65 ..      31      73 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.4e-05
                      FlaC_arch  1 ridelEnklsklsteletvkkeneelsksveelke 35
                                   ri  +E++ls l+++l+ +++ ++e+  sv+ l +
  gi|119720342|ref|YP_920837.1| 31 RIAYVEKRLSGLESRLGGLESRLDEITRSVNSLVD 65
                                   78889*************************99865 PP

>> Prefoldin_3  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   3.7e-05     0.096      70      98 ..      25      53 ..       7      54 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.7e-05
                    Prefoldin_3 70 vdlisrRiDYVkqniktlekrleaaenkl 98
                                   v  i+rRi YV++ ++ le rl   e++l
  gi|119720342|ref|YP_920837.1| 25 VVYIERRIAYVEKRLSGLESRLGGLESRL 53
                                   6789******************9999998 PP

>> PAH  Paired amphipathic helix repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0     3e-05     0.076      15      36 ..     100     121 ..      62     125 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3e-05
                            PAH  15 keqidskeVyeqVskLFhdhpd 36 
                                    k ++++keVye++ +L++++pd
  gi|119720342|ref|YP_920837.1| 100 KTKYYTKEVYERLGQLLSKDPD 121
                                    34699****************9 PP

>> Filo_VP35  Filoviridae VP35
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0     5e-05      0.13      68     109 ..      17      58 ..       8      90 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5e-05
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHH CS
                      Filo_VP35  68 vkrtladllivvnrqiidiestlseletrvtelerqlheikp 109
                                    v  ++a l++ ++r+i+ +e  ls le r+  le  l ei+ 
  gi|119720342|ref|YP_920837.1|  17 VATAIAILVVYIERRIAYVEKRLSGLESRLGGLESRLDEITR 58 
                                    5778999********************************985 PP

>> DASH_Dam1  DASH complex subunit Dam1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   7.2e-05      0.18       2      36 ..      36      70 ..      35      73 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.2e-05
                      DASH_Dam1  2 epafaeLaDsletLdknledLqqihesLsdfNeSF 36
                                   e++++ L+  l  L+++l+++ +  +sL+dfNe++
  gi|119720342|ref|YP_920837.1| 36 EKRLSGLESRLGGLESRLDEITRSVNSLVDFNEAL 70
                                   5778899999***********************87 PP

>> Sugarporin_N  Maltoporin periplasmic N-terminal extension
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.5   0.00026      0.66      13      40 ..      28      54 ..       9      56 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00026
                   Sugarporin_N 13 llstaasvaaaasltiEaRLaaLEkrLq 40
                                   +   +a+ + + ++ +E RL  LE+rL 
  gi|119720342|ref|YP_920837.1| 28 IERRIAY-VEKRLSGLESRLGGLESRLD 54
                                   4444444.66666666666666666664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1197.71
//
Query:       gi|119720343|ref|YP_920838.1|  [L=375]
Description: hypothetical protein Tpen_1438 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.65    8.9  37.3      0.049   12.5  31.3    1.9  1  MFS_1     Major Facilitator Superfamily


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5  31.3   2.8e-06     0.049     120     350 ..     111     333 ..     103     336 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.8e-06
                          MFS_1 120 graigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllllpeepperkrkspkeeekgt.gpaplvp 198
                                     r++++l +++s++++ gp+l++++as++    +  i a+v+l +  l  +ll++   +r+ ++p+    g  + ++l  
  gi|119720343|ref|YP_920838.1| 111 ERVNAVLEVSYSIAMVAGPPLAAWMASAG----PAGISAAVALELSAL--ALLTAVLARRGLNAPIGP--GGgFLQALCR 182
                                    6899**********************554....455555555555444..555555555555555555..2203333333 PP

                          MFS_1 199 awkallkdpvlwillialllfffgfsglltllplylqevlgls..glllaglllallalvgailallagrlsdrlgr..r 274
                                     +   ++++    l ++l ++  g+ +l+  +  ++  +lg    g ++a+  ++ll++++  ++l a++l+ r g   +
  gi|119720343|ref|YP_920838.1| 183 -LAGSRAPR----LALVLSTAISGVGALVNVSVALVAGRLGEVlpG-FTAS--YSLLSALTGLGSLAASALAARRGVlgE 254
                                    .44444444....666666666666666666666667777777888.7888..888888888889*******88676557 PP

                          MFS_1 275 rrlllallllllaalglallavtssavllll..vlvl.....iGfglgfvfpsllalasdlappeeagtasglfntagsl 347
                                     +l+ +llll++  ++l l   + +++lll+  +  l      Gfg g +f  +l++++++++    g+a++   ++g+l
  gi|119720343|ref|YP_920838.1| 255 GFLYAGLLLLSAYPALLGLSMSA-EPSLLLAtiL--LafstlNGFGNGAFFLWILSAVQRSMG-GDVGKALATLYVLGAL 330
                                    78888888888888888777777.5555555342..224667999*****************8.9999999999999999 PP

                          MFS_1 348 gga 350
                                    +g+
  gi|119720343|ref|YP_920838.1| 331 AGL 333
                                    886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      185  (0.0103185); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2557.54
//
Query:       gi|119720344|ref|YP_920839.1|  [L=238]
Description: hypothetical protein Tpen_1439 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0051   16.2   0.2      0.006   15.9   0.2    1.3  1  Marek_SORF3  Marek's disease-like virus SORF3 protein
  ------ inclusion threshold ------
       0.11   12.6   0.3       0.22   11.6   0.3    1.4  1  DUF4501      Domain of unknown function (DUF4501)
        1.7    8.6   5.2        8.8    6.3   0.4    2.4  2  SLATT_1      SMODS and SLOG-associating 2TM effector domain 1


Domain annotation for each model (and alignments):
>> Marek_SORF3  Marek's disease-like virus SORF3 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.2     1e-06     0.006     110     186 ..     119     195 ..      17     227 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1e-06
                    Marek_SORF3 110 tGkleilyrlwdvrdalki..kvlGpklmalfsavlenatailsiainkGydrhntrsmdmtvqsarlvlslamevvry 186
                                    +G + +l   w v   lk+  + l p l+ lf av +++t i+  a  k   +h + ++ m + sa ++++++  v  +
  gi|119720344|ref|YP_920839.1| 119 WGVFVVL--GWFVGRDLKLanPFLFPALPLLFMAVGDGVTGIVRNALFKRRVKHWSGNLAMFIVSAAMAVAMGFGVPGV 195
                                    5555444..3555444555236899************************999*************99999888876433 PP

>> DUF4501  Domain of unknown function (DUF4501)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.3   3.7e-05      0.22      88     140 ..      18      69 ..       2      75 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.7e-05
                        DUF4501  88 aslllgtlfislfLilsvasf.fylkrssklPkvfYrrnkasvlqpseaaamip 140
                                    ++l+  ++f+   L+++ a++ f++krs++   ++Y r+   +l  +  aa+i 
  gi|119720344|ref|YP_920839.1|  18 IALFAWVMFVV--LVVAKATYnFFVKRSNERVAIYYARKVIHILAGGLVAAVIA 69 
                                    44555555555..444444444789**********************9999985 PP

>> SLATT_1  SMODS and SLOG-associating 2TM effector domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.3    0.0061        36      20      70 ..      44      94 ..      32     102 .. 0.77
   2 ?    6.3   0.4    0.0015       8.8      20      66 ..     164     204 ..     159     211 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0061
                        SLATT_1 20 neraakrwrlllillellalllaalrafgelsvdlvgvlaavaaallaWle 70
                                   ner a    + +i + + +l++a++  f+ +s  ++ ++ a++ all++l 
  gi|119720344|ref|YP_920839.1| 44 NERVAIYYARKVIHILAGGLVAAVIAYFPIFSTPVLPFAMAMVLALLTYLP 94
                                   445555555667777788999999999999999889999999999998875 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0015
                        SLATT_1  20 neraakrwrlllillellalllaalrafgelsvdlvgvlaavaaall 66 
                                     +r+ k+w+  l+++ + a++++a++ fg   v   gvl+a+ a+l+
  gi|119720344|ref|YP_920839.1| 164 FKRRVKHWSGNLAMFIVSAAMAVAMG-FG---V--PGVLSAALASLV 204
                                    6899999**99999999999999999.44...3..666777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       921  (0.0513693); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1501.42
//
Query:       gi|119720345|ref|YP_920840.1|  [L=539]
Description: hypothetical protein Tpen_1440 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.7e-14   53.4   0.0      1e-13   52.0   0.0    1.7  2  DUF87          Helicase HerA, central domain
    0.00021   20.8   0.1     0.0004   19.8   0.1    1.4  1  FtsK_SpoIIIE   FtsK/SpoIIIE family
  ------ inclusion threshold ------
      0.051   12.5   0.0       0.11   11.4   0.0    1.4  1  AAA_10         AAA-like domain
       0.12   11.2   0.0        0.2   10.5   0.0    1.2  1  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-


Domain annotation for each model (and alignments):
>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.0   0.0   2.2e-17     1e-13       2     129 ..     129     285 ..     128     327 .. 0.78
   2 ?   -2.2   0.0      0.81   3.6e+03     121     164 ..     371     407 ..     336     455 .. 0.67

  Alignments for each domain:
  == domain 1  score: 52.0 bits;  conditional E-value: 2.2e-17
                          DUF87   2 eiGrll...sgsevpvyldlnklvtrHlAilgsTGsGKSntvavLleelle.kkgatililDpHGEYgkal......... 68 
                                     iGr+    s+ +v+v ld  k + +H++++g TG+GKSn+ +vL +++l  + +++++++D  +EY   +         
  gi|119720345|ref|YP_920840.1| 129 PIGRVRfghSAVDVEVALDGAKTIPHHILVVGGTGAGKSNFGRVLAASILHlRGRYSLVVFDCESEYLLGSkpgemglah 208
                                    5777777667788*************************************877788***********9999666777765 PP

                          DUF87  69 .....ekllsekvkvitpspsa...........................kdkelkinpwsldpeelldlleeddkpaaav 116
                                         e                                            +++lk+++++l+p +++   e    p+++ 
  gi|119720345|ref|YP_920840.1| 209 lpfseE---------------YlflvsarvprpgrlrvelpelgeersiPAYPLKMDVSRLKPGDFALTGEF-SSPQEEL 272
                                    544331...............2333333333555577888888888899999**************999888.5555555 PP

                          DUF87 117 qrsvleealdqak 129
                                    ++ +++++ + ++
  gi|119720345|ref|YP_920840.1| 273 LWLAYKQFGEGWV 285
                                    6666655555555 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.81
                          DUF87 121 leealdqakakeekeklssdepveklleelkkekeelrklknqa 164
                                    + +a+++++ ke+ ek+s   pv  + ee +      r+l +qa
  gi|119720345|ref|YP_920840.1| 371 VFRAYERMR-KELPEKWSQLPPVLIMVEEAH------RYLGSQA 407
                                    334555555.577788888777777777776......3333333 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.1   8.9e-08    0.0004      20      64 ..     133     178 ..     124     186 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 8.9e-08
                                    EEEEEETTS-EEEEEGGGS-..SEEEE--TTSSHHHHHHHHHHHHH CS
                   FtsK_SpoIIIE  20 valgkeisgnplvldlkkma.shllvaGatgsGKStalntLilSla 64 
                                    v +g+  ++  + ld +k    h+lv+G+tg GKS++ ++L +S++
  gi|119720345|ref|YP_920840.1| 133 VRFGHSAVDVEVALDGAKTIpHHILVVGGTGAGKSNFGRVLAASIL 178
                                    6667777777777776554349*******************99997 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   2.4e-05      0.11      13      51 ..     145     183 ..     141     196 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.4e-05
                         AAA_10  13 evkgsktnasasliiGdlGnGKSvlakllvlyisllggk 51 
                                    +++g+kt   + l++G++G+GKS + ++l   i+ l g+
  gi|119720345|ref|YP_920840.1| 145 ALDGAKTIPHHILVVGGTGAGKSNFGRVLAASILHLRGR 183
                                    5899*******************9999998877655544 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   4.4e-05       0.2      16      55 ..     154     195 ..     144     198 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 4.4e-05
                  TrwB_AAD_bind  16 qhilivGttGsGKtqalekllrairargdr..aivlDltGaf 55 
                                    +hil+vG+tG+GK++  + l ++i +   r   +v+D + ++
  gi|119720345|ref|YP_920840.1| 154 HHILVVGGTGAGKSNFGRVLAASILHLRGRysLVVFDCESEY 195
                                    7*****************999999775544227999988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (539 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.45
# Mc/sec: 3616.70
//
Query:       gi|119720346|ref|YP_920841.1|  [L=374]
Description: hypothetical protein Tpen_1441 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00065   19.5   0.0      0.031   13.9   0.0    2.3  1  NurA      NurA domain


Domain annotation for each model (and alignments):
>> NurA  NurA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   1.8e-06     0.031     185     242 .]     268     327 ..     112     327 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.8e-06
                                    EEEEEEESSTTTTEEEEEHHHHHHCCHHHHHHHHHH....TTB-SSSBCCHHHHHHHHCC CS
                           NurA 185 iyfaYvrlegggsilrleipaevstakdedvlslla..sqrlsisGYprpLalAhelaki 242
                                      +   rl+++   +r+++  e+ +  d d+l  ++  +q + ++GYp pL+++h+l +i
  gi|119720346|ref|YP_920841.1| 268 LGVGAARLSPDAAAFRVDVTWELAVRADFDYLAGMLayLQDFTSPGYPLPLKIVHNLSRI 327
                                    55555788899999999988888877777888888789******************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       256  (0.0142785); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.53
# Mc/sec: 2113.68
//
Query:       gi|119720347|ref|YP_920842.1|  [L=281]
Description: hypothetical protein Tpen_1442 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      0.009   16.5   0.2      0.033   14.7   0.2    2.0  1  HTH_27     Winged helix DNA-binding domain
  ------ inclusion threshold ------
      0.062   13.2   0.2       0.25   11.2   0.2    2.0  2  MarR_2     MarR family
      0.091   12.8   0.1       0.84    9.7   0.1    2.2  2  HTH_Crp_2  Crp-like helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.2   5.6e-06     0.033      33      68 .]     216     248 ..     214     248 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.6e-06
                         HTH_27  33 shisyslkkLtekGLvertgdeadrrekrvrlTdkG 68 
                                    +++s  +++L+e+GLv+r    +++r++ v+lTd G
  gi|119720347|ref|YP_920842.1| 216 ASYSRLVSELEERGLVVRR---HEGRNRSVELTDLG 248
                                    678999**********777...778********987 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       1.3   7.7e+03      13      27 ..     144     156 ..     143     157 .. 0.80
   2 ?   11.2   0.2   4.2e-05      0.25      35      55 ..     215     235 ..     214     240 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.3
                                    HHHCTTTSEEEHHHH CS
                         MarR_2  13 aLgrrpgrdltvgel 27 
                                    ++++ +   lt+++l
  gi|119720347|ref|YP_920842.1| 144 FIRAKDN--LTASDL 156
                                    6778887..999998 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 4.2e-05
                                    HHHHHHHHHHHHHTTSEEEEE CS
                         MarR_2  35 ksavsrilkrLvaaGLverrp 55 
                                    k++ sr++ +L+++GLv+rr 
  gi|119720347|ref|YP_920842.1| 215 KASYSRLVSELEERGLVVRRH 235
                                    6788**************993 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.13   7.7e+02      20      29 ..      68      77 ..      51      79 .. 0.63
   2 ?    9.7   0.1   0.00014      0.84      37      62 ..     217     247 ..     215     249 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.13
                                   EEHHHHHHHH CS
                      HTH_Crp_2 20 lpltqeelAs 29
                                    pl+qe +As
  gi|119720347|ref|YP_920842.1| 68 NPLSQESIAS 77
                                   49******98 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00014
                                    HHHHHHHHHHHTTSEE.E..T.EE.EEES-H CS
                      HTH_Crp_2  37 tvsrilseLkreglis.r..g.rr.irildl 62 
                                    + sr+ seL+++gl+  r  g +r ++++dl
  gi|119720347|ref|YP_920842.1| 217 SYSRLVSELEERGLVVrRheGrNRsVELTDL 247
                                    679*************644432357999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1913.40
//
Query:       gi|119720348|ref|YP_920843.1|  [L=142]
Description: hypothetical protein Tpen_1443 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-06   27.7   1.7    4.6e-06   26.5   0.4    2.0  2  PaREP1          Archaeal PaREP1/PaREP8 family
     0.0015   18.7   0.0     0.0034   17.6   0.0    1.6  1  DUF5618         Domain of unknown function (DUF5618)
     0.0036   17.2   0.0     0.0079   16.1   0.0    1.5  2  Maf             Maf-like protein
  ------ inclusion threshold ------
      0.095   12.5   0.6       0.24   11.2   0.0    1.8  2  COX2-transmemb  Cytochrome C oxidase subunit II, transmembran


Domain annotation for each model (and alignments):
>> PaREP1  Archaeal PaREP1/PaREP8 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.2     0.085   3.8e+02      27      36 ..       8      17 ..       3      30 .. 0.83
   2 !   26.5   0.4     1e-09   4.6e-06      12     113 ..      23     120 ..      12     122 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.085
                         PaREP1 27 eKaykAvkal 36
                                    Ka+kAv+ +
  gi|119720348|ref|YP_920843.1|  8 TKAWKAVELA 17
                                   6999999865 PP

  == domain 2  score: 26.5 bits;  conditional E-value: 1e-09
                         PaREP1  12 eAeellekGdlrqAaeKaykAvkalvkalaeknnlklleeaeekerwstkellkavaklleelgdkevvdlw.klAldLH 90 
                                    e ++  e   lr+A+eK + Av  +  al+++     l + + +  ++ +ell ++++   e+ + +++d + +  + LH
  gi|119720348|ref|YP_920843.1|  23 EYRKDREPLRLRNACEKGWLAVVLATDALLVA-----LGYGKPESYRERRELLGKLEREKPEIARLGLRDRFgARGYYLH 97 
                                    55555555569*********************.....322333333344566666666666666777998773579**** PP

                         PaREP1  91 eyqfheaklelsdveskeeavkd 113
                                    + ++he+ l +++v+++ e+v++
  gi|119720348|ref|YP_920843.1|  98 VQGYHEGALGADEVAEELEKVER 120
                                    ********************997 PP

>> DUF5618  Domain of unknown function (DUF5618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   7.7e-07    0.0034      21     122 ..      17     126 ..       5     127 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 7.7e-07
                                    S-EETTEE.--HHH..HHHHHHHHHHHHHHHHHHHH---S...SS-.--HHHHHHHHHC........C-HHHHHHHHHHH CS
                        DUF5618  21 akkedklY.kdkky..vkeAggtAYsgvLlaldellgkkglekkkrpksvetYkealkk........ldkkllkefnsay 89 
                                    a++e + Y kd+ +  ++ A++  +++v+la d+ll   g    ++p+s  + +e l k            l  +f    
  gi|119720348|ref|YP_920843.1|  17 ARREVDEYrKDREPlrLRNACEKGWLAVVLATDALLVALG---YGKPESYRERRELLGKlerekpeiARLGLRDRFGARG 93 
                                    5666566624555522679*******************99...5677777777777777554544433344667899999 PP

                                    HHHIIIICCT---BHHHHHHHHHHHHHHHHHHH CS
                        DUF5618  90 dvLhlagyydGiksakvvkeglkaaeklikkie 122
                                    + Lh++gy +G+  a+ v+e+l+++e+ +  +e
  gi|119720348|ref|YP_920843.1|  94 YYLHVQGYHEGALGADEVAEELEKVERYVGDVE 126
                                    9************************99887766 PP

>> Maf  Maf-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.8e-06    0.0079      20      80 ..      14      77 ..       3      83 .. 0.69
   2 ?   -2.2   0.0      0.72   3.2e+03      50      63 ..     106     118 ..      91     134 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.8e-06
                                   EEEE------....HHHHHHHHHHHHHHHHHTCEEEEEEEEEE.CE---SSHHHHHHHHHHHTTSE CS
                            Maf 20 fevvpsdvde....aeelvlrlAeaKaeavaalvigaDtvvvl.ilgKPkdeeealemLkklsgrt 80
                                   +e+   +vde    +e l lr A +K    +a+v++ D ++v   +gKP++  e +e L kl+ ++
  gi|119720348|ref|YP_920843.1| 14 VELARREVDEyrkdREPLRLRNACEKGW--LAVVLATDALLVAlGYGKPESYRERRELLGKLEREK 77
                                   4555566666665533344555555543..488*******99746**************9998655 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.72
                                    EEEEEEEEECE--- CS
                            Maf  50 igaDtvvvlilgKP 63 
                                    +gaD v+  +l+K 
  gi|119720348|ref|YP_920843.1| 106 LGADEVAE-ELEKV 118
                                    56666666.45554 PP

>> COX2-transmemb  Cytochrome C oxidase subunit II, transmembrane
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1      0.57   2.6e+03      14      22 ..       9      17 ..       6      18 .. 0.62
   2 ?   11.2   0.0   5.3e-05      0.24      11      29 ..      36      54 ..      34      56 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.57
                                   HHHHHHHHH CS
                 COX2-transmemb 14 KGWLAFsLA 22
                                   K W A  LA
  gi|119720348|ref|YP_920843.1|  9 KAWKAVELA 17
                                   667666665 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 5.3e-05
                                   HHHHHHHHHHHHHHHHHHH CS
                 COX2-transmemb 11 AYEKGWLAFsLAmLFvFiA 29
                                   A EKGWLA  LA     +A
  gi|119720348|ref|YP_920843.1| 36 ACEKGWLAVVLATDALLVA 54
                                   78*********97555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 997.95
//
Query:       gi|119720349|ref|YP_920844.1|  [L=279]
Description: NAD+ synthetase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.5e-72  242.4   0.0      4e-72  242.2   0.0    1.0  1  NAD_synthase   NAD synthase
    7.5e-06   25.8   0.0      1e-05   25.4   0.0    1.2  1  Asn_synthase   Asparagine synthase
    2.4e-05   23.3   0.0      0.015   14.1   0.0    2.4  2  tRNA_Me_trans  tRNA methyl transferase
  ------ inclusion threshold ------
      0.016   14.8   0.0       0.43   10.3   0.0    2.4  2  Sigma70_r4_2   Sigma-70, region 4
      0.017   14.6   0.2      0.068   12.7   0.1    2.0  2  Sigma70_r4     Sigma-70, region 4
       0.11   12.1   0.0       0.25   10.9   0.0    1.5  2  ThiI           Thiamine biosynthesis protein (ThiI)
       0.19   11.9   0.2       0.45   10.6   0.2    1.6  1  Sigma70_r3     Sigma-70 region 3


Domain annotation for each model (and alignments):
>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  242.2   0.0   1.6e-75     4e-72       3     242 .]      15     258 ..      13     258 .. 0.95

  Alignments for each domain:
  == domain 1  score: 242.2 bits;  conditional E-value: 1.6e-75
                                    HHHHHHHHHHHHHCTT.SEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTS...EEEE CS
                   NAD_synthase   3 eelvdflkeyvkkaga.kgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgi...evkt 78 
                                    e++   l+ yv+++   +  v+G+SGGvDS++va l+ +alg+en    +lPs  +++edvedal ++e lg+   + ++
  gi|119720349|ref|YP_920844.1|  15 EYIARRLRWYVREYAGkRAGVVGVSGGVDSAVVAFLTARALGPENTYCYVLPSFATPKEDVEDALRVIEALGLpdgNWEV 94 
                                    56778899999998772566***************************************************984445688 PP

                                    ---HHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHTEEEB---BHHHHTTT-S-TTTTT--SBETTTTS-HHH CS
                   NAD_synthase  79 idikpivrafeqelkeakedlakgNlkaRiRmailyaianklnllvlgTgnksElvvGyfTkyGDgaadlapiaellKte 158
                                    i+++pi+++fe+ l e    +a+gN+ aRiRm+il + a  +n lv+gTg+ksEl++GyfTkyGDg++d++pi++l+Kt+
  gi|119720349|ref|YP_920844.1|  95 ISVDPILKSFEEVLGEMD-RVARGNVMARIRMIILHEKAYAHNALVIGTGDKSELLLGYFTKYGDGGVDVLPIGGLYKTH 173
                                    99*********9999887.9************************************************************ PP

                                    HHHHHHHTT--HHHHCS--B--SSTT-BHHHHHSS-HHHHHHHHT.HSSSS...HHHHHTTT--HHHHHHHHHHHHHTGG CS
                   NAD_synthase 159 vkeLakelnvPervlkkpPsAdLkpgqtDeeeLgikYdelDeiLk.lvekkkspeeiikekelpaevvekieklvkkseh 237
                                    v++La++l+vPer+++kp s +L+pgqt e eLg +Y+ +D +L   +ek   +e i++e++++  vv++i ++vk+s+h
  gi|119720349|ref|YP_920844.1| 174 VRQLARYLGVPERIVEKPSSPRLWPGQTAEGELGAPYELVDSVLYlRFEKWLPEERIAEELGVEVGVVKRILEMVKRSQH 253
                                    ********************************************977999999999************************ PP

                                    GGSSS CS
                   NAD_synthase 238 Krklp 242
                                    Kr +p
  gi|119720349|ref|YP_920844.1| 254 KRMMP 258
                                    **987 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0     4e-09     1e-05      24     221 ..      38     227 ..      21     239 .. 0.74

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 4e-09
                   Asn_synthase  24 LSGGlDSSliaalaarqsksplktFsigfee..kgsdeakyakevaehlgte.htelvlteeelldalpdviyhlee..p 98 
                                     SGG+DS+++a+l ar +  p +t+   + +     ++++ a +v e+lg++     v++++ +l+ +++v+  +++   
  gi|119720349|ref|YP_920844.1|  38 VSGGVDSAVVAFLTARALG-PENTYCYVLPSfaTPKEDVEDALRVIEALGLPdGNWEVISVDPILKSFEEVLGEMDRvaR 116
                                    6****************97.99***99994466999****************65677899999**************976 PP

                   Asn_synthase  99 fadrsaiplyllsrlakrkgvkvvLsGeGaDElfgGYpyfykaalsrsrefeklplarslrasllarklrklaellelae 178
                                        + i + +l+++a +++  v+ +G+ + El  GY + y +  +     + lp       +l+++++r+la+ l+ + 
  gi|119720349|ref|YP_920844.1| 117 GNVMARIRMIILHEKAYAHNALVIGTGDKS-ELLLGYFTKYGDGGV-----DVLP-----IGGLYKTHVRQLARYLG-VP 184
                                    67788899********9**99999999998.777799866665522.....2223.....33344444444444444.22 PP

                   Asn_synthase 179 ardleelaelyrlkasdsaeaelegedelhrelyldlktllpg 221
                                    +r +e+++    + +++ + +  + ++ +++ lyl+++++lp+
  gi|119720349|ref|YP_920844.1| 185 ERIVEKPSSPRLWPGQTAEGELGAPYELVDSVLYLRFEKWLPE 227
                                    2222232222233333333466667777777777777777765 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0     6e-06     0.015       4      64 ..      35      88 ..      33      97 .. 0.73
   2 !    6.6   0.0    0.0011       2.8     165     193 ..     163     193 ..     161     196 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6e-06
                  tRNA_Me_trans  4 vvalSgGVDSsvaaallkeq.gyevigvflklweeedeegkeccaeedlkdaervaeklgip 64
                                   vv++SgGVDS+v+a+l +++ g e + +++  +          + +ed++da rv e lg+p
  gi|119720349|ref|YP_920844.1| 35 VVGVSGGVDSAVVAFLTARAlGPENTYCYVLPSFA--------TPKEDVEDALRVIEALGLP 88
                                   79************998776357777666654433........4567788888888888776 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0011
                  tRNA_Me_trans 165 lfPlgeltKeevrkiAkeagla..vaekkdS 193
                                    ++P+g l K++vr++A+  g++  + ek+ S
  gi|119720349|ref|YP_920844.1| 163 VLPIGGLYKTHVRQLARYLGVPerIVEKPSS 193
                                    68****************9998777777766 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.074   1.9e+02      30      43 ..     175     188 ..     173     190 .. 0.83
   2 ?   10.3   0.0   0.00017      0.43      18      45 ..     216     243 ..     213     250 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.074
                                    HHHHHHHT--HHHH CS
                   Sigma70_r4_2  30 kEIAellgisegtV 43 
                                    ++ A++lg++e+ V
  gi|119720349|ref|YP_920844.1| 175 RQLARYLGVPERIV 188
                                    678*******9866 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00017
                                    HHHHHHTS---HHHHHHHHT--HHHHHH CS
                   Sigma70_r4_2  18 ifllryleglsykEIAellgisegtVks 45 
                                    ++ lr+++ l+ + IAe+lg+ +g Vk+
  gi|119720349|ref|YP_920844.1| 216 VLYLRFEKWLPEERIAEELGVEVGVVKR 243
                                    789999999****************997 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.3   3.3e+03      25      32 ..     176     183 ..     172     187 .. 0.57
   2 ?   12.7   0.1   2.7e-05     0.068      12      41 ..     216     245 ..     214     248 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.3
                                    HHHHHHTS CS
                     Sigma70_r4  25 EIgerlgi 32 
                                    ++++ lg+
  gi|119720349|ref|YP_920844.1| 176 QLARYLGV 183
                                    45555555 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 2.7e-05
                                    HHHHHHTTT--HHHHHHHHTS-HHHHHHHH CS
                     Sigma70_r4  12 vlelrfgeglTleEIgerlgiSrerVrqie 41 
                                    vl+lrf++ l+ e I+e+lg+  + V++i+
  gi|119720349|ref|YP_920844.1| 216 VLYLRFEKWLPEERIAEELGVEVGVVKRIL 245
                                    9***************************96 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   9.9e-05      0.25       7     101 ..      35     130 ..      30     146 .. 0.61
   2 ?   -3.3   0.0       2.2   5.7e+03     143     162 ..     165     184 ..     163     191 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 9.9e-05
                           ThiI   7 laLlSgGiDSpVaaylllkR.Gcrvvlvhlknepgtseeaiekveklaellaeyqts...levklvvvdfkevlkeilek 82 
                                    ++ +SgG+DS V a+l  +  G +  ++++  +  t++e  e   ++ e l   +++   ++v  +  +f+evl e+ + 
  gi|119720349|ref|YP_920844.1|  35 VVGVSGGVDSAVVAFLTARAlGPENTYCYVLPSFATPKEDVEDALRVIEALGLPDGNwevISVDPILKSFEEVLGEMDRV 114
                                    6669************9875599999999988888887777777777777766665300023333444455555544443 PP

                           ThiI  83 vkekltivllkrkmlriAe 101
                                    ++     v+ +  m+ + e
  gi|119720349|ref|YP_920844.1| 115 ARG---NVMARIRMIILHE 130
                                    332...3455555555555 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.2
                           ThiI 143 PLigldKeeiiklAkeigty 162
                                    P+ gl K ++ +lA+ +g  
  gi|119720349|ref|YP_920844.1| 165 PIGGLYKTHVRQLARYLGVP 184
                                    77789999999999999865 PP

>> Sigma70_r3  Sigma-70 region 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.2   0.00018      0.45      23      48 ..     227     252 ..     226     253 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00018
                                    HHHHHHHHTXXHHHHHHHHHHHXXXE CS
                     Sigma70_r3  23 peEiAeeLglseekVrevleaarepv 48 
                                    +e iAeeLg+++  V+++le++++++
  gi|119720349|ref|YP_920844.1| 227 EERIAEELGVEVGVVKRILEMVKRSQ 252
                                    589*******************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1793.12
//
Query:       gi|119720350|ref|YP_920845.1|  [L=279]
Description: Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.4e-40  137.4   0.0    6.3e-40  137.1   0.0    1.0  1  CN_hydrolase  Carbon-nitrogen hydrolase


Domain annotation for each model (and alignments):
>> CN_hydrolase  Carbon-nitrogen hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.1   0.0   3.5e-44   6.3e-40       1     260 [.       6     259 ..       6     260 .. 0.85

  Alignments for each domain:
  == domain 1  score: 137.1 bits;  conditional E-value: 3.5e-44
                                    EEEEEEBB-STTHHHHHHHHHHHHHHHHHHTTESEEEEETTTTTBSSSHHHHHHHHBHSSSHHHHHHHHHHHH.HTEEEE CS
                   CN_hydrolase   1 rvAvvQlpqkaadleanlqklleliaeAarkgadLivlPElfitgykeeahfleaAeaglgetlallaalark.ngiavv 79 
                                    rv v+Q+++   d   nl+k+le++++A + g++++++PEl++tgy      +++A ++  +  ++l ++a+   g  v 
  gi|119720350|ref|YP_920845.1|   6 RVGVAQIHSLLGDVRRNLEKHLEYVERARELGVEVLAFPELSLTGY----LLRDLAYEVSDAAREALGEIAEAsRGLCVL 81 
                                    7999*****99****************9999***************....334444445556666666666541456677 PP

                                    EEEEEEECCTTEEEEEEEEEEEETTSEEEEEEE-SS--E.ECTTSCECCGHHTSCS-SSS-EEEETTEEEEEEEGGGGGS CS
                   CN_hydrolase  80 igliereltngklqayntavlldldgklvgkyrKlhLfp.geprpptaverelfepgdgipvfdtpvgkiGaaiCyeigf 158
                                    +gl ++      +  y + v + +dg+++g  +Kl L + g +++++++ +  +++++   vf++ ++++   iC++ ++
  gi|119720350|ref|YP_920845.1|  82 VGLVHE--PRAGI--YENSVAVVRDGSVAGVVSKLYLPDyGLFEESRYFREGSCSREG---VFECGGWRVAPIICEDAWH 154
                                    778888..44555..99999999*************9766665555555555555555...******************* PP

                                    HHHHHHHHHTT-SEEEE..........BH.GCCCTCHHHHHHHHHHHHHHHHHHTSEEEEEEBEEEHCETTEEEE--EEE CS
                   CN_hydrolase 159 pellralalkgaeilvn..........lserapvpksmgppqwellgraralengcfviaanqvggyeqlilwpvghSai 228
                                    pe +   a++ga++++           +      +++  + +we+++ +ra+en c+v+ an+vg   ++   ++g+S++
  gi|119720350|ref|YP_920845.1| 155 PEPAELAARRGADVVFIhasspirglyG-----SGEANIERVWEAIAVTRAVENACYVVFANRVGP--EDEEYFWGGSMV 227
                                    *****************99988776553.....48999****************************..9*********** PP

                                    E-TTS-EEEECCSSSTEEEEEEEEHHHHHHHH CS
                   CN_hydrolase 229 idpdGrilaglgeeeegvliaeidladvratr 260
                                    ++pdG+++a++ + ee++l+a++dl ++ra r
  gi|119720350|ref|YP_920845.1| 228 VAPDGEVVARAKKMEEELLVADLDLYRLRASR 259
                                    *************************9999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 1667.76
//
Query:       gi|119720351|ref|YP_920846.1|  [L=422]
Description: ABC-2 type transporter [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.3e-20   71.8  15.1    1.9e-19   70.0  15.1    1.7  1  ABC2_membrane_3  ABC-2 family transporter protein
    1.1e-18   67.4  21.1    1.5e-16   60.5  11.6    2.5  3  ABC2_membrane    ABC-2 type transporter
  ------ inclusion threshold ------
      0.099   12.1   0.0       0.15   11.4   0.0    1.3  1  SBP_bac_3        Bacterial extracellular solute-binding prote
       0.17   12.3   0.1       0.44   10.9   0.1    1.8  1  Smr              Smr domain


Domain annotation for each model (and alignments):
>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.0  15.1   4.1e-23   1.9e-19       1     340 [.      21     408 ..      21     413 .. 0.71

  Alignments for each domain:
  == domain 1  score: 70.0 bits;  conditional E-value: 4.1e-23
                ABC2_membrane_3   1 ksfliitlllPiilvlllglifsnsve..ddentpiavvdedn..sslsqqlvealea..spsve...lvyevdseeeak 71 
                                    ks+l++++ +P+ l+ +++++f  +     + ++++avv  +   + ++++ +++l+a  + s++   +     ++++a+
  gi|119720351|ref|YP_920846.1|  21 KSTLFWSFAFPLMLLSFYVFLFAPGAGqgRAVSINVAVVPGSEavAAYAEETAKYLKApwNASLKlsvNATVWGNLSSAM 100
                                    89*******************9844442367777779999999**9999********988888889999*********** PP

                ABC2_membrane_3  72 kalkngdidgilvipkgfskdllkgesatvtvli..nssnlnsskailnalns.llqqlnasalv............... 133
                                    +alk+g +d+++ ++ g   +l+      vtv++   + +++   +++ +l+s ++q    +al+               
  gi|119720351|ref|YP_920846.1| 101 NALKKGYLDAVVLVEPGSGGTLN------VTVYVlrGTPDPSREELVAAYLYSfFYQVAHFEALGelsrfvnatasrvpg 174
                                    ******************86664......555554334445666777777887777665433333544444433222333 PP

                ABC2_membrane_3 134 .lqseatstsaninvestql..........................eeelsnvasf..........lvgliliilifita 176
                                             +a                                                        ++++++ ++f ++
  gi|119720351|ref|YP_920846.1| 175 lA-------PA--------AaevverawraalnpgvrvvgvvpgeeG--------AqlrsrvvgwlTLSVVFMSFMFEGV 231
                                    31.......22........1223333335554444556666765431........0222232332255577777788889 PP

                ABC2_membrane_3 177 sfiavsiveEkesrikelqlvsgvsplqywlsk...ilgdflvyllqlllilllafgl....gipfgnlglllllfllfg 249
                                    +  a+++++E +++ + ++l++ ++p++y+ +     l++++++++++ l+ ++a+g      i   + ++llll+l+ g
  gi|119720351|ref|YP_920846.1| 232 VGGAAAVASEAKRGFLRRLLSTKLTPSEYFAGLaisWLALMAASAVPTCLLGFVAYGGslavKILSAEALFLLLLVLVAG 311
                                    99999************************998722244555555555555555577776655454558899999999999 PP

                ABC2_membrane_3 250 layialgyllsslfknsetaqilifivilllsgffgglfpledlpsalkwifsiiPffapglgllrli.tgdplwe.... 324
                                    l++ + g+l++ +fk++e+a++++ i+ ++++++ g+  p   lp++l+ ++ ++Pf+ ++ +   ++ +g +++     
  gi|119720351|ref|YP_920846.1| 312 LLAFSAGLLIGLFFKSPESASVVANIIVWPTMAAGGFWLPKWMLPDPLRAFAEVNPFSILFSATSEVAvFGRSISGyllp 391
                                    99999******************9999996666666666666799**********************7666655554444 PP

                ABC2_membrane_3 325 .illsliilalfavvyl 340
                                     ++  l+ lalfav+ +
  gi|119720351|ref|YP_920846.1| 392 tVAAVLLSLALFAVAAV 408
                                    46666666666666554 PP

>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.1   7.3e-06     0.033       4      41 ..       7      43 ..       5      64 .. 0.85
   2 !   60.5  11.6   3.3e-20   1.5e-16      52     205 ..     212     375 ..     194     380 .. 0.86
   3 ?   -3.6   0.2       1.4   6.2e+03     132     143 ..     395     406 ..     382     413 .. 0.46

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.3e-06
                  ABC2_membrane  4 kallkreflqrwrdpslgllwrliqplllalvfgtvfg 41
                                    a++ r++++++rd+s++ +w++++pl+l+ ++ ++f 
  gi|119720351|ref|YP_920846.1|  7 AAVVVRSVKLFLRDKSTL-FWSFAFPLMLLSFYVFLFA 43
                                   57899**********888.******************8 PP

  == domain 2  score: 60.5 bits;  conditional E-value: 3.3e-20
                  ABC2_membrane  52 r......pgllffsvlflafsaltsvapvferergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflvgl 125
                                    r      + ++f+s++f + +   ++a+ +e +rg+l r+l+++l ++s+y+++ +++ l+++++ a+   l+ ++  g 
  gi|119720351|ref|YP_920846.1| 212 RvvgwltLSVVFMSFMFEG-VVGGAAAVASEAKRGFLRRLLSTKL-TPSEYFAGLAISWLALMAASAVPTCLLGFVAYGG 289
                                    2544555788999999999.5555666******************.**********************999999999988 PP

                  ABC2_membrane 126 dls....rf..flflllllltalaasslgllisalapsfedasqlaslvllpllllsGffipidsmpkwlqwiaylnPlt 199
                                     l     +   +++lll+l+ +l+a s glli+ +++s e as++a++++ p++  +Gf  p++++p  l+++a++nP++
  gi|119720351|ref|YP_920846.1| 290 SLAvkilSAeaLFLLLLVLVAGLLAFSAGLLIGLFFKSPESASVVANIIVWPTMAAGGFWLPKWMLPDPLRAFAEVNPFS 369
                                    88775652266999999999**********************************************99************ PP

                  ABC2_membrane 200 yaveal 205
                                     +++a 
  gi|119720351|ref|YP_920846.1| 370 ILFSAT 375
                                    *99986 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 1.4
                  ABC2_membrane 132 lflllllltala 143
                                     +ll l l+a+a
  gi|119720351|ref|YP_920846.1| 395 AVLLSLALFAVA 406
                                    222222222222 PP

>> SBP_bac_3  Bacterial extracellular solute-binding proteins, family 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   3.4e-05      0.15     113     161 ..      56     116 ..      48     168 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.4e-05
                                    EEEETTSHHHHHHHHHHHC............TSEEEEESSHHHHHHHHHTTSSSEEEEEHH CS
                                    xxxxxxxxxxxxxxxxxxx............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      SBP_bac_3 113 vgvqagstaeellkeelkk............gaeivefdtleealqaLkngrvdavvadsp 161
                                    v+v+ gs a ++++ee +k            +++++++ +l++a++aLk+g  davv  +p
  gi|119720351|ref|YP_920846.1|  56 VAVVPGSEAVAAYAEETAKylkapwnaslklSVNATVWGNLSSAMNALKKGYLDAVVLVEP 116
                                    8889998877775554444566777777766666689*******************97655 PP

>> Smr  Smr domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   9.8e-05      0.44      10      56 ..     178     220 ..     155     246 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 9.8e-05
                                    HHHHHHHHHHHHHHHTT-SEEEEE--STTSTTHCHHHHHHHHHHHCS CS
                            Smr  10 ealnvletfldaasakglrsvevihGkGahagvgvLrpavmgwLagk 56 
                                     a +v+e+  +aa + g+r v v+ G       + Lr++v gwL+ +
  gi|119720351|ref|YP_920846.1| 178 AAAEVVERAWRAALNPGVRVVGVVPGEEG----AQLRSRVVGWLTLS 220
                                    577888899999999***********877....79*********866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       835  (0.0465726); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 2671.39
//
Query:       gi|119720352|ref|YP_920847.1|  [L=310]
Description: ABC transporter related [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.6e-27   95.2   0.0      7e-27   94.6   0.0    1.3  1  ABC_tran   ABC transporter
    1.6e-14   54.4   0.0    2.3e-09   37.5   0.0    2.2  2  AAA_21     AAA domain, putative AbiEii toxin, Type IV TA syst
    0.00038   20.1   0.1      0.001   18.7   0.0    1.7  2  AAA_29     P-loop containing region of AAA domain
     0.0005   19.6   0.0       0.18   11.2   0.1    2.1  2  SMC_N      RecF/RecN/SMC N terminal domain
      0.001   19.5   0.4       0.82   10.0   0.2    2.4  2  AAA_16     AAA ATPase domain
     0.0032   17.5   0.1       0.78    9.8   0.0    2.9  3  AAA_14     AAA domain
     0.0053   16.5   0.0       0.11   12.2   0.0    2.1  2  IstB_IS21  IstB-like ATP binding protein
     0.0087   16.3   0.0       0.11   12.8   0.0    2.4  1  SbcCD_C    Putative exonuclease SbcCD, C subunit
  ------ inclusion threshold ------
      0.021   14.4   0.1      0.068   12.7   0.1    2.0  1  AAA_25     AAA domain
      0.051   14.1   0.0       0.09   13.3   0.0    1.3  1  AAA_23     AAA domain
      0.088   12.5   0.3       0.38   10.4   0.0    1.9  2  AAA_30     AAA domain
      0.099   12.3   0.0       0.43   10.2   0.0    1.8  2  AAA_15     AAA ATPase domain
       0.16   12.1   0.7        1.7    8.8   0.2    2.3  3  AAA_33     AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.6   0.0   5.1e-30     7e-27       1     137 []      23     167 ..      23     167 .. 0.92

  Alignments for each domain:
  == domain 1  score: 94.6 bits;  conditional E-value: 5.1e-30
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEET.TCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilld.gkdlkeqeleslrkeigvlpqepqlfpeltvren 79 
                                    l+ +s++++ege+va++G+nG+GKSt++ + ag ++pt G++l+  g++ ++     +r +i+++pq+  l  elt  en
  gi|119720352|ref|YP_920847.1|  23 LRGISIEVREGEVVALLGPNGSGKSTFMGIAAGVVRPTRGRLLVYgGEPYSD---AGVRGRISYMPQDYGLYAELTGIEN 99 
                                    6789**************************************9996777777...99*******************8899 PP

                                    .............HHHTCHHHHHHHSTTGG.TTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    .............xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 .............esdeeiekalsklglke.lkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                                 e+++++e++   lgl e + +++v    s++SgG+k++ +la al+++p+llllDEpt+
  gi|119720352|ref|YP_920847.1| 100 yefyaalmevdakEAKRRLEELSGLLGLGEwFYKRRV----STYSGGMKRKASLALALASNPDLLLLDEPTS 167
                                    9*****9999988888889999999999885566677....*****************************96 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.2   1.8e-05     0.025       2      21 ..      36      55 ..      35      73 .. 0.85
   2 !   37.5   0.0   1.6e-12   2.3e-09     235     297 ..     137     196 ..     126     197 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.8e-05
                         AAA_21  2 nvliGpNgsGKSnLLdaldl 21
                                    +l GpNgsGKS+++ +  +
  gi|119720352|ref|YP_920847.1| 36 VALLGPNGSGKSTFMGIAAG 55
                                   689***********988755 PP

  == domain 2  score: 37.5 bits;  conditional E-value: 1.6e-12
                         AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                    +  S G+kr + l++al++ +   +lll+DEp +gL+P + r+++++++  +r g  v+l+TH
  gi|119720352|ref|YP_920847.1| 137 STYSGGMKRKASLALALASNP---DLLLLDEPTSGLDPNARREVWGVVDGMRRSGKTVVLATH 196
                                    5569***************99...9***********************9999999******** PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   7.6e-07     0.001      16      39 ..      27      50 ..      21      63 .. 0.79
   2 ?   -3.1   0.0       5.1   7.1e+03      29      38 ..     183     192 ..     177     195 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 7.6e-07
                         AAA_29 16 tieidlkgatlltGpsGsGKSTll 39
                                   +ie+++ +++ l Gp+GsGKST++
  gi|119720352|ref|YP_920847.1| 27 SIEVREGEVVALLGPNGSGKSTFM 50
                                   567775559*************98 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5.1
                         AAA_29  29 GpsGsGKSTl 38 
                                    G   sGK+ +
  gi|119720352|ref|YP_920847.1| 183 GMRRSGKTVV 192
                                    6666888766 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.1   0.00013      0.18      25      41 ..      34      50 ..      23      53 .. 0.84
   2 !    6.3   0.0    0.0042       5.8     137     195 ..     139     193 ..      95     214 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00013
                                   SEEEEEESTTSSHHHHH CS
                                   xxxxxxxxxxxxxxxxx RF
                          SMC_N 25 sftaivGpNGSGKsnll 41
                                   ++ a++GpNGSGKs ++
  gi|119720352|ref|YP_920847.1| 34 EVVALLGPNGSGKSTFM 50
                                   57899*********987 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0042
                                    S-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 137 LSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivi 195
                                     SgG k  ++laL +A +      l llDe  + LD + +++v  +++  + +   +v 
  gi|119720352|ref|YP_920847.1| 139 YSGGMKRKASLALALASN----PDLLLLDEPTSGLDPNARREVWGVVDGMRRSGKTVVL 193
                                    69**********999864....35899**************999999876666555553 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.2    0.0006      0.82      10      41 ..      21      50 ..      16     130 .. 0.82
   2 !    7.4   0.0    0.0037       5.1      28      59 ..     180     214 ..     169     259 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0006
                         AAA_16 10 eqLlsalervrsgrpelvllsGesGvGKsslv 41
                                   e+L+ +   vr+g  e+v l G+ G+GKs+ +
  gi|119720352|ref|YP_920847.1| 21 EALRGISIEVREG--EVVALLGPNGSGKSTFM 50
                                   5555555567766..89************976 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0037
                         AAA_16  28 llsGesGvGKsslv.rellralekd..ggiflrgk 59 
                                    ++ G++ +GK+ ++ ++l++ +e+   +++++rg 
  gi|119720352|ref|YP_920847.1| 180 VVDGMRRSGKTVVLaTHLFEDAERLadRVVVMRGG 214
                                    788**********9899999777655545555554 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.028        38       3      19 ..      34      50 ..      32      55 .. 0.89
   2 !    9.8   0.0   0.00057      0.78       6      22 ..     180     196 ..     178     211 .. 0.80
   3 ?   -2.1   0.0       2.6   3.6e+03      80     105 ..     202     226 ..     195     231 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.028
                         AAA_14  3 kilvitGaRrvGKTtll 19
                                   +++++ G+  +GK+t++
  gi|119720352|ref|YP_920847.1| 34 EVVALLGPNGSGKSTFM 50
                                   7999***********97 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00057
                         AAA_14   6 vitGaRrvGKTtllkql 22 
                                    v+ G+Rr+GKT++l + 
  gi|119720352|ref|YP_920847.1| 180 VVDGMRRSGKTVVLATH 196
                                    799********998654 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 2.6
                         AAA_14  80 ekalkslvdegknldvivtGSnskll 105
                                    e+   ++v  +  ++v+++GS+  l+
  gi|119720352|ref|YP_920847.1| 202 ERLADRVVVMR-GGEVVAAGSQEDLK 226
                                    55555555544.67899999987665 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   8.2e-05      0.11      30      70 ..      15      57 ..       6      68 .. 0.79
   2 ?    2.0   0.0      0.11   1.5e+02     102     148 ..     150     195 ..     140     209 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.2e-05
                      IstB_IS21 30 ldkrkvkeLatlsf.iekkenivllGpsGvGKs.hlaialgve 70
                                   + +r+v++L++ s  +++ e ++llGp G GKs ++ ia gv 
  gi|119720352|ref|YP_920847.1| 15 SGERRVEALRGISIeVREGEVVALLGPNGSGKStFMGIAAGVV 57
                                   5689999999999768999*************73667777765 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.11
                      IstB_IS21 102 alkrllkvdllilDdlgllpldqaeaellfeviekryerrsiiitsn 148
                                    al+   ++dll+lD+  +  ld +++++++ v++       +++ + 
  gi|119720352|ref|YP_920847.1| 150 ALALASNPDLLLLDEP-TSGLDPNARREVWGVVDGMRRSGKTVVLAT 195
                                    55566788******96.6789************97665555555444 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   7.7e-05      0.11      26      87 ..     132     180 ..      99     183 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.7e-05
                        SbcCD_C  26 lsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllel 87 
                                     +r+++t SGG k   a+lala      + s      +++l++LDE  s+lD++ ++++ ++
  gi|119720352|ref|YP_920847.1| 132 YKRRVSTYSGGMK-RKASLALA------LAS------NPDLLLLDEPTSGLDPNARREVWGV 180
                                    5778888888888.55555555......344......589****************998776 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   4.9e-05     0.068      31      97 ..      31      88 ..      14     202 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.9e-05
                         AAA_25 31 pagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsed.elrrRlravgeal 97
                                   ++ge+++l G+ g+GK+t+   +a+ v+         +p++g+ l++ +E   d ++r R++ + +++
  gi|119720352|ref|YP_920847.1| 31 REGEVVALLGPNGSGKSTFM-GIAAGVV---------RPTRGRLLVYGGEPYSDaGVRGRISYMPQDY 88
                                   69****************94.4444444.........3466677777777653336666666666666 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   6.5e-05      0.09      15      36 ..      28      50 ..      20      51 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.5e-05
                         AAA_23 15 idF.skgltlItGpNGaGKTTil 36
                                   i+  +  ++++ GpNG+GK+T++
  gi|119720352|ref|YP_920847.1| 28 IEVrEGEVVALLGPNGSGKSTFM 50
                                   55544468899**********86 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00028      0.38      18      46 ..      33      61 ..      26      71 .. 0.81
   2 ?   -1.0   0.0      0.87   1.2e+03      23      48 ..     181     207 ..     174     234 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00028
                         AAA_30 18 drvavltGpAGtGKttalkalreaweaag 46
                                     v++l Gp G+GK+t ++ ++ +++   
  gi|119720352|ref|YP_920847.1| 33 GEVVALLGPNGSGKSTFMGIAAGVVRPTR 61
                                   35999**************9998887664 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.87
                         AAA_30  23 ltGpAGtGKttalkal.reaweaaggr 48 
                                    + G   +GKt +l++   e +e+   r
  gi|119720352|ref|YP_920847.1| 181 VDGMRRSGKTVVLATHlFEDAERLADR 207
                                    445555666666654323333333333 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00031      0.43      14      40 ..      23      50 ..      21      52 .. 0.85
   2 ?   -0.5   0.0      0.58     8e+02     322     364 ..     155     196 ..     142     196 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00031
                         AAA_15 14 lkdveidlsee.ltvliGkNnsGKSsil 40
                                   l+ ++i++ e  +  l G+N+sGKS+++
  gi|119720352|ref|YP_920847.1| 23 LRGISIEVREGeVVALLGPNGSGKSTFM 50
                                   56678888888899************97 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.58
                         AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                    +++++ll++EP   L p+a ++++     + +++k  v++ TH
  gi|119720352|ref|YP_920847.1| 155 SNPDLLLLDEPTSGLDPNARREVWGVVDGMRRSGK-TVVLATH 196
                                    57899*****************9999999999998.7888888 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.2    0.0013       1.7       1      16 [.      35      50 ..      35      60 .. 0.91
   2 ?   -3.2   0.0       6.4   8.8e+03      97     116 ..     100     119 ..      96     121 .. 0.80
   3 ?    1.0   0.0      0.31   4.3e+02       6     116 ..     183     205 ..     132     227 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0013
                         AAA_33  1 lvllvGlpGsGKstla 16
                                   +v l G++GsGKst+ 
  gi|119720352|ref|YP_920847.1| 35 VVALLGPNGSGKSTFM 50
                                   78999*********95 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 6.4
                         AAA_33  97 vpvrivvvetdeetlkeRla 116
                                    +++ +  +e+d +++k+Rl+
  gi|119720352|ref|YP_920847.1| 100 YEFYAALMEVDAKEAKRRLE 119
                                    66777888999999999986 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.31
                         AAA_33   6 GlpGsGKstlaerllkklgavllssdtlrrrlfgtdqqsktdytrvldrlyqilnelarkalsagrnvildatnlsrrer 85 
                                    G+  sGK+ ++  +l                                                                 
  gi|119720352|ref|YP_920847.1| 183 GMRRSGKTVVLATHL----------------------------------------------------------------- 197
                                    333344444444443................................................................. PP

                         AAA_33  86 arflklarrlgvpvrivvvetdeetlkeRla 116
                                                           ++ +eRla
  gi|119720352|ref|YP_920847.1| 198 -----------------------FEDAERLA 205
                                    .......................33333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2065.25
//
Query:       gi|119720353|ref|YP_920848.1|  [L=117]
Description: hypothetical protein Tpen_1448 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-11   45.3   0.1    2.7e-11   43.9   0.1    1.7  2  Asp_protease_2   Aspartyl protease
    2.2e-10   41.0   0.1    3.4e-10   40.4   0.1    1.3  1  gag-asp_proteas  gag-polyprotein putative aspartyl protease
  ------ inclusion threshold ------
      0.024   14.4   0.0      0.032   14.0   0.0    1.3  1  Asp_protease     Aspartyl protease
       0.03   13.6   0.0      0.041   13.2   0.0    1.2  1  Peptidase_U4     Sporulation factor SpoIIGA
      0.054   13.0   0.0       0.06   12.8   0.0    1.1  1  Peptidase_A3     Cauliflower mosaic virus peptidase (A3)
       0.14   11.5   0.0       0.14   11.5   0.0    1.1  1  Asp              Eukaryotic aspartyl protease
       0.17   11.0   0.0        3.1    6.9   0.0    2.0  2  AdoHcyase        S-adenosyl-L-homocysteine hydrolase


Domain annotation for each model (and alignments):
>> Asp_protease_2  Aspartyl protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9   0.1   1.1e-14   2.7e-11       8      75 ..      17      81 ..       6     100 .. 0.84
   2 ?   -0.2   0.0      0.64   1.6e+03      22      39 ..      87     104 ..      84     111 .. 0.77

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 1.1e-14
                 Asp_protease_2  8 kpvrfllDTGasttlispelaeklglkvreseltvrvsgaggevkarlvrldslklggltlknvpalv 75
                                    +v++l+DTGa+t+++++++ae+lgl+v ++   + v++a+g+vk+  + + +++l g +++ + a+v
  gi|119720353|ref|YP_920848.1| 17 LEVKALVDTGATTLVLPRSVAEELGLRVLGK---MDVELADGTVKKVDYSIVEVELSGRRAPVLVAIV 81
                                   589***************************6...8***********************7776655555 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.64
                 Asp_protease_2  22 lispelaeklglkvrese 39 
                                    ++  e+ e+lgl v++ +
  gi|119720353|ref|YP_920848.1|  87 CVGVEALERLGLAVDPAT 104
                                    67778999****999864 PP

>> gag-asp_proteas  gag-polyprotein putative aspartyl protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   0.1   1.3e-13   3.4e-10       9      76 ..      18      82 ..      14      95 .. 0.84

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 1.3e-13
                                   EEEEEEETT-SS-EEEHHHHHHTTGGGGEB..TT--EE-TTSTT-EEEEEEEEEE.EETTEEEEEEEE CS
                gag-asp_proteas  9 pvkflvDTGAsstiiseelaerlglsrkedkgkvevktangeveakrvrldsvkiggielrnvsavvl 76
                                   +vk+lvDTGA++ ++++++ae+lgl+ +    k+ v+ a+g+v++  + + +v++ g ++  + a+v 
  gi|119720353|ref|YP_920848.1| 18 EVKALVDTGATTLVLPRSVAEELGLRVLG---KMDVELADGTVKKVDYSIVEVELSGRRAPVLVAIVE 82
                                   79**************************8...7**********************9998885555543 PP

>> Asp_protease  Aspartyl protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.2e-05     0.032      34     119 ..      17      96 ..       4     101 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.2e-05
                   Asp_protease  34 vkvkafvdsGaqksilskkcaercglmrlldtrfkgiakGvGtkkilGrvhsaevklgdlflpvalsvledkevdlllGl 113
                                     +vka+vd+Ga + +l +++ae+ gl  +l +    +a G  +kk+      +ev+l++   pv + ++e+ ev   +G+
  gi|119720353|ref|YP_920848.1|  17 LEVKALVDTGATTLVLPRSVAEELGLR-VLGKMDVELADGT-VKKVDYS--IVEVELSGRRAPVLVAIVERGEV--CVGV 90 
                                    579*********************985.4455445566664.3444333..35667777777777777776654..5566 PP

                   Asp_protease 114 dllkrh 119
                                    + l r 
  gi|119720353|ref|YP_920848.1|  91 EALERL 96 
                                    666665 PP

>> Peptidase_U4  Sporulation factor SpoIIGA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.6e-05     0.041     147     168 ..       5      26 ..       1      30 [. 0.90

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.6e-05
                   Peptidase_U4 147 iyeveielkgkkievkallDTG 168
                                    + +v++++++k++evkal+DTG
  gi|119720353|ref|YP_920848.1|   5 YAPVKLYHGEKSLEVKALVDTG 26 
                                    678******************* PP

>> Peptidase_A3  Cauliflower mosaic virus peptidase (A3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.4e-05      0.06       6      82 ..       5      79 ..       2      90 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.4e-05
                   Peptidase_A3  6 yikvrlykknykkielhcyvdtGaslciakkkvipeenWvilkrPkevkiadkskitiskvikdvdlkienkifliP 82
                                   y  v+ly+ + k +e+++ vdtGa+  +  + v  ee    +   + v +ad++   +   i +v+l       l+ 
  gi|119720353|ref|YP_920848.1|  5 YAPVKLYH-GEKSLEVKALVDTGATTLVLPRSVA-EELGLRVLGKMDVELADGTVKKVDYSIVEVELSGRRAPVLVA 79
                                   55566664.66889*******************9.666666666789*********999999999997665555555 PP

>> Asp  Eukaryotic aspartyl protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   5.5e-05      0.14     197     230 ..      17      50 ..       8      97 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.5e-05
                                    EEEEEEEETTCSSEEEEHHHHHHHHHHHTTEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            Asp 197 sgcqailDtGTsllalptsivekiakaigakkse 230
                                     +++a++DtG++ l+lp+s++e++   + +k + 
  gi|119720353|ref|YP_920848.1|  17 LEVKALVDTGATTLVLPRSVAEELGLRVLGKMDV 50 
                                    5789******************998887776655 PP

>> AdoHcyase  S-adenosyl-L-homocysteine hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0    0.0012       3.1     236     290 ..       6      68 ..       2      75 .. 0.80
   2 ?    2.3   0.0     0.029        74      56      80 ..      87     111 ..      79     115 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0012
                                    HHHHHHHTTSSS-SS........EEE--CHHHHHHHHHCCCCCT-------HHHHHCCTSXTT CS
                                    xxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      AdoHcyase 236 aqielfkkekkyekk........vyvlpkklDekvarlhleklgaklteltkeqaeyigveve 290
                                    a ++l++ ek+ e k          vlp+++ e++    l k++++l + t ++ +y  veve
  gi|119720353|ref|YP_920848.1|   6 APVKLYHGEKSLEVKalvdtgatTLVLPRSVAEELGLRVLGKMDVELADGTVKKVDYSIVEVE 68 
                                    66777776665665566666666889*************************999999777654 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.029
                                    HHHHHHHHHTT-EEEEE-SSTTT-- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxx RF
                      AdoHcyase  56 avLietLvalGaevrWasCnifstq 80 
                                     v +e+L +lG  v  a+  i+st+
  gi|119720353|ref|YP_920848.1|  87 CVGVEALERLGLAVDPATGSIYSTR 111
                                    5779*******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 786.55
//
Query:       gi|119720354|ref|YP_920849.1|  [L=284]
Description: UbiA prenyltransferase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.5e-35  120.4  20.6    9.9e-35  120.0  20.6    1.2  1  UbiA      UbiA prenyltransferase family
  ------ inclusion threshold ------
        2.5    8.4   0.0        2.5    8.4   0.0    4.1  5  DUF3040   Protein of unknown function (DUF3040)


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.0  20.6   1.1e-38   9.9e-35       5     229 ..      32     248 ..      28     280 .. 0.83

  Alignments for each domain:
  == domain 1  score: 120.0 bits;  conditional E-value: 1.1e-38
                           UbiA   5 alvglalaaggspdlllllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivllilgllll 84 
                                    a+ g++++ ggs++    +l+++ ++l+aa++n++NdyfD e+Da+   +p+RPl+s+risp  a+ +++ ll++gl+l+
  gi|119720354|ref|YP_920849.1|  32 AYTGYVAGRGGSLPQ--GVLVAASAALVAAWGNIVNDYFDLESDAI--SKPWRPLPSRRISPGSAVSASLPLLAAGLALG 107
                                    567788887777666..566666789********************..******************************** PP

                           UbiA  85 alllnpltallgllalllyvvYtglrlKrrtllgtvvggiafglppllgwaavtgslsllalllalavflltwaialand 164
                                     +l++pl+ ++++la +l+++Y+  r K  +l g+v++++  +l ++ g+ a   + ++  ll+++  fl +++  + + 
  gi|119720354|ref|YP_920849.1| 108 -FLVSPLCGFTAVLASALLFLYS-WRVKALGLPGNVLIAFLAALNVVYGALAS-PE-PWRSLLPSAYAFLIILGREVLKG 183
                                    .**********************.6**********************999996.55.89999999999************ PP

                           UbiA 165 lrdregDrkagiktlpvvlGrkaaril.lalllavlllallllllalllllylllalllaalallr 229
                                    ++d+egD+++g+kt + +lG++aa+++ ++lllav+ l+  l ll +++ ly+l+a++ + ++++ 
  gi|119720354|ref|YP_920849.1| 184 VEDLEGDAARGVKTVASTLGARAALRVsAVLLLAVVALS-PLPLLSGYGALYALFAFGGVDAPIAL 248
                                    **************************9555555555555.34444444444444444444333333 PP

>> DUF3040  Protein of unknown function (DUF3040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.7      0.32   2.9e+03      67      77 ..      47      57 ..      12      65 .. 0.50
   2 ?    8.4   0.0   0.00028       2.5      39      83 ..      80     124 ..      69     125 .. 0.82
   3 ?   -1.0   0.1      0.24   2.2e+03      50      69 ..     142     162 ..     133     178 .. 0.58
   4 ?   -0.4   3.3      0.16   1.4e+03      37      79 ..     204     236 ..     184     251 .. 0.47
   5 ?   -0.2   0.3      0.14   1.3e+03      46      62 ..     265     281 ..     241     284 .] 0.54

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.32
                        DUF3040 67 avvlgvvGfvv 77
                                    v++++  ++v
  gi|119720354|ref|YP_920849.1| 47 GVLVAASAALV 57
                                   22222222222 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00028
                        DUF3040  39 rslrrlavlavllfvaGllllvlGvaaaavvlgvvGfvvmlagvv 83 
                                    r l+ +++ +  ++ a l ll +G+a+  +v +++Gf+++la ++
  gi|119720354|ref|YP_920849.1|  80 RPLPSRRISPGSAVSASLPLLAAGLALGFLVSPLCGFTAVLASAL 124
                                    4455567888999999********999999**********99875 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.24
                        DUF3040  50 llfvaGllllvlG.vaaaavv 69 
                                    l++++++l +v G +a   ++
  gi|119720354|ref|YP_920849.1| 142 LIAFLAALNVVYGaLASPEPW 162
                                    555556677777734444333 PP

  == domain 4  score: -0.4 bits;  conditional E-value: 0.16
                        DUF3040  37 rrrslrrlavlavllfvaGllllvlGvaaaavvlgvvGfvvml 79 
                                    +r +lr          v+++lll + ++   ++l+  G++ +l
  gi|119720354|ref|YP_920849.1| 204 ARAALR----------VSAVLLLAVVALSPLPLLSGYGALYAL 236
                                    222223..........333333333233333455555554443 PP

  == domain 5  score: -0.2 bits;  conditional E-value: 0.14
                        DUF3040  46 vlavllfvaGllllvlG 62 
                                     +  + +++Gll++++G
  gi|119720354|ref|YP_920849.1| 265 RILKVPLLMGLLAFLVG 281
                                    22333445577765555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      217  (0.0121033); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 2050.26
//
Query:       gi|119720355|ref|YP_920850.1|  [L=197]
Description: phosphatidate cytidylyltransferase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1395.94
//
Query:       gi|119720356|ref|YP_920851.1|  [L=444]
Description: binding-protein-dependent transport systems inner membrane component [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-13   50.4  19.4    2.1e-13   50.4  19.4    2.1  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.3     0.091   1.6e+03      52      71 ..      19      38 ..      10      53 .. 0.56
   2 !   50.4  19.4   1.2e-17   2.1e-13      20     177 ..     244     430 ..     227     438 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.091
                   BPD_transp_1 52 lilpviillllsaapyvrli 71
                                   + l+++++++l ++ y +++
  gi|119720356|ref|YP_920851.1| 19 TLLALVVMGVLLFPVYYMFM 38
                                   33444444444444444433 PP

  == domain 2  score: 50.4 bits;  conditional E-value: 1.2e-17
                   BPD_transp_1  20 lrpliivllslPsfv...........laillvlvf.........................vilsilghlilpviilllls 63 
                                    l+++  +l+ +Ps                     +                          +   l + i+ + ++++ +
  gi|119720356|ref|YP_920851.1| 244 LTVVLTLLFVVPSAYafsrlkffgkgH-------IlysylmftqvagglgiaglvalygmLVRLNLVNNIFVLPVIYAAG 316
                                    455555555555555333333333331.......03333333455555555555556666455556666777889999** PP

                   BPD_transp_1  64 aapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG...lgtl 140
                                    ++p+++++ +++l+s++ d+ eaa+++Gas+ qi+ +v++P+alp i+t +i++f+g +++ +l+ +l+++       + 
  gi|119720356|ref|YP_920851.1| 317 SVPFNTWLLKGYLDSISPDFDEAALVDGASYAQIIGQVLVPMALPGIATVAIFSFIGGWTELILANLLLNQENhplTVYI 396
                                    *********************************************************************99877766677 PP

                   BPD_transp_1 141 lleailgydyseisnggvlalviavlllnlvadilqr 177
                                     +  ++ +++s+++   ++a++++++l ++v+++l++
  gi|119720356|ref|YP_920851.1| 397 YVLLTNLRNVSWNQ---FAAAALIFALPVVVMFLLAQ 430
                                    77777778888777...55555555555555444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (444 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       663  (0.0369792); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 3214.24
//
Query:       gi|119720357|ref|YP_920852.1|  [L=300]
Description: binding-protein-dependent transport systems inner membrane component [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-17   63.6  20.6    1.9e-17   63.6  20.6    1.9  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
       0.03   14.5   1.1        0.1   12.7   1.1    1.9  1  TM_PBP2_N     N-terminal of TM subunit in PBP-dependent ABC t


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   3.3      0.32   2.9e+03      47      47 ..      72      72 ..       5     105 .. 0.42
   2 !   63.6  20.6   2.1e-21   1.9e-17       2     176 ..      89     288 ..      88     293 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.32
                   BPD_transp_1 47 s 47
                                   +
  gi|119720357|ref|YP_920852.1| 72 T 72
                                   1 PP

  == domain 2  score: 63.6 bits;  conditional E-value: 2.1e-21
                   BPD_transp_1   2 illGilaa...lnrnkkldkllrpliivllslPsfvlaillvlvf....................vilsilghlilpvii 58 
                                    +l+Gi++    +++  +++ + r l i++++lP +  + ++ ++f                     + ++++++++++ i
  gi|119720357|ref|YP_920852.1|  89 VLTGIFLSvlyNSKYVRGRAIYRSLLIIPWALPLLFTITVWRFMFdpvvgpvngvlralgvanppDWTTDITWGFIALNI 168
                                    5678888877668888999***********************9************************************* PP

                   BPD_transp_1  59 llllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlg 138
                                    + ++ a p+++ ++ aal+s+p  l+eaa ++Gas+wq++ kv++P +  pii   il++++++  ++++ fl++++ l 
  gi|119720357|ref|YP_920852.1| 169 IEVWLAYPFMLTVITAALQSVPYTLIEAAIVDGASYWQRLTKVIIPIVSKPIIFATILTSAASFQYFLVP-FLFNGS-LF 246
                                    ****************************************************************988777.555555.99 PP

                   BPD_transp_1 139 tllleailgydyseis....nggvlalviavlllnlvadilq 176
                                      ++  + gy  +++s    +g ++a++++v l+++v+++++
  gi|119720357|ref|YP_920852.1| 247 EDRFLLLYGYKKAFGSavpeYGKAAAILVIVTLVLAVYMFVN 288
                                    999999999999999999998999999888888888888765 PP

>> TM_PBP2_N  N-terminal of TM subunit in PBP-dependent ABC transporters
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.1   1.1e-05       0.1       4      22 ..      20      38 ..      18      44 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.1e-05
                      TM_PBP2_N  4 lvfqvfpvlyTistafTNy 22
                                   l+f+v+p++y++ +afTN 
  gi|119720357|ref|YP_920852.1| 20 LFFNVYPIFYSVFIAFTNA 38
                                   68****************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       695  (0.038764); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 2066.30
//
Query:       gi|119720358|ref|YP_920853.1|  [L=415]
Description: extracellular solute-binding protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.3e-53  180.9   1.9    5.9e-53  180.5   1.9    1.1  1  SBP_bac_8  Bacterial extracellular solute-binding protein
      2e-42  146.3   9.7    2.9e-42  145.7   9.7    1.2  1  SBP_bac_1  Bacterial extracellular solute-binding protein
    5.8e-07   29.2   0.1    2.8e-05   23.7   0.0    2.2  2  SBP_bac_6  Bacterial extracellular solute-binding protein


Domain annotation for each model (and alignments):
>> SBP_bac_8  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.5   1.9   9.9e-57   5.9e-53       2     278 ..      64     356 ..      63     359 .. 0.85

  Alignments for each domain:
  == domain 1  score: 180.5 bits;  conditional E-value: 9.9e-57
                                    HHHHHHHH-.TEEEEEEE--SSSHHHHHHHHHHTT---SEE.EEE-HHHHHHHHHTTSB--GG...GSTTHHH-HH.HHH CS
                      SBP_bac_8   2 lakefekkt.gvkvnvvtaasndleqklkaalaagtapdidvvwanedalatlaeeglladls...dldnlddltd.ala 76 
                                    ++++f  ++  ++v++++   +dle+ lk+a++ag++pd  ++++++d+++++ae+gll++++   +   l+++++   +
  gi|119720358|ref|YP_920853.1|  64 VIADFHVQHpEITVKLEQK--ADLETSLKTAIPAGQGPD--LFIWAHDWIGKFAEAGLLEPIDeyvTPSVLNKFSPiGQN 139
                                    78999999*99*****888..58***************7..667779****************64433455556665666 PP

                                    TT--TS.----EEEEEEE-EEEEEHHHHHHS.---BHHHHHHHHHHH....HHH-SE..GG---GGGGGGTHHETTEE-- CS
                      SBP_bac_8  77 avgydgklygvPyasetpyvliynkdllekaedpktwdellaaakkl....kgkfgl..pdpasgwlqaallakdgksld 150
                                    a +y g++y++P+a+et  +liynk+l++ + +pkt+de++++ +k+    kg +gl  p ++++   + + + +g+++d
  gi|119720358|ref|YP_920853.1| 140 AIEYRGHYYAMPLAAET-VALIYNKALVP-N-PPKTFDEMKSIMAKFtnpdKGTYGLatPIDPYFLSGWVHAF-GGYYFD 215
                                    66**************9.7**********.6.***************88777888884456788899******.*****8 PP

                                    -H.......HHH.HHHHHHH.HHHHHTT-EE-S..--SSTTTTTSBSEEEE-TTHHHHHH-TTTSEEEE.--......S- CS
                      SBP_bac_8 151 ddg.....gkdglkealell.kklkdngktydtgadavsefanGevaftingswdiaaaqkagkklgai.vp......kq 217
                                    d++     +k+++ + ++++  + ++++  + +++++vs+f +G++ ++ing+w+i +++kag ++g++ +p       +
  gi|119720358|ref|YP_920853.1| 216 DKTkqpglDKPETIKGFKFFfEQVYPYVAKTRDYNAQVSLFLEGKAPMMINGPWSIGDVKKAGINFGVApLPpidsssVP 295
                                    888899998888888888761557799865556677889******************************63446655446 PP

                                    -EEEEEEEEEEBTTS-HHHHHHHHHHHHHTTSHHHHHHHH.HH---BS-S-TTTHHHHHH-H CS
                      SBP_bac_8 218 gsfaggkglavpknaknedlaAldFlkwltspenqaalae.ktgyipvnksaalspevkkdp 278
                                     +  g+k ++v k+ k+++ a + Fl+wlt++ n  + +    gyipv+k++ ++pe++++p
  gi|119720358|ref|YP_920853.1| 296 HPYGGVKLVYVAKGVKDKA-AVWTFLEWLTTNPNVIKQFAiRNGYIPVLKEVLNDPEIQNNP 356
                                    699999*************.6********977766665555*******************98 PP

>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.7   9.7   4.8e-46   2.9e-42       3     312 ..      56     327 ..      54     330 .. 0.90

  Alignments for each domain:
  == domain 1  score: 145.7 bits;  conditional E-value: 4.8e-46
                                    SHHHHHHHHHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHHHHTTSSSCSEEEECGGHHHHHHHTTSBECCHHHHHHTT CS
                      SBP_bac_1   3 sltegaalqalvakafekehpgikVeiesvgsgslaqkltlaiaaGdgpaDviavdndwiarlakaglllpldpyvkayl 82 
                                    ++ +  +l+ ++ ++f  +hp i+V++e+    +l + l++ai aG+gp D++++++dwi+++a+agll+p+d+yv +  
  gi|119720358|ref|YP_920853.1|  56 EEVK--TLEDVI-ADFHVQHPEITVKLEQK--ADLETSLKTAIPAGQGP-DLFIWAHDWIGKFAEAGLLEPIDEYVTPSV 129
                                    5666..899999.***999***********..*****************.*****************************5 PP

                                    ECTTCCTEEEEHHHHTHHHHCEEE.ES.EEEEE.EEEEEEETTTHHCTTGGGSHBHHHHHHHHHHHHHHCTCTHCCHCCE CS
                      SBP_bac_1  83 apgvkdaadklsssvlpkildskv.ly.vPlya.argliYNkdlfekagldppwtWdelveaakklkekgkkpiggargg 159
                                            ++ +s  +++ +++++ +y +Pl a + +liYNk l+     +pp+t+de      k++ ++k++     +g
  gi|119720358|ref|YP_920853.1| 130 --------LNKFSPIGQNAIEYRGhYYaMPLAAeTVALIYNKALVP----NPPKTFDEMKSIMAKFTNPDKGT-----YG 192
                                    ........55678889888888778*******77************....7899*******************.....** PP

                                    EHHHHHHHHHHHHHHHHTGGGEECCCT..HHCSHHHHS.HHHHHHHHHHHHHHHHHHHTTEEECSSHHHHHHHHHTTSCS CS
                      SBP_bac_1 160 sasgtayyfalalakslggkvfdkdgg..gldnpegvt.aatylvklyavanltkelkgkgaenkdgaaalalfeaGeaa 236
                                     a     yf++ +   +gg++fd++ +  gld+pe  +  +          + +++  +++a + d +a ++lf +G+a+
  gi|119720358|ref|YP_920853.1| 193 LATPIDPYFLSGWVHAFGGYYFDDKTKqpGLDKPETIKgFK----------FFFEQVYPYVAKTRDYNAQVSLFLEGKAP 262
                                    ************************99888777776666444..........4444556********************** PP

                                    EEEEEHHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEE..EEEEEEEEBTTCSTHHHHHHHHHHHTSHH CS
                      SBP_bac_1 237 maivglwaalaamkvapkvafaadkekpkeelgvaplPagkggkpgi..lgayglaipkgsknpeaAkkFldfllspe 312
                                    m+i+g+w+             + d +k+++++gvaplP ++    +    g+  + + kg k+++a++ Fl++l+++ 
  gi|119720358|ref|YP_920853.1| 263 MMINGPWS-------------IGDVKKAGINFGVAPLPPIDSSSVPHpyGGVKLVYVAKGVKDKAAVWTFLEWLTTNP 327
                                    ********.............999999999999999999988888889445555*********************986 PP

>> SBP_bac_6  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   4.7e-09   2.8e-05       4      79 ..      99     175 ..      96     178 .. 0.86
   2 !    3.4   0.0    0.0072        43     182     234 ..     304     357 ..     299     367 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 4.7e-09
                      SBP_bac_6   4 pdlilsfdkdflekfieeglfqpldpanlpnvnkdfa..eeglkdpdgkyy..pygvgplvlavnkdrlkgrpvPksWaD 79 
                                    pdl++    d+++kf+e+gl++p+d+   p+v ++f+   ++  + +g+yy  p++ +++ l++nk  +++   Pk++++
  gi|119720358|ref|YP_920853.1|  99 PDLFI-WAHDWIGKFAEAGLLEPIDEYVTPSVLNKFSpiGQNAIEYRGHYYamPLAAETVALIYNKALVPNP--PKTFDE 175
                                    89999.999****************9999999999997644444447888889****************766..999986 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.0072
                      SBP_bac_6 182 mlvkkg.kkkelakafidfllspe.vqailakaggvfPvvtnpavlnelpegakl 234
                                    ++v kg k k+ ++ f+++l+ +  v +++a  +g +Pv ++  +++++++++++
  gi|119720358|ref|YP_920853.1| 304 VYVAKGvKDKAAVWTFLEWLTTNPnVIKQFAIRNGYIPV-LKEVLNDPEIQNNPV 357
                                    5677888999**********87655**********9**9.766666666666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1056  (0.058899); expected 358.6 (0.02)
Passed bias filter:                      934  (0.0520944); expected 358.6 (0.02)
Passed Vit filter:                       108  (0.00602376); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.45
# Mc/sec: 2780.43
//
Query:       gi|119720359|ref|YP_920854.1|  [L=739]
Description: alpha amylase, catalytic region [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.9e-59  199.7   5.2    1.3e-58  199.2   5.2    1.2  1  Alpha-amylase   Alpha amylase, catalytic domain
      6e-15   54.9   0.3      2e-14   53.3   0.0    2.1  2  CBM_20          Starch binding domain
    2.1e-07   30.9   1.0    4.8e-07   29.7   1.0    1.7  1  TIG             IPT/TIG domain
  ------ inclusion threshold ------
      0.018   14.8   0.0      0.054   13.3   0.0    1.8  1  Bac_A_amyl_C    Bacterial Alpha amylase C-terminal domain
      0.032   14.4   0.0      0.081   13.1   0.0    1.7  1  Malt_amylase_C  Maltogenic Amylase, C-terminal domain


Domain annotation for each model (and alignments):
>> Alpha-amylase  Alpha amylase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.2   5.2   3.6e-62   1.3e-58       1     331 [.      81     402 ..      81     407 .. 0.83

  Alignments for each domain:
  == domain 1  score: 199.2 bits;  conditional E-value: 3.6e-62
                                    --CHHHHCTCCCCCCCT-SCEEE-B-CE...........-S-TTTTSS-SCECCE-CCC--CCCCCCHHHHHHCTT-EEE CS
                  Alpha-amylase   1 GDLkGiiekLdYlkeLGvtaiwlsPifk...........spqadhgYdiadytkidpefGtnedlkeLiskahekgikvi 69 
                                    GD++Gii kL+Yl eLGvtaiw+sP+f+            ++ +hgY+ +d++ i+++fG    + +Li++a++ +i vi
  gi|119720359|ref|YP_920854.1|  81 GDIDGIIAKLPYLYELGVTAIWISPVFDnidvaintssgLQAGYHGYWPKDFKVIEEHFGSWSTFYKLIQEARKYNITVI 160
                                    9***********************************9987789************************************* PP

                                    EEE--SC--TTSCCCHCCHHSTTSG......GGCCC-E......ESS-STTC-TTTT.CSCEECTTTTCEEESSS-TTS- CS
                  Alpha-amylase  70 lDlVvNHtsdehewfkeslkkkgep......krdyyiwkegkeekeppnnwkslfdg.saweydekaqeyylhlflkklp 142
                                    +D+VvNH+  + +    +l  +g        +++y+   +   ++   +n +++++g ++w++ ++      +++l +l+
  gi|119720359|ref|YP_920854.1| 161 IDFVVNHSNPSDAGEYGALYDNGTFvtdyptDAKYATVDPI--TR-SLSNIYNHNGGiTNWNDRWEV----RYKNLFNLA 233
                                    *******9777666444444445440000014444444444..22.233334445441455544444....499****** PP

                                    BB-TTTCCCCCCCCCCCCCCCTTT-SEEEETTCCCTTTCCCCHCCHCCHHHHHHHHHHHTCCGTT-EEEEE-TT-SCCCH CS
                  Alpha-amylase 143 dLnteneevrkelkdvvkfwlekgidGfRlDvvkhvskvealesngeflheftqalnetvasrkevmtvgEvssdasedl 222
                                    d+n  n+ v+++lk+   ++l+ gi G+RlD+vkhv+          +l++++  + +     k+v+++gE++++ ++++
  gi|119720359|ref|YP_920854.1| 234 DFNQLNPWVDRYLKESTALYLKAGIGGIRLDAVKHVEP--------GWLKTYADYVYAI----KNVFMFGEWYQSFNDEM 301
                                    **************************************........9999999999977....6***********99988 PP

                                    CCCC-CGG-SIC.ECCITTCGGGCC-CTSTTSB-SS-HHHHHHHHHHHHHHS-CCCTTCEEES--TTS--HHHHTTSSTT CS
                  Alpha-amylase 223 rvyttearlele.mvldfphldvaqkakikeqlksisakklkellkkwlkaleeaaeeavtflgnHDqeRilsrlgddsa 301
                                    + ++ +   ++  +v+++p ++v  +++   +  + ++++l++++kk+ ++ +  +++ v+f+++HD +R+ls  ++   
  gi|119720359|ref|YP_920854.1| 302 YWDMVKFANDSGiSVINIPLQQVLVDVF---AYDTKTMYDLDNAVKKYTSNFMW-QNKLVNFIDSHDVPRFLSLSKSIT- 376
                                    8777665554431366666666666666...777778****************7.9********************999. PP

                                    TTHHHHHHHHHCCCTSSSEEEEETTCCCT- CS
                  Alpha-amylase 302 eaekklklaaillltlrGvpviYyGeEigm 331
                                        + ++++++++t +G+pviYyG+E+++
  gi|119720359|ref|YP_920854.1| 377 ----RFHQVLAFVMTAPGIPVIYYGDEQYL 402
                                    ....8***********************86 PP

>> CBM_20  Starch binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.1       2.7   9.6e+03      47      64 ..     578     595 ..     573     596 .. 0.80
   2 !   53.3   0.0   5.6e-18     2e-14       2      91 ..     635     729 ..     634     734 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2.7
                         CBM_20  47 yplWsttvslpagtkieY 64 
                                    + +Ws+tv+  ++++ie+
  gi|119720359|ref|YP_920854.1| 578 QSTWSATVTYWSDKSIEF 595
                                    678999999988888887 PP

  == domain 2  score: 53.3 bits;  conditional E-value: 5.6e-18
                         CBM_20   2 vsVtFkv.na.....ttqlgesvyivGsiseLGnWnpkkavklsaseqtssyplWsttvslpagtkieYkyikkdsdgsv 75 
                                    ++V F+v n+     +t +ge + ++Gs++eL nW+p+   ++ +  +    p+W++ +s+pa+t ie+k++k    g+ 
  gi|119720359|ref|YP_920854.1| 635 IPVIFEVqNTkgttlETVPGEFLWLTGSVPELSNWSPATTRAVGPMLC-PAWPNWFVVASVPANTYIEFKFLKAPLGGTG 713
                                    677777754456667899*******************99988888888.79***************************** PP

                         CBM_20  76 tWesgenrsltvpssg 91 
                                    +We+g+n+ +t+ps+g
  gi|119720359|ref|YP_920854.1| 714 VWEPGSNHAYTTPSDG 729
                                    *************976 PP

>> TIG  IPT/TIG domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   1.0   1.4e-10   4.8e-07       3      85 .]     544     629 ..     542     629 .. 0.91

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 1.4e-10
                            TIG   3 issisPnsgsasgGttititGtnFgtnssdssvtiggtpctvta.svssttlvcttPpgp.....sgllnvsvlvdgaql 76 
                                    + +i P++g a  G  ++i+G +Fg++  ++ +t g +   +t+ ++s+ ++++++P+g+     +++++v+v++ + + 
  gi|119720359|ref|YP_920854.1| 544 VGAIDPTMGRA--GNVVVISGEGFGSQPGQVLITNGQSTWSATVtYWSDKSIEFIVPSGVttplnDNHVTVIVKRAD-GA 620
                                    6789*******..***********999999999999887777778***************9*997779999999999.** PP

                            TIG  77 rsdnttftY 85 
                                    +s++  f+Y
  gi|119720359|ref|YP_920854.1| 621 TSNGIAFQY 629
                                    *******99 PP

>> Bac_A_amyl_C  Bacterial Alpha amylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.5e-05     0.054      33      63 ..     490     524 ..     486     527 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.5e-05
                                    EEEE--S-SEEEEE....TTTSEEEEEETTEEEEE CS
                   Bac_A_amyl_C  33 gevkvdlpDGsYkN....lidgseveVkdGklalk 63 
                                    ++v ++lpDG+Y +    li+g++++V +Gk++++
  gi|119720359|ref|YP_920854.1| 490 SNVYTSLPDGVYSDylggLINGTSIKVVGGKFSVT 524
                                    6899*********9777789***********9987 PP

>> Malt_amylase_C  Maltogenic Amylase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   2.3e-05     0.081      11      71 ..     461     528 ..     454     532 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.3e-05
                                    TTEEEEEEEETTEEEEEEEE...SS-EEEE...E--G.GGTT-EEEETTTTEE-----SSEEEEE-TT CS
                 Malt_amylase_C  11 rkvlaYlReyedetilvvaN...rsaqave...ldls.elagrvpvelfggeefpaigelytltLppy 71 
                                     +v++++R+  ++ +lv++N   +s+ av+    +l+  +    +  l++g+  + +g+++ +tLpp 
  gi|119720359|ref|YP_920854.1| 461 SDVYIFERKFFGNVVLVAINrnlNSPVAVSnvyTSLPdGVYSDYLGGLINGTSIKVVGGKFSVTLPPG 528
                                    479*****************96644444431114444777777777788899**************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (739 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.43
# Mc/sec: 5108.22
//
Query:       gi|119720360|ref|YP_920855.1|  [L=290]
Description: pyruvate ferredoxin/flavodoxin oxidoreductase, beta subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.5e-29  101.6   0.0    6.3e-29  100.7   0.0    1.4  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
    1.6e-20   73.0   1.3    3.1e-20   72.1   1.3    1.5  1  PFO_beta_C    Pyruvate ferredoxin oxidoreductase beta subunit


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.7   0.0   7.1e-33   6.3e-29       2     153 .]      55     202 ..      54     202 .. 0.94

  Alignments for each domain:
  == domain 1  score: 100.7 bits;  conditional E-value: 7.1e-33
                                    SSHHHHHHHHHHTTSSSSEEEC.ETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEEEEE CS
                   TPP_enzyme_C   2 iGcltlwaarllkvkrprsylt.sgglgtmGyglpaAiGaklakpdrevvaivGDGgflmi.lqelatavrrnlpitvvv 79 
                                    iGc+               y++ +++ + +G+++ +A+G+k+a+p+ +vv++vGDG+ +   l++l+ a++rn+ i+v+v
  gi|119720360|ref|YP_920855.1|  55 IGCHDK----------IVDYINlNSFRSLHGRAITVATGIKIANPRLQVVVFVGDGDAYGEgLEHLVFAAKRNIGIKVIV 124
                                    667766..........667888888999**************************************************** PP

                                    EE-SBCCCHHHH...HHHHTCCTTTTSBB.BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHHCSSSEEEEEE CS
                   TPP_enzyme_C  80 lnNegygmtggq...qepfggkrksgpagkdlkpvdfaklaealGak.garvekadveeleealkealekkgpaliev 153
                                    ++N++yg+t gq   ++p+g   +s+p+g+ ++p++++kl  a Ga+ +ar  +a +++l+  +k+a++++g+a+i+v
  gi|119720360|ref|YP_920855.1| 125 HDNRVYGLTTGQytpTSPKGFPGRSTPKGSVEDPLNPVKLLLASGASfVARGYSARPDHLKGLIKQAIMHRGFAVIDV 202
                                    ************9999999999999****9*****************9998788899*******************98 PP

>> PFO_beta_C  Pyruvate ferredoxin oxidoreductase beta subunit C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.1   1.3   3.5e-24   3.1e-20       1      62 [.     206     271 ..     206     275 .. 0.95

  Alignments for each domain:
  == domain 1  score: 72.1 bits;  conditional E-value: 3.5e-24
                                    XTTTXSSSXSXXXXX-EEEGGGST---EEHHHHHHHHT----......-EEEEEEEETTS--HHHHHH CS
                     PFO_beta_C   1 CvtFNkvnTfdwYkervykleedgyDpsdlekAlekalewgd......kiplGifYkeekptyeerle 62 
                                    CvtF  ++T+++Y+ rvy+l+e g+D + +e+A++ka+ew+       +ip+GifYk ekptyee + 
  gi|119720360|ref|YP_920855.1| 206 CVTF--FDTYKYYNARVYDLQEAGHDYTSYEAAMRKAEEWNYgvddsgRIPIGIFYKAEKPTYEETIL 271
                                    ****..****************9****************998888999*****************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2119.07
//
Query:       gi|119720361|ref|YP_920856.1|  [L=554]
Description: pyruvate flavodoxin/ferredoxin oxidoreductase domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.5e-54  183.6   0.0    6.5e-54  183.1   0.0    1.2  1  POR_N            Pyruvate flavodoxin/ferredoxin oxidoreductas
    3.4e-24   85.9   0.3    1.3e-23   84.0   0.3    1.9  1  POR              Pyruvate ferredoxin/flavodoxin oxidoreductas
    3.2e-08   33.4   1.1    1.8e-07   30.9   1.1    2.0  2  TPP_enzyme_N     Thiamine pyrophosphate enzyme, N-terminal TP
  ------ inclusion threshold ------
      0.016   15.1   0.0      0.045   13.6   0.0    1.7  1  Transketolase_C  Transketolase, C-terminal domain
      0.055   13.8   0.0       0.15   12.4   0.0    1.8  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma


Domain annotation for each model (and alignments):
>> POR_N  Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.1   0.0   1.8e-57   6.5e-54       2     220 ..     196     420 ..     195     430 .. 0.90

  Alignments for each domain:
  == domain 1  score: 183.1 bits;  conditional E-value: 1.8e-57
                                    HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCCHHH CS
                          POR_N   2 aaiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmienlgl 81 
                                    +a++ag++ ++aYP+TPss+i++ la+  +k+++   +v+  e+Ei+ i+ + GAa+aGar+a+ TSg G++Lm+e+l l
  gi|119720361|ref|YP_920856.1| 196 GAVKAGMKLYVAYPMTPSSSILHYLAANEDKFGI---VVIHPENEIAVIGIAEGAAYAGARVAVGTSGGGFALMVEHLSL 272
                                    78999***************************97...******************************************* PP

                                    HHHTT--EEEEEEEEE-STTBEEEEE--TTCHHHH.....S---EEEE-SSHHHHHHHHHHHHHHHHHCTSEEEEEEEHH CS
                          POR_N  82 aageelPvvivvvaRalpstglsirtdqsDlmaar.....dtglivlasenvqeafdlalvAfnlAekvrvPvivlfDgf 156
                                    a+ +e+Pvvi++++R +p+tg++++t+q+Dl++a+     +++ +vla++++ eaf+l  +A+nlA+k++vPvivl+D++
  gi|119720361|ref|YP_920856.1| 273 AGQAEIPVVIFLAQRPGPATGVPTYTEQGDLFFAIfaghgEFPRVVLAPGDADEAFQLSGEAMNLAWKFQVPVIVLSDKH 352
                                    ******************************************************************************** PP

                                    HH.HEEEEEEC-SGG.GS-----SBXXXXXXXX.....SXXXBXXTXXTSSXXEEESBXBXTTSXBXXX CS
                          POR_N 157 llshevekvelpdeedelklikekleeyerkey.....aldpekpiargtaanpdtglehrekgneaed 220
                                    l  ++v +  + +  ++++ +k      e k+y     +++p  ++ + +a ++++++eh+e+g  +ed
  gi|119720361|ref|YP_920856.1| 353 LS-ESVYTAIVDEGSVKVEQEKLWDGTGEYKRYlftedGVSPLAFPGTPGAIVKANSYEHDEYGLTTED 420
                                    99.66666555544433333333333333344466999***************************9998 PP

>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.0   0.3   3.6e-27   1.3e-23       1     176 [.      13     164 ..      11     165 .. 0.96

  Alignments for each domain:
  == domain 1  score: 84.0 bits;  conditional E-value: 3.6e-27
                                    CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHHHHGGGEEEEE CS
                            POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetlsehldglkpgg 80 
                                    +G+G+  +g i+a+ + + Gy+ + +++y+s irGgh ++ vr+s++ +v++ + +++++lval++e++++h  +l + +
  gi|119720361|ref|YP_920856.1|  13 AGDGIRQTGVIIANLFNKMGYWTFVYDDYQSLIRGGHNFAIVRASRR-KVQAHR-DRVEILVALNQESVEKHSWRLGERS 90 
                                    5*********************************************9.99**99.************************* PP

                                    EEEEECTCGTT-CCHHHCTS-HHHHHHHT-EEEEE-HHHHHHHCCC.CCHHHHHHHHHHHHHHTS-HHHHHHHHHCCS-C CS
                            POR  81 iiiynseelkpdelkkakeeerelkerlgvrvygvdatkiakeiggneraaNtvmlGalaallglplealeeaikkrfpk 160
                                    +++++s+ +k + l                   g+++ ++ak+ g   +++N v++Gala +lg+++  +e ++++++ +
  gi|119720361|ref|YP_920856.1|  91 LVVFDSGSVKAEGL-------------------GIPMAEMAKRRGLPLIMRNSVAVGALASMLGVEFSLVESVVRRAISR 151
                                    ******87555555...................99********************************************7 PP

                                    H.HHHHHHHHHHHHHH CS
                            POR 161 kkeviekNlkafragy 176
                                        +e+Nl+ +r+gy
  gi|119720361|ref|YP_920856.1| 152 ---NVEENLELAREGY 164
                                    ...6***********9 PP

>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   1.1   5.1e-11   1.8e-07       2     140 ..     188     328 ..     187     356 .. 0.78
   2 ?    0.5   0.0      0.11     4e+02      82     106 ..     334     358 ..     327     383 .. 0.78

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 5.1e-11
                                    EHHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT....TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHH CS
                   TPP_enzyme_N   2 tvaealvraLkalgvehvfgvpGsrilplldalseeq...girvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatn 78 
                                    t+ eal     ++g + ++++p + + ++l +l++++   gi v+   +E +++++A+g a a     v++ tsg G++ 
  gi|119720361|ref|YP_920856.1| 188 TGNEALSLGAVKAGMKLYVAYPMTPSSSILHYLAANEdkfGIVVIHPENEIAVIGIAEGAAYAG--ARVAVGTSGGGFAL 265
                                    56677777778999*******************9999988888888889999999999998887..46788999****** PP

                                    CHHHHHHHHHHT--EEEEEEE--CCCHHS..TC--T-.CCHHHCCCSSEEEE-SSGGGHHHHH CS
                   TPP_enzyme_N  79 altalaeAkvdriPllvlsgdrptslrgqgvlqqeld.qlalfrpvtkyaervtspeelpeal 140
                                    ++  l  A ++ iP++++ ++rp   +g ++  ++ d   a+f+ + ++ + v  p ++ ea+
  gi|119720361|ref|YP_920856.1| 266 MVEHLSLAGQAEIPVVIFLAQRPGPATGVPTYTEQGDlFFAIFAGHGEFPRVVLAPGDADEAF 328
                                    ***********************9999944444333225555665555555555555555554 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.11
                                    HHHHHHHHT--EEEEEEE--CCCHH CS
                   TPP_enzyme_N  82 alaeAkvdriPllvlsgdrptslrg 106
                                    a+  A++ ++P++vls  + ++++ 
  gi|119720361|ref|YP_920856.1| 334 AMNLAWKFQVPVIVLSDKHLSESVY 358
                                    56789**********9877766655 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.3e-05     0.045       7      70 ..     453     511 ..     449     521 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.3e-05
                                    ETTSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEE CS
                Transketolase_C   7 regkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveea 70 
                                    +eg++ +lv++Gs+  +++e+ae+L     +  Vv + ++ pl +  +++++   +r+v ve +
  gi|119720361|ref|YP_920856.1| 453 NEGSETVLVTWGSTKGVVVEVAERL-----GLYVVQPLCLYPLPTWELKKLIDPGRRIVSVEVN 511
                                    589*********************9.....588************************9999855 PP

>> PFOR_II  Pyruvate:ferredoxin oxidoreductase core domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   4.1e-05      0.15       2      72 ..     457     518 ..     456     544 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.1e-05
                                    SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHH CS
                        PFOR_II   2 evvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlve 72 
                                    e+v+v+ Gs+ g++ +++++l        ++++  l+P P+ elk+l++  +++v+++ n +    Gql++
  gi|119720361|ref|YP_920856.1| 457 ETVLVTWGSTKGVVVEVAERLGLY-----VVQPLCLYPLPTWELKKLIDPGRRIVSVEVNST----GQLAT 518
                                    678888888877776666665444.....79*****************************94....77765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (554 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.24s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 3938.15
//
Query:       gi|119720362|ref|YP_920857.1|  [L=58]
Description: rubredoxin-type Fe(Cys)4 protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-24   86.3   3.2    1.2e-24   86.1   3.2    1.0  1  Rubredoxin       Rubredoxin
    3.2e-05   23.4   0.6       0.15   11.6   0.0    2.2  2  TF_Zn_Ribbon     TFIIB zinc-binding
     0.0022   17.8   1.8      0.035   13.9   0.5    2.1  2  zf-C2H2_3        zinc-finger of acetyl-transferase ESCO
     0.0028   17.3   1.8      0.035   13.8   0.2    2.1  2  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
     0.0074   16.4   3.2      0.089   12.9   3.2    2.1  1  Zn-ribbon_8      Zinc ribbon domain
     0.0085   16.2   0.7      0.012   15.6   0.7    1.3  1  PHD_4            PHD-finger
     0.0095   16.0   0.2       0.53   10.4   0.0    2.1  2  zf-Sec23_Sec24   Sec23/Sec24 zinc finger
     0.0098   15.6   4.8       0.48   10.2   0.4    2.1  2  Rubredoxin_2     Rubredoxin metal binding domain
  ------ inclusion threshold ------
       0.01   15.2   0.1       0.15   11.5   0.0    2.1  2  Vps36-NZF-N      Vacuolar protein sorting 36 NZF-N zinc-finge
      0.013   15.3   2.3          3    7.6   0.9    2.1  2  zinc_ribbon_10   Predicted integral membrane zinc-ribbon meta
      0.013   15.4   0.2        5.3    7.0   0.1    2.0  2  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.027   14.4   0.8        6.6    6.8   0.2    2.3  2  Nudix_N_2        Nudix N-terminal
      0.028   14.0   3.8       0.17   11.6   1.9    2.1  2  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
      0.031   14.2   1.3        2.4    8.1   0.1    2.1  2  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
      0.039   13.9   6.7        0.6   10.1   1.3    2.1  2  Zn_ribbon_SprT   SprT-like zinc ribbon domain
      0.039   14.0   0.2        9.3    6.4   0.1    2.1  2  DZR              Double zinc ribbon
      0.043   14.3   2.3        8.1    7.0   0.4    2.5  2  Zn-C2H2_12       Autophagy receptor zinc finger-C2H2 domain
      0.044   13.7   1.1        5.7    6.9   0.1    2.1  2  Prok-RING_1      Prokaryotic RING finger family 1
      0.046   13.5   1.4       0.61    9.9   0.3    2.1  2  zf-MIZ           MIZ/SP-RING zinc finger
      0.051   14.0   4.2       0.76   10.3   0.9    2.2  2  zf-H2C2_2        Zinc-finger double domain
      0.062   13.5   2.2       0.79   10.0   0.1    2.1  2  zf-nanos         Nanos RNA binding domain
      0.091   13.7   2.0        6.4    7.9   0.3    2.2  2  zf-C2H2_4        C2H2-type zinc finger
      0.096   12.6   3.3       0.57   10.1   1.2    2.1  2  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
      0.099   12.7   2.3        3.7    7.7   0.7    2.2  2  zf-C2H2_6        C2H2-type zinc finger
        0.1   12.6   2.7       0.75    9.8   2.6    2.0  1  ADK_lid          Adenylate kinase, active site lid
        0.1   12.7   1.4        4.1    7.6   0.2    2.1  2  zf-Mss51         Zinc-finger of mitochondrial splicing suppre
       0.11   12.5   0.1       0.14   12.1   0.1    1.2  1  HypA             Hydrogenase/urease nickel incorporation, met
       0.16   11.3   2.7       0.62    9.4   0.3    2.1  2  zf-RanBP         Zn-finger in Ran binding protein and others
       0.17   12.3   1.7        4.5    7.7   0.5    2.1  2  C1_2             C1 domain
       0.19   11.6   2.4        4.4    7.2   0.6    2.1  2  TFIIS_C          Transcription factor S-II (TFIIS)
       0.23   12.0   4.0        1.6    9.4   0.6    2.2  2  zf-C2H2          Zinc finger, C2H2 type
       0.28   11.9   1.6        4.4    8.1   0.4    2.0  2  MRNIP            MRN-interacting protein
       0.43   10.4   4.1        7.6    6.4   0.2    2.5  2  zinc_ribbon_2    zinc-ribbon domain


Domain annotation for each model (and alignments):
>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.1   3.2   2.2e-27   1.2e-24       1      47 []       8      54 ..       8      54 .. 0.98

  Alignments for each domain:
  == domain 1  score: 86.1 bits;  conditional E-value: 2.2e-27
                                   EEEETTT-BEEETTTBBGGGTB-TT--GGGS-TT-BBTTTB-BGGGE CS
                     Rubredoxin  1 kyeCkvCgyvYdpakGdpdegiapgTkFedlPddWvCPdCgvekeqF 47
                                   ky+C+vCgyvY p+ Gdpd++i+pgT+Fe+lP++WvCP+Cg++k+ F
  gi|119720362|ref|YP_920857.1|  8 KYRCTVCGYVYSPELGDPDSNIPPGTPFEELPENWVCPVCGATKDLF 54
                                   7*******************************************987 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   0.00028      0.15      20      37 ..       9      26 ..       5      29 .. 0.87
   2 !   10.6   0.1   0.00058      0.31       2      14 ..      43      55 ..      42      58 .] 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00028
                                   EEESSSSBEEEECCCCCC CS
                   TF_Zn_Ribbon 20 lvCtdCGlVlednsideg 37
                                   ++Ct CG+V   +  d+ 
  gi|119720362|ref|YP_920857.1|  9 YRCTVCGYVYSPELGDPD 26
                                   89*******999999886 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00058
                                   EETTTTCEECHEE CS
                   TF_Zn_Ribbon  2 kCPnCgstnlveD 14
                                   +CP+Cg t+++++
  gi|119720362|ref|YP_920857.1| 43 VCPVCGATKDLFE 55
                                   7******997765 PP

>> zf-C2H2_3  zinc-finger of acetyl-transferase ESCO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.5   6.5e-05     0.035       9      26 ..       4      21 ..       1      26 [. 0.84
   2 ?    3.5   0.0      0.12        64      15      20 ..      43      48 ..      34      50 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.5e-05
                      zf-C2H2_3  9 ksfgasqCkeCgMvYnpg 26
                                   k++++ +C++Cg vY+p 
  gi|119720362|ref|YP_920857.1|  4 KKYKKYRCTVCGYVYSPE 21
                                   7778899********995 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.12
                      zf-C2H2_3 15 qCkeCg 20
                                    C++Cg
  gi|119720362|ref|YP_920857.1| 43 VCPVCG 48
                                   4****9 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1      0.12        65       6      11 ..      10      15 ..       7      17 .. 0.91
   2 !   13.8   0.2   6.4e-05     0.035       4      16 ..      41      55 ..      39      58 .] 0.78

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.12
                        zf-RRN7  6 pCgvCg 11
                                   +C vCg
  gi|119720362|ref|YP_920857.1| 10 RCTVCG 15
                                   7****9 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 6.4e-05
                        zf-RRN7  4 gppCgvCgc..rsft 16
                                   +++C+vCg+  ++f 
  gi|119720362|ref|YP_920857.1| 41 NWVCPVCGAtkDLFE 55
                                   79*******866776 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   3.2   0.00016     0.089       6      34 ..       9      49 ..       7      53 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00016
                    Zn-ribbon_8  6 YrCeeCghefe...........vlqsisdaplta.CPeCgs 34
                                   YrC+ Cg ++            +  ++ + p+   CP Cg+
  gi|119720362|ref|YP_920857.1|  9 YRCTVCGYVYSpelgdpdsnipPGTPFEELPENWvCPVCGA 49
                                   ***********988888888775555557778888****98 PP

>> PHD_4  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.7   2.3e-05     0.012      25      67 ..       3      47 ..       1      48 [. 0.81

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.3e-05
                          PHD_4 25 etpsslmeCsvCyeivHpeClkek..egegvvnedlpnsWeCpkC 67
                                   e++ +   C+vC  +  pe  +      +g+  e+lp++W Cp C
  gi|119720362|ref|YP_920857.1|  3 EKKYKKYRCTVCGYVYSPELGDPDsnIPPGTPFEELPENWVCPVC 47
                                   55666778*****99999988765434578*************** PP

>> zf-Sec23_Sec24  Sec23/Sec24 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.081        44      22      31 ..       7      16 ..       1      20 [. 0.67
   2 !   10.4   0.0   0.00097      0.53      22      34 ..      40      52 ..      29      55 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.081
                 zf-Sec23_Sec24 22 krwiCnfCnh 31
                                   k+++C  C+ 
  gi|119720362|ref|YP_920857.1|  7 KKYRCTVCGY 16
                                   5677777764 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00097
                 zf-Sec23_Sec24 22 krwiCnfCnhkne 34
                                     w+C+ C+   +
  gi|119720362|ref|YP_920857.1| 40 ENWVCPVCGATKD 52
                                   57******98766 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.4   0.00089      0.48       1      11 [.       9      19 ..       9      23 .. 0.90
   2 !    7.7   0.4    0.0054         3      15      22 ..      42      49 ..      41      50 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00089
                   Rubredoxin_2  1 YvCsqCGfesa 11
                                   Y+C  CG++++
  gi|119720362|ref|YP_920857.1|  9 YRCTVCGYVYS 19
                                   9*******985 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0054
                   Rubredoxin_2 15 GrCpsCgs 22
                                   + Cp Cg+
  gi|119720362|ref|YP_920857.1| 42 WVCPVCGA 49
                                   99999996 PP

>> Vps36-NZF-N  Vacuolar protein sorting 36 NZF-N zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.21   1.2e+02      35      40 ..      10      15 ..       2      30 .. 0.71
   2 ?   11.5   0.0   0.00027      0.15       7      17 ..      39      49 ..      33      54 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.21
                    Vps36-NZF-N 35 pClaCG 40
                                    C+ CG
  gi|119720362|ref|YP_920857.1| 10 RCTVCG 15
                                   466666 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00027
                    Vps36-NZF-N  7 tatWvCpICsf 17
                                     +WvCp+C  
  gi|119720362|ref|YP_920857.1| 39 PENWVCPVCGA 49
                                   579******86 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.9    0.0056         3      39      52 ..       3      16 ..       1      18 [. 0.84
   2 ?    7.6   0.0    0.0058       3.2      44      53 ..      41      50 ..      30      51 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0056
                 zinc_ribbon_10 39 eleevkyrCpkCga 52
                                   e+++ kyrC  Cg 
  gi|119720362|ref|YP_920857.1|  3 EKKYKKYRCTVCGY 16
                                   67888*******97 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0058
                 zinc_ribbon_10 44 kyrCpkCgal 53
                                   +++Cp Cga+
  gi|119720362|ref|YP_920857.1| 41 NWVCPVCGAT 50
                                   7*******85 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1    0.0098       5.3      42      56 ..       4      18 ..       1      22 [. 0.81
   2 ?    7.0   0.0    0.0098       5.3      44      56 ..      39      51 ..      31      53 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0098
                 OrfB_Zn_ribbon 42 lsgrtfkCpnCgfea 56
                                   ++ ++++C+ Cg+++
  gi|119720362|ref|YP_920857.1|  4 KKYKKYRCTVCGYVY 18
                                   4778999****9986 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0098
                 OrfB_Zn_ribbon 44 grtfkCpnCgfea 56
                                   +++++Cp Cg++ 
  gi|119720362|ref|YP_920857.1| 39 PENWVCPVCGATK 51
                                   5689999999875 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.2     0.012       6.6      23      31 ..       9      17 ..       5      18 .. 0.88
   2 ?    6.3   0.0     0.017       9.1      24      31 ..      43      50 ..      29      51 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.012
                                   EEETTTTEE CS
                      Nudix_N_2 23 lvCpaCgti 31
                                   ++C+ Cg++
  gi|119720362|ref|YP_920857.1|  9 YRCTVCGYV 17
                                   68*****98 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.017
                                   EETTTTEE CS
                      Nudix_N_2 24 vCpaCgti 31
                                   vCp Cg++
  gi|119720362|ref|YP_920857.1| 43 VCPVCGAT 50
                                   89999875 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.9    0.0003      0.17       3      14 ..       5      16 ..       3      19 .. 0.83
   2 ?    2.6   0.0      0.19   1.1e+02       8      13 ..      43      48 ..      37      55 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0003
                                   TT-EEE-TTT-- CS
                Desulfoferrod_N  3 klevYkCevCGn 14
                                   k  +Y+C+vCG 
  gi|119720362|ref|YP_920857.1|  5 KYKKYRCTVCGY 16
                                   6789*******6 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.19
                                   E-TTT- CS
                Desulfoferrod_N  8 kCevCG 13
                                    C vCG
  gi|119720362|ref|YP_920857.1| 43 VCPVCG 48
                                   699**9 PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.2     0.032        17      13      21 ..      10      18 ..       8      22 .. 0.85
   2 ?    8.1   0.1    0.0045       2.4      24      34 ..      39      50 ..      38      53 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.032
                        DUF35_N 13 rCpdCGtvq 21
                                   rC+ CG v+
  gi|119720362|ref|YP_920857.1| 10 RCTVCGYVY 18
                                   9*****996 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0045
                        DUF35_N 24 Pr.avCphCgsd 34
                                   P+ +vCp Cg++
  gi|119720362|ref|YP_920857.1| 39 PEnWVCPVCGAT 50
                                   44489****987 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   1.3    0.0011       0.6       4      14 ..       8      18 ..       4      22 .. 0.80
   2 ?    7.1   0.3    0.0096       5.2       5      12 ..      42      49 ..      41      51 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0011
                 Zn_ribbon_SprT  4 vYrCtgCgrey 14
                                   +YrCt Cg  y
  gi|119720362|ref|YP_920857.1|  8 KYRCTVCGYVY 18
                                   6*******655 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0096
                 Zn_ribbon_SprT  5 YrCtgCgr 12
                                   ++C+ Cg 
  gi|119720362|ref|YP_920857.1| 42 WVCPVCGA 49
                                   99****95 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1     0.017       9.3      28      41 ..       8      21 ..       1      23 [. 0.76
   2 ?    6.3   0.0     0.018       9.6      26      37 ..      39      50 ..      27      56 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.017
                            DZR 28 edrCpsCgekvdpe 41
                                   ++rC  Cg+  +pe
  gi|119720362|ref|YP_920857.1|  8 KYRCTVCGYVYSPE 21
                                   799****9998775 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.018
                            DZR 26 aaedrCpsCgek 37
                                   +++ +Cp Cg+ 
  gi|119720362|ref|YP_920857.1| 39 PENWVCPVCGAT 50
                                   445566666654 PP

>> Zn-C2H2_12  Autophagy receptor zinc finger-C2H2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1     0.021        12       3      13 ..      11      21 ..      10      23 .. 0.87
   2 ?    7.0   0.4     0.015       8.1       2       7 ..      43      48 ..      43      50 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.021
                     Zn-C2H2_12  3 CPlCseqFpkn 13
                                   C +C+++++++
  gi|119720362|ref|YP_920857.1| 11 CTVCGYVYSPE 21
                                   779******97 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.015
                     Zn-C2H2_12  2 eCPlCs 7 
                                   +CP+C+
  gi|119720362|ref|YP_920857.1| 43 VCPVCG 48
                                   7****8 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1      0.02        11       1      12 [.       5      16 ..       5      25 .. 0.81
   2 ?    6.9   0.1      0.01       5.7      22      29 ..      43      50 ..      32      52 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.02
                    Prok-RING_1  1 nytgkkCpvCgk 12
                                   +y++ +C+vCg 
  gi|119720362|ref|YP_920857.1|  5 KYKKYRCTVCGY 16
                                   589999****86 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.01
                    Prok-RING_1 22 vCpeCgtp 29
                                   vCp+Cg+ 
  gi|119720362|ref|YP_920857.1| 43 VCPVCGAT 50
                                   89999985 PP

>> zf-MIZ  MIZ/SP-RING zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.17        92      36      47 ..       3      14 ..       1      16 [. 0.77
   2 ?    9.9   0.3    0.0011      0.61      40      48 ..      40      48 ..      35      50 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.17
                                   HHHS---B-TTT CS
                         zf-MIZ 36 nertetWnCPvC 47
                                    ++ ++ +C vC
  gi|119720362|ref|YP_920857.1|  3 EKKYKKYRCTVC 14
                                   5667789***** PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0011
                                   ---B-TTT- CS
                         zf-MIZ 40 etWnCPvCs 48
                                   e+W CPvC 
  gi|119720362|ref|YP_920857.1| 40 ENWVCPVCG 48
                                   67******6 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.9    0.0014      0.76      13      24 ..       7      18 ..       1      19 [. 0.77
   2 ?    5.2   0.1     0.058        32      15      21 ..      42      48 ..      30      50 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0014
                      zf-H2C2_2 13 kpyeCplCdkaF 24
                                   k+y C +C++++
  gi|119720362|ref|YP_920857.1|  7 KKYRCTVCGYVY 18
                                   579*******98 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.058
                      zf-H2C2_2 15 yeCplCd 21
                                   + Cp+C+
  gi|119720362|ref|YP_920857.1| 42 WVCPVCG 48
                                   68****8 PP

>> zf-nanos  Nanos RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.4      0.18        99      32      40 ..       7      15 ..       5      18 .. 0.87
   2 ?   10.0   0.1    0.0015      0.79      34      44 ..      42      52 ..      40      53 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.18
                       zf-nanos 32 rkyvCpiCg 40
                                   +ky C++Cg
  gi|119720362|ref|YP_920857.1|  7 KKYRCTVCG 15
                                   589*****8 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0015
                       zf-nanos 34 yvCpiCgatgd 44
                                    vCp+Cgat+d
  gi|119720362|ref|YP_920857.1| 42 WVCPVCGATKD 52
                                   69*******98 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.3     0.012       6.4       1      11 [.       9      19 ..       9      22 .. 0.84
   2 ?    5.5   0.1     0.069        37       2       9 ..      43      50 ..      42      54 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.012
                      zf-C2H2_4  1 fkCpiCgksFs 11
                                   ++C++Cg ++s
  gi|119720362|ref|YP_920857.1|  9 YRCTVCGYVYS 19
                                   89****99883 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.069
                      zf-C2H2_4  2 kCpiCgks 9 
                                    Cp+Cg++
  gi|119720362|ref|YP_920857.1| 43 VCPVCGAT 50
                                   7****976 PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   1.2    0.0011      0.57      18      31 ..       3      18 ..       1      21 [. 0.77
   2 ?    2.7   0.0      0.21   1.1e+02      18      30 ..      40      50 ..      37      53 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0011
                                   CCCE..EEESSSS-EE CS
                 RNA_POL_M_15KD 18 egkn..feCrqCgYee 31
                                   e+k+  + C  CgY++
  gi|119720362|ref|YP_920857.1|  3 EKKYkkYRCTVCGYVY 18
                                   44555599******98 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.21
                                   CCCEEEESSSS-E CS
                 RNA_POL_M_15KD 18 egknfeCrqCgYe 30
                                   e+++  C  Cg+ 
  gi|119720362|ref|YP_920857.1| 40 ENWV--CPVCGAT 50
                                   5666..8888875 PP

>> zf-C2H2_6  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.7    0.0068       3.7       2      11 ..       9      18 ..       8      19 .. 0.84
   2 ?    4.8   0.0     0.055        30       3      10 ..      43      50 ..      42      50 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0068
                      zf-C2H2_6  2 heCsvCsksF 11
                                   ++C+vC+ ++
  gi|119720362|ref|YP_920857.1|  9 YRCTVCGYVY 18
                                   9*****9776 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.055
                      zf-C2H2_6  3 eCsvCsks 10
                                   +C+vC+++
  gi|119720362|ref|YP_920857.1| 43 VCPVCGAT 50
                                   6*****86 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   2.6    0.0014      0.75       4      29 ..      11      49 ..       9      50 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0014
                                   -TTT--EEETT......TB--S.......STTB-TTT-- CS
                        ADK_lid  4 CpkCGrsYhvv......fnpPk.......veglCDkCGe 29
                                   C  CG +Y+ +       +pP        ++ +C +CG 
  gi|119720362|ref|YP_920857.1| 11 CTVCGYVYSPElgdpdsNIPPGtpfeelpENWVCPVCGA 49
                                   899999998666665532444467777779999999996 PP

>> zf-Mss51  Zinc-finger of mitochondrial splicing suppressor 51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.2    0.0076       4.1      11      26 ..       3      18 ..       1      21 [. 0.83
   2 ?    4.8   0.1     0.056        31      14      24 ..      39      49 ..      25      53 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0076
                       zf-Mss51 11 apkhvdfeCpdCGipt 26
                                   ++k  ++ C  CG+++
  gi|119720362|ref|YP_920857.1|  3 EKKYKKYRCTVCGYVY 18
                                   467789*******986 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.056
                       zf-Mss51 14 hvdfeCpdCGi 24
                                   + +  Cp CG 
  gi|119720362|ref|YP_920857.1| 39 PENWVCPVCGA 49
                                   56789***996 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00027      0.14      68      95 ..       6      50 ..       2      55 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00027
                                   --EEEETTTS-EEECHH.HHH.................S-TTTSSS CS
                           HypA 68 pvkvrCreCgkefelee.kal.................rCpkCgsa 95
                                     k+rC++Cg+ ++ e  +                    Cp Cg++
  gi|119720362|ref|YP_920857.1|  6 YKKYRCTVCGYVYSPELgD-PdsnippgtpfeelpenwVCPVCGAT 50
                                   56899********977543.234689******************86 PP

>> zf-RanBP  Zn-finger in Ran binding protein and others
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1      0.19     1e+02       7      12 ..      11      16 ..      10      18 .. 0.83
   2 ?    9.4   0.3    0.0011      0.62       4      11 ..      41      48 ..      38      51 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.19
                                   -SSS-- CS
                       zf-RanBP  7 CskClv 12
                                   C++C++
  gi|119720362|ref|YP_920857.1| 11 CTVCGY 16
                                   999996 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0011
                                   SEE-SSS- CS
                       zf-RanBP  4 dWdCskCl 11
                                    W C++C+
  gi|119720362|ref|YP_920857.1| 41 NWVCPVCG 48
                                   69999998 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.5    0.0082       4.5      29      41 ..       5      17 ..       1      20 [. 0.60
   2 ?    4.1   0.0      0.11        60      17      28 ..      40      51 ..      34      55 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0082
                           C1_2 29 dgffYsCseCdfs 41
                                   ++++Y+C+ C ++
  gi|119720362|ref|YP_920857.1|  5 KYKKYRCTVCGYV 17
                                   3444777777664 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.11
                           C1_2 17 esfnCsaCgrki 28
                                   e++ C +Cg + 
  gi|119720362|ref|YP_920857.1| 40 ENWVCPVCGATK 51
                                   7899****9875 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.6    0.0081       4.4      27      38 ..       7      18 ..       2      19 .. 0.81
   2 ?    4.4   0.0     0.061        33       3      10 ..      44      51 ..      42      55 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0081
                        TFIIS_C 27 vfykCtkCghrW 38
                                     y+Ct Cg+ +
  gi|119720362|ref|YP_920857.1|  7 KKYRCTVCGYVY 18
                                   67*******987 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.061
                        TFIIS_C  3 CpkCgsre 10
                                   Cp Cg ++
  gi|119720362|ref|YP_920857.1| 44 CPVCGATK 51
                                   ****9987 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.6    0.0029       1.6       1      11 [.       9      19 ..       9      21 .. 0.91
   2 ?    3.9   0.1      0.16        87       2       7 ..      43      48 ..      42      52 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0029
                                   EEETTTTEEES CS
                        zf-C2H2  1 ykCpdCgksFk 11
                                   y+C++Cg++++
  gi|119720362|ref|YP_920857.1|  9 YRCTVCGYVYS 19
                                   9*******996 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.16
                                   EETTTT CS
                        zf-C2H2  2 kCpdCg 7 
                                   +Cp+Cg
  gi|119720362|ref|YP_920857.1| 43 VCPVCG 48
                                   7****9 PP

>> MRNIP  MRN-interacting protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.4     0.008       4.4      14      27 ..       2      15 ..       1      19 [. 0.90
   2 ?    3.3   0.0      0.25   1.3e+02      19      31 ..      40      52 ..      36      55 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.008
                          MRNIP 14 qvkKskkwkCkvCn 27
                                   q+kK kk++C vC+
  gi|119720362|ref|YP_920857.1|  2 QEKKYKKYRCTVCG 15
                                   89***********8 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.25
                          MRNIP 19 kkwkCkvCnekqs 31
                                   ++w C vC++ + 
  gi|119720362|ref|YP_920857.1| 40 ENWVCPVCGATKD 52
                                   58******98765 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.3     0.046        25      16      21 ..      11      16 ..       5      20 .. 0.69
   2 ?    6.4   0.2     0.014       7.6       2       7 ..      44      49 ..      43      51 .. 0.61

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.046
                  zinc_ribbon_2 16 CpyCGt 21
                                   C+ CG+
  gi|119720362|ref|YP_920857.1| 11 CTVCGY 16
                                   555554 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.014
                  zinc_ribbon_2  2 CpnCGa 7 
                                   Cp CGa
  gi|119720362|ref|YP_920857.1| 44 CPVCGA 49
                                   666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); expected 17.9 (0.001)
Passed Fwd filter:                        33  (0.00184059); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              33  [number of targets reported over threshold]
# CPU time: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 419.11
//
Query:       gi|119720363|ref|YP_920858.1|  [L=644]
Description: alpha amylase, catalytic region [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-58  197.9   0.0    4.3e-58  197.5   0.0    1.1  1  Alpha-amylase    Alpha amylase, catalytic domain
    3.2e-09   37.0   0.0    2.7e-08   34.0   0.0    2.3  2  Alpha-amylase_N  Alpha amylase, N-terminal ig-like domain
    1.2e-06   28.8   0.1    2.5e-06   27.7   0.1    1.6  1  DUF3459          Domain of unknown function (DUF3459)
    0.00072   19.7   0.0     0.0014   18.8   0.0    1.4  1  AMPK1_CBM        Glycogen recognition site of AMP-activated p
     0.0031   17.6   0.0      0.037   14.1   0.0    2.3  2  Malt_amylase_C   Maltogenic Amylase, C-terminal domain


Domain annotation for each model (and alignments):
>> Alpha-amylase  Alpha amylase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.5   0.0   1.2e-61   4.3e-58       1     335 [.     232     536 ..     232     538 .. 0.89

  Alignments for each domain:
  == domain 1  score: 197.5 bits;  conditional E-value: 1.2e-61
                                    --CHHHHCTCCCCCCCT-SCEEE-B-CE-S-TTTTSS-SCECCE-CCC--CCCCCCHHHHHHCTT-EEEEEE--SC--TT CS
                  Alpha-amylase   1 GDLkGiiekLdYlkeLGvtaiwlsPifkspqadhgYdiadytkidpefGtnedlkeLiskahekgikvilDlVvNHtsde 80 
                                    G L+ i e+L+ + +LG +a++l+Pif+s   +hgYd+ dy+ +  + G  e++ +L+++++++g++v+lD V+ Hts  
  gi|119720363|ref|YP_920858.1| 232 GGLEEIAERLNHVSGLGANALYLTPIFEST-TYHGYDVVDYYRVAGRLGGDEAFGRLLAELKKRGMRVVLDGVFHHTSFF 310
                                    668889***********************9.************************************************* PP

                                    SCCCHCCHHSTTSG.GGCCC-E......ESS-STTC-..TTTTCSCEECTTTTCEEESSS-TTS-BB-TTTCCCCCCCCC CS
                  Alpha-amylase  81 hewfkeslkkkgep.krdyyiwkegkeekeppnnwks..lfdgsaweydekaqeyylhlflkklpdLnteneevrkelkd 157
                                    h +f++ ++k +e+ ++ +y      + + +p +  +    + ++ e ++    y  + +++ +p Ln++n+evr  +  
  gi|119720363|ref|YP_920858.1| 311 HPYFQDLVEKGEESrYKGFYR---VLGFPVVPREFLEalRSGAPRHELKKYPRRYESFFDVWLMPRLNHDNPEVRSFITG 387
                                    ********9766444444444...445567777666643456667777888889999*********************** PP

                                    CCCCCCTTT-SEEEETTCCCTTTCCCCHCCHCCHHHHHHHHHHHTCCGTT-EEEEE-TT-SCCCHCCCC-CGG-SICECC CS
                  Alpha-amylase 158 vvkfwlekgidGfRlDvvkhvskvealesngeflheftqalnetvasrkevmtvgEvssdasedlrvyttearlelemvl 237
                                    v ++w+ +g+dG+RlDv++ v+         e ++ef+++l+       +v+++gEv++da+     +++++ +      
  gi|119720363|ref|YP_920858.1| 388 VGRYWVSRGVDGWRLDVAHGVPP--------ELWREFRETLP------GDVYLFGEVMDDARI-WLFDKFHGAM------ 446
                                    ***********************........***********......689*******98884.3455555555...... PP

                                    ITTCGGGCC-CTSTTSB-SS-HHHHHHHHHHHHHHS-CCCTTCEEES--TTS--HHHHTTSSTTTTHHHHHHHHHCCCTS CS
                  Alpha-amylase 238 dfphldvaqkakikeqlksisakklkellkkwlkaleeaaeeavtflgnHDqeRilsrlgddsaeaekklklaaillltl 317
                                    ++  +d+  +++   +  +i+a+++ ++l+    ++   ++ + +fl+nHD  R+ls +gd+      k   a+++l+t+
  gi|119720363|ref|YP_920858.1| 447 NYLLYDAVLRFF---AYREITAEEFLNRLELLSVYYGPGEYAMYNFLDNHDVDRLLSLVGDRD-----KYLCALVFLFTY 518
                                    555889988888...899999*********999999999************************.....8999******** PP

                                    SSEEEEETTCCCT----S CS
                  Alpha-amylase 318 rGvpviYyGeEigmtggk 335
                                    +Gvp iYyG+E+g+ + +
  gi|119720363|ref|YP_920858.1| 519 KGVPSIYYGDEVGLENTD 536
                                    **************9976 PP

>> Alpha-amylase_N  Alpha amylase, N-terminal ig-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.34   1.2e+03      68      89 ..      51      72 ..      46      95 .. 0.86
   2 !   34.0   0.0   7.5e-12   2.7e-08       3     100 ..     115     200 ..     113     216 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.34
                                   EEEEEEEE-TTS-EEEEEEEE- CS
                Alpha-amylase_N 68 dYweaeltlkkkrlrYlFelee 89
                                   d w +e++l++    YlF l +
  gi|119720363|ref|YP_920858.1| 51 DRWVVEVELPEGVWYYLFSLGG 72
                                   6699**************9965 PP

  == domain 2  score: 34.0 bits;  conditional E-value: 7.5e-12
                                    GGG-B--SSTTTEEEEETTEEEEEEEEETTT-SEEEEEEEETTS-.TTS--EEEEEEEEEE-SSEEEEEEEEE-TTS-EE CS
                Alpha-amylase_N   3 keAiyHrpeseyayaydektlhirLrtkkddvekveliygdpyeweekwkseetemkkiasdelfdYweaeltlkkkrlr 82 
                                     eA+yH p   y+y++    l +rLr+ ++ ++k+ l+++ +           +em+  a+de+fdY+ea+l++  + + 
  gi|119720363|ref|YP_920858.1| 115 EEALYHYPSLTYVYPFG-GVLFVRLRALRGSLQKAFLVVDGRR----------LEMRLKARDEVFDYYEASLEAGGE-VS 182
                                    59*************65.5789****************98876..........57******************9988.** PP

                                    EEEEEE-TS-EEEEESSE CS
                Alpha-amylase_N  83 YlFeleedgeslvytekg 100
                                    Y+Fe+ ++g+   y+e  
  gi|119720363|ref|YP_920858.1| 183 YYFEVLGGGRLHRYGEFS 200
                                    *******99999999876 PP

>> DUF3459  Domain of unknown function (DUF3459)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.1     7e-10   2.5e-06       2      89 ..     562     639 ..     561     641 .. 0.86

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 7e-10
                                    HHHHHHHHHHHCCCTT--CGGEEEEEEECTCEEEEEEEETTEEEEEEEE-SSCGCCS-SS---SEEEEECT--S....SS CS
                        DUF3459   2 yrdLLaLRreePaLadarrgglevavlgdgallvrwrlgdgrllrllaNLgdepvtlppegaagkllfsseaaraggdag 81 
                                    +r+L +LRr+  aL++ +++ ++   ++ g l+ r+rlgd + +++++N ++ ++ l+  ++a  +lf+s++      ++
  gi|119720363|ref|YP_920858.1| 562 TRALASLRRRSAALQRGAFEPVR---FEGGLLVYRRRLGD-ESILVAINYSESEAVLE--EPAQSVLFRSGSVK----EK 631
                                    699**************999999...79999999999955.5589*******999999..9**********988....67 PP

                                    EE-TTEEE CS
                        DUF3459  82 rlppesvv 89 
                                     l p s v
  gi|119720363|ref|YP_920858.1| 632 LLGPFSSV 639
                                    77775554 PP

>> AMPK1_CBM  Glycogen recognition site of AMP-activated protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   3.9e-07    0.0014       5      66 ..      21      83 ..      17      89 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 3.9e-07
                      AMPK1_CBM  5 ikWkggGkkVyvtGsfnnWkk.kipLkksekdfsvilkLpeGthqykFiVDgewrvdpdlpta 66
                                   ++ +++G+  y+ G+fn +++ +++++  +++++v ++LpeG+  y F   g+  vdp+ p +
  gi|119720363|ref|YP_920858.1| 21 FSAPREGEYAYLLGNFNAFNEgSFRMRGAGDRWVVEVELPEGVWYYLFSLGGRRAVDPENPET 83
                                   5556799************65389**********************************99866 PP

>> Malt_amylase_C  Maltogenic Amylase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.16   5.7e+02       1      22 [.      71      92 ..      71     100 .. 0.79
   2 !   14.1   0.0     1e-05     0.037      12      39 ..     588     615 ..     578     630 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.16
                                   -EEEE---S-TTEEEEEEEETT CS
                 Malt_amylase_C  1 GsfefleadnrkvlaYlReyed 22
                                   G  + ++++n++  +Y R+  +
  gi|119720363|ref|YP_920858.1| 71 GGRRAVDPENPETTVYSRRAYK 92
                                   667899************9766 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 1e-05
                                    TEEEEEEEETTEEEEEEEESS-EEEEE- CS
                 Malt_amylase_C  12 kvlaYlReyedetilvvaNrsaqaveld 39 
                                      l+Y R+++de ilv++N s+ ++ l+
  gi|119720363|ref|YP_920858.1| 588 GLLVYRRRLGDESILVAINYSESEAVLE 615
                                    689****************888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (644 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.56
# Mc/sec: 3493.37
//
Query:       gi|119720364|ref|YP_920859.1|  [L=113]
Description: DNA polymerase beta subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.9e-12   45.5   0.2      1e-11   45.0   0.2    1.2  1  NTP_transf_2    Nucleotidyltransferase domain
    3.5e-08   33.4   0.0    4.3e-08   33.1   0.0    1.3  1  Polbeta         Polymerase beta, Nucleotidyltransferase
     0.0055   16.5   0.1     0.0067   16.2   0.1    1.3  1  DUF294          Putative nucleotidyltransferase DUF294
  ------ inclusion threshold ------
      0.011   16.0   0.0      0.012   15.8   0.0    1.1  1  DNA_pol_B_palm  DNA polymerase beta palm


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.0   0.2   2.2e-15     1e-11       4      87 ..      26     107 ..      23     111 .. 0.84

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 2.2e-15
                                    HHHHHHHHTT.TSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEECEEECCCC CS
                   NTP_transf_2   4 lleelkelep.vakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevdlvtrekledp 82 
                                    +++++ e+   + +v+lfGS+arG+++ +SD+D+lvv+++ v+      ++e  a+i + l    ++e ++ t  ++e++
  gi|119720364|ref|YP_920859.1|  26 IKRICVEEVDrDCRVILFGSAARGDYRVDSDVDVLVVTEKAVD---ALSRAEVAAKIYERLGFRDPVELHVATPREFEEW 102
                                    667777777789*****************************98...6777788888888888888899999988888888 PP

                                    TEEEE CS
                   NTP_transf_2  83 llvks 87 
                                    +++ +
  gi|119720364|ref|YP_920859.1| 103 YKRFI 107
                                    87765 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.0   9.5e-12   4.3e-08      16      66 ..      40      91 ..      24     107 .. 0.82

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 9.5e-12
                                   TTEEEEEE-S------EEEEEEEESS---HHHHHHHHHHHHHH..SSSEEEE CS
                        Polbeta 16 aylFGSrakgkareeSDiDlavllkekldleeelelaaeledi.klgkkvDl 66
                                   ++lFGS a+g++r +SD+D+ v++++  d   ++e+aa++ ++   ++ v+l
  gi|119720364|ref|YP_920859.1| 40 VILFGSAARGDYRVDSDVDVLVVTEKAVDALSRAEVAAKIYERlGFRDPVEL 91
                                   89*************************9999999999999887444444444 PP

>> DUF294  Putative nucleotidyltransferase DUF294
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   1.5e-06    0.0067      39      96 ..      30      81 ..      10     110 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.5e-06
                         DUF294 39 aeeelgkppvpfallvmGSeGReEqtlktDqDnalvledeeeeaareyfaelaervne 96
                                   ++ee    ++++ ++ +GS++R++  + +D D   v e+   + ++   ae+a+++ e
  gi|119720364|ref|YP_920859.1| 30 CVEE---VDRDCRVILFGSAARGDYRVDSDVDVLVVTEK---AVDALSRAEVAAKIYE 81
                                   3333...4788999**********************999...3333333444444444 PP

>> DNA_pol_B_palm  DNA polymerase beta palm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.8   0.0   2.7e-06     0.012      13      78 ..      25      91 ..      12     107 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.7e-06
                                   HHHH.HHHHH-TT-EEEE-HHHHTT-SEE.SSEEEEEEBTTBSTTSS--HHHHHHHHHHHHHTTSEEE CS
                 DNA_pol_B_palm 13 lvkk.aakeldpevevivcGSYRRgaess.GDvDvlitkkdakseskklkklleklvkklkkkgfltd 78
                                   l+k+  ++e+d++++vi  GS  Rg      DvDvl+  ++a  +  ++ ++ +k+ ++l  ++ ++ 
  gi|119720364|ref|YP_920859.1| 25 LIKRiCVEEVDRDCRVILFGSAARGDYRVdSDVDVLVVTEKAVDAL-SRAEVAAKIYERLGFRDPVEL 91
                                   555415799***************9876437*****9999888854.577788887777766665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 736.90
//
Query:       gi|119720365|ref|YP_920860.1|  [L=173]
Description: hypothetical protein Tpen_1460 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.3e-27   94.4   0.0    8.9e-27   94.1   0.0    1.1  1  DUF488    Protein of unknown function, DUF488
  ------ inclusion threshold ------
       0.12   12.2   0.0       0.88    9.4   0.0    2.4  3  BTRD1     Bacterial tandem repeat domain 1


Domain annotation for each model (and alignments):
>> DUF488  Protein of unknown function, DUF488
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.1   0.0   9.9e-31   8.9e-27       2     122 .]      14     139 ..      13     139 .. 0.93

  Alignments for each domain:
  == domain 1  score: 94.1 bits;  conditional E-value: 9.9e-31
                         DUF488   2 lervydllkkdgvrvlvDVRlwPrSrnpgfskealkedlkeagiaYvwlkelgpsrelrkwfk..hdp.rweefferYaa 78 
                                     er+ ++  + gvrv+vDVR++PrS+ ++fs ++l+++l+eag++Y w+ elg     r++ +  + p   +  f+ Y a
  gi|119720365|ref|YP_920860.1|  14 PERFAEKVFSLGVRVVVDVRRYPRSKVEFFSGDKLSAWLAEAGVGYEWMGELGALGMARRRGElgEAPcTDSPTFRVYVA 93 
                                    58999999999******************************************99888887664366666********** PP

                         DUF488  79 eleskeaakealeelkelakkg..vaLlcaekdperchrvvlaeyl 122
                                    +l s++ a +al ++ e+a++g   +Llc e++pe+chr+++a++l
  gi|119720365|ref|YP_920860.1|  94 YLVSDPGALAALSRIGEMASRGlrPLLLCRERKPEHCHRQFVADAL 139
                                    ****88999**********************************986 PP

>> BTRD1  Bacterial tandem repeat domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.42   3.8e+03      34      44 ..       8      18 ..       4      18 .. 0.76
   2 ?   -1.7   0.0      0.29   2.6e+03      19      31 ..     108     120 ..     105     122 .. 0.77
   3 ?    9.4   0.0   9.8e-05      0.88      20      36 ..     137     153 ..     133     168 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.42
                          BTRD1 34 gYgvg.gearya 44
                                   gYg g ++ r+a
  gi|119720365|ref|YP_920860.1|  8 GYG-GlSPERFA 18
                                   899.76888997 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.29
                          BTRD1  19 fdklkakGYrpvh 31 
                                    + ++ ++G rp  
  gi|119720365|ref|YP_920860.1| 108 IGEMASRGLRPLL 120
                                    567899****975 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 9.8e-05
                          BTRD1  20 dklkakGYrpvhvsgYg 36 
                                    d+l+a+G+r vhv g +
  gi|119720365|ref|YP_920860.1| 137 DALVARGFRVVHVVGDE 153
                                    89***********8865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       188  (0.0104858); expected 358.6 (0.02)
Passed bias filter:                      178  (0.00992805); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.29s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 1204.10
//
Query:       gi|119720366|ref|YP_920861.1|  [L=140]
Description: hypothetical protein Tpen_1461 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       197  (0.0109878); expected 358.6 (0.02)
Passed bias filter:                      188  (0.0104858); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 941.91
//
Query:       gi|119720367|ref|YP_920862.1|  [L=252]
Description: ABC transporter related [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.5e-27   94.3   0.0    1.3e-26   93.7   0.0    1.3  1  ABC_tran  ABC transporter
    1.4e-12   48.0   0.1    1.2e-05   25.3   0.0    2.1  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
     0.0037   17.7   0.0      0.016   15.6   0.0    2.1  1  AAA       ATPase family associated with various cellular acti
  ------ inclusion threshold ------
       0.02   14.6   0.0       0.05   13.3   0.0    1.6  1  AAA_29    P-loop containing region of AAA domain
      0.021   14.5   0.0        0.5   10.0   0.0    2.0  2  AAA_15    AAA ATPase domain
      0.021   14.5   0.0      0.027   14.2   0.0    1.4  1  AAA_30    AAA domain
      0.047   13.3   0.1      0.082   12.5   0.1    1.3  1  SRP54     SRP54-type protein, GTPase domain
      0.063   13.8   0.5       0.11   13.0   0.5    1.3  1  AAA_23    AAA domain
       0.11   12.4   0.0       0.19   11.7   0.0    1.3  1  Rad17     Rad17 P-loop domain
       0.12   12.7   0.1       0.16   12.4   0.1    1.4  1  AAA_16    AAA ATPase domain
       0.19   12.0   0.0       0.31   11.3   0.0    1.4  1  AAA_28    AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.7   0.0   8.2e-30   1.3e-26       1     137 []      23     167 ..      23     167 .. 0.95

  Alignments for each domain:
  == domain 1  score: 93.7 bits;  conditional E-value: 8.2e-30
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren. 79 
                                    l+ +++ + +ge+++++G+nGaGK+t lk+lagllkp  G  ++ g ++++ ++ ++ + +g++p++p +f++ltv+e  
  gi|119720367|ref|YP_920862.1|  23 LNGLTMRIGPGEIYGLLGPNGAGKTTTLKILAGLLKPSRGYARIYGVEVSS-RRVEALRLVGYVPENPVVFQNLTVEEFl 101
                                    68899**********************************************.66667778******************** PP

                                    ............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    ............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                                e + ++e +l+ +gl + kd+ +     +LS G+ q+v + +a+l +pk+ll+DEpta
  gi|119720367|ref|YP_920862.1| 102 rfvaalrgldwrEVSGDAEYYLEVFGLAGRKDSFM----GELSRGMVQKVLVSAAFLVRPKVLLMDEPTA 167
                                    *******9998777778************999998....*****************************97 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.1   1.7e-07   0.00027       2      26 ..      36      61 ..      35      99 .. 0.65
   2 !   25.3   0.0   7.1e-09   1.2e-05     235     298 ..     137     197 ..     100     201 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.7e-07
                         AAA_21  2 nvliGpNgsGKSnLLdaldllarl.d 26
                                    +l GpNg+GK++ L++l +l    +
  gi|119720367|ref|YP_920862.1| 36 YGLLGPNGAGKTTTLKILAGLLKPsR 61
                                   689****************9965443 PP

  == domain 2  score: 25.3 bits;  conditional E-value: 7.1e-09
                         AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHS 298
                                     elS G+ +   + +a+l ++   ++ll DEp +g++P+ ++ + e +++ls++g+  ++++H+
  gi|119720367|ref|YP_920862.1| 137 GELSRGMVQKVLVSAAFLVRP---KVLLMDEPTAGMDPESQHVFKEEVRRLSSKGVTSLISSHQ 197
                                    689*******99999999999...9**************************************8 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   9.9e-06     0.016       3      66 ..      38     164 ..      36     213 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 9.9e-06
                                    EESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSS........................................... CS
                            AAA   3 lyGppGtGKTllakavakelg..vefleisgsellsk........................................... 37 
                                    l Gp G GKT++ k +a  l+  + + +i g e+ s                                            
  gi|119720367|ref|YP_920862.1|  38 LLGPNGAGKTTTLKILAGLLKpsRGYARIYGVEVSSRrvealrlvgyvpenpvvfqnltveeflrfvaalrgldwrevsg 117
                                    78*****************9654333444443333333334555555555666666665555555666666666666666 PP

                                    .................STTH.HHHHHHHHHHHHHHTSTSEEEEEET CS
                            AAA  38 .................yvge.sekkirelfkeakekakpsilfiDE 66 
                                                     ++ge s   +++++ +a    +p++l++DE
  gi|119720367|ref|YP_920862.1| 118 daeyylevfglagrkdsFMGElSRGMVQKVLVSAAFLVRPKVLLMDE 164
                                    66666666666666666555513334455554443333567777776 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.1e-05      0.05      13      50 ..      24      61 ..      21      66 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.1e-05
                         AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                   +g t++i + +++ l Gp+G+GK+T l  ++ lL p++
  gi|119720367|ref|YP_920862.1| 24 NGLTMRIGPGEIYGLLGPNGAGKTTTLKILAGLLKPSR 61
                                   56788999888999***********9988888887775 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00031       0.5      28      50 ..      38      60 ..      30     101 .. 0.84
   2 ?    2.5   0.0     0.061        99     324     356 ..     157     189 ..     150     198 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00031
                         AAA_15 28 liGkNnsGKSsilealdlFlnnk 50
                                   l G+N++GK++ l++l  +l+ +
  gi|119720367|ref|YP_920862.1| 38 LLGPNGAGKTTTLKILAGLLKPS 60
                                   67**************9999987 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.061
                         AAA_15 324 nvilliEEPEahLHpqaqkvlikllkelandnk 356
                                    +++ll++EP a   p+ q v+ +  ++l++++ 
  gi|119720367|ref|YP_920862.1| 157 PKVLLMDEPTAGMDPESQHVFKEEVRRLSSKGV 189
                                    6799*************************9986 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.7e-05     0.027      20      63 ..      35      80 ..      27     203 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.7e-05
                         AAA_30 20 vavltGpAGtGKttalkalreaweaa.g.grviglAptgkaAkvLa 63
                                   +  l Gp G+GKtt+lk l+ +++ + g  r+ g+  +++  ++L+
  gi|119720367|ref|YP_920862.1| 35 IYGLLGPNGAGKTTTLKILAGLLKPSrGyARIYGVEVSSRRVEALR 80
                                   56689****************9998877657777777777777766 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1     5e-05     0.082       6      27 ..      38      59 ..      34      69 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5e-05
                                   EEESTTSSHHHHHHHHHHHHHH CS
                          SRP54  6 lvGlqGaGKTttlaKLaallkk 27
                                   l+G++GaGKTttl  La llk 
  gi|119720367|ref|YP_920862.1| 38 LLGPNGAGKTTTLKILAGLLKP 59
                                   89************99998875 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.5   6.7e-05      0.11      21      39 ..      35      53 ..      17      58 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.7e-05
                         AAA_23 21 ltlItGpNGaGKTTildAi 39
                                   ++ + GpNGaGKTT l  +
  gi|119720367|ref|YP_920862.1| 35 IYGLLGPNGAGKTTTLKIL 53
                                   67789*********99766 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00011      0.19      47      70 ..      35      58 ..      20      74 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00011
                          Rad17 47 iLLisGPsGCgkstvvkvLskelg 70
                                   i  + GP G gk+t++k+L+  l 
  gi|119720367|ref|YP_920862.1| 35 IYGLLGPNGAGKTTTLKILAGLLK 58
                                   66688**************97765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   9.7e-05      0.16      25      65 ..      34      75 ..      22     193 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.7e-05
                         AAA_16 25 elvllsGesGvGKsslvrellralekdggif.lrgkcdqles 65
                                   e+  l G+ G GK++ ++ l+  l+ ++g++ ++g  +++++
  gi|119720367|ref|YP_920862.1| 34 EIYGLLGPNGAGKTTTLKILAGLLKPSRGYArIYGVEVSSRR 75
                                   777799***************999999999888888887733 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00019      0.31       4      25 ..      38      64 ..      36     111 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00019
                         AAA_28  4 itGgestGKTtlleaLa.....argyp 25
                                   ++G+ ++GKTt+l+ La     +rgy 
  gi|119720367|ref|YP_920862.1| 38 LLGPNGAGKTTTLKILAgllkpSRGYA 64
                                   68***************7766655665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1648.99
//
Query:       gi|119720368|ref|YP_920863.1|  [L=545]
Description: hypothetical protein Tpen_1463 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (545 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       721  (0.0402142); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 3621.07
//
Query:       gi|119720369|ref|YP_920864.1|  [L=116]
Description: PadR-like family transcriptional regulator [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.9e-09   35.8   0.2    1.2e-08   34.8   0.2    1.5  1  PadR           Transcriptional regulator PadR-like family
  ------ inclusion threshold ------
      0.016   15.3   0.0      0.068   13.3   0.1    1.9  2  Mrr_N          Mrr N-terminal domain
      0.041   13.9   0.0      0.072   13.1   0.0    1.5  1  HTH_45         Winged helix-turn-helix
      0.053   13.3   0.0      0.064   13.0   0.0    1.2  1  DUF4364        Domain of unknown function (DUF4364)
      0.053   13.4   0.1      0.081   12.8   0.1    1.3  1  DUF3116        Protein of unknown function (DUF3116)
       0.14   12.0   0.0       0.19   11.5   0.0    1.2  1  Peptidase_C93  Bacterial transglutaminase-like cysteine prote
       0.15   12.2   0.0       0.36   11.0   0.0    1.6  2  HTH_34         Winged helix DNA-binding domain


Domain annotation for each model (and alignments):
>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   0.2   4.5e-12   1.2e-08       1      75 []      24      91 ..      24      91 .. 0.91

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 4.5e-12
                                   HHHHHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHHHH CS
                           PadR  1 iLalleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrelae 75
                                   +La l++++ y y++++++ e + g +++ +   Y +  +Le+eg++e++ ++     +rkyYr+T++Grr l+e
  gi|119720369|ref|YP_920864.1| 24 VLAELAKGDCYPYALRRAVLEDF-G-VDAGKVVFYVVTGKLEAEGFIEGYYRD-----RRKYYRITERGRRLLKE 91
                                   7899999*********9987775.7.79999999****************998.....8************9975 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.67   1.7e+03       5      34 ..      21      49 ..      18      53 .. 0.79
   2 ?   13.3   0.1   2.7e-05     0.068      69      86 ..      73      90 ..      58      91 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.67
                          Mrr_N  5 mlplLealadgsehrlkeirervaerfgls 34
                                    l +L  la+g  +    +r++v e+fg++
  gi|119720369|ref|YP_920864.1| 21 WLYVLAELAKGDCYP-YALRRAVLEDFGVD 49
                                   567888888899888.88999999999876 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 2.7e-05
                          Mrr_N 69 spkrgvwkiTekGrevlk 86
                                   +++r +++iTe+Gr++lk
  gi|119720369|ref|YP_920864.1| 73 RDRRKYYRITERGRRLLK 90
                                   678*************98 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   2.8e-05     0.072      43      68 ..      62      91 ..      55     101 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.8e-05
                         HTH_45 43 Lvekgli....kkskekYvlTekGlellek 68
                                   L  +g+i    +++ + Y++Te+G++ll++
  gi|119720369|ref|YP_920864.1| 62 LEAEGFIegyyRDRRKYYRITERGRRLLKE 91
                                   7889999888889999************97 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.5e-05     0.064      42      72 ..      61      91 ..      39      99 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.5e-05
                        DUF4364 42 eLvesglieeeekenktlykiTekGketlel 72
                                   +L+ +g+ie   ++ +++y+iTe+G++ l++
  gi|119720369|ref|YP_920864.1| 61 KLEAEGFIEGYYRDRRKYYRITERGRRLLKE 91
                                   7999*******99*************99975 PP

>> DUF3116  Protein of unknown function (DUF3116)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   3.1e-05     0.081      51      82 ..      62      91 ..      47      95 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.1e-05
                        DUF3116 51 LElkgyilRkeekannkkrYelTekGellyke 82
                                   LE +g+i       + +k+Y++Te+G  l+ke
  gi|119720369|ref|YP_920864.1| 62 LEAEGFIEGYYR--DRRKYYRITERGRRLLKE 91
                                   899999976555..89************9986 PP

>> Peptidase_C93  Bacterial transglutaminase-like cysteine proteinase BTLCP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   7.3e-05      0.19      60     107 ..      13      61 ..       4      68 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.3e-05
                  Peptidase_C93  60 elygveerWey..pkdgaGdCedyallKrkeLieaGlpasallltvvrde 107
                                    e  gve+ W y  ++ ++GdC  yal +r  L + G+ a ++ + vv+ +
  gi|119720369|ref|YP_920864.1|  13 EKTGVENLWLYvlAELAKGDCYPYAL-RRAVLEDFGVDAGKVVFYVVTGK 61 
                                    567999999873356789*******8.6999**********999999765 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       2.2   5.7e+03      12      27 ..       3      18 ..       1      28 [. 0.66
   2 ?   11.0   0.0   0.00014      0.36      34      78 ..      58      98 ..      48     100 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.2
                         HTH_34 12 vdeadfvelkealeat 27
                                   vd+  +++l+e++++ 
  gi|119720369|ref|YP_920864.1|  3 VDSKPMRRLREKTGVE 18
                                   6666677788877665 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00014
                         HTH_34 34 hlkkLekagYievdkefkgkkprtllriTpeGreafkkyvkaLks 78
                                    + kLe+ g+ie       + +r  +riT+ Gr   k+ +++L+ 
  gi|119720369|ref|YP_920864.1| 58 VTGKLEAEGFIEGY----YRDRRKYYRITERGRRLLKEGIAYLRT 98
                                   56677778877654....345678*************99999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 837.73
//
Query:       gi|119720370|ref|YP_920865.1|  [L=215]
Description: class II aldolase/adducin family protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.6e-51  172.7   0.0    8.8e-51  172.5   0.0    1.0  1  Aldolase_II  Class II Aldolase and Adducin N-terminal domain


Domain annotation for each model (and alignments):
>> Aldolase_II  Class II Aldolase and Adducin N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.5   0.0   4.9e-55   8.8e-51       2     185 ..       9     183 ..       8     184 .. 0.96

  Alignments for each domain:
  == domain 1  score: 172.5 bits;  conditional E-value: 4.9e-55
                                    HHHHHHHHHHHTTSSCTTBCEEEEEETSTTEEEEEBTSS-GGGHTGGGEEEEETTSCEEEECECSSSTB-TTHHHHHHHH CS
                    Aldolase_II   2 elaeasrllarrglvegtgGniSvrvpeedsflitpsgvdfeeltaedlvvvdldsgevvegkekggkpssetplHlaiy 81 
                                    e+a+a+r+l ++gl+ g++GniSvr   ++ +++ psgv +++l++ed++vv+ d g+vv+g   +gkps+e+ +Hla+y
  gi|119720370|ref|YP_920865.1|   9 EVADAFRRLEELGLNWGYSGNISVRAG-QGVYVVSPSGVLKSKLRPEDVLVVRED-GSVVDG---RGKPSVEFKTHLAVY 83 
                                    89***********************77.88888********************66.****55...689************ PP

                                    HH-TT-SEEEEE--HHHHHHHTCCSTSCHCCSSHHHHC.HSSSEEEEES-SSTTCHHHHHHHHHHHHHS-SEEEETTTEE CS
                    Aldolase_II  82 karpdaravvHtHspaavalsalagkeglppltqeaaklllgdevpvipyaapgteelgealaealkedakavllrnHGl 161
                                    +ar+d++avvH+H+ +  +l+al  + gl+p+ +e    +lg+ + v++ya+pgteel++++++al+ d++avl++nHG+
  gi|119720370|ref|YP_920865.1|  84 RARRDVNAVVHAHPVYSGVLAAL--RVGLKPVLEELVL-YLGGPIEVAEYAPPGTEELARNVVKALG-DRCAVLMANHGA 159
                                    *********************99..89*********98.99999**********************8.99********** PP

                                    EEEESSHHHHHHHHHHHHHHHHHH CS
                    Aldolase_II 162 ltvGetleeAvalaetleeaaeiq 185
                                    l++G tleeA a++ +le+aa+++
  gi|119720370|ref|YP_920865.1| 160 LACGSTLEEAIANLGYLERAAKVA 183
                                    *********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1481.76
//
Query:       gi|119720371|ref|YP_920866.1|  [L=144]
Description: UspA domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-34  119.1   2.8    2.3e-34  118.9   2.8    1.1  1  Usp       Universal stress protein family


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.9   2.8   1.3e-38   2.3e-34       1     141 []       1     144 []       1     144 [] 0.96

  Alignments for each domain:
  == domain 1  score: 118.9 bits;  conditional E-value: 1.3e-38
                                    S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH...HHHHHHC CS
                            Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada...akaaaea 77 
                                    m+ rIlVa+Dgse+++kAle A++la ++ga+l+++ v+d+++ +++  + ++    +   e + ++        ++a+ 
  gi|119720371|ref|YP_920866.1|   1 MFARILVAYDGSEHARKALEVAVDLASKYGAKLFVVEVVDSKSLTSSLREVPSLDVGRVIAEIKSKASVDvreCLRLAQS 80 
                                    899********************************************999999999999999998888889988899999 PP

                                    TTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                            Usp  78 ggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                    +gv+ e +v+egdpa eil++aee +adliV+Gsrg+s  +r+++GSvs++++ ++++pVlvV+
  gi|119720371|ref|YP_920866.1|  81 RGVDAEGDVLEGDPASEILRYAEEVKADLIVTGSRGLSLWKRIFIGSVSSKIVSESKVPVLVVK 144
                                    ***************************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 1004.21
//
Query:       gi|119720372|ref|YP_920867.1|  [L=475]
Description: trimethylamine methyltransferase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-81  272.7   0.0    4.2e-81  272.4   0.0    1.0  1  MTTB      Trimethylamine methyltransferase (MTTB)


Domain annotation for each model (and alignments):
>> MTTB  Trimethylamine methyltransferase (MTTB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  272.4   0.0   2.4e-85   4.2e-81      29     493 ..       3     459 ..       1     467 [. 0.94

  Alignments for each domain:
  == domain 1  score: 272.4 bits;  conditional E-value: 2.4e-85
                           MTTB  29 ppyellseeeleaieeaalriLeeiGiefldpealellkaaGakvegervrfdrglvreliakapreftlharnPerdve 108
                                    p++++ls  e e+i  +alr+Le++G+ f d+ + ++  + G ++++ rv +++++v+e++++apr++ l  r+ ++  +
  gi|119720372|ref|YP_920867.1|   3 PSVSVLSRREAEEITGEALRVLETVGVFFEDKGVERIALEGGGRLKDGRVLIPEDVVKEALRTAPRRIRLYDRDGREVAV 82 
                                    7899**************************************************************************** PP

                           MTTB 109 iggknvvfapvagaPfvrDlerg.rregtledfrnlvkLaqmldvlhhsggtvvepvDvpvnkrhldvlyakltlsdkvf 187
                                    +g  + +f p+++a  + D  ++  r++tled+++lv +a++l+ l+ ++  +v p +vp+++++   ly  l++s k++
  gi|119720372|ref|YP_920867.1|  83 LGEGARIFNPGSAAIRILDHGSQtPRNPTLEDLKKLVIVADYLKGLKAQSTALV-PFEVPAEVKDAVRLYVVLKYSGKPV 161
                                    ********************99989*************************9999.************************9 PP

                           MTTB 188 mgsvtekeraedsiemlrivfGaeeeefranpvvttiinvnsPlkfdetmlealeayaragqavivtpfilaGAmaPvtv 267
                                    ++ +   e+   ++eml +v+    e+++++p+ +  +  ++Pl + + +   l ++ar g ++ +++    GA++Pvtv
  gi|119720372|ref|YP_920867.1| 162 VTGAFTVENLPLMVEMLGAVR----EDYAEKPFAIFDVCPTPPLSWSTVTSRNLVDLARLGVPAEIISMPGLGATSPVTV 237
                                    988888888888888876655....556679************************************************* PP

                           MTTB 268 agavaqalAEaLagialtqlvrpgapviyGtftssvdlksGApafGtpeaalatlvagqlArrlglPlrssggltasklp 347
                                     ga+ q +AE+L+gial+qlv+pgapviyG  ++ +    G p+  +pea+l++l+   lAr+l+lP  +  gl++sk+ 
  gi|119720372|ref|YP_920867.1| 238 YGAIIQHHAEVLSGIALSQLVKPGAPVIYGGSPTMIHPYYGTPSITAPEAVLISLAYRDLARYLDLPSHTYMGLSDSKTV 317
                                    ******************************************************************************** PP

                           MTTB 348 DaQaayesanslwaavlaganlvlhaAGwleggLvasyekfilDadvlgmiarllegievseealaldairevgpg..gh 425
                                    D Qa++e+a++ + a+lag  ++   AG+le   v s+ek++lD++ +    rl++g+ev++  +alda++e   +  g+
  gi|119720372|ref|YP_920867.1| 318 DYQAGAETAYTAALAALAGFDVI-SGAGMLEYESVQSLEKLVLDNEACLIAERLARGVEVDP--QALDALKEGVLEkkGN 394
                                    ********************976.689*********************************87..589***88544335** PP

                           MTTB 426 flgtahTlaryetafyepelsdnknfeeWeeeGakdaeerAnekvkkiLaeyeepkldeaideeLrdf 493
                                    fl+  hT ++y+++   p++ d +   +  ++G    +e A+++v++iLae+++p ld +  + L+++
  gi|119720372|ref|YP_920867.1| 395 FLALRHTRQHYRSEILVPKVWDLAPRAK--STG-VPLAELAHREVERILAEHKPPLLDGDALRRLDAV 459
                                    **********************998764..555.56889********************999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 3011.07
//
Query:       gi|119720373|ref|YP_920868.1|  [L=218]
Description: methionine synthase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-26   92.9   0.5    2.2e-26   92.3   0.5    1.3  1  B12-binding      B12 binding domain
    9.3e-22   77.3   0.1    1.8e-21   76.3   0.1    1.5  1  B12-binding_2    B12 binding domain
  ------ inclusion threshold ------
      0.049   13.9   2.6        4.7    7.6   0.8    3.1  3  TetR_C_11        Tetracyclin repressor-like, C-terminal domai
      0.053   13.5   0.0      0.077   12.9   0.0    1.3  1  Glyco_tran_WecB  Glycosyl transferase WecB/TagA/CpsF family
      0.064   13.0   0.0        0.1   12.3   0.0    1.3  1  FGGY_C           FGGY family of carbohydrate kinases, C-termi
       0.11   12.5   0.0         11    6.1   0.0    2.8  3  TnpV             Transposon-encoded protein TnpV
       0.12   12.7   0.1       0.22   11.9   0.1    1.4  1  Radical_SAM      Radical SAM superfamily


Domain annotation for each model (and alignments):
>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.3   0.5   8.6e-30   2.2e-26       3     120 ..      97     208 ..      95     209 .. 0.94

  Alignments for each domain:
  == domain 1  score: 92.3 bits;  conditional E-value: 8.6e-30
                    B12-binding   3 vllatvggdlhplGlavlaaalrdagfeVqllganvenedivaairaekpdvvglSalltsqleavkelvel..lkrirp 80 
                                    ++ +tv gd+h+lG+++ aa+++++gf+V++lg++v++e++++a+++ +++vvg+Sal+t+++ + ++++e+  +++ r+
  gi|119720373|ref|YP_920868.1|  97 AVFGTVRGDIHELGKNLAAAVFEAEGFHVVDLGVDVPPEKFAEAVEKYNARVVGMSALMTTTMLEQRNVIEElkKRGLRD 176
                                    6889********************************************************************99999*** PP

                    B12-binding  81 rvkvvvGGahpsldpeetleaklgiddvvvgegedaleal 120
                                    +v+v++GGa+  +++e++ e  +g+d+    +g+da+ea+
  gi|119720373|ref|YP_920868.1| 177 KVIVIAGGAP--VTEEWVRE--IGADV----WGRDAFEAV 208
                                    ********99..77888555..**777....******997 PP

>> B12-binding_2  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.3   0.1   7.2e-25   1.8e-21       2      74 ..       9      81 ..       8      82 .. 0.97

  Alignments for each domain:
  == domain 1  score: 76.3 bits;  conditional E-value: 7.2e-25
                  B12-binding_2  2 aerlhwaivhgdkegieelidealaqgsaavdvlndvllpamkeVGdlfgagelflpqvllsaevmkkavahL 74
                                   +e+l +a+v+gd++++ee +++++++g  + +++ +vl+pam++VG+l+++ge+f+p++++sae++++ +++L
  gi|119720373|ref|YP_920868.1|  9 REKLFQAVVEGDEAAAEEYTRRLVERGLGPREIVSEVLVPAMRRVGELYEKGEYFIPELVMSAEAFRRSMEVL 81
                                   799*******************************************************************998 PP

>> TetR_C_11  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.8    0.0018       4.7      42      83 ..       6      47 ..       1      52 [. 0.85
   2 ?    3.9   0.0     0.026        66       5      37 ..     100     131 ..      98     164 .. 0.77
   3 ?   -0.2   0.0      0.46   1.2e+03      95     111 ..     181     197 ..     179     199 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0018
                      TetR_C_11 42 pelaealrerlleprraalravlrrAvarGelradadvelvl 83
                                    el+e l ++++e   aa+++  rr v+rG  + ++  e+++
  gi|119720373|ref|YP_920868.1|  6 GELREKLFQAVVEGDEAAAEEYTRRLVERGLGPREIVSEVLV 47
                                   6899999999********************888877777665 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.026
                      TetR_C_11   5 GslrgDLrallralaealaspragallrallae 37 
                                    G++rgD+++l ++la+a+ + ++g  + +l  +
  gi|119720373|ref|YP_920868.1| 100 GTVRGDIHELGKNLAAAVFE-AEGFHVVDLGVD 131
                                    99***********9998877.466655555555 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.46
                      TetR_C_11  95 lltgeplddafaerlvd 111
                                    + +g+p+++++++++ +
  gi|119720373|ref|YP_920868.1| 181 IAGGAPVTEEWVREIGA 197
                                    56899********9865 PP

>> Glyco_tran_WecB  Glycosyl transferase WecB/TagA/CpsF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0     3e-05     0.077      58     116 ..     135     195 ..      87     205 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3e-05
                Glyco_tran_WecB  58 ekaaerlrekypglriagthdgy..keeeeeaiieainas..kpdlllvglGapkqEkwiarl 116
                                    ek+ae++++   + r++g+++       e++++ie++++   + ++++++ Gap  E+w+++ 
  gi|119720373|ref|YP_920868.1| 135 EKFAEAVEKY--NARVVGMSALMttTMLEQRNVIEELKKRglRDKVIVIAGGAPVTEEWVREI 195
                                    4444444433..677788877754335899********9955779**************9986 PP

>> FGGY_C  FGGY family of carbohydrate kinases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0     4e-05       0.1     124     175 ..     151     202 ..     141     213 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4e-05
                         FGGY_C 124 arAaleavalqlrailealekdsgkpldrlavdGGgs.kndllmqllAdilgv 175
                                    + A++  ++l  r+++e+l+k  g   + +++ GG+  + + ++++ Ad+ g+
  gi|119720373|ref|YP_920868.1| 151 MSALMTTTMLEQRNVIEELKKR-GLRDKVIVIAGGAPvTEEWVREIGADVWGR 202
                                    67999**************999.**************8999999999**9995 PP

>> TnpV  Transposon-encoded protein TnpV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.49   1.2e+03      49      72 ..       9      33 ..       7      45 .. 0.72
   2 ?    2.5   0.0     0.052   1.3e+02       4      19 ..      58      73 ..      56      80 .. 0.83
   3 ?    6.1   0.0    0.0042        11      51      89 ..     136     174 ..     133     194 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.49
                           TnpV 49 sgkLnehlaeideqaeerl.erlvk 72
                                   ++kL + + e de a e + +rlv+
  gi|119720373|ref|YP_920868.1|  9 REKLFQAVVEGDEAAAEEYtRRLVE 33
                                   6789999999999877665145555 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.052
                           TnpV  4 kvgdyllPnltlpeee 19
                                   ++g+y++P+l ++ e+
  gi|119720373|ref|YP_920868.1| 58 EKGEYFIPELVMSAEA 73
                                   689********99885 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0042
                           TnpV  51 kLnehlaeideqaeerlerlvkqlaekegvteelkakdq 89 
                                    k +e +++++ +   +   +++ ++e+++v eelk++  
  gi|119720373|ref|YP_920868.1| 136 KFAEAVEKYNARVVGMSALMTTTMLEQRNVIEELKKRGL 174
                                    566777888888888999999**************9865 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   8.5e-05      0.22      76     163 ..      94     195 ..      61     199 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.5e-05
                                    CTEEEEEEECSSCHG..HHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHTCTSHH.............HHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxx..xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx.............xxxxxxxxxxxx RF
                    Radical_SAM  76 pgiritvetngtlpd..eeklerllelg.vdrvslgleaaddekvlklmnrghtf.............eevlealeklre 139
                                    +++ ++ ++ g  ++  +  +++  e++ + +v lg++ + ++ + + +  +++               e+ +++e l++
  gi|119720373|ref|YP_920868.1|  94 RWVAVFGTVRGDIHElgKNLAAAVFEAEgFHVVDLGVDVPPEK-FAEAV-EKYNArvvgmsalmtttmLEQRNVIEELKK 171
                                    556666666666666776666666676679************9.88888.5566667888999999997777******** PP

                                    TTSETEEEEEEEBTTTSHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM 140 agikrvvdrivglpGendeeleel 163
                                    +g+++ v++i g+  +++e ++e+
  gi|119720373|ref|YP_920868.1| 172 RGLRDKVIVIAGGAPVTEEWVREI 195
                                    *****9*******99***988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1455.90
//
Query:       gi|119720374|ref|YP_920869.1|  [L=229]
Description: hypothetical protein Tpen_1469 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.039   14.1   0.0       0.14   12.4   0.0    1.9  2  Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase


Domain annotation for each model (and alignments):
>> Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.35   6.3e+03      20      27 ..      49      56 ..      33      72 .. 0.52
   2 ?   12.4   0.0   7.8e-06      0.14      51      88 .]     145     181 ..     141     181 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.35
                                   EETTSEEE CS
                 Putative_PNPOx 20 vdedGrPn 27
                                   vd    +n
  gi|119720374|ref|YP_920869.1| 49 VDGRIEVN 56
                                   33333333 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 7.8e-06
                                    HHHHHHHHH-EEEEEEEETTGSEEEEEEEEEEEESCHH CS
                 Putative_PNPOx  51 rklrnleenprvallflddelgrgvrieGtaelvsdge 88 
                                    +++  +++nprv+l+f+ ++   +++++G a ++ d+e
  gi|119720374|ref|YP_920869.1| 145 HTWTLIQRNPRVSLVFFQPP-SLSFEVKGYASIHLDDE 181
                                    556669**************.57899999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1645.28
//
Query:       gi|119720375|ref|YP_920870.1|  [L=342]
Description: radical SAM domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.9e-14   53.8   0.0    5.3e-14   52.9   0.0    1.4  1  Radical_SAM     Radical SAM superfamily
    0.00094   19.1   0.1    0.00094   19.1   0.1    2.5  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
     0.0032   17.4   0.1     0.0032   17.4   0.1    3.0  3  DZR             Double zinc ribbon
     0.0046   17.0   1.3        2.2    8.4   0.1    2.7  2  zf-ACC          Acetyl-coA carboxylase zinc finger domain
     0.0054   16.5   6.4       0.33   10.8   0.1    3.6  3  zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
     0.0063   16.1   4.4       0.26   10.9   0.1    2.9  3  zf_UBZ          Ubiquitin-Binding Zinc Finger
  ------ inclusion threshold ------
      0.049   13.1  12.3       0.79    9.2   0.1    3.8  4  zf-ribbon_3     zinc-ribbon domain
      0.059   13.3   0.1      0.059   13.3   0.1    3.4  3  zf-HIT          HIT zinc finger
       0.18   11.9   0.0       0.36   11.0   0.0    1.5  1  Fer4_14         4Fe-4S single cluster domain
       0.36   10.9   0.1       0.36   10.9   0.1    3.5  3  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
       0.37   11.5   0.2       0.37   11.5   0.2    3.3  3  zf-ISL3         zinc-finger of transposase IS204/IS1001/IS109
       0.44   10.6   4.0        1.9    8.5   0.0    2.9  3  zinc-ribbons_6  zinc-ribbons
       0.49    9.9   7.4          1    8.9   4.1    2.9  3  TF_Zn_Ribbon    TFIIB zinc-binding
       0.84    9.7   4.0        3.6    7.6   0.0    3.0  3  CpXC            CpXC protein
        1.2    8.8  10.6        3.1    7.5   0.2    3.5  3  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
        1.2    8.9  13.1        2.1    8.2   0.6    3.5  3  zinc_ribbon_2   zinc-ribbon domain
        2.3    7.8   8.1       0.77    9.3   0.3    3.0  3  DUF2688         Protein of unknown function (DUF2688)
        3.8    7.7  13.3       0.64   10.2   0.2    3.6  3  Zn-ribbon_8     Zinc ribbon domain
        8.7    5.9   9.6        5.3    6.6   0.3    2.9  3  Mu-like_Com     Mu-like prophage protein Com
        9.1    6.3  14.4        8.5    6.4   0.0    3.7  3  Zn_ribbon_SprT  SprT-like zinc ribbon domain
        9.7    6.3   7.2        2.1    8.4   0.1    2.8  2  HypA            Hydrogenase/urease nickel incorporation, meta


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.9   0.0   6.2e-17   5.3e-14       6     162 ..      81     226 ..      78     231 .. 0.93

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 6.2e-17
                                    EESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEEC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM   6 gCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritvetn 85 
                                    gCn+ C++C++++  +   +++ l + + +++++ + ++ g+ ++  +  ep+ + d+v+++ ++a++  +g+   ++tn
  gi|119720375|ref|YP_920870.1|  81 GCNFHCPWCQNHHL-SFSLPPEGLEPVDPEALADLA-VSAGAQGISASFNEPITNLDYVVDASEAARK--RGLYSMMVTN 156
                                    9***********95.999999999999999999999.999****************************..7********* PP

                                    SSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  86 gtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGendeelee 162
                                     +      l++ le+gvd ++ +++   +   ++ +  + +   v ++ + + ++g + v ++++++pG nd++  e
  gi|119720375|ref|YP_920870.1| 157 MYFT-TSSLRLVLEAGVDGFAASVKGCPSA--RRVL-ANVDHYVVFRNARVALDSGAH-VEIVYLVVPGANDSK--E 226
                                    ***8.************************7..7777.778999999************.*************84..5 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.1   1.1e-06   0.00094      10      54 ..     271     330 ..     266     332 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.1e-06
                 OrfB_Zn_ribbon  10 ykakeyGikveev....npayTSktCseCgsknke...........alsgrtfkCpnCgf 54 
                                    + a ++G+k+++v    +p+  S++C++Cg+++ +           + +g ++kCp+Cg 
  gi|119720375|ref|YP_920870.1| 271 DYAVKEGVKYVYVgnvhDPELESTRCPRCGKTLVRregyrvvefnlDFEGGRYKCPRCGE 330
                                    6688899999998666679999***********9999*******9999**********95 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.4      0.72   6.2e+02      28      40 ..      14      26 ..       3      35 .. 0.66
   2 ?   -0.9   0.6       2.1   1.8e+03      14      19 ..      85      90 ..      78      96 .. 0.67
   3 !   17.4   0.1   3.8e-06    0.0032      11      43 ..     292     337 ..     287     340 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.72
                            DZR 28 edrCpsCgekvdp 40
                                     +C +C++ +  
  gi|119720375|ref|YP_920870.1| 14 VVACLACERRCRV 26
                                   5789999998655 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.1
                            DZR 14 fCseCg 19
                                    C++C+
  gi|119720375|ref|YP_920870.1| 85 HCPWCQ 90
                                   455554 PP

  == domain 3  score: 17.4 bits;  conditional E-value: 3.8e-06
                            DZR  11 darfCseCgtklkavaa.............edrCpsCgekvdpear 43 
                                    ++  C++Cg++l + +               ++Cp+Cge+v+ + r
  gi|119720375|ref|YP_920870.1| 292 ESTRCPRCGKTLVRREGyrvvefnldfeggRYKCPRCGEPVPIKGR 337
                                    5678*******9865559***********************98876 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.1    0.0026       2.2       2      15 ..     294     307 ..     294     307 .. 0.89
   2 !    6.8   0.2    0.0084       7.2       3      10 ..     324     331 ..     323     332 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0026
                         zf-ACC   2 tKCpsCgemlykke 15 
                                    t+Cp+Cg +l ++e
  gi|119720375|ref|YP_920870.1| 294 TRCPRCGKTLVRRE 307
                                    79*******99886 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0084
                         zf-ACC   3 KCpsCgem 10 
                                    KCp+Cge 
  gi|119720375|ref|YP_920870.1| 324 KCPRCGEP 331
                                    9*****96 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1      0.18   1.5e+02       3      10 ..      85      92 ..      83      95 .. 0.77
   2 !   10.8   0.1   0.00039      0.33       3      16 ..     295     308 ..     293     314 .. 0.88
   3 ?    4.8   0.4     0.029        25       3      13 ..     324     334 ..     322     337 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.18
                                   E-SSS--E CS
                 zf-C4_Topoisom  3 kCPkCggd 10
                                    CP+C ++
  gi|119720375|ref|YP_920870.1| 85 HCPWCQNH 92
                                   5****943 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00039
                                    E-SSS--EEEEEE- CS
                 zf-C4_Topoisom   3 kCPkCggdLvlkrg 16 
                                     CP Cg+ Lv+++g
  gi|119720375|ref|YP_920870.1| 295 RCPRCGKTLVRREG 308
                                    6***********98 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.029
                                    E-SSS--EEEE CS
                 zf-C4_Topoisom   3 kCPkCggdLvl 13 
                                    kCP Cg+++ +
  gi|119720375|ref|YP_920870.1| 324 KCPRCGEPVPI 334
                                    8*****98755 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       2.9   2.5e+03       3      11 ..      84      92 ..      83      99 .. 0.74
   2 !    6.2   0.2    0.0091       7.8       3      12 ..     294     303 ..     292     307 .. 0.82
   3 !   10.9   0.1   0.00031      0.26       2      14 ..     322     334 ..     321     337 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2.9
                         zf_UBZ  3 ylCerCgke 11
                                   + C+ C+ +
  gi|119720375|ref|YP_920870.1| 84 FHCPWCQNH 92
                                   78**9*977 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0091
                         zf_UBZ   3 ylCerCgkei 12 
                                      C+rCgk++
  gi|119720375|ref|YP_920870.1| 294 TRCPRCGKTL 303
                                    57*****986 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00031
                         zf_UBZ   2 tylCerCgkeipe 14 
                                     y C+rCg+++p+
  gi|119720375|ref|YP_920870.1| 322 RYKCPRCGEPVPI 334
                                    59*********96 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       7.3   6.2e+03      11      22 ..       9      20 ..       8      21 .. 0.73
   2 ?    1.6   0.8      0.23     2e+02      18      23 ..      85      90 ..      84      92 .. 0.85
   3 ?    9.2   0.1   0.00092      0.79       3      13 ..     294     305 ..     292     307 .. 0.83
   4 ?    8.4   0.4    0.0017       1.5       3      12 ..     323     332 ..     322     336 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 7.3
                    zf-ribbon_3 11 plssddnvCpyC 22
                                   pl  ++++C  C
  gi|119720375|ref|YP_920870.1|  9 PLGGGVVACLAC 20
                                   566788899777 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.23
                    zf-ribbon_3 18 vCpyCG 23
                                   +Cp+C+
  gi|119720375|ref|YP_920870.1| 85 HCPWCQ 90
                                   7****7 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.00092
                    zf-ribbon_3   3 vrCPnCGa.pls 13 
                                    +rCP+CG+ +++
  gi|119720375|ref|YP_920870.1| 294 TRCPRCGKtLVR 305
                                    69*****98876 PP

  == domain 4  score: 8.4 bits;  conditional E-value: 0.0017
                    zf-ribbon_3   3 vrCPnCGapl 12 
                                    ++CP+CG+p+
  gi|119720375|ref|YP_920870.1| 323 YKCPRCGEPV 332
                                    58*****975 PP

>> zf-HIT  HIT zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1       8.1   6.9e+03      15      21 ..      85      91 ..      83      92 .. 0.71
   2 ?    2.1   0.9      0.21   1.8e+02      15      21 ..     295     301 ..     294     303 .. 0.86
   3 ?   13.3   0.1   6.9e-05     0.059      12      22 ..     321     331 ..     318     332 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 8.1
                                   E-TTT-- CS
                         zf-HIT 15 kCpkCnt 21
                                    Cp C  
  gi|119720375|ref|YP_920870.1| 85 HCPWCQN 91
                                   5998875 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.21
                                    E-TTT-- CS
                         zf-HIT  15 kCpkCnt 21 
                                    +Cp+C+ 
  gi|119720375|ref|YP_920870.1| 295 RCPRCGK 301
                                    8****85 PP

  == domain 3  score: 13.3 bits;  conditional E-value: 6.9e-05
                                    -SEE-TTT--E CS
                         zf-HIT  12 akYkCpkCntr 22 
                                    ++YkCp+C+++
  gi|119720375|ref|YP_920870.1| 321 GRYKCPRCGEP 331
                                    79*******98 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00042      0.36       7      24 ..      81      97 ..      77     161 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00042
                        Fer4_14  7 gCnlsCkgCdnketwkse 24
                                   gCn++C++C n++  +++
  gi|119720375|ref|YP_920870.1| 81 GCNFHCPWCQNHH-LSFS 97
                                   8*********987.5554 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   1.3       1.1   9.6e+02       1       6 [.      85      90 ..      85      92 .. 0.83
   2 ?   10.9   0.1   0.00043      0.36       1      14 [.     295     308 ..     295     320 .. 0.90
   3 ?    3.6   2.1     0.082        70       1       9 [.     324     332 ..     324     333 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.1
                 DNA_ligase_ZBD  1 hCPvCG 6 
                                   hCP C 
  gi|119720375|ref|YP_920870.1| 85 HCPWCQ 90
                                   9****7 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00043
                 DNA_ligase_ZBD   1 hCPvCGsavvReeg 14 
                                    +CP CG  +vR eg
  gi|119720375|ref|YP_920870.1| 295 RCPRCGKTLVRREG 308
                                    5*********9997 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.082
                 DNA_ligase_ZBD   1 hCPvCGsav 9  
                                    +CP CG +v
  gi|119720375|ref|YP_920870.1| 324 KCPRCGEPV 332
                                    6*****998 PP

>> zf-ISL3  zinc-finger of transposase IS204/IS1001/IS1096/IS1165
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.3       5.6   4.8e+03       4      11 ..      85      92 ..      83      94 .. 0.76
   2 ?   11.5   0.2   0.00043      0.37       3      20 ..     294     311 ..     292     314 .. 0.87
   3 ?    4.3   0.4     0.076        65       4      11 ..     324     331 ..     322     339 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 5.6
                        zf-ISL3  4 rCPnCgsk 11
                                   +CP C++ 
  gi|119720375|ref|YP_920870.1| 85 HCPWCQNH 92
                                   79999875 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00043
                        zf-ISL3   3 hrCPnCgsktvvkhgkke 20 
                                    +rCP+Cg++ v++ g++ 
  gi|119720375|ref|YP_920870.1| 294 TRCPRCGKTLVRREGYRV 311
                                    79*******99**99875 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.076
                        zf-ISL3   4 rCPnCgsk 11 
                                    +CP+Cg++
  gi|119720375|ref|YP_920870.1| 324 KCPRCGEP 331
                                    69999988 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.3       4.9   4.2e+03      18      27 ..      16      25 ..      12      36 .. 0.62
   2 ?    2.3   0.0      0.19   1.7e+02      16      28 ..      83      95 ..      73     107 .. 0.72
   3 ?    8.5   0.0    0.0022       1.9       2      38 ..     295     331 ..     294     337 .. 0.68

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 4.9
                                   E-TTT--EEE CS
                 zinc-ribbons_6 18 hCeaCqedlk 27
                                    C aC+++++
  gi|119720375|ref|YP_920870.1| 16 ACLACERRCR 25
                                   4555655443 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.19
                                   EEE-TTT--EEEE CS
                 zinc-ribbons_6 16 qyhCeaCqedlkk 28
                                   ++hC  Cq++   
  gi|119720375|ref|YP_920870.1| 83 NFHCPWCQNHHLS 95
                                   6788888887655 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0022
                                    --SSS-S--EE-S.............SEEE-TTT--EEEEEEE-SSS-S- CS
                 zinc-ribbons_6   2 kCpeCqqelekrg.............eqyhCeaCqedlkkealCpeCeqe 38 
                                     Cp+C + l++r+              +y+C  C e             +
  gi|119720375|ref|YP_920870.1| 295 RCPRCGKTLVRREgyrvvefnldfegGRYKCPRCGE-------------P 331
                                    6*********88746666666666665666666654.............4 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       3.7   3.1e+03       2       9 ..      85      92 ..      84      96 .. 0.76
   2 ?    6.7   0.1    0.0062       5.3      12      26 ..     286     300 ..     277     305 .. 0.82
   3 ?    8.9   4.1    0.0012         1       2      27 ..     295     330 ..     294     333 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 3.7
                                   EETTTTCE CS
                   TF_Zn_Ribbon  2 kCPnCgst 9 
                                    CP C + 
  gi|119720375|ref|YP_920870.1| 85 HCPWCQNH 92
                                   59*99876 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0062
                                    HEETSTTCEEESSSS CS
                   TF_Zn_Ribbon  12 veDpergelvCtdCG 26 
                                    v Dpe   ++C++CG
  gi|119720375|ref|YP_920870.1| 286 VHDPELESTRCPRCG 300
                                    678999999999998 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0012
                                    EETTTTCEEC..........HEETSTTCEEESSSSB CS
                   TF_Zn_Ribbon   2 kCPnCgstnl..........veDpergelvCtdCGl 27 
                                    +CP Cg t +           +D+e g + C++CG+
  gi|119720375|ref|YP_920870.1| 295 RCPRCGKTLVrregyrvvefNLDFEGGRYKCPRCGE 330
                                    7*****99868*****9977777***********96 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.8       4.8   4.1e+03      38      46 ..      84      92 ..      82      97 .. 0.66
   2 ?    7.6   0.0    0.0043       3.6      29      47 ..     285     303 ..     276     313 .. 0.86
   3 ?    2.0   0.1      0.24   2.1e+02      38      47 ..     323     332 ..     319     339 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 4.8
                           CpXC 38 atCpkCgat 46
                                   ++Cp C++ 
  gi|119720375|ref|YP_920870.1| 84 FHCPWCQNH 92
                                   667777654 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0043
                           CpXC  29 klldgslfeatCpkCgata 47 
                                    ++ d +l +++Cp+Cg+t 
  gi|119720375|ref|YP_920870.1| 285 NVHDPELESTRCPRCGKTL 303
                                    6778899*********986 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.24
                           CpXC  38 atCpkCgata 47 
                                    ++Cp+Cg+ +
  gi|119720375|ref|YP_920870.1| 323 YKCPRCGEPV 332
                                    6788888755 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.9      0.45   3.8e+02      23      31 ..      85      93 ..      84      94 .. 0.93
   2 ?    7.5   0.2    0.0037       3.1       6      20 ..     296     310 ..     293     312 .. 0.87
   3 ?    5.1   0.3     0.021        18       6      12 ..     325     331 ..     325     334 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.45
                  zf-NADH-PPase 23 vCpaCgleh 31
                                   +Cp C+++h
  gi|119720375|ref|YP_920870.1| 85 HCPWCQNHH 93
                                   8******99 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0037
                  zf-NADH-PPase   6 CgrCGaptepaeggw 20 
                                    C+rCG   ++ eg +
  gi|119720375|ref|YP_920870.1| 296 CPRCGKTLVRREGYR 310
                                    ******999999876 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.021
                  zf-NADH-PPase   6 CgrCGap 12 
                                    C+rCG p
  gi|119720375|ref|YP_920870.1| 325 CPRCGEP 331
                                    *****98 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   2.0       3.5     3e+03       2       6 ..      86      90 ..      81      94 .. 0.68
   2 ?    7.9   0.1     0.003       2.6       1       9 [.     295     303 ..     295     307 .. 0.86
   3 ?    8.2   0.6    0.0024       2.1       1      10 [.     324     333 ..     324     335 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 3.5
                  zinc_ribbon_2  2 CpnCG 6 
                                   Cp C 
  gi|119720375|ref|YP_920870.1| 86 CPWCQ 90
                                   66665 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.003
                  zinc_ribbon_2   1 fCpnCGael 9  
                                    +Cp+CG++l
  gi|119720375|ref|YP_920870.1| 295 RCPRCGKTL 303
                                    6*****987 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0024
                  zinc_ribbon_2   1 fCpnCGaelq 10 
                                    +Cp+CG++++
  gi|119720375|ref|YP_920870.1| 324 KCPRCGEPVP 333
                                    7999998875 PP

>> DUF2688  Protein of unknown function (DUF2688)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1      0.78   6.6e+02      30      51 ..       6      27 ..       4      30 .. 0.81
   2 ?    9.3   0.3    0.0009      0.77       7      19 ..     293     305 ..     289     308 .. 0.87
   3 ?    1.4   0.3      0.26   2.2e+02       9      17 ..     324     332 ..     322     337 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.78
                        DUF2688 30 LkqklGdICsdClipEElaeIe 51
                                   L+  lG+   +Cl  E + ++ 
  gi|119720375|ref|YP_920870.1|  6 LQEPLGGGVVACLACERRCRVR 27
                                   66778999999**999998875 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0009
                        DUF2688   7 tTqCrRCGkslst 19 
                                    +T+C RCGk l++
  gi|119720375|ref|YP_920870.1| 293 STRCPRCGKTLVR 305
                                    8*********986 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.26
                        DUF2688   9 qCrRCGksl 17 
                                    +C RCG ++
  gi|119720375|ref|YP_920870.1| 324 KCPRCGEPV 332
                                    7*****986 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1       1.8   1.5e+03       7      34 ..      85      91 ..      83      95 .. 0.60
   2 ?   10.2   0.2   0.00075      0.64      25      38 ..     292     305 ..     283     307 .. 0.67
   3 ?    5.4   0.1     0.023        20       6      35 ..     323     331 ..     315     334 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.8
                    Zn-ribbon_8  7 rCeeCghefevlqsisdapltaCPeCgs 34
                                   +                     CP C+ 
  gi|119720375|ref|YP_920870.1| 85 H---------------------CPWCQN 91
                                   4.....................666654 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00075
                    Zn-ribbon_8  25 pltaCPeCgsevrr 38 
                                    + t CP+Cg+++ r
  gi|119720375|ref|YP_920870.1| 292 ESTRCPRCGKTLVR 305
                                    3455******5554 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.023
                    Zn-ribbon_8   6 YrCeeCghefevlqsisdapltaCPeCgse 35 
                                    Y+                     CP+Cg++
  gi|119720375|ref|YP_920870.1| 323 YK---------------------CPRCGEP 331
                                    45.....................5555554 PP

>> Mu-like_Com  Mu-like prophage protein Com
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.4       6.3   5.3e+03      26      36 ..      85      93 ..      82     102 .. 0.65
   2 ?    5.0   0.2     0.019        17      26      31 ..     295     300 ..     290     308 .. 0.82
   3 ?    6.6   0.3    0.0062       5.3      25      32 ..     323     330 ..     318     338 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 6.3
                    Mu-like_Com 26 KCPRCGtLnHl 36
                                    CP C   nH 
  gi|119720375|ref|YP_920870.1| 85 HCPWCQ--NHH 93
                                   699994..554 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.019
                    Mu-like_Com  26 KCPRCG 31 
                                    +CPRCG
  gi|119720375|ref|YP_920870.1| 295 RCPRCG 300
                                    8****9 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.0062
                    Mu-like_Com  25 iKCPRCGt 32 
                                     KCPRCG 
  gi|119720375|ref|YP_920870.1| 323 YKCPRCGE 330
                                    59*****5 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.2     0.045        39       6      20 ..      85      96 ..      84      98 .. 0.86
   2 ?    4.5   0.2     0.038        32      26      34 ..     295     303 ..     287     310 .. 0.79
   3 ?    6.4   0.0      0.01       8.5       5      11 ..     323     329 ..     311     334 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.045
                 Zn_ribbon_SprT  6 rCtgCgreythhlsi 20
                                   +C+ C+   +hhls+
  gi|119720375|ref|YP_920870.1| 85 HCPWCQ---NHHLSF 96
                                   599999...***996 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.038
                 Zn_ribbon_SprT  26 rCrrCkgtL 34 
                                    rC+rC+ tL
  gi|119720375|ref|YP_920870.1| 295 RCPRCGKTL 303
                                    677777666 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.01
                 Zn_ribbon_SprT   5 YrCtgCg 11 
                                    Y+C++Cg
  gi|119720375|ref|YP_920870.1| 323 YKCPRCG 329
                                    7777777 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   3.4       3.3   2.8e+03      87      97 ..      73      94 ..       4      98 .. 0.54
   2 ?    8.4   0.1    0.0025       2.1      70      94 ..     293     330 ..     281     338 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3.3
                                   H...........S-TTTSSS-E CS
                           HypA 87 l...........rCpkCgsadv 97
                                   l           +Cp C+++++
  gi|119720375|ref|YP_920870.1| 73 LaltysnfgcnfHCPWCQNHHL 94
                                   0444444444447888887765 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0025
                                    EEEETTTS-EEECHH.HHH............S-TTTSS CS
                           HypA  70 kvrCreCgkefelee.kal............rCpkCgs 94 
                                    ++rC +Cgk+   +e +++            +Cp+Cg+
  gi|119720375|ref|YP_920870.1| 293 STRCPRCGKTLVRREgYRVvefnldfeggryKCPRCGE 330
                                    679*****99986654322567999999999*****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                        38  (0.00211947); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 2206.89
//
Query:       gi|119720376|ref|YP_920871.1|  [L=258]
Description: hypothetical protein Tpen_1471 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.1e-40  135.8   0.0    1.1e-39  135.3   0.0    1.2  1  DUF364    Putative heavy-metal chelation
    5.5e-20   71.4   0.2    1.2e-19   70.3   0.2    1.6  1  DUF4213   Putative heavy-metal chelation


Domain annotation for each model (and alignments):
>> DUF364  Putative heavy-metal chelation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.3   0.0   1.2e-43   1.1e-39       1     144 [.     109     250 ..     109     253 .. 0.96

  Alignments for each domain:
  == domain 1  score: 135.3 bits;  conditional E-value: 1.2e-43
                         DUF364   1 daldlleikkgkkVvvVGyfapvlkklkekgaeltvlelnpnlleeeegdlpdeaaeellpeadvviitGstLvngtler 80 
                                    dal+ + +++g+ Vv+VGyfap+++ l+ ++++l vle+ +  +e+ e ++p++a + +l++ad ++itGs++vn+t+++
  gi|119720376|ref|YP_920871.1| 109 DALEQVGVAPGDSVVLVGYFAPYVEALRGRVRRLAVLEFASVVVEGVE-VYPWWAYAAVLRDADKLLITGSSIVNHTINY 187
                                    78999************************************9999998.57***************************** PP

                         DUF364  81 llelakkaaevvlvGPsapllpevlfdyGvdviagvvvtdpdkllraiaeGggtkhlkrkgakk 144
                                    ll+     ae+ lvGPs+pl+pev+ +yGv+ i ++vv+dp++++++++eGgg+  ++r+g  +
  gi|119720376|ref|YP_920871.1| 188 LLTAPT-RAEKHLVGPSSPLAPEVFGRYGVKTINTAVVVDPESCATILMEGGGFSSCFREGCLR 250
                                    ***999.***************************************************998766 PP

>> DUF4213  Putative heavy-metal chelation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.3   0.2   1.3e-23   1.2e-19       1      74 []      17      98 ..      17      98 .. 0.95

  Alignments for each domain:
  == domain 1  score: 70.3 bits;  conditional E-value: 1.3e-23
                        DUF4213  1 yeelieaapedltVedvviGlnwtlVelsdggaGlAyt.........eagklvgkparelaelllswnplersvGlAaiNAl 73
                                   ye ++++a    +V++vviG++ tlVel+dg+aG+Ayt           g+l+g+++ +++ llls   le svGlAa+NAl
  gi|119720376|ref|YP_920871.1| 17 YEYALSRA-GSERVKRVVIGVHATLVELEDGRAGVAYTnregplssvTPGRLRGMNVSDALGLLLSPRGLEVSVGLAAVNAL 97
                                   89999999.9*****************************9999988877888*****************************9 PP

                        DUF4213 74 l 74
                                   l
  gi|119720376|ref|YP_920871.1| 98 L 98
                                   6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1840.95
//
Query:       gi|119720377|ref|YP_920872.1|  [L=135]
Description: PilT domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-16   61.4   0.2    1.4e-16   61.1   0.2    1.1  1  PIN          PIN domain
  ------ inclusion threshold ------
      0.069   13.0   0.1       0.12   12.3   0.1    1.4  1  Phage-MuB_C  Mu B transposition protein, C terminal


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.1   0.2   1.5e-20   1.4e-16       1     120 [.       2     122 ..       2     124 .. 0.89

  Alignments for each domain:
  == domain 1  score: 61.1 bits;  conditional E-value: 1.5e-20
                                    EEE-HHHHHHHH.TTSHHHHHHHHHHHTS.SEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCH.HH CS
                            PIN   1 ivlDTsvliall.rgeekaeaarklleel.eelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpida.ei 77 
                                    i+lDTsv+++++ ++++++ +a++ll +l e+ v s+l+l El++v++r   +      l    l+  + +++++d  ++
  gi|119720377|ref|YP_920872.1|   2 IYLDTSVIVSYVdEEDPNHGRAVELLGRLmEDRVASQLTLLELAAVYSR--AGLPNPVSLAVYSLRVVGASLVDVDLnQV 79 
                                    79***********************************************..77777777777777777788888775156 PP

                                    HHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHHHH CS
                            PIN  78 aeeaaeialkygllpnDaliaAtAkehgikliatfDedfrrva 120
                                     ++a+++a  ++l+++D+l+++ A+  g++++a+fD+++++ a
  gi|119720377|ref|YP_920872.1|  80 SRQALRYAQLLRLRTLDLLHVVAARMLGASAVASFDKEIAERA 122
                                    788999999999**************************98865 PP

>> Phage-MuB_C  Mu B transposition protein, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   1.3e-05      0.12       9      47 ..      89     127 ..      80     129 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.3e-05
                                    -SS-SGGGTTHHHHSSSSSSSHHHHHHHTTSSS-S-HHH CS
                    Phage-MuB_C   9 ikktkkeDvkaiaaAwgltdeelmkllqeiaekpGaLRa 47 
                                    + +    D+  ++aA+ l  +++ ++  eiae++Ga+R+
  gi|119720377|ref|YP_920872.1|  89 LLRLRTLDLLHVVAARMLGASAVASFDKEIAERAGAIRE 127
                                    5566677999***************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      200  (0.0111551); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.49
# Mc/sec: 836.45
//
Query:       gi|119720378|ref|YP_920873.1|  [L=88]
Description: hypothetical protein Tpen_1473 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.058   14.2   0.0      0.073   13.9   0.0    1.1  1  DUF3349   Protein of unknown function (DUF3349)


Domain annotation for each model (and alignments):
>> DUF3349  Protein of unknown function (DUF3349)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   4.1e-06     0.073      37      94 ..      11      69 ..       7      70 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.1e-06
                                   HHHHHHHHHHHHH--..SSS.BSHHHCHHHHHHHCTS---HHHHHHHHHHHHTTT-GCC CS
                        DUF3349 37 eevkevaeelvaeaa.eadeavdeedieelitkvteeepseedvarVaarLaaggwpla 94
                                   +ev+++ae++v+ +  ++ ++  ++ ie+ +++v +e +  ++v r a++L+++g++l 
  gi|119720378|ref|YP_920873.1| 11 KEVAQLAEKMVRYGLaRNRSHAFNIMIERGLEEVKREVAFWDEVYRSAEELEKSGFRLR 69
                                   79***********9658899999*********************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 605.09
//
Query:       gi|119720379|ref|YP_920874.1|  [L=243]
Description: ABC-2 type transporter [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.4e-12   45.3  15.2    8.6e-12   44.9  15.2    1.1  1  ABC2_membrane    ABC-2 type transporter
      9e-08   31.6   7.4      9e-08   31.6   7.4    1.3  2  ABC2_membrane_3  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.9  15.2   9.6e-16   8.6e-12      16     207 ..      22     206 ..      12     208 .. 0.86

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 9.6e-16
                  ABC2_membrane  16 rdpslgllwrliqplllalvfgtvfgnlgnsedglnrpgllffsvlflafsaltsvapvferergvlerelvsplyslsa 95 
                                    r++ +     ++q  +++l + ++f+ +g  +   + + + f ++ +++ ++l ++ + + r  ++ e + +spl s+s+
  gi|119720379|ref|YP_920874.1|  22 RQW-MW----IAQDAVWTLSLPLIFYFWGGLKALKSLVVASFVATGWTVGVNLVGQTVGWQRVSRIQEALVASPL-SPSD 95 
                                    333.33....678888999999999988733333356888888888888899999989999999999********.**** PP

                  ABC2_membrane  96 yvlakvlvelpvsllqalifllivyflvgldlsrf.flflllllltalaasslgllisalapsfedasqlaslvllplll 174
                                    y+++ vl+++p+ l + ++f+l++++l  + +  + + +++l +++++++s+l+l++    ++  ++s +++ +++++++
  gi|119720379|ref|YP_920874.1|  96 YFVGTVLGQIPYFLTEYTAFTLLALWL-EVSPA-GvAALYALSFASLVLGSFLSLAVVLRIKNPMNISAVTNPLVTVTII 173
                                    **************************9.88886.558889999999999999**************************** PP

                  ABC2_membrane 175 lsGffipidsmpkwlqwiaylnPltyavealrs 207
                                    l ++ +p++++p++ +  a l P + + e+ r+
  gi|119720379|ref|YP_920874.1| 174 LPPVWYPLSALPEVARLPALLAPTAALAELARW 206
                                    ***********99***99999999999998886 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0      0.33     3e+03       5      16 ..      32      43 ..      32      51 .. 0.79
   2 !   31.6   7.4     1e-11     9e-08     160     338 ..      51     232 ..      45     235 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.33
                ABC2_membrane_3  5 iitlllPiilvl 16
                                   ++tl lP+i+++
  gi|119720379|ref|YP_920874.1| 32 VWTLSLPLIFYF 43
                                   489999999987 PP

  == domain 2  score: 31.6 bits;  conditional E-value: 1e-11
                ABC2_membrane_3 160 asflvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilll..afglgipfgn 237
                                    +s +v+ +++   +++++ + + +  ++ sri e ++ s++sp+ y+++ +lg    +l+ +  ++ll  ++   ++  +
  gi|119720379|ref|YP_920874.1|  51 KSLVVASFVATGWTVGVNLVGQTVGWQRVSRIQEALVASPLSPSDYFVGTVLGQIPYFLTEYTAFTLLalWLE--VSPAG 128
                                    555666777778889999999999999**********************************998877534888..9999* PP

                ABC2_membrane_3 238 lglllllfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlpsalkwifsiiPffapglgllrli 317
                                    + +l  l++  + + ++l++++   +kn+ + ++++ ++  +++++  + +pl++lp+ ++  + + P+ a++++   ++
  gi|119720379|ref|YP_920874.1| 129 VAALYALSFASLVLGSFLSLAVVLRIKNPMNISAVTNPLVTVTIILPPVWYPLSALPEVARLPALLAPTAALAELARWVA 208
                                    ***************************************9988888888899**********************999998 PP

                ABC2_membrane_3 318 ....tgdplweillsliilalfavv 338
                                        + dp +++l  +++ a+++v+
  gi|119720379|ref|YP_920874.1| 209 glgcM-DPAVPLLVTFVWIAGTGVA 232
                                    87755.5778888888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      205  (0.011434); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1517.15
//
Query:       gi|119720380|ref|YP_920875.1|  [L=293]
Description: ABC transporter related [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-25   90.7   0.0    1.6e-25   90.2   0.0    1.2  1  ABC_tran      ABC transporter
    3.5e-13   50.1   0.1    1.3e-08   35.0   0.0    2.5  3  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
      8e-05   22.6   0.0     0.0002   21.4   0.0    1.6  2  Rad17         Rad17 P-loop domain
     0.0003   21.2   0.1    0.00046   20.6   0.1    1.4  1  AAA_16        AAA ATPase domain
     0.0035   16.7   0.0     0.0062   15.8   0.0    1.3  1  Zeta_toxin    Zeta toxin
     0.0036   17.3   0.0     0.0058   16.6   0.0    1.3  1  TsaE          Threonylcarbamoyl adenosine biosynthesis protei
     0.0038   17.5   0.1      0.018   15.3   0.1    1.9  1  AAA_22        AAA domain
  ------ inclusion threshold ------
      0.012   15.1   0.0        1.4    8.3   0.0    2.1  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.013   15.1   0.1      0.033   13.8   0.0    1.6  2  AAA_27        AAA domain
      0.021   14.3   0.0          2    7.8   0.0    2.1  2  SMC_N         RecF/RecN/SMC N terminal domain
      0.023   15.2   0.0      0.034   14.6   0.0    1.2  1  AAA_23        AAA domain
      0.029   14.4   0.2        4.3    7.3   0.1    2.9  2  AAA_5         AAA domain (dynein-related subfamily)
      0.044   14.0   0.0       0.53   10.6   0.0    2.2  1  SbcCD_C       Putative exonuclease SbcCD, C subunit
      0.053   13.9   0.0       0.25   11.8   0.0    1.9  2  AAA           ATPase family associated with various cellular 
      0.054   13.8   0.3       0.12   12.6   0.3    1.8  1  AAA_28        AAA domain
      0.054   13.3   0.1      0.096   12.5   0.1    1.3  1  MukB          MukB N-terminal
      0.077   12.7   0.1       0.16   11.7   0.1    1.5  1  AAA_30        AAA domain
      0.096   12.4   0.0       0.19   11.5   0.0    1.5  1  AAA_29        P-loop containing region of AAA domain
       0.11   12.1   0.0       0.19   11.4   0.0    1.2  1  SRP54         SRP54-type protein, GTPase domain
       0.19   12.0   0.1       0.51   10.7   0.1    1.6  2  AAA_19        AAA domain
        0.2   11.3   0.0        3.9    7.1   0.0    2.0  2  AAA_15        AAA ATPase domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.2   0.0   1.9e-28   1.6e-25       1     136 [.      19     161 ..      19     162 .. 0.96

  Alignments for each domain:
  == domain 1  score: 90.2 bits;  conditional E-value: 1.9e-28
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren. 79 
                                    l+ vsl+ ++ge++++ G+nGaGK+t +++++ +l+p++Ge ++ g d+ + e +++r++i+++pq  + f e+t +e  
  gi|119720380|ref|YP_920875.1|  19 LRGVSLEARKGELLVLAGPNGAGKTTTVRIFTTNLRPDAGEARVLGYDVVR-EYREVRRRIAYIPQGFEPFWEHTPEEYv 97 
                                    6789**********************************************9.9999***********9999999999989 PP

                                    ............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    ............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                e++++++++l+ lgl++ + +++    + LSgGq +r ++a++l++++++l+lDEpt
  gi|119720380|ref|YP_920875.1|  98 tavlmmrgwsfwEARAQAKRWLDALGLSD-ARRPI----RVLSGGQVRRAVVAAVLATEAEVLFLDEPT 161
                                    ***********999***************.78888....9****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.1   0.00012       0.1       2      26 ..      32      50 ..      31      64 .. 0.79
   2 ?   -3.3   0.0       7.1     6e+03     131     161 ..      76     106 ..      66     111 .. 0.76
   3 !   35.0   0.0   1.5e-11   1.3e-08     229     298 ..     126     192 ..     124     195 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00012
                         AAA_21  2 nvliGpNgsGKSnLLdaldllarld 26
                                    vl GpNg+GK++  +++       
  gi|119720380|ref|YP_920875.1| 32 LVLAGPNGAGKTTTVRIF------T 50
                                   69***********99998......4 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 7.1
                         AAA_21 131 svsepndlqfgkaltditsrawsllllldgl 161
                                     ++ ++ + f++++ + +++++++ l+++g+
  gi|119720380|ref|YP_920875.1|  76 RRIAYIPQGFEPFWEHTPEEYVTAVLMMRGW 106
                                    5667777888888899999999988888876 PP

  == domain 3  score: 35.0 bits;  conditional E-value: 1.5e-11
                         AAA_21 229 gqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHS 298
                                    +  +p+r lS G+ r  a+++a+l++     +l++DEp  gL+ ++ r++++ l+e  r g+ +++tTH+
  gi|119720380|ref|YP_920875.1| 126 DARRPIRVLSGGQVRR-AVVAAVLATEA--EVLFLDEPTEGLDVEVRREVWRALRERLRDGSSILMTTHD 192
                                    56789***********.*******9997..9***********************666666*********8 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   2.3e-07    0.0002      33      70 ..      17      54 ..      11      61 .. 0.88
   2 ?   -2.6   0.0         5   4.3e+03      32      52 ..     116     136 ..     113     151 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 2.3e-07
                          Rad17 33 ewlkadvLesrkkriLLisGPsGCgkstvvkvLskelg 70
                                   e+l+  +Le rk ++L+++GP G gk+t+v++ + +l 
  gi|119720380|ref|YP_920875.1| 17 EALRGVSLEARKGELLVLAGPNGAGKTTTVRIFTTNLR 54
                                   578999*************************9987765 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 5
                          Rad17  32 kewlkadvLesrkkriLLisG 52 
                                    k+wl+a  L  +++ i ++sG
  gi|119720380|ref|YP_920875.1| 116 KRWLDALGLSDARRPIRVLSG 136
                                    789999999999888988888 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.1   5.4e-07   0.00046      12     106 ..      19     120 ..       9     189 .. 0.61

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 5.4e-07
                         AAA_16  12 LlsalervrsgrpelvllsGesGvGKsslvrellralekd..ggif....lrgkcdqlesaipy.....salaqalaree 80 
                                    L+ +   +r+g  el++l G+ G GK++ vr + + l+ d  ++ +    +  ++++ ++ i+y      ++++    ee
  gi|119720380|ref|YP_920875.1|  19 LRGVSLEARKG--ELLVLAGPNGAGKTTTVRIFTTNLRPDagEARVlgydVVREYREVRRRIAYipqgfEPFWEHT-PEE 95 
                                    44444445555..89************************9762444333444444444666777777767788888.558 PP

                         AAA_16  81 llrqlldeaesaeleawrekleeala 106
                                    +++++l +   + +e +r++ +++l 
  gi|119720380|ref|YP_920875.1|  96 YVTAVLMMRGWSFWE-ARAQAKRWLD 120
                                    888888883332222.2222233333 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   7.2e-06    0.0062      16      57 ..      29      71 ..      18      79 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 7.2e-06
                     Zeta_toxin 16 PklillgGqpGAGKselaellkdele.rqgnvvrldpDdlRel 57
                                     l++l+G  GAGK+++ + ++++l+  +g++ +l  D +Re+
  gi|119720380|ref|YP_920875.1| 29 GELLVLAGPNGAGKTTTVRIFTTNLRpDAGEARVLGYDVVREY 71
                                   56899********************988899999999999987 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   6.8e-06    0.0058      14      62 ..      24      74 ..       6      81 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 6.8e-06
                                   HHHCHTEEEEEEESTTSSHHHHHHHHHHHTT--..----TTTTSEEEEEE. CS
                           TsaE 14 lakalgdvilLeGdLGaGKTtlvrglakalgve..evkSPTFtlveeYele 62
                                   l +  g++++L G+ GaGKTt vr +  +l  +  e +   + +v+eY++ 
  gi|119720380|ref|YP_920875.1| 24 LEARKGELLVLAGPNGAGKTTTVRIFTTNLRPDagEARVLGYDVVREYREV 74
                                   33333788**********************887788999999999999765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   2.1e-05     0.018       4      38 ..      28      70 ..      25     195 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.1e-05
                         AAA_22  4 tagilvvtGesGtGKTtllrrlleqldeeakaee........e 38
                                   +  +lv+ G+ G+GKTt++r ++ +l  +a  ++        e
  gi|119720380|ref|YP_920875.1| 28 KGELLVLAGPNGAGKTTTVRIFTTNLRPDAGEARvlgydvvrE 70
                                   56789*****************999954433333555544440 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0016       1.4       7      49 ..      14      57 ..       9      84 .. 0.78
   2 ?    4.8   0.0     0.019        16      92     136 ..     136     186 ..     130     216 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0016
                   Mg_chelatase  7 GqeeakraleiaaaGgHnlllvGppGsGKtmlakrlpsll.ppl 49
                                   G+ ea r + + a  g  l+l+Gp G+GKt   + +++ l p+ 
  gi|119720380|ref|YP_920875.1| 14 GNVEALRGVSLEARKGELLVLAGPNGAGKTTTVRIFTTNLrPDA 57
                                   6677778888888888899***********99998776441555 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.019
                   Mg_chelatase  92 Gggs.kpkpGeislahnGvLfLDElp.....efkrkvlevLRePledgevt 136
                                    Gg+  ++   ++  ++  vLfLDE +     e +r+v  +LRe l dg+  
  gi|119720380|ref|YP_920875.1| 136 GGQVrRAVVAAVLATEAEVLFLDEPTegldvEVRREVWRALRERLRDGSSI 186
                                    555534444455555678******86222336899999****999988654 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.8e-05     0.033       9      45 ..      11      48 ..       8      53 .. 0.86
   2 ?   -2.5   0.0       3.7   3.2e+03     112     146 ..     162     195 ..     145     200 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.8e-05
                         AAA_27  9 eryGkftd.rsldfsaeeadlhliyGpNEAGKstalrA 45
                                   +r+G+++  r ++++a + +l ++ GpN AGK+t++r 
  gi|119720380|ref|YP_920875.1| 11 KRFGNVEAlRGVSLEARKGELLVLAGPNGAGKTTTVRI 48
                                   78999886367999999*****************9875 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.7
                         AAA_27 112 ggldretFealFgLdherLreGGealleaegelgq 146
                                    +gld e  ++++    erLr+G  ++l ++ ++g+
  gi|119720380|ref|YP_920875.1| 162 EGLDVEVRREVWRALRERLRDGS-SILMTTHDMGE 195
                                    55555555555555567787764.56666666666 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.023        19      26      39 ..      31      44 ..      15      50 .. 0.83
   2 ?    7.8   0.0    0.0024         2     136     204 ..     133     198 ..      81     209 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.023
                                   EEEEEESTTSSHHH CS
                                   xxxxxxxxxxxxxx RF
                          SMC_N 26 ftaivGpNGSGKsn 39
                                   + ++ GpNG+GK+ 
  gi|119720380|ref|YP_920875.1| 31 LLVLAGPNGAGKTT 44
                                   56899*******96 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0024
                                    CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
                          SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreemlek 204
                                    +LSgG+   + +a ++A++    a + +lDe    LD + +++v + l+e+  + + +++++++ +  e 
  gi|119720380|ref|YP_920875.1| 133 VLSGGQVRRAVVAAVLATE----AEVLFLDEPTEGLDVEVRREVWRALRERLRDgSSILMTTHDMGEAEV 198
                                    79****9888888887765....456789********************876654888888887766655 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0     4e-05     0.034      11      40 ..      20      50 ..      12      63 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4e-05
                         AAA_23 11 rdqeidFsk.gltlItGpNGaGKTTildAik 40
                                   r+++++  k  l ++ GpNGaGKTT ++ ++
  gi|119720380|ref|YP_920875.1| 20 RGVSLEARKgELLVLAGPNGAGKTTTVRIFT 50
                                   555555534258899**********988766 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.1     0.005       4.3       2      23 ..      32      53 ..      31     164 .. 0.77
   2 ?    3.3   0.0      0.09        77      12      45 ..     169     202 ..     167     217 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.005
                                   EEEE--SSSSHHHHHHHGGGGB CS
                          AAA_5  2 vlLvGppGtgKselaerlaaal 23
                                   ++L Gp G gK++ ++ +   l
  gi|119720380|ref|YP_920875.1| 32 LVLAGPNGAGKTTTVRIFTTNL 53
                                   6899***********9988776 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.09
                                    HHHHHHHGGGGBS--EEEEE--TT--HHHHH--B CS
                          AAA_5  12 Kselaerlaaalnreveyvqltrdtteedlkgrr 45 
                                    ++e+++ l ++l++   + + t d+ e++++  r
  gi|119720380|ref|YP_920875.1| 169 RREVWRALRERLRDGSSILMTTHDMGEAEVVADR 202
                                    789*************************998765 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00062      0.53      26      89 ..     127     177 ..      98     178 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00062
                        SbcCD_C  26 lsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                     +r ++ lSGG+ + ++  a++              +  +++fLDE  ++lD e ++++ ++l+
  gi|119720380|ref|YP_920875.1| 127 ARRPIRVLSGGQVRRAVVAAVL-------A------TEAEVLFLDEPTEGLDVEVRREVWRALR 177
                                    5666677777776333332222.......2......23468*****************999987 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0    0.0003      0.25       2      23 ..      33      54 ..      32      93 .. 0.80
   2 ?   -0.3   0.0       1.5   1.3e+03      58      67 ..     151     160 ..     119     198 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0003
                                   EEESSTTSSHHHHHHHHHHHHT CS
                            AAA  2 llyGppGtGKTllakavakelg 23
                                   +l Gp G GKT++++   ++l 
  gi|119720380|ref|YP_920875.1| 33 VLAGPNGAGKTTTVRIFTTNLR 54
                                   799************9988874 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.5
                                    TSEEEEEETG CS
                            AAA  58 kpsilfiDEi 67 
                                    +  +lf+DE 
  gi|119720380|ref|YP_920875.1| 151 EAEVLFLDEP 160
                                    3489999985 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.3   0.00014      0.12       3      30 ..      33      71 ..      31     182 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00014
                         AAA_28  3 vitGgestGKTtlleaLa.........ar..gypvvpEa 30
                                   v+ G+ ++GKTt+++ ++         ar  gy vv+E+
  gi|119720380|ref|YP_920875.1| 33 VLAGPNGAGKTTTVRIFTtnlrpdageARvlGYDVVREY 71
                                   899***********9999655565554338888888665 PP

>> MukB  MukB N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   0.00011     0.096      30      54 ..      33      57 ..      28      64 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                                   HHHS--SHHHHHHHHHHHHHHS--T CS
                           MukB 30 tlsGgnGaGksttmaafvtaliPdl 54
                                    l G nGaGk+tt+  f t l Pd 
  gi|119720380|ref|YP_920875.1| 33 VLAGPNGAGKTTTVRIFTTNLRPDA 57
                                   689********************97 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00019      0.16      18      44 ..      29      55 ..      19      68 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00019
                         AAA_30 18 drvavltGpAGtGKttalkalreawea 44
                                     + vl Gp G+GKtt+++  +  ++ 
  gi|119720380|ref|YP_920875.1| 29 GELLVLAGPNGAGKTTTVRIFTTNLRP 55
                                   45899*************998655544 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00022      0.19      16      39 ..      23      46 ..      14      60 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00022
                         AAA_29 16 tieidlkg.atlltGpsGsGKSTll 39
                                   ++e + kg   +l+Gp+G+GK+T +
  gi|119720380|ref|YP_920875.1| 23 SLEAR-KGeLLVLAGPNGAGKTTTV 46
                                   55555.445899***********76 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00022      0.19       4      41 ..      32      69 ..      30      70 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00022
                                   EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSS CS
                          SRP54  4 illvGlqGaGKTttlaKLaallkkegkkvllvaaDtfR 41
                                   ++l+G++GaGKTtt+      l+ ++ ++ +   D+ R
  gi|119720380|ref|YP_920875.1| 32 LVLAGPNGAGKTTTVRIFTTNLRPDAGEARVLGYDVVR 69
                                   789***********987777777766666666666655 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1    0.0006      0.51       7      32 ..      25      51 ..      19      63 .. 0.75
   2 ?   -2.1   0.0         5   4.3e+03      57      77 ..     175     195 ..     145     244 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0006
                         AAA_19  7 alkekvllvtaGp.GtGKTrvlkhiva 32
                                   +++++ llv+aGp G GKT++++   +
  gi|119720380|ref|YP_920875.1| 25 EARKGELLVLAGPnGAGKTTTVRIFTT 51
                                   55666777777777*******987655 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 5
                         AAA_19  57 elrerlaalgaeatTiHrlal 77 
                                     lrerl+      +T H +++
  gi|119720380|ref|YP_920875.1| 175 ALRERLRDGSSILMTTHDMGE 195
                                    455555544444666666654 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0    0.0046       3.9      24      43 ..      29      49 ..      16      54 .. 0.80
   2 ?    2.0   0.0      0.16   1.4e+02     325     365 ..     153     192 ..     139     193 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0046
                         AAA_15 24 e.ltvliGkNnsGKSsileal 43
                                     l vl G+N++GK++ ++++
  gi|119720380|ref|YP_920875.1| 29 GeLLVLAGPNGAGKTTTVRIF 49
                                   3599************99876 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.16
                         AAA_15 325 villiEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                     +l+++EP   L  +  ++++++l+e ++d++  +++tTH 
  gi|119720380|ref|YP_920875.1| 153 EVLFLDEPTEGLDVEVRREVWRALRERLRDGS-SILMTTHD 192
                                    57899**************************9.9******5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 1819.36
//
Query:       gi|119720381|ref|YP_920876.1|  [L=348]
Description: hypothetical protein Tpen_1476 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       232  (0.0129399); expected 358.6 (0.02)
Passed bias filter:                      191  (0.0106531); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2427.47
//
Query:       gi|119720382|ref|YP_920877.1|  [L=154]
Description: PilT domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.1e-14   52.0   0.0    1.2e-13   51.6   0.0    1.2  1  PIN       PIN domain
    0.00085   20.1   0.1     0.0012   19.6   0.0    1.5  1  PIN_3     PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.6   0.0   1.4e-17   1.2e-13       2     109 ..       8     126 ..       7     131 .. 0.90

  Alignments for each domain:
  == domain 1  score: 51.6 bits;  conditional E-value: 1.4e-17
                                    EE-HHHHHHHH.TTSHHHHHHHHHHHTS....SEEEEEHHHHHHHHHHHHS......SCHCHHHHHHHHHHHHHHHTSEE CS
                            PIN   2 vlDTsvliall.rgeekaeaarklleel....eelvtsalvlaEllyvlar......rkskrekaaelvelllllsalki 70 
                                     lDTsv+++++  + + +++a+  + +l     e +++  vlaE++yv+ar        + ++ a +lv +l +l+++++
  gi|119720382|ref|YP_920877.1|   8 ALDTSVIVEYIdARGDLHRQAELVFSALlsgrLEALIPHPVLAETYYVAARlyralgAGDPEGTASRLVSWLYRLPSVSV 87 
                                    59*********855555555555555557889************************99999******************* PP

                                    EEBCHHHHHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE CS
                            PIN  71 lpidaeiaeeaaeialkygllpnDaliaAtAkehgikli 109
                                     + + e+a ea++++++yg+ + D++++A+A+ + +k++
  gi|119720382|ref|YP_920877.1|  88 PEGGVELAVEAGRVKARYGVALTDCYVLAVARVYACKAL 126
                                    ************************************987 PP

>> PIN_3  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   1.3e-07    0.0012       1      55 [.       6      61 ..       6     127 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.3e-07
                          PIN_3  1 rvvlDtnvlldallfdsp...aarkildaletgaitlvvsprlldElervlarelayp 55
                                   rv lDt+v+++++  ++     a+ +++al +g++++++   +l E ++v+ar   y+
  gi|119720382|ref|YP_920877.1|  6 RVALDTSVIVEYIDARGDlhrQAELVFSALLSGRLEALIPHPVLAETYYVAARL--YR 61
                                   899********9999998999******************************998..44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 1070.62
//
Query:       gi|119720383|ref|YP_920878.1|  [L=85]
Description: AbrB family transcriptional regulator [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-10   41.1   2.0    1.1e-10   41.1   2.0    1.6  2  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
  ------ inclusion threshold ------
      0.027   14.9   0.0      0.028   14.9   0.0    1.2  1  PrlF_antitoxin  prlF antitoxin for toxin YhaV_toxin
      0.048   13.8   0.0      0.064   13.4   0.0    1.2  1  AbrB-like       AbrB-like transcriptional regulator
       0.14   12.3   0.7       0.27   11.3   0.1    1.7  2  SymE_toxin      Toxin SymE, type I toxin-antitoxin system


Domain annotation for each model (and alignments):
>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   2.0   2.5e-14   1.1e-10       3      45 ..       5      47 ..       3      48 .. 0.95
   2 ?   -1.9   0.1       0.8   3.6e+03      16      24 ..      77      85 .]      75      85 .] 0.82

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 2.5e-14
                                   ETTEEEEEE-CCCHHHCCEECTCEEEEEECTTCCCCCCCHHSX CS
                 MazE_antitoxin  3 vGnsgavriPkevrfelgireGdevelevdgdkiilrplkslp 45
                                   v+++g+v+iPkevr++lg+ +G+ + ++v+g + +l+p++++p
  gi|119720383|ref|YP_920878.1|  5 VSRKGQVVIPKEVREKLGLVPGTVLRVRVEGKRVVLEPVEEPP 47
                                   89**************************************988 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.8
                                   HHHCCEECT CS
                 MazE_antitoxin 16 rfelgireG 24
                                    ++lg++eG
  gi|119720383|ref|YP_920878.1| 77 LRDLGVEEG 85
                                   578999998 PP

>> PrlF_antitoxin  prlF antitoxin for toxin YhaV_toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   6.2e-06     0.028       4      46 ..       5      45 ..       2      74 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 6.2e-06
                 PrlF_antitoxin  4 ltergqttiPasvRkaLklkkgrdkiaytilddgkvvisraee 46
                                   + ++gq  iP+ vR+ L+l +g+  +  +  ++++vv++  ee
  gi|119720383|ref|YP_920878.1|  5 VSRKGQVVIPKEVREKLGLVPGT--VLRVRVEGKRVVLEPVEE 45
                                   7899****************976..555556777888876655 PP

>> AbrB-like  AbrB-like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.4e-05     0.064      32      68 ..       2      38 ..       1      40 [. 0.90

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.4e-05
                      AbrB-like 32 rvsVqknGnLliGsaYTkklgLkpGdefeIklgrkhi 68
                                   ++ V + G+++i +   +klgL pG+ ++++++ k++
  gi|119720383|ref|YP_920878.1|  2 KTVVSRKGQVVIPKEVREKLGLVPGTVLRVRVEGKRV 38
                                   578999************************9998876 PP

>> SymE_toxin  Toxin SymE, type I toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1      0.57   2.6e+03      45      52 ..       6      13 ..       3      15 .. 0.75
   2 ?   11.3   0.1   6.1e-05      0.27      31      53 ..      19      41 ..      19      42 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.57
                     SymE_toxin 45 Vmegrlvi 52
                                    ++g++vi
  gi|119720383|ref|YP_920878.1|  6 SRKGQVVI 13
                                   67899998 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 6.1e-05
                     SymE_toxin 31 eqaGFatGqpltisVmegrlvit 53
                                   e +G+ +G+ l+++V+ +r+v++
  gi|119720383|ref|YP_920878.1| 19 EKLGLVPGTVLRVRVEGKRVVLE 41
                                   679******************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       248  (0.0138323); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 623.67
//
Query:       gi|119720384|ref|YP_920879.1|  [L=517]
Description: potassium-transporting ATPase subunit A [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   2.2e-119  399.1  28.4     2e-116  389.4  28.4    2.1  1  KdpA      Potassium-transporting ATPase A subunit


Domain annotation for each model (and alignments):
>> KdpA  Potassium-transporting ATPase A subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  389.4  28.4  1.1e-120    2e-116       3     544 ..      15     515 ..      13     517 .] 0.96

  Alignments for each domain:
  == domain 1  score: 389.4 bits;  conditional E-value: 1.1e-120
                                    HHHHHHHHHHHHHHHHHHHHTT-...--SS-SHHHHHHHHHHT---.----HHHHHHHHHHHHHHHHHHHHHHHHTTTTS CS
                           KdpA   3 llllllllalplgkylakvfegektlldkllkpverllyrllgvdeeeemtwkeYalalllfnlvlllllylllrlqgvl 82 
                                    ll+ + l+a +lg+ + k++ + ++   ++l+ +e  ++ +l+vd++ + +w+eY+++ll++n+++++l++l l+lqgv+
  gi|119720384|ref|YP_920879.1|  15 LLVSVSLAASLLGRLISKLVVDWHRNPPEALALIEGRVLGALRVDTKPKTSWREYLASLLALNFASIALATLALYLQGVV 94 
                                    6677889999********8777777788899***********************************************99 PP

                                    S--SS------HHHHHHHHHHHHTT-----S-HHHH--HHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHS-S-S----HH CS
                           KdpA  83 plnpeglealspdlafntavSFvtntnlQhYsgestlsylsqmlgltvlnFvsaatGlavavalirglarketkelGnfy 162
                                           + +s dlafntavS vtnt lQhY ge+ ls l q+l+++ + Fv++atGl+vava++r+l+  e    Gnf+
  gi|119720384|ref|YP_920879.1|  95 RAG----PPVSLDLAFNTAVSLVTNTGLQHYVGERDLSALLQVLVVIPMSFVASATGLSVAVAFMRSLVVGE---PGNFF 167
                                    887....789**********************************************************9765...9**** PP

                                    HHHHHHHHHTHHHHHHHHHHHHHHHT--------EEEE-SSS-EEEE--SSHHHHHHHHHHTT----SSSSTTTSTTTS- CS
                           KdpA 163 vdlvrailrvLLPlslvvalllvaqGvpqtlsgkaevttlegakqtialGpvAsleaIkqlGtnGGGffgaNsahpfenp 242
                                    +d++r++l v  P+s+++al+lva+Gvp                     GpvAsl+aIk lG+ G G+fgaNsahp+enp
  gi|119720384|ref|YP_920879.1| 168 ADFLRSLLVVYAPISVLAALALVAAGVP--------------------AGPVASLVAIKLLGNVGAGYFGANSAHPLENP 227
                                    **************************97....................59****************************** PP

                                    SHHHHHHHHHHHHHHHHHHHHHHHHHTS-THHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHH..-----TTB-SSS-H CS
                           KdpA 243 taltnlleilaillipaalvftfGrmvkdkrqglailavmlvlflvllvvvvvaeaagnpalaeeqaggnmeGkEvrfGi 322
                                    +altn++e++++ll+p++l+f++ r++++ r g+ ++a+ lvl+ +ll+++     +g p+l +        G E r+G 
  gi|119720384|ref|YP_920879.1| 228 SALTNFFEAFLMLLVPLSLPFAYERIAGRGR-GYSLYAIDLVLLSLLLAIA---PLSGFPLLGR--------GVEPRLGG 295
                                    ****************************998.9999999998888777655...6678899877........******** PP

                                    HHHHHHHHHHHHTT----SS-GGGS-HHHHHHHHHHHHTS-TT-TTTHHHHHHHHHHHHHHHHHHHHHTS--EETTEE-- CS
                           KdpA 323 aasalfavvttatstGavnamhdsltplgglvpllnmmlevvfGGvGvGllnllvfvilavFiagLmvGrtPeylgkkie 402
                                    + + +f+vv+  t+tGa  +++  + p +  + l+ m+++ ++G    G+++l v+v++ vFi +LmvG+tP +lg+ ++
  gi|119720384|ref|YP_920879.1| 296 SPTLIFNVVSALTNTGATSSSLTPMGPSAVSSILMGMFIQSAPG-SALGFVYLTVYVVIVVFIGSLMVGKTPRFLGRAVS 374
                                    ****************************************9986.579******************************** PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHTTSHHHTT--S-THHHHHHHHHHHHHHHTT-----S-S---SHHHHHHHHHHHHH CS
                           KdpA 403 arevklaalaiLvhpllilvgtalalalpalaslsnpgahglsevLYeftSaaanNGSafeGlgdntvfwnltlglamll 482
                                     r +k+a+ ++Lvhp++ilv+t +a ++ a   l  pg+  +++vL ef+Saa+n G ++ G ++nt+fwn++++++mll
  gi|119720384|ref|YP_920879.1| 375 PRAIKYAVALFLVHPVIILVPTVVAQLTGACGFLGPPGPATFTKVLLEFSSAASNTGMSYLGDAANTPFWNVSTAIVMLL 454
                                    ****************************99999*********************************************** PP

                                    HHHHHHHHHHHHHHHHHTS------TT---SSHHHHHHHHHHHHHHHHHHHHHHHHHTTHHH CS
                           KdpA 483 gRflpiiavlaiAgslaakkkvpesagtlktdtplFvvllvgvilivgaLtFlPalaLGPia 544
                                    gR++pi+++l+iA+ la   +v +    ++t++ lFv++ + +il++  LtF+P++a+GP+a
  gi|119720384|ref|YP_920879.1| 455 GRYVPIALMLLIAEDLAGTPPV-SLPDPVETRGLLFVAFSTLMILVLFLLTFFPFIAIGPLA 515
                                    *******************999.67899********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (517 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 3406.09
//
Query:       gi|119720385|ref|YP_920880.1|  [L=701]
Description: K+-transporting ATPase, B subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.1e-40  137.6   5.2    6.2e-40  136.6   0.6    2.4  2  E1-E2_ATPase    E1-E2 ATPase
    2.5e-32  112.9   0.9    5.4e-32  111.8   0.9    1.6  1  Hydrolase       haloacid dehalogenase-like hydrolase
    9.6e-10   38.6   0.9      2e-05   24.5   0.1    2.2  2  Hydrolase_3     haloacid dehalogenase-like hydrolase
    2.1e-05   25.0   0.4    0.00071   20.0   0.1    3.3  3  HAD             haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.016   14.5   0.3      0.038   13.3   0.3    1.5  1  Hydantoinase_A  Hydantoinase/oxoprolinase
      0.025   14.7   0.0      0.085   13.0   0.0    1.9  1  Hydrolase_6     Haloacid dehalogenase-like hydrolase
      0.046   13.7   0.1       0.26   11.3   0.0    2.2  2  DNA_photolyase  DNA photolyase
      0.083   12.3   0.2        0.2   11.0   0.2    1.6  1  AroM            AroM protein
       0.12   12.4   0.1       0.34   11.0   0.1    1.7  1  HAD_2           Haloacid dehalogenase-like hydrolase
       0.12   12.2   0.0       0.26   11.1   0.0    1.5  1  Aminotran_4     Amino-transferase class IV


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.6   0.6   3.5e-43   6.2e-40       7     179 ..     101     271 ..      95     273 .. 0.96
   2 ?    2.5   0.4      0.05        89     113     167 ..     598     655 ..     573     660 .. 0.68

  Alignments for each domain:
  == domain 1  score: 136.6 bits;  conditional E-value: 3.5e-43
                                    EEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-SEEE-TTTS---S-EE-G-TTEE-TT-EEEE-EEEEEEE CS
                   E1-E2_ATPase   7 akvirdgteeeidakelvpGDivllkagdrvpaDgrivegsaevdesaLTGEslpvekekgdmvfsGtvvvsgeakavVt 86 
                                    a+++ ++++++++++elvpGD+v++ +g+ vp Dg ++eg a vdes+LTGEs+pvek+k d+v++Gt vv+g+++++++
  gi|119720385|ref|YP_920880.1| 101 AHKLVGDRVVDVRSSELVPGDVVVVGEGEYVPRDGYVLEGIAYVDESMLTGESEPVEKKKDDRVIGGTRVVRGRIRVEIV 180
                                    566788999*********************************************************************** PP

                                    E-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHHHHS-TTHHHH CS
                   E1-E2_ATPase  87 atgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgkslaeallralallvaaiPcaLpla 166
                                    a   +++++++++l+++ak+ k + + +l+ l + l+++ l+i++ +++++ ++g++     + a+a+lva +P  ++ +
  gi|119720385|ref|YP_920880.1| 181 AEPGKSYIDRLMALIQTAKRPKMKSEVMLSILLGGLSLTFLVITASLYFALRSVGGW--ADPVLAVAFLVALMPTTIGGL 258
                                    ***************************************************999999..5999***************** PP

                                    HHHHHHHHHHHHH CS
                   E1-E2_ATPase 167 vplalalgarrla 179
                                    +p + ++g++rl+
  gi|119720385|ref|YP_920880.1| 259 LPAIGVAGVTRLM 271
                                    **********996 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.05
                                    HHHHHHHHHHHHHHHHHHHHH...HHS-STTTSSTTHHHHHHHHHHHHHS-TTHHHHH CS
                   E1-E2_ATPase 113 kkldklgkvlvpvvlliallv...flialllgkslaeallralallvaaiPcaLplav 167
                                     +++ ++k+++++ +++a  +     ++++  +s+  a+l ++ +  ++iP  +pla+
  gi|119720385|ref|YP_920880.1| 598 SIMNDIAKYFTIFPMIVARSFpqlSWLNFMGLHSPESAILATMIFNAVIIPSLIPLAL 655
                                    35666777777666666655410045556666777799**************999986 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.8   0.9     3e-35   5.4e-32       1     210 []     289     549 ..     289     549 .. 0.75

  Alignments for each domain:
  == domain 1  score: 111.8 bits;  conditional E-value: 3e-35
                                    SSEEEEESBTTTBCHHHHHHHHHHHH.....CHHHHHHHHHH.HHCHHHHHHHHHHHHH.............HHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxx.xxxxxxxxxxxxxxxx.............xxxxxxxx RF
                      Hydrolase   1 iktvvfDkdGTLttgepsvedvivsa.....alalaaaletg.sehpigkalvaaakar.............sgaltgfa 61 
                                    ++++vfDk+GT+t+g++s + +i+       ++a aa l+ +  +++ g  +++ ak               s       
  gi|119720385|ref|YP_920880.1| 289 VDVIVFDKTGTITEGSRSAVAFIPLKnyterDVAVAAYLASVgDRTHEGISIIELAKSKgyvpedllvnealS------- 361
                                    689**********************999988888888888889888888888888888877854444433320....... PP

                                    HETTTE...............................................HHHHTHHHHHHHHHCHHHHHHHHHHHH CS
                                    xxxxxx...............................................xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase  62 tfigrg...............................................ayaigkpewltaldippdlgaaigsaq 94 
                                        r                                                +                          
  gi|119720385|ref|YP_920880.1| 362 ---ARKisfdvrtrfsgvefswyrrkspfagtvtplsevsrrilearergervT-------------------------- 412
                                    ...222344444433333344444444444444444444444444333334443.......................... PP

                                    HHCHHHHHH........................................TTHHHHHHHHHHTHHBHTTHHHHHHHHHHTT CS
                                    xxxxxxxxx........................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase  95 sqgrtvall........................................qaralavftiadplkvkpeaaeavasLkaag 134
                                           +                                         +++a++v+ ++d   +k++++e +++Lk++g
  gi|119720385|ref|YP_920880.1| 413 -------VIkgsvdsvlevvredratreaiariveevgrrgetpllvalNDEAVGVVVLKDR--IKEGVKEKIRRLKKMG 483
                                    .......4455555555555556666666666666777777777777**99***********..**************** PP

                                    EEEEEEESSEHHHHHHHHHHTTGGGESEEEEHHCES.STTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase 135 ievvlltgdnpetaeraanqlGddyfdaviasdiet.vakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                    +++v++tgdnp tae++a+++G           i+  va ++pe+k++ ++e q +++ va+ GDg nDa+ala+A+
  gi|119720385|ref|YP_920880.1| 484 VKLVMITGDNPVTAEAIAREVG-----------IKHyVARAKPEDKLRRVEEEQLEGHVVAVLGDGTNDAPALAKAD 549
                                    **********************...........7777**************************************98 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.1   5.1e-05     0.091      14      58 ..     466     510 ..     463     513 .. 0.93
   2 !   24.5   0.1   1.1e-08     2e-05     203     242 ..     529     568 ..     520     579 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.1e-05
                                    S---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEE CS
                    Hydrolase_3  14 kkisektkeaikklkekgikvviATGRslravlpvleelgldlpv 58 
                                     +i+e  ke i++lk+ g+k+v  TG ++++++ +++e+g++ +v
  gi|119720385|ref|YP_920880.1| 466 DRIKEGVKEKIRRLKKMGVKLVMITGDNPVTAEAIAREVGIKHYV 510
                                    569999************************************877 PP

  == domain 2  score: 24.5 bits;  conditional E-value: 1.1e-08
                                    GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEE CS
                    Hydrolase_3 203 leeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyv 242
                                       v++ GDg ND + L +a++g+Am+++++ +k+aA+++
  gi|119720385|ref|YP_920880.1| 529 GHVVAVLGDGTNDAPALAKADVGIAMNSGTRAAKEAANMI 568
                                    5668999******************************997 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.69   1.2e+03      99     136 ..     215     250 ..     181     288 .. 0.66
   2 ?   -1.2   0.0       1.3   2.4e+03      89     119 ..     396     426 ..     378     441 .. 0.77
   3 !   20.0   0.1   3.9e-07   0.00071      83     187 ..     466     545 ..     444     546 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.69
                            HAD  99 aaGdrvvvvSgglrplvepllaelg.adevlatelevdd 136
                                        ++ v++++l + ++ +    g ad vla  + v  
  gi|119720385|ref|YP_920880.1| 215 GLSLTFLVITASLYFALRSVG---GwADPVLAVAFLVAL 250
                                    445578999*******99999...888888887666555 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.3
                            HAD  89 galellaahraaGdrvvvvSgglrplvepll 119
                                    ++ +++ ++r++G rv+v+ g+ + ++e + 
  gi|119720385|ref|YP_920880.1| 396 EVSRRILEARERGERVTVIKGSVDSVLEVVR 426
                                    6677777899********9999999998776 PP

  == domain 3  score: 20.0 bits;  conditional E-value: 3.9e-07
                            HAD  83 pklldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelglegkpvrgegkvaalrewl 162
                                     + +++g++e +++ ++ G+++v+++g +   +e++++e+g    + +      ++ +         + e+k+++++e  
  gi|119720385|ref|YP_920880.1| 466 DR-IKEGVKEKIRRLKKMGVKLVMITGDNPVTAEAIAREVG----IKH------YVARA--------KPEDKLRRVEE-- 524
                                    34.779***********************************....988......66666........78889999999.. PP

                            HAD 163 aaegegidleevvayGDspsDlpll 187
                                        e ++ + v + GD+ +D p+l
  gi|119720385|ref|YP_920880.1| 525 ----EQLEGHVVAVLGDGTNDAPAL 545
                                    ....55666556666********98 PP

>> Hydantoinase_A  Hydantoinase/oxoprolinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.3   2.1e-05     0.038     194     273 ..     430     514 ..     423     517 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.1e-05
                 Hydantoinase_A 194 larrafeelakelnlk........veevAegilsvavenmanavrklsvergldpkeltlvvfGGaGaqhaaalaeelgv 265
                                    ++r+a++ + +e++          +++ A g++ v+++ +++ v++    r+l++  + lv+++G  ++ a+a+a+e+g+
  gi|119720385|ref|YP_920880.1| 430 ATREAIARIVEEVGRRgetpllvaLNDEAVGVV-VLKDRIKEGVKEK--IRRLKKMGVKLVMITGDNPVTAEAIAREVGI 506
                                    556666777777777777777777777777765.6788999999988..799**************************** PP

                 Hydantoinase_A 266 kkvivppy 273
                                    k++++++ 
  gi|119720385|ref|YP_920880.1| 507 KHYVARAK 514
                                    ***99875 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   4.7e-05     0.085       7      51 ..     460     504 ..     457     519 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.7e-05
                                    TTSEETTEE-TTHHHHHHHHHHTT-EEEEEE---SS-HHHHHHHH CS
                    Hydrolase_6   7 GvLwrgdkaipgaaealnalraagkpvvllTNnsskseeeyakkl 51 
                                    Gv++ +d++ +g++e +++l+++g+++v++T  +  + e++a ++
  gi|119720385|ref|YP_920880.1| 460 GVVVLKDRIKEGVKEKIRRLKKMGVKLVMITGDNPVTAEAIAREV 504
                                    9******************************99988888887665 PP

>> DNA_photolyase  DNA photolyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.4   2.5e+03      63     103 ..     405     444 ..     401     468 .. 0.60
   2 ?   11.3   0.0   0.00014      0.26      59     108 ..     476     525 ..     465     534 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.4
                                    HHTT--EEEEESSHHHHHHHHHHHCTECEEEEE---SHHHH CS
                 DNA_photolyase  63 relgirLvvrrgdpadvlpelakelgasavvanreyepder 103
                                    re+g r  v++g++ +vl e+++e  a++  + r +e  +r
  gi|119720385|ref|YP_920880.1| 405 RERGERVTVIKGSVDSVL-EVVREDRATREAIARIVEEVGR 444
                                    788888888888876654.4445555554444444444444 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00014
                                    HHHHHHTT--EEEEESSHHHHHHHHHHHCTECEEEEE---SHHHHHHHHH CS
                 DNA_photolyase  59 deeLrelgirLvvrrgdpadvlpelakelgasavvanreyepdererdea 108
                                     ++L+++g++Lv+++gd     +++a+e+g+++ va +++e + r+ +e+
  gi|119720385|ref|YP_920880.1| 476 IRRLKKMGVKLVMITGDNPVTAEAIAREVGIKHYVARAKPEDKLRRVEEE 525
                                    579**************9999******************99998887764 PP

>> AroM  AroM protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.2   0.00011       0.2      35      92 ..     428     489 ..     406     498 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00011
                           AroM  35 Dglseeeiaalape...egeavlvsrlrdGes.vvlskekveprlqaaiakleeegvdlill 92 
                                    D+ ++e+ia++  e    ge++l+  l+d    vv+ k+++++ ++++i++l++ gv+l+++
  gi|119720385|ref|YP_920880.1| 428 DRATREAIARIVEEvgrRGETPLLVALNDEAVgVVVLKDRIKEGVKEKIRRLKKMGVKLVMI 489
                                    777888887665441115699999999998766*************************9986 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00019      0.34      81     164 ..     469     541 ..     463     554 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00019
                          HAD_2  81 ydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekkKPdpeviekaleklklkkeeviyvGD 160
                                     +gvke +  Lk++g+kl  +T  +  ++e   +++gi++y      +++            + +e+ +l+ + v + GD
  gi|119720385|ref|YP_920880.1| 469 KEGVKEKIRRLKKMGVKLVMITGDNPVTAEAIAREVGIKHYVARAKPEDKL-----------RRVEEEQLEGHVVAVLGD 537
                                    68*************************************996544333333...........333555555555555555 PP

                          HAD_2 161 sptD 164
                                     ++D
  gi|119720385|ref|YP_920880.1| 538 GTND 541
                                    5555 PP

>> Aminotran_4  Amino-transferase class IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00015      0.26     130     157 ..     282     311 ..     267     316 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00015
                    Aminotran_4 130 akergad.evllvdedgnvtEgstsNv.fi 157
                                    a e+  d +v+++d+ g +tEgs+s v fi
  gi|119720385|ref|YP_920880.1| 282 AVEAAGDvDVIVFDKTGTITEGSRSAVaFI 311
                                    44444456*******************776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (701 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.68u 0.30s 00:00:00.98 Elapsed: 00:00:00.48
# Mc/sec: 4354.98
//
Query:       gi|119720386|ref|YP_920881.1|  [L=141]
Description: hypothetical protein Tpen_1481 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-11   44.8   0.1    9.5e-08   32.1   0.0    2.1  2  KdpC      K+-transporting ATPase, c chain


Domain annotation for each model (and alignments):
>> KdpC  K+-transporting ATPase, c chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.2   1.8e-05      0.31       3      29 ..      10      36 ..       8      43 .. 0.85
   2 !   32.1   0.0   5.3e-12   9.5e-08     119     181 ..      63     130 ..      60     131 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 1.8e-05
                                   HHHHHHHHHHHHHHTHHHHHHHHHHHH CS
                           KdpC  3 kalrlllvltvllgliYplavtgiaql 29
                                   ++l l   l+++lg++Yp++v++++ +
  gi|119720386|ref|YP_920881.1| 10 ASLALSATLMLVLGFAYPALVWALSLA 36
                                   67889999**************99865 PP

  == domain 2  score: 32.1 bits;  conditional E-value: 5.3e-12
                                    BSSS---EE-HHHHHHTHHHHHHHHT--HHHHHHHHHHTEE-...-SSTTT--..-EEEHHHHHHHHH CS
                           KdpC 119 SgSGLDPhIspeaAelQvarvakarglseeeveklvaenteg...rllgilGe..prVnVlklNlaLd 181
                                      SG DP + +++A  Qv+ v++++gl+ee v+++++en e+    +l +lG   + VnV+++N +L 
  gi|119720386|ref|YP_920881.1|  63 TSSGCDPFVPLDYALRQVPEVSRKTGLPEELVARVLRENAEKyraANLYVLGPgyDIVNVVEVNKELA 130
                                    57***********************************88876222567788652267*******9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 946.98
//
Query:       gi|119720387|ref|YP_920882.1|  [L=268]
Description: hypothetical protein Tpen_1482 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-09   36.5   0.0    3.9e-09   35.8   0.0    1.3  1  GATase_4  Glutamine amidotransferases class-II
     0.0002   21.6   0.0    0.00029   21.0   0.0    1.2  1  GATase_6  Glutamine amidotransferase domain


Domain annotation for each model (and alignments):
>> GATase_4  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   0.0   4.3e-13   3.9e-09      25     113 ..      37     129 ..      24     147 .. 0.76

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 4.3e-13
                       GATase_4  25 rggltdahadGwGiafye...gkaarvfkdpepsaespl.aelvreypiksk.nvvaHiRkatqGevklenthpFvRelw 99 
                                    + g+ + h dGwG+a       + ++      p  e +   e +r+  ++ + ++v+H Rka+ G+v+ +nthp    + 
  gi|119720387|ref|YP_920882.1|  37 GTGKCGRHGDGWGFAAVTleeYQRVEHYRSTIPVYEDAWgFEKLRR-ALRGEgVLVVHARKASAGSVSARNTHPIHYGWR 115
                                    567889********99886333334444455555544431466777.4665426799*********************** PP

                       GATase_4 100 grewifAHnGdlke 113
                                    g e+ +AHnG+++ 
  gi|119720387|ref|YP_920882.1| 116 GYEMFLAHNGSMRA 129
                                    ***********964 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   3.3e-08   0.00029       9      96 ..      83     174 ..      72     204 .. 0.67

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 3.3e-08
                       GATase_6   9 lv.edevalaHvRlaivglaeeega.qPfpsedgr..lllvhNGeiynykelreelpalkgla.frsrsDtevlla.lle 82 
                                    +  +++v+++H+R a+ g   ++++ +P++  +++  + l+hNG++++ + l++ l      + + + +Dt  l   +++
  gi|119720387|ref|YP_920882.1|  83 ALrGEGVLVVHARKASAGSV-SARNtHPIHYGWRGyeMFLAHNGSMRAGD-LAASLGV----PvLPDVTDTFYLGEyVYR 156
                                    44255799***********7.88888***55555444899*******995.7766666....334479999888887887 PP

                       GATase_6  83 elG....eevlerlrGmf 96 
                                    +l+      ++e++ +++
  gi|119720387|ref|YP_920882.1| 157 RLDlpgaGNLAEAFGEAA 174
                                    777544222223333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 2078.17
//
Query:       gi|119720388|ref|YP_920883.1|  [L=233]
Description: hypothetical protein Tpen_1483 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.055   14.0   2.5      0.055   14.0   2.5    2.9  3  LPAM_1    Prokaryotic membrane lipoprotein lipid attachment s


Domain annotation for each model (and alignments):
>> LPAM_1  Prokaryotic membrane lipoprotein lipid attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   2.5   3.1e-06     0.055       1      16 [.       1      16 [.       1      16 [. 0.98
   2 ?   -2.8   0.5      0.66   1.2e+04      14      17 ..     172     175 ..     172     175 .. 0.95
   3 ?    1.2   0.7     0.036   6.4e+02       5      13 ..     200     208 ..     195     208 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.1e-06
                         LPAM_1  1 MKKillalgalllLsG 16
                                   M++ ll+++al++L++
  gi|119720388|ref|YP_920883.1|  1 MRRVLLLACALAVLAA 16
                                   **************97 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.66
                         LPAM_1  14 LsGC 17 
                                    Ls+C
  gi|119720388|ref|YP_920883.1| 172 LSAC 175
                                    9*** PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.036
                         LPAM_1   5 llalgalll 13 
                                    ll+++al++
  gi|119720388|ref|YP_920883.1| 200 LLVAVALAV 208
                                    788888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1718.69
//
Query:       gi|119720389|ref|YP_920884.1|  [L=273]
Description: Mg2+ transporter protein, CorA family protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-41  142.1   0.1    1.6e-40  139.2   0.1    1.9  1  CorA             CorA-like Mg2+ transporter protein
  ------ inclusion threshold ------
      0.059   13.5   0.0        1.8    8.7   0.0    2.6  2  DUF2730          Protein of unknown function (DUF2730)
       0.87    9.7   2.1        3.4    7.8   0.0    2.4  3  Antimicrobial10  Metchnikowin family


Domain annotation for each model (and alignments):
>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.2   0.1   2.7e-44   1.6e-40      34     292 .]      25     269 ..       5     270 .. 0.83

  Alignments for each domain:
  == domain 1  score: 139.2 bits;  conditional E-value: 2.7e-44
                           CorA  34 lldseerprvedyddylllvlpsveldkseeeeeevplsillgdnflitvrreplealdevikrlk.deggkpkspgell 112
                                    ++++ er+rv++y+d l +vl ++       +++   ++ ll+ +++     +   +l  ++++++ +  g ++sp  +l
  gi|119720389|ref|YP_920884.1|  25 VARDAERTRVTAYKDALVVVLGYPG------KGR---FAALLRGDTVAVAAPRG--LLARLREDFEkNSYGCRSSPDAFL 93 
                                    5555555555555555555554432......211...23444444444333333..3567777777766799******** PP

                           CorA 113 yrlldeivdrlfellekleeeldeledeledstkkeilrelaqlrrrlvklrralapnrevlkrllakaddkllddedke 192
                                    +  l +++d++ ++ ++le+e+d led + ++ ++ ++ +  ++r +lv++rr l  +r++  +ll  +    l++ +k+
  gi|119720389|ref|YP_920884.1|  94 ALSLLRLIDEYYAYYDALEDEIDGLEDSVAEDPTRVDVARFRRVRGSLVEFRRDLYSLRAAA-SLLLGEGVYDLSEGAKR 172
                                    **************************************************************.99999************ PP

                           CorA 193 ylrdlldelerllemlealrerleslqdtyssllserlNrvmkvLTvltaiflPlTlitGiyGmNfkglPelewsygypf 272
                                    + +++++++ +ll+m+e+++erl  ++d++ s ls  lN+vmk+LT + +i lPl +i+GiyGmN + +Pe+ w+y yp+
  gi|119720389|ref|YP_920884.1| 173 LVQEVYEDAVQLLDMVESQKERLADIRDLHLSALSLALNEVMKKLTAINVIALPLLVIAGIYGMNLE-IPEARWPYAYPA 251
                                    *******************************************************************.************ PP

                           CorA 273 vlllglmallailllfwfkr 292
                                    v  l +ma l+++l + +++
  gi|119720389|ref|YP_920884.1| 252 V--LTAMATLTAILAYALRK 269
                                    *..88888888887777765 PP

>> DUF2730  Protein of unknown function (DUF2730)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0    0.0003       1.8      46      99 ..     112     161 ..     102     164 .. 0.90
   2 ?    1.7   0.1     0.045   2.7e+02      33      64 ..     179     200 ..     168     225 .. 0.58

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0003
                        DUF2730  46 dkrlteletkvenLPtakdlekLkllladlrgelkaleaevrqlshqvdLLLen 99 
                                    +  ++ le +v++ Pt++d+++     + +rg l + ++++ +l+  + LLL +
  gi|119720389|ref|YP_920884.1| 112 EDEIDGLEDSVAEDPTRVDVARF----RRVRGSLVEFRRDLYSLRAAASLLLGE 161
                                    677899**************986....68**********************965 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.045
                        DUF2730  33 edleklaekveendkrlteletkvenLPtakd 64 
                                    ed  +l ++ve++++rl++           +d
  gi|119720389|ref|YP_920884.1| 179 EDAVQLLDMVESQKERLAD----------IRD 200
                                    4455555666666666554..........444 PP

>> Antimicrobial10  Metchnikowin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.3      0.11   6.7e+02       3      21 ..     201     219 ..     200     226 .. 0.85
   2 ?   -1.8   0.1      0.56   3.4e+03       5      20 ..     217     232 ..     214     233 .. 0.80
   3 ?    7.8   0.0   0.00057       3.4       9      31 ..     249     271 ..     247     273 .] 0.92

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.11
                Antimicrobial10   3 LnlsklfllLLgllllltv 21 
                                    L ls+l l+L  ++  lt+
  gi|119720389|ref|YP_920884.1| 201 LHLSALSLALNEVMKKLTA 219
                                    789***********98886 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.56
                Antimicrobial10   5 lsklfllLLglllllt 20 
                                    l+++  + L+ll++++
  gi|119720389|ref|YP_920884.1| 217 LTAINVIALPLLVIAG 232
                                    5678888899999987 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.00057
                Antimicrobial10   9 fllLLgllllltvvlaEasRrqG 31 
                                    ++++L  +++lt++la a R+ G
  gi|119720389|ref|YP_920884.1| 249 YPAVLTAMATLTAILAYALRKRG 271
                                    5899****************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1975.97
//
Query:       gi|119720390|ref|YP_920885.1|  [L=470]
Description: extracellular solute-binding protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      9e-34  117.0   1.0    4.4e-33  114.7   0.4    2.1  2  SBP_bac_6   Bacterial extracellular solute-binding protein
    1.1e-24   87.7   0.2    1.1e-24   87.7   0.2    2.1  2  SBP_bac_8   Bacterial extracellular solute-binding protein
    6.3e-22   78.9   3.2    6.3e-22   78.9   3.2    2.0  2  SBP_bac_1   Bacterial extracellular solute-binding protein
    2.9e-19   69.7   0.0    1.7e-18   67.3   0.0    2.0  2  SBP_bac_11  Bacterial extracellular solute-binding protein


Domain annotation for each model (and alignments):
>> SBP_bac_6  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0     0.078   3.5e+02      97     152 ..      36      91 ..      24      95 .. 0.76
   2 !  114.7   0.4   9.8e-37   4.4e-33       3     218 ..      96     313 ..      94     331 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.078
                      SBP_bac_6  97 sdlfealllalykdfg.edgvkkllrnlkanlhpaq.mvkaagslesgepavsvvpyf 152
                                    +++ ++l+l++  ++  +++v++ ++n+++n   +   vk +++ +++   ++ ++++
  gi|119720390|ref|YP_920885.1|  36 QQYENTLVLITPSNTLlLKAVTTAFKNYAKNKLGVDvDVKLIQAGSPEC--MNRIIAW 91 
                                    67888888888886666**************999998888888888776..6666666 PP

  == domain 2  score: 114.7 bits;  conditional E-value: 9.8e-37
                      SBP_bac_6   3 lpdlilsfdkdflekfieeglfqpld..panlpnvnkdfaeeglkdpdgkyypygvgplvlavnkdrlkgrpv..PksWa 78 
                                     +d++++ d  ++ k++e+gl++ ++  ++  + ++  f    lkdpd  + p  +   ++++n+++l+++ +  Pk+W+
  gi|119720390|ref|YP_920885.1|  96 EADIFFGGDLIYHWKLKEKGLLESYKpkSPGYDAIPSTFLGFPLKDPDEMWHPKLWWGHGFMYNTKVLEKLGLqpPKTWD 175
                                    589**999999**************97777889999999999***************************9999989**** PP

                      SBP_bac_6  79 DLldPeykgkvalpgnngsdlfealllalykdfgedgvkkllrnlkanlhpaq..mvkaagslesgepavsvvpyffadi 156
                                    DLldP++k+ ++++++++s++ ++ + ++ ++ g+d++++++r l+an+      + + ++ +++ge  + v+++++  +
  gi|119720390|ref|YP_920885.1| 176 DLLDPKWKDLIVMCTPSRSSSTYINVGIIIQNRGWDQGWAFWRRLAANVGAFVqrSADVVDLVSKGE--YAVGFAYSQGA 253
                                    ******************9999999999999*****************998777*************..*********** PP

                      SBP_bac_6 157 lpekkkgknlkvvwPedGalvspifmlvkkgkkkelakafidfllspevqailakaggvfPv 218
                                    + +++ g ++ +  +  G +vs +++l+ +  +++ akaf+d+ + +++q++   agg +Pv
  gi|119720390|ref|YP_920885.1| 254 IINRYNGYPVSMYMDPTGFIVSGVSLLKGAP-HPNIAKAFLDWWYTEDAQQAALSAGG-IPV 313
                                    *****999***********************.****************9888777777.776 PP

>> SBP_bac_8  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.7   0.2   2.5e-28   1.1e-24       4     269 ..      61     318 ..      58     331 .. 0.80
   2 ?    2.0   1.4     0.033   1.5e+02     140     194 ..     360     420 ..     328     440 .. 0.66

  Alignments for each domain:
  == domain 1  score: 87.7 bits;  conditional E-value: 2.5e-28
                                    HHHHHH-.T..EEEEEEE--SSSHHHHHHHHHHTT---SEE.EEE-HHHH..HHHHHTTSB--GG.GSTTHHH-HHHHHT CS
                      SBP_bac_8   4 kefekkt.g..vkvnvvtaasndleqklkaalaagtapdidvvwanedal..atlaeeglladls.dldnlddltdalaa 77 
                                    k + k + g  v+v++++a+s++ ++ + a    g+ p++d++++ +d +  ++l+e+gll+  + +++ +d +++++ +
  gi|119720390|ref|YP_920885.1|  61 KNYAKNKlGvdVDVKLIQAGSPECMNRIIAW--NGK-PEADIFFG-GDLIyhWKLKEKGLLESYKpKSPGYDAIPSTFLG 136
                                    66777666666999****************4..466.56676655.67761156677*****999899************ PP

                                    T...--TS.----EEEEEEE-EEEEEHHHHHHS...---BHHHHHHHHHHHHHH-SEGG---G..GGGGGTHHETTEE-- CS
                      SBP_bac_8  78 v...gydgklygvPyasetpyvliynkdlleka..edpktwdellaaakklkgkfglpdpasg..wlqaallakdgksld 150
                                    +   + d    + P  +   ++++yn+++lek   ++pktwd+ll+  +k+k  + + +p+ +  +++   ++       
  gi|119720390|ref|YP_920885.1| 137 FplkDPDE--MWHPKLWWG-HGFMYNTKVLEKLglQPPKTWDDLLD--PKWKDLIVMCTPSRSssTYINVGII------- 204
                                    *8766677..999999985.9**********84667**********..****999885555431244444444....... PP

                                    -H..HHH.HHHHHHHHHHHHTT-.EE-S..--SSTTTTTSBSEEEE-TTHHHHHH-TTTSEEEE--S--EEEEEEEEEEB CS
                      SBP_bac_8 151 ddggkdglkealellkklkdngk.tydtgadavsefanGevaftingswdiaaaqkagkklgaivpkqgsfaggkglavp 229
                                      +++ g+++ +++++ l +n+  +++ +ad+v+++ +Ge+a ++++s+ ++  + +g ++ + + ++g ++ g  +  +
  gi|119720390|ref|YP_920885.1| 205 --IQNRGWDQGWAFWRRLAANVGaFVQRSADVVDLVSKGEYAVGFAYSQGAIINRYNGYPVSMYMDPTGFIVSG--VSLL 280
                                    ..1489*************9976599*********************999999998899998877567877776..6779 PP

                                    TTS-HHHHHHHHHHHHHTTSHHHHHHHHHH---BS-S-TT CS
                      SBP_bac_8 230 knaknedlaAldFlkwltspenqaalaektgyipvnksaa 269
                                    k+a+++++ A++Fl w++++++q+a     g ipv++++ 
  gi|119720390|ref|YP_920885.1| 281 KGAPHPNI-AKAFLDWWYTEDAQQAALS-AGGIPVLPTVK 318
                                    *******9.************9998888.55566666554 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.033
                                    GTHHETTEE---H.....HHH.HHHHHHHHHHHHTT-EE....-S...--SSTTTTTSBSEEE CS
                      SBP_bac_8 140 allakdgksldddg...gkdglkealellkklkdngkty....dtg.adavsefanGevafti 194
                                    a++  +  +  d++      +lk+a+  + + ++++k +        a+a+s+f +G++a++ 
  gi|119720390|ref|YP_920885.1| 360 AMYT-NISKIFDNTivaKHSELKDAWSTILSVQAKVKGVpdaeA-KlAQAISAFDKGDYATAK 420
                                    3333.444444444466667789999999999999887655433.247999999999998765 PP

>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.9   3.2   1.4e-25   6.3e-22      10     315 .]      52     303 ..      45     303 .. 0.82
   2 ?   -1.1   0.2      0.31   1.4e+03     202     237 ..     387     418 ..     315     448 .. 0.58

  Alignments for each domain:
  == domain 1  score: 78.9 bits;  conditional E-value: 1.4e-25
                                    HHHHHHHHH.....HHHHTTEEEEEEEECHHHHHHHHHHHHHTTSSSCSEEEE..CGGHHHHHHHTTSBECCHHHHHHTT CS
                      SBP_bac_1  10 lqalvakaf.....ekehpgikVeiesvgsgslaqkltlaiaaGdgpaDviav..dndwiarlakaglllpldpyvkayl 82 
                                    l ++v++af     +k++ +++V++++ gs + ++  ++   +G+++aD++++    +++ +l+++gll+   p    y 
  gi|119720390|ref|YP_920885.1|  52 LLKAVTTAFknyakNKLGVDVDVKLIQAGSPECMN--RIIAWNGKPEADIFFGgdLIYHW-KLKEKGLLESYKPKSPGYD 128
                                    556666776666779********************..99999999********6544444.46788********999995 PP

                                    ECTTCCTEEEEHHHHTHHHHCEEE.ESEEEEE.EEEEEEETTTHHCTTGGGSHBHHHHHHHHHHHHHHCTCTHCCHCCEE CS
                      SBP_bac_1  83 apgvkdaadklsssvlpkildskv.lyvPlya.argliYNkdlfekagldppwtWdelveaakklkekgkkpiggarggs 160
                                    a           s +l+  l + +  + P      g++YN++++ek gl+pp+tWd+l+++  k     ++p       s
  gi|119720390|ref|YP_920885.1| 129 AIP---------STFLGFPLKDPDeMWHPKLWwGHGFMYNTKVLEKLGLQPPKTWDDLLDPKWKDLIVMCTP-------S 192
                                    544.........556666666422433455544*********************************999999.......7 PP

                                    HHHHHHHHHHHHHHHHTGGGEECCCTHHCSHHHHSHHHHHHHHHHHHHHHHHHHTTEEECSSHHHHHHHHHTTSCSEEEE CS
                      SBP_bac_1 161 asgtayyfalalakslggkvfdkdgggldnpegvtaatylvklyavanltkelkgkgaenkdgaaalalfeaGeaamaiv 240
                                     s  +y++   ++++ g                        + +++a++ +  +++ga  + +a++++l+++Ge a++++
  gi|119720390|ref|YP_920885.1| 193 RSSSTYINVGIIIQNRG------------------------WDQGWAFWRRLAANVGAFVQRSADVVDLVSKGEYAVGFA 248
                                    77777777777777777........................778888999****************************** PP

                                    EHHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEEEEEEEEEEBTTCSTHHHHHHHHHHHTSHHHHH CS
                      SBP_bac_1 241 glwaalaamkvapkvafaadkekpkeelgvaplPagkggkpgilgayglaipkgsknpeaAkkFldfllspeaqa 315
                                    ++  a    + +++++  + +++ ++                  +++g+ ++kg+++p  Ak+Fld+ ++++aq+
  gi|119720390|ref|YP_920885.1| 249 YSQGA--IINRYNGYPVSMYMDPTGF------------------IVSGVSLLKGAPHPNIAKAFLDWWYTEDAQQ 303
                                    *9994..4445666666666666666..................****************************995 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.31
                                    HHHHHHHHHHHHHTTEEECSSHHHHHHHHHTTSCSE CS
                      SBP_bac_1 202 klyavanltkelkgkgaenkdgaaalalfeaGeaam 237
                                     l     ++++ kg++ ++++ a+a ++f +G+ a 
  gi|119720390|ref|YP_920885.1| 387 ILS----VQAKVKGVPDAEAKLAQAISAFDKGDYAT 418
                                    222....44555666666666666666666665554 PP

>> SBP_bac_11  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.3   0.0   3.7e-22   1.7e-18      12     228 ..      52     309 ..      42     309 .. 0.78
   2 ?   -0.7   0.2      0.22   9.7e+02     113     149 ..     400     435 ..     372     458 .. 0.56

  Alignments for each domain:
  == domain 1  score: 67.3 bits;  conditional E-value: 3.7e-22
                                    HHHHHHHHHHHHH-......--EEEEESSHHHHHHHH..HHH...-SEEEESSH.HHHHHHHHGGGGG.....GG-EEEE CS
                     SBP_bac_11  12 alrelaaaFeahtg......vkvevsaggsgklarqi..adga.rpDvwipassawlellaaaglvqa.....esavpla 77 
                                     l+++  aF+++ +      v+v++  +gs +++++i   +g+ ++D+++ ++  +  +l+++gl+ +     + + ++ 
  gi|119720390|ref|YP_920885.1|  52 LLKAVTTAFKNYAKnklgvdVDVKLIQAGSPECMNRIiaWNGKpEADIFFGGDLIYHWKLKEKGLLESykpksPGYDAIP 131
                                    56666666665333346788999**************6433448************************665443333334 PP

                                    EEEEEEEESTT-T..........................T---SHHHHHHSS--..EEEE--T-TTTTHH.HHHHGGG-- CS
                     SBP_bac_11  78 ssplviavpkgnp..........................kkikgwadLlkpglk..lavadPttspsGlaalalleaaga 129
                                    s+ l +  +   p                          +++k+w+dLl+p++k  +++ +P++s+s +  ++++ +  +
  gi|119720390|ref|YP_920885.1| 132 STFLGFPLKD--PdemwhpklwwghgfmyntkvleklglQPPKTWDDLLDPKWKdlIVMCTPSRSSSTYINVGIIIQNRG 209
                                    4445555544..44466668888888888888888888789************777********9999955555554322 PP

                                    ....HHHHHHHHHTEEEEESSHHHHHHHHHTTT-SEEEEEHHHHH..HSTTSSEEE.E--TTT--...EEEEEEEE-TT- CS
                     SBP_bac_11 130 ....qellkalekkvvklgessrqlltaveageadagivyeseakaaengdkleav.ylpeglnldpldypaavlkkaak 204
                                         +++++l+ +v  +++ s ++++ v  ge+++g++y + a+ +    + ++  y  ++     ++ ++ +lk+a++
  gi|119720390|ref|YP_920885.1| 210 wdqgWAFWRRLAANVGAFVQRSADVVDLVSKGEYAVGFAYSQGAIINR-YNGYPVSmYMDPTGF---IVSGVSLLKGAPH 285
                                    466688************************************999775.555555535555554...5899********* PP

                                    -HHHHHHHHHTTSHHHHHHHHHTT CS
                     SBP_bac_11 205 reaAraFlafLrspeaqailrkyG 228
                                    ++ A+aFl++ ++++aq+++ ++G
  gi|119720390|ref|YP_920885.1| 286 PNIAKAFLDWWYTEDAQQAALSAG 309
                                    *******************99887 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.22
                                    -TTTTHH.HHHHGGG--HHHHHHHHHTEEEEESSHHH CS
                     SBP_bac_11 113 tspsGlaalalleaagaqellkalekkvvklgessrq 149
                                    +++   +a++++++ g+++++kal+  ++k +e++  
  gi|119720390|ref|YP_920885.1| 400 AEAKLAQAISAFDK-GDYATAKALALEAAKIAETAPK 435
                                    23333344444444.4444444444444444444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (470 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       670  (0.0373696); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 3291.27
//
Query:       gi|119720391|ref|YP_920886.1|  [L=358]
Description: ABC transporter related [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      5e-38  130.7   0.0    8.2e-38  130.0   0.0    1.3  1  ABC_tran      ABC transporter
    1.5e-12   47.6   1.5    2.2e-07   31.1   0.0    2.7  2  TOBE          TOBE domain
    1.6e-12   47.4   0.1    6.1e-12   45.5   0.1    2.1  1  TOBE_2        TOBE domain
    8.2e-10   39.0   0.1    0.00042   20.2   0.0    2.3  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
      0.001   19.5   0.0     0.0015   19.0   0.0    1.4  1  AAA_16        AAA ATPase domain
     0.0011   18.9   1.0       0.01   15.7   0.2    2.5  2  TOBE_3        TOBE-like domain
     0.0014   18.6   0.0     0.0024   17.8   0.0    1.3  1  Rad17         Rad17 P-loop domain
     0.0043   16.5   0.1       0.14   11.5   0.0    2.1  2  SMC_N         RecF/RecN/SMC N terminal domain
  ------ inclusion threshold ------
       0.01   16.3   0.1      0.051   14.0   0.1    2.1  1  AAA           ATPase family associated with various cellular 
      0.014   15.3   0.0      0.025   14.5   0.0    1.3  1  RsgA_GTPase   RsgA GTPase
      0.015   15.3   0.0      0.037   14.0   0.0    1.6  1  AAA_5         AAA domain (dynein-related subfamily)
      0.024   13.8   0.0      0.029   13.5   0.0    1.2  1  G-alpha       G-protein alpha subunit
      0.028   14.1   0.0      0.052   13.3   0.0    1.4  1  AAA_29        P-loop containing region of AAA domain
      0.029   13.7   0.0      0.072   12.5   0.0    1.6  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.033   13.9   0.0      0.064   13.0   0.0    1.4  1  AAA_30        AAA domain
      0.034   14.1   0.3       0.07   13.0   0.1    1.6  2  NACHT         NACHT domain
      0.039   14.0   0.0      0.091   12.8   0.0    1.6  1  AAA_14        AAA domain
       0.04   14.4   0.0        0.1   13.1   0.0    1.6  2  AAA_23        AAA domain
      0.045   13.3   0.0      0.098   12.2   0.0    1.6  1  AAA_25        AAA domain
      0.049   13.6   0.0      0.077   13.0   0.0    1.2  1  MIT_C         Phospholipase D-like domain at C-terminus of MI
      0.062   13.8   0.0       0.25   11.9   0.0    2.1  2  AAA_18        AAA domain
      0.068   13.3   0.2          1    9.5   0.1    2.2  2  MotA_activ    Transcription factor MotA, activation domain
       0.09   12.7   0.0       0.17   11.8   0.0    1.4  1  ATPase_2      ATPase domain predominantly from Archaea
       0.13   12.5   0.3       0.33   11.2   0.0    1.7  2  AAA_22        AAA domain
       0.13   11.4   0.0       0.22   10.7   0.0    1.3  1  NB-ARC        NB-ARC domain
       0.14   11.9   0.0       0.27   11.0   0.0    1.3  1  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
       0.17   12.1   0.0       0.45   10.7   0.0    1.7  1  AAA_28        AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.0   0.0   1.2e-40   8.2e-38       1     136 [.      19     161 ..      19     162 .. 0.97

  Alignments for each domain:
  == domain 1  score: 130.0 bits;  conditional E-value: 1.2e-40
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren. 79 
                                    l+ v+l++ ege+v ++G++G+GK+tLl++++gl++pt G++ +d++d++e  ++ +++++g ++q+  l+p+l+v++n 
  gi|119720391|ref|YP_920886.1|  19 LRGVNLEVAEGELVTLLGPSGCGKTTLLRVISGLYRPTRGRVYFDSEDVTE--KNPWERNVGLVFQDYALWPHLKVYDNi 96 
                                    6789**********************************************9..999************************ PP

                                    ............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    ............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                e de++++++s lg+++l d+      ++LSgGq+qrvalara++ +p++lllDEp 
  gi|119720391|ref|YP_920886.1|  97 ayglrlrkipkdEIDERVHRVASLLGIEDLLDRYP----HQLSGGQQQRVALARAVVINPSVLLLDEPL 161
                                    ***********999***************999998....*****************************7 PP

>> TOBE  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.5     4e-05     0.026       4      62 ..     237     286 ..     235     288 .. 0.94
   2 !   31.1   0.0   3.3e-10   2.2e-07       6      63 ..     299     354 ..     296     355 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4e-05
                           TOBE   4 rNqlpgtVvvveplgseveVrvdlgggatLtArvtrrsaeeLgLapGeeVfalikaakv 62 
                                     N+++g+V +v p  +e +V+ ++g  +     v+ +  ++    +GeeV++++ ++ v
  gi|119720391|ref|YP_920886.1| 237 VNIVKGKVAEVAPDTGELVVESEIGELH-----VSADEKAS----KGEEVYLAFRPENV 286
                                    69**************************.....88899999....***********998 PP

  == domain 2  score: 31.1 bits;  conditional E-value: 3.3e-10
                           TOBE   6 qlpgtVvvveplgseveVrvdlgggatLtArvtrrsaeeLgLapGeeVfalikaakvh 63 
                                     l+g+V+ v +lgs  +V+v++gg+  + A +   +++   ++pGe+V+++++++ ++
  gi|119720391|ref|YP_920886.1| 299 LLEGRVDSVQFLGSLLRVDVEVGGKR-IRAEIHNPARAG-LFSPGEKVYLRVDPGNIR 354
                                    69************************.******999999.79************9876 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.5   0.1   9.1e-15   6.1e-12       1      76 []     279     356 ..     279     356 .. 0.86

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 9.1e-15
                         TOBE_2   1 laiRPEklrla..aagg.anglsGtVedveylGsstryvvelaggqlvvvrqpnadrdsalapGdtVelswdpddavvl 76 
                                    la RPE++++   ++gg a+ l+G+V++v++lGs +r+ ve++g ++ +++ +n +r+  + pG++V l++dp  ++vl
  gi|119720391|ref|YP_920886.1| 279 LAFRPENVEILraPRGGsAGLLEGRVDSVQFLGSLLRVDVEVGGKRI-RAEIHNPARAGLFSPGEKVYLRVDPGNIRVL 356
                                    688*******997666645688********************99988.666666665579***************9997 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   6.3e-07   0.00042       3      96 ..      33     123 ..      31     131 .. 0.78
   2 !   19.2   0.0   1.3e-06   0.00084     206     298 ..     104     193 ..      80     197 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 6.3e-07
                         AAA_21   3 vliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrlersq 82 
                                     l Gp g+GK++LL+ +++l r  r      +e+     + k p++ + +   ++ ++  ++++ +++ y  +lr   ++
  gi|119720391|ref|YP_920886.1|  33 TLLGPSGCGKTTLLRVISGLYRPTRGRVYFDSED----VTEKNPWERNVGLVFQDYALWPHLKVYDNIAYGLRLRKIPKD 108
                                    699*****************98733333333333....688999999999999999999999999999999999999999 PP

                         AAA_21  83 v.eeklssvetlles 96 
                                       e++ +v +ll++
  gi|119720391|ref|YP_920886.1| 109 EiDERVHRVASLLGI 123
                                    977777766666655 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 1.3e-06
                         AAA_21 206 eeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkel 285
                                    +   +++der  +    +l  +d  ++ +++lS G+++  al+ a+   +   s+ll+DEp ++L+ k+   + + +++l
  gi|119720391|ref|YP_920886.1| 104 KIPKDEIDERVHR-VASLLGIEDLLDRYPHQLSGGQQQRVALARAVVINP---SVLLLDEPLSNLDAKIRINVRTEIRKL 179
                                    3333334444433.7777888899999************9*******999...************************777 PP

                         AAA_21 286 sr.ngaQviltTHS 298
                                    ++  ++  i +TH+
  gi|119720391|ref|YP_920886.1| 180 QKeLKITSIYVTHD 193
                                    77688888999998 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   2.2e-06    0.0015      19      55 ..      26      62 ..      15     159 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.2e-06
                         AAA_16 19 vrsgrpelvllsGesGvGKsslvrellralekd..ggif 55
                                   v++g  elv l G+sG+GK++l+r +   ++ +  +++f
  gi|119720391|ref|YP_920886.1| 26 VAEG--ELVTLLGPSGCGKTTLLRVISGLYRPTrgRVYF 62
                                   4444..89***************9998665555322444 PP

>> TOBE_3  TOBE-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.64   4.2e+02      37      59 ..     263     281 ..     245     282 .. 0.64
   2 !   15.7   0.2   1.6e-05      0.01       4      59 ..     297     348 ..     294     349 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.64
                         TOBE_3  37 velprdrfeelglaeGetvylrP 59 
                                      +++d+    + ++Ge+vyl  
  gi|119720391|ref|YP_920886.1| 263 LHVSADE----KASKGEEVYLAF 281
                                    3455555....8888*****976 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1.6e-05
                         TOBE_3   4 egglpatvrrirpvGpivRlELerlgdtgeliEvelprdrfeelglae.GetvylrP 59 
                                    +g l+++v +++ +G   R+++e +   g  i +e++  +  + gl+  Ge+vylr 
  gi|119720391|ref|YP_920886.1| 297 AGLLEGRVDSVQFLGSLLRVDVEVG---GKRIRAEIHNPA--RAGLFSpGEKVYLRV 348
                                    56799*****************877...677777777777..4477777******95 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   3.6e-06    0.0024      33      67 ..      17      51 ..       6      70 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.6e-06
                          Rad17 33 ewlkadvLesrkkriLLisGPsGCgkstvvkvLsk 67
                                   e+l+   Le ++ +++ + GPsGCgk+t ++v+s 
  gi|119720391|ref|YP_920886.1| 17 EALRGVNLEVAEGELVTLLGPSGCGKTTLLRVISG 51
                                   56778889999999******************985 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.099        66      26      44 ..      31      49 ..      20      52 .. 0.83
   2 !   11.5   0.0   0.00022      0.14     133     201 ..     130     196 ..      74     211 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.099
                                   EEEEEESTTSSHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxx RF
                          SMC_N 26 ftaivGpNGSGKsnlldAi 44
                                   +  ++Gp G+GK+ ll  i
  gi|119720391|ref|YP_920886.1| 31 LVTLLGPSGCGKTTLLRVI 49
                                   66799********998766 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00022
                                    STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEE..EEE-SSHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxx RF
                          SMC_N 133 skelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQf..ivislreem 201
                                    ++++LSgG+++ vala  + i   +p ++ llDe  ++LD+k + +v + +++ +k+  +  i +++++e 
  gi|119720391|ref|YP_920886.1| 130 YPHQLSGGQQQRVALARAVVI---NP-SVLLLDEPLSNLDAKIRINVRTEIRKLQKELKItsIYVTHDQEE 196
                                    4569*******9999877554...44.5779*********************9999966522666666554 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   7.7e-05     0.051       2      22 ..      33      53 ..      32     200 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.7e-05
                                   EEESSTTSSHHHHHHHHHHHH CS
                            AAA  2 llyGppGtGKTllakavakel 22
                                    l Gp G+GKT+l + +    
  gi|119720391|ref|YP_920886.1| 33 TLLGPSGCGKTTLLRVISGLY 53
                                   699************998765 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   3.8e-05     0.025      96     121 ..      26      51 ..       6      63 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.8e-05
                                    HCTTSEEEEECSTTSSHHHHHHHHCT CS
                    RsgA_GTPase  96 llkdktsvlvGqSGvGKStLinallp 121
                                    + ++++++l+G+SG GK+tL+ ++ +
  gi|119720391|ref|YP_920886.1|  26 VAEGELVTLLGPSGCGKTTLLRVISG 51 
                                    445699***************99875 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   5.5e-05     0.037       2      26 ..      32      57 ..      31      76 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.5e-05
                                   EEEE--SSSSHHHHHHHGGGGB.S-- CS
                          AAA_5  2 vlLvGppGtgKselaerlaaal.nre 26
                                   v L+Gp+G+gK++l + ++ ++  ++
  gi|119720391|ref|YP_920886.1| 32 VTLLGPSGCGKTTLLRVISGLYrPTR 57
                                   679****************9997443 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   4.4e-05     0.029      26      61 ..      32      72 ..      22     226 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.4e-05
                                   EEEEESTTSSHHHHHHHHHHHCS--.....--HHHHHCCHH CS
                        G-alpha 26 llllGqseSGKsTilkqlkllykkg.....fseeelatwra 61
                                   + llG s++GK+T+l+ +  ly+++     f+ e++ + ++
  gi|119720391|ref|YP_920886.1| 32 VTLLGPSGCGKTTLLRVISGLYRPTrgrvyFDSEDVTEKNP 72
                                   579*******************9999999877776644333 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   7.8e-05     0.052      15      48 ..      22      55 ..      10      64 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.8e-05
                         AAA_29 15 htieidlkgatlltGpsGsGKSTllDAiqalLvp 48
                                     +e+ + + + l GpsG GK+Tll  i+ l  p
  gi|119720391|ref|YP_920886.1| 22 VNLEVAEGELVTLLGPSGCGKTTLLRVISGLYRP 55
                                   45666655588999**********9766666555 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00011     0.072       6      49 ..      13      56 ..       8      78 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                   Mg_chelatase  6 kGqeeakraleiaaaGgHnlllvGppGsGKtmlakrlpsllppl 49
                                    G+ ea r +++ +a g  + l+Gp+G+GKt l + +++l  p 
  gi|119720391|ref|YP_920886.1| 13 FGKVEALRGVNLEVAEGELVTLLGPSGCGKTTLLRVISGLYRPT 56
                                   5788899999999999999****************999997765 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   9.6e-05     0.064      17      49 ..      29      60 ..      21      67 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.6e-05
                         AAA_30 17 gdrvavltGpAGtGKttalkalreaweaaggrv 49
                                   g  +++l Gp G GKtt+l+++  +++   grv
  gi|119720391|ref|YP_920886.1| 29 G-ELVTLLGPSGCGKTTLLRVISGLYRPTRGRV 60
                                   3.48999***************99998876565 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   0.00011      0.07       2      21 ..      31      50 ..      30      58 .. 0.88
   2 ?   -2.9   0.0       8.4   5.6e+03      91     114 ..     158     181 ..     113     196 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00011
                                   CEEEEC-TTTCHHHHHHHHH CS
                          NACHT  2 lvilqGeaGsGKTtLlqkla 21
                                   lv l G++G+GKTtLl+ + 
  gi|119720391|ref|YP_920886.1| 31 LVTLLGPSGCGKTTLLRVIS 50
                                   6899************9875 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 8.4
                                    TT-SS-TCH.........HHHHHC CS
                          NACHT  91 DelvtdlgqkekqpvrtlLselir 114
                                    De  + l++k + +vrt +++l +
  gi|119720391|ref|YP_920886.1| 158 DEPLSNLDAKIRINVRTEIRKLQK 181
                                    344444444455555555555544 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00014     0.091       3      45 ..      30      71 ..      28      97 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00014
                         AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkk 45
                                   +++++ G+  +GKTtll+ + + l+ + +  +y++ +d ++k+
  gi|119720391|ref|YP_920886.1| 30 ELVTLLGPSGCGKTTLLRVI-SGLYRPTRGRVYFDSEDVTEKN 71
                                   6799************8655.5666688888999888877654 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00015       0.1      14      40 ..      23      50 ..      11      72 .. 0.81
   2 ?   -2.2   0.0       7.7   5.1e+03     183     192 ..     174     183 ..     109     199 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00015
                         AAA_23 14 eidF.skgltlItGpNGaGKTTildAik 40
                                   +++  +  l+ + Gp G+GKTT+l+ i 
  gi|119720391|ref|YP_920886.1| 23 NLEVaEGELVTLLGPSGCGKTTLLRVIS 50
                                   4555555788999***********9885 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 7.7
                         AAA_23 183 keleeleeel 192
                                     e+ +l++el
  gi|119720391|ref|YP_920886.1| 174 TEIRKLQKEL 183
                                    2222222222 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00015     0.098      31      50 ..      27      46 ..      17      83 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00015
                         AAA_25 31 pagelallaGapgtGKttla 50
                                   ++gel+ l G++g+GKttl+
  gi|119720391|ref|YP_920886.1| 27 AEGELVTLLGPSGCGKTTLL 46
                                   69****************97 PP

>> MIT_C  Phospholipase D-like domain at C-terminus of MIT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00012     0.077      62     121 ..     169     230 ..     145     244 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00012
                          MIT_C  62 edeqkenleelkesleklgielevefsst..ihdreirldngwiikigrGLdifkkseskfs 121
                                    + ++++++++l+++l+ ++i ++ + +++  i dr  ++++g+i ++g  Ldi++++++ f 
  gi|119720391|ref|YP_920886.1| 169 RINVRTEIRKLQKELKITSIYVTHDQEEAlvISDRIAVMNKGFIEQVGSPLDIYYRPRTLFV 230
                                    567788999*******99999999986653389***********************988775 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00038      0.25       1      21 [.      32      52 ..      32     118 .. 0.72
   2 ?   -2.1   0.0         8   5.3e+03      60      84 ..     176     205 ..     153     215 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00038
                         AAA_18  1 IlltGtpGvGKttlakeLskr 21
                                   + l G++G+GKttl + +s +
  gi|119720391|ref|YP_920886.1| 32 VTLLGPSGCGKTTLLRVISGL 52
                                   6799************99755 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 8
                         AAA_18  60 lldaleenss.....aleegknlvidghla 84 
                                    + ++ +e        + ++++ lvi++++a
  gi|119720391|ref|YP_920886.1| 176 IRKLQKELKItsiyvTHDQEEALVISDRIA 205
                                    333333322255555555555556655555 PP

>> MotA_activ  Transcription factor MotA, activation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0       0.6     4e+02      40      68 ..     191     219 ..     180     226 .. 0.79
   2 ?    9.5   0.1    0.0016         1      31      55 ..     239     263 ..     226     277 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.6
                                    -TTS-HHHHHHHHHHHHHTTSEEEETTEE CS
                     MotA_activ  40 hpdlgnavvnsnigvlikkglveksgdgl 68 
                                      d  +a+v s+   +++kg++e+ g  l
  gi|119720391|ref|YP_920886.1| 191 THDQEEALVISDRIAVMNKGFIEQVGSPL 219
                                    5577788888887778899*****99877 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0016
                                    B-HHHHHHT-TTS-HHHHHHHHHHH CS
                     MotA_activ  31 itaaevrevhpdlgnavvnsnigvl 55 
                                    i   +v ev pd g+ vv+s+ig l
  gi|119720391|ref|YP_920886.1| 239 IVKGKVAEVAPDTGELVVESEIGEL 263
                                    566789*****************87 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00025      0.17      21      42 ..      30      51 ..      17      75 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00025
                       ATPase_2 21 eiyfiYGpegsGKtaLlkeiie 42
                                   e + + Gp g+GKt+Ll+ i  
  gi|119720391|ref|YP_920886.1| 30 ELVTLLGPSGCGKTTLLRVISG 51
                                   667788***********98754 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00049      0.33       7      23 ..      31      47 ..      26      67 .. 0.88
   2 ?   -2.1   0.0       6.3   4.2e+03      84      99 ..     141     159 ..     110     190 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00049
                         AAA_22  7 ilvvtGesGtGKTtllr 23
                                   ++++ G+sG+GKTtllr
  gi|119720391|ref|YP_920886.1| 31 LVTLLGPSGCGKTTLLR 47
                                   67899**********98 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 6.3
                         AAA_22  84 qalrarav...ielliiDE 99 
                                    + + arav   +++l++DE
  gi|119720391|ref|YP_920886.1| 141 RVALARAVvinPSVLLLDE 159
                                    3333333356667777777 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00033      0.22      17      40 ..      28      49 ..      14      64 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00033
                                   TSCSEEEEEEESTTSSHHHHHHHH CS
                         NB-ARC 17 elqslvvalvGmgGvGKttlakqi 40
                                   e +  +v+l G  G+GKttl++ i
  gi|119720391|ref|YP_920886.1| 28 EGE--LVTLLGPSGCGKTTLLRVI 49
                                   555..89*************9877 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00041      0.27       4      23 ..      32      51 ..      30      58 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00041
                      PduV-EutP  4 illiGkvgsGKttLtqalkg 23
                                   + l+G++g+GKttL + ++g
  gi|119720391|ref|YP_920886.1| 32 VTLLGPSGCGKTTLLRVISG 51
                                   679************99987 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00067      0.45       2      20 ..      32      50 ..      31      71 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00067
                         AAA_28  2 ivitGgestGKTtlleaLa 20
                                   + ++G++++GKTtll+ ++
  gi|119720391|ref|YP_920886.1| 32 VTLLGPSGCGKTTLLRVIS 50
                                   6799***********9776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              27  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2249.72
//
Query:       gi|119720392|ref|YP_920887.1|  [L=544]
Description: binding-protein-dependent transport systems inner membrane component [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.3e-26   92.7  42.1      2e-14   53.7  18.1    3.4  4  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   1.4       0.1   1.9e+03      24      50 ..      17      55 ..       3      82 .. 0.42
   2 !   53.2  16.1   1.7e-18     3e-14       6     170 ..      73     259 ..      68     268 .. 0.75
   3 ?    0.6   1.9     0.022   3.9e+02      30      70 ..     305     368 ..     286     373 .. 0.52
   4 !   53.7  18.1   1.1e-18     2e-14       3     173 ..     359     537 ..     357     544 .] 0.82

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.1
                   BPD_transp_1 24 iivllslPsfvlaillvlvf..................vilsilg 50
                                   + v+   P   l+      +                   +ls+l+
  gi|119720392|ref|YP_920887.1| 17 VAVFILYPLAYLV------LfvvsprslsevvaflesdLFLSSLK 55
                                   2222222222222......12234455555556566663333333 PP

  == domain 2  score: 53.2 bits;  conditional E-value: 1.7e-18
                   BPD_transp_1   6 ilaa...lnrnkkldkllrpliivllslPsfvlaillvlvf..................vilsilghlilpviillllsa 64 
                                    +  a    +++  +++ ++  ++++ ++P+fv a+ +++++                       + ++  +vi++ ++++
  gi|119720392|ref|YP_920887.1|  73 VPYAyalHRYKVLGKNYVLSATFMPTMVPPFVGALSVIFLLgrfgtvnlllmewglierP--INFIYGLHGVILVQTITL 150
                                    444444557788899999999***********5555444446778888888899998553..347788889********* PP

                   BPD_transp_1  65 apyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG.lgtllle 143
                                    +p++ +++++ l  l+++l+eaa+ lGa+++++f++v+lP++ p ++tgl+++f +++++++ +  lg++     + +++
  gi|119720392|ref|YP_920887.1| 151 FPWIAINVYNSLLKLDRSLEEAAESLGAPPIRRFFTVTLPAVTPGLMTGLFMVFSFAFTDYATPIVLGQYELlAPQAFVN 230
                                    ********************************************************************887543333344 PP

                   BPD_transp_1 144 ailgydyseis..nggvlalviavlllnl 170
                                    ++++ d s       +v++++++v+ l l
  gi|119720392|ref|YP_920887.1| 231 IQQAIDESRVRtgTYMVFFMLVIVIGLFL 259
                                    44444444333321333333333333333 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.022
                   BPD_transp_1  30 lPsfvlaillvlvf..............................vilsilghlilp.viillllsaapyvrl 70 
                                    lP++ +       f                               + + + +++++ +i ll+ ++++yv +
  gi|119720392|ref|YP_920887.1| 305 LPHVFV-------FvislskawsltplptsyslenfatifhsptPFVNTAIYAAIGtAICLLVGMFGAYV-V 368
                                    333333.......133444447777777777777777777777744455555555524444444444444.3 PP

  == domain 4  score: 53.7 bits;  conditional E-value: 1.1e-18
                   BPD_transp_1   3 llGilaa...lnrnkkldkllrpliivllslPsfvlaillvlvf....vilsilghlilpviillllsaapyvrlirraa 75 
                                    l+G++ a   ++ n +l+++++    +++ +P +v++  ++++f     ++++lg+++l + ++l++  + y+++  +a 
  gi|119720392|ref|YP_920887.1| 359 LVGMFGAyvvTRTNHPLNEVIDSALSMMFVVPGIVVGTSFLFAFrkdiPVMGVLGSTWLIMPLMLATRRITYTIRYAYAT 438
                                    567777777799*****************************9************************************** PP

                   BPD_transp_1  76 lrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG...lgtllleailgydyse 152
                                      ++ ++l+eaa++ G ++  +f+k+v+Pna+  i++g +++f+ ++++ ++ +fl  +pG   ++ +++  i + +++ 
  gi|119720392|ref|YP_920887.1| 439 YVTIRRSLEEAAYVFGEKPLGTFFKIVMPNAIYGILAGTLFSFIEIVNELTASLFLY-KPGwetVTIQMFIQITAGQFPV 517
                                    *********************************************************.6655554444444444444443 PP

                   BPD_transp_1 153 isnggvlalviavlllnlvad 173
                                     + +++++l ++ ++l +va+
  gi|119720392|ref|YP_920887.1| 518 SA-AYAVVLFVVSIALATVAM 537
                                    33.333333333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (544 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       787  (0.0438954); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 3487.41
//
Query:       gi|119720393|ref|YP_920888.1|  [L=322]
Description: biotin--acetyl-CoA-carboxylase ligase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.2e-15   56.2   0.1    1.3e-14   54.3   0.0    1.9  2  BPL_LplA_LipB   Biotin/lipoate A/B protein ligase family
    3.3e-13   49.4   0.1    6.8e-13   48.4   0.1    1.5  1  HTH_11          HTH domain
    1.7e-08   34.2   3.5    3.3e-08   33.3   3.5    1.5  1  BPL_C           Biotin protein ligase C terminal domain
    2.2e-07   30.7   0.6    5.5e-07   29.4   0.6    1.6  1  MarR_2          MarR family
    5.2e-05   23.0   0.4    0.00012   21.8   0.0    1.7  2  HTH_IclR        IclR helix-turn-helix domain
    0.00021   21.7   0.2    0.00038   20.9   0.2    1.5  1  HTH_27          Winged helix DNA-binding domain
    0.00031   20.8   0.2    0.00086   19.4   0.2    1.8  1  AbiEi_4         Transcriptional regulator, AbiEi antitoxin
     0.0012   19.0   0.0     0.0025   18.0   0.0    1.5  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
  ------ inclusion threshold ------
      0.013   15.2   0.9      0.025   14.2   0.9    1.5  1  GntR            Bacterial regulatory proteins, gntR family
      0.024   14.2   0.0      0.046   13.3   0.0    1.5  1  HTH_24          Winged helix-turn-helix DNA-binding
      0.053   13.9   0.0       0.11   12.9   0.0    1.5  1  Rrf2            Transcriptional regulator
      0.061   13.2   0.1       0.18   11.7   0.1    1.9  1  TrmB            Sugar-specific transcriptional regulator TrmB
       0.11   12.3   0.0        0.4   10.5   0.0    1.9  1  HTH_10          HTH DNA binding domain
       0.11   12.5   0.1        6.1    6.9   0.0    2.8  3  Put_DNA-bind_N  Putative DNA-binding protein N-terminus
       0.14   12.6   0.4          3    8.3   0.2    2.4  2  FaeA            FaeA-like protein


Domain annotation for each model (and alignments):
>> BPL_LplA_LipB  Biotin/lipoate A/B protein ligase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.3   0.0   1.1e-17   1.3e-14       7     131 .]      93     211 ..      87     211 .. 0.84
   2 ?   -1.2   0.1       1.5   1.8e+03      28      39 ..     302     313 ..     293     317 .. 0.83

  Alignments for each domain:
  == domain 1  score: 54.3 bits;  conditional E-value: 1.1e-17
                                    -HHHHHH..GCGGG--TT-EEEEEEESS-B....-B--B-TTSEEEEEEEEESS...-CCGTHHHHHHHHHHHHHHH... CS
                  BPL_LplA_LipB   7 stntllkeslnsselesgglvvvrrqtgGr....nvwhspkgeltyslllspeqktfqnrvlelyvsllvlavlealgyr 82 
                                    st+++++  l s+  e g++vv++  t+Gr    + w+   g+l+++++l+p+q     + l+l+ +   l+v++++   
  gi|119720393|ref|YP_920888.1|  93 STQDVAD-ALASQGAEEGTVVVAESMTSGRgrlgRRWFAGPGGLWFTVILRPQQ----MKHLQLLSLAAGLSVAKSV--- 164
                                    5656555.7889999*******************8888889**********886....4566777777777777777... PP

                                    ...HHTT-TTEEEETTTEEEETTEEEEEEEEEEEE.TTS-EEEEEEEEEE CS
                  BPL_LplA_LipB  83 dskpgiegipvfikwpnDlyvngrKlaGiavtstr.gktlhhivigvgvn 131
                                       +g  gi ++ kwpnD++v+ rKl Gi+v+ +     l ++ +gvgvn
  gi|119720393|ref|YP_920888.1| 165 ---RGLYGIDARLKWPNDVVVGERKLCGILVEGKAeADALKYLLLGVGVN 211
                                    ...8******************************9555667788888887 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.5
                                    EEEEESS-B-B- CS
                  BPL_LplA_LipB  28 vvrrqtgGrnvw 39 
                                    vv+  tgGr+++
  gi|119720393|ref|YP_920888.1| 302 VVQKDTGGRVTV 313
                                    8999*****985 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.4   0.1   5.7e-16   6.8e-13       3      55 .]       8      60 ..       7      60 .. 0.91

  Alignments for each domain:
  == domain 1  score: 48.4 bits;  conditional E-value: 5.7e-16
                         HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvpIesepgrGYr 55
                                   + +le L +  g++ g eLAe+L+vS+ +++r I  L+++g+ +es p+rGYr
  gi|119720393|ref|YP_920888.1|  8 RRVLEVLARRGGYVRGGELAEKLGVSKVAIHRAIVGLRKMGYVVESHPRRGYR 60
                                   6789999555555***************************************8 PP

>> BPL_C  Biotin protein ligase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   3.5   2.8e-11   3.3e-08       1      47 [.     273     320 ..     273     321 .. 0.97

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 2.8e-11
                                    STTSEEEEEE.TSCEEEEEEEEE-TTSEEEEEETTE.EEEESSCCEEE CS
                          BPL_C   1 hsGqeVtled.edgkveGiavGIdddGaLllktddglqpdinsGdisl 47 
                                    ++G++V++   ++g+veG+av+++++G L+++ d+g ++++++Gd+++
  gi|119720393|ref|YP_920888.1| 273 TLGRRVRVSIvGGGVVEGVAVDVTSRGELVVQKDTGGRVTVDAGDVEH 320
                                    69********************************************98 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.6   4.6e-10   5.5e-07       8      54 ..       8      53 ..       6      60 .. 0.93

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 4.6e-10
                                   HHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                         MarR_2  8 arvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                   +rvL +L+rr+g+ ++ gela++lg+sk a++r++  L + G+v+++
  gi|119720393|ref|YP_920888.1|  8 RRVLEVLARRGGY-VRGGELAEKLGVSKVAIHRAIVGLRKMGYVVES 53
                                   89**********9.9*****************************987 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   9.8e-08   0.00012       7      49 ..       9      51 ..       9      54 .. 0.96
   2 ?   -3.2   0.0       6.5   7.8e+03      21      31 ..     149     159 ..     143     163 .. 0.47

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 9.8e-08
                                   HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                       HTH_IclR  7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                   ++L+ la++++ ++  elA+++g++k + hR +  L ++Gyv 
  gi|119720393|ref|YP_920888.1|  9 RVLEVLARRGGYVRGGELAEKLGVSKVAIHRAIVGLRKMGYVV 51
                                   69***************************************96 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 6.5
                                    HHHHHHHHTS- CS
                       HTH_IclR  21 lselArrtglp 31 
                                    l+ l+ ++gl+
  gi|119720393|ref|YP_920888.1| 149 LQLLSLAAGLS 159
                                    44444444443 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.2   3.2e-07   0.00038       8      64 ..      10      63 ..       4      66 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 3.2e-07
                         HTH_27  8 vLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrl 64
                                   vL+++++r++ ++  +l+++l v++ +i+ ++  L ++G+v+++   ++rr  r+  
  gi|119720393|ref|YP_920888.1| 10 VLEVLARRGGYVRGGELAEKLGVSKVAIHRAIVGLRKMGYVVES---HPRRGYRLVS 63
                                   89999999999999***************************776...7888888755 PP

>> AbiEi_4  Transcriptional regulator, AbiEi antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.2   7.2e-07   0.00086       1      32 [.       8      40 ..       8      41 .. 0.95

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 7.2e-07
                        AbiEi_4  1 erlpelasrqvGlfttrelea.aGispsalrrL 32
                                   +r++e ++r++G+++  el++ +G+s  a++r+
  gi|119720393|ref|YP_920888.1|  8 RRVLEVLARRGGYVRGGELAEkLGVSKVAIHRA 40
                                   799****************999**********8 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   2.1e-06    0.0025      19      56 ..      17      54 ..       8      59 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.1e-06
                                   HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                 Fe_dep_repress 19 ekkvvktkdlaerLnvspssVsemlkkLekdGyveyek 56
                                    +++v+  +lae L+vs+  +   +  L+k+Gyv+ ++
  gi|119720393|ref|YP_920888.1| 17 RGGYVRGGELAEKLGVSKVAIHRAIVGLRKMGYVVESH 54
                                   5789*****************************86543 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.9   2.1e-05     0.025       8      62 ..       5      59 ..       3      61 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.1e-05
                                   HHHHHHHTTSS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTS.EEEETTCEE CS
                           GntR  8 rLredIlsgelrpGdkLPsereLaaefgVsrttvReALrrLeaegl.verrqgrGt 62
                                   +Lr+++l+   r G    +  eLa+++gVs+  + +A+  L   g+ ve++++rG 
  gi|119720393|ref|YP_920888.1|  5 ELRRRVLEVLARRGGYV-RGGELAEKLGVSKVAIHRAIVGLRKMGYvVESHPRRGY 59
                                   78999999999999999.99***********************9962578888885 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.8e-05     0.046       3      47 ..       5      50 ..       4      51 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.8e-05
                         HTH_24  3 etdrkILelLqknpr.isqreLAerlglSpstvnrrlkrLeeeGlI 47
                                   e++r++Le+L + ++     eLAe+lg+S+ +++r +  L ++G++
  gi|119720393|ref|YP_920888.1|  5 ELRRRVLEVLARRGGyVRGGELAEKLGVSKVAIHRAIVGLRKMGYV 50
                                   5789********8888********************9999999998 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   9.1e-05      0.11      13      59 ..      10      54 ..       5      73 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.1e-05
                                   HHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                           Rrf2 13 allyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvr 59
                                   +l +La++ +   v+  e+ae+ ++s++ + + +  Lrk g+v    
  gi|119720393|ref|YP_920888.1| 10 VLEVLARRGG--YVRGGELAEKLGVSKVAIHRAIVGLRKMGYVVESH 54
                                   5556666666..48999************************996544 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00015      0.18      23      56 ..      21      54 ..       8      86 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00015
                                   CHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                           TrmB 23 atadeiaeelgvprskvYevLrsLedkGlVerek 56
                                    +  e+ae+lgv++  + +++  L ++G+V  ++
  gi|119720393|ref|YP_920888.1| 21 VRGGELAEKLGVSKVAIHRAIVGLRKMGYVVESH 54
                                   56679************************98764 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00033       0.4      25      42 ..      22      39 ..      20      42 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00033
                         HTH_10 25 tlkeLAkelGIskstlse 42
                                   +  eLA++lG+sk +++ 
  gi|119720393|ref|YP_920888.1| 22 RGGELAEKLGVSKVAIHR 39
                                   678************986 PP

>> Put_DNA-bind_N  Putative DNA-binding protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0    0.0051       6.1      15      44 ..       9      37 ..       8      39 .. 0.90
   2 ?    2.1   0.0      0.16     2e+02      18      36 ..      52      70 ..      49      75 .. 0.80
   3 ?   -2.7   0.0       5.2   6.2e+03      10      17 ..     248     255 ..     236     260 .. 0.56

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0051
                                   HHHHHHHHTT--EE-HHHHHHHCTS-HHHH CS
                 Put_DNA-bind_N 15 ryLeelkeegveriSSteLaealgvtaaqv 44
                                   r+Le l ++g  ++   eLae+lgv+ + +
  gi|119720393|ref|YP_920888.1|  9 RVLEVLARRG-GYVRGGELAEKLGVSKVAI 37
                                   8999999999.9*************99876 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.16
                                   HHHHHTT--EE-HHHHHHH CS
                 Put_DNA-bind_N 18 eelkeegveriSSteLaea 36
                                   e+  ++g   +SS+ La+a
  gi|119720393|ref|YP_920888.1| 52 ESHPRRGYRLVSSDNLADA 70
                                   6667889999*******97 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 5.2
                                    HHHHHHHH CS
                 Put_DNA-bind_N  10 LplYlryL 17 
                                    L  Y+ +L
  gi|119720393|ref|YP_920888.1| 248 LDGYYAAL 255
                                    44566666 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.2    0.0025         3       5      54 ..      10      59 ..       6      62 .. 0.89
   2 ?    1.8   0.0      0.26   3.1e+02      12      26 ..      88     102 ..      81     104 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0025
                                   HHHHHHH.S----HHHHHHHHTS-HHHHHHHHHHHHHHSSEEEE--SSSS CS
                           FaeA  5 IleylnsikapckTreiAdalglsaYQaRyYLeqLekegkikrspvrrGv 54
                                   +le l + ++ ++  e+A+ lg+s   +   +  L+k g +  s  rrG 
  gi|119720393|ref|YP_920888.1| 10 VLEVLARRGGYVRGGELAEKLGVSKVAIHRAIVGLRKMGYVVESHPRRGY 59
                                   67777777788999*********************************996 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.26
                                    .S----HHHHHHHHT CS
                           FaeA  12 ikapckTreiAdalg 26 
                                    +k+ + T+++Adal+
  gi|119720393|ref|YP_920888.1|  88 VKTCGSTQDVADALA 102
                                    468899*******86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2360.71
//
Query:       gi|119720394|ref|YP_920889.1|  [L=207]
Description: hypothetical protein Tpen_1489 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        1.2    8.8   6.9       0.64    9.7   0.1    2.6  2  DUF697    Domain of unknown function (DUF697)


Domain annotation for each model (and alignments):
>> DUF697  Domain of unknown function (DUF697)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   2.6      0.02   3.5e+02      68     125 ..      56     113 ..      28     132 .. 0.77
   2 ?    9.7   0.1   3.6e-05      0.64      56      79 ..     151     174 ..     131     188 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.02
                         DUF697  68 elgyegaqrLarsvlknlaglGlvelgtdllkqllslnlatklsaraaQGvvagllTa 125
                                     l+ +ga+r a  +l ++ +lG+ ++++ + + ll+   + ++++ +a  +++ ll++
  gi|119720394|ref|YP_920889.1|  56 SLTVAGARRTAAAILLSAPFLGFYAVSSTAAQLLLGFFDPLYAASTLARHLSVVLLSY 113
                                    688899999999999999*****99999998888887444444444444444444444 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 3.6e-05
                         DUF697  56 rlirelaelYgielgyegaqrLar 79 
                                       r+l+elYg++lg ++a+rL+ 
  gi|119720394|ref|YP_920889.1| 151 LTLRQLGELYGVNLGGRRARRLVA 174
                                    4579*****************974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1499.42
//
Query:       gi|119720395|ref|YP_920890.1|  [L=408]
Description: ABC transporter related [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-38  131.8   0.0    1.4e-19   71.0   0.0    2.7  2  ABC_tran         ABC transporter
      3e-24   86.4   8.2    3.6e-09   36.8   0.1    4.1  4  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    4.8e-10   39.8   0.3     0.0013   19.1   0.1    3.2  2  AAA_22           AAA domain
    1.4e-09   37.4   0.2    0.00031   19.9   0.2    2.3  2  T2SSE            Type II/IV secretion system protein
    8.1e-09   35.1   1.2     0.0024   17.6   0.1    2.4  2  AAA_29           P-loop containing region of AAA domain
    1.8e-08   35.1   0.0     0.0046   17.5   0.0    2.1  2  AAA_23           AAA domain
    1.1e-07   32.3   2.3     0.0049   17.3   0.4    2.6  2  AAA_16           AAA ATPase domain
    1.1e-06   28.7   0.9       0.02   14.8   0.0    2.7  2  NACHT            NACHT domain
    1.1e-06   28.2   0.0       0.72    9.3   0.0    3.6  4  SMC_N            RecF/RecN/SMC N terminal domain
    1.4e-06   28.1   5.4     0.0039   16.9   0.2    3.0  2  AAA_30           AAA domain
    6.4e-06   25.9   0.4      0.049   13.2   0.1    3.1  3  AAA_25           AAA domain
    2.2e-05   24.5   0.2      0.034   14.1   0.0    2.2  2  ATPase_2         ATPase domain predominantly from Archaea
    2.6e-05   24.8   2.3      0.054   14.0   0.1    2.6  2  AAA_18           AAA domain
    5.6e-05   23.1   3.9      0.092   12.7   0.3    2.4  2  NTPase_1         NTPase
    6.7e-05   23.1   0.0       0.35   11.0   0.2    2.8  2  AAA_33           AAA domain
    7.3e-05   22.8   0.2       0.13   12.2   0.0    2.2  2  Rad17            Rad17 P-loop domain
    0.00014   22.3   0.9       0.74   10.2   0.2    2.9  3  AAA              ATPase family associated with various cellul
    0.00021   21.1   0.6        2.7    7.7   0.1    3.2  3  IstB_IS21        IstB-like ATP binding protein
    0.00024   21.0   1.3      0.085   12.8   0.1    2.3  2  RsgA_GTPase      RsgA GTPase
    0.00028   21.2   4.6       0.28   11.4   0.2    2.7  2  AAA_28           AAA domain
    0.00028   20.9   0.3       0.73    9.8   0.0    2.4  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
     0.0004   20.0   5.8      0.064   12.8   0.8    2.3  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
    0.00044   19.7   0.1        0.3   10.4   0.0    2.2  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    0.00061   19.6   0.0       0.26   11.0   0.0    2.8  3  AAA_15           AAA ATPase domain
      0.001   19.4   0.0        1.5    9.2   0.0    2.2  2  RNA_helicase     RNA helicase
     0.0011   19.0   0.6        1.1    9.3   0.1    2.8  2  AAA_14           AAA domain
     0.0013   19.1   3.2        1.1    9.5   0.2    3.0  2  AAA_19           AAA domain
     0.0017   18.2   1.2       0.96    9.3   0.0    2.2  2  dNK              Deoxynucleoside kinase
     0.0018   17.5   0.1        1.7    7.7   0.1    2.1  2  PIF1             PIF1-like helicase
     0.0025   17.7   0.3        1.2    8.9   0.1    2.4  2  ATP_bind_1       Conserved hypothetical ATP binding protein
     0.0044   16.9   1.5       0.93    9.4   0.2    2.6  2  MobB             Molybdopterin guanine dinucleotide synthesis
     0.0051   16.0   0.6        1.3    8.1   0.1    2.2  2  NB-ARC           NB-ARC domain
      0.007   15.7   0.3          2    7.7   0.0    2.2  2  FtsK_SpoIIIE     FtsK/SpoIIIE family
     0.0071   16.1   1.5          2    8.1   0.1    2.3  2  AAA_24           AAA domain
     0.0086   15.8   0.5        2.2    8.0   0.0    2.3  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
  ------ inclusion threshold ------
      0.015   15.5   0.0        5.1    7.4   0.0    2.7  2  SbcCD_C          Putative exonuclease SbcCD, C subunit
      0.015   15.3   1.2        2.9    7.9   0.1    2.6  2  AAA_5            AAA domain (dynein-related subfamily)
      0.021   14.9   1.6        3.7    7.7   0.2    2.4  2  MMR_HSR1         50S ribosome-binding GTPase
      0.021   14.5   3.8        1.3    8.6   0.1    2.5  2  SRP54            SRP54-type protein, GTPase domain
      0.033   13.5   0.5        6.8    5.9   0.0    2.3  2  Zeta_toxin       Zeta toxin
      0.033   13.7   0.5        4.2    6.8   0.1    2.2  2  AAA_7            P-loop containing dynein motor region
      0.035   13.9   0.2          9    6.0   0.0    2.3  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
       0.04   13.4   0.2        8.2    5.8   0.0    2.1  2  Pox_A32          Poxvirus A32 protein
      0.044   12.6   1.1       0.79    8.5   0.1    2.1  2  DLIC             Dynein light intermediate chain (DLIC)
      0.046   13.5   1.5        1.8    8.3   0.3    2.5  2  DEAD             DEAD/DEAH box helicase
      0.048   13.1   1.0        1.8    7.9   0.1    2.4  2  PhoH             PhoH-like protein
       0.05   12.8   0.0       0.89    8.7   0.0    2.1  2  KAP_NTPase       KAP family P-loop domain
      0.061   12.7   1.1        4.3    6.6   0.1    2.4  2  ATPase           KaiC
      0.066   12.8   0.2        1.6    8.3   0.0    2.2  2  AAA_27           AAA domain
      0.071   11.9   2.6        5.1    5.8   0.1    2.8  3  ABC_ATPase       Predicted ATPase of the ABC class
      0.085   12.6   0.5        5.3    6.7   0.0    2.4  2  PRK              Phosphoribulokinase / Uridine kinase family
       0.11   12.5   0.0       0.23   11.4   0.0    1.5  1  DUF1876          Domain of unknown function (DUF1876)
       0.12   11.6   0.1         13    4.8   0.1    2.3  2  DAP3             Mitochondrial ribosomal death-associated pro
       0.14    9.7   1.5       0.33    8.4   0.1    1.8  2  DUF3584          Protein of unknown function (DUF3584)
       0.19   11.8   0.6         18    5.3   0.1    2.3  2  Dynamin_N        Dynamin family
       0.21   11.2   0.4        5.1    6.7   0.0    2.2  2  Thymidylate_kin  Thymidylate kinase
       0.26    9.9   1.1        1.1    7.8   0.2    1.9  2  AAA_13           AAA domain
       0.28   10.9   0.9         16    5.2   0.1    2.9  3  Cytidylate_kin   Cytidylate kinase
        0.3    9.9   1.1        9.5    5.0   0.1    2.2  2  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
       0.49   10.8   1.9         17    5.8   0.1    2.3  2  AAA_17           AAA domain
       0.53   10.3   7.0        8.1    6.5   0.9    2.6  2  DUF87            Helicase HerA, central domain
       0.66    9.7   4.1        8.8    6.0   0.7    2.6  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
        1.5    8.0   3.9         15    4.7   0.7    2.1  2  DUF2075          Uncharacterized conserved protein (DUF2075)
        7.3    6.7   5.6         38    4.3   0.5    2.5  2  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.9   0.0   5.4e-18   1.5e-15       1     137 []       9     144 ..       9     144 .. 0.85
   2 !   71.0   0.0   4.9e-22   1.4e-19       2     136 ..     229     355 ..     228     356 .. 0.91

  Alignments for each domain:
  == domain 1  score: 57.9 bits;  conditional E-value: 5.4e-18
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--......SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp......teGeilldgkdlkeqeleslrkeigvlpqe.pqlfpe 73 
                                    l+ +s++++ege+ +++G++G+GK+tLlk+lag            G++++ g d  e      r  ++++pq+ +  f +
  gi|119720395|ref|YP_920890.1|   9 LEGLSFEVEEGELAVVTGPTGSGKTTLLKVLAGVIPGlydsyrVTGSVKVYGLDPLE---AAGRGLVAYVPQDpHYYFLG 85 
                                    6789****************************9988766556666666666555555...6788999******767899* PP

                                    SBHHHH.HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  74 ltvren.esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                    +tv+e+ +    ++ ++++l       +++     +LS G+  r+  a al   +kllllDEpta
  gi|119720395|ref|YP_920890.1|  86 VTVGEEvALAGGVAGFAEHLLRYP--SRRI----DELSDGELYRLLAATALSGGAKLLLLDEPTA 144
                                    **9999777777999999887555..8888....*****************************97 PP

  == domain 2  score: 71.0 bits;  conditional E-value: 4.9e-22
                                    EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvrenes 81 
                                    +  sl ++ege+va++G+nG+GK+tLlk+lag lkp +G++l+++  +     + +  +++ +++e +lf e        
  gi|119720395|ref|YP_920890.1| 229 RGASLRVREGECVAVTGRNGSGKTTLLKILAGILKPSAGTLLVEKPVFLVPAAPLYWYSSASVEEEVELFAEAW----GF 304
                                    6789*************************************999887777888888888999999999988883....56 PP

                                    HTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  82 deeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                    + ++ ++l+ ++l+ l  ++     ++LS G+ +r++la a +++++ lllDEpt
  gi|119720395|ref|YP_920890.1| 305 RGDVGEVLELFDLERLGGRNP----YELSAGESRRLSLALAYVSRAETLLLDEPT 355
                                    778999999999999888888....*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   1.1e-05     0.003       1      22 [.      21      42 ..      21      66 .. 0.79
   2 !   13.4   0.2   0.00018     0.049     234     285 ..     113     161 ..     107     173 .. 0.77
   3 !   21.6   0.2   5.8e-07   0.00016       3      36 ..     242     273 ..     240     301 .. 0.72
   4 !   36.8   0.1   1.3e-11   3.6e-09     222     300 ..     313     388 ..     286     391 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.1e-05
                         AAA_21  1 lnvliGpNgsGKSnLLdaldll 22
                                   l+v++Gp gsGK++LL+ l ++
  gi|119720395|ref|YP_920890.1| 21 LAVVTGPTGSGKTTLLKVLAGV 42
                                   689****************776 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00018
                         AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkel 285
                                    ++elSdG +  l  +tal   +   +lll+DEp +  +P+ l ++le l+el
  gi|119720395|ref|YP_920890.1| 113 IDELSDGELYRLLAATALSGGA---KLLLLDEPTARVDPWGLGEVLETLSEL 161
                                    7899999988777777777666...9*************8777777777443 PP

  == domain 3  score: 21.6 bits;  conditional E-value: 5.8e-07
                         AAA_21   3 vliGpNgsGKSnLLdaldllarldrdvegltdel 36 
                                    +++G+NgsGK++LL++l ++    +++  l  e+
  gi|119720395|ref|YP_920890.1| 242 AVTGRNGSGKTTLLKILAGIL--KPSAGTLLVEK 273
                                    799**************9986..45555555555 PP

  == domain 4  score: 36.8 bits;  conditional E-value: 1.3e-11
                         AAA_21 222 vflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSpl 300
                                     +++ ++ + ++++elS G  r l l++a+ +++    +ll+DEp +gL+    r lle+l+e +++g+ v+++TH+  
  gi|119720395|ref|YP_920890.1| 313 ELFDLERLGGRNPYELSAGESRRLSLALAYVSRA---ETLLLDEPTLGLDAPSKRALLEMLEEFASRGSSVVVATHDLA 388
                                    55666778899***********************...89**********************999999*********975 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.1   4.5e-06    0.0013       5     128 ..      19     172 ..      16     180 .. 0.75
   2 !   15.9   0.0   4.1e-05     0.011       4     104 ..     237     359 ..     234     389 .. 0.59

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 4.5e-06
                         AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaee.........................erpevvfvtlpsst......ss 53 
                                      + vvtG++G+GKTtll+ l+   +  ++  +                         ++p+++f  +++++      + 
  gi|119720395|ref|YP_920890.1|  19 GELAVVTGPTGSGKTTLLKVLAGVIPGLYDSYRvtgsvkvygldpleaagrglvayvpQDPHYYFLGVTVGEevalagGV 98 
                                    56789**************9999887665555588899999999999999999999988888886666666644555566 PP

                         AAA_22  54 kdllrellralglelkaerlsseellealeqalraravielliiDEaqh.lrs...eealeeLrsllnlsrkgvqliLv 128
                                    + ++++llr   ++ ++  ls  el+++l+  + + ++ +ll++DE    +++    e+le+L++l +  + g++ +Lv
  gi|119720395|ref|YP_920890.1|  99 AGFAEHLLRYPSRRIDE--LSDGELYRLLAATALSGGA-KLLLLDEPTArVDPwglGEVLETLSELGE--ERGLTTLLV 172
                                    66666666655555555..8888888888888888888.99999998776862457999999988888..887777776 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 4.1e-05
                         AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee..................erpevv.fvtlpsst.sskdllrellra 63 
                                    +  +++vtG  G+GKTtll+ l+  l+   +a +                   +++v  +v+l ++  + +    e+l+ 
  gi|119720395|ref|YP_920890.1| 237 EGECVAVTGRNGSGKTTLLKILAGILKP--SAGTllvekpvflvpaaplywySSASVEeEVELFAEAwGFRGDVGEVLEL 314
                                    57899****************9999853..33335577777777666666644444446777777777777777777777 PP

                         AAA_22  64 lglelka....erlsseellealeqalraravielliiDEaqh.lr 104
                                    ++le+ +    ++ls  e +++    +   ++ e l++DE    l+
  gi|119720395|ref|YP_920890.1| 315 FDLERLGgrnpYELSAGESRRLSLALAYVSRA-ETLLLDEPTLgLD 359
                                    77766665555333333333222222222222.4466666666665 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.2   1.1e-06   0.00031     119     153 ..       9      43 ..       4      49 .. 0.83
   2 !   15.3   0.0   2.7e-05    0.0076     102     167 ..     211     275 ..     168     292 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.1e-06
                          T2SSE 119 aevlrkavrerglilvsGgTgsGKttllyallkei 153
                                     e l+  v+e  l +v+G+TgsGKttll +l   i
  gi|119720395|ref|YP_920890.1|   9 LEGLSFEVEEGELAVVTGPTGSGKTTLLKVLAGVI 43 
                                    55667778888899**************9988776 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 2.7e-05
                          T2SSE 102 eltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeinksderivtvEDpv 167
                                    ++  d+l+++ +    + +  +  vre   + v+G  gsGKttll +l  +++ s    ++vE pv
  gi|119720395|ref|YP_920890.1| 211 KVYADKLAYAYERGRPVLRGASLRVREGECVAVTGRNGSGKTTLLKILAGILKPS-AGTLLVEKPV 275
                                    5555666666666666666666778899999*****************9999999.7777888776 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   2.5e-05    0.0071      16      39 ..      13      36 ..       7      45 .. 0.81
   2 !   17.6   0.1   8.5e-06    0.0024      16      49 ..     232     265 ..     227     268 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.5e-05
                         AAA_29 16 tieidlkgatlltGpsGsGKSTll 39
                                   ++e+++ +  ++tGp+GsGK+Tll
  gi|119720395|ref|YP_920890.1| 13 SFEVEEGELAVVTGPTGSGKTTLL 36
                                   56777555999************8 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 8.5e-06
                         AAA_29  16 tieidlkgatlltGpsGsGKSTllDAiqalLvpa 49 
                                    ++++++ + + +tG++GsGK+Tll  ++ +L p+
  gi|119720395|ref|YP_920890.1| 232 SLRVREGECVAVTGRNGSGKTTLLKILAGILKPS 265
                                    5677755599*************97777777665 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.6e-05    0.0046      15      39 ..      14      39 ..       6      50 .. 0.79
   2 !   15.6   0.0   6.3e-05     0.018      22      43 ..     241     262 ..     236     324 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.6e-05
                         AAA_23 15 idF.skgltlItGpNGaGKTTildAi 39
                                   ++  +  l ++tGp+G+GKTT+l  +
  gi|119720395|ref|YP_920890.1| 14 FEVeEGELAVVTGPTGSGKTTLLKVL 39
                                   444445799*************9866 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 6.3e-05
                         AAA_23  22 tlItGpNGaGKTTildAiklaL 43 
                                    +++tG NG+GKTT+l  +  +L
  gi|119720395|ref|YP_920890.1| 241 VAVTGRNGSGKTTLLKILAGIL 262
                                    578************9887666 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   0.00013     0.035      24      45 ..      19      40 ..       8      80 .. 0.86
   2 !   17.3   0.4   1.7e-05    0.0049      17      52 ..     233     266 ..     220     388 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 0.00013
                         AAA_16 24 pelvllsGesGvGKsslvrell 45
                                   +el +++G+ G+GK++l++ l+
  gi|119720395|ref|YP_920890.1| 19 GELAVVTGPTGSGKTTLLKVLA 40
                                   38999*************8776 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 1.7e-05
                         AAA_16  17 ervrsgrpelvllsGesGvGKsslvrellralekdg 52 
                                     rvr+g  e+v ++G  G+GK++l++ l+  l+ + 
  gi|119720395|ref|YP_920890.1| 233 LRVREG--ECVAVTGRNGSGKTTLLKILAGILKPSA 266
                                    467766..89***************99997777663 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.3   0.00069      0.19       3      21 ..      22      40 ..      20      43 .. 0.88
   2 !   14.8   0.0   7.3e-05      0.02       3      27 ..     241     265 ..     239     292 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00069
                                   EEEEC-TTTCHHHHHHHHH CS
                          NACHT  3 vilqGeaGsGKTtLlqkla 21
                                    +++G+ GsGKTtLl+ la
  gi|119720395|ref|YP_920890.1| 22 AVVTGPTGSGKTTLLKVLA 40
                                   689************9876 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 7.3e-05
                                    EEEEC-TTTCHHHHHHHHHHHHCTS CS
                          NACHT   3 vilqGeaGsGKTtLlqklalawaeg 27 
                                    v+++G++GsGKTtLl+ la  ++ +
  gi|119720395|ref|YP_920890.1| 241 VAVTGRNGSGKTTLLKILAGILKPS 265
                                    89**************999877755 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.025         7      25      43 ..      20      38 ..       5      44 .. 0.81
   2 ?   -1.6   0.0       5.4   1.5e+03     149     188 ..     124     163 ..     105     187 .. 0.74
   3 !    9.3   0.0    0.0026      0.72      26      42 ..     240     256 ..     232     273 .. 0.85
   4 !    8.2   0.0    0.0055       1.5     136     208 ..     327     396 ..     293     401 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.025
                                   SEEEEEESTTSSHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxx RF
                          SMC_N 25 sftaivGpNGSGKsnlldA 43
                                   ++ +++Gp GSGK+ ll  
  gi|119720395|ref|YP_920890.1| 20 ELAVVTGPTGSGKTTLLKV 38
                                   57899*********99865 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 5.4
                                    HHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 149 LlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksk 188
                                    Ll A+     a l llDe  a  D     +v e l e  +
  gi|119720395|ref|YP_920890.1| 124 LLAATALSGGAKLLLLDEPTARVDPWGLGEVLETLSELGE 163
                                    5556666667778888888888888777777777776655 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0026
                                    EEEEEESTTSSHHHHHH CS
                                    xxxxxxxxxxxxxxxxx RF
                          SMC_N  26 ftaivGpNGSGKsnlld 42 
                                      a++G+NGSGK+ ll 
  gi|119720395|ref|YP_920890.1| 240 CVAVTGRNGSGKTTLLK 256
                                    679**********9986 PP

  == domain 4  score: 8.2 bits;  conditional E-value: 0.0055
                                    CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-SCE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx RF
                          SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreemlekadkl 208
                                    +LS Ge   +     +A+  v++a   llDe    LD+   +++ e+l+e  ++ + ++v +++  + +  d++
  gi|119720395|ref|YP_920890.1| 327 ELSAGESRRL----SLALAYVSRAETLLLDEPTLGLDAPSKRALLEMLEEFASRgSSVVVATHDLAFASLLDRV 396
                                    5777776654....4556688999999**********************9877647888888876666665655 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.2   1.4e-05    0.0039      18      45 ..      19      46 ..      14     164 .. 0.77
   2 !   13.4   0.2   0.00017     0.047      18      46 ..     238     266 ..     230     384 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.4e-05
                         AAA_30 18 drvavltGpAGtGKttalkalreaweaa 45
                                     +av+tGp G+GKtt+lk+l+ ++   
  gi|119720395|ref|YP_920890.1| 19 GELAVVTGPTGSGKTTLLKVLAGVIPGL 46
                                   4599*****************9887655 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00017
                         AAA_30  18 drvavltGpAGtGKttalkalreaweaag 46 
                                      ++++tG+ G+GKtt+lk l+ +++ + 
  gi|119720395|ref|YP_920890.1| 238 GECVAVTGRNGSGKTTLLKILAGILKPSA 266
                                    45899****************99988773 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.1   0.00017     0.049      31      54 ..      17      40 ..       8      45 .. 0.89
   2 ?   -1.7   0.0       6.3   1.8e+03     166     188 ..     152     174 ..     143     175 .. 0.89
   3 !    9.2   0.0     0.003      0.85      30      50 ..     235     255 ..     209     317 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00017
                         AAA_25 31 pagelallaGapgtGKttlaldla 54
                                    +gela+++G++g+GKttl+  la
  gi|119720395|ref|YP_920890.1| 17 EEGELAVVTGPTGSGKTTLLKVLA 40
                                   68*****************97776 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 6.3
                         AAA_25 166 galvealeriarrtgaavllvhH 188
                                    g+++e l ++ ++ g ++llv H
  gi|119720395|ref|YP_920890.1| 152 GEVLETLSELGEERGLTTLLVEH 174
                                    67899999999**********99 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.003
                         AAA_25  30 lpagelallaGapgtGKttla 50 
                                    +++ge ++++G+ g+GKttl+
  gi|119720395|ref|YP_920890.1| 235 VREGECVAVTGRNGSGKTTLL 255
                                    679****************98 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   0.00012     0.034      16      41 ..      15      40 ..       7      52 .. 0.86
   2 !    8.3   0.0    0.0072         2      21      40 ..     239     258 ..     232     268 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 0.00012
                       ATPase_2 16 erepneiyfiYGpegsGKtaLlkeii 41
                                   e e+ e  +++Gp gsGKt+Llk ++
  gi|119720395|ref|YP_920890.1| 15 EVEEGELAVVTGPTGSGKTTLLKVLA 40
                                   55678899**************9865 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0072
                       ATPase_2  21 eiyfiYGpegsGKtaLlkei 40 
                                    e + ++G+ gsGKt+Llk +
  gi|119720395|ref|YP_920890.1| 239 ECVAVTGRNGSGKTTLLKIL 258
                                    56789************965 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.1   0.00019     0.054       2      20 ..      23      41 ..      23     157 .. 0.66
   2 !   10.0   0.3    0.0033      0.93       1      19 [.     241     259 ..     241     278 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 0.00019
                         AAA_18  2 lltGtpGvGKttlakeLsk 20
                                   ++tG+ G+GKttl k L+ 
  gi|119720395|ref|YP_920890.1| 23 VVTGPTGSGKTTLLKVLAG 41
                                   59**************964 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0033
                         AAA_18   1 IlltGtpGvGKttlakeLs 19 
                                    +++tG  G+GKttl k L+
  gi|119720395|ref|YP_920890.1| 241 VAVTGRNGSGKTTLLKILA 259
                                    689*************996 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.3   0.00091      0.25       3      23 ..      23      43 ..      22      56 .. 0.83
   2 !   12.7   0.3   0.00033     0.092       2      24 ..     241     263 ..     240     269 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00091
                                   EEE--TTSSHHHHHHHHHHHH CS
                       NTPase_1  3 fiTGppGvGKtTlvkkvlell 23
                                   ++TGp G+GKtTl+k ++ ++
  gi|119720395|ref|YP_920890.1| 23 VVTGPTGSGKTTLLKVLAGVI 43
                                   69***********99887665 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00033
                                    EEEE--TTSSHHHHHHHHHHHH. CS
                       NTPase_1   2 vfiTGppGvGKtTlvkkvlellk 24 
                                    v++TG+ G+GKtTl+k ++  lk
  gi|119720395|ref|YP_920890.1| 241 VAVTGRNGSGKTTLLKILAGILK 263
                                    89*************99988886 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.2    0.0013      0.35       2      21 ..      22      41 ..      21     178 .. 0.84
   2 !    9.3   0.0    0.0043       1.2       3      33 ..     242     310 ..     241     391 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0013
                         AAA_33  2 vllvGlpGsGKstlaerllk 21
                                    ++ G+ GsGK+tl++ l+ 
  gi|119720395|ref|YP_920890.1| 22 AVVTGPTGSGKTTLLKVLAG 41
                                   6789***********98875 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0043
                         AAA_33   3 llvGlpGsGKstlaerllkklg....avllssdt..................................l 33 
                                     + G +GsGK+tl++ l+  l+    + l+++++                                  +
  gi|119720395|ref|YP_920890.1| 242 AVTGRNGSGKTTLLKILAGILKpsagTLLVEKPVflvpaaplywyssasveeevelfaeawgfrgdvgE 310
                                    57799**********996655555566777777766666666666555555555555555555555553 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   0.00045      0.13      38      67 ..      12      41 ..       6      50 .. 0.82
   2 !    8.4   0.1    0.0067       1.9      37      72 ..     230     265 ..     222     271 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00045
                          Rad17 38 dvLesrkkriLLisGPsGCgkstvvkvLsk 67
                                    + e ++ ++ +++GP+G gk+t +kvL+ 
  gi|119720395|ref|YP_920890.1| 12 LSFEVEEGELAVVTGPTGSGKTTLLKVLAG 41
                                   556666677999****************85 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0067
                          Rad17  37 advLesrkkriLLisGPsGCgkstvvkvLskelgik 72 
                                      +L  r+ + + ++G  G gk+t +k+L+ +l ++
  gi|119720395|ref|YP_920890.1| 230 GASLRVREGECVAVTGRNGSGKTTLLKILAGILKPS 265
                                    56677777778899****************998765 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.2    0.0027      0.74       2      21 ..      23      42 ..      22      74 .. 0.86
   2 !    9.2   0.0    0.0055       1.6       2      23 ..     242     263 ..     241     309 .. 0.83
   3 ?   -1.2   0.0       8.8   2.5e+03      87     111 ..     364     386 ..     359     403 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0027
                                   EEESSTTSSHHHHHHHHHHH CS
                            AAA  2 llyGppGtGKTllakavake 21
                                   +++Gp G GKT+l k +a  
  gi|119720395|ref|YP_920890.1| 23 VVTGPTGSGKTTLLKVLAGV 42
                                   589*************9975 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0055
                                    EEESSTTSSHHHHHHHHHHHHT CS
                            AAA   2 llyGppGtGKTllakavakelg 23 
                                     ++G  G GKT+l k +a  l+
  gi|119720395|ref|YP_920890.1| 242 AVTGRNGSGKTTLLKILAGILK 263
                                    579***************9886 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 8.8
                                    HHHHHHHHHTTTSSSTEEEEEEESS CS
                            AAA  87 nqLlteldgvkkkeskvivigatnr 111
                                     +Ll++l+++ ++ s   v++at++
  gi|119720395|ref|YP_920890.1| 364 RALLEMLEEFASRGS--SVVVATHD 386
                                    689999999999755..66666665 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.1    0.0096       2.7      39      65 ..      10      37 ..       6      43 .. 0.80
   2 ?    5.7   0.0     0.039        11      44      64 ..     235     255 ..     222     261 .. 0.86
   3 ?    4.3   0.0      0.11        30      96     149 ..     333     385 ..     327     397 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0096
                      IstB_IS21 39 atlsf.iekkenivllGpsGvGKshlai 65
                                    +lsf +e+ e  v++Gp+G GK+ l  
  gi|119720395|ref|YP_920890.1| 10 EGLSFeVEEGELAVVTGPTGSGKTTLLK 37
                                   5666657888999***********9865 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.039
                      IstB_IS21  44 iekkenivllGpsGvGKshla 64 
                                    +++ e+++++G  G GK+ l 
  gi|119720395|ref|YP_920890.1| 235 VREGECVAVTGRNGSGKTTLL 255
                                    7889**************885 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.11
                      IstB_IS21  96 dgklaralkrllkvdllilDdlgllpldqaeaellfeviekryerrsiiitsnl 149
                                      +l+ al+ + +++ l+lD+   l ld  +++ l+e++e+   r s ++ +  
  gi|119720395|ref|YP_920890.1| 333 SRRLSLALAYVSRAETLLLDEPT-LGLDAPSKRALLEMLEEFASRGSSVVVATH 385
                                    557778899999*********75.679**************9999887765543 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.1    0.0003     0.085      90     121 ..       9      41 ..       1      52 [. 0.84
   2 ?    7.1   0.1     0.017       4.6      98     121 ..     237     260 ..     231     270 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.0003
                                    HHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                    RsgA_GTPase  90 leelkellkd.ktsvlvGqSGvGKStLinallp 121
                                    le l+ ++++ +++v+ G++G GK+tL+++l++
  gi|119720395|ref|YP_920890.1|   9 LEGLSFEVEEgELAVVTGPTGSGKTTLLKVLAG 41 
                                    667777787779*****************9986 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.017
                                    TTSEEEEECSTTSSHHHHHHHHCT CS
                    RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallp 121
                                    +++++++ G  G GK+tL++ l++
  gi|119720395|ref|YP_920890.1| 237 EGECVAVTGRNGSGKTTLLKILAG 260
                                    458999**************9987 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.2   0.00099      0.28       3      20 ..      23      40 ..      21      53 .. 0.89
   2 !   11.0   0.2    0.0014      0.38       2      20 ..     241     259 ..     240     278 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00099
                         AAA_28  3 vitGgestGKTtlleaLa 20
                                   v+tG+ ++GKTtll+ La
  gi|119720395|ref|YP_920890.1| 23 VVTGPTGSGKTTLLKVLA 40
                                   89*************998 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0014
                         AAA_28   2 ivitGgestGKTtlleaLa 20 
                                    +++tG  ++GKTtll+ La
  gi|119720395|ref|YP_920890.1| 241 VAVTGRNGSGKTTLLKILA 259
                                    89****************9 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.1    0.0056       1.6      19      40 ..      19      40 ..       5      55 .. 0.81
   2 !    9.8   0.0    0.0026      0.73      19      44 ..     238     263 ..     219     279 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0056
                                   TEEEEEEESTTSSHHHHHHHHH CS
                           TsaE 19 gdvilLeGdLGaGKTtlvrgla 40
                                   g++ + +G+ G+GKTtl + la
  gi|119720395|ref|YP_920890.1| 19 GELAVVTGPTGSGKTTLLKVLA 40
                                   667899************9887 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0026
                                    TEEEEEEESTTSSHHHHHHHHHHHTT CS
                           TsaE  19 gdvilLeGdLGaGKTtlvrglakalg 44 
                                    g++++ +G  G+GKTtl + la  l+
  gi|119720395|ref|YP_920890.1| 238 GECVAVTGRNGSGKTTLLKILAGILK 263
                                    789****************9987765 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.8   0.00023     0.064       3      20 ..      22      39 ..      20      46 .. 0.89
   2 !    9.5   0.3    0.0024      0.67       3      20 ..     241     258 ..     239     268 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00023
                                   EEEEESTTCCHHHHHHHH CS
                           cobW  3 tvltGflGsGKTtLlnhl 20
                                    v+tG+ GsGKTtLl+ l
  gi|119720395|ref|YP_920890.1| 22 AVVTGPTGSGKTTLLKVL 39
                                   69*************865 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0024
                                    EEEEESTTCCHHHHHHHH CS
                           cobW   3 tvltGflGsGKTtLlnhl 20 
                                    + +tG  GsGKTtLl+ l
  gi|119720395|ref|YP_920890.1| 241 VAVTGRNGSGKTTLLKIL 258
                                    679************865 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0    0.0011       0.3      26      51 ..      23      48 ..      17      81 .. 0.86
   2 ?    7.0   0.1     0.012       3.4      26      50 ..     242     266 ..     233     275 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0011
                   Mg_chelatase 26 llvGppGsGKtmlakrlpsllpplse 51
                                   +++Gp GsGKt l k l++++p l +
  gi|119720395|ref|YP_920890.1| 23 VVTGPTGSGKTTLLKVLAGVIPGLYD 48
                                   578*******************8865 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.012
                   Mg_chelatase  26 llvGppGsGKtmlakrlpsllppls 50 
                                     ++G  GsGKt l k l+++l p  
  gi|119720395|ref|YP_920890.1| 242 AVTGRNGSGKTTLLKILAGILKPSA 266
                                    5789*****************8865 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0      0.11        31      22      43 ..      19      39 ..      11      43 .. 0.82
   2 !   11.0   0.0   0.00091      0.26      27      50 ..     242     265 ..     232     284 .. 0.86
   3 ?    0.4   0.0       1.5   4.1e+02     306     368 ..     337     389 ..     326     390 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.11
                         AAA_15 22 seeltvliGkNnsGKSsileal 43
                                    e l v+ G+ +sGK+++l++l
  gi|119720395|ref|YP_920890.1| 19 GE-LAVVTGPTGSGKTTLLKVL 39
                                   44.89999************98 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00091
                         AAA_15  27 vliGkNnsGKSsilealdlFlnnk 50 
                                     + G+N+sGK+++l++l  +l+ +
  gi|119720395|ref|YP_920890.1| 242 AVTGRNGSGKTTLLKILAGILKPS 265
                                    567*************98777755 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 1.5
                         AAA_15 306 llillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSphi 368
                                    +l+l  ++            +ll++EP + L    ++ l + l e a+ ++  v++ TH   +
  gi|119720395|ref|YP_920890.1| 337 SLALAYVSRA---------ETLLLDEPTLGLDAPSKRALLEMLEEFASRGS-SVVVATHDLAF 389
                                    4444444444.........4599***************************9.9******8765 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0     0.012       3.5       2      19 ..      23      40 ..      22      59 .. 0.88
   2 !    9.2   0.0    0.0054       1.5       2      83 ..     242     327 ..     241     334 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.012
                   RNA_helicase  2 wlyGpsgeGKStlakeLa 19
                                   +++Gp+g GK+tl k La
  gi|119720395|ref|YP_920890.1| 23 VVTGPTGSGKTTLLKVLA 40
                                   689***********9987 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0054
                   RNA_helicase   2 wlyGpsgeGKStlakeLakallkkl.klkkkdsvysrnpeddfwdgYt..gqevvvidDfgqvkdee.npsdlaelirlv 77 
                                     ++G++g GK+tl k La  l  +   l  ++ v+  +++  +w++    ++ev ++ +    + +  +  +l++l rl 
  gi|119720395|ref|YP_920890.1| 242 AVTGRNGSGKTTLLKILAGILKPSAgTLLVEKPVFLVPAAPLYWYSSAsvEEEVELFAEAWGFRGDVgEVLELFDLERLG 321
                                    689*************9888874443445556666777777777544334666666666665554443333556666666 PP

                   RNA_helicase  78 sstpyp 83 
                                      +py+
  gi|119720395|ref|YP_920890.1| 322 GRNPYE 327
                                    555555 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.1    0.0038       1.1       3      23 ..      20      40 ..      18      44 .. 0.87
   2 ?    6.9   0.1     0.021       5.9       3      23 ..     239     259 ..     237     273 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0038
                         AAA_14  3 kilvitGaRrvGKTtllkqli 23
                                   ++ v+tG+  +GKTtllk l+
  gi|119720395|ref|YP_920890.1| 20 ELAVVTGPTGSGKTTLLKVLA 40
                                   5689*************9775 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.021
                         AAA_14   3 kilvitGaRrvGKTtllkqli 23 
                                    + +++tG   +GKTtllk l+
  gi|119720395|ref|YP_920890.1| 239 ECVAVTGRNGSGKTTLLKILA 259
                                    6789************99776 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.2    0.0041       1.1      10      30 ..      19      39 ..      13      47 .. 0.83
   2 !    8.8   0.1     0.007         2       9      35 ..     237     263 ..     230     277 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0041
                         AAA_19 10 ekvllvtaGpGtGKTrvlkhi 30
                                    ++ +vt++ G+GKT++lk  
  gi|119720395|ref|YP_920890.1| 19 GELAVVTGPTGSGKTTLLKVL 39
                                   567899999********9875 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.007
                         AAA_19   9 kekvllvtaGpGtGKTrvlkhivallv 35 
                                    + ++++vt+  G+GKT++lk    +l+
  gi|119720395|ref|YP_920890.1| 237 EGECVAVTGRNGSGKTTLLKILAGILK 263
                                    67899*************998776665 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0    0.0034      0.96       2      20 ..      23      41 ..      22      51 .. 0.89
   2 !    7.8   0.2    0.0094       2.6       2      21 ..     242     261 ..     241     273 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0034
                                   EEEESTTSSHHHHHHHHHC CS
                            dNK  2 vveGnIgaGKstlvklLsk 20
                                   vv G+ g+GK+tl+k+L+ 
  gi|119720395|ref|YP_920890.1| 23 VVTGPTGSGKTTLLKVLAG 41
                                   799*************985 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0094
                                    EEEESTTSSHHHHHHHHHCC CS
                            dNK   2 vveGnIgaGKstlvklLskk 21 
                                    +v G  g+GK+tl+k+L+  
  gi|119720395|ref|YP_920890.1| 242 AVTGRNGSGKTTLLKILAGI 261
                                    689999***********865 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.1    0.0061       1.7      18      48 ..      15      45 ..       5      58 .. 0.82
   2 !    7.6   0.0    0.0067       1.9      18      50 ..     234     266 ..     226     272 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0061
                                   ..HCTS-EEEEESTTSSCHHHHHHHHHHCHC CS
                           PIF1 18 lnekgklfFvtGsgGtgKtflwkallkklrs 48
                                     e+g+l  vtG  G+gKt l+k l  ++ +
  gi|119720395|ref|YP_920890.1| 15 EVEEGELAVVTGPTGSGKTTLLKVLAGVIPG 45
                                   4589999******************999875 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0067
                                    ..HCTS-EEEEESTTSSCHHHHHHHHHHCHCTC CS
                           PIF1  18 lnekgklfFvtGsgGtgKtflwkallkklrseg 50 
                                      ++g+ + vtG  G+gKt l+k l  +l+++ 
  gi|119720395|ref|YP_920890.1| 234 RVREGECVAVTGRNGSGKTTLLKILAGILKPSA 266
                                    557899999*****************9999864 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.1    0.0042       1.2       1      20 [.      24      43 ..      24      53 .. 0.84
   2 ?    6.5   0.0     0.022       6.2       1      22 [.     243     264 ..     243     294 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0042
                     ATP_bind_1  1 vvGpaGsGKttfvgalseil 20
                                   v+Gp GsGKtt+ + l+ ++
  gi|119720395|ref|YP_920890.1| 24 VTGPTGSGKTTLLKVLAGVI 43
                                   89**********99887665 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.022
                     ATP_bind_1   1 vvGpaGsGKttfvgalseilel 22 
                                    v+G  GsGKtt+ + l+ il+ 
  gi|119720395|ref|YP_920890.1| 243 VTGRNGSGKTTLLKILAGILKP 264
                                    89***********999888765 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.1     0.037        10       4      20 ..      24      40 ..      21      57 .. 0.80
   2 !    9.4   0.2    0.0033      0.93       2      24 ..     241     263 ..     240     269 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.037
                           MobB  4 ivgksgsGKTtLlekli 20
                                   ++g  gsGKTtLl+ l 
  gi|119720395|ref|YP_920890.1| 24 VTGPTGSGKTTLLKVLA 40
                                   56899********9875 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0033
                           MobB   2 lgivgksgsGKTtLleklipelk 24 
                                    ++++g++gsGKTtLl+ l  +lk
  gi|119720395|ref|YP_920890.1| 241 VAVTGRNGSGKTTLLKILAGILK 263
                                    6899***********99988776 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.019       5.3      22      38 ..      21      37 ..       6      52 .. 0.77
   2 !    8.1   0.1    0.0047       1.3      22      38 ..     240     256 ..     232     261 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.019
                                   EEEEEESTTSSHHHHHH CS
                         NB-ARC 22 vvalvGmgGvGKttlak 38
                                   +  + G  G+GKttl+k
  gi|119720395|ref|YP_920890.1| 21 LAVVTGPTGSGKTTLLK 37
                                   45689**********87 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0047
                                    EEEEEESTTSSHHHHHH CS
                         NB-ARC  22 vvalvGmgGvGKttlak 38 
                                     va+ G+ G+GKttl+k
  gi|119720395|ref|YP_920890.1| 240 CVAVTGRNGSGKTTLLK 256
                                    799************86 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0     0.007         2      43      59 ..      23      39 ..       5      66 .. 0.84
   2 ?    6.0   0.0     0.024       6.8      42      59 ..     241     258 ..     221     262 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.007
                                   EEE--TTSSHHHHHHHH CS
                   FtsK_SpoIIIE 43 lvaGatgsGKStalntL 59
                                   +v G tgsGK+t l++L
  gi|119720395|ref|YP_920890.1| 23 VVTGPTGSGKTTLLKVL 39
                                   899***********988 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.024
                                    EEEE--TTSSHHHHHHHH CS
                   FtsK_SpoIIIE  42 llvaGatgsGKStalntL 59 
                                    + v G+ gsGK+t l+ L
  gi|119720395|ref|YP_920890.1| 241 VAVTGRNGSGKTTLLKIL 258
                                    789**********99865 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.2     0.016       4.6       6      22 ..      23      39 ..      20      46 .. 0.88
   2 !    8.1   0.1    0.0072         2       4      22 ..     240     258 ..     237     277 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.016
                         AAA_24  6 liyGpsgiGKTtlakel 22
                                   +++Gp g+GKTtl+k l
  gi|119720395|ref|YP_920890.1| 23 VVTGPTGSGKTTLLKVL 39
                                   799**********9865 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0072
                         AAA_24   4 kiliyGpsgiGKTtlakel 22 
                                     ++++G +g+GKTtl+k l
  gi|119720395|ref|YP_920890.1| 240 CVAVTGRNGSGKTTLLKIL 258
                                    5899***********9987 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0079       2.2       5      23 ..      23      41 ..      20      61 .. 0.76
   2 ?    5.8   0.1     0.037        10       4      23 ..     241     260 ..     239     264 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0079
                      PduV-EutP  5 lliGkvgsGKttLtqalkg 23
                                   ++ G++gsGKttL + l g
  gi|119720395|ref|YP_920890.1| 23 VVTGPTGSGKTTLLKVLAG 41
                                   578************9987 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.037
                      PduV-EutP   4 illiGkvgsGKttLtqalkg 23 
                                    + + G+ gsGKttL + l g
  gi|119720395|ref|YP_920890.1| 241 VAVTGRNGSGKTTLLKILAG 260
                                    5678**********998875 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.078        22      64      89 ..     134     159 ..     109     160 .. 0.82
   2 ?    7.4   0.0     0.018       5.1      62      89 ..     344     371 ..     325     372 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.078
                        SbcCD_C  64 lrlvfLDEAFsklDeesiatllelle 89 
                                     +l++LDE  +++D+  + ++le+l 
  gi|119720395|ref|YP_920890.1| 134 AKLLLLDEPTARVDPWGLGEVLETLS 159
                                    589************99999999875 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.018
                        SbcCD_C  62 palrlvfLDEAFsklDeesiatllelle 89 
                                    ++ ++++LDE   +lD+ s ++lle+le
  gi|119720395|ref|YP_920890.1| 344 SRAETLLLDEPTLGLDAPSKRALLEMLE 371
                                    35579********************997 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.1      0.01       2.9       4      23 ..      24      43 ..      22      54 .. 0.85
   2 ?    5.4   0.1     0.059        17       4      24 ..     243     263 ..     241     276 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.01
                                   EE--SSSSHHHHHHHGGGGB CS
                          AAA_5  4 LvGppGtgKselaerlaaal 23
                                   + Gp+G+gK++l + la ++
  gi|119720395|ref|YP_920890.1| 24 VTGPTGSGKTTLLKVLAGVI 43
                                   68************999877 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.059
                                    EE--SSSSHHHHHHHGGGGBS CS
                          AAA_5   4 LvGppGtgKselaerlaaaln 24 
                                    + G  G+gK++l + la  l+
  gi|119720395|ref|YP_920890.1| 243 VTGRNGSGKTTLLKILAGILK 263
                                    68**************99884 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1     0.039        11       3      21 ..      23      41 ..      21      62 .. 0.83
   2 ?    7.7   0.2     0.013       3.7       2      21 ..     241     260 ..     240     273 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.039
                                   EEEESTTSSHHHHHHHHHT CS
                       MMR_HSR1  3 aivGrpNvGKStLinaltg 21
                                   ++ G + +GK+tL++ l g
  gi|119720395|ref|YP_920890.1| 23 VVTGPTGSGKTTLLKVLAG 41
                                   789************9987 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.013
                                    EEEEESTTSSHHHHHHHHHT CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltg 21 
                                    va+ Gr  +GK+tL++ l g
  gi|119720395|ref|YP_920890.1| 241 VAVTGRNGSGKTTLLKILAG 260
                                    89*************99987 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.5     0.028       7.7       4      23 ..      22      41 ..      20      46 .. 0.85
   2 ?    8.6   0.1    0.0046       1.3       4      28 ..     241     265 ..     239     274 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.028
                                   EEEEESTTSSHHHHHHHHHH CS
                          SRP54  4 illvGlqGaGKTttlaKLaa 23
                                    ++ G++G+GKTt l  La 
  gi|119720395|ref|YP_920890.1| 22 AVVTGPTGSGKTTLLKVLAG 41
                                   5789*********9998885 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0046
                                    EEEEESTTSSHHHHHHHHHHHHHHT CS
                          SRP54   4 illvGlqGaGKTttlaKLaallkke 28 
                                    +++ G +G+GKTt l  La +lk +
  gi|119720395|ref|YP_920890.1| 241 VAVTGRNGSGKTTLLKILAGILKPS 265
                                    6799************999988765 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.024       6.8      18      37 ..      21      40 ..       8      49 .. 0.85
   2 ?    5.4   0.1     0.034       9.6      19      41 ..     241     263 ..     231     273 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.024
                     Zeta_toxin 18 lillgGqpGAGKselaellk 37
                                   l ++ G +G+GK++l++ l+
  gi|119720395|ref|YP_920890.1| 21 LAVVTGPTGSGKTTLLKVLA 40
                                   67899**********99876 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.034
                     Zeta_toxin  19 illgGqpGAGKselaellkdele 41 
                                    + + G  G+GK++l++ l+  l+
  gi|119720395|ref|YP_920890.1| 241 VAVTGRNGSGKTTLLKILAGILK 263
                                    6789***********99887665 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1     0.015       4.2      32      52 ..      18      38 ..      12      54 .. 0.82
   2 ?    5.0   0.1     0.056        16      30      53 ..     235     258 ..     231     269 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.015
                          AAA_7 32 nkkpvllvGptGtGKtviikd 52
                                   ++   +++GptG+GKt+++k 
  gi|119720395|ref|YP_920890.1| 18 EGELAVVTGPTGSGKTTLLKV 38
                                   5666789**********9875 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.056
                          AAA_7  30 lknkkpvllvGptGtGKtviikdl 53 
                                    ++++  v ++G  G+GKt+++k l
  gi|119720395|ref|YP_920890.1| 235 VREGECVAVTGRNGSGKTTLLKIL 258
                                    67888999***********98755 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.046        13      37      54 ..      23      40 ..      15      53 .. 0.88
   2 ?    6.0   0.0     0.032         9      23      57 ..     228     262 ..     222     272 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.046
                         RuvB_N 37 llyGpPGlGkttlakiia 54
                                   +++Gp G Gkttl k++a
  gi|119720395|ref|YP_920890.1| 23 VVTGPTGSGKTTLLKVLA 40
                                   689************998 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.032
                         RuvB_N  23 ieaakkreealdhvllyGpPGlGkttlakiiakel 57 
                                    ++ a  r ++ + v ++G  G Gkttl ki+a  l
  gi|119720395|ref|YP_920890.1| 228 LRGASLRVREGECVAVTGRNGSGKTTLLKILAGIL 262
                                    566778888889999***************99655 PP

>> Pox_A32  Poxvirus A32 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.029       8.2      17      34 ..      23      40 ..      15      52 .. 0.81
   2 ?    5.5   0.0     0.037        10      16      33 ..     241     258 ..     231     265 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.029
                        Pox_A32 17 alvGgsGsGktvyLlsLl 34
                                   +++G +GsGkt+ L+ L 
  gi|119720395|ref|YP_920890.1| 23 VVTGPTGSGKTTLLKVLA 40
                                   57899*******999874 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.037
                        Pox_A32  16 lalvGgsGsGktvyLlsL 33 
                                    +a++G  GsGkt+ L+ L
  gi|119720395|ref|YP_920890.1| 241 VAVTGRNGSGKTTLLKIL 258
                                    6899*********99866 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1      0.15        41      28      48 ..      22      42 ..      14      46 .. 0.88
   2 ?    8.5   0.1    0.0028      0.79      22      54 ..     235     267 ..     227     272 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.15
                           DLIC 28 vlvlGedgsGkttliaklqGv 48
                                    +v G  gsGkttl+  l Gv
  gi|119720395|ref|YP_920890.1| 22 AVVTGPTGSGKTTLLKVLAGV 42
                                   5899************99998 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0028
                           DLIC  22 lPsgksvlvlGedgsGkttliaklqGveeekkG 54 
                                    +  g  v v G +gsGkttl+  l G+ ++  G
  gi|119720395|ref|YP_920890.1| 235 VREGECVAVTGRNGSGKTTLLKILAGILKPSAG 267
                                    56688999******************9888776 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.3    0.0066       1.8      13      30 ..      18      35 ..       6     191 .. 0.89
   2 ?    4.0   0.0      0.13        37      13      33 ..     237     257 ..     229     281 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0066
                                   TTCEEEEEESTTSSHHHH CS
                                   xxxxxxxxxxxxxxxxxx RF
                           DEAD 13 gggdvlvaaeTGsGKTla 30
                                   +g+  +v ++TGsGKT+ 
  gi|119720395|ref|YP_920890.1| 18 EGELAVVTGPTGSGKTTL 35
                                   6777899*********86 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.13
                                    TTCEEEEEESTTSSHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  13 gggdvlvaaeTGsGKTlafli 33 
                                    +g+ v v ++ GsGKT+   i
  gi|119720395|ref|YP_920890.1| 237 EGECVAVTGRNGSGKTTLLKI 257
                                    788999**********97554 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.1    0.0066       1.8      17      37 ..      17      37 ..       6      43 .. 0.78
   2 ?    3.3   0.1      0.17        47      18      36 ..     237     255 ..     231     269 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0066
                                   HH-SEEEEE--TTSSTTHHHH CS
                           PhoH 17 kkndivfaiGpaGtGKtylav 37
                                   ++ ++ +++Gp+G+GKt l  
  gi|119720395|ref|YP_920890.1| 17 EEGELAVVTGPTGSGKTTLLK 37
                                   5678999*********97644 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.17
                                    H-SEEEEE--TTSSTTHHH CS
                           PhoH  18 kndivfaiGpaGtGKtyla 36 
                                    + + v ++G+ G+GKt l 
  gi|119720395|ref|YP_920890.1| 237 EGECVAVTGRNGSGKTTLL 255
                                    667899*********9764 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.32        91      25      40 ..      24      39 ..      15      42 .. 0.86
   2 ?    8.7   0.0    0.0032      0.89      18      48 ..     236     266 ..     212     388 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.32
                     KAP_NTPase 25 LygkWGsGKssllnkl 40
                                   ++g+ GsGK++ll+ l
  gi|119720395|ref|YP_920890.1| 24 VTGPTGSGKTTLLKVL 39
                                   78888********976 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0032
                     KAP_NTPase  18 atpivvgLygkWGsGKssllnkledelkefa 48 
                                    +++ +v+++g  GsGK++ll+ l   lk  a
  gi|119720395|ref|YP_920890.1| 236 REGECVAVTGRNGSGKTTLLKILAGILKPSA 266
                                    56779****************9987776665 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.1     0.083        23      18      35 ..      18      35 ..      11      39 .. 0.88
   2 ?    6.6   0.1     0.015       4.3      17      35 ..     236     254 ..     231     260 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.083
                         ATPase 18 egrvvlitGepGtGKtif 35
                                   eg+   +tG +G+GKt++
  gi|119720395|ref|YP_920890.1| 18 EGELAVVTGPTGSGKTTL 35
                                   678899**********97 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.015
                         ATPase  17 pegrvvlitGepGtGKtif 35 
                                     eg+ v +tG  G+GKt++
  gi|119720395|ref|YP_920890.1| 236 REGECVAVTGRNGSGKTTL 254
                                    68999************97 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0058       1.6      18      47 ..      11      40 ..       5      49 .. 0.87
   2 ?    2.2   0.0      0.41   1.2e+02      29      46 ..     241     258 ..     229     262 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0058
                         AAA_27 18 sldfsaeeadlhliyGpNEAGKstalrAis 47
                                    l+f+ ee +l ++ Gp  +GK+t+l+ + 
  gi|119720395|ref|YP_920890.1| 11 GLSFEVEEGELAVVTGPTGSGKTTLLKVLA 40
                                   5899999******************98765 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.41
                         AAA_27  29 hliyGpNEAGKstalrAi 46 
                                      + G N +GK+t+l+ +
  gi|119720395|ref|YP_920890.1| 241 VAVTGRNGSGKTTLLKIL 258
                                    5699*********99855 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.1     0.018       5.1     242     265 ..      16      40 ..       6      50 .. 0.84
   2 ?   -2.2   0.0       4.7   1.3e+03     336     350 ..     129     143 ..     126     145 .. 0.85
   3 ?    5.0   0.2     0.032       9.1     242     264 ..     235     258 ..     227     263 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.018
                                    E-SS.EEEEEE-TTSSHHHHHHHHH CS
                     ABC_ATPase 242 ipkG.vtlIvGggfhGKsTLLeAle 265
                                    + +G + +++G+   GK+TLL+ l+
  gi|119720395|ref|YP_920890.1|  16 VEEGeLAVVTGPTGSGKTTLLKVLA 40 
                                    5677799***************986 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 4.7
                                    HHHTT-SEEEEEGGG CS
                     ABC_ATPase 336 aleagakllLiDEDt 350
                                    al  gakllL+DE t
  gi|119720395|ref|YP_920890.1| 129 ALSGGAKLLLLDEPT 143
                                    7889*********77 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.032
                                    E-SS.EEEEEE-TTSSHHHHHHHH CS
                     ABC_ATPase 242 ipkG.vtlIvGggfhGKsTLLeAl 264
                                    +++G  ++++G++  GK+TLL+ l
  gi|119720395|ref|YP_920890.1| 235 VREGeCVAVTGRNGSGKTTLLKIL 258
                                    67777889*************976 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1      0.16        46       4      21 ..      24      41 ..      21      56 .. 0.86
   2 ?    6.7   0.0     0.019       5.3       2      24 ..     241     263 ..     240     280 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.16
                            PRK  4 vagsSGaGkttvarklek 21
                                   v+g+ G+Gktt+ + l  
  gi|119720395|ref|YP_920890.1| 24 VTGPTGSGKTTLLKVLAG 41
                                   8**********9988765 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.019
                            PRK   2 IgvagsSGaGkttvarklekifg 24 
                                    ++v+g  G+Gktt+ + l  i++
  gi|119720395|ref|YP_920890.1| 241 VAVTGRNGSGKTTLLKILAGILK 263
                                    79************999998887 PP

>> DUF1876  Domain of unknown function (DUF1876)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00082      0.23      26      76 ..      62     116 ..      48     121 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00082
                                    TTEEEEEEEEEES-SSS---....SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        DUF1876  26 detelrgvGlArrnpaDedv....peiGdElAaaRALsdLaeqLleaaaedieav 76 
                                    d  e  g+Gl    p+D++      ++G+E+A a  ++  ae+Ll+  +++i++ 
  gi|119720395|ref|YP_920890.1|  62 DPLEAAGRGLVAYVPQDPHYyflgVTVGEEVALAGGVAGFAEHLLRYPSRRIDEL 116
                                    56677788888888888886333358**********************9999986 PP

>> DAP3  Mitochondrial ribosomal death-associated protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1     0.047        13      26      40 ..      22      36 ..      14      40 .. 0.89
   2 ?    4.5   0.0      0.06        17      26      40 ..     241     255 ..     231     294 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.047
                                   EEEE-SSSSSTTTTH CS
                           DAP3 26 lvltGekgsGKSvlL 40
                                    v+tG +gsGK++lL
  gi|119720395|ref|YP_920890.1| 22 AVVTGPTGSGKTTLL 36
                                   69***********99 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.06
                                    EEEE-SSSSSTTTTH CS
                           DAP3  26 lvltGekgsGKSvlL 40 
                                    + +tG++gsGK++lL
  gi|119720395|ref|YP_920890.1| 241 VAVTGRNGSGKTTLL 255
                                    569*********998 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1      0.36     1e+02      20      37 ..      22      39 ..       7      41 .. 0.78
   2 ?    8.4   0.1    0.0012      0.33      13      37 ..     234     258 ..     226     259 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.36
                        DUF3584 20 tnieGtNaaGKTtLlrLi 37
                                     + G  ++GKTtLl+++
  gi|119720395|ref|YP_920890.1| 22 AVVTGPTGSGKTTLLKVL 39
                                   5688999********875 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0012
                        DUF3584  13 eldldghtnieGtNaaGKTtLlrLi 37 
                                    +++  + + + G N++GKTtLl+++
  gi|119720395|ref|YP_920890.1| 234 RVREGECVAVTGRNGSGKTTLLKIL 258
                                    5555567999************976 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0      0.11        31       2      20 ..      23      41 ..      22      44 .. 0.92
   2 ?    5.3   0.1     0.065        18       1      20 [.     241     260 ..     241     277 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.11
                                   EEEEBTTTTHHHHHHHHHT CS
                      Dynamin_N  2 avvGsqSsGKSSvlnaLlg 20
                                   +v G + sGK+++l  L g
  gi|119720395|ref|YP_920890.1| 23 VVTGPTGSGKTTLLKVLAG 41
                                   799***********99988 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.065
                                    EEEEEBTTTTHHHHHHHHHT CS
                      Dynamin_N   1 iavvGsqSsGKSSvlnaLlg 20 
                                    +av G   sGK+++l  L g
  gi|119720395|ref|YP_920890.1| 241 VAVTGRNGSGKTTLLKILAG 260
                                    79*************99988 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1      0.36     1e+02       3      18 ..      26      41 ..      24      49 .. 0.85
   2 ?    6.7   0.0     0.018       5.1       3      25 ..     245     267 ..     243     275 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.36
                                   ESTTSSHHHHHHHHHH CS
                Thymidylate_kin  3 GlDGaGKttqaellke 18
                                   G  G+GKtt ++ l+ 
  gi|119720395|ref|YP_920890.1| 26 GPTGSGKTTLLKVLAG 41
                                   778********99975 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.018
                                    ESTTSSHHHHHHHHHHHHHHTTE CS
                Thymidylate_kin   3 GlDGaGKttqaellkerlkeegi 25 
                                    G +G+GKtt +++l+  lk ++ 
  gi|119720395|ref|YP_920890.1| 245 GRNGSGKTTLLKILAGILKPSAG 267
                                    889************99998764 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1      0.65   1.8e+02      23      38 ..      26      41 ..      19      48 .. 0.84
   2 ?    7.8   0.2     0.004       1.1      23      39 ..     245     261 ..     242     273 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.65
                         AAA_13 23 GwNGaGKTtLSrllrs 38
                                   G  G+GKTtL ++l+ 
  gi|119720395|ref|YP_920890.1| 26 GPTGSGKTTLLKVLAG 41
                                   888*******999986 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.004
                         AAA_13  23 GwNGaGKTtLSrllrsl 39 
                                    G+NG+GKTtL ++l+ +
  gi|119720395|ref|YP_920890.1| 245 GRNGSGKTTLLKILAGI 261
                                    9*********9999876 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1     0.056        16       3      20 ..      24      41 ..      22      56 .. 0.88
   2 ?   -1.0   0.0       4.3   1.2e+03      27      43 ..     116     132 ..     111     178 .. 0.77
   3 ?    2.5   0.1      0.37     1e+02       1      21 [.     241     261 ..     241     266 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.056
                                   EE-STTSSHHHHHHHHHH CS
                 Cytidylate_kin  3 iDGPagsGKssvaralae 20
                                   + GP+gsGK ++ + la 
  gi|119720395|ref|YP_920890.1| 24 VTGPTGSGKTTLLKVLAG 41
                                   57************9995 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 4.3
                                    EEHHHHHHHHHHHHHHT CS
                 Cytidylate_kin  27 ldtgalYRalalaalrr 43 
                                    l+ g+lYR la  al  
  gi|119720395|ref|YP_920890.1| 116 LSDGELYRLLAATALSG 132
                                    78899******999986 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.37
                                    EEEE-STTSSHHHHHHHHHHH CS
                 Cytidylate_kin   1 iaiDGPagsGKssvaralaek 21 
                                    +a+ G  gsGK ++ ++la  
  gi|119720395|ref|YP_920890.1| 241 VAVTGRNGSGKTTLLKILAGI 261
                                    689999************975 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1     0.034       9.5       7      35 ..      12      39 ..       6      43 .. 0.72
   2 ?    3.5   0.1     0.096        27      13      37 ..     236     259 ..     231     271 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.034
                  TrwB_AAD_bind  7 vplpkeretqhilivGttGsGKtqalekl 35
                                   +++++e e + ++++G tGsGKt+ l+ l
  gi|119720395|ref|YP_920890.1| 12 LSFEVE-EGELAVVTGPTGSGKTTLLKVL 39
                                   555443.44556789********998765 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.096
                  TrwB_AAD_bind  13 retqhilivGttGsGKtqalekllr 37 
                                    re + ++++G  GsGKt+ l+ +l+
  gi|119720395|ref|YP_920890.1| 236 REGECVAVTGRNGSGKTTLLK-ILA 259
                                    57777899*********9775.444 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.1     0.061        17       1      16 [.      25      40 ..      25      51 .. 0.88
   2 ?    4.3   0.2      0.18        51       1      16 [.     244     259 ..     244     273 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.061
                                   EE-TTSSHHHHHHHHH CS
                         AAA_17  1 lGgPGsGKgtqceklv 16
                                   +G+ GsGK+t+++ l+
  gi|119720395|ref|YP_920890.1| 25 TGPTGSGKTTLLKVLA 40
                                   699*********8765 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.18
                                    EE-TTSSHHHHHHHHH CS
                         AAA_17   1 lGgPGsGKgtqceklv 16 
                                    +G  GsGK+t+++ l+
  gi|119720395|ref|YP_920890.1| 244 TGRNGSGKTTLLKILA 259
                                    5889********6664 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   1.2     0.043        12      28      43 ..      24      39 ..      21      43 .. 0.89
   2 ?    6.5   0.9     0.029       8.1      26      57 ..     241     270 ..     238     271 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.043
                          DUF87 28 ilgsTGsGKSntvavL 43
                                   + g TGsGK+++ +vL
  gi|119720395|ref|YP_920890.1| 24 VTGPTGSGKTTLLKVL 39
                                   6799***********9 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.029
                          DUF87  26 lAilgsTGsGKSntvavLleellekkgatili 57 
                                    +A+ g+ GsGK+++ ++ l+ +l k++a +l+
  gi|119720395|ref|YP_920890.1| 241 VAVTGRNGSGKTTLLKI-LAGIL-KPSAGTLL 270
                                    79**********99985.56777.67776654 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.7     0.031       8.8       2      18 ..      23      39 ..      22      43 .. 0.88
   2 ?    4.0   0.1      0.13        35       3      19 ..     243     259 ..     241     274 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.031
                Viral_helicase1  2 vvhGvpGcGKStlirkl 18
                                   vv G  G+GK+tl++ l
  gi|119720395|ref|YP_920890.1| 23 VVTGPTGSGKTTLLKVL 39
                                   899**********9866 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.13
                Viral_helicase1   3 vhGvpGcGKStlirkll 19 
                                    v G  G+GK+tl++ l+
  gi|119720395|ref|YP_920890.1| 243 VTGRNGSGKTTLLKILA 259
                                    78889******998665 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.7     0.055        15       3      21 ..      21      39 ..      19      60 .. 0.83
   2 ?    4.5   0.1     0.063        18       3      20 ..     240     257 ..     238     283 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.055
                        DUF2075  3 vvlVtGvaGtGKtvvllnl 21
                                   + +VtG +G+GKt +l  l
  gi|119720395|ref|YP_920890.1| 21 LAVVTGPTGSGKTTLLKVL 39
                                   789**********998655 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.063
                        DUF2075   3 vvlVtGvaGtGKtvvlln 20 
                                    +v VtG+ G+GKt +l  
  gi|119720395|ref|YP_920890.1| 240 CVAVTGRNGSGKTTLLKI 257
                                    789**********98754 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.5      0.14        38       1      20 [.      21      40 ..      21      47 .. 0.86
   2 ?    4.2   0.6      0.15        41       4      24 ..     243     263 ..     240     272 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.14
                                   EEEEESSTTSSHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxx RF
                           CbiA  1 iaiastkGGvGKTtlaanLa 20
                                   +a++ +  G+GKTtl+  La
  gi|119720395|ref|YP_920890.1| 21 LAVVTGPTGSGKTTLLKVLA 40
                                   5899999*******987666 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.15
                                    EESSTTSSHHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxx RF
                           CbiA   4 astkGGvGKTtlaanLarala 24 
                                    + +  G+GKTtl+  La +l+
  gi|119720395|ref|YP_920890.1| 243 VTGRNGSGKTTLLKILAGILK 263
                                    56778********99999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                       112  (0.00624686); expected 17.9 (0.001)
Passed Fwd filter:                        64  (0.00356964); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              64  [number of targets reported over threshold]
# CPU time: 0.71u 0.31s 00:00:01.02 Elapsed: 00:00:00.49
# Mc/sec: 2481.05
//
Query:       gi|119720396|ref|YP_920891.1|  [L=220]
Description: BioY protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-27   95.9  17.4    4.1e-27   94.9  17.4    1.5  1  BioY      BioY family


Domain annotation for each model (and alignments):
>> BioY  BioY family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.9  17.4   2.3e-31   4.1e-27       2     132 ..      37     207 ..      36     210 .. 0.79

  Alignments for each domain:
  == domain 1  score: 94.9 bits;  conditional E-value: 2.3e-31
                           BioY   2 gpvpitlqtlavllaglllgprrgalavllYlllGalglPvfag.ggGlavllgptgGYllGFlvaalvvgll....... 73 
                                    gpvp t+q+ +v+laglll p  +a ++l+Ylll alg+Pv ag +gGlavllg tgGYllGF++ a+++++l       
  gi|119720396|ref|YP_920891.1|  37 GPVPYTMQNAGVVLAGLLLDPADAATSMLVYLLLIALGAPVAAGlRGGLAVLLGYTGGYLLGFVPSAFLMSVLsrlylrg 116
                                    8*******************************************99***************************9999999 PP

                           BioY  74 .......kk.laelllallagllviyalGvlwlal..........vls..............laaalaagvlpfipgdlv 121
                                           ++ l  ll+  +++++ +y+lG+l+++l          +                +   ++a+v++f+p dl+
  gi|119720396|ref|YP_920891.1| 117 rgldsanRRdLLVLLALSAVAVTPTYLLGFLVFSLyavpgsklyaW-AsgvagwlglggapgWLVLFVASVAVFVPQDLL 195
                                    999876423566667777779999********99965444433320.0233344444444446666999*********97 PP

                           BioY 122 k.avlaallaka 132
                                       v+a+l a++
  gi|119720396|ref|YP_920891.1| 196 MdHVVAVLAARE 207
                                    615555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      201  (0.0112109); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1393.27
//
Query:       gi|119720397|ref|YP_920892.1|  [L=215]
Description: hypothetical protein Tpen_1492 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.8e-18   66.9   8.6    7.7e-18   64.8   8.7    2.0  1  MS_channel  Mechanosensitive ion channel
  ------ inclusion threshold ------
          4    7.1  14.6        0.4   10.4   9.4    1.8  2  FtsK_4TM    4TM region of DNA translocase FtsK/SpoIIIE
        4.1    7.8  11.4        3.8    7.9   0.8    2.9  3  DUF4396     Domain of unknown function (DUF4396)


Domain annotation for each model (and alignments):
>> MS_channel  Mechanosensitive ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.8   8.7   1.3e-21   7.7e-18      28     106 ..     129     207 ..     104     213 .. 0.91

  Alignments for each domain:
  == domain 1  score: 64.8 bits;  conditional E-value: 1.3e-21
                                    HHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESSSEEEEEEEE-SSEEEEEETTSEEEEEEHHHHHTS-E CS
                     MS_channel  28 lavlGalglalglalkdlisnlvaGiillfekpfkiGDlveigdieGtVediglrttkirtfdgrivtiPnsslvtsni 106
                                    +a+ G++g ++g+a+++++ + +aG++ l+ +p++iGD+v++++ eG Vedi++++t ir+ dg++  iPn++++ s+i
  gi|119720397|ref|YP_920892.1| 129 VALGGFIGMVVGFASQQVLGQALAGLFTLIVRPIRIGDRVNVAGEEGVVEDISTLFTVIRKSDGSLALIPNNMVIGSKI 207
                                    8999*********************************************************************998876 PP

>> FtsK_4TM  4TM region of DNA translocase FtsK/SpoIIIE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.2      0.19   1.2e+03      82     100 ..      24      42 ..       8      57 .. 0.44
   2 ?   10.4   9.4   6.8e-05       0.4      57     150 ..      69     159 ..      62     164 .. 0.64

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.19
                       FtsK_4TM  82 rrkslerrllrllgallll 100
                                    r++ ++ +l+ ++++++++
  gi|119720397|ref|YP_920892.1|  24 RKSLQKLALWIVTYVVVTA 42 
                                    3322222222222222222 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 6.8e-05
                       FtsK_4TM  57 lllslfGlsawllvvlllawglrllrrkslerrllrllgalllllasaalfalrlasledelpggaGGvlGrllaaalst 136
                                     l  +fG+  +   +  ++w+lr    ++++++++ l+ +l + + +a++++ +    + +  +++GG++G +++ a+++
  gi|119720397|ref|YP_920892.1|  69 GLSLFFGYMIIRAFADTVYWTLRAKYPHPTAAAVRSLFTILGIGALLAGIAGGTA---GGAAGVALGGFIGMVVGFASQQ 145
                                    4445666655555555555555555545444444444444444445555555333...3466799*************** PP

                       FtsK_4TM 137 llgftGatllllvl 150
                                    +lg + a l  l++
  gi|119720397|ref|YP_920892.1| 146 VLGQALAGLFTLIV 159
                                    ****9999988876 PP

>> DUF4396  Domain of unknown function (DUF4396)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.7    0.0025        15      88     131 ..       5      50 ..       1      58 [. 0.80
   2 ?   -0.2   0.1      0.19   1.1e+03      44      60 ..      66      78 ..      51     106 .. 0.64
   3 ?    7.9   0.8   0.00064       3.8       6      44 ..     119     157 ..     116     160 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0025
                        DUF4396  88 evgmnlvmllllgamda..eleltsplfWfslqlsllaGflvalPv 131
                                     v+++ + +l+++++++  + +l+++++W++  + ++a  ++a+P+
  gi|119720397|ref|YP_920892.1|   5 HVIEAYWKVLAVSSVATnvRKSLQKLALWIVTYVVVTATVFTAVPY 50 
                                    5667777777755554446779***********************9 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.19
                        DUF4396 44 lsvvlalllgllletal 60
                                   +s+ l+l++g++    +
  gi|119720397|ref|YP_920892.1| 66 ISIGLSLFFGYM----I 78
                                   333333333333....3 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.00064
                        DUF4396   6 alatlhClaGcaiGdilgmviltslslalglpmaatmil 44 
                                    a  t  ++aG a+G ++gmv++++ + +lg+++a  + l
  gi|119720397|ref|YP_920892.1| 119 AGGTAGGAAGVALGGFIGMVVGFASQQVLGQALAGLFTL 157
                                    56788899***************9999999999877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       720  (0.0401584); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1508.62
//
Query:       gi|119720398|ref|YP_920893.1|  [L=228]
Description: metal-dependent hydrolase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-24   85.8   0.1    3.4e-24   85.5   0.1    1.1  1  Lactamase_B_2  Beta-lactamase superfamily domain
    6.2e-21   75.0   0.0    7.9e-21   74.6   0.0    1.1  1  Lactamase_B_3  Beta-lactamase superfamily domain
    2.6e-12   47.2   2.2    6.6e-12   45.8   2.2    1.6  1  Lactamase_B    Metallo-beta-lactamase superfamily


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.5   0.1   5.8e-28   3.4e-24       1     201 []      24     191 ..      24     191 .. 0.88

  Alignments for each domain:
  == domain 1  score: 85.5 bits;  conditional E-value: 5.8e-28
                                    SEEEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCH CS
                  Lactamase_B_2   1 rriLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylale 80 
                                    rriL+D++++   ++++  +P   r   +++d +++th+H DHl ++  l++ ++  ++++a  +++++l+++       
  gi|119720398|ref|YP_920893.1|  24 RRILLDPWLE--NPLSPV-KPSDYRG--ARVDYIFVTHDHGDHLGNAVELARATG--AKVVAVYELAEELSKE------- 89 
                                    8*********..443444.3555455..59*********************9555..6799999999999999....... PP

                                    TTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---HH.HHHHHCT-SE CS
                  Lactamase_B_2  81 eepavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyipee.igerlggadl 159
                                       +v+++  ++g++++l+  g++  +tpa h+s +      g   G++++g + +vy++gDtg + ++ +  +l+ +d+
  gi|119720398|ref|YP_920893.1|  90 ---GVQAVGANIGGPLALE--GIQAVFTPALHSSSK------GAPTGVVVRGRDTAVYHAGDTGLFGDMrLIGELYAPDV 158
                                    ...678999*********8..899************......9************************6655568999*** PP

                                    EEEE-S-SSTTHHHHHHT---STSHHHHCTTSSSSEEEEESB CS
                  Lactamase_B_2 160 lllditayeddemirhmgHltpeeaveaaadlgakrlvliHi 201
                                    +ll+i+         +++++ + ea++a++ l+++ ++++H+
  gi|119720398|ref|YP_920893.1| 159 ALLPIG---------GHFTMGVVEALKAVELLRPRLAIPMHY 191
                                    ******.........8999999*******************7 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.6   0.0   1.3e-24   7.9e-21       1     163 []       3     190 ..       3     190 .. 0.79

  Alignments for each domain:
  == domain 1  score: 74.6 bits;  conditional E-value: 1.3e-24
                  Lactamase_B_3   1 eltwlghnsflletag.....arilvDPf.....kanlgyeppaeeaDlvlisqaledHahle.tlkqlaenvkvlee.. 67 
                                    +l++lgh++f +e +g      ril+DP+     ++ +  ++   ++D + +++++ dH   + +l++ a+ +kv++   
  gi|119720398|ref|YP_920893.1|   3 RLRYLGHAAFDVELEGfdgrkRRILLDPWlenplSPVKPSDYRGARVDYIFVTHDHGDHLGNAvELAR-ATGAKVVAVye 81 
                                    589*******9998642225579******444432234444455***************755414555.77788888877 PP

                  Lactamase_B_3  68 .................geslevggleiravatshdavggsergenngflleqdgltiyhlGhlahelsseelkelgrvD 130
                                                     g+ l+++g++   +++ h +++g++ g     +++ ++  +yh G+++   ++  + el  +D
  gi|119720398|ref|YP_920893.1|  82 laeelskegvqavganiGGPLALEGIQAVFTPALHSSSKGAPTG----VVVRGRDTAVYHAGDTGLFGDMRLIGELYAPD 157
                                    77777777776666666666888888888888888777666666....69999*************************** PP

                  Lactamase_B_3 131 vvltPvggpltlgqeealelakrLkpklvlPmh 163
                                    v l+P+gg++t+g  eal+++++L+p+l +Pmh
  gi|119720398|ref|YP_920893.1| 158 VALLPIGGHFTMGVVEALKAVELLRPRLAIPMH 190
                                    ********************************9 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   2.2   1.1e-15   6.6e-12      13     170 ..      21     169 ..      14     190 .. 0.71

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 1.1e-15
                                    ETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHHHHHHH CS
                    Lactamase_B  13 gdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmeeaddaas 92 
                                    g ++ iL D+ ++++ +  +      ++ + +vd++++TH H DH G++ +l++at+++v+av+e a++l +e+++    
  gi|119720398|ref|YP_920893.1|  21 GRKRRILLDPWLENPLSPVKP----SDYRGARVDYIFVTHDHGDHLGNAVELARATGAKVVAVYELAEELSKEGVQAVGA 96 
                                    567888888888888888875....9999**********************************************65322 PP

                                    HCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTST.SCCEEEEEETTCCEEEECTTTSSHHCCCCCC......... CS
                    Lactamase_B  93 rkglllagvsadkpdvdeeeldgnaggrralyvtggpgh.ghghgvveygggkvlftGDallagetgridl......... 162
                                                   +   +l++++   +++++ +      ++++vv+ ++  v  +GD++l g+  +i++         
  gi|119720398|ref|YP_920893.1|  97 ---------------NIGGPLALEGIQAVFTPALHSSSKgAPTGVVVRGRDTAVYHAGDTGLFGDMRLIGElyapdvall 161
                                    ...............33333333333333333333333314677777778888888999999999999999777555555 PP

                                    .TTCEEE- CS
                    Lactamase_B 163 tlrgaevr 170
                                    +++g++++
  gi|119720398|ref|YP_920893.1| 162 PIGGHFTM 169
                                    44444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1671.05
//
Query:       gi|119720399|ref|YP_920894.1|  [L=701]
Description: glycoside hydrolase family 3 protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.6e-60  202.8   0.0    1.3e-59  202.2   0.0    1.2  1  Glyco_hydro_3    Glycosyl hydrolase family 3 N terminal domai
    1.2e-47  162.5   0.0    3.2e-47  161.2   0.0    1.7  1  Glyco_hydro_3_C  Glycosyl hydrolase family 3 C-terminal domai
    1.8e-24   85.6   0.2    4.2e-24   84.5   0.2    1.7  1  Fn3-like         Fibronectin type III-like domain


Domain annotation for each model (and alignments):
>> Glyco_hydro_3  Glycosyl hydrolase family 3 N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  202.2   0.0   2.1e-63   1.3e-59      60     319 .]      32     279 ..      19     279 .. 0.92

  Alignments for each domain:
  == domain 1  score: 202.2 bits;  conditional E-value: 2.1e-63
                                    SS....S--EEEE---BTTB---SS...S..---S-HHHHHHHT-HHHHHHHHHHHHHHHHHHT--EE---B-----STT CS
                  Glyco_hydro_3  60 eksrlgiPlllavDqegGlvqrlge...g..tlfPsalalaatssldlikelgriiakelralgididfaPvvdvnrdpr 134
                                    e  ++ +P ++++D  +Gl+ + +       t fP ++ laat++++ ++ +gr+i++e ra g+d+ +aP v+ +r+p 
  gi|119720399|ref|YP_920894.1|  32 ETRPVRVPSIVTADGPSGLRVEPSGgrrWfaTAFPVPTMLAATWNPEVVERVGRAIGEECRAYGVDVLLAPGVNMHRHPL 111
                                    566788999999999999876432211213599*********************************************** PP

                                    SSSGGGSS-SSHHHHHHHHHHHHHHHHHTT-EEEEEEETTGTT-SSETTTSEEB----HHHHHHTTHHHHHHHH.HTT-S CS
                  Glyco_hydro_3 135 ngigvrsFsedpelvaalaaamvkGlqgagvaatvKHFpghGdgavdshkelptvdhseeelrevdlvpfqaai.eagvd 213
                                     g+++++Fsedp l + +aaa+v+G+q+ gv at+KHF++   +++++++ ++++  se++lre++l+pf+ a+ +a+  
  gi|119720399|ref|YP_920894.1| 112 CGRNFEYFSEDPLLSGEMAAAYVRGVQSVGVGATLKHFAA---NDQETNRTVIDTVVSERALREIYLKPFEIAVkKAKPW 188
                                    ****************************************...5************************************ PP

                                    EEEE---B-TTT---BGGG-HHHHIIIIIIIS---SEEEES-TTSHHHHCCS-HHHHHHHHHHHT-SBEES-S---SGHH CS
                  Glyco_hydro_3 214 sVMtaHvqfpaldgtpatgskklltdvLRkelGFdGvvvsDalamkeiadrggkeeavvlaLkAGvDilLvpeertseik 293
                                     VM +   +++l+g+  + +++llt vLR+e+GFdGvv++D+             + +v  ++AG+D+++  ++    ++
  gi|119720399|ref|YP_920894.1| 189 CVMSS---YNKLNGKYSSQNEWLLTRVLREEWGFDGVVMTDWG----------AGDDSVEQVNAGNDLIMPGSDEA--VE 253
                                    *****...**********************************9..........44567889*********999996..9* PP

                                    HHHHHHHTTSS-HHHHHHHHHHHHHH CS
                  Glyco_hydro_3 294 alkkavkeGeltearidesvrrvlrl 319
                                    +l++a+++G+l  +++++s++rvlrl
  gi|119720399|ref|YP_920894.1| 254 KLLEAARSGRLRLEALEASAERVLRL 279
                                    ************************96 PP

>> Glyco_hydro_3_C  Glycosyl hydrolase family 3 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.2   0.0   5.3e-51   3.2e-47       1     204 []     312     578 ..     312     578 .. 0.89

  Alignments for each domain:
  == domain 1  score: 161.2 bits;  conditional E-value: 5.3e-51
                                    -EEEEEGSS--S-S-STEEEEEESGGGSSS-SS-BSSS----S---HHHHHHHHHHH....................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...................... RF
                Glyco_hydro_3_C   1 iVLLkNennlLPLkkklkkiaviGpnadetlklGggsgtvtvsylvsplegirerles...................... 58 
                                    +VLLkNe ++LPL + + ++a++G    etlk G gsg+++++y+v++leg++                           
  gi|119720399|ref|YP_920894.1| 312 VVLLKNE-GALPLGPGA-RVALFGTGQVETLKGGMGSGHTHPRYVVTVLEGLKSGGLLvdeelssiyeryvreargeefl 389
                                    7******.*****8886.******99999***********************987644889******************* PP

                                    .................-HHHHHHHHHHHTSEEEEEEEES...SB-TTSC....SGHHSSTTHHHHHHHHH....HTTSS CS
                                    ................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxx....xxxxx RF
                Glyco_hydro_3_C  59 ................eegideaveaakeaDvavvvvgedpeiegEgvDr....tdlalpeaqdelikava....aankn 114
                                                      ++ +a++ a+++D+avvv+ +    +gEg+Dr     d+ l+e++++l++ v+      +k+
  gi|119720399|ref|YP_920894.1| 390 eklyldevyadplpqdIVSEGDAARFAERNDAAVVVLYRV---SGEGWDRrpvrGDFYLTESEERLLRLVSrefrGRGKK 466
                                    **************9856788999****************...******999999*************9996655677** PP

                                    EEEEEEESSGG--TTTGTTTEEEEEE-S--GCCHHHHHHHHHTTSS---B--SS-EESSSGGG................. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx.xx..... RF
                Glyco_hydro_3_C 115 vvvvlqsggpvavepwkeenvkAilaawlpGqegGtaiadvLfGdvnPsGkLpvtfpksledlpd.dyyeek.dt..... 187
                                    vvvvl+  gp++v++w  + v+Ail +wlpGqe+G+ +advL G+vnPsGkLp+t+p++++d+p  +   ++ ++     
  gi|119720399|ref|YP_920894.1| 467 VVVVLNVCGPIEVASW-RDLVDAILVVWLPGQEAGRVVADVLAGRVNPSGKLPMTWPRDWTDVPAaK--APEcYPglpve 543
                                    ****************.77********************************************8832..22232234445 PP

                                    ..................S.-----SETTTT-BCH CS
                                    .................xx.xxxxxxxxxxxxxxx RF
                Glyco_hydro_3_C 188 .................yk.fegtplYpeGlglsY 204
                                                     y+ f  +p Y++G+glsY
  gi|119720399|ref|YP_920894.1| 544 dprrvvycegvyvgyryYDtFGVEPAYEFGYGLSY 578
                                    56778888889889888778888888999999998 PP

>> Fn3-like  Fibronectin type III-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.5   0.2     7e-28   4.2e-24       1      71 []     611     682 ..     611     682 .. 0.99

  Alignments for each domain:
  == domain 1  score: 84.5 bits;  conditional E-value: 7e-28
                                    EEEEEEEEESS-STTSBS-EEEEEEEEE.E-TT-EEEEEEEEECGGG-EEETTTTEEE--SCEEEEEEESSS CS
                       Fn3-like   1 evvqlYvsdpessverpvkeLkgFekve.LapGesktvtftldrkdlsvwdeekqkwvvepGeytvlvgtss 71 
                                    ev+q+Yv++p +++++p +eLk+F+k++ L+pGe ++++++++ +dl+++de+++ wvvepGey+v vg+ss
  gi|119720399|ref|YP_920894.1| 611 EVAQVYVRAPRGRIDKPFQELKAFRKTRlLEPGEAERIKLRVSLRDLASFDEREKVWVVEPGEYEVRVGSSS 682
                                    8*********************************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (701 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       283  (0.0157845); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 4859.62
//
Query:       gi|119720400|ref|YP_920895.1|  [L=101]
Description: AbrB family transcriptional regulator [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-08   34.7   0.4      2e-08   34.0   0.4    1.4  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
  ------ inclusion threshold ------
      0.011   15.7   0.1      0.019   15.0   0.1    1.7  1  MraZ            MraZ protein, putative antitoxin-like


Domain annotation for each model (and alignments):
>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   0.4   2.2e-12     2e-08       3      42 ..      16      56 ..      14      59 .. 0.88

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 2.2e-12
                                   ETTEEEEEE-CCCHHHCCEECTCEEEEEECTT.CCCCCCCH CS
                 MazE_antitoxin  3 vGnsgavriPkevrfelgireGdevelevdgd.kiilrplk 42
                                   v+  g+v+iPkevr+ lg+ eG+++ l++ +d  i lr+l 
  gi|119720400|ref|YP_920895.1| 16 VDAEGRVVIPKEVRERLGLAEGSRLLLVELSDdTIALRKLD 56
                                   56669**************************9999888876 PP

>> MraZ  MraZ protein, putative antitoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1   2.1e-06     0.019       6      32 ..      12      41 ..       9      96 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.1e-06
                                   EEEEB-TTSEEE--CHHHHHTTSC...SEE CS
                           MraZ  6 tevelDakGRlllPaklreeakle...kev 32
                                     v +Da GR+ +P++ re ++l    +++
  gi|119720400|ref|YP_920895.1| 12 KVVVVDAEGRVVIPKEVRERLGLAegsRLL 41
                                   56779***************9987444555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1471  (0.0820458); expected 358.6 (0.02)
Passed bias filter:                      776  (0.0432818); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 692.57
//
Query:       gi|119720401|ref|YP_920896.1|  [L=101]
Description: hypothetical protein Tpen_1496 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0049   16.8   1.9     0.0062   16.5   1.9    1.3  1  PaREP1    Archaeal PaREP1/PaREP8 family


Domain annotation for each model (and alignments):
>> PaREP1  Archaeal PaREP1/PaREP8 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   1.9   3.4e-07    0.0062       3      58 ..      12      66 ..      10      98 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.4e-07
                         PaREP1  3 leeaekeleeAeellekGdlrqAaeKaykAvkalvkalaeknnlklleeaeekerw 58
                                   l++a++el+e ++     +lrqAaeK + A+  +v   ++    +  +  +ek+  
  gi|119720401|ref|YP_920896.1| 12 LKAARRELDEYRKTGDSMKLRQAAEKGWLAINKAVEEFLKTLGVEA-KTYREKRDA 66
                                   67778888887888788889********887777777777643333.333333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       921  (0.0513693); expected 358.6 (0.02)
Passed bias filter:                      603  (0.0336327); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 757.29
//
Query:       gi|119720402|ref|YP_920897.1|  [L=437]
Description: peptidase U34, dipeptidase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-13   50.7   0.1    3.5e-13   49.2   0.1    1.7  1  Peptidase_C69  Peptidase family C69
    0.00014   21.7   0.0    0.00024   20.9   0.0    1.3  1  AAT            Acyl-coenzyme A:6-aminopenicillanic acid acyl-


Domain annotation for each model (and alignments):
>> Peptidase_C69  Peptidase family C69
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.2   0.1   3.9e-17   3.5e-13       2     177 ..       2     172 ..       1     191 [. 0.76

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 3.9e-17
                  Peptidase_C69   2 CttllVGkkASlDGstiiarneDsagealnpkrfvvvkpeeqpreYksvlsnleldlPenplrytsvpnalgkegileea 81 
                                    C tl+  + A  DG ti a+n D   e ++++ +  v p  ++ e +  ++ +e++  ++++   +   +       +e 
  gi|119720402|ref|YP_920897.1|   2 CDTLVALRGATRDGVTIFAKNSD--REPNEAQVLEFV-PRMRHTEERVRVTYVEVEQVDETYAVLISRPFWM---WGAEM 75 
                                    899999999**************..444434444333.4444445677888899999999887665555543...33688 PP

                  Peptidase_C69  82 gineanvamsatetittnervlgadPlvskggigeedlitlvLpyiksARegvkrlgdlleeyGtye..........sng 151
                                    g+ne  va+        ne+v++   +  k+g++  dl+ l L+++++ARe++k ++ lleeyG+ +           n+
  gi|119720402|ref|YP_920897.1|  76 GVNEFGVAVG-------NEAVFTRGGYS-KTGLTGMDLVRLALERSRTAREALKWITSLLEEYGQGGncsyfrkmfyNNS 147
                                    9999999976.......56777777776.***********************************8752333333333589 PP

                  Peptidase_C69 152 vafsDkneiWylEtigGhhWvAvRvP 177
                                    + ++D+ e W lEt+ G +WvA Rv 
  gi|119720402|ref|YP_920897.1| 148 FLVADPREAWVLETV-GREWVAERVE 172
                                    **************9.699*****93 PP

>> AAT  Acyl-coenzyme A:6-aminopenicillanic acid acyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   2.6e-08   0.00024       4      98 ..      13     126 ..      11     162 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2.6e-08
                                    SE...EEEEEEEE-S-S--EEEEE--S..................SS--EEEE.SSSS-SEEEEEETTS-EEEE-TTS-T CS
                            AAT   4 kdgk.llgrNeDldpetlsnrflvvased................sgfaslgy.agslpGrtdGiNeaGLavtinllslk 65 
                                    +dg  ++++N D  p+ ++ + +v                     + +a+l   +  ++G ++G+Ne G+av++  +  +
  gi|119720402|ref|YP_920897.1|  13 RDGVtIFAKNSDREPNEAQVLEFVPRMRHteervrvtyveveqvdETYAVLISrPFWMWGAEMGVNEFGVAVGNEAVFTR 92 
                                    566669999999888888888887655445579999999999999****9988788899***************766555 PP

                                    .TT---------HHHHHHH.--SHHHHHHTHHHH CS
                            AAT  66 .klrakGfprafitRllLekcesveeAvellkei 98 
                                       + +G+  + + Rl Le++++  eA + + ++
  gi|119720402|ref|YP_920897.1|  93 gGYSKTGLTGMDLVRLALERSRTAREALKWITSL 126
                                    267899*********************9988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (437 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2949.53
//
Query:       gi|119720403|ref|YP_920898.1|  [L=682]
Description: hypothetical protein Tpen_1498 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
   4.9e-113  378.7   0.0   5.7e-113  378.5   0.0    1.0  1  Beta_propel  Beta propeller domain
  ------ inclusion threshold ------
      0.055   13.3   0.1       0.15   12.0   0.1    1.7  1  PsbN         Photosystem II reaction centre N protein (psbN)
       0.09   12.5   0.0       0.14   11.9   0.0    1.2  1  DUF2225      Uncharacterized protein conserved in bacteria (D


Domain annotation for each model (and alignments):
>> Beta_propel  Beta propeller domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  378.5   0.0  9.5e-117  5.7e-113       2     514 .]      97     673 ..      96     673 .. 0.96

  Alignments for each domain:
  == domain 1  score: 378.5 bits;  conditional E-value: 9.5e-117
                    Beta_propel   2 SeTNvqvegVdEaDivktDGkyiyvvsgskvvivdaeaeelklvseikleekfkieelyldgdrLvvisseeeeeeseae 81 
                                    S+TNvqv gVdE+Divk    +i v++gs+v+iv    +e k++++i+  +  ++  l+l+g+rL+vi+s+   ++    
  gi|119720403|ref|YP_920898.1|  97 SKTNVQVVGVDEPDIVKAGSGVIAVARGSEVYIVG--IAERKVLGKISAGS--QVFGLFLEGSRLAVITSTPLIRPLVVL 172
                                    9**********************************..999**********9..*******************99998877 PP

                    Beta_propel  82 ..eeeepilskee.tkvliyDisdkenpkllreleldGsyvssRkigdklylvsskeaeeeeenekeaeeakleellPkv 158
                                        + p+l   + t++l+y+i+d+++p+ll + +++G+ + +R+ g+ +y+++s               a+le  lP v
  gi|119720403|ref|YP_920898.1| 173 pgAGSPPYLGGVAnTTLLVYSIEDPSSPRLLYSSSVSGYPLGARMLGGVVYILTS---------------APLEVKLPLV 237
                                    64555555544448*****************************************...............678889**** PP

                    Beta_propel 159 seeeeklvacediylpdesesssylvvtsldlakdkavdskavlgsgeevYvseenlYlas................... 219
                                       +++ ++  ++  +d s+s  ylv++ +dl++ k++ +++  + ++++Y+ e++lY+as                   
  gi|119720403|ref|YP_920898.1| 238 ---DGEPIPPGSVAKIDPSASW-YLVLLCMDLSTGKHSAYAFTSAPSSWIYMGENRLYVASypsvyeealkefleavskr 313
                                    ...88899*********99999.********************************************************* PP

                    Beta_propel 220 .........................................eeyeeeeeksedkTeiykfalsdgkveyaasgeVpGtll 258
                                                                             e++++e     dkT +  fa+s+ kv+y++s+eVpG++l
  gi|119720403|ref|YP_920898.1| 314 lpggvsgrvsglafqgllgealnaledylssvsydvardilEKAAAEVPPIPDKTIFKVFAVSGLKVSYRGSVEVPGRVL 393
                                    *****************************************8899999******************************** PP

                    Beta_propel 259 nqFsldeydgyLRvatt........................................................leteese 282
                                    +qFs++e +gy+ vatt                                                        +  +e +
  gi|119720403|ref|YP_920898.1| 394 DQFSMEELGGYFVVATTsgewrvrasiaktlitppsppsrnvtvevcsggscreivvpitvqptslragrpivYVGVEPA 473
                                    *************************************************************************889999* PP

                    Beta_propel 283 aetsnnvyvLd.eklkevGkleglapgEriysvRFmgdraYlVTfrqtDPLFviDLsdpanPkilGeLkIpGySeYLhpy 361
                                    a+tsnnv+    e+lk+ G+l+glapgEr+y++R +g+++YlVT+rq+DPLF++DLsdp++P++lG++k pG+SeYLhp+
  gi|119720403|ref|YP_920898.1| 474 ADTSNNVFSVSlEDLKVKGNLTGLAPGERVYASRLVGSTMYLVTYRQVDPLFAVDLSDPSSPRVLGYVKAPGFSEYLHPV 553
                                    **********6688****************************************************************** PP

                    Beta_propel 362 denhLlGiGkeadeegeeeqglklslFDVsDpanpkevakvvigdrgsdsealydhkAllfdkeknllaipvseesnses 441
                                      ++LlG+G         ++ lk+slFDVsDp++++e+++v+i+ +   s++++dh+A+ fd+++++ +ipvs     ++
  gi|119720403|ref|YP_920898.1| 554 TGKLLLGVGFT------DDRRLKVSLFDVSDPKAIREASTVTIAAS---SPVTSDHHAFSFDPSNGRAYIPVS----LWY 620
                                    *********77......2378**********************555...8***********************....79* PP

                    Beta_propel 442 sssqgayvykvdaekgfklkgkitheelakeetlkkakdlyeysskvrRslyigdklytvseskiksadletl 514
                                    + s g++v++v+ + +++ ++ ++h+                      R++y+ d+++tvs++++++++ +tl
  gi|119720403|ref|YP_920898.1| 621 TGSGGVMVVEVK-NGRLSFVKLLEHPG-------------------ALRTVYTPDEVFTVSQASVNVYSSSTL 673
                                    ************.9***********66...................89********************99885 PP

>> PsbN  Photosystem II reaction centre N protein (psbN)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   2.5e-05      0.15       4      31 ..       4      31 ..       1      33 [. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.5e-05
                           PsbN  4 AtvlsisiaavlvaiTgfsiYtaFGPPs 31
                                    +++++ ++a++ a+T f++Y+a GP +
  gi|119720403|ref|YP_920898.1|  4 RMLVAVVLLALIGALTPFALYVALGPRA 31
                                   5789999999999*************86 PP

>> DUF2225  Uncharacterized protein conserved in bacteria (DUF2225)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.4e-05      0.14      98     154 ..     254     312 ..     246     319 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.4e-05
                        DUF2225  98 esYkLallcyelkkekkskkAklalrlAWlyrdked..eekeklflkkAlelykeayek 154
                                    +s++L llc++l   k+s  A ++   +W+y  ++    ++    +++Al+ + ea++k
  gi|119720403|ref|YP_920898.1| 254 ASWYLVLLCMDLSTGKHSAYAFTSAPSSWIYMGENRlyVASYPSVYEEALKEFLEAVSK 312
                                    689*****************************999944344457899999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (682 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.50
# Mc/sec: 4131.49
//
Query:       gi|119720404|ref|YP_920899.1|  [L=132]
Description: transcriptional regulator, TrmB [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-12   46.8   0.1    3.6e-12   45.9   0.1    1.4  1  HTH_5            Bacterial regulatory protein, arsR family
    4.9e-12   45.2   0.0    8.8e-12   44.4   0.0    1.5  1  HTH_24           Winged helix-turn-helix DNA-binding
      2e-11   43.5   0.8    1.4e-10   40.7   0.2    2.2  2  HTH_IclR         IclR helix-turn-helix domain
    2.3e-10   40.2   0.1    3.7e-10   39.5   0.1    1.4  1  TrmB             Sugar-specific transcriptional regulator Trm
      2e-09   37.2   0.0    4.1e-09   36.2   0.0    1.5  1  MarR_2           MarR family
    1.6e-08   34.5   0.1    2.6e-08   33.8   0.1    1.4  1  HTH_20           Helix-turn-helix domain
    1.3e-05   25.1   0.0    1.8e-05   24.6   0.0    1.2  1  MarR             MarR family
    2.7e-05   23.9   1.2    5.2e-05   23.0   0.0    2.1  1  HTH_AsnC-type    AsnC-type helix-turn-helix domain
     0.0001   22.0   0.0    0.00022   20.9   0.0    1.5  1  HTH_38           Helix-turn-helix domain
    0.00014   21.8   0.0    0.00025   21.0   0.0    1.4  1  HTH_Crp_2        Crp-like helix-turn-helix domain
    0.00023   21.2   0.0    0.00066   19.8   0.0    1.8  2  HTH_28           Helix-turn-helix domain
    0.00029   20.5   0.0     0.0029   17.2   0.0    2.2  2  Sigma70_r4_2     Sigma-70, region 4
    0.00034   20.8   0.0    0.00062   19.9   0.0    1.4  1  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
    0.00076   19.2   0.0     0.0013   18.5   0.0    1.3  1  LexA_DNA_bind    LexA DNA binding domain
    0.00081   19.1   0.0    0.00098   18.9   0.0    1.1  1  DUF4423          Domain of unknown function (DUF4423)
     0.0011   18.7   0.0     0.0028   17.4   0.0    1.6  1  HTH_10           HTH DNA binding domain
     0.0014   18.3   0.0     0.0023   17.6   0.0    1.3  1  HTH_psq          helix-turn-helix, Psq domain
     0.0014   18.4   0.0      0.004   16.9   0.0    1.8  1  HTH_30           PucR C-terminal helix-turn-helix domain
     0.0018   18.3   0.1     0.0084   16.1   0.0    1.9  2  HTH_29           Winged helix-turn helix
     0.0024   18.2   0.0     0.0038   17.6   0.0    1.3  1  Rrf2             Transcriptional regulator
     0.0034   17.1   0.0     0.0057   16.4   0.0    1.3  1  HTH_DeoR         DeoR-like helix-turn-helix domain
     0.0034   17.5   0.0     0.0056   16.8   0.0    1.4  1  B-block_TFIIIC   B-block binding subunit of TFIIIC
     0.0065   16.6   0.1     0.0065   16.6   0.1    1.9  1  DprA_WH          DprA winged helix domain
  ------ inclusion threshold ------
      0.011   15.7   0.0      0.019   14.9   0.0    1.4  1  HTH_11           HTH domain
      0.014   15.0   0.0      0.025   14.2   0.0    1.4  1  RP-C             Replication protein C N-terminal domain
      0.017   14.9   0.0      0.041   13.7   0.0    1.7  1  HTH_23           Homeodomain-like domain
      0.019   15.4   0.0      0.038   14.5   0.0    1.5  1  HTH_27           Winged helix DNA-binding domain
      0.028   14.4   0.0       0.16   12.0   0.0    2.2  1  HTH_36           Helix-turn-helix domain
      0.034   14.6   0.0      0.051   14.0   0.0    1.3  1  HTH_40           Helix-turn-helix domain
      0.048   13.8   0.0       0.08   13.0   0.0    1.4  1  MerR_1           MerR HTH family regulatory protein
      0.049   13.6   0.0      0.091   12.7   0.0    1.5  1  HTH_1            Bacterial regulatory helix-turn-helix protei
      0.051   13.2   0.0      0.093   12.4   0.0    1.4  1  CENP-B_N         CENP-B N-terminal DNA-binding domain
      0.063   13.1   0.0       0.12   12.2   0.0    1.4  1  DUF742           Protein of unknown function (DUF742)
      0.067   12.8   0.0       0.12   11.9   0.0    1.4  1  GerE             Bacterial regulatory proteins, luxR family
      0.068   12.8   0.0       0.14   11.9   0.0    1.5  1  GntR             Bacterial regulatory proteins, gntR family
      0.088   12.6   0.0       0.25   11.2   0.0    1.8  1  MerR             MerR family regulatory protein
      0.099   13.0   0.0       0.14   12.6   0.0    1.2  1  Penicillinase_R  Penicillinase repressor
        0.1   12.7   0.0       0.24   11.5   0.0    1.6  1  HTH_9            RNA polymerase III subunit RPC82 helix-turn-
       0.14   12.3   0.0       0.21   11.7   0.0    1.3  1  DUF2250          Uncharacterized protein conserved in archaea
       0.14   12.1   0.0       0.23   11.5   0.0    1.3  1  Cdc6_C           CDC6, C terminal winged helix domain
       0.27   10.2   0.0       0.32    9.9   0.0    1.1  1  TnsD             Tn7-like transposition protein D


Domain annotation for each model (and alignments):
>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.9   0.1   8.3e-15   3.6e-12       8      47 .]      16      55 ..       9      55 .. 0.93

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 8.3e-15
                                   HHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                          HTH_5  8 LklLaegelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                   L lL++ge+ v ela+elgl++stv +HL++L+++GLV+k
  gi|119720404|ref|YP_920899.1| 16 LELLQSGEMGVRELARELGLPPSTVHYHLNRLEDLGLVKK 55
                                   778999********************************87 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.4   0.0     2e-14   8.8e-12       3      48 .]       9      54 ..       7      54 .. 0.95

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 2e-14
                         HTH_24  3 etdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                    t ++I+ +L + + +  reLA++lgl+pstv+++l+rLe+ Gl+k
  gi|119720404|ref|YP_920899.1|  9 GTALRIYLELLQSGEMGVRELARELGLPPSTVHYHLNRLEDLGLVK 54
                                   5789****************************************97 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7   0.2   3.3e-13   1.4e-10      16      50 ..      21      55 ..      16      57 .. 0.94
   2 ?    0.7   0.0       1.1   4.7e+02       3      12 ..     109     118 ..     108     121 .. 0.86

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 3.3e-13
                                   BSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                       HTH_IclR 16 pqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                    +e++++elAr++glp+Stvh +L+ L+ lG+v++
  gi|119720404|ref|YP_920899.1| 21 SGEMGVRELARELGLPPSTVHYHLNRLEDLGLVKK 55
                                   689******************************96 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1.1
                                    HHHHHHHCT- CS
                       HTH_IclR   3 dRalaiLdal 12 
                                    dRa+aiL  l
  gi|119720404|ref|YP_920899.1| 109 DRAAAILASL 118
                                    8******876 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   0.1   8.6e-13   3.7e-10       6      61 ..       7      62 ..       1      69 [. 0.89

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 8.6e-13
                                   HHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTE CS
                           TrmB  6 LseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpkl 61
                                   Ls +  ++Yl Ll++g++ ++e+a+elg+p s+v   L++Led GlV++ +  +++
  gi|119720404|ref|YP_920899.1|  7 LSGTALRIYLELLQSGEMGVRELARELGLPPSTVHYHLNRLEDLGLVKKGEDGYTV 62
                                   6777789*****************************************99988776 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   0.0   9.4e-12   4.1e-09       3      54 ..       7      56 ..       6      65 .. 0.88

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 9.4e-12
                                   --HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                         MarR_2  3 ltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                   l+++ +r+ ++L  +++  + v+elar+lgl++s+v+++l+rL++ GLv + 
  gi|119720404|ref|YP_920899.1|  7 LSGTALRIYLELLQSGE--MGVRELARELGLPPSTVHYHLNRLEDLGLVKKG 56
                                   56677777789999999..99****************************876 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.1   5.9e-11   2.6e-08      11      56 ..      10      55 ..       7      60 .. 0.91

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 5.9e-11
                                   HHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                         HTH_20 11 vRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                                   + +ri+ +L + +++ + ela++l+l+++t++yHL+ Le+ gLv+ 
  gi|119720404|ref|YP_920899.1| 10 TALRIYLELLQSGEMGVRELARELGLPPSTVHYHLNRLEDLGLVKK 55
                                   7899999999**********************************85 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   4.1e-08   1.8e-05       4      49 ..      10      55 ..       7      58 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 4.1e-08
                                   HHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                           MarR  4 tqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieR 49
                                   t ++i   l ++g++ v eLa+ lg+ +stv   l rLe+ Gl+++
  gi|119720404|ref|YP_920899.1| 10 TALRIYLELLQSGEMGVRELARELGLPPSTVHYHLNRLEDLGLVKK 55
                                   5566667899*********************************986 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   1.2e-07   5.2e-05       7      42 .]      13      48 ..      10      48 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 1.2e-07
                  HTH_AsnC-type  7 kILeaLqedaRisyaeLAervGlSestvlrRvrrLe 42
                                   +I  +L + + + ++eLA+++Gl +stv+  ++rLe
  gi|119720404|ref|YP_920899.1| 13 RIYLELLQSGEMGVRELARELGLPPSTVHYHLNRLE 48
                                   666778889*************************98 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0     5e-07   0.00022      15      43 ..      17      46 ..      13      47 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 5e-07
                         HTH_38 15 rllaeG.lslreIArrLgrspsTIsRElkR 43
                                    ll+ G +++re Ar+Lg  psT++++l R
  gi|119720404|ref|YP_920899.1| 17 ELLQSGeMGVRELARELGLPPSTVHYHLNR 46
                                   4788888*******************9988 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   5.6e-07   0.00025      25      68 .]      27      71 ..      14      71 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 5.6e-07
                                   HHHHHHTTSSHHHHHHHHHHHHHTTSEEETEE.EEES-HHHHHHH CS
                      HTH_Crp_2 25 eelAsmlGltretvsrilseLkreglisrgrr.irildleaLral 68
                                   +elA+ lGl ++tv   l++L++ gl+++g +  ++  + +L+++
  gi|119720404|ref|YP_920899.1| 27 RELARELGLPPSTVHYHLNRLEDLGLVKKGEDgYTVAKRIKLKDY 71
                                   79**************************87444999999999875 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   1.5e-06   0.00066       7      40 ..      17      51 ..      12      56 .. 0.87
   2 ?   -1.9   0.0       8.9   3.9e+03       6      22 ..      98     115 ..      96     116 .. 0.60

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.5e-06
                         HTH_28  7 kllaaGh.svreaArelgisrrtvyrWikryeegG 40
                                   +ll++G+  vre+Arelg+ ++tv   ++r+e  G
  gi|119720404|ref|YP_920899.1| 17 ELLQSGEmGVRELARELGLPPSTVHYHLNRLEDLG 51
                                   56779999****************99999999877 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 8.9
                         HTH_28   6 ikllaaGh.svreaArel 22 
                                    ++ l+ G+ + + aA++l
  gi|119720404|ref|YP_920899.1|  98 LLTLQGGElNPDRAAAIL 115
                                    455555667777777765 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   6.7e-06    0.0029      25      49 ..      22      46 ..      12      47 .. 0.87
   2 ?    0.4   0.0       1.2   5.4e+02      10      27 ..     105     122 ..     104     123 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 6.7e-06
                                   S---HHHHHHHHT--HHHHHHHHHH CS
                   Sigma70_r4_2 25 eglsykEIAellgisegtVksrlsR 49
                                    ++  +E A++lg++++tV ++l R
  gi|119720404|ref|YP_920899.1| 22 GEMGVRELARELGLPPSTVHYHLNR 46
                                   678899*****************88 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.2
                                    TS-HHHHHHHHHHHTS-- CS
                   Sigma70_r4_2  10 eLperqreifllrylegl 27 
                                    eL +++ +++l + l gl
  gi|119720404|ref|YP_920899.1| 105 ELNPDRAAAILASLLSGL 122
                                    799*******99988886 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   1.4e-06   0.00062      21      53 ..      22      54 ..      13      60 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.4e-06
                                   SSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                 Fe_dep_repress 21 kvvktkdlaerLnvspssVsemlkkLekdGyve 53
                                   +  ++ +la++L+  ps+V   l++Le+ G+v+
  gi|119720404|ref|YP_920899.1| 22 GEMGVRELARELGLPPSTVHYHLNRLEDLGLVK 54
                                   556789**************************8 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   2.9e-06    0.0013      28      57 ..      26      54 ..      23      59 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.9e-06
                                   HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE CS
                  LexA_DNA_bind 28 ireiaralglkSpsaveehLkaLerKGyie 57
                                   +re+ar+lgl  ps+v+ hL++Le  G+++
  gi|119720404|ref|YP_920899.1| 26 VRELARELGLP-PSTVHYHLNRLEDLGLVK 54
                                   8**********.*************99986 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   2.3e-06   0.00098      35      85 ..      22      70 ..      10      87 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.3e-06
                        DUF4423 35 fkadpeelakrlrpkisaeevekalefLlklgllkkdedgkyrqteksltt 85
                                   ++  ++ela+ l+  ++ + v+  l++L++lgl+kk edg  +  + +l+ 
  gi|119720404|ref|YP_920899.1| 22 GEMGVRELARELG--LPPSTVHYHLNRLEDLGLVKKGEDGYTVAKRIKLKD 70
                                   456799*******..************************877777777764 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   6.5e-06    0.0028      25      48 ..      25      48 ..      22      49 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 6.5e-06
                         HTH_10 25 tlkeLAkelGIskstlsehLrkae 48
                                    ++eLA elG+ +st+++hL++ e
  gi|119720404|ref|YP_920899.1| 25 GVRELARELGLPPSTVHYHLNRLE 48
                                   689******************976 PP

>> HTH_psq  helix-turn-helix, Psq domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   5.3e-06    0.0023      12      41 ..      19      48 ..      10      51 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 5.3e-06
                        HTH_psq 12 vvnGkmSirkAArkYgiPrsTLwrrkrgky 41
                                    ++G+m++r++Ar+ g P sT ++++++ +
  gi|119720404|ref|YP_920899.1| 19 LQSGEMGVRELARELGLPPSTVHYHLNRLE 48
                                   35**********************999855 PP

>> HTH_30  PucR C-terminal helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   9.1e-06     0.004      13      39 ..      24      50 ..      10      52 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 9.1e-06
                                   T-HHHHHHHHTS-HHHHHHHHHHHHHH CS
                         HTH_30 13 gnisatAkaLhvHrnTlryRLrrieel 39
                                   + +++ A++L++ + T++y L+r+e+l
  gi|119720404|ref|YP_920899.1| 24 MGVRELARELGLPPSTVHYHLNRLEDL 50
                                   568999*******************97 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.9e-05    0.0084       7      41 ..      18      52 ..      15      65 .. 0.86
   2 ?   -0.6   0.0       3.1   1.4e+03       4      22 ..      97     115 ..      96     116 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.9e-05
                         HTH_29  7 llaeGvstvsqiAkllglsrrtvyrwlkrfeegGl 41
                                   ll  G++ v+++A+ lgl ++tv  +l+r e  Gl
  gi|119720404|ref|YP_920899.1| 18 LLQSGEMGVRELARELGLPPSTVHYHLNRLEDLGL 52
                                   67777778***********************9995 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 3.1
                         HTH_29   4 allllaeGvstvsqiAkll 22 
                                    all l  G+ ++ ++A++l
  gi|119720404|ref|YP_920899.1|  97 ALLTLQGGELNPDRAAAIL 115
                                    7788888999999999887 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   8.6e-06    0.0038      15      69 ..      14      64 ..       7      70 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 8.6e-06
                                   HHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT-TCEEESS CS
                           Rrf2 15 lyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvrGkgGGyrLak 69
                                   +yL++ +++e + ++e+a++ +++ps +   l++L+  glvk  +G   Gy+ ak
  gi|119720404|ref|YP_920899.1| 14 IYLELLQSGE-MGVRELARELGLPPSTVHYHLNRLEDLGLVK--KGE-DGYTVAK 64
                                   6777777777.99****************************7..566.5566555 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.3e-05    0.0057       8      55 ..      17      64 ..      13      65 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.3e-05
                       HTH_DeoR  8 llkqqgklsveelvellgvSeaTiRRDLneLeeqglltRthGGavsis 55
                                    l q+g + v el+ +lg  + T+   Ln Le  gl+++   G+++ +
  gi|119720404|ref|YP_920899.1| 17 ELLQSGEMGVRELARELGLPPSTVHYHLNRLEDLGLVKKGEDGYTVAK 64
                                   689************************************999998865 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.3e-05    0.0056      22      50 ..      27      55 ..      20      74 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.3e-05
                 B-block_TFIIIC 22 sdLakeskqdprslfyrlksLekkgLIvk 50
                                   ++La+e++  p+ ++y+l+ Le+ gL++k
  gi|119720404|ref|YP_920899.1| 27 RELARELGLPPSTVHYHLNRLEDLGLVKK 55
                                   7899***********************99 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   1.5e-05    0.0065       8      56 ..       5      54 ..       2      59 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.5e-05
                        DprA_WH  8 pplddlerrvL.aaLgpePvhvDqLvrrtglpaaevsaaLleLELaGlve 56
                                   p+l++++ r+  ++L++  + v +L+r++glp+++v  +L  LE  Glv+
  gi|119720404|ref|YP_920899.1|  5 PELSGTALRIYlELLQSGEMGVRELARELGLPPSTVHYHLNRLEDLGLVK 54
                                   6777777777549******************************9777776 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   4.3e-05     0.019       4      48 ..      13      54 ..      10      65 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.3e-05
                         HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvpIes 48
                                    i+  Ll++ + +   eLA+eL++  +tv+ ++ +Le+lg  +++
  gi|119720404|ref|YP_920899.1| 13 RIYLELLQSGE-MGVRELARELGLPPSTVHYHLNRLEDLG--LVK 54
                                   67777767777.999************************9..444 PP

>> RP-C  Replication protein C N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   5.7e-05     0.025      75     102 ..      27      54 ..      25      69 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.7e-05
                           RP-C  75 aqLsralglsestlrrhlaaLveaGlii 102
                                    ++L+r+lgl++st+ +hl +L ++Gl+ 
  gi|119720404|ref|YP_920899.1|  27 RELARELGLPPSTVHYHLNRLEDLGLVK 54 
                                    689***********************95 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   9.4e-05     0.041      17      42 ..      23      48 ..      12      59 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 9.4e-05
                         HTH_23 17 GlsvreIAreLgvsrrTvyrwlkryr 42
                                    + vre AreLg +++Tv   l+r +
  gi|119720404|ref|YP_920899.1| 23 EMGVRELARELGLPPSTVHYHLNRLE 48
                                   5679***************9999864 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   8.6e-05     0.038       8      53 ..      15      58 ..      12      66 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 8.6e-05
                         HTH_27  8 vLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgd 53
                                   +L+l++   +++  ++l++ l +  s+++y l++L+  GLv++ +d
  gi|119720404|ref|YP_920899.1| 15 YLELLQ--SGEMGVRELARELGLPPSTVHYHLNRLEDLGLVKKGED 58
                                   566666..7888899**************************65544 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00036      0.16       3      55 .]       7      53 ..       6      53 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00036
                         HTH_36  3 LspsaklllgslasfanknggcfpsqetlakrlglsknTvsraikeLeqlGyi 55
                                   Ls +a +++++l+      +     ++ la+ lgl  +Tv  +++ Le+lG++
  gi|119720404|ref|YP_920899.1|  7 LSGTALRIYLELLQSG---EM---GVRELARELGLPPSTVHYHLNRLEDLGLV 53
                                   7778888888887666...44...5799***********************85 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   0.00012     0.051       3      40 ..      13      51 ..      11      75 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 0.00012
                         HTH_40  3 eetlelleeg.lsieeIAkerglkesTIegHLaelieeg 40
                                   ++ lell++g + + e A+e gl +sT+  HL +l   g
  gi|119720404|ref|YP_920899.1| 13 RIYLELLQSGeMGVRELARELGLPPSTVHYHLNRLEDLG 51
                                   6789999665499*******************9876655 PP

>> MerR_1  MerR HTH family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00018      0.08       3      29 ..      26      53 ..      24      63 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00018
                                   HHHHHHHHTS-HHHHHHHHHHTT.-S-E CS
                         MerR_1  3 igevakilgvtthtlrywekegl.lkpk 29
                                   ++e+a++lg++++t++y+ ++   l   
  gi|119720404|ref|YP_920899.1| 26 VRELARELGLPPSTVHYHLNRLEdLGLV 53
                                   78****************9998766555 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00021     0.091      17      39 ..      27      49 ..      10      51 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00021
                                   HHHHHHHTS-HHHHHHHHHHHHH CS
                          HTH_1 17 trAAeeLglsqpavsrqikrLEe 39
                                   ++ A+eLgl +++v  +++rLE+
  gi|119720404|ref|YP_920899.1| 27 RELARELGLPPSTVHYHLNRLED 49
                                   5559******************8 PP

>> CENP-B_N  CENP-B N-terminal DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00021     0.093      22      44 ..      22      45 ..      17      50 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00021
                                   TT.-HHHHHHHHT--CCHHHHHHH CS
                       CENP-B_N 22 ge.Skaelarrfnvpestlsdilk 44
                                   ge  ++elar++++p+st+   l+
  gi|119720404|ref|YP_920899.1| 22 GEmGVRELARELGLPPSTVHYHLN 45
                                   666899************976555 PP

>> DUF742  Protein of unknown function (DUF742)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00026      0.12      49      87 ..      16      55 ..       3      75 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00026
                         DUF742 49 lrLcre.plsVaelaAelklPvgvvrvLlsdLldaglltv 87
                                   l+L ++  + V ela el lP ++v+  l  L d gl++ 
  gi|119720404|ref|YP_920899.1| 16 LELLQSgEMGVRELARELGLPPSTVHYHLNRLEDLGLVKK 55
                                   7788877999**************************9976 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00028      0.12      10      41 ..      15      47 ..      13      49 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00028
                                   HHHHHCTTS-.HHHHHHHHTS-HHHHHHHHHHH CS
                           GerE 10 vLrllaeGks.nkeIAeelniSekTVkvhksni 41
                                   +L+ll +G++ + e A+el++ + TV++h+ ++
  gi|119720404|ref|YP_920899.1| 15 YLELLQSGEMgVRELARELGLPPSTVHYHLNRL 47
                                   5788888864489****************9875 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00031      0.14      26      54 ..      25      53 ..      13      57 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00031
                                   -HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                           GntR 26 sereLaaefgVsrttvReALrrLeaeglv 54
                                    +reLa e+g   +tv   L+rLe  glv
  gi|119720404|ref|YP_920899.1| 25 GVRELARELGLPPSTVHYHLNRLEDLGLV 53
                                   69**************************9 PP

>> MerR  MerR family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00056      0.25       3      18 ..      27      42 ..      26      59 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00056
                                   HHHHHHHTTTHHHHHH CS
                           MerR  3 gevAeltGvsprtLRy 18
                                   +e+A+ +G++p+t++y
  gi|119720404|ref|YP_920899.1| 27 RELARELGLPPSTVHY 42
                                   79************98 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00031      0.14      20      58 ..      26      60 ..      12      69 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00031
                                   HHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETT CS
                Penicillinase_R 20 vkevveeleeekelaysTVktllrrLvkKgllsrekegr 58
                                   v     el++e  l +sTV+  l+rL++ gl+++ ++g 
  gi|119720404|ref|YP_920899.1| 26 V----RELARELGLPPSTVHYHLNRLEDLGLVKKGEDGY 60
                                   4....4566666677*******************99985 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00055      0.24      17      57 ..      13      53 ..       9      55 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00055
                                   HHHHHHHHHSSBEHHHHHHHHSSTHHHHHHHHHHHHHTTSE CS
                          HTH_9 17 kVvetLlrkgrltlrelvkktkLsldqVkksLvvLiqhrlV 57
                                   +++  Ll++g   +rel+++++L+++ V+  L  L  ++lV
  gi|119720404|ref|YP_920899.1| 13 RIYLELLQSGEMGVRELARELGLPPSTVHYHLNRLEDLGLV 53
                                   78889***********************9888766666555 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00048      0.21      26      61 ..      27      62 ..      11      73 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00048
                        DUF2250 26 ksiakeleipleevrellkkLeelGLlervegktik 61
                                   + +a+el +p + v+  l++Le+lGL+++ e     
  gi|119720404|ref|YP_920899.1| 27 RELARELGLPPSTVHYHLNRLEDLGLVKKGEDGYTV 62
                                   678999**********************98854433 PP

>> Cdc6_C  CDC6, C terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00052      0.23      39      75 ..      37      69 ..      26      71 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00052
                                   HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEES CS
                         Cdc6_C 39 qrevsdllseLemlgileleksskGrregrtrkisLn 75
                                    ++v+ +l++Le+lg+++  +     ++   ++i+L+
  gi|119720404|ref|YP_920899.1| 37 PSTVHYHLNRLEDLGLVKKGED----GYTVAKRIKLK 69
                                   4789****************99....89999999996 PP

>> TnsD  Tn7-like transposition protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00073      0.32     193     228 ..      17      52 ..       8      74 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00073
                           TnsD 193 eLveeeglslkeiAkelgvdiktVlryakklgllke 228
                                    eL+++ ++ ++e A+elg+ ++tV  ++++l++l  
  gi|119720404|ref|YP_920899.1|  17 ELLQSGEMGVRELARELGLPPSTVHYHLNRLEDLGL 52 
                                    4556699************************99874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                       111  (0.00619109); expected 17.9 (0.001)
Passed Fwd filter:                        41  (0.0022868); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              41  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 855.94
//
Query:       gi|119720405|ref|YP_920900.1|  [L=82]
Description: hypothetical protein Tpen_1500 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 601.89
//
Query:       gi|119720406|ref|YP_920901.1|  [L=162]
Description: PaREP8 domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.6e-24   84.3   3.6      9e-24   83.6   3.6    1.3  1  PaREP1    Archaeal PaREP1/PaREP8 family
    0.00015   21.9   2.8    0.00031   20.9   2.8    1.5  1  HEPN      HEPN domain


Domain annotation for each model (and alignments):
>> PaREP1  Archaeal PaREP1/PaREP8 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.6   3.6     1e-27     9e-24       2     115 .]      47     150 ..      46     150 .. 0.98

  Alignments for each domain:
  == domain 1  score: 83.6 bits;  conditional E-value: 1e-27
                         PaREP1   2 rleeaekeleeAeellekGdlrqAaeKaykAvkalvkalaeknnlklleeaeekerwstkellkavaklleelgdkevvd 81 
                                    +le+++++l++A+e l+kGdlrqA+eK+++A++ ++ka+a +         e+++  s+ el+ + ++++++lg  +v+ 
  gi|119720406|ref|YP_920901.1|  47 YLEASLRLLQQAREELSKGDLRQAGEKVWGACALAIKAYALA--------TEGRRLESHAELWVYKDRVARRLG-GWVRV 117
                                    89****************************************........8999********************.***** PP

                         PaREP1  82 lwklAldLHeyqfheaklelsdveskeeavkdlv 115
                                    +++lA ++H++ f+e+ ++++dve++ ++v++lv
  gi|119720406|ref|YP_920901.1| 118 AFMLASSMHVN-FYEGLATREDVEDALREVERLV 150
                                    ***********.*******************986 PP

>> HEPN  HEPN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   2.8   3.5e-08   0.00031       2     116 ..      45     154 ..      44     157 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 3.5e-08
                                    HHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHTT--..SSCCHHHHHHCCHHHT...-HHHHHHHHHH CS
                           HEPN   2 eewlrrAeedleaAellleegdydlacfhaqqaaekalKAlllkkgge.ppkthdlreLleelkkelkeseelreeleeL 80 
                                    e++l+ + + l++A++ l++gd + a  ++  a+ +a+KA+ l+ +g+  +++  l     ++++ l     + + +  L
  gi|119720406|ref|YP_920901.1|  45 EKYLEASLRLLQQAREELSKGDLRQAGEKVWGACALAIKAYALATEGRrLESHAELWVYKDRVARRL---GGWVRVAFML 121
                                    78899999********************************998888772555555555555666666...59******** PP

                                    HCCCHHCCCTSS--S--HHHHHHHHHHHHHHHHHHH CS
                           HEPN  81 ekayiesrYpdakeeyteedaeealkdaeevlelve 116
                                        +   Y+  +   t+ed+e+al+ +e+++++v 
  gi|119720406|ref|YP_920901.1| 122 ASSMHVNFYEGLA---TREDVEDALREVERLVKAVA 154
                                    **********988...69**************9974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       901  (0.0502538); expected 358.6 (0.02)
Passed bias filter:                      644  (0.0359195); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.49
# Mc/sec: 999.82
//
Query:       gi|119720407|ref|YP_920902.1|  [L=92]
Description: hypothetical protein Tpen_1502 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      4e-15   55.2   3.2      4e-15   55.2   3.2    1.9  2  DUF131     Protein of unknown function DUF131
  ------ inclusion threshold ------
      0.038   13.9   1.1      0.038   13.9   1.1    2.4  2  Ycf9       YCF9
        1.1    9.1   5.0        2.1    8.2   5.0    1.5  1  Fig1       Ca2+ regulator and membrane fusion protein Fig1


Domain annotation for each model (and alignments):
>> DUF131  Protein of unknown function DUF131
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   2.3      0.22   1.3e+03      46      61 ..      10      25 ..       3      31 .. 0.65
   2 !   55.2   3.2   6.8e-19     4e-15      15      61 ..      33      79 ..      24      81 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.22
                         DUF131 46 taiiLaIilmilllil 61
                                    ++  +++l+++ +il
  gi|119720407|ref|YP_920902.1| 10 ALVAASVVLVLVGFIL 25
                                   4555566777776665 PP

  == domain 2  score: 55.2 bits;  conditional E-value: 6.8e-19
                         DUF131 15 aekeesrvkgGGVvliGPIPIiFGsdkrlaktaiiLaIilmilllil 61
                                    + +es+v++GGV+++GPIP+iFGs++++a+++ +LaI +m+l+++l
  gi|119720407|ref|YP_920902.1| 33 GSPGESKVEAGGVLVVGPIPVIFGSSPEAARKVAYLAIAIMFLSVFL 79
                                   56789**************************************9876 PP

>> Ycf9  YCF9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   6.7     0.072   4.3e+02       2      17 ..       5      19 ..       4      31 .. 0.82
   2 ?   13.9   1.1   6.3e-06     0.038      15      57 ..      45      86 ..      40      87 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.072
                                   HHHHHHHHHHHHHHHH CS
                           Ycf9  2 fqlalaaLvllSfvlV 17
                                   fq+ l+aLv++S vlV
  gi|119720407|ref|YP_920902.1|  5 FQV-LIALVAASVVLV 19
                                   554.6799****9999 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 6.3e-06
                                   HHHHH.HHHHHHSTSTHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           Ycf9 15 vlVvg.VPVayatpqnwsqsknlifsgsalWvaLVllvgilnfl 57
                                   vlVvg +PV++   ++++ ++++ +++ a+ ++ V+l  +lnfl
  gi|119720407|ref|YP_920902.1| 45 VLVVGpIPVIFG--SSPEAARKVAYLAIAIMFLSVFLLILLNFL 86
                                   7999989****9..5678899**********************8 PP

>> Fig1  Ca2+ regulator and membrane fusion protein Fig1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   5.0   0.00035       2.1      80     136 ..      10      83 ..       2      90 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00035
                           Fig1  80 yllmvaiiLtlllfllllyfpl................gseipllPfkska.vskvalvlsflllllwlvgalw 136
                                     l+ ++++L+l++f+l++ + l                   ip++ + s + ++kva++++++++l +++ +l+
  gi|119720407|ref|YP_920902.1|  10 ALVAASVVLVLVGFILVALSALrgspgeskveaggvlvVGPIPVIFGSSPEaARKVAYLAIAIMFLSVFLLILL 83 
                                    577899***********997779999999999998888345666555554458888888888888887776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1054  (0.0587874); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 645.38
//
Query:       gi|119720408|ref|YP_920903.1|  [L=91]
Description: hypothetical protein Tpen_1503 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0014   18.3   2.1     0.0014   18.3   2.1    1.5  2  DUF131          Protein of unknown function DUF131
  ------ inclusion threshold ------
       0.03   14.5   3.5       0.03   14.5   3.5    2.2  2  GHMP_kinases_N  GHMP kinases N terminal domain
        4.8    7.3   6.4        6.1    6.9   1.4    2.2  2  Lipase3_N       Lipase 3 N-terminal region


Domain annotation for each model (and alignments):
>> DUF131  Protein of unknown function DUF131
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.2       0.6   3.6e+03      49      57 ..      17      21 ..      10      31 .. 0.50
   2 !   18.3   2.1   2.3e-07    0.0014      21      60 ..      37      76 ..      32      78 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.6
                         DUF131 49 iLaIilmil 57
                                   +La+     
  gi|119720408|ref|YP_920903.1| 17 LLAV----A 21
                                   3332....2 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 2.3e-07
                         DUF131 21 rvkgGGVvliGPIPIiFGsdkrlaktaiiLaIilmillli 60
                                   +v ++G v+iG +P+ FG  +++  ++ +La+ l++l+ +
  gi|119720408|ref|YP_920903.1| 37 SVGFAGCVVIGFVPLCFGYGSSAGLVLALLAVALTALVAL 76
                                   789*******************************999765 PP

>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.6     0.086   5.1e+02      21      32 ..      19      30 ..      17      39 .. 0.83
   2 ?   14.5   3.5   5.1e-06      0.03       7      39 ..      48      74 ..      42      83 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.086
                                   HHHHHHHHHHHT CS
                 GHMP_kinases_N 21 avalvaAllall 32
                                   ava ++Al+a+ 
  gi|119720408|ref|YP_920903.1| 19 AVASILALAAYS 30
                                   899999999875 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 5.1e-06
                                   SSHTTSSSCHHHHHHHHHHHHHHHHTTEHHHHH CS
                 GHMP_kinases_N  7 eiPvgaGLGSSAAlavalvaAllallglsleea 39
                                    +P+  G GSSA l++al+a +l +l      +
  gi|119720408|ref|YP_920903.1| 48 FVPLCFGYGSSAGLVLALLAVALTAL------V 74
                                   58999****************99988......4 PP

>> Lipase3_N  Lipase 3 N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.3     0.017        99       4      21 ..      20      37 ..      17      45 .. 0.85
   2 ?    6.9   1.4     0.001       6.1       2      16 ..      70      84 ..      69      87 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.017
                      Lipase3_N  4 allalaaatwaektstes 21
                                   + ++la+a+++ ++s+ s
  gi|119720408|ref|YP_920903.1| 20 VASILALAAYSFIASPAS 37
                                   5689*********99865 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.001
                      Lipase3_N  2 fsallalaaatwaek 16
                                   ++al+ala+++w+++
  gi|119720408|ref|YP_920903.1| 70 LTALVALAVLAWLWL 84
                                   79************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1000  (0.0557756); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 684.22
//
Query:       gi|119720409|ref|YP_920904.1|  [L=81]
Description: hypothetical protein Tpen_1504 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.075   13.0   1.0        0.2   11.7   0.6    1.7  2  DUF2095   Uncharacterized protein conserved in archaea (DUF20


Domain annotation for each model (and alignments):
>> DUF2095  Uncharacterized protein conserved in archaea (DUF2095)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1     0.017     3e+02      69      98 ..      11      41 ..       8      46 .. 0.68
   2 ?   11.7   0.6   1.1e-05       0.2      34      70 ..      40      77 ..      23      80 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.017
                        DUF2095 69 idflrrce..tdeealeiinwmeergeithem 98
                                   + +l +ce  +dee +ei + +  rge   em
  gi|119720409|ref|YP_920904.1| 11 LGYLEKCEliSDEELMEIEDRL-SRGEDVLEM 41
                                   5688899854577777876655.467766666 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 1.1e-05
                        DUF2095 34 ergleidairl.deeevleeeeeegkidfsgynptiid 70
                                   e g+ + ++   +e+ v+e e++eg+    gynp  + 
  gi|119720409|ref|YP_920904.1| 40 EMGIRVLGYDEkKEDYVVEVEDLEGLLSENGYNPDYVR 77
                                   67999999975156779999**************8765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.29s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 569.80
//
Query:       gi|119720410|ref|YP_920905.1|  [L=396]
Description: cytochrome bd-type quinol oxidase subunit 1-like [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-19   69.4  19.0    2.2e-19   69.4  19.0    2.0  2  Cyt_bd_oxida_I  Cytochrome bd terminal oxidase subunit I


Domain annotation for each model (and alignments):
>> Cyt_bd_oxida_I  Cytochrome bd terminal oxidase subunit I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.4  19.0   1.2e-23   2.2e-19       6     239 ..       8     237 ..       6     259 .. 0.90
   2 !    4.7   2.5   0.00053       9.6     314     411 ..     264     385 ..     252     393 .. 0.55

  Alignments for each domain:
  == domain 1  score: 69.4 bits;  conditional E-value: 1.2e-23
                 Cyt_bd_oxida_I   6 faltavfHflfvpltlGlalllailetlylrtgdekykklakfwgklfainFavGvvtGivlefqfgtnWseysrfvGdi 85 
                                    +al   +H++ v ++++l+ ++ +l  +    gd+  + +a+ + k++a +++++ v G+   + +   ++e+  ++G+ 
  gi|119720410|ref|YP_920905.1|   8 MALVFGVHIVAVNIGIALSTIVPLLVKRSRALGDKGLEGVARSLFKVYAATYGLAGVMGTAFTVFLASFYPEFVGVAGNL 87 
                                    789999************************************************************************** PP

                 Cyt_bd_oxida_I  86 fgapLaiEgllAFflEstflglmlfgwdrvskklhllatwlvaigtllSalwIlaanswmqtPvGaelnpdtgraeltdf 165
                                     + p+ i  +++ +l    +  +++gwdr+s+k+h ++ wl+a  +++  l   a+ ++++tP+G  l ++       ++
  gi|119720410|ref|YP_920905.1|  88 TMVPFGIS-IVSIMLHFFAIVAFWYGWDRFSPKVHEAVGWLLAATAYTIPLGFRAVFAFLNTPAGLVLGEK----PSLNV 162
                                    ********.7**********************************************************633....45799 PP

                 Cyt_bd_oxida_I 166 lavlfnpsalakflHtvlaalltaaffvagvsawyllr.rekefarkslkialvvalvaallqallGdlsgkeva 239
                                    +++l+np+++  +l  v++al+++ +fva+v a++ lr + +++ r  + ++l +a ++++++++lG + + +++
  gi|119720410|ref|YP_920905.1| 163 VQALLNPTFPPLYLKSVVGALVAGFLFVAAVLAFKGLRtALTDAERGLYVFSLRYASMLLFAMMFLGAWYAVSLV 237
                                    **************************************7444455666666666666677777777777766665 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.00053
                 Cyt_bd_oxida_I 314 wsfri.mvglgvlllllallalll............rwllrllllaiplpfiaveaGWivtevGRqPWivy......... 371
                                    w f + mv + v  ++l+l+   l             +  ++++ a+++++++v +G ++  +   P+ v+         
  gi|119720410|ref|YP_920905.1| 264 WLFLVkMVLVAVQGAALLLV---LlprgkgesllesPAGYKATITAAVAAALTVLTGEYLNAFSQYPFFVAnapliadkl 340
                                    33333123333333333333...1356889999999668999****************************9666666666 PP

                 Cyt_bd_oxida_I 372 .....gllrta...davspvsagevllslilflllylvLlvvevylll 411
                                          +l+ a   + vsp+   +    l++ ++l +++l++ + +++
  gi|119720410|ref|YP_920905.1| 341 pepyrTILTRAlnlENVSPL---AQDPALYAATVLGVLVLFAAAGYMI 385
                                    66665233333111334553...2222222222222222222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       818  (0.0456244); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2765.09
//
Query:       gi|119720411|ref|YP_920906.1|  [L=541]
Description: cytochrome bd ubiquinol oxidase, subunit I [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-65  221.4  30.1    4.6e-65  219.9  30.1    1.7  1  Cyt_bd_oxida_I  Cytochrome bd terminal oxidase subunit I


Domain annotation for each model (and alignments):
>> Cyt_bd_oxida_I  Cytochrome bd terminal oxidase subunit I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  219.9  30.1   2.6e-69   4.6e-65       3     411 ..      16     532 ..      14     538 .. 0.92

  Alignments for each domain:
  == domain 1  score: 219.9 bits;  conditional E-value: 2.6e-69
                 Cyt_bd_oxida_I   3 RlqfaltavfHflfvpltlGlalllailetlylrtgdekykklakfwgklfainFavGvvtGivlefqfgtnWseysrfv 82 
                                    R+   + + +H++++   lGl+l+++++ ++y rt +e ++kla++ +k +++ FavG+++G+  ef + ++W++  +++
  gi|119720411|ref|YP_920906.1|  16 RILSIIGIEIHWFILQYVLGLPLVILVALLAYKRTANESWLKLARTSAKALGLVFAVGAASGTASEFGLLVIWPNLLEAA 95 
                                    888899999*********************************************************************** PP

                 Cyt_bd_oxida_I  83 GdifgapLaiEgllAFflEstflglmlfgwdrvskklhllatwlvaigtllSalwIlaanswmqtPvG............ 150
                                    G  +  pL++E ++AF++E tf+ l++fgw+++s   ++++++l+ +g++lS  +I+++ns+m  P+G            
  gi|119720411|ref|YP_920906.1|  96 GRYIYFPLYVE-IFAFLTEITFIYLLVFGWGKLSLNGRIAVAFLALLGAWLSGAMIMSVNSYMVAPTGvspafsqeagwl 174
                                    ***********.7******************************************************************* PP

                 Cyt_bd_oxida_I 151 ................................................................................ 150
                                                                                                                    
  gi|119720411|ref|YP_920906.1| 175 ysqgypkillvvperlvdaldvgklqslgmevvgrvgggvavympsrivarlayeawggrtvgesvlalvvkpealpslk 254
                                    **************************************************************************999999 PP

                 Cyt_bd_oxida_I 151 .........aelnpdtgraeltdflavlf.npsalakflHtvlaalltaaffvagvsawyllr..rekefarkslkialv 218
                                             a l  +  +++++ + +v f +p+++ +flH v aal++++f +ag +a+  l   re++++   l++++v
  gi|119720411|ref|YP_920906.1| 255 atlvkdvvdAVLT-E--TVRTVGYTTVTFkSPVFVGSFLHAVGAALTVTGFTIAGAYALLSLLsrRESKYYADGLRFGVV 331
                                    6666555332222.2..333445555554389***********************99986655569999*********** PP

                 Cyt_bd_oxida_I 219 valvaallqal.lGdlsgkevaetqpaKlAAmeglweteeaplslfgipdeeeeknefaieiPgllsllatgsldgevkG 297
                                    + lva+++q + +G+  g e+a+++p+KlAAmeg  +      +++ ip++        + i  l+  +  g++ + ++ 
  gi|119720411|ref|YP_920906.1| 332 FSLVAVAVQGAvFGHVIGTEIAKYNPEKLAAMEGTSK------AVLSIPRA--------LGIESLMKAIIFGNPGAAMPS 397
                                    ********97669*********************996......47888877........99******************* PP

                 Cyt_bd_oxida_I 298 lndlpk............eevPpvalvfwsfrimvglgvlllllallalll........rwllrllllaiplpfiaveaG 357
                                    ++++p             + +Pp +++++ ++  +gl +ll llal++++l        r+ l+ ++++ +++   + +G
  gi|119720411|ref|YP_920906.1| 398 YDEIPVdycrldnlppvqDCRPP-LILHYLYYSKIGLSLLLGLLALAGTVLiytgrapgRLTLYGFAVSPVIAHAVSFLG 476
                                    ****889****999999989998.99999******************9988899****988899999999999999**** PP

                 Cyt_bd_oxida_I 358 WivtevGRqPWivygllrtadavsp..vsagevllslilflllylvLlvvevylll 411
                                    W+v+e+GR+PW++yg+++++ a +     a+e +++  +fl + ++L+ + +++ll
  gi|119720411|ref|YP_920906.1| 477 WAVREMGRKPWTIYGVMTVDVAHTAnpAGAAEYAVVASIFLGVLAALIYASWRILL 532
                                    *******************9998664578888899999999999999998887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (541 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 3669.81
//
Query:       gi|119720412|ref|YP_920907.1|  [L=480]
Description: hypothetical protein Tpen_1507 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.7e-27   93.9   0.0    1.1e-26   93.5   0.0    1.1  1  UxaE           tagaturonate epimerase
  ------ inclusion threshold ------
       0.06   12.8   0.0        2.8    7.3   0.0    2.2  2  F_bP_aldolase  Fructose-bisphosphate aldolase class-II


Domain annotation for each model (and alignments):
>> UxaE  tagaturonate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.5   0.0   1.3e-30   1.1e-26     156     388 ..     132     378 ..     129     454 .. 0.86

  Alignments for each domain:
  == domain 1  score: 93.5 bits;  conditional E-value: 1.3e-30
                           UxaE 156 dveealea.gftmitlDlsekikneveklsekelkekyeel.eeelrekleekylgkkfkik.ee..elelsekellkav 230
                                    +++ea+ea g+ ++t+D+ e i+ + +k+ ++e+++ yee+ + + r+ lee+y g ++ ++ ++  +++ls++++++ +
  gi|119720412|ref|YP_920907.1| 132 ELREAAEAgGVDFVTIDTCELIDYSYDKVGAEEVAAAYEEVfDGDERRALEERYEGVHYFLGgDRvvAVRLSREDVARLA 211
                                    667777762689***************************9835799999************96432257899******** PP

                           UxaE 231 liYekaikfvekvyekilkkkekefdlEiSiDEtetptspeeHlFvaeeLkrkgveftslAprFiGefqKgiDYiGdlke 310
                                    ++Y   ++++e++y+   ++++ e+ +E++ DEt  + ++ e +F  +eL r+g+++  +Ap     f+K  DY Gdl+ 
  gi|119720412|ref|YP_920907.1| 212 VKYRRSLDYAERIYRAAREAMGVELGFEVAFDETPGVSEAREVFFYLSELLRRGLRVDFIAPNV--GFRKREDYSGDLHA 289
                                    ***************99999999***************************************85..4************* PP

                           UxaE 311 fekelkkHaaiakefggyklSlHSGS......DK.fsvykiigkltegkfHvKtaGtswLeAvrvvae.....kdpelyr 378
                                    + + l++  a+  +++ y lS+HSGS      DK f v+ ++g++t g +  K +G      + v+a+     + ++ly 
  gi|119720412|ref|YP_920907.1| 290 LYERLRNLHAVVSSMNAY-LSIHSGSgshpysDKgFGVWGVVGRATGGAVKYKMSGVLVQLLLEVMASyppgsETRRLYE 368
                                    *****9988899999677.******54454448889********************987777788876222224557888 PP

                           UxaE 379 eiykfalekl 388
                                    eiy+   e+l
  gi|119720412|ref|YP_920907.1| 369 EIYSEVVEHL 378
                                    8888777765 PP

>> F_bP_aldolase  Fructose-bisphosphate aldolase class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0   0.00032       2.8      52      98 ..      61     107 ..      32     141 .. 0.84
   2 ?    3.5   0.0    0.0047        42     167     214 ..     266     318 ..     223     384 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00032
                                    HHHH-HHHHHHHHHHHHHHHHT...-EEEEEE----GHHHHHHHHHH CS
                  F_bP_aldolase  52 akyaggaealaelvraaaeaykkasvpvalhlDHgakleglkkaiea 98 
                                     ++++  +++  ++r++ e+ k+ svpv +  DH + l  +++a+++
  gi|119720412|ref|YP_920907.1|  61 FYFGHTGTSIGGFIRSVKEYSKALSVPVEVEADHVSILGSVERALKK 107
                                    4565667788999******99999***********999999999876 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.0047
                                    HH-EEEE--SS---SS.--SS..--THHHHHHHHHH....--SEE-SGTTS-H CS
                  F_bP_aldolase 167 tgvdalAvaiGnvHGv.ykpkpkLdferlkeiqkav....vplVlHGgsgvpd 214
                                    + vd++A+ +G    + y+   +  +erl+++++ v      l +H gsg+ +
  gi|119720412|ref|YP_920907.1| 266 LRVDFIAPNVGFRKREdYSGDLHALYERLRNLHAVVssmnAYLSIHSGSGSHP 318
                                    56999999999877764766666779**********9966559******9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (480 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.58
# Mc/sec: 2501.56
//
Query:       gi|119720413|ref|YP_920908.1|  [L=163]
Description: hydrogenase maturation protease [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-08   34.7   0.0    1.8e-08   34.3   0.0    1.2  1  HycI      Hydrogenase maturation protease


Domain annotation for each model (and alignments):
>> HycI  Hydrogenase maturation protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.0     1e-12   1.8e-08      35     129 ..      68     154 ..      50     155 .. 0.86

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 1e-12
                                    C..-SEEEEEEE--SSS-TT-EEEEECCHHHHHHTTC.CGCCCHCHHHHHHHHHHCCS--SEEEEEEE--S-BST.CCS- CS
                           HycI  35 e..adkliivDavdfglepGevkiikddevpkklkakkmsaHqlplaevlklleekgeipkevillgvqpesledvgiel 112
                                        +  +ivDavd+glepG++++ + d   +       s+H+lpl  v ++l        ev +lg+q ++le  + ++
  gi|119720413|ref|YP_920908.1|  68 RagVKVALIVDAVDAGLEPGSIVLSRLDAAYE--AL--PSTHKLPLRLVAEYLGLE-----EVYVLGIQVQNLEV-SQGV 137
                                    4557888*********************9995..44..59******9999999888.....68889999999998.89** PP

                                    -HHHHCCHHHHHHHCCC CS
                           HycI 113 seevkkavekavelile 129
                                    s++v+++  +++e++le
  gi|119720413|ref|YP_920908.1| 138 SRPVAESARRLAEALLE 154
                                    ***********999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1056.26
//
Query:       gi|119720414|ref|YP_920909.1|  [L=292]
Description: transcriptional regulator, TrmB [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-10   39.7   0.0    4.2e-10   39.0   0.0    1.4  1  HTH_24         Winged helix-turn-helix DNA-binding
    2.5e-07   30.5   0.0    5.6e-07   29.3   0.0    1.7  1  HTH_5          Bacterial regulatory protein, arsR family
    3.6e-05   23.9   0.0    0.00023   21.3   0.0    2.1  2  HTH_34         Winged helix DNA-binding domain
    5.7e-05   22.8   0.0    0.00017   21.3   0.0    1.8  1  HTH_IclR       IclR helix-turn-helix domain
    0.00011   22.2   0.0    0.00032   20.7   0.0    1.9  1  HTH_20         Helix-turn-helix domain
    0.00016   21.5   0.9    0.00047   20.0   0.1    2.1  2  TrmB           Sugar-specific transcriptional regulator TrmB
    0.00052   19.8   0.0    0.00092   19.0   0.0    1.3  1  DUF4423        Domain of unknown function (DUF4423)
    0.00098   19.0   0.0     0.0024   17.7   0.0    1.6  1  MarR_2         MarR family
     0.0013   18.5   0.0     0.0033   17.2   0.0    1.6  1  HTH_AsnC-type  AsnC-type helix-turn-helix domain
     0.0023   18.3   0.2     0.0073   16.6   0.1    1.8  2  FaeA           FaeA-like protein
  ------ inclusion threshold ------
      0.022   14.9   0.2       0.12   12.5   0.0    2.3  2  DprA_WH        DprA winged helix domain
      0.037   14.1   0.0      0.071   13.2   0.0    1.4  1  DUF2250        Uncharacterized protein conserved in archaea (
      0.039   13.7   1.0        0.1   12.4   0.0    2.2  3  HTH_23         Homeodomain-like domain


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   0.0     3e-13   4.2e-10       2      48 .]     181     227 ..     180     227 .. 0.95

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 3e-13
                         HTH_24   2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                    +e++ +ILe+L++np+ s+r +++++g+S + v ++l  Le+ G+++
  gi|119720414|ref|YP_920909.1| 181 SEKRVRILEYLKQNPGASMRRISRETGVSFGEVQWHLSILERLGYVQ 227
                                    67889****************************************95 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.0   4.1e-10   5.6e-07       1      46 [.     181     227 ..     181     228 .. 0.97

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 4.1e-10
                                    SHHHHHHHHHHTTSS.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_5   1 dptRlkILklLaege.lcvcelaeelglsqstvShHLkkLreaGLVe 46 
                                    +++R++IL +L +++ ++   +++e+g+s + v  HL++L+ +G+V+
  gi|119720414|ref|YP_920909.1| 181 SEKRVRILEYLKQNPgASMRRISRETGVSFGEVQWHLSILERLGYVQ 227
                                    589*******************************************6 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       1.2   1.7e+03      59      69 ..     150     160 ..     144     166 .. 0.78
   2 !   21.3   0.0   1.7e-07   0.00023       2      46 ..     184     228 ..     184     233 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.2
                         HTH_34  59 lriTpeGreaf 69 
                                    l++T+ Gr++ 
  gi|119720414|ref|YP_920909.1| 150 LTLTESGRQKL 160
                                    799*****975 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 1.7e-07
                         HTH_34   2 RlavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYiev 46 
                                    R  +l yL ++  a++++++ +++++ g+   hl++Le  gY+++
  gi|119720414|ref|YP_920909.1| 184 RVRILEYLKQNPGASMRRISRETGVSFGEVQWHLSILERLGYVQR 228
                                    789***************************************975 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   1.2e-07   0.00017       6      50 ..     185     228 ..     182     230 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.2e-07
                                    HHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                       HTH_IclR   6 laiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50 
                                    ++iL++l + p++ + + ++r+tg++   v  +L+ L++lGyv++
  gi|119720414|ref|YP_920909.1| 185 VRILEYLKQNPGA-SMRRISRETGVSFGEVQWHLSILERLGYVQR 228
                                    79**********8.9****************************98 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   2.3e-07   0.00032       6      60 ..     178     232 ..     158     233 .. 0.94

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.3e-07
                                    HHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                         HTH_20   6 ALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvreg 60 
                                    +L ++ R ril +L+++ g++   + ++ ++s  ++  HL +Le+ g+v +vr g
  gi|119720414|ref|YP_920909.1| 178 VLRSEKRVRILEYLKQNPGASMRRISRETGVSFGEVQWHLSILERLGYVQRVRIG 232
                                    567889**********************************************987 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1       1.6   2.2e+03       9      19 ..       6      16 ..       4      31 .. 0.81
   2 !   20.0   0.1   3.4e-07   0.00047      12      64 ..     186     239 ..     181     242 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.6
                                   HCCCHCHHHHH CS
                           TrmB  9 yEakvYlaLlk 19
                                   +E +++laLl 
  gi|119720414|ref|YP_920909.1|  6 MEKRAFLALLL 16
                                   69999999994 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 3.4e-07
                                    CHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES.STTTEEEE CS
                           TrmB  12 kvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerek.grpklYra 64 
                                    ++  +L ++  a+++ i++e+gv+   v+  L+ Le+ G+V+r++ g++++Y +
  gi|119720414|ref|YP_920909.1| 186 RILEYLKQNPGASMRRISRETGVSFGEVQWHLSILERLGYVQRVRiGKYTVYYP 239
                                    666777789999*********************************77799**98 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   6.7e-07   0.00092      17      78 ..     178     236 ..     169     239 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 6.7e-07
                        DUF4423  17 yfssWyypvirellplkdfkadpeelakrlrpkisaeevekalefLlklgllkkdedgkyrq 78 
                                    +++s + + i+e l+ +++ a+++ +++ ++  +s  ev+  l++L++lg +++ + gky +
  gi|119720414|ref|YP_920909.1| 178 VLRSEKRVRILEYLKQNPG-ASMRRISRETG--VSFGEVQWHLSILERLGYVQRVRIGKYTV 236
                                    788888999**********.***********..**************************975 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   1.7e-06    0.0024       8      54 ..     185     229 ..     183     232 .. 0.96

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.7e-06
                                    HHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                         MarR_2   8 arvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54 
                                     r+L +L  +pg   +++ + r++g+s + v+ +l  L++ G+v+r+
  gi|119720414|ref|YP_920909.1| 185 VRILEYLKQNPG--ASMRRISRETGVSFGEVQWHLSILERLGYVQRV 229
                                    69**********..9*****************************997 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.4e-06    0.0033       7      35 ..     186     214 ..     185     214 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.4e-06
                  HTH_AsnC-type   7 kILeaLqedaRisyaeLAervGlSestvl 35 
                                    +ILe L +++ +s++++++++G+S  +v+
  gi|119720414|ref|YP_920909.1| 186 RILEYLKQNPGASMRRISRETGVSFGEVQ 214
                                    8***********************88885 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       3.8   5.2e+03      24      38 ..     138     152 ..     132     157 .. 0.72
   2 !   16.6   0.1   5.3e-06    0.0073       4      52 ..     186     233 ..     183     237 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3.8
                                    HHTS-HHHHHHHHHH CS
                           FaeA  24 alglsaYQaRyYLeq 38 
                                    a++++a  a +YL  
  gi|119720414|ref|YP_920909.1| 138 AVAVAAVAATSYLTL 152
                                    567888889999865 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 5.3e-06
                                    HHHHHHHH.S----HHHHHHHHTS-HHHHHHHHHHHHHHSSEEEE--SS CS
                           FaeA   4 eIleylnsikapckTreiAdalglsaYQaRyYLeqLekegkikrspvrr 52 
                                     Ileyl++ + ++  r i   +g+s   +   L  Le+ g ++r+ +++
  gi|119720414|ref|YP_920909.1| 186 RILEYLKQ-NPGASMRRISRETGVSFGEVQWHLSILERLGYVQRVRIGK 233
                                    69******.999999******************************9987 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.3       1.7   2.4e+03      11      22 ..     154     165 ..     125     169 .. 0.52
   2 ?   12.5   0.0   8.4e-05      0.12      11      57 ..     181     228 ..     172     230 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.7
                        DprA_WH  11 ddlerrvLaaLg 22 
                                    ++ +++++aaL+
  gi|119720414|ref|YP_920909.1| 154 ESGRQKLFAALS 165
                                    445556666665 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 8.4e-05
                        DprA_WH  11 ddlerrvLaaLgpePv.hvDqLvrrtglpaaevsaaLleLELaGlver 57 
                                    ++ + r+L+ L + P  ++  ++r+tg++++ev+ +L+ LE  G+v+r
  gi|119720414|ref|YP_920909.1| 181 SEKRVRILEYLKQNPGaSMRRISRETGVSFGEVQWHLSILERLGYVQR 228
                                    678889999998887548899********************9999998 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   5.1e-05     0.071       5      56 ..     179     230 ..     175     236 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.1e-05
                        DUF2250   5 eedelalkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLlerve 56 
                                     ++e+ +++l++lk+      + i++e+ +++ ev+  l  Le+lG ++rv 
  gi|119720414|ref|YP_920909.1| 179 LRSEKRVRILEYLKQNPGASMRRISRETGVSFGEVQWHLSILERLGYVQRVR 230
                                    5677899******************************************996 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       6.5     9e+03       5      14 ..       7      17 ..       4      29 .. 0.60
   2 ?   12.4   0.0   7.4e-05       0.1       5      30 ..     182     209 ..     179     210 .. 0.93
   3 ?   -1.9   0.0       2.3   3.1e+03      35      43 ..     245     253 ..     244     259 .. 0.70

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 6.5
                         HTH_23  5 reRlr.illll 14
                                   ++R+  +llll
  gi|119720414|ref|YP_920909.1|  7 EKRAFlALLLL 17
                                   45554144444 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 7.4e-05
                         HTH_23   5 reRlrillllae..GlsvreIAreLgvs 30 
                                    ++R ril  l++  G+s r+I+re gvs
  gi|119720414|ref|YP_920909.1| 182 EKRVRILEYLKQnpGASMRRISRETGVS 209
                                    799************************9 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 2.3
                         HTH_23  35 yrwlkryre 43 
                                     rwl  ++e
  gi|119720414|ref|YP_920909.1| 245 ERWLACFAE 253
                                    59**99953 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 2086.29
//
Query:       gi|119720415|ref|YP_920910.1|  [L=133]
Description: hypothetical protein Tpen_1510 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.025   14.5  13.0       0.03   14.2  13.0    1.1  1  7TMR-DISM_7TM    7TM diverse intracellular signalling
      0.083   13.2   1.2        9.5    6.6   0.0    2.2  2  Phage_holin_5_2  Phage holin family Hol44, in holin superfami
        1.8    6.7  12.8        1.9    6.7  12.8    1.0  1  DUF2070          Predicted membrane protein (DUF2070)
        2.2    7.7   6.3       0.46    9.9   2.2    1.8  2  DUF4349          Domain of unknown function (DUF4349)


Domain annotation for each model (and alignments):
>> 7TMR-DISM_7TM  7TM diverse intracellular signalling
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2  13.0   6.7e-06      0.03      71     170 ..      14     120 ..       6     132 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6.7e-06
                  7TMR-DISM_7TM  71 ltlllllilfllFarsflelkk.kp......rllklllllavllsllllllpllpyteslslaqllallvillllligik 143
                                    +++ +l++l+++ +  +l+l k kp        + + ++la++ +++++ l  ++ ++++++++ ++l ++l +l+++++
  gi|119720415|ref|YP_920910.1|  14 MLVPTLSGLVAVLTSAVLRLAKgKPssedewSAFAAGIVLAFIDGFMIAYLVPFFPYFASKFLFHVYLYTLLASLTAVLY 93 
                                    45566666888899999***99999****99888899999999999999999999999999999**************** PP

                  7TMR-DISM_7TM 144 awrkgnkparyfliawlllligvlidi 170
                                    a++k   + r +++a ++ ++ +l+ +
  gi|119720415|ref|YP_920910.1|  94 AMYKAVTDLRVYAAASIPWILVILLVA 120
                                    ********************9999865 PP

>> Phage_holin_5_2  Phage holin family Hol44, in holin superfamily V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0021       9.5      22      63 ..      15      55 ..       4      61 .. 0.87
   2 ?    5.6   0.2    0.0046        20       2      35 ..      89     122 ..      88     129 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0021
                Phage_holin_5_2 22 yIPlilgiiGiilgvvivfta.dfqaedilifgaiiqGilsgg 63
                                   ++P++ g++ ++ ++v  +++ +   ed +   a++ Gi+ + 
  gi|119720415|ref|YP_920910.1| 15 LVPTLSGLVAVLTSAVLRLAKgKPSSEDEWS--AFAAGIVLAF 55
                                   789999********999999889999999*9..******9886 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0046
                Phage_holin_5_2   2 vvilyiiGeilKktekvkdkyIPlilgiiGiilg 35 
                                    +++ly++ +++   +  +   IP+il+i+ ++++
  gi|119720415|ref|YP_920910.1|  89 TAVLYAMYKAVTDLRVYAAASIPWILVILLVAVA 122
                                    677777777777777777799******9977766 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7  12.8   0.00043       1.9      43     148 ..      16     122 ..       2     133 .] 0.63

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.00043
                        DUF2070  43 lfglpalvaflltlpvlrilggrltykrs..lflalltelivviisllaillsall..qalvllalvlslalvfalrllv 118
                                    + +l+  + ++lt+ vlr+++g++ ++    +f a + + ++  ++++ ++   ++   a+ +l+ v  ++l ++l+ ++
  gi|119720415|ref|YP_920910.1|  16 VPTLS-GLVAVLTSAVLRLAKGKPSSEDEwsAFAAGIVLAFIDGFMIAYLV--PFFpyFASKFLFHVYLYTLLASLTAVL 92 
                                    44444.35568999******9995444432255555555444443333333..334564555555555577888889999 PP

                        DUF2070 119 lvavsdesllkavlpaliqpllailllvly 148
                                    + ++   + l++++ a+i  +l+ill+ + 
  gi|119720415|ref|YP_920910.1|  93 YAMYKAVTDLRVYAAASIPWILVILLVAVA 122
                                    999999999999999998888888888776 PP

>> DUF4349  Domain of unknown function (DUF4349)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1      0.16   7.4e+02     183     205 ..      52      72 ..      23      80 .. 0.61
   2 ?    9.9   2.2    0.0001      0.46     172     209 ..      84     121 ..      78     124 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.16
                        DUF4349 183 lveflagllvvlgallPwllvla 205
                                    +++f+ g+  ++++l+P+++ +a
  gi|119720415|ref|YP_920910.1|  52 VLAFIDGF--MIAYLVPFFPYFA 72 
                                    33344444..3477788777665 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0001
                        DUF4349 172 flealsggwnalveflagllvvlgallPwllvlalvla 209
                                    +l+ l + ++a+++++++l v ++a +Pw+lv++lv++
  gi|119720415|ref|YP_920910.1|  84 LLASLTAVLYAMYKAVTDLRVYAAASIPWILVILLVAV 121
                                    567788999*************************7665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.35s 00:00:00.96 Elapsed: 00:00:00.57
# Mc/sec: 706.16
//
Query:       gi|119720416|ref|YP_920911.1|  [L=460]
Description: Alpha-galactosidase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.8e-46  156.1   0.0    9.5e-46  155.6   0.0    1.2  1  Glyco_hydro_4   Family 4 glycosyl hydrolase
    4.4e-40  138.0   0.0    7.7e-40  137.2   0.0    1.4  1  Glyco_hydro_4C  Family 4 glycosyl hydrolase C-terminal domain
     0.0013   18.8   0.0      0.033   14.3   0.0    2.2  2  Ldh_1_N         lactate/malate dehydrogenase, NAD binding dom
  ------ inclusion threshold ------
      0.013   14.8   0.0       0.02   14.2   0.0    1.2  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
      0.082   13.0   0.0       0.16   12.1   0.0    1.4  1  OTCace          Aspartate/ornithine carbamoyltransferase, Asp


Domain annotation for each model (and alignments):
>> Glyco_hydro_4  Family 4 glycosyl hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.6   0.0   2.7e-49   9.5e-46       1     178 [.       8     188 ..       8     192 .. 0.97

  Alignments for each domain:
  == domain 1  score: 155.6 bits;  conditional E-value: 2.7e-49
                                    EEEEETTTSSSHHHHHHHHHHTTTTCTEEEEEEE-SSHHHHHHHHHHHHHHHHHCTTTCEEEEESSHHHHHTT-SEEEE- CS
                  Glyco_hydro_4   1 kiviiGgGStifaklllgdlkkteelsvselaLvDideerldaiqtlakklveeagadlkieattdrkealkdadfVita 80 
                                    ki +iG+GS  ++ +l+ dl +t+ l +s++  +Di+eerl +   la+k+  e+ga+ ++  ttdrkea++d d Vi++
  gi|119720416|ref|YP_920911.1|   8 KISVIGAGSVAWSSKLVHDLLHTPSLYGSDVYFMDINEERLRILRGLAEKYKSEVGAEYNFFYTTDRKEAVRDSDVVINT 87 
                                    89****************************************************************************** PP

                                    --TT....HHHHHHHHHHCCHTTTTT-CTTSSSHHHHHHHHHHHHHHHHHHHHHHHHH-TTSEEEE-SSSHHHHHHHHHH CS
                  Glyco_hydro_4  81 irvG....lekareidekiplryGieqtiqdtvgpggifrglrtipvlleIakdieelcPdawvlnytNPaavvteallr 156
                                    ++ G    +e +re+ ek ++++G++  + ++v+++ ++ g+ + +  ++Ia+d+eel+P aw+++++NP++++t+++ r
  gi|119720416|ref|YP_920911.1|  88 AMYGghryYELMREVSEKHGYYRGVNSVEWNMVSDYHTIWGYYQWKLAMDIARDVEELAPGAWLIQMANPVFELTTLISR 167
                                    *******9999********************************************************************8 PP

                                    HSTTSEEEEE-SHHHHHHHHHH CS
                  Glyco_hydro_4 157 lvpnikavglChsvigvkeela 178
                                     +   k+vglCh ++g ke+ +
  gi|119720416|ref|YP_920911.1| 168 ETR-VKVVGLCHGHLGYKEIAQ 188
                                    877.************998755 PP

>> Glyco_hydro_4C  Family 4 glycosyl hydrolase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.2   0.0   2.2e-43   7.7e-40       2     208 .]     202     433 ..     201     433 .. 0.77

  Alignments for each domain:
  == domain 1  score: 137.2 bits;  conditional E-value: 2.2e-43
                                    EEETTEEEEEEEECTTEEHHHHHHHHHHH.......HHHHHHCTGGG..........TSHHHHHHHHHHSSEEE...... CS
                 Glyco_hydro_4C   2 aGlNHlaWllkledkGeDlypelrelvee.......dewleeiaekk..........aervridllrrlgllpt...... 58 
                                    +G NH++Wl+k++++GeD+yp + + vee       +     +   +           +++++d++rr+gl+p       
  gi|119720416|ref|YP_920911.1| 202 IGFNHVIWLTKFTYDGEDAYPLIDRWVEEkaeqywsQ-----W---RmrqvnpfdiqMSPAAVDMYRRYGLFPVgdtvrg 273
                                    7**********************99888876544431.....2...1334566678899********************* PP

                                    .CGGHHCTTSS.HCHHHH...............SHHHHHHH....HHHHHHHHHHHTTTTTHHHHHHH.....SSCHTS- CS
                 Glyco_hydro_4C  59 .eysrhyaEYvpylkrea...............peliekek....traevvkevekelfeelekekle.....lekrsge 113
                                     ++++h       lk +                + ++ +++    t a+++ + +                   + r++e
  gi|119720416|ref|YP_920911.1| 274 gTWKYHS-----SLKTKQywygptggpdseigwALYTAHQEywlaTLAQAASDPRI-----------PvsslfPQTRTEE 337
                                    *999999.....66643344554444422222222222111223333333333333...........2555556689*** PP

                                    SHHHHHHHHHHTS-EEEEEEEE-TTSSTTS-TTSEEEEEEEEETTEEEEB--CS-HHHHHH.CHHHHHHHHHHHHHHHHH CS
                 Glyco_hydro_4C 114 yavdiieaivtdkprrlvvnvpNnglIpnLpddavVEvpclvdkngirpvavgelpeqlaa.llrtniaveeltveAale 192
                                     +v +ie+++ dkp +++vnv N ++I+++p++++VEvp++vd++gi+p +  +lp+++ + ++++++ + e+++ A+le
  gi|119720416|ref|YP_920911.1| 338 SVVPLIESLMLDKPGEYQVNVLNGNAIEGIPSNVAVEVPARVDARGIHPKTGLRLPRKILSlVMQPRLLRAEMAIAAFLE 417
                                    *******************************************************88876616889************** PP

                                    TBHHHHHHHHHCSTT- CS
                 Glyco_hydro_4C 193 gdrelalqallldplv 208
                                    g r+ ++ +l+ldp++
  gi|119720416|ref|YP_920911.1| 418 GGRQFLIDWLMLDPRT 433
                                    **************97 PP

>> Ldh_1_N  lactate/malate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   9.2e-06     0.033       1      77 [.       7      88 ..       7      93 .. 0.81
   2 ?    2.0   0.0     0.056     2e+02      98     129 ..     135     166 ..     131     174 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 9.2e-06
                                   EEEEEETTTSHHH..HHHHHHHHHT..TSSSEEEEE-SSHH..HHHHHHHHHHHCHCCSTS-EEEEESSGGGGTTESEEEE- CS
                        Ldh_1_N  1 vkvavvGaaGgiG..qslalllank..kladelaLlDiake..kleGvaldlshistflsvkvkvsekeeealkdadvvvit 76
                                   +k++v+Ga G ++  ++l + l+     +++++ ++Di++e  ++    ++    ++ ++ +   + + +ea++d+dvv+ t
  gi|119720416|ref|YP_920911.1|  7 IKISVIGA-GSVAwsSKLVHDLLHTpsLYGSDVYFMDINEErlRILRGLAEKYKSEVGAEYNFFYTTDRKEAVRDSDVVINT 87
                                   59******.***822445556666556799***********7744445678888999999*******************988 PP

                                   - CS
                        Ldh_1_N 77 a 77
                                   a
  gi|119720416|ref|YP_920911.1| 88 A 88
                                   7 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.056
                                    HHHHHHHHHHHTTTSEEEE-SSSHHHHHHHHH CS
                        Ldh_1_N  98 vkeiveaiakvapnaivlvvsNPvdiltevlk 129
                                      +i++ +++ ap a ++ ++NPv  lt +++
  gi|119720416|ref|YP_920911.1| 135 AMDIARDVEELAPGAWLIQMANPVFELTTLIS 166
                                    678999******************76665555 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   5.5e-06      0.02      23     109 ..       4      98 ..       1     103 [. 0.75

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.5e-06
                                    ETCB---EEEEESTSHHHHHH......HHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEE......HCHHHHHHHHHHH CS
                    AlaDh_PNT_C  23 vpgvepakvlviGgGvaGlqA......iatakglgakVtvlDvrparleqleslgakfvev......lksqeellaeavk 90 
                                    vp   + k+ viG+G + +++      ++t +  g +V+ +D++++rl+ l+ l +k  +               +eav+
  gi|119720416|ref|YP_920911.1|   4 VP---KIKISVIGAGSVAWSSklvhdlLHTPSLYGSDVYFMDINEERLRILRGLAEK-YKSevgaeyNFFYTTDRKEAVR 79 
                                    44...899**********99844444345667779****************997777.3333455554444556689*** PP

                                    H-SEEEE---BTTSS---S CS
                    AlaDh_PNT_C  91 eadvvigtvlipGkkaPkL 109
                                    ++dvvi t+   G++   L
  gi|119720416|ref|YP_920911.1|  80 DSDVVINTAMYGGHRYYEL 98 
                                    *********9988876655 PP

>> OTCace  Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   4.4e-05      0.16      12      98 ..      20     107 ..       6     116 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.4e-05
                                    TSHHHHHHHHHHHHCT-EEEEES-TTSSH-HHHHHHHHHHHHHH.T..-EEEEESSCHHHHTT-SEEEE--SSETTCCGG CS
                         OTCace  12 knnvanslikllarlgmdvvlvaPkglepdkevleeakknakks.g..gsititedleeavkgaDvvytdvwvsmgeeke 88 
                                     ++ +++l+++ + +g dv+++  ++ +    +l+ +++++k++ g   ++ +t+d +eav + Dvv+ + ++  + + e
  gi|119720416|ref|YP_920911.1|  20 SSKLVHDLLHTPSLYGSDVYFMDINEERL--RILRGLAEKYKSEvGaeYNFFYTTDRKEAVRDSDVVINTAMYGGHRYYE 97 
                                    35789999999999****99999998544..577777777777766345677789**************99987777777 PP

                                    HHHHHHHHCC CS
                         OTCace  89 reerlkklkd 98 
                                     ++++ + ++
  gi|119720416|ref|YP_920911.1|  98 LMREVSEKHG 107
                                    7776666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (460 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.53
# Mc/sec: 2609.86
//
Query:       gi|119720417|ref|YP_920912.1|  [L=128]
Description: hypothetical protein Tpen_1512 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 807.47
//
Query:       gi|119720418|ref|YP_920913.1|  [L=423]
Description: amino acid permease-associated region [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.8e-46  157.8  29.7    4.8e-46  157.5  29.7    1.1  1  AA_permease_2   Amino acid permease
    4.2e-43  147.7  29.9    6.7e-43  147.0  29.9    1.3  1  AA_permease     Amino acid permease
      1e-13   50.9   6.0      1e-13   50.9   6.0    1.5  2  Spore_permease  Spore germination protein


Domain annotation for each model (and alignments):
>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.5  29.7     8e-50   4.8e-46       1     385 [.      11     378 ..      11     416 .. 0.85

  Alignments for each domain:
  == domain 1  score: 157.5 bits;  conditional E-value: 8e-50
                  AA_permease_2   1 lsllsafalvigsvigsgifvkn..laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkkvaf 78 
                                    l+ll+a+ + +g++ig+gifv    +a+ +gpa++l v+++ l  s   +l +aEl+salpr gG+y y++ + ++ v+f
  gi|119720418|ref|YP_920913.1|  11 LTLLDAVSVGLGAIIGAGIFVLIgiAAGLAGPAVVLAVLVSGLSAS-LTALSFAELGSALPRAGGVYEYGHTLLHPAVGF 89 
                                    6789999**************99877888***************97.6999*****999********************* PP

                  AA_permease_2  79 lsawfnwfayvpvlasilsvaasyllnalgpdlqgntwltyliaiaililvalinirgikesakiqnilgilkillplii 158
                                    l++w+ w+a  +vl +++s +++y+l+al p++++     ++ a a+++lv+l+n++g k sa ++ + + +k+  +l++
  gi|119720418|ref|YP_920913.1|  90 LMGWM-WVAGNIVLGATASQGFGYYLSALVPSVNP-----RVAALALVVLVTLLNALGAKLSAVVNDVFVAVKV-SVLLL 162
                                    ****9.6666666889****************977.....68999*****************************.8**** PP

                  AA_permease_2 159 liilglitvdgggfsslstetdtffpngwpgvllgllivlwsfdGfesaanvseevkk..kdvpkaifigllivlvlyll 236
                                    l+++g ++v++  f+        f p g   v+ + + + ++++Gf  ++  +eevk   k++p+ai ++l++++ ly l
  gi|119720418|ref|YP_920913.1| 163 LVAAGAALVKPENFQ-------PFAPKGLLPVMEASALFYFAYIGFPRISTLAEEVKDpeKNIPRAILLALAVSAALYAL 235
                                    *********999886.......688887777777777789***************886669******************* PP

                  AA_permease_2 237 vniaflgvvpddeianlsnlgsvaalffeavggkvvaiivvilialsllgaintavigssrvlealardgvlPrffakvn 316
                                    v+++++gv + + +a+++    +++ ++++vg   v ++v +++ ++ +  ++t v+g+srv++a+ar +++P+ +a +n
  gi|119720418|ref|YP_920913.1| 236 VAVVAVGVAGYEALASSNA---PLEEVARRVG---VGWVVGVGGLVATFSVVLTSVMGQSRVFYAMARNREIPDKIAEIN 309
                                    ***************8665...5777777777...7777888999999999***************************** PP

                  AA_permease_2 317 .kfgspiraiiltaivslillllfllassaaynfllsvsslgliisyllliigalilrkkrphl.kr....pgki 385
                                     k g+p++++ l+ +v l+l+ lf      +++ l+ v+s+++++s  l+ ++ ++l+ +  +   r    p+ +
  gi|119720418|ref|YP_920913.1| 310 eKLGTPVYSVLLSGTVMLVLVALF------DISRLAMVTSFLVLVSHVLTNVADVKLYLDGVDPpFRsplrPWHA 378
                                    ****************87766555......578999999999999999999999998877544431232233322 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.0  29.9   1.1e-46   6.7e-43       2     370 ..      16     347 ..      15     356 .. 0.89

  Alignments for each domain:
  == domain 1  score: 147.0 bits;  conditional E-value: 1.1e-46
                    AA_permease   2 vlvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviGln 81 
                                    ++   lg +iG+g+fv +g++++ aGp +++la+l++g+   l++ls++e+ ++ p++gg y y +  l+p++Gf +G++
  gi|119720418|ref|YP_920913.1|  16 AVSVGLGAIIGAGIFVLIGIAAGLAGP-AVVLAVLVSGLSASLTALSFAELGSALPRAGGVYEYGHTLLHPAVGFLMGWM 94 
                                    67889**********************.999************************************************* PP

                    AA_permease  82 ylfswitvlaleltaasiliqfwelvtdlpkawvtgavflvvlliinlvgvkvygeaefilalikiiaiiafiivgiill 161
                                     +   i+  a +  + +++++ +  v++++   v ++ ++v+++++n +g+k+++ +  ++  +k+  ++ ++  g+   
  gi|119720418|ref|YP_920913.1|  95 WVAGNIVLGATASQGFGYYLSAL--VPSVN-PRVAALALVVLVTLLNALGAKLSAVVNDVFVAVKVSVLLLLVAAGAA-- 169
                                    88888999999999999****99..*****.*************************************9999999943.. PP

                    AA_permease 162 aggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiagEvkdPeksiPkailqvvi 241
                                       kp+++             + + p+g        ++ ++ + + ++fa+ G+  + ++a+EvkdPek+iP+ail ++ 
  gi|119720418|ref|YP_920913.1| 170 -LVKPENF-------------QPFAPKG--------LLPVMEASALFYFAYIGFPRISTLAEEVKDPEKNIPRAILLALA 227
                                    .3333334.............3346777........******************************************** PP

                    AA_permease 242 ritifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplinaviltaalssansslysasRvlyslakd 321
                                      + +Y l++++++ + ++ +l + n       p++ +   +   +++ ++ ++ l+a++s+++ s++  sRv+y++a++
  gi|119720418|ref|YP_920913.1| 228 VSAALYALVAVVAVGVAGYEALASSN------APLEEV---ARRVGVGWVVGVGGLVATFSVVLTSVMGQSRVFYAMARN 298
                                    *********************88888......255555...555678999****************************** PP

                    AA_permease 322 glaP.kvlkkvskrgvPlraillsmiisllal.llaslnlaapivfnflla 370
                                    + +P k+++  +k g P+ ++lls  + l+++ l + + la   v+ fl+ 
  gi|119720418|ref|YP_920913.1| 299 REIPdKIAEINEKLGTPVYSVLLSGTVMLVLVaLFDISRLA--MVTSFLVL 347
                                    ************************77777766355555555..55555554 PP

>> Spore_permease  Spore germination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.9   6.0   1.7e-17     1e-13      12     252 ..      21     262 ..      11     287 .. 0.90
   2 ?   -4.1   0.6      0.88   5.2e+03      44      53 ..     324     333 ..     315     353 .. 0.49

  Alignments for each domain:
  == domain 1  score: 50.9 bits;  conditional E-value: 1.7e-17
                 Spore_permease  12 vsfqlGvgiltlprsvaeqatpdgWisvllagiiililvllmlkllkkfpe.ktliellkkilgkwLGsllsilfilyFl 90 
                                      +++G+gi +l +++a  a+p   ++vl+ g+ + + +l + +l +  p    ++e+ + +l   +G+l++ ++++  +
  gi|119720418|ref|YP_920913.1|  21 LGAIIGAGIFVLIGIAAGLAGPAVVLAVLVSGLSASLTALSFAELGSALPRaGGVYEYGHTLLHPAVGFLMGWMWVAGNI 100
                                    5689********************************************9972679************************* PP

                 Spore_permease  91 llaafelRefseliqvflledtplwiiilllllvilYlvvkG.ieslareflfiivilliilllillfslklaeiknlrP 169
                                    +l a+    f+  ++  +    p ++ ++l++lv+l+ + +  ++ +  ++ +++ + + +lll++     l++++n +P
  gi|119720418|ref|YP_920913.1| 101 VLGATASQGFGYYLSALVPSVNPRVAALALVVLVTLLNALGAkLSAV--VNDVFVAVKVSVLLLLVAAGAALVKPENFQP 178
                                    **********************************9998887624444..5677777888888888899999********* PP

                 Spore_permease 170 vlgngikpvlkslkttslsflgveillllvpflkdk.kkvkkaallgvlistllyllttlivilvlsveqlkkatwptls 248
                                     + +g+ pv++++  ++++++g+  +  l + +kd+ k++ +a+ll++++s  ly+l+ +++++v + e+l +++ p+ +
  gi|119720418|ref|YP_920913.1| 179 FAPKGLLPVMEASALFYFAYIGFPRISTLAEEVKDPeKNIPRAILLALAVSAALYALVAVVAVGVAGYEALASSNAPLEE 258
                                    ***********************988888888888725689*****************************9999988876 PP

                 Spore_permease 249 llkv 252
                                    +++ 
  gi|119720418|ref|YP_920913.1| 259 VARR 262
                                    6665 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 0.88
                 Spore_permease  44 iiililvllm 53 
                                     ++l+lv+l+
  gi|119720418|ref|YP_920913.1| 324 TVMLVLVALF 333
                                    3333333322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1054  (0.0587874); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.50
# Mc/sec: 2528.89
//
Query:       gi|119720419|ref|YP_920914.1|  [L=253]
Description: hypothetical protein Tpen_1514 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0045   17.3  15.1      0.011   16.0   6.1    2.5  2  DUF996         Protein of unknown function (DUF996)
  ------ inclusion threshold ------
        0.4   10.4  37.0       0.39   10.4  22.3    2.1  2  Yip1           Yip1 domain


Domain annotation for each model (and alignments):
>> DUF996  Protein of unknown function (DUF996)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.4   0.00072       6.4      27      89 ..      20      82 ..      16     101 .. 0.66
   2 !   16.0   6.1   1.2e-06     0.011      30     120 ..     118     211 ..     108     217 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00072
                         DUF996 27 snaliafilsiialvvailalllvlgalatalelpgleeaaslilllllvliiayvlliisav 89
                                   + +l++ +++++al+v++l+l + l ++   +  +++ +  ++++  ll+l+++++l+i+ +v
  gi|119720419|ref|YP_920914.1| 20 EAMLASQLVNLVALLVFALLLPGFLPSVPELWAGKEALRLGAALARHLLLLLLVLILFIAGGV 82
                                   5678899999*******9999888888876666655555555444444444445555554433 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 1.2e-06
                         DUF996  30 liafilsiialvvailalllvlgalatalelpgleeaaslilllllvliiayvlliisa...vflkksyellgkrtgvkl 106
                                     +++ l++ a+v++++  l ++ ala  +   g+e ++++++++++vl+++++++i+s    +     + +l+++tg + 
  gi|119720419|ref|YP_920914.1| 118 WASLALAVLAVVALVAFALPAMPALAGRYPPVGPEAMLAVMTGFIVVLLLVVLAAIASFvarIGEILMLFELSSATGLDS 197
                                    444455555555555555555555555555666666666777777777555555555550005566778899******** PP

                         DUF996 107 FetagllyfiGaiL 120
                                    F+ta++l ++  +L
  gi|119720419|ref|YP_920914.1| 198 FKTAAILEVVQILL 211
                                    ******98876666 PP

>> Yip1  Yip1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   6.1   0.00038       3.4     106     160 ..      24     105 ..       9     113 .. 0.76
   2 ?   10.4  22.3   4.3e-05      0.39      18     145 ..     113     237 ..      95     247 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00038
                           Yip1 106 yallPlilgaliaillllllgt...........................llllvgllaliWslvllylglkaahnlskkk 158
                                     ++l++++++l+++lll+ + +                           +l+l+++ +++W +++++  ++aa +l k++
  gi|119720419|ref|YP_920914.1|  24 ASQLVNLVALLVFALLLPGFLPsvpelwagkealrlgaalarhllllllVLILFIAGGVLWLFAVFARLIPAADRLAKWR 103
                                    3456666666666666655555777888888*************999988888899999999999999999999998887 PP

                           Yip1 159 al 160
                                     +
  gi|119720419|ref|YP_920914.1| 104 EA 105
                                    55 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 4.3e-05
                           Yip1  18 ilrapdlallllalltlllgllas......lnlgqtlasgeevqgltlssllgaiiggylglllgllllalllhl..iak 89 
                                    i   ++  l+l++l+ ++l+++a           +  ++     g + + ++++ ++ +l+l++ +++ +++  +  i +
  gi|119720419|ref|YP_920914.1| 113 IKYGYWASLALAVLAVVALVAFALpampalA---GRYPPV----GPEAMLAVMTGFIVVLLLVVLAAIASFVARIgeILM 185
                                    5556677777777777777777774453322...222222....333555555555555555666666666666566666 PP

                           Yip1  90 llg.gkgsfkqtlsvvgyallPlilgaliaillllllgtllllvgllaliWslvlly 145
                                    l+  ++ +  +++  ++   +++il++++++++  l+ +     gll+++  +++l+
  gi|119720419|ref|YP_920914.1| 186 LFElSSATGLDSFKTAAILEVVQILLSFLSAVPHALAVA-----GLLSVALFIAALV 237
                                    666*99999***********************9987776.....3333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1160  (0.0646996); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.50
# Mc/sec: 1511.63
//
Query:       gi|119720420|ref|YP_920915.1|  [L=89]
Description: hypothetical protein Tpen_1515 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.45
# Mc/sec: 598.26
//
Query:       gi|119720421|ref|YP_920916.1|  [L=328]
Description: alcohol dehydrogenase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.8e-27   94.3   0.0    6.1e-27   93.7   0.0    1.3  1  ADH_N           Alcohol dehydrogenase GroES-like domain
    1.9e-16   60.2   0.1    3.2e-16   59.5   0.1    1.3  1  ADH_zinc_N      Zinc-binding dehydrogenase
    1.2e-10   41.3   0.1    1.6e-10   40.8   0.1    1.1  1  Glu_dehyd_C     Glucose dehydrogenase C-terminus
    8.6e-09   36.6   0.0    3.6e-08   34.5   0.0    1.9  2  ADH_zinc_N_2    Zinc-binding dehydrogenase
  ------ inclusion threshold ------
      0.017   15.7   0.7      0.047   14.2   0.7    1.8  1  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
      0.037   13.4   0.0      0.046   13.1   0.0    1.3  1  PALP            Pyridoxal-phosphate dependent enzyme
      0.051   14.0   0.1      0.089   13.2   0.1    1.3  1  NAD_binding_7   Putative NAD(P)-binding
      0.093   12.6   0.2       0.31   10.9   0.0    1.8  2  LpxI_N          LpxI N-terminal domain
       0.14   10.9   0.0       0.25   10.0   0.0    1.4  1  Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase


Domain annotation for each model (and alignments):
>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.7   0.0   3.1e-30   6.1e-27       2     107 ..      25     125 ..      24     127 .. 0.95

  Alignments for each domain:
  == domain 1  score: 93.7 bits;  conditional E-value: 3.1e-30
                                    TEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SSSHHHHTT-GGG- CS
                          ADH_N   2 gevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVvvepliscgeCaaCkegeenlC 81 
                                    g++l+k+ a+giCg+D  ++kg + +  k pli+GHE++G+v+e  +e     vG+ Vv e++++c +C++C++g +++C
  gi|119720421|ref|YP_920916.1|  25 GWALVKTLAVGICGTDKAFYKG-TYPLFKKPLIPGHEVSGVVVEGPEE----LVGRLVVSEINFPCWRCEYCRSGLYTHC 99 
                                    799*******************.8********************6655....49************************** PP

                                    TTBEETTTSS-SSSBSEEEECGGGEE CS
                          ADH_N  82 eeakllgvsldGgfaeyvvvpekklv 107
                                    +++k+lg+++dGg+aey+v+p++ l+
  gi|119720421|ref|YP_920916.1| 100 PYKKTLGIDFDGGLAEYFVAPATALH 125
                                    *********************98876 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.5   0.1   1.6e-19   3.2e-16       4     128 ..     169     290 ..     167     292 .. 0.88

  Alignments for each domain:
  == domain 1  score: 59.5 bits;  conditional E-value: 1.6e-19
                                    HHHHHHHHHTT-EEEEEES.SHHHHHHHHHTTESEEEETTTCHHHHHHHHHTT.TSSEEEEEESSCSHHHHHHHHHCEEE CS
                     ADH_zinc_N   4 laavqlAkalGaeviavds.seeklelakklGadevinykeadlverikeltg.gegvdvvfecvGsgatleaalkllkp 81 
                                    +++vq++k +G+++++v++  ++k+e++++l +++v  + +    +r+    g g g+dvvfe++G++++l+ a++l+kp
  gi|119720421|ref|YP_920916.1| 169 VMLVQVLKDAGFRPVVVSRaGSSKAEILRSLDVEVVTAE-Q---ASRLGGESGdGVGFDVVFEVSGDPSALNLAVDLVKP 244
                                    799*********77776661577*********9999999.4...355555554477************************ PP

                                    EEEEEECSCTSSEEEEEHHHHHHTT-EEEEE-SSCHHHHHHHHHHHH CS
                     ADH_zinc_N  82 gGrlvvvGggkgeeefdlrnlllkeksilGsllgslreefkealdll 128
                                    +G++ +  +++++ +++l + + ke+ ++Gs +g+  +ef+ea++ll
  gi|119720421|ref|YP_920916.1| 245 RGTVHLKSTPGNPGSVNLTKAVVKEVAVIGSRCGT-FREFREAIRLL 290
                                    ***********************************.9*******997 PP

>> Glu_dehyd_C  Glucose dehydrogenase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   0.1   8.1e-14   1.6e-10      31     210 ..     156     326 ..     133     327 .. 0.83

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 8.1e-14
                    Glu_dehyd_C  31 pesalvlGaGslGLLalalleaeerglervyvlgrrdrpdptidlveelGatYvdsre.tpvdeipeaseemdlvvEaTG 109
                                     +s+ v+G+G+l ++ + +l+  + g+  v v+ r    + +++++++l+   v+ ++ + +   +     +d+v+E  G
  gi|119720421|ref|YP_920916.1| 156 GDSVAVVGTGNLAVMLVQVLK--DAGFRPV-VVSR--AGSSKAEILRSLDVEVVTAEQaSRLGGESGDGVGFDVVFEVSG 230
                                    47999***********99998..589*866.6776..4578999*******999876516789999999*********** PP

                    Glu_dehyd_C 110 sakhafeaiealapnGvaaLlGvpeds.evevdggelhrelvleNkalvGsvNanrrhfeaavdtLaalpeslldelvtk 188
                                     + ++  a++ ++p G + L   p +  +v+       ++ v++  a++Gs     r+f++a++ L +     ++ ++t+
  gi|119720421|ref|YP_920916.1| 231 DPSALNLAVDLVKPRGTVHLKSTPGNPgSVN------LTKAVVKEVAVIGSRCGTFREFREAIRLLREG---RVRPVITS 301
                                    ********************98886541332......356699999*****************999764...58999*** PP

                    Glu_dehyd_C 189 vv.dldeleeAfedd..detiKtvv 210
                                    v+ +l++++eAfe++    ++K+vv
  gi|119720421|ref|YP_920916.1| 302 VYgGLEKAREAFERSfrPGEVKVVV 326
                                    99459*******9752268999998 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       1.4   2.8e+03     112     120 ..     141     149 ..     119     208 .. 0.50
   2 !   34.5   0.0   1.8e-11   3.6e-08      16     121 ..     215     315 ..     197     322 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.4
                                    GGGHHHHHH CS
                   ADH_zinc_N_2 112 leeaaeAhr 120
                                    l+++  A+r
  gi|119720421|ref|YP_920916.1| 141 LAALLNALR 149
                                    333333222 PP

  == domain 2  score: 34.5 bits;  conditional E-value: 1.8e-11
                                    HHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE----.S-EEE-CHHHCTTT-EEEE--GGG...-.-HHHHHHHHH CS
                   ADH_zinc_N_2  16 aatggegvDvvldtvggealleaslkvlpggGrlvsiggpplsaallkpakkrkgrsvkyeflfsmkasaqadileelaa 95 
                                    ++ +g g+Dvv++  g +++l  ++++++++G++   + p    + + ++    ++ vk + ++  + +  ++ ++e  +
  gi|119720421|ref|YP_920916.1| 215 ESGDGVGFDVVFEVSGDPSALNLAVDLVKPRGTVHLKSTP---GNPGSVN--LTKAVVKEVAVIGSRCGTFRE-FREAIR 288
                                    5556789*********99999*******888**9433332...2222222..333444444444323334788.****** PP

                                    HHHHHH----EEEE.EEGGGHHHHHHH CS
                   ADH_zinc_N_2  96 lieeGklrpvvdrv.fpleeaaeAhry 121
                                    l+ eG++rpv+++v  +le+a+eA+++
  gi|119720421|ref|YP_920916.1| 289 LLREGRVRPVITSVyGGLEKAREAFER 315
                                    **************555********97 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.7   2.4e-05     0.047       1      69 [.     158     215 ..     158     227 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.4e-05
                                    EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEE CS
                      Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegs 69 
                                    +v+vvG G+++++l ++l++ g +  vv r+               +e l+ + +ev++ +++ ++ g+
  gi|119720421|ref|YP_920916.1| 158 SVAVVGTGNLAVMLVQVLKDAGFRPVVVSRAGSSK-----------AEILRSLDVEVVTAEQASRLGGE 215
                                    699***************************98887...........67777777777777777777655 PP

>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   2.3e-05     0.046      49     108 ..     150     207 ..     127     289 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.3e-05
                                    HHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-EEEEEEETTS-HHHHHHHHHTT-EEEEEC CS
                           PALP  49 lkegtgaktvveassGNhgralAaaaallGlkvtivvpadaspekvallrllGaevvevg 108
                                    lk+  +++ v++ ++GN ++ l  + + +G++ ++v  a++s  k++ lr+l  evv  +
  gi|119720421|ref|YP_920916.1| 150 LKPPAPGDSVAVVGTGNLAVMLVQVLKDAGFRPVVVSRAGSS--KAEILRSLDVEVVTAE 207
                                    3333699*****************************999998..9*********999883 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   4.5e-05     0.089       8      73 ..     157     233 ..     154     249 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.5e-05
                  NAD_binding_7   8 kkvlvvGgGevAarkvrklleagakvtvvapevkeele.......elvklaeeel....ekdlegadlviaatddre 73 
                                     +v vvG G++A   v+ l +ag + +vv+ + ++++e       e v++++       ++d  g+d+v+ +  d++
  gi|119720421|ref|YP_920916.1| 157 DSVAVVGTGNLAVMLVQVLKDAGFRPVVVSRAGSSKAEilrsldvEVVTAEQASRlggeSGDGVGFDVVFEVSGDPS 233
                                    6799****************************755555565555554555444334554455666777777777665 PP

>> LpxI_N  LpxI N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00016      0.31       6      44 ..     162     200 ..     159     212 .. 0.82
   2 ?   -1.7   0.0       1.3   2.5e+03      52      70 ..     281     299 ..     260     315 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00016
                         LpxI_N   6 AGsGrlPllvaeaakaagrevvvvalegeadeelekivd 44 
                                     G G+l++++++ +k+ag ++vvv+  g+ ++e+ +  d
  gi|119720421|ref|YP_920916.1| 162 VGTGNLAVMLVQVLKDAGFRPVVVSRAGSSKAEILRSLD 200
                                    69**************************99999888555 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.3
                         LpxI_N  52 gqlgklikaLkregvtevv 70 
                                     ++ ++i++L++ +v+ v+
  gi|119720421|ref|YP_920916.1| 281 REFREAIRLLREGRVRPVI 299
                                    4667778888888887776 PP

>> Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00013      0.25     267     304 ..     151     188 ..     119     210 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00013
                                    HHHHTT-EEEEECSSHHHHHHHHHHHHHT-EEEEEEES CS
                 Oxidored_nitro 267 heylagkrvaiygdpdrvvalarllkelGmevvaagte 304
                                    ++   g  va++g + ++v l+++lk+ G+++v+++  
  gi|119720421|ref|YP_920916.1| 151 KPPAPGDSVAVVGTGNLAVMLVQVLKDAGFRPVVVSRA 188
                                    55666999**************************9755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2152.13
//
Query:       gi|119720422|ref|YP_920917.1|  [L=148]
Description: hypothetical protein Tpen_1517 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.7e-06   26.7   0.0    1.2e-05   25.4   0.0    1.8  1  XhlA             Haemolysin XhlA
    1.7e-05   24.7   7.2     0.0095   15.9   0.2    3.6  3  Sugarporin_N     Maltoporin periplasmic N-terminal extension
    5.3e-05   23.2   2.6    7.4e-05   22.7   2.6    1.3  1  Prefoldin_3      Prefoldin subunit
    0.00014   22.0   0.3    0.00026   21.2   0.3    1.5  1  Tropomyosin_1    Tropomyosin like
     0.0022   17.8   1.4       0.02   14.7   0.3    2.7  3  HSBP1            Heat shock factor binding protein 1
     0.0023   18.3   1.3     0.0083   16.5   1.3    2.1  1  CLZ              C-terminal leucine zipper domain of cyclic n
     0.0026   18.0   0.4     0.0085   16.4   0.4    1.8  1  BLOC1_2          Biogenesis of lysosome-related organelles co
     0.0038   17.7   0.5     0.0071   16.8   0.4    1.4  1  DUF16            Protein of unknown function DUF16
     0.0043   17.1   2.1     0.0043   17.1   2.1    2.0  2  DHR10            Designed helical repeat protein 10 domain
     0.0046   17.3   2.2     0.0063   16.9   0.5    2.2  1  FlaC_arch        Flagella accessory protein C (FlaC)
  ------ inclusion threshold ------
       0.01   16.0   0.2       0.01   16.0   0.2    1.6  1  Jnk-SapK_ap_N    JNK_SAPK-associated protein-1
      0.014   15.6   4.7       0.82   10.0   0.9    3.1  3  ABC_tran_CTD     ABC transporter C-terminal domain
      0.014   15.6   2.6       0.81   10.0   0.1    2.7  2  Osmo_CC          Osmosensory transporter coiled coil
      0.016   15.4   0.9      0.023   14.9   0.9    1.5  1  Fib_alpha        Fibrinogen alpha/beta chain family
      0.017   14.8   2.1       0.15   11.7   0.6    2.7  3  Vac_Fusion       Chordopoxvirus multifunctional envelope prot
      0.019   14.9   0.4      0.019   14.9   0.4    2.2  2  TMF_DNA_bd       TATA element modulatory factor 1 DNA binding
       0.02   15.3   1.3       0.02   15.3   1.3    1.5  1  HrpB7            Bacterial type III secretion protein (HrpB7)
      0.021   14.5   0.3      0.051   13.2   0.3    1.7  1  DUF4988          Domain of unknown function
      0.021   14.4   1.0      0.021   14.4   1.0    1.4  1  MscS_porin       Mechanosensitive ion channel porin domain
      0.021   14.8   0.4      0.049   13.7   0.4    1.6  1  DUF1664          Protein of unknown function (DUF1664)
      0.035   13.4   0.1      0.049   12.9   0.1    1.3  1  DUF3450          Protein of unknown function (DUF3450)
      0.041   14.2   0.4       0.09   13.1   0.5    1.6  1  DUF5082          Domain of unknown function (DUF5082)
      0.042   12.9   0.0      0.056   12.5   0.0    1.2  1  MCM              MCM P-loop domain
      0.044   13.2   2.9      0.039   13.4   1.9    1.4  1  DUF3552          Domain of unknown function (DUF3552)
      0.045   13.6   0.9      0.045   13.6   0.9    1.9  2  DASH_Spc19       Spc19
      0.046   13.8   2.0       0.16   12.1   0.4    2.4  2  TRPM_tetra       Tetramerisation domain of TRPM
      0.048   14.1   0.4       0.13   12.7   0.5    1.6  2  CCDC53           Subunit CCDC53 of WASH complex
      0.048   13.7   0.7      0.048   13.7   0.7    1.7  1  ADIP             Afadin- and alpha -actinin-Binding
      0.048   13.6   0.8      0.066   13.2   0.8    1.4  1  Ax_dynein_light  Axonemal dynein light chain
      0.052   13.9   5.1         15    5.9   2.5    3.1  2  Lzipper-MIP1     Leucine-zipper of ternary complex factor MIP
      0.052   14.2   1.0      0.052   14.2   1.0    2.2  2  SlyX             SlyX
      0.071   12.4   1.0       0.15   11.4   0.9    1.6  1  Dynamitin        Dynamitin
      0.079   11.6   0.1        0.1   11.2   0.1    1.1  1  AAA_13           AAA domain
      0.079   13.0   0.0       0.11   12.5   0.0    1.3  1  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
      0.094   11.9   3.0        8.4    5.7   0.0    3.4  4  MRF_C1           Myelin gene regulatory factor -C-terminal do
      0.095   12.1   7.0       0.32   10.3   7.1    1.7  1  Tropomyosin      Tropomyosin
      0.098   13.1   0.1        0.2   12.1   0.1    1.5  1  NPV_P10          Nucleopolyhedrovirus P10 protein
       0.15   11.5   0.0       0.18   11.2   0.0    1.1  1  FliD_C           Flagellar hook-associated protein 2 C-termin
       0.34   10.9   3.2       0.19   11.7   0.5    2.0  1  Prefoldin_2      Prefoldin subunit
       0.34   11.5  12.0       0.51   10.9   0.2    3.6  3  MerR-DNA-bind    MerR, DNA binding
        1.4    8.8   7.1       0.19   11.5   1.7    2.3  1  DivIC            Septum formation initiator
        1.4    9.2   4.8        1.4    9.2   1.1    2.1  2  KLRAQ            Predicted coiled-coil domain-containing prot
          2    8.3   5.7          1    9.2   0.6    2.6  3  CdvA             CdvA-like coiled-coil domain
        2.5    8.2   5.5       0.64   10.2   1.2    2.0  2  Med9             RNA polymerase II transcription mediator com
        4.4    7.5  11.6       0.21   11.7   1.7    3.0  2  bZIP_2           Basic region leucine zipper


Domain annotation for each model (and alignments):
>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   3.1e-08   1.2e-05       2      48 ..      73     119 ..      72     142 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 3.1e-08
                           XhlA   2 ikerlerietkldnleervdkleekaaeaeekiknleedlkklesnq 48 
                                    +++++  +e++ ++le+r++ le+k + +e ++ +le ++++le ++
  gi|119720422|ref|YP_920917.1|  73 VEQKIGALEQRFNSLEQRINLLEQKIDLVERRVGSLEQRIARLEGMM 119
                                    789*****************************************986 PP

>> Sugarporin_N  Maltoporin periplasmic N-terminal extension
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.2   2.4e-05    0.0095      25      45 ..      70      90 ..      66      90 .. 0.89
   2 !   11.0   2.7   0.00079      0.32      26      53 ..      85     112 ..      84     114 .. 0.89
   3 ?    4.9   0.3     0.063        25      27      36 ..     107     116 ..     105     118 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.4e-05
                   Sugarporin_N 25 sltiEaRLaaLEkrLqeAeqr 45
                                   ++t+E+++ aLE+r ++ eqr
  gi|119720422|ref|YP_920917.1| 70 ADTVEQKIGALEQRFNSLEQR 90
                                   57**************99998 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00079
                   Sugarporin_N  26 ltiEaRLaaLEkrLqeAeqraqaAeara 53 
                                    +++E+R+++LE+     e r  + e+r+
  gi|119720422|ref|YP_920917.1|  85 NSLEQRINLLEQKIDLVERRVGSLEQRI 112
                                    69************99999999888887 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.063
                   Sugarporin_N  27 tiEaRLaaLE 36 
                                    ++E+R+a LE
  gi|119720422|ref|YP_920917.1| 107 SLEQRIARLE 116
                                    89*******9 PP

>> Prefoldin_3  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   2.6   1.9e-07   7.4e-05      27      95 ..      47     116 ..       7     119 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.9e-07
                    Prefoldin_3  27 eddateedllriardfegslvte.kEveeilGekqgvtrskqQvvdlisrRiDYVkqniktlekrleaae 95 
                                    +d at++dl ++++   g++v + + ve+ +G  ++   s +Q ++l++++iD V++ + +le+r++  e
  gi|119720422|ref|YP_920917.1|  47 RDVATKQDLKELREGIRGDIVSRaDTVEQKIGALEQRFNSLEQRINLLEQKIDLVERRVGSLEQRIARLE 116
                                    6889*****************97256999****999999***************************9877 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.3   6.5e-07   0.00026      13      59 ..      67     113 ..      50     119 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 6.5e-07
                  Tropomyosin_1  13 qekaeeleekvKeleqenlekeqeiksLtkknqqleeevekleeklk 59 
                                    + +a+ +e+k+ +leq+  + eq i+ L++k++++e  v  le+++ 
  gi|119720422|ref|YP_920917.1|  67 VSRADTVEQKIGALEQRFNSLEQRINLLEQKIDLVERRVGSLEQRIA 113
                                    689****************************************9876 PP

>> HSBP1  Heat shock factor binding protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       5.9   2.3e+03       6      16 ..       5      15 ..       2      16 .. 0.78
   2 ?    6.9   0.0     0.014       5.6      21      47 ..      62      88 ..      53      92 .. 0.82
   3 !   14.7   0.3     5e-05      0.02       7      46 ..      73     115 ..      70     120 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 5.9
                          HSBP1  6 vVenlLqqlqd 16
                                   ++e+lL++l +
  gi|119720422|ref|YP_920917.1|  5 IAEKLLEELRQ 15
                                   67999999876 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.014
                          HSBP1 21 msdqilsriDdMssriDdLEksiadlm 47
                                   +  +i+sr D  +++i  LE+  ++l 
  gi|119720422|ref|YP_920917.1| 62 IRGDIVSRADTVEQKIGALEQRFNSLE 88
                                   567899999999999999999887775 PP

  == domain 3  score: 14.7 bits;  conditional E-value: 5e-05
                          HSBP1   7 VenlLqqlqdkFqtmsdqils...riDdMssriDdLEksiadl 46 
                                    Ve+    l+++F+++++ i     +iD  ++r+ +LE+ ia l
  gi|119720422|ref|YP_920917.1|  73 VEQKIGALEQRFNSLEQRINLleqKIDLVERRVGSLEQRIARL 115
                                    677777899******999985556****************987 PP

>> CLZ  C-terminal leucine zipper domain of cyclic nucleotide-gated channels
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   1.3   2.1e-05    0.0083      25      69 ..      69     116 ..      51     118 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.1e-05
                            CLZ  25 eqkeleekverLessLeaLqtrlarLlaeyessqrk...LkqRitkLE 69 
                                     ++++e+k+  Le++ ++L++r++ L ++ + ++r+   L+qRi++LE
  gi|119720422|ref|YP_920917.1|  69 RADTVEQKIGALEQRFNSLEQRINLLEQKIDLVERRvgsLEQRIARLE 116
                                    67899*****************99999998877775444999**9999 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.4   2.1e-05    0.0085      42      86 ..      69     117 ..      46     121 .. 0.63

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.1e-05
                        BLOC1_2  42 vaaslekkleklnekyeelqp....ylqqidqiekqvteLeeavseLDe 86 
                                    +a+ +e+k+ +l+++ ++l++    + q+id +e++v +Le+ +++L+ 
  gi|119720422|ref|YP_920917.1|  69 RADTVEQKIGALEQRFNSLEQrinlLEQKIDLVERRVGSLEQRIARLEG 117
                                    4555566666666644444331111446677777777777777776664 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.4   1.8e-05    0.0071      32      85 ..      66     119 ..      42     130 .. 0.59

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.8e-05
                                    BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HH CS
                          DUF16  32 nkqrLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetl 85 
                                       r   +e+k+ +l++++n leq ++ +++ki+  + ++   ++++ +++  +
  gi|119720422|ref|YP_920917.1|  66 IVSRADTVEQKIGALEQRFNSLEQRINLLEQKIDLVERRVGSLEQRIARLEGMM 119
                                    334444556666677777777777777777777777777777766666555555 PP

>> DHR10  Designed helical repeat protein 10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.2       6.1   2.4e+03      45      54 ..       9      18 ..       3      28 .. 0.41
   2 !   17.1   2.1   1.1e-05    0.0043      49      98 ..      67     116 ..      38     119 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 6.1
                          DHR10 45 ieaelaklee 54
                                   + +el++ e+
  gi|119720422|ref|YP_920917.1|  9 LLEELRQRED 18
                                   2222222222 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 1.1e-05
                          DHR10  49 lakleeakkklkelrdaleekeielrelerkeerlqrqlenaeeklerlr 98 
                                    + + +++++k+ +l+++ +++e++ + le+k+++++r++ + e++++rl+
  gi|119720422|ref|YP_920917.1|  67 VSRADTVEQKIGALEQRFNSLEQRINLLEQKIDLVERRVGSLEQRIARLE 116
                                    5688999*****************************************96 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.5   1.6e-05    0.0063       1      40 [.      76     115 ..      69     122 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.6e-05
                      FlaC_arch   1 ridelEnklsklsteletvkkeneelsksveelkenVkdl 40 
                                    +i+ lE+++++l+ +++ ++++++ ++  v  l++++ +l
  gi|119720422|ref|YP_920917.1|  76 KIGALEQRFNSLEQRINLLEQKIDLVERRVGSLEQRIARL 115
                                    6788888888888888888888888888888888888554 PP

>> Jnk-SapK_ap_N  JNK_SAPK-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.0   0.2   2.6e-05      0.01      66     129 ..      52     115 ..      36     119 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.6e-05
                  Jnk-SapK_ap_N  66 yerekelrkraeeeleeiedqweeerkelqekveqleeenrelelkaknaadqlsrleekeael 129
                                    +++ kelr+    ++    d++e++  +l++++++le++++ le+k++ ++ ++ +le++ a l
  gi|119720422|ref|YP_920917.1|  52 KQDLKELREGIRGDIVSRADTVEQKIGALEQRFNSLEQRINLLEQKIDLVERRVGSLEQRIARL 115
                                    677889999999999999****************************************998766 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1       4.5   1.8e+03      14      32 ..      10      28 ..       5      59 .. 0.48
   2 ?   10.0   0.9    0.0021      0.82      11      32 ..      71      92 ..      51     104 .. 0.75
   3 ?    6.3   0.1     0.028        11      10      28 ..      98     116 ..      92     120 .. 0.55

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 4.5
                   ABC_tran_CTD 14 eaeIeaLEeeiaeleaela 32
                                    +e+ + E     l +el 
  gi|119720422|ref|YP_920917.1| 10 LEELRQREDLRRGLAEELV 28
                                   4444444444444444444 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0021
                   ABC_tran_CTD 11 eeleaeIeaLEeeiaeleaela 32
                                   +++e++I aLE++  +le++++
  gi|119720422|ref|YP_920917.1| 71 DTVEQKIGALEQRFNSLEQRIN 92
                                   4677777777777777777765 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.028
                   ABC_tran_CTD  10 leeleaeIeaLEeeiaele 28 
                                    ++ +e++  +LE++ia le
  gi|119720422|ref|YP_920917.1|  98 IDLVERRVGSLEQRIARLE 116
                                    4445555566666666665 PP

>> Osmo_CC  Osmosensory transporter coiled coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.055        22      15      34 ..      71      90 ..      66      92 .. 0.84
   2 ?   10.0   0.1     0.002      0.81       9      32 ..      93     116 ..      91     124 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.055
                                   THHHHHHHHHHHHHHHHHHH CS
                        Osmo_CC 15 dnIEqkvedideeIaaLeek 34
                                   d +Eqk++ +++  + Le++
  gi|119720422|ref|YP_920917.1| 71 DTVEQKIGALEQRFNSLEQR 90
                                   78999999999999999876 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.002
                                    XXXXXXTHHHHHHHHHHHHHHHHH CS
                        Osmo_CC   9 lLqehYdnIEqkvedideeIaaLe 32 
                                    lL+++ d +E++v+ +++ Ia+Le
  gi|119720422|ref|YP_920917.1|  93 LLEQKIDLVERRVGSLEQRIARLE 116
                                    9*********************98 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.9   5.7e-05     0.023      93     129 ..      66     102 ..       7     119 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.7e-05
                                    HHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Fib_alpha  93 lketidaqesnirvLqnvlesneqkiqkLeqdidqke 129
                                    +  + d+ e++i +L + ++s+eq+i+ Leq+id  e
  gi|119720422|ref|YP_920917.1|  66 IVSRADTVEQKIGALEQRFNSLEQRINLLEQKIDLVE 102
                                    3333344455555555555555555555555555333 PP

>> Vac_Fusion  Chordopoxvirus multifunctional envelope protein A27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0       0.9   3.6e+02       7      23 ..      37      53 ..      34      63 .. 0.80
   2 ?    7.3   0.4    0.0088       3.5       4      35 ..      72     103 ..      69     104 .. 0.89
   3 ?   11.7   0.6   0.00038      0.15       2      34 ..      84     116 ..      83     119 .. 0.95

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.9
                                   HHHHHHHHHHHHHHHHH CS
                     Vac_Fusion  7 erllvlekdfqlvikcc 23
                                   +r+ vl+ ++ +v+ ++
  gi|119720422|ref|YP_920917.1| 37 LRIAVLTALYRDVATKQ 53
                                   6999*******999876 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0088
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH- CS
                     Vac_Fusion   4 dleerllvlekdfqlvikcckrvnealkRlEn 35 
                                     +e+++  le+ f+ ++++    ++ ++ +E+
  gi|119720422|ref|YP_920917.1|  72 TVEQKIGALEQRFNSLEQRINLLEQKIDLVER 103
                                    68999*************99999999999887 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.00038
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Vac_Fusion   2 lkdleerllvlekdfqlvikcckrvnealkRlE 34 
                                    +++le+r+  le++  lv+ +    ++++ RlE
  gi|119720422|ref|YP_920917.1|  84 FNSLEQRINLLEQKIDLVERRVGSLEQRIARLE 116
                                    789*****************************9 PP

>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.2       4.5   1.8e+03      60      69 ..       7      16 ..       3      27 .. 0.62
   2 ?   14.9   0.4   4.9e-05     0.019      32      73 ..      74     115 ..      68     116 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 4.5
                     TMF_DNA_bd 60 ekeleeleer 69
                                   ek leel++r
  gi|119720422|ref|YP_920917.1|  7 EKLLEELRQR 16
                                   4444444444 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 4.9e-05
                     TMF_DNA_bd  32 nntikkLrkknkelekeikelkkkleklekeleeleerlkea 73 
                                    +++i  L +  + le+ i+ l++k++ +e+ + +le+r ++ 
  gi|119720422|ref|YP_920917.1|  74 EQKIGALEQRFNSLEQRINLLEQKIDLVERRVGSLEQRIARL 115
                                    577888888888888888888999999999988888887776 PP

>> HrpB7  Bacterial type III secretion protein (HrpB7)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   1.3   5.1e-05      0.02      82     134 ..      64     116 ..      38     119 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.1e-05
                          HrpB7  82 dvlegrvraaeaelaaarqaldaaedavaatarkiaRndaqidacrerierlr 134
                                    + +  r   +e+++ a++q+++  e++++  ++ki   ++++   ++ri+rl+
  gi|119720422|ref|YP_920917.1|  64 GDIVSRADTVEQKIGALEQRFNSLEQRINLLEQKIDLVERRVGSLEQRIARLE 116
                                    56667778889999999999999999999999999999999999999999886 PP

>> DUF4988  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.3   0.00013     0.051       1      30 [.      80     109 ..      68     126 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00013
                        DUF4988   1 leddvndlkdrvaaleeqvkelndniealk 30 
                                    le++ n+l++r++ le++++ ++  + +l+
  gi|119720422|ref|YP_920917.1|  80 LEQRFNSLEQRINLLEQKIDLVERRVGSLE 109
                                    577778888888888888887777777765 PP

>> MscS_porin  Mechanosensitive ion channel porin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   1.0   5.2e-05     0.021     161     204 ..      73     116 ..      42     119 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.2e-05
                     MscS_porin 161 leaqieeleqellsnnnrqeLlklqrdllklriqqleqelqaLq 204
                                     e++i  leq   s  +r++Ll+++ dl + r+  leq+++ L+
  gi|119720422|ref|YP_920917.1|  73 VEQKIGALEQRFNSLEQRINLLEQKIDLVERRVGSLEQRIARLE 116
                                    6899999*********************************9997 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.4   0.00012     0.049      63     115 ..      65     117 ..      42     122 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00012
                        DUF1664  63 hLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegles 115
                                    ++ sr d+v++k+ + ++  +++++ ++ ++++++ +++ v s+++ +  le+
  gi|119720422|ref|YP_920917.1|  65 DIVSRADTVEQKIGALEQRFNSLEQRINLLEQKIDLVERRVGSLEQRIARLEG 117
                                    44555566666666666666666666666666666666666666666665555 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   0.00012     0.049      38      92 ..      69     116 ..      39     124 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00012
                        DUF3450  38 kidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeie 92 
                                    +       ++++++++ al+++ +sle   + le+ ++ +e+++ sle++i+++e
  gi|119720422|ref|YP_920917.1|  69 R-------ADTVEQKIGALEQRFNSLEQRINLLEQKIDLVERRVGSLEQRIARLE 116
                                    3.......44455555555555555555555555555555555555555555544 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.5   0.00023      0.09      69     121 ..      60     115 ..      51     117 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00023
                        DUF5082  69 dgirsnlessyqtyvdkldelida...ieeEIerLenqiseaqgvldtlqsqlnsl 121
                                    +gir ++ s  +t+++k+ +l+++   +e+ I+ Le++i   ++ +++l++ +  l
  gi|119720422|ref|YP_920917.1|  60 EGIRGDIVSRADTVEQKIGALEQRfnsLEQRINLLEQKIDLVERRVGSLEQRIARL 115
                                    67888999999999999877776433388999999999999999999999999877 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00014     0.056       3      58 ..       8      66 ..       6      77 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00014
                                   HHHHHHHTSSTHHHHHHHHSSTTSSS-HHHHHHHHHHHH---EBBBSSSSB....BCSS- CS
                            MCM  3 eeikelakekdiieklvksiapsiyghedvkkaillqlfggvkkkledktk....lrgdi 58
                                   + ++el++++d+ + l++ ++ +i+g++  + a+l +l   v+ k +d ++    +rgdi
  gi|119720422|ref|YP_920917.1|  8 KLLEELRQREDLRRGLAEELVSEIFGDRRLRIAVLTALYRDVATK-QDLKElregIRGDI 66
                                   66899*********************************9888743.34344112355555 PP

>> DUF3552  Domain of unknown function (DUF3552)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   1.9   9.8e-05     0.039      58     123 ..      51     116 ..      40     121 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.8e-05
                        DUF3552  58 akeeihklreelekelkerrnelqrlekRllqkeetLdrkeeslekkeesleekekelkqkeqsle 123
                                    +k+++++lre +  ++ +r + +++    l+q+ ++L+++ + le+k + +e++  +l+q+ ++le
  gi|119720422|ref|YP_920917.1|  51 TKQDLKELREGIRGDIVSRADTVEQKIGALEQRFNSLEQRINLLEQKIDLVERRVGSLEQRIARLE 116
                                    677888888888888888888888888888888888888888888888888888877777766665 PP

>> DASH_Spc19  Spc19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.3       6.7   2.6e+03      71      84 ..       5      18 ..       2      27 .. 0.66
   2 ?   13.6   0.9   0.00011     0.045      55      99 ..      56     100 ..      47     119 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 6.7
                                   HHHHHHHHHHHHHH CS
                     DASH_Spc19 71 kaekeleklerree 84
                                    aek le+l++re+
  gi|119720422|ref|YP_920917.1|  5 IAEKLLEELRQRED 18
                                   56677777766664 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 0.00011
                                    HHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     DASH_Spc19  55 aslaeeiePqieellekaekeleklerreetLkaklelqegrlsn 99 
                                    ++l+e i+  i +  +++e+++  le+r ++L+++++l+e++++ 
  gi|119720422|ref|YP_920917.1|  56 KELREGIRGDIVSRADTVEQKIGALEQRFNSLEQRINLLEQKIDL 100
                                    467777788888888888888888888888888888888887764 PP

>> TRPM_tetra  Tetramerisation domain of TRPM
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1     0.056        22      16      43 ..      68      95 ..      64      98 .. 0.76
   2 ?   12.1   0.4   0.00041      0.16       6      50 ..      79     123 ..      74     126 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.056
                     TRPM_tetra 16 mkveevneKenlikaSLqsldfrLgkLe 43
                                    + + v++K  + ++   sl++r+  Le
  gi|119720422|ref|YP_920917.1| 68 SRADTVEQKIGALEQRFNSLEQRINLLE 95
                                   5667788888888888888888888776 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00041
                     TRPM_tetra   6 vttERvEnmsmkveevneKenlikaSLqsldfrLgkLedlsaltv 50 
                                    +   R   + ++++ +++K  l+++ + sl++r+++Le +++l v
  gi|119720422|ref|YP_920917.1|  79 ALEQRFNSLEQRINLLEQKIDLVERRVGSLEQRIARLEGMMGLFV 123
                                    556688888999999***********************9999877 PP

>> CCDC53  Subunit CCDC53 of WASH complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.5   0.00033      0.13      17      48 ..      71     102 ..      69     116 .. 0.85
   2 ?   -0.4   0.0       3.4   1.3e+03      19      38 ..     101     120 ..      99     124 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00033
                         CCDC53  17 tecEekLvevekrlqrleitlalLEakLsSip 48 
                                    +  E+k+  +e+r + le +++lLE+k++ ++
  gi|119720422|ref|YP_920917.1|  71 DTVEQKIGALEQRFNSLEQRINLLEQKIDLVE 102
                                    678************************98665 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 3.4
                         CCDC53  19 cEekLvevekrlqrleitla 38 
                                     E+++ ++e+r+ rle ++ 
  gi|119720422|ref|YP_920917.1| 101 VERRVGSLEQRIARLEGMMG 120
                                    68999999999999998775 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.7   0.00012     0.048      62     108 ..      70     116 ..      39     119 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00012
                           ADIP  62 irkleaeierlqskierlktqleqlerelalvqakerqlekklktle 108
                                      + e  i  l++++++l+++   le++++lv+++  +le+++++le
  gi|119720422|ref|YP_920917.1|  70 ADTVEQKIGALEQRFNSLEQRINLLEQKIDLVERRVGSLEQRIARLE 116
                                    45666677778888999999999999999999999999999888876 PP

>> Ax_dynein_light  Axonemal dynein light chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.8   0.00017     0.066     118     156 ..      65     105 ..       6     116 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00017
                Ax_dynein_light 118 e..qgkselekkikeLeeekeelekqvaelkaklealekre 156
                                    +   + + +e+ki +Le++ ++le++++ l++k++ +e+r 
  gi|119720422|ref|YP_920917.1|  65 DivSRADTVEQKIGALEQRFNSLEQRINLLEQKIDLVERRV 105
                                    25556788999************************999986 PP

>> Lzipper-MIP1  Leucine-zipper of ternary complex factor MIP1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   2.5     0.038        15      15      81 ..       8      91 ..       4      96 .. 0.56
   2 ?    4.8   0.1     0.086        34      59      78 ..      97     116 ..      92     119 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.038
                   Lzipper-MIP1 15 qLqerLqeeeklrraLekal......ssssdgsllslstllp.kkakellkei............allEeevvkLEqkllsL 77
                                   +L e+L++ e+lrr L + l      +++    +  l++l +  ++k++lke+             ++E+ +  LEq+ +sL
  gi|119720422|ref|YP_920917.1|  8 KLLEELRQREDLRRGLAEELvseifgDRR--LRIAVLTALYRdVATKQDLKELregirgdivsraDTVEQKIGALEQRFNSL 87
                                   67777777777777777777665553222..222333332221344444444422222222222248899999999999999 PP

                   Lzipper-MIP1 78 yrkl 81
                                   ++++
  gi|119720422|ref|YP_920917.1| 88 EQRI 91
                                   8765 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.086
                   Lzipper-MIP1  59 eiallEeevvkLEqkllsLy 78 
                                     i l+E  v  LEq++  L+
  gi|119720422|ref|YP_920917.1|  97 KIDLVERRVGSLEQRIARLE 116
                                    68899999999999998885 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1       5.1     2e+03      12      24 ..       3      15 ..       1      27 [. 0.72
   2 ?   14.2   1.0   0.00013     0.052       4      52 ..      69     117 ..      66     121 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 5.1
                                   HHHHHHHHHHHHH CS
                           SlyX 12 lafqedtieeLnd 24
                                   l+  e+++eeL +
  gi|119720422|ref|YP_920917.1|  3 LSIAEKLLEELRQ 15
                                   6667777777754 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 0.00013
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXX CS
                           SlyX   4 rleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkelee 52 
                                    r +  E k+  +e+  ++L + +   +q+id  +r++  l++r++ le 
  gi|119720422|ref|YP_920917.1|  69 RADTVEQKIGALEQRFNSLEQRINLLEQKIDLVERRVGSLEQRIARLEG 117
                                    6677899999999999999999999999999999999999999988875 PP

>> Dynamitin  Dynamitin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.9   0.00037      0.15     240     280 ..      77     116 ..      55     120 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00037
                      Dynamitin 240 prplletlsrLeaklslLqtahLDaierRlksllaeldela 280
                                      +l +  ++Le++++lL+ +++D +erR+ sl +++ +l+
  gi|119720422|ref|YP_920917.1|  77 IGALEQRFNSLEQRINLLE-QKIDLVERRVGSLEQRIARLE 116
                                    4577788899*******95.68************9999875 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00026       0.1     392     450 ..      55     116 ..      47     120 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00026
                         AAA_13 392 keeakkklelhlv...eeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLe 450
                                     +e+++ ++ ++v     +e+++ ++++ +++le+ i+ le++++  e+++  le++i+ Le
  gi|119720422|ref|YP_920917.1|  55 LKELREGIRGDIVsraDTVEQKIGALEQRFNSLEQRINLLEQKIDLVERRVGSLEQRIARLE 116
                                    45666666666662223344555566666666666666666666666666666666666555 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00029      0.11      30     103 ..      39     114 ..      28     124 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00029
                   Baculo_PEP_C  30 vqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq...dtlrneLtnlnsiltnLlssvtN 103
                                    + +l++l +++++ +  L++l e ++  + + ++ +++ + +L++  n+l+   + l+++++ ++  + +L   ++ 
  gi|119720422|ref|YP_920917.1|  39 IAVLTALYRDVATKQ-DLKELREGIRGDIVSRADTVEQKIGALEQRFNSLEqriNLLEQKIDLVERRVGSLEQRIAR 114
                                    556666666666433.4777777777777766666667777777777777644444556677777777766666654 PP

>> MRF_C1  Myelin gene regulatory factor -C-terminal domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       1.5   6.1e+02      26      35 ..      73      82 ..      71      83 .. 0.80
   2 ?    3.6   0.1     0.093        37      24      35 ..      85      96 ..      82      97 .. 0.89
   3 ?    2.5   0.1      0.21        84      26      35 ..      94     103 ..      92     104 .. 0.89
   4 ?    5.7   0.0     0.021       8.4      24      34 ..     106     116 ..     103     118 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.5
                         MRF_C1 26 LEtrIeelEk 35
                                    E++I +lE+
  gi|119720422|ref|YP_920917.1| 73 VEQKIGALEQ 82
                                   5999999996 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.093
                         MRF_C1 24 gnLEtrIeelEk 35
                                   ++LE+rI+ lE+
  gi|119720422|ref|YP_920917.1| 85 NSLEQRINLLEQ 96
                                   58******9996 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.21
                         MRF_C1  26 LEtrIeelEk 35 
                                    LE++I+ +E+
  gi|119720422|ref|YP_920917.1|  94 LEQKIDLVER 103
                                    9*****9996 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.021
                         MRF_C1  24 gnLEtrIeelE 34 
                                    g+LE+rI +lE
  gi|119720422|ref|YP_920917.1| 106 GSLEQRIARLE 116
                                    79********9 PP

>> Tropomyosin  Tropomyosin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   7.1    0.0008      0.32     143     225 ..      20     103 ..       2     118 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0008
                    Tropomyosin 143 iveLeeeLkvvgnnlksLevseekaseredeyeeeirtLeekLk.eaeeRaeeAErsvqkLekevdrledeleaekekyk 221
                                     + L eeL       + L ++   a  r+ + ++ +++L e ++ + + Ra+  E+++  Le+  ++le++++   +k++
  gi|119720422|ref|YP_920917.1|  20 RRGLAEELVSEIFGDRRLRIAVLTALYRDVATKQDLKELREGIRgDIVSRADTVEQKIGALEQRFNSLEQRINLLEQKID 99 
                                    44555555555555677777777777777777777788877776456778888888888888888888777776666665 PP

                    Tropomyosin 222 aise 225
                                     +++
  gi|119720422|ref|YP_920917.1| 100 LVER 103
                                    5544 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00051       0.2      14      64 ..      71     118 ..      60     124 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00051
                        NPV_P10  14 kavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdi 64 
                                      v++k+ al+q+ +++++ ++    l++k+d     + +le+ +   + +
  gi|119720422|ref|YP_920917.1|  71 DTVEQKIGALEQRFNSLEQRINL---LEQKIDLVERRVGSLEQRIARLEGM 118
                                    5799**************97777...99**************999887766 PP

>> FliD_C  Flagellar hook-associated protein 2 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00045      0.18     183     231 ..      71     119 ..      36     125 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00045
                                    HHHSTT.SHHHHHHHHXXXXHHHHHHHHHHHHHCHHHHHHHHHHHHHHH CS
                         FliD_C 183 syvkssngtlqtasknltkqikdldkkiedldkrletleerlkkqfaal 231
                                    ++v+ + g+l+++ ++l+++i+ l++ki+ +++r+ +le+r+ +   ++
  gi|119720422|ref|YP_920917.1|  71 DTVEQKIGALEQRFNSLEQRINLLEQKIDLVERRVGSLEQRIARLEGMM 119
                                    5667777999999999999999999999999999999999887766555 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.5   0.00048      0.19      60      99 ..      73     112 ..      66     118 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00048
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    Prefoldin_2  60 keevkeeLeerketlekeiktlekqleklekeleelkeel 99 
                                    +e+ +  Le+r ++le++i+ le++++ +e+++  l++ +
  gi|119720422|ref|YP_920917.1|  73 VEQKIGALEQRFNSLEQRINLLEQKIDLVERRVGSLEQRI 112
                                    6666778999999999999999999999999888888776 PP

>> MerR-DNA-bind  MerR, DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   1.9       1.8   7.2e+02      21      58 ..       7      45 ..       1      52 [. 0.57
   2 ?    5.6   0.6      0.06        24      34      56 ..      73      95 ..      53      99 .. 0.62
   3 ?   10.9   0.2    0.0013      0.51      39      58 ..      99     118 ..      94     121 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 1.8
                                   HHHH.HHHHSTTTBHHHHHHHHHHHHHHHHHHHHHHHHH CS
                  MerR-DNA-bind 21 relL.alyddrappcqdvrallarklaeleeriaeLqal 58
                                     lL +l+++++ ++ ++++l+ +   + + ria L+al
  gi|119720422|ref|YP_920917.1|  7 EKLLeELRQREDLRRGLAEELVSEIFGDRRLRIAVLTAL 45
                                   345555555566666666666666666666666666665 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.06
                                   HHHHHHHHHHHHHHHHHHHHHHH CS
                  MerR-DNA-bind 34 cqdvrallarklaeleeriaeLq 56
                                    ++    l+++ ++le+ri+ L+
  gi|119720422|ref|YP_920917.1| 73 VEQKIGALEQRFNSLEQRINLLE 95
                                   33334456666666666666555 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.0013
                                    HHHHHHHHHHHHHHHHHHHH CS
                  MerR-DNA-bind  39 allarklaeleeriaeLqal 58 
                                    +l++r++ +le+ria+L+ +
  gi|119720422|ref|YP_920917.1|  99 DLVERRVGSLEQRIARLEGM 118
                                    699**************988 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.7   0.00047      0.19      29      59 ..      73     103 ..      67     116 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00047
                                    HHHHHHHHHHHHHHHHHHHCC-XXXXXXXXX CS
                          DivIC  29 lqaelaklkaeneeLeaevkdLksdedyiee 59 
                                     ++++ +l ++ ++Le+++++L++  d +e+
  gi|119720422|ref|YP_920917.1|  73 VEQKIGALEQRFNSLEQRINLLEQKIDLVER 103
                                    4455555555555555555555544444444 PP

>> KLRAQ  Predicted coiled-coil domain-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.5      0.82   3.3e+02      29      63 ..       7      41 ..       4      60 .. 0.73
   2 ?    9.2   1.1    0.0034       1.4      29      77 ..      56     105 ..      41     120 .. 0.69

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.82
                          KLRAQ 29 aslkeelkekeqslrkseqEvdsLtFrNkqLekrv 63
                                   ++l eel+++e   r   +E+ s  F  ++L   v
  gi|119720422|ref|YP_920917.1|  7 EKLLEELRQREDLRRGLAEELVSEIFGDRRLRIAV 41
                                   57889999999888888888888888888886444 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0034
                          KLRAQ  29 aslkeelkeke.qslrkseqEvdsLtFrNkqLekrvellqeeleveekkv 77 
                                    ++l+e ++    +   ++eq + +L+ r + Le+r++ll ++++  e++v
  gi|119720422|ref|YP_920917.1|  56 KELREGIRGDIvSRADTVEQKIGALEQRFNSLEQRINLLEQKIDLVERRV 105
                                    55666666443134456788888888888888888888888888776654 PP

>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.2       2.5     1e+03      24      45 ..       6      27 ..       4      31 .. 0.55
   2 ?    9.2   0.6    0.0026         1      16      62 ..      51      97 ..      37     109 .. 0.84
   3 ?    0.8   0.1         1     4e+02      44      60 ..     100     116 ..      94     126 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 2.5
                           CdvA 24 kekleealkklkekakelkekl 45
                                    ekl e+l++ ++ +  l+e+l
  gi|119720422|ref|YP_920917.1|  6 AEKLLEELRQREDLRRGLAEEL 27
                                   4555556666555555555555 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0026
                           CdvA 16 pkstyeeikekleealkklkekakelkeklkkrlkeledqiksleka 62
                                    k++ +e++e ++  +    ++ ++ +  l++r ++le+ i+ le+ 
  gi|119720422|ref|YP_920917.1| 51 TKQDLKELREGIRGDIVSRADTVEQKIGALEQRFNSLEQRINLLEQK 97
                                   68999999999999999999999999999999999999999999875 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 1
                           CdvA  44 klkkrlkeledqiksle 60 
                                     +++r+++le+ i++le
  gi|119720422|ref|YP_920917.1| 100 LVERRVGSLEQRIARLE 116
                                    45667777777777666 PP

>> Med9  RNA polymerase II transcription mediator complex subunit 9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.2       4.6   1.8e+03      56      70 ..       7      21 ..       2      30 .. 0.64
   2 ?   10.2   1.2    0.0016      0.64      19      63 ..      68     116 ..      53     121 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 4.6
                           Med9 56 eaeieeleeqlakKr 70
                                   e+ +eel+++ + +r
  gi|119720422|ref|YP_920917.1|  7 EKLLEELRQREDLRR 21
                                   455666666655555 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0016
                           Med9  19 lsskdletktgelrhkLkkarelirelpg....idrsveeqeaeieele 63 
                                    + +  +e+k+g+l +++++  + i+ l+     ++r v + e++i+ le
  gi|119720422|ref|YP_920917.1|  68 SRADTVEQKIGALEQRFNSLEQRINLLEQkidlVERRVGSLEQRIARLE 116
                                    567889********************99998888888888888888887 PP

>> bZIP_2  Basic region leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.7   0.00052      0.21      26      53 ..      76     103 ..      72     104 .. 0.88
   2 ?    4.9   0.1     0.068        27      26      45 ..      97     116 ..      96     119 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00052
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         bZIP_2  26 keeeleervkeLeeeNaqLrqkveqLek 53 
                                    k   le+r ++Le++++ L+qk++ +e+
  gi|119720422|ref|YP_920917.1|  76 KIGALEQRFNSLEQRINLLEQKIDLVER 103
                                    55679******************99886 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.068
                                    HHHHHHHHHHHHHHHHHHHH CS
                         bZIP_2  26 keeeleervkeLeeeNaqLr 45 
                                    k    e+rv +Le+++a+L+
  gi|119720422|ref|YP_920917.1|  97 KIDLVERRVGSLEQRIARLE 116
                                    66678999999999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1118  (0.0623571); expected 358.6 (0.02)
Passed bias filter:                      850  (0.0474092); expected 358.6 (0.02)
Passed Vit filter:                       200  (0.0111551); expected 17.9 (0.001)
Passed Fwd filter:                        46  (0.00256568); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              45  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.47
# Mc/sec: 939.51
//
Query:       gi|119720423|ref|YP_920918.1|  [L=312]
Description: phosphoesterase, DHHA1 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.2e-17   61.8   0.1    1.8e-16   60.8   0.1    1.5  1  DHHA1            DHHA1 domain
    0.00028   21.1   0.0     0.0005   20.3   0.0    1.3  1  DHH              DHH family
     0.0038   16.9   0.0     0.0061   16.2   0.0    1.3  1  Glyco_trans_4_5  Glycosyl-transferase family 4
  ------ inclusion threshold ------
      0.033   14.5   0.4       0.23   11.8   0.1    2.4  2  Nitro_FeMo-Co    Dinitrogenase iron-molybdenum cofactor


Domain annotation for each model (and alignments):
>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.8   0.1   4.1e-20   1.8e-16      28     136 ..     199     308 ..     186     310 .. 0.87

  Alignments for each domain:
  == domain 1  score: 60.8 bits;  conditional E-value: 4.1e-20
                                    HHHHHTCEEEC..TCEEEEEECHCCHHH.HHHHHHHHHHHTHGBT.TCEEEEEEEECTEEEEEEEESSHSS-HHHHHHHH CS
                          DHHA1  28 eellekaeevk..gvkvlvaevgeewda.galgiaadklksklkk.pvivfvakeegdkvkvsarskkdgvdagelakea 103
                                    ++ll+++ +v+  ++ ++v +v+  +d+ g lg+aa + +   ++ + + ++++ +g+++  s+rs++ gvd+++l++++
  gi|119720423|ref|YP_920918.1| 199 QSLLNEELRVRvrEKALVVGQVAYVMDPgGSLGTAAFYARV--ERgVKVGVAVERRGETCVMSLRSTG-GVDLNALLRRI 275
                                    3344443344466999******9******************..**9999999999999**********.*********** PP

                                    HHHTTCCEEEETCEEEEEEEHCHHHHHHHHHHH CS
                          DHHA1 104 aaklgggGGGHdlAaGagipaekleealealee 136
                                    a+  gg GGGH++AaGa+ip ++le++l++l +
  gi|119720423|ref|YP_920918.1| 276 APRHGGHGGGHRQAAGARIPCGELEKFLAELAA 308
                                    ****************************99875 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   1.1e-07    0.0005       8      84 ..       7     117 ..       4     131 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.1e-07
                                    CSSSHHHHHH.HHHHHH................................CECS--TCGGCGCCHHCCCSEEEEEEE-S-- CS
                                    xxxxxxxxxx.xxxxxx................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DHH   8 knpDtDsigS.aialan................................llvDhneksqavegeakeeaedviiiDHHrl 54 
                                     + D D++++ aia +                                 + vD   + + +e  +++ + +v+ +DHH  
  gi|119720423|ref|YP_920918.1|   7 AHGDSDGVTAaAIAKSVyrdaevffthpvglakdleefargrspviildVAVDEAGAPRLAEV-LRSLGAEVVYVDHHPG 85 
                                    6789******55555557788888888888777777777777777555557776665555554.8*************** PP

                                    -S..S---SS--EEEE-SSS-HHHHHHHHHHH CS
                                    xx..xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DHH  55 ge..efetlapilflnepvgstaeivaellee 84 
                                    ge  e  +   + +++e+  ++ae+++++++ 
  gi|119720423|ref|YP_920918.1|  86 GEalEKIRVPGVRVVHEEGPCAAELAYRFFKP 117
                                    *966555566789999*************864 PP

>> Glyco_trans_4_5  Glycosyl-transferase family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.4e-06    0.0061       6      70 ..      52     112 ..      46     114 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.4e-06
                Glyco_trans_4_5   6 llishelsltGaPlvlmelatlLrsvgaevvvltlskkggllkeladrgikvleakaeelfklal 70 
                                    +++    + +GaP+    la +Lrs+gaevv +  + +g+ l++++  g++v+++ ++ + +la 
  gi|119720423|ref|YP_920918.1|  52 IILDVAVDEAGAPR----LAEVLRSLGAEVVYVDHHPGGEALEKIRVPGVRVVHEEGPCAAELAY 112
                                    44455677788886....79***********************************9988877765 PP

>> Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   5.1e-05      0.23      41      85 ..      61     105 ..      51     114 .. 0.85
   2 ?   -0.5   0.0      0.35   1.6e+03      61      85 ..     228     252 ..     227     262 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.1e-05
                                    CSSTHHHHHHHHTT-SEEEESSS.CHHHHHHHCTTTSEEEES-SSB CS
                  Nitro_FeMo-Co  41 ggggklaqllaeegvdvvivgki.Gpralakleaagievykgaggt 85 
                                     g  +la++l + g++vv+v +  G++al+k++  g++v+  ++g+
  gi|119720423|ref|YP_920918.1|  61 AGAPRLAEVLRSLGAEVVYVDHHpGGEALEKIRVPGVRVVH-EEGP 105
                                    56789***************8766****************9.5555 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.35
                                    SSSCHHHHHHHCTTTSEEEES-SSB CS
                  Nitro_FeMo-Co  61 gkiGpralakleaagievykgaggt 85 
                                    g+ G  a+ +  ++g++v ++ ++ 
  gi|119720423|ref|YP_920918.1| 228 GSLGTAAFYARVERGVKVGVAVERR 252
                                    578999999999****998875554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1998.31
//
Query:       gi|119720424|ref|YP_920919.1|  [L=107]
Description: dinitrogenase iron-molybdenum cofactor biosynthesis [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-14   54.1   0.2    1.7e-14   53.9   0.2    1.1  1  Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor


Domain annotation for each model (and alignments):
>> Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.9   0.2   9.6e-19   1.7e-14       6      90 ..       2      88 ..       1      93 [. 0.90

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 9.6e-19
                                   -STCCC-SEEEEEEESSSCEEEEEEE.E.GCCCTSSCSSTHHHHHHHHTT-SEEEESSSCHHHHHHHCTTTSEEEES.-SSB CS
                  Nitro_FeMo-Co  6 dqhFGrapyFaiyeveegevkivenr.veeaadaegggggklaqllaeegvdvvivgkiGpralakleaagievykg.aggt 85
                                   ++hFGrap+Fa++ ve g++k+  ++ ++ a + e+g+g ++  ++ +   d+v+v+ iG +a+ +l++ag+evy + ++ +
  gi|119720424|ref|YP_920919.1|  2 SPHFGRAPFFAVVVVEGGSAKLERVErNPVAPTVEEGRGHAVLGFVLSLRPDAVVVKDIGAGAFYRLREAGVEVYAVdRHVE 83
                                   89*******************99999877777888899**************************************888877 PP

                                   HHHHH CS
                  Nitro_FeMo-Co 86 veeal 90
                                   v ea 
  gi|119720424|ref|YP_920919.1| 84 VVEAA 88
                                   77775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       268  (0.0149478); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 774.90
//
Query:       gi|119720425|ref|YP_920920.1|  [L=133]
Description: thioesterase superfamily protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-08   34.8   0.2    4.9e-08   33.2   0.1    1.7  2  4HBT      Thioesterase superfamily


Domain annotation for each model (and alignments):
>> 4HBT  Thioesterase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   0.1   2.8e-12   4.9e-08       2      75 ..      29     102 ..      28     105 .. 0.96
   2 ?   -1.2   0.0      0.15   2.8e+03      12      26 ..     119     133 .]     118     133 .] 0.85

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 2.8e-12
                                    SSB-HHHHHHHHHHHHHHHHHHTTSTTEEEEEEEEEEEESS-BBTTCEEEEEEEEEEEESSEEEEEEEEEETTS CS
                           4HBT   2 GvvhgGvylallDeaagaalrslggrgilvvvvelsidflrpvrlgdeltvearvlrlgrtsavvevevrdedg 75 
                                    G++  ++++a+++ea  ++l +  g+++  v+v++ +++++p+ lg+ ++v++r+lr  ++++++ +e ++++ 
  gi|119720425|ref|YP_920920.1|  29 GILSTPNLVAFMEEASRVFLDEKLGKDYTTVGVRIDVHHVAPALLGSQVEVRGRILRSDGRRVTLWIEAWSGKT 102
                                    999*******************************************************************9875 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.15
                                    HHHHHHHHHHHHTTS CS
                           4HBT  12 llDeaagaalrslgg 26 
                                    +l+++++++ ++ gg
  gi|119720425|ref|YP_920920.1| 119 YLERIRSMLSSRAGG 133
                                    99******9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       260  (0.0145016); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 973.14
//
Query:       gi|119720426|ref|YP_920921.1|  [L=201]
Description: abortive infection protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.8e-08   32.4  20.5    3.9e-06   27.2  20.5    2.4  1  CPBP      CPBP intramembrane metalloprotease


Domain annotation for each model (and alignments):
>> CPBP  CPBP intramembrane metalloprotease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2  20.5   2.2e-10   3.9e-06       8      89 ..     107     190 ..       2     193 .. 0.90

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 2.2e-10
                                    HHHHHHHHHHHHHHHHTTCHHHHHHHH..S-HHHHHHHHHHHHHCSGGG.HHH.HHHHHHHHHHHHHHHHHTT-HHHHHH CS
                           CPBP   8 fllalllapllEEllfRglllqllqer.gsstlailissilFglaHlpn.gps.vllaalaGlvlgylylktgsllaail 84 
                                    +  al   +  EE+++Rg ll+ l er gs ++a+++    ++l+H+++ +p+ +l a+++G + g+++ + g l+aa+ 
  gi|119720426|ref|YP_920921.1| 107 LATALCAIGASEEVYWRGGLLSFLVERfGSTRAALAVMVSYYTLVHVYTlNPAlMLGALVVGAYTGLVATRLG-LAAAVS 185
                                    3347777889*****************6666999***************98889*******************.****** PP

                                    HHHHH CS
                           CPBP  85 lHall 89 
                                    +H+++
  gi|119720426|ref|YP_920921.1| 186 THVAW 190
                                    **997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1546.55
//
Query:       gi|119720427|ref|YP_920922.1|  [L=280]
Description: hypothetical protein Tpen_1522 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-16   59.9   0.3    2.5e-16   59.9   0.3    2.2  4  DUF3267   Putative zincin peptidase


Domain annotation for each model (and alignments):
>> DUF3267  Putative zincin peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.3      0.29   5.3e+03      79      88 ..      23      32 ..      11      47 .. 0.46
   2 !   59.9   0.3   1.4e-20   2.5e-16       2     107 ..      49     157 ..      48     158 .. 0.88
   3 ?   -3.3   0.3      0.63   1.1e+04      77      83 ..     192     198 ..     177     207 .. 0.43
   4 ?   -4.0   0.2      0.99   1.8e+04      61      64 ..     241     244 ..     229     252 .. 0.45

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.29
                        DUF3267 79 lllllalnaa 88
                                   ll+ +a+ ++
  gi|119720427|ref|YP_920922.1| 23 LLFYVAVLLL 32
                                   2222222222 PP

  == domain 2  score: 59.9 bits;  conditional E-value: 1.4e-20
                        DUF3267   2 lvlvilHEllHglffklfgkkpkkkvkfgik..lliayatsseallskkqfiiillaPfvllgilllllalllpsstl.l 78 
                                    l+++ lHE++H+ +   fg++  +   f+++  l+ +y+ ++++l ++ ++++++laP+++l+ + l++a  l+  +  +
  gi|119720427|ref|YP_920922.1|  49 LATLALHEGIHVAVAYAFGARGISVKPFRASwiLVGVYVSTKTSL-RRDEWLVVALAPLLVLTPAALVAAKTLEGLAReT 127
                                    7899****************9888888876454566666666666.****************************77667* PP

                        DUF3267  79 lllllalnaagsagD.lliallllkapkda 107
                                    + +++++n++g+ gD +l++++ll+a++da
  gi|119720427|ref|YP_920922.1| 128 AEFIVVFNTMGAGGDlFLALAVLLSAKRDA 157
                                    ***************99********99987 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 0.63
                        DUF3267  77 lllllll 83 
                                    +++l+l+
  gi|119720427|ref|YP_920922.1| 192 FCCLWLG 198
                                    1222222 PP

  == domain 4  score: -4.0 bits;  conditional E-value: 0.99
                        DUF3267  61 lgil 64 
                                    + ++
  gi|119720427|ref|YP_920922.1| 241 VALI 244
                                    1111 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 2120.57
//
Query:       gi|119720428|ref|YP_920923.1|  [L=189]
Description: hypothetical protein Tpen_1524 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1377.90
//
Query:       gi|119720429|ref|YP_920924.1|  [L=469]
Description: hypothetical protein Tpen_1525 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (469 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 3485.91
//
Query:       gi|119720430|ref|YP_920925.1|  [L=525]
Description: hypothetical protein Tpen_1526 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.4e-24   83.8   0.2    3.9e-23   81.8   0.0    2.2  2  DUF2341   Domain of unknown function (DUF2341)
    0.00058   20.0   0.1     0.0028   17.8   0.1    2.2  1  DUF1080   Domain of Unknown Function (DUF1080)


Domain annotation for each model (and alignments):
>> DUF2341  Domain of unknown function (DUF2341)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.8   0.0   4.4e-27   3.9e-23       1      73 [.     237     312 ..     237     331 .. 0.91
   2 ?   -2.9   0.0       1.2     1e+04      17      55 ..     434     471 ..     427     481 .. 0.59

  Alignments for each domain:
  == domain 1  score: 81.8 bits;  conditional E-value: 4.4e-27
                        DUF2341   1 dgsdiRf....vdsdgttLpywieswdantekaliWvkvpsip.angnktikiyygnptatstsngdatfelFDdfsg 73 
                                    d++d+Rf     d ++ ++pyw+es  ++ ++a++Wvkvpsip + g+++i++yygnp+ats+sng+atf++F+dfs+
  gi|119720430|ref|YP_920925.1| 237 DFGDLRFsylqPDGREVAIPYWVES--VSGGCATVWVKVPSIPaSPGTARIYVYYGNPSATSESNGAATFIYFNDFSS 312
                                    799*****9888888888******6..9***************8899*****************************98 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.2
                        DUF2341  17 ywiesw.dantekaliWvkvpsipangnktikiyygnpta 55 
                                      +e++  + + +a  W k++       + i +y+ ++++
  gi|119720430|ref|YP_920925.1| 434 SEVEPVhVYYSLQANTWYKLEM--RLYGGHITVYVDDSKV 471
                                    5555554445556777777765..3445556666666555 PP

>> DUF1080  Domain of Unknown Function (DUF1080)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   3.1e-07    0.0028     120     162 ..     441     483 ..     319     506 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.1e-07
                                    S--S--TTSEEEEEEEEETTEEEEEETTEEEEEEETTSHHHHH CS
                        DUF1080 120 akaakppgeWntyeiivkgdrvtvwlNGvlvldftdldaetek 162
                                    + ++ ++++W ++e + +g ++tv++++ +v+d td+++ t+ 
  gi|119720430|ref|YP_920925.1| 441 VYYSLQANTWYKLEMRLYGGHITVYVDDSKVIDWTDSSPITSG 483
                                    56778999******************************98743 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (525 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 3634.48
//
Query:       gi|119720431|ref|YP_920926.1|  [L=75]
Description: hypothetical protein Tpen_1527 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       206  (0.0114898); expected 358.6 (0.02)
Passed bias filter:                      178  (0.00992805); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 531.85
//
Query:       gi|119720432|ref|YP_920927.1|  [L=311]
Description: peptidase S1 and S6, chymotrypsin/Hap [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-34  119.4   2.9      4e-34  118.7   2.9    1.3  1  Trypsin_2      Trypsin-like peptidase domain
    1.9e-13   50.5   0.0    4.1e-13   49.5   0.0    1.6  1  PDZ_2          PDZ domain
      2e-13   50.7   0.0    3.3e-13   50.0   0.0    1.3  1  Trypsin        Trypsin
    1.3e-10   40.9   1.6    3.1e-10   39.7   0.5    2.1  2  PDZ_6          PDZ domain
    3.3e-05   24.2   0.0    7.7e-05   23.0   0.0    1.6  1  PDZ            PDZ domain
    0.00015   20.6   0.3      0.033   12.8   0.0    2.1  2  Peptidase_S46  Peptidase S46
  ------ inclusion threshold ------
      0.071   13.1   0.1       0.18   11.8   0.1    1.7  1  Tricorn_PDZ    Tricorn protease PDZ domain


Domain annotation for each model (and alignments):
>> Trypsin_2  Trypsin-like peptidase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.7   2.9   1.5e-37     4e-34       1     150 []      42     180 ..      42     180 .. 0.96

  Alignments for each domain:
  == domain 1  score: 118.7 bits;  conditional E-value: 1.5e-37
                      Trypsin_2   1 GsGflvgsdglilTnaHvvdsadgaavkaikkkveeagadgrevpakvvaadpelDlAllkvssderaglpplplgpsea 80 
                                    GsG+ v++dgl+ TnaHvv++ ++ +v         +++ g  v+a+vv +dp++D+A+l+v   era l p++lg+s++
  gi|119720432|ref|YP_920927.1|  42 GSGVAVSEDGLVATNAHVVEGFEEISV---------TTPGGDHVRAEVVDVDPHYDIAFLRV---ERARLKPAELGDSDS 109
                                    9**************************.........****************999*******...*************** PP

                      Trypsin_2  81 lkggepvyvvGyplggeksg.svssGivsgvvesesaasgegesflqtdaatspGsSGGplfdsdGrvvGl 150
                                    l++g+ v++vG+p g+  +g s+++G+vsg+ +s  a++   e+++qtda+++pG+SGGpl+d +GrvvG+
  gi|119720432|ref|YP_920927.1| 110 LRVGQFVVAVGNPFGQLLGGpSLTFGVVSGLGRSLRAEGKIYENLIQTDAPVNPGNSGGPLVDLEGRVVGI 180
                                    *************99998889************7777788888888************************8 PP

>> PDZ_2  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.5   0.0   1.6e-16   4.1e-13       9      82 .]     224     307 ..     216     307 .. 0.87

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 1.6e-16
                                    ----............-EEEEEE-TTSGGGGT.--TT-EEEEETTB--SSHHHHHHHHHTS-TT-EEEEEEEETTEEEEE CS
                          PDZ_2   9 deed..........tggvlvvsVkeggPaakaglkagDvilkvdgkkvksledlislllkkkpGdtVkltvlRdgkkktv 78 
                                    d+++          + gvlv  V +g+Paa+ag+k+g vilk+dg +vk + dl s+l++k+ G++  l+v+  g+ + +
  gi|119720432|ref|YP_920927.1| 224 DVNPaiayqlglprAAGVLVLRVVPGSPAARAGVKPGAVILKLDGSEVKGTGDLVSKLRQKEVGEKAVLEVFYAGTLRRL 303
                                    5555555566666678**************************************************************** PP

                                    EEE- CS
                          PDZ_2  79 evkl 82 
                                    +v++
  gi|119720432|ref|YP_920927.1| 304 QVTV 307
                                    9986 PP

>> Trypsin  Trypsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.0   0.0   1.3e-16   3.3e-13      27     219 ..      42     202 ..      30     204 .. 0.78

  Alignments for each domain:
  == domain 1  score: 50.0 bits;  conditional E-value: 1.3e-16
                                    EEEEEEETT.EEEEEGGGTTTGGGEEEEESESBTTSCTTTEEEEEEEEEEEETTEBTTTTTTTEEEEEESSSSTSBSSBH CS
                        Trypsin  27 CgGslisen.wvlTAaHCvsnasdvkvvlgehnlkksegkeqklkvekvivhpnynpstldnDiallklkepvklgdtvr 105
                                     +G+ +se+  v T+aH+v++ ++++v       +   g+  ++  e v    +++p    +Dia l++++      + +
  gi|119720432|ref|YP_920927.1|  42 GSGVAVSEDgLVATNAHVVEGFEEISV-------TTPGGD--HVRAEVV----DVDPH---YDIAFLRVERA-----RLK 100
                                    4689999997899*******9333333.......444444..4444442....35665...5*********9.....*** PP

                                    CCBBCSTTHTTSTTTEEEEEESSBSSTSSBSSBEEEEEEEEEEHHHHHHHTTTTSTTTEEEEESTTSSSBCTTTTTTSEE CS
                        Trypsin 106 piclpaassslpvgttclvsGwgrtkekgksdtlqevevpvvsretcksaykgkvtenmlcagakeggkdacqGDSGGPl 185
                                    p++l + s+sl vg+ ++++G +  +  g   +l+ + v+ + r+   +   gk+ en ++++a       ++G+SGGPl
  gi|119720432|ref|YP_920927.1| 101 PAELGD-SDSLRVGQFVVAVGNPFGQLLG-GPSLTFGVVSGLGRSLRAE---GKIYENLIQTDA-----PVNPGNSGGPL 170
                                    ******.7778999666666666655555.4678888888888864444...78**********.....7********** PP

                                    EETTTEEEEEEEEESSSSCTTSEEEEEEGGGGHH CS
                        Trypsin 186 vcsdgelvGivswgkgcakgnrpgvytkvssyld 219
                                    v  +g +vGi+++    a+g  +g+++++++++ 
  gi|119720432|ref|YP_920927.1| 171 VDLEGRVVGITTAMIPFAQG--IGFAIPINEVKY 202
                                    ********************..9*****998875 PP

>> PDZ_6  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.61   1.6e+03      15      26 ..     109     120 ..      80     121 .. 0.76
   2 !   39.7   0.5   1.2e-13   3.1e-10       2      54 ..     243     294 ..     242     294 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.61
                          PDZ_6  15 GlrvGDiilsvN 26 
                                     lrvG  +++v+
  gi|119720432|ref|YP_920927.1| 109 SLRVGQFVVAVG 120
                                    499999999997 PP

  == domain 2  score: 39.7 bits;  conditional E-value: 1.2e-13
                          PDZ_6   2 VtaVdpgsPAdrAGlrvGDiilsvNGqpveglsladvaallr.gsagesvvlvv 54 
                                    V  V+pgsPA+rAG+++G +il+++G +v  + + d+++ lr   +ge+ vl+v
  gi|119720432|ref|YP_920927.1| 243 VLRVVPGSPAARAGVKPGAVILKLDGSEV--KGTGDLVSKLRqKEVGEKAVLEV 294
                                    778**************************..***********889999998876 PP

>> PDZ  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0     3e-08   7.7e-05      25      74 ..     238     287 ..     219     294 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 3e-08
                                    SSSEEEEEECTTSHHHHHTSSTTEEEEEETTEETTTSHHHHHHHHHHTTT CS
                            PDZ  25 dkgifvsevlpggaaeadglkvGDkIlsvNgvdvenvsheeavqaikgsk 74 
                                    + g+ v +v+pg++a+++g+k+G +Il+ +g  v++  ++   +  k+ +
  gi|119720432|ref|YP_920927.1| 238 AAGVLVLRVVPGSPAARAGVKPGAVILKLDGSEVKGTGDLVSKLRQKEVG 287
                                    5799********9999999************9999887666555555555 PP

>> Peptidase_S46  Peptidase S46
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   1.3e-05     0.033      47      69 ..      40      62 ..      35      69 .. 0.88
   2 !    5.8   0.0    0.0017       4.3     632     650 ..     162     180 ..     144     183 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.3e-05
                                   TTEE-EE-STT-EEEE-HHHHHH CS
                  Peptidase_S46 47 ggCtasfVSpeGLvlTNHHCayg 69
                                   g  ++  VS++GLv TN H++ g
  gi|119720432|ref|YP_920927.1| 40 GLGSGVAVSEDGLVATNAHVVEG 62
                                   889****************9865 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0017
                                    -TT-TT-EEE-TTS-EEEE CS
                  Peptidase_S46 632 tGGNSGSPvlngkgelvGl 650
                                      GNSG P+++ +g++vG+
  gi|119720432|ref|YP_920927.1| 162 NPGNSGGPLVDLEGRVVGI 180
                                    56****************8 PP

>> Tricorn_PDZ  Tricorn protease PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   7.2e-05      0.18      31      77 ..     250     295 ..     247     307 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.2e-05
                                    -GGGGGS---.TT-EEEEETTEE-BTTB-HHHHHHTTT.TSEEEEEEE CS
                    Tricorn_PDZ  31 SPLaepGvnvreGdlilavdgepvskekgiaelLvgka.gkeveLtvk 77 
                                    SP a+ Gv+   G++il++dg +v+ + ++ + L +k+ g+++ L+v 
  gi|119720432|ref|YP_920927.1| 250 SPAARAGVK--PGAVILKLDGSEVKGTGDLVSKLRQKEvGEKAVLEVF 295
                                    899999999..9****************99999987753566666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.46u 0.20s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2451.32
//
Query:       gi|119720433|ref|YP_920928.1|  [L=394]
Description: major facilitator transporter [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.2e-26   91.7  45.9    2.5e-18   66.1  21.0    2.1  2  MFS_1       Major Facilitator Superfamily
    1.8e-05   23.8  15.9     0.0044   15.9   0.1    3.0  3  MFS_1_like  MFS_1 like family
  ------ inclusion threshold ------
       0.45    9.3  14.1      0.022   13.7   4.2    3.0  3  Sugar_tr    Sugar (and other) transporter


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.1  21.0   4.3e-22   2.5e-18       6     224 ..      33     245 ..      28     253 .. 0.87
   2 !   30.0  20.0   4.2e-11   2.5e-07      22     172 ..     246     393 ..     236     394 .] 0.73

  Alignments for each domain:
  == domain 1  score: 66.1 bits;  conditional E-value: 4.3e-22
                          MFS_1   6 flsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalglllllfass 84 
                                    + s++a ++++p++ l+l    g    ++g++  +  ++++++ l+++rlsd  G+r+ ++ l+l++ +l++l+l+fass
  gi|119720433|ref|YP_920928.1|  33 LASSFAGNLVSPFMALYLYGLAGGRFFQAGIASQAPVAVSVIMGLFWARLSDTNGSRKkFVQLSLATGSLASLALSFASS 112
                                    5678888899999999777777889999*************************998888************888889877 PP

                          MFS_1  85 lwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivslla 164
                                    +   +++ +l +++++a+ +a  al+a++f++ +rg+ +g+++a++ +G   g +l+g+l+ ++g+r++  ++a++++l 
  gi|119720433|ref|YP_920928.1| 113 INDAILVQILGAFTGSAGGAAFSALMAEVFKD-KRGSRLGVYNASTVIGGFAGSMLSGFLYNWIGFRWMLRLNALLGVLP 191
                                    7789999************************9.*********************************************** PP

                          MFS_1 165 fvlfllllpeepperkrkspkeeekgtgpaplvp..awkallkdpvlwillialllfffgfs 224
                                    +vl  + +  e+ +r ++s++++    +  p +p   wk+ l++ vl   l ++l+++++  
  gi|119720433|ref|YP_920928.1| 192 LVL--ISMIPEEGNRNPVSSRKL----VSIPKIPrrFWKLYLARLVL--SLPGALSGGVFSV 245
                                    776..888888888888888888....88888888899999999988..6666666653333 PP

  == domain 2  score: 30.0 bits;  conditional E-value: 4.2e-11
                          MFS_1  22 alaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa.sslwlllvlrvlqGlgag 100
                                    +  + l+  p + ++l+++ + ++++as+p+Grl+dr++ r +++l+ l++ +  +l+ f  +++ ++ ++ v+  +   
  gi|119720433|ref|YP_920928.1| 246 YFVKYLNGPPEAWSTLVAV-TTLFGLASIPYGRLADRLSTREMFVLAGLGWTAL-YLGYFLsPNYLVFSLFFVI-PVW-P 321
                                    5566677555555555555.44599*****************666666666666.4555431553333333333.333.6 PP

                          MFS_1 101 alfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllll 172
                                    a++ a   ++ d++ ++er+  +++ ++ ++l      +++gl+a++++ r +f++  + +ll++ ++++ll
  gi|119720433|ref|YP_920928.1| 322 AFWLAYSKALMDLSDESERATFYAFEGTLSALFGSAVGVAAGLVADLYSPRTLFLLSSASALLGAAVAGVLL 393
                                    8**************************96655555555999***********************99877765 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   7.4e-07    0.0044      18      86 ..      42     111 ..      28     116 .. 0.89
   2 !    3.9   3.5    0.0033        20     316     382 ..     116     180 ..     104     183 .. 0.63
   3 !   12.1   1.9     1e-05     0.063     242     384 ..     241     376 ..     184     377 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 7.4e-07
                     MFS_1_like  18 llPYltiylk.skglkaseigiitlilpltsilsppiwgvlaDrfgkrkkvvilslllsavlflsllfip 86 
                                    + P++ +yl    g    + gi + +  ++s++  ++w+ l+D  g rkk v lsl    ++ l+l f +
  gi|119720433|ref|YP_920928.1|  42 VSPFMALYLYgLAGGRFFQAGIASQAPVAVSVIMGLFWARLSDTNGSRKKFVQLSLATGSLASLALSFAS 111
                                    47*******989999*******************************************999999999876 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.0033
                     MFS_1_like 316 vlpievLhgisfgllwaaaveyvskiapksleatgqgllsglyfglGralGsliGGllwdlksaifl 382
                                    ++++++L +++  +  aa    +++++ k  ++   g++++    +G++ Gs+++G+l+++ + +++
  gi|119720433|ref|YP_920928.1| 116 AILVQILGAFTGSAGGAAFSALMAEVF-KDKRGSRLGVYNAS-TVIGGFAGSMLSGFLYNWIGFRWM 180
                                    444455555544444444444455555.44566677888765.779**************9988776 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 1e-05
                     MFS_1_like 242 giienFlflYL.kelgasntllGslvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaiienawlvlpie 320
                                    g++    ++Y+ k l+ + + +++lva++++  +    +  +l ++l+ +++ ++a l  ++ +l+y  + ++  +++  
  gi|119720433|ref|YP_920928.1| 241 GVF----SVYFvKYLNGPPEAWSTLVAVTTLFGLASIPY-GRLADRLSTREMFVLAGLGWTALYLGY--FLSPNYLVFSL 313
                                    333....4444466699***************9998777.58**********999988877766665..55555555555 PP

                     MFS_1_like 321 vLhgisfgllwaaaveyvskiapksleatgqgllsglyfglGralGsliGGllwdlksaiflFr 384
                                    ++      ++w+a  +   ++  +s +at  ++  +l+  +G+a+G  +G l+ dl+s+++lF 
  gi|119720433|ref|YP_920928.1| 314 FFVIPVWPAFWLAYSKALMDLSDESERATFYAFEGTLSALFGSAVGVAAG-LVADLYSPRTLFL 376
                                    5555667889************************************8776.999*******996 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.4     0.072   4.3e+02     298     333 ..      70     106 ..      28     145 .. 0.57
   2 ?   13.7   4.2   3.6e-06     0.022      45     145 ..     147     267 ..     121     338 .. 0.78
   3 ?   -1.4   3.4      0.13     8e+02      53      89 ..     350     385 ..     241     393 .. 0.58

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.072
                                    HHHHHHHHHHHHHHHHS-.SHHHHHHHHHHHHHHHHH CS
                       Sugar_tr 298 vvnfvatfvaiflvdrfG.RRtllllGaagmaicfvi 333
                                    +v +++ ++++ l+d  G R++++ l++a+++++ + 
  gi|119720433|ref|YP_920928.1|  70 AVSVIMGLFWARLSDTNGsRKKFVQLSLATGSLASLA 106
                                    3334444444444444332333333444444444444 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 3.6e-06
                                    ..HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTT..................SS-TGGG CS
                       Sugar_tr  45 svlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgk..................nsvevli 106
                                     +++g+  +++++G+++Gs+++g+l +++G ++ l   a+l v   vl+ +++++                  + ++ l+
  gi|119720433|ref|YP_920928.1| 147 GSRLGVYNASTVIGGFAGSMLSGFLYNWIGFRWMLRLNALLGVLPLVLISMIPEEgnrnpvssrklvsipkipRRFWKLY 226
                                    46789999***************************************999999778999999999999999999999999 PP

                                    GGHHHHHHHHHHHHHHHHHHHHTTS..-SCCHHHHHHHHHH CS
                       Sugar_tr 107 vgRvlvGigvGlasvlvPmyisEiA..pkklRgalvslyql 145
                                    ++R+++ ++  l  ++ ++y  ++   p++  ++lv ++ l
  gi|119720433|ref|YP_920928.1| 227 LARLVLSLPGALSGGVFSVYFVKYLngPPEAWSTLVAVTTL 267
                                    99999988877777777777666533355555555555555 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.13
                                    HTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHH CS
                       Sugar_tr  53 siflvGaiiGslfagllgdrfGRkkslliaavlfvig 89 
                                     ++l+G+++G + agl++d ++ +  +l +++ ++ g
  gi|119720433|ref|YP_920928.1| 350 LSALFGSAVG-VAAGLVADLYSPRTLFLLSSASALLG 385
                                    3333444443.23344444444444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 2800.59
//
Query:       gi|119720434|ref|YP_920929.1|  [L=243]
Description: ABC transporter related [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.2e-16   59.4   0.0    7.5e-16   58.9   0.0    1.2  1  ABC_tran    ABC transporter
    5.4e-09   36.3   0.1    0.00052   19.9   0.0    2.1  2  AAA_21      AAA domain, putative AbiEii toxin, Type IV TA sys
    0.00037   20.2   0.1    0.00054   19.6   0.1    1.2  1  AAA_27      AAA domain
     0.0011   18.4   0.0       0.35   10.3   0.0    2.1  2  SMC_N       RecF/RecN/SMC N terminal domain
  ------ inclusion threshold ------
      0.015   15.0   0.0      0.037   13.8   0.0    1.6  1  AAA_29      P-loop containing region of AAA domain
      0.023   14.3   0.6       0.09   12.3   0.0    2.1  2  AAA_25      AAA domain
      0.055   14.0   0.0      0.077   13.5   0.0    1.2  1  AAA_23      AAA domain
       0.18   12.0   0.0       0.27   11.4   0.0    1.3  1  AAA_33      AAA domain
       0.18   12.0   0.0       0.31   11.3   0.0    1.4  1  AAA_28      AAA domain
       0.21   10.4   0.2        0.3    9.8   0.2    1.1  1  ABC_ATPase  Predicted ATPase of the ABC class


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.9   0.0   4.2e-19   7.5e-16       1     136 [.      19     162 ..      19     163 .. 0.87

  Alignments for each domain:
  == domain 1  score: 58.9 bits;  conditional E-value: 4.2e-19
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--..SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp..teGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvr 77 
                                    l+ vsl + e e++ ++G+n aGK+tLl++lagl +    +G++lldg+d++     e++r+ ++   q p    ++ +r
  gi|119720434|ref|YP_920929.1|  19 LRGVSLGVGEAEVHFLMGPNAAGKTTLLSALAGLPRVrvVSGRVLLDGEDVTGlPVVERARRGVALAYQIPPELVGVPLR 98 
                                    6789*****************************9887779*************888899999999999996666666566 PP

                                    HH........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    xx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  78 en........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                    +            + +e++ ++l+l++l  +      + +SgG+++r +l  + l +p+l llDEp 
  gi|119720434|ref|YP_920929.1|  99 SLaklvsgrfGTGAYVEELSRRLRLEHLMGRDS---FRGFSGGERKRAELFLVALMRPRLALLDEPD 162
                                    666666666666666***********9888775...7****************************95 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   2.9e-07   0.00052       2      25 ..      32      55 ..      31      80 .. 0.79
   2 !   14.5   0.1   1.3e-05     0.023     233     301 ..     131     197 ..     116     199 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2.9e-07
                         AAA_21  2 nvliGpNgsGKSnLLdaldllarl 25
                                    +l GpN++GK++LL al +l r+
  gi|119720434|ref|YP_920929.1| 32 HFLMGPNAAGKTTLLSALAGLPRV 55
                                   5789**************999555 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 1.3e-05
                         AAA_21 233 parelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSpll 301
                                    ++r +S G ++ + l++  l ++   +l l+DEp++g +   l  +++ l+  s+  g+  i++TH   l
  gi|119720434|ref|YP_920929.1| 131 SFRGFSGGERKRAELFLVALMRP---RLALLDEPDSGVDLDSLWLIADALSFVSEeFGTAMIVVTHTRAL 197
                                    5788999****998888888888...99************999999999977777445555999996555 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1     3e-07   0.00054      19      48 ..      22      51 ..       9      53 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 3e-07
                         AAA_27 19 ldfsaeeadlhliyGpNEAGKstalrAisd 48
                                   ++++ +ea++h+++GpN AGK+t+l+A+  
  gi|119720434|ref|YP_920929.1| 22 VSLGVGEAEVHFLMGPNAAGKTTLLSALAG 51
                                   6677889********************975 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   0.0    0.0036       6.5      24      44 ..      29      49 ..      23      52 .. 0.88
   2 !   10.3   0.0   0.00019      0.35     137     205 ..     135     201 ..     106     211 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0036
                                   SSEEEEEESTTSSHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 24 ksftaivGpNGSGKsnlldAi 44
                                    ++ +++GpN +GK+ ll A+
  gi|119720434|ref|YP_920929.1| 29 AEVHFLMGPNAAGKTTLLSAL 49
                                   56889*************998 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00019
                                    S-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxx RF
                          SMC_N 137 LSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQfivislreemleka 205
                                    +SgGe++ + l L+ A+ +  p  l llDe d+  D      +a+ l   s++  + +iv+++++ ++ek+
  gi|119720434|ref|YP_920929.1| 135 FSGGERKRAELFLV-ALMR--P-RLALLDEPDSGVDLDSLWLIADALSFVSEEfgTAMIVVTHTRALIEKV 201
                                    79****99999777.5544..3.489*********************9777775589********999986 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.1e-05     0.037      19      43 ..      26      50 ..      17      52 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.1e-05
                         AAA_29 19 idlkgatlltGpsGsGKSTllDAiq 43
                                   + ++++++l+Gp+ +GK+Tll A++
  gi|119720434|ref|YP_920929.1| 26 VGEAEVHFLMGPNAAGKTTLLSALA 50
                                   55566899*************9986 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0     5e-05      0.09      31      54 ..      27      50 ..      19      93 .. 0.76
   2 ?   -1.3   0.0      0.75   1.3e+03     171     190 ..     176     195 ..     171     196 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5e-05
                         AAA_25 31 pagelallaGapgtGKttlaldla 54
                                    + e++ l+G+ ++GKttl++ la
  gi|119720434|ref|YP_920929.1| 27 GEAEVHFLMGPNAAGKTTLLSALA 50
                                   57899*****************99 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.75
                         AAA_25 171 aleriarrtgaavllvhHvg 190
                                    al  +++++g a ++v H++
  gi|119720434|ref|YP_920929.1| 176 ALSFVSEEFGTAMIVVTHTR 195
                                    455568899*********96 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   4.3e-05     0.077      23      39 ..      33      49 ..      23      52 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.3e-05
                         AAA_23 23 lItGpNGaGKTTildAi 39
                                    + GpN aGKTT+l A+
  gi|119720434|ref|YP_920929.1| 33 FLMGPNAAGKTTLLSAL 49
                                   578************98 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00015      0.27       1      26 [.      31      55 ..      31      86 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00015
                         AAA_33  1 lvllvGlpGsGKstlaerllkklgav 26
                                   + +l G++++GK+tl+  l+  l+ v
  gi|119720434|ref|YP_920929.1| 31 VHFLMGPNAAGKTTLLSALA-GLPRV 55
                                   6799*************998.44433 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00017      0.31       4      27 ..      34      58 ..      31      87 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00017
                         AAA_28  4 itGgestGKTtlleaLaar.gypvv 27
                                   ++G+  +GKTtll+aLa    ++vv
  gi|119720434|ref|YP_920929.1| 34 LMGPNAAGKTTLLSALAGLpRVRVV 58
                                   79***************54333333 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.2   0.00017       0.3     234     265 ..      16      50 ..       5      52 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00017
                                    TEEEEEEEE-SS...EEEEEE-TTSSHHHHHHHHH CS
                     ABC_ATPase 234 gkkvsGmgipkG...vtlIvGggfhGKsTLLeAle 265
                                     + ++G+ +  G   v  ++G+++ GK+TLL+Al+
  gi|119720434|ref|YP_920929.1|  16 AEVLRGVSLGVGeaeVHFLMGPNAAGKTTLLSALA 50 
                                    555555444333336999***************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1655.94
//
Query:       gi|119720435|ref|YP_920930.1|  [L=406]
Description: SufBD protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-39  135.3   0.0    2.8e-39  135.0   0.0    1.1  1  UPF0051   Uncharacterized protein family (UPF0051)


Domain annotation for each model (and alignments):
>> UPF0051  Uncharacterized protein family (UPF0051)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.0   0.0   1.6e-43   2.8e-39       2     218 .]     154     377 ..     153     377 .. 0.93

  Alignments for each domain:
  == domain 1  score: 135.0 bits;  conditional E-value: 1.6e-43
                        UPF0051   2 qfertlivveegaevtiieeyagc............gvveifvgenAklkyvkvqnwsedavnlstkraeegrdaklelt 69 
                                    qf +++++++egae+ +    +gc            g +e+fvg +A+l +++++ w+e++++ +++++++++  ++ ++
  gi|119720435|ref|YP_920930.1| 154 QFAHNVVYLDEGAEAVVT---TGClvphgvkgglhvGLSEFFVGPGARLVFTMLHAWGEGTHVRPRTAVRVEEGGEYVSY 230
                                    899***************...999999999999999*******************************9988777777777 PP

                        UPF0051  70 tvslggkltrk.epsvelkgegaeaelnglylakgkqhldtrtkvdhngpntssrilskgvlkdearavfrgkikvrkga 148
                                    ++  +   +++ +p+v+l  ++a+a+l++++ ++g    d++  + + g+++s++++s+   + ++++v rg +  +++a
  gi|119720435|ref|YP_920930.1| 231 YAVYSPVASLQtYPRVYL-YRRASAKLTSVVAGTGPGVYDVGGGAVLLGEGSSAELVSRVLGSKGSTIVSRGSV--EAEA 307
                                    777776655552777777.5******************************************************..99** PP

                        UPF0051 149 qktdahqenrnLllsdkaradtiPeleidaddvkasHgAtvGkideeqlfYLmsRGlseeeArrlivrgf 218
                                    +  ++h+e+   +l++ ++++++P l+ + + ++++H+A++G ++ e++ YLm+RG+seeeAr++++rg+
  gi|119720435|ref|YP_920930.1| 308 NDVKGHIECLGVMLDPSSTIEAVPVLKSRVERAELTHEAAIGMLSGEKIEYLMARGFSEEEARSILLRGY 377
                                    ********************************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2640.88
//
Query:       gi|119720436|ref|YP_920931.1|  [L=636]
Description: phosphoenolpyruvate carboxykinase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   1.9e-104  349.4   0.0   2.4e-104  349.0   0.0    1.1  1  PEPCK_GTP  Phosphoenolpyruvate carboxykinase C-terminal P-loo
    2.9e-57  193.8   0.0      4e-57  193.3   0.0    1.1  1  PEPCK_N    Phosphoenolpyruvate carboxykinase N-terminal domai


Domain annotation for each model (and alignments):
>> PEPCK_GTP  Phosphoenolpyruvate carboxykinase C-terminal P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  349.0   0.0  2.6e-108  2.4e-104       1     358 []     257     617 ..     257     617 .. 0.94

  Alignments for each domain:
  == domain 1  score: 349.0 bits;  conditional E-value: 2.6e-108
                                    -EEES-EEEEEE-TTS-EEEEEEE-TTTSSHHHHHT---SSTT-EEEEEESS-EEEEE-TTSBEEEE---SEEEEE-TT- CS
                      PEPCK_GTP   1 wLaEhmlilgvtspegkkkyvaaafpsacGKtnlamleptlegwkvetvgdDiawlkfgedgrlraiNpeaGfFgvapgt 80 
                                    wLaEhm+i+g++   g+ +y+a+afp++cGKt++am+++t       +vgdD+a ++   +g   a+Npe G+Fg+++g+
  gi|119720436|ref|YP_920931.1| 257 WLAEHMFIVGLKGRGGRLTYFAGAFPAGCGKTSTAMIADT-------VVGDDLALIHAV-NGVAVAVNPEVGMFGIIDGV 328
                                    9*************************************95.......9**********9.******************** PP

                                    STTT-HHHHHHT.TBS..-EEES-EEETTS-EE-TT--------EE-TTSSEE-T.T-S.......SS-TT-EEEEEGGG CS
                      PEPCK_GTP  81 nektnpnalktl.kkn..tiftNvaltedgdvwWegleeeapaelidwkgkkwtkekek.......aahpnsrftvpakq 150
                                    n  ++p++++ l + +  +if+Nv+lt+dg+vwW+g+  e+p+e+++++g +w+++k++        +hpn+rft+++++
  gi|119720436|ref|YP_920931.1| 329 NPADDPEIYSLLtNPEveVIFSNVLLTRDGEVWWRGKP-EEPREGLNYAG-EWWPGKRDeggkevpPSHPNARFTLSIRH 406
                                    **********99644467*******************7.55669******.788875555777889************** PP

                                    STTB-TTTT-TT-EEEEEEEEEEB-SSSS-SEEE-SSHHHHHHH.HHT-EEE--TTSSS-TT-EEE-GGG-GGG-SS-HH CS
                      PEPCK_GTP 151 lpiiapewedpeGvpisaiifggrrsetvplvleafdwehGvfl.gatlesetTaaaegkvgvvrrdPfamlpFlgynlg 229
                                    +p+++p+++dp Gvp+sa++fggr+s+t+p+vle+fdw+hGv++ ga+lese+Taa+ g+vgv++ +P+a+l+Fl+++ g
  gi|119720436|ref|YP_920931.1| 407 FPKLDPRIDDPGGVPLSAMVFGGRDSSTLPPVLESFDWNHGVVMmGAALESEKTAAVIGQVGVTELNPYAILDFLPISPG 486
                                    *****************************************9877*********************************** PP

                                    HHHHHHHHHTTSTT-B--EEEEEES--B-TTSSBSS--GGGHHHHHHHHHHHHTT..S-EEETTEEEE-BTTC--TT-.. CS
                      PEPCK_GTP 230 dYlehwlelgkklekklPkifsvNwfrkdeegkflWPGfgenlrvlkWilkrvegeakavetpiGlvPkkedldlkgl.. 307
                                     ++e +++++ k  + +Pkif vN+f+++++g++l    ++ l  l+W+  rv+ge+ av+tp+G+vP +edl   ++  
  gi|119720436|ref|YP_920931.1| 487 AFTELHFRFAGK-LRVTPKIFGVNYFLRGKDGNYLA-EKRDKLAWLRWMEARVNGEVGAVKTPVGYVPVYEDLR--EIfd 562
                                    *********999.99********************7.78899999***************************64..4445 PP

                                    .......TT--HHHHS---HHHHHHHHHHHHHHHHHTGGGS-HHHHHHHHHHHHHH CS
                      PEPCK_GTP 308 .....dlskedleellsvdkeewkeeveeieelfeklgeklPkelleeleelekrl 358
                                         ++++  +ee++sv++ +++ +ve++ +++ + +++ P  l+e l+++e+rl
  gi|119720436|ref|YP_920931.1| 563 khlgkEFPEGLYEEMFSVRVLNYLGKVERVYKAYLE-DSDAPPLLFEILRDQERRL 617
                                    556999****************************88.89*************9987 PP

>> PEPCK_N  Phosphoenolpyruvate carboxykinase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.3   0.0   4.5e-61     4e-57       3     217 ..      44     252 ..      43     253 .. 0.96

  Alignments for each domain:
  == domain 1  score: 193.3 bits;  conditional E-value: 4.5e-61
                                    HHHHHHHH--SEEEE----HHHHHHHHHHHHHTTSEEE-TTSBS-EEE---TTSSS--GGGEEEE-SSHHHH-SS--EE- CS
                        PEPCK_N   3 veevaelcqPdkvvvcdgseeeneellkelvekgeliklekypnsylarsdpkDvARvesrTfictekeedagplnnwmd 82 
                                    ++ v+ + +P++++v++gse+++e+++++++++ge+ +  +y++++++++  kD AR+  +T i+ +  +++ ++ n+ d
  gi|119720436|ref|YP_920931.1|  44 IAAVILVAKPSSLFVNTGSESDREYIRRRALDNGEELPT-RYERHTVHFDGAKDLARDVANTRILYPGGRRV-AMVNTYD 121
                                    56788899*******************************.*******************************9.9999*** PP

                                    HHHHHHHHHHHSTTTTTTSEEEEEEEEES-TTSTT-EEEEEEES-HHHHHHHHHHSEESHHHHTT-SS..TSEEEEEE-S CS
                        PEPCK_N  83 peemkeelkelfkgcmkGrtmyVipfsmGpvgsplskigveiTdsaYVvlsmrimtrvgkkvleklgeeeefvkclHsvg 162
                                    + +  eel+elf+g+m+Gr+ +V +++ Gp gsp+s +gv++TdsaYV +s+++++r++++ + + ge+ e++ ++Hs+g
  gi|119720436|ref|YP_920931.1| 122 RGRGVEELRELFEGVMRGREAFVSFYLYGPRGSPFSLYGVQVTDSAYVTHSEELLYRNAYRDFVEKGEDVEYMLFVHSAG 201
                                    ******************************************************************************** PP

                                    --SS-SS-BTB---G.G-EEEEEGGGTEEEEES--SHHHH-TCCHHHHCHHHHHHH CS
                        PEPCK_N 163 aplegqkdvkWpcne.kkyivhfpeereilsvgsgYgGNaLlgKkcfalRiasvia 217
                                    + +    +  W  n+ k++i+++ e+++++sv+++Y+GN++++Kk +alR+a++++
  gi|119720436|ref|YP_920931.1| 202 ERD----ERGWSKNTdKRRIYIDVENSTVYSVNTQYAGNTVGLKK-LALRLAVYKG 252
                                    844....345999988*****************************.*******987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (636 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 4126.82
//
Query:       gi|119720437|ref|YP_920932.1|  [L=452]
Description: citrate transporter [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-28   99.5  40.4    5.3e-16   58.7  21.2    2.2  2  CitMHS         Citrate transporter
    0.00023   20.3  23.4     0.0023   17.0   8.4    2.6  2  Na_sulph_symp  Sodium:sulfate symporter transmembrane region


Domain annotation for each model (and alignments):
>> CitMHS  Citrate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.7  21.2   5.9e-20   5.3e-16      13     168 ..      65     226 ..      40     276 .. 0.72
   2 !   46.8  11.1   2.4e-16   2.1e-12      15     167 ..     290     450 ..     280     452 .] 0.83

  Alignments for each domain:
  == domain 1  score: 58.7 bits;  conditional E-value: 5.9e-20
                                    xxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         CitMHS  13 vvallvlvll......vltieealsgiaspiillllgamiigaaleetGlfdrlaakllrlaggkrdllvllvlltalls 86 
                                    +++      +      +l+i+++ + +++++il+l+g++ i+++ e +Gl    + ++++++ ++ +l+ + ++l +ll+
  gi|119720437|ref|YP_920932.1|  65 FAS------FivvatgLLGIDDVRKSVDVDVILFLVGMFSIVGLAETSGLLTAASYFFVSRFHSRVKLFYASAVLFGLLA 138
                                    233......13334479**********************************************8655************* PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............ RF
                         CitMHS  87 afvsndgvvlimipivlslakrlkklppl.lliplalaaniggaltpiGtpttraaarpglslpnlll............ 153
                                    af+ nd+ v++m+p+v  +  r +++ p  ++++la++  ig+a+tpiG+p            +n+l+            
  gi|119720437|ref|YP_920932.1| 139 AFAVNDT-VALMGPAVAYVISRAAGIDPKaMFLLLAFSITIGSAMTPIGNP------------QNVLIasgsgmpapmlv 205
                                    ******9.66777777777777788888879999*****************............77777777776665544 PP

                                    ......xxxxxxxxxxxxxxx RF
                         CitMHS 154 ......lalllvgllplvllf 168
                                          ++ l+++ll+ +ll 
  gi|119720437|ref|YP_920932.1| 206 ftarlaVPTLVNLLLTAYLLS 226
                                    444444334444443333332 PP

  == domain 2  score: 46.8 bits;  conditional E-value: 2.4e-16
                                    xxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
                         CitMHS  15 allvlvll....vltieealsgiaspiillllgamiigaaleetGlfdrlaakll.rlaggkrdllvllvlltallsafv 89 
                                    a     ++    +  +  +ls ++++++++++ ++i +a++ ++G++d+  + ll  +a g rd l++++ll+  ls f+
  gi|119720437|ref|YP_920932.1| 290 AA----AAiypfTSNPRRILSRVDWSTVVFFITMFITVAGVMRSGVVDPALRLLLpEKATGARD-LFAIALLSLALSQFL 364
                                    22....223566677888**********************************999956666799.99************* PP

                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................ RF
                         CitMHS  90 sndgvvlimipivlslakrlkklppllliplalaaniggaltpiGtpttraaarpglslpnlll................ 153
                                    sn++ + im+  +  l+ +   + +++ + la+a+ i g lt+ G               n+++                
  gi|119720437|ref|YP_920932.1| 365 SNVPLASIMVEYMRGLGYS--STDVRAWLTLATASTIAGNLTLLGAA------------SNIIIlemlerrfkttitfte 430
                                    *****************96..4444445679999999999*******............*****9999999999999999 PP

                                    ......xxxxxxxxxxxxxx RF
                         CitMHS 154 ......lalllvgllplvll 167
                                          l+ +l++l++  +l
  gi|119720437|ref|YP_920932.1| 431 flrvgvLVTALNMLVYAPFL 450
                                    99955544455555665555 PP

>> Na_sulph_symp  Sodium:sulfate symporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   8.4   2.6e-07    0.0023     303     434 ..      69     195 ..      39     232 .. 0.79
   2 !    8.8   7.0     8e-05      0.72     320     459 ..     308     447 ..     303     452 .] 0.68

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.6e-07
                  Na_sulph_symp 303 illllrvldWkDivkqktaWntllllgglialakllersgliewlgnklttslsglspavaiiiilslfvlvhylfaSat 382
                                    i++ + +l  +D+ ++    +++l+l g+ ++  l e sgl+   + ++++    ++  v ++    +++ +   fa + 
  gi|119720437|ref|YP_920932.1|  69 IVVATGLLGIDDV-RKSVDVDVILFLVGMFSIVGLAETSGLLTAASYFFVS---RFHSRVKLFYASAVLFGLLAAFAVND 144
                                    4455556666654.4456678889999999999999999987766666655...45566666666666777777788775 PP

                  Na_sulph_symp 383 Attaallpillavaqaipgappllvalllalatslagfllpyatgpnpivfg 434
                                     t+a + p ++ v   ++g++p  + llla+++ +++ ++p++ ++n+++ +
  gi|119720437|ref|YP_920932.1| 145 -TVALMGPAVAYVISRAAGIDPKAMFLLLAFSITIGSAMTPIGNPQNVLIAS 195
                                    .7999*********9999*****************************98754 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 8e-05
                  Na_sulph_symp 320 taWntllllgglialakllersgliewlgnklttslsglspavaiiiilslfvlvhylfaSatAttaallpillavaqai 399
                                      W t++++ ++     +  rsg+++     l +  +   +a  +++i +l++++  +f S++ + ++++  +  ++ + 
  gi|119720437|ref|YP_920932.1| 308 VDWSTVVFFITMFITVAGVMRSGVVDPALRLLLPEKA--TGARDLFAIALLSLAL-SQFLSNVPLASIMVEYMRGLGYSS 384
                                    5688888888877777778888888877777777777..5555555555544433.467788888888888888888877 PP

                  Na_sulph_symp 400 pgappllvalllalatslagfllpyatgpnpivfga......gylkvkdywrlGfilsiigllill 459
                                    +    + + l+la a+ +ag l+ ++++ n i++ +       ++   ++ r+G++++ +++l+++
  gi|119720437|ref|YP_920932.1| 385 T---DVRAWLTLATASTIAGNLTLLGAASNIIILEMlerrfkTTITFTEFLRVGVLVTALNMLVYA 447
                                    3...45777888888888888888888888888875332222356667788888888877777754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (452 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       624  (0.0348039); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.51
# Mc/sec: 2663.88
//
Query:       gi|119720438|ref|YP_920933.1|  [L=191]
Description: hypothetical protein Tpen_1534 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.5e-36  123.9  14.8    7.7e-36  123.7  14.8    1.0  1  ECF-ribofla_trS  ECF-type riboflavin transporter, S component
    2.7e-07   30.8  13.9    3.7e-07   30.4  13.9    1.1  1  ECF_trnsprt      ECF transporter, substrate-specific componen
  ------ inclusion threshold ------
       0.44   11.0  11.7         13    6.3  10.9    2.6  2  SNARE_assoc      SNARE associated Golgi protein


Domain annotation for each model (and alignments):
>> ECF-ribofla_trS  ECF-type riboflavin transporter, S component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.7  14.8   1.3e-39   7.7e-36       2     171 ..      12     181 ..      11     182 .. 0.95

  Alignments for each domain:
  == domain 1  score: 123.7 bits;  conditional E-value: 1.3e-39
                                    ..TTHHHHHHHHHHHHHHHHHH---B-S.SS-B.--TTHHHHHHHHHHSS--STHHHHHHHHHHHHHHHSS-G.GGHHHH CS
                ECF-ribofla_trS   2 lstkkvvatailaAlvvvltlfisIplpanteg.sinlgdavlalaallfGpvvGflvGaiGsalaDllsgYg.iwapft 79 
                                    lst ++va++i++Al++++ +f++I  +++++  s++++ ++ ++++++fGpvvGf+vG++G++++D++s +g +w+++ 
  gi|119720438|ref|YP_920933.1|  12 LSTTDIVAMGIGTALYAAFNVFFNILQIPGSQLvSVRPSVSIPMFFGHVFGPVVGFVVGFLGNTISDAVS-WGgFWWNW- 89 
                                    699***********************99999999**********************************55.888*****. PP

                                    HHHHHHHHHHHHHH--S-S-SSH...HHHHHHHHHHHHHHHHHHHHHHHH.............S-HHHHHHHHHHHHHHH CS
                ECF-ribofla_trS  80 liikgliGlivGliakklkknkengvfkilalvlfaivmvigyviaegll.pildiiiy..sepaekvalqsipaniiqa 156
                                     + +gl+Gli Gl+++ +   k+++++++++l+++++++v+g ++++g++ ++ +i+ y  s+++e++++  +pa++++a
  gi|119720438|ref|YP_920933.1|  90 DVGNGLLGLISGLASYII---KREELLEKKGLMVASVLAVVGSIVGMGFAsFTDYIFGYgiSTIEEAIYALFLPAAVTDA 166
                                    ******************...44568************************88888888899******************* PP

                                    HHHHHHHHHHHHHHH CS
                ECF-ribofla_trS 157 vvgaiialpLlkala 171
                                    v gai++ +L+ka++
  gi|119720438|ref|YP_920933.1| 167 VNGAILTPVLIKAYS 181
                                    *************96 PP

>> ECF_trnsprt  ECF transporter, substrate-specific component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4  13.9   6.2e-11   3.7e-07       3     167 ..      17     175 ..      12     181 .. 0.63

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 6.2e-11
                                    HHHHHHHHHHHHHHHHHHEEE.STS......E.EESHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHCHT-SSTTHHHHHH CS
                    ECF_trnsprt   3 lvitglliAisivlsllgyiplpni......k.itiihipvllggllfGpikGailgiitsvlkailtggtgalssfvpi 75 
                                    +v +g+ +A+ + ++   +++++ i      +    + ip++  g +fGp++G+++g+++++++  +  g+  ++   + 
  gi|119720438|ref|YP_920933.1|  17 IVAMGIGTALYAAFN--VFFNILQIpgsqlvSvRPSVSIPMF-FGHVFGPVVGFVVGFLGNTISDAVSWGG--FW---WN 88 
                                    688999999999999..5555555555677761455677777.5***********************7776..55...77 PP

                                    HHHHHHCHHHHHHHHHHCCCHTTHHHH...HHHHHHHHCCCCCHHHHHHHCCCHHHHS.............--HHHHHHH CS
                    ECF_trnsprt  76 aflsriligliagllykkgkkknlkei...vvsfilagvlgtivatllvlliilplylklktakaiaiagkallaailgp 152
                                      + ++l+gli gl   ++k+  l e+    v+++la+v + + + + + +  ++ y+    ++ i      ++ a+++p
  gi|119720438|ref|YP_920933.1|  89 WDVGNGLLGLISGLASYIIKREELLEKkglMVASVLAVVGSIVGMGFASFTDYIFGYG----ISTI----EEAIYALFLP 160
                                    7888888888888544344444333321224444444443333333333333344443....3333....3667777777 PP

                                    HHCCTTCCHHHHHHH CS
                    ECF_trnsprt 153 iivkglieaiiaaii 167
                                    + v+++++++i   +
  gi|119720438|ref|YP_920933.1| 161 AAVTDAVNGAILTPV 175
                                    777777777765544 PP

>> SNARE_assoc  SNARE associated Golgi protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3  10.9    0.0022        13       2      72 ..      49     122 ..      48     159 .. 0.60
   2 ?    3.1   2.1     0.021   1.3e+02      15      41 ..     117     143 ..      92     186 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0022
                    SNARE_assoc   2 PsevllvaaGvlfglllgtlvtslgallGaslay...llgrylgrkalrrkllsekrvkalerlverygflall 72 
                                    Ps  + +++G +fg+++g++v +lg ++++ +++   +    +g+  l+   +   ++ + e+l+e++g +++ 
  gi|119720438|ref|YP_920933.1|  49 PSVSIPMFFGHVFGPVVGFVVGFLGNTISDAVSWggfWWNWDVGNGLLGLISGLASYIIKREELLEKKGLMVAS 122
                                    6777779**********************988750003333333344444444445555566666665554443 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.021
                    SNARE_assoc  15 glllgtlvtslgallGaslayllgryl 41 
                                    gl+++ +++++g+++G+ +a ++ +++
  gi|119720438|ref|YP_920933.1| 117 GLMVASVLAVVGSIVGMGFASFTDYIF 143
                                    344444445555555544444443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1288.05
//
Query:       gi|119720439|ref|YP_920934.1|  [L=263]
Description: cobalt transport protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.2e-26   91.4   6.2      1e-25   90.7   6.2    1.3  1  CbiQ      Cobalt transport protein
  ------ inclusion threshold ------
        4.1    7.8  12.2          4    7.8   8.6    2.6  2  DUF2516   Protein of unknown function (DUF2516)
        4.6    7.4   5.3        1.5    9.0   0.1    2.8  3  COX6C     Cytochrome c oxidase subunit VIc


Domain annotation for each model (and alignments):
>> CbiQ  Cobalt transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.7   6.2   1.7e-29     1e-25       2     211 ..      12     223 ..      11     229 .. 0.93

  Alignments for each domain:
  == domain 1  score: 90.7 bits;  conditional E-value: 1.7e-29
                                    SCCCCS-HHHHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHTTS---.....HHHHHHHCCCHCHHHHHHHHHHE... CS
                           CbiQ   2 ksvlhrldprvkliwlfllllalvlapnlvtlliiiallllllllvilp.....rvlaqalilpllflllgllillfqli 76 
                                    +s+ hrldprvkl+++ +++la++l++nl+++++  al l  +ll+ lp       + ++li++l + +l+ l+++++  
  gi|119720439|ref|YP_920934.1|  12 SSIVHRLDPRVKLFFVGSVVLAASLSYNLLLAVLTLALGLSFYLLARLPfsktkNTWKFILIVALVLSFLNYLFVAVLYH 91 
                                    799********************************************999999999*********************666 PP

                                    ....EECTTEEE...E-TTHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHHHHCCCSS--HHHHHHHHHHHHHHHHHHHH CS
                           CbiQ  77 ttegefvfagggqisitseGllrglllalRiltllslllllalTTppeeltsslerlgvPlelalillLayRfiflLlee 156
                                    ++ ge++ a ++      e l r+++ +l+ l++ +++++++ TTpp   +++l +lg     a+++ L++R+++ +++e
  gi|119720439|ref|YP_920934.1|  92 RPRGELLEAFMS-----AELLSRSITPVLKLLAVATVTVAFVYTTPPHLYAPALGQLGLSYRAAYAVHLGFRYFPQFVDE 166
                                    666666666666.....8889*********************************************************** PP

                                    HHHHHHHHHHTTTTS.....SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS-SS CS
                           CbiQ 157 vqrikqAqklRlgds...klgirrslrslgkliaalflralkraervalAmeaRGYtg 211
                                    ++r  +Aq++R+ +    k ++ r + ++++li+++ ++a     +v  Ame RG+ g
  gi|119720439|ref|YP_920934.1| 167 LRRTLEAQMARGYRPrggKNPLGR-ILAVIPLIVPVTVSATLSIYDVSDAMELRGFGG 223
                                    **************9887777777.********************************9 PP

>> DUF2516  Protein of unknown function (DUF2516)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   8.6   0.00067         4      40      79 ..      63     130 ..      25     132 .. 0.96
   2 ?   -0.2   0.1       0.2   1.2e+03      66      80 ..     241     255 ..     221     258 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00067
                        DUF2516  40 rtKpfWlailgvallvlll............................glfgalsllgliavvaalvYl 79 
                                    +tK++W  il+val++++l                            +++  l+ll+++ v++a+vY 
  gi|119720439|ref|YP_920934.1|  63 KTKNTWKFILIVALVLSFLnylfvavlyhrprgelleafmsaellsrSITPVLKLLAVATVTVAFVYT 130
                                    79********************************************9999999*************95 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.2
                        DUF2516  66 llgliavvaalvYlv 80 
                                     ++++++v++lv+l+
  gi|119720439|ref|YP_920934.1| 241 AFAILSAVISLVFLA 255
                                    578888999999886 PP

>> COX6C  Cytochrome c oxidase subunit VIc
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.2      0.57   3.4e+03      11      34 ..      32      54 ..      29      60 .. 0.57
   2 ?    9.0   0.1   0.00026       1.5      13      50 ..      66     103 ..      62     105 .. 0.90
   3 ?   -0.9   0.1      0.32   1.9e+03      10      33 ..     106     129 ..     102     131 .. 0.64

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.57
                          COX6C 11 lakrlkrhlvvafvlslgvaaayk 34
                                   la++l  +l++a+ l+l+ +++++
  gi|119720439|ref|YP_920934.1| 32 LAASLSYNLLLAV-LTLALGLSFY 54
                                   5666777776664.3444444444 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00026
                          COX6C  13 krlkrhlvvafvlslgvaaaykfavaepRKkayadFYk 50 
                                    ++ k+ l+va+vls++ ++++ ++   pR +  + F++
  gi|119720439|ref|YP_920934.1|  66 NTWKFILIVALVLSFLNYLFVAVLYHRPRGELLEAFMS 103
                                    667999***********************998888875 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.32
                          COX6C  10 llakrlkrhlvvafvlslgvaaay 33 
                                    ll +++   l++ +v +++va++y
  gi|119720439|ref|YP_920934.1| 106 LLSRSITPVLKLLAVATVTVAFVY 129
                                    566666666666666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       971  (0.0541581); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 1690.31
//
Query:       gi|119720440|ref|YP_920935.1|  [L=222]
Description: hypothetical protein Tpen_1536 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.6e-66  222.1  22.1    6.3e-66  222.0  22.1    1.0  1  DUF554     Protein of unknown function (DUF554)
     0.0024   16.6   5.7     0.0028   16.4   5.7    1.1  1  CitMHS_2   Putative citrate transport
  ------ inclusion threshold ------
        1.7    8.4  13.1       0.88    9.3   5.9    2.6  3  Mntp       Putative manganese efflux pump


Domain annotation for each model (and alignments):
>> DUF554  Protein of unknown function (DUF554)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  222.0  22.1   1.1e-69   6.3e-66       1     219 [.       2     217 ..       2     218 .. 0.98

  Alignments for each domain:
  == domain 1  score: 222.0 bits;  conditional E-value: 1.1e-69
                         DUF554   1 lGtivNvlaillGsllGlllkkrlperlqktlmqalGlvvlliGismalksenvllvilslvlGaviGelldleerlerl 80 
                                    lGt+vN+l++l+Gsl+Glll+k ++ +  + + ++lGl++++iG++mal+ ++++++i+sl+lG+++Ge+l +e +l+rl
  gi|119720440|ref|YP_920935.1|   2 LGTLVNTLTVLAGSLVGLLLRKSVNAERVAFVADVLGLFTVAIGVQMALQARKPVAMIVSLLLGSLVGEALGVEGALQRL 81 
                                    69****************************************************************************** PP

                         DUF554  81 gealkkkvkkskrfaegfvtasllfcvGamailGslqeGltgdatlLltKslLDgvtaiilasslGigvlfsalpvlvyq 160
                                    +e+++++  +s+ +++g++ta l+fcvG+m+++Gs+++Gl gd+++Ll+Ks++Dgv++++ a+++G+gv+fs++ vl +q
  gi|119720440|ref|YP_920935.1|  82 SERVSRT--RSQGVVDGMLTAFLTFCVGPMTVVGSIRDGL-GDPSILLAKSVMDGVASVAYAAAMGVGVVFSSVLVLAFQ 158
                                    ***9998..44558*************************9.9************************************** PP

                         DUF554 161 gaitllAgllapllteaviaeltavGgllilaiGlnlleikkikvanllPalllavllv 219
                                    g+++ll+ l  +ll ea ++elta+Gg+l++++G+nll++k+i+v+n+lPallla++l+
  gi|119720440|ref|YP_920935.1| 159 GSLALLGALTGALLPEASVNELTAAGGVLLIGVGINLLKLKRIRVGNMLPALLLAPILA 217
                                    ********************************************************986 PP

>> CitMHS_2  Putative citrate transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   5.7   4.7e-07    0.0028      46     180 ..       5     143 ..       1     163 [. 0.75

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 4.7e-07
                       CitMHS_2  46 lvplavllgveaaleellhallaeylpFivlllaLfvvaggilikgnlkgtplvntlllligavlasligttGasmlliR 125
                                    lv ++++l+ +     l +++ ae ++F++ +l+Lf+va g+++  +++ +p++ ++ ll+g+++ + +g  Ga   l  
  gi|119720440|ref|YP_920935.1|   5 LVNTLTVLAGSLVGLLLRKSVNAERVAFVADVLGLFTVAIGVQMALQAR-KPVAMIVSLLLGSLVGEALGVEGALQRLSE 83 
                                    55555555556666667788999*******************9998765.899999******************888888 PP

                       CitMHS_2 126 pllrankeRkkkvhvvvFfiflvan..iGGsL.tPlGDPPlflG..flkGvdFfWtlkhl 180
                                     + r+ ++      +  F+ f v    + Gs+   lGDP ++l    + Gv  +  +  +
  gi|119720440|ref|YP_920935.1|  84 RVSRTRSQGVVDGMLTAFLTFCVGPmtVVGSIrDGLGDPSILLAksVMDGVASVAYAAAM 143
                                    88888888888888899999999742245666268*****99952256677655555444 PP

>> Mntp  Putative manganese efflux pump
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.3     0.011        64      16      59 ..       5      52 ..       1      58 [. 0.67
   2 ?   -1.5   0.2      0.32   1.9e+03     118     125 ..      58      65 ..      37      78 .. 0.48
   3 ?    9.3   5.9   0.00015      0.88      98     152 .]     142     196 ..     123     196 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.011
                           Mntp 16 lfqalmpliGwllGkllselie.avdhwiafll...LlllGlkmivea 59
                                   l+++l+ l+G l+G ll++ ++ +   ++a +l    + +G++m ++a
  gi|119720440|ref|YP_920935.1|  5 LVNTLTVLAGSLVGLLLRKSVNaERVAFVADVLglfTVAIGVQMALQA 52
                                   567888999999999999998833334444333211467899998776 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.32
                           Mntp 118 sllGlllG 125
                                    +++ lllG
  gi|119720440|ref|YP_920935.1|  58 MIVSLLLG 65 
                                    22333333 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.00015
                           Mntp  98 llkvnillavlliGlvtlvlsllGlllGrklgsllgkkaeilGGliLiliGlkil 152
                                     ++v ++++ +l+  +   l+llG l+G  l ++  ++ +++GG+ Li++G+++l
  gi|119720440|ref|YP_920935.1| 142 AMGVGVVFSSVLVLAFQGSLALLGALTGALLPEASVNELTAAGGVLLIGVGINLL 196
                                    5678888888888889999*********************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.51
# Mc/sec: 1317.21
//
Query:       gi|119720441|ref|YP_920936.1|  [L=325]
Description: threonine synthase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-59  200.5   3.0    4.5e-59  200.3   3.0    1.0  1  PALP      Pyridoxal-phosphate dependent enzyme


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.3   3.0   2.5e-63   4.5e-59       7     294 .]      15     318 ..      10     318 .. 0.92

  Alignments for each domain:
  == domain 1  score: 200.3 bits;  conditional E-value: 2.5e-63
                                    S--EEEECCTCCCCCCE...EEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-EEEE CS
                           PALP   7 pTPlvrlprlskelgvp...lflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallGlkvti 83 
                                     TPl++l +l k l+ +   ++lK+E+ nptg +KdR+a   + ++  + g +tv++++ GN g+a+A++a+l+Gl+++i
  gi|119720441|ref|YP_920936.1|  15 STPLLKLTSLRKLLNLDgaaVYLKYEGYNPTGTHKDRAALAHVGEAVLN-GYDTVTVGTCGNYGVAVAYYARLAGLRAVI 93 
                                    69*********999999999*************************9999.9***************************** PP

                                    EEETTS-HHHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTT..SHHHHHHHHTHHHHHHHHTTTTEEEE CS
                           PALP  84 vvpadaspekvallrllGaevvevggdydeavaaaaelaaegegaylvsqfd..nptviegygtiglEileqlggkpdav 161
                                    +vp++ s+++v  ++++Ga+vvev+g y++ava+    a+  +g+y +++++  +   ie+y+ i+ Ei++qlg++p +v
  gi|119720441|ref|YP_920936.1|  94 FVPKGYSNSRVPEMKRYGARVVEVEGPYEDAVAVSVSSARA-NGWYDANPGSvnDHVSIEAYSLIAREIVRQLGDAPAVV 172
                                    **********************************8888888.9*********956667888******************* PP

                                    EEE-SSSHHHHHHHHHHHH..HSTT....-EEEEEEECTTCGGTTCCS..S.SS..B........SSS.CCSTCS.CGTT CS
                           PALP 162 vvpvGgGgliaGiaaglke..rrpd....vrvigvepegsdalarslragrrvtvpvs.......dtiadglavg.spse 227
                                     vpvG+G ++ Gi++g+    r ++    +r++++ +++++ l  s+ +g+ +++pv+       +   + +a++  ++e
  gi|119720441|ref|YP_920936.1| 173 AVPVGNGTTLVGIYHGFYRlyRAGEttriPRMVAASTSNANQLVYSWSRGSTEPLPVEvsevretPVNEPLVAIRsLNAE 252
                                    *******************8844445689*********************999999998888866333333444466889 PP

                                    CCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHH.HHHHHHCCTTCEEEEEEE-B CS
                           PALP 228 lafelldrlvdeivtvsdeealeamrllarregivvepssaaalaal.klreagelkegdrvvviltg 294
                                    +a++++ ++ + + + sd e++e+  ll   eg+ + p+sa al a+ + ++a+e+++   vv+++tg
  gi|119720441|ref|YP_920936.1| 253 EALRAIYASKGAAFGFSDSEMVEMSILLRAFEGVSALPASASALLAVrEYLKANEVDGP--VVAVITG 318
                                    9999999****************************************999999999999..***9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 2067.48
//
Query:       gi|119720442|ref|YP_920937.1|  [L=353]
Description: hypothetical protein Tpen_1538 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      2e-65  219.9   0.0    2.5e-65  219.5   0.0    1.1  1  DUF1611    Domain of unknown function (DUF1611_C) P-loop doma
    2.9e-32  110.8   0.0    6.7e-32  109.6   0.0    1.7  1  DUF1611_N  Domain of unknown function (DUF1611_N) Rossmann-li
     0.0051   16.9   0.1      0.033   14.3   0.0    2.3  2  DapB_N     Dihydrodipicolinate reductase, N-terminus
  ------ inclusion threshold ------
      0.019   15.1   0.2        3.6    7.7   0.0    2.7  3  DUF498     Protein of unknown function (DUF498/DUF598)
      0.041   14.0   0.3      0.089   12.9   0.3    1.5  1  DUF150_C   RimP C-terminal SH3 domain
      0.071   12.9   0.2       0.56   10.0   0.1    2.3  2  AAA_26     AAA domain


Domain annotation for each model (and alignments):
>> DUF1611  Domain of unknown function (DUF1611_C) P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  219.5   0.0   8.4e-69   2.5e-65       2     200 .]     144     341 ..     143     341 .. 0.99

  Alignments for each domain:
  == domain 1  score: 219.5 bits;  conditional E-value: 8.4e-69
                        DUF1611   2 vadgkarevkakrvlvvGTdcavGKrttaleleealeerGlkaafvaTgqtgili.agegvvldavvvdfvaGaveglvk 80 
                                    +++gk++evka +v+v+GTd+avGKrt a++++++l++rG+ka fv+Tgqt++++ a++ +vld+v++dfv+G +e++v+
  gi|119720442|ref|YP_920937.1| 144 FYTGKIKEVKALKVVVIGTDSAVGKRTVAHMVTDELNARGIKAVFVGTGQTAWMQgAKYVFVLDSVINDFVPGVLEDVVW 223
                                    79****************************************************************************** PP

                        DUF1611  81 kaaeeeepdlilveGQgsLthpaysgvtlglLlGsqPdalvLchrpgrkhirglpeialppleeeieliealaakkkvvg 160
                                    +a++ee+p++i+v GQgsL+hp+++g ++++L   +P++ +L+h+pgrkh++g+pe+++pple+ ++l+e +++++ v++
  gi|119720442|ref|YP_920937.1| 224 RAYSEEKPKVIVVPGQGSLLHPVFPG-SYEILNLLKPEVTILHHAPGRKHLDGFPEYPVPPLEKFLKLVEIITDRR-VFA 301
                                    **************************.************************************************9.*** PP

                        DUF1611 161 islNtknlseeeakealeeleeelglpvvdpvregaeklv 200
                                    i+l t+ lse+e+ ++ e+le+elg+pvv p+ eg+ ++v
  gi|119720442|ref|YP_920937.1| 302 ITLSTEGLSEREVLAEREKLEKELGIPVVVPMIEGVGRIV 341
                                    ************************************9986 PP

>> DUF1611_N  Domain of unknown function (DUF1611_N) Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.6   0.0   2.3e-35   6.7e-32       2      93 ..      41     136 ..      40     137 .. 0.98

  Alignments for each domain:
  == domain 1  score: 109.6 bits;  conditional E-value: 2.3e-35
                      DUF1611_N   2 ekaGkdagelldd..rgipvvssleea..laagaevlviGiapeggklpeswreavkeAleaGldvvsGlHerLsddpel 77 
                                    ++aG+dage+ld+  rgi+++ssleea  +++g++ l+iG+a++gg+lp+s+re+vkeAl++G++vvsGlHe+Lsddpel
  gi|119720442|ref|YP_920937.1|  41 TLAGRDAGEVLDGkpRGIKIYSSLEEAlkEHPGVKFLIIGVATPGGRLPPSYREVVKEALKRGISVVSGLHEFLSDDPEL 120
                                    689*********99****************************************************************** PP

                      DUF1611_N  78 aalakkkgvkiiDvRk 93 
                                    +++a+++g++iiDvRk
  gi|119720442|ref|YP_920937.1| 121 SRIARETGAEIIDVRK 136
                                    ***************8 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   1.1e-05     0.033      13      97 ..      19     109 ..      17     132 .. 0.77
   2 ?   -1.1   0.4      0.65   1.9e+03       2      22 ..     156     177 ..     155     234 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.1e-05
                                    HHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEBSSHHHHHHH....-SEEEE-S-HH.....HHHHH CS
                         DapB_N  13 Gkevvkaveeaedlelvaavdrkeselegkdagellglgklgvavtddleevlek....advliDFTtpe.....avlen 83 
                                    Gk+   +v+++ ++++v+++d++   l g+dage+l+ ++ g++++++lee+l++       +i   tp      +  e+
  gi|119720442|ref|YP_920937.1|  19 GKTAHGLVRKSLRYKIVGVIDST---LAGRDAGEVLDGKPRGIKIYSSLEEALKEhpgvKFLIIGVATPGgrlppSYREV 95 
                                    7777888999999********97...59*************************996553336777777651111145677 PP

                                    HHHHHHTT-EEEE- CS
                         DapB_N  84 lklalekgvklViG 97 
                                    +k al++g+++V G
  gi|119720442|ref|YP_920937.1|  96 VKEALKRGISVVSG 109
                                    88888888888876 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.65
                                    EEEEETTTSHHHHH.HHHHHHH CS
                         DapB_N   2 kvavvGasGrmGke.vvkavee 22 
                                    kv+v+G    +Gk+ v+++v++
  gi|119720442|ref|YP_920937.1| 156 KVVVIGTDSAVGKRtVAHMVTD 177
                                    6677777666665413334433 PP

>> DUF498  Protein of unknown function (DUF498/DUF598)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.011        33      43      82 ..      64     106 ..       7     108 .. 0.76
   2 ?    7.7   0.0    0.0012       3.6      51      88 ..     153     192 ..     122     198 .. 0.84
   3 ?   -2.7   0.0         2     6e+03      50      77 ..     228     256 ..     211     265 .. 0.60

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.011
                                    HHHHCT..T..SEEEEE-TTS-----H...HHHHHHHCCTSEE CS
                         DUF498  43 lellellepkpellilGtGkrqlplsp...evrealnelgigv 82 
                                    le++   +p + +li+G+ +   +l+p   ev++   ++gi+v
  gi|119720442|ref|YP_920937.1|  64 LEEALKEHPGVKFLIIGVATPGGRLPPsyrEVVKEALKRGISV 106
                                    44444457899*******9997777772334444455566665 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0012
                                    T..SEEEEE-TTS..-----HHHHHHHHCCTSEEEEE-HH CS
                         DUF498  51 pkpellilGtGkr..qlplspevrealnelgigvevmdtr 88 
                                    + + ++++Gt +    + +   v++ ln++gi+  +  t+
  gi|119720442|ref|YP_920937.1| 153 KALKVVVIGTDSAvgKRTVAHMVTDELNARGIKAVFVGTG 192
                                    34799********999****************98877766 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 2
                                    .T..SEEEE.E-TTS-----HHHHHHHHC CS
                         DUF498  50 epkpellil.GtGkrqlplspevrealne 77 
                                    e+kp ++++ G G+ ++p+ p   e ln 
  gi|119720442|ref|YP_920937.1| 228 EEKPKVIVVpGQGSLLHPVFPGSYEILNL 256
                                    56666665546666666665555555554 PP

>> DUF150_C  RimP C-terminal SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.3     3e-05     0.089      17      54 ..     134     170 ..     125     179 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3e-05
                       DUF150_C  17 vklklpvegrkkftGkivevdeetitlevdgkkrkket 54 
                                    v+ k+ ++ rk +tGki+ev++ +++++ ++ + +k+t
  gi|119720442|ref|YP_920937.1| 134 VR-KIYYNTRKFYTGKIKEVKALKVVVIGTDSAVGKRT 170
                                    55.66789****************99988888777766 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00019      0.56       3      36 ..     157     190 ..     156     212 .. 0.85
   2 ?   -0.7   0.0      0.35   1.1e+03      89     117 ..     219     249 ..     206     263 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00019
                         AAA_26   3 ifvtgtdtgvGKTvvslgLvralkrkgvkvgyfK 36 
                                    ++v+gtd  vGK +v+ ++++ l+++g+k+ ++ 
  gi|119720442|ref|YP_920937.1| 157 VVVIGTDSAVGKRTVAHMVTDELNARGIKAVFVG 190
                                    79***************************99875 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.35
                         AAA_26  89 ekiv..kelekdadivvVEGagglgvpitee 117
                                    e++v     e++ +++vV G g+l+ p++ +
  gi|119720442|ref|YP_920937.1| 219 EDVVwrAYSEEKPKVIVVPGQGSLLHPVFPG 249
                                    555555456677899*********9999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2394.22
//
Query:       gi|119720443|ref|YP_920938.1|  [L=484]
Description: hypothetical protein Tpen_1539 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (484 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 3245.50
//
Query:       gi|119720444|ref|YP_920939.1|  [L=170]
Description: hypothetical protein Tpen_1540 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-05   23.7   0.9    3.8e-05   23.1   0.9    1.6  1  YdjM      LexA-binding, inner membrane-associated putative hy
  ------ inclusion threshold ------
          2    8.1   7.0        6.4    6.4   7.0    1.8  1  DUF4184   Domain of unknown function (DUF4184)


Domain annotation for each model (and alignments):
>> YdjM  LexA-binding, inner membrane-associated putative hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.9   4.2e-09   3.8e-05      68     127 ..      52     128 ..       1     165 [. 0.84

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 4.2e-09
                           YdjM  68 gftHSllflallalvlllllrlfgrsa.................lrlglllllgvlsHlllDlltkyGvpllwPfsk 127
                                    g  H++ ++all+l l ll++  ++                     ++++ +lg+ +H+llD+     ++ l+P   
  gi|119720444|ref|YP_920939.1|  52 GYLHTFAGAALLGLCLGLLMHATEKVLgnawkrallegsrsvgfEGFAVAGILGCTVHVLLDSPLYPDIRPLYPYAA 128
                                    789*********************9989*************9887777889999********************964 PP

>> DUF4184  Domain of unknown function (DUF4184)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   7.0   0.00071       6.4       1     121 [.       1     114 [.       1     115 [. 0.58

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.00071
                        DUF4184   1 MPfTlsHpaavlplkllkrkrlslsaLviGslaPDveyf......lrlkakstltHtllglllvdlplalllalvfhlvi 74 
                                    MPfT  H+  +l + l  r+r++ +  ++ s+a Dve +      l   + + + Ht++g+ l+ l l+l    ++h++ 
  gi|119720444|ref|YP_920939.1|   1 MPFTPFHLGPALAVGLPLRERIHAPTFILASIAVDVEPLvvlvlgL-DYPLHGYLHTFAGAALLGLCLGL----LMHATE 75 
                                    *******65555555577*******************995444221.12334455666666555555555....555432 PP

                        DUF4184  75 kkpllallPaalarrlkksaerkslkallvvvvsaliGaatHvlwDs 121
                                    k  l     +a +r      e ++   +  ++v+ ++G + Hvl+Ds
  gi|119720444|ref|YP_920939.1|  76 K-VL----GNAWKRA---LLEGSRSVGFEGFAVAGILGCTVHVLLDS 114
                                    2.22....2222222...11123334456677777777777777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      199  (0.0110993); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 1169.02
//
Query:       gi|119720445|ref|YP_920940.1|  [L=548]
Description: ABC transporter related [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-57  193.8   0.0    6.2e-28   98.0   0.0    2.3  2  ABC_tran         ABC transporter
    1.9e-11   44.3   0.5     0.0033   17.3   0.0    4.1  4  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    1.4e-10   40.7   0.3    1.1e-05   25.0   0.0    2.4  2  AAA_29           P-loop containing region of AAA domain
    4.7e-10   39.3   0.4    2.3e-06   27.2   0.2    3.5  3  SMC_N            RecF/RecN/SMC N terminal domain
    1.8e-07   31.7   0.1      0.005   17.2   0.2    2.6  2  AAA_16           AAA ATPase domain
      2e-07   31.1   0.1     0.0064   16.4   0.0    2.5  2  RsgA_GTPase      RsgA GTPase
    1.2e-05   25.9   0.0      0.014   15.9   0.0    2.3  2  AAA_23           AAA domain
    3.3e-05   23.5   0.4      0.062   12.9   0.0    3.0  3  AAA_25           AAA domain
    5.1e-05   23.1   0.1     0.0088   15.8   0.0    2.4  2  AAA_30           AAA domain
    5.9e-05   22.6   0.2       0.21   10.9   0.0    2.3  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    6.4e-05   22.2   0.1      0.007   15.6   0.0    2.2  2  DUF815           Protein of unknown function (DUF815)
      7e-05   22.2   0.3      0.056   12.7   0.0    2.4  2  Zeta_toxin       Zeta toxin
    0.00018   21.6   1.0       0.23   11.6   0.4    2.8  2  MMR_HSR1         50S ribosome-binding GTPase
    0.00022   21.1   0.0      0.084   12.6   0.0    2.4  2  AAA_15           AAA ATPase domain
    0.00029   20.9   1.1       0.72    9.9   0.1    2.8  2  AAA_5            AAA domain (dynein-related subfamily)
    0.00033   20.9   0.0       0.27   11.5   0.0    2.6  2  AAA_22           AAA domain
    0.00047   20.1   0.6        0.1   12.5   0.0    2.3  2  NACHT            NACHT domain
     0.0005   20.6   1.0       0.62   10.6   0.0    3.3  3  AAA_18           AAA domain
    0.00063   19.9   0.1        1.2    9.4   0.0    3.2  2  SbcCD_C          Putative exonuclease SbcCD, C subunit
    0.00066   18.8   0.0       0.12   11.4   0.0    2.5  2  T2SSE            Type II/IV secretion system protein
    0.00069   18.9   0.5      0.026   13.7   0.0    2.4  2  NB-ARC           NB-ARC domain
    0.00069   19.4   0.9       0.92    9.2   0.0    2.9  3  AAA_24           AAA domain
    0.00074   18.8   0.0       0.12   11.5   0.0    2.1  2  G-alpha          G-protein alpha subunit
     0.0022   18.2   0.9       0.77    9.9   0.1    3.0  3  AAA_33           AAA domain
     0.0026   17.8   0.2        1.4    8.9   0.0    2.4  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
     0.0027   17.2   0.2          2    7.9   0.0    2.3  2  AAA_7            P-loop containing dynein motor region
     0.0027   17.4   0.1        7.3    6.3   0.0    3.2  3  IstB_IS21        IstB-like ATP binding protein
     0.0051   16.9   0.6       0.53   10.3   0.0    2.5  2  DUF87            Helicase HerA, central domain
     0.0058   17.0   0.1          5    7.6   0.0    2.5  2  RNA_helicase     RNA helicase
     0.0061   16.5   2.3       0.54   10.2   0.1    2.9  2  NTPase_1         NTPase
     0.0099   14.6   0.1        4.6    5.8   0.0    3.6  4  AAA_13           AAA domain
  ------ inclusion threshold ------
      0.012   15.4   0.2        5.5    6.7   0.0    2.3  2  Sigma54_activat  Sigma-54 interaction domain
      0.012   15.5   0.1       0.38   10.6   0.1    2.6  2  CPT              Chloramphenicol phosphotransferase-like prot
      0.012   15.2   1.7        4.5    6.8   0.1    3.4  3  SRP54            SRP54-type protein, GTPase domain
      0.012   16.0   1.5        5.8    7.3   0.1    3.3  3  AAA              ATPase family associated with various cellul
      0.015   14.7   0.4        0.5    9.7   0.1    2.4  2  FtsK_SpoIIIE     FtsK/SpoIIIE family
       0.02   14.8   0.3        1.2    9.0   0.0    2.5  2  APS_kinase       Adenylylsulphate kinase
      0.023   14.4   0.1        1.2    8.9   0.0    2.4  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
      0.024   14.0   0.2        5.4    6.3   0.0    2.4  2  Gtr1_RagA        Gtr1/RagA G protein conserved region
      0.026   13.6   0.1       0.27   10.3   0.0    2.1  2  MCM              MCM P-loop domain
      0.028   13.4   0.1        4.7    6.1   0.0    2.4  2  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
      0.029   13.9   0.5        0.8    9.1   0.2    2.4  2  KdpD             Osmosensitive K+ channel His kinase sensor d
       0.03   13.9   0.3        3.2    7.3   0.0    2.3  2  AAA_27           AAA domain
       0.04   13.0   0.0      0.068   12.3   0.0    1.3  1  Propeptide_C25   Propeptide_C25
      0.043   13.2   1.1        5.6    6.2   0.1    2.6  3  ATPase           KaiC
      0.052   13.5   0.1       0.33   10.8   0.0    2.2  2  Rad17            Rad17 P-loop domain
      0.086   13.1   0.2         14    5.9   0.0    2.4  2  Roc              Ras of Complex, Roc, domain of DAPkinase
      0.087   11.6   0.2        0.3    9.9   0.0    1.9  2  ABC_ATPase       Predicted ATPase of the ABC class
      0.087   12.0   0.0        2.1    7.4   0.0    2.2  2  PIF1             PIF1-like helicase
       0.09   11.7   0.1        1.5    7.7   0.0    2.2  2  AAA_10           AAA-like domain
       0.13   11.2   0.3        1.9    7.3   0.0    2.4  3  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
       0.13   12.1   0.4         11    5.9   0.0    2.6  2  MobB             Molybdopterin guanine dinucleotide synthesis
       0.45   10.8   2.2         36    4.5   0.1    3.3  3  AAA_28           AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.0   0.0   1.8e-30   6.2e-28       1     136 [.      33     183 ..      33     184 .. 0.95
   2 !   93.7   0.0   3.9e-29   1.3e-26       1     137 []     296     442 ..     296     442 .. 0.92

  Alignments for each domain:
  == domain 1  score: 98.0 bits;  conditional E-value: 1.8e-30
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--.....SEEEEEETTCEGGGB-HHHCCHCEEEE-SS..--S-TT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxx RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp.....teGeilldgkdlkeqeleslrkeigvlpqe..pqlfpe 73 
                                    l+nvsl++ +ge+v + G++G+GKStLlk++ gl         +G ++++g  + e++  +l++ +g++ qe  +qlf  
  gi|119720445|ref|YP_920940.1|  33 LRNVSLEVDKGEVVLLAGRSGSGKSTLLKAINGLIPHrysgtYKGAVRVRGLTVAETPVYELSRIVGTVMQEvsKQLFLP 112
                                    78********************************9889999999****************************87777777 PP

                                    SBHHHH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    xxxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  74 ltvren.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                    + v++              e ++++e+als+lg+ +lkd+ v    ++LSgG+kqrva+a +l+ kp+++l+DEp 
  gi|119720445|ref|YP_920940.1| 113 T-VADDvafgpsnlciereEIERRVEEALSRLGILHLKDRDV----NELSGGEKQRVAIAGVLAMKPEIILMDEPL 183
                                    7.77777***********999999******************....*****************************7 PP

  == domain 2  score: 93.7 bits;  conditional E-value: 3.9e-29
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS..--S-TTSBHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxx RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe..pqlfpeltvre 78 
                                    lk ++l+++ege+va++G+nGaGKSt++kl++gllkpteG++l+ g+d+++ e  ++   +g ++q+  + lf e+ vre
  gi|119720445|ref|YP_920940.1| 296 LKGINLEIREGERVALLGNNGAGKSTMAKLMLGLLKPTEGSVLVYGRDTHTMEVYEVAPMVGLVFQDpfSMLFAET-VRE 374
                                    789************************************************999*************866777777.999 PP

                                    H.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    x.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  79 n.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                    +             e   ++e+a+++   k+l d          S+G+k+r+++a +l  kp++l+lDEpta
  gi|119720445|ref|YP_920940.1| 375 EiafgprnlgvppsEIPGRVEEAAERCFVKHLLDFSP----FASSHGEKKRICVASILSMKPRILVLDEPTA 442
                                    9******999888777788888888888888777776....9****************************97 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   9.8e-06    0.0033       2      35 ..      46      76 ..      45     101 .. 0.84
   2 !    7.9   0.0    0.0071       2.4     228     294 ..     147     210 ..     102     213 .. 0.78
   3 ?    5.4   0.0      0.04        13       3      22 ..     310     329 ..     309     352 .. 0.83
   4 !    9.1   0.0     0.003         1     231     301 ..     408     477 ..     384     480 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 9.8e-06
                         AAA_21  2 nvliGpNgsGKSnLLdaldllarldrdvegltde 35
                                    +l G+ gsGKS+LL+a+ +l   +++  ++t++
  gi|119720445|ref|YP_920940.1| 46 VLLAGRSGSGKSTLLKAINGL---IPHRYSGTYK 76
                                   6899****************9...6666666555 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0071
                         AAA_21 228 dgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQvil 294
                                    + ++++++elS G k+  a++  l+  +    ++l DEp ++L+ + ++++ e++k+ +++g  v++
  gi|119720445|ref|YP_920940.1| 147 HLKDRDVNELSGGEKQRVAIAGVLAMKP---EIILMDEPLANLDSEGVATVQEVIKSFREEGKTVVI 210
                                    667788999****************988...9***********997777777777777776666665 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.04
                         AAA_21   3 vliGpNgsGKSnLLdaldll 22 
                                    +l G Ng+GKS+  +++ +l
  gi|119720445|ref|YP_920940.1| 310 ALLGNNGAGKSTMAKLMLGL 329
                                    799********988777766 PP

  == domain 4  score: 9.1 bits;  conditional E-value: 0.003
                         AAA_21 231 elparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr..ngaQviltTHSpll 301
                                    +++++  S G k+ ++++++l   +   ++l++DEp +g +++  + ++e++++l +      ++l TH++ l
  gi|119720445|ref|YP_920940.1| 408 DFSPFASSHGEKKRICVASILSMKP---RILVLDEPTAGQDYATYTAFMEFVDSLVNagVIKTLVLITHDTDL 477
                                    5566666777877767777777655...************************666665333677999999765 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   3.3e-08   1.1e-05      15      45 ..      36      66 ..      32      75 .. 0.84
   2 !   13.4   0.1   0.00014     0.047      17      41 ..     301     325 ..     295     337 .. 0.75

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 3.3e-08
                         AAA_29 15 htieidlkgatlltGpsGsGKSTllDAiqal 45
                                    ++e+d  +++ll+G+sGsGKSTll Ai+ l
  gi|119720445|ref|YP_920940.1| 36 VSLEVDKGEVVLLAGRSGSGKSTLLKAINGL 66
                                   567888666******************9866 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00014
                         AAA_29  17 ieidlkgatlltGpsGsGKSTllDA 41 
                                    +ei++ + + l G++G+GKST+   
  gi|119720445|ref|YP_920940.1| 301 LEIREGERVALLGNNGAGKSTMAKL 325
                                    5676555999***********9655 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.2   6.7e-09   2.3e-06      25     197 ..      44     212 ..      32     232 .. 0.73
   2 ?    5.7   0.0     0.026       8.9      27      43 ..     309     325 ..     292     377 .. 0.87
   3 ?   -2.0   0.0       5.7   1.9e+03     138     187 ..     415     460 ..     391     485 .. 0.76

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 6.7e-09
                                    SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrrvk 104
                                    ++  + G+ GSGKs ll Ai  ++ +r + + + +   + ++  +e +  +  ++  t+ +e +k    +  + +    +
  gi|119720445|ref|YP_920940.1|  44 EVVLLAGRSGSGKSTLLKAINGLIPHRYSGTYKGAVRVRGLTV-AETPVYELSRIVGTVMQEVSK----QLFLPTVADDV 118
                                    356788**************99999998878887655444444.466777777766665444444....22334444555 PP

                                    TTSEEEEEETTEEE-HHHHHHHHHCTT-STT......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 105 rkgeseykingkevtkkevsellesagiske......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkk 178
                                      g s+  i+++e+++  v+e l++ gi         +LSgGek+ va+a ++A++   p+ + l+De  a+LD + v+ 
  gi|119720445|ref|YP_920940.1| 119 AFGPSNLCIEREEIER-RVEEALSRLGILHLkdrdvnELSGGEKQRVAIAGVLAMK---PE-IILMDEPLANLDSEGVAT 193
                                    6677899999988865.67888888777543334444**************99975...44.889*************** PP

                                    HHHHHHHHCTTSEEEEE-S CS
                                    xxxxxxxxxxxxxxxxxxx RF
                          SMC_N 179 vaellkeksknaQfivisl 197
                                    v e++k+ +++   +vi+ 
  gi|119720445|ref|YP_920940.1| 194 VQEVIKSFREEGKTVVIAE 212
                                    **********999999874 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.026
                                    EEEEESTTSSHHHHHHH CS
                                    xxxxxxxxxxxxxxxxx RF
                          SMC_N  27 taivGpNGSGKsnlldA 43 
                                     a++G+NG+GKs +   
  gi|119720445|ref|YP_920940.1| 309 VALLGNNGAGKSTMAKL 325
                                    5899********98765 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 5.7
                                    -HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 138 SgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeks 187
                                    S Gek+ + +a +++   +kp+ + +lDe  a  D +  +++ e++++  
  gi|119720445|ref|YP_920940.1| 415 SHGEKKRICVASILS---MKPR-ILVLDEPTAGQDYATYTAFMEFVDSLV 460
                                    678887777776654...5555.668899999888888888888877655 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.2   1.5e-05     0.005      21      88 ..      42     112 ..      32     213 .. 0.59
   2 !   11.8   0.0   0.00071      0.24      24      72 ..     306     358 ..     299     440 .. 0.61

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.5e-05
                         AAA_16  21 sgrpelvllsGesGvGKsslvrellralekd......ggif.lrgkcdqlesaipy...salaqalareellrqllde 88 
                                    +g  e+vll G sG+GKs+l++++   +  +      g  + +rg ++     +p    s ++ +  + e+ +ql  +
  gi|119720445|ref|YP_920940.1|  42 KG--EVVLLAGRSGSGKSTLLKAINGLIPHRysgtykG-AVrVRGLTVAE---TPVyelSRIVGTVMQ-EVSKQLFLP 112
                                    33..89***************99997777665444431.22233333333...444232444444434.555555555 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00071
                         AAA_16  24 pelvllsGesGvGKsslvrellralekdggif.lrgkcdqlesa....ipysal 72 
                                    +e v l G+ G GKs++++  l  l+ ++g + ++g+ ++  ++    +p++ l
  gi|119720445|ref|YP_920940.1| 306 GERVALLGNNGAGKSTMAKLMLGLLKPTEGSVlVYGRDTHT-MEvyevAPMVGL 358
                                    47899*****************9999887555488887776.333344444332 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.9e-05    0.0064      94     121 ..      37      65 ..      15      85 .. 0.80
   2 !   12.0   0.0   0.00044      0.15      80     131 ..     286     338 ..     275     363 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.9e-05
                                    HHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                    RsgA_GTPase  94 kellkd.ktsvlvGqSGvGKStLinallp 121
                                    + ++++ ++++l+G SG GKStL++a+++
  gi|119720445|ref|YP_920940.1|  37 SLEVDKgEVVLLAGRSGSGKSTLLKAING 65 
                                    445555599**************999876 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00044
                                    EE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S--- CS
                    RsgA_GTPase  80 llvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallpelelktgevs 131
                                    +  s ++k  l+ ++ ++++ + ++l+G+ G+GKSt+ + +l+ l+   g+v 
  gi|119720445|ref|YP_920940.1| 286 VSFSYEDKPVLKGINLEIREgERVALLGNNGAGKSTMAKLMLGLLKPTEGSVL 338
                                    56667777778888888888799**************9999887666555554 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   4.3e-05     0.014      11      40 ..      34      64 ..      28      85 .. 0.84
   2 ?    7.7   0.0     0.014       4.7      23      36 ..     310     323 ..     289     330 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.3e-05
                         AAA_23 11 rdqeidFsk.gltlItGpNGaGKTTildAik 40
                                   r+++++ +k  ++l+ G  G+GK+T+l Ai 
  gi|119720445|ref|YP_920940.1| 34 RNVSLEVDKgEVVLLAGRSGSGKSTLLKAIN 64
                                   6667777663599*****************7 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.014
                         AAA_23  23 lItGpNGaGKTTil 36 
                                    ++ G+NGaGK+T  
  gi|119720445|ref|YP_920940.1| 310 ALLGNNGAGKSTMA 323
                                    678*********75 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   0.00018     0.062      30      50 ..      40      60 ..      16      63 .. 0.87
   2 ?   -0.9   0.0       3.1     1e+03      82     117 ..     128     179 ..     124     210 .. 0.54
   3 ?    7.0   0.0     0.012       3.9      30      50 ..     303     323 ..     281     340 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00018
                         AAA_25 30 lpagelallaGapgtGKttla 50
                                   + +ge++llaG++g+GK+tl+
  gi|119720445|ref|YP_920940.1| 40 VDKGEVVLLAGRSGSGKSTLL 60
                                   479****************97 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 3.1
                         AAA_25  82 sedelrrRlravgeal...............rddarllvldlagv.eslpLf 117
                                     ++e++rR+++++  l                +++r+++  +  +  ++ L+
  gi|119720445|ref|YP_920940.1| 128 EREEIERRVEEALSRLgilhlkdrdvnelsgGEKQRVAIAGVLAMkPEIILM 179
                                    6778999999998887777777766666666555555555544444444443 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.012
                         AAA_25  30 lpagelallaGapgtGKttla 50 
                                    +++ge ++l G  g+GK+t+a
  gi|119720445|ref|YP_920940.1| 303 IREGERVALLGNNGAGKSTMA 323
                                    679****************98 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   2.6e-05    0.0088      17      75 ..      42     107 ..      34     135 .. 0.80
   2 ?    4.6   0.0     0.069        23      21      52 ..     309     340 ..     301     353 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.6e-05
                         AAA_30  17 gdrvavltGpAGtGKttalkalreaweaa.g......grviglAptgkaAkvLaeelgieastiak 75 
                                    +  v++l G+ G+GK+t+lka++ ++ ++         rv gl+  ++   +L++ +g+  + + k
  gi|119720445|ref|YP_920940.1|  42 KGEVVLLAGRSGSGKSTLLKAINGLIPHRySgtykgaVRVRGLTVAETPVYELSRIVGTVMQEVSK 107
                                    44699*******************999885368888888888888888888888777766655555 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.069
                         AAA_30  21 avltGpAGtGKttalkalreaweaaggrvigl 52 
                                    ++l G  G+GK+t+ k +  +++  +g+v+++
  gi|119720445|ref|YP_920940.1| 309 VALLGNNGAGKSTMAKLMLGLLKPTEGSVLVY 340
                                    6788**********999888888776677665 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   0.00062      0.21      24      49 ..      45      70 ..      29      90 .. 0.84
   2 !    9.3   0.0     0.002      0.69      24      51 ..     308     335 ..     296     368 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00062
                   Mg_chelatase 24 nlllvGppGsGKtmlakrlpsllppl 49
                                    +ll+G +GsGK+ l k++++l+p+ 
  gi|119720445|ref|YP_920940.1| 45 VVLLAGRSGSGKSTLLKAINGLIPHR 70
                                   689********************975 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.002
                   Mg_chelatase  24 nlllvGppGsGKtmlakrlpsllpplse 51 
                                     + l+G+ G+GK+ +ak + +ll p + 
  gi|119720445|ref|YP_920940.1| 308 RVALLGNNGAGKSTMAKLMLGLLKPTEG 335
                                    67899******************98765 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   2.1e-05     0.007      52     120 ..      42     122 ..      32     128 .. 0.79
   2 ?    4.3   0.1     0.058        20      54      75 ..     307     328 ..     300     342 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.1e-05
                         DUF815  52 pannvLLwGarGtGKSslvkallneyaeeg.........Lrlievekedlkelpklvellrerperfil...fvDDLsFe 119
                                    + + vLL G  G+GKS+l+ka+   + ++          +r + v+++ + el+++v ++ ++  + +    + DD++F 
  gi|119720445|ref|YP_920940.1|  42 KGEVVLLAGRSGSGKSTLLKAINGLIPHRYsgtykgavrVRGLTVAETPVYELSRIVGTVMQEVSKQLFlptVADDVAFG 121
                                    56679****************98766666566678998888899999**********99987655544313368999997 PP

                         DUF815 120 e 120
                                     
  gi|119720445|ref|YP_920940.1| 122 P 122
                                    5 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.058
                         DUF815  54 nnvLLwGarGtGKSslvkalln 75 
                                    + v L G+ G+GKS++ k +l 
  gi|119720445|ref|YP_920940.1| 307 ERVALLGNNGAGKSTMAKLMLG 328
                                    67889***********998875 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   0.00017     0.056      14      39 ..      41      66 ..      32      83 .. 0.77
   2 !    7.0   0.0    0.0091       3.1      21      51 ..     311     341 ..     303     348 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00017
                     Zeta_toxin 14 erPklillgGqpGAGKselaellkde 39
                                   ++  ++ll+G +G+GKs+l+++++  
  gi|119720445|ref|YP_920940.1| 41 DKGEVVLLAGRSGSGKSTLLKAINGL 66
                                   56679****************99765 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0091
                     Zeta_toxin  21 lgGqpGAGKselaellkdelerqgnvvrldp 51 
                                    l G  GAGKs++a+l+   l+++++ v +++
  gi|119720445|ref|YP_920940.1| 311 LLGNNGAGKSTMAKLMLGLLKPTEGSVLVYG 341
                                    6699*************99997777776654 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.4   0.00068      0.23       2      21 ..      46      65 ..      45     210 .. 0.87
   2 !    8.0   0.0    0.0087         3       1      22 [.     308     329 ..     308     362 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00068
                                   EEEEESTTSSHHHHHHHHHT CS
                       MMR_HSR1  2 vaivGrpNvGKStLinaltg 21
                                   v+++Gr+ +GKStL++a+ g
  gi|119720445|ref|YP_920940.1| 46 VLLAGRSGSGKSTLLKAING 65
                                   789**************976 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0087
                                    EEEEEESTTSSHHHHHHHHHTS CS
                       MMR_HSR1   1 evaivGrpNvGKStLinaltge 22 
                                    +va++G+  +GKSt+ + ++g 
  gi|119720445|ref|YP_920940.1| 308 RVALLGNNGAGKSTMAKLMLGL 329
                                    69*************9999873 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   0.00025     0.084      14      46 ..      33      66 ..      32     117 .. 0.90
   2 ?    5.9   0.0     0.026       8.6      25      50 ..     308     333 ..     296     368 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00025
                         AAA_15 14 lkdveidlsee.ltvliGkNnsGKSsilealdlF 46
                                   l++v++++++  + +l G+ +sGKS++l+a++ +
  gi|119720445|ref|YP_920940.1| 33 LRNVSLEVDKGeVVLLAGRSGSGKSTLLKAINGL 66
                                   789999999988*******************866 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.026
                         AAA_15  25 ltvliGkNnsGKSsilealdlFlnnk 50 
                                       l G N++GKS+ ++++  +l+ +
  gi|119720445|ref|YP_920940.1| 308 RVALLGNNGAGKSTMAKLMLGLLKPT 333
                                    56899************998888765 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.1    0.0043       1.4       2      25 ..      46      69 ..      45      77 .. 0.85
   2 !    9.9   0.1    0.0021      0.72       2      36 ..     309     344 ..     308     352 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0043
                                   EEEE--SSSSHHHHHHHGGGGBS- CS
                          AAA_5  2 vlLvGppGtgKselaerlaaalnr 25
                                   vlL G +G+gKs+l + +  ++  
  gi|119720445|ref|YP_920940.1| 46 VLLAGRSGSGKSTLLKAINGLIPH 69
                                   89**************99988844 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0021
                                    EEEE--SSSSHHHHHHHGGGGB.S--EEEEE--TT- CS
                          AAA_5   2 vlLvGppGtgKselaerlaaal.nreveyvqltrdt 36 
                                    v L+G+ G gKs++a+ ++ +l  +e  +    rdt
  gi|119720445|ref|YP_920940.1| 309 VALLGNNGAGKSTMAKLMLGLLkPTEGSVLVYGRDT 344
                                    679******************985555555555555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   0.00079      0.27       5      36 ..      43      74 ..      39     181 .. 0.79
   2 ?    6.8   0.0     0.023       7.7       9      30 ..     310     331 ..     304     410 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00079
                         AAA_22  5 agilvvtGesGtGKTtllrrlleqldeeakae 36
                                     ++++ G sG+GK+tll+ +    + +++ +
  gi|119720445|ref|YP_920940.1| 43 GEVVLLAGRSGSGKSTLLKAINGLIPHRYSGT 74
                                   567899*************9887766555554 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.023
                         AAA_22   9 vvtGesGtGKTtllrrlleqld 30 
                                    ++ G  G+GK+t ++ +l  l+
  gi|119720445|ref|YP_920940.1| 310 ALLGNNGAGKSTMAKLMLGLLK 331
                                    688************9998874 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0    0.0003       0.1       2      21 ..      45      64 ..      44      76 .. 0.86
   2 ?    5.7   0.1     0.037        13       2      19 ..     308     325 ..     307     339 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.0003
                                   CEEEEC-TTTCHHHHHHHHH CS
                          NACHT  2 lvilqGeaGsGKTtLlqkla 21
                                   +v+l G++GsGK+tLl+ + 
  gi|119720445|ref|YP_920940.1| 45 VVLLAGRSGSGKSTLLKAIN 64
                                   799**************986 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.037
                                    CEEEEC-TTTCHHHHHHH CS
                          NACHT   2 lvilqGeaGsGKTtLlqk 19 
                                     v+l G +G GK+t+++ 
  gi|119720445|ref|YP_920940.1| 308 RVALLGNNGAGKSTMAKL 325
                                    689***********8764 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0    0.0018      0.62       1      21 [.      46      66 ..      46     116 .. 0.67
   2 ?    2.8   0.0      0.47   1.6e+02      69      99 ..     199     229 ..     130     241 .. 0.81
   3 ?    4.3   0.1      0.16        55       1      17 [.     309     325 ..     309     358 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0018
                         AAA_18  1 IlltGtpGvGKttlakeLskr 21
                                   +ll+G +G+GK+tl k+++ +
  gi|119720445|ref|YP_920940.1| 46 VLLAGRSGSGKSTLLKAINGL 66
                                   79**************99654 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.47
                         AAA_18  69 s.aleegknlvidghlaeleseaakdikkvvL 99 
                                    +  +eegk++vi  h++e + e  +d++ +v+
  gi|119720445|ref|YP_920940.1| 199 KsFREEGKTVVIAEHRVEEVLEVGVDRV-FVM 229
                                    136789************9999999888.555 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.16
                         AAA_18   1 IlltGtpGvGKttlake 17 
                                    ++l G  G+GK+t+ak 
  gi|119720445|ref|YP_920940.1| 309 VALLGNNGAGKSTMAKL 325
                                    678999*********96 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0    0.0035       1.2      28      88 ..     151     198 ..     141     200 .. 0.75
   2 ?    4.7   0.0       0.1        35      63      88 ..     431     456 ..     414     458 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0035
                        SbcCD_C  28 rssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllell 88 
                                    r++++lSGGekq +a       +a ++        +++++++DE  ++lD+e +at+ e++
  gi|119720445|ref|YP_920940.1| 151 RDVNELSGGEKQRVA-------IAGVLAM------KPEIILMDEPLANLDSEGVATVQEVI 198
                                    788899999995433.......3333334......47899999999999999999887766 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.1
                        SbcCD_C  63 alrlvfLDEAFsklDeesiatllell 88 
                                    ++r+++LDE  ++ D  + ++ +e++
  gi|119720445|ref|YP_920940.1| 431 KPRILVLDEPTAGQDYATYTAFMEFV 456
                                    69*************99999999986 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   0.00035      0.12     120     155 ..      34      69 ..       7      73 .. 0.76
   2 ?    4.8   0.0     0.036        12      79     160 ..     254     337 ..     191     373 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00035
                          T2SSE 120 evlrkavrerglilvsGgTgsGKttllyallkeink 155
                                    + ++  v +  ++l++G  gsGK+tll a+   i++
  gi|119720445|ref|YP_920940.1|  34 RNVSLEVDKGEVVLLAGRSGSGKSTLLKAINGLIPH 69 
                                    455667788899*****************9988876 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.036
                          T2SSE  79 rlrvvllPvvag.ealviR..kksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeink 155
                                      ++ l+P + + +++++   ++ + ++++++++++ ++k  + + ++  +re   + + G  g GK+t++  +l  ++ 
  gi|119720445|ref|YP_920940.1| 254 PAEAYLPPGIVEaPRISLPhhSPGVVAVEFRNVSFSYEDK-PVLKGINLEIREGERVALLGNNGAGKSTMAKLMLGLLKP 332
                                    4466677777666777777334444555667766665554.4666788888999999999************99999998 PP

                          T2SSE 156 sderi 160
                                    ++  +
  gi|119720445|ref|YP_920940.1| 333 TEGSV 337
                                    85544 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   7.7e-05     0.026      21      78 ..      44     107 ..      33     192 .. 0.69
   2 ?    2.9   0.0      0.16        53      23      38 ..     309     324 ..     300     335 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.7e-05
                                    EEEEEEESTTSSHHHHHHHHCCSHCC.CCCCBTEEEEE......................EEESXXHHHHHHHXXHHHHH CS
                         NB-ARC  21 lvvalvGmgGvGKttlakqilnksde.vegrFdsvawv......................vvsktdkseeiletilkeLs 77 
                                     vv l G+ G+GK+tl+k i+    +   g++ + + v                                        +s
  gi|119720445|ref|YP_920940.1|  44 EVVLLAGRSGSGKSTLLKAINGLIPHrYSGTYKGAVRVrgltvaetpvyelsrivgtvmqE-----------------VS 106
                                    4999****************98765415568988888888866555555555555544441.................33 PP

                                    C CS
                         NB-ARC  78 l 78 
                                    +
  gi|119720445|ref|YP_920940.1| 107 K 107
                                    2 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.16
                                    EEEEESTTSSHHHHHH CS
                         NB-ARC  23 valvGmgGvGKttlak 38 
                                    val G  G GK+t+ak
  gi|119720445|ref|YP_920940.1| 309 VALLGNNGAGKSTMAK 324
                                    899***********98 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.1    0.0092       3.1       4      22 ..      45      63 ..      42      80 .. 0.88
   2 !    9.2   0.0    0.0027      0.92       3      26 ..     307     337 ..     305     356 .. 0.76
   3 ?   -1.6   0.0       5.5   1.9e+03      49     131 ..     449     474 ..     427     488 .. 0.62

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0092
                         AAA_24  4 kiliyGpsgiGKTtlakel 22
                                    +l+ G sg+GK+tl+k +
  gi|119720445|ref|YP_920940.1| 45 VVLLAGRSGSGKSTLLKAI 63
                                   789************9976 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0027
                         AAA_24   3 lkiliyGpsgiGKTtlakel.......gpkp 26 
                                     ++++ G +g+GK+t+ak +       + ++
  gi|119720445|ref|YP_920940.1| 307 ERVALLGNNGAGKSTMAKLMlgllkptEGSV 337
                                    5899**************9966655544444 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 5.5
                         AAA_24  49 wedfldevvelaaeladyktlviDtideleelclaevirqnekaeskedkgdgkGygelaeefrrllkklqelrk..nvi 126
                                    +++                                                           f+++++ l +++   + +
  gi|119720445|ref|YP_920940.1| 449 YTA-----------------------------------------------------------FMEFVDSLVNAGVikTLV 469
                                    444...........................................................555555555555555555 PP

                         AAA_24 127 fiahe 131
                                    +i h 
  gi|119720445|ref|YP_920940.1| 470 LITHD 474
                                    55554 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0   0.00036      0.12      25      48 ..      45      68 ..      30     167 .. 0.85
   2 ?    5.2   0.0     0.028       9.6      25      48 ..     308     331 ..     291     349 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00036
                                   EEEEEESTTSSHHHHHHHHHHHCS CS
                        G-alpha 25 kllllGqseSGKsTilkqlkllyk 48
                                    +ll G s+SGKsT+lk +  l  
  gi|119720445|ref|YP_920940.1| 45 VVLLAGRSGSGKSTLLKAINGLIP 68
                                   389**************9985544 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.028
                                    EEEEEESTTSSHHHHHHHHHHHCS CS
                        G-alpha  25 kllllGqseSGKsTilkqlkllyk 48 
                                    ++ llG+++ GKsT+ k +  l k
  gi|119720445|ref|YP_920940.1| 308 RVALLGNNGAGKSTMAKLMLGLLK 331
                                    799************998875554 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.1    0.0023      0.77       1      18 [.      45      62 ..      45      94 .. 0.90
   2 ?   -1.3   0.0       6.7   2.3e+03      75     101 ..     227     257 ..     190     260 .. 0.69
   3 ?    5.4   0.0     0.055        19       3      21 ..     310     328 ..     309     355 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0023
                         AAA_33  1 lvllvGlpGsGKstlaer 18
                                   +vll G +GsGKstl++ 
  gi|119720445|ref|YP_920940.1| 45 VVLLAGRSGSGKSTLLKA 62
                                   89*************986 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 6.7
                         AAA_33  75 l...datnlsr.rerarflklarrlgvpvri 101
                                    +     t +++ ++ +++ ++a +l+vp ++
  gi|119720445|ref|YP_920940.1| 227 FvmrEGTIVREvERVEELANFADELKVPAEA 257
                                    3334678888845558999999999998776 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.055
                         AAA_33   3 llvGlpGsGKstlaerllk 21 
                                     l G +G+GKst a+ +l 
  gi|119720445|ref|YP_920940.1| 310 ALLGNNGAGKSTMAKLMLG 328
                                    57799*********98764 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0    0.0041       1.4      15      40 ..      41      64 ..      28      76 .. 0.77
   2 ?    6.3   0.1     0.028       9.3      19      41 ..     306     328 ..     291     337 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0041
                                   HHCHTEEEEEEESTTSSHHHHHHHHH CS
                           TsaE 15 akalgdvilLeGdLGaGKTtlvrgla 40
                                    k  g+v+lL G  G+GK+tl +++ 
  gi|119720445|ref|YP_920940.1| 41 DK--GEVVLLAGRSGSGKSTLLKAIN 64
                                   33..889***************9985 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.028
                                    TEEEEEEESTTSSHHHHHHHHHH CS
                           TsaE  19 gdvilLeGdLGaGKTtlvrglak 41 
                                    g+ ++L G+ GaGK+t+++ ++ 
  gi|119720445|ref|YP_920940.1| 306 GERVALLGNNGAGKSTMAKLMLG 328
                                    6679**************98875 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0     0.006         2      30      54 ..      40      64 ..      35     115 .. 0.87
   2 ?    7.1   0.0      0.01       3.5      29      60 ..     302     333 ..     298     346 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.006
                          AAA_7 30 lknkkpvllvGptGtGKtviikdll 54
                                   ++++  vll G +G+GK++++k + 
  gi|119720445|ref|YP_920940.1| 40 VDKGEVVLLAGRSGSGKSTLLKAIN 64
                                   678899*************998765 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.01
                          AAA_7  29 llknkkpvllvGptGtGKtviikdllkkldke 60 
                                     ++++  v l G+ G GK++++k +l  l+++
  gi|119720445|ref|YP_920940.1| 302 EIREGERVALLGNNGAGKSTMAKLMLGLLKPT 333
                                    5788999***************9988777765 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.023       7.9      44      67 ..      40      63 ..      25      76 .. 0.89
   2 ?    0.5   0.0       1.3   4.5e+02     107     156 ..     172     220 ..     154     228 .. 0.79
   3 ?    6.3   0.0     0.022       7.3      44      65 ..     303     324 ..     284     352 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.023
                      IstB_IS21 44 iekkenivllGpsGvGKshlaial 67
                                   ++k e ++l G sG GKs l  a+
  gi|119720445|ref|YP_920940.1| 40 VDKGEVVLLAGRSGSGKSTLLKAI 63
                                   78999*************998887 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1.3
                      IstB_IS21 107 lkvdllilDdlgllpldqaeaellfeviekryerrsiiitsnlpfaewde 156
                                    +k++++++D+  l +ld++  +++ evi++  e   +++ ++  ++e  e
  gi|119720445|ref|YP_920940.1| 172 MKPEIILMDE-PLANLDSEGVATVQEVIKSFREEGKTVVIAEHRVEEVLE 220
                                    4556666666.7999***************99999999999988887655 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.022
                      IstB_IS21  44 iekkenivllGpsGvGKshlai 65 
                                    i++ e ++llG  G+GKs +a 
  gi|119720445|ref|YP_920940.1| 303 IREGERVALLGNNGAGKSTMAK 324
                                    678999************9996 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1      0.12        41      28      43 ..      48      63 ..      34      67 .. 0.85
   2 !   10.3   0.0    0.0016      0.53      24      56 ..     307     338 ..     299     340 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.12
                          DUF87 28 ilgsTGsGKSntvavL 43
                                     g++GsGKS++ + +
  gi|119720445|ref|YP_920940.1| 48 LAGRSGSGKSTLLKAI 63
                                   6699********9876 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0016
                          DUF87  24 rHlAilgsTGsGKSntvavLleellekkgatil 56 
                                    +++A lg  G+GKS+ ++++l  l     +++l
  gi|119720445|ref|YP_920940.1| 307 ERVALLGNNGAGKSTMAKLMLGLLK-PTEGSVL 338
                                    579****************997776.5555555 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0     0.024       8.1       1      18 [.      46      63 ..      46      86 .. 0.80
   2 ?    7.6   0.0     0.015         5       2      36 ..     310     339 ..     309     361 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.024
                   RNA_helicase  1 iwlyGpsgeGKStlakeL 18
                                   ++l G+sg GKStl k +
  gi|119720445|ref|YP_920940.1| 46 VLLAGRSGSGKSTLLKAI 63
                                   5789**********9984 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.015
                   RNA_helicase   2 wlyGpsgeGKStlakeLakallkklklkkkdsvys 36 
                                     l G++g GKSt+ak +   ll    +++++sv +
  gi|119720445|ref|YP_920940.1| 310 ALLGNNGAGKSTMAKLML-GLL----KPTEGSVLV 339
                                    588***********9933.333....344455544 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.1    0.0016      0.54       2      42 ..      46      83 ..      45      95 .. 0.84
   2 ?    5.1   0.0     0.057        19       2      26 ..     309     333 ..     308     348 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0016
                                   EEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE---- CS
                       NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvkvgGfyteevregg 42
                                   v++ G++G+GK+Tl+k +  l+     +++G y   vr +g
  gi|119720445|ref|YP_920940.1| 46 VLLAGRSGSGKSTLLKAINGLI---PHRYSGTYKGAVRVRG 83
                                   789*************999999...5568888877777665 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.057
                                    EEEE--TTSSHHHHHHHHHHHH... CS
                       NTPase_1   2 vfiTGppGvGKtTlvkkvlellkss 26 
                                    v++ G+ G GK+T+ k +l llk  
  gi|119720445|ref|YP_920940.1| 309 VALLGNNGAGKSTMAKLMLGLLKPT 333
                                    7889************999999855 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.66   2.2e+02      23      45 ..      50      72 ..      43      93 .. 0.78
   2 ?    1.3   0.0      0.29        99     498     570 ..     154     214 ..     119     222 .. 0.72
   3 ?    5.8   0.0     0.014       4.6      23      66 ..     313     350 ..     306     353 .. 0.75
   4 ?    1.0   0.0      0.37   1.2e+02     524     579 ..     430     483 ..     423     499 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.66
                         AAA_13 23 GwNGaGKTtLSrllrslelgete 45
                                   G+ G+GK+tL ++++ l  ++ +
  gi|119720445|ref|YP_920940.1| 50 GRSGSGKSTLLKAINGLIPHRYS 72
                                   899*********99998555544 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.29
                         AAA_13 498 etLSeGEktaIaflYFlkslkeddseigkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHn 570
                                    ++LS GEk  +a+      l      + k +i+ +D P   LDs+ +  v   iks     ++ k + i  H 
  gi|119720445|ref|YP_920940.1| 154 NELSGGEKQRVAIA---GVLA-----M-KPEIILMDEPLANLDSEGVATVQEVIKSFR---EEGKTVVIAEHR 214
                                    56666666666654...2222.....3.899**************9999999999875...666666666665 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.014
                         AAA_13  23 GwNGaGKTtLSrllrslelgetepkfangsieitngeeldirVf 66 
                                    G NGaGK+t+++l+  l       k ++gs+ +   + + + V+
  gi|119720445|ref|YP_920940.1| 313 GNNGAGKSTMAKLMLGLL------KPTEGSVLVYGRDTHTMEVY 350
                                    9************98882......23566666666666666666 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.37
                         AAA_13 524 igkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleffkevkk 579
                                    + k +i v+D P    D       + +++s + ++  +k l + TH +++  e ++
  gi|119720445|ref|YP_920940.1| 430 M-KPRILVLDEPTAGQDYATYTAFMEFVDSLV-NAGVIKTLVLITHDTDLAVEYTD 483
                                    4.99*************999888889999998.9999*********9998766665 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0     0.016       5.5      19      43 ..      40      64 ..      27      79 .. 0.79
   2 ?    6.4   0.0      0.02       6.9      19      44 ..     303     328 ..     290     341 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.016
                                   CTSSS-EEEECSTTSSHHHHHHHHH CS
                Sigma54_activat 19 aktdlsvlitGesGtGKellaraih 43
                                   +++   vl+ G sG+GK++l +ai 
  gi|119720445|ref|YP_920940.1| 40 VDKGEVVLLAGRSGSGKSTLLKAIN 64
                                   5566789************999985 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.02
                                    CTSSS-EEEECSTTSSHHHHHHHHHH CS
                Sigma54_activat  19 aktdlsvlitGesGtGKellaraihe 44 
                                    ++   +v ++G++G+GK+++a+++  
  gi|119720445|ref|YP_920940.1| 303 IREGERVALLGNNGAGKSTMAKLMLG 328
                                    555678999*************9976 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1    0.0011      0.38       1      26 [.      43      68 ..      43      73 .. 0.88
   2 ?    2.0   0.0      0.47   1.6e+02       4      24 ..     309     329 ..     306     354 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0011
                                   --EEEEEE-TTSSHHHHHHHHHHHSS CS
                            CPT  1 ariilLnGgsssGKsslaralqevld 26
                                   ++++lL G s sGKs+l +a+  +++
  gi|119720445|ref|YP_920940.1| 43 GEVVLLAGRSGSGKSTLLKAINGLIP 68
                                   689*****************987765 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.47
                                    EEEEE-TTSSHHHHHHHHHHH CS
                            CPT   4 ilLnGgsssGKsslaralqev 24 
                                    + L G   +GKs++a+ +  +
  gi|119720445|ref|YP_920940.1| 309 VALLGNNGAGKSTMAKLMLGL 329
                                    6688999********987655 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.29     1e+02       3      18 ..      45      60 ..      43      70 .. 0.88
   2 ?    2.9   0.0      0.21        71      59     112 ..     197     251 ..     186     260 .. 0.81
   3 ?    6.8   0.1     0.013       4.5       4      40 ..     309     345 ..     307     351 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.29
                                   EEEEEESTTSSHHHHH CS
                          SRP54  3 villvGlqGaGKTttl 18
                                   v+ll+G  G+GK t l
  gi|119720445|ref|YP_920940.1| 45 VVLLAGRSGSGKSTLL 60
                                   89***********987 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.21
                                    EEE.SSTTSCHHHHHHHHHHHHHHTTSSEEEEEE--SSTTHHHHHHHHHHHHHHH CS
                          SRP54  59 vik.kkeeadpaavakeavekakeekidvvlvDTaGrlqndkelmeelkkikkvv 112
                                    vik  +ee +++ +a++ ve+  e ++d v+v   G    + e +eel+++++ +
  gi|119720445|ref|YP_920940.1| 197 VIKsFREEGKTVVIAEHRVEEVLEVGVDRVFVMREGTIVREVERVEELANFADEL 251
                                    4443455668999************************************998776 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.013
                                    EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTS CS
                          SRP54   4 illvGlqGaGKTttlaKLaallkkegkkvllvaaDtf 40 
                                    ++l+G +GaGK t +  +  llk  + +vl+   Dt 
  gi|119720445|ref|YP_920940.1| 309 VALLGNNGAGKSTMAKLMLGLLKPTEGSVLVYGRDTH 345
                                    6899*******98766666667777999999988885 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.1     0.017       5.8       1      21 [.      46      66 ..      46     115 .. 0.72
   2 ?   -0.2   0.0       3.7   1.3e+03      56      72 ..     170     187 ..     137     225 .. 0.67
   3 ?    5.5   0.0     0.066        22       2      22 ..     310     330 ..     309     374 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.017
                                   EEEESSTTSSHHHHHHHHHHH CS
                            AAA  1 vllyGppGtGKTllakavake 21
                                   vll G  G GK++l ka+   
  gi|119720445|ref|YP_920940.1| 46 VLLAGRSGSGKSTLLKAINGL 66
                                   79***************9766 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 3.7
                                    TS.TSEEEEEETGGGHHH CS
                            AAA  56 ka.kpsilfiDEidalak 72 
                                     a kp i+++DE  a   
  gi|119720445|ref|YP_920940.1| 170 LAmKPEIILMDEPLANLD 187
                                    335688999998544444 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.066
                                    EEESSTTSSHHHHHHHHHHHH CS
                            AAA   2 llyGppGtGKTllakavakel 22 
                                     l G+ G GK+++ak +   l
  gi|119720445|ref|YP_920940.1| 310 ALLGNNGAGKSTMAKLMLGLL 330
                                    689************987765 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1    0.0015       0.5      41      58 ..      45      62 ..      26      67 .. 0.83
   2 ?    2.5   0.0      0.22        75      38      64 ..     306     330 ..     292     358 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0015
                                   SEEEE--TTSSHHHHHHH CS
                   FtsK_SpoIIIE 41 hllvaGatgsGKStalnt 58
                                    +l+aG++gsGKSt l++
  gi|119720445|ref|YP_920940.1| 45 VVLLAGRSGSGKSTLLKA 62
                                   589************987 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.22
                                    S-.SEEEE--TTSSHHHHHHHHHHHHH CS
                   FtsK_SpoIIIE  38 mashllvaGatgsGKStalntLilSla 64 
                                     +  + ++G  g GKSt+ + L+l+l+
  gi|119720445|ref|YP_920940.1| 306 GE-RVALLGNNGAGKSTMAK-LMLGLL 330
                                    45.68899********9754.666665 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0    0.0036       1.2       2      23 ..      43      64 ..      42      81 .. 0.86
   2 ?    3.3   0.0      0.21        71       5      27 ..     309     331 ..     305     347 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0036
                                   -EEEEEESSTTSSHHHHHHHHH CS
                     APS_kinase  2 gvvvwltGlsgsGKstianale 23
                                   g vv+l+G sgsGKst+ +a++
  gi|119720445|ref|YP_920940.1| 43 GEVVLLAGRSGSGKSTLLKAIN 64
                                   789**************98886 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.21
                                    EEEESSTTSSHHHHHHHHHHHHH CS
                     APS_kinase   5 vwltGlsgsGKstianalekkLv 27 
                                    v l G  g+GKst+a+ +   L+
  gi|119720445|ref|YP_920940.1| 309 VALLGNNGAGKSTMAKLMLGLLK 331
                                    678899*********98766665 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0    0.0034       1.2       4      24 ..      46      66 ..      43      78 .. 0.86
   2 ?    3.0   0.0      0.23        79       3      23 ..     308     328 ..     306     353 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0034
                      PduV-EutP  4 illiGkvgsGKttLtqalkge 24
                                   +ll G++gsGK tL +a++g 
  gi|119720445|ref|YP_920940.1| 46 VLLAGRSGSGKSTLLKAINGL 66
                                   899***************985 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.23
                      PduV-EutP   3 killiGkvgsGKttLtqalkg 23 
                                    ++ l+G+ g+GK t+++ + g
  gi|119720445|ref|YP_920940.1| 308 RVALLGNNGAGKSTMAKLMLG 328
                                    899***********9987654 PP

>> Gtr1_RagA  Gtr1/RagA G protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.033        11       2      19 ..      46      63 ..      45      71 .. 0.89
   2 ?    6.3   0.0     0.016       5.4       2      33 ..     309     340 ..     308     358 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.033
                      Gtr1_RagA  2 vLLmGksgsGKtsmrsii 19
                                   vLL G+sgsGK+++ + i
  gi|119720445|ref|YP_920940.1| 46 VLLAGRSGSGKSTLLKAI 63
                                   8************98876 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.016
                      Gtr1_RagA   2 vLLmGksgsGKtsmrsiiFdnylardtlrlga 33 
                                    v L+G++g+GK++m + +   + +++   l  
  gi|119720445|ref|YP_920940.1| 309 VALLGNNGAGKSTMAKLMLGLLKPTEGSVLVY 340
                                    779*************9988888887766655 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00079      0.27      60     100 ..      46      87 ..      35      96 .. 0.86
   2 ?    0.6   0.0      0.71   2.4e+02      53      78 ..     302     327 ..     292     349 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00079
                                    EEEEESSTSTHHHHHHHHHHHSSSEEEEESSSSSSS.HSSSE CS
                            MCM  60 vllvgdpgtaKsqlLkyveklapravytsgkgssaa.gLtaa 100
                                    vll g +g +Ks+lLk+++ l+p+    + kg+  + gLt+a
  gi|119720445|ref|YP_920940.1|  46 VLLAGRSGSGKSTLLKAINGLIPHRYSGTYKGAVRVrGLTVA 87 
                                    89*********************9999888887654399976 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.71
                                    BBCSS-EEEEEESSTSTHHHHHHHHH CS
                            MCM  53 klrgdinvllvgdpgtaKsqlLkyve 78 
                                    ++r    v l+g+ g +Ks++ k + 
  gi|119720445|ref|YP_920940.1| 302 EIREGERVALLGNNGAGKSTMAKLML 327
                                    68888899***********9988764 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.014       4.7      18      50 ..      32      64 ..      19      75 .. 0.84
   2 ?    4.6   0.0      0.04        13      14      49 ..     291     326 ..     278     339 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.014
                                   HHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHH CS
                           MeaB 18 llerllakaGraqvvGltGvPGaGkstlvealg 50
                                    l++++ +  + +vv l G  G+Gkstl++a+ 
  gi|119720445|ref|YP_920940.1| 32 ALRNVSLEVDKGEVVLLAGRSGSGKSTLLKAIN 64
                                   5778888888999***************99875 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.04
                                    HHHHHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHH CS
                           MeaB  14 eakellerllakaGraqvvGltGvPGaGkstlveal 49 
                                    e k +l+ +  +  + ++v l G  GaGkst+ + +
  gi|119720445|ref|YP_920940.1| 291 EDKPVLKGINLEIREGERVALLGNNGAGKSTMAKLM 326
                                    56777888888888899**************97644 PP

>> KdpD  Osmosensitive K+ channel His kinase sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.2    0.0024       0.8      49      97 ..     137     189 ..     125     247 .. 0.79
   2 ?    2.5   0.0      0.25        85      69     116 ..     418     464 ..     403     490 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0024
                           KdpD  49 ealleglevi...prkeveykgkeleeldldailarkpevvlvDe.lahtnap 97 
                                    e+ l++l ++   +r   e +g e +++ +  +la+kpe++l+De la  + +
  gi|119720445|ref|YP_920940.1| 137 EEALSRLGILhlkDRDVNELSGGEKQRVAIAGVLAMKPEIILMDEpLANLDSE 189
                                    444444544422144455677889999*****************966655555 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.25
                           KdpD  69 eleeldldailarkpevvlvDelahtnapgsrhekryqdveelLeagi 116
                                    e +++ + +il++kp+++++De    + + +  +   + v++l++ag+
  gi|119720445|ref|YP_920940.1| 418 EKKRICVASILSMKPRILVLDEPTAGQ-DYATYTAFMEFVDSLVNAGV 464
                                    566778999*************76554.45555666666777777775 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0095       3.2      18      49 ..      35      66 ..      26      74 .. 0.88
   2 ?    4.2   0.1     0.082        28      31      49 ..     311     329 ..     297     333 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0095
                         AAA_27 18 sldfsaeeadlhliyGpNEAGKstalrAisdl 49
                                   +++++ ++ ++ l+ G   +GKst+l+Ai+ l
  gi|119720445|ref|YP_920940.1| 35 NVSLEVDKGEVVLLAGRSGSGKSTLLKAINGL 66
                                   667777899999*****************987 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.082
                         AAA_27  31 iyGpNEAGKstalrAisdl 49 
                                    ++G N AGKst+ + +  l
  gi|119720445|ref|YP_920940.1| 311 LLGNNGAGKSTMAKLMLGL 329
                                    57*********98877666 PP

>> Propeptide_C25  Propeptide_C25
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0    0.0002     0.068      18     103 ..     275     361 ..     266     369 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0002
                                    ETTEEEEEEE--S-EEEEEEETTEEEEEEE-TT-B-.---TTSB---BEEEEEE--SSEEEEEEEEEEEEEEE-S--B-B CS
                 Propeptide_C25  18 eqsvtkiefrvanlkftsvekdkgvfqrisiteges.lsekGepelPilsksiavpetreakvevvssktetlenvdiaP 96 
                                      +v+ +efr +   +++    kg+   i   e +  l+++G  +  + ++++++   +e  v v   +t+t+e +++aP
  gi|119720445|ref|YP_920940.1| 275 SPGVVAVEFRNVSFSYEDKPVLKGINLEIREGERVAlLGNNGAGKSTMAKLMLGLLKPTEGSVLVYGRDTHTMEVYEVAP 354
                                    557778888888888888888888877776666655369***************************************** PP

                                    ---S-BT CS
                 Propeptide_C25  97 sksvvve 103
                                    + + v++
  gi|119720445|ref|YP_920940.1| 355 MVGLVFQ 361
                                    *****98 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1     0.017       5.6      18      35 ..      42      59 ..      39      65 .. 0.90
   2 ?   -2.7   0.0       9.1   3.1e+03      30      58 ..     204     232 ..     195     245 .. 0.73
   3 ?    4.8   0.0     0.044        15      16      37 ..     303     324 ..     297     363 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.017
                         ATPase 18 egrvvlitGepGtGKtif 35
                                   +g+vvl++G +G+GK+++
  gi|119720445|ref|YP_920940.1| 42 KGEVVLLAGRSGSGKSTL 59
                                   689************997 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 9.1
                         ATPase  30 tGKtifalqFlikgaekygepgvfvtvee 58 
                                     GKt++ ++  ++ + ++g   vfv  e 
  gi|119720445|ref|YP_920940.1| 204 EGKTVVIAEHRVEEVLEVGVDRVFVMREG 232
                                    58888888888888888888888876665 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.044
                         ATPase  16 ipegrvvlitGepGtGKtifal 37 
                                    i eg+ v + G+ G+GK+++a+
  gi|119720445|ref|YP_920940.1| 303 IREGERVALLGNNGAGKSTMAK 324
                                    678999**************97 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00099      0.33      34      65 ..      32      63 ..      28      79 .. 0.88
   2 ?   -1.1   0.0       4.5   1.5e+03      38      64 ..     299     325 ..     291     331 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00099
                          Rad17 34 wlkadvLesrkkriLLisGPsGCgkstvvkvL 65
                                   +l+  +Le  k +++L++G sG gkst +k +
  gi|119720445|ref|YP_920940.1| 32 ALRNVSLEVDKGEVVLLAGRSGSGKSTLLKAI 63
                                   678889****9******************986 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 4.5
                          Rad17  38 dvLesrkkriLLisGPsGCgkstvvkv 64 
                                      Le r+ + + + G  G gkst+ k 
  gi|119720445|ref|YP_920940.1| 299 INLEIREGERVALLGNNGAGKSTMAKL 325
                                    5566665555566799*******9886 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1     0.093        31       2      19 ..      46      63 ..      45      89 .. 0.84
   2 ?    5.9   0.0     0.041        14       1      19 [.     308     326 ..     308     355 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.093
                                   EEEESSTTSSHHHHHHCH CS
                            Roc  2 vvlvGdsgvGKtsllkrf 19
                                   v+l G sg+GK++llk +
  gi|119720445|ref|YP_920940.1| 46 VLLAGRSGSGKSTLLKAI 63
                                   6899**********9875 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.041
                                    EEEEESSTTSSHHHHHHCH CS
                            Roc   1 KvvlvGdsgvGKtsllkrf 19 
                                    +v l+G++g+GK++++k +
  gi|119720445|ref|YP_920940.1| 308 RVALLGNNGAGKSTMAKLM 326
                                    589***********98744 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00087       0.3     242     265 ..      40      64 ..      33      73 .. 0.86
   2 ?   -2.5   0.0       4.8   1.6e+03     328     348 ..     161     181 ..     154     247 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00087
                                    E-SS.EEEEEE-TTSSHHHHHHHHH CS
                     ABC_ATPase 242 ipkG.vtlIvGggfhGKsTLLeAle 265
                                    + kG v+l++G+   GKsTLL+A++
  gi|119720445|ref|YP_920940.1|  40 VDKGeVVLLAGRSGSGKSTLLKAIN 64 
                                    67888******************97 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.8
                                    HHHHHHHHHHHTT-SEEEEEG CS
                     ABC_ATPase 328 sqAanimealeagakllLiDE 348
                                     q ++i+  l ++ +++L+DE
  gi|119720445|ref|YP_920940.1| 161 KQRVAIAGVLAMKPEIILMDE 181
                                    555555555555555555555 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0    0.0063       2.1      16      49 ..      37      70 ..      30      82 .. 0.85
   2 ?    2.2   0.0      0.25        84       5      55 ..     291     339 ..     287     341 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0063
                                   ....HCTS-EEEEESTTSSCHHHHHHHHHHCHCT CS
                           PIF1 16 avlnekgklfFvtGsgGtgKtflwkallkklrse 49
                                   ++  +kg+++ + G +G+gK+ l+ka+   +  +
  gi|119720445|ref|YP_920940.1| 37 SLEVDKGEVVLLAGRSGSGKSTLLKAINGLIPHR 70
                                   556689*********************9988766 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.25
                                    HHHHHHHHH......HCTS-EEEEESTTSSCHHHHHHHHHHCHCTCCCEEE CS
                           PIF1   5 eQkkvfdaiieavlnekgklfFvtGsgGtgKtflwkallkklrsegkivla 55 
                                    e k v++ i   +  ++g+ + + G  G+gK+ + k +l  l++++  vl+
  gi|119720445|ref|YP_920940.1| 291 EDKPVLKGI--NLEIREGERVALLGNNGAGKSTMAKLMLGLLKPTEGSVLV 339
                                    566666777..566688999999********************99888875 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.33   1.1e+02      20      41 ..      42      63 ..      30      68 .. 0.76
   2 ?    7.7   0.0    0.0045       1.5      23      68 ..     308     353 ..     296     367 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.33
                         AAA_10 20 nasasliiGdlGnGKSvlakll 41
                                   +   +l+ G  G GKS l k +
  gi|119720445|ref|YP_920940.1| 42 KGEVVLLAGRSGSGKSTLLKAI 63
                                   4555699***********9987 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0045
                         AAA_10  23 asliiGdlGnGKSvlakllvlyisllggkaliiDpkkerekfketl 68 
                                     ++++G+ G+GKS +akl+   +   +g +l+  +   + + +e +
  gi|119720445|ref|YP_920940.1| 308 RVALLGNNGAGKSTMAKLMLGLLKPTEGSVLVYGRDTHTMEVYEVA 353
                                    5699***************999998888888877776666666655 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.56   1.9e+02      18      34 ..      46      62 ..      33      70 .. 0.83
   2 ?   -2.1   0.0       4.2   1.4e+03     258     285 ..     191     218 ..     177     221 .. 0.72
   3 ?    7.3   0.0    0.0056       1.9      13      58 ..     304     349 ..     295     355 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.56
                  TrwB_AAD_bind 18 ilivGttGsGKtqalek 34
                                   +l++G  GsGK++ l++
  gi|119720445|ref|YP_920940.1| 46 VLLAGRSGSGKSTLLKA 62
                                   799**********9876 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.2
                  TrwB_AAD_bind 258 leelksllaegRkfGgavvlglqsiaql 285
                                    + +++++++  R+ G  vv++ + ++ +
  gi|119720445|ref|YP_920940.1| 191 VATVQEVIKSFREEGKTVVIAEHRVEEV 218
                                    7888899999999999999988877665 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0056
                  TrwB_AAD_bind  13 retqhilivGttGsGKtqalekllrairargdraivlDltGafvsr 58 
                                    re + ++++G  G+GK+++++ +l  ++  +  ++v+    + ++ 
  gi|119720445|ref|YP_920940.1| 304 REGERVALLGNNGAGKSTMAKLMLGLLKPTEGSVLVYGRDTHTMEV 349
                                    5778899*****************9999999999998777666665 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.032        11       1      19 [.      45      63 ..      45      76 .. 0.84
   2 ?    3.5   0.0      0.18        61       2      42 ..     309     349 ..     308     352 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.032
                           MobB  1 vlgivgksgsGKTtLlekl 19
                                   v+ ++g+sgsGK tLl+ +
  gi|119720445|ref|YP_920940.1| 45 VVLLAGRSGSGKSTLLKAI 63
                                   57899**********9875 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.18
                           MobB   2 lgivgksgsGKTtLleklipelkarglrvgtiKhahhgfdv 42 
                                    +++ g++g+GK t+ + ++  lk  + +v +   ++h ++v
  gi|119720445|ref|YP_920940.1| 309 VALLGNNGAGKSTMAKLMLGLLKPTEGSVLVYGRDTHTMEV 349
                                    5789******************9999999888888888775 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1      0.11        36       2      20 ..      46      64 ..      45      81 .. 0.84
   2 ?    0.1   0.0       2.4   8.2e+02     133     153 ..     128     148 ..     123     155 .. 0.86
   3 ?    3.2   0.1      0.27        92       1      17 [.     308     324 ..     308     338 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.11
                         AAA_28  2 ivitGgestGKTtlleaLa 20
                                   + + G +++GK+tll+a++
  gi|119720445|ref|YP_920940.1| 46 VLLAGRSGSGKSTLLKAIN 64
                                   6788999********9986 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 2.4
                         AAA_28 133 ereaiderlrealrelgipvi 153
                                    ere+i++r++eal +lgi  +
  gi|119720445|ref|YP_920940.1| 128 EREEIERRVEEALSRLGILHL 148
                                    899**************9755 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.27
                         AAA_28   1 kivitGgestGKTtlle 17 
                                    +++++G  ++GK+t+++
  gi|119720445|ref|YP_920940.1| 308 RVALLGNNGAGKSTMAK 324
                                    799***********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (548 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); expected 17.9 (0.001)
Passed Fwd filter:                        53  (0.0029561); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              53  [number of targets reported over threshold]
# CPU time: 0.70u 0.27s 00:00:00.97 Elapsed: 00:00:00.45
# Mc/sec: 3655.06
//
Query:       gi|119720446|ref|YP_920941.1|  [L=317]
Description: paREP7 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-07   31.3   9.7        1.2    9.6   0.0    5.3  6  Snapin_Pallidin  Snapin/Pallidin
    1.3e-05   25.2   2.7       0.12   12.4   0.6    2.6  2  DUF1664          Protein of unknown function (DUF1664)
    4.6e-05   24.0   8.7        0.1   13.3   0.6    3.4  4  YabA             Initiation control protein YabA
    5.4e-05   23.1  13.4    5.4e-05   23.1  13.4    2.5  2  KASH_CCD         Coiled-coil region of CCDC155 or KASH
    0.00042   20.7   0.1         16    6.0   0.0    4.6  4  LPP              Lipoprotein leucine-zipper
    0.00048   20.2  11.8       0.05   13.7   4.4    2.5  2  Mod_r            Modifier of rudimentary (Mod(r)) protein
     0.0006   20.3  36.2     0.0052   17.3   8.4    3.1  3  APG6_N           Apg6 coiled-coil region
     0.0013   19.1  26.7       0.91   10.0   6.5    4.7  4  Latarcin         Latarcin precursor
     0.0023   17.7   7.9        5.4    6.8   6.5    3.6  2  SKA2             Spindle and kinetochore-associated protein 2
     0.0041   17.5   6.6      0.021   15.2   6.6    2.0  2  zf-C4H2          Zinc finger-containing protein
     0.0053   16.0   0.4        1.5    8.0   0.0    2.2  2  ATP-synt_10      ATP10 protein
  ------ inclusion threshold ------
      0.012   15.9   4.6       0.85    9.9   0.2    3.7  3  DUF4709          Domain of unknown function (DUF4709)
      0.014   15.1  14.2       0.71    9.7   0.8    5.1  5  Rbsn             Rabenosyn Rab binding domain
      0.015   15.5  15.6       0.03   14.5   9.7    3.1  4  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
      0.019   14.2   0.1      0.034   13.4   0.1    1.5  1  DUF1394          Protein of unknown function (DUF1394)
      0.019   14.9   3.8      0.019   14.9   3.8    3.8  3  TMF_DNA_bd       TATA element modulatory factor 1 DNA binding
      0.028   14.2   1.2        1.6    8.5   0.4    2.9  4  Lectin_N         Hepatic lectin, N-terminal domain
      0.031   12.9   5.7       0.41    9.2   7.1    1.9  3  FapA             Flagellar Assembly Protein A
      0.032   14.1   1.8          4    7.3   0.4    2.8  3  Sec34            Sec34-like family
      0.035   14.3  11.8         12    6.2   0.0    6.4  6  VPS11_C          Vacuolar protein sorting protein 11 C termin
      0.037   14.0  12.7       0.76    9.8   1.4    3.8  5  DUF2205          Short coiled-coil protein
      0.039   13.0   4.2        1.9    7.5   0.8    2.6  2  TelA             Toxic anion resistance protein (TelA)
      0.046   14.0   0.1         10    6.5   0.0    3.4  3  DUF948           Bacterial protein of unknown function (DUF94
      0.062   13.3  11.1       0.51   10.3   7.7    3.0  3  Serine_rich      Serine rich protein interaction domain
      0.079   13.4  36.8        2.3    8.7  12.0    4.6  3  ZapB             Cell division protein ZapB
      0.081   12.9  26.9        7.1    6.5  23.4    3.2  1  JAKMIP_CC3       JAKMIP CC3 domain
      0.088   12.9  14.9      0.096   12.8   0.7    2.7  2  ADIP             Afadin- and alpha -actinin-Binding
       0.09   12.4   6.5       0.21   11.2   5.1    2.1  2  PI3K_P85_iSH2    Phosphatidylinositol 3-kinase regulatory sub
       0.12   12.5  17.5        3.8    7.7   2.8    4.6  5  bZIP_1           bZIP transcription factor
       0.16   12.2  23.1        1.3    9.3   1.0    4.8  4  JIP_LZII         JNK-interacting protein  leucine zipper II
       0.19   11.3  13.3        1.6    8.3   3.3    2.7  3  DUF2968          Protein of unknown function (DUF2968)
       0.26   11.3  25.6      0.031   14.3   7.4    3.3  3  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
       0.26   11.8  10.5        2.7    8.5   1.8    3.3  3  UPF0449          Uncharacterised protein family UPF0449
        0.3   10.4  16.5        3.2    7.0  15.5    2.7  2  DUF2353          Uncharacterized coiled-coil protein (DUF2353
       0.31   11.6   9.8         56    4.3   7.2    3.3  1  DUF16            Protein of unknown function DUF16
       0.35    8.7   2.2       0.53    8.1   2.2    1.3  1  V_ATPase_I       V-type ATPase 116kDa subunit family
       0.42   10.8  21.4        5.1    7.3   3.5    2.7  2  ATG16            Autophagy protein 16 (ATG16)
       0.45    9.7   5.1       0.52    9.5   4.2    1.6  1  TMPIT            TMPIT-like protein
       0.49   10.4   8.9         22    5.0   0.0    3.1  2  DUF1640          Protein of unknown function (DUF1640)
       0.52    9.5  18.5        1.3    8.2  18.5    1.7  1  HAP1_N           HAP1 N-terminal conserved region
       0.54   10.1  21.6        2.4    8.0   3.0    4.2  4  DivIC            Septum formation initiator
       0.56    9.5  15.4        2.8    7.2  14.0    2.3  2  GAS              Growth-arrest specific micro-tubule binding
       0.59    9.7   7.6        6.4    6.3   3.5    2.8  3  DUF4795          Domain of unknown function (DUF4795)
       0.65    9.7  15.9        1.1    9.0   1.1    3.4  3  DUF4201          Domain of unknown function (DUF4201)
       0.66   10.3  11.3        2.8    8.3   1.8    4.1  4  DUF4061          Domain of unknown function (DUF4061)
       0.86    8.1  15.8       0.29    9.6   9.2    2.1  2  FUSC             Fusaric acid resistance protein family
       0.94    8.8   9.3        9.9    5.4   2.2    2.9  3  CASP_C           CASP C terminal
        1.3    7.1  11.6        4.3    5.4   2.3    3.1  4  EzrA             Septation ring formation regulator, EzrA
        1.3    8.3   9.7          6    6.1   1.5    2.4  2  DUF4763          Domain of unknown function (DUF4763)
        1.4    9.2  15.7        8.6    6.7   0.4    5.5  6  HALZ             Homeobox associated leucine zipper
        1.5    8.8   5.9         13    5.8   0.6    3.2  5  DUF4446          Protein of unknown function (DUF4446)
        1.5    8.4   9.6        0.2   11.3   4.0    2.1  2  PTRF_SDPR        PTRF/SDPR family
        1.6    8.3  11.9        3.8    7.1   6.6    2.8  2  Laminin_I        Laminin Domain I
        2.3    7.0   6.6        1.7    7.5   5.2    1.6  1  5_nucleotid      5' nucleotidase family
        2.6    5.7  13.9         24    2.6  14.0    2.0  1  Nup88            Nuclear pore component
        2.7    8.2  21.1        6.1    7.1   9.1    3.3  3  TMF_TATA_bd      TATA element modulatory factor 1 TATA bindin
        2.7    8.0   6.5        1.5    8.9   1.0    2.7  3  Laminin_II       Laminin Domain II
        3.9    8.0   6.2         42    4.7   0.4    3.8  3  COMP             Cartilage oligomeric matrix protein
        4.4    7.4  16.5         31    4.6  16.5    2.2  1  UPF0242          Uncharacterised protein family (UPF0242) N-t
        6.4    6.5  26.7        1.6    8.5  20.1    2.4  2  ERM              Ezrin/radixin/moesin family


Domain annotation for each model (and alignments):
>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.3     0.035        11      13      51 ..      44      82 ..      31      84 .. 0.77
   2 !    8.6   0.3    0.0082       2.4      11      43 ..      63      95 ..      60     101 .. 0.84
   3 !    8.8   0.5    0.0074       2.2      17      41 ..      83     107 ..      75     117 .. 0.85
   4 ?    4.3   0.1      0.18        54      18      42 ..      98     122 ..      96     129 .. 0.83
   5 ?    8.0   0.6     0.012       3.7      17      42 ..     125     150 ..     116     161 .. 0.80
   6 !    9.6   0.0    0.0041       1.2      17      51 ..     160     194 ..     154     203 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.035
                Snapin_Pallidin 13 pkldeldeklkelrqsQeeLleqldrlnekLkeleeaqe 51
                                   +++++l+e  ++l ++Qe+L  ++++l e+++ l+e+q 
  gi|119720446|ref|YP_920941.1| 44 SEIKALREGQEQLWRKQEKLWGEVRKLWEEVRALREDQR 82
                                   567777777788888888888888888888888888775 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0082
                Snapin_Pallidin 11 lepkldeldeklkelrqsQeeLleqldrlnekL 43
                                   l+ ++++l e++++lr+ Q++L e+++ l+e+ 
  gi|119720446|ref|YP_920941.1| 63 LWGEVRKLWEEVRALREDQRKLWEEVKALRENQ 95
                                   667899999*****************9998865 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0074
                Snapin_Pallidin  17 eldeklkelrqsQeeLleqldrlne 41 
                                    +l e++k+lr++Qe+L e++++l+e
  gi|119720446|ref|YP_920941.1|  83 KLWEEVKALRENQEKLWEEVKSLRE 107
                                    56689****************9987 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.18
                Snapin_Pallidin  18 ldeklkelrqsQeeLleqldrlnek 42 
                                    l e++k+lr+ Q +L e+++ l+e+
  gi|119720446|ref|YP_920941.1|  98 LWEEVKSLREGQGKLWEEVKALRED 122
                                    56889**************999886 PP

  == domain 5  score: 8.0 bits;  conditional E-value: 0.012
                Snapin_Pallidin  17 eldeklkelrqsQeeLleqldrlnek 42 
                                    +l e++k+lr++Qe+L e+++ l+e+
  gi|119720446|ref|YP_920941.1| 125 RLWEEVKALRENQEKLWEEVRALRED 150
                                    667899**************999886 PP

  == domain 6  score: 9.6 bits;  conditional E-value: 0.0041
                Snapin_Pallidin  17 eldeklkelrqsQeeLleqldrlnekLkeleeaqe 51 
                                    +l e++++lr+ Qe L+ ++d l++++++l ea  
  gi|119720446|ref|YP_920941.1| 160 RLWEEVRALREGQERLRGDVDGLRASFRQLGEAVG 194
                                    56689***********************9998765 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.6   0.00041      0.12      48     124 .]      47     123 ..      33     123 .. 0.87
   2 !   12.3   0.0   0.00044      0.13      54     117 ..     130     193 ..     117     197 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00041
                        DUF1664  48 kqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerieekQ 124
                                    k l + +e+l + +++L  ++ ++ +++ +  e ++++ eev+++re+ +++ e+v+s++e   +l ++++ + e Q
  gi|119720446|ref|YP_920941.1|  47 KALREGQEQLWRKQEKLWGEVRKLWEEVRALREDQRKLWEEVKALRENQEKLWEEVKSLREGQGKLWEEVKALREDQ 123
                                    667788899999999********************************************999999988888887766 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00044
                        DUF1664  54 seslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskl 117
                                     ++l++ +++L +++  + + + +  e ++ + eev ++re+ ++++ dv+ +++ +++l++ +
  gi|119720446|ref|YP_920941.1| 130 VKALRENQEKLWEEVRALREDQGKLWEGQQRLWEEVRALREGQERLRGDVDGLRASFRQLGEAV 193
                                    56889999***********************************************999998765 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   2.1    0.0018      0.53      11      79 ..      33     101 ..      29     102 .. 0.88
   2 !   11.0   1.3    0.0017       0.5       4      53 ..      68     117 ..      59     125 .. 0.58
   3 !   11.7   2.8    0.0011      0.32       2      58 ..      80     136 ..      79     139 .. 0.87
   4 !   13.3   0.6   0.00033       0.1       2      52 ..     122     172 ..     111     192 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0018
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                           YabA  11 eeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkkelsegkenLarlYee 79 
                                    ++l e+++++l+e+++l+e  ++l  + ++L  e +kl e+++  ++++++  +e++  +en ++l+ee
  gi|119720446|ref|YP_920941.1|  33 RDLLEKMDATLSEIKALREGQEQLWRKQEKLWGEVRKLWEEVRALREDQRKLWEEVKALRENQEKLWEE 101
                                    677889999999999999999999999999999999999999988999999999999999999999887 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0017
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHX CS
                           YabA   4 kelfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerle 53 
                                    ++l +++++l e+ ++l ee+++l+e+ ++l ee ++L+  + kl e+++
  gi|119720446|ref|YP_920941.1|  68 RKLWEEVRALREDQRKLWEEVKALRENQEKLWEEVKSLREGQGKLWEEVK 117
                                    44556666666666666666666666666666666666655555555543 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.0011
                                    -HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXX CS
                           YabA   2 dkkelfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekk 58 
                                    d+++l +++++l e+ e+l ee+++l+e   +l ee ++L+ ++++l e+++  +++
  gi|119720446|ref|YP_920941.1|  80 DQRKLWEEVKALRENQEKLWEEVKSLREGQGKLWEEVKALREDQRRLWEEVKALREN 136
                                    78999*************************************999999998544444 PP

  == domain 4  score: 13.3 bits;  conditional E-value: 0.00033
                                    -HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           YabA   2 dkkelfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerl 52 
                                    d++ l +++++l e+ e+l ee+++l+e+  +l e  ++L  e + lre +
  gi|119720446|ref|YP_920941.1| 122 DQRRLWEEVKALRENQEKLWEEVRALREDQGKLWEGQQRLWEEVRALREGQ 172
                                    678899999999999999999999999999999999999999999999866 PP

>> KASH_CCD  Coiled-coil region of CCDC155 or KASH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1  13.4   1.8e-07   5.4e-05      17     140 ..      60     180 ..      53     205 .. 0.75
   2 ?   -0.9   0.1       4.1   1.2e+03      93     109 ..     257     273 ..     243     304 .. 0.67

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1.8e-07
                       KASH_CCD  17 NkkLaeenskLkkavetaeetnakLteeieeLkkklkstQqalqkaklleeEleelkalvkeleEkrarlkaqnkqleke 96 
                                      kL +e++kL + v +  e   kL ee+++L++      ++ ++ k+l e    l + vk l E ++rl  + k l  +
  gi|119720446|ref|YP_920941.1|  60 QEKLWGEVRKLWEEVRALREDQRKLWEEVKALRENQ---EKLWEEVKSLREGQGKLWEEVKALREDQRRLWEEVKALREN 136
                                    567888888888888888888888888888887653...45667778888888888888888888888888888888888 PP

                       KASH_CCD  97 nqsLiakiesLqeenikllaekdelkkklkeLlkekaeLkkqlh 140
                                    ++ L +++ +L e+  kl   ++ l + ++ L + ++ L+ +++
  gi|119720446|ref|YP_920941.1| 137 QEKLWEEVRALREDQGKLWEGQQRLWEEVRALREGQERLRGDVD 180
                                    88888888888888888888887777777777777777776554 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 4.1
                       KASH_CCD  93 lekenqsLiakiesLqe 109
                                    +e+e   L+++++  +e
  gi|119720446|ref|YP_920941.1| 257 AEREAAKLMERVKVVEE 273
                                    44444444444444433 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.054        16       8      35 ..      66      93 ..      38     101 .. 0.68
   2 ?    5.3   0.0     0.087        26       4      36 ..      97     129 ..      94     137 .. 0.77
   3 ?    3.6   0.0      0.29        88       6      29 ..     127     150 ..     124     160 .. 0.84
   4 ?    1.5   0.0       1.3   3.9e+02       5      30 ..     161     186 ..     158     192 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.054
                            LPP  8 qVsqLkskvdqlssdvnsakaaaqaake 35
                                   +V +L ++v +l +d+ ++ ++++a +e
  gi|119720446|ref|YP_920941.1| 66 EVRKLWEEVRALREDQRKLWEEVKALRE 93
                                   4555555555555555555444444433 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.087
                            LPP   4 eLssqVsqLkskvdqlssdvnsakaaaqaakeE 36 
                                    +L ++V++L + + +l ++v++++++     eE
  gi|119720446|ref|YP_920941.1|  97 KLWEEVKSLREGQGKLWEEVKALREDQRRLWEE 129
                                    677889999999999999999999988777666 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.29
                            LPP   6 ssqVsqLkskvdqlssdvnsakaa 29 
                                     ++V++L +++++l ++v +++++
  gi|119720446|ref|YP_920941.1| 127 WEEVKALRENQEKLWEEVRALRED 150
                                    578999999999999999999988 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 1.3
                            LPP   5 LssqVsqLkskvdqlssdvnsakaaa 30 
                                    L ++V +L + ++ l  dv+ ++a  
  gi|119720446|ref|YP_920941.1| 161 LWEEVRALREGQERLRGDVDGLRASF 186
                                    55789999999999999999988765 PP

>> Mod_r  Modifier of rudimentary (Mod(r)) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   4.4   0.00017      0.05       8      87 ..      26     105 ..      23     111 .. 0.92
   2 !   10.5   0.9    0.0017       0.5      25      80 ..     126     182 ..     109     211 .. 0.54

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00017
                          Mod_r   8 Lqelledeeklealvktlpevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqeldel 87 
                                    L  ll   ++le++  tl+e+k+l+e +e+l  ++e+l  +  +l +e++ lr++  +  ee+k+l+++ e++++e ++l
  gi|119720446|ref|YP_920941.1|  26 LAGLLGFRDLLEKMDATLSEIKALREGQEQLWRKQEKLWGEVRKLWEEVRALREDQRKLWEEVKALRENQEKLWEEVKSL 105
                                    56677778999999999**********************************************************99887 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0017
                          Mod_r  25 l.pevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeek 80 
                                    l +evk+l+e++e+l +e ++l e++ +l +  + l +e+ + +e  ++l+  ++ +
  gi|119720446|ref|YP_920941.1| 126 LwEEVKALRENQEKLWEEVRALREDQGKLWEGQQRLWEEVRALREGQERLRGDVDGL 182
                                    224555555555555555555555555555544445555544444444444444444 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5  12.4   0.00013     0.037      32     108 ..      33     105 ..       7     112 .. 0.78
   2 !   17.3   8.4   1.7e-05    0.0052      51     127 ..     111     187 ..     103     191 .. 0.91
   3 ?   -1.2   1.1         9   2.7e+03      48      75 ..     275     302 ..     241     308 .. 0.42

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 0.00013
                         APG6_N  32 lkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynel 108
                                     + l+k + +     +e+++l+e  e+l +++e+l  e ++l +e ++l+++ ++l+ee +al e++e+ w+e ++l
  gi|119720446|ref|YP_920941.1|  33 RDLLEKMDAT----LSEIKALREGQEQLWRKQEKLWGEVRKLWEEVRALREDQRKLWEEVKALRENQEKLWEEVKSL 105
                                    3344444333....459999999999999999999999999999999999999999999999999999999998776 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 1.7e-05
                         APG6_N  51 eleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynelqlelleleeeldsleaqye 127
                                    +l ee+++l++++++l ee k+l +++e+l +e++al+e   +l e ++r w+e ++l+  +++l  + d l a+++
  gi|119720446|ref|YP_920941.1| 111 KLWEEVKALREDQRRLWEEVKALRENQEKLWEEVRALREDQGKLWEGQQRLWEEVRALREGQERLRGDVDGLRASFR 187
                                    6779******************************************************9999999988888888765 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 9
                         APG6_N  48 eleeleeeleklekeeeelleeLkelek 75 
                                    + ++ e  + ++ +  +e+le L++l +
  gi|119720446|ref|YP_920941.1| 275 SGRKVELAVLAVANLGREALEVLEKLHR 302
                                    2222233334444444555555555555 PP

>> Latarcin  Latarcin precursor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   5.2     0.019       5.5      21      59 ..      66     102 ..      37     109 .. 0.80
   2 !   10.0   6.5     0.003      0.91      13      67 ..     101     148 ..      94     156 .. 0.77
   3 ?    7.7   2.4     0.015       4.6      25      76 ..     139     192 ..     134     204 .. 0.66
   4 ?    4.7   0.4      0.13        39      15      40 ..     255     293 ..     251     306 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.019
                       Latarcin  21 ainrklmemvnnlRkvqgRLeemvenlrkvedledtEEA 59 
                                    ++ rkl e v  lR++q +L e v +lr+ ++    EE 
  gi|119720446|ref|YP_920941.1|  66 EV-RKLWEEVRALREDQRKLWEEVKALRENQEK-LWEEV 102
                                    44.999999999999999999999999966554.45555 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.003
                       Latarcin  13 eLdelergainrklmemvnnlRkvqgRLeemvenlrkvedledtEEARgafkklk 67 
                                    e+  l +g+   kl e v  lR++q RL e v +lr+ ++    EE R     l+
  gi|119720446|ref|YP_920941.1| 101 EVKSLREGQG--KLWEEVKALREDQRRLWEEVKALRENQEK-LWEEVRA----LR 148
                                    5555555555..99**********************76665.6899998....44 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.015
                       Latarcin  25 klmemvnnlRkvqgR.......LeemvenlrkvedledtEEARgafkklkdkfkkmgek 76 
                                    kl e v  lR++qg+       L e v +lr     e  E  Rg ++ l+  f+++ge+
  gi|119720446|ref|YP_920941.1| 139 KLWEEVRALREDQGKlwegqqrLWEEVRALR-----EGQERLRGDVDGLRASFRQLGEA 192
                                    6667777777777772222222444444444.....45677899888899999888876 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.13
                       Latarcin  15 delergainrklmemvnnlRkvqgR...............L 40 
                                    +++er+a+  klme v  + ++ gR                
  gi|119720446|ref|YP_920941.1| 255 EDAEREAA--KLMERVKVVEEISGRkvelavlavanlgreA 293
                                    89999999..**************97777776666654441 PP

>> SKA2  Spindle and kinetochore-associated protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   6.5     0.018       5.4      36      78 ..      60     105 ..      28     175 .. 0.60
   2 ?   -1.5   0.0       6.8     2e+03      35      51 ..     256     272 ..     250     279 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.018
                           SKA2  36 na...eNpvkLlerlkkvkeelqaLkeqceellaekkelidkirtt 78 
                                    ++    +++kL e++++++e+  +L e++++l +++++l +++++ 
  gi|119720446|ref|YP_920941.1|  60 QEklwGEVRKLWEEVRALREDQRKLWEEVKALRENQEKLWEEVKSL 105
                                    4445555566666666666666666666666666666555544433 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 6.8
                           SKA2  35 dnaeNpvkLlerlkkvk 51 
                                    d +++ +kL+er+k v 
  gi|119720446|ref|YP_920941.1| 256 DAEREAAKLMERVKVVE 272
                                    44478899999998776 PP

>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   6.6     7e-05     0.021       2     103 ..      46     151 ..      28     166 .. 0.62
   2 !    9.5   1.7    0.0038       1.1      14     105 ..      93     182 ..      90     207 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 7e-05
                        zf-C4H2   2 ikeirektleleklknklakevealekeekcleeyk....kelelLeqEkmaHveeLrlIhaDinalEsvikeaeeekek 77 
                                    ik +re  ++l ++++kl  ev  l +e + l+e +    +e++ L + +++  ee++ +++   +l + +k  +e++++
  gi|119720446|ref|YP_920941.1|  46 IKALREGQEQLWRKQEKLWGEVRKLWEEVRALREDQrklwEEVKALRENQEKLWEEVKSLREGQGKLWEEVKALREDQRR 125
                                    56666666666666666666666666666666554311113455566666666666666666666666666666666666 PP

                        zf-C4H2  78 slekakklyeeykklkeevnelrsel 103
                                     +e++k l e+ +kl eev  lr++ 
  gi|119720446|ref|YP_920941.1| 126 LWEEVKALRENQEKLWEEVRALREDQ 151
                                    66666666666666666666666664 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0038
                        zf-C4H2  14 klknklakevealekeekcleeykkelelLeqEkmaHveeLrlIhaDinalEsvikeaeeekekslekakklyeeykklk 93 
                                    + ++kl +ev++l++ +  l    +e++ L ++++   ee++ +++  ++l + ++  +e++ k +e  ++l ee+++l+
  gi|119720446|ref|YP_920941.1|  93 ENQEKLWEEVKSLREGQGKLW---EEVKALREDQRRLWEEVKALRENQEKLWEEVRALREDQGKLWEGQQRLWEEVRALR 169
                                    556666677776666666554...47788888888899999999999999999999999999999999999999999999 PP

                        zf-C4H2  94 eevnelrse.lgl 105
                                    e  ++lr +  gl
  gi|119720446|ref|YP_920941.1| 170 EGQERLRGDvDGL 182
                                    8888888875555 PP

>> ATP-synt_10  ATP10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.3     0.021       6.1      22      84 ..      52     115 ..      36     127 .. 0.80
   2 !    8.0   0.0     0.005       1.5      62      95 ..     135     168 ..     120     169 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.021
                    ATP-synt_10  22 Gldkppsknent.skkyslgnslkdlfdeektekrrkeLeeelkksyfydlkefrktnGKlFls 84 
                                    G ++  +k+e+   + ++l+++++ l +++++  ++ +  +e ++  + ++k++r+ +GKl+  
  gi|119720446|ref|YP_920941.1|  52 GQEQLWRKQEKLwGEVRKLWEEVRALREDQRKLWEEVKALRENQEKLWEEVKSLREGQGKLWEE 115
                                    5556666666667778899999999999988887777777888999***************975 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.005
                    ATP-synt_10  62 elkksyfydlkefrktnGKlFlspksyfkadkal 95 
                                    e ++  + ++  +r+ +GKl+ + ++++ + +al
  gi|119720446|ref|YP_920941.1| 135 ENQEKLWEEVRALREDQGKLWEGQQRLWEEVRAL 168
                                    55677899********************999887 PP

>> DUF4709  Domain of unknown function (DUF4709)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.4      0.14        41      32      60 ..      63      91 ..      29     105 .. 0.69
   2 ?    5.0   0.1     0.096        29      28      59 ..      87     118 ..      84     124 .. 0.87
   3 ?    9.9   0.2    0.0028      0.85      28     103 ..     115     190 ..     100     196 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.14
                        DUF4709 32 ltevtqkLvkevkslkrdfeflkqllqak 60
                                   l  +++kL +ev++l++d++ l++ ++a 
  gi|119720446|ref|YP_920941.1| 63 LWGEVRKLWEEVRALREDQRKLWEEVKAL 91
                                   44556666666666666666666666553 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.096
                        DUF4709  28 elkeltevtqkLvkevkslkrdfeflkqllqa 59 
                                    e+k l e+ +kL +evksl++ ++ l++ ++a
  gi|119720446|ref|YP_920941.1|  87 EVKALRENQEKLWEEVKSLREGQGKLWEEVKA 118
                                    68999****************99999998876 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.0028
                        DUF4709  28 elkeltevtqkLvkevkslkrdfeflkqllqakyee..klkeealelytrlndklkeleklykekvevvRksfkqQLa 103
                                    e+k l e  ++L +evk+l++++e l++ ++a  e+  kl e   +l+++++  l+e ++  +  v+ +R sf+ QL 
  gi|119720446|ref|YP_920941.1| 115 EVKALREDQRRLWEEVKALRENQEKLWEEVRALREDqgKLWEGQQRLWEEVR-ALREGQERLRGDVDGLRASFR-QLG 190
                                    6788889999999999999999999999998877764467788888888875.467777777888888888887.455 PP

>> Rbsn  Rabenosyn Rab binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       7.5   2.2e+03      22      30 ..      71      79 ..      68      84 .. 0.81
   2 ?    8.4   0.8    0.0059       1.8      21      41 ..      84     104 ..      79     105 .. 0.83
   3 ?   -1.1   0.0       5.4   1.6e+03      22      29 ..     113     120 ..     109     121 .. 0.85
   4 ?    9.7   0.8    0.0024      0.71      18      40 ..     123     145 ..     122     147 .. 0.87
   5 ?    2.3   0.1      0.46   1.4e+02      18      30 ..     158     170 ..     157     182 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 7.5
                           Rbsn 22 fDEvatLee 30
                                   ++Ev +L e
  gi|119720446|ref|YP_920941.1| 71 WEEVRALRE 79
                                   79***9976 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0059
                           Rbsn  21 rfDEvatLeeNLkELqeEidr 41 
                                     ++Ev++L eN + L eE++ 
  gi|119720446|ref|YP_920941.1|  84 LWEEVKALRENQEKLWEEVKS 104
                                    48*************999875 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 5.4
                           Rbsn  22 fDEvatLe 29 
                                    ++Ev++L 
  gi|119720446|ref|YP_920941.1| 113 WEEVKALR 120
                                    79****97 PP

  == domain 4  score: 9.7 bits;  conditional E-value: 0.0024
                           Rbsn  18 karrfDEvatLeeNLkELqeEid 40 
                                    ++r ++Ev++L eN + L eE+ 
  gi|119720446|ref|YP_920941.1| 123 QRRLWEEVKALRENQEKLWEEVR 145
                                    67889***********9999875 PP

  == domain 5  score: 2.3 bits;  conditional E-value: 0.46
                           Rbsn  18 karrfDEvatLee 30 
                                    ++r ++Ev +L e
  gi|119720446|ref|YP_920941.1| 158 QQRLWEEVRALRE 170
                                    7999*******87 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   3.6      0.13        40       4      52 ..      46      95 ..       7      98 .. 0.59
   2 ?   14.5   9.7    0.0001      0.03       4      95 ..      46     142 ..      43     148 .. 0.72
   3 ?    2.9   0.0      0.43   1.3e+02      23      61 ..     157     195 ..     138     199 .. 0.79
   4 ?   -1.5   0.1       9.7   2.9e+03      63      79 ..     255     271 ..     246     284 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.13
                                   HHHHHH-HHHHHHHHCC.CTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   Seryl_tRNA_N  4 iklirenpeavkeklkk.Rgedkadvdelleldekrrelqveleelqaer 52
                                   ik +re  e++ +k++k  ge  ++ +e+ +l e +r+l  e+ +l++++
  gi|119720446|ref|YP_920941.1| 46 IKALREGQEQLWRKQEKlWGEVRKLWEEVRALREDQRKLWEEVKALRENQ 95
                                   44445533333333322023445555555555555555555555555444 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 0.0001
                                    HHHHHH-HHHHHHHHCC.CTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT....S-TCCCCCCCHH CS
                   Seryl_tRNA_N   4 iklirenpeavkeklkk.RgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkk....edaeeliaevke 78 
                                    ik +re  e++ +k++k  ge  ++ +e+ +l e +r+l  e+ +l++++ +l +e++++ + +    e+ ++l+++ + 
  gi|119720446|ref|YP_920941.1|  46 IKALREGQEQLWRKQEKlWGEVRKLWEEVRALREDQRKLWEEVKALRENQEKLWEEVKSLREGQgklwEEVKALREDQRR 125
                                    8999996666666555415699999**********************************996544555555555555555 PP

                                    HHHHHHHHHHHHHHHHH CS
                   Seryl_tRNA_N  79 lkeelkaleaelkelea 95 
                                    l ee+kal +++++l +
  gi|119720446|ref|YP_920941.1| 126 LWEEVKALRENQEKLWE 142
                                    55555555555555544 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.43
                                    CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC CS
                   Seryl_tRNA_N  23 edkadvdelleldekrrelqveleelqaerNelskeIgk 61 
                                    +++ + +e+ +l e +++l+ +++ l+a   +l++++g+
  gi|119720446|ref|YP_920941.1| 157 GQQRLWEEVRALREGQERLRGDVDGLRASFRQLGEAVGM 195
                                    566778999999999999999999999999999988886 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 9.7
                                    CCTTS-TCCCCCCCHHH CS
                   Seryl_tRNA_N  63 kkkkedaeeliaevkel 79 
                                     +++ +a++l+++vk +
  gi|119720446|ref|YP_920941.1| 255 EDAEREAAKLMERVKVV 271
                                    44456777777777655 PP

>> DUF1394  Protein of unknown function (DUF1394)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   0.00011     0.034      16     125 ..      82     199 ..      51     204 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00011
                        DUF1394  16 revyeeveevlkeaeeileelksYkgaeeeireaisnpsd............eeaqekawkavlplvaklkefyefsskl 83 
                                    r+++eev+++ +++e++ ee+ks ++ + ++ e +++ ++            +e+qek w+ v  l + + + +e  ++l
  gi|119720446|ref|YP_920941.1|  82 RKLWEEVKALRENQEKLWEEVKSLREGQGKLWEEVKALREdqrrlweevkalRENQEKLWEEVRALREDQGKLWEGQQRL 161
                                    44444444444444444444444433333333333333211112333333333666666666666666666666666555 PP

                        DUF1394  84 ekvvpklleelcseklsakesLeqkqalakqfaeildfvlkF 125
                                     ++    +++l ++++  + +++   a ++q++e + ++l+F
  gi|119720446|ref|YP_920941.1| 162 WEE----VRALREGQERLRGDVDGLRASFRQLGEAVGMTLEF 199
                                    555....45666777777777777777777777777777777 PP

>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   1.2     0.017         5      12      52 ..      44      84 ..      33      85 .. 0.87
   2 ?   14.9   3.8   6.5e-05     0.019      14      72 ..      67     125 ..      65     127 .. 0.93
   3 ?    9.1   0.5    0.0043       1.3      12      71 ..     128     187 ..     127     190 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.017
                     TMF_DNA_bd 12 eqIaqLmeEGekLskkelklnntikkLrkknkelekeikel 52
                                    +I++L+e  e+L  k+ kl   + kL ++++ l +++++l
  gi|119720446|ref|YP_920941.1| 44 SEIKALREGQEQLWRKQEKLWGEVRKLWEEVRALREDQRKL 84
                                   589****************************9999999886 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 6.5e-05
                     TMF_DNA_bd  14 IaqLmeEGekLskkelklnntikkLrkknkelekeikelkkkleklekeleeleerlke 72 
                                    + +L eE  +L+  ++kl + +k Lr+  ++l +e+k+l +   kl +e++ l+e +++
  gi|119720446|ref|YP_920941.1|  67 VRKLWEEVRALREDQRKLWEEVKALRENQEKLWEEVKSLREGQGKLWEEVKALREDQRR 125
                                    67899*****************************************9999999998765 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0043
                     TMF_DNA_bd  12 eqIaqLmeEGekLskkelklnntikkLrkknkelekeikelkkkleklekeleeleerlk 71 
                                    e++++L+e+ ekL  + ++l++ + kL +  + l +e++ l +  e+l  +++ l+++++
  gi|119720446|ref|YP_920941.1| 128 EEVKALRENQEKLWEEVRALREDQGKLWEGQQRLWEEVRALREGQERLRGDVDGLRASFR 187
                                    78999**********************999999999999999999998888888777665 PP

>> Lectin_N  Hepatic lectin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.2      0.17        51      71     120 ..      42      94 ..      31     105 .. 0.64
   2 ?    8.5   0.4    0.0053       1.6      69     124 ..      68     126 ..      49     133 .. 0.70
   3 ?    6.8   0.2     0.017       5.2      70     124 ..     111     168 ..      94     171 .. 0.78
   4 ?   -0.5   0.0       3.2   9.7e+02      51      73 ..     173     195 ..     169     203 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.17
                       Lectin_N  71 tlaeiqalssqggslsekvtsleaklek...kqqdlkadhselllhvkqlvkd 120
                                    tl+ei+al+  +++l +k + l  +++k   + ++l++d+ +l   vk l+++
  gi|119720446|ref|YP_920941.1|  42 TLSEIKALREGQEQLWRKQEKLWGEVRKlweEVRALREDQRKLWEEVKALREN 94 
                                    67777777776666666655555444431115566777777777777777665 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0053
                       Lectin_N  69 sstlaeiqalssqggslsekvtsleaklek...kqqdlkadhselllhvkqlvkdLrtL 124
                                     +   e++al+  +++l e+v+ l+ + ek   + ++l++ + +l   vk l++d r L
  gi|119720446|ref|YP_920941.1|  68 RKLWEEVRALREDQRKLWEEVKALRENQEKlweEVKSLREGQGKLWEEVKALREDQRRL 126
                                    55567888888888888888888876555422266778888888888888888888877 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.017
                       Lectin_N  70 stlaeiqalssqggslsekvtsleaklek...kqqdlkadhselllhvkqlvkdLrtL 124
                                    +   e++al+  +++l e+v+ l+ + ek   + ++l++d+ +l    ++l +++r+L
  gi|119720446|ref|YP_920941.1| 111 KLWEEVKALREDQRRLWEEVKALRENQEKlweEVRALREDQGKLWEGQQRLWEEVRAL 168
                                    5567999***********9999987666522266789999999999999999999998 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 3.2
                       Lectin_N  51 sqLqreLetLketfsnfssstla 73 
                                     +L+ ++  L+++f+ + + + +
  gi|119720446|ref|YP_920941.1| 173 ERLRGDVDGLRASFRQLGEAVGM 195
                                    689***********988776655 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   2.1      0.01         3     334     415 ..      34     108 ..      21     117 .. 0.66
   2 ?    9.2   7.1    0.0014      0.41     334     428 ..      76     166 ..      43     176 .. 0.85
   3 ?    7.3   0.1    0.0053       1.6     334     408 ..     118     193 ..     110     222 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.01
                           FapA 334 elkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeeleskke 413
                                    +l ek+++   e+++l+e +e+l +k       ++ +    +  e++  l+e++ kl ee+++l+e++++l ee++s  +
  gi|119720446|ref|YP_920941.1|  34 DLLEKMDATLSEIKALREGQEQLWRKQ------EKLWGEVRKLWEEVRALREDQRKLWEEVKALRENQEKLWEEVKSL-R 106
                                    444555555555555555555555552......334444455668888888888999999999999999998888888.3 PP

                           FapA 414 ea 415
                                    e+
  gi|119720446|ref|YP_920941.1| 107 EG 108
                                    33 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0014
                           FapA 334 elkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeelesk.k 412
                                    +l+e +++l ee+++l+e++ekl +++k+l++ +       +  e++k l+e++ +l ee+++l+e++++l ee++   +
  gi|119720446|ref|YP_920941.1|  76 ALREDQRKLWEEVKALRENQEKLWEEVKSLREGQ------GKLWEEVKALREDQRRLWEEVKALRENQEKLWEEVRALrE 149
                                    6778889999999999**********99999933......35679****************************9999963 PP

                           FapA 413 eea.kikvnkeiypgvk 428
                                    +++  ++ +++++ +v+
  gi|119720446|ref|YP_920941.1| 150 DQGkLWEGQQRLWEEVR 166
                                    44447777777777765 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0053
                           FapA 334 elkeklkeleeeleeleeeleklkkkikklpklka.ekqlesekkeqlkklletkeklkeeleeleeelkelkeel 408
                                    +l+e +++l ee+++l+e++ekl ++++ l++ +   ++ +++  e++  l+e +e+l+ ++  l++ + +l e +
  gi|119720446|ref|YP_920941.1| 118 ALREDQRRLWEEVKALRENQEKLWEEVRALREDQGkLWEGQQRLWEEVRALREGQERLRGDVDGLRASFRQLGEAV 193
                                    6788889999999999999999999988888866568999999999999999999999999999999999988876 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.4     0.013         4      12      58 ..      60     106 ..      30     117 .. 0.63
   2 ?    6.7   0.6      0.02         6      10      67 ..      79     136 ..      72     145 .. 0.72
   3 ?    4.5   0.1       0.1        30      12      58 ..     116     162 ..     107     180 .. 0.52

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.013
                          Sec34  12 cdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrle 58 
                                     ++l  +++++ e+++ l+e+ ++  e+ ++l+e+ e+l ee k+l+
  gi|119720446|ref|YP_920941.1|  60 QEKLWGEVRKLWEEVRALREDQRKLWEEVKALRENQEKLWEEVKSLR 106
                                    34555666666666666666666666666666666666666666655 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.02
                          Sec34  10 eecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieek 67 
                                    e  ++l e+++++ e+ e+l e++ks  e   +l e+ + l e+q+rl e +++++e+
  gi|119720446|ref|YP_920941.1|  79 EDQRKLWEEVKALRENQEKLWEEVKSLREGQGKLWEEVKALREDQRRLWEEVKALREN 136
                                    5566777788888888888888888888888888888888888888877766666654 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.1
                          Sec34  12 cdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrle 58 
                                    +++l e+ +++ e+++ l+e+ ++  e+ ++l+e+  +l e q+rl 
  gi|119720446|ref|YP_920941.1| 116 VKALREDQRRLWEEVKALRENQEKLWEEVRALREDQGKLWEGQQRLW 162
                                    33444444444444444444444444444444444444444444443 PP

>> VPS11_C  Vacuolar protein sorting protein 11 C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0      0.17        49       2      19 ..      44      61 ..      43      68 .. 0.81
   2 ?    0.5   0.1       2.5   7.3e+02       2      14 ..      72      84 ..      71      87 .. 0.88
   3 ?    2.3   0.1      0.65   1.9e+02       2      14 ..      86      98 ..      85     107 .. 0.88
   4 ?   -0.1   0.0       3.8   1.1e+03       2      13 ..     114     125 ..     113     126 .. 0.87
   5 ?    2.1   0.2      0.75   2.2e+02       2      14 ..     128     140 ..     127     148 .. 0.89
   6 ?    6.2   0.0     0.042        12       2      24 ..     163     185 ..     162     191 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.17
                        VPS11_C  2 etirelrraQeesadrhd 19
                                    +i++lr+ Qe++  + +
  gi|119720446|ref|YP_920941.1| 44 SEIKALREGQEQLWRKQE 61
                                   589*********966655 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 2.5
                        VPS11_C  2 etirelrraQees 14
                                   e++r+lr++Q+++
  gi|119720446|ref|YP_920941.1| 72 EEVRALREDQRKL 84
                                   689*******985 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.65
                        VPS11_C  2 etirelrraQees 14
                                   e++++lr++Qe++
  gi|119720446|ref|YP_920941.1| 86 EEVKALRENQEKL 98
                                   689********86 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 3.8
                        VPS11_C   2 etirelrraQee 13 
                                    e++++lr++Q++
  gi|119720446|ref|YP_920941.1| 114 EEVKALREDQRR 125
                                    689*******97 PP

  == domain 5  score: 2.1 bits;  conditional E-value: 0.75
                        VPS11_C   2 etirelrraQees 14 
                                    e++++lr++Qe++
  gi|119720446|ref|YP_920941.1| 128 EEVKALRENQEKL 140
                                    689********86 PP

  == domain 6  score: 6.2 bits;  conditional E-value: 0.042
                        VPS11_C   2 etirelrraQeesadrhdlFkaa 24 
                                    e++r+lr+ Qe++ ++ d + a+
  gi|119720446|ref|YP_920941.1| 163 EEVRALREGQERLRGDVDGLRAS 185
                                    689************99988776 PP

>> DUF2205  Short coiled-coil protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   2.9     0.061        18      15      59 ..      50      94 ..      37     109 .. 0.72
   2 ?    7.8   2.5     0.011       3.2      12      56 ..      75     119 ..      66     121 .. 0.83
   3 ?    7.5   4.7     0.014       4.1      13      57 ..      90     134 ..      86     140 .. 0.89
   4 ?    9.8   1.4    0.0026      0.76      13      53 ..     118     158 ..     113     163 .. 0.85
   5 ?    0.6   0.0         2   5.8e+02      13      37 ..     167     191 ..     158     195 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.061
                        DUF2205 15 rearerLqqqakeLqssLqaLaervdeVkeehdKLesenrfLqqY 59
                                   re +e+L ++ ++L    ++L e v + +e++ KL  e + L + 
  gi|119720446|ref|YP_920941.1| 50 REGQEQLWRKQEKLWGEVRKLWEEVRALREDQRKLWEEVKALREN 94
                                   677777777777777788888888888888888888777777654 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.011
                        DUF2205  12 klerearerLqqqakeLqssLqaLaervdeVkeehdKLesenrfL 56 
                                    ++ re++ +L + +k+L +  ++L e v + +e + KL  e + L
  gi|119720446|ref|YP_920941.1|  75 RALREDQRKLWEEVKALRENQEKLWEEVKSLREGQGKLWEEVKAL 119
                                    445788889999999999999999999999999999999988877 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.014
                        DUF2205  13 lerearerLqqqakeLqssLqaLaervdeVkeehdKLesenrfLq 57 
                                    + re++e+L + +k+L ++  +L e v + +e++ +L  e + L 
  gi|119720446|ref|YP_920941.1|  90 ALRENQEKLWEEVKSLREGQGKLWEEVKALREDQRRLWEEVKALR 134
                                    55899********************************99999886 PP

  == domain 4  score: 9.8 bits;  conditional E-value: 0.0026
                        DUF2205  13 lerearerLqqqakeLqssLqaLaervdeVkeehdKLesen 53 
                                    + re++ rL + +k+L +  ++L e v + +e++ KL    
  gi|119720446|ref|YP_920941.1| 118 ALREDQRRLWEEVKALRENQEKLWEEVRALREDQGKLWEGQ 158
                                    4579999*****************************96655 PP

  == domain 5  score: 0.6 bits;  conditional E-value: 2
                        DUF2205  13 lerearerLqqqakeLqssLqaLae 37 
                                    + re +erL+  ++ L +s ++L e
  gi|119720446|ref|YP_920941.1| 167 ALREGQERLRGDVDGLRASFRQLGE 191
                                    4467788888888888888887766 PP

>> TelA  Toxic anion resistance protein (TelA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.8    0.0063       1.9      78     135 ..      47     107 ..      33     121 .. 0.68
   2 ?    5.4   0.3     0.028       8.3     104     135 ..     118     149 ..     114     179 .. 0.59

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0063
                           TelA  78 kkaknkieklfakYekaeeqidkI...vkeLekgqdellkdnaaLdqlyeknleyfkeLek 135
                                    k +++  e+l +k ek+  ++ k+   v++L++ q++l + ++aL + +ek++e +k L++
  gi|119720446|ref|YP_920941.1|  47 KALREGQEQLWRKQEKLWGEVRKLweeVRALREDQRKLWEEVKALRENQEKLWEEVKSLRE 107
                                    4455555666667777777777763334567788888888888888888888888888765 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.028
                           TelA 104 eLekgqdellkdnaaLdqlyeknleyfkeLek 135
                                    +L++ q++l + ++aL + +ek++e +++L++
  gi|119720446|ref|YP_920941.1| 118 ALREDQRRLWEEVKALRENQEKLWEEVRALRE 149
                                    56666666666666666666666666666654 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0     0.034        10      39      87 ..      47     105 ..      24     121 .. 0.61
   2 ?    2.7   0.0      0.49   1.5e+02      47      65 ..     128     146 ..     104     195 .. 0.53
   3 ?    0.0   0.1       3.4     1e+03      47      72 ..     252     281 ..     242     296 .. 0.45

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.034
                         DUF948  39 e..........kqvdpilkevedllakvnelledvneklekvdplteavadlgesvsel 87 
                                    +          ++ +++  ev++l ++v++l ed ++  e+v++l e+ ++l e v++l
  gi|119720446|ref|YP_920941.1|  47 KalregqeqlwRKQEKLWGEVRKLWEEVRALREDQRKLWEEVKALRENQEKLWEEVKSL 105
                                    33333333333666666666666666666666666666666666666666665555555 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.49
                         DUF948  47 kevedllakvnelledvne 65 
                                    +ev++l ++ ++l e+v+ 
  gi|119720446|ref|YP_920941.1| 128 EEVKALRENQEKLWEEVRA 146
                                    4444444444444444432 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 3.4
                         DUF948  47 kevedllakvnelledvne....klekvdp 72 
                                    + +ed+ +++ +l+e v+        kv+ 
  gi|119720446|ref|YP_920941.1| 252 RSAEDAEREAAKLMERVKVveeiSGRKVEL 281
                                    333333333333333333322233344444 PP

>> Serine_rich  Serine rich protein interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   7.7    0.0017      0.51      16     107 ..      41     137 ..      31     153 .. 0.87
   2 ?    1.2   0.0       1.1   3.4e+02      33      53 ..     169     190 ..     135     206 .. 0.47
   3 ?    1.3   0.0         1     3e+02      25      72 ..     244     291 ..     241     308 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0017
                    Serine_rich  16 evesavskLlsfvsskWRskenleanlqeirlavdrlrtslrefleFargalanaaklsd.....knlqtkLrkqlqkle 90 
                                    +  s +++L +  ++ WR++e+l  +++++++ v +lr+  r++ e  +  + n  kl +     ++ q kL +++++l+
  gi|119720446|ref|YP_920941.1|  41 ATLSEIKALREGQEQLWRKQEKLWGEVRKLWEEVRALREDQRKLWEEVKALRENQEKLWEevkslREGQGKLWEEVKALR 120
                                    55678999999999*******************************************9888866777799********** PP

                    Serine_rich  91 dsdqilqetsqeLdsce 107
                                    ++++ l e  ++L +++
  gi|119720446|ref|YP_920941.1| 121 EDQRRLWEEVKALRENQ 137
                                    *********99998875 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 1.1
                    Serine_rich  33 Rs.kenleanlqeirlavdrlr 53 
                                    R  +e+l+ +++ +r+++ +l 
  gi|119720446|ref|YP_920941.1| 169 REgQERLRGDVDGLRASFRQLG 190
                                    2213444444444444444444 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 1
                    Serine_rich  25 lsfvsskWRskenleanlqeirlavdrlrtslrefleFargalanaak 72 
                                    ++ v++  Rs e  e++++++ + v+ +++     +e+a  a+an  +
  gi|119720446|ref|YP_920941.1| 244 VGEVTTYLRSAEDAEREAAKLMERVKVVEEISGRKVELAVLAVANLGR 291
                                    5667788899999************99999999999999988888664 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7  12.0    0.0077       2.3      20      63 ..      60     103 ..      31     105 .. 0.59
   2 ?    6.2  12.8     0.046        14       9      64 ..      91     146 ..      82     147 .. 0.62
   3 ?    7.6   5.8     0.017         5      13      65 ..     130     182 ..     125     188 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0077
                           ZapB  20 itlLqmeieeLkeeneelkeenreleeeneqlkeereawqerlk 63 
                                     ++L  e+++L ee+++l e +r+l ee+++l+e++e++ e +k
  gi|119720446|ref|YP_920941.1|  60 QEKLWGEVRKLWEEVRALREDQRKLWEEVKALRENQEKLWEEVK 103
                                    34555566666666666666666666777777777776666665 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.046
                           ZapB   9 LEskiqkaidtitlLqmeieeLkeeneelkeenreleeeneqlkeereawqerlkk 64 
                                    L +  +k+ +++++L++   +L ee+++l e +r+l ee+++l+e++e++ e +++
  gi|119720446|ref|YP_920941.1|  91 LRENQEKLWEEVKSLREGQGKLWEEVKALREDQRRLWEEVKALRENQEKLWEEVRA 146
                                    33444455556666666666666666666666666669999999999988776665 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.017
                           ZapB  13 iqkaidtitlLqmeieeLkeeneelkeenreleeeneqlkeereawqerlkkL 65 
                                    ++++ ++ ++L +e+++L+e++ +l e +++l ee+ +l+e +e ++  +++L
  gi|119720446|ref|YP_920941.1| 130 VKALRENQEKLWEEVRALREDQGKLWEGQQRLWEEVRALREGQERLRGDVDGL 182
                                    56666777888888888888888888888888899999999999887766655 PP

>> JAKMIP_CC3  JAKMIP CC3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5  23.4     0.024       7.1      93     185 ..      35     131 ..       7     191 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.024
                     JAKMIP_CC3  93 Lreklggeldaerelka.reqleselrktkskikdLeeaLaqkGqdskwveekQalikrnqe.LvekikkleeeeskLkq 170
                                    L ek+ ++l   + l++ +eql    +k   ++++L e+ +   +d++ + e  + +++nqe L e +k+l+e ++kL +
  gi|119720446|ref|YP_920941.1|  35 LLEKMDATLSEIKALREgQEQLWRKQEKLWGEVRKLWEEVRALREDQRKLWEEVKALRENQEkLWEEVKSLREGQGKLWE 114
                                    33444444444455544355555555666666666655555555666666555566777888899999999999999999 PP

                     JAKMIP_CC3 171 eiqdlr.dqnelLE.fr 185
                                    e+++lr dq++l E  +
  gi|119720446|ref|YP_920941.1| 115 EVKALReDQRRLWEeVK 131
                                    99999944677776333 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   5.0     0.021       6.3      59     129 ..      36     106 ..      10     111 .. 0.74
   2 ?   12.8   0.7   0.00032     0.096      56     133 ..     110     187 ..     106     189 .. 0.93

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.021
                           ADIP  59 netirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrlknalqqik 129
                                     e++    +ei+ l+   e+l ++ e+l  e+  + ++ r l+ ++++l + +k ++e  ++l   +++++
  gi|119720446|ref|YP_920941.1|  36 LEKMDATLSEIKALREGQEQLWRKQEKLWGEVRKLWEEVRALREDQRKLWEEVKALRENQEKLWEEVKSLR 106
                                    34455556778888888888888888888899988889999999999999999999999999888888776 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00032
                           ADIP  56 eslnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrlknalqqiktqya 133
                                     +l e+++ l+ +  rl  +++ l ++ e+l  e+ ++ +++ +l   +++l + ++ ++e  +rl+ +++ ++++++
  gi|119720446|ref|YP_920941.1| 110 GKLWEEVKALREDQRRLWEEVKALRENQEKLWEEVRALREDQGKLWEGQQRLWEEVRALREGQERLRGDVDGLRASFR 187
                                    56778999**************************************************************99999987 PP

>> PI3K_P85_iSH2  Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   5.1   0.00071      0.21      48     132 ..      55     137 ..      33     143 .. 0.83
   2 ?    1.6   0.1      0.63   1.9e+02      82     120 ..     129     167 ..     127     196 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00071
                  PI3K_P85_iSH2  48 qlkrqaleaFneaikmFeeqiklqekfskeaqehEieklqenleqlksrlkelhsskekLeedlkqqkeeereleReina 127
                                    ql r + + ++e+ k++ee  +l e   k    +E++ l en e+l + +k+l++ + kL e++k+  e++r l  e+ a
  gi|119720446|ref|YP_920941.1|  55 QLWRKQEKLWGEVRKLWEEVRALREDQRK--LWEEVKALRENQEKLWEEVKSLREGQGKLWEEVKALREDQRRLWEEVKA 132
                                    45566667788888888888888888555..4579***************************************999999 PP

                  PI3K_P85_iSH2 128 lkpel 132
                                    l+ + 
  gi|119720446|ref|YP_920941.1| 133 LRENQ 137
                                    98765 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.63
                  PI3K_P85_iSH2  82 EieklqenleqlksrlkelhsskekLeedlkqqkeeere 120
                                    E++ l en e+l + +  l++ + kL e  +   ee r 
  gi|119720446|ref|YP_920941.1| 129 EVKALRENQEKLWEEVRALREDQGKLWEGQQRLWEEVRA 167
                                    555555555555555555555555554433333333333 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   3.3     0.023       6.8      27      59 ..      66      98 ..      45     103 .. 0.62
   2 ?    7.7   2.8     0.013       3.8      28      62 ..      81     115 ..      78     124 .. 0.58
   3 ?    7.5   1.5     0.015       4.4      28      63 ..     109     144 ..     103     145 .. 0.88
   4 ?    6.1   1.9      0.04        12      26      55 ..     121     150 ..     114     156 .. 0.66
   5 ?    0.7   0.0       1.9   5.7e+02      28      59 ..     158     189 ..     153     193 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.023
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         bZIP_1 27 eieeLerrvkaLekeNksLkseleelkkevekL 59
                                   e+ +L ++v aL +   +L +e++ l+++ ekL
  gi|119720446|ref|YP_920941.1| 66 EVRKLWEEVRALREDQRKLWEEVKALRENQEKL 98
                                   455666666666666666666666666666666 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.013
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         bZIP_1  28 ieeLerrvkaLekeNksLkseleelkkevekLksk 62 
                                    + +L ++vkaL +  ++L +e+++l++   kL ++
  gi|119720446|ref|YP_920941.1|  81 QRKLWEEVKALRENQEKLWEEVKSLREGQGKLWEE 115
                                    55666666666666666666666666555444333 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.015
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         bZIP_1  28 ieeLerrvkaLekeNksLkseleelkkevekLkskv 63 
                                    + +L ++vkaL +    L +e++ l+++ ekL ++v
  gi|119720446|ref|YP_920941.1| 109 QGKLWEEVKALREDQRRLWEEVKALRENQEKLWEEV 144
                                    678999***********************9997765 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.04
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         bZIP_1  26 aeieeLerrvkaLekeNksLkseleelkke 55 
                                    + + +L ++vkaL +  ++L +e+  l+++
  gi|119720446|ref|YP_920941.1| 121 EDQRRLWEEVKALRENQEKLWEEVRALRED 150
                                    556667777777777777777777777665 PP

  == domain 5  score: 0.7 bits;  conditional E-value: 1.9
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         bZIP_1  28 ieeLerrvkaLekeNksLkseleelkkevekL 59 
                                    +++L ++v aL +  + L+  ++ l+    +L
  gi|119720446|ref|YP_920941.1| 158 QQRLWEEVRALREGQERLRGDVDGLRASFRQL 189
                                    67888889999988888888888887666655 PP

>> JIP_LZII  JNK-interacting protein  leucine zipper II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   1.0    0.0042       1.3       5      70 ..       7      74 ..       5      75 .. 0.77
   2 ?    6.7   1.9     0.026       7.9      31      66 ..      70     105 ..      67     109 .. 0.85
   3 ?    7.8   2.0     0.012       3.7      32      68 ..     113     149 ..     109     152 .. 0.89
   4 ?    1.3   0.0       1.3   3.9e+02      41      64 ..     157     180 ..     152     187 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0042
                       JIP_LZII  5 kevenLikENteLletknaLn..vvkddLIarvdeLtsereiLreEleslqkakerlesrikelEeel 70
                                   +e+e Lik  +e +e + aL      +dL+++ d   se ++Lre  e+l   +e+l  ++++l ee+
  gi|119720446|ref|YP_920941.1|  7 REWERLIKALEEDRELRYALAglLGFRDLLEKMDATLSEIKALREGQEQLWRKQEKLWGEVRKLWEEV 74
                                   667777664444444444443114568********************************999998886 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.026
                       JIP_LZII  31 LIarvdeLtsereiLreEleslqkakerlesrikel 66 
                                    L ++v  L +++  L eE+++l++++e+l +++k l
  gi|119720446|ref|YP_920941.1|  70 LWEEVRALREDQRKLWEEVKALRENQEKLWEEVKSL 105
                                    55678889999999*************999999987 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.012
                       JIP_LZII  32 IarvdeLtsereiLreEleslqkakerlesrikelEe 68 
                                     ++v  L +++  L eE+++l++++e+l +++++l e
  gi|119720446|ref|YP_920941.1| 113 WEEVKALREDQRRLWEEVKALRENQEKLWEEVRALRE 149
                                    5679999**********************99999876 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 1.3
                       JIP_LZII  41 ereiLreEleslqkakerlesrik 64 
                                     ++ L eE+++l++ +erl+  + 
  gi|119720446|ref|YP_920941.1| 157 GQQRLWEEVRALREGQERLRGDVD 180
                                    577888999999999999887665 PP

>> DUF2968  Protein of unknown function (DUF2968)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   2.1    0.0094       2.8     127     179 ..      44      96 ..      35      97 .. 0.89
   2 ?    2.8   7.6      0.27        82     108     177 ..      82     150 ..      73     154 .. 0.66
   3 ?    8.3   3.3    0.0054       1.6     112     174 ..     127     189 ..     114     194 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0094
                        DUF2968 127 adlavarqQeqavaerQkqarkeaaaLeaqreaaqaqlralqrqirqLqaqqe 179
                                    ++++  r+ ++++ ++Q+++  e+++L ++ +a+++  r+l +++++L ++qe
  gi|119720446|ref|YP_920941.1|  44 SEIKALREGQEQLWRKQEKLWGEVRKLWEEVRALREDQRKLWEEVKALRENQE 96 
                                    678888999999************************************99886 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.27
                        DUF2968 108 kaqlerqiaasearaerLqadlavarqQeqavaerQkqarkeaaaLeaqreaaqaqlralqrqirqLqaq 177
                                    ++  e +++a +++ e+L ++++  r+ + ++ e+ k++r++ + L ++ +a++++ ++l +++r+L ++
  gi|119720446|ref|YP_920941.1|  82 RKLWE-EVKALRENQEKLWEEVKSLREGQGKLWEEVKALREDQRRLWEEVKALRENQEKLWEEVRALRED 150
                                    33333.3444445557777777777777777777777777777777777777777777777777777665 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0054
                        DUF2968 112 erqiaasearaerLqadlavarqQeqavaerQkqarkeaaaLeaqreaaqaqlralqrqirqL 174
                                     ++++a +++ e+L ++++  r+ + ++ e Q+ + +e++aL++ +e+++  ++ l+   rqL
  gi|119720446|ref|YP_920941.1| 127 WEEVKALRENQEKLWEEVRALREDQGKLWEGQQRLWEEVRALREGQERLRGDVDGLRASFRQL 189
                                    334555556667788888888888888888888888888888888888888888887777777 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   7.4    0.0001     0.031      24      91 ..      37     104 ..      32     111 .. 0.89
   2 ?    5.6   9.1     0.052        16      38      92 ..      93     147 ..      93     178 .. 0.64
   3 ?   -0.3   0.5       3.4     1e+03      15      49 ..     257     288 ..     248     315 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 0.0001
                 CENP-F_leu_zip  24 dkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelqk 91 
                                    +k ++  +e++ + e qe++ +  E+   ev +l ee++ l+e  r+l  +++alr+++e+L +e++ 
  gi|119720446|ref|YP_920941.1|  37 EKMDATLSEIKALREGQEQLWRKQEKLWGEVRKLWEEVRALREDQRKLWEEVKALRENQEKLWEEVKS 104
                                    455556689999**************************************************988775 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.052
                 CENP-F_leu_zip  38 enqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelqkk 92 
                                    enqek+  e+ + ++   +l ee++ l+e  r+l  +++alr+++e+L +e++  
  gi|119720446|ref|YP_920941.1|  93 ENQEKLWEEVKSLREGQGKLWEEVKALREDQRRLWEEVKALRENQEKLWEEVRAL 147
                                    5677777777777777777777777777777777777777777777776554332 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 3.4
                 CENP-F_leu_zip  15 serkadsLkdkvenLerelemseenqekvileaEt 49 
                                    +er+a++L ++v+  e   e+s+++ e ++l + +
  gi|119720446|ref|YP_920941.1| 257 AEREAAKLMERVKVVE---EISGRKVELAVLAVAN 288
                                    5677777777777666...5666666666666554 PP

>> UPF0449  Uncharacterised protein family UPF0449
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   1.8    0.0089       2.7      48     100 ..      51     103 ..      32     108 .. 0.75
   2 ?    4.3   1.0      0.18        55      57      97 ..     109     149 ..     103     153 .. 0.82
   3 ?    5.6   1.8     0.073        22      48      99 ..     128     179 ..     114     198 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0089
                        UPF0449  48 seeedleaeveelYeqvrtylelnerLeeakeeLkqkceeLktageeLeeeie 100
                                    + +e+l  ++e+l+ +vr++ e  + L+e + +L ++++ L+ + e+L ee++
  gi|119720446|ref|YP_920941.1|  51 EGQEQLWRKQEKLWGEVRKLWEEVRALREDQRKLWEEVKALRENQEKLWEEVK 103
                                    35566666788888888888888888888888888888888888888888775 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.18
                        UPF0449  57 veelYeqvrtylelnerLeeakeeLkqkceeLktageeLee 97 
                                    + +l+e+v+++ e ++rL e+ + L+++ e+L    + L+e
  gi|119720446|ref|YP_920941.1| 109 QGKLWEEVKALREDQRRLWEEVKALRENQEKLWEEVRALRE 149
                                    66788899999999999999999999999999988888776 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.073
                        UPF0449  48 seeedleaeveelYeqvrtylelnerLeeakeeLkqkceeLktageeLeeei 99 
                                    +e ++l++++e+l+e+vr++ e + +L e +++L +++  L+   e+L+ ++
  gi|119720446|ref|YP_920941.1| 128 EEVKALRENQEKLWEEVRALREDQGKLWEGQQRLWEEVRALREGQERLRGDV 179
                                    4455667778888888888888888888888888888888887777776555 PP

>> DUF2353  Uncharacterized coiled-coil protein (DUF2353)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0  15.5     0.011       3.2      31     173 ..      35     175 ..      30     179 .. 0.66
   2 ?    2.1   0.4      0.34     1e+02      75     106 ..     156     187 ..     142     201 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.011
                        DUF2353  31 maeqLqerlsalkkqleeekakaadlkeekekekklsqlleesreenkalkleveeLrqklkeaqgDiklLReqlarqrl 110
                                     +e++  +ls++k   e +++ ++++++   + +kl + ++  re +++l +ev++Lr+  + + + +k LRe + +  l
  gi|119720446|ref|YP_920941.1|  35 LLEKMDATLSEIKALREGQEQLWRKQEKLWGEVRKLWEEVRALREDQRKLWEEVKALRENQEKLWEEVKSLREGQGK--L 112
                                    56777777788887777888888777766777777777778888888888888888888888888888888843332..2 PP

                        DUF2353 111 glkdedlletrhssaeereelvkqlEklkekiqqlerdlkavldekeelvterdaykeKaerL 173
                                      +++ l e++    ee + l ++ Ekl e  + l+ d  ++ + ++ l  e  a +e  erL
  gi|119720446|ref|YP_920941.1| 113 WEEVKALREDQRRLWEEVKALRENQEKLWEEVRALREDQGKLWEGQQRLWEEVRALREGQERL 175
                                    333444444444446666666677777777777777777777777777777766666666666 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.34
                        DUF2353  75 eenkalkleveeLrqklkeaqgDiklLReqla 106
                                    e +++l +ev +Lr+  + ++gD++ LR+++ 
  gi|119720446|ref|YP_920941.1| 156 EGQQRLWEEVRALREGQERLRGDVDGLRASFR 187
                                    55677888899999999999999999986554 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   7.2      0.19        56      58      79 ..      82     103 ..      32     199 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.19
                                    HHHHHHHHHHHHHHHHHHH... CS
                          DUF16  58 ekqgekikelkveqkaqgeeln 79 
                                    +k+ e++k l+++q++  ee++
  gi|119720446|ref|YP_920941.1|  82 RKLWEEVKALRENQEKLWEEVK 103
                                    2222222222222222222222 PP

>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   2.2    0.0018      0.53      19     114 ..      78     173 ..      32     192 .. 0.61

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0018
                     V_ATPase_I  19 nafqrkfvkevrrcdemerklrfleeeieklekavikeeeaeesleapeekeldeleeelekleeelkelnenleklkke 98 
                                    ++ qrk  +ev+ + e ++kl    + +++ + + ++e +a ++ +++  +e++ l e+ ekl ee++ l+e + kl + 
  gi|119720446|ref|YP_920941.1|  78 REDQRKLWEEVKALRENQEKLWEEVKSLREGQGKLWEEVKALREDQRRLWEEVKALRENQEKLWEEVRALREDQGKLWEG 157
                                    33355555555555555555554444555545555555555555555555555555666666666666666666666665 PP

                     V_ATPase_I  99 lnelvelkavlekake 114
                                    +++l e+   l++ +e
  gi|119720446|ref|YP_920941.1| 158 QQRLWEEVRALREGQE 173
                                    5555555555555554 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0  13.9      0.02         6      75     180 ..      38     143 ..      32     143 .. 0.90
   2 ?    7.3   3.5     0.017       5.1     107     193 ..     126     213 ..     121     217 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.02
                          ATG16  75 kiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvq 154
                                    k+ ++ +++++lre +++l +++++l   +++l ee+++l+e  ++  e++++l+++ ++l +++k+++e    + + v+
  gi|119720446|ref|YP_920941.1|  38 KMDATLSEIKALREGQEQLWRKQEKLWGEVRKLWEEVRALREDQRKLWEEVKALRENQEKLWEEVKSLREGQGKLWEEVK 117
                                    56677789**************************************************************9999999999 PP

                          ATG16 155 dlqDElsaLqlqlnqaEeklrklekE 180
                                    +l+++   L  +++ + e+ +kl +E
  gi|119720446|ref|YP_920941.1| 118 ALREDQRRLWEEVKALRENQEKLWEE 143
                                    99999988888888888888887665 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.017
                          ATG16 107 lneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDElsaLqlqlnqaEeklr.klekENkeLv 185
                                    l ee+++l+e+ ++  e++++l+++  +l +  +++ ee+r +++  + l+ +++ L+  + q+ e+   +le  ++  +
  gi|119720446|ref|YP_920941.1| 126 LWEEVKALRENQEKLWEEVRALREDQGKLWEGQQRLWEEVRALREGQERLRGDVDGLRASFRQLGEAVGmTLEFYAAAFL 205
                                    56899999999999************************************************997776549999999999 PP

                          ATG16 186 eRWmkrka 193
                                    eR++++k+
  gi|119720446|ref|YP_920941.1| 206 ERLLAEKG 213
                                    99999986 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   4.2    0.0017      0.52       3      77 ..      66     139 ..      64     173 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0017
                          TMPIT   3 eweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk..eeeeeeveelkeelke 77 
                                    e+++l +e+++l+e ++++ ++++ l + q+k+ +e+k+ ++   +l++++k l+++++      eev+ l+e+ ++
  gi|119720446|ref|YP_920941.1|  66 EVRKLWEEVRALREDQRKLWEEVKALRENQEKLWEEVKSLREGQGKLWEEVKALREDQRrlW---EEVKALRENQEK 139
                                    67788889999999999999999999999999999999999999999999999887744331...222222222222 PP

>> DUF1640  Protein of unknown function (DUF1640)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   7.8      0.35     1e+02      71     143 ..      71     148 ..      18     155 .. 0.66
   2 ?    5.0   0.0     0.075        22      72      97 ..     163     188 ..     154     195 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.35
                        DUF1640  71 rsefaalrseteklqreleklk...qkLreeidklkadirldlnleKgrireelakleakiqel...nnkidrevsalr 143
                                     +e+ alr+++ kl +e+++l+   +kL ee++ l+++ + +l +e +  re++ +l ++++ l   ++k+ +ev alr
  gi|119720446|ref|YP_920941.1|  71 WEEVRALREDQRKLWEEVKALRenqEKLWEEVKSLREG-QGKLWEEVKALREDQRRLWEEVKALrenQEKLWEEVRALR 148
                                    35677777777777777777762224677777777777.7777777777777777777766544333667777777776 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.075
                        DUF1640  72 sefaalrseteklqreleklkqkLre 97 
                                    +e+ alr+ +e+l+ +++ l+ ++r+
  gi|119720446|ref|YP_920941.1| 163 EEVRALREGQERLRGDVDGLRASFRQ 188
                                    68999****************99986 PP

>> HAP1_N  HAP1 N-terminal conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2  18.5    0.0043       1.3     185     296 ..      52     169 ..      14     192 .. 0.53

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0043
                         HAP1_N 185 easqLktetdtlEekEqqLvldcveqlseanqqiaelseelarkleelerqqeeissLlaqivdlqqklkelgveneelk 264
                                      +qL +++++l  +    v ++ e+++  +++  +l ee++  +e++e+  ee++sL+    +l + +k l +++  l 
  gi|119720446|ref|YP_920941.1|  52 GQEQLWRKQEKLWGE----VRKLWEEVRALREDQRKLWEEVKALRENQEKLWEEVKSLREGQGKLWEEVKALREDQRRLW 127
                                    444443333333222....2233344444445555555666666666666666666666655666666666666666666 PP

                         HAP1_N 265 qhLaaskeaqrqLtaE..........LqdlqekyaevegmLh 296
                                    ++ +a +e+q++L +E          L + q++  e    L+
  gi|119720446|ref|YP_920941.1| 128 EEVKALRENQEKLWEEvralredqgkLWEGQQRLWEEVRALR 169
                                    666666666666666633333333333333333333333333 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.9      0.14        43      21      50 ..      41      70 ..      26      80 .. 0.69
   2 ?    8.0   3.0    0.0081       2.4      16      53 ..      71     108 ..      67     112 .. 0.85
   3 ?    7.9   3.1    0.0088       2.6      16      54 ..     113     151 ..     110     156 .. 0.85
   4 ?    4.0   0.2      0.15        44      24      57 ..     142     175 ..     139     189 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.14
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHCC- CS
                          DivIC 21 qlkqeiaalqaelaklkaeneeLeaevkdL 50
                                   ++ +ei+al +  ++l  ++e+L  ev++L
  gi|119720446|ref|YP_920941.1| 41 ATLSEIKALREGQEQLWRKQEKLWGEVRKL 70
                                   455677777777777777777777777777 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0081
                                    XXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXX CS
                          DivIC  16 llaykqlkqeiaalqaelaklkaeneeLeaevkdLksd 53 
                                    +  +++l+++  +l +e+++l++ +e+L +evk L+ +
  gi|119720446|ref|YP_920941.1|  71 WEEVRALREDQRKLWEEVKALRENQEKLWEEVKSLREG 108
                                    66788999999999999999999999999999999865 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0088
                                    XXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXX CS
                          DivIC  16 llaykqlkqeiaalqaelaklkaeneeLeaevkdLksde 54 
                                    +  +k+l+++  +l +e+++l++ +e+L +ev+ L+ d+
  gi|119720446|ref|YP_920941.1| 113 WEEVKALREDQRRLWEEVKALRENQEKLWEEVRALREDQ 151
                                    566788999999999999999999999999999998775 PP

  == domain 4  score: 4.0 bits;  conditional E-value: 0.15
                                    HHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXX CS
                          DivIC  24 qeiaalqaelaklkaeneeLeaevkdLksdedyi 57 
                                    +e+ al ++  kl + +++L +ev+ L+ +++++
  gi|119720446|ref|YP_920941.1| 142 EEVRALREDQGKLWEGQQRLWEEVRALREGQERL 175
                                    7899999999999999999999999999999986 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2  14.0    0.0094       2.8      25     130 ..      43     145 ..      39     153 .. 0.84
   2 ?    4.8   7.3     0.051        15      29     105 ..      96     169 ..      93     198 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0094
                            GAS  25 LelIkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdl 104
                                    L+ Ik l+e  e+l +k+e+   e+ ++ +e + l+e  +k+ eev+ Lr+   n+ek  ++ k+l++   +l +e+k+l
  gi|119720446|ref|YP_920941.1|  43 LSEIKALREGQEQLWRKQEKLWGEVRKLWEEVRALREDQRKLWEEVKALRE---NQEKLWEEVKSLREGQGKLWEEVKAL 119
                                    889**********************************************97...56666777777778888888888888 PP

                            GAS 105 kwehevleqrfekvekerdelykkfe 130
                                    +++++ l ++++++ +  ++l ++ +
  gi|119720446|ref|YP_920941.1| 120 REDQRRLWEEVKALRENQEKLWEEVR 145
                                    88888888888888888777766554 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.051
                            GAS  29 kslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlk 105
                                    ++l ee++ l++ + +   e++++ ++ +rl e++k+++e+ e+L ++++  ++d+ +l + ++rl e  +    l+
  gi|119720446|ref|YP_920941.1|  96 EKLWEEVKSLREGQGKLWEEVKALREDQRRLWEEVKALRENQEKLWEEVRALREDQGKLWEGQQRLWEEVRA---LR 169
                                    567788888888888888888888888888888888888888888888888888888887777766543333...33 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.2      0.26        79     120     143 ..      33      58 ..       6      79 .. 0.44
   2 ?    6.3   3.5     0.022       6.4      14     154 ..      65     110 ..      30     132 .. 0.39
   3 ?    5.8   2.3     0.031       9.2       5      55 ..      95     148 ..      86     192 .. 0.61

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.26
                        DUF4795 120 eelkekld..rlelepLkeqleerlk 143
                                    ++l ek+d    e++ L+e  e+ ++
  gi|119720446|ref|YP_920941.1|  33 RDLLEKMDatLSEIKALREGQEQLWR 58 
                                    44444444444444444444332222 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.022
                        DUF4795  14 eaieklqeelekleekvkelekrledkekklealkkqieelekvkadkeeveeelaekadkeaLatkvsrdqfDeakkeL 93 
                                     +++kl ee+  l e +++l                                                            
  gi|119720446|ref|YP_920941.1|  65 GEVRKLWEEVRALREDQRKL------------------------------------------------------------ 84 
                                    22222222222222222222............................................................ PP

                        DUF4795  94 ekmleellekleeqeealkkaldtLqeelkekldrlelepLkeqleerlkelqkelqeame 154
                                                                        e++ L+e+ e+ ++e++  l+e   
  gi|119720446|ref|YP_920941.1|  85 ----------------------------------WEEVKALRENQEKLWEEVK-SLREGQG 110
                                    ..................................2333333333333333333.2222223 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.031
                        DUF4795   5 sael...lkklqeaieklqeelekleekvkelekrledkekklealkkqieele 55 
                                    +++l   +k l+e   kl ee++ l e +++l ++ ++++++ e l++++++l+
  gi|119720446|ref|YP_920941.1|  95 QEKLweeVKSLREGQGKLWEEVKALREDQRRLWEEVKALRENQEKLWEEVRALR 148
                                    333333334444444444444444555555555555555555555555555444 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.2     0.029       8.6     128     172 ..      19      64 ..      10      69 .. 0.81
   2 ?    4.6   6.9     0.082        24      95     169 ..      69     145 ..      65     147 .. 0.80
   3 ?    9.0   1.1    0.0036       1.1      63     134 ..     114     185 ..     111     191 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.029
                        DUF4201 128 neklkqq.ggllrvPaLlkDYdktkekveekrksvkkLrrkvkile 172
                                     ++l++   gll+  +Ll+ +d t ++++ +r+  ++L rk ++l 
  gi|119720446|ref|YP_920941.1|  19 DRELRYAlAGLLGFRDLLEKMDATLSEIKALREGQEQLWRKQEKLW 64 
                                    555655515899999*************************999985 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.082
                        DUF4201  95 elkkelkekeerlaklrkelykvklerdklrkqneklkqqggll..rvPaLlkDYdktkekveekrksvkkLrrkvk 169
                                    +l +e + + e+++kl++e+  ++++ +kl ++ + l++  g l  +v aL +D  +  e+v+ +r+  +kL ++v+
  gi|119720446|ref|YP_920941.1|  69 KLWEEVRALREDQRKLWEEVKALRENQEKLWEEVKSLREGQGKLweEVKALREDQRRLWEEVKALRENQEKLWEEVR 145
                                    55677888899999999999999999999999999999988877556778888888888888888888888888776 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0036
                        DUF4201  63 keLkrlkkkttktvhalthlkeklhmleselselkkelkekeerlaklrkelykvklerdklrkqneklkqq 134
                                    +e+k+l++   +   +++ l+e+   l +e+++l+++  ++ e +++l++e+  +++  ++lr + + l+++
  gi|119720446|ref|YP_920941.1| 114 EEVKALREDQRRLWEEVKALRENQEKLWEEVRALREDQGKLWEGQQRLWEEVRALREGQERLRGDVDGLRAS 185
                                    578888888888889999999999999999999999999999999999999999999999999887777765 PP

>> DUF4061  Domain of unknown function (DUF4061)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   1.8    0.0095       2.8      28      80 ..      40      91 ..      37     107 .. 0.67
   2 ?    3.1   3.9       0.4   1.2e+02      31      79 ..      85     132 ..      73     149 .. 0.59
   3 ?    3.0   0.8      0.43   1.3e+02      30      46 ..     126     142 ..     108     161 .. 0.62
   4 ?    0.9   0.2         2   5.9e+02      26      44 ..     157     175 ..     142     186 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0095
                        DUF4061 28 dcsleqleeiReqQekLarlhfeldaeeeelaekeedalresdenlkkLvskL 80
                                   d +l +++++Re Qe+L r++ +l  e ++l e+   alre +++l + v+ L
  gi|119720446|ref|YP_920941.1| 40 DATLSEIKALREGQEQLWRKQEKLWGEVRKLWEEV-RALREDQRKLWEEVKAL 91
                                   5688999*****************99998777433.34444444433333333 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.4
                        DUF4061  31 leqleeiReqQekLarlhfeldaeeeelaekeedalresdenlkkLvsk 79 
                                     e+++++Re QekL +   +l + + +l e e +alre ++ l + v+ 
  gi|119720446|ref|YP_920941.1|  85 WEEVKALRENQEKLWEEVKSLREGQGKLWE-EVKALREDQRRLWEEVKA 132
                                    678888899999988888888777766553.333344333333322222 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.43
                        DUF4061  30 sleqleeiReqQekLar 46 
                                      e+++++Re QekL +
  gi|119720446|ref|YP_920941.1| 126 LWEEVKALRENQEKLWE 142
                                    45677777777777754 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 2
                        DUF4061  26 GkdcsleqleeiReqQekL 44 
                                    G++   e++ ++Re Qe+L
  gi|119720446|ref|YP_920941.1| 157 GQQRLWEEVRALREGQERL 175
                                    6666778888899999988 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   9.2   0.00098      0.29     221     336 ..      32     145 ..      15     153 .. 0.83
   2 ?    4.7   1.0      0.03       8.9     237     308 ..     139     209 ..     136     214 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00098
                           FUSC 221 lrrllsrmlallallsslarllarlraeeaaavpelaallaelaaleaaaaaealeaalaalrarlralrraleadadta 300
                                     r ll +m a l+ + +l++ +++l +++++ + e+++l +e++al  ++++ +l ++++alr+  ++l ++ +  ++ +
  gi|119720446|ref|YP_920941.1|  32 FRDLLEKMDATLSEIKALREGQEQLWRKQEKLWGEVRKLWEEVRAL--REDQRKLWEEVKALRENQEKLWEEVKSLREGQ 109
                                    688999999************************************5..56788888888888888888888888888888 PP

                           FUSC 301 alllarlaellaelaqllaslraleaaiaaarraer 336
                                    + l+++++ l ++ ++l+++++al++  ++ +++ r
  gi|119720446|ref|YP_920941.1| 110 GKLWEEVKALREDQRRLWEEVKALRENQEKLWEEVR 145
                                    888888888888888888888888888777555444 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.03
                           FUSC 237 slarllarlraeeaaavpelaallaelaaleaaaaaealeaalaalrarlralrrale.adadtaalllarla 308
                                    +l+++ ++lr+ + + ++  + l +e++al  ++ +e+l+++++ lra +r+l +a        aa++l+rl+
  gi|119720446|ref|YP_920941.1| 139 KLWEEVRALREDQGKLWEGQQRLWEEVRAL--REGQERLRGDVDGLRASFRQLGEAVGmTLEFYAAAFLERLL 209
                                    5788999999999999999**********5..6689****************999998766666677776665 PP

>> CASP_C  CASP C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   2.2     0.033       9.9     108     140 ..      61      93 ..      47     107 .. 0.61
   2 ?    4.7   3.2     0.055        16      99     141 ..      94     136 ..      90     154 .. 0.69
   3 ?    3.8   0.7       0.1        31     102     133 ..     125     156 ..     118     170 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.033
                         CASP_C 108 rkqeetvsslraeiaslqkDNlkLYEkvRYlqs 140
                                    +k   +v++l +e+ +l++D  kL+E v+ l +
  gi|119720446|ref|YP_920941.1|  61 EKLWGEVRKLWEEVRALREDQRKLWEEVKALRE 93 
                                    555556666667777777777777776665444 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.055
                         CASP_C  99 rnaeLEeelrkqeetvsslraeiaslqkDNlkLYEkvRYlqsY 141
                                      ++L ee+++ +e   +l +e+++l++D   L+E v+ l + 
  gi|119720446|ref|YP_920941.1|  94 NQEKLWEEVKSLREGQGKLWEEVKALREDQRRLWEEVKALREN 136
                                    5566777777777777778888888888888888877755544 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.1
                         CASP_C 102 eLEeelrkqeetvsslraeiaslqkDNlkLYE 133
                                     L ee++  +e+ ++l +e+ +l++D  kL+E
  gi|119720446|ref|YP_920941.1| 125 RLWEEVKALRENQEKLWEEVRALREDQGKLWE 156
                                    56677777778888888888888888888776 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   2.3     0.014       4.3     103     143 ..      67     107 ..      38     118 .. 0.64
   2 ?    4.3   0.9     0.031       9.2     377     410 ..     119     152 ..     116     170 .. 0.81
   3 ?    1.6   0.1       0.2        60     380     425 ..     143     188 ..     136     201 .. 0.57
   4 ?   -2.6   0.1       3.8   1.1e+03     442     488 ..     247     293 ..     241     299 .. 0.57

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.014
                                    HHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHHH CS
                           EzrA 103 laeleeeldeveekikkileelkelteseeknreeieklke 143
                                    +++l ee+  ++e+ +k+ ee+k l+e++ek  ee+++l+e
  gi|119720446|ref|YP_920941.1|  67 VRKLWEEVRALREDQRKLWEEVKALRENQEKLWEEVKSLRE 107
                                    45555556666666666666666666666666666666655 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.031
                                    TGGGTHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           EzrA 377 lqeeleeleekleeieekqeeileslkslrkdEk 410
                                    l+e++++l e+++++ e+qe+++e++++lr+d  
  gi|119720446|ref|YP_920941.1| 119 LREDQRRLWEEVKALRENQEKLWEEVRALREDQG 152
                                    7888899999999999999999999999999975 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.2
                                    GTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           EzrA 380 eleeleekleeieekqeeileslkslrkdEkrAreqldeikkelke 425
                                    e++ l e+  ++ e q++++e++++lr+  +r r  +d ++   ++
  gi|119720446|ref|YP_920941.1| 143 EVRALREDQGKLWEGQQRLWEEVRALREGQERLRGDVDGLRASFRQ 188
                                    5555555555555555555555555555555555555554444333 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 3.8
                                    HHHHSTTTSTTTHHHHHHHT-TT--HHHHHHHHHTTTTTSGGGTHHH CS
                           EzrA 442 yleelkeasdeieelakeLekkpinikevnkrldeardlveklyekt 488
                                    + ++l+ a+d+ +e ak +e++++  +   ++++ a  +v +l +++
  gi|119720446|ref|YP_920941.1| 247 VTTYLRSAEDAEREAAKLMERVKVVEEISGRKVELAVLAVANLGREA 293
                                    55566666666666666666666654444455666666666665555 PP

>> DUF4763  Domain of unknown function (DUF4763)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   2.1     0.026       7.7      94     154 ..      38      98 ..      33     107 .. 0.76
   2 ?    6.1   1.5      0.02         6     101     154 ..     101     154 ..      96     167 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.026
                        DUF4763  94 lltseqpeileLqrnnhkLrqqlaelqqhlkasrkslkelreslcqekkrlrklqkrlnel 154
                                    + + +  ei+ L+  + +L  ++++l    ++ ++++++lre+++++ + +++l++  ++l
  gi|119720446|ref|YP_920941.1|  38 KMDATLSEIKALREGQEQLWRKQEKLWGEVRKLWEEVRALREDQRKLWEEVKALRENQEKL 98 
                                    5556677888888888888888888888888888888888888888888888887766554 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.02
                        DUF4763 101 eileLqrnnhkLrqqlaelqqhlkasrkslkelreslcqekkrlrklqkrlnel 154
                                    e++ L+  + kL  +++ l +  ++ ++++k+lre + ++ + +r+l++  ++l
  gi|119720446|ref|YP_920941.1| 101 EVKSLREGQGKLWEEVKALREDQRRLWEEVKALRENQEKLWEEVRALREDQGKL 154
                                    778888888888888888888888888888888888888888888888766555 PP

>> HALZ  Homeobox associated leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.2         1   3.1e+02      15      40 ..      54      79 ..      45      82 .. 0.72
   2 ?    5.5   0.8     0.066        20      21      40 ..      74      93 ..      68      96 .. 0.86
   3 ?    5.0   1.9     0.098        29      16      40 ..      83     107 ..      75     109 .. 0.60
   4 ?    6.7   0.4     0.029       8.6      20      40 ..     115     135 ..     110     138 .. 0.86
   5 ?    3.7   0.2      0.25        75      21      40 ..     130     149 ..     126     152 .. 0.86
   6 ?    0.6   0.1       2.3   6.8e+02      23      40 ..     153     170 ..     145     173 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 1
                           HALZ 15 daLksdydsLkkenekLkaelqeLke 40
                                   ++L  + + L  e +kL  e++ L+e
  gi|119720446|ref|YP_920941.1| 54 EQLWRKQEKLWGEVRKLWEEVRALRE 79
                                   55556667777788888889888887 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.066
                           HALZ 21 ydsLkkenekLkaelqeLke 40
                                   + +L+++ +kL  e++ L+e
  gi|119720446|ref|YP_920941.1| 74 VRALREDQRKLWEEVKALRE 93
                                   569***************98 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.098
                           HALZ  16 aLksdydsLkkenekLkaelqeLke 40 
                                    +L  ++ +L++  ekL  e+++L+e
  gi|119720446|ref|YP_920941.1|  83 KLWEEVKALRENQEKLWEEVKSLRE 107
                                    4445566777777777777777765 PP

  == domain 4  score: 6.7 bits;  conditional E-value: 0.029
                           HALZ  20 dydsLkkenekLkaelqeLke 40 
                                    ++ +L+++ ++L  e++ L+e
  gi|119720446|ref|YP_920941.1| 115 EVKALREDQRRLWEEVKALRE 135
                                    6779***************98 PP

  == domain 5  score: 3.7 bits;  conditional E-value: 0.25
                           HALZ  21 ydsLkkenekLkaelqeLke 40 
                                    + +L++  ekL  e++ L+e
  gi|119720446|ref|YP_920941.1| 130 VKALRENQEKLWEEVRALRE 149
                                    568999999*********98 PP

  == domain 6  score: 0.6 bits;  conditional E-value: 2.3
                           HALZ  23 sLkkenekLkaelqeLke 40 
                                     L +  ++L  e++ L+e
  gi|119720446|ref|YP_920941.1| 153 KLWEGQQRLWEEVRALRE 170
                                    5666679*********98 PP

>> DUF4446  Protein of unknown function (DUF4446)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1      0.47   1.4e+02      41      85 ..      33      77 ..      19      83 .. 0.83
   2 ?    5.8   0.6     0.043        13      22      83 ..      44     103 ..      35     106 .. 0.80
   3 ?    5.0   1.5     0.075        22      24      84 ..      88     146 ..      76     156 .. 0.74
   4 ?   -0.8   0.0       4.6   1.4e+03      39      83 ..     150     194 ..     137     196 .. 0.71
   5 ?   -1.8   0.0       9.3   2.8e+03      49      73 ..     249     273 ..     243     283 .. 0.64

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.47
                        DUF4446 41 ksleellkekleeveelkeeseelekeieeleeklkkslqkvglv 85
                                   ++l e++  +l+e+++l+e +e+l +++e+l  +++k  ++v+ +
  gi|119720446|ref|YP_920941.1| 33 RDLLEKMDATLSEIKALREGQEQLWRKQEKLWGEVRKLWEEVRAL 77
                                   577788999999999999999999999999999999888877655 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.043
                        DUF4446  22 vklkklkkkykklmkgkdgksleellkekleeveelkeeseelekeieeleeklkkslqkvg 83 
                                     ++k l++  ++l +  ++++l   +++  eev++l+e++++l +e+++l+e+++k  ++v+
  gi|119720446|ref|YP_920941.1|  44 SEIKALREGQEQLWR--KQEKLWGEVRKLWEEVRALREDQRKLWEEVKALRENQEKLWEEVK 103
                                    556667777777776..577888889999999999999999999999999999999887776 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.075
                        DUF4446  24 lkklkkkykklmkgkdgksleellkekleeveelkeeseelekeieeleeklkkslqkvgl 84 
                                    +k l+++ +kl +  + ksl e   +  eev++l+e++++l +e+++l+e+++k  ++v+ 
  gi|119720446|ref|YP_920941.1|  88 VKALRENQEKLWE--EVKSLREGQGKLWEEVKALREDQRRLWEEVKALRENQEKLWEEVRA 146
                                    5566666666665..5677777788888888888888888888888888888877777665 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 4.6
                        DUF4446  39 dgksleellkekleeveelkeeseelekeieeleeklkkslqkvg 83 
                                    d+ +l e  ++  eev++l+e +e+l+ +++ l++++++  + vg
  gi|119720446|ref|YP_920941.1| 150 DQGKLWEGQQRLWEEVRALREGQERLRGDVDGLRASFRQLGEAVG 194
                                    445555556677888999999999999998888888887766666 PP

  == domain 5  score: -1.8 bits;  conditional E-value: 9.3
                        DUF4446  49 ekleeveelkeeseelekeieelee 73 
                                    ++l++ e++++e ++l+++++ +ee
  gi|119720446|ref|YP_920941.1| 249 TYLRSAEDAEREAAKLMERVKVVEE 273
                                    5566666666666666666666655 PP

>> PTRF_SDPR  PTRF/SDPR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   4.0   0.00066       0.2      10      98 ..      35     126 ..      32     131 .. 0.87
   2 ?    5.8   4.0     0.031       9.3      16      98 ..      72     154 ..      69     159 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00066
                                    HHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      PTRF_SDPR  10 lLdkvvgi...vdsvqesqkrlEerqaelenavksiqgdllkLakshssTsntvnklleksrkvsvnvkevrerlekqav 86 
                                    lL+k+ +    + +++e q++l ++q++l + v+ +  ++  L  ++ +  + v+ l e   k   +vk++re   k   
  gi|119720446|ref|YP_920941.1|  35 LLEKMDATlseIKALREGQEQLWRKQEKLWGEVRKLWEEVRALREDQRKLWEEVKALRENQEKLWEEVKSLREGQGKLWE 114
                                    66666655011455568899************************************************************ PP

                                    HHHHHHHHHHHH CS
                      PTRF_SDPR  87 qvkklEaneael 98 
                                    +vk l ++++ l
  gi|119720446|ref|YP_920941.1| 115 EVKALREDQRRL 126
                                    ****99999877 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.031
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      PTRF_SDPR  16 givdsvqesqkrlEerqaelenavksiqgdllkLakshssTsntvnklleksrkvsvnvkevrerlekqavqvkklEane 95 
                                    + v +++e q++l e  + l ++ + +  ++  L   + +  + v+ l e  r+   +vk +re+ ek   +v+ l +++
  gi|119720446|ref|YP_920941.1|  72 EEVRALREDQRKLWEEVKALRENQEKLWEEVKSLREGQGKLWEEVKALREDQRRLWEEVKALRENQEKLWEEVRALREDQ 151
                                    55677889999999999999999999999999999999999999*9999*******************999999999988 PP

                                    HHH CS
                      PTRF_SDPR  96 ael 98 
                                     +l
  gi|119720446|ref|YP_920941.1| 152 GKL 154
                                    877 PP

>> Laminin_I  Laminin Domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   6.6     0.013       3.8      44     115 ..      69     140 ..      29     168 .. 0.56
   2 ?    2.6   0.2      0.31        92     140     162 ..     248     270 ..     244     299 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.013
                      Laminin_I  44 ilekelesLaqeteeLqkkatqvlakaqkvnaesertlnnakeLaekikkladnikeilekvatlneneeal 115
                                     l +e+  L ++ ++L ++++  +++ +k+ +e++   +   +L e++k+l+++   + e v++l en+e+l
  gi|119720446|ref|YP_920941.1|  69 KLWEEVRALREDQRKLWEEVKALRENQEKLWEEVKSLREGQGKLWEEVKALREDQRRLWEEVKALRENQEKL 140
                                    223445566666666666666666666666666666666666666666666666666666666666655554 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.31
                      Laminin_I 140 tkqleeaeaelkaAqkLLsrvqt 162
                                    t+ l+ ae+  ++A kL++rv+ 
  gi|119720446|ref|YP_920941.1| 248 TTYLRSAEDAEREAAKLMERVKV 270
                                    56778899999999999999864 PP

>> 5_nucleotid  5' nucleotidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   5.2    0.0056       1.7     330     402 ..      67     141 ..      39     183 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0056
                                    -TTHHHHHHHHHHTHHH..HHHHHHHHHHHHHHHHHHHHHHHT.TTHHHHHHHHHHHHHHHHHHHHHHHHHHCCS CS
                    5_nucleotid 330 vpELeeElevleekkek..eeleelekleelledelkklksseeeskekleeleedleelkkeirelreelkelf 402
                                    v+ L eE+++l+e+++k  ee++ l++ +e+l +e+k+l+  + +  e++++l+ed ++l +e+++lre+ ++l+
  gi|119720446|ref|YP_920941.1|  67 VRKLWEEVRALREDQRKlwEEVKALRENQEKLWEEVKSLREGQGKLWEEVKALREDQRRLWEEVKALRENQEKLW 141
                                    677888899888888888888888888888888888888888555677777777777777777777777776655 PP

>> Nup88  Nuclear pore component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6  14.0     0.081        24     561     676 ..      54     168 ..      32     175 .. 0.67

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.081
                          Nup88 561 kllkkqkeqqleelqsleeerkslseraeklAekyeeikdkQeklvrrvkkvlkrlnsklpvlseaeremkkelek.... 636
                                    ++l  ++e+   e+++l ee + l+e+  kl e+    +++Qekl + vk++ ++ + kl   ++a re ++ l++    
  gi|119720446|ref|YP_920941.1|  54 EQLWRKQEKLWGEVRKLWEEVRALREDQRKLWEEVKALRENQEKLWEEVKSL-REGQGKLWEEVKALREDQRRLWEevka 132
                                    567788999999************************************9985.666666666666666555555540000 PP

                          Nup88 637 ikeklkslknalkqvkkkldkqrkqiakskeeekksslel 676
                                    ++e+ ++l ++++ +++     + ++ +++++  ++  +l
  gi|119720446|ref|YP_920941.1| 133 LRENQEKLWEEVRALRED----QGKLWEGQQRLWEEVRAL 168
                                    444444444444444433....333333555545555555 PP

>> TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   9.1      0.02       6.1      19     100 ..      41     122 ..      32     133 .. 0.78
   2 ?    6.9   5.8     0.023         7      15     111 ..      96     189 ..      95     192 .. 0.87
   3 ?    2.7   0.3      0.46   1.4e+02      39      69 ..     251     281 ..     242     313 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.02
                    TMF_TATA_bd  19 seirrlEgElaslkeelerleaerdeareeivklmkeneelkelk....keleelekeleelqeryetlLellGeksEev 94 
                                    +++    +E+++l+e  e+l ++++++  e+ kl +e+ +l+e +    +e++ l+++ e+l e+ ++l e  G+  Eev
  gi|119720446|ref|YP_920941.1|  41 ATL----SEIKALREGQEQLWRKQEKLWGEVRKLWEEVRALREDQrklwEEVKALRENQEKLWEEVKSLREGQGKLWEEV 116
                                    444....6999***********************9987666554411116778888888999999999999999999999 PP

                    TMF_TATA_bd  95 eELraD 100
                                    + Lr+D
  gi|119720446|ref|YP_920941.1| 117 KALRED 122
                                    999998 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.023
                    TMF_TATA_bd  15 erlsseirrlEgElaslkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqeryetlLellGeksEev 94 
                                    e+l  e+++l     +l ee++ l + ++++ ee+ +l ++ e+l e+ + l+e + +l e q+r+ +    l e +E+ 
  gi|119720446|ref|YP_920941.1|  96 EKLWEEVKSLREGQGKLWEEVKALREDQRRLWEEVKALRENQEKLWEEVRALREDQGKLWEGQQRLWEEVRALREGQER- 174
                                    566677787777778899999**************99999999999999999999999999999999999999888876. PP

                    TMF_TATA_bd  95 eELraDvaDlKemykeq 111
                                      Lr Dv+ l++ ++++
  gi|119720446|ref|YP_920941.1| 175 --LRGDVDGLRASFRQL 189
                                    ..999999999988875 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.46
                    TMF_TATA_bd  39 eaerdeareeivklmkeneelkelkkeleel 69 
                                     ++ ++a++e +klm+++  ++e +++  el
  gi|119720446|ref|YP_920941.1| 251 LRSAEDAEREAAKLMERVKVVEEISGRKVEL 281
                                    5566778888888888888888877766555 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   1.0    0.0049       1.5       6      97 ..      33     121 ..      31     125 .. 0.88
   2 ?    4.1   1.0      0.15        44      27      96 ..      82     148 ..      69     170 .. 0.52
   3 ?    0.9   0.1       1.4   4.2e+02      33      76 ..     257     301 ..     244     306 .. 0.60

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0049
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH. CS
                     Laminin_II   6 aeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeas 85 
                                    ++ +e++ ++l+ +++l +  e++  k +++ ++v++  e+v+++ +  r   ++vk L ++ ++L +    +k l+e++
  gi|119720446|ref|YP_920941.1|  33 RDLLEKMDATLSEIKALREGQEQLWRKQEKLWGEVRKLWEEVRALREDQRKLWEEVKALRENQEKLWEE---VKSLREGQ 109
                                    567899999*********************************************************998...55556665 PP

                                    ..HHHHHHHHHH CS
                     Laminin_II  86 sslsdniseike 97 
                                    + l ++++ ++e
  gi|119720446|ref|YP_920941.1| 110 GKLWEEVKALRE 121
                                    558777777775 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.15
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH...HHHHHHHHH CS
                     Laminin_II  27 entkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeassslsdniseik 96 
                                     ++ e+++ ++++ e+  e+vk++ ++     ++vk L +   +L + +k l++ +e+   l +++  ++
  gi|119720446|ref|YP_920941.1|  82 RKLWEEVKALRENQEKLWEEVKSLREGQGKLWEEVKALREDQRRLWEEVKALRENQEK---LWEEVRALR 148
                                    3444444444444444444455555555555555555555555555443333332222...444444443 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 1.4
                                    XXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXX--TTTTTGGGHH CS
                     Laminin_II  33 lseinrsveetnekvk.dankairdArrsvkkLeklapqLldklk 76 
                                    +++ ++++ e  ++v+  + + +++A  +v +L ++a ++l+kl+
  gi|119720446|ref|YP_920941.1| 257 AEREAAKLMERVKVVEeISGRKVELAVLAVANLGREALEVLEKLH 301
                                    333333333333444423445677888888888888888888876 PP

>> COMP  Cartilage oligomeric matrix protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       7.8   2.3e+03      19      35 ..      34      50 ..      32      52 .. 0.73
   2 ?    4.7   0.4      0.14        42       5      35 ..      62      92 ..      59      94 .. 0.84
   3 ?    3.7   0.2      0.28        85      17      36 ..     116     135 ..     110     136 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 7.8
                           COMP 19 eLreelrqQvkEisfLR 35
                                   +L e +     Ei++LR
  gi|119720446|ref|YP_920941.1| 34 DLLEKMDATLSEIKALR 50
                                   56677777778999998 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.14
                           COMP  5 qLlrqLseltqllkeLreelrqQvkEisfLR 35
                                   +L ++ + l   ++ Lre+ r+  +E+++LR
  gi|119720446|ref|YP_920941.1| 62 KLWGEVRKLWEEVRALREDQRKLWEEVKALR 92
                                   666777788888999***************9 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.28
                           COMP  17 lkeLreelrqQvkEisfLRn 36 
                                    +k Lre+ r+  +E+++LR 
  gi|119720446|ref|YP_920941.1| 116 VKALREDQRRLWEEVKALRE 135
                                    789***************95 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6  16.5       0.1        31      65     155 ..      64     166 ..       8     181 .. 0.60

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.1
                        UPF0242  65 l........ekskleekeaklteld....eglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaed 132
                                    +        e   l e+++kl e+     e+ ++  e+++ l+e + +L ee++a  e  +rl ee + L+e  e+  e+
  gi|119720446|ref|YP_920941.1|  64 WgevrklweEVRALREDQRKLWEEVkalrENQEKLWEEVKSLREGQGKLWEEVKALREDQRRLWEEVKALRENQEKLWEE 143
                                    13333333455556666666666552222333333335555555555555555555555555555555555555555555 PP

                        UPF0242 133 feelkleleeqLaekqellqeyq 155
                                    + +l+ +  +  + +q l +e +
  gi|119720446|ref|YP_920941.1| 144 VRALREDQGKLWEGQQRLWEEVR 166
                                    55555555544444444444443 PP

>> ERM  Ezrin/radixin/moesin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5  20.1    0.0053       1.6       2     121 ..      55     174 ..      54     193 .. 0.87
   2 ?    1.1   0.2      0.99   2.9e+02       1      19 [.     255     273 ..     249     301 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0053
                            ERM   2 eaerekreleerLkqlqeeaekaqeaLreseetaelLaekarraeeeaelLeqkaaeaeeeiqrlkesaekeeeekekle 81 
                                    +  r++++l  + ++l ee+++ +e+ r+  e+++ L e+++++ ee + L + + ++ ee ++l+e++++  ee ++l 
  gi|119720446|ref|YP_920941.1|  55 QLWRKQEKLWGEVRKLWEEVRALREDQRKLWEEVKALRENQEKLWEEVKSLREGQGKLWEEVKALREDQRRLWEEVKALR 134
                                    56688899999999999999999999999999999999999999999999999999999999999999999999999999 PP

                            ERM  82 rklreaeleaarleeeserkeeeaerLkeeleeareaeee 121
                                    ++ ++  +e++ l+e++ +  e ++rL ee+++ re +e+
  gi|119720446|ref|YP_920941.1| 135 ENQEKLWEEVRALREDQGKLWEGQQRLWEEVRALREGQER 174
                                    9999999999999999999999999999999998888876 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.99
                            ERM   1 eeaerekreleerLkqlqe 19 
                                    e+aere ++l+er k ++e
  gi|119720446|ref|YP_920941.1| 255 EDAEREAAKLMERVKVVEE 273
                                    6788888888888877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1280  (0.0713927); expected 358.6 (0.02)
Passed bias filter:                      636  (0.0354733); expected 358.6 (0.02)
Passed Vit filter:                       149  (0.00831056); expected 17.9 (0.001)
Passed Fwd filter:                        83  (0.00462937); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              60  [number of targets reported over threshold]
# CPU time: 1.15u 0.34s 00:00:01.49 Elapsed: 00:00:00.52
# Mc/sec: 1836.94
//
Query:       gi|119720447|ref|YP_920942.1|  [L=250]
Description: hypothetical protein Tpen_1543 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-07   31.3  12.6    1.8e-07   31.3  12.6    2.0  2  ECF-ribofla_trS  ECF-type riboflavin transporter, S component
    3.8e-06   27.0   3.9    3.8e-06   27.0   3.9    1.9  2  Thia_YuaJ        Thiamine transporter protein (Thia_YuaJ)
      3e-05   24.2  12.9    4.5e-05   23.6  12.9    1.3  1  ECF_trnsprt      ECF transporter, substrate-specific componen


Domain annotation for each model (and alignments):
>> ECF-ribofla_trS  ECF-type riboflavin transporter, S component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3  12.6     3e-11   1.8e-07       2     164 ..      15     176 ..      14     183 .. 0.77
   2 ?   -0.8   2.6      0.22   1.3e+03      82     161 ..     162     232 ..     153     241 .. 0.48

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 3e-11
                                    ..TTHHHHHHHHHHHHHHHHHH---B-S.SS-B--TTHHHHHHHHHHSS--STHHHHHHHHHHHHHHHSS-GGGHHHHHH CS
                ECF-ribofla_trS   2 lstkkvvatailaAlvvvltlfisIplpantegsinlgdavlalaallfGpvvGflvGaiGsalaDllsgYgiwapftli 81 
                                    +st++v+++a++aAl  vl++ + Ip p n   ++++  + ++l+a+  Gp+ G+l G++G  +  +   Yg w    ++
  gi|119720447|ref|YP_920942.1|  15 ISTQDVALVAVMAALANVLGF-FAIPGPWNI--QFSMTGIPILLVAFTRGPLLGALTGLLGGYVQAV--KYG-WEGY-VV 87 
                                    79******************9.99****888..999999*************************999..552.3444.78 PP

                                    HHHHHHHHHHHH--S-S-SSH......HHHHHHHHHHHH..HHHHHHHHHHHH.............S-HHHHHHHHHHHH CS
                ECF-ribofla_trS  82 ikgliGlivGliakklkknke...ngvfkilalvlfaiv..mvigyviaegll..pildiiiy.sepaekvalqsipani 153
                                      +++G ++G++akk  + ++      f   +++l + v  m  g v +e l+      +  +  e + +v  +si++ +
  gi|119720447|ref|YP_920942.1|  88 YTAIQGGVAGFFAKKV-RLLRvlaPPFFFFGGFFLTWWVdqMRYGKVTFEDLVsmTQRAVA-AgPETGLAVPYVSIVSGV 165
                                    89999********999.33334554455555544444442277788888888852233333.248888888888998888 PP

                                    HHHHHHHHHHH CS
                ECF-ribofla_trS 154 iqavvgaiial 164
                                    + a+v a+++l
  gi|119720447|ref|YP_920942.1| 166 VAAAVAALLVL 176
                                    88888888765 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.22
                                    HHHHHH.HHHHHH--S-S-SSH...HHHHHHHHHHHHHHHHHHHHHHHH..........S-HHHHHHHHHHHHHHHHHHH CS
                ECF-ribofla_trS  82 ikgliG.livGliakklkknkengvfkilalvlfaivmvigyviaegllpildiiiysepaekvalqsipaniiqavvga 160
                                    ++g+++  +++l++ +  +n +      l l+l++ ++ i+yv  ++++    + + +++ +      +   ++q +v a
  gi|119720447|ref|YP_920942.1| 162 VSGVVAaAVAALLVLRFPENRR------LLLTLAGCMGAIAYVPYDAFA----LYVVQQYPWIPTWFVLAKDLVQDFVAA 231
                                    4444331344445555544444......556777777777887777777....222233333333333333344444444 PP

                                    H CS
                ECF-ribofla_trS 161 i 161
                                     
  gi|119720447|ref|YP_920942.1| 232 G 232
                                    3 PP

>> Thia_YuaJ  Thiamine transporter protein (Thia_YuaJ)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   3.9   6.4e-10   3.8e-06       4      60 ..      23      78 ..      20     105 .. 0.84
   2 ?   -2.6   0.0      0.79   4.8e+03      41      45 ..     162     166 ..     131     181 .. 0.60

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 6.4e-10
                      Thia_YuaJ  4 iallaalalvLslikliklpqggsislsmiPilllalrrGlkagllaGllwGllqli 60
                                   +a++aala vL ++ +   p  ++ s+  iPill+a++rG+  g+l+Gll G +q +
  gi|119720447|ref|YP_920942.1| 23 VAVMAALANVLGFFAIPG-PWNIQFSMTGIPILLVAFTRGPLLGALTGLLGGYVQAV 78
                                   799********9997665.8899999999************************9987 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.79
                      Thia_YuaJ  41 rrGlk 45 
                                      G+ 
  gi|119720447|ref|YP_920942.1| 162 VSGVV 166
                                    22222 PP

>> ECF_trnsprt  ECF transporter, substrate-specific component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6  12.9   7.5e-09   4.5e-05       2     170 ..      19     236 ..      18     238 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 7.5e-09
                                    HHHHHHHHHHHHHHHHHHHEEE.STSEEESHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHCHT-SSTTHHHHHHHHHHHH CS
                    ECF_trnsprt   2 klvitglliAisivlsllgyiplpnikitiihipvllggllfGpikGailgiitsvlkailtggtgalssfvpiaflsri 81 
                                     ++++++++A++ vl+++ ++   ni+++   ip+ll+++  Gp+ Ga+ g+++  ++a+  g          ++++  +
  gi|119720447|ref|YP_920942.1|  19 DVALVAVMAALANVLGFFAIPGPWNIQFSMTGIPILLVAFTRGPLLGALTGLLGGYVQAVKYGW--------EGYVVYTA 90 
                                    5899************53444444899**************************99999999433........35666666 PP

                                    CHHHHHHHHHHCCCHTTHHHH.................................................HHHHHHHHCC CS
                    ECF_trnsprt  82 ligliagllykkgkkknlkei.................................................vvsfilagvl 112
                                    + g +ag+     kk++l ++                                                 +vs+++++v+
  gi|119720447|ref|YP_920942.1|  91 IQGGVAGFFA---KKVRLLRVlappffffggffltwwvdqmrygkvtfedlvsmtqravaagpetglavpYVSIVSGVVA 167
                                    6666666444...4454444456777888888888888999999999999********************9***999999 PP

                                    CCCHHHHH........HHCCCHHHHS................--HHHHHHHHHCCTTCCHHHHHHHHHH CS
                    ECF_trnsprt 113 gtivatll........vlliilplylklktakaiaiag...kallaailgpiivkglieaiiaaiivvl 170
                                     +++a+l+        +ll +   ++ +++++ +a+a    +++ ++ ++ ++ k+l++  +aa i+  
  gi|119720447|ref|YP_920942.1| 168 AAVAALLVlrfpenrrLLLTLAGCMGAIAYVPYDAFALyvvQQYPWIPTWFVLAKDLVQDFVAAGITAS 236
                                    999999998888988733333334445666666666666777788888888888999888888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       692  (0.0385967); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1698.54
//
Query:       gi|119720448|ref|YP_920943.1|  [L=510]
Description: ABC transporter related [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.8e-56  189.4   0.0    9.3e-27   94.2   0.0    2.3  2  ABC_tran      ABC transporter
    4.7e-13   49.6   2.7     0.0046   16.8   0.0    4.1  4  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    1.9e-10   40.3   0.2    9.5e-05   22.1   0.1    2.3  2  AAA_29        P-loop containing region of AAA domain
    2.1e-10   40.4   0.0     0.0039   16.6   0.0    3.8  2  SMC_N         RecF/RecN/SMC N terminal domain
      1e-07   32.5   0.2     0.0041   17.5   0.0    2.5  2  AAA_16        AAA ATPase domain
    1.6e-06   28.4   0.2       0.34   11.2   0.1    4.0  2  AAA_22        AAA domain
    2.2e-06   27.7   0.1      0.026   14.4   0.0    2.7  2  RsgA_GTPase   RsgA GTPase
    1.1e-05   25.1   0.2        0.2   11.2   0.0    3.5  2  AAA_25        AAA domain
    5.7e-05   22.6   0.0       0.27   10.6   0.0    2.5  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
    0.00053   19.8   0.0      0.037   13.8   0.0    2.2  2  AAA_15        AAA ATPase domain
    0.00056   20.0   0.2       0.67   10.1   0.0    2.7  2  MMR_HSR1      50S ribosome-binding GTPase
    0.00078   18.6   0.0       0.16   11.0   0.0    3.0  3  T2SSE         Type II/IV secretion system protein
     0.0008   19.2   0.0      0.029   14.1   0.0    2.5  2  AAA_30        AAA domain
    0.00081   19.6   1.5       0.14   12.3   0.2    3.5  2  AAA_33        AAA domain
     0.0017   18.3   0.3        0.3   11.0   0.0    3.2  3  NTPase_1      NTPase
     0.0018   17.7   0.4        3.8    6.9   0.0    3.9  4  TniB          Bacterial TniB protein
     0.0026   18.1   0.0       0.38   11.2   0.0    2.4  2  RNA_helicase  RNA helicase
     0.0039   16.8   0.0        3.2    7.3   0.0    2.3  2  AAA_27        AAA domain
      0.005   16.6   0.1       0.73    9.5   0.0    2.3  2  AAA_24        AAA domain
     0.0056   17.2   0.0       0.43   11.0   0.0    2.2  2  AAA_23        AAA domain
     0.0088   16.3   0.0        1.4    9.2   0.0    3.2  2  SbcCD_C       Putative exonuclease SbcCD, C subunit
     0.0097   16.2   0.0         18    5.6   0.0    3.3  3  AAA_28        AAA domain
  ------ inclusion threshold ------
       0.01   16.4   0.0        5.8    7.5   0.0    2.9  2  AAA_18        AAA domain
       0.01   15.8   0.6       0.19   11.7   0.0    3.0  3  AAA_5         AAA domain (dynein-related subfamily)
      0.011   15.6   0.4        4.1    7.1   0.1    2.4  2  ATP_bind_1    Conserved hypothetical ATP binding protein
      0.012   14.8   0.3       0.25   10.5   0.0    2.6  3  NB-ARC        NB-ARC domain
      0.013   15.0   0.0       0.73    9.3   0.0    2.2  2  AAA_7         P-loop containing dynein motor region
      0.014   15.3   0.0       0.45   10.4   0.0    2.2  2  ATPase_2      ATPase domain predominantly from Archaea
      0.015   15.2   0.0       0.16   11.8   0.0    2.2  2  NACHT         NACHT domain
      0.017   14.9   0.1        1.1    9.0   0.1    2.3  2  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
      0.017   14.6   0.3        3.9    6.9   0.0    2.3  2  KdpD          Osmosensitive K+ channel His kinase sensor doma
      0.024   14.5   0.1        1.2    9.1   0.0    2.6  2  APS_kinase    Adenylylsulphate kinase
      0.025   13.4   0.3       0.42    9.4   0.1    2.1  2  DLIC          Dynein light intermediate chain (DLIC)
      0.027   14.2   0.1         23    4.6   0.0    3.5  4  IstB_IS21     IstB-like ATP binding protein
      0.029   13.8   0.1      0.077   12.4   0.0    1.7  2  Fer4_NifH     4Fe-4S iron sulfur cluster binding proteins, Ni
      0.037   13.4   0.7        7.6    5.8   0.0    3.2  3  ATPase        KaiC
      0.041   12.8   0.1        1.3    7.9   0.0    2.3  2  AAA_PrkA      PrkA AAA domain
      0.057   12.6   0.0       0.33   10.1   0.0    1.9  2  G-alpha       G-protein alpha subunit
      0.059   13.2   0.0        8.4    6.2   0.0    3.1  3  CPT           Chloramphenicol phosphotransferase-like protein
      0.061   12.5   0.0       0.46    9.6   0.0    2.1  2  PIF1          PIF1-like helicase
       0.12   11.6   0.0       0.38   10.0   0.0    1.8  1  Zeta_toxin    Zeta toxin
       0.15   12.1   0.0         24    5.0   0.0    2.7  2  AAA_14        AAA domain
       0.21   11.6   0.0        1.2    9.2   0.0    2.0  2  TsaE          Threonylcarbamoyl adenosine biosynthesis protei
       0.24   11.3   0.0         27    4.6   0.0    2.3  2  Rad17         Rad17 P-loop domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.1   0.0   4.9e-29     2e-26       1     137 []      21     172 ..      21     172 .. 0.92
   2 !   94.2   0.0   2.3e-29   9.3e-27       1     136 [.     279     424 ..     279     425 .. 0.92

  Alignments for each domain:
  == domain 1  score: 93.1 bits;  conditional E-value: 4.9e-29
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--.....SEEEEEETTCEGGGB-HHHCCHCEEEE-SS..--S-TT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxx RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp.....teGeilldgkdlkeqeleslrkeigvlpqe..pqlfpe 73 
                                    l+ vsl++++ge va++G++ +GKStL+ +l+gl         +G++++dg d++e++  +l k++gv+ q+  +ql + 
  gi|119720448|ref|YP_920943.1|  21 LDSVSLSISQGEFVAVMGPSPSGKSTLVYALSGLIPHcvkgeIKGSVKVDGLDTREHPVAELAKRVGVILQDpeAQLLEL 100
                                    789*******************************9889888899999*************************75555555 PP

                                    SBHHHH............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    xxxxxx............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  74 ltvren............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                      v e             e + ++ +al+ +gl + +++      s+LSgG+kqr+a+a +l+ +pk+++lDEpta
  gi|119720448|ref|YP_920943.1| 101 RAVDEValplenlgvpaeEIRLRVGEALEMVGLRGYEERSP----SELSGGEKQRLAIASVLALRPKVIVLDEPTA 172
                                    557776********998777778************999998....*****************************97 PP

  == domain 2  score: 94.2 bits;  conditional E-value: 2.3e-29
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltvren 79 
                                    l++v+l+l+ege+v ++G+nG+GKStL+k + gllkp +G++l+dg d+++ ++ +l++ +g ++q+ ++   + +v+++
  gi|119720448|ref|YP_920943.1| 279 LDHVDLTLREGEVVFLMGRNGSGKSTLVKHMNGLLKPSSGRVLVDGCDTRTCPTYRLSRIVGLVFQNpAHQIVGESVYDE 358
                                    789****************************************************************6444444448888 PP

                                    .............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    .............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 .............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                 + ++e++++++ ++l+++ d +     ++LS G+ +r+++a +++ +pk+l+lDEp+
  gi|119720448|ref|YP_920943.1| 359 iamglrhlgvggdDVRREVARIARAFELEDKLDMIP----EELSVGELKRLMIASIVAMRPKVLVLDEPM 424
                                    9**********8888888**********99888887....*****************************7 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.055        23       3      22 ..      35      54 ..      33      69 .. 0.86
   2 !   16.8   0.0   1.1e-05    0.0046     225     277 ..     132     181 ..      70     200 .. 0.71
   3 !   10.4   0.1   0.00098       0.4       2      22 ..     292     312 ..     291     327 .. 0.83
   4 !   15.1   0.0   3.8e-05     0.016     220     301 ..     380     458 ..     352     460 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.055
                         AAA_21  3 vliGpNgsGKSnLLdaldll 22
                                   ++ Gp  sGKS+L +al++l
  gi|119720448|ref|YP_920943.1| 35 AVMGPSPSGKSTLVYALSGL 54
                                   6678888***********99 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 1.1e-05
                         AAA_21 225 engdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHP...kllrr 277
                                       ++ e++++elS G k+ la+++ l+ ++   +++++DEp ++ +P        
  gi|119720448|ref|YP_920943.1| 132 GLRGYEERSPSELSGGEKQRLAIASVLALRP---KVIVLDEPTANVDPpgtL---Q 181
                                    556788999***********66666666666...8*************4432...3 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00098
                         AAA_21   2 nvliGpNgsGKSnLLdaldll 22 
                                     +l G+NgsGKS+L + + +l
  gi|119720448|ref|YP_920943.1| 292 VFLMGRNGSGKSTLVKHMNGL 312
                                    5789**********9877666 PP

  == domain 4  score: 15.1 bits;  conditional E-value: 3.8e-05
                         AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell..kelsrngaQviltTH 297
                                      + +e +d  +  + elS G ++   +++++ + ++  ++l++DEp +g+  +  rr+l+ +   + ++  + +++ TH
  gi|119720448|ref|YP_920943.1| 380 IARAFELEDKLDMIPEELSVGELKR-LMIASIVAMRP--KVLVLDEPMTGMTSAHSRRVLDTVlgMLGES--STIVVITH 454
                                    56667778888888999********.99999999999..7*************99999994444655655..99****** PP

                         AAA_21 298 Spll 301
                                    +p l
  gi|119720448|ref|YP_920943.1| 455 DPRL 458
                                    **87 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.9e-05    0.0077      14      44 ..      23      53 ..      19      57 .. 0.82
   2 !   22.1   0.1   2.3e-07   9.5e-05      14      50 ..     281     317 ..     276     321 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.9e-05
                         AAA_29 14 ghtieidlkgatlltGpsGsGKSTllDAiqa 44
                                     +++i++ +++ ++Gps sGKSTl+ A++ 
  gi|119720448|ref|YP_920943.1| 23 SVSLSISQGEFVAVMGPSPSGKSTLVYALSG 53
                                   56778886669***************99875 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 2.3e-07
                         AAA_29  14 ghtieidlkgatlltGpsGsGKSTllDAiqalLvpak 50 
                                    + ++++++ ++++l+G++GsGKSTl+  ++ lL p++
  gi|119720448|ref|YP_920943.1| 281 HVDLTLREGEVVFLMGRNGSGKSTLVKHMNGLLKPSS 317
                                    55667775559***************99999999986 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   9.7e-06    0.0039      25     200 ..      32     203 ..      19     218 .. 0.71
   2 !   14.3   0.1     5e-05      0.02      25     202 ..     290     459 ..     279     476 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 9.7e-06
                                    SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEE.EEEEEEEETTEESSSSSSCEEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkka.eveitfdnedkklkiekeevsisrrv 103
                                    +f a++Gp  SGKs l+ A++ ++ +  + +++ +   d +   +e++ ++ a +v +++++++++l + +   ++   +
  gi|119720448|ref|YP_920943.1|  32 EFVAVMGPSPSGKSTLVYALSGLIPHCVKGEIKGSVKVDGLDT-REHPVAELAkRVGVILQDPEAQLLELRAVDEVALPL 110
                                    5777777777777777777777777666666666655555554.455555544257777777777755555555666666 PP

                                    ETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 104 krkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaell 183
                                    ++ g    +i  +  +  e+  l   ++ s+++LSgGek+ +a+a ++A++   p+ + +lDe  a+ D   + +v e l
  gi|119720448|ref|YP_920943.1| 111 ENLGVPAEEIRLRVGEALEMVGLRGYEERSPSELSGGEKQRLAIASVLALR---PK-VIVLDEPTANVDPPGTLQVYETL 186
                                    66666666666666666777777777777777*************999985...44.679******************** PP

                                    HHHCTTSEEEEE-SSHH CS
                                    xxxxxxxxxxxxxxxxx RF
                          SMC_N 184 keksknaQfivislree 200
                                    k+ +++  + vi ++++
  gi|119720448|ref|YP_920943.1| 187 KRLNEEHGLTVIVVENK 203
                                    *9999988777776654 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 5e-05
                                    SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--..BTTCSSTT.EEEEEEEEEETTEE..SSSSSSCEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxx.xxxxxxxxxxxxxx..xxxxxxxxxx RF
                          SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk..skekasvk.kaeveitfdnedkk..lkiekeevsi 99 
                                    ++ +++G+NGSGKs l+  +           l+ ++ + l+    +++ +    +  v ++f+n+ ++   +   +e+ +
  gi|119720448|ref|YP_920943.1| 290 EVVFLMGRNGSGKSTLVKHMNG--------LLKPSSGRVLVDGcdTRTCPTYRlSRIVGLVFQNPAHQivGESVYDEIAM 361
                                    57899***********998833........46666667777764433333333145578899999999432233344444 PP

                                    EEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 100 srrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkv 179
                                      r    g     + ++ ++ +   el  + ++ +e+LS Ge + +++a ++A+   +p+   +lDe    +  ++ ++v
  gi|119720448|ref|YP_920943.1| 362 GLRHLGVGG--DDVRREVARIARAFELEDKLDMIPEELSVGELKRLMIASIVAM---RPKV-LVLDEPMTGMTSAHSRRV 435
                                    433333333..3566777777777777788888899999999998888877765...5554.578888888888777777 PP

                                    HH.HHHHHCTTSEEEEE-SSHHHC CS
                                    xx.xxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 180 ae.llkeksknaQfivislreeml 202
                                     + +l    +++ ++vi+++ ++ 
  gi|119720448|ref|YP_920943.1| 436 LDtVLGMLGESSTIVVITHDPRLA 459
                                    651455777778888888887654 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   0.00027      0.11      19     143 ..      26     169 ..      18     200 .. 0.58
   2 !   17.5   0.0     1e-05    0.0041      20      63 ..     287     328 ..     276     452 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00027
                         AAA_16  19 vrsgrpelvllsGesGvGKsslvrellralekdggif....lrgkcdqlesaipysalaqalareellrqlldeaesael 94 
                                    ++ +++e v + G+s +GKs+lv +l   l  +   +    ++g  +  + +++  ++a++++r   +  +l+++e+ +l
  gi|119720448|ref|YP_920943.1|  26 LSISQGEFVAVMGPSPSGKSTLVYALSG-LIPH---CvkgeIKGSVKVDGLDTREHPVAELAKR---VGVILQDPEA-QL 97 
                                    44556699***************88874.4444...2012244444444444554668888855...4444555444.45 PP

                         AAA_16  95 eawrekleeala..............................avpelagaeasrllellkrllallsrderplvlvlDd 143
                                     + r+  e al                               + +el+g e++rl+ +   +l       rp v+vlD+
  gi|119720448|ref|YP_920943.1|  98 LELRAVDEVALPlenlgvpaeeirlrvgealemvglrgyeerSPSELSGGEKQRLAIASVLAL-------RPKVIVLDE 169
                                    555554444444666777777777777778877777777766666666666666655522222.......234777775 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 1e-05
                         AAA_16  20 rsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdql 63 
                                    r  ++e+v+l G  G+GKs+lv++    l+ + g +l   cd  
  gi|119720448|ref|YP_920943.1| 287 R--EGEVVFLMGRNGSGKSTLVKHMNGLLKPSSGRVLVDGCDTR 328
                                    3..3489*******************999999899988888887 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0    0.0028       1.1       5     128 ..      31     200 ..      27     209 .. 0.62
   2 !   11.2   0.1   0.00085      0.34       6      99 ..     290     422 ..     286     427 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0028
                         AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaee....................erpevvfvtlpsstsskdllrellral 64 
                                      +++v+G+s +GK+tl+  l    +   k e                     +                         +
  gi|119720448|ref|YP_920943.1|  31 GEFVAVMGPSPSGKSTLVYALSGLIPHCVKGEIkgsvkvdgldtrehpvaelaK------------------------RV 86 
                                    567888888888888888888877643222222333333333333333333331........................33 PP

                         AAA_22  65 glelka............................................erlsseell.ealeqalrarav...ielli 96 
                                    g+ l +                                            e+ s +el     ++ + a      +++++
  gi|119720448|ref|YP_920943.1|  87 GVILQDpeaqllelravdevalplenlgvpaeeirlrvgealemvglrgyEERSPSELSgGEKQRLAIASVLalrPKVIV 166
                                    33333333335555555555555555555555566667777777777788777788887566666655555588889999 PP

                         AAA_22  97 iDEaqh.lr...seealeeLrsllnlsrkgvqliLv 128
                                    +DE    ++   + +++e+L++l +  ++g+++i+v
  gi|119720448|ref|YP_920943.1| 167 LDEPTAnVDppgTLQVYETLKRLNE--EHGLTVIVV 200
                                    9998887887655999999999999..999999987 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00085
                         AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaee...................erpevvfvtlpsstsskdllrellralgl 66 
                                     +++++G  G+GK+tl++ +   l+   +                      + +++vf +++++   ++++ e++  l +
  gi|119720448|ref|YP_920943.1| 290 EVVFLMGRNGSGKSTLVKHMNGLLKP--S--SgrvlvdgcdtrtcptyrlsRIVGLVFQNPAHQIVGESVYDEIAMGLRH 365
                                    67899**************9998842..2..1234455555555555544322222222222222333333333333333 PP

                         AAA_22  67 elka.........................erlsseellealeqalraravielliiDE 99 
                                     + +                         e+ls  el +++   + a +  ++l++DE
  gi|119720448|ref|YP_920943.1| 366 LGVGgddvrrevariarafeledkldmipEELSVGELKRLMIASIVAMRP-KVLVLDE 422
                                    33335556666666666666666677777777777777777777777777.7777777 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0    0.0011      0.46      90     122 ..      21      54 ..       6      93 .. 0.75
   2 !   14.4   0.0   6.4e-05     0.026      90     122 ..     279     312 ..     263     329 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0011
                                    HHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT CS
                    RsgA_GTPase  90 leelkellkd.ktsvlvGqSGvGKStLinallpe 122
                                    l++++  +++ ++++++G+S  GKStL+ al + 
  gi|119720448|ref|YP_920943.1|  21 LDSVSLSISQgEFVAVMGPSPSGKSTLVYALSGL 54 
                                    5555555655599***************999874 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 6.4e-05
                                    HHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT CS
                    RsgA_GTPase  90 leelkellkd.ktsvlvGqSGvGKStLinallpe 122
                                    l+++   l++ ++++l+G  G GKStL++++++ 
  gi|119720448|ref|YP_920943.1| 279 LDHVDLTLREgEVVFLMGRNGSGKSTLVKHMNGL 312
                                    566666777779*****************99875 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.1    0.0024      0.97      30      54 ..      28      52 ..      24     209 .. 0.85
   2 !   11.2   0.0   0.00049       0.2      29      51 ..     285     307 ..     279     311 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0024
                         AAA_25 30 lpagelallaGapgtGKttlaldla 54
                                   +  ge+++++G++ +GK+tl++ l+
  gi|119720448|ref|YP_920943.1| 28 ISQGEFVAVMGPSPSGKSTLVYALS 52
                                   5689*****************9987 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00049
                         AAA_25  29 llpagelallaGapgtGKttlal 51 
                                     l++ge++ l+G+ g+GK+tl+ 
  gi|119720448|ref|YP_920943.1| 285 TLREGEVVFLMGRNGSGKSTLVK 307
                                    6889****************985 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0    0.0016      0.64      16      66 ..      25      75 ..      16      89 .. 0.79
   2 !   10.6   0.0   0.00065      0.27      25      51 ..     292     318 ..     280     350 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0016
                   Mg_chelatase 16 eiaaaGgHnlllvGppGsGKtmlakrlpsllpplseeealevakiasvagk 66
                                    ++++ g  + ++Gp+ sGK+ l  +l++l+p+  + e+  + k+  + ++
  gi|119720448|ref|YP_920943.1| 25 SLSISQGEFVAVMGPSPSGKSTLVYALSGLIPHCVKGEIKGSVKVDGLDTR 75
                                   5556666678899*********************99999888888777664 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00065
                   Mg_chelatase  25 lllvGppGsGKtmlakrlpsllpplse 51 
                                    ++l+G  GsGK+ l k +++ll p s 
  gi|119720448|ref|YP_920943.1| 292 VFLMGRNGSGKSTLVKHMNGLLKPSSG 318
                                    789*******************98775 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.098        40      12      44 ..      19      52 ..      19      77 .. 0.87
   2 !   13.8   0.0     9e-05     0.037      15      50 ..     280     316 ..     278     349 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.098
                         AAA_15 12 Rslkdveidlsee.ltvliGkNnsGKSsileald 44
                                   R+l++v++++s   +  + G+  sGKS++++al 
  gi|119720448|ref|YP_920943.1| 19 RALDSVSLSISQGeFVAVMGPSPSGKSTLVYALS 52
                                   6788888888887899****************96 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 9e-05
                         AAA_15  15 kdveidlsee.ltvliGkNnsGKSsilealdlFlnnk 50 
                                    ++v++ l e  + +l G+N+sGKS++++ ++ +l+ +
  gi|119720448|ref|YP_920943.1| 280 DHVDLTLREGeVVFLMGRNGSGKSTLVKHMNGLLKPS 316
                                    5666777776799****************99999977 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0    0.0016      0.67       2      21 ..      34      53 ..      33     213 .. 0.86
   2 !    7.5   0.0    0.0099       4.1       2      21 ..     292     311 ..     291     335 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0016
                                   EEEEESTTSSHHHHHHHHHT CS
                       MMR_HSR1  2 vaivGrpNvGKStLinaltg 21
                                   va++G + +GKStL+ al+g
  gi|119720448|ref|YP_920943.1| 34 VAVMGPSPSGKSTLVYALSG 53
                                   89****************97 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0099
                                    EEEEESTTSSHHHHHHHHHT CS
                       MMR_HSR1   2 vaivGrpNvGKStLinaltg 21 
                                    v ++Gr  +GKStL++ + g
  gi|119720448|ref|YP_920943.1| 292 VFLMGRNGSGKSTLVKHMNG 311
                                    789***********998755 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0   0.00038      0.16     106     156 ..       8      58 ..       2      65 .. 0.80
   2 ?   -1.3   0.0       2.3   9.3e+02     143     175 ..     179     212 ..     142     236 .. 0.76
   3 ?    3.7   0.0     0.066        27     122     160 ..     282     320 ..     242     326 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00038
                          T2SSE 106 ddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeinks 156
                                    ++l+++  +  +  + ++ ++++   + v G+  sGK+tl+yal   i+++
  gi|119720448|ref|YP_920943.1|   8 ENLSFSYPNGRRALDSVSLSISQGEFVAVMGPSPSGKSTLVYALSGLIPHC 58 
                                    5566666666667777888888899999*****************999876 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.3
                          T2SSE 143 ttllyallkeinks.derivtvEDpvEiqlegan 175
                                    t  +y  lk +n++    +++vE  vE+  + a+
  gi|119720448|ref|YP_920943.1| 179 TLQVYETLKRLNEEhGLTVIVVENKVEVARRYAK 212
                                    5566888888888756678888999998776555 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.066
                          T2SSE 122 lrkavrerglilvsGgTgsGKttllyallkeinksderi 160
                                    +   +re  ++ + G  gsGK+tl+  +   ++ s+ r+
  gi|119720448|ref|YP_920943.1| 282 VDLTLREGEVVFLMGRNGSGKSTLVKHMNGLLKPSSGRV 320
                                    55556667888999**********998888887776665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0      0.22        88      16      45 ..      29      58 ..      21     201 .. 0.80
   2 !   14.1   0.0   7.2e-05     0.029      13      82 ..     285     408 ..     279     457 .. 0.59

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.22
                         AAA_30 16 sgdrvavltGpAGtGKttalkalreaweaa 45
                                   s+  ++++ Gp  +GK+t++ al  ++ + 
  gi|119720448|ref|YP_920943.1| 29 SQGEFVAVMGPSPSGKSTLVYALSGLIPHC 58
                                   444589999**********99998777655 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 7.2e-05
                         AAA_30  13 lltsgdrvavltGpAGtGKttalkalreaweaa.g.................grviglAptgkaAkvLae.......... 64 
                                    +l +g  v++l G+ G+GK+t++k+++ +++ + g                  r++gl  ++ a + ++e          
  gi|119720448|ref|YP_920943.1| 285 TLREG-EVVFLMGRNGSGKSTLVKHMNGLLKPSsGrvlvdgcdtrtcptyrlSRIVGLVFQNPAHQIVGEsvydeiamgl 363
                                    45555.59**********************99955777777777777777664555555555554444432222222222 PP

                         AAA_30  65 .elgieastiakllkrlk..........................g 82 
                                     +lg+ ++ + + + r +                          +
  gi|119720448|ref|YP_920943.1| 364 rHLGVGGDDVRREVARIArafeledkldmipeelsvgelkrlmiA 408
                                    244554444444444444444455566666666666666666552 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1      0.17        67       2      17 ..      34      49 ..      33      58 .. 0.86
   2 !   12.3   0.2   0.00034      0.14       1      21 [.     291     314 ..     291     465 .. 0.62

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.17
                         AAA_33  2 vllvGlpGsGKstlae 17
                                   v + G++ sGKstl+ 
  gi|119720448|ref|YP_920943.1| 34 VAVMGPSPSGKSTLVY 49
                                   5689*********986 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00034
                         AAA_33   1 lvllvGlpGsGKstlaerl...lk 21 
                                    +v+l G +GsGKstl++++   lk
  gi|119720448|ref|YP_920943.1| 291 VVFLMGRNGSGKSTLVKHMnglLK 314
                                    89**************99733343 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0      0.23        95       2      46 ..      34      87 ..      33     105 .. 0.67
   2 !   11.0   0.0   0.00074       0.3       2      33 ..     292     325 ..     291     336 .. 0.80
   3 ?    0.1   0.1       1.6   6.7e+02      79     135 ..     400     456 ..     394     476 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.23
                                   EEEE--TTSSHHHHHHHHHHHH..........GGGEEEEEEEEE-..------E CS
                       NTPase_1  2 vfiTGppGvGKtTlvkkvlell....kss...gvkvgGfyteevr..eggrrig 46
                                   v++ Gp+ +GK+Tlv  ++ l+    k +    vkv+G+ t+e+   e  +r+g
  gi|119720448|ref|YP_920943.1| 34 VAVMGPSPSGKSTLVYALSGLIphcvKGEikgSVKVDGLDTREHPvaELAKRVG 87
                                   67889999******9876655411111111124778887777766445555555 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00074
                                    EEEE--TTSSHHHHHHHHHHHH.....GGGEEEE CS
                       NTPase_1   2 vfiTGppGvGKtTlvkkvlellkss..gvkvgGf 33 
                                    vf+ G+ G+GK+Tlvk +  llk s   v v+G 
  gi|119720448|ref|YP_920943.1| 292 VFLMGRNGSGKSTLVKHMNGLLKPSsgRVLVDGC 325
                                    899***************9999866223555665 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 1.6
                                    HHHHHHHHHHHHHHHHHH-EEEE--..-STTGGG-HHHHHHHHHHHTTTSEEEEE--SS CS
                       NTPase_1  79 esfeelalealrkalseadviviDE..iGkmElkskkfkeaveevLksekpvlavihrr 135
                                     ++++l+++++     ++ v+v+DE   G     s+++ ++v  +L ++  ++++ h +
  gi|119720448|ref|YP_920943.1| 400 GELKRLMIASIVA--MRPKVLVLDEpmTGMTSAHSRRVLDTVLGMLGESSTIVVITHDP 456
                                    5677777777765..57899999996668888888888899999998666666666665 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       1.6   6.4e+02      38      53 ..      34      49 ..      29      80 .. 0.84
   2 ?    3.5   0.0       0.1        41     105     160 ..     147     200 ..     133     207 .. 0.82
   3 ?    1.5   0.0       0.4   1.6e+02      38      55 ..     292     309 ..     281     319 .. 0.85
   4 !    6.9   0.0    0.0094       3.8     103     158 ..     398     452 ..     387     462 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.6
                           TniB 38 lllvGdsnnGKtmive 53
                                   + ++G+s  GK+++v 
  gi|119720448|ref|YP_920943.1| 34 VAVMGPSPSGKSTLVY 49
                                   6799*********986 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.1
                           TniB 105 skleqqvlrllrelkvrvLiiDEihnllagsarkqreflnalksLgnelkipivlv 160
                                     ++++ +++   +l+++v+++DE    +        ++ ++lk+L++e  +++++v
  gi|119720448|ref|YP_920943.1| 147 GEKQRLAIASVLALRPKVIVLDEPTANV--DPPGTLQVYETLKRLNEEHGLTVIVV 200
                                    56778888888999*********87665..67777889999999999999999876 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.4
                           TniB  38 lllvGdsnnGKtmivekF 55 
                                    + l+G+   GK+++v++ 
  gi|119720448|ref|YP_920943.1| 292 VFLMGRNGSGKSTLVKHM 309
                                    6799***********986 PP

  == domain 4  score: 6.9 bits;  conditional E-value: 0.0094
                           TniB 103 rvskleqqvlrllrelkvrvLiiDEihnllagsarkqreflnalksLgnelkipiv 158
                                    +v +l++ +++ + +++++vL++DE    +  sa+++r +  +l +Lg+   i ++
  gi|119720448|ref|YP_920943.1| 398 SVGELKRLMIASIVAMRPKVLVLDEPMTGM-TSAHSRRVLDTVLGMLGESSTIVVI 452
                                    677899999999*************88887.6778888888899999998888776 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0      0.11        45       2      19 ..      35      52 ..      34      71 .. 0.84
   2 !   11.2   0.0   0.00092      0.38       1      48 [.     292     334 ..     292     348 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.11
                   RNA_helicase  2 wlyGpsgeGKStlakeLa 19
                                    + Gps  GKStl++ L+
  gi|119720448|ref|YP_920943.1| 35 AVMGPSPSGKSTLVYALS 52
                                   689***********9975 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00092
                   RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYt 48 
                                    ++l G++g GKStl+k+ ++ ll    ++++++v + ++++  +  Y+
  gi|119720448|ref|YP_920943.1| 292 VFLMGRNGSGKSTLVKH-MNGLL----KPSSGRVLVDGCDTRTCPTYR 334
                                    6899*************.55555....566677777777776666665 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0    0.0079       3.2      18      49 ..      23      54 ..       7      56 .. 0.87
   2 !    7.0   0.0    0.0094       3.8      18      50 ..     281     313 ..     271     314 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0079
                         AAA_27 18 sldfsaeeadlhliyGpNEAGKstalrAisdl 49
                                   s+++s ++ ++  ++Gp  +GKst++ A+s l
  gi|119720448|ref|YP_920943.1| 23 SVSLSISQGEFVAVMGPSPSGKSTLVYALSGL 54
                                   5666777899******************9977 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0094
                         AAA_27  18 sldfsaeeadlhliyGpNEAGKstalrAisdll 50 
                                    ++d+   e ++ +++G N +GKst+++ ++ ll
  gi|119720448|ref|YP_920943.1| 281 HVDLTLREGEVVFLMGRNGSGKSTLVKHMNGLL 313
                                    5667767889999************99888776 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.051        21       5      22 ..      34      51 ..      31      77 .. 0.82
   2 !    9.5   0.0    0.0018      0.73       4      23 ..     291     314 ..     288     329 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.051
                         AAA_24  5 iliyGpsgiGKTtlakel 22
                                   ++++Gps +GK+tl++ l
  gi|119720448|ref|YP_920943.1| 34 VAVMGPSPSGKSTLVYAL 51
                                   689***********9988 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0018
                         AAA_24   4 kiliyGpsgiGKTtlakel....g 23 
                                     ++++G +g+GK+tl+k++    +
  gi|119720448|ref|YP_920943.1| 291 VVFLMGRNGSGKSTLVKHMngllK 314
                                    689***************955551 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0      0.19        77      21      40 ..      33      52 ..      16      78 .. 0.84
   2 !   11.0   0.0    0.0011      0.43      18      37 ..     288     307 ..     274     315 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.19
                         AAA_23 21 ltlItGpNGaGKTTildAik 40
                                   ++++ Gp  +GK+T++ A+ 
  gi|119720448|ref|YP_920943.1| 33 FVAVMGPSPSGKSTLVYALS 52
                                   567889*********99885 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0011
                         AAA_23  18 skgltlItGpNGaGKTTild 37 
                                    +  ++ + G NG+GK+T++ 
  gi|119720448|ref|YP_920943.1| 288 EGEVVFLMGRNGSGKSTLVK 307
                                    55678899*********986 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0    0.0034       1.4      27      88 ..     138     186 ..     120     188 .. 0.73
   2 ?    2.0   0.0      0.62   2.5e+02      63      87 ..     414     438 ..     405     440 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0034
                        SbcCD_C  27 srssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllell 88 
                                    +rs ++lSGGekq l       a+a+++        ++++++LDE  +++D+  + ++ e+l
  gi|119720448|ref|YP_920943.1| 138 ERSPSELSGGEKQRL-------AIASVLAL------RPKVIVLDEPTANVDPPGTLQVYETL 186
                                    6777899*****765.......45555555......47788888888888888777777666 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.62
                        SbcCD_C  63 alrlvfLDEAFsklDeesiatllel 87 
                                    ++++++LDE   ++ +  ++++l++
  gi|119720448|ref|YP_920943.1| 414 RPKVLVLDEPMTGMTSAHSRRVLDT 438
                                    6889************999999986 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.043        18       2      22 ..      34      54 ..      33      94 .. 0.81
   2 ?    2.4   0.0      0.41   1.7e+02      94     159 ..     138     203 ..     130     209 .. 0.72
   3 ?    4.2   0.0      0.11        45       2      20 ..     292     310 ..     291     323 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.043
                         AAA_28  2 ivitGgestGKTtlleaLaar 22
                                   ++++G++ +GK+tl+ aL+  
  gi|119720448|ref|YP_920943.1| 34 VAVMGPSPSGKSTLVYALSGL 54
                                   799**************9865 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.41
                         AAA_28  94 geaeaelea.aarekrydlvfllppapeidddgeRredleereaiderlrealrelgipviivpsgd 159
                                    ++ + el   + ++  ++ v+ l+p   + d  +   d+    +++e l+ + +e+g  vi+v+   
  gi|119720448|ref|YP_920943.1| 138 ERSPSELSGgEKQRLAIASVLALRPKVIVLDEPTANVDPPGTLQVYETLKRLNEEHGLTVIVVE-NK 203
                                    4555556553444555677888888776646666678999999********************4.43 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.11
                         AAA_28   2 ivitGgestGKTtlleaLa 20 
                                    + ++G  ++GK+tl+++++
  gi|119720448|ref|YP_920943.1| 292 VFLMGRNGSGKSTLVKHMN 310
                                    678999*********9975 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.045        18       1      24 [.      34      58 ..      34     102 .. 0.78
   2 ?    7.5   0.0     0.014       5.8       1      22 [.     292     313 ..     292     349 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.045
                         AAA_18  1 IlltGtpGvGKttlakeLskrl.gf 24
                                   ++++G++ +GK+tl  +Ls +  ++
  gi|119720448|ref|YP_920943.1| 34 VAVMGPSPSGKSTLVYALSGLIpHC 58
                                   689************9998776555 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.014
                         AAA_18   1 IlltGtpGvGKttlakeLskrl 22 
                                    ++l+G  G+GK+tl k+ + +l
  gi|119720448|ref|YP_920943.1| 292 VFLMGRNGSGKSTLVKHMNGLL 313
                                    7899***********9986655 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       2.3   9.5e+02       4      23 ..      36      55 ..      34      64 .. 0.83
   2 ?   -0.8   0.0       3.5   1.4e+03      65     124 ..     161     230 ..     135     241 .. 0.58
   3 ?   11.7   0.0   0.00047      0.19       2      24 ..     292     314 ..     291     327 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 2.3
                                   EE--SSSSHHHHHHHGGGGB CS
                          AAA_5  4 LvGppGtgKselaerlaaal 23
                                   + Gp+ +gKs+l+  l+ ++
  gi|119720448|ref|YP_920943.1| 36 VMGPSPSGKSTLVYALSGLI 55
                                   679999*******9999888 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 3.5
                                    G-SEEEEESGGG--HHHHHHHHHHHHSSEEE..-SSSEEE---.................-EEEEEESS-- CS
                          AAA_5  65 egeilvlDEveraesevlnsLlslleerrllleeggelvkakndd.ller..........frviatanpld 124
                                    +++++vlDE + a+ +  ++L+ +   +rl  e g +++ ++n+   ++r           rv+a ++p +
  gi|119720448|ref|YP_920943.1| 161 RPKVIVLDEPT-ANVDPPGTLQVYETLKRLNEEHGLTVIVVENKVeVARRyakravlmegGRVVADGEPSK 230
                                    66777777755.55555555544444555555555555555555444444555455555555555555554 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.00047
                                    EEEE--SSSSHHHHHHHGGGGBS CS
                          AAA_5   2 vlLvGppGtgKselaerlaaaln 24 
                                    v+L G  G+gKs+l++++  +l+
  gi|119720448|ref|YP_920943.1| 292 VFLMGRNGSGKSTLVKHMNGLLK 314
                                    89****************99983 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.018       7.2       1      22 [.      36      57 ..      36      63 .. 0.88
   2 ?    7.1   0.1      0.01       4.1       2      21 ..     295     314 ..     294     322 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.018
                     ATP_bind_1  1 vvGpaGsGKttfvgalseilel 22
                                   v+Gp  sGK+t+v als +++ 
  gi|119720448|ref|YP_920943.1| 36 VMGPSPSGKSTLVYALSGLIPH 57
                                   89*************9987775 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.01
                     ATP_bind_1   2 vGpaGsGKttfvgalseile 21 
                                    +G  GsGK+t+v+ ++ +l+
  gi|119720448|ref|YP_920943.1| 295 MGRNGSGKSTLVKHMNGLLK 314
                                    7999**********987765 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.47   1.9e+02      21      37 ..      32      48 ..      22      52 .. 0.86
   2 ?   10.5   0.0   0.00061      0.25      21      40 ..     290     309 ..     279     318 .. 0.86
   3 ?   -2.5   0.0       5.8   2.3e+03      62     110 ..     371     421 ..     353     422 .. 0.66

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.47
                                   EEEEEEESTTSSHHHHH CS
                         NB-ARC 21 lvvalvGmgGvGKttla 37
                                    +va++G   +GK+tl+
  gi|119720448|ref|YP_920943.1| 32 EFVAVMGPSPSGKSTLV 48
                                   599************97 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00061
                                    EEEEEEESTTSSHHHHHHHH CS
                         NB-ARC  21 lvvalvGmgGvGKttlakqi 40 
                                     vv+l+G+ G+GK+tl+k++
  gi|119720448|ref|YP_920943.1| 290 EVVFLMGRNGSGKSTLVKHM 309
                                    39**************9976 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 5.8
                                    XXHHHHHHHXXHHHHHCCCTTSSSS-STTS....HHHHHHHHCCCTTEEEEEE CS
                         NB-ARC  62 tdkseeiletilkeLslseddleekeeves....lkrklvrlLltkrfllvlD 110
                                     d  +e+ + i++ ++l++ +l+  +e+ s    +  ++  +   +  +lvlD
  gi|119720448|ref|YP_920943.1| 371 DDVRREVAR-IARAFELED-KLDMIPEELSvgelKRLMIASIVAMRPKVLVLD 421
                                    555566666.899998884.444444444346655567777777777777777 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0      0.13        52      27      91 ..      25      87 ..      20     112 .. 0.72
   2 ?    9.3   0.0    0.0018      0.73      26      58 ..     282     314 ..     274     331 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.13
                          AAA_7 27 elllknkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdiiesklekrrk 91
                                   +l ++++  v ++Gp+ +GK++++  l   ++  +++   i+ s + +  ++++   ++l kr +
  gi|119720448|ref|YP_920943.1| 25 SLSISQGEFVAVMGPSPSGKSTLVYALSGLIP--HCVKGEIKGSVKVDGLDTREHPVAELAKRVG 87
                                   5678899999*************998776666..6666666666666666666666666666655 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0018
                          AAA_7  26 lelllknkkpvllvGptGtGKtviikdllkkld 58 
                                    ++l l+++  v+l+G  G+GK++++k++   l+
  gi|119720448|ref|YP_920943.1| 282 VDLTLREGEVVFLMGRNGSGKSTLVKHMNGLLK 314
                                    5788999999***************99876655 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.29   1.2e+02      19      37 ..      30      48 ..      18      52 .. 0.83
   2 ?   10.4   0.0    0.0011      0.45      20      42 ..     289     311 ..     276     334 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.29
                       ATPase_2 19 pneiyfiYGpegsGKtaLl 37
                                   + e++ + Gp  sGK++L+
  gi|119720448|ref|YP_920943.1| 30 QGEFVAVMGPSPSGKSTLV 48
                                   467899***********97 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0011
                       ATPase_2  20 neiyfiYGpegsGKtaLlkeiie 42 
                                     e++f+ G+ gsGK++L+k++  
  gi|119720448|ref|YP_920943.1| 289 GEVVFLMGRNGSGKSTLVKHMNG 311
                                    689****************9755 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0       1.1   4.6e+02       3      20 ..      34      51 ..      32      57 .. 0.85
   2 ?   11.8   0.0    0.0004      0.16       2      21 ..     291     310 ..     290     319 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 1.1
                                   EEEEC-TTTCHHHHHHHH CS
                          NACHT  3 vilqGeaGsGKTtLlqkl 20
                                   v++ G++ sGK+tL+  l
  gi|119720448|ref|YP_920943.1| 34 VAVMGPSPSGKSTLVYAL 51
                                   7899**********9776 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.0004
                                    CEEEEC-TTTCHHHHHHHHH CS
                          NACHT   2 lvilqGeaGsGKTtLlqkla 21 
                                    +v+l G++GsGK+tL++++ 
  gi|119720448|ref|YP_920943.1| 291 VVFLMGRNGSGKSTLVKHMN 310
                                    799*************9975 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0      0.14        57       4      23 ..      34      53 ..      32      60 .. 0.89
   2 ?    9.0   0.1    0.0027       1.1       4      23 ..     292     311 ..     289     314 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.14
                      PduV-EutP  4 illiGkvgsGKttLtqalkg 23
                                   + ++G++ sGK tL  al+g
  gi|119720448|ref|YP_920943.1| 34 VAVMGPSPSGKSTLVYALSG 53
                                   679*************9987 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0027
                      PduV-EutP   4 illiGkvgsGKttLtqalkg 23 
                                    ++l+G+ gsGK tL ++++g
  gi|119720448|ref|YP_920943.1| 292 VFLMGRNGSGKSTLVKHMNG 311
                                    89**************9987 PP

>> KdpD  Osmosensitive K+ channel His kinase sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0    0.0095       3.9      62      93 ..     141     172 ..     117     204 .. 0.76
   2 ?    5.5   0.1     0.025        10      50      92 ..     385     424 ..     372     454 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0095
                           KdpD  62 eveykgkeleeldldailarkpevvlvDelah 93 
                                      e +g e ++l + ++la +p+v+++De   
  gi|119720448|ref|YP_920943.1| 141 PSELSGGEKQRLAIASVLALRPKVIVLDEPTA 172
                                    45677889999******************543 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.025
                           KdpD  50 allegleviprkeveykgkeleeldldailarkpevvlvDela 92 
                                    +l ++l++ip+   e +  el++l + +i+a++p+v+++De  
  gi|119720448|ref|YP_920943.1| 385 ELEDKLDMIPE---ELSVGELKRLMIASIVAMRPKVLVLDEPM 424
                                    45567888887...456678999*****************943 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0      0.25     1e+02       4      24 ..      33      53 ..      30     110 .. 0.82
   2 ?    9.1   0.0    0.0028       1.2       2      38 ..     289     324 ..     288     335 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.25
                                   EEEEESSTTSSHHHHHHHHHH CS
                     APS_kinase  4 vvwltGlsgsGKstianalek 24
                                    v + G s sGKst+ +al+ 
  gi|119720448|ref|YP_920943.1| 33 FVAVMGPSPSGKSTLVYALSG 53
                                   67788**********999974 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0028
                                    -EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEH CS
                     APS_kinase   2 gvvvwltGlsgsGKstianalekkLvekgisvylLdG 38 
                                    g vv+l G  gsGKst+ ++++  L+ +  +v l+dG
  gi|119720448|ref|YP_920943.1| 289 GEVVFLMGRNGSGKSTLVKHMNGLLKPSSGRV-LVDG 324
                                    779***************99997776554443.4455 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.22        89      24      54 ..      30      61 ..      23      92 .. 0.84
   2 ?    9.4   0.1     0.001      0.42      24      56 ..     288     320 ..     282     323 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.22
                           DLIC 24 sgksvlvlGedgsGkttliaklqG.veeekkG 54
                                    g  v v+G + sGk+tl+  l G + +  kG
  gi|119720448|ref|YP_920943.1| 30 QGEFVAVMGPSPSGKSTLVYALSGlIPHCVKG 61
                                   567799***************99933455665 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.001
                           DLIC  24 sgksvlvlGedgsGkttliaklqGveeekkGrG 56 
                                     g  v+++G +gsGk+tl+  + G+ ++  Gr 
  gi|119720448|ref|YP_920943.1| 288 EGEVVFLMGRNGSGKSTLVKHMNGLLKPSSGRV 320
                                    677899*******************99999986 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.057        23      44      68 ..      28      52 ..      16      57 .. 0.88
   2 ?   -1.9   0.0       5.8   2.4e+03     106     141 ..     159     193 ..     148     212 .. 0.70
   3 ?    2.4   0.0      0.28   1.2e+02      44      64 ..     286     306 ..     258     311 .. 0.84
   4 ?    2.0   0.0      0.36   1.5e+02     105     148 ..     411     454 ..     384     465 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.057
                      IstB_IS21 44 iekkenivllGpsGvGKshlaialg 68
                                   i++ e ++++Gps  GKs l  al+
  gi|119720448|ref|YP_920943.1| 28 ISQGEFVAVMGPSPSGKSTLVYALS 52
                                   678899***************9985 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 5.8
                      IstB_IS21 106 llkvdllilDdlgllpldqaeaellfeviekryerr 141
                                     l++++++lD+  + ++d   + +++e +++  e +
  gi|119720448|ref|YP_920943.1| 159 ALRPKVIVLDEP-TANVDPPGTLQVYETLKRLNEEH 193
                                    568899999996.56788888888888887766554 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.28
                      IstB_IS21  44 iekkenivllGpsGvGKshla 64 
                                    +++ e + l+G  G GKs l 
  gi|119720448|ref|YP_920943.1| 286 LREGEVVFLMGRNGSGKSTLV 306
                                    46778999**********986 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.36
                      IstB_IS21 105 rllkvdllilDdlgllpldqaeaellfeviekryerrsiiitsn 148
                                      +++++l+lD+  +   + +++++l  v+    e ++i++ + 
  gi|119720448|ref|YP_920943.1| 411 VAMRPKVLVLDEPMTGMTSAHSRRVLDTVLGMLGESSTIVVITH 454
                                    346789*******9999999999999999998888888877655 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00019     0.077       4      43 ..     293     332 ..     290     358 .. 0.90
   2 ?   -2.7   0.0       7.9   3.2e+03     240     266 ..     380     407 ..     372     410 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00019
                      Fer4_NifH   4 aiyGkGGiGksttsqnlsaalaemgkkvlivGCDPkaDst 43 
                                     + G+ G+Gkst ++ +   l+    +vl+ GCD ++  t
  gi|119720448|ref|YP_920943.1| 293 FLMGRNGSGKSTLVKHMNGLLKPSSGRVLVDGCDTRTCPT 332
                                    5689******************************987555 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 7.9
                      Fer4_NifH 240 larki.lenkklviPkplsedeLeelle 266
                                    +ar+  le+k  +iP++ls  eL+ l++
  gi|119720448|ref|YP_920943.1| 380 IARAFeLEDKLDMIPEELSVGELKRLMI 407
                                    5555424667789*********999976 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.57   2.3e+02      15      36 ..      27      48 ..      15      69 .. 0.86
   2 ?    5.8   0.0     0.019       7.6      16      38 ..     286     308 ..     273     314 .. 0.86
   3 ?    2.8   0.0      0.15        62      61     164 ..     357     456 ..     342     470 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.57
                         ATPase 15 GipegrvvlitGepGtGKtifa 36
                                    i +g+ v ++G + +GK++++
  gi|119720448|ref|YP_920943.1| 27 SISQGEFVAVMGPSPSGKSTLV 48
                                   58899**************986 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.019
                         ATPase  16 ipegrvvlitGepGtGKtifalq 38 
                                    + eg+vv ++G  G+GK++++++
  gi|119720448|ref|YP_920943.1| 286 LREGEVVFLMGRNGSGKSTLVKH 308
                                    789****************9875 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.15
                         ATPase  61 edlrenakslGwdlekleeegklaiidasesaeesaeekdkedleelieelaeaikeikakrvviDsitglayeekeava 140
                                     ++    ++lG+  +++++e    i  a+e +++     ++ ++ el++ +   i +++ k +v+D    + + +++a  
  gi|119720448|ref|YP_920943.1| 357 DEIAMGLRHLGVGGDDVRRE-VARIARAFELEDKLDMIPEELSVGELKRLMIASIVAMRPKVLVLDEP--M-TGMTSAHS 432
                                    56666677777777777777.455666666666555558899999*********************63..3.44688899 PP

                         ATPase 141 ReilrqlvrvlkklgvTailvsek 164
                                    R+ l++++ +l +  +  +++ + 
  gi|119720448|ref|YP_920943.1| 433 RRVLDTVLGMLGESSTIVVITHDP 456
                                    999999999999888888888775 PP

>> AAA_PrkA  PrkA AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.16        65      92     114 ..      35      57 ..      28      97 .. 0.72
   2 ?    7.9   0.0    0.0031       1.3      89     123 ..     290     325 ..     283     350 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.16
                       AAA_PrkA  92 yllGPvggGksslverlkkllea 114
                                     ++GP  +Gks+lv +l  l+ +
  gi|119720448|ref|YP_920943.1|  35 AVMGPSPSGKSTLVYALSGLIPH 57 
                                    589***********999877755 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0031
                       AAA_PrkA  89 qilyllGPvggGksslverlkklleaapiyal.egs 123
                                    ++++l+G  g+Gks+lv+++  ll+ ++  +l +g+
  gi|119720448|ref|YP_920943.1| 290 EVVFLMGRNGSGKSTLVKHMNGLLKPSSGRVLvDGC 325
                                    699*****************9999877555444444 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       1.1   4.5e+02      28      43 ..      36      51 ..      30      61 .. 0.84
   2 ?   10.1   0.0    0.0008      0.33      26      49 ..     292     315 ..     280     330 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.1
                                   EEESTTSSHHHHHHHH CS
                        G-alpha 28 llGqseSGKsTilkql 43
                                   ++G s SGKsT++  l
  gi|119720448|ref|YP_920943.1| 36 VMGPSPSGKSTLVYAL 51
                                   6899*******98765 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0008
                                    EEEEESTTSSHHHHHHHHHHHCS- CS
                        G-alpha  26 llllGqseSGKsTilkqlkllykk 49 
                                    + l+G ++SGKsT++k++  l k+
  gi|119720448|ref|YP_920943.1| 292 VFLMGRNGSGKSTLVKHMNGLLKP 315
                                    7899**************977665 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0      0.17        69       3      28 ..      33      58 ..      31      60 .. 0.83
   2 ?   -1.6   0.0       5.1   2.1e+03      67      89 ..     203     225 ..     185     239 .. 0.73
   3 ?    6.2   0.0     0.021       8.4       1      25 [.     289     313 ..     289     366 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.17
                                   EEEEEE-TTSSHHHHHHHHHHHSSS- CS
                            CPT  3 iilLnGgsssGKsslaralqevldep 28
                                    +   G s sGKs+l+ al  +++++
  gi|119720448|ref|YP_920943.1| 33 FVAVMGPSPSGKSTLVYALSGLIPHC 58
                                   6777899***********98887765 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 5.1
                                    HHHHHHHHHHHHHHHTT-EEEEE CS
                            CPT  67 lllaalyeavaamaraGnnvivD 89 
                                    +++ a++ a +a++ +G +v++D
  gi|119720448|ref|YP_920943.1| 203 KVEVARRYAKRAVLMEGGRVVAD 225
                                    45567777888999999999999 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.021
                                    --EEEEEE-TTSSHHHHHHHHHHHS CS
                            CPT   1 ariilLnGgsssGKsslaralqevl 25 
                                    +++++L G   sGKs+l++ +  +l
  gi|119720448|ref|YP_920943.1| 289 GEVVFLMGRNGSGKSTLVKHMNGLL 313
                                    689***************9887666 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       1.1   4.7e+02       9      47 ..      20      56 ..      16      70 .. 0.82
   2 ?    9.6   0.0    0.0011      0.46      20      54 ..     287     321 ..     277     324 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.1
                                   HHHHH......HCTS-EEEEESTTSSCHHHHHHHHHHCH CS
                           PIF1  9 vfdaiieavlnekgklfFvtGsgGtgKtflwkallkklr 47
                                   ++d++  +++ ++g+++ v G + +gK+ l  al+  + 
  gi|119720448|ref|YP_920943.1| 20 ALDSV--SLSISQGEFVAVMGPSPSGKSTLVYALSGLIP 56
                                   56666..667799*****************999998876 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0011
                                    HCTS-EEEEESTTSSCHHHHHHHHHHCHCTCCCEE CS
                           PIF1  20 ekgklfFvtGsgGtgKtflwkallkklrsegkivl 54 
                                    ++g+++F+ G  G+gK+ l k++   l+++   vl
  gi|119720448|ref|YP_920943.1| 287 REGEVVFLMGRNGSGKSTLVKHMNGLLKPSSGRVL 321
                                    789**********************9999887776 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00093      0.38      18      56 ..     291     329 ..     285     337 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00093
                     Zeta_toxin  18 lillgGqpGAGKselaellkdelerqgnvvrldpDdlRe 56 
                                    +++l G  G+GKs+l + ++  l++ ++ v +d+ d R+
  gi|119720448|ref|YP_920943.1| 291 VVFLMGRNGSGKSTLVKHMNGLLKPSSGRVLVDGCDTRT 329
                                    799*********************999999999988886 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.098        40       3      22 ..      32      51 ..      30      84 .. 0.89
   2 ?    5.0   0.0     0.058        24       3      22 ..     290     309 ..     288     334 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.098
                         AAA_14  3 kilvitGaRrvGKTtllkql 22
                                   + ++++G+  +GK+tl++ l
  gi|119720448|ref|YP_920943.1| 32 EFVAVMGPSPSGKSTLVYAL 51
                                   6799************9876 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.058
                         AAA_14   3 kilvitGaRrvGKTtllkql 22 
                                    ++++++G   +GK+tl+k++
  gi|119720448|ref|YP_920943.1| 290 EVVFLMGRNGSGKSTLVKHM 309
                                    7899*************987 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       3.8   1.6e+03      19      39 ..      31      51 ..      18      59 .. 0.78
   2 ?    9.2   0.0    0.0029       1.2      19      42 ..     289     312 ..     276     338 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 3.8
                                   TEEEEEEESTTSSHHHHHHHH CS
                           TsaE 19 gdvilLeGdLGaGKTtlvrgl 39
                                   g++++  G+  +GK+tlv +l
  gi|119720448|ref|YP_920943.1| 31 GEFVAVMGPSPSGKSTLVYAL 51
                                   7789999999*******9776 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0029
                                    TEEEEEEESTTSSHHHHHHHHHHH CS
                           TsaE  19 gdvilLeGdLGaGKTtlvrglaka 42 
                                    g+v++L G  G+GK+tlv+++   
  gi|119720448|ref|YP_920943.1| 289 GEVVFLMGRNGSGKSTLVKHMNGL 312
                                    789****************98654 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.066        27      33      67 ..      19      53 ..      16      70 .. 0.83
   2 ?    4.1   0.0     0.093        38      40      72 ..     284     316 ..     276     380 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.066
                          Rad17 33 ewlkadvLesrkkriLLisGPsGCgkstvvkvLsk 67
                                   ++l++ +L   + + + + GPs  gkst v  Ls 
  gi|119720448|ref|YP_920943.1| 19 RALDSVSLSISQGEFVAVMGPSPSGKSTLVYALSG 53
                                   57888888888888999*************99986 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.093
                          Rad17  40 LesrkkriLLisGPsGCgkstvvkvLskelgik 72 
                                    L  r+ +++ + G  G gkst vk +   l ++
  gi|119720448|ref|YP_920943.1| 284 LTLREGEVVFLMGRNGSGKSTLVKHMNGLLKPS 316
                                    5566667999**************987766654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (510 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                       107  (0.00596798); expected 17.9 (0.001)
Passed Fwd filter:                        44  (0.00245412); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              44  [number of targets reported over threshold]
# CPU time: 0.72u 0.30s 00:00:01.02 Elapsed: 00:00:00.49
# Mc/sec: 3113.54
//
Query:       gi|119720449|ref|YP_920944.1|  [L=276]
Description: cobalt transport protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.1e-32  110.4  10.8    1.4e-31  109.9  10.8    1.3  1  CbiQ      Cobalt transport protein


Domain annotation for each model (and alignments):
>> CbiQ  Cobalt transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.9  10.8   7.6e-36   1.4e-31       3     214 ..       8     230 ..       6     234 .. 0.87

  Alignments for each domain:
  == domain 1  score: 109.9 bits;  conditional E-value: 7.6e-36
                                    CCCCS-HHHHHHHHHHHHHHHHHS-H.HHHHHHHHHHHHHHHHTTS---..HHHHHHHCCCHCHHHHHHHHHHE...... CS
                           CbiQ   3 svlhrldprvkliwlfllllalvlap.nlvtlliiiallllllllvilp..rvlaqalilpllflllgllillf....ql 75 
                                    +v+hrldpr k +wl +l++++ ++   l++l  +++++ +lll+++     + +++++   l+  + ll+l++     +
  gi|119720449|ref|YP_920944.1|   8 TVIHRLDPRAKIVWLTSLMVIALIVIdPLYLLPPLAFAVAFLLLSRVYElkEFHSKWIM-STLLGSTLLLVLFNglfaAV 86 
                                    79**************99988766550556667899***99999999888877777777.66666666666666677655 PP

                                    .....EECTTEEE......E-TTHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHHHHCCCSS--HHHHHHHHHHHHHHHH CS
                           CbiQ  76 ittegefvfaggg...qisitseGllrglllalRiltllslllllalTTppeeltsslerlgvPlelalillLayRfifl 152
                                      ++g+++f +     ++ +t eG   g+  alR l++++  l +a+TT p +l++sle++g P el+++++L++Rfi++
  gi|119720449|ref|YP_920944.1|  87 EVKKGTVLFYISFlglKYPVTVEGFYLGVGAALRLLVIMLSFLTVAFTTYPRDLANSLEKVGLPYELTFTVALTFRFIPF 166
                                    66677777766656699*******************99999999************************************ PP

                                    HHHHHHHHHHHHHHTTTTS....SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS-SS... CS
                           CbiQ 153 LleevqrikqAqklRlgds..klgirrslrslgkliaalflralkraervalAmeaRGYtgsee 214
                                    L ee++ri +A k+R+ +   + g+ ++lr++ +l+  l++ +l   +rv   +eaR++  s++
  gi|119720449|ref|YP_920944.1| 167 LEEEARRIADALKSRGYRGfeEGGFLERLRAYSTLFTVLIVNSLSLVRRVGMVLEARCFGASPR 230
                                    ******************99***************************************88554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1858.92
//
Query:       gi|119720450|ref|YP_920945.1|  [L=324]
Description: hypothetical protein Tpen_1546 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
        0.1   12.1   0.0       0.29   10.7   0.0    1.8  2  Pribosyltran  Phosphoribosyl transferase domain
       0.13   11.7   0.0       0.31   10.5   0.0    1.7  2  UPRTase       Uracil phosphoribosyltransferase


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   3.2e-05      0.29      80     117 ..     137     177 ..      93     216 .. 0.76
   2 ?   -2.9   0.0      0.48   4.3e+03     120     143 ..     259     282 ..     258     285 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 3.2e-05
                                    EE----TTSEEEEE-SEESSSHHHHHHHHHHHCC-BS...E CS
                   Pribosyltran  80 rlledpagkkVliVDDildtGgTllaalelLkekgpe...e 117
                                    ++ e + ++ ++iV D ++tG Tl   l +Lk +  e   +
  gi|119720450|ref|YP_920945.1| 137 ENFEALPDRAIVIVGDTIATGATLSGSLLRLKQAALEkgyR 177
                                    47888899*****************9999999887775552 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.48
                                    EEEEEE-HHHHHHHHHH-TTS... CS
                   Pribosyltran 120 iavlvdkpateeevdknakrvfsl 143
                                    ++ ++d ++++++++k+ +++++l
  gi|119720450|ref|YP_920945.1| 259 LCSIFDWGDRTKNPEKHLRELVEL 282
                                    678889999999999999998865 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.24   2.2e+03      95     131 ..       8      45 ..       3      49 .. 0.80
   2 ?   10.5   0.0   3.4e-05      0.31     112     171 ..     136     198 ..      53     214 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.24
                        UPRTase  95 ghlglqreeetlepveyynkLPkki.aertvlllDpvi 131
                                    g++ l r ++  e v  y  + +++ ++++++++D v+
  gi|119720450|ref|YP_920945.1|   8 GKARLVRVDTPVEGVVLYRVVREDLpRNQYIMVCDEVL 45 
                                    56677777788888899999999998888899999886 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 3.4e-05
                        UPRTase 112 ynkLPkkiaertvlllDpviaTGgsaaaaiqlLker....gvgeekIlvlsvlaseegvkrlae 171
                                    y+++ + + +r ++++  +iaTG+++   + +Lk++    g +++k+ vl++  + eg +rl +
  gi|119720450|ref|YP_920945.1| 136 YENFEA-LPDRAIVIVGDTIATGATLSGSLLRLKQAalekGYRVDKVAVLTISGAVEGSRRLRK 198
                                    555554.467788888889*******99999997654444999**********99999987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2450.33
//
Query:       gi|119720451|ref|YP_920946.1|  [L=353]
Description: ABC transporter related [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-33  115.1   0.0      5e-33  114.5   0.0    1.3  1  ABC_tran         ABC transporter
    1.2e-11   45.3   0.2    6.4e-11   42.9   0.1    2.4  1  OB_MalK          MalK OB fold domain
    1.3e-07   32.0   1.2    4.6e-07   30.3   0.6    2.3  2  CysA_C_terminal  CysA C-terminal regulatory domain
      3e-07   30.5   0.0     0.0096   15.8   0.0    2.2  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    5.9e-06   26.4   0.7    1.6e-05   25.0   0.1    2.1  2  TOBE_2           TOBE domain
    0.00046   20.6   0.0      0.062   13.7   0.0    2.3  2  AAA              ATPase family associated with various cellul
    0.00092   19.2   0.0     0.0016   18.4   0.0    1.3  1  Rad17            Rad17 P-loop domain
     0.0058   17.0   0.1      0.011   16.1   0.1    1.6  1  AAA_16           AAA ATPase domain
  ------ inclusion threshold ------
      0.012   15.1   0.0        0.5    9.8   0.0    2.3  2  SMC_N            RecF/RecN/SMC N terminal domain
      0.013   15.8   0.4      0.038   14.3   0.4    1.9  1  AAA_22           AAA domain
      0.038   14.2   0.2        0.1   12.8   0.0    1.8  2  AAA_28           AAA domain
      0.044   14.1   0.0        1.2    9.5   0.0    2.9  2  TOBE             TOBE domain
      0.054   13.2   0.1       0.14   11.8   0.0    1.6  2  AAA_30           AAA domain
      0.057   13.3   0.1       0.19   11.7   0.0    1.8  2  RsgA_GTPase      RsgA GTPase
      0.065   13.4   0.4        8.2    6.6   0.0    3.3  3  Fn3-like         Fibronectin type III-like domain
      0.086   12.7   0.0       0.14   12.0   0.0    1.3  1  ATPase_2         ATPase domain predominantly from Archaea
      0.094   13.2   0.0       0.16   12.4   0.0    1.3  1  AAA_23           AAA domain
       0.14   11.9   0.0       0.26   11.0   0.0    1.4  1  AAA_29           P-loop containing region of AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.5   0.0   5.1e-36     5e-33       2     136 ..      20     161 ..      19     162 .. 0.97

  Alignments for each domain:
  == domain 1  score: 114.5 bits;  conditional E-value: 5.1e-36
                                    EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                       ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                    ++vsl++kege  +++G++G+GK+t l+++agl++p+eG++ + ++d+++  l+  +++i++++q   ++p+++v++n  
  gi|119720451|ref|YP_920946.1|  20 DDVSLEVKEGEFFVLLGPSGCGKTTTLRIIAGLEEPDEGRVFFGEEDVTR--LPPGKRKISMVFQSYAVWPHMKVYDNia 97 
                                    89************************************************..**************************** PP

                                    ...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                               e ++++ +a++ +++++l d+      ++LSgGq+qrva+aral+  p++ll+DEp 
  gi|119720451|ref|YP_920946.1|  98 lplkvqgyppeEIERRVREAARLVQIEDLLDRYP----QQLSGGQRQRVAVARALAVTPRVLLMDEPL 161
                                    *******999999999999999999999888888....*****************************7 PP

>> OB_MalK  MalK OB fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   0.1   6.4e-14   6.4e-11       1      52 [.     235     281 ..     235     282 .. 0.97

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 6.4e-14
                        OB_MalK   1 GSPaMNflpatveedgvlvegggvtlplpeeqklalklyagkevilGiRPEh 52 
                                    GSP+ N++++tv+  g  v+ g v lp+ ++    l++y gk+vi+GiRPE+
  gi|119720451|ref|YP_920946.1| 235 GSPPINLFEGTVTPRG--VDVGFVVLPVGAGS---LEEYSGKRVIVGIRPED 281
                                    9************999..**********9998...****************9 PP

>> CysA_C_terminal  CysA C-terminal regulatory domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       4.2   4.2e+03       8      22 ..      56      71 ..      56      76 .. 0.79
   2 !   30.3   0.6   4.6e-10   4.6e-07       1      43 []     240     284 ..     240     284 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 4.2
                CysA_C_terminal  8 edGklriGglalp.vP 22
                                   ++G++ +G+ ++  +P
  gi|119720451|ref|YP_920946.1| 56 DEGRVFFGEEDVTrLP 71
                                   5899*9**98887677 PP

  == domain 2  score: 30.3 bits;  conditional E-value: 4.6e-10
                CysA_C_terminal   1 NlFhGrve.dGklriGglalpvP..elagadgqevvayVRPhDlei 43 
                                    NlF+G+v   G + +G + lpv    l+++ g++v++++RP+D+++
  gi|119720451|ref|YP_920946.1| 240 NLFEGTVTpRG-VDVGFVVLPVGagSLEEYSGKRVIVGIRPEDVHL 284
                                    9******9566.***********8999999**************97 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   9.6e-06    0.0096       1      44 [.      31      66 ..      31      86 .. 0.73
   2 !   12.8   0.0   7.8e-05     0.077     213     299 ..     111     194 ..      80     197 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 9.6e-06
                         AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirk 44
                                   + vl Gp g+GK++ L+++ +l         + de + ++g+ +
  gi|119720451|ref|YP_920946.1| 31 FFVLLGPSGCGKTTTLRIIAGL--------EEPDEGRVFFGEED 66
                                   68*****************999........34444444444444 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 7.8e-05
                         AAA_21 213 derlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQ 291
                                     +r re   +++  +d  ++ + +lS G+++  a++ al+ ++   ++ll DEp ++L+  l       lk+l+r ++  
  gi|119720451|ref|YP_920946.1| 111 ERRVRE-AARLVQIEDLLDRYPQQLSGGQRQRVAVARALAVTP---RVLLMDEPLSNLDALLRVQARAELKRLQRdTRLT 186
                                    333333.7888889999999************9*******999...**************77755555566666656688 PP

                         AAA_21 292 viltTHSp 299
                                     i +TH+ 
  gi|119720451|ref|YP_920946.1| 187 TIYVTHDQ 194
                                    89999985 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       7.4   7.4e+03      38      52 ..     133     147 ..     129     152 .. 0.71
   2 !   25.0   0.1   1.6e-08   1.6e-05       1      76 []     275     343 ..     275     343 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 7.4
                         TOBE_2  38 elaggqlvvvrqpna 52 
                                    +l ggq+++v+++ a
  gi|119720451|ref|YP_920946.1| 133 QLSGGQRQRVAVARA 147
                                    677888888877665 PP

  == domain 2  score: 25.0 bits;  conditional E-value: 1.6e-08
                         TOBE_2   1 laiRPEklrlaaaggan.glsGtVedveylGsstryvvelaggqlvvvrqpnadrdsalapGdtVelswdpddavvl 76 
                                    ++iRPE+++l +a+++   ++G V  +e lG +++++v++++  l ++r    +      + ++V + +dp +++++
  gi|119720451|ref|YP_920946.1| 275 VGIRPEDVHL-TASPGFiEVEGSVWVTENLGGEYVVLVSVGDVIL-RARSREKP------ESERVKVYLDPSKLHFF 343
                                    79********.333344799*********************9876.44444444......56999999999999987 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   6.3e-05     0.062       2      20 ..      33      51 ..      32      86 .. 0.89
   2 ?    4.8   0.0     0.035        35      30      72 ..     122     169 ..     104     206 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.3e-05
                                   EEESSTTSSHHHHHHHHHH CS
                            AAA  2 llyGppGtGKTllakavak 20
                                   +l Gp G+GKT++ + +a 
  gi|119720451|ref|YP_920946.1| 33 VLLGPSGCGKTTTLRIIAG 51
                                   689*************996 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.035
                                    ETTTCSSSSTTHHHHHHHHHHHHHHHTS.TSEEEEEET....GGGHHH CS
                            AAA  30 sgsellskyvgesekkirelfkeakeka.kpsilfiDE....idalak 72 
                                    +  +ll+ y ++ +   r+ ++ a++ a +p +l++DE    +dal +
  gi|119720451|ref|YP_920946.1| 122 QIEDLLDRYPQQLSGGQRQRVAVARALAvTPRVLLMDEplsnLDALLR 169
                                    56788888999999999********************95444555555 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.6e-06    0.0016      36      66 ..      20      50 ..      10      58 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.6e-06
                          Rad17 36 kadvLesrkkriLLisGPsGCgkstvvkvLs 66
                                   +  +Le ++ +  ++ GPsGCgk+t++++++
  gi|119720451|ref|YP_920946.1| 20 DDVSLEVKEGEFFVLLGPSGCGKTTTLRIIA 50
                                   56689999999999**************987 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   1.1e-05     0.011      24      63 ..      29      68 ..      18     196 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.1e-05
                         AAA_16 24 pelvllsGesGvGKsslvrellralekdggiflrgkcdql 63
                                   +e  +l G+sG+GK++ +r ++   e d+g ++ g+ d  
  gi|119720451|ref|YP_920946.1| 29 GEFFVLLGPSGCGKTTTLRIIAGLEEPDEGRVFFGEEDVT 68
                                   37899**************999655555688777777765 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.065        65      24      40 ..      29      45 ..      13      50 .. 0.78
   2 ?    9.8   0.0    0.0005       0.5     133     207 ..     130     200 ..      83     212 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.065
                                   SSEEEEEESTTSSHHHH CS
                                   xxxxxxxxxxxxxxxxx RF
                          SMC_N 24 ksftaivGpNGSGKsnl 40
                                    +f +++Gp G+GK+  
  gi|119720451|ref|YP_920946.1| 29 GEFFVLLGPSGCGKTTT 45
                                   468899********976 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0005
                                    STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SC CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 133 skelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadk 207
                                    ++++LSgG+++ va+a  +A+    p+ + l+De  ++LD+  + +    lk+ + ++ +  i ++++++e +  
  gi|119720451|ref|YP_920946.1| 130 YPQQLSGGQRQRVAVARALAVT---PR-VLLMDEPLSNLDALLRVQARAELKRLQRDTRLTTIYVTHDQVEAMVL 200
                                    5679*************99975...44.5699********98887777778887778777777777777776643 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.4   3.8e-05     0.038       4      29 ..      28      53 ..      24     199 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.8e-05
                         AAA_22  4 tagilvvtGesGtGKTtllrrlleql 29
                                   +  + v+ G+sG+GKTt+lr ++   
  gi|119720451|ref|YP_920946.1| 28 EGEFFVLLGPSGCGKTTTLRIIAGLE 53
                                   567899*************9887765 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0    0.0001       0.1       2      21 ..      32      53 ..      31      70 .. 0.75
   2 ?   -2.1   0.1         4   3.9e+03      72      91 ..     151     170 ..     112     204 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.0001
                         AAA_28  2 ivitGgestGKTtlleaLa..a 21
                                   +v++G++++GKTt+l+ +a  +
  gi|119720451|ref|YP_920946.1| 32 FVLLGPSGCGKTTTLRIIAglE 53
                                   79*************9988442 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4
                         AAA_28  72 ankvlfcDrglldtlaYara 91 
                                    +++vl++D  l +  a +r+
  gi|119720451|ref|YP_920946.1| 151 TPRVLLMDEPLSNLDALLRV 170
                                    34444444433333333333 PP

>> TOBE  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.52   5.2e+02      50      64 .]     270     284 ..     261     284 .. 0.91
   2 ?    9.5   0.0    0.0012       1.2       7      63 ..     293     341 ..     292     342 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.52
                           TOBE  50 GeeVfalikaakvhl 64 
                                    G++V + i +++vhl
  gi|119720451|ref|YP_920946.1| 270 GKRVIVGIRPEDVHL 284
                                    99************7 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0012
                           TOBE   7 lpgtVvvveplgseveVrvdlgggatLtArvtrrsaeeLgLapGeeVfalikaakvh 63 
                                    ++g V v e lg+e++V v +g+   L Ar  r+  e+      e+V + ++++k+h
  gi|119720451|ref|YP_920946.1| 293 VEGSVWVTENLGGEYVVLVSVGDVI-LRARS-REKPES------ERVKVYLDPSKLH 341
                                    57999999*****************.****9.888888......8888888888888 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00014      0.14      18      49 ..      29      60 ..      22      65 .. 0.82
   2 ?   -2.5   0.1       3.6   3.6e+03     125     159 ..     138     172 ..     131     203 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00014
                         AAA_30 18 drvavltGpAGtGKttalkalreaweaaggrv 49
                                     + vl Gp G GKtt+l+ ++ + e ++grv
  gi|119720451|ref|YP_920946.1| 29 GEFFVLLGPSGCGKTTTLRIIAGLEEPDEGRV 60
                                   35889***************999888776665 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.6
                         AAA_30 125 erQlasVeaGgvlrdlveaagigtaeLtevvRqke 159
                                    +rQ  +V +  +++  v   + +  +L+ + R + 
  gi|119720451|ref|YP_920946.1| 138 QRQRVAVARALAVTPRVLLMDEPLSNLDALLRVQA 172
                                    55555555444443333233444445555555533 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00019      0.19      90     121 ..      19      51 ..       3      60 .. 0.79
   2 ?   -1.9   0.0       2.7   2.7e+03       7      29 ..     155     177 ..     151     211 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00019
                                    HHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                    RsgA_GTPase  90 leelkellkd.ktsvlvGqSGvGKStLinallp 121
                                    +++++ ++k+ ++ vl+G+SG GK+t +  +++
  gi|119720451|ref|YP_920946.1|  19 VDDVSLEVKEgEFFVLLGPSGCGKTTTLRIIAG 51 
                                    5566666666699*************9988876 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.7
                                    EETTTTEES--EEEEEEESTTTT CS
                    RsgA_GTPase   7 elvrpkvaNvdqllivvslkepe 29 
                                    +l++++ +N+d ll v + +e +
  gi|119720451|ref|YP_920946.1| 155 LLMDEPLSNLDALLRVQARAELK 177
                                    57778888888888887766333 PP

>> Fn3-like  Fibronectin type III-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       2.9   2.9e+03      48      70 ..      16      38 ..       8      38 .. 0.73
   2 ?    2.6   0.1      0.15   1.5e+02      48      67 ..     290     311 ..     265     314 .. 0.81
   3 ?    6.6   0.0    0.0083       8.2      33      56 ..     327     350 ..     324     352 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2.9
                                   EEETTTTEEE--SCEEEEEEESS CS
                       Fn3-like 48 vwdeekqkwvvepGeytvlvgts 70
                                   v+ ++  +  v +Ge+ vl g s
  gi|119720451|ref|YP_920946.1| 16 VVAVDDVSLEVKEGEFFVLLGPS 38
                                   55566667789999999999976 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.15
                                    EEETTTTEEE--..SCEEEEEE CS
                       Fn3-like  48 vwdeekqkwvve..pGeytvlv 67 
                                    + ++e + wv+e   Gey vlv
  gi|119720451|ref|YP_920946.1| 290 FIEVEGSVWVTEnlGGEYVVLV 311
                                    56779999****555*****98 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.0083
                                    -EEEEEEEEECGGG-EEETTTTEE CS
                       Fn3-like  33 esktvtftldrkdlsvwdeekqkw 56 
                                    es++v++ ld++ l ++d e++++
  gi|119720451|ref|YP_920946.1| 327 ESERVKVYLDPSKLHFFDKETEAR 350
                                    9******************98765 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00014      0.14      16      53 ..      25      61 ..      21      70 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00014
                       ATPase_2 16 erepneiyfiYGpegsGKtaLlkeiienledkdkyviy 53
                                   e ++ e+ ++ Gp g+GKt+ l+ i+    + d+ +++
  gi|119720451|ref|YP_920946.1| 25 EVKEGEFFVLLGPSGCGKTTTLRIIAGLE-EPDEGRVF 61
                                   556678999***********998665544.55555555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00016      0.16      19      39 ..      29      49 ..      13      51 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00016
                         AAA_23 19 kgltlItGpNGaGKTTildAi 39
                                     ++++ Gp G+GKTT l+ i
  gi|119720451|ref|YP_920946.1| 29 GEFFVLLGPSGCGKTTTLRII 49
                                   4689************99877 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00026      0.26      13      39 ..      20      46 ..      17      57 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00026
                         AAA_29 13 dghtieidlkgatlltGpsGsGKSTll 39
                                   d+ ++e+++ ++++l GpsG GK+T l
  gi|119720451|ref|YP_920946.1| 20 DDVSLEVKEGEFFVLLGPSGCGKTTTL 46
                                   556788886669************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2401.34
//
Query:       gi|119720452|ref|YP_920947.1|  [L=270]
Description: binding-protein-dependent transport systems inner membrane component [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.6e-15   55.8  15.6    4.6e-15   55.8  15.6    2.1  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
       0.17   11.4   3.9        2.6    7.6   0.2    2.5  2  DUF4791       Domain of unknown function (DUF4791)


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   1.4     0.079   7.1e+02     106     171 ..       6      80 ..       3      81 .. 0.64
   2 !   55.8  15.6   5.2e-19   4.6e-15       1     179 [.      82     260 ..      82     261 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.079
                   BPD_transp_1 106 alppiitglilafggllggavlleflgswpGlgtllleailgydyseis.........nggvlalviavlllnlv 171
                                    ++   i g++l++ +l+  a  ++  +++p   ++ + ++ +   + +          ++ ++ +++++++++++
  gi|119720452|ref|YP_920947.1|   6 SILLSIVGALLSAWILVPLAYTMLAAFADPEDYYRHVIPTKYTLENVNVflelgaldaMARSVLVAFLTIAISFA 80 
                                    555556666666666666666666666677777777777777777766677877777777777777777777665 PP

  == domain 2  score: 55.8 bits;  conditional E-value: 5.2e-19
                   BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalrslp 80 
                                    g+++G+ ++ +  +++++  r  +  ++++P++v+ai+l   ++i  +l+++ l+v+++ +  a+p+v+li+++++ s+p
  gi|119720452|ref|YP_920947.1|  82 GVPAGYAVG-RWVFRGKDSYRLAVLSMRMFPVMVMAIPLAS-LYIRLGLYDSLLGVALVHAALALPFVVLITSSIFVSIP 159
                                    799999999.99999***********************884.48999********************************* PP

                   BPD_transp_1  81 kdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis...... 154
                                    +dl+ea ++ G+sr q+f k++ P+alp + + ++++f+ ++++ ++  +l+    l  ++l a+    + + +      
  gi|119720452|ref|YP_920947.1| 160 RDLEEAGLVFGLSRVQVFTKITAPLALPGLSAAAMFTFVTSWNEVFASTILT----LKERTLPALTVATTILSTgaaapd 235
                                    ********************************************99999999....555544444444444333556778 PP

                   BPD_transp_1 155 nggvlalviavlllnlvadilqrll 179
                                       ++a++++ l+  +v+  + ++l
  gi|119720452|ref|YP_920947.1| 236 PYRFAAATLLALPAFIVMLYMRKYL 260
                                    7888888888888888888777776 PP

>> DUF4791  Domain of unknown function (DUF4791)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.2   0.00029       2.6      65     132 ..      14      81 ..      11     116 .. 0.92
   2 ?    4.9   1.7    0.0019        17      22      86 ..      89     157 ..      70     232 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00029
                        DUF4791  65 alghglfvvpLlldlllslvkdedeetetlkdltllGNivSllylavkesnllylgmallalvakyga 132
                                    al  +  +vpL++ +l+ +++ ed    ++ +   l N+   l l++ +     + +a+l++++++++
  gi|119720452|ref|YP_920947.1|  14 ALLSAWILVPLAYTMLAAFADPEDYYRHVIPTKYTLENVNVFLELGALDAMARSVLVAFLTIAISFAV 81 
                                    667778899***************99***********************************9999976 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0019
                        DUF4791  22 lvralsedeeckkarevtssilevvpLplvNielYlkseg....salalghglfvvpLlldlllslvkd 86 
                                    + r ++  ++  +++ ++  +  v+ +++    lY +        ++al+h+   +p ++ +  s++ +
  gi|119720452|ref|YP_920947.1|  89 VGRWVFRGKDSYRLAVLSMRMFPVMVMAIPLASLYIRLGLydslLGVALVHAALALPFVVLITSSIFVS 157
                                    5555556666667777777776666555555555554322222489**********9999998888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.34s 00:00:00.92 Elapsed: 00:00:00.55
# Mc/sec: 1489.95
//
Query:       gi|119720453|ref|YP_920948.1|  [L=284]
Description: binding-protein-dependent transport systems inner membrane component [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-10   40.8  21.5    1.9e-10   40.8  21.5    2.3  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   4.1       0.1   1.8e+03      28      73 ..      10      56 ..       3      80 .. 0.67
   2 !   40.8  21.5   1.1e-14   1.9e-10       5     171 ..      81     274 ..      77     280 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.1
                   BPD_transp_1 28 lslPsfvlaillvlvfvilsilghlilp.viillllsaapyvrlirr 73
                                    ++P++++++ ++++++++++     l+ +++    +++p+vr++++
  gi|119720453|ref|YP_920948.1| 10 KAMPYLLILPSMLYMLAFIGYPLVQSLSwALLPDSHGSIPIVRILTS 56
                                   58999999999999995555555444443555555555555555554 PP

  == domain 2  score: 40.8 bits;  conditional E-value: 1.1e-14
                   BPD_transp_1   5 Gilaa..lnrnkkldkllrpliivllslPsfvlaillvlvf.....................vilsilghlilp.viill 60 
                                    ++la   l ++++++++++ ++ v+l+l  +  a++++ ++                     ++  ++ ++ +  ++++ 
  gi|119720453|ref|YP_920948.1|  81 ALLASlvLVQRFPGREVSLYFFTVPLALSDVSAALIWYTMLssrgflnkllmeaglisspiqFFGYAFRNMEFLaIVLTE 160
                                    555557677889999999999999**999999999999999*****************9998777777777766588888 PP

                   BPD_transp_1  61 llsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtl 140
                                    ++ a+++v+++++a++++++++l eaa + G+s  q +r+v+lP+++p+i + li++  ++l  ++ +++l+   G+  +
  gi|119720453|ref|YP_920948.1| 161 VWRATAIVFINIYAGFQTINRELLEAADVFGLSSLQKLRYVTLPLLKPSIQSALIIRTLFALQTFAPVLILA---GFDIP 237
                                    ************************************************************************...9**** PP

                   BPD_transp_1 141 lleailgydyseis......nggvlalviavlllnlv 171
                                    +l ++  y+y++ +      ++++l++++ ++l  + 
  gi|119720453|ref|YP_920948.1| 238 VLATEAFYQYTLVMdvptaaAWSLLIGAVTFALGAFY 274
                                    ***********99998877655555555555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      180  (0.0100396); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1859.42
//
Query:       gi|119720454|ref|YP_920949.1|  [L=428]
Description: extracellular solute-binding protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    8.3e-32  111.1   1.8    1.1e-31  110.7   1.8    1.1  1  SBP_bac_8   Bacterial extracellular solute-binding protein
    1.1e-30  107.7   6.9    1.5e-30  107.2   6.9    1.2  1  SBP_bac_1   Bacterial extracellular solute-binding protein
    2.5e-05   23.8   0.8    0.00019   20.9   0.2    2.4  2  SBP_bac_6   Bacterial extracellular solute-binding protein
     0.0013   18.6   0.0     0.0041   16.9   0.0    1.9  1  SBP_bac_11  Bacterial extracellular solute-binding protein
  ------ inclusion threshold ------
       0.11   12.4   0.1       0.26   11.1   0.1    1.7  1  DUF4307     Domain of unknown function (DUF4307)
       0.13   12.5   0.3       0.69   10.3   0.1    2.2  2  Wzz         Chain length determinant protein


Domain annotation for each model (and alignments):
>> SBP_bac_8  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.7   1.8   3.6e-35   1.1e-31       3     270 ..      55     350 ..      53     361 .. 0.82

  Alignments for each domain:
  == domain 1  score: 110.7 bits;  conditional E-value: 3.6e-35
                                    HHHHHHH-TEEEEEEE--SSSHHHHHHHHHHTT---SEE.EEE-HHHHHHHHHTTSB--GG...GSTTHHH-HH...HHH CS
                      SBP_bac_8   3 akefekktgvkvnvvtaasndleqklkaalaagtapdidvvwanedalatlaeeglladls...dldnlddltd...ala 76 
                                     ++f  +tg+kv +v+ ++ d+++k+ a++++g++ + +++ + ++ ++ +a +gl++dls   +l+  + +++   a++
  gi|119720454|ref|YP_920949.1|  55 LSRFGNETGIKVDFVPLGYTDMVAKVEAEVNSGKVST-NIIGGLSSEVDYFASKGLVEDLSkfgSLPGRTFYPAleqASK 133
                                    578999*****************************76.8899999****************6655566666544221444 PP

                                    TT--TS.----EEEEEEE-EEEEEHHHHHH......S.......---BHHHHHHHHHHH.....HHH-SEGG---G.GGG CS
                      SBP_bac_8  77 avgydgklygvPyasetpyvliynkdllek......a......edpktwdellaaakkl.....kgkfglpdpasg.wlq 138
                                     +g++   + vP+++ t  v+++n ++++       +       d +t+d+lla+ak +     k+++glp+ + g  ++
  gi|119720454|ref|YP_920949.1| 134 MYGIK---AMVPWMTAT-FVIVVNNKAFDYlppgltKddvikgTDKWTYDALLAWAKNIyektgKQAVGLPAGGGGlLHR 209
                                    44554...599**9998.9*********654444431356667899********88877777555555777777777778 PP

                                    GGTHHETTEE---H......HHH.HHHHHHHHHHHHTT-EE.-S..--SSTTTTTSBSEEEE-TTHHHHHH-TTT.SEEE CS
                      SBP_bac_8 139 aallakdgksldddg....gkdglkealellkklkdngkty.dtgadavsefanGevaftingswdiaaaqkagk.klga 212
                                    +++ + ++ s++++     ++++ +e +++l++l ++      t++++ + + +G+v+++    +++ aa   ++ ++++
  gi|119720454|ref|YP_920949.1| 210 FLHGY-LYPSYTGYQakafNSPEAVELWKYLRELWKYTNPAsTTYDAMADPLLKGDVWIAWDHVARVKAAITTSPdQFTV 288
                                    88888.99999888788888999999999999999999855156688888*********************998637888 PP

                                    E.--....S--EEEEEEEEEEBTTS-HHHHHHHHHHHHHTTSHHHHHHHHHH---BS-S-TTT CS
                      SBP_bac_8 213 i.vp....kqgsfaggkglavpknaknedlaAldFlkwltspenqaalaektgyipvnksaal 270
                                      vp      g+++  +gla+pk+a+++d  A++++++lt pe qa+ ae+ g++p+ k+a+ 
  gi|119720454|ref|YP_920949.1| 289 CpVPrgpkGRGYIVVLAGLAIPKGAPDQDS-AWKLVEFLTRPEVQAKVAENVGFFPTVKEASP 350
                                    86676643348******************8.*****************************984 PP

>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.2   6.9     5e-34   1.5e-30       6     315 .]      47     333 ..      43     333 .. 0.83

  Alignments for each domain:
  == domain 1  score: 107.2 bits;  conditional E-value: 5e-34
                                    HHHHHHHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHHHHTTSSSCSEEEECGGHHHHHHHTTSBECCHHHHHHTTECT CS
                      SBP_bac_1   6 egaalqalvakafekehpgikVeiesvgsgslaqkltlaiaaGdgpaDviavdndwiarlakaglllpldpyvkaylapg 85 
                                    e a ++ l+  +f   ++gikV +++ g+ ++  k+ + + +G+    +i + ++ ++ +a++gl+++l+++      + 
  gi|119720454|ref|YP_920949.1|  47 EQAFMRSLL-SRFGN-ETGIKVDFVPLGYTDMVAKVEAEVNSGKVSTNIIGGLSSEVDYFASKGLVEDLSKFGSLPGRTF 124
                                    334666666.99978.7***************************77577777************************9999 PP

                                    TCCTEEEEHHHHTHHHHCEEEES.EEEEE.EEEEEEETTTHH..CTTGGG........SHBHHHHHHHHHHHHHHCTCTH CS
                      SBP_bac_1  86 vkdaadklsssvlpkildskvly.vPlya.argliYNkdlfe..kagldp........pwtWdelveaakklkekgkkpi 153
                                    ++  +        ++i+       vP+++ + ++++N + f+  ++gl+         +wt+d l+++ak++ ek++k  
  gi|119720454|ref|YP_920949.1| 125 YPALEQAS---KMYGIK-----AmVPWMTaTFVIVVNNKAFDylPPGLTKddvikgtdKWTYDALLAWAKNIYEKTGKQA 196
                                    88776663...334444.....45****77*************************************************5 PP

                                    CCHCCEEHHHHHHHHHHHHHHHHTGGGEECCCTHHCSHHHHSHHHHHHHHHHHHHHHHHHHTTEEECSSHHHHHHHHHTT CS
                      SBP_bac_1 154 ggarggsasgtayyfalalakslggkvfdkdgggldnpegvtaatylvklyavanltkelkgkgaenkdgaaalalfeaG 233
                                    +g+  g ++     +  +l+ s+ g+ ++             a++  ++ +++++l + +k  ++++++ +a+++ + +G
  gi|119720454|ref|YP_920949.1| 197 VGLPAGGGGLLHRFLHGYLYPSYTGYQAK-------------AFNSPEAVELWKYLRELWKYTNPASTTYDAMADPLLKG 263
                                    55555555555555555555555544333.............55556666666688899********************* PP

                                    SCSEEEEEHHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEEEEEEEEEEBTTCSTHHHHHHHHHHHTSHHH CS
                      SBP_bac_1 234 eaamaivglwaalaamkvapkvafaadkekpkeelgvaplPagkggkpgilgayglaipkgsknpeaAkkFldfllspea 313
                                    ++ +a++                 +a+    ++ + v+p+P g++g + i++  glaipkg+++++ A+k+++fl+ pe 
  gi|119720454|ref|YP_920949.1| 264 DVWIAWDHVAR------------VKAAITTSPDQFTVCPVPRGPKGRGYIVVLAGLAIPKGAPDQDSAWKLVEFLTRPEV 331
                                    **999998666............677777777889********************************************9 PP

                                    HH CS
                      SBP_bac_1 314 qa 315
                                    qa
  gi|119720454|ref|YP_920949.1| 332 QA 333
                                    96 PP

>> SBP_bac_6  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.24     7e+02     197     220 ..     101     124 ..      97     150 .. 0.71
   2 !   20.9   0.2   6.4e-08   0.00019     117     220 ..     236     348 ..     212     361 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.24
                      SBP_bac_6 197 idfllspevqailakaggvfPvv.t 220
                                    +d++ s+ + ++l+k+g+ +P    
  gi|119720454|ref|YP_920949.1| 101 VDYFASKGLVEDLSKFGS-LPGRtF 124
                                    79**************98.776541 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 6.4e-08
                      SBP_bac_6 117 kkllrnlkanlhpaq..mvkaagslesgepavsvvpyffadilpekkkgk...nlkvvw.....Ped.Galvspifmlvk 185
                                    +k+lr+l +  +pa    + +a++l +g+  v+++++  a++ ++           v       P+  G +v+   ++++
  gi|119720454|ref|YP_920949.1| 236 WKYLRELWKYTNPASttYDAMADPLLKGD--VWIAWDHVARVKAAITTSPdqfT--V-CpvprgPKGrGYIVVLAGLAIP 310
                                    44444444444444476777777888888..88888888877776653333221..2.123344677799********** PP

                      SBP_bac_6 186 kg.kkkelakafidfllspevqailakaggvfPvv..t 220
                                    kg + ++ a+++++fl+ pevqa +a++ g fP+v  +
  gi|119720454|ref|YP_920949.1| 311 KGaPDQDSAWKLVEFLTRPEVQAKVAENVGFFPTVkeA 348
                                    *****************************99**96433 PP

>> SBP_bac_11  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.4e-06    0.0041      11     226 ..      49     337 ..      40     341 .. 0.54

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.4e-06
                                    HHHHHHHHHHHHHH---EEEEESSHHHHHHHH....HHH..-SEEEESSH.HHHHHHHHGGGGG................ CS
                     SBP_bac_11  11 aalrelaaaFeahtgvkvevsaggsgklarqi....adgarpDvwipassawlellaaaglvqa................ 70 
                                    a +r l  +F ++tg+kv++   g  ++++++     +g+  + +i + s  ++  a++glv                  
  gi|119720454|ref|YP_920949.1|  49 AFMRSLLSRFGNETGIKVDFVPLGYTDMVAKVeaevNSGKVSTNIIGGLSSEVDYFASKGLVEDlskfgslpgrtfypal 128
                                    56777788888888844444444443333333222233333333333334444444444444444444444448888888 PP

                                    .........GG-EEEEEEEEEEEESTT-.....T.............T---SHHHHHHS..................... CS
                     SBP_bac_11  71 .........esavplassplviavpkgn.....p.............kkikgwadLlkp..................... 102
                                             ++ vp  +++ vi+v+  +     p                 + ++Ll+                      
  gi|119720454|ref|YP_920949.1| 129 eqaskmygiKAMVPWMTATFVIVVNNKAfdylpPgltkddvikgtdkW---TYDALLAWakniyektgkqavglpagggg 205
                                    855555555555566666666666666566664133333333221110...12223321233333333333333333332 PP

                                    ...S--EEEE--T-TTTTHH.HHHHGGG--HHHHHHHHHTEEEEESSHHHHHHHHHT..TT-SEEEEEHHHH..H....H CS
                     SBP_bac_11 103 ...glklavadPttspsGlaalalleaagaqellkalekkvvklgessrqlltavea..geadagivyesea..kaa..e 173
                                        +  ++  P+  ++   a++  ea    el+k l++    +++ ++++++a+++   + d++i++ + a  kaa  +
  gi|119720454|ref|YP_920949.1| 206 llhRFLHGYLYPSYTGYQAKAFNSPEA---VELWKYLRELWK-YTNPASTTYDAMADplLKGDVWIAWDHVArvKAAitT 281
                                    222222333333333333333333334...559999998776.8888899999977733479999999998866333548 PP

                                    STTSSEEEE--TTT--......EEEEEEEE-TT--HHHHHHHHHTTSHHHHHHHHH CS
                     SBP_bac_11 174 ngdkleavylpeglnl.dpl..dypaavlkkaakreaAraFlafLrspeaqailrk 226
                                     +d +++ ++p g     ++    ++a++k+a+++  A ++++fL+ pe+qa +++
  gi|119720454|ref|YP_920949.1| 282 SPDQFTVCPVPRGPKGrGYIvvLAGLAIPKGAPDQDSAWKLVEFLTRPEVQAKVAE 337
                                    999999999999886655551156778889*********************98765 PP

>> DUF4307  Domain of unknown function (DUF4307)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   8.9e-05      0.26       3      41 ..       4      42 ..       2      50 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 8.9e-05
                        DUF4307  3 rllvillvvlvvvalalvawigysqgsadvsaevvgfev 41
                                   + +++++vv++vv++al+a+++y+ + ++v+ + v+ + 
  gi|119720454|ref|YP_920949.1|  4 KKVLVAAVVALVVLVALAAYVLYRPKPKSVTLTFVSTQL 42
                                   7789999*****************999999888777665 PP

>> Wzz  Chain length determinant protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00023      0.69      15      53 ..       4      42 ..       2      64 .. 0.88
   2 ?   -1.3   0.0      0.95   2.8e+03      39      67 ..     142     171 ..     134     187 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00023
                                   XXXXXXXXXXXXXXXXXXXXXXXXX-EEEEEEEES--CH CS
                            Wzz 15 rkklIilvtllfallaviyaflatpkYtataqilvpekk 53
                                   +k+l+++v++l++l+a++  +l +pk ++ ++  v+++ 
  gi|119720454|ref|YP_920949.1|  4 KKVLVAAVVALVVLVALAAYVLYRPKPKSVTLTFVSTQL 42
                                   799****************************99998865 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.95
                                    X-EEEEEEEES--CHHHHH.HHHHCCHHHH CS
                            Wzz  39 pkYtataqilvpekkqvea.ssltaqdvqa 67 
                                    p+ tat +i v++k      ++lt+ dv +
  gi|119720454|ref|YP_920949.1| 142 PWMTATFVIVVNNKAFDYLpPGLTKDDVIK 171
                                    555777777777664323344555544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       752  (0.0419432); expected 358.6 (0.02)
Passed bias filter:                      678  (0.0378158); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.43
# Mc/sec: 2961.92
//
Query:       gi|119720455|ref|YP_920950.1|  [L=342]
Description: transcriptional regulator, TrmB [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-54  184.8   0.1    1.7e-54  184.5   0.1    1.1  1  Regulator_TrmB  Archaeal transcriptional regulator TrmB
    1.2e-13   50.7   0.1    2.1e-13   50.0   0.1    1.4  1  TrmB            Sugar-specific transcriptional regulator TrmB
    2.9e-05   23.5   0.0    6.6e-05   22.4   0.0    1.6  1  HTH_24          Winged helix-turn-helix DNA-binding
    0.00031   20.8   0.0    0.00066   19.7   0.0    1.5  1  HTH_9           RNA polymerase III subunit RPC82 helix-turn-h
    0.00031   21.2   0.0     0.0008   19.8   0.0    1.6  1  HTH_27          Winged helix DNA-binding domain
     0.0004   20.1   0.1    0.00086   19.1   0.1    1.6  1  HTH_IclR        IclR helix-turn-helix domain
     0.0012   18.7   0.1     0.0022   17.8   0.1    1.4  1  HTH_5           Bacterial regulatory protein, arsR family
     0.0029   17.6   0.0     0.0059   16.6   0.0    1.5  1  HTH_20          Helix-turn-helix domain
     0.0077   16.1   0.0      0.018   14.9   0.0    1.6  1  MarR_2          MarR family
  ------ inclusion threshold ------
      0.024   15.0   0.0      0.046   14.1   0.0    1.4  1  Rrf2            Transcriptional regulator


Domain annotation for each model (and alignments):
>> Regulator_TrmB  Archaeal transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.5   0.1   9.3e-58   1.7e-54      10     231 ..     122     340 ..     113     342 .] 0.96

  Alignments for each domain:
  == domain 1  score: 184.5 bits;  conditional E-value: 9.3e-58
                                    HHHHHHHHHHHH-SSEEEEEE-GGGHHHHHHHHHHHHHTT-EEEEEESS----GGGSSSSEEEEEE-S---S.EEEEETT CS
                 Regulator_TrmB  10 tvierieelIesAenelivslpselLeelreeliaaaergvtVllliypdedleeldleevatevrvrrsgapllvivDr 89 
                                    +   r  e+I+sA++++iv+++s++++ ++eel++++e+gv+V++++y+ ++ + +++e v+ ++r++ sg+ ++v+vD+
  gi|119720455|ref|YP_920950.1| 122 AFRIRGLEYIRSAKCDVIVCGDSSFVKPYWEELRKKEEEGVNVFVILYELPGIPVREDEVVVRKARKAVSGD-MMVVVDS 200
                                    55556679****************************************************************.******* PP

                                    TEEEEE-SSS-EEEE--HHHHHHHHHHHHHH........HHH-EEEEEEES-TT-EEES-HHHHHHHHHHHT.TTS-EEE CS
                 Regulator_TrmB  90 krgvvaprevlrdkeeeyaiifkekelihvlshyFlttlWktseviktdepvekpitfssirlavedikkllraglkvea 169
                                    + ++va+r++  +++ ey++ ++e+ li++l + F+++ W +++vi+ depv++p +f+  rla+ ++++ll++g+++++
  gi|119720455|ref|YP_920950.1| 201 RVALVAQRRLGPGERPEYGLSVEEPVLIDYLEQDFFNR-WLRGSVIR-DEPVRLPSCFTVNRLALIEAQRLLSEGRRLSL 278
                                    *********99***************************.********.******************************** PP

                                    EEEEEETTT--EEEEEEEEEEEEEETTTTEEEEEEEETTEEEEEE-TT--SSSEEEEEEEEE CS
                 Regulator_TrmB 170 eveGrdtetgeevtieGrvveatlnstpgvaslvvetedgevtVGGlgAvlEDieaeeitle 231
                                    +++Gr+t +++e+ +eG v +a++++ +gva++vv+t+ g++++GG +Av+E+++a++i+l+
  gi|119720455|ref|YP_920950.1| 279 TAYGRYTGSRGEAIVEGIVRDAVVDQATGVAHFVVDTRAGSIRIGGPDAVVEEFAASRIELR 340
                                    ***********************************************************997 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.0   0.1   1.2e-16   2.1e-13       5      68 .]      14      77 ..      10      77 .. 0.94

  Alignments for each domain:
  == domain 1  score: 50.0 bits;  conditional E-value: 1.2e-16
                                   HHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE--HH CS
                           TrmB  5 GLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYravdpe 68
                                   G    Ea++Y+aLlk+gp+t +e++ +++   s+  ++L++L++ GlVe+++g+p +Yrav++e
  gi|119720455|ref|YP_920950.1| 14 GAGRPEAEIYQALLKYGPSTLRELSDKVDMVGSQLHQYLKRLVRLGLVEVSRGKPSIYRAVSVE 77
                                   55567********************************************************976 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   3.7e-08   6.6e-05       7      48 .]      21      62 ..      20      62 .. 0.96

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 3.7e-08
                         HTH_24  7 kILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                   +I+++L k +  + reL++++++  s ++++lkrL++ Gl++
  gi|119720455|ref|YP_920950.1| 21 EIYQALLKYGPSTLRELSDKVDMVGSQLHQYLKRLVRLGLVE 62
                                   5999************************************96 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   3.7e-07   0.00066      16      57 ..      20      61 ..      17      64 .. 0.95

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 3.7e-07
                                   HHHHHHHHHHSSBEHHHHHHHHSSTHHHHHHHHHHHHHTTSE CS
                          HTH_9 16 akVvetLlrkgrltlrelvkktkLsldqVkksLvvLiqhrlV 57
                                   a +++ Ll++g +tlrel+ k+++  +q ++ L  L++++lV
  gi|119720455|ref|YP_920950.1| 20 AEIYQALLKYGPSTLRELSDKVDMVGSQLHQYLKRLVRLGLV 61
                                   5799************************************99 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   4.5e-07    0.0008      15      52 ..      28      65 ..      16      75 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 4.5e-07
                         HTH_27 15 rrrrkkladlcgrlnvedshisyslkkLtekGLvertg 52
                                    +++++l++l++++++  s+ +  lk+L++ GLve ++
  gi|119720455|ref|YP_920950.1| 28 KYGPSTLRELSDKVDMVGSQLHQYLKRLVRLGLVEVSR 65
                                   5899******************************4433 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.1   4.8e-07   0.00086      18      49 ..      31      62 ..       9      65 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 4.8e-07
                                   S-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                       HTH_IclR 18 eltlselArrtglpkStvhRlLqtLvelGyve 49
                                   + tl+el+++ ++  S  h +L+ Lv+lG+ve
  gi|119720455|ref|YP_920950.1| 31 PSTLRELSDKVDMVGSQLHQYLKRLVRLGLVE 62
                                   369****************************8 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   1.2e-06    0.0022       7      46 ..      22      62 ..      20      63 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.2e-06
                                   HHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_5  7 ILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                   I ++L + g+ +  el++++++  s + ++Lk+L  +GLVe
  gi|119720455|ref|YP_920950.1| 22 IYQALLKyGPSTLRELSDKVDMVGSQLHQYLKRLVRLGLVE 62
                                   66789999********************************8 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   3.3e-06    0.0059      14      59 ..      21      66 ..      10      68 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3.3e-06
                                   HHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
                         HTH_20 14 rilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvre 59
                                   +i++aL   ++ t+ el + +d+  ++l++ L+ L++ gLvev r 
  gi|119720455|ref|YP_920950.1| 21 EIYQALLKYGPSTLRELSDKVDMVGSQLHQYLKRLVRLGLVEVSRG 66
                                   799****************************************985 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0     1e-05     0.018      14      56 ..      26      66 ..      14      68 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1e-05
                                   HHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                         MarR_2 14 LgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                   L   ++   t +el ++ ++  s +++ lkrLv+ GLve ++g
  gi|119720455|ref|YP_920950.1| 26 LLKYGP--STLRELSDKVDMVGSQLHQYLKRLVRLGLVEVSRG 66
                                   455555..699****************************9987 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.6e-05     0.046      24      61 ..      30      67 ..      22      76 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.6e-05
                                   C-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT CS
                           Rrf2 24 epvsseeiaerqnispsylekilakLrkaglvksvrGk 61
                                   +p +++e+++++++  s l + l++L + glv++ rGk
  gi|119720455|ref|YP_920950.1| 30 GPSTLRELSDKVDMVGSQLHQYLKRLVRLGLVEVSRGK 67
                                   46899********************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2345.55
//
Query:       gi|119720456|ref|YP_920951.1|  [L=718]
Description: hypothetical protein Tpen_1552 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-38  131.0   0.0    7.9e-38  129.7   0.0    1.7  1  GHL6             Hypothetical glycosyl hydrolase 6
    1.7e-08   33.9   0.0    2.6e-08   33.3   0.0    1.2  1  GHL10            Glycosyl hydrolase-like 10
    7.9e-08   31.7   0.0    1.2e-07   31.1   0.0    1.2  1  DUF4015          Putative glycosyl hydrolase domain
    5.5e-06   26.0   0.0    1.6e-05   24.5   0.0    1.8  2  Glyco_hydro_42M  Beta-galactosidase trimerisation domain
  ------ inclusion threshold ------
      0.014   15.4   0.0      0.024   14.6   0.0    1.3  1  DUF4434          Domain of unknown function (DUF4434)
      0.028   14.9   0.0         19    5.8   0.0    3.1  2  CoA_binding_2    CoA binding domain
       0.19   11.6   0.0       0.34   10.8   0.0    1.3  1  GHL15            Hypothetical glycosyl hydrolase family 15


Domain annotation for each model (and alignments):
>> GHL6  Hypothetical glycosyl hydrolase 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.7   0.0   3.1e-41   7.9e-38       4     137 .]      24     157 ..      21     157 .. 0.92

  Alignments for each domain:
  == domain 1  score: 129.7 bits;  conditional E-value: 3.1e-41
                           GHL6   4 elveelkeagadtlvifardaggvvyYrtkldfvtehpklk.rdllkelvkachregikvvvrvdfskaderiyeqhpeW 82 
                                    ++v  + e++ dt+vifarda+g++yY++ +    +   lk rdll+e+v+++hr+gikvv++++++  + ++y  hpeW
  gi|119720456|ref|YP_920951.1|  24 DIVGLAAELHCDTVVIFARDAWGRAYYDSAV--ARKVASLKsRDLLREVVEEAHRRGIKVVAMIGHT-TNPELYSSHPEW 100
                                    788999*************************..888888887*************************.************ PP

                           GHL6  83 aavkenGeviiiegervgepg...wptlCinsgyqeklaeeleealkrldlDGifldi 137
                                    a++++nG+vi ++++++g ++   wp +C+ns++ +++++e+ee+l r+++DG+fld+
  gi|119720456|ref|YP_920951.1| 101 AQRDRNGRVIHMDTDPQGVKDkvrWPLMCLNSPFLDYVLREAEEVL-RYGVDGVFLDS 157
                                    **********88887765443347999******************5.8********95 PP

>> GHL10  Glycosyl hydrolase-like 10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   0.0     1e-11   2.6e-08      17     222 ..      18     224 ..       8     246 .. 0.72

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 1e-11
                          GHL10  17 dkvqkkeaikkLddlqlntvyvqvkn.dgtalypsavakwselktgkkgedpGrDvLaevideahkrnlkvlaWFevgln 95 
                                    d+v   +++ + ++l+ +tv++  ++  g a+y+sava++        ++   rD+L ev++eah+r++kv+a     + 
  gi|119720456|ref|YP_920951.1|  18 DRVTGADIVGLAAELHCDTVVIFARDaWGRAYYDSAVARKVAS-----LKS--RDLLREVVEEAHRRGIKVVAM----IG 86 
                                    5666666666667777777765555415999999999986543.....344..89*****************96....45 PP

                          GHL10  96 akelselvkahPasltvqkrdevktses...aagerlwlnPliPevqdfitklvvev..vkrYdvDgvqlDDyfylpes. 169
                                    ++   el ++hP +   ++++ v+ + +   +  +  +  Pl+     f+  ++ e+  v rY vDgv lD + y+p+  
  gi|119720456|ref|YP_920951.1|  87 HTTNPELYSSHPEWAQRDRNGRVIHMDTdpqGVKD-KVRWPLMCLNSPFLDYVLREAeeVLRYGVDGVFLDSFRYMPDVe 165
                                    6677899*******999999999887542213333.4455888777777777775543389************9998751 PP

                          GHL10 170 .fGydlidvalYrqetkkealsnked.dl.....widWRrdkisqlvkklnatikavkPn 222
                                     +    +  + Y +e + + l+++ed d         WR     + ++++++ ++ +kP+
  gi|119720456|ref|YP_920951.1| 166 rACFCENCRKAYAEEVG-GELPSEEDwDSeafrrAFAWRYRVNVKALERVKDFVRKAKPG 224
                                    15555566789999998.555555551446666667788766666778899999999997 PP

>> DUF4015  Putative glycosyl hydrolase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.0   4.6e-11   1.2e-07      17     179 ..      24     221 ..      14     225 .. 0.76

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 4.6e-11
                                    HHHHHHHHSS--EEEEEEE-TTS-BSS----HHHHHCT-B--S.--HHHHHHHHHHTT-EEEEEEE-S--TTHHHHSGGG CS
                        DUF4015  17 ellelidetelnavviDvKddeGnvtyesklelaeelgaskkyisdleellkklkergiyviaRivvfkDkvlaearpel 96 
                                    +++ l+ e + ++vvi  +d  G+ +y+s++ ++ +  +s+++   l+e+++++++rgi v+a i     + l++++pe+
  gi|119720456|ref|YP_920951.1|  24 DIVGLAAELHCDTVVIFARDAWGRAYYDSAVARKVASLKSRDL---LREVVEEAHRRGIKVVAMIGHTTNPELYSSHPEW 100
                                    567788888999***************8887776666666666...9********************************* PP

                                    B-EETTSSB---TTS--.......-.B-TT-GGGHHHHHHHHHHHHHHT-SEEEEE--S---.------EE---TT--.. CS
                        DUF4015  97 avkkkdgevwkdsegea.......w.vdpykeevwdynieiAkeaaelGfdeiqfDYvRfpe.dskkkeleyseeeteee 167
                                    a ++++g+v +  ++ +       w +   ++   dy ++ A+e+ ++G+d +  D  R+    +++   e  ++ + ee
  gi|119720456|ref|YP_920951.1| 101 AQRDRNGRVIHMDTDPQgvkdkvrWpLMCLNSPFLDYVLREAEEVLRYGVDGVFLDSFRYMPdVERACFCENCRKAYAEE 180
                                    ********98876663344455557456788999*************************965133333333333444434 PP

                                    .............................HHHHHHHHHHHH CS
                        DUF4015 168 .............................rveaisdflaya 179
                                                                   e ++df+++a
  gi|119720456|ref|YP_920951.1| 181 vggelpseedwdseafrrafawryrvnvkALERVKDFVRKA 221
                                    56666666666666666666666666665556666666665 PP

>> Glyco_hydro_42M  Beta-galactosidase trimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   6.4e-09   1.6e-05       5     119 ..     363     473 ..     359     511 .. 0.76
   2 ?   -3.4   0.0       2.3   5.8e+03     166     189 ..     561     582 ..     548     587 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 6.4e-09
                Glyco_hydro_42M   5 ivfdwesk.waiesqegpssrdldyrsevrkyYrallelgvpvDvvseea....dlsgYklvvaPtlylvseelvkklea 79 
                                    +v++ +s+ w  +s+  p+    ++++e+r  Y al+  g pvD+vs ++    +l+gY+++++  +  +s   v  l++
  gi|119720456|ref|YP_920951.1| 363 VVYSNRSRdWLGRSD--PR----HVTDEARGLYYALAYSGYPVDFVSDTQldsgELKGYRVLLLGSVASMSRRGVASLAE 436
                                    566666542555555..66....6899999*****************87766679************************* PP

                Glyco_hydro_42M  80 fvenGGtlvltylsGvvdendrihlggvpgpLrellGikv 119
                                     +++G  +v+tyl+   de+ r  ++   ++L   lG++ 
  gi|119720456|ref|YP_920951.1| 437 RAARGLGVVATYLTSTMDEDGRQLEEFQLSEL---LGVSY 473
                                    *********************99977655544...44443 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.3
                Glyco_hydro_42M 166 agtpAvtrnnygkGkaiYvgsrle 189
                                     g+pA+t++  ++ +++Y + +l+
  gi|119720456|ref|YP_920951.1| 561 TGAPAITAR--EEPRVVYFSGQLG 582
                                    589****99..7888888877666 PP

>> DUF4434  Domain of unknown function (DUF4434)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   9.5e-06     0.024      30      87 ..      30      89 ..      25     112 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 9.5e-06
                                   HHTT--EEEES-SEETTEESS--HHHHTT----SB-HHHHHHHHHHHTT-EEE..EE--B CS
                        DUF4434 30 kelgmntlilqrvsykgkafypskllkekfekkakdlveaiLdaAdklgmkvf..lglny 87
                                   +el ++t+++    + g a+y+s+++ + +  k+ dl+ ++ ++A + g+kv+  +g   
  gi|119720456|ref|YP_920951.1| 30 AELHCDTVVIFARDAWGRAYYDSAVARKVASLKSRDLLREVVEEAHRRGIKVVamIGHTT 89
                                   5789*********************9889999*******************962245444 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0    0.0072        19      66      95 ..      65      94 ..      17     110 .. 0.73
   2 ?    5.3   0.0      0.01        27      64      96 ..     265     297 ..     262     312 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0072
                                   HHHGGGHHHHHHH--SEEEE-TT---HHHH CS
                  CoA_binding_2 66 eatpeivkealalgakavwlqpgsedeeaa 95
                                   + + e+v+ea+++g+k+v +  ++ ++e++
  gi|119720456|ref|YP_920951.1| 65 DLLREVVEEAHRRGIKVVAMIGHTTNPELY 94
                                   445677777777777777777777776665 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.01
                                    -HHHHGGGHHHHHHH--SEEEE-TT---HHHHH CS
                  CoA_binding_2  64 ppeatpeivkealalgakavwlqpgsedeeaae 96 
                                    pp  ++eivk  +a+gak+vw   +s++ ++  
  gi|119720456|ref|YP_920951.1| 265 PPGFLAEIVKLSKAMGAKRVWATRNSFHMALTT 297
                                    7788999****************9999988765 PP

>> GHL15  Hypothetical glycosyl hydrolase family 15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00013      0.34      40      97 ..      94     158 ..      75     181 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00013
                          GHL15  40 qnehpdwflrdskgkri......skyqgh..yqmdvsnpefrewWvksalnelrdsgiDGvfaDnd 97 
                                     ++hp+w  rd +g+ i      ++++++  +     n  f  +  + a + lr  g+DGvf+D++
  gi|119720456|ref|YP_920951.1|  94 YSSHPEWAQRDRNGRVIhmdtdpQGVKDKvrWPLMCLNSPFLDYVLREAEEVLRY-GVDGVFLDSF 158
                                    479**************77643333555556777778999***999999855555.********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (718 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.43
# Mc/sec: 5039.90
//
Query:       gi|119720457|ref|YP_920952.1|  [L=362]
Description: spermidine/putrescine ABC transporter ATPase subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-37  128.0   0.0      5e-37  127.5   0.0    1.2  1  ABC_tran  ABC transporter
    2.2e-08   34.3   0.0    0.00034   20.5   0.0    2.2  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    5.2e-07   29.7   0.5    5.2e-07   29.7   0.5    2.5  3  TOBE_2    TOBE domain
    0.00088   19.2   0.0     0.0013   18.7   0.0    1.2  1  Rad17     Rad17 P-loop domain
     0.0013   19.5   0.1      0.014   16.2   0.0    2.8  2  OB_MalK   MalK OB fold domain
     0.0017   18.8   0.2      0.017   15.6   0.2    2.2  1  AAA       ATPase family associated with various cellular acti
     0.0057   16.1   0.1       0.11   11.9   0.1    2.1  2  TniB      Bacterial TniB protein
     0.0064   16.0   0.1      0.041   13.3   0.0    1.9  2  SMC_N     RecF/RecN/SMC N terminal domain
  ------ inclusion threshold ------
      0.024   15.0   0.8      0.067   13.6   0.8    1.8  1  AAA_16    AAA ATPase domain
      0.032   14.2   0.4       0.21   11.6   0.4    2.1  1  AAA_5     AAA domain (dynein-related subfamily)
      0.054   13.8   1.0       0.74   10.1   0.1    2.4  2  AAA_22    AAA domain
      0.088   13.1   0.1       0.73   10.1   0.1    2.2  1  SbcCD_C   Putative exonuclease SbcCD, C subunit


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.5   0.0   3.4e-40     5e-37       2     136 ..      20     161 ..      19     162 .. 0.97

  Alignments for each domain:
  == domain 1  score: 127.5 bits;  conditional E-value: 3.4e-40
                                    EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                       ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                    ++vs+++++ge+++++G++G+GK+t l+++agl+ p+eG++l++g+d+++   +  ++ +g+++q+  l+p++tv++n  
  gi|119720457|ref|YP_920952.1|  20 DHVSFSVERGEMLGLLGPSGCGKTTTLRIIAGLTVPDEGRVLVEGEDITN--APPEKRGMGMVFQNYALWPHMTVYDNva 97 
                                    79************************************************..99999*********************** PP

                                    ...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                               e ++++++al+ ++l elkd+      ++LSgGq+qrvalaral+ +p+++llDEp 
  gi|119720457|ref|YP_920952.1|  98 fplrargmpadEVQRRVKEALEIVRLYELKDRYP----HQLSGGQQQRVALARALAVQPRVILLDEPL 161
                                    *********9999999************999998....*****************************7 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0     9e-05      0.13       3      23 ..      33      53 ..      31      79 .. 0.80
   2 !   20.5   0.0   2.3e-07   0.00034     228     298 ..     125     193 ..      81     199 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9e-05
                         AAA_21  3 vliGpNgsGKSnLLdaldlla 23
                                   +l Gp g+GK++ L+++ +l 
  gi|119720457|ref|YP_920952.1| 33 GLLGPSGCGKTTTLRIIAGLT 53
                                   799**************9994 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 2.3e-07
                         AAA_21 228 dgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHS 298
                                      +++ +++lS G+++  al+ al+ ++   +++l+DEp ++L+ kl ++    lkel+r  g+  + +TH+
  gi|119720457|ref|YP_920952.1| 125 ELKDRYPHQLSGGQQQRVALARALAVQP---RVILLDEPLSNLDAKLREEMRFELKELQRkLGVTAVYVTHD 193
                                    45667889*********9*******999...*********************88888888899********8 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       4.6   6.8e+03      38      53 ..     133     148 ..     129     154 .. 0.68
   2 ?   -1.1   0.0       1.5   2.2e+03      28      54 ..     247     272 ..     238     283 .. 0.69
   3 !   29.7   0.5   3.5e-10   5.2e-07       4      75 ..     291     354 ..     278     355 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 4.6
                         TOBE_2  38 elaggqlvvvrqpnad 53 
                                    +l ggq+++v+ + a 
  gi|119720457|ref|YP_920952.1| 133 QLSGGQQQRVALARAL 148
                                    6778888888776665 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.5
                         TOBE_2  28 ylGsstryvvelaggqlvvvrqpnadr 54 
                                    +lG+ + ++v++++g  v++++   ++
  gi|119720457|ref|YP_920952.1| 247 FLGEGY-VLVRVGDGLYVKAYTKRVHE 272
                                    666655.46899999888888877775 PP

  == domain 3  score: 29.7 bits;  conditional E-value: 3.5e-10
                         TOBE_2   4 RPEklrlaaagganglsGtVedveylGsstryvvelaggqlvvvrqpnadrdsalapGdtVelswdpddavv 75 
                                    RPEk+     ++ n ++G+V++ +ylG+ ++y+v++ +g    +r+++++   ++++G+++ l +++d+++v
  gi|119720457|ref|YP_920952.1| 291 RPEKVDE---SRVNVFEGVVVRKTYLGDVYDYRVRVSEGVT--LRVEARE---NYDVGSKLYLVVPADRTLV 354
                                    5555555...7779*************************55..6667776...889***********99987 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   8.5e-07    0.0013      45      73 ..      29      57 ..      14     136 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 8.5e-07
                          Rad17 45 kriLLisGPsGCgkstvvkvLskelgikl 73
                                    ++L + GPsGCgk+t++++++   +++ 
  gi|119720457|ref|YP_920952.1| 29 GEMLGLLGPSGCGKTTTLRIIAGLTVPDE 57
                                   4589999**************98887764 PP

>> OB_MalK  MalK OB fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   9.3e-06     0.014       5      50 ..     237     282 ..     236     285 .. 0.87
   2 ?   -1.3   0.0       2.8   4.2e+03       6      38 ..     301     331 ..     300     344 .. 0.58

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 9.3e-06
                        OB_MalK   5 MNflpatveedgvlvegggvtlplpeeq..kl.alklyagkevilGiRP 50 
                                     Nfl++++e    ++ +g v +++ ++   k+  ++ ++  +vi+G+RP
  gi|119720457|ref|YP_920952.1| 237 INFLEGRIE---EFLGEGYVLVRVGDGLyvKAyTKRVHEKAPVIVGVRP 282
                                    6********...4899999999999999764479*************** PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.8
                        OB_MalK   6 Nflpatveedgvlvegggvtlplpeeqklalkl 38 
                                    N +++ v+++ +l +  + +++++e+    l+ 
  gi|119720457|ref|YP_920952.1| 301 NVFEGVVVRKTYLGDVYDYRVRVSEGV--TLRV 331
                                    778888887775555555556665555..3333 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.2   1.1e-05     0.017       3      66 ..      34     159 ..      32     194 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.1e-05
                                    EESSTTSSHHHHHHHHHHHH..THEEEEEETTTCSSS........................................... CS
                            AAA   3 lyGppGtGKTllakavakel..gvefleisgsellsk........................................... 37 
                                    l Gp G+GKT++ + +a  +  +   + ++g ++++                                            
  gi|119720457|ref|YP_920952.1|  34 LLGPSGCGKTTTLRIIAGLTvpDEGRVLVEGEDITNAppekrgmgmvfqnyalwphmtvydnvafplrargmpadevqrr 113
                                    89***************986442223444445554444444444444445555555555555555555555555555555 PP

                                    ................STTHHHHHHHHHHHHHHHTS.TSEEEEEET CS
                            AAA  38 ................yvgesekkirelfkeakeka.kpsilfiDE 66 
                                                    y  + +   ++ ++ a++ a +p ++++DE
  gi|119720457|ref|YP_920952.1| 114 vkealeivrlyelkdrYPHQLSGGQQQRVALARALAvQPRVILLDE 159
                                    5555555555555555777777777777777777777777777777 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0     0.083   1.2e+02      34      53 ..      28      47 ..       3      58 .. 0.84
   2 !   11.9   0.1   7.2e-05      0.11      92     167 ..     124     197 ..      90     205 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.083
                           TniB 34 rmpnlllvGdsnnGKtmive 53
                                   r + l l+G+s +GKt+ ++
  gi|119720457|ref|YP_920952.1| 28 RGEMLGLLGPSGCGKTTTLR 47
                                   66678899********9876 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 7.2e-05
                           TniB  92 ealgaplkararvskleqqvlrllrelkvrvLiiDEihnllagsarkqreflnalksLgnelkipivlvGteealr 167
                                     +l+ ++  + +  ++++ +l+   ++++rv+++DE  + l   a+ ++e+   lk L+++l ++ v+v  ++a +
  gi|119720457|ref|YP_920952.1| 124 YELKDRYPHQLSGGQQQRVALARALAVQPRVILLDEPLSNL--DAKLREEMRFELKELQRKLGVTAVYVTHDQAEA 197
                                    566667766667777777777788899*********87777..67778888899**************98777754 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0       0.3   4.5e+02      26      40 ..      31      45 ..      15      50 .. 0.79
   2 !   13.3   0.0   2.8e-05     0.041     121     200 ..     118     193 ..     100     212 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.3
                                   EEEEEESTTSSHHHH CS
                                   xxxxxxxxxxxxxxx RF
                          SMC_N 26 ftaivGpNGSGKsnl 40
                                   +  ++Gp G+GK+  
  gi|119720457|ref|YP_920952.1| 31 MLGLLGPSGCGKTTT 45
                                   55689*******976 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 2.8e-05
                                    HHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 121 kevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislree 200
                                     e+ +l e ++ ++++LSgG+++ vala  +A+q      + llDe  ++LD+k ++++   lke + +  +  + ++++
  gi|119720457|ref|YP_920952.1| 118 LEIVRLYELKDRYPHQLSGGQQQRVALARALAVQPR----VILLDEPLSNLDAKLREEMRFELKELQRKLGVTAVYVTHD 193
                                    4666677777778889**************998754....679****************999999998865544444444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.8   4.5e-05     0.067      23      63 ..      28      69 ..      18     205 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.5e-05
                         AAA_16 23 rpelvllsGesGvGKsslvrellralekdggif.lrgkcdql 63
                                   r+e++ l G+sG+GK++ +r ++     d+g + ++g+   +
  gi|119720457|ref|YP_920952.1| 28 RGEMLGLLGPSGCGKTTTLRIIAGLTVPDEGRVlVEGEDITN 69
                                   3478999*************9997666665555466665555 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.4   0.00014      0.21       4      34 ..      34      66 ..      32     178 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00014
                                   EE--SSSSHHHHHHHGGGGB..S--EEEEE--T CS
                          AAA_5  4 LvGppGtgKselaerlaaal..nreveyvqltr 34
                                   L+Gp+G+gK++  + +a ++      + v + +
  gi|119720457|ref|YP_920952.1| 34 LLGPSGCGKTTTLRIIAGLTvpDEGRVLVEGED 66
                                   99***************9999544444444444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1    0.0005      0.74       6      24 ..      30      48 ..      26      60 .. 0.84
   2 ?    2.1   0.1      0.15   2.2e+02      73     124 ..     132     186 ..      98     223 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0005
                         AAA_22  6 gilvvtGesGtGKTtllrr 24
                                    +l + G+sG+GKTt+lr 
  gi|119720457|ref|YP_920952.1| 30 EMLGLLGPSGCGKTTTLRI 48
                                   567789**********986 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.15
                         AAA_22  73 lsseellealeqalrarav.ielliiDEaqh.lr...seealeeLrsllnlsrkgvq 124
                                    ++++   ++    +ra av ++++++DE    l+   +ee+  eL++l+   + gv+
  gi|119720457|ref|YP_920952.1| 132 HQLSGGQQQRVALARALAVqPRVILLDEPLSnLDaklREEMRFELKELQR--KLGVT 186
                                    33333333333334444447779999995444766444666666666655..44444 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00049      0.73      33      84 ..     134     172 ..     124     177 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00049
                        SbcCD_C  33 lSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatl 84 
                                    lSGG++q    +ala     ++        ++r+++LDE  s+lD++ ++++
  gi|119720457|ref|YP_920952.1| 134 LSGGQQQR---VALA----RALAV------QPRVILLDEPLSNLDAKLREEM 172
                                    56666632...2333....22333......4899************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 2404.70
//
Query:       gi|119720458|ref|YP_920953.1|  [L=354]
Description: extracellular solute-binding protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    8.7e-31  107.2   0.3    1.4e-30  106.6   0.3    1.2  1  SBP_bac_6   Bacterial extracellular solute-binding protein
    1.1e-19   71.1   0.0    1.6e-19   70.5   0.0    1.2  1  SBP_bac_11  Bacterial extracellular solute-binding protein
    2.1e-19   70.5   0.3    3.1e-19   69.9   0.3    1.3  1  SBP_bac_8   Bacterial extracellular solute-binding protein
    5.4e-16   59.4   3.4    7.7e-16   58.9   3.4    1.2  1  SBP_bac_1   Bacterial extracellular solute-binding protein
  ------ inclusion threshold ------
      0.099   13.0   0.6         58    4.1   0.1    3.3  3  Wzz         Chain length determinant protein


Domain annotation for each model (and alignments):
>> SBP_bac_6  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.6   0.3   3.8e-34   1.4e-30       4     237 ..     111     330 ..     110     333 .. 0.86

  Alignments for each domain:
  == domain 1  score: 106.6 bits;  conditional E-value: 3.8e-34
                      SBP_bac_6   4 pdlilsfdkdflekfieeglfqpldpanlpnvnkdfaeeglkdpdgkyypygvgplvlavnkdrlkgrpvPksWaDLldP 83 
                                    +d+++  ++  +e +i+e ++++++   +p+++     ++++dp+g+y+  +v  +v+++n   +++   PksW+DL++P
  gi|119720458|ref|YP_920953.1| 111 ADVVYIASPFEFETLINESIIEKFP--DIPELKYIP--QEYRDPRGYYVWGRVLVMVIVYNPNIVTDP--PKSWQDLVKP 184
                                    79999999999***********987..677777444..***************************766..********** PP

                      SBP_bac_6  84 eykgkvalpgnngsdlfealllalykdfgedgvkkllrnlkanlhpaq..mvkaagslesgepavsvvpyffadilpekk 161
                                    e+kgkv++ ++  s++ +++++al+ +fg    + ++++lk+n   +     + a  ++ ge  v v+ +++  ++p   
  gi|119720458|ref|YP_920953.1| 185 EWKGKVVIANPLYSGSTQVAVAALASKFG----WSYFEKLKENDVLVVqdVPDVARVVATGERPVGVTLTMYLGAYPTL- 259
                                    **********99999999**9*9999776....6677777777777776566777888888866666666666666655. PP

                      SBP_bac_6 162 kgknlkvvwPedGalvspifmlvkkg.kkkelakafidfllspevqailakaggvfPvvtnpavlnelpegaklkwl 237
                                         k+v Pe+Ga++ p  + ++k+ k++e+ak f+ flls+ ++++l++a+  + +  ++++ + lp+  +lk+l
  gi|119720458|ref|YP_920953.1| 260 -----KFVAPEEGAIAIPSPVGLVKNaKHPEDAKVFLRFLLSKLGAQALTDAYT-YSTRIDAPAPKGLPPLSQLKIL 330
                                    .....6***********************************************8.9888888888888887777765 PP

>> SBP_bac_11  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.5   0.0   4.6e-23   1.6e-19      29     227 ..      87     306 ..      67     308 .. 0.87

  Alignments for each domain:
  == domain 1  score: 70.5 bits;  conditional E-value: 4.6e-23
                                    EEEESSHHHHHHHH....HHH...-SEEEESSH.HHHHHHHHGGGGG...............GG-EEEEEEE...EEEEE CS
                     SBP_bac_11  29 evsaggsgklarqi....adga.rpDvwipassawlellaaaglvqa...............esavplassp...lviav 85 
                                    ev   g gk+++++    ++g+ ++Dv+  as+   e l+++  + +               +++  ++  +   +vi++
  gi|119720458|ref|YP_920953.1|  87 EVWRSGTGKVVAKLlaekKAGSvEADVVYIASPFEFETLINESIIEKfpdipelkyipqeyrDPRGYYVWGRvlvMVIVY 166
                                    55566788888888665555559*******************99999************997666666666678788888 PP

                                    STT-.TT---SHHHHHHSS-..-EEEE--T-TTTTHH.HHHHGGG--HHHHHHHHHTEEEEESSHHHHHHHHHTTT-SEE CS
                     SBP_bac_11  86 pkgn.pkkikgwadLlkpgl..klavadPttspsGlaalalleaagaqellkalekkvvklgessrqlltaveageadag 162
                                    +++   +++k+w+dL kp++  k+++a+P  s+s + a+a+l+   +  ++++l+++ v  ++++ +++  v++ge  +g
  gi|119720458|ref|YP_920953.1| 167 NPNIvTDPPKSWQDLVKPEWkgKVVIANPLYSGSTQVAVAALASKFGWSYFEKLKENDVLVVQDVPDVARVVATGERPVG 246
                                    88866789************889**************9999997633558999999988799****************** PP

                                    EEEHHHHH..HSTTSSEEEE--TTT--...EEEEEEEE-TT--HHHHHHHHHTTSHHHHHHHHHT CS
                     SBP_bac_11 163 ivyeseakaaengdkleavylpeglnldpldypaavlkkaakreaAraFlafLrspeaqailrky 227
                                    ++    +    + + l++v++ eg  +  ++ p++++k+a+++e A+ Fl+fL+s+ + ++l+++
  gi|119720458|ref|YP_920953.1| 247 VTLTMYLG---AYPTLKFVAPEEGAIA--IPSPVGLVKNAKHPEDAKVFLRFLLSKLGAQALTDA 306
                                    *9987776...7**************6..*******************************99876 PP

>> SBP_bac_8  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.9   0.3   8.6e-23   3.1e-19      13     263 ..      85     311 ..      56     320 .. 0.88

  Alignments for each domain:
  == domain 1  score: 69.9 bits;  conditional E-value: 8.6e-23
                                    EEEEEE--SSSHHHHHHHHHHTT---SEE.EEE-HHH.HHHHHHTTSB--GGGSTTHHH-HHHHHTT--TS.----EEEE CS
                      SBP_bac_8  13 kvnvvtaasndleqklkaalaagtapdidvvwaneda.latlaeeglladlsdldnlddltdalaavgydgklygvPyas 91 
                                     ++v  ++++++++kl a+ +ag++  +dvv++++ + + tl++e  ++ + d+++l+++++ +++    g  y v+  +
  gi|119720458|ref|YP_920953.1|  85 SLEVWRSGTGKVVAKLLAEKKAGSVE-ADVVYIASPFeFETLINESIIEKFPDIPELKYIPQEYRD--PRG--YYVWGRV 159
                                    4566667899**************96.58888887777************************8884..567..9999888 PP

                                    EEE-EEEEEHHHHHHS.---BHHHHHHHHHHHHHH-SEGG---GGGGGGTHHETTEE---H..HHH.HHHHHHHHHHHHT CS
                      SBP_bac_8  92 etpyvliynkdllekaedpktwdellaaakklkgkfglpdpasgwlqaallakdgksldddggkdglkealellkklkdn 171
                                       +v++yn  ++ +  +pk+w++l++  +++kgk+ +++p ++   + ++a++           + k  + ++ klk+n
  gi|119720458|ref|YP_920953.1| 160 LV-MVIVYNPNIVTD--PPKSWQDLVK--PEWKGKVVIANPLYSGSTQVAVAAL-----------ASKFGWSYFEKLKEN 223
                                    75.9**********5..**********..************9865555555514...........346689*******99 PP

                                    T-.EE-S..--SSTTTTTSBSEEEE-TTHHHHHH-TTTSEEEE--S--EEEEEEEEEEBTTS-HHHHHHHHHHHHHTTSH CS
                      SBP_bac_8 172 gk.tydtgadavsefanGevaftingswdiaaaqkagkklgaivpkqgsfaggkglavpknaknedlaAldFlkwltspe 250
                                     + ++++ +d+   +a+Ge   +++ +  + a+    ++l++++p +g++a  +++   knak+++  A++Fl++l+s+ 
  gi|119720458|ref|YP_920953.1| 224 DVlVVQDVPDVARVVATGERPVGVTLTMYLGAY----PTLKFVAPEEGAIAIPSPVGLVKNAKHPED-AKVFLRFLLSKL 298
                                    87488999********************99996....55***************************7.************ PP

                                    HHHHHHHHH---B CS
                      SBP_bac_8 251 nqaalaektgyip 263
                                    + +al +++ y +
  gi|119720458|ref|YP_920953.1| 299 GAQALTDAYTYST 311
                                    *999999988865 PP

>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.9   3.4   2.1e-19   7.7e-16      30     311 ..      89     297 ..      68     302 .. 0.80

  Alignments for each domain:
  == domain 1  score: 58.9 bits;  conditional E-value: 2.1e-19
                                    EEECHHHHHHHHHHHHHTTSSSCSEEEE.CGGHHHHHHHTTSBECCHHHHHHTTECTTCCTEEEEHHHHTHHHHCEEEES CS
                      SBP_bac_1  30 esvgsgslaqkltlaiaaGdgpaDviav.dndwiarlakaglllpldpyvkaylapgvkdaadklsssvlpkildskvly 108
                                      +g+g +  kl +   aG+ +aDv+++ +++ + +l+++   + + ++ + + +p+  ++ d+     ++++++     
  gi|119720458|ref|YP_920953.1|  89 WRSGTGKVVAKLLAEKKAGSVEADVVYIaSPFEFETLINESIIEKFPDIPELKYIPQ--EYRDP----RGYYVWG----- 157
                                    3457777888**************************************888886555..44444....3334444..... PP

                                    EEEEE.EEEEEEETTTHHCTTGGGSHBHHHHHHHHHHHHHHCTCTHCCHCCEEHHHHHHHHHHHHHHHHTGGGEECCCTH CS
                      SBP_bac_1 109 vPlya.argliYNkdlfekagldppwtWdelveaakklkekgkkpiggarggsasgtayyfalalakslggkvfdkdggg 187
                                          +++++YN+ ++     dpp++W++lv++  k k    +p        +sg +++                    
  gi|119720458|ref|YP_920953.1| 158 ---RVlVMVIVYNPNIVT----DPPKSWQDLVKPEWKGKVVIANP-------LYSGSTQV-------------------- 203
                                    ...23389**********....899*******9999888888888.......33333333.................... PP

                                    HCSHHHHSHHHHHHHHHHHHHHHHHHHTTEEECSSHHHHHHHHHTTSCSEEEEEHHHHHHHHCEEEEECHHCHHHHTTST CS
                      SBP_bac_1 188 ldnpegvtaatylvklyavanltkelkgkgaenkdgaaalalfeaGeaamaivglwaalaamkvapkvafaadkekpkee 267
                                            a+++l  ++++ + +k + +++   +d++++++ +++Ge ++++  + +          +a+++ k  ++ee
  gi|119720458|ref|YP_920953.1| 204 --------AVAALASKFGWSYFEKLKENDVLVVQDVPDVARVVATGERPVGVTLTMY---------LGAYPTLKFVAPEE 266
                                    ........77888888889999*****************************999998.........55555555555444 PP

                                    EEEECEEBETTTTSEEEEEEEEEEBTTCSTHHHHHHHHHHHTSH CS
                      SBP_bac_1 268 lgvaplPagkggkpgilgayglaipkgsknpeaAkkFldfllsp 311
                                     + ++            + ++++++k++k+pe Ak Fl+flls+
  gi|119720458|ref|YP_920953.1| 267 GA-IA------------IPSPVGLVKNAKHPEDAKVFLRFLLSK 297
                                    44.44............99***********************97 PP

>> Wzz  Chain length determinant protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1     0.016        58      19      40 ..       9      30 ..       4      62 .. 0.80
   2 ?    1.6   0.0     0.096   3.4e+02      35      55 ..     191     211 ..     183     240 .. 0.70
   3 ?    3.4   0.0     0.026        93      36      63 ..     302     330 ..     289     348 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.016
                                   XXXXXXXXXXXXXXXXXXXXX- CS
                            Wzz 19 Iilvtllfallaviyaflatpk 40
                                   I+lv++l++++++++ f ++p 
  gi|119720458|ref|YP_920953.1|  9 ILLVIVLAVAIGALVYFGSKPS 30
                                   8889999999888888877764 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.096
                                    XXXXX-EEEEEEEES--CHHH CS
                            Wzz  35 flatpkYtataqilvpekkqv 55 
                                    ++a p Y+ ++q++v    ++
  gi|119720458|ref|YP_920953.1| 191 VIANPLYSGSTQVAVAALASK 211
                                    689999999999999987765 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.026
                                    XXXX-EEEEEEEES--CHHH.HHHHHHCC CS
                            Wzz  36 latpkYtataqilvpekkqv.eassltaq 63 
                                    ++t+ Yt +++i  p +k+    s+l  +
  gi|119720458|ref|YP_920953.1| 302 ALTDAYTYSTRIDAPAPKGLpPLSQLKIL 330
                                    68999************997533555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2335.17
//
Query:       gi|119720459|ref|YP_920954.1|  [L=561]
Description: binding-protein-dependent transport systems inner membrane component [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.8e-30  104.4  51.6    1.1e-17   64.4  14.8    3.5  4  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
      0.064   13.4   0.1        2.6    8.2   0.0    2.5  2  HTH_28        Helix-turn-helix domain
       0.11   12.8   0.5       0.22   11.7   0.5    1.5  1  DUF5534       Family of unknown function (DUF5534)


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.2      0.15   9.2e+02      49      75 ..      21      47 ..      11      56 .. 0.78
   2 !   64.4  14.8   1.8e-21   1.1e-17       1     176 [.      90     275 ..      86     284 .. 0.84
   3 ?   -0.6   1.1      0.16   9.5e+02     109     154 ..     317     362 ..     302     381 .. 0.54
   4 !   53.8  17.6   3.2e-18   1.9e-14       3     173 ..     373     547 ..     371     551 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.15
                   BPD_transp_1 49 lghlilpviillllsaapyvrlirraa 75
                                    ++l  +++++++   +p+++li++++
  gi|119720459|ref|YP_920954.1| 21 PKWLTVALLVAAVALVLPPILLIFSDV 47
                                   677788888888888888888888776 PP

  == domain 2  score: 64.4 bits;  conditional E-value: 1.8e-21
                   BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf..........vilsilg.hlilpviillllsaapyvr 69 
                                    g+++++l+a ++n + ++ll+ l   ++ +Psf++a  ++++            + s l  ++ l ++++l+l++ p+++
  gi|119720459|ref|YP_920954.1|  90 GLMFAWLLA-RYNIPRRELLLSLLTGPYVIPSFLIATGWIMLWtnrglyeqftGMRSPLNpYGPLNLVFVLALHNYPLAM 168
                                    677788888.************************99999977799*******97777777699999************** PP

                   BPD_transp_1  70 lirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgyd 149
                                    l ++ al +l+ +l+eaar+ G+s+++i   +vlP++lp++++g+il+f++++ ++ ++  lg    +g+++l +++++ 
  gi|119720459|ref|YP_920954.1| 169 LSIYPALLNLDASLEEAARIHGVSPRRIATGIVLPLVLPSVLSGFILTFAYSISEFGAPAVLGLP--VGYTTLVTQIYSL 246
                                    ***************************************************************55..7877777777777 PP

                   BPD_transp_1 150 yseis..nggvlalviavlllnlvadilq 176
                                    ++     ++++ +l +++ +++l+a  l+
  gi|119720459|ref|YP_920954.1| 247 MTVSPvdYAAAEVLSVVLSAISLLALYLN 275
                                    77666554444444444444444444444 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.16
                   BPD_transp_1 109 piitglilafggllggavlleflgswpGlgtllleailgydyseis 154
                                    pi++ ++ ++++ +g+ + l+ lg ++ l  l +e +    ++  +
  gi|119720459|ref|YP_920954.1| 317 PILAVIVGSLVRTWGEPITLSNLGVDHYLKILAMERSRRALVATLL 362
                                    5666666666666777777766665544444444444444444444 PP

  == domain 4  score: 53.8 bits;  conditional E-value: 3.2e-18
                   BPD_transp_1   3 llGilaa...lnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilp.viillllsaapyvrlirraalrs 78 
                                    ++G+l+a   +++ + l+++++ ++++++s+P +v+++ l++++  l +  ++  + +++++++ ++py++++ + al +
  gi|119720459|ref|YP_920954.1| 373 IVGLLVAyvaVRSPSLLSRIIDYIVFLPFSIPGLVIGVGLLVAAGKLYGPLYGTVGiLLVAFVIRFLPYATRTLAPALLQ 452
                                    68889999989******************************99988888888888879********************** PP

                   BPD_transp_1  79 lpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG..lgtllleailgydyseisng 156
                                    ++++l+ea+r+ G+s  +++ +vvlP+++  ++++ i++f +++++ ++  +l ++    +   +l ++ gy  + +  +
  gi|119720459|ref|YP_920954.1| 453 IDESLEEASRIHGVSFGKTLARVVLPLSAGALLSSWIFVFNSSMKELSASAILSTQVEtaIVVAFLLFTDGYFSDGA--A 530
                                    **********************************************9999888866544466666666666666644..5 PP

                   BPD_transp_1 157 gvlalviavlllnlvad 173
                                    +++++v+++lll++va 
  gi|119720459|ref|YP_920954.1| 531 LSIIIVLVTLLLTAVAS 547
                                    99999999999988875 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0   0.00043       2.6      14      30 ..     181     197 ..     174     198 .. 0.83
   2 ?    2.3   0.0     0.031   1.8e+02      10      31 ..     451     474 ..     444     476 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00043
                         HTH_28  14 svreaArelgisrrtvy 30 
                                    s  eaAr++g+s+r++ 
  gi|119720459|ref|YP_920954.1| 181 SLEEAARIHGVSPRRIA 197
                                    789***********985 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.031
                         HTH_28  10 aaGh.svreaArelgisr.rtvyr 31 
                                    ++ + s  ea+r++g+s   t+ r
  gi|119720459|ref|YP_920954.1| 451 LQIDeSLEEASRIHGVSFgKTLAR 474
                                    4655599*********98666655 PP

>> DUF5534  Family of unknown function (DUF5534)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.5   3.7e-05      0.22      61     101 ..     343     383 ..     317     386 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.7e-05
                        DUF5534  61 kllrklaliphrPaLvkviliacvalsialicGiaisyviY 101
                                    ++l+ la+ + r aLv  +l++  a sia i+G+ ++yv  
  gi|119720459|ref|YP_920954.1| 343 HYLKILAMERSRRALVATLLLSLGAASIASIVGLLVAYVAV 383
                                    567899********************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (561 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       734  (0.0409393); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.44
# Mc/sec: 3830.70
//
Query:       gi|119720460|ref|YP_920955.1|  [L=117]
Description: HEPN domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-13   51.3   0.4    1.4e-13   51.0   0.4    1.2  1  HEPN      HEPN domain


Domain annotation for each model (and alignments):
>> HEPN  HEPN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.0   0.4   8.1e-18   1.4e-13       2      68 ..      19      84 ..      18     110 .. 0.82

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 8.1e-18
                                   HHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHTT--.SSCCHHHHHHCCHHHT.. CS
                           HEPN  2 eewlrrAeedleaAellleegdydlacfhaqqaaekalKAlllkkggeppkthdlreLleelkkelk 68
                                   ++ + +A +dl+a +++  ++ y++acf aqqaa ka++All++++ + +++h++ +L+ +   e+ 
  gi|119720460|ref|YP_920955.1| 19 KKRFLQALRDLKATRDSSATDSYEWACFQAQQAAGKAVRALLYALTPS-AWGHSVVDLATLRGYEDV 84
                                   677889*****************************************8.*********986665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 763.66
//
Query:       gi|119720461|ref|YP_920956.1|  [L=269]
Description: major facilitator superfamily permease [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        4.5    6.1  34.3       0.34    9.8  25.7    2.0  2  MFS_1     Major Facilitator Superfamily


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   4.2     0.046   8.2e+02     135     183 ..      17      69 ..      13     108 .. 0.63
   2 ?    9.8  25.7   1.9e-05      0.34       7     163 ..      94     254 ..      88     257 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.046
                          MFS_1 135 ilg.pllggllasslg...Wravfyilaivsllafv.lfllllpeepperkrks 183
                                    ++  pllg +l+ +l     r  f++la++ + +++ + +l++p++ +e +  s
  gi|119720461|ref|YP_920956.1|  17 AISyPLLGYALS-ALRpgsVREGFLALAVAHVALAIyVLALFYPVTLKEGEEGS 69 
                                    344155555555.33323577778888888888888666666666665555554 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 1.9e-05
                          MFS_1   7 lsalarsilgpalpl.alaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa.ss 84 
                                    l+ la+ ++ +++   ++ e +g +   + l  +  + ++++++l++ r+  r+G r + l ++ ++a++ lll+ a ++
  gi|119720461|ref|YP_920956.1|  94 LYLLAWQLTPAFVLVnYVVEGYGGNLFHVALFDASMSTASVASMLVVDRVPARLGFRAMALSAAGVSASM-LLLS-AkPP 171
                                    5556666655555556889999999999999999999999999999999999999999999999999999.6666.569* PP

                          MFS_1  85 lwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllgglla.sslg...Wravfyilaiv 160
                                    lw+l+vl +   ++ +a++  + a++    ++ee +++ + lsa +    +  pll+glla  s g     ++f+++a +
  gi|119720461|ref|YP_920956.1| 172 LWALMVLGFALRMFDSAFLVFSRAWLYGSIAREEAALVSSGLSALSLTVLLAVPLLAGLLAaVSPGlpyLAGSFLVAATL 251
                                    ********************************999999999999888888888********6666644444446666666 PP

                          MFS_1 161 sll 163
                                     l+
  gi|119720461|ref|YP_920956.1| 252 PLI 254
                                    555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      163  (0.00909142); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1825.12
//
Query:       gi|119720462|ref|YP_920957.1|  [L=451]
Description: L-fucose isomerase and related proteins-like [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.071   13.6   0.0       0.16   12.5   0.0    1.6  1  DUF3681   Protein of unknown function (DUF3681)
       0.16   12.0   0.0       0.26   11.3   0.0    1.3  1  DUF3849   Protein of unknown function (DUF3849)


Domain annotation for each model (and alignments):
>> DUF3681  Protein of unknown function (DUF3681)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.7e-05      0.16      23      68 ..      94     139 ..      84     173 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.7e-05
                        DUF3681  23 lalfrspggvflrhgkallylYYgiLvavvvfGlaeasvgfWvsgd 68 
                                     +++r p +vflrh +++lyl+Y i+ a ++    + +  +W++ d
  gi|119720462|ref|YP_920957.1|  94 GVAYRGPTVVFLRHRSGPLYLWYEIIDARLIRRYNDRIGQVWLDYD 139
                                    5789**********************99999888777777776655 PP

>> DUF3849  Protein of unknown function (DUF3849)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   2.9e-05      0.26      66     107 ..     202     244 ..     196     259 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.9e-05
                        DUF3849  66 LantvqekdwDgrfseenkewaktiavpedkd.ernlefvvds 107
                                    La+ +++++ D+r  ee+k++ak++  +e    e++ efvv++
  gi|119720462|ref|YP_920957.1| 202 LAERIKKAMGDERCLEEAKRMAKEYLSEEGVRlETREEFVVNA 244
                                    8999*********************9999887999*****986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 3141.57
//
Query:       gi|119720463|ref|YP_920958.1|  [L=344]
Description: ABC transporter related [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-29  103.5   0.0    1.8e-29  103.0   0.0    1.3  1  ABC_tran      ABC transporter
    8.7e-12   45.5   0.0      2e-06   27.8   0.0    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    3.8e-09   37.1   0.0    8.2e-09   36.1   0.0    1.6  1  DUF4162       Domain of unknown function (DUF4162)
    0.00026   21.4   0.0    0.00078   19.9   0.0    1.8  1  AAA_16        AAA ATPase domain
     0.0016   18.2   0.0      0.003   17.3   0.0    1.4  1  AAA_30        AAA domain
     0.0085   15.8   0.0      0.018   14.8   0.0    1.5  1  AAA_29        P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.012   16.1   0.0       0.02   15.4   0.0    1.2  1  AAA_23        AAA domain
      0.017   15.4   0.0      0.042   14.1   0.0    1.9  1  AAA_22        AAA domain
      0.021   15.1   0.0      0.047   13.9   0.0    1.6  1  AAA_28        AAA domain
      0.029   14.0   0.0       0.05   13.2   0.0    1.3  1  AAA_27        AAA domain
      0.033   14.6   0.0      0.058   13.8   0.0    1.4  1  RNA_helicase  RNA helicase
      0.064   13.2   0.0       0.12   12.3   0.0    1.4  1  RsgA_GTPase   RsgA GTPase
      0.072   12.7   0.1       0.19   11.3   0.1    1.6  1  AAA_25        AAA domain
      0.085   13.3   0.1       0.54   10.7   0.1    2.3  1  AAA           ATPase family associated with various cellular 
      0.085   12.3   0.0       0.56    9.6   0.0    2.0  2  SMC_N         RecF/RecN/SMC N terminal domain
       0.11   12.1   0.0       0.18   11.4   0.0    1.4  1  ATP-synt_ab   ATP synthase alpha/beta family, nucleotide-bind
       0.16   11.9   0.0       0.25   11.2   0.0    1.2  1  ATPase_2      ATPase domain predominantly from Archaea
       0.16   11.9   0.0       0.26   11.2   0.0    1.3  1  NACHT         NACHT domain
       0.25    9.9   0.0       0.38    9.3   0.0    1.2  1  AAA_13        AAA domain
       0.27    8.7   0.0       0.36    8.3   0.0    1.0  1  DUF3584       Protein of unknown function (DUF3584)


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.0   0.0     2e-32   1.8e-29       1     136 [.      32     175 ..      32     176 .. 0.97

  Alignments for each domain:
  == domain 1  score: 103.0 bits;  conditional E-value: 2e-32
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren. 79 
                                    l+ vs+ ++ege++a++G+nGaGK+tL+++l+ + kp +G+ ++ g+++ + e  ++r+ ig++pqe +++ +lt +en 
  gi|119720463|ref|YP_920958.1|  32 LDGVSMVVEEGEIHAVLGPNGAGKTTLMRVLTTQIKPSSGDAWVLGRHVVK-EAARVREVIGYVPQEFSVWTDLTGYENa 110
                                    789******************************************999999.99************************** PP

                                    ............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    ............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                e+++ +e++l+ +gl e k++ v    +++SgG+ +r++l  al++kp++l+lDEpt
  gi|119720463|ref|YP_920958.1| 111 miyaklygvppsERRRVVEDMLEFMGLGEAKHRLV----KTYSGGMIRRLELGIALMTKPRVLFLDEPT 175
                                    **********8777777******************....*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.2e-05      0.01       2      19 ..      45      62 ..      44      78 .. 0.83
   2 !   27.8   0.0   2.2e-09     2e-06     238     297 ..     149     206 ..     112     209 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.2e-05
                         AAA_21  2 nvliGpNgsGKSnLLdal 19
                                    ++ GpNg+GK++L++ l
  gi|119720463|ref|YP_920958.1| 45 HAVLGPNGAGKTTLMRVL 62
                                   6899************99 PP

  == domain 2  score: 27.8 bits;  conditional E-value: 2.2e-09
                         AAA_21 238 SdGtkrllalltallralkkgsllliDEpEngLHPkllrrll.ellkelsrngaQviltTH 297
                                    S G+ r l l  al   +   ++l++DEp  gL+P++ + ++ ++l+++ ++g+ v++ TH
  gi|119720463|ref|YP_920958.1| 149 SGGMIRRLELGIALMTKP---RVLFLDEPTIGLDPRARELVWsRILEYAGEGGVTVVFNTH 206
                                    778888878888888766...******************999999999999********** PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.0   9.1e-12   8.2e-09       7      81 .]     236     318 ..     230     318 .. 0.79

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 9.1e-12
                                    HTTS.-SSEEEEE..--.-----..---EEEE-TT..S-EEEEE--.-----------.----EEEEEEEE---HHHHHH CS
                        DUF4162   7 Krsy.gknrieve..ad.aeelleepgveeveeeg..gelelkled.eeaanellkal.tsgveirsFeeeePsLndIFi 78 
                                     ++  g+ ++++e  ++ +++l +++gv+ ve     + ++l++ed e++   +++al  +gv+++++++++PsL+d+F+
  gi|119720463|ref|YP_920958.1| 236 VEKAgGGATVKIEfdGElEKALGALSGVRGVEVVSagNPVVLRVEDlEVQVAGVFRALlGNGVNVKKVSLQPPSLEDVFL 315
                                    555545667779976443555556678999977776577*******************77******************** PP

                                    HHH CS
                        DUF4162  79 ekv 81 
                                    +++
  gi|119720463|ref|YP_920958.1| 316 RLT 318
                                    975 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   8.7e-07   0.00078      25     143 ..      43     173 ..      30     188 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 8.7e-07
                         AAA_16  25 elvllsGesGvGKsslvrellralekd..ggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekle 102
                                    e+  + G+ G GK++l+r l ++++ +  ++++l  + ++            a+  +e++  + +e     ++ w +   
  gi|119720463|ref|YP_920958.1|  43 EIHAVLGPNGAGKTTLMRVLTTQIKPSsgDAWVLGRHVVKE-----------AARVREVIGYVPQE-----FSVWTDLT- 105
                                    78889**********************74355555555555...........44444777777777.....55555522. PP

                         AAA_16 103 eala......avpelagaeasrllellkrllallsrder......................plvlvlDd 143
                                      ++          ++++e++r+ e + +++ l + ++r                      p vl+lD+
  gi|119720463|ref|YP_920958.1| 106 -GYEnamiyaKLYGVPPSERRRVVEDMLEFMGLGEAKHRlvktysggmirrlelgialmtkPRVLFLDE 173
                                    .22224555577788999999999999999999998666888888888888888888888888888885 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   3.4e-06     0.003      14      63 ..      39      88 ..      33     128 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.4e-06
                         AAA_30 14 ltsgdrvavltGpAGtGKttalkalreaweaa.ggrviglAptgkaAkvLa 63
                                   +++g  ++++ Gp G+GKtt++++l+  ++ + g   ++  +  k A++++
  gi|119720463|ref|YP_920958.1| 39 VEEG-EIHAVLGPNGAGKTTLMRVLTTQIKPSsGDAWVLGRHVVKEAARVR 88
                                   4444.599*****************88777764633333333334444444 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0     2e-05     0.018      13      41 ..      33      61 ..      30      72 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2e-05
                         AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDA 41
                                   dg ++ +++ +++ + Gp+G+GK+Tl+  
  gi|119720463|ref|YP_920958.1| 33 DGVSMVVEEGEIHAVLGPNGAGKTTLMRV 61
                                   566677775559**************954 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.0   2.2e-05      0.02      23      40 ..      46      63 ..      29      65 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.2e-05
                         AAA_23 23 lItGpNGaGKTTildAik 40
                                   ++ GpNGaGKTT+++ ++
  gi|119720463|ref|YP_920958.1| 46 AVLGPNGAGKTTLMRVLT 63
                                   678***********9876 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   4.6e-05     0.042       6      43 ..      43      91 ..      39     229 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.6e-05
                         AAA_22  6 gilvvtGesGtGKTtllrrlleqldeeakaee...........erpevv 43
                                    i +v G+ G+GKTtl+r l+ q +  +  ++           + +ev+
  gi|119720463|ref|YP_920958.1| 43 EIHAVLGPNGAGKTTLMRVLTTQIKPSSGDAWvlgrhvvkeaaRVREVI 91
                                   567899***************9985544444476666666665444444 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   5.2e-05     0.047       3      32 ..      46      86 ..      44      91 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.2e-05
                         AAA_28  3 vitGgestGKTtlleaLaar...........gypvvpEaar 32
                                   +++G+ ++GKTtl++ L+ +           g  vv+Eaar
  gi|119720463|ref|YP_920958.1| 46 AVLGPNGAGKTTLMRVLTTQikpssgdawvlGRHVVKEAAR 86
                                   789***************66666666777889999999998 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   5.5e-05      0.05      24      47 ..      40      63 ..      32      70 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.5e-05
                         AAA_27 24 eeadlhliyGpNEAGKstalrAis 47
                                   ee ++h ++GpN AGK+t++r ++
  gi|119720463|ref|YP_920958.1| 40 EEGEIHAVLGPNGAGKTTLMRVLT 63
                                   57789**************99775 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   6.5e-05     0.058       3      62 ..      47     108 ..      45     119 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.5e-05
                   RNA_helicase   3 lyGpsgeGKStlakeLakallkklklkk..kdsvysrnpeddfwdgYtgqevvvidDfgqvk 62 
                                    + Gp+g GK+tl++ L++++  ++++ +    +v+  +++   + gY  qe+ v+ D+   +
  gi|119720463|ref|YP_920958.1|  47 VLGPNGAGKTTLMRVLTTQIKPSSGDAWvlGRHVVKEAARVREVIGYVPQEFSVWTDLTGYE 108
                                    68******************977744441134455566677777888888888888886655 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00013      0.12      94     124 ..      36      67 ..      21      89 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                                    HHHCTT.SEEEEECSTTSSHHHHHHHHCTT-- CS
                    RsgA_GTPase  94 kellkd.ktsvlvGqSGvGKStLinallpele 124
                                    + ++++ ++ +++G+ G+GK+tL+ +l+ + +
  gi|119720463|ref|YP_920958.1|  36 SMVVEEgEIHAVLGPNGAGKTTLMRVLTTQIK 67 
                                    5555555999*****************98865 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00021      0.19      29      66 ..      38      79 ..      32      90 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00021
                         AAA_25 29 llpagelallaGapgtGKttlaldlalava..tGkpwlg..p 66
                                   ++ +ge++++ G+ g+GKttl   l   +   +G+ w    +
  gi|119720463|ref|YP_920958.1| 38 VVEEGEIHAVLGPNGAGKTTLMRVLTTQIKpsSGDAWVLgrH 79
                                   6789*****************999998888878888866543 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1    0.0006      0.54       3      23 ..      47      67 ..      46     175 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0006
                                   EESSTTSSHHHHHHHHHHHHT CS
                            AAA  3 lyGppGtGKTllakavakelg 23
                                   + Gp G GKT+l++ + ++++
  gi|119720463|ref|YP_920958.1| 47 VLGPNGAGKTTLMRVLTTQIK 67
                                   57**************99975 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00062      0.56      24      42 ..      42      60 ..      21      82 .. 0.84
   2 ?    0.1   0.0      0.51   4.6e+02     157     210 ..     165     216 ..     152     225 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00062
                                   SSEEEEEESTTSSHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxx RF
                          SMC_N 24 ksftaivGpNGSGKsnlld 42
                                    ++ a++GpNG+GK+ l+ 
  gi|119720463|ref|YP_920958.1| 42 GEIHAVLGPNGAGKTTLMR 60
                                   45899**********9986 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.51
                                    S--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 157 kpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadklvg 210
                                    kp+ l +lDe    LD + ++ v +++ e   +  + v+ ++++ + +a+++ g
  gi|119720463|ref|YP_920958.1| 165 KPRVL-FLDEPTIGLDPRARELVWSRILEYAGEGGVTVV-FNTHYMDEAERFAG 216
                                    44444.58***************9999998877666555.66666677777665 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0    0.0002      0.18       1      88 [.      28     215 ..      28     229 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0002
                                    SSHHHHHHS-EB.TT-EEEEEESTTSSHHHHHHHHHHHSSTS..SEEEEEE............................. CS
                                    xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxx............................. RF
                    ATP-synt_ab   1 GirvlDalfpiv.qGqrtlipgafgvGktvisqslskqsnsd..daiiyvg............................. 48 
                                    G+r+lD +  +v +G+  +++g +g Gkt++++ l+ q + +  da ++                               
  gi|119720463|ref|YP_920958.1|  28 GVRALDGVSMVVeEGEIHAVLGPNGAGKTTLMRVLTTQIKPSsgDAWVLGRhvvkeaarvrevigyvpqefsvwtdltgy 107
                                    899***9987772578889*************999988765544466665566666667777777777777777777777 PP

                                    ....................................................................ESEEHHHHHHHH CS
                                    ....................................................................xxxxxxxxxxxx RF
                    ATP-synt_ab  49 ....................................................................iGergnevaevl 60 
                                                                                                        iG   +  + v+
  gi|119720463|ref|YP_920958.1| 108 enamiyaklygvppserrrvvedmlefmglgeakhrlvktysggmirrlelgialmtkprvlfldeptIGLDPRARELVW 187
                                    77777777777777777777777777777777777777777777777777777777777777777776666666666666 PP

                                    HHCHHSSGGGGEEEEEEETTS-HHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    ATP-synt_ab  61 eefpegtimkrtvlvantsnepvaarea 88 
                                    +++ e      +++v+nt  +  a+r+a
  gi|119720463|ref|YP_920958.1| 188 SRILEYAGEGGVTVVFNTHYMDEAERFA 215
                                    6666666666666666666666666665 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00028      0.25      14      43 ..      38      65 ..      28      79 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00028
                       ATPase_2 14 ilerepneiyfiYGpegsGKtaLlkeiien 43
                                   ++e+   ei  + Gp g GKt+L++ + ++
  gi|119720463|ref|YP_920958.1| 38 VVEE--GEIHAVLGPNGAGKTTLMRVLTTQ 65
                                   5555..7899**************987665 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00029      0.26       4      25 ..      46      67 ..      43      75 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00029
                                   EEEC-TTTCHHHHHHHHHHHHC CS
                          NACHT  4 ilqGeaGsGKTtLlqklalawa 25
                                   ++ G++G GKTtL++ l ++++
  gi|119720463|ref|YP_920958.1| 46 AVLGPNGAGKTTLMRVLTTQIK 67
                                   689************9998877 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00043      0.38      21      39 ..      47      65 ..      37      80 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00043
                         AAA_13 21 iYGwNGaGKTtLSrllrsl 39
                                   + G NGaGKTtL r+l  +
  gi|119720463|ref|YP_920958.1| 47 VLGPNGAGKTTLMRVLTTQ 65
                                   77************99875 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0004      0.36      22      37 ..      47      62 ..      35      63 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0004
                        DUF3584 22 ieGtNaaGKTtLlrLi 37
                                   + G N+aGKTtL+r++
  gi|119720463|ref|YP_920958.1| 47 VLGPNGAGKTTLMRVL 62
                                   6799**********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2478.61
//
Query:       gi|119720464|ref|YP_920959.1|  [L=252]
Description: ABC-2 type transporter [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-34  119.1  13.9    1.7e-34  119.1  13.9    1.4  2  ABC2_membrane    ABC-2 type transporter
    2.4e-15   56.5  17.7    2.9e-15   56.2  17.7    1.0  1  ABC2_membrane_3  ABC-2 family transporter protein
    2.7e-07   30.1  17.0    3.5e-07   29.8  17.0    1.1  1  ABC2_membrane_2  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.1  13.9   2.9e-38   1.7e-34      10     209 ..      13     217 ..       5     218 .. 0.90
   2 ?   -3.4   0.2      0.88   5.2e+03     142     154 ..     232     244 ..     225     249 .. 0.58

  Alignments for each domain:
  == domain 1  score: 119.1 bits;  conditional E-value: 2.9e-38
                  ABC2_membrane  10 eflqrwrdpslgllwrliqplllalvfgtvfgnlg....nsedglnr..pgllffsvlflafsaltsvapvferergvle 83 
                                    e+++  +dp+   ++r +qp l++ vfgtv +++      s d+l++  pg+l+ s+ f+a  ++ ++++v+er+ g+l+
  gi|119720464|ref|YP_920959.1|  13 ELRRLRHDPTEV-FTRAVQPALWIGVFGTVMSRVRaiptGSVDYLTFiaPGVLMQSTSFIA--IAYGIMLVWERDSGILK 89 
                                    677777777666.********************7754433444444499************..***************** PP

                  ABC2_membrane  84 relvsplyslsayvlakvlvelpvsllqalifllivyflvgldls....rfflflllllltalaasslgllisalapsfe 159
                                    r l+ p+  ++ +vl++ l+ ++++l q +++lli+++l g +l+    + +l+ l++++++  +++l++++++ +++ e
  gi|119720464|ref|YP_920959.1|  90 RVLTLPV-NRFLIVLGRSLSGATRALSQLFVVLLIALPL-GARLNvnplALCLAALAVYVCSTGLTALSIIMASAMKTRE 167
                                    *******.******************************9.999998555558888888888888999************* PP

                  ABC2_membrane 160 dasqlaslvllpllllsGffipidsmpkwlqwiaylnPltyavealrsnl 209
                                     ++ +++++++pl+++s +++p++ mp+ lq+++ +nPlty+++alr++l
  gi|119720464|ref|YP_920959.1| 168 RFMGIIQAITMPLFFTSNALYPVEFMPQPLQYVSLFNPLTYTIQALRASL 217
                                    **************************99*******************986 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 0.88
                  ABC2_membrane 142 laasslgllisal 154
                                    la+ sl++l++a 
  gi|119720464|ref|YP_920959.1| 232 LATFSLAMLLAAT 244
                                    4455555555554 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.2  17.7   4.9e-19   2.9e-15     155     344 ..      51     244 ..      39     245 .. 0.84

  Alignments for each domain:
  == domain 1  score: 56.2 bits;  conditional E-value: 4.9e-19
                ABC2_membrane_3 155 elsnvasflvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilllafgl..g 232
                                     + ++  f+++ +l+ + +++a+    ++v E+ s+i+++ l+ +v+++ ++l++ l+ ++ +l ql+++ll+a+ l   
  gi|119720464|ref|YP_920959.1|  51 GSVDYLTFIAPGVLMQSTSFIAIAYGIMLVWERDSGILKRVLTLPVNRFLIVLGRSLSGATRALSQLFVVLLIALPLgaR 130
                                    5678889999988888877777777779******************************************9997775333 PP

                ABC2_membrane_3 233 ipfg.nlglllllfllfgl...ayialgyllsslfknsetaqilifivilllsgffgglfpledlpsalkwifsiiPffa 308
                                    +  + n ++l+l  l  +     ++al+  + s++k+ e  +++i +++++l++ + +l+p+e +p +l++++ ++P+++
  gi|119720464|ref|YP_920959.1| 131 L--NvNPLALCLAALAVYVcstGLTALSIIMASAMKTRERFMGIIQAITMPLFFTSNALYPVEFMPQPLQYVSLFNPLTY 208
                                    3..3555555544444444011567778889999********************************************** PP

                ABC2_membrane_3 309 pglgllrlitgdplweillsliilalfavvylllal 344
                                     +++l   + +  +w++l + +ila f++++ll+a 
  gi|119720464|ref|YP_920959.1| 209 TIQALRASLIYCDYWSTLANTGILATFSLAMLLAAT 244
                                    *****888765579*****************99985 PP

>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8  17.0   5.9e-11   3.5e-07      87     276 ..      70     244 ..      29     249 .. 0.74

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 5.9e-11
                ABC2_membrane_2  87 viaalfgadaiagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvllalaiilalgivlaledllllvv 166
                                    +ia++ g+  ++ E+++g lk+ L++Pv R  i+lg  ++g++     +  l+++    l+i l lg  l++  l l ++
  gi|119720464|ref|YP_920959.1|  70 FIAIAYGIM-LVWERDSGILKRVLTLPVNRFLIVLGRSLSGATR---ALSQLFVV----LLIALPLGARLNVNPLALCLA 141
                                    567788874.567*****************************99...44444444....335677777777777776666 PP

                ABC2_membrane_2 167 asvlllllvvflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavpqeindflsllsptsayntll 246
                                    a  +++  + ++al++ ++s ++++++ + +  ++  + +++ +++ly+v  ++++ ++       +sl++p  +  ++l
  gi|119720464|ref|YP_920959.1| 142 ALAVYVCSTGLTALSIIMASAMKTRERFMGIIQAI-TMPLFFTSNALYPVEFMPQPLQY-------VSLFNPLTYTIQAL 213
                                    655555555469***********666666665555.5666*********9999999999.......9*****88755555 PP

                ABC2_membrane_2 247 neilagsdlna.lgstatnllilllllavll 276
                                    ++ l   d ++ l+ t+  + ++l++l++ +
  gi|119720464|ref|YP_920959.1| 214 RASLIYCDYWStLANTGILATFSLAMLLAAT 244
                                    5555555466655555555555555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1734.59
//
Query:       gi|119720465|ref|YP_920960.1|  [L=233]
Description: transcriptional regulator, TrmB [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    7.1e-22   77.1   0.4    2.8e-21   75.1   0.1    2.2  2  TrmB        Sugar-specific transcriptional regulator TrmB
    0.00038   20.4   0.0     0.0012   18.8   0.0    2.0  1  HTH_29      Winged helix-turn helix
     0.0015   18.3   0.3     0.0059   16.4   0.0    2.2  2  HTH_IclR    IclR helix-turn-helix domain
      0.004   17.5   0.0      0.011   16.1   0.0    1.7  1  Rrf2        Transcriptional regulator
     0.0077   16.2   0.2        0.4   10.7   0.0    2.6  2  HTH_Crp_2   Crp-like helix-turn-helix domain
  ------ inclusion threshold ------
      0.011   15.8   0.0      0.027   14.6   0.0    1.6  1  HTH_28      Helix-turn-helix domain
       0.02   15.3   0.1        4.1    7.9   0.0    2.3  2  FaeA        FaeA-like protein
      0.024   14.5   0.1       0.13   12.1   0.1    2.0  2  ATP-synt_D  ATP synthase subunit D
      0.032   14.4   0.8      0.057   13.6   0.8    1.4  1  DUF3958     Protein of unknown function (DUF3958)
      0.079   12.8   0.0       0.18   11.6   0.0    1.7  1  HTH_23      Homeodomain-like domain
       0.18   12.4   0.3       0.39   11.3   0.3    1.5  1  BST2        Bone marrow stromal antigen 2


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.1   0.1   1.7e-24   2.8e-21       1      68 []      17      84 ..      17      84 .. 0.98
   2 ?   -1.8   0.0       1.8     3e+03       8      22 ..     200     214 ..     199     216 .. 0.81

  Alignments for each domain:
  == domain 1  score: 75.1 bits;  conditional E-value: 1.7e-24
                                   HHHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE--HH CS
                           TrmB  1 LqklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYravdpe 68
                                   L+ lG+s yE+k+YlaLl +g at++e+a  +g++++k+Y+vL+sLe+kGl   ++grp +++a+dpe
  gi|119720465|ref|YP_920960.1| 17 LASLGFSRYEIKAYLALLIRGVATVSEVADLSGISYTKAYDVLSSLENKGLLASVPGRPLRFQALDPE 84
                                   678***************************************************************97 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.8
                                    HHCCCHCHHHHHHCC CS
                           TrmB   8 eyEakvYlaLlklgp 22 
                                    + Ea  Y++++++++
  gi|119720465|ref|YP_920960.1| 200 DVEANSYTVVVNSER 214
                                    579999**9998876 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   7.6e-07    0.0012       5      47 ..      31      74 ..      28      86 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 7.6e-07
                         HTH_29  5 llllaeGvstvsqiAkllglsrrtvyrwlkrfeegGlaalld.r 47
                                   l+ll +Gv tvs++A l g+s+++ y++l   e++Gl a  + r
  gi|119720465|ref|YP_920960.1| 31 LALLIRGVATVSEVADLSGISYTKAYDVLSSLENKGLLASVPgR 74
                                   788999******************************87766533 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   3.6e-06    0.0059      19      50 ..      39      70 ..      29      72 .. 0.88
   2 ?   -2.3   0.1       2.4     4e+03       6      14 ..     220     228 ..     219     231 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.6e-06
                                   -BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                       HTH_IclR 19 ltlselArrtglpkStvhRlLqtLvelGyveq 50
                                    t+se+A+ +g++ ++++  L++L++ G++  
  gi|119720465|ref|YP_920960.1| 39 ATVSEVADLSGISYTKAYDVLSSLENKGLLAS 70
                                   38***************************975 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.4
                                    HHHHCT-CT CS
                       HTH_IclR   6 laiLdalae 14 
                                    l++L+al+ 
  gi|119720465|ref|YP_920960.1| 220 LRLLEALRG 228
                                    677888765 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   6.7e-06     0.011      16      61 ..      30      74 ..      23      76 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 6.7e-06
                                   HHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT CS
                           Rrf2 16 yLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvrGk 61
                                   yLa+  ++  ++++e+a+  +is + +  +l+ L+++gl+ sv G+
  gi|119720465|ref|YP_920960.1| 30 YLALLIRGV-ATVSEVADLSGISYTKAYDVLSSLENKGLLASVPGR 74
                                   677777765.9*********************************97 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   0.00024       0.4      23      63 ..      40      84 ..      12      85 .. 0.82
   2 ?    2.7   0.2     0.075   1.2e+02       1      12 [.     213     224 ..     213     232 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00024
                                   HHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.E.TE..EEEES-HH CS
                      HTH_Crp_2 23 tqeelAsmlGltretvsrilseLkreglis.r.gr..ririldle 63
                                   t  e A++ G++      +ls L+++gl+    gr  r++ ld+e
  gi|119720465|ref|YP_920960.1| 40 TVSEVADLSGISYTKAYDVLSSLENKGLLAsVpGRplRFQALDPE 84
                                   67899************************9733532226666665 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.075
                                    HHHHHHHHHHHC CS
                      HTH_Crp_2   1 qRlArfLlrlae 12 
                                    +RlA +Llrl e
  gi|119720465|ref|YP_920960.1| 213 ERLAGLLLRLLE 224
                                    7********943 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.6e-05     0.027       7      51 ..      32      75 ..      27      75 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.6e-05
                         HTH_28  7 kllaaGh.svreaArelgisrrtvyrWikryeegGiagLvprrrrp 51
                                    ll++G+ +v+e+A + gis++  y+ ++ +e  G+  L+  ++rp
  gi|119720465|ref|YP_920960.1| 32 ALLIRGVaTVSEVADLSGISYTKAYDVLSSLENKGL--LASVPGRP 75
                                   56789****************************998..66666665 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1     0.012        20      16      39 ..      11      34 ..       6      38 .. 0.86
   2 ?    7.9   0.0    0.0025       4.1      14      50 ..      37      73 ..      34      75 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.012
                                   --HHHHHHHHTS-HHHHHHHHHHH CS
                           FaeA 16 ckTreiAdalglsaYQaRyYLeqL 39
                                    +  e+   lg s Y ++ YL  L
  gi|119720465|ref|YP_920960.1| 11 SRVEEVLASLGFSRYEIKAYLALL 34
                                   577899999************998 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0025
                                   ----HHHHHHHHTS-HHHHHHHHHHHHHHSSEEEE-- CS
                           FaeA 14 apckTreiAdalglsaYQaRyYLeqLekegkikrspv 50
                                   + ++ +e+Ad  g+s   a   L  Le +g +  +p 
  gi|119720465|ref|YP_920960.1| 37 GVATVSEVADLSGISYTKAYDVLSSLENKGLLASVPG 73
                                   556779************************9998885 PP

>> ATP-synt_D  ATP synthase subunit D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   7.9e-05      0.13      15      84 ..      87     154 ..      81     179 .. 0.84
   2 ?   -0.3   0.0      0.48   7.9e+02      66      99 ..     192     224 ..     182     230 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.9e-05
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSTSTTSTSHHHHHHHSSS.SS-..TSS-SE CS
                     ATP-synt_D  15 ghslLkkKrdaLilefreilkelkelreeleeelkeayfslaeafaaggeediesavlesvklakvvkve 84 
                                    +++lL+++r++L+ e++++ +++ e+  el++ ++  + s    f++ ge+++  +v+e  + a+ + v 
  gi|119720465|ref|YP_920960.1|  87 MRNLLERRRSELLGEIKRLEEKVSEATSELRKLYSPEARSPV--FLVRGERALPTLVQEALRSAEATVVC 154
                                    679*****************************9997777766..78888999999999988877744444 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.48
                                    HHHHSSS.SS-..TSS-SEEEEEEBTTSEEEEEE CS
                     ATP-synt_D  66 diesavlesvklakvvkvelktenvaGVkvpvfe 99 
                                    ++e +v+e+v+ a++++v +++e +aG+ +  +e
  gi|119720465|ref|YP_920960.1| 192 RVEVYVKEDVE-ANSYTVVVNSERLAGLLLRLLE 224
                                    57778899998.555**********999877665 PP

>> DUF3958  Protein of unknown function (DUF3958)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.8   3.5e-05     0.057      68     107 .]      80     119 ..      73     119 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.5e-05
                        DUF3958  68 vqrlsrklredLEeeeeeLkrekrqLedqeeelyyekrkl 107
                                    +   +  +r+ LE+ + eL  e ++Le++++e ++e rkl
  gi|119720465|ref|YP_920960.1|  80 ALDPETAMRNLLERRRSELLGEIKRLEEKVSEATSELRKL 119
                                    5566778999****************************97 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00011      0.18       6      46 ..      27      67 ..      15      72 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00011
                         HTH_23  6 eRlrillllaeGlsvreIAreLgvsrrTvyrwlkryreeGl 46
                                   +++  +ll +  ++v+e+A++ g+s+   y +l+  +++Gl
  gi|119720465|ref|YP_920960.1| 27 IKAYLALLIRGVATVSEVADLSGISYTKAYDVLSSLENKGL 67
                                   4555555556599*********************9977994 PP

>> BST2  Bone marrow stromal antigen 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.3   0.00024      0.39      53      90 ..      80     117 ..      77     118 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00024
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC CS
                           BST2  53 sLekekaqsqkqqakvqelqgeikkLnqkLqdaeaeve 90 
                                    +L+ e+a  +  +++  el geik+L++k+ +a  e++
  gi|119720465|ref|YP_920960.1|  80 ALDPETAMRNLLERRRSELLGEIKRLEEKVSEATSELR 117
                                    7889999999999********************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       733  (0.0408835); expected 358.6 (0.02)
Passed bias filter:                      651  (0.0363099); expected 358.6 (0.02)
Passed Vit filter:                       103  (0.00574488); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 1654.07
//
Query:       gi|119720466|ref|YP_920961.1|  [L=237]
Description: putative circadian clock protein, KaiC [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.9e-26   91.2   0.0      7e-26   91.0   0.0    1.1  1  ATPase    KaiC
  ------ inclusion threshold ------
      0.044   12.8   0.0      0.058   12.4   0.0    1.1  1  FMN_dh    FMN-dependent dehydrogenase
      0.069   13.0   0.0       0.14   12.0   0.0    1.6  1  MEDS      MEDS: MEthanogen/methylotroph, DcmR Sensory domain
      0.082   12.0   0.0       0.49    9.5   0.0    1.9  2  PAXNEB    PAXNEB protein


Domain annotation for each model (and alignments):
>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.0   0.0   1.6e-29     7e-26       2     138 ..       5     149 ..       4     181 .. 0.84

  Alignments for each domain:
  == domain 1  score: 91.0 bits;  conditional E-value: 1.6e-29
                         ATPase   2 ktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekleeeg 81 
                                    +tgI+glDe l+gG+p+ ++vl++G+ G+ K +fa++ l++g+ + ge+g++vtv+  +ed+ en+++ G+  +++ eeg
  gi|119720466|ref|YP_920961.1|   5 RTGIKGLDEALEGGLPRPSSVLVAGSIGSKKNTFAQRILYEGLLE-GEKGIYVTVDLFPEDIVENMEKYGMSARRFIEEG 83 
                                    7********************************************.********************************** PP

                         ATPase  82 klaiidasesaeesaee.....kdkedleelieelaeaikeika....krvviDsitglayeekea 138
                                    +l++id ++ + + +++     ++ +dl+e+++e+  a +e+ +     r+vi  +++l  +++++
  gi|119720466|ref|YP_920961.1|  84 RLVFIDCFSPRVGVESSarylvENPFDLDEVLREIVVAKREFLEpgdrYRLVISHLSTLFFSASKE 149
                                    ***********9987778877777777777777776666666445655778888887775555555 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.3e-05     0.058     276     338 ..      15      77 ..       9      86 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.3e-05
                                    EESS--SHHHHHHHHHTT-SEEEESHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-SBH CS
                         FMN_dh 276 vDgGirrGsDvlkAlalGAdavllGRpflyglaagGeeGvervleilraelertmallGvksv 338
                                    + gG  r s vl A  +G +   ++  +ly   ++Ge+G+  +++++ +++ ++m+  G++  
  gi|119720466|ref|YP_920961.1|  15 LEGGLPRPSSVLVAGSIGSKKNTFAQRILYEGLLEGEKGIYVTVDLFPEDIVENMEKYGMSAR 77 
                                    679*******************************************************99765 PP

>> MEDS  MEDS: MEthanogen/methylotroph, DcmR Sensory domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   3.2e-05      0.14      21      68 ..      43      90 ..      37     151 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.2e-05
                           MEDS 21 ikaglargekvlyvasastldelrealrkagldvdaalesgqleilda 68
                                   + +gl +gek +yv+ +   +++ e ++k+g+ + ++ e+g+l ++d+
  gi|119720466|ref|YP_920961.1| 43 LYEGLLEGEKGIYVTVDLFPEDIVENMEKYGMSARRFIEEGRLVFIDC 90
                                   568*****************************************9997 PP

>> PAXNEB  PAXNEB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00011      0.49      21      83 ..       6      67 ..       4      76 .. 0.77
   2 ?    0.2   0.0      0.07   3.2e+02     208     281 ..     131     196 ..     107     200 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00011
                         PAXNEB 21 tGtpsLDklLgGGLplGsillie...EdgttdfakvLlkyFlAeGvvqkhevlvlsldddpeewlr 83
                                   tG++ LD+ L GGLp  s++l+     +++++fa+ +    l eG++++ + +++++d  pe++++
  gi|119720466|ref|YP_920961.1|  6 TGIKGLDEALEGGLPRPSSVLVAgsiGSKKNTFAQRI----LYEGLLEGEKGIYVTVDLFPEDIVE 67
                                   9*********************933334555555544....4588888888888888777777765 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.07
                         PAXNEB 208 vlRivipsLlspllydyppeeskpedllkFLhsLrallrssnlvalitlplsliarssslvrkieqlvDtvieL 281
                                      R+vi  L    +      ++++e +  F+  L a +r+s+ + ++  +  ++  ++++   +++l D v+eL
  gi|119720466|ref|YP_920961.1| 131 RYRLVISHLSTLFF------SASKELIPGFIGRLHAEARRSRGIHVMVYSEGVL--NKHYECFLKSLPDVVFEL 196
                                    46777766654444......5677777888888888888888888888877777..666666777777777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1712.36
//
Query:       gi|119720467|ref|YP_920962.1|  [L=493]
Description: anion transporter [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      3e-83  280.5  40.0    3.7e-83  280.2  40.0    1.0  1  Na_sulph_symp  Sodium:sulfate symporter transmembrane region
    7.1e-24   84.5  31.8    7.1e-24   84.5  31.8    1.8  2  CitMHS         Citrate transporter


Domain annotation for each model (and alignments):
>> Na_sulph_symp  Sodium:sulfate symporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  280.2  40.0   4.1e-87   3.7e-83       9     471 ..      20     484 ..      14     485 .. 0.93

  Alignments for each domain:
  == domain 1  score: 280.2 bits;  conditional E-value: 4.1e-87
                  Na_sulph_symp   9 lllvvlliilllPapdgleskawrllaifiaaivglileplplavialialsllavligvlaakalsevlsgfssdttlL 88 
                                    l++++ll i l+P+p gl++ ++r la+f++a + + + p+p   ++l+a++ll++ +g+      +++ +   +d+++L
  gi|119720467|ref|YP_920962.1|  20 LAIFALLAISLMPTPPGLTVWGQRALAVFTFALILWLTSPIPFWLTSLLAIALLPITGGYSV----TSTFQQLGQDVIWL 95 
                                    679999***************************************************99988....999999******** PP

                  Na_sulph_symp  89 vfaalliaaavektgLgkRiAlvlvkivGkrtliLgyalvladlllapatpsntAraggivfpvikslssafgsepekqs 168
                                    ++ a+++++a+ektg+gkR+A++l+ ++G ++     +l+l++l+la ++ps+tAra +i++p+   +++a++ +p ++ 
  gi|119720467|ref|YP_920962.1|  96 MVCAFILSSAMEKTGIGKRLAYRLLLVFGGSPSLTLLGLILINLALAFVVPSTTARA-SIMLPIALLIAEAYNLKPGES- 173
                                    ********************************77788*******************7.5777**************995. PP

                  Na_sulph_symp 169 erkigaylmltvvqsasitsiaflTamApNllllglinsilgveitwasWflaaiptgvillllvplllyvlyppeikkk 248
                                      + g++lm+   +++ ++ +++lTa+Ap +l+ ++++ ++gve+ w+ W++a +p+ +++l++ +++  +l+ppei ++
  gi|119720467|ref|YP_920962.1| 174 --NYGKILMMQQPMANNLSTSMILTATAPQILAWSFLKGMAGVEVPWLTWLVAQMPVILVMLVVLWIVGLKLFPPEIGST 251
                                    ..57*************************************************************************888 PP

                  Na_sulph_symp 249 e..eakavaktelkelGpltarekallilfvlllllWifge.......slnidattvaivvlvillllrvldWkDivkqk 319
                                       e  a  k+elk +Gpl+++ek  l++f+l+l+lW++++        l i  +  a+++ ++l+l+++   k     k
  gi|119720467|ref|YP_920962.1| 252 AstEWRAKLKEELKSMGPLSREEKYTLAVFLLVLFLWATDQwhevmfaGLSIPYALAAVIGASLLFLPKLGPLKKWGDAK 331
                                    6335667789******************************977666444449*****************5555555589* PP

                  Na_sulph_symp 320 taWntllllgglialakllersgliewlgnklttsls...glspavaiiiilslfvlvhylfaSatAttaallpillava 396
                                     +W+ +++ +g +a+   l+ sg  +wl  +l++ l    g+   va + +l l++++h++f+S+t  ta+++p+ +a+a
  gi|119720467|ref|YP_920962.1| 332 IPWDLMIFSAGAYAVGLALNDSGGGQWLVMQLVNALGlqkGVDLFVAYALLLALMLYSHVFFSSKTTRTAIFIPLYIALA 411
                                    *******************************998765333777788889999999************************* PP

                  Na_sulph_symp 397 qaipgappllvalllalatslagfllpyatgpnpivfgagylkvkdywrlGfilsiigllillllgalwwklLvl 471
                                     a+ g pp+ +al+ a+ +s   ++ py+  pn i+fg+gy+ ++d+ + G+ +  ig++++l +g  w ++L++
  gi|119720467|ref|YP_920962.1| 412 RAL-GLPPVAIALPAAFVISWD-LTFPYNCKPNLIYFGTGYFTMRDMIIYGLTICTIGYVLYLAVGWPWLNFLAS 484
                                    ***.*****************9.*******************************************888777765 PP

>> CitMHS  Citrate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.5  31.8     8e-28   7.1e-24       1     299 [.      52     425 ..      52     432 .. 0.82
   2 ?   -3.5   0.8       0.5   4.5e+03     207     225 ..     466     488 ..     443     489 .. 0.70

  Alignments for each domain:
  == domain 1  score: 84.5 bits;  conditional E-value: 8e-28
                                    xxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx RF
                         CitMHS   1 lvllileklrldvvallvlvll....vltieealsgiaspiillllgamiigaaleetGlfdrlaakllrlaggkrd.ll 75 
                                    l+l++++ ++  +++ll+++ll      +  + ++ ++ ++i+l++ a+i+++a+e+tG+ +rla +ll ++gg++   l
  gi|119720467|ref|YP_920962.1|  52 LILWLTSPIPFWLTSLLAIALLpitgGYSVTSTFQQLGQDVIWLMVCAFILSSAMEKTGIGKRLAYRLLLVFGGSPSlTL 131
                                    589*************99999997776666669999*****************************************989 PP

                                    xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxx...... RF
                         CitMHS  76 vllvlltallsafvsndgv.vlimipivlslakrlkklppl.......lliplalaaniggaltpiGtpttraa...... 141
                                    + l+l+   l+ +v  +++ + im+pi+l +a+   +l+p        l++   +a+n+  ++++  t + + a      
  gi|119720467|ref|YP_920962.1| 132 LGLILINLALAFVVPSTTArASIMLPIALLIAEA-YNLKPGesnygkiLMMQQPMANNLSTSMILTATAPQILAwsflkg 210
                                    99********9999997777*************8.6777777*****999999999999876666666654444999999 PP

                                    ....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                         CitMHS 142 ....arpglslpnllllalllvgllplvllfmfgvalalpvnap.........kvkkqkaiieaiarsllpvatillla. 207
                                        + p+l++++  ++++l+  l++l++++    +  +p++++         k k+  + +  ++r  +   +++ll+ 
  gi|119720467|ref|YP_920962.1| 211 magvEVPWLTWLVAQMPVILVM-LVVLWIVG----LKLFPPEIGstastewraKLKEELKSMGPLSREEKYTLAVFLLVl 285
                                    9887777777777777777666.88888888....566666666666677666666666666666666665555555556 PP

                                    ...........................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
                         CitMHS 208 ...........................................ykkveWsvlllfaGvfllvgaleqtGilealadll.g 243
                                                                                 k++W+++++ aG+  ++ al+++G +++l+  l +
  gi|119720467|ref|YP_920962.1| 286 flwatdqwhevmfaglsipyalaavigasllflpklgplkkwgDAKIPWDLMIFSAGAYAVGLALNDSGGGQWLVMQLvN 365
                                    777888888888888889999999999999999**********9*************************77777766644 PP

                                    x.....x.xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         CitMHS 244 a.....g.gplvalalvlglial.lsafisnvavaalmapialgmapalgllspsplalalav 299
                                    a     g  ++va+al+l+l+     +f s ++ +a+++p+ +++a alg   + p+a+al +
  gi|119720467|ref|YP_920962.1| 366 AlglqkGvDLFVAYALLLALMLYsHVFFSSKTTRTAIFIPLYIALARALG---LPPVAIALPA 425
                                    47677757899999888888888555666666668*************99...7777887765 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 0.5
                                    x....xxxxxxxxxxxxxxxxxx RF
                         CitMHS 207 a....ykkveWsvlllfaGvfll 225
                                    +    y +v W+ l ++a +++l
  gi|119720467|ref|YP_920962.1| 466 IgyvlYLAVGWPWLNFLASIGML 488
                                    13334888899999999888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (493 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       782  (0.0436165); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.41
# Mc/sec: 3575.35
//
Query:       gi|119720468|ref|YP_920963.1|  [L=289]
Description: hypothetical protein Tpen_1565 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.13   12.5   2.5        4.4    7.6   0.1    3.3  3  NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosi


Domain annotation for each model (and alignments):
>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1     0.072   1.3e+03      18      35 ..     111     131 ..     106     150 .. 0.62
   2 ?    7.6   0.1   0.00025       4.4      21      38 ..     182     200 ..     168     214 .. 0.73
   3 ?    2.6   0.1    0.0089   1.6e+02      40      62 ..     226     250 ..     221     261 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.072
                    NPCBM_assoc  18 taaatnvslslslP...eGWt 35 
                                    t+++++v+++l+ P   + W 
  gi|119720468|ref|YP_920963.1| 111 TKPLSRVEIALKKPvsgPKWA 131
                                    788999999999883222355 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00025
                    NPCBM_assoc  21 atnvslslslPeGWt.vve 38 
                                    + +v++++  P+GW+ v +
  gi|119720468|ref|YP_920963.1| 182 LPGVRIRVCPPSGWNaVYA 200
                                    5689***********4323 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.0089
                    NPCBM_assoc  40 spasaa..slapGetveatvkVtpp 62 
                                    + ++++  sl pG +++a+v+V p 
  gi|119720468|ref|YP_920963.1| 226 DEKTVTpkSLSPGSSFSAEVAVLPA 250
                                    455555569************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 2222.30
//
Query:       gi|119720469|ref|YP_920964.1|  [L=441]
Description: beta-lactamase domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      3e-11   43.6   0.0    6.3e-11   42.6   0.0    1.5  1  Beta-Casp      Beta-Casp domain
    1.5e-07   31.6   0.2    3.6e-07   30.4   0.2    1.7  1  Lactamase_B    Metallo-beta-lactamase superfamily
    9.2e-06   25.3   0.0    2.4e-05   24.0   0.0    1.7  2  Lactamase_B_2  Beta-lactamase superfamily domain
    3.8e-05   23.2   0.0    7.8e-05   22.2   0.0    1.4  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain
     0.0009   19.1   0.1     0.0025   17.7   0.0    1.8  2  RMMBL          Zn-dependent metallo-hydrolase RNA specificity


Domain annotation for each model (and alignments):
>> Beta-Casp  Beta-Casp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.6   0.0   1.7e-14   6.3e-11      21     110 .]     249     350 ..     233     350 .. 0.68

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 1.7e-14
                                    S-EEEEE-HHHHHHHHH..GGGGGGE-SHH.....HHHH..HH..............HS-SSEEEEES-TTSSSSHHHHH CS
                      Beta-Casp  21 klpiyldsplaskatev..Ykeyaeveaks.lewmeskkeeln..............sskgpkvilassgmlegGrsrel 83 
                                     +pi++  ++a+ + +v  Y+ y    + + le  ++k  +l+               + +p+v+la++ ml + +sr+ 
  gi|119720469|ref|YP_920964.1| 249 GAPIFVEKSIAEGVERVaaYEGY---VKPEfLEVAKRKP-HLAepfhvfskdevdevARVKPSVVLATDLMLME-TSRRF 323
                                    37999999999666555114555...3344444444442.222344555555555566679***********76.***** PP

                                    HHHHTTSTTSEEEESS---TTSHHHHH CS
                      Beta-Casp  84 lkklledprntvilvgyqaegTlgrkl 110
                                    ++kl edp ++vil+gyqa+gT+gr+l
  gi|119720469|ref|YP_920964.1| 324 FEKLREDPSSSVILTGYQAPGTFGRRL 350
                                    *************************97 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.2     1e-10   3.6e-07       5      98 ..      13     115 ..       9     194 .. 0.73

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 1e-10
                                    SSEEEEEEETTCEEEES--SCHHHHHHHH..HHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCC CS
                    Lactamase_B   5 pvnsyliegdggviLiDtGtsteaaraal..elaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapal 82 
                                    + ++  +e++g+ +++D G+   ++  ++   +++  ++  +v+av+++HlH DH ++++ lv++  + +++ ++ +++l
  gi|119720469|ref|YP_920964.1|  13 GRSCLALEHGGRYYVFDVGVKKVYSGGKYgePPFLGLIDAGKVEAVFVSHLHEDHLAAVPALVRRGFNGPIYMSAPTAEL 92 
                                    5689999*******************999955555567999***************************999999998888 PP

                                    HCHHHHHHHHHCCHH.......T CS
                    Lactamase_B  83 fmeeaddaasrkgll.......l 98 
                                         +++++ +++        +
  gi|119720469|ref|YP_920964.1|  93 GIKQWYKWTVLEEDGkplfteeD 115
                                    88887777777776655555432 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   6.7e-09   2.4e-05      27     116 ..      51     150 ..      40     191 .. 0.74
   2 ?   -3.5   0.0       1.7   6.3e+03     177     200 ..     379     403 ..     371     404 .. 0.69

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 6.7e-09
                                    -..SEEEEE-SS--HHHHGGGGCCCC..C--EEEEEEEEHHHHH..........HCCTTCGHHHCHTTTTEEEEEE-.TT CS
                  Lactamase_B_2  27 elppidaVllthaHyDHlaglltlre..lrpkklplyapkgvla..........vleanfvylaleeepavnvheld.wg 93 
                                    +  +++aV+++h H DHla ++ l +  +   + p+y ++ +++          vle+ +++l++ee++ ++++ ++  g
  gi|119720469|ref|YP_920964.1|  51 DAGKVEAVFVSHLHEDHLAAVPALVRrgF---NGPIYMSAPTAElgikqwykwtVLEEDGKPLFTEEDCDEARKMVKtVG 127
                                    55799*******************99432...469**9999999999999999999999999999999777666666323 PP

                                    SEEEECSTTEEEEEEEE-EE--C CS
                  Lactamase_B_2  94 esfelgdggleitatparhksgr 116
                                    +   +++g++e+ +++  h+ g 
  gi|119720469|ref|YP_920964.1| 128 DGSVVTSGDVEVAFHQSGHALGS 150
                                    33333445777777766666555 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.7
                                    T---STSHHHHCTTSS.SSEEEEES CS
                  Lactamase_B_2 177 gHltpeeaveaaadlg.akrlvliH 200
                                     H+++++ ve+++++   + lv++H
  gi|119720469|ref|YP_920964.1| 379 MHFDVRDNVELVQRTLkEEGLVVLH 403
                                    6999999999988754244555555 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   2.2e-08   7.8e-05      35     164 ..      54     170 ..      50     177 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 2.2e-08
                  Lactamase_B_6  35 tvdliLLshatlehlGayallyakfksklllnipvyatlpvvkLGrvslldlyaskgllgpedseeleledideafdkik 114
                                    +v+++ +sh   +hl+a + l+       + n p+y + p+++LG    +     +++l++  +  ++ ed dea + +k
  gi|119720469|ref|YP_920964.1|  54 KVEAVFVSHLHEDHLAAVPALVR-----RGFNGPIYMSAPTAELGIKQWYK----WTVLEEDGKPLFTEEDCDEARKMVK 124
                                    799**************887774.....3679*************655544....56777778888999*********** PP

                  Lactamase_B_6 115 tlkYsQklelkskldgltitaynaGhtlGGtiWkiskesekivYavdwnh 164
                                    t+     +  +    ++ +  +++Gh+lG  + ++s +  +++Ya d+n 
  gi|119720469|ref|YP_920964.1| 125 TVGDGSVV--T--SGDVEVAFHQSGHALGSMYMEVSVGGWSMLYAADINR 170
                                    *9744443..3..25799999***************************97 PP

>> RMMBL  Zn-dependent metallo-hydrolase RNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.8   6.3e+03      28      46 ..      52      70 ..      47      80 .. 0.74
   2 !   17.7   0.0   6.9e-07    0.0025       3      51 ..     367     417 ..     365     429 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.8
                          RMMBL 28 klkprnvilvHGeeeatsa 46
                                     k + v++ H +e++++a
  gi|119720469|ref|YP_920964.1| 52 AGKVEAVFVSHLHEDHLAA 70
                                   5566679999999998876 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 6.9e-07
                          RMMBL   3 pvkarieeidfSgHadknellelirklkprn..vilvHGeeeatsalarll 51 
                                    +  +r++++ +  H d ++  el++++ ++   v+l HGee    +la +l
  gi|119720469|ref|YP_920964.1| 367 RFSCRVYDVPVKMHFDVRDNVELVQRTLKEEglVVLHHGEEPNSTRLALHL 417
                                    6689***********************99999***************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 3022.01
//
Query:       gi|119720470|ref|YP_920965.1|  [L=429]
Description: phosphonopyruvate decarboxylase-related protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.3e-57  191.9   0.0      1e-56  191.4   0.0    1.2  1  PhosphMutase     2,3-bisphosphoglycerate-independent phosphog
    8.8e-37  126.8   0.0      1e-36  126.6   0.0    1.0  1  Metalloenzyme    Metalloenzyme superfamily
    5.1e-05   22.4   0.0    7.5e-05   21.8   0.0    1.2  1  Alk_phosphatase  Alkaline phosphatase
  ------ inclusion threshold ------
        0.1   12.7   0.0       0.32   11.1   0.0    1.9  1  DUF2384          Protein of unknown function (DUF2384)
       0.13   12.8   0.0        2.2    8.8   0.0    2.6  3  CoA_binding_2    CoA binding domain


Domain annotation for each model (and alignments):
>> PhosphMutase  2,3-bisphosphoglycerate-independent phosphoglycerate mutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.4   0.0   2.9e-60     1e-56       1     170 []      47     225 ..      47     225 .. 0.98

  Alignments for each domain:
  == domain 1  score: 191.4 bits;  conditional E-value: 2.9e-60
                                    HHTSEEEEEE-----------TCHHHHTT--HHCH---HHHHHHHHTT----TT-EEEEEEEEEEC....TTCEEETTGG CS
                   PhosphMutase   1 AkkGetGlldtvpegiapgSdvAnlsilGydpkkyytGRGplEAlgiGlelkpgdvafRcnlvtvdee..dgiiidrrag 78 
                                    A++G+tG++d +++g++pg+d+++++++Gydp ++y+GRGplEA+giG+elkpgdva+R+n++tv+ee  + i++drrag
  gi|119720470|ref|YP_920965.1|  47 AAEGVTGIMDVIEPGVRPGTDTGHMALFGYDPYRFYPGRGPLEAAGIGVELKPGDVALRANFATVREEggRLIVVDRRAG 126
                                    899***************************************************************9988889******* PP

                                    G-.-TTHHHHHHHT-EEE...TTEEEEEEE-STTEEEEEE....--S-B--S--..SSTTS------BS..SGGGHHHHH CS
                   PhosphMutase  79 risteeakeLikalneel.e.egvevkfypgveyrhllvl....lsdkitdtdpphdkegkeikellpl.kseeaketae 151
                                    ri  e+a++L+++lne++ + ++v+v+f++++ +r ++vl    ls +++d+dp   +eg++++e++pl +++e+++ta+
  gi|119720470|ref|YP_920965.1| 127 RIRGEDAEALTRYLNERIgSvDDVRVSFHHATAHRLVVVLrgdsLSPRVSDSDPGTAREGEPVREVKPLtNDPESERTAR 206
                                    *******************789***********************************************99********* PP

                                    HHHHHHHHHHHHHHHSHHH CS
                   PhosphMutase 152 llnelieksqeiLedhpvN 170
                                    +l +l+++++e Le  pvN
  gi|119720470|ref|YP_920965.1| 207 ILWKLLLRAHEELERCPVN 225
                                    ******************9 PP

>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.6   0.0   2.8e-40     1e-36       3     244 ..      13     416 ..      11     420 .. 0.97

  Alignments for each domain:
  == domain 1  score: 126.6 bits;  conditional E-value: 2.8e-40
                                    EEEEEETTBB----GGGTT...HHHS--HHHHHHHHH.......SEEEEEESSSTT----HHHHHHHH............ CS
                                    xxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............ RF
                  Metalloenzyme   3 vvlvvlDGlGeapadelna...ihvAktPtldkLkkeaPerwlikahgtavglpeddmgnsevgHlel............ 67 
                                     v+++lDGlG++p  el++   ++vA++Ptld+L++e       + +g++  ++ + ++++++gH++l            
  gi|119720470|ref|YP_920965.1|  13 SVVLILDGLGDRPVPELGGrtpLQVARKPTLDSLAAE-------GVTGIMDVIEPGVRPGTDTGHMALfgydpyrfypgr 85 
                                    689**********************************.......89********************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                  Metalloenzyme  68 ................................................................................ 67 
                                                                                                                    
  gi|119720470|ref|YP_920965.1|  86 gpleaagigvelkpgdvalranfatvreeggrlivvdrragrirgedaealtrylnerigsvddvrvsfhhatahrlvvv 165
                                    ******************************************************************************** PP

                                    .............................................................HHHHTT-----EEEEEEEE CS
                                    .............................................................xxxxxxxxxxxxxxxxxxx RF
                  Metalloenzyme  68 .............................................................lrisetvkfahvtffwngg 86 
                                                                                                  r++++  +a+ ++++++g
  gi|119720470|ref|YP_920965.1| 166 lrgdslsprvsdsdpgtaregepvrevkpltndpesertarilwklllraheelercpvneERVKRGLLPANAVLTRGAG 245
                                    *************************************************************999**************** PP

                                    -S--.-SSHHHHHT--EEEE--SHH....................STT--HHHHHHHHHHHH.CC.-SEEEEEE-HHHHH CS
                                    xxxx.xxxxxxxxxxxxxxxxxxxx....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  Metalloenzyme  87 rsgy.fnpleereeipsdtvitfdl....................qpemkavevaekaldailsgkfdlvvvniknaDmv 145
                                    + +y + p+ e+++  +  v++                         +++  +++++alda   g +++v++++k +D +
  gi|119720470|ref|YP_920965.1| 246 MVPYgIVPFREQFGATAYLVAEEATvlgvarilgiegeipggstaDLDTDLDAIFNRALDAYRRG-YEFVFIHVKGTDIA 324
                                    *9994555999999999999987777999***************999***************888.************** PP

                                    HHTT-HHHHHHHHHHHHHHHHHHHTTS-TTTEEEEEE-SSB--TTTSS........-----EEEEEESTT----S--S.S CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
                  Metalloenzyme 146 GHtgdleatiaaieaaDeavkeildaieqvdgilvvtADHgnaedmvkrdkqplTsHtlepVPilivgkglapdkvke.g 224
                                    GH+ ++ ++++ ie++Dea +  l++i+  ++i++vtADH+++ ++ +        H+ +pVP+li g+g+++d+v++ +
  gi|119720470|ref|YP_920965.1| 325 GHDAKPLEKARFIERVDEAFAGFLSRIDRGKTIVAVTADHSTPCTVRD--------HSGDPVPLLINGPGVRRDDVTSfD 396
                                    ************************************************........************************ PP

                                    HHHHTT-TTEEEEGGGHHHH CS
                                    xxxxxxxxxxxxxxxxxxxx RF
                  Metalloenzyme 225 akfrekggLanvaatllnll 244
                                    + ++++ggL+++++  l  +
  gi|119720470|ref|YP_920965.1| 397 EISCARGGLGRIRGVNLVRI 416
                                    ************99877655 PP

>> Alk_phosphatase  Alkaline phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   2.1e-08   7.5e-05     232     314 ..     293     372 ..     264     393 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 2.1e-08
                                    E--HHHHHHHHHHHHTTSTT-EEEEEEETCHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHCHHCTTEEEEEEESSEESEE CS
                Alk_phosphatase 232 dPsLkemtevAiklLsknekGFFLlVEGsrIDhaaHendavgalsEvvefdeAvkaalefakkeketlvvvTaDHshvfs 311
                                    d +L    + A+++ ++  +  F+ V G+  D a+H++++ ++ + +  +deA++  l   +   +t+v vTaDHs+ ++
  gi|119720470|ref|YP_920965.1| 293 DTDLDAIFNRALDAYRRGYEFVFIHVKGT--DIAGHDAKPLEKARFIERVDEAFAGFLSRID-RGKTIVAVTADHSTPCT 369
                                    45788888899999999999999999998..559*************************999.899**********9766 PP

                                    EES CS
                Alk_phosphatase 312 fgg 314
                                    +  
  gi|119720470|ref|YP_920965.1| 370 VRD 372
                                    655 PP

>> DUF2384  Protein of unknown function (DUF2384)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0     9e-05      0.32      18      33 ..      24      39 ..      23      56 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9e-05
                        DUF2384 18 rPnpaLggrtPldlld 33
                                   rP p LggrtPl++++
  gi|119720470|ref|YP_920965.1| 24 RPVPELGGRTPLQVAR 39
                                   8************986 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.28     1e+03      22      50 ..     110     138 ..      93     176 .. 0.66
   2 ?   -2.1   0.0       1.4   5.2e+03      11      36 ..     200     227 ..     197     241 .. 0.81
   3 ?    8.8   0.0    0.0006       2.2      25      95 ..     308     393 ..     296     399 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.28
                                    HHHHHT--EEEESSS-SEETTEES----T CS
                  CoA_binding_2  22 yllehglpvvpVnpkeeeilgekvyasla 50 
                                     ++e+g + ++V  ++++i ge++ a + 
  gi|119720470|ref|YP_920965.1| 110 TVREEGGRLIVVDRRAGRIRGEDAEALTR 138
                                    45667779999999999999988655444 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.4
                                    -TTSHHHHHHHHHHH..HT--EEEESSS CS
                  CoA_binding_2  11 npgkfgykvlrylle..hglpvvpVnpk 36 
                                    +++++++ +++ ll+  ++l+ +pVn  
  gi|119720470|ref|YP_920965.1| 200 ESERTARILWKLLLRahEELERCPVNEE 227
                                    6788999999999998666999999976 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0006
                                    HHT--EEEESSS-SEETTEES----T.....T--..............EEEE-S-HHHHGGGHHHHHHH--SEEEE-TT- CS
                  CoA_binding_2  25 ehglpvvpVnpkeeeilgekvyaslaed.pepvd..............lvdvftppeatpeivkealalgakavwlqpgs 89 
                                    ++g++ v ++ k++ i g+++ +  ++   e vd              +++ +t  + tp +v++ +   ++ ++  pg+
  gi|119720470|ref|YP_920965.1| 308 RRGYEFVFIHVKGTDIAGHDAKPLEKARfIERVDeafagflsridrgkTIVAVTADHSTPCTVRDHSGDPVPLLINGPGV 387
                                    39****************87766655535999999999**********9999999*********9999999999999999 PP

                                    --HHHH CS
                  CoA_binding_2  90 edeeaa 95 
                                    + +++ 
  gi|119720470|ref|YP_920965.1| 388 RRDDVT 393
                                    888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       222  (0.0123822); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2993.76
//
Query:       gi|119720471|ref|YP_920966.1|  [L=140]
Description: hypothetical protein Tpen_1568 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.037   14.2   0.0      0.061   13.6   0.0    1.3  1  Cu_amine_oxidN2  Copper amine oxidase, N2 domain


Domain annotation for each model (and alignments):
>> Cu_amine_oxidN2  Copper amine oxidase, N2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   3.4e-06     0.061      41      75 ..      67     101 ..      58     107 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.4e-06
                                    HHHHHHHHHCH---S-EEEEEEEEETSSSSEEEEE CS
                Cu_amine_oxidN2  41 KkavlqflekgeppppRkAsvvilfGkqtkelvvd 75 
                                    ++a + ++   +p+p R A++v+  G+++ e +v+
  gi|119720471|ref|YP_920966.1|  67 REAWRTHRTLAGPLPMRAARAVAVIGGEKREVLVE 101
                                    77888999999*******************99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       134  (0.00747392); expected 358.6 (0.02)
Passed bias filter:                      123  (0.00686039); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.45
# Mc/sec: 940.90
//
Query:       gi|119720472|ref|YP_920967.1|  [L=122]
Description: hypothetical protein Tpen_1569 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.071   13.3   0.0       0.16   12.1   0.0    1.5  1  ParG      ParG


Domain annotation for each model (and alignments):
>> ParG  ParG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   8.8e-06      0.16      41      73 ..       8      40 ..       3      42 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.8e-06
                           ParG 41 fdeekhtrfkaacakkGtsitdvinqlvdnwlk 73
                                    de k   fka  +++G +++  i++ +d wl 
  gi|119720472|ref|YP_920967.1|  8 VDERKLREFKAEAIRRGLTLSQAIEEAMDLWLS 40
                                   68899999***********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 865.56
//
Query:       gi|119720473|ref|YP_920968.1|  [L=221]
Description: peroxidase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.1e-36  124.0   0.0    4.5e-36  123.5   0.0    1.3  1  AhpC-TSA    AhpC/TSA family
    2.2e-17   63.1   0.0      3e-17   62.7   0.0    1.1  1  Redoxin     Redoxin
    8.3e-13   47.9   0.1    1.5e-12   47.2   0.1    1.4  1  1-cysPrx_C  C-terminal domain of 1-Cys peroxiredoxin
  ------ inclusion threshold ------
      0.069   13.3   0.0      0.083   13.0   0.0    1.3  1  AhpC-TSA_2  AhpC/TSA antioxidant enzyme


Domain annotation for each model (and alignments):
>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.5   0.0     1e-39   4.5e-36       2     123 ..      10     138 ..       9     139 .. 0.95

  Alignments for each domain:
  == domain 1  score: 123.5 bits;  conditional E-value: 1e-39
                                    TSB----EEESTTCEEEEC.HHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHHHH- CS
                       AhpC-TSA   2 gdkapdfelknadgetvsl.sdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfieke 80 
                                    g+kap+f++k+++ + +++ +d++gk+vvlf +p+d++pvCtte  +++k++eefk+++v++ig+s+d+++sh k++e +
  gi|119720473|ref|YP_920968.1|  10 GEKAPSFTAKTTH-GVINFpDDFRGKWVVLFSHPADFTPVCTTEFVSFQKKMEEFKKLNVQLIGLSIDQVFSHIKWVEWI 88 
                                    99********999.666666999********************************************************* PP

                                    H.......SSEEEE-TTSHHHHHTT-EETT.TTECSCEEEEE-TTSBEEE CS
                       AhpC-TSA  81 s......lnfpllsDeegkvakaygvlkee.kglalratfvidkegkiry 123
                                    +      ++fp+++D +g++ak+yg++++   + ++ra+fvid++g++r+
  gi|119720473|ref|YP_920968.1|  89 KeklgveIEFPIIADDTGEIAKKYGMIHPGkGTNTVRAVFVIDPNGVLRA 138
                                    ***************************999777899***********997 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.7   0.0   6.7e-21     3e-17       3     137 ..      10     146 ..       8     154 .. 0.80

  Alignments for each domain:
  == domain 1  score: 62.7 bits;  conditional E-value: 6.7e-21
                                    TSBB---ECCEETTCEEEEEHHH.HTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHH...HHH CS
                        Redoxin   3 gdkaPdftlplaatdgnsvslse.fkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndaf...vke 78 
                                    g+kaP+ft ++  t+g  ++  + f+gk vv+++ p+ f+P+C++e + ++k  e++k+ +v+ +++++d+        e
  gi|119720473|ref|YP_920968.1|  10 GEKAPSFTAKT--THGV-INFPDdFRGKWVVLFSHPADFTPVCTTEFVSFQKKMEEFKKLNVQLIGLSIDQVFShikWVE 86 
                                    89******644..5555.555555************************888887778************99888777555 PP

                                    HHHH...TT-TSEEEE-TTSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEEEEEEESSSCH CS
                        Redoxin  79 fwgk...eglkfpvlsDgsaaftkalGlrleedaseglrtpryavidedgkvvylevepepe 137
                                    ++++    ++ fp+++D +++++k++G+     +++    ++++vid +g+++++ + p ++
  gi|119720473|ref|YP_920968.1|  87 WIKEklgVEIEFPIIADDTGEIAKKYGMI-HPGKGT-NTVRAVFVIDPNGVLRAVLYYPQEV 146
                                    5555788667*****************55.333333.59*************9988777765 PP

>> 1-cysPrx_C  C-terminal domain of 1-Cys peroxiredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.2   0.1   3.3e-16   1.5e-12       1      39 [.     159     201 ..     159     202 .. 0.96

  Alignments for each domain:
  == domain 1  score: 47.2 bits;  conditional E-value: 3.3e-16
                                    HHHHHHHHT-BB-TTT.T.....BT-EEE---SSHHHHHHHHHH CS
                     1-cysPrx_C   1 ALQladkhgvatPAnWkp.....GdkvivpPpateedavkryle 39 
                                    ALQ++dkhgva PAnW p     G kvi+pP+++e+ a++r+++
  gi|119720473|ref|YP_920968.1| 159 ALQVSDKHGVALPANW-PnneliGGKVIIPPASDEKTAKERLEK 201
                                    9***************.99********************99975 PP

>> AhpC-TSA_2  AhpC/TSA antioxidant enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.8e-05     0.083       3      54 ..      57     115 ..      55     205 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.8e-05
                     AhpC-TSA_2   3 srdkpeldaagvklvaigigdp.s...akkFvkl...tgfpfelyvDpsaklyqalglk 54 
                                    +++ +e+++ +v+l++ +i+++ s     +++k+   +++ f++++D ++++ ++ g+ 
  gi|119720473|ref|YP_920968.1|  57 QKKMEEFKKLNVQLIGLSIDQVfShikWVEWIKEklgVEIEFPIIADDTGEIAKKYGMI 115
                                    77889*****************997444577777999999**************99996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1604.56
//
Query:       gi|119720474|ref|YP_920969.1|  [L=433]
Description: hypothetical protein Tpen_1571 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-15   57.4   3.1    6.8e-15   55.4   3.1    2.1  1  NurA      NurA domain


Domain annotation for each model (and alignments):
>> NurA  NurA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.4   3.1   3.8e-19   6.8e-15       4     202 ..      55     348 ..      53     401 .. 0.75

  Alignments for each domain:
  == domain 1  score: 55.4 bits;  conditional E-value: 3.8e-19
                                    EEEEEEEEEEEETTCEEEEEEEEEEECCEEECCCEEEECEBTCCHHEEEEEHHHHHHHHHHHHHHHHHHHCGGCCSCEEE CS
                           NurA   4 aAvDGSngvvrlsggilyilsayavvgggkerleealslasvdsispsdelerrirllmetlElklgallleekgedlll 83 
                                    +AvD+S+  +++ gg+++++ +  + + g+e++ e   +a ++     d+ ++  rl++e++E+   al++ e+g++l+l
  gi|119720474|ref|YP_920969.1|  55 YAVDSSSDDIEVQGGGVVLVTRSLALSAGGEEIRELRLDAFYPRNV-RDY-DDFKRLVREHVEHV-VALRAVEEGARLVL 131
                                    9*********999999999988888888888888888888877644.344.**************.9999999******* PP

                                    EECSHHCCCH....HHHHHHHHHHHHHHHHHHHHHTT-....TTCEEEEESS-SCTCCHCCC.................. CS
                           NurA  84 lDGsligslv....efdelheeleyeeylyslsrllea....glnlvgvaKsfrskellnll.................. 137
                                    +DGsl+g  +    e + +  e+ + ey+  +s+l+ +    g+ +vgv+K++rs+ l+++l                  
  gi|119720474|ref|YP_920969.1| 132 IDGSLYGRMIhvlrELEVEGREDFMFEYVELYSELFSKarsrGALVVGVSKDSRSTVLKEELlylrlksvlkglgeplag 211
                                    **********9998888889999999************************************999999999999999999 PP

                                    .......................................S--HHHHCCHHCCHCH---STTS-HHHHTT........... CS
                           NurA 138 .................................letlligesisDiallgallrkpgytspllkilrek........... 173
                                                                      +  + + s++D  ++ a+ +  g++ pl  +l++            
  gi|119720474|ref|YP_920969.1| 212 avlgywrllkrrprealenvrklvreglspevyELFEEATSSVPDSKVILACDPGRGFSRPLRLSLEKVstgvtdilltd 291
                                    99999888888888888888888888888888777777788888888888888888888777776655566666666666 PP

                                    ...........................-HCCHHHHHH-.EEEEEEESSTTTTEEEEE CS
                           NurA 174 ...........................pllrealidke.iyfaYvrlegggsilrle 202
                                                                   e  ++++ +++ Y  +++g+ +lr++
  gi|119720474|ref|YP_920969.1| 292 gargaallrdvfektaerlgeefderaSQVLECMKKYPpVVTSYAVFSRGDDPLRVD 348
                                    666666666666666666666666555333444445555666666666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 3014.78
//
Query:       gi|119720475|ref|YP_920970.1|  [L=531]
Description: hypothetical protein Tpen_1572 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-39  136.5   0.0    2.5e-39  135.7   0.0    1.4  1  DUF87            Helicase HerA, central domain
    3.2e-06   26.3   0.0    0.00023   20.2   0.0    2.1  2  AAA_10           AAA-like domain
      7e-06   24.9   0.0     0.0041   15.8   0.0    2.1  2  DUF853           Bacterial protein of unknown function (DUF85
    1.3e-05   24.3   0.0      0.045   12.7   0.0    2.2  2  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
    3.4e-05   23.9   0.3    0.00039   20.5   0.1    2.6  2  HAS-barrel       HAS barrel domain
    4.3e-05   22.5   0.0    5.8e-05   22.1   0.0    1.3  1  T4SS-DNA_transf  Type IV secretory system Conjugative DNA tra
     0.0016   18.1   0.0     0.0037   16.9   0.0    1.6  1  Zot              Zonular occludens toxin (Zot)
     0.0025   18.2   0.1      0.015   15.7   0.0    2.2  2  AAA              ATPase family associated with various cellul
  ------ inclusion threshold ------
      0.015   15.6   0.0        2.1    8.6   0.0    2.6  1  AAA_22           AAA domain
      0.021   14.2   0.1       0.66    9.3   0.0    2.3  2  FtsK_SpoIIIE     FtsK/SpoIIIE family
       0.19   11.5   0.0         17    5.1   0.0    2.4  2  DEAD             DEAD/DEAH box helicase
       0.22   11.5   0.0        3.4    7.6   0.0    2.3  2  ResIII           Type III restriction enzyme, res subunit


Domain annotation for each model (and alignments):
>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.7   0.0   1.7e-42   2.5e-39       1     227 []     141     364 ..     141     364 .. 0.87

  Alignments for each domain:
  == domain 1  score: 135.7 bits;  conditional E-value: 1.7e-42
                          DUF87   1 ieiGrllsgsevpvyldlnklvtrHlAilgsTGsGKSntvavLleellekkgatililDpHGEYgkal......ekllse 74 
                                    i+iG+l+s+++v+vyl +n + +rH+A++++TG+GKS+tv+v+leell + gat +++DpH +Y+ ++      + ++s+
  gi|119720475|ref|YP_920970.1| 141 IRIGSLVSRRNVDVYLSVNGF-RRHVAVIAQTGAGKSYTVGVILEELL-RLGATAVVIDPHADYVFLSrdrdmrRHEYSD 218
                                    68****************888.**************************.******************************* PP

                          DUF87  75 kvkvitpspsa.........kdkelkinpwsldpeelldlleeddkpaaavqrsvleealdqakakeekeklssdepvek 145
                                    +v v+++++s+         + +el++++++l+ e++++++++  ++++++ r+++++ald+++      ++++d+++ +
  gi|119720475|ref|YP_920970.1| 219 RVLVFRNPNSTgrydpsqmdNVHELTVKFSDLSAEDVARIAGI--PEKWTNVRKAIRDALDKLR----GRDYTIDDLLGE 292
                                    *******9999********************************..****************776....99******9997 PP

                          DUF87 146 lleelkkekeelrklknqaiarlldkledllrkggsfsnsstdliallleklekegkitiidlsgvdelaqqlvvsvilr 225
                                    l++  +    + + +  +++ + l kl+++   g+      t++ +++     k+g+++++dlsg+++  q+++vs +l+
  gi|119720475|ref|YP_920970.1| 293 LEKMSR--GGGKEAAYASSAYNHLVKLRKFSVFGRYT----TSVKDEI----LKPGHVSVLDLSGLNDASQDYIVSTVLE 362
                                    666666..33444444444444444444444444444....5666666....9***********************9998 PP

                          DUF87 226 ri 227
                                    +i
  gi|119720475|ref|YP_920970.1| 363 EI 364
                                    76 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   1.5e-07   0.00023      23     161 ..     164     305 ..     157     354 .. 0.69
   2 ?    4.0   0.0     0.013        19     259     293 ..     400     434 ..     379     454 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.5e-07
                         AAA_10  23 asliiGdlGnGKSvlakllvlyisllggkaliiDpkkerekfketlpeiak.kinvvtLdseeenegvLdPlvllk.... 97 
                                    ++++i ++G+GKS+++ ++   ++ lg  a++iDp ++     +      +   ++v + ++ +  g  dP  + +    
  gi|119720475|ref|YP_920970.1| 164 HVAVIAQTGAGKSYTVGVILEELLRLGATAVVIDPHADYVFLSRDRDMRRHeYSDRVLVFRNPNSTGRYDPSQMDNvhel 243
                                    789***********************************444444433333314577877889999999999988773332 PP

                         AAA_10  98 eekeaeslaedilelllgvkkkesekkaalseaveavlegkqrgllavieelrkedekvareia 161
                                      k +   aed+   + g+ +k ++ ++a+++a ++ l+g +  + +++ el+k +   ++e+a
  gi|119720475|ref|YP_920970.1| 244 TVKFSDLSAEDVAR-IAGIPEKWTNVRKAIRDALDK-LRGRDYTIDDLLGELEKMSRGGGKEAA 305
                                    23333333333332.455555555555567777654.446666777777777666555555554 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.013
                         AAA_10 259 kkllkelvRiGRsynaavylvtqsadDvlkeelkn 293
                                     ++++ +   GR++  +++lvtq ++ ++ + l++
  gi|119720475|ref|YP_920970.1| 400 SEIINTIAAEGRKFGVFLILVTQRPSKIDADALSQ 434
                                    678999999****************9998877654 PP

>> DUF853  Bacterial protein of unknown function (DUF853)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0    0.0012       1.8       9      64 ..     150     205 ..     145     227 .. 0.87
   2 !   15.8   0.0   2.7e-06    0.0041     240     361 ..     360     477 ..     322     513 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0012
                         DUF853   9 aeqelalalklanrhGliaGatGtGktvtLqvlaeslseaGvpvfladvkGdLsgi 64 
                                    ++ +++l+++   rh  +   tG+Gk  t+ v+ e+l + G + ++ d   d   +
  gi|119720475|ref|YP_920970.1| 150 RNVDVYLSVNGFRRHVAVIAQTGAGKSYTVGVILEELLRLGATAVVIDPHADYVFL 205
                                    5678899999999****************************999999988776655 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 2.7e-06
                         DUF853 240 llseLfeeLPevGdldkPklvfffdeahLLf.ndapkallekveqvvrLi....rskGvGvyfvtqnPldlPdtvLaqLG 314
                                    +l e+++ L   G+   P +v+  +eah +   +a+k        ++  i    r  Gv + +vtq P+ +  + L+q  
  gi|119720475|ref|YP_920970.1| 360 VLEEIYR-LRYSGEFRYPVFVV-VEEAHRFVpSKASKR-STMSSEIINTIaaegRKFGVFLILVTQRPSKIDADALSQCN 436
                                    4566663.66677777787776.578886651344443.2333344444511115556666689**************98 PP

                         DUF853 315 nrvqhalraftpkdqkavkaaadtfranpefdveeaiteLgvGealv 361
                                    +++   lr   p dq+av  a++ + +    d+++ +  L+vGea++
  gi|119720475|ref|YP_920970.1| 437 SQI--ILRITNPSDQRAVAEASERLGE----DLMRDLPGLNVGEAII 477
                                    765..7************999987654....6778888899999876 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0     3e-05     0.045      12      56 ..     159     203 ..     152     211 .. 0.89
   2 !    9.3   0.0   0.00032      0.48     261     325 ..     403     462 ..     399     469 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3e-05
                  TrwB_AAD_bind  12 eretqhilivGttGsGKtqalekllrairargdraivlDltGafv 56 
                                    +  ++h++++  tG+GK+ ++  +l+++ + g +a+v+D++ ++v
  gi|119720475|ref|YP_920970.1| 159 NGFRRHVAVIAQTGAGKSYTVGVILEELLRLGATAVVIDPHADYV 203
                                    55679***********************************99986 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00032
                  TrwB_AAD_bind 261 lksllaegRkfGgavvlglqsiaqlrevYGedaaqsilslvntklilrvs...daetAeelsellGeq 325
                                    +++++aegRkfG+ ++l  q  +++ +       +  ls +n+++ilr++   d+++  e+se lGe 
  gi|119720475|ref|YP_920970.1| 403 INTIAAEGRKFGVFLILVTQRPSKIDA-------D-ALSQCNSQIILRITnpsDQRAVAEASERLGED 462
                                    67899******************9964.......3.47899*****9965455888889999999985 PP

>> HAS-barrel  HAS barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.1   2.6e-07   0.00039       1      89 [.       8      98 ..       8     101 .. 0.81
   2 ?   -0.1   0.0       0.7     1e+03      15      34 ..     132     152 ..     130     184 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.6e-07
                     HAS-barrel  1 iGevigestssslifrvegskdvkvGeyVeielp.......dgeivlGmvtdirrgnselsndlalvlsleeleeangddev 75
                                   +G++++e+t+ s+if+ + +  +  +eyV ++ +        +  vl++vt ++++++ +s+ l+l +sle++ ea+ dd+ 
  gi|119720475|ref|YP_920970.1|  8 VGRIVEEATPESFIFVTTKQDHPPKYEYVLVKSRevvageeREVDVLCQVTGVVSRSDAYSSRLDL-ESLERIHEAGIDDAN 88
                                   79******************************99*****99999***********75555555544.456666666667777 PP

                     HAS-barrel 76 alatedtgvkvlGe 89
                                   +l ++    + lG+
  gi|119720475|ref|YP_920970.1| 89 LLCAA----RTLGY 98
                                   77766....66776 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.7
                     HAS-barrel  15 frvegsk.dvkvGeyVeielp 34 
                                    f++++++ ++++G++V+ ++ 
  gi|119720475|ref|YP_920970.1| 132 FFSYPGEeGIRIGSLVSRRNV 152
                                    6666666699****9987766 PP

>> T4SS-DNA_transf  Type IV secretory system Conjugative DNA transfer
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   3.9e-08   5.8e-05      37     100 ..     155     223 ..     133     363 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 3.9e-08
                T4SS-DNA_transf  37 llntdGdf.ehvlvvAptrsgK..gvgvviPnllkwkqsiVvlDpkgElaelts..kiRkkqgr.kVfvl 100
                                    +l  +G f  hv v+A t++gK  +vgv++  ll  + ++Vv+Dp ++ + l     +R+ +    V v+
  gi|119720475|ref|YP_920970.1| 155 YLSVNG-FrRHVAVIAQTGAGKsyTVGVILEELLRLGATAVVIDPHADYVFLSRdrDMRRHEYSdRVLVF 223
                                    677788.669************6669*********************98766541145666665566665 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   2.5e-06    0.0037      83     134 ..     378     431 ..     364     442 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.5e-06
                            Zot  83 llviDEcqeifpvrakegrkd.pevi.naftehRhlgwDivlltqdiskihkev 134
                                    ++v+ E++++ p +a +   +  e+i    +e R++g  ++l+tq +ski+ ++
  gi|119720475|ref|YP_920970.1| 378 FVVVEEAHRFVPSKASKRSTMsSEIInTIAAEGRKFGVFLILVTQRPSKIDADA 431
                                    99**********999964444456774455789*****************9876 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       1.3   1.9e+03       4      23 ..     168     190 ..     165     208 .. 0.75
   2 !   15.7   0.0     1e-05     0.015      58     128 ..     375     439 ..     340     443 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.3
                                    ESSTTSSHHHHHHHHHHHH...T CS
                            AAA   4 yGppGtGKTllakavakel...g 23 
                                    +   G GK++++  + +el   g
  gi|119720475|ref|YP_920970.1| 168 IAQTGAGKSYTVGVILEELlrlG 190
                                    56789*******99999963334 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1e-05
                                    TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSSEEE CS
                            AAA  58 kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfdrki 128
                                     p+ ++++E++++++s+     ++++++ +++++ +  + +k + v++i++t+rp+k+d   l + ++++i
  gi|119720475|ref|YP_920970.1| 375 YPVFVVVEEAHRFVPSK----ASKRSTMSSEIINTIAAEGRKFG-VFLILVTQRPSKIDADAL-SQCNSQI 439
                                    47899************....55666666666666666666545.9****************9.8998887 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0    0.0014       2.1       6      31 ..     163     188 ..     160     449 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0014
                         AAA_22   6 gilvvtGesGtGKTtllrrlleqlde 31 
                                    ++++v++++G+GK++++  +le+l +
  gi|119720475|ref|YP_920970.1| 163 RHVAVIAQTGAGKSYTVGVILEELLR 188
                                    67889999999999888777777643 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.062        93      36      60 ..     159     183 ..     140     190 .. 0.76
   2 ?    9.3   0.0   0.00044      0.66     164     225 ..     399     461 ..     373     473 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.062
                                    GGS-.SEEEE--TTSSHHHHHHHHH CS
                   FtsK_SpoIIIE  36 kkmashllvaGatgsGKStalntLi 60 
                                    ++   h+ v+  tg GKS ++ +++
  gi|119720475|ref|YP_920970.1| 159 NGFRRHVAVIAQTGAGKSYTVGVIL 183
                                    34448*************9998776 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00044
                                    ..............-----------B-----EEEEEEC-HHHHHHHHHHH....HHHHHHHHHH CS
                   FtsK_SpoIIIE 164 e..ritsLsnqgpsygvhvlvtagrelekrpslvvivderieLrlaapkdssvlvedaivRlar 225
                                        i+ ++++g ++gv +++ ++r +++    +++  + i Lr + p+d +++v +a  Rl++
  gi|119720475|ref|YP_920970.1| 399 SseIINTIAAEGRKFGVFLILVTQRPSKIDADALSQCNSQIILRITNPSD-QRAVAEASERLGE 461
                                    14467888888888888888888888888888888888888888888888.8888888888775 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.011        17      15      34 ..     163     182 ..     153     202 .. 0.73
   2 ?    3.8   0.0     0.028        42      98     148 ..     353     405 ..     299     418 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.011
                                    CEEEEEESTTSSHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxx RF
                           DEAD  15 gdvlvaaeTGsGKTlaflip 34 
                                    ++v v a+TG+GK+    + 
  gi|119720475|ref|YP_920970.1| 163 RHVAVIAQTGAGKSYTVGVI 182
                                    7899*********9876544 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.028
                                    CSEEEEEH.HHHHHHHHCTSSHCTTEEEEEEETHHHHHHT...TTHHHHHHHHHH CS
                                    xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxx RF
                           DEAD  98 vdivvgtp.grlddllstgklnlsqvrflVlDEadrlldq...gfsdfinrilnq 148
                                     d++v+t  + + +l  +g+  ++   f+V+ Ea+r+  +   ++s   ++i+n+
  gi|119720475|ref|YP_920970.1| 353 QDYIVSTVlEEIYRLRYSGE--FRYPVFVVVEEAHRFVPSkasKRSTMSSEIINT 405
                                    56566555244444444555..778889********9987333333334444444 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0    0.0023       3.4      25      53 ..     163     191 ..     142     211 .. 0.82
   2 ?    1.2   0.0      0.21   3.2e+02     129     148 ..     369     391 ..     308     415 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0023
                                    SEEEEEESTTSTHHHHHHHHHHHH-S... CS
                         ResIII  25 krglikmaTGtGKTlvaaklierllkkgk 53 
                                    +++ + + TG+GK+++   + e+ll+ g 
  gi|119720475|ref|YP_920970.1| 163 RHVAVIAQTGAGKSYTVGVILEELLRLGA 191
                                    46779999************999998654 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.21
                                    HTTT-S...EEEEETGGGTTS.T CS
                         ResIII 129 lrdrfd...viiiDEaHrlgakk 148
                                     +++f    ++++ EaHr+  +k
  gi|119720475|ref|YP_920970.1| 369 YSGEFRypvFVVVEEAHRFVPSK 391
                                    344444566899******98864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (531 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.47
# Mc/sec: 3404.61
//
Query:       gi|119720476|ref|YP_920971.1|  [L=391]
Description: metallophosphoesterase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-12   48.7   0.1    2.2e-12   47.9   0.1    1.4  1  Metallophos    Calcineurin-like phosphoesterase
    2.3e-07   31.2   0.0    8.6e-07   29.3   0.0    1.8  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.9   0.1   2.4e-16   2.2e-12       1      90 [.       4     116 ..       4     209 .. 0.70

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 2.4e-16
                                    EEEEEEESBTB............TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSS....HHHHHHHHHHHHHHHHT CS
                    Metallophos   1 lrilvigDlHl............algggqlddllkllddllreekpdlvllaGDlvdrg....dlekellellaalvkyp 64 
                                    lri++++D Hl            ++++  l+++++++d + +  kp l+l+ GDl+d      ++   +++ +++l++++
  gi|119720476|ref|YP_920971.1|   4 LRIVHTADNHLdpkftflgpkvrDRREDFLNAFRRVVDFAVEA-KPHLFLVSGDLFDSVnprnPVRVQVIRAFRRLYSEG 82 
                                    69******************99999999999999999888888.**************88999889999999******** PP

                                    SEEEEEC-TTS.....................CHHHHHHHHHHHHHH CS
                    Metallophos  65 ipvylllGNHe.....................gfeeellnkygylgi 90 
                                    ++vy+++GNH+                                    
  gi|119720476|ref|YP_920971.1|  83 VRVYVIAGNHDmprsleeglsplkeveasgyaR-------------F 116
                                    ***********8877766444333322222220.............2 PP

>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.0   9.6e-11   8.6e-07       2     154 ..       5     234 ..       4     248 .. 0.67

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 9.6e-11
                  Metallophos_2   2 klaiiSDlH.................snldaleavlealkevgvdaiihaGDl.eeeep......evleellela....p 53 
                                    ++++ +D H                 + l+a ++v++ + e+++ + +++GDl   ++p      +v++++++l+    +
  gi|119720476|ref|YP_920971.1|   5 RIVHTADNHldpkftflgpkvrdrreDFLNAFRRVVDFAVEAKPHLFLVSGDLfDSVNPrnpvrvQVIRAFRRLYsegvR 84 
                                    56677777777777777777777777778999********************98555554446666999999999***** PP

                  Metallophos_2  54 vlaVrGNnD.............................................eevveedvlreaaelgtdlpeeaele 88 
                                    v+++ GN+D                                             ++    +v+  +++l+++  ++   e
  gi|119720476|ref|YP_920971.1|  85 VYVIAGNHDmprsleeglsplkeveasgyarffektsefevdhfevngfdvavaGISYNPEVGLDEHPLRKYN-ARVPRE 163
                                    **********999988888887776666655555555544444433333332221113333333333332222.222222 PP

                  Metallophos_2  89 lagekvlliHgdpl.....gvkdalaellkeaeegsd.vvvcGHtHvp.evekeggvlvvnPGsvgeprdgdp 154
                                     ++ +v l+H+         ++ +  + ++e   ++  ++++GH H + ++   +g +  +PGs +++++ ++
  gi|119720476|ref|YP_920971.1| 164 -GDIEVVLMHYN-FagvevPGAWRAPRITREDIPDNCvYAALGHVHSRvTIPLGNGGVAAYPGSTERRSFIEE 234
                                    .56668888887.469966445555555555445555899*******9555555688999*****99987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2835.97
//
Query:       gi|119720477|ref|YP_920972.1|  [L=840]
Description: SMC domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.3e-21   76.7   1.6    3.3e-21   76.7   1.6    5.5  2  AAA_23          AAA domain
    6.9e-09   35.5   0.0    4.9e-08   32.7   0.0    2.0  1  SMC_N           RecF/RecN/SMC N terminal domain
    9.9e-05   22.0   0.0    9.9e-05   22.0   0.0    4.2  4  AAA_27          AAA domain
    0.00035   21.0   7.3         19    5.8   0.2    5.7  6  NPV_P10         Nucleopolyhedrovirus P10 protein
    0.00044   20.4   0.2     0.0021   18.3   0.0    2.3  1  SbcCD_C         Putative exonuclease SbcCD, C subunit
    0.00051   19.9   1.9    0.00051   19.9   1.9    2.5  2  AAA_15          AAA ATPase domain
    0.00056   19.6   0.0     0.0051   16.5   0.0    2.4  2  AAA_29          P-loop containing region of AAA domain
     0.0019   17.6   3.2     0.0019   17.6   3.2    6.0  5  DUF3450         Protein of unknown function (DUF3450)
     0.0026   17.6  33.0       0.16   11.7   0.3    5.5  5  Phage_GP20      Phage minor structural protein GP20
     0.0084   16.0   9.0       0.48   10.2   0.0    4.3  5  AAA_21          AAA domain, putative AbiEii toxin, Type IV TA
  ------ inclusion threshold ------
      0.012   15.6   2.3         13    5.8   0.0    4.5  4  Baculo_PEP_C    Baculovirus polyhedron envelope protein, PEP,
      0.014   15.7   9.9      0.014   15.7   9.9    4.7  5  DUF5082         Domain of unknown function (DUF5082)
      0.016   15.5  42.9       0.15   12.4   0.6    6.1  6  BLOC1_2         Biogenesis of lysosome-related organelles com
      0.028   12.6  47.6     0.0097   14.1  20.3    3.3  3  FPP             Filament-like plant protein, long coiled-coil
      0.076   12.4  77.0      0.017   14.5   3.0    5.1  4  GAS             Growth-arrest specific micro-tubule binding
       0.13   12.3  88.3       0.22   11.5  28.7    5.8  6  CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein C
       0.32   11.1  58.9      0.065   13.3   0.7    5.8  5  ADIP            Afadin- and alpha -actinin-Binding
       0.61   10.1  32.0        3.8    7.6   2.6    6.1  7  DUF1664         Protein of unknown function (DUF1664)
          1    9.2  12.2         18    5.2   0.3    4.8  4  Sec8_exocyst    Sec8 exocyst complex component specific domai
        1.1    9.6   7.8       0.15   12.4   0.9    3.1  2  Retrotrans_gag  Retrotransposon gag protein
        2.1    8.1  10.3         43    3.9   1.0    4.4  5  Bacillus_HBL    Bacillus haemolytic enterotoxin (HBL)
        5.6    5.7  53.3        2.7    6.8   9.9    3.1  3  DUF812          Protein of unknown function (DUF812)
        6.8    6.6  27.9        6.5    6.7   4.6    5.7  6  Cauli_AT        Aphid transmission protein


Domain annotation for each model (and alignments):
>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.7   1.6   4.3e-24   3.3e-21       1     199 [.       6     235 ..       6     236 .. 0.66
   2 ?    5.5   0.1     0.028        22     142     193 ..     625     680 ..     588     685 .. 0.69

  Alignments for each domain:
  == domain 1  score: 76.7 bits;  conditional E-value: 4.3e-24
                         AAA_23   1 kLkienfrsfrdqe.idFskgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiesegkvkayveltf 79 
                                    +Lk +nfr ++ qe + F kg+++I G N+aGK+Til+A+ ++L+g+ +     +g +    d  ++++ +++a ve+ f
  gi|119720477|ref|YP_920972.1|   6 SLKAQNFRRLNFQEpLVFPKGFVVIRGRNEAGKSTILEAVLFGLFGDYRIIQELRGAREAGLDSVVNHR-SGRARVEVVF 84 
                                    6899******99988********************************9888887776666666656665.899******* PP

                         AAA_23  80 enkdgrytrsiererelskkkgkttkkaklellei.........deleqfisellgskkiilnlilflgqerfeefelkd 150
                                    e +++r  +++er  e+ ++ g+++     e+++          +  ++++s+l+ ++ +++     ++q++ e ++++ 
  gi|119720477|ref|YP_920972.1|  85 EVEGRR--YRVERVVERGREGGRQVEARLVEITQGgerliatspSRVNEEVSKLVRVNWREMLATNVIAQKDLEHLLRMG 162
                                    ***998..577777777777777775443333333444444467777888888777777766555555555544444433 PP

                         AAA_23 151 kke.........rleelekeleeledekkllekl...............eqekekekeleeleeeleeilkel 199
                                    k+e           e+++k++e+le+e++ ++++                +++e + + ee ++elee++kel
  gi|119720477|ref|YP_920972.1| 163 KNErekvinmmmGFESYNKAIEKLEEERRAMQQElekkvlekssledklRNLEELKVKVEEYRRELEEVEKEL 235
                                    3333445556665555555555555555555555222233332222224466666668888888888888776 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.028
                         AAA_23 142 r...feefelkdkkerleelekeleeledekkllekle.qekekekeleeleeele 193
                                    r   ++e+++     +l+++ek+leel ++++ l kle +  e e e ++ +e+ +
  gi|119720477|ref|YP_920972.1| 625 RrlaEAEERRRVLTGELRDAEKKLEELPAVRDRLAKLEsEVRELEVEVNARREAVK 680
                                    23333333444455588888888888888888888885255666667777776655 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.0   6.3e-11   4.9e-08       2     197 ..       4     810 ..       3     815 .. 0.86

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 6.3e-11
                                    EEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHC.TT..TTTTTTCHCCCCCC--BTTCSSTTEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N   2 lkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvL.Ge.rsakklrseklsdlihkskekasvkkaev 79 
                                    l +l+ +nF+ ++  +  l f k+f +i G+N +GKs +l+A+lF L G+ r  ++lr ++   l +    ++++ +a+v
  gi|119720477|ref|YP_920972.1|   4 LVSLKAQNFRRLN-FQEPLVFPKGFVVIRGRNEAGKSTILEAVLFGLfGDyRIIQELRGAREAGLDSV--VNHRSGRARV 80 
                                    667999*****95.99999**************************65365235677887777766554..566899**** PP

                                    EEEEEETTEE.........SSSSSSCEEEEEEEETTSE......EEEEETTEEE-H..HHHHHHHHCTT-STT....... CS
                                    xxxxxxxxxx.........xxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxx..xxxxxxxxxxxxxxx....... RF
                          SMC_N  80 eitfdnedkk.........lkiekeevsisrrvkrkge......seykingkevtk..kevsellesagiske....... 135
                                    e++f+ e+++          ++   +v+ +   +++g       s  ++n++  +    + +e                 
  gi|119720477|ref|YP_920972.1|  81 EVVFEVEGRRyrvervverGREGGRQVEARLVEITQGGerliatSPSRVNEEVSKLvrVNWRE---------Mlatnvia 151
                                    ****99998855555443322222233333333333331111122333333333331122234.........14444555 PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                          SMC_N 136 ................................................................................ 135
                                                                                                                    
  gi|119720477|ref|YP_920972.1| 152 qkdlehllrmgknerekvinmmmgfesynkaiekleeerramqqelekkvlekssledklrnleelkvkveeyrreleev 231
                                    55999999999999999999999999999999999999999999999999999999999999999999999999999999 PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                          SMC_N 136 ................................................................................ 135
                                                                                                                    
  gi|119720477|ref|YP_920972.1| 232 ekelpalrseeersrkvreyldgllrvlrerektsrsieeverrireleeerrsleekavklkgeleaqrrrlgeleerg 311
                                    99999999999999999999999999999999999999999999999999999999999999999999999999999999 PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                          SMC_N 136 ................................................................................ 135
                                                                                                                    
  gi|119720477|ref|YP_920972.1| 312 ravreafrkaeeerrraiefsgkalelldkyqslldekrrtleriaeldkrleerpkllgesarlaeearsvesriages 391
                                    99999999999999999999999999999999999999999999999999999999999999999999999999999999 PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                          SMC_N 136 ................................................................................ 135
                                                                                                                    
  gi|119720477|ref|YP_920972.1| 392 lpawskvasaallvasavlllvnpallalsiagallavlslaagayrksvtvsrlrlererlereralveerlkslerdv 471
                                    99999999999999999999999999999999999999999999999999999999999999999999999999999999 PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                          SMC_N 136 ................................................................................ 135
                                                                                                                    
  gi|119720477|ref|YP_920972.1| 472 adreslskrleeidarllraeeelkgvlgeefsklplqevrervsrerarreeeyeraraekealekeaasvgervsqle 551
                                    99999999999999999999999999999999999999999999999999999999999999999999999999999999 PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                          SMC_N 136 ................................................................................ 135
                                                                                                                    
  gi|119720477|ref|YP_920972.1| 552 kqleeversveerverlgelakrreelldalsrlvvpeppfeieglvwpvderdiegvevvyntydrlyqqvsrrlaeae 631
                                    99999999999999999999999999999999999999999999999999999999999999999999999999999999 PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                          SMC_N 136 ................................................................................ 135
                                                                                                                    
  gi|119720477|ref|YP_920972.1| 632 errrvltgelrdaekkleelpavrdrlaklesevrelevevnarreavkllrevsakrraafapsveqnmnwivsyvtng 711
                                    99999999999999999999999999999999999999999999999999999999999999999999999999999999 PP

                                    ............................CS-HHHHHHHHHHHHHH.......HHCCS--SEEEECTTTTTS-HHHHHHHH CS
                                    ............................xxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 136 ............................lLSgGektLvalaLlfA.......iqkvkpaplyllDeidaaLDeknvkkva 180
                                                                  SgG      la+++A         k     + +lDe     D++++ +++
  gi|119720477|ref|YP_920972.1| 712 rykavkidperydvsvydaeagrwmqrdIYSGGTNDQFLLAMRIAftlsllpSAKGTYPRFLFLDEPLGSSDAERRGRIV 791
                                    99999999999999999999999999999999988777777777766777543333333588899999999999999999 PP

                                    HHHHHHCTT..SEEEEE-S CS
                                    xxxxxxxxx..xxxxxxxx RF
                          SMC_N 181 ellkekskn..aQfivisl 197
                                    ell ++ ++   Q++ i++
  gi|119720477|ref|YP_920972.1| 792 ELLARELTRffDQVFLITH 810
                                    9998776664569988887 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   1.3e-07   9.9e-05      21      52 ..      17      51 ..      10     101 .. 0.88
   2 ?   -1.2   0.2       1.6   1.2e+03     153     180 ..     174     201 ..     114     232 .. 0.65
   3 ?   -1.0   1.8       1.4   1.1e+03     138     199 ..     259     320 ..     245     327 .. 0.61
   4 ?   -0.8   1.4       1.3   9.8e+02     164     188 ..     528     552 ..     434     576 .. 0.65

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.3e-07
                         AAA_27 21 fsae...eadlhliyGpNEAGKstalrAisdllfG 52
                                   f++     +++ +i G NEAGKst+l+A+   lfG
  gi|119720477|ref|YP_920972.1| 17 FQEPlvfPKGFVVIRGRNEAGKSTILEAVLFGLFG 51
                                   5542333689******************9988887 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.6
                         AAA_27 153 aGlaslrevleaLeaeadelfkprkskk 180
                                     G++s ++ +e+Le+e++++ ++ ++k 
  gi|119720477|ref|YP_920972.1| 174 MGFESYNKAIEKLEEERRAMQQELEKKV 201
                                    5566666666666666665554444433 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1.4
                         AAA_27 138 leaegelgqlLfeasaGlaslrevleaLeaeadelfkprkskkrainealeeleeakkelre 199
                                    l+++++ ++++ e +  +++l+e + +Le++a +l  + ++++r++ e +e+ ++++++ r+
  gi|119720477|ref|YP_920972.1| 259 LREREKTSRSIEEVERRIRELEEERRSLEEKAVKLKGELEAQRRRLGELEERGRAVREAFRK 320
                                    55555555555555555666666666666666666666666665666665555555555555 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 1.3
                         AAA_27 164 aLeaeadelfkprkskkraineale 188
                                    + +ae+++l k+ +s  +++ + ++
  gi|119720477|ref|YP_920972.1| 528 RARAEKEALEKEAASVGERVSQLEK 552
                                    2223333333333333333333333 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.2     0.024        19      12      58 ..     182     235 ..     179     245 .. 0.83
   2 ?    5.0   0.0     0.044        35      12      56 ..     268     309 ..     255     323 .. 0.85
   3 ?   -1.2   0.0       3.7   2.9e+03      23      52 ..     342     371 ..     336     384 .. 0.81
   4 ?    1.5   0.0      0.55   4.3e+02      23      55 ..     460     492 ..     455     500 .. 0.67
   5 ?    4.4   0.0     0.069        54      19      74 ..     539     591 ..     530     592 .. 0.66
   6 ?    2.1   0.1      0.34   2.6e+02      22      59 ..     636     673 ..     621     688 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.024
                        NPV_P10  12 dikavddkVdalqqqv.......ddvqenlpdvtelnekLdaqsaqLaeletkv 58 
                                    +i+++++   a+qq++        +++++l++++el+ k+++   +L+e+e+++
  gi|119720477|ref|YP_920972.1| 182 AIEKLEEERRAMQQELekkvlekSSLEDKLRNLEELKVKVEEYRRELEEVEKEL 235
                                    6777777777888877777788889999***************99999999876 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.044
                        NPV_P10  12 dikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaelet 56 
                                     i++v+ ++  l+++  +++e+  +   l+ +L+aq   L ele+
  gi|119720477|ref|YP_920972.1| 268 SIEEVERRIRELEEERRSLEEKAVK---LKGELEAQRRRLGELEE 309
                                    5889999999999999999997666...99*************98 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 3.7
                        NPV_P10  23 lqqqvddvqenlpdvtelnekLdaqsaqLa 52 
                                     q+ +d+ +  l+ + el ++L++ ++ L 
  gi|119720477|ref|YP_920972.1| 342 YQSLLDEKRRTLERIAELDKRLEERPKLLG 371
                                    566778888889999999999999888776 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.55
                        NPV_P10  23 lqqqvddvqenlpdvtelnekLdaqsaqLaele 55 
                                    +++++++++ ++ d + l+++L+++ a L   e
  gi|119720477|ref|YP_920972.1| 460 VEERLKSLERDVADRESLSKRLEEIDARLLRAE 492
                                    455667777777777777777777777665544 PP

  == domain 5  score: 4.4 bits;  conditional E-value: 0.069
                        NPV_P10  19 kVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiLnpdevPdlp 74 
                                       ++ ++v +++++l++v+     +++  + L el +  e+  d L+  +vP++p
  gi|119720477|ref|YP_920972.1| 539 EAASVGERVSQLEKQLEEVE---RSVEERVERLGELAKRREELLDALSRLVVPEPP 591
                                    45566667777777776644...677777777777777777777777755577766 PP

  == domain 6  score: 2.1 bits;  conditional E-value: 0.34
                        NPV_P10  22 alqqqvddvqenlpdvtelnekLdaqsaqLaeletkve 59 
                                    +l  ++ d +++l+++  + ++L ++  ++ ele +v+
  gi|119720477|ref|YP_920972.1| 636 VLTGELRDAEKKLEELPAVRDRLAKLESEVRELEVEVN 673
                                    56666777777777777777777777777777776665 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   2.7e-06    0.0021      33      89 ..     741     795 ..     720     796 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.7e-06
                        SbcCD_C  33 lSGGek.qflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                     SGG + qfl+++ +a+ l+ l s +    + +r++fLDE  ++ D+e++ +++ell+
  gi|119720477|ref|YP_920972.1| 741 YSGGTNdQFLLAMRIAFTLSLLPSAK---GTYPRFLFLDEPLGSSDAERRGRIVELLA 795
                                    47776526777777777777777774...899***********************986 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   1.9   6.5e-07   0.00051       4     227 ..       5     278 ..       3     368 .. 0.47
   2 ?   -3.1   0.2       6.2   4.9e+03     150     177 ..     524     551 ..     461     577 .. 0.51

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 6.5e-07
                         AAA_15   4 kkikikNFRslkd.veidlseeltvliGkNnsGKSsilealdlFlnnkekkn...........kkvikiekedleifeni 71 
                                     ++k +NFR+l     + + + + v+ G+N +GKS+ilea  + l  +++             +            +  +
  gi|119720477|ref|YP_920972.1|   5 VSLKAQNFRRLNFqEPLVFPKGFVVIRGRNEAGKSTILEAVLFGLFGDYRIIqelrgareaglD------------SVVN 72 
                                    68999******95455555555******************955444444444444444333330............3344 PP

                         AAA_15  72 seskdikIdvef.......................................aekekakeyektlkskekkkadlllkkk. 111
                                     +s + +++v f                                          + + ++e+ +k  + +++++l ++  
  gi|119720477|ref|YP_920972.1|  73 HRSGRARVEVVFevegrryrvervvergreggrqvearlveitqggerliaT--SPSRVNEEVSKLVRVNWREMLATNVi 150
                                    5556666666666677777777777777777777777777777776666431..23333333333344444444444431 PP

                         AAA_15 112 .esdlkktikdkklklkknelsdekisvekkkskkelpkekeeklekekeelkid..kedlkklikkleeslkkee.... 184
                                     ++dl  +++  k + +k  ++ + ++ ++k  +k  ++ +   +e+ek+ l++    ++l++l ++l+ +++++     
  gi|119720477|ref|YP_920972.1| 151 aQKDLEHLLRMGKNEREKVINMMMGFESYNKAIEKLEEERRAMQQELEKKVLEKSslEDKLRNL-EELKVKVEEYRrele 229
                                    1344444444444444444444445554444444444444444455555555444422222222.223333333333333 PP

                         AAA_15 185 elknvlksaiiklllisakRnvsd......edsekkssllgklkekile 227
                                    e+++ l+++  + +   ++R++ d       + ek+s +++++ ++i e
  gi|119720477|ref|YP_920972.1| 230 EVEKELPALRSEEERSRKVREYLDgllrvlREREKTSRSIEEVERRIRE 278
                                    2222222222333333333333333333322222222222222222222 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 6.2
                         AAA_15 150 ekeeklekekeelkidkedlkklikkle 177
                                    e++e +  eke l+++  ++ +  ++le
  gi|119720477|ref|YP_920972.1| 524 EEYERARAEKEALEKEAASVGERVSQLE 551
                                    2222222233333333333333333333 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   6.5e-06    0.0051      19      48 ..      22      51 ..       4      56 .. 0.74
   2 ?   -0.3   0.0       1.1   8.8e+02      38      50 ..     578     590 ..     577     593 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.5e-06
                         AAA_29 19 idlkgatlltGpsGsGKSTllDAiqalLvp 48
                                   + +kg++++ G++++GKST+l A+ + L +
  gi|119720477|ref|YP_920972.1| 22 VFPKGFVVIRGRNEAGKSTILEAVLFGLFG 51
                                   4468999****************9876665 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.1
                         AAA_29  38 llDAiqalLvpak 50 
                                    llDA++ l vp+ 
  gi|119720477|ref|YP_920972.1| 578 LLDALSRLVVPEP 590
                                    89*********86 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   8.1    0.0071       5.5      35      93 ..     179     237 ..     171     261 .. 0.64
   2 ?    0.6   9.1      0.37   2.9e+02      25      84 ..     262     321 ..     255     384 .. 0.61
   3 ?    3.3   0.1     0.054        42      37      84 ..     441     488 ..     404     499 .. 0.56
   4 !   17.6   3.2   2.4e-06    0.0019      36     122 ..     509     595 ..     506     604 .. 0.94
   5 ?    3.1   0.9     0.064        50      28      88 ..     616     676 ..     596     687 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0071
                        DUF3450  35 sqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeiee 93 
                                     +k i+kl++e++ +++e+++   e++sle + ++le+l  ++e+ + +lee  +e+ +
  gi|119720477|ref|YP_920972.1| 179 YNKAIEKLEEERRAMQQELEKKVLEKSSLEDKLRNLEELKVKVEEYRRELEEVEKELPA 237
                                    45666777777777777777777777766666666666666666555555554444433 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.37
                        DUF3450  25 aekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasl 84 
                                     ek+ ++ ++++++i +l++e+++l+++  +lk ele+ +    +le+  +++++ + + 
  gi|119720477|ref|YP_920972.1| 262 REKTSRSIEEVERRIRELEEERRSLEEKAVKLKGELEAQRRRLGELEERGRAVREAFRKA 321
                                    444444444444444444444444444444444444444444444444444444444444 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.054
                        DUF3450  37 kkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasl 84 
                                      +++l  e++ l++e   ++e+l+sle   +  e+l + +e+  a+l
  gi|119720477|ref|YP_920972.1| 441 VTVSRLRLERERLERERALVEERLKSLERDVADRESLSKRLEEIDARL 488
                                    445555555555555555555555555555555555555555444444 PP

  == domain 4  score: 17.6 bits;  conditional E-value: 2.4e-06
                        DUF3450  36 qkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeierelvpllekmidrLeqfvel 115
                                    q+  +++++e++  ++ey+++++e+e+le++ + + + v+++e++++++e++ ee  e   el    e+++d+L ++v  
  gi|119720477|ref|YP_920972.1| 509 QEVRERVSRERARREEEYERARAEKEALEKEAASVGERVSQLEKQLEEVERSVEERVERLGELAKRREELLDALSRLVVP 588
                                    777889999**********************************************999999******************* PP

                        DUF3450 116 dlPflle 122
                                     +Pf  e
  gi|119720477|ref|YP_920972.1| 589 EPPFEIE 595
                                    ***9877 PP

  == domain 5  score: 3.1 bits;  conditional E-value: 0.064
                        DUF3450  28 avaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqi 88 
                                      +  +q++++  + ++ ++ l  e+r+++++le+l + +++l++l +++++   +++ + 
  gi|119720477|ref|YP_920972.1| 616 YDRLYQQVSRRLAEAEERRRVLTGELRDAEKKLEELPAVRDRLAKLESEVRELEVEVNARR 676
                                    5556677777777888888888888888888888888888888777776666555555554 PP

>> Phage_GP20  Phage minor structural protein GP20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   5.2   0.00079      0.62      10      87 ..     165     250 ..     156     255 .. 0.81
   2 ?    2.4   0.8      0.16   1.2e+02      39      75 ..     264     300 ..     241     330 .. 0.52
   3 !    8.3   0.1    0.0024       1.9      21      73 ..     444     496 ..     434     502 .. 0.88
   4 ?    2.9   1.3      0.11        89      24      59 ..     530     562 ..     509     584 .. 0.50
   5 !   11.7   0.3   0.00021      0.16      18      68 ..     625     675 ..     610     688 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00079
                     Phage_GP20  10 engkdit........kakldeveeerdtlkeqlkdrdkqLedLkkkakdneeLqkqieelqaknkkakaeyeakiadlkl 81 
                                    e +k+i+        +++++++eeer  ++++l+++  + + L++k  + eeL+ ++ee+  ++++ ++e  a  ++ + 
  gi|119720477|ref|YP_920972.1| 165 EREKVINmmmgfesyNKAIEKLEEERRAMQQELEKKVLEKSSLEDKLRNLEELKVKVEEYRRELEEVEKELPALRSEEER 244
                                    5566664444444568999*****************99999***************************999887666666 PP

                     Phage_GP20  82 dnaiel 87 
                                    +  +++
  gi|119720477|ref|YP_920972.1| 245 SRKVRE 250
                                    666655 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.16
                     Phage_GP20  39 kqLedLkkkakdneeLqkqieelqaknkkakaeyeak 75 
                                    k+   ++++     eL+++  +l++k+ k k e ea+
  gi|119720477|ref|YP_920972.1| 264 KTSRSIEEVERRIRELEEERRSLEEKAVKLKGELEAQ 300
                                    4444444444444444444444444444444443333 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0024
                     Phage_GP20  21 deveeerdtlkeqlkdrdkqLedLkkkakdneeLqkqieelqaknkkakaeye 73 
                                    +++  er+ l+ + +  ++ L+ L+ ++ d e+L k +ee+ a + +a++e +
  gi|119720477|ref|YP_920972.1| 444 SRLRLERERLERERALVEERLKSLERDVADRESLSKRLEEIDARLLRAEEELK 496
                                    556778999999999999**************************999999876 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.11
                     Phage_GP20  24 eeerdtlkeqlkdrdkqLedLkkkakdneeLqkqie 59 
                                     +e++ l+++ +   + +++L+k+ +++e   + +e
  gi|119720477|ref|YP_920972.1| 530 RAEKEALEKEAASVGERVSQLEKQLEEVE---RSVE 562
                                    44444444444433333333333322222...1111 PP

  == domain 5  score: 11.7 bits;  conditional E-value: 0.00021
                     Phage_GP20  18 akldeveeerdtlkeqlkdrdkqLedLkkkakdneeLqkqieelqaknkka 68 
                                     +l+e+ee r  l+++l d++k+Le+L ++    ++L+ ++ el+ ++++ 
  gi|119720477|ref|YP_920972.1| 625 RRLAEAEERRRVLTGELRDAEKKLEELPAVRDRLAKLESEVRELEVEVNAR 675
                                    67899***************************************9988764 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0   0.00062      0.48       1      59 [.      27      67 ..      27     121 .. 0.61
   2 ?   -1.7   0.4       2.5     2e+03     182     182 ..     259     259 ..     178     332 .. 0.52
   3 ?    1.7   0.2      0.24   1.8e+02      87     210 ..     346     475 ..     329     505 .. 0.71
   4 ?   -2.2   0.0       3.6   2.8e+03      71     153 ..     610     693 ..     596     727 .. 0.65
   5 !    6.3   0.0    0.0092       7.2     243     297 ..     754     810 ..     741     811 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00062
                         AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfe 59
                                   + v+ G+N +GKS++L+a  +                    +++++  + l+  ++++ 
  gi|119720477|ref|YP_920972.1| 27 FVVIRGRNEAGKSTILEAVLFGL------------------FGDYRIIQELRGAREAGL 67
                                   67899**************8874..................333333333333333333 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.5
                         AAA_21 182 k 182
                                    +
  gi|119720477|ref|YP_920972.1| 259 L 259
                                    1 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.24
                         AAA_21  87 lssvetllesgllldkrsleeedvfnpeargirggvsvfslkelsvsepndlqfgkaltditsrawsllllldglrke.. 164
                                    l +++++le+   ldkr +e+++     ar + + +sv+s+++ +  +++++  ++al+  ++ +   ++ l +l  +  
  gi|119720477|ref|YP_920972.1| 346 LDEKRRTLERIAELDKRLEERPKLLGESARLAEEARSVESRIAGESLPAWSKVASAALLVASAVLLLVNPALLALSIAga 425
                                    55677788888888888888888888888888888888888888888888888888888888888887777777776666 PP

                         AAA_21 165 ....rigllnifadyfgfakekrllqrlvrslklveielsdlgegeelia 210
                                         ++ + + ++ ++ ++++  ++rl+r++ lve +l  l+  + + +
  gi|119720477|ref|YP_920972.1| 426 llavLSLAAGAYRKSVTVSRLRLERERLERERALVEERLKSLERDVADRE 475
                                    66666666666666666666666666666666666665555544444443 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 3.6
                         AAA_21  71 ryryglrlersqv.eeklssvetllesgllldkrsleeedvfnpeargirggvsvfslkelsvsepndlqfgkaltdits 149
                                    +  y+      q  +++l + e++++  +   ++++++  + +++ ++  +++s+ ++ e +v+   +  +  + ++ ++
  gi|119720477|ref|YP_920972.1| 610 EVVYNTYDRLYQQvSRRLAEAEERRRVLTGELRDAEKKLEELPAVRDRLAKLESEVRELEVEVNARREAVKLLREVSAKR 689
                                    55555555555555777777777777777777777777777777777777777777777766666665555555555555 PP

                         AAA_21 150 raws 153
                                    ra++
  gi|119720477|ref|YP_920972.1| 690 RAAF 693
                                    5544 PP

  == domain 5  score: 6.3 bits;  conditional E-value: 0.0092
                         AAA_21 243 rllalltallralkkg..sllliDEpEngLHPkllrrllell.kelsrngaQviltTH 297
                                    r+ a+ ++ll  +k +  ++l++DEp  + + ++  r++ell +el+r   Qv+l TH
  gi|119720477|ref|YP_920972.1| 754 RI-AFTLSLLPSAKGTypRFLFLDEPLGSSDAERRGRIVELLaRELTRFFDQVFLITH 810
                                    55.888888888877799*************************999999********* PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1      0.62   4.8e+02      50      99 ..     186     240 ..     169     242 .. 0.54
   2 ?    1.2   0.0      0.45   3.5e+02      36      83 ..     453     499 ..     447     509 .. 0.76
   3 ?    2.5   0.1      0.18   1.4e+02      35      76 ..     542     582 ..     533     587 .. 0.51
   4 ?    5.8   0.0     0.016        13      42     102 ..     611     673 ..     607     709 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.62
                   Baculo_PEP_C  50 lsedlksllaeldt......rldtlltnLtdalnalq......dtlrneLtnlnsiltnLls 99 
                                    l+e+ +++ +el++       l++ l nL       +      ++ r eL+ ++++l  L s
  gi|119720477|ref|YP_920972.1| 186 LEEERRAMQQELEKkvleksSLEDKLRNL-------EelkvkvEEYRRELEEVEKELPALRS 240
                                    33333333333333111112444444444.......44444456888899999988888776 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.45
                   Baculo_PEP_C  36 latlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtl 83 
                                    l++  + +e++L++l+ d+ +  ++l++rl++  ++L +a  +l+  l
  gi|119720477|ref|YP_920972.1| 453 LERERALVEERLKSLERDVAD-RESLSKRLEEIDARLLRAEEELKGVL 499
                                    566667788889999999888.77788888888888888888777554 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.18
                   Baculo_PEP_C  35 qlatlldaietqLnalsedlksllaeldtrldtlltnLtdal 76 
                                     + + + ++e+qL++++ ++++ ++ l  +l++  ++L dal
  gi|119720477|ref|YP_920972.1| 542 SVGERVSQLEKQLEEVERSVEERVERLG-ELAKRREELLDAL 582
                                    4455555666666666665555443332.3444444444444 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.016
                   Baculo_PEP_C  42 aietqLnalsedlksllaeldtrldtlltnLtdalnalq..dtlrneLtnlnsiltnLlssvt 102
                                     + ++ + l +++++ lae ++r   l+ +L da ++l+   ++r +L  l+s++ +L  +v 
  gi|119720477|ref|YP_920972.1| 611 VVYNTYDRLYQQVSRRLAEAEERRRVLTGELRDAEKKLEelPAVRDRLAKLESEVRELEVEVN 673
                                    566777888999999999999999999999****99999777999999999999999988775 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   9.9   1.8e-05     0.014       2     122 ..     187     308 ..     186     309 .. 0.92
   2 ?   -1.6   0.0       3.9     3e+03      69     100 ..     332     363 ..     323     395 .. 0.63
   3 ?   -1.6   0.3         4   3.1e+03       4      37 ..     449     482 ..     443     501 .. 0.58
   4 ?    7.4   0.5    0.0066       5.2      65     114 ..     533     582 ..     513     586 .. 0.72
   5 ?    4.6   0.4     0.047        36      12      45 ..     634     667 ..     620     683 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.8e-05
                        DUF5082   2 ktkisklqaqiaelrseiaaleekIerLkeaktklsdekeslkqkkkklekplnssesWkGkeennydgirs..nlessy 79 
                                     ++++++q++ +++  e ++le+k++ L+e k k++++  +l++ +k+l     ++ +   k ++  dg ++     +++
  gi|119720477|ref|YP_920972.1| 187 EEERRAMQQELEKKVLEKSSLEDKLRNLEELKVKVEEYRRELEEVEKELPALRSEE-ERSRKVREYLDGLLRvlREREKT 265
                                    689*********************************************98776666.5567799999999998888899* PP

                        DUF5082  80 qtyvdkldelidaieeEIerLenqiseaqgvldtlqsqlnslk 122
                                    ++++++++  i+++eeE + Le++  +++g l+ + + l++l+
  gi|119720477|ref|YP_920972.1| 266 SRSIEEVERRIRELEEERRSLEEKAVKLKGELEAQRRRLGELE 308
                                    *************************************999986 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.9
                        DUF5082  69 dgirsnlessyqtyvdkldelidaieeEIerL 100
                                    +g++ +l ++yq   d+ + +  +i e  +rL
  gi|119720477|ref|YP_920972.1| 332 SGKALELLDKYQSLLDEKRRTLERIAELDKRL 363
                                    55555555555555555555555554433333 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 4
                        DUF5082   4 kisklqaqiaelrseiaaleekIerLkeaktkls 37 
                                    ++++l+++ a  ++++++le +++  ++ +++l+
  gi|119720477|ref|YP_920972.1| 449 ERERLERERALVEERLKSLERDVADRESLSKRLE 482
                                    5566666666666666666666655444444444 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.0066
                        DUF5082  65 ennydgirsnlessyqtyvdkldelidaieeEIerLenqiseaqgvldtl 114
                                    ++  + +++++ + +++ +++l+e+++++ee +erL +  +  +  ld l
  gi|119720477|ref|YP_920972.1| 533 KEALEKEAASVGERVSQLEKQLEEVERSVEERVERLGELAKRREELLDAL 582
                                    33334444478888888888888888888888888877777777777666 PP

  == domain 5  score: 4.6 bits;  conditional E-value: 0.047
                        DUF5082  12 iaelrseiaaleekIerLkeaktklsdekeslkq 45 
                                       l +e+++ e+k+e+L +++++l + ++++ +
  gi|119720477|ref|YP_920972.1| 634 RRVLTGELRDAEKKLEELPAVRDRLAKLESEVRE 667
                                    55678999****************9998887766 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   9.8   0.00096      0.75      17      93 ..     150     230 ..     142     233 .. 0.85
   2 ?    5.9   0.7      0.02        16      34      84 ..     243     293 ..     238     304 .. 0.84
   3 ?   -0.6   0.1       2.2   1.7e+03      36      71 ..     321     357 ..     292     370 .. 0.47
   4 ?   -0.0   0.3       1.4   1.1e+03      70      93 ..     460     483 ..     442     493 .. 0.75
   5 ?    6.7   2.0     0.012       9.1      33      89 ..     523     580 ..     508     585 .. 0.70
   6 ?   12.4   0.6   0.00019      0.15      15      83 ..     606     674 ..     603     684 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00096
                        BLOC1_2  17 atvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqq....idqiekqvteLeeavseLDeyskeLE 92 
                                    ++++d+++L ++ ++  ek+ ++    +s +k +ekl+e+  ++q+ l++       +e++++ Lee+  +++ey +eLE
  gi|119720477|ref|YP_920972.1| 150 IAQKDLEHLLRMGKNEREKVINMMMGFESYNKAIEKLEEERRAMQQELEKkvleKSSLEDKLRNLEELKVKVEEYRRELE 229
                                    6899*********************************99876665555432211578**********************9 PP

                        BLOC1_2  93 a 93 
                                    +
  gi|119720477|ref|YP_920972.1| 230 E 230
                                    6 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.02
                        BLOC1_2  34 ekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseL 84 
                                    e+  k+++ +++l + l + ++++ ++++  ++i ++e++ ++Lee + +L
  gi|119720477|ref|YP_920972.1| 243 ERSRKVREYLDGLLRVLREREKTSRSIEEVERRIRELEEERRSLEEKAVKL 293
                                    666788888999999999999999999999999999999999999988777 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 2.2
                        BLOC1_2  36 ykklkdvaaslekkleklnekye.elqpylqqidqie 71 
                                     ++ +++a +++ k+ +l  ky+  l+++ + +++i 
  gi|119720477|ref|YP_920972.1| 321 AEEERRRAIEFSGKALELLDKYQsLLDEKRRTLERIA 357
                                    3334444444454544555555522333333333333 PP

  == domain 4  score: -0.0 bits;  conditional E-value: 1.4
                        BLOC1_2  70 iekqvteLeeavseLDeyskeLEa 93 
                                    +e+++++Le  v+  ++ sk+LE+
  gi|119720477|ref|YP_920972.1| 460 VEERLKSLERDVADRESLSKRLEE 483
                                    566677777777777777777764 PP

  == domain 5  score: 6.7 bits;  conditional E-value: 0.012
                        BLOC1_2  33 sekykklkdvaaslekkleklnekyeelqpylqqid.qiekqvteLeeavseLDeysk 89 
                                    +e+y+  + + + lek++  + e+  +l+++l++++  +e++v++L e++++ +e   
  gi|119720477|ref|YP_920972.1| 523 EEEYERARAEKEALEKEAASVGERVSQLEKQLEEVErSVEERVERLGELAKRREELLD 580
                                    4667777777777777777777777777777777763477777777777776555554 PP

  == domain 6  score: 12.4 bits;  conditional E-value: 0.00019
                        BLOC1_2  15 leatvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavse 83 
                                    +e++   y++  +l +++s++ ++ +++   l+ +l + ++k eel    +++ ++e +v+eLe  v++
  gi|119720477|ref|YP_920972.1| 606 IEGVEVVYNTYDRLYQQVSRRLAEAEERRRVLTGELRDAEKKLEELPAVRDRLAKLESEVRELEVEVNA 674
                                    56666679999999**************************************************88875 PP

>> FPP  Filament-like plant protein, long coiled-coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1  20.3   1.2e-05    0.0097     681     815 ..     177     324 ..     125     337 .. 0.77
   2 ?    5.7   9.9    0.0046       3.6     714     806 ..     477     572 ..     431     583 .. 0.51
   3 ?    4.2   1.8     0.013       9.8     259     320 ..     614     678 ..     603     701 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.2e-05
                            FPP 681 gsnesk....keenkllkeeleelksekenlevelksate...nleslkaqlqesEqllaelkseLeslkeskslaetql 753
                                    +s+++     +ee++ +++ele+  +ek+ le +l++ +e   ++e+    l+e E+ l  l+se e++++ ++ ++  l
  gi|119720477|ref|YP_920972.1| 177 ESYNKAieklEEERRAMQQELEKKVLEKSSLEDKLRNLEElkvKVEEYRRELEEVEKELPALRSEEERSRKVREYLDGLL 256
                                    22222245558999999***************999988887779****************************99998654 PP

                            FPP 754 ......kcmkesyesletrateleaelnelkqkieaLeveLeeekksheeleakckelqeqlervekk 815
                                          ++ + s e++e r +ele+e ++l++k+ +L+ eLe +++   ele + + ++e + ++e++
  gi|119720477|ref|YP_920972.1| 257 rvlrerEKTSRSIEEVERRIRELEEERRSLEEKAVKLKGELEAQRRRLGELEERGRAVREAFRKAEEE 324
                                    222211567778999*************************************9999999988887765 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0046
                            FPP 714 atenleslkaqlqesEqllae.lkseLes..lkeskslaetqlkcmkesyesletrateleaelnelkqkieaLeveLee 790
                                     +++le++ a+l   E+ l+  l +e+++  l+e ++ +  +    +e ye     ++ le+e  ++ +++++Le++Lee
  gi|119720477|ref|YP_920972.1| 477 LSKRLEEIDARLLRAEEELKGvLGEEFSKlpLQEVRERVSRERARREEEYERARAEKEALEKEAASVGERVSQLEKQLEE 556
                                    33344444444444444444312333433223444444444444445555555555555555555555555555555555 PP

                            FPP 791 ekksheeleakckelq 806
                                     ++s ee   +  el 
  gi|119720477|ref|YP_920972.1| 557 VERSVEERVERLGELA 572
                                    5555555544444444 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.013
                            FPP 259 eklqkenefLterLlameeEtkmLKEaL...akrnsELqaSrnmcAktaskLsqlEaqleelskq 320
                                    ++  +  +   +rL + ee  ++L   L   +k+ +EL a r  +Ak  s  ++lE+++++  + 
  gi|119720477|ref|YP_920972.1| 614 NTYDRLYQQVSRRLAEAEERRRVLTGELrdaEKKLEELPAVRDRLAKLESEVRELEVEVNARREA 678
                                    55566667778999999999999999985445999999999999999999999999998855443 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9  16.7   0.00026      0.21      26     111 ..     160     245 ..     155     253 .. 0.91
   2 ?    1.5  13.6      0.21   1.7e+02      55     169 ..     261     374 ..     255     387 .. 0.75
   3 ?    0.8  20.4      0.33   2.6e+02      50     169 ..     444     572 ..     432     583 .. 0.72
   4 ?   14.5   3.0   2.2e-05     0.017      56     116 ..     620     680 ..     610     699 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00026
                            GAS  26 elIkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlk 105
                                     + k+ +e++ ++    e+ +k ++++++e + ++++L+k   e+  L+ +l+n e+ k++ ++ +++l+e+ekel +l+
  gi|119720477|ref|YP_920972.1| 160 RMGKNEREKVINMMMGFESYNKAIEKLEEERRAMQQELEKKVLEKSSLEDKLRNLEELKVKVEEYRRELEEVEKELPALR 239
                                    55577788888899999999************************************************************ PP

                            GAS 106 wehevl 111
                                     e e  
  gi|119720477|ref|YP_920972.1| 240 SEEERS 245
                                    999865 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.21
                            GAS  55 enkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrfekvekerd...elykkfea 131
                                    e ++ +  ++++e+ + eL+++ +  e++     +lk +l+ + + l +l++  + +++ f k+e+er    e++ k  +
  gi|119720477|ref|YP_920972.1| 261 EREKTSRSIEEVERRIRELEEERRSLEEKA---VKLKGELEAQRRRLGELEERGRAVREAFRKAEEERRraiEFSGKALE 337
                                    556666677777777777777766666644...46788899999999999999999999999999998733345666777 PP

                            GAS 132 aiqevqqktglknllLekklkalqeelEkkeaqleevl 169
                                     ++++q   + k   Le+ +++l+++lE++ + l e  
  gi|119720477|ref|YP_920972.1| 338 LLDKYQSLLDEKRRTLER-IAELDKRLEERPKLLGESA 374
                                    788999999999999985.8899999999888887765 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.33
                            GAS  50 seisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdl...kwehevleqrfekvekerdely 126
                                    s +  e +rl+ +   +ee ++ L++++++ e+  ++l+++ arl ++e+elk +   + ++  l++  e+v++er + +
  gi|119720477|ref|YP_920972.1| 444 SRLRLERERLERERALVEERLKSLERDVADRESLSKRLEEIDARLLRAEEELKGVlgeEFSKLPLQEVRERVSRERARRE 523
                                    56677888888888999999*********************************873323334446777788999998888 PP

                            GAS 127 kkfeaa......iqevqqktglknllLekklkalqeelEkkeaqleevl 169
                                    +++e+a      +++    +g +   Lek+l++++ ++E++ ++l e+ 
  gi|119720477|ref|YP_920972.1| 524 EEYERAraekeaLEKEAASVGERVSQLEKQLEEVERSVEERVERLGELA 572
                                    8888874333334444445555555566666666666666655555554 PP

  == domain 4  score: 14.5 bits;  conditional E-value: 2.2e-05
                            GAS  56 nkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrfe 116
                                     ++ +  L +aee +  L  +l++ ek+ ++l +++ rl +le+e+++l++e +  ++ ++
  gi|119720477|ref|YP_920972.1| 620 YQQVSRRLAEAEERRRVLTGELRDAEKKLEELPAVRDRLAKLESEVRELEVEVNARREAVK 680
                                    5788899********************************************9987776655 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5  10.8      0.34   2.7e+02      79     130 ..     152     203 ..      79     216 .. 0.84
   2 ?    9.2  16.6    0.0014       1.1      24      84 ..     181     244 ..     176     251 .. 0.90
   3 ?   11.5  28.7   0.00028      0.22       9     133 ..     204     341 ..     198     348 .. 0.88
   4 ?    1.7   6.4      0.31   2.4e+02      74     119 ..     442     487 ..     438     501 .. 0.74
   5 ?    0.5  25.3      0.73   5.7e+02       3     113 ..     455     564 ..     452     585 .. 0.71
   6 ?    9.0   4.1    0.0017       1.4      20      93 ..     617     689 ..     612     692 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.34
                 CENP-F_leu_zip  79 rsekeeLekelqkkqervseLeslnsslenlleekEqekvqmkeeskaavee 130
                                    +++ e+L ++ ++++e+v ++ +  +s ++ +e++E+e++ m++e +++v e
  gi|119720477|ref|YP_920972.1| 152 QKDLEHLLRMGKNEREKVINMMMGFESYNKAIEKLEEERRAMQQELEKKVLE 203
                                    5667888888899999999999999999999999999999999999888753 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0014
                 CENP-F_leu_zip  24 dkvenLerelemseenqekvilea...EtskaevetlkeeieelaeelreleldLvalrsekee 84 
                                      +e+Le e   +++++ek +le+   E++   +e+lk ++ee ++el+e e +L alrse e 
  gi|119720477|ref|YP_920972.1| 181 KAIEKLEEERRAMQQELEKKVLEKsslEDKLRNLEELKVKVEEYRRELEEVEKELPALRSEEER 244
                                    579******************99655599999*****************************986 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.00028
                 CENP-F_leu_zip   9 lekLKeserkadsLkdkvenLerelemseenqekvileaEtskaevet.............lkeeieelaeelreleldL 75 
                                    ++ L    r+ + Lk kve+  rele++e+++ ++  e E s++  e                  iee +++ rele + 
  gi|119720477|ref|YP_920972.1| 204 KSSLEDKLRNLEELKVKVEEYRRELEEVEKELPALRSEEERSRKVREYldgllrvlrerekTSRSIEEVERRIRELEEER 283
                                    4557777788899******************************9998877787777777667788999999999999999 PP

                 CENP-F_leu_zip  76 valrsekeeLekelqkkqervseLeslnsslenlleekEqekvqmkeeskaaveeLqt 133
                                     +l +   +L+ el+ +++r  eLe++   +++  +++E+e+++  e s +a+e+L +
  gi|119720477|ref|YP_920972.1| 284 RSLEEKAVKLKGELEAQRRRLGELEERGRAVREAFRKAEEERRRAIEFSGKALELLDK 341
                                    9999999************************************************987 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 0.31
                 CENP-F_leu_zip  74 dLvalrsekeeLekelqkkqervseLeslnsslenlleekEqekvq 119
                                     ++ lr e+e Le+e     er ++Le+   + e+l +++E+ +++
  gi|119720477|ref|YP_920972.1| 442 TVSRLRLERERLERERALVEERLKSLERDVADRESLSKRLEEIDAR 487
                                    5778999999999999999999999999887777776666665333 PP

  == domain 5  score: 0.5 bits;  conditional E-value: 0.73
                 CENP-F_leu_zip   3 kkklhvlekLKeserk...adsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalr 79 
                                    +++  v+e+LK  er+    +sL  + e++++ l  +ee++  v l  E sk  +++++e     ++e+ + e + +  r
  gi|119720477|ref|YP_920972.1| 455 RERALVEERLKSLERDvadRESLSKRLEEIDARLLRAEEELKGV-LGEEFSKLPLQEVRER---VSRERARREEEYERAR 530
                                    44555666777666642224567777777777777777776554.4556777666666655...5669999999****** PP

                 CENP-F_leu_zip  80 sekeeLekelqkkqervseLeslnsslenlleek 113
                                     eke Leke     ervs+Le+  +++e+ +ee 
  gi|119720477|ref|YP_920972.1| 531 AEKEALEKEAASVGERVSQLEKQLEEVERSVEER 564
                                    ****************************999875 PP

  == domain 6  score: 9.0 bits;  conditional E-value: 0.0017
                 CENP-F_leu_zip  20 dsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelqkkq 93 
                                    d L ++v +  +e e+  + ++   ++aE++ +e+ ++++ + +l++e rele++++a r+e  +L +e+  k+
  gi|119720477|ref|YP_920972.1| 617 DRLYQQVSRRLAEAEERRRVLTGELRDAEKKLEELPAVRDRLAKLESEVRELEVEVNA-RREAVKLLREVSAKR 689
                                    66677777777777888888888899*****************************876.667777778877766 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   7.5      0.62   4.8e+02      70     110 ..     177     217 ..     152     240 .. 0.64
   2 ?    7.5  13.0    0.0051         4      27     113 ..     241     327 ..     226     365 .. 0.82
   3 ?   13.3   0.7   8.4e-05     0.065      70     123 ..     437     490 ..     428     505 .. 0.85
   4 ?    6.1   6.7     0.014        11      48     120 ..     512     584 ..     506     587 .. 0.63
   5 ?    3.8   2.7     0.072        56      84     135 ..     645     696 ..     615     701 .. 0.67

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.62
                           ADIP  70 erlqskierlktqleqlerelalvqakerqlekklktleqk 110
                                    e+ +++ie+l+++  + ++el+    ++ +le kl++le+ 
  gi|119720477|ref|YP_920972.1| 177 ESYNKAIEKLEEERRAMQQELEKKVLEKSSLEDKLRNLEEL 217
                                    55567777777777777777775555555666666555542 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0051
                           ADIP  27 tekveeniaaiinviysLlqardrdleqreslnetirkleaeierlqskierlktqleqlerelalvqakerqlekklkt 106
                                    +e++ +++++ ++ + ++l+ r++  +  e+++++ir+le e  +l+ k  +lk +le+++r+l  ++++ r  + + ++
  gi|119720477|ref|YP_920972.1| 241 EEERSRKVREYLDGLLRVLREREKTSRSIEEVERRIRELEEERRSLEEKAVKLKGELEAQRRRLGELEERGRAVREAFRK 320
                                    4667777777888888999********************************************************99999 PP

                           ADIP 107 leqklkn 113
                                    +e+  ++
  gi|119720477|ref|YP_920972.1| 321 AEEERRR 327
                                    9987665 PP

  == domain 3  score: 13.3 bits;  conditional E-value: 8.4e-05
                           ADIP  70 erlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrlkn 123
                                     r++ +++rl  + e+lere alv++++++le+++++ e+  k++ e  +rl +
  gi|119720477|ref|YP_920972.1| 437 YRKSVTVSRLRLERERLERERALVEERLKSLERDVADRESLSKRLEEIDARLLR 490
                                    5788899************************************99987777765 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.014
                           ADIP  48 rdrdleqreslnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqr 120
                                    r+r  ++r   +e+ ++ +ae+e l+++  ++ ++++qle++l+ v++   +   +l +l +   ++ + l+r
  gi|119720477|ref|YP_920972.1| 512 RERVSRERARREEEYERARAEKEALEKEAASVGERVSQLEKQLEEVERSVEERVERLGELAKRREELLDALSR 584
                                    4444555666666677777777777777777777777777777766666666666666666666666666555 PP

  == domain 5  score: 3.8 bits;  conditional E-value: 0.072
                           ADIP  84 eqlerelalvqakerqlekklktleqklknekeelqrlknalqqiktqyahe 135
                                    e++  el +v  ++++le ++++le  ++  +e ++ l+   +++++++a +
  gi|119720477|ref|YP_920972.1| 645 EKKLEELPAVRDRLAKLESEVRELEVEVNARREAVKLLREVSAKRRAAFAPS 696
                                    3333455577788888888888888888888888888888888888887755 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   2.7     0.042        33      39     106 ..     172     238 ..     168     243 .. 0.80
   2 ?    3.6   0.7     0.084        65      60     107 ..     261     308 ..     239     324 .. 0.64
   3 ?    6.1   0.1     0.014        11      52      88 ..     340     376 ..     324     392 .. 0.73
   4 ?    2.4   0.2      0.19   1.5e+02      39      80 ..     453     493 ..     446     517 .. 0.76
   5 ?    7.6   2.6    0.0049       3.8      44     122 ..     475     559 ..     465     561 .. 0.76
   6 ?    7.0   0.8    0.0075       5.8      94     122 ..     531     559 ..     500     580 .. 0.52
   7 ?    4.2   0.3     0.055        43      48     106 ..     621     682 ..     610     688 .. 0.64

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.042
                        DUF1664  39 lsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesv 106
                                    +    es  k +e++ e+ +a +++L++++ +  ++l++  +  +e+k +v+e r++l+e+++++ ++
  gi|119720477|ref|YP_920972.1| 172 MMMGFESYNKAIEKLEEERRAMQQELEKKVLE-KSSLEDKLRNLEELKVKVEEYRRELEEVEKELPAL 238
                                    55666777788888888888888888888866.56789999999999999999999999999988665 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.084
                        DUF1664  60 tkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvk 107
                                     +++ s+ i++v++++ e +e  ++++e+  +++++l++ ++ + +++
  gi|119720477|ref|YP_920972.1| 261 EREKTSRSIEEVERRIRELEEERRSLEEKAVKLKGELEAQRRRLGELE 308
                                    345556666666666666666666666666666666666665555554 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.014
                        DUF1664  52 qvseslaatkrhLssridrvdkkldeqkeiskeikee 88 
                                    + ++sl + kr+  +ri+++dk+l+e  ++  e ++ 
  gi|119720477|ref|YP_920972.1| 340 DKYQSLLDEKRRTLERIAELDKRLEERPKLLGESARL 376
                                    34689999999999***********998877665554 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.19
                        DUF1664  39 lsdavesvskqleqvseslaatkrhLssridrvdkkldeqke 80 
                                    l+   + v ++l+++  ++a+ ++ Ls+r++++d++l   +e
  gi|119720477|ref|YP_920972.1| 453 LERERALVEERLKSLERDVAD-RESLSKRLEEIDARLLRAEE 493
                                    666677788888888888875.78999999999998866554 PP

  == domain 5  score: 7.6 bits;  conditional E-value: 0.0049
                        DUF1664  44 esvskqleqvseslaatkrhLssridrvdkkl......deqkeiskeikeevtevredlseigedvesvkeavegleskl 117
                                    es+sk+le++ + l ++ ++L+  + +  +kl      + +++  +  +ee +++r + ++++++  sv e v++le++l
  gi|119720477|ref|YP_920972.1| 475 ESLSKRLEEIDARLLRAEEELKGVLGEEFSKLplqevrERVSRERARREEEYERARAEKEALEKEAASVGERVSQLEKQL 554
                                    7889999999999999999988887765555422111133344455667889999************************* PP

                        DUF1664 118 eriee 122
                                    e++e 
  gi|119720477|ref|YP_920972.1| 555 EEVER 559
                                    **996 PP

  == domain 6  score: 7.0 bits;  conditional E-value: 0.0075
                        DUF1664  94 edlseigedvesvkeavegleskleriee 122
                                     + ++++++  sv e v++le++le++e 
  gi|119720477|ref|YP_920972.1| 531 AEKEALEKEAASVGERVSQLEKQLEEVER 559
                                    33333333333333333333333333332 PP

  == domain 7  score: 4.2 bits;  conditional E-value: 0.055
                        DUF1664  48 kqleqvseslaatkrhLssridrvdkkldeqkeis...keikeevtevredlseigedvesv 106
                                    +q+ +  ++ ++ +r L+ ++   +kkl+e  ++    +++++ev e++ ++++ +e v+ +
  gi|119720477|ref|YP_920972.1| 621 QQVSRRLAEAEERRRVLTGELRDAEKKLEELPAVRdrlAKLESEVRELEVEVNARREAVKLL 682
                                    55555556666778899999999999999987665111345556666666666665555554 PP

>> Sec8_exocyst  Sec8 exocyst complex component specific domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   1.5     0.026        20      80     129 ..     206     255 ..     132     272 .. 0.87
   2 ?   -0.3   0.1       1.2   9.2e+02      76     121 ..     271     316 ..     262     321 .. 0.70
   3 ?    5.2   0.3     0.023        18      86     124 ..     545     583 ..     534     587 .. 0.85
   4 ?    2.2   0.0       0.2   1.6e+02      74     104 ..     620     650 ..     610     694 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.026
                   Sec8_exocyst  80 siqesqekvselKesleeakkklstkkkeLkelnarsakykevieiLdai 129
                                    s+++  ++++elK ++ee +++l++ +keL  l  +  + ++v e Ld +
  gi|119720477|ref|YP_920972.1| 206 SLEDKLRNLEELKVKVEEYRRELEEVEKELPALRSEEERSRKVREYLDGL 255
                                    56666778899999999999999999999999998888888888888765 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.2
                   Sec8_exocyst  76 kilssiqesqekvselKesleeakkklstkkkeLkelnarsakyke 121
                                    ++ + i e +e+ + l e+  + k +l++++  L el++r ++++e
  gi|119720477|ref|YP_920972.1| 271 EVERRIRELEEERRSLEEKAVKLKGELEAQRRRLGELEERGRAVRE 316
                                    4455566666666777777777778888888888888888776665 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.023
                   Sec8_exocyst  86 ekvselKesleeakkklstkkkeLkelnarsakykevie 124
                                    e+vs+l ++lee +++++++ + L el++r  ++ + ++
  gi|119720477|ref|YP_920972.1| 545 ERVSQLEKQLEEVERSVEERVERLGELAKRREELLDALS 583
                                    799*************************99877666555 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.2
                   Sec8_exocyst  74 YskilssiqesqekvselKesleeakkklst 104
                                    Y+++ + ++e++e+ + l  +l++a+kkl++
  gi|119720477|ref|YP_920972.1| 620 YQQVSRRLAEAEERRRVLTGELRDAEKKLEE 650
                                    8999999999999999999999999998864 PP

>> Retrotrans_gag  Retrotransposon gag protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.9   0.00019      0.15      34      94 ..     195     255 ..     181     257 .. 0.81
   2 ?   -0.3   0.1       1.7   1.4e+03      36      70 ..     259     293 ..     253     320 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00019
                 Retrotrans_gag  34 kaflktflpserkdqleeelsslrQgtesvreYvtrfktladqlde...vlte..eakiekflaGL 94 
                                    +++ k+ l+   k+ le++l++l + + +v+eY ++++++  +l+       e    k++ +l+GL
  gi|119720477|ref|YP_920972.1| 195 QELEKKVLE---KSSLEDKLRNLEELKVKVEEYRRELEEVEKELPAlrsE--EerSRKVREYLDGL 255
                                    555666665...8999******************************6433..23467888888888 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.7
                 Retrotrans_gag  36 flktflpserkdqleeelsslrQgtesvreYvtrf 70 
                                    ++++   s+  ++ e+++++l ++ +s++e + ++
  gi|119720477|ref|YP_920972.1| 259 LREREKTSRSIEEVERRIRELEEERRSLEEKAVKL 293
                                    55566667788899999999999999998855555 PP

>> Bacillus_HBL  Bacillus haemolytic enterotoxin (HBL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   1.0     0.056        43     103     169 ..     179     244 ..     169     251 .. 0.88
   2 ?    3.8   0.0     0.058        45     114     172 ..     258     316 ..     242     321 .. 0.83
   3 ?   -2.7   0.0       5.6   4.4e+03      97     125 ..     471     499 ..     461     506 .. 0.80
   4 ?    2.5   0.1      0.15   1.2e+02      98     133 ..     538     573 ..     526     578 .. 0.82
   5 ?    0.7   0.0       0.5   3.9e+02     103     148 ..     654     699 ..     613     707 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.056
                   Bacillus_HBL 103 llellekLqeeiqqnqkevkqlikeLkklklklakdsknFktdvdeltsilagdsgvisqlqneied 169
                                      +++ekL+ee    q+e ++++ e ++l++kl  + +++k +v+e    l+  ++++++l+ e e+
  gi|119720477|ref|YP_920972.1| 179 YNKAIEKLEEERRAMQQELEKKVLEKSSLEDKLR-NLEELKVKVEEYRRELEEVEKELPALRSEEER 244
                                    5688999999999999999999999999999996.78999999999999999999999999988665 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.058
                   Bacillus_HBL 114 iqqnqkevkqlikeLkklklklakdsknFktdvdeltsilagdsgvisqlqneiedlqg 172
                                    +    +++ ++i+e+++   +l+++ +++++++ +l+  l+++   + +l+++   +++
  gi|119720477|ref|YP_920972.1| 258 VLREREKTSRSIEEVERRIRELEEERRSLEEKAVKLKGELEAQRRRLGELEERGRAVRE 316
                                    45567788899*************************************99998766665 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 5.6
                   Bacillus_HBL  97 kkdkaellellekLqeeiqqnqkevkqli 125
                                      d+++l+++le++ + +   ++e k ++
  gi|119720477|ref|YP_920972.1| 471 VADRESLSKRLEEIDARLLRAEEELKGVL 499
                                    47899999999999999999999888776 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.15
                   Bacillus_HBL  98 kdkaellellekLqeeiqqnqkevkqlikeLkklkl 133
                                    k+ a++ e++++L++++ + + +v++ ++ L +l++
  gi|119720477|ref|YP_920972.1| 538 KEAASVGERVSQLEKQLEEVERSVEERVERLGELAK 573
                                    566788899999999999999999999999998875 PP

  == domain 5  score: 0.7 bits;  conditional E-value: 0.5
                   Bacillus_HBL 103 llellekLqeeiqqnqkevkqlikeLkklklklakdsknFktdvde 148
                                    + ++l kL++e+ + + ev++  +++k l++  ak  + F   v++
  gi|119720477|ref|YP_920972.1| 654 VRDRLAKLESEVRELEVEVNARREAVKLLREVSAKRRAAFAPSVEQ 699
                                    6789999*************99999999999999999999888876 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5  27.4    0.0084       6.5     273     484 ..     150     368 ..     100     373 .. 0.79
   2 ?    6.8   9.9    0.0034       2.7     261     377 ..     459     578 ..     434     584 .. 0.68
   3 ?    4.5   1.0     0.016        13     344     409 ..     604     669 ..     602     700 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0084
                         DUF812 273 ksksdlaellsefseksetdslktkgsrfthaekl..qftkeelakkaeteeelkkkreeeleelqeqieeleskieele 350
                                     +++dl++ll+    k+e++++ + +  f++ +k+  ++++e+   ++++e e k  ++ +le+  +++eel+ k+ee++
  gi|119720477|ref|YP_920972.1| 150 IAQKDLEHLLRMG--KNEREKVINMMMGFESYNKAieKLEEER--RAMQQELEKKVLEKSSLEDKLRNLEELKVKVEEYR 225
                                    4566777766655..6666667777888888888877777774..45666666666666777777788999999****** PP

                         DUF812 351 eeikklessikqveeeleeekeeneelekevkl...kkktlellpdaeeniekLqalveasaqrlvelakqWekhRvpl. 426
                                     e++++e+++  + +e e+ ++ +e l   +++   ++kt   +++ e  i++L+++  + +++ v+l+ + e++R+ l 
  gi|119720477|ref|YP_920972.1| 226 RELEEVEKELPALRSEEERSRKVREYLDGLLRVlreREKTSRSIEEVERRIRELEEERRSLEEKAVKLKGELEAQRRRLg 305
                                    ********999999999888888888776554322299**************************************9873 PP

                         DUF812 427 ..ieeyrelkesksekekeaerkle...eikklrekmkevaeelrqkeellkqLvaeleklpk 484
                                       e  r+ +e+ ++ e+e++r +e   +  +l +k + + +e r+  e + +L ++le++pk
  gi|119720477|ref|YP_920972.1| 306 elEERGRAVREAFRKAEEERRRAIEfsgKALELLDKYQSLLDEKRRTLERIAELDKRLEERPK 368
                                    314567899999999999999999865566778899999********************9998 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0034
                         DUF812 261 alkseeae.ssasksksdlaellsefseksetdslktkgsrfthaeklqftkeela...kkaeteeelkkkreeeleelq 336
                                    +++++ ++ +++  ++++l++ l+e++ +  + +++ kg   ++  kl +++ + +   ++a+ eee + +r e+ e+l+
  gi|119720477|ref|YP_920972.1| 459 LVEERLKSlERDVADRESLSKRLEEIDARLLRAEEELKGVLGEEFSKLPLQEVRERvsrERARREEEYERARAEK-EALE 537
                                    334444445667777777888888887777777777777777777777555442223345666666766666655.7888 PP

                         DUF812 337 eqieeleskieeleeeikklessikqveeeleeekeeneel 377
                                    ++  ++ +++++le++++++e s+++  e l e+ + +eel
  gi|119720477|ref|YP_920972.1| 538 KEAASVGERVSQLEKQLEEVERSVEERVERLGELAKRREEL 578
                                    88888888888888888888888888888888887777776 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.016
                         DUF812 344 skieeleeeikklessikqveeeleeekeeneelekevklkkktlellpdaeeniekLqalveasa 409
                                    ++ie +e   ++++   +qv+  l e +e +  l+ e++ ++k le lp     ++kL+++v + +
  gi|119720477|ref|YP_920972.1| 604 RDIEGVEVVYNTYDRLYQQVSRRLAEAEERRRVLTGELRDAEKKLEELPAVRDRLAKLESEVRELE 669
                                    567777777788888889999999999999999999999999999999999999999998887765 PP

>> Cauli_AT  Aphid transmission protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   4.6    0.0083       6.5      90     158 ..     153     221 ..     147     225 .. 0.92
   2 ?    4.2   0.9     0.046        36     107     142 ..     263     299 ..     254     321 .. 0.71
   3 ?   -1.5   0.0       2.7   2.1e+03      95     143 ..     317     366 ..     311     386 .. 0.47
   4 ?    4.7   0.1     0.034        26     122     163 .]     459     500 ..     434     500 .. 0.85
   5 ?    2.2   0.2       0.2   1.5e+02      81     136 ..     504     563 ..     502     585 .. 0.66
   6 ?    2.3   0.1      0.18   1.4e+02     104     142 ..     642     680 ..     609     705 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0083
                       Cauli_AT  90 kklkkifkeggedkekktklletLkeaqnrikkleeetkklaekivtekllkeevkdlderlseirdsl 158
                                    k+l++ ++ g +++ek  + +   +  ++ i+kleee + ++++++ + l k+ + d  ++l+e++ ++
  gi|119720477|ref|YP_920972.1| 153 KDLEHLLRMGKNEREKVINMMMGFESYNKAIEKLEEERRAMQQELEKKVLEKSSLEDKLRNLEELKVKV 221
                                    678899999************************************************999999998776 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.046
                       Cauli_AT 107 tklletLkeaqnrikkleeetkklaek.ivtekllke 142
                                     k   +++e++ ri++leee ++l+ek ++ +  l++
  gi|119720477|ref|YP_920972.1| 263 EKTSRSIEEVERRIRELEEERRSLEEKaVKLKGELEA 299
                                    456678999999**************95544444443 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 2.7
                       Cauli_AT  95 ifkeggedkekktklletLkeaqnrikkleeetkklaek.ivtekllkee 143
                                     f++++e++ ++ +      e  ++ + l +e+++  e+  + +k l+e 
  gi|119720477|ref|YP_920972.1| 317 AFRKAEEERRRAIEFSGKALELLDKYQSLLDEKRRTLERiAELDKRLEER 366
                                    55555555555554433333333333333222222222213333433333 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.034
                       Cauli_AT 122 kleeetkklaekivtekllkeevkdlderlseirdslkaiiG 163
                                     +ee+ k+l+ ++  ++ l + + ++d rl + +++lk ++G
  gi|119720477|ref|YP_920972.1| 459 LVEERLKSLERDVADRESLSKRLEEIDARLLRAEEELKGVLG 500
                                    468999*********************************998 PP

  == domain 5  score: 2.2 bits;  conditional E-value: 0.2
                       Cauli_AT  81 sksPfgsvfkklkkifkeggedkekktklletLkeaqn....rikkleeetkklaekivt 136
                                    sk P+++v +++++   + +e++e++  + e L++       r+++le++ ++++  ++ 
  gi|119720477|ref|YP_920972.1| 504 SKLPLQEVRERVSRERARREEEYERARAEKEALEKEAAsvgeRVSQLEKQLEEVERSVEE 563
                                    688888888888888777888888888888888765544555666666666666555543 PP

  == domain 6  score: 2.3 bits;  conditional E-value: 0.18
                       Cauli_AT 104 ekktklletLkeaqnrikkleeetkklaekivtekllke 142
                                     ++ k+le L  +++r  kle e+++l+ ++++++   +
  gi|119720477|ref|YP_920972.1| 642 RDAEKKLEELPAVRDRLAKLESEVRELEVEVNARREAVK 680
                                    455667777888888999999999999887776655444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (840 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2598  (0.144905); expected 358.6 (0.02)
Passed bias filter:                      971  (0.0541581); expected 358.6 (0.02)
Passed Vit filter:                       254  (0.014167); expected 17.9 (0.001)
Passed Fwd filter:                       143  (0.0079759); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 2.35u 0.45s 00:00:02.80 Elapsed: 00:00:00.65
# Mc/sec: 3907.63
//
Query:       gi|119720478|ref|YP_920973.1|  [L=320]
Description: D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.5e-56  188.1   0.0    1.1e-55  187.8   0.0    1.1  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
    9.6e-18   64.1   0.0    1.2e-17   63.8   0.0    1.1  1  2-Hacid_dh       D-isomer specific 2-hydroxyacid dehydrogenas
    2.9e-06   27.5   0.0    4.9e-06   26.7   0.0    1.3  1  AdoHcyase_NAD    S-adenosyl-L-homocysteine hydrolase, NAD bin
    4.8e-05   23.0   0.0      9e-05   22.1   0.0    1.4  1  IlvN             Acetohydroxy acid isomeroreductase, NADPH-bi
    5.1e-05   23.8   0.3    0.00022   21.7   0.0    2.1  3  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    0.00014   22.1   0.0    0.00025   21.2   0.0    1.4  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
    0.00054   19.3   0.0     0.0016   17.8   0.0    1.7  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
    0.00076   19.7   0.1     0.0054   17.0   0.0    2.4  2  TrkA_N           TrkA-N domain
     0.0012   19.3   0.0     0.0024   18.4   0.0    1.5  1  XdhC_C           XdhC Rossmann domain
     0.0072   16.9   0.3       0.23   12.0   0.0    2.7  2  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
     0.0073   16.4   0.0      0.015   15.4   0.0    1.5  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
     0.0095   15.5   0.0      0.052   13.1   0.0    2.0  2  DUF364           Putative heavy-metal chelation
  ------ inclusion threshold ------
      0.014   15.8   0.1      0.058   13.8   0.0    2.0  2  NAD_binding_7    Putative NAD(P)-binding
      0.031   14.2   0.4       0.69    9.8   0.0    2.4  2  NAD_binding_10   NAD(P)H-binding
       0.05   13.6   0.1        1.5    8.8   0.0    2.4  2  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
      0.056   13.1   0.0       0.13   11.9   0.0    1.5  1  ELFV_dehydrog    Glutamate/Leucine/Phenylalanine/Valine dehyd
      0.077   13.0   0.0        5.8    6.9   0.0    2.4  2  ADH_zinc_N       Zinc-binding dehydrogenase
      0.079   13.0   0.0       0.17   11.9   0.0    1.6  1  DpaA_N           Dipicolinate synthase subunit A N-terminal d
      0.081   13.2   0.0       0.27   11.5   0.0    1.9  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
       0.09   13.1   0.0        0.2   12.0   0.0    1.6  1  Gp_dh_N          Glyceraldehyde 3-phosphate dehydrogenase, NA
       0.15   12.0   0.0       0.28   11.1   0.0    1.5  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding


Domain annotation for each model (and alignments):
>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.8   0.0   1.3e-58   1.1e-55       1     178 []     102     283 ..     102     283 .. 0.94

  Alignments for each domain:
  == domain 1  score: 187.8 bits;  conditional E-value: 1.3e-58
                                    HHHHHHHHTTHHHHHHHHHTTCC.HTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHT CS
                   2-Hacid_dh_C   1 lalllallrrlaeadeevregew.ksekallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelg 79 
                                    +al+lal++r+ e d ev++g w +  ++    +l g+tv i+G+G+IG++va+++kaf+m+v+a++++++k++  +++ 
  gi|119720478|ref|YP_920973.1| 102 FALILALAKRVVEQDGEVKRGLWrSFTEENFLADLDGSTVTIVGYGNIGREVARIAKAFNMRVLAVKKNPEKDS-LADEV 180
                                    589********************7667788888************************************99887.88888 PP

                                    CEECSHHHHHHH-SEEEE-S--STTTTTSBSHHHHHCSTTTEEEEESS-GGGB-HHHHHHHHHTTSCCEEEES--SSSSS CS
                   2-Hacid_dh_C  80 velvsleellaesDivslhlpltpetrhlinaeelakmkkgailiNtaRGglvdeeaLleaLksgkiagaalDvfeeepl 159
                                    + ++ l e+l+++D+v+l+lplt et+ li+++el++mkk+a+l+N++RG++vdeeaL++aL +g+iaga++Dv++  p+
  gi|119720478|ref|YP_920973.1| 181 YPVERLAEALSQADFVVLALPLTRETYRLIGEKELKSMKKTAYLVNVGRGAVVDEEALYRALSEGWIAGAGIDVWWRYPP 260
                                    8999**************************************************************************** PP

                                    GTC..HHH..HHSTTEEE-SS-T CS
                   2-Hacid_dh_C 160 ped..spl..lelpnviltPHia 178
                                    ++d  spl   +lpnv+ tPH a
  gi|119720478|ref|YP_920973.1| 261 DKDypSPLgvHKLPNVVATPHKA 283
                                    *99444668899*********76 PP

>> 2-Hacid_dh  D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.8   0.0   1.4e-20   1.2e-17      37     132 ..      39     313 ..      15     315 .. 0.97

  Alignments for each domain:
  == domain 1  score: 63.8 bits;  conditional E-value: 1.4e-20
                                    HTTESEEEE-TTS-BSHHHHHHHTT--EEEESSSSCTTB-HHHHHHTT-EEEE-TTTTHHHHHHHH.............. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............. RF
                     2-Hacid_dh  37 akdadalivrsntkvtaevlealpkLkviaragvGvDnvDldaakerGilVtnvpgystesvAElt.............. 102
                                    +++ad+ i +      ++  +a+ +Lk+++  ++G Dn+Dl+++ erG++V+   g+++++vAE++              
  gi|119720478|ref|YP_920973.1|  39 IEEADVAIAFILP---RDAAQAAGRLKFVQVPAAGADNLDLEYLFERGVKVATSKGCNARAVAEHAfalilalakrvveq 115
                                    5666666666644...8888999********************************************************* PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                     2-Hacid_dh 103 ................................................................................ 102
                                                                                                                    
  gi|119720478|ref|YP_920973.1| 116 dgevkrglwrsfteenfladldgstvtivgygnigrevariakafnmrvlavkknpekdsladevypverlaealsqadf 195
                                    ******************************************************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                     2-Hacid_dh 103 ................................................................................ 102
                                                                                                                    
  gi|119720478|ref|YP_920973.1| 196 vvlalpltretyrligekelksmkktaylvnvgrgavvdeealyralsegwiagagidvwwryppdkdypsplgvhklpn 275
                                    ******************************************************************************** PP

                                    ........T-BHHHHHHHHHHHHHHHHHHHTTCCGTTB CS
                                    ........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     2-Hacid_dh 103 ........aaTeeaqeniaeeaaenlvaflkgespana 132
                                            ++T++a+en  + a+en+++f++ge+p n 
  gi|119720478|ref|YP_920973.1| 276 vvatphkaGWTRKARENCLRFACENVLRFVRGEEPLNL 313
                                    **********************************9986 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0   5.7e-09   4.9e-06      21     111 ..     136     229 ..     131     245 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 5.7e-09
                                    -TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHHHHHCTT-EE--HHHCTTT-SEEEE-....SSSSSSB-HHH CS
                  AdoHcyase_NAD  21 laGkvavvaGyGdvGkGcaaslkglGarvivtevdPicalqaameGfevvtleevvkkadivvtt....tGnkdiitleh 96 
                                    l G ++ ++GyG++G+  a+  k++  rv+    +P      a e + v +l e++++ad+vv +      +  +i  ++
  gi|119720478|ref|YP_920973.1| 136 LDGSTVTIVGYGNIGREVARIAKAFNMRVLAVKKNPEKDSL-ADEVYPVERLAEALSQADFVVLAlpltRETYRLIGEKE 214
                                    56999*******************************87654.5799****************9752221456789***** PP

                                    HCCS-TTEEEEE-SS CS
                  AdoHcyase_NAD  97 lkkmkddaivcniGh 111
                                    lk+mk++a + n+G 
  gi|119720478|ref|YP_920973.1| 215 LKSMKKTAYLVNVGR 229
                                    *************97 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   1.1e-07     9e-05       2      86 ..     136     219 ..     135     240 .. 0.73

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.1e-07
                                    HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHHH..HHHHHH CS
                           IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDelq..kevyee 79 
                                    l+g +++++GyG+ G+  a+  +   + v    + +    ++  +e + v ++aea ++ad+v++ +P + +  + + e+
  gi|119720478|ref|YP_920973.1| 136 LDGSTVTIVGYGNIGREVARIAKAFNMRVLAVKK-NP-EKDSLADEVYPVERLAEALSQADFVVLALPLTREtyRLIGEK 213
                                    6789******************999888865443.33.466667889********************9543310333344 PP

                                    HTGGG-- CS
                           IlvN  80 eiepnlk 86 
                                    e++ ++k
  gi|119720478|ref|YP_920973.1| 214 ELK-SMK 219
                                    443.344 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       6.9   5.9e+03      59      81 ..      39      61 ..      34      75 .. 0.82
   2 ?   -1.9   0.0         6   5.2e+03      48      68 ..      86     107 ..      53     115 .. 0.59
   3 !   21.7   0.0   2.6e-07   0.00022       2      71 ..     141     202 ..     140     225 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 6.9
                                   HHH-SEEEE-S-HHHHHHHHHHC CS
                  F420_oxidored 59 aeeadvvvlavkpedveevlsel 81
                                   +eeadv +  + p+d+++++  l
  gi|119720478|ref|YP_920973.1| 39 IEEADVAIAFILPRDAAQAAGRL 61
                                   57899999988888888887766 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 6
                                    -EEECECHHHHHH.H-SEEEE- CS
                  F420_oxidored  48 vkvtavdneeaae.eadvvvla 68 
                                    v ++++ n+ a++ +a  ++la
  gi|119720478|ref|YP_920973.1|  86 VATSKGCNARAVAeHAFALILA 107
                                    4444445666655244444444 PP

  == domain 3  score: 21.7 bits;  conditional E-value: 2.6e-07
                                    EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-H CS
                  F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkp 71 
                                    + i+G+Gn+g+ +a+ + a +     ++ a ++npek  +la+e++    +   +ea+++ad+vvla++ 
  gi|119720478|ref|YP_920973.1| 141 VTIVGYGNIGREVARIAKAFN---MRVL-AVKKNPEKD-SLADEVY--PVE-RLAEALSQADFVVLALPL 202
                                    789************666666...8888.769999975.6777765..344.589************997 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0     3e-07   0.00025       2     106 ..     141     244 ..     140     252 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 3e-07
                                    EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHS.HCCC- CS
                  NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdevieg.lleal 80 
                                    + ++G G++G++ a+  ++ +++v ++  +    ++ +a+++ ++e ++e+++++d+v++ ++ ++++  +i +  l+++
  gi|119720478|ref|YP_920973.1| 141 VTIVGYGNIGREVARIAKAFNMRVLAVKKN--PEKDSLADEVYPVERLAEALSQADFVVLALPLTRETYRLIGEkELKSM 218
                                    789***********9877777777766666..55677778899*****************************9988999* PP

                                    -TT-EEEE-S---HHHHHHHHHHHHH CS
                  NAD_binding_2  81 kkgdilidgstsspedtrelakelke 106
                                    kk ++l++++  ++ d + l+++l+e
  gi|119720478|ref|YP_920973.1| 219 KKTAYLVNVGRGAVVDEEALYRALSE 244
                                    **********9999999998888776 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.8e-06    0.0016      29     127 ..     139     227 ..     132     235 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.8e-06
                                    -EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHHHHHHHHHHH-SEEEE---BTTSS--- CS
                    AlaDh_PNT_C  29 akvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvevlksqeellaeavkeadvvigtvlipGkkaPk 108
                                    ++v+++G G  G + +++ak+++ +V ++ ++p++    +++            e laea+++ad v+ +     +++ +
  gi|119720478|ref|YP_920973.1| 139 STVTIVGYGNIGREVARIAKAFNMRVLAVKKNPEKDSLADEVYPV---------ERLAEALSQADFVVLALP-LTRETYR 208
                                    78*******************************987666664433.........689***********9955.568999* PP

                                    SC-HHHHHTS-TTEEEEET CS
                    AlaDh_PNT_C 109 LvteemvksMkpgsVivDv 127
                                    L+ e+ +ksMk+ + +v v
  gi|119720478|ref|YP_920973.1| 209 LIGEKELKSMKKTAYLVNV 227
                                    ************9999876 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1       1.6   1.4e+03      58      70 ..      37      49 ..      35      59 .. 0.79
   2 !   17.0   0.0   6.3e-06    0.0054       1      33 [.     141     173 ..     141     206 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.6
                                   TTGGGESEEEE-S CS
                         TrkA_N 58 agiekadaviaat 70
                                   agie+ad+ ia +
  gi|119720478|ref|YP_920973.1| 37 AGIEEADVAIAFI 49
                                   89*****999875 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 6.3e-06
                                    EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHH CS
                         TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeer 33 
                                    + i+G+G++Gr++a+  ++ +++v+++ k++e+
  gi|119720478|ref|YP_920973.1| 141 VTIVGYGNIGREVARIAKAFNMRVLAVKKNPEK 173
                                    579****************5557********87 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   2.8e-06    0.0024       2      66 ..     142     243 ..     141     251 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.8e-06
                                    EEE--STTHHHHHHHHHHHTEEEEEEES-GGGG...............-GGG-TT-SE...................... CS
                         XdhC_C   2 vifGaghvaqalarlaaalgfrvtvvdpreefa...............tkerfpeade...................... 44 
                                     i+G g++++++ar+a+a+++rv  v++++e                          +                      
  gi|119720478|ref|YP_920973.1| 142 TIVGYGNIGREVARIAKAFNMRVLAVKKNPEKDsladevypverlaeaL--------Sqadfvvlalpltretyrligek 213
                                    79****************************7557777777555443330........25556666666666777777777 PP

                                    ........-EEEE--S-HHHHHHHHHHHSS CS
                         XdhC_C  45 ........tavvvlthdhklDaealeaalr 66 
                                            +++v + ++   D+eal +al+
  gi|119720478|ref|YP_920973.1| 214 elksmkktAYLVNVGRGAVVDEEALYRALS 243
                                    78888888888999999999***9999993 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1      0.38   3.3e+02       6      60 ..      33      89 ..      32      95 .. 0.66
   2 !   12.0   0.0   0.00027      0.23       2      32 ..     141     171 ..     140     194 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.38
                                   CSSHHHHHHHHHHHHTTSEEEEEESSSSSS.TTSSHHHHHHH.HHHHHHTTEEEECS CS
                      Pyr_redox  6 GgGyiglElAgalaelgkkVtvversdkll.rllDeeaskil.qeklekngievlln 60
                                   G G+ g+E+A ++ ++       +++ +l   + +++ +++l  e+l ++g++v ++
  gi|119720478|ref|YP_920973.1| 33 GKGFAGIEEADVAIAFILPRDAAQAAGRLKfVQVPAAGADNLdLEYLFERGVKVATS 89
                                   889999999988776666666666666666656666666666567777777777665 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00027
                                    EEEECSSHHHHHHHHHHHHTTSEEEEEESSS CS
                      Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversd 32 
                                    v++vG G+ig E+A ++++++ +V  v  ++
  gi|119720478|ref|YP_920973.1| 141 VTIVGYGNIGREVARIAKAFNMRVLAVKKNP 171
                                    89********************998887765 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.7e-05     0.015       7     100 ..     133     220 ..     127     232 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.7e-05
                                    HS..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-...S CS
                   Shikimate_DH   7 leslkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisa...t 83 
                                    l +l++++v+++G G+++++va+   a +++ v+ +  + e+ ++la+e+        ++e l e+l++ad v+ a   t
  gi|119720478|ref|YP_920973.1| 133 LADLDGSTVTIVGYGNIGREVARIAKAFNMR-VLAVKKNPEK-DSLADEV-------YPVERLAEALSQADFVVLAlplT 203
                                    558999*****************99999999.7777788877.6798888.......688*************9995545 PP

                                    SSSS-SB-HHHHHCCHH CS
                   Shikimate_DH  84 aseepilekeeveealk 100
                                      +  ++ ++e+++++k
  gi|119720478|ref|YP_920973.1| 204 RETYRLIGEKELKSMKK 220
                                    55666777777776664 PP

>> DUF364  Putative heavy-metal chelation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   6.1e-05     0.052       8      68 ..     135     198 ..     130     200 .. 0.74
   2 ?   -0.8   0.0       1.2     1e+03     116     131 ..     230     245 ..     223     249 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.1e-05
                         DUF364   8 ikkgkkVvvVGy..fapvlkklkekgaeltvlelnpnllee..eegdlpdeaaeellpeadvvii 68 
                                      +g +V++VGy  +++ + ++  k+ +++vl  ++n +++  +++++p e+ +e+l++ad v++
  gi|119720478|ref|YP_920973.1| 135 DLDGSTVTIVGYgnIGREVARIA-KAFNMRVLAVKKNPEKDslADEVYPVERLAEALSQADFVVL 198
                                    66899******988888888887.555555555555555550055566**************996 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.2
                         DUF364 116 vvvtdpdkllraiaeG 131
                                      v+d+++l+ra++eG
  gi|119720478|ref|YP_920973.1| 230 GAVVDEEALYRALSEG 245
                                    5699***********9 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0         4   3.4e+03      64      86 ..       3      27 ..       1      34 [. 0.76
   2 ?   13.8   0.0   6.8e-05     0.058       3      75 ..     134     206 ..     132     229 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 4
                  NAD_binding_7 64 lviaatddrelneriaeaa..karr 86
                                   +v++a d +e ++ri+e+   +++r
  gi|119720478|ref|YP_920973.1|  3 TVYVALDLKEWERRIVEETlsREAR 27
                                   7999999999999999987434444 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 6.8e-05
                  NAD_binding_7   3 ldlkgkkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvk..laeeelekdlegadlviaatddreln 75 
                                     dl+g +v +vG G+++ + +r   +++ +v  v ++  +e ++l +  +  e l + l++ad+v+ a + + + 
  gi|119720478|ref|YP_920973.1| 134 ADLDGSTVTIVGYGNIGREVARIAKAFNMRVLAVKKN--PEKDSLADevYPVERLAEALSQADFVVLALPLTRET 206
                                    5899*************99888888887777777777..444444443233455678899999999998655444 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1      0.17   1.5e+02      77     103 ..      44      73 ..      15     103 .. 0.71
   2 ?    9.8   0.0    0.0008      0.69       4      69 ..     147     202 ..     145     235 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.17
                                    HHHHHH...HHHHHCT--EEEEEEETTTTS CS
                 NAD_binding_10  77 gakniv...daakeagvkRfvlvsaigvgd 103
                                    +a++ +   daa++ag  +fv v a+g+++
  gi|119720478|ref|YP_920973.1|  44 VAIAFIlprDAAQAAGRLKFVQVPAAGADN 73 
                                    3555555559*****************996 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0008
                                    SHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES-.- CS
                 NAD_binding_10   4 GkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsal.g 69 
                                    G++Gr++++ + a  +++v a+  npek + l++         +v  ve laeal++ad Vv al  
  gi|119720478|ref|YP_920973.1| 147 GNIGREVARIAKAF-NMRVLAVKKNPEKDS-LAD---------EVYPVERLAEALSQADFVVLALpL 202
                                    99**********99.6***********976.654.........56667899*********9999852 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.15   1.3e+02       2      27 ..     141     166 ..     140     174 .. 0.80
   2 ?    8.8   0.0    0.0017       1.5      52     106 ..     175     231 ..     157     245 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.15
                                    EEEE--SHHHHHHHHHHHTTT--EEE CS
                 NAD_Gly3P_dh_N   2 iavlGaGswGtalAkvlaenghevrl 27 
                                    ++++G G+ G  +A++ +  + +v  
  gi|119720478|ref|YP_920973.1| 141 VTIVGYGNIGREVARIAKAFNMRVLA 166
                                    9*************998877776665 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0017
                                    ---TTEEEES-HHHHHTT--EEEE---..HHHHHHHHHHHCCC--TT-EEEE---SE CS
                 NAD_Gly3P_dh_N  52 klpenlvattdlaealkgadiivlvvP..sqalrevlkklkgllkkkailvsliKGi 106
                                    +l +++  ++ laeal++ad++vl++P   ++ r + +k  + +kk a lv++ +G 
  gi|119720478|ref|YP_920973.1| 175 SLADEVYPVERLAEALSQADFVVLALPltRETYRLIGEKELKSMKKTAYLVNVGRGA 231
                                    5788999999****************9333567777777777788888888887776 PP

>> ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00016      0.13      28      62 ..     134     168 ..     123     172 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00016
                                    S-STTEEEEEE--SHHHHHHHHHHHHCT-EEEEEE CS
                  ELFV_dehydrog  28 dslegkrvaisGsGnvgsyaallltelgakvvavs 62 
                                     +l+g++v+i G+Gn+g  +a++++  +++v+av 
  gi|119720478|ref|YP_920973.1| 134 ADLDGSTVTIVGYGNIGREVARIAKAFNMRVLAVK 168
                                    4699****************************985 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.072        62      79     128 ..      55     105 ..      51     107 .. 0.77
   2 ?    6.9   0.0    0.0067       5.8       5      33 ..     152     180 ..     149     254 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.072
                                    EEEEEEEEECSCTSSEEE.EEHHHHHHTT-EEEEE-SSCHHHHHHH.HHHHH CS
                     ADH_zinc_N  79 lkpgGrlvvvGggkgeee.fdlrnlllkeksilGsllgslreefke.aldll 128
                                    ++  Grl +v ++  + + +dl +l+ + +++  s +++  ++++e a++l+
  gi|119720478|ref|YP_920973.1|  55 AQAAGRLKFVQVPAAGADnLDLEYLFERGVKVATSKGCN-ARAVAEhAFALI 105
                                    56789999****5555555*****************999.455544477665 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0067
                                    HHHHHHHHTT-EEEEEESSHHHHHHHHHT CS
                     ADH_zinc_N   5 aavqlAkalGaeviavdsseeklelakkl 33 
                                     +  +Aka++++v av  ++ek  la + 
  gi|119720478|ref|YP_920973.1| 152 EVARIAKAFNMRVLAVKKNPEKDSLADEV 180
                                    57789*****************9888774 PP

>> DpaA_N  Dipicolinate synthase subunit A N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0    0.0002      0.17      24      68 ..     163     209 ..     150     233 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0002
                                    EEEEES-..TSSS-BTTEEEE-GGGS-GGG-SEEE--TT-BETTTEE CS
                         DpaA_N  24 kvslygl..eleekiegvekaesleealedadviilPvpgtkdggei 68 
                                    +v +++   e+++  ++v  +e l+eal++ad+++l +p+t++  ++
  gi|119720478|ref|YP_920973.1| 163 RVLAVKKnpEKDSLADEVYPVERLAEALSQADFVVLALPLTRETYRL 209
                                    34444337788889999************************998766 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00031      0.27       1      54 [.     141     190 ..     141     210 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00031
                                    EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE- CS
                Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaial 54 
                                    v i+G+G++G+ va+  a+ f++  ++  + ++ ek + la+++  v+  a+al
  gi|119720478|ref|YP_920973.1| 141 VTIVGYGNIGREVARI-AKAFNM--RVLAVKKNPEK-DSLADEVYPVERLAEAL 190
                                    679**********985.666788..9*******999.88887765555444444 PP

>> Gp_dh_N  Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00024       0.2       2      34 ..     140     171 ..     139     181 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00024
                                    EEEEESTSHHHHHHHHHHHHHTTCEEEEEE-TS CS
                        Gp_dh_N   2 kvainGfGRIGrlvlralleekelevvaindlt 34 
                                     v i G+G IGr v+r++    +++v+a+++  
  gi|119720478|ref|YP_920973.1| 140 TVTIVGYGNIGREVARIAK-AFNMRVLAVKKNP 171
                                    589************9874.5688999888754 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00033      0.28       1      35 [.     140     174 ..     140     208 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00033
                                    EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHH CS
                        3HCDH_N   1 kvaviGaGtmGagiaavfasagleVvlvdiseeal 35 
                                    +v+++G G +G+++a ++ + +++V  v  ++e+ 
  gi|119720478|ref|YP_920973.1| 140 TVTIVGYGNIGREVARIAKAFNMRVLAVKKNPEKD 174
                                    69**************************9987764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 1973.27
//
Query:       gi|119720479|ref|YP_920974.1|  [L=427]
Description: extracellular ligand-binding receptor [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-41  143.2   5.7    1.9e-41  142.9   5.7    1.1  1  Peripla_BP_6     Periplasmic binding protein
    2.3e-32  112.5   0.0    2.8e-32  112.2   0.0    1.1  1  ANF_receptor     Receptor family ligand binding region
    1.2e-09   37.5   0.3    1.7e-09   37.1   0.3    1.1  1  LppC             LppC putative lipoprotein
    6.6e-08   31.9   0.1    3.7e-07   29.4   0.1    2.0  1  Peripla_BP_5     Periplasmic binding protein domain
     0.0017   17.8   0.0       0.83    9.0   0.0    2.2  2  Peripla_BP_1     Periplasmic binding proteins and sugar bindi
  ------ inclusion threshold ------
      0.094   12.3   0.1       0.22   11.1   0.0    1.7  2  PrpR_N           Propionate catabolism activator
       0.11   12.6   0.0       0.25   11.5   0.0    1.6  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
       0.12   11.7   0.1       0.27   10.6   0.1    1.5  1  HEM4             Uroporphyrinogen-III synthase HemD
          2    8.2   0.0          2    8.2   0.0    2.9  3  Ribosomal_L12_N  Ribosomal protein L7/L12 dimerisation domain


Domain annotation for each model (and alignments):
>> Peripla_BP_6  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.9   5.7   9.3e-45   1.9e-41       2     333 ..      56     394 ..      55     405 .. 0.86

  Alignments for each domain:
  == domain 1  score: 142.9 bits;  conditional E-value: 9.3e-45
                                    EEEEEEE-SSSTTHHHHHHHHHHHHHHHHHHHHTTEETT..EEEEEEEEE-TTSHHHHHHHHHHHHHCT--SEEEE-BSH CS
                   Peripla_BP_6   2 ikiGlltplsGpyassgksllagaqaafeeiNaaGGinG..rkielverDdaydpdraaeaarrlvdqdgvdalvgplss 79 
                                    ++iG+  pl+G ++s+gk +++ + +a++++N++   +G  ++++ v+ Dd+ +p++a+++++ l + +g+++++gp  s
  gi|119720479|ref|YP_920974.1|  56 YTIGFTLPLTGELSSIGKIWEKVVYLAIDDLNKEAQAYGfnVEFKAVILDDGTTPEKALQNVQTLAQ-QGIKVIIGPAAS 134
                                    68*******************************99999722577778******************99.************ PP

                                    HHHHHHHHHHHHHT-EEEESS-HHCC..TTSTTEEESS--HHHHHHHHHHHHHHHTTSCEEEEEEESSHHHHHHHHHHHH CS
                   Peripla_BP_6  80 avaaavaevlakdgvpvigpagltge..kcspyvfslgpsysaqasalveylakelggkkvalvyadyafgregiaalka 157
                                    + ++av  +++ +++++i+p++++++     + +f++ +s++ qa+ l+  la ++g++kv ++  ++ +g++ ++ +k+
  gi|119720479|ref|YP_920974.1| 135 SQVKAVKGFVDSNQIVLISPSSTAPTlaIPGDFIFRTVGSDAGQARVLAT-LAYQEGARKVIVFHRNDEYGNAFADFFKK 213
                                    *********************999863377777****************9.67778************************ PP

                                    HHHCCTEEEEEEEEE-TTHHHHHH....HHHHHHTTT-SEEEEESSHHHHHHHHHHHHHTT-SSSCEEEE..CCC-CHHH CS
                   Peripla_BP_6 158 aakaaGgevvgeepvplgttdfsa....qvlqikaagadavllagtgadlaallkaaaeaGldakrillv..swsgseed 231
                                    ++ ++Gg  + ++p+++g +d++a    ++ +++++++dav+l+++ +d  ++l  aae  +      +v  ++ g++e 
  gi|119720479|ref|YP_920974.1| 214 YFSELGGSSI-DVPYQTGLSDYAAevasLASKVQSEKVDAVVLISFDTDGGNILSHAAESPVLSSVRWFVseGPHGAAEL 292
                                    ********77.7899988866655222288888999*************************9986555555666677776 PP

                                    HHHHHHHHHTT..EEEEESCSTCCCSHHHHHHHHHHHHHHTTGGC--HHHHHHHHHHHHHHHHHHCCTHCCHHHHHHHHH CS
                   Peripla_BP_6 232 lkalggeaaeg..vlavtpyfpdldnpavrafvaayeaayggapppsqfaaggyiaadlllealkaagsltreavraale 309
                                     +++ g+ a++  +l++ p f    np  ++f+++++++yg +   s f    y+a++l   a+ +ags ++ a+r+al 
  gi|119720479|ref|YP_920974.1| 293 KAPAVGAFAAKtkLLGTRPLF--IGNPLYEDFKKRLKEKYGVD--ASVFCDTLYDAVMLAGWAMLRAGSSDGNAIRSALI 368
                                    555555566651156666655..78*****************8..9*********************************8 PP

                                    HS-..BECCCTCCBEECTTSBEE--E CS
                   Peripla_BP_6 310 slg..fdgllgplkftaedhqasrpv 333
                                    ++   + g+ g   f+++  +a +++
  gi|119720479|ref|YP_920974.1| 369 EVAkhYYGVSGWAIFDEAGDKAYQDY 394
                                    8555899**99888887777676664 PP

>> ANF_receptor  Receptor family ligand binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.2   0.0   1.4e-35   2.8e-32       2     350 ..      75     399 ..      74     403 .. 0.90

  Alignments for each domain:
  == domain 1  score: 112.2 bits;  conditional E-value: 1.4e-35
                                    HHHHHHHHHHHHHT-TTSST.TEEEEEEEEE-TT-HHHHHHHHHHHCCCCEEEEEE-SSHHHHHHHHHHHCCTT-EEEES CS
                   ANF_receptor   2 vleAmklAveeinsdpnllp.giklgyeiidtccdfslaleaaldflkgkvvaviGpssssvsdavaslanlfkiPvisy 80 
                                    ++ ++ lA++++n+    ++ ++++ + i+d+  ++++al+ ++++ ++ ++++iGp+ ss+++av+ + + ++i +is+
  gi|119720479|ref|YP_920974.1|  75 WEKVVYLAIDDLNKEAQAYGfNVEFKAVILDDGTTPEKALQNVQTLAQQGIKVIIGPAASSQVKAVKGFVDSNQIVLISP 154
                                    678899********988876255888899*******************88****************************** PP

                                    S---GGGG-TTTTTTEEESS--CHHHHHHHHHHHHHTT--EEEEEEESSHHHHHHHHHHHH...HHHHTT-EEEEEEEES CS
                   ANF_receptor  81 gstspelsdknryptflrtvpsdtsqaqAivdilkhfgWkkvaliysdddygesglqalee...eleergicvalkekip 157
                                    +st+p+l       +++rtv sd+ qa++++ +  + g +kv++ + +d+yg+  ++ +++   el+  +i v +++ ++
  gi|119720479|ref|YP_920974.1| 155 SSTAPTLAIPGD--FIFRTVGSDAGQARVLATLAYQEGARKVIVFHRNDEYGNAFADFFKKyfsELGGSSIDVPYQTGLS 232
                                    *********999..55*********************************************999999999********** PP

                                    TCHHHCHHHHHHHHHHTT.T--EEEEEE-HHHHHHHHHHHHHTTS-STTEEEEETCHCCCECTTS-CC..HHHHHTT-EE CS
                   ANF_receptor 158 essnddevvrkllkeiks.karvivlfcssedarellkaarrlgltgeeyvwiasdawtsslvldkpeltgleaaegvlg 236
                                       ++   v++l ++++s k +++vl +  +d  ++l  a +  + + +  w++s++ + + +l+ p +  + a  ++lg
  gi|119720479|ref|YP_920974.1| 233 ---DYAAEVASLASKVQSeKVDAVVLISFDTDGGNILSHAAESPVLS-SVRWFVSEGPHGAAELKAPAVGAFAAKTKLLG 308
                                    ...999999999889999899******************99999999.5******************97788899***** PP

                                    EEE--B-HHHHHHHHHST--CCCSSSTCCGSTTCCHHHHH...HHHHHHHHHHHHHHHCHHSSSHCCB-HHHHCCHHHHH CS
                   ANF_receptor 237 frlkdpnspkfsefldkreklsdekqnyenegkeqisyqaalmYdaVyllaeAlnkllrkkkpgralscntlkpweggqk 316
                                     r     +p +++f          k  +e++g    s ++ ++YdaV+l + A+ ++++                 +g +
  gi|119720479|ref|YP_920974.1| 309 TRPLFIGNPLYEDFK---------KRLKEKYGVDA-SVFCDTLYDAVMLAGWAMLRAGS----------------SDGNA 362
                                    ***************.........66677777775.8899999***************4................35555 PP

                                    HHHHHHT-..EEEETTSCEEB-TTSBBE.-EEEEEEE CS
                   ANF_receptor 317 llrylrnv..nfeGltGdvkfdengdrv.ptydilnl 350
                                    + ++l +v  ++ G++G   fde gd +  +y ++++
  gi|119720479|ref|YP_920974.1| 363 IRSALIEVakHYYGVSGWAIFDEAGDKAyQDYGVWAI 399
                                    5666655522566999999999999999888888876 PP

>> LppC  LppC putative lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   0.3   8.4e-13   1.7e-09     201     406 ..      41     257 ..      38     273 .. 0.77

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 8.4e-13
                                    HHS--HHHHHHHT--------EEEEE--SSTTHHHHHHHHHHHHHHH...........TT--S-EEEEE..TTTS-HHHH CS
                           LppC 201 akllPkaltdllnlqqtkltkvalLLPlsGklakvaetirdGFlaak........daetqsnaqvkvfD..taaesledi 270
                                    a + P a ++      +k+  ++  LPl+G+l  +++   +    a             + + +  + D  t+ e + + 
  gi|119720479|ref|YP_920974.1|  41 AGQAPGAAQQ----APKKVYTIGFTLPLTGELSSIGKIWEKVVYLAIddlnkeaqAYGFNVEFKAVILDdgTTPEKALQN 116
                                    5556666666....56788899**************98877766666555432101122333444467757666655566 PP

                                    HHHHHHTT--EEE---SHHHHHHHHHSGG.GTTSEEEES---TT---BTTEEE----HHH..HHHHHHHHHHHTT-SSEE CS
                           LppC 271 yaqakaagidlvVGPLlkqnvdkllaqeqlvqsidvLaLNssdnsraiaqlcyfgLspEd..eaesaAsklwadgvRnpl 348
                                    ++ + ++gi++++GP    +v+++  +  +  +i +++  s+  + ai++ + f     d  +a+  A  ++++g R+++
  gi|119720479|ref|YP_920974.1| 117 VQTLAQQGIKVIIGPAASSQVKAVKGFVDS-NQIVLISPSSTAPTLAIPGDFIFRTVGSDagQARVLATLAYQEGARKVI 195
                                    6788899********************999.778888888888899****99998766662267889************* PP

                                    EEEESSHHHHHHHHHHHHHHHHHHSS--EEEEESSGGGHHHHHH....HH-.TTTEEEEE-- CS
                           LppC 349 vlvpqndlGrRvveAFnerwqqlagtdaaielvdqpadlaqqlk....dasrqdidavyiva 406
                                    v+  ++++G+  ++ F++ + +l+g+ + + +     d a +++    + +++++dav ++ 
  gi|119720479|ref|YP_920974.1| 196 VFHRNDEYGNAFADFFKKYFSELGGSSIDVPYQTGLSDYAAEVAslasKVQSEKVDAVVLIS 257
                                    ****************************9988766666666666444466778899998876 PP

>> Peripla_BP_5  Periplasmic binding protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.1   1.9e-10   3.7e-07       3     310 ..      58     370 ..      56     407 .. 0.78

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 1.9e-10
                   Peripla_BP_5   3 vGvLhSlsGtmaisekslkdaallaieeinaagGvlgrkie..avvvdpasdwelfaekaeklieedkvevvfGcwtSas 80 
                                    +G    l+G ++ + k   +++ lai++ n+++   g ++e  av+ d   ++e+  ++ + l ++++++v++G   S+ 
  gi|119720479|ref|YP_920974.1|  58 IGFTLPLTGELSSIGKIWEKVVYLAIDDLNKEAQAYGFNVEfkAVILDDGTTPEKALQNVQTL-AQQGIKVIIGPAASSQ 136
                                    6667779**************************999977763378888877777776666665.669************* PP

                   Peripla_BP_5  81 RkavlpvveelnalLfYpvqYEG.eEssknviYtGaapnqqaipavdyllselgakrvflvGsdyvypretnrilkallk 159
                                     kav+  v++++ +L+ p        +  + i+     +     +++ l+ ++ga++v++   +  y    +  +k++++
  gi|119720479|ref|YP_920974.1| 137 VKAVKGFVDSNQIVLISPSSTAPtLAIPGDFIFRTVGSDAGQARVLATLAYQEGARKVIVFHRNDEYGNAFADFFKKYFS 216
                                    ******************9876515667777777666666666666677777799************************* PP

                   Peripla_BP_5 160 akggevvgeeYlp.lgs..sdvqkivakikkakpd.vvlstinGdsnvafykelkeagikaekipvvslsvaeeelaaid 235
                                    + gg+ ++  Y + l +   +v+++ +k+++ k d vvl +   d    + ++ ++  +++ +  v     + +el+a  
  gi|119720479|ref|YP_920974.1| 217 ELGGSSIDVPYQTgLSDyaAEVASLASKVQSEKVDaVVLISFDTDGGNILSHAAESPVLSSVRWFVSEGPHGAAELKA-- 294
                                    ***********6524434467777778888888874666778888888888888888889999999999999999976.. PP

                   Peripla_BP_5 236 aealvGhlaawnYfqs.....vdtpenkafvakfkarvgedrvtndpmeaayiqvklwaqAvekagstdvekvreallgq 310
                                      ++vG +aa + +       + +p  ++f ++ k+++g d+     + + y +v+l   A+ +ags+d +++r+al+++
  gi|119720479|ref|YP_920974.1| 295 --PAVGAFAAKTKLLGtrplfIGNPLYEDFKKRLKEKYGVDAS--VFCDTLYDAVMLAGWAMLRAGSSDGNAIRSALIEV 370
                                    ..34444444433222111116788888888888888887654..35678899999******************999876 PP

>> Peripla_BP_1  Periplasmic binding proteins and sugar binding domain of LacI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.0    0.0023       4.5      18      96 ..      85     164 ..      79     219 .. 0.66
   2 !    9.0   0.0   0.00042      0.83      41      90 ..     234     282 ..     231     297 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0023
                                    HHHHHHHHHHHHHTEEEEEEE-SSHHHHH.HHHHHHHHTT-SEEEEE-S-GGHHHHHHHHHHT-EEEEESS--B-T.TTS CS
                   Peripla_BP_1  18 dlvkgitkaakehgvdvlllaageeedla.kaidllkakgidgliiatsdtsfdditakaesgipvialedaidap.dgv 95 
                                    dl+k ++  +++ +++ ++l +g  ++ a + ++ l+++gi+ +i   +  ++ +++  + s  ++++++  + ap  ++
  gi|119720479|ref|YP_920974.1|  85 DLNKEAQAYGFNVEFKAVILDDGTTPEKAlQNVQTLAQQGIKVIIGPAASSQVKAVKGFVDS-NQIVLISPSSTAPtLAI 163
                                    555555666666667778999999998888************65544444446666666666.67777777777773334 PP

                                    - CS
                   Peripla_BP_1  96 P 96 
                                    P
  gi|119720479|ref|YP_920974.1| 164 P 164
                                    4 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00042
                                    SHHHHHHHHHHHHHTT-SEEEEE-S-GGHHHHHHHHHHT-EEEEESS--B CS
                   Peripla_BP_1  41 eeedlakaidllkakgidgliiatsdtsfdditakaesgipvialedaid 90 
                                    + +++a+ ++ ++++++d++++ + dt++ +i+  a++  pv+  ++ ++
  gi|119720479|ref|YP_920974.1| 234 YAAEVASLASKVQSEKVDAVVLISFDTDGGNILSHAAE-SPVLSSVRWFV 282
                                    5677889999******************9999999998.9**98887766 PP

>> PrpR_N  Propionate catabolism activator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00011      0.22     103     132 ..     108     137 ..      68     158 .. 0.77
   2 ?   -3.6   0.0       3.5     7e+03      16      33 ..     237     254 ..     226     254 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00011
                         PrpR_N 103 nseeeaeaavkelkaegvevvvGdgvvadl 132
                                    +++e+a + v++l+++g++v++G+  ++++
  gi|119720479|ref|YP_920974.1| 108 TTPEKALQNVQTLAQQGIKVIIGPAASSQV 137
                                    68899******************9887665 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 3.5
                         PrpR_N  16 eavelakeleaegvdvii 33 
                                    e ++la + ++e+vd+++
  gi|119720479|ref|YP_920974.1| 237 EVASLASKVQSEKVDAVV 254
                                    566778888889988876 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00012      0.25      70     101 ..     103     134 ..      65     154 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00012
                                    EEEE-S-HHHHHHHHHHHHHTT-EEEE--SS- CS
                         DapB_N  70 vliDFTtpeavlenlklalekgvklViGTTGl 101
                                    +l D Ttpe +l+n+++++++g+k++iG    
  gi|119720479|ref|YP_920974.1| 103 ILDDGTTPEKALQNVQTLAQQGIKVIIGPAAS 134
                                    33478**********************97654 PP

>> HEM4  Uroporphyrinogen-III synthase HemD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00013      0.27      96     177 ..     171     257 ..     128     260 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00013
                                    EE-..SSSHHHHGGGS-.---EEEEEE.....-SS.S--HHHHHHHHHTTEEEEEE-SEEEEE-HH..HHHHHHHHHHTT CS
                           HEM4  96 lvpseegtaegLaeelaeslagkrvll.....lrgeiarddlaegLeergaevdevevYetvpaee..epeelkealkag 168
                                     v+s++g+a+ La  la + ++++v++      +g+   d ++++++e g +  +v +Y+t   ++  e+++l  +++++
  gi|119720479|ref|YP_920974.1| 171 TVGSDAGQARVLAT-LAYQEGARKVIVfhrndEYGNAFADFFKKYFSELGGSSIDV-PYQTGLSDYaaEVASLASKVQSE 248
                                    39999****99998.77555557766645666666666999999999***988887.6***555555699********** PP

                                    --SEEEESS CS
                           HEM4 169 evdavvftS 177
                                    +vdavv+ S
  gi|119720479|ref|YP_920974.1| 249 KVDAVVLIS 257
                                    ******998 PP

>> Ribosomal_L12_N  Ribosomal protein L7/L12 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   4.9       2.6   5.2e+03      40      47 ..      34      43 ..      14      51 .. 0.57
   2 ?   -4.6   1.4         9   1.8e+04      34      40 ..     294     301 ..     289     303 .. 0.51
   3 ?    8.2   0.0     0.001         2      19      33 ..     321     335 ..     320     351 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.6
                                   .H..HHHHHH CS
                Ribosomal_L12_N 40 aa..aaaaaa 47
                                   aa  ++aa+ 
  gi|119720479|ref|YP_920974.1| 34 AAifGGAAGQ 43
                                   2233333322 PP

  == domain 2  score: -4.6 bits;  conditional E-value: 9
                                    HHHHHH.. CS
                Ribosomal_L12_N  34 APvava.a 40 
                                    AP+++a a
  gi|119720479|ref|YP_920974.1| 294 APAVGAfA 301
                                    66554424 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.001
                                    HHHHHHHHHTTHHHH CS
                Ribosomal_L12_N  19 eLvkalEekFGVsAA 33 
                                    +++k l+ek+GV+A+
  gi|119720479|ref|YP_920974.1| 321 DFKKRLKEKYGVDAS 335
                                    799*********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       911  (0.0508115); expected 358.6 (0.02)
Passed bias filter:                      722  (0.04027); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.47
# Mc/sec: 2745.84
//
Query:       gi|119720480|ref|YP_920975.1|  [L=319]
Description: inner-membrane translocator [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      6e-31  107.6  35.2    8.4e-31  107.1  35.2    1.2  1  BPD_transp_2  Branched-chain amino acid transport system / pe
  ------ inclusion threshold ------
        4.9    7.1   8.4        5.8    6.8   0.4    3.6  4  DUF5337       Family of unknown function (DUF5337)


Domain annotation for each model (and alignments):
>> BPD_transp_2  Branched-chain amino acid transport system / permease component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.1  35.2   9.3e-35   8.4e-31       2     267 ..       9     294 ..       8     297 .. 0.83

  Alignments for each domain:
  == domain 1  score: 107.1 bits;  conditional E-value: 9.3e-35
                   BPD_transp_2   2 ilnlltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsl.lllallvallvgaavglllgllvlrl 80 
                                    iln+  ++  +++++++l+l+++ + vin++h+ f+  G y+a  l  ll++  l+la l+a++vg+ ++l++ llv r 
  gi|119720480|ref|YP_920975.1|   9 ILNFFQYTFFYILFSIPLTLSYRNTKVINFAHANFISYGIYTAVFLNGLLGNTsLALACLAAFAVGGSIALVNHLLVFRP 88 
                                    789999999********************************9999999988889************************** PP

                   BPD_transp_2  81 kvdeliitllllsvlvgltlllltgitsgvkgqssvkellgfaga.llsflsaviv.................llalllv 142
                                     +++ ++  l++++  gl  +++  +    + +++  +l  f ++  + ++                      l al+lv
  gi|119720480|ref|YP_920975.1|  89 LEKRGASMSLIMIASMGLWIMYNYALYM-LADIAHYYTLKNFISYgRIVYADV--PevellglrlqqsfvaggLAALVLV 165
                                    *****77777665555555522222222.222233333322222202222222..134666667777788899******* PP

                   BPD_transp_2 143 lavllllrrtrfGralravgeneeaaralGinvkrvklltfvisgalAglaGallalllgsippnigvglgfnaiaavvl 222
                                    + ++l+l +t +G a+rav++n+ +a+ +Gi+ + +  lt++i+g+ A++ Ga+ + ++g++ p     ++++++++ ++
  gi|119720480|ref|YP_920975.1| 166 ASLYLFLEKTTLGKAMRAVADNPVLAEISGIPRNTIVNLTWLIAGGAAAVGGAIWTSFSGTVTPTSADAMILQVFTVSFI 245
                                    ****************************************************************99999*********** PP

                   BPD_transp_2 223 GgagsllgtviGaliigvvksllltllgi....ptelarvllgallilv 267
                                    Gg+ sll t +Ga++i++++++++++l      p +++ +l+++ l+ +
  gi|119720480|ref|YP_920975.1| 246 GGLVSLLRTGLGAVAIAFIENVGIAALNTyfgvPISFRPFLTFVTLLTI 294
                                    *********************9999997787777777777777777655 PP

>> DUF5337  Family of unknown function (DUF5337)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1      0.27   2.4e+03      49      56 ..      65      72 ..      62      88 .. 0.71
   2 ?    6.8   0.4   0.00065       5.8      10      57 ..      90     137 ..      86     153 .. 0.74
   3 ?    3.4   0.1    0.0074        66      13      37 ..     157     181 ..     146     185 .. 0.88
   4 ?   -1.3   0.0      0.23     2e+03      25      44 ..     293     312 ..     286     313 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.27
                        DUF5337 49 LaAlAali 56
                                   La lAa++
  gi|119720480|ref|YP_920975.1| 65 LACLAAFA 72
                                   78888886 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.00065
                        DUF5337  10 arkgrlvalviavtmllwlgaqwigeqlglsnRyalLfdLaAlAaliw 57 
                                     ++g  ++l++ ++m lw+  +++  +l   + y  L +++  + +++
  gi|119720480|ref|YP_920975.1|  90 EKRGASMSLIMIASMGLWIMYNYALYMLADIAHYYTLKNFISYGRIVY 137
                                    6889999*************9987766655555656666655555555 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.0074
                        DUF5337  13 grlvalviavtmllwlgaqwigeql 37 
                                    g l+alv++++  l+l  + +g+++
  gi|119720480|ref|YP_920975.1| 157 GGLAALVLVASLYLFLEKTTLGKAM 181
                                    6789****************99987 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 0.23
                        DUF5337  25 llwlgaqwigeqlglsnRya 44 
                                     + +++  +g++ gl+ R++
  gi|119720480|ref|YP_920975.1| 293 TILIAFPPLGAAGGLPFRFR 312
                                    3556777899999**99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       751  (0.0418874); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 2133.08
//
Query:       gi|119720481|ref|YP_920976.1|  [L=344]
Description: inner-membrane translocator [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.3e-45  154.9  27.9    2.7e-45  154.6  27.9    1.0  1  BPD_transp_2  Branched-chain amino acid transport system / pe
  ------ inclusion threshold ------
        1.8    8.8  12.6        1.3    9.2   0.1    4.0  4  DUF350        Domain of Unknown Function (DUF350)


Domain annotation for each model (and alignments):
>> BPD_transp_2  Branched-chain amino acid transport system / permease component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.6  27.9     3e-49   2.7e-45       2     268 .]       8     317 ..       7     317 .. 0.94

  Alignments for each domain:
  == domain 1  score: 154.6 bits;  conditional E-value: 3e-49
                   BPD_transp_2   2 ilnlltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsl........................... 54 
                                    ++++ltl +i+ai+Al l++  g +Gv n+g   f++lGayv a+l ++l  l                           
  gi|119720481|ref|YP_920976.1|   8 LISWLTLLGIYAILALTLNFESGTSGVTNFGKVFFYGLGAYVGATLTVYLFLLlngvdvsktppydvsgivllgelagkn 87 
                                    6789**************************************9999888777779************************* PP

                   BPD_transp_2  55 .......lllallvallvgaavglllgllvlrlkvdeliitllllsvlvgltlllltgitsgvkgqssvkellgf..aga 125
                                           l+l+l+ a+lv++++g ll ++++r++   + +tll + +l++++l  + ++ +g+ g  s+++++ +   + 
  gi|119720481|ref|YP_920976.1|  88 palnlglLALSLATAFLVAGVIGYLLSYPIIRVGPAFVGFTLLSTGELFRIFL-QHYEPVGGSRGLMSIPGPFSWvpQPR 166
                                    *****************************************************.88888888888888888888833444 PP

                   BPD_transp_2 126 llsflsavivllalllvlavllllrrtrfGralravgeneeaaralGinvkrvklltfvisgalAglaGallalllgsip 205
                                    l+  l+ ++vl +l+++++v+ +l+++++Gr lrav+++e aa ++G+ v ++k+++ +i+++++g+aG+lla +l+s++
  gi|119720481|ref|YP_920976.1| 167 LREVLFLALVLAVLAATYLVMDRLTNSPLGRTLRAVRDDEVAALCMGKHVPKLKATVLFIGSGFSGVAGVLLAYYLTSVN 246
                                    55556666669999****************************************************************** PP

                   BPD_transp_2 206 p.nigvglgfnaiaavvlGgagsllgtviGaliigvvksllltllgi.......ptelarvllgallilvl 268
                                    p  + +  +fn++a+ +lGg+g+l+g+++Ga i+ +++  l++++++       p  ++ + +g++++lvl
  gi|119720481|ref|YP_920976.1| 247 PdMFVPAVTFNVWAMIILGGMGNLRGALLGASIFTFIDRALSFVTPQlgvtvisPDYVRGFAVGLVMVLVL 317
                                    *999999**************************************99**9999889999999*****9997 PP

>> DUF350  Domain of Unknown Function (DUF350)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.7    0.0011        10      19      54 .]      69     109 ..      43     109 .. 0.73
   2 ?    9.2   0.1   0.00015       1.3       2      35 ..     173     209 ..     172     214 .. 0.89
   3 ?   -3.6   0.0       1.4   1.3e+04       6      15 ..     233     242 ..     229     249 .. 0.61
   4 ?   -1.9   0.7      0.45     4e+03      34      40 ..     308     314 ..     273     319 .. 0.57

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0011
                         DUF350  19 lTpgklgelIkqg.....nnAaaivlagviiglaiivaaAi 54 
                                    + p++++ ++  g     n+A  + l + ++++a++va  i
  gi|119720481|ref|YP_920976.1|  69 TPPYDVSGIVLLGelagkNPALNLGLLALSLATAFLVAGVI 109
                                    3359999988888555534499999*************987 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00015
                         DUF350   2 gvvGivllllgffvfdllT..p.gklgelIkqgnnAa 35 
                                    +++ +++l++ ++v+d+lT  p g+  + ++++++Aa
  gi|119720481|ref|YP_920976.1| 173 LALVLAVLAATYLVMDRLTnsPlGRTLRAVRDDEVAA 209
                                    678899*************999************976 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 1.4
                         DUF350   6 ivllllgffv 15 
                                    ++  ll++++
  gi|119720481|ref|YP_920976.1| 233 VAGVLLAYYL 242
                                    4444555554 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 0.45
                         DUF350  34 Aaaivla 40 
                                    A+++v++
  gi|119720481|ref|YP_920976.1| 308 AVGLVMV 314
                                    4444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2488.45
//
Query:       gi|119720482|ref|YP_920977.1|  [L=261]
Description: ABC transporter related [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.5e-24   85.2   0.0    6.9e-24   84.9   0.0    1.1  1  ABC_tran      ABC transporter
    5.2e-09   35.8   0.1    8.7e-09   35.1   0.1    1.3  1  BCA_ABC_TP_C  Branched-chain amino acid ATP-binding cassette 
    2.4e-07   30.9   2.9    0.00035   20.5   0.6    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    9.2e-05   23.0   0.1    0.00014   22.4   0.1    1.2  1  AAA_23        AAA domain
    0.00011   21.8   0.0     0.0002   21.0   0.0    1.4  1  AAA_29        P-loop containing region of AAA domain
    0.00037   20.0   0.1      0.099   12.1   0.1    2.1  2  SMC_N         RecF/RecN/SMC N terminal domain
  ------ inclusion threshold ------
      0.047   14.1   0.0      0.066   13.6   0.0    1.4  1  AAA_16        AAA ATPase domain
      0.066   12.9   0.0       0.14   11.9   0.0    1.7  1  AAA_30        AAA domain
       0.12   11.4   0.0       0.34    9.9   0.0    1.6  2  T2SSE         Type II/IV secretion system protein
       0.14   12.5   0.0       0.34   11.2   0.0    1.7  2  AAA_22        AAA domain
       0.21   11.1   0.2       0.36   10.3   0.2    1.3  1  FeoB_N        Ferrous iron transport protein B
       0.22   10.6   0.1       0.34   10.1   0.1    1.2  1  NB-ARC        NB-ARC domain
       0.31   10.7   0.0       0.42   10.3   0.0    1.1  1  AAA_15        AAA ATPase domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.9   0.0     5e-27   6.9e-24       1     136 [.      23     186 ..      23     187 .. 0.94

  Alignments for each domain:
  == domain 1  score: 84.9 bits;  conditional E-value: 5e-27
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEET.TCEGGG....B-HHHCCHCEEEE-SS--S-TTSB CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx....xxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilld.gkdlke....qeleslrkeigvlpqepqlfpelt 75 
                                    l++vsl++    +v+++G+nG+GK+tL+++++g + p++Ge++++ g+ +++    ++ e++ k i   +q p+lf+ lt
  gi|119720482|ref|YP_920977.1|  23 LQDVSLSVPSQGIVGLIGPNGSGKTTLFNVVTGFYVPDKGEVWFNdGNRSERidglNPNEVFAKGIVRTFQIPRLFKSLT 102
                                    789******************************************77777779*************************** PP

                                    HHHH...........................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSS CS
                                    xxxx...........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  76 vren...........................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpk 128
                                    v en                           +  +++  +l+++gl e ++ +v    s+LSg + + ++  r l++ +k
  gi|119720482|ref|YP_920977.1| 103 VLENllvtpfaqkgenplkalkpsswieeerALARKAVSLLRRFGLLEYANVRV----SELSGAHIKLLETIRGLMTPAK 178
                                    *********************999988766666666999999999999999999....********************** PP

                                    EEEEESTT CS
                                    xxxxxxxx RF
                       ABC_tran 129 llllDEpt 136
                                    l+llDEp 
  gi|119720482|ref|YP_920977.1| 179 LFLLDEPA 186
                                    *******7 PP

>> BCA_ABC_TP_C  Branched-chain amino acid ATP-binding cassette transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.1   6.3e-12   8.7e-09       1      23 []     235     257 ..     235     257 .. 0.96

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 6.3e-12
                   BCA_ABC_TP_C   1 rvIAeGtPaEvrndPrVieAYLG 23 
                                    +++AeG+P+Ev ++P+V+eAY G
  gi|119720482|ref|YP_920977.1| 235 QLLAEGKPEEVTSNPKVVEAYIG 257
                                    689******************88 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.6   2.5e-07   0.00035       2      56 ..      36      82 ..      35     135 .. 0.68
   2 !   11.5   0.2   0.00014       0.2     257     294 ..     176     213 ..      71     236 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.5e-07
                         AAA_21  2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpei 56
                                    +liGpNgsGK++L+    ++           d+    ++ +  + ++d+ +p++
  gi|119720482|ref|YP_920977.1| 36 VGLIGPNGSGKTTLFNVVTGFY--------VPDKGEVWFNDGNRSERIDGLNPNE 82
                                   68*************9998773........3333333444444444444444444 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00014
                         AAA_21 257 kgsllliDEpEngLHPkllrrllellkelsrngaQvil 294
                                    +++l+l+DEp +g +  + ++l++l++el+++g  +++
  gi|119720482|ref|YP_920977.1| 176 PAKLFLLDEPAAGVEAGAAHELFRLVRELRSEGYTFLI 213
                                    349*************************9998888766 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.1     1e-07   0.00014      11      39 ..      24      53 ..      15      57 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1e-07
                         AAA_23 11 rdqeidF.skgltlItGpNGaGKTTildAi 39
                                   +d+++   s+g++ ++GpNG+GKTT+++ +
  gi|119720482|ref|YP_920977.1| 24 QDVSLSVpSQGIVGLIGPNGSGKTTLFNVV 53
                                   5555544799*****************865 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   1.4e-07    0.0002      15      56 ..      26      68 ..      21      73 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.4e-07
                         AAA_29 15 htieidlkgatlltGpsGsGKSTllDAiqalLvpak.kvrfNk 56
                                    ++++  +g++ l+Gp+GsGK+Tl+  ++   vp+k +v fN 
  gi|119720482|ref|YP_920977.1| 26 VSLSVPSQGIVGLIGPNGSGKTTLFNVVTGFYVPDKgEVWFND 68
                                   566777789999**********************999999996 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.1   7.2e-05     0.099      23      43 ..      32      52 ..      22      61 .. 0.84
   2 !    6.0   0.0    0.0052       7.1     156     211 ..     174     230 ..     130     237 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.2e-05
                                   TSSEEEEEESTTSSHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 23 sksftaivGpNGSGKsnlldA 43
                                   s+++  ++GpNGSGK+ l++ 
  gi|119720482|ref|YP_920977.1| 32 SQGIVGLIGPNGSGKTTLFNV 52
                                   5678899*********99875 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0052
                                    CS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-SCEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 156 vkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreemlekadklvgv 211
                                    + pa l+llDe +a   +   +++ +l++e +++   f+++ +r e+l +    v v
  gi|119720482|ref|YP_920977.1| 174 MTPAKLFLLDEPAAGVEAGAAHELFRLVRELRSEgYTFLIVEHRIEILMQYVDYVYV 230
                                    57999************************98777699*******9998887655555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   4.8e-05     0.066      23      63 ..      30      74 ..      21     214 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.8e-05
                         AAA_16 23 rp..elvllsGesGvGKsslvrellralekd.g.giflrgkcdql 63
                                    p  ++v l+G+ G+GK++l + +   +  d g ++f  g+  + 
  gi|119720482|ref|YP_920977.1| 30 VPsqGIVGLIGPNGSGKTTLFNVVTGFYVPDkGeVWFNDGNRSER 74
                                   44448999*************999986666653477766666666 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0    0.0001      0.14      19      62 ..      34      88 ..      26     214 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0001
                         AAA_30 19 rvavltGpAGtGKttalkalreaweaa.g..........grviglAptgkaAkvL 62
                                    ++ l Gp G+GKtt+ ++++  +  + g          +r+ gl p++  Ak +
  gi|119720482|ref|YP_920977.1| 34 GIVGLIGPNGSGKTTLFNVVTGFYVPDkGevwfndgnrsERIDGLNPNEVFAKGI 88
                                   478899**************99988773466666666666666666666666665 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00025      0.34     124     152 ..      28      56 ..      20      67 .. 0.82
   2 ?   -1.6   0.0      0.82   1.1e+03     145     181 ..     196     232 ..     152     240 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00025
                          T2SSE 124 kavrerglilvsGgTgsGKttllyallke 152
                                     +v ++g++ + G+ gsGKttl +++  +
  gi|119720482|ref|YP_920977.1|  28 LSVPSQGIVGLIGPNGSGKTTLFNVVTGF 56 
                                    466789999999***********998765 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.82
                          T2SSE 145 llyallkeinksderivtvEDpvEiqleganqvqlna 181
                                     l  l+ e+ ++   +++vE  +Ei ++ +++v + +
  gi|119720482|ref|YP_920977.1| 196 ELFRLVRELRSEGYTFLIVEHRIEILMQYVDYVYVLH 232
                                    5667788888888889999999999998888887765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00025      0.34       4      26 ..      32      54 ..      30     109 .. 0.87
   2 ?   -1.8   0.0       2.5   3.5e+03      88     102 ..     172     187 ..     134     215 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00025
                         AAA_22  4 tagilvvtGesGtGKTtllrrll 26
                                   ++gi+ ++G+ G+GKTtl + ++
  gi|119720482|ref|YP_920977.1| 32 SQGIVGLIGPNGSGKTTLFNVVT 54
                                   588999***********987665 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.5
                         AAA_22  88 arav.ielliiDEaqh 102
                                      ++  +l+++DE   
  gi|119720482|ref|YP_920977.1| 172 GLMTpAKLFLLDEPAA 187
                                    3333555666666444 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.2   0.00026      0.36       3      23 ..      36      56 ..      35      59 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00026
                                   EEEEESTTSSHHHHHHHHHTT CS
                         FeoB_N  3 valvGnpnvGkttlfnaltga 23
                                   v l+G   +Gkttlfn +tg 
  gi|119720482|ref|YP_920977.1| 36 VGLIGPNGSGKTTLFNVVTGF 56
                                   6799*999***********97 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00025      0.34      18      39 ..      33      52 ..      22      56 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00025
                                   SCSEEEEEEESTTSSHHHHHHH CS
                         NB-ARC 18 lqslvvalvGmgGvGKttlakq 39
                                       +v+l G  G+GKttl++ 
  gi|119720482|ref|YP_920977.1| 33 Q--GIVGLIGPNGSGKTTLFNV 52
                                   3..49**************975 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0    0.0003      0.42      14      41 ..      23      51 ..      22      76 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0003
                         AAA_15 14 lkdveidlsee.ltvliGkNnsGKSsile 41
                                   l+dv++++ ++ +  liG+N+sGK+++ +
  gi|119720482|ref|YP_920977.1| 23 LQDVSLSVPSQgIVGLIGPNGSGKTTLFN 51
                                   566666666666888***********865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1666.85
//
Query:       gi|119720483|ref|YP_920978.1|  [L=237]
Description: ABC transporter related [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.4e-33  113.8   0.0    1.1e-32  113.3   0.0    1.2  1  ABC_tran     ABC transporter
    6.3e-12   45.9   0.2    2.3e-05   24.3   0.0    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    9.4e-06   25.2   0.3      0.031   13.7   0.1    2.3  2  SMC_N        RecF/RecN/SMC N terminal domain
    1.7e-05   25.1   0.1      9e-05   22.8   0.1    1.9  1  AAA_22       AAA domain
     0.0007   19.3   0.1     0.0015   18.2   0.1    1.5  1  AAA_29       P-loop containing region of AAA domain
     0.0011   19.0   0.0      0.004   17.2   0.0    1.8  1  Dynamin_N    Dynamin family
     0.0012   19.4   0.5     0.0022   18.5   0.3    1.4  1  AAA_23       AAA domain
     0.0014   18.6   0.3     0.0028   17.6   0.1    1.6  2  RsgA_GTPase  RsgA GTPase
  ------ inclusion threshold ------
      0.011   16.0   0.0        0.2   11.9   0.0    2.2  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
      0.012   14.5   0.6        3.5    6.3   0.0    2.9  3  ABC_ATPase   Predicted ATPase of the ABC class
      0.024   14.2   1.1      0.027   14.1   0.1    1.5  2  AAA_27       AAA domain
      0.027   14.9   0.1      0.052   13.9   0.1    1.7  1  AAA_16       AAA ATPase domain
       0.04   13.6   0.9        0.1   12.3   0.1    1.9  3  AAA_30       AAA domain
       0.07   13.6   0.1       0.54   10.7   0.1    2.1  1  AAA          ATPase family associated with various cellular a
       0.11   12.6   0.2       0.91    9.6   0.1    2.0  2  MMR_HSR1     50S ribosome-binding GTPase
       0.12   11.0   0.0        2.5    6.6   0.0    2.0  2  AAA_13       AAA domain
       0.14   11.7   0.6        0.3   10.7   0.1    1.7  2  cobW         CobW/HypB/UreG, nucleotide-binding domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.3   0.0   1.1e-35   1.1e-32       1     137 []      20     166 ..      20     166 .. 0.94

  Alignments for each domain:
  == domain 1  score: 113.3 bits;  conditional E-value: 1.1e-35
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvren 79 
                                    l+ vs++l +ge+ a++G+nGaGK+t+l+++ gl +   Ge+ ++g +l+  ++ e+++  +++ pq +++fp+ltv+en
  gi|119720483|ref|YP_920978.1|  20 LHGVSFELGKGEIAAVLGPNGAGKTTMLNTIFGLATLHRGEVSFNGVKLNGrKPSEIVKLGVSYAPQLDNVFPNLTVEEN 99 
                                    689***********************************************999*************************** PP

                                    ............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    ............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                                  +++ie++l+ +  ++   ++ ++++++LSgG++q++a+aral+++p++lllDEpt+
  gi|119720483|ref|YP_920978.1| 100 lvvgafirgkdpGIRSDIEDILDLFPEIK---RRRNQKAKTLSGGERQMLAVARALMTRPSVLLLDEPTS 166
                                    ******99988888888******999887...3334578*****************************96 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.2   2.8e-07    0.0003       1     110 [.      32     133 ..      32     138 .. 0.57
   2 !   24.3   0.0   2.2e-08   2.3e-05     230     289 ..     131     188 ..     124     194 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.8e-07
                         AAA_21   1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrler 80 
                                    ++++ GpNg+GK++ L ++ +la l r   + + ++ +g ++++i +l  +y+p  + +f    +++++ +   ++r ++
  gi|119720483|ref|YP_920978.1|  32 IAAVLGPNGAGKTTMLNTIFGLATLHRGEVSFNGVKLNGRKPSEIVKLGVSYAPQLDNVFPNL-TVEENLVVGAFIRGKD 110
                                    67899*****************88733333333333333444444444444444444444444.4445555555555555 PP

                         AAA_21  81 sqveeklssvetllesgllldkrsleeedv 110
                                     ++       +++ e+ l l++++++++++
  gi|119720483|ref|YP_920978.1| 111 PGI-------RSDIEDILDLFPEIKRRRNQ 133
                                    555.......66666666666666655554 PP

  == domain 2  score: 24.3 bits;  conditional E-value: 2.2e-08
                         AAA_21 230 qelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ng 289
                                    ++  a  lS G +++la++ al  ++   s+ll+DEp +gL Pk+ ++l+  +ke ++ +g
  gi|119720483|ref|YP_920978.1| 131 RNQKAKTLSGGERQMLAVARALMTRP---SVLLLDEPTSGLSPKAGATLMNKIKEIQQtRG 188
                                    55556679*******88888888888...****************9999977766555455 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.1     3e-05     0.031      25      49 ..      31      54 ..      21      66 .. 0.85
   2 !    9.6   0.0   0.00053      0.56     133     199 ..     134     196 ..      80     211 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3e-05
                                   SEEEEEESTTSSHHHHHHHHHHHCT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 25 sftaivGpNGSGKsnlldAilFvLG 49
                                   ++ a++GpNG+GK+ +l+ i F L 
  gi|119720483|ref|YP_920978.1| 31 EIAAVLGPNGAGKTTMLNTI-FGLA 54
                                   6789****************.8776 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00053
                                    STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 133 skelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislre 199
                                    + ++LSgGe++++a+a      + +p+ + llDe  + L  k  + + + +ke +++  + +  +++
  gi|119720483|ref|YP_920978.1| 134 KAKTLSGGERQMLAVARA---LMTRPS-VLLLDEPTSGLSPKAGATLMNKIKEIQQTRGVAILLVEQ 196
                                    4459********999865...355555.6689**999999999999999999988766555555554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.1   8.5e-08     9e-05       5     130 ..      30     196 ..      26     202 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 8.5e-08
                         AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaee.....................................erpevv..fv 45 
                                      i +v G+ G+GKTt l++++  ++ +   +                                      e+  vv  f+
  gi|119720483|ref|YP_920978.1|  30 GEIAAVLGPNGAGKTTMLNTIFGLATLH---RGevsfngvklngrkpseivklgvsyapqldnvfpnltvEENLVVgaFI 106
                                    56899*****************998643...3357799***********************9999999988888888777 PP

                         AAA_22  46 tlpsstsskdllrellralglelka...erlsseellealeqalrarav.ielliiDEaqh.lrs....eealeeLrsll 116
                                      + ++  ++  +++l  + + + +   + ++++   +++   +ra ++ +++l++DE    l s    +++++++++++
  gi|119720483|ref|YP_920978.1| 107 RGKDPG-IRSDIEDILDLFPEIKRRrnqKAKTLSGGERQMLAVARALMTrPSVLLLDEPTSgL-SpkagATLMNKIKEIQ 184
                                    777777.66666777777776666633244444444466666666666699************.44577*********** PP

                         AAA_22 117 nlsrkgvqliLvGt 130
                                       + gv+++Lv +
  gi|119720483|ref|YP_920978.1| 185 Q--TRGVAILLVEQ 196
                                    *..*******9965 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   1.5e-06    0.0015      13      55 ..      21      64 ..      15      66 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.5e-06
                         AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDAiqalLvpak.kvrfN 55
                                   +g ++e+   ++  + Gp+G+GK+T+l  i  l + ++ +v+fN
  gi|119720483|ref|YP_920978.1| 21 HGVSFELGKGEIAAVLGPNGAGKTTMLNTIFGLATLHRgEVSFN 64
                                   6677778755599***************9999999888889998 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   3.8e-06     0.004       2     133 ..      34     191 ..      33     211 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.8e-06
                                    EEEEBTTTTHHHHHHHHHTS--S---SSS---S-EEEEE......................CCT---CCS...SSEEEE. CS
                      Dynamin_N   2 avvGsqSsGKSSvlnaLlgedilprgpnptTrrplelql......................geeeeaseravkeelkek. 58 
                                    av+G   +GK+++ln + g + l+rg+       l  ++                                    ++e+ 
  gi|119720483|ref|YP_920978.1|  34 AVLGPNGAGKTTMLNTIFGLATLHRGEVSFNGVKLNGRKpseivklgvsyapqldnvfpnlT-------------VEENl 100
                                    799********************999876654433333333333366644444444444331.............33333 PP

                                    .............T-EB--CHHHHHHHHHHHHHHHTSSSS--SS-EEEEEEETTS-SEEEEE--..-B-SSSGTTS...H CS
                      Dynamin_N  59 .............ekkledfsevreeieketekiagankgiskkvillkilsllvkgltlvDlP..Gldsvnkrdq...e 120
                                                 ++++ed+ ++  ei+++++++a++++g  ++++ +     +++ + l+D P  Gl    k      +
  gi|119720483|ref|YP_920978.1| 101 vvgafirgkdpgiRSDIEDILDLFPEIKRRRNQKAKTLSGGERQMLAVARALMTRPSVLLLDEPtsGLSP--KAGAtlmN 178
                                    3334444455589999999999999999999999999999999999999999999999999988334433..33322345 PP

                                    HHHHHHSTTEEEE CS
                      Dynamin_N 121 lvkeyikkadiil 133
                                     +ke+ + + + +
  gi|119720483|ref|YP_920978.1| 179 KIKEIQQTRGVAI 191
                                    5555554444444 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.3   2.1e-06    0.0022      12      40 ..      22      51 ..      12      78 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.1e-06
                         AAA_23 12 dqeidFsk.gltlItGpNGaGKTTildAik 40
                                   +++++++k  + ++ GpNGaGKTT l+ i 
  gi|119720483|ref|YP_920978.1| 22 GVSFELGKgEIAAVLGPNGAGKTTMLNTIF 51
                                   5667886636999*************9986 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   2.6e-06    0.0028      95     131 ..      25      62 ..      10      78 .. 0.85
   2 ?   -2.8   0.0         5   5.2e+03      66      84 ..     178     196 ..     171     213 .. 0.56

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.6e-06
                                    HHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S--- CS
                    RsgA_GTPase  95 ellkd.ktsvlvGqSGvGKStLinallpelelktgevs 131
                                     +l + ++++++G+ G+GK+t++n++ + ++l+ gevs
  gi|119720483|ref|YP_920978.1|  25 FELGKgEIAAVLGPNGAGKTTMLNTIFGLATLHRGEVS 62 
                                    55555499********************9999999998 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 5
                                    HHHHHHHHHTTSEEEE--T CS
                    RsgA_GTPase  66 eelkeelealgyevllvsa 84 
                                    +++ke  ++ g+++llv++
  gi|119720483|ref|YP_920978.1| 178 NKIKEIQQTRGVAILLVEQ 196
                                    4445555555555555544 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00019       0.2      25      86 ..     130     178 ..     125     182 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00019
                        SbcCD_C  25 elsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatlle 86 
                                    + +++++tlSGGe+q+la       +a ++        ++++++LDE  s+l+++  atl++
  gi|119720483|ref|YP_920978.1| 130 RRNQKAKTLSGGERQMLA-------VARALMT------RPSVLLLDEPTSGLSPKAGATLMN 178
                                    467899********6543.......3333333......467888888888888888888876 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.4     0.055        58     244     264 ..      29      50 ..      19      53 .. 0.88
   2 ?    6.3   0.0    0.0034       3.5     300     351 ..     115     166 ..     113     169 .. 0.93
   3 ?    2.3   0.0     0.055        58     375     410 ..     175     210 ..     170     215 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.055
                                    SS.EEEEEE-TTSSHHHHHHHH CS
                     ABC_ATPase 244 kG.vtlIvGggfhGKsTLLeAl 264
                                    kG + ++ G++  GK+T+L+ +
  gi|119720483|ref|YP_920978.1|  29 KGeIAAVLGPNGAGKTTMLNTI 50 
                                    667999*************987 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0034
                                    E--TTTB---CCC--STTEEESS--HHHHHHHHHHHHHHTT-SEEEEEGGGS CS
                     ABC_ATPase 300 vDispFinnLPegkdttkfstedASGStsqAanimealeagakllLiDEDts 351
                                     Di   ++  Pe k+ ++   ++ SG   q  ++++al  + ++lL+DE ts
  gi|119720483|ref|YP_920978.1| 115 SDIEDILDLFPEIKRRRNQKAKTLSGGERQMLAVARALMTRPSVLLLDEPTS 166
                                    58888999999999999999*****************************998 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.055
                                    -HHHCHHHHHHHH--EEEEEESS-GCCTTT-SEEEE CS
                     ABC_ATPase 375 plvdrvrelykklgvstilvvggsgdyldvAdtvil 410
                                    +l+++++e+ ++ gv ++lv   +   l++Ad+  +
  gi|119720483|ref|YP_920978.1| 175 TLMNKIKEIQQTRGVAILLVEQNVARALEIADRAAV 210
                                    7899****************************9755 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   2.5e-05     0.027      11      47 ..      14      51 ..      10      59 .. 0.81
   2 ?   -3.5   0.1       6.2   6.5e+03      85     101 ..     129     145 ..     126     152 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.5e-05
                         AAA_27 11 yGkftd.rsldfsaeeadlhliyGpNEAGKstalrAis 47
                                   yGk++  + ++f+ ++ ++  ++GpN AGK+t+l+ i 
  gi|119720483|ref|YP_920978.1| 14 YGKMEVlHGVSFELGKGEIAAVLGPNGAGKTTMLNTIF 51
                                   5665542457888889999***************9885 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 6.2
                         AAA_27  85 aRrkgrkktlldaddqa 101
                                    +Rr ++ ktl + + q 
  gi|119720483|ref|YP_920978.1| 129 RRRNQKAKTLSGGERQM 145
                                    34455556666666554 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   4.9e-05     0.052      22      51 ..      28      57 ..      20     192 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.9e-05
                         AAA_16 22 grpelvllsGesGvGKsslvrellralekd 51
                                   g +e+  + G+ G GK++++++++  ++ +
  gi|119720483|ref|YP_920978.1| 28 GKGEIAAVLGPNGAGKTTMLNTIFGLATLH 57
                                   5568999***************99655544 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   9.8e-05       0.1      17      43 ..      30      55 ..      24      69 .. 0.80
   2 ?   -1.4   0.0       1.5   1.6e+03      88      96 ..     155     163 ..     126     197 .. 0.50
   3 ?   -1.4   0.0       1.5   1.6e+03      33      52 ..     175     194 ..     148     213 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9.8e-05
                         AAA_30 17 gdrvavltGpAGtGKttalkalreawe 43
                                   g  +a++ Gp G+GKtt+l+++  +++
  gi|119720483|ref|YP_920978.1| 30 G-EIAAVLGPNGAGKTTMLNTIFGLAT 55
                                   3.48999************99866655 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.5
                         AAA_30  88 pgtllivDE 96 
                                    + ++l+ DE
  gi|119720483|ref|YP_920978.1| 155 RPSVLLLDE 163
                                    334555555 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 1.5
                         AAA_30  33 talkalreaweaaggrvigl 52 
                                    t++++++e+ +++g  ++++
  gi|119720483|ref|YP_920978.1| 175 TLMNKIKEIQQTRGVAILLV 194
                                    56666666666666444333 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00051      0.54       3      35 ..      35      69 ..      33     208 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00051
                                   EESSTTSSHHHHHHHHHHHHTHE..EEEEETTTCS CS
                            AAA  3 lyGppGtGKTllakavakelgve..fleisgsell 35
                                   + Gp G GKT++ + +   +  +   ++++g +l 
  gi|119720483|ref|YP_920978.1| 35 VLGPNGAGKTTMLNTIFGLATLHrgEVSFNGVKLN 69
                                   68**************9997544222333333333 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1   0.00086      0.91       3      21 ..      34      52 ..      32      75 .. 0.82
   2 ?    0.9   0.0      0.46   4.8e+02      61      84 ..     171     195 ..     123     228 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00086
                                   EEEESTTSSHHHHHHHHHT CS
                       MMR_HSR1  3 aivGrpNvGKStLinaltg 21
                                   a++G   +GK+t++n+++g
  gi|119720483|ref|YP_920978.1| 34 AVLGPNGAGKTTMLNTIFG 52
                                   899**************98 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.46
                                    HHHHHHHHHHHHHHCT.SEEEEEEE CS
                       MMR_HSR1  61 seekglgkaflaleea.dlillvvd 84 
                                    + +  l +++++++++  +++l+v+
  gi|119720483|ref|YP_920978.1| 171 KAGATLMNKIKEIQQTrGVAILLVE 195
                                    3444555556655554244444444 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0024       2.5      21      39 ..      35      53 ..      29     103 .. 0.72
   2 ?    2.4   0.0     0.047        49     488     509 ..     127     147 ..     122     154 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0024
                         AAA_13 21 iYGwNGaGKTtLSrllrsl 39
                                   + G NGaGKTt+ + +  l
  gi|119720483|ref|YP_920978.1| 35 VLGPNGAGKTTMLNTIFGL 53
                                   679********87665444 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.047
                         AAA_13 488 ivrkggsqaaetLSeGEktaIa 509
                                    i r   +q+a+tLS GE+ + a
  gi|119720483|ref|YP_920978.1| 127 IKRR-RNQKAKTLSGGERQMLA 147
                                    6775.558**********9887 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00028       0.3       4      21 ..      34      51 ..      31      65 .. 0.82
   2 ?   -1.8   0.0       1.9   2.1e+03      15      35 ..     175     195 ..     168     210 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00028
                                   EEEESTTCCHHHHHHHHH CS
                           cobW  4 vltGflGsGKTtLlnhll 21
                                    + G+ G+GKTt+ln++ 
  gi|119720483|ref|YP_920978.1| 34 AVLGPNGAGKTTMLNTIF 51
                                   5789***********987 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.9
                                    HHHHHHHCT--SS-EEEEESS CS
                           cobW  15 tLlnhllenraglklavivNe 35 
                                    tL+n++ e ++ + +a+++ e
  gi|119720483|ref|YP_920978.1| 175 TLMNKIKEIQQTRGVAILLVE 195
                                    455555555555555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                       106  (0.00591221); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 1436.87
//
Query:       gi|119720484|ref|YP_920979.1|  [L=236]
Description: glycerophosphoryl diester phosphodiesterase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-35  122.9   0.0    1.8e-33  116.4   0.0    2.1  1  GDPD           Glycerophosphoryl diester phosphodiesterase fa
    0.00023   21.5   0.2     0.0035   17.8   0.1    2.3  2  GDPD_2         Glycerophosphoryl diester phosphodiesterase fa
    0.00098   18.7   0.0     0.0016   18.0   0.0    1.2  1  PI-PLC-X       Phosphatidylinositol-specific phospholipase C,
  ------ inclusion threshold ------
      0.024   14.1   0.0      0.048   13.2   0.0    1.5  1  EAL            EAL domain
      0.044   13.6   0.0      0.083   12.7   0.0    1.4  1  Abhydrolase_3  alpha/beta hydrolase fold
       0.12   11.8   0.1        9.2    5.6   0.0    2.1  2  PEP_mutase     Phosphoenolpyruvate phosphomutase


Domain annotation for each model (and alignments):
>> GDPD  Glycerophosphoryl diester phosphodiesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.4   0.0     6e-37   1.8e-33       1     258 [.      18     229 ..      18     230 .. 0.82

  Alignments for each domain:
  == domain 1  score: 116.4 bits;  conditional E-value: 6e-37
                                    TTTTTTTSSTTSHHHHHHHHHTT-SEEEEEEEE-TTS-EEE-SSSBSTTTCSCCCH.BGGGS-HHHHHTSTECCTTCCCC CS
                           GDPD   1 HRGasgnlpEnTlesfakAaelGadyiEfDvqlTkDgvpVvlHDfnldrttdvagrldvkdltleelkrldkiakenkaq 80 
                                    HRGasg+ pEnTl + ++A+e G+d++E+Dv+l+ DgvpVv+HD++l+rtt ++g  +v+d  ++el+ ld +++     
  gi|119720484|ref|YP_920979.1|  18 HRGASGYEPENTLRAVRRALEMGVDAVEVDVRLSADGVPVVIHDETLERTTSGRG--RVRDYPVDELRMLD-AGS----- 89 
                                    *******************************************************..**************.444..... PP

                                    SCCCSSGCCB...BHHHHHHHHHHCCSEEEEEEECCCCCCCHHHHHHTCHHHCCCCCSCHHTT..STTCSCEEEESTHHH CS
                           GDPD  81 lsenrvrlefpfptleevlkkpqnvglnieikipmlseakeeeelqivkeilksvdeilkkvlkkadkrkvifssfnpdi 160
                                      ++r+      p l+evl++  + ++ +  +++      e e    +   l  v e +          +v f s +p++
  gi|119720484|ref|YP_920979.1|  90 --GERI------PLLAEVLDE-VKGKAALFLELK------EVEA---AAPSLSLVEEKG-------MLGDVLFISLQPEA 144
                                    ..5566......9******86.444444444333......3333...223333344444.......34678899****** PP

                                    HHHHHHTCTCTEEEE.EEHHHHHHC-E.EECHCCCCCCCTCCCCHHCCCHCCCEB.CHHHHHHHTT-EEEEBSB-THSHH CS
                           GDPD 161 lkllrekqpklpllf.lteggteaeadssleraakfakadallgevsavaeglgdpdlVkraksrglvvhvytvnnedee 239
                                    l  +r+++p+  l + +++ g++          ak ++++ +l+   +++e       V+ a++ +l+v+++tv+++  +
  gi|119720484|ref|YP_920979.1| 145 LAEVRRMSPRAYLGLiYFKPGEWIL-------EAKRLGCSFVLPHYRLATEK-----AVSFAHRLKLRVVAWTVDDP--A 210
                                    *********4444330344444444.......469*************9999.....9*******************..* PP

                                    HHHHHHCCC-SEEEES-HH CS
                           GDPD 240 emkrlleagvdgvitDfpd 258
                                    + + l++ gvdgv  +fpd
  gi|119720484|ref|YP_920979.1| 211 TAAELKKRGVDGVASNFPD 229
                                    ******************8 PP

>> GDPD_2  Glycerophosphoryl diester phosphodiesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.17     5e+02      11      23 ..      31      43 ..      24      44 .. 0.73
   2 !   17.8   0.1   1.2e-06    0.0035       1      27 [.     200     226 ..     200     229 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.17
                         GDPD_2 11 avwrelvgaGVdg 23
                                   ++ r ++++GVd 
  gi|119720484|ref|YP_920979.1| 31 RAVRRALEMGVDA 43
                                   4558899****96 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 1.2e-06
                         GDPD_2   1 kvrfWttddeavwrelvgaGVdgInTD 27 
                                    +v +Wt+dd+a+ +el + GVdg+  +
  gi|119720484|ref|YP_920979.1| 200 RVVAWTVDDPATAAELKKRGVDGVASN 226
                                    799********************9666 PP

>> PI-PLC-X  Phosphatidylinositol-specific phospholipase C, X domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   5.4e-07    0.0016      28      66 ..      29      67 ..      24      74 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 5.4e-07
                                   -SS-HHHHHHTT--EEEEEE-...TT.SEEEETTEEE.E CS
                       PI-PLC-X 28 sveayrnaLlrGcRcvEidvwdgedeepvvlhgytltkk 66
                                   +  a+r+aL++G+  vE+dv+ ++d+ pvv+h  tl ++
  gi|119720484|ref|YP_920979.1| 29 TLRAVRRALEMGVDAVEVDVRLSADGVPVVIHDETLERT 67
                                   56799*****************************99765 PP

>> EAL  EAL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.6e-05     0.048     192     230 ..     185     223 ..     177     224 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.6e-05
                                    HHHHHCHHHHCCCT-EEEE-S--SHHHHHHHHHHT-SEE CS
                            EAL 192 alvkalialakelgikvvaegVeteeqlealrelgcdlv 230
                                      ++  +++a++l+++vva  V++++++  l++ g+d v
  gi|119720484|ref|YP_920979.1| 185 LATEKAVSFAHRLKLRVVAWTVDDPATAAELKKRGVDGV 223
                                    5677889*****************************976 PP

>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.8e-05     0.083      25      65 ..     171     212 ..     168     223 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.8e-05
                                    HHHHTSEEEEEE---TTTS-TTHHHHHHHHHHHHHHHTHH.H CS
                  Abhydrolase_3  25 akelgavvvsvdYrlAPehpfPaavedalaalrwlaeqaw.e 65 
                                    ak+lg+  v ++YrlA e+ +  a+   l+++ w ++  + +
  gi|119720484|ref|YP_920979.1| 171 AKRLGCSFVLPHYRLATEKAVSFAHRLKLRVVAWTVDDPAtA 212
                                    89********************************99986534 PP

>> PEP_mutase  Phosphoenolpyruvate phosphomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0    0.0091        27      78     105 ..      22      47 ..      16      76 .. 0.84
   2 ?    5.6   0.0    0.0031       9.2     167     217 ..     173     223 ..     170     226 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0091
                     PEP_mutase  78 dGygespeevaetvrrliaaGvvgvniE 105
                                    +Gy  +pe+  ++vrr++++Gv +v ++
  gi|119720484|ref|YP_920979.1|  22 SGY--EPENTLRAVRRALEMGVDAVEVD 47 
                                    788..59***************999876 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0031
                     PEP_mutase 167 eAGAdgvfvpglqkdaeiaelvaavdvplnvvplkgtlsvaelaelGvari 217
                                      G++ v+ + +  +++  ++++++++++++   ++  + ael++ Gv  +
  gi|119720484|ref|YP_920979.1| 173 RLGCSFVLPHYRLATEKAVSFAHRLKLRVVAWTVDDPATAAELKKRGVDGV 223
                                    579***********************999999965569*********9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1606.23
//
Query:       gi|119720485|ref|YP_920980.1|  [L=256]
Description: radical SAM domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.6e-21   75.6   0.0      1e-20   74.8   0.0    1.4  1  Radical_SAM  Radical SAM superfamily
     0.0022   18.3   0.0     0.0036   17.6   0.0    1.3  1  Fer4_12      4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.017   15.2   0.0      0.027   14.6   0.0    1.3  1  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.8   0.0   1.7e-24     1e-20       6     147 ..      47     189 ..      45     208 .. 0.94

  Alignments for each domain:
  == domain 1  score: 74.8 bits;  conditional E-value: 1.7e-24
                                    EESS--TTTSCCTT.HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEE CS
                                    xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM   6 gCnlrCsfCarpet.vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritvet 84 
                                    gCnlrC+fC+ ++   r+ g gr+ s+ee+ e + +++ ++g + v ++g ep+  +d    + +l + +   +r+++et
  gi|119720485|ref|YP_920980.1|  47 GCNLRCVFCWGWRVrDRPSGAGRFYSPEEVYERLASIAGRRGYRLVRISGNEPTIAWDHLLRVIELLEAD-GRFRFVLET 125
                                    9************9***********************87777**************************97.********* PP

                                    CSSCHG..HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEE CS
                                    xxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  85 ngtlpd..eeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvd 147
                                    ng+l+   + k++ l +    +v ++l+ a++e+++ l++ r++ +  +leal++l + g++   +
  gi|119720485|ref|YP_920980.1| 126 NGILIGadKSKARDLSKFSSVHVRVSLKGASEEEFHLLTGaRREFYRLQLEALRNLLDEGVP--AH 189
                                    *****999****************************************************99..34 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   6.1e-07    0.0036      14     125 ..      47     158 ..      38     169 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 6.1e-07
                        Fer4_12  14 gCnlsCkgCfnketwsfk..sgkef.tkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekdiwl 90 
                                    gCnl+C +C    +++    +g+ + ++e+ e++   +  +  + + ++G EP      + ll++++ +++ +    +++
  gi|119720485|ref|YP_920980.1|  47 GCNLRCVFCWGWRVRDRPsgAGRFYsPEEVYERLASIAGRRGYRLVRISGNEPTI--AWDHLLRVIELLEADGRFRFVLE 124
                                    9********9777765442245555359999999999999999************..99***********9999779*** PP

                        Fer4_12  91 ytgytleelskkekeellkeidvlvdGkfeesled 125
                                    ++g  + + ++k  ++l k   v v + ++ + e+
  gi|119720485|ref|YP_920980.1| 125 TNGILIGADKSK-ARDLSKFSSVHVRVSLKGASEE 158
                                    *******99875.8888888888888887765555 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   4.6e-06     0.027       7      92 ..      47     130 ..      44     154 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.6e-06
                        Fer4_14   7 gCnlsCkgCd..nketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekkiw 84 
                                    gCnl C++C   +  +  s +g  ++ e++ ++l++   ++   + + ++G eP +    ++ll++++ l   +  ++  
  gi|119720485|ref|YP_920980.1|  47 GCNLRCVFCWgwRVRDRPSGAGRFYSPEEVYERLASIAGRRG-YRLVRISGNEPTIA--WDHLLRVIELLEADG-RFRFV 122
                                    9*********88666667788888888888888876666555.35699*******66..679**********99.99*** PP

                        Fer4_14  85 letngtle 92 
                                    letng l 
  gi|119720485|ref|YP_920980.1| 123 LETNGILI 130
                                    ****9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1642.12
//
Query:       gi|119720486|ref|YP_920981.1|  [L=295]
Description: hypothetical protein Tpen_1583 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2161.02
//
Query:       gi|119720487|ref|YP_920982.1|  [L=356]
Description: ATPase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.8e-13   50.9   0.0      8e-13   48.8   0.0    2.1  1  ATPase_2    ATPase domain predominantly from Archaea
    1.2e-09   38.3   0.0     0.0014   18.7   0.0    2.7  3  AAA_14      AAA domain
    3.9e-07   30.4   0.1    2.7e-06   27.7   0.0    2.2  2  AAA_22      AAA domain
    8.2e-07   29.6   2.8    9.8e-07   29.3   0.3    2.3  2  AAA_16      AAA ATPase domain
  ------ inclusion threshold ------
      0.011   15.7   0.3      0.045   13.7   0.2    2.2  1  PadR        Transcriptional regulator PadR-like family
      0.041   13.7   0.0      0.073   12.9   0.0    1.3  1  Whirly      Whirly transcription factor
      0.042   13.7   0.3       0.15   12.0   0.1    2.0  2  HxlR        HxlR-like helix-turn-helix
      0.066   12.4   0.0       0.11   11.7   0.0    1.3  1  KAP_NTPase  KAP family P-loop domain


Domain annotation for each model (and alignments):
>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.8   0.0   3.6e-16     8e-13       2     227 ..      15     247 ..      14     252 .. 0.76

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 3.6e-16
                       ATPase_2   2 fdRekelkeleeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkkleka 81 
                                    +d e+el ele+ + +   + +++ G ++ GKt+L+  ++++l +    v  y +lre ++s +  +   +  ++++ ++
  gi|119720487|ref|YP_920982.1|  15 YDFERELGELEKFVGE---PLVVVSGLRRTGKTSLILTALNELGE----VYVYVDLREGASSAAGIY---KLLSRSFGET 84 
                                    67799*********99...99**********************44....444556666666665555...2333334444 PP

                       ATPase_2  82 l.................giavpkaeleeilk...eksklvfkaielllekikkkgkkiiiiiDelqklidlglngaell 141
                                                         v    le  l+   + + l+ + +++l e  ++ g+k+++++De+q+++  g+      
  gi|119720487|ref|YP_920982.1|  85 YrrlgggvgelfrrvlsrVRGVSFMGLEVSLDwspRGRPLLSELFDALDELGERLGRKVVVVLDEFQRAR-TGFG----- 158
                                    4466666677777775552333333344445566778888888888888888888999************.5555..... PP

                       ATPase_2 142 vkeLlnliesltk.ekhlcvviclsSeglfiervyn.eselegrhky.ilvddldketalnflkegfkel.eelskedfe 217
                                      +L+n++ + +  ++++ +v+ +s+ g++  ++ n e++l+gr+   +  + l  e++l+fl++gf+e   e +  ++e
  gi|119720487|ref|YP_920982.1| 159 -LALQNAVAHSYDfNRNVSFVLSGSEMGVLYGVLGNpEGPLYGRAYVeVRTRKLSAEESLDFLRRGFEEAgLEVEGRELE 237
                                    .56788887777626788899***********776549*******999**********************7777****** PP

                       ATPase_2 218 eiyryvGGkP 227
                                    ++++ ++G+ 
  gi|119720487|ref|YP_920982.1| 238 RAVNELDGII 247
                                    *******986 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   6.1e-07    0.0014       3      43 ..      31      68 ..      29      88 .. 0.83
   2 !   16.8   0.0   2.4e-06    0.0053      56     107 ..     135     189 ..     111     217 .. 0.68
   3 ?   -2.8   0.0       2.8   6.2e+03      56      76 ..     325     344 ..     305     347 .. 0.53

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 6.1e-07
                         AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderd 43
                                   +++v++G+Rr+GKT l+ + ++el    e ++y++l +   
  gi|119720487|ref|YP_920982.1| 31 PLVVVSGLRRTGKTSLILTALNELG---EVYVYVDLREGAS 68
                                   679******************9999...99****9988655 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 2.4e-06
                         AAA_14  56 ileklkeekktylflDEiqev.....pewekalkslvdegknldvivtGSnskllsk 107
                                    + e+l   +k +++lDE q++       +++a+ + +d ++n+ ++++GS  ++l+ 
  gi|119720487|ref|YP_920982.1| 135 LGERL--GRKVVVVLDEFQRArtgfgLALQNAVAHSYDFNRNVSFVLSGSEMGVLYG 189
                                    33322..48999*********54444456777777777779**********999965 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 2.8
                         AAA_14  56 ileklkeekktylflDEiqev 76 
                                    + e l++  k+  ++DE  e+
  gi|119720487|ref|YP_920982.1| 325 LYEVLQH-LKKHSLIDENNEY 344
                                    2222222.3456788886665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.0   1.2e-09   2.7e-06       7     131 ..      32     183 ..      28     187 .. 0.89
   2 ?   -0.6   0.1      0.67   1.5e+03      52      91 ..     304     334 ..     266     344 .. 0.50

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 1.2e-09
                         AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.sskdllrellralglelka............... 70 
                                    ++vv G   tGKT l+ + l++l         +  +v+v+l ++  s + +++ l r +g+   +               
  gi|119720487|ref|YP_920982.1|  32 LVVVSGLRRTGKTSLILTALNEL---------GEVYVYVDLREGAsSAAGIYKLLSRSFGETYRRlgggvgelfrrvlsr 102
                                    789********************.........9999*********999999*********98888*************** PP

                         AAA_22  71 ..................erlsseellealeqalraravielliiDEaqhlr.s..eealeeLrsllnlsrkgvqliLvG 129
                                                       r  ++el++al +  ++ ++++++++DE+q+ r     ++ + + + ++    +v+++L G
  gi|119720487|ref|YP_920982.1| 103 vrgvsfmglevsldwsprGRPLLSELFDALDELGERLGRKVVVVLDEFQRARtGfgLALQNAVAHSYD-FNRNVSFVLSG 181
                                    **************9998888899999999999999999************75263555555566666.78999999999 PP

                         AAA_22 130 tp 131
                                     +
  gi|119720487|ref|YP_920982.1| 182 SE 183
                                    75 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.67
                         AAA_22  52 sskdllrellralglelkaerlsseellealeqalrarav 91 
                                    ++++l rel ra g+e ++         +al++ l++ ++
  gi|119720487|ref|YP_920982.1| 304 EWSELKRELERAEGREVSD---------RALYEVLQHLKK 334
                                    4444444444444433333.........333333333333 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.3   4.4e-10   9.8e-07      24     159 ..      29     165 ..       7     178 .. 0.60
   2 ?   -0.7   0.2      0.73   1.6e+03     132     132 ..     289     289 ..     209     338 .. 0.55

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 4.4e-10
                         AAA_16  24 p.elvllsGesGvGKsslvrellralekdggif.lrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekl 101
                                    + +lv++sG + +GK+sl+ ++l++l + ++++ lr+ + +       + + ++l+r   + +  ++    + +   e +
  gi|119720487|ref|YP_920982.1|  29 GePLVVVSGLRRTGKTSLILTALNELGEVYVYVdLREGASSA------AGIYKLLSR--SFGETYRR----LGGGVGELF 96 
                                    3489*******************9***999888777777777......224444422..22222222....222222222 PP

                         AAA_16 102 eeala...........avpelagaea...........srllellkrllallsrderplvlvlDdlqwadeaslqllaaLl 159
                                    +++l+                    +           s l+++l +l    +r +r++v+vlD++q+a+++   +l++ +
  gi|119720487|ref|YP_920982.1|  97 RRVLSrvrgvsfmgleV--------SldwsprgrpllSELFDALDELG---ERLGRKVVVVLDEFQRARTGFGLALQNAV 165
                                    22233111343333320........13344666344466666666666...444556***********987666666555 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.73
                         AAA_16 132 r 132
                                    r
  gi|119720487|ref|YP_920982.1| 289 R 289
                                    1 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2     2e-05     0.045      14      54 ..     307     345 ..     294     353 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2e-05
                                    HHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-S CS
                           PadR  14 eiikeleelsegllelseGslYpaLkrLekeglvesewees 54 
                                    e+++ele+  eg +e+s+  lY +L+ L+k+ l+++++e +
  gi|119720487|ref|YP_920982.1| 307 ELKRELERA-EG-REVSDRALYEVLQHLKKHSLIDENNEYT 345
                                    899999999.78.9********************9998865 PP

>> Whirly  Whirly transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   3.2e-05     0.073      35      65 ..     159     188 ..     125     197 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.2e-05
                                    EEEEEEEETTEE-GGG-EEEEE-HHHHHHHH CS
                         Whirly  35 LefapavgerqYdwekkqvfaLSatElgell 65 
                                    L + +av+ + Yd+++  +f LS +E+g l 
  gi|119720487|ref|YP_920982.1| 159 LALQNAVA-HSYDFNRNVSFVLSGSEMGVLY 188
                                    33446665.57*****************997 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0       6.3   1.4e+04      68      79 ..     232     243 ..     229     247 .. 0.76
   2 ?   12.0   0.1   6.6e-05      0.15       8      59 ..     292     348 ..     287     353 .. 0.84

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 6.3
                                    CGGGGHHHHHHH CS
                           HxlR  68 kGrslepvlqel 79 
                                    +Gr+le +++el
  gi|119720487|ref|YP_920982.1| 232 EGRELERAVNEL 243
                                    688998888877 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 6.6e-05
                                    HHHHHHHTTS-EEHHHHHHHST.....TS-HHHHHHHHHHHHHTTSEEEEEESSSS- CS
                           HxlR   8 llilvellkgkkRfselkralp.....kisqkmLaqrLreLeqdglierevypevPp 59 
                                     l+++ l +g k +selkr+l      ++s + L + L++L+++ li+ +   + P+
  gi|119720487|ref|YP_920982.1| 292 RLVMRLLARGVKEWSELKRELEraegrEVSDRALYEVLQHLKKHSLIDENNEYTDPV 348
                                    588999999**********9963333369******************9998888776 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   5.1e-05      0.11     160     211 ..     124     180 ..     120     183 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.1e-05
                     KAP_NTPase 160 lladmektLda....lqkrlVvviDdLDrceteevlqlleavkllfsl.kpvvfila 211
                                    ll++++++Ld+    l +++Vvv+D+  r +t + l l +av +  ++ ++v+f+l+
  gi|119720487|ref|YP_920982.1| 124 LLSELFDALDElgerLGRKVVVVLDEFQRARTGFGLALQNAVAHSYDFnRNVSFVLS 180
                                    5677888888888889**************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2363.69
//
Query:       gi|119720488|ref|YP_920983.1|  [L=161]
Description: GCN5-related N-acetyltransferase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-17   62.8   0.3    4.2e-17   62.5   0.3    1.2  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    5.2e-11   42.6   0.2    6.7e-11   42.2   0.2    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    7.9e-11   42.2   0.4      1e-10   41.8   0.4    1.2  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    1.5e-10   40.9   0.3    2.9e-10   40.0   0.3    1.5  1  FR47             FR47-like protein
    2.8e-09   37.3   0.0    3.1e-09   37.1   0.0    1.1  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
    4.9e-08   33.1   0.2    6.6e-08   32.7   0.2    1.2  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
    1.1e-07   32.7   0.1    1.5e-07   32.2   0.1    1.2  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
    6.1e-05   22.7   0.1    0.00011   21.9   0.1    1.4  1  Acetyltransf_8   Acetyltransferase (GNAT) domain
     0.0062   16.3   0.1     0.0082   15.9   0.1    1.2  1  PanZ             Acetyltransferase (GNAT) domain, PanZ
  ------ inclusion threshold ------
      0.052   13.7   0.1       0.11   12.7   0.1    1.6  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.5   0.3   2.3e-20   4.2e-17      21     117 .]      30     129 ..       8     129 .. 0.86

  Alignments for each domain:
  == domain 1  score: 62.5 bits;  conditional E-value: 2.3e-20
                                    HHH.HHHHHHSTTC.EEEEEEETTEEEEEEEEEEEET.TSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEE CS
                 Acetyltransf_1  21 eee.feesfsleae.gllvaeedgeliGfisllkipd.ekggvayieslaVspeyrgkGlGsaLlealeerareegikki 97 
                                    e + +++s +l    ++lvae dg+++G + ++      +g+ +++  laV++e+r++G+G+ L+ea+e+++re+g+ ++
  gi|119720488|ref|YP_920983.1|  30 EGAeRYWSTRLLGYlETLVAEIDGRVVGVAEIYETEArGYGRLGVVSYLAVKREFRRMGVGRSLVEAAEKIFRERGCAYV 109
                                    3334556655555568999***********99999999999************************************998 PP

                                    EEEEETTEHHHHHHHHHTTE CS
                 Acetyltransf_1  98 vlaveedndaairlYeklGF 117
                                     + ++++n+a+++l++klG+
  gi|119720488|ref|YP_920983.1| 110 AASTRKSNKASQALFRKLGY 129
                                    99*************88**8 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2   0.2   3.7e-14   6.7e-11      29     109 ..      42     132 ..      20     142 .. 0.86

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 3.7e-14
                Acetyltransf_10  29 gealllvaeeggkivGvielrdgs........hisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp.yav 98 
                                    g   +lvae +g++vGv+e+++++         +s l+V++e+r+ G+g++L+ea+e+ ++++g +  + + ++s+ + +
  gi|119720488|ref|YP_920983.1|  42 GYLETLVAEIDGRVVGVAEIYETEargygrlgVVSYLAVKREFRRMGVGRSLVEAAEKIFRERGCAYvAASTRKSNkASQ 121
                                    667899**************6666699************************************99999777777776999 PP

                Acetyltransf_10  99 pfYeklGFkav 109
                                    ++++klG++  
  gi|119720488|ref|YP_920983.1| 122 ALFRKLGYELY 132
                                    ********977 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.8   0.4   5.8e-14     1e-10       4      75 ..      45     130 ..      32     131 .. 0.75

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 5.8e-14
                                    EEEEEEETTEEEEEEEEEEES....TCTEE......EEE-GGGTTSSHHHHHHHHTT.....SEEEEE.EEEE..THHHH CS
                 Acetyltransf_7   4 evfVaeddgkivGfialslld....aeitr......laVdpeyrgkGiGraLleaae.....kgiile.qlel..naeka 65 
                                    e++Vae dg++vG + +++++    +   r      laV+ e+r+ G+Gr L+eaae     +g+  +    +  +++++
  gi|119720488|ref|YP_920983.1|  45 ETLVAEIDGRVVGVAEIYETEargyG---RlgvvsyLAVKREFRRMGVGRSLVEAAEkifreRGCAYVaA-STrkSNKAS 120
                                    4679*********9999998887551...2345667******************7333566688874432.222344477 PP

                                    HHHHHHTTEE CS
                 Acetyltransf_7  66 ikfYeklGFe 75 
                                    +++++klG+e
  gi|119720488|ref|YP_920983.1| 121 QALFRKLGYE 130
                                    88*******8 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   0.3   1.6e-13   2.9e-10      22      84 ..      73     136 ..      58     138 .. 0.84

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 1.6e-13
                                    SSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-.EEEEEETT-HHHHHHHHHHT-EEEEEEE CS
                           FR47  22 gelgalqvlpehrrrGlgsrlvkalakeiaergkt.vllvvvasNtpsirlyeklGfekieete 84 
                                    g ++ l v+ e+rr+G g++lv+a  k  +erg   v + ++ sN++s++l+ klG+e++e   
  gi|119720488|ref|YP_920983.1|  73 GVVSYLAVKREFRRMGVGRSLVEAAEKIFRERGCAyVAASTRKSNKASQALFRKLGYELYERGS 136
                                    7778899*****************888888899762567899*****************97655 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   0.0   1.7e-12   3.1e-09      53     142 ..      47     137 ..       6     143 .. 0.91

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 1.7e-12
                 Acetyltransf_4  53 lvae.sdrivGyaylgqfkkrakdwkaelsvylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhka 131
                                    lvae ++r+vG a + + ++r++   + +s++ ++r  + +g+gr l++a e++++e +  +  a++ ++n++s++++ +
  gi|119720488|ref|YP_920983.1|  47 LVAEiDGRVVGVAEIYETEARGYGRLGVVSYLAVKREFRRMGVGRSLVEAAEKIFRERGCAYVAASTRKSNKASQALFRK 126
                                    68999**************************999999******************************************* PP

                 Acetyltransf_4 132 lGFelvgifkk 142
                                    lG+el  +  +
  gi|119720488|ref|YP_920983.1| 127 LGYELYERGSR 137
                                    ****9876555 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.2   3.7e-11   6.6e-08       2     127 ..      10     131 ..       9     132 .. 0.93

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 3.7e-11
                                    EEEE-GGGHHHHHHHHHHHTT----H..HHHHHHHHHHTTSEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEEEEEE CS
                 Acetyltransf_9   2 irelteedldevlellkyaFqdeespleeireyfrklleesrvlgaedngelvgqlallplelnvpGktlkaagvtgVav 81 
                                    ir lt  dl++++e+l++aF+  e++      +  +ll+  ++l+ae +g++vg++ ++  e + +G+    + v+  av
  gi|119720488|ref|YP_920983.1|  10 IRWLTAGDLPAAMEVLEEAFEGAERY------WSTRLLGYLETLVAEIDGRVVGVAEIYETEARGYGR---LGVVSYLAV 80 
                                    7899*****************99997......7899****************************9996...7999***** PP

                                    -CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--.....SSHHHHHTTT-EE CS
                 Acetyltransf_9  82 apehrgrgvlskLlaraleemreegqplsllfP.....ssipiYrrfGyei 127
                                    + e r+ gv ++L+++a +  re+g   +         +s +++r++Gye 
  gi|119720488|ref|YP_920983.1|  81 KREFRRMGVGRSLVEAAEKIFRERGCAYVAASTrksnkASQALFRKLGYEL 131
                                    ************************999888888888888889999999985 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.1   8.3e-11   1.5e-07      38     138 .]      26     130 ..       4     130 .. 0.72

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 8.3e-11
                 Acetyltransf_3  38 eewlera...waeeseeegyg.waivlkdtgviGsvglrdleeedee..aelgymla.psfwgkGyateavralleyafe 110
                                    ee +e a   w ++    gy   ++ + d++v+G++ +++ e +     + ++y+   ++f++ G+++  v+a+ +++ +
  gi|119720488|ref|YP_920983.1|  26 EEAFEGAeryWSTR--LLGYLeTLVAEIDGRVVGVAEIYETEARGYGrlGVVSYLAVkREFRRMGVGRSLVEAAEKIF-R 102
                                    44444334445442..2333335565677768*******988887646666666654377*************99998.8 PP

                 Acetyltransf_3 111 elglerlvavidkeNeaSirvleklGfe 138
                                    e g  ++ a + k+N+aS+++++klG+e
  gi|119720488|ref|YP_920983.1| 103 ERGCAYVAASTRKSNKASQALFRKLGYE 130
                                    888***********************86 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.1   6.3e-08   0.00011      30     140 ..      32     132 ..       4     136 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 6.3e-08
                                    HHHHHHHHHC.STTEEEEEEEETTEEEEEEEEEEGGGCGGGGCS---TT-EEEEEEES.SHHHCTTTCHHHHHHHHHHHH CS
                 Acetyltransf_8  30 evrellakldadphsepliglldgepvgyfeiYwakedelaeyydaepgdrGiHllig.eaeargkglttallralvhyl 108
                                     +r++ ++l    + e+l++++dg+ vg +eiY+ ++           g +G+   ++ + e+r+ g++++l++a ++ +
  gi|119720488|ref|YP_920983.1|  32 AERYWSTRLL--GYLETLVAEIDGRVVGVAEIYETEAR--------GYGRLGVVSYLAvKREFRRMGVGRSLVEA-AEKI 100
                                    4455555664..89999****************99999........77999999999956678888888888876.7999 PP

                                    HCCTT--EEEE--BTT-HHHHHHHHHTT-EEE CS
                 Acetyltransf_8 109 fadprtrrvvvEPdvrNerairllekaGfeke 140
                                    f++++++ v +  + +N+++ +l++k+G+e  
  gi|119720488|ref|YP_920983.1| 101 FRERGCAYVAASTRKSNKASQALFRKLGYELY 132
                                    ****************************9865 PP

>> PanZ  Acetyltransferase (GNAT) domain, PanZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   4.6e-06    0.0082      44     121 ..      50     130 ..      31     137 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.6e-06
                           PanZ  44 rFNdRlLgAvkveledk.....eaelsdlcVRevTRrRGVgsyLleearrqaPevkswvlaeedvkeldlavlqafleal 118
                                        R  g +++  +++      + +s l V+++ Rr GVg+ L+e a +   e  + ++a ++ k  ++++ qa++++l
  gi|119720488|ref|YP_920983.1|  50 EIDGRVVGVAEIYETEArgygrLGVVSYLAVKREFRRMGVGRSLVEAAEKIFRERGCAYVAASTRK--SNKASQALFRKL 127
                                    555566666555443332222267899******************998887766666666666655..345667777777 PP

                           PanZ 119 gfa 121
                                    g++
  gi|119720488|ref|YP_920983.1| 128 GYE 130
                                    774 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   5.9e-05      0.11      28      65 ..      76     107 ..      46     122 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.9e-05
                Acetyltransf_CG  28 thTeVpeelrGkGiAkkLvkaalddareeglkvvptCs 65 
                                        V+ e+r+ G+++ Lv+aa +  re+g        
  gi|119720488|ref|YP_920983.1|  76 SYLAVKREFRRMGVGRSLVEAAEKIFRERGC------A 107
                                    55679*****************999999984......4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1129.50
//
Query:       gi|119720489|ref|YP_920984.1|  [L=208]
Description: pyrrolidone-carboxylate peptidase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-60  204.2   0.0    2.6e-60  204.0   0.0    1.0  1  Peptidase_C15  Pyroglutamyl peptidase
  ------ inclusion threshold ------
      0.098   12.1   0.0        0.2   11.1   0.0    1.5  1  DUF3343        Protein of unknown function (DUF3343)


Domain annotation for each model (and alignments):
>> Peptidase_C15  Pyroglutamyl peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  204.0   0.0   2.9e-64   2.6e-60       1     199 [.       1     201 [.       1     204 [. 0.95

  Alignments for each domain:
  == domain 1  score: 204.0 bits;  conditional E-value: 2.9e-64
                                    -EEEEEEE---TT-S--HHHHHHHHHT.T-EETTEEEEEEEE-SSTTHHHHHHHHHHHHH--SEEEEEEE-TT--SEEEE CS
                  Peptidase_C15   1 mkvLvtGfdPfgkekinPaleavkeLd.gaeiaeativkrevPtvfkksadvlkkaiaeikpdivlaiGqagGrsaitve 79 
                                    m++L+tGf+Pfg+e++nP+  ++ e     + a+ + +++e+P++++++ +++++a+ae kp +++a+G +gG +++ ve
  gi|119720489|ref|YP_920984.1|   1 MRILLTGFGPFGEEDVNPSSTVAIEASrRLREAGYEAKALELPVSYRRAGQMIENAVAEYKPWLAIALGLYGGVTHVRVE 80 
                                    89****************9987766650334566788999**************************************** PP

                                    -EEES-BE-SS--TTS---ESB-SSTTS-SEEE--S-HHHHHHHHHHTT--EEEES---SSHHHHHHHHHHHHHHHHS-- CS
                  Peptidase_C15  80 rvainldDaripDnegkqlidepispdgeaaYfstlPvkamvkalkeaGvPaavsntaGtfvCnhllYqvlylldkklpe 159
                                    rva+n+ D   +D +g q++dep++p+g++aYfs +P +++v++l+ +G+Paa+s++aGt++Cn+++Y++l l+d ++ +
  gi|119720489|ref|YP_920984.1|  81 RVALNIMDFSTSDVDGAQPVDEPVDPEGPPAYFSSIPTRRVVERLRAEGIPAALSYSAGTYLCNYVMYKLLRLSDVRGAP 160
                                    ******************************************************************************** PP

                                    SEEEEEEE-B-GGGTHHHHHT.-B--HHHHHHHHHHHHHHH CS
                  Peptidase_C15 160 vraGfihiPylpeqvidkpet.pslsldkevagvkaaieai 199
                                    vraGfih+Py pe +  k++  psl+l+ +v++v +a+e  
  gi|119720489|ref|YP_920984.1| 161 VRAGFIHLPYTPELASRKKGLpPSLPLELQVKAVLIAVEES 201
                                    *******************9999**************9865 PP

>> DUF3343  Protein of unknown function (DUF3343)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   2.2e-05       0.2       7      36 ..      18      47 ..      16      50 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.2e-05
                        DUF3343  7 ssthhAiaaekalkeggiearliplPreis 36
                                   +s++ Ai+a + l+e+g+ea+   lP +++
  gi|119720489|ref|YP_920984.1| 18 PSSTVAIEASRRLREAGYEAKALELPVSYR 47
                                   6999**********************8887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1556.42
//
Query:       gi|119720490|ref|YP_920985.1|  [L=297]
Description: hypothetical protein Tpen_1587 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 2049.64
//
Query:       gi|119720491|ref|YP_920986.1|  [L=452]
Description: extracellular solute-binding protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.7e-33  115.8  11.6    6.4e-33  115.0  11.6    1.4  1  SBP_bac_1   Bacterial extracellular solute-binding protein
    1.6e-23   84.0   2.0    2.3e-23   83.4   2.0    1.2  1  SBP_bac_8   Bacterial extracellular solute-binding protein
     0.0072   16.1   0.1        3.5    7.3   0.0    2.4  2  SBP_bac_11  Bacterial extracellular solute-binding protein
  ------ inclusion threshold ------
      0.012   15.6   0.1      0.032   14.2   0.1    1.7  1  SasG_E      E domain
      0.045   13.6   0.3       0.36   10.7   0.0    2.2  2  DUF5572     Family of unknown function (DUF5572)
       0.32   11.3   0.6        2.9    8.2   0.7    2.2  2  WXG100      Proteins of 100 residues with WXG


Domain annotation for each model (and alignments):
>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.0  11.6   2.2e-36   6.4e-33       2     313 ..      85     366 ..      84     368 .. 0.88

  Alignments for each domain:
  == domain 1  score: 115.0 bits;  conditional E-value: 2.2e-36
                                    GSHHHHHHHHHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHHHHTTSSSCSEEEECGGHHHHHHHTTSBECCHHHHHHT CS
                      SBP_bac_1   2 gsltegaalqalvakafekehpgikVeiesvgsgslaqkltlaiaaGdgpaDviavdndwiarlakaglllpldpyvkay 81 
                                    g++++  ++qa++ +a+ k+hp++++e+ +    ++a  + +++aaG +p Dvi+++ ++ia++ k+g l +l+ ++k++
  gi|119720491|ref|YP_920986.1|  85 GDEAK--YFQAVI-DAYVKTHPNVEIEYRTMRAEDVAATMPIQFAAGVAPGDVIFGWAWFIAKMGKEGHLVDLTGIIKEN 161
                                    67778..******.*****************************************************************9 PP

                                    TECTTCCTEEEEHHHHTHHHHCE.EE...ES.EEEE.E.EEEEEEETTTHHCTTGGGSHBHHHHHHHHHHHHHHCTCTHC CS
                      SBP_bac_1  82 lapgvkdaadklsssvlpkilds.kv...ly.vPly.a.argliYNkdlfekagldppwtWdelveaakklkekgkkpig 154
                                                   ++p+i d+ k    ++  P+      g++Y+k+ f k+gl++p+++ e+v +++k+k+  + +  
  gi|119720491|ref|YP_920986.1| 162 E--------------YVPGIVDAvKAdgkIWgAPFTmWlKPGFWYRKSFFQKYGLTEPKSYAEFVQLLEKIKGIPGVKNP 227
                                    5..............99999996666899*************************************************66 PP

                                    CHCCEEHHHHHHHHHHHHHHHHTGGGEECCCTHHCSHHHHSHHHHHHHHHHHHHHHHHHHTTEEECSSHHHHHHHHHTTS CS
                      SBP_bac_1 155 garggsasgtayyfalalakslggkvfdkdgggldnpegvtaatylvklyavanltkelkgkgaenkdgaaalalfeaGe 234
                                    +a g   ++  +   ++++  +gg+ +  +   l++++   ++  ++k +   +    +kg+ +e   ++ + + + aGe
  gi|119720491|ref|YP_920986.1| 228 IATGDGVGWPISDIVEHFIIAYGGPQMQLN---LISGKTRFTDPSVRKVFSDYLIPLLQKGYFSEPIEWTTVIPKWWAGE 304
                                    777777777777777788888885555333...34444444555555555555556679********************* PP

                                    CSEEEEEHHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEEEEEEEEEEBTTCSTHHHHHHHHHHHTSHHH CS
                      SBP_bac_1 235 aamaivglwaalaamkvapkvafaadkekpkeelgvaplPagkggkpgilgayglaipkgsknpeaAkkFldfllspea 313
                                     +++++g+w               + + + +++l+++plP  kg  +   ga++  +pk s n +aA +F+++l+++++
  gi|119720491|ref|YP_920986.1| 305 YGLYFMGTWI--------------TGMVEDPNDLDFFPLPESKGVVG---GADYAFVPKYSRNVDAALDFIKYLATEGQ 366
                                    *********7..............99999999********9999999...9*************************987 PP

>> SBP_bac_8  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.4   2.0   7.8e-27   2.3e-23       1     274 [.      93     389 ..      93     394 .. 0.78

  Alignments for each domain:
  == domain 1  score: 83.4 bits;  conditional E-value: 7.8e-27
                                    HHHHHHHHH-.TEEEEEEE--SSSHHHHHHHHHHTT---SEE.EEE-HHHHHHHHHTTSB--GGGS.TTHHH-HHHHHTT CS
                      SBP_bac_8   1 klakefekkt.gvkvnvvtaasndleqklkaalaagtapdidvvwanedalatlaeeglladlsdl.dnlddltdalaav 78 
                                    ++++++ k++ +v++++ t+  +d+++++  + aag ap  dv+++++ ++a++ +eg l+dl+ + ++ ++++  ++av
  gi|119720491|ref|YP_920986.1|  93 AVIDAYVKTHpNVEIEYRTMRAEDVAATMPIQFAAGVAPG-DVIFGWAWFIAKMGKEGHLVDLTGIiKENEYVPGIVDAV 171
                                    589*****************99*****************9.8899999****************99677788899***** PP

                                    --TS.----EEEEEEE-EEEEEHHHHHHS...---BHHHHHHHHHHHHHH-............SEGG---GGGGGGTHHE CS
                      SBP_bac_8  79 gydgklygvPyasetpyvliynkdlleka..edpktwdellaaakklkgkf............glpdpasgwlqaallak 144
                                    + dgk+ g P+++    ++ y+k+ ++k     pk+++e++++++k+kg              g+p   s+ ++ + +a+
  gi|119720491|ref|YP_920986.1| 172 KADGKIWGAPFTMWLKPGFWYRKSFFQKYglTEPKSYAEFVQLLEKIKGIPgvknpiatgdgvGWPI--SDIVEHFIIAY 249
                                    ************87544**********94566***************86663334544444333332..23332222331 PP

                                    TTEE---H..........HHH..HHHHHHHHHHHHTT-EE.-.S..--SSTTTTTSBSEEEE-TTHHHHHH-TTTSEEEE CS
                      SBP_bac_8 145 dgksldddg........gkdgl.kealellkklkdngkty.d.tgadavsefanGevaftingswdiaaaqkagkklgai 213
                                    +g ++ + +        +++ + k + ++l  l ++g++  +  +++++ ++  Ge+  ++ g+w+   +++   +l + 
  gi|119720491|ref|YP_920986.1| 250 GGPQM-QLNlisgktrfTDPSVrKVFSDYLIPLLQKGYFSePiEWTTVIPKWWAGEYGLYFMGTWITGMVEDP-NDLDFF 327
                                    33333.22224333234334442444577778889999886357899999*********************94.366788 PP

                                    .--S--EEEEEEEEE.EBTTS-HHHHHHHHHHHHHTTSHHHHHHHHHH---BS-S-TTTHHHH CS
                      SBP_bac_8 214 .vpkqgsfaggkgla.vpknaknedlaAldFlkwltspenqaalaektgyipvnksaalspev 274
                                     +p ++ ++gg+ +a vpk + n d aAldF+k+l+++ +    +  +g ip+ ++a+  + +
  gi|119720491|ref|YP_920986.1| 328 pLPESKGVVGGADYAfVPKYSRNVD-AALDFIKYLATEGQVVHASVPSGKIPTWTKAPVEKLW 389
                                    5678889999987666*********.6**********99999888899999999888866655 PP

>> SBP_bac_11  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0    0.0012       3.5       7      51 ..      85     135 ..      83     153 .. 0.86
   2 !    6.2   0.0    0.0025       7.4     174     218 ..     320     364 ..     302     367 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0012
                                    SSTHHHHHHHHHHH.HHHH---EEEEESSHHHHHHHH....HHH...-SEE CS
                     SBP_bac_11   7 gslaaalrelaaaF.eahtgvkvevsaggsgklarqi....adga.rpDvw 51 
                                    g+ a+ ++++++a+ + h++v++e+++  + ++a+++    a+g  + Dv+
  gi|119720491|ref|YP_920986.1|  85 GDEAKYFQAVIDAYvKTHPNVEIEYRTMRAEDVAATMpiqfAAGVaPGDVI 135
                                    555788999*****999******************7777777776688887 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0025
                                    STTSSEEEE--TTT--....EEEEEEEE-TT--HHHHHHHHHTTSH CS
                     SBP_bac_11 174 ngdkleavylpeglnl.dpldypaavlkkaakreaAraFlafLrsp 218
                                     + +l++++lpe+  +   +dy++ v+k +++  aA +F+++L+++
  gi|119720491|ref|YP_920986.1| 320 DPNDLDFFPLPESKGVvGGADYAF-VPKYSRNVDAALDFIKYLATE 364
                                    56789999999988777899**88.9*****************975 PP

>> SasG_E  E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   1.1e-05     0.032      20      47 ..     216     244 ..     212     245 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.1e-05
                                    EEE--B-EEEET.TTTEEEE--B-EEEEE CS
                         SasG_E  20 eevPGKPGvKnP.dtGevvtpPvDdvtKy 47 
                                    e++ G PGvKnP  tG+ v  P+ d++ +
  gi|119720491|ref|YP_920986.1| 216 EKIKGIPGVKNPiATGDGVGWPISDIVEH 244
                                    7899********77**********99876 PP

>> DUF5572  Family of unknown function (DUF5572)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.28   8.4e+02       9      22 ..     154     167 ..     151     169 .. 0.84
   2 ?   10.7   0.0   0.00012      0.36       2      23 ..     204     225 ..     203     226 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.28
                        DUF5572   9 lveLIesGkpIPgI 22 
                                    l   I++++ +PgI
  gi|119720491|ref|YP_920986.1| 154 LTGIIKENEYVPGI 167
                                    56679********9 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00012
                        DUF5572   2 yplsFaelveLIesGkpIPgIk 23 
                                    +p+s+ae v+L+e+ k IPg k
  gi|119720491|ref|YP_920986.1| 204 EPKSYAEFVQLLEKIKGIPGVK 225
                                    69******************98 PP

>> WXG100  Proteins of 100 residues with WXG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.7   0.00098       2.9       4      38 ..      28      62 ..      27      64 .. 0.90
   2 ?   -0.2   0.0      0.39   1.2e+03      39      58 ..      81     100 ..      73     114 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00098
                                   SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCG CS
                         WXG100  4 vdpeelrqaaarfqkqaeeledelqrlkaevdalq 38
                                   v+ + l++a+++++++ ++l++ +++l+++v +++
  gi|119720491|ref|YP_920986.1| 28 VTVQSLASAISDLKASISNLQGTVSSLQQQVGKIS 62
                                   78899*************************99884 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.39
                                    CGCTHHHCHHHHHHHHHHHH CS
                         WXG100  39 sgWsGaaadafqaefeewkq 58 
                                    + W G+ a+ fqa+++ + +
  gi|119720491|ref|YP_920986.1|  81 GPWAGDEAKYFQAVIDAYVK 100
                                    67**********99987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (452 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       776  (0.0432818); expected 358.6 (0.02)
Passed bias filter:                      689  (0.0384294); expected 358.6 (0.02)
Passed Vit filter:                       110  (0.00613531); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.47
# Mc/sec: 2907.90
//
Query:       gi|119720492|ref|YP_920987.1|  [L=297]
Description: binding-protein-dependent transport systems inner membrane component [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      6e-21   75.0  24.7      6e-21   75.0  24.7    2.0  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
       0.14   12.3   0.2        0.4   10.8   0.2    1.8  1  TM_PBP2_N     N-terminal of TM subunit in PBP-dependent ABC t


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   1.6     0.041   3.7e+02      26      44 ..      11      54 ..       8      87 .. 0.60
   2 !   75.0  24.7   6.7e-25     6e-21       2     171 ..      89     282 ..      88     294 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.041
                   BPD_transp_1 26 vllslPsfvlaillvlvf.........................v 44
                                   v+l++P  v+++++v+ +                         +
  gi|119720492|ref|YP_920987.1| 11 VFLGIPLSVILVFVVYPIvatvvlsftadgalsaknyvevlteS 54
                                   78888988988888887766655555555555555555555550 PP

  == domain 2  score: 75.0 bits;  conditional E-value: 6.7e-25
                   BPD_transp_1   2 illGilaa.lnrnkkldkllrpliivllslPsfvlaillvlvf.....................vilsilghlilpviil 59 
                                    ++lG+l+a + r+ +++ ++ + i++++ lP +v ++++ ++f                      +  + +++ l++i+ 
  gi|119720492|ref|YP_920987.1|  89 VFLGMLLAyTLRGVPGSSFIAGAIFLGMVLPGVVSGLIIRFMFddslgifprifgalgvpllskTWTIYPQTALLALILG 168
                                    789************************************************************8888888899999**** PP

                   BPD_transp_1  60 lllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgt 139
                                    +++ ++++ + ++ a+l+s+p++ veaa+++Gas w+if ++++P+++p ++   +++++++l+ + +++ ++++++ g+
  gi|119720492|ref|YP_920987.1| 169 SVWLWLGFSVTLYLAGLDSIPSSMVEAALVDGASQWEIFTRIIVPQLKPITVVVTLMTVMWILKIFDIVYVVTGGGPGGS 248
                                    ***************************************************************************99*** PP

                   BPD_transp_1 140 llleailgydyseis..nggvlalviavlllnlv 171
                                     ++ a+++y y + s  +g ++a++++++ll+lv
  gi|119720492|ref|YP_920987.1| 249 STVLALIMYTYFASSleYGKAAAVAVILALLTLV 282
                                    ************999**77777777777777665 PP

>> TM_PBP2_N  N-terminal of TM subunit in PBP-dependent ABC transporters
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2   4.5e-05       0.4       3      26 ..      20      41 ..      19      53 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 4.5e-05
                      TM_PBP2_N  3 LlvfqvfpvlyTistafTNyGdGh 26
                                   +lvf v+p++ T+ ++fT   dG 
  gi|119720492|ref|YP_920987.1| 20 ILVFVVYPIVATVVLSFTA--DGA 41
                                   68****************5..555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       838  (0.0467399); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2038.11
//
Query:       gi|119720493|ref|YP_920988.1|  [L=279]
Description: binding-protein-dependent transport systems inner membrane component [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.9e-23   81.3  16.5    6.9e-23   81.3  16.5    1.9  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.3     0.032   5.7e+02      20      40 ..      15      35 ..       5      63 .. 0.69
   2 !   81.3  16.5   3.9e-27   6.9e-23       2     182 ..      88     271 ..      87     274 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.032
                   BPD_transp_1 20 lrpliivllslPsfvlaillv 40
                                    ++++ +l+ lP+++l+++ v
  gi|119720493|ref|YP_920988.1| 15 ALWVFTALWLLPFVALVVMSV 35
                                   455666666777776666655 PP

  == domain 2  score: 81.3 bits;  conditional E-value: 3.9e-27
                   BPD_transp_1   2 illGilaa...lnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalrs 78 
                                    +++++++a   ++ +++ + ll + i v++s+P   ++i+l+  ++++++l++   ++i+l     +p++ +++r+++r 
  gi|119720493|ref|YP_920988.1|  88 VVFAAMMAyslTYLSFRYRTLLFVSILVFMSVPQQMVVIPLFS-LYVKTGLHDKLAGIILLHSAWGTPWIAFFMRNYFRM 166
                                    678999999***************************9999994.36666666666668888888889************* PP

                   BPD_transp_1  79 lpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG...lgtllleailgydyseisn 155
                                    lp+++veaar++Gas+++if+k++lP++lp +++  +++f++++g+++ +  ++ +p    ++++l     ++ +++++ 
  gi|119720493|ref|YP_920988.1| 167 LPQSFVEAARIDGASEFTIFWKILLPLSLPAVVAASAIQFTWVWGDFFYAMVFLPSPSnyvVTQRLALLKGEFHIDWGL- 245
                                    *************************************************999998886777777777777777777777. PP

                   BPD_transp_1 156 ggvlalviavlllnlvadilqrlldpr 182
                                     +++ +++a+l+ +lv+ ++ ++  + 
  gi|119720493|ref|YP_920988.1| 246 -LSAGAILAMLPPLLVYVAFKKYYVRG 271
                                    .99***************999998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.55
# Mc/sec: 1521.01
//
Query:       gi|119720494|ref|YP_920989.1|  [L=345]
Description: transcriptional regulator, TrmB [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-49  167.5   0.0    4.4e-49  166.8   0.0    1.4  2  Regulator_TrmB  Archaeal transcriptional regulator TrmB
      1e-19   70.2   0.4    2.2e-19   69.1   0.4    1.6  1  TrmB            Sugar-specific transcriptional regulator TrmB
    1.5e-05   24.8   0.2    9.8e-05   22.2   0.0    2.4  2  MarR_2          MarR family
    0.00031   20.8   0.3    0.00079   19.4   0.0    1.9  2  HTH_20          Helix-turn-helix domain
    0.00032   20.5   0.2     0.0013   18.4   0.0    2.1  2  HTH_IclR        IclR helix-turn-helix domain
     0.0047   16.8   0.0       0.01   15.7   0.0    1.6  1  HTH_5           Bacterial regulatory protein, arsR family
  ------ inclusion threshold ------
      0.067   13.7   0.7       0.44   11.0   0.1    2.6  2  RuvA_C          RuvA, C-terminal domain
      0.081   13.3   0.1       0.22   11.9   0.0    1.8  2  Rrf2            Transcriptional regulator


Domain annotation for each model (and alignments):
>> Regulator_TrmB  Archaeal transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       2.9   6.4e+03     171     189 ..      29      47 ..      25      57 .. 0.70
   2 !  166.8   0.0     2e-52   4.4e-49       2     231 ..     119     339 ..     118     341 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 2.9
                                    EEEEETTT--EEEEEEEEE CS
                 Regulator_TrmB 171 veGrdtetgeevtieGrvv 189
                                    ++Gr++  +e v ++G + 
  gi|119720494|ref|YP_920989.1|  29 ADGRERTANEIVALTGVPQ 47 
                                    6777777777777777764 PP

  == domain 2  score: 166.8 bits;  conditional E-value: 2e-52
                                    EEEESSHHHHHHHHHHHHHH-SSEEEEEE-GGGHHHHHHHHHHHHHTT-EEEEEESS----GGGSSSSEEEEEE-S---S CS
                 Regulator_TrmB   2 vwvvksretvierieelIesAenelivslpselLeelreeliaaaergvtVllliypdedleeldleevatevrvrrsga 81 
                                    v v+k+++++i r+++++e+A+++ +v++p++l+ e+ ++      ++ +V +++y+  + ee+  +e +  +r+r+ g 
  gi|119720494|ref|YP_920989.1| 119 VRVIKNKSEAILRARKMLENASYDALVAGPPRLVGEILPHSVGGGAARRLVAVVYYE--GVEEPLPAEPWLGLRLRSVGV 196
                                    899******************************************************..********************* PP

                                    .EEEEETTTEEEEE-SSS-EEEE--HHHHHHHHHHHHHH........HHH-EEEEE.EES-TT-EEES-HHHHHHHHHHH CS
                 Regulator_TrmB  82 pllvivDrkrgvvaprevlrdkeeeyaiifkekelihvlshyFlttlWktsevikt.depvekpitfssirlavedikkl 160
                                      lvi+D++r+v+          e+ya+ + e++li++++ ++++ lW+ s+v+k+ +  + +++t +si+l+ e++k++
  gi|119720494|ref|YP_920989.1| 197 IPLVIADSARAVILR--------ESYALEIAEEDLIRTFLDFYYHALWRVSSVVKPfEPVEGFEYTATSIWLLNEVLKEC 268
                                    667***********4........58*******************************999999****************** PP

                                    T.TTS-EEEEEEEEETTT--EEEEEEEEEEEEEETTTTEEEEEEEETTEEEEEE-TT--SSSEEEEEEEEE CS
                 Regulator_TrmB 161 lraglkveaeveGrdtetgeevtieGrvveatlnstpgvaslvvetedgevtVGGlgAvlEDieaeeitle 231
                                    l +gl  e++v G++++tg++vt++Gr+ e++ n ++ + slv+e++++++tVGGlgA+lED+e++ ++l+
  gi|119720494|ref|YP_920989.1| 269 LGRGLGAEVTVAGVERRTGRSVTLTGRPAEISENGQGVRVSLVLEVGQRKITVGGLGARLEDVEGRVFRLK 339
                                    ******************************************************************99996 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.1   0.4   9.8e-23   2.2e-19       3      67 ..      14      78 ..      12      79 .. 0.97

  Alignments for each domain:
  == domain 1  score: 69.1 bits;  conditional E-value: 9.8e-23
                                   HCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE--H CS
                           TrmB  3 klGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYravdp 67
                                   +lGL+ yEa+vYla+    + ta+ei   +gvp+++vYe+L+sL +kGlVe+  ++pk+Yra++p
  gi|119720494|ref|YP_920989.1| 14 ELGLKPYEARVYLAIADGRERTANEIVALTGVPQPRVYETLESLASKGLVEVALSKPKRYRAIEP 78
                                   79*************************************************************99 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   4.4e-08   9.8e-05       2      53 ..      16      65 ..      15      73 .. 0.88
   2 ?   -1.4   0.0         1   2.2e+03      14      33 ..     269     288 ..     263     291 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 4.4e-08
                                   T--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                         MarR_2  2 gltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53
                                   gl+p +arv +a++++ +   t++e+++ +g+++++v  +l+ L ++GLve 
  gi|119720494|ref|YP_920989.1| 16 GLKPYEARVYLAIADGRE--RTANEIVALTGVPQPRVYETLESLASKGLVEV 65
                                   788888888888888777..7*****************************96 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1
                                    HHCTTTSEEEHHHHHHHHTS CS
                         MarR_2  14 Lgrrpgrdltvgelarrlgl 33 
                                    Lgr+ g ++tv+ ++rr+g 
  gi|119720494|ref|YP_920989.1| 269 LGRGLGAEVTVAGVERRTGR 288
                                    67777778999999999986 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   3.5e-07   0.00079      10      57 ..      19      66 ..      12      70 .. 0.93
   2 ?   -3.3   0.1       4.4   9.9e+03       7      17 ..     201     211 ..     200     212 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 3.5e-07
                                   HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                         HTH_20 10 PvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevv 57
                                   P  +r++ a+a+++++ta+e+ ++ ++++  ++  L+ L++ gLvev 
  gi|119720494|ref|YP_920989.1| 19 PYEARVYLAIADGRERTANEIVALTGVPQPRVYETLESLASKGLVEVA 66
                                   777899****************************************95 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4.4
                                    HS-HHHHHHHH CS
                         HTH_20   7 LahPvRrrilr 17 
                                    +a+  R+ ilr
  gi|119720494|ref|YP_920989.1| 201 IADSARAVILR 211
                                    68999**9998 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0     6e-07    0.0013      11      49 ..      27      64 ..      23      66 .. 0.92
   2 ?   -2.1   0.0       1.5   3.4e+03       4      16 ..      80      92 ..      79      98 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 6e-07
                                   T-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                       HTH_IclR 11 alaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                   a+a ++++ t  e+ + tg+p + v+  L +L   G+ve
  gi|119720494|ref|YP_920989.1| 27 AIADGRER-TANEIVALTGVPQPRVYETLESLASKGLVE 64
                                   57777777.9****************************8 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.5
                                   HHHHHHCT-CTTB CS
                       HTH_IclR  4 RalaiLdalaeap 16
                                   Ra++iL  la+++
  gi|119720494|ref|YP_920989.1| 80 RAIEILAGLASRR 92
                                   9999999888765 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   4.6e-06      0.01      11      46 ..      28      64 ..      24      65 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 4.6e-06
                                   HTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_5 11 Lae.gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                    a+ +e+++ e+++ +g++q+ v + L  L   GLVe
  gi|119720494|ref|YP_920989.1| 28 IADgRERTANEIVALTGVPQPRVYETLESLASKGLVE 64
                                   566689******************************8 PP

>> RuvA_C  RuvA, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1    0.0002      0.44       3      21 ..       5      23 ..       3      40 .. 0.90
   2 ?   -0.1   0.1      0.58   1.3e+03      19      35 ..      99     114 ..      96     132 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0002
                                   HHHHHHHHHHCTS-HHHHH CS
                         RuvA_C  3 ledaveALlaLGYkekeae 21
                                    eda +AL+ LG k+ ea+
  gi|119720494|ref|YP_920989.1|  5 FEDAYNALVELGLKPYEAR 23
                                   59*************9996 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.58
                                    HHHHHHHHHHC-TTS-H CS
                         RuvA_C  19 eaekAvakvlanpgasv 35 
                                     a kA+++v+  ++++v
  gi|119720494|ref|YP_920989.1|  99 RALKALSRVY-LQAEDV 114
                                    5778888887.555554 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   9.7e-05      0.22      15      58 ..      24      66 ..       8      86 .. 0.85
   2 ?   -3.4   0.0       5.7   1.3e+04       5      23 ..      95     113 ..      92     121 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.7e-05
                                   HHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                           Rrf2 15 lyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksv 58
                                   +yLa  +++e  +++ei + ++++++ +   l+ L+ +glv++ 
  gi|119720494|ref|YP_920989.1| 24 VYLAIADGRE-RTANEIVALTGVPQPRVYETLESLASKGLVEVA 66
                                   7899999988.9*****************************976 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 5.7
                                    HHHHHHHHHHHHHHHSSTC CS
                           Rrf2   5 skteyalhallyLakeeee 23 
                                    s  e al+al    +++e+
  gi|119720494|ref|YP_920989.1|  95 SNKERALKALSRVYLQAED 113
                                    5667788888777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2506.89
//
Query:       gi|119720495|ref|YP_920990.1|  [L=414]
Description: glycosyl transferase, group 1 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.2e-18   65.5   0.1    1.4e-17   63.8   0.1    1.9  1  Glycos_transf_1  Glycosyl transferases group 1
    1.2e-10   41.9   0.9    1.9e-10   41.3   0.3    1.6  2  Glyco_trans_1_4  Glycosyl transferases group 1
    1.5e-08   34.9   0.0    3.7e-08   33.7   0.0    1.7  1  Glyco_trans_1_2  Glycosyl transferases group 1
  ------ inclusion threshold ------
      0.041   13.6   0.0       0.07   12.9   0.0    1.3  1  Cu-oxidase_2     Multicopper oxidase
       0.15   12.5   0.0         34    4.9   0.0    2.6  3  Aida_N           Aida N-terminus


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.8   0.1   3.8e-21   1.4e-17       5     171 ..     218     389 ..     214     390 .. 0.84

  Alignments for each domain:
  == domain 1  score: 63.8 bits;  conditional E-value: 3.8e-21
                                    HHHHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES..........STTHHHHHHHHHHHCTTCGG CS
                Glycos_transf_1   5 krkklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaG.........ngeeekelkklaeelelsdnv 75 
                                     +k+ g + ++++i  v+r++++K+v  ++++f+++kk+  p ++l+++           + +ek l +   e ++   +
  gi|119720495|ref|YP_920990.1| 218 VFKRFGVDPERPVITKVARFDPWKDVFSAVDVFREVKKE-VPGAQLLLVSsmarddpegAVFYEKVLGYVKGEEGVHILT 296
                                    577888999***************************987.**********9***87644444555555555555554444 PP

                                    GEEECCHSSSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHH CS
                Glycos_transf_1  76 iflgevsredleellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairkl 155
                                      +g  +  ++ ++ +   + ++++i+EgfG++++E +  ++pv+a  +gg++++v+dg+tG+   ++  ++lae+++ l
  gi|119720495|ref|YP_920990.1| 297 DAIGVRD-LEVNAFQRGTTVGLHTAIREGFGLAVTEMLWKKVPVVARPVGGVKKQVVDGVTGFTAWSV--QELAERVKAL 373
                                    4444443.556677777*********************************************998888..********** PP

                                    HHSHHHHHHHHHHHHH CS
                Glycos_transf_1 156 ledeelrerlgenark 171
                                    l d++lr rlge++r+
  gi|119720495|ref|YP_920990.1| 374 LADNQLRGRLGEAGRE 389
                                    **************97 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0         2   7.2e+03      66      97 ..      32      63 ..       9      75 .. 0.55
   2 !   41.3   0.3   5.4e-14   1.9e-10       1     134 []     228     376 ..     228     376 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2
                                   HHHHHHH-SEEEE-----SHHHHHHHHTT-EE CS
                Glyco_trans_1_4 66 laellaaadvfvaPsegfglkllEamaaglpv 97
                                   +a+ l+ ++v+ + s   g  + E + + +pv
  gi|119720495|ref|YP_920990.1| 32 VAKRLKGVSVVHVNSTAYGGGVAEILHSMVPV 63
                                   33334444444444455555555555555555 PP

  == domain 2  score: 41.3 bits;  conditional E-value: 5.4e-14
                                    SEEEEEES---GG.GTHHHHHHHHHHHH.H.H.EEEEEES---..........HHHHHHHTT-T.TEEEE---...TH.. CS
                Glyco_trans_1_4   1 rpvilfvGrleenvkgvdllleavpllrkk.d.vrlvivGdgprp........eeleelaagleerveftGfv...ed.. 65 
                                    rpvi  v r+ +++k v   ++ + +++k+ + ++l++v +  r+        e++  +++g ee+v+++       d  
  gi|119720495|ref|YP_920990.1| 228 RPVITKVARF-DPWKDVFSAVDVFREVKKEvPgAQLLLVSSMARDdpegavfyEKVLGYVKG-EEGVHILTDAigvRDle 305
                                    588999****.667**************88758*******6542234554444333334444.57888877666885556 PP

                                    HHHHHHH-SEEEE--..---SHHHHHHHHTT-EEEE-TGGGT.TT--.TTSSEE--TT-HHHHHHHHHHHHH- CS
                Glyco_trans_1_4  66 laellaaadvfvaPs..egfglkllEamaaglpvVatdvggi.aevv.gengllvppgdpealaeailrLled 134
                                    ++++ +  +v + +   egfgl++ E++  ++pvVa +vgg+ ++vv g++g+ +   ++++lae++ +Ll+d
  gi|119720495|ref|YP_920990.1| 306 VNAFQRGTTVGLHTAirEGFGLAVTEMLWKKVPVVARPVGGVkKQVVdGVTGFTAW--SVQELAERVKALLAD 376
                                    ****************99**********************9945566*****9997..9************87 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   0.0     1e-11   3.7e-08       2      91 ..     316     405 ..     315     406 .. 0.94

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 1e-11
                Glyco_trans_1_2   2 vLnpsrsespnlrlfEaaacGafaltddaegleelftpgkevilfedleelaekiryllanpeerraiaeaarervlaeh 81 
                                    +L++  +e++ l + E +   +++++ +  g+ + + +g +++++ +++elae++++lla+ ++r +++ea+re+v++++
  gi|119720495|ref|YP_920990.1| 316 GLHTAIREGFGLAVTEMLWKKVPVVARPVGGVKKQVVDGVTGFTAWSVQELAERVKALLADNQLRGRLGEAGREHVRRNF 395
                                    788999999******************99***************99*********************************9 PP

                Glyco_trans_1_2  82 tydhraeqll 91 
                                      ++ ++++l
  gi|119720495|ref|YP_920990.1| 396 VITQHVKRYL 405
                                    9988888776 PP

>> Cu-oxidase_2  Multicopper oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0     2e-05      0.07      90     120 ..     124     155 ..      93     160 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2e-05
                                    BSEEEE-TTEEEEEE.EES.S-EEEEEEESSH CS
                   Cu-oxidase_2  90 rdtvqvppggwvair.fkadnpGvwllHCHil 120
                                     d+v v+  + +a+  fk    Gvw+++CHi+
  gi|119720495|ref|YP_920990.1| 124 ADVVLVHDPQPMALPmFKRGARGVWVWRCHID 155
                                    5999998877777766***************8 PP

>> Aida_N  Aida N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.013        45      13      49 ..      68     105 ..      63     116 .. 0.76
   2 ?    4.9   0.0    0.0096        34      10      34 ..     233     257 ..     229     271 .. 0.87
   3 ?   -3.2   0.0       3.2   1.2e+04      70      95 ..     352     377 ..     349     378 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.013
                         Aida_N  13 dfdsWGqlveAvdeYerlakqlkkeaes.qsseltedq 49 
                                    ++d+  +++eA de+ +++k++++ ++   s  lt++ 
  gi|119720495|ref|YP_920990.1|  68 GIDARWEVLEAEDEFFQVTKKIHNGLQGnPSLVLTDED 105
                                    56666689***************999984455555555 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0096
                         Aida_N  10 kavdfdsWGqlveAvdeYerlakql 34 
                                    k   fd W ++  Avd +++++k++
  gi|119720495|ref|YP_920990.1| 233 KVARFDPWKDVFSAVDVFREVKKEV 257
                                    66789****************9988 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 3.2
                         Aida_N  70 vdgeesitledlkkleevlksilsde 95 
                                    vdg  ++t  ++++l e +k++l+d+
  gi|119720495|ref|YP_920990.1| 352 VDGVTGFTAWSVQELAERVKALLADN 377
                                    56666777888888888888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 2748.80
//
Query:       gi|119720496|ref|YP_920991.1|  [L=255]
Description: daunorubicin resistance ABC transporter, inner membrane subunit B [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.6e-39  133.0  20.6    1.3e-38  132.5  20.6    1.2  1  ABC2_membrane    ABC-2 type transporter
    7.6e-19   68.0  19.9    1.1e-18   67.5  19.9    1.2  1  ABC2_membrane_3  ABC-2 family transporter protein
      9e-08   31.7  16.8    1.6e-07   30.9  16.8    1.5  1  ABC2_membrane_2  ABC-2 family transporter protein
  ------ inclusion threshold ------
          6    7.2  14.9        3.5    8.0   2.2    2.5  2  DUF3021          Protein of unknown function (DUF3021)


Domain annotation for each model (and alignments):
>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.5  20.6   2.9e-42   1.3e-38       4     208 ..       5     217 ..       2     219 .. 0.90

  Alignments for each domain:
  == domain 1  score: 132.5 bits;  conditional E-value: 2.9e-42
                  ABC2_membrane   4 kallkreflqrwrdpslgllwrliqplllalvfgtvfgnlgnsedglnr.................pgllffsvlflafs 66 
                                     +++ r++++++  +s + +++++qp+ ++++fg  ++++ +      +                  g++++++++ +  
  gi|119720496|ref|YP_920991.1|   5 ATMVYRQVKRFVNARSRL-VMSVVQPVTWLVFFGMGWSRAFS------FpgaramfggldylsylaSGMVAMTIIMGS-- 75 
                                    6899***********888.*******************8441......122223346667788899999999999999.. PP

                  ABC2_membrane  67 altsvapvferergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflv.gldlsrf.flflllllltalaa 144
                                    ++++++++++++ g+l++ lv+p  s+++++++++l++ +v ++q+li++++++++  gl++  + + ++ + ll++l +
  gi|119720496|ref|YP_920991.1|  76 FMSGISVIWDKQFGFLKETLVAPA-SRAEIIIGRALGDSLVVVFQSLIIMALMFLVApGLNPY-GvLPAVGYGLLLSLGF 153
                                    99**********************.**************************777764499995.46************** PP

                  ABC2_membrane 145 sslgllisalapsfedasqlaslvllpllllsGffipidsmpkwlqwiaylnPltyavealrsn 208
                                     s+g+++s+  +s+e ++++++lv++pll+lsG+f+pi++mp w++ +ayl P tyav+++r+ 
  gi|119720496|ref|YP_920991.1| 154 ASIGIALSTKITSMEGFQMIVNLVTMPLLFLSGIFYPINTMPDWMKVLAYLDPATYAVDGMRYC 217
                                    **************************************************************86 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.5  19.9   2.5e-22   1.1e-18     158     344 ..      57     245 ..      51     246 .. 0.92

  Alignments for each domain:
  == domain 1  score: 67.5 bits;  conditional E-value: 2.5e-22
                ABC2_membrane_3 158 nvasflvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilllafgl..gipf 235
                                    ++ s+l++ ++++ i++++++   s++ +k+ + ++  lv++ s++++++++ lgd lv ++q+l+i++l+f +  g++ 
  gi|119720496|ref|YP_920991.1|  57 DYLSYLASGMVAMTIIMGSFMSGISVIWDKQFGFLKETLVAPASRAEIIIGRALGDSLVVVFQSLIIMALMFLVapGLNP 136
                                    5788999955555555666667779**********999*******************************97776678999 PP

                ABC2_membrane_3 236 gnlglllllfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlpsalkwifsiiPffapglgllr 315
                                    ++++ ++ + ll +l ++++g +ls+ ++++e  q ++ +v+++l++++g+++p++++p+++k+++++ P ++  +g+  
  gi|119720496|ref|YP_920991.1| 137 YGVLPAVGYGLLLSLGFASIGIALSTKITSMEGFQMIVNLVTMPLLFLSGIFYPINTMPDWMKVLAYLDPATYAVDGMRY 216
                                    9*****************************************************************************99 PP

                ABC2_membrane_3 316 litgdplweillsliilalfavvylllal 344
                                     +tg++ ++   ++++l++++ v+l++a+
  gi|119720496|ref|YP_920991.1| 217 CLTGVSSIDPRVDVGLLVALTSVFLVVAA 245
                                    99***8889889*******9999999987 PP

>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9  16.8   3.7e-11   1.6e-07      89     285 ..      74     250 ..       7     253 .. 0.75

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 3.7e-11
                ABC2_membrane_2  89 aalfgadaiagEkergTlkllLskPvsRdeillgKfigglaigla.iavallatvllalaiilalgivlaledllllvva 167
                                    +  ++  ++  +k  g lk  L  P+sR+ei++g ++g +++ ++  ++++   +l+  a+ l    vl++  +      
  gi|119720496|ref|YP_920991.1|  74 GSFMSGISVIWDKQFGFLKETLVAPASRAEIIIGRALGDSLVVVFqSLIIMALMFLV--APGLNPYGVLPAVGYG----- 146
                                    444555567778899999************************554444444333333..3333333333333333..... PP

                ABC2_membrane_2 168 svlllllvvflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavpqeindflsllsptsayntlln 247
                                       lll + f+++g++lS+ +  s e  ++ + l+ + +++ +++ y+++ ++  ++v       l +l+p+ +   + +
  gi|119720496|ref|YP_920991.1| 147 ---LLLSLGFASIGIALSTKIT-SMEGFQMIVNLVTMPLLFLSGIFYPINTMPDWMKV-------LAYLDPATYAVDGMR 215
                                    ...22222369**********9.9******************************8888.......******999766666 PP

                ABC2_membrane_2 248 eilagsdlnalgstatnllilllllavllvlgyvlFkr 285
                                      l+g +   ++     +++l++l+ v+lv+++ +F++
  gi|119720496|ref|YP_920991.1| 216 YCLTGVS---SIDPRVDVGLLVALTSVFLVVAAKSFEK 250
                                    6666663...4556889*******************98 PP

>> DUF3021  Protein of unknown function (DUF3021)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   2.2   0.00078       3.5      25      71 ..      52      96 ..      22     100 .. 0.73
   2 ?    4.5   5.1     0.009        40      17      92 ..     123     200 ..     102     243 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00078
                        DUF3021 25 fsgettllestavlkqvllsaliGvlfalaslifeserlsllkqtli 71
                                   ++g   +  s+ +  +v +++++G +++++s+i++++ + +lk+tl+
  gi|119720496|ref|YP_920991.1| 52 MFGGLDY-LSYLASGMVAMTIIMGSFMSGISVIWDKQ-FGFLKETLV 96
                                   4444444.677777889999***************98.888888875 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.009
                        DUF3021  17 iislvislfsgettllestavlkqvlls.aliGvlfalaslifeserlsllkqtl.ihflvvlllvlllalllgWfpl 92 
                                    i+ l++ +  g + +  + av   +lls ++ ++++al++ i ++e +++ ++++ + +l+++ ++ +++++  W+++
  gi|119720496|ref|YP_920991.1| 123 IMALMFLVAPGLNPYGVLPAVGYGLLLSlGFASIGIALSTKITSMEGFQMIVNLVtMPLLFLSGIFYPINTMPDWMKV 200
                                    4466777777777777888888888888788999999****************998899999**************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1765.71
//
Query:       gi|119720497|ref|YP_920992.1|  [L=323]
Description: daunorubicin resistance ABC transporter ATPase subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-35  121.2   0.0    6.3e-35  120.7   0.0    1.3  1  ABC_tran  ABC transporter
    1.2e-10   41.7   0.0    7.7e-06   25.9   0.0    2.2  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
      3e-09   37.5   0.0    7.8e-09   36.1   0.0    1.8  1  DUF4162   Domain of unknown function (DUF4162)
    0.00081   19.2   0.0        1.6    8.4   0.0    2.2  2  AAA_15    AAA ATPase domain
     0.0026   17.4   0.1      0.005   16.6   0.1    1.4  1  AAA_29    P-loop containing region of AAA domain
      0.004   17.6   0.3       0.19   12.1   0.3    2.9  1  AAA       ATPase family associated with various cellular acti
     0.0095   15.6   0.1       0.03   14.0   0.1    1.8  2  SRP54     SRP54-type protein, GTPase domain
  ------ inclusion threshold ------
      0.012   16.1   1.0      0.023   15.2   1.0    1.7  1  AAA_23    AAA domain
      0.034   13.6   0.0      0.084   12.3   0.0    1.6  1  SMC_N     RecF/RecN/SMC N terminal domain
      0.042   13.8   0.0      0.065   13.2   0.0    1.2  1  Rad17     Rad17 P-loop domain
      0.069   13.3   0.0       0.14   12.3   0.0    1.5  1  AAA_33    AAA domain
       0.11   12.2   0.2       0.26   11.0   0.0    1.7  3  AAA_30    AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.7   0.0   4.2e-38   6.3e-35       2     136 ..      22     164 ..      21     165 .. 0.98

  Alignments for each domain:
  == domain 1  score: 120.7 bits;  conditional E-value: 4.2e-38
                                    EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                       ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.. 79 
                                    + vs++++ege+++++G+nGaGK+t + +l+ ll+pt+G+ l+ g d+ + + +++rk+ig+++q+p+l+++lt+ +n  
  gi|119720497|ref|YP_920992.1|  22 DGVSFTVREGEIYGLLGPNGAGKTTTIHILTTLLRPTSGRALVAGYDVVK-QPSEVRKRIGIVFQDPSLDNQLTAWDNmy 100
                                    78**********************************************99.67789************************ PP

                                    ...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                               e +++i+++l+ ++lk+++++ v    + +SgG+++r+++arall +p++l+lDEpt
  gi|119720497|ref|YP_920992.1| 101 ihgmlyglggqELKRKINELLDFVELKNFANKQV----KYFSGGMRRRLEIARALLHEPEILFLDEPT 164
                                    **********************************....9****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   2.4e-05     0.036       2      24 ..      34      56 ..      33     103 .. 0.74
   2 !   25.9   0.0   5.2e-09   7.7e-06     237     297 ..     137     195 ..     105     198 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.4e-05
                         AAA_21  2 nvliGpNgsGKSnLLdaldllar 24
                                    +l GpNg+GK++ + +l  l r
  gi|119720497|ref|YP_920992.1| 34 YGLLGPNGAGKTTTIHILTTLLR 56
                                   689***************98876 PP

  == domain 2  score: 25.9 bits;  conditional E-value: 5.2e-09
                         AAA_21 237 lSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTH 297
                                    +S G++r l ++ all  +    +l++DEp  gL+P+   ++++ +  +++++g  ++ltTH
  gi|119720497|ref|YP_920992.1| 137 FSGGMRRRLEIARALLHEP---EILFLDEPTIGLDPQTRVKIWDYImAIKKEKGMTIVLTTH 195
                                    4999999999999999988...9********************66657777789******** PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.0   5.2e-12   7.8e-09       1      80 [.     219     303 ..     219     304 .. 0.88

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 5.2e-12
                                    E-HHHHHTTS-SSEEEEE..-------..---EEEE-TT.S-EEEEE--.-----------.----EEEEEEEE---HHH CS
                        DUF4162   1 GtleeiKrsygknrieve..adaeelleepgveeveeeg.gelelkled.eeaanellkal.tsgveirsFeeeePsLnd 75 
                                    Gt +e+K+  g++ i+++  + a + le + +++ +    g +el +++ ++a++++++ + ++g++i++++ ++P+Ln+
  gi|119720497|ref|YP_920992.1| 219 GTSDELKALVGNEVIYLKldGSAPACLEADFISSCRIVSgGLVELSVKNaSQAMPRVFELAeEKGLKIVEVTYRRPTLNE 298
                                    899***************644477777777788887776588*******9***********77***************** PP

                                    HHHHH CS
                        DUF4162  76 IFiek 80 
                                    +Fi++
  gi|119720497|ref|YP_920992.1| 299 VFIHL 303
                                    ***97 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0    0.0011       1.6      28      50 ..      36      58 ..      30     132 .. 0.84
   2 !    8.4   0.0     0.001       1.6     323     364 ..     154     195 ..     133     196 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0011
                         AAA_15 28 liGkNnsGKSsilealdlFlnnk 50
                                   l G+N++GK++ +++l  +l  +
  gi|119720497|ref|YP_920992.1| 36 LLGPNGAGKTTTIHILTTLLRPT 58
                                   67**************9999865 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.001
                         AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                    ++ il+++EP + L pq    +++++  + +++ + +++tTH
  gi|119720497|ref|YP_920992.1| 154 EPEILFLDEPTIGLDPQTRVKIWDYIMAIKKEKGMTIVLTTH 195
                                    5689************************************** PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   3.4e-06     0.005      13      50 ..      22      59 ..      19      63 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3.4e-06
                         AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                   dg ++++++ +++ l Gp+G+GK+T +  +++lL p++
  gi|119720497|ref|YP_920992.1| 22 DGVSFTVREGEIYGLLGPNGAGKTTTIHILTTLLRPTS 59
                                   66778887666999********************9987 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.3   0.00013      0.19       3      66 ..      36     162 ..      34     213 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                                    EESSTTSSHHHHHHHHHHHHTHE......................................................... CS
                            AAA   3 lyGppGtGKTllakavakelgve......................................................... 25 
                                    l Gp G GKT++++ + + l  +                                                         
  gi|119720497|ref|YP_920992.1|  36 LLGPNGAGKTTTIHILTTLLRPTsgralvagydvvkqpsevrkrigivfqdpsldnqltawdnmyihgmlyglggqelkr 115
                                    78**************9998422222333344444444555555555555555555555555555555555555555555 PP

                                    .......EEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS.TSEEEEEET CS
                            AAA  26 .......fleisgsellskyvgesekkirelfkeakeka.kpsilfiDE 66 
                                           f+e  ++++ +k v+  +  +r  ++ a++   +p ilf+DE
  gi|119720497|ref|YP_920992.1| 116 kinelldFVE--LKNFANKQVKYFSGGMRRRLEIARALLhEPEILFLDE 162
                                    5555433322..2334444666667777777777766666777777777 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.2   1.8e+03     131     152 ..      10      31 ..       6      35 .. 0.81
   2 !   14.0   0.1     2e-05      0.03       5      40 ..      35      70 ..      31      75 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.2
                                    HHHHHHHHHSSCSEEEEESTTS CS
                          SRP54 131 kqakaFkeavgitgviltklDg 152
                                    + +k+Fk+++ ++gv +t  +g
  gi|119720497|ref|YP_920992.1|  10 NLVKRFKDVTAVDGVSFTVREG 31 
                                    57899*********99996655 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 2e-05
                                   EEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTS CS
                          SRP54  5 llvGlqGaGKTttlaKLaallkkegkkvllvaaDtf 40
                                    l+G++GaGKTtt+  L  ll+    ++l++  D+ 
  gi|119720497|ref|YP_920992.1| 35 GLLGPNGAGKTTTIHILTTLLRPTSGRALVAGYDVV 70
                                   589******************999999999988875 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   1.0   1.6e-05     0.023      17      43 ..      26      55 ..       6     207 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.6e-05
                         AAA_23 17 F...skgltlItGpNGaGKTTildAiklaL 43
                                   F   +  ++ + GpNGaGKTT +  ++  L
  gi|119720497|ref|YP_920992.1| 26 FtvrEGEIYGLLGPNGAGKTTTIHILTTLL 55
                                   44455678899***********99998776 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   5.6e-05     0.084      26     208 ..      33     203 ..       8     215 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.6e-05
                                    EEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--..BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  26 ftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk..skekasvkkaeveitfdnedkklkiekeevsisrrv 103
                                    +  ++GpNG+GK+  +  +         + lr ++ ++l+      +++s  + ++ i+f++++ +     ++++   ++
  gi|119720497|ref|YP_920992.1|  33 IYGLLGPNGAGKTTTIHIL----T----TLLRPTSGRALVAGydVVKQPSEVRKRIGIVFQDPSLD-----NQLTAWDNM 99 
                                    56789********987655....4....34777777777776555566777888999***988877.....556666666 PP

                                    ETTSEEEEEETTEEE-H..HHHHHHHHCTT-...STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHH CS
                                    xxxxxxxxxxxxxxxxx..xxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 104 krkgeseykingkevtk..kevsellesagi...skelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkk 178
                                    + +g   y + g+e ++  +e+ +++e +++   + +++SgG +  + +a        +   + +lDe    LD + + k
  gi|119720497|ref|YP_920992.1| 100 YIHGM-LYGLGGQELKRkiNELLDFVELKNFankQVKYFSGGMRRRLEIAR----ALLHEPEILFLDEPTIGLDPQTRVK 174
                                    66665.666666665543455555555555511145689***988655543....33344456779************** PP

                                    HHHHHHHHCTTSEEEEE-SSHHHCCC-SCE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 179 vaellkeksknaQfivislreemlekadkl 208
                                    + +++ + +k+  +  i l+++ + +a++l
  gi|119720497|ref|YP_920992.1| 175 IWDYIMAIKKEKGM-TIVLTTHYMDEAEQL 203
                                    *****987766444.344555555555554 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.3e-05     0.065      35     166 ..      21     151 ..      11     165 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.3e-05
                          Rad17  35 lkadvLesrkkriLLisGPsGCgkstvvkvLskelgikl.rewlnpvslkepdnqksdfkgltekesrflsqiesfkele 113
                                    ++  +   r+ +i  + GP G gk+t++++L+  l +   r  + +  + + + ++    g++ ++ ++  q+ ++ ++ 
  gi|119720497|ref|YP_920992.1|  21 VDGVSFTVREGEIYGLLGPNGAGKTTTIHILTTLLRPTSgRALVAGYDVVKQPSEVRKRIGIVFQDPSLDNQLTAWDNMY 100
                                    55556666667788899***************998765415666777766666666666777777777888888888887 PP

                          Rad17 114 LkdakylklqklGddlrtdkk.lilvedlPnkfyrdsdalrevirkylrsseal 166
                                    +++  y  l   G++l+ + + l+   +l n  +++++ +   +r+ l + +al
  gi|119720497|ref|YP_920992.1| 101 IHGMLY-GLG--GQELKRKINeLLDFVELKNFANKQVKYFSGGMRRRLEIARAL 151
                                    777777.444..666665543133344566666666677777777777777765 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   9.3e-05      0.14       5      78 ..      37     124 ..      35     165 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9.3e-05
                         AAA_33   5 vGlpGsGKstlaerl...lkklg.......avllssdtlrrrlfg..tdqqsktdytrvldr..lyqilnelarkalsag 70 
                                     G++G+GK+t ++ l   l+++        + ++ ++++ r+  g   +++s+ ++ +++d+  ++++l +l  + l+++
  gi|119720497|ref|YP_920992.1|  37 LGPNGAGKTTTIHILttlLRPTSgralvagYDVVKQPSEVRKRIGivFQDPSLDNQLTAWDNmyIHGMLYGLGGQELKRK 116
                                    6*********99988444444447888888********999888878888888888888888778888988888888888 PP

                         AAA_33  71 rnvildat 78 
                                    +n +ld  
  gi|119720497|ref|YP_920992.1| 117 INELLDFV 124
                                    88888766 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00017      0.26      19      48 ..      32      62 ..      23     115 .. 0.84
   2 ?   -3.6   0.0         5   7.4e+03      44      67 ..     185     208 ..     179     228 .. 0.67
   3 ?   -3.1   0.0       3.7   5.5e+03     102     120 ..     269     287 ..     262     289 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00017
                         AAA_30 19 rvavltGpAGtGKttalkalreaweaa.ggr 48
                                    +  l Gp G+GKtt++  l+ +++   g+ 
  gi|119720497|ref|YP_920992.1| 32 EIYGLLGPNGAGKTTTIHILTTLLRPTsGRA 62
                                   477899**************99998775544 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 5
                         AAA_30  44 aaggrviglAptgkaAkvLaeelg 67 
                                    ++g+++++ ++    A++L + + 
  gi|119720497|ref|YP_920992.1| 185 EKGMTIVLTTHYMDEAEQLCDRIA 208
                                    447777777777777777766555 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 3.7
                         AAA_30 102 tkqlaallkaaekagakvi 120
                                    ++ + ++++ ae++g k++
  gi|119720497|ref|YP_920992.1| 269 SQAMPRVFELAEEKGLKIV 287
                                    5678899999999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       632  (0.0352502); expected 358.6 (0.02)
Passed bias filter:                      618  (0.0344693); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2147.23
//
Query:       gi|119720498|ref|YP_920993.1|  [L=157]
Description: PadR-like family transcriptional regulator [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-16   59.8   0.0      1e-15   57.4   0.0    2.0  2  PadR      Transcriptional regulator PadR-like family
    6.3e-05   23.6   0.0     0.0001   22.9   0.0    1.4  1  RTP       Replication terminator protein
     0.0023   18.1   0.0     0.0055   16.9   0.0    1.8  2  HTH_34    Winged helix DNA-binding domain
  ------ inclusion threshold ------
      0.038   13.8   0.3        0.3   11.0   0.1    2.5  2  HTH_5     Bacterial regulatory protein, arsR family
      0.076   13.0   0.0       0.24   11.4   0.0    1.8  2  HTH_45    Winged helix-turn-helix


Domain annotation for each model (and alignments):
>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.4   0.0   2.9e-19     1e-15       1      74 [.      16      86 ..      16      87 .. 0.95
   2 ?   -0.2   0.0      0.29     1e+03       8      25 ..     106     123 ..     101     132 .. 0.80

  Alignments for each domain:
  == domain 1  score: 57.4 bits;  conditional E-value: 2.9e-19
                                   HHHHHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHHH CS
                           PadR  1 iLalleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrela 74
                                   +La le++p++ y ++kele+++ g +++s+G lYp+L++L +e+lv++e + s  + ++++Y++T++Gr+ l+
  gi|119720498|ref|YP_920993.1| 16 VLAALEKGPLHAYGLMKELEKSL-G-FRPSPGALYPILRKLIREDLVVAELRGS-GDVKTRVYNITEKGRSFLE 86
                                   89********************7.7.9***********************9997.88999**********9886 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.29
                                    S-EEHHHHHHHHHCCSTT CS
                           PadR   8 qpsyGyeiikeleelseg 25 
                                    ++  Gy + ++++e ++ 
  gi|119720498|ref|YP_920993.1| 106 EEVKGYRLFHAIDEILDS 123
                                    677899999999998776 PP

>> RTP  Replication terminator protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   2.9e-08    0.0001       4      94 ..       6      90 ..       4     108 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 2.9e-08
                                   --HHHHHHHHHHHHHHTT-EBCTCHHHHHHHHHTTTT----HHHHHHHHHHHHHTTSEEEEEEEBTSSSSSEEEEEEESS.. CS
                            RTP  4 lkqrAFlklylitlvekkklyglklldelkkeFkelgykPnhseiyralhelvedgilkrrkelkekaklqevviYsltdeG 85
                                   lk + +lkl ++  +ek +l+++ l+ el    k+lg++P++  +y  l+ l+ + ++    el+   +++   +Y++t++G
  gi|119720498|ref|YP_920993.1|  6 LKLKGYLKLLVLAALEKGPLHAYGLMKELE---KSLGFRPSPGALYPILRKLIREDLVVA--ELRGSGDVK-TRVYNITEKG 81
                                   78999**************99999999997...689*****************8888864..555445554.3579999999 PP

                                   HHHHHHHHH CS
                            RTP 86 kekaklykk 94
                                   +  ++  + 
  gi|119720498|ref|YP_920993.1| 82 RSFLEHHRG 90
                                   887776665 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.98   3.5e+03      36      46 ..       4      14 ..       2      33 .. 0.80
   2 !   16.9   0.0   1.5e-06    0.0055      27      78 ..      43      94 ..      12      96 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.98
                         HTH_34 36 kkLekagYiev 46
                                   kkL+ +gY++ 
  gi|119720498|ref|YP_920993.1|  4 KKLKLKGYLKL 14
                                   68888899874 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 1.5e-06
                         HTH_34 27 tdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafkkyvkaLks 78
                                   + g+L+  l+kL   + ++ ++  +g  +  +++iT++Gr+  + +  +L++
  gi|119720498|ref|YP_920993.1| 43 SPGALYPILRKLIREDLVVAELRGSGDVKTRVYNITEKGRSFLEHHRGELEE 94
                                   6799******************************************999987 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   8.3e-05       0.3       4      28 ..      13      37 ..      12      62 .. 0.87
   2 ?   -3.6   0.0         3   1.1e+04      24      35 ..      77      88 ..      76      88 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 8.3e-05
                                   HHHHHHHHTTSSEEHHHHHHHHTS- CS
                          HTH_5  4 RlkILklLaegelcvcelaeelgls 28
                                   +l +L +L++g+l +  l++el++s
  gi|119720498|ref|YP_920993.1| 13 KLLVLAALEKGPLHAYGLMKELEKS 37
                                   6899*******************98 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 3
                                   HHTS-HHHHHHH CS
                          HTH_5 24 elglsqstvShH 35
                                   ++++ +s + hH
  gi|119720498|ref|YP_920993.1| 77 ITEKGRSFLEHH 88
                                   688889999999 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   6.6e-05      0.24      40      69 ..      51      88 ..      46      95 .. 0.82
   2 ?   -3.0   0.0       2.1   7.5e+03       8      16 ..     117     125 ..     111     130 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.6e-05
                         HTH_45 40 LdmLvekgli........kkskekYvlTekGlellekl 69
                                   L +L+ ++l+        + ++  Y +TekG+ +le+ 
  gi|119720498|ref|YP_920993.1| 51 LRKLIREDLVvaelrgsgDVKTRVYNITEKGRSFLEHH 88
                                   677888888888888876668999***********975 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.1
                         HTH_45   8 iadILeais 16 
                                    i +IL++i+
  gi|119720498|ref|YP_920993.1| 117 IDEILDSIN 125
                                    557777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1184.51
//
Query:       gi|119720499|ref|YP_920994.1|  [L=69]
Description: hypothetical protein Tpen_1596 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.5e-06   27.2   0.0    3.5e-06   27.2   0.0    1.1  1  NTP_transf_2  Nucleotidyltransferase domain
    0.00018   21.5   0.0    0.00018   21.5   0.0    1.1  1  Polbeta       Polymerase beta, Nucleotidyltransferase
  ------ inclusion threshold ------
      0.013   15.3   0.0      0.014   15.2   0.0    1.1  1  DUF294        Putative nucleotidyltransferase DUF294


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.0   5.8e-10   3.5e-06      14      47 ..      13      46 ..       1      67 [. 0.79

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 5.8e-10
                                   TSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHH CS
                   NTP_transf_2 14 vakvvlfGSyarGtalkgSDiDllvvlpeevsre 47
                                      v+l GS ar +++  SD D++vv++++  r+
  gi|119720499|ref|YP_920994.1| 13 ALAVILIGSLARSDYTAFSDADVVVVVERDCRRP 46
                                   6789************************997664 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   3.1e-08   0.00018      12      45 ..      12      47 ..       2      65 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 3.1e-08
                                   HHHSTTEEEEEE-S------EEEEEEEESS-..--H CS
                        Polbeta 12 eielaylFGSrakgkareeSDiDlavllkek..ldl 45
                                   +  +++l GS a+ +++  SD D+ v+++++  + +
  gi|119720499|ref|YP_920994.1| 12 GALAVILIGSLARSDYTAFSDADVVVVVERDcrRPM 47
                                   56799***********************99865333 PP

>> DUF294  Putative nucleotidyltransferase DUF294
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   2.4e-06     0.014      47      85 ..      11      48 ..       2      63 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.4e-06
                         DUF294 47 pvpfallvmGSeGReEqtlktDqDnalvledeeeeaare 85
                                   + + a++ +GS +R + t  +D D   v+e+ ++++  +
  gi|119720499|ref|YP_920994.1| 11 RGALAVILIGSLARSDYTAFSDADVVVVVER-DCRRPMD 48
                                   567899***********************99.4444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       221  (0.0123264); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 538.56
//
Query:       gi|119720500|ref|YP_920995.1|  [L=76]
Description: hypothetical protein Tpen_1597 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-11   43.8   0.0    2.6e-11   43.7   0.0    1.0  1  HEPN      HEPN domain


Domain annotation for each model (and alignments):
>> HEPN  HEPN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.7   0.0   1.4e-15   2.6e-11      35      96 ..       7      73 ..       5      76 .] 0.92

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 1.4e-15
                                   HHHHHHHHHHHTT--.SSCCHHHHHHCCHHHT...-HHHHHHHHHHHCCCHHCCCTSS--S......- CS
                           HEPN 35 aekalKAlllkkggeppkthdlreLleelkkelkeseelreeleeLekayiesrYpdakee......y 96
                                   aek +KAl+  +g+e  ++ +++++le l  elk s+e+++  +eL+++yi++rYp+a++e      y
  gi|119720500|ref|YP_920995.1|  7 AEKVVKALYQCLGIE-IWGYSVSKMLEHLPSELKPSQEIIDASKELDRHYIPTRYPNAHVEgapmdyY 73
                                   8*************9.******************************************9986666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 556.50
//
Query:       gi|119720501|ref|YP_920996.1|  [L=195]
Description: hypothetical protein Tpen_1598 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-06   29.1   1.8    2.6e-05   24.6   0.9    2.1  2  Rubrerythrin  Rubrerythrin
  ------ inclusion threshold ------
       0.12   12.3   0.4       0.21   11.5   0.4    1.4  1  CK2S          Casein Kinase 2 substrate
        0.2   11.9   1.3       0.36   11.1   0.1    2.0  3  FliG_M        FliG middle domain


Domain annotation for each model (and alignments):
>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.9   4.4e-09   2.6e-05       9     126 ..      38     152 ..      36     176 .. 0.77
   2 !    6.7   0.3    0.0015       8.8      13      59 ..     137     185 ..     133     192 .. 0.67

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 4.4e-09
                                    HHHHHHHHHHHHHHCHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS-------TTGGHHHHHHHH CS
                   Rubrerythrin   9 gEssarrlYkelaekakegypqiaelFeelAeeEreHakilnklleklepelelevkekvreyaeakpkflttaknLeea 88 
                                     E+ a+++Y++la+k+k   p +++++e +  e + H +i+  +++k  + ++  ++    e + + +++l  a+ L++ 
  gi|119720501|ref|YP_920996.1|  38 LEEAACKFYTALARKVK--DPRLSKALEVVGLESKNHYEIIVAFFGKPAGAED-CRRFFGEEGFRMVEEMLQVAERLSSG 114
                                    69***************..****************************999999.66777777888889999999999966 PP

                                    HHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHHH CS
                   Rubrerythrin  89 iegayaeeeemyrfyeelaekegneeakklfkklaeaE 126
                                    +e   +e   + + ++ + + +g+e   kl   l+ +E
  gi|119720501|ref|YP_920996.1| 115 VEVSLEEVASLLERFNSVEKVAGEEIYSKLYSVLIAEE 152
                                    66666666666666666666666554444444444444 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0015
                                    HHHHHHHHHHCHH.TT-HHHHH.HHHHHHHHHHHHHHHHHHHHHHCSTT CS
                   Rubrerythrin  13 arrlYkelaekak.egypqiae.lFeelAeeEreHakilnklleklepe 59 
                                    ++++Y  l++ +  e+ + +a  l++ +A +E  H k+++++ + l+ e
  gi|119720501|ref|YP_920996.1| 137 GEEIYSKLYSVLIaEECKGLASlLMRSIASQEDFHYKVVEEVARTLRRE 185
                                    4556666666655555555555257888888888888888888877765 PP

>> CK2S  Casein Kinase 2 substrate
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.4   3.4e-05      0.21       6      98 ..      98     187 ..      95     194 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.4e-05
                           CK2S   6 frkveeqrekWkellseseslleslsnlaeqlqalqnvklygtplrdfpdlqerLrekqlealeevl.akLrekleelqk 84 
                                    fr vee  +  ++l+s +e  le +++l+e+ +++++v+ ++     +++l + L+++  ++l ++l +++ ++ +  +k
  gi|119720501|ref|YP_920996.1|  98 FRMVEEMLQVAERLSSGVEVSLEEVASLLERFNSVEKVAGEE----IYSKLYSVLIAEECKGLASLLmRSIASQEDFHYK 173
                                    999***********************************9654....4677777777777666666532556666555566 PP

                           CK2S  85 vrdsleklvrdalq 98 
                                    v++++++ +r  +q
  gi|119720501|ref|YP_920996.1| 174 VVEEVARTLRREAQ 187
                                    66666666666666 PP

>> FliG_M  FliG middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       1.5   8.9e+03      49      63 ..      26      40 ..      21      41 .. 0.73
   2 ?   -2.4   0.0         1     6e+03      58      65 ..     119     126 ..     102     133 .. 0.57
   3 ?   11.1   0.1     6e-05      0.36      43      73 ..     160     190 ..     154     192 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.5
                                   TCCTCSHHHHHHHHH CS
                         FliG_M 49 tlekvspevlkevee 63
                                    +e  +pe l ++ee
  gi|119720501|ref|YP_920996.1| 26 VIEGFKPECLAILEE 40
                                   567788888888886 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1
                                    HHHHHHHH CS
                         FliG_M  58 lkeveevL 65 
                                    l+ev+++L
  gi|119720501|ref|YP_920996.1| 119 LEEVASLL 126
                                    34444444 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 6e-05
                                    HHHHHHTCCTCSHHHHHHHHHHHHHHCHHHH CS
                         FliG_M  43 virriatlekvspevlkeveevLekklssvg 73 
                                    ++r ia+ e+ + +v++ev+++L+++ +++ 
  gi|119720501|ref|YP_920996.1| 160 LMRSIASQEDFHYKVVEEVARTLRREAQANR 190
                                    799***********************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       676  (0.0377043); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1302.56
//
Query:       gi|119720502|ref|YP_920997.1|  [L=421]
Description: major facilitator transporter [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.6e-43  147.5  52.1    2.3e-26   92.5  19.4    2.0  2  MFS_1       Major Facilitator Superfamily
    3.6e-23   81.8  34.4    1.1e-22   80.3  34.4    1.6  1  MFS_2       MFS/sugar transport protein
    4.7e-05   22.4  23.1    0.00017   20.6  22.1    2.2  1  MFS_1_like  MFS_1 like family
     0.0018   16.6   0.7     0.0018   16.6   0.7    2.1  2  BT1         BT1 family
  ------ inclusion threshold ------
        8.9    4.5  15.1        4.3    5.5   1.8    3.2  3  OATP        Organic Anion Transporter Polypeptide (OATP) fami


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.5  19.4   6.5e-30   2.3e-26       2     239 ..      13     262 ..      12     269 .. 0.89
   2 !   60.7  26.0   3.1e-20   1.1e-16      27     167 ..     261     408 ..     260     420 .. 0.86

  Alignments for each domain:
  == domain 1  score: 92.5 bits;  conditional E-value: 6.5e-30
                          MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsd....rfGrrr.vlllglllfalg. 75 
                                     +++f +++ +si+++ +p +  +++g++   +g+++t+  ++a+v+ + +G+lsd    r+Grr+ +++lg+   al+ 
  gi|119720502|ref|YP_920997.1|  13 GFGFFGISILWSIYNSYVP-IFLKEFGLASWLVGFIMTIDNIFAVVLLPYIGVLSDvtrtRIGRRKpYIILGAPPAALTf 91 
                                    6899***************.777************************************9*******************7 PP

                          MFS_1  76 lllllfasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravf 154
                                    +l++l+  + + ++l++ v++ + ++++ + ++a++ d++p e+r++a+g+++ + ++G++l+  +g+ l+   + +++f
  gi|119720502|ref|YP_920997.1|  92 ALIPLL-RGDFyAMLAVIVVMNFSMALFRSPVIAFMPDITPSEKRSQANGIINFMGGVGSLLAFFVGAKLY-EMNPSYPF 169
                                    777777.67777***********************************************************.668999** PP

                          MFS_1 155 yilaivsllafvlfllllpeepperkrkspkeee...kgtgpaplvpawkallkdpvl.....w.illialllfffgfsg 225
                                    +++a+ +lla +l++ll+ e++  ++r  +++++      +++++++ ++a l+  +l     + ++l++++l+f+g+++
  gi|119720502|ref|YP_920997.1| 170 VAAAVTMLLASLLVVLLVDEPEEFKARGGSVRLGellRESFRKSFSE-LSANLREAFLgedksLlFMLASIFLWFIGYNA 248
                                    ************97777777777777777777768888888888888.999999998855555269************** PP

                          MFS_1 226 lltllplylqevlg 239
                                    + t++++y++  lg
  gi|119720502|ref|YP_920997.1| 249 IETFFTSYAKWYLG 262
                                    *****999765555 PP

  == domain 2  score: 60.7 bits;  conditional E-value: 3.1e-20
                          MFS_1  27 lgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllf.a.....sslw.lllvlrvlqGlga 99 
                                    lgi +++ +l+l+++alg++v+slp+G+++ r+Grr+++ lgl+l+++  l l+f a     ++   ++l + ++ G +a
  gi|119720502|ref|YP_920997.1| 261 LGIGEAAGSLILGFVALGFLVFSLPAGFIGARLGRRKTMTLGLALLVVL-LGLAFyAstavkTGAViYVLGAIFFFGGFA 339
                                    6788888999***************************************.777754434467444446777777777777 PP

                          MFS_1 100 .galfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvl 167
                                     ++++ +++  ++d++++e+ g ++gl++ +++ +ai +p+l+gl+++ lg++a+f    +++l ++v 
  gi|119720502|ref|YP_920997.1| 340 wALVNVNSLPTVVDMTSRERLGAYTGLYYFASQSAAITAPPLAGLFIDVLGYQALFPYSIVFLLASAVT 408
                                    7*******************************************************9999999999882 PP

>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.3  34.4     3e-26   1.1e-22       3     388 ..      13     393 ..      11     409 .. 0.85

  Alignments for each domain:
  == domain 1  score: 80.3 bits;  conditional E-value: 3e-26
                          MFS_2   3 glgalaanilsvllatylliFytdvlglsaalvglvllvarlvDaitDpivGtlidktstrwGrrrPwlllsaiilavsi 82 
                                    g+g +++ il+++   y  iF+ +  gl  +lvg+++ + +++ ++  p++G+l+d t+tr+Grr+P++ l+a+++a+++
  gi|119720502|ref|YP_920997.1|  13 GFGFFGISILWSIYNSYVPIFLKEF-GLASWLVGFIMTIDNIFAVVLLPYIGVLSDVTRTRIGRRKPYIILGAPPAALTF 91 
                                    89********************887.***************************************************888 PP

                          MFS_2  83 illftppelsqsakfiwllvtyillrilytlfeipyvslvpvltkdydeRtsltsvrsflsvlggvlaailafllvlilg 162
                                    +l+ +       + f  +l++ +++   ++lf  p ++ +p +t+ ++ R++++++ +f+  +g++la ++   l  +  
  gi|119720502|ref|YP_920997.1|  92 ALIPLL-----RGDFYAMLAVIVVMNFSMALFRSPVIAFMPDITP-SEKRSQANGIINFMGGVGSLLAFFVGAKLYEMNP 165
                                    877443.....47999999999999******************66.568*******************999999966666 PP

                          MFS_2 163 glkserkgylifaliialLmllgviivvlgtkervem.......rkkekteqkeklslleqlkevf..rnraflillllf 233
                                    +        +++a++  lL+ l+v+++v    e ++        +  ++  +k+  +l+ +l+e f  +++ +l +l+++
  gi|119720502|ref|YP_920997.1| 166 S------YPFVAAAVTMLLASLLVVLLVDEPEEFKARggsvrlgELLRESFRKSFSELSANLREAFlgEDKSLLFMLASI 239
                                    6......4455555555555555555554444443333334345555677778888888899987655999********* PP

                          MFS_2 234 llaalalgvlnglllYyltyvlg.ngsaasvfllvvtisallgiplwqplakrlgkkntyllgalltivllvlvlll.qp 311
                                    +l + +++  ++ +  y++ +lg  ++a s++l++v ++ l++++ +  + +rlg+++t+ lg++l++vll l++ + ++
  gi|119720502|ref|YP_920997.1| 240 FLWFIGYNAIETFFTSYAKWYLGiGEAAGSLILGFVALGFLVFSLPAGFIGARLGRRKTMTLGLALLVVLLGLAFYAsTA 319
                                    *********************************************************99999999999999999999744 PP

                          MFS_2 312 snl.llflvllviagfgvgvaallpwsmladvvDygelktGkrregvffavlsfisklatgiglgvsgllLsafgyra 388
                                     ++ ++ +vl +i++fg  + al+    l++vvD       + r g +++++ f+s+ a+  +  ++gl ++  gy+a
  gi|119720502|ref|YP_920997.1| 320 VKTgAVIYVLGAIFFFGGFAWALVNVNSLPTVVDMTS----RERLGAYTGLYYFASQSAAITAPPLAGLFIDVLGYQA 393
                                    4441455666677777777788888899******877....999********************************65 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6  22.1   4.8e-08   0.00017      18     361 ..      26     374 ..       8     397 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 4.8e-08
                     MFS_1_like  18 llPYltiylkskglkaseigiitlilpltsilsppiwgvlaD....rfgkrkkvvilslllsavlflsllfippskerqe 93 
                                       Y+ i+lk+ gl    +g+i++i  +++++  p +gvl+D    r+g+rk+ +il++  +a++f+   +ip       
  gi|119720502|ref|YP_920997.1|  26 YNSYVPIFLKEFGLASWLVGFIMTIDNIFAVVLLPYIGVLSDvtrtRIGRRKPYIILGAPPAALTFA---LIP------- 95 
                                    44699*************************************66666789999**************...577....... PP

                     MFS_1_like  94 esklevsvaqdvdaektfwilfllvvlasfflaailvlldaatlkelgedrkdyGrqrlfGsvGyaifafitGilidhys 173
                                                d+   +++++++ + + +f +++++ +  +t    +++++  G +   G vG    af++G+ +  ++
  gi|119720502|ref|YP_920997.1|  96 --------LLRGDFYAMLAVIVVMNFSMALFRSPVIAFMPDITPS--EKRSQANGIINFMGGVGSL-LAFFVGAKLYEMN 164
                                    ........556889999999999999999*********9998866..5777788**********65.5777888776666 PP

                     MFS_1_like 174 vnllpysallyvlaallvisllvvlilnetekesklkvtksl.................qvllnilknpeviifllva.l 235
                                     ++ p   +++ +  +l++sllvvl ++e e  ++ +    l                 +   + l + + ++f+l+  +
  gi|119720502|ref|YP_920997.1| 165 PSY-P---FVAAAVTMLLASLLVVLLVDEPEEFKARGGSVRLgellresfrksfselsaNLREAFLGEDKSLLFMLASiF 240
                                    654.5...55556666667777777777766655555443347889*********9996333455666677777666505 PP

                     MFS_1_like 236 ilgmswgiienFlflYL.kelgasntllGslvalgvvaeiplfffaeklleklGhvklliial..layilrfllyaii.. 310
                                    +  + +++ie+F++ Y    lg  +   + ++ + +++ +++ + a  +  +lG +k ++++l  l++ l +  ya++  
  gi|119720502|ref|YP_920997.1| 241 LWFIGYNAIETFFTSYAkWYLGIGEAAGSLILGFVALGFLVFSLPAGFIGARLGRRKTMTLGLalLVVLLGLAFYASTav 320
                                    5567799****988888556788888888888889999999999999999999998877766500555555666777777 PP

                     MFS_1_like 311 ...enawlvlpievLhgisfgllwaaaveyvskiapksleatgqgllsglyfgl 361
                                        +  ++  i ++ g++ +l+ +     v ++++++  + + gl+  ++ ++
  gi|119720502|ref|YP_920997.1| 321 ktgAVIYVLGAIFFFGGFAWALVNVNSLPTVVDMTSRERLGAYTGLYYFASQSA 374
                                    766666777788899999999999999999999999999999999998877665 PP

>> BT1  BT1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.7     5e-07    0.0018      12     182 ..      29     196 ..      21     224 .. 0.71
   2 ?   -0.7   3.5     0.087   3.1e+02      55     168 ..     294     406 ..     249     419 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5e-07
                            BT1  12 vqfmltdrlgidparyqrlsglatl.gwvikpltallsDgfallGytkrwYlvvscllgaafallygllpakeasakvaa 90 
                                      + + +++g+    +  + ++ ++   v+ p +++lsD+      ++++Y+++++  +a+   l+ ll +  +      
  gi|119720502|ref|YP_920997.1|  29 YVPIFLKEFGLASWLVGFIMTIDNIfAVVLLPYIGVLSDVTRTRIGRRKPYIILGAPPAALTFALIPLLRGDFYA---ML 105
                                    5577888899999999999999886367889***********************999888887777777777666...88 PP

                            BT1  91 afillsslgkaivdvlsdalvselarq.spkagpsLvSwiwlvsavGgiiasvlsGpLldagktr..isvlvsaalqllt 167
                                    a+i+++++++a+    + a +  +  + +++++      i ++  vG+++a+ ++  L +   +   ++ +v+ +l++l 
  gi|119720502|ref|YP_920997.1| 106 AVIVVMNFSMALFRSPVIAFMPDITPSeKRSQA---NGIINFMGGVGSLLAFFVGAKLYEMNPSYpfVAAAVTMLLASLL 182
                                    999999****99887777777666655344444...44677777899999998877777655432113334444444444 PP

                            BT1 168 vvvflfnwygerknr 182
                                    vv+ l++  +e k r
  gi|119720502|ref|YP_920997.1| 183 VVL-LVDEPEEFKAR 196
                                    444.55545555554 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.087
                            BT1  55 GytkrwYlvvscllgaafallyg.llpakeasakvaaafillsslgkaivdvlsdalvselarqspkagpsLvSwiwlvs 133
                                    G +k   l ++ l+  +    y+ + +++ a++ v++a+ +++ +  a+v+v s   v+ +  +++   ++   + +++s
  gi|119720502|ref|YP_920997.1| 294 GRRKTMTLGLALLVVLLGLAFYAsTAVKTGAVIYVLGAIFFFGGFAWALVNVNSLPTVVDMTSRERL--GAYTGLYYFAS 371
                                    5555555555555444444444414567788999999999***********9999999988766554..45889999999 PP

                            BT1 134 avGgiiasvlsGpLldagktrisvlvsaalqlltv 168
                                       +i a  l G  +d    +  +  s ++ l + 
  gi|119720502|ref|YP_920997.1| 372 QSAAITAPPLAGLFIDVLGYQALFPYSIVFLLASA 406
                                    99999999999999998888877765555555444 PP

>> OATP  Organic Anion Transporter Polypeptide (OATP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.9     0.014        51      13      56 ..      19      62 ..       9      73 .. 0.69
   2 ?    5.5   0.3    0.0012       4.5     461     506 ..     102     147 ..      98     166 .. 0.54
   3 ?    5.5   1.8    0.0012       4.3     292     384 ..     228     319 ..     188     378 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.014
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           OATP 13 qamvsgyfkstittiEkrFklpsstsgliassneignillilfv 56
                                     +  ++ +s +  + k+F+l s  +g+i+++ +i +++l+  +
  gi|119720502|ref|YP_920997.1| 19 ISILWSIYNSYVPIFLKEFGLASWLVGFIMTIDNIFAVVLLPYI 62
                                   34455566777777889*************98888777666554 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0012
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           OATP 461 llflillflvsflgalgrvpallvilRcVkkedksfalGlqlllir 506
                                    ++ l+++++++f +al r p + ++  + ++e++s a G++ ++  
  gi|119720502|ref|YP_920997.1| 102 YAMLAVIVVMNFSMALFRSPVIAFMPDITPSEKRSQANGIINFMGG 147
                                    5555566666666666666666666566666666666665555532 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.0012
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           OATP 292 knpifllvilssvfeillvaGfitFlpkylEtqFslsaseAnlltGvvvipgaalGillgGllvkklklsakklaklvlv 371
                                    +++ +l+++ s  + +++++++ tF + y     ++ ++  +l++G+v++ + ++  l +G++  +l  +   ++ l+l+
  gi|119720502|ref|YP_920997.1| 228 EDKSLLFMLASIFLWFIGYNAIETFFTSYAKWYLGIGEAAGSLILGFVALGFLVFS-LPAGFIGARLGRRKTMTLGLALL 306
                                    56677777777777888999999***********************9999888876.56788888888888888888888 PP

                                    xxxxxxxxxxxxx RF
                           OATP 372 vsllsllllllll 384
                                    v ll l+++++ +
  gi|119720502|ref|YP_920997.1| 307 VVLLGLAFYASTA 319
                                    8888888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       892  (0.0497518); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.67u 0.27s 00:00:00.94 Elapsed: 00:00:00.46
# Mc/sec: 2760.25
//
Query:       gi|119720503|ref|YP_920998.1|  [L=299]
Description: phosphate uptake regulator, PhoU [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-08   34.8   0.7    1.7e-08   34.8   0.7    1.7  2  PhoU      PhoU domain


Domain annotation for each model (and alignments):
>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   0.7   9.5e-13   1.7e-08       1      87 [.     137     221 ..     137     223 .. 0.82
   2 ?   -2.6   0.1      0.46   8.2e+03      14      33 ..     248     266 ..     233     273 .. 0.44

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 9.5e-13
                                    HHHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SH..HHHHHHHHHHHHHHHHHH CS
                           PhoU   1 lrrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplae..dlrellsllriardlERi 78 
                                    ++rm ++++eml +a ++l  +    a +v ++dd++drl+++  r  +++  ++  l+   +lr  l+++  a++lE  
  gi|119720503|ref|YP_920998.1| 137 IYRMDSTTREMLLKATDLLLGG--GDASAVSALDDRVDRLYFLAVRI-MRRRIRDPTLSPdeRLRL-LDMRLTAKNLENL 212
                                    689***************9998..569999999***********998.555544444444323665.8************ PP

                                    HHHHHHHHH CS
                           PhoU  79 gDhavniae 87 
                                    gD  +++a+
  gi|119720503|ref|YP_920998.1| 213 GDSYESLAR 221
                                    ***999998 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.46
                                    HHHHHHHCT-HHHHHHHHHH CS
                           PhoU  14 dalealeekdtelarevier 33 
                                    + le  e++d el+ + +++
  gi|119720503|ref|YP_920998.1| 248 LFLEGSESRD-ELLLDYRRL 266
                                    2222222333.444444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2096.06
//
Query:       gi|119720504|ref|YP_920999.1|  [L=169]
Description: hypothetical protein Tpen_1601 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1134.19
//
Query:       gi|119720505|ref|YP_921000.1|  [L=226]
Description: CRISPR-associated Cas4 family protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-07   31.5   4.3    2.1e-05   24.6   3.6    2.8  2  PDDEXK_1  PD-(D/E)XK nuclease superfamily
  ------ inclusion threshold ------
      0.053   13.9   0.0      0.077   13.4   0.0    1.2  1  PDDEXK_3  PD-(D/E)XK nuclease superfamily


Domain annotation for each model (and alignments):
>> PDDEXK_1  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.8   0.0    0.0025        22      28      49 ..      69      91 ..      48     107 .. 0.70
   2 !   24.6   3.6   2.3e-09   2.1e-05     113     255 .]     102     220 ..      86     220 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0025
                       PDDEXK_1 28 eeeleap.dlGtlvHaaleefye 49
                                   +e +++p  lGtlvH+ le++ +
  gi|119720505|ref|YP_921000.1| 69 SEFFSPPlVLGTLVHRGLEALLS 91
                                   445667779**********9987 PP

  == domain 2  score: 24.6 bits;  conditional E-value: 2.3e-09
                       PDDEXK_1 113 gfrpvale....lefggekvrLkGriDrvd.dkegelriiDyKtgsappkskelaelkegl.QlllYllalaegeelkee 186
                                    +   v+ e    +++++ k++LkGr D+v  ++eg    ++ Kt +    + +   l++++ Q ++Y l+   +      
  gi|119720505|ref|YP_921000.1| 102 E---VEPErsleVSVDDAKYTLKGRADLVVtTPEGARIGVEIKTLR---GDAA-LPLEHHVdQARIYNLLFDLE------ 168
                                    2...22222212555578999*******99899998888****998...4444.35899999*********999...... PP

                       PDDEXK_1 187 gepagalylrleepkvkdeevvkkmalteeeleallqeleelaeeilagefparpskkCeyCpyksvCr 255
                                      ++ ++y++        e+++++ + ++  l++++++++e          ++r + +C+yCp++ +C+
  gi|119720505|ref|YP_921000.1| 169 --KSYLVYISP-------ERLAQYEVGDRMGLDEVASRIREP--------RAPRYTWECRYCPFSVICP 220
                                    ..667788887.......777777788888888888888885........46677777**********7 PP

>> PDDEXK_3  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   8.6e-06     0.077      36     104 ..      97     173 ..      77     184 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.6e-06
                       PDDEXK_3  36 kkrglkveeqvelpvvYkgkevgeeyrlDllv....eekvivElKa...veel.keeheaqllnYlkltklklGlli 104
                                    k+  ++ve +++l+v+ ++ + + + r+Dl+v      ++ vE+K+     +l  e+h  q   Y  l++l+  +l+
  gi|119720505|ref|YP_921000.1|  97 KQYRVEVEPERSLEVSVDDAKYTLKGRADLVVttpeGARIGVEIKTlrgDAALpLEHHVDQARIYNLLFDLEKSYLV 173
                                    4567889999**********************998778999*****4332344236677888899888888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1481.72
//
Query:       gi|119720506|ref|YP_921001.1|  [L=167]
Description: hypothetical protein Tpen_1603 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0015   18.3  29.0     0.0015   18.3  29.0    1.5  1  DUF4203   Domain of unknown function (DUF4203)
  ------ inclusion threshold ------
          2    9.0   4.6       0.89   10.1   0.8    2.4  2  DUF1240   Protein of unknown function (DUF1240)


Domain annotation for each model (and alignments):
>> DUF4203  Domain of unknown function (DUF4203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3  29.0   1.6e-07    0.0015       4     150 ..      10     140 ..       9     143 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.6e-07
                        DUF4203   4 ailillGlvlcffGyrlfkltlflsgfllgsllvlvlilkvvvlpsslvqgaslvaalvvGllgGllallfwelglfllg 83 
                                    +++i+lG+v +++Gyr+ +l + ++ +++++ +++++ +        l + ++ ++ +++G+++G+l  + + +  ++++
  gi|119720506|ref|YP_921001.1|  10 VLMIVLGFVTAVWGYRIARLWVSFISAIAVGYAFYAFSTPA------LKSALTPLVLFLIGFFVGAL--IGFAVFKLAVS 81 
                                    689***********************************866......45556666666666666666..44446677888 PP

                        DUF4203  84 algGlllallilsllegglitslpskaiflvivvlgllgavlslklqklllivatsvvGaaavvlgi 150
                                    +++G+++a+++ s     +++ ++       ++vl+l++a+l     + ll++a+++ G+ +v+lg+
  gi|119720506|ref|YP_921001.1|  82 LIAGFAIAYALESHG--YVVPGEGP------LLVLALVFALLIYAVIDKLLVLAFALAGSSMVFLGL 140
                                    899999999998866..66666666......5789*****9999999******************95 PP

>> DUF1240  Protein of unknown function (DUF1240)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.8    0.0001      0.89      41      75 ..      65      99 ..      25     104 .. 0.80
   2 ?   -0.4   0.1      0.19   1.7e+03      39      39 ..     128     128 ..     101     159 .. 0.50

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0001
                        DUF1240 41 klvkllaiiailsfvlslflslYvdyklksegYlv 75
                                    +v++l   a++ + +sl   + ++y l+s+gY+v
  gi|119720506|ref|YP_921001.1| 65 FFVGALIGFAVFKLAVSLIAGFAIAYALESHGYVV 99
                                   6788899999***********************97 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.19
                        DUF1240  39 n 39 
                                     
  gi|119720506|ref|YP_921001.1| 128 F 128
                                    1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1088  (0.0606838); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 1102.96
//
Query:       gi|119720507|ref|YP_921002.1|  [L=168]
Description: nuclease [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.5e-07   29.6   0.0    9.4e-07   29.0   0.0    1.2  1  ParBc     ParB-like nuclease domain


Domain annotation for each model (and alignments):
>> ParBc  ParB-like nuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.0   5.3e-11   9.4e-07       9      76 ..      52     113 ..      44     124 .. 0.86

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 5.3e-11
                          ParBc   9 rpnplqprkd.spekieelvasIkkkGll.qPiivrktrqgryeiiaGerRlrAakrlglkevpvivlei 76 
                                    r     p+ + +p++++ l ++I ++G l  P++v+ +      i++G++R+ ++  lg++ vp+++   
  gi|119720507|ref|YP_921002.1|  52 R-----PHEEvDPSRLRSLEEEILGAGYLeRPVLVECET---LIILDGHHRVAVLRKLGKTVVPALLVSY 113
                                    3.....444458*****************9********9...**********************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 1375.85
//
Query:       gi|119720508|ref|YP_921003.1|  [L=382]
Description: pyridoxal-5'-phosphate-dependent enzyme, beta subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-45  155.1   0.1    4.7e-45  154.2   0.1    1.4  1  PALP      Pyridoxal-phosphate dependent enzyme


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.2   0.1   2.6e-49   4.7e-45       5     291 ..      89     360 ..      85     363 .. 0.88

  Alignments for each domain:
  == domain 1  score: 154.2 bits;  conditional E-value: 2.6e-49
                                    SSS--EEEECCTCCCCCCEEEEEEGGGST.TSBTTHHHHHHHHHHHHTT..TTTSEEEEEBSSHHHHHHHHHHHHHT-EE CS
                           PALP   5 igpTPlvrlprlskelgvplflKlEslnp.tgSfKdRgaeyllarlkeg..tgaktvveassGNhgralAaaaallGlkv 81 
                                     +pTPlvrl++l  + +v+ ++KlE++np + S+KdR   y++++l e+   +   + ea+s N+g+alAa++a  G++v
  gi|119720508|ref|YP_921003.1|  89 NWPTPLVRLNSLG-DGKVRAWAKLEFFNPfSMSVKDRIGWYMVKKLLEKhpGASLALYEATSTNTGMALAAMGAIKGFRV 167
                                    689*********8.66777*********99***************6666577889999********************** PP

                                    EEEEETTS-HHHHHHHHHTT-EEEEECCH.HHHHHHHHHHHHHHSTTCEE--TTTSHHHHHH.HHTHHHHHHHHTT...T CS
                           PALP  82 tivvpadaspekvallrllGaevvevggd.ydeavaaaaelaaegegaylvsqfdnptvieg.ygtiglEileqlg...g 156
                                     +++p++  ++   ll  +Gaev++v+++ + e  + ++ la+e eg ++++qf+n +++      ++ E+  q+     
  gi|119720508|ref|YP_921003.1| 168 KLFLPETIQKASDTLLSVMGAEVRRVPKSlTVEFIDDVEHLAKE-EGGVHLNQFENDANFGVhLRYTAKELDLQVRsakL 246
                                    **************************88844444445888****.**************************855556447 PP

                                    TEEEEEEE-SSSHHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTCCS..S.SS..B.SSS.CCSTCSCGTTCCHHHHSEE CS
                           PALP 157 kpdavvvpvGgGgliaGiaaglkerrpdvrvigvepegsdalarslragrrvtvpvsdtiadglavgspselafelldrl 236
                                    ++  +v ++G+ g +++++ ++k+r +dv+++gv+p+                       ++g++   ++ + + ++  +
  gi|119720508|ref|YP_921003.1| 247 NLRGIVGGLGTSGHLSALSLYFKSRYSDVKIYGVQPAPGTV-------------------IPGIRRV-ETGMKWVHY-VS 305
                                    7889*********************************5444...................5555555.566777555.58 PP

                                    EEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHH.HHHHHHCCTTCEEEEEE CS
                           PALP 237 vdeivtvsdeealeamrllarregivvepssaaalaal.klreagelkegdrvvvi 291
                                    vd++v v+ eea++ ++++arregi+v+ ss+a+ aa   l + gel+egd v ++
  gi|119720508|ref|YP_921003.1| 306 VDKVVDVTPEEAVAHAVKVARREGILVGLSSGAVTAAFeALYSGGELPEGDYV-LV 360
                                    999***********************************************555.44 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2596.90
//
Query:       gi|119720509|ref|YP_921004.1|  [L=185]
Description: rubrerythrin [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.8e-29  101.5   0.7    5.8e-29  101.2   0.7    1.1  1  Rubrerythrin    Rubrerythrin
    0.00013   21.9   0.1    0.00031   20.7   0.1    1.7  1  Ferritin        Ferritin-like domain
  ------ inclusion threshold ------
      0.022   14.8   0.6       0.24   11.5   0.0    2.2  2  zf-Sec23_Sec24  Sec23/Sec24 zinc finger
       0.04   14.4   4.2          6    7.4   0.2    3.3  3  Zn-C2H2_12      Autophagy receptor zinc finger-C2H2 domain
      0.054   13.5   4.5        0.1   12.6   4.5    1.4  1  ADK_lid         Adenylate kinase, active site lid
      0.058   13.4   0.2      0.086   12.9   0.2    1.2  1  DZR             Double zinc ribbon
      0.063   13.3   4.6        2.6    8.2   0.2    2.4  2  Rubredoxin      Rubredoxin
      0.075   12.5   4.0        2.1    7.8   0.6    2.2  2  zf-ribbon_3     zinc-ribbon domain
        0.1   12.7   5.8        2.4    8.3   0.2    2.5  2  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
       0.11   12.5   3.5       0.14   12.1   0.0    2.2  2  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
       0.15   11.6   3.7        3.7    7.1   0.2    2.5  2  TF_Zn_Ribbon    TFIIB zinc-binding
       0.16   11.9   4.9        2.5    8.1   0.5    2.3  2  zf-FPG_IleRS    Zinc finger found in FPG and IleRS
        0.4   10.4   5.7        3.3    7.5   0.7    2.5  2  zf-RRN7         Zinc-finger of RNA-polymerase I-specific TFII
       0.43   10.5   1.9          1    9.3   0.0    2.1  2  DUF3797         Domain of unknown function (DUF3797)
       0.69    9.7   4.1        3.9    7.3   4.0    2.1  2  zinc_ribbon_2   zinc-ribbon domain
       0.71    9.7   4.1        1.5    8.6   4.1    1.6  1  DUF3039         Protein of unknown function (DUF3039)
       0.84    9.0   4.6        9.1    5.7   0.4    2.2  2  zf-RanBP        Zn-finger in Ran binding protein and others
        4.5    7.5   6.3         51    4.1   6.3    2.2  2  Zn-ribbon_8     Zinc ribbon domain
          9    6.2   5.6         31    4.5   0.2    2.5  2  Rad50_zn_hook   Rad50 zinc hook motif


Domain annotation for each model (and alignments):
>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.2   0.7   6.1e-32   5.8e-29       1     136 [.       9     137 ..       9     138 .. 0.97

  Alignments for each domain:
  == domain 1  score: 101.2 bits;  conditional E-value: 6.1e-32
                                    HHHHHHHHHHHHHHHHHHHHHHCHH.TT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS-------TTG CS
                   Rubrerythrin   1 eiLekAiagEssarrlYkelaekak.egypqiaelFeelAeeEreHakilnklleklepelelevkekvreyaeakpkfl 79 
                                    ++L  A+ gEs+a+++Y  +ae a+ eg+p++a+lF+++A +E  Hak+++  l+++++            ya +++   
  gi|119720509|ref|YP_921004.1|   9 DLLLSAFGGESMAHMRYLVFAEIADrEGFPNVARLFRAIAYAEFVHAKNHYGNLGDYKEAFP--------VYAGTPAGPG 80 
                                    6899****************************************************998888........8********* PP

                                    GHHHHHHHHHHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHHHHHHH CS
                   Rubrerythrin  80 ttaknLeeaiegayaeeeemyrfyeelaekegneeakklfkklaeaEkkHeerlrkl 136
                                    tt knLe ai g+++e  emy+ y e+a+++g++ a+++f+++ eaEk H++++r++
  gi|119720509|ref|YP_921004.1|  81 TTSKNLELAIMGEEYEVNEMYPAYIEVARFQGEKGAERSFRWALEAEKIHAKLYREA 137
                                    ******************************************************986 PP

>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.1   3.3e-07   0.00031       3     130 ..      10     132 ..       8     143 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 3.3e-07
                                    HHHHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS....SHHHHHHC-SSSS..CS. CS
                       Ferritin   3 aLneqladeltaayqylamawyvkgpgleglaeffdeqaeeerehadklaerilalGgtpvltraeleeieapke..fg. 79 
                                    +L +++  e  a++ yl +a  ++ +g++++a +f+  a  e  ha+  +  + +  +          +++a      g 
  gi|119720509|ref|YP_921004.1|  10 LLLSAFGGESMAHMRYLVFAEIADREGFPNVARLFRAIAYAEFVHAKNHYGNLGDYKE--------AFPVYAGTPagPGt 81 
                                    67788889999************************************98887666555........44433333335563 PP

                                    SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHH CS
                       Ferritin  80 sveevleaalehekkvteslrelielaeeegDpatadfledfleeqeehew 130
                                    ++++   a++  e++v+e++   ie+a+ +g  + +  + + le +  h++
  gi|119720509|ref|YP_921004.1|  82 TSKNLELAIMGEEYEVNEMYPAYIEVARFQGEKGAERSFRWALEAEKIHAK 132
                                    55555556678899*****************************99887776 PP

>> zf-Sec23_Sec24  Sec23/Sec24 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00026      0.24      20      32 ..     150     162 ..     146     167 .. 0.86
   2 ?    1.2   0.1       0.4   3.8e+02      25      31 ..     171     177 ..     171     180 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00026
                 zf-Sec23_Sec24  20 ggkrwiCnfCnhk 32 
                                    +gk w+C+ C+h 
  gi|119720509|ref|YP_921004.1| 150 DGKVWVCPVCGHT 162
                                    579********96 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.4
                 zf-Sec23_Sec24  25 iCnfCnh 31 
                                    +C++C+ 
  gi|119720509|ref|YP_921004.1| 171 KCPICGA 177
                                    6****86 PP

>> Zn-C2H2_12  Autophagy receptor zinc finger-C2H2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.56   5.3e+02       8      20 ..      99     111 ..      98     112 .. 0.91
   2 ?    7.4   0.2    0.0064         6       2      10 ..     155     163 ..     155     164 .. 0.90
   3 ?    5.0   0.6     0.037        35       2       7 ..     171     176 ..     170     177 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.56
                     Zn-C2H2_12   8 eqFpknvdqdeFe 20 
                                    e++p+ ++++ F+
  gi|119720509|ref|YP_921004.1|  99 EMYPAYIEVARFQ 111
                                    89********998 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0064
                     Zn-C2H2_12   2 eCPlCseqF 10 
                                    +CP+C+ ++
  gi|119720509|ref|YP_921004.1| 155 VCPVCGHTY 163
                                    7*****988 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.037
                     Zn-C2H2_12   2 eCPlCs 7  
                                    +CP+C+
  gi|119720509|ref|YP_921004.1| 171 KCPICG 176
                                    7****8 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   4.5   0.00011       0.1       2      30 ..     154     178 ..     154     179 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00011
                                    EE-TTT--EEETTTB--SSTTB-TTT--. CS
                        ADK_lid   2 rvCpkCGrsYhvvfnpPkveglCDkCGep 30 
                                    +vCp CG +Y      P  + +C  CG p
  gi|119720509|ref|YP_921004.1| 154 WVCPVCGHTYV----GPEPPEKCPICGAP 178
                                    9*********8....578889*****987 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   9.1e-05     0.086      14      39 ..     155     180 ..     146     185 .] 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.1e-05
                            DZR  14 fCseCgtklkavaaedrCpsCgekvd 39 
                                    +C+ Cg++   ++ +++Cp Cg++ +
  gi|119720509|ref|YP_921004.1| 155 VCPVCGHTYVGPEPPEKCPICGAPRE 180
                                    7*******998889********9865 PP

>> Rubredoxin  Rubredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.2    0.0027       2.6      35      42 ..     154     161 ..     137     164 .. 0.82
   2 ?    6.4   0.6    0.0097       9.1      36      47 .]     171     182 ..     169     182 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0027
                                    -BBTTTB- CS
                     Rubredoxin  35 WvCPdCgv 42 
                                    WvCP+Cg 
  gi|119720509|ref|YP_921004.1| 154 WVCPVCGH 161
                                    99999985 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0097
                                    BBTTTB-BGGGE CS
                     Rubredoxin  36 vCPdCgvekeqF 47 
                                    +CP Cg+++e++
  gi|119720509|ref|YP_921004.1| 171 KCPICGAPREKY 182
                                    6*******9986 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1     0.011        10       5      10 ..     156     161 ..     147     167 .. 0.79
   2 ?    7.8   0.6    0.0023       2.1       4      11 ..     171     178 ..     169     181 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.011
                    zf-ribbon_3   5 CPnCGa 10 
                                    CP CG+
  gi|119720509|ref|YP_921004.1| 156 CPVCGH 161
                                    888887 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0023
                    zf-ribbon_3   4 rCPnCGap 11 
                                    +CP CGap
  gi|119720509|ref|YP_921004.1| 171 KCPICGAP 178
                                    69999987 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   1.2     0.011        10       2       7 ..     156     161 ..     155     167 .. 0.86
   2 ?    8.3   0.2    0.0025       2.4       1      13 [.     171     183 ..     171     184 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.011
                 DNA_ligase_ZBD   2 CPvCGs 7  
                                    CPvCG+
  gi|119720509|ref|YP_921004.1| 156 CPVCGH 161
                                    *****7 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0025
                 DNA_ligase_ZBD   1 hCPvCGsavvRee 13 
                                    +CP+CG++ ++ +
  gi|119720509|ref|YP_921004.1| 171 KCPICGAPREKYQ 183
                                    6*****9977766 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00015      0.14      16      27 ..     150     161 ..     138     163 .. 0.96
   2 ?   -0.1   1.2      0.97   9.1e+02       4      10 ..     171     177 ..     167     178 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00015
                 PhnA_Zn_Ribbon  16 dgallvCpeCah 27 
                                    dg ++vCp C+h
  gi|119720509|ref|YP_921004.1| 150 DGKVWVCPVCGH 161
                                    899********9 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.97
                 PhnA_Zn_Ribbon   4 kCplCaS 10 
                                    kCp C++
  gi|119720509|ref|YP_921004.1| 171 KCPICGA 177
                                    8999975 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.2    0.0039       3.7       2      10 ..     155     163 ..     154     167 .. 0.87
   2 ?    4.9   0.5      0.02        19       2       9 ..     171     178 ..     170     181 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0039
                                    EETTTTCEE CS
                   TF_Zn_Ribbon   2 kCPnCgstn 10 
                                    +CP+Cg+t+
  gi|119720509|ref|YP_921004.1| 155 VCPVCGHTY 163
                                    7*****997 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.02
                                    EETTTTCE CS
                   TF_Zn_Ribbon   2 kCPnCgst 9  
                                    kCP+Cg +
  gi|119720509|ref|YP_921004.1| 171 KCPICGAP 178
                                    8*****75 PP

>> zf-FPG_IleRS  Zinc finger found in FPG and IleRS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.4     0.015        14       3      10 ..     155     162 ..     155     164 .. 0.86
   2 ?    8.1   0.5    0.0026       2.5       2      13 ..     170     181 ..     170     183 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.015
                                    B-TTT--B CS
                   zf-FPG_IleRS   3 pCpRCwry 10 
                                    +Cp+C+++
  gi|119720509|ref|YP_921004.1| 155 VCPVCGHT 162
                                    6*****98 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0026
                                    SB-TTT--BBEE CS
                   zf-FPG_IleRS   2 epCpRCwryier 13 
                                    e+Cp C+ + e+
  gi|119720509|ref|YP_921004.1| 170 EKCPICGAPREK 181
                                    8*******9987 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.7    0.0035       3.3       2      11 ..     151     160 ..     150     167 .. 0.81
   2 ?    5.3   0.4     0.017        16       5      13 ..     170     179 ..     166     183 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0035
                        zf-RRN7   2 ekgppCgvCg 11 
                                    +k+++C+vCg
  gi|119720509|ref|YP_921004.1| 151 GKVWVCPVCG 160
                                    6899*****9 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.017
                        zf-RRN7   5 ppCgvCgc.r 13 
                                    + C++Cg+ r
  gi|119720509|ref|YP_921004.1| 170 EKCPICGApR 179
                                    78*****964 PP

>> DUF3797  Domain of unknown function (DUF3797)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0    0.0011         1       8      25 ..     148     165 ..     145     167 .. 0.88
   2 ?   -0.2   0.5      0.97   9.2e+02      15      21 ..     171     177 ..     170     180 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0011
                        DUF3797   8 kLdekYvqCPeCgNnkvl 25 
                                    ++d+k   CP+Cg  +v+
  gi|119720509|ref|YP_921004.1| 148 PIDGKVWVCPVCGHTYVG 165
                                    67999999******9996 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.97
                        DUF3797  15 qCPeCgN 21 
                                    +CP Cg 
  gi|119720509|ref|YP_921004.1| 171 KCPICGA 177
                                    6****95 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   4.0    0.0042       3.9       2      22 ..     156     178 ..     155     179 .. 0.93
   2 ?    5.8   0.3     0.013        12       1       8 [.     171     178 ..     171     185 .] 0.70

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0042
                  zinc_ribbon_2   2 CpnCGaelqdnakF..CpyCGtp 22 
                                    Cp CG++    ++   Cp CG+p
  gi|119720509|ref|YP_921004.1| 156 CPVCGHTYVGPEPPekCPICGAP 178
                                    *********999999******98 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.013
                  zinc_ribbon_2   1 fCpnCGae 8  
                                    +Cp CGa+
  gi|119720509|ref|YP_921004.1| 171 KCPICGAP 178
                                    67777776 PP

>> DUF3039  Protein of unknown function (DUF3039)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   4.1    0.0016       1.5      26      54 ..     155     183 ..     147     185 .] 0.87

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0016
                        DUF3039  26 VvALCGkvwvptrdpkkfPvCpeCkeiye 54 
                                    V   CG+++v    p+k P+C + +e y+
  gi|119720509|ref|YP_921004.1| 155 VCPVCGHTYVGPEPPEKCPICGAPREKYQ 183
                                    6678*****************99999887 PP

>> zf-RanBP  Zn-finger in Ran binding protein and others
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.4    0.0096       9.1       5      11 ..     154     160 ..     151     163 .. 0.87
   2 ?    5.0   0.4     0.016        15      20      29 ..     171     180 ..     169     181 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0096
                                    EE-SSS- CS
                       zf-RanBP   5 WdCskCl 11 
                                    W C++C+
  gi|119720509|ref|YP_921004.1| 154 WVCPVCG 160
                                    ******8 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.016
                                    B-TTT--BTS CS
                       zf-RanBP  20 kCvaCqapkp 29 
                                    kC +C+ap++
  gi|119720509|ref|YP_921004.1| 171 KCPICGAPRE 180
                                    899*****97 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.2     0.065        61      28      34 ..     155     161 ..     147     165 .. 0.75
   2 ?    4.1   6.3     0.054        51       8      35 ..     156     178 ..     153     182 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.065
                    Zn-ribbon_8  28 aCPeCgs 34 
                                    +CP Cg+
  gi|119720509|ref|YP_921004.1| 155 VCPVCGH 161
                                    4999997 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.054
                    Zn-ribbon_8   8 CeeCghefevlqsisdapltaCPeCgse 35 
                                    C  Cgh++       + p+++CP Cg++
  gi|119720509|ref|YP_921004.1| 156 CPVCGHTYV----GPE-PPEKCPICGAP 178
                                    888998887....223.4466*****95 PP

>> Rad50_zn_hook  Rad50 zinc hook motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.2     0.033        31      21      27 ..     155     161 ..     151     162 .. 0.85
   2 ?    3.3   1.2      0.08        76      20      28 ..     170     178 ..     167     178 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.033
                                    E-TTT-- CS
                  Rad50_zn_hook  21 cCPlCgR 27 
                                     CP+Cg+
  gi|119720509|ref|YP_921004.1| 155 VCPVCGH 161
                                    6****96 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.08
                                    EE-TTT--E CS
                  Rad50_zn_hook  20 gcCPlCgRe 28 
                                    ++CP Cg +
  gi|119720509|ref|YP_921004.1| 170 EKCPICGAP 178
                                    59****975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1300.39
//
Query:       gi|119720510|ref|YP_921005.1|  [L=96]
Description: hypothetical protein Tpen_1607 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.5e-06   26.0   0.2    1.8e-05   25.1   0.2    1.5  1  HMA       Heavy-metal-associated domain


Domain annotation for each model (and alignments):
>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.2     1e-09   1.8e-05       1      57 [.       7      58 ..       7      62 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1e-09
                            HMA  1 tvrvsgmhCagCaakvekvLselpgVesvkvdlatktvtVegdaestklrkiieaie 57
                                   t++vsg+ C++C+a  +  L+++pgV +v v    ++v+V++d+e t+l +    ++
  gi|119720510|ref|YP_921005.1|  7 TLKVSGIGCGSCVAPSKAHLLRVPGVVAVYVFG--SRVEVVYDEERTSLDE---VLK 58
                                   789***********************8887755..6**********65544...444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 624.93
//
Query:       gi|119720511|ref|YP_921006.1|  [L=71]
Description: hypothetical protein Tpen_1608 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-13   50.4   0.0    2.9e-13   50.1   0.0    1.1  1  TrmO      tRNA-methyltransferase O


Domain annotation for each model (and alignments):
>> TrmO  tRNA-methyltransferase O
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.1   0.0   1.6e-17   2.9e-13      64     113 ..       8      55 ..       2      60 .. 0.92

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 1.6e-17
                                    -E.EGGGS--S-SSS-EEEEEEEEEEEETTEEEEES----TT-EEEEEEE CS
                           TrmO  64 ervGvfatRsphRpnpiglsvvklekvegnvlevsgvDlldgtpvlDiKP 113
                                    er  v+a+R  +  +p++lsvv+l k eg+ l v+g+Dl+dgtpvlDiKP
  gi|119720511|ref|YP_921006.1|   8 ER--VLACRYSCFRSPVALSVVRLVKREGRLLCVEGLDLFDGTPVLDIKP 55 
                                    44..9******999************************************ PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       197  (0.0109878); expected 358.6 (0.02)
Passed bias filter:                      177  (0.00987227); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.33s 00:00:00.84 Elapsed: 00:00:00.55
# Mc/sec: 389.45
//
Query:       gi|119720512|ref|YP_921007.1|  [L=131]
Description: PilT domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-12   48.0   0.0    1.9e-12   47.7   0.0    1.1  1  PIN            PIN domain
  ------ inclusion threshold ------
       0.04   13.7   0.0       0.05   13.4   0.0    1.2  1  RNase_Zc3h12a  Zc3h12a-like Ribonuclease NYN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.7   0.0   2.2e-16   1.9e-12       2     121 ..       3     124 ..       3     125 .. 0.83

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 2.2e-16
                                    EE-HHHHHHHHTTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHS...SCHCHHHHHHHHHHHHH.HHTSEEEEBCHHH CS
                            PIN   2 vlDTsvliallrgeekaeaarklleeleelvtsalvlaEllyvlar...rkskrekaaelvellll.lsalkilpidaei 77 
                                    v+DT +l+al  g++++ +a++ll     l +++ +l E+  vl++   ++ ++ +a + ++      +  ++  i++e+
  gi|119720512|ref|YP_921007.1|   3 VVDTEFLFALSPGDPRHGRALRLLSM-KGLKVPDTALLEFQVVLRArgrKPGEIAAAMNALKHVFKsYRVREVSTIGTEL 81 
                                    79**********************85.*******************98544444444444444444155555555***** PP

                                    HHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHHHHH CS
                            PIN  78 aeeaaeialkygllpnDaliaAtAkehgikliatfDedfrrvak 121
                                    + + ae+ +kygl+ +D +iaA A++ +  +i++ D+ f+rv +
  gi|119720512|ref|YP_921007.1|  82 FVRQAELEEKYGLSYFDSMIAASALAVDG-VIVSDDRAFDRVPG 124
                                    *****************************.565********975 PP

>> RNase_Zc3h12a  Zc3h12a-like Ribonuclease NYN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   5.6e-06      0.05      77     112 ..      83     118 ..      54     123 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.6e-06
                  RNase_Zc3h12a  77 tpskyldgkksvsyddrlilelAeekdGvivsndny 112
                                    + + +l+ k   sy d++i   A   dGvivs d+ 
  gi|119720512|ref|YP_921007.1|  83 VRQAELEEKYGLSYFDSMIAASALAVDGVIVSDDRA 118
                                    5566667777789*********************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 882.65
//
Query:       gi|119720513|ref|YP_921008.1|  [L=79]
Description: AbrB family transcriptional regulator [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-11   44.2   1.4    1.8e-11   43.7   1.4    1.2  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
  ------ inclusion threshold ------
      0.015   15.7   0.0      0.019   15.4   0.0    1.1  1  PrlF_antitoxin  prlF antitoxin for toxin YhaV_toxin


Domain annotation for each model (and alignments):
>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.7   1.4     2e-15   1.8e-11       1      41 [.       5      45 ..       5      49 .. 0.93

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 2e-15
                                   EEETTEEEEEE-CCCHHHCCEECTCEEEEEECTTCCCCCCC CS
                 MazE_antitoxin  1 fkvGnsgavriPkevrfelgireGdevelevdgdkiilrpl 41
                                   ++vG+   v+iPk vr++ g++eGd +e++v+g++i+l+ +
  gi|119720513|ref|YP_921008.1|  5 VRVGKRFTVVIPKSVREKVGLKEGDLLEVRVEGGRIVLERK 45
                                   69***********************************9865 PP

>> PrlF_antitoxin  prlF antitoxin for toxin YhaV_toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.0   2.1e-06     0.019       3      44 ..       6      45 ..       3      53 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.1e-06
                 PrlF_antitoxin  3 tltergqttiPasvRkaLklkkgrdkiaytilddgkvvisra 44
                                   ++ +r+   iP+svR+ ++lk+  d ++ ++ ++g++v++r+
  gi|119720513|ref|YP_921008.1|  6 RVGKRFTVVIPKSVREKVGLKE-GDLLEVRV-EGGRIVLERK 45
                                   6889999**************9.66888776.6788999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.48
# Mc/sec: 491.01
//
Query:       gi|119720514|ref|YP_921009.1|  [L=588]
Description: AMP-dependent synthetase and ligase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-40  138.6   0.0    9.7e-24   83.7   0.0    2.2  2  AMP-binding    AMP-binding enzyme
    7.8e-14   51.3   0.1    7.8e-14   51.3   0.1    2.0  2  ACAS_N         Acetyl-coenzyme A synthetase N-terminus
      8e-07   29.9   2.9    1.4e-06   29.2   2.1    1.9  2  AMP-binding_C  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.7   0.0   4.4e-18   2.6e-14      10     100 ..      88     187 ..      79     222 .. 0.85
   2 !   83.7   0.0   1.6e-27   9.7e-24     189     423 .]     277     513 ..     266     513 .. 0.88

  Alignments for each domain:
  == domain 1  score: 52.7 bits;  conditional E-value: 4.4e-18
                                    TSEEEEE...CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS-HHHH CS
                    AMP-binding  10 dkvalvd...sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptltaeel 86 
                                     kva+ +   sg+ + lTY+ ld+ + r+A +L+s Gv++gd V +++p+ pe ++ +la++++Ga   p+ ++++  el
  gi|119720514|ref|YP_921009.1|  88 RKVAVLYeseSGDAEVLTYEGLDALAGRIAGWLESVGVGRGDWVTVYSPPNPESLAFMLAAMRVGAPFEPVFTGFGYYEL 167
                                    57888888999999****************************************************************** PP

                                    HHHHHHHTESEEE......E CS
                    AMP-binding  87 ayiledseakvli......a 100
                                    a  ++  +++v++      +
  gi|119720514|ref|YP_921009.1| 168 AKRIARRGSRVVFtvdgytR 187
                                    *************5444331 PP

  == domain 2  score: 83.7 bits;  conditional E-value: 1.6e-27
                                    HHHHHHHC.SCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGCCH.HHHHHHHHHHHT-SEEEEEHHHHHH CS
                    AMP-binding 189 aslkletr.fklkeddvvlsilplahifglilelllallsGatvvllpkdaald.pklllelieklkvtviagvPrvlea 266
                                    ++   + r  +lk++++++ ++   +i+g+++ ++++l+ G+tvvl+++ ++++  ++++  +e ++vt++ ++  +l+ 
  gi|119720514|ref|YP_921009.1| 277 YA---TSRwIGLKPRETLFNTVWPGWITGVSYLVFGPLMTGSTVVLYDGAPDWRgWDRWISIVESYGVTLLLTTSGALRL 353
                                    33...2342458899999**********************************66699************99999999999 PP

                                    HHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTC.................EEEEEEEEGGGSSECEE... CS
                    AMP-binding 267 llesgalkaakkakdlsslrlvllggeplspellrffralfge.................evlegYGlTEttgvvtv... 326
                                    + +++a+    +++d  sl+ vl+ +epl +e++ ++++++g+                 +vl++Y ++E +++++    
  gi|119720514|ref|YP_921009.1| 354 MSRQPAEL--FRSHDYDSLKAVLVTAEPLDAETWGWAYSVLGTlkrplvdsvpselsgaiPVLDLYIQSEVGTFLVGnlp 431
                                    98876554..56789***********************************************************965554 PP

                                    CHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEETTS-SEBTT-HHHHHHHEEETCCEEEEEEEEEEET CS
                    AMP-binding 327 lpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgpgvmkgYlkkpeataeafdsegrwlrTGDlgrlde 406
                                     +    + ++g++G+p+pg  v+++++           G l+vr+p+ +      p    e++  e +++ TGD +r+  
  gi|119720514|ref|YP_921009.1| 432 SY-TFTHIVPGTCGPPMPGFHVEVLED-----------GRLVVRKPWPAIPVE-APGDFWEKWR-E-GFYDTGDAARYSV 496
                                    22.3333478***************98...........99******9998865.8899999998.6.7**********99 PP

                                    TSEEEEEEECCCEEEET CS
                    AMP-binding 407 dGyleivgRkkdliklr 423
                                    dGy+e++gR + ++k++
  gi|119720514|ref|YP_921009.1| 497 DGYIEVLGRRDGVMKVS 513
                                    **************985 PP

>> ACAS_N  Acetyl-coenzyme A synthetase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.3   0.1   1.3e-17   7.8e-14       1      54 [.      24      76 ..      24      77 .. 0.95
   2 ?   -1.4   0.3      0.37   2.2e+03       9      20 ..     471     482 ..     470     486 .. 0.79

  Alignments for each domain:
  == domain 1  score: 51.3 bits;  conditional E-value: 1.3e-17
                                   HHHHHHHHHH-HHHHHHHHHCCS--SB--S-SECSTTTCT-EESTT-EE-HHHH CS
                         ACAS_N  1 ykelykeSiedpeaFWaeqakeldWekpfdkvldgskgpfikWFeGGklNicyN 54
                                   y+++y+eS+ed  +FW++ a+ l W kp+++v++g ++p ++WF+GG+l+  +N
  gi|119720514|ref|YP_921009.1| 24 YRRVYRESVEDVYGFWSSYARLLLWRKPWERVVEG-EAPRVRWFAGGELSPYEN 76
                                   99*********************************.************986665 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.37
                                    HH-HHHHHHHHH CS
                         ACAS_N   9 iedpeaFWaeqa 20 
                                    +e p  FW++  
  gi|119720514|ref|YP_921009.1| 471 VEAPGDFWEKWR 482
                                    68899***9865 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0         3   1.8e+04      28      49 ..     385     402 ..     370     411 .. 0.50
   2 !   29.2   2.1   2.3e-10   1.4e-06       2      64 ..     522     580 ..     521     585 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 3
                                    --EEEEEE------HHHHHHHH CS
                  AMP-binding_C  28 alvafVvlkdgsealeeeLkah 49 
                                    +  a+ vl  g+  l++ L++ 
  gi|119720514|ref|YP_921009.1| 385 WGWAYSVL--GT--LKRPLVDS 402
                                    34555555..43..33444444 PP

  == domain 2  score: 29.2 bits;  conditional E-value: 2.3e-10
                                    HHHHHHSSTTEEEEEEE-----TTS---EEEEEE------HHHHHHHHHHHHT-TTTS-SEEE CS
                  AMP-binding_C   2 vEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgsealeeeLkahvrkelgpyavpkkvv 64 
                                    +E +++ +p+V+ + V++ pd++k e++v+ V  +++    +e++++ vr++lgp+  p +v 
  gi|119720514|ref|YP_921009.1| 522 IERVVAGVPGVRGVRVYARPDPLKFEVPVVSVEGSAD----PEAVRKAVREKLGPILEPAQVT 580
                                    8******************************997444....4*****************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (588 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 4139.61
//
Query:       gi|119720515|ref|YP_921010.1|  [L=181]
Description: hypothetical protein Tpen_1612 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.4e-11   43.3   0.0    4.5e-11   42.9   0.0    1.1  1  Lactamase_B_3  Beta-lactamase superfamily domain
    9.8e-07   28.5   0.0    1.4e-06   28.0   0.0    1.1  1  Lactamase_B_2  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   0.0     5e-15   4.5e-11      63     162 ..      61     154 ..      50     155 .. 0.91

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 5e-15
                  Lactamase_B_3  63 kvleegeslevggleiravatshdavggsergenngflleqdgltiyhlGhlahelsseelkelgrvDvvltPvggpltl 142
                                    +v+++g++le++g+++r v+++ +    +e+g+++g+++  +g+++y+ G ++   ++      +++Dv l+P g++  +
  gi|119720515|ref|YP_921010.1|  61 RVVKPGDALELEGFRVRVVSGYRR----AEQGGGVGYVFYLGGVKVYYAGPTGLV-EEIVGLRGEDIDVALLPLGEG-AM 134
                                    79*********************6....56999********************84.444445778***********9.9* PP

                  Lactamase_B_3 143 gqeealelakrLkpklvlPm 162
                                     +eea+e+++ ++p++ +P 
  gi|119720515|ref|YP_921010.1| 135 TPEEASEVVRTVRPRVAVPL 154
                                    ******************96 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   1.5e-10   1.4e-06      96     198 ..      63     153 ..      58     154 .. 0.89

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 1.5e-10
                                    EEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---HHHHHHHCT-SEEEEE-S-SSTTHHHHH CS
                  Lactamase_B_2  96 felgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyipeeigerlggadllllditayeddemirh 175
                                    +++gd  le++ + +r  sg  ++ ++g  +G+++  gg +vyy+g tg ++e +g r +++d++ll+ +          
  gi|119720515|ref|YP_921010.1|  63 VKPGD-ALELEGFRVRVVSGY-RRAEQGGGVGYVFYLGGVKVYYAGPTGLVEEIVGLRGEDIDVALLPLG---------- 130
                                    55665.578888888888888.7888899***************************************88.......... PP

                                    HT---STSHHHHCTTSSSSEEEE CS
                  Lactamase_B_2 176 mgHltpeeaveaaadlgakrlvl 198
                                    +g +tpeea e+++ ++++++v+
  gi|119720515|ref|YP_921010.1| 131 EGAMTPEEASEVVRTVRPRVAVP 153
                                    69*****************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       235  (0.0131073); expected 358.6 (0.02)
Passed bias filter:                      197  (0.0109878); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 1308.95
//
Query:       gi|119720516|ref|YP_921011.1|  [L=353]
Description: hydrogenase expression/formation protein HypE [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-22   79.0   0.0    6.1e-22   78.4   0.0    1.3  1  AIRS_C           AIR synthase related protein, C-terminal dom
      2e-17   63.6   0.4    4.1e-17   62.6   0.4    1.5  1  AIRS             AIR synthase related protein, N-terminal dom
  ------ inclusion threshold ------
       0.16   10.7   0.0       0.23   10.2   0.0    1.1  1  AdoMet_Synthase  S-adenosylmethionine synthetase (AdoMet synt


Domain annotation for each model (and alignments):
>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.4   0.0     1e-25   6.1e-22       3     152 ..     175     326 ..     173     330 .. 0.85

  Alignments for each domain:
  == domain 1  score: 78.4 bits;  conditional E-value: 1e-25
                                    TEEEEEEETSSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHHHHHHHHT CS
                         AIRS_C   3 GdvliltgslGlggagtslkrkileeeglddsavqlgdvlleptliyvkralaalkglvkaahDvTgGGLlgalaemapa 82 
                                    Gd++++t   G +ga++++ +++  + ++ +s++ ++d   +  l+ v ++ a   g ++aa+D T+GGL+g l+e+a+ 
  gi|119720516|ref|YP_921011.1| 175 GDKIVVTDYVGDHGAVILMLQMGMGDVEEIASGSLKSDSKPLTPLLPVFEKFA---GYIHAARDPTRGGLAGVLNEWARS 251
                                    9***************7776666666554434666777777744444444444...68********************** PP

                                    TTEEEEEECGTHHHHHHHH.....HHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEEESSSEE CS
                         AIRS_C  83 sgvgaeidldkvpifdele.....splemllsensGrllvavppeeadavlaileeeglpeaavIGevtakeels 152
                                    +g+ a+i +++vp++d ++     ++ ++l+ +++G  +++v+pe a++v+++l+ +g p+a+vIGe  + ++ +
  gi|119720516|ref|YP_921011.1| 252 GGLLAVIREEEVPVRDAVRrfaemLGVDPLYLASEGAAVLSVSPEVAEEVVSELRGRGFPNARVIGEFRENPKYR 326
                                    ****************9998888899999999***********************************99988766 PP

>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.6   0.4   6.9e-21   4.1e-17       1      93 [.      51     163 ..      51     164 .. 0.86

  Alignments for each domain:
  == domain 1  score: 62.6 bits;  conditional E-value: 6.9e-21
                                    SSSE.........EEEEEEEEE.EECCTCCCC....HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC......HHHHHHHH CS
                           AIRS   1 dDaa.........vvvttdshnrpvlvepvhf....iGakavavnlsDlaamGArPlalllslalp......wleevvrg 61 
                                    dD a         +vvt+d    ++ v+p  f    iG +av++ ++D+++mG+rP+a+l+++ ++      +le++v++
  gi|119720516|ref|YP_921011.1|  51 DDGAliplpgggfLVVTAD----SYTVNPPFFpggnIGSLAVHGSINDVVMMGGRPVAMLDTIVVEegfpmgDLEAIVNS 126
                                    6777544444444599999....6666776677*********************************************** PP

                                    HHHHHHHTT-EEEEEEEEEESS.....EEEEEEEEEE CS
                           AIRS  62 laeaaeelgvplvgGdtsfsne.....ptisvtavGl 93 
                                    + ea+e+ gvpl+gGd +++++     +t++++ +G+
  gi|119720516|ref|YP_921011.1| 127 MLEALEKEGVPLIGGDFKVMPKgqldrITVTTVGLGV 163
                                    ********************88899777777766665 PP

>> AdoMet_Synthase  S-adenosylmethionine synthetase (AdoMet synthetase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   3.8e-05      0.23     164     211 ..     115     158 ..      90     172 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 3.8e-05
                                    ES--HHHHHHHHHHHHHTSHHHHHH-TTEEEEEEEEEEEETTEEEEEE CS
                AdoMet_Synthase 164 aplseleklvleterllnskelkkklpevGeDiKvmglRekkkielTv 211
                                    +p+ +le +v ++ + l+    k+ +p +G D Kvm   + ++i++T 
  gi|119720516|ref|YP_921011.1| 115 FPMGDLEAIVNSMLEALE----KEGVPLIGGDFKVMPKGQLDRITVTT 158
                                    699999999999888887....788*******************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2502.75
//
Query:       gi|119720517|ref|YP_921012.1|  [L=99]
Description: hypothetical protein Tpen_1614 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.6e-15   57.0   0.2    2.3e-15   56.5   0.2    1.3  1  HupF_HypC  HupF/HypC family
  ------ inclusion threshold ------
       0.13   13.0   2.3        6.7    7.5   0.1    2.4  2  PCB_OB     Penicillin-binding protein OB-like domain


Domain annotation for each model (and alignments):
>> HupF_HypC  HupF/HypC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.5   0.2   2.6e-19   2.3e-15       1      64 [.       1      66 [.       1      67 [. 0.96

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 2.6e-19
                                   CCEEEEEEEEEEETTEEEEECT.TEEEEEEGTTC.TTB-TT-EEEEETTEEEEEE-HHHHHHHHHH CS
                      HupF_HypC  1 MCLaiPgkvveiedelAlvdvg.Gvrrevslalv.eevkvGdyVLvhvGfAiekideeeaeetlel 64
                                   MC++ P+ v+e+++++A+vd+g Gv rev +++  + v+ Gd V+vh+G+ i+ki++e  +e +e+
  gi|119720517|ref|YP_921012.1|  1 MCWGTPAVVLEVSGSTARVDYGdGVVREVFVGIAgDRVSRGDIVVVHAGVIISKISPEGLREEIEF 66
                                   **********************************878**********************9998876 PP

>> PCB_OB  Penicillin-binding protein OB-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.1   0.00075       6.7      36      55 ..       6      25 ..       4      35 .. 0.85
   2 ?    5.2   0.3    0.0038        34      83      97 ..      34      48 ..      27      51 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00075
                                   EEEEEEEETTEEEEEETTS- CS
                         PCB_OB 36 pAvVlsvseksarvglrdge 55
                                   pAvVl+vs + arv   dg 
  gi|119720517|ref|YP_921012.1|  6 PAVVLEVSGSTARVDYGDGV 25
                                   9*************997774 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0038
                                   HCCC--TTEEEEEEE CS
                         PCB_OB 83 asdvlkpGdvvlvrk 97
                                   a d++++Gd+v+v++
  gi|119720517|ref|YP_921012.1| 34 AGDRVSRGDIVVVHA 48
                                   6799*********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 633.05
//
Query:       gi|119720518|ref|YP_921013.1|  [L=411]
Description: hydrogenase formation HypD protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   2.2e-121  405.3   0.0   2.6e-121  405.0   0.0    1.0  1  HypD       Hydrogenase formation hypA family
  ------ inclusion threshold ------
       0.02   14.8   0.0      0.051   13.5   0.0    1.7  1  zf-RING_6  zf-RING of BARD1-type protein


Domain annotation for each model (and alignments):
>> HypD  Hydrogenase formation hypA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  405.0   0.0  2.9e-125  2.6e-121       6     350 ..      36     391 ..      32     392 .. 0.95

  Alignments for each domain:
  == domain 1  score: 405.0 bits;  conditional E-value: 2.9e-125
                                    HHHHHHHHHHTSS-EEEEE--HHHHHHHHHTTHHHHS-TTEEEEE-S--TTTTS-HHHHHHHHHHHHH--EEEEE-CCHH CS
                           HypD   6 llekikkeakkerelkimevCGghthaivryglrslLpenielisGPGCpVCvtpeeeidkaielaekeevilatfgDml 85 
                                     +e+i+++  ++ ++kim++CG+h+++iv++glrsl+pe +el++GPGCpVCvtp+ +i++aiel+ + +v+++t+gD++
  gi|119720518|ref|YP_921013.1|  36 KFEEIRAREGRDYRIKIMDFCGTHEWTIVHFGLRSLMPEGVELVAGPGCPVCVTPSWYIERAIELSLS-GVTVYTYGDTF 114
                                    568899999999******************************************************99.*********** PP

                                    G---T.....T--HHHHHHTT-EEEE-SSHHHHHHHHHH-TTSEEEEEEEE-HHHHHHHHHHHHHHHHHT-SSEEEEEEE CS
                           HypD  86 rvpgs.....kksLleakaegadvrivyspldalkiakenpdkevvflavGFEttapatalalleakkeglknfsvlssh 160
                                    ++++       +sL+ea+a+g++vr+v+s +da++ a+++   e vfl++GFEt ap +a a+ +   + ++n++++s  
  gi|119720518|ref|YP_921013.1| 115 KLRAVnpvdgVSSLEEARAAGGRVRLVVSLVDAVRDASRH-GGESVFLGIGFETVAPGYARAVVS--GSLPENLKLMSLV 191
                                    **9987887779***************************9.8999******************99..999********** PP

                                    E-HHHHHHHHHHTT......---SEEEEEHHHHHHHTTHHHHHHHHHH---EEEE-SSHHHHHHHHHHHHHHHHTT---E CS
                           HypD 161 klvppaleallesee.....lkidgfiapghvstviGlkayeelaeeykvpvvvaGFepldilqailmlvkqleegeaev 235
                                    kl+ppa+ + l+  +       + g+iapghvstv+G+ka+e++ae+++vpvvv+GFep+d+l++i+++++ql++ge+ v
  gi|119720518|ref|YP_921013.1| 192 KLTPPAMFYSLDILRdkptePPVMGVIAPGHVSTVTGAKAWEPVAEQFQVPVVVSGFEPIDVLMGIAEIMRQLARGEYGV 271
                                    ******9875443222223588********************************************************** PP

                                    EETTTTT--TT--HHHHHHHHHHEEEEEEEETTTEEEEEEEEEE-GGGGGGBGGGT---.....-S---SS-TT--HHHH CS
                           HypD 236 eneYkrvvkeegnkkaqklieevfevrdaewRglgvipksglklreeyaefdaekkfel.....ekeeekekkackcgev 310
                                    + eY+r+v++eg+ +aq++i+e fe++d++wRg+g +p sgl+lre+y ++da ++f +     ek +++++++c+c+ev
  gi|119720518|ref|YP_921013.1| 272 KVEYTRAVTWEGDLEAQAAIHEAFEAVDDAWRGIGFLPLSGLRLREKYGRLDALRHFGIeeltpEKWRKDTPPGCRCAEV 351
                                    *********************************************************98888888899999********* PP

                                    HTTS--GGGSTTBTTTB-SSS-SSHHHHSTT-HHHHHHHT CS
                           HypD 311 lkGkakPedCklFgkaCtpenpvGacmvSsEGaCaayyky 350
                                      GkakP+dC++F+k+Ctpe+p+G+cmvS EG+Ca++ ++
  gi|119720518|ref|YP_921013.1| 352 TLGKAKPTDCPMFMKKCTPEKPYGPCMVSLEGTCAVWARF 391
                                    *************************************998 PP

>> zf-RING_6  zf-RING of BARD1-type protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   5.7e-06     0.051      39      57 ..      80      98 ..      74     105 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.7e-06
                      zf-RING_6 39 fgsgcpvcytpawiqdvki 57
                                    g gcpvc tp+w  +  i
  gi|119720518|ref|YP_921013.1| 80 AGPGCPVCVTPSWYIERAI 98
                                   589**********876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2767.49
//
Query:       gi|119720519|ref|YP_921014.1|  [L=510]
Description: carbohydrate kinase, FGGY [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-39  134.8   0.0      5e-39  134.3   0.0    1.2  1  FGGY_N    FGGY family of carbohydrate kinases, N-terminal dom
      4e-29  101.8   0.0    5.6e-29  101.3   0.0    1.2  1  FGGY_C    FGGY family of carbohydrate kinases, C-terminal dom
  ------ inclusion threshold ------
        0.2   11.5   0.0       0.42   10.4   0.0    1.4  1  RibD_C    RibD C-terminal domain


Domain annotation for each model (and alignments):
>> FGGY_N  FGGY family of carbohydrate kinases, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.3   0.0   8.3e-43     5e-39       2     245 .]       3     240 ..       2     240 .. 0.95

  Alignments for each domain:
  == domain 1  score: 134.3 bits;  conditional E-value: 8.3e-43
                                    EEEEEEESSEEEEEEEETTS-EEEEEEEE--EB-SSTT--EE-HHHHHHHHHHHHHHHHHHCT.-GCCEEEEEEEE-SS- CS
                         FGGY_N   2 ilglDcGttstkaivldekgkvvasaqaelelsspkegwaeqdpeeiwqalaeairkvleqagisekqikaIgisgqreg 81 
                                    i+++D+Gtt++k+ +++e+g++++s ++ ++l+ +  g+aeq+p ei+ ++ +++r++ +    ++ +++aI +++q+++
  gi|119720519|ref|YP_921014.1|   3 IVVVDIGTTNIKTGIFNEDGRLLHSFTERVTLEVDASGRAEQNPYEIYSKVVSSLRQAAKF---TKGEAEAIFFTSQMHS 79 
                                    799****************************************************998765...59************** PP

                                    EEEEETTTEESSEEE-TT--TTHHHHHHHHHTTCHCCHHHHHSS-SSTTSHHHHHHHHHHHSCCHHCCHCEEEEHHHHHH CS
                         FGGY_N  82 lvllDkndkpLynailwkdrrtaeiveklkeegnekklyektglvlstgftlsklkWlkenepevfekiekflliddyLi 161
                                    +++lD++++pL   +++ d+r ++ ++++ +  +  +ly+ tg +   +++l k+  l++     ++  +  + ++++  
  gi|119720519|ref|YP_921014.1|  80 AMILDREGEPLSGLVTYLDTRPSQFIDEIDA--ESYELYQETGCPPLYVYPLIKIIYLRRLLN-PRAGFKVAVSVKEFPL 156
                                    *****************************99..7789*********************98654.4567888999****** PP

                                    HHHCT--EEEHHHHCTTTSEETTTTEE-HHHHHHTT--GGGS-EEE-TCCEEEEEECCCCCCTT.S-EEEEEEEEEHHHH CS
                         FGGY_N 162 wrLtgqfvtdvtnasesmlfnikklewdeellailgipeelLPklvesseiigelkpelaaklGlkegvpvvggggDqqa 241
                                    ++Ltg+ ++dv+ as+ ++++i++l+w+e++++i+g+ ee LP+l+ +++   el +e+++ +G+k+ +p+ +g +D  a
  gi|119720519|ref|YP_921014.1| 157 FKLTGHLAVDVSTASGAQMVDIRSLKWSEKAIEIAGLGEENLPELYIGEKEHLELSSEASTLTGFKKATPIYPGVSDAGA 236
                                    *****************************************************************************988 PP

                                    HHHH CS
                         FGGY_N 242 aalG 245
                                      +G
  gi|119720519|ref|YP_921014.1| 237 HSFG 240
                                    7776 PP

>> FGGY_C  FGGY family of carbohydrate kinases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.3   0.0   9.4e-33   5.6e-29       3     191 ..     251     440 ..     249     446 .. 0.87

  Alignments for each domain:
  == domain 1  score: 101.3 bits;  conditional E-value: 9.4e-33
                         FGGY_C   3 vslGTssflllvgtkpv.isehglltpvagedgkpeyalegsiavagslvawlldnlglreeirdagev...eeslaela 78 
                                    + +GTs  + ++ + pv    h+    ++   g   + + g+++ ag +v+w+l+n +++eei ++  +   +++l+  +
  gi|119720519|ref|YP_921014.1| 251 LNVGTSAAIRVTEPSPVlDGRHMRFFSYY--AGNSRWIVGGAVNNAGVAVEWFLRNFATAEEIVSETANidrFTLLD-IE 327
                                    678**************766677777777..6789*********************988888887777778666666.78 PP

                         FGGY_C  79 aaeavadaggvvfvpafsglrapywdpdargtitglsssttlahiarAaleavalqlrailealekdsgkpldrlavdGG 158
                                     + + + a+g+vf+p+++g+r p+ dp +rg++ g s stt  ++ rA++e+va+ l+ ileal+++    l++l+++GG
  gi|119720519|ref|YP_921014.1| 328 TRLSPPGANGLVFLPYLTGERFPIRDPYFRGAFYGASLSTTRNDMLRAIMEGVAFTLKMILEALKEH---GLNPLLTHGG 404
                                    88889999********************************************************555...5555655555 PP

                         FGGY_C 159 gs..kndllmqllAdilgvpVerpkt.aeatalGaA 191
                                    g   +   ++q++ d++g+p++++++  e+t++G  
  gi|119720519|ref|YP_921014.1| 405 GGglRIGTWRQIFSDVFGMPLYVVREhVEPTLVGGW 440
                                    4444**********************9******975 PP

>> RibD_C  RibD C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0     7e-05      0.42     118     144 ..     374     405 ..     362     409 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 7e-05
                                    C.....ESE-HHHHHHHHHHTT--EEEEEETH CS
                         RibD_C 118 k.....vrvdlkelleeLkergirsllveGGa 144
                                    +     v ++lk +le+Lke+g+++ll++GG+
  gi|119720519|ref|YP_921014.1| 374 RaimegVAFTLKMILEALKEHGLNPLLTHGGG 405
                                    3333445899*********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (510 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 3152.13
//
Query:       gi|119720520|ref|YP_921015.1|  [L=291]
Description: binding-protein-dependent transport systems inner membrane component [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.9e-20   72.8  17.2    2.9e-20   72.8  17.2    1.8  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.2     0.054   9.7e+02      28      43 ..      17      32 ..       5      92 .. 0.69
   2 !   72.8  17.2   1.6e-24   2.9e-20       1     182 [.      98     283 ..      98     286 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.054
                   BPD_transp_1 28 lslPsfvlaillvlvf 43
                                   +++  ++++i+ +++f
  gi|119720520|ref|YP_921015.1| 17 SAILLLWIVIPTFWAF 32
                                   4444444444444433 PP

  == domain 2  score: 72.8 bits;  conditional E-value: 1.6e-24
                   BPD_transp_1   1 gillGilaa...lnrnkkldkllrpliivllslPsfvlaillvlvfvilsilg..hlilpviillllsaapyvrlirraa 75 
                                    g++lG+la+    ++  k+++++++l+ + + +P+f+l+++++    i   lg  ++  +++++ l +++py +l++r++
  gi|119720520|ref|YP_921015.1|  98 GVILGSLAGynlARFDYKGKRVVTWLVLFAYVFPVFILIVPVLI---IVRNLGlyNTLHGLALVHLAYTLPYSTLMMRSY 174
                                    79999999999999999********************7777663...456666204444478888999************ PP

                   BPD_transp_1  76 lrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis. 154
                                    ++ +p+ l+eaa+++G++r++ +++vv+P ++p +it +i++f++++++ ++++ l+s++   tl + ++      ei  
  gi|119720520|ref|YP_921015.1| 175 FYGIPRVLEEAALIDGCTRFEALWRVVIPVSVPGFITAFIFSFTLSWNDLLFALVLLSSSRNYTLPIATTFFLWGGEIVd 254
                                    *********************************************************99954433333333333344448 PP

                   BPD_transp_1 155 .nggvlalviavlllnlvadilqrlldpr 182
                                      g+++++++a l+ +++++++q+++   
  gi|119720520|ref|YP_921015.1| 255 pGGLAATAIFAGLVPSVLYMLVQKYVVAG 283
                                    88***********************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       624  (0.0348039); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1825.73
//
Query:       gi|119720521|ref|YP_921016.1|  [L=283]
Description: binding-protein-dependent transport systems inner membrane component [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.4e-25   89.3  16.1    2.4e-25   89.3  16.1    2.2  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   5.1      0.23   4.1e+03      24      51 ..       8      30 ..       4      79 .. 0.73
   2 !   89.3  16.1   1.3e-29   2.4e-25       4     174 ..      83     275 ..      80     278 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.23
                   BPD_transp_1 24 iivllslPsfvlaillvlvfvilsilgh 51
                                   ++ l+ +P++ l+i+++        +g+
  gi|119720521|ref|YP_921016.1|  8 SQWLYVVPTLTLIIIIFI-----IPIGY 30
                                   555677788877777663.....23333 PP

  == domain 2  score: 89.3 bits;  conditional E-value: 1.3e-29
                   BPD_transp_1   4 lGilaa..lnrnkkldkllrpliivllslPsfvlaillvlvf...................vilsilghlilpviillll 62 
                                    +G+ +a  ln++++++ +lr+++i+++++Psfv+a+l+   f                   v++ +   ++ +vi++ ++
  gi|119720521|ref|YP_921016.1|  83 IGLGVAllLNKKFWGRGFLRGFSILPWAFPSFVVAVLFW--FnydyrgtfntvlklmglqpVHWMSYDMAMASVILINIW 160
                                    6777777799***********************999977..6679**************99666566666666******* PP

                   BPD_transp_1  63 saapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtlll 142
                                    +  p++++ + a+l+++p++l+eaa+++Gas  q f +v++P+++p++ t ++l+ ++ lg+++ ++++++++++  +++
  gi|119720521|ref|YP_921016.1| 161 HGWPFFFMGYLAGLQAIPEELYEAAEIDGASALQKFIHVTIPQLKPVLYTVALLSTMWTLGEFTQIYMTTGGGPVDATTT 240
                                    ************************************************************************99999999 PP

                   BPD_transp_1 143 eailgydyseis...nggvlalviavlllnlvadi 174
                                     +i  + +++++   + +++a++i+vl++ lv+  
  gi|119720521|ref|YP_921016.1| 241 IPIATFKIAFMTeinFPLAAAYTILVLPIYLVLIY 275
                                    999999999999999999999*******9999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2100.64
//
Query:       gi|119720522|ref|YP_921017.1|  [L=450]
Description: extracellular solute-binding protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.9e-25   90.3   3.3    2.5e-25   89.8   3.3    1.1  1  SBP_bac_8  Bacterial extracellular solute-binding protein
    5.1e-19   69.4   7.9    7.9e-19   68.7   7.9    1.2  1  SBP_bac_1  Bacterial extracellular solute-binding protein


Domain annotation for each model (and alignments):
>> SBP_bac_8  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.8   3.3   2.8e-29   2.5e-25       4     269 ..      60     363 ..      57     378 .. 0.78

  Alignments for each domain:
  == domain 1  score: 89.8 bits;  conditional E-value: 2.8e-29
                                    HHHHHH-TEEEEEEE--SSSHHHHHHHHHHTT---SEE.EEE-HHHHHHHHHTTSB--GGGS.TTHHH...-HHHHHTT- CS
                      SBP_bac_8   4 kefekktgvkvnvvtaasndleqklkaalaagtapdidvvwanedalatlaeeglladlsdl.dnldd...ltdalaavg 79 
                                     e+  k++v+v+++ +a +d+  kl+aa++ag+ pdi+   +n+ ++a +ae+gll +l+d+ ++l++   ++ +l+ ++
  gi|119720522|ref|YP_921017.1|  60 REWASKNNVDVEITWYAVADIGKKLTAAVEAGNPPDIV---INGHPVAIFAEKGLLLPLDDViEKLNKsdfYEIKLKICS 136
                                    578899*****************************975...8889***************88777777653444888889 PP

                                    -TS.----EEEEEEE-EEEEEHHHHHHS......---BHHHHHHHHHHH....HHH-.........SEGG---GGGGGGT CS
                      SBP_bac_8  80 ydgklygvPyasetpyvliynkdlleka.....edpktwdellaaakkl....kgkf.........glpdpasgwlqaal 141
                                    + g++y+vP   e  + l+++ d+++ka      + k++d++  aak+l    +g +         g+ +++++ ++++ 
  gi|119720522|ref|YP_921017.1| 137 WGGHYYCVPMGFEM-TWLHVRWDIVQKAgaqnlFPLKSLDDFYVAAKALhnvePGVYgvglplglnGYDTWWTFEHFWGG 215
                                    9************7.8***********888999999******99899997777677777666666654455555444544 PP

                                    HH........ETTEE---H..HHH.HHHHHHHHHHHHTT-EE.....-S..--SSTTTTTSBSEEEE-TTHHHHHH-TTT CS
                      SBP_bac_8 142 la........kdgksldddggkdglkealellkklkdngkty.....dtgadavsefanGevaftingswdiaaaqkagk 208
                                    +          +g+ +d+  ++ +lk+a+e+ +k+   + t+     + +a++++++ +G++a+tin+ +++ a+  +++
  gi|119720522|ref|YP_921017.1| 216 YGgamlanrsVAGVIMDKEPYRSALKKAFEIERKIWVEKLTPpdsdqWVDASNNNAYIQGKIAMTINPASIYYALMTQNP 295
                                    4444444676666666554488888999998888665555555554444578899*********************9999 PP

                                    SEEEE....--S--EEEEEEEEEEBTTS-HHHHHHHHHHHHHT..TSHHHHHHHHHH--..-BS-S-TT CS
                      SBP_bac_8 209 klgai....vpkqgsfaggkglavpknaknedlaAldFlkwlt..spenqaalaektgy..ipvnksaa 269
                                    +l+a     v++ ++  g +++ ++k +k++dl A+d++ +l    +++ + ++e++ +  +p++ks  
  gi|119720522|ref|YP_921017.1| 296 ELAAKtklfVLPISVDCGDESTFIFKTTKYPDL-AKDLVYYLFadKDDYRRGFVEAGALyfLPPFKSQM 363
                                    8887644335688999****************9.********744445888899944444489988754 PP

>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.7   7.9   8.8e-23   7.9e-19       8     312 ..      53     340 ..      49     343 .. 0.81

  Alignments for each domain:
  == domain 1  score: 68.7 bits;  conditional E-value: 8.8e-23
                                    HHHHHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHHHHTTSSSCSEEEECGGHHHHHHHTTSBECCHHHHHHTTECTTC CS
                      SBP_bac_1   8 aalqalvakafekehpgikVeiesvgsgslaqkltlaiaaGdgpaDviavdndwiarlakaglllpldpyvkaylapgvk 87 
                                    +++++ v  ++   +++++Vei++    +   klt+a++aG++p D+++ ++  +a +a++glllpld+++++ ++    
  gi|119720522|ref|YP_921017.1|  53 YWIEKKV-REWAS-KNNVDVEITWYAVADIGKKLTAAVEAGNPP-DIVINGH-PVAIFAEKGLLLPLDDVIEKLNKSD-- 126
                                    5677788.88755.457777777776699999**********66.*****44.3449************999986433.. PP

                                    CTEEEEHHHHTHHHHCE.EE...ES.EEEE.EEEEEEEETTTHHCTTGGG...SHBHHHHHHHHHHHHHHCTCT.HCCHC CS
                      SBP_bac_1  88 daadklsssvlpkilds.kv...ly.vPly.aargliYNkdlfekagldp...pwtWdelveaakklkekgkkp.iggar 157
                                     ++ k         l +  +   +y vP+  + + l ++ d++ kag +     ++ d+++ aak l    ++  ++g+ 
  gi|119720522|ref|YP_921017.1| 127 FYEIK---------LKIcSWgghYYcVPMGfEMTWLHVRWDIVQKAGAQNlfpLKSLDDFYVAAKALHNVEPGVyGVGLP 197
                                    22222.........33455579********999999999*****88866688789*******************9***** PP

                                    CEEHHHHHHHHHHHHHHHHTGGGEECCCT...HHCSHHHHS...HHHHHHHHHHHHHHHHHHHTTEEECSSHHHHHHHHH CS
                      SBP_bac_1 158 ggsasgtayyfalalakslggkvfdkdgg...gldnpegvt...aatylvklyavanltkelkgkgaenkdgaaalalfe 231
                                     g ++ +++++++++++++gg    ++      +d++++      a  ++ +++v   +k  ++++ +++d ++  ++  
  gi|119720522|ref|YP_921017.1| 198 LGLNGYDTWWTFEHFWGGYGGAMLANRSVagvIMDKEPYRSalkKAFEIERKIWV---EKLTPPDSDQWVDASN-NNAYI 273
                                    ********************99888888899977777777754455555555533...3355555555555555.77788 PP

                                    TTSCSEEEEEHHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEEEEEEEEEEBTTCSTHHHHHHHHHHHTSH CS
                      SBP_bac_1 232 aGeaamaivglwaalaamkvapkvafaadkekpkeelgvaplPagkggkpgilgayglaipkgsknpeaAkkFldfllsp 311
                                    +G++am+i+  +  +a m ++p+ a++++   +++ ++               g     i+k++k+p+ Ak+++ +l+++
  gi|119720522|ref|YP_921017.1| 274 QGKIAMTINPASIYYALMTQNPELAAKTKLFVLPISVDC--------------GDESTFIFKTTKYPDLAKDLVYYLFAD 339
                                    9*************9999999999999999999999998..............9999*******************9988 PP

                                    H CS
                      SBP_bac_1 312 e 312
                                    +
  gi|119720522|ref|YP_921017.1| 340 K 340
                                    6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 3054.09
//
Query:       gi|119720523|ref|YP_921018.1|  [L=297]
Description: dihydrodipicolinate synthetase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-53  181.1   0.0    2.1e-53  180.9   0.0    1.0  1  DHDPS     Dihydrodipicolinate synthetase family
  ------ inclusion threshold ------
      0.021   14.5   0.3      0.039   13.7   0.3    1.5  1  UVR       UvrB/uvrC motif
       0.18   11.7   0.2       0.27   11.2   0.2    1.2  1  DeoRC     DeoR C terminal sensor domain


Domain annotation for each model (and alignments):
>> DHDPS  Dihydrodipicolinate synthetase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.9   0.0   3.6e-57   2.1e-53       3     288 ..       7     290 ..       5     291 .. 0.97

  Alignments for each domain:
  == domain 1  score: 180.9 bits;  conditional E-value: 3.6e-57
                                    SEEEEE----B-TTSSB-HHHHHHHHHHHHHCT-SEEEESSCCCTGGGS-HHHHHHHHHHHHHHHTTSSEEEEE---SSH CS
                          DHDPS   3 sgiitalvtpfdedgkldkealrklieflinkgvdglvvaGttGEsatlsteekeqlveiaveaakgripviagvGsnst 82 
                                     gii++l+tpfd++g+l    l+ ++ef  +  v g + +Gt G  +++ t+++++++e ++e+++g+  ++ +vGs  t
  gi|119720523|ref|YP_921018.1|   7 YGIIPPLITPFDTKGNLSVDRLSGIVEFT-KPYVHGYYLCGTYGLGPLMRTDQRKKVAERVAELVGGEKLIVVHVGSADT 85 
                                    69**************************7.788*********************************************** PP

                                    HHHHHHHHCCCCCT-SEEEEE---SS---HHHHHHHHHHHHHCHSS-EEEEE-HHHHSHHHHHHHHHHHHTSTTEEEEEE CS
                          DHDPS  83 seaiklakkaeeaGadgvlavtPYYnkpsqeglyqhfkaiieatdlpvilYnvpsrtgadlspetvkrLaelenivgvKe 162
                                    ++a++lak+a++ Ga++v +v+P+Y++ s   + ++f++ + + + pv  Yn p r g  ++pe   +L e+  ++g+K+
  gi|119720523|ref|YP_921018.1|  86 ETAVELAKHAQDIGAHAVASVPPFYYHHSETHILNFFRELVDSVSIPVYAYNNPPRVGYPITPELALKLKEV-GVAGIKD 164
                                    *****************************************9999************************997.7****** PP

                                    -SS-CTHHHHHHCCCSTTSEEEES-GGGHHHHHHTT-SEEEESCHHCHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                          DHDPS 163 avgdleevikikkevgkdlviysGddelllsalslGadGvisvtsniagermrqlikalkeGdlaeaaelnekllpliki 242
                                     + d+++ i+ k + g+d+ +  G ++l+l++  lGa+  i   sn+a+e++ +l+kal++ d+++aa+++ k++++  +
  gi|119720523|ref|YP_921018.1| 165 SSFDVQAFIDYKVTLGEDFDVVVGTEALMLPTYVLGARAFIPGMSNYAPEIVFKLFKALENRDFENAAKIQYKINKVRRQ 244
                                    ******************************************************************************99 PP

                                    CCCC.SCCHHHHHHHHCTTSSSBB.--TTS--S-HHHHHHHHHHHHH CS
                          DHDPS 243 lfae.pnvilvktalellGlvveatlrkPltpleeeekeeleallka 288
                                    +    p + lv  al+l G++++   rkP++p+ +e +e l++ +++
  gi|119720523|ref|YP_921018.1| 245 VQRLgPTIPLVYLALKLRGVDAGF-PRKPFLPAPHEVQEILKSYIEE 290
                                    9888688888999**********9.*************999988875 PP

>> UVR  UvrB/uvrC motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.3   6.6e-06     0.039       6      36 .]     214     244 ..     209     244 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.6e-06
                            UVR   6 eLeeemeeAaenedFEkAAklRDqinalkkq 36 
                                    e+  ++ +A en dFE AAk+  +in++++q
  gi|119720523|ref|YP_921018.1| 214 EIVFKLFKALENRDFENAAKIQYKINKVRRQ 244
                                    56678999*******************9976 PP

>> DeoRC  DeoR C terminal sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   4.5e-05      0.27       3      42 ..      56      95 ..      54     104 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.5e-05
                          DeoRC  3 aeeKrrIAkaAaeliedgdtifldaGtTtlelaraLaekk 42
                                   +++++++A+++ael+  ++ i++  G+  +e a +La+++
  gi|119720523|ref|YP_921018.1| 56 TDQRKKVAERVAELVGGEKLIVVHVGSADTETAVELAKHA 95
                                   6899*******************************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2006.03
//
Query:       gi|119720524|ref|YP_921019.1|  [L=228]
Description: bacterio-opsin activator [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.3e-21   74.8   0.0    6.8e-21   73.8   0.0    1.6  1  HTH_10        HTH DNA binding domain
     0.0019   17.6   0.1     0.0073   15.8   0.1    2.0  1  Sigma70_r4    Sigma-70, region 4
     0.0029   17.1   1.2      0.012   15.2   0.1    2.7  3  HTH_24        Winged helix-turn-helix DNA-binding
      0.003   17.4   0.0      0.041   13.7   0.0    2.4  2  HTH_5         Bacterial regulatory protein, arsR family
  ------ inclusion threshold ------
      0.017   15.7   1.9      0.064   13.8   0.1    2.5  3  Mga           Mga helix-turn-helix domain
      0.033   13.9   0.4        8.8    6.1   0.2    2.4  2  Sigma70_r4_2  Sigma-70, region 4
      0.039   14.0   0.5       0.18   11.9   0.1    2.2  3  ENT           ENT domain
      0.074   13.0   0.0        7.5    6.6   0.0    2.5  2  HTH_6         Helix-turn-helix domain, rpiR family


Domain annotation for each model (and alignments):
>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.8   0.0     3e-24   6.8e-21       1      53 []     165     217 ..     165     217 .. 0.98

  Alignments for each domain:
  == domain 1  score: 73.8 bits;  conditional E-value: 3e-24
                         HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaesklie 53 
                                    LT+ q+++l +A+ +GYFd+PR+ +l++L++elGIsk+tl eh+r++esk+++
  gi|119720524|ref|YP_921019.1| 165 LTPLQRKILSKAIIKGYFDWPRKYSLSDLSQELGISKATLAEHIRRSESKILK 217
                                    9**************************************************85 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   3.3e-06    0.0073       1      46 [.     161     217 ..     161     219 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.3e-06
                                    HHHHS-HHHHHHHHHHH.......TTT--HHHHHHHHTS-H....HHHHHHHHHHHH CS
                     Sigma70_r4   1 aLasLpererevlelrf.......geglTleEIgerlgiSr....erVrqiekrAlr 46 
                                    +L++L++ +r++l+           ++++l++++++lgiS+    e++r+ e++ l+
  gi|119720524|ref|YP_921019.1| 161 LLSKLTPLQRKILSKAIikgyfdwPRKYSLSDLSQELGISKatlaEHIRRSESKILK 217
                                    599**********999999999999***************74444777877777776 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       2.2     5e+03       7      14 ..      30      37 ..      27      46 .. 0.70
   2 !   15.2   0.1   5.3e-06     0.012      18      40 ..     188     210 ..     165     214 .. 0.85
   3 ?   -1.6   0.0      0.93   2.1e+03       6      14 ..     213     221 ..     210     223 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.2
                         HTH_24  7 kILelLqk 14
                                    +L+++q 
  gi|119720524|ref|YP_921019.1| 30 TVLNIIQS 37
                                   57888885 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 5.3e-06
                         HTH_24  18 isqreLAerlglSpstvnrrlkr 40 
                                     s ++L+++lg+S++t+ ++++r
  gi|119720524|ref|YP_921019.1| 188 YSLSDLSQELGISKATLAEHIRR 210
                                    6889******************8 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.93
                         HTH_24   6 rkILelLqk 14 
                                     kIL++L +
  gi|119720524|ref|YP_921019.1| 213 SKILKYLLE 221
                                    69***9987 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   1.8e-05     0.041      15      37 ..     187     209 ..     177     210 .. 0.92
   2 ?    0.5   0.0      0.25   5.6e+02       5      14 ..     213     222 ..     212     227 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.8e-05
                                    SEEHHHHHHHHTS-HHHHHHHHH CS
                          HTH_5  15 elcvcelaeelglsqstvShHLk 37 
                                    +++ ++l+ elg+s++t+ +H +
  gi|119720524|ref|YP_921019.1| 187 KYSLSDLSQELGISKATLAEHIR 209
                                    6789*****************87 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.25
                                    HHHHHHHTTS CS
                          HTH_5   5 lkILklLaeg 14 
                                    +kILk+L eg
  gi|119720524|ref|YP_921019.1| 213 SKILKYLLEG 222
                                    59*****994 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.2      0.53   1.2e+03       8      44 ..      30      66 ..      26      80 .. 0.77
   2 ?   -2.1   0.0       2.6   5.9e+03      22      36 ..      81      95 ..      62      96 .. 0.73
   3 ?   13.8   0.1   2.9e-05     0.064      29      62 ..     186     219 ..     171     221 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.53
                                   HHHHHHHHSHHHHHHHHHHHHSEEEHHHHHHHCT--H CS
                            Mga  8 llqellkeslkyqllkflfeeeevsieelaqelyiSe 44
                                    + +++++  +y+ l++  ++ ++++++  +e+ + +
  gi|119720524|ref|YP_921019.1| 30 TVLNIIQSGSTYKTLAHATTSGNLKFYQVLEEMKFKN 66
                                   5567788888999999999999999999888886655 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.6
                                   HHHHHHHSEEEHHHH CS
                            Mga 22 lkflfeeeevsieel 36
                                   ++f++e+++++++++
  gi|119720524|ref|YP_921019.1| 81 VTFILERDYCTFYDY 95
                                   567788888887775 PP

  == domain 3  score: 13.8 bits;  conditional E-value: 2.9e-05
                                    SEEEHHHHHHHCT--HHHHHHHHHHHHHHCHCCT CS
                            Mga  29 eevsieelaqelyiSestlkrkikelnklLkefd 62 
                                    ++ s+ +l+qel iS++tl  +i++ +  + ++ 
  gi|119720524|ref|YP_921019.1| 186 RKYSLSDLSQELGISKATLAEHIRRSESKILKYL 219
                                    68899*******************9988887775 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.006        13       6      21 ..     160     175 ..     159     181 .. 0.81
   2 ?    6.1   0.2    0.0039       8.8      27      53 ..     188     214 ..     186     215 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.006
                                    HHHTTS-HHHHHHHHH CS
                   Sigma70_r4_2   6 ealaeLperqreifll 21 
                                    ++l++L++ qr+i+  
  gi|119720524|ref|YP_921019.1| 160 DLLSKLTPLQRKILSK 175
                                    689**********965 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0039
                                    --HHHHHHHHT--HHHHHHHHHHHHHH CS
                   Sigma70_r4_2  27 lsykEIAellgisegtVksrlsRArkk 53 
                                    +s  + +++lgis +t   +++R   k
  gi|119720524|ref|YP_921019.1| 188 YSLSDLSQELGISKATLAEHIRRSESK 214
                                    6778999***************98665 PP

>> ENT  ENT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.6   3.7e+03      28      39 ..      13      24 ..      11      36 .. 0.75
   2 ?   -2.5   0.0       2.4   5.4e+03      37      61 ..     114     138 ..     111     145 .. 0.67
   3 ?   11.9   0.1   7.9e-05      0.18      20      54 ..     177     211 ..     170     216 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.6
                            ENT 28 ekkkllteLrke 39
                                   ++k+ll+eL ++
  gi|119720524|ref|YP_921019.1| 13 PQKSLLSELTNL 24
                                   679999999865 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.4
                            ENT  37 rkeLsIsterHraelrrvksDerlk 61 
                                    rk + Is+e+   +l+r k+  +++
  gi|119720524|ref|YP_921019.1| 114 RKFFIISEEEPSILLDRLKKYGTVT 138
                                    5677788888777777776655555 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 7.9e-05
                            ENT  20 raqgdLseekkkllteLrkeLsIsterHraelrrv 54 
                                     ++g + +++k  l++L++eL Is+ + ++ +rr 
  gi|119720524|ref|YP_921019.1| 177 IIKGYFDWPRKYSLSDLSQELGISKATLAEHIRRS 211
                                    5678899***********************99995 PP

>> HTH_6  Helix-turn-helix domain, rpiR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0033       7.5      12      51 ..     163     204 ..     157     206 .. 0.79
   2 ?    4.3   0.0     0.018        40      12      28 ..     206     222 ..     204     228 .] 0.83

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0033
                                    ----HHHHHHHH..HHHH-S---TT--HHHHHHHTT--HHHH CS
                          HTH_6  12 ekltksekkiae..yilaspdkaielsikalAkaaavSeati 51 
                                    +klt+  +ki+   +i+   d  ++ s+++l++++++S+at+
  gi|119720524|ref|YP_921019.1| 163 SKLTPLQRKILSkaIIKGYFDWPRKYSLSDLSQELGISKATL 204
                                    67777777776433677777888899**************97 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.018
                                    ----HHHHHHHHHHHH- CS
                          HTH_6  12 ekltksekkiaeyilas 28 
                                    e++  se+ki++y+l+ 
  gi|119720524|ref|YP_921019.1| 206 EHIRRSESKILKYLLEG 222
                                    67889*********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 1378.96
//
Query:       gi|119720525|ref|YP_921020.1|  [L=499]
Description: carbohydrate kinase, FGGY [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.9e-50  171.1   0.0    4.9e-50  170.4   0.0    1.3  1  FGGY_N        FGGY family of carbohydrate kinases, N-terminal
    1.1e-30  106.8   0.0    1.6e-30  106.3   0.0    1.2  1  FGGY_C        FGGY family of carbohydrate kinases, C-terminal
     0.0054   16.7   0.0     0.0095   15.9   0.0    1.3  1  Hexokinase_1  Hexokinase
  ------ inclusion threshold ------
      0.077   12.7   0.1       0.15   11.7   0.1    1.4  1  Raco_middle   RACo middle region


Domain annotation for each model (and alignments):
>> FGGY_N  FGGY family of carbohydrate kinases, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.4   0.0   1.1e-53   4.9e-50       2     245 .]       3     244 ..       2     244 .. 0.98

  Alignments for each domain:
  == domain 1  score: 170.4 bits;  conditional E-value: 1.1e-53
                                    EEEEEEESSEEEEEEEETTS-EEEEEEEE--EB-SSTT--EE-HHHHHHHHHHHHHHHHHHCT.-GCCEEEEEEEE-SS- CS
                         FGGY_N   2 ilglDcGttstkaivldekgkvvasaqaelelsspkegwaeqdpeeiwqalaeairkvleqagisekqikaIgisgqreg 81 
                                    il++D+Gt+ +k +++d ++ v +  ++e+++ +p+++ ae+dpe ++  + e ++++l++a    +++  +  sg   g
  gi|119720525|ref|YP_921020.1|   3 ILAVDVGTSTLKSALVDLEKGVTGFVRKEIPILRPEPEAAEHDPETLFRMVLENLKETLAKA--GVSEVDCLVLSGYLFG 80 
                                    799**************9999*****************************************..567899999******* PP

                                    EEEEETTTEESSEEE-TT--TTHHHHHHHHHTTCHCCHHHHHSS-SSTTSHHHHHHHHHHHSCCHHCCHCEEEEHHHHHH CS
                         FGGY_N  82 lvllDkndkpLynailwkdrrtaeiveklkeegnekklyektglvlstgftlsklkWlkenepevfekiekflliddyLi 161
                                    + +lD +++pL+n+++w drr+  + + l + +n+  +y +tg +   +++l k+ Wlk+  ++++++++ fl  + yL 
  gi|119720525|ref|YP_921020.1|  81 VLALDSKGEPLTNVLTWLDRRATRTLRTLFQVLNPVDVYRRTGCPPLFIYPLAKIFWLKTARENTYRATKRFLDAKGYLL 160
                                    ******************************************************************************** PP

                                    HHHCT--EEEHHHHCTTTSEETTTTEE-HHHHHHTT--GGGS-EEE-TCCEEEEEECCCCCCTT.S-EEEEEEEEEHHHH CS
                         FGGY_N 162 wrLtgqfvtdvtnasesmlfnikklewdeellailgipeelLPklvesseiigelkpelaaklGlkegvpvvggggDqqa 241
                                     rLtg+ v +v+ as+s+l+n++ ++wd+e+++++g++ ++LP+lve+  i+g +  ++a  +Glk  vpvv+g +D +a
  gi|119720525|ref|YP_921020.1| 161 LRLTGEEVMEVSSASGSQLLNLERKDWDHEIIHSAGLDLDKLPQLVEPDTIVGDVPVSIARSIGLKSPVPVVAGVFDGAA 240
                                    ******************************************************************************99 PP

                                    HHHH CS
                         FGGY_N 242 aalG 245
                                      lG
  gi|119720525|ref|YP_921020.1| 241 VSLG 244
                                    8776 PP

>> FGGY_C  FGGY family of carbohydrate kinases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.3   0.0   3.6e-34   1.6e-30       7     197 ..     259     450 ..     253     451 .. 0.87

  Alignments for each domain:
  == domain 1  score: 106.3 bits;  conditional E-value: 3.6e-34
                         FGGY_C   7 Tssflllvgtkpv..isehglltpvagedgkpeyalegsiavagslvawlldnl.glreeirdagev..eeslaelaaae 81 
                                    Ts++l + ++ pv   s ++  ++++    +++++  g+++    ++ w++dn  +l + ++++  v  +e+l+ ++aa 
  gi|119720525|ref|YP_921020.1| 259 TSTMLRVASRIPVidSSPKMRFQTYY--SLRGYWLPGGAVNSGAVVLRWFRDNFaQLERLVAQELGVseYELLD-NEAAL 335
                                    88888889999999888899999999..67888888888888888888*****854444444444448555555.78888 PP

                         FGGY_C  82 avadaggvvfvpafsglrapywdpdargtitglsssttlahiarAaleavalqlrailealekdsgkpldrlavdGGgsk 161
                                    + + ++gvvf+p+ sg+r p   ++a+g+i gl++ +t  ++ rA++e+va+ l  + eal +  g  +++++++GGg++
  gi|119720525|ref|YP_921020.1| 336 SPPGSNGVVFLPYISGERFPEFGNNASGVIYGLREWHTRKDVLRAIMEGVAFNLNLVNEALREN-GLSFREVRITGGGAN 414
                                    89999********************************************************988.*************** PP

                         FGGY_C 162 ndllmqllAdilgvpVerpktaeatalGaAilAava 197
                                    ++l++q+lAd+lgvp++ +   +a++lG   +A +a
  gi|119720525|ref|YP_921020.1| 415 SRLWLQILADVLGVPIKAFTKGDAALLGSSFVAKIA 450
                                    ****************************98887665 PP

>> Hexokinase_1  Hexokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   2.1e-06    0.0095      57     119 ..       3      67 ..       2      74 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.1e-06
                                    EEEEEESSSEEEEEEEEEESSS-EEEEEEE..EE--GGGGGSBHHHHHHHHHHHHHHHHHHH... CS
                   Hexokinase_1  57 ylAlDlGgtnlRvllveLlgeskveitqek..ykipeelktgtaeeLFdfiakciaefleeegee 119
                                    +lA+D+G ++l+ +lv+L++  +  +++e    + + e  +++ e+LF ++ ++++e l++ g +
  gi|119720525|ref|YP_921020.1|   3 ILAVDVGTSTLKSALVDLEKGVTGFVRKEIpiLRPEPEAAEHDPETLFRMVLENLKETLAKAGVS 67 
                                    79****************964433333333446888889999*****************998766 PP

>> Raco_middle  RACo middle region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   3.4e-05      0.15       3      23 ..       4      24 ..       3      31 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.4e-05
                    Raco_middle  3 lavDiGtTtvvaaLvdletgk 23
                                   lavD+Gt+t+  aLvdle+g 
  gi|119720525|ref|YP_921020.1|  4 LAVDVGTSTLKSALVDLEKGV 24
                                   79****************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (499 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 3256.54
//
Query:       gi|119720526|ref|YP_921021.1|  [L=338]
Description: D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-65  218.5   0.0    6.1e-65  217.9   0.0    1.3  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
    1.4e-23   83.0   0.1    1.9e-23   82.6   0.1    1.2  1  2-Hacid_dh       D-isomer specific 2-hydroxyacid dehydrogenas
    5.6e-05   23.3   0.5    0.00027   21.0   0.3    2.0  2  AdoHcyase_NAD    S-adenosyl-L-homocysteine hydrolase, NAD bin
    0.00015   22.0   0.2    0.00034   20.8   0.1    1.6  2  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
     0.0093   15.5   0.1       0.02   14.4   0.0    1.6  2  IlvN             Acetohydroxy acid isomeroreductase, NADPH-bi
     0.0097   16.3   0.1       0.17   12.3   0.0    2.3  2  NAD_binding_7    Putative NAD(P)-binding
  ------ inclusion threshold ------
      0.016   15.8   0.1       0.11   13.1   0.0    2.4  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
      0.053   13.6   0.1       0.18   11.8   0.0    1.9  2  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
       0.17   12.1   0.9        1.6    9.0   0.2    2.7  3  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma


Domain annotation for each model (and alignments):
>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  217.9   0.0   3.1e-68   6.1e-65       1     178 []     114     291 ..     114     291 .. 0.98

  Alignments for each domain:
  == domain 1  score: 217.9 bits;  conditional E-value: 3.1e-68
                                    HHHHHHHHTTHHHHHHHHHTTCCHTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHH.HTT-EEEEESSSHHHHHCHHHHT CS
                   2-Hacid_dh_C   1 lalllallrrlaeadeevregewksekallgkelsgktvGiiGlGrIGqavakrlk.afgmkviaydrskkkeeeeeelg 79 
                                    +al+l+++r++ +a + vreg+w ++ ++ g ++sgktvGiiGlG+IG++va++++ +f++kv+ayd++  k+  +++ g
  gi|119720526|ref|YP_921021.1| 114 VALCLNVARKVCQAATLVREGKWAERGKIVGVNISGKTVGIIGLGNIGSRVAEIFSrGFNAKVVAYDPFVGKDY-AARFG 192
                                    689****************************************************99************99776.9999* PP

                                    CEECSHHHHHHH-SEEEE-S--STTTTTSBSHHHHHCSTTTEEEEESS-GGGB-HHHHHHHHHTTSCCEEEES--SSSSS CS
                   2-Hacid_dh_C  80 velvsleellaesDivslhlpltpetrhlinaeelakmkkgailiNtaRGglvdeeaLleaLksgkiagaalDvfeeepl 159
                                    +elv+l++ll+esDi+ lh+plt+et+h+i+++e++kmkkg+i++NtaRG+l+d++aL++ L+sgkiag++lDv+e ep+
  gi|119720526|ref|YP_921021.1| 193 AELVDLDTLLRESDIILLHAPLTKETYHMIGEKEIDKMKKGVIVVNTARGELIDTNALIKGLESGKIAGVGLDVVEGEPI 272
                                    ******************************************************************************** PP

                                    GTCHHHHHSTTEEE-SS-T CS
                   2-Hacid_dh_C 160 pedspllelpnviltPHia 178
                                     +d+pll+  nv++tPHi+
  gi|119720526|ref|YP_921021.1| 273 GADHPLLKYRNVVITPHIG 291
                                    *****************98 PP

>> 2-Hacid_dh  D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.6   0.1   9.5e-27   1.9e-23       7     130 ..      15     319 ..       5     324 .. 0.95

  Alignments for each domain:
  == domain 1  score: 82.6 bits;  conditional E-value: 9.5e-27
                                    .CHHHHHHHHHTTE.EEEEES...CSSHHHCHHHHTTESEEEE-TTS-BSHHHHHHHTT--EEEESSSSCTTB-HHHHHH CS
                                    xxxxxxxxxxxxxx.xxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     2-Hacid_dh   7 lreeelellkeegv.evevkd...ellteellekakdadalivrsntkvtaevlealpkLkviaragvGvDnvDldaake 82 
                                    + ++ l+ l+e  v ++++ d   +l  + l+ek+++++++i  ++  +++e++e+  +L +iar+g+G+DnvD+daa+e
  gi|119720526|ref|YP_921021.1|  15 IAPDVLQKLQE--VaQIDFIDvekTLRGKALAEKLEGYHFIIASVTPLYDREFFENNRSLLLIARHGIGYDNVDVDAATE 92 
                                    46677777788..5566666666599999*************************************************** PP

                                    TT-EEEE-TTTTH.HHHHHHH........................................................... CS
                                    xxxxxxxxxxxxx.xxxxxxx........................................................... RF
                     2-Hacid_dh  83 rGilVtnvpgyst.esvAElt........................................................... 102
                                    +G++Vt+vpg+   ++vAEl+                                                           
  gi|119720526|ref|YP_921021.1|  93 QGVIVTRVPGSRErDAVAELAvalclnvarkvcqaatlvregkwaergkivgvnisgktvgiiglgnigsrvaeifsrgf 172
                                    **********875268**************************************************************** PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                     2-Hacid_dh 103 ................................................................................ 102
                                                                                                                    
  gi|119720526|ref|YP_921021.1| 173 nakvvaydpfvgkdyaarfgaelvdldtllresdiillhapltketyhmigekeidkmkkgvivvntargelidtnalik 252
                                    ******************************************************************************** PP

                                    .......................................T-BHHHHHHHHHHHHHHHHHHHTTCCGT CS
                                    .......................................xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     2-Hacid_dh 103 .......................................aaTeeaqeniaeeaaenlvaflkgespa 130
                                                                           a+T e ++ + e  a++++++++ge p 
  gi|119720526|ref|YP_921021.1| 253 glesgkiagvgldvvegepigadhpllkyrnvvitphigANTYEGLRGMDEANADAILKVIRGEAPL 319
                                    ***************************************************************8775 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.47   9.4e+02     120     151 ..      46      77 ..       4      91 .. 0.74
   2 !   21.0   0.3   1.4e-07   0.00027      19     111 ..     145     241 ..     138     261 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.47
                                    HHHTTT-EEEEEETTEEEEE-TTS-EEEEEGG CS
                  AdoHcyase_NAD 120 aleanalkkeevkpqvdrvtlkdgkkiillae 151
                                    +le +   + +v p +dr  ++++++++l+a+
  gi|119720526|ref|YP_921021.1|  46 KLEGYHFIIASVTPLYDREFFENNRSLLLIAR 77 
                                    45555666778899999999999999999885 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 1.4e-07
                                    S--TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHHH.HHCTT-EE--HHHCTTT-SEEEE....-SSSSSSB- CS
                  AdoHcyase_NAD  19 vllaGkvavvaGyGdvGkGcaaslkglGarvivtevdPicalq.aameGfevvtleevvkkadivvt....ttGnkdiit 93 
                                    v ++Gk++ ++G G++G   a+ + + G    v   dP      aa  G e+v l+++++++di++     t  +  +i 
  gi|119720526|ref|YP_921021.1| 145 VNISGKTVGIIGLGNIGSRVAEIF-SRGFNAKVVAYDPFVGKDyAARFGAELVDLDTLLRESDIILLhaplTKETYHMIG 223
                                    679***************999865.56777777889**8876438899****************98522224567789** PP

                                    HHHHCCS-TTEEEEE-SS CS
                  AdoHcyase_NAD  94 lehlkkmkddaivcniGh 111
                                     ++++kmk+ +iv n   
  gi|119720526|ref|YP_921021.1| 224 EKEIDKMKKGVIVVNTAR 241
                                    **************9865 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       2.8   5.5e+03      51      75 ..      88     112 ..      67     131 .. 0.67
   2 !   20.8   0.1   1.7e-07   0.00034       1     120 [.     151     270 ..     151     279 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.8
                                    HHHHHCSEEEE-SSSHHHHHHHHHS CS
                  NAD_binding_2  51 elvasldvvitmvkagkavdevieg 75 
                                    +++++  v++t v+ +++ d+v e 
  gi|119720526|ref|YP_921021.1|  88 DAATEQGVIVTRVPGSRERDAVAEL 112
                                    5666667777777777766666654 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 1.7e-07
                                    EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHS.HCCC CS
                  NAD_binding_2   1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdevieg.llea 79 
                                    ++g+iGlG++Gs  a+ + ++g++  v+  ++   ++ +a+    + ++  l+++ d++++  + +k++ ++i +  +++
  gi|119720526|ref|YP_921021.1| 151 TVGIIGLGNIGSRVAE-IFSRGFNAKVVAYDPFVGKDYAARFGAELVDLDTLLRESDIILLHAPLTKETYHMIGEkEIDK 229
                                    58***********986.6778888888888888999999998778889999**********************99899** PP

                                    --TT-EEEE-S---HHHHHHHHHHHHHTT-EEEEEEEESHH CS
                  NAD_binding_2  80 lkkgdilidgstsspedtrelakelkekglkfldaPVSGGe 120
                                    +kkg i+++++  +  dt+ l k l++ ++  ++  V  Ge
  gi|119720526|ref|YP_921021.1| 230 MKKGVIVVNTARGELIDTNALIKGLESGKIAGVGLDVVEGE 270
                                    **************************999999988876665 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       3.4   6.7e+03     107     122 ..      88     103 ..      74     119 .. 0.51
   2 !   14.4   0.0     1e-05      0.02       2      91 ..     147     236 ..     146     252 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 3.4
                                    -TTSEEEEEEESS-SH CS
                           IlvN 107 pkdvdvvlvAPkgpGh 122
                                     +  +  ++  + pG+
  gi|119720526|ref|YP_921021.1|  88 DAATEQGVIVTRVPGS 103
                                    3333333333333333 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 1e-05
                                    HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-..HHHHHHHHHH CS
                           IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliP..Delqkevyee 79 
                                    ++gk++ +iG G+ G   a+ +   g++  v  ++     + A + g e ++++ + +++d++++ +P   e+ + + e+
  gi|119720526|ref|YP_921021.1| 147 ISGKTVGIIGLGNIGSRVAEIF-SRGFNAKVVAYDPFVGKDYAARFGAELVDLDTLLRESDIILLHAPltKETYHMIGEK 225
                                    789*************999877.689***9999999999***************************99323444556666 PP

                                    HTGGG--TT-EE CS
                           IlvN  80 eiepnlkegkal 91 
                                    ei +++k+g ++
  gi|119720526|ref|YP_921021.1| 226 EI-DKMKKGVIV 236
                                    66.566776644 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0       0.2     4e+02      35      69 ..      14      57 ..       5      77 .. 0.68
   2 !   12.3   0.0   8.5e-05      0.17       3      50 ..     145     198 ..     143     248 .. 0.58

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.2
                  NAD_binding_7 35 vvapevkeeleelvk.........laeeelekdlegadlviaat 69
                                   v+ap+v ++l+e  +         l+ + l ++leg++++ia +
  gi|119720526|ref|YP_921021.1| 14 VIAPDVLQKLQEVAQidfidvektLRGKALAEKLEGYHFIIASV 57
                                   89999755555333311211222234455677799999999865 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 8.5e-05
                  NAD_binding_7   3 ldlkgkkvlvvGgGevAarkvrklle.agakvtvvapev..keele.....elvkl 50 
                                    ++++gk+v ++G G+++ r ++ + + ++akv+ ++p v            elv+l
  gi|119720526|ref|YP_921021.1| 145 VNISGKTVGIIGLGNIGSRVAEIFSRgFNAKVVAYDPFVgkD--YAarfgaELVDL 198
                                    6899*************9888877776667777777776431..223344433332 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.78   1.5e+03      56      81 ..      87     112 ..      38     129 .. 0.74
   2 ?   13.1   0.0   5.5e-05      0.11       1      94 [.     151     239 ..     151     242 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.78
                                    HHHHHH-SEEEE-S-HHHHHHHHHHC CS
                  F420_oxidored  56 eeaaeeadvvvlavkpedveevlsel 81 
                                     +aa+e+ v+v  v+ +   ++++el
  gi|119720526|ref|YP_921021.1|  87 VDAATEQGVIVTRVPGSRERDAVAEL 112
                                    56777777777777777666666666 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 5.5e-05
                                    EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHH..HHHHH CS
                  F420_oxidored   1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkped..veevl 78 
                                    ++giiG Gn+g+ +a+ + ++g+ + ++v     +p   +  a+++g  ++ vd  ++++e+d+++l  + ++  ++ + 
  gi|119720526|ref|YP_921021.1| 151 TVGIIGLGNIGSRVAE-IFSRGF-NAKVV---AYDPFVGKDYAARFG--AELVDLDTLLRESDIILLHAPLTKetYHMIG 223
                                    59**************.666672.34444...578888899999998..66666999999*****998887541133333 PP

                                    HHCGHHHHTTSEEEEE CS
                  F420_oxidored  79 selakdalkgklvisv 94 
                                    ++  ++ +kg +v+ +
  gi|119720526|ref|YP_921021.1| 224 EKEIDKMKKGVIVVNT 239
                                    3335666667777665 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       2.7   5.3e+03      48      61 ..      39      52 ..      17      61 .. 0.65
   2 ?   11.8   0.0   9.2e-05      0.18       7      81 ..     143     210 ..     138     240 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.7
                                   HHHHHHHHHT.ET- CS
                   Shikimate_DH 48 rakelaeelkgeei 61
                                   r k+lae+l+g+++
  gi|119720526|ref|YP_921021.1| 39 RGKALAEKLEGYHF 52
                                   55666666666544 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 9.2e-05
                                    HS...TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE CS
                   Shikimate_DH   7 le.slkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvis 81 
                                    ++ ++++k+v +iG G+++++va+ +++  ++   v+  +    k+ a ++++e      l +l++ll+e+d+++ 
  gi|119720526|ref|YP_921021.1| 143 VGvNISGKTVGIIGLGNIGSRVAEIFSRG-FN-AKVVAYDPFVGKDYAARFGAE------LVDLDTLLRESDIILL 210
                                    4558999*****************99865.44.346667788889999999666......8899999999999875 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.36   7.3e+02       8      56 ..      14      59 ..      12      68 .. 0.66
   2 ?   -1.5   0.0       1.5   2.9e+03      45      60 ..      78      93 ..      40     132 .. 0.54
   3 ?    9.0   0.2   0.00078       1.6       1      31 [.     152     180 ..     152     241 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.36
                                   HHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--T CS
                Sacchrp_dh_NADP  8 svGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialda 56
                                    ++  v+++l++  ++  +++ +++++++ +ala+k+ g  f+++++++
  gi|119720526|ref|YP_921021.1| 14 VIAPDVLQKLQEVAQI--DFIDVEKTLRG-KALAEKLEGYHFIIASVTP 59
                                   4555555555555555..55555666665.7888888999999999986 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.5
                                   TTTCEEEEE--TTTHH CS
                Sacchrp_dh_NADP 45 lgvrfeaialdaenye 60
                                   +g+  +++ +da+ ++
  gi|119720526|ref|YP_921021.1| 78 HGIGYDNVDVDAATEQ 93
                                   3334444444444444 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.00078
                                    EEEE--SHHHHHHHHHHHCTCCT-GEEEEEE CS
                Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvad 31 
                                    v iiG G++G+ vae  +r f+   +++  d
  gi|119720526|ref|YP_921021.1| 152 VGIIGLGNIGSRVAEIFSRGFNA--KVVAYD 180
                                    689****************9998..677665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 2108.33
//
Query:       gi|119720527|ref|YP_921022.1|  [L=253]
Description: 2-dehydro-3-deoxyglucarate aldolase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.2e-39  134.8   0.0    2.8e-39  134.5   0.0    1.1  1  HpcH_HpaI  HpcH/HpaI aldolase/citrate lyase family
  ------ inclusion threshold ------
       0.08   11.8   0.0       0.12   11.3   0.0    1.2  1  PK         Pyruvate kinase, barrel domain


Domain annotation for each model (and alignments):
>> HpcH_HpaI  HpcH/HpaI aldolase/citrate lyase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.5   0.0   3.2e-43   2.8e-39       3     217 ..      17     234 ..      15     237 .. 0.91

  Alignments for each domain:
  == domain 1  score: 134.5 bits;  conditional E-value: 3.2e-43
                                    EEEEESTSHHHHHHHCTC--SEEEEESSTSSSHHHHHHHHHHHHHHHHHHHHCTTTSSEEEEE-SSTTHHHHHHHGGHHH CS
                      HpcH_HpaI   3 glflpganaalaekaaiagaDsvliDlEdavalaeKdaARvlvsealkqldalaaaasevvVRvnsldselikqdlevld 82 
                                    g ++   n+++ e +++ g+D++l+D+E+a+          + + +   l a++   +++ VRv+ +d++++k+   vld
  gi|119720527|ref|YP_921022.1|  17 GAWVTIGNPEVPEMLSLLGFDWLLFDMEHAP---------LDFQLLEYMLIAVK-NDATPLVRVPFNDPVYVKR---VLD 83 
                                    6799999************************.........66666655566654.4479***************...*** PP

                                    TTSSEEEESS--SHHHHHHHHHHTSHTTTS---..................HCCC-EEEEEE-SHHHHHTHHHHHTSTTE CS
                      HpcH_HpaI  83 lgaqvvlvPkvetaeealevvsalrepekgirg..................anketrllaqiEsaegvknaeeIaavegl 144
                                    lg+ ++l+P v++ e+a+ +v+ +++p++girg                  +++++ +++qiE++e+vkn+eeI++++g+
  gi|119720527|ref|YP_921022.1|  84 LGVAGILFPLVNKSEDAKLAVASTKYPPRGIRGvgprraasyglrtneyfeEAGKVLVVVQIETQEAVKNIEEILSTDGV 163
                                    ******************************************************************************** PP

                                    EEEEE-HHHHHHHTT-TTSTTSHHHHHHHHHHHHTTHCEEEEEEE.E-SSHHHHHHHHHTTHCEEEEEEHHHH CS
                      HpcH_HpaI 145 dgvflGaeDlsadlgtkrspegtevldareriltaaraagiaaldtvasdiddaegflaegalfvalGfdgkl 217
                                    d+ f+G++Dls + g+++  +++ v  a+er++ a+r  g+   ++  sd +  e  l  g   +alG+d   
  gi|119720527|ref|YP_921022.1| 164 DAFFIGPNDLSFSFGYRS-WKEEAVRRAIERVADASRSLGV-PGGMYCSDDESLEFALSLGFSLIALGSDYRF 234
                                    ***************865.88899*****************.666677777788888999********99765 PP

>> PK  Pyruvate kinase, barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   1.3e-05      0.12     214     243 ..     135     163 ..     120     183 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.3e-05
                                    CCTTSEEEEEE-SCHHHHTHHHHHHHSSEE CS
                             PK 214 egkeikiiakienqegvenldeileasDgi 243
                                    e+ ++ ++ +ie qe+v+n++eil + Dg+
  gi|119720527|ref|YP_921022.1| 135 EAGKVLVVVQIETQEAVKNIEEILST-DGV 163
                                    445688999**************974.443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1607.38
//
Query:       gi|119720528|ref|YP_921023.1|  [L=243]
Description: hypothetical protein Tpen_1625 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      9e-08   32.1   0.0    1.1e-07   31.8   0.0    1.3  1  SBP_bac_11  Bacterial extracellular solute-binding protein


Domain annotation for each model (and alignments):
>> SBP_bac_11  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.0   6.4e-12   1.1e-07      97     229 ..     113     237 ..      44     238 .. 0.83

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 6.4e-12
                                    HHHHH.SS--EEEE--T-TTTTHH.HHHHGGG.--HHHHHHHHHTEEEEESSH..HHHHHHHHTTT-SEEEEEHHHHH.. CS
                     SBP_bac_11  97 adLlk.pglklavadPttspsGlaalalleaa.gaqellkalekkvvklgess..rqlltaveageadagivyeseakaa 172
                                    +dL +  + ++a+++P t++ G     ++  a g  ++l+ + k+ v l+  +  r +++ ++ g +dag+ + +ea   
  gi|119720528|ref|YP_921023.1| 113 EDLCDiRNRRVAIPNPVTEGIGALLRDMYSEAcG--DYLELITKGSVYLTR-IhhREIPELMRHGVVDAGVMWVTEAR-- 187
                                    4444434669****************99997746..677777777775544.34799*********************.. PP

                                    HSTTSSEEEE--TTT--...EEEEEEEE-TT--HHHHHHHHHTTSHHHHHHHHHTT- CS
                     SBP_bac_11 173 engdkleavylpeglnldpldypaavlkkaakreaAraFlafLrspeaqailrkyGf 229
                                        +l++++++ g     l++++  ++++     Ar + + Lrs+++++i +kyGf
  gi|119720528|ref|YP_921023.1| 188 --YWGLPYFAPSTGRRG-KLVFALLPWATD----KARQLFRQLRSQKVKEIYEKYGF 237
                                    ..89************8.899999999987....7999999**************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1615.92
//
Query:       gi|119720529|ref|YP_921024.1|  [L=110]
Description: hypothetical protein Tpen_1626 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.6e-10   38.9   0.0    1.1e-09   38.7   0.0    1.2  1  DrsE      DsrE/DsrF-like family
     0.0067   16.5   0.0     0.0092   16.1   0.0    1.1  1  DsrH      DsrH like protein
  ------ inclusion threshold ------
      0.026   14.4   0.0      0.029   14.3   0.0    1.2  1  DrsE_2    DsrE/DsrF/DrsH-like family


Domain annotation for each model (and alignments):
>> DrsE  DsrE/DsrF-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.7   0.0   1.8e-13   1.1e-09      33     115 ..      33     108 ..       7     110 .] 0.87

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 1.8e-13
                                    EEEEEE-GGGGGGGBS---TGGGTS---GGGGGGCGGGT-EEEEEHHHHHHTT--GGGE-.T--EEEE-HHHHHHHHHH- CS
                           DrsE  33 evsvffygdGvllllkgqtanpadeknlaellkalkeygvklyvCgqaakargldededl.gvgvevsglgelaelqneg 111
                                     v+++f++ ++++l+k        +k + + ++ ++e gv + +C++++  rg+ +++++ gv+v+ sg++e++++ +eg
  gi|119720529|ref|YP_921024.1|  33 VVEIVFHQTAINALVK--------GKGFDDEIRGFVERGVVIAACRNSMRDRGIRSEDLVdGVTVVNSGVAEIVKKESEG 104
                                    467*************........356999*************************77655889****************9 PP

                                    SEEE CS
                           DrsE 112 drvi 115
                                    + ++
  gi|119720529|ref|YP_921024.1| 105 WLYL 108
                                    9777 PP

>> DsrH  DsrH like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   1.5e-06    0.0092       8      73 ..      18      91 ..      14     102 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.5e-06
                                   -HHHHHHT--TT-....EEEE-GGGGGGGBTTBTTHHHHHTS...SSEEEEEHHHHHHTT-T.TSB-TTSEEE- CS
                           DsrH  8 alksclrllqegD....avlLieDgVyaalkgsrllkalkea...svklyaLkeDleARGlt.eqlsegvkvid 73
                                   alksc +ll+e      ++++ + +++a++kg+ +  +++     +v + a ++ +  RG+  e+l +gv+v++
  gi|119720529|ref|YP_921024.1| 18 ALKSCRNLLSEVPdavvEIVFHQTAINALVKGKGFDDEIRGFverGVVIAACRNSMRDRGIRsEDLVDGVTVVN 91
                                   6888888886653477789***********************999999**************999********8 PP

>> DrsE_2  DsrE/DsrF/DrsH-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   4.9e-06     0.029     105     145 ..      59     101 ..      20     108 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.9e-06
                                    HHHTT-EEEEEHHHHHHHT--GGGB-TT-..EEE-HHHHHHHH CS
                         DrsE_2 105 akeagvklvaCqmtmdlmglkkeelidgv..eiagaatylkea 145
                                      e+gv + aC+ +m   g++ e+l+dgv     g+a+ +k+ 
  gi|119720529|ref|YP_921024.1|  59 FVERGVVIAACRNSMRDRGIRSEDLVDGVtvVNSGVAEIVKKE 101
                                    5789*************************43345777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.36u 0.28s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 788.67
//
Query:       gi|119720530|ref|YP_921025.1|  [L=204]
Description: hypothetical protein Tpen_1627 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.1e-09   37.5   0.0      3e-09   37.0   0.0    1.3  1  Protoglobin  Protoglobin


Domain annotation for each model (and alignments):
>> Protoglobin  Protoglobin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   0.0   1.7e-13     3e-09       9     123 ..      24     139 ..      17     161 .. 0.92

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 1.7e-13
                                    HHHTT-SHHHHHHHHHHHHHHHHCHHHHHHHHHHHHCTSHHHHHHHCH.HCHHHHHHHHHHHHHHHCCCSSCCHHHHHHH CS
                    Protoglobin   9 lsflglteedlaaLralapliealipavvdafYekllsfpetarifet.ssqierlkdflksyllklfsgpfdsayveyl 87 
                                    ++ +g++e+d+++Lr+ +  ++ali+ vv+ f  ++ + +e ar +++   ++e+l++f ks+l  +f+g++d+a   +l
  gi|119720530|ref|YP_921025.1|  24 RKVVGISEADIELLRSSWSDANALIDGVVEGFLGRVYEDEEVARLIKEgALSLEELREFCKSHLILVFNGNYDRAHGLWL 103
                                    6899*******************************************9888***************************** PP

                                    HHHHHHHCHCT--HHHHHHCHHHHHHHHHHHHCCCS CS
                    Protoglobin  88 dkvGkmhtrlgleprwyiaalglvqevllealleke 123
                                      vG +    g+++r  + +lg+ ++ ll+   +  
  gi|119720530|ref|YP_921025.1| 104 FWVGLRNLSRGVPVRLDMEFLGFALSELLTRFDDRV 139
                                    *************************99998777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1403.14
//
Query:       gi|119720531|ref|YP_921026.1|  [L=1032]
Description: glycoside hydrolase family protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.2e-70  235.3   0.0    1.3e-69  234.8   0.0    1.1  1  Glyco_hydro_38N  Glycosyl hydrolases family 38 N-terminal dom
    2.4e-27   96.4   0.0    6.6e-27   95.0   0.0    1.7  2  Glyco_hydro_38C  Glycosyl hydrolases family 38 C-terminal dom
    1.2e-21   76.6   0.2    3.5e-21   75.1   0.2    1.7  2  Alpha-mann_mid   Alpha mannosidase middle domain
    2.1e-06   27.8   0.0    5.1e-06   26.5   0.0    1.7  1  Glyco_hydro38C2  Glycosyl hydrolases family 38 C-terminal bet


Domain annotation for each model (and alignments):
>> Glyco_hydro_38N  Glycosyl hydrolases family 38 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  234.8   0.0   2.9e-73   1.3e-69       2     288 ..     259     515 ..     258     521 .. 0.96

  Alignments for each domain:
  == domain 1  score: 234.8 bits;  conditional E-value: 2.9e-73
                                    EEEEEEEE--SSSSS-HHHHHCCTCHHHHHHHHHHHHHSTT--EEES-CHHHHHHHCCS-CCCHHHHHHHHHCTSEEECT CS
                Glyco_hydro_38N   2 vhvvpHsHiDvgWlktvdeyqrrkvqrilssvlellerdpdrkFilseaslferwweeapeekkelvkklvaegrlevvg 81 
                                    +++v+HsHiD +Wl++v+e+ r+kv+r++ +v++ll+++    +++s+a ++e+++e++pe+++e+ k+lv++gr+++vg
  gi|119720531|ref|YP_921026.1| 259 LFIVGHSHIDAAWLWPVQET-REKVARTFANVVSLLREYGGPVYAQSSALYYEWVEEDYPELFREI-KRLVESGRWIPVG 336
                                    689*****************.*********************************************.************* PP

                                    T-SS-B-SSSS-HHHHHHHHHCCCHHHHCCH--EESEEEESSSSSB-TCHHHHHHCTT--EEEESSS-HHCHCCHHHTT- CS
                Glyco_hydro_38N  82 GgwvenDealpsgeslirqlleGqrflkeefgvrpkvaWliDpFGysatlPqllkkaGidsfltqrlsyndknkfaeqkh 161
                                    G+wve+D  l+ gesl+rq+l+Gqr+++++fg + +++W +D+FG+  +lPqll k+G++ f+t+++ +nd+n+f   ++
  gi|119720531|ref|YP_921026.1| 337 GMWVESDVQLVEGESLARQFLYGQRYFYSRFGRTARIGWIPDSFGFPYSLPQLLVKSGLECFVTHKVLWNDTNEF---PY 413
                                    ***************************************************************************...** PP

                                    SCEEEE-TTSTEEEEEE--TT.SSHCCCCCC.GGGTTTHHHCHHHHHHCHHHHHTTSSSSEEEEEECEETHCCCCHHHHC CS
                Glyco_hydro_38N 162 lefiWrgsdgteilthmlpadsydptygfqfdfkrdenvkeraekllaqvkklaektrtnevllplGddfadgqggntek 241
                                    ++f Wrg dg+ i +++l +     +y+  +          ++ ++ a+++++++    + + + +G++  dg+gg+t++
  gi|119720531|ref|YP_921026.1| 414 HSFLWRGVDGSTIPVQILLN-----SYNEML----------TPGSVKAYWSRYKQRGEVPFLPYAYGYG--DGGGGPTRE 476
                                    *******************8.....588889..........9*************99999999999999..********* PP

                                    CHHHHHHHHHHCSSEEEEC--HHHHHHHHHHHS...HCE-ESSB-S- CS
                Glyco_hydro_38N 242 lleeinrsnekeslpkvqfgtpseYfdalekenaefptkdsddfpvy 288
                                    +le +   ++ ++lp+++  + +eY+++l++++        +++pv+
  gi|119720531|ref|YP_921026.1| 477 MLESLDVVKRLPGLPRLRHLEEEEYLARLKASE--------GSMPVW 515
                                    *******************************44........444444 PP

>> Glyco_hydro_38C  Glycosyl hydrolases family 38 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.0   0.0   1.5e-30   6.6e-27       4     213 ..     700     899 ..     697     900 .. 0.94
   2 ?   -2.0   0.0      0.72   3.2e+03      97     123 ..     973    1006 ..     971    1016 .. 0.60

  Alignments for each domain:
  == domain 1  score: 95.0 bits;  conditional E-value: 1.5e-30
                                    SS-EEEE.TTTSSEEEEESTTTS-EEE...EEEEEEEEEEECS-S-SSS--.BSTT-EEEE--.S-EEECEE-SS-EEEE CS
                Glyco_hydro_38C   4 gflkveidaknGtlksiydkeakrevlkeqvgnqfaayedapdssdaydfk.pdneekplevsekeveviesgplvaevt 82 
                                    g ++v + +++G l s+     ++evl    +nq++++ d+p+ +da+++   + ++ + +++ +e + +e+g l+a v+
  gi|119720531|ref|YP_921026.1| 700 GAVEVVV-DRDGSLGSVRLLPGGEEVLSRP-SNQLRVHFDRPGVFDAWELTdDFLSRWEEARTLSEPRLVERGRLRACVE 777
                                    6688999.888****************876.8******************95666666666666**************** PP

                                    EEETTES...EEEEEEEEECCCCEEEEEEEE-TTECEEEEEEEE---TTCEEEEETTTCEEEEESSTTTT...S..SEGG CS
                Glyco_hydro_38C  83 vkfkieaestisqeirLykgkkriefevkvdweekevllkvafpidiqaefatdengfgvikRptdqntsweaakfevia 162
                                        + ++s+++q + +y+ ++ +e++++++w +k  l+k++++ + + + a +e+++gv+ R   +++s ++akfe   
  gi|119720531|ref|YP_921026.1| 778 YVKGF-GKSRVTQRVCVYRFSPVVEVKTRLEWFDKGFLVKAWMKPAFKPTAAVFETPYGVVYRSPAWASSIDRAKFEA-- 854
                                    *****.9***********************************************************************.. PP

                                    GG-EEESSEEEEE-SSEEEEEEECS-EEEEE-SSTTEEEEEEEEEBSSS-T CS
                Glyco_hydro_38C 163 gnyypiqsfvdlqdesygvavlndskyGvssleqggqleLsLlRrplypdp 213
                                        p+ ++vd++d+  g+av+  + +G+s+  +++ ++LsLl++p++p+p
  gi|119720531|ref|YP_921026.1| 855 ----PALRWVDVSDGARGFAVIAPGRHGYSV--REDYVSLSLLKSPTFPNP 899
                                    ....***************************..89*************986 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.72
                                     EEEE.ECCCCEEEEEEEE-T...TECEE...EEE CS
                Glyco_hydro_38C   97 irLy.kgkkriefevkvdwe...ekevl...lkv 123 
                                      rLy ++   +e+ev+v+     + ev+   l+v
  gi|119720531|ref|YP_921026.1|  973 MRLYnPHRGEVEVEVEVNVPfreAVEVDipeLRV 1006
                                     6788767777777777765533444444555555 PP

>> Alpha-mann_mid  Alpha mannosidase middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       2.3     1e+04       9      31 ..     228     250 ..     226     270 .. 0.81
   2 !   75.1   0.2   7.9e-25   3.5e-21       1      94 [.     522     615 ..     522     616 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.3
                                    SSCHHHHHHHHHHHHHHHHHHHC CS
                 Alpha-mann_mid   9 SrarlKrlnrkleslLraaells 31 
                                    S  + Kr++ +le lL+ +e l 
  gi|119720531|ref|YP_921026.1| 228 SLDDVKRACDRLEPLLSLLEELR 250
                                    56688999999999999988775 PP

  == domain 2  score: 75.1 bits;  conditional E-value: 7.9e-25
                                    EE--GGGTSSCHHHHHHHHHHHHHHHHHHHCCTTT-SCGC-HHHHHHHHHHHHHHHTCTTTTTT-S-HHHHHHCCHHHHH CS
                 Alpha-mann_mid   1 elhrgtfTSrarlKrlnrkleslLraaellssaaaskgyeypkeeleelwkalllnqfHDilpGtsieeVyedaeerlae 80 
                                    e+hrgt+T++ + K+l+ ++e  L +ae ++s a+s   e  + +le+lwk+lll+qfHDilpG+s++eVyeda + l++
  gi|119720531|ref|YP_921026.1| 522 EFHRGTYTTNLQVKELMWRAELALLTAEEVASLASSRTGEGLSARLERLWKTLLLHQFHDILPGSSMKEVYEDAYRDLSM 601
                                    79******************************7778999999************************************** PP

                                    HHHHHHHHCCCCCC CS
                 Alpha-mann_mid  81 alkelekllesalr 94 
                                    +l+e+ +l+++al+
  gi|119720531|ref|YP_921026.1| 602 VLREASSLAREALE 615
                                    **********9986 PP

>> Glyco_hydro38C2  Glycosyl hydrolases family 38 C-terminal beta sandwich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0   1.1e-09   5.1e-06       4      69 .]     959    1030 ..     957    1030 .. 0.89

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 1.1e-09
                                     EEEEEE-TTT--EEEEEEESSSSSBEEE-EETT.SCEEEEE-TTSSB-..........-TTSEEXTTXEEEEE CS
                Glyco_hydro38C2    4 lltlkkaededdlllRlynlseegedatlslsqpvksvnvknllEttl..ape.....eleielkPmEIrTfi 69  
                                     l ++k aed+d+ ++Rlyn + ++ +++++++ p  ++ ++++ E             +l++ lkP+E++T++
  gi|119720531|ref|YP_921026.1|  959 LGAFKAAEDGDGYVMRLYNPHRGEVEVEVEVNVPFREAVEVDIPELRVlgR-VevsggKLRLRLKPFEVKTVK 1030
                                     5689***************************99999******999999552.0467789************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1032 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.87u 0.36s 00:00:01.23 Elapsed: 00:00:00.58
# Mc/sec: 5324.78
//
Query:       gi|119720532|ref|YP_921027.1|  [L=113]
Description: hypothetical protein Tpen_1629 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        6.4    6.5  14.7        7.5    6.3  14.7    1.1  1  Bax1-I    Inhibitor of apoptosis-promoting Bax1


Domain annotation for each model (and alignments):
>> Bax1-I  Inhibitor of apoptosis-promoting Bax1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3  14.7   0.00042       7.5      15     107 ..      12     105 ..       1     112 [. 0.57

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.00042
                         Bax1-I  15 llltalvaavvlsspaqlflslhivlflvvilaplalv.flslsaarlkkkssalalallllftlleGlslspillvyt. 92 
                                    +++ al+a v++++   l +   +++f+ v+ + l+l  + + + +  +  ++ + +al++++++ +++   + llv++ 
  gi|119720532|ref|YP_921027.1|  12 VVVLALAASVASTF--ILPPAFAPAVFWFVVGGWLVLAaL-LAGVEESRVVPARALYALYGGLAVTASAAYTVHLLVADa 88 
                                    22223333333222..244455666777777777888844.445556666777777*****9999999999999999985 PP

                         Bax1-I  93 ..gaiilqaflltaaif 107
                                      + ++l a ++++++ 
  gi|119720532|ref|YP_921027.1|  89 rvSLLVLLAGVGATGVA 105
                                    55444444433333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       743  (0.0414412); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 755.91
//
Query:       gi|119720533|ref|YP_921028.1|  [L=181]
Description: hypothetical protein Tpen_1630 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.9e-53  180.6   0.1    2.2e-53  180.4   0.1    1.0  1  NTPase_I-T  Protein of unknown function DUF84


Domain annotation for each model (and alignments):
>> NTPase_I-T  Protein of unknown function DUF84
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.4   0.1   1.2e-57   2.2e-53       1     163 []       8     171 ..       8     171 .. 0.99

  Alignments for each domain:
  == domain 1  score: 180.4 bits;  conditional E-value: 1.2e-57
                                    S---HHHHHHHHHHHHHHCTTEEEEEEE---SS-SS-BSHHHHHHHHHHHHHHHHHHSTTSSEEEEEEEEEET....TEE CS
                     NTPase_I-T   1 gSkNpvKveAvkeafeklfkdvevegvsvpsgvsdqPmgdeetlkGAinRaknaleaaeeadygvGlEgGveeleeklld 80 
                                    gS Np K+++v++af+++f dv v+g+ v+sgv+ qP++  e+l+GA+nRa +alea+ e+ +gvG+E+G++ +++ ++d
  gi|119720533|ref|YP_921028.1|   8 GSANPSKIAGVEKAFKRYFGDVVVKGFRVESGVARQPFSLGEILRGARNRALRALEACGECAFGVGVEAGIFAVDGFYMD 87 
                                    8******************************************************************************* PP

                                    EEEE.EEEESS-EEEEE---EE--HHHHHHHC.TT--HHHHHHHHHTHCCHHHTTHHHHHHTTTSS-HHHHHHHHHHHHT CS
                     NTPase_I-T  81 vawaavvdkegrvsvgrsasfelPeevveevk.egeelgevmdelfgtenikqkeGaigllTkglvtRedlyeqavilAl 159
                                    ++ a+vv++ g ++vg+s+sf +P+ +vee++ eg el+e++d+ fgt+n+++ eG++gllT+g+v Redl eqav++Al
  gi|119720533|ref|YP_921028.1|  88 TQAAVVVKRGGAEGVGFSSSFAVPPFIVEEILsEGLELEEAVDRHFGTRNVGEGEGFVGLLTRGVVVREDLAEQAVLMAL 167
                                    *******************************88*********************************************** PP

                                    HHHH CS
                     NTPase_I-T 160 ipfl 163
                                    ip+l
  gi|119720533|ref|YP_921028.1| 168 IPVL 171
                                    *985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       270  (0.0150594); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1222.96
//
Query:       gi|119720534|ref|YP_921029.1|  [L=647]
Description: formate dehydrogenase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.7e-48  163.2   0.0    2.4e-47  161.9   0.0    1.6  1  Molybdopterin    Molybdopterin oxidoreductase
    7.1e-18   64.7   0.0    1.8e-17   63.4   0.0    1.7  1  Molydop_binding  Molydopterin dinucleotide binding domain
    0.00012   22.0   0.0    0.00023   21.1   0.0    1.4  1  Molybdop_Fe4S4   Molybdopterin oxidoreductase Fe4S4 domain


Domain annotation for each model (and alignments):
>> Molybdopterin  Molybdopterin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.9   0.0   4.1e-51   2.4e-47       1     431 [.      58     455 ..      58     456 .. 0.88

  Alignments for each domain:
  == domain 1  score: 161.9 bits;  conditional E-value: 4.1e-51
                                    B--S-EEECTTTTTSEEEE--HHHHHHHHHHHHHHHHHHCSGGGEEEEEBTSSCSHHHHHHHHHHHHHTT-EEE-BEECC CS
                  Molybdopterin   1 RlkyPmvRkqargeGkFvrvsWdeAleliaaslkytikkygpdrvagfssgplmsmeslaslkkllsllggknlsfydwy 80 
                                    R+  P+ R + +    F+rv+W  Al+++a++lk++ +++gp +v      + m + +++  ++l + lg     +  + 
  gi|119720534|ref|YP_921029.1|  58 RVLFPYRRAGGKPGRSFERVEWGSALDEVASRLKEVLEEHGPGAVLHLEYAGNMGLLTWYYPQRLWNWLGA--ARTDYSI 135
                                    8999****9999999****************************99997777888899**************..4444444 PP

                                    GGGTTHHHHCHHCCCCCTTTS-SS-CCGGGG-SEEEEESS-HHHHSHHHHHHHHHHHHTTC-EEEEECSSB-HCGGGCSE CS
                  Molybdopterin  81 adlppasaqqtigsdsrsnyessnpledlensdliilwGsNvreerpilnarirkaalkkkakvivigpryaellkfade 160
                                    + ++ ++ +     ++ +  +++ + e+ e s+l++ wG N     p l a  ++  ++ +  +++++pr +e++ + d 
  gi|119720534|ref|YP_921029.1| 136 CSKS-GHEA----LSLHYGLSYGRTPEEAEGSRLFVFWGFNASVSSPHLWAAALRGRRR-GSVIAAVDPRRSETALKSDF 209
                                    4443.3332....3345566677777799********************5555554444.388**********889**** PP

                                    EEEEHTTTHHHHHHHHHHHHHHCCCCTCHHHHHHEECHHHCCCCCCCEECCSHHHHHHCCHHHHHHHHHHHHHHTSSEEE CS
                  Molybdopterin 161 wlaikpgtdaalalamghvilqelkvdkeflrkytygkeetdmpllvtleeetgkkkevvariarelarnaaktagksmi 240
                                     + ++pgtd+ala +  +++++e+++d++f+++yt+g+ee++   +  +  +++  ++v  + + +la+ +a+ ++ s  
  gi|119720534|ref|YP_921029.1| 210 AVHPRPGTDVALAYGVINYLISEGLYDEDFVERYTVGFEELRREASRWSLSRVSGVTGVGEKDVARLAELYAELKP-STT 288
                                    ****************************************************************************.666 PP

                                    EECHHHHTSTTHHHHHHHHHHHHHHCTHCSSTTCEEEEESSCTTHHHCHHHHTCCTTCCCCCCCTTHHHHHCCCTTTCST CS
                  Molybdopterin 241 ivGaglnhrqdgdaiyravinLallvgnvgqpgGgwahlnGqlilagaaekvgalpvllsvkslkeekikfaaeqpgnlg 320
                                    ++G g+++  +g++++rav  + +lvg+ +    g+   n+   l + a+ +g+                     pg ++
  gi|119720534|ref|YP_921029.1| 289 FIGFGVQKGVNGAEAVRAVSLIPALVGQHR----GFYYSNSRRWLVDLAAVTGER-----------------HAPPGRVV 347
                                    66***********************98665....344445555666666666666.................68999999 PP

                                    SS--ECGGCHHHHHHTTSSSEEEEESH.HHHHSTTSCCCHCHHHCSSEEEEE.ESCSSHHHHTSSEEEEBE-CCGSEEEE CS
                  Molybdopterin 321 nfprnlfversnllkssgkkvlyllgnnpevdhadenevekalekldlvvvl.dgrltstalyaDiiLPaatwyEkedly 399
                                           v  ++l++++++k++y+ + np  + + ++++ + l ++d++vvl d ++++ta yaD++LPaat++Ek+d++
  gi|119720534|ref|YP_921029.1| 348 S-----QVALAELVERGEFKFIYVYNMNPLLTLPGQGKLRRGLSRSDVFVVLhDTHWNETADYADVVLPAATYLEKDDVV 422
                                    9.....667899***********************************9999846666*********************** PP

                                    E-TTSEEEE.EEESSS-STT-BEHHHHHHHHHH CS
                  Molybdopterin 400 tndegrfqh.lkqavsppgeaksdwkIlkaLak 431
                                    +   +      +++++p ge++s+ ++ ++La+
  gi|119720534|ref|YP_921029.1| 423 IPYAHGYVAmSRKVIEPLGESRSEVWVTCELAR 455
                                    *9999988889********************97 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.4   0.0     3e-21   1.8e-17      27     110 ..     556     637 ..     535     638 .. 0.88

  Alignments for each domain:
  == domain 1  score: 63.4 bits;  conditional E-value: 3e-21
                                    SSS-EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESSB-TTEEEEESSHCC.....S-GHCTS--SCSTTT--CS CS
                Molydop_binding  27 pepevveinpedAaalGikdGdlVevesrrGsvevrakvtervrpGvvfmpfgwweagekggnaNaltddatdplsgtpe 106
                                    p p+vv +np dA++lG++dGdlVe+++++Gsv+v+a+vte v+pGv++ p +      +g++ N+l++ +t  + g+p 
  gi|119720534|ref|YP_921029.1| 556 PIPAVVHVNPVDAERLGVRDGDLVELYNEHGSVVVKAQVTELVPPGVLWSPRQLVG--LDGSPQNSLVPTETQRIGGGPV 633
                                    33479*************************************************55..********************** PP

                                    TT-E CS
                Molydop_binding 107 fksv 110
                                    f+s+
  gi|119720534|ref|YP_921029.1| 634 FNST 637
                                    9986 PP

>> Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   3.8e-08   0.00023       2      50 ..       2      50 ..       1      54 [. 0.91

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 3.8e-08
                                   EEEEEE-S.SBTT--EEEEEEETTEEEEEEE-TTSTTTTT---HHHHTCH CS
                 Molybdop_Fe4S4  2 kvvktaCp.yCgvgCglevhvkdgkivkvegdpdhpvnegrlCvKGrtll 50
                                   +  k++Cp  C   C l v+  +g+  +v +dp    + g lC++G+  +
  gi|119720534|ref|YP_921029.1|  2 AALKSVCPrDCYDTCHLAVSLDGGEL-RVAPDPGFAFTAGFLCPRGAVEA 50
                                   5679*********************9.*******************9655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (647 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 4044.01
//
Query:       gi|119720535|ref|YP_921030.1|  [L=284]
Description: 4-vinyl reductase, 4VR [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-07   30.5   0.0    5.2e-07   29.6   0.0    1.5  1  V4R       V4R domain
  ------ inclusion threshold ------
      0.043   13.6   0.2      0.081   12.7   0.2    1.5  1  ACT       ACT domain


Domain annotation for each model (and alignments):
>> V4R  V4R domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0   5.8e-11   5.2e-07       2      61 ..     211     273 ..     210     274 .. 0.90

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 5.8e-11
                                    -EEEEEES-S-TT---SS---HHHHHHHHHHHHHHHS...SEEEEEEEE-GGGT-SSEEEEEE CS
                            V4R   2 elsieespelaglpgkeePvCyleaGllagalsellg...krveveEveCaaeGhdhCeFeve 61 
                                    + ++++++e+++l+g+e+    + +Gllag ls+  g   k v+ +E++C a+G+ +Ce +++
  gi|119720535|ref|YP_921030.1| 211 VAQVYDNVECKSLVGIEGAEGTIIRGLLAGWLSGYWGvdiKTVRPKETKCIARGDPYCEYVFR 273
                                    6789*****************************888844467788**************9876 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   9.1e-06     0.081      10      66 ..      41      97 ..      32      98 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.1e-06
                                   STTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHTTC CS
                            ACT 10 rPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkkle 66
                                   ++G+L +++ ++a   + i    +++  ++ ++ + v+i +d +++ e+++ + +l 
  gi|119720535|ref|YP_921030.1| 41 VVGVLRDILDVFAGEKVPILLFKTSTPPRGSGEDIRVIIAADIKEDREAEKIVAALR 97
                                   58****************************999999999999999999999888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2140.93
//
Query:       gi|119720536|ref|YP_921031.1|  [L=237]
Description: SPP-like hydrolase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-23   82.9   0.0    2.7e-13   50.3   0.0    2.1  2  Hydrolase_3      haloacid dehalogenase-like hydrolase
     0.0002   21.8   2.0        0.2   12.0   0.0    2.7  4  HAD              haloacid dehalogenase-like hydrolase
    0.00043   19.5   0.0    0.00085   18.5   0.0    1.4  2  Trehalose_PPase  Trehalose-phosphatase
     0.0015   18.9   0.5       0.12   12.7   0.3    2.2  2  Hydrolase        haloacid dehalogenase-like hydrolase
     0.0065   16.0   0.0       0.16   11.4   0.0    2.1  2  S6PP             Sucrose-6F-phosphate phosphohydrolase


Domain annotation for each model (and alignments):
>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.0   6.4e-11   2.3e-07       1      83 [.       6      87 ..       6      95 .. 0.88
   2 !   50.3   0.0   7.5e-17   2.7e-13     173     253 ..     142     222 ..     132     224 .. 0.94

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 6.4e-11
                                   EEEEIIIIIS-TTS---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEEEEGGGTEE.ECTTTEEEEE--B-H CS
                    Hydrolase_3  1 ialDlDGTLlnsdkkisektkeaikklkekgikvviATGRslravlpvleelgldlpvialNGali.ddekgkilykstisk 81
                                   +++D+D TL + + +is + +ea+++l+ +g+ vv+A++  +  v  + + l  +  +++ NG+++ d  + +il   +i+k
  gi|119720536|ref|YP_921031.1|  6 VFVDVDWTLTDRERRISSRVVEALERLQREGYFVVLASATAYPIVYGLSRYLPTSGVAVGENGGVVgDGRRLEIL--GRIDK 85
                                   699**************************************************99***********766666665..55665 PP

                                   HH CS
                    Hydrolase_3 82 ed 83
                                   e 
  gi|119720536|ref|YP_921031.1| 86 EL 87
                                   55 PP

  == domain 2  score: 50.3 bits;  conditional E-value: 7.5e-17
                                    EESTTEEEEEETT-SHHHHHHHHHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE--GGGTHHH CS
                    Hydrolase_3 173 ssskgyleimpkgvsKgtalkklakelnisleeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtksnnedGVa 252
                                    ++s+  l + p+gv+Kg +l+k +++l+   + v+a+GD+e D+ M+ +a+++ + + a eevkk A+yv k   +dG +
  gi|119720536|ref|YP_921031.1| 142 KYSGVALHVHPPGVNKGVGLRKALEMLGGGFDYVVAVGDSEVDVDMFRVADFSACPAHAPEEVKKEASYVAKAPYSDGFL 221
                                    567788999***************************************************************99999976 PP

                                    H CS
                    Hydrolase_3 253 k 253
                                    +
  gi|119720536|ref|YP_921031.1| 222 E 222
                                    5 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.3   4.5e+03       1      12 [.       6      17 ..       6      23 .. 0.86
   2 !    9.0   0.1   0.00047       1.7      88     123 ..      26      58 ..      10     112 .. 0.75
   3 !   12.0   0.0   5.6e-05       0.2     132     188 .]     139     189 ..     113     189 .. 0.70
   4 ?   -3.3   0.0       2.8     1e+04     137     155 ..     216     234 ..     202     236 .. 0.61

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.3
                            HAD  1 alfDfDgTLldg 12
                                   ++ D+D TL+d 
  gi|119720536|ref|YP_921031.1|  6 VFVDVDWTLTDR 17
                                   689******986 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00047
                            HAD  88 pgalellaahraaGdrvvvvSgglrplvepllaelg 123
                                     +ale+l+   ++G+ vv+ S++  p+v  l + l 
  gi|119720536|ref|YP_921031.1|  26 VEALERLQ---REGYFVVLASATAYPIVYGLSRYLP 58 
                                    27888888...*****************99998776 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 5.6e-05
                            HAD 132 levddrltge..lglegkpvrgegkvaalrewlaaegegidleevvayGDspsDlpllr 188
                                    lev+  ++g   + +++++ +g      lr+ l++ g g d+  vva+GDs+ D+ ++r
  gi|119720536|ref|YP_921031.1| 139 LEVK--YSGValHVHPPGVNKG----VGLRKALEMLGGGFDY--VVAVGDSEVDVDMFR 189
                                    4443..3333333467777777....8899966666666666..*************87 PP

  == domain 4  score: -3.3 bits;  conditional E-value: 2.8
                            HAD 137 rltgelglegkpvrgegkv 155
                                    + +g l++ + + rg+gk+
  gi|119720536|ref|YP_921031.1| 216 YSDGFLEIVDVVLRGAGKP 234
                                    5566666677777777766 PP

>> Trehalose_PPase  Trehalose-phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0      0.67   2.4e+03       8      35 ..      14      36 ..       7      46 .. 0.62
   2 !   18.5   0.0   2.4e-07   0.00085     145     205 ..     138     195 ..     129     222 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.67
                                   TB---SSGGG--B-TTHHHHHHHHHTTS CS
                Trehalose_PPase  8 lspivedpdaavpssellslLkkLasdp 35
                                   l++      + ++ss+++++L++L  + 
  gi|119720536|ref|YP_921031.1| 14 LTD-----RERRISSRVVEALERLQREG 36
                                   433.....44588899999999886664 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 2.4e-07
                                    --EEEE-SSEEEEE-S---HHHHHHHHHHTS--------EEEEEE-SSTTHHHHTTS-TT. CS
                Trehalose_PPase 145 dlevtqgkkvvevrpqgvsKGkaverlleslgsadseddfvlciGDdrtDedmFsvlrktk 205
                                    +lev+     + v+p gv+KG  +++ le lg+     d+v+++GD   D dmF+v    +
  gi|119720536|ref|YP_921031.1| 138 GLEVKYSGVALHVHPPGVNKGVGLRKALEMLGGG---FDYVVAVGDSEVDVDMFRVADFSA 195
                                    677777777899*********************9...******************987765 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.9   0.0    0.0078        28       3      65 ..       5      72 ..       4     136 .. 0.67
   2 !   12.7   0.3   3.2e-05      0.12     174     210 .]     156     192 ..     114     192 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0078
                                   EEEEESBTTTBCHHHHHHHHHHHH.....CHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase  3 tvvfDkdGTLttgepsvedvivsa.....alalaaaletgsehpigkalvaaakarsgaltgfatfig 65
                                   +v+ D+d TLt+ e+++   +v+a          ++l+ ++  pi   l ++    + a+ +++ + g
  gi|119720536|ref|YP_921031.1|  5 AVFVDVDWTLTDRERRISSRVVEAlerlqREGYFVVLASATAYPIVYGLSRYLPTSGVAVGENGGVVG 72
                                   68899999999999555555554422223333333333336666666666666666666655555444 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 3.2e-05
                                    TSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase 174 pspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                     +  g+++a++ L+g    v++VGD+  D+ +++ A+
  gi|119720536|ref|YP_921031.1| 156 NKGVGLRKALEMLGGGFDYVVAVGDSEVDVDMFRVAD 192
                                    4777999*******88888**************9997 PP

>> S6PP  Sucrose-6F-phosphate phosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.025        91       4      41 ..       5      42 ..       2      57 .. 0.81
   2 !   11.4   0.0   4.6e-05      0.16     153     239 ..     144     221 ..     133     225 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.025
                                   EEEE-TBTTTB.S-HHHHHHHHHHHH.GGGGGEEEEEE CS
                           S6PP  4 llvsdLDntlvdgdnealarlnelleaeerkdvllvfa 41
                                   ++  d+D tl+d++++   r  e le  +r+   +v+a
  gi|119720536|ref|YP_921031.1|  5 AVFVDVDWTLTDRERRISSRVVEALERLQREGYFVVLA 42
                                   6778**********************666666655555 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 4.6e-05
                                    TTTEEEEEETT-SHHHHHHHHHHHHT--GGGEEEEE-SGGGHHHHTSSSEEEE-TT--HHHHHHHHHH--TTE..EE-SS CS
                           S6PP 153 sgkdlDvlPkraskgeAlryLakkleleleqilvcGdsgnDeellignvlgVvVgnaqeellqwllenakeneriylaee 232
                                    sg +l v P + +kg  lr  ++ l+   + ++ +Gds+ D ++++    + + + a ee         ke    y+a++
  gi|119720536|ref|YP_921031.1| 144 SGVALHVHPPGVNKGVGLRKALEMLGGGFDYVVAVGDSEVDVDMFRVADFSACPAHAPEE-------VKKEA--SYVAKA 214
                                    46789999*************************************777777776666665.......22222..355666 PP

                                    -THHHHH CS
                           S6PP 233 rcaaGil 239
                                    ++ +G l
  gi|119720536|ref|YP_921031.1| 215 PYSDGFL 221
                                    6666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1543.76
//
Query:       gi|119720537|ref|YP_921032.1|  [L=334]
Description: oligopeptide/dipeptide ABC transporter, ATPase subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-37  129.1   0.0    2.1e-37  128.7   0.0    1.2  1  ABC_tran      ABC transporter
    1.3e-20   73.7   0.2    2.2e-20   72.9   0.2    1.4  1  oligo_HPY     Oligopeptide/dipeptide transporter, C-terminal 
    2.9e-06   27.3   0.7      0.012   15.4   0.3    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    0.00027   21.2   0.8     0.0027   18.0   0.8    2.1  1  AAA_22        AAA domain
     0.0006   20.2   2.0     0.0012   19.3   2.0    1.8  1  AAA_16        AAA ATPase domain
     0.0012   18.5   0.1     0.0021   17.8   0.1    1.3  1  AAA_29        P-loop containing region of AAA domain
     0.0056   16.1   0.0      0.038   13.4   0.0    1.9  1  SMC_N         RecF/RecN/SMC N terminal domain
     0.0076   16.7   0.0      0.015   15.7   0.0    1.5  1  AAA           ATPase family associated with various cellular 
  ------ inclusion threshold ------
       0.03   13.7   0.0      0.064   12.6   0.0    1.5  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.036   13.3   0.1      0.055   12.7   0.1    1.2  1  NB-ARC        NB-ARC domain
      0.042   13.6   0.1       0.08   12.7   0.1    1.4  1  AAA_30        AAA domain
      0.043   13.2   0.0        3.7    6.9   0.0    2.2  2  TniB          Bacterial TniB protein
      0.068   13.3   0.3       0.14   12.3   0.3    1.8  1  AAA_33        AAA domain
      0.087   12.7   0.1       0.18   11.7   0.1    1.5  1  NACHT         NACHT domain
       0.11   12.1   0.1       0.18   11.3   0.1    1.5  1  AAA_25        AAA domain
       0.13   12.0   0.0       0.17   11.6   0.0    1.2  1  AAA_24        AAA domain
       0.14   12.6   0.0        0.2   12.2   0.0    1.2  1  AAA_23        AAA domain
       0.15   11.8   0.1       0.21   11.3   0.1    1.2  1  PRK           Phosphoribulokinase / Uridine kinase family
       0.15   11.9   0.1        0.3   11.0   0.1    1.4  1  RsgA_GTPase   RsgA GTPase
       0.16   11.9   0.1       0.29   11.2   0.1    1.3  1  TsaE          Threonylcarbamoyl adenosine biosynthesis protei
       0.17   10.9   0.0       0.28   10.2   0.0    1.3  1  T2SSE         Type II/IV secretion system protein
       0.21   10.8   0.0       0.34   10.2   0.0    1.3  1  Zeta_toxin    Zeta toxin


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.7   0.0   2.5e-40   2.1e-37       2     136 ..      40     192 ..      39     193 .. 0.94

  Alignments for each domain:
  == domain 1  score: 128.7 bits;  conditional E-value: 2.5e-40
                                    EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG...B-HHHCCHCEEEE-SS..--S-TTSBH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxx..xxxxxxxxx RF
                       ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke...qeleslrkeigvlpqe..pqlfpeltv 76 
                                    + vs++l+ ge++a+vGe+G+GK+t+++++ gl+kpt+G+il+dg+d+++   +el+s+r+++++++q+   +l+p+++v
  gi|119720537|ref|YP_921032.1|  40 DGVSFSLRSGEIMALVGESGSGKTTVARAVVGLVKPTSGRILFDGRDISRldgRELRSYRRSVQMVFQDpsVSLNPRMKV 119
                                    78*******************************************************************9899******* PP

                                    HHH..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    xxx..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  77 ren..............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                    +e+              e++e + kal+++gl+  +++  ++ p++LSgGq+qrva+aral+ +p+lll+DEp 
  gi|119720537|ref|YP_921032.1| 120 GEQvkypldvnkvgsedERREAALKALERVGLVP-PEDFYSRYPHQLSGGQRQRVAIARALVLNPRLLLADEPI 192
                                    *************975555555899999999999.888888999*****************************7 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.9   0.2   2.7e-23   2.2e-20       1      65 []     244     310 ..     244     310 .. 0.98

  Alignments for each domain:
  == domain 1  score: 72.9 bits;  conditional E-value: 2.7e-23
                      oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekd..klekikgeapslerldeGCpFapRCpfaleeC 65 
                                    vE gp++++f++plHPYTkaLl++vp+l+++    + +++kge ps+ + ++GC+ +pRCpfa+e+C
  gi|119720537|ref|YP_921032.1| 244 VEAGPVQEVFSNPLHPYTKALLSAVPSLTPGGAarRRVTLKGEIPSPLNPPAGCRLHPRCPFATEKC 310
                                    8*****************************998889******************************* PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   0.00026      0.21       1      47 [.      51      88 ..      51     120 .. 0.77
   2 !   15.4   0.3   1.5e-05     0.012     181     299 ..     102     225 ..      76     227 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00026
                         AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkips 47
                                   +++l+G  gsGK+++ +a  +l          +++++++   + ++s
  gi|119720537|ref|YP_921032.1| 51 IMALVGESGSGKTTVARAVVGL---------VKPTSGRILFDGRDIS 88
                                   689****************998.........4444444444444444 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1.5e-05
                         AAA_21 181 ekrllqrlvrslklveielsdlgegeeliasvderlrer.......gvvflengdgqelparelSdGtkrllalltallr 253
                                    ++  +q+ + sl+++    +  ++  + ++  +e++r++        v ++ ++d + + +++lS G+++  a++ al  
  gi|119720537|ref|YP_921032.1| 102 VQMVFQDPSVSLNPRMKVGEQVKYPLDVNKVGSEDERREaalkaleRVGLVPPEDFYSRYPHQLSGGQRQRVAIARALVL 181
                                    4555555555555555555555555555555555555558888888999**********************999999998 PP

                         AAA_21 254 alkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSp 299
                                     +   +lll DEp ++ + ++ + +l llk+l++ +   ++  TH+ 
  gi|119720537|ref|YP_921032.1| 182 NP---RLLLADEPISNVDVSARAQILALLKSLRDeRSLSILYITHDL 225
                                    88...*********************99999998889********96 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.8   3.3e-06    0.0027       4      29 ..      48      73 ..      46     226 .. 0.59

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3.3e-06
                         AAA_22  4 tagilvvtGesGtGKTtllrrlleql 29
                                   +  i++++GesG+GKTt++r ++   
  gi|119720537|ref|YP_921032.1| 48 SGEIMALVGESGSGKTTVARAVVGLV 73
                                   56799***************998765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   2.0   1.5e-06    0.0012       3      47 ..      30      72 ..      28     285 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.5e-06
                         AAA_16  3 vGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellra 47
                                    GR++ l+++  +  ++rsg  e++ l+GesG+GK++++r++   
  gi|119720537|ref|YP_921032.1| 30 RGRQRLLRAVDGVSFSLRSG--EIMALVGESGSGKTTVARAVVGL 72
                                   56666666666655566666..8*****************98744 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   2.5e-06    0.0021      13      50 ..      40      77 ..      37      83 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.5e-06
                         AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                   dg +++++  +++ l+G+sGsGK+T+  A+  l  p++
  gi|119720537|ref|YP_921032.1| 40 DGVSFSLRSGEIMALVGESGSGKTTVARAVVGLVKPTS 77
                                   66778887556***************999988888776 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   4.7e-05     0.038      25     189 ..      50     213 ..      43     240 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.7e-05
                                    SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--.BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk.skekasvkkaeveitfdnedkklkiekeevsisrrv 103
                                    ++ a+vG+ GSGK+ +  A+  +   +s + l      + i++   ++ ++ + +v+++f++++         vs++ r+
  gi|119720537|ref|YP_921032.1|  50 EIMALVGESGSGKTTVARAVVGLVKPTSGRIL---FDGRDISRlDGRELRSYRRSVQMVFQDPS---------VSLNPRM 117
                                    57899**************9433333333322...22222222234455555666666666555.........5566666 PP

                                    ETTSEEEEEETTEEE-HHHHHHHHHCTT-STT..............CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 104 krkgeseykingkevtkkevsellesagiske..............lLSgGektLvalaLlfAiqkvkpaplyllDeida 169
                                    k +++ +y ++ ++v +++ ++  + + +++               +LSgG+++ va+a  + ++   p  l l De  +
  gi|119720537|ref|YP_921032.1| 118 KVGEQVKYPLDVNKVGSEDERREAALKALERVglvppedfysryphQLSGGQRQRVAIARALVLN---P-RLLLADEPIS 193
                                    6666666766666665555444444444444444444899999999********99998765543...3.3778899999 PP

                                    TS-HHHHHHHHHHHHHHCTT CS
                                    xxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 170 aLDeknvkkvaellkekskn 189
                                    + D + ++++  llk+ +++
  gi|119720537|ref|YP_921032.1| 194 NVDVSARAQILALLKSLRDE 213
                                    99999999999999987766 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.9e-05     0.015       1      51 [.      52     107 ..      52     118 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.9e-05
                                    EEEESSTTSSHHHHHHHHHHHH..........THEEEEEETTTCSSSSTTHHHHHHHHHHH CS
                            AAA   1 vllyGppGtGKTllakavakel..........gvefleisgsellskyvgesekkirelfk 51 
                                    + l+G  G GKT++a+av+  +          g+++ +++g el+        ++++++f+
  gi|119720537|ref|YP_921032.1|  52 MALVGESGSGKTTVARAVVGLVkptsgrilfdGRDISRLDGRELR-----SYRRSVQMVFQ 107
                                    679****************99844444334444668888888888.....45566666665 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   7.9e-05     0.064      25      84 ..      52     112 ..      31     129 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.9e-05
                   Mg_chelatase  25 lllvGppGsGKtmlakrlpsllpplseeealevakiasvag.kkeeekllkrrpfraphhs 84 
                                    + lvG +GsGKt +a+++ +l+ p s +  ++ + i+ + g + ++ +   +  f++p  s
  gi|119720537|ref|YP_921032.1|  52 MALVGESGSGKTTVARAVVGLVKPTSGRILFDGRDISRLDGrELRSYRRSVQMVFQDPSVS 112
                                    789*********************9999999988888888844445555566667777655 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   6.7e-05     0.055      21      42 ..      50      71 ..      37      85 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.7e-05
                                   EEEEEEESTTSSHHHHHHHHCC CS
                         NB-ARC 21 lvvalvGmgGvGKttlakqiln 42
                                    ++alvG  G+GKtt+a+ ++ 
  gi|119720537|ref|YP_921032.1| 50 EIMALVGESGSGKTTVARAVVG 71
                                   49***************99975 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   9.8e-05      0.08      15      45 ..      47      76 ..      40      83 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.8e-05
                         AAA_30 15 tsgdrvavltGpAGtGKttalkalreaweaa 45
                                    sg+ +++l+G  G+GKtt+ +a++ +++  
  gi|119720537|ref|YP_921032.1| 47 RSGE-IMALVGESGSGKTTVARAVVGLVKPT 76
                                   4564.99*****************9888766 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.037        30      38      53 ..      52      67 ..      42      77 .. 0.87
   2 ?    6.9   0.0    0.0045       3.7     117     159 ..     180     220 ..     156     228 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.037
                           TniB 38 lllvGdsnnGKtmive 53
                                   + lvG+s  GKt++++
  gi|119720537|ref|YP_921032.1| 52 MALVGESGSGKTTVAR 67
                                   789**********987 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0045
                           TniB 117 elkvrvLiiDEihnllagsarkqreflnalksLgnelkipivl 159
                                     l++r+L+ DE   + +  ++++ ++l++lksL +e +++i +
  gi|119720537|ref|YP_921032.1| 180 VLNPRLLLADEP--ISNVDVSARAQILALLKSLRDERSLSILY 220
                                    5789******95..45557999999***********9999976 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.3   0.00018      0.14       3      20 ..      53      70 ..      51     226 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00018
                         AAA_33  3 llvGlpGsGKstlaerll 20
                                    lvG +GsGK+t+a+ ++
  gi|119720537|ref|YP_921032.1| 53 ALVGESGSGKTTVARAVV 70
                                   689************985 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00022      0.18       2      22 ..      51      71 ..      50      78 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00022
                                   CEEEEC-TTTCHHHHHHHHHH CS
                          NACHT  2 lvilqGeaGsGKTtLlqklal 22
                                   +++l Ge+GsGKTt ++ ++ 
  gi|119720537|ref|YP_921032.1| 51 IMALVGESGSGKTTVARAVVG 71
                                   5899************99875 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00022      0.18      31      97 ..      47     123 ..      38     223 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00022
                         AAA_25  31 pagelallaGapgtGKttlaldlalava..tGkpwlg..........pvapeqgkVlyvsaEdsedelrrRlravgeal 97 
                                    + ge+ +l+G +g+GKtt+a  ++  v   +G+ +++          ++++ ++ V +v + d+   l++R++ vge++
  gi|119720537|ref|YP_921032.1|  47 RSGEIMALVGESGSGKTTVARAVVGLVKptSGRILFDgrdisrldgrELRSYRRSVQMV-FQDPSVSLNPRMK-VGEQV 123
                                    67999**************9777655555577777767777777766665555555554.4555557777776.66666 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0    0.0002      0.17       5      23 ..      52      74 ..      48     128 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0002
                         AAA_24  5 iliyGpsgiGKTtlakel....g 23
                                   ++++G+sg+GKTt+a+      +
  gi|119720537|ref|YP_921032.1| 52 MALVGESGSGKTTVARAVvglvK 74
                                   799************98766553 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00024       0.2      14      39 ..      43      69 ..      36     138 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00024
                         AAA_23 14 eidF.skgltlItGpNGaGKTTildAi 39
                                   ++ + s  + +++G+ G+GKTT+ +A+
  gi|119720537|ref|YP_921032.1| 43 SFSLrSGEIMALVGESGSGKTTVARAV 69
                                   55555567999************9986 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00026      0.21       1      22 [.      51      72 ..      51      91 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00026
                            PRK  1 vIgvagsSGaGkttvarkleki 22
                                   ++++ g+SG+Gkttvar+++ +
  gi|119720537|ref|YP_921032.1| 51 IMALVGESGSGKTTVARAVVGL 72
                                   67899************98765 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00037       0.3      91     121 ..      40      71 ..      28      82 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00037
                                    HHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                    RsgA_GTPase  91 eelkellkd.ktsvlvGqSGvGKStLinallp 121
                                    + ++  l++ ++++lvG+SG GK+t+  a+++
  gi|119720537|ref|YP_921032.1|  40 DGVSFSLRSgEIMALVGESGSGKTTVARAVVG 71 
                                    55666777779**************9988765 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00035      0.29      19      40 ..      49      70 ..      29      78 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00035
                                   TEEEEEEESTTSSHHHHHHHHH CS
                           TsaE 19 gdvilLeGdLGaGKTtlvrgla 40
                                   g++++L G+ G+GKTt +r+++
  gi|119720537|ref|YP_921032.1| 49 GEIMALVGESGSGKTTVARAVV 70
                                   788****************987 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00034      0.28     127     161 ..      47      81 ..      24      96 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00034
                          T2SSE 127 rerglilvsGgTgsGKttllyallkeinksderiv 161
                                    r+  ++ + G  gsGKtt++ a++  ++ ++ ri+
  gi|119720537|ref|YP_921032.1|  47 RSGEIMALVGESGSGKTTVARAVVGLVKPTSGRIL 81 
                                    555677788*******************9999986 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00042      0.34      18      50 ..      51      83 ..      43     113 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00042
                     Zeta_toxin 18 lillgGqpGAGKselaellkdelerqgnvvrld 50
                                   ++ l+G +G+GK+++a+++   ++++++ + +d
  gi|119720537|ref|YP_921032.1| 51 IMALVGESGSGKTTVARAVVGLVKPTSGRILFD 83
                                   56799*************998877555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                       102  (0.00568911); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 2238.64
//
Query:       gi|119720538|ref|YP_921033.1|  [L=315]
Description: oligopeptide/dipeptide ABC transporter, ATPase subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.3e-26   91.5   0.0    8.6e-26   91.1   0.0    1.2  1  ABC_tran   ABC transporter
    9.8e-20   70.9   0.1    1.7e-19   70.1   0.1    1.4  1  oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal reg
      4e-08   33.0   0.1      2e-07   30.7   0.1    1.8  1  SMC_N      RecF/RecN/SMC N terminal domain
    1.2e-06   28.5   1.1      0.002   18.0   0.0    2.4  3  AAA_21     AAA domain, putative AbiEii toxin, Type IV TA syst
    0.00033   20.9   0.1     0.0016   18.7   0.1    1.9  1  AAA_22     AAA domain
     0.0025   17.5   0.0     0.0043   16.8   0.0    1.4  1  AAA_29     P-loop containing region of AAA domain
     0.0047   17.3   0.4      0.011   16.2   0.2    1.5  1  AAA_16     AAA ATPase domain
  ------ inclusion threshold ------
      0.046   12.9   0.0      0.061   12.5   0.0    1.1  1  DUF2075    Uncharacterized conserved protein (DUF2075)
        0.1   12.3   0.2         13    5.5   0.1    2.1  2  IstB_IS21  IstB-like ATP binding protein
       0.17   11.2   0.7        9.5    5.5   0.1    2.1  2  ATPase     KaiC
       0.18   11.3   0.0       0.51    9.8   0.0    1.7  2  NIR_SIR    Nitrite and sulphite reductase 4Fe-4S domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.1   0.0   5.3e-29   8.6e-26       3     136 ..      25     180 ..      23     181 .. 0.89

  Alignments for each domain:
  == domain 1  score: 91.1 bits;  conditional E-value: 5.3e-29
                                    EEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--....SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS..--S-T CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxx....xxxxxxxxxxxxxxxx..xxxxx RF
                       ABC_tran   3 nvslklkegekvaivGenGaGKStLlkllagllkp....teGeilldgkdlke....qeleslrkeigvlpqe..pqlfp 72 
                                     v+l++++ge++++vGe+G+GKStL  ++++ll      + G++l++g+dl +    + +++  +ei++++q+  ++l+p
  gi|119720538|ref|YP_921033.1|  25 GVTLSVNPGEVLGVVGESGSGKSTLGLAILRLLPRyarvERGQVLYNGADLLKlgeeELRRIRGREISIVFQDpySSLNP 104
                                    799**********************98888888777777**************999777778889********999**** PP

                                    TSBHHHH...............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    xxxxxxx...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  73 eltvren...............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                     ++++++               e+ +++ ++l+++g +    +++++ p++LSgGq+qrva+  al+ +pkl+++DE t
  gi|119720538|ref|YP_921033.1| 105 VMRIGDHfvelfeehgygysreEALRRAGDILERMGVPR---ERLSDYPHQLSGGQRQRVAIGLALALNPKLVVADEIT 180
                                    *****************9866555556777777777555...899999*****************************88 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.1   0.1   1.1e-22   1.7e-19       1      65 []     232     295 ..     232     295 .. 0.98

  Alignments for each domain:
  == domain 1  score: 70.1 bits;  conditional E-value: 1.1e-22
                      oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekdklekikgeapslerldeGCpFapRCpfaleeC 65 
                                    vE g++ +++ +plHPYTkaLl++vp++   ++ ++ i+g++p+ ++ ++GC+F+pRCpfa+e+C
  gi|119720538|ref|YP_921033.1| 232 VELGSTGEVVGDPLHPYTKALLAAVPSIGGSRE-VKPIPGDPPDMRNPPRGCRFHPRCPFATEKC 295
                                    8***************************99999.******************************* PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.1   1.2e-10     2e-07      27     211 ..      36     225 ..      25     232 .. 0.72

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 1.2e-10
                                    EEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCC...CCCC--.BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  27 taivGpNGSGKsnlldAilFvLGersakklrsekl...sdlihk.skekasvkkaeveitfdnedkklkiekeevsisrr 102
                                      +vG+ GSGKs l  Ail +L  r a+  r + l    dl++  ++e +++   e++i+f+++ ++    ++ + i  +
  gi|119720538|ref|YP_921033.1|  36 LGVVGESGSGKSTLGLAILRLLP-RYARVERGQVLyngADLLKLgEEELRRIRGREISIVFQDPYSS---LNPVMRIGDH 111
                                    579***************99999.4553444433222245666578888999999******999998...4555666555 PP

                                    EETTSE.EEEEETTEEE-HHHHHHHHHCTT-STT.......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HH CS
                                    xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 103 vkrkge.seykingkevtkkevsellesagiske.......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDek 174
                                     ++  e   y   ++e+  +   ++le++g+ +e       +LSgG+++ va+ L +A++      l++ Dei  aLD+ 
  gi|119720538|ref|YP_921033.1| 112 FVELFEeHGYGYSREEA-LRRAGDILERMGVPRErlsdyphQLSGGQRQRVAIGLALALNP----KLVVADEITTALDAL 186
                                    44433313344444443.34455566666665555555566*****************975....499************ PP

                                    HHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC-SCEEEE CS
                                    xxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 175 nvkkvaellkekskn..aQfivislreemlekadklvgv 211
                                      +++ +ll+e +k+  + ++ i+++ +++++    v v
  gi|119720538|ref|YP_921033.1| 187 VEAQIMDLLREVKKEydTSILFITHNMGLVAELADRVAV 225
                                    **********98887557888999998888776444444 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.1    0.0011       1.8       3      22 ..      37      56 ..      35      68 .. 0.87
   2 ?   -2.1   0.0       1.6   2.7e+03     261     285 ..      93     119 ..      87     134 .. 0.80
   3 !   18.0   0.0   1.2e-06     0.002     234     302 ..     150     216 ..     124     217 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0011
                         AAA_21  3 vliGpNgsGKSnLLdaldll 22
                                   +++G  gsGKS+L  a+  l
  gi|119720538|ref|YP_921033.1| 37 GVVGESGSGKSTLGLAILRL 56
                                   79************999887 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.6
                         AAA_21 261 lliDEpEngLHP..kllrrllellkel 285
                                    +++ +p ++L+P  ++  +++el++e+
  gi|119720538|ref|YP_921033.1|  93 IVFQDPYSSLNPvmRIGDHFVELFEEH 119
                                    678899999999544448888888664 PP

  == domain 3  score: 18.0 bits;  conditional E-value: 1.2e-06
                         AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSplll 302
                                    +++lS G+++  a+ +al+  +   +l++ DE+ + L+  + + +++ll+e ++  ++ +++ TH+  l+
  gi|119720538|ref|YP_921033.1| 150 PHQLSGGQRQRVAIGLALALNP---KLVVADEITTALDALVEAQIMDLLREVKKeYDTSILFITHNMGLV 216
                                    6899******999999999888...99**********************66666699*********9887 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   9.6e-07    0.0016       8     129 ..      36     210 ..      31     216 .. 0.65

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 9.6e-07
                         AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee........................................erpevvfvtl 47 
                                    l v+GesG+GK+tl   +l+ l+++a  e+                                        +         
  gi|119720538|ref|YP_921033.1|  36 LGVVGESGSGKSTLGLAILRLLPRYARVERgqvlyngadllklgeeelrrirgreisivfqdpysslnpvM--------- 106
                                    569**********************9999999***999999999999999998555555555555544442......... PP

                         AAA_22  48 psstsskdllrellralglelka...................erlsseellealeqalrarav........ielliiDEa 100
                                            +  ++++ +++ + +                   +r +++++ ++l    r+r +        ++l++ DE+
  gi|119720538|ref|YP_921033.1| 107 -------RIGDHFVELFEEHGYGysreealrragdilermgvPRERLSDYPHQLSGGQRQRVAiglalalnPKLVVADEI 179
                                    .......3333333333332222333444444444444455534444444444433333333355566678999999999 PP

                         AAA_22 101 qh.lr...seealeeLrsllnlsrkgvqliLvG 129
                                       l+   +++++  Lr+  +  +++++++++ 
  gi|119720538|ref|YP_921033.1| 180 TTaLDalvEAQIMDLLREVKK--EYDTSILFIT 210
                                    998876655777777777777..9999998875 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   2.6e-06    0.0043      14      46 ..      25      57 ..      21      73 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.6e-06
                         AAA_29 14 ghtieidlkgatlltGpsGsGKSTllDAiqalL 46
                                   g t+++++ ++  ++G+sGsGKSTl  Ai  lL
  gi|119720538|ref|YP_921033.1| 25 GVTLSVNPGEVLGVVGESGSGKSTLGLAILRLL 57
                                   4678888888889************77777766 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.2   6.4e-06     0.011       5      63 ..      16      71 ..      12     103 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 6.4e-06
                         AAA_16  5 ReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdql 63
                                   R+ e+e+L  +  +v+ g  e++ ++GesG+GKs+l  ++l +l  +++ + rg+   +
  gi|119720538|ref|YP_921033.1| 16 RQGEVEALGGVTLSVNPG--EVLGVVGESGSGKSTLGLAIL-RLLPRYARVERGQVLYN 71
                                   666777776666667766..78999***********98888.45555455555544444 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   3.8e-05     0.061       3      75 ..      35     106 ..      33     118 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.8e-05
                        DUF2075   3 vvlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlrealakkeekkkkkeafeklssfinnls 75 
                                    v+ V G++G+GK+ ++l++l  l + ++ ++ ++l+   +l++  +e+l++ + +++++ +f+++ s  n++ 
  gi|119720538|ref|YP_921033.1|  35 VLGVVGESGSGKSTLGLAILRLLPRYARVERGQVLYNGADLLKLGEEELRRIR-GREISIVFQDPYSSLNPVM 106
                                    56689******************999999999999999999999999998888.9999999999988888765 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.012        20      46      67 ..      32      53 ..       9      76 .. 0.84
   2 ?    5.5   0.1    0.0077        13      99     150 ..     161     214 ..     145     224 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.012
                      IstB_IS21 46 kkenivllGpsGvGKshlaial 67
                                     e + ++G sG GKs l  a+
  gi|119720538|ref|YP_921033.1| 32 PGEVLGVVGESGSGKSTLGLAI 53
                                   5677889***********9997 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0077
                      IstB_IS21  99 laralkrllkvdllilDdl..gllpldqaeaellfeviekryerrsiiitsnlp 150
                                    +a  l+  l+++l++ D++  +l  l +a+  +l++ ++k y+++ + it n+ 
  gi|119720538|ref|YP_921033.1| 161 VAIGLALALNPKLVVADEIttALDALVEAQIMDLLREVKKEYDTSILFITHNMG 214
                                    555566778899******833567899***********************9975 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1    0.0058       9.5      19      37 ..      33      51 ..      29      55 .. 0.87
   2 ?    4.0   0.1     0.016        26     118     162 ..     169     209 ..     163     228 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0058
                         ATPase 19 grvvlitGepGtGKtifal 37
                                   g+v  ++Ge+G+GK++++l
  gi|119720538|ref|YP_921033.1| 33 GEVLGVVGESGSGKSTLGL 51
                                   678889**********997 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.016
                         ATPase 118 ikakrvviDsitglayeekeavaReilrqlvrvlkklgvTailvs 162
                                    ++ k vv D it+      +a++ ++++ l+r++kk + T+il  
  gi|119720538|ref|YP_921033.1| 169 LNPKLVVADEITTA----LDALVEAQIMDLLREVKKEYDTSILFI 209
                                    67899999999998....68899999********99999988754 PP

>> NIR_SIR  Nitrite and sulphite reductase 4Fe-4S domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00031      0.51     102     145 ..      95     142 ..      36     145 .. 0.88
   2 ?   -1.7   0.0       1.1   1.8e+03     103     122 ..     172     191 ..     155     201 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00031
                                    E..EEEEGGGHHHHHHHHHHHHHHHS-CSSGGG-..SHHHHHHHHHHH CS
                                    x..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxx RF
                        NIR_SIR 102 l..gfvpeeevlevveaivevyrdhgdrknrkke..RlkylverlGve 145
                                    +  ++   + v+++ ++ ve++++hg+   r+ +  R ++++er+Gv 
  gi|119720538|ref|YP_921033.1|  95 FqdPYSSLNPVMRIGDHFVELFEEHGYGYSREEAlrRAGDILERMGVP 142
                                    255777777899999*********999999999999**********96 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.1
                                    EEEEGGGHHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxx RF
                        NIR_SIR 103 gfvpeeevlevveaivevyr 122
                                      v ++e++ +++a+ve + 
  gi|119720538|ref|YP_921033.1| 172 KLVVADEITTALDALVEAQI 191
                                    55667779999999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.57u 0.34s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 1922.80
//
Query:       gi|119720539|ref|YP_921034.1|  [L=293]
Description: binding-protein-dependent transport systems inner membrane component [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      1e-24   87.3  10.2      1e-24   87.3  10.2    1.7  3  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.2      0.52   9.4e+03     162     167 ..      19      24 ..      11      35 .. 0.40
   2 ?   -3.1   0.2      0.31   5.5e+03     154     172 ..      85     102 ..      68     106 .. 0.51
   3 !   87.3  10.2   5.8e-29     1e-24       1     183 [.     107     290 ..     107     292 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 0.52
                   BPD_transp_1 162 viavll 167
                                    + +v+l
  gi|119720539|ref|YP_921034.1|  19 TSLVAL 24 
                                    222222 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.31
                   BPD_transp_1 154 snggvlalviavlllnlva 172
                                    +  + + +v+av+ l++++
  gi|119720539|ref|YP_921034.1|  85 L-LAGARFVLAVAFLSTAV 102
                                    3.33333444444444444 PP

  == domain 3  score: 87.3 bits;  conditional E-value: 5.8e-29
                   BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilp.viillllsaapyvrlirraalrsl 79 
                                    g+llG+l++ + ++ ld++l+ +++ l+slP +++ai l         lg+++    +++++ +++ y+r++r ++l+  
  gi|119720539|ref|YP_921034.1| 107 GVLLGLLSG-YVGGLLDRALSLVMDSLYSLPGLIVAIALA------ALLGTGVVNmSMAIAVAYIPSYFRMVRGQVLSLK 179
                                    89*******.******************************......99*******99*********************** PP

                   BPD_transp_1  80 pkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis..... 154
                                    +  +veaar+ Ga++  +  + ++Pn++p i+++l+++f+ ++   + l+flg    lg    ++ +g+d++ +      
  gi|119720539|ref|YP_921034.1| 180 SAPFVEAARVAGAGPLDVALRQIMPNTFPAIASLLPITFADAIITEAGLSFLG----LGIEPPTPDWGFDLNKGRqffla 255
                                    *****************************************************....***************999***** PP

                   BPD_transp_1 155 ......nggvlalviavlllnlvadilqrlldprv 183
                                          +++ la+v+ vl ++l+   l+++l+p+ 
  gi|119720539|ref|YP_921034.1| 256 gywwigVFPGLAIVVTVLGFLLLGEGLNEMLNPKR 290
                                    *********************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1948.76
//
Query:       gi|119720540|ref|YP_921035.1|  [L=341]
Description: binding-protein-dependent transport systems inner membrane component [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.3e-37  128.5   8.7    2.3e-37  128.5   8.7    1.8  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
        9.8    5.8  13.8      0.031   13.9   2.5    2.5  3  MlaE          Permease MlaE


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.3      0.15   1.3e+03     106     122 ..      12      28 ..       5      45 .. 0.58
   2 !  128.5   8.7   2.5e-41   2.3e-37       1     185 []     116     340 ..     116     340 .. 0.99

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.15
                   BPD_transp_1 106 alppiitglilafggll 122
                                    +l+p++ +++l+f+++l
  gi|119720540|ref|YP_921035.1|  12 LLTPVMLFVLLSFVFIL 28 
                                    33333333333333332 PP

  == domain 2  score: 128.5 bits;  conditional E-value: 2.5e-41
                   BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf..................................... 43 
                                    gi lG+l+a+++   ++++ r+++ v++s+P+f l++ll++ +                                     
  gi|119720540|ref|YP_921035.1| 116 GIALGLLSARYQYTGVQYFARFYSSVVYSVPVFYLGLLLQAYLakplgfpttgrlspvnmvavdslpvrtgfvfidslaa 195
                                    899*************************************999************************************* PP

                   BPD_transp_1  44 ....vilsilghlilpviillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafg 119
                                        ++l++l h  lp+++l+++ ++ + r+++ ++ +++++d+ +aar +G ++w++++++ l+nal+pi+t  +l+++
  gi|119720540|ref|YP_921035.1| 196 grldILLDYLAHISLPALTLGVYLSGVFSRVTYLSVEDAMSQDYTQAARGRGIREWTVVKRYGLRNALIPILTMTGLQVA 275
                                    ******************************************************************************** PP

                   BPD_transp_1 120 gllggavlleflgswpGlgtllleailgydyseisnggvlalviavlllnlvadilqrlldprvrk 185
                                    +llggavl+e++++w G+g+l+ e il +dy+  + g+v +++++v l +lv+d+l++++dprvr+
  gi|119720540|ref|YP_921035.1| 276 ALLGGAVLTETTFNWEGVGLLVYEGILKRDYAIVQ-GAVTIYAVLVTLTSLVVDVLYAYVDPRVRY 340
                                    ***********************************.****************************95 PP

>> MlaE  Permease MlaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   2.5   3.5e-06     0.031      96     152 ..      89     143 ..      83     160 .. 0.82
   2 ?   -3.8   0.0       0.9   8.1e+03     110     127 ..     208     225 ..     204     242 .. 0.53
   3 ?   -2.2   1.4       0.3   2.7e+03     113     135 ..     265     288 ..     261     327 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.5e-06
                           MlaE  96 pikylvvPrvlAlvialplLtviadlvgilggylvavlllgispgaylqsvqealsl 152
                                    p++ylv+ r+ A++  ++  t+ia ++gi+ g l a +  + +  +y++++ +++  
  gi|119720540|ref|YP_921035.1|  89 PVAYLVASRLPATIELTVAATLIAAALGIALGLLSARY--QYTGVQYFARFYSSVVY 143
                                    99*******************************99887..47777788888777644 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 0.9
                           MlaE 110 ialplLtviadlvgilgg 127
                                    i+lp Lt+ + l g+++ 
  gi|119720540|ref|YP_921035.1| 208 ISLPALTLGVYLSGVFSR 225
                                    445555555555554433 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.3
                           MlaE 113 plLtviad.lvgilggylvavlll 135
                                    p+Lt+  + ++++lgg++++ +++
  gi|119720540|ref|YP_921035.1| 265 PILTMTGLqVAALLGGAVLTETTF 288
                                    666665541445555555544433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.22s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2499.14
//
Query:       gi|119720541|ref|YP_921036.1|  [L=529]
Description: extracellular solute-binding protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.7e-89  299.8   4.9    3.4e-89  299.4   4.9    1.1  1  SBP_bac_5  Bacterial extracellular solute-binding proteins, f
  ------ inclusion threshold ------
      0.022   14.3   0.1       0.13   11.8   0.0    2.0  2  OpuAC      Substrate binding domain of ABC-type glycine betai
      0.058   12.9   0.0       0.19   11.2   0.0    1.9  2  SieB       Super-infection exclusion protein B


Domain annotation for each model (and alignments):
>> SBP_bac_5  Bacterial extracellular solute-binding proteins, family 5 Middle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  299.4   4.9   5.7e-93   3.4e-89       1     376 [.      81     448 ..      81     449 .. 0.91

  Alignments for each domain:
  == domain 1  score: 299.4 bits;  conditional E-value: 5.7e-93
                                    SEEESSEEEEEEEETTTTEEEEEE-TT-B-TTSSB-SHHHHHHHHHHHHTGGGHCTTHHHHHCTCTEEEEEEEETTEEEE CS
                      SBP_bac_5   1 evvpaLAeswwevsdDgktytfkLRkgvkFsDGtpltAeDvvfsferlldpdtasgyaslleedqdikkveavddytvrf 80 
                                    ++v  LA s +++s+D k++++k+R ++kF+DGtpltA++vv+s+er+++ ++ +           i+k+eav d t+r+
  gi|119720541|ref|YP_921036.1|  81 KIVNKLAVS-YTISPDRKVWEIKIRRDAKFQDGTPLTAQAVVWSWERTIKLNQDPAFLIAD----LIEKAEAVSDDTIRV 155
                                    68999****.8*********************************************99998....6************** PP

                                    EESSETT..TTTTHCHHHHHHHGCCHTCTCTTTTTGTTTSE-BSSSEEEEEEETTTEEEEEE-TTSTTTSCSSSSEEEEE CS
                      SBP_bac_5  81 tlkkpna..lfltllaavpasiakkaaekeddkdkdtnekpvgtGPYklkefkpgqkivlernpdYwgggkpkldriefk 158
                                    +lk+p+   +  +lla + a ++  + + +  +  ++++ +   GPYkl+++kpg++i+l++np+Y+ g+kpk +ri+++
  gi|119720541|ref|YP_921036.1| 156 YLKQPFEetYVKSLLATWVAFPV--NPKTTPMEVVKPPNTVDMIGPYKLASWKPGEYIELVANPNYY-GEKPKTERIIIR 232
                                    *****996556777777777777..3434444444444444449**********************9.************ PP

                                    E-.SHHHHHHHHHTTSSSEE.ESTTCCTHCHHHHHTTEEEEEEEE.EEEEEEEEETTTSTGGGSHHHHHHHHHHS-HHHH CS
                      SBP_bac_5 159 vipdsdaraaalqsGeiddv.aepppsdieqlkeakglkvlyesp.gggvtylafNtkkppfddkrvRqAlsyAiDreei 236
                                    +++d+++ ++a+++Ge+d++   ++p+d++ + ++ +l+v +++p  + + yl+fN kk+pf+dkrvRqA++y iDr++i
  gi|119720541|ref|YP_921036.1| 233 FYKDAQSLRLAVENGEVDVAfRTLSPADVKDIIAKGQLQV-VSGPgIAPIRYLVFNVKKEPFNDKRVRQAIAYLIDRNQI 311
                                    **9999999999*****99888999999999999999999.6666156789***************************** PP

                                    HHHCT.TTSSEEESSSSTTTSTTCCSCHCCCSHH.SHHHHHHHHHHHTT-BCSSTSCEETCEEEEEEEEETTSHHHHHHH CS
                      SBP_bac_5 237 vkavl.egyatpansllppsspgadeeykpayka.ydpekAkklLkeaGykdgdggglrekklkltlllasgspaekaia 314
                                    v++v+ +  a+p +s++p ++ g+++++k+ y +  ++e+A++lL +aG+  ++  ++     +l ++ + ++pae +ia
  gi|119720541|ref|YP_921036.1| 312 VNTVFmGTFAQPLYSMVPIGFIGHKDSFKERYGDkPNVEAARQLLRQAGFSESNPLKM-----ELWFTPVRYTPAEPDIA 386
                                    ****967789********************9988999****************99887.....89*************** PP

                                    HHHHHHHHHTT.EEEEEEEECHHHHHHHHHHCTTESEEEEEEECTTSTTHHHHHHHHSTTCTT CS
                      SBP_bac_5 315 eliqqqlkkiG.ikvevktvdwaatylervkdgdfdmillgwgadypdpdnflnpflsssgag 376
                                    ++i+q+l++ G ikve+k+ dw aty +  k+ +  ++llgw++d+ d dn++ pf++s+++g
  gi|119720541|ref|YP_921036.1| 387 AIIKQNLEASGmIKVELKSADW-ATYRSLFKQEKIAVWLLGWFPDFLDSDNYVRPFYHSGANG 448
                                    **********************.************************************9887 PP

>> OpuAC  Substrate binding domain of ABC-type glycine betaine transport system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.12   7.3e+02      40      60 ..     238     258 ..     233     285 .. 0.73
   2 ?   11.8   0.0   2.2e-05      0.13      16     110 ..     385     483 ..     383     499 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.12
                                    HHHHHHHHTTSSSEEEEEEHH CS
                          OpuAC  40 avlfaalasGdiDvypeewtg 60 
                                    ++l+ a+++G++Dv+    ++
  gi|119720541|ref|YP_921036.1| 238 QSLRLAVENGEVDVAFRTLSP 258
                                    6788999******99855554 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 2.2e-05
                                    HHHHHHHHHHHTTE.EEEEEEEESHHHHHHHHHTTSSSEEEEEEHHHH..HHHHHHHHHHHHEEEEEEEESEEECEEEEE CS
                          OpuAC  16 laeilkqllekkGy.kveltnlgstavlfaalasGdiDvypeewtgta..yeaykkaveekkglevlgplgagnteglav 92 
                                    +a+i+kq le+ G  kvel +++  a+++   ++ +i v++ +w++ +  ++ y + +       +l  ++ + +    +
  gi|119720541|ref|YP_921036.1| 385 IAAIIKQNLEASGMiKVELKSADW-ATYRSLFKQEKIAVWLLGWFPDFldSDNYVRPFYHSGANGWLHVNYKNPVVDELI 463
                                    699********************8.8888888***************999666666666677778888888888888888 PP

                                    EHHHHH..HHTTTBHHHHCT CS
                          OpuAC  93 pkyvae..kygiksisDLkk 110
                                    +k v +  ++ ik+++++++
  gi|119720541|ref|YP_921036.1| 464 DKQVLQptEERIKTLAQIQD 483
                                    88887754477888888766 PP

>> SieB  Super-infection exclusion protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       1.1   6.7e+03      96     114 ..     156     174 ..     154     179 .. 0.79
   2 ?   11.2   0.0   3.2e-05      0.19      85     124 ..     437     477 ..     433     496 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.1
                           SieB  96 vltlplndpavkeLlekgi 114
                                    +l+ p ++ +vk+Ll++ +
  gi|119720541|ref|YP_921036.1| 156 YLKQPFEETYVKSLLATWV 174
                                    6778899999999998766 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 3.2e-05
                           SieB  85 vLreflnqgks.vltlplndpavkeLlekgiltkasnvsni 124
                                    ++r+f+ +g +  l   +++p+v eL++k++l+++ +  ++
  gi|119720541|ref|YP_921036.1| 437 YVRPFYHSGANgWLHVNYKNPVVDELIDKQVLQPTEERIKT 477
                                    67777877765145999*****************9985444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (529 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       729  (0.0406604); expected 358.6 (0.02)
Passed bias filter:                      648  (0.0361426); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.40
# Mc/sec: 3962.34
//
Query:       gi|119720542|ref|YP_921037.1|  [L=390]
Description: major facilitator transporter [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.6e-14   52.1  41.1    1.6e-13   50.3  38.1    2.1  2  MFS_1     Major Facilitator Superfamily
     0.0054   15.3  23.6       0.34    9.4   8.2    2.2  2  MFS_2     MFS/sugar transport protein


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.3  38.1   1.8e-17   1.6e-13       2     352 ..      13     346 ..      12     346 .. 0.74
   2 !   14.4  16.6   1.5e-06     0.013       2     177 ..     211     383 ..     210     390 .] 0.79

  Alignments for each domain:
  == domain 1  score: 50.3 bits;  conditional E-value: 1.8e-17
                          MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllf 81 
                                    + ++++ +la ++l++++p++l  +lg++++e+glll++  l+++++++p+++++d  Gr+++ +++++l + ++l+l  
  gi|119720542|ref|YP_921037.1|  13 AALYVIFSLANGLLAVVMPPYL-LHLGFTGAEAGLLLAVMNLAMIAGMVPFSYVADLKGRKPLAIAAFALALPAGLALY- 90 
                                    668999*************755.89*************************************99999999999955555. PP

                          MFS_1  82 asslw.lllvlrvlqGlgagalfpagaaliadwfpk.eergraigllsagfslGailgpllggllasslg......Wrav 153
                                     s    +++++ +l Gl+ ++++ + + l+ad + + e   +a+  l++ + +++  g+l++++   slg         +
  gi|119720542|ref|YP_921037.1|  91 -SANKaAVFAAYLLNGLANSMAVVSLNPLVADSAGRrEVMEKAFTALQVLSLVSSSAGMLVAAAYP-SLGaadrvsAYRS 168
                                    .445559*****************************555679****************99999554.5555766665556 PP

                          MFS_1 154 fyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllply 233
                                    +++ a ++lla+++  ll ++e+ ++++ ++ ++          + ++++        +l+a+l++  g  + +  +  y
  gi|119720542|ref|YP_921037.1| 169 MILYAYLGLLAGLV-PLLGVREEYRPGPRNGLRL----------S-FSKVSLEL----ALLAALTGL-GAGIGVWNSGYY 231
                                    68888888888885.4444455555555555555..........3.55565555....444444442.333333333334 PP

                          MFS_1 234 lqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvl.iGf 312
                                    + + +g   ++++g+   +  ++ a++ lla   s+rlg   + + + l+ + ++++ al + +    ++++++++  ++
  gi|119720542|ref|YP_921037.1| 232 FSKKFGVE-AFELGIRGVAENALLAAATLLAPLASRRLGTLGAVVAFQLASVPLLAATALSPSF----VYAAAFFTaRSM 306
                                    46667777.5666655555555555555566666688886445555555555555555555444....333344444788 PP

                          MFS_1 313 glgfvfpsllalasdlappeeagtasglfntagslggalg 352
                                     +  ++p+l al ++l+ + e++++s l ++a++l g++g
  gi|119720542|ref|YP_921037.1| 307 LMNAANPLLSALQMSLVEEGERARLSMLLTLAFQLPGSIG 346
                                    99999********************************997 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 1.5e-06
                          MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll. 80 
                                    +l+a+l++l+++i   +   + ++ +g+ + e+g+  ++  ++ a+a+l++   s r+G    +++  l+++   l+++ 
  gi|119720542|ref|YP_921037.1| 211 ALLAALTGLGAGIGVWNSGYYFSKKFGVEAFELGIRGVAENALLAAATLLAPLASRRLGTLGAVVAFQLASVPL-LAATa 289
                                    56667777777763333333999************999977777777777777777787777666666666666.33332 PP

                          MFS_1  81 fasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilai 159
                                    + s+++ + +++    ++ + a++p+  al   ++ + er+r   ll+++f+l   +g ++gg+l+  +   ++ y+  +
  gi|119720542|ref|YP_921037.1| 290 L-SPSFvYAAAFFTARSMLMNAANPLLSALQMSLVEEGERARLSMLLTLAFQLPGSIGSAIGGYLM-DVQIDLPIYLTSA 367
                                    4.67776999999999**************************************************.7789999999999 PP

                          MFS_1 160 vsllafvlfllllpeepp 177
                                    v+++   l  l+ + +p+
  gi|119720542|ref|YP_921037.1| 368 VYAVQTAL--LYTLLKPH 383
                                    99998776..55555554 PP

>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3  10.3   4.2e-05      0.37     225     349 ..       8     129 ..       3     153 .. 0.88
   2 !    9.4   8.2   3.8e-05      0.34     175     347 ..     169     327 ..     132     374 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 4.2e-05
                          MFS_2 225 aflillllfllaalalgvlnglllYyltyvlgngsaasvfllvvtisallgiplwqplakrlgkkntyllgalltivllv 304
                                     + +l++l+++++la g+l+  +  yl +   +g++a ++l+v+ +++++g++ ++++a   g+k +++++++l+++ ++
  gi|119720542|ref|YP_921037.1|   8 NLKLLAALYVIFSLANGLLAVVMPPYLLHLGFTGAEAGLLLAVMNLAMIAGMVPFSYVADLKGRKPLAIAAFALALPAGL 87 
                                    56678999999999999999999988887555************************************************ PP

                          MFS_2 305 lvlllqpsnlllflvllviagfgvgvaallpwsmladvvDygelk 349
                                     ++ +   n +++++++++ g++  +a++ +  ++ad++   e++
  gi|119720542|ref|YP_921037.1|  88 ALYSA---NKAAVFAAYLLNGLANSMAVVSLNPLVADSAGRREVM 129
                                    **999...8899999999999999999999999999998776665 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 3.8e-05
                          MFS_2 175 aliialLmllgviivvlgtkervemrkkekteqkeklslleqlkevfrnraflillllfllaalalgvlnglllYyltyv 254
                                    ++++a L ll+ ++  lg++e+  +          +   +++l+ +f++   l l+ll+ l+ l+ g++  ++ Yy+ + 
  gi|119720542|ref|YP_921037.1| 169 MILYAYLGLLAGLVPLLGVREE--Y----------RPGPRNGLRLSFSK-VSLELALLAALTGLGAGIGVWNSGYYFSKK 235
                                    4556666666666666666655..2..........34456777888877.455677777778888899999999999999 PP

                          MFS_2 255 lg.ngsaasvfllvvtisallgiplwqplakrlgkkntyllgalltivllvlvlllqpsnlllflvllviagfgvgvaal 333
                                     g ++++  +  ++  ++ +++++l++ + +rlg   ++++++l+ ++ll+ + l  ps ++++ ++++ +++ + +a+ 
  gi|119720542|ref|YP_921037.1| 236 FGvEAFELGIRGVAENALLAAATLLAPLASRRLGTLGAVVAFQLASVPLLAATALS-PSFVYAAAFFTARSML-MNAANP 313
                                    999**********************************************9999998.6666665555555444.488999 PP

                          MFS_2 334 lpwsmladvvDyge 347
                                    l+ ++ + +v++ge
  gi|119720542|ref|YP_921037.1| 314 LLSALQMSLVEEGE 327
                                    99999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2556.05
//
Query:       gi|119720543|ref|YP_921038.1|  [L=503]
Description: amino acid permease-associated region [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-55  189.1  37.6    1.8e-55  188.5  37.6    1.3  1  AA_permease_2   Amino acid permease
    9.9e-36  123.3  42.2    2.7e-35  121.9  42.2    1.7  1  AA_permease     Amino acid permease
     0.0024   16.8  11.2      0.026   13.4  11.2    2.4  1  Spore_permease  Spore germination protein


Domain annotation for each model (and alignments):
>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.5  37.6     3e-59   1.8e-55       1     405 [.       8     415 ..       8     455 .. 0.86

  Alignments for each domain:
  == domain 1  score: 188.5 bits;  conditional E-value: 3e-59
                  AA_permease_2   1 lsllsafalvigsvigsgifvkn..laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkkvaf 78 
                                    l+ll ++++++g +igsgif+ +   + ++g +++l +++a +++ + v+lv+aEl+sa+ + gG yvy++aafg+ v+f
  gi|119720543|ref|YP_921038.1|   8 LGLLELVGISVGGIIGSGIFMMPslTLSTAGLSALLAWILAGVAM-TVVALVFAELGSAFGDTGGPYVYARAAFGRTVGF 86 
                                    7899*******************9544457777777777777765.9*********998********************* PP

                  AA_permease_2  79 lsawfnwfayvpvlasilsvaasyllnalgp..dlqgntwltyliaiaililvalinirgikesakiqnilgilkillpl 156
                                    l++w + ++ v+++++++++++syl +++ +  ++q  t   +l + a+l++++l+n++g+k ++ +++ +++lk+ + l
  gi|119720543|ref|YP_921038.1|  87 LVGWGYYVSCVLTVSAVTAAFVSYLGFFVPGlvEGQRLTPVGVLAGLAFLWFLTLLNYVGVKYGGLYASATTLLKV-FAL 165
                                    ***************************9955454444466789999******************************.59* PP

                  AA_permease_2 157 iiliilglitvdgggfsslstetdtffpngwpg.vllgllivlwsfdGfesaanvseevkk..kdvpkaifigllivlvl 233
                                    +i+ ++gl++  ++ f+        ++ +       l+ + ++w + Gfes++  +eevkk  +dvp+ i+++++iv+ +
  gi|119720543|ref|YP_921038.1| 166 AIFAAAGLAYPEPSRFN--------VLEGLDAVsLGLAVSLAVWPYMGFESVTIPVEEVKKpqRDVPLSIILSMGIVTAV 237
                                    ***********999997........55555554235556669****************998889**************** PP

                  AA_permease_2 234 yllvniaflgvvpddei.......anlsnlgsvaalffeavggkvvaiivvilialsllgaintavigssrvlealardg 306
                                    y+l+ ++fl  + ++++        +l+nl s+++ +++  g  +va++v++++++s  ga   +++ s r+ +a+++ g
  gi|119720543|ref|YP_921038.1| 238 YVLIVLSFLSLLDWKSLglaqgdwGSLANLSSPLSDVARSRGLLAVAVAVMLGAVFSTGGASGVWLLDSGRFPYAFSQAG 317
                                    *****************7766666445555555666666655559999******************************** PP

                  AA_permease_2 307 vlPrffakvn.kfgspiraiiltaivslillllfllassaaynfllsvsslgliisyllliigalilrkkrphlkr...p 382
                                     lP+++ kv+ ++g+p +++ l+ iv++++l+l+ l     + +++ ++++ +i++y++ ++g+ +lr +   ++    p
  gi|119720543|ref|YP_921038.1| 318 DLPKVLGKVHdRYGTPHVGLLLSSIVASAVLVLLPL-----FPAIALLGVMTSIVPYAVSSLGLAVLRGRGDYRPAfrnP 392
                                    ****************************99999988.....78*************************997766444454 PP

                  AA_permease_2 383 gkilvaiigalfllfllvalffp 405
                                       lva ++++f++++ ++ ++p
  gi|119720543|ref|YP_921038.1| 393 FGKLVAYVSFVFSTLVAYWSCWP 415
                                    44667888888887777777776 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.9  42.2   4.5e-39   2.7e-35       4     436 ..      15     433 ..      12     469 .. 0.87

  Alignments for each domain:
  == domain 1  score: 121.9 bits;  conditional E-value: 4.5e-39
                    AA_permease   4 vialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviGlnyl 83 
                                     i++gg+iG g+f+  + +ls+aG+ +alla++lagv ++ v+l ++e+ +++  +gg y+ya+   g+ +Gf +G+ y 
  gi|119720543|ref|YP_921038.1|  15 GISVGGIIGSGIFMMPSLTLSTAGL-SALLAWILAGVAMTVVALVFAELGSAFGDTGGPYVYARAAFGRTVGFLVGWGYY 93 
                                    589**********************.9***************************************************** PP

                    AA_permease  84 fswitvlaleltaasiliqfwelvtdlpkawvt.......gavflvvlliinlvgvkvygeaefilalikiiaiiafiiv 156
                                    +s ++++ + ++a +++++f   v+ l +           g+ fl +l+++n+vgvk+ g     ++l+k+ a+++f   
  gi|119720543|ref|YP_921038.1|  94 VSCVLTVSAVTAAFVSYLGFF--VPGLVEGQRLtpvgvlaGLAFLWFLTLLNYVGVKYGGLYASATTLLKVFALAIFAAA 171
                                    *********************..999995444489******************************************999 PP

                    AA_permease 157 giillaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvi..vvfaftGielvaiiagEvkdPeksiPk 234
                                    g   la  +p+++               n+ +g        + ++  ++++  +v  ++G+e+v+i  +Evk P++++P 
  gi|119720543|ref|YP_921038.1| 172 G---LAYPEPSRF---------------NVLEG--------LDAVSLGLAVslAVWPYMGFESVTIPVEEVKKPQRDVPL 225
                                    9...778888889...............78888........5555555544116788*********************** PP

                    AA_permease 235 ailqvviritifYvlsllligllvprndlgllndsasa....aspfvifikesgvsvlaplinaviltaalssansslys 310
                                    +i+  + ++t +Yvl++l+  +l+++++lgl ++        +sp+  + +++g+ ++a+ + ++   ++ +++   l  
  gi|119720543|ref|YP_921038.1| 226 SIILSMGIVTAVYVLIVLSFLSLLDWKSLGLAQGDWGSlanlSSPLSDVARSRGLLAVAVAVMLGAVFSTGGASGVWLLD 305
                                    *******************************99655448899*****************999999999999999999999 PP

                    AA_permease 311 asRvlyslakdglaPkvl.kkvskrgvPlraillsmiisllalllaslnlaapivfnfllaisaliglivwlliilsyl. 388
                                    + R  y++++ g +Pkvl k+++++g P++++lls+i++ ++l+l  l +a  i+   ++++   ++++ ++l+ l    
  gi|119720543|ref|YP_921038.1| 306 SGRFPYAFSQAGDLPKVLgKVHDRYGTPHVGLLLSSIVASAVLVLLPLFPA--IALLGVMTSIVPYAVSSLGLAVLRGRg 383
                                    ***************6652778*********************99999999..9*******************9999887 PP

                    AA_permease 389 rfRkalky.qgrsie.elgfkaallplgvilvlaaliiillilalyaylt 436
                                     +R+a++   g+ ++  +++ + l+ +++++ ++++ ++l+++ +  +++
  gi|119720543|ref|YP_921038.1| 384 DYRPAFRNpFGKLVAyVSFVFSTLVAYWSCWPWTLVGALLTLAVVPVFAR 433
                                    89999976244444414555677788888888888888877666555555 PP

>> Spore_permease  Spore germination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4  11.2   4.4e-06     0.026      12     237 ..      18     252 ..       8     258 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.4e-06
                 Spore_permease  12 vsfqlGvgiltlprsvaeqatpdgWisvllagiiililvllmlkllkkfpe.ktliellkkilgkwLGsllsilfilyFl 90 
                                    v  ++G+gi ++p     +a+ ++ ++ +lag+++ +++l++ +l + f +    + + ++ +g+ +G+l +  + +  +
  gi|119720543|ref|YP_921038.1|  18 VGGIIGSGIFMMPSLTLSTAGLSALLAWILAGVAMTVVALVFAELGSAFGDtGGPYVYARAAFGRTVGFLVGWGYYVSCV 97 
                                    6678*********************************************862679************************* PP

                 Spore_permease  91 llaafelRefseliqvfl......ledtplwiii.lllllvilYlvvkGieslar...eflfiivilliilllillfslk 160
                                    l+++ ++  f+  + +f+         tp+ ++  l +l+   +l + G++          ++ v+ l+i+ +  l   +
  gi|119720543|ref|YP_921038.1|  98 LTVSAVTAAFVSYLGFFVpglvegQRLTPVGVLAgLAFLWFLTLLNYVGVKYGGLyasATTLLKVFALAIFAAAGLAYPE 177
                                    *****************933322112355544433556666666666666543310012344444444444444444444 PP

                 Spore_permease 161 laeiknlrPvlgngikpvlks..lkttslsflgveillllvpflkdkkk.vkkaallgvlistllyllttlivilvlsve 237
                                       ++     + +g+  v  +  ++ ++ +++g+e +++ v+ +k++++ v   ++l+++i+t +y+l++l  ++ l+ +
  gi|119720543|ref|YP_921038.1| 178 PSRFN-----VLEGLDAVSLGlaVSLAVWPYMGFESVTIPVEEVKKPQRdVPLSIILSMGIVTAVYVLIVLSFLSLLDWK 252
                                    44444.....44677777666557788999************999987615667889***********999999888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (503 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       823  (0.0459033); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.42
# Mc/sec: 3577.10
//
Query:       gi|119720544|ref|YP_921039.1|  [L=486]
Description: major facilitator transporter [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-52  176.9  81.2    6.1e-40  137.2  56.1    2.7  2  MFS_1     Major Facilitator Superfamily
    2.9e-09   36.3  11.2    2.9e-09   36.3  11.2    2.6  3  Sugar_tr  Sugar (and other) transporter


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.2  56.1   6.8e-44   6.1e-40       2     352 ..      17     408 ..      16     409 .. 0.89
   2 !   53.7  17.1   1.6e-18   1.5e-14       3     146 ..     271     418 ..     269     472 .. 0.82

  Alignments for each domain:
  == domain 1  score: 137.2 bits;  conditional E-value: 6.8e-44
                          MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll. 80 
                                     l+af+++l++ i+ + l   +a++l ++  e+ + + +y+lg+ ++ l++G l+d +Gr +++  g+llf lg  +l+ 
  gi|119720544|ref|YP_921039.1|  17 TLGAFMAGLDARIVVVGLD-VIASALKADIEEALWFTQAYMLGSTLMLLLAGKLADLYGRVKLYAYGFLLFTLG-SILSg 94 
                                    589****************.9*****************************************************.44442 PP

                          MFS_1  81 fasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilai 159
                                      +  +  l+++r+lqGlgag+l++++a++i+d++ +   ++a+++ s++f lG+ilg  ++gl++ +lgWr++fy++ +
  gi|119720544|ref|YP_921039.1|  95 A-AATPlQLAASRFLQGLGAGVLTTLSATIITDVAVGGPLAFALSINSLAFRLGSILGLTASGLIIGLLGWRGIFYVNVP 173
                                    3.555669************************************************************************ PP

                          MFS_1 160 vsllafvlfllllpeepperkrkspkeee...............................................kgtg 192
                                    v++ +++l     + +++  +r++p  ++                                               + + 
  gi|119720544|ref|YP_921039.1| 174 VGIAGAIL--SRKRLRETYTPREKPLIDWvgfclftvsllglllaltfyayglsyrsfarllllvsaacfllfiavEARS 251
                                    *****999..777778888888888888888*******************999988777776655554444444444444 PP

                          MFS_1 193 paplvpawkallkdpvl.......w...illialllfffgfsglltllplylqevlglsglllaglllallalvgailal 262
                                     +p+            l       w      ia +l++++f +++ ll+ly    l  s ++++g+ l  + l +++++l
  gi|119720544|ref|YP_921039.1| 252 DHPI------------LdlslfriWgftGGNIAQFLNAVAFGAVMLLLTLYYEVALRKS-AFETGISLLPFELSFLAFGL 318
                                    4444............243333335666688888888889999********99999999.8******************* PP

                          MFS_1 263 lagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvliGfglgfvfpsllalasdlappeeagtasglfn 342
                                    l+grlsdr+g  ++ +l+ll+++la l+l  l v++s++l+++ ++l+G g g++ ++ ++++++++ppe++g as++  
  gi|119720544|ref|YP_921039.1| 319 LSGRLSDRYGYVKFAILGLLVGSLAQLLLGGLTVSTSPALVAAYSALLGAGNGLFLSPNTSAIMSSVPPERRGVASAIRA 398
                                    ******************************************************************************** PP

                          MFS_1 343 tagslggalg 352
                                    +++++g+ ++
  gi|119720544|ref|YP_921039.1| 399 IVFNVGMTIS 408
                                    ******9986 PP

  == domain 2  score: 53.7 bits;  conditional E-value: 1.6e-18
                          MFS_1   3 laaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll.f 81 
                                    +a+fl+a a+++++++l+l++  +l  s+ e g+ l  + l ++++ l+ Grlsdr+G  ++ +lgll+ +l+ lll  +
  gi|119720544|ref|YP_921039.1| 271 IAQFLNAVAFGAVMLLLTLYYEVALRKSAFETGISLLPFELSFLAFGLLSGRLSDRYGYVKFAILGLLVGSLAQLLLGgL 350
                                    68899999999999999887777777777777777777999999999999999999999999999999999994444446 PP

                          MFS_1  82 a.sslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllgglla.s 146
                                    + s+++ l+++  +l G+g g++++   ++i   +p+e+rg a ++ ++ f++G+ +   ++ +l+ +
  gi|119720544|ref|YP_921039.1| 351 TvSTSPaLVAAYSALLGAGNGLFLSPNTSAIMSSVPPERRGVASAIRAIVFNVGMTISLNIAVILIsT 418
                                    56888988999999999999999999999999999999999999999999999999987777777734 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3  11.2   3.2e-13   2.9e-09      48     187 ..      48     181 ..      13     189 .. 0.87
   2 ?   -5.9   2.7         2   1.8e+04     320     360 ..     206     245 ..     202     249 .. 0.40
   3 ?    1.5   5.9     0.012   1.1e+02      49     161 ..     303     415 ..     263     435 .. 0.78

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 3.2e-13
                                    HHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHH CS
                       Sugar_tr  48 sglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyi 127
                                      +++ ++++G+++  l+ag+l+d +GR k ++ + +lf  g++l++aa    +  +l+++R+l G+g+G+ ++l+ + i
  gi|119720544|ref|YP_921039.1|  48 ALWFTQAYMLGSTLMLLLAGKLADLYGRVKLYAYGFLLFTLGSILSGAAA---TPLQLAASRFLQGLGAGVLTTLSATII 124
                                    579***********************************************...9************************** PP

                                    HTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHH CS
                       Sugar_tr 128 sEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllil 187
                                      +A      +  s++ la  +G +++ +    +    +   wr  +++++   ++ +il
  gi|119720544|ref|YP_921039.1| 125 TDVAVGGPLAFALSINSLAFRLGSILGLTASGLIIGLLG---WRGIFYVNVPVGIAGAIL 181
                                    ****99999999999*****9999999877666555555...888888888887776665 PP

  == domain 2  score: -5.9 bits;  conditional E-value: 2
                                    HHHHHHHHHHHHHHHH..HHHHTTSS...CHHHHHHHHHHH CS
                       Sugar_tr 320 lllGaagmaicfvilgivalllvakskaasivaivfialfi 360
                                    + ++++g ++++++++   l +++       v+ ++++lfi
  gi|119720544|ref|YP_921039.1| 206 FTVSLLGLLLALTFYA-YGLSYRSFARLLLLVSAACFLLFI 245
                                    3444444444444444.222222222333333444444444 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.012
                                    HHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHH CS
                       Sugar_tr  49 glivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyis 128
                                    g+++  f +  ++ +l++g l+dr+G+ k  + + ++ + +++l +  +  +s  ++++   l+G g Gl+    +  i 
  gi|119720544|ref|YP_921039.1| 303 GISLLPFELSFLAFGLLSGRLSDRYGYVKFAILGLLVGSLAQLLLGGLTVSTSPALVAAYSALLGAGNGLFLSPNTSAIM 382
                                    5555555555566678999999*****99999999999999999999999999999999999999999998777777777 PP

                                    TTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Sugar_tr 129 EiApkklRgalvslyqlaitfGilvaaifglgl 161
                                       p++ Rg    +      +G+ ++  + ++l
  gi|119720544|ref|YP_921039.1| 383 SSVPPERRGVASAIRAIVFNVGMTISLNIAVIL 415
                                    777889999888888888888877766665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (486 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 3162.42
//
Query:       gi|119720545|ref|YP_921040.1|  [L=203]
Description: multiple antibiotic resistance (MarC)-related proteins [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.6e-37  127.1  12.4    6.9e-37  126.8  12.4    1.0  1  MarC      MarC family integral membrane protein


Domain annotation for each model (and alignments):
>> MarC  MarC family integral membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.8  12.4   3.8e-41   6.9e-37       7     202 ..      15     198 ..       9     199 .. 0.93

  Alignments for each domain:
  == domain 1  score: 126.8 bits;  conditional E-value: 3.8e-41
                           MarC   7 afvsLlaiinplgnvpvflslleevskeerkrialkasilallillvfllfGelilklfgisidalkiaGgillfliaid 86 
                                    ++v L+a++np++ +p f+ l+e  +++e+ + ++kas++++ +++vf l+G+ +l+l+++si +l+++Gg+ll++ia+d
  gi|119720545|ref|YP_921040.1|  15 VAVQLYAVLNPVSVIPTFVNLTEGLDSREKVHAVRKASMIVFSLMVVFSLIGDPLLRLLNVSIASLRLGGGVLLMVIAVD 94 
                                    5799**************************************************************************** PP

                           MarC  87 mlkakqkkekkkkseeeeseekdeiavvPLAlPliaGPgaittvlvlaseassivekvavvlaillaalitllilllssl 166
                                    ml++  ++    k      e+ de  vvP+A+Pl+ GPg+itt++vl+++        +++l  lla+l+++ +l   ++
  gi|119720545|ref|YP_921040.1|  95 MLSGMSRT----KGL----ESGDEALVVPIATPLLVGPGTITTLIVLSASEGLP----VTLLGALLATLLVYATLAFGES 162
                                    ****9993....233....34699***********************9998874....788888999999999******* PP

                           MarC 167 ilrllgktginaleRlmGllLvalavqlivdGikei 202
                                    +l+llg++ ++ l R m+++++ ++ ++i  ++ e+
  gi|119720545|ref|YP_921040.1| 163 LLELLGRNFVRSLGRFMAIIIAGISAEMIHRALLEW 198
                                    *****************************9999775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1367.20
//
Query:       gi|119720546|ref|YP_921041.1|  [L=81]
Description: hypothetical protein Tpen_1643 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       231  (0.0128842); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 617.49
//
Query:       gi|119720547|ref|YP_921042.1|  [L=247]
Description: GCN5-related N-acetyltransferase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.2e-16   58.9   0.1      2e-15   57.0   0.1    1.8  2  Acetyltransf_1   Acetyltransferase (GNAT) family
    1.6e-13   50.7   0.0      1e-11   44.9   0.0    2.1  2  Acetyltransf_10  Acetyltransferase (GNAT) domain
    8.6e-11   42.1   0.1      2e-10   41.0   0.1    1.6  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    0.00021   21.5   0.1    0.00045   20.4   0.1    1.5  1  Acetyltransf_6   Acetyltransferase (GNAT) domain
     0.0023   17.9   0.0     0.0046   16.9   0.0    1.5  1  FR47             FR47-like protein
  ------ inclusion threshold ------
      0.063   13.4   0.0       0.33   11.0   0.0    2.2  2  Acetyltransf_9   Acetyltransferase (GNAT) domain
      0.073   13.2   0.0       0.52   10.4   0.0    2.0  2  Acetyltransf_4   Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.0   0.1   7.9e-19     2e-15      35     117 .]      11      89 ..       3      89 .. 0.93
   2 ?   -0.6   0.0       0.6   1.5e+03      31      55 ..     151     176 ..     125     232 .. 0.58

  Alignments for each domain:
  == domain 1  score: 57.0 bits;  conditional E-value: 7.9e-19
                                    EEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETTEHHHHHHHHH CS
                 Acetyltransf_1  35 llvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlaveedndaairlYek 114
                                     lvae++ e++Gf+ ++k  +    +ay++slaV+p+yr  G+G +Ll  lee + ++g+++i l v ++n +a  +Y +
  gi|119720547|ref|YP_921042.1|  11 VLVAERGSEVLGFVIAYKHRE----RAYVDSLAVDPAYRDLGIGGRLLSGLEELLAKRGVERIALSVKDSNLRALDFYLR 86 
                                    4569999************99....9****************************************************99 PP

                                    TTE CS
                 Acetyltransf_1 115 lGF 117
                                     G+
  gi|119720547|ref|YP_921042.1|  87 RGY 89 
                                    998 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.6
                                    TTC.EEEEEEETTEEEEEEEEEEEET CS
                 Acetyltransf_1  31 eae.gllvaeedgeliGfisllkipd 55 
                                     a+  +l a++ g++ G + ++ +++
  gi|119720547|ref|YP_921042.1| 151 GAGeKTLTAYKSGRVRGVAEFSADDE 176
                                    44445556777777777776666666 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.9   0.0   3.9e-15     1e-11      29     110 ..       7      93 ..       2      95 .. 0.89
   2 ?    3.7   0.0     0.021        54      30     111 ..     153     237 ..     129     241 .. 0.82

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 3.9e-15
                Acetyltransf_10  29 gealllvaeeggkivGvi.elrdgs..hisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp.yavpfYek 103
                                    ++ ++lvae+g +++G++ +++ ++  ++  l+Vdp+yr  Gig +Ll  +ee + k+g +  +l+v+ s+  a +fY +
  gi|119720547|ref|YP_921042.1|   7 SRRIVLVAERGSEVLGFViAYKHREraYVDSLAVDPAYRDLGIGGRLLSGLEELLAKRGVERiALSVKDSNlRALDFYLR 86 
                                    566799**********99644444456***************************99************************ PP

                Acetyltransf_10 104 lGFkavg 110
                                     G+ +vg
  gi|119720547|ref|YP_921042.1|  87 RGYGVVG 93 
                                    ***8875 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.021
                Acetyltransf_10  30 ealllvaeeggkivGviel.rdgshisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp.yavpfYeklGF 106
                                      ++l a+++g++ Gv+e   d++  +  +  ++y +    +aLl+  ++   ++gi +  + v++s+   v+   + GF
  gi|119720547|ref|YP_921042.1| 153 GEKTLTAYKSGRVRGVAEFsADDEVFADYVALSSYSSVEALRALLKGFRDFGLEAGIDTlVIPVDSSKqVVVEELSRSGF 232
                                    45678899999********8888899999999999999999999999999977999999999999999778888888888 PP

                Acetyltransf_10 107 kavge 111
                                    ++++ 
  gi|119720547|ref|YP_921042.1| 233 RTLKT 237
                                    87755 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   0.1   7.6e-14     2e-10       4      74 ..      10      89 ..       7      91 .. 0.76

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 7.6e-14
                                   EEEEEEETTEEEEEEEEEEES..TCTEEEEE-GGGTTSSHHHHHHH.HTT....SEEEEEEEEE..THH.HHHHHHHHTTE CS
                 Acetyltransf_7  4 evfVaeddgkivGfialslld..aeitrlaVdpeyrgkGiGraLle.aae....kgiileqlel..nae.kaikfYeklGF 74
                                    v+Vae++ +++Gf++++ +   a+   laVdp+yr  GiG +Ll  ++e    +g++ + l +  + + +a++fY + G+
  gi|119720547|ref|YP_921042.1| 10 IVLVAERGSEVLGFVIAYKHRerAYVDSLAVDPAYRDLGIGGRLLSgLEEllakRGVERIALSVkdS-NlRALDFYLRRGY 89
                                   689************9999987666666*****************8642234557755223333323.2599********9 PP

>> Acetyltransf_6  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.1   1.8e-07   0.00045      73     137 ..      11      75 ..       3      80 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.8e-07
                 Acetyltransf_6  73 lyvlrldgrpvAvalglrsgdrlyywlggydpelaklspgllllweliedaaeeGlrrfdlgggd 137
                                    ++v++ + +++++++++++++r+y    ++dp++++l++g  ll  l e +a +G++r+ l   d
  gi|119720547|ref|YP_921042.1|  11 VLVAERGSEVLGFVIAYKHRERAYVDSLAVDPAYRDLGIGGRLLSGLEELLAKRGVERIALSVKD 75 
                                    67888999*************************************************99987766 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.8e-06    0.0046      19      77 ..      30      89 ..      16      94 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.8e-06
                                   -TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-.EEEEEETT-HHHHHHHHHHT- CS
                           FR47 19 kdggelgalqvlpehrrrGlgsrlvkalakeiaergkt.vllvvvasNtpsirlyeklGf 77
                                   ++  ++ +l v+p  r  G g+rl + l + +a+rg + + l v+ sN ++  +y + G+
  gi|119720547|ref|YP_921042.1| 30 RERAYVDSLAVDPAYRDLGIGGRLLSGLEELLAKRGVErIALSVKDSNLRALDFYLRRGY 89
                                   555677899*************************9966156678889********99888 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00013      0.33      72     127 ..      31      91 ..       5      92 .. 0.87
   2 ?   -2.1   0.0       1.5   3.8e+03     112     126 ..     139     153 ..     124     155 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00013
                                    EEEEEEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--.....SSHHHHHTTT-EE CS
                 Acetyltransf_9  72 kaagvtgVavapehrgrgvlskLlaraleemreegqplsllfP.....ssipiYrrfGyei 127
                                    + a+v + av+p +r  g+  +Ll  + e ++++g++ + l       ++ ++Y r Gy++
  gi|119720547|ref|YP_921042.1|  31 ERAYVDSLAVDPAYRDLGIGGRLLSGLEELLAKRGVERIALSVkdsnlRALDFYLRRGYGV 91 
                                    5589999*******************************9999999887778********97 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.5
                                    E--SSHHHHHTTT-E CS
                 Acetyltransf_9 112 lfPssipiYrrfGye 126
                                      P  + iY+++G +
  gi|119720547|ref|YP_921042.1| 139 TEPVDRMIYKKYGAG 153
                                    567888999999976 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0    0.0002      0.52      86     138 ..      41      93 ..      10     100 .. 0.87
   2 ?    0.6   0.0      0.22   5.7e+02      97     140 ..     195     238 ..     146     244 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0002
                 Acetyltransf_4  86 erdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhkalGFelvg 138
                                    + + ++ g+g  l+  le+ l++ ++e++  ++  +n  + +f+ + G+ +vg
  gi|119720547|ref|YP_921042.1|  41 DPAYRDLGIGGRLLSGLEELLAKRGVERIALSVKDSNLRALDFYLRRGYGVVG 93 
                                    466788999999*************************************9998 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.22
                 Acetyltransf_4  97 elidaleqvlkeqnienllaeiaspnensiqfhkalGFelvgif 140
                                    +l++   ++  e +i +l++++ s+++  ++ ++++GF+ ++ +
  gi|119720547|ref|YP_921042.1| 195 ALLKGFRDFGLEAGIDTLVIPVDSSKQVVVEELSRSGFRTLKTE 238
                                    55555556667889999999999999999999999999988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1806.15
//
Query:       gi|119720548|ref|YP_921043.1|  [L=289]
Description: Sec-independent periplasmic protein translocase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-41  141.1  20.0    4.7e-41  140.9  20.0    1.1  1  TatC      Sec-independent protein translocase protein (TatC)


Domain annotation for each model (and alignments):
>> TatC  Sec-independent protein translocase protein (TatC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.9  20.0   2.6e-45   4.7e-41       2     207 .]      31     266 ..      26     266 .. 0.80

  Alignments for each domain:
  == domain 1  score: 140.9 bits;  conditional E-value: 2.6e-45
                                    HHHHHHHHHHHHHHHHHHHHHHH...HHTHHHHHHHCCHHHHC.C.......................TTS-EE--SSS- CS
                           TatC   2 hLeeLrkrlirallavaiafiit...fvfaeeliafllepleeae.......................eevelivlsple 55 
                                    +Le Lr+ li   +a++i +i++   +++ + ++ ++++ +++++                        +v li +  ++
  gi|119720548|ref|YP_921043.1|  31 FLETLRRILIEF-IAFLILLIFLpapWMLPRSYYPLVFALMNATNhymldfndnpfsgpfarlfgvngSRVVLISHGWFD 109
                                    577777777743.333333333311122233333333333322223455666666666666666655534889******* PP

                                    HHHHHHHHHHHHHHHHSHHHHHHHHHCCCTTTTS---STTTHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHT....TTTS CS
                           TatC  56 afllklkvslvaglvlasPvilyqlwafvapgLykherrlvlvfliaslllfllGaafayfvvlplvlkfll....seev 131
                                     +++ l +s+v++  + sP+i+y++++fv+pgLy+he+r+v+++ +++l lf++G++++yfvv+p+v+++ +      ++
  gi|119720548|ref|YP_921043.1| 110 SLTAALLLSVVIAAGVLSPLIAYEVYRFVEPGLYSHEKRVVKRYTVFALSLFVAGLLYGYFVVMPIVFSVAVwlatLGGA 189
                                    *********************************************************************88855552334 PP

                                    STTEEHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHTTSS-HHHHHTTHHHHHHHHHHHHHHH-S..SHHHHHHHHHH CS
                           TatC 132 epllslseylsfvlllllafgiaFelPlvlvllarlglvsaetlrkkrryaivvilvvaavltP.pdvisqlllavP 207
                                    +  +s++e+++ ++l +la+g++F +Plv++ l+++g+v++etlr ++ry++++++ + +++tP p+++s l+l +P
  gi|119720548|ref|YP_921043.1| 190 SLFFSIQEFYQNIMLGTLATGVFFMFPLVVLALHKIGVVTYETLRGNWRYVVFAVFAFLVMVTPdPTFFSDLVLGAP 266
                                    667**********************************************************************9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       796  (0.0443973); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1923.23
//
Query:       gi|119720549|ref|YP_921044.1|  [L=393]
Description: hypothetical protein Tpen_1646 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.15   12.0   0.2        3.2    7.8   0.1    2.2  2  DNA_primase_S  DNA primase small subunit


Domain annotation for each model (and alignments):
>> DNA_primase_S  DNA primase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.1   0.00018       3.2      20      64 ..     111     154 ..     103     167 .. 0.75
   2 ?    1.9   0.0     0.011     2e+02     132     167 ..     179     214 ..     156     223 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00018
                                    HHHHHHHHHHHHHHHH-----GGGEEEEE--SEEEEEEE--TTEE CS
                  DNA_primase_S  20 cwkfvsvavkvldellredfgfkdilwvfsgrrGfHcwvsdkdar 64 
                                     w+   +a++ +  +l+ +   k ++w+  ++rG+H++ + + + 
  gi|119720549|ref|YP_921044.1| 111 HWRATIEAARAIVDYLEREGVVK-SVWLKWSGRGMHVHLHEYAVT 154
                                    488899999***9***7776666.555555558*****9998654 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.011
                                    ..............-----------------....- CS
                  DNA_primase_S 132 eakedivlvllyprldeqvtkgikhllkapfcihgk 167
                                    ++k+ +v +++  +++++   + +++++ap ++h++
  gi|119720549|ref|YP_921044.1| 179 KEKIREVNAKHGSKIKVENLMDPQRVFTAPLSLHRA 214
                                    567778888999999999999*************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       640  (0.0356964); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.40
# Mc/sec: 2948.88
//
Query:       gi|119720550|ref|YP_921045.1|  [L=524]
Description: carbohydrate kinase, YjeF related protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.1e-50  169.7   0.5      8e-50  169.1   0.5    1.3  1  YjeF_N        YjeF-related protein N-terminus
    3.3e-49  167.6   3.4    8.6e-49  166.2   0.2    2.0  2  Carb_kinase   Carbohydrate kinase
    4.2e-06   26.3   0.0    7.1e-06   25.6   0.0    1.3  1  Phos_pyr_kin  Phosphomethylpyrimidine kinase
    0.00047   19.6   1.6     0.0013   18.1   0.1    2.0  2  PfkB          pfkB family carbohydrate kinase
     0.0011   18.4   0.1     0.0019   17.6   0.1    1.3  1  HK            Hydroxyethylthiazole kinase family


Domain annotation for each model (and alignments):
>> YjeF_N  YjeF-related protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.1   0.5   2.2e-53     8e-50       2     171 .]      25     192 ..      24     192 .. 0.95

  Alignments for each domain:
  == domain 1  score: 169.1 bits;  conditional E-value: 2.2e-53
                         YjeF_N   2 eeLmenagravaevlrallgnspaekkvlvlvGsgnnGgdglaaArhLaqegakVtvllleeeekldedaeralellkka 81 
                                    e+Lmenag++va+++ +l+     + +  v++G+gnnGgdgl+aArhL ++ga+V+v+l++ ++kl + +++++e++ ka
  gi|119720550|ref|YP_921045.1|  25 EILMENAGASVARLAVSLI---GLPMSAAVVCGPGNNGGDGLVAARHLSSMGADVKVFLVAAPDKLAGIVKENYERVVKA 101
                                    79*****************...899999**************************************************** PP

                         YjeF_N  82 ggkvveekpeedleekls.apvdlviDAllGiglrgelreelaeliewlnsseapvlavDiPSGldadtGavsgtavkad 160
                                    g+ v   ++e ++    + +  d+v+DAl+G+gl+++l++ + +++e +n s+++v++vDiPSG+++dtG+v+g+av+ad
  gi|119720550|ref|YP_921045.1| 102 GIAVEVVDEERAEGLSEElSLFDVVVDALFGTGLSRPLEGVYRKVVEAINGSGSLVISVDIPSGVHGDTGQVLGVAVRAD 181
                                    ****9988887765444489************************************************************ PP

                         YjeF_N 161 vtvtfgapkrg 171
                                    +tvtfg+pk g
  gi|119720550|ref|YP_921045.1| 182 YTVTFGLPKLG 192
                                    *********86 PP

>> Carb_kinase  Carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.3     0.024        87       2      79 ..      50     137 ..      49     161 .. 0.77
   2 !  166.2   0.2   2.4e-52   8.6e-49       2     243 ..     248     501 ..     247     502 .. 0.94

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.024
                                    EEEE-BTTCHHHHHHHHHHHHCTT-SE.EEEEESSTTTCCCCTTTTTCEECCTT.....HTTTS....--SSS-SEEE.. CS
                    Carb_kinase   2 lvigGsedytGAallaalaalrlgagl.vsvateseaiavlksylpevivhpll.....edeqa.kileklerldavv.. 72 
                                     v++G  +  G +l aa   +++ga++ v  ++ +++ a + +  +e +v+         +e+a    e+l+  d+vv  
  gi|119720550|ref|YP_921045.1|  50 AVVCGPGNNGGDGLVAARHLSSMGADVkVFLVAAPDKLAGIVKENYERVVKAGIavevvDEERAeGLSEELSLFDVVVda 129
                                    68999999****************99745566678898888888888888887778897556665667889999999766 PP

                                    .E-TT-SS CS
                    Carb_kinase  73 .iGpGLgr 79 
                                      G GL r
  gi|119720550|ref|YP_921045.1| 130 lFGTGLSR 137
                                    57888876 PP

  == domain 2  score: 166.2 bits;  conditional E-value: 2.4e-52
                                    EEEE-BTTCHHHHHHHHHHHHCTT-SEEEEEESSTTTCCCCTTTTTCEECCTT........HTTTS...--SSS-SEEEE CS
                    Carb_kinase   2 lvigGsedytGAallaalaalrlgaglvsvateseaiavlksylpevivhpll........edeqakileklerldavvi 73 
                                    l ++Gs  y GA+ll+ ++ l++g g  + at +  +  l +  pev+ + l+         ++   ile+ +  d+v++
  gi|119720550|ref|YP_921045.1| 248 LFVAGSRRYMGAPLLCSKSFLKAGGGYSRLATIKSIVPFLGVRAPEVVYEALEetasgtvaYGNLERILELSKSSDIVAV 327
                                    679*****************************8889999999999999999999999998733334789*********** PP

                                    -TT-SSSHCHHH.HCHHHCCCCS-EEEEGGGGGSGGGG....TTTTSSEEEE--HHHHHHHCTTTCH.HCCSHHHHHHHH CS
                    Carb_kinase  74 GpGLgrdekikk.lleevlekdeplviDAdgLnllaqkne.lserkaeviLTPhkkEfkrLlkaivk.keddrlelarel 150
                                    GpGLg +e++   + + +++ ++pl++D+dgL+ +a   e +ser+a+++LTPh++E +rL++ +v+    +r+++a el
  gi|119720550|ref|YP_921045.1| 328 GPGLGLEEETLRlVCDLARSVEKPLIVDGDGLTAVARCGEyISERRAPTVLTPHAGEMSRLTGKSVEeVRASRVDAALEL 407
                                    *****99999985778999*******************99**********************999987999********* PP

                                    HHHHTTEEEEESTTSEEEECTTEEEEE----GGG-STTHHHHHHHHHHHHHHCTSSHHHHHHHHHHHHHHHHHHHCCCT- CS
                    Carb_kinase 151 aqklnavvllkgekdvivspegevlinstgssalakGGsGDvLaGligalLaqneasyeaaiaaawlhgaasdeaaekkg 230
                                    a kl+a v+lkg+++vi++p+g  +in  g++++a++GsGDvL G+i+al        ea+  ++++hg a+d aae++g
  gi|119720550|ref|YP_921045.1| 408 AGKLKAYVVLKGAHTVIATPDGRAYINLSGNPGMATAGSGDVLVGAIAALYGLGLGFEEAVRMGVFVHGLAGDIAAEERG 487
                                    ******************************************************************************** PP

                                    T.S-HCHHHHHHHC CS
                    Carb_kinase 231 v.gmlatelskiip 243
                                      g+++  l++++p
  gi|119720550|ref|YP_921045.1| 488 QdGLTSVTLMNYLP 501
                                    *9999999998887 PP

>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0     2e-09   7.1e-06     121     224 ..     376     471 ..     331     480 .. 0.82

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 2e-09
                                    SEEE-BHHHHHHHHT---SSHH.HHHHHHHHHHHTT-SEEEEEEGGS-SSSEEEEEEEETSSEEEEEEEE----S--BTH CS
                   Phos_pyr_kin 121 tvitPNlpEaeaLlgekiktee.dmkeaakkllklgakaVlikGghlegeeavvtdvlydgeeveeleaerietknthGt 199
                                    tv+tP   E+++L+g++++++  +  +aa +l+   + +V++kG h+         v+ + ++   ++ +  +   t G+
  gi|119720550|ref|YP_921045.1| 376 TVLTPHAGEMSRLTGKSVEEVRaSRVDAALELAGKLKAYVVLKGAHT---------VIATPDGRAYINLSGNPGMATAGS 446
                                    8**************9999776467789999999999*********4.........34433444444444445569**** PP

                                    HHHHHHHHHHHHHCTSSHHHHHHHH CS
                   Phos_pyr_kin 200 GCtlssaiaaelakgesleeAvkkA 224
                                    G++l  aiaa    g   eeAv+++
  gi|119720550|ref|YP_921045.1| 447 GDVLVGAIAALYGLGLGFEEAVRMG 471
                                    **********************986 PP

>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.2      0.11   3.9e+02      35      64 ..      58      87 ..      55     108 .. 0.83
   2 !   18.1   0.1   3.6e-07    0.0013     140     283 ..     330     472 ..     307     478 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.11
                                   EESHHHHHHHHHHHTT-EEEEEEEEESSHH CS
                           PfkB 35 aGGagaNvAvalarlgadvafigavGdDnf 64
                                   +GG+g+  A+ l+++gadv ++ +   D++
  gi|119720550|ref|YP_921045.1| 58 NGGDGLVAARHLSSMGADVKVFLVAAPDKL 87
                                   7*****************998877666665 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 3.6e-07
                                    CTTSHHHHHHHHHHHHHHTTEEEEEECESSSHH....HHHHHHHHHCTESEEEEEHHHHHHHHTSCT.HSHHHHHHHHHH CS
                           PfkB 140 sselpeavleelaeaaknggtfdpnlldplgaq....fkeallellaladllkpneeElealtgekl.edieealaalhk 214
                                      +l e++l+++ ++a++    +p ++d  g        e ++e  + +++l+p + E ++ltg++  e  ++ ++a+ +
  gi|119720550|ref|YP_921045.1| 330 GLGLEEETLRLVCDLARSVE--KPLIVDGDGLTavarCGEYISE-RRAPTVLTPHAGEMSRLTGKSVeEVRASRVDAALE 406
                                    46788999999999999999..9999999998864323333333.379******************87556666677666 PP

                                    HHHTTS.SEEEEEEGGGEEEEEETTEEEEEEE.SSSS-SBGTTHHHHHHHHHHHHHHTTHHHHHHHHHHH CS
                           PfkB 215 lkakga.ktvvvtlGkeGalvvekdgelkvpavpkvkvvDttGAGDsfvggflaallegksleealrfan 283
                                    l  +g+ k  vv +G+  +++   dg  +++    +    t G GD  vg+++a +  g  +eea+r+++
  gi|119720550|ref|YP_921045.1| 407 L--AGKlKAYVVLKGAHTVIAT-PDGRAYINL-SGNPGMATAGSGDVLVGAIAALYGLGLGFEEAVRMGV 472
                                    5..4555899999999988888.666666665.5677799****************************96 PP

>> HK  Hydroxyethylthiazole kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   5.3e-07    0.0019      66     240 ..     336     500 ..     303     506 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 5.3e-07
                                    HHHHHHHHHHHHTT--EEEE-TTBTTBHHHHHHHHHHHHHS--SEEEEEHHHHHHHHTSSCCSCSSSSSS-SHHHHHHHH CS
                             HK  66 ealkaAvksakevnrPvvlDPVgvgAtelRrelalellkevklavikGNasEilslaglelkvkGvDskeaataavaavq 145
                                    e+l+   + a++v++P+++D  g +A +   e + e      + v+   a+E+  l+g+++     +  e +++ v a+ 
  gi|119720550|ref|YP_921045.1| 336 ETLRLVCDLARSVEKPLIVDGDGLTAVARCGEYISE---RRAPTVLTPHAGEMSRLTGKSV-----E--EVRASRVDAAL 405
                                    666777777888888888888777777654444443...4567788888888888877653.....2..23333588999 PP

                                    HHHHHHTSEEEEESSSEEEE..ESSEEEEEE-S-GGGGGSTTHHHHHHHHHHHHHTTBSSHHHHHHHHHHHHHHHH.HHH CS
                             HK 146 kvAqklrvvvvvtGevDvvs..dgkkvyklknGtellgkitasGCllgsvvaaflavkkdkllaaveavllykvAgkeaa 223
                                    ++A kl++ vv+ G+  v++  dg+  ++l +G++ ++   +sG +l  ++aa  ++  +  +a+  +v +  +Ag+ aa
  gi|119720550|ref|YP_921045.1| 406 ELAGKLKAYVVLKGAHTVIAtpDGRAYINL-SGNPGMAT-AGSGDVLVGAIAALYGLGLGFEEAVRMGVFVHGLAGDIAA 483
                                    *******************95566666665.68998875.79***********************9**********9999 PP

                                    HHHHTTHHHHHHHHHHH CS
                             HK 224 arsegsgsFqvelldal 240
                                    ++  ++g   v+l++ l
  gi|119720550|ref|YP_921045.1| 484 EERGQDGLTSVTLMNYL 500
                                    99988899888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (524 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 3712.97
//
Query:       gi|119720551|ref|YP_921046.1|  [L=272]
Description: fructose-bisphosphate aldolase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.1e-33  116.8   0.0    1.3e-33  116.6   0.0    1.0  1  DeoC       DeoC/LacD family aldolase
  ------ inclusion threshold ------
      0.041   13.2   0.1       0.07   12.4   0.1    1.4  1  ThiG       Thiazole biosynthesis protein ThiG
      0.046   13.3   0.0       0.12   11.9   0.0    1.5  1  OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS famil


Domain annotation for each model (and alignments):
>> DeoC  DeoC/LacD family aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.6   0.0   2.2e-37   1.3e-33       2     235 .]      22     242 ..      21     242 .. 0.92

  Alignments for each domain:
  == domain 1  score: 116.6 bits;  conditional E-value: 2.2e-37
                                    EEEEECCSHHHHHHHHCTSSHHHHHHHHHHHHHHGGGSSEEEEETTTHHHHHHCSCTTSEEEEETECSSCCTTSTTEEEE CS
                           DeoC   2 vilavDqrvankddtasaqneqledlkalvkealtpgasavlldpgviasaskeyakdiallvkldkgtyllkskqrdvd 81 
                                    v++a+D++v+++++++        +++++ ++++ +  +av++ pg++a  s   + +++l+vk+ ++t l +++++++ 
  gi|119720551|ref|YP_921046.1|  22 VVFAFDHGVEHGPGDFP---GETVNPRKILSKVV-GEVDAVMMLPGIAALTSEVWQGKVPLIVKVTSKTSLRPEAEKLLQ 97 
                                    689*************9...47799999999986.89*********************************9999977776 PP

                                    .TTCHHHHHHHTT-SEEEEEEEEHTTTTCHHHHHHHHHHHHHHHHHHHTEEEEEEEEE-CTTBSSTTCHHHHHHHHHHHH CS
                           DeoC  82 .evasveeakalGAdavkvvvyyradgseeeqqklaeikrvkeacheeglplilelylrdeaikdekvdpdlvaeAarvs 160
                                     ++  ve a+alGAdav ++vy+   gs  e  +l+   +vk a++ +glp +   y+r++aik+ + d ++v+ + r++
  gi|119720551|ref|YP_921046.1|  98 sPFGFVEDAVALGADAVAATVYW---GSNFEDLMLERWFQVKRAAETYGLPCLQLSYPRGPAIKNMY-DVEVVRYGVRAA 173
                                    9**********************...*****************************************.************ PP

                                    TCCT-SEEEE--SSCC.B.HHHHHHHHHHHHH.CHSSTEEEEETTSSHHHHHHHHHHHHH..HHTHCEEEESHHHHTT CS
                           DeoC 161 aelGaDiiKvevpkevvnateedaevfkdvik.aapvpgvvlsGGvseedfletvedAvk..eagasGvlsGRaifqk 235
                                    +e GaD+iK+ ++        ++ e+f++v++ aa vp v++sGG++++++l+ +    +  +aga+Gv++GR+ifq+
  gi|119720551|ref|YP_921046.1| 174 IESGADLIKTYYT--------GSTESFRRVVEvAAGVP-VLMSGGAKARTLLDFLYVVKSvmDAGAQGVVVGRNIFQH 242
                                    *************........99999999887477899.*******7776666544444344**************97 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   1.2e-05      0.07     175     233 ..     201     265 ..     167     270 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.2e-05
                                    SS-BEEES---SHH..H....HHHHHHTT-SEEEESHHHHTSSSHHHHHHHHHHHHHHHHHHHHH CS
                           ThiG 175 kvPvivDAGigsps..d....aaqamelGadavllntavaeakdpvamArafklaveaGrlayla 233
                                     vPv++  G    +  d    +  +m+ Ga++v++   + + +dp   A+a+ + v+ G+   +a
  gi|119720551|ref|YP_921046.1| 201 GVPVLMSGGAKARTllDflyvVKSVMDAGAQGVVVGRNIFQHEDPTLAAKAIMYVVHEGYAPEEA 265
                                    6666666665443311122215689********************************99877666 PP

>> OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.1e-05      0.12     198     225 .]     225     252 ..     219     252 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.1e-05
                                    HHHTTCSEEEESHHHHTSSSHHHHHHHH CS
                      OMPdecase 198 igiagadiiivGRgIlkagdpveeaery 225
                                    + +aga+ ++vGR I++ +dp  +a+++
  gi|119720551|ref|YP_921046.1| 225 VMDAGAQGVVVGRNIFQHEDPTLAAKAI 252
                                    45699******************99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2072.76
//
Query:       gi|119720552|ref|YP_921047.1|  [L=308]
Description: ribokinase-like domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-57  194.9   0.4    2.3e-57  194.6   0.4    1.0  1  PfkB          pfkB family carbohydrate kinase
    9.7e-07   28.4   0.0    1.5e-06   27.8   0.0    1.2  1  Phos_pyr_kin  Phosphomethylpyrimidine kinase


Domain annotation for each model (and alignments):
>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  194.6   0.4   2.6e-61   2.3e-57       3     297 ..       5     290 ..       4     294 .. 0.91

  Alignments for each domain:
  == domain 1  score: 194.6 bits;  conditional E-value: 2.6e-61
                                    EEEEEEEEEEEEEEECSSH.TTSEE.EESEEEEEEESHHHHHHHHHHHTT-EEEEEEEEESSHHHHHHHHHHHHTTEEET CS
                           PfkB   3 kvvviGealidliavsekl.egelv.evktveksaGGagaNvAvalarlgadvafigavGdDnfGeflleelkkegvdtd 80 
                                    +vv +G++l dl  +++++  ++     k+ +++ GG++aNvA ++ rlg+++a+ig+vG D+fG+  le l  egvd++
  gi|119720552|ref|YP_921047.1|   5 DVVTLGHILLDLRFCVDAFaTPDREgVIKSQSHGVGGSAANVAIGVRRLGGRSAVIGKVGFDDFGKNALEDLVREGVDIS 84 
                                    5899****************777777****************************************************** PP

                                    TEEEESS.SEEEEEEEEETTTSEEEEEEEEGGGGGHHHHHHHHHHHHHGCTSEEEEESEECTTSHHHHHHHHHHHHHHTT CS
                           PfkB  81 yvkided.trtglalivvdedgertivfnrgaaadltkeeleededlleeadllyisgllsselpeavleelaeaakngg 159
                                     v+id+   +tg +++++d++g+  ++ + g a  ++ ++ e ++++l+e  +l+i++     l++++ + +a+aak+ g
  gi|119720552|ref|YP_921047.1|  85 NVRIDALnGKTGFTIVIIDSQGQIVMYGDKGVA--ESLQPEEVNLKILKETGHLHIAS-----LRVDTSAFVAKAAKELG 157
                                    ******88***********98744444444444..44445568**************9.....9**************** PP

                                    EEEEEECESSSHH...HHHHHHHHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTSSEEEEEEGGGEEEEEE CS
                           PfkB 160 tfdpnlldplgaq...fkeallellaladllkpneeElealtgekledieealaalhklkakgaktvvvtlGkeGalvve 236
                                      +++  dp   q     eal+ +++lad++ pne E +a++g +  d++ea+++l     +ga +v+v++G++G++vv+
  gi|119720552|ref|YP_921047.1| 158 --VRVSWDPGRRQarmGIEALKPIVRLADIVLPNEIEVKAIAGVE--DVKEAANVLLG---EGAGLVIVKRGSRGVYVVS 230
                                    ..8888888888878779999999*********************..99999998887...9****************** PP

                                    TTEEEEEEE.SSSS-SBGTTHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHTSSSSST CS
                           PfkB 237 kdgelkvpavpkvkvvDttGAGDsfvggflaallegksleealrfanavAalvvqkkgaia 297
                                    kd+e++vpa ++++vvDttGAGD+f++g+l +l +  +l++a+rfa+ vA l v++ g+ +
  gi|119720552|ref|YP_921047.1| 231 KDEEFEVPAYRPETVVDTTGAGDAFAAGLLMGLKR-FDLRDAVRFATVVAGLKVTRLGSHE 290
                                    *********************************99.79******************99865 PP

>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.0   1.7e-10   1.5e-06     109     224 ..     173     275 ..     157     281 .. 0.83

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 1.7e-10
                                    HHHHHHHTGGG-SEEE-BHHHHHHHHT---SSHHHHHHHHHHHHHTT-SEEEEEEGGS-SSSEEEEEEEETSSEEEEEEE CS
                   Phos_pyr_kin 109 vealkeeLlplatvitPNlpEaeaLlgekikteedmkeaakkllklgakaVlikGghlegeeavvtdvlydgeeveelea 188
                                    +ealk  +++la+++ PN  E++a++g     +ed+keaa+ ll  ga  V++k g     + v  +v+ ++e ++e++a
  gi|119720552|ref|YP_921047.1| 173 IEALKP-IVRLADIVLPNEIEVKAIAG-----VEDVKEAANVLLGEGAGLVIVKRGS----RGV--YVVSKDE-EFEVPA 239
                                    677776.99*****************9.....9*********************997....345..5555555.555666 PP

                                    E----.S--BTHHHHHHHHHHHHHHCTSSHHHHHHHH CS
                   Phos_pyr_kin 189 eriet.knthGtGCtlssaiaaelakgesleeAvkkA 224
                                     r et  +t G+G+++++ +   l +  +l++Av+ A
  gi|119720552|ref|YP_921047.1| 240 YRPETvVDTTGAGDAFAAGLLMGLKR-FDLRDAVRFA 275
                                    66555269***********9999966.7899999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2216.37
//
Query:       gi|119720553|ref|YP_921048.1|  [L=290]
Description: hypothetical protein Tpen_1650 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-08   34.6  28.6    1.2e-05   25.3  11.6    2.9  3  VIT1          VIT family
    6.9e-06   26.5   3.7    8.5e-05   23.0   3.5    2.1  1  Rubrerythrin  Rubrerythrin
     0.0017   18.6   0.3        1.2    9.3   0.3    2.7  2  Ferritin_2    Ferritin-like domain
  ------ inclusion threshold ------
      0.013   15.0   0.3      0.019   14.5   0.3    1.4  1  DUF1129       Protein of unknown function (DUF1129)
      0.044   13.6   1.1      0.044   13.6   1.1    2.9  3  DUF4190       Domain of unknown function (DUF4190)


Domain annotation for each model (and alignments):
>> VIT1  VIT family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.21   7.6e+02      83     109 ..      91     117 ..      25     133 .. 0.75
   2 !   18.0   5.9   5.7e-07     0.002       3      60 ..     139     195 ..     137     198 .. 0.91
   3 !   25.3  11.6   3.4e-09   1.2e-05     132     214 ..     197     279 ..     193     280 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.21
                           VIT1  83 aeelaeilearglseelaqevaaellk 109
                                     ee +++le+ glsee+ +++   + +
  gi|119720553|ref|YP_921048.1|  91 VEEYVRVLESAGLSEEQREALKGIIED 117
                                    367788888889998888774444433 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 5.7e-07
                           VIT1   3 davlGanDGLvspfalvaGlsaaslgssktvllaGlaellAGaiSMgiGeYlsvkser 60 
                                    ++ lG++D ++   ++ aG  + + +s+    ++Gl   ++ ++SM++ +Yl +k+e+
  gi|119720553|ref|YP_921048.1| 139 AMALGMSDAIIELSGVHAGFLGYT-SSPIYTGISGLIVGISASMSMAAAAYLQAKQEK 195
                                    788******************887.588999999999999***************997 PP

  == domain 3  score: 25.3 bits;  conditional E-value: 3.4e-09
                           VIT1 132 asplkaAlssalsfliGgliPllpylfvesvglalvvsiavtllalllfGavkalltgssklvsalrmlliGalAaaaay 211
                                    +sp  +Al+++l++++  ++   p+++v+sv +al++s+a++++al++f +++++++g + l++ l+++ i +l  ++ y
  gi|119720553|ref|YP_921048.1| 197 KSPAVNALVTGLMYMLTVVMLTSPFFLVPSVATALAASVALAVAALAAFSYFSSVILGGNFLREFLENTSIVFLVVLVGY 276
                                    6899**********************************************************************999999 PP

                           VIT1 212 lig 214
                                    l+g
  gi|119720553|ref|YP_921048.1| 277 LFG 279
                                    987 PP

>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   3.5   2.4e-08   8.5e-05      13     134 ..      13     126 ..       9     129 .. 0.73

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 2.4e-08
                                    HHHHHHHHHHCHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS-------TTGGHHHHHHHHHHHH CS
                   Rubrerythrin  13 arrlYkelaekakegypqiaelFeelAeeEreHakilnklleklepelelevkekvreyaeakpkflttaknLeeaiega 92 
                                    + +lY+ la   k  +p  +e++e+l+++Er H ++  ++ +++e+++    +  +  ++     +l +   ++ +++ +
  gi|119720553|ref|YP_921048.1|  13 DSELYRRLAGIEK--NPANREILEKLSQQERSHYEFWSRFSGSVELGRW---DRLKLAFLVLSSRILGKVFIIKFLERHE 87 
                                    6788999998888..****************************999999...3444445555555544444455445555 PP

                                    HHHHHCHHHHHHHHHHHTT.SHHHHHHHHHHHHHHHHHHHHHH CS
                   Rubrerythrin  93 yaeeeemyrfyeelaekeg.neeakklfkklaeaEkkHeerlr 134
                                      +     ++y +++e +g  ee ++ +k ++e+Ek+Hee l+
  gi|119720553|ref|YP_921048.1|  88 GRVV----EEYVRVLESAGlSEEQREALKGIIEDEKYHEEALA 126
                                    5555....555555555541456789**************987 PP

>> Ferritin_2  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.0    0.0024       8.6      34      60 ..      24      50 ..       4      66 .. 0.80
   2 !    9.3   0.3   0.00035       1.2      22      68 ..      96     135 ..      79     209 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0024
                     Ferritin_2 34 lldaevrevaeeiakheeaHveflkaa 60
                                     +++ re++e++ ++e++H+ef+++ 
  gi|119720553|ref|YP_921048.1| 24 EKNPANREILEKLSQQERSHYEFWSRF 50
                                   457889*****************9875 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00035
                     Ferritin_2  22 aalegaslddkalldaevrevaeeiakheeaHveflkaaleGaaava 68 
                                    ++le      +a+l++e re ++ i ++e+ H e+l++ +  + av+
  gi|119720553|ref|YP_921048.1|  96 RVLE------SAGLSEEQREALKGIIEDEKYHEEALASQID-EFAVR 135
                                    3333......99**************************994.55554 PP

>> DUF1129  Protein of unknown function (DUF1129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.3   5.2e-06     0.019     111     194 ..     168     247 ..      98     250 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.2e-06
                        DUF1129 111 iGlitlllvalvgGlamvlvyrlltrekkkkkrpplwkrllilllllvvwlvlftlval.lpaviNpvLpplvliiigvi 189
                                    +G+  l +v++ + + m   + +l+  k++k + p+++ l+  l+ +  ++v+++   + l +++   L + v ++++++
  gi|119720553|ref|YP_921048.1| 168 TGISGL-IVGISASMSMAAAA-YLQA-KQEKGKSPAVNALVTGLMYM--LTVVMLTSPFfLVPSVATALAASVALAVAAL 242
                                    333222.23444434443332.2322.45555666666655555555..5555555555577888899999999998888 PP

                        DUF1129 190 afvvr 194
                                    a +++
  gi|119720553|ref|YP_921048.1| 243 AAFSY 247
                                    87665 PP

>> DUF4190  Domain of unknown function (DUF4190)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   1.1   1.2e-05     0.044       9      60 ..     157     215 ..     152     217 .. 0.80
   2 ?    1.8   2.6     0.057   2.1e+02       2      22 ..     200     221 ..     200     255 .. 0.82
   3 ?   -2.7   0.5       1.4   5.1e+03      11      22 ..     268     282 ..     265     288 .. 0.44

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.2e-05
                        DUF4190   9 gilgllfl.iitgivavilGhvAlrqirrsg......erGkglAiaGivlGwigllllv 60 
                                    g lg ++  i tgi ++i+G+ A   ++         e+Gk  A+ ++v+G  ++l +v
  gi|119720553|ref|YP_921048.1| 157 GFLGYTSSpIYTGISGLIVGISASMSMAAAAylqakqEKGKSPAVNALVTGLMYMLTVV 215
                                    6678788779**********98877766555555556**************99988776 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.057
                        DUF4190   2 AiasLvlgilgllfl.iitgiv 22 
                                    A+ +Lv+g++ +l++ ++t+++
  gi|119720553|ref|YP_921048.1| 200 AVNALVTGLMYMLTVvMLTSPF 221
                                    78899**999999955677654 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 1.4
                        DUF4190  11 lgllf..l.iitgiv 22 
                                    + l++  + +++++v
  gi|119720553|ref|YP_921048.1| 268 VFLVVlvGyLFGSLV 282
                                    322222233566655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1116  (0.0622455); expected 358.6 (0.02)
Passed bias filter:                      609  (0.0339673); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2040.50
//
Query:       gi|119720554|ref|YP_921049.1|  [L=138]
Description: hypothetical protein Tpen_1651 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-16   61.4   1.3    1.4e-16   60.9   1.3    1.2  1  CxxCxxCC  Putative zinc- or iron-chelating domain
  ------ inclusion threshold ------
      0.053   13.7   0.1       0.17   12.1   0.0    1.9  2  PMBR      Pseudomurein-binding repeat


Domain annotation for each model (and alignments):
>> CxxCxxCC  Putative zinc- or iron-chelating domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.9   1.3   1.5e-20   1.4e-16       5      84 ..      15     100 ..       7     101 .. 0.83

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 1.5e-20
                       CxxCxxCC   5 CgaCCkelkvklteedlerlkaaevaeeeeeskkiak.......adgrCvfldeetklCkiYeeRpkicrlfpas.ekee 76 
                                    Cg+CC+++ v lt +d+er++  ++  e++ + +          +d +Cvfld++t+ C+iYe+Rp++crl+p + + + 
  gi|119720554|ref|YP_921049.1|  15 CGKCCYKAVVPLTRRDIERITSRGYRFEDFAEYR--AgvpvlknVDSHCVFLDPTTNACTIYEDRPTACRLYPLAySPKL 92 
                                    *************************555554444..24699999*****************************9866666 PP

                       CxxCxxCC  77 llaraetC 84 
                                    +  ++++C
  gi|119720554|ref|YP_921049.1|  93 WVHVDPAC 100
                                    67777777 PP

>> PMBR  Pseudomurein-binding repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.51   4.6e+03       5      16 ..      26      37 ..      25      41 .. 0.74
   2 ?   12.1   0.0   1.9e-05      0.17       2      23 ..     103     124 ..     102     127 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.51
                           PMBR  5 isyeeyldmasr 16
                                   ++++++ ++ sr
  gi|119720554|ref|YP_921049.1| 26 LTRRDIERITSR 37
                                   688888888887 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 1.9e-05
                           PMBR   2 sgkisyeeyldmasrvlafies 23 
                                    +g + +e ++++asrvl+++e+
  gi|119720554|ref|YP_921049.1| 103 AGEVPKEAVVRLASRVLDYYEE 124
                                    57788999************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 1034.93
//
Query:       gi|119720555|ref|YP_921050.1|  [L=171]
Description: nitroreductase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.6e-29  100.6   0.2    1.5e-18   67.4   0.2    2.0  2  Nitroreductase  Nitroreductase family
    1.1e-10   41.5   0.0    0.00011   21.8   0.0    3.0  3  TM1586_NiRdase  Putative TM nitroreductase


Domain annotation for each model (and alignments):
>> Nitroreductase  Nitroreductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.4   0.2   1.7e-22   1.5e-18       2      59 ..      14      71 ..      13      80 .. 0.93
   2 !   32.0   0.0   1.3e-11   1.1e-07      88     169 ..      76     148 ..      69     149 .. 0.89

  Alignments for each domain:
  == domain 1  score: 67.4 bits;  conditional E-value: 1.7e-22
                                   HH--B---B-S----HHHHHHHHHHHHTS--GGG---EEEEEE.-CCCHHHHHHHHHH CS
                 Nitroreductase  2 rkRrSiRkFddepvpkeelekileaarraPsagnlqpwrfvvvqdkelryklaeaale 59
                                   ++RrS+RkF+depvp+e + + ++ ar+aPsa+n+qpw f+vv+d+e+++kla++ + 
  gi|119720555|ref|YP_921050.1| 14 LSRRSVRKFSDEPVPDELIYRAIDIARFAPSAHNAQPWSFLVVKDREKLEKLAKIHRW 71
                                   69***************************************************98766 PP

  == domain 2  score: 32.0 bits;  conditional E-value: 1.3e-11
                                    HHSSEEEEE---TTS---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GGGGGHHHHHHHHT-S..SEEEEEEE CS
                 Nitroreductase  88 agapvlivivatldkserkaaerayryalldagaaaqnllLaAtalGlgscpiggfdeaaeevrkllglpdeeeivvlia 167
                                    a++ v i++          +++ +    l+d +++a+ l+La++ lGl +++i ++++a+ e+r++ + p++  +v++++
  gi|119720555|ref|YP_921050.1|  76 ANSKVAIIV--------FSDEKVSPKSHLVDGAIVATYLWLALHCLGLSTVWIYTLEQAE-EIRRIVNAPPHLFPVAIFP 146
                                    555666666........578889999999****************************999.7****************** PP

                                    EE CS
                 Nitroreductase 168 vG 169
                                    vG
  gi|119720555|ref|YP_921050.1| 147 VG 148
                                    *9 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0   0.00027       2.4       8      25 ..      15      32 ..      10      34 .. 0.88
   2 !   21.8   0.0   1.3e-08   0.00011     161     195 ..      33      67 ..      30      75 .. 0.75
   3 !    9.3   0.0   8.8e-05      0.79      91     152 ..     106     169 ..      82     171 .] 0.83

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00027
                                   H--B---B--S---HHHH CS
                 TM1586_NiRdase  8 kRhsvRkYkdealeeell 25
                                    R+svRk++de++++el+
  gi|119720555|ref|YP_921050.1| 15 SRRSVRKFSDEPVPDELI 32
                                   7*************9875 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 1.3e-08
                                    HHHHHHHHTS--GGG----EEE.E-SSEE......E CS
                 TM1586_NiRdase 161 keileaarlAPsAlNqqpwrfelkdddeikika.sv 195
                                     +++++ar APsA N qpw f +++d + k+ +   
  gi|119720555|ref|YP_921050.1|  33 YRAIDIARFAPSAHNAQPWSFLVVKD-REKLEKlAK 67 
                                    5789*****************98885.555543344 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 8.8e-05
                                    HHHHHHHTT-EEEEES--SST.............T-S-EEEEE-BS----.-----HHHHBSS- CS
                 TM1586_NiRdase  91 lvLkltalGlgtcWvggtykkkkak..velkkgeklvivIalGyaktklveakrkpleelcevk 152
                                    l L l  lGl+t W+    + ++    v+++     v++  +G+++++  ++ r++leel++v+
  gi|119720555|ref|YP_921050.1| 106 LWLALHCLGLSTVWIYTLEQAEEIRriVNAPPHLFPVAIFPVGFPAESPPPRPRRSLEELVHVD 169
                                    6799999********98888766651144445555588999*******************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1195.17
//
Query:       gi|119720556|ref|YP_921051.1|  [L=388]
Description: major facilitator transporter [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-42  144.9  27.3    5.8e-25   88.0   3.5    2.0  2  MFS_1            Major Facilitator Superfamily
    4.9e-12   45.4  11.2    1.3e-05   24.3   0.2    2.1  2  MFS_1_like       MFS_1 like family
    1.7e-09   37.1  12.4    0.00026   20.0   5.9    3.0  3  Sugar_tr         Sugar (and other) transporter
    9.7e-09   34.3  17.8    3.4e-08   32.5  17.8    1.8  1  MFS_2            MFS/sugar transport protein
      1e-07   30.8  13.1    2.4e-07   29.5  13.1    1.6  1  MFS_3            Transmembrane secretion effector
    8.7e-07   28.1   0.2    8.7e-07   28.1   0.2    3.0  3  LacY_symp        LacY proton/sugar symporter
  ------ inclusion threshold ------
      0.013   14.2  13.1        0.6    8.7   7.0    2.7  2  ATG22            Vacuole effluxer Atg22 like
      0.016   14.8   0.1      0.051   13.1   0.1    1.8  1  PMT_4TMC         C-terminal four TMM region of protein-O-mann
       0.49    9.2   9.9      0.026   13.4   2.0    2.1  2  PTR2             POT family
       0.58   10.5   9.1      0.086   13.1   2.6    2.8  2  Transgly_assoc   Transglycosylase associated protein


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.0   3.5   3.2e-28   5.8e-25       3     229 ..      18     233 ..      16     236 .. 0.87
   2 !   60.2  22.2   8.9e-20   1.6e-16       3     169 ..     216     382 ..     214     387 .. 0.90

  Alignments for each domain:
  == domain 1  score: 88.0 bits;  conditional E-value: 3.2e-28
                          MFS_1   3 laaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalglllllf 81 
                                    ++ +++  +  +++  lp +l ++lg++ + +gl+ ++  l+  ++ l+ G++sdr+Grr+ ++++g+ l+a++  l++f
  gi|119720556|ref|YP_921051.1|  18 FVSLFTDVSTEMINGYLPVFLVQELGATRALLGLIEGIGELANYFFRLVSGYISDRLGRRKaLVFAGYSLSAVSKPLFAF 97 
                                    677778888999**************************************************************444445 PP

                          MFS_1  82 asslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivs 161
                                    a+s w  lv+ +l   g g+ ++   ali++   +e  g+a+gl  +  + Ga++gpll+ ll+ ++g r +f++  i +
  gi|119720556|ref|YP_921051.1|  98 AHSPWDALVVKALDRTGKGIRTSPRDALISQSIDEESSGKAFGLHRTIDQSGAMIGPLLATLLLPLIGPRNLFLVSFIPA 177
                                    677777889999******************************************************************** PP

                          MFS_1 162 llafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltl 229
                                    ++a+ + l+++++ ++e++  +  +              +++l ++ l+++l+a++++++g++ +++l
  gi|119720556|ref|YP_921051.1| 178 VIALAILLAFVVDVKTESREARILKG------------ARQVLGNKRLLLVLAAFAVMGLGYYDFSFL 233
                                    ***77656666666666666666666............677888887866777777777777655554 PP

  == domain 2  score: 60.2 bits;  conditional E-value: 8.9e-20
                          MFS_1   3 laaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa 82 
                                    ++a+++ ++ + + +++ l  +++ g++++ + l++ +  l+  +  +p G+lsdr+G  +vl+ +l++fal+  ++l a
  gi|119720556|ref|YP_921051.1| 216 VLAAFAVMGLGYYDFSFLLVRSREVGVAADLVPLVYLAINLFHTAVGYPSGVLSDRVGKEKVLVGSLVFFALA-SIAL-A 293
                                    5556666666667777766789***************************************************.5555.3 PP

                          MFS_1  83 ..sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaiv 160
                                       +l  ++v+ vl G++ g++ +++ a++ + +p+e rg ++g+++++++l+++ g+ + g+l + +g  ++f   a +
  gi|119720556|ref|YP_921051.1| 294 rtENLAGFAVAVVLYGVFFGSYETVSRAILPRFAPPELRGTVYGVFYIATGLATLAGMTVVGYLWDTAGRAVAFTYSATL 373
                                    3377669************************************************************************* PP

                          MFS_1 161 sllafvlfl 169
                                    sl+a++lf+
  gi|119720556|ref|YP_921051.1| 374 SLIAALLFA 382
                                    ****99744 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.2   7.1e-09   1.3e-05     226     330 ..      12     118 ..      10     172 .. 0.80
   2 !   24.1   7.1   8.2e-09   1.5e-05     179     384 ..     166     368 ..     123     369 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 7.1e-09
                     MFS_1_like 226 eviifllvalilgmswgiienFlflYL.kelgasntllGslvalgvvaeiplfffaeklleklGhvk.lliiallayilr 303
                                    +v ++ +v l+  +s  +i+ +l ++L +elga++ llG +  +g +a+  + +++ ++ ++lG +k l++++ ++ ++ 
  gi|119720556|ref|YP_921051.1|  12 NVYALGFVSLFTDVSTEMINGYLPVFLvQELGATRALLGLIEGIGELANYFFRLVSGYISDRLGRRKaLVFAGYSLSAVS 91 
                                    57788999********************************************************9873677889999*** PP

                     MFS_1_like 304 fllyaiienawlvlpievLhgisfgll 330
                                      l a+ +++w +l++ +L     g+ 
  gi|119720556|ref|YP_921051.1|  92 KPLFAFAHSPWDALVVKALDRTGKGIR 118
                                    ****************99986665555 PP

  == domain 2  score: 24.1 bits;  conditional E-value: 8.2e-09
                     MFS_1_like 179 ysallyvlaallvisllvvlilnetekesklkvtkslqvllnilknpeviifllvalilgmswgiienFlflYL..kelg 256
                                     + l++v  +  vi+l+++l++  + k ++ + + +l+   ++l n++++++l++ +++g     ++ F fl     e+g
  gi|119720556|ref|YP_921051.1| 166 PRNLFLVSFIPAVIALAILLAFVVDVKTESRE-ARILKGARQVLGNKRLLLVLAAFAVMGLG---YYDFSFLLVrsREVG 241
                                    45677777777777777766665555444444.44778899999999999999999999975...455555555446777 PP

                     MFS_1_like 257 asntllGslvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaiienawlvlpievLhgisfgllwaaave 336
                                        l+  +     +    + + +  l +++G +k+l+ +l++++l  + +a +en+    ++ vL+g+ fg +  +   
  gi|119720556|ref|YP_921051.1| 242 VAADLVPLVYLAINLFHTAVGYPSGVLSDRVGKEKVLVGSLVFFALASIALARTENLAGFAVAVVLYGVFFGSYETVSRA 321
                                    77777766666666666666777899****************************************************** PP

                     MFS_1_like 337 yvskiapksleatgqgllsglyfglGralGsliGGllwdlksaiflFr 384
                                       ++ap++l++t+ g++ ++  gl +  G  + G+lwd+ + +++F 
  gi|119720556|ref|YP_921051.1| 322 ILPRFAPPELRGTVYGVFYIA-TGLATLAGMTVVGYLWDTAGRAVAFT 368
                                    ******************987.9*******************999997 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.4   2.9e-07   0.00052      43     188 ..      44     184 ..       9     189 .. 0.73
   2 ?    2.0   0.3      0.04        72     301     338 ..     151     189 ..     148     226 .. 0.62
   3 !   20.0   5.9   1.4e-07   0.00026      66     185 ..     265     382 ..     249     387 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.9e-07
                                    H...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHH.HHHHHHHHHHHHH-TTTT.SS-TGGGGGHHHHHHHHHHHH CS
                       Sugar_tr  43 essvlsglivsiflvGaiiGslfagllgdrfGRkkslli.aavlfvigavlqaaakgk.nsvevlivgRvlvGigvGlas 120
                                    ++  l+gli +i  +   +  l++g+++dr+GR+k+l++ +  l+ ++  l a+a++   ++ v ++ R   Gi      
  gi|119720556|ref|YP_921051.1|  44 ATRALLGLIEGIGELANYFFRLVSGYISDRLGRRKALVFaGYSLSAVSKPLFAFAHSPwDALVVKALDRTGKGIRTSPRD 123
                                    35667888888888888888999****************6678999**********443333334444888999999999 PP

                                    HHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHG CS
                       Sugar_tr 121 vlvPmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllill 188
                                    +l++  i+E +  k  g   ++ q++  +G l+a+ +   l  ++     r l+ ++++pa++ l++l
  gi|119720556|ref|YP_921051.1| 124 ALISQSIDEESSGKAFGLHRTIDQSGAMIGPLLATLL---LPLIGP----RNLFLVSFIPAVIALAIL 184
                                    9999999999999999999999999999999999754...444455....456777777776655554 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.04
                                    HHHHHHHHHHHHHS-SHHHHHHHHHHHHHHHHHHH...H CS
                       Sugar_tr 301 fvatfvaiflvdrfGRRtllllGaagmaicfvilg.iva 338
                                    ++  + a +l   +G R+l+l++++ + i+++il   v+
  gi|119720556|ref|YP_921051.1| 151 MIGPLLATLLLPLIGPRNLFLVSFIPAVIALAILLaFVV 189
                                    444455556666667777777777776666666653333 PP

  == domain 3  score: 20.0 bits;  conditional E-value: 1.4e-07
                                    HHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHH CS
                       Sugar_tr  66 agllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvslyql 145
                                    +g l+dr+G+ k+l+ + v+f  +++  a ++   ++  ++v+ vl G++ G   +++   +  +Ap++lRg++ +++  
  gi|119720556|ref|YP_921051.1| 265 SGVLSDRVGKEKVLVGSLVFFALASIALARTE---NLAGFAVAVVLYGVFFGSYETVSRAILPRFAPPELRGTVYGVFYI 341
                                    799**********************9999999...99******************************************* PP

                                    HHHHHHHHHHHH.HHHHHTSS-TTHHHHHHHCCHHHHHHHH CS
                       Sugar_tr 146 aitfGilvaaif.glglnktsnadgwrillglqlvpallll 185
                                    a+ +  l + ++ g+  ++ + a+ + +   l+l+ all++
  gi|119720556|ref|YP_921051.1| 342 ATGLATLAGMTVvGYLWDTAGRAVAFTYSATLSLIAALLFA 382
                                    *******9986515555888889************998775 PP

>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5  17.8   1.9e-11   3.4e-08       4     404 ..      18     380 ..      15     388 .] 0.82

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 1.9e-11
                          MFS_2   4 lgalaanilsvllatylliFytdvlglsaalvglvllvarlvDaitDpivGtlidktstrwGrrrPwlllsaiilavsii 83 
                                    + +l +++++ ++  yl +F+++ lg + al+gl+  +  l + ++  ++G+++d+    +Grr+++++++  + avs  
  gi|119720556|ref|YP_921051.1|  18 FVSLFTDVSTEMINGYLPVFLVQELGATRALLGLIEGIGELANYFFRLVSGYISDR----LGRRKALVFAGYSLSAVSKP 93 
                                    556667788888999****************************************6....5******************* PP

                          MFS_2  84 llftppelsqsakfiwllvtyill.rilytlfeipyvslvpvltkdydeRtsltsvrsflsvlggvlaailafllvlilg 162
                                    l+ ++++        w +++  +l r+     + p  +l+++   d +   ++++  +++   g +++ +la+ll+   g
  gi|119720556|ref|YP_921051.1|  94 LFAFAHS-------PWDALVVKALdRTGKGIRTSPRDALISQS-IDEESSGKAFGLHRTIDQSGAMIGPLLATLLLPLIG 165
                                    9999999.......46666666663677777777777777765.99999**************************99999 PP

                          MFS_2 163 glkserkgylifaliialLmllgviivvlgtkervemrkkekteqkeklslleqlkevfrnraflillllfllaalalgv 242
                                          ++ +++ +i a+++l+  ++ v  +k           ++ +  ++l++ ++v+ n+ +l++l++f   +++lg 
  gi|119720556|ref|YP_921051.1| 166 P-----RNLFLVSFIPAVIALAILLAFVVDVK-----------TESREARILKGARQVLGNKRLLLVLAAFA--VMGLGY 227
                                    6.....78888888888888877777766666...........357789************99988887765..555677 PP

                          MFS_2 243 lnglllYyltyvlg.ngsaasvfllvvtisallgiplwqplakrlgkkntyllgalltivllvlvlllqpsnlllflvll 321
                                    +   +l++    +g +++ + +++l++ +  +++     +l  r gk ++ + ++ + ++l  ++l+  ++nl+ f v++
  gi|119720556|ref|YP_921051.1| 228 YDFSFLLVRSREVGvAADLVPLVYLAINLFHTAVGYPSGVLSDRVGKEKVLVGSL-VFFALASIALAR-TENLAGFAVAV 305
                                    777788888888888999999999999888777777799*********9876655.445555555555.9********** PP

                          MFS_2 322 viagfgvgvaallpwsmladvvDygelktGkrregvffavlsfisklatgiglgvsgllLsafgyrakasvqspqvvlal 401
                                    v++g+++g+  ++  ++l+  +           +g++++v+ +++ lat  g+ v+g+l +++g  a a ++s++  l+ 
  gi|119720556|ref|YP_921051.1| 306 VLYGVFFGSYETVSRAILPRFAPP-------ELRGTVYGVFYIATGLATLAGMTVVGYLWDTAGR-AVAFTYSATLSLIA 377
                                    ********************9754.......469*************************999997.55555555444333 PP

                          MFS_2 402 rll 404
                                    +ll
  gi|119720556|ref|YP_921051.1| 378 ALL 380
                                    333 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5  13.1   1.4e-10   2.4e-07      35     390 ..      37     381 ..      27     387 .. 0.84

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 1.4e-10
                          MFS_3  35 WlmtdisasplmvAlvqaaatLPifllsilaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllaltllig 114
                                    +l+ ++ a+ +   l+   + L   ++ +++G ++D + rRk l+ +   l +vs  l  +a+    spw  l++  l  
  gi|119720556|ref|YP_921051.1|  37 FLVQELGATRALLGLIEGIGELANYFFRLVSGYISDRLGRRKALVFAGYSLSAVSKPLFAFAH----SPWDALVVKALDR 112
                                    57888999999999****************************999988888889999888875....8************ PP

                          MFS_3 115 iGaalndPaWqAsvgelvkrrdvpaAvaLnsvginiaRsvGPAlgGvlvaavGaalafavnalsylalivallrwkrevr 194
                                     G  + +   +A +++ ++ +   +A  L+         +GP l+ +l+ ++G+   f v  +  ++ +++ll+   +v+
  gi|119720556|ref|YP_921051.1| 113 TGKGIRTSPRDALISQSIDEESSGKAFGLHRTIDQSGAMIGPLLATLLLPLIGPRNLFLVSFIPAVIALAILLAFVVDVK 192
                                    *****************************9888888889********************999999999999888877776 PP

                          MFS_3 195 ksslprEkllealraglRftaasreikavlvRaalFglsasavlaLLPlvardqldgdalvyGillgalGvGAilgalll 274
                                    ++     +  + +  g+R +   + +  vl+  a+ gl       L  lv  ++++  a    ++  a+ +   + +  +
  gi|119720556|ref|YP_921051.1| 193 TE-----SREARILKGARQVLGNKRLLLVLAAFAVMGLGYYDFSFL--LVRSREVGVAADLVPLVYLAINLFHTAVGYPS 265
                                    54.....444567788999999999999998888888876665444..34455566666666666677777777778889 PP

                          MFS_3 275 srLRerlsserlvllaavalAlvllslalasslwvavlvlllgGaaWitalstlnvavqlavPrW....vvgRalavYlt 350
                                      L +r+++e+++  + v +Al  ++la +++l+  +++++l G      + ++++   +++Pr+    ++g +  v++ 
  gi|119720556|ref|YP_921051.1| 266 GVLSDRVGKEKVLVGSLVFFALASIALARTENLAGFAVAVVLYGVF----FGSYETVSRAILPRFappeLRGTVYGVFYI 341
                                    99****************************************9964....344444444444444222289********9 PP

                          MFS_3 351 vlaGglaaGsllWGavaealsvtlaLlaaaaalllaaail 390
                                    ++  +  aG  + G + ++++ ++a + +a++ l+aa+++
  gi|119720556|ref|YP_921051.1| 342 ATGLATLAGMTVVGYLWDTAGRAVAFTYSATLSLIAALLF 381
                                    9988888999999999999999999999998888777665 PP

>> LacY_symp  LacY proton/sugar symporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.2   4.9e-10   8.7e-07      23     198 ..      27     198 ..      10     224 .. 0.77
   2 ?    3.6   1.3     0.013        24      27      89 ..     230     287 ..     213     323 .. 0.66
   3 ?    1.1   0.3     0.074   1.3e+02     345     391 ..     331     376 ..     318     386 .. 0.74

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 4.9e-10
                      LacY_symp  23 msayfplfpvwlkevlglsktetGivfsvislfsilfqplfGlisdklGlkkellwvislllvlfapfliyvfepllqln 102
                                      ++  ++pv+l + lg +++ +G++  + +l    f+ + G isd+lG +k l+++   l  +  p++ + ++p   l 
  gi|119720556|ref|YP_921051.1|  27 TEMINGYLPVFLVQELGATRALLGLIEGIGELANYFFRLVSGYISDRLGRRKALVFAGYSLSAVSKPLFAFAHSPWDALV 106
                                    34566799*******************************************************************98877 PP

                      LacY_symp 103 ilvGalvGgvflGlvysagagaieayiekvsraskfeyGkarvfGclGyalcaslaGilfsidpslvfwlasgf.alill 181
                                    + +   +G    G+  s + ++i   i+  s  +   +G  r +   G  ++  la +l+ +    +++l+s + a+i l
  gi|119720556|ref|YP_921051.1| 107 VKALDRTG---KGIRTSPRDALISQSIDEESSGK--AFGLHRTIDQSGAMIGPLLATLLLPLIGPRNLFLVSFIpAVIAL 181
                                    77666666...59999999999999999877655..56899999999999*****9999986666666666666144444 PP

                      LacY_symp 182 lllllskpdksssakva 198
                                     +ll +  d+++++  a
  gi|119720556|ref|YP_921051.1| 182 AILLAFVVDVKTESREA 198
                                    45555555555444433 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.013
                      LacY_symp  27 fplfpvwlkevlglsktetGivfsvislfsilfqplfGlisdklGlkkellwvislllvlfap 89 
                                    f+++ v  +  +g++   + +v+ +i+lf        G++sd++G  k l+ ++     +fa 
  gi|119720556|ref|YP_921051.1| 230 FSFLLVR-SREVGVAADLVPLVYLAINLFHTAVGYPSGVLSDRVGKEKVLVGSLV----FFAL 287
                                    3333333.34467777788899*******9999999************9987654....4443 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.074
                      LacY_symp 345 lsatifligfqlskqlaivllstlaGklydkvGfqtaylvlgiivls 391
                                    l  t++ + f ++  la++   t++G l+d++G   a+   +++ l 
  gi|119720556|ref|YP_921051.1| 331 LRGTVYGV-FYIATGLATLAGMTVVGYLWDTAGRAVAFTYSATLSLI 376
                                    55677765.78899999999999999999999988877654444433 PP

>> ATG22  Vacuole effluxer Atg22 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.3   0.00038      0.68     407     477 ..     127     198 ..      25     199 .. 0.77
   2 ?    8.7   7.0   0.00033       0.6     384     466 ..     301     382 ..     200     386 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00038
                          ATG22 407 seLiPrGkEaaFFsLyaitdkgssvigplivglItDrtgnirsafv.flavLlvvplpllllvdvergrrea 477
                                    s+ i + +  + F+L  ++d+++++igpl+ +l+    g  +  +v f+ +++ +++ l ++vdv+   rea
  gi|119720556|ref|YP_921051.1| 127 SQSIDEESSGKAFGLHRTIDQSGAMIGPLLATLLLPLIGPRNLFLVsFIPAVIALAILLAFVVDVKTESREA 198
                                    555555555666*************************99755433325667788888888999*99988887 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00033
                          ATG22 384 fyvlavvyglvlgglssysRslfseLiPrGkEaaFFsLyaitdkgssvigplivglItDrtgnirsafvflavLlvvplp 463
                                    f v  v+yg+++g+++++sR++     P+    + ++ + i    + + g+ +vg + D  g + +af   a L++++  
  gi|119720556|ref|YP_921051.1| 301 FAVAVVLYGVFFGSYETVSRAILPRFAPPELRGTVYGVFYIATGLATLAGMTVVGYLWDTAGRA-VAFTYSATLSLIAAL 379
                                    4466789***********************999999988888888889***********99875.799999999999888 PP

                          ATG22 464 lll 466
                                    l+ 
  gi|119720556|ref|YP_921051.1| 380 LFA 382
                                    775 PP

>> PMT_4TMC  C-terminal four TMM region of protein-O-mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   2.9e-05     0.051     117     177 ..     166     231 ..     142     236 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.9e-05
                       PMT_4TMC 117 gRvlflhhYlpAllfailllaalldfllkslkkslkkk.....klvklivvvvllvlviavFiffs 177
                                     R lfl  ++pA+++ ++lla+++d+ ++s+++++ k       + +l++v++ ++++ + ++ fs
  gi|119720556|ref|YP_921051.1| 166 PRNLFLVSFIPAVIALAILLAFVVDVKTESREARILKGarqvlGNKRLLLVLAAFAVMGLGYYDFS 231
                                    699************************988888875547766645555555555555556666555 PP

>> PTR2  POT family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   1.1      0.17     3e+02      86     122 ..     152     187 ..     149     193 .. 0.79
   2 ?   13.4   2.0   1.4e-05     0.026      70     127 ..     329     386 ..     326     388 .] 0.95

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.17
                                    HHHHHHHHHHHHHHCTT-HHHHHHHHHHHHHHHHHHH CS
                           PTR2  86 vGSLlsliitpylqenvgyplgFgipavlmiiallvF 122
                                    +G Ll+++++p++  +  + + F ipav+ +  ll F
  gi|119720556|ref|YP_921051.1| 152 IGPLLATLLLPLIGPRNLFLVSF-IPAVIALAILLAF 187
                                    899*******************9.5555544445555 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 1.4e-05
                                    SCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTT-HHHHHHHHHHHHHHHHHHHHCTTT CS
                           PTR2  70 prersrfFsiFyfsiNvGSLlsliitpylqenvgyplgFgipavlmiiallvFllGsr 127
                                    p+ r+ ++ +Fy++  +  L  +++++yl +++g +++F  +a l +ia l F++++r
  gi|119720556|ref|YP_921051.1| 329 PELRGTVYGVFYIATGLATLAGMTVVGYLWDTAGRAVAFTYSATLSLIAALLFAYSTR 386
                                    7889999***********************************************9987 PP

>> Transgly_assoc  Transglycosylase associated protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   2.6   4.8e-05     0.086       5      43 ..     151     187 ..     149     192 .. 0.77
   2 ?   -0.8   0.5         1   1.9e+03      10      35 ..     279     306 ..     278     307 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.8e-05
                 Transgly_assoc   5 ivGAfvGgfllgllgigvgggelaslivaiiGAiILLfi 43 
                                    ++G +++++ll+l+g+  +  +l s+i+a+i   ILL+ 
  gi|119720556|ref|YP_921051.1| 151 MIGPLLATLLLPLIGP--RNLFLVSFIPAVIALAILLAF 187
                                    4666777777777777..9999*********98888864 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1
                 Transgly_assoc  10 vGgfllgllgi..gvgggelaslivaii 35 
                                    vG +++ +l      ++ +la++ va++
  gi|119720556|ref|YP_921051.1| 279 VGSLVFFALASiaLARTENLAGFAVAVV 306
                                    5555533333334567788899988886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       632  (0.0352502); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.69u 0.28s 00:00:00.97 Elapsed: 00:00:00.48
# Mc/sec: 2419.79
//
Query:       gi|119720557|ref|YP_921052.1|  [L=413]
Description: hypothetical protein Tpen_1654 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0065   16.2   0.0       0.11   12.2   0.0    2.4  2  Fucose_iso_C     L-fucose isomerase, C-terminal domain
  ------ inclusion threshold ------
      0.081   12.1   0.0       0.15   11.3   0.0    1.4  1  Arabinose_Isome  L-arabinose isomerase


Domain annotation for each model (and alignments):
>> Fucose_iso_C  L-fucose isomerase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0     0.033   2.9e+02       1      15 [.     111     124 ..     111     151 .. 0.79
   2 !   12.2   0.0   1.2e-05      0.11      43     140 ..     321     407 ..     309     410 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.033
                                    EE-SS---GGGEE-T CS
                   Fucose_iso_C   1 linsGnaaldgaars 15 
                                    l+++G+++ dg +++
  gi|119720557|ref|YP_921052.1| 111 LFHCGSFS-DGNCAA 124
                                    79*****9.775544 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 1.2e-05
                                    E-B--TT-EEEEEEEEEETTTEEE.EEEEEEEE----HHHHHHHHHHH-TTS-BEEEEE---SSHHHHT-SSSEEEEEES CS
                   Fucose_iso_C  43 vegtikpgpvTllRlnlikgdGkvklqiaeGefvdlpeetfgslgvrtipewpttffkprltgksvmenwganHvavvyG 122
                                    v+ + +pg+vT++ l+  + + +v  ++a G++v+    +   ++ rt+ +  ++    +++++++     anH  v  G
  gi|119720557|ref|YP_921052.1| 321 VASQLQPGEVTVASLS--RDLSEV--YVARGRVVRSGFIS--RAMCRTQAHV-EF----DFDAEVIPLVAPANHHLVMPG 389
                                    6677899*********..999999..*******8876544..5566666666.32....334688999999********* PP

                                    --HHHHHHHHHHHT--EE CS
                   Fucose_iso_C 123 hvgkdlielakyLripvv 140
                                    +v+ +++ + k+L+ +v 
  gi|119720557|ref|YP_921052.1| 390 DVVREVKSVSKLLGLRVK 407
                                    **************9986 PP

>> Arabinose_Isome  L-arabinose isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   1.7e-05      0.15     196     318 ..     158     274 ..     114     288 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.7e-05
                                    HHHH--EEEEE-HHHHHHHHHTS-HHHHHHHHHHHHHHSEE-GGGSTTSTTHHHHHHHHHHHHHHHHHHHHHT-SEE.EE CS
                Arabinose_Isome 196 eiklGvsvntygvgdlvevveavsdeevdalveeyekkYelaeelkeeeereeslreaarielglrkfLeekgfkaf.tt 274
                                      +lG++++ ++ ++l+++ e++  e+v++ +++ +    ++         ++sl++   +  +lr++ eek ++a+ ++
  gi|119720557|ref|YP_921052.1| 158 SSRLGWTIEVVPAEELFSAAESAPREAVESFLSRVSGVPGFE-------LYRSSLEHVGGVYYALRRLSEEKRLDAVaVD 230
                                    568899999999999999999999998888888776543333.......3466788889999*************98358 PP

                                    -TT--TTSSS-SSHHHHHHHHHT-EEESTT-HHHHHHHHHHHHH CS
                Arabinose_Isome 275 tFedlgglkqlpglavqrLmaeGyGfgaEGDwktaalvrilkvm 318
                                     F  l + +  p +a   L a+G+  + E D  +a l+ + + +
  gi|119720557|ref|YP_921052.1| 231 CFPYLVEHRVSPCVALALLNADGFAAACEADLYSALLMLVSREL 274
                                    9**********************************999877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2795.84
//
Query:       gi|119720558|ref|YP_921053.1|  [L=96]
Description: hypothetical protein Tpen_1655 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.4e-09   36.8   0.2    5.1e-09   36.7   0.2    1.1  1  Rubrerythrin  Rubrerythrin
     0.0012   18.7   0.0     0.0015   18.4   0.0    1.2  1  DUF2202       Uncharacterized protein domain (DUF2202)
     0.0059   16.9   0.0     0.0084   16.4   0.0    1.3  1  DUF2383       Domain of unknown function (DUF2383)
  ------ inclusion threshold ------
      0.015   15.1   0.0      0.017   14.9   0.0    1.2  1  COQ7          Ubiquinone biosynthesis protein COQ7
      0.017   15.2   0.1       0.31   11.1   0.0    2.1  2  HTH_20        Helix-turn-helix domain
      0.029   14.3   0.0       0.55   10.2   0.0    2.1  2  RHH_4         Ribbon-helix-helix domain
      0.038   13.9   0.1      0.045   13.7   0.1    1.2  1  Ferritin      Ferritin-like domain


Domain annotation for each model (and alignments):
>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.2     2e-12   5.1e-09       4      72 ..      25      91 ..      22      96 .] 0.87

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 2e-12
                                   HHHHHHHHHHHHHHHHHHHCHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS--- CS
                   Rubrerythrin  4 ekAiagEssarrlYkelaekakegypqiaelFeelAeeEreHakilnklleklepelelevkekvreya 72
                                     +i++E +a +lY  la  ++   p  +++Fe++A+eE+ H + +  lle l+pe+  e ++ ++e++
  gi|119720558|ref|YP_921053.1| 25 RLSIIAELDAVNLYLQLANATD--DPLARKVFEDIAREEKTHVGEFLSLLERLDPEQVKELEKGKKEVL 91
                                   679*******************..9999***************************99955555555555 PP

>> DUF2202  Uncharacterized protein domain (DUF2202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   5.7e-07    0.0015      15      65 ..      34      87 ..      17      95 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 5.7e-07
                        DUF2202 15 arDvYlelYdrwk....lqiflniakseqthtdavksllekYeledpvkederGk 65
                                   a ++Yl+l + ++     ++f++ia+ e+th+ +  slle+ + e+  ke e+Gk
  gi|119720558|ref|YP_921053.1| 34 AVNLYLQLANATDdplaRKVFEDIAREEKTHVGEFLSLLERLDPEQV-KELEKGK 87
                                   66788888877652222689*********************997654.4444566 PP

>> DUF2383  Domain of unknown function (DUF2383)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   3.3e-06    0.0084      12      60 ..      30      78 ..      20      86 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.3e-06
                                   HHHHHHHHHHHHHHT--SHHHHHHHHHHHHHHHHHHHHHHHHHHHCT-- CS
                        DUF2383 12 tlkdgeegykeaaekvkdpqlktlleriaeereeaaeeLqseiralgge 60
                                   ++ d+++ y + a   +dp  ++++e+ia+e + ++ e+ s +++l  e
  gi|119720558|ref|YP_921053.1| 30 AELDAVNLYLQLANATDDPLARKVFEDIAREEKTHVGEFLSLLERLDPE 78
                                   5679**********************************99999888655 PP

>> COQ7  Ubiquinone biosynthesis protein COQ7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   6.8e-06     0.017       2      59 ..      20      75 ..      19      86 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 6.8e-06
                           COQ7  2 ldrllRvdhaGElgAvaiYkgqlavlakkdpelkpllkemleqEkeHlatfeellker 59
                                   l++++R     El Av +Y   + +  ++dp  ++++++++++Ek H+  f +ll++ 
  gi|119720558|ref|YP_921053.1| 20 LAQAVRLSIIAELDAVNLYLQLANA--TDDPLARKVFEDIAREEKTHVGEFLSLLERL 75
                                   6789999999*********977777..799999****************999998875 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.079     2e+02       7      19 ..      20      32 ..      11      37 .. 0.82
   2 ?   11.1   0.0   0.00012      0.31       2      37 ..      40      76 ..      39      84 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.079
                                   HS-HHHHHHHHHH CS
                         HTH_20  7 LahPvRrrilraL 19
                                   La+ vR+ i ++L
  gi|119720558|ref|YP_921053.1| 20 LAQAVRLSIIAEL 32
                                   7888999999998 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00012
                                   HHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHH.TS- CS
                         HTH_20  2 qiaeALahPvRrrilraLaraegltaselaerl.dls 37
                                   q+a A+++P  r+++  +ar+e   ++e+  +l +l+
  gi|119720558|ref|YP_921053.1| 40 QLANATDDPLARKVFEDIAREEKTHVGEFLSLLeRLD 76
                                   899*******************999999998885455 PP

>> RHH_4  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.072   1.8e+02      51      64 ..      18      31 ..      11      32 .. 0.80
   2 ?   10.2   0.0   0.00021      0.55      24      45 ..      53      74 ..      49      86 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.072
                                   .THHHHHHHHHHHH CS
                          RHH_4 51 anLasalRvfvlry 64
                                   + La a+R+ ++++
  gi|119720558|ref|YP_921053.1| 18 EELAQAVRLSIIAE 31
                                   589******99876 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00021
                                   HHHHHHHHTT--HHHHHHHH.H CS
                          RHH_4 24 aLeeiArregltvnaLiaeida 45
                                   ++e+iAr+e++ v ++++ +++
  gi|119720558|ref|YP_921053.1| 53 VFEDIAREEKTHVGEFLSLLER 74
                                   789***************9954 PP

>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   1.8e-05     0.045      83     139 ..      22      75 ..       4      94 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.8e-05
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Ferritin  83 evleaalehekkvteslrelielaeeegDpatadfledfleeqeeheweleallekl 139
                                    ++++  + +e ++++ + +l++ ++   Dp  +  +ed+ +e+  h+ e+ +lle+l
  gi|119720558|ref|YP_921053.1|  22 QAVRLSIIAELDAVNLYLQLANATD---DPLARKVFEDIAREEKTHVGEFLSLLERL 75 
                                    5555555555555556655555555...56666666666666666666666666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       718  (0.0400469); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 739.38
//
Query:       gi|119720559|ref|YP_921054.1|  [L=152]
Description: NUDIX hydrolase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-23   82.4   0.0    3.4e-23   82.1   0.0    1.0  1  NUDIX     NUDIX domain
    0.00045   20.2   0.0    0.00064   19.7   0.0    1.3  1  NUDIX_4   NUDIX domain


Domain annotation for each model (and alignments):
>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.1   0.0   3.8e-27   3.4e-23       4     115 ..       8     119 ..       4     135 .. 0.79

  Alignments for each domain:
  == domain 1  score: 82.1 bits;  conditional E-value: 3.8e-27
                                    EEEEEEEEETTSEEEEEEESSSSTTT.EESSEEECBTTSHHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEEEEEEEEE CS
                          NUDIX   4 ravgvvllnekgevLlvrrskkpfpg.WelPgGkvepgEtpeeAArREleEEtGleaellellgrlhylapydgpygdeh 82 
                                    +av++ +  + g++Llv+r k+p +g W++PgG +e+gE + +AA REl EEtGl+a+ l ++g+++  +++ g+ +  h
  gi|119720559|ref|YP_921054.1|   8 AAVSC-VVKKGGKFLLVKRGKDPGRGlWAFPGGVIEAGEGVFDAAKRELYEETGLSANPLGVVGVTEVIHTDGGRVK-HH 85 
                                    34444.5555567*******999999*************888**********************9999999888888.45 PP

                                    EEEEEEE.EEECSGCSSTSTTTEEEEEEEEHHHH CS
                          NUDIX  83 eilyvfl.eevegelepndenevsevrwvpleel 115
                                    ++++ +l +e+  e  p++ ++v+ev w++l+e+
  gi|119720559|ref|YP_921054.1|  86 YVILSVLfDEESLEGSPRAGGDVEEVAWMSLDEI 119
                                    55544444666666666678*************9 PP

>> NUDIX_4  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   7.2e-08   0.00064       3      63 ..      12      86 ..       9     132 .. 0.56

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 7.2e-08
                                   EEEEECTEEEEEE--TTSSSTT-EE-SEEE.-TTS-HHHHHH...HHHHS-EEE...........EEEEEEEEEEE CS
                        NUDIX_4  3 llirddgrvllekRpekgllggLwefPgge.eegeeleeala...reelgieve...........elepgtvkHvf 63
                                   +++ ++g++ll kR ++    gLw fPgg  e+ge + +a++    ee+g++++           +++ g+vkH +
  gi|119720559|ref|YP_921054.1| 12 CVVKKGGKFLLVKRGKD-PGRGLWAFPGGViEAGEGVFDAAKrelYEETGLSANplgvvgvteviHTDGGRVKHHY 86
                                   455555********996.99*******9887777754344332333455554332332222222223336666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       229  (0.0127726); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1099.68
//
Query:       gi|119720560|ref|YP_921055.1|  [L=220]
Description: hypothetical protein Tpen_1657 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1667.44
//
Query:       gi|119720561|ref|YP_921056.1|  [L=444]
Description: rhomboid family protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-36  125.9  17.3    1.2e-36  125.9  17.3    1.9  2  Rhomboid  Rhomboid family
     0.0086   16.6   0.4     0.0086   16.6   0.4    2.7  3  DUF1751   Eukaryotic integral membrane protein (DUF1751)


Domain annotation for each model (and alignments):
>> Rhomboid  Rhomboid family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.9  17.3   1.4e-40   1.2e-36       4     147 ..      61     218 ..      59     221 .. 0.96
   2 ?   -2.1   0.1      0.37   3.4e+03      50      58 ..     255     263 ..     226     278 .. 0.48

  Alignments for each domain:
  == domain 1  score: 125.9 bits;  conditional E-value: 1.4e-40
                                    CC-TTHHHHGGG--SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-S........-EESSHHH CS
                       Rhomboid   4 rgelwrlltsmflHagwlHllfNmlallvfGsplerrlGslrflllyllsglagsllsllfsaeses.....plvGaSGa 78 
                                    +++l+rl+tsmflHa+++H++fNml+l+ fG+++e +lGs r++lly++sg+++s+++ +f +  ++     p++GaSGa
  gi|119720561|ref|YP_921056.1|  61 PEHLYRLFTSMFLHANLAHIFFNMLYLYTFGKSVEAVLGSERYFLLYFASGILASVFHTAFLPIEGAssafvPALGASGA 140
                                    789***********************************************************99888999********** PP

                                    HHHHHHHHHHHHHCCCCGS----HC............CCCCCCCCCCHHHCTSSSTTTHHHHHHHHHHHHHHHHHHCC CS
                       Rhomboid  79 ifgllgallvlvprnrkllrkliia.........llllllfillnlvlgllpraggvsnlAHlgGllaGlllgllllr 147
                                    i+g+lga+l+l+p +r ++ ++ ++           +l+++++l+++ g+l+   gv+ +AH gG+++Gl+l  +l++
  gi|119720561|ref|YP_921056.1| 141 ISGVLGAYLLLFPGTRLTMCFFYVFiplcftmkaAAYLVFWFALQILQGFLGASLGVAVFAHAGGFIGGLALLPVLVS 218
                                    *******************99999999******999***********************************9988876 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.37
                                    HHHHHHHHH CS
                       Rhomboid  50 yllsglags 58 
                                     l++ +a++
  gi|119720561|ref|YP_921056.1| 255 VLIGLVAAA 263
                                    111222222 PP

>> DUF1751  Eukaryotic integral membrane protein (DUF1751)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.4   9.5e-07    0.0086       8      94 ..      64     145 ..      55     150 .. 0.83
   2 ?   -0.9   0.2      0.27   2.4e+03      63      94 ..     160     198 ..     145     202 .. 0.43
   3 ?   -1.9   0.1      0.55     5e+03      13      35 ..     265     287 ..     245     291 .. 0.61

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 9.5e-07
                        DUF1751   8 pwtlltasfveqnvwkvlvslltlllggkylErlWgskEllkFilvvnvitnllvvlltlllylvtkseelllvpisGla 87 
                                     + l+t++f  +n+ ++ +++l l+ +gk +E + gs+ ++    ++ +++++l+ ++++++  +   ++  +vp  G+ 
  gi|119720561|ref|YP_921056.1|  64 LYRLFTSMFLHANLAHIFFNMLYLYTFGKSVEAVLGSERYF----LLYFASGILASVFHTAFLPIEGASS-AFVPALGAS 138
                                    6889********************************87653....4567788888899988888888888.778888888 PP

                        DUF1751  88 gilagfl 94 
                                    g  +g+l
  gi|119720561|ref|YP_921056.1| 139 GAISGVL 145
                                    8888887 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.27
                        DUF1751  63 vlltlllylvtkseelll.......vpisGlagilagfl 94 
                                    +++++++ l ++ + + +         ++G+ g   g++
  gi|119720561|ref|YP_921056.1| 160 CFFYVFIPLCFTMKAAAYlvfwfalQILQGFLGASLGVA 198
                                    333333322222222211000101123455555555555 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.55
                        DUF1751  13 tasfveqnvwkvlvslltlllgg 35 
                                    ++s ve++  + + ++lt+ + g
  gi|119720561|ref|YP_921056.1| 265 VYSAVEAETTGGVNKVLTVSVTG 287
                                    34456666666666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (444 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 3291.79
//
Query:       gi|119720562|ref|YP_921057.1|  [L=388]
Description: tyrosyl-tRNA synthetase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-33  116.8   0.0    4.4e-21   75.5   0.0    2.1  2  tRNA-synt_1b  tRNA synthetases class I (W and Y)


Domain annotation for each model (and alignments):
>> tRNA-synt_1b  tRNA synthetases class I (W and Y)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.5   0.0   2.5e-25   4.4e-21       5     195 ..      44     234 ..      40     237 .. 0.88
   2 !   39.4   0.0   2.4e-14   4.3e-10     199     292 ..     263     362 ..     254     363 .. 0.79

  Alignments for each domain:
  == domain 1  score: 75.5 bits;  conditional E-value: 2.5e-25
                                    --EEEEEEETSSS-BGG.GHHHHHHHHHHHHTTSEEEEEEEHHHHHTTTTT-SSHHHHHHHHHHHHHH.HHHHH.HHTCH CS
                   tRNA-synt_1b   5 plrvysGidPTgklHlG.ylvplkklvelqkaghevffliaDlhAiigdpskaeerklrkreevlena.ikaql.akgld 81 
                                    pl  y G++ +g +HlG  l++++k+++lq+ g+++ +++aD h  i+++   ++  +r  +  + +   +  l  +g d
  gi|119720562|ref|YP_921057.1|  44 PLVHYIGFEISGLVHLGtGLISMQKVADLQSVGVKTKVFLADYHSWINRKLGGDLDVIRRVAGGYFKEaLRVSLrIVGGD 123
                                    67789**********************************************8899999887665554446666625679* PP

                                    TTTEEEEETHHHHTTHHHHHH..HHHHHTTCBHHHHHHHHHCCHHCSSSC--BHHHHHHHHHHHHHHHHTCHSEEEEEGG CS
                   tRNA-synt_1b  82 pekaevvlqsewlehlelael..lrdlgklgslnrmlqfksvkkrleegegislgeftYplLqaaDilllkadlvpgGsD 159
                                    p+k+e++l+se +e+l l ++  + +++  ++l+r+ +  ++  r e+ e +s+++++Y  +q aDi+ + +++  gG+D
  gi|119720562|ref|YP_921057.1| 124 PDKTEFILGSELYEKLGLDYFtnVLRVSMETTLSRVRRSVTILGRSES-EALSFAQLLYVPMQVADIFSMGVNIPHGGMD 202
                                    ****************6655511456777799****************.79***************************** PP

                                    GHHHHHHHHHHHHHHHHHSTTSS-EEEEET-BBSTT CS
                   tRNA-synt_1b 160 Qkqnielgrdlarrfnkkevfkkpegltvplltgld 195
                                    Q++  ++++++ +++       kp++l ++ll+gl+
  gi|119720562|ref|YP_921057.1| 203 QRKAHVIAIEVGEKLFGY----KPVALHHHLLPGLQ 234
                                    **************9888....9*********9986 PP

  == domain 2  score: 39.4 bits;  conditional E-value: 2.4e-14
                                    BTTCETTCGC-BTTCCHHHHHHHHHHCHCSTTC.SHHHHHHH.HHTHHH...CHHHHHHHHCCSEE.ESSHHHHHHHHHC CS
                   tRNA-synt_1b 199 KmSKSagnsaIfLddekesvkkkiqkavtdsde.evekllkl.ktelsn...elierleavsgkkp.kreaeellaeevt 272
                                    KmSKS++++a+f+ d++e++++ki++a++  +e e+  ll++ ++ ++    e +e + + +g+    +++ el++++++
  gi|119720562|ref|YP_921057.1| 263 KMSKSKPETALFIHDSEEEIRSKIGRAFCPAGEvEMNPLLEIaRYIVFRnrkEPFEVVNKKTGERRaFNTYGELEEAFRE 342
                                    9********************************955555554144444434433444555555555567899******** PP

                                    CCCHHHHHHHHHHHHHHHHH CS
                   tRNA-synt_1b 273 klvhggdlkkalaealnell 292
                                    +lvh+ dlk+al+++l e+l
  gi|119720562|ref|YP_921057.1| 343 RLVHPADLKEALSRELAEIL 362
                                    **************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 2484.65
//
Query:       gi|119720563|ref|YP_921058.1|  [L=387]
Description: myo-inositol-1-phosphate synthase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-21   76.3   0.0    3.2e-21   75.6   0.0    1.3  1  Inos-1-P_synth  Myo-inositol-1-phosphate synthase
    0.00075   19.0   0.0     0.0012   18.3   0.0    1.4  2  NAD_binding_5   Myo-inositol-1-phosphate synthase


Domain annotation for each model (and alignments):
>> Inos-1-P_synth  Myo-inositol-1-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.6   0.0   3.5e-25   3.2e-21       1     109 []     209     314 ..     209     314 .. 0.95

  Alignments for each domain:
  == domain 1  score: 75.6 bits;  conditional E-value: 3.5e-25
                                    SHHHHHHHHHHHHHHTT-EEEEEEEEEEE-HHHHHHTTSHHHHHHHHHHHHHHHHHHHSS--EEE....EEE.EE-GGGT CS
                 Inos-1-P_synth   1 GqTklksvLaellverglkvksivslNilGnnDgknlseeerfksKkisKssvvddivkanellyvdhevvi.kYvpylg 79 
                                    G+T l   Lae+l+er+ +v si+++Ni+Gn+D+++l+e+er+ +K+++Ks +++di+++++     h ++   Y+++lg
  gi|119720563|ref|YP_921058.1| 209 GATPLTVDLAEHLKERNRRVLSIAQFNIGGNTDFLALTEPERNLAKENTKSGFLKDILGYEPP----HFIRPtGYLEPLG 284
                                    99**********************************************************775....444447******* PP

                                    TEEEEEEEEEEEEGGGEEEEEEEEEEEEH. CS
                 Inos-1-P_synth  80 DsKvaldeieseiflggkntielkleceDS 109
                                    D+K+  ++++   f+g++ +++++++++DS
  gi|119720563|ref|YP_921058.1| 285 DKKFVSMHVQWVSFGGFTDELVVNMRINDS 314
                                    *****************************9 PP

>> NAD_binding_5  Myo-inositol-1-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0      0.55   4.9e+03       3      26 ..       8      30 ..       6      34 .. 0.86
   2 !   18.3   0.0   1.3e-07    0.0012     202     262 ..     157     218 ..     146     363 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 0.55
                                   xxxxxxxxxxxxxxxxxxxxxxxx RF
                  NAD_binding_5  3 vllvGlgGnngtTlvagvlankkg 26
                                   v lvG  G ++t +  g++  kkg
  gi|119720563|ref|YP_921058.1|  8 VALVGQ-GYVATIFAWGLCKLKKG 30
                                   789998.*******9999999886 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 1.3e-07
                                    xxxxxxxxxxxxxxxx.xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                  NAD_binding_5 202 eispstiyavAaileg.vpyingsPqntl.vpglvelAekkgvfiaGdDfKtlLAaPlilDLv 262
                                    +++ s++ya+  +++g ++y+n  P      p+ ve A+++g+++ GdD  t  A+Pl +DL+
  gi|119720563|ref|YP_921058.1| 157 DLPHSQVYAFLVLRHGrSSYVNLQPAYVAcSPAFVEKARENGLLVLGDDGAT-GATPLTVDLA 218
                                    57889*****999987468*******99989*******************99.6999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 2289.53
//
Query:       gi|119720564|ref|YP_921059.1|  [L=535]
Description: hypothetical protein Tpen_1661 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-58  196.5   0.0    6.5e-58  196.0   0.0    1.2  1  DUF2192   Uncharacterized protein conserved in archaea (DUF21
  ------ inclusion threshold ------
      0.026   14.0   0.0       0.13   11.7   0.0    2.1  2  MauJ      Methylamine utilization protein MauJ


Domain annotation for each model (and alignments):
>> DUF2192  Uncharacterized protein conserved in archaea (DUF2192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  196.0   0.0   7.3e-62   6.5e-58       2     229 .]      33     252 ..      32     252 .. 0.97

  Alignments for each domain:
  == domain 1  score: 196.0 bits;  conditional E-value: 7.3e-62
                        DUF2192   2 elykkrievlvdllsklleeekltReelvellkkvYeekgiePlrGlskPediYdkElatlYvvgkyGlgleeelkelfd 81 
                                    +l+k+r++v++d+ls+ll++e++tR+e++ ll+++Y e+g+ePlrGls+P+++Y +E++ +Y vgkyGlgl+eel e ++
  gi|119720564|ref|YP_921059.1|  33 YLQKRRLQVVTDVLSRLLAGEAATRDEAIGLLRRAYLEAGLEPLRGLSTPRSFY-REMSLVYAVGKYGLGLDEEL-EGLR 110
                                    579***************************************************.*******************9.**** PP

                        DUF2192  82 kifsvEekleealeiilskkkeeavekvkevlgkidenkvarvlrlvltkvvlgfadeeelikllrkleeafpelektvk 161
                                    +if+vE+ +++al +++s+      e v +v g+++e++v  +l++vl++ +lg++  eel+k+l  l    +++ + ++
  gi|119720564|ref|YP_921059.1| 111 EIFEVEALCDAALGLVRSG--AGVEESVFRVFGRLKESDVRSFLNYVLAASLLGYVGFEELLKVLGGL----EAYGNVAR 184
                                    ******************7..555566777789*********************************99....88999*** PP

                        DUF2192 162 kyarfyiAfkiaekiaegeirnrlekealkkalalrlgiekalPsdeyiaeiakevfkvpkkvlkkvl 229
                                    +y  +++A+++a+ + ++++++r+ekea+k +la +lg ekalPsd ++++ia +v+ v++ v ++vl
  gi|119720564|ref|YP_921059.1| 185 DYRILVVAYRLADFVGSNKFSRRSEKEAAKLDLARSLGDEKALPSDGLVWRIAVNVYGVDEGVANRVL 252
                                    ******************************************************************97 PP

>> MauJ  Methylamine utilization protein MauJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   1.4e-05      0.13     156     205 ..     290     339 ..     268     414 .. 0.83
   2 ?   -1.0   0.0      0.11   9.6e+02      60      91 ..     481     512 ..     472     530 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.4e-05
                           MauJ 156 ddlkpllrLyqraRnatdpawRllaayailkaararkaPfevgadqsdfa 205
                                    + l+ +l L ++ R a  +++Rl+aa a+ +a ++++ P +++a  ++  
  gi|119720564|ref|YP_921059.1| 290 EWLQAYLYLEKKLRKAFPASSRLVAAAAVDQAKAEGASPESLTARSVNIE 339
                                    3457899999*****************************98777766654 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.11
                           MauJ  60 aleldgvplelalygneaGkLseiiyrveaas 91 
                                    +lel g+++     g + GkL+e + ++ + +
  gi|119720564|ref|YP_921059.1| 481 TLELGGRRIATLKLGSDPGKLEEKVEKILSHN 512
                                    678889999988999********999887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (535 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 3606.70
//
Query:       gi|119720565|ref|YP_921060.1|  [L=226]
Description: hypothetical protein Tpen_1662 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1706.60
//
Query:       gi|119720566|ref|YP_921061.1|  [L=220]
Description: cyclase family protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-35  121.1   0.0    4.6e-35  120.8   0.0    1.1  1  Cyclase   Putative cyclase


Domain annotation for each model (and alignments):
>> Cyclase  Putative cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.8   0.0   2.6e-39   4.6e-35       1     136 []      13     165 ..      13     165 .. 0.91

  Alignments for each domain:
  == domain 1  score: 120.8 bits;  conditional E-value: 2.6e-39
                        Cyclase   1 idLshplsedtpvwp...dp.................islsehtGTHlDapgHfae..ktidelpleelvgpavvldvsa 58 
                                    +dL+++l+ + pv+p    p                 + l ehtGTH+D+p+Hf+e   tid++ple+++g+++v+d s+
  gi|119720566|ref|YP_921061.1|  13 VDLTMELKTGAPVFPgypVPivhtwttikehgyysnlLMLVEHTGTHVDSPAHFIEgaPTIDKVPLERFMGRGIVVDASH 92 
                                    7*************6565226667899999******9999****************988********************9 PP

                        Cyclase  59 kaaaedyeiitaedleaalakqgveikpgdivlirTgwskrledkeky.rnpglseeaaewlaekgvkavGvDtlsvDa 136
                                           + it+e le+al+ +g  + +g +vlirTg++++ ++++++ ++pgl+e +a++la+ gv+avG+D++s+D+
  gi|119720566|ref|YP_921061.1|  93 LP---PKAPITREFLEKALEGKG--VGNGWVVLIRTGYDAK-AGTPDWfNHPGLDEGGARYLADLGVNAVGIDAPSIDQ 165
                                    94...44578**********999..88*************9.7787887****************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       161  (0.00897987); expected 358.6 (0.02)
Passed bias filter:                      157  (0.00875676); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1593.61
//
Query:       gi|119720567|ref|YP_921062.1|  [L=403]
Description: aminotransferase, class I and II [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-67  227.3   0.0    3.5e-67  227.1   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
      7e-09   35.5   0.0    9.6e-09   35.0   0.0    1.1  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
     0.0014   19.0   0.1       0.39   11.1   0.0    2.5  2  Radical_SAM      Radical SAM superfamily
      0.003   16.1   0.0     0.0043   15.6   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
  ------ inclusion threshold ------
      0.035   13.4   0.0      0.052   12.8   0.0    1.2  1  Beta_elim_lyase  Beta-eliminating lyase
       0.06   13.2   0.0       0.29   11.1   0.0    2.2  3  HHH              Helix-hairpin-helix motif
      0.093   13.0   0.0       0.68   10.2   0.0    2.3  2  DUF1611_N        Domain of unknown function (DUF1611_N) Rossm


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  227.1   0.0   1.4e-70   3.5e-67       2     358 ..      36     388 ..      35     393 .. 0.96

  Alignments for each domain:
  == domain 1  score: 227.1 bits;  conditional E-value: 1.4e-70
                                    EEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHH CS
                  Aminotran_1_2   2 dvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagali 81 
                                    dvi +g++++++     ++ e+++a ke  +  +++++y  + g pel+e++a+++g+++++++k++ +v v+ Ga+a++
  gi|119720567|ref|YP_921062.1|  36 DVISFGIGQPDFQ----PPREALEAIKE--ALDRGYTRYISPLGIPELREEIARYVGEKYGVDVKPS-EVAVTVGAKAAL 108
                                    79***********....**********9..99999********************************.************ PP

                                    HHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT CS
                  Aminotran_1_2  82 ealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPt 161
                                     + i ll   pgde++v dp ++ y+ ++r++gg  v ++l +e +f+l +e++e+ ++ ++    ++++i+v+sphNPt
  gi|119720567|ref|YP_921062.1| 109 FMTISLL-TRPGDEVVVQDPAFPTYECVIRYAGGRPVFVRLAEERGFRLSAEDVERTVEGLH----RVRGIVVNSPHNPT 183
                                    *******.7***************************************************98....89************ PP

                                    --B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTT...EEEEEESSSTTSSGGG-EEEEEEEHH CS
                  Aminotran_1_2 162 GtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepn...llivgslsKafGlaGeRvGyilgnaa 238
                                    G+++ ++++e+ll+la+++++++++De+Y++ v++ +      +++++ ++   ++ v+++sK ++++G+R+Gy+++ ++
  gi|119720567|ref|YP_921062.1| 184 GSALEEKDVEALLELARRKGMFVISDEIYEDYVYEGKH----ASFLQAPDWrdyVVYVSGFSKTWAMTGLRLGYVVAREE 259
                                    ***********************************774....45666655577899************************ PP

                                    HHHHHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS.TEEEECCSCSSEEEEEETHH CS
                  Aminotran_1_2 239 vvsqlrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLael.glkvlasqsgmflltdlsae 315
                                    v+++l+ ++++++s  +++lq+ +++al+       +++   +++ +rr+  ++eL ++ g++ ++s ++++l+  +++ 
  gi|119720567|ref|YP_921062.1| 260 VIRALEVFATNMYScpPAPLQYGALKALQLGTG---WFKPLLEEYRRRRDAAFEELSKIpGVSTVKSRGAFYLFPNFKEV 336
                                    ****************************99886...******************************************** PP

                                    .......CHHHHHHHHHHTCTEEEEEGGGGTS...TTEEEEECTTS-HHHHHH CS
                  Aminotran_1_2 316 .......takelskkLleevgvyvtpgtsftv...pgrlRitvAglteeelee 358
                                           + +el+k Ll e gv+++pgt f +    g  R+++  l+ e+++e
  gi|119720567|ref|YP_921062.1| 337 lratglrSVDELAKRLLFEAGVVLLPGTAFPLrggDGYMRVSY-VLPVEKIRE 388
                                    *******99*************************999*****9.888888876 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.0   3.7e-12   9.6e-09       5     144 ..      52     209 ..      48     210 .. 0.82

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 3.7e-12
                                    HHHHHHHHHHTSS..-SSSSHHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHH...TTTT....TT-EEEEESSS-TH CS
                DegT_DnrJ_EryC1   5 eeleaveevlksg..wltsgpeveeFEkafaaylgvkhaiavssGtaAlhlaLra...lgvg....pgdeVIvpsltFva 75 
                                    e+lea++e+l+ g   ++s   + e+ +++a+y+g+k+ + v     A+ ++ +a   + ++    pgdeV+v    F +
  gi|119720567|ref|YP_921062.1|  52 EALEAIKEALDRGytRYISPLGIPELREEIARYVGEKYGVDVKPSEVAVTVGAKAalfMTISlltrPGDEVVVQDPAFPT 131
                                    678888999999844455577789999*************99999999999998877755557777************** PP

                                    HHHHHHHTT-EEEEE-B-TT.TSSB-GGGCGGG--TTE..EEEEEB...-GGGB--...-HHHHHHHHHHCT-EEEEE CS
                DegT_DnrJ_EryC1  76 tanavlelgakpvfvDvdpd.tynidpaaieaaitert..kaIlpV...hlyGqva...dmdalkaiaakhglkvieD 144
                                       +++++g +pvfv   ++  + ++++++e+ ++     ++I++    +  G +    d++al ++a+++g+ vi+D
  gi|119720567|ref|YP_921062.1| 132 YECVIRYAGGRPVFVRLAEErGFRLSAEDVERTVEGLHrvRGIVVNsphNPTGSALeekDVEALLELARRKGMFVISD 209
                                    ****************97661699***********7544499996422145666655669****************99 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   0.00015      0.39      36     101 ..      25      85 ..      22      98 .. 0.75
   2 !    5.3   0.0    0.0091        23      23      90 ..     150     214 ..     137     273 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00015
                                    HHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  36 eevkelkaekgvkevilgggepllypdfvellerlaklavpgiritvetngtlpdeeklerllelg 101
                                    +++ e++ +kg++++ +g g p+++p+ + l +   +l  +   ++++++ + p+    e+++++ 
  gi|119720567|ref|YP_921062.1|  25 DLAAEAR-RKGIDVISFGIGQPDFQPPREALEAIKEAL--DRGYTRYISPLGIPE--LREEIARYV 85 
                                    5677784.899***************996666666666..799999999999975..444444444 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0091
                                    HHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHG CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  23 egrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritvetngtlpd 90 
                                    e+rg  ls e++++ v+ l ++   + v+ +  +p+  + +++++e+l +la +   ++v++ ++  d
  gi|119720567|ref|YP_921062.1| 150 EERGFRLSAEDVERTVEGL-HRV-RGIVVNSPHNPTGSALEEKDVEALLELA-RRKGMFVISDEIYED 214
                                    5677889************.687.8999999*******99999999999997.555555555444433 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.7e-06    0.0043      71     174 ..      98     210 ..      58     216 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.7e-06
                                    EEESSH.HHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEEST....TSHHHHHHHCCT..TEEEEEE CS
                Cys_Met_Meta_PP  71 lavssG.maAiaaailallkaGdeivvsddlYggtqrllkkvlkklgievkfvdt....sdleelekaike..ntklvyl 143
                                    +av+ G  aA++++i  l + Gde+vv+d ++   + ++++ +    + v+  +      ++e++e+ ++   +++ + +
  gi|119720567|ref|YP_921062.1|  98 VAVTVGaKAALFMTISLLTRPGDEVVVQDPAFPTYECVIRY-AGGRPVFVRLAEErgfrLSAEDVERTVEGlhRVRGIVV 176
                                    445555268999999999999*********99655445554.444445555555434446889999999977799***** PP

                                    ESS-TTT...T----HHHHHHHHHHTT-EEEEEG CS
                Cys_Met_Meta_PP 144 Etptnpl...lkvvDiekiaklakkagvlvvvDn 174
                                     +p np+   l+  D+e++++la+ +g+ v+ D 
  gi|119720567|ref|YP_921062.1| 177 NSPHNPTgsaLEEKDVEALLELARRKGMFVISDE 210
                                    ******85557789***************99986 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     2e-05     0.052      34     167 ..      74     209 ..      48     210 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2e-05
                                    HHHHHHHHHHHTT-SEEEE.......ES-HHHHHHHHH.HHH--TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBT CS
                Beta_elim_lyase  34 vnrLedavaelfgkeaalf.......vpqGtaAnsill.killqrgeevivtepahihfdetgaiaelagvklrdlknke 105
                                    + +L +++a+++g ++++        v+ G  A  ++  ++l+++g+ev+v++pa   f +   +  +ag +++ ++ +e
  gi|119720567|ref|YP_921062.1|  74 IPELREEIARYVGEKYGVDvkpsevaVTVGAKAALFMTiSLLTRPGDEVVVQDPA---FPTYECVIRYAGGRPVFVRLAE 150
                                    5678888888888888885566777666676666655448888***********8...5666667788888888887666 PP

                                    T..TBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEE CS
                Beta_elim_lyase 106 a..GkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlD 167
                                    +    +++e++e+ ++       +++ i++   +n   G +++ + ++++ ++a+++g+ ++ D
  gi|119720567|ref|YP_921062.1| 151 ErgFRLSAEDVERTVEG--L--HRVRGIVVNSPHNP-TGSALEEKDVEALLELARRKGMFVISD 209
                                    654689*********99..5..67***********5.9********************998877 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       4.1   1.1e+04       5      19 ..     160     174 ..     159     174 .. 0.77
   2 ?   11.1   0.0   0.00011      0.29       2      20 ..     301     319 ..     300     322 .. 0.84
   3 ?   -2.5   0.0       2.4   6.1e+03       8      15 ..     343     350 ..     343     350 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 4.1
                                    HHTSSHHHHHTSTT- CS
                            HHH   5 lipasreeLlalPGV 19 
                                    ++++++e L  + G+
  gi|119720567|ref|YP_921062.1| 160 DVERTVEGLHRVRGI 174
                                    578999999777776 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00011
                                    HHHHHTSSHHHHHTSTT-S CS
                            HHH   2 leglipasreeLlalPGVG 20 
                                    + + ++a +eeL ++PGV 
  gi|119720567|ref|YP_921062.1| 301 YRRRRDAAFEELSKIPGVS 319
                                    566789************7 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 2.4
                                    SSHHHHHT CS
                            HHH   8 asreeLla 15 
                                    +s++eL++
  gi|119720567|ref|YP_921062.1| 343 RSVDELAK 350
                                    599***87 PP

>> DUF1611_N  Domain of unknown function (DUF1611_N) Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00027      0.68      23      61 ..      27      65 ..      12      67 .. 0.87
   2 ?   -0.9   0.0      0.78     2e+03      40      65 ..     182     208 ..     175     209 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00027
                      DUF1611_N 23 leealaagaevlviGiapeggklpeswreavkeAleaGl 61
                                    +ea ++g++v+ +Gi+ ++ + p +  ea+keAl++G+
  gi|119720567|ref|YP_921062.1| 27 AAEARRKGIDVISFGIGQPDFQPPREALEAIKEALDRGY 65
                                   455589*******************************96 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.78
                      DUF1611_N  40 peggklpeswreavke.AleaGldvvs 65 
                                    p g +l+e+ +ea+ e A ++G+ v+s
  gi|119720567|ref|YP_921062.1| 182 PTGSALEEKDVEALLElARRKGMFVIS 208
                                    788999988777765548888988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 2450.96
//
Query:       gi|119720568|ref|YP_921063.1|  [L=183]
Description: hypothetical protein Tpen_1665 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-27   94.8  16.0    5.8e-27   94.6  16.0    1.0  1  DUF1097   Protein of unknown function (DUF1097)


Domain annotation for each model (and alignments):
>> DUF1097  Protein of unknown function (DUF1097)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.6  16.0   3.3e-31   5.8e-27       2     144 ..      21     174 ..      20     176 .. 0.93

  Alignments for each domain:
  == domain 1  score: 94.6 bits;  conditional E-value: 3.3e-31
                        DUF1097   2 lsvgvlaglwallaatlgelpvWagFigwasffaaGggkkgllkslltnllGvvwAllaillisllggnlgllalll... 78 
                                    l+v+ la+l+ l+++ +++lpvWa+F++wa +fa+G++kk++++++ +  lG v+++la+++++++ ++++++++++   
  gi|119720568|ref|YP_921063.1|  21 LTVAYLAALSLLVTLPPLGLPVWATFVTWAGYFALGADKKAFKEIYKATPLGGVFGWLAVVGFDYAVKAMPGVHYIIpvm 100
                                    79*************************************************************************99996 PP

                        DUF1097  79 .vvgivaflmvllakipllsfiPaiflGlastfatllktava........lsnpllavivslllGavfGylseal 144
                                     v ++ +++++++ ++++  +  a+f+++ s+f+t+++++++        ++ +l++ ++++llG +fGyls +l
  gi|119720568|ref|YP_921063.1| 101 lVEFLDVLVLMYIISVFK-FTGAAVFFAFPSYFGTYYGGFYPktgqllldATLALVWQVAANLLGPIFGYLSIRL 174
                                    666777777777777766.567899**********************************************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      206  (0.0114898); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1332.74
//
Query:       gi|119720569|ref|YP_921064.1|  [L=301]
Description: dihydrodipicolinate synthase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.4e-70  234.6   0.0    1.1e-69  234.4   0.0    1.0  1  DHDPS     Dihydrodipicolinate synthetase family


Domain annotation for each model (and alignments):
>> DHDPS  Dihydrodipicolinate synthetase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  234.4   0.0   5.9e-74   1.1e-69       2     287 ..       5     295 ..       4     297 .. 0.97

  Alignments for each domain:
  == domain 1  score: 234.4 bits;  conditional E-value: 5.9e-74
                                    -SEEEEE----B-TTSSB-HHHHHHHHHHHHHCT-SEEEESSCCCTGGGS-HHHHHHHHHHHHHHHTTSSEEEEE---SS CS
                          DHDPS   2 fsgiitalvtpfdedgkldkealrklieflinkgvdglvvaGttGEsatlsteekeqlveiaveaakgripviagvGsns 81 
                                    f g+i++ +tpf ed  ld+ea++ l++++ +kgv g++   ttGE+  ls ee +++ + + ea++g++ vi g+ +n 
  gi|119720569|ref|YP_921064.1|   5 FYGVISPFITPFREDLSLDREAVAWLARYQAEKGVHGIFPNSTTGEFVHLSREEAVEVTRLVLEAVGGKVWVIPGISANY 84 
                                    789***************************************************************************** PP

                                    HHHHHHHHHCCCCCT-SEEEEE---SS---HHHHHHHHHHHHHCHSS-EEEEE-HHHHSHHHHHHHHHHHHT.STTEEEE CS
                          DHDPS  82 tseaiklakkaeeaGadgvlavtPYYnkpsqeglyqhfkaiieatdlpvilYnvpsrtgadlspetvkrLae.lenivgv 160
                                    t++++ l++ +++ G+dg+++ +PY+ k+s+e l+ hf +i+e+ dlp+i+Yn+p+ tg ++ +    +La+  +n++g 
  gi|119720569|ref|YP_921064.1|  85 TEDSVALGRTFKDLGVDGAVVTPPYFFKVSPERLKVHFSTILEKVDLPIIVYNIPATTGINIPVGLYLELAKeHSNLAGA 164
                                    ***********************************************************************99******* PP

                                    EE-SS-C...THHHHHHCCCSTTSEEEES-GGGHHHHHHTT-SEEEESCHHCHHHHHHHHHHHHHTT-HHHHHHHHHHHH CS
                          DHDPS 161 Keavgdl...eevikikkevgkdlviysGddelllsalslGadGvisvtsniagermrqlikalkeGdlaeaaelnekll 237
                                    K++v+++   +++++++k  +kd++++ G d+lll++l +G+dG i + +n a+++ r++++a++ Gdl+ a e  +kll
  gi|119720569|ref|YP_921064.1| 165 KATVESFtyfRQLVQVVKAERKDFAVLTGLDDLLLPVLMMGGDGGIMALANAAPQIHREVYDAYRSGDLKRALEAWHKLL 244
                                    ******966678888889999*********************************************************** PP

                                    HHHHHCCCC.SCCHHHHHHHHCTTSSSBB.--TTS--S-HHHHHHHHHHHH CS
                          DHDPS 238 plikilfae.pnvilvktalellGlvveatlrkPltpleeeekeeleallk 287
                                    +l+  +  + +++  vkt l+++G +v++++r Pltp + e +e+++++++
  gi|119720569|ref|YP_921064.1| 245 RLVRVYDYAtSFPTSVKTLLKVMGAPVKPYARTPLTPETREVEEKIAQIAR 295
                                    ****9976659********************************99998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2173.50
//
Query:       gi|119720570|ref|YP_921065.1|  [L=335]
Description: AIR synthase-like protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-29  101.8   2.4    9.1e-29  100.6   2.4    1.6  1  AIRS_C    AIR synthase related protein, C-terminal domain
    9.4e-14   51.8   0.6    2.2e-13   50.7   0.6    1.6  1  AIRS      AIR synthase related protein, N-terminal domain


Domain annotation for each model (and alignments):
>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.6   2.4     1e-32   9.1e-29       1     150 [.     153     307 ..     153     312 .. 0.86

  Alignments for each domain:
  == domain 1  score: 100.6 bits;  conditional E-value: 1e-32
                                    STTEEEEEEETSSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHH.....HTTECEEEE--TTHHHHH CS
                         AIRS_C   1 kpGdvliltgslGlggagtslkrkileeeglddsavqlgdvlleptliyvkralaal.....kglvkaahDvTgGGLlga 75 
                                    +pGd+lilt++ G+ g ++++ +  +e +     +v +  +++ +  iy++     +      g+v+a+hD T+GG+lg 
  gi|119720570|ref|YP_921065.1| 153 RPGDALILTKGAGIEGTAILATELYDELSR----KVDREVLERAKSFIYEVSVVKDAltavrAGGVHAMHDPTEGGVLGG 228
                                    79****************777663333333....35566666666777766655555555577***************** PP

                                    HHHHHHTTTEEEEEECGTHHHHHHHH.....HHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEEESSS CS
                         AIRS_C  76 laemapasgvgaeidldkvpifdele.....splemllsensGrllvavppeeadavlaileeeglpeaavIGevtakee 150
                                    l+ema a++ g++++++k+p+++e++     ++ ++l+  +sG ll+av+  +a  v+++l++eg+p aavIG++t++ e
  gi|119720570|ref|YP_921065.1| 229 LQEMAIAANAGLVVEEEKIPVREETKavcraLGVDPLRLISSGSLLIAVEGSRARDVVDALSREGIP-AAVIGRLTEGSE 307
                                    ******************************************************************7.*********975 PP

>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.7   0.6   2.4e-17   2.2e-13       2      93 ..      37     140 ..      25     141 .. 0.85

  Alignments for each domain:
  == domain 1  score: 50.7 bits;  conditional E-value: 2.4e-17
                                    SSEEEEEEEEEE.EECCTCCCC....HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC......HHHHHHHHHHHHHHHTT- CS
                           AIRS   2 Daavvvttdshnrpvlvepvhf....iGakavavnlsDlaamGArPlalllslalp......wleevvrglaeaaeelgv 71 
                                    Daa ++   +    v  +p+++    iG+++v+v ++D+a+ G +P++l+ ++ lp       l +++ +l++aa+e+g+
  gi|119720570|ref|YP_921065.1|  37 DAA-LIDLGDKVLVVHADPITGavsnIGWLSVHVSANDVATRGVQPRWLVTVVLLPegagqdVLWDIAGQLRKAADEIGA 115
                                    666.22222222223336777788889*********************99999999******9***************** PP

                                    EEEEEEEEEESS...EEEEEEEEEE CS
                           AIRS  72 plvgGdtsfsne...ptisvtavGl 93 
                                     +vgG+t+f+++   p++++ta+G+
  gi|119720570|ref|YP_921065.1| 116 TIVGGHTEFTPGldrPILVTTAMGV 140
                                    **********999999999999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 2265.43
//
Query:       gi|119720571|ref|YP_921066.1|  [L=168]
Description: hypothetical protein Tpen_1668 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-43  148.7  12.4    1.8e-43  148.5  12.4    1.0  1  ECF-ribofla_trS  ECF-type riboflavin transporter, S component
    2.9e-08   34.0  13.3    4.9e-08   33.3  13.3    1.3  1  ECF_trnsprt      ECF transporter, substrate-specific componen
     0.0022   17.5  11.7     0.0033   17.0  11.6    1.4  1  5TM-5TMR_LYT     5TMR of 5TMR-LYT
  ------ inclusion threshold ------
        2.5    8.1  10.7          3    7.8   3.1    2.3  2  Thia_YuaJ        Thiamine transporter protein (Thia_YuaJ)
        3.7    7.7   7.2       0.37   11.0   2.2    1.8  2  YbjM             Putative inner membrane protein of Enterobac
          5    7.5   9.6       0.21   11.9   1.8    2.5  2  DUF4730          Domain of unknown function (DUF4730)


Domain annotation for each model (and alignments):
>> ECF-ribofla_trS  ECF-type riboflavin transporter, S component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.5  12.4   6.1e-47   1.8e-43       4     171 ..       7     158 ..       4     159 .. 0.95

  Alignments for each domain:
  == domain 1  score: 148.5 bits;  conditional E-value: 6.1e-47
                                    TTHHHHHHHHHHHHHHHHHH---B-S.SS-B--TTHHHHHHHHHHSS--STHHHHHHHHHHHHHHHSS-GGGHHHHHHHH CS
                ECF-ribofla_trS   4 tkkvvatailaAlvvvltlfisIplpantegsinlgdavlalaallfGpvvGflvGaiGsalaDllsgYgiwapftliik 83 
                                     k v++++++aAl++v+t++++Ip+p +t+g+inlgdav++l+++++Gp +G+l+G+iGsalaD+lsgY++wapftl+ik
  gi|119720571|ref|YP_921066.1|   7 SKLVATVGVFAALTTVATVIVQIPVP-ETKGYINLGDAVVLLSGIVLGPAAGALAGGIGSALADVLSGYAHWAPFTLVIK 85 
                                    578999*******************9.***************************************************** PP

                                    HHHHHHHHHH--S-S-SSH...HHHHHHHHHHHHHHHHHHHHHHHH..........S-HHHHHHHHHHHHHHHHHHHHHH CS
                ECF-ribofla_trS  84 gliGlivGliakklkknkengvfkilalvlfaivmvigyviaegllpildiiiysepaekvalqsipaniiqavvgaiia 163
                                    g++G+++Gl++++ k+ ++     +l+++l+a+ m++gy+++e+ll          +++ +al+++p+n++qav+ga++a
  gi|119720571|ref|YP_921066.1|  86 GVEGFLAGLLSRTGKTALR-----TLGVLLAAFEMILGYFLVETLL----------YGVGAALAELPGNVFQAVFGALVA 150
                                    **************66665.....99********************..........************************ PP

                                    HHHHHHHH CS
                ECF-ribofla_trS 164 lpLlkala 171
                                    l+   +l+
  gi|119720571|ref|YP_921066.1| 151 LLAGEQLR 158
                                    99887776 PP

>> ECF_trnsprt  ECF transporter, substrate-specific component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3  13.3   1.6e-11   4.9e-08       2     141 ..       9     145 ..       8     157 .. 0.84

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 1.6e-11
                                    HHHHHHHHHHHHHHHHHH.HEEE.STSE..EESHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHCHT-SSTTHHHHHHHHH CS
                    ECF_trnsprt   2 klvitglliAisivlsll.gyiplpnik..itiihipvllggllfGpikGailgiitsvlkailtggtgalssfvpiafl 78 
                                     ++++g+++A+  v       ip+p  k  i + +  vll+g+++Gp +Ga++g+i+s l+ +l  g + ++   p+  +
  gi|119720571|ref|YP_921066.1|   9 LVATVGVFAALTTVAT-ViVQIPVPETKgyINLGDAVVLLSGIVLGPAAGALAGGIGSALADVL-SGYAHWA---PFTLV 83 
                                    5899************.4477777777445**********************************.6776665...***** PP

                                    HHHCHHHHHHHHHHCCCHTTHHHHHHHHHHHHCCCCCHHHHHHHCCCHHHHS........... CS
                    ECF_trnsprt  79 sriligliagllykkgkkknlkeivvsfilagvlgtivatllvlliilplylklktakaiaia 141
                                    + ++ g++agll + gk  ++   v+  ++ ++lg+++   l++++   l   l++  ++a+ 
  gi|119720571|ref|YP_921066.1|  84 IKGVEGFLAGLLSRTGKTALRTLGVLLAAFEMILGYFLVETLLYGVGAALA-ELPGNVFQAVF 145
                                    *********************999999999999999988888888887666.45555555544 PP

>> 5TM-5TMR_LYT  5TMR of 5TMR-LYT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0  11.6   1.1e-06    0.0033      18     120 ..       6     116 ..       2     153 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.1e-06
                   5TM-5TMR_LYT  18 klllglifglfsilgtytgieie......gaiantRaigvvvaGllgGplvGliagliaglhRyllgGftala..cgist 89 
                                    k  l++ +g+f+ l t   + ++      + ++n+   +v+++G++ Gp  G++ag i+ ++  +l G + +a   +++ 
  gi|119720571|ref|YP_921066.1|   6 KSKLVATVGVFAALTTVATVIVQipvpetKGYINLGDAVVLLSGIVLGPAAGALAGGIGSALADVLSGYAHWApfTLVIK 85 
                                    5667788899999999999988888888779***************************9999999999554441145555 PP

                   5TM-5TMR_LYT  90 ilagllaGlihrklkrrrkkltvlvalligl 120
                                     ++g+laGl++r  k   ++l vl a++  +
  gi|119720571|ref|YP_921066.1|  86 GVEGFLAGLLSRTGKTALRTLGVLLAAFEMI 116
                                    689*******999887554444444433322 PP

>> Thia_YuaJ  Thiamine transporter protein (Thia_YuaJ)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   3.1     0.001         3       2      63 ..      11      73 ..      10     104 .. 0.84
   2 ?    5.0   0.9    0.0076        23       6      51 ..     109     154 ..     103     156 .. 0.94

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.001
                      Thia_YuaJ  2 veiallaalalvLsli.kliklpqggsislsmiPilllalrrGlkagllaGllwGllqlilgk 63
                                   ++++++aal++v ++i ++ +  + g i+l+   +ll  +  G++ag+laG +   l+ +l  
  gi|119720571|ref|YP_921066.1| 11 ATVGVFAALTTVATVIvQIPVPETKGYINLGDAVVLLSGIVLGPAAGALAGGIGSALADVLSG 73
                                   5789************6666666789****888899***************998877666555 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0076
                      Thia_YuaJ   6 llaalalvLslikliklpqggsislsmiPilllalrrGlkagllaG 51 
                                    llaa+ ++L ++ + +l  g+  +l+ +P  ++   +G  ++llaG
  gi|119720571|ref|YP_921066.1| 109 LLAAFEMILGYFLVETLLYGVGAALAELPGNVFQAVFGALVALLAG 154
                                    789**********99999*************************998 PP

>> YbjM  Putative inner membrane protein of Enterobacteriaceae
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.2      0.56   1.7e+03      62      79 ..      10      27 ..       2      68 .. 0.60
   2 ?   11.0   2.2   0.00012      0.37      46     112 ..      87     153 ..      70     158 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.56
                           YbjM 62 vpllGallaapvcllvlk 79
                                   v+ +G+++a++++  v+ 
  gi|119720571|ref|YP_921066.1| 10 VATVGVFAALTTVATVIV 27
                                   455666666555443332 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00012
                           YbjM  46 lPGivaallskekrllvpllGallaapvcllvlklvlaseeslwqelayllSavFWcalGallvlll 112
                                    + G++a lls+  +     lG+llaa  ++l + lv +  + +   la l   vF +++Gal+ ll+
  gi|119720571|ref|YP_921066.1|  87 VEGFLAGLLSRTGKTALRTLGVLLAAFEMILGYFLVETLLYGVGAALAELPGNVFQAVFGALVALLA 153
                                    569***********************999999999889999999999999************99987 PP

>> DUF4730  Domain of unknown function (DUF4730)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   1.8   7.1e-05      0.21      13      41 ..      23      53 ..      10      60 .. 0.85
   2 ?   -0.6   1.2      0.56   1.7e+03       9      39 ..     109     140 ..     100     154 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.1e-05
                        DUF4730 13 lslllvipgvEAk..ldaGDaiALlLGivlt 41
                                     ++  ip+ E k  ++ GDa+ Ll Givl+
  gi|119720571|ref|YP_921066.1| 23 ATVIVQIPVPETKgyINLGDAVVLLSGIVLG 53
                                   4568899*****999**************97 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.56
                        DUF4730   9 livllslllvipgvEAk.ldaGDaiALlLGiv 39 
                                    l++ + ++l+   vE      G a+A l G v
  gi|119720571|ref|YP_921066.1| 109 LLAAFEMILGYFLVETLlYGVGAALAELPGNV 140
                                    45566677777777776445677777666644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1153.58
//
Query:       gi|119720572|ref|YP_921067.1|  [L=169]
Description: magnesium-dependent phosphatase-1 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.1e-13   49.5   0.0    5.3e-13   49.2   0.0    1.2  1  Acid_PPase   Acid Phosphatase
    2.8e-11   44.1   0.0    7.4e-08   32.9   0.0    2.1  2  Hydrolase    haloacid dehalogenase-like hydrolase
    1.2e-08   35.3   0.0    1.1e-07   32.1   0.0    2.0  2  HAD_2        Haloacid dehalogenase-like hydrolase
    0.00012   21.8   0.0    0.00015   21.6   0.0    1.2  1  NIF          NLI interacting factor-like phosphatase
      0.009   16.1   0.0      0.018   15.1   0.0    1.8  1  Hydrolase_6  Haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.022   14.3   0.0      0.048   13.1   0.0    1.5  2  DUF2608      Protein of unknown function (DUF2608)
        0.1   13.0   1.0        1.7    9.0   0.0    2.3  2  HAD          haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> Acid_PPase  Acid Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.2   0.0   2.1e-16   5.3e-13       4     138 ..       4     127 ..       2     155 .. 0.89

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 2.1e-16
                                    SEEEE-STTTSSSS-TTTSS-S-EEE-TTS.-EEETT--EE---TTHHHHHHHHHHTT--EEEEE--S-HHHHHHHHHHT CS
                     Acid_PPase   4 klivFDLDyTLWpfevdtlvsaplkkeskksevvDrrgeelklypdveeileelkskevklavaSrtdepdlarelLkll 83 
                                    k++v DLD TLW+      + +p+++ s++  vvD++g+e++l p vee+l++ ++++ +lavaS  + p+ a e+Lk+l
  gi|119720572|ref|YP_921067.1|   4 KALVVDLDGTLWSHRDISRTRPPFRRVSDG-VVVDSTGQEVRLNPCVEEALRAAREAGLRLAVASW-NDPEPAVEALKAL 81 
                                    67899*******988888899*********.**********************************7.67*********** PP

                                    T-G..........GGESEEEESSS.-HHHHHHHHHHHH---GGGEEEEES-HHHHH CS
                     Acid_PPase  84 eindakekekklldvfddveiykg.sktkhfeklkkktgieyedmlfFDdesrnie 138
                                     +            +fd + i ++  k + +ek+ ++  ++  +++f Dd +  +e
  gi|119720572|ref|YP_921067.1|  82 GVY----------GYFDLLVIEPHpGKDRMLEKILRELRLSPGEVVFVDDTEYMVE 127
                                    *99..........8999999999767999999999999999999999999876555 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0    0.0004         1       1      16 [.       3      18 ..       3      34 .. 0.84
   2 !   32.9   0.0   2.9e-11   7.4e-08     116     200 ..      42     123 ..      24     133 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0004
                                   SSEEEEESBTTTBCHH CS
                                   xxxxxxxxxxxxxxxx RF
                      Hydrolase  1 iktvvfDkdGTLttge 16
                                   ik++v D+dGTL+  +
  gi|119720572|ref|YP_921067.1|  3 IKALVVDLDGTLWSHR 18
                                   89***********654 PP

  == domain 2  score: 32.9 bits;  conditional E-value: 2.9e-11
                                    THHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT.GGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Hydrolase 116 plkvkpeaaeavasLkaagievvlltgdnpetaeraanqlG.ddyfdaviasdietvakpspegkvaaireLqgkpeeva 194
                                    + ++ p ++ea+++ ++ag+++++++ ++pe+a +a++ lG   yfd  +     +    + +++++++reL+ +p ev+
  gi|119720572|ref|YP_921067.1|  42 EVRLNPCVEEALRAAREAGLRLAVASWNDPEPAVEALKALGvYGYFDLLVIEPHPG----KDRMLEKILRELRLSPGEVV 117
                                    55688999*********************************555554444333333....779***************** PP

                                    EEESSH CS
                                    xxxxxx RF
                      Hydrolase 195 mVGDgv 200
                                    +V+D+ 
  gi|119720572|ref|YP_921067.1| 118 FVDDTE 123
                                    ****85 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.14   3.6e+02       3      15 ..       8      20 ..       6      23 .. 0.82
   2 !   32.1   0.0   4.4e-11   1.1e-07      76     162 ..      41     123 ..      28     133 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.14
                          HAD_2  3 FDlDgTlldteel 15
                                    DlDgTl   +++
  gi|119720572|ref|YP_921067.1|  8 VDLDGTLWSHRDI 20
                                   6******998876 PP

  == domain 2  score: 32.1 bits;  conditional E-value: 4.4e-11
                          HAD_2  76 kevkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekkKPdpeviekaleklklkkeev 155
                                    +ev++ + v+e+L   +eag++l++++ ++ e + e l++lg+  yFd  v++ + +k     +++ek+l++l l++ ev
  gi|119720572|ref|YP_921067.1|  41 QEVRLNPCVEEALRAAREAGLRLAVASWNDPEPAVEALKALGVYGYFDLLVIEPHPGKD----RMLEKILRELRLSPGEV 116
                                    478888999******************************************99987777....9**************** PP

                          HAD_2 156 iyvGDsp 162
                                    ++v D+ 
  gi|119720572|ref|YP_921067.1| 117 VFVDDTE 123
                                    *****97 PP

>> NIF  NLI interacting factor-like phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   5.8e-08   0.00015       1     119 [.       4     128 ..       4     156 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 5.8e-08
                            NIF   1 ktLVLDLDetLv.hskleksk....klkve....gekvevsvlkRpgldefLkelskl.yevvifTasseeyaeavidil 70 
                                    k LV+DLD+tL+ h+  ++++    +  v+      +++  v + p ++e L+ + +    + + + + +e a + +++l
  gi|119720572|ref|YP_921067.1|   4 KALVVDLDGTLWsHRDISRTRppfrR--VSdgvvVDSTGQEVRLNPCVEEALRAAREAgLRLAVASWNDPEPAVEALKAL 81 
                                    679*********76665333245442..22335544568999999*********99988********************* PP

                            NIF  71 dpekkllshrlyrescvkkkgeyvKdLsllgrdlsrvvivDdspdsfel 119
                                      ++ +++  + + +   k+++  K L+ l  +  +vv+vDd+++ +el
  gi|119720572|ref|YP_921067.1|  82 GVYG-YFDLLVIEPHP-GKDRMLEKILRELRLSPGEVVFVDDTEYMVEL 128
                                    ***9.79999999999.7899*********99***********998776 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   7.1e-06     0.018       2      55 ..       7      82 ..       6     157 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 7.1e-06
                                   EEESTTTSE.........................ETTEE-TTHHHHHHHHHHTT-EEEEEE---SS-HHHHHHHHHHTT CS
                    Hydrolase_6  2 lfDidGvLw.........................rgdkaipgaaealnalraagkpvvllTNnsskseeeyakkleklg 55
                                   ++D+dG+Lw                         ++ ++ p ++eal+a r+ag ++++ + n  ++    ++ l++lg
  gi|119720572|ref|YP_921067.1|  7 VVDLDGTLWshrdisrtrppfrrvsdgvvvdstgQEVRLNPCVEEALRAAREAGLRLAVASWNDPEP---AVEALKALG 82
                                   89******************************999999*******************9998776555...455555555 PP

>> DUF2608  Protein of unknown function (DUF2608)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       1.4   3.5e+03      21      31 ..       6      16 ..       5      20 .. 0.81
   2 ?   13.1   0.0   1.9e-05     0.048     165     199 ..      98     132 ..      92     135 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.4
                        DUF2608 21 vvfDiDdtLlt 31
                                   +v+D+D tL +
  gi|119720572|ref|YP_921067.1|  6 LVVDLDGTLWS 16
                                   799*****976 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 1.9e-05
                        DUF2608 165 KGeaLlklLdkigrepksviFiDDkkknlasveea 199
                                    K  +L k+L  +  +p +v+F+DD+++ ++ v+ea
  gi|119720572|ref|YP_921067.1|  98 KDRMLEKILRELRLSPGEVVFVDDTEYMVELVREA 132
                                    5679***********************99999876 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.3     0.059   1.5e+02       2      11 ..       7      16 ..       6      21 .. 0.85
   2 ?    9.0   0.0   0.00066       1.7      71     128 ..      37      83 ..      17     124 .. 0.71

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.059
                            HAD  2 lfDfDgTLld 11
                                   + D+DgTL+ 
  gi|119720572|ref|YP_921067.1|  7 VVDLDGTLWS 16
                                   78******96 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00066
                            HAD  71 aelerfvaevirpklldpgalellaahraaGdrvvvvSgg.lrplvepllaelgadevl 128
                                    +  ++ v      + l p + e+l+a+r+aG r++v S + ++p ve+l  +lg    +
  gi|119720572|ref|YP_921067.1|  37 DSTGQEV------R-LNPCVEEALRAAREAGLRLAVASWNdPEPAVEALK-ALG----V 83 
                                    4444555......3.569999*****************996777777777.777....3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1224.83
//
Query:       gi|119720573|ref|YP_921068.1|  [L=322]
Description: aldo/keto reductase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-62  211.7   0.0    1.5e-62  211.5   0.0    1.0  1  Aldo_ket_red    Aldo/keto reductase family
  ------ inclusion threshold ------
      0.017   15.0   0.0      0.047   13.6   0.0    1.7  1  RNA_pol_Rpb6    RNA polymerase Rpb6
      0.021   14.2   0.0      0.035   13.5   0.0    1.2  1  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family


Domain annotation for each model (and alignments):
>> Aldo_ket_red  Aldo/keto reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  211.5   0.0   2.5e-66   1.5e-62       1     292 [.      15     305 ..      15     307 .. 0.96

  Alignments for each domain:
  == domain 1  score: 211.5 bits;  conditional E-value: 2.5e-66
                                    .EEEE-SSS-ST..TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH-TTTGGG-EEEEEE--SSSTTSS CS
                   Aldo_ket_red   1 elglGtwqlgsk.eeiskeealellrraleaGinffDtAevYgkgqseellGealkksrkkreeviiatKvdlrdaeiks 79 
                                    ++glG+w ++   + ++ e+a  +++rale GinffDtA vYg+g se+ lG al + ++kr+e+i++tK+      + +
  gi|119720573|ref|YP_921068.1|  15 RIGLGAWEFSEAwGLTDYEKAKSVVKRALELGINFFDTAMVYGNGFSEKTLGSALRELGAKRDEIIVSTKI------PGE 88 
                                    59********99999********************************************************......99* PP

                                    SS-HHHHHHHHHHHHHHHT-S-EEEEEE-S--TTS-.HHHHH.HHHHHHHHTTSEEEEEEES--HHHHHHH.HHTTT--E CS
                   Aldo_ket_red  80 glskeniresleeslkrLgtdyvDllllHrpdpslpsieevl.daleelvkeGkiraiGvSnfsveqleka.kkkkkvki 157
                                     l++ +i +++e s+k Lg+ yvD+ll H+p +++ + ++v+ +a+e+lv  G++r++G+Snf+ve +e+  ++ +  ++
  gi|119720573|ref|YP_921068.1|  89 FLNPLDIPRAVEHSVKLLGLGYVDVLLAHWPPCWHNYPTKVYaRAMEQLVNVGLVRYLGLSNFPVELVESFrSSLARADV 168
                                    ************************************99999879***************************99999**** PP

                                    EEEE-B-BTT-HHHHTTHHHHHHHTT-EEEEBSTTGGGTTGTTTSS---SSSCCC-------..TS-HHHHHHHHHHHHH CS
                   Aldo_ket_red 158 vavqveynllreleeegllelckkkgvpliaysplggGlltgkyqseedkedkeprkdlkrd..ertsknldaaeelsel 235
                                     + q +ynl+++ +e++++++++k+ + + a+sp+++G+ltgky++++ ++  + r +   +  e+++k    ++ l++ 
  gi|119720573|ref|YP_921068.1| 169 EVFQHRYNLVERWAEAEVIPYAEKHRITVQAWSPIAKGALTGKYTPDNLPQFADVRAREPVFhpENFEKVWRVVQLLKST 248
                                    *********************************************9999986665555444499**************** PP

                                    HHHTT--HHHHHHHHHTTSTT-SEEEE--SSHHHHHHHHGGGG----HHHHHHHHHH CS
                   Aldo_ket_red 236 akehgvslaqlalryalsqpavgivipgasnieqlednldalelklseeevaeldel 292
                                    ++++g+++ q+al++++ +++ +++ipga++++q+e+ ++a  ++l++e++a+l+e+
  gi|119720573|ref|YP_921068.1| 249 GEKYGKTPVQVALNWLITSSPAVVPIPGAKSPAQVEELAGAAGWRLKPEDWAALEEA 305
                                    ******************************************************997 PP

>> RNA_pol_Rpb6  RNA polymerase Rpb6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   7.8e-06     0.047       7      45 ..      29      75 ..      28      78 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.8e-06
                                   --HHHHHHHHHHHHHHH.........HT....S.S-SSSSTTCHHHHTT CS
                   RNA_pol_Rpb6  7 ltrYelvriaakRArQieeg.e....sl....e.tqkpvviAlrEiaeg 45
                                   lt Ye++  + kRA+++  g +     +      ++k ++ AlrE+ ++
  gi|119720573|ref|YP_921068.1| 29 LTDYEKAKSVVKRALEL--GiNffdtAMvygnGfSEKTLGSALRELGAK 75
                                   577**************..44444364477774447*********9776 PP

>> Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   5.9e-06     0.035      73     109 ..     217     253 ..     212     265 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.9e-06
                                    HHHHHHCT-SEEEEE-ST-TTHHHHHHHHHHTTSEEE CS
                 Ribul_P_3_epim  73 vpefaeagasiisvHaEalehlkrtiqeikeaGakag 109
                                    +p+fa+++a+  ++H+E+ e++ r++q +k++G k g
  gi|119720573|ref|YP_921068.1| 217 LPQFADVRAREPVFHPENFEKVWRVVQLLKSTGEKYG 253
                                    79*******************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 2087.50
//
Query:       gi|119720574|ref|YP_921069.1|  [L=372]
Description: hypothetical protein Tpen_1671 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2629.75
//
Query:       gi|119720575|ref|YP_921070.1|  [L=640]
Description: glycoside hydrolase family 42 protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.7e-07   28.8   0.0    1.3e-06   28.1   0.0    1.3  1  Cellulase        Cellulase (glycosyl hydrolase family 5)
    2.5e-06   27.1   0.1      0.042   13.2   0.1    2.3  2  Glyco_hydro_42   Beta-galactosidase
    0.00016   21.7   0.0    0.00038   20.5   0.0    1.6  1  DUF4434          Domain of unknown function (DUF4434)
    0.00066   19.3   0.2     0.0022   17.7   0.0    1.9  2  Glyco_hydro_42C  Beta-galactosidase C-terminal domain
     0.0014   18.5   0.1     0.0027   17.6   0.1    1.4  1  LBP_C            Lacto-N-biose phosphorylase C-terminal domai
  ------ inclusion threshold ------
       0.15   11.3   0.0        3.7    6.7   0.0    2.1  2  Glyco_hydro_72   Glucanosyltransferase


Domain annotation for each model (and alignments):
>> Cellulase  Cellulase (glycosyl hydrolase family 5)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   4.2e-10   1.3e-06      11     278 ..      18     273 ..       8     276 .. 0.75

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 4.2e-10
                                    EEECET..TSCGGSHHHHHHHHHHHT-SEEEEEEECTGGTTSSTTTGCTHHHHHHHHHHHHHHHHTT-EEEEEEESS... CS
                      Cellulase  11 kglsts..wgnpyttkalidevkdagfntvRlpvswgelvenapdykvdenslerveevvkyakenglyvildiHse... 85 
                                    ++++++  w  + + k+ i+++k+ g+ +vR+ +  +  ++++ ++   e+sl++++ ++++  e++l++++ +      
  gi|119720575|ref|YP_921070.1|  18 YNVKMWkeWDEE-SLKKDIEKMKELGVRVVRIFLR-DIDFADERGI-PIEESLQKLQRFLDLLHEKNLQAFVTLLVGhms 94 
                                    556666666654.89999****************9.6666444444.7799******************99887554334 PP

                                    .....TTTCSSSSTTTTHHHHHHHHHHHHHHHHHHHTTTTTTEEEESSSS--STTCTCCTCHHHTTHHHHHHHHHHHHHH CS
                      Cellulase  86 .....egwltkadgnssedtaeeffkklwtqiAerykkndevvifelmNEPhgnntgaewtseeadevkayaeeaikaIR 160
                                           w      + ++ ++ e+ +++ ++iAer+++ +   ++ l NE   +++  +     +++  ++ e+++k+ +
  gi|119720575|ref|YP_921070.1|  95 gknfpIPW--TSFDSLYTPSSVEKTATFARKIAERLASHPALAGWILSNELSLVKRA-TT----REDALRLLEAFTKTMK 167
                                    76666555..22234455556777788889******99999************8774.33....67777788******** PP

                                    HHTTSSEEEEECHHHHTBHHHHHCTSGSSSSTTEEEEEEEETTTHHHTGCGSHSCTHHHHHHHHHHHHHHHHHHTTS.EE CS
                      Cellulase 161 avgpnrliivegnswsgnldgavlndPndsqdnliysvHfYgpsdfaqtefgkdltdktnlaqrledaakylvekgi.pv 239
                                    +v+pn+++  +       +d+ ++++Pn       + +H Y  +d          td   l   + ++ + + + g  pv
  gi|119720575|ref|YP_921070.1| 168 SVDPNHIVSSGD-----IPDSFMQETPNVRHLVDYVGPHLYL-YD----------TDLVRLGYFYGAMLELFSNAGDlPV 231
                                    ****88777666.....78887888**9977778899*****.44..........34566788888899988777655** PP

                                    EEEEEESSTTSSHHHHHHHHHH.....HHHHHHTTTEEEEEEES CS
                      Cellulase 240 iigEfGgsnadgdlakeeaekw.....ldylkekgiswiyWsln 278
                                    i++EfG s+ +    +e+ ++      ++ l+ +  + ++W+++
  gi|119720575|ref|YP_921070.1| 232 ILEEFGFSTLQF--SEESHARFveeilYTSLAHEASGAFIWCFS 273
                                    ******985554..333333332333477778888888888876 PP

>> Glyco_hydro_42  Beta-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.1   1.4e-05     0.042       5      63 ..      24      84 ..      18      88 .. 0.79
   2 !   11.6   0.0   4.4e-05      0.13     110     140 ..     115     145 ..     107     168 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.4e-05
                                   GGS-CCHHHHHHHHHHHHT--EEEE-T....T-HHHH-SBTTB---HHHHHHHHHHHCTT-EE CS
                 Glyco_hydro_42  5 eqwpeeaweedirlmkeagvnvvrlge....faWaklePeegkydFewLdevldllekagikv 63
                                   ++w+ee++++di++mke+gv+vvr+      fa ++  P e++   + L+++ldll+++++++
  gi|119720575|ref|YP_921070.1| 24 KEWDEESLKKDIEKMKELGVRVVRIFLrdidFADERGIPIEESL--QKLQRFLDLLHEKNLQA 84
                                   57999*******************95333338888888888874..67888888888888765 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 4.4e-05
                                    HHHHHHHHHHHHHHTT-TTEEEEE-SSSTTT CS
                 Glyco_hydro_42 110 ekvakivealaerYkdhpavilwhidnEygc 140
                                    ek+a  ++++aer ++hpa+++w ++nE++ 
  gi|119720575|ref|YP_921070.1| 115 EKTATFARKIAERLASHPALAGWILSNELSL 145
                                    6788999*********************876 PP

>> DUF4434  Domain of unknown function (DUF4434)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   1.3e-07   0.00038      11     154 ..      20     168 ..       7     177 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.3e-07
                                    SSS-----HHHHHHHHHHHHHTT--EE..EES-SEETTEESS--HHHHTT----SB-HHHHHHHHHHHTT-EEEEE--B- CS
                        DUF4434  11 sdleqnltdkqWkeklrelkelgmntl..ilqrvsykgkafypskllkekfekkakdlveaiLdaAdklgmkvflglnyd 88 
                                      + ++++++  k++++++kelg++ +  +l +  + ++   p + + +k++   + l e+ L+a   l +  + g n+ 
  gi|119720575|ref|YP_921070.1|  20 VKMWKEWDEESLKKDIEKMKELGVRVVriFLRDIDFADERGIPIEESLQKLQRFLDLLHEKNLQAFVTLLVGHMSGKNFP 99 
                                    444589******************98732466788888888887664445555555555556666555666656666777 PP

                                    SHHHH.HS-GGG.GHHHHHHHHHHHHHHTTT-TTEEEEEE----SS--TTH..HHHHHHHHHHHHHHTT CS
                        DUF4434  89 eewwdveedlsw.eielakrvaeelakkYghhkafyGWYiseEidnankea..vealkelkkhlkelse 154
                                      w +++  ++   +e+   +a  +a++  +h+a++GW +s+E++  ++++   +al+ l++  k+++ 
  gi|119720575|ref|YP_921070.1| 100 IPWTSFDSLYTPsSVEKTATFARKIAERLASHPALAGWILSNELSLVKRATtrEDALRLLEAFTKTMKS 168
                                    77777665555578899999*************************998654445555555555555444 PP

>> Glyco_hydro_42C  Beta-galactosidase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.7     5e+03      45      57 ..      34      47 ..      28      47 .. 0.76
   2 !   17.7   0.0   7.3e-07    0.0022       2      44 ..     570     611 ..     569     617 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.7
                                   ..SEE-TTEEEEEE CS
                Glyco_hydro_42C 45 g.vtlePygvaVlr 57
                                   +  +++  gv+V+r
  gi|119720575|ref|YP_921070.1| 34 DiEKMKELGVRVVR 47
                                   556789999*9997 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 7.3e-07
                                    EEEEE....ETTEEEEEE-SSS-EE----TT-EEEES-..... CS
                Glyco_hydro_42C   2 vevqrRengegrylFvlNfsneevtvtlpasagdlltgelaeg 44 
                                    ve+q  ++++ ++l+v+N+sne v+  + +sa++++ ++   g
  gi|119720575|ref|YP_921070.1| 570 VELQVYTGEKDDLLIVINHSNENVETSI-TSATRIVEAQVIGG 611
                                    7788889******************999.99999998876655 PP

>> LBP_C  Lacto-N-biose phosphorylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   8.9e-07    0.0027       1      35 [.     563     599 ..     563     605 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 8.9e-07
                          LBP_C   1 wysdNvnvEvayY..pesgklvViNNsdeeqtTtvyt 35 
                                    + s++++vE  +Y  ++++ l+ViN+s+e+ +T+++ 
  gi|119720575|ref|YP_921070.1| 563 YASKDPRVELQVYtgEKDDLLIVINHSNENVETSITS 599
                                    7899*********5557889***************86 PP

>> Glyco_hydro_72  Glucanosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0013       3.7      51      78 ..      26      53 ..       2      70 .. 0.73
   2 ?    2.3   0.0     0.028        84     230     286 ..     218     278 ..     207     317 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0013
                                   G-HHHHHHHHHHHHHHT-SEEEES---T CS
                 Glyco_hydro_72 51 adaeaCkrdikllkelgvntvrvyavdn 78
                                    d e+ k+di+ +kelgv +vr++  d 
  gi|119720575|ref|YP_921070.1| 26 WDEESLKKDIEKMKELGVRVVRIFLRDI 53
                                   467899*****************97665 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.028
                                    HHHHHHTT-S.S-EEEEEE---SSS...S---THHHHHTSHHHHTTEEEEEES-SB--SSS CS
                 Glyco_hydro_72 230 ertkefenys.iPlflseyGCnkvt...prkftevealyseemtsvfsGGlvyeyseeann 286
                                    +  + f+n++ +P++l e+G  + +   + +   ve+++++++ +  sG +++ +s+ +++
  gi|119720575|ref|YP_921070.1| 218 AMLELFSNAGdLPVILEEFGFSTLQfseESHARFVEEILYTSLAHEASGAFIWCFSDFTEE 278
                                    556677777448********99987666566667999999999999999999998875554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (640 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.66u 0.27s 00:00:00.93 Elapsed: 00:00:00.44
# Mc/sec: 4338.84
//
Query:       gi|119720576|ref|YP_921071.1|  [L=159]
Description: hypothetical protein Tpen_1673 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       747  (0.0416643); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 1080.35
//
Query:       gi|119720577|ref|YP_921072.1|  [L=73]
Description: hypothetical protein Tpen_1674 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.9e-06   26.6   0.2    1.4e-05   24.8   0.0    1.9  2  RHH_1         Ribbon-helix-helix protein, copG family
    0.00035   21.3   0.2    0.00041   21.1   0.2    1.2  1  VAPB_antitox  Putative antitoxin
  ------ inclusion threshold ------
      0.044   13.7   0.1      0.055   13.4   0.1    1.2  1  XH            XH domain


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   2.4e-09   1.4e-05       3      37 ..       3      38 ..       3      39 .. 0.97
   2 ?   -1.3   0.1      0.41   2.4e+03       5      14 ..      50      59 ..      48      60 .. 0.72

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 2.4e-09
                                   EEEEEHHHHHHHHHHHHHHT.SSHHHHHHHHHHHHH CS
                          RHH_1  3 sirldeellerLdelarrrg.rSrSelIReAlreyl 37
                                   +i +de + +rL+el++++g +S  ++IR+++++++
  gi|119720577|ref|YP_921072.1|  3 TIAVDEATWKRLRELKDKLGfQSYNDVIRALVEQWH 38
                                   89********************************96 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.41
                                   EEEHHHHHHH CS
                          RHH_1  5 rldeellerL 14
                                    +d + +e+L
  gi|119720577|ref|YP_921072.1| 50 EIDVDAAEAL 59
                                   5778888877 PP

>> VAPB_antitox  Putative antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.2   6.8e-08   0.00041       1      49 [.       2      49 ..       2      71 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 6.8e-08
                   VAPB_antitox  1 KtIsIsdevYekLkklKr..egeSFsdvIerLlekkkkgkkkellelfgil 49
                                   KtI +++ + ++L++lK     +S++dvI+ L+e+  +   +++ e +++l
  gi|119720577|ref|YP_921072.1|  2 KTIAVDEATWKRLRELKDklGFQSYNDVIRALVEQWHV---SRVQESVEKL 49
                                   9****************955579**********95444...4566666665 PP

>> XH  XH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   9.2e-06     0.055      65      92 ..      12      39 ..       2      54 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.2e-06
                             XH 65 ekLkeLkeeyGeevykaVtkallelney 92
                                   ++L+eLk+++G + y+ V +al+e  ++
  gi|119720577|ref|YP_921072.1| 12 KRLRELKDKLGFQSYNDVIRALVEQWHV 39
                                   68*********************97665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       794  (0.0442858); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 487.24
//
Query:       gi|119720578|ref|YP_921073.1|  [L=513]
Description: glycoside hydrolase family protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.9e-56  189.6   0.1    1.7e-43  148.7   0.0    2.7  2  Glyco_hydro_1  Glycosyl hydrolase family 1


Domain annotation for each model (and alignments):
>> Glyco_hydro_1  Glycosyl hydrolase family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.2   0.3   6.3e-14   1.1e-09       3      89 ..       4      96 ..       2     107 .. 0.80
   2 !  148.7   0.0   9.2e-48   1.7e-43      95     450 ..     131     496 ..     126     498 .. 0.83

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 6.3e-14
                                   GGS-TT-EEEEE--HHHHH--..TTSTT---BHHHHHHHHGGGS....TTS---SSTT-HHHHHHHHHHHHHHTT-SEEEEE CS
                  Glyco_hydro_1  3 etfpedFlwgaataayqiEGa..wnedGkgesiwDtftetpgkv....legsngdvacdsYhrykeDvallkelgvkayrfS 78
                                    +fp++F wg++ + +q E +  ++    +++ w ++ + p ++    ++g+  + ++++++ + +D +l +elg+++yr+ 
  gi|119720578|ref|YP_921073.1|  4 MMFPQKFRWGVSESGFQFEMGdeYRRFIDTNTDWWHWVRDPHNIssrlVSGDLPEDGINYFELFGKDHELARELGLNTYRLG 85
                                   57*****************76235555667777888988887761111455556678999********************** PP

                                   --HHHHSTTST CS
                  Glyco_hydro_1 79 isWpRilPkGe 89
                                   i W+Ri+P+++
  gi|119720578|ref|YP_921073.1| 86 IEWSRIFPHPT 96
                                   ********974 PP

  == domain 2  score: 148.7 bits;  conditional E-value: 9.2e-48
                                    HHHHHHHHHHHHHHHTT-EEEEEEESS--BHHHHH..H-GGG-............SHHHHHHHHHHHHHHHHHTTT--EE CS
                  Glyco_hydro_1  95 kGlayYerLidelleagieplvTlyHwdlPqaLqd..eGgwen............rsiidafkeyaevvfkrfgdkvklw 160
                                    k ++ Y++++  l ++g + +v l H+ lP++++d      ++            +s   +  +ya++v  +fgd v++w
  gi|119720578|ref|YP_921073.1| 131 KAVQMYREILLDLRKRGFKVIVNLVHFTLPYWIHDpiR--AKSselsegplglleESFPIEMAKYAAYVAWKFGDLVDMW 208
                                    67899****************************99532..22212344444333366666789***************** PP

                                    EEEE-HHHHHHHHHT..SS-STT-S-TTTHHHHHHHHHHHHHHHHHHHHHHHT.........TT-EEEEEEEEEEEEESS CS
                  Glyco_hydro_1 161 lTfnEpnvvallgyl..tgefaPgkkdleaayeaaHnlllaharavklykeva.........qkgkigivlnlslaepls 229
                                     TfnEp v   lgyl  ++ f+Pg+++ +a+ +a  n  +aha a++++k+           + +++g+++n+  a+   
  gi|119720578|ref|YP_921073.1| 209 STFNEPVVPIELGYLgtYTGFPPGVNKPQAVPKALVNTAIAHALAYDMIKKFDnvkadpdsnSPAEVGLIYNIIPAYSP- 287
                                    **************733578*************************9988877666788876667899999988777644. PP

                                    SSHHHH.HHHHHHHHHHTHHHHHHHHHSS--HHHHHHHGGG..S----HHHHHHHTT--SEEEEEEEEEEEEEE--...- CS
                  Glyco_hydro_1 230 eseedk.eaaeraleflngwfldpvvkGdYpeemkellrergalpeiteedkellkgkadflglnyYtsrlvknkeseea 308
                                     +  +  +a+e++  f+n+  l++v +G+    +      +++l        + l gk d+lg+nyYt+ +vk++     
  gi|119720578|ref|YP_921073.1| 288 -EGTKSeKAVEHYSYFHNELLLEAVKNGRLDVALD----GKNIL------KPAALGGKLDWLGVNYYTRIVVKESS---R 353
                                    .4333338********************9765443....33222......24689*****************9998...4 PP

                                    STT---SSGGGGG-............SBSS-B-SSSS-B-HHHHHHHHHHHHHTS----EEEEE----EE-BSSSHHH-- CS
                  Glyco_hydro_1 309 slskteekkleeev............dpslpktdigwiiepeglrkllellkkeYqklpiyiteNGlgakdeieegkveD 376
                                     ++ +    +e               +      ++gw+ +pegl + l+ + + Y   ++++teNG ++          D
  gi|119720578|ref|YP_921073.1| 354 RFNGHPVLDFEAVAgygyacvpfglsKIGRACDGMGWEFYPEGLIDALR-IGSTYA-SKLLVTENGTSDPR--------D 423
                                    4555555444444455678899999655566678**************7.5799*9.99*******98776........7 PP

                                    HHHHHHHHHHHHHHHHHHHTT--EEEEEEE-SB----GGGTTSEE--SEEEETTTTTEEEE-HHHHHHHHHHH- CS
                  Glyco_hydro_1 377 dkRidYlkehlnevkkaiedgvdlkgYvawsllDnfewaegyskrfGlvyvdrnetleRtpkkSakwykeviek 450
                                      R +Yl +hl ++  aie+g++++gY+ w+l+Dn+ewa+g+++rfGl+ vd   t++R+p++S + yk++i++
  gi|119720578|ref|YP_921073.1| 424 VIRPSYLVNHLYALLLAIEEGINVEGYLHWALTDNYEWAHGFRQRFGLFEVD-LITKSRIPRHSSRIYKHIIQQ 496
                                    89**************************************************.99****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (513 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 3398.19
//
Query:       gi|119720579|ref|YP_921074.1|  [L=636]
Description: extracellular solute-binding protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-66  225.4   7.4    1.6e-66  224.8   7.4    1.2  1  SBP_bac_5        Bacterial extracellular solute-binding prote
  ------ inclusion threshold ------
      0.024   14.4   0.1      0.083   12.7   0.0    1.9  2  ECSCR            Endothelial cell-specific chemotaxis regulat
      0.082   13.0   0.1       0.13   12.3   0.1    1.3  1  DUF4366          Domain of unknown function (DUF4366)
      0.089   12.3   1.5       0.18   11.4   1.5    1.4  1  DUF5527          Family of unknown function (DUF5527)
       0.22   12.0   0.2       0.38   11.2   0.2    1.3  1  MGC-24           Multi-glycosylated core protein 24 (MGC-24),
        2.4    8.2   5.6        3.8    7.5   5.6    1.2  1  TMEM119          TMEM119 family


Domain annotation for each model (and alignments):
>> SBP_bac_5  Bacterial extracellular solute-binding proteins, family 5 Middle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  224.8   7.4   5.5e-70   1.6e-66       2     369 ..      77     458 ..      76     463 .. 0.87

  Alignments for each domain:
  == domain 1  score: 224.8 bits;  conditional E-value: 5.5e-70
                                    EEESSEEEEE..EEETTTTEEEEEE-TT-B-TTSSB-SHHHHHHHHHHHHTGGGHCTTHHHHHCTCTEEEEEEEETTEEE CS
                      SBP_bac_5   2 vvpaLAesww..evsdDgktytfkLRkgvkFsDGtpltAeDvvfsferlldpdtasgyaslleedqdikkveavddytvr 79 
                                    ++p++A+  +  +vs +   +t+kL++ ++++DG+plt+eDv+++f+ + +++ta +y+s l+      +ve++d++tv+
  gi|119720579|ref|YP_921074.1|  77 FIPWIADGQPsfQVSGNTVRITIKLKE-ARWQDGQPLTSEDVAYTFYEFPKKNTAVYYSSILN---YLLSVETPDTRTVV 152
                                    789999995566788888888888888.**********************************5...9************* PP

                                    EEESSETT......TTTTHCHHHHHHHGCCHTCTCTTTTTGTTTSE-BSSSEEEEEEETTTEEEEEE-TTST...TTSCS CS
                      SBP_bac_5  80 ftlkkpna......lfltllaavpasiakkaaekeddkdkdtnekpvgtGPYklkefkpgqkivlernpdYw...gggkp 150
                                    f+ ++++       +fl+ +a +p+    + +++++++ +d n +p+g+G Yk  +++  ++++++r +++w   + g p
  gi|119720579|ref|YP_921074.1| 153 FVCNATTVnypqiyDFLRSVAIIPK----HVWVNKEKPLEDANWPPIGSGMYKASSYTS-DRMIWVRDDNWWgtkYFGTP 227
                                    ******8877644334444444444....556999999*********************.************99888999 PP

                                    SSSEEEEEE-.SHHHHHHHHHTTSSSEEESTTCCTHCHHHHHTTEEE....EEEEEEEEEEEEEETTTSTGGGSHHHHHH CS
                      SBP_bac_5 151 kldriefkvipdsdaraaalqsGeiddvaepppsdieqlkeakglkv....lyespgggvtylafNtkkppfddkrvRqA 226
                                     + +i++ +++++++++a+l  Ge+d+ +++ p++   +++++ l           +++v +l++Ntkk+p+d++ +R+A
  gi|119720579|ref|YP_921074.1| 228 GPRYIVYVMVSSNAVALAMLARGELDWSNYFLPGFSSLVQQYPFLVTwynkSPWNLPANVAFLFVNTKKTPMDNPTFRKA 307
                                    **********6666666666*****5555555555555566665555977777777************************ PP

                                    HHHHS-HHHHHHHCTTTSSEEESSSSTTTSTTCCSCHCCCSHH.......SHHHHHHHHHHHTT-BCSSTSCEETC.... CS
                      SBP_bac_5 227 lsyAiDreeivkavlegyatpansllppsspgadeeykpayka.......ydpekAkklLkeaGykdgdggglrek.... 295
                                    l yAiD ++i+++v+eg+ ++a  +    +pg+++  +++          ydpekAk+lL++ G+kd +g+g re     
  gi|119720579|ref|YP_921074.1| 308 LYYAIDVDKIINTVFEGGVIKALPIGILDIPGYKPFIDTE--LisrygykYDPEKAKQLLDSIGIKDYNGDGWRELpggk 385
                                    *********************************9998885..25699999************************99**** PP

                                    EEEEEEEEETTSHHHHHHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHCTTESEEEEEEECTTSTTHHHHHHH CS
                      SBP_bac_5 296 klkltlllasgspaekaiaeliqqqlkkiGikvevktvdwaatylervkdgdfdmillgwgadypdpdnflnpf 369
                                    +lklt+++++g++++ ++a li+++l+++G+ ve +  d  ++y e+  +g+fdm + ++g+  +  ++ ++++
  gi|119720579|ref|YP_921074.1| 386 PLKLTIIVPYGWTDWMEAARLIASDLQRVGLYVEAQFPDY-SAYSEALYKGTFDMLINNFGSFASISPWVIYNW 458
                                    ****************************************.******************999865555555554 PP

>> ECSCR  Endothelial cell-specific chemotaxis regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.2   3.5e+03      42      73 ..     172     204 ..     143     208 .. 0.66
   2 ?   12.7   0.0   2.8e-05     0.083      12      61 ..     588     636 .]     579     636 .] 0.87

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.2
                          ECSCR  42 vsvvslrfkcrknkesedpqkpei.sglsescs 73 
                                    v+++     + k+k  ed + p i sg+++++s
  gi|119720579|ref|YP_921074.1| 172 VAIIPKHVWVNKEKPLEDANWPPIgSGMYKASS 204
                                    445555556678888899887765478887755 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 2.8e-05
                          ECSCR  12 psptsetvltvaafgvisfivilvvvviilvsvvslrfkcrknkesedpq 61 
                                     +pt+ t  t  a     +iv l+v+v il +v  + f  rk+ke   pq
  gi|119720579|ref|YP_921074.1| 588 TTPTAPTTPTAPAPDYTPYIVALIVIVAIL-AVAYMFFVQRKKKEETKPQ 636
                                    47999999999999**********999998.6888999*******99998 PP

>> DUF4366  Domain of unknown function (DUF4366)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   4.5e-05      0.13      95     145 ..     571     631 ..     565     632 .. 0.51

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.5e-05
                        DUF4366  95 eepepekeaepee.........peeepekksn.......nglllvvlavaligggaayyfkvlkpkk 145
                                    ++p+++++++p++         p++              +  +++++++++i + a+++f  +k+k+
  gi|119720579|ref|YP_921074.1| 571 KTPTTTPTTTPTTpttpttptaPTT------PtapapdyTPYIVALIVIVAILAVAYMFFVQRKKKE 631
                                    3444444433333222222332222......022334457777777777777778877777777776 PP

>> DUF5527  Family of unknown function (DUF5527)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.5   5.9e-05      0.18      10      62 ..     575     625 ..     570     630 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.9e-05
                        DUF5527  10 tsptlsllallvsttelvPlspaslaekadplpiiialvCiflllatflifvt 62 
                                    t+pt++  +  + tt  +P++p+++  ++d  p i+al+ i+ +la   +f++
  gi|119720579|ref|YP_921074.1| 575 TTPTTTPTTPTTPTTPTAPTTPTAP--APDYTPYIVALIVIVAILAVAYMFFV 625
                                    4444444444566677777777776..8999***************9888865 PP

>> MGC-24  Multi-glycosylated core protein 24 (MGC-24), sialomucin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   0.00013      0.38      75     134 ..     574     631 ..     566     634 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00013
                         MGC-24  75 stttstsvatsgttnttvtptsqparkstFDaAsFiGGivLvLgvqAviFFlykfcksKd 134
                                    +tt++t+ +t +t++t  +pt+  +  ++ D   +i  +++++++ Av++ ++   k K+
  gi|119720579|ref|YP_921074.1| 574 TTTPTTTPTTPTTPTTPTAPTT--PTAPAPDYTPYIVALIVIVAILAVAYMFFVQRKKKE 631
                                    2223333334444444445555..3578889999**999999999999876655555555 PP

>> TMEM119  TMEM119 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   5.6    0.0013       3.8      30      88 ..     567     625 ..     564     628 .. 0.95

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0013
                        TMEM119  30 lpPprtPalsptsvgpqptalaGpkpptnfldGivdffrqyvlliavvGslaflllfiv 88 
                                    l P +tP+ +pt+  + pt+ + p+ pt       d+    v li +v  la+  +f v
  gi|119720579|ref|YP_921074.1| 567 LRPVKTPTTTPTTTPTTPTTPTTPTAPTTPTAPAPDYTPYIVALIVIVAILAVAYMFFV 625
                                    789**********************************99999**************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (636 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       897  (0.0500307); expected 358.6 (0.02)
Passed bias filter:                      714  (0.0398237); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.70u 0.32s 00:00:01.02 Elapsed: 00:00:00.47
# Mc/sec: 4107.98
//
Query:       gi|119720580|ref|YP_921075.1|  [L=347]
Description: binding-protein-dependent transport systems inner membrane component [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.2e-39  135.1   8.2    2.2e-39  135.1   8.2    2.3  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
      0.054   12.9   0.1      0.054   12.9   0.1    1.7  2  Chs7          Chitin synthase export chaperone


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   4.5      0.35   3.2e+03      13      40 ..      13      40 ..       5     134 .. 0.52
   2 !  135.1   8.2   2.5e-43   2.2e-39       4     184 ..     138     343 ..     135     344 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.35
                   BPD_transp_1 13 nkkldkllrpliivllslPsfvlaillv 40
                                   ++ l+++l +l+i+lls+  +v +  l+
  gi|119720580|ref|YP_921075.1| 13 SGLLNYFLKRLFILLLSFFLIVTINWLI 40
                                   5667777788888887777777444443 PP

  == domain 2  score: 135.1 bits;  conditional E-value: 2.5e-43
                   BPD_transp_1   4 lGilaalnrnkkldkllrpliivllslPsfvlaillvlvf.............................vilsilghlil 54 
                                    lG+laa  +++ ld++l pl + l   P+f+l+++l++vf                             ++++++ h+il
  gi|119720580|ref|YP_921075.1| 138 LGALAA--KKRLLDNILVPLAYYLANAPYFWLGVVLQFVFsvelckstpiclpsgfpysrgltpslnvtFLWDAFMHWIL 215
                                    899999..*************************************************************9********** PP

                   BPD_transp_1  55 pviillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgsw 134
                                    p +  +l++++++++ +r++++++l +++ ++++ lG s+   + k+v+++al p +tgl++++g l+   v++ef++s+
  gi|119720580|ref|YP_921075.1| 216 PFASYVLVQMGGWMIGMRNMIIYELGSNYAKYMEDLGFSDSM-LSKYVYRHALLPQVTGLGIQIGMLVSLGVAVEFVFSY 294
                                    ******************************************.************************************* PP

                   BPD_transp_1 135 pGlgtllleailgydyseisnggvlalviavlllnlvadilqrlldprvr 184
                                    pGlg+ l++ai+++dy +++ g+vl+++i+vl+ n+++dil+ +ldpr+r
  gi|119720580|ref|YP_921075.1| 295 PGLGYYLVNAIQNRDYFLTQ-GIVLVVTISVLVANFIIDILYGVLDPRTR 343
                                    ********************.***************************97 PP

>> Chs7  Chitin synthase export chaperone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1     6e-06     0.054     191     251 ..     122     186 ..     110     210 .. 0.73
   2 ?   -3.0   0.8      0.41   3.7e+03     191     214 ..     299     322 ..     298     337 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6e-06
                           Chs7 191 lyllnlvllvvyvvlql...ilvlrvLeer.wplgalllgvllfvigqvllyvlskkiCegvkhy 251
                                      +++++l+  y+  +l       r L+++  pl ++l+ +  f +g vl++v+s+++C+++   
  gi|119720580|ref|YP_921075.1| 122 APVAPALLVSWYIGNKLgalAAKKRLLDNIlVPLAYYLANAPYFWLGVVLQFVFSVELCKSTPIC 186
                                    5566666666666554421022235677752689999999********************98655 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.41
                           Chs7 191 lyllnlvllvvyvvlqlilvlrvL 214
                                    +yl+n++    y+++q i+ + ++
  gi|119720580|ref|YP_921075.1| 299 YYLVNAIQNRDYFLTQGIVLVVTI 322
                                    577777777777777755554443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2492.53
//
Query:       gi|119720581|ref|YP_921076.1|  [L=289]
Description: binding-protein-dependent transport systems inner membrane component [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-22   80.1  19.3    1.7e-22   80.1  19.3    1.6  2  BPD_transp_1  Binding-protein-dependent transport system inne
    5.9e-05   23.0   0.5    5.9e-05   23.0   0.5    3.2  5  OppC_N        N-terminal TM domain of oligopeptide transport 


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1      0.24   2.1e+03      38      38 ..      40      40 ..      18      99 .. 0.59
   2 !   80.1  19.3   1.9e-26   1.7e-22       1     184 [.     101     287 ..     101     288 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.24
                   BPD_transp_1 38 l 38
                                   +
  gi|119720581|ref|YP_921076.1| 40 V 40
                                   1 PP

  == domain 2  score: 80.1 bits;  conditional E-value: 1.9e-26
                   BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilg..hlilpviillllsaapyvrlirraalrs 78 
                                    g+llG++++ ++++ +d+++++++++ll++P+++++il++      +++g   l + +++++ll++ +++r +r+   + 
  gi|119720581|ref|YP_921076.1| 101 GVLLGLVSG-YFGGLVDEIVSFVVNLLLTIPPLLIVILVL------TYIGfrGLEFNGLLIGLLQWHWVARAVRSITKSL 173
                                    89*******.****************************99......55553156666*********************** PP

                   BPD_transp_1  79 lpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG....lgtllleailgydyseis 154
                                    +++d+v ++r+ G+s ++++ + +lPn+l++++  ++l+f +++  +v lef+g  pG    +g  l +a l++ ++++ 
  gi|119720581|ref|YP_921076.1| 174 RSRDFVLVSRMSGLSAFETILNDILPNMLSYVALVFVLQFSSAVFFSVTLEFFGLVPGnimsIGFILQQAVLWNAIQMNV 253
                                    *****************************************************************************999 PP

                   BPD_transp_1 155 ....nggvlalviavlllnlvadilqrlldprvr 184
                                        +++ + +++++  l +++  l +l++pr+r
  gi|119720581|ref|YP_921076.1| 254 wwwaIIPGILITLFLGSLYVISSSLDELFNPRLR 287
                                    *99999999***********************98 PP

>> OppC_N  N-terminal TM domain of oligopeptide transport permease C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.5   6.6e-09   5.9e-05       8      51 .]      16      60 ..       3      60 .. 0.78
   2 ?   -3.1   0.4      0.93   8.4e+03      16      30 ..      94     108 ..      92     116 .. 0.73
   3 ?   -4.2   1.8         2   1.8e+04      20      26 ..     133     139 ..     132     144 .. 0.50
   4 ?   -3.4   0.3       1.1     1e+04      16      24 ..     203     211 ..     200     223 .. 0.60
   5 ?   -1.2   0.1      0.22     2e+03      22      32 ..     262     272 ..     261     286 .. 0.71

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 6.6e-09
                         OppC_N  8 rrFkrNklAvvglvilllllliaifaPliaPydp.qdliqn..llpP 51
                                   + ++r  +  ++l+++l+ +++a+++Pli+Pydp q        +pP
  gi|119720581|ref|YP_921076.1| 16 KYLLRKQRVRFALFWVLFTIVLAAVGPLITPYDPtQ-TA-GppRQPP 60
                                   678888888999999999999999********9953.32.1226666 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.93
                         OppC_N  16 Avvglvillllllia 30 
                                    A+vg  + +ll l++
  gi|119720581|ref|YP_921076.1|  94 AIVGTTVGVLLGLVS 108
                                    888888888887776 PP

  == domain 3  score: -4.2 bits;  conditional E-value: 2
                         OppC_N  20 lvillll 26 
                                    l+++l+l
  gi|119720581|ref|YP_921076.1| 133 LIVILVL 139
                                    4444444 PP

  == domain 4  score: -3.4 bits;  conditional E-value: 1.1
                         OppC_N  16 Avvglvill 24 
                                      v+lv++l
  gi|119720581|ref|YP_921076.1| 203 SYVALVFVL 211
                                    456666655 PP

  == domain 5  score: -1.2 bits;  conditional E-value: 0.22
                         OppC_N  22 illlllliaif 32 
                                    il++l+l +++
  gi|119720581|ref|YP_921076.1| 262 ILITLFLGSLY 272
                                    78889988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       821  (0.0457917); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1954.46
//
Query:       gi|119720582|ref|YP_921077.1|  [L=320]
Description: oligopeptide/dipeptide ABC transporter, ATPase subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-23   84.2   0.0    1.5e-23   83.8   0.0    1.2  1  ABC_tran      ABC transporter
    3.6e-18   65.8   0.1    6.5e-18   65.0   0.1    1.4  1  oligo_HPY     Oligopeptide/dipeptide transporter, C-terminal 
      6e-05   22.7   0.0    0.00011   21.8   0.0    1.4  1  AAA_29        P-loop containing region of AAA domain
    0.00041   20.3   0.0    0.00078   19.4   0.0    1.4  1  RsgA_GTPase   RsgA GTPase
     0.0013   18.8   0.0     0.0023   18.0   0.0    1.6  1  MMR_HSR1      50S ribosome-binding GTPase
     0.0037   17.5   0.2      0.013   15.8   0.2    1.9  1  AAA_22        AAA domain
  ------ inclusion threshold ------
       0.01   15.3   0.2       0.84    9.0   0.0    2.1  2  SMC_N         RecF/RecN/SMC N terminal domain
      0.012   16.0   0.2      0.024   15.0   0.1    1.4  1  AAA_16        AAA ATPase domain
      0.022   14.8   0.1      0.041   14.0   0.1    1.4  1  Dynamin_N     Dynamin family
      0.026   15.0   0.1      0.048   14.2   0.1    1.3  1  AAA_23        AAA domain
      0.041   13.2   0.0      0.061   12.6   0.0    1.2  1  Septin        Septin
      0.045   13.7   0.1       0.13   12.2   0.0    1.7  2  NACHT         NACHT domain
      0.046   13.6   0.0      0.087   12.7   0.0    1.4  1  MobB          Molybdopterin guanine dinucleotide synthesis pr
      0.046   13.9   0.0      0.063   13.4   0.0    1.3  1  AAA_33        AAA domain
       0.05   12.8   0.1      0.071   12.3   0.1    1.2  1  NB-ARC        NB-ARC domain
      0.071   11.9   1.3       0.89    8.3   0.1    2.2  2  ABC_ATPase    Predicted ATPase of the ABC class
      0.076   12.6   0.0       0.14   11.7   0.0    1.4  1  cobW          CobW/HypB/UreG, nucleotide-binding domain
      0.081   12.7   3.4        1.1    9.0   0.4    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
      0.094   12.0   0.1       0.16   11.3   0.1    1.2  1  FtsK_SpoIIIE  FtsK/SpoIIIE family
       0.16   11.4   0.1       0.66    9.4   0.0    1.8  2  Proteasome    Proteasome subunit


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.8   0.0   1.7e-26   1.5e-23       2     136 ..      25     178 ..      24     179 .. 0.92

  Alignments for each domain:
  == domain 1  score: 83.8 bits;  conditional E-value: 1.7e-26
                                    EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--...SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS..--S-T CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxx....xxxxxxxxxxxxxxxx..xxxxx RF
                       ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkp...teGeilldgkdlke....qeleslrkeigvlpqe..pqlfp 72 
                                    + vs++++ege+++ivGe+G+GKStLl+ l +   p     G+ l+dgk+l +    +++++l  ++ ++pq   + l p
  gi|119720582|ref|YP_921077.1|  25 DGVSFEVHEGEILGIVGESGSGKSTLLNSLVNVRPPmkyIGGDALFDGKNLYRmskeEKKSVLGTRLTIIPQYalDALPP 104
                                    78*******************************99988899*********9998988888899999999***98888888 PP

                                    TSBHHHH..........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    xxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  73 eltvren..........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                      ++++            ++e i+ a+++l+ + l ++v++  p +LSgG++qrva++ a l+ p+lll DE t
  gi|119720582|ref|YP_921077.1| 105 VFRIKQYladfakthglSESEIIKLARERLKEVSLSEKVLDMYPIELSGGMRQRVAIVIASLTSPRLLLGDEIT 178
                                    8888887999999999777777999***********************************************98 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.0   0.1   7.3e-21   6.5e-18       2      65 .]     232     297 ..     231     297 .. 0.97

  Alignments for each domain:
  == domain 1  score: 65.0 bits;  conditional E-value: 7.3e-21
                      oligo_HPY   2 ErgpssklfdeplHPYTkaLlrsvprldrekd..klekikgeapslerldeGCpFapRCpfaleeC 65 
                                    E++p++++ ++plHPYT +L++s+ +l  +    +l +ikg +psl + + GC+FapRCp+a+  C
  gi|119720582|ref|YP_921077.1| 232 EIAPAEEIAKKPLHPYTNMLISSLTKLGVKASqqRLSGIKGLPPSLANPPPGCRFAPRCPYAVGRC 297
                                    99*************************99988889*****************************99 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   1.3e-07   0.00011      13      45 ..      25      57 ..      21      64 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.3e-07
                         AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDAiqal 45
                                   dg ++e+++ ++  ++G+sGsGKSTll ++  +
  gi|119720582|ref|YP_921077.1| 25 DGVSFEVHEGEILGIVGESGSGKSTLLNSLVNV 57
                                   77889999666999*************988776 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   8.7e-07   0.00078      86     121 ..      20      56 ..       4      66 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 8.7e-07
                                    THTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                    RsgA_GTPase  86 tkegleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                    + ++++ ++ ++++ ++  +vG+SG GKStL+n+l++
  gi|119720582|ref|YP_921077.1|  20 EVKAVDGVSFEVHEgEILGIVGESGSGKSTLLNSLVN 56 
                                    445677777777776999****************985 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   2.6e-06    0.0023       3      22 ..      38      57 ..      36     145 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.6e-06
                                   EEEESTTSSHHHHHHHHHTS CS
                       MMR_HSR1  3 aivGrpNvGKStLinaltge 22
                                   +ivG + +GKStL+n+l++ 
  gi|119720582|ref|YP_921077.1| 38 GIVGESGSGKSTLLNSLVNV 57
                                   8****************985 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.2   1.4e-05     0.013       6      29 ..      35      58 ..      31     215 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.4e-05
                         AAA_22  6 gilvvtGesGtGKTtllrrlleql 29
                                    il ++GesG+GK+tll+ l++  
  gi|119720582|ref|YP_921077.1| 35 EILGIVGESGSGKSTLLNSLVNVR 58
                                   67889*************999865 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   0.00094      0.84      25      44 ..      35      54 ..      19      64 .. 0.84
   2 ?    4.7   0.0      0.02        18     128     184 ..     142     194 ..      68     229 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00094
                                   SEEEEEESTTSSHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 25 sftaivGpNGSGKsnlldAi 44
                                   ++  ivG+ GSGKs ll+++
  gi|119720582|ref|YP_921077.1| 35 EILGIVGESGSGKSTLLNSL 54
                                   4668*************998 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.02
                                    HCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 128 esagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellk 184
                                    +  ++++ +LSgG ++ va  +++A  +     l l Dei +aLD    k +   ++
  gi|119720582|ref|YP_921077.1| 142 KVLDMYPIELSGGMRQRVA--IVIA--SLTSPRLLLGDEITSALDVVTQKGIMLNIR 194
                                    3344445589999998655..5544..4444558888********998887776665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1   2.7e-05     0.024      20      45 ..      32      55 ..      17      76 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.7e-05
                         AAA_16 20 rsgrpelvllsGesGvGKsslvrell 45
                                   ++  +e++ ++GesG+GKs+l+++l 
  gi|119720582|ref|YP_921077.1| 32 HE--GEILGIVGESGSGKSTLLNSLV 55
                                   34..48999*************9985 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   4.5e-05     0.041       2      22 ..      38      58 ..      37      64 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.5e-05
                                   EEEEBTTTTHHHHHHHHHTS- CS
                      Dynamin_N  2 avvGsqSsGKSSvlnaLlged 22
                                    +vG+  sGKS++ln+L+  +
  gi|119720582|ref|YP_921077.1| 38 GIVGESGSGKSTLLNSLVNVR 58
                                   68***************9765 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   5.3e-05     0.048      20      39 ..      35      54 ..      18      55 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.3e-05
                         AAA_23 20 gltlItGpNGaGKTTildAi 39
                                    +  I+G+ G+GK+T+l+ +
  gi|119720582|ref|YP_921077.1| 35 EILGIVGESGSGKSTLLNSL 54
                                   5778*************976 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   6.8e-05     0.061       9      26 ..      39      56 ..      34      86 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.8e-05
                                   EEEBTTSSCCCCCCTTSS CS
                         Septin  9 vvGesglGkttlintlfe 26
                                   +vGesg Gk+tl+n+l++
  gi|119720582|ref|YP_921077.1| 39 IVGESGSGKSTLLNSLVN 56
                                   8***************97 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00014      0.13       5      21 ..      39      55 ..      35      58 .. 0.89
   2 ?   -2.4   0.0       4.4     4e+03     135     164 ..     108     135 ..     102     136 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00014
                                   EEC-TTTCHHHHHHHHH CS
                          NACHT  5 lqGeaGsGKTtLlqkla 21
                                   + Ge+GsGK+tLl +l+
  gi|119720582|ref|YP_921077.1| 39 IVGESGSGKSTLLNSLV 55
                                   89************997 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.4
                                    HCTTSSCE..EEEE--TCCHHHHHHHHCTT CS
                          NACHT 135 leeqleeaivlevegfsesrrkqlvrkyfs 164
                                    ++++l++   ++  g+ses++ +l+r+ ++
  gi|119720582|ref|YP_921077.1| 108 IKQYLADF--AKTHGLSESEIIKLARERLK 135
                                    66777777..78889999999999998765 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   9.7e-05     0.087       1      22 [.      36      57 ..      36      63 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.7e-05
                           MobB  1 vlgivgksgsGKTtLleklipe 22
                                   +lgivg sgsGK tLl+ l+++
  gi|119720582|ref|YP_921077.1| 36 ILGIVGESGSGKSTLLNSLVNV 57
                                   79*****************975 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0     7e-05     0.063       4      35 ..      39      71 ..      36     135 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7e-05
                         AAA_33  4 lvGlpGsGKstlaerllkklg.avllssdtlrr 35
                                   +vG +GsGKstl+ +l++ ++ +  +  d+l++
  gi|119720582|ref|YP_921077.1| 39 IVGESGSGKSTLLNSLVNVRPpMKYIGGDALFD 71
                                   69***************9999899999998776 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1     8e-05     0.071      15      42 ..      31      56 ..      18      87 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8e-05
                                   TTTSCSEEEEEEESTTSSHHHHHHHHCC CS
                         NB-ARC 15 kdelqslvvalvGmgGvGKttlakqiln 42
                                    +e +  ++++vG  G+GK+tl+++ +n
  gi|119720582|ref|YP_921077.1| 31 VHEGE--ILGIVGESGSGKSTLLNSLVN 56
                                   55556..9***************99887 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1     0.001      0.89     235     265 ..      22      55 ..      11      59 .. 0.80
   2 ?    2.5   0.2     0.057        51     390     431 ..     204     244 ..     151     258 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.001
                                    EEEEEEE..E-SS.EEEEEE-TTSSHHHHHHHHH CS
                     ABC_ATPase 235 kkvsGmg..ipkG.vtlIvGggfhGKsTLLeAle 265
                                    k+v G+   + +G +  IvG    GKsTLL++l 
  gi|119720582|ref|YP_921077.1|  22 KAVDGVSfeVHEGeILGIVGESGSGKSTLLNSLV 55 
                                    56666543367888999**************985 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.057
                                    EEEEEESS-GCCTTT-SEEEEEETTEEEE-HHHHHHHHHCHT CS
                     ABC_ATPase 390 stilvvggsgdyldvAdtvilmeeykpkdvtekakeiaeela 431
                                    s +lv+  ++   +vAdt+++m + k+ ++   a+eia++  
  gi|119720582|ref|YP_921077.1| 204 SAVLVTHDISLIYQVADTIMVMYAGKVAEIA-PAEEIAKKPL 244
                                    8899999999999*********999999887.7888887754 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00016      0.14       3      24 ..      37      58 ..      35      64 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00016
                                   EEEEESTTCCHHHHHHHHHCT- CS
                           cobW  3 tvltGflGsGKTtLlnhllenr 24
                                   ++++G  GsGK+tLln+l++ r
  gi|119720582|ref|YP_921077.1| 37 LGIVGESGSGKSTLLNSLVNVR 58
                                   7899**************9765 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.4    0.0012       1.1       2      19 ..      37      54 ..      36      80 .. 0.80
   2 ?    5.1   0.2      0.02        17     236     302 ..     150     215 ..      56     215 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0012
                         AAA_21  2 nvliGpNgsGKSnLLdal 19
                                    +++G  gsGKS+LL  l
  gi|119720582|ref|YP_921077.1| 37 LGIVGESGSGKSTLLNSL 54
                                   579************887 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.02
                         AAA_21 236 elSdGtkrllalltallralkkgsllliDEpEngLHPkllrrll....ellkelsrngaQviltTHSplll 302
                                    elS G+++  a++ a l  +   +lll DE+ + L+   ++ ++    ++++e     +  +l+TH+ +l+
  gi|119720582|ref|YP_921077.1| 150 ELSGGMRQRVAIVIASLTSP---RLLLGDEITSALDVVTQKGIMlnirRFVDEGLI--GSAVLVTHDISLI 215
                                    56999999877777777666...9*************9999999888777788888..8889999997775 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00017      0.16      44      60 ..      39      55 ..      23      56 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00017
                                   EE--TTSSHHHHHHHHH CS
                   FtsK_SpoIIIE 44 vaGatgsGKStalntLi 60
                                   ++G +gsGKSt ln+L+
  gi|119720582|ref|YP_921077.1| 39 IVGESGSGKSTLLNSLV 55
                                   9**************97 PP

>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1       1.2     1e+03     155     175 ..     118     138 ..     108     146 .. 0.75
   2 ?    9.4   0.0   0.00074      0.66      27      68 ..     203     244 ..     195     261 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.2
                                    STTBSHHHHHHHHHHHHHHHH CS
                     Proteasome 155 kedltleeavelavkalkeal 175
                                    ++ l++ e+++la++ lke++
  gi|119720582|ref|YP_921077.1| 118 THGLSESEIIKLARERLKEVS 138
                                    567999999999999999886 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00074
                                    TTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHH CS
                     Proteasome  27 gskllskstveKifkiddhigvafaGlaaDartlvrraraea 68 
                                    gs +l +++++ i+++ d+i+v++aG++a++    ++a++ +
  gi|119720582|ref|YP_921077.1| 203 GSAVLVTHDISLIYQVADTIMVMYAGKVAEIAPAEEIAKKPL 244
                                    688889999********************9987777777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      560  (0.0312343); expected 358.6 (0.02)
Passed Vit filter:                       112  (0.00624686); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 1982.83
//
Query:       gi|119720583|ref|YP_921078.1|  [L=324]
Description: oligopeptide/dipeptide ABC transporter, ATPase subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.7e-31  108.1   0.0    7.1e-31  107.5   0.0    1.3  1  ABC_tran      ABC transporter
    3.3e-14   53.2   0.2    5.9e-14   52.3   0.2    1.5  1  oligo_HPY     Oligopeptide/dipeptide transporter, C-terminal 
    1.7e-05   25.1   0.1    0.00011   22.5   0.1    2.0  1  AAA_22        AAA domain
    0.00023   21.6   0.0    0.00035   21.0   0.0    1.4  1  AAA_16        AAA ATPase domain
    0.00089   19.0   0.0     0.0013   18.5   0.0    1.2  1  PRK           Phosphoribulokinase / Uridine kinase family
    0.00092   19.0   0.1     0.0013   18.6   0.1    1.2  1  AAA_15        AAA ATPase domain
     0.0015   18.3   0.0     0.0029   17.3   0.0    1.4  1  AAA_29        P-loop containing region of AAA domain
     0.0019   18.1   0.3      0.077   12.8   0.0    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
     0.0027   17.2   0.0     0.0075   15.7   0.0    1.6  1  SMC_N         RecF/RecN/SMC N terminal domain
      0.008   15.6   0.0      0.015   14.7   0.0    1.4  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
  ------ inclusion threshold ------
       0.01   16.3   0.0      0.015   15.8   0.0    1.3  1  AAA_23        AAA domain
      0.011   16.1   0.1       0.69   10.2   0.0    2.1  2  AAA_19        AAA domain
      0.026   14.5   0.0      0.054   13.5   0.0    1.5  1  TsaE          Threonylcarbamoyl adenosine biosynthesis protei
       0.03   13.5   0.0      0.043   13.0   0.0    1.2  1  G-alpha       G-protein alpha subunit
      0.034   13.9   0.0      0.047   13.4   0.0    1.2  1  AAA_24        AAA domain
      0.041   13.1   0.0      0.078   12.1   0.0    1.4  1  NB-ARC        NB-ARC domain
      0.041   13.9   0.1      0.073   13.1   0.1    1.4  1  AAA_5         AAA domain (dynein-related subfamily)
      0.052   14.0   0.0      0.087   13.2   0.0    1.4  1  AAA           ATPase family associated with various cellular 
      0.059   13.8   0.0        0.1   13.0   0.0    1.4  1  RNA_helicase  RNA helicase
      0.081   12.8   0.0       0.14   12.1   0.0    1.3  1  RsgA_GTPase   RsgA GTPase
      0.082   13.0   0.0       0.15   12.2   0.0    1.3  1  DUF87         Helicase HerA, central domain
      0.088   12.0   0.0       0.13   11.4   0.0    1.2  1  TIP49         TIP49 P-loop domain
       0.11   12.3   0.0       0.43   10.3   0.0    1.8  2  AAA_30        AAA domain
       0.12   12.3   0.1       0.24   11.3   0.1    1.5  1  NACHT         NACHT domain
       0.17   11.1   0.0       0.28   10.4   0.0    1.3  1  Zeta_toxin    Zeta toxin
       0.18   11.2   0.0         11    5.4   0.0    2.2  2  TniB          Bacterial TniB protein


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.5   0.0     1e-33   7.1e-31       2     136 ..      28     177 ..      27     178 .. 0.95

  Alignments for each domain:
  == domain 1  score: 107.5 bits;  conditional E-value: 1e-33
                                    EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG...B-HHHCCHCEEEE-SS..--S-TTSBH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxx..xxxxxxxxx RF
                       ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke...qeleslrkeigvlpqe..pqlfpeltv 76 
                                    ++vs+k+ +g+++a++Ge+G+GK+t+++++++ l+pt+G++ ++gkd+     +e   + ++++ ++q+  ++++p +tv
  gi|119720583|ref|YP_921078.1|  28 EDVSFKVDKGKILALIGESGSGKTTIARIILRILRPTSGRVIFEGKDIFAfdaEESAAYYRNVQGIFQDpySSFNPLKTV 107
                                    79**********************************************999999999999*********98888888889 PP

                                    HHH............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    xxx............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  77 ren............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                     +             + ++ i+++l+++gl+   ++v+++ p++LSgGq qrv++arall kp+ll++DEp 
  gi|119720583|ref|YP_921078.1| 108 DDIleltckkytcseYPENAIKQVLERVGLDP--QSVLGKFPHQLSGGQLQRVSIARALLVKPRLLVADEPV 177
                                    888******99999888888*********999..99999********************************7 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.3   0.2   8.5e-17   5.9e-14       4      64 ..     232     297 ..     229     300 .. 0.88

  Alignments for each domain:
  == domain 1  score: 52.3 bits;  conditional E-value: 8.5e-17
                      oligo_HPY   4 gpssklfdeplHPYTkaLlrsvprldrekdklekikgeapslerlde......GCpFapRCpfalee 64 
                                    g+ ++++++plHPYT  Ll+svp l +++ + eki+  +  le+ +e      GC++a+RCp+a+e+
  gi|119720583|ref|YP_921078.1| 232 GD-ATILEKPLHPYTTNLLASVPTLSSRWATEEKIRAARLRLEAEEEtvytttGCKYASRCPYASEK 297
                                    54.4799***********************9999999998777777789999************986 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.1   1.6e-07   0.00011       4     128 ..      36     206 ..      33     212 .. 0.66

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.6e-07
                         AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee......................................erpevvfv 45 
                                    + +il+++GesG+GKTt +r +l+ l  ++   +                                        +++++ 
  gi|119720583|ref|YP_921078.1|  36 KGKILALIGESGSGKTTIARIILRIL--RPTSGRvifegkdifafdaeesaayyrnvqgifqdpyssfnplkTVDDILEL 113
                                    6799********************99..3333337786667777766666666655555555555555444444444455 PP

                         AAA_22  46 tlpsst...sskdllrellralglelka.erlsseell.ealeqalrarav...ielliiDEaqh.lr...seealeeLr 113
                                    t+++ t    +++  +++l+ +gl+  +  ++  ++l   +l++ + ara    ++ll+ DE    l+   + ++l+ L 
  gi|119720583|ref|YP_921078.1| 114 TCKKYTcseYPENAIKQVLERVGLDPQSvLGKFPHQLSgGQLQRVSIARALlvkPRLLVADEPVSmLDastRVDILNILY 193
                                    55555544444455555555555555558666777777778888777777788888999999888566744377777777 PP

                         AAA_22 114 sllnlsrkgvqliLv 128
                                    +l      +++ +L+
  gi|119720583|ref|YP_921078.1| 194 DLKT--GENISTLLI 206
                                    7766..777777665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   5.1e-07   0.00035      25      69 ..      38      86 ..      24     152 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 5.1e-07
                         AAA_16 25 elvllsGesGvGKsslvrellralekdggiflrgkcdql....esaipy 69
                                    ++ l+GesG+GK++++r +lr l+ + g ++ +  d +    e++++y
  gi|119720583|ref|YP_921078.1| 38 KILALIGESGSGKTTIARIILRILRPTSGRVIFEGKDIFafdaEESAAY 86
                                   799******************9999997777666655554444444555 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.9e-06    0.0013       1      82 [.      39     119 ..      39     128 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.9e-06
                            PRK   1 vIgvagsSGaGkttvarklekifgrekvkaaeiegdsflrldraekdleleerkrakekevsflspeandfdllyevlke 80 
                                    ++++ g+SG+Gktt+ar +  i++ ++   +  eg+ ++ +d  e  +  ++ ++ ++  +s ++p     d l+ + k+
  gi|119720583|ref|YP_921078.1|  39 ILALIGESGSGKTTIARIILRILRPTS-GRVIFEGKDIFAFDAEESAAYYRNVQGIFQDPYSSFNPLKTVDDILELTCKK 117
                                    67899*******************444.44777*******************************9987777777777777 PP

                            PRK  81 lk 82 
                                    + 
  gi|119720583|ref|YP_921078.1| 118 YT 119
                                    75 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.1   1.8e-06    0.0013      11      63 ..      24      73 ..      24     118 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.8e-06
                         AAA_15 11 FRslkdveidlsee.ltvliGkNnsGKSsilealdlFlnnkekknkkvikieke 63
                                   FR+ +dv+ ++++  +  liG+ +sGK++i++++  +l  +   +   + +e +
  gi|119720583|ref|YP_921078.1| 24 FRAVEDVSFKVDKGkILALIGESGSGKTTIARIILRILRPT---S-GRVIFEGK 73
                                   99999988888887799*****************9999877...2.33333333 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   4.2e-06    0.0029      15      50 ..      30      65 ..      23      71 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.2e-06
                         AAA_29 15 htieidlkg.atlltGpsGsGKSTllDAiqalLvpak 50
                                    ++++d kg +  l+G+sGsGK+T+   i  +L p++
  gi|119720583|ref|YP_921078.1| 30 VSFKVD-KGkILALIGESGSGKTTIARIILRILRPTS 65
                                   556677.44699************9777777777765 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   0.00011     0.077       2      25 ..      40      63 ..      39     104 .. 0.76
   2 ?    3.5   0.1     0.077        53     236     298 ..     149     209 ..     147     211 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00011
                         AAA_21  2 nvliGpNgsGKSnLLdaldllarl 25
                                    +liG  gsGK+++ +++  + r 
  gi|119720583|ref|YP_921078.1| 40 LALIGESGSGKTTIARIILRILRP 63
                                   58****************888664 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.077
                         AAA_21 236 elSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTHS 298
                                    +lS G+++   ++ all    k++ll+ DEp + L+ +    +l +l ++++ +++  +l TH+
  gi|119720583|ref|YP_921078.1| 149 QLSGGQLQRVSIARALL---VKPRLLVADEPVSMLDASTRVDILNILyDLKTGENISTLLITHD 209
                                    55666665544444555...555************************65555599********8 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.1e-05    0.0075      25     199 ..      38     210 ..      22     229 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.1e-05
                                    SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSS.SCEEEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                          SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiek.eevsisrrv 103
                                    ++ a++G+ GSGK+ +   il +L  +s + +   + +d+    +e++++   +v+ +f+++ ++++  k  +  ++ + 
  gi|119720583|ref|YP_921078.1|  38 KILALIGESGSGKTTIARIILRILRPTSGRVIF--EGKDIFAFDAEESAAYYRNVQGIFQDPYSSFNPLKtVDDILELTC 115
                                    4789****************9999987775443..344555556888888899999999999888332220223333333 PP

                                    ETTSEEEEEETTEEE-HHHHHHHHHCTT-STT........CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 104 krkgeseykingkevtkkevsellesagiske........lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDekn 175
                                    k     +y+   +e  ++ ++++le++g++++        +LSgG+ + v++a  +    vkp+ l + De  + LD++ 
  gi|119720583|ref|YP_921078.1| 116 K-----KYTC--SEYPENAIKQVLERVGLDPQsvlgkfphQLSGGQLQRVSIARAL---LVKPR-LLVADEPVSMLDAST 184
                                    3.....3433..3457889999999999999999999999******9988887653...35665.7789*********** PP

                                    HHHHHHHHH..HHCTTSEEEEE-SSH CS
                                    xxxxxxxxx..xxxxxxxxxxxxxxx RF
                          SMC_N 176 vkkvaellk..eksknaQfivislre 199
                                    +  + ++l   ++ +n   + i+++ 
  gi|119720583|ref|YP_921078.1| 185 RVDILNILYdlKTGENISTLLITHDV 210
                                    *9999999855566777888888765 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   2.1e-05     0.015      25      68 ..      40      83 ..      30     107 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.1e-05
                   Mg_chelatase 25 lllvGppGsGKtmlakrlpsllpplseeealevakiasvagkke 68
                                   l l+G +GsGKt +a+ +  +l p s + ++e + i +   +++
  gi|119720583|ref|YP_921078.1| 40 LALIGESGSGKTTIARIILRILRPTSGRVIFEGKDIFAFDAEES 83
                                   679***********************999999999988776433 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.8   0.0   2.2e-05     0.015       7      43 ..      24      61 ..      22     130 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.2e-05
                         AAA_23  7 frsfrdqeidFsk.gltlItGpNGaGKTTildAiklaL 43
                                   fr  +d+++  +k ++ +++G+ G+GKTTi + i  +L
  gi|119720583|ref|YP_921078.1| 24 FRAVEDVSFKVDKgKILALIGESGSGKTTIARIILRIL 61
                                   666677777776647999************99987766 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0     0.001      0.69       9      37 ..      36      64 ..      28      84 .. 0.87
   2 ?    4.0   0.0     0.082        57      99     145 ..     164     217 ..     104     218 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.001
                         AAA_19  9 kekvllvtaGpGtGKTrvlkhivallvel 37
                                   k k+l++++  G+GKT++ + i+++l  +
  gi|119720583|ref|YP_921078.1| 36 KGKILALIGESGSGKTTIARIILRILRPT 64
                                   578999*************9999988765 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.082
                         AAA_19  99 klqeeellivDE.fqdvd.elqyrLlkallgekkk.....lllvGDpdQliyvf 145
                                     l +  ll+ DE ++++d  + + +l+ l++ k+      ll+  D  Q+ yv+
  gi|119720583|ref|YP_921078.1| 164 LLVKPRLLVADEpVSMLDaSTRVDILNILYDLKTGenistLLITHDVSQAYYVG 217
                                    444666999***88****999999999998655335677799999999999998 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   7.9e-05     0.054      14      43 ..      34      61 ..      21      68 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.9e-05
                                   HHHCHTEEEEEEESTTSSHHHHHHHHHHHT CS
                           TsaE 14 lakalgdvilLeGdLGaGKTtlvrglakal 43
                                   + k  g++++L G+ G+GKTt++r +++ l
  gi|119720583|ref|YP_921078.1| 34 VDK--GKILALIGESGSGKTTIARIILRIL 61
                                   333..789******************9987 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   6.2e-05     0.043      26      62 ..      40      90 ..      26     145 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.2e-05
                                   EEEEESTTSSHHHHHHHHHHHCS--.............--HHHHHC.CHHH CS
                        G-alpha 26 llllGqseSGKsTilkqlkllykkg.............fseeelat.wrav 62
                                   l l+G+s+SGK+Ti + + ++ +++             f+ ee+a+ +r+v
  gi|119720583|ref|YP_921078.1| 40 LALIGESGSGKTTIARIILRILRPTsgrvifegkdifaFDAEESAAyYRNV 90
                                   6799**************999999989999999999999999996658875 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   6.8e-05     0.047       3      37 ..      38      86 ..      36     122 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.8e-05
                         AAA_24  3 lkiliyGpsgiGKTtlakel..............gpkplfidtekGlks 37
                                   + ++++G+sg+GKTt+a+ +              g++++ +d e++++ 
  gi|119720583|ref|YP_921078.1| 38 KILALIGESGSGKTTIARIIlrilrptsgrvifeGKDIFAFDAEESAAY 86
                                   6689*************99988888887777777777777777776654 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00011     0.078      19      42 ..      37      59 ..      24      72 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00011
                                   CSEEEEEEESTTSSHHHHHHHHCC CS
                         NB-ARC 19 qslvvalvGmgGvGKttlakqiln 42
                                   +  ++al G  G+GKtt+a+ il+
  gi|119720583|ref|YP_921078.1| 37 G-KILALIGESGSGKTTIARIILR 59
                                   3.59***************99986 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   0.00011     0.073       3      24 ..      41      63 ..      39      73 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00011
                                   EEE--SSSSHHHHHHHGGGGB.S CS
                          AAA_5  3 lLvGppGtgKselaerlaaal.n 24
                                    L+G++G+gK+++a+ +++ l  
  gi|119720583|ref|YP_921078.1| 41 ALIGESGSGKTTIARIILRILrP 63
                                   69***************999852 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00013     0.087       2      34 ..      41      75 ..      40     138 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00013
                                   EEESSTTSSHHHHHHHHHHHH....THEEEEEETTTC CS
                            AAA  2 llyGppGtGKTllakavakel....gvefleisgsel 34
                                    l+G  G GKT++a+ + + l    g   + ++g+++
  gi|119720583|ref|YP_921078.1| 41 ALIGESGSGKTTIARIILRILrptsG--RVIFEGKDI 75
                                   599***************99843321..233333333 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00015       0.1       3      62 ..      42     114 ..      40     140 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00015
                   RNA_helicase   3 lyGpsgeGKStlakeLakallkkl............klkkkdsvysrnpeddfwdgYt.gqevvvidDfgqvk 62 
                                    l G+sg GK+t+a+ + + l  ++             + +++  y+rn++  f d Y+  ++   +dD+ + +
  gi|119720583|ref|YP_921078.1|  42 LIGESGSGKTTIARIILRILRPTSgrvifegkdifaFDAEESAAYYRNVQGIFQDPYSsFNPLKTVDDILELT 114
                                    78*************88888866688899999999855566889999**999999999889999999987766 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0    0.0002      0.14      89     119 ..      26      57 ..      11      68 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0002
                                    THHHHHHHCTT.SEEEEECSTTSSHHHHHHHH CS
                    RsgA_GTPase  89 gleelkellkd.ktsvlvGqSGvGKStLinal 119
                                    ++e+++ ++++ k+ +l+G+SG GK+t+   +
  gi|119720583|ref|YP_921078.1|  26 AVEDVSFKVDKgKILALIGESGSGKTTIARII 57 
                                    677888888877***************98765 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00021      0.15      26      47 ..      40      61 ..      23      81 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00021
                          DUF87 26 lAilgsTGsGKSntvavLleel 47
                                   lA +g++GsGK++ ++++l+ l
  gi|119720583|ref|YP_921078.1| 40 LALIGESGSGKTTIARIILRIL 61
                                   89**************999855 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00019      0.13      49      96 ..      36      83 ..       5      91 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00019
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          TIP49 49 aGravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkt 96
                                    G+ + l G+sg+Gkt +a  i + l      v++ g ++++ + + +
  gi|119720583|ref|YP_921078.1| 36 KGKILALIGESGSGKTTIARIILRILRPTSGRVIFEGKDIFAFDAEES 83
                                   378888*********************99999999***9999887665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00062      0.43      18      50 ..      37      69 ..      28      86 .. 0.86
   2 ?   -0.9   0.0       1.7   1.1e+03      73     111 ..     143     191 ..     121     201 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00062
                         AAA_30 18 drvavltGpAGtGKttalkalreaweaaggrvi 50
                                    ++ +l G  G+GKtt+ + + ++++   grvi
  gi|119720583|ref|YP_921078.1| 37 GKILALIGESGSGKTTIARIILRILRPTSGRVI 69
                                   468899***************999998876776 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.7
                         AAA_30  73 iakllkrlk.........grarlepgtllivDE.agmvdtkqlaallka 111
                                    + k+ ++l          +ra l + +ll+ DE ++m+d+++  ++l++
  gi|119720583|ref|YP_921078.1| 143 LGKFPHQLSggqlqrvsiARALLVKPRLLVADEpVSMLDASTRVDILNI 191
                                    4455555556666666665566777799999997799998887777765 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00034      0.24       3      23 ..      40      60 ..      38      68 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00034
                                   EEEEC-TTTCHHHHHHHHHHH CS
                          NACHT  3 vilqGeaGsGKTtLlqklala 23
                                   ++l Ge+GsGKTt ++ + + 
  gi|119720583|ref|YP_921078.1| 40 LALIGESGSGKTTIARIILRI 60
                                   789***********9988765 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0    0.0004      0.28      15      50 ..      36      71 ..      25     108 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0004
                     Zeta_toxin 15 rPklillgGqpGAGKselaellkdelerqgnvvrld 50
                                   + k++ l G +G+GK+++a+ + + l+++++ v ++
  gi|119720583|ref|YP_921078.1| 36 KGKILALIGESGSGKTTIARIILRILRPTSGRVIFE 71
                                   557778889**************9999666665554 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.015        11      36      53 ..      38      55 ..      22     109 .. 0.87
   2 ?    3.7   0.0     0.052        36     117     157 ..     165     203 ..     144     215 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.015
                           TniB 36 pnlllvGdsnnGKtmive 53
                                   + l l+G+s  GKt+i++
  gi|119720583|ref|YP_921078.1| 38 KILALIGESGSGKTTIAR 55
                                   6789************87 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.052
                           TniB 117 elkvrvLiiDEihnllagsarkqreflnalksLgnelkipi 157
                                     +k+r+L+ DE  ++l   a+++  +ln+l  L+   +i+ 
  gi|119720583|ref|YP_921078.1| 165 LVKPRLLVADEPVSML--DASTRVDILNILYDLKTGENIST 203
                                    5899************..66778889999888877666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      581  (0.0324056); expected 358.6 (0.02)
Passed Vit filter:                       117  (0.00652574); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 2172.73
//
Query:       gi|119720584|ref|YP_921079.1|  [L=325]
Description: glycoside hydrolase family protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-20   73.4   0.0    3.5e-20   72.9   0.0    1.2  1  Glyco_hydro_12  Glycosyl hydrolase family 12


Domain annotation for each model (and alignments):
>> Glyco_hydro_12  Glycosyl hydrolase family 12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.9   0.0   1.9e-24   3.5e-20       4     198 ..      64     291 ..      61     302 .. 0.82

  Alignments for each domain:
  == domain 1  score: 72.9 bits;  conditional E-value: 1.9e-24
                                    EEEE--TTEEEEEEEEEEEE-SSEEEEEEEEEEEEESSG..........B--EEEEE-BGGGTB--.....TT----EEG CS
                 Glyco_hydro_12   4 svennlWgskegsgsvavkvdgekitssgasahtswkek..........gypevygGeksvksysn.....sgvalpvkv 68 
                                    s++ nlWg  + +gs  v+        +g+   ++ + +          +y ev +G k++    +     + + lp ++
  gi|119720584|ref|YP_921079.1|  64 SIDPNLWGLVDFEGSGLVRGSARMECRAGGPLLIETALEvdaplrqgvvAYHEVIYGVKPFGVDPAhplprDPLPLPARL 143
                                    7888999999999999988775555566665555555445677888898999*99999998765541111145678889* PP

                                    GGEEEEEEEEEEEEE-TT--EEEEEEEEEESSTT-S.--TT-EEEEEEEE.EES---SSEEEE....EEEETTE....EE CS
                 Glyco_hydro_12  69 ssvssiptevsfsiddtnvkanvaydlflaaeknqv.tsigdvElmiWlarygniqPiGekie....tavvgGe....tW 139
                                    + +  + + +++s++ ++  +nvayd++l++ + +   s gd E+m+Wl+ ++n +P G+ +     ++ v+       W
  gi|119720584|ref|YP_921079.1| 144 DLLPRVVALAEYSVHWSSTGVNVAYDVWLKRRAGEPgVSRGDLEVMVWLY-WDNATPAGSAVSrfeaPVLVNCTlkplNW 222
                                    ********************************99988999**********.***********9999988888888888** PP

                                    EEEE...EESSSEEEEEEESS--.EEEE.EEHHHHHHHHH......-SS---GGGSEE-EEEEE--B.. CS
                 Glyco_hydro_12 140 elwlG..aeaeqdvlsFvakspi.kgys.fDvkdFldalt......sargldaedlylislqiGtEpft 198
                                    ++w     ++++ + +F  + p+ +g +  D+k Fld +       +     a dl+++s+++G E f 
  gi|119720584|ref|YP_921079.1| 223 TVWIQrsIGGGWTYVAFTPSAPVrSGSVaVDLKLFLDKAVelleesTPGQWSARDLHVVSVEFGSEVFY 291
                                    ***9877899*************7666679*******98778877444567899************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 2188.44
//
Query:       gi|119720585|ref|YP_921080.1|  [L=548]
Description: HEPN domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-09   36.5   2.5    7.8e-09   35.7   2.5    1.4  1  HEPN      HEPN domain
  ------ inclusion threshold ------
      0.049   13.5   0.7         23    5.0   0.0    3.2  2  TPR_10    Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> HEPN  HEPN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   2.5   8.7e-13   7.8e-09       4     114 ..     411     525 ..     408     530 .. 0.82

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 8.7e-13
                                    HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHH......TT--.SSCCHHHHHHCCHHHT...-HHHHHHH CS
                           HEPN   4 wlrrAeedleaAellleegdydlacfhaqqaaekalKAlllk......kggeppkthdlreLleelkkelkeseelreel 77 
                                    ++r+A++++e A ++ ++g  d ++f+a+q++e+++ Al lk       ++e  + h l +++ +l +++  +++++e+l
  gi|119720585|ref|YP_921080.1| 411 YYREAQKYMELAYEMRRRGLLDQSMFYAEQSVEFLVDALALKvkrivpSEIEDFRKHRLFSMMLFLVEGDAVPRKVEECL 490
                                    689***************************************533333333334455555555599999999******** PP

                                    HHHHCCCHHCCCTSS--S--HHHHHHHHHHHHHHHHH CS
                           HEPN  78 eeLekayiesrYpdakeeyteedaeealkdaeevlel 114
                                     +L+k y+  rY      +t ++a +a++++e+ +e+
  gi|119720585|ref|YP_921080.1| 491 HFLSKSYTR-RYKLESA-VTWDEADRAVECMERAWEY 525
                                    *******86.8888888.4*************98876 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.3    0.0026        24      18      34 ..     412     428 ..     410     432 .. 0.92
   2 ?    5.0   0.0    0.0026        23       4      26 ..     489     511 ..     487     524 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0026
                         TPR_10  18 ydeAealleealairrr 34 
                                    y eA +++e a+++rrr
  gi|119720585|ref|YP_921080.1| 412 YREAQKYMELAYEMRRR 428
                                    78**************9 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0026
                         TPR_10   4 slnNLanalrqrgrydeAealle 26 
                                    +l+ L+  +++r++++ A+ + e
  gi|119720585|ref|YP_921080.1| 489 CLHFLSKSYTRRYKLESAVTWDE 511
                                    8999999*************944 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (548 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 3720.61
//
Query:       gi|119720586|ref|YP_921081.1|  [L=415]
Description: major facilitator transporter [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.3e-38  132.0  51.7    3.4e-26   92.0  31.1    2.1  2  MFS_1       Major Facilitator Superfamily
    2.9e-34  118.7  15.9    7.4e-34  117.4  15.9    1.8  1  Sugar_tr    Sugar (and other) transporter
  ------ inclusion threshold ------
      0.034   13.5  36.0       0.31   10.3  11.6    2.1  2  MFS_4       Uncharacterised MFS-type transporter YbfB
        0.1   10.8   2.1       0.76    8.0   0.3    2.5  2  OATP        Organic Anion Transporter Polypeptide (OATP) fami
       0.13   11.1   7.6        4.4    6.0   6.3    2.4  2  MFS_1_like  MFS_1 like family


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.0  31.1   9.4e-30   3.4e-26       9     266 ..      17     282 ..       8     285 .. 0.82
   2 !   45.8  16.0     1e-15   3.7e-12      42     176 ..     271     406 ..     263     414 .. 0.87

  Alignments for each domain:
  == domain 1  score: 92.0 bits;  conditional E-value: 9.4e-30
                          MFS_1   9 alarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfasslw.l 87 
                                    a+ +++++ +l+ ++  +l + + e+g +l+   lg+++++ ++G+lsdr+Grr  l+++++l++++ + ++ a+  w  
  gi|119720586|ref|YP_921081.1|  17 AMYAGVVSGTLT-LIRAELAMGAEEAGRVLSSWLLGMLLGASLIGYLSDRVGRRASLVASYALMGVF-TPMSAAARGWlD 94 
                                    344445777777.99****************************************************.666634555647 PP

                          MFS_1  88 llvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvl 167
                                    l v rvl+G+g ++++ ++ +l+a+++p + rgr +++l ++++lG +   +l+ l+a s+gWravf++  ++++l+ v 
  gi|119720586|ref|YP_921081.1|  95 LSVYRVLAGAGNAGYMVTASVLLAEYAPTSSRGRQVAVLESAWALGWLASLVLSRLIAPSYGWRAVFLASSAALALLPV- 173
                                    *****************************************************************************99. PP

                          MFS_1 168 fllllpeepperkrkspkeee...................kgtgpaplvpawkallkdpvlwillialllfffgfsgllt 228
                                      l++ ++++ r  +s+ ++                    ++ g + lv   ++l+++    +l+i++++  ++++g++ 
  gi|119720586|ref|YP_921081.1| 174 --LYVAVPESLRFLVSKGRLAeaealagrlgvevpraqpaARAGLRDLVG-RRYLRRSV---MLWIHWFMLVLAYWGIFL 247
                                    ..899888888888888888788888888887765554444444444444.55555555...69**************** PP

                          MFS_1 229 llplylqevlglsglllaglllallalvgailallagr 266
                                    +lp +    +g++ ++ ++  +a+l  +++i + l+g+
  gi|119720586|ref|YP_921081.1| 248 WLPDI-LYKRGIP-FVRSL-DYAILITLAQIPGYLSGA 282
                                    ****7.9999999.33333.555555555555555554 PP

  == domain 2  score: 45.8 bits;  conditional E-value: 1e-15
                          MFS_1  42 algaavaslplGrlsdrfGrrrvlllglllfalglllllfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergr 121
                                    +l+++ + l +++l++  Gr++vl + +l+ +++++ l+ a +    l+  vl +++  +++ + +a++ +++p e rg 
  gi|119720586|ref|YP_921081.1| 271 TLAQIPGYLSGAYLVEVAGRKPVLAAYMLGAGIASAGLWAAKTDLEALAWGVLVSFFNLGAWGVTYAYTPELYPTELRGT 350
                                    678899999999**********************666664477778********************************** PP

                          MFS_1 122 aigllsagfslGailgpllggllasslg.Wravfyilaivsllafvlfllllpeep 176
                                    + g+++a+  +G ilgp ++g++++s+g  +a+f ++a++ ++++ ++++l +e++
  gi|119720586|ref|YP_921081.1| 351 GSGWANAFGRIGGILGPYVAGVMIQSYGnPSAPFAVFALAHVVSAAVVAALGVETK 406
                                    ************************666648888**********9987776665554 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.4  15.9   2.1e-37   7.4e-34      42     449 ..      40     414 ..       4     415 .] 0.83

  Alignments for each domain:
  == domain 1  score: 117.4 bits;  conditional E-value: 2.1e-37
                                    HH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHH CS
                       Sugar_tr  42 eessvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasv 121
                                    e      g ++s+ l+G ++G+ ++g+l+dr+GR+ sl+++ +l+ + + ++aaa     +  l v Rvl+G g  +  v
  gi|119720586|ref|YP_921081.1|  40 E-----AGRVLSSWLLGMLLGASLIGYLSDRVGRRASLVASYALMGVFTPMSAAAR---GWLDLSVYRVLAGAGNAGYMV 111
                                    3.....489***********************************************...9******************** PP

                                    HHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGGGS---HHHHHHT CS
                       Sugar_tr 122 lvPmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllilllflPESPrylvek 201
                                    +++++++E+Ap++ Rg+ v + ++a+++G l + ++   ++ + +   wr  +  +++   ll +l + +PES r+lv+k
  gi|119720586|ref|YP_921081.1| 112 TASVLLAEYAPTSSRGRQVAVLESAWALGWLASLVLSRLIAPSYG---WRAVFLASSAALALLPVLYVAVPESLRFLVSK 188
                                    *******************************99999999999888...*976655555555999**************** PP

                                    T-HHHHHHHHHHHHHC.HHHHHHHHHHHHHHHHHHH.....HTTHHHHSH...HHHHHHHHHHHHHHTTHHHHHHHTTTH CS
                       Sugar_tr 202 gkeeeakevlaklrge.edadrelaeekdsleaeqeeekaswkellssktvrqrlligvvlqifqqltGinaimyyspti 280
                                    g+  ea++   +l  e + a++++ +  + l              +++  +++r ++    +++  l +   i+   p i
  gi|119720586|ref|YP_921081.1| 189 GRLAEAEALAGRLGVEvPRAQPAARAGLRDL--------------VGR-RYLRRSVMLWIHWFMLVLAY-WGIFLWLPDI 252
                                    ************4333244444444444444..............444.45667777777777777776.5677777888 PP

                                    HHHSS-THH..HHHHHHHHHHHHHHHHHHHHHHHHS-SHHHHHHHHHHHHHHHHHHH..HHHHTTSS...CHHHHHHHHH CS
                       Sugar_tr 281 fenlglsks..llvtiivgvvnfvatfvaiflvdrfGRRtllllGaagmaicfvilgivalllvakskaasivaivfial 358
                                    + + g+     l   i++   ++   + +++lv+ +GR+++l   ++g+ i+ + l        ak    + +   +  +
  gi|119720586|ref|YP_921081.1| 253 LYKRGIPFVrsLDYAILITLAQIPGYLSGAYLVEVAGRKPVLAAYMLGAGIASAGLW------AAK----TDLEALAWGV 322
                                    88888776665889999999999999999************9988888888877773......333....2233445555 PP

                                    HHHHHHTTTTHHHHHHHHHHSHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHT-HH.HHHHHHHHHHHHHHHHHHS CS
                       Sugar_tr 359 fialfalgwgpvpwvlvsElfpqsvRskalaiavavnwlanflisllfpiiteaigggyv.flvfaglavlfiifvfffv 437
                                     + +f+lg  +v + + +El+p+++R++++  a a   +  +l  ++  ++ +++g++   f+vfa   v+++ +v    
  gi|119720586|ref|YP_921081.1| 323 LVSFFNLGAWGVTYAYTPELYPTELRGTGSGWANAFGRIGGILGPYVAGVMIQSYGNPSApFAVFALAHVVSAAVVAALG 402
                                    66899***************************************************5543389***************** PP

                                    --STT--CCCCG CS
                       Sugar_tr 438 petkgrtleeie 449
                                    +etkgr+lee++
  gi|119720586|ref|YP_921081.1| 403 VETKGRSLEEVS 414
                                    **********86 PP

>> MFS_4  Uncharacterised MFS-type transporter YbfB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0  16.4   0.00021      0.74      19     165 ..      30     176 ..      25     200 .. 0.79
   2 ?   10.3  11.6   8.6e-05      0.31     193     362 ..     228     398 ..     190     399 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00021
                          MFS_4  19 llaegqlslsqagllaaaNylGYLvGallaafalsagaeRlrllagllatvllllamaltesfaaflliRflaGvasAvv 98 
                                    ++ae+ + + +ag + +  +lG L+Ga l  +   +   R  l a+  +  + +  +a++++ + +++ R+laG + A  
  gi|119720586|ref|YP_921081.1|  30 IRAELAMGAEEAGRVLSSWLLGMLLGASLIGYLSDRVGRRASLVASYALMGVFTPMSAAARGWLDLSVYRVLAGAGNAGY 109
                                    56788899999*****************9988888888888899999999999999999********************* PP

                          MFS_4  99 lvfgsslvlahaaaarrervgallfaGvGlGiavsgllvlll.lqlglsasslWlalavlsavllllv 165
                                    +v +s l  + a  + r+r  a+l +   lG ++s +l  l+   +g+ a       a+l+++ +l v
  gi|119720586|ref|YP_921081.1| 110 MVTASVLLAEYAPTSSRGRQVAVLESAWALGWLASLVLSRLIaPSYGWRAV-FLASSAALALLPVLYV 176
                                    ********9999999999999999999999998887665444034444444.2233444554444443 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 8.6e-05
                          MFS_4 193 llalllaYglaGfGYiitatFlvaiardgaggalleallWllvGlaaivgvlvwlrvakrsglrralaaallieavgvll 272
                                     + l + +++  ++Y  +  +l++i  +++   +    + +l+ la i+g l    + +  g +++laa +l  +++ + 
  gi|119720586|ref|YP_921081.1| 228 SVMLWIHWFMLVLAYWGIFLWLPDILYKRGIPFVRSLDYAILITLAQIPGYLSGAYLVEVAGRKPVLAAYMLGAGIASAG 307
                                    45566778888888888888999998885444444445667899*************************99999999888 PP

                          MFS_4 273 sllspsplglivssvllGltflaitalvlqlarelappatrrllglmTasfg.igQilGpllasllaeatgslalallva 351
                                      + ++ l  +  +vl+  + l+   ++ +++ el+p + r + +    +fg ig ilGp++a+++ +  g+ +++ +v 
  gi|119720586|ref|YP_921081.1| 308 LWAAKTDLEALAWGVLVSFFNLGAWGVTYAYTPELYPTELRGTGSGWANAFGrIGGILGPYVAGVMIQSYGNPSAPFAVF 387
                                    8888888888888899999999*********************9999999*99*************************** PP

                          MFS_4 352 aaalvlaaliv 362
                                    a a v++a++v
  gi|119720586|ref|YP_921081.1| 388 ALAHVVSAAVV 398
                                    ******99886 PP

>> OATP  Organic Anion Transporter Polypeptide (OATP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.3   0.00021      0.76      11      80 ..      14      83 ..       5      90 .. 0.84
   2 ?    1.7   0.1     0.017        62     140     192 ..     100     152 ..      92     162 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00021
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           OATP 11 lvqamvsgyfkstittiEkrFklpsstsgliassneignillilfvsYfggrghrPrwigigallmalgs 80
                                    + am+ g+++ t+t i  +  +  ++ g ++ss  +g +l + +++Y+ +r+ r   + ++  lm++++
  gi|119720586|ref|YP_921081.1| 14 AIGAMYAGVVSGTLTLIRAELAMGAEEAGRVLSSWLLGMLLGASLIGYLSDRVGRRASLVASYALMGVFT 83
                                   4459************************************************777666666777777765 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.017
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           OATP 140 lllGiGatpiytlGisYidDnvkkknsplylgilyalrilGpalGfllGslll 192
                                    +l+G+G++ ++  +   + +++ +++    +++l ++++lG+    +l+ l++
  gi|119720586|ref|YP_921081.1| 100 VLAGAGNAGYMVTASVLLAEYAPTSSRGRQVAVLESAWALGWLASLVLSRLIA 152
                                    799***************************************99999988776 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0    0.0054        19      33      74 ..      38      79 ..      31      89 .. 0.81
   2 ?    6.0   6.3    0.0012       4.4     265     378 ..     266     378 ..     135     386 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.0054
                     MFS_1_like 33 aseigiitlilpltsilsppiwgvlaDrfgkrkkvvilslll 74
                                   a+e g +++   l  +l++ ++g l+Dr+g+r+ +v+  +l+
  gi|119720586|ref|YP_921081.1| 38 AEEAGRVLSSWLLGMLLGASLIGYLSDRVGRRASLVASYALM 79
                                   567777777788888999***************998766655 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0012
                     MFS_1_like 265 lvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaiienawlvlpievLhgisfgllwaaaveyvskiapk 344
                                    + +l ++a+ip ++ + +l+e  G   +l + +l   +   ++ + +    +l   vL ++     w++   y  ++ p 
  gi|119720586|ref|YP_921081.1| 266 YAILITLAQIPGYLSGAYLVEVAGRKPVLAAYMLGAGIASAGLWAAKTDLEALAWGVLVSFFNLGAWGVTYAYTPELYPT 345
                                    55677999*****************99999888877777777777777777888888999988999************** PP

                     MFS_1_like 345 sleatgqgllsglyfglGralGsliGGllwdlks 378
                                    +l++tg g  +++   +G+ lG +++G++++ ++
  gi|119720586|ref|YP_921081.1| 346 ELRGTGSGWANAF-GRIGGILGPYVAGVMIQSYG 378
                                    ********98877.569*************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.40
# Mc/sec: 3130.70
//
Query:       gi|119720587|ref|YP_921082.1|  [L=450]
Description: cation diffusion facilitator family transporter [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.1e-41  140.1  15.0    8.9e-41  139.8  15.0    1.1  1  Cation_efflux    Cation efflux family
    1.9e-34  117.6  10.1    2.1e-14   53.4   0.1    3.2  3  ZT_dimer         Dimerisation domain of Zinc Transporter
      0.004   17.1   4.7      0.004   17.1   4.7    1.8  2  DUF5134          Domain of unknown function (DUF5134)
  ------ inclusion threshold ------
      0.011   15.5   0.1      0.031   14.0   0.1    1.9  1  CT_C_D           Carboxyltransferase domain, subdomain C and 
      0.028   14.7   1.9        1.1    9.6   0.7    2.5  2  AMP-binding_C_2  AMP-binding enzyme C-terminal domain
      0.029   14.4   3.2      0.097   12.7   0.3    2.7  2  SsgA             Streptomyces sporulation and cell division p
        0.1   13.0   0.4        5.1    7.5   0.1    2.6  2  Arm-DNA-bind_3   Arm DNA-binding domain
        0.1   12.9   1.4        6.8    7.1   0.2    2.7  2  FtsZ_C           FtsZ family, C-terminal domain
        1.5    9.0   8.2         10    6.4   0.1    3.9  5  CinA_KH          Damage-inducible protein CinA KH domain
        7.2    6.4   6.3        2.6    7.8   0.1    3.1  3  Ribosomal_L12_N  Ribosomal protein L7/L12 dimerisation domain


Domain annotation for each model (and alignments):
>> Cation_efflux  Cation efflux family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.8  15.0     5e-44   8.9e-41       3     199 .]      13     209 ..      11     209 .. 0.98

  Alignments for each domain:
  == domain 1  score: 139.8 bits;  conditional E-value: 5e-44
                  Cation_efflux   3 lsllanlilalvelivglltnSlalladafhslsdlvsllllllalklsrkppderfpfGygrlevlgalvsgllllgla 82 
                                     sll++l+++   l+v++ltnSla+ladafhsl+d++++++++ a+ +s+k pd+++++G++++e+lg+l+++ ll ++ 
  gi|119720587|ref|YP_921082.1|  13 TSLLVTLLILSLRLAVYALTNSLAVLADAFHSLVDILGNVFAVAAVAVSSKGPDADHSYGHEKAESLGTLFVAGLLTVIF 92 
                                    689***************************************************************************** PP

                  Cation_efflux  83 vfllleaiqklikegereihaglalvvalvslvvnlalllilrragrklrsaalkaaalhvlgDaltslgvlvsalvill 162
                                    +f+++e++q++++++  +  +++  +++++ + + ++ +++l r++r +rs++l+a+alh  +D +++  +l  ++v  l
  gi|119720587|ref|YP_921082.1|  93 AFIVYESLQRALAPSYSVAFTAWSSLLLAFTMSMDMWRARALSRGARLYRSTVLEADALHYTSDFYATGTILALSVVGTL 172
                                    *********************************************************************99999999999 PP

                  Cation_efflux 163 fnlksgplaDpvaslligliilysalkllkeslseLl 199
                                    ++ +  +++D ++s++i+ + +ys+l+l+k+++ eL+
  gi|119720587|ref|YP_921082.1| 173 YKGPYLKYLDMAVSVAIAGYFAYSSLRLAKTAVDELM 209
                                    988877*****************************97 PP

>> ZT_dimer  Dimerisation domain of Zinc Transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.4   0.1   1.1e-17   2.1e-14       3      78 ..     214     287 ..     212     288 .. 0.90
   2 !   46.5   2.2   1.7e-15     3e-12       7      79 .]     297     367 ..     289     367 .. 0.88
   3 !   21.8   0.1   8.6e-08   0.00015       3      78 ..     372     449 ..     370     450 .] 0.88

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 1.1e-17
                                    ..HHHHHHHHHTT-SS-EEEEEEEEE-S----EEEEEEEE-TTS-HHHHHHHHHHHHHHHHHH-TT--EEEEEEEE CS
                       ZT_dimer   3 eeeeeeireiiksvpgvkgvhdlrtrksGskifvdlhievdgdlsvkeaHeiadevekrikeefpgvadvliHveP 78 
                                     e+++ +re+++s  g + v+++r+rk+G+++f d   ++++ ++++eaH+++deve++++ +     dv+iH+eP
  gi|119720587|ref|YP_921082.1| 214 TEVVALFREVASS-RG-LPVERVRARKAGPRVFLDAVARIPPGMTLEEAHRLVDEVEEELRGRAGVDVDVTIHMEP 287
                                    5677777888876.34.789********************************************9999******** PP

  == domain 2  score: 46.5 bits;  conditional E-value: 1.7e-15
                                    HHHHHHHTT-SS-EEEEEEEEE-S----EEEEEEEE-TTS-HHHHHHHHHHHHHHHHHH-TT--EEEEEEEE. CS
                       ZT_dimer   7 eeireiiksvpgvkgvhdlrtrksGskifvdlhievdgdlsvkeaHeiadevekrikeefpgvadvliHvePe 79 
                                    ++++e+++  +gv++vh l   +    ++v +h+e ++d sv+ea +iade++++++ + pgv+ v++HveP+
  gi|119720587|ref|YP_921082.1| 297 RRVEEAAR-REGVVRVHGLELARGEGGVHVRFHVEAKPDVSVEEAKRIADELKREVE-STPGVSSVVVHVEPA 367
                                    45556555.69**********99999******************************6.679***********5 PP

  == domain 3  score: 21.8 bits;  conditional E-value: 8.6e-08
                                    ..HHHHHHHHHTT..-SS-EEEEEEEEE-S----EEEEEEEE-TTS-HHHHHHHHHHHHHHHHHH-TT--EEEEEEEE CS
                       ZT_dimer   3 eeeeeeireiiks..vpgvkgvhdlrtrksGskifvdlhievdgdlsvkeaHeiadevekrikeefpgvadvliHveP 78 
                                    e++++++++++++    g ++v d+++ k   k +vd+  +v++  s++eaH+ + ++e  ++ee+ +   v++ +eP
  gi|119720587|ref|YP_921082.1| 372 EDVRKAVERVLSRegLRGKLEVADVKVVKTEGKTLVDIVCKVPRGESIEEAHRSVGRLEGVLREELGEKYLVTVCLEP 449
                                    566777777776546778999*******9999**********************************997778999999 PP

>> DUF5134  Domain of unknown function (DUF5134)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   4.7   2.3e-06     0.004      30     145 ..      13     125 ..       5     131 .. 0.81
   2 ?   -1.8   0.1       1.4   2.6e+03     103     126 ..     184     211 ..     159     249 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.3e-06
                        DUF5134  30 agqlavvfalaalwflvlavvrrrataarrlahlyhavmmlAMvyMaaamalaaggghsghaaagasmpgg.vplvtgvl 108
                                    +  l v  ++++l+ +v a+++   + a  + + +++v+ l  v+ +aa a++++g  + h  ++++++   +  v+g+l
  gi|119720587|ref|YP_921082.1|  13 TS-LLVTLLILSLRLAVYALTN---SLAVLADAFHSLVDILGNVFAVAAVAVSSKGPDADHSYGHEKAESLgTLFVAGLL 88 
                                    44.4777788888888888875...4889999******************7777777777776666655554899***** PP

                        DUF5134 109 avyFaaaalvwlarllpapapaelaracrlvMalGMa 145
                                    +v+Fa ++  +l r+l++ + ++ +++  l+ a+ M 
  gi|119720587|ref|YP_921082.1|  89 TVIFAFIVYESLQRALAPSYSVAFTAWSSLLLAFTMS 125
                                    *****************77778888888888888885 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.4
                        DUF5134 103 lvtgvlavyFaaaalvwlarllp....a 126
                                    +v++++a yFa   l+ +  +++    +
  gi|119720587|ref|YP_921082.1| 184 AVSVAIAGYFAYSSLRLAKTAVDelmdR 211
                                    5666777777777766664444444431 PP

>> CT_C_D  Carboxyltransferase domain, subdomain C and D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   1.7e-05     0.031       8      77 ..     320     389 ..     315     446 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.7e-05
                                    TTEEEEEE-SS--H.HHHHHHHHHHHHHHT..STTECEEEE-SSEEEEEESCCCCHHHHHH.HHHHHHHH..... CS
                         CT_C_D   8 deallvefgeeise.alskrvlalaaalrakalpgvvelvpayrsllvefdpealdaaellaalkallee....a 77 
                                    +  + v+f  e+++  + ++++++a++l     ++ ve +p++ s++v+++p+a + +++++a++++l++     
  gi|119720587|ref|YP_921082.1| 320 EGGVHVRFHVEAKPdVSVEEAKRIADEL-----KREVESTPGVSSVVVHVEPAAKSEEDVRKAVERVLSReglrG 389
                                    5556666654433312334445555555.....5578***************************99988755430 PP

>> AMP-binding_C_2  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.045        81      50      86 ..     257     293 ..     247     302 .. 0.78
   2 ?    9.6   0.7   0.00061       1.1      26      83 ..     315     370 ..     297     384 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.045
                                    HHHHHHHHHHHHHHHHHHHSS--EEEEE-TT-S---- CS
                AMP-binding_C_2  50 lkelealekkiakklksklgvsvkvelvepgtlprse 86 
                                    l+e ++l ++++++l+ + gv+v+v++  + + + + 
  gi|119720587|ref|YP_921082.1| 257 LEEAHRLVDEVEEELRGRAGVDVDVTIHMEPQDEVAA 293
                                    56788999*****************997665555555 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00061
                                    EEEEETTEEEEEEEEEE-TT----HHHHHHHHHHHHHHHHHHHSS--EEEEE-TT-S- CS
                AMP-binding_C_2  26 vvtregelDelevkvEvkegfsdelkelealekkiakklksklgvsvkvelvepgtlp 83 
                                     + r ++  +++ +vE+k+++  +++e ++++++++++++s+ gvs  v  vep    
  gi|119720587|ref|YP_921082.1| 315 ELARGEGGVHVRFHVEAKPDV--SVEEAKRIADELKREVESTPGVSSVVVHVEPAAKS 370
                                    56666666688999*****99..5679*******************999999987544 PP

>> SsgA  Streptomyces sporulation and cell division protein, SsgA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.2      0.19   3.3e+02      37      56 ..     311     330 ..     274     357 .. 0.65
   2 ?   12.7   0.3   5.4e-05     0.097      13      70 ..     360     415 ..     353     429 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.19
                                    HHHTTS-EEETTEEEEEEE. CS
                           SsgA  37 aeGlrapageGdVrvwPaer 56 
                                     +Gl+ + geG V+v+ + +
  gi|119720587|ref|YP_921082.1| 311 VHGLELARGEGGVHVRFHVE 330
                                    45777888888888876654 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 5.4e-05
                                    TEEEEEEE-SS---EEEEEEHHHHHHHTTS-EEETTEEEEEEE.ETTEEEEEEE--TT CS
                           SsgA  13 faVrlafptdgdeevewvfaRelLaeGlrapageGdVrvwPaereeedelvlelrspe 70 
                                    ++V+++  ++++e v+ +++R l +eGlr++   +dV+v  +e +  + + +  + p+
  gi|119720587|ref|YP_921082.1| 360 VVVHVEPAAKSEEDVRKAVERVLSREGLRGKLEVADVKVVKTEGK--TLVDIVCKVPR 415
                                    56888888999****************************999864..33334444444 PP

>> Arm-DNA-bind_3  Arm DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1     0.078   1.4e+02      24      62 ..     235     272 ..     200     282 .. 0.64
   2 ?    7.5   0.1    0.0029       5.1      43      63 ..     333     353 ..     295     360 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.078
                 Arm-DNA-bind_3  24 rvtpsGaktfvlryrlGr.ypavslaeARkkarelralia 62 
                                    r ++ G ++f+    + r  p ++l+eA +  +e+ ++++
  gi|119720587|ref|YP_921082.1| 235 RARKAGPRVFLDA--VARiPPGMTLEEAHRLVDEVEEELR 272
                                    3333355555522..34425779********999999885 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0029
                 Arm-DNA-bind_3  43 pavslaeARkkarelraliaq 63 
                                    p+vs++eA++ a+el++++++
  gi|119720587|ref|YP_921082.1| 333 PDVSVEEAKRIADELKREVES 353
                                    78***************9975 PP

>> FtsZ_C  FtsZ family, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.2    0.0038       6.8      48      89 ..     254     295 ..     248     298 .. 0.93
   2 ?    4.0   0.0     0.034        61      35      68 ..     321     354 ..     296     378 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0038
                                    T--HHHHHHHHHHHHHHS-TTSEEEEEEEE-TT--SEEEEEE CS
                         FtsZ_C  48 dltlkEveevaetireevdeeanvivGavideeledeirvtv 89 
                                     +tl+E+ + +++++ee+   a v v  +i+ e +de+  t+
  gi|119720587|ref|YP_921082.1| 254 GMTLEEAHRLVDEVEEELRGRAGVDVDVTIHMEPQDEVAATI 295
                                    79*******************************999998775 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.034
                                    G-SEEEEEEEE-TT--HHHHHHHHHHHHHHS-TT CS
                         FtsZ_C  35 gAkgvlvnitggsdltlkEveevaetireevdee 68 
                                    g   v +++ + +d++++E++++a+++++ev++ 
  gi|119720587|ref|YP_921082.1| 321 GGVHVRFHVEAKPDVSVEEAKRIADELKREVEST 354
                                    55556679999*****************999865 PP

>> CinA_KH  Damage-inducible protein CinA KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       7.1   1.3e+04      17      27 ..     204     214 ..     201     220 .. 0.54
   2 ?    6.4   0.1    0.0056        10      47      68 ..     255     276 ..     250     279 .. 0.88
   3 ?    0.9   0.1      0.28     5e+02      36      66 ..     275     305 ..     273     309 .. 0.79
   4 ?    5.3   0.1     0.013        22      34      65 ..     319     353 ..     310     360 .. 0.84
   5 ?   -2.1   0.0       2.5   4.4e+03      45      70 ..     415     440 ..     412     441 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 7.1
                                    HHGGGS-BSSS CS
                        CinA_KH  17 kladlidrenp 27 
                                    ++++l+dr+  
  gi|119720587|ref|YP_921082.1| 204 AVDELMDRTPT 214
                                    56666666443 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0056
                                    EEHHHHHHHHH....HHHHHTT CS
                        CinA_KH  47 aneeeaealiapveeeirerlg 68 
                                     + eea++l+++veee+r r g
  gi|119720587|ref|YP_921082.1| 255 MTLEEAHRLVDEVEEELRGRAG 276
                                    5789**************9988 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.28
                                    TEEEEEEE...EEHHHHHHHHH....HHHHH CS
                        CinA_KH  36 gevtvRltakaaneeeaealiapveeeirer 66 
                                    ++v+v +t   + ++e++a ia+ +ee  +r
  gi|119720587|ref|YP_921082.1| 275 AGVDVDVTIHMEPQDEVAATIARRVEEAARR 305
                                    6899999999999999999998877776655 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.013
                                    ETTEEEEEEE...E...EHHHHHHHHH....HHHH CS
                        CinA_KH  34 kegevtvRltakaa...neeeaealiapveeeire 65 
                                     eg+v+vR  ++a+   + eea+++++++++e+++
  gi|119720587|ref|YP_921082.1| 319 GEGGVHVRFHVEAKpdvSVEEAKRIADELKREVES 353
                                    5799****999887555789999999999999986 PP

  == domain 5  score: -2.1 bits;  conditional E-value: 2.5
                                    ..EEHHHHHHHHH....HHHHHTTTT CS
                        CinA_KH  45 kaaneeeaealiapveeeirerlgdy 70 
                                    ++++ eea++ + ++e  +re lg++
  gi|119720587|ref|YP_921082.1| 415 RGESIEEAHRSVGRLEGVLREELGEK 440
                                    67888999999999999999999986 PP

>> Ribosomal_L12_N  Ribosomal protein L7/L12 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.5       1.1   1.9e+03      29      39 ..      51      61 ..      51      69 .. 0.62
   2 ?    7.8   0.1    0.0014       2.6      11      28 ..     254     271 ..     253     272 .. 0.94
   3 ?   -0.2   0.1      0.45   8.1e+02      18      44 ..     345     368 ..     343     372 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.1
                                   THHHHHHHHHH CS
                Ribosomal_L12_N 29 GVsAAAPvava 39
                                   +V A+A+vav 
  gi|119720587|ref|YP_921082.1| 51 NVFAVAAVAVS 61
                                   56678888887 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0014
                                    TSBHHHHHHHHHHHHHHT CS
                Ribosomal_L12_N  11 eltvLElseLvkalEekF 28 
                                    ++t+ E+  Lv++ Ee++
  gi|119720587|ref|YP_921082.1| 254 GMTLEEAHRLVDEVEEEL 271
                                    6***************96 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.45
                                    HHHHHHHHHHTTHHHHHHHHHH.HHHH CS
                Ribosomal_L12_N  18 seLvkalEekFGVsAAAPvavaaaaaa 44 
                                     eL+ + E++ GVs    v+v   +aa
  gi|119720587|ref|YP_921082.1| 345 DELKREVESTPGVSS---VVVHVEPAA 368
                                    5999**********6...333333444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       827  (0.0461264); expected 358.6 (0.02)
Passed bias filter:                      550  (0.0306766); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.41
# Mc/sec: 3291.63
//
Query:       gi|119720588|ref|YP_921083.1|  [L=386]
Description: hypothetical protein Tpen_1685 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-06   28.5  18.6      0.024   15.0   0.1    4.1  4  OmpH             Outer membrane protein (OmpH-like)
     0.0018   18.0  17.8      0.018   14.8   5.9    3.0  3  YkyA             Putative cell-wall binding lipoprotein
     0.0037   16.8  27.8     0.0073   15.8   8.0    3.2  3  Golgin_A5        Golgin subfamily A member 5
     0.0042   14.7  18.3     0.0082   13.7  18.3    1.5  1  DUF3584          Protein of unknown function (DUF3584)
     0.0065   16.5  30.0      0.035   14.2   5.1    4.9  4  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
  ------ inclusion threshold ------
       0.01   16.1   7.9          6    7.2   0.1    5.0  4  DUF4709          Domain of unknown function (DUF4709)
      0.022   15.0  22.5       0.27   11.5   0.6    5.1  6  KxDL             Uncharacterized conserved protein
       0.03   13.9  20.5       0.71    9.4   9.0    2.2  2  Exonuc_VII_L     Exonuclease VII, large subunit
      0.044   13.6   1.1         12    5.7   0.0    3.1  4  Bacillus_HBL     Bacillus haemolytic enterotoxin (HBL)
       0.21   11.7   8.8        1.7    8.9   1.5    2.9  3  Fib_alpha        Fibrinogen alpha/beta chain family
       0.22   10.4  24.2       0.53    9.1  13.0    2.6  2  Spc7             Spc7 kinetochore protein
       0.45   10.3   8.9        5.2    6.8   0.1    3.4  3  Sulfotransfer_4  Sulfotransferase domain
       0.56    9.8  14.1        1.9    8.0  14.1    2.1  1  DUF885           Bacterial protein of unknown function (DUF88
       0.79    9.5  18.7          2    8.2   0.2    4.6  5  SKA2             Spindle and kinetochore-associated protein 2
        1.4    9.4  13.1        4.1    7.9   0.4    4.0  3  DUF16            Protein of unknown function DUF16
        1.5    8.1  12.9         63    2.8  12.9    2.2  1  DUF4407          Domain of unknown function (DUF4407)
        1.6    9.3   8.2         27    5.3   0.2    4.0  4  YusW             YusW-like protein
        2.6    7.2  13.1        2.3    7.4   1.3    2.9  4  TMPIT            TMPIT-like protein
        2.9    7.5   5.5        3.8    7.1   1.0    2.6  3  SLATT_4          SMODS and SLOG-associating 2TM effector doma
          3    7.9   9.3         23    5.1   0.5    3.6  4  DUF1664          Protein of unknown function (DUF1664)
        3.3    7.9  16.3        4.9    7.3   9.6    3.3  3  Nmad5            Nucleotide modification associated domain 5
        4.4    7.6   5.1         58    4.0   0.1    4.7  5  DUF3130          Protein of unknown function (DUF3130
        4.6    7.2  38.2       0.14   12.2   5.7    4.2  3  YscO-like        YscO-like protein
          6    4.6  21.8        0.1   10.4  11.9    2.1  2  Nup88            Nuclear pore component
        6.9    6.3  14.8         76    2.9  12.0    2.6  2  SHE3             SWI5-dependent HO expression protein 3
        8.1    7.1  26.0         12    6.6   2.4    4.4  5  HIP1_clath_bdg   Clathrin-binding domain of Huntingtin-intera
        9.6    5.2  12.8        1.8    7.6   0.9    3.8  3  RmuC             RmuC family
         10    6.4  18.0       0.95    9.7   1.1    4.0  5  DUF4375          Domain of unknown function (DUF4375)


Domain annotation for each model (and alignments):
>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   1.5    0.0015      0.93      21      90 ..      38     105 ..      26     117 .. 0.61
   2 !   10.9   2.8   0.00069      0.44      27      91 ..     115     181 ..     110     186 .. 0.80
   3 !   15.0   0.1   3.7e-05     0.024       3      92 ..     183     278 ..     181     294 .. 0.76
   4 ?    2.4   0.0      0.28   1.8e+02      62     116 ..     331     383 ..     297     386 .] 0.76

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0015
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS.-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           OmpH  21 qeqlekkfkklqaeleakekelqklqeelqkkakklekeekeqelqkkeqelqqkqqqkaqelqkkqqel 90 
                                     e++++ ++++ a +++ ++ l++l++ l+k +++   ++  +el ++++++++ +++  ++l+k ++++
  gi|119720588|ref|YP_921083.1|  38 AEEMKRLREEMHAGFAKHGEILERLEKILEKHEEA--LRRHDEELIRLREDMNKGFARHDEQLAKLREDM 105
                                    45555555666666666666666666666544444..345555677777777776777767777766554 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00069
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHTTTS...-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           OmpH  27 kfkklqaeleakekelqklqeelqkkakkl.e.keekeqelqkkeqelqqkqqqkaqelqkkqqell 91 
                                     +++ +++l +++++++kl+e+++k  +   e  ++ e+el k+++++++ ++++ +el + ++++ 
  gi|119720588|ref|YP_921083.1| 115 ASRRHEEQLVKLREDFNKLREDMNKGFARHdEaLKRHEEELVKLREDMNAGFARQDKELTRLREDMN 181
                                    5677899999999999999999987776665577777777999999999999999999999887765 PP

  == domain 3  score: 15.0 bits;  conditional E-value: 3.7e-05
                                    EEE-HHHHHHHS.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS..-HHHHHH.HHHHHHHHHHHHHHH CS
                           OmpH   3 avvdvqkilees.pegkaaqeqlekkfkklqaeleakekelqklqeelqkkakkl.ekeekeqe.lqkkeqelqqkqqqk 79 
                                    ++  ++++++ + +e+k  +e+++k f++ +++l++ e+el kl+e+++k  +   e  ++ +e l+k  +el +++++ 
  gi|119720588|ref|YP_921083.1| 183 GFARHDELFRRHeEEMKGLREDMNKGFARHDEALRRHEEELVKLREDMNKGFARHdEALRRHEEiLEKHSEELAKLRSAM 262
                                    677788899999889*********************************97777664455555557999999998865555 PP

                                    H...HHHHHHHHHHHH CS
                           OmpH  80 a...qelqkkqqellk 92 
                                        +el k     ++
  gi|119720588|ref|YP_921083.1| 263 IagfGELSKFAGMTFE 278
                                    5666666665555444 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.28
                                    HHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEEEE CS
                           OmpH  62 eqelqkkeqelqqkqqqka.qelqkkqqellkpildkinkaikevakekgydlvld 116
                                     +el+k++++ +   ++k+ +e +k    l++p    + + ++++a ekg+ l++ 
  gi|119720588|ref|YP_921083.1| 331 LEELEKLVRKAEL-VKAKYgKEPRKILVILTAP--RDLAEKLEKIAGEKGVELIIG 383
                                    4556666666666.4444456666666667777..8899999**********9986 PP

>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   5.4    0.0061       3.9      47     140 ..      42     135 ..      32     138 .. 0.75
   2 !   14.8   5.9   2.7e-05     0.018      17     126 ..      88     196 ..      78     199 .. 0.93
   3 !   13.7   7.0   5.8e-05     0.037      16     133 ..     137     253 ..     125     263 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0061
                           YkyA  47 de.fdkikklsdealenveeReellekekesieeakeefekikeeieeiedeelkkeaeelieameeryeaydklykaYk 125
                                    ++  +++++  ++  e++e  e++lek +e++ +  ee+  ++e++++       +++ +l e m++ ++ +d+   + +
  gi|119720588|ref|YP_921083.1|  42 KRlREEMHAGFAKHGEILERLEKILEKHEEALRRHDEELIRLREDMNKGF-ARHDEQLAKLREDMNSGFARHDEASRRHE 120
                                    44345555566666677777788888888888888888888888888883.34678******************999999 PP

                           YkyA 126 ealeldkeLYemLkk 140
                                    e l + +e +++L +
  gi|119720588|ref|YP_921083.1| 121 EQLVKLREDFNKLRE 135
                                    999887777777765 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 2.7e-05
                           YkyA  17 EkefeeqqekLtelekkeqelyeeiielgmdefdkikklsdealenveeReellekekesieeakeefekikeeieeied 96 
                                     k+f+   e+L +l ++ +  + +  e++  + ++++kl ++  ++ e+ ++ ++   e++++ +ee+ k++e+++    
  gi|119720588|ref|YP_921083.1|  88 NKGFARHDEQLAKLREDMNSGFARHDEASRRHEEQLVKLREDFNKLREDMNKGFARHDEALKRHEEELVKLREDMNAGF- 166
                                    6899999**********************************************************************94. PP

                           YkyA  97 eelkkeaeelieameeryeaydklykaYke 126
                                      + ke++ l e m+  ++ +d+l+ + +e
  gi|119720588|ref|YP_921083.1| 167 ARQDKELTRLREDMNAGFARHDELFRRHEE 196
                                    44789*******************987766 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 5.8e-05
                           YkyA  16 lEkefeeqqekLtelekkeqelyeeiielgmdefdkikklsdealenveeReellekekesieeakeefekikeeieeie 95 
                                      k+f+   e L++ e++  +l e++++    + ++++ l +++ +      el+   +e ++  +e ++k  +  +e  
  gi|119720588|ref|YP_921083.1| 137 MNKGFARHDEALKRHEEELVKLREDMNAGFARQDKELTRLREDMNAGFARHDELFRRHEEEMKGLREDMNKGFARHDEA- 215
                                    3589999*******************9877777899**********************************999999999. PP

                           YkyA  96 deelkkeaeelieameeryeaydklykaYkealeldke 133
                                        ++e+ +l e m++ ++ +d+ + + +e+le++ e
  gi|119720588|ref|YP_921083.1| 216 LRRHEEELVKLREDMNKGFARHDEALRRHEEILEKHSE 253
                                    556799***************************99865 PP

>> Golgin_A5  Golgin subfamily A member 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   4.1   0.00087      0.56      90     156 ..      36     106 ..      28     111 .. 0.75
   2 !   15.8   8.0   1.1e-05    0.0073      67     156 ..      95     181 ..      92     189 .. 0.94
   3 ?    5.8   3.2     0.013       8.1     103     157 ..     196     250 ..     184     262 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00087
                      Golgin_A5  90 slreqlqeleeqleeerkak....eeveaelerlkeelryleeelvrskatlqsrikdrekeieklrnqlt 156
                                    sl e++++l+e++++  +++    e++e+ le+++e lr+  eel+r ++++++   ++++++ klr+++ 
  gi|119720588|ref|YP_921083.1|  36 SLAEEMKRLREEMHAGFAKHgeilERLEKILEKHEEALRRHDEELIRLREDMNKGFARHDEQLAKLREDMN 106
                                    45555555555555554444111166788889999********************************9876 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 1.1e-05
                      Golgin_A5  67 nqqieqlrtelqdleaqqqaeaeslreqlqeleeqleeerkakeeveaelerlkeelryleeelvrskatlqsrikdrek 146
                                     +q+ +lr +++   a++ + ++  +eql +l+e ++   k +e++++  +r++e l++ eeelv+ ++++++   +++k
  gi|119720588|ref|YP_921083.1|  95 DEQLAKLREDMNSGFARHDEASRRHEEQLVKLREDFN---KLREDMNKGFARHDEALKRHEEELVKLREDMNAGFARQDK 171
                                    57999*************999999************9...8999************************************ PP

                      Golgin_A5 147 eieklrnqlt 156
                                    e+ +lr+++ 
  gi|119720588|ref|YP_921083.1| 172 ELTRLREDMN 181
                                    ******9875 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.013
                      Golgin_A5 103 eeerkakeeveaelerlkeelryleeelvrskatlqsrikdrekeieklrnqltt 157
                                    ee +  +e++++  +r++e lr+ eeelv+ ++++++   ++++ + + ++ l +
  gi|119720588|ref|YP_921083.1| 196 EEMKGLREDMNKGFARHDEALRRHEEELVKLREDMNKGFARHDEALRRHEEILEK 250
                                    3334557777777888888888888888888888777777777777666554444 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7  18.3   1.3e-05    0.0082     237     452 ..      31     247 ..      18     273 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.3e-05
                        DUF3584 237 laaiekvrpeieklqeefeq.leslelrLsllkgelkadeerlaekqeevqeakaelkqqlrtledelkeaidelnqels 315
                                    l+++ + ++e+++l ee+++ ++   + L  l++ l+++ee+l+++ ee     +++++ ++  +++l++ ++ +n+   
  gi|119720588|ref|YP_921083.1|  31 LRRLDSLAEEMKRLREEMHAgFAKHGEILERLEKILEKHEEALRRHDEELIRLREDMNKGFARHDEQLAKLREDMNSGFA 110
                                    55566666666666655544144444455666666666666666666666666666666666666666666666666666 PP

                        DUF3584 316 aakaklaakeselealeeqkkkyedadieklkadldqlpsirseleeleeeldaltekhqdvqekydrrkqkikeeleee 395
                                      +++  + e++l +l e+ +k  ++     + + ++l   ++el +l e+++a   ++ +   ++ ++  +   +  e 
  gi|119720588|ref|YP_921083.1| 111 RHDEASRRHEEQLVKLREDFNKLREDMNKGFARHDEALKRHEEELVKLREDMNAGFARQDKELTRLREDMNAGFARHDEL 190
                                    66666666666666666666666666666666666666666666666666666543333332233333333344444444 PP

                        DUF3584 396 leklkerleaireekdrlkaaieealealesqlrkqleaqkeelneeekelesrlse 452
                                     ++ +e+ + +re  ++  a+++eal   e++l+k +e  ++ ++++ + l+++ + 
  gi|119720588|ref|YP_921083.1| 191 FRRHEEEMKGLREDMNKGFARHDEALRRHEEELVKLREDMNKGFARHDEALRRHEEI 247
                                    455555566666666666666666666666666666666655555555554443333 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   1.6      0.06        38      61     116 ..      33      88 ..      27      91 .. 0.67
   2 !   14.2   5.1   5.5e-05     0.035      18     115 ..      92     190 ..      85     192 .. 0.87
   3 !   10.0   2.1    0.0011      0.69      12      61 ..     211     260 ..     202     262 .. 0.91
   4 ?    2.5   0.2      0.21   1.4e+02      48      72 ..     323     347 ..     322     351 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.06
                     TPR_MLP1_2  61 alreelnelkaeiaelkaeaesakaeleeseesweeqkeelekelselekriedln 116
                                    +l + ++e+k  ++e+ a   +  + le+ e+ +e+++e+l+++ +el + +ed+n
  gi|119720588|ref|YP_921083.1|  33 RLDSLAEEMKRLREEMHAGFAKHGEILERLEKILEKHEEALRRHDEELIRLREDMN 88 
                                    45555666666666677777777777777777777777777777777777777766 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 5.5e-05
                     TPR_MLP1_2  18 eeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqa.lreelnelkaeiaelkaeaesakaeleeseeswee 96 
                                    ++++++l+kl+ed+++  ++  ea ++ e++lvk  ed ++l++ +++ +++  + ++  ++e+ ++++++++  +  ++
  gi|119720588|ref|YP_921083.1|  92 ARHDEQLAKLREDMNSGFARHDEASRRHEEQLVKLREDFNKLREdMNKGFARHDEALKRHEEELVKLREDMNAGFARQDK 171
                                    7899*************************************975489999999999999999999999999999999999 PP

                     TPR_MLP1_2  97 qkeelekelselekriedl 115
                                    + ++l+++++   +r ++l
  gi|119720588|ref|YP_921083.1| 172 ELTRLREDMNAGFARHDEL 190
                                    9999998888777777776 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.0011
                     TPR_MLP1_2  12 slkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqa 61 
                                    + +e   ++e++l kl+ed++k  ++  ea ++ e+ l kh+e++ +l++
  gi|119720588|ref|YP_921083.1| 211 RHDEALRRHEEELVKLREDMNKGFARHDEALRRHEEILEKHSEELAKLRS 260
                                    66788999************************************999975 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.21
                     TPR_MLP1_2  48 elvkhaedvkelqalreelnelkae 72 
                                    e++ hae ++el++l  +++ +ka+
  gi|119720588|ref|YP_921083.1| 323 EVTAHAESLEELEKLVRKAELVKAK 347
                                    8999*********998888888776 PP

>> DUF4709  Domain of unknown function (DUF4709)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.4      0.21   1.3e+02      63      97 ..      42      76 ..      28      96 .. 0.85
   2 ?    1.8   0.0      0.44   2.8e+02       4      31 ..     101     128 ..      98     134 .. 0.84
   3 ?    7.2   0.1    0.0094         6       4      51 ..     133     181 ..     130     199 .. 0.84
   4 ?    5.0   0.0     0.044        28       5      33 ..     202     230 ..     199     266 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.21
                        DUF4709 63 eklkeealelytrlndklkeleklykekvevvRks 97
                                   ++l+ee  + + +  + l++lek+ ++++e++R+ 
  gi|119720588|ref|YP_921083.1| 42 KRLREEMHAGFAKHGEILERLEKILEKHEEALRRH 76
                                   57888888888888889999999999999999875 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.44
                        DUF4709   4 isddlkvGffatDhatQTdvsEilelke 31 
                                    + +d++ Gf ++D+a+  +++ +++l+e
  gi|119720588|ref|YP_921083.1| 101 LREDMNSGFARHDEASRRHEEQLVKLRE 128
                                    6789999999999999999999998876 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0094
                        DUF4709   4 isddlkvGffatDhatQTdvsEilelke.ltevtqkLvkevkslkrdfe 51 
                                    + +d++ Gf ++D+a   +++E+++l+e + +   +  ke+++l++d++
  gi|119720588|ref|YP_921083.1| 133 LREDMNKGFARHDEALKRHEEELVKLREdMNAGFARQDKELTRLREDMN 181
                                    678999********************96466677777778888887765 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.044
                        DUF4709   5 sddlkvGffatDhatQTdvsEilelkelt 33 
                                     +d++ Gf ++D+a   +++E+++l+e +
  gi|119720588|ref|YP_921083.1| 202 REDMNKGFARHDEALRRHEEELVKLREDM 230
                                    589999******************98744 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.4     0.072        46      30      72 ..      32      74 ..      29      82 .. 0.81
   2 ?    5.4   1.1     0.035        23      25      70 ..      66     111 ..      48     122 .. 0.83
   3 ?    5.3   1.4     0.036        23      15      69 ..      81     135 ..      76     139 .. 0.82
   4 ?    3.8   0.8      0.11        71      30      65 ..     128     163 ..     117     168 .. 0.70
   5 ?   11.5   0.6   0.00042      0.27      19      69 ..     160     210 ..     153     214 .. 0.88
   6 ?    5.3   0.8     0.038        24      25      67 ..     216     258 ..     213     263 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.072
                           KxDL 30 reLlelnalsqerlaklrarfkqgtkllkevkkdLesifkkir 72
                                   r+L  l +++++  ++++a f+++ + l ++ k Le+  + +r
  gi|119720588|ref|YP_921083.1| 32 RRLDSLAEEMKRLREEMHAGFAKHGEILERLEKILEKHEEALR 74
                                   5688888888888899999999999999999998888776665 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.035
                           KxDL  25 lnkknreLlelnalsqerlaklrarfkqgtkllkevkkdLesifkk 70 
                                    l+k ++ L +  +++ +  +++++ f+++ + l ++++d++s f +
  gi|119720588|ref|YP_921083.1|  66 LEKHEEALRRHDEELIRLREDMNKGFARHDEQLAKLREDMNSGFAR 111
                                    6777888888888888888999999999999999999999987765 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.036
                           KxDL  15 lalQaqtsgrlnkknreLlelnalsqerlaklrarfkqgtkllkevkkdLesifk 69 
                                    ++l +++ + +    ++L +l++ +++ +a++ +  +++ + l ++++d +++++
  gi|119720588|ref|YP_921083.1|  81 IRLREDMNKGFARHDEQLAKLREDMNSGFARHDEASRRHEEQLVKLREDFNKLRE 135
                                    5566677777888899999999999999999999999999999999999888766 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.11
                           KxDL  30 reLlelnalsqerlaklrarfkqgtkllkevkkdLe 65 
                                    +   +l++ +++ +a++ + +k++ + l ++++d++
  gi|119720588|ref|YP_921083.1| 128 EDFNKLREDMNKGFARHDEALKRHEEELVKLREDMN 163
                                    555667777777788888888888888888887776 PP

  == domain 5  score: 11.5 bits;  conditional E-value: 0.00042
                           KxDL  19 aqtsgrlnkknreLlelnalsqerlaklrarfkqgtkllkevkkdLesifk 69 
                                    +++ + +  + +eL++l++ +++ +a++ + f+++ + +k +++d+++ f 
  gi|119720588|ref|YP_921083.1| 160 EDMNAGFARQDKELTRLREDMNAGFARHDELFRRHEEEMKGLREDMNKGFA 210
                                    56777888999***********************************98775 PP

  == domain 6  score: 5.3 bits;  conditional E-value: 0.038
                           KxDL  25 lnkknreLlelnalsqerlaklrarfkqgtkllkevkkdLesi 67 
                                    l   ++eL +l++ +++ +a++ + ++++ + l +  ++L ++
  gi|119720588|ref|YP_921083.1| 216 LRRHEEELVKLREDMNKGFARHDEALRRHEEILEKHSEELAKL 258
                                    6678899**********************99999999888776 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   9.0    0.0011      0.71     147     256 ..      35     155 ..      20     159 .. 0.64
   2 ?    8.9   8.0    0.0016         1     156     256 ..     133     255 ..     126     276 .. 0.48

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0011
                   Exonuc_VII_L 147 eqleelerrlekaikrlleekkqrleklasrlkspeellerkrqrldeleerleralkkqlkkkrerleelkerlk.... 222
                                    ++l+e ++rl+++++  + ++ + le+l++ l++ ee l+r+ ++l +l+e++++     ++++ e+l +l+e ++    
  gi|119720588|ref|YP_921083.1|  35 DSLAEEMKRLREEMHAGFAKHGEILERLEKILEKHEEALRRHDEELIRLREDMNK----GFARHDEQLAKLREDMNsgfa 110
                                    5677778899999999999999999999999999999999999998887777777....555666666666666633555 PP

                   Exonuc_VII_L 223 ...ekleekkerlkklkerle........lleekkerleeleekl 256
                                       e  ++++e+l kl+e ++         +++++e+l++ ee+l
  gi|119720588|ref|YP_921083.1| 111 rhdEASRRHEEQLVKLREDFNklredmnkGFARHDEALKRHEEEL 155
                                    555444444455544444444322222243555555555555555 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0016
                   Exonuc_VII_L 156 lekaikrlleekkqrleklasrl....kspeellerkrqrldeleerleralkkq...lkkkrerleelkerl.k..... 222
                                    l++ +++ + ++ + l++ +++l    ++ ++ ++r+ ++l++l+e++++  +++   +++++e+++ l+e + k     
  gi|119720588|ref|YP_921083.1| 133 LREDMNKGFARHDEALKRHEEELvklrEDMNAGFARQDKELTRLREDMNAGFARHdelFRRHEEEMKGLREDMnKgfarh 212
                                    55555555555555555555555433224444555555555555555555444444445555555555555553355555 PP

                   Exonuc_VII_L 223 .ekleekkerlkklkerle........lleekkerleeleekl 256
                                     e l++++e+l kl+e ++         l++++e le+ +e+l
  gi|119720588|ref|YP_921083.1| 213 dEALRRHEEELVKLREDMNkgfarhdeALRRHEEILEKHSEEL 255
                                    4445555555555544444433332222333333333333333 PP

>> Bacillus_HBL  Bacillus haemolytic enterotoxin (HBL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.25   1.6e+02     122     175 ..      35      88 ..      27      90 .. 0.78
   2 ?    1.2   0.0      0.44   2.8e+02     105     148 ..      57     100 ..      41     108 .. 0.79
   3 ?    2.4   0.2      0.19   1.2e+02     101     168 ..      96     163 ..      91     172 .. 0.78
   4 ?    5.7   0.0     0.018        12     101     166 ..     196     261 ..     191     268 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.25
                   Bacillus_HBL 122 kqlikeLkklklklakdsknFktdvdeltsilagdsgvisqlqneiedlqgkik 175
                                    ++l++e+k+l++++ +  ++  + ++ l++il+  +  +    +e+ +l++ ++
  gi|119720588|ref|YP_921083.1|  35 DSLAEEMKRLREEMHAGFAKHGEILERLEKILEKHEEALRRHDEELIRLREDMN 88 
                                    567788888888888888888888888888888888888888777777777766 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.44
                   Bacillus_HBL 105 ellekLqeeiqqnqkevkqlikeLkklklklakdsknFktdvde 148
                                    e le+L++ + + +++ ++  +eL +l+++++k  +  ++++++
  gi|119720588|ref|YP_921083.1|  57 EILERLEKILEKHEEALRRHDEELIRLREDMNKGFARHDEQLAK 100
                                    67899999999999999999999999999999876666666655 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.19
                   Bacillus_HBL 101 aellellekLqeeiqqnqkevkqlikeLkklklklakdsknFktdvdeltsilagdsgvisqlqneie 168
                                    ++l +l e+++++     +++++  ++L kl+++++k  ++ ++  +  ++ l+  + ++ +l+++++
  gi|119720588|ref|YP_921083.1|  96 EQLAKLREDMNSGFARHDEASRRHEEQLVKLREDFNKLREDMNKGFARHDEALKRHEEELVKLREDMN 163
                                    55666667777788888888888888888888888888888888888888888888888888887765 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.018
                   Bacillus_HBL 101 aellellekLqeeiqqnqkevkqlikeLkklklklakdsknFktdvdeltsilagdsgvisqlqne 166
                                    +e++ l e+++++     ++ ++  +eL kl+++++k  +  ++++   ++il+  s ++++l+ +
  gi|119720588|ref|YP_921083.1| 196 EEMKGLREDMNKGFARHDEALRRHEEELVKLREDMNKGFARHDEALRRHEEILEKHSEELAKLRSA 261
                                    566667789999999999******************************************999865 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       7.9   5.1e+03     110     125 ..      33      48 ..      16      54 .. 0.73
   2 ?    8.9   1.5    0.0026       1.7      32     120 ..      54     139 ..      40     140 .. 0.87
   3 ?    6.5   0.2     0.013       8.6      30     124 ..     166     261 ..     157     264 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 7.9
                                    HHHHHHHHHHHHHHHH CS
                      Fib_alpha 110 vlesneqkiqkLeqdi 125
                                     l+s+ +++++L++++
  gi|119720588|ref|YP_921083.1|  33 RLDSLAEEMKRLREEM 48 
                                    4677777888877654 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0026
                                    CCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHH CS
                      Fib_alpha  32 dvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnvl 111
                                    +  + le+le+ le++++  +  +e   ++++ +++  + ++   + + k+++++++  +r +e   ++e+++ +L++ +
  gi|119720588|ref|YP_921083.1|  54 KHGEILERLEKILEKHEEALRRHDEELIRLREDMNKGFARHD---EQLAKLREDMNSGFARHDEASRRHEEQLVKLREDF 130
                                    555678999999999999999999999999999988887765...7999******************************* PP

                                    HHHHHHHHH CS
                      Fib_alpha 112 esneqkiqk 120
                                    ++++++++k
  gi|119720588|ref|YP_921083.1| 131 NKLREDMNK 139
                                    *****9975 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.013
                                    CCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHH CS
                      Fib_alpha  30 ekdvkkdlekleneleeisnstkeaeelvkeikdslrekqksk.kdndnvikksskeleeeilrlketidaqesnirvLq 108
                                        +k+l++l+++++    ++ e ++  +e ++ lre+ ++  + +d+++++ ++el +  +++++   ++ + +r   
  gi|119720588|ref|YP_921083.1| 166 FARQDKELTRLREDMNAGFARHDELFRRHEEEMKGLREDMNKGfARHDEALRRHEEELVKLREDMNKGFARHDEALRRHE 245
                                    555677777888887777777777666666555555555544404458999999999999999***************** PP

                                    HHHHHHHHHHHHHHHH CS
                      Fib_alpha 109 nvlesneqkiqkLeqd 124
                                    ++le+ +++++kL+++
  gi|119720588|ref|YP_921083.1| 246 EILEKHSEELAKLRSA 261
                                    ***********99986 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1  13.0   0.00083      0.53     136     244 ..      58     163 ..      55     179 .. 0.82
   2 ?    6.0   8.3    0.0071       4.5     153     261 ..     143     252 ..     138     289 .. 0.53

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00083
                           Spc7 136 llegLkegleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaei 215
                                     le L++ le++ e+l++ +e+L + +e +++   + +e+ a+l+e +++  ++++e +   +e+L +lre++++l +++
  gi|119720588|ref|YP_921083.1|  58 ILERLEKILEKHEEALRRHDEELIRLREDMNKGFARHDEQLAKLREDMNSGFARHDEASRRHEEQLVKLREDFNKLREDM 137
                                    6899**************************************************************************** PP

                           Spc7 216 eekkkelaelqeqleeleekieelkeqks 244
                                    +   k  a+  e l++ ee++ +l+e ++
  gi|119720588|ref|YP_921083.1| 138 N---KGFARHDEALKRHEEELVKLREDMN 163
                                    9...5666666666666666555554443 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0071
                           Spc7 153 edkelLekqeeeldellpeleeekaeleeeleklqe.......aaeelesidkeeLeelreelae....lkaeieekkke 221
                                    + +e L+++eeel +l +++++ +a+  +el++l+e       +++el    +ee++ lre++++    +++ ++++++e
  gi|119720588|ref|YP_921083.1| 143 RHDEALKRHEEELVKLREDMNAGFARQDKELTRLREdmnagfaRHDELFRRHEEEMKGLREDMNKgfarHDEALRRHEEE 222
                                    55677888888888888888888888888888888843333334444444444444444443322111123333333333 PP

                           Spc7 222 laelqeqleeleekieelkeqkseleeeiaeaervleeck 261
                                    l +l+e++          ++  +++ e+++++e++le++ 
  gi|119720588|ref|YP_921083.1| 223 LVKLREDM----------NKGFARHDEALRRHEEILEKHS 252
                                    33333333..........3333444444444444444333 PP

>> Sulfotransfer_4  Sulfotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1    0.0081       5.2     122     174 ..      27      76 ..      18      93 .. 0.86
   2 ?    2.6   1.1      0.16     1e+02     112     177 ..     131     197 ..      76     211 .. 0.68
   3 ?    5.1   0.6     0.028        18     110     173 ..     197     257 ..     186     262 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0081
                Sulfotransfer_4 122 llalldpllellaklvellralvrrlfgagsdaedeeaakeayeehnervrev 174
                                    +l+ l++l++l++++++l +++  ++ ++g   e  e++++++e+h+e +r++
  gi|119720588|ref|YP_921083.1|  27 VLEVLRRLDSLAEEMKRLREEMHAGFAKHG---EILERLEKILEKHEEALRRH 76 
                                    577788899999**********99999986...999***********999986 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.16
                Sulfotransfer_4 112 lalrsetlsrllalldpllellaklvellralvrrlfgag.sdaedeeaakeayeehnervrevvpa 177
                                    ++lr++  + + ++ + l+++ ++lv+l +++  ++ +++   ++ +e + + + +h e  r++ ++
  gi|119720588|ref|YP_921083.1| 131 NKLREDMNKGFARHDEALKRHEEELVKLREDMNAGFARQDkELTRLREDMNAGFARHDELFRRHEEE 197
                                    4445555555555555666677777777777766666665445677777777777777776666554 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.028
                Sulfotransfer_4 110 tllalrsetlsrllalldpllellaklvellralvrrlfgagsdaedeeaakeayeehnervre 173
                                     ++ lr++  + + ++ + l+++ ++lv+l +++ +++ +++   e  ++++e++e+h+e++ +
  gi|119720588|ref|YP_921083.1| 197 EMKGLREDMNKGFARHDEALRRHEEELVKLREDMNKGFARHD---EALRRHEEILEKHSEELAK 257
                                    555666666677777777788899999999999988888885...999**********999866 PP

>> DUF885  Bacterial protein of unknown function (DUF885)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0  14.1     0.003       1.9      77     309 ..      34     271 ..       5     371 .. 0.57

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.003
                                    T-CCCCHHHHHHHHHCGTTSSCHHHHHHHHHHCCCHHHHH...HHHHHHHHHHHHTT.-S-HHHHHHHHHHHHHHHGTSS CS
                         DUF885  77 lralagpvqqlpsllseepfateedleaylarlaavpaal...dqaranlregaaaglvpprrqvekvieqlrgllagaa 153
                                    l +la  +  l++ + + +++  e le++ + l++  +al   d+ + +lre++++g  ++++q+ k  e++++ +a  +
  gi|119720588|ref|YP_921083.1|  34 LDSLAEEMKRLREEMHAGFAKHGEILERLEKILEKHEEALrrhDEELIRLREDMNKGFARHDEQLAKLREDMNSGFARHD 113
                                    44444445555555555555555555555555555555553336677778888888888888888888888888777544 PP

                                    HHCCCHH.CCCCCC....HHHHHHHHHH.HHHHHHHHHHHHHHHH...HCC....HHHS-BSS..HHHHHHHHHHHHHSS CS
                         DUF885 154 aeasalvaplaeleaek.ealraeleaalaeavkpayaeladfle...eel....lpaarkdapdGeelYarllrsfttt 225
                                    +++           +e+  +lr++++++ +e + + +a++ + l+   eel    +        d  + +ar+ ++ t  
  gi|119720588|ref|YP_921083.1| 114 EASRR--------HEEQlVKLREDFNKL-REDMNKGFARHDEALKrheEELvklrE--------DMNAGFARQDKELTRL 176
                                    44333........222224566666666.666666666666666533112211120........2233333333333333 PP

                                    SS-.......HHHHHHHHHHHHHHHHHHHHHHHHHH.HH-.HHHHHHHHHC..H-GGGEEESHHHHH..HHHHHHHHHHH CS
                         DUF885 226 dlt.......peeihelglaelariraemeaiakev.gfkgdlaevlaalr..tdprfyleetdagr..eellaaaraai 293
                                      +        +e+ ++ ++e++ +r+ m +  ++  +     +e l +lr   ++ f+ + ++a+r  ee+l++  +++
  gi|119720588|ref|YP_921083.1| 177 REDmnagfarHDELFRRHEEEMKGLREDMNKGFARHdEALRRHEEELVKLRedMNKGFA-RHDEALRrhEEILEKHSEEL 255
                                    33300111113334444444444444444333333322211233333333322111221.12222223367777777777 PP

                                    HHHCCHHHCCT---TT CS
                         DUF885 294 aeldaklpehfgllpk 309
                                    a+l+ ++ + fg+l k
  gi|119720588|ref|YP_921083.1| 256 AKLRSAMIAGFGELSK 271
                                    7777777777766665 PP

>> SKA2  Spindle and kinetochore-associated protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.2    0.0031         2      26      87 ..      12      74 ..       9      80 .. 0.77
   2 ?    6.0   2.2     0.015       9.8      37      94 ..     115     181 ..      85     197 .. 0.70
   3 ?    1.4   0.1      0.41   2.6e+02      45      80 ..     171     206 ..     152     212 .. 0.83
   4 ?    4.1   0.4      0.06        38      33      80 ..     216     263 ..     200     272 .. 0.81
   5 ?   -1.4   0.1         3   1.9e+03      38      75 ..     332     369 ..     323     375 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0031
                           SKA2 26 ekefqqsypdna.eNpvkLlerlkkvkeelqaLkeqceellaekkelidkirttlvanrellq 87
                                   e++++  y+  +   ++++l+rl  + ee++ L+e++++  a+  e+ +++++ l +  e l+
  gi|119720588|ref|YP_921083.1| 12 EEDVEFRYAVAGyLGVLEVLRRLDSLAEEMKRLREEMHAGFAKHGEILERLEKILEKHEEALR 74
                                   555555555555667889999999999999999999999999999988888888887777765 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.015
                           SKA2  37 a.....eNpvkLlerlkkvkeelqaLkeqceellaekk....elidkirttlvanrellqqLqasae 94 
                                    a     e +vkL e+++k++e++++  ++++e l++ +    +l + +++ ++++ + l++L+++++
  gi|119720588|ref|YP_921083.1| 115 AsrrheEQLVKLREDFNKLREDMNKGFARHDEALKRHEeelvKLREDMNAGFARQDKELTRLREDMN 181
                                    1335558999999999999999999999999999988844444556666666677777777777765 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.41
                           SKA2  45 erlkkvkeelqaLkeqceellaekkelidkirttlv 80 
                                    ++l++++e+++a  ++++el  + +e ++ +r  ++
  gi|119720588|ref|YP_921083.1| 171 KELTRLREDMNAGFARHDELFRRHEEEMKGLREDMN 206
                                    578889999999999999999999988888888775 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.06
                           SKA2  33 ypdnaeNpvkLlerlkkvkeelqaLkeqceellaekkelidkirttlv 80 
                                    +++++e++vkL e+++k  +++ +  +++ee+l++  e   k+r+ ++
  gi|119720588|ref|YP_921083.1| 216 LRRHEEELVKLREDMNKGFARHDEALRRHEEILEKHSEELAKLRSAMI 263
                                    344448999999999999999999999999999999999999888876 PP

  == domain 5  score: -1.4 bits;  conditional E-value: 3
                           SKA2  38 eNpvkLlerlkkvkeelqaLkeqceellaekkelidki 75 
                                    e++ kL+++ + vk+++ +  +++  +l++ ++l++k+
  gi|119720588|ref|YP_921083.1| 332 EELEKLVRKAELVKAKYGKEPRKILVILTAPRDLAEKL 369
                                    56667777777777777666666666666666666654 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.4    0.0064       4.1      38      93 ..      47     106 ..      32     115 .. 0.74
   2 ?    5.6   0.9     0.033        21      40      78 ..     120     162 ..      89     190 .. 0.47
   3 ?    2.9   2.8      0.24   1.5e+02      25      73 ..     130     182 ..     126     272 .. 0.56

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0064
                                    HHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH...........HHHHHHHHHH CS
                          DUF16  38 kieakvdklgeqinkleqkvekqgekikelkveqkaqgeeln....kvdetleliletLq 93 
                                    ++ a  +k+ge +++le++ ek +e +++  +e    +e++n    + de l  + e ++
  gi|119720588|ref|YP_921083.1|  47 EMHAGFAKHGEILERLEKILEKHEEALRRHDEELIRLREDMNkgfaRHDEQLAKLREDMN 106
                                    34455569*******************************999777766666666655555 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.033
                                    HHHHH...HHHHHHHHHHHH....HHHHHHHHHHHHHHHHH.. CS
                          DUF16  40 eakvdklgeqinkleqkvek....qgekikelkveqkaqgeel 78 
                                    e+++ kl e +nkl + ++k     +e +k+ ++e  + +e++
  gi|119720588|ref|YP_921083.1| 120 EEQLVKLREDFNKLREDMNKgfarHDEALKRHEEELVKLREDM 162
                                    3333333333333333332211112333333333333333333 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.24
                                    HHHB-..BHHHHHHHHHHHH...HHHHHHHHHHH....HHHHHHHHHHHHHHH CS
                          DUF16  25 lnefkdsnkqrLkkieakvdklgeqinkleqkve....kqgekikelkveqka 73 
                                    +n+ +++ ++ + + ++ ++ ++e++ kl + ++    +q++++++l+++++a
  gi|119720588|ref|YP_921083.1| 130 FNKLREDMNKGFARHDEALKRHEEELVKLREDMNagfaRQDKELTRLREDMNA 182
                                    66666665555555555555555555555554431111344444444444433 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8  12.9     0.099        63     153     238 ..      91     174 ..      29     266 .. 0.47

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.099
                        DUF4407 153 earldalraeaqkeldgtkgtgttgvaGkgpaakekkaqldaaqaelaelkakld.....atarlaalraelaeleaera 227
                                     ar d++ a++++ ++       +g a+  +a ++ ++ql +++++ ++l+++++      +++l+++++el +l+++++
  gi|119720588|ref|YP_921083.1|  91 FARHDEQLAKLREDMN-------SGFARHDEASRRHEEQLVKLREDFNKLREDMNkgfarHDEALKRHEEELVKLREDMN 163
                                    3333333333332222.......224444455555555555555555555555444444433333333333333333333 PP

                        DUF4407 228 keraasqaaaa 238
                                    +  a+++++  
  gi|119720588|ref|YP_921083.1| 164 AGFARQDKELT 174
                                    33333333221 PP

>> YusW  YusW-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.2     0.043        27      23      66 ..      94     137 ..      91     142 .. 0.86
   2 ?    1.9   0.1      0.51   3.2e+02      29      56 ..     132     159 ..     124     165 .. 0.84
   3 ?    1.6   0.1      0.61   3.9e+02      25      56 ..     197     227 ..     187     231 .. 0.76
   4 ?    5.0   0.2     0.055        35      25      54 ..     221     250 ..     215     265 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.043
                           YusW  23 kdeteakiedgankekleGdeAleelealLseLsvdsetsedev 66 
                                     de+ ak+++++n    ++deA ++ e+ L +L  d ++  +++
  gi|119720588|ref|YP_921083.1|  94 HDEQLAKLREDMNSGFARHDEASRRHEEQLVKLREDFNKLREDM 137
                                    57889*************************99988777766665 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.51
                           YusW  29 kiedgankekleGdeAleelealLseLs 56 
                                    k+++++nk   ++deAl++ e+ L +L 
  gi|119720588|ref|YP_921083.1| 132 KLREDMNKGFARHDEALKRHEEELVKLR 159
                                    677999*************999998886 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.61
                           YusW  25 eteakiedgankekleGdeAleelealLseLs 56 
                                    e++  +++++nk   ++deAl++ e+ L +L 
  gi|119720588|ref|YP_921083.1| 197 EMKG-LREDMNKGFARHDEALRRHEEELVKLR 227
                                    3333.4489*************9999888775 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.055
                           YusW  25 eteakiedgankekleGdeAleelealLse 54 
                                    e+  k+++++nk   ++deAl++ e++L++
  gi|119720588|ref|YP_921083.1| 221 EELVKLREDMNKGFARHDEALRRHEEILEK 250
                                    45678889*******************987 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   2.0      0.03        20       5      86 ..      35     120 ..      31     127 .. 0.48
   2 ?    4.1   4.7     0.036        23      21      82 ..      73     137 ..      53     192 .. 0.55
   3 ?    7.4   1.3    0.0036       2.3       2      87 ..     128     221 ..     127     229 .. 0.68
   4 ?    5.0   1.0     0.018        12       3      75 ..     172     255 ..     170     269 .. 0.64

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.03
                          TMPIT   5 eelekefkeleeta....keykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkk 80 
                                    ++l++e+k+l+e+      +  + le+l+k  +k  ++++++ ++l +l+++++k  ++ +e+ ++  e++++ +++ ++
  gi|119720588|ref|YP_921083.1|  35 DSLAEEMKRLREEMhagfAKHGEILERLEKILEKHEEALRRHDEELIRLREDMNKGFARHDEQLAKLREDMNSGFARHDE 114
                                    55666666665544111122233344444444445555555555555555555555555445555555555555555555 PP

                          TMPIT  81 vlkeve 86 
                                      ++ e
  gi|119720588|ref|YP_921083.1| 115 ASRRHE 120
                                    555555 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.036
                          TMPIT  21 ykqkleelsklqskcskeikkqkkrlkelksslkklkksvk...eeeeeeveelkeelkerkkvl 82 
                                    ++++ eel +l +++ k  +++ ++l +l++++++  ++ +   +++ee++ +l+e++++ ++ +
  gi|119720588|ref|YP_921083.1|  73 LRRHDEELIRLREDMNKGFARHDEQLAKLREDMNSGFARHDeasRRHEEQLVKLREDFNKLREDM 137
                                    44455566666666666666666666666666655444433122333444444444444333322 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0036
                          TMPIT   2 eeweelekefkeleeta.keykqkleelsklqskcskeikkqkkrlkelksslkklkksvk.......eeeeeeveelke 73 
                                    e++++l++++++  +++ + +k++ eel kl +++    ++q k+l++l+++++   ++ +       ee +   e++++
  gi|119720588|ref|YP_921083.1| 128 EDFNKLREDMNKGFARHdEALKRHEEELVKLREDMNAGFARQDKELTRLREDMNAGFARHDelfrrheEEMKGLREDMNK 207
                                    567778888776544442778888999************************99987666555664333333444455555 PP

                          TMPIT  74 elkerkkvlkeves 87 
                                     +++ ++ l++ e+
  gi|119720588|ref|YP_921083.1| 208 GFARHDEALRRHEE 221
                                    55555555555555 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.018
                          TMPIT   3 eweelekefkeleeta.keykqkleelsklqskcskeikkqkkrlkelksslkklkksvk..........eeeeeeveel 71 
                                    e+++l++++++  +++ + ++++ ee++ l +++ k  +++ + l++ +++l kl+++++          +++ee++e+ 
  gi|119720588|ref|YP_921083.1| 172 ELTRLREDMNAGFARHdELFRRHEEEMKGLREDMNKGFARHDEALRRHEEELVKLREDMNkgfarhdealRRHEEILEKH 251
                                    66667777665444442667788888999999999999999999999999999999887656644433333333333333 PP

                          TMPIT  72 keel 75 
                                    +eel
  gi|119720588|ref|YP_921083.1| 252 SEEL 255
                                    3333 PP

>> SLATT_4  SMODS and SLOG-associating 2TM effector domain family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   1.0    0.0059       3.8     103     159 ..      98     154 ..      61     160 .. 0.76
   2 ?    1.0   0.1      0.46     3e+02     119     161 ..     182     224 ..     173     228 .. 0.84
   3 ?   -0.2   0.1         1   6.7e+02     100     132 ..     220     252 ..     211     257 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0059
                        SLATT_4 103 ylsLltdlksgalsleearkkrDeLqeelsevYsgaprTtskaYkkAqkaLkkneel 159
                                    +  L  d++sg   ++ea ++ +e + +l+e +++  +  +k +++ ++aLk +ee 
  gi|119720588|ref|YP_921083.1|  98 LAKLREDMNSGFARHDEASRRHEEQLVKLREDFNKLREDMNKGFARHDEALKRHEEE 154
                                    555666777777777777777777777777777777777777777777777777765 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.46
                        SLATT_4 119 earkkrDeLqeelsevYsgaprTtskaYkkAqkaLkkneeltf 161
                                       ++ DeL ++ +e  +g  +  +k +++ ++aL+ +ee   
  gi|119720588|ref|YP_921083.1| 182 AGFARHDELFRRHEEEMKGLREDMNKGFARHDEALRRHEEELV 224
                                    5567899999999999999999**************9999765 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 1
                        SLATT_4 100 RekylsLltdlksgalsleearkkrDeLqeels 132
                                     e+++ L  d+++g   ++ea+++ +e +e+ s
  gi|119720588|ref|YP_921083.1| 220 EEELVKLREDMNKGFARHDEALRRHEEILEKHS 252
                                    578888888999999999998888888877765 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.5     0.035        23      44      97 ..      35      88 ..      26     104 .. 0.55
   2 ?    2.6   0.2       0.2   1.3e+02      64     105 ..      98     139 ..      85     150 .. 0.68
   3 ?    1.2   0.3      0.56   3.6e+02      86     105 ..     120     139 ..     111     196 .. 0.62
   4 ?    4.2   0.2     0.063        41      36      95 ..     202     261 ..     193     274 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.035
                        DUF1664 44 esvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredls 97
                                   +s++++++++ e+++a   +  + ++r++k l++ +e+ +  +ee+ ++red++
  gi|119720588|ref|YP_921083.1| 35 DSLAEEMKRLREEMHAGFAKHGEILERLEKILEKHEEALRRHDEELIRLREDMN 88
                                   344444444444444444444455555555555555555555555555555543 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.2
                        DUF1664  64 Lssridrvdkkldeqkeiskeikeevtevredlseigedves 105
                                    L++  + +++      e+s+  +e++ ++red ++++ed+++
  gi|119720588|ref|YP_921083.1|  98 LAKLREDMNSGFARHDEASRRHEEQLVKLREDFNKLREDMNK 139
                                    444445555556666677777778888888888888877764 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.56
                        DUF1664  86 keevtevredlseigedves 105
                                    +e++ ++red ++++ed+++
  gi|119720588|ref|YP_921083.1| 120 EEQLVKLREDFNKLREDMNK 139
                                    45555555555555555443 PP

  == domain 4  score: 4.2 bits;  conditional E-value: 0.063
                        DUF1664  36 krslsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevred 95 
                                    +  +++  ++  + l +  e+l + ++++++  +r d+ l   +ei ++ +ee++++r+ 
  gi|119720588|ref|YP_921083.1| 202 REDMNKGFARHDEALRRHEEELVKLREDMNKGFARHDEALRRHEEILEKHSEELAKLRSA 261
                                    5667777778888899999************************************99976 PP

>> Nmad5  Nucleotide modification associated domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.6      0.56   3.6e+02      44      76 ..      63      96 ..      38     117 .. 0.61
   2 ?    7.3   9.6    0.0077       4.9      18     149 ..     113     259 ..      99     262 .. 0.63
   3 ?    6.0   2.2     0.019        12      24      77 ..     186     249 ..     180     349 .. 0.64

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.56
                          Nmad5 44 lg.gkkteaalreiikeieklqsklpkeglstnk 76
                                    +  +k e+alr++ +e+  l +++ k++++ ++
  gi|119720588|ref|YP_921083.1| 63 EKiLEKHEEALRRHDEELIRLREDMNKGFARHDE 96
                                   3333456677777777777777777777766554 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0077
                          Nmad5  18 khgiaekekalrkeradlaeevrldalg.gkkteaalreiikeieklqsklpkeglstnk.pkstgsvidvnlaGa.... 91 
                                    +++ + +e++l+k r+d+  ++r d  +   + ++al+++ +e+ kl +++ +++++++k  ++ ++++++ +a +    
  gi|119720588|ref|YP_921083.1| 113 DEASRRHEEQLVKLREDFN-KLREDMNKgFARHDEALKRHEEELVKLREDMNAGFARQDKeLTRLREDMNAGFA-Rhdel 190
                                    5566778999999999996.678888876899***************************988888888888888.32455 PP

                          Nmad5  92 ..rvelyfng.........kkletvvlasvdeiaketkslp........kvvleadnplvkrfdelekaqeelrekr 149
                                      r+e  ++g                  + de  + ++++         k +   d++l++  + lek  eel++ r
  gi|119720588|ref|YP_921083.1| 191 frRHEEEMKGlredmnkgfA--------RHDEALRRHEEELvklredmnKGFARHDEALRRHEEILEKHSEELAKLR 259
                                    55445555554333332221........2222222222222222222323344445555555555566666666555 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.019
                          Nmad5  24 kekalrkeradlaeevrldalg.gkkteaalreiikeieklqsklpkeglstnk.........p 77 
                                    +  +l+++ ++ ++ +r d  +   + ++alr++ +e+ kl +++ k++++ ++          
  gi|119720588|ref|YP_921083.1| 186 RHDELFRRHEEEMKGLREDMNKgFARHDEALRRHEEELVKLREDMNKGFARHDEalrrheeilE 249
                                    4555666666666666666666566777777777777777777777777766664333333331 PP

>> DUF3130  Protein of unknown function (DUF3130
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       2.7   1.7e+03      72      85 ..      86      99 ..      58     106 .. 0.76
   2 ?    0.5   0.0       1.2   7.5e+02      65      86 ..     128     150 ..     122     153 .. 0.79
   3 ?    4.0   0.1     0.091        58      72      86 ..     161     175 ..     149     181 .. 0.86
   4 ?   -1.8   0.0         6   3.8e+03      72      86 ..     204     218 ..     197     221 .. 0.84
   5 ?   -1.1   0.0       3.5   2.3e+03      73      86 ..     230     243 ..     224     263 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 2.7
                        DUF3130 72 klgaafikkDkele 85
                                   ++++ f+++D++l 
  gi|119720588|ref|YP_921083.1| 86 DMNKGFARHDEQLA 99
                                   59999999998875 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1.2
                        DUF3130  65 kDaerlkk.lgaafikkDkeler 86 
                                    +D ++l++ +++ f+++D+ l+r
  gi|119720588|ref|YP_921083.1| 128 EDFNKLREdMNKGFARHDEALKR 150
                                    677777644*********99887 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.091
                        DUF3130  72 klgaafikkDkeler 86 
                                    +++a f+++Dkel r
  gi|119720588|ref|YP_921083.1| 161 DMNAGFARQDKELTR 175
                                    69**********976 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 6
                        DUF3130  72 klgaafikkDkeler 86 
                                    ++++ f+++D+ l r
  gi|119720588|ref|YP_921083.1| 204 DMNKGFARHDEALRR 218
                                    6999******99876 PP

  == domain 5  score: -1.1 bits;  conditional E-value: 3.5
                        DUF3130  73 lgaafikkDkeler 86 
                                    +++ f+++D+ l r
  gi|119720588|ref|YP_921083.1| 230 MNKGFARHDEALRR 243
                                    66666666666554 PP

>> YscO-like  YscO-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       3.1     2e+03      51      67 ..      36      52 ..      29      59 .. 0.72
   2 ?   12.2   5.7   0.00022      0.14      17      67 ..      59     109 ..      53     125 .. 0.92
   3 ?    1.7  18.0      0.36   2.3e+02       8     130 ..     122     247 ..     115     254 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 3.1
                                   HHHHHHHHHHHHHHH-- CS
                      YscO-like 51 hkkaKvaqlreeldkGt 67
                                      + ++ lree+  G 
  gi|119720588|ref|YP_921083.1| 36 SLAEEMKRLREEMHAGF 52
                                   45667888888888875 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00022
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-- CS
                      YscO-like  17 veeAEkvvkdkkkaLekEkeklrkleeerdkvkkhkkaKvaqlreeldkGt 67 
                                    +e+ Ek++++  +aL +  e+l +l+e+ +k +  + +++a+lre ++ G 
  gi|119720588|ref|YP_921083.1|  59 LERLEKILEKHEEALRRHDEELIRLREDMNKGFARHDEQLAKLREDMNSGF 109
                                    6899********************************************995 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.36
                                    HHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHH CS
                      YscO-like   8 qlldikk...rrveeAEkvvkdkkkaLekEkeklrkleeerdkvkkhkkaKvaqlreeldkGttsdkikkmkryikvvke 84 
                                    ql+++++   +  e+  k ++   +aL++ +e+l kl+e+ +  +  + + ++ lre ++ G +    +  +r+++ +k 
  gi|119720588|ref|YP_921083.1| 122 QLVKLREdfnKLREDMNKGFARHDEALKRHEEELVKLREDMNAGFARQDKELTRLREDMNAGFARHD-ELFRRHEEEMKG 200
                                    56666652224679999*********************************************87665.567899999999 PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHH CS
                      YscO-like  85 elkqeekkvekQkekVkvAerkvEqareelakk.rkeveklekhkee 130
                                      +  +k  ++  e+ +  e ++ + re+++k  ++  e+l+ h e 
  gi|119720588|ref|YP_921083.1| 201 LREDMNKGFARHDEALRRHEEELVKLREDMNKGfARHDEALRRHEEI 247
                                    99999999999*****9999999999999988536667788888765 PP

>> Nup88  Nuclear pore component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4  11.9   0.00016       0.1     555     679 ..      29     153 ..       5     181 .. 0.82
   2 ?   -0.9   2.4      0.41   2.6e+02     569     620 ..     211     262 ..     184     272 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00016
                          Nup88 555 eiekrvkllkkqkeqqleelqsleeerkslseraeklAekyeeikdkQ.eklvrrvkkvlkrlnsklpvlseaeremkke 633
                                    e+ +r + l+++ ++  ee++    +  ++ er ek+ ek+ee+  +  e+l+r  +++ k +  +  +l +   +m++ 
  gi|119720588|ref|YP_921083.1|  29 EVLRRLDSLAEEMKRLREEMHAGFAKHGEILERLEKILEKHEEALRRHdEELIRLREDMNKGFARHDEQLAKLREDMNSG 108
                                    889****************************************97765166666667777789999999*********** PP

                          Nup88 634 lekikeklkslknalkqvkkkldkqrkqiakskeeekksslelsek 679
                                    +++ +e+ +  +++l ++++ ++k r+ ++k+  + + ++l+ +e+
  gi|119720588|ref|YP_921083.1| 109 FARHDEASRRHEEQLVKLREDFNKLREDMNKGFAR-HDEALKRHEE 153
                                    ******************************98666.4444443333 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.41
                          Nup88 569 qqleelqsleeerkslseraeklAekyeeikdkQeklvrrvkkvlkrlnskl 620
                                    +  e l++ eee  +l+e+ +k   +++e+  + e+++++ ++ l +l+s++
  gi|119720588|ref|YP_921083.1| 211 RHDEALRRHEEELVKLREDMNKGFARHDEALRRHEEILEKHSEELAKLRSAM 262
                                    4556788888899999999999999999999999999999999888888765 PP

>> SHE3  SWI5-dependent HO expression protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   9.4      0.18   1.1e+02      79     174 ..      66     162 ..      29     180 .. 0.63
   2 ?    2.9  12.0      0.12        76      21     200 ..      72     263 ..      65     289 .. 0.68

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.18
                                    HHHHHHH.HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSSXXXX CS
                           SHE3  79 kesveel.klekkqlkkrlenssaseteleeelerlkvqYdalvdsqkeYkehYqqeieeLkesleklklenekqleelq 157
                                     e++ee+ + + ++l    e+ ++  ++  e+l +l+ + ++  + + e   + ++++ +L+e ++kl+++ +k +  + 
  gi|119720588|ref|YP_921083.1|  66 LEKHEEAlRRHDEELIRLREDMNKGFARHDEQLAKLREDMNSGFARHDEASRRHEEQLVKLREDFNKLREDMNKGFARHD 145
                                    22333320233333333333444444455677777777778878888877777788888888888888888888777777 PP

                                    XXXXXXX.XXXXXXXXX CS
                           SHE3 158 erissndkdidtkldsy 174
                                    e + + ++++ ++ +++
  gi|119720588|ref|YP_921083.1| 146 EALKRHEEELVKLREDM 162
                                    77777766655544444 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.12
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHH........HHHH CS
                           SHE3  21 qLtqqsqeLleklelaqkkeskflenlaslkhE.NdnL...sslLkRKerrlkdlekelselkesvee........lkle 88 
                                    +L++ ++eL++  e  +k  +++ e+la+l+++ N          +R e +l  l +++++l+e +++        lk +
  gi|119720588|ref|YP_921083.1|  72 ALRRHDEELIRLREDMNKGFARHDEQLAKLREDmNSGFarhDEASRRHEEQLVKLREDFNKLREDMNKgfarhdeaLKRH 151
                                    66777777777777777777777777777775412211000122345555555555555555554443111111012333 PP

                                    HHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSSXXXXXXXXXXX.XXX CS
                           SHE3  89 kkqlkkrlenssaseteleeelerlkvqYdalvdsqkeYkehYqqeieeLkesleklklenekqleelqerissndkdid 168
                                    +++l k  e+ +a  ++  +el rl+ + +a  + + e   + ++e++ L+e ++k    +++ l  ++e++++  +d++
  gi|119720588|ref|YP_921083.1| 152 EEELVKLREDMNAGFARQDKELTRLREDMNAGFARHDELFRRHEEEMKGLREDMNKGFARHDEALRRHEEELVKLREDMN 231
                                    33344444444444556678899999999999999998888889999999999999777777799999999999999999 PP

                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                           SHE3 169 tkldsynnkkknlesieeeknkkllkklesla 200
                                    + +   ++  ++ e+i e++ ++l k+ + ++
  gi|119720588|ref|YP_921083.1| 232 KGFARHDEALRRHEEILEKHSEELAKLRSAMI 263
                                    99999999999999999999999998877776 PP

>> HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interacting protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   4.8     0.046        29      24      75 ..      29      80 ..      27     103 .. 0.81
   2 ?    1.1   1.2      0.97   6.2e+02      33      63 ..      77     107 ..      69     125 .. 0.62
   3 ?    0.2   4.4       1.9   1.2e+03      23      83 ..      96     156 ..      91     172 .. 0.51
   4 ?    5.4   2.7     0.044        28      22      77 ..     127     182 ..     118     192 .. 0.83
   5 ?    6.6   2.4     0.018        12       8      89 ..     181     262 ..     180     271 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.046
                 HIP1_clath_bdg 24 everekkeleeelerlkeeaerkleeqkeelekLkreleakraelarlkssL 75
                                   ev r  + l+ee++rl+ee +   ++  e le+L++ le++++ l r  + L
  gi|119720588|ref|YP_921083.1| 29 EVLRRLDSLAEEMKRLREEMHAGFAKHGEILERLEKILEKHEEALRRHDEEL 80
                                   68888899*************************9999999988888766655 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.97
                 HIP1_clath_bdg  33 eeelerlkeeaerkleeqkeelekLkrelea 63 
                                    +eel rl+e+ ++  +   e+l kL++++++
  gi|119720588|ref|YP_921083.1|  77 DEELIRLREDMNKGFARHDEQLAKLREDMNS 107
                                    4555666666666666666666666666654 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 1.9
                 HIP1_clath_bdg  23 eeverekkeleeelerlkeeaerkleeqkeel.ekLkreleakraelarlkssLesseqsge 83 
                                    e++++ +++++  + r  e + r+ eeq  +l e +++  e+ ++ +ar  ++L+++e++  
  gi|119720588|ref|YP_921083.1|  96 EQLAKLREDMNSGFARHDEAS-RRHEEQLVKLrEDFNKLREDMNKGFARHDEALKRHEEELV 156
                                    566667777777776644433.3333333322133333333334444455555555554444 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.044
                 HIP1_clath_bdg  22 qeeverekkeleeelerlkeeaerkleeqkeelekLkreleakraelarlkssLes 77 
                                    +e+ ++ ++++++ + r  e  +r++ee  +  e +++ ++++ +el+rl++ ++ 
  gi|119720588|ref|YP_921083.1| 127 REDFNKLREDMNKGFARHDEALKRHEEELVKLREDMNAGFARQDKELTRLREDMNA 182
                                    57888889999999999999999999999999999999999999999999988875 PP

  == domain 5  score: 6.6 bits;  conditional E-value: 0.018
                 HIP1_clath_bdg   8 nAevtkqlsvarqaqeeverekkeleeelerlkeeaerkleeqkeelekLkreleakraelarlkssLesseqsgeqlss 87 
                                    nA  ++     r + ee++  ++++++ + r  e  +r++ee  +  e +++ ++++ + l r ++ Le++ ++ ++l s
  gi|119720588|ref|YP_921083.1| 181 NAGFARHDELFRRHEEEMKGLREDMNKGFARHDEALRRHEEELVKLREDMNKGFARHDEALRRHEEILEKHSEELAKLRS 260
                                    56666666677888888888888888888888888888888888888888888888888888888888888777777766 PP

                 HIP1_clath_bdg  88 ql 89 
                                     +
  gi|119720588|ref|YP_921083.1| 261 AM 262
                                    55 PP

>> RmuC  RmuC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1      0.13        84     227     264 ..      37      74 ..      27      80 .. 0.71
   2 ?    7.6   0.9    0.0028       1.8     221     289 ..      70     138 ..      68     140 .. 0.92
   3 ?    1.9   0.2      0.15        97     222     266 ..     214     258 ..     208     271 .. 0.65

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.13
                           RmuC 227 naeeiaellgelydkfekfgedleklgkklekaqksyd 264
                                     aee  +l +e++  f+k+ge le+l+k lek +++++
  gi|119720588|ref|YP_921083.1|  37 LAEEMKRLREEMHAGFAKHGEILERLEKILEKHEEALR 74 
                                    46777777777888888888888888888777776655 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0028
                           RmuC 221 qeaqeknaeeiaellgelydkfekfgedleklgkklekaqksydkavkklegnilrkaeklkelgvkek 289
                                    +ea++++ ee+ +l +++ + f+++ e+l kl++ +++     d+a  + e+++++  e++++l ++ +
  gi|119720588|ref|YP_921083.1|  70 EEALRRHDEELIRLREDMNKGFARHDEQLAKLREDMNSGFARHDEASRRHEEQLVKLREDFNKLREDMN 138
                                    67899999*************************************999999****99999999987765 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.15
                           RmuC 222 eaqeknaeeiaellgelydkfekfgedleklgkklekaqksydka 266
                                    ea++++ ee+++l +++ + f+++ e l++ ++ lek ++++ k+
  gi|119720588|ref|YP_921083.1| 214 EALRRHEEELVKLREDMNKGFARHDEALRRHEEILEKHSEELAKL 258
                                    566666666666666666666666666666666666666665554 PP

>> DUF4375  Domain of unknown function (DUF4375)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   1.1    0.0015      0.95      48     111 ..      50     111 ..      36     119 .. 0.85
   2 ?    2.6   0.9      0.24   1.6e+02      77     108 ..     127     158 ..      98     167 .. 0.67
   3 ?    1.3   3.3      0.61   3.9e+02      74     104 ..     167     197 ..     126     204 .. 0.45
   4 ?    2.6   2.0      0.25   1.6e+02      54     107 ..     174     225 ..     168     240 .. 0.65
   5 ?    1.5   1.3      0.53   3.4e+02      58     107 ..     203     250 ..     195     259 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0015
                                    TT--HHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHH.-GGGHHHHHHHHHHHHHHHHHHHH CS
                        DUF4375  48 iGaeelakllekakklykkgkeelereerdeelealyeeeeeefdelDdefyeyeeeltellae 111
                                     G +++ ++le+  k+++k++e+l+r ++  el  l e+ ++ f   D++  +  e++++ +a+
  gi|119720588|ref|YP_921083.1|  50 AGFAKHGEILERLEKILEKHEEALRRHDE--ELIRLREDMNKGFARHDEQLAKLREDMNSGFAR 111
                                    4889999********99999999877655..6788989989***********999998877766 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.24
                                    TT-HHHHHHH.-GGGHHHHHHHHHHHHHHHHH CS
                        DUF4375  77 deelealyeeeeeefdelDdefyeyeeeltel 108
                                    +e++++l e+ ++ f   D++   +eeel +l
  gi|119720588|ref|YP_921083.1| 127 REDFNKLREDMNKGFARHDEALKRHEEELVKL 158
                                    23488888888899999999998888888765 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.61
                                    HHHTT-HHHHHHH.-GGGHHHHHHHHHHHHH CS
                        DUF4375  74 eerdeelealyeeeeeefdelDdefyeyeee 104
                                    +++d+el  l e+ +  f   D+ f  +eee
  gi|119720588|ref|YP_921083.1| 167 ARQDKELTRLREDMNAGFARHDELFRRHEEE 197
                                    2223345666555566666666666666665 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.25
                                    HHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHH.-GGGHHHHHHHHHHHHHHHH CS
                        DUF4375  54 akllekakklykkgkeelereerdeelealyeeeeeefdelDdefyeyeeelte 107
                                     +l e++++ + ++ e ++r e+  e++ l e+ ++ f   D++   +eeel +
  gi|119720588|ref|YP_921083.1| 174 TRLREDMNAGFARHDELFRRHEE--EMKGLREDMNKGFARHDEALRRHEEELVK 225
                                    45555555555555555544443..57777777777777777777777777665 PP

  == domain 5  score: 1.5 bits;  conditional E-value: 0.53
                                    HHHHHHHHHHHHHHHHHHHTT-HHHHHHH.-GGGHHHHHHHHHHHHHHHH CS
                        DUF4375  58 ekakklykkgkeelereerdeelealyeeeeeefdelDdefyeyeeelte 107
                                    e+++k + ++ e+l+r e+  el +l e+ ++ f   D++   +ee l++
  gi|119720588|ref|YP_921083.1| 203 EDMNKGFARHDEALRRHEE--ELVKLREDMNKGFARHDEALRRHEEILEK 250
                                    4455555566666555554..56777777788888888887777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1422  (0.0793128); expected 358.6 (0.02)
Passed bias filter:                      610  (0.0340231); expected 358.6 (0.02)
Passed Vit filter:                       107  (0.00596798); expected 17.9 (0.001)
Passed Fwd filter:                        63  (0.00351386); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              28  [number of targets reported over threshold]
# CPU time: 1.27u 0.36s 00:00:01.63 Elapsed: 00:00:00.58
# Mc/sec: 2015.87
//
Query:       gi|119720589|ref|YP_921084.1|  [L=121]
Description: DNA polymerase beta subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.9e-10   39.9   0.1      5e-10   39.5   0.1    1.3  1  NTP_transf_2    Nucleotidyltransferase domain
    0.00063   19.8   0.0    0.00069   19.6   0.0    1.3  1  Polbeta         Polymerase beta, Nucleotidyltransferase
  ------ inclusion threshold ------
      0.062   13.5   0.0      0.081   13.1   0.0    1.2  1  DNA_pol_B_palm  DNA polymerase beta palm
      0.092   12.6   0.1       0.66    9.8   0.0    2.0  2  ETF             Electron transfer flavoprotein domain


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   0.1   1.1e-13     5e-10       2      48 ..       9      71 ..       8     116 .. 0.69

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 1.1e-13
                                   HHHHHHHHHHTTTSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHH................H CS
                   NTP_transf_2  2 kklleelkelepvakvvlfGSyarGtalkgSDiDllvvlpeevsre................k 48
                                   k++le  ++l++++ +vl+GSyarG++++ SD+D+++v+ e++  +                +
  gi|119720589|ref|YP_921084.1|  9 KEALEWASRLRGSVTAVLVGSYARGDFNEWSDVDVVLVSGEFKGGPlerlkaievppgyeviP 71
                                   677888889999***************************999664455555555554444442 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   1.5e-07   0.00069      14      42 ..      22      50 ..       8      98 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.5e-07
                                   HSTTEEEEEE-S------EEEEEEEESS- CS
                        Polbeta 14 elaylFGSrakgkareeSDiDlavllkek 42
                                     a+l GS+a+g+++e SD+D+ ++  e 
  gi|119720589|ref|YP_921084.1| 22 VTAVLVGSYARGDFNEWSDVDVVLVSGEF 50
                                   578999****************9887665 PP

>> DNA_pol_B_palm  DNA polymerase beta palm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.8e-05     0.081      15      52 ..      12      50 ..       1      62 [. 0.76

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.8e-05
                                   HHHHHHH-TT-EEEE-HHHHTT-.SEESSEEEEEEBTTB CS
                 DNA_pol_B_palm 15 kkaakeldpevevivcGSYRRga.essGDvDvlitkkda 52
                                    + a++l  +v+++ +GSY Rg  ++  DvDv++   ++
  gi|119720589|ref|YP_921084.1| 12 LEWASRLRGSVTAVLVGSYARGDfNEWSDVDVVLVSGEF 50
                                   3446778889***********9746789****9987665 PP

>> ETF  Electron transfer flavoprotein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00015      0.66      16      42 ..       7      29 ..       2      36 .. 0.77
   2 ?    0.6   0.0       0.1   4.7e+02      17      30 ..      88     101 ..      82     106 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00015
                                   HHHHHHHHHHHHHHHHT--EEEEEEES CS
                            ETF 16 vdlealeaArrlkekaggevtavvvGp 42
                                   v +eale A rl     g+vtav+vG+
  gi|119720589|ref|YP_921084.1|  7 VVKEALEWASRL----RGSVTAVLVGS 29
                                   456677777777....69********8 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.1
                                    HHHHHHHHHHHHHH CS
                            ETF  17 dlealeaArrlkek 30 
                                     lea+e +++l++ 
  gi|119720589|ref|YP_921084.1|  88 ALEAVERGVKLRDD 101
                                    79*********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 805.56
//
Query:       gi|119720590|ref|YP_921085.1|  [L=136]
Description: HEPN domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-35  120.9   0.0    3.6e-35  120.7   0.0    1.0  1  HEPN      HEPN domain
    0.00075   19.4   0.1     0.0023   17.8   0.0    1.7  2  PaREP1    Archaeal PaREP1/PaREP8 family


Domain annotation for each model (and alignments):
>> HEPN  HEPN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.7   0.0     4e-39   3.6e-35       1     117 [.       7     128 ..       7     129 .. 0.98

  Alignments for each domain:
  == domain 1  score: 120.7 bits;  conditional E-value: 4e-39
                                    HHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHTT--.SSCCHHHHHHCCHHHT...-HHHHHHHHHH CS
                           HEPN   1 aeewlrrAeedleaAellleegdydlacfhaqqaaekalKAlllkkggeppkthdlreLleelkkelkeseelreeleeL 80 
                                    +e+w++ A+++l++A+ +le+gdy++acf+aqqaae+a+KAll+ +g  p ++h++++Ll+    ++  ++++ + +  L
  gi|119720590|ref|YP_921085.1|   7 YERWMETARRTLSSARGDLERGDYNWACFKAQQAAEFAVKALLYGLGL-PHHGHSVSRLLRVMPGGISVPQDVMQAAITL 85 
                                    699*********************************************.6*****************99*********** PP

                                    HCCCHHCCCTSS--S......--HHHHHHHHHHHHHHHHHHHH CS
                           HEPN  81 ekayiesrYpdakee......yteedaeealkdaeevlelvee 117
                                    +k+y+++rYp+a+ e      y++ daeea+++aee++++ve+
  gi|119720590|ref|YP_921085.1|  86 DKYYVPTRYPNAWHEgipaeyYSRMDAEEAIRHAEEIVRWVER 128
                                    ****************************************986 PP

>> PaREP1  Archaeal PaREP1/PaREP8 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   2.6e-07    0.0023       4      43 ..      12      51 ..       9      64 .. 0.90
   2 ?   -1.1   0.0      0.19   1.7e+03      10      15 ..     116     121 ..      92     132 .. 0.55

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.6e-07
                         PaREP1  4 eeaekeleeAeellekGdlrqAaeKaykAvkalvkalaek 43
                                   e a++ l+ A+  le+Gd+  A+ Ka +A++ +vkal+  
  gi|119720590|ref|YP_921085.1| 12 ETARRTLSSARGDLERGDYNWACFKAQQAAEFAVKALLYG 51
                                   7899999******************************875 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.19
                         PaREP1  10 leeAee 15 
                                    ++ Aee
  gi|119720590|ref|YP_921085.1| 116 IRHAEE 121
                                    222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 952.90
//
Query:       gi|119720591|ref|YP_921086.1|  [L=138]
Description: HEPN domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      5e-17   62.1   1.8    7.3e-17   61.6   1.8    1.3  1  HEPN      HEPN domain


Domain annotation for each model (and alignments):
>> HEPN  HEPN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.6   1.8   4.1e-21   7.3e-17       2     117 ..       7     130 ..       6     131 .. 0.84

  Alignments for each domain:
  == domain 1  score: 61.6 bits;  conditional E-value: 4.1e-21
                                    HHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHTT--.SSCCHHHHHHCCHHHT............... CS
                           HEPN   2 eewlrrAeedleaAellleegdydlacfhaqqaaekalKAlllkkggeppkthdlreLleelkkelke............ 69 
                                    e ++rrA + l+ A+   ++    la+f a+q+a++++KA+++++ ge  ++h+lreLl++ ++ l e            
  gi|119720591|ref|YP_921086.1|   7 ETLKRRAVKLLQVARSIEDA---GLALFLAEQSAQLYIKAVHYELLGEKVRGHGLRELLGLFARSLREagyekeadaitg 83 
                                    67788888888888765555...57***********************************55555555587666677777 PP

                                    .-HHHHHHHHHHHCCCHHCCCTSS--S--HHHHHHHHHHHHHHHHHHHH CS
                           HEPN  70 .seelreeleeLekayiesrYpdakeeyteedaeealkdaeevlelvee 117
                                       e r+ l  Le+ay++ rY+ + +   +ed+e a++++e+++e +e+
  gi|119720591|ref|YP_921086.1|  84 lALEHRRALALLEEAYTMGRYGTYVY--GSEDVEIAVRTVEKLVETLEK 130
                                    767777777****************9..9****************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 997.97
//
Query:       gi|119720592|ref|YP_921087.1|  [L=122]
Description: DNA polymerase beta subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.3e-06   27.8   0.0    3.1e-06   27.4   0.0    1.3  1  NTP_transf_2  Nucleotidyltransferase domain
     0.0059   16.7   0.0     0.0073   16.4   0.0    1.3  1  Polbeta       Polymerase beta, Nucleotidyltransferase
  ------ inclusion threshold ------
        0.1   12.2   0.2       0.24   11.0   0.2    1.6  1  Kelch_1       Kelch motif


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   5.2e-10   3.1e-06       5      74 ..      23      85 ..      19     110 .. 0.68

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 5.2e-10
                                   HHHHHHHTTTSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEE CS
                   NTP_transf_2  5 leelkelepvakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevdlv 74
                                   +++  +  p+a+v++ G +a +  +  SDiD+lvv+p  +      +gl++++ ++  + +  gl++d  
  gi|119720592|ref|YP_921087.1| 23 AKAAMDVVPGARVYVIGGVAEDRVTALSDIDILVVVPGGAR-----KGLYADVLERAIDAY--GLPWDAP 85
                                   5666666789*****************************76.....445554444444444..4444433 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.2e-06    0.0073      15      53 ..      34      72 ..      16     104 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.2e-06
                                   STTEEEEEE-S------EEEEEEEESS---HHHHHHHHH CS
                        Polbeta 15 laylFGSrakgkareeSDiDlavllkekldleeelelaa 53
                                    +y+ G +a+++ +  SDiD+ v++    ++  ++++ +
  gi|119720592|ref|YP_921087.1| 34 RVYVIGGVAEDRVTALSDIDILVVVPGGARKGLYADVLE 72
                                   59**********************988855555555444 PP

>> Kelch_1  Kelch motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.2     4e-05      0.24      11      31 ..      32      54 ..      29      58 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4e-05
                                   TTEEEEEEEBCS..SSBEEEEEE CS
                        Kelch_1 11 ggkiYviGGsdg..gnalssvev 31
                                   g ++YviGG  +   +als++ +
  gi|119720592|ref|YP_921087.1| 32 GARVYVIGGVAEdrVTALSDIDI 54
                                   558*********99999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 886.33
//
Query:       gi|119720593|ref|YP_921088.1|  [L=129]
Description: HEPN domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.7e-30  104.5   2.8    4.3e-30  104.3   2.8    1.0  1  HEPN       HEPN domain
  ------ inclusion threshold ------
      0.027   14.4   1.1      0.027   14.4   1.1    1.8  2  PaREP1     Archaeal PaREP1/PaREP8 family
      0.049   13.8   0.7      0.065   13.4   0.7    1.3  1  HEPN_AbiV  AbiV


Domain annotation for each model (and alignments):
>> HEPN  HEPN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.3   2.8   7.1e-34   4.3e-30       2     116 ..       6     126 ..       5     128 .. 0.94

  Alignments for each domain:
  == domain 1  score: 104.3 bits;  conditional E-value: 7.1e-34
                                    HHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHTT--.SSCCHHHHHHC.CHHHT...-HHHHHHHHHH CS
                           HEPN   2 eewlrrAeedleaAellleegdydlacfhaqqaaekalKAlllkkggeppkthdlreLle.elkkelkeseelreeleeL 80 
                                     +wl++Ae dle+Ae l ++g+y++a+f+a+qaaeka KAll++ +   p++h++r Lle + +  +  ++el  +++eL
  gi|119720593|ref|YP_921088.1|   6 LRWLSEAEWDLETAEILHKAGRYNAAAFYAHQAAEKACKALLYSIHEA-PWGHSVRVLLErYFEARGLRIDELLSYAREL 84 
                                    58*********************************************9.***********855555556*********** PP

                                    HCCCHHCCCTSS--S......--HHHHHHHHHHHHHHHHHHH CS
                           HEPN  81 ekayiesrYpdakee......yteedaeealkdaeevlelve 116
                                    +++yi++rYp+a++       y++e   +a++ a++++++++
  gi|119720593|ref|YP_921088.1|  85 DRHYIPARYPNAHPAgtpheaYDSEASSRAISAAKAIVDFAR 126
                                    **************************************9976 PP

>> PaREP1  Archaeal PaREP1/PaREP8 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   1.1   4.5e-06     0.027       3      46 ..       9      52 ..       7      86 .. 0.87
   2 ?   -1.8   0.3      0.47   2.8e+03      24      37 ..     109     122 ..     105     125 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.5e-06
                         PaREP1  3 leeaekeleeAeellekGdlrqAaeKaykAvkalvkalaeknnl 46
                                   l+eae  le Ae l++ G +  Aa  a +A++ + kal+ + ++
  gi|119720593|ref|YP_921088.1|  9 LSEAEWDLETAEILHKAGRYNAAAFYAHQAAEKACKALLYSIHE 52
                                   789999********************************998555 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.47
                         PaREP1  24 qAaeKaykAvkalv 37 
                                    +A+ +a  A+ka+v
  gi|119720593|ref|YP_921088.1| 109 EASSRAISAAKAIV 122
                                    68999999999988 PP

>> HEPN_AbiV  AbiV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.7   1.1e-05     0.065      17      50 ..      16      48 ..       7      84 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.1e-05
                      HEPN_AbiV 17 ledAelLaengsyarAysLlilaiEElgKallly 50
                                   le Ae+L+++g+y  A + ++ a E + Kall y
  gi|119720593|ref|YP_921088.1| 16 LETAEILHKAGRYNAAAFYAHQAAEKACKALL-Y 48
                                   799**************************975.4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 873.51
//
Query:       gi|119720594|ref|YP_921089.1|  [L=130]
Description: DNA polymerase beta subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.5e-12   45.2   0.3    1.2e-11   44.7   0.3    1.5  1  NTP_transf_2   Nucleotidyltransferase domain
    3.8e-09   36.5   0.0    5.7e-09   35.9   0.0    1.5  1  Polbeta        Polymerase beta, Nucleotidyltransferase
  ------ inclusion threshold ------
      0.014   15.0   0.0      0.019   14.6   0.0    1.2  1  RlaP           RNA repair pathway DNA polymerase beta family
       0.13   11.4   0.0       0.17   11.0   0.0    1.2  1  Adenyl_transf  Streptomycin adenylyltransferase
       0.13   12.1   0.0        0.2   11.5   0.0    1.4  1  DUF294         Putative nucleotidyltransferase DUF294


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.7   0.3   3.3e-15   1.2e-11       2      57 ..       5      58 ..       4     123 .. 0.72

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 3.3e-15
                                   HHHHHHHHHHTTTSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHH CS
                   NTP_transf_2  2 kklleelkelepvakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeeglekla 57
                                   + + e+lk +++v+ v+lfGS+arG++++ SD Dllv+++ +++    +++ e l 
  gi|119720594|ref|YP_921089.1|  5 SDVVERLKNRFKVYAVILFGSRARGDWKPWSDYDLLVIGDFDKDY--LDRIGEVLD 58
                                   568899**********************************99542..222222222 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   0.0   1.6e-12   5.7e-09       5      58 ..       9      63 ..       5     104 .. 0.76

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 1.6e-12
                                   TTHHHHHHHHSTTEEEEEE-S------EEEEEEEESS---HHH.HHHHHHHHHHH CS
                        Polbeta  5 eilekekeielaylFGSrakgkareeSDiDlavllkekldlee.elelaaeledi 58
                                   e l+++ ++ +++lFGSra+g+ ++ SD+Dl v+ + ++d+ +   e+ ++l d+
  gi|119720594|ref|YP_921089.1|  9 ERLKNRFKVYAVILFGSRARGDWKPWSDYDLLVIGDFDKDYLDrIGEVLDALRDV 63
                                   6688999****************************99966655255666666666 PP

>> RlaP  RNA repair pathway DNA polymerase beta family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   5.3e-06     0.019      13     115 ..      12     110 ..       2     127 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.3e-06
                           RlaP  13 eeeeevkilyacesGSrawGfpspdsDyDvrfiyiepaewylglertrdvielpiddelDl..vgwelrKalrLllksNp 90 
                                    ++  ++k+  +++ GSra G   p sDyD+  i    ++++ ++    +v++   d  l++  + + l  al+++ k+Np
  gi|119720594|ref|YP_921089.1|  12 KN--RFKVYAVILFGSRARGDWKPWSDYDLLVIGDFDKDYLDRI---GEVLDALRDVRLPVepHPYTLSEALEMVEKGNP 86 
                                    33..3577778899********************9999999999...7777777788887522789************** PP

                           RlaP  91 tvlewlsspivyledtseleellrl 115
                                     ++  l   +v l+ t e e+l ++
  gi|119720594|ref|YP_921089.1|  87 LIISALEEGVV-LHSTGEFEKLVKA 110
                                    *******9999.7776666666554 PP

>> Adenyl_transf  Streptomycin adenylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   4.8e-05      0.17      12      68 ..       8      56 ..       2      78 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4.8e-05
                                   HHHHHH-TTEEEEEE----------------EEEEEEES-HHHHHT-SGGGGGG--E CS
                  Adenyl_transf 12 levAkkderiravilnGSranpnakkDefqDyDivyvvtdiesfiedkswldkFGer 68
                                   +e  k+  ++ avil GSra+ + k   ++DyD+  + +    f  dk++ld+ Ge+
  gi|119720594|ref|YP_921089.1|  8 VERLKNRFKVYAVILFGSRARGDWK--PWSDYDLLVIGD----F--DKDYLDRIGEV 56
                                   5556778899**************7..9*****987654....2..45555555555 PP

>> DUF294  Putative nucleotidyltransferase DUF294
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   5.5e-05       0.2      41      86 ..       9      49 ..       2      74 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.5e-05
                         DUF294 41 eelgkppvpfallvmGSeGReEqtlktDqDnalvledeeeeaarey 86
                                   e+l+++   +a++ +GS +R++    +D D  lv+ d     +++y
  gi|119720594|ref|YP_921089.1|  9 ERLKNRFKVYAVILFGSRARGDWKPWSDYDL-LVIGD----FDKDY 49
                                   5566667789*******************95.66666....33333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       709  (0.0395449); expected 358.6 (0.02)
Passed bias filter:                      648  (0.0361426); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 949.81
//
Query:       gi|119720595|ref|YP_921090.1|  [L=139]
Description: DNA polymerase beta subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.3e-13   50.0   0.0    2.9e-13   49.7   0.0    1.1  1  Polbeta       Polymerase beta, Nucleotidyltransferase
    4.5e-06   26.9   0.1    6.6e-06   26.3   0.1    1.3  1  NTP_transf_2  Nucleotidyltransferase domain


Domain annotation for each model (and alignments):
>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.7   0.0   3.3e-17   2.9e-13       2      90 ..      19     103 ..      18     105 .. 0.96

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 3.3e-17
                                    STTTTHHHHHHHHSTTEEEEEE-S------EEEEEEEESS---HHHHHHHHHHHHHH.SSSEEEEEETTTS-HHHHHHHH CS
                        Polbeta   2 kikeilekekeielaylFGSrakgkareeSDiDlavllkekldleeelelaaelediklgkkvDlvdlneapplllyeil 81 
                                    k++e+l +e+e+ la++FGS+++ +  +  D+Dlav++k+  dl + + l+a le + lg  vD+v l+e pp ++y++l
  gi|119720595|ref|YP_921090.1|  19 KLREVLGSEEEVLLAVVFGSFVSLDSYR--DVDLAVYTKRG-DLGYLAALSARLELA-LGVPVDVVPLDEIPPRFRYSVL 94 
                                    8999******************999988..***********.99***********99.9********************* PP

                                    HS-EEEES- CS
                        Polbeta  82 kegkllysk 90 
                                    ++g +++++
  gi|119720595|ref|YP_921090.1|  95 TKGVVVLER 103
                                    *****9987 PP

>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.1   7.3e-10   6.6e-06       1      92 [.      17      97 ..      17     100 .. 0.90

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 7.3e-10
                                   HHHHHHHHHHHTTTSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEECEEECCCC CS
                   NTP_transf_2  1 lkklleelkelepvakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevdlvtrekledp 82
                                   l+kl+e l ++e v  +v+fGS++   + ++ D+Dl+v++++          l +la     le+ lg++vd+v+ ++++ p
  gi|119720595|ref|YP_921090.1| 17 LAKLREVLGSEEEVLLAVVFGSFVS--LDSYRDVDLAVYTKRGD--------LGYLAALSARLELALGVPVDVVPLDEIP-P 87
                                   5799********************6..77999***********4........4899***********************9.9 PP

                                   TEEEEEECEE CS
                   NTP_transf_2 83 llvksileer 92
                                   + + s+l ++
  gi|119720595|ref|YP_921090.1| 88 RFRYSVLTKG 97
                                   9888887666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       250  (0.0139439); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1032.91
//
Query:       gi|119720596|ref|YP_921091.1|  [L=92]
Description: hypothetical protein Tpen_1693, partial [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-17   63.4   0.0    1.8e-17   63.3   0.0    1.0  1  DUF86     Protein of unknown function DUF86


Domain annotation for each model (and alignments):
>> DUF86  Protein of unknown function DUF86
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.3   0.0     1e-21   1.8e-17      37     118 ..       2      85 ..       1      86 [. 0.96

  Alignments for each domain:
  == domain 1  score: 63.3 bits;  conditional E-value: 1e-21
                                    HHHHHHHHHHHHHHHTT----SSC..HHHHHHHTTSS-HHHHHHHHHHHCCHHHHHT-CCCTTHHHHHHHHHHTCHHHHH CS
                          DUF86  37 igEaaidiakhlakklgikkpgdy..ifeilaekgviaeepeepwrkmiglRNrLvHgYlgidpeivwsiikenlpdlee 114
                                    ++Ea+i ++ h+a++  +  p++   +f++l+ekg+ ++ + e++ k+++lRN L+H+Y+ +d+++v+++++++ + ++e
  gi|119720596|ref|YP_921091.1|   2 LVEALIALCYHIARNAYGVRPETPvrTFSVLVEKGLMNAWEFEELVKLVRLRNLLIHRYWVVDDRRVYDSVRKDFKAVRE 81 
                                    68************99999999999******************************************************* PP

                                    HHHH CS
                          DUF86 115 fles 118
                                    fle+
  gi|119720596|ref|YP_921091.1|  82 FLER 85 
                                    *997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 715.76
//
Query:       gi|119720597|ref|YP_921092.1|  [L=147]
Description: PilT domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-10   42.0   0.4    1.9e-10   41.3   0.4    1.3  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   0.4     1e-14   1.9e-10       1     121 [.       6     137 ..       6     138 .. 0.92

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 1e-14
                                    EEE-HHHHHHHHTTSHHHHHHHHHHHTS....SEEEEEHHHHHHHHHHHHS.........SCHCHHHHHHHHHHHHHHHT CS
                            PIN   1 ivlDTsvliallrgeekaeaarklleel....eelvtsalvlaEllyvlar.........rkskrekaaelvelllllsa 67 
                                    ++lDTs++++ +  ee+++ + ++++++     ++ +s   + E++ v  +         +++   k   +v +l +l +
  gi|119720597|ref|YP_921092.1|   6 VYLDTSAIVKRYVVEEGTDVLDEIYAGAyagdVTIGFSLFNIGEVAVVFDKyrrrgviadVNDCFSKFLSEVSTLARLGS 85 
                                    69**********77777777888887777777**************************99999999999999******** PP

                                    SEEEEBCHHHHHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHHHHH CS
                            PIN  68 lkilpidaeiaeeaaeialkygllpnDaliaAtAkehgikliatfDedfrrvak 121
                                    l+++ i+++i+ e  ++  +yg+ ++Dal +A Ak   +  ++tfDe++++va 
  gi|119720597|ref|YP_921092.1|  86 LRVVRISKPILVESVRYVFRYGVYIADALQIASAKNFEA--FLTFDERLAEVAV 137
                                    **********************************98777..55********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1132.00
//
Query:       gi|119720598|ref|YP_921093.1|  [L=90]
Description: hypothetical protein Tpen_1695 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00015   21.6   0.5    0.00032   20.5   0.5    1.5  1  RHH_1     Ribbon-helix-helix protein, copG family


Domain annotation for each model (and alignments):
>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.5   1.8e-08   0.00032       2      36 ..       5      39 ..       4      39 .. 0.97

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.8e-08
                                   EEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHH CS
                          RHH_1  2 vsirldeellerLdelarrrgrSrSelIReAlrey 36
                                   v+++ld++l+ r+  + + +grS Sel++e+l +y
  gi|119720598|ref|YP_921093.1|  5 VTLSLDRDLVSRVKSRLAFEGRSLSELVEELLSMY 39
                                   89******************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 663.64
//
Query:       gi|119720599|ref|YP_921094.1|  [L=162]
Description: PaREP8 domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.2e-36  123.1   3.3    6.5e-36  122.7   3.3    1.1  1  PaREP1      Archaeal PaREP1/PaREP8 family
  ------ inclusion threshold ------
      0.089   12.9   2.3        0.7   10.0   2.3    2.1  1  HEPN        HEPN domain
       0.09   13.0   0.0       0.76   10.0   0.0    2.0  2  SesA        N-terminal domain on NACHT_NTPase and P-loop NTPa
       0.13   10.9   0.0       0.18   10.4   0.0    1.1  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family


Domain annotation for each model (and alignments):
>> PaREP1  Archaeal PaREP1/PaREP8 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.7   3.3   1.5e-39   6.5e-36       1     115 []      37     151 ..      37     151 .. 0.98

  Alignments for each domain:
  == domain 1  score: 122.7 bits;  conditional E-value: 1.5e-39
                         PaREP1   1 arleeaekeleeAeellekGdlrqAaeKaykAvkalvkalaeknnlklleeaeekerwstkellkavaklleelgdkevv 80 
                                    ar++ ae++l+eAee+++kG+++qA+eK+ykAv+++vkalae +n k+lee ++++rw+ ++l +a ++l++ lg+++++
  gi|119720599|ref|YP_921094.1|  37 ARIDFAEEMLREAEEYVAKGNVVQASEKIYKAVEECVKALAERFNVKQLEEVRRRGRWDAWLLGQASTDLSRILGEDRIR 116
                                    68999*************************************************************************** PP

                         PaREP1  81 dlwklAldLHeyqfheaklelsdveskeeavkdlv 115
                                     +w++A+d H+++fheak++l+dves+ + +++l+
  gi|119720599|ref|YP_921094.1| 117 FAWATAYDVHVWGFHEAKYRLEDVESALPIARWLL 151
                                    *****************************999985 PP

>> HEPN  HEPN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   2.3   0.00016       0.7       5      48 ..      39      82 ..      35     158 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00016
                                   HHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHTT- CS
                           HEPN  5 lrrAeedleaAellleegdydlacfhaqqaaekalKAlllkkgg 48
                                   ++ Aee l++Ae+   +g    a  +++ a+e ++KAl  + + 
  gi|119720599|ref|YP_921094.1| 39 IDFAEEMLREAEEYVAKGNVVQASEKIYKAVEECVKALAERFNV 82
                                   6779*********************************9766554 PP

>> SesA  N-terminal domain on NACHT_NTPase and P-loop NTPases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00017      0.76      31      73 ..      35      76 ..      26      93 .. 0.85
   2 ?    0.8   0.0      0.12   5.2e+02      28      48 ..     130     150 ..     128     162 .] 0.68

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00017
                           SesA 31 vgkrLplvqetLedaksqlesskldedtesaikpvlesckeka 73
                                   +g+r+   +e+L++a++ + +++  +++e+ i++++e+c +++
  gi|119720599|ref|YP_921094.1| 35 AGARIDFAEEMLREAEEYVAKGNVVQASEK-IYKAVEECVKAL 76
                                   78899999******************9999.********9854 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.12
                           SesA  28 FrevgkrLplvqetLedaksq 48 
                                    F+e++ rL+ v+ +L  a+  
  gi|119720599|ref|YP_921094.1| 130 FHEAKYRLEDVESALPIARWL 150
                                    777888888887777666544 PP

>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0     4e-05      0.18      69     113 ..      41      81 ..      39      93 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 4e-05
                                    HHHHHHHHHHHHHHCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBX CS
                     Cpn60_TCP1  69 LageLleeaekliaagvhpttiiegyekalekaleaLkeiaveis 113
                                    +a+e+l+eae+++a+g + ++  e + ka+e++++aL e    ++
  gi|119720599|ref|YP_921094.1|  41 FAEEMLREAEEYVAKG-NVVQASEKIYKAVEECVKALAER---FN 81 
                                    799*********9777.89999***************655...33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1033  (0.0576162); expected 358.6 (0.02)
Passed bias filter:                      755  (0.0421105); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1073.33
//
Query:       gi|119720600|ref|YP_921095.1|  [L=92]
Description: DNA polymerase beta subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-13   50.1   0.0    2.9e-13   49.9   0.0    1.2  1  NTP_transf_2  Nucleotidyltransferase domain
    2.4e-07   30.7   0.0    3.1e-07   30.4   0.0    1.3  1  Polbeta       Polymerase beta, Nucleotidyltransferase
  ------ inclusion threshold ------
      0.018   15.3   0.0      0.027   14.8   0.0    1.3  1  BolA          BolA-like protein


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.9   0.0   4.9e-17   2.9e-13      13      86 ..       9      82 ..       1      91 [. 0.74

  Alignments for each domain:
  == domain 1  score: 49.9 bits;  conditional E-value: 4.9e-17
                                   TTSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEECEEECCC....CTEEE CS
                   NTP_transf_2 13 pvakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevdlvtrekled....pllvk 86
                                   ++a+v+lfGSyarGt+ ++SD+Dl+vv++ +       e  e++ + +   ++ l+ e  ++t e++e+    + +v 
  gi|119720600|ref|YP_921095.1|  9 GDARVYLFGSYARGTWVEDSDVDLVVVSRCFEGM----EPGERYRFVRGLASRELAFEFLVYTPEEFEEalkrSVVVQ 82
                                   49*****************************664....5556777777888887888888887777776444344444 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.0   5.1e-11   3.1e-07      16      42 ..      13      39 ..       4      85 .. 0.75

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 5.1e-11
                                   TTEEEEEE-S------EEEEEEEESS- CS
                        Polbeta 16 aylFGSrakgkareeSDiDlavllkek 42
                                   +ylFGS+a+g+  e+SD+Dl v+ +  
  gi|119720600|ref|YP_921095.1| 13 VYLFGSYARGTWVEDSDVDLVVVSRCF 39
                                   9*********************98866 PP

>> BolA  BolA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   4.5e-06     0.027      31      61 ..      30      60 ..      18      70 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.5e-06
                           BolA 31 FkvvivseaFegkslvarhRlvyalLkeela 61
                                    ++v+vs  Feg++  +r R v  l + ela
  gi|119720600|ref|YP_921095.1| 30 VDLVVVSRCFEGMEPGERYRFVRGLASRELA 60
                                   5789********************9999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 665.79
//
Query:       gi|119720601|ref|YP_921096.1|  [L=133]
Description: HEPN domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-27   94.3   0.0    6.1e-27   94.1   0.0    1.0  1  HEPN      HEPN domain
  ------ inclusion threshold ------
      0.059   14.0   3.6        0.8   10.4   0.5    2.2  2  DUF4398   Domain of unknown function (DUF4398)
        9.8    6.2   6.4        1.7    8.6   1.1    2.5  3  TPR_10    Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> HEPN  HEPN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.1   0.0     1e-30   6.1e-27       2     117 ..       7     128 ..       6     129 .. 0.97

  Alignments for each domain:
  == domain 1  score: 94.1 bits;  conditional E-value: 1e-30
                                    HHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHTT--..SSCCHHHHHHCCHHHT...-HHHHHHHHHH CS
                           HEPN   2 eewlrrAeedleaAellleegdydlacfhaqqaaekalKAlllkkgge.ppkthdlreLleelkkelkeseelreeleeL 80 
                                     +wl++A  dle A ++   gdy+lacf+aqqa+eka KA+++ + ++ pp+ hdl  L +elk  l  + +++e l eL
  gi|119720601|ref|YP_921096.1|   7 VDWLEEAVADLERAVRAEGVGDYSLACFMAQQAVEKAFKACYIGLLRRrPPRAHDLVMLYSELKGTLSLPGDVEEALPEL 86 
                                    58******************************************98888***************99999*********** PP

                                    HCCCHHCCCTSS--S.....--HHHHHHHHHHHHHHHHHHHH CS
                           HEPN  81 ekayiesrYpdakee.....yteedaeealkdaeevlelvee 117
                                    +++y+++rYp+a        +++ +a +a+++a+ v+e v+e
  gi|119720601|ref|YP_921096.1|  87 SQYYVTARYPNAGLRrpsasFSRAQAVRAIEVARGVVERVRE 128
                                    ************9999**********************9986 PP

>> DUF4398  Domain of unknown function (DUF4398)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.5   0.00013       0.8      21      62 ..       5      46 ..       2      47 .. 0.85
   2 ?    4.5   0.1    0.0091        54       8      34 ..     105     131 ..      99     132 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00013
                        DUF4398 21 yApaeleeAreaLaqAeaamaekdyeeAdhlaylAerdaelA 62
                                   +A + leeA   L++A +a + +dy+ A  +a++A ++a +A
  gi|119720601|ref|YP_921096.1|  5 EAVDWLEEAVADLERAVRAEGVGDYSLACFMAQQAVEKAFKA 46
                                   444449*****************************9998665 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0091
                        DUF4398   8 aaleaAraagaeeyApaeleeAreaLa 34 
                                    a++++A+a  a e A    e+ reaLa
  gi|119720601|ref|YP_921096.1| 105 ASFSRAQAVRAIEVARGVVERVREALA 131
                                    8899*******9999999******997 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   1.1   0.00029       1.7      18      36 ..       3      21 ..       3      22 .. 0.90
   2 ?   -2.7   0.0       1.1   6.3e+03       6      15 ..      60      69 ..      59      70 .. 0.79
   3 ?   -2.2   0.2       0.7   4.2e+03      28      36 ..     115     123 ..     109     131 .. 0.50

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00029
                         TPR_10 18 ydeAealleealairrrll 36
                                   ++eA+++leea+a  +r++
  gi|119720601|ref|YP_921096.1|  3 REEAVDWLEEAVADLERAV 21
                                   68***********999985 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.1
                         TPR_10  6 nNLanalrqr 15
                                   ++L ++++++
  gi|119720601|ref|YP_921096.1| 60 HDLVMLYSEL 69
                                   7899999976 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.7
                         TPR_10  28 alairrrll 36 
                                    a+++ r ++
  gi|119720601|ref|YP_921096.1| 115 AIEVARGVV 123
                                    444443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 959.99
//
Query:       gi|119720602|ref|YP_921097.1|  [L=155]
Description: hypothetical protein Tpen_1699 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-06   27.1   1.6    6.8e-06   26.0   1.6    1.6  1  PaREP1           Archaeal PaREP1/PaREP8 family
    0.00012   22.3   3.4    0.00016   21.9   3.4    1.1  1  DUF5618          Domain of unknown function (DUF5618)
    0.00019   21.5   4.6    0.00039   20.5   4.6    1.4  1  HEPN             HEPN domain
  ------ inclusion threshold ------
       0.05   13.3   0.9        0.2   11.3   0.1    2.0  2  Retrotran_gag_2  gag-polypeptide of LTR copia-type
      0.072   12.8   0.8      0.097   12.3   0.8    1.2  1  DUF1367          Protein of unknown function (DUF1367)


Domain annotation for each model (and alignments):
>> PaREP1  Archaeal PaREP1/PaREP8 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   1.6   1.9e-09   6.8e-06       3     115 .]      15     116 ..      13     116 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 1.9e-09
                         PaREP1   3 leeaekeleeAeellekGdlrqAaeKaykAvkalvkalaeknnlklleeaeekerwstkellkavaklleelgdkevvdl 82 
                                    l+ ae+e+e A +     ++r+Aa Ka+ ++  +v+ ++          + +   +s+ e+ + ++k+    ++++++ l
  gi|119720602|ref|YP_921097.1|  15 LKYAEEEFEKAIKTRDVMLYRNAADKAFFSMVLAVNSYIYR--------KMNVTPKSHSERRSLLRKM----NREDLRAL 82 
                                    7889*************************************........4444444555555555555....47888888 PP

                         PaREP1  83 wklAld.LHeyqfheaklelsdveskeeavkdlv 115
                                     +  ++ LH+++f+e+ +++++ e + ++vk+++
  gi|119720602|ref|YP_921097.1|  83 YSDIMKtLHDEAFYEGVYNPKEAEYAIKQVKKML 116
                                    7765555***********************9985 PP

>> DUF5618  Domain of unknown function (DUF5618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   3.4   4.3e-08   0.00016      12     121 ..      10     119 ..       2     121 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 4.3e-08
                                    HHHHHHHHHS-EETTEE--HHHH...HHHHHHHHHHHHHHHHHHH---S...SS-.--HHHHHHHHHCC-HHHHHHH.HH CS
                        DUF5618  12 nAkeiLsekakkedklYkdkkyv...keAggtAYsgvLlaldellgkkglekkkrpksvetYkealkkldkkllkef.ns 87 
                                     A eiL + a+ e +  +  + v   + A+  A+ +++la+++++ +k    + +pks  + ++ l+k++++ l+++  +
  gi|119720602|ref|YP_921097.1|  10 TAEEIL-KYAEEEFEKAIKTRDVmlyRNAADKAFFSMVLAVNSYIYRKM---NVTPKSHSERRSLLRKMNREDLRALySD 85 
                                    577777.555555554444444434499*****************9998...78899999999*****999988876257 PP

                                    HHHHHIIIICCT---BHHHHHHHHHHHHHHHHHH CS
                        DUF5618  88 aydvLhlagyydGiksakvvkeglkaaeklikki 121
                                    + ++Lh    y+G+++ k ++ ++k+++k+++  
  gi|119720602|ref|YP_921097.1|  86 IMKTLHDEAFYEGVYNPKEAEYAIKQVKKMLEEF 119
                                    99****************************9876 PP

>> HEPN  HEPN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   4.6   1.1e-07   0.00039       1     116 [.      11     120 ..      11     122 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.1e-07
                                    HHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHTT--..SSCCHHHHHHCCHHHT...-HHHHHHHHH CS
                           HEPN   1 aeewlrrAeedleaAellleegdydlacfhaqqaaekalKAlllkkgge.ppkthdlreLleelkkelkeseelreelee 79 
                                    aee l+ Aee +e+A +  +   y+ a+ +a  ++ +a+ +++++k    p++++  r+Ll++  +e+      + + + 
  gi|119720602|ref|YP_921097.1|  11 AEEILKYAEEEFEKAIKTRDVMLYRNAADKAFFSMVLAVNSYIYRKMNVtPKSHSERRSLLRKMNREDL----RALYSDI 86 
                                    58899***************************************9998846666667778888776554....3344455 PP

                                    HHCCCHHCCCTSS--S--HHHHHHHHHHHHHHHHHHH CS
                           HEPN  80 LekayiesrYpdakeeyteedaeealkdaeevlelve 116
                                    +  +  e+ Y+  ++    ++ae a+k+++++le  +
  gi|119720602|ref|YP_921097.1|  87 MKTLHDEAFYEGVYN---PKEAEYAIKQVKKMLEEFK 120
                                    666666777777665...8*************99865 PP

>> Retrotran_gag_2  gag-polypeptide of LTR copia-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0       0.2     7e+02      29      54 ..      10      35 ..       5      39 .. 0.86
   2 ?   11.3   0.1   5.7e-05       0.2       9      67 ..      83     142 ..      74     145 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.2
                Retrotran_gag_2 29 takevWdkLkelyekksaankltlrk 54
                                   ta e+ +  +e++ek  +++ ++l++
  gi|119720602|ref|YP_921097.1| 10 TAEEILKYAEEEFEKAIKTRDVMLYR 35
                                   788999999999***99999999987 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 5.7e-05
                Retrotran_gag_2   9 lalIvlsisdsllelvk.eektakevWdkLkelyekksaankltlrkklfslkmkegesv 67 
                                     + I++++ d+ +++   ++k+a  +++  k++ e+ ++a+    r++ +sl+  ++ ++
  gi|119720602|ref|YP_921097.1|  83 YSDIMKTLHDEAFYEGVyNPKEAEYAIKQVKKMLEEFKKARATSARRQPHSLRVIDEHTI 142
                                    478*********998776***********************************9888776 PP

>> DUF1367  Protein of unknown function (DUF1367)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.8   2.7e-05     0.097      91     194 ..      13     113 ..       2     115 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.7e-05
                        DUF1367  91 svlkeaadeylakvakkRaeklisidksldafrewvtveaGfydivelpdGslkkeaksisfanmdeeeFqelYkavlnv 170
                                    + + + a+e ++k  k R   l+    +   f   + v++  y  +++     + e++s+   +m+ e+  +lY ++++ 
  gi|119720602|ref|YP_921097.1|  13 E-ILKYAEEEFEKAIKTRDVMLYRNAADKAFFSMVLAVNSYIYRKMNVTPK-SHSERRSL-LRKMNREDLRALYSDIMKT 89 
                                    3.4456677777777888666666666655556666777877877665554.58889998.68***************** PP

                        DUF1367 171 lWnliLsrkfeseeeaenaadqll 194
                                    l  +  ++     +eae a++q+ 
  gi|119720602|ref|YP_921097.1|  90 LHDEAFYEGVYNPKEAEYAIKQVK 113
                                    **********************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1398  (0.0779742); expected 358.6 (0.02)
Passed bias filter:                      774  (0.0431703); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1092.86
//
Query:       gi|119720603|ref|YP_921098.1|  [L=163]
Description: PaREP8 domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.8e-27   94.2   4.2    7.9e-27   93.5   4.2    1.4  1  PaREP1          Archaeal PaREP1/PaREP8 family
    0.00038   20.6   0.9     0.0014   18.7   0.9    1.9  1  HEPN            HEPN domain
  ------ inclusion threshold ------
      0.035   14.6   0.0      0.064   13.8   0.0    1.5  1  CopG_antitoxin  CopG antitoxin of type II toxin-antitoxin sys
       0.12   12.6   0.0       0.37   11.0   0.0    1.7  2  DUF5618         Domain of unknown function (DUF5618)


Domain annotation for each model (and alignments):
>> PaREP1  Archaeal PaREP1/PaREP8 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.5   4.2   1.8e-30   7.9e-27       2     115 .]      47     150 ..      46     150 .. 0.98

  Alignments for each domain:
  == domain 1  score: 93.5 bits;  conditional E-value: 1.8e-30
                         PaREP1   2 rleeaekeleeAeellekGdlrqAaeKaykAvkalvkalaeknnlklleeaeekerwstkellkavaklleelgdkevvd 81 
                                    ++e a+++l+ A+e l++Gd+rqAaeK ++A++ +vka+a++        +++++ +s++el+++ + + +elg ++v+d
  gi|119720603|ref|YP_921098.1|  47 YVEVALYLLDRAREELKRGDVRQAAEKTWGAAALAVKAYAMW--------KDGRRLTSHGELWDYESLIESELG-EWVYD 117
                                    899***************************************........9***********************.***** PP

                         PaREP1  82 lwklAldLHeyqfheaklelsdveskeeavkdlv 115
                                    +w++A  +H++ f+e++++ s+ve++ ++v+ lv
  gi|119720603|ref|YP_921098.1| 118 AWMAANGMHTC-FYEGWCKESHVETAIKHVEGLV 150
                                    ***********.******************9875 PP

>> HEPN  HEPN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.9   3.2e-07    0.0014       2     115 ..      45     153 ..      44     158 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 3.2e-07
                                    HHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHTT--.SSCCHHHHHHCCHHHT...-HHHHHHHHHHH CS
                           HEPN   2 eewlrrAeedleaAellleegdydlacfhaqqaaekalKAlllkkggeppkthdlreLleelkkelkeseelreeleeLe 81 
                                    +e+++ A + l+ A++ l++gd + a+ +   aa +a+KA+   k+g+    h+  eL+ + +  + e  e+  ++  + 
  gi|119720603|ref|YP_921098.1|  45 REYVEVALYLLDRAREELKRGDVRQAAEKTWGAAALAVKAYAMWKDGRRLTSHG--ELWDYESLIESELGEWVYDAWMAA 122
                                    678899*****************************************9666665..555544444444578888888888 PP

                                    CCCHHCCCTSS--S--HHHHHHHHHHHHHHHHHH CS
                           HEPN  82 kayiesrYpdakeeyteedaeealkdaeevlelv 115
                                    +  ++  Y+  +  ++e  +e+a+k++e +++ v
  gi|119720603|ref|YP_921098.1| 123 NGMHTCFYEG-W--CKESHVETAIKHVEGLVKTV 153
                                    8888888887.3..47999999999999999875 PP

>> CopG_antitoxin  CopG antitoxin of type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.4e-05     0.064      45      78 ..       3      36 ..       1      37 [. 0.90

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.4e-05
                 CopG_antitoxin 45 islrlpedlLealkekAnkrdvpyqslikellee 78
                                   + ++lp +l +++ e+A+kr+v ++++i ++l +
  gi|119720603|ref|YP_921098.1|  3 VPIALPPSLAKKILEEARKRGVTIEEYIVDFLTR 36
                                   6679************************999975 PP

>> DUF5618  Domain of unknown function (DUF5618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.45     2e+03      13      24 ..      12      22 ..       2      35 .. 0.65
   2 ?   11.0   0.0   8.3e-05      0.37       5     122 ..      43     154 ..      39     155 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.45
                                   HHHHHHHHS-EE CS
                        DUF5618 13 AkeiLsekakke 24
                                   Ak+iL e+a+k 
  gi|119720603|ref|YP_921098.1| 12 AKKIL-EEARKR 22
                                   56666.555554 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 8.3e-05
                                    HHHHHHHHHHHHHHHHS-EETTEE--HHHHHHHHHHHHHHHHHHHHHHH---S...SS-.--HHHHHHHHHCC-HHHHHH CS
                        DUF5618   5 eakrylenAkeiLsekakkedklYkdkkyvkeAggtAYsgvLlaldellgkkglekkkrpksvetYkealkkldkkllke 84 
                                    +a+ y+e A  +L ++a+ e      +  v++A++  + ++ la+ ++ + k+ ++ + + ++  Y++ +++  ++ + +
  gi|119720603|ref|YP_921098.1|  43 RAREYVEVALYLL-DRAREEL----KRGDVRQAAEKTWGAAALAVKAYAMWKDGRRLTSHGELWDYESLIESELGEWVYD 117
                                    6777778787777.7777664....4678************************9999999***********999999999 PP

                                    HHHHHHHHIIIICCT---BHHHHHHHHHHHHHHHHHHH CS
                        DUF5618  85 fnsaydvLhlagyydGiksakvvkeglkaaeklikkie 122
                                       a + +h +  y+G  + + v++++k++e l+k ++
  gi|119720603|ref|YP_921098.1| 118 AWMAANGMHTC-FYEGWCKESHVETAIKHVEGLVKTVA 154
                                    99999999*87.69**999999************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       773  (0.0431145); expected 358.6 (0.02)
Passed bias filter:                      582  (0.0324614); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1070.32
//
Query:       gi|119720604|ref|YP_921099.1|  [L=84]
Description: hypothetical protein Tpen_1701 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       194  (0.0108205); expected 358.6 (0.02)
Passed bias filter:                      183  (0.0102069); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 652.29
//
Query:       gi|119720605|ref|YP_921100.1|  [L=132]
Description: hypothetical protein Tpen_1702 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.061   13.2   0.0      0.091   12.6   0.0    1.3  1  ACP_syn_III  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase 


Domain annotation for each model (and alignments):
>> ACP_syn_III  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   5.1e-06     0.091      35      64 ..       9      39 ..       3      55 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.1e-06
                                   EEGGGCS-TT.THHHHTTB-EEEEEEEEEEE CS
                    ACP_syn_III 35 etlskilDwk.drstavlfGDGAgAvvleas 64
                                   e l++ ++w+ +r+  +l+G GA Avv e++
  gi|119720605|ref|YP_921100.1|  9 EELARAVNWRgKRADYLLVGEGAVAVVEETE 39
                                   7899*****95599***********986665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      591  (0.0329634); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 976.56
//
Query:       gi|119720606|ref|YP_921101.1|  [L=457]
Description: hypothetical protein Tpen_1703 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.8e-23   82.2   0.0    3.1e-14   53.5   0.0    2.1  2  AAA_15    AAA ATPase domain
    5.4e-21   75.7   0.1    1.7e-15   57.6   0.0    2.2  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    0.00046   19.6   0.0      0.047   13.0   0.0    2.1  2  DUF2813   Protein of unknown function (DUF2813)
     0.0079   16.7   0.0      0.011   16.2   0.0    1.2  1  AAA_23    AAA domain
  ------ inclusion threshold ------
       0.03   13.7   0.0        4.2    6.7   0.0    2.2  2  SMC_N     RecF/RecN/SMC N terminal domain
       0.13   11.8   0.3        3.4    7.2   0.1    2.2  2  AAA_25    AAA domain
       0.15   11.8   0.1       0.46   10.3   0.0    1.8  2  AAA_29    P-loop containing region of AAA domain
       0.16   11.6   0.0       0.32   10.6   0.0    1.4  1  AAA_27    AAA domain


Domain annotation for each model (and alignments):
>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0   1.9e-09   4.2e-06       5      45 ..       8      47 ..       7      51 .. 0.92
   2 !   53.5   0.0   1.4e-17   3.1e-14     287     368 ..     298     379 ..     253     380 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 1.9e-09
                         AAA_15  5 kikikNFRslkdveidlseeltvliGkNnsGKSsilealdl 45
                                   ++ ++ F+ +++++i++ + ltvl+G+N++GKS +l++ + 
  gi|119720606|ref|YP_921101.1|  8 RVYVRDFGPFEEASIEVRP-LTVLVGRNSVGKSMLLQLVWA 47
                                   578999*************.****************98775 PP

  == domain 2  score: 53.5 bits;  conditional E-value: 1.4e-17
                         AAA_15 287 k.......ddeelplnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQv 359
                                    +       ++++lpl ++ sGv++ l ++l ++  e+         +++iEEPEahLHp aqk l++l++++++++ + v
  gi|119720606|ref|YP_921101.1| 298 RavyvntwSGQRLPLPRAPSGVRESLAVALALVVPEQP-------WLVFIEEPEAHLHPRAQKALARLIARAVKKHGKVV 370
                                    14444677999**********************99999.......********************************999 PP

                         AAA_15 360 iitTHSphi 368
                                    +++THS+++
  gi|119720606|ref|YP_921101.1| 371 VLSTHSDYL 379
                                    *******97 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   3.3e-06    0.0075       1      22 [.      27      48 ..      27      75 .. 0.88
   2 !   57.6   0.0   7.5e-19   1.7e-15     219     302 ..     295     380 ..     212     380 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.3e-06
                         AAA_21  1 lnvliGpNgsGKSnLLdaldll 22
                                   l+vl+G+N++GKS LL++ + l
  gi|119720606|ref|YP_921101.1| 27 LTVLVGRNSVGKSMLLQLVWAL 48
                                   79****************9887 PP

  == domain 2  score: 57.6 bits;  conditional E-value: 7.5e-19
                         AAA_21 219 r..gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQv.ilt 295
                                         v++   +gq lp+  +++G+++ la+++al    ++  l++i+EpE++LHP++++ l++l+ ++ ++ ++v +l+
  gi|119720606|ref|YP_921101.1| 295 GgvRAVYVNTWSGQRLPLPRAPSGVRESLAVALALVVPEQP-WLVFIEEPEAHLHPRAQKALARLIARAVKKHGKVvVLS 373
                                    3666667777789*************************999.************************88888788888*** PP

                         AAA_21 296 THSplll 302
                                    THS +ll
  gi|119720606|ref|YP_921101.1| 374 THSDYLL 380
                                    ****997 PP

>> DUF2813  Protein of unknown function (DUF2813)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   2.1e-05     0.047      12      44 ..      15      47 ..       7      57 .. 0.77
   2 !    4.4   0.0    0.0085        19     286     303 ..     337     354 ..     328     383 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.1e-05
                        DUF2813 12 RGinrLSlsleentvLiGENaWGKSSLldALsl 44
                                      +  S++++++tvL+G N+ GKS Ll+  + 
  gi|119720606|ref|YP_921101.1| 15 GPFEEASIEVRPLTVLVGRNSVGKSMLLQLVWA 47
                                   556677********************9984433 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0085
                        DUF2813 286 illlEdpearLHPtmlai 303
                                    ++ +E+pea+LHP+  + 
  gi|119720606|ref|YP_921101.1| 337 LVFIEEPEAHLHPRAQKA 354
                                    4578*********97555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0     5e-06     0.011       1      43 [.       8      48 ..       8      67 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5e-06
                         AAA_23  1 kLkienfrsfrdqeidFskgltlItGpNGaGKTTildAiklaL 43
                                   ++ ++ f++f++ +i+   +lt+++G N  GK+ +l+   +aL
  gi|119720606|ref|YP_921101.1|  8 RVYVRDFGPFEEASIEVR-PLTVLVGRNSVGKSMLLQL-VWAL 48
                                   578899***********9.****************984.3555 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0019       4.2       5      49 ..       9      49 ..       7      61 .. 0.81
   2 ?    4.7   0.0     0.008        18     146     208 ..     322     386 ..     318     396 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0019
                                   EEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCT CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N  5 leienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLG 49
                                   + +++F  +  +++++++ + +t++vG+N  GKs ll+ + + L 
  gi|119720606|ref|YP_921101.1|  9 VYVRDFGPF--EEASIEVRP-LTVLVGRNSVGKSMLLQLV-WALT 49
                                   667778888..678888888.9************999877.8776 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.008
                                    HHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-.SCE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx.xxx RF
                          SMC_N 146 alaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreemleka.dkl 208
                                    +la+ +A+   ++  l+++ e +a+L  +  k++a+l+ ++ k+   ++v s +++ l  a +++
  gi|119720606|ref|YP_921101.1| 322 SLAVALALVVPEQPWLVFIEEPEAHLHPRAQKALARLIARAVKKhGKVVVLSTHSDYLLYAvSNM 386
                                    577778888888888999********************976655378888776666554442555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.1    0.0015       3.4      35      70 ..      27      64 ..      22      85 .. 0.82
   2 ?    2.5   0.0     0.042        95      75     109 ..     336     375 ..     321     413 .. 0.61

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0015
                         AAA_25 35 lallaGapgtGKttla.ldlalava.tGkpwlgpvape 70
                                   l++l+G+  +GK++l+ l +al+va  + ++lg+ ++e
  gi|119720606|ref|YP_921101.1| 27 LTVLVGRNSVGKSMLLqLVWALTVAmPDLKLLGEAVSE 64
                                   799***********985899999998777778855555 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.042
                         AAA_25  75 lyvsaEdsedelrrRlravgeal.....rddarllvldla 109
                                    ++v  E++e++l++R++++++ l     +  +++ vl+ +
  gi|119720606|ref|YP_921101.1| 336 WLVFIEEPEAHLHPRAQKALARLiaravKKHGKVVVLSTH 375
                                    5666799999999999999988877766555555555533 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0    0.0002      0.46       6      40 ..      11      43 ..       7      56 .. 0.74
   2 ?   -2.8   0.2       2.5   5.7e+03      36      46 ..     195     205 ..     195     206 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0002
                         AAA_29  6 lvNWgtfdghtieidlkgatlltGpsGsGKSTllD 40
                                   + + g f++ +ie++    t+l+G++ +GKS ll 
  gi|119720606|ref|YP_921101.1| 11 VRDFGPFEEASIEVR--PLTVLVGRNSVGKSMLLQ 43
                                   556677777777776..569***********9985 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.5
                         AAA_29  36 STllDAiqalL 46 
                                    S l+DA+  +L
  gi|119720606|ref|YP_921101.1| 195 SDLVDAVLKVL 205
                                    669****9998 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00014      0.32       8      50 ..      11      49 ..       7      56 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00014
                         AAA_27  8 LeryGkftdrsldfsaeeadlhliyGpNEAGKstalrAisdll 50
                                   ++ +G+f++ s++ +     l++++G N  GKs +l+ + +l 
  gi|119720606|ref|YP_921101.1| 11 VRDFGPFEEASIEVR----PLTVLVGRNSVGKSMLLQLVWALT 49
                                   678***********8....7*************9998776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (457 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 3223.91
//
Query:       gi|119720607|ref|YP_921102.1|  [L=121]
Description: hypothetical protein Tpen_1704 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.092   12.2   0.0       0.16   11.4   0.0    1.4  1  AP_endonuc_2  Xylose isomerase-like TIM barrel


Domain annotation for each model (and alignments):
>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0     9e-06      0.16      65     101 ..      47      82 ..      17     102 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9e-06
                                    HHHHHHHHHHHHHHHHHHTBSEEEEEBCCGBCTTTSG CS
                   AP_endonuc_2  65 reesvdalkraielaaaLGapllvlhpGtagagpkgs 101
                                     +e+++ ++ra+ +a+ LG+p+l+ ++G  +++p+++
  gi|119720607|ref|YP_921102.1|  47 AREALELWERAAGAARLLGVPVLIYWTG-PTDPPPSE 82 
                                    2578************************.33333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       225  (0.0125495); expected 358.6 (0.02)
Passed bias filter:                      201  (0.0112109); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 844.95
//
Query:       gi|119720608|ref|YP_921103.1|  [L=271]
Description: hypothetical protein Tpen_1705 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.6e-11   41.7  12.4    1.2e-10   41.3   3.0    3.7  2  DUF3782        Protein of unknown function (DUF3782)
    7.1e-07   29.2   3.7    2.6e-06   27.4   0.9    2.6  3  MCPsignal      Methyl-accepting chemotaxis protein (MCP) sign
    0.00012   21.6   3.6    0.00016   21.2   3.6    1.1  1  DUF4618        Domain of unknown function (DUF4618)
    0.00019   21.3   0.5    0.00049   20.0   0.5    1.8  1  PDDEXK_10      PD-(D/E)XK nuclease superfamily
    0.00024   20.8   3.3    0.00038   20.1   3.3    1.3  1  Exonuc_VII_L   Exonuclease VII, large subunit
    0.00024   21.3   3.2      0.022   15.0   1.7    2.7  2  BLOC1_2        Biogenesis of lysosome-related organelles comp
     0.0012   19.1  10.5     0.0027   17.9  10.5    1.5  1  ATG16          Autophagy protein 16 (ATG16)
      0.002   18.7   7.6      0.084   13.4   0.4    2.6  2  Syntaxin-6_N   Syntaxin 6, N-terminal
     0.0021   17.0   9.7     0.0037   16.2   8.9    1.7  1  Spc7           Spc7 kinetochore protein
     0.0023   18.2   5.6       0.13   12.6   0.4    2.9  2  DUF2383        Domain of unknown function (DUF2383)
     0.0035   15.6   5.6     0.0047   15.2   5.6    1.1  1  EzrA           Septation ring formation regulator, EzrA
     0.0037   16.0   2.3     0.0048   15.6   2.3    1.1  1  AAA_13         AAA domain
     0.0037   17.1   7.4     0.0053   16.6   7.4    1.2  1  FAM184         Family with sequence similarity 184, A and B
      0.004   16.9   1.8      0.006   16.3   1.8    1.2  1  DUF4559        Domain of unknown function (DUF4559)
     0.0044   17.2   0.5      0.096   13.0   0.5    2.4  1  DUF948         Bacterial protein of unknown function (DUF948)
     0.0078   15.7   3.6       0.01   15.4   3.6    1.1  1  HMMR_N         Hyaluronan mediated motility receptor N-termin
  ------ inclusion threshold ------
      0.011   14.9   4.4      0.015   14.4   4.4    1.3  1  APG17          Autophagy protein Apg17
      0.011   13.9   6.5      0.015   13.4   6.5    1.1  1  HOOK           HOOK protein
      0.012   15.5   4.8        1.1    9.3   0.2    2.5  3  Noelin-1       Neurogenesis glycoprotein
      0.013   14.5   5.1      0.016   14.2   5.1    1.1  1  IFT57          Intra-flagellar transport protein 57
      0.014   15.6   3.8       0.33   11.3   0.5    2.5  3  KxDL           Uncharacterized conserved protein
      0.016   15.4  13.2       0.12   12.6   2.7    2.5  2  TMF_TATA_bd    TATA element modulatory factor 1 TATA binding
      0.017   14.5   4.1      0.022   14.2   4.1    1.1  1  FAM76          FAM76 protein
      0.024   12.6   1.8      0.028   12.3   1.8    1.1  1  V_ATPase_I     V-type ATPase 116kDa subunit family
      0.028   14.3   3.3       0.68    9.8   0.2    2.2  2  Sec34          Sec34-like family
      0.032   13.7   0.4          4    6.8   0.2    2.6  3  DUF1487        Protein of unknown function (DUF1487)
      0.032   13.1   6.5      0.057   12.3   6.5    1.3  1  DUF812         Protein of unknown function (DUF812)
      0.039   14.0   3.0       0.79    9.8   3.0    2.2  1  DUF1664        Protein of unknown function (DUF1664)
      0.063   13.9   3.3        2.8    8.6   0.5    3.0  2  SlyX           SlyX
      0.064   13.7   0.0         20    5.7   0.0    2.5  2  T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX d
      0.091   12.6   0.4       0.62    9.9   0.0    2.1  2  Nsp1_C         Nsp1-like C-terminal region
      0.098   11.2   2.7       0.14   10.7   2.7    1.3  1  FapA           Flagellar Assembly Protein A
        0.1   12.6   5.9       0.23   11.5   0.7    2.5  2  baeRF_family2  Bacterial archaeo-eukaryotic release factor fa
       0.12   11.6   6.5       0.39    9.9   5.5    1.8  2  MPS2           Monopolar spindle protein 2
       0.13   12.1   0.6        3.1    7.6   0.0    2.2  2  BDV_P24        Borna disease virus P24 protein
       0.16   11.2   3.9       0.51    9.5   4.0    1.6  2  TMPIT          TMPIT-like protein
       0.17   11.9   1.7       0.69    9.9   1.5    1.9  1  Serine_rich    Serine rich protein interaction domain
       0.18   11.1   9.5       0.99    8.7   9.0    1.9  2  GAS            Growth-arrest specific micro-tubule binding
       0.19   11.6   7.0       0.46   10.3   1.9    2.1  2  Spc29          Spindle Pole Component 29
       0.21   10.9   5.9       0.36   10.1   5.9    1.3  1  CorA           CorA-like Mg2+ transporter protein
       0.22    9.4   1.1       0.56    8.1   1.1    1.5  1  Prominin       Prominin
       0.24   10.6   3.8          1    8.5   3.7    1.9  1  ISG65-75       Invariant surface glycoprotein
       0.25   11.5   4.8       0.92    9.6   3.4    2.1  3  Spore_III_AB   Stage III sporulation protein AB (spore_III_AB
       0.32   11.3   9.5       0.51   10.6   7.4    2.0  2  zf-C4H2        Zinc finger-containing protein
       0.34   11.0   7.5       0.27   11.3   5.6    1.6  1  UPF0242        Uncharacterised protein family (UPF0242) N-ter
       0.37   10.8  10.7       0.79    9.8   5.8    2.5  2  TMF_DNA_bd     TATA element modulatory factor 1 DNA binding
        0.4   10.5   5.9       0.15   11.9   2.0    2.3  2  DUF919         Nucleopolyhedrovirus protein of unknown functi
       0.56   10.4   8.6       0.74   10.0   6.0    2.1  2  CREPT          Cell-cycle alteration and expression-elevated 
       0.66   10.1   3.7        2.4    8.3   3.7    1.8  1  Fib_alpha      Fibrinogen alpha/beta chain family
       0.67    9.8   3.6        3.9    7.4   0.5    2.2  2  Sec8_exocyst   Sec8 exocyst complex component specific domain
       0.76    9.1   5.3        1.7    8.0   2.0    2.5  3  Helo_like_N    Fungal N-terminal domain of STAND proteins
       0.77    9.5   8.4        0.3   10.8   2.7    2.5  3  DUF745         Protein of unknown function (DUF745)
       0.89    9.6   6.8       0.74    9.8   1.3    2.5  2  Sec2p          GDP/GTP exchange factor Sec2p
          1    9.8   5.5          3    8.3   0.2    3.0  3  FlaC_arch      Flagella accessory protein C (FlaC)
        1.4    9.5   9.4        2.2    8.8   9.4    1.3  1  APG6_N         Apg6 coiled-coil region
        1.4    9.3   8.4        2.1    8.8   7.6    1.7  1  DUF4200        Domain of unknown function (DUF4200)
        1.7    9.4   8.8        7.3    7.3   0.9    2.7  2  DUF4404        Domain of unknown function (DUF4404)
        1.9    7.7   5.4        1.3    8.3   1.7    2.0  2  DUF3450        Protein of unknown function (DUF3450)
        2.2    8.5   5.8        4.9    7.3   5.8    1.6  1  MutS_III       MutS domain III
        2.4    8.2   9.0       0.24   11.4   3.3    2.2  2  Laminin_II     Laminin Domain II
        3.2    6.7   8.9        4.6    6.2   8.6    1.4  1  Atg14          Vacuolar sorting 38 and autophagy-related subu
        3.8    7.8   8.2        2.1    8.6   1.1    2.6  2  Seryl_tRNA_N   Seryl-tRNA synthetase N-terminal domain
        4.5    7.7   8.4         11    6.4   7.8    2.0  1  CENP-H         Centromere protein H (CENP-H)
        4.5    7.3   8.6         14    5.7   1.4    2.5  2  SOAR           STIM1 Orai1-activating region
          6    6.9   8.4         45    4.0   8.4    2.0  1  RP-C_C         Replication protein C C-terminal region
        7.2    7.5  13.5          2    9.2   1.9    3.7  3  VAPB_antitox   Putative antitoxin
          9    6.8  11.1          4    8.0   2.3    3.0  2  Cep57_MT_bd    Centrosome microtubule-binding domain of Cep57


Domain annotation for each model (and alignments):
>> DUF3782  Protein of unknown function (DUF3782)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   5.6       3.8     1e+03       9       9 ..      93      93 ..      10     124 .. 0.71
   2 !   41.3   3.0   4.6e-13   1.2e-10       9      77 ..     118     192 ..     106     193 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 3.8
                        DUF3782  9 e 9 
                                   e
  gi|119720608|ref|YP_921103.1| 93 E 93
                                   1 PP

  == domain 2  score: 41.3 bits;  conditional E-value: 4.6e-13
                        DUF3782   9 e...eeetkedleelekeieklertigaLGaRWGlvsEeafReglkeiLeealgv....kVekwlyyDkeGeVygy 77 
                                    +    ee++e+l+el+k++ +l+ ++g++G+RWG + E+ + e +k++L    gv    k+ek++y+D +G +y +
  gi|119720608|ref|YP_921103.1| 118 HsriLEEHSERLKELTKSVGELKAAVGSIGRRWGRDLEKLVYELYKDALLGL-GVkdvgKIEKYTYVDIDGKYYRR 192
                                    144589*********************************************9.*999999************9975 PP

>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.9   9.6e-09   2.6e-06      74     169 ..      24     119 ..      21     122 .. 0.96
   2 ?    5.1   0.0     0.067        18     106     147 ..     105     146 ..     101     149 .. 0.61
   3 ?    0.7   0.0       1.5     4e+02      50      62 ..     243     258 ..     215     262 .. 0.73

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 9.6e-09
                                    HHHHHHHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      MCPsignal  74 AdEVrkLAersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaasee 153
                                    AdE r+LAe  +  a+ +++  +   + i+d  +++ee +++v + s + ee  ++l e + +++e+a ++++ ++  ee
  gi|119720608|ref|YP_921103.1|  24 ADELRDLAEAVKVLAEYMKTGFESTLRAIEDHSKMIEELTKEVRNNSRILEEHSKVLGEHSRRIEELAGEIRNHSRVLEE 103
                                    9******************************************************************************* PP

                                    HHHHHHHHHHHHHHHH CS
                      MCPsignal 154 qsasieevnqaveeva 169
                                     s+ +ee ++ v + +
  gi|119720608|ref|YP_921103.1| 104 HSKRLEELTREVRNHS 119
                                    *******999998765 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.067
                                    ....HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHH CS
                      MCPsignal 106 vesleetrqrveegselveetgealkeiveavaevadlvqei 147
                                     + lee +++v + s + ee  e lke++++v+e+++ v  i
  gi|119720608|ref|YP_921103.1| 105 SKRLEELTREVRNHSRILEEHSERLKELTKSVGELKAAVGSI 146
                                    445566666666666666666666776666666666666555 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 1.5
                                    HHHHHHHH...HHHHH CS
                      MCPsignal  50 NlLALNAa...iEAAR 62 
                                     ++A+NAa   iEAAR
  gi|119720608|ref|YP_921103.1| 243 IIVAVNAAkeaIEAAR 258
                                    5789999633377777 PP

>> DUF4618  Domain of unknown function (DUF4618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   3.6     6e-07   0.00016      95     230 ..      25     158 ..      10     167 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 6e-07
                        DUF4618  95 akvqklqeelnvLstYkDkeYpvkavqIanlvrqlqqlkdsqqdeldeleelikevleklskkiqkkkekllkslaektl 174
                                    ++++ l e ++vL  Y+   +      I+ +++ +++l ++ +++   lee  ++vl + s++i++   ++ ++   ++l
  gi|119720608|ref|YP_921103.1|  25 DELRDLAEAVKVLAEYMKTGFESTLRAIEDHSKMIEELTKEVRNNSRILEEH-SKVLGEHSRRIEELAGEIRNHS--RVL 101
                                    46788999***********************************999988885.6799*********999999986..99* PP

                        DUF4618 175 katqeaLlqktlenqvlkkeiekfrefieeleeeipeLkaeveqLqaqae.eprevi 230
                                    +++++ L++ t+e ++ ++ +e++ e  +el++ + eLka+v  + ++   +  + +
  gi|119720608|ref|YP_921103.1| 102 EEHSKRLEELTREVRNHSRILEEHSERLKELTKSVGELKAAVGSIGRRWGrDLEKLV 158
                                    ******************************************988776655555555 PP

>> PDDEXK_10  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.5   1.8e-06   0.00049       2      74 .]     195     263 ..     194     263 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.8e-06
                      PDDEXK_10   2 evelDvvvkdgkvilvEiksslkrgDlavikrkkelYekakgvkvdrlivvtpfiddrnpervkavAerlgie 74 
                                    ++elD+ ++d +v  +E+ks l+  D++ ++ k  +  k  g+  +r i+v+    ++    ++++A++lgi+
  gi|119720608|ref|YP_921103.1| 195 RIELDIYMHDTSVYFIEVKSLLEVDDVYWFNEKCGIVSKIIGRTPTRRIIVAVNAAKE----AIEAARELGID 263
                                    79******************************************88888887555555....99*******95 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   3.3   1.4e-06   0.00038     147     246 ..      35     136 ..      12     165 .. 0.58

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.4e-06
                   Exonuc_VII_L 147 eqleelerrlekaikrlleekkqrleklasrlkspeellerkrqrldeleerleralkkqlkkkrerleelkerl.k..e 223
                                    + l+e+++   +++ r++e++++++e+l++++++++++le++++ l e ++r+e+ l+ +++++++ lee ++rl +  +
  gi|119720608|ref|YP_921103.1|  35 KVLAEYMKTGFESTLRAIEDHSKMIEELTKEVRNNSRILEEHSKVLGEHSRRIEE-LAGEIRNHSRVLEEHSKRLeEltR 113
                                    2333333333333445557777777788777777777777777777777777777.666666666666666666632433 PP

                   Exonuc_VII_L 224 kleekkerlkklkerlelleekk 246
                                    +++++++ l++ +erl++l+++ 
  gi|119720608|ref|YP_921103.1| 114 EVRNHSRILEEHSERLKELTKSV 136
                                    33333333333333333333222 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.2     0.011       2.9      19      81 ..       5      66 ..       1      68 [. 0.81
   2 !   15.0   1.7   8.2e-05     0.022       2      88 ..      57     143 ..      50     162 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.011
                        BLOC1_2 19 vedyklLeklNeaase..kykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeav 81
                                   + d++ Le++ e+a +  + ++l+d a+ +++ +e+++     +++ l+ i++  k ++eL++ v
  gi|119720608|ref|YP_921103.1|  5 SIDWSRLEEVVERAVRraRADELRDLAEAVKVLAEYMKT---GFESTLRAIEDHSKMIEELTKEV 66
                                   567888888888876511568999999999999999999...9****************999877 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 8.2e-05
                        BLOC1_2   2 rmfekvskyleaeleatvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeav 81 
                                    +m+e+++k ++++  +  e+ k+L +  ++ +e   ++++    le+ +++l+e+  e++++ + +++  ++++eL++ v
  gi|119720608|ref|YP_921103.1|  57 KMIEELTKEVRNNSRILEEHSKVLGEHSRRIEELAGEIRNHSRVLEEHSKRLEELTREVRNHSRILEEHSERLKELTKSV 136
                                    67888888888888888888888888888888888888888888888888888888888888888888888888888888 PP

                        BLOC1_2  82 seLDeys 88 
                                     eL + +
  gi|119720608|ref|YP_921103.1| 137 GELKAAV 143
                                    8886655 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9  10.5     1e-05    0.0027      69     158 ..      52     141 ..      16     146 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1e-05
                          ATG16  69 nskqsakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelre 148
                                     ++ s+ i++l++++      l+e  k  ge++ r+ el  e++   + l+e ++rl+el++e+++ ++ l+++ e+l+e
  gi|119720608|ref|YP_921103.1|  52 IEDHSKMIEELTKEVRNNSRILEEHSKVLGEHSRRIEELAGEIRNHSRVLEEHSKRLEELTREVRNHSRILEEHSERLKE 131
                                    345788999999999999999*********************************************************** PP

                          ATG16 149 keklvqdlqD 158
                                    ++k v +l+ 
  gi|119720608|ref|YP_921103.1| 132 LTKSVGELKA 141
                                    ***9999886 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.4   0.00031     0.084      48      97 ..      17      68 ..       5      70 .. 0.80
   2 ?    8.1   1.9     0.015       3.9      17      64 ..      90     136 ..      68     165 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00031
                   Syntaxin-6_N 48 kalrsiewd.ledLeetvriveknpsk.fkidekelsrrrafveevreevke 97
                                   +a+r ++ d l+dL e+v+++ +  +  f+ + ++++ + +++ee+ +ev++
  gi|119720608|ref|YP_921103.1| 17 RAVRRARADeLRDLAEAVKVLAEYMKTgFESTLRAIEDHSKMIEELTKEVRN 68
                                   55555554339********997766556*********************975 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.015
                   Syntaxin-6_N  17 aeslyrrwerlledtssstseeldetrteLrka...lrsiewdledLeetv 64 
                                    +++ +r+ +r+le+     s+ l+e+++e+r+    l++ ++ l++L ++v
  gi|119720608|ref|YP_921103.1|  90 LAGEIRNHSRVLEEH----SKRLEELTREVRNHsriLEEHSERLKELTKSV 136
                                    334444444444332....44444444444444111334444444444444 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   8.9   1.4e-05    0.0037     134     240 ..      56     140 ..      29     150 .. 0.51

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.4e-05
                           Spc7 134 mqllegLkegleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelka 213
                                    ++++e+L +++++n  +lee +++L ++   ++el  e++++   lee  ++l+e  +e                     
  gi|119720608|ref|YP_921103.1|  56 SKMIEELTKEVRNNSRILEEHSKVLGEHSRRIEELAGEIRNHSRVLEEHSKRLEELTRE--------------------- 114
                                    34445555555555555555555555555555555555555555555555555554444..................... PP

                           Spc7 214 eieekkkelaelqeqleeleekieelk 240
                                     ++++++ l+e  e+l+el++++ elk
  gi|119720608|ref|YP_921103.1| 115 -VRNHSRILEEHSERLKELTKSVGELK 140
                                    .44444444444444444444444443 PP

>> DUF2383  Domain of unknown function (DUF2383)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.4   0.00048      0.13      38      92 ..      50     102 ..      35     103 .. 0.87
   2 !    8.5   0.4    0.0095       2.5      38      85 ..      99     146 ..      96     166 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00048
                                    HHHHHHHHHHHHHHHHHHHCT----------------------------HHHHHH CS
                        DUF2383  38 riaeereeaaeeLqseiralggepedggslagklhrawvdlksaltsndeeaile 92 
                                    r +e++++ +eeL +e+r++ +  e+++ ++g+  r + +l + + ++++  +le
  gi|119720608|ref|YP_921103.1|  50 RAIEDHSKMIEELTKEVRNNSRILEEHSKVLGEHSRRIEELAGEIRNHSR--VLE 102
                                    6799******************************9999888887777664..555 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0095
                                    HHHHHHHHHHHHHHHHHHHCT--------------------------- CS
                        DUF2383  38 riaeereeaaeeLqseiralggepedggslagklhrawvdlksaltsn 85 
                                    r+ ee++++ eeL  e+r++ +  e+++  + +l + + +lk+a++s 
  gi|119720608|ref|YP_921103.1|  99 RVLEEHSKRLEELTREVRNHSRILEEHSERLKELTKSVGELKAAVGSI 146
                                    6779**************************************999885 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   5.6   1.8e-05    0.0047     310     406 ..      44     140 ..      25     143 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.8e-05
                                    SSSHHHHT--HHHHTTGGG-TTTS-GGGSSTTTSTTHHHHHHHHHHHHHHHHHHHHHHS-SS---STTGGGTHHHHHHHH CS
                           EzrA 310 elkeklehlekqnkelkeeldrlkqsYeLseeeleklrelekelkelekdyeeleekleekkvaYSelqeeleeleekle 389
                                     +++ l  +e+ +k+++e +++++++ ++ ee  + l e +++++el  ++++    lee++    el+ e+++ ++ le
  gi|119720608|ref|YP_921103.1|  44 GFESTLRAIEDHSKMIEELTKEVRNNSRILEEHSKVLGEHSRRIEELAGEIRNHSRVLEEHSKRLEELTREVRNHSRILE 123
                                    589999************************************************************************** PP

                                    HHHHHHHHHHHHHHHHH CS
                           EzrA 390 eieekqeeileslkslr 406
                                    e +e+++e+ +s+++l+
  gi|119720608|ref|YP_921103.1| 124 EHSERLKELTKSVGELK 140
                                    **************998 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   2.3   1.8e-05    0.0048     364     460 ..      38     143 ..       6     153 .. 0.48

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.8e-05
                         AAA_13 364 iesikklvaeineliakhNekvanleeekeeakkklelhlv.........eeleseldeykkkykklekaieklekelke 434
                                    +e +k   ++  + i++h +++++l++e+ +    le h           eel  e+ +  + +++ +k +e+l++e+++
  gi|119720608|ref|YP_921103.1|  38 AEYMKTGFESTLRAIEDHSKMIEELTKEVRNNSRILEEHSKvlgehsrriEELAGEIRNHSRVLEEHSKRLEELTREVRN 117
                                    23445555555555555555555555555555555555543344444444444444444444444444444444444444 PP

                         AAA_13 435 eeaelkkleeeikeLekqlrdekpaa 460
                                    +++ l++  e+ keL k++ + k a+
  gi|119720608|ref|YP_921103.1| 118 HSRILEEHSERLKELTKSVGELKAAV 143
                                    44444444444444444444444443 PP

>> FAM184  Family with sequence similarity 184, A and B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   7.4     2e-05    0.0053      71     181 ..      32     143 ..      10     165 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2e-05
                         FAM184  71 qalaefeqykrrveerelkleaehsqkvvelsreveevkrkFeeklrqfaqlqeqle..qekekaLeelrkkhreeveeL 148
                                    +a++   +y ++  e++l + ++hs+ + el +ev +  r  ee ++ + +   ++e  + + ++ +++ ++h++ +eeL
  gi|119720608|ref|YP_921103.1|  32 EAVKVLAEYMKTGFESTLRAIEDHSKMIEELTKEVRNNSRILEEHSKVLGEHSRRIEelAGEIRNHSRVLEEHSKRLEEL 111
                                    56666677888888999999999999999999999999999999999999999999988667777888888899999999 PP

                         FAM184 149 lkeqeaqsekllkeqekleekhkaeveklkeev 181
                                     +e +++s+ l++  e+l+e  k +v +lk++v
  gi|119720608|ref|YP_921103.1| 112 TREVRNHSRILEEHSERLKELTK-SVGELKAAV 143
                                    99999999999999999988654.566676665 PP

>> DUF4559  Domain of unknown function (DUF4559)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   1.8   2.2e-05     0.006     185     304 ..      26     146 ..       9     151 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.2e-05
                        DUF4559 185 eleeaeeaieellkilkqefeislke....ddevrvltdvllslqklkeleeellkedatkldelvlraeeqkiskeell 260
                                    el ++ ea++ l + +k  fe  l++       ++ lt+ +++++ ++e ++++l e+  +++el+ +  ++    ee++
  gi|119720608|ref|YP_921103.1|  26 ELRDLAEAVKVLAEYMKTGFESTLRAiedhSKMIEELTKEVRNNSRILEEHSKVLGEHSRRIEELAGEIRNHSRVLEEHS 105
                                    566777888888888999999999987333333455566667778999*****************888777777777775 PP

                        DUF4559 261 kelqvlkeflnknkdLkenlkedvkklqeieekldkldedvtel 304
                                    k+l+    + +++++  + l+e  ++l+e+ + +++l+  v ++
  gi|119720608|ref|YP_921103.1| 106 KRLEE---LTREVRNHSRILEEHSERLKELTKSVGELKAAVGSI 146
                                    55554...444444444444566667777777777777666655 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.5   0.00036     0.096      20      85 ..      79     144 ..      15     147 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00036
                         DUF948  20 vllklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvs 85 
                                    vl + ++ ++e+a  i++  + +++ +k +e+l+++v++    ++e++e++++lt++v++l ++v 
  gi|119720608|ref|YP_921103.1|  79 VLGEHSRRIEELAGEIRNHSRVLEEHSKRLEELTREVRNHSRILEEHSERLKELTKSVGELKAAVG 144
                                    444556666777777777777777778888888888888777788889999999999988888775 PP

>> HMMR_N  Hyaluronan mediated motility receptor N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   3.6   3.8e-05      0.01     191     292 ..      34     136 ..      15     155 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.8e-05
                         HMMR_N 191 lqvtqknLee.skakvaqLkeklvslekekieekseteklleyieelsnvseqlekykldiaqleellkekndeiesLks 269
                                    ++v+ + +++ + ++++++++  + +e++ +e + +++ l+e  + l + s+++e    +i++   +l+e+ + +e+L  
  gi|119720608|ref|YP_921103.1|  34 VKVLAEYMKTgFESTLRAIEDHSKMIEELTKEVRNNSRILEEHSKVLGEHSRRIEELAGEIRNHSRVLEEHSKRLEELTR 113
                                    55555555542578999*************************************************************** PP

                         HMMR_N 270 sLeekeqelskqvkdlnekckll 292
                                    ++++ +  l+++ + l+e  k +
  gi|119720608|ref|YP_921103.1| 114 EVRNHSRILEEHSERLKELTKSV 136
                                    ***99998888888888777665 PP

>> APG17  Autophagy protein Apg17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   4.4   5.7e-05     0.015     234     323 ..      53     139 ..      13     143 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.7e-05
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHHHHHH...HHHHH CS
                          APG17 234 ekDaaeledVvkelqerleemekakkllsekkeeiekllsalkkaleeleevgkklpeylaifkaeeeflerweeekeki 313
                                    e  ++ +e+  ke++++ +++e+ +k l e+ ++ie+l  ++++  + lee +k+l+e    +++ +++le+   + e++
  gi|119720608|ref|YP_921103.1|  53 EDHSKMIEELTKEVRNNSRILEEHSKVLGEHSRRIEELAGEIRNHSRVLEEHSKRLEELTREVRNHSRILEE---HSERL 129
                                    55567789999**************************************************77777777777...55555 PP

                                    HHHHHHHHHH CS
                          APG17 314 eekleeleeL 323
                                    +e ++ + eL
  gi|119720608|ref|YP_921103.1| 130 KELTKSVGEL 139
                                    5555555554 PP

>> HOOK  HOOK protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   6.5   5.8e-05     0.015     444     547 ..      35     140 ..       9     155 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.8e-05
                           HOOK 444 nlaaellpaevreklirLqhENKmLklkqeg..seeekltelqelledanrrkneLetenrlanqrileLeaqveelqka 521
                                    ++ ae + + +  +l  ++   Km+++  ++  ++++ l+e ++ l +  rr++eL  e r +   ++e ++++eel+++
  gi|119720608|ref|YP_921103.1|  35 KVLAEYMKTGFESTLRAIEDHSKMIEELTKEvrNNSRILEEHSKVLGEHSRRIEELAGEIRNHSRVLEEHSKRLEELTRE 114
                                    44456666666666666666666664332221022333455566666666666666666666666666666666666666 PP

                           HOOK 522 lqeqgskaedssllkkkleehleklk 547
                                     +++    e+ s+  k+l++ + +lk
  gi|119720608|ref|YP_921103.1| 115 VRNHSRILEEHSERLKELTKSVGELK 140
                                    66655555554444444444444443 PP

>> Noelin-1  Neurogenesis glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.2    0.0041       1.1      34      90 ..      20      77 ..      14      84 .. 0.72
   2 ?    7.9   0.7     0.011       2.9      37      92 ..      83     138 ..      79     145 .. 0.90
   3 ?    2.7   0.0      0.47   1.2e+02      37      68 ..     125     156 ..     121     158 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0041
                       Noelin-1 34 rDarsrqlrqllekvqnlsqsievldlRtsrdlqyvrkt.etllktlesklkvveedr 90
                                   r ar  +lr+l e v+ l++ ++   + t r+++  +k+ e+l k+++++ + +ee+ 
  gi|119720608|ref|YP_921103.1| 20 RRARADELRDLAEAVKVLAEYMKTGFESTLRAIEDHSKMiEELTKEVRNNSRILEEHS 77
                                   67999****************9998888877776444432455555655555555554 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.011
                       Noelin-1  37 rsrqlrqllekvqnlsqsievldlRtsrdlqyvrktetllktlesklkvveedrke 92 
                                    +sr++ +l  +++n s+ +e  ++R ++   +vr+   +l++ +++lk+++++  e
  gi|119720608|ref|YP_921103.1|  83 HSRRIEELAGEIRNHSRVLEEHSKRLEELTREVRNHSRILEEHSERLKELTKSVGE 138
                                    6899********************************************99887655 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.47
                       Noelin-1  37 rsrqlrqllekvqnlsqsievldlRtsrdlqy 68 
                                    +s++l++l++ v  l   +  + +R  rdl+ 
  gi|119720608|ref|YP_921103.1| 125 HSERLKELTKSVGELKAAVGSIGRRWGRDLEK 156
                                    6789*************************985 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   5.1   6.1e-05     0.016     204     321 ..      27     143 ..       9     150 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6.1e-05
                          IFT57 204 leRvlpqLkvtikadakdWrahleqmkkhkksieeslpetksqlkklhedisktlekiesrEkylnsqleellqeyreaq 283
                                    l+  + + kv  +  +  ++++l ++++h+k iee ++e++++ +++ e+ sk+l + + r + l  ++++  + ++e +
  gi|119720608|ref|YP_921103.1|  27 LRDLAEAVKVLAEYMKTGFESTLRAIEDHSKMIEELTKEVRNN-SRILEEHSKVLGEHSRRIEELAGEIRNHSRVLEEHS 105
                                    5555555566445555589999999999999999999998876.678888999999999999999999999999999999 PP

                          IFT57 284 eelsevkekykqlsegvseltrelaeiseelekvkqem 321
                                    ++l+e+++++++ s+ ++e ++ l+e+++ + ++k  +
  gi|119720608|ref|YP_921103.1| 106 KRLEELTREVRNHSRILEEHSERLKELTKSVGELKAAV 143
                                    99999999999999999999999999999988888765 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.2      0.24        64      31      66 ..      33      68 ..      21      83 .. 0.57
   2 ?    5.5   1.1     0.075        20      38      71 ..      82     115 ..      46     116 .. 0.63
   3 ?   11.3   0.5    0.0012      0.33      36      78 ..     101     143 ..      95     146 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.24
                           KxDL 31 eLlelnalsqerlaklrarfkqgtkllkevkkdLes 66
                                    ++ l +++++ ++++   ++++ k++ e+ k+ ++
  gi|119720608|ref|YP_921103.1| 33 AVKVLAEYMKTGFESTLRAIEDHSKMIEELTKEVRN 68
                                   444455555555555555555555555555555444 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.075
                           KxDL  38 lsqerlaklrarfkqgtkllkevkkdLesifkki 71 
                                    + ++r ++l  +++++ ++l e  k Le +++ +
  gi|119720608|ref|YP_921103.1|  82 EHSRRIEELAGEIRNHSRVLEEHSKRLEELTREV 115
                                    4456666777777777777777777777766665 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.0012
                           KxDL  36 nalsqerlaklrarfkqgtkllkevkkdLesifkkirslkakl 78 
                                     ++ ++rl++l+ +++++ + l e  + L+ ++k +  lka +
  gi|119720608|ref|YP_921103.1| 101 LEEHSKRLEELTREVRNHSRILEEHSERLKELTKSVGELKAAV 143
                                    567899*******************************999875 PP

>> TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   2.3    0.0065       1.8      58     101 ..      51      94 ..      28      96 .. 0.89
   2 ?   12.6   2.7   0.00045      0.12      60     107 ..      95     142 ..      92     145 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0065
                    TMF_TATA_bd  58 elkelkkeleelekeleelqeryetlLellGeksEeveELraDv 101
                                    + ++ +k +eel+ke+++ ++ +e+  ++lGe s ++eEL  ++
  gi|119720608|ref|YP_921103.1|  51 AIEDHSKMIEELTKEVRNNSRILEEHSKVLGEHSRRIEELAGEI 94 
                                    56788999********************************8777 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00045
                    TMF_TATA_bd  60 kelkkeleelekeleelqeryetlLellGeksEeveELraDvaDlKem 107
                                    ++ ++ lee +k+leel+++  +   +l e sE+ +EL + v +lK+ 
  gi|119720608|ref|YP_921103.1|  95 RNHSRVLEEHSKRLEELTREVRNHSRILEEHSERLKELTKSVGELKAA 142
                                    66778899999***********************************86 PP

>> FAM76  FAM76 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   4.1   8.1e-05     0.022     205     297 ..      43     141 ..      11     144 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 8.1e-05
                          FAM76 205 tskksldsnssdhlvavtqLkeeiaslkkqleqkdqellekdkkitelkae...llekekelreklkelekeakekiekl 281
                                    t  +s+  +  dh  ++++L +e+++  + le++ ++l e  + i el +e   + +  +e+ ++l+el +e++++   l
  gi|119720608|ref|YP_921103.1|  43 TGFESTLRAIEDHSKMIEELTKEVRNNSRILEEHSKVLGEHSRRIEELAGEirnHSRVLEEHSKRLEELTREVRNHSRIL 122
                                    44456777889*************************************99822244555667778888887776665555 PP

                          FAM76 282 ...ekkirellkevaelsk 297
                                       +++ +el+k v el+ 
  gi|119720608|ref|YP_921103.1| 123 eehSERLKELTKSVGELKA 141
                                    1115677888888888875 PP

>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.8   0.00011     0.028      21     116 ..      41     129 ..      10     168 .. 0.47

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00011
                     V_ATPase_I  21 fqrkfvkevrrcdemerklrfleeeieklekavikeeeaeesleapeekeldeleeelekleeelkelnenleklkkeln 100
                                    ++  f + +r +++ +++++ l++e+++++ +  ++++       +++++++el  e++++ + l+e ++ le+l++e++
  gi|119720608|ref|YP_921103.1|  41 MKTGFESTLRAIEDHSKMIEELTKEVRNNSRILEEHSK----VLGEHSRRIEELAGEIRNHSRVLEEHSKRLEELTREVR 116
                                    45556666666666666666666666663333333332....22222333333333333333333333333333332222 PP

                     V_ATPase_I 101 elvelkavlekakefl 116
                                    +   ++ +le+ +e l
  gi|119720608|ref|YP_921103.1| 117 N---HSRILEEHSERL 129
                                    1...111222111111 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.2    0.0025      0.68      18      67 ..      48      97 ..      39     100 .. 0.90
   2 ?    4.8   0.3     0.086        23       5      45 ..     101     141 ..      97     148 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0025
                          Sec34 18 qtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieek 67
                                    +++++++ + +ee  k+v ++++ l+e+++ l e+ +r+eela ei+++
  gi|119720608|ref|YP_921103.1| 48 TLRAIEDHSKMIEELTKEVRNNSRILEEHSKVLGEHSRRIEELAGEIRNH 97
                                   5677888999999999*******************************985 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.086
                          Sec34   5 LeskeeecdelleqtdealeqLeeleekfksvsektsslhe 45 
                                    Le+++++++el +++++  + Lee +e+ k+ +++  +l++
  gi|119720608|ref|YP_921103.1| 101 LEEHSKRLEELTREVRNHSRILEEHSERLKELTKSVGELKA 141
                                    56666666666666666666666666666666666665554 PP

>> DUF1487  Protein of unknown function (DUF1487)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.2     0.015         4      15      65 ..      29      78 ..      26     110 .. 0.80
   2 ?   -1.4   0.0       4.8   1.3e+03      54      71 ..     105     122 ..      89     136 .. 0.75
   3 ?    4.1   0.0       0.1        27     118     174 ..     197     255 ..     183     263 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.015
                        DUF1487 15 DlnsalealveslkePfaegavatvlveesirdefvervrsklkplseeva 65
                                   Dl++a+++l+e +k  f + + a +  + ++ +e+ + vr++ + l+e+ +
  gi|119720608|ref|YP_921103.1| 29 DLAEAVKVLAEYMKTGFESTLRA-IEDHSKMIEELTKEVRNNSRILEEHSK 78
                                   99***************987655.78999*************998887754 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 4.8
                        DUF1487  54 rsklkplseevaeHpsyl 71 
                                     ++l++l +ev +H+  l
  gi|119720608|ref|YP_921103.1| 105 SKRLEELTREVRNHSRIL 122
                                    578899999999998654 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.1
                        DUF1487 118 TlhtFrnakEvvkllakeslkfasvsvwneklaavyelvarln..vdvftiNCakvslk 174
                                     l ++   + v  +  k  l+ + v+ +nek + v +++ r +    ++++N ak+ ++
  gi|119720608|ref|YP_921103.1| 197 ELDIYMHDTSVYFIEVKSLLEVDDVYWFNEKCGIVSKIIGRTPtrRIIVAVNAAKEAIE 255
                                    5667777778888999999**********************995456788999888876 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   6.5   0.00021     0.057     325     437 ..      20     133 ..       8     164 .. 0.50

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00021
                         DUF812 325 kkkreeeleelqeqieeleskiee.leeeikklessikqveeeleeekeeneelekevklkkktlellpdaeeniekLqa 403
                                    + +r +el++l e ++ l + +++  e++++++e++ k +ee ++e +++   le+  k+       +++  + i++  +
  gi|119720608|ref|YP_921103.1|  20 RRARADELRDLAEAVKVLAEYMKTgFESTLRAIEDHSKMIEELTKEVRNNSRILEEHSKVLGEHSRRIEELAGEIRNHSR 99 
                                    44555555555555555555444324555555555555555555555555555555555544444444444555555555 PP

                         DUF812 404 lveasaqrlvelakqWekhRvplieeyrelkesk 437
                                    ++e+ ++rl el ++  +h + l e  ++lke  
  gi|119720608|ref|YP_921103.1| 100 VLEEHSKRLEELTREVRNHSRILEEHSERLKELT 133
                                    5555555555555555555444444444444432 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   3.0     0.003      0.79      62     116 ..      88     142 ..      22     163 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.003
                        DUF1664  62 rhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesk 116
                                    ++L+ +i +  + l+e ++  +e+++ev + ++ l+e +e ++++ + v +l++ 
  gi|119720608|ref|YP_921103.1|  88 EELAGEIRNHSRVLEEHSKRLEELTREVRNHSRILEEHSERLKELTKSVGELKAA 142
                                    2444455555555555555555555555555555555555555555555555555 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.3     0.079        21       5      45 ..      59      99 ..      51     109 .. 0.58
   2 ?    8.6   0.5     0.011       2.8      17      50 ..     106     139 ..      84     149 .. 0.53

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.079
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           SlyX  5 leeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllae 45
                                   +eeL  ++    + +ee ++v+ e+ ++i++l  ++r   +
  gi|119720608|ref|YP_921103.1| 59 IEELTKEVRNNSRILEEHSKVLGEHSRRIEELAGEIRNHSR 99
                                   44444444455556666666666666666666666665544 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.011
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXX CS
                           SlyX  17 dtieeLndvvaeqqqqidrlqrqlrllaerlkel 50 
                                    + +eeL ++v ++ + +++  ++l++l++ + el
  gi|119720608|ref|YP_921103.1| 106 KRLEELTREVRNHSRILEEHSERLKELTKSVGEL 139
                                    3345555555555555555555555555555555 PP

>> T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX diderm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.094        25       8      38 ..      23      53 ..      21      78 .. 0.88
   2 ?    5.7   0.0     0.076        20       9      76 ..      91     157 ..      84     165 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.094
                  T7SS_ESX_EspC  8 dpdhlrelaakhdevaaeiasavaaaagasa 38
                                    +d+lr la+ ++  a+++++  +++++a +
  gi|119720608|ref|YP_921103.1| 23 RADELRDLAEAVKVLAEYMKTGFESTLRAIE 53
                                   589*******************999977665 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.076
                  T7SS_ESX_EspC   9 pdhlrelaakhdevaaeiasavaaaagasaavldshGpicaatndavaaaeaarraagealaaasteL 76 
                                    ++++r ++  ++e +++++ +++ + ++ +++l+ h     +++++v +++aa  + g+++ +++++L
  gi|119720608|ref|YP_921103.1|  91 AGEIRNHSRVLEEHSKRLEELTREV-RNHSRILEEHSERLKELTKSVGELKAAVGSIGRRWGRDLEKL 157
                                    6778888888888888888888888.888888888888888888888888888888888887777776 PP

>> Nsp1_C  Nsp1-like C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       3.4     9e+02      73      95 ..      42      64 ..      24      85 .. 0.54
   2 ?    9.9   0.0    0.0023      0.62      22      73 ..      92     143 ..      83     155 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 3.4
                         Nsp1_C 73 qnkidqeLeyiesqqdeLeslLd 95
                                   ++  + +L  ie   + +e+l +
  gi|119720608|ref|YP_921103.1| 42 KTGFESTLRAIEDHSKMIEELTK 64
                                   44455555555544444333333 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0023
                         Nsp1_C  22 elinkWtteLeeqekeFeeqakkvneWDrvLvengekIskLysevleaeqeq 73 
                                      i + +  Lee +k  ee + +v++  r+L e +e++++L ++v e +++ 
  gi|119720608|ref|YP_921103.1|  92 GEIRNHSRVLEEHSKRLEELTREVRNHSRILEEHSERLKELTKSVGELKAAV 143
                                    557888999************************************9988775 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   2.7   0.00054      0.14     335     415 ..      55     142 ..      22     157 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00054
                           FapA 335 lkeklkeleeeleeleeeleklkkk.......ikklpk.lkaekqlesekkeqlkklletkeklkeeleeleeelkelke 406
                                    + ++++el +e+++  + le++ k        i++l   +++ +++ +e+++ l++l+++  +++++lee+ e+lkel +
  gi|119720608|ref|YP_921103.1|  55 HSKMIEELTKEVRNNSRILEEHSKVlgehsrrIEELAGeIRNHSRVLEEHSKRLEELTREVRNHSRILEEHSERLKELTK 134
                                    33344444444444433333333333334455555543134477788888888888888888888888888888888888 PP

                           FapA 407 eleskkeea 415
                                    ++ +  ++a
  gi|119720608|ref|YP_921103.1| 135 SVGEL-KAA 142
                                    88777.344 PP

>> baeRF_family2  Bacterial archaeo-eukaryotic release factor family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.5      0.28        74     116     143 ..       7      34 ..       4      37 .. 0.82
   2 ?   11.5   0.7   0.00085      0.23      81     123 ..      90     132 ..      54     142 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.28
                  baeRF_family2 116 drealaeevaealaerrarrreevlerf 143
                                    d   l+e v++a+++ ra++ ++++e +
  gi|119720608|ref|YP_921103.1|   7 DWSRLEEVVERAVRRARADELRDLAEAV 34 
                                    5567899999999999999999999865 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00085
                  baeRF_family2  81 laGDvrarsllrdeLpervrelvvevegggraagadrealaee 123
                                    laG++r  s + +e ++r++el+ ev +++r  + + e l+e 
  gi|119720608|ref|YP_921103.1|  90 LAGEIRNHSRVLEEHSKRLEELTREVRNHSRILEEHSERLKEL 132
                                    9*****************************9888777777665 PP

>> MPS2  Monopolar spindle protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.8      0.41   1.1e+02     163     197 ..      56      90 ..      10      98 .. 0.57
   2 ?    9.9   5.5    0.0015      0.39     115     208 ..      56     150 ..      50     160 .. 0.70

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.41
                           MPS2 163 evrveslkdELeakdevlrekeRelleLkkrlsey 197
                                       +e+l +E+++  ++l+e+ + l e  +r++e+
  gi|119720608|ref|YP_921103.1|  56 SKMIEELTKEVRNNSRILEEHSKVLGEHSRRIEEL 90 
                                    33345555555555555555555555555555443 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0015
                           MPS2 115 vkrlvvlssknsekdslstprkkilldllkkqesPekl.rrsnrklkaLevrveslkdELeakdevlrekeRelleLkkr 193
                                    +k++ +l  +  ++ ++     k+l +  ++ e+ ++  r++ r l     r+e+l +E++++ ++l+e+   l eL+k 
  gi|119720608|ref|YP_921103.1|  56 SKMIEELTKEVRNNSRILEEHSKVLGEHSRRIEELAGEiRNHSRVLEEHSKRLEELTREVRNHSRILEEHSERLKELTKS 135
                                    5555555555555555555555555555555555554404455666777789**************************** PP

                           MPS2 194 lseykekYellqref 208
                                    ++e+k    ++ r++
  gi|119720608|ref|YP_921103.1| 136 VGELKAAVGSIGRRW 150
                                    ****99888887776 PP

>> BDV_P24  Borna disease virus P24 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0     0.011       3.1     117     151 ..      13      47 ..       6      55 .. 0.87
   2 ?    2.8   0.4      0.35        95      72     106 ..      56      89 ..      47     143 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.011
                        BDV_P24 117 etiqtaqrcdhsdsirilgenikildrsmktmmet 151
                                    e ++ a r   +d +r l e +k+l   mkt +e+
  gi|119720608|ref|YP_921103.1|  13 EVVERAVRRARADELRDLAEAVKVLAEYMKTGFES 47 
                                    6788899999*********************9886 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.35
                        BDV_P24  72 delikklvtelaensmieaeevrgtlgdisariea 106
                                     ++i  l  e+ +ns i  ee    lg+ s rie 
  gi|119720608|ref|YP_921103.1|  56 SKMIEELTKEVRNNSRIL-EEHSKVLGEHSRRIEE 89 
                                    568999999999999996.6667799999999984 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   4.0    0.0019      0.51       3      70 ..      58     131 ..      21     148 .. 0.52
   2 ?    7.8   0.4    0.0065       1.7       4      61 ..      87     144 ..      84     166 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0019
                          TMPIT   3 eweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk......eeeeeevee 70 
                                     +eel+ke+++ +   +e  + l e s+ +++++ ei+++++ l+e +++l++l+++v+      ee++e+++e
  gi|119720608|ref|YP_921103.1|  58 MIEELTKEVRNNSRILEEHSKVLGEHSRRIEELAGEIRNHSRVLEEHSKRLEELTREVRnhsrilEEHSERLKE 131
                                    33444444444444444444444444444444444444444444444444444444433222222333333333 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0065
                          TMPIT   4 weelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk 61 
                                    +eel+ e+++ +   +e  ++leel++   + s+ ++++++rlkel++s+ +lk++v+
  gi|119720608|ref|YP_921103.1|  87 IEELAGEIRNHSRVLEEHSKRLEELTREVRNHSRILEEHSERLKELTKSVGELKAAVG 144
                                    5556666666666666666666666666666666666666666666666666666554 PP

>> Serine_rich  Serine rich protein interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   1.5    0.0026      0.69      16     114 ..      29     133 ..      15     159 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0026
                    Serine_rich  16 evesavskLlsfvsskWRs.kenleanlqeirlavdrlrtslrefleFargalanaaklsd.....knlqtkLrkqlqkl 89 
                                    ++ +av+ L +++++++ s    +e + + i + ++++r+  r + e ++     + ++++     +n ++ L+++ ++l
  gi|119720608|ref|YP_921103.1|  29 DLAEAVKVLAEYMKTGFEStLRAIEDHSKMIEELTKEVRNNSRILEEHSKVLGEHSRRIEElageiRNHSRVLEEHSKRL 108
                                    56677888888888877775566788888888888888888777777777777777777777777744444444444444 PP

                    Serine_rich  90 edsdqilqetsqeLdsceWsleala 114
                                    e+  + + ++s+ L++ + +l+ l+
  gi|119720608|ref|YP_921103.1| 109 EELTREVRNHSRILEEHSERLKELT 133
                                    4444444444444444444444443 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.5      0.21        56      16      52 ..      40      76 ..      14      83 .. 0.46
   2 ?    8.7   9.0    0.0037      0.99      35     105 ..      73     140 ..      31     149 .. 0.54

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.21
                            GAS 16 YYnditrnNLelIkslKeeieelkkkeernekelsei 52
                                   Y ++  ++ L  I+   + ieel k+ + n++ l+e+
  gi|119720608|ref|YP_921103.1| 40 YMKTGFESTLRAIEDHSKMIEELTKEVRNNSRILEEH 76
                                   2222233333333333344444444444444444333 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0037
                            GAS  35 ieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlk 105
                                    +ee  k   +++++++e++ e ++ +  L++  + +eeL ++++n+++    l++  +rlkel+k + +lk
  gi|119720608|ref|YP_921103.1|  73 LEEHSKVLGEHSRRIEELAGEIRNHSRVLEEHSKRLEELTREVRNHSR---ILEEHSERLKELTKSVGELK 140
                                    344444444455555555555555555555555555555555555554...44555555555555544444 PP

>> Spc29  Spindle Pole Component 29
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.7     0.063        17     122     164 ..      48      90 ..      20      98 .. 0.64
   2 ?   10.3   1.9    0.0017      0.46     111     166 ..      86     141 ..      76     150 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.063
                          Spc29 122 lekklddqkleIkeLkreleqqrtvnseLqekvaeleeevkrl 164
                                    + + ++d+  +I+eL +e+ ++  + +e  + + e  +++++l
  gi|119720608|ref|YP_921103.1|  48 TLRAIEDHSKMIEELTKEVRNNSRILEEHSKVLGEHSRRIEEL 90 
                                    4457777777777777777666666555444444444444443 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0017
                          Spc29 111 siyssvkkivelekklddqkleIkeLkreleqqrtvnseLqekvaeleeevkrlaa 166
                                    +i +   +i +  ++l+++  +++eL re+ ++  + +e  e+++el ++v +l+a
  gi|119720608|ref|YP_921103.1|  86 RIEELAGEIRNHSRVLEEHSKRLEELTREVRNHSRILEEHSERLKELTKSVGELKA 141
                                    45555566777889999999999999999999999999999999999999988776 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   5.9    0.0014      0.36      90     210 ..      14     135 ..       6     146 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0014
                           CorA  90 aldevikrlkdeggkpkspgellyrlldeivdrlfellekleeeldeledel.....edstkkeilrelaqlrrrlvklr 164
                                    +++ +++r++   ++ ++ +e +  l + +   ++ +l+++e++ + +e+       ++++ +e+ + l +  rr+ +l 
  gi|119720608|ref|YP_921103.1|  14 VVERAVRRAR--ADELRDLAEAVKVLAEYMKTGFESTLRAIEDHSKMIEELTkevrnNSRILEEHSKVLGEHSRRIEELA 91 
                                    3444444444..57888888888888888888888888888888888888887445333333444444555558899998 PP

                           CorA 165 ralapnrevlkrllakaddkllddedkeylrdlldelerllemlea 210
                                      ++++ +vl+++ +  + ++l++e +++ r l+++ erl e +++
  gi|119720608|ref|YP_921103.1|  92 GEIRNHSRVLEEHSK--RLEELTREVRNHSRILEEHSERLKELTKS 135
                                    888888888866666..88888888888888888888887776654 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   1.1    0.0021      0.56     313     412 ..      23     126 ..       9     137 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0021
                       Prominin 313 cldqlpnvdevlealeevletnlssivk...eglarlneipekvknqtaevvpdlkkalakgreqikklakkip..real 387
                                      d+l ++ e ++ l e ++t ++s+ +   +  + ++e+ + v+n+ ++++++  k l + +  i++la +i+  +++l
  gi|119720608|ref|YP_921103.1|  23 RADELRDLAEAVKVLAEYMKTGFESTLRaieDHSKMIEELTKEVRNN-SRILEEHSKVLGEHSRRIEELAGEIRnhSRVL 101
                                    34788888888888888888888876540004444455555555554.56788888899999999999999998766778 PP

                       Prominin 388 davisdlenterssktfddvvekye 412
                                    ++ ++ le++ r++++ ++ +e+ +
  gi|119720608|ref|YP_921103.1| 102 EEHSKRLEELTREVRNHSRILEEHS 126
                                    8889999999988888888888765 PP

>> ISG65-75  Invariant surface glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   3.7    0.0039         1      53     119 ..      60     128 ..      26     156 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0039
                       ISG65-75  53 dyllketkdklayienakekvdyyvekleslleeakekgtltesdaeklkkaceeAka..knkkareka 119
                                    ++l ke++++ + +e++ + + +++ ++e+l  e ++ +   e+ +++l+++ +e+ +   + +++++ 
  gi|119720608|ref|YP_921103.1|  60 EELTKEVRNNSRILEEHSKVLGEHSRRIEELAGEIRNHSRVLEEHSKRLEELTREVRNhsRILEEHSER 128
                                    567777777777777777777777777777777777777777777777777777776622233333333 PP

>> Spore_III_AB  Stage III sporulation protein AB (spore_III_AB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.3      0.32        86     104     153 ..      24      72 ..       9      75 .. 0.58
   2 ?    9.6   3.4    0.0034      0.92      19     120 ..      41     139 ..      36     143 .. 0.66
   3 ?    9.2   1.0    0.0046       1.2      25      94 ..      75     155 ..      70     170 .. 0.56

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.32
                                    HHHHHHHHHHHHHHT--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XX CS
                   Spore_III_AB 104 kedkeilkelgeslgysdregqlkalelaleeleeeieeareeakkkekl 153
                                    ++++  l+e  + l +  ++g +++l+ a+e+ +++iee+ +e ++++++
  gi|119720608|ref|YP_921103.1|  24 ADELRDLAEAVKVLAEYMKTGFESTLR-AIEDHSKMIEELTKEVRNNSRI 72 
                                    445555555555666555555555554.4455566677777777776665 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0034
                                    XXXXXXHHHHHHHHHHHHHHHHHHHHHH-SS-HHHHHHHHHHCS-T..THHHHHHHHHHHHH.STSS-HHHHHHHHHHHH CS
                   Spore_III_AB  19 lakrlkrrlkeleelkralellegeirygatpLpealeklaekses..plseffeevaerleekegesfeeaweeavekl 96 
                                    + +++   l+ +e+  +++e l+ e+r + + L+e  + l+e+s+   +l+  +++ ++ lee   + +ee     +++ 
  gi|119720608|ref|YP_921103.1|  41 MKTGFESTLRAIEDHSKMIEELTKEVRNNSRILEEHSKVLGEHSRRieELAGEIRNHSRVLEE-HSKRLEE----LTREV 115
                                    566778888999999999999999999999999997777776666522233333333333332.4444444....44444 PP

                                    GGGS---HHHHHHHHHHHHHHT-- CS
                   Spore_III_AB  97 lkklaLkkedkeilkelgeslgys 120
                                    ++++ + +e+ e lkel +s g++
  gi|119720608|ref|YP_921103.1| 116 RNHSRILEEHSERLKELTKSVGEL 139
                                    444888889999999998888875 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0046
                                    HHHHHHHHHHHHHHHHHHHHHH-SS-HHHHHHHHHHCS-T..THHHHHHHHHHHHH.S.........TSS-HHHHHHHHH CS
                   Spore_III_AB  25 rrlkeleelkralellegeirygatpLpealeklaekses..plseffeevaerleek.........egesfeeaweeav 93 
                                    ++ k l e  r +e l geir   + L+e  ++l+e +++  + s+++ee +erl+e            +s++++w + +
  gi|119720608|ref|YP_921103.1|  75 EHSKVLGEHSRRIEELAGEIRNHSRVLEEHSKRLEELTREvrNHSRILEEHSERLKELtksvgelkaAVGSIGRRWGRDL 154
                                    66667777777777777777777777777666666444433345555555555555421222222224455555555555 PP

                                    H CS
                   Spore_III_AB  94 e 94 
                                    e
  gi|119720608|ref|YP_921103.1| 155 E 155
                                    5 PP

>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0       2.9   7.8e+02      63      91 ..      14      42 ..       7      46 .. 0.85
   2 ?   10.6   7.4    0.0019      0.51       2     104 ..      49     151 ..      48     164 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 2.9
                        zf-C4H2 63 alEsvikeaeeekekslekakklyeeykk 91
                                    +E+ +++a+ ++ + l++a k+++ey k
  gi|119720608|ref|YP_921103.1| 14 VVERAVRRARADELRDLAEAVKVLAEYMK 42
                                   57889999999999999999999999976 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0019
                        zf-C4H2   2 ikeirektleleklknklakevealekeekcleeykkelelLeqEkmaHveeLrlIhaDinalEsvikeaeeekekslek 81 
                                    ++ i + ++ +e+l ++++++   le+++k+l e ++ +e+L  E ++H+  L    + +++l + +++     e++ e+
  gi|119720608|ref|YP_921103.1|  49 LRAIEDHSKMIEELTKEVRNNSRILEEHSKVLGEHSRRIEELAGEIRNHSRVLEEHSKRLEELTREVRNHSRILEEHSER 128
                                    56788999999***************************************999999999999999998888889999999 PP

                        zf-C4H2  82 akklyeeykklkeevnelrselg 104
                                     k+l++ + +lk  v ++ +  g
  gi|119720608|ref|YP_921103.1| 129 LKELTKSVGELKAAVGSIGRRWG 151
                                    99999999999999988876655 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   5.6     0.001      0.27      86     180 ..      22     116 ..       8     119 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.001
                        UPF0242  86 tkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelkleleeqLaekqellqeyqetieeqrsvl 165
                                      +++l++l e  + L+e ++   e   r  e+  ++ e+l + ++++++ + e  + L e   +++e++ +i +   vl
  gi|119720608|ref|YP_921103.1|  22 ARADELRDLAEAVKVLAEYMKTGFESTLRAIEDHSKMIEELTKEVRNNSRILEEHSKVLGEHSRRIEELAGEIRNHSRVL 101
                                    567799999999999999999999999999999*********************************************** PP

                        UPF0242 166 ekrqdqieqLeskVr 180
                                    e+  ++ e+L   Vr
  gi|119720608|ref|YP_921103.1| 102 EEHSKRLEELTREVR 116
                                    **********99887 PP

>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   5.8     0.003      0.79       5      73 ..      50     118 ..      46     119 .. 0.91
   2 ?    7.7   2.5     0.013       3.4       7      52 ..     101     146 ..      96     161 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.003
                     TMF_DNA_bd   5 kklkeKDeqIaqLmeEGekLskkelklnntikkLrkknkelekeikelkkkleklekeleeleerlkea 73 
                                      ++   ++I++L +E  + s    ++++ + +    ++el  ei++ ++ le+ +k leel+++ +++
  gi|119720608|ref|YP_921103.1|  50 RAIEDHSKMIEELTKEVRNNSRILEEHSKVLGEHSRRIEELAGEIRNHSRVLEEHSKRLEELTREVRNH 118
                                    556677789*****************************************************9998765 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.013
                     TMF_DNA_bd   7 lkeKDeqIaqLmeEGekLskkelklnntikkLrkknkelekeikel 52 
                                    l+e  +++++L  E  + s    ++++ +k+L k + el   + + 
  gi|119720608|ref|YP_921103.1| 101 LEEHSKRLEELTREVRNHSRILEEHSERLKELTKSVGELKAAVGSI 146
                                    6677777888888888888888888888888888888887766655 PP

>> DUF919  Nucleopolyhedrovirus protein of unknown function (DUF919)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.3       5.6   1.5e+03      24      37 ..     102     115 ..      94     124 .. 0.72
   2 ?   11.9   2.0   0.00058      0.15       9      41 ..     107     140 ..     102     143 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 5.6
                         DUF919  24 sqHfErlkkitKnp 37 
                                     +H  rl+ +t + 
  gi|119720608|ref|YP_921103.1| 102 EEHSKRLEELTREV 115
                                    57888888888665 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00058
                         DUF919   9 qLdeinqaKrk.ltiksqHfErlkkitKnpkElq 41 
                                    +L+e+++  r+  +i  +H Erlk +tK   El+
  gi|119720608|ref|YP_921103.1| 107 RLEELTREVRNhSRILEEHSERLKELTKSVGELK 140
                                    56666655443157899*************9997 PP

>> CREPT  Cell-cycle alteration and expression-elevated protein in tumour
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   1.5     0.012       3.1      50     120 ..      27      98 ..       7     101 .. 0.80
   2 ?   10.0   6.0    0.0028      0.74      35     126 ..      47     139 ..      45     146 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.012
                          CREPT  50 lkqveealellaeYnkr.LeaeleeRkklakmledfleaqkellakaeekleelkeklekvksvrkelkshi 120
                                    l+   ea+++laeY+k   e+ l   +  +km+e++++ ++++ +  ee+ + l e  +++++   e+++h 
  gi|119720608|ref|YP_921103.1|  27 LRDLAEAVKVLAEYMKTgFESTLRAIEDHSKMIEELTKEVRNNSRILEEHSKVLGEHSRRIEELAGEIRNHS 98 
                                    355679999*****9865888888889999999999999999999999999999999999999999998885 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0028
                          CREPT  35 sllekikdkee.aekllkqveealellaeYnkrLeaeleeRkklakmledfleaqkellakaeekleelkeklekvksvr 113
                                    s l+ i+d+++  e+l+k+v++  ++l+e  k L +     ++la  +++  +++ e+ ++ ee  +e+++  + +++  
  gi|119720608|ref|YP_921103.1|  47 STLRAIEDHSKmIEELTKEVRNNSRILEEHSKVLGEHSRRIEELAGEIRNHSRVLEEHSKRLEELTREVRNHSRILEEHS 126
                                    578899987662699*******************999999999*****99999999999999999999999999999999 PP

                          CREPT 114 kelkshiqsLPdL 126
                                    + lk+  +s  +L
  gi|119720608|ref|YP_921103.1| 127 ERLKELTKSVGEL 139
                                    8888887776655 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   3.7    0.0091       2.4      27     120 ..      42     138 ..      31     146 .. 0.46

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0091
                                    CCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHH...HHHCCHHH CS
                      Fib_alpha  27 lkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlke...tidaqesn 103
                                    ++  +++ + +e+  + +ee++++ ++ +++ +e +++l e+ +  ++    i++ s+ lee+  rl+e   ++ ++ + 
  gi|119720608|ref|YP_921103.1|  42 KTGFESTLRAIEDHSKMIEELTKEVRNNSRILEEHSKVLGEHSRRIEELAGEIRNHSRVLEEHSKRLEEltrEVRNHSRI 121
                                    44444444444444444555555555555555555555555555555555555555555554444444300023333333 PP

                                    HHHHHHHHHHHHHHHHH CS
                      Fib_alpha 104 irvLqnvlesneqkiqk 120
                                    +++  + l+++ +++ +
  gi|119720608|ref|YP_921103.1| 122 LEEHSERLKELTKSVGE 138
                                    33333344444444444 PP

>> Sec8_exocyst  Sec8 exocyst complex component specific domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.5     0.015       3.9      53     124 ..      31     102 ..      23     105 .. 0.81
   2 ?    3.9   0.3      0.17        47      80     116 ..     100     136 ..      91     145 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.015
                   Sec8_exocyst  53 eeaLqevvnehhqaFnssiasYskilssiqesqekvselKesleeakkklstkkkeLkelnarsakykevie 124
                                    +ea++  ++  + +F s   + +   ++i+e +++v++  + lee  k l++++  ++el+ + +++++v+e
  gi|119720608|ref|YP_921103.1|  31 AEAVKVLAEYMKTGFESTLRAIEDHSKMIEELTKEVRNNSRILEEHSKVLGEHSRRIEELAGEIRNHSRVLE 102
                                    566777777778888888888888888888888999999999999999999999999999988888888876 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.17
                   Sec8_exocyst  80 siqesqekvselKesleeakkklstkkkeLkelnars 116
                                     ++e  ++++el +++++  + l+++++ Lkel ++ 
  gi|119720608|ref|YP_921103.1| 100 VLEEHSKRLEELTREVRNHSRILEEHSERLKELTKSV 136
                                    4556667777788888888888888888888887665 PP

>> Helo_like_N  Fungal N-terminal domain of STAND proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.5      0.13        35      26      57 ..      47      78 ..      11      88 .. 0.60
   2 ?    8.0   2.0    0.0063       1.7      26      97 ..      47     117 ..      33     123 .. 0.87
   3 ?    4.5   0.4     0.075        20      21      57 ..     105     141 ..      94     162 .. 0.66

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.13
                    Helo_like_N 26 etvksfrsrdktvreLkeeleaLeevLesLee 57
                                   +t++   +++k + eL++e+++ +++Le+ ++
  gi|119720608|ref|YP_921103.1| 47 STLRAIEDHSKMIEELTKEVRNNSRILEEHSK 78
                                   44455555556666666666655555555444 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0063
                    Helo_like_N  26 etvksfrsrdktvreLkeeleaLeevLesLeevavaeeeselalLklpllrCgkaCkefeqvikkcskkssk 97 
                                    +t++   +++k + eL++e+++ +++Le+ ++ +  e++  ++ L   +++ +++ +e  + ++++++  ++
  gi|119720608|ref|YP_921103.1|  47 STLRAIEDHSKMIEELTKEVRNNSRILEEHSK-VLGEHSRRIEELAGEIRNHSRVLEEHSKRLEELTREVRN 117
                                    67888899************************.55999999*********9999999999999999987654 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.075
                    Helo_like_N  21 sksLyetvksfrsrdktvreLkeeleaLeevLesLee 57 
                                    sk L e  ++ r++++ + e  e l++L++ + +L+ 
  gi|119720608|ref|YP_921103.1| 105 SKRLEELTREVRNHSRILEEHSERLKELTKSVGELKA 141
                                    5555666666666666666666666666666555555 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   2.7    0.0011       0.3      70     159 ..      29     119 ..      18     131 .. 0.85
   2 ?    9.6   0.3    0.0026      0.69      64     123 ..      87     146 ..      78     149 .. 0.90
   3 ?   -0.5   0.2       3.3   8.7e+02      12      24 ..     245     257 ..     240     260 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0011
                         DUF745  70 elreaeavvqee.kkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaektqlleaAkkRv 148
                                    +l+ea +v+ e  k+  +s+ ++++  +k+ ++ ++++   +++l++ ++ l +  +  ++ + e+++ +  le+  kR+
  gi|119720608|ref|YP_921103.1|  29 DLAEAVKVLAEYmKTGFESTLRAIEDHSKMIEELTKEVRNNSRILEEHSKVLGEHSRRIEELAGEIRNHSRVLEEHSKRL 108
                                    67888888887614567888899999999999999999999999999999999999999999999999999999999999 PP

                         DUF745 149 eeLkkqlkear 159
                                    eeL++++++  
  gi|119720608|ref|YP_921103.1| 109 EELTREVRNHS 119
                                    99999988765 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0026
                         DUF745  64 veqleqelreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlena 123
                                    +e+l  e+r+ ++v++e +k l++  + ++  +++ ++  + l+ l++ + + k+++ ++
  gi|119720608|ref|YP_921103.1|  87 IEELAGEIRNHSRVLEEHSKRLEELTREVRNHSRILEEHSERLKELTKSVGELKAAVGSI 146
                                    799999*****************************************9999999887665 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 3.3
                         DUF745  12 iAqkAAqeAkaAn 24 
                                    +A +AA+eA +A 
  gi|119720608|ref|YP_921103.1| 245 VAVNAAKEAIEAA 257
                                    6788888887775 PP

>> Sec2p  GDP/GTP exchange factor Sec2p
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   2.1      0.15        40      24      76 ..      60     111 ..      21     113 .. 0.77
   2 ?    9.8   1.3    0.0028      0.74      46      83 ..     102     139 ..      94     144 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.15
                                    HHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHTTHCHCCCHCTSSSSHH CS
                          Sec2p  24 edLtasLFeeANkmVaaar.kekealekkneklkeqLkeketlleslqeqLkeL 76 
                                    e+Lt+++    N+ + +++ k   +  ++ e+l  ++++   +le++++ L+eL
  gi|119720608|ref|YP_921103.1|  60 EELTKEVR--NNSRILEEHsKVLGEHSRRIEELAGEIRNHSRVLEEHSKRLEEL 111
                                    55555543..34444444434455677889999999999999999999999998 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0028
                                    HHHHHHHHHHHHHHTTHCHCCCHCTSSSSHHHHCTTTX CS
                          Sec2p  46 ealekkneklkeqLkeketlleslqeqLkeLkevlekm 83 
                                    e+  k+ e+l++++++   +le+++e LkeL + + ++
  gi|119720608|ref|YP_921103.1| 102 EEHSKRLEELTREVRNHSRILEEHSERLKELTKSVGEL 139
                                    66788999***********************8876655 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.2      0.99   2.7e+02      14      38 ..      43      67 ..      38      74 .. 0.78
   2 ?    3.0   2.6      0.53   1.4e+02       1      37 [.      86     115 ..      58     121 .. 0.69
   3 ?    8.3   0.2     0.011         3       1      37 [.     107     143 ..     107     162 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.99
                      FlaC_arch 14 teletvkkeneelsksveelkenVk 38
                                   t +e+  + +e+ sk +eel ++V+
  gi|119720608|ref|YP_921103.1| 43 TGFESTLRAIEDHSKMIEELTKEVR 67
                                   5666777888999999999999986 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.53
                      FlaC_arch   1 ridelEnklsklsteletvkkeneelsksveelkenV 37 
                                    ri+el         e+ +  + +ee sk +eel ++V
  gi|119720608|ref|YP_921103.1|  86 RIEEL-------AGEIRNHSRVLEEHSKRLEELTREV 115
                                    44444.......4455555555555555555555555 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.011
                      FlaC_arch   1 ridelEnklsklsteletvkkeneelsksveelkenV 37 
                                    r++el  ++ ++s  le   + ++el ksv elk  V
  gi|119720608|ref|YP_921103.1| 107 RLEELTREVRNHSRILEEHSERLKELTKSVGELKAAV 143
                                    899******************************9988 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   9.4    0.0081       2.2      30     123 ..      44     133 ..      18     141 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0081
                         APG6_N  30 eflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynelq 109
                                     f+++l++ ++    + + +eel +e+++ ++  ee  + L e  +  eel+ e+++ ++ le+  +  e+  re ++++
  gi|119720608|ref|YP_921103.1|  44 GFESTLRAIED----HSKMIEELTKEVRNNSRILEEHSKVLGEHSRRIEELAGEIRNHSRVLEEHSKRLEELTREVRNHS 119
                                    24444444433....34578888888888888888888888888888888888888888888888888888888888888 PP

                         APG6_N 110 lelleleeeldsle 123
                                    + l+e+ e+l+ l+
  gi|119720608|ref|YP_921103.1| 120 RILEEHSERLKELT 133
                                    88888888887765 PP

>> DUF4200  Domain of unknown function (DUF4200)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   7.6    0.0077       2.1       6      94 ..      50     141 ..      45     163 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0077
                        DUF4200   6 remfevqealeakkeeiqrleealkqreeelekkeqelee...dllkfdkflkendakraralkkaeeerklkkekeaei 82 
                                    r +++  +++e+  +e ++  + l+++ + l +  +++ee   ++ +  + l+e+ ++ ++  +++ + ++  +e  + +
  gi|119720608|ref|YP_921103.1|  50 RAIEDHSKMIEELTKEVRNNSRILEEHSKVLGEHSRRIEElagEIRNHSRVLEEHSKRLEELTREVRNHSRILEEHSERL 129
                                    77888899999********999999999999988866665222678999******************************* PP

                        DUF4200  83 kklkaeietlks 94 
                                    k+l++++ +lk+
  gi|119720608|ref|YP_921103.1| 130 KELTKSVGELKA 141
                                    *********996 PP

>> DUF4404  Domain of unknown function (DUF4404)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.3     0.043        11       3      38 ..      57      92 ..      56     104 .. 0.88
   2 ?    7.3   0.9     0.027       7.3       3      36 ..     106     139 ..     104     146 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.043
                        DUF4404  3 elLekLheeLeqnesldeetralLeslaedieella 38
                                   +++e+L++e+++n+++ ee  ++L +  + ieel  
  gi|119720608|ref|YP_921103.1| 57 KMIEELTKEVRNNSRILEEHSKVLGEHSRRIEELAG 92
                                   5789****************************9865 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.027
                        DUF4404   3 elLekLheeLeqnesldeetralLeslaedieel 36 
                                    ++Le+L+ e+++++++ ee  ++L++l + + el
  gi|119720608|ref|YP_921103.1| 106 KRLEELTREVRNHSRILEEHSERLKELTKSVGEL 139
                                    68*************************9988765 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1       3.6   9.6e+02     131     160 ..      11      41 ..       8      43 .. 0.61
   2 ?    8.3   1.7    0.0048       1.3      34      93 ..      82     141 ..      61     146 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 3.6
                        DUF3450 131 Lkelmdradv.slaekyrrvleayqiEaeYg 160
                                    L+e+++ra   + a+ +r + ea ++ aeY 
  gi|119720608|ref|YP_921103.1|  11 LEEVVERAVRrARADELRDLAEAVKVLAEYM 41 
                                    5555555533134667777888888888775 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0048
                        DUF3450  34 qsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeiee 93 
                                    + +++i++l+ e +++++ +++ +++le+l+ + ++ +r++++  +++++l+++  e+++
  gi|119720608|ref|YP_921103.1|  82 EHSRRIEELAGEIRNHSRVLEEHSKRLEELTREVRNHSRILEEHSERLKELTKSVGELKA 141
                                    557899999999999999999999999999999999999999999999999999988875 PP

>> MutS_III  MutS domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   5.8     0.018       4.9      83     170 ..      18     118 ..       7     145 .. 0.55

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.018
                                    HHHHHHTT---HHHHHHHHHHHHHHHTTTTT---SSTHHHHHHHHHHHHHHHB-SS--SSGGGS--B-T........... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........... RF
                       MutS_III  83 llsrislgkakardlkallealkaleelvallekeklaeseeeslaelleeaideeplalekegedlra........... 151
                                    +++     +a+a++l+ l+ea+k l+e +++  +++l   e  + ++++ee + +e  ++++  e++ +           
  gi|119720608|ref|YP_921103.1|  18 AVR-----RARADELRDLAEAVKVLAEYMKTGFESTLRAIE--DHSKMIEE-LTKEVRNNSRILEEHSKvlgehsrriee 89 
                                    332.....456677778888888766655555444433222..33388887.7777777777777777744445555555 PP

                                    ...........HHHHHHHHHHHHHHHHHHT CS
                                    ...........xxxxxxxxxxxxxxxxxxx RF
                       MutS_III 152 ...........iealeqelfqelleeveea 170
                                               + +++++ ++el +ev+++
  gi|119720608|ref|YP_921103.1|  90 lageirnhsrvL-EEHSKRLEELTREVRNH 118
                                    555555555432.22233355555555544 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   1.9     0.023       6.1       5      92 ..      24     115 ..      20     117 .. 0.55
   2 ?   11.4   3.3   0.00089      0.24       4      89 ..      58     140 ..      47     152 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.023
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXX--TTTTTGGGHHHHHH CS
                     Laminin_II   5 aaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankaird....ArrsvkkLeklapqLldklkelkq 80 
                                    a+e  + a++v+   + +++  e t   ++   + +ee +++v++ ++++++     ++ ++ +e+la ++ +  + l++
  gi|119720608|ref|YP_921103.1|  24 ADELRDLAEAVKVLAEYMKTGFESTLRAIEDHSKMIEELTKEVRNNSRILEEhskvLGEHSRRIEELAGEIRNHSRVLEE 103
                                    55666666666666666666666666666666666666666666555555431111345556666666666666666666 PP

                                    HHHH...HHHHH CS
                     Laminin_II  81 leeassslsdni 92 
                                    +++  + l +++
  gi|119720608|ref|YP_921103.1| 104 HSKRLEELTREV 115
                                    666555555554 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00089
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHH CS
                     Laminin_II   4 laaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqlee 83 
                                    +++e  + + +  ++l++ s+ l + +  ++e+++++++   ++++ +k +++  r+v++  + +++  ++lkel +   
  gi|119720608|ref|YP_921103.1|  58 MIEELTKEVRNNSRILEEHSKVLGEHSRRIEELAGEIRNHSRVLEEHSKRLEELTREVRNHSRILEEHSERLKELTKSVG 137
                                    67777777888888888888889999999999999988888888888888777777777777777777777776655443 PP

                                    H...HH CS
                     Laminin_II  84 asssls 89 
                                    +   l+
  gi|119720608|ref|YP_921103.1| 138 E---LK 140
                                    3...33 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   8.6     0.017       4.6      52     117 ..      63     135 ..      28     161 .. 0.58

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.017
                          Atg14  52 ke.......eaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklkkRrsd 117
                                    ++         e+ ++ +  ++ ++eel  +i+  ++ l+e +++l++l++e+++ ++ l+++s+ lk+ +++
  gi|119720608|ref|YP_921103.1|  63 TKevrnnsrILEEHSKVLGEHSRRIEELAGEIRNHSRVLEEHSKRLEELTREVRNHSRILEEHSERLKELTKS 135
                                    2222222233344444555555555555555555555555555555555555555555555555555544444 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   1.6      0.83   2.2e+02      41      90 ..      41      80 ..       9      97 .. 0.46
   2 ?    8.6   1.1    0.0078       2.1      23      65 ..     100     142 ..      87     148 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.83
                                   HHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHH CS
                   Seryl_tRNA_N 41 lqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleael 90
                                   +++ +e+  +     sk I+++ k+  + +++++e ++           l
  gi|119720608|ref|YP_921103.1| 41 MKTGFESTLRAIEDHSKMIEELTKEVRNNSRILEEHSK----------VL 80
                                   44445555555555555555555555444444444333..........33 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0078
                                    CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCT CS
                   Seryl_tRNA_N  23 edkadvdelleldekrrelqveleelqaerNelskeIgkakkk 65 
                                    + ++  ++l el ++ r++   lee  ++ +el+k++g++k++
  gi|119720608|ref|YP_921103.1| 100 VLEEHSKRLEELTREVRNHSRILEEHSERLKELTKSVGELKAA 142
                                    6778889999*****************************9975 PP

>> CENP-H  Centromere protein H (CENP-H)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   7.8     0.042        11       5      62 ..      49     123 ..      45     150 .. 0.60

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.042
                         CENP-H   5 ieqrdelssellklsqelrelqeeltevekenlrlkrknrelaael.l.elakekesek...............e 62 
                                    ++ +++ s+ +++l++e+r+  + l+e  k   + +r+ +ela e+       e++s++               e
  gi|119720608|ref|YP_921103.1|  49 LRAIEDHSKMIEELTKEVRNNSRILEEHSKVLGEHSRRIEELAGEIrNhSRVLEEHSKRleeltrevrnhsrilE 123
                                    666777788888888888888888888888888888888888888832233333333335333333222223333 PP

>> SOAR  STIM1 Orai1-activating region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   1.4     0.054        14      47      93 ..      42      90 ..       9      94 .. 0.77
   2 ?    5.6   1.0     0.056        15      58      97 ..      97     136 ..      89     140 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.054
                           SOAR 47 rssllgslrla..hssslddvdkkileakqaleevtkelkerqeRWqqi 93
                                   ++ + ++lr +  hs+ ++++ k++ +  + lee +k l e+++R +++
  gi|119720608|ref|YP_921103.1| 42 KTGFESTLRAIedHSKMIEELTKEVRNNSRILEEHSKVLGEHSRRIEEL 90
                                   34567889999889*****************************997765 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.056
                           SOAR  58 hssslddvdkkileakqaleevtkelkerqeRWqqieklc 97 
                                    hs+ l++  k++ e+ +++++ ++ l+e++eR +++ k +
  gi|119720608|ref|YP_921103.1|  97 HSRVLEEHSKRLEELTREVRNHSRILEEHSERLKELTKSV 136
                                    999999999***********************99987755 PP

>> RP-C_C  Replication protein C C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   8.4      0.17        45       7      84 ..       9      93 ..       7     180 .. 0.61

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.17
                         RP-C_C  7 qrfralverlprkatlaeleelleelealreevenal.......esalkaenssanesqnerhiqnsnpdsssesepaseke 81
                                   +r++++ver  r+a ++el++l+e+ + l+e  ++ +       e+++k  ++ ++e +n+++i + +++   e + + e+ 
  gi|119720608|ref|YP_921103.1|  9 SRLEEVVERAVRRARADELRDLAEAVKVLAEYMKTGFestlraiEDHSKMIEELTKEVRNNSRILEEHSKVLGEHSRRIEEL 90
                                   4667777777777778888888888888877777777444455566666666666677777777777774333322222222 PP

                         RP-C_C 82 ree 84
                                   ++e
  gi|119720608|ref|YP_921103.1| 91 AGE 93
                                   221 PP

>> VAPB_antitox  Putative antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.2      0.47   1.3e+02      25      67 ..      13      55 ..      11      57 .. 0.86
   2 ?    9.2   1.9    0.0075         2      24      68 ..      56      98 ..      53      99 .. 0.79
   3 ?    1.1   0.2       2.6   6.9e+02      51      68 ..     102     119 ..      98     120 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.47
                   VAPB_antitox 25 dvIerLlekkkkgkkkellelfgilseeeadeiekaskelrke 67
                                   +v+er + + + ++ ++l e++++l e   + +e++++ +++ 
  gi|119720608|ref|YP_921103.1| 13 EVVERAVRRARADELRDLAEAVKVLAEYMKTGFESTLRAIEDH 55
                                   89999999999999**********9888878888888888765 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0075
                   VAPB_antitox 24 sdvIerLlekkkkgkkkellelfgilseeeadeiekaskelrkef 68
                                   s +Ie+L++  ++++++++le   ++  e+ ++ie+   e+r+ +
  gi|119720608|ref|YP_921103.1| 56 SKMIEELTK--EVRNNSRILEEHSKVLGEHSRRIEELAGEIRNHS 98
                                   678****86..44566777777777779999***********976 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 2.6
                   VAPB_antitox  51 eeeadeiekaskelrkef 68 
                                    ee+ +++e+ ++e+r+ +
  gi|119720608|ref|YP_921103.1| 102 EEHSKRLEELTREVRNHS 119
                                    667799*******99876 PP

>> Cep57_MT_bd  Centrosome microtubule-binding domain of Cep57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   3.4      0.14        37      17      74 ..      59     111 ..      46     113 .. 0.68
   2 ?    8.0   2.3     0.015         4      14      47 ..     105     138 ..      93     163 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.14
                    Cep57_MT_bd  17 lkeLedEfehlklelqelaaqynaldpslgkrkR..kdLaeeleelvkrlEaKadqIykL 74 
                                    +       e+l +e    ++ ++++ + lg+++R  ++La e+++  + lE++++   +L
  gi|119720608|ref|YP_921103.1|  59 I-------EELTKEVRNNSRILEEHSKVLGEHSRriEELAGEIRNHSRVLEEHSKRLEEL 111
                                    4.......4555555555555556666664444411689999999999999999988887 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.015
                    Cep57_MT_bd  14 aevlkeLedEfehlklelqelaaqynaldpslgk 47 
                                    ++ l+eL+ E++ ++ +l+e ++++++l++s+g+
  gi|119720608|ref|YP_921103.1| 105 SKRLEELTREVRNHSRILEEHSERLKELTKSVGE 138
                                    899**************************99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1397  (0.0779185); expected 358.6 (0.02)
Passed bias filter:                      841  (0.0469072); expected 358.6 (0.02)
Passed Vit filter:                       185  (0.0103185); expected 17.9 (0.001)
Passed Fwd filter:                        75  (0.00418317); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              67  [number of targets reported over threshold]
# CPU time: 0.96u 0.33s 00:00:01.29 Elapsed: 00:00:00.51
# Mc/sec: 1607.62
//
Query:       gi|119720609|ref|YP_921104.1|  [L=111]
Description: hypothetical protein Tpen_1706 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.02   15.6   0.0       0.04   14.6   0.0    1.4  1  Asp_protease_2   Aspartyl protease
       0.06   13.9   0.0       0.09   13.3   0.0    1.2  1  gag-asp_proteas  gag-polyprotein putative aspartyl protease
       0.15   11.9   0.0       0.21   11.4   0.0    1.2  1  NUC153           NUC153 domain
       0.21   11.0   0.0        2.8    7.3   0.0    2.0  2  Asp              Eukaryotic aspartyl protease


Domain annotation for each model (and alignments):
>> Asp_protease_2  Aspartyl protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0     9e-06      0.04      10      54 ..      13      54 ..      10      62 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 9e-06
                 Asp_protease_2 10 vrfllDTGasttlispelaeklglkvreseltvrvsgaggevkar 54
                                   +++l+DTG+ +t i     + lg+++++    +++ ++gg+v  r
  gi|119720609|ref|YP_921104.1| 13 FELLVDTGSMYTWIEGGRLRGLGIEPTGR---RVFGTIGGRVVER 54
                                   579***********************995...8999999996544 PP

>> gag-asp_proteas  gag-polyprotein putative aspartyl protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0     2e-05      0.09      10      91 ..      13      89 ..      11      90 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2e-05
                                   EEEEEETT-SS-EEEHHHHHHTTGGGGEB..TT--EE-TTSTT-EEEEEEEEEE.EETTEEEEEEEEEESSSSEEEEHHHHH CS
                gag-asp_proteas 10 vkflvDTGAsstiiseelaerlglsrkedkgkvevktangeveakrvrldsvkiggielrnvsavvlegelddlLLGldfLk 91
                                   +++lvDTG   t i     + lg+++     ++ ++t  g+v  +++  +   ig +  r   +vv+  e d+ +LG+ +L+
  gi|119720609|ref|YP_921104.1| 13 FELLVDTGSMYTWIEGGRLRGLGIEPTG---RRVFGTIGGRVVEREIGEA--VIGCMGERATCIVVFAREGDAEVLGVTALE 89
                                   578***********************98...5889999999988855544..455555554456677778899999999997 PP

>> NUC153  NUC153 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   4.7e-05      0.21      12      27 ..      92     107 ..      87     108 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.7e-05
                         NUC153  12 dFaIDptspeFkktnp 27 
                                      ++Dpt+ +F++ ++
  gi|119720609|ref|YP_921104.1|  92 ALEVDPTTKQFRRVEA 107
                                    569*********9887 PP

>> Asp  Eukaryotic aspartyl protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0   0.00061       2.8      15      29 ..      13      27 ..       9      44 .. 0.90
   2 ?    2.1   0.0     0.024   1.1e+02     271     301 ..      65      93 ..      41     104 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00061
                                   EEEEEETT--SEEEE CS
                                   xxxxxxxxxxxxxxx RF
                            Asp 15 ftvifDTGSsdlWVp 29
                                   f++++DTGS ++W+ 
  gi|119720609|ref|YP_921104.1| 13 FELLVDTGSMYTWIE 27
                                   899**********96 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.024
                                    STTSEEEESEEECCTSSSEEEEHHHHTTEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            Asp 271 seesqCilglvseeegdlwiLGdvFlrsayv 301
                                    +e+++Ci+ +   +egd+ +LG + l++   
  gi|119720609|ref|YP_921104.1|  65 GERATCIVVF--AREGDAEVLGVTALENLAL 93 
                                    45689**999..99999*****999987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       209  (0.0116571); expected 358.6 (0.02)
Passed bias filter:                      191  (0.0106531); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.37u 0.29s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 776.93
//
Query:       gi|119720610|ref|YP_921105.1|  [L=100]
Description: hypothetical protein Tpen_1707 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 731.30
//
Query:       gi|119720611|ref|YP_921106.1|  [L=101]
Description: transcriptional regulator/antitoxin, MazE [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.8e-08   33.1   0.3    5.4e-08   32.6   0.3    1.3  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
  ------ inclusion threshold ------
      0.054   13.5   0.1      0.086   12.8   0.1    1.3  1  DUF1246         Protein of unknown function (DUF1246)


Domain annotation for each model (and alignments):
>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.3     6e-12   5.4e-08       7      44 ..      31      68 ..      25      70 .. 0.88

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 6e-12
                                   EEEEE-CCCHHHCCEECTCEEEEEECTTCCCCCCCHHS CS
                 MazE_antitoxin  7 gavriPkevrfelgireGdevelevdgdkiilrplksl 44
                                       iPk ++++ gireG+++ l+v+g +ii++p+ ++
  gi|119720611|ref|YP_921106.1| 31 NTLYIPKSIAKAVGIREGSKLKLRVEGHRIIIEPVPDP 68
                                   5567******************************9765 PP

>> DUF1246  Protein of unknown function (DUF1246)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   9.6e-06     0.086      51      98 ..      16      62 ..       4      67 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.6e-06
                                   ..TTSS--HHHHHHTTCEE--BTTHHHHC-HHHHHC-SS-EES-TTHH CS
                        DUF1246 51 kdilkeevqeklreenailvPhgsfveYvgiekieelkvpifGnrkll 98
                                   + i+ +ev  +l ++n++ +P+ s+++ vgi++ ++lk+++ G r ++
  gi|119720611|ref|YP_921106.1| 16 EKIMISEVRVRLSKKNTLYIPK-SIAKAVGIREGSKLKLRVEGHRIII 62
                                   4577788999***********5.9*********************887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 689.95
//
Query:       gi|119720612|ref|YP_921107.1|  [L=149]
Description: hypothetical protein Tpen_1709 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0015   19.0   0.0      0.002   18.6   0.0    1.2  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.1e-07     0.002      21     116 ..      23     117 ..       2     123 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.1e-07
                                    HHHHHHTS..SEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCHHHHHHHHHHHHHHHSBHHHHHHH CS
                            PIN  21 arklleel..eelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpidaeiaeeaaeialkygllpnDalia 98 
                                    ++k l +    e + ++  + E++ +l+r   + + +++l  l  + +++   + + e + +a+e+++k  ++++D+l++
  gi|119720612|ref|YP_921107.1|  23 LLKKLRDSgvAEYYYTQFNILEIVGKLSR--VGYNSSRALAGLASIFEEFIEESPTVEGVMKALELRRKGHRDLIDLLLY 100
                                    44444444578899999999999999999..666666666666666556666667999********************** PP

                                    HHHHHHT-EEE.ESSTHH CS
                            PIN  99 AtAkehgikliatfDedf 116
                                     t + +g+ l++t+D ++
  gi|119720612|ref|YP_921107.1| 101 TTSLTRGL-LFLTRDVHL 117
                                    ********.787***775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 1074.55
//
Query:       gi|119720613|ref|YP_921108.1|  [L=72]
Description: hypothetical protein Tpen_1710 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0072   16.5   0.1     0.0086   16.2   0.1    1.1  1  DALR_1        DALR anticodon binding domain
  ------ inclusion threshold ------
      0.071   13.5   0.5      0.074   13.4   0.5    1.2  1  Phostensin_N  PP1-regulatory protein, Phostensin N-terminal


Domain annotation for each model (and alignments):
>> DALR_1  DALR anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   9.6e-07    0.0086       7      57 ..      11      60 ..       8      67 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 9.6e-07
                                   HHHHHHHHTTCTTCCCCHCCHCCS-SHHHHHHHHHHHTHHHHHHHHHHHT- CS
                         DALR_1  7 RiksilrkaeeegekleeealalleeeeekeLlkalaqfpevleeaaeele 57
                                   R+k+il+k +++++k +++a    e+  e+eL kal +f ++l++ ++ ++
  gi|119720613|ref|YP_921108.1| 11 RVKKILEKRGAKVSKPTGKAPTA-EKTGEEELRKALDEFASTLKDKIDPRA 60
                                   9************9999999888.999****************99887665 PP

>> Phostensin_N  PP1-regulatory protein, Phostensin N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.5   8.2e-06     0.074       6      38 ..       6      38 ..       2      72 .] 0.72

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.2e-06
                   Phostensin_N  6 aqmPAWKReiLERrRAKlgllsgeadpvkgaae 38
                                   a++P   ++iLE+r AK++ ++g+a   ++++e
  gi|119720613|ref|YP_921108.1|  6 AKVPNRVKKILEKRGAKVSKPTGKAPTAEKTGE 38
                                   67888899************8887776666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       851  (0.047465); expected 358.6 (0.02)
Passed bias filter:                      618  (0.0344693); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 528.78
//
Query:       gi|119720614|ref|YP_921109.1|  [L=121]
Description: hypothetical protein Tpen_1711 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       648  (0.0361426); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 863.77
//
Query:       gi|119720615|ref|YP_921110.1|  [L=190]
Description: dTDP-4-dehydrorhamnose 3,5-epimerase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-59  200.7   0.0    1.4e-59  200.6   0.0    1.0  1  dTDP_sugar_isom  dTDP-4-dehydrorhamnose 3,5-epimerase
    0.00043   19.9   0.1    0.00059   19.5   0.1    1.2  1  Cupin_1          Cupin
     0.0067   16.1   0.0      0.011   15.4   0.0    1.4  1  Cupin_2          Cupin domain
  ------ inclusion threshold ------
      0.094   12.5   0.2       0.19   11.6   0.2    1.4  1  Toxin_24         Conotoxin TVIIA/GS family


Domain annotation for each model (and alignments):
>> dTDP_sugar_isom  dTDP-4-dehydrorhamnose 3,5-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.6   0.0   3.1e-63   1.4e-59       2     168 ..      14     180 ..      13     181 .. 0.98

  Alignments for each domain:
  == domain 1  score: 200.6 bits;  conditional E-value: 3.1e-63
                                    -SSTTCEEEEE-EEEETTEEEEEEEEHHHHHHHTS-----EEEEEEEETTBEEEEEEESSCS---EEEEEEESEEEEEEE CS
                dTDP_sugar_isom   2 teiegvlliepkvfgDeRGfflesfneeefaeagleaefvqdnlsvskkgvlRGlHfqkepkaqaklvrvvrGevldvaV 81 
                                    +ei++v+l+e +vf DeRGff+e ++++ef + g++  fvq nls+s++gv+R lH+q +p +q+klv+vv+G+v+dvaV
  gi|119720615|ref|YP_921110.1|  14 LEIPDVVLVEYAVFPDERGFFAELYKRTEFLSGGVPYGFVQVNLSFSRAGVVRALHYQLKPMEQGKLVYVVSGRVFDVAV 93 
                                    68****************************************************************************** PP

                                    E-BTTSTTTT-EEEEEEETTT--EEEE-TTEEEEEEE-SSEEEEEEEESS---GGGEEEE-TT-TTTT---...SS.B-- CS
                dTDP_sugar_isom  82 DlRkgSptfgkwvgveLsaenkrqlyipegfahGflvlsdeaevlYkvteyyapesergirwnDpelgidw...eelilS 158
                                    D+R+gSp fg++v+v L+     +l++p+gfahGf++l+d + +lY vt+ y+p++er+i w Dp+lgi+w   e +++S
  gi|119720615|ref|YP_921110.1|  94 DIRRGSPWFGRHVSVVLE--PGFALWVPPGFAHGFQALED-SFFLYFVTKEYSPQHERCIFWRDPDLGIRWprvEGAVVS 170
                                    *****************9..99****************98.899*****99***********************899*** PP

                                    HHHHT-B-HH CS
                dTDP_sugar_isom 159 ekDkaapsla 168
                                     +D++ p ++
  gi|119720615|ref|YP_921110.1| 171 GRDSRCPLFR 180
                                    *****99987 PP

>> Cupin_1  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.1   1.3e-07   0.00059      45     121 ..      65     147 ..      50     154 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.3e-07
                                    EEEEEEE...SSS-EEEEEEESEEEEEEEETTSS.....EEEEEEEETTEEEEE-TT-EEEEEEESSSSEEEEEEEESSS CS
                        Cupin_1  45 lllPhyh...pnateiayvlqGegrvgfvvpgng....nrdfhkklreGdvfvvPaglvhfqynsgdepavaivvfdtnn 117
                                    ++++hy    +   +++yv+ G+++ + v   +g     r  + +l++G +++vP+g++h +++ + ++ + ++v +  +
  gi|119720615|ref|YP_921110.1|  65 VRALHYQlkpMEQGKLVYVVSGRVFDVAVDIRRGspwfGRHVSVVLEPGFALWVPPGFAHGFQALE-DSFFLYFVTKEYS 143
                                    5566666333445689*********88888888877765666666********************7.8888999888888 PP

                                    TT-E CS
                        Cupin_1 118 pgnq 121
                                    p+++
  gi|119720615|ref|YP_921110.1| 144 PQHE 147
                                    8766 PP

>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   2.5e-06     0.011      21      62 ..      79     131 ..      69     139 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.5e-06
                                    EEEEEEESE.EEEEEC........TE..EEEEETTEEEEE-TT-EEEEEE-SS CS
                        Cupin_2  21 effyVleGe.geltvd........ge..eveleaGdsvyfpagtpHrfrNtgd 62 
                                     ++yV++G+ + + vd        g+   v+le+G ++ +p+g  H+f   +d
  gi|119720615|ref|YP_921110.1|  79 KLVYVVSGRvFDVAVDirrgspwfGRhvSVVLEPGFALWVPPGFAHGFQALED 131
                                    799******99999**988777774477*******************987665 PP

>> Toxin_24  Conotoxin TVIIA/GS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   4.2e-05      0.19       3      10 ..     170     177 ..     168     178 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.2e-05
                       Toxin_24   3 SGRdSRCP 10 
                                    SGRdSRCP
  gi|119720615|ref|YP_921110.1| 170 SGRDSRCP 177
                                    9******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       241  (0.0134419); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1384.89
//
Query:       gi|119720616|ref|YP_921111.1|  [L=94]
Description: hypothetical protein Tpen_1713 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00032   19.9   0.0    0.00034   19.8   0.0    1.0  1  RmlD_sub_bind  RmlD substrate binding domain


Domain annotation for each model (and alignments):
>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   1.9e-08   0.00034     216     267 ..      25      77 ..      13      93 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.9e-08
                                    S-EEHHHHHHHHHHHHCHTTSEEEEE-CCCS-.-SS---SBE-B--HHHHHCC CS
                  RmlD_sub_bind 216 getswlefArailkeagadseevkpistaeyp.tpAkRPanSvLdtekleatf 267
                                    + +s++efA   ++++g+++  v ++s+ae+    A+RP++S+Ldt++++ + 
  gi|119720616|ref|YP_921111.1|  25 KRMSRYEFAVRLAERLGYSADLVDAVSAAEMKgWVARRPRDSSLDTSRARGIL 77 
                                    459***********************999986268***********9987654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 700.68
//
Query:       gi|119720617|ref|YP_921112.1|  [L=1293]
Description: peptidase S8/S53 subtilisin kexin sedolisin [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      4e-28   98.6   0.0    1.1e-27   97.1   0.0    1.7  1  Peptidase_S8  Subtilase family
    6.2e-08   32.8   2.4    5.3e-05   23.3   0.1    2.9  3  ASH           Abnormal spindle-like microcephaly-assoc'd, ASP
     0.0028   18.4   3.0      0.043   14.5   0.6    2.9  3  fn3_5         Fn3-like domain


Domain annotation for each model (and alignments):
>> Peptidase_S8  Subtilase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.1   0.0   1.9e-31   1.1e-27       1     287 [.     191     671 ..     191     681 .. 0.78

  Alignments for each domain:
  == domain 1  score: 97.1 bits;  conditional E-value: 1.9e-31
                                    -TT-EEEEECS-B-TT-TTTGGGEEE..EEEE---TTSG......................................... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................................ RF
                   Peptidase_S8   1 gkgvlvavlDtGvdpshpdlsvttdgerklvdvideegag........................................ 40 
                                    g+gv +a++DtGvd +hpdl + +        + + + +g                                        
  gi|119720617|ref|YP_921112.1| 191 GSGVNIAIVDTGVDFGHPDLTSALA-------YWSGTYKGewvveplvfdadesqvllfqdvqlvnsthvyvggksyttl 263
                                    79******************94433.......333334445677888888********************9999999999 PP

                                    ................................................................................ CS
                                    ................................................................................ RF
                   Peptidase_S8  41 ................................................................................ 40 
                                                                                                                    
  gi|119720617|ref|YP_921112.1| 264 ipwpvdiyppydyyriplsvynmvsqpggglrfgvtylwrydgirivgvllvkpytfgyyayalidvnnngrfddevapp 343
                                    99999999999999999999999999999999999999999999999999999999999999999988888888888888 PP

                                    ............................GGEETT-SS-TT-SC-S..............................SS... CS
                                    ............................xxxxxxxxxxxxxxxxx..............................xxxxx RF
                   Peptidase_S8  41 ............................fngadsettstnwardd..............................ngnsi 62 
                                                                                d                               ++si
  gi|119720617|ref|YP_921112.1| 344 idpygrgsvlrysanrviapdydrngfpD---------------DsfgvaggffydwwwyfnypaeifpgwdrqgRWLSI 408
                                    88888888877775555555555555550...............255555555555555555555555555554455555 PP

                                    ......HHHHHHHHHH-B..........SSSSSB-SSTTSEEEEEE-SSTTSB-HH..HHHHHH..........HHHHHH CS
                                    x.....xxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..........xxxxxx RF
                   Peptidase_S8  63 e.....HGthvAGiaaan........apeegekngvapgakilsvkvldtsggsmetgtelira..........ieeaae 119
                                          HGt +A+ aa+              +  g+apgaki +vk+l    g+ e    l++a          +++   
  gi|119720617|ref|YP_921112.1| 409 FydfygHGTSCASAAAGRgvvaynvtGLGVVKLTGIAPGAKIVGVKALW--IGNVEV-GMLWAAgfdvnpydgkFYYTGS 485
                                    466677**************99777777778999*********888772..222222.3333334556666666777777 PP

                                    CT-SEEEE-EESCETTCHHCHHHHHH.........HHHHHH.CC.T-EEEEE--SS-T-HHEEE-TTCEECTTTSTTCEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Peptidase_S8 120 dkvdvinmslgestslpktgrsieal.........ainravnkk.gvlvviSaGNngktgsslqagspvgtpstsknvit 189
                                     ++++i++s+g s+ + ++g    +l         +   +  ++ g+l+v + GN g      +   ++ +p+ s +v+t
  gi|119720617|ref|YP_921112.1| 486 RRAHIISNSWGTSYFTYDVGAFGYDLesvfvaglsMPGFLDPRYpGILIVQAGGNGG------PGYGTITSPGASPGVLT 559
                                    8888*******6665555555444445559999984445555556************......9999************* PP

                                    EEEES.......................TTSSB-TT--B-TT.......-EEEE-S-CCCCCCCCCHHHTTTHHEEEE-S CS
                                    xxxxx.......................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Peptidase_S8 190 vgayt.......................tegkiapfSsrGpssdgklkpdivapGgnivstwsrqsnnsaglssyqsmsG 246
                                    vga t                         +++ ++S rGp+++g +kpd+v  G+ ++  ++          +y+ + G
  gi|119720617|ref|YP_921112.1| 560 VGASTsmhfayvlskqgygsvfmsgggwAFDEVVSWSLRGPTVAGYVKPDVVNVGAFGFTAAPVTV-------NYTIFGG 632
                                    ****************************9999************************9444444444.......499**** PP

                                    HHHCHHHHHHHHHHHHHHHTT--HHHHHHHHHCCS-EE... CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Peptidase_S8 247 TSmAsPnaagaaAlllsalpkltpetvraallntAqdlgka 287
                                    TS A+P+ ag+aAl+ + lp   p+ v++++  tAq +   
  gi|119720617|ref|YP_921112.1| 633 TSYATPLTAGVAALVYQVLPTADPDLVKSIIASTAQGV--G 671
                                    ***********************************855..2 PP

>> ASH  Abnormal spindle-like microcephaly-assoc'd, ASPM-SPD-2-Hydin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       0.8   4.8e+03      26      50 ..      89     114 ..      87     119 .. 0.84
   2 !   23.3   0.1   8.9e-09   5.3e-05      13      68 ..     761     816 ..     754     820 .. 0.92
   3 !    7.9   0.2   0.00058       3.5      43      80 ..     939     976 ..     929     993 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.8
                                    EEE-EEESS-SS-.-EEEEEEEE--X CS
                            ASH  26 erlLtveNpseep.aevkvskvpaae 50 
                                    er+L v N+++ +  evkvs+++ ++
  gi|119720617|ref|YP_921112.1|  89 ERTLSVANGKQVKvREVKVSRLVMDK 114
                                    79999****99999999999987555 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 8.9e-09
                                    EEEE-----EEEEEEE-EEESS-SS--EEEEEEEE--XXXXXXXXXXXXXXXXXXX CS
                            ASH  13 fvsFgdvkvGssaerlLtveNpseepaevkvskvpaaekgfsveetelevqpgesv 68 
                                    ++ Fgdv+vG +++ +Ltv+Np++++++v +s+ + + ++ +v  ++l ++pg+s+
  gi|119720617|ref|YP_921112.1| 761 SLFFGDVPVGGNKSITLTVKNPTNKTVSVSLSPRIFKLTNTTVLSRSLSLSPGTSY 816
                                    577******************************99999999999999*****9875 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.00058
                                    EEEEE--XXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXX CS
                            ASH  43 vskvpaaekgfsveetelevqpgesvtltvtwt.Pteeg 80 
                                    + +++  +  +sv++++ +++pg+s+t+t+t++ P+ ++
  gi|119720617|ref|YP_921112.1| 939 YVDTA-GDSWVSVSPSTATISPGGSQTFTLTLKvPSNAV 976
                                    44444.566799*******************96455555 PP

>> fn3_5  Fn3-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1      0.04   2.4e+02       9      31 ..     772     794 ..     766     828 .. 0.82
   2 !   14.5   0.6   7.2e-06     0.043      58     114 ..     947     999 ..     932    1000 .. 0.86
   3 ?   -2.2   0.0       1.1   6.6e+03       8      27 ..    1234    1253 ..    1232    1257 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.04
                          fn3_5   9 kfsftltlkNtsnkaltykvsan 31 
                                     +s+tlt+kN +nk+++ ++s  
  gi|119720617|ref|YP_921112.1| 772 NKSITLTVKNPTNKTVSVSLSPR 794
                                    6899***********99998876 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 7.2e-06
                          fn3_5  58 altfetskvtvpAnssktvtvtldlpsdakkkngyfveGfvtlkdsedknpelsvPY 114
                                     +++++s+ t+ +++s+t+t+tl +ps+a     +++   v +++ +++     +PY
  gi|119720617|ref|YP_921112.1| 947 WVSVSPSTATISPGGSQTFTLTLKVPSNAVP--TTYIGEVVAVNNVTGH--ATAIPY 999
                                    67899**********************8888..7777778999999999..889998 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.1
                          fn3_5    8 dkfsftltlkNtsnkaltyk 27  
                                     + f+f + ++N++ + + ++
  gi|119720617|ref|YP_921112.1| 1234 TVFTFSFMVQNYGAEGQKFD 1253
                                     55899********9998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.77u 0.30s 00:00:01.07 Elapsed: 00:00:00.44
# Mc/sec: 8840.41
//
Query:       gi|119720618|ref|YP_921113.1|  [L=362]
Description: UDP-N-acetylglucosamine 2-epimerase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   2.6e-109  365.3   0.0   3.3e-109  364.9   0.0    1.0  1  Epimerase_2      UDP-N-acetylglucosamine 2-epimerase
     0.0018   17.4   0.0      0.052   12.6   0.0    2.2  2  DUF354           Protein of unknown function (DUF354)
     0.0069   16.4   0.0      0.014   15.4   0.0    1.5  1  Glyco_transf_4   Glycosyltransferase Family 4
  ------ inclusion threshold ------
      0.044   13.8   0.0      0.076   13.1   0.0    1.3  1  Glyco_transf_28  Glycosyltransferase family 28 N-terminal dom
      0.045   13.7   0.1       0.12   12.3   0.1    1.6  2  DB_JBP1          Thymine dioxygenase JBP1 DNA-binding domain
       0.14   12.7   0.0       0.56   10.7   0.0    1.9  2  Rhodanese        Rhodanese-like domain


Domain annotation for each model (and alignments):
>> Epimerase_2  UDP-N-acetylglucosamine 2-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  364.9   0.0  1.1e-112  3.3e-109       7     346 ..      26     356 ..      22     357 .. 0.96

  Alignments for each domain:
  == domain 1  score: 364.9 bits;  conditional E-value: 1.1e-112
                                    -..EEEEEEE-S--SGGGTHHHHHHTT----SEEE---S--HHHHHHHHHHHHHHHHHHH--SEEEEESSSHHHHHHHHH CS
                    Epimerase_2   7 selelqlvvtGqHldremgdtvfeeleiekpdydlnsdsqslakstgrvligleevleeekpDlvlvlGDtnetlagala 86 
                                    +e+e+++++tGqH+d+em++++fe+l++++pd++l+++s+s + ++g+++++ ee l++ +pD+v+v+GDtn+tlagala
  gi|119720618|ref|YP_921113.1|  26 REFEHTVIHTGQHYDYEMSKVFFEQLRLRDPDIHLGVGSGSQGYQVGEIVKKAEEHLKSINPDVVVVYGDTNSTLAGALA 105
                                    579***************************************************************************** PP

                                    HHHTT-EEEEET-----S-TT..SHHHHHHHHHHHT-SEEEESSHHHHHHHHHTT--GGGEEE---HHHHHHHHHHHHHH CS
                    Epimerase_2  87 AfklripvaHveAGlRsfdltegmpeEinRhlidklsdlhfapteearenLlkegeeeerifvvGntviDalllskeeie 166
                                    A+k++ pvaHveAGlRs+d++  m eEinR+++d++s l+fapt++ar+nLlke++ + ++f +G++ +D l+   e+i+
  gi|119720618|ref|YP_921113.1| 106 AAKAGYPVAHVEAGLRSHDMK--MQEEINRRVVDHVSALLFAPTPSARDNLLKENV-PGKVFLTGDVHVDVLQKWIESIQ 182
                                    *********************..********************************9.779************99999995 PP

                                    ...T-HHHHHH..--SS-EEEEE---HHHHTSHHHHHHHHHHHHHHHHHH--EEEEE--..HHHHHHH.....HHHHHH- CS
                    Epimerase_2 167 eklkaseilke..lkekkyvlvtlHrrenedeperlkeilealkalakekdvevvvpvhnnprtrkrl.....leeleel 239
                                        +s+il +  l e +yv++t+Hr+en+d+p++l+e++++lk+la+   ++vv+p+h  prtr+r+     ++el + 
  gi|119720618|ref|YP_921113.1| 183 ----RSNILGRlgLLEGEYVMATIHRAENVDDPAKLAEVIKCLKELAAL--TKVVFPIH--PRTRSRAeeaglEKELYSN 254
                                    ....6689998999**********************************9..889*****..*******888876677777 PP

                                    TTEEEE----HHHHHHHHHC-SEEEES-HHHHHHHHHCT--EEESSSS-S-THHHHTTSEEE-TT-HHHHHHHHHHHCT- CS
                    Epimerase_2 240 envtlieplgyldflsllknaklvltdSgGiqeEapslgvpvvnlReeteRpegveagtnvlvgtdkeeIvaaleklled 319
                                    +n+ +++plgy+dfl+l+  +klv+tdSgG+q+Ea++lg+p+++lR++te+ e v+a +++l++++++++v++++klle+
  gi|119720618|ref|YP_921113.1| 255 PNLVATKPLGYVDFLRLVTGSKLVVTDSGGVQREAYLLGKPAIVLRDRTEWIELVQAEWVRLADANPARLVQEYKKLLEK 334
                                    7*****************************************************************************77 PP

                                    ..--......--TT-SS-HHHHHHHHH CS
                    Epimerase_2 320 kkelekmanaknpYgdGkaseriveil 346
                                           a +    gdGka+eri++++
  gi|119720618|ref|YP_921113.1| 335 -----PPAPQPGLLGDGKAAERITKTI 356
                                    .....6667789************987 PP

>> DUF354  Protein of unknown function (DUF354)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.035   1.1e+02     194     215 ..     162     183 ..     150     190 .. 0.81
   2 !   12.6   0.0   1.7e-05     0.052     208     276 ..     216     297 ..     207     303 .. 0.67

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.035
                         DUF354 194 asyldadchkdvltkiveklkd 215
                                      +l +d+h dvl k +e ++ 
  gi|119720618|ref|YP_921113.1| 162 KVFLTGDVHVDVLQKWIESIQR 183
                                    56899*************9985 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 1.7e-05
                         DUF354 208 kiveklkdrid..ilvi...prdee.......qkeiyeevdnvivike..tvdalsllkrsdlviGaGGtmnreaallGi 273
                                    ++++ lk+ +    +v+   pr +        +ke+y + +  +  k+   vd l l+  s lv+   G ++rea llG 
  gi|119720618|ref|YP_921113.1| 216 EVIKCLKELAAltKVVFpihPRTRSraeeaglEKELYSNPN-LVATKPlgYVDFLRLVTGSKLVVTDSGGVQREAYLLGK 294
                                    55555655555432333111455541111222467888877.555555336***************************** PP

                         DUF354 274 pvv 276
                                    p++
  gi|119720618|ref|YP_921113.1| 295 PAI 297
                                    *98 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   4.6e-06     0.014      59     158 ..      73     162 ..      19     166 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 4.6e-06
                 Glyco_transf_4  59 aflrrlrrllkrekpDvv.HahspaalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrrad.r 136
                                      ++++ ++lk  +pDvv  + +  + +a++la+++  g p+ +   gl          +   ++ +++ rr+++++   
  gi|119720618|ref|YP_921113.1|  73 EIVKKAEEHLKSINPDVVvVYGDTNSTLAGALAAAK-AGYPVAHVEAGLR---------SHDMKMQEEINRRVVDHVSaL 142
                                    45678999**********867777888899999998.9****99977776.........233334444445555554417 PP

                 Glyco_transf_4 137 viavSeatadelrerygvppek 158
                                    ++a++++++d+l++  +vp  k
  gi|119720618|ref|YP_921113.1| 143 LFAPTPSARDNLLK-ENVPG-K 162
                                    899**********9.88884.4 PP

>> Glyco_transf_28  Glycosyltransferase family 28 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   2.5e-05     0.076      15     117 ..      17     116 ..       4     122 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.5e-05
                                    HHHHHHHHHCT.T-EEEEEEETCCCHHHHHHCCT-EEEE---GHCTT..CHHHHCCHHHHHHHHHHHHHHHHHHHHCCCC CS
                Glyco_transf_28  15 alAlakeLkke.gheVrylgtkrgleerlveeaglefepiageklrrklspknlkeilkvlkavvkakkilkeakpdavv 93 
                                      A+a+++ +e +h V  + t + ++ ++   +++ fe++ ++     l ++  ++  +v++ v+ka ++lk+++pd+vv
  gi|119720618|ref|YP_921113.1|  17 LAAVAETFDREfEHTV--IHTGQHYDYEM---SKVFFEQLRLRDPDIHLGVGSGSQGYQVGEIVKKAEEHLKSINPDVVV 91 
                                    5688888865415555..45555555555...999*******999999999999999999999***************** PP

                                    CCCCCCCH.CCCCCHCCCTTHCCCC CS
                Glyco_transf_28  94 gtggyvsl.paviaaplaripviih 117
                                     +g   s+ +  +aa++a+ pv   
  gi|119720618|ref|YP_921113.1|  92 VYGDTNSTlAGALAAAKAGYPVAHV 116
                                    ***8776515579999999998655 PP

>> DB_JBP1  Thymine dioxygenase JBP1 DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       2.1   6.4e+03      38      53 ..      74      89 ..      72     101 .. 0.81
   2 ?   12.3   0.1   4.2e-05      0.12      30      55 ..     300     325 ..     295     333 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.1
                        DB_JBP1 38 lvkkewkklkernPer 53
                                   +vkk+ ++lk++nP+ 
  gi|119720618|ref|YP_921113.1| 74 IVKKAEEHLKSINPDV 89
                                   7999999999999985 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 4.2e-05
                        DB_JBP1  30 qarekwlelvkkewkklkernPerkd 55 
                                    + r++w+elv+ ew +l + nP r  
  gi|119720618|ref|YP_921113.1| 300 RDRTEWIELVQAEWVRLADANPARLV 325
                                    679*******************9965 PP

>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00019      0.56      55     102 ..      75     121 ..      63     125 .. 0.72
   2 ?   -1.5   0.0       1.2   3.7e+03      28      78 ..     200     239 ..     194     290 .. 0.50

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00019
                      Rhodanese  55 peellel.gidnkktvvvycdgggraaaaaallkklGyknvsvldGGfk 102
                                    +++++e+ +  n + vvvy+d+++  a a a++k +G + v +++ G++
  gi|119720618|ref|YP_921113.1|  75 VKKAEEHlKSINPDVVVVYGDTNSTLAGALAAAK-AG-YPVAHVEAGLR 121
                                    333333343458999*******999555566666.**.79999999986 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.2
                      Rhodanese  28 ghIpgAvnvskdtlsrakkseapllelpeellelgidnkktvvvycdgggr 78 
                                      I  A nv          ++a+l+e ++ l+el     ++vv+  + + r
  gi|119720618|ref|YP_921113.1| 200 ATIHRAENV---------DDPAKLAEVIKCLKEL--AALTKVVFPIHPRTR 239
                                    555555555.........4444444444444444..333444433333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 2811.29
//
Query:       gi|119720619|ref|YP_921114.1|  [L=274]
Description: FkbM family methyltransferase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-19   70.1   0.0      3e-19   69.7   0.0    1.1  1  Methyltransf_21  Methyltransferase FkbM domain
    3.4e-05   23.7   0.1    5.8e-05   22.9   0.1    1.3  1  Met_10           Met-10+ like-protein
  ------ inclusion threshold ------
       0.06   12.6   0.0       0.17   11.2   0.0    1.7  1  V_cholerae_RfbT  Vibrio cholerae RfbT protein


Domain annotation for each model (and alignments):
>> Methyltransf_21  Methyltransferase FkbM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.7   0.0   4.9e-23     3e-19       1     172 [.     105     255 ..     105     256 .. 0.80

  Alignments for each domain:
  == domain 1  score: 69.7 bits;  conditional E-value: 4.9e-23
                Methyltransf_21   1 dvGanigvwdsfanltarlcggggevlaiEPvpnslpkfeklranlltlavgndvglyelivegksg..gkyfpfavgdt 78 
                                    dvGan+g  ++++  + r    g++v+a+EPvp    + + l+an   l ++   g + +   ++ +  g+ ++f  ++ 
  gi|119720619|ref|YP_921114.1| 105 DVGANVG--YYTLLGVLR----GARVVAMEPVPQ---TVAVLKAN---LRLNGFSGVIVVDKCAW-StrGRVTLFVPSGR 171
                                    9******..777766666....************...********...99996666655444333.36644444444443 PP

                Methyltransf_21  79 .ngfstssvlggedaryievpvvtldsfleeikksridllkiDvEGaElevLeGaqkglkrcqpnlivvEvhkfkefete 157
                                      g s++++  g+ ++ + v++v+ld++l+ +   ri l+k+DvEGaE++vL+G +  l+r+++ +  vEv+        
  gi|119720619|ref|YP_921114.1| 172 yYGLSSAYHDRGVKGSLVGVEAVRLDDVLRGF--DRIRLVKLDVEGAEYDVLKGMESVLERVDFIV--VEVSRR------ 241
                                    15555557667*******************99..***************************99988..6**974...... PP

                Methyltransf_21 158 lfdeirqflrecgyr 172
                                      ++i+ +l+++g++
  gi|119720619|ref|YP_921114.1| 242 -AKDIICLLKSHGFK 255
                                    .57888888888887 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.1   9.7e-09   5.8e-05      96     153 ..      95     150 ..      89     157 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 9.7e-09
                                    TT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCE CS
                         Met_10  96 klveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvv 153
                                    +  ++g+v vdv A +G++++      ++ rv+a++  P++v  lk n++lN  + v+
  gi|119720619|ref|YP_921114.1|  95 SALSPGDVFVDVGANVGYYTLLGVL--RGARVVAMEPVPQTVAVLKANLRLNGFSGVI 150
                                    5689****************96555..8999*********************999988 PP

>> V_cholerae_RfbT  Vibrio cholerae RfbT protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   2.8e-05      0.17      43     213 ..      64     227 ..      39     240 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2.8e-05
                V_cholerae_RfbT  43 efglhcfprvqlnhalsyknpnfdlgmrhwivnhckhdttyidiganvgtfcgiaarhitqgkiiaiepltemensirmn 122
                                    e+g+ +f r      l y  p  +  +  +i         ++d+ganvg +  +    +   +++a+ep+ +    ++ n
  gi|119720619|ref|YP_921114.1|  64 ELGVVVFVRGGT-EDLYYLLPGREGPVDEFIRSALSPGDVFVDVGANVGYYTLLGV--LRGARVVAMEPVPQTVAVLKAN 140
                                    566666666543.3466666666666777777777777899********9987765..56779***************** PP

                V_cholerae_RfbT 123 vqlnnplvefhhfgcaigenegenifevyefdnrvsslyfkkntdiadkvknsqvlvrklssldisp..tnsvvikidae 200
                                    ++ln     +    ca        +f        +ss y ++       vk s v v  +   d+        ++k+d e
  gi|119720619|ref|YP_921114.1| 141 LRLNGFSGVIVVDKCAWSTRGRVTLFVPSGRYYGLSSAYHDR------GVKGSLVGVEAVRLDDVLRgfDRIRLVKLDVE 214
                                    ***987777777778877766666666555555566666544......36666666666555555431134456788888 PP

                V_cholerae_RfbT 201 gaeieilnqiyef 213
                                    gae ++l+ +  +
  gi|119720619|ref|YP_921114.1| 215 GAEYDVLKGMESV 227
                                    8888877766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       263  (0.014669); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2052.39
//
Query:       gi|119720620|ref|YP_921115.1|  [L=426]
Description: glycosyl transferase, group 1 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.9e-43  146.0   0.0    1.5e-42  145.1   0.0    1.4  1  Glycos_transf_1  Glycosyl transferases group 1
    2.1e-33  115.6   0.1    9.5e-33  113.5   0.0    2.1  2  Glyco_trans_1_4  Glycosyl transferases group 1
    3.2e-20   72.8   1.5    1.1e-19   71.0   1.0    2.1  2  Glyco_transf_4   Glycosyltransferase Family 4
    8.5e-14   52.3   0.1    8.5e-14   52.3   0.1    2.0  3  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    6.4e-12   45.7   0.2    5.7e-11   42.6   0.2    2.4  2  Glyco_trans_4_2  Glycosyl transferase 4-like
    7.6e-11   42.3   0.0    1.8e-10   41.1   0.0    1.6  1  Glyco_trans_1_2  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.1   0.0   4.9e-46   1.5e-42       6     171 ..     239     402 ..     236     403 .. 0.97

  Alignments for each domain:
  == domain 1  score: 145.1 bits;  conditional E-value: 4.9e-46
                                    HHHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSS CS
                Glycos_transf_1   6 rkklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsred 85 
                                    rk+lg+ e+k +++s    +++ g+++lika+al+ k  +++v++vi G+g+ + + +kl+e l+l++nvif+g+++r++
  gi|119720620|ref|YP_921115.1| 239 RKRLGI-ENKFVVFSARHHRPVYGLEYLIKAAALVVKL-RSDVVFVIGGEGPLRTYHEKLVEMLNLENNVIFTGRIPRDE 316
                                    677777.8999***********************9986.***************************************** PP

                                    HHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHHHHH CS
                Glycos_transf_1  86 leellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeelrerl 165
                                    +++++ ++d++v+ps  E++ +v++EAma+g+pv+ + +gg+ +++ dg +G+lv+p +++a+ae+i +l++++++++r+
  gi|119720620|ref|YP_921115.1| 317 MPHYYAASDAVVVPSLQEAWSLVVTEAMASGKPVVGTRVGGIVDQIIDGYNGFLVPPRDPKAIAEKILWLIDNPDEAKRM 396
                                    ******************************************************************************** PP

                                    HHHHHH CS
                Glycos_transf_1 166 genark 171
                                    g n+r+
  gi|119720620|ref|YP_921115.1| 397 GMNGRR 402
                                    ***985 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.82   2.4e+03      59      81 ..     178     201 ..     152     222 .. 0.69
   2 !  113.5   0.0   3.2e-36   9.5e-33       4     134 .]     249     389 ..     246     389 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.82
                                    EE---TH..HHHHHHH-SEEEE--- CS
                Glyco_trans_1_4  59 ftGfved..laellaaadvfvaPse 81 
                                    +  +  d  ++e+l +ad +++ s+
  gi|119720620|ref|YP_921115.1| 178 LSKRY-DalVREVLVNADAVIVASR 201
                                    44444.2247778888888887773 PP

  == domain 2  score: 113.5 bits;  conditional E-value: 3.2e-36
                                    EEEES---GG.GTHHHHHHHHHHHH.H..HEEEEEES---...HHHHHHHT..T-T.TEEEE---..THHHHHHHH-SEE CS
                Glyco_trans_1_4   4 ilfvGrleenvkgvdllleavpllrkk..dvrlvivGdgp.rpeeleelaa..gleerveftGfv..edlaellaaadvf 76 
                                    ++f  r +++v g+++l++a++l+ k   dv +vi G+gp r    e+l++  +le++v+ftG++  ++++ ++aa+d +
  gi|119720620|ref|YP_921115.1| 249 VVFSARHHRPVYGLEYLIKAAALVVKLrsDVVFVIGGEGPlRT-YHEKLVEmlNLENNVIFTGRIprDEMPHYYAASDAV 327
                                    8999999999***********999955445**********755.444444455899*********9777*********** PP

                                    EE--..---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHHH- CS
                Glyco_trans_1_4  77 vaPs..egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrLled 134
                                    v+Ps  e ++l++ Eama+g+pvV t+vggi + +  g ng+lvpp+dp+a+ae+il L+++
  gi|119720620|ref|YP_921115.1| 328 VVPSlqEAWSLVVTEAMASGKPVVGTRVGGIVDQIidGYNGFLVPPRDPKAIAEKILWLIDN 389
                                    *****99***********************866555***********************986 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.0   1.0   3.8e-23   1.1e-19       7     170 .]      45     228 ..      44     228 .. 0.76
   2 ?   -1.0   0.0      0.52   1.5e+03     128     148 ..     318     338 ..     290     351 .. 0.78

  Alignments for each domain:
  == domain 1  score: 71.0 bits;  conditional E-value: 3.8e-23
                 Glyco_transf_4   7 hvleLaraLarrGheVtvv.......tpgddgpleeev................elvvrvprvplp....llkrllrsla 59 
                                    +v++ a +L +rG++V+vv       +                           el++++p + ++    ++  l++   
  gi|119720620|ref|YP_921115.1|  45 FVFDEAYRLVQRGVNVHVVraaveesS-------SSYGinfhgirrrvdaeafvELLKNLPLYSPFallrNPLMLYWENL 117
                                    67888999***********66544331.......3333345666778888778855555555444400003344445555 PP

                 Glyco_transf_4  60 flrrlrrllkrekpDvvHahspaalgaallalrrrlgiplVltvHglye.krllkarlkplsrllralerrllrradrvi 138
                                    +++ + +++++ ++D++Hah++++ g+++l ++rr+++plV+t+Hg +    +  ++  +ls+++ al r +l +ad+vi
  gi|119720620|ref|YP_921115.1| 118 YALNISNVVENLRIDLIHAHFAYPEGFSGLIAKRRTKKPLVVTLHGYDIlVEPSVKYGIRLSKRYDALVREVLVNADAVI 197
                                    677889999999************************************983344445556777888899999******** PP

                 Glyco_transf_4 139 avSeatadelrerygvppekitVipnGvDler 170
                                    + S+a+ +e +++ g + +  + ++nGvD++r
  gi|119720620|ref|YP_921115.1| 198 VASRAVFEEAVKLRGRK-SGTYLVHNGVDIKR 228
                                    ************88855.8**********986 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.52
                 Glyco_transf_4 128 rrllrradrviavSeatadel 148
                                     + + ++d+v+++S ++a  l
  gi|119720620|ref|YP_921115.1| 318 PHYYAASDAVVVPSLQEAWSL 338
                                    566889999999998777665 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.3   0.1   2.8e-17   8.5e-14      12     160 .]      51     223 ..      46     223 .. 0.69
   2 ?   -2.6   0.0       2.3   6.8e+03      50      79 ..     255     282 ..     249     289 .. 0.75
   3 ?   -3.2   0.1       3.3   9.9e+03     128     141 ..     322     335 ..     319     342 .. 0.78

  Alignments for each domain:
  == domain 1  score: 52.3 bits;  conditional E-value: 2.8e-17
                Glyco_trans_4_4  12 raLaarGheVtvltpapapg...........apeleedgvrvhrlpvprrpspladlaal..........ralrrllrqr 70 
                                     +L++rG+ V+v+ +a  ++           ++ ++ + + v  l+  +  sp+a l+ +               ++  +
  gi|119720620|ref|YP_921115.1|  51 YRLVQRGVNVHVVRAAVEESsssyginfhgiRR-RVDAEAFVELLKNLPLYSPFALLRNPlmlywenlyaLNISNVV--E 127
                                    589**********96666654444455544322.4555566665554444455665553322232222112224445..* PP

                Glyco_trans_4_4  71 rerpdvvhahs.ptaglaarlarrrrgiplvvtlhgll......lrrgsgavrrlyralerrllrradavlvvseaeaee 143
                                      r+d++hah  ++ g+ +++a+rr++ plvvtlhg +      + + + ++   y+al r +l +adav+v s+a+ ee
  gi|119720620|ref|YP_921115.1| 128 NLRIDLIHAHFaYPEGFSGLIAKRRTKKPLVVTLHGYDilvepsVKY-GIRLSKRYDALVREVLVNADAVIVASRAVFEE 206
                                    **********97899********999*********844433332333.567778899*********************** PP

                Glyco_trans_4_4 144 lralgvpadrvvvvpng 160
                                    ++ l ++ + + +v+ng
  gi|119720620|ref|YP_921115.1| 207 AVKLRGRKSGTYLVHNG 223
                                    *9977776666666665 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.3
                Glyco_trans_4_4  50 rpspladlaalralrrllrqrrerpdvvha 79 
                                    +++p++ l++l  +++l+   + r dvv +
  gi|119720620|ref|YP_921115.1| 255 HHRPVYGLEYLIKAAALV--VKLRSDVVFV 282
                                    456888888888888888..8888888876 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 3.3
                Glyco_trans_4_4 128 rradavlvvseaea 141
                                    +  dav+v+s +ea
  gi|119720620|ref|YP_921115.1| 322 AASDAVVVPSLQEA 335
                                    56799999997766 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.4   4.1e+03      15      41 ..      15      41 ..       6      54 .. 0.74
   2 !   42.6   0.2   1.9e-14   5.7e-11      17     139 .]      50     200 ..      32     200 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.4
                Glyco_trans_4_2 15 rlakeLakrgyeVhvitpkkgakdele 41
                                   r++ e+ + ++ V+++++ +g++ +++
  gi|119720620|ref|YP_921115.1| 15 RRMMEAGSSDISVAIVSSVVGKSPREV 41
                                   446667788999999999888765554 PP

  == domain 2  score: 42.6 bits;  conditional E-value: 1.9e-14
                Glyco_trans_4_2  17 akeLakrgyeVhvitpkkgakdeleaegihvhrlkvd......................rkgpleylka........... 63 
                                    a  L +rg++Vhv+   ++  + + ++gi++h ++ +                      r                    
  gi|119720620|ref|YP_921115.1|  50 AYRLVQRGVNVHVVRAAVE--ESSSSYGINFHGIRRRvdaeafvellknlplyspfallR--------Nplmlywenlya 119
                                    55699***********998..7788999*9999953333555555555555554444421........033444444454 PP

                Glyco_trans_4_2  64 fklkklikkikPDvvhahyakpygllgslaarlsgvipvvlsvwGldvlkfpkksk....lkkl...llklalkkatkvi 136
                                    + + ++++ + +D++hah a p g+ g +a+r+++ +p+v++ +G d+l +p  +       k    l++  l +a++vi
  gi|119720620|ref|YP_921115.1| 120 LNISNVVENLRIDLIHAHFAYPEGFSGLIAKRRTK-KPLVVTLHGYDILVEPSVKYgirlS-KRydaLVREVLVNADAVI 197
                                    8**************************99999998.***************9999866642.225779999999****99 PP

                Glyco_trans_4_2 137 stn 139
                                    + +
  gi|119720620|ref|YP_921115.1| 198 VAS 200
                                    875 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   0.0     6e-14   1.8e-10       4      91 ..     329     418 ..     324     419 .. 0.94

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 6e-14
                Glyco_trans_1_2   4 npsrsespnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaarervlaeh 81 
                                     ps +e  +l++ Ea+a+G +++ ++  g+ + + +g  ++l+   d++ +aeki  l++np+e+++++ ++r+ +++++
  gi|119720620|ref|YP_921115.1| 329 VPSLQEAWSLVVTEAMASGKPVVGTRVGGIVDQIIDGYNGFLVPprDPKAIAEKILWLIDNPDEAKRMGMNGRRLAEEKF 408
                                    5788889999*****************999999999999999999*********************************** PP

                Glyco_trans_1_2  82 tydhraeqll 91 
                                    + ++r+e+++
  gi|119720620|ref|YP_921115.1| 409 DIEKRIEKII 418
                                    *******996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.38
# Mc/sec: 3354.83
//
Query:       gi|119720621|ref|YP_921116.1|  [L=696]
Description: glycosyl transferase family protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0032   17.7  21.2     0.0032   17.7  21.2    3.4  3  PMT_2     Dolichyl-phosphate-mannose-protein mannosyltransfer


Domain annotation for each model (and alignments):
>> PMT_2  Dolichyl-phosphate-mannose-protein mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0      0.45     8e+03      76      93 ..      11      28 ..       6      41 .. 0.59
   2 !   17.7  21.2   1.8e-07    0.0032      31     152 ..     101     227 ..      80     232 .. 0.82
   3 ?   -3.3  14.1      0.52   9.2e+03       9      98 ..     308     400 ..     300     463 .. 0.72

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.45
                          PMT_2 76 aplvllwalalylllral 93
                                    ++v+++++++  ++ al
  gi|119720621|ref|YP_921116.1| 11 KMFVAFLVIIYSSVYFAL 28
                                   455555555555555554 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 1.8e-07
                          PMT_2  31 agvltilllyllarrlfgkraallaalllavvplfvalsalftpdaplvllwalalylllraleknk.lkywllagvlfG 109
                                    + ++ ++  y l+r+l++   al+    +a+ p+ v++   + +d ++  l +l++y+l+  l +   l   l ++++++
  gi|119720621|ref|YP_921116.1| 101 FLLVYLASTYMLIRELVDFPEALILWTAVAFNPFAVVYFNFYLTDFAFASLSLLSIYYLIWSLRRWAkLTGILKSYIVAA 180
                                    567788899***************************************************999976557888******** PP

                          PMT_2 110 lgflsKytaallliaall.yllis.arr.ilkekkpyl.alllalll 152
                                    l++l+K +++l++   +l  +++  ++  +l + ++ l ++++al +
  gi|119720621|ref|YP_921116.1| 181 LALLVKLNMLLVIAHWILlVVVFAwKKYwRLSKWHKTLfIVAIALPV 227
                                    **************966646666644554444444444455555544 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 0.52
                          PMT_2   9 llalftklfgf.selairlvsalagvltilllyllarrlfg.kraallaalllavvplfvalsa.lftpdaplvllwala 85 
                                    l+ l+  lf +    +i l   l+ +l ++++ +l  +l + +r +lla ++l+v+ l + +++   ++ ++  +++a  
  gi|119720621|ref|YP_921116.1| 308 LALLSPLLFWKeRRHGIMLSLLLFLLLPVFYFHILNGNLWDlARNSLLAFVILEVTGLTALYAVtRSNTQVVVAAFVASQ 387
                                    5556666775546677777788889999999999999******************9888888886788899999999999 PP

                          PMT_2  86 lylllraleknkl 98 
                                    l+l+++++ + + 
  gi|119720621|ref|YP_921116.1| 388 LLLYAEYIVSLNY 400
                                    9999998876654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (696 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       725  (0.0404373); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 4804.84
//
Query:       gi|119720622|ref|YP_921117.1|  [L=447]
Description: UDP-glucose 6-dehydrogenase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.2e-60  202.9   0.0    6.2e-60  202.0   0.0    1.5  2  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
    2.1e-34  117.6   0.0    2.5e-33  114.1   0.0    2.2  2  UDPG_MGDP_dh    UDP-glucose/GDP-mannose dehydrogenase family,
    1.9e-29  102.1   0.0    7.6e-29  100.2   0.0    1.9  2  UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family,
    2.2e-08   34.6   0.0     0.0083   16.7   0.0    3.3  3  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
    1.3e-07   32.0   0.1    1.3e-06   28.7   0.0    2.3  2  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
    0.00023   21.2   0.0     0.0025   17.8   0.0    2.3  2  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
    0.00044   20.2   0.0    0.00098   19.1   0.0    1.6  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
     0.0022   18.0   0.1      0.012   15.5   0.0    2.3  2  ADH_zinc_N      Zinc-binding dehydrogenase
     0.0043   16.3   0.0     0.0086   15.3   0.0    1.5  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
      0.008   16.4   0.1      0.039   14.2   0.0    2.2  2  TrkA_N          TrkA-N domain
     0.0096   15.8   0.5       0.38   10.6   0.1    2.4  2  NAD_binding_10  NAD(P)H-binding
  ------ inclusion threshold ------
       0.01   16.6   0.0       0.39   11.5   0.0    2.5  2  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f
      0.034   13.2   0.0      0.046   12.8   0.0    1.2  1  GIDA            Glucose inhibited division protein A
      0.058   13.4   0.0       0.12   12.4   0.0    1.7  1  CbiA            CobQ/CobB/MinD/ParA nucleotide binding domain
      0.072   12.2   0.2       0.13   11.3   0.2    1.3  1  FAD_binding_2   FAD binding domain
       0.08   12.2   0.2       0.18   11.0   0.1    1.6  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
       0.14   11.5   0.1        1.1    8.6   0.1    2.5  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase


Domain annotation for each model (and alignments):
>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  202.0   0.0   5.8e-63   6.2e-60       2     186 ..       3     190 ..       2     191 .. 0.97
   2 ?   -3.8   0.0       7.4   7.8e+03      62      83 ..     376     397 ..     368     398 .. 0.81

  Alignments for each domain:
  == domain 1  score: 202.0 bits;  conditional E-value: 5.8e-63
                                    EEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS--TTHHHHHHHHCHTTTEEEES-HHHHHHC-SEEE CS
                 UDPG_MGDP_dh_N   2 kisviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipiyepgLeelvkkavesgrlsfttdvekaveeadvif 81 
                                    +++viGlGY Gl+ a++la++g++v+gvD deekv+ +n+g +p+yep L++++k ++e g +++tt+v ka+ee+dv+f
  gi|119720622|ref|YP_921117.1|   3 RVAVIGLGYAGLPFAVALAHRGFKVVGVDTDEEKVELINKGVSPVYEPALNDYLKGVLERGLFKATTSVAKAIEESDVVF 82 
                                    89****************************************************************************** PP

                                    E-----B-TTTTCB-THHHHHHHHHHHHHHHC...EEEEEE-S---TTHHHHCHHHHHHHHCSS-.TTCEEEEE------ CS
                 UDPG_MGDP_dh_N  82 iaVgTPskkkgkaaDlkyvesaarsiaealkk...gkvvvvkSTvpvgtaeelvkkileeaskkk.gvdfdvvsnPEflr 157
                                    + VgTP+k  + + Dl+++e+a+++i++alk+   +k++vv+STv +gt+e +vk+i+ee+s k  g+df++ +nPEflr
  gi|119720622|ref|YP_921117.1|  83 VFVGTPTKA-DGSLDLTQLENASEDIGRALKDeggYKLIVVRSTVLPGTTEGVVKRIIEERSGKIcGRDFGLCMNPEFLR 161
                                    *********.7778*****************99999**************************9889************** PP

                                    TTSHHHHHHS-S-EEEEESSCHHHHHHHH CS
                 UDPG_MGDP_dh_N 158 egsavkdllnpdrvviGveekkaeaalee 186
                                    eg+a++d++np r+viG+ +k+++++le+
  gi|119720622|ref|YP_921117.1| 162 EGKALYDIFNPARIVIGEYDKRSGDILES 190
                                    **********************9998876 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 7.4
                                    TTEEEES-HHHHHHC-SEEEE- CS
                 UDPG_MGDP_dh_N  62 grlsfttdvekaveeadvifia 83 
                                    g++ f +dv + ++++d+i++a
  gi|119720622|ref|YP_921117.1| 376 GNVAFFSDVYECARRCDAIVVA 397
                                    6888999999999999999876 PP

>> UDPG_MGDP_dh  UDP-glucose/GDP-mannose dehydrogenase family, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.1   0.0   2.4e-36   2.5e-33       2      93 ..     210     302 ..     209     303 .. 0.98
   2 ?    0.9   0.0      0.51   5.4e+02      26      53 ..     414     440 ..     408     445 .. 0.81

  Alignments for each domain:
  == domain 1  score: 114.1 bits;  conditional E-value: 2.4e-36
                   UDPG_MGDP_dh   2 tAEliKlaaNaflatkIsfiNelanlceal.gidveeVieavgldprigpkflkpglGvGGsclpkDvkaLvalaeelgl 80 
                                    +AEliK+aaNafla+k+sfiN +a+++++l   dv eV++++gldprig+ fl++glG+GGsclpkD++aL++la++lg+
  gi|119720622|ref|YP_921117.1| 210 NAELIKYAANAFLAMKVSFINLIARIAQRLpRGDVIEVASGIGLDPRIGRDFLDAGLGFGGSCLPKDLRALIKLAKSLGV 289
                                    69****************************89************************************************ PP

                   UDPG_MGDP_dh  81 eaelleavrevNe 93 
                                    +a+llea+ evNe
  gi|119720622|ref|YP_921117.1| 290 DAKLLEAILEVNE 302
                                    ************8 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.51
                   UDPG_MGDP_dh  26 nlcealgidveeVieavgldprigpkfl 53 
                                    ++++++ id +++i+av++ +  g+k++
  gi|119720622|ref|YP_921117.1| 414 TMARRVVIDCRHIIDAVKASKA-GFKYY 440
                                    5788899***********9998.56665 PP

>> UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       2.7   2.9e+03      51      74 ..      62      85 ..      19      99 .. 0.70
   2 !  100.2   0.0   7.2e-32   7.6e-29       1     104 [.     325     428 ..     325     429 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.7
                                   BTCCEEES-CHHHHTT-SEEEE-S CS
                 UDPG_MGDP_dh_C 51 ekgvevvdsleealkgadaivilt 74
                                   +   + ++s+++a++++d++ + +
  gi|119720622|ref|YP_921117.1| 62 RGLFKATTSVAKAIEESDVVFVFV 85
                                   344566777889999999988776 PP

  == domain 2  score: 100.2 bits;  conditional E-value: 7.2e-32
                                    EEE-SSSSTT-S--TT-HHHHHHHHHHHCTSEEEEE-SSTHHCCCCHHGGBTCCEEES-CHHHHTT-SEEEE-S--GGGG CS
                 UDPG_MGDP_dh_C   1 ailGlafKkdtdDlReSpaldiieeLleegaevkiyDPkvkeeaveaeleekgvevvdsleealkgadaiviltehdefk 80 
                                    a+lGlafK++tdD+ReS++++++++L++ega ++++DP + ++a++  +   +v + ++++e+++ +daiv++t++ +++
  gi|119720622|ref|YP_921117.1| 325 AVLGLAFKPGTDDVRESQSIKLVKRLAKEGAVLHAHDPLALDAAKRVLQGIGNVAFFSDVYECARRCDAIVVATDWGDYR 404
                                    89*******************************************9988899**************************** PP

                                    GS-HHHHHHCCSS-EEEESSS-CC CS
                 UDPG_MGDP_dh_C  81 eldlaklkelmkpavvfDgrnvld 104
                                    +l +++l e+m+++vv+D+r+++d
  gi|119720622|ref|YP_921117.1| 405 NLCFERLGETMARRVVIDCRHIID 428
                                    *********************998 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   7.8e-06    0.0083       1      70 [.       3      86 ..       3     104 .. 0.94
   2 ?    1.2   0.0      0.52   5.5e+02      51      85 ..     206     239 ..     157     250 .. 0.65
   3 !   12.5   0.0   0.00016      0.17      39      94 ..     368     423 ..     343     425 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 7.8e-06
                                   EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC...................-EEECECHHHHHHH-S CS
                  F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg...................vkvtavdneeaaeead 63
                                   ++++iG G  g  +a  l+++g    ++v + + ++ek+e + + ++                    k+t+ + ++a+ee+d
  gi|119720622|ref|YP_921117.1|  3 RVAVIGLGYAGLPFAVALAHRG---FKVV-GVDTDEEKVELINKGVSpvyepalndylkgvlerglFKATT-SVAKAIEESD 79
                                   69********************...****.99**********************************99999.********** PP

                                   EEEE-S- CS
                  F420_oxidored 64 vvvlavk 70
                                   vv++ v 
  gi|119720622|ref|YP_921117.1| 80 VVFVFVG 86
                                   ***9885 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.52
                                    ECECHHHHHHH-SEEEE-S-HHHHHHHHHHCGHHH CS
                  F420_oxidored  51 tavdneeaaeeadvvvlavkpedveevlselakda 85 
                                    t+  n+e+++ a   +la+k + +  ++  +a+++
  gi|119720622|ref|YP_921117.1| 206 TSIVNAELIKYAANAFLAMKVSFINLIA-RIAQRL 239
                                    333799999*9*********98775444.443444 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 0.00016
                                    HHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHHHHCGHHHHTTSEEEEE CS
                  F420_oxidored  39 aeelaeelgvkvtavdneeaaeeadvvvlavkpedveevlselakdalkgklvisv 94 
                                    a+   + +g  ++ +d  e+a+++d +v+a  + d+ +++ e   ++ ++++vi++
  gi|119720622|ref|YP_921117.1| 368 AKRVLQGIGNVAFFSDVYECARRCDAIVVATDWGDYRNLCFERLGETMARRVVIDC 423
                                    444445555445555999************************99**********97 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0   1.2e-09   1.3e-06       2      75 ..       4      97 ..       3     144 .. 0.80
   2 ?    0.5   0.0      0.59   6.2e+02      14      67 ..     346     402 ..     344     433 .. 0.66

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 1.2e-09
                                   EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT....................EEE-SSHHHHHHHCSEEEE-S CS
                  NAD_binding_2  2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg....................akaaesieelvasldvvitmv 63
                                   +++iGlG  G ++a  l+++g+kv++++ ++ekve + +                      +ka++s+++++++ dvv+++v
  gi|119720622|ref|YP_921117.1|  4 VAVIGLGYAGLPFAVALAHRGFKVVGVDTDEEKVELINKGVspvyepalndylkgvlerglFKATTSVAKAIEESDVVFVFV 85
                                   89****************************9999877666599*************************************** PP

                                   SSHHHHHHHHHS CS
                  NAD_binding_2 64 kagkavdevieg 75
                                      ++ d  ++ 
  gi|119720622|ref|YP_921117.1| 86 GTPTKADGSLDL 97
                                   *99998877654 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.59
                                    HHHHHHHTT-EEEEE-.SSHHHHHHHHHTT...EEE-SSHHHHHHHCSEEEE-SSSHH CS
                  NAD_binding_2  14 malnllkagykvavyn.rtkekveelvaeg...akaaesieelvasldvvitmvkagk 67 
                                    ++++l+k+g  +++++ +  +++++++ +g   +  ++++ e+++++d++++    g+
  gi|119720622|ref|YP_921117.1| 346 LVKRLAKEGAVLHAHDpLALDAAKRVL-QGignVAFFSDVYECARRCDAIVVATDWGD 402
                                    788899999999999944445555555.444568888888899999999887655544 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   2.3e-06    0.0025       2      79 ..       4      87 ..       3     112 .. 0.85
   2 ?    0.5   0.0       0.5   5.2e+02      56      89 ..     377     410 ..     369     429 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.3e-06
                                   EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHH......HSSBTTTBTT----TTEEEES-HHHHHTT--EEEE-- CS
                 NAD_Gly3P_dh_N  2 iavlGaGswGtalAkvlaenghevrlwvreeelieeine......ehenvkyLpgiklpenlvattdlaealkgadiivlvv 77
                                   +av+G G  G  +A +la++g +v+    +ee +e in+      e   ++yL+g+      +att +a+a++++d++++ v
  gi|119720622|ref|YP_921117.1|  4 VAVIGLGYAGLPFAVALAHRGFKVVGVDTDEEKVELINKgvspvyEPALNDYLKGVLERGLFKATTSVAKAIEESDVVFVFV 85
                                   9*************************************9222222334568****88888889**************99887 PP

                                   -H CS
                 NAD_Gly3P_dh_N 78 Ps 79
                                    +
  gi|119720622|ref|YP_921117.1| 86 GT 87
                                   55 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.5
                                    TEEEES-HHHHHTT--EEEE---HHHHHHHHHHH CS
                 NAD_Gly3P_dh_N  56 nlvattdlaealkgadiivlvvPsqalrevlkkl 89 
                                    n+ + +d+ e+++++d iv++      r+ + + 
  gi|119720622|ref|YP_921117.1| 377 NVAFFSDVYECARRCDAIVVATDWGDYRNLCFER 410
                                    788899**************98877777776544 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   9.2e-07   0.00098       2      44 ..       4      46 ..       3      82 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 9.2e-07
                                   EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHH CS
                        3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekiek 44
                                   vaviG G  G   a ++a++g++Vv vd++ee++e  ++ ++ 
  gi|119720622|ref|YP_921117.1|  4 VAVIGLGYAGLPFAVALAHRGFKVVGVDTDEEKVELINKGVSP 46
                                   9********************************9988887765 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.2e-05     0.012       9      79 ..      19      98 ..       8     101 .. 0.74
   2 ?   -0.7   0.0       1.2   1.3e+03      88      88 ..     327     327 ..     278     398 .. 0.53

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.2e-05
                                   HHHHTT-EEEEEESSHHHHHHHHHTTESEEEET...........TTC.HHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHHC CS
                     ADH_zinc_N  9 lAkalGaeviavdsseeklelakklGadeviny...........kea.dlverikeltggegvdvvfecvGsgatleaalkl 78
                                   ++++ G++v++vd +eek+el  k G+  v+ +           +   +    ++++   e  dvvf +vG+++  + +l+l
  gi|119720622|ref|YP_921117.1| 19 ALAHRGFKVVGVDTDEEKVELINK-GVSPVYEPalndylkgvleRGLfKATTSVAKAI--EESDVVFVFVGTPTKADGSLDL 97
                                   3347899**************999.899999996666666666533344555555555..699********99999888887 PP

                                   E CS
                     ADH_zinc_N 79 l 79
                                   +
  gi|119720622|ref|YP_921117.1| 98 T 98
                                   6 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.2
                                    C CS
                     ADH_zinc_N  88 v 88 
                                     
  gi|119720622|ref|YP_921117.1| 327 L 327
                                    0 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   8.1e-06    0.0086       2      46 ..       3      56 ..       2     107 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 8.1e-06
                                   SEEEE--SHHHHHHHHHHHHHTS-EEEEE.........TTHCHHHCSHHHHCHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlve.........legtclnggcllskal 46
                                   +v+viG G AGl +a  la+ g+kv+ v+          +g  +   + l   l
  gi|119720622|ref|YP_921117.1|  3 RVAVIGLGYAGLPFAVALAHRGFKVVGVDtdeekveliNKGVSPVYEPALNDYL 56
                                   79**************************76654444444444555555555544 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   3.7e-05     0.039       1      40 [.       4      43 ..       4      55 .. 0.84
   2 ?   -2.6   0.0       6.1   6.4e+03      62      74 ..     390     402 ..     388     437 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.7e-05
                                   EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHT CS
                         TrkA_N  1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelree 40
                                   +++iGlG  G   a  L ++g +vv++d+dee+ve + + 
  gi|119720622|ref|YP_921117.1|  4 VAVIGLGYAGLPFAVALAHRGFKVVGVDTDEEKVELINKG 43
                                   68*****************7756***********987644 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 6.1
                                    GESEEEE-SSSHH CS
                         TrkA_N  62 kadaviaatgdde 74 
                                    ++da+++at+  +
  gi|119720622|ref|YP_921117.1| 390 RCDAIVVATDWGD 402
                                    5677777776333 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.1   0.00036      0.38      49      99 ..      66     125 ..      10     145 .. 0.82
   2 ?    3.1   0.1     0.072        75      40      89 ..     370     434 ..     344     438 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00036
                                    T-CCHHHHHHTT-SEEEES---TCC.........HHHHHHHHHHHHHHCT--EEEEEEET CS
                 NAD_binding_10  49 tdvedlaealkgadaVvsalggggk.........deegaknivdaakeagvkRfvlvsai 99 
                                      + ++a+a++  d+V++ +g+  k          e++ + i +a+k +g  ++++v + 
  gi|119720622|ref|YP_921117.1|  66 KATTSVAKAIEESDVVFVFVGTPTKadgsldltqLENASEDIGRALKDEGGYKLIVVRST 125
                                    56789***************988887777765555555899999****999999999875 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.072
                                    TCEEEE--TT-CCHHHHHHTT-SEEEES-..--TCC....HHHH...........HHHHHHHHHHCT CS
                 NAD_binding_10  40 glevvegdvtdvedlaealkgadaVvsal..ggggk....deeg...........aknivdaakeag 89 
                                    ++    g+v   +d+ e  + +da+v+a+  g  ++    +              +++i+da+k+++
  gi|119720622|ref|YP_921117.1| 370 RVLQGIGNVAFFSDVYECARRCDAIVVATdwGDYRNlcfeR--LgetmarrvvidCRHIIDAVKASK 434
                                    444444677777889999999*******9763333356440..234445667899*******99875 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00037      0.39       2      74 ..       3      91 ..       3     106 .. 0.73
   2 ?    2.3   0.0      0.27   2.9e+02      47      71 ..     377     399 ..     322     422 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00037
                                   EEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHH...HHHTTHEEESS....................HHHHHTC CS
                   GFO_IDH_MocA  2 rvaiiGaGkigskhlrplnesqrleevvalldpdaeraeav...aesfgveaysd....................leellad 60
                                   rva+iG+G++g +++ +l +  r+ +vv++ d+d+e+ e +         ++y+                     +++  ++
  gi|119720622|ref|YP_921117.1|  3 RVAVIGLGYAGLPFAVALAH--RGFKVVGV-DTDEEKVELInkgV----SPVYEPalndylkgvlerglfkattsVAKAIEE 77
                                   79************944444..699***95.99999999884431....223333444566688888888877778888888 PP

                                   TTESEEEE-S-GGG CS
                   GFO_IDH_MocA 61 peidavivatpngt 74
                                   +++ +v+v+tp++ 
  gi|119720622|ref|YP_921117.1| 78 SDVVFVFVGTPTKA 91
                                   89999999999854 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.27
                                    THEEESSHHHHHTCTTESEEEE-S- CS
                   GFO_IDH_MocA  47 gveaysdleelladpeidavivatp 71 
                                    +v+++sd+ e ++  ++da++vat 
  gi|119720622|ref|YP_921117.1| 377 NVAFFSDVYECAR--RCDAIVVATD 399
                                    3459999999999..9******996 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   4.4e-05     0.046       2      72 ..       4      80 ..       3     125 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.4e-05
                                   EEEE-SSHHHHHHHHHHHHTT--EEEE......ES-GGGTT--SSSSEEE-TTHHHHHHHHHHHT-SHHHHHHHHEE CS
                           GIDA  2 viViGgGhAGceAAlaaarlGakvlLi......thkldtiaelsCnpsiggiakgllvrEidalggliikaadkagi 72
                                   v ViG G AG+  A+a+a +G+kv+ +      ++ +++ ++ ++ p++    kg l r + +    ++ka++++ +
  gi|119720622|ref|YP_921117.1|  4 VAVIGLGYAGLPFAVALAHRGFKVVGVdtdeekVELINKGVSPVYEPALNDYLKGVLERGLFKATTSVAKAIEESDV 80
                                   89*************************99988888888888999999999999999999999999999999999887 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00012      0.12      19      87 ..      16     183 ..      14     343 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00012
                                    HHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH............................................ CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................................ RF
                           CbiA  19 LaralarrglrVllvDaDpqannlaileglendiep............................................ 54 
                                    +a+ala rg++V+ vD+D +   l i +g+++  ep                                            
  gi|119720622|ref|YP_921117.1|  16 FAVALAHRGFKVVGVDTDEEKVEL-INKGVSPVYEPalndylkgvlerglfkattsvakaieesdvvfvfvgtptkadgs 94 
                                    589***************994444.488888888889999*****99999999999999999999999999999999999 PP

                                    .....................................................CCHCCCHHH.HHHCHCHHHH.....EE CS
                                    .....................................................xxxxxxxxx.xxxxxxxxxx...xxxx RF
                           CbiA  55 .....................................................dlkrllell.ealgkkkall...lkia 77 
                                                                                         +++ +l++  e l+++ka l   +++a
  gi|119720622|ref|YP_921117.1|  95 ldltqlenasedigralkdeggyklivvrstvlpgttegvvkriieersgkicGRDFGLCMNpEFLREGKA-LydiFNPA 173
                                    98888888888888888888888888888888888888888888888888888555555555233333322.23555555 PP

                                    EEEEEEESS. CS
                                    xxxxxxxxxx RF
                           CbiA  78 gvvlnrvdge 87 
                                    ++v+  +d++
  gi|119720622|ref|YP_921117.1| 174 RIVIGEYDKR 183
                                    5555555555 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   0.00012      0.13       2      32 ..       4      34 ..       3      37 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00012
                                   EEEE--SHHHHHHHHHHHHTTT-EEEEESSS CS
                  FAD_binding_2  2 viViGsGlAGLaAAleaaeaGlkvavvekeq 32
                                   v ViG G AGL  A+++a++G kv+ v+  +
  gi|119720622|ref|YP_921117.1|  4 VAVIGLGYAGLPFAVALAHRGFKVVGVDTDE 34
                                   89**********************9887665 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00017      0.18      30     100 ..       3      86 ..       2      95 .. 0.81
   2 ?   -3.6   0.0       5.2   5.5e+03      45      73 ..     386     414 ..     367     432 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00017
                                    EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEE.............HCHHHHHHHHHHHH-SEEE CS
                    AlaDh_PNT_C  30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvev.............lksqeellaeavkeadvvi 96 
                                    +v viG G aGl  + + +  g kV+ +D+++++ e +++  + + e              l +   ++a+a++e+dvv 
  gi|119720622|ref|YP_921117.1|   3 RVAVIGLGYAGLPFAVALAHRGFKVVGVDTDEEKVELINKGVSPVYEPalndylkgvlergLFKATTSVAKAIEESDVVF 82 
                                    799*********866666667**************999994444344467778999999999999999999999999996 PP

                                    E--- CS
                    AlaDh_PNT_C  97 gtvl 100
                                      v 
  gi|119720622|ref|YP_921117.1|  83 VFVG 86 
                                    6555 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 5.2
                                    HHHHHTT-EEEEEESSHHHHHHHHHTTTC CS
                    AlaDh_PNT_C  45 atakglgakVtvlDvrparleqleslgak 73 
                                    + a++ +a+V+++D    r   +e lg++
  gi|119720622|ref|YP_921117.1| 386 ECARRCDAIVVATDWGDYRNLCFERLGET 414
                                    56788888888888777766666666655 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.1     0.001       1.1      38      75 ..       3      39 ..       1     106 [. 0.91

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.001
                                   EEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCH CS
                   2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlkafgmkviaydrskkkeeee 75
                                   +v++iGlG  G  +a  l+  g+kv+++d+ ++k e  
  gi|119720622|ref|YP_921117.1|  3 RVAVIGLGYAGLPFAVALAHRGFKVVGVDTDEEKVE-L 39
                                   799**************************9988665.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.52
# Mc/sec: 2563.50
//
Query:       gi|119720623|ref|YP_921118.1|  [L=296]
Description: nucleotidyl transferase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.5e-30  104.0   0.0    1.7e-29  103.2   0.0    1.4  1  NTP_transferase  Nucleotidyl transferase
    2.5e-06   27.9   0.0    4.1e-06   27.2   0.0    1.4  1  NTP_transf_3     MobA-like NTP transferase domain


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.2   0.0   1.9e-33   1.7e-29       1     242 [.       4     277 ..       4     282 .. 0.89

  Alignments for each domain:
  == domain 1  score: 103.2 bits;  conditional E-value: 1.9e-33
                                    EEEEE--S--GGGTTCCTTSSGGGSEETT...ET....ETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGT. CS
                NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlg...ke....rliqatlsrlansgieeiivvltqehsflveeqlkegskfg. 72 
                                    kavI a G GtRL P+t++l+k ++p      +     ++i ++++ l+  g+ e+ +++ + ++++ +    +++ ++ 
  gi|119720623|ref|YP_921118.1|   4 KAVITAAGLGTRLLPITKELPKEMLPLFSvsdNAvglkPIIHIVFESLLGVGVSEVCFIVGKSKRAIEDYFTPDADFIEv 83 
                                    79********************9988532111212334*****************9999998888766666666654459 PP

                                    ......................SEEEEEEESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEEST...THHHHHHHHH CS
                NTP_transferase  73 ......................vevlialepegkgtAdAvalaaelledeksdelvlvLggDhlikd...ayeeavkkai 127
                                                           ++ ++ +pe++g  dAv+ a+ +++ +     ++  g+D +i++   +++++vk ++
  gi|119720623|ref|YP_921118.1|  84 lrakgvenranelmkfysairnAKIFFINQPEPRGFGDAVLRAEPFVGADPF---IVHAGDDAVISEghnHLRRLVKVFQ 160
                                    99*******************99*************************9996...999999****999999********* PP

                                    THSSTTSEEEEEEESS-CTTSEEEEEC...TTS...BEEEEECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSS CS
                NTP_transferase 128 ekaakgtvtfgivpveeateyGviead...eeg...rverfvEKPkeakaselassGiYvfnsevllflakdleelkrge 201
                                    e++   ++t+++++ve++++yGv + +   + g   rv +++EKP+e++ +++a+  +Y f+++++ +l +++++   ge
  gi|119720623|ref|YP_921118.1| 161 EYDC--DATLLAEDVEDPRAYGVLRGKvvnDYGsilRVLDIIEKPREPP-TNIAAIAVYAFKPKIFSYL-RNVKPDSGGE 236
                                    **99..9*****************998886333567*************.*******************.88******** PP

                                    CHHHHHHHHHHHTTEEEEEECSTTEE-EEEXSSHHHHHHHH CS
                NTP_transferase 202 deitdilpkaleegkvalaflfkdaeyWsDvGtldsllean 242
                                     ++t+++++++++g +  a+  k  e   DvGt++s+++a 
  gi|119720623|ref|YP_921118.1| 237 VQLTAAIKAMIDDGCDVCAVKLKPGERRLDVGTPQSYWKAL 277
                                    **************99999988877789**********986 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.0   4.6e-10   4.1e-06       1     128 [.       5     213 ..       5     247 .. 0.75

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 4.6e-10
                                    EEEEEESS-TTT....TT.THHHHCC....CCC.....CHHHHHHHHHCTT.-CEEEEECSH..CHHHH........... CS
                   NTP_transf_3   1 aviLAGGrSsRm....gg.dKallpl....ggk.....pllervldalraagvdevvvvggd..eevla........... 53 
                                    avi A+G ++R+    ++ +K +lpl    +       p+++ v+++l  +gv+ev+ ++g   +++++           
  gi|119720623|ref|YP_921118.1|   5 AVITAAGLGTRLlpitKElPKEMLPLfsvsD-NavglkPIIHIVFESLLGVGVSEVCFIVGKskRAIEDyftpdadfiev 83 
                                    7999********6665458*******76651.156666****************99999887444566688899999999 PP

                                    ..................HHTTCTS-EEE-TTSS-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHH..HHHHHHCHHH CS
                   NTP_transf_3  54 ..................alarlgvrvvededpgkgplaslaaalraaadadavlvlacDmPlltpel..verllaaaaa 113
                                                      a++  ++ ++++++  +g + +++ a   + +ad+++v a+D + +++ +  ++rl++ +++
  gi|119720623|ref|YP_921118.1|  84 lrakgvenranelmkfysAIRNAKIFFINQPE-PRGFGDAVLRAEPFV-GADPFIVHAGDDAVISEGHnhLRRLVKVFQE 161
                                    99999999999888887777777787887775.69***********99.9**********9999986555********** PP

                                    HTSSEEEEESSSEE.....................................E CS
                   NTP_transf_3 114 sgadvvvptyeger.....................................g 128
                                     ++d++ ++ + e                                      +
  gi|119720623|ref|YP_921118.1| 162 YDCDATLLAEDVEDpraygvlrgkvvndygsilrvldiiekprepptniaaI 213
                                    ****999888877755566666666666655555555555555555554443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2153.97
//
Query:       gi|119720624|ref|YP_921119.1|  [L=402]
Description: glycosyl transferase, group 1 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-20   74.0   0.1    2.4e-20   73.3   0.1    1.3  1  Glyco_trans_1_4  Glycosyl transferases group 1
    1.3e-15   57.3   0.0    2.4e-15   56.5   0.0    1.4  1  Glycos_transf_1  Glycosyl transferases group 1
    0.00029   20.9   0.1     0.0017   18.4   0.1    2.3  2  Glyco_transf_4   Glycosyltransferase Family 4
  ------ inclusion threshold ------
      0.024   15.1   0.0       0.17   12.4   0.0    2.1  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain
      0.067   13.6   0.0       0.12   12.8   0.0    1.3  1  Glyco_trans_1_2  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.3   0.1   6.8e-24   2.4e-20       3     133 ..     226     368 ..     224     369 .. 0.80

  Alignments for each domain:
  == domain 1  score: 73.3 bits;  conditional E-value: 6.8e-24
                                    EEEEES---GG.GTHHHHHHHHHHHH.H.H.EEEEEES---...HHHHHHHTT-T.TEEEE---.THHHHHH..HH-SEE CS
                Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkk.d.vrlvivGdgp.rpeeleelaagleerveftGfv.edlaell..aaadvf 76 
                                    +++f+G l ++++gvd+l+  v++l +    ++l +vGdgp +++ l+ ++ +l   ve+tGfv + +a ++  ++ dv+
  gi|119720624|ref|YP_921119.1| 226 TVGFLGFL-APWQGVDMLCSIVAELNRLgYkAKLKVVGDGPlKRQLLK-ECTKLGVPVEITGFVsHPVALCIarRDFDVM 303
                                    789***99.567**********999945526**********8764555.55445446*******6556666511567999 PP

                                    EE--...-....--SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHHH CS
                Glyco_trans_1_4  77 vaPs...e....gfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrLle 133
                                    v+P    e     +++k++Ea+a+g+pvVat+++   e     e gl  + +dp+a+ae i+r+l+
  gi|119720624|ref|YP_921119.1| 304 VLPRvstEttatIMPIKVIEALALGIPVVATELPV-YESSafREKGLYTSRRDPKAFAETIARILR 368
                                    99999984444469*******************65.564557899******************996 PP

>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.5   0.0   6.6e-19   2.4e-15       7     159 ..     217     370 ..     211     376 .. 0.90

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 6.6e-19
                                    HHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCH.SSS CS
                Glycos_transf_1   7 kklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevs.red 85 
                                    +k+ k e++ ++ ++g l +++gvd l   +a+l++    ++kl ++G+g+ + +l k++ +l++   v+++g+vs + +
  gi|119720624|ref|YP_921119.1| 217 RKT-KTENEVTVGFLGFLAPWQGVDMLCSIVAELNRL-GYKAKLKVVGDGPLKRQLLKECTKLGV--PVEITGFVShPVA 292
                                    444.55999*************************886.*********************999999..999******6666 PP

                                    HHHHHHCESEEEEEESS.....BSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSH CS
                Glycos_transf_1  86 leellknadifvlpsis.....EgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairkllede 159
                                    l    +  d++vlp  s       ++i ++EA+a+g+pv+a+  + +      ++ Gl     +++a+ae i+++l+++
  gi|119720624|ref|YP_921119.1| 293 LCIARRDFDVMVLPRVStettaTIMPIKVIEALALGIPVVATELPVYESSAFREK-GLYTSRRDPKAFAETIARILRES 370
                                    6666666*******999*8988889******************999999888888.9******************9875 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   4.8e-07    0.0017      72     167 ..     110     204 ..      50     207 .. 0.66
   2 ?   -0.8   0.0      0.36   1.3e+03      91     102 ..     325     334 ..     291     376 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 4.8e-07
                 Glyco_transf_4  72 kpDvvHahspaalgaallalrr..rlgiplVltvHglyekrllka.rlkplsrllralerrllrradrviavSeatadel 148
                                    ++D++ ++++  +++ ++  r+  +  +++ + + +      ++   +++   l++ + r++l r+  +i+ S   a+ l
  gi|119720624|ref|YP_921119.1| 110 HFDIIYVRDSRLALLLAFSPRLarKCFVKIAAILEDGI----YQVlLRQLTLMLINSIDRHVLERTAGIITHSADFAKSL 185
                                    67777777766665555555542233333333333333....3330344555678999999******************* PP

                 Glyco_transf_4 149 rerygvppekitVipnGvD 167
                                    + r +v p++i Vip+G+ 
  gi|119720624|ref|YP_921119.1| 186 VLRKKVLPKRIIVIPPGIM 204
                                    *****************95 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.36
                 Glyco_transf_4  91 lrrrlgiplVlt 102
                                    l  +lgip+V+t
  gi|119720624|ref|YP_921119.1| 325 L--ALGIPVVAT 334
                                    2..378888887 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   4.6e-05      0.17      73     160 .]     110     202 ..     105     202 .. 0.66
   2 ?    0.0   0.0      0.29     1e+03      93     120 ..     325     360 ..     245     373 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.6e-05
                Glyco_trans_4_4  73 rpdvvhahsptaglaarlarrrrgiplvvtlhglllrrg..sgavrrly....ralerrllrradavlvvseaeaeelra 146
                                    ++d++++ ++ ++l+ ++   r   +++v + + l ++g  +  +r+l       ++r +l r +++++ s+++a+ l+ 
  gi|119720624|ref|YP_921119.1| 110 HFDIIYVRDSRLALLLAFSP-RLARKCFVKIAAIL-EDGiyQVLLRQLTlmliNSIDRHVLERTAGIITHSADFAKSLVL 187
                                    57888888875333222222.23455666666432.12222233444431133677********************9996 PP

                Glyco_trans_4_4 147 .lgvpadrvvvvpng 160
                                     + v + r+ v+p+g
  gi|119720624|ref|YP_921119.1| 188 rKKVLPKRIIVIPPG 202
                                    588*99*******97 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.29
                Glyco_trans_4_4  93 rrrgiplvvtlh....glllrrg....sgavrrlyr 120
                                    ++ gip+v t      + ++r+     s++++ +++
  gi|119720624|ref|YP_921119.1| 325 LALGIPVVATELpvyeSSAFREKglytSRRDPKAFA 360
                                    234777777765444423333222333444444444 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   3.3e-05      0.12      13      62 ..     319     369 ..     292     372 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.3e-05
                Glyco_trans_1_2  13 lrlfEaaacGafaltddaegleelftpgkevilfe.dleelaekiryllan 62 
                                     ++ Ea+a G+++++++ + +e     +k + + + d++ +ae i++ l++
  gi|119720624|ref|YP_921119.1| 319 IKVIEALALGIPVVATELPVYESSAFREKGLYTSRrDPKAFAETIARILRE 369
                                    599*************99*****977776777777************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       641  (0.0357521); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2712.42
//
Query:       gi|119720625|ref|YP_921120.1|  [L=394]
Description: glycosyl transferase, group 1 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.1e-27   93.7   0.0      2e-24   86.1   0.0    2.2  2  Glycos_transf_1  Glycosyl transferases group 1
      4e-19   69.4   0.0    7.5e-18   65.3   0.0    2.3  2  Glyco_trans_1_4  Glycosyl transferases group 1
    4.2e-05   23.6   0.4    0.00022   21.2   0.0    2.4  3  Glyco_transf_4   Glycosyltransferase Family 4
    0.00022   21.5   0.0    0.00043   20.6   0.0    1.5  1  Glyco_trans_1_2  Glycosyl transferases group 1
    0.00057   20.4   0.0    0.00088   19.7   0.0    1.4  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.4   0.0    0.0034        12      13      77 ..      57     118 ..      49     131 .. 0.78
   2 !   86.1   0.0   5.6e-28     2e-24       5     166 ..     191     353 ..     188     358 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0034
                                    TT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGE CS
                Glycos_transf_1  13 ekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnvif 77 
                                     +k++ ++++   + Kg+ l ++++ +l    +++ +lviaG+ ++  +l +   +  l+++ i+
  gi|119720625|ref|YP_921120.1|  57 PEKELDFVINKGPRIKGIRLPVTLLFHLL---KQRPHLVIAGDSTYPSTLIAFLTSKMLRAKFIL 118
                                    55566666777777788888888877775...5699*************9999998888887765 PP

  == domain 2  score: 86.1 bits;  conditional E-value: 5.6e-28
                                    HHHHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES....STTHHHHHHHHHHHCTTCGGGEE..E CS
                Glycos_transf_1   5 krkklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaG...ngeeekelkklaeelelsdnvifl..g 79 
                                     r+klg+ ++k ++l++gr+ + Kgv+l++ka+ +++   + n++l+i G   +  ++  l + +++ +l+ +v++l  +
  gi|119720625|ref|YP_921120.1| 191 LRRKLGL-DNKIVVLYIGRVIPLKGVHLILKALTKIN---EYNLHLLIPGtfvDPWYKRLLDDIVKASKLESKVTMLslK 266
                                    5788888.79************************995...89**********9999999999999999999999986337 PP

                                    CCHSSSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSH CS
                Glycos_transf_1  80 evsredleellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairkllede 159
                                    +v +ed   +++ adi+++ps++E++G+v+ EA +ag+pvi++ ++ +a  +  g+  l+++p+n+e+la+ ++ l  d 
  gi|119720625|ref|YP_921120.1| 267 FVRVEDRGIYYELADIVCYPSYYEAWGMVVNEAAYAGKPVISTRTCAAAYDILFGHPELVIPPGNVEELAKSLKLLAMDA 346
                                    999*******************************************999999999999******************9999 PP

                                    HHHHHHH CS
                Glycos_transf_1 160 elrerlg 166
                                    ++r+++g
  gi|119720625|ref|YP_921120.1| 347 NKRKAIG 353
                                    9999876 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0       0.1   3.6e+02      13      46 ..      70     103 ..      52     126 .. 0.66
   2 !   65.3   0.0   2.1e-21   7.5e-18       3     131 ..     202     342 ..     200     345 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.1
                                    G.GTHHHHHHHH.HHHH.HHEEEEEES---..HHH CS
                Glyco_trans_1_4  13 nvkgvdllleav.pllrkkdvrlvivGdgprpeel 46 
                                    ++kg++l +  + +ll+ ++ +lvi+Gd++ p+ l
  gi|119720625|ref|YP_921120.1|  70 RIKGIRLPVTLLfHLLK-QRPHLVIAGDSTYPSTL 103
                                    45555555555645555.4489*****88743344 PP

  == domain 2  score: 65.3 bits;  conditional E-value: 2.1e-21
                                    EEEEES---GG.GTHHHHHHHHHHHH.HHEEEEEES-..--...HHHHHHHT..T-T.TEEEE-..--..THHHHHHHH- CS
                Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkkdvrlvivGd..gp.rpeeleelaa..gleerveftG..fv..edlaellaaa 73 
                                    v+l++Gr+  + kgv+l+l+a+ ++ + +++l+i G   +p  ++ l++ ++  +le++v+++   fv  ed   +++ a
  gi|119720625|ref|YP_921120.1| 202 VVLYIGRV-IPLKGVHLILKALTKINEYNLHLLIPGTfvDPwYKRLLDDIVKasKLESKVTMLSlkFVrvEDRGIYYELA 280
                                    79******.678**************779*******5223333333333333568999999887446688********** PP

                                    SEEEE--..---SHHHHHHHHTT-EEEE-TGG.GTTT--.TTSSEE--TT-HHHHHHHHHHH CS
                Glyco_trans_1_4  74 dvfvaPs..egfglkllEamaaglpvVatdvg.giaevv.gengllvppgdpealaeailrL 131
                                    d+++ Ps  e +g+++ Ea+ ag+pv++t++  ++ +++ g   l++ppg++e+la+ +  L
  gi|119720625|ref|YP_921120.1| 281 DIVCYPSyyEAWGMVVNEAAYAGKPVISTRTCaAAYDILfGHPELVIPPGNVEELAKSLKLL 342
                                    *****************************8752668888*****************998766 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   6.2e-08   0.00022      56     165 ..      72     175 ..      33     179 .. 0.81
   2 ?   -1.8   0.0      0.73   2.6e+03     145     163 ..     188     205 ..     187     207 .. 0.85
   3 ?   -2.2   0.0         1   3.7e+03      72     102 ..     279     309 ..     240     310 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 6.2e-08
                 Glyco_transf_4  56 rslaflrrlrrllkrekpDvvHah..spaalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrr 133
                                    + ++ +  l  +l +++p++v a   ++++ + a l +++ l+++++l    ++      +++++ls+ll+ + r ++ +
  gi|119720625|ref|YP_921120.1|  72 KGIRLPVTLLFHLLKQRPHLVIAGdsTYPSTLIAFLTSKM-LRAKFILWEERWF------WHSSLLSNLLWPFSRTVALK 144
                                    4566777788888889999996552234555666666666.9999998877777......89999*************** PP

                 Glyco_transf_4 134 adrviavSeatadelrerygvppekitVipnG 165
                                    ad++i++    ++ ++   gv++ +i V pn+
  gi|119720625|ref|YP_921120.1| 145 ADALIVPGTLSKEFYKN-IGVEKGRIFVAPNA 175
                                    *****************.************96 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.73
                 Glyco_transf_4 145 adelrerygvppekitVip 163
                                    a+ lr+++g++ +ki+V++
  gi|119720625|ref|YP_921120.1| 188 ARALRRKLGLD-NKIVVLY 205
                                    5789999****.7**9998 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1
                 Glyco_transf_4  72 kpDvvHahspaalgaallalrrrlgiplVlt 102
                                      D+v + s++ ++ +++  ++  g+p++ t
  gi|119720625|ref|YP_921120.1| 279 LADIVCYPSYYEAWGMVVNEAAYAGKPVIST 309
                                    5688877777777666665555688888876 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   1.2e-07   0.00043       5      90 ..     286     373 ..     279     375 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.2e-07
                Glyco_trans_1_2   5 psrsespnlrlfEaaacGafaltdda..egleelftpgkevilfe.dleelaekiryllanpeerraiaeaarervlaeh 81 
                                    ps +e   +++ Eaa +G +++++++   +++ lf    e+++   ++eela+ ++ l  +  +r+ai+ + ++ + +++
  gi|119720625|ref|YP_921120.1| 286 PSYYEAWGMVVNEAAYAGKPVISTRTcaAAYDILFGHP-ELVIPPgNVEELAKSLKLLAMDANKRKAIGMELKRLISEKY 364
                                    666788899****************9*88888899988.6666666**********9999******************** PP

                Glyco_trans_1_2  82 tydhraeql 90 
                                    +y+  ++ +
  gi|119720625|ref|YP_921120.1| 365 SYEEMLKGF 373
                                    **9877666 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   2.5e-07   0.00088      68     159 ..      83     174 ..      29     175 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 2.5e-07
                Glyco_trans_4_4  68 rqrrerpdvvhahspt..aglaarlarrrrgiplvvtlhglllrrgsgavrrlyralerrllrradavlvvseaeaeelr 145
                                       ++rp++v+a ++t  + l+a l +   ++++++    +   ++s+ + +l++++ r+++  ada++v+ +   e + 
  gi|119720625|ref|YP_921120.1|  83 HLLKQRPHLVIAGDSTypSTLIAFLTSKMLRAKFILWEERWF--WHSSLLSNLLWPFSRTVALKADALIVPGTLSKEFYK 160
                                    3479*******9986544889999999899*****9555543..56899******************************* PP

                Glyco_trans_4_4 146 algvpadrvvvvpn 159
                                      gv   r+ v pn
  gi|119720625|ref|YP_921120.1| 161 NIGVEKGRIFVAPN 174
                                    *************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2551.91
//
Query:       gi|119720626|ref|YP_921121.1|  [L=380]
Description: glycosyl transferase, group 1 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-36  124.1   0.0      8e-36  123.1   0.0    1.5  1  Glycos_transf_1  Glycosyl transferases group 1
    4.8e-33  114.4   0.0    7.9e-33  113.7   0.0    1.3  1  Glyco_trans_1_4  Glycosyl transferases group 1
    8.7e-19   68.1   0.1    2.6e-18   66.6   0.0    1.7  2  Glyco_transf_4   Glycosyltransferase Family 4
    1.7e-08   35.1   0.0    4.2e-08   33.8   0.0    1.7  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    3.3e-06   27.4   0.0    9.2e-06   26.0   0.0    1.8  1  Glyco_trans_1_2  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.1   0.0   2.2e-39     8e-36      13     159 ..     191     335 ..     186     352 .. 0.93

  Alignments for each domain:
  == domain 1  score: 123.1 bits;  conditional E-value: 2.2e-39
                                    TT-EEEEEESS-TTTTTHHHHHHHHHCCCCC.HCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHHH CS
                Glycos_transf_1  13 ekkkiilsvgrlekeKgvdllikafallkkq.lnpnvklviaGngeeekelkklaeelelsdnviflgevsredleellk 91 
                                    +++  i++vgrl k Kgvd+l++ + l++++   ++vk++i+G+g+ e+ +kkla+++++   v flg+v++e+++++++
  gi|119720626|ref|YP_921121.1| 191 SEDFNIVFVGRLLKDKGVDTLLRIIYLINDElNLHDVKFTIVGSGPLEEDIKKLAQKYQN---VVFLGYVKHENMPSIYR 267
                                    577889**********************9998889***********************99...***************** PP

                                    CESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSH CS
                Glycos_transf_1  92 nadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairkllede 159
                                     a++f+lps+sEg++++llEA a+glp++as+++g++++v+dg+tG lv+++++  ++ ai++  +  
  gi|119720626|ref|YP_921121.1| 268 EANLFLLPSRSEGMPLSLLEAQACGLPAVASKIPGVLDIVRDGVTGRLVDAEDVRGFVSAIEECYRLW 335
                                    *************************************************************9987666 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.7   0.0   2.2e-36   7.9e-33       2     132 ..     194     332 ..     193     333 .. 0.92

  Alignments for each domain:
  == domain 1  score: 113.7 bits;  conditional E-value: 2.2e-36
                                    EEEEEES---GG.GTHHHHHHHHHHHH.H.H...EEEEEES---...HHHHHHHTT-T.TEEEE---..THHHHHHHH-S CS
                Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkk.d...vrlvivGdgp.rpeeleelaagleerveftGfv..edlaellaaad 74 
                                    ++i+fvGrl  + kgvd ll+ + l+ ++ +   v+++ivG+gp + e++++la+++ ++v+f+G+v  e++++++++a+
  gi|119720626|ref|YP_921121.1| 194 FNIVFVGRLL-KDKGVDTLLRIIYLINDElNlhdVKFTIVGSGPlE-EDIKKLAQKY-QNVVFLGYVkhENMPSIYREAN 270
                                    589******4.55**************8884567**********55.69*9888877.6********9888********* PP

                                    EEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHH CS
                Glyco_trans_1_4  75 vfvaPs..egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrLl 132
                                    +f++Ps  eg++l+llEa a+glp Va++++g+ ++v  g++g lv+++d+  ++ ai++++
  gi|119720626|ref|YP_921121.1| 271 LFLLPSrsEGMPLSLLEAQACGLPAVASKIPGVLDIVrdGVTGRLVDAEDVRGFVSAIEECY 332
                                    ******999*************************************************9876 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.6   0.0   7.1e-22   2.6e-18       1     169 [.      14     180 ..      14     181 .. 0.83
   2 ?   -1.5   0.0      0.63   2.2e+03     110     145 ..     333     368 ..     322     378 .. 0.75

  Alignments for each domain:
  == domain 1  score: 66.6 bits;  conditional E-value: 7.1e-22
                 Glyco_transf_4   1 vGGverhvleLaraLarrGheVtvv....tpgddgpleeev...elvvrvprvplpllkrllrslaflrrlrrllkrekp 73 
                                    +GG er+++e+  +L +rGheV v+    +p++   +++e    +++ ++++  + +l+r ++ +  +r l +  k  ++
  gi|119720626|ref|YP_921121.1|  14 PGGGERFAVEVLTRLSKRGHEVGVLhinwAPHPATSAGNESkllDRGAELHKCGYIKLPR-GFPVVDPRCLVKPSK--QY 90 
                                    59***********************76666666666666667777777777776555554.467778899999999..99 PP

                 Glyco_transf_4  74 DvvHahspaal..gaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrradrviavSeatadelrer 151
                                    Dv+ +  + +    ++ll+  ++l +p V+ +H +          + l rl+  l+  ++++ d++ +  ++ ++ l++ 
  gi|119720626|ref|YP_921121.1|  91 DVLYIPAYSPNelTVSLLKKSKALSVPAVAVFHCML-------ADNVLARLYTPLYIAAFNSFDKLHVLNRFQRNFLKS- 162
                                    9997776666511555565555**************.......789999999999999*********************. PP

                 Glyco_transf_4 152 ygvppekitVipnGvDle 169
                                    +g+p+eki+ ipnGvD++
  gi|119720626|ref|YP_921121.1| 163 HGIPEEKIEFIPNGVDTS 180
                                    ****************97 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.63
                 Glyco_transf_4 110 rllkarlkplsrllralerrllrradrviavSeata 145
                                    rl+++  + +++l++++ ++++r+ d  ++v + ++
  gi|119720626|ref|YP_921121.1| 333 RLWESSPQEYYNLNKKIREYIVRNYDLEVVVGKIEK 368
                                    677888888889999999999999998887766665 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.0   1.2e-11   4.2e-08       1     160 []      15     176 ..      15     176 .. 0.81

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 1.2e-11
                Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvlt....papapg...apeleedgvrvhrlpvprrpspladlaalralrrllrqrrer 73 
                                    gG++r + e++ +L +rGheV vl     p+pa++   +  l  +g+++h +     p++++ ++     r l+   + +
  gi|119720626|ref|YP_921121.1|  15 GGGERFAVEVLTRLSKRGHEVGVLHinwaPHPATSagnESKLLDRGAELHKCGYIKLPRGFPVVDP----RCLV-KPSKQ 89 
                                    8**********************8877765555553223347799*****9997777655554433....3344.56899 PP

                Glyco_trans_4_4  74 pdvvhahs.ptaglaarlar..rrrgiplvvtlhglllrrgsgavrrlyralerrllrradavlvvseaeaeelralgvp 150
                                    +dv+++   ++  l + l++   + ++p v  +h  l +     ++rly++l  ++++++d ++v+ ++ +  l  +g+p
  gi|119720626|ref|YP_921121.1|  90 YDVLYIPAySPNELTVSLLKksKALSVPAVAVFHCMLAD---NVLARLYTPLYIAAFNSFDKLHVLNRFQRNFLKSHGIP 166
                                    ******88467888888887434569********87654...5799********************************** PP

                Glyco_trans_4_4 151 adrvvvvpng 160
                                     ++++ +png
  gi|119720626|ref|YP_921121.1| 167 EEKIEFIPNG 176
                                    *********8 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   2.6e-09   9.2e-06       2      82 ..     272     358 ..     270     368 .. 0.79

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 2.6e-09
                Glyco_trans_1_2   2 vLnpsrsespnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekirylla....npeerraiaeaare 75 
                                    +L psrse++ l l+Ea acG +a++++++g+ +++++g ++ l++  d+  ++ +i+++ +    +p+e+  + ++ re
  gi|119720626|ref|YP_921121.1| 272 FLLPSRSEGMPLSLLEAQACGLPAVASKIPGVLDIVRDGVTGRLVDaeDVRGFVSAIEECYRlwesSPQEYYNLNKKIRE 351
                                    688*************************************9999988899999999987654333456666666666666 PP

                Glyco_trans_1_2  76 rvlaeht 82 
                                     + ++++
  gi|119720626|ref|YP_921121.1| 352 YIVRNYD 358
                                    5555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2691.10
//
Query:       gi|119720627|ref|YP_921122.1|  [L=383]
Description: glycosyl transferase, group 1 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.9e-36  123.6   0.0    1.1e-35  122.7   0.0    1.4  1  Glycos_transf_1  Glycosyl transferases group 1
    2.1e-26   92.9   0.2    4.1e-25   88.8   0.1    2.2  2  Glyco_trans_1_4  Glycosyl transferases group 1
    4.2e-10   39.9   0.1    7.8e-09   35.8   0.0    2.5  3  Glyco_transf_4   Glycosyltransferase Family 4
     0.0035   17.8   0.0      0.087   13.3   0.0    2.4  3  Glyco_trans_4_4  Glycosyl transferase 4-like domain
     0.0063   16.9   0.0      0.013   15.9   0.0    1.5  1  Glyco_trans_1_2  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.7   0.0   3.1e-39   1.1e-35      11     156 ..     195     339 ..     192     356 .. 0.94

  Alignments for each domain:
  == domain 1  score: 122.7 bits;  conditional E-value: 3.1e-39
                                    TTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHH CS
                Glycos_transf_1  11 knekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleell 90 
                                     + +++++++vgrlek+K +d++i af+ + k+ +pn+kl+i+G+g+ + +l +l+ +  l  nv++lg vs+e++ +ll
  gi|119720627|ref|YP_921122.1| 195 RDPEENTFIMVGRLEKRKHYDHAIVAFKAVAKA-EPNAKLLIVGEGPLRPYLAQLIRKFSLVRNVQLLGSVSEEEKLSLL 273
                                    57899*************************998.********************************************** PP

                                    HCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHH CS
                Glycos_transf_1  91 knadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairkll 156
                                    ++a ++++  + EgfGivl+EA+aag+pvia++++++ evv++g tG+lv++ ++  la+ai ++ 
  gi|119720627|ref|YP_921122.1| 274 SKAQALIHLGYPEGFGIVLIEALAAGVPVIAYDIPPLNEVVEHGATGILVPKDDVRVLARAIVRFN 339
                                    *************************************************************98775 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0     0.076   2.7e+02       3      58 ..       5      54 ..       3      77 .. 0.72
   2 !   88.8   0.1   1.1e-28   4.1e-25       2     130 ..     200     337 ..     199     340 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.076
                                   EEEEES--.-GG.GTHHHHHHHHHHHH.HHEEEEEES---...HHHHHHHTT-T.TEE CS
                Glyco_trans_1_4  3 vilfvGrl.eenvkgvdllleavpllrkkdvrlvivGdgp.rpeeleelaagleerve 58
                                   +i+f+  + + +  gv +l e +++++ k +r+ i+  g  + e+l++     e+ v+
  gi|119720627|ref|YP_921122.1|  5 RIIFLTDYlTTKSGGVGFLYEVMKKIAGK-YRIDIIA-GRvE-ESLQK-----EDYVR 54
                                   788888887778899************66.8887777.4423.35652.....23344 PP

  == domain 2  score: 88.8 bits;  conditional E-value: 1.1e-28
                                    EEEEEES---GG.GTHHHHHHHHHHHH.H.H.EEEEEES---...HHHHHHHT..T-T.TEEEE---..THHHHHHHH-S CS
                Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkk.d.vrlvivGdgp.rpeeleelaa..gleerveftGfv..edlaellaaad 74 
                                    +++++vGrl e++k  d  + a+++++k+ + ++l+ivG+gp rp  l +l++   l  +v+++G v  e++ +ll++a+
  gi|119720627|ref|YP_921122.1| 200 NTFIMVGRL-EKRKHYDHAIVAFKAVAKAePnAKLLIVGEGPlRP-YLAQLIRkfSLVRNVQLLGSVseEEKLSLLSKAQ 277
                                    6899*****.777**********999977536**********776.99988875777799*******9777********* PP

                                    EEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHH CS
                Glyco_trans_1_4  75 vfvaPs..egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailr 130
                                     ++     egfg++l+Ea+aag+pv+a d++ ++evv  g +g+lvp++d+  la+ai+r
  gi|119720627|ref|YP_921122.1| 278 ALIHLGypEGFGIVLIEALAAGVPVIAYDIPPLNEVVehGATGILVPKDDVRVLARAIVR 337
                                    ***9999************************99*****99******************97 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   0.0   2.2e-12   7.8e-09       7     168 ..      22     187 ..      17     189 .. 0.78
   2 ?    0.9   0.0      0.11   3.9e+02      72     101 ..     276     304 ..     205     306 .. 0.62
   3 ?   -1.8   0.0      0.77   2.8e+03      64      92 ..     348     374 ..     307     379 .. 0.58

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 2.2e-12
                 Glyco_transf_4   7 hvleLaraLarrGheVtvvtpgddgpleeev..elvvrvprvpl...pllkrllrslaflrrlrrllkre.....kpDvv 76 
                                    +++e+ +  a + +++++++ ++++ l++e+  +    +    +   ++++++ + + fl    ++lkr      +  ++
  gi|119720627|ref|YP_921122.1|  22 FLYEVMKKIAGK-YRIDIIAGRVEESLQKEDyvR---ILNLNVYrddLPSAQPENAVKFLNLSTKMLKRIvkctgEEELI 97 
                                    567777777777.999*********999995541...3333333112455566666777777777777777777977777 PP

                 Glyco_transf_4  77 .HahspaalgaallalrrrlgiplVltvHglye.krllkarlkplsrllralerrllrradrviavSeatadelrerygv 154
                                     H +++++ +  ++       +p V+++H+l+e   + +   k+++ +++ + + + + +  v++vS+++++ l+++  v
  gi|119720627|ref|YP_921122.1|  98 lHFNNHFPNLIPWFIVN---SVPKVCSIHHLEEtAQFSGVIPKLAKVAVQDVFE-VNSPCTVVLTVSKSVRQKLASLRAV 173
                                    7********99988776...9***********9877777777888877777666.579******************999* PP

                 Glyco_transf_4 155 ppekitVipnGvDl 168
                                    ++  i+Vip+G+D+
  gi|119720627|ref|YP_921122.1| 174 RKGGIVVIPPGIDT 187
                                    *************9 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.11
                 Glyco_transf_4  72 kpDvvHahspaalgaallalrrrlgiplVl 101
                                       ++H  +p  +g +l+ +++  g+p+++
  gi|119720627|ref|YP_921122.1| 276 AQALIHLGYPEGFGIVLIEALA-AGVPVIA 304
                                    4457799999999999888887.9999987 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.77
                 Glyco_transf_4  64 lrrllkrekpDvvHahspaalgaallalr 92 
                                    lr++++  ++D+  +  ++a ++  la++
  gi|119720627|ref|YP_921122.1| 348 LRKRAE--RYDINIIAREFARLYDTLACC 374
                                    333333..555554455555555555555 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   2.4e-05     0.087      36     160 .]      49     184 ..      25     184 .. 0.73
   2 ?   -0.3   0.0      0.36   1.3e+03      75     100 ..     278     303 ..     237     355 .. 0.68
   3 ?    1.7   0.0     0.089   3.2e+02      36      80 ..     296     361 ..     275     379 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.4e-05
                Glyco_trans_4_4  36 eedgvrvhrlpvprrpspladlaalral........rrllrqrrerpdvvhahsptaglaarlarrrrgiplvvtlhgll 107
                                     ed vr+ +l v+r   p a ++ +  +        +r+++   e   ++h ++   +l+ +++    ++p v+++h l+
  gi|119720627|ref|YP_921122.1|  49 KEDYVRILNLNVYRDDLPSAQPENAVKFlnlstkmlKRIVKCTGEEELILHFNNHFPNLIPWFIV--NSVPKVCSIHHLE 126
                                    46778888888888876666666554442223222255555567777788888866666666666..59********988 PP

                Glyco_trans_4_4 108 lrrg.sgavrrlyraler...rllrradavlvvseaeaeelra.lgvpadrvvvvpng 160
                                     + + sg  + l++ + +    + + + +vl+vs +++++l+  + v+   +vv+p+g
  gi|119720627|ref|YP_921122.1| 127 ETAQfSGVIPKLAKVAVQdvfEVNSPCTVVLTVSKSVRQKLASlRAVRKGGIVVIPPG 184
                                    77777888888997775546678888*****************888**********97 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.36
                Glyco_trans_4_4  75 dvvhahsptaglaarlarrrrgiplv 100
                                     ++h+ +p + +++++ ++++g+p++
  gi|119720627|ref|YP_921122.1| 278 ALIHLGYPEGFGIVLIEALAAGVPVI 303
                                    56677776544444444446677764 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.089
                Glyco_trans_4_4  36 eedgvrvhrlpvprrp......splad............laalralrrll......rqrrerpdvvhah 80 
                                     ++gv+v+  ++p+        +   +            ++a+ ++ ++       r r+er+d+ ++ 
  gi|119720627|ref|YP_921122.1| 296 LAAGVPVIAYDIPPLNevvehgA---TgilvpkddvrvlARAIVRFNSYTfeektlRKRAERYDINIIA 361
                                    46777777777666652222110...0222222343333556666655433344448889999886555 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   3.6e-06     0.013       9      61 ..     286     340 ..     263     363 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.6e-06
                Glyco_trans_1_2   9 espnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekirylla 61 
                                    e++  +l Ea+a+G+++++ d++ l e ++ g ++il+   d+  la++i ++ +
  gi|119720627|ref|YP_921122.1| 286 EGFGIVLIEALAAGVPVIAYDIPPLNEVVEHGATGILVPkdDVRVLARAIVRFNS 340
                                    789999********************************99888888888877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2419.78
//
Query:       gi|119720628|ref|YP_921123.1|  [L=354]
Description: glycosyl transferase, group 1 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-18   67.7   0.1    3.4e-18   66.2   0.0    1.7  2  Glyco_transf_4   Glycosyltransferase Family 4
    9.7e-15   54.5   0.0    1.6e-14   53.8   0.0    1.3  1  Glycos_transf_1  Glycosyl transferases group 1
    1.6e-12   48.0   0.0    3.1e-12   47.1   0.0    1.4  1  Glyco_trans_1_4  Glycosyl transferases group 1
    6.2e-11   43.0   0.0    1.1e-10   42.2   0.0    1.4  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
  ------ inclusion threshold ------
       0.02   15.0   0.0       0.09   12.8   0.0    2.0  2  Glyco_trans_4_2  Glycosyl transferase 4-like
       0.11   12.2   0.0       0.22   11.2   0.0    1.6  1  Glyco_transf_5   Starch synthase catalytic domain
       0.17   12.3   0.0        0.4   11.1   0.0    1.6  1  Glyco_trans_1_2  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.2   0.0   1.3e-21   3.4e-18       1     168 [.      15     174 ..      15     176 .. 0.86
   2 ?   -1.6   0.0      0.94   2.4e+03      11      29 ..     229     247 ..     225     273 .. 0.69

  Alignments for each domain:
  == domain 1  score: 66.2 bits;  conditional E-value: 1.3e-21
                 Glyco_transf_4   1 vGGverhvleLaraLarrGheVtvvtpgddgpleeevelvvrvprvplpllkrllrslaflrrlrrllkrekpDvvHahs 80 
                                    +GG+er  + La++L +rGh+V+ vt ++++ +     ++  ++ +   +++rll  l f ++ ++l+++ k Dvv +  
  gi|119720628|ref|YP_921123.1|  15 YGGAERRYYILAKELMKRGHDVVYVTYDYGESEIPLATVGPPPRLYDEKGRRRLLPALEFGWKTAKLVEKLKCDVVDVTV 94 
                                    7*************************99998877774555555556666777777788999***************9999 PP

                 Glyco_transf_4  81 paalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrradrviavSeatadelrerygvppekit 160
                                    p++  + +      +   +Vlt+H  + k++ ++++kpl  l+   e+rllr+a  vi++S+ +a+++++  g    k++
  gi|119720628|ref|YP_921123.1|  95 PYTTALFM------KPRSFVLTYHEYWGKYWEHYFSKPLGTLAAIAEKRLLRKAVLVITPSKLVANRILSEVG--TVKVA 166
                                    99996554......4778*********99999*************************************9777..34677 PP

                 Glyco_transf_4 161 VipnGvDl 168
                                     +p G ++
  gi|119720628|ref|YP_921123.1| 167 PVPIGLNP 174
                                    77777666 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.94
                 Glyco_transf_4  11 LaraLarrGheVtvvtpgd 29 
                                    ++ +L ++ heV+ +  ++
  gi|119720628|ref|YP_921123.1| 229 VTAQLEKLHHEVHSYRKAS 247
                                    6778999999999774333 PP

>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.8   0.0   6.4e-18   1.6e-14      13     154 ..     184     319 ..     175     322 .. 0.86

  Alignments for each domain:
  == domain 1  score: 53.8 bits;  conditional E-value: 6.4e-18
                                    TT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHHHC CS
                Glycos_transf_1  13 ekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleellkn 92 
                                    +++  + ++gr++++Kg  +li++++++    ++++++ ++G+g+  +e+ ++ e+l+  ++v+ + + s+e++ ell +
  gi|119720628|ref|YP_921123.1| 184 SRDIDVTMIGRFTYTKGWWRLIEVLRQV----DKPLRVAVVGDGPLYNEVTAQLEKLH--HEVHSYRKASEEEKLELLAR 257
                                    6678899*******************98....789***********999998877665..69999999999********* PP

                                    ESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHH CS
                Glycos_transf_1  93 adifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairk 154
                                    ++ ++  s  Egf i+ lEA+ +g   i+ ++g +a v   +etG  + ++n  ++ae+++k
  gi|119720628|ref|YP_921123.1| 258 SKYYLNLSDAEGFSIATLEAILCGATPIVLDTGLNAAVEIVEETGCGYIAKNLREIAEQVAK 319
                                    *******************************9988776666666666666666777777765 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.1   0.0   1.2e-15   3.1e-12       4     129 ..     189     318 ..     186     322 .. 0.83

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 1.2e-15
                                    EEEES---GG.GTHHHHHHHHHHHH.HHEEEEEES---...HHHHHHHTT-T.TEEEE---..THHHHHHHH-SEEEE-- CS
                Glyco_trans_1_4   4 ilfvGrleenvkgvdllleavpllrkkdvrlvivGdgp.rpeeleelaagleerveftGfv..edlaellaaadvfvaPs 80 
                                    + ++Gr+    kg   l+e + ++  k++r+ +vGdgp  + e+ +++++l+++v+   +   e++ ella+++ +++ s
  gi|119720628|ref|YP_921123.1| 189 VTMIGRF-TYTKGWWRLIEVLRQVD-KPLRVAVVGDGPlYN-EVTAQLEKLHHEVHSYRKAseEEKLELLARSKYYLNLS 265
                                    7899***.556**************.56**********765.99988888877788777778777*************** PP

                                    ..---SHHHHHHHHTT-EEEE-TGGGTTT--...TTSSEE--TT-HHHHHHHHH CS
                Glyco_trans_1_4  81 ..egfglkllEamaaglpvVatdvggiaevv...gengllvppgdpealaeail 129
                                      egf++++lEa  +g   ++ d+ g++++v   +e+g+   +++  ++ae+++
  gi|119720628|ref|YP_921123.1| 266 daEGFSIATLEAILCGATPIVLDT-GLNAAVeivEETGCGYIAKNLREIAEQVA 318
                                    *99********************9.54444444588885333348889998876 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2   0.0   4.3e-14   1.1e-10       1     159 [.      16     170 ..      16     171 .. 0.82

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 4.3e-14
                Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvltpapapgape..leedgvrvhrlpvprrpspladlaalralrrllrqrrerpdvvh 78 
                                    gG++r+ + la++L +rGh+V+ +t ++ +++ +   +++  r++  + +rr  +l+ l++ +  + l+  ++ + dvv 
  gi|119720628|ref|YP_921123.1|  16 GGAERRYYILAKELMKRGHDVVYVTYDYGESEIPlaTVGPPPRLYDEKGRRR--LLPALEFGWKTAKLV--EKLKCDVVD 91 
                                    8************************988777665225566666666555555..689999*********..********* PP

                Glyco_trans_4_4  79 ahsptaglaarlarrrrgiplvvtlhgll...lrrg.sgavrrlyralerrllrradavlvvseaeaeelralgvpadrv 154
                                    +  p++ ++ +  r      +v+t+h+ +   ++++ s +++ l++ +e+rllr a +v+++s  +a ++    +   +v
  gi|119720628|ref|YP_921123.1|  92 VTVPYTTALFMKPR-----SFVLTYHEYWgkyWEHYfSKPLGTLAAIAEKRLLRKAVLVITPSKLVANRILSEVGT-VKV 165
                                    ***98888888888.....7******8663334444799****************************999884444.477 PP

                Glyco_trans_4_4 155 vvvpn 159
                                    + vp 
  gi|119720628|ref|YP_921123.1| 166 APVPI 170
                                    77775 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   3.5e-05      0.09       1     136 [.       2     146 ..       2     149 .. 0.64
   2 ?   -0.9   0.0       0.6   1.5e+03      26      76 ..     216     271 ..     196     290 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.5e-05
                Glyco_trans_4_2   1 killlanlssvh........tlrlakeLakrgyeVhvitpkkgakdeleaegihvhrl.....kvdrkgpleylk.afkl 66 
                                    k++++  + ++h        ++ lakeL krg++V+ +t + g++++     ++v +      +++r+  l  l    k 
  gi|119720628|ref|YP_921123.1|   2 KVCFVCSHLWPHsyggaerrYYILAKELMKRGHDVVYVTYDYGESEIPL---ATVGPPprlydEKGRRRLLPALEfGWKT 78 
                                    899999999999555543333346****************999544444...4444443335544688899999955699 PP

                Glyco_trans_4_2  67 kklikkikPDvvhahyakpygllgslaarlsgvipvvlsv...wGldv.lkfpkksk.lkklllklalkkatkvi 136
                                    +kl++k+k Dvv +    py   + l+    +   +vl+    wG    ++f k+   l  +++k +l+ka +vi
  gi|119720628|ref|YP_921123.1|  79 AKLVEKLKCDVVDVTV--PYT-TA-LF---MKPRSFVLTYheyWGKYWeHYFSKPLGtLAAIAEKRLLRKAVLVI 146
                                    ************6654..553.34.33...333445555500044433544444433466668888888888777 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.6
                Glyco_trans_4_2  26 eVhvitpkkgakdele...aegihvhrlkvdrkg.pleylk.afklkklikkikPD 76 
                                    +V+v+  ++ + +++        +vh+ ++ ++  +le+l+  + + +l +++++ 
  gi|119720628|ref|YP_921123.1| 216 RVAVVGDGPLYNEVTAqleKLHHEVHSYRKASEEeKLELLArSKYYLNLSDAEGFS 271
                                    55555555555333330002223344444444446777776455666666666655 PP

>> Glyco_transf_5  Starch synthase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   8.5e-05      0.22       1      48 [.       2      48 ..       2     134 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 8.5e-05
                 Glyco_transf_5  1 kilfvasEvaplaktGGLadvvgaLpkaLaklghdvrvilPrygaike 48
                                   k++fv+s   p    GG  +  + L+k+L k+ghdv  ++ +yg+ + 
  gi|119720628|ref|YP_921123.1|  2 KVCFVCSHLWP-HSYGGAERRYYILAKELMKRGHDVVYVTYDYGESEI 48
                                   7999*****99.999****************************55443 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00016       0.4       2      57 ..     261     318 ..     260     321 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00016
                Glyco_trans_1_2   2 vLnpsrsespnlrlfEaaacGafaltdda..egleelftpgkevilfedleelaekir 57 
                                    +Ln+s +e+++  ++Ea  cGa+ ++ d+   +  e++++   + ++++l e+ae+++
  gi|119720628|ref|YP_921123.1| 261 YLNLSDAEGFSIATLEAILCGATPIVLDTglNAAVEIVEETGCGYIAKNLREIAEQVA 318
                                    79********************888887755444445444434445559999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2600.52
//
Query:       gi|119720629|ref|YP_921124.1|  [L=262]
Description: nucleotidyl transferase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-22   80.7   0.0    1.4e-22   80.5   0.0    1.0  1  NTP_transferase  Nucleotidyl transferase
    8.8e-16   58.7   0.3    9.2e-16   58.6   0.3    1.2  1  NTP_transf_3     MobA-like NTP transferase domain
    0.00051   19.8   0.0    0.00072   19.4   0.0    1.2  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
  ------ inclusion threshold ------
      0.027   14.4   0.0      0.044   13.7   0.0    1.3  1  CTP_transf_3     Cytidylyltransferase


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.5   0.0   3.2e-26   1.4e-22       3     242 ..      17     251 ..      15     255 .. 0.86

  Alignments for each domain:
  == domain 1  score: 80.5 bits;  conditional E-value: 3.2e-26
                                    EEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEEEESS CS
                NTP_transferase   3 vILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlialepe 82 
                                    v++aGG+G R+  +   ++k+l+   gk +l++++++  a+ g+++   vlt ++++ +e+  ++g+k+gv+v++++ p+
  gi|119720629|ref|YP_921124.1|  17 VVMAGGEGRRMGLV--PVPKPLLELNGK-PLLEHCIEYYARCGFKD-FTVLT-RQEPVAEKAREAGKKLGVNVKVSMDPP 91 
                                    9*********6432..369999999999.*****************.66666.4555667777778899*******9998 PP

                                    --..BGGHHHHHTHHHHTTSSE..EEEEETTEEEEST.THHHHHHHHHTHSSTT.SEEEEEEESS-CTTSEEEEECTTSB CS
                NTP_transferase  83 gk..gtAdAvalaaelledeksdelvlvLggDhlikd.ayeeavkkaiekaakg.tvtfgivpveeateyGvieadeegr 158
                                        g  +A++ a++  + + +   ++v+++D + +d    +++++++e+a+++   + ++v    a  yGv+e+d eg 
  gi|119720629|ref|YP_921124.1|  92 LPkvGKGKALKHALQTGAVDPERRALVVFPDDLYLDDtLPLRFLASHVEAARRMgAWASVAVTLGLALPYGVVEIDAEGM 171
                                    7678*********99999999999*************76789***********98999999******************* PP

                                    EEEEECS-SSHSHCSEECCSEEEEETTHHHHHHH.CCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEEXSSHHH CS
                NTP_transferase 159 verfvEKPkeakaselassGiYvfnsevllflak.dleelkrgedeitdilpkaleegkvalaflfkdaeyWsDvGtlds 237
                                    + +f+EKP  +     as G+Y f++++l+ l++    ++++  ++ + +lp + e+ + +++ +      W  + tl+ 
  gi|119720629|ref|YP_921124.1| 172 AVSFKEKPVLPI---HASIGLYAFEPQALKLLLEvVDMDSPSAVEFESTLLPLLAEQRRLHAYPVPHH--AWLPLNTLKE 246
                                    **********99...79*****************8778888888888888888888887777655555..4987777777 PP

                                    HHHHH CS
                NTP_transferase 238 llean 242
                                    l ea+
  gi|119720629|ref|YP_921124.1| 247 LDEAS 251
                                    76665 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.6   0.3   2.1e-19   9.2e-16       1     118 [.      16     145 ..      16     262 .] 0.70

  Alignments for each domain:
  == domain 1  score: 58.6 bits;  conditional E-value: 2.1e-19
                                    EEEEEESS-TTTTT...THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSHCHHHHHHTTC....T..S-EEE-.TTSS- CS
                   NTP_transf_3   1 aviLAGGrSsRmgg...dKallplggkpllervldalraagvdevvvvggdeevlaalarl....g..vrvved.edpgk 70 
                                    +v++AGG+++Rmg    +K+ll+l+gkplle++++  +++g+++ +v +++e+v++ +++     g  v+v  d + p  
  gi|119720629|ref|YP_921124.1|  16 VVVMAGGEGRRMGLvpvPKPLLELNGKPLLEHCIEYYARCGFKDFTVLTRQEPVAEKAREAgkklGvnVKVSMDpPLPKV 95 
                                    69***********5568**********************************98887665443333522555555234478 PP

                                    SHHHHHHHHHHH..H..SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSE CS
                   NTP_transf_3  71 gplaslaaalra..aa.dadavlvlacDmPlltpelverllaaaaasgadv 118
                                    g +++l++al+   +  +  a++v++ D+ +l+  l  r+la++ ++  ++
  gi|119720629|ref|YP_921124.1|  96 GKGKALKHALQTgaVDpERRALVVFPDDL-YLDDTLPLRFLASHVEAARRM 145
                                    **********9864333556666666666.667777555555553333222 PP

>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   1.6e-07   0.00072       3      39 ..      16      53 ..      14      82 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.6e-07
                                   EEEECTTSSCTT-.SSS-GGGSEETTEEHHHHHHHHHH CS
                           IspD  3 vvipAAGsGkRmk.aglpKqflelkgqtllehtvdall 39
                                   vv+ A G+G+Rm+ + +pK +lel+g++lleh ++  +
  gi|119720629|ref|YP_921124.1| 16 VVVMAGGEGRRMGlVPVPKPLLELNGKPLLEHCIEYYA 53
                                   89**********95689***************998665 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   9.8e-06     0.044      16      60 ..      34      77 ..      32      88 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 9.8e-06
                                   GGGSEETTEEHHHHHHHHHHHTTTTSEEEEEES-HHHHHHHHHTT CS
                   CTP_transf_3 16 KnlldlggkpliayvleaalkskafekvivaTDseeiknvakefg 60
                                   K+ll+l+gkpl+++++e    +++ ++  v T +e +++ a e+g
  gi|119720629|ref|YP_921124.1| 34 KPLLELNGKPLLEHCIEYYARCGF-KDFTVLTRQEPVAEKAREAG 77
                                   9*****************999998.55677788888887777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1753.21
//
Query:       gi|119720630|ref|YP_921125.1|  [L=329]
Description: glycosyl transferase family protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-18   67.0   0.0    2.3e-18   66.6   0.0    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
    8.1e-07   29.5   0.0    1.3e-06   28.9   0.0    1.3  1  NTP_transf_3     MobA-like NTP transferase domain
    6.4e-06   26.2   0.1      1e-05   25.5   0.1    1.3  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
  ------ inclusion threshold ------
      0.086   12.4   0.0       0.12   12.0   0.0    1.2  1  NTP_transferase  Nucleotidyl transferase
        0.4   10.7   2.9       0.33   11.0   0.8    1.9  2  Phage_holin_2_1  Bacteriophage P21 holin S


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.6   0.0   6.4e-22   2.3e-18       1     169 [.      18     172 ..      18     173 .. 0.94

  Alignments for each domain:
  == domain 1  score: 66.6 bits;  conditional E-value: 6.4e-22
                                    EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--S CS
                Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraatg 80 
                                    ++vipt  ee  +  +++ l+         i+vvD gStD+t+e++ e      + rv+ +e + Gka a++++lr++ +
  gi|119720630|ref|YP_921125.1|  18 TIVIPTLKEERGVGLVIDELKGE---GWTNILVVDGGSTDRTREVAAEK-----GARVVLQEGR-GKADAVRTALRYVET 88 
                                    69*******************99...55678889999************.....9*******55.*************** PP

                                    SEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTTCSTCCCE CS
                Glycos_transf_2  81 dyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsfeigsaal 160
                                     yi+++D D +++  ++ +l++ + + g d v+g+r r + +    +r       + + +++ +   + nls++++++ l
  gi|119720630|ref|YP_921125.1|  89 PYIVVMDGDYTYPARHVAELLRTARERGLDEVIGARTRGRENIPLLNRF-----GNWVITETFNVLFGTNLSDVCSGMYL 163
                                    ***********************************************95.....78999999999*************** PP

                                    EEEHHHHHC CS
                Glycos_transf_2 161 lrrealeel 169
                                    +r e+++e+
  gi|119720630|ref|YP_921125.1| 164 VRTEVAREV 172
                                    ****99876 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0   3.6e-10   1.3e-06      29     132 ..      32     134 ..      22     169 .. 0.85

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 3.6e-10
                                    HHHHHHCTT.-CEEEEECSH..CHHHHHHTTCTS-EEE-TTSS-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHH CS
                   NTP_transf_3  29 rvldalraagvdevvvvggd..eevlaalarlgvrvvededpgkgplaslaaalraaadadavlvlacDmPlltpelver 106
                                     v+d l+  g+ +++vv g   +  ++ +a++g+rvv +e  g+g + ++++alr + ++ +++v+ +D  + ++ +v++
  gi|119720630|ref|YP_921125.1|  32 LVIDELKGEGWTNILVVDGGstDRTREVAAEKGARVVLQE--GRGKADAVRTALRYV-ETPYIVVMDGDYTY-PARHVAE 107
                                    589999999999*****544356777788999*******9..9*************9.9***********88.6777777 PP

                                    HHHCHHHHT.SSEEEEESSSEEEECCE CS
                   NTP_transf_3 107 llaaaaasg.advvvptyegerghpll 132
                                    ll+ a+++g ++v+ ++++g++  pll
  gi|119720630|ref|YP_921125.1| 108 LLRTARERGlDEVIGARTRGRENIPLL 134
                                    777776666589999****99988885 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.1   2.9e-09     1e-05       3      99 ..      16      99 ..      14     126 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 2.9e-09
                Glyco_tranf_2_3  3 dlavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnealr 84
                                   ++++++pt++ee+ +g v+++l    ++ + + vv+ +s++ t+eva e     ++   rvv + +  g +gk++a+  alr
  gi|119720630|ref|YP_921125.1| 16 EVTIVIPTLKEERGVGLVIDELKG--EGWTNILVVDGGSTDRTREVAAE-----KG--ARVVLQ-E--G-RGKADAVRTALR 84
                                   589******************987..68899999************988.....44..466544.3..5.6*********** PP

                Glyco_tranf_2_3 85 avksdlvllvDdDtv 99
                                    v++ +++++D+D  
  gi|119720630|ref|YP_921125.1| 85 YVETPYIVVMDGDYT 99
                                   *************75 PP

>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   3.3e-05      0.12      78     132 ..      67     118 ..      18     148 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.3e-05
                                    EEESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEEST.THHHHHHHHHTHSST CS
                NTP_transferase  78 alepegkgtAdAvalaaelledeksdelvlvLggDhlikd.ayeeavkkaiekaak 132
                                    ++ +eg+g AdAv+ a++++e  +    ++v+ gD  +   ++ e+++ a+e++ +
  gi|119720630|ref|YP_921125.1|  67 VVLQEGRGKADAVRTALRYVETPY----IVVMDGDYTYPArHVAELLRTARERGLD 118
                                    4556899**************777....9*********999**********99874 PP

>> Phage_holin_2_1  Bacteriophage P21 holin S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1      0.82   2.9e+03      23      39 ..      33      49 ..      29      50 .. 0.82
   2 ?   11.0   0.8   9.2e-05      0.33      21      62 ..     258     301 ..     248     303 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.82
                Phage_holin_2_1 23 lldklspeeWsaigvlg 39
                                   ++d+l +e W  i v+ 
  gi|119720630|ref|YP_921125.1| 33 VIDELKGEGWTNILVVD 49
                                   78999*****9998885 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 9.2e-05
                Phage_holin_2_1  21 kqlldklspeeWsaigvlg.gl.vigllTyltnlYFKrketrrk 62 
                                    + l++++ ++ W +i+++g g+ +++ll  +++lY Kr e r+ 
  gi|119720630|ref|YP_921125.1| 258 RWLVQGVKHQVWGIIAIVGtGVgLVALLNAIMSLYLKRLELRIT 301
                                    458999************9444357899999*******999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       798  (0.0445089); expected 358.6 (0.02)
Passed bias filter:                      614  (0.0342462); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2371.36
//
Query:       gi|119720631|ref|YP_921126.1|  [L=479]
Description: hypothetical protein Tpen_1728 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (479 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.20s 00:00:00.70 Elapsed: 00:00:00.37
# Mc/sec: 3928.26
//
Query:       gi|119720632|ref|YP_921127.1|  [L=639]
Description: hypothetical protein Tpen_1729 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.9e-51  173.4   1.1    2.3e-49  168.4   1.1    2.1  1  DUF3131          Protein of unknown function (DUF3131)
      3e-09   37.0   7.0      0.002   18.3   0.1    4.3  4  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
    0.00028   20.8   0.2     0.0032   17.4   0.0    2.7  3  CarbopepD_reg_2  CarboxypepD_reg-like domain
    0.00054   20.1   0.1       0.68   10.1   0.0    3.3  3  MG4              Macroglobulin domain MG4
  ------ inclusion threshold ------
      0.046   14.0   7.0       0.49   10.7   0.7    4.3  4  NPCBM_assoc      NPCBM-associated, NEW3 domain of alpha-galac
       0.15   11.9   1.1        8.1    6.4   0.0    3.1  2  DUF824           Salmonella repeat of unknown function (DUF82
       0.62   10.4   6.5        4.4    7.7   0.1    3.4  3  Invasin_D3       Invasin, domain 3
        1.6    8.8  11.2       0.43   10.6   0.1    4.5  4  Big_1            Bacterial Ig-like domain (group 1)


Domain annotation for each model (and alignments):
>> DUF3131  Protein of unknown function (DUF3131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.4   1.1     1e-52   2.3e-49       2     364 ..      37     372 ..      36     374 .. 0.88

  Alignments for each domain:
  == domain 1  score: 168.4 bits;  conditional E-value: 1e-52
                        DUF3131   2 yAraAWsYfernyq.peTGLvnsvddypsvTlWdvGsyllAlvaAreLglidkkefderirklLktLaklplfkgelPnk 80 
                                     AraAW Yf      ++ G+  ++ + + vT WdvGsyl A+v A +Lgli+++e  +r +k+L+ L++ pl+   +P  
  gi|119720632|ref|YP_921127.1|  37 LARAAWGYFSPGFGlSQRGINYATPSWHYVTDWDVGSYLSAIVDAAWLGLISRDEAISRAEKVLAFLSTRPLHPSGVPYS 116
                                    7********9865427889999********************************************************** PP

                        DUF3131  81 vyntrtlemvdygnnpkeegig.wsAlDigRllaaLkvlktrypeyadaveaivarWslsrlvkdgqlygaivkkdeklq 159
                                    +y+++t+ + +        ++g     D gRll+aL++lk+ +pe+a  v+ +v+r  +s+          + +  +   
  gi|119720632|ref|YP_921127.1| 117 AYSSDTGMPAE--------NAGpSNPSDAGRLLIALYRLKKSFPELAPTVDYVVERNGFSAFAGS------VPD-SG--- 178
                                    *********64........44314579*****************************999987665......333.23... PP

                        DUF3131 160 vvqegrlgyeeYaarglqlwgfdvekalskepyktvevegvevpvdrrdlkkt.eannyvvsepylleglElGfdaelke 238
                                            y++Y a+g++lwgf++++ ++       ++ g+   +++ d+         v+ ep ll+++El   +e  e
  gi|119720632|ref|YP_921127.1| 179 -------FYSYYYAYGFHLWGFNTPQVMKA-----LSMLGRLPYTRTVDAYGVrLPYVEVTMEPILLTIFELDPPPEFYE 246
                                    .......5999************9999654.....44444444444444443324477899******************* PP

                        DUF3131 239 laerlleaqkeryeetgkltAvsednidraPyfvystvian..gepWavitddgkevpelrlvStkaAfawsalfedeYt 316
                                     a ++++aq++ry +tgk tA +e++++ +Py++y+ ++    ge+W+v + +  + + + +v +kaA++++a+++++Yt
  gi|119720632|ref|YP_921127.1| 247 WAYKVYKAQENRYLATGKPTAFTEGQVNAPPYYIYEWIVDIytGETWTVWSGSLGKLSMTPVVYAKAALGMHAIWNTNYT 326
                                    ************************************98654449************************************ PP

                        DUF3131 317 qelleavkeladperGyyeGlyeetgkvnksltantNgiiLeaLlYka 364
                                      l e+v ++++p + +yeG+ e+ g+v  ++t +tN++i +a  Y +
  gi|119720632|ref|YP_921127.1| 327 AFLAEYVMKAKTP-NCFYEGVDEN-GNVVYAITDKTNAMIVSAARYAL 372
                                    ********99998.69********.****************9988865 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.3   2.9e+03      52      73 ..     363     384 ..     347     401 .. 0.71
   2 ?    4.8   0.1     0.015        34      43      69 ..     441     467 ..     439     473 .. 0.68
   3 !   18.3   0.1     9e-07     0.002       1      81 [.     475     549 ..     475     550 .. 0.90
   4 !   14.9   0.1   1.1e-05     0.024       7      61 ..     557     610 ..     552     628 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.3
                CarboxypepD_reg  52 vtvsapGyatatreevtltagq 73 
                                    + vsa+ ya ++ +  ++tag 
  gi|119720632|ref|YP_921127.1| 363 MIVSAARYALQRASKPSVTAGA 384
                                    6678888888888777777776 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.015
                CarboxypepD_reg  43 rglppgtysvtvsapGyatatreevtl 69 
                                    +gl+pg+y+vtv  +  a  +  ++t+
  gi|119720632|ref|YP_921127.1| 441 QGLAPGNYTVTVKVSTIAHNETLTLTV 467
                                    6899********776666555434444 PP

  == domain 3  score: 18.3 bits;  conditional E-value: 9e-07
                CarboxypepD_reg   1 tisGrVtdasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatreevtltagqtttldit 80 
                                    t++ rV+da g p++gat+ +        +   tda+G+  ++    g+ ++t+ ++G + a    ++++ ++++tl ++
  gi|119720632|ref|YP_921127.1| 475 TLRVRVVDACGDPVPGATLLLN-----GLKAGETDAKGEAEVK-HVEGEATLTAIYAGLEVAGPLKISVNSDTNATLKAN 548
                                    6788******************.....67788**********8.5569************99988899999999999887 PP

                CarboxypepD_reg  81 L 81 
                                    L
  gi|119720632|ref|YP_921127.1| 549 L 549
                                    7 PP

  == domain 4  score: 14.9 bits;  conditional E-value: 1.1e-05
                CarboxypepD_reg   7 tdasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyat 61 
                                    t ++g+p +g  V++   + +t ++++t+++G+  l+ +pp ++++++  p  + 
  gi|119720632|ref|YP_921127.1| 557 TTPDGKPATGILVVAL-LGRTTLSTAKTNSTGHALLPRIPPANITLQAYTPDGKL 610
                                    5689**********99.688899************************97665555 PP

>> CarbopepD_reg_2  CarboxypepD_reg-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.7   3.8e+03      44      56 ..     446     458 ..     442     475 .. 0.50
   2 !   17.4   0.0   1.4e-06    0.0032       5      76 ..     480     549 ..     476     558 .. 0.79
   3 ?   -0.5   0.0      0.55   1.2e+03      23      49 ..     576     602 ..     554     604 .. 0.67

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.7
                CarbopepD_reg_2  44 gkytLvvsyvGyk 56 
                                    g+yt++v++    
  gi|119720632|ref|YP_921127.1| 446 GNYTVTVKVSTIA 458
                                    5555544443332 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 1.4e-06
                CarbopepD_reg_2   5 VvdketkeplpgatVyvkgtkkgtvTdenGnFelknlpagkytLvvsyvGyktq.ekkvtvskektldvnill 76 
                                    Vvd+  ++p+pgat +++g k+g  Td++G+ e+k++ +g+ tL++ y G + +   k++v+++++ +++ +l
  gi|119720632|ref|YP_921127.1| 480 VVDA-CGDPVPGATLLLNGLKAG-ETDAKGEAEVKHV-EGEATLTAIYAGLEVAgPLKISVNSDTNATLKANL 549
                                    7886.569************998.69********988.6***********99752456666666665555555 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.55
                CarbopepD_reg_2  23 gtkkgtvTdenGnFelknlpagkytLv 49 
                                     t   + T++ G+  l ++p+ + tL+
  gi|119720632|ref|YP_921127.1| 576 TTLSTAKTNSTGHALLPRIPPANITLQ 602
                                    333455699999999999999999987 PP

>> MG4  Macroglobulin domain MG4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1      0.47     1e+03      57      78 ..     449     470 ..     425     474 .. 0.68
   2 !   10.1   0.0    0.0003      0.68      16      60 ..     474     511 ..     471     548 .. 0.72
   3 !    5.6   0.0    0.0079        18      18      59 ..     552     590 ..     551     605 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.47
                            MG4  57 takfsintpedaksltitvktk 78 
                                    t+ + + t +++++lt+tv+ k
  gi|119720632|ref|YP_921127.1| 449 TVTVKVSTIAHNETLTLTVTVK 470
                                    4556666666777777777666 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0003
                            MG4  16 fsikVlvkdpdgspaknvpVkiealkseteekeslttdedGtakf 60 
                                    ++++V+v+d+ g p+++ ++ ++ lk       + +td++G a++
  gi|119720632|ref|YP_921127.1| 474 YTLRVRVVDACGDPVPGATLLLNGLK-------AGETDAKGEAEV 511
                                    99**********************65.......334444444433 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.0079
                            MG4  18 ikVlvkdpdgspaknvpVkiealkseteekeslttdedGtak 59 
                                    i V  + pdg+pa +++V+  + +   +  ++ +t++ G a 
  gi|119720632|ref|YP_921127.1| 552 IAVAFTTPDGKPATGILVVALL-G--RTTLSTAKTNSTGHAL 590
                                    679999*************999.4..5677788888888875 PP

>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.22   4.9e+02      42      60 ..     383     401 ..     377     403 .. 0.82
   2 ?   10.7   0.7   0.00022      0.49       3      77 ..     390     455 ..     388     457 .. 0.79
   3 ?    5.2   0.1     0.011        25      44      64 ..     454     474 ..     453     483 .. 0.88
   4 ?   -1.9   0.0       1.8   4.1e+03      16      33 ..     543     561 ..     512     565 .. 0.66

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.22
                    NPCBM_assoc  42 asaaslapGetveatvkVt 60 
                                      +++l pGe ++ t++Vt
  gi|119720632|ref|YP_921127.1| 383 GAVPALYPGENATITLNVT 401
                                    4677999********9998 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00022
                    NPCBM_assoc   3 pGetvtltltvtndgtaaatnvslslslPeGWtvvevspasaaslapGetveatvkVtppagaaaGdyevtakar 77 
                                    pGe  t+tl vt +   +   + ls+++P+G t  ev+p ++      + ++a +kV++ +g a+G y+vt+k++
  gi|119720632|ref|YP_921127.1| 390 PGENATITLNVTHQLPLP---ITLSAEAPPGIT-AEVEPSTG-----KANLTARLKVSARQGLAPGNYTVTVKVS 455
                                    566777777666655444...569999999999.66666665.....689***********************98 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.011
                    NPCBM_assoc  44 aaslapGetveatvkVtppag 64 
                                    ++++a +et++ tv+V+pp  
  gi|119720632|ref|YP_921127.1| 454 VSTIAHNETLTLTVTVKPPGY 474
                                    578999*************75 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 1.8
                    NPCBM_assoc  16 dg.taaatnvslslslPeG 33 
                                     + +a ++++ ++ ++P+G
  gi|119720632|ref|YP_921127.1| 543 ATlKANLRKIAVAFTTPDG 561
                                    2224556666666666665 PP

>> DUF824  Salmonella repeat of unknown function (DUF824)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.6     0.064   1.4e+02      13      22 ..     461     470 ..     450     471 .. 0.86
   2 ?    6.4   0.0    0.0036       8.1      16      36 ..     475     495 ..     474     497 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.064
                         DUF824  13 Esipltitvk 22 
                                    E+++lt+tvk
  gi|119720632|ref|YP_921127.1| 461 ETLTLTVTVK 470
                                    9********8 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0036
                         DUF824  16 pltitvkDasGnPvpnapftl 36 
                                    +l + v+Da G Pvp a+  l
  gi|119720632|ref|YP_921127.1| 475 TLRVRVVDACGDPVPGATLLL 495
                                    6889************98766 PP

>> Invasin_D3  Invasin, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.4     0.027        59      50      80 ..     436     467 ..     392     471 .. 0.68
   2 ?    7.7   0.1     0.002       4.4      23      81 ..     475     540 ..     473     554 .. 0.69
   3 ?   -0.2   0.1      0.56   1.3e+03      31      60 ..     559     587 ..     547     590 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.027
                     Invasin_D3  50 tlsavtdngdGtytatLta.ttagtatitptv 80 
                                    ++sa +  + G yt+t++  t a + t+t tv
  gi|119720632|ref|YP_921127.1| 436 KVSARQGLAPGNYTVTVKVsTIAHNETLTLTV 467
                                    45555556667777777765555444444444 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.002
                     Invasin_D3  23 tltvtlkDangnpvsgltvtfsttsag........tlsavt.dngdGtytatLta.ttagtatitptvn 81 
                                    tl v + Da g+pv g+t  ++  +ag            v+  +g+ t ta+  + + ag ++i++  +
  gi|119720632|ref|YP_921127.1| 475 TLRVRVVDACGDPVPGATLLLNGLKAGetdakgeaE---VKhVEGEATLTAIYAGlEVAGPLKISVNSD 540
                                    799***************999855555433211222...322455568888888888888888887665 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.56
                     Invasin_D3  31 angnpvsglt.vtfsttsagtlsavtdngdG 60 
                                     +g+p++g   v++     +tls++++n+ G
  gi|119720632|ref|YP_921127.1| 559 PDGKPATGILvVALL-G-RTTLSTAKTNSTG 587
                                    578999995515555.3.5799999999998 PP

>> Big_1  Bacterial Ig-like domain (group 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   0.0       7.4   1.7e+04      43      53 ..     347     357 ..     347     360 .. 0.52
   2 ?   -2.5   0.1       2.3   5.2e+03       5      14 ..     461     470 ..     459     470 .. 0.76
   3 ?   10.6   0.1   0.00019      0.43       8      51 ..     475     512 ..     474     523 .. 0.76
   4 ?    2.6   0.1     0.062   1.4e+02      14      48 ..     557     589 ..     550     591 .. 0.72

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 7.4
                          Big_1  43 danGkatvtlt 53 
                                    d+nG+++  +t
  gi|119720632|ref|YP_921127.1| 347 DENGNVVYAIT 357
                                    45555555555 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.3
                          Big_1   5 dtntltatvk 14 
                                    +t tlt+tvk
  gi|119720632|ref|YP_921127.1| 461 ETLTLTVTVK 470
                                    5678999986 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00019
                          Big_1   8 tltatvkDangnpvagatVtfsvsggalsassgtTdanGkatvt 51 
                                    tl+++v+Da g pv+gat  ++  +       g Tda+G+a+v+
  gi|119720632|ref|YP_921127.1| 475 TLRVRVVDACGDPVPGATLLLNGLK------AGETDAKGEAEVK 512
                                    899**************99887433......5667777777775 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.062
                          Big_1  14 kDangnpvagatVtfsvsggalsassgtTdanGka 48 
                                    +  +g+p  g+ V      ++l  s+++T++ G+a
  gi|119720632|ref|YP_921127.1| 557 TTPDGKPATGILVVALLGRTTL--STAKTNSTGHA 589
                                    5567777777777777666555..89*******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (639 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.45
# Mc/sec: 4308.00
//
Query:       gi|119720633|ref|YP_921128.1|  [L=420]
Description: glycosyl transferase family protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-44  152.7   0.1    1.9e-44  152.3   0.1    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
      2e-32  112.7   4.0      2e-32  112.7   4.0    2.6  3  Glyco_trans_2_3  Glycosyl transferase family group 2
    2.4e-28   99.1   0.0    3.2e-28   98.7   0.0    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
    4.7e-20   71.8   0.0    7.7e-20   71.1   0.0    1.3  1  Glyco_transf_21  Glycosyl transferase family 21
    1.3e-05   24.9   0.0    1.7e-05   24.4   0.0    1.1  1  Glyco_tranf_2_2  Glycosyltransferase like family 2


Domain annotation for each model (and alignments):
>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.3   0.1   5.3e-48   1.9e-44       1     230 []      67     294 ..      67     294 .. 0.94

  Alignments for each domain:
  == domain 1  score: 152.3 bits;  conditional E-value: 5.3e-48
                Glyco_tranf_2_3   1 prdlavlVptfneedvlgevlesllaqeypr..vevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksra 78 
                                    pr ++v+Vp+ +e ++++++l+++l+++yp   +ev+vv+  sd  + e ++ + +++p++ vr+++     +++gk  a
  gi|119720633|ref|YP_921128.1|  67 PR-VTVIVPSKDEGRRVERCLNAILSSDYPLekLEVIVVDASSDGYVEEIVRRAGERYPGA-VRLIRE---EEPRGKPAA 141
                                    67.**************************6666*******99**99999***********5.**9944...4588***** PP

                Glyco_tranf_2_3  79 lnealravksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvflln.rstlvsalgalefaerhlrflaarralg. 156
                                    ln+alr +++++v+++D+D+v e d+++r++  ++ p+v+av+++ ++ln r+++++++   e + +++   + r++lg 
  gi|119720633|ref|YP_921128.1| 142 LNRALREATGEVVAVFDADSVPERDAIRRAVKHLEEPGVAAVQGKTLVLNeRESVLARVASKEEKAWFHALIRGRERLGl 221
                                    ************************************************98466777777777*****************7 PP

                Glyco_tranf_2_3 157 vltlnGsgslirrevlkelegldplflltdDyelglrlrragfrtayvpgaavrevfpsslkayikqrnRwvyg 230
                                    +++l+Gs+ ++ r+ l+e +g+++   l++D+el++ l ++g+r++y+++++ + + p+sl  +  qrnRw++g
  gi|119720633|ref|YP_921128.1| 222 FVPLTGSCQFVKRSALEEVGGWRE-DALAEDLELSMDLLARGYRVKYANDVVSWQEAPTSLRSLAVQRNRWYRG 294
                                    7***********************.***********************************************86 PP

>> Glyco_trans_2_3  Glycosyl transferase family group 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   1.4       1.6   5.7e+03     169     195 ..      25      52 ..      14      54 .. 0.42
   2 ?   -0.2   0.0      0.23   8.2e+02     120     143 ..     126     151 ..     102     152 .. 0.79
   3 !  112.7   4.0   5.5e-36     2e-32       1     195 [.     153     394 ..     153     396 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.6
                Glyco_trans_2_3 169 lhlallllfsllalalvl.llllllaal 195
                                    l++al+ll+   +la+++ ++++++a+l
  gi|119720633|ref|YP_921128.1|  25 LLDALSLLTLAGILAWSAyHAPIIVAGL 52 
                                    3333333333333333332444444444 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.23
                Glyco_trans_2_3 120 s..lvkekspltlraalrQrkRwayG 143
                                    +  l++e+ p+   aal+++ R a G
  gi|119720633|ref|YP_921128.1| 126 AvrLIREEEPRGKPAALNRALREATG 151
                                    35689*****************8887 PP

  == domain 3  score: 112.7 bits;  conditional E-value: 5.5e-36
                Glyco_trans_2_3   1 iilllDaDtvlppdclreiaaelaspevaivqgpvlvm.nvanwleelaalffaedhgkdilvrealgrvvpsvGsgafl 79 
                                    ++++ DaD+v+ +d +r+++ +l++p va+vqg++lv  ++ ++l+++a  + + ++  +i+ re+lg +vp++Gs+ f+
  gi|119720633|ref|YP_921128.1| 153 VVAVFDADSVPERDAIRRAVKHLEEPGVAAVQGKTLVLnERESVLARVASKEEKAWFHALIRGRERLGLFVPLTGSCQFV 232
                                    58899*******************************964789**********98888889******************** PP

                Glyco_trans_2_3  80 rrsalqevggwdgdessvsEDfdmglrlqrkGyrvrfvpeslvkekspltlraalrQrkRwayGc.el..eklil..... 151
                                     rsal+evggw+  e++++ED+++++ l+++Gyrv ++++++ +++ p +lr    Qr Rw++G+ e   ++l+l     
  gi|119720633|ref|YP_921128.1| 233 KRSALEEVGGWR--EDALAEDLELSMDLLARGYRVKYANDVVSWQEAPTSLRSLAVQRNRWYRGYmEAfaRHLRLalagr 310
                                    ************..**************************************************8522442222245555 PP

                Glyco_trans_2_3 152 ..........................lvrllgylgsllwsalplhla....llllfslla.............lalvlll 188
                                                              +   +  l+++ +++ p++l+    ++ lfs++              la+v+++
  gi|119720633|ref|YP_921128.1| 311 rgldaailsagpylmalsllavaawlA---STALPHVNHFSTPAALVaalnAVSLFSVSValalserpvsaknLAWVPVI 387
                                    555665555555555555444432210...12223333333332222101122333333366666677777777777777 PP

                Glyco_trans_2_3 189 llllaal 195
                                    ++++++l
  gi|119720633|ref|YP_921128.1| 388 YAYWFTL 394
                                    7777765 PP

>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.7   0.0   8.9e-32   3.2e-28       1     170 []      70     241 ..      70     241 .. 0.94

  Alignments for each domain:
  == domain 1  score: 98.7 bits;  conditional E-value: 8.9e-32
                                    EEEEEESS-TTTHHHHHHHHHHH.GGCCEEEEEEEEES-SSCHHHHHGGGCH.C-TTEEEEEESSS-HHHHHHHHHHHH- CS
                Glycos_transf_2   1 svviptyNeektlletlesllaq.dpypdfeiivvDDgStDetveileelak.edprvrvirreenvGkagalnaglraa 78 
                                    +v++p+  e   ++++l+++l+  +p +++e+ivvD +S  + +ei++++ + +++ vr+ir ee +Gk +aln++lr+a
  gi|119720633|ref|YP_921128.1|  70 TVIVPSKDEGRRVERCLNAILSSdYPLEKLEVIVVDASSDGYVEEIVRRAGErYPGAVRLIREEEPRGKPAALNRALREA 149
                                    69*************************************777777777777789999*********************** PP

                                    -SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTTCSTCC CS
                Glycos_transf_2  79 tgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsfeigsa 158
                                    tg++++++DaD++p++d +++ v++le++g+++v g++ + +  +    r    +e+  +   +r r++ g     +gs+
  gi|119720633|ref|YP_921128.1| 150 TGEVVAVFDADSVPERDAIRRAVKHLEEPGVAAVQGKTLVLNERESVLARVASKEEKAWFHALIRGRERLGLFVPLTGSC 229
                                    ****************************************9999999999988899999999999999999********* PP

                                    CEEEEHHHHHCH CS
                Glycos_transf_2 159 allrrealeell 170
                                      ++r+alee++
  gi|119720633|ref|YP_921128.1| 230 QFVKRSALEEVG 241
                                    *********985 PP

>> Glyco_transf_21  Glycosyl transferase family 21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.1   0.0   2.1e-23   7.7e-20      13     172 ..     133     292 ..     124     293 .. 0.87

  Alignments for each domain:
  == domain 1  score: 71.1 bits;  conditional E-value: 2.1e-23
                Glyco_transf_21  13 vgvnpKvnnllqaleaakydllvisDsdvrvkpdyLeellaaledpkvglVtslpvgsdak.glaaaleaafl.ntlagv 90 
                                    ++ + K  +l++al++a  +++ + D+d + ++d++++ +++le+p+v+ V++  ++ +++ ++ a++++    + ++++
  gi|119720633|ref|YP_921128.1| 133 EEPRGKPAALNRALREATGEVVAVFDADSVPERDAIRRAVKHLEEPGVAAVQGKTLVLNEReSVLARVASKEEkAWFHAL 212
                                    455667788********************************************777655543889999888874555666 PP

                Glyco_transf_21  91 lqa..klsglgfavGksmalrreaLeaiGGfealadeLAeDyalgkllraaGlkvvlspapiaqtsvprrsslrallaRq 168
                                    +    +l+ +   +G++  ++r+aLe++GG ++  d LAeD++l++ l a+G++v  +++++ ++++p+  slr+l+ + 
  gi|119720633|ref|YP_921128.1| 213 IRGreRLGLFVPLTGSCQFVKRSALEEVGGWRE--DALAEDLELSMDLLARGYRVKYANDVVSWQEAPT--SLRSLAVQR 288
                                    666788999************************..*******************************996..899999888 PP

                Glyco_transf_21 169 lrWa 172
                                     rW 
  gi|119720633|ref|YP_921128.1| 289 NRWY 292
                                    8886 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   4.8e-09   1.7e-05      23     237 ..      92     301 ..      70     306 .. 0.74

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 4.8e-09
                Glyco_tranf_2_2  23 akyy.deeielivvddgSsekfleevssiidln..llvylkdeddkayslaaarNrGaskaesdlvlFlDaDcfissDkf 99 
                                       y  e++e+ivvd  Ss+ ++ee+      +  + v l  e ++  ++ aa Nr   +a +++v   DaD     D +
  gi|119720633|ref|YP_921128.1|  92 SD-YpLEKLEVIVVDA-SSDGYVEEIVRRAGERypGAVRLIRE-EEPRGKPAALNRALREATGEVVAVFDADSVPERDAI 168
                                    33.337899***9987.55666777766665551245554444.56889******************************* PP

                Glyco_tranf_2_2 100 ekilklitikklrenidaavvlpvvdlnkedsevlkdvedltassrvledllaakstlvkffapssssilinrraflevG 179
                                     + +k     +l+e   aav    +   +e   vl +v  +  ++ +   l+  ++ l  f+   +s   ++r a+ evG
  gi|119720633|ref|YP_921128.1| 169 RRAVK-----HLEEPGVAAVQG-KTLVLNERESVLARVASKEEKAWFH-ALIRGRERLGLFVPLTGSCQFVKRSALEEVG 241
                                    *9999.....887766666555.55555677789*******9999999.88888888888888888************** PP

                Glyco_tranf_2_2 180 GyDErfrGhgaEDfdlllRlakaikslekmpvellykaraksls.....nykGfrrflealak 237
                                    G+ E      aED +l + l+++   ++     +++++   sl+       + +r ++ea a+
  gi|119720633|ref|YP_921128.1| 242 GWREDA---LAEDLELSMDLLARGYRVKYANDVVSWQEAPTSLRslavqRNRWYRGYMEAFAR 301
                                    ***997...799999999999998888777777778877777776656544556666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       664  (0.037035); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.53
# Mc/sec: 2373.56
//
Query:       gi|119720634|ref|YP_921129.1|  [L=403]
Description: Fis family transcriptional regulator [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.35   11.0   5.0       0.31   11.2   0.2    3.1  3  MHYT      Bacterial signalling protein N terminal repeat


Domain annotation for each model (and alignments):
>> MHYT  Bacterial signalling protein N terminal repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.2      0.13   2.2e+03      37      46 ..       7      16 ..       5      32 .. 0.51
   2 ?   -0.7   0.0      0.09   1.6e+03      11      29 ..     300     317 ..     300     319 .. 0.85
   3 ?   11.2   0.2   1.7e-05      0.31      26      53 ..     364     391 ..     356     396 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.13
                           MHYT 37 vasvlAlala 46
                                   va+++Al+la
  gi|119720634|ref|YP_921129.1|  7 VAALAALLLA 16
                                   3444444442 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.09
                           MHYT  11 GMaAftlpgpigydpalta 29 
                                    G aA+++ gp +y+++lt+
  gi|119720634|ref|YP_921129.1| 300 GYAAVRV-GPHTYNVTLTG 317
                                    5688888.899*****997 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 1.7e-05
                           MHYT  26 altalSlliaivasvlAlalavrrrdtr 53 
                                     +t+l+ll+ i+as++A+al+vrr+  +
  gi|119720634|ref|YP_921129.1| 364 VTTGLALLAIILASAAAVALLVRRAAKL 391
                                    689******************9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 2313.58
//
Query:       gi|119720635|ref|YP_921130.1|  [L=91]
Description: hypothetical protein Tpen_1732 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.025   13.5   0.0      0.027   13.4   0.0    1.0  1  LMBR1            LMBR1-like membrane protein
       0.12   11.1   0.1       0.13   11.0   0.1    1.1  1  DUF2207          Predicted membrane protein (DUF2207)
       0.12   12.4   8.9      0.043   13.8   6.6    1.4  2  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
       0.16   12.1   0.2       0.18   11.9   0.2    1.1  1  DUF2614          Zinc-ribbon containing domain


Domain annotation for each model (and alignments):
>> LMBR1  LMBR1-like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0     6e-06     0.027     132     212 ..      11      88 ..       3      91 .] 0.74

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6e-06
                          LMBR1 132 lllvivlglliyvliilqklsllsiksllpilislantwGlvllilllGyGlvel.Prslwreiksdldeelkklyfeaa 210
                                    ++l+ + g+l+y +i++   +++    ll  l   + + G++ ++  +G+ l+ + P + + ei+++++eelkkl++e++
  gi|119720635|ref|YP_921130.1|  11 IMLASIAGILVYGWILF-FTQWS---LLLLQLTGFVAVAGVLGILAWIGFTLATTpPPKPIEEIEKEIEEELKKLEAEEK 86 
                                    45555555555555552.22233...6688899999999****************86677788************88887 PP

                          LMBR1 211 kl 212
                                    k 
  gi|119720635|ref|YP_921130.1|  87 KE 88 
                                    64 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   2.9e-05      0.13     384     442 ..      13      75 ..       2      86 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 2.9e-05
                        DUF2207 384 salglgliilglilillallllvlllvfllilllillliaiivlllfsrllgrr....teeGa 442
                                     a + g+++ g+il++    ll l l++++ ++ +l+++a+i + l+++  +++     +e  
  gi|119720635|ref|YP_921130.1|  13 LASIAGILVYGWILFFTQWSLLLLQLTGFVAVAGVLGILAWIGFTLATTPPPKPieeiEKEIE 75 
                                    333444444444444444444444499999999999999999999998866666322244444 PP

>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   6.6   9.7e-06     0.043      33     109 ..       6      74 ..       2      81 .. 0.53
   2 ?   -1.7   0.0      0.63   2.8e+03      20      30 ..      77      87 ..      71      89 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9.7e-06
                Phage_holin_3_6  33 agsgagllgaagvlallalllllval.alalaalwlaalivaavllvlagvlalvglkklkkakplpertieelkedv 109
                                    ++  a++l+  + +++++++l++    +l+l       l  +++++ + g+la++g   +     +p + iee+++ +
  gi|119720635|ref|YP_921130.1|   6 LVGTAIMLASIAGILVYGWILFFTQWsLLLL------QLTGFVAVAGVLGILAWIGFTLATT---PPPKPIEEIEKEI 74 
                                    4444445444444444444444444413444......3444555555667777777774444...4666777777655 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.63
                Phage_holin_3_6 20 eLakaElkeea 30
                                   eL k+E++e++
  gi|119720635|ref|YP_921130.1| 77 ELKKLEAEEKK 87
                                   56667777766 PP

>> DUF2614  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   3.9e-05      0.18      12      61 ..       9      57 ..       1      73 [. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.9e-05
                        DUF2614 12 falllvfiglivmyigllfkeselllvlflllGlllvlastvvyfwiGll 61
                                    a++l  i+ i++y  +lf + ++ l l+ l G+++v     +  wiG++
  gi|119720635|ref|YP_921130.1|  9 TAIMLASIAGILVYGWILFFT-QWSLLLLQLTGFVAVAGVLGILAWIGFT 57
                                   577888777778887776654.5666678899****************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1964  (0.109543); expected 358.6 (0.02)
Passed bias filter:                      924  (0.0515366); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.50
# Mc/sec: 549.57
//
Query:       gi|119720636|ref|YP_921131.1|  [L=97]
Description: hypothetical protein Tpen_1733 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00016   20.7   6.0    0.00018   20.5   6.0    1.0  1  Spc7            Spc7 kinetochore protein
    0.00028   19.3   1.3     0.0003   19.2   1.3    1.0  1  Gp58            gp58-like protein
    0.00041   20.7   0.0    0.00052   20.4   0.0    1.2  1  MtrB            Tetrahydromethanopterin S-methyltransferase s
     0.0007   19.2   3.6    0.00083   19.0   3.6    1.0  1  PspA_IM30       PspA/IM30 family
    0.00076   19.7   3.5    0.00089   19.4   3.5    1.1  1  Tropomyosin_1   Tropomyosin like
    0.00078   19.2   0.0    0.00093   18.9   0.0    1.1  1  MotA_ExbB       MotA/TolQ/ExbB proton channel family
    0.00079   19.1   3.0    0.00093   18.9   3.0    1.1  1  Lebercilin      Ciliary protein causing Leber congenital amau
    0.00084   18.1   0.0    0.00084   18.1   0.0    1.0  1  AAA_13          AAA domain
    0.00099   18.8   3.5     0.0011   18.6   3.5    1.0  1  Filament        Intermediate filament protein
     0.0011   19.0   4.0       0.31   11.1   0.1    2.2  2  DUF1043         Protein of unknown function (DUF1043)
     0.0019   17.7   1.7     0.0023   17.4   1.7    1.0  1  DUF2353         Uncharacterized coiled-coil protein (DUF2353)
     0.0019   18.2   8.4     0.0025   17.8   8.4    1.1  1  TMF_DNA_bd      TATA element modulatory factor 1 DNA binding
     0.0021   17.6   5.3     0.0026   17.4   5.3    1.1  1  MscS_porin      Mechanosensitive ion channel porin domain
     0.0028   17.8   3.9     0.0037   17.5   3.9    1.1  1  End3            Actin cytoskeleton-regulatory complex protein
     0.0035   16.7   4.8     0.0041   16.5   4.8    1.0  1  Tropomyosin     Tropomyosin
     0.0037   16.6   0.2     0.0039   16.5   0.2    1.2  1  HemX            HemX, putative uroporphyrinogen-III C-methylt
     0.0044   17.3   0.6     0.0065   16.7   0.3    1.4  1  DUF5082         Domain of unknown function (DUF5082)
     0.0061   16.2   0.1      0.007   16.0   0.1    1.2  1  SseC            Secretion system effector C (SseC) like famil
     0.0062   16.1   1.1      0.008   15.7   1.1    1.1  1  DegS            Sensor protein DegS
     0.0068   16.4   1.7      0.014   15.4   1.7    1.6  1  Bap31_Bap29_C   Bap31/Bap29 cytoplasmic coiled-coil domain
      0.007   16.7   6.1      0.071   13.5   1.2    2.1  2  Csm1_N          Csm1 N-terminal domain
     0.0084   14.8   3.1     0.0097   14.7   3.1    1.1  1  WEMBL           Weak chloroplast movement under blue light
     0.0095   16.4   0.9      0.012   16.0   0.9    1.2  1  NPV_P10         Nucleopolyhedrovirus P10 protein
  ------ inclusion threshold ------
       0.01   16.1   3.2      0.012   15.9   3.2    1.1  1  Jnk-SapK_ap_N   JNK_SAPK-associated protein-1
      0.011   14.6   3.6      0.013   14.4   3.6    1.0  1  CALCOCO1        Calcium binding and coiled-coil domain (CALCO
      0.011   16.2   1.7      0.019   15.5   1.7    1.4  1  Syntaxin-6_N    Syntaxin 6, N-terminal
      0.013   15.6   5.7      0.015   15.3   5.7    1.1  1  CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein C
      0.013   15.8   7.7      0.015   15.6   7.7    1.0  1  ATG16           Autophagy protein 16 (ATG16)
      0.013   15.3   1.9      0.017   14.9   1.9    1.1  1  Phage_GP20      Phage minor structural protein GP20
      0.014   15.5   0.4      0.014   15.5   0.4    1.4  1  DUF1664         Protein of unknown function (DUF1664)
      0.014   15.5   0.6      0.017   15.2   0.6    1.2  1  DUF2730         Protein of unknown function (DUF2730)
      0.016   15.2   0.2       0.03   14.3   0.2    1.4  1  UPF0154         Uncharacterised protein family (UPF0154)
      0.017   14.6   2.2      0.022   14.3   2.2    1.1  1  HMMR_N          Hyaluronan mediated motility receptor N-termi
      0.017   13.3   3.8      0.019   13.2   3.8    1.0  1  FPP             Filament-like plant protein, long coiled-coil
      0.018   15.5   0.2      0.019   15.4   0.2    1.1  1  Fez1            Fez1
      0.018   15.1   8.1       0.04   14.0   8.1    1.5  1  TPR_MLP1_2      TPR/MLP1/MLP2-like protein
      0.019   14.4   2.8      0.024   14.0   2.8    1.1  1  Rab5-bind       Rabaptin-like protein
      0.022   13.7   2.3      0.025   13.5   2.3    1.0  1  DUF812          Protein of unknown function (DUF812)
      0.023   14.1   3.7      0.029   13.7   3.7    1.1  1  GAS             Growth-arrest specific micro-tubule binding
      0.024   14.0   0.9      0.029   13.7   0.9    1.1  1  FAM76           FAM76 protein
      0.026   14.3   3.4      0.032   14.0   3.4    1.1  1  DUF4201         Domain of unknown function (DUF4201)
      0.027   12.7   4.3       0.03   12.6   4.3    1.0  1  Cast            RIM-binding protein of the cytomatrix active 
      0.027   14.8   2.0      0.066   13.6   1.1    2.0  2  FlaC_arch       Flagella accessory protein C (FlaC)
      0.028   12.3   3.2      0.033   12.0   3.2    1.0  1  Myosin_tail_1   Myosin tail
      0.029   14.5   1.4      0.038   14.1   1.4    1.2  1  COG2            COG (conserved oligomeric Golgi) complex comp
      0.031   13.6   2.9      0.037   13.3   2.9    1.0  1  FmiP_Thoc5      Fms-interacting protein/Thoc5
      0.033   14.3   5.6      0.044   13.9   5.6    1.1  1  ADIP            Afadin- and alpha -actinin-Binding
      0.033   14.6   3.9       0.25   11.8   3.9    2.1  1  DUF4094         Domain of unknown function (DUF4094)
      0.034   13.7   0.1      0.034   13.7   0.1    1.0  1  Exonuc_VII_L    Exonuclease VII, large subunit
      0.035   13.9   0.4      0.044   13.6   0.4    1.1  1  SKA1            Spindle and kinetochore-associated protein 1
      0.036   13.3   4.1      0.041   13.1   4.1    1.1  1  HAP1_N          HAP1 N-terminal conserved region
      0.037   14.1   5.9      0.036   14.1   4.6    1.7  1  Cep57_CLD_2     Centrosome localisation domain of PPC89
      0.039   13.9   0.1      0.044   13.7   0.1    1.1  1  EMP24_GP25L     emp24/gp25L/p24 family/GOLD
      0.041   14.1   3.2       0.07   13.4   3.2    1.4  1  ABC_tran_CTD    ABC transporter C-terminal domain
      0.043   12.0   2.8      0.057   11.6   2.8    1.1  1  EzrA            Septation ring formation regulator, EzrA
       0.05   13.6   0.5      0.058   13.4   0.5    1.1  1  Baculo_PEP_C    Baculovirus polyhedron envelope protein, PEP,
      0.056   13.4   3.6        0.2   11.6   0.7    2.0  2  Prefoldin_2     Prefoldin subunit
      0.057   12.2   2.4      0.067   11.9   2.4    1.1  1  Tektin          Tektin family
       0.06   13.1   6.3      0.068   13.0   6.3    1.1  1  OEP             Outer membrane efflux protein
      0.067   13.1   1.1       0.25   11.3   0.0    2.4  1  Pox_A_type_inc  Viral A-type inclusion protein repeat
      0.069   13.4   0.4      0.069   13.4   0.4    2.5  2  XhlA            Haemolysin XhlA
       0.07   13.2   1.3       0.14   12.2   0.2    2.0  1  Tom5            Mitochondrial import receptor subunit or tran
       0.07   13.0   0.2      0.083   12.7   0.2    1.1  1  Bacillus_HBL    Bacillus haemolytic enterotoxin (HBL)
      0.072   13.4   0.3       0.11   12.8   0.3    1.3  1  TSC22           TSC-22/dip/bun family
      0.079   12.1   4.8        0.1   11.7   4.8    1.2  1  CCDC144C        CCDC144C protein coiled-coil region
      0.081   11.9   0.0      0.083   11.9   0.0    1.1  1  MT              Microtubule-binding stalk of dynein motor
      0.083   11.8   0.0      0.088   11.7   0.0    1.0  1  FemAB           FemAB family
      0.088   12.0   0.1        0.1   11.8   0.1    1.0  1  TMPIT           TMPIT-like protein
      0.091   12.9   4.0       0.17   12.0   0.8    2.0  2  Swi5            Swi5
      0.095   10.9   2.4       0.11   10.7   2.4    1.0  1  COG6            Conserved oligomeric complex COG6
        0.1   12.7   3.6       0.15   12.2   3.6    1.2  1  TolA_bind_tri   TolA binding protein trimerisation
        0.1   12.9   1.3       0.19   12.0   0.7    1.6  2  KxDL            Uncharacterized conserved protein
       0.11   11.9  10.9        1.4    8.3   0.2    2.0  2  DUF3552         Domain of unknown function (DUF3552)
       0.11   12.0   3.7       0.14   11.8   3.7    1.0  1  HAUS-augmin3    HAUS augmin-like complex subunit 3
       0.12   12.8   3.5       0.45   10.9   3.5    1.8  1  CLZ             C-terminal leucine zipper domain of cyclic nu
       0.12   11.4   3.7       0.14   11.2   3.7    1.0  1  Atg14           Vacuolar sorting 38 and autophagy-related sub
       0.15   11.4   3.6       0.17   11.1   3.6    1.1  1  DUF4763         Domain of unknown function (DUF4763)
       0.15   12.0   0.7        5.9    6.9   0.0    2.1  2  Nas2_N          Nas2 N_terminal domain
       0.17   11.9   3.7       0.25   11.4   2.9    1.6  1  Sec2p           GDP/GTP exchange factor Sec2p
       0.18   10.9   2.5       0.23   10.6   2.5    1.1  1  DLP_helical     Dynamin-like helical domain
       0.18   12.0   3.6       0.31   11.3   3.6    1.4  1  Seryl_tRNA_N    Seryl-tRNA synthetase N-terminal domain
       0.19   12.1   7.1        1.4    9.4   3.4    2.1  2  LPP             Lipoprotein leucine-zipper
        0.2   12.1   7.2        1.2    9.6   7.2    1.9  1  DUF4140         N-terminal domain of unknown function (DUF414
        0.2   12.3   3.3       0.36   11.5   3.3    1.4  1  SlyX            SlyX
        0.2   11.7   4.5       0.24   11.5   4.5    1.1  1  UPF0242         Uncharacterised protein family (UPF0242) N-te
        0.2   11.4   1.9       0.27   11.1   1.9    1.1  1  DUF724          Protein of unknown function (DUF724)
       0.21   10.5   2.5       0.23   10.4   2.5    1.0  1  IFT57           Intra-flagellar transport protein 57
       0.21   12.1   8.3       0.25   11.9   8.3    1.1  1  APG6_N          Apg6 coiled-coil region
       0.22   10.0   3.5       0.28    9.7   3.5    1.0  1  Macoilin        Macoilin family
       0.24   11.7   5.8       0.34   11.1   5.8    1.3  1  TMF_TATA_bd     TATA element modulatory factor 1 TATA binding
       0.24   11.3   2.2       0.28   11.0   2.2    1.1  1  Sec34           Sec34-like family
       0.25   11.8   1.4       0.33   11.5   1.4    1.2  1  DUF16           Protein of unknown function DUF16
       0.26   11.2   3.1        6.6    6.7   0.4    1.9  2  Prefoldin       Prefoldin subunit
       0.27   11.2   8.6       0.53   10.3   8.6    1.5  1  Sugarporin_N    Maltoporin periplasmic N-terminal extension
       0.28   11.0   5.1       0.39   10.5   3.8    1.7  2  DivIC           Septum formation initiator
       0.29   11.3   3.0       0.76   10.0   3.0    1.8  1  JIP_LZII        JNK-interacting protein  leucine zipper II
       0.31   11.6   5.0       0.85   10.2   0.3    2.3  2  YtxH            YtxH-like protein
       0.33   11.2   3.8       0.62   10.3   3.8    1.5  1  Spc24           Spc24 subunit of Ndc80
       0.34   11.0   7.7       0.56   10.3   7.7    1.3  1  DHR10           Designed helical repeat protein 10 domain
       0.36   10.2   6.1       0.13   11.6   3.9    1.4  1  DUF4407         Domain of unknown function (DUF4407)
       0.38    9.3   3.3        1.4    7.5   3.3    1.8  1  DUF3138         Protein of unknown function (DUF3138)
       0.44   10.5   7.0        1.8    8.5   7.0    1.7  1  YscO            Type III secretion protein YscO
       0.45   11.0   4.9        0.6   10.6   4.9    1.2  1  ZapB            Cell division protein ZapB
       0.45    8.4   1.3       0.55    8.1   1.3    1.1  1  Prominin        Prominin
       0.46    7.9   3.7       0.55    7.7   3.7    1.0  1  DUF3584         Protein of unknown function (DUF3584)
       0.54   10.5   4.6        5.9    7.1   0.3    2.1  2  Cnn_1N          Centrosomin N-terminal motif 1
       0.61   10.0   5.5        1.3    9.0   0.6    2.0  2  EspB            Enterobacterial EspB protein
       0.71   10.3   8.0        1.4    9.3   8.1    1.5  1  Uso1_p115_C     Uso1 / p115 like vesicle tethering protein, C
        3.5    8.3   8.7         33    5.2   8.7    2.4  1  DUF883          Bacterial protein of unknown function (DUF883


Domain annotation for each model (and alignments):
>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   6.0   1.1e-06   0.00018     198     256 ..       3      61 ..       1      65 [. 0.94

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.1e-06
                           Spc7 198 keeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaerv 256
                                    +eeL+++re++++l++++++++ +l++ q++l +l++++++l++q se ++++aeae  
  gi|119720636|ref|YP_921131.1|   3 EEELKSYRENVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSESRSRLAEAEAR 61 
                                    689****************************************************9975 PP

>> Gp58  gp58-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   1.3   1.8e-06    0.0003     268     319 ..       5      56 ..       2      73 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.8e-06
                           Gp58 268 eiknregavsrvqqdldsyqrrlqdaeknyssLtqtvkGlqstvsdpnskle 319
                                    e+k   ++v+r+q d++s+q +l +a+ + s+L+  v+ l++++s+  s+l 
  gi|119720636|ref|YP_921131.1|   5 ELKSYRENVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSESRSRLA 56 
                                    77888899************************************99888764 PP

>> MtrB  Tetrahydromethanopterin S-methyltransferase subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   3.1e-06   0.00052      23      89 ..      17      85 ..       6      87 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 3.1e-06
                           MtrB 23 redv..vllsldpvleeidkLekiaddlvnsLdpetallesypgRektlviaGlltnlfyGfivglvia 89
                                   +edv  + ++l+  ++ +  L++ +  l+ +L+ +++ l+  + R + + +aG++ +l+ Gf++g +++
  gi|119720636|ref|YP_921131.1| 17 QEDVksLQVKLSSAQTDLSALKAQVSSLEAQLSESRSRLAEAEARAQLVGVAGTVVGLVVGFAIGYFVS 85
                                   45543367888999999************************************************9986 PP

>> PspA_IM30  PspA/IM30 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   3.6   5.1e-06   0.00083      91     152 ..       4      65 ..       3      75 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 5.1e-06
                      PspA_IM30  91 aeikslekqaealetqlaqqrsaveqlrkqlealetkieelkakkellkarekaakaqeavq 152
                                    +e+ks+ +++++l++ ++ ++     +++ l+al+++++ l+a+  +  +r++ a a++++ 
  gi|119720636|ref|YP_921131.1|   4 EELKSYRENVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSESRSRLAEAEARAQLV 65 
                                    578999***************************************************99985 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   3.5   5.4e-06   0.00089      20      77 ..       3      60 ..       1      66 [. 0.93

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 5.4e-06
                  Tropomyosin_1 20 eekvKeleqenlekeqeiksLtkknqqleeevekleeklkeakekaeesekkktnnea 77
                                   ee++K++ ++ ++  +++ksL+ k++ ++ ++  l+++++  +++++es ++ +++ea
  gi|119720636|ref|YP_921131.1|  3 EEELKSYRENVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSESRSRLAEAEA 60
                                   78999**********************************************9999996 PP

>> MotA_ExbB  MotA/TolQ/ExbB proton channel family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   5.7e-06   0.00093      19      72 ..      25      78 ..       5      81 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 5.7e-06
                                   -HHHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      MotA_ExbB 19 vdgaepeelrraleealsreeerlekglsilatigslaPllGLlGTVlGlieaf 72
                                   v+ ++ ++  +al++++s  e++l+++ s la + + a l+G+ GTV+Gl+  f
  gi|119720636|ref|YP_921131.1| 25 VKLSSAQTDLSALKAQVSSLEAQLSESRSRLAEAEARAQLVGVAGTVVGLVVGF 78
                                   667778888899**************************************9866 PP

>> Lebercilin  Ciliary protein causing Leber congenital amaurosis disease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   3.0   5.6e-06   0.00093      65     120 ..       2      59 ..       1      69 [. 0.87

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 5.6e-06
                     Lebercilin  65 hneEvrvlrerlRksqekerelekklkekeaellrlkdklkklkk.Lsedkn.Laere 120
                                    ++eE++ +re++ ++qe +++l+ kl +++ +l  lk +++ l++ Lse ++ Lae e
  gi|119720636|ref|YP_921131.1|   2 REEELKSYRENVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAqLSESRSrLAEAE 59 
                                    68******************************************99*99886255554 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   5.1e-06   0.00084     408     462 ..       3      57 ..       1      94 [. 0.82

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 5.1e-06
                         AAA_13 408 eseldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaaee 462
                                    e+el+ y +++ +l++++++l+ +l+ ++++l +l+++++ Le+ql++ +   +e
  gi|119720636|ref|YP_921131.1|   3 EEELKSYRENVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSESRSRLAE 57 
                                    6889999999999999999999999999999999999999999999887766555 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   3.5   6.9e-06    0.0011     203     260 ..       5      62 ..       1      66 [. 0.65

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 6.9e-06
                                    XXXXXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Filament 203 aaeknsealrsakeeitelrrqiqsleieleslkkqkasleaqlaeleerleaelekl 260
                                    + ++  e++ + +e+++ l+ ++ s +++l++lk+q +sleaql+e   rl+++ +++
  gi|119720636|ref|YP_921131.1|   5 ELKSYRENVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSESRSRLAEAEARA 62 
                                    4555666677777777777777777777777777777777777777777766665554 PP

>> DUF1043  Protein of unknown function (DUF1043)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   1.1    0.0083       1.4      36      82 ..      12      59 ..       2      68 .. 0.57
   2 !   11.1   0.1    0.0019      0.31       2      18 ..      71      87 ..      70      95 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0083
                        DUF1043 36 akaeleeqkqeledHfaqsaelLetlaedyqkLyqhlaksseeLlp.e 82
                                   + ++l+e  + l+  ++++++ L+ l+ + + L  +l++s ++L   e
  gi|119720636|ref|YP_921131.1| 12 NVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSESRSRLAEaE 59
                                   333444445555556666666667777777777777777766665522 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0019
                        DUF1043  2 liglvvGiiiGalilrl 18
                                   ++glvvG+ iG++++r 
  gi|119720636|ref|YP_921131.1| 71 VVGLVVGFAIGYFVSRK 87
                                   79************996 PP

>> DUF2353  Uncharacterized coiled-coil protein (DUF2353)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   1.7   1.4e-05    0.0023      69     132 ..       5      65 ..       2      68 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.4e-05
                        DUF2353  69 lleesreenkalkleveeLrqklkeaqgDiklLReqlarqrlglkdedlletrhssaeereelv 132
                                     l+ +re+  +l+++v++L+ kl+ aq D  +L++q+ + + +l++   +++r  +ae+r +lv
  gi|119720636|ref|YP_921131.1|   5 ELKSYRENVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSE---SRSRLAEAEARAQLV 65 
                                    57899*****************************888877666543...456667788888887 PP

>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   8.4   1.5e-05    0.0025      19      74 .]       4      59 ..       3      59 .. 0.98

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.5e-05
                     TMF_DNA_bd 19 eEGekLskkelklnntikkLrkknkelekeikelkkkleklekeleeleerlkeae 74
                                   eE++ ++ +  +l + +k+L+ k++ + ++++ lk ++++le +l+e ++rl+eae
  gi|119720636|ref|YP_921131.1|  4 EELKSYRENVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSESRSRLAEAE 59
                                   8999*************************************************998 PP

>> MscS_porin  Mechanosensitive ion channel porin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   5.3   1.6e-05    0.0026      87     142 ..       6      61 ..       3      69 .. 0.60

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.6e-05
                     MscS_porin  87 llqtssqlqelqeqlaqlnsqlvelqtrperaqqqltearqrlqeirnrLnstaaa 142
                                    l++  +++ +lqe+ ++l+ +l ++qt ++ + +q ++   +l+e r+rL++ +a+
  gi|119720636|ref|YP_921131.1|   6 LKSYRENVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSESRSRLAEAEAR 61 
                                    55555566666666666666666666666666666666666666666666555433 PP

>> End3  Actin cytoskeleton-regulatory complex protein END3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   3.9   2.2e-05    0.0037     142     197 ..       4      57 ..       2      59 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.2e-05
                           End3 142 eqLLkYKeeqlreleegegkskeknlksvkedietveeqVegLesylssrkeeLeq 197
                                    e+L  Y+e+  r +e+ +  s + +l+s + d+++++ qV++Le+ ls+ ++ L++
  gi|119720636|ref|YP_921131.1|   4 EELKSYRENVTRLQEDVK--SLQVKLSSAQTDLSALKAQVSSLEAQLSESRSRLAE 57 
                                    678899999887777665..55699***********************99998875 PP

>> Tropomyosin  Tropomyosin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   4.8   2.5e-05    0.0041       7      65 ..       3      61 ..       1      67 [. 0.85

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.5e-05
                    Tropomyosin  7 eeeldeaeerlekakkkleeaekkaekaeaEvaalnrriqlleeelerteerleealek 65
                                   eeel +++e+ +++++ +++ + k  +a+++ +al+ +++ le++l ++ +rl+ea ++
  gi|119720636|ref|YP_921131.1|  3 EEELKSYRENVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSESRSRLAEAEAR 61
                                   68888999999999999999999999999999999999999999999999999988765 PP

>> HemX  HemX, putative uroporphyrinogen-III C-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.2   2.4e-05    0.0039      60     117 ..       5      66 ..       1      83 [. 0.83

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.4e-05
                           HemX  60 qkqeleerlqqlaeklealekeleqlqkqleelqqqlskvsga.erkdWlLaeAd...fLlk 117
                                    + +   e++  l+e++++l+ +l++ q +l++l++q+s ++++ +++  +LaeA+   +L+ 
  gi|119720636|ref|YP_921131.1|   5 ELKSYRENVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQlSESRSRLAEAEaraQLVG 66 
                                    556667888899999999***********************998888889***984444555 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.3   3.9e-05    0.0065      90     122 ..      13      45 ..       4      46 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.9e-05
                        DUF5082  90 idaieeEIerLenqiseaqgvldtlqsqlnslk 122
                                    + +++e+++ L+ ++s+aq++l+ l+ q++sl+
  gi|119720636|ref|YP_921131.1|  13 VTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLE 45 
                                    6799**************************997 PP

>> SseC  Secretion system effector C (SseC) like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   4.3e-05     0.007      10      68 ..      20      77 ..       4      82 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.3e-05
                           SseC 10 skaaedsleskqkllkelqekqeklrqeqveeireqikkaeekakkaGiigkIfGwila 68
                                   +k+++ +l+s+q++l +l++ q  +++ q+ e r+ +++ae  a+  G++g ++G +++
  gi|119720636|ref|YP_921131.1| 20 VKSLQVKLSSAQTDLSALKA-QVSSLEAQLSESRSRLAEAEARAQLVGVAGTVVGLVVG 77
                                   57888899999999999976.5666******************************9985 PP

>> DegS  Sensor protein DegS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   1.1   4.9e-05     0.008      72     134 ..       7      68 ..       3      73 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 4.9e-05
                           DegS  72 kkyseeeikeaYeeakelqvelallrekEkqlrerRdelerrLkklketierAeklvsqvgvv 134
                                    k+y+e ++ +  e +k+lqv+l+ ++   + l+++  +le +L + ++ +  Ae  ++ vgv+
  gi|119720636|ref|YP_921131.1|   7 KSYRE-NVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSESRSRLAEAEARAQLVGVA 68 
                                    55655.56677899****************************************999999987 PP

>> Bap31_Bap29_C  Bap31/Bap29 cytoplasmic coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   1.7   8.3e-05     0.014       2      29 ..      19      46 ..      18      61 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 8.3e-05
                  Bap31_Bap29_C  2 eiekLkkeLkkkkkDlealKkQaeglak 29
                                    +++L+ +L +++ Dl alK Q  +l +
  gi|119720636|ref|YP_921131.1| 19 DVKSLQVKLSSAQTDLSALKAQVSSLEA 46
                                   799*********************9986 PP

>> Csm1_N  Csm1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   1.1    0.0056      0.92      33      63 ..       3      33 ..       1      36 [. 0.78
   2 !   13.5   1.2   0.00043     0.071      32      67 ..      23      58 ..      22      61 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0056
                         Csm1_N 33 sqkletkdqeiesLkeqlaeleekvkeleer 63
                                   +++l+++ + + +L+e +++l+ k+++++++
  gi|119720636|ref|YP_921131.1|  3 EEELKSYRENVTRLQEDVKSLQVKLSSAQTD 33
                                   6778888888888888888888888888775 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00043
                         Csm1_N 32 LsqkletkdqeiesLkeqlaeleekvkeleerrkkq 67
                                   L+ kl++ ++ +++Lk+q+ +le++++e+ +r +++
  gi|119720636|ref|YP_921131.1| 23 LQVKLSSAQTDLSALKAQVSSLEAQLSESRSRLAEA 58
                                   67789999********************99988765 PP

>> WEMBL  Weak chloroplast movement under blue light
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   3.1   5.9e-05    0.0097     300     343 ..       4      47 ..       1      71 [. 0.58

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.9e-05
                          WEMBL 300 kELeevkaniekakdevklLkvaaasLrseLekekaeLaslrqr 343
                                    +EL+  ++n+ + +++vk+L+v  +s +++L+  ka+++sl  +
  gi|119720636|ref|YP_921131.1|   4 EELKSYRENVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQ 47 
                                    56666666666666666666666666666666666666666442 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.9   7.5e-05     0.012      15      65 ..       8      55 ..       3      65 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 7.5e-05
                        NPV_P10 15 avddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiL 65
                                      + V+ lq+ v+++q +l      ++ L a+ aq+ +le+++++  + L
  gi|119720636|ref|YP_921131.1|  8 SYRENVTRLQEDVKSLQVKLSS---AQTDLSALKAQVSSLEAQLSESRSRL 55
                                   5567889999999999988888...45889999999999998888766655 PP

>> Jnk-SapK_ap_N  JNK_SAPK-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.9   3.2   7.2e-05     0.012      88     139 ..       3      54 ..       1      68 [. 0.84

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 7.2e-05
                  Jnk-SapK_ap_N  88 eeerkelqekveqleeenrelelkaknaadqlsrleekeaelkkeysklher 139
                                    eee k ++e v++l+e+++ l++k+++a++ ls+l+ + ++l+ + s+  +r
  gi|119720636|ref|YP_921131.1|   3 EEELKSYRENVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSESRSR 54 
                                    6889999*************************99999988887777766654 PP

>> CALCOCO1  Calcium binding and coiled-coil domain (CALCOCO1) like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   3.6   7.7e-05     0.013     178     236 ..       4      62 ..       1      69 [. 0.85

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 7.7e-05
                       CALCOCO1 178 akleqseeelrslskelqelrnslaerdtqvlqLqdtittltqkLttAqrkeaenEall 236
                                     +l++ +e++ +l +++++l+ +l   +t++  L+ +++ l+ +L++ + + ae Ea  
  gi|119720636|ref|YP_921131.1|   4 EELKSYRENVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSESRSRLAEAEARA 62 
                                    57888888999999999999999999999999999999999999999999999999854 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   1.7   0.00011     0.019      36      89 ..      13      66 ..       1      73 [. 0.86

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 0.00011
                   Syntaxin-6_N 36 seeldetrteLrkalrsiewdledLeetvriveknpskfkidekelsrrrafve 89
                                      l+e  + L+ +l+s+++dl+ L+  v+ +e++ s+ + + +e + r ++v 
  gi|119720636|ref|YP_921131.1| 13 VTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSESRSRLAEAEARAQLVG 66
                                   5678889999***************************************99986 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   5.7   9.4e-05     0.015      47     102 ..       6      61 ..       2      65 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 9.4e-05
                 CENP-F_leu_zip  47 aEtskaevetlkeeieelaeelreleldLvalrsekeeLekelqkkqervseLesl 102
                                      + ++ v  l+e ++ l+ +l+  ++dL+al+ +  +Le +l ++++r  e e++
  gi|119720636|ref|YP_921131.1|   6 LKSYRENVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSESRSRLAEAEAR 61 
                                    55678999999999999999999999999999999999999999999999998765 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   7.7     9e-05     0.015      73     132 ..       3      62 ..       1      66 [. 0.87

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 9e-05
                          ATG16  73 sakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaer 132
                                    +++++s  +++++l+e+++ l+ + +  ++ l +l+++++ le++l+e ++rlae+ea+ 
  gi|119720636|ref|YP_921131.1|   3 EEELKSYRENVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSESRSRLAEAEARA 62 
                                    567888899999999999999999999999999999999999999999999999999876 PP

>> Phage_GP20  Phage minor structural protein GP20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   1.9   0.00011     0.017      19      72 ..      12      62 ..       3      65 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 0.00011
                     Phage_GP20 19 kldeveeerdtlkeqlkdrdkqLedLkkkakdneeLqkqieelqaknkkakaey 72
                                   ++++++e++++l+ +l  ++++L+ Lk++   + +L++q+ e    +++a+a +
  gi|119720636|ref|YP_921131.1| 12 NVTRLQEDVKSLQVKLSSAQTDLSALKAQ---VSSLEAQLSESRSRLAEAEARA 62
                                   678899********************999...9999999999999999988765 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.4   8.3e-05     0.014      74     119 ..       5      50 ..       2      54 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 8.3e-05
                        DUF1664  74 kldeqkeiskeikeevtevredlseigedvesvkeavegleskler 119
                                    +l++  e  + ++e+v++++ +ls+ ++d++++k+ v++le++l++
  gi|119720636|ref|YP_921131.1|   5 ELKSYRENVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSE 50 
                                    5677788889999999999999999999999999999999999875 PP

>> DUF2730  Protein of unknown function (DUF2730)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.6    0.0001     0.017      33      93 ..       4      62 ..       1      74 [. 0.70

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 0.0001
                        DUF2730 33 edleklaekveendkrlteletkvenLPtakdlekLkllladlrgelkaleaevrqlshqv 93
                                   e+l++  e+v++ ++ +++l++k+++   + dl++Lk +++ l+++l++ + ++++ + ++
  gi|119720636|ref|YP_921131.1|  4 EELKSYRENVTRLQEDVKSLQVKLSS--AQTDLSALKAQVSSLEAQLSESRSRLAEAEARA 62
                                   56666677777777777777777765..566777777777777777777777776666555 PP

>> UPF0154  Uncharacterised protein family (UPF0154)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.2   0.00018      0.03       2      21 ..      71      90 ..      70      92 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 0.00018
                        UPF0154  2 vialivGlvlGffiarkymk 21
                                   v++l+vG+++G+f++rk + 
  gi|119720636|ref|YP_921131.1| 71 VVGLVVGFAIGYFVSRKRLG 90
                                   899*************9875 PP

>> HMMR_N  Hyaluronan mediated motility receptor N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   2.2   0.00013     0.022     175     218 ..       8      54 ..       2      67 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 0.00013
                         HMMR_N 175 akekevsvkQed...meaklqvtqknLeeskakvaqLkeklvsleke 218
                                    + + +v+ +Qed   +++kl ++q++L + ka+v+ L+ +l+++   
  gi|119720636|ref|YP_921131.1|   8 SYRENVTRLQEDvksLQVKLSSAQTDLSALKAQVSSLEAQLSESRSR 54 
                                    44455666665522245677777777777777777777777665544 PP

>> FPP  Filament-like plant protein, long coiled-coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   3.8   0.00012     0.019     688     744 ..       4      60 ..       1      66 [. 0.62

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00012
                            FPP 688 eenkllkeeleelksekenlevelksatenleslkaqlqesEqllaelkseLeslke 744
                                    ee k+ +e++++l+ + + l+v+l+sa+ +l +lkaq +  E +l+e +s L++++ 
  gi|119720636|ref|YP_921131.1|   4 EELKSYRENVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSESRSRLAEAEA 60 
                                    455666666666666666666666666666666666666666666666666666654 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.2   0.00012     0.019      51     108 ..       3      60 ..       1      80 [. 0.59

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 0.00012
                           Fez1  51 eeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelselsl 108
                                    eee+k+++e+++  +++++ ++ +l+ ++++ + l+ +v++le++l+e r++l+e+++
  gi|119720636|ref|YP_921131.1|   3 EEELKSYRENVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSESRSRLAEAEA 60 
                                    5555555555555555555555555555555555555555555555555555555433 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   8.1   0.00024      0.04      29      85 ..       4      60 ..       1      65 [. 0.49

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 0.00024
                     TPR_MLP1_2 29 edlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesaka 85
                                   e+l++ +e +++ q++ ++  vk +++ ++l+al++++++l+a+++e ++++ +a+a
  gi|119720636|ref|YP_921131.1|  4 EELKSYRENVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSESRSRLAEAEA 60
                                   444555555555555555555555555555555555555555555555555544444 PP

>> Rab5-bind  Rabaptin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   2.8   0.00015     0.024       8      58 ..       3      53 ..       2      66 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 0.00015
                      Rab5-bind  8 EkqLqaiqeqEaelrdqvkklqellrraneqLekerkdkkeLedslkelse 58
                                   E++L+++ e+  +l+++vk lq+ l  a+ +L++ + +   Le +l e+  
  gi|119720636|ref|YP_921131.1|  3 EEELKSYRENVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSESRS 53
                                   788999999999999999999999999999999999999999998887754 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   2.3   0.00015     0.025     321     380 ..       3      61 ..       1      69 [. 0.72

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00015
                         DUF812 321 eeelkkkreeeleelqeqieeleskieeleeeikklessikqveeeleeekeeneeleke 380
                                    eeelk  re +++ lqe +++l+ k+++ + ++++l+++++ +e +l e ++  +e e+ 
  gi|119720636|ref|YP_921131.1|   3 EEELKSYRE-NVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSESRSRLAEAEAR 61 
                                    677777776.55788888888888888888888888888888888888877777776655 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   3.7   0.00017     0.029      54     106 ..       4      53 ..       2      66 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00017
                            GAS  54 qenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkw 106
                                    +e k+++e++++++e+v+ L+ +l   + d   l +lka++++le +l++ + 
  gi|119720636|ref|YP_921131.1|   4 EELKSYRENVTRLQEDVKSLQVKLSSAQTD---LSALKAQVSSLEAQLSESRS 53 
                                    678999999999999999999999998886...55556666666666655544 PP

>> FAM76  FAM76 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.9   0.00018     0.029     221     264 ..      13      56 ..       6      65 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00018
                          FAM76 221 vtqLkeeiaslkkqleqkdqellekdkkitelkaellekekelr 264
                                    vt+L+e+++sl+ +l++ +++l++ + ++++l a+l e++++l 
  gi|119720636|ref|YP_921131.1|  13 VTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSESRSRLA 56 
                                    899*******************************9998887664 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   3.4   0.00019     0.032      61     120 ..       2      61 ..       1      65 [. 0.88

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 0.00019
                        DUF4201  61 rnkeLkrlkkkttktvhalthlkeklhmleselselkkelkekeerlaklrkelykvkle 120
                                    r++eLk  ++++t+    ++ l+ kl+  ++ ls+lk + +++e++l + r +l +++++
  gi|119720636|ref|YP_921131.1|   2 REEELKSYRENVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSESRSRLAEAEAR 61 
                                    789999999999999999999999999999999999999999999999999999998765 PP

>> Cast  RIM-binding protein of the cytomatrix active zone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   4.3   0.00018      0.03     466     523 ..       2      59 ..       1      65 [. 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00018
                           Cast 466 rleeleslkkenkelkeklsalqaeltekesslldlkekasslassglkkdsklksle 523
                                    r eel+s++ +   l+e +++lq +l++ ++ l+ lk + ssl+ +  ++ s+l + e
  gi|119720636|ref|YP_921131.1|   2 REEELKSYRENVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSESRSRLAEAE 59 
                                    789*****************************************99988888887655 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.2      0.17        28      20      40 ..       3      23 ..       1      27 [. 0.86
   2 ?   13.6   1.1    0.0004     0.066       2      36 ..      13      47 ..      12      65 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.17
                      FlaC_arch 20 kkeneelsksveelkenVkdl 40
                                   ++e+++ +++v++l+e+Vk l
  gi|119720636|ref|YP_921131.1|  3 EEELKSYRENVTRLQEDVKSL 23
                                   6789999999*****999976 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 0.0004
                      FlaC_arch  2 idelEnklsklsteletvkkeneelsksveelken 36
                                   +  l++++++l+++l++++++++ l+ +v  l+ +
  gi|119720636|ref|YP_921131.1| 13 VTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQ 47
                                   66799999******************999999876 PP

>> Myosin_tail_1  Myosin tail
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   3.2    0.0002     0.033     429     485 ..       7      64 ..       2      70 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0002
                  Myosin_tail_1 429 eelaekvsklqaelesvsslleeaegksiklskdvsslesqlqDtqellqe.etrqkL 485
                                    +   e v++lq ++ s++  l++a++  + l+ +vssle+ql + ++ l e e r++L
  gi|119720636|ref|YP_921131.1|   7 KSYRENVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSESRSRLAEaEARAQL 64 
                                    56689999**********************************9999877664788776 PP

>> COG2  COG (conserved oligomeric Golgi) complex component, COG2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   1.4   0.00023     0.038      64     111 ..       6      53 ..       3      74 .. 0.55

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 0.00023
                           COG2  64 Lvglqeeleevesplaaarkkvesvreklsereeeveskleeakelee 111
                                    L++++e++ +++ ++++++ k++s++  ls+ +++v+s  ++ +e ++
  gi|119720636|ref|YP_921131.1|   6 LKSYRENVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSESRS 53 
                                    666666666666666666666666666666666655554444443333 PP

>> FmiP_Thoc5  Fms-interacting protein/Thoc5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   2.9   0.00022     0.037     109     162 ..       4      57 ..       2      66 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00022
                     FmiP_Thoc5 109 eqlkeleekkkkleqeieekkkfLssLppkLkslkkatkplqealglpltkerk 162
                                    e+lk+  e+++ l++++++ + +Lss ++ L++lk++++ l+ +l+ + ++  +
  gi|119720636|ref|YP_921131.1|   4 EELKSYRENVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSESRSRLAE 57 
                                    7999****************************************9864443333 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   5.6   0.00027     0.044      68     120 ..       5      57 ..       2      65 .. 0.49

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00027
                           ADIP  68 eierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqr 120
                                    e+++ + ++ rl++ +++l+ +l+++q ++  l++++ +le++l + +  l+ 
  gi|119720636|ref|YP_921131.1|   5 ELKSYRENVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSESRSRLAE 57 
                                    44444455555555555555555555555555555555555555555444433 PP

>> DUF4094  Domain of unknown function (DUF4094)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   3.9    0.0015      0.25      52      87 ..      17      53 ..       1      54 [. 0.61

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0015
                        DUF4094 52 srskdilg.evskthkaiqtLdktissLemeLaaara 87
                                   +++ + l+ + s +++++++L+ ++ssLe +L+  r+
  gi|119720636|ref|YP_921131.1| 17 QEDVKSLQvKLSSAQTDLSALKAQVSSLEAQLSESRS 53
                                   2233556667777777777778888888888887776 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   0.00021     0.034     163     221 ..       5      62 ..       1      88 [. 0.75

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00021
                   Exonuc_VII_L 163 lleekkqrleklasrlkspeellerkrqrldeleerleralkkqlkkkrerleelkerl 221
                                     l++ ++++++l++++ks + +l++++  l+ l++++++ l+ ql+++r+rl e+++r 
  gi|119720636|ref|YP_921131.1|   5 ELKSYRENVTRLQEDVKSLQVKLSSAQTDLSALKAQVSS-LEAQLSESRSRLAEAEARA 62 
                                    566677777777777787777888888888888888877.7777888888877777554 PP

>> SKA1  Spindle and kinetochore-associated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.4   0.00027     0.044       3      51 ..      14      60 ..       7      66 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00027
                                   XXXXX................XXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                           SKA1  3 selrelvslrainqdpallkedlskieaevsaleellnklkkelqeeee 51
                                   + l+e  ++++++ + +++++dls+++a+vs+le +l++ + +l+e e 
  gi|119720636|ref|YP_921131.1| 14 TRLQE--DVKSLQVKLSSAQTDLSALKAQVSSLEAQLSESRSRLAEAEA 60
                                   55666..4555567778889999***********999999999998765 PP

>> HAP1_N  HAP1 N-terminal conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   4.1   0.00025     0.041     222     272 ..       3      53 ..       1      65 [. 0.77

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00025
                         HAP1_N 222 seelarkleelerqqeeissLlaqivdlqqklkelgveneelkqhLaaske 272
                                    +eel++ +e+++r qe+++sL+ ++ + q+ l  l+++   l+++L+ s+ 
  gi|119720636|ref|YP_921131.1|   3 EEELKSYRENVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSESRS 53 
                                    478888888888888888888888888888888888888888888877764 PP

>> Cep57_CLD_2  Centrosome localisation domain of PPC89
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   4.6   0.00022     0.036       4      49 ..      12      57 ..       9      63 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 0.00022
                    Cep57_CLD_2  4 evktLqnrLdsltrklqvheeelkrLnkERdsalrqLgvAyeelne 49
                                    v++Lq++ +sl+ kl+++++ l +L +  +s + qL++ +++l e
  gi|119720636|ref|YP_921131.1| 12 NVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSESRSRLAE 57
                                   5899**********************************99998876 PP

>> EMP24_GP25L  emp24/gp25L/p24 family/GOLD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   0.00027     0.044     107     171 ..      14      78 ..       2      87 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00027
                    EMP24_GP25L 107 sakkekletleselkkleekldsikreqkylrereerlrdtnestnsrvvwwsilqllvlvlvav 171
                                    +  +e++++l+++l   ++ l+ +k ++ +l+++ ++ r  + +++ r   + ++ ++v ++v++
  gi|119720636|ref|YP_921131.1|  14 TRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSESRSRLAEAEARAQLVGVAGTVVGLVVGF 78 
                                    34489999999999999999999999999999999999999999999999999999999888876 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   3.2   0.00042      0.07       8      62 ..       4      60 ..       1      61 [. 0.68

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00042
                   ABC_tran_CTD  8 releeleaeIeaLEeeiaeleaeladpelysdp..eklaelsaeleeleaeLeelye 62
                                    el+   +   +L+e+ ++l+ +l++++       ++++ l a+l e ++ L+e+++
  gi|119720636|ref|YP_921131.1|  4 EELKSYRENVTRLQEDVKSLQVKLSSAQTDLSAlkAQVSSLEAQLSESRSRLAEAEA 60
                                   68999999999**************99833112244455555555555555555555 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   2.8   0.00035     0.057     351     403 ..       4      56 ..       2      65 .. 0.45

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00035
                                    HHHHHHHHHHHHHHHHHS-SS---STTGGGTHHHHHHHHHHHHHHHHHHHHHH CS
                           EzrA 351 kelkelekdyeeleekleekkvaYSelqeeleeleekleeieekqeeileslk 403
                                    +elk+ ++++ +l+e++++ +v  S+ q +l  l+ +++ +e ++ e +  l+
  gi|119720636|ref|YP_921131.1|   4 EELKSYRENVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSESRSRLA 56 
                                    44444444444444444444444444444444444444444444444333332 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.5   0.00035     0.058      26      84 ..       7      61 ..       4      76 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00035
                   Baculo_PEP_C 26 rlqnvqilaqlatlldaietqLnalsedlksllaeldt...rldtlltnLtdalnalqdtlr 84
                                   ++   ++ + l++++++++ +L++ ++dl++l a++++   +l+++ ++L +a +      r
  gi|119720636|ref|YP_921131.1|  7 KSYRENV-TRLQEDVKSLQVKLSSAQTDLSALKAQVSSleaQLSESRSRLAEAEA------R 61
                                   5555667.88999999999999999999988766544444455555555555444......3 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.7     0.044       7.3      75     103 ..       3      31 ..       2      33 .. 0.70
   2 ?   11.6   0.7    0.0012       0.2       3      37 ..      23      57 ..      21      64 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.044
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHCCT CS
                    Prefoldin_2  75 ekeiktlekqleklekeleelkeelqkkl 103
                                    e+e+k++ ++ ++l+++++ l+ +l +++
  gi|119720636|ref|YP_921131.1|   3 EEELKSYRENVTRLQEDVKSLQVKLSSAQ 31 
                                    56777777777777777777777776655 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.0012
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    Prefoldin_2  3 linkfqqlqqqlqqlaqqikqletqlkelelvlee 37
                                   l+ k++  q +l++l++q+ +le+ql+e+ + l e
  gi|119720636|ref|YP_921131.1| 23 LQVKLSSAQTDLSALKAQVSSLEAQLSESRSRLAE 57
                                   56677788888888888888888888877665554 PP

>> Tektin  Tektin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   2.4   0.00041     0.067     324     362 ..      11      49 ..       3      58 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00041
                         Tektin 324 eEvkeleetieaLkeklaeaeaslkaLertrleleedia 362
                                    e+v+ l+e++++L+ kl+ a++ l+aL+ + ++le +++
  gi|119720636|ref|YP_921131.1|  11 ENVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLS 49 
                                    6899*******************************9986 PP

>> OEP  Outer membrane efflux protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   6.3   0.00041     0.068     123     183 ..       5      64 ..       2      69 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00041
                            OEP 123 qlelaeealklaekalelaearykaGlislldvlqaqvrllqaraelaeaeqqlqlaraqL 183
                                    +l+ ++e+++++++ ++  + ++    ++l + l aqv+ l+a++++  ++ + + araqL
  gi|119720636|ref|YP_921131.1|   5 ELKSYRENVTRLQEDVKSLQVKLSSAQTDL-SALKAQVSSLEAQLSESRSRLAEAEARAQL 64 
                                    555555555555555555555555555555.555555555555555555555555555554 PP

>> Pox_A_type_inc  Viral A-type inclusion protein repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0    0.0015      0.25       3      21 ..      34      52 ..      32      53 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0015
                 Pox_A_type_inc  3 msrlRsRIsDLErqLseCr 21
                                   +s+l+  +s+LE qLse r
  gi|119720636|ref|YP_921131.1| 34 LSALKAQVSSLEAQLSESR 52
                                   799*************977 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.4   0.00042     0.069      10      47 ..       3      40 ..       2      49 .. 0.79
   2 ?    1.2   2.5       2.7   4.4e+02      53      66 ..      69      82 ..      40      83 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00042
                           XhlA 10 etkldnleervdkleekaaeaeekiknleedlkklesn 47
                                   e++l+++ e v++l+e+    + k+ +++ dl+ l+++
  gi|119720636|ref|YP_921131.1|  3 EEELKSYRENVTRLQEDVKSLQVKLSSAQTDLSALKAQ 40
                                   67788888888888888888888888888888888875 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 2.7
                           XhlA 53 rtiiGalisaviyl 66
                                   +t++G +++++i++
  gi|119720636|ref|YP_921131.1| 69 GTVVGLVVGFAIGY 82
                                   89999999999876 PP

>> Tom5  Mitochondrial import receptor subunit or translocase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   0.00083      0.14       8      35 ..      47      74 ..      43      76 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00083
                           Tom5  8 qpSeeEikaaeaeArqtvknfaaaaalL 35
                                   q+Se   ++aeaeAr+++  +a +++ L
  gi|119720636|ref|YP_921131.1| 47 QLSESRSRLAEAEARAQLVGVAGTVVGL 74
                                   99********************999987 PP

>> Bacillus_HBL  Bacillus haemolytic enterotoxin (HBL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2    0.0005     0.083     137     175 ..      11      49 ..       3      58 .. 0.52

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0005
                   Bacillus_HBL 137 kdsknFktdvdeltsilagdsgvisqlqneiedlqgkik 175
                                    ++++ +++dv+ l+  l++ + ++s+l++++++l+ +++
  gi|119720636|ref|YP_921131.1|  11 ENVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLS 49 
                                    344555555555555555555555555555555554443 PP

>> TSC22  TSC-22/dip/bun family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.3   0.00066      0.11      13      46 ..      10      43 ..       8      56 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00066
                          TSC22 13 rEeVevLkekIkeLeernseleeENslLkalasp 46
                                   rE V  L+e +k L+ + s  +++ s Lka++s+
  gi|119720636|ref|YP_921131.1| 10 RENVTRLQEDVKSLQVKLSSAQTDLSALKAQVSS 43
                                   9****************************99986 PP

>> CCDC144C  CCDC144C protein coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   4.8   0.00061       0.1      78     125 ..       5      52 ..       1      64 [. 0.55

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00061
                       CCDC144C  78 kLekekqnkerleaevesyrsrLaaAiqdheqsqtskrdlelalqrer 125
                                    +L++ ++n  rl+++v+s++ +L++A  d+   ++  + le +l  +r
  gi|119720636|ref|YP_921131.1|   5 ELKSYRENVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSESR 52 
                                    555555555555555555555555555555555555555555554444 PP

>> MT  Microtubule-binding stalk of dynein motor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00051     0.083     225     263 ..      22      60 ..       6      82 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00051
                             MT 225 kanaelaaaqeklaaikakiaelnanlaeltaafekata 263
                                      + +l++aq  l+a+ka+++ l+a+l+e  +++  a a
  gi|119720636|ref|YP_921131.1|  22 SLQVKLSSAQTDLSALKAQVSSLEAQLSESRSRLAEAEA 60 
                                    456678899999999999999999999999888877765 PP

>> FemAB  FemAB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00053     0.088     241     311 ..       3      71 ..       1      83 [. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00053
                          FemAB 241 aeylkelqekleklekklakleekleknpe..kkkkkklkelekqlaslekelkeaeefiekdgeevvlaaal 311
                                    +e lk+++e+   l+++++ l+ kl+ +++  +  k +++ le ql++ + +l+eae   +     v +a+++
  gi|119720636|ref|YP_921131.1|   3 EEELKSYRENVTRLQEDVKSLQVKLSSAQTdlSALKAQVSSLEAQLSESRSRLAEAEARAQL----VGVAGTV 71 
                                    6778899999999*********9999999999999999999****99999999999985444....4444443 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00061       0.1       5      58 ..       7      60 ..       3      78 .. 0.48

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00061
                          TMPIT  5 eelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkk 58
                                   ++ ++++ +l+e  k+++ kl + ++  s+++ ++++ + +l+e +s+l + ++
  gi|119720636|ref|YP_921131.1|  7 KSYRENVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSESRSRLAEAEA 60
                                   444444444444444444444444444444444444444444444444444333 PP

>> Swi5  Swi5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.2      0.35        58       4      24 ..      12      32 ..       2      36 .. 0.50
   2 ?   12.0   0.8     0.001      0.17       2      34 ..      31      63 ..      30      68 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.35
                                   HHHHHHHHHHHHHHHHHHHHH CS
                           Swi5  4 eikeleeqleelekelaelke 24
                                   ++ +l+e +++l+ +l++++ 
  gi|119720636|ref|YP_921131.1| 12 NVTRLQEDVKSLQVKLSSAQT 32
                                   344445555555555544444 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.001
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHH CS
                           Swi5  2 eaeikeleeqleelekelaelkeelkekkdpee 34
                                   ++++++l++q+++le++l+e +++l e ++ ++
  gi|119720636|ref|YP_921131.1| 31 QTDLSALKAQVSSLEAQLSESRSRLAEAEARAQ 63
                                   78999********************98876555 PP

>> COG6  Conserved oligomeric complex COG6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   2.4   0.00066      0.11      44      94 ..       4      54 ..       2      66 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00066
                           COG6 44 eqLkriesdveklnelcdemkkklssakeetsdlleeaeeLkeekkklelk 94
                                   e+Lk+ +++v+ l+e +++++ klssa+++ s l  ++++L++++ + +++
  gi|119720636|ref|YP_921131.1|  4 EELKSYRENVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSESRSR 54
                                   567777777777777777777777777777777777777777777665554 PP

>> TolA_bind_tri  TolA binding protein trimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   3.6   0.00088      0.15       3      54 ..      10      61 ..       8      64 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00088
                  TolA_bind_tri  3 edrvarLErilearsqlllelqqqlealqqelreLRGqiEelqyqleqleer 54
                                    + v+rL + +++ +  l   q+ l+al++++++L  q+ e + +l ++e r
  gi|119720636|ref|YP_921131.1| 10 RENVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSESRSRLAEAEAR 61
                                   5789999999999999999999999999999999999999999999999888 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.7    0.0012      0.19      41      79 ..       4      42 ..       1      51 [. 0.62
   2 ?    1.7   0.1       1.9   3.1e+02      26      49 ..      38      61 ..      36      64 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0012
                           KxDL 41 erlaklrarfkqgtkllkevkkdLesifkkirslkakla 79
                                   e+l+++r+++ + ++++k+++  L s +  +++lka+++
  gi|119720636|ref|YP_921131.1|  4 EELKSYRENVTRLQEDVKSLQVKLSSAQTDLSALKAQVS 42
                                   566666666666666666666666666666666666654 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 1.9
                           KxDL 26 nkknreLlelnalsqerlaklrar 49
                                   +++   L+++  +s +rla+++ar
  gi|119720636|ref|YP_921131.1| 38 KAQVSSLEAQLSESRSRLAEAEAR 61
                                   455556777777777777777776 PP

>> DUF3552  Domain of unknown function (DUF3552)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   5.5     0.019       3.1      70     130 ..       3      63 ..       1      66 [. 0.74
   2 ?    8.3   0.2    0.0082       1.4       3      24 ..      67      88 ..      65      95 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.019
                        DUF3552  70 ekelkerrnelqrlekRllqkeetLdrkeeslekkeesleekekelkqkeqsleekeeele 130
                                    e+elk+ r++++rl++ +++ + +L   +++l+   +++++ e +l++ +++l e e++++
  gi|119720636|ref|YP_921131.1|   3 EEELKSYRENVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSESRSRLAEAEARAQ 63 
                                    6788888888888888888888888888888888888888888888888887777776654 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0082
                        DUF3552  3 iilaivalvvglvvgylvrkki 24
                                   ++ ++v+lvvg+++gy+v +k+
  gi|119720636|ref|YP_921131.1| 67 VAGTVVGLVVGFAIGYFVSRKR 88
                                   566799***********97765 PP

>> HAUS-augmin3  HAUS augmin-like complex subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   3.7   0.00083      0.14      85     143 ..       4      62 ..       2      70 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00083
                   HAUS-augmin3  85 qelqeLqkekalklkrlnkLqvqaaslqqelrkleeeekeakkklkeaqeelraenaet 143
                                    +el+  ++   ++++  + Lqv  +s+q  l++l+++ ++ + +l e+ + l+++ a++
  gi|119720636|ref|YP_921131.1|   4 EELKSYRENVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSESRSRLAEAEARA 62 
                                    34444444444566666666666666666666666666666666666666666665554 PP

>> CLZ  C-terminal leucine zipper domain of cyclic nucleotide-gated channels
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   3.5    0.0027      0.45      24      60 ..      11      47 ..       1      61 [. 0.43

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0027
                            CLZ 24 aeqkeleekverLessLeaLqtrlarLlaeyessqrk 60
                                   ++   l+e v++L+ +L + qt l  L a+++s +++
  gi|119720636|ref|YP_921131.1| 11 ENVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQ 47
                                   3333333334444444444444444444444444443 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   3.7   0.00084      0.14      68     121 ..       5      58 ..       1      66 [. 0.52

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00084
                          Atg14  68 kleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklkkRrsdlesl 121
                                     l++ +  + +l+e ++ l+ kls+ +  + + k+++++l ++l++ rs+l+ +
  gi|119720636|ref|YP_921131.1|   5 ELKSYRENVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSESRSRLAEA 58 
                                    344444455555555555555555555555555555555555555555554444 PP

>> DUF4763  Domain of unknown function (DUF4763)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   3.6    0.0011      0.17      94     151 ..       5      62 ..       1      65 [. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0011
                        DUF4763  94 lltseqpeileLqrnnhkLrqqlaelqqhlkasrkslkelreslcqekkrlrklqkrl 151
                                    +l+s    +  Lq +   L+ +l+++q  l a +++++ l+++l+++++rl++ ++r+
  gi|119720636|ref|YP_921131.1|   5 ELKSYRENVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSESRSRLAEAEARA 62 
                                    4455667788899999999999999999999999999999999999888888777765 PP

>> Nas2_N  Nas2 N_terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0     0.036       5.9      49      72 ..       6      29 ..       4      34 .. 0.86
   2 ?    3.9   0.1       0.3        49       2      26 ..      35      59 ..      34      72 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.036
                         Nas2_N 49 vrtaRnriiclqNDlkelmkeiee 72
                                    ++ R+++++lq D+k+l+ ++ +
  gi|119720636|ref|YP_921131.1|  6 LKSYRENVTRLQEDVKSLQVKLSS 29
                                   5789**************999876 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.3
                         Nas2_N  2 keLekkkdeiekeieelsevLesqn 26
                                   ++L+++ +++e++++e  ++L +++
  gi|119720636|ref|YP_921131.1| 35 SALKAQVSSLEAQLSESRSRLAEAE 59
                                   6788999999999999999998554 PP

>> Sec2p  GDP/GTP exchange factor Sec2p
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   2.9    0.0015      0.25      44      89 ..       5      50 ..       1      53 [. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0015
                                   HHHHHHHHHHHHHHHHTTHCHCCCHCTSSSSHHHHCTTTXXXXXXX CS
                          Sec2p 44 ekealekkneklkeqLkeketlleslqeqLkeLkevlekmeeesee 89
                                   e ++++++ ++l+e +k  +  l+s q++L+ Lk  ++++e++ +e
  gi|119720636|ref|YP_921131.1|  5 ELKSYRENVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSE 50
                                   55667788899************************99999988665 PP

>> DLP_helical  Dynamin-like helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   2.5    0.0014      0.23      74     125 ..       4      55 ..       2      64 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0014
                    DLP_helical  74 rqlpeaeerleelekevekleesakriekelaelkkeieearielreelkay 125
                                    ++l+  +e++ +l+++v+ l+ +++  +++l+ lk +++  +++l+e+ +++
  gi|119720636|ref|YP_921131.1|   4 EELKSYRENVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSESRSRL 55 
                                    67888999*************************************9987776 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   3.6    0.0019      0.31      35      97 ..       3      62 ..       1      66 [. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0019
                                   HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHH CS
                   Seryl_tRNA_N 35 dekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleael 97
                                   +e+ ++ +  +  lq+  ++l+ + ++a     d ++l+a+v++l ++l++   +l+e+ea+ 
  gi|119720636|ref|YP_921131.1|  3 EEELKSYRENVTRLQEDVKSLQVKLSSAQT---DLSALKAQVSSLEAQLSESRSRLAEAEARA 62
                                   567777778888888888877777666664...789999999999999999999999999875 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.8     0.015       2.5       8      33 ..      12      37 ..       4      38 .. 0.77
   2 ?    9.4   3.4    0.0082       1.4       6      37 ..      31      62 ..      26      63 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.015
                            LPP  8 qVsqLkskvdqlssdvnsakaaaqaa 33
                                   +V +L+++v++l+ +++sa++++ a 
  gi|119720636|ref|YP_921131.1| 12 NVTRLQEDVKSLQVKLSSAQTDLSAL 37
                                   67888888888888888888888765 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0082
                            LPP  6 ssqVsqLkskvdqlssdvnsakaaaqaakeEA 37
                                    +++s+Lk++v++l+++++++++ +++a + A
  gi|119720636|ref|YP_921131.1| 31 QTDLSALKAQVSSLEAQLSESRSRLAEAEARA 62
                                   5799****************999999987665 PP

>> DUF4140  N-terminal domain of unknown function (DUF4140)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   7.2    0.0075       1.2      54      97 ..      22      64 ..       1      65 [. 0.76

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0075
                        DUF4140 54 vervpnreaeeeelkalraeleeledelaaledelaaaearlaf 97
                                     +v  ++a++ +l+al+a++ +le++l++ +++la aear ++
  gi|119720636|ref|YP_921131.1| 22 SLQVKLSSAQT-DLSALKAQVSSLEAQLSESRSRLAEAEARAQL 64
                                   33334444444.499*********************99999876 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   3.3    0.0022      0.36      12      58 ..      13      59 ..       3      64 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0022
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXXXX CS
                           SlyX 12 lafqedtieeLndvvaeqqqqidrlqrqlrllaerlkeleessgase 58
                                   ++ +++ +++L+  +   q ++++l++q+  l+ +l+e +++ +++e
  gi|119720636|ref|YP_921131.1| 13 VTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSESRSRLAEAE 59
                                   55667777888888888888888888888888888877777766554 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   4.5    0.0014      0.24     102     153 ..       3      57 ..       1      64 [. 0.65

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0014
                        UPF0242 102 keeldakeeelerlkeenqqLqekleaiaedfeelkle...leeqLaekqellqe 153
                                    +eel++  e++ rl+e+ ++Lq+kl+ ++ d ++lk +   le+qL e + +l e
  gi|119720636|ref|YP_921131.1|   3 EEELKSYRENVTRLQEDVKSLQVKLSSAQTDLSALKAQvssLEAQLSESRSRLAE 57 
                                    6677777777888888888888888888877776665411156666666665555 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.9    0.0016      0.27      96     149 ..       5      58 ..       2      67 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0016
                         DUF724  96 kLlslkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlall 149
                                    +L s +++ t+l+e  k l+ k++ ++++ + l+++++ le + +e + +la +
  gi|119720636|ref|YP_921131.1|   5 ELKSYRENVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSESRSRLAEA 58 
                                    566777888888888888888888888888888888888888888777766644 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   2.5    0.0014      0.23     278     329 ..       5      56 ..       1      64 [. 0.55

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0014
                          IFT57 278 eyreaqeelsevkekykqlsegvseltrelaeiseelekvkqemeergssmt 329
                                    e+++ +e+++ ++e++k l+ ++s+ +++l+ ++ ++++++ ++ e  s+++
  gi|119720636|ref|YP_921131.1|   5 ELKSYRENVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSESRSRLA 56 
                                    4455555555555555555555555555555555555555555555555554 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   8.3    0.0015      0.25      35      96 ..       6      60 ..       1      64 [. 0.69

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0015
                         APG6_N 35 lkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealee 96
                                   lk+        +e++ +l+e+++ l+ + +++++ L +l+++ ++lea+l++ ++ l++ e+
  gi|119720636|ref|YP_921131.1|  6 LKS-------YRENVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSESRSRLAEAEA 60
                                   333.......3567778888888888888888888888888888888888887777776654 PP

>> Macoilin  Macoilin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   3.5    0.0017      0.28     393     442 ..       8      57 ..       3      65 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0017
                       Macoilin 393 skkdalvrLeadikkLkaeLqasrqteqelrskissltseerslkselqq 442
                                    s +++++rL++d+k L+ +L++++   + l+ ++ssl ++  + +s l +
  gi|119720636|ref|YP_921131.1|   8 SYRENVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSESRSRLAE 57 
                                    55677788888888888888888888888888888888877777776654 PP

>> TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   5.8    0.0021      0.34      24      81 ..       2      56 ..       1      65 [. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0021
                    TMF_TATA_bd 24 lEgElaslkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqerye 81
                                   +E El+s++e+++rl++  ++++   vkl++   +l++lk+++++le++l+e ++r+ 
  gi|119720636|ref|YP_921131.1|  2 REEELKSYRENVTRLQEDVKSLQ---VKLSSAQTDLSALKAQVSSLEAQLSESRSRLA 56
                                   68899999999999888777776...77788888888888888888888888888765 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   2.2    0.0017      0.28       3      49 ..       4      50 ..       2      65 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0017
                          Sec34  3 dqLeskeeecdelleqtdealeqLeeleekfksvsektsslheaceq 49
                                   ++L+s++e++++l e++++++ +L++ +++ ++ +++ ssl+++  +
  gi|119720636|ref|YP_921131.1|  4 EELKSYRENVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSE 50
                                   68999999999999**********99999999999999999976543 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.4     0.002      0.33      47     101 ..       3      57 ..       1      65 [. 0.77

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.002
                                    .HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHHHHHHHHH CS
                          DUF16  47 geqinkleqkvekqgekikelkveqkaqgeelnkvdetleliletLqkinkRlDs 101
                                    +e+++   ++v++++e +k l+v+    + +l +++  + ++   L +   Rl +
  gi|119720636|ref|YP_921131.1|   3 EEELKSYRENVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSESRSRLAE 57 
                                    6777788888888888888888888888888888888888888888887777765 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.3     0.066        11      92     118 ..       5      31 ..       2      36 .. 0.49
   2 ?    6.7   0.4      0.04       6.6      85     115 ..      33      63 ..      29      68 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.066
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Prefoldin  92 qlekleeeleklkdqittleanlaqly 118
                                     l+++ e+++ l++ +++l+++l+  +
  gi|119720636|ref|YP_921131.1|   5 ELKSYRENVTRLQEDVKSLQVKLSSAQ 31 
                                    444455555555555555555544443 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.04
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Prefoldin  85 kleelekqlekleeeleklkdqittleanla 115
                                     l+ l++q+ +le++l + ++++ ++ea ++
  gi|119720636|ref|YP_921131.1|  33 DLSALKAQVSSLEAQLSESRSRLAEAEARAQ 63 
                                    6788899999999999999999999988877 PP

>> Sugarporin_N  Maltoporin periplasmic N-terminal extension
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   8.6    0.0032      0.53      19      54 ..      28      63 ..      22      64 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0032
                   Sugarporin_N 19 svaaaasltiEaRLaaLEkrLqeAeqraqaAearak 54
                                   s a+++++++ a    LE+ L e  +r+++Aeara+
  gi|119720636|ref|YP_921131.1| 28 SSAQTDLSALKAQVSSLEAQLSESRSRLAEAEARAQ 63
                                   44999999**************************98 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1      0.61     1e+02      31      50 ..       4      23 ..       2      29 .. 0.62
   2 ?   10.5   3.8    0.0024      0.39      16      64 ..      17      63 ..      12      65 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.61
                                   HHHHHHHHHHHHHHHHHCC- CS
                          DivIC 31 aelaklkaeneeLeaevkdL 50
                                   +el++ ++   +L++ vk L
  gi|119720636|ref|YP_921131.1|  4 EELKSYRENVTRLQEDVKSL 23
                                   55666666666666666666 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0024
                                   XXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXXXXXXXXX CS
                          DivIC 16 llaykqlkqeiaalqaelaklkaeneeLeaevkdLksdedyieerARse 64
                                   + ++k+l+ ++   q +l +lka+  +Lea++++ +s     e+ AR +
  gi|119720636|ref|YP_921131.1| 17 QEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSESRSR--LAEAEARAQ 63
                                   67888999999999999999999999999999999744..445555544 PP

>> JIP_LZII  JNK-interacting protein  leucine zipper II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   3.0    0.0046      0.76      35      70 ..      13      48 ..       1      63 [. 0.94

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0046
                       JIP_LZII 35 vdeLtsereiLreEleslqkakerlesrikelEeel 70
                                   v+ L+++ ++L+  l+s q+ +++l+ +++ lE++l
  gi|119720636|ref|YP_921131.1| 13 VTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQL 48
                                   88999****************************987 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.7      0.62     1e+02      35      65 ..       7      43 ..       3      59 .. 0.52
   2 ?   10.2   0.3    0.0052      0.85       2      21 ..      68      87 ..      67      88 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.62
                           YtxH 35 ddlkekakelleeakeka......kekaedlkekvke 65
                                   + ++e++++l e++k+        +   ++lk +v++
  gi|119720636|ref|YP_921131.1|  7 KSYRENVTRLQEDVKSLQvklssaQTDLSALKAQVSS 43
                                   5555555555555544444444454444444444444 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0052
                           YtxH  2 lglliGaavGaaaglLlAPk 21
                                   +g ++G++vG a+g++ + k
  gi|119720636|ref|YP_921131.1| 68 AGTVVGLVVGFAIGYFVSRK 87
                                   799*************8866 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   3.8    0.0038      0.62       7      50 ..      14      57 ..       2      72 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0038
                          Spc24  7 friakelsdleselesleselaelkeeleeleeeseekeserve 50
                                    r+++++++l+ +l+s ++ l+ lk+++  le + +e++s+++e
  gi|119720636|ref|YP_921131.1| 14 TRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSESRSRLAE 57
                                   56777788888888888888888888888888888885554433 PP

>> DHR10  Designed helical repeat protein 10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   7.7    0.0034      0.56      44     102 ..       5      63 ..       2      65 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0034
                          DHR10  44 eieaelakleeakkklkelrdaleekeielrelerkeerlqrqlenaeeklerlreqae 102
                                    e+++  + +   ++++k+l+ +l++ +++l+ l+++ + l+ ql+  + +l+ ++ +a+
  gi|119720636|ref|YP_921131.1|   5 ELKSYRENVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSESRSRLAEAEARAQ 63 
                                    44444555555667777777778888888888888888888888888888777777664 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   3.9   0.00081      0.13     125     163 ..      11      62 ..       1      71 [. 0.47

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00081
                        DUF4407 125 eqlaaa.............ltaelaeleaqiaalqaeidaaearldalraea 163
                                    e+++               ++++l++l+aq+++l+a++++ ++rl++++a a
  gi|119720636|ref|YP_921131.1|  11 ENVTRLqedvkslqvklssAQTDLSALKAQVSSLEAQLSESRSRLAEAEARA 62 
                                    2222222223332333333455555555555555555555555555555544 PP

>> DUF3138  Protein of unknown function (DUF3138)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   3.3    0.0083       1.4      22      55 ..      29      62 ..       1      79 [. 0.72

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0083
                        DUF3138 22 atadrikalkaqltalqrqvkelraalaaakaaa 55
                                   +   ++ alkaq+++l++q++e r+ la a+a a
  gi|119720636|ref|YP_921131.1| 29 SAQTDLSALKAQVSSLEAQLSESRSRLAEAEARA 62
                                   3455678888888888888888888887777655 PP

>> YscO  Type III secretion protein YscO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   7.0     0.011       1.8      66     130 ..       4      59 ..       1      66 [. 0.39

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.011
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           YscO  66 kelekvkqqvalLrekeaelekqveeakqqleaerealrqarkelqearraveKfaelarlvrae 130
                                    +el  ++++v+ L+e +++l+ ++  a+  l a   ++ +++++l e r  +++          e
  gi|119720636|ref|YP_921131.1|   4 EELKSYRENVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSESRSRLAEA---------E 59 
                                    3344444444444444444444444444444444444444444444433333332.........2 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   4.9    0.0037       0.6      18      63 ..      11      56 ..       3      62 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0037
                           ZapB 18 dtitlLqmeieeLkeeneelkeenreleeeneqlkeereawqerlk 63
                                   +++t+Lq+ ++ L+ + ++ +    +l+++++ l+++ ++ ++rl 
  gi|119720636|ref|YP_921131.1| 11 ENVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSESRSRLA 56
                                   7899999999999999999999999999999999999999999985 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   1.3    0.0033      0.55     239     286 ..      11      58 ..       2      66 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0033
                       Prominin 239 aelerllenlkeakeqLeqvnklekeLrksgsqLrdglrgvkrdlnqa 286
                                    ++++rl e++k+ + +L++ +  ++ L+ + s L++ l++ + +l +a
  gi|119720636|ref|YP_921131.1|  11 ENVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSESRSRLAEA 58 
                                    678999999999999999999999999999999999999999998765 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   3.7    0.0034      0.55     597     648 ..       9      60 ..       2      67 .. 0.42

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0034
                        DUF3584 597 yaaseeeLrerlqaleealqsaeakqkqaeeelkqlnaeleeakravaeaat 648
                                    y ++ + L+e ++ l+ +l sa+   +++ +++++l+a+l e++  +aea++
  gi|119720636|ref|YP_921131.1|   9 YRENVTRLQEDVKSLQVKLSSAQTDLSALKAQVSSLEAQLSESRSRLAEAEA 60 
                                    3333334444444444444444444444444444444444444444444333 PP

>> Cnn_1N  Centrosomin N-terminal motif 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.6     0.073        12      44      72 ..       5      33 ..       1      35 [. 0.69
   2 ?    7.1   0.3     0.036       5.9      45      71 ..      34      60 ..      29      62 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.073
                         Cnn_1N 44 enielkveveslqkelkekkkllreaeka 72
                                   e+   +++v  lq ++k+++ +l +a+++
  gi|119720636|ref|YP_921131.1|  5 ELKSYRENVTRLQEDVKSLQVKLSSAQTD 33
                                   55566677777888888888888777764 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.036
                         Cnn_1N 45 nielkveveslqkelkekkkllreaek 71
                                   +  lk +v sl+ +l e + +l eae 
  gi|119720636|ref|YP_921131.1| 34 LSALKAQVSSLEAQLSESRSRLAEAEA 60
                                   6679********************996 PP

>> EspB  Enterobacterial EspB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.6    0.0079       1.3     159     199 ..       3      43 ..       1      44 [. 0.91
   2 ?    5.8   1.0     0.075        12      33      73 ..      38      79 ..      35      87 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0079
                           EspB 159 esnleeykktvresqDkiasvlqdlrstardlndlinrvaq 199
                                    e+ l++y ++v++ q+++ s   +l s  +dl  l ++v++
  gi|119720636|ref|YP_921131.1|   3 EEELKSYRENVTRLQEDVKSLQVKLSSAQTDLSALKAQVSS 43 
                                    67899**************************9999888875 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.075
                           EspB 33 eiQkaafqtqkkaIeekkAgAta.allegvlsivlGilgsaa 73
                                   ++Q+ ++++q        A A+a a+l gv+++v G++  +a
  gi|119720636|ref|YP_921131.1| 38 KAQVSSLEAQLSESRSRLAEAEArAQLVGVAGTVVGLVVGFA 79
                                   67888888887766666666655378889*******986654 PP

>> Uso1_p115_C  Uso1 / p115 like vesicle tethering protein, C terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   8.1    0.0087       1.4       7      75 ..       3      62 ..       1      65 [. 0.68

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0087
                    Uso1_p115_C  7 eseaaslkdeneklkaelqslskalesleqkeakkaaesqakeleaenkklekeleklraelkeekeke 75
                                   e+e +s+++  ++l+ +++sl+ +l s++            + l+a++++le +l + r++l+e++ ++
  gi|119720636|ref|YP_921131.1|  3 EEELKSYRENVTRLQEDVKSLQVKLSSAQTD---------LSALKAQVSSLEAQLSESRSRLAEAEARA 62
                                   5555666666666666666666666666666.........88888888888888888888888887765 PP

>> DUF883  Bacterial protein of unknown function (DUF883)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   8.7       0.2        33      34      94 .]      28      87 ..       2      87 .. 0.49

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.2
                         DUF883 34 erleerlerarerlrdaeeavaerakeaaeaaddyVrenPwqavGiAagvGlllGlLlarR 94
                                   + ++  l++++++++ +e ++ e+ ++ ae a+  ++   ++   ++++vG+ +G++++r+
  gi|119720636|ref|YP_921131.1| 28 SSAQTDLSALKAQVSSLEAQLSESRSRLAE-AEARAQLVGVAGTVVGLVVGFAIGYFVSRK 87
                                   223444555555555555555444333332.333444444444444555888888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2004  (0.111774); expected 358.6 (0.02)
Passed bias filter:                     1471  (0.0820458); expected 358.6 (0.02)
Passed Vit filter:                       372  (0.0207485); expected 17.9 (0.001)
Passed Fwd filter:                       109  (0.00607954); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):             109  [number of targets reported over threshold]
# CPU time: 0.72u 0.39s 00:00:01.10 Elapsed: 00:00:00.52
# Mc/sec: 559.94
//
Query:       gi|119720637|ref|YP_921132.1|  [L=94]
Description: hypothetical protein Tpen_1734 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-06   27.6   0.1    3.4e-06   27.2   0.1    1.2  1  DUF2283   Protein of unknown function (DUF2283)


Domain annotation for each model (and alignments):
>> DUF2283  Protein of unknown function (DUF2283)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.1   1.9e-10   3.4e-06       2      46 ..      11      56 ..      10      58 .. 0.92

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 1.9e-10
                        DUF2283  2 itYDpeaDalYIyl.segpveeseevdddiilDfDedGrlvGIEiL 46
                                   + Y pe D+l ++l ++g+   se ++d+i+l +De  +++G+Ei 
  gi|119720637|ref|YP_921132.1| 11 VYYAPELDTLDLWLdEPGRESFSEPLNDNIVLKLDERREVIGLEIV 56
                                   7899**********98888888999********************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.49
# Mc/sec: 579.48
//
Query:       gi|119720638|ref|YP_921133.1|  [L=90]
Description: hypothetical protein Tpen_1735 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       283  (0.0157845); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.48
# Mc/sec: 568.71
//
Query:       gi|119720639|ref|YP_921134.1|  [L=271]
Description: hypothetical protein Tpen_1736 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.5e-25   87.0   0.0    1.1e-24   86.3   0.0    1.4  1  Polbeta       Polymerase beta, Nucleotidyltransferase
    1.5e-20   73.2   0.0      5e-20   71.5   0.0    1.9  3  DUF86         Protein of unknown function DUF86
    2.7e-09   37.2   0.1    5.4e-09   36.2   0.1    1.6  1  NTP_transf_2  Nucleotidyltransferase domain


Domain annotation for each model (and alignments):
>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.3   0.0   1.9e-28   1.1e-24       1      93 []     148     239 ..     148     239 .. 0.98

  Alignments for each domain:
  == domain 1  score: 86.3 bits;  conditional E-value: 1.9e-28
                                    -STTTTHHHHHHHHSTTEEEEEE-S------EEEEEEEESS---HHHHHHHHHHHHHH.SSSEEEEEETTTS-HHHHHHH CS
                        Polbeta   1 ekikeilekekeielaylFGSrakgkareeSDiDlavllkekldleeelelaaelediklgkkvDlvdlneapplllyei 80 
                                    e i  +l++++++ +ay+FGSrakg+ar +SDiD+av+++ + +++  +el++eled+ lg +vDlv+lneap++l+ye+
  gi|119720639|ref|YP_921134.1| 148 ETIARVLSNRSNVVFAYIFGSRAKGQARCRSDIDVAVYTRGEASWKHLVELKNELEDA-LGLDVDLVHLNEAPLTLAYEV 226
                                    68999*****************************************************.9******************** PP

                                    HHS-EEEES-SHH CS
                        Polbeta  81 lkegkllyskdee 93 
                                    +++g l++++d+e
  gi|119720639|ref|YP_921134.1| 227 VSTGVLVLDRDSE 239
                                    **********975 PP

>> DUF86  Protein of unknown function DUF86
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.5   0.0   8.4e-24     5e-20       2     116 ..      11     126 ..      10     129 .. 0.95
   2 ?   -3.5   0.0       1.5   9.2e+03      97     115 ..     146     164 ..     146     165 .. 0.80
   3 ?   -3.0   0.0         1   6.1e+03      76      89 ..     189     202 ..     186     202 .. 0.83

  Alignments for each domain:
  == domain 1  score: 71.5 bits;  conditional E-value: 8.4e-24
                                    HHHHHHHCCHH...TSTSCCGSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----SSC..HHHHHHHTTSS-HHHHHHH CS
                          DUF86   2 kealeklkefteeldeeeflsdeleydavernlqvigEaaidiakhlakklgikkpgdy..ifeilaekgviaeepeepw 79 
                                    +e++ +lke+ ++ + e++  d + + aver+l++++Ea+id + +l++ l+++kp++y  + +il+ +g++++ ++ ++
  gi|119720639|ref|YP_921134.1|  11 LEYIGLLKELRRRASPEALAGDYVVRGAVERYLHLAIEAVIDAGMRLCSLLRLGKPESYrdVARILRGAGMLSAASAGKL 90 
                                    6999*******9999***************************************************************** PP

                                    HHHHCCHHHHHT-CCCTTHHHHHHHHHHTCHHHHHHH CS
                          DUF86  80 rkmiglRNrLvHgYlgidpeivwsiikenlpdleefl 116
                                       +glRN+LvHgY++id+ ++ +++ e +++le+++
  gi|119720639|ref|YP_921134.1|  91 ELWVGLRNVLVHGYARIDYGKLAEALGE-VEELENIV 126
                                    ************************9998.78888776 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.5
                                    THHHHHHHHHHTCHHHHHH CS
                          DUF86  97 dpeivwsiikenlpdleef 115
                                    d e++ ++++++ ++++++
  gi|119720639|ref|YP_921134.1| 146 DAETIARVLSNRSNVVFAY 164
                                    7899999999988887765 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 1
                                    HHHHHHHHCCHHHH CS
                          DUF86  76 eepwrkmiglRNrL 89 
                                    e  w++++ l+N L
  gi|119720639|ref|YP_921134.1| 189 EASWKHLVELKNEL 202
                                    5689******9965 PP

>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   0.1     9e-13   5.4e-09       4      78 ..     150     217 ..     147     249 .. 0.85

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 9e-13
                                    HHHHHHHHTTTSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEE..CEEE CS
                   NTP_transf_2   4 lleelkelepvakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevdlv..trek 78 
                                    +++ l+ ++ v+ +++fGS+a+G a+  SDiD++v+++ e+       + + l+e   +le  lgl vdlv     +
  gi|119720639|ref|YP_921134.1| 150 IARVLSNRSNVVFAYIFGSRAKGQARCRSDIDVAVYTRGEA-------SWKHLVELKNELEDALGLDVDLVhlN--E 217
                                    6677777888******************************5.......5799******************9652..2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1798.29
//
Query:       gi|119720640|ref|YP_921135.1|  [L=257]
Description: hypothetical protein Tpen_1737 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-10   39.9   2.1     0.0051   17.0   0.3    3.8  3  XhlA             Haemolysin XhlA
    8.2e-10   38.8   3.5    0.00028   21.1   0.0    3.7  2  ABC_tran_CTD     ABC transporter C-terminal domain
    8.8e-10   38.4   8.2    8.8e-10   38.4   8.2    1.9  2  Tropomyosin      Tropomyosin
    1.4e-08   35.0   5.4       0.08   13.3   0.0    3.7  3  FlaC_arch        Flagella accessory protein C (FlaC)
    7.9e-08   32.1   0.0       0.01   15.4   0.0    2.4  2  MscS_porin       Mechanosensitive ion channel porin domain
    7.4e-07   29.4  10.3     0.0068   16.7   3.2    4.1  2  CCDC-167         Coiled-coil domain-containing protein 167
    7.8e-07   29.3   4.0    7.8e-07   29.3   4.0    2.2  2  Tropomyosin_1    Tropomyosin like
    1.6e-06   28.0   3.6      0.063   13.2   0.3    4.1  4  Prefoldin_2      Prefoldin subunit
      2e-06   28.3   0.6       0.59   10.5   0.1    3.2  3  CCDC53           Subunit CCDC53 of WASH complex
    2.5e-06   27.8   0.4       0.13   12.7   0.0    4.2  3  Snapin_Pallidin  Snapin/Pallidin
    2.6e-06   27.3  25.9     0.0085   16.0   0.6    5.4  5  Sugarporin_N     Maltoporin periplasmic N-terminal extension
    2.6e-06   27.5   0.4    0.00015   21.7   0.1    2.6  2  DUF1664          Protein of unknown function (DUF1664)
    6.2e-06   26.3   0.2    0.00031   20.8   0.1    2.4  2  Laminin_II       Laminin Domain II
    7.4e-06   25.7   0.1    2.1e-05   24.3   0.1    1.8  1  Exonuc_VII_L     Exonuclease VII, large subunit
    8.7e-06   24.2   0.1     0.0023   16.2   0.1    2.4  2  EzrA             Septation ring formation regulator, EzrA
    1.1e-05   25.9   2.0     0.0018   18.7   0.2    3.1  4  DUF16            Protein of unknown function DUF16
    1.5e-05   25.4   0.0       0.12   12.8   0.0    3.1  2  NPV_P10          Nucleopolyhedrovirus P10 protein
    2.6e-05   24.5   6.1        1.5    9.3   3.9    4.1  3  CLZ              C-terminal leucine zipper domain of cyclic n
      3e-05   24.2   1.4    6.3e-05   23.1   0.4    2.0  2  Nup54            Nucleoporin complex subunit 54
    5.4e-05   23.6  11.0      0.018   15.4   0.5    3.5  4  HrpB7            Bacterial type III secretion protein (HrpB7)
    5.5e-05   22.4   0.2      0.055   12.6   0.1    2.4  2  RmuC             RmuC family
    6.2e-05   23.0   2.2        2.3    8.4   0.0    4.1  3  Prefoldin_3      Prefoldin subunit
    6.6e-05   21.3   0.2    9.7e-05   20.8   0.2    1.3  1  FPP              Filament-like plant protein, long coiled-coi
    9.6e-05   20.4   9.5    0.00015   19.8   9.5    1.3  1  Myosin_tail_1    Myosin tail
    0.00012   22.2   0.2        1.8    8.8   0.0    3.6  2  SesA             N-terminal domain on NACHT_NTPase and P-loop
    0.00012   22.3   0.5      0.035   14.3   0.1    2.7  3  FliJ             Flagellar FliJ protein
    0.00014   21.9   1.7        2.9    8.0   0.3    4.0  4  TRPM_tetra       Tetramerisation domain of TRPM
    0.00016   21.7   0.0      0.013   15.5   0.0    2.4  3  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
    0.00017   21.9   4.3    0.00049   20.4   4.1    1.9  1  ATG16            Autophagy protein 16 (ATG16)
    0.00018   21.2   0.1     0.0056   16.3   0.1    2.7  1  DUF4795          Domain of unknown function (DUF4795)
    0.00025   20.8   6.1       0.36   10.7   0.1    4.6  3  Matrilin_ccoil   Trimeric coiled-coil oligomerisation domain 
    0.00027   18.6   1.5    0.00035   18.3   1.5    1.2  1  DUF3584          Protein of unknown function (DUF3584)
    0.00028   21.2   0.2       0.94    9.9   0.0    3.6  2  UPF0184          Uncharacterised protein family (UPF0184)
    0.00032   20.1   2.3    0.00076   18.9   0.4    2.4  1  GAS              Growth-arrest specific micro-tubule binding
    0.00033   20.9   0.1       0.42   11.0   0.0    3.1  3  Flagellin_C      Bacterial flagellin C-terminal helical regio
    0.00038   20.7  12.8      0.092   13.0   4.9    2.7  2  DUF4164          Domain of unknown function (DUF4164)
    0.00038   20.2   2.1     0.0012   18.6   0.3    2.3  1  Laminin_I        Laminin Domain I
    0.00042   19.4   0.0      0.024   13.6   0.1    1.9  1  IFT57            Intra-flagellar transport protein 57
    0.00049   19.1   1.4    0.00049   19.1   1.4    2.1  2  Spc7             Spc7 kinetochore protein
    0.00058   20.1   0.2        2.9    8.2   0.1    3.8  4  V-SNARE_C        Snare region anchored in the vesicle membran
    0.00083   19.5   6.9       0.24   11.5   1.3    3.4  3  COG2             COG (conserved oligomeric Golgi) complex com
      0.001   18.7   3.6        2.4    7.9   0.1    3.8  4  Vac_Fusion       Chordopoxvirus multifunctional envelope prot
      0.001   18.8   0.1       0.39   10.5   0.0    3.5  3  SKA2             Spindle and kinetochore-associated protein 2
     0.0014   18.7   5.9        7.6    6.7   0.1    4.9  3  DUF2802          Protein of unknown function (DUF2802)
     0.0018   17.1   0.2      0.013   14.3   0.2    2.0  1  Tektin           Tektin family
      0.002   18.0   8.4       0.25   11.2   0.8    3.4  3  DASH_Spc19       Spc19
     0.0021   18.1   5.9     0.0021   18.1   5.9    2.0  2  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
     0.0021   17.8   0.7       0.13   12.0   0.1    2.7  2  DUF4201          Domain of unknown function (DUF4201)
     0.0022   17.8   0.4        3.4    7.5   0.0    3.1  2  Nsp1_C           Nsp1-like C-terminal region
     0.0025   18.1   0.1         14    6.1   0.0    3.5  4  KxDL             Uncharacterized conserved protein
     0.0026   17.6   5.8        6.6    6.7   0.1    5.0  4  MtrG             Tetrahydromethanopterin S-methyltransferase,
     0.0031   16.7   2.6        1.5    7.9   0.1    2.9  3  FH2              Formin Homology 2 Domain
     0.0045   17.3   8.0      0.049   14.0   0.7    3.7  3  Trns_repr_metal  Metal-sensitive transcriptional repressor
      0.005   15.8   0.8        0.2   10.5   0.3    2.1  1  DUF812           Protein of unknown function (DUF812)
     0.0051   16.5   2.0     0.0051   16.5   2.0    2.0  2  Lebercilin       Ciliary protein causing Leber congenital ama
     0.0055   16.3   0.1       0.01   15.4   0.1    1.5  1  Leu_zip          Leucine zipper
     0.0055   16.9   0.1        1.4    9.3   0.0    3.0  1  DUF948           Bacterial protein of unknown function (DUF94
     0.0059   16.7   2.4       0.22   11.6   0.4    3.6  2  DUF2730          Protein of unknown function (DUF2730)
     0.0063   15.8   0.1      0.074   12.3   0.0    2.4  2  HemX             HemX, putative uroporphyrinogen-III C-methyl
     0.0065   16.2   0.1      0.017   14.8   0.0    1.8  1  DUF745           Protein of unknown function (DUF745)
     0.0067   17.0   5.1       0.11   13.1   1.1    3.6  4  SlyX             SlyX
     0.0072   16.1   0.0        4.7    7.0   0.0    3.6  5  DASH_Duo1        DASH complex subunit Duo1
     0.0075   15.6   0.0          1    8.6   0.1    2.2  2  DUF3450          Protein of unknown function (DUF3450)
     0.0083   15.8   1.3       0.56    9.8   0.0    2.7  3  YkyA             Putative cell-wall binding lipoprotein
     0.0085   16.6   2.6       0.15   12.6   0.2    2.5  2  Syntaxin-6_N     Syntaxin 6, N-terminal
     0.0094   14.7   0.2       0.04   12.6   0.1    1.7  1  AAA_13           AAA domain
     0.0099   15.7   2.0      0.034   13.9   0.0    2.4  2  TACC_C           Transforming acidic coiled-coil-containing p
  ------ inclusion threshold ------
       0.01   15.3  12.4       0.36   10.3   2.3    3.8  3  DUF4349          Domain of unknown function (DUF4349)
      0.011   15.2  12.4      0.099   12.1   4.5    2.9  3  DUF3552          Domain of unknown function (DUF3552)
      0.011   15.5   9.9        2.8    7.7   1.5    3.8  3  DUF241           Arabidopsis protein of unknown function
      0.011   15.2   0.5        1.6    8.2   0.1    3.0  4  WASH_WAHD        WAHD domain of WASH complex
      0.012   15.1   4.8      0.015   14.7   2.5    2.4  1  HMMR_N           Hyaluronan mediated motility receptor N-term
      0.012   14.7   2.2        0.1   11.7   0.5    2.6  3  APG17            Autophagy protein Apg17
      0.014   15.6   1.1       0.16   12.1   0.2    2.5  2  EcoEI_R_C        EcoEI R protein C-terminal
      0.015   15.2   2.4         12    5.8   0.6    4.2  3  HSBP1            Heat shock factor binding protein 1
      0.017   15.6   9.1        7.9    7.0   0.1    3.8  2  DUF4140          N-terminal domain of unknown function (DUF41
      0.018   13.9   0.5      0.065   12.1   0.5    1.9  1  Fmp27_WPPW       RNA pol II promoter Fmp27 protein domain
      0.021   14.8   4.6        1.1    9.3   0.1    4.3  3  SNARE            SNARE domain
      0.022   15.2   1.2       0.27   11.7   0.7    2.9  1  Spectrin         Spectrin repeat
      0.023   14.5   5.6      0.043   13.6   5.7    1.6  1  ERM              Ezrin/radixin/moesin family
      0.024   14.7  16.9       0.32   11.1   2.9    3.9  3  DHR10            Designed helical repeat protein 10 domain
      0.025   14.7   0.2       0.33   11.0   0.1    2.6  2  ADIP             Afadin- and alpha -actinin-Binding
      0.027   14.7   5.3       0.55   10.4   2.9    3.0  2  MutS_III         MutS domain III
      0.034   12.6   0.0        2.8    6.2   0.0    2.2  2  Sec3_C           Exocyst complex component Sec3
      0.038   12.2   3.2      0.043   12.0   3.2    1.3  1  HOOK             HOOK protein
      0.044   13.3   0.1        1.9    8.0   0.0    2.7  3  Vps5             Vps5 C terminal like
      0.048   13.8   0.0       0.13   12.4   0.0    1.8  1  Fib_alpha        Fibrinogen alpha/beta chain family
      0.062   13.1   0.3       0.43   10.4   0.1    1.9  2  DUF724           Protein of unknown function (DUF724)
      0.063   13.1  11.6        1.3    8.8   1.0    3.9  3  Glyco_H_20C_C    Glycoside Hydrolase 20C C-terminal domain
      0.064   12.6   0.9          4    6.7   1.0    2.4  2  Cluap1           Clusterin-associated protein-1
      0.065   12.5   1.1       0.27   10.4   0.1    2.3  4  ISG65-75         Invariant surface glycoprotein
      0.072   12.2   2.9       0.72    8.9   0.4    2.5  2  CCDC144C         CCDC144C protein coiled-coil region
      0.084   12.1   0.5        3.6    6.8   0.1    2.7  2  FmiP_Thoc5       Fms-interacting protein/Thoc5
      0.098   13.1   5.3        1.3    9.4   5.3    2.2  1  Fez1             Fez1
       0.11   13.3   0.0        3.1    8.6   0.0    2.7  2  Occludin_ELL     Occludin homology domain
       0.11   12.6   3.0        2.4    8.2   2.0    2.6  2  Cep57_CLD        Centrosome localisation domain of Cep57
       0.11   11.7   0.0       0.36   10.0   0.0    1.9  1  TMPIT            TMPIT-like protein
       0.12   12.6   3.3        2.8    8.1   0.6    3.5  3  T3SS_needle_E    Type III secretion system, cytoplasmic E com
       0.13   10.6   8.3       0.19   10.0   7.4    1.7  1  MAD              Mitotic checkpoint protein
       0.14   11.6   4.2        3.1    7.2   4.2    2.8  1  DegS             Sensor protein DegS
       0.16   11.0   0.2         20    4.1   0.0    2.4  2  TelA             Toxic anion resistance protein (TelA)
       0.17   12.0   7.0        1.1    9.3   1.6    3.2  2  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
        0.2   10.7   0.1        5.2    6.0   0.1    2.3  2  DUF2333          Uncharacterized protein conserved in bacteri
       0.21   10.9   2.1       0.64    9.3   1.3    2.2  2  CorA             CorA-like Mg2+ transporter protein
       0.22    9.4   0.1       0.42    8.5   0.1    1.4  2  V_ATPase_I       V-type ATPase 116kDa subunit family
       0.22   11.4  12.0       0.76    9.6   0.6    3.7  3  Dynactin_p22     Dynactin subunit p22
       0.22   11.6   0.2       0.12   12.5   2.9    3.5  2  TolA_bind_tri    TolA binding protein trimerisation
       0.25   10.9   3.5          1    8.9   1.2    2.7  2  PTRF_SDPR        PTRF/SDPR family
       0.33   11.2  11.3        8.6    6.7   3.4    4.2  3  Rx_N             Rx N-terminal domain
       0.38   10.3   6.7       0.13   11.8   1.6    2.5  1  PspA_IM30        PspA/IM30 family
       0.54   10.2  11.8       0.16   11.9   3.3    3.0  3  YscO             Type III secretion protein YscO
       0.69    9.1   5.8       0.14   11.4   0.5    2.0  2  MPS2             Monopolar spindle protein 2
       0.78    9.9  11.4         18    5.5   0.2    5.1  4  GreA_GreB_N      Transcription elongation factor, N-terminal
       0.84    9.8   8.1        3.5    7.8   3.9    3.4  1  Uds1             Up-regulated During Septation
       0.91    9.8  12.3        2.6    8.3   5.1    3.0  2  Cortex-I_coil    Cortexillin I, coiled coil
          1    9.8  19.9        7.2    7.0   1.9    6.0  5  HalX             HalX domain
        2.3    8.3   9.2         33    4.6   0.1    4.3  4  Tnp_22_trimer    L1 transposable element trimerization domain
        2.5    8.4  10.8        3.6    7.9   1.9    3.2  4  TMF_TATA_bd      TATA element modulatory factor 1 TATA bindin
        3.3    8.2  11.0       0.84   10.2   3.9    2.8  3  APG6_N           Apg6 coiled-coil region
        3.5    8.0   7.5       0.48   10.8   0.2    2.8  1  DUF4200          Domain of unknown function (DUF4200)
        3.6    8.0  16.1         77    3.7   1.4    5.9  4  Val_tRNA-synt_C  Valyl tRNA synthetase tRNA binding arm
        3.6    7.4   9.7         11    5.9   2.8    2.5  2  CEP63            Centrosomal protein of 63 kDa
        3.6    7.4   7.2          2    8.3   0.1    3.5  3  Asp4             Accessory secretory protein Sec Asp4
        8.1    6.6   5.9         11    6.1   0.4    3.1  2  PspB             Phage shock protein B


Domain annotation for each model (and alignments):
>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.3   3.5e-05    0.0051       2      41 ..      12      51 ..       8      56 .. 0.73
   2 !   12.3   0.2     0.001      0.14       2      43 ..      54      95 ..      53     105 .. 0.77
   3 !    9.3   0.0     0.009       1.3       3      46 ..      90     133 ..      88     136 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.5e-05
                           XhlA  2 ikerlerietkldnleervdkleekaaeaeekiknleedl 41
                                   i  rl r+e++l   e+r++ +e + +++ee+++++ee+l
  gi|119720640|ref|YP_921135.1| 12 INARLDRVEERLGGVEKRLEGVEGRLDKVEERLESVEENL 51
                                   6667777777777777777777777777777777777777 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.001
                           XhlA  2 ikerlerietkldnleervdkleekaaeaeekiknleedlkk 43
                                   ++erl++ e++l +le r++k+e + +  e +++ +e+ l +
  gi|119720640|ref|YP_921135.1| 54 VQERLTKAERRLADLEGRLSKVEGRLEALERRVDGVEKALGD 95
                                   688888888888888888888888888888887777776654 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.009
                           XhlA   3 kerlerietkldnleervdkleekaaeaeekiknleedlkkles 46 
                                    ++ l  + ++ld  e r++++e + + ae+++  +e+ l+k es
  gi|119720640|ref|YP_921135.1|  90 EKALGDVGERLDAVEARLSRVEGRLEGAESRLAGVEHGLEKVES 133
                                    56677778889999999999999999999999999888888876 PP

>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.5   3.4e-05    0.0049       4      63 ..       3      64 ..       1      72 [. 0.62
   2 !   21.1   0.0   1.9e-06   0.00028       5      63 ..      60     120 ..      57     123 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.4e-05
                   ABC_tran_CTD  4 ykeqreleeleaeIeaLEeeiaeleaeladpelysdp..eklaelsaeleeleaeLeelyer 63
                                   y   r++e++ a++++ Ee++  +e++l+  e   d   e+l  + + l  +++ L +++ r
  gi|119720640|ref|YP_921135.1|  3 YWLGRKFEKINARLDRVEERLGGVEKRLEGVEGRLDKveERLESVEENLGGVQERLTKAERR 64
                                   66678888888888888888888888888888554443444555555555555555555444 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 1.9e-06
                   ABC_tran_CTD   5 keqreleeleaeIeaLEeeiaeleaeladpely.sdp.eklaelsaeleeleaeLeelyer 63 
                                    k +r+l+ le ++ + E ++++le ++   e    d  e+l ++ a+l ++e  Le +++r
  gi|119720640|ref|YP_921135.1|  60 KAERRLADLEGRLSKVEGRLEALERRVDGVEKAlGDVgERLDAVEARLSRVEGRLEGAESR 120
                                    6678888888888888888888888888888765666799999999999999999998887 PP

>> Tropomyosin  Tropomyosin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   8.2   6.1e-12   8.8e-10      23     155 ..       8     140 ..       4     147 .. 0.94
   2 ?   -1.4   0.5       8.7   1.3e+03      91     112 ..     200     221 ..     176     250 .. 0.57

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 6.1e-12
                    Tropomyosin  23 kleeaekkaekaeaEvaalnrriqlleeelerteerleealekLeeaekaadeserarKvlEnrelkdeekleeleaqlk 102
                                    k e+ +++ ++ e+    +++r++ +e  l+++eerle+  e L  ++++    er +  lE r  k e +le le++++
  gi|119720640|ref|YP_921135.1|   8 KFEKINARLDRVEERLGGVEKRLEGVEGRLDKVEERLESVEENLGGVQERLTKAERRLADLEGRLSKVEGRLEALERRVD 87 
                                    6778888999999999999************************************************************* PP

                    Tropomyosin 103 eakeiaeeadrkyeEvarklvvvesdLeraeeraeaaeskiveLeeeLkvvgn 155
                                      ++   +  ++++ v+ +l  ve+ Le ae+r    e+  ++ e++L  v +
  gi|119720640|ref|YP_921135.1|  88 GVEKALGDVGERLDAVEARLSRVEGRLEGAESRLAGVEHGLEKVESRLSRVVK 140
                                    *********************************************99987765 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 8.7
                    Tropomyosin  91 eekleeleaqlkeakeiaeead 112
                                    e  +ee e+ l+ a++  ee  
  gi|119720640|ref|YP_921135.1| 200 EFTMEEAEDFLRLARKAVEEHG 221
                                    3334444444444444444444 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.6   0.00065     0.094       1      37 [.      15      51 ..      15      60 .. 0.91
   2 ?    9.0   0.0     0.013       1.9       6      36 ..      62      92 ..      56      98 .. 0.58
   3 !   13.3   0.0   0.00056      0.08       1      42 [.      99     140 ..      99     144 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00065
                      FlaC_arch  1 ridelEnklsklsteletvkkeneelsksveelkenV 37
                                   r+d +E++l+ ++ +le v+  ++++++ +e ++en 
  gi|119720640|ref|YP_921135.1| 15 RLDRVEERLGGVEKRLEGVEGRLDKVEERLESVEENL 51
                                   78999*****************************996 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.013
                      FlaC_arch  6 Enklsklsteletvkkeneelsksveelken 36
                                   E +l +l+ +l+ v+  +e l+  v+ +++ 
  gi|119720640|ref|YP_921135.1| 62 ERRLADLEGRLSKVEGRLEALERRVDGVEKA 92
                                   5566666666666666666666666655554 PP

  == domain 3  score: 13.3 bits;  conditional E-value: 0.00056
                      FlaC_arch   1 ridelEnklsklsteletvkkeneelsksveelkenVkdlls 42 
                                    r+d +E +ls+++ +le +++ +  ++  +e+++ +  ++++
  gi|119720640|ref|YP_921135.1|  99 RLDAVEARLSRVEGRLEGAESRLAGVEHGLEKVESRLSRVVK 140
                                    899**********************************99997 PP

>> MscS_porin  Mechanosensitive ion channel porin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   7.3e-05      0.01      80     138 ..      16      74 ..       7      78 .. 0.77
   2 !   14.2   0.0   0.00016     0.024      80     138 ..      79     137 ..      76     148 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 7.3e-05
                     MscS_porin  80 leeLeqrllqtssqlqelqeqlaqlnsqlvelqtrperaqqqltearqrlqeirnrLns 138
                                    l+  e rl  ++ +l+ ++ +l + +++l + +  +  +q++lt+a +rl++++ rL++
  gi|119720640|ref|YP_921135.1|  16 LDRVEERLGGVEKRLEGVEGRLDKVEERLESVEENLGGVQERLTKAERRLADLEGRLSK 74 
                                    66778888888888888888888888888888888888888888888888888887765 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 0.00016
                     MscS_porin  80 leeLeqrllqtssqlqelqeqlaqlnsqlvelqtrperaqqqltearqrlqeirnrLns 138
                                    le+Le+r++ ++ +l ++ e+l   +++l   + r+e a ++l+     l+++++rL+ 
  gi|119720640|ref|YP_921135.1|  79 LEALERRVDGVEKALGDVGERLDAVEARLSRVEGRLEGAESRLAGVEHGLEKVESRLSR 137
                                    799****************************************************9975 PP

>> CCDC-167  Coiled-coil domain-containing protein 167
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   3.2   4.7e-05    0.0068       5      64 ..      15      71 ..       9      83 .. 0.86
   2 !   11.0   0.5    0.0028      0.41       6      59 ..      86     136 ..      81     203 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.7e-05
                       CCDC-167  5 eIdkleeklascrerLeaverrlrkeelseeeResleeEeaslkeqleenekeLksLrke 64
                                    +d++ee+l  +++rLe ve rl k+e   e+ es+ee ++ ++e+l++ e++L+ L + 
  gi|119720640|ref|YP_921135.1| 15 RLDRVEERLGGVEKRLEGVEGRLDKVE---ERLESVEENLGGVQERLTKAERRLADLEGR 71
                                   679999999999999999999999986...66679*******************999765 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0028
                       CCDC-167   6 IdkleeklascrerLeaverrlrkeelseeeResleeEeaslkeqleenekeLk 59 
                                    +d++e++l ++ erL+ave rl ++e   e   ++e  +a ++  le+ e++L+
  gi|119720640|ref|YP_921135.1|  86 VDGVEKALGDVGERLDAVEARLSRVEGRLE---GAESRLAGVEHGLEKVESRLS 136
                                    677777777777777777777777765554...444444444444444444443 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   4.0   5.4e-09   7.8e-07      10     138 ..      10     142 ..       5     147 .. 0.78
   2 ?   -0.7   0.2       9.8   1.4e+03      49      59 ..     185     195 ..     173     226 .. 0.61

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 5.4e-09
                  Tropomyosin_1  10 eeaqekaeeleekvKeleqenlekeqeiksLtkknqqleeevekleeklkeakekaeesekkktnne....altrkiqlL 85 
                                    e+  ++ + +ee++   e++ +  e  + + +++++ +ee++  ++e+l++a++ + + e + ++ e    al+r+++ +
  gi|119720640|ref|YP_921135.1|  10 EKINARLDRVEERLGGVEKRLEGVEGRLDKVEERLESVEENLGGVQERLTKAERRLADLEGRLSKVEgrleALERRVDGV 89 
                                    44556777777777777777777777777777777777777777777777777777777777777778888999999999 PP

                  Tropomyosin_1  86 EeeleesdkkLkettekLretdvkaeelERkvkaLeqerdewekkyeeleeky 138
                                    E  l +  ++L     +L+ ++ + e  E + + +e+  ++ e+++  + + +
  gi|119720640|ref|YP_921135.1|  90 EKALGDVGERLDAVEARLSRVEGRLEGAESRLAGVEHGLEKVESRLSRVVKGF 142
                                    99999999999999999999999999999999999999999999988776655 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 9.8
                  Tropomyosin_1  49 eevekleeklk 59 
                                    eevekl e l+
  gi|119720640|ref|YP_921135.1| 185 EEVEKLREYLE 195
                                    44444444443 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.3   0.00043     0.063      65      99 ..      17      51 ..       9      61 .. 0.85
   2 ?    6.9   0.0     0.041       5.9      65      97 ..      59      91 ..      52      95 .. 0.55
   3 ?    6.3   0.0     0.061       8.8      71     100 ..     100     129 ..      88     149 .. 0.50
   4 ?   -0.6   0.1       8.5   1.2e+03      57      69 ..     184     196 ..     169     234 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00043
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    Prefoldin_2 65 eeLeerketlekeiktlekqleklekeleelkeel 99
                                   +++eer+  +ek+++ +e +l+k+e++le ++e+l
  gi|119720640|ref|YP_921135.1| 17 DRVEERLGGVEKRLEGVEGRLDKVEERLESVEENL 51
                                   67899999999999999999999999999999998 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.041
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    Prefoldin_2 65 eeLeerketlekeiktlekqleklekeleelke 97
                                   ++ e r+++le +++++e +le le++++ +++
  gi|119720640|ref|YP_921135.1| 59 TKAERRLADLEGRLSKVEGRLEALERRVDGVEK 91
                                   344555555555666666666666555555555 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.061
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    Prefoldin_2  71 ketlekeiktlekqleklekeleelkeelq 100
                                    ++ +e++++++e +le  e +l+ ++  l 
  gi|119720640|ref|YP_921135.1| 100 LDAVEARLSRVEGRLEGAESRLAGVEHGLE 129
                                    444444444444444444444333333332 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 8.5
                                    EE-HHHHHHHHHH CS
                    Prefoldin_2  57 kqdkeevkeeLee 69 
                                    k+++e+++e Le+
  gi|119720640|ref|YP_921135.1| 184 KEEVEKLREYLEK 196
                                    3333333333333 PP

>> CCDC53  Subunit CCDC53 of WASH complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.1    0.0041      0.59      17      49 ..      17      50 ..       7      61 .. 0.81
   2 ?    8.4   0.0     0.019       2.8      17      48 ..      59      90 ..      55     100 .. 0.84
   3 ?    6.6   0.0     0.068       9.9      21      56 ..      98     134 ..      93     148 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0041
                         CCDC53 17 tecEekLvevekrlqrleitlalLEakLsSip.g 49
                                   +  Ee+L  vekrl+ +e +l  +E +L+S++ +
  gi|119720640|ref|YP_921135.1| 17 DRVEERLGGVEKRLEGVEGRLDKVEERLESVEeN 50
                                   67899*************************9853 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.019
                         CCDC53 17 tecEekLvevekrlqrleitlalLEakLsSip 48
                                   t+ E++L+++e rl+++e +l+ LE + + ++
  gi|119720640|ref|YP_921135.1| 59 TKAERRLADLEGRLSKVEGRLEALERRVDGVE 90
                                   56899999999999999999999999988876 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.068
                         CCDC53  21 ekLvevekrlqrleitlalLEakLsSip.gleeveae 56 
                                    e+L  ve rl+r+e +l+  E++L+ ++ gle+ve++
  gi|119720640|ref|YP_921135.1|  98 ERLDAVEARLSRVEGRLEGAESRLAGVEhGLEKVESR 134
                                    6777777777777777777777777777677777665 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0     0.012       1.7      54      88 ..      12      46 ..       6      49 .. 0.83
   2 !   12.7   0.0   0.00089      0.13      43      89 ..      37      82 ..      35      90 .. 0.82
   3 ?    3.4   0.0      0.71     1e+02      64      86 ..      99     121 ..      84     140 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.012
                Snapin_Pallidin 54 vlpdlkeyakKLvnikkrmsslnerlqklkkRaek 88
                                   + ++l++  ++L  ++kr++ ++ rl k+++R+e 
  gi|119720640|ref|YP_921135.1| 12 INARLDRVEERLGGVEKRLEGVEGRLDKVEERLES 46
                                   56688888999999999999999999999999986 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00089
                Snapin_Pallidin 43 LkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqklkkRaekL 89
                                   L+++ee  e +v ++l   +++L+++++r+  l+ rl+k++ R+e L
  gi|119720640|ref|YP_921135.1| 37 LDKVEERLE-SVEENLGGVQERLTKAERRLADLEGRLSKVEGRLEAL 82
                                   566666666.6677888889999999999999999999999999987 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.71
                Snapin_Pallidin  64 KLvnikkrmsslnerlqklkkRa 86 
                                    +L +++ r+s+++ rl+ ++ R+
  gi|119720640|ref|YP_921135.1|  99 RLDAVEARLSRVEGRLEGAESRL 121
                                    44444444444444444444444 PP

>> Sugarporin_N  Maltoporin periplasmic N-terminal extension
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.5    0.0007       0.1      26      54 ..      17      45 ..      12      46 .. 0.88
   2 !   11.9   1.2    0.0011      0.16      28      53 ..      40      65 ..      32      67 .. 0.93
   3 ?    8.6   4.2     0.012       1.8      29      53 ..      62      86 ..      61      87 .. 0.92
   4 ?    7.1   0.9     0.037       5.4      28      40 ..      75      87 ..      71     100 .. 0.85
   5 !   16.0   0.6   5.9e-05    0.0085      25      48 ..     100     123 ..      92     130 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0007
                   Sugarporin_N 26 ltiEaRLaaLEkrLqeAeqraqaAearak 54
                                   + +E+RL   EkrL+  e r+ + e+r++
  gi|119720640|ref|YP_921135.1| 17 DRVEERLGGVEKRLEGVEGRLDKVEERLE 45
                                   569**********************9986 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.0011
                   Sugarporin_N 28 iEaRLaaLEkrLqeAeqraqaAeara 53
                                   +E+RL+  E  L   + r+++Ae+r+
  gi|119720640|ref|YP_921135.1| 40 VEERLESVEENLGGVQERLTKAERRL 65
                                   9***********************97 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.012
                   Sugarporin_N 29 EaRLaaLEkrLqeAeqraqaAeara 53
                                   E RLa+LE rL + e r+ a e+r 
  gi|119720640|ref|YP_921135.1| 62 ERRLADLEGRLSKVEGRLEALERRV 86
                                   89*****************999985 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.037
                   Sugarporin_N 28 iEaRLaaLEkrLq 40
                                   +E RL+aLE r+ 
  gi|119720640|ref|YP_921135.1| 75 VEGRLEALERRVD 87
                                   9*********985 PP

  == domain 5  score: 16.0 bits;  conditional E-value: 5.9e-05
                   Sugarporin_N  25 sltiEaRLaaLEkrLqeAeqraqa 48 
                                    ++++EaRL   E rL+ Ae+r++ 
  gi|119720640|ref|YP_921135.1| 100 LDAVEARLSRVEGRLEGAESRLAG 123
                                    689******************986 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.1   1.1e-06   0.00015      44     122 ..      10      91 ..       5      93 .. 0.88
   2 ?    8.8   0.0     0.011       1.6      61     118 ..      79     136 ..      69     147 .. 0.57

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.1e-06
                        DUF1664  44 esvskqleqvseslaatkrhLs...sridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleri 120
                                    e++  +l++v e l  + ++L+    r+d+v+++l++++e    ++e +t++++ l++++  +++v+   e le +++ +
  gi|119720640|ref|YP_921135.1|  10 EKINARLDRVEERLGGVEKRLEgveGRLDKVEERLESVEENLGGVQERLTKAERRLADLEGRLSKVEGRLEALERRVDGV 89 
                                    678899999999999999888533379***********************************************999998 PP

                        DUF1664 121 ee 122
                                    e+
  gi|119720640|ref|YP_921135.1|  90 EK 91 
                                    85 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.011
                        DUF1664  61 krhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskle 118
                                     + L++r+d v+k l ++ e   ++++ +++v++ l+  ++ +  v++  e++es+l+
  gi|119720640|ref|YP_921135.1|  79 LEALERRVDGVEKALGDVGERLDAVEARLSRVEGRLEGAESRLAGVEHGLEKVESRLS 136
                                    3445555555555555555555555555555555555555555555555555555555 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.1   2.1e-06   0.00031       6      84 ..      10      88 ..       7      96 .. 0.86
   2 ?    3.8   0.0      0.36        53      10      48 ..      98     136 ..      85     196 .. 0.65

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.1e-06
                                   XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH CS
                     Laminin_II  6 aeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleea 84
                                   +++n  +  v+e l +++++le ++  l ++++ +e ++e++   ++ +  A+r   +Le  + +++ +l+ l+ + ++
  gi|119720640|ref|YP_921135.1| 10 EKINARLDRVEERLGGVEKRLEGVEGRLDKVEERLESVEENLGGVQERLTKAERRLADLEGRLSKVEGRLEALERRVDG 88
                                   6788899999999999999999999999999999999999999999999999999999999999999999999988665 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.36
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                     Laminin_II  10 etakevleqlaplsqnlentkeklseinrsveetnekvk 48 
                                    e + +v++ l  ++ +le  ++ l +++  +e+++  ++
  gi|119720640|ref|YP_921135.1|  98 ERLDAVEARLSRVEGRLEGAESRLAGVEHGLEKVESRLS 136
                                    333444444444444444444444444444444443333 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.1   1.4e-07   2.1e-05     143     259 ..      10     131 ..       1     241 [. 0.62

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 1.4e-07
                   Exonuc_VII_L 143 aeleeqleelerrlekaikrlleekkqrleklasrlkspeellerkrqrldeleerleralkkqlkkkrerleelkerlk 222
                                    ++++++l+++e+rl   ++++le  + rl+k+++rl+s ee l   ++rl+++e+rl   l+ +l+k + rle l++r+ 
  gi|119720640|ref|YP_921135.1|  10 EKINARLDRVEERLGG-VEKRLEGVEGRLDKVEERLESVEENLGGVQERLTKAERRLAD-LEGRLSKVEGRLEALERRVD 87 
                                    4444444555444433.233344444444444444444444444444444444444444.44444444444444444442 PP

                   Exonuc_VII_L 223 ...ekleekkerlkklkerle....lleekkerleeleekleal 259
                                       + l +  erl+++++rl+    +le +++rl+ +e+ le++
  gi|119720640|ref|YP_921135.1|  88 gveKALGDVGERLDAVEARLSrvegRLEGAESRLAGVEHGLEKV 131
                                    24433333334444444444333333444444444444444433 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   1.6e-05    0.0023     359     431 ..       8      80 ..       5      83 .. 0.88
   2 !    7.5   0.0    0.0071         1     345     414 ..      78     147 ..      75     226 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.6e-05
                                    HHHHHHHHHS-SS---STTGGGTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSS CS
                           EzrA 359 dyeeleekleekkvaYSelqeeleeleekleeieekqeeileslkslrkdEkrAreqldeikkelkeikrkie 431
                                    ++e+++ +l+  +     ++++le +e +l+++ee++e+++e+l++ ++  ++A+++l++++ +l++++ ++e
  gi|119720640|ref|YP_921135.1|   8 KFEKINARLDRVEERLGGVEKRLEGVEGRLDKVEERLESVEENLGGVQERLTKAERRLADLEGRLSKVEGRLE 80 
                                    67777777777777777899***********************************************998887 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0071
                                    THHHHHHHHHHHHHHHHHHHHHHS-SS---STTGGGTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           EzrA 345 klrelekelkelekdyeeleekleekkvaYSelqeeleeleekleeieekqeeileslkslrkdEkrAre 414
                                    +l+ le++++ +ek + ++ e+l++ ++  S+++ +le +e++l+ +e  +e+++  l+   k  +  +e
  gi|119720640|ref|YP_921135.1|  78 RLEALERRVDGVEKALGDVGERLDAVEARLSRVEGRLEGAESRLAGVEHGLEKVESRLSRVVKGFESHQE 147
                                    67889999*********************************************99999988776665555 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1     0.072        10      71     103 ..       9      41 ..       4      42 .. 0.66
   2 !   18.7   0.2   1.3e-05    0.0018      35     103 ..      36     104 ..      34     121 .. 0.80
   3 !   11.0   0.0    0.0033      0.47      33     101 ..      69     137 ..      65     144 .. 0.89
   4 ?   -0.1   0.0       9.1   1.3e+03      38      67 ..     109     138 ..     104     187 .. 0.59

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.072
                                    HHHHHH.......HHHHHHHHHHHHHHHHHHHC CS
                          DUF16  71 qkaqgeelnkvdetleliletLqkinkRlDsie 103
                                     ++ +++l++v+e l  + + L+ ++ RlD++e
  gi|119720640|ref|YP_921135.1|   9 FEKINARLDRVEERLGGVEKRLEGVEGRLDKVE 41 
                                    444555566777777777777777777777776 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 1.3e-05
                                    HHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHHHHHHHHHHC CS
                          DUF16  35 rLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetleliletLqkinkRlDsie 103
                                    rL k+e+++++ +e++  +++  +k + ++ +l+ +  + + +l+++++ ++ + ++L ++++RlD +e
  gi|119720640|ref|YP_921135.1|  36 RLDKVEERLESVEENLGGVQERLTKAERRLADLEGRLSKVEGRLEALERRVDGVEKALGDVGERLDAVE 104
                                    788888888888888888888888888888888888888888888888888888888888888888877 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.0033
                                    HHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHHHHHHHHH CS
                          DUF16  33 kqrLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetleliletLqkinkRlDs 101
                                    + rL k+e ++++l+ +++ +e++    ge+++  +++    + +l+  ++ l  + + L+k++ Rl +
  gi|119720640|ref|YP_921135.1|  69 EGRLSKVEGRLEALERRVDGVEKALGDVGERLDAVEARLSRVEGRLEGAESRLAGVEHGLEKVESRLSR 137
                                    568999999999999999999999999999999999999999999999999999999999999999976 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 9.1
                                    HHHHHHH...HHHHHHHHHHHHHHHHHHHH CS
                          DUF16  38 kieakvdklgeqinkleqkvekqgekikel 67 
                                    ++e +++  + +++ +e+  ek + ++++ 
  gi|119720640|ref|YP_921135.1| 109 RVEGRLEGAESRLAGVEHGLEKVESRLSRV 138
                                    555555544444444444444444443333 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0     0.012       1.7      17      66 ..      13      59 ..       6      77 .. 0.57
   2 !   12.8   0.0   0.00085      0.12      15      64 ..      74     120 ..      70     138 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.012
                        NPV_P10 17 ddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiLn 66
                                   + ++d +++++  v++ l+    ++ +Ld+  + L+++e+++  +q+ L+
  gi|119720640|ref|YP_921135.1| 13 NARLDRVEERLGGVEKRLEG---VEGRLDKVEERLESVEENLGGVQERLT 59
                                   44455555555555555555...335666666666666666666655555 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00085
                        NPV_P10  15 avddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdi 64 
                                    +v+ +++al+ +vd v++ l dv    e+Lda  a L  +e  +e  ++ 
  gi|119720640|ref|YP_921135.1|  74 KVEGRLEALERRVDGVEKALGDV---GERLDAVEARLSRVEGRLEGAESR 120
                                    788999****************5...59**********999887766555 PP

>> CLZ  C-terminal leucine zipper domain of cyclic nucleotide-gated channels
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   3.9      0.01       1.5      27      69 ..      38      83 ..       5      85 .. 0.58
   2 ?    8.6   1.4     0.016       2.3      19      61 ..      58     100 ..      54     122 .. 0.69
   3 ?    7.6   0.0     0.032       4.7      31      69 ..     105     143 ..     100     151 .. 0.51

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.01
                            CLZ 27 keleekverLessLeaLqtrl...arLlaeyessqrkLkqRitkLE 69
                                   +++ee++e++e++L   q rl   +r la++e   +k + R+++LE
  gi|119720640|ref|YP_921135.1| 38 DKVEERLESVEENLGGVQERLtkaERRLADLEGRLSKVEGRLEALE 83
                                   4556666666666666665441113445555555555555666666 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.016
                            CLZ  19 aakagaeqkeleekverLessLeaLqtrlarLlaeyessqrkL 61 
                                      ka+    +le +++++e++LeaL+ r+  + + +  + ++L
  gi|119720640|ref|YP_921135.1|  58 LTKAERRLADLEGRLSKVEGRLEALERRVDGVEKALGDVGERL 100
                                    5567777889999999999999999999876655555544444 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.032
                            CLZ  31 ekverLessLeaLqtrlarLlaeyessqrkLkqRitkLE 69 
                                     +++r+e++Le  + rla +   +e+++++L + ++  E
  gi|119720640|ref|YP_921135.1| 105 ARLSRVEGRLEGAESRLAGVEHGLEKVESRLSRVVKGFE 143
                                    555555555555555555555555555555544444333 PP

>> Nup54  Nucleoporin complex subunit 54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.4   4.4e-07   6.3e-05      34     134 ..      19     115 ..       7     124 .. 0.88
   2 !    9.7   0.1    0.0059      0.85      32     100 ..      80     147 ..      79     196 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 4.4e-07
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SS---SSHHHHH CS
                          Nup54  34 LakRvkaQqkevaqhrerlkeisdrleeleqkhqletsvrlekakkrhvelshRllrllrkleilrsrgyaldaeEeelr 113
                                    +++R+   +k ++  + rl+++++rle++e ++   +++rl ka +r + l+ Rl ++  +le l++r  ++++    + 
  gi|119720640|ref|YP_921135.1|  19 VEERLGGVEKRLEGVEGRLDKVEERLESVE-ENLGGVQERLTKAERRLADLEGRLSKVEGRLEALERRVDGVEKALGDVG 97 
                                    5677777888999999999***********.777899******************************************* PP

                                    HHHHHHHHHHS-HHH.HHHHH CS
                          Nup54 114 arletleaqlndpaqlkgrvn 134
                                    +rl+++ea+l++   ++gr++
  gi|119720640|ref|YP_921135.1|  98 ERLDAVEARLSR---VEGRLE 115
                                    **********96...345544 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0059
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                          Nup54  32 edLakRvkaQqkevaqhrerlkeisdrleeleqkhqletsvrlekakkrhvelshRllrllrkleilrs 100
                                    e+L++Rv+  +k++    erl++++ rl+ +e  +   + +rl+ + +   + ++Rl r+++  e  + 
  gi|119720640|ref|YP_921135.1|  80 EALERRVDGVEKALGDVGERLDAVEARLSRVE-GRLEGAESRLAGVEHGLEKVESRLSRVVKGFESHQE 147
                                    6899****************************.888899*********************997776554 PP

>> HrpB7  Bacterial type III secretion protein (HrpB7)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.1    0.0059      0.86      94     136 ..       8      50 ..       5      57 .. 0.86
   2 !   15.4   0.5   0.00013     0.018      82     139 ..      73     130 ..      70     136 .. 0.91
   3 ?    7.8   0.2     0.029       4.1      84     125 ..      96     137 ..      90     162 .. 0.66
   4 ?    0.5   0.2         5   7.2e+02      69     107 ..     182     222 ..     160     250 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0059
                          HrpB7  94 elaaarqaldaaedavaatarkiaRndaqidacrerierlrra 136
                                    + ++ +++ld+ e+++  +++++   ++++d+++er+e ++++
  gi|119720640|ref|YP_921135.1|   8 KFEKINARLDRVEERLGGVEKRLEGVEGRLDKVEERLESVEEN 50 
                                    567888999999************************9998765 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 0.00013
                          HrpB7  82 dvlegrvraaeaelaaarqaldaaedavaatarkiaRndaqidacrerierlrraaer 139
                                    + +egr++a+e+++   ++al +  +++ a++++++R +++++  + r++ ++  +e+
  gi|119720640|ref|YP_921135.1|  73 SKVEGRLEALERRVDGVEKALGDVGERLDAVEARLSRVEGRLEGAESRLAGVEHGLEK 130
                                    6899*********************************************998887776 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.029
                          HrpB7  84 legrvraaeaelaaarqaldaaedavaatarkiaRndaqida 125
                                    + +r+ a+ea+l + +++l+ ae ++a ++  + + ++++ +
  gi|119720640|ref|YP_921135.1|  96 VGERLDAVEARLSRVEGRLEGAESRLAGVEHGLEKVESRLSR 137
                                    556666666666666666666666666666666666665544 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 5
                          HrpB7  69 fsiadylacrayrdvlegrvr..aaeaelaaarqaldaaed 107
                                    ++ +++  +r y++   g+ +  +ae  l+ ar+a+++  d
  gi|119720640|ref|YP_921135.1| 182 LTKEEVEKLREYLEKDPGEFTmeEAEDFLRLARKAVEEHGD 222
                                    55555555555555555544311333335555555555544 PP

>> RmuC  RmuC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.1   0.00038     0.055     222     273 ..      10      60 ..       5      78 .. 0.58
   2 ?    7.4   0.0     0.015       2.2     222     278 ..      80     139 ..      74     148 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00038
                           RmuC 222 eaqeknaeeiaellgelydkfekfgedleklgkklekaqksydkavkklegn 273
                                    e+++ + +++ e+lg + +++e+++ +l+k++++le++++++  + ++l+ +
  gi|119720640|ref|YP_921135.1|  10 EKINARLDRVEERLGGVEKRLEGVEGRLDKVEERLESVEENLGGVQERLT-K 60 
                                    56666666666666666666666666666666666666666666333333.2 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.015
                           RmuC 222 eaqeknaeeiaellgelydkfekfgedleklgkklekaqksydkavkkle...gnilrka 278
                                    ea+e++++ + ++lg++ +++  ++++l++++ +le a++ +  + + le   ++++r +
  gi|119720640|ref|YP_921135.1|  80 EALERRVDGVEKALGDVGERLDAVEARLSRVEGRLEGAESRLAGVEHGLEkveSRLSRVV 139
                                    677888888888888888888888888888888888888877765444444434444433 PP

>> Prefoldin_3  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0     0.062       8.9      72      98 ..      11      37 ..       8      38 .. 0.91
   2 ?    5.7   0.1       0.1        15      71      99 .]      38      66 ..      37      66 .. 0.92
   3 ?    8.4   0.0     0.016       2.3      70      98 ..      79     107 ..      71     122 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.062
                    Prefoldin_3 72 lisrRiDYVkqniktlekrleaaenkl 98
                                    i+ R+D V++ +  +ekrle  e +l
  gi|119720640|ref|YP_921135.1| 11 KINARLDRVEERLGGVEKRLEGVEGRL 37
                                   5899******************99988 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.1
                    Prefoldin_3 71 dlisrRiDYVkqniktlekrleaaenkla 99
                                   d ++ R+  V++n+  ++ rl++ae++la
  gi|119720640|ref|YP_921135.1| 38 DKVEERLESVEENLGGVQERLTKAERRLA 66
                                   56899*********************996 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.016
                    Prefoldin_3  70 vdlisrRiDYVkqniktlekrleaaenkl 98 
                                    +++++rR+D V++ +  +  rl+a e +l
  gi|119720640|ref|YP_921135.1|  79 LEALERRVDGVEKALGDVGERLDAVEARL 107
                                    57899999999999999999999999988 PP

>> FPP  Filament-like plant protein, long coiled-coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.2   6.7e-07   9.7e-05     705     814 ..      10     119 ..       5     148 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 6.7e-07
                            FPP 705 enlevelksatenleslkaqlqesEqllaelkseLeslkeskslaetqlkcmkesyesletrateleaelnelkqkieaL 784
                                    e+++++l + +e+l  +  +l+  E  l+++++ Les++e  + +++ l + +    +le r++++e  l+ l+++++ +
  gi|119720640|ref|YP_921135.1|  10 EKINARLDRVEERLGGVEKRLEGVEGRLDKVEERLESVEENLGGVQERLTKAERRLADLEGRLSKVEGRLEALERRVDGV 89 
                                    67888899999999999999999999999999999999999888888899999999999999999999999999999999 PP

                            FPP 785 eveLeeekksheeleakckelqeqlervek 814
                                    e+ L +  +     ea+   ++ +le +e+
  gi|119720640|ref|YP_921135.1|  90 EKALGDVGERLDAVEARLSRVEGRLEGAES 119
                                    999999999999999999988888887764 PP

>> Myosin_tail_1  Myosin tail
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   9.5     1e-06   0.00015     359     563 ..      10     144 ..       6     225 .. 0.58

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1e-06
                  Myosin_tail_1 359 eelseqleqakrskaslekakqaLesenkelqaelkslqqakqdseqkrkkleaqlqelqvklseserqreelaekvskl 438
                                    e+++ +l+++      +ek  + +e    ++++ l+s++++   + ++  k+e +l +l+ +ls+ e + e l+ +v  +
  gi|119720640|ref|YP_921135.1|  10 EKINARLDRVEERLGGVEKRLEGVEGRLDKVEERLESVEENLGGVQERLTKAERRLADLEGRLSKVEGRLEALERRVDGV 89 
                                    45555555555555555555555555555555555555555555555555555555555555555555555555555555 PP

                  Myosin_tail_1 439 qaelesvsslleeaegksiklskdvsslesqlqDtqellqeetrqkLalssrlrqleeeknalkeqleeeeeakknvekq 518
                                    ++ l +v + l+ +e++ ++++  ++  es+l  ++                                            
  gi|119720640|ref|YP_921135.1|  90 EKALGDVGERLDAVEARLSRVEGRLEGAESRLAGVE-------------------------------------------- 125
                                    555555555555555555555555555555555544............................................ PP

                  Myosin_tail_1 519 lstlqaqlsdlkkkleeeasavealeeakkrlqrelealtqrlee 563
                                                               +  +++  l  + + +e+
  gi|119720640|ref|YP_921135.1| 126 --------------------------HGLEKVESRLSRVVKGFES 144
                                    ..........................4444444333333333333 PP

>> SesA  N-terminal domain on NACHT_NTPase and P-loop NTPases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0     0.012       1.8      28      81 ..       9      59 ..       4      86 .. 0.49
   2 ?    8.7   0.0     0.013       1.8      21      55 ..      86     120 ..      79     145 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.012
                           SesA 28 FrevgkrLplvqetLedaksqlesskldedtesaikpvlesckekatkleeife 81
                                   F+++++rL  v+e L  ++++le+ +   d+   +++ les++e++  ++e ++
  gi|119720640|ref|YP_921135.1|  9 FEKINARLDRVEERLGGVEKRLEGVEGRLDK---VEERLESVEENLGGVQERLT 59
                                   5555555555555555555555555444442...33333333333333333333 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.013
                           SesA  21 ikglpeaFrevgkrLplvqetLedaksqlesskld 55 
                                    + g  +a+ +vg+rL  v++ L++++ +le++++ 
  gi|119720640|ref|YP_921135.1|  86 VDGVEKALGDVGERLDAVEARLSRVEGRLEGAESR 120
                                    56788999999999999999999999999988765 PP

>> FliJ  Flagellar FliJ protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.1   0.00024     0.035      13      93 ..       8      83 ..       5      94 .. 0.47
   2 !   13.5   0.0   0.00045     0.065       2      82 ..      60     135 ..      58     148 .. 0.94
   3 ?    3.7   0.0      0.47        68       2      53 ..     102     148 ..     101     197 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 0.00024
                           FliJ 13 elqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqvekareewqearqerkkle 93
                                   ++++ +++l+++e+ +   +k+l+g        +l ++++ +++++e +   ++ l++ae+++   + ++ + + ++++le
  gi|119720640|ref|YP_921135.1|  8 KFEKINARLDRVEERLGGVEKRLEGVE-----GRLDKVEERLESVEENLGGVQERLTKAERRLADLEGRLSKVEGRLEALE 83
                                   344444455555555555555555554.....4444444444444444444444444444444444444444444444444 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00045
                           FliJ   2 eaareLaeaqrelqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqvekaree 81 
                                    +a+r+La  + +l + e +le+le+  +  +k l + +     ++l +++a +s+++ +++ +++ la  e+ +ek +++
  gi|119720640|ref|YP_921135.1|  60 KAERRLADLEGRLSKVEGRLEALERRVDGVEKALGDVG-----ERLDAVEARLSRVEGRLEGAESRLAGVEHGLEKVESR 134
                                    79************************************.....**************************99999998887 PP

                           FliJ  82 w 82 
                                    +
  gi|119720640|ref|YP_921135.1| 135 L 135
                                    6 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.47
                           FliJ   2 eaareLaeaqrelqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqaf 53 
                                    + + +L +++ +l+ ae++l+ +e  +++ +++ls          +   q+f
  gi|119720640|ref|YP_921135.1| 102 AVEARLSRVEGRLEGAESRLAGVEHGLEKVESRLSRVV-----KGFESHQEF 148
                                    67788999999999999999999999999999998887.....555555555 PP

>> TRPM_tetra  Tetramerisation domain of TRPM
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.3      0.02       2.9      11      44 ..       9      42 ..       7      49 .. 0.85
   2 ?    7.0   0.3     0.043       6.2       8      43 ..      41      76 ..      39      82 .. 0.93
   3 ?    5.2   0.0      0.16        23      10      40 ..      85     115 ..      76     119 .. 0.80
   4 ?   -0.3   0.0       8.2   1.2e+03      28      41 ..     124     137 ..     115     139 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.02
                     TRPM_tetra 11 vEnmsmkveevneKenlikaSLqsldfrLgkLed 44
                                    E +  +++ v+e+   +++ L  ++ rL k+e+
  gi|119720640|ref|YP_921135.1|  9 FEKINARLDRVEERLGGVEKRLEGVEGRLDKVEE 42
                                   6888999999999999999999999999999987 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.043
                     TRPM_tetra  8 tERvEnmsmkveevneKenlikaSLqsldfrLgkLe 43
                                    ER E +   ++ v+e+    ++ L +l+ rL+k+e
  gi|119720640|ref|YP_921135.1| 41 EERLESVEENLGGVQERLTKAERRLADLEGRLSKVE 76
                                   5999999***************************98 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.16
                     TRPM_tetra  10 RvEnmsmkveevneKenlikaSLqsldfrLg 40 
                                    Rv+ +   +++v e+  +++a L+ ++ rL+
  gi|119720640|ref|YP_921135.1|  85 RVDGVEKALGDVGERLDAVEARLSRVEGRLE 115
                                    6667777789999999999999999999885 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 8.2
                     TRPM_tetra  28 ikaSLqsldfrLgk 41 
                                    +++ L ++++rL++
  gi|119720640|ref|YP_921135.1| 124 VEHGLEKVESRLSR 137
                                    56779999999987 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   9.1e-05     0.013      34     110 ..      24      95 ..       5     104 .. 0.75
   2 !   10.4   0.0    0.0034      0.49      34     105 ..      66     132 ..      62     144 .. 0.49
   3 ?    4.5   0.0      0.22        32      35      77 ..      95     140 ..      91     184 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 9.1e-05
                   Baculo_PEP_C  34 aqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtnlnsiltnLlssvtNinstLnn 110
                                    + +++ l+ +e++L++++e+l+s    ++++l  + ++Lt+a  +l+ +l+ +L  ++  l  L   v +++++L  
  gi|119720640|ref|YP_921135.1|  24 GGVEKRLEGVEGRLDKVEERLES----VEENLGGVQERLTKAERRLA-DLEGRLSKVEGRLEALERRVDGVEKALGD 95 
                                    55777788888888888887777....78888888888888888888.68888888888888888888888887755 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0034
                   Baculo_PEP_C  34 aqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtnlnsiltnLlssvtNin 105
                                    a+l+  l ++e++L+al+ ++      ++++l ++ ++L++  ++l+  ++ +L++ +s l+     +  ++
  gi|119720640|ref|YP_921135.1|  66 ADLEGRLSKVEGRLEALERRVDG----VEKALGDVGERLDAVEARLS-RVEGRLEGAESRLAGVEHGLEKVE 132
                                    44444444444444444443332....44566666666666666665.555555555555544433333333 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.22
                   Baculo_PEP_C  35 qlatlldaietqLnalsedlksl...laeldtrldtlltnLtdaln 77 
                                    ++ + lda+e +L+ ++ +l+ +   la +++ l+++ ++L++ ++
  gi|119720640|ref|YP_921135.1|  95 DVGERLDAVEARLSRVEGRLEGAesrLAGVEHGLEKVESRLSRVVK 140
                                    4555556666666666665543311144444455555555555444 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   4.1   3.4e-06   0.00049      98     175 ..      38     115 ..       8     122 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 3.4e-06
                          ATG16  98 gelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDElsaLqlqlnqaEeklr 175
                                     + ++rl +++e l   +e+l++ e+rla+le + +++e +l+ +e ++ + ek++ d+ + l+a + +l+ +E +l+
  gi|119720640|ref|YP_921135.1|  38 DKVEERLESVEENLGGVQERLTKAERRLADLEGRLSKVEGRLEALERRVDGVEKALGDVGERLDAVEARLSRVEGRLE 115
                                    456788888888888888888888888888888888888888888888888888888888888888888888888876 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   3.8e-05    0.0056       5     141 ..      40     197 ..       5     226 .. 0.52

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.8e-05
                        DUF4795   5 saellkklqeaieklqeelekleekvkelekrledkekklealkkqieelekvkadkeeveeelaekadkeaLatkvsrd 84 
                                    ++e l+ ++e++  +qe+l k e + ++le+rl++ e  leal+  ++                                
  gi|119720640|ref|YP_921135.1|  40 VEERLESVEENLGGVQERLTKAERRLADLEGRLSKVEGRLEALERRVDGV------------------------------ 89 
                                    22223333333333333333333333333333333333333333333333.............................. PP

                        DUF4795  85 q............fDeakkeLekmleellekleeqeealkkaldtLq................................. 119
                                    +            +++++++ e  le + ++l ++e+ l+k+ + L+                                 
  gi|119720640|ref|YP_921135.1|  90 EkalgdvgerldaVEARLSRVEGRLEGAESRLAGVEHGLEKVESRLSrvvkgfeshqeflidylasegvikektalvvra 169
                                    34444444444455556666666666666666666666666666666666666666666667777777777776666665 PP

                        DUF4795 120 ......eelkekldrlelepLkeqleer 141
                                          + l + l + e+e+L+e+le+ 
  gi|119720640|ref|YP_921135.1| 170 elrsvlSLLSNPLTKEEVEKLREYLEKD 197
                                    5544444444444499999999999854 PP

>> Matrilin_ccoil  Trimeric coiled-coil oligomerisation domain of matrilin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.6      0.21        30      21      44 ..      20      43 ..       8      51 .. 0.57
   2 !   10.7   0.1    0.0025      0.36      18      44 ..      59      85 ..      58      86 .. 0.94
   3 ?    4.4   0.0      0.23        34      25      44 ..      94     113 ..      87     121 .. 0.58

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.21
                                   HHHHHHHHHHHHHHHHHHHHHHHH CS
                 Matrilin_ccoil 21 eseiqaLtqkLeavtkRlealEnk 44
                                   e+++    ++Le v  Rl + E +
  gi|119720640|ref|YP_921135.1| 20 EERLGGVEKRLEGVEGRLDKVEER 43
                                   444444444455555555444444 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0025
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                 Matrilin_ccoil 18 tkVeseiqaLtqkLeavtkRlealEnk 44
                                   tk+e ++ +L  +L+ v  RlealE +
  gi|119720640|ref|YP_921135.1| 59 TKAERRLADLEGRLSKVEGRLEALERR 85
                                   68999********************88 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.23
                                    HHHHHHHHHHHHHHHHHHHH CS
                 Matrilin_ccoil  25 qaLtqkLeavtkRlealEnk 44 
                                     +  ++L+av  Rl   E +
  gi|119720640|ref|YP_921135.1|  94 GDVGERLDAVEARLSRVEGR 113
                                    44555666666666655544 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   1.5   2.4e-06   0.00035     278     438 ..      26     192 ..       5     226 .. 0.57

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.4e-06
                        DUF3584 278 laekqeevqeakaelkqqlrtlede...lkeaidelnqelsaakaklaakeselealeeqkkkyeda..di.eklkadld 351
                                    +++++e v+++  +++++l++ e++   ++e+  +++ +l ++++ l++ e +leale++ +  e+a  d+ e+l a   
  gi|119720640|ref|YP_921135.1|  26 VEKRLEGVEGRLDKVEERLESVEENlggVQERLTKAERRLADLEGRLSKVEGRLEALERRVDGVEKAlgDVgERLDAVEA 105
                                    33444444444444444444444431114555555666677777777777777777777665444432222244444444 PP

                        DUF3584 352 qlpsirseleeleeeldaltekhqdvqekydrrkqkikeeleeeleklkerleaireekdrl.kaaieealealesqlrk 430
                                    +l  ++  le +e +l++++   ++v++++ r ++  +++ e  +  l ++  +i+e+ + + +a+ +++l+ l ++l k
  gi|119720640|ref|YP_921135.1| 106 RLSRVEGRLEGAESRLAGVEHGLEKVESRLSRVVKGFESHQEFLIDYLASE-GVIKEKTALVvRAELRSVLSLLSNPLTK 184
                                    555556666666666666666666666666666655555555555555544.7788877777788888888888888887 PP

                        DUF3584 431 qleaqkee 438
                                    ++ ++ +e
  gi|119720640|ref|YP_921135.1| 185 EEVEKLRE 192
                                    76555544 PP

>> UPF0184  Uncharacterised protein family (UPF0184)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0    0.0065      0.94      28      62 ..       9      46 ..       6      64 .. 0.75
   2 ?    6.5   0.1     0.074        11      29      56 ..      80     107 ..      40     126 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0065
                        UPF0184 28 yeainsmLDqinsaLDalEernDdlnskL...rELles 62
                                   +e in  LD ++  L  +E+r + ++++L   +E les
  gi|119720640|ref|YP_921135.1|  9 FEKINARLDRVEERLGGVEKRLEGVEGRLdkvEERLES 46
                                   78999999999999999999999999988222355665 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.074
                        UPF0184  29 eainsmLDqinsaLDalEernDdlnskL 56 
                                    ea+   +D ++ aL ++ er D ++++L
  gi|119720640|ref|YP_921135.1|  80 EALERRVDGVEKALGDVGERLDAVEARL 107
                                    4444455555555555555555555555 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.4   5.3e-06   0.00076      35     170 ..       9     140 ..       5     151 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 5.3e-06
                            GAS  35 ieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqr 114
                                     e+++++ +r e +l  ++++ +  +  L k+ee +e  +++l   ++   +l+++++rl +le  l++++   e le r
  gi|119720640|ref|YP_921135.1|   9 FEKINARLDRVEERLGGVEKRLEGVEGRLDKVEERLESVEENLGGVQE---RLTKAERRLADLEGRLSKVEGRLEALERR 85 
                                    466667777777777777778888888888888888888777777776...78888888888888888888888888888 PP

                            GAS 115 fekvekerdelykkfeaaiqevqqktglknllLekklkalqeelEkkeaqleevla 170
                                    ++ vek+  ++ ++ +a ++    +++ +    e +l+ +++ lEk e +l+ v++
  gi|119720640|ref|YP_921135.1|  86 VDGVEKALGDVGERLDA-VEARLSRVEGRLEGAESRLAGVEHGLEKVESRLSRVVK 140
                                    88888888888888766.66666777777777888888888888888888887775 PP

>> Flagellin_C  Bacterial flagellin C-terminal helical region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0       2.7   3.9e+02       9      38 ..      14      43 ..       7      46 .. 0.73
   2 !   11.0   0.0    0.0029      0.42       5      47 ..      38      80 ..      34      85 .. 0.87
   3 ?    5.9   0.0      0.11        17      16      50 ..      91     125 ..      81     138 .. 0.60

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 2.7
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHCH CS
                    Flagellin_C  9 tdldkvrselGavqnRlesaitnlkaqsen 38
                                     ld v   lG v++Rle    +l++  e 
  gi|119720640|ref|YP_921135.1| 14 ARLDRVEERLGGVEKRLEGVEGRLDKVEER 43
                                   567778888999999999888888776665 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0029
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHCHHC CS
                    Flagellin_C  5 deaitdldkvrselGavqnRlesaitnlkaqsenlkaaesrle 47
                                   d+  + l++v  +lG vq+Rl++a  +l      l++ e+rle
  gi|119720640|ref|YP_921135.1| 38 DKVEERLESVEENLGGVQERLTKAERRLADLEGRLSKVEGRLE 80
                                   6667788899999***************999999999999987 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.11
                                    HHHHHHHHHHHHHHHHHHHHHCHHHHHHCHHCCHH CS
                    Flagellin_C  16 selGavqnRlesaitnlkaqsenlkaaesrledvD 50 
                                      lG v +Rl+   ++l+     l+ aesrl +v 
  gi|119720640|ref|YP_921135.1|  91 KALGDVGERLDAVEARLSRVEGRLEGAESRLAGVE 125
                                    55666666666666666666666666666666654 PP

>> DUF4164  Domain of unknown function (DUF4164)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   7.4   0.00083      0.12      11      86 ..      10      89 ..       5      92 .. 0.88
   2 !   13.0   4.9   0.00063     0.092       5      79 ..      64     138 ..      60     143 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00083
                        DUF4164 11 trLeaaldsLEka...vdrrleaerkr.deleaeiealgedrsRLaeeLdqaearaarleevnrEvsrrLkaaietirav 86
                                   ++++a ld+ E++   v++rle  + r d++e+++e ++e      e+L++ae r+a le   + v +rL+a+   + +v
  gi|119720640|ref|YP_921135.1| 10 EKINARLDRVEERlggVEKRLEGVEGRlDKVEERLESVEENLGGVQERLTKAERRLADLEGRLSKVEGRLEALERRVDGV 89
                                   5688899999987444689999988888*******************************************998888665 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00063
                        DUF4164   5 eleaaltrLeaaldsLEkavdrrleaerkr.deleaeiealgedrsRLaeeLdqaearaarleevnrEvsrrLkaa 79 
                                    +l++   rL++   +LE a++rr++  +k  +++ +++ a+++  sR + +L +ae r+a +e + + v +rL ++
  gi|119720640|ref|YP_921135.1|  64 RLADLEGRLSKVEGRLE-ALERRVDGVEKAlGDVGERLDAVEARLSRVEGRLEGAESRLAGVEHGLEKVESRLSRV 138
                                    45555666666656665.57888887666669*****************************************876 PP

>> Laminin_I  Laminin Domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.3   8.6e-06    0.0012     157     243 ..      16     105 ..      10     118 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 8.6e-06
                      Laminin_I 157 LsrvqtllqklqeenkaLk...ealrdsLaeyeakLsDlrelleeAaaktrdanrlnlanqanlreiekkkeevseeknq 233
                                    L rv+++l    + +++ +    +++++L+  e++L   +e+l +A+ + +d ++++++++ +l+++e++++ v++   +
  gi|119720640|ref|YP_921135.1|  16 LDRVEERLGGVEKRLEGVEgrlDKVEERLESVEENLGGVQERLTKAERRLADLEGRLSKVEGRLEALERRVDGVEKALGD 95 
                                    66777777766666666542225678999999999999999999999999999999999999999999999999988777 PP

                      Laminin_I 234 leetlktard 243
                                    + e l + ++
  gi|119720640|ref|YP_921135.1|  96 VGERLDAVEA 105
                                    7777765555 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.1   0.00016     0.024     253     325 ..      11      83 ..       5      93 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00016
                          IFT57 253 disktlekiesrEkylnsqleellqeyreaqeelsevkekykqlsegvseltrelaeiseelekvkqemeerg 325
                                    +i+  l+++e+r   ++++le     + +++e+l++v+e++  ++e++++ +r la+++ +l+kv+ ++e  +
  gi|119720640|ref|YP_921135.1|  11 KINARLDRVEERLGGVEKRLEGVEGRLDKVEERLESVEENLGGVQERLTKAERRLADLEGRLSKVEGRLEALE 83 
                                    5666677777777777777777777777777777777777777777777777777777777777776666544 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   1.4   3.4e-06   0.00049     137     239 ..      33     131 ..       5     163 .. 0.41
   2 ?   -0.2   0.2       2.5   3.6e+02     176     216 ..     184     225 ..     154     233 .. 0.60

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 3.4e-06
                           Spc7 137 legLkegleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeie 216
                                    +eg  +++ee+le++ee    ++++  ++++ l +le + +++e +le l+++++ +e    + L  + e+l++++a ++
  gi|119720640|ref|YP_921135.1|  33 VEGRLDKVEERLESVEENLGGVQERLTKAERRLADLEGRLSKVEGRLEALERRVDGVE----KALGDVGERLDAVEARLS 108
                                    1222222222222222222222222222222222333333333333333333222222....233333333333333333 PP

                           Spc7 217 ekkkelaelqeqleeleekieel 239
                                    + + +l+  +++l+ +e  +e++
  gi|119720640|ref|YP_921135.1| 109 RVEGRLEGAESRLAGVEHGLEKV 131
                                    33333333333333333333333 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 2.5
                           Spc7 176 kaeleeeleklqeaaeelesid.keeLeelreelaelkaeie 216
                                    k+e+e+  e l++   e++  + ++ L+ +r++++e+  ++e
  gi|119720640|ref|YP_921135.1| 184 KEEVEKLREYLEKDPGEFTMEEaEDFLRLARKAVEEHGDKYE 225
                                    334444444444455555544435556666666666666555 PP

>> V-SNARE_C  Snare region anchored in the vesicle membrane C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0      0.17        25      35      57 ..      20      42 ..      11      48 .. 0.79
   2 ?    8.2   0.1      0.02       2.9      26      66 .]      46      86 ..      37      86 .. 0.84
   3 ?    0.5   0.0       5.2   7.5e+02      38      56 ..      93     111 ..      90     121 .. 0.67
   4 ?    2.1   0.0       1.6   2.4e+02      37      65 ..     106     134 ..      97     138 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.17
                      V-SNARE_C 35 retLkrarsklhnvanrlgksns 57
                                    e+L+++ ++l +v  rl+k+  
  gi|119720640|ref|YP_921135.1| 20 EERLGGVEKRLEGVEGRLDKVEE 42
                                   57899999999999999999876 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.02
                      V-SNARE_C 26 ailedLhsQretLkrarsklhnvanrlgksnsiLrsikrRv 66
                                   ++ e+L+   e+L  a ++l ++  rl k+   L + +rRv
  gi|119720640|ref|YP_921135.1| 46 SVEENLGGVQERLTKAERRLADLEGRLSKVEGRLEALERRV 86
                                   66688888899999999999999999999999999999995 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 5.2
                      V-SNARE_C  38 Lkrarsklhnvanrlgksn 56 
                                    L+++ ++l  v +rl ++ 
  gi|119720640|ref|YP_921135.1|  93 LGDVGERLDAVEARLSRVE 111
                                    6777777777777777664 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 1.6
                      V-SNARE_C  37 tLkrarsklhnvanrlgksnsiLrsikrR 65 
                                    +L+r+  +l ++ +rl  + + L +++ R
  gi|119720640|ref|YP_921135.1| 106 RLSRVEGRLEGAESRLAGVEHGLEKVESR 134
                                    56777777777777777666666665544 PP

>> COG2  COG (conserved oligomeric Golgi) complex component, COG2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   1.3    0.0017      0.24      62     131 ..      21      91 ..      16      93 .. 0.77
   2 ?    6.5   0.2     0.059       8.5      66     102 ..      53      89 ..      49     119 .. 0.54
   3 ?    7.1   0.3     0.038       5.5      63     112 ..     113     162 ..     107     191 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0017
                           COG2  62 ghLvglqeeleevesplaaarkkvesvreklsereeeveskleeakeleekr.ellklllkldevveklea 131
                                    ++L g++++le ve  l ++ +++esv+e+l   +e++++  +  ++le    ++  +l  l+++v+ +e+
  gi|119720640|ref|YP_921135.1|  21 ERLGGVEKRLEGVEGRLDKVEERLESVEENLGGVQERLTKAERRLADLEGRLsKVEGRLEALERRVDGVEK 91 
                                    57889999999999999999999999999999999999988777777776544666666666666666665 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.059
                           COG2  66 glqeeleevesplaaarkkvesvreklsereeevesk 102
                                    g+qe+l + e  la +  ++++v+  l++ e++v++ 
  gi|119720640|ref|YP_921135.1|  53 GVQERLTKAERRLADLEGRLSKVEGRLEALERRVDGV 89 
                                    5555555555555555555555555555555555433 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.038
                           COG2  63 hLvglqeeleevesplaaarkkvesvreklsereeeveskleeakeleek 112
                                    +L g +++l  ve+ l+++ ++++ v++  + ++e + + l+    ++ek
  gi|119720640|ref|YP_921135.1| 113 RLEGAESRLAGVEHGLEKVESRLSRVVKGFESHQEFLIDYLASEGVIKEK 162
                                    56666666666666666666666666666666555554444433333333 PP

>> Vac_Fusion  Chordopoxvirus multifunctional envelope protein A27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.1     0.016       2.4       2      34 ..      16      48 ..       8      55 .. 0.63
   2 ?    5.4   0.0     0.093        13       6      44 ..      55      93 ..      51     102 .. 0.79
   3 ?    7.6   0.0      0.02       2.8       2      37 ..      79     114 ..      71     117 .. 0.83
   4 ?    0.2   0.0       3.9   5.7e+02       2      18 ..     128     144 ..     126     149 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.016
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Vac_Fusion  2 lkdleerllvlekdfqlvikcckrvnealkRlE 34
                                   l ++eerl  +ek  + v+ +  +v+e+l+ +E
  gi|119720640|ref|YP_921135.1| 16 LDRVEERLGGVEKRLEGVEGRLDKVEERLESVE 48
                                   445666666666666666666666666666655 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.093
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-XXXXXXXXX CS
                     Vac_Fusion  6 eerllvlekdfqlvikcckrvnealkRlEnHleTlRkam 44
                                    erl++ e    +++ + ++v+ +l+ lE+ ++ + ka+
  gi|119720640|ref|YP_921135.1| 55 QERLTKAERRLADLEGRLSKVEGRLEALERRVDGVEKAL 93
                                   678888888888888888888888888888888777765 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.02
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-XX CS
                     Vac_Fusion   2 lkdleerllvlekdfqlvikcckrvnealkRlEnHl 37 
                                    l+ le+r+  +ek   +v ++   v+ +l+R+E  l
  gi|119720640|ref|YP_921135.1|  79 LEALERRVDGVEKALGDVGERLDAVEARLSRVEGRL 114
                                    678899999999999999999999999999998665 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 3.9
                                    HHHHHHHHHHHHHHHHH CS
                     Vac_Fusion   2 lkdleerllvlekdfql 18 
                                    l+++e rl ++ k f+ 
  gi|119720640|ref|YP_921135.1| 128 LEKVESRLSRVVKGFES 144
                                    57889999999888865 PP

>> SKA2  Spindle and kinetochore-associated protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0       2.1     3e+02       8      25 ..       6      23 ..       4      25 .. 0.88
   2 !   10.5   0.0    0.0027      0.39       2      67 ..      28      92 ..      25     103 .. 0.77
   3 ?    2.3   0.0      0.98   1.4e+02       4      27 ..     107     130 ..     104     140 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 2.1
                           SKA2  8 ealFqkaesdLdyvqhrL 25
                                      F+k ++ Ld v++rL
  gi|119720640|ref|YP_921135.1|  6 GRKFEKINARLDRVEERL 23
                                   5689************99 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0027
                           SKA2  2 savdklealFqkaesdLdyvqhrLekefqqsypdnaeNpvkLlerlkkvkeelqaLkeqceellae 67
                                   + ++++e  ++k e+ L+ v++ L    ++ ++ + + ++ L  rl+kv  +l+aL+++++ + ++
  gi|119720640|ref|YP_921135.1| 28 KRLEGVEGRLDKVEERLESVEENLGGVQERLTKAE-RRLADLEGRLSKVEGRLEALERRVDGVEKA 92
                                   56677888888888888888888877766666666.588899999999999999999998877665 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.98
                           SKA2   4 vdklealFqkaesdLdyvqhrLek 27 
                                    ++ +e  ++ aes L  v+h Lek
  gi|119720640|ref|YP_921135.1| 107 LSRVEGRLEGAESRLAGVEHGLEK 130
                                    667777888888888888888876 PP

>> DUF2802  Protein of unknown function (DUF2802)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1     0.052       7.6       1      25 [.      25      49 ..      24      51 .. 0.91
   2 ?    6.0   0.2     0.088        13       4      25 ..      56      77 ..      53      96 .. 0.60
   3 ?    4.1   0.1      0.35        51       2      23 ..      96     117 ..      88     149 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.052
                        DUF2802  1 gmgqrlaelekrlkqleerleeleq 25
                                   g+++rl+ +e rl+++eerle++e+
  gi|119720640|ref|YP_921135.1| 25 GVEKRLEGVEGRLDKVEERLESVEE 49
                                   6889*****************9986 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.088
                        DUF2802  4 qrlaelekrlkqleerleeleq 25
                                   +rl + e+rl  le rl+++e 
  gi|119720640|ref|YP_921135.1| 56 ERLTKAERRLADLEGRLSKVEG 77
                                   5555555555555555555533 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.35
                        DUF2802   2 mgqrlaelekrlkqleerleel 23 
                                    +g+rl+++e rl+++e rle  
  gi|119720640|ref|YP_921135.1|  96 VGERLDAVEARLSRVEGRLEGA 117
                                    5677777777777777766644 PP

>> Tektin  Tektin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.2   8.8e-05     0.013     250     357 ..      27     131 ..       5     137 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8.8e-05
                         Tektin 250 rkrieetedaknkleeqlkkvleeiaeleknieeLekairdkeaplklaqtRlenRtqRp.nvElcrDeaqyrLveEvke 328
                                    +kr+e +e   +k+ee l+ v+e++  +++ +++ e+ ++d e+ l  ++ Rle+ ++R  +vE     + +rL    + 
  gi|119720640|ref|YP_921135.1|  27 EKRLEGVEGRLDKVEERLESVEENLGGVQERLTKAERRLADLEGRLSKVEGRLEALERRVdGVEKALGDVGERL----DA 102
                                    68888899999999999999999999999999999999999999999999999999999535777776666666....55 PP

                         Tektin 329 leetieaLkeklaeaeaslkaLertrlel 357
                                    +e+ +++ + +l+ ae+ l   e+   ++
  gi|119720640|ref|YP_921135.1| 103 VEARLSRVEGRLEGAESRLAGVEHGLEKV 131
                                    55555566666666666555555555555 PP

>> DASH_Spc19  Spc19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.2      0.03       4.3      70     105 ..      10      45 ..       5      52 .. 0.61
   2 !   11.2   0.8    0.0018      0.25      64     103 ..      46      85 ..      40      98 .. 0.83
   3 ?    5.4   0.4      0.11        16      64      99 ..     102     137 ..      81     197 .. 0.59

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.03
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...... CS
                     DASH_Spc19  70 ekaekeleklerreetLkaklelqegrlsnaesskk 105
                                    ek+++ l++ e+r    +++le  egrl++ e++ +
  gi|119720640|ref|YP_921135.1|  10 EKINARLDRVEERLGGVEKRLEGVEGRLDKVEERLE 45 
                                    666666666666666666777666666666444333 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.0018
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.... CS
                     DASH_Spc19  64 qieellekaekeleklerreetLkaklelqegrlsnaess 103
                                    ++ee+l  +++ l+k err   L+ +l + egrl+  e++
  gi|119720640|ref|YP_921135.1|  46 SVEENLGGVQERLTKAERRLADLEGRLSKVEGRLEALERR 85 
                                    6899999999999999999999999999999999986554 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.11
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     DASH_Spc19  64 qieellekaekeleklerreetLkaklelqegrlsn 99 
                                    ++e  l+++e  le  e+r    +  le+ e+rls+
  gi|119720640|ref|YP_921135.1| 102 AVEARLSRVEGRLEGAESRLAGVEHGLEKVESRLSR 137
                                    344444444444444444444444444444444444 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   5.9   1.4e-05    0.0021       3     119 ..       7     123 ..       6     147 .. 0.90
   2 ?   -0.4   0.3       7.3     1e+03      98     121 ..     170     193 ..     161     205 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.4e-05
                 CENP-F_leu_zip   3 kkklhvlekLKeserkadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsek 82 
                                    +k++++  +L ++e++   ++ + e+ e  l  +ee +e+v+ +    ++ + + +  +  l+ +l++ e  L+al +  
  gi|119720640|ref|YP_921135.1|   7 RKFEKINARLDRVEERLGGVEKRLEGVEGRLDKVEERLESVEENLGGVQERLTKAERRLADLEGRLSKVEGRLEALERRV 86 
                                    688999999999999999************************************************************** PP

                 CENP-F_leu_zip  83 eeLekelqkkqervseLeslnsslenlleekEqekvq 119
                                    + +ek l +  er +  e++ s +e  le +E   + 
  gi|119720640|ref|YP_921135.1|  87 DGVEKALGDVGERLDAVEARLSRVEGRLEGAESRLAG 123
                                    *****************************99987544 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 7.3
                 CENP-F_leu_zip  98 eLeslnsslenlleekEqekvqmk 121
                                    eL s+ s l+n l ++E ek +++
  gi|119720640|ref|YP_921135.1| 170 ELRSVLSLLSNPLTKEEVEKLREY 193
                                    667777777777777777776654 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.1   0.00086      0.13      71     135 ..       8      72 ..       5      77 .. 0.88
   2 ?    3.0   0.0      0.52        76      65     121 ..      79     135 ..      76     141 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00086
                        DUF4201  71 kttktvhalthlkeklhmleselselkkelkekeerlaklrkelykvklerdklrkqneklkqqg 135
                                    k  k   +l  + e+l  +e+ l+  + +l++ eerl++++++l  v+++ +k++++ ++l+ ++
  gi|119720640|ref|YP_921135.1|   8 KFEKINARLDRVEERLGGVEKRLEGVEGRLDKVEERLESVEENLGGVQERLTKAERRLADLEGRL 72 
                                    5566677788899999*****************************************99998665 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.52
                        DUF4201  65 Lkrlkkkttktvhalthlkeklhmleselselkkelkekeerlaklrkelykvkler 121
                                    L++l +++    +al ++ e+l+++e+ ls+ + +l+  e rla +++ l+kv+ + 
  gi|119720640|ref|YP_921135.1|  79 LEALERRVDGVEKALGDVGERLDAVEARLSRVEGRLEGAESRLAGVEHGLEKVESRL 135
                                    556666666666777788899999999999999999999999999999999988765 PP

>> Nsp1_C  Nsp1-like C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1     0.034       4.9      57     101 ..       7      51 ..       4      60 .. 0.67
   2 ?    7.5   0.0     0.023       3.4      53     111 ..      59     117 ..      54     154 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.034
                         Nsp1_C  57 ekIskLysevleaeqeqnkidqeLeyiesqqdeLeslLdnyEkel 101
                                     k +k++  + ++e+    ++++Le +e   d  e+ L++ E++l
  gi|119720640|ref|YP_921135.1|   7 RKFEKINARLDRVEERLGGVEKRLEGVEGRLDKVEERLESVEENL 51 
                                    556666777777777777777777777777777777777777765 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.023
                         Nsp1_C  53 vengekIskLysevleaeqeqnkidqeLeyiesqqdeLeslLdnyEkeleellsklesq 111
                                     +   ++++L   + ++e   ++++++ + +e+   +  + Ld  E++l+++ ++le +
  gi|119720640|ref|YP_921135.1|  59 TKAERRLADLEGRLSKVEGRLEALERRVDGVEKALGDVGERLDAVEARLSRVEGRLEGA 117
                                    45555667777777788888888888888888888888888888888887777766655 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0       0.2        29      37      74 ..      10      47 ..       5      52 .. 0.55
   2 ?    6.1   0.0     0.093        14      39      76 ..      54      91 ..      45      96 .. 0.80
   3 ?    4.7   0.0      0.25        36      35      78 ..      71     114 ..      56     120 .. 0.65
   4 ?    0.9   0.0         4   5.8e+02      36      57 ..     128     149 ..     114     152 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.2
                           KxDL 37 alsqerlaklrarfkqgtkllkevkkdLesifkkirsl 74
                                   ++ ++rl ++++r+    k l  v   L+++ ++++s 
  gi|119720640|ref|YP_921135.1| 10 EKINARLDRVEERLGGVEKRLEGVEGRLDKVEERLESV 47
                                   34455555555555555555555555555555555555 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.093
                           KxDL 39 sqerlaklrarfkqgtkllkevkkdLesifkkirslka 76
                                   +qerl+k++ r+++    l++v   Le + ++++  ++
  gi|119720640|ref|YP_921135.1| 54 VQERLTKAERRLADLEGRLSKVEGRLEALERRVDGVEK 91
                                   68899999999999999999999999999888887666 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.25
                           KxDL  35 lnalsqerlaklrarfkqgtkllkevkkdLesifkkirslkakl 78 
                                       +++ rl+ l+ r+    k+l +v + L+ +  ++++ + +l
  gi|119720640|ref|YP_921135.1|  71 RLSKVEGRLEALERRVDGVEKALGDVGERLDAVEARLSRVEGRL 114
                                    34566777777777777777777777777777777777766655 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 4
                           KxDL  36 nalsqerlaklrarfkqgtkll 57 
                                     +++++rl+++ + f+++++ l
  gi|119720640|ref|YP_921135.1| 128 LEKVESRLSRVVKGFESHQEFL 149
                                    5789999999999999998765 PP

>> MtrG  Tetrahydromethanopterin S-methyltransferase, subunit G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1     0.045       6.6      11      26 ..       8      23 ..       6      31 .. 0.88
   2 ?    5.3   0.2      0.12        17      13      30 ..      31      48 ..      26      60 .. 0.80
   3 ?    2.5   0.1      0.94   1.4e+02      13      27 ..      73      87 ..      48     100 .. 0.76
   4 ?    2.1   0.0       1.3   1.8e+02      13      30 ..     101     118 ..      89     127 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.045
                           MtrG 11 dfnevkkrLdeieekv 26
                                    f+++++rLd++ee++
  gi|119720640|ref|YP_921135.1|  8 KFEKINARLDRVEERL 23
                                   69************97 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.12
                           MtrG 13 nevkkrLdeieekvefvn 30
                                   + v+ rLd++ee++e v+
  gi|119720640|ref|YP_921135.1| 31 EGVEGRLDKVEERLESVE 48
                                   568899999999999765 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.94
                           MtrG 13 nevkkrLdeieekve 27
                                   ++v+ rL+ +e++v+
  gi|119720640|ref|YP_921135.1| 73 SKVEGRLEALERRVD 87
                                   567777777777776 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 1.3
                           MtrG  13 nevkkrLdeieekvefvn 30 
                                    ++v++rL ++e ++e ++
  gi|119720640|ref|YP_921135.1| 101 DAVEARLSRVEGRLEGAE 118
                                    456666666666666555 PP

>> FH2  Formin Homology 2 Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.1      0.01       1.5     277     343 ..      15      81 ..       7      84 .. 0.86
   2 ?    5.5   0.0     0.055         8     280     351 ..      74     145 ..      68     153 .. 0.79
   3 ?    4.1   0.7      0.14        21     118     156 ..     175     217 ..     166     230 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.01
                                    -HHHHHHHHHHHHHHHHHHHHHHHHCCTTSSTT-THHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            FH2 277 nleslekevkklekglkklekelessekkeepsdkflevlkeflkeaeeklkkleeelkeakelvke 343
                                     l+ +e+ +  +ek+l+ +e  l++ e+  e  ++ l  ++e l++ae++l++le  l++++ ++++
  gi|119720640|ref|YP_921135.1|  15 RLDRVEERLGGVEKRLEGVEGRLDKVEERLESVEENLGGVQERLTKAERRLADLEGRLSKVEGRLEA 81 
                                    5788999999999999999999999999999999999999999999999999999999999988876 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.055
                                    HHHHHHHHHHHHHHHHHHHHHHCCTTSSTT-THHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-- CS
                            FH2 280 slekevkklekglkklekelessekkeepsdkflevlkeflkeaeeklkkleeelkeakelvkelveYfged 351
                                    ++e  +++le++++ +ek l +  +  +  ++ l+ ++  l+ ae++l+ +e  l+++++++ ++v+ f ++
  gi|119720640|ref|YP_921135.1|  74 KVEGRLEALERRVDGVEKALGDVGERLDAVEARLSRVEGRLEGAESRLAGVEHGLEKVESRLSRVVKGFESH 145
                                    667778888888888888888888888888888888889999999999999999999999998888877654 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.14
                                    HHHHHHCGGHHHHHHHHCTCTS...GTTB-HHHHHHHHHTT.S CS
                            FH2 118 enLlkmaPtkeelkklkeykge...vseLseaeqFllelvk.i 156
                                     +Ll +  tkee++kl+ey ++     ++ eae Fl    k +
  gi|119720640|ref|YP_921135.1| 175 LSLLSNPLTKEEVEKLREYLEKdpgEFTMEEAEDFLRLARKaV 217
                                    567888899*******999888788889999999998776655 PP

>> Trns_repr_metal  Metal-sensitive transcriptional repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.5      0.17        24       3      50 ..      10      58 ..       8      65 .. 0.75
   2 !   14.0   0.7   0.00034     0.049       4      48 ..      67     112 ..      64     140 .. 0.91
   3 ?    5.6   0.4      0.15        21       4      20 ..     102     118 ..      99     196 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.17
                                   HHHHHHHHHHHHHHHHHHHHHHT.T--HHHHHHHHHHHHHHHHHHHHHH CS
                Trns_repr_metal  3 kkllnrLkrieGQvrgiqrmiee.dryCidiltQlaAvrsalnkvglel 50
                                   +k+ +rL r+e  + g+++ +e  +    ++   l +v++ l +v++ l
  gi|119720640|ref|YP_921135.1| 10 EKINARLDRVEERLGGVEKRLEGvEGRLDKVEERLESVEENLGGVQERL 58
                                   5788999999999999999999545567777777777777777776655 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 0.00034
                                    HHHHHHHHHHHHHHHHHHHHHT.T--HHHHHHHHHHHHHHHHHHHH CS
                Trns_repr_metal   4 kllnrLkrieGQvrgiqrmiee.dryCidiltQlaAvrsalnkvgl 48 
                                    +l  rL+++eG +++++r ++  ++   d+   l Av++ l +v+ 
  gi|119720640|ref|YP_921135.1|  67 DLEGRLSKVEGRLEALERRVDGvEKALGDVGERLDAVEARLSRVEG 112
                                    5667*****************76999***************99976 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.15
                                    HHHHHHHHHHHHHHHHH CS
                Trns_repr_metal   4 kllnrLkrieGQvrgiq 20 
                                    ++ +rL+r+eG ++g +
  gi|119720640|ref|YP_921135.1| 102 AVEARLSRVEGRLEGAE 118
                                    5779*********9965 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.3    0.0014       0.2     332     417 ..       9      98 ..       6     109 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0014
                         DUF812 332 leelqeqieeleskieeleeeikklessikqveeeleeekeeneelekevklkkk.tlel...lpdaeeniekLqalvea 407
                                     e+++ +++++e+++  +e+ ++ +e ++ +vee le  +e+    ++ + ++++ +++l   l + e+ +e+L++ v+ 
  gi|119720640|ref|YP_921135.1|   9 FEKINARLDRVEERLGGVEKRLEGVEGRLDKVEERLESVEENLGGVQERLTKAERrLADLegrLSKVEGRLEALERRVDG 88 
                                    57888889999999999999999999999999999998888877777666555541444433355688888888888887 PP

                         DUF812 408 saqrlvelak 417
                                     ++ l  +++
  gi|119720640|ref|YP_921135.1|  89 VEKALGDVGE 98 
                                    7777766655 PP

>> Lebercilin  Ciliary protein causing Leber congenital amaurosis disease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   2.0   3.5e-05    0.0051      45     156 ..      27     137 ..      13     148 .. 0.88
   2 ?    0.0   0.3       3.9   5.7e+02      83     155 ..     132     202 ..     127     211 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.5e-05
                     Lebercilin  45 ekaLskyedteaeLpqllarhneEvrvlrerlRksqekerelekklkekeaellrlkdklkklkkLsedknLaer.eeLq 123
                                    ek+L+ +e++  +  + l++ +e +  ++erl k++ +  +le +l + e +l+ l++ ++  +k     +  er + ++
  gi|119720640|ref|YP_921135.1|  27 EKRLEGVEGRLDKVEERLESVEENLGGVQERLTKAERRLADLEGRLSKVEGRLEALERRVDGVEKALG--DVGERlDAVE 104
                                    78999999999999999999999999999999999999999999999999999999999999999663..5667735678 PP

                     Lebercilin 124 kkLeeleakleekeekikeLerkleleeksfrr 156
                                     +L+++e +le +e ++   e+ le  e+  +r
  gi|119720640|ref|YP_921135.1| 105 ARLSRVEGRLEGAESRLAGVEHGLEKVESRLSR 137
                                    89****************999999998888777 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 3.9
                     Lebercilin  83 erelekklkekeaellrlkdklkklkkLsedknLaereeLqkkLeeleakleekeekikeLerkleleeksfr 155
                                    e++l++ +k  e++ + l d l     + e+  L  r+eL + L+ l++ l +  e++++L+ +le    +f+
  gi|119720640|ref|YP_921135.1| 132 ESRLSRVVKGFESHQEFLIDYLASEGVIKEKTALVVRAELRSVLSLLSNPLTK--EEVEKLREYLEKDPGEFT 202
                                    55666666666666666666666666677777888888888888888888864..556667766666655555 PP

>> Leu_zip  Leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1     7e-05      0.01     133     243 ..       7     121 ..       2     155 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 7e-05
                        Leu_zip 133 keierLkeenekLkerlkelEkqatsaleeksklekalkelqkelgekkde.kenskeiskleeklaelkldlek...tl 208
                                     + e+++   ++++erl  +Ek+++ +     k+e+ l++++++lg  +++ ++ ++++++le +l++++  le     +
  gi|119720640|ref|YP_921135.1|   7 RKFEKINARLDRVEERLGGVEKRLEGVEGRLDKVEERLESVEENLGGVQERlTKAERRLADLEGRLSKVEGRLEAlerRV 86 
                                    56778888888899999999999999999999999999999999987655415578899999999999987776611144 PP

                        Leu_zip 209 eektasaksleedlastkhelLkvqeqLelaekeL 243
                                    +  ++   ++ e l     +l +v+ +Le ae+ L
  gi|119720640|ref|YP_921135.1|  87 DGVEKALGDVGERLDAVEARLSRVEGRLEGAESRL 121
                                    44455556667888888888888888888888766 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0    0.0093       1.4      29      58 ..      38      63 ..       3     146 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0093
                         DUF948 29 deaaatieelekqvdpilkevedllakvne 58
                                   d++++++e++e++++     v++ l+k+++
  gi|119720640|ref|YP_921135.1| 38 DKVEERLESVEENLG----GVQERLTKAER 63
                                   222222222222222....22222222333 PP

>> DUF2730  Protein of unknown function (DUF2730)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.4    0.0016      0.22      38      90 ..      33      90 ..       5      96 .. 0.63
   2 ?    6.2   0.1     0.073        10      43      91 ..      73     126 ..      67     135 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0016
                        DUF2730 38 laekveendkrlteletkvenLP.....takdlekLkllladlrgelkaleaevrqls 90
                                   ++  +++ ++rl+++e ++  +       ++ l++L+  l++++g+l+ale++v+ ++
  gi|119720640|ref|YP_921135.1| 33 VEGRLDKVEERLESVEENLGGVQerltkAERRLADLEGRLSKVEGRLEALERRVDGVE 90
                                   4445566677777777666543200001233455556666666666666666555555 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.073
                        DUF2730  43 eendkrlteletkvenLPta.....kdlekLkllladlrgelkaleaevrqlsh 91 
                                    ++ + rl++le +v+ +  a     + l++++  l+ ++g+l+ +e +++ ++h
  gi|119720640|ref|YP_921135.1|  73 SKVEGRLEALERRVDGVEKAlgdvgERLDAVEARLSRVEGRLEGAESRLAGVEH 126
                                    344445555555554443322111134566667777777777777776666666 PP

>> HemX  HemX, putative uroporphyrinogen-III C-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   0.00051     0.074      41     106 ..      41     111 ..       2     137 .. 0.59
   2 ?   -1.3   0.0       7.3   1.1e+03      94     121 ..     188     215 ..     169     223 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00051
                           HemX  41 qqqlaaleqqlaq....veaekeqkqeleerlqqlaeklealekeleqlqkqleelqqqlskvsga.erkd 106
                                    +++l+++e++l+     +++ +++ ++le rl + +++leale++++  +k+l  + ++l +v+++ +r +
  gi|119720640|ref|YP_921135.1|  41 EERLESVEENLGGvqerLTKAERRLADLEGRLSKVEGRLEALERRVDGVEKALGDVGERLDAVEARlSRVE 111
                                    33333333333222222444556666666666666666666666666666666666666666665543333 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 7.3
                           HemX  94 qqlskvsgaerkdWlLaeAdfLlklAgr 121
                                    ++l +   +++ +  + eA+  l+lA +
  gi|119720640|ref|YP_921135.1| 188 EKLREYLEKDPGEFTMEEAEDFLRLARK 215
                                    4455555559999999999999999976 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   0.00012     0.017      67     163 ..      26     122 ..      14     148 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 0.00012
                         DUF745  67 leqelreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaektqlleaAkk 146
                                    +e+ l+  e  ++++++ l+s e+n+  +++  ++a++ l+ l+  l +++ +le +e+  +g+++ l +  + l+a ++
  gi|119720640|ref|YP_921135.1|  26 VEKRLEGVEGRLDKVEERLESVEENLGGVQERLTKAERRLADLEGRLSKVEGRLEALERRVDGVEKALGDVGERLDAVEA 105
                                    56777777888999999999999999999999999999999999999999999999999999999999999999999999 PP

                         DUF745 147 RveeLkkqlkearkdle 163
                                    R+ +++ +l+ a + l+
  gi|119720640|ref|YP_921135.1| 106 RLSRVEGRLEGAESRLA 122
                                    99999999999887665 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0       7.4   1.1e+03       3      45 ..      14      28 ..       6      35 .. 0.48
   2 !   13.1   1.1   0.00078      0.11       2      53 ..      34      85 ..      26      93 .. 0.71
   3 !   11.5   0.2    0.0025      0.36       2      57 ..      62     117 ..      61     134 .. 0.68
   4 ?    2.3   0.0       1.9   2.7e+02       3      47 ..      98     142 ..      96     161 .. 0.66

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 7.4
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           SlyX  3 erleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllae 45
                                   +rl++ E++l                              +++
  gi|119720640|ref|YP_921135.1| 14 ARLDRVEERL----------------------------GGVEK 28
                                   3344444433............................33333 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00078
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXX CS
                           SlyX  2 eerleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkelees 53
                                   e rl++ E++l   e+ +   ++ +++ +++++ l+ +l +++ rl++le +
  gi|119720640|ref|YP_921135.1| 34 EGRLDKVEERLESVEENLGGVQERLTKAERRLADLEGRLSKVEGRLEALERR 85
                                   4577777777777777777777777777777777777777777777777765 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.0025
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXXX CS
                           SlyX   2 eerleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkeleessgas 57 
                                    e rl +LE +l+  e  +e+L + v   ++ +    ++l++++ rl+ +e + +++
  gi|119720640|ref|YP_921135.1|  62 ERRLADLEGRLSKVEGRLEALERRVDGVEKALGDVGERLDAVEARLSRVEGRLEGA 117
                                    56777777777777777777777777777777777777777777776666655543 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 1.9
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT- CS
                           SlyX   3 erleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerl 47 
                                    erl++ E +l+  e  +e     +a  ++ +++ + +l ++++ +
  gi|119720640|ref|YP_921135.1|  98 ERLDAVEARLSRVEGRLEGAESRLAGVEHGLEKVESRLSRVVKGF 142
                                    566777777766666666666666666666666666666655555 PP

>> DASH_Duo1  DASH complex subunit Duo1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0     0.033       4.7       8      41 ..      15      48 ..       8      51 .. 0.82
   2 ?    6.2   0.0     0.062         9       9      41 ..      30      62 ..      28      68 .. 0.77
   3 ?    0.3   0.0       4.2     6e+02       7      38 ..      56      87 ..      50      93 .. 0.79
   4 ?    2.3   0.0         1   1.5e+02       7      40 ..      84     117 ..      78     122 .. 0.80
   5 ?    0.5   0.0       3.6   5.3e+02      16      44 ..     121     149 ..     114     154 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.033
                      DASH_Duo1  8 qLrkinevienviesLkkaksniervketvestn 41
                                    L+++ e + +v++ L+ +++ +++v+e++es++
  gi|119720640|ref|YP_921135.1| 15 RLDRVEERLGGVEKRLEGVEGRLDKVEERLESVE 48
                                   6888888999999999999999999999998875 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.062
                      DASH_Duo1  9 LrkinevienviesLkkaksniervketvestn 41
                                   L+ +   +++v+e L+++++n+  v+e++++++
  gi|119720640|ref|YP_921135.1| 30 LEGVEGRLDKVEERLESVEENLGGVQERLTKAE 62
                                   555666688899999999999999999888776 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 4.2
                      DASH_Duo1  7 eqLrkinevienviesLkkaksniervketve 38
                                   e L+k  + + ++++ L k+++ +e ++++v+
  gi|119720640|ref|YP_921135.1| 56 ERLTKAERRLADLEGRLSKVEGRLEALERRVD 87
                                   66777788888899999999999998888876 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 1
                      DASH_Duo1   7 eqLrkinevienviesLkkaksniervketvest 40 
                                    + ++ + +++ +v e L++++  ++rv+ ++e +
  gi|119720640|ref|YP_921135.1|  84 RRVDGVEKALGDVGERLDAVEARLSRVEGRLEGA 117
                                    5788899999999999999999999998877655 PP

  == domain 5  score: 0.5 bits;  conditional E-value: 3.6
                      DASH_Duo1  16 ienviesLkkaksniervketvestntLL 44 
                                    + +v+  L+k++s ++rv +  es ++ L
  gi|119720640|ref|YP_921135.1| 121 LAGVEHGLEKVESRLSRVVKGFESHQEFL 149
                                    56788889999999999988888877766 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.1     0.007         1      40     110 ..      10      80 ..       5      82 .. 0.81
   2 ?    7.8   0.0     0.013       1.9      36     114 ..      62     140 ..      56     147 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.007
                        DUF3450  40 dklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeierelvpllekmidrLe 110
                                    +k++   + +++++  ++++le  e   +++e+ ++s+e+++  ++e+++++e+  ++l+  l k+  rLe
  gi|119720640|ref|YP_921135.1|  10 EKINARLDRVEERLGGVEKRLEGVEGRLDKVEERLESVEENLGGVQERLTKAERRLADLEGRLSKVEGRLE 80 
                                    56666667788888999999999999999999999999999999999999999988888888888777776 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.013
                        DUF3450  36 qkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeierelvpllekmidrLeqfve 114
                                    +++  +l+   ++++ +++al+++++  e+    + + ++++e++++++e ++e +e   ++++  lek+ +rL ++v+
  gi|119720640|ref|YP_921135.1|  62 ERRLADLEGRLSKVEGRLEALERRVDGVEKALGDVGERLDAVEARLSRVEGRLEGAESRLAGVEHGLEKVESRLSRVVK 140
                                    5566667777788889999999999999999999999999999999999999999999999999999999999999886 PP

>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.2     0.097        14      50      94 ..      20      68 ..       7      87 .. 0.39
   2 !    9.8   0.0    0.0039      0.56      11     126 ..      42     154 ..      33     157 .. 0.85
   3 ?    2.8   0.6      0.55        79      80     125 ..     183     228 ..     181     233 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.097
                           YkyA 50 dkikklsdealenveeReellek....ekesieeakeefekikeeieei 94
                                   ++    +++ le ve R +++e+     +e++   +e ++k++  + ++
  gi|119720640|ref|YP_921135.1| 20 EERLGGVEKRLEGVEGRLDKVEErlesVEENLGGVQERLTKAERRLADL 68
                                   3333333333333333333333300002223333344444444444444 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0039
                           YkyA  11 eeavelEkefeeqqekLtelekkeqelyeeiiel..gmdefdkikklsdealenveeReellekekesieeakeefekik 88 
                                    e +++ E+++   qe Lt++e+   +l  ++ +     + +++ ++ +++al  v eR + +e     +++ +  +e ++
  gi|119720640|ref|YP_921135.1|  42 ERLESVEENLGGVQERLTKAERRLADLEGRLSKVegRLEALERRVDGVEKALGDVGERLDAVEA---RLSRVEGRLEGAE 118
                                    5677889999999*********999999888665325667999999999999999999999999...9999999****** PP

                           YkyA  89 eeieeiedeelkkeaeelieameeryeaydklykaYke 126
                                    + +  +e     +++e+  + + + +e++++++ +Y +
  gi|119720640|ref|YP_921135.1| 119 SRLAGVEHG--LEKVESRLSRVVKGFESHQEFLIDYLA 154
                                    ****99766..89999999999999999**99999965 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.55
                           YkyA  80 akeefekikeeieeiedeelkkeaeelieameeryeaydklykaYk 125
                                    +kee+ek++e++e+   e   +eae++     +  e + + y+ Yk
  gi|119720640|ref|YP_921135.1| 183 TKEEVEKLREYLEKDPGEFTMEEAEDFLRLARKAVEEHGDKYEVYK 228
                                    5899***********9999999******999999999999999998 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.2     0.001      0.15      10      86 ..      33     108 ..      24     125 .. 0.74
   2 ?    3.9   0.3      0.54        78       9      80 ..     130     207 ..      95     226 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.001
                   Syntaxin-6_N  10 VqkslnkaeslyrrwerlledtssstseeldetrteLrkalrsiewdledLeetvriveknpskfkidekelsrrra 86 
                                    V+  l+k+e+ +++ e+ l   ++ +  + ++   +L+  l+++e  le Le+ v+ vek   +++ + ++++ r +
  gi|119720640|ref|YP_921135.1|  33 VEGRLDKVEERLESVEENLGGVQE-RLTKAERRLADLEGRLSKVEGRLEALERRVDGVEKALGDVGERLDAVEARLS 108
                                    555566666666666543333332.67888888899***********************988777777777777755 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.54
                   Syntaxin-6_N   9 eVqkslnkaeslyrrwerlledtsss........tseeldetrteLrkalrsiewdl..edLeetvriveknpskfkide 78 
                                    +V++ l+++ + +++ ++ l     +        +++     r eLr+ l+ +++ l  e+ e+  + +ek+p +f ++e
  gi|119720640|ref|YP_921135.1| 130 KVESRLSRVVKGFESHQEFLI----DylasegviKEKTALVVRAELRSVLSLLSNPLtkEEVEKLREYLEKDPGEFTMEE 205
                                    445555555555555543333....0333345666666777788888888888776644677777788899999998888 PP

                   Syntaxin-6_N  79 ke 80 
                                    +e
  gi|119720640|ref|YP_921135.1| 206 AE 207
                                    76 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.1   0.00027      0.04     387     463 ..      18     103 ..       5     119 .. 0.42

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00027
                         AAA_13 387 nleeekeeakkklelhlv.........eeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdek 457
                                    ++ee+   ++k le  +          e++e++l   ++ + k+e+ + +le +l++ e +l++le ++   ek l d+ 
  gi|119720640|ref|YP_921135.1|  18 RVEERLGGVEKRLEGVEGrldkveerlESVEENLGGVQERLTKAERRLADLEGRLSKVEGRLEALERRVDGVEKALGDVG 97 
                                    44444444444444433211111111133333333444444444444444444444444444444444444444444444 PP

                         AAA_13 458 paaeei 463
                                    +  + +
  gi|119720640|ref|YP_921135.1|  98 ERLDAV 103
                                    444444 PP

>> TACC_C  Transforming acidic coiled-coil-containing protein (TACC), C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.1     0.012       1.7      65     114 ..      39      88 ..       6     121 .. 0.44
   2 !   13.9   0.0   0.00024     0.034       8     118 ..      49     162 ..      44     172 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.012
                         TACC_C  65 lakkeiqkvleekeqlladlnsveksfsdlfkryekqkevlegykknees 114
                                    + ++ ++ v e+   +++ l++ e+ ++dl  r+ k    le + +  + 
  gi|119720640|ref|YP_921135.1|  39 KVEERLESVEENLGGVQERLTKAERRLADLEGRLSKVEGRLEALERRVDG 88 
                                    22333333333333333333333333333333333333333333333333 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 0.00024
                         TACC_C   8 aalekvkeeveekeeeiqelkkkveelkkenqemkkivaefektiaqlieekqkqk...elakkeiqkvleekeqlladl 84 
                                    + l  v+e  +++e+++++l+ + ++ + + + +++ v+  ek++ ++ e  ++ +   +  +  ++ + +    + + l
  gi|119720640|ref|YP_921135.1|  49 ENLGGVQERLTKAERRLADLEGRLSKVEGRLEALERRVDGVEKALGDVGERLDAVEarlSRVEGRLEGAESRLAGVEHGL 128
                                    555668999999********************************9999888766551114445566666677888999** PP

                         TACC_C  85 nsveksfsdlfkryekqkevlegykkneeslkkc 118
                                    ++ve  +s ++k +e  +e l +y + e + k++
  gi|119720640|ref|YP_921135.1| 129 EKVESRLSRVVKGFESHQEFLIDYLASEGVIKEK 162
                                    ************************9999999986 PP

>> DUF4349  Domain of unknown function (DUF4349)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.3      0.12        18     122     145 ..      20      43 ..      10      57 .. 0.55
   2 ?   10.3   2.3    0.0025      0.36     102     147 ..      41      87 ..      37      91 .. 0.70
   3 ?    6.3   0.1     0.041       5.9     120     142 ..     102     124 ..      94     130 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.12
                        DUF4349 122 ereLsevqaeieslegqlryLdnq 145
                                    e++L  v++++e  eg+l   +++
  gi|119720640|ref|YP_921135.1|  20 EERLGGVEKRLEGVEGRLDKVEER 43 
                                    444444444444444444444433 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0025
                        DUF4349 102 edrllallekaksv.edlleiereLsevqaeieslegqlryLdnqva 147
                                    e+rl+++ e+ + v e l ++er+L++ + ++ + eg+l++L+++v+
  gi|119720640|ref|YP_921135.1|  41 EERLESVEENLGGVqERLTKAERRLADLEGRLSKVEGRLEALERRVD 87 
                                    45555555553333044778899999999999999999999998887 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.041
                        DUF4349 120 eiereLsevqaeieslegqlryL 142
                                    ++e +Ls+v+ ++e +e++l+  
  gi|119720640|ref|YP_921135.1| 102 AVEARLSRVEGRLEGAESRLAGV 124
                                    79*****************9875 PP

>> DUF3552  Domain of unknown function (DUF3552)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   4.5   0.00068     0.099      78     140 ..      21      82 ..       7      84 .. 0.64
   2 ?    8.8   0.2    0.0069         1      79     132 ..      78     131 ..      67     156 .. 0.63
   3 ?   -1.2   0.3       7.8   1.1e+03      59      73 ..     184     198 ..     181     220 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00068
                        DUF3552  78 nelqrlekRllqkeetLdrkeeslekkeesleekekelkqkeqsleekeeeleelveeqrqeL 140
                                    + l  +ekRl+  e +Ld+ ee le+ ee+l   +++l++ e++l   e +l++ ve + + L
  gi|119720640|ref|YP_921135.1|  21 ERLGGVEKRLEGVEGRLDKVEERLESVEENLGGVQERLTKAERRLADLEGRLSK-VEGRLEAL 82 
                                    445556777777777777777777777777777777777777777777776666.44445555 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0069
                        DUF3552  79 elqrlekRllqkeetLdrkeeslekkeesleekekelkqkeqsleekeeeleel 132
                                     l++le+R+   e++L    e l+  e++l++ e +l+  e++l   e+ le++
  gi|119720640|ref|YP_921135.1|  78 RLEALERRVDGVEKALGDVGERLDAVEARLSRVEGRLEGAESRLAGVEHGLEKV 131
                                    455666666666666666666666666666666666666666555555555443 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 7.8
                        DUF3552  59 keeihklreelekel 73 
                                    kee+ klre lek+ 
  gi|119720640|ref|YP_921135.1| 184 KEEVEKLREYLEKDP 198
                                    889999999888874 PP

>> DUF241  Arabidopsis protein of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   1.5     0.019       2.8     178     225 ..      10      59 ..       5      65 .. 0.54
   2 ?    7.7   1.6     0.019       2.8     174     223 ..      41      85 ..      37     100 .. 0.56
   3 ?    6.3   0.1     0.051       7.4     195     224 ..     104     135 ..      86     140 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.019
                         DUF241 178 ekvdaalesllssskkek..vqsalkrleeleecieelEeglekvfRrLI 225
                                    ek++a l ++ ++    +  ++ ++ rl+++ee +e++Ee+l  v  rL 
  gi|119720640|ref|YP_921135.1|  10 EKINARLDRVEERLGGVEkrLEGVEGRLDKVEERLESVEENLGGVQERLT 59 
                                    44444444444443222235666666666666666666666666666654 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.019
                         DUF241 174 enelekvdaalesllssskkekvqsalkrleeleecieelEeglekvfRr 223
                                    e+ le+v++ l  ++++     +++a++rl +le  ++++E  le + Rr
  gi|119720640|ref|YP_921135.1|  41 EERLESVEENLGGVQER-----LTKAERRLADLEGRLSKVEGRLEALERR 85 
                                    45566667766666666.....4555555555555555555555555444 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.051
                         DUF241 195 k..vqsalkrleeleecieelEeglekvfRrL 224
                                    +  + +++ rle  e+ + ++E glekv  rL
  gi|119720640|ref|YP_921135.1| 104 EarLSRVEGRLEGAESRLAGVEHGLEKVESRL 135
                                    24577889999999999999999999998888 PP

>> WASH_WAHD  WAHD domain of WASH complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.1     0.011       1.6      37      74 ..       9      46 ..       5      49 .. 0.87
   2 ?    6.2   0.0     0.045       6.5      37      70 ..      37      70 ..      31      76 .. 0.91
   3 ?    1.9   0.0      0.89   1.3e+02      38      69 ..      52      83 ..      44      92 .. 0.73
   4 ?    2.0   0.0      0.87   1.3e+02      34      64 ..      90     120 ..      69     140 .. 0.61

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.011
                      WASH_WAHD 37 fgridarvernreklqaineRveiaqakiaklkeskka 74
                                   f++i+ar++r+ e+l  +++R+e ++ + +k++e  ++
  gi|119720640|ref|YP_921135.1|  9 FEKINARLDRVEERLGGVEKRLEGVEGRLDKVEERLES 46
                                   89999999999999999999999999999999887665 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.045
                      WASH_WAHD 37 fgridarvernreklqaineRveiaqakiaklke 70
                                   ++++++r+e++ e l  ++eR+++a+ + a l++
  gi|119720640|ref|YP_921135.1| 37 LDKVEERLESVEENLGGVQERLTKAERRLADLEG 70
                                   689************************9999987 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.89
                      WASH_WAHD 38 gridarvernreklqaineRveiaqakiaklk 69
                                   g +++r+ +  ++l  ++ R+++++ + ++l+
  gi|119720640|ref|YP_921135.1| 52 GGVQERLTKAERRLADLEGRLSKVEGRLEALE 83
                                   56777888888888888888888887777775 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.87
                      WASH_WAHD  34 ndvfgridarvernreklqaineRveiaqak 64 
                                    ++ +g + +r++ + ++l++++ R+e a+ +
  gi|119720640|ref|YP_921135.1|  90 EKALGDVGERLDAVEARLSRVEGRLEGAESR 120
                                    3345555566666666666666666655554 PP

>> HMMR_N  Hyaluronan mediated motility receptor N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   2.5   0.00011     0.015     184     319 ..      44     176 ..      36     194 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 0.00011
                         HMMR_N 184 QedmeaklqvtqknLeeskakvaqLkeklvslekekieekset.eklleyiee.lsnvseqlekykldiaqleellkekn 261
                                     e++e +l  +q+ L+++  ++a L+ +l      k+e + e  e+ ++ +e+ l  v e+l+  + ++  +e  l+ ++
  gi|119720640|ref|YP_921135.1|  44 LESVEENLGGVQERLTKAERRLADLEGRL-----SKVEGRLEAlERRVDGVEKaLGDVGERLDAVEARLSRVEGRLEGAE 118
                                    45667777777777777777777777777.....4566666665666666554399999999999*************** PP

                         HMMR_N 262 deiesLkssLeekeqelskqvkdlnekckllekekeelvreeeekeqtlsaEleelke 319
                                    + +  + + Le+ e  ls+ vk  +++ + l   +  +   +e+ +  + aEl ++  
  gi|119720640|ref|YP_921135.1| 119 SRLAGVEHGLEKVESRLSRVVKGFESHQEFLIDYLASEGVIKEKTALVVRAELRSVLS 176
                                    ********************99988877766655444433344444555555555555 PP

>> APG17  Autophagy protein Apg17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1      0.19        27      42      92 ..      13      63 ..       5      73 .. 0.59
   2 ?   11.7   0.5    0.0007       0.1      21     160 ..      55     194 ..      44     220 .. 0.74
   3 ?    1.1   0.6       1.2   1.7e+02     273     348 ..     176     246 ..     160     251 .. 0.67

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.19
                                   HHHHHHHHHHHHHHHHIIIIIIIIIIIIIIIIIHHHHHHHHHHHHHHHHHH CS
                          APG17 42 eflrdglkqQlkllekirkslerklekgkeefkdlikeldaanerLektle 92
                                   +   d +++ l  +ek  +++e +l+k++e++++++++l  ++erL+k   
  gi|119720640|ref|YP_921135.1| 13 NARLDRVEERLGGVEKRLEGVEGRLDKVEERLESVEENLGGVQERLTKAER 63
                                   444455555555555555666666666666666666666666666665544 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.0007
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHIIIIIIIIIIIIIIIIIHHHHHHHHHHHHHHHHHHHHHTSS-T CS
                          APG17  21 nelltsarqeleeavkllakteflrdglkqQlkllekirkslerklekgkeefkdlikeldaanerLektlekLrktkve 100
                                    +e lt+a+ +l + +  l+k+e   ++l++ ++ +ek    ++++l+ ++ ++ +++ +l+ a +rL    + L+k++  
  gi|119720640|ref|YP_921135.1|  55 QERLTKAERRLADLEGRLSKVEGRLEALERRVDGVEKALGDVGERLDAVEARLSRVEGRLEGAESRLAGVEHGLEKVESR 134
                                    78889999999999999999999999999999999999999999999999999999999999999999999999888877 PP

                                    TS..........STGGGCS--TTTTHHHHHHHHHHHHHHHHHHHHHTTHH..HHHHHHHHHHH CS
                          APG17 101 psfrpegee...ktLlDFvdedsveelkealkesidelqaaqkkldssllefdtdlrelkkel 160
                                    +s   +g e   + L D+   ++v + k al  +++el ++ + l++ l+  ++++++l++ l
  gi|119720640|ref|YP_921135.1| 135 LSRVVKGFEshqEFLIDYLASEGVIKEKTALV-VRAELRSVLSLLSNPLT--KEEVEKLREYL 194
                                    77666666688899****99999976666663.23444444444444444..44444444444 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 1.2
                                    HHHHHHHHHHH....HHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHH CS
                          APG17 273 salkkaleeleevgkklpeylaifkaeeeflerweeekekieekleeleeLrefYegF.lsaYdklllEveRRrave 348
                                    s l++ l++ e   +kl+eyl+  k+  ef+ ++   ++ +    + +ee  + Ye + l+ Y++l++   RRr ++
  gi|119720640|ref|YP_921135.1| 176 SLLSNPLTKEE--VEKLREYLE--KDPGEFTMEE--AEDFLRLARKAVEEHGDKYEVYkLHLYAALVRGWTRRRLAK 246
                                    44444444444..579999999..8999999884..44444445556666666777775688999999998888665 PP

>> EcoEI_R_C  EcoEI R protein C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0       1.5   2.2e+02      68      99 ..      63      95 ..      27     167 .. 0.55
   2 ?   12.1   0.2    0.0011      0.16      20      63 ..     170     215 ..     167     237 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 1.5
                      EcoEI_R_C 68 q.ltdlidlirkiagldeeletrserverafkr 99
                                   + l+dl   + k+ g  e le r + ve+a  +
  gi|119720640|ref|YP_921135.1| 63 RrLADLEGRLSKVEGRLEALERRVDGVEKALGD 95
                                   245566666666666666666666666655544 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.0011
                      EcoEI_R_C  20 aLqiiws..dreltkellkeLeekLkepppgitpealweayellek 63 
                                    +L+ + s    +ltke++++L+e L+++p  +t e+ ++ ++l  k
  gi|119720640|ref|YP_921135.1| 170 ELRSVLSllSNPLTKEEVEKLREYLEKDPGEFTMEEAEDFLRLARK 215
                                    788888888999**********************999988877644 PP

>> HSBP1  Heat shock factor binding protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0       2.1   3.1e+02      24      43 ..      11      30 ..       7      34 .. 0.81
   2 ?    5.8   0.6     0.086        12      25      41 ..      75      91 ..      33      99 .. 0.54
   3 ?    4.4   0.0      0.23        33      27      46 ..      77      96 ..      75     112 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 2.1
                          HSBP1 24 qilsriDdMssriDdLEksi 43
                                   +i  r+D  ++r+   Ek +
  gi|119720640|ref|YP_921135.1| 11 KINARLDRVEERLGGVEKRL 30
                                   79999999999998888765 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.086
                          HSBP1 25 ilsriDdMssriDdLEk 41
                                   + +r++ +++r+D  Ek
  gi|119720640|ref|YP_921135.1| 75 VEGRLEALERRVDGVEK 91
                                   33455555555555555 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.23
                          HSBP1 27 sriDdMssriDdLEksiadl 46
                                   +r++ +++r+D  Ek + d+
  gi|119720640|ref|YP_921135.1| 77 GRLEALERRVDGVEKALGDV 96
                                   57888888888888877665 PP

>> DUF4140  N-terminal domain of unknown function (DUF4140)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   2.7     0.056       8.1      64      96 ..      48      80 ..       7      89 .. 0.56
   2 ?    7.0   0.1     0.055       7.9      66      96 ..      92     122 ..      83     129 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.056
                        DUF4140 64 eeelkalraeleeledelaaledelaaaearla 96
                                   ee l  ++++l+++e++la+le +l+ +e rl+
  gi|119720640|ref|YP_921135.1| 48 EENLGGVQERLTKAERRLADLEGRLSKVEGRLE 80
                                   222444444444444444444444444444444 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.055
                        DUF4140  66 elkalraeleeledelaaledelaaaearla 96 
                                    +l  + ++l+++e++l+++e +l+ ae+rla
  gi|119720640|ref|YP_921135.1|  92 ALGDVGERLDAVEARLSRVEGRLEGAESRLA 122
                                    46677899999*************9999987 PP

>> Fmp27_WPPW  RNA pol II promoter Fmp27 protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.5   0.00045     0.065     176     241 ..      33     101 ..       9     231 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00045
                     Fmp27_WPPW 176 leeRleeleeqiekleekleelelkseke...deelkeeieelekeikelkeklefletlledlkesee 241
                                    +e Rl+++ee++e++ee+l+ ++++  k     ++l+ +++++e  ++ l+++++ +e++l d+ e+ +
  gi|119720640|ref|YP_921135.1|  33 VEGRLDKVEERLESVEENLGGVQERLTKAerrLADLEGRLSKVEGRLEALERRVDGVEKALGDVGERLD 101
                                    344555555555555555555555555443333445555555555555555555555555555555444 PP

>> SNARE  SNARE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0      0.44        63       3      29 ..      16      42 ..      15      44 .. 0.90
   2 ?    9.3   0.1    0.0078       1.1       3      30 ..      37      64 ..      36      67 .. 0.91
   3 ?    2.6   0.0      0.94   1.4e+02       3      28 ..     100     125 ..      98     127 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.44
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          SNARE  3 vDrIdtnVenaqsnveraqkeLkkavk 29
                                   +Dr +     ++ ++e++ ++L+k+++
  gi|119720640|ref|YP_921135.1| 16 LDRVEERLGGVEKRLEGVEGRLDKVEE 42
                                   79999999999*************986 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0078
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          SNARE  3 vDrIdtnVenaqsnveraqkeLkkavky 30
                                   +D  +   e++++n+ ++q++L ka+++
  gi|119720640|ref|YP_921135.1| 37 LDKVEERLESVEENLGGVQERLTKAERR 64
                                   68889999*****************997 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.94
                                    HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          SNARE   3 vDrIdtnVenaqsnveraqkeLkkav 28 
                                    +D  ++   +++ ++e+a ++L+ ++
  gi|119720640|ref|YP_921135.1| 100 LDAVEARLSRVEGRLEGAESRLAGVE 125
                                    6888899999999*******999776 PP

>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.7    0.0019      0.27      13      96 ..      33     114 ..       4     147 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0019
                                    HHHHHHHHHHHHCCSSCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHTTHHHHHHHHHHHHHHHHHH CS
                       Spectrin  13 leeWieekeellssedlgkdleevqallkkhkaleaelaaqqervkalnelaeklldeghsaseeieerleelnerWeeL 92 
                                    +e  +++ ee l  e +++ l +vq+ l+k ++  a+l+ +  +v+   e  e+ +d  ++a  ++ erl++++ r   +
  gi|119720640|ref|YP_921135.1|  33 VEGRLDKVEERL--ESVEENLGGVQERLTKAERRLADLEGRLSKVEGRLEALERRVDGVEKALGDVGERLDAVEARLSRV 110
                                    333334444444..222224444444444333333333333333332223333333444444555555555555555555 PP

                                    HHHH CS
                       Spectrin  93 kela 96 
                                    + ++
  gi|119720640|ref|YP_921135.1| 111 EGRL 114
                                    5555 PP

>> ERM  Ezrin/radixin/moesin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   5.7    0.0003     0.043       4     102 ..      34     132 ..       7     220 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.0003
                            ERM   4 erekreleerLkqlqeeaekaqeaLreseetaelLaekarraeeeaelLeqkaaeaeeeiqrlkesaekeeeekeklerk 83 
                                    e + +++eerL++++e+    qe L+++e++   L+ ++ ++e   e Le++   +e++   + e+  + e+  +++e +
  gi|119720640|ref|YP_921135.1|  34 EGRLDKVEERLESVEENLGGVQERLTKAERRLADLEGRLSKVEGRLEALERRVDGVEKALGDVGERLDAVEARLSRVEGR 113
                                    45556777888888888888888888888888888888888888888888888777777777777777777777777777 PP

                            ERM  84 lreaeleaarleeeserke 102
                                    l+ ae+++a +e   e+ e
  gi|119720640|ref|YP_921135.1| 114 LEGAESRLAGVEHGLEKVE 132
                                    7777777666665444433 PP

>> DHR10  Designed helical repeat protein 10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   2.9    0.0022      0.32      47     100 ..      11      64 ..       6      69 .. 0.71
   2 ?   10.8   2.7    0.0026      0.38      50      94 ..      42      86 ..      35      91 .. 0.65
   3 ?   10.5   0.1    0.0034      0.49      51     102 ..      78     129 ..      72     137 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0022
                          DHR10  47 aelakleeakkklkelrdaleekeielrelerkeerlqrqlenaeeklerlreq 100
                                    +  a+l+ ++++l   +++le  e +l ++e + e ++  l   +e+l++++++
  gi|119720640|ref|YP_921135.1|  11 KINARLDRVEERLGGVEKRLEGVEGRLDKVEERLESVEENLGGVQERLTKAERR 64 
                                    445677777777777777777777777777777777777777777777777765 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0026
                          DHR10 50 akleeakkklkelrdaleekeielrelerkeerlqrqlenaeekl 94
                                   ++le+++++l   +++l++ e++l++le + + ++ +le  e++ 
  gi|119720640|ref|YP_921135.1| 42 ERLESVEENLGGVQERLTKAERRLADLEGRLSKVEGRLEALERRV 86
                                   566666777777777777777777777777777777777666665 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.0034
                          DHR10  51 kleeakkklkelrdaleekeielrelerkeerlqrqlenaeeklerlreqae 102
                                    +le  +++++  ++al + +++l  +e++ +r++ +le ae +l+ +++  e
  gi|119720640|ref|YP_921135.1|  78 RLEALERRVDGVEKALGDVGERLDAVEARLSRVEGRLEGAESRLAGVEHGLE 129
                                    6788899999999999999999999999999999999999999987776655 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1    0.0023      0.33      70     118 ..      31      79 ..      10      94 .. 0.75
   2 ?    6.0   0.1     0.081        12      60     104 ..      56     100 ..      54     114 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0023
                           ADIP  70 erlqskierlktqleqlerelalvqakerqlekklktleqklknekeel 118
                                    e  + + ++++++le+ e  l  vq++++++e++l++le  l +    l
  gi|119720640|ref|YP_921135.1|  31 EGVEGRLDKVEERLESVEENLGGVQERLTKAERRLADLEGRLSKVEGRL 79 
                                    5556678899999999999999999999999999999998776655555 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.081
                           ADIP  60 etirkleaeierlqskierlktqleqlerelalvqakerqlekkl 104
                                    e++ k e  ++ l+ + ++++ +le+ler+++ v++++ +   +l
  gi|119720640|ref|YP_921135.1|  56 ERLTKAERRLADLEGRLSKVEGRLEALERRVDGVEKALGDVGERL 100
                                    677778888889999999999999999999999998876666555 PP

>> MutS_III  MutS domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0       1.1   1.6e+02      49      61 ..      10      23 ..       7      33 .. 0.82
   2 ?   10.4   2.9    0.0038      0.55      48     106 ..      37     105 ..      35     246 .. 0.51

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 1.1
                                   HHHHHHHHHHHH.T CS
                                   xxxxxxxxxxxx.x RF
                       MutS_III 49 eeInaRldaVee.l 61
                                   e+InaRld Vee l
  gi|119720640|ref|YP_921135.1| 10 EKINARLDRVEErL 23
                                   79*********866 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0038
                                    HHHHHHHHHHHHH.T..TT.HHHHHHHHTT---HHHHHHHHHTT....................---HHHHHHHHHHHHH CS
                                    xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................xxxxxxxxxxxxxxxx RF
                       MutS_III  48 leeInaRldaVee.leneelreelrellrrlpDleRllsrislg....................kakardlkallealka 106
                                    l+++++Rl+ Vee l    ++e+l+++ rrl Dle  ls++  +                    +         l+a++a
  gi|119720640|ref|YP_921135.1|  37 LDKVEERLESVEEnL--GGVQERLTKAERRLADLEGRLSKVEGRlealerrvdgvekalgdvgeR---------LDAVEA 105
                                    6899*********88..8889*****************988553222222222222111111110.........111111 PP

>> Sec3_C  Exocyst complex component Sec3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0      0.11        16      31      77 ..       8      54 ..       5      61 .. 0.68
   2 ?    6.2   0.0     0.019       2.8       5      72 ..      63     126 ..      59     135 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.11
                         Sec3_C 31 kveelkkdidkalkecdeldalltlysveLstlsedieyIEsqnngL 77
                                   k+e+++ ++d + + ++ ++++l+  +  L +++e +e +E++  g 
  gi|119720640|ref|YP_921135.1|  8 KFEKINARLDRVEERLGGVEKRLEGVEGRLDKVEERLESVEENLGGV 54
                                   56677777777777777777777777777777777777777765444 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.019
                         Sec3_C   5 eleerLsreLskleaanikrllesdkkveelkkdidkalkecdeldalltlysveLstlsedieyIEs 72 
                                      +++L+ +Lsk+e+    rl +++ +v+ + k + ++ + +d ++a+l++ +  L+  ++ ++ +E+
  gi|119720640|ref|YP_921135.1|  63 RRLADLEGRLSKVEG----RLEALERRVDGVEKALGDVGERLDAVEARLSRVEGRLEGAESRLAGVEH 126
                                    556677777888776....6788888888888888888888888888888888777777777777765 PP

>> HOOK  HOOK protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   3.2    0.0003     0.043     478     583 ..      28     130 ..       6     218 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0003
                           HOOK 478 ekltelqelledanrrkneLetenrlanqrileLeaqveelqkalqeqgskaedssllkkkleehleklkevqeelqkkk 557
                                    ++l+ ++  l+  ++r++++e++    ++r+++ e+++ +l+ +l++ +++ e    l+++++   + l +v e l   +
  gi|119720640|ref|YP_921135.1|  28 KRLEGVEGRLDKVEERLESVEENLGGVQERLTKAERRLADLEGRLSKVEGRLEA---LERRVDGVEKALGDVGERLDAVE 104
                                    344444444444444444444444444444444444444444444444444443...33333333333333333333333 PP

                           HOOK 558 eqleelepklssnkqkieeleeaLkk 583
                                    + l  +e +l+ + ++ + +e+ L+k
  gi|119720640|ref|YP_921135.1| 105 ARLSRVEGRLEGAESRLAGVEHGLEK 130
                                    33333333333333333333333333 PP

>> Vps5  Vps5 C terminal like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0       2.4   3.5e+02     152     189 ..      10      47 ..       7      51 .. 0.51
   2 ?    8.0   0.0     0.013       1.9     135     192 ..      42      99 ..      36     104 .. 0.90
   3 ?    1.4   0.0       1.3   1.9e+02     150     188 ..     106     144 ..     100     149 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 2.4
                           Vps5 152 eKlekaaksqqdklqqlkkeveelerkvqeaekeFeei 189
                                    eK+++     +++l  ++k +e +e +++++e+  e +
  gi|119720640|ref|YP_921135.1|  10 EKINARLDRVEERLGGVEKRLEGVEGRLDKVEERLESV 47 
                                    44444444445555555666666666655555554444 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.013
                           Vps5 135 qkwqsaeqelskkkeqleKlekaaksqqdklqqlkkeveelerkvqeaekeFeeiset 192
                                    ++++s+e++l   +e+l+K+e+   + + +l +++  +e ler+v+ +ek   +++e+
  gi|119720640|ref|YP_921135.1|  42 ERLESVEENLGGVQERLTKAERRLADLEGRLSKVEGRLEALERRVDGVEKALGDVGER 99 
                                    567899999999***********99999*********************999998876 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 1.3
                           Vps5 150 qleKlekaaksqqdklqqlkkeveelerkvqeaekeFee 188
                                    +l ++e   + ++ +l+ +++ +e++e+++ ++ k Fe 
  gi|119720640|ref|YP_921135.1| 106 RLSRVEGRLEGAESRLAGVEHGLEKVESRLSRVVKGFES 144
                                    556677777777889999999999999999999999985 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00091      0.13      32     122 ..      25     111 ..      11     120 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00091
                                    CCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHH CS
                      Fib_alpha  32 dvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnvl 111
                                     v+k+le +e +l++++++ +++ee    +++ l+++++  +d +  ++k++ +le     l++++d  e+ +    + l
  gi|119720640|ref|YP_921135.1|  25 GVEKRLEGVEGRLDKVEERLESVEENLGGVQERLTKAERRLADLEGRLSKVEGRLE----ALERRVDGVEKALGDVGERL 100
                                    5899**************************************99999999999999....89999999999999998888 PP

                                    HHHHHHHHHHH CS
                      Fib_alpha 112 esneqkiqkLe 122
                                    ++ e ++++ e
  gi|119720640|ref|YP_921135.1| 101 DAVEARLSRVE 111
                                    88888888776 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1     0.003      0.43     106     184 ..      11      89 ..       5     110 .. 0.62
   2 ?    9.9   0.2    0.0042       0.6     102     186 ..      49     133 ..      36     147 .. 0.51

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.003
                         DUF724 106 klleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaekleeeledveqeFeav 184
                                    k+  ++ ++e+++   e++ + +e  +d++e++   +e++l  ++e+  +a++++a+l+   +k+e +le+ e++++ v
  gi|119720640|ref|YP_921135.1|  11 KINARLDRVEERLGGVEKRLEGVEGRLDKVEERLESVEENLGGVQERLTKAERRLADLEGRLSKVEGRLEALERRVDGV 89 
                                    5555555666666666666666666666666666666666666666666666666666666666666666666555443 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0042
                         DUF724 102 deqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaekleeeledveqeF 181
                                    ++   ++e++ k+e+++++ e + +k+e  ++ le+++  +e+ l  + e+ +a +++++r++   e +e +l  ve+  
  gi|119720640|ref|YP_921135.1|  49 ENLGGVQERLTKAERRLADLEGRLSKVEGRLEALERRVDGVEKALGDVGERLDAVEARLSRVEGRLEGAESRLAGVEHGL 128
                                    33333344444444444444444444444444444444444444444446666666666666666666666666666655 PP

                         DUF724 182 eavas 186
                                    e+v s
  gi|119720640|ref|YP_921135.1| 129 EKVES 133
                                    55543 PP

>> Glyco_H_20C_C  Glycoside Hydrolase 20C C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   1.0    0.0091       1.3     143     174 ..      19      49 ..      16      50 .. 0.89
   2 ?    7.7   1.2      0.02       2.8     143     173 ..      47      76 ..      44      92 .. 0.82
   3 ?    2.3   0.3      0.89   1.3e+02     144     159 ..     118     133 ..      79     161 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0091
                  Glyco_H_20C_C 143 ldiRlGGllaRlesaeeRLeaYlegkierieE 174
                                    ++ RlGG+ +Rle +e RL++ +e+++e++eE
  gi|119720640|ref|YP_921135.1|  19 VEERLGGVEKRLEGVEGRLDK-VEERLESVEE 49 
                                    678****************98.7888999998 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.02
                  Glyco_H_20C_C 143 ldiRlGGllaRlesaeeRLeaYlegkierie 173
                                    ++  lGG+ +Rl +ae+RL + leg+++++e
  gi|119720640|ref|YP_921135.1|  47 VEENLGGVQERLTKAERRLAD-LEGRLSKVE 76 
                                    67789**************98.788877776 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.89
                  Glyco_H_20C_C 144 diRlGGllaRlesaee 159
                                    + Rl G+   le++e+
  gi|119720640|ref|YP_921135.1| 118 ESRLAGVEHGLEKVES 133
                                    3444444444444444 PP

>> Cluap1  Clusterin-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   1.0     0.028         4     168     203 ..      38      73 ..       5      91 .. 0.48
   2 ?    4.7   0.0      0.12        17     170     219 ..      75     124 ..      63     155 .. 0.58

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.028
                         Cluap1 168 kalkeaikkvkeelektkkalenlesdeanLeakie 203
                                     +++e++++v+e+l  ++++l++ e+  a Le ++ 
  gi|119720640|ref|YP_921135.1|  38 DKVEERLESVEENLGGVQERLTKAERRLADLEGRLS 73 
                                    223344444444444444444444444444444444 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.12
                         Cluap1 170 lkeaikkvkeelektkkalenlesdeanLeakiekkkqeleraqkrLqsl 219
                                    ++ ++++++++++ ++kal ++ +  +++ea++ + +  le a+ rL+ +
  gi|119720640|ref|YP_921135.1|  75 VEGRLEALERRVDGVEKALGDVGERLDAVEARLSRVEGRLEGAESRLAGV 124
                                    44445555555555555555555555555555555555555555555443 PP

>> ISG65-75  Invariant surface glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1    0.0019      0.27      57     147 ..      10      99 ..       6     110 .. 0.83
   2 ?    2.6   0.0      0.46        66      54     105 ..      84     135 ..      72     149 .. 0.72
   3 ?   -1.1   0.0       6.3     9e+02      56      85 ..     114     143 ..     102     164 .. 0.67
   4 ?   -1.6   0.1       8.8   1.3e+03      76     110 ..     186     218 ..     167     228 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0019
                       ISG65-75  57 ketkdklayienakekvdyyvekleslleeakekgtltesdaeklkkaceeAkaknkkarekakkalekaekaskkakea 136
                                    ++++ +l+ +e+ +  v++++e++e++l++ +e  ++ e++   +++ +++A++  ++ + +  k+    e + +++   
  gi|119720640|ref|YP_921135.1|  10 EKINARLDRVEERLGGVEKRLEGVEGRLDKVEERLESVEENLGGVQERLTKAERRLADLEGRLSKVEGRLEALERRVD-G 88 
                                    678888999999999999999999999999999999999999999999999999999999999998888888777764.5 PP

                       ISG65-75 137 akkAlGeelee 147
                                     +kAlG+  e+
  gi|119720640|ref|YP_921135.1|  89 VEKALGDVGER 99 
                                    67888887665 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.46
                       ISG65-75  54 yllketkdklayienakekvdyyvekleslleeakekgtltesdaeklkkac 105
                                    + ++ ++++l+ + + +++v+++++++e++le a+      e   ek+++ +
  gi|119720640|ref|YP_921135.1|  84 RRVDGVEKALGDVGERLDAVEARLSRVEGRLEGAESRLAGVEHGLEKVESRL 135
                                    5566778888888888888888888888888887776666666666665555 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 6.3
                       ISG65-75  56 lketkdklayienakekvdyyvekleslle 85 
                                    l+ ++ +la +e+ +ekv+ +++++ +  e
  gi|119720640|ref|YP_921135.1| 114 LEGAESRLAGVEHGLEKVESRLSRVVKGFE 143
                                    455566666666666666666666655555 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 8.8
                       ISG65-75  76 yvekleslleeakekgtltesdaeklkkaceeAka 110
                                    +vekl++ le+    g+ t+++ae+  +++++A +
  gi|119720640|ref|YP_921135.1| 186 EVEKLREYLEK--DPGEFTMEEAEDFLRLARKAVE 218
                                    44555555554..3555566665555555555544 PP

>> CCDC144C  CCDC144C protein coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.4     0.005      0.72     147     226 ..      10      89 ..       5      92 .. 0.86
   2 ?    3.2   0.1      0.28        41      63     112 ..      98     147 ..      89     196 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.005
                       CCDC144C 147 evLsqqLskaeskansLenelhetrdaLrektlllesvqrdlsqaqcqikeleqmyqneeekvnkyiakqesleerlaql 226
                                    e +  +L ++e ++   e+ l+ ++  L +    lesv+ +l   q ++ + e+ +   e++++k+ ++ e+le r+  +
  gi|119720640|ref|YP_921135.1|  10 EKINARLDRVEERLGGVEKRLEGVEGRLDKVEERLESVEENLGGVQERLTKAERRLADLEGRLSKVEGRLEALERRVDGV 89 
                                    55667888999999999999999999999999999999999999999999999999999999999999999999998655 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.28
                       CCDC144C  63 gqLnvlkaentmlnskLekekqnkerleaevesyrsrLaaAiqdheqsqt 112
                                    ++L++++a  ++++ +Le        +e  +e + srL+ +++  e +q+
  gi|119720640|ref|YP_921135.1|  98 ERLDAVEARLSRVEGRLEGAESRLAGVEHGLEKVESRLSRVVKGFESHQE 147
                                    67888888888888888888888888999999999999988888887765 PP

>> FmiP_Thoc5  Fms-interacting protein/Thoc5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1     0.025       3.6     110     158 ..       8      59 ..       5      74 .. 0.67
   2 ?    4.6   0.0      0.11        16     108     154 ..      55     101 ..      53     183 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.025
                     FmiP_Thoc5 110 qlkeleekkkkleqeieekkkfLssLppkLkslkkatkplqealgl...plt 158
                                    ++++++++   +e+     +k+L+  + +L+++++ ++ ++e+lg    +lt
  gi|119720640|ref|YP_921135.1|   8 KFEKINARLDRVEERLGGVEKRLEGVEGRLDKVEERLESVEENLGGvqeRLT 59 
                                    5677777777777777777888888888888888888888888853222333 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.11
                     FmiP_Thoc5 108 aeqlkeleekkkkleqeieekkkfLssLppkLkslkkatkplqealg 154
                                    +e l++ e++   le   ++ + +L++L+ +++ ++ka+  + e l+
  gi|119720640|ref|YP_921135.1|  55 QERLTKAERRLADLEGRLSKVEGRLEALERRVDGVEKALGDVGERLD 101
                                    56666666666666666667777777777777777776666666664 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   5.3     0.009       1.3      21     106 ..      53     138 ..       5     226 .. 0.51

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.009
                           Fez1  21 dsqaevtqklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelr 100
                                     +q  +t+    +  l ++l  ++ +le+ e++++ +e++l +  + l+ +e++l+r + + e  + ++  +e+ l+++ 
  gi|119720640|ref|YP_921135.1|  53 GVQERLTKAERRLADLEGRLSKVEGRLEALERRVDGVEKALGDVGERLDAVEARLSRVEGRLEGAESRLAGVEHGLEKVE 132
                                    22333333333333333344444444444444444444444444444444444444443333333333333333333333 PP

                           Fez1 101 eelsel 106
                                    ++ls++
  gi|119720640|ref|YP_921135.1| 133 SRLSRV 138
                                    333333 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0     0.021       3.1      23      96 ..       8      79 ..       5      87 .. 0.81
   2 ?    1.3   0.0       3.8   5.6e+02      31      70 ..     100     139 ..      85     155 .. 0.57

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.021
                   Occludin_ELL 23 eYkelhaeleevskkfseLerelkelkegskeykkieeeilqeykklkkdpeyqekkkrceyLkekLshiKkli 96
                                   ++ +++a+l+ v++++  +e++l+  + + ++++++ e++ +++  +  +++  ++++r+ +L+ +Ls +  ++
  gi|119720640|ref|YP_921135.1|  8 KFEKINARLDRVEERLGGVEKRLEGVEGRLDKVEERLESVEENLGGV--QERLTKAERRLADLEGRLSKVEGRL 79
                                   56788888999999999999999999888889999988888888888..7778888899999999998776555 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 3.8
                   Occludin_ELL  31 leevskkfseLerelkelkegskeykkieeeilqeykklk 70 
                                    l++v++++s++e +l+ ++ +   +++  e++ ++++++ 
  gi|119720640|ref|YP_921135.1| 100 LDAVEARLSRVEGRLEGAESRLAGVEHGLEKVESRLSRVV 139
                                    5555555555555555555554444444444444444332 PP

>> Cep57_CLD  Centrosome localisation domain of Cep57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   2.0     0.016       2.4      75     156 ..      32      78 ..       6     109 .. 0.44
   2 ?    7.9   2.1      0.02       2.9      48     130 ..      54     136 ..      36     149 .. 0.55

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.016
                      Cep57_CLD  75 lLEkqLeymrkmvesaekerkavlekqaslekekkqesselqaklekLekLEkeylrLtatqklaekkikeLeekLkeEe 154
                                      E +L+++ +                                   +Le +E++   ++++ ++ae+++++Le +L++ e
  gi|119720640|ref|YP_921135.1|  32 GVEGRLDKVEE-----------------------------------RLESVEENLGGVQERLTKAERRLADLEGRLSKVE 76 
                                    33333333333...................................3333333333333333333333333333333322 PP

                      Cep57_CLD 155 hq 156
                                     +
  gi|119720640|ref|YP_921135.1|  77 GR 78 
                                    22 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.02
                      Cep57_CLD  48 kekekseeskqnqelesqLaaaesrcslLEkqLeymrkmvesaekerkavlekqaslekek.kqesselqaklekLekLE 126
                                     +++ ++++++  +le +L+ +e r + LE++ + + k +     er +++e + s  + + +  +s+l      Lek+E
  gi|119720640|ref|YP_921135.1|  54 VQERLTKAERRLADLEGRLSKVEGRLEALERRVDGVEKALGDV-GERLDAVEARLSRVEGRlEGAESRLAGVEHGLEKVE 132
                                    3334445555556667777777777777777777766666643.345555554444333332444455555555566666 PP

                      Cep57_CLD 127 keyl 130
                                    ++ +
  gi|119720640|ref|YP_921135.1| 133 SRLS 136
                                    5555 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0    0.0025      0.36       9      80 ..      28      98 ..       5     156 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0025
                          TMPIT  9 kefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkk 80
                                   k+++ +e + ++++++le++++    ++++++k ++rl +l+ +l+k++ +++   e++v+ +++ l +  +
  gi|119720640|ref|YP_921135.1| 28 KRLEGVEGRLDKVEERLESVEENLGGVQERLTKAERRLADLEGRLSKVEGRLE-ALERRVDGVEKALGDVGE 98
                                   33334444444444444444444444444444444444444444444444432.223333333333333333 PP

>> T3SS_needle_E  Type III secretion system, cytoplasmic E component of needle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.6      0.02       2.8       4      39 ..      40      74 ..      37      94 .. 0.81
   2 ?    2.2   0.1       1.4     2e+02      11      37 ..      95     121 ..      79     126 .. 0.60
   3 ?    1.6   0.0       2.2   3.2e+02       4      32 ..     110     137 ..     102     148 .. 0.61

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.02
                                   HHHHHCCCCTHHHHHHHHHHHHHHHHHHHHHCCTSS CS
                  T3SS_needle_E  4 LEdrLrhapgeqakelqdrLeaArarLkqalsspqs 39
                                    E+rL  ++ e +  +q+rL +A++rL+    ++ +
  gi|119720640|ref|YP_921135.1| 40 VEERLESVE-ENLGGVQERLTKAERRLADLEGRLSK 74
                                   69*******.*****************976666555 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 1.4
                                    CCTHHHHHHHHHHHHHHHHHHHHHCCT CS
                  T3SS_needle_E  11 apgeqakelqdrLeaArarLkqalssp 37 
                                    + ge ++++ +rL++ + rL+ a s++
  gi|119720640|ref|YP_921135.1|  95 DVGERLDAVEARLSRVEGRLEGAESRL 121
                                    345566666666666666666555555 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 2.2
                                    HHHHHCCCCTHHHHHHHHHHHHHHHHHHH CS
                  T3SS_needle_E   4 LEdrLrhapgeqakelqdrLeaArarLkq 32 
                                     E rL  a+ + ++ + + Le+ + rL +
  gi|119720640|ref|YP_921135.1| 110 VEGRLEGAE-SRLAGVEHGLEKVESRLSR 137
                                    455666666.6666666666666666655 PP

>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   7.4    0.0013      0.19     395     555 ..       8     173 ..       4     203 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0013
                            MAD 395 hneeveaqlevaeeevggykqqastlerelqalr.qqesladass..skeevdslkkkleeLelerqrLreqkeelElel 471
                                    ++e+++a+l+++ee +gg  ++ + +e  l++   + es +++     +e +++  ++l +Le   ++ + + e lE ++
  gi|119720640|ref|YP_921135.1|   8 KFEKINARLDRVEERLGGVEKRLEGVEGRLDKVEeRLESVEEN-LggVQERLTKAERRLADLEGRLSKVEGRLEALERRV 86 
                                    6789999999999999999999999999999999444555554.557899999999999999999999999999999888 PP

                            MAD 472 e..rreLqgd...ydlkktkVlhlseNPaakakqqkkeqlekLqaEierlkellkkleedkekkvaslpessltlafkev 546
                                        + L  +    d  + +     e     a+ + +   + L++  +rl +++k  e+++e  ++ l++++  + +k +
  gi|119720640|ref|YP_921135.1|  87 DgvEKALGDVgerLDAVEARL-SRVEGRLEGAESRLAGVEHGLEKVESRLSRVVKGFESHQEFLIDYLASEG-VIKEKTA 164
                                    876566654411144445543.33345566677777888888999999999999999999998888998885.5788888 PP

                            MAD 547 leLrkeles 555
                                    l +r+el s
  gi|119720640|ref|YP_921135.1| 165 LVVRAELRS 173
                                    888888876 PP

>> DegS  Sensor protein DegS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   4.2     0.022       3.1      45     154 ..      11     119 ..       5     150 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.022
                           DegS  45 evikevdklekkerkarkrLaeVskdFkkyseeeikeaYeeakelqvelallrekEkqlrerRdelerrLkklketierA 124
                                    ++ ++ d++e++     krL  V+ + +k  ee+++++ e+   +q +l+ + ++ ++l  r  ++e rL+ l++ ++  
  gi|119720640|ref|YP_921135.1|  11 KINARLDRVEERLGGVEKRLEGVEGRLDKV-EERLESVEENLGGVQERLTKAERRLADLEGRLSKVEGRLEALERRVDGV 89 
                                    445566666777777777777777777664.5667777777778888888888888888888888888888888888888 PP

                           DegS 125 eklvsqvgvvlnyLsgdlkqvsekledlkq 154
                                    ek +  vg  l+ ++  l++v+ +le +++
  gi|119720640|ref|YP_921135.1|  90 EKALGDVGERLDAVEARLSRVEGRLEGAES 119
                                    888888888888888888888887777665 PP

>> TelA  Toxic anion resistance protein (TelA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0      0.18        26      85     134 ..      10      59 ..       4      74 .. 0.43
   2 ?    4.1   0.0      0.14        20      40      96 ..      90     147 ..      71     155 .. 0.62

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.18
                           TelA  85 eklfakYekaeeqidkIvkeLekgqdellkdnaaLdqlyeknleyfkeLe 134
                                    ek+ a+ +++ee +  + k+Le  + +l k  + L++  e++    ++L+
  gi|119720640|ref|YP_921135.1|  10 EKINARLDRVEERLGGVEKRLEGVEGRLDKVEERLESVEENLGGVQERLT 59 
                                    34444444444444444444444444444444444444333333333333 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.14
                           TelA  40 tkdlgevgklLseLvkelkeldpdelkeekkl.gllplfkkaknkieklfakYekaee 96 
                                    +k+lg+vg+ L  + ++l++++ +  + e +l g+   ++k++++++++++ +e+ +e
  gi|119720640|ref|YP_921135.1|  90 EKALGDVGERLDAVEARLSRVEGRLEGAESRLaGVEHGLEKVESRLSRVVKGFESHQE 147
                                    4666777777777777777777665555555544444667777777777766666554 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   1.6    0.0079       1.1      61     116 ..      11      69 ..       7      92 .. 0.68
   2 ?    3.7   0.0      0.43        62      61     106 ..      95     140 ..      88     151 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0079
                     TPR_MLP1_2  61 alreelnelkaeiaelkaeaesakaeleeseesweeqkeel...ekelselekriedln 116
                                    +++++l+++++++  +++++e ++  l++ ee +e+ +e+l   +++l+++e+r+ dl+
  gi|119720640|ref|YP_921135.1|  11 KINARLDRVEERLGGVEKRLEGVEGRLDKVEERLESVEENLggvQERLTKAERRLADLE 69 
                                    56666777777777777777777777777776666666665444677777777777765 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.43
                     TPR_MLP1_2  61 alreelnelkaeiaelkaeaesakaeleeseesweeqkeelekels 106
                                    ++ e+l+ ++a+++ ++ ++e a++ l+  e  +e+ +++l + ++
  gi|119720640|ref|YP_921135.1|  95 DVGERLDAVEARLSRVEGRLEGAESRLAGVEHGLEKVESRLSRVVK 140
                                    5555666666666666666666666666666666666666655554 PP

>> DUF2333  Uncharacterized protein conserved in bacteria (DUF2333)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0      0.19        28     153     200 ..      13      60 ..       6      64 .. 0.60
   2 ?    6.0   0.1     0.036       5.2     150     205 ..      59     114 ..      44     140 .. 0.66

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.19
                        DUF2333 153 ikalerYlkrlsdekekdaqFyaradnLneyleevekRLgslsqrLsa 200
                                    +  l+r  +rl   +++      r d ++e le+ve+ Lg + +rL++
  gi|119720640|ref|YP_921135.1|  13 NARLDRVEERLGGVEKRLEGVEGRLDKVEERLESVEENLGGVQERLTK 60 
                                    445555556666655655566666666666666666666666666655 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.036
                        DUF2333 150 rkgikalerYlkrlsdekekdaqFyaradnLneyleevekRLgslsqrLsasvgka 205
                                     k+ + l +   rls+ + +      r d +++ l +v +RL+++  rLs+  g+ 
  gi|119720640|ref|YP_921135.1|  59 TKAERRLADLEGRLSKVEGRLEALERRVDGVEKALGDVGERLDAVEARLSRVEGRL 114
                                    45555666666666666666666667777777777777777777777777665554 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   1.3    0.0045      0.64     122     215 ..      18     121 ..       5     139 .. 0.49
   2 ?    4.5   0.3      0.13        19     112     144 ..      78     111 ..      56     201 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0045
                           CorA 122 rlfellekleeeldeledel.edstkkeilrelaq.lrrrlvklrralapnrevlk.......rlla.kaddkllddedk 191
                                    r++e l  +e++l+ +e +l + +++ e ++e +  +++rl+k +r la+++  l+       +l +  +  ++   +  
  gi|119720640|ref|YP_921135.1|  18 RVEERLGGVEKRLEGVEGRLdKVEERLESVEENLGgVQERLTKAERRLADLEGRLSkvegrleALERrVDGVEKALGDVG 97 
                                    55555555555555555555433333333333222255555555555555555553233211111111111112222222 PP

                           CorA 192 eylrdlldelerllemlealrerl 215
                                    e+l+ ++ +l+r++  le   +rl
  gi|119720640|ref|YP_921135.1|  98 ERLDAVEARLSRVEGRLEGAESRL 121
                                    346666666666665555555554 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.13
                           CorA 112 lyrlldeivdrlfellekleeeldeledel.eds 144
                                     ++ l++ vd ++++l ++ e+ld +e +l + +
  gi|119720640|ref|YP_921135.1|  78 RLEALERRVDGVEKALGDVGERLDAVEARLsRVE 111
                                    4566788888888888888888888888885333 PP

>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.1    0.0029      0.42      23     100 ..       7      94 ..       4     165 .. 0.65
   2 ?    0.5   0.0      0.74   1.1e+02      33     118 ..      87     168 ..      77     209 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0029
                     V_ATPase_I  23 rkfvkevrrcdemerklrfleeeieklekavikeeea..........eesleapeekeldeleeelekleeelkelnenl 92 
                                    rkf k   r+d +e++l  +e+ +e  e    k ee           ++++ ++ e++l +le +l+k+e +l+ l++  
  gi|119720640|ref|YP_921135.1|   7 RKFEKINARLDRVEERLGGVEKRLEGVEGRLDKVEERlesveenlggVQERLTKAERRLADLEGRLSKVEGRLEALERRV 86 
                                    67777777888888888888888777777666666654554444444445555555555555555555555555555555 PP

                     V_ATPase_I  93 eklkkeln 100
                                    + ++k l 
  gi|119720640|ref|YP_921135.1|  87 DGVEKALG 94 
                                    55555544 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.74
                     V_ATPase_I  33 demerklrfleeeieklekavikeeea...eesleapeekeldeleeelekleeelkelnenleklkkelnelvelkavl 109
                                    d +e+ l  + e ++  e            +e + +  e++l  +e+ lek+e++l+++ +  e+ ++ l + +  + v+
  gi|119720640|ref|YP_921135.1|  87 DGVEKALGDVGERLDAVEA-------RlsrVEGRLEGAESRLAGVEHGLEKVESRLSRVVKGFESHQEFLIDYLASEGVI 159
                                    3333333333333333222.......122234455556667777788888888888888777777777777777777777 PP

                     V_ATPase_I 110 ekakeflee 118
                                    ++ ++++ +
  gi|119720640|ref|YP_921135.1| 160 KEKTALVVR 168
                                    666555544 PP

>> Dynactin_p22  Dynactin subunit p22
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   4.9       1.1   1.5e+02       2      28 ..      37      63 ..      10      92 .. 0.54
   2 ?    2.7   0.1      0.71     1e+02       2      21 ..      72      91 ..      71      98 .. 0.84
   3 ?    9.6   0.6    0.0053      0.76       2      66 ..     100     154 ..      99     228 .. 0.71

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 1.1
                   Dynactin_p22  2 ldaLEeriaeLEkrvlGeekekekede 28
                                   ld+ Eer+++ E+ + G ++  +k + 
  gi|119720640|ref|YP_921135.1| 37 LDKVEERLESVEENLGGVQERLTKAER 63
                                   444555555555555555554444442 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.71
                   Dynactin_p22  2 ldaLEeriaeLEkrvlGeek 21
                                   l++ E r+++LE+rv G ek
  gi|119720640|ref|YP_921135.1| 72 LSKVEGRLEALERRVDGVEK 91
                                   678999*******9988776 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.0053
                   Dynactin_p22   2 ldaLEeriaeLEkrvlGeekekekedesiidsLakvqkklssavskrekikellkkleelekyLd 66 
                                    lda E+r+++ E r+ G+e+  +  +    + L+kv+++ls++v++ e+ +e+      l +yL 
  gi|119720640|ref|YP_921135.1| 100 LDAVEARLSRVEGRLEGAESRLAGVE----HGLEKVESRLSRVVKGFESHQEF------LIDYLA 154
                                    7999***********99999977777....****************9999888......444554 PP

>> TolA_bind_tri  TolA binding protein trimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   2.9   0.00083      0.12       2      68 ..      40     106 ..      32     112 .. 0.83
   2 ?   11.6   0.2    0.0015      0.22       2      49 ..      75     122 ..      74     147 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00083
                  TolA_bind_tri   2 ledrvarLErilearsqlllelqqqlealqqelreLRGqiEelqyqleqleerQrdlYldlDerlrk 68 
                                    +e+r++++E+ l + ++ l++  ++l +l+  l++  G +E l+ +++ +e+   d  + lD++ ++
  gi|119720640|ref|YP_921135.1|  40 VEERLESVEENLGGVQERLTKAERRLADLEGRLSKVEGRLEALERRVDGVEKALGDVGERLDAVEAR 106
                                    7899999999999999999999999999999999999999999999999998877777777766555 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.0015
                  TolA_bind_tri   2 ledrvarLErilearsqlllelqqqlealqqelreLRGqiEelqyqle 49 
                                    +e r++ LEr +++ +++l ++ ++l+a ++ l++  G +E  + +l 
  gi|119720640|ref|YP_921135.1|  75 VEGRLEALERRVDGVEKALGDVGERLDAVEARLSRVEGRLEGAESRLA 122
                                    799*************************************98777665 PP

>> PTRF_SDPR  PTRF/SDPR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   1.2     0.007         1      11      88 ..      44     121 ..       7     139 .. 0.65
   2 ?    0.2   0.1       3.2   4.6e+02     154     198 ..     151     196 ..     129     204 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.007
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      PTRF_SDPR  11 LdkvvgivdsvqesqkrlEerqaelenavksiqgdllkLakshssTsntvnklleksrkvsvnvkevrerlekqavqv 88 
                                    L+ v + +  vqe  ++ E+r a+le+ ++ + g l  L ++     +++  + e+   v +++  v  rle  ++++
  gi|119720640|ref|YP_921135.1|  44 LESVEENLGGVQERLTKAERRLADLEGRLSKVEGRLEALERRVDGVEKALGDVGERLDAVEARLSRVEGRLEGAESRL 121
                                    444444445555555556666666666666666666666666666666666666666666666666666666655555 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 3.2
                                    .XXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXX CS
                      PTRF_SDPR 154 eveveeeaeesraerlkrsslkkvdsl.KkaFskenlektrqniek 198
                                    ++ ++e + + +++ + r+ l+ v sl  +  +ke++ek r+ +ek
  gi|119720640|ref|YP_921135.1| 151 DYLASEGVIKEKTALVVRAELRSVLSLlSNPLTKEEVEKLREYLEK 196
                                    4566677777778888888888887752567899999999999998 PP

>> Rx_N  Rx N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   3.4     0.059       8.6      11      49 ..      21      59 ..      10     101 .. 0.62
   2 ?    4.9   0.1      0.21        31       2      37 ..     103     138 ..     102     174 .. 0.86
   3 ?   -0.3   0.1       9.1   1.3e+03      24      35 ..     184     195 ..     166     225 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.059
                           Rx_N 11 dllaeeakllkgvkeeleklkdeLesiqavLedaeerqi 49
                                   + l    k+l+gv++ l+k +++Les++  L  + er +
  gi|119720640|ref|YP_921135.1| 21 ERLGGVEKRLEGVEGRLDKVEERLESVEENLGGVQERLT 59
                                   555555556666666666666666665555554444433 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.21
                           Rx_N   2 vsallqkLadllaeeakllkgvkeeleklkdeLesi 37 
                                    v+a l++++  l+   ++l gv++ lek +++L+++
  gi|119720640|ref|YP_921135.1| 103 VEARLSRVEGRLEGAESRLAGVEHGLEKVESRLSRV 138
                                    677788888889999999999999999999999876 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 9.1
                           Rx_N  24 keeleklkdeLe 35 
                                    kee+ekl++ Le
  gi|119720640|ref|YP_921135.1| 184 KEEVEKLREYLE 195
                                    344444444333 PP

>> PspA_IM30  PspA/IM30 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   1.6   0.00088      0.13     102     180 ..      39     120 ..      28     137 .. 0.48

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00088
                      PspA_IM30 102 aletqlaqqrsaveqlrkqlealetkieelkakkellkareka.akaqeavqkslgkls..tesatdslerieeKieere 178
                                    + e+ l+ +++    +++ l+++e+++++l+    ++  r++a  +    v+k+lg +        + l r+e + e  e
  gi|119720640|ref|YP_921135.1|  39 KVEERLESVEENLGGVQERLTKAERRLADLEGRLSKVEGRLEAlERRVDGVEKALGDVGerLDAVEARLSRVEGRLEGAE 118
                                    44444444444444455555555555555555555555554441233444555555554433333344555555555555 PP

                      PspA_IM30 179 ar 180
                                     r
  gi|119720640|ref|YP_921135.1| 119 SR 120
                                    44 PP

>> YscO  Type III secretion protein YscO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   3.3    0.0011      0.16      67     134 ..      15      82 ..      12      90 .. 0.87
   2 ?    3.0   0.5       0.6        87      68     120 ..      79     131 ..      69     147 .. 0.58
   3 ?    0.2   0.1       4.6   6.7e+02     102     119 ..     202     219 ..     173     249 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0011
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           YscO  67 elekvkqqvalLrekeaelekqveeakqqleaerealrqarkelqearraveKfaelarlvraeasrq 134
                                    +l++v ++++  +++ +  e ++++++++le  +e+l   ++ l++a+r ++ ++   ++v+   +++
  gi|119720640|ref|YP_921135.1|  15 RLDRVEERLGGVEKRLEGVEGRLDKVEERLESVEENLGGVQERLTKAERRLADLEGRLSKVEGRLEAL 82 
                                    69***********************************************9988776666666655555 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.6
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           YscO  68 lekvkqqvalLrekeaelekqveeakqqleaerealrqarkelqearraveKf 120
                                    le++ ++v   +++  +  ++++ ++++l + + +l+ a+  l+  ++ +eK+
  gi|119720640|ref|YP_921135.1|  79 LEALERRVDGVEKALGDVGERLDAVEARLSRVEGRLEGAESRLAGVEHGLEKV 131
                                    45555555555555555555555555555555555555555555555555554 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 4.6
                                    HHHHHHHHHHHHHHHHHH CS
                           YscO 102 alrqarkelqearraveK 119
                                    ++++a++ l+ ar+ave+
  gi|119720640|ref|YP_921135.1| 202 TMEEAEDFLRLARKAVEE 219
                                    334444444444444443 PP

>> MPS2  Monopolar spindle protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.5   0.00094      0.14     159     210 ..      37      89 ..      27     105 .. 0.88
   2 ?   -0.2   0.5       3.2   4.6e+02     162     260 ..     103     200 ..      96     227 .. 0.50

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00094
                           MPS2 159 lkaLevrveslkdELeakdevlrekeRelleLkkrlseykekYellqrefs.l 210
                                    l ++e r+es++++L   +e l++ eR l +L+ rls+ + + e l+r+ + +
  gi|119720640|ref|YP_921135.1|  37 LDKVEERLESVEENLGGVQERLTKAERRLADLEGRLSKVEGRLEALERRVDgV 89 
                                    567899*****************************************997745 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 3.2
                           MPS2 162 LevrveslkdELeakdevlrekeRelleLkkrlseykekYellqrefs.lykarrveksqnslktaikheviisElkrkl 240
                                    +e+r+  ++  Le  ++ l+  e  l ++++rls     +e+ q+    +     v k++ +l+   +   ++s l   l
  gi|119720640|ref|YP_921135.1| 103 VEARLSRVEGRLEGAESRLAGVEHGLEKVESRLSRVVKGFESHQEFLIdYLASEGVIKEKTALVVRAELRSVLSLLSNPL 182
                                    56666666666666666666666666666666666655555544322223344444444445444444455555555555 PP

                           MPS2 241 qeqteiisilkeqiqreeGa 260
                                    ++  e +++l+e +++++G 
  gi|119720640|ref|YP_921135.1| 183 TK--EEVEKLREYLEKDPGE 200
                                    43..2345555555555554 PP

>> GreA_GreB_N  Transcription elongation factor, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1       1.3   1.8e+02      44      69 ..      15      40 ..      10      48 .. 0.58
   2 ?    5.5   0.2      0.13        18      49      69 ..      55      75 ..      52      76 .. 0.90
   3 ?    1.4   0.0       2.5   3.7e+02      50      69 ..      98     117 ..      93     118 .. 0.85
   4 ?    3.9   0.1       0.4        59       2      17 ..     181     196 ..     180     225 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 1.3
                                   HHHHHHHHHHHHHHHHHHHHHHHHTE CS
                    GreA_GreB_N 44 eYdaAkeeqaeiearIreLedkLana 69
                                    +d   e+++ +e+r++  e +L+++
  gi|119720640|ref|YP_921135.1| 15 RLDRVEERLGGVEKRLEGVEGRLDKV 40
                                   55555556666666666555555543 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.13
                                   HHHHHHHHHHHHHHHHHHHTE CS
                    GreA_GreB_N 49 keeqaeiearIreLedkLana 69
                                   +e++++ e+r+++Le +L+++
  gi|119720640|ref|YP_921135.1| 55 QERLTKAERRLADLEGRLSKV 75
                                   68999*************986 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 2.5
                                    HHHHHHHHHHHHHHHHHHTE CS
                    GreA_GreB_N  50 eeqaeiearIreLedkLana 69 
                                    e++  +ear++  e +L+ a
  gi|119720640|ref|YP_921135.1|  98 ERLDAVEARLSRVEGRLEGA 117
                                    78889999999999999877 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.4
                                    EE-HHHHHHHHHHHHH CS
                    GreA_GreB_N   2 ylTkegyekleeeLee 17 
                                    +lTke  ekl+e Le+
  gi|119720640|ref|YP_921135.1| 181 PLTKEEVEKLREYLEK 196
                                    89**********9986 PP

>> Uds1  Up-regulated During Septation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   3.9     0.024       3.5      30     117 ..      37     105 ..       7     146 .. 0.53

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.024
                           Uds1  30 lkaLeerlealrkkLa.letklrdaarsLsrlyssskksakssaarsnskssreslakaeeelaeserkvdelaselekl 108
                                    l ++eerle+++++L  ++ +l +a r+L+ l                       l k e  l+++er+vd +++ l  +
  gi|119720640|ref|YP_921135.1|  37 LDKVEERLESVEENLGgVQERLTKAERRLADLE--------------------GRLSKVEGRLEALERRVDGVEKALGDV 96 
                                    333444444444444224444444444444444....................233333333333333333333333333 PP

                           Uds1 109 eeraaevrr 117
                                     er+  v+ 
  gi|119720640|ref|YP_921135.1|  97 GERLDAVEA 105
                                    333333333 PP

>> Cortex-I_coil  Cortexillin I, coiled coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   5.1     0.018       2.6       8      71 ..      13      76 ..       7     115 .. 0.66
   2 ?    4.1   1.4      0.37        54      13      94 ..     116     197 ..     104     209 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.018
                                   XXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                  Cortex-I_coil  8 easknelanklaglenslesekvsreelikqkdelesllasleseaaerekrlreleakldeal 71
                                   +a  + + ++l g+e+ le+     +++  + + +e+ l  ++++  + e+rl++le +l ++ 
  gi|119720640|ref|YP_921135.1| 13 NARLDRVEERLGGVEKRLEGVEGRLDKVEERLESVEENLGGVQERLTKAERRLADLEGRLSKVE 76
                                   4555556677777777777777777777777777777777777777777777777775544332 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.37
                                    XHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                  Cortex-I_coil  13 elanklaglenslesekvsreelikqkdelesll.asleseaaerekrlreleakldealknleleklarlelesrlskt 91 
                                       ++lag+e+ le       +++k  +  ++ l   l se+  +ek    ++a l  +l  l  + l++ e+e     +
  gi|119720640|ref|YP_921135.1| 116 GAESRLAGVEHGLEKVESRLSRVVKGFESHQEFLiDYLASEGVIKEKTALVVRAELRSVLSLLS-NPLTKEEVEKLREYL 194
                                    4568999999999988877888899877776654268999999999999999999988886554.567777777766667 PP

                                    HHH CS
                  Cortex-I_coil  92 ekd 94 
                                    ekd
  gi|119720640|ref|YP_921135.1| 195 EKD 197
                                    776 PP

>> HalX  HalX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   2.5      0.69     1e+02      40      57 ..      33      50 ..       7      61 .. 0.64
   2 ?    7.0   1.9      0.05       7.2      36      60 ..      71      95 ..      55     103 .. 0.71
   3 ?    2.8   0.2         1   1.5e+02      42      60 ..      98     116 ..      91     124 .. 0.68
   4 ?    2.2   0.0       1.6   2.3e+02      44      64 ..     128     148 ..     117     149 .. 0.87
   5 ?    0.6   0.2       4.9     7e+02      42      66 ..     185     211 ..     181     213 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.69
                           HalX 40 Learleelraqldetlde 57
                                    e+rl+ ++++l+ + ++
  gi|119720640|ref|YP_921135.1| 33 VEGRLDKVEERLESVEEN 50
                                   345666666666666555 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.05
                           HalX 36 eYqeLearleelraqldetldeldd 60
                                   + +  e+rle+l++++d +  +l+d
  gi|119720640|ref|YP_921135.1| 71 RLSKVEGRLEALERRVDGVEKALGD 95
                                   6677889999999999999988888 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 1
                           HalX  42 arleelraqldetldeldd 60 
                                    +rl++++a+l+++  +l+ 
  gi|119720640|ref|YP_921135.1|  98 ERLDAVEARLSRVEGRLEG 116
                                    6777777777777766655 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 1.6
                           HalX  44 leelraqldetldelddaddf 64 
                                    le ++++l++++  ++++++f
  gi|119720640|ref|YP_921135.1| 128 LEKVESRLSRVVKGFESHQEF 148
                                    8999************99998 PP

  == domain 5  score: 0.6 bits;  conditional E-value: 4.9
                           HalX  42 arleelraqldetldeldd..addfea 66 
                                    +++e lr+ l+    e++   a+df++
  gi|119720640|ref|YP_921135.1| 185 EEVEKLREYLEKDPGEFTMeeAEDFLR 211
                                    889999999999999955544888775 PP

>> Tnp_22_trimer  L1 transposable element trimerization domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1      0.22        33       1      17 [.      15      31 ..      15      35 .. 0.87
   2 ?    2.4   0.2       1.1   1.6e+02       1      16 [.      36      51 ..      36      62 .. 0.86
   3 ?    4.1   0.0      0.32        47       1      28 [.      64      91 ..      64      94 .. 0.80
   4 ?   -0.3   0.1       7.5   1.1e+03       1      17 [.      99     115 ..      99     133 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.22
                                   HHHHHHHHHHHHHHHHH CS
                  Tnp_22_trimer  1 RidelEERvSaaEDeie 17
                                   R d  EER  + E  +e
  gi|119720640|ref|YP_921135.1| 15 RLDRVEERLGGVEKRLE 31
                                   899**********8877 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 1.1
                                   HHHHHHHHHHHHHHHH CS
                  Tnp_22_trimer  1 RidelEERvSaaEDei 16
                                   R d+ EER    E ++
  gi|119720640|ref|YP_921135.1| 36 RLDKVEERLESVEENL 51
                                   89******99998765 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.32
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                  Tnp_22_trimer  1 RidelEERvSaaEDeieeidrevKereK 28
                                   R  +lE R S  E  +e ++r v   eK
  gi|119720640|ref|YP_921135.1| 64 RLADLEGRLSKVEGRLEALERRVDGVEK 91
                                   6778999999999999999998865555 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 7.5
                                    HHHHHHHHHHHHHHHHH CS
                  Tnp_22_trimer   1 RidelEERvSaaEDeie 17 
                                    R d  E R S  E  +e
  gi|119720640|ref|YP_921135.1|  99 RLDAVEARLSRVEGRLE 115
                                    56666666666664443 PP

>> TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   1.9     0.025       3.6      54     104 ..      18      68 ..       8      70 .. 0.87
   2 ?    7.4   3.6     0.035         5      28      95 ..      37     101 ..      28     108 .. 0.71
   3 ?    4.9   0.4       0.2        29      59      97 ..      65     103 ..      63     153 .. 0.79
   4 ?    1.3   0.6       2.6   3.8e+02      18      59 ..     104     145 ..      96     196 .. 0.62

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.025
                    TMF_TATA_bd  54 keneelkelkkeleelekeleelqeryetlLellGeksEeveELraDvaDl 104
                                    +  e+l   +k+le +e +l++++er+e++ e lG  +E+    +  +aDl
  gi|119720640|ref|YP_921135.1|  18 RVEERLGGVEKRLEGVEGRLDKVEERLESVEENLGGVQERLTKAERRLADL 68 
                                    55678888999*****************************99988888887 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.035
                    TMF_TATA_bd  28 laslkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqeryetlLellGeksEeve 95 
                                    l +++e   rle+  +++     +l+k   +l++l+++l+++e +le+l++r + + + lG   E+ +
  gi|119720640|ref|YP_921135.1|  37 LDKVEE---RLESVEENLGGVQERLTKAERRLADLEGRLSKVEGRLEALERRVDGVEKALGDVGERLD 101
                                    444444...44444444444445788888999999999999999********9999999999998876 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.2
                    TMF_TATA_bd  59 lkelkkeleelekeleelqeryetlLellGeksEeveEL 97 
                                    l++l+++l+++e +le+l++r + + + lG   E+ +  
  gi|119720640|ref|YP_921135.1|  65 LADLEGRLSKVEGRLEALERRVDGVEKALGDVGERLDAV 103
                                    556777788888888888888888877777777776544 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 2.6
                    TMF_TATA_bd  18 sseirrlEgElaslkeelerleaerdeareeivklmkeneel 59 
                                    ++++ r Eg l+ ++++l+ +e+  +++++ + +++k  e+ 
  gi|119720640|ref|YP_921135.1| 104 EARLSRVEGRLEGAESRLAGVEHGLEKVESRLSRVVKGFESH 145
                                    455556666666666666666666665555555555555544 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   3.9    0.0058      0.84      19      93 ..      31     102 ..       7     121 .. 0.46
   2 ?    8.4   0.4     0.021         3      50      97 ..      59     106 ..      51     149 .. 0.49
   3 ?   -0.3   1.1       9.7   1.4e+03      45      58 ..     183     196 ..     125     225 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0058
                         APG6_N  19 eqaekerdaYeeflkklkkekkeeek....qdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelea 93 
                                    e +e   d+ ee l+ ++       +     +e l ++e++l++le   ++ +  L++le+  + +e++l +  e l+a
  gi|119720640|ref|YP_921135.1|  31 EGVEGRLDKVEERLESVE-------EnlggVQERLTKAERRLADLEGRLSKVEGRLEALERRVDGVEKALGDVGERLDA 102
                                    222222222222222222.......122222344444444444444444444444444444444444444444444443 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.021
                         APG6_N  50 eeleeeleklekeeeelleeLkelekereeleaelaaleeelealeee 97 
                                     ++e++l++le   ++ +  L++le+  + +e++l +  e l+a+e+ 
  gi|119720640|ref|YP_921135.1|  59 TKAERRLADLEGRLSKVEGRLEALERRVDGVEKALGDVGERLDAVEAR 106
                                    333444444444444444444444444444444444443333333332 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 9.7
                         APG6_N  45 qdeeleeleeelek 58 
                                    ++ee+e+l+e lek
  gi|119720640|ref|YP_921135.1| 183 TKEEVEKLREYLEK 196
                                    44444455444444 PP

>> DUF4200  Domain of unknown function (DUF4200)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2    0.0033      0.48      15     103 ..       5      93 ..       1      98 [. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0033
                        DUF4200  15 leakkeeiqrleealkqreeelekkeqeleedllkfdkflkendakraralkkaeeerklkkekeaeikklkaeietlks 94 
                                    l++k e+i+ + +++++r   +ek+ +  e +l k+++ l++ +++    +++  + +++  + e  + k +  +e+l+ 
  gi|119720640|ref|YP_921135.1|   5 LGRKFEKINARLDRVEERLGGVEKRLEGVEGRLDKVEERLESVEENLGGVQERLTKAERRLADLEGRLSKVEGRLEALER 84 
                                    67777888888888888888888888888899999999999999999999999999999999999999999999999999 PP

                        DUF4200  95 eiekleekl 103
                                    + +  e++l
  gi|119720640|ref|YP_921135.1|  85 RVDGVEKAL 93 
                                    998888877 PP

>> Val_tRNA-synt_C  Valyl tRNA synthetase tRNA binding arm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   5.4       1.8   2.6e+02       8      28 ..      18      38 ..       8      83 .. 0.56
   2 ?    3.7   1.4      0.53        77      15      37 ..      60      82 ..      54     114 .. 0.53
   3 ?    3.2   0.1      0.77   1.1e+02      12      27 ..     120     135 ..      95     145 .. 0.60
   4 ?   -0.2   0.4       8.7   1.3e+03       2      18 ..     187     203 ..     184     216 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 1.8
                Val_tRNA-synt_C  8 RLeKeLaklekeiervqkKLa 28
                                   R e +L  +ek +e+v+++L 
  gi|119720640|ref|YP_921135.1| 18 RVEERLGGVEKRLEGVEGRLD 38
                                   445555555555555555553 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.53
                Val_tRNA-synt_C 15 klekeiervqkKLanpgFveKAP 37
                                   k+e  ++ ++++L+  + +  A 
  gi|119720640|ref|YP_921135.1| 60 KAERRLADLEGRLSKVEGRLEAL 82
                                   44444444444444433333344 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.77
                Val_tRNA-synt_C  12 eLaklekeiervqkKL 27 
                                    +La +e  +e+v+++L
  gi|119720640|ref|YP_921135.1| 120 RLAGVEHGLEKVESRL 135
                                    3333334444444444 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 8.7
                Val_tRNA-synt_C   2 vekeraRLeKeLaklek 18 
                                    vek+r+ LeK+  +++ 
  gi|119720640|ref|YP_921135.1| 187 VEKLREYLEKDPGEFTM 203
                                    67777888887666655 PP

>> CEP63  Centrosomal protein of 63 kDa
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   2.8     0.074        11      33     101 ..      12      83 ..       5      91 .. 0.52
   2 ?    5.4   0.1     0.099        14     190     229 ..     102     141 ..      95     183 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.074
                          CEP63  33 letrlkireeeLasarnaldekhkEvgllrqqleeleke...kqelvakyeqqlqklreelsklkrsyekLq 101
                                    +++rl+  ee L  + + l+  +    + +++le++e++    qe+ +k e++l  l+  lsk++   e L 
  gi|119720640|ref|YP_921135.1|  12 INARLDRVEERLGGVEKRLEGVEGRLDKVEERLESVEENlggVQERLTKAERRLADLEGRLSKVEGRLEALE 83 
                                    344555555555555555555554444455444444443111455555555555555555555555555555 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.099
                          CEP63 190 dsqseiqrLrskleraqdtleaqelelerLrllveelgks 229
                                    ++++++ r++ +le a+++l + e  le+ +++++ ++k 
  gi|119720640|ref|YP_921135.1| 102 AVEARLSRVEGRLEGAESRLAGVEHGLEKVESRLSRVVKG 141
                                    467999***************************9999874 PP

>> Asp4  Accessory secretory protein Sec Asp4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.4       8.1   1.2e+03       8      15 ..      39      46 ..      26      64 .. 0.66
   2 ?    8.3   0.1     0.014         2       8      25 ..      74      91 ..      70      95 .. 0.86
   3 ?    0.7   0.1       3.2   4.7e+02       8      23 ..     109     124 ..     107     133 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 8.1
                           Asp4  8 eveGrmes 15
                                    ve r+es
  gi|119720640|ref|YP_921135.1| 39 KVEERLES 46
                                   35555555 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.014
                           Asp4  8 eveGrmeslkrrPaekek 25
                                    veGr+e+l rr    ek
  gi|119720640|ref|YP_921135.1| 74 KVEGRLEALERRVDGVEK 91
                                   69**********877776 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 3.2
                           Asp4   8 eveGrmeslkrrPaek 23 
                                     veGr+e    r a  
  gi|119720640|ref|YP_921135.1| 109 RVEGRLEGAESRLAGV 124
                                    59*****988887765 PP

>> PspB  Phage shock protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.3       1.6   2.3e+02      40      62 ..      27      49 ..      10      53 .. 0.78
   2 ?    6.1   0.4     0.078        11      36      65 ..      59      87 ..      50      95 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 1.6
                           PspB 40 ekrLeellekAekleeRietLEr 62
                                   ekrLe +  + +k eeR+e++E+
  gi|119720640|ref|YP_921135.1| 27 EKRLEGVEGRLDKVEERLESVEE 49
                                   56788888888889999998886 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.078
                           PspB 36 saedekrLeellekAekleeRietLEriLd 65
                                   ++  e+rL++l  + +k e R+e+LEr +d
  gi|119720640|ref|YP_921135.1| 59 TK-AERRLADLEGRLSKVEGRLEALERRVD 87
                                   43.467899999999**********98665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1186  (0.0661498); expected 358.6 (0.02)
Passed bias filter:                      912  (0.0508673); expected 358.6 (0.02)
Passed Vit filter:                       216  (0.0120475); expected 17.9 (0.001)
Passed Fwd filter:                       132  (0.00736237); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):             124  [number of targets reported over threshold]
# CPU time: 1.41u 0.39s 00:00:01.79 Elapsed: 00:00:00.58
# Mc/sec: 1338.12
//
Query:       gi|119720641|ref|YP_921136.1|  [L=514]
Description: polysaccharide biosynthesis protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-24   87.1  23.5    2.2e-24   86.3  17.0    2.1  2  Polysacc_synt    Polysaccharide biosynthesis protein
    1.8e-22   80.0   5.7    1.8e-22   80.0   5.7    1.9  2  Polysacc_synt_3  Polysaccharide biosynthesis protein
    9.5e-10   38.7   7.7    9.5e-10   38.7   7.7    4.0  4  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai


Domain annotation for each model (and alignments):
>> Polysacc_synt  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.3  17.0   3.6e-28   2.2e-24       5     273 ..      18     286 ..      15     287 .. 0.87
   2 !    4.8   0.4    0.0026        16     112     189 ..     337     413 ..     309     431 .. 0.89

  Alignments for each domain:
  == domain 1  score: 86.3 bits;  conditional E-value: 3.6e-28
                  Polysacc_synt   5 vivlllsqlitkllafvtlvylarilgpegfGlvalalaivtllviltdlGlnaalvreiakyrekkelvslillnvllv 84 
                                    + ++l +q  + l+a +  ++larilgpeg+G++ala+++++ll+i+td+G++aa+ re ++  +  e v+ ++  +l  
  gi|119720641|ref|YP_921136.1|  18 AVSILGGQASATLVAGIASILLARILGPEGYGKYALATTVASLLSIFTDFGVSAAVAREASRRGR--EGVAGLVGLALAF 95 
                                    5677888999999999************************************************9..6666555555555 PP

                  Polysacc_synt  85 llvlvllfllllliaa....flglpelavlylilalmll.llvgvasfrrglfqglermkyaavsqvveqlsrvilvlia 159
                                    +l ++l+ ++l  +      +l l ++ ++ l+l +  + +l++   f +  + gl +  ++a   v++ lsr +l+l++
  gi|119720641|ref|YP_921136.1|  96 TLASALVSTALGALLSerltLLLLNRAEMVQLTLLALPTvFLNSALNFSYFALLGLGDTASLAALPVIRDLSRSVLSLAL 175
                                    555555555554444457877777777777666666666688888889999999************************** PP

                  Polysacc_synt 160 vflfldivaavlgavlaalvggivslavlrkkfrprfvilslklvrellsfsapltisslaillytyidsillglllgae 239
                                        + + +av+g+v+++ +++  +la l++++++    +     + ll +++pl +ss++++l+      ++++++ ++
  gi|119720641|ref|YP_921136.1| 176 AAAYG-VPGAVAGLVAGYALAAASGLAALYRRLGRLPLAP-AGELKPLLGYGLPLYASSVLGTLSGIYQNSVAAWFATDV 253
                                    *****.9***********************9998777777.899**********************99999********* PP

                  Polysacc_synt 240 avGiYnaayqllvaisgllapivtaalfPvfsel 273
                                    +vG++ +a +++ +i+ l+api   +l P+fs+l
  gi|119720641|ref|YP_921136.1| 254 EVGNFKVAMNFAALIQLLVAPISL-SLLPAFSRL 286
                                    **********************99.*******97 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0026
                  Polysacc_synt 112 lilalmllllvgvasfrrglfqglermkyaavsqvveqlsrvilvliavflfldivaavlgavlaalvggivslavlr 189
                                     +++++lll   +++   ++fqg+ + ++++  +++   + + l + ++   + ++++v+++v+++  ++ ++ +  r
  gi|119720641|ref|YP_921136.1| 337 SLYSASLLLSGLGTAALPSFFQGVGDTRANLEASLAGLAVLLPLAAPLTQRLG-LYGLVASLVASSASSAAYGVWRAR 413
                                    678899999***************************99999999999999999.*************99999988776 PP

>> Polysacc_synt_3  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.0   5.7   2.9e-26   1.8e-22       1     289 [.      38     330 ..      38     332 .. 0.81
   2 ?   -0.5   0.1     0.098   5.8e+02     117     161 ..     365     412 ..     361     431 .. 0.77

  Alignments for each domain:
  == domain 1  score: 80.0 bits;  conditional E-value: 2.9e-26
                Polysacc_synt_3   1 vLARLLspedFGvvaialvvislanlfvdmGlssaliqke.dlteedlstvftfnlvlgllialvlfllaplias..... 74 
                                    +LAR+L pe +G +a+a++v sl+++f+d+G+s a+ ++  ++ +e +  +  + l++ l+ alv  +l  l+++     
  gi|119720641|ref|YP_921136.1|  38 LLARILGPEGYGKYALATTVASLLSIFTDFGVSAAVAREAsRRGREGVAGLVGLALAFTLASALVSTALGALLSErltll 117
                                    69*************************************95555555555555555555555555555555555444446 PP

                Polysacc_synt_3  75 fynqpelvtvlrvlalvlilsglssvqeallrrelkFkklfkitlvssvvgvivaivlAll..glgvwA.Lvigtllssl 151
                                    ++n +e+v+++ ++  +++l+++ + +   l    +  +l++  ++  +   +++++lA +    g+ A Lv g  l+++
  gi|119720641|ref|YP_921136.1| 118 LLNRAEMVQLTLLALPTVFLNSALNFSYFALLGLGDTASLAALPVIRDLSRSVLSLALAAAygVPGAVAgLVAGYALAAA 197
                                    789999999888888899*******************************9988877776540044544435555555555 PP

                Polysacc_synt_3 152 lslvllwlaskwrprlkfslkslkelfsfglklllsnllnylarnldnlliGkvlssaaLGlYsvakrlaslpvaeitsv 231
                                      l++l+ ++   p       +lk+l+++gl l +s++l +l+   +n + +++ ++ ++G ++va+++a  +++ + ++
  gi|119720641|ref|YP_921136.1| 198 SGLAALYRRLGRLPL--APAGELKPLLGYGLPLYASSVLGTLSGIYQNSVAAWFATDVEVGNFKVAMNFAA-LIQLLVAP 274
                                    555555444444444..4678***********************************************986.5799**** PP

                Polysacc_synt_3 232 iakVlfPalSrlqddkkklrelylkvlrlialivlPiavglavvaellvkvllGsqWl 289
                                    i+  l+Pa+Srl+ d  +  + ++ + r ++li +P+ v+ av ++ lv +++G+++ 
  gi|119720641|ref|YP_921136.1| 275 ISLSLLPAFSRLSGD--DSGRFFRYAARYTGLILVPAGVYAAVESRDLVALVYGREYA 330
                                    **************9..66899********************************9985 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.098
                Polysacc_synt_3 117 itlvssvvgvivaivlAl...lglgvwALvigtllssllslvllwlas 161
                                    ++l +s++g++v + lA      lg++ Lv + ++ss+ s++  ++++
  gi|119720641|ref|YP_921136.1| 365 ANLEASLAGLAVLLPLAApltQRLGLYGLVASLVASSASSAAYGVWRA 412
                                    6677888888888888862224589********999999988877765 PP

>> Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.9   8.9         3   1.8e+04      39      85 ..      33      78 ..      25     119 .. 0.41
   2 ?   -0.8   5.8      0.24   1.4e+03      54      99 ..      87     132 ..      84     160 .. 0.56
   3 !   11.2   9.2   4.9e-05      0.29       6     120 ..     132     261 ..     127     280 .. 0.77
   4 !   38.7   7.7   1.6e-13   9.5e-10       1     142 [.     335     471 ..     335     472 .. 0.84

  Alignments for each domain:
  == domain 1  score: -4.9 bits;  conditional E-value: 3
                Polysacc_synt_C 39 alvklilnllliplfgivG.aaiatvlallvvavlnlyalrrllgikl 85
                                    ++ ++l  +l p    +G  a+at++a l++++  +       +   
  gi|119720641|ref|YP_921136.1| 33 GIASILLARILGP--EGYGkYALATTVASLLSIFTDFGVSAAVAREAS 78
                                   4444444444444..236677777777777766655333333222222 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.24
                Polysacc_synt_C  54 givGaaiatvlallvvavlnlyalrrllgikl.ellrrllkpllaal 99 
                                    g+vG a+a +la ++v+  +  +l+ +l + l + +  ++ + l+al
  gi|119720641|ref|YP_921136.1|  87 GLVGLALAFTLASALVSTALGALLSERLTLLLlN-RAEMVQLTLLAL 132
                                    7889777777777666666666666666665532.333333333333 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 4.9e-05
                Polysacc_synt_C   6 alsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplfgivGaaiatvlallvvavlnlyalrrllgikl 85 
                                     +++++ s  +++   L glg +  ++   vi  l   +l+l l   +g+ Ga+++ v++++++a+  l al+r+lg  +
  gi|119720641|ref|YP_921136.1| 132 LPTVFLNSALNFSYFALLGLGDTASLAALPVIRDLSRSVLSLALAAAYGVPGAVAGLVAGYALAAASGLAALYRRLGRLP 211
                                    5677888888999999999999999999999999******************************************9999 PP

                Polysacc_synt_C  86 .......ellrrllkpllaalvmgivvylllllllglllla.........a 120
                                           + l     pl a+ v+g +  ++++  + +++           a
  gi|119720641|ref|YP_921136.1| 212 lapagelKPLLGYGLPLYASSVLGTL-SGIYQNSVAAWFATdvevgnfkvA 261
                                    99897443344444899999998888.446666555555545555544441 PP

  == domain 4  score: 38.7 bits;  conditional E-value: 1.6e-13
                Polysacc_synt_C   1 vLailalsiiflsls.tvlssiLqglgrqkialkalvigalvklilnllliplfgivGaaiatvlallvvavlnlyalrr 79 
                                    +L++++ s+++++l    l s +qg+g +++ l a+++g++v l l  +l+ ++g++G +++ v++ + +a++ ++++rr
  gi|119720641|ref|YP_921136.1| 335 YLSLYSASLLLSGLGtAALPSFFQGVGDTRANLEASLAGLAVLLPLAAPLTQRLGLYGLVASLVASSASSAAYGVWRARR 414
                                    5899***********999*************************************************************9 PP

                Polysacc_synt_C  80 llgiklellrrllkpllaalvmgivvylllllllgllllaalalllavlvgalvYlllllllr 142
                                     +g  +++l  + ++++aal+  + +    l ll++ +  al +++ + + al+Y++l+ l++
  gi|119720641|ref|YP_921136.1| 415 -VGAEVDFLHAT-RTCAAALAALAPL--APLALLNVHP--ALRVAATATAYALAYGALAPLFG 471
                                    .55566545544.8888888888883..3344444443..46778888899999999987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (514 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 3061.66
//
Query:       gi|119720642|ref|YP_921137.1|  [L=204]
Description: cobalamin (vitamin B12) biosynthesis CbiM protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-64  216.9  19.2    2.9e-64  216.7  19.2    1.0  1  CbiM      Cobalt uptake substrate-specific transmembrane regi


Domain annotation for each model (and alignments):
>> CbiM  Cobalt uptake substrate-specific transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  216.7  19.2   1.6e-68   2.9e-64       1     207 []       2     201 ..       2     201 .. 0.96

  Alignments for each domain:
  == domain 1  score: 216.7 bits;  conditional E-value: 1.6e-68
                           CbiM   1 HipdgiLspavllaayavalallalalrrlrkeldearvpllallaafifaaqminipipggtslHllgavlaaiLlGpw 80 
                                    Hipdg+L+pa+++++ya++la+la+++ ++r+    ++  l+ +laa+ifaaqm+n+pipggtslHl+g++la iL+Gpw
  gi|119720642|ref|YP_921137.1|   2 HIPDGYLDPAMCAVTYALSLAVLAFSALKARSA-GSEQKTLVPVLAAAIFAAQMLNWPIPGGTSLHLVGGALASILVGPW 80 
                                    *******************************99.666678**************************************** PP

                           CbiM  81 aaflavavvlllqallfgdGGitaLGaNilnmavigvllaylvyrllsrlasskkrvalaaflaallsvvlaallvalel 160
                                    +a l++++vll qal+f+dGGit+LGaN+lnm++++v+++yl yr+++++      ++++afla++ls++la++++++el
  gi|119720642|ref|YP_921137.1|  81 LASLTMFLVLLTQALVFHDGGITTLGANVLNMGIVAVFAGYLAYRAFPER-----LRVVGAFLAGWLSITLAGVVCGVEL 155
                                    *********************************************99555.....689********************** PP

                           CbiM 161 alsgleaslsltaalaamllvhlpvgilEgviTaaivkalkkvrpel 207
                                    +ls++ + ++l +++++m  +h+++g++Eg+iTa ++++lk+ +p+l
  gi|119720642|ref|YP_921137.1| 156 GLSKQ-FLYGLSVTVPVMGGWHALLGVVEGLITASVYAYLKSKAPQL 201
                                    ***66.78*********************************999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       662  (0.0369234); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1324.79
//
Query:       gi|119720643|ref|YP_921138.1|  [L=100]
Description: cobalamin biosynthesis protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.6e-09   36.1   0.2    9.7e-09   35.0   0.2    1.5  1  PDGLE     PDGLE domain
  ------ inclusion threshold ------
       0.12   12.8   0.5       0.25   11.8   0.5    1.7  1  DUF4014   Protein of unknown function (DUF4014)
        2.6    8.2   8.9        2.2    8.4   2.5    2.2  2  TPPK_C    Thiamine pyrophosphokinase C terminal


Domain annotation for each model (and alignments):
>> PDGLE  PDGLE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.2   1.6e-12   9.7e-09       2      87 ..      21      95 ..      20      97 .. 0.88

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 1.6e-12
                          PDGLE  2 aalliggvlswfAS..anPdGLEwsiekvagtaeleasgdlhealaeiqektalLpDYsfkgaeekkagtsvAgivGvlltl 81
                                   + l+  ++ +w+A+  ++++ L+ ++e +          +l+e+++ei+  ++++ DY+++g +++ +g++v+g++Gv+++l
  gi|119720643|ref|YP_921138.1| 21 MVLVSPVFGVWLANlvGYHEPLDLAAEAL----------GLNETTEEIN--WTPFLDYTVPGLPDW-LGYIVSGFLGVAVVL 89
                                   66788888999998889999999999995..........6888888888..***************.*************** PP

                          PDGLE 82 alagli 87
                                   al +l+
  gi|119720643|ref|YP_921138.1| 90 ALGYLL 95
                                   **9876 PP

>> DUF4014  Protein of unknown function (DUF4014)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.5   4.2e-05      0.25      23      42 ..      16      35 ..       5      67 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.2e-05
                        DUF4014 23 lflilmvpispiffiwlagv 42
                                   l ++ mv +sp+f +wla +
  gi|119720643|ref|YP_921138.1| 16 LAVLAMVLVSPVFGVWLANL 35
                                   67789************975 PP

>> TPPK_C  Thiamine pyrophosphokinase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   2.5   0.00037       2.2      23      45 ..      14      36 ..      14      38 .. 0.91
   2 ?    3.6   0.5     0.012        70      16      33 ..      74      91 ..      68      92 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00037
                         TPPK_C 23 aLvAvavallvspagqsfldlli 45
                                   a +Av++ +lvsp++ ++l +l+
  gi|119720643|ref|YP_921138.1| 14 AALAVLAMVLVSPVFGVWLANLV 36
                                   568****************9985 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.012
                         TPPK_C 16 llllvlAaLvAvavallv 33
                                   +l  +++++++vav+l++
  gi|119720643|ref|YP_921138.1| 74 WLGYIVSGFLGVAVVLAL 91
                                   888899*********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       711  (0.0396564); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 597.42
//
Query:       gi|119720644|ref|YP_921139.1|  [L=242]
Description: cobalt transport protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-13   49.9   9.6      7e-13   48.7   9.6    1.6  1  CbiQ      Cobalt transport protein


Domain annotation for each model (and alignments):
>> CbiQ  Cobalt transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.7   9.6   3.9e-17     7e-13      41     211 ..      36     210 ..      32     217 .. 0.85

  Alignments for each domain:
  == domain 1  score: 48.7 bits;  conditional E-value: 3.9e-17
                                    HHHHTTS---.HHHHHHHCCCHCHHHHHHHHHHE.......EECTTEEE..........E-TTHHHHHHHHHHHHHHHHH CS
                           CbiQ  41 llllllvilp.rvlaqalilpllflllgllillfqlittegefvfaggg.......qisitseGllrglllalRiltlls 112
                                    l+l++l+++    +a+ ++ p + + lg++++++ + +  g+++++  +        +    +G   + l++lR ++++s
  gi|119720644|ref|YP_921139.1|  36 LVLVGLAADVeASYASGPATPAMAIALGAVLAAT-SRKLRGWLTVTLVSaffaglvALPALLRGDPGAPLFVLRAVAASS 114
                                    5666777777778888899999999999999999.5555555555555533333335666667777889*********** PP

                                    HHHHHHHHS-HHHHHHHCCCSS--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTS..SHHHHHHHHHHHHHHHHHH CS
                           CbiQ 113 lllllalTTppeeltsslerlgvPlelalillLayRfiflLleevqrikqAqklRlgdsklgirrslrslgkliaalflr 192
                                    + + ++++  +  l+ +le+l+ P+ l+  l L++R+i++++  ++r+  A+++Rl+ s  ++++ ++ +  +++ l+l 
  gi|119720644|ref|YP_921139.1| 115 AFTGVLASLGWLWLLRGLEELRLPRGLVWELGLTLRAIPVFARDASRMLAAREARLLAS--SRAS-WSVVSSVAGDLLLA 191
                                    ***********************************************************..5555.************** PP

                                    HHHHHHHHHHHHHTTS-SS CS
                           CbiQ 193 alkraervalAmeaRGYtg 211
                                     ++ra++++ A+eaR +  
  gi|119720644|ref|YP_921139.1| 192 GVRRARALQMALEARSFGE 210
                                    ***************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.51
# Mc/sec: 1417.23
//
Query:       gi|119720645|ref|YP_921140.1|  [L=239]
Description: ABC transporter related [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.1e-33  114.5   0.0    7.2e-33  114.0   0.0    1.2  1  ABC_tran      ABC transporter
    3.6e-16   59.8   0.1    8.1e-08   32.4   0.0    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    2.5e-05   23.9   0.1    4.7e-05   23.0   0.1    1.4  1  AAA_29        P-loop containing region of AAA domain
    0.00012   21.6   0.0      0.085   12.3   0.0    2.1  2  SMC_N         RecF/RecN/SMC N terminal domain
    0.00026   21.4   0.5    0.00042   20.7   0.5    1.4  1  AAA_16        AAA ATPase domain
    0.00084   19.9   0.0     0.0013   19.3   0.0    1.2  1  AAA_23        AAA domain
     0.0011   18.5   0.3     0.0025   17.4   0.3    1.6  1  AAA_25        AAA domain
     0.0013   18.4   0.0     0.0036   17.0   0.0    1.7  2  SRP54         SRP54-type protein, GTPase domain
     0.0073   16.2   0.2      0.016   15.2   0.2    1.6  1  NACHT         NACHT domain
  ------ inclusion threshold ------
      0.011   15.5   0.0      0.021   14.6   0.0    1.5  2  AAA_15        AAA ATPase domain
      0.017   15.4   0.1       0.03   14.6   0.1    1.8  1  AAA_28        AAA domain
      0.018   15.2   0.1       0.04   14.1   0.1    1.8  1  AAA_33        AAA domain
      0.022   15.2   0.0      0.037   14.5   0.0    1.4  1  AAA           ATPase family associated with various cellular 
      0.038   13.7   0.2        0.1   12.3   0.1    1.6  2  AAA_30        AAA domain
      0.065   12.5   0.0       0.12   11.7   0.0    1.4  1  Zeta_toxin    Zeta toxin
      0.079   12.4   0.0       0.14   11.6   0.0    1.3  1  RecA          recA bacterial DNA recombination protein
      0.093   12.5   0.0       0.21   11.3   0.0    1.6  2  IstB_IS21     IstB-like ATP binding protein
      0.098   12.7   0.2        0.2   11.7   0.2    1.5  1  AAA_5         AAA domain (dynein-related subfamily)
        0.1   13.2   0.0       0.17   12.4   0.0    1.5  1  AAA_18        AAA domain
       0.15   10.9   0.1       0.21   10.4   0.1    1.1  1  DLIC          Dynein light intermediate chain (DLIC)
       0.16   11.6   0.3       0.26   10.9   0.3    1.3  1  cobW          CobW/HypB/UreG, nucleotide-binding domain
       0.16   12.2   0.0       0.95    9.7   0.0    2.1  1  SbcCD_C       Putative exonuclease SbcCD, C subunit
       0.17   11.2   0.0       0.25   10.7   0.0    1.2  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
       0.17   12.2   0.1        1.6    9.0   0.1    2.0  2  AAA_19        AAA domain
       0.18   11.0   0.1        1.7    7.8   0.1    2.0  2  NB-ARC        NB-ARC domain
       0.25   11.4   0.0       0.59   10.2   0.0    1.6  1  AAA_14        AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.0   0.0     1e-35   7.2e-33       1     137 []      18     163 ..      18     163 .. 0.97

  Alignments for each domain:
  == domain 1  score: 114.0 bits;  conditional E-value: 1e-35
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS..--S-TTSBHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxx RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe..pqlfpeltvre 78 
                                    l+ v+l l++ge+va++G+nG+GK+tLl +lagllkp  G++lldg+dl + +l+ +r++ig ++q+  +qlf+ + v+e
  gi|119720645|ref|YP_921140.1|  18 LRGVTLGLERGEVVALLGPNGSGKTTLLLALAGLLKPSRGSVLLDGRDLWS-QLPGARRRIGLVFQDpdDQLFNPT-VEE 95 
                                    6789*********************************************99.9**************988999998.999 PP

                                    H.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    x.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  79 n.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                    +             e+ +++e+a++ lg ++l d++v    + LS+G+k+rvala +l+ +p+ lllDEpta
  gi|119720645|ref|YP_921140.1|  96 ElafalnqlglpeaEKASRLERAARMLGVEGLLDRPV----HALSYGEKRRVALASVLVYDPEYLLLDEPTA 163
                                    99***********999999******************....*****************************97 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.1     5e-09   3.5e-06       2      88 ..      31     113 ..      30     122 .. 0.75
   2 !   32.4   0.0   1.2e-10   8.1e-08     220     298 ..     118     193 ..      79     198 .. 0.80

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 5e-09
                         AAA_21   2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrlers 81 
                                     +l GpNgsGK++LL al +l           +  s   + r+ +s l++   +i  +f++++ ++ ++  + +l +  +
  gi|119720645|ref|YP_921140.1|  31 VALLGPNGSGKTTLLLALAGLLK--------PSRGSVLLDGRDLWSQLPGARRRIGLVFQDPDDQLFNPTVEEELAFALN 102
                                    689******************64........3444445567888888888888888888888888888888888888888 PP

                         AAA_21  82 qv....eekls 88 
                                    q+    +ek s
  gi|119720645|ref|YP_921140.1| 103 QLglpeAEKAS 113
                                    87666555554 PP

  == domain 2  score: 32.4 bits;  conditional E-value: 1.2e-10
                         AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHS 298
                                      + l  ++  ++p++ lS G kr  al++ l +++     ll+DEp ++L+P+  + lle + +l+r+g  v+l+T++
  gi|119720645|ref|YP_921140.1| 118 AARMLGVEGLLDRPVHALSYGEKRRVALASVLVYDP---EYLLLDEPTANLDPRSASALLEAVCRLKREGRGVLLATQD 193
                                    555566677788999999******************...56**********************999999********98 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.1   6.8e-08   4.7e-05      15      50 ..      21      56 ..      16      59 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 6.8e-08
                         AAA_29 15 htieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                    t+ +++ +++ l Gp+GsGK+Tll A++ lL p++
  gi|119720645|ref|YP_921140.1| 21 VTLGLERGEVVALLGPNGSGKTTLLLALAGLLKPSR 56
                                   56667766699*********************9986 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   0.00012     0.085      25      45 ..      29      49 ..      21      64 .. 0.86
   2 !    7.7   0.0    0.0031       2.2     136     188 ..     134     182 ..      73     208 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00012
                                   SEEEEEESTTSSHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 25 sftaivGpNGSGKsnlldAil 45
                                   ++ a++GpNGSGK+ ll A+ 
  gi|119720645|ref|YP_921140.1| 29 EVVALLGPNGSGKTTLLLALA 49
                                   57799***********99885 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0031
                                    CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksk 188
                                    +LS Gek  vala +     ++p+ l llDe  a+LD +  +++ e + + + 
  gi|119720645|ref|YP_921140.1| 134 ALSYGEKRRVALASV---LVYDPEYL-LLDEPTANLDPRSASALLEAVCRLKR 182
                                    79******9999966...67888865.79*************99999887655 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.5   6.1e-07   0.00042      23     119 ..      27     173 ..      16     194 .. 0.53

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 6.1e-07
                         AAA_16  23 rpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekle 102
                                    r+e+v l G+ G+GK++l+ +l+  l+ ++g +l    d          + q+  +++ +  + ++++++++++     e
  gi|119720645|ref|YP_921140.1|  27 RGEVVALLGPNGSGKTTLLLALAGLLKPSRGSVLLDGRDL---------WSQLPGARRRIGLVFQDPDDQLFNPT---VE 94 
                                    4599*******************88888865554444444.........45666666677777777444333333...33 PP

                         AAA_16 103 eala..............................................................avpelagaeasrl 119
                                    e+la                                                              ++++l++ +as+l
  gi|119720645|ref|YP_921140.1|  95 EELAfalnqlglpeaekasrleraarmlgveglldrpvhalsygekrrvalasvlvydpeyllldePTANLDPRSASAL 173
                                    3333434444444433333333333333344444444444444444444444444444444444443333333333333 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.8e-06    0.0013      11      40 ..      19      49 ..      12      55 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.8e-06
                         AAA_23 11 rdqeidFsk.gltlItGpNGaGKTTildAik 40
                                   r++++ +++  ++++ GpNG+GKTT+l A+ 
  gi|119720645|ref|YP_921140.1| 19 RGVTLGLERgEVVALLGPNGSGKTTLLLALA 49
                                   55666665525899*************9986 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.3   3.6e-06    0.0025      30      54 ..      25      49 ..      17      87 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.6e-06
                         AAA_25 30 lpagelallaGapgtGKttlaldla 54
                                   l +ge+++l G+ g+GKttl+l la
  gi|119720645|ref|YP_921140.1| 25 LERGEVVALLGPNGSGKTTLLLALA 49
                                   479*******************998 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   5.2e-06    0.0036       3      40 ..      30      67 ..      28      78 .. 0.92
   2 ?   -2.3   0.0       4.2   2.9e+03     158     178 ..     120     140 ..     114     146 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 5.2e-06
                                   EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTS CS
                          SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvllvaaDtf 40
                                   v++l+G++G+GKTt l  La llk +  +vll   D +
  gi|119720645|ref|YP_921140.1| 30 VVALLGPNGSGKTTLLLALAGLLKPSRGSVLLDGRDLW 67
                                   899***********************999999888865 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4.2
                                    HHHHHHHHHTS-EEEEE-SSS CS
                          SRP54 158 aalsiaaelklPikfigvGek 178
                                     +l ++  l+ P+  +++Gek
  gi|119720645|ref|YP_921140.1| 120 RMLGVEGLLDRPVHALSYGEK 140
                                    578888899999*99999998 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.2   2.3e-05     0.016       2      26 ..      30      54 ..      29      61 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.3e-05
                                   CEEEEC-TTTCHHHHHHHHHHHHCT CS
                          NACHT  2 lvilqGeaGsGKTtLlqklalawae 26
                                   +v+l G++GsGKTtLl  la +++ 
  gi|119720645|ref|YP_921140.1| 30 VVALLGPNGSGKTTLLLALAGLLKP 54
                                   799*************999988775 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0     3e-05     0.021      25      50 ..      30      55 ..      18     117 .. 0.84
   2 ?   -1.8   0.0       2.9     2e+03     326     355 ..     155     184 ..     128     191 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3e-05
                         AAA_15 25 ltvliGkNnsGKSsilealdlFlnnk 50
                                   +  l G+N+sGK+++l al  +l+ +
  gi|119720645|ref|YP_921140.1| 30 VVALLGPNGSGKTTLLLALAGLLKPS 55
                                   78999**************9999977 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.9
                         AAA_15 326 illiEEPEahLHpqaqkvlikllkelandn 355
                                     ll++EP a+L p   + l ++ ++l +++
  gi|119720645|ref|YP_921140.1| 155 YLLLDEPTANLDPRSASALLEAVCRLKREG 184
                                    489999999999999999999988886665 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   4.4e-05      0.03       2      21 ..      31      55 ..      30     237 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.4e-05
                         AAA_28  2 ivitGgestGKTtlleaLa.....a 21
                                   ++++G+ ++GKTtll aLa     +
  gi|119720645|ref|YP_921140.1| 31 VALLGPNGSGKTTLLLALAgllkpS 55
                                   899***************9555443 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   5.8e-05      0.04       1      39 [.      30      72 ..      30     225 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.8e-05
                         AAA_33  1 lvllvGlpGsGKstlaerllkklg....avllssdtlrrrlfg 39
                                   +v l G++GsGK+tl+  l+  l+     vll+  +l ++l g
  gi|119720645|ref|YP_921140.1| 30 VVALLGPNGSGKTTLLLALAGLLKpsrgSVLLDGRDLWSQLPG 72
                                   78999**********9988666555557777777776665555 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   5.3e-05     0.037       2      41 ..      32      73 ..      31      93 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.3e-05
                                   EEESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSSSTTH CS
                            AAA  2 llyGppGtGKTllakavakelg..vefleisgsellskyvge 41
                                    l Gp G GKT+l  a+a  l+  +  + ++g +l+s++ g+
  gi|119720645|ref|YP_921140.1| 32 ALLGPNGSGKTTLLLALAGLLKpsRGSVLLDGRDLWSQLPGA 73
                                   699****************99754557888888888765554 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00015       0.1      18      49 ..      28      59 ..      21      64 .. 0.82
   2 ?   -1.6   0.0       2.7   1.9e+03      90     112 ..     154     177 ..     101     206 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00015
                         AAA_30 18 drvavltGpAGtGKttalkalreaweaaggrv 49
                                     v++l Gp G+GKtt+l al+ +++ + g+v
  gi|119720645|ref|YP_921140.1| 28 GEVVALLGPNGSGKTTLLLALAGLLKPSRGSV 59
                                   45999***************999888775555 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.7
                         AAA_30  90 tllivDE.agmvdtkqlaallkaa 112
                                    + l+ DE ++ +d +++ all+a+
  gi|119720645|ref|YP_921140.1| 154 EYLLLDEpTANLDPRSASALLEAV 177
                                    555555523344555555555554 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00017      0.12      18      62 ..      30      74 ..      21      94 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00017
                     Zeta_toxin 18 lillgGqpGAGKselaellkdelerqgnvvrldpDdlRelhPeye 62
                                   ++ l G  G+GK++l+ +l+  l++ ++ v ld+ dl ++ P ++
  gi|119720645|ref|YP_921140.1| 30 VVALLGPNGSGKTTLLLALAGLLKPSRGSVLLDGRDLWSQLPGAR 74
                                   6778899***************************99999999876 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0    0.0002      0.14      49      73 ..      24      48 ..      15      64 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0002
                                   SEETTSEEEEEESTTSSHHHHHHHH CS
                           RecA 49 GlpkGriieiyGpessGkttlalha 73
                                   Gl +G ++ + Gp+ sGkttl l +
  gi|119720645|ref|YP_921140.1| 24 GLERGEVVALLGPNGSGKTTLLLAL 48
                                   899*****************98764 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00031      0.21      45      68 ..      26      49 ..      21      75 .. 0.90
   2 ?   -3.1   0.0       7.8   5.4e+03     111     135 ..     155     178 ..     141     194 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00031
                      IstB_IS21 45 ekkenivllGpsGvGKshlaialg 68
                                   e+ e ++llGp G GK+ l  al+
  gi|119720645|ref|YP_921140.1| 26 ERGEVVALLGPNGSGKTTLLLALA 49
                                   78899**************99997 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 7.8
                      IstB_IS21 111 llilDdlgllpldqaeaellfevie 135
                                     l+lD+  + +ld  +a+ l+e + 
  gi|119720645|ref|YP_921140.1| 155 YLLLDEP-TANLDPRSASALLEAVC 178
                                    5666664.45677777777776554 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   0.00029       0.2       2      24 ..      31      53 ..      30      66 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00029
                                   EEEE--SSSSHHHHHHHGGGGBS CS
                          AAA_5  2 vlLvGppGtgKselaerlaaaln 24
                                   v L+Gp G+gK++l   la +l+
  gi|119720645|ref|YP_921140.1| 31 VALLGPNGSGKTTLLLALAGLLK 53
                                   569****************9994 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00025      0.17       1      44 [.      31      72 ..      31     104 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00025
                         AAA_18  1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpe 44
                                   ++l G+ G+GKttl  +L+ +l      ++v+ +++ l+++ p 
  gi|119720645|ref|YP_921140.1| 31 VALLGPNGSGKTTLLLALAGLL--KPSRGSVLLDGRDLWSQLPG 72
                                   6899**************9887..55566666666666666555 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1    0.0003      0.21      24      56 ..      27      59 ..      15      62 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0003
                           DLIC 24 sgksvlvlGedgsGkttliaklqGveeekkGrG 56
                                    g  v +lG +gsGkttl+  l G+ ++ +G+ 
  gi|119720645|ref|YP_921140.1| 27 RGEVVALLGPNGSGKTTLLLALAGLLKPSRGSV 59
                                   577899*******************99999985 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.3   0.00038      0.26       2      21 ..      30      49 ..      29      61 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00038
                                   EEEEEESTTCCHHHHHHHHH CS
                           cobW  2 vtvltGflGsGKTtLlnhll 21
                                   v+ l G+ GsGKTtLl +l 
  gi|119720645|ref|YP_921140.1| 30 VVALLGPNGSGKTTLLLALA 49
                                   67899***********9876 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0    0.0014      0.95      63      87 ..     152     176 ..     112     179 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0014
                        SbcCD_C  63 alrlvfLDEAFsklDeesiatllel 87 
                                    +++ ++LDE  ++lD++s+++lle+
  gi|119720645|ref|YP_921140.1| 152 DPEYLLLDEPTANLDPRSASALLEA 176
                                    47899****************9997 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00037      0.25      25      56 ..      31      62 ..      19      83 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00037
                   Mg_chelatase 25 lllvGppGsGKtmlakrlpsllpplseeeale 56
                                   + l+Gp GsGKt l  +l++ll p   +  l+
  gi|119720645|ref|YP_921140.1| 31 VALLGPNGSGKTTLLLALAGLLKPSRGSVLLD 62
                                   6799******************9987666555 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1    0.0024       1.6      10      35 ..      28      53 ..      22      61 .. 0.84
   2 ?    0.9   0.0      0.74   5.1e+02      99     127 ..     149     179 ..      92     191 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0024
                         AAA_19 10 ekvllvtaGpGtGKTrvlkhivallv 35
                                    +v++++++ G+GKT++l +   ll+
  gi|119720645|ref|YP_921140.1| 28 GEVVALLGPNGSGKTTLLLALAGLLK 53
                                   57999************988776665 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.74
                         AAA_19  99 klqeeellivDE.fqdvd.elqyrLlkallg 127
                                     + + e+l+ DE + ++d   + +Ll+a++ 
  gi|119720645|ref|YP_921140.1| 149 LVYDPEYLLLDEpTANLDpRSASALLEAVCR 179
                                    3446668999995578998899999999984 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.1    0.0024       1.7      21      37 ..      29      45 ..      22      49 .. 0.87
   2 ?    0.7   0.0      0.35   2.4e+02     128     154 ..     181     207 ..     170     212 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0024
                                   EEEEEEESTTSSHHHHH CS
                         NB-ARC 21 lvvalvGmgGvGKttla 37
                                    vval G  G+GKttl+
  gi|119720645|ref|YP_921140.1| 29 EVVALLGPNGSGKTTLL 45
                                   499************96 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.35
                                    CHTTSEEEEEESBCCCCCCS-S-EEEE CS
                         NB-ARC 128 renrlrvllTTRdeevanavsatseki 154
                                    + ++  vll T d+ va++v++++ +i
  gi|119720645|ref|YP_921140.1| 181 KREGRGVLLATQDVGVASRVADRYAVI 207
                                    4567779*************9986655 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00085      0.59       3      23 ..      29      49 ..      27      69 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00085
                         AAA_14  3 kilvitGaRrvGKTtllkqli 23
                                   +++++ G+  +GKTtll  l+
  gi|119720645|ref|YP_921140.1| 29 EVVALLGPNGSGKTTLLLALA 49
                                   7999*************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                       108  (0.00602376); expected 17.9 (0.001)
Passed Fwd filter:                        26  (0.00145016); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              26  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 1587.08
//
Query:       gi|119720646|ref|YP_921141.1|  [L=420]
Description: glycosyl transferase, group 1 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-21   76.7   0.0    2.7e-21   75.8   0.0    1.3  1  Glycos_transf_1  Glycosyl transferases group 1
    1.8e-17   64.0   0.0    3.5e-17   63.1   0.0    1.5  1  Glyco_trans_1_4  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.8   0.0     3e-25   2.7e-21       8     162 ..     235     389 ..     231     394 .. 0.85

  Alignments for each domain:
  == domain 1  score: 75.8 bits;  conditional E-value: 3e-25
                                    HTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES...STTHHHHHHHHHHHCTTCGGGEEECCHSSS CS
                Glycos_transf_1   8 klgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaG..ngeeekelkklaeelelsdnviflgevsred 85 
                                    k++ +ek++ il+ g l+++Kg+  ++ a++l++k+ + ++klvi G  + +   +l    ++l+l+d v ++g++sre+
  gi|119720646|ref|YP_921141.1| 235 KSV-KEKENCILYKGGLTPVKGILDVLLAYRLIRKE-RGDLKLVITGklDSKTHRKLLVALKKLNLKDYVVLTGFISREQ 312
                                    444.49***************************886.**********99555555555556******************* PP

                                    HHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHH CS
                Glycos_transf_1  86 leellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeelr 162
                                    l el  +a ++++ps++++f+ ++lE++ ag+pv+ ++++ ++ +        lv ++++eala + +++le +++ 
  gi|119720646|ref|YP_921141.1| 313 LFELNAKARLLLHPSHMDSFPYTVLESLHAGTPVVGYDIPALKIYYGGLPGVRLVREGDVEALATEAIDMLERSPKE 389
                                    **************************************998877766544334666668888888888888776555 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.1   0.0   3.8e-21   3.5e-17       3     133 ..     243     384 ..     241     385 .. 0.84

  Alignments for each domain:
  == domain 1  score: 63.1 bits;  conditional E-value: 3.8e-21
                                    EEEEES---GG.GTHHHHHHHHHHHH.H..HEEEEEES---....HHHHHHHT..T-T.TEEEE---..THHHHHHHH-S CS
                Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkk..dvrlvivGdgp.rp.eeleelaa..gleerveftGfv..edlaellaaad 74 
                                     il+ G l  +vkg+  +l a  l+rk+  d++lvi G+ + +  ++l   ++  +l++ v++tGf+  e+l el a+a+
  gi|119720646|ref|YP_921141.1| 243 CILYKGGL-TPVKGILDVLLAYRLIRKErgDLKLVITGKLDsKThRKLLVALKklNLKDYVVLTGFIsrEQLFELNAKAR 321
                                    6899999*.678**************88544*******6543223344323334889999*******9888********* PP

                                    EEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--.TTSS.EE--TT-HHHHHHHHHHHHH CS
                Glyco_trans_1_4  75 vfvaPs..egfglkllEamaaglpvVatdvggiaevv.geng.llvppgdpealaeailrLle 133
                                    +++ Ps   +f++++lE++ ag+pvV  d+++++ +  g  g  lv +gd+eala + +++le
  gi|119720646|ref|YP_921141.1| 322 LLLHPShmDSFPYTVLESLHAGTPVVGYDIPALKIYYgGLPGvRLVREGDVEALATEAIDMLE 384
                                    ******988*********************99666558888878************9999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 2602.74
//
Query:       gi|119720647|ref|YP_921142.1|  [L=343]
Description: glycosyl transferase, group 1 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-28   99.6   0.0    2.7e-28   98.6   0.0    1.5  2  Glycos_transf_1  Glycosyl transferases group 1
    5.6e-27   94.8   0.0    2.7e-26   92.6   0.0    1.9  2  Glyco_trans_1_4  Glycosyl transferases group 1
    8.1e-13   48.7   1.0    5.1e-12   46.1   1.1    2.0  2  Glyco_transf_4   Glycosyltransferase Family 4
    5.8e-07   30.1   6.3    6.4e-07   30.0   4.9    1.7  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    1.2e-06   28.8   0.0    3.5e-06   27.3   0.0    1.8  1  Glyco_trans_1_2  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       1.7   6.3e+03     114     124 ..     120     130 ..     115     134 .. 0.77
   2 !   98.6   0.0   7.6e-32   2.7e-28      14     170 ..     166     318 ..     154     320 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.7
                                    HTT--EEEETT CS
                Glycos_transf_1 114 aaglpviasna 124
                                    +ag+pv++  +
  gi|119720647|ref|YP_921142.1| 120 EAGVPVVTISN 130
                                    689****9875 PP

  == domain 2  score: 98.6 bits;  conditional E-value: 7.6e-32
                                    T-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHHHCE CS
                Glycos_transf_1  14 kkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleellkna 93 
                                       ++l  +rl+  K + ++++a++l+k   +  +  vi G+g+ + e++     ++l+d+v+f  +++ e+l++l+++a
  gi|119720647|ref|YP_921142.1| 166 IHHVVLWNSRLVGFKEPFTFLEAIRLVKG--KASFEAVIRGDGPLKREVEGYLRRHGLEDTVRFAERIPFEKLPQLYRSA 243
                                    55678888999999***********9986..6************************************************ PP

                                    SEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHHHHHHHHHH CS
                Glycos_transf_1  94 difvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeelrerlgenar 170
                                     if++++ +E+fG+++lEAma+glpvi+ +agg+aev  d+   l + p++ e+lae++  ll+d++l+e ++ ++ 
  gi|119720647|ref|YP_921142.1| 244 TIFIHTCSKEPFGLAVLEAMASGLPVIVPDAGGAAEVAGDAG--LKFRPGDSEDLAEKLLVLLTDQQLYETFSARSI 318
                                    *************************************98876..999999*******************99988765 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.47   1.7e+03      87     103 ..     115     131 ..     113     151 .. 0.70
   2 !   92.6   0.0   7.4e-30   2.7e-26       2     134 .]     168     306 ..     167     306 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.47
                                    HHHHHHTT-EEEE-TGG CS
                Glyco_trans_1_4  87 llEamaaglpvVatdvg 103
                                    ll+   ag+pvV+ +  
  gi|119720647|ref|YP_921142.1| 115 LLQLYEAGVPVVTISNF 131
                                    5677789*****98753 PP

  == domain 2  score: 92.6 bits;  conditional E-value: 7.4e-30
                                    EEEEEES---GG.GTHHHHHHHHHHHH.HH.EEEEEES---...HHHHHHHT..T-T.TEEEE---..THHHHHHHH-SE CS
                Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkkd.vrlvivGdgp.rpeeleelaa..gleerveftGfv..edlaellaaadv 75 
                                    +v+l+ +rl    k    +lea+ l++ k  ++ vi Gdgp + +e+e +++  gle++v+f+ ++  e+l++l+++a++
  gi|119720647|ref|YP_921142.1| 168 HVVLWNSRL-VGFKEPFTFLEAIRLVKGKAsFEAVIRGDGPlK-REVEGYLRrhGLEDTVRFAERIpfEKLPQLYRSATI 245
                                    578888899.456999***********8845**********66.5999888668************9999********** PP

                                    EEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--TTSSEE--TT-HHHHHHHHHHHHH- CS
                Glyco_trans_1_4  76 fvaPs..egfglkllEamaaglpvVatdvggiaevvgengllvppgdpealaeailrLled 134
                                    f+ +   e fgl++lEama+glpv++ d+gg+aev g++gl + pgd+e+lae++l Ll+d
  gi|119720647|ref|YP_921142.1| 246 FIHTCskEPFGLAVLEAMASGLPVIVPDAGGAAEVAGDAGLKFRPGDSEDLAEKLLVLLTD 306
                                    ***99999***********************9**88**********************997 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.1   1.1   1.4e-15   5.1e-12       4     166 ..       9     152 ..       9     155 .. 0.85
   2 ?   -0.1   0.0      0.22     8e+02      76     100 ..     247     270 ..     204     271 .. 0.83

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 1.4e-15
                 Glyco_transf_4   4 verhvleLaraLarrGheVtvvtpgddgpleeevelvvrvprvplpllkrllrslaflrrlrrllkrekpDvvHahspaa 83 
                                    ve +++ La +L rr ++V+++++++ + ++++      vpr p p++++ll    +  +l++l++  ++DvvH++++  
  gi|119720647|ref|YP_921142.1|   9 VEHYTVGLAGELSRR-IKVELLAFARYPVSARQ----MVVPRLPVPGHRDLL----YKYALKALAR--RYDVVHVNTASH 77 
                                    7899***********.*******9999999999....445555544444444....4445666666..9********666 PP

                 Glyco_transf_4  84 lgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrradrviavSeatadelrerygvppekitVip 163
                                    +   +l  +   +  l lt Hg+ e+ l+++ +++++  +r+ + +l+ +   v+++S++ a+ lrer+gv++   +V++
  gi|119720647|ref|YP_921142.1|  78 G---AL--LG-PRDNLLLTEHGWPEPELVEREQRRFYEKERESLLQLYEAGVPVVTISNFSARMLRERLGVKA--TAVVY 149
                                    5...22..22.5779*********************************************************9..9**** PP

                 Glyco_transf_4 164 nGv 166
                                    +Gv
  gi|119720647|ref|YP_921142.1| 150 HGV 152
                                    **8 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.22
                 Glyco_transf_4  76 vHahspaalgaallalrrrlgiplV 100
                                    +H+ s  ++g+a+l +++ +g+p++
  gi|119720647|ref|YP_921142.1| 247 IHTCSKEPFGLAVLEAMA-SGLPVI 270
                                    699999999999999998.999998 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   4.9   1.8e-10   6.4e-07       4     156 ..      10     149 ..       9     152 .. 0.79
   2 ?   -2.0   0.0       1.2   4.2e+03      72     101 ..     240     271 ..     199     278 .. 0.60

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 1.8e-10
                Glyco_trans_4_4   4 gryvaelaraLaarGheVtvltpapapgapeleedgvrvhrlpvprrpspladlaalralrrllrqrrerpdvvhahs.p 82 
                                    + y+  la +L +r   V++l+ a +p++     ++  v rlpvp ++    dl +  al++l    ++r+dvvh+++ +
  gi|119720647|ref|YP_921142.1|  10 EHYTVGLAGELSRR-IKVELLAFARYPVSA----RQMVVPRLPVPGHR----DLLYKYALKAL----ARRYDVVHVNTaS 76 
                                    6799**********.********9999988....5667889****887....56666777777....59*********44 PP

                Glyco_trans_4_4  83 taglaarlarrrrgiplvvtlhglllrrg.sgavrrlyralerrllrrada...vlvvseaeaeelra.lgvpadrvvv 156
                                    +++l++       +  l++t hg+  ++   + +rr+y      ll+   a   v+++s++ a+ lr+ lgv a+ vv+
  gi|119720647|ref|YP_921142.1|  77 HGALLG------PRDNLLLTEHGWPEPELvEREQRRFYEKERESLLQLYEAgvpVVTISNFSARMLRErLGVKATAVVY 149
                                    455544......45669******9988886777777775444455555555778*************99****988775 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.2
                Glyco_trans_4_4  72 erpdvvhahs.pt..aglaarlarrrrgiplvv 101
                                    +r   + +h+ ++   gl a+l +++ g+p++v
  gi|119720647|ref|YP_921142.1| 240 YRSATIFIHTcSKepFGL-AVLEAMASGLPVIV 271
                                    444445555533342333.33333477777765 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   9.7e-10   3.5e-06       3      92 .]     247     335 ..     243     335 .. 0.91

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 9.7e-10
                Glyco_trans_1_2   3 LnpsrsespnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaarervlae 80 
                                    +++  +e + l ++Ea+a+G ++++ da g +e    g+ ++ f+  d e+laek+  ll++ ++++  +++ +er  a 
  gi|119720647|ref|YP_921142.1| 247 IHTCSKEPFGLAVLEAMASGLPVIVPDAGGAAEVA--GDAGLKFRpgDSEDLAEKLLVLLTDQQLYETFSARSIER-SAF 323
                                    444555889999****************9999996..888************************************.9** PP

                Glyco_trans_1_2  81 htydhraeqlla 92 
                                    +t++++a ++l+
  gi|119720647|ref|YP_921142.1| 324 FTWEKAASTYLD 335
                                    *******99885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 2194.25
//
Query:       gi|119720648|ref|YP_921143.1|  [L=353]
Description: glycosyl transferase family protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.1e-18   65.5   0.0    7.1e-18   65.0   0.0    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
    2.8e-14   53.6   0.1    8.8e-14   51.9   0.1    1.7  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    4.1e-06   26.8   0.0    7.3e-06   26.0   0.0    1.5  1  Glyco_trans_2_3  Glycosyl transferase family group 2
      0.001   18.6   0.0     0.0016   18.0   0.0    1.2  1  Glyco_tranf_2_2  Glycosyltransferase like family 2


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.0   0.0   1.6e-21   7.1e-18       1     129 [.      11     140 ..      11     175 .. 0.87

  Alignments for each domain:
  == domain 1  score: 65.0 bits;  conditional E-value: 1.6e-21
                                    EEEEEESS-TTTHHHHHHHHHHH.GGCCEEEEEEEEES-SSCHHHHHGGGCH..C-TTEEEEEESSS-HHHHHHHHHHHH CS
                Glycos_transf_2   1 svviptyNeektlletlesllaq.dpypdfeiivvDDgStDetveileelak..edprvrvirreenvGkagalnaglra 77 
                                    +v +++ N+e  +  +l+sll+q +p++++  ++vD gS D+tve+++e+ +     ++ v+ +  n     a+n ++++
  gi|119720648|ref|YP_921143.1|  11 TVAMVALNREWIIGHALKSLLSQtYPHDRIFFVLVDGGSVDRTVEVVREALSgsDLAGFEVVVQRSN--IPEARNIAIER 88 
                                    58899******************777888888999*****************766667777777777..*********** PP

                                    --SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC CS
                Glycos_transf_2  78 atgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiern 129
                                     +g+ i+f D+D+  +pd l+ l+ea+ + g d+  + +  i++++ e  ++
  gi|119720648|ref|YP_921143.1|  89 MRGEAIFFWDSDVLLEPDGLKMLYEAASDYGIDILSADTLSIKVSSVEEGWR 140
                                    *********************************9999999988888777665 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.9   0.1     2e-17   8.8e-14       4     209 ..      10     213 ..       8     239 .. 0.81

  Alignments for each domain:
  == domain 1  score: 51.9 bits;  conditional E-value: 2e-17
                Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaqeypr.vevvvvvde.sdaetlevaeelaaalpdvrvrvvvnarnlgstgksralne 81 
                                    ++v+ +++n+e  +g  l sll+q+yp    ++v vd+ s + t+ev++e+   ++ ++  vvv+  n       +a n 
  gi|119720648|ref|YP_921143.1|  10 ITVAMVALNREWIIGHALKSLLSQTYPHdRIFFVLVDGgSVDRTVEVVREALSGSDLAGFEVVVQRSN-----IPEARNI 84 
                                    689999********************66255556666648899*******999999889998877442.....345679* PP

                Glyco_tranf_2_3  82 alravksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfllnrstlvsalgalefaerhlrflaarralgv.ltl 160
                                    a+++ +++ + + D+D+++ePd lk+l  ++ + +++++ ++ ++   s++   +  le      + ++ r  +gv l +
  gi|119720648|ref|YP_921143.1|  85 AIERMRGEAIFFWDSDVLLEPDGLKMLYEAASDYGIDILSADTLSIKVSSVEEGWRVLE------ELCKKRGKIGVeLVP 158
                                    *******************************788*********9999999977777777......567778888876666 PP

                Glyco_tranf_2_3 161 nGsg..slirrevlkelegldplflltdDyelglrlrragfrtayvpgaa.....v 209
                                    + ++  +lir  vl++  ++dp   +++D++ ++ +r+ g+r+a++ g++     v
  gi|119720648|ref|YP_921143.1| 159 AVAMgaTLIRKIVLDRV-RFDPELTFGEDADFCVKARSLGYRVAVHRGVVavdvnV 213
                                    65555699**9999999.****9***********************9998555551 PP

>> Glyco_trans_2_3  Glycosyl transferase family group 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   1.6e-09   7.3e-06       2     192 ..      94     298 ..      93     336 .. 0.63

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 1.6e-09
                Glyco_trans_2_3   2 illlDaDtvlppdclreiaaelaspevaivqgpvlvmnvanwleelaalffaedhgkdilvrealgrvvpsvGsgaflrr 81 
                                    i + D+D +l pd l+ +++  ++  ++i++  +l   v+++ e + +l+      k +  +    + vp v  ga l r
  gi|119720648|ref|YP_921143.1|  94 IFFWDSDVLLEPDGLKMLYEAASDYGIDILSADTLSIKVSSVEEGWRVLEE--LCKKRGKIG---VELVPAVAMGATLIR 168
                                    67889**********999888888899********99999*******9875..333433343...356888888888888 PP

                Glyco_trans_2_3  82 salqevggwdgdessvsEDfdmglrlqrkGyrvrfv.............peslvkeksplt.lraalrQrkR.wayGc.. 144
                                    + + + +++d  e + +ED d++++++++Gyrv  +             ++s ++ + plt l   +r +++  ++G   
  gi|119720648|ref|YP_921143.1| 169 KIVLDRVRFD-PELTFGEDADFCVKARSLGYRVAVHrgvvavdvnvtgrAGSDIYVSKPLTeLLKGIRKKAKvKVLGLsf 247
                                    8877666777.479*******************99977778888887776668888888867444444444436666433 PP

                Glyco_trans_2_3 145 el......eklillvrllgylgsllwsalplhlallllfsllalalvlllllll 192
                                     +       +++++    +yl  l   +++++l++ l  +l +l l++ +++l 
  gi|119720648|ref|YP_921143.1| 248 DPglkdvlVYMWRYK---RYLYYLGYLPMLVALIVGLAKNLPMLTLLFPAYVLP 298
                                    113322222222111...222222222233333333333333333333222222 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   3.5e-07    0.0016      20     102 ..      30     111 ..      10     123 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3.5e-07
                Glyco_tranf_2_2  20 lqkakyydeeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNrGaskaesdlvlFlDaDcfissDkf 99 
                                    l+ ++y  + i +++vd+gS + ++e+v+       l  ++   +++     arN  +++  ++ ++F D+D +  +D +
  gi|119720648|ref|YP_921143.1|  30 LLSQTYPHDRIFFVLVDGGSVDRTVEVVREALSGSDLAGFEVVVQRS-NIPEARNIAIERMRGEAIFFWDSDVLLEPDGL 108
                                    33344447788899***************999999999777776665.56689*************************98 PP

                Glyco_tranf_2_2 100 eki 102
                                    + +
  gi|119720648|ref|YP_921143.1| 109 KML 111
                                    654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.67u 0.33s 00:00:01.00 Elapsed: 00:00:00.55
# Mc/sec: 1927.28
//
Query:       gi|119720649|ref|YP_921144.1|  [L=346]
Description: glycosyl transferase, group 1 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-39  135.0   0.0    2.5e-39  134.6   0.0    1.1  1  Glycos_transf_1  Glycosyl transferases group 1
    1.7e-33  115.9   0.1    3.1e-33  115.0   0.1    1.4  1  Glyco_trans_1_4  Glycosyl transferases group 1
    3.6e-21   75.9   5.6    4.9e-19   69.0   3.9    2.7  2  Glyco_transf_4   Glycosyltransferase Family 4
    1.3e-17   64.7  14.8    3.8e-15   56.7  10.1    3.7  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain
      3e-16   59.6   0.0    5.1e-16   58.8   0.0    1.4  1  Glyco_trans_1_2  Glycosyl transferases group 1
    0.00024   20.1   0.0    0.00042   19.3   0.0    1.3  1  Epimerase_2      UDP-N-acetylglucosamine 2-epimerase
     0.0006   19.6   1.2      0.063   13.0   0.2    2.9  2  Glyco_transf_5   Starch synthase catalytic domain
     0.0051   16.8   0.0      0.098   12.7   0.0    2.8  1  Glyco_trans_4_2  Glycosyl transferase 4-like
  ------ inclusion threshold ------
       0.19   10.2   0.0       0.31    9.5   0.0    1.2  1  Glycogen_syn     Glycogen synthase


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.6   0.0   1.3e-42   2.5e-39      14     171 ..     173     322 ..     163     323 .. 0.96

  Alignments for each domain:
  == domain 1  score: 134.6 bits;  conditional E-value: 1.3e-42
                                    T-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHHHCE CS
                Glycos_transf_1  14 kkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleellkna 93 
                                     ++ ++++grl++eKgvdll+kaf+ l    + +++lv++G+g+ e+el++l   ++   +++flg ++re+   + k +
  gi|119720649|ref|YP_921144.1| 173 YERQVVYSGRLSREKGVDLLVKAFRAL----DVDAHLVVVGGGPLEEELRSL---AGGDPRIHFLGPMPRERALRVVKGS 245
                                    5789*********************98....89*******************...7999********************* PP

                                    SEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHHHHHHHHHHH CS
                Glycos_transf_1  94 difvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeelrerlgenark 171
                                    d+fvlps++Eg+ ++llEAma g+pv+a+++gg+ e+v+dg+tGllv+p  +e+ a+a+r lled++l++rl  +a++
  gi|119720649|ref|YP_921144.1| 246 DVFVLPSRYEGLSTALLEAMAMGVPVVATKVGGNTELVEDGKTGLLVEPS-PEEVARAVRLLLEDSDLAARLASAAKR 322
                                    *************************************************9.**********************99985 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.0   0.1   1.6e-36   3.1e-33       2     134 .]     175     309 ..     174     309 .. 0.92

  Alignments for each domain:
  == domain 1  score: 115.0 bits;  conditional E-value: 1.6e-36
                                    EEEEEES---GG.GTHHHHHHHHHHHH.HHEEEEEES---...HHHHHHHTT-T.TEEEE---..THHHHHHHH-SEEEE CS
                Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkkdvrlvivGdgp.rpeeleelaagleerveftGfv..edlaellaaadvfva 78 
                                    + +++ Grl  ++kgvdll++a+ +l   d++lv+vG+gp + eel++la g ++r++f+G +  e   ++++ +dvfv+
  gi|119720649|ref|YP_921144.1| 175 RQVVYSGRL-SREKGVDLLVKAFRALD-VDAHLVVVGGGPlE-EELRSLA-GGDPRIHFLGPMprERALRVVKGSDVFVL 250
                                    579******.566**********9999.569*********55.6**9777.5589********8777999********** PP

                                    --..---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHHH- CS
                Glyco_trans_1_4  79 Ps..egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrLled 134
                                    Ps  eg++ +llEama+g+pvVat+vgg  e+v  g++gllv+p +pe+ a+a+  Lled
  gi|119720649|ref|YP_921144.1| 251 PSryEGLSTALLEAMAMGVPVVATKVGGNTELVedGKTGLLVEP-SPEEVARAVRLLLED 309
                                    **999*************************************87.6***********997 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.0   3.9   2.4e-22   4.9e-19       2     169 ..      17     163 ..      16     164 .. 0.82
   2 !    5.7   0.0    0.0067        13       8     102 ..     189     274 ..     186     275 .. 0.73

  Alignments for each domain:
  == domain 1  score: 69.0 bits;  conditional E-value: 2.4e-22
                 Glyco_transf_4   2 GGverhvleLaraLarrGheVtvvtpgddgpleeevelvvrvprvplpllkrllrslaflrr.lrrllkrekpDvvHahs 80 
                                    GGv+ hv  L++ L+r+GheV+vv+ +  + l+ +             +l ++ +  +++++ +  +lk  ++DvvHah+
  gi|119720649|ref|YP_921144.1|  17 GGVAQHVGKLVELLRRDGHEVEVVSAENTPILPVK-------------GLMNPSFAATSALKvALGRLKGRRYDVVHAHN 83 
                                    9***********************96666655555.............34444444444433145678888********* PP

                 Glyco_transf_4  81 paalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrradrviavSeatadelrerygvppekit 160
                                     +++  a++a+r       Vlt+Hg +     + + ++l rl    er +l +adrv+ vS+ata+++ +  gv+   ++
  gi|119720649|ref|YP_921144.1|  84 VPSA-PAMRAARG----GRVLTLHGVFSEQVGYLHGGLLGRLSGVAERVALGWADRVTSVSRATAEHYSR-IGVN---VV 154
                                    8776.77777774....47********9888888889999999999************************.**88...9* PP

                 Glyco_transf_4 161 VipnGvDle 169
                                     +pn+vD++
  gi|119720649|ref|YP_921144.1| 155 HVPNAVDPS 163
                                    *******86 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0067
                 Glyco_transf_4   8 vleLaraLarrGheVtvvtpgddgpleeevelvvrvprvplpllkrllrslaflrrlrrllkrekpDvvHahspaalgaa 87 
                                    v  L++a++++ ++ ++v+ g+++ +ee        ++     ++ + + + ++ r+ r++k  + Dv    s + ++  
  gi|119720649|ref|YP_921144.1| 189 VDLLVKAFRALDVDAHLVVVGGGPLEEEL-------RSLAGGDPRIHFLGPMPRERALRVVK--GSDVFVLPSRYEGLST 259
                                    56799999**********98887777666.......55555555666666777788888888..7888877777777665 PP

                 Glyco_transf_4  88 llalrrrlgiplVlt 102
                                    +l  +++ g+p+V+t
  gi|119720649|ref|YP_921144.1| 260 ALLEAMAMGVPVVAT 274
                                    55555569****998 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.7  10.1   1.9e-18   3.8e-15       1     159 [.      17     158 ..      17     159 .. 0.82
   2 !    5.8   0.1    0.0086        17      10     134 ..     192     324 ..     186     337 .. 0.53

  Alignments for each domain:
  == domain 1  score: 56.7 bits;  conditional E-value: 1.9e-18
                Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvltpapapgapeleedgvrvhrlpvprrpspladlaalralrrll.rqrrerpdvvha 79 
                                    gG++++v  l++ L+++GheV+v+ ++ +p  p     g+         +p    + aa+ al+ +l r + +r+dvvha
  gi|119720649|ref|YP_921144.1|  17 GGVAQHVGKLVELLRRDGHEVEVVSAENTPILP---VKGLM--------NP----SFAATSALKVALgRLKGRRYDVVHA 81 
                                    8*************************8888877...33333........22....456777777777777********** PP

                Glyco_trans_4_4  80 hsptaglaarlarrrrgiplvvtlhglllrrg.sgavrrlyralerrllrradavlvvseaeaeelralgvpadrvvvvp 158
                                    h+ ++++a+r+ar + ++  ++ +++  + +  +g ++rl   +er +l  ad+v++vs+a ae++ + gv    vv vp
  gi|119720649|ref|YP_921144.1|  82 HNVPSAPAMRAAR-GGRVLTLHGVFSEQVGYLhGGLLGRLSGVAERVALGWADRVTSVSRATAEHYSRIGVN---VVHVP 157
                                    *************.7555544444443333335899***********************************6...77788 PP

                Glyco_trans_4_4 159 n 159
                                    n
  gi|119720649|ref|YP_921144.1| 158 N 158
                                    7 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0086
                Glyco_trans_4_4  10 laraLaarGheVtvltpapapgapele...edgvrvhrl.pvprrpspladlaalralrrllrqrrerpdvvhahs.pta 84 
                                    l++a++a+ ++ ++++ ++ p ++el+   ++  r+h l p+pr+           ++ r++     + dv ++ s + +
  gi|119720649|ref|YP_921144.1| 192 LVKAFRALDVDAHLVVVGGGPLEEELRslaGGDPRIHFLgPMPRE-----------RALRVV----KGSDVFVLPSrYEG 256
                                    667777777777777655555555533332444555544344444...........234444....66778888884445 PP

                Glyco_trans_4_4  85 glaarlarrrrgiplvvtlh............glllrrg.sgavrrlyraler.....rllrradavl 134
                                     + a+l +++ g+p+v t              gll+++     +r+++  le+     rl++ a +v+
  gi|119720649|ref|YP_921144.1| 257 LSTALLEAMAMGVPVVATKVggntelvedgktGLLVEPSpEEVARAVRLLLEDsdlaaRLASAAKRVV 324
                                    55555556667888888887554444444333233333322222222222222232226666666666 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.8   0.0   2.6e-19   5.1e-16       2      92 .]     248     339 ..     247     339 .. 0.97

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 2.6e-19
                Glyco_trans_1_2   2 vLnpsrsespnlrlfEaaacGafaltddaegleelftpgkevilfe.dleelaekiryllanpeerraiaeaarervlae 80 
                                    ++ psr+e++++ l+Ea+a+G+++++++  g  el+++gk+++l+e ++ee+a+++r ll++ ++++++a aa++ v ++
  gi|119720649|ref|YP_921144.1| 248 FVLPSRYEGLSTALLEAMAMGVPVVATKVGGNTELVEDGKTGLLVEpSPEEVARAVRLLLEDSDLAARLASAAKRVVAEK 327
                                    6779**************************************************************************** PP

                Glyco_trans_1_2  81 htydhraeqlla 92 
                                    +++d+ ++q+l+
  gi|119720649|ref|YP_921144.1| 328 YSWDKVYAQYLD 339
                                    *********985 PP

>> Epimerase_2  UDP-N-acetylglucosamine 2-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   2.1e-07   0.00042     228     328 ..     213     318 ..     183     328 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 2.1e-07
                                    HHHHHHHHHHH-TTEEEE----HHHHHHHHHC-SEEE......ES-HHHHHHHHHCT--EEESSSS-S-THHHHTTSEEE CS
                    Epimerase_2 228 trkrlleeleelenvtlieplgyldflsllknaklvl......tdSgGiqeEapslgvpvvnlReeteRpegveagtnvl 301
                                     +++l++   + ++++++ p+  ++ l+++k +++ +      + S  +  Ea+++gvpvv   + +   e ve g+  l
  gi|119720649|ref|YP_921144.1| 213 LEEELRSLAGGDPRIHFLGPMPRERALRVVKGSDVFVlpsryeGLSTALL-EAMAMGVPVVAT-KVGGNTELVEDGKTGL 290
                                    4444443333335*********************9883444434455677.************.99999*******9999 PP

                                    .-TT-HHHHHHHHHHHCT-..--..... CS
                    Epimerase_2 302 .vgtdkeeIvaaleklledkkelekman 328
                                     v++++ee+ +a++ lled++  +++a+
  gi|119720649|ref|YP_921144.1| 291 lVEPSPEEVARAVRLLLEDSDLAARLAS 318
                                    9****************99666666655 PP

>> Glyco_transf_5  Starch synthase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.2   3.2e-05     0.063      13      41 ..      14      42 ..       6      52 .. 0.88
   2 ?    3.9   0.0     0.018        36     119     170 ..      60     102 ..      51     149 .. 0.53

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.2e-05
                 Glyco_transf_5 13 aktGGLadvvgaLpkaLaklghdvrvilP 41
                                   +  GG+a++vg+L + L++ gh+v+v++ 
  gi|119720649|ref|YP_921144.1| 14 SGLGGVAQHVGKLVELLRRDGHEVEVVSA 42
                                   558***********************975 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.018
                 Glyco_transf_5 119 sraalellek.l.gwkpdvihahDWhtalvpallkelykerglfkkiktvftiH 170
                                    +  al+++   l g + dv+hah   +a +    ++++           v+t+H
  gi|119720649|ref|YP_921144.1|  60 ATSALKVALGrLkGRRYDVVHAHNVPSAPAM---RAAR--------GGRVLTLH 102
                                    5555555555343446999999987777772...3322........23355555 PP

>> Glyco_trans_4_2  Glycosyl transferase 4-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   4.9e-05     0.098      12     108 ..      22     103 ..      13     139 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.9e-05
                Glyco_trans_4_2  12 htlrlakeLakrgyeVhvitpkkgakdeleaegihvhrlkvdrkgpleylk.afklkklikkikPDvvhahyakpygllg 90 
                                    h+ +l++ L+  g+eV+v++ ++    +l  +g+       ++  + + lk a  l + +k + +Dvvhah++++    +
  gi|119720649|ref|YP_921144.1|  22 HVGKLVELLRRDGHEVEVVSAENT--PILPVKGLMN-----PSFAATSALKvA--LGR-LKGRRYDVVHAHNVPSAP--A 89 
                                    777889999999999999999877..6777777622.....333345555533..333.57899********99863..3 PP

                Glyco_trans_4_2  91 slaarlsgvipvvlsvwG 108
                                      aar ++    vl+ +G
  gi|119720649|ref|YP_921144.1|  90 MRAARGGR----VLTLHG 103
                                    33455554....666664 PP

>> Glycogen_syn  Glycogen synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00016      0.31     465     508 ..     241     284 ..     238     289 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00016
                                    HHHH-SEEE---SSBSS-HHHHHHHHTT--EEEETTBHHHHHHH CS
                   Glycogen_syn 465 fvrGchlGvfpsyyepwGytpaectvmGipsvttnlsGfGcfme 508
                                     v+G+ + v+ps ye    +  e   mG+p v+t + G    +e
  gi|119720649|ref|YP_921144.1| 241 VVKGSDVFVLPSRYEGLSTALLEAMAMGVPVVATKVGGNTELVE 284
                                    599*********************************99766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.66u 0.35s 00:00:01.01 Elapsed: 00:00:00.54
# Mc/sec: 1911.94
//
Query:       gi|119720650|ref|YP_921145.1|  [L=111]
Description: hypothetical protein Tpen_1747 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.34s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 635.18
//
Query:       gi|119720651|ref|YP_921146.1|  [L=289]
Description: hypothetical protein Tpen_1748 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.7e-17   62.4   0.1    8.3e-17   61.2   0.1    1.6  1  DUF58         Protein of unknown function DUF58
    4.6e-06   26.2   0.0     0.0015   18.0   0.0    2.2  2  VWA_CoxE      VWA domain containing CoxE-like protein
  ------ inclusion threshold ------
      0.057   13.1   0.1       0.11   12.2   0.1    1.4  1  HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor


Domain annotation for each model (and alignments):
>> DUF58  Protein of unknown function DUF58
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.2   0.1   1.4e-20   8.3e-17       1      79 [.      35     118 ..      35     130 .. 0.87

  Alignments for each domain:
  == domain 1  score: 61.2 bits;  conditional E-value: 1.4e-20
                          DUF58   1 gldfaglReYvpgDplrrIdWkatAR......tgelyvrefeaerartvllvldlspemslgstgdekletavsaaasla 74 
                                    gl++ ++ReY+p D++r+IdW+atAR      + +++v+ + aer+++v l++dls++m  +s++ + l +a+++ a++a
  gi|119720651|ref|YP_921146.1|  35 GLEYVDFREYQPFDDARHIDWRATARspgpdgGYRPIVKVYRAERKTRVALAVDLSASMLYQSKP-KTLVYALAVIAAVA 113
                                    67999*********************888877777************************998876.67777777777777 PP

                          DUF58  75 rqlld 79 
                                    ++l d
  gi|119720651|ref|YP_921146.1| 114 DTLED 118
                                    77765 PP

>> VWA_CoxE  VWA domain containing CoxE-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   2.5e-07    0.0015      19      98 ..      44     126 ..      28     180 .. 0.74
   2 !    6.2   0.0     0.001         6     130     171 ..     179     220 ..     177     232 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.5e-07
                       VWA_CoxE  19 rkrrrrgrriDlrrtlranlrhgge.lvelvrrkprerkprelvllvDvSgSmaays.....aiflallhAllqqlprte 92 
                                    ++    +r+iD+r+t r+    gg  ++  v+r    ++++++ l vD S+Sm   s     +  la+++A+ ++l++t 
  gi|119720651|ref|YP_921146.1|  44 YQPFDDARHIDWRATARSPGPDGGYrPIVKVYRA---ERKTRVALAVDLSASMLYQSkpktlVYALAVIAAVADTLEDTF 120
                                    55556789**********9998886555555555...3345899*********654422221456788899999998777 PP

                       VWA_CoxE  93 vfaFdt 98 
                                    +++ +t
  gi|119720651|ref|YP_921146.1| 121 TLVLST 126
                                    776666 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.001
                       VWA_CoxE 130 TrigaalaeflelvtrpaLsrravvvlvsDglergdreella 171
                                    T+++ +l++f ++ +  a sr+a+ +lv D +e  + + +la
  gi|119720651|ref|YP_921146.1| 179 TDYAHSLEDFERSSKTLAASRGAAYLLVYDWWEVHPPPDALA 220
                                    99*************9999**************988776655 PP

>> HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor, HrcA DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   1.8e-05      0.11      56      72 ..      61      77 ..      58      83 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.8e-05
                   HrcA_DNA-bdg 56 vpGPkGGYkPtlkayea 72
                                    pGP GGY+P +k y+a
  gi|119720651|ref|YP_921146.1| 61 SPGPDGGYRPIVKVYRA 77
                                   69*************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.33s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 1680.93
//
Query:       gi|119720652|ref|YP_921147.1|  [L=274]
Description: hypothetical protein Tpen_1749 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       268  (0.0149478); expected 358.6 (0.02)
Passed bias filter:                      217  (0.0121033); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 1591.17
//
Query:       gi|119720653|ref|YP_921148.1|  [L=353]
Description: ATPase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.8e-54  180.7   0.2      1e-52  177.4   0.2    2.2  1  AAA_3            ATPase family associated with various cellul
    9.5e-14   51.0   0.2    2.2e-13   49.8   0.2    1.6  1  AAA_lid_2        AAA lid domain
      1e-12   48.3   0.0    3.9e-12   46.4   0.0    2.1  1  AAA_5            AAA domain (dynein-related subfamily)
    8.3e-05   23.0   0.0    0.00037   20.9   0.0    2.0  1  AAA              ATPase family associated with various cellul
    0.00032   20.1   0.5     0.0037   16.7   0.1    2.1  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    0.00079   19.2   0.1      0.022   14.5   0.1    2.3  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
     0.0072   16.7   0.1      0.017   15.5   0.1    1.6  1  AAA_16           AAA ATPase domain
  ------ inclusion threshold ------
      0.013   15.3   0.1      0.057   13.1   0.1    1.9  1  Sigma54_activat  Sigma-54 interaction domain
      0.091   12.9   0.0       0.18   12.0   0.0    1.6  1  AAA_33           AAA domain
       0.11   12.4   0.0       0.24   11.3   0.0    1.5  1  NACHT            NACHT domain
       0.14   11.2   0.0        8.9    5.3   0.0    2.2  2  MCM              MCM P-loop domain
       0.15   12.5   0.0       0.33   11.4   0.0    1.6  1  MCM_lid          MCM AAA-lid domain


Domain annotation for each model (and alignments):
>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  177.4   0.2     7e-56     1e-52       1     131 []      42     191 ..      42     191 .. 0.90

  Alignments for each domain:
  == domain 1  score: 177.4 bits;  conditional E-value: 7e-56
                          AAA_3   1 hvllegvPGlaktllvkalakaldle..............fkriqftpdllPsdilGtevfeekekefefkkGpvfanll 66 
                                    hvllegvPG+akt+l+k+la+ l+l+              f+r+qftpdl+Psdi+G  vf+ ++++fe + Gpvf+ +l
  gi|119720653|ref|YP_921148.1|  42 HVLLEGVPGIAKTTLAKSLARLLGLSegyaleldgvayrgFSRVQFTPDLMPSDITGNLVFNPSTRSFEPRFGPVFTYFL 121
                                    9********************987643344444455555599************************************** PP

                          AAA_3  67 ladeinrappktqsalleameerqvtvegethklp.....epflvlatqnPieqeGtyplpeaqldrfll 131
                                    ladeinra p+tqsall+am+er+vt+++++++l+     + f+v+atqnP+eqeGtyplpeaqldrfl+
  gi|119720653|ref|YP_921148.1| 122 LADEINRAVPRTQSALLQAMQEREVTIGDRSYRLEvrergKFFFVIATQNPVEQEGTYPLPEAQLDRFLM 191
                                    ********************************99744444679*************************98 PP

>> AAA_lid_2  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.8   0.2   1.5e-16   2.2e-13       7      56 ..     269     317 ..     266     337 .. 0.88

  Alignments for each domain:
  == domain 1  score: 49.8 bits;  conditional E-value: 1.5e-16
                      AAA_lid_2   7 laielgvsgrRadlallraArAlAalegrdyVtpeDvkeaaplVLaHRlr 56 
                                    +++elg+s+r   +al++a++AlAa++g + V   Dv +a  +VL+HRl+
  gi|119720653|ref|YP_921148.1| 269 EYFELGASPR-SGIALVKASKALAAMRGSTVVERVDVDRALFPVLNHRLV 317
                                    789*******.*************************************98 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.4   0.0   2.6e-15   3.9e-12       1     138 []      42     189 ..      42     189 .. 0.91

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 2.6e-15
                                    EEEEE--SSSSHHHHHHHGGGGB..............S--EEEEE--TT--HHHHH--B--...........-------- CS
                          AAA_5   1 dvlLvGppGtgKselaerlaaal..............nreveyvqltrdtteedlkgrreikngttslvd..splvraar 64 
                                    +vlL G pG++K++la++la++l               r +  vq+t d+ ++d++g + ++++t+s+++  +p+     
  gi|119720653|ref|YP_921148.1|  42 HVLLEGVPGIAKTTLAKSLARLLglsegyaleldgvaYRGFSRVQFTPDLMPSDITGNLVFNPSTRSFEPrfGPVF---- 117
                                    79***************************99999998899999*******************99999999444555.... PP

                                    G-SEEEEESGGG--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--..-TT-TTHHHHTT- CS
                          AAA_5  65 egeilvlDEveraesevlnsLlslleerrllleeggelvkaknddllerfrviatanpld.rslnelspalrsRf 138
                                        l+ DE++ra + ++++Ll+ + er++ + ++  +  +++ +  + f viat np++  +  +l +a ++Rf
  gi|119720653|ref|YP_921148.1| 118 -TYFLLADEINRAVPRTQSALLQAMQEREVTIGDRSYRLEVRERG--KFFFVIATQNPVEqEGTYPLPEAQLDRF 189
                                    .6999******************************9999999854..44***********888888888888888 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   2.5e-07   0.00037       1     130 [.      43     195 ..      43     197 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2.5e-07
                                    EEEESSTTSSHHHHHHHHHHHHT...HEEEEEETTTCSSS..................STTHHHHHHHHHHHHHHHTSTS CS
                            AAA   1 vllyGppGtGKTllakavakelg...vefleisgsellsk..................yvgesekkirelfkeakekakp 59 
                                    vll G pG+ KT+lak++a+ lg    + le++g   +                    ++  s ++++  f  + +    
  gi|119720653|ref|YP_921148.1|  43 VLLEGVPGIAKTTLAKSLARLLGlseGYALELDGVAYRGFsrvqftpdlmpsditgnlVFNPSTRSFEPRFGPVFT---- 118
                                    79*******************9643333555555555522345555556666777777788888888888877754.... PP

                                    EEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS............SSTEEEEEEESS......GGGSTHHHHS CS
                            AAA  60 silfiDEidalaksrsgseseeeervvnqLlteldgvkkk............eskvivigatnr......pdkldpallr 121
                                      l+ DEi + +++            +++Ll+++++ +              ++k+++++at++         l++a l 
  gi|119720653|ref|YP_921148.1| 119 YFLLADEINRAVPRT-----------QSALLQAMQEREVTigdrsyrlevreRGKFFFVIATQNpveqegTYPLPEAQL- 186
                                    58**********999...........*************9***********9888999999988553332233555555. PP

                                    TTSSEEEET CS
                            AAA 122 gRfdrkiei 130
                                    +Rf +++++
  gi|119720653|ref|YP_921148.1| 187 DRFLMRVFV 195
                                    777776666 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   2.5e-06    0.0037       5      47 ..      23      65 ..      19      80 .. 0.73
   2 ?    1.3   0.0      0.12   1.8e+02     110     158 ..     121     172 ..     118     184 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.5e-06
                   Mg_chelatase  5 vkGqeeakraleia.aaGgHnlllvGppGsGKtmlakrlpsllp 47
                                   v+G ee k  +  + +aGgH +ll G pG  Kt lak l+ ll 
  gi|119720653|ref|YP_921148.1| 23 VVGYEEEKALVLASlIAGGH-VLLEGVPGIAKTTLAKSLARLLG 65
                                   56666655544444246666.889****************9995 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.12
                   Mg_chelatase 110 LfLDElpefkrkvlevLRePledgevtisrakakvefp..arfq.lvaamNp 158
                                    L+ DE+     ++  +L + ++++evti   ++++e     +f  ++a+ Np
  gi|119720653|ref|YP_921148.1| 121 LLADEINRAVPRTQSALLQAMQEREVTIGDRSYRLEVRerGKFFfVIATQNP 172
                                    67799999999*****************887776655411444404555676 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   1.5e-05     0.022      34      58 ..      41      65 ..      36      70 .. 0.90
   2 ?    2.0   0.0       0.1   1.5e+02      88     115 ..     121     148 ..     118     172 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.5e-05
                         RuvB_N 34 dhvllyGpPGlGkttlakiiakelg 58
                                    hvll G PG+ kttlak +a+ lg
  gi|119720653|ref|YP_921148.1| 41 GHVLLEGVPGIAKTTLAKSLARLLG 65
                                   5*****************9998776 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.1
                         RuvB_N  88 lfideihrlsraveevlysamedfrldi 115
                                    l+ dei r  + ++  l +am++ ++ i
  gi|119720653|ref|YP_921148.1| 121 LLADEINRAVPRTQSALLQAMQEREVTI 148
                                    7789999999999999999999887654 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   1.1e-05     0.017      21      63 ..      39      79 ..      27     147 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.1e-05
                         AAA_16 21 sgrpelvllsGesGvGKsslvrellralekdggiflrgkcdql 63
                                   +g  + vll G +G+ K++l+++l+r l  ++g++l+ + + +
  gi|119720653|ref|YP_921148.1| 39 AG--GHVLLEGVPGIAKTTLAKSLARLLGLSEGYALELDGVAY 79
                                   44..78*******************999999888877666666 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   3.8e-05     0.057      24     129 ..      42     152 ..      26     178 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.8e-05
                                    -EEEECSTTSSHHHHHHHHHH........HSTTTTS-EEEEETTTS-TTCHHHHHHEBSSSSSTTTSS-BEHHHHHTTTS CS
                Sigma54_activat  24 svlitGesGtGKellaraihe........askrkekpfvavncaaipeelleseLFGhekGaFtGAekekkGlfekadgG 95 
                                    +vl++G  G  K++la+++ +        a + +   +  +   +++++l+ s++ G     F  ++++ + +f      
  gi|119720653|ref|YP_921148.1|  42 HVLLEGVPGIAKTTLAKSLARllglsegyALELDGVAYRGFSRVQFTPDLMPSDITGNL--VFNPSTRSFEPRFGPVFTY 119
                                    56666666666666666666633333322222223333334444446666666666654..4666666666666666677 PP

                                    EEEEETGGGS-HHHHHHHHHHHHHSEEESBTSSS CS
                Sigma54_activat  96 tlfLDeigelplelQekLlrvlqegevervGssk 129
                                     l+ Dei++  +++Q+ Ll+++qe+ev+ +G+++
  gi|119720653|ref|YP_921148.1| 120 FLLADEINRAVPRTQSALLQAMQEREVT-IGDRS 152
                                    8999**********************96.77654 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00012      0.18       2      31 ..      43      75 ..      43     171 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00012
                         AAA_33  2 vllvGlpGsGKstlaerllkklg...avllssd 31
                                   vll G+pG  K+tla++l++ lg   ++ l+ d
  gi|119720653|ref|YP_921148.1| 43 VLLEGVPGIAKTTLAKSLARLLGlseGYALELD 75
                                   7899***************99987665555555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00016      0.24       3      31 ..      43      71 ..      42      93 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00016
                                   EEEEC-TTTCHHHHHHHHHHHHCTS-SCC CS
                          NACHT  3 vilqGeaGsGKTtLlqklalawaegklpq 31
                                   v+l+G +G+ KTtL+++la+++  ++ ++
  gi|119720653|ref|YP_921148.1| 43 VLLEGVPGIAKTTLAKSLARLLGLSEGYA 71
                                   79*****************9998766655 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.006       8.9      53      80 ..      36      63 ..       9      73 .. 0.83
   2 ?    3.5   0.0     0.021        32     127     164 ..     123     160 ..     120     183 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.006
                                   BBCSS-EEEEEESSTSTHHHHHHHHHHH CS
                            MCM 53 klrgdinvllvgdpgtaKsqlLkyvekl 80
                                   +l++  +vll g pg+aK++l k++++l
  gi|119720653|ref|YP_921148.1| 36 SLIAGGHVLLEGVPGIAKTTLAKSLARL 63
                                   4566679**************9998876 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.021
                                    EESGGGSTCHHHHHHHHHHHHSEEEEESSSCEEEEE-- CS
                            MCM 127 iDefdkmkeedrsalhEamEqqtisiaKaGivatLnar 164
                                     De+++   +++sal+ am + +++i   +    ++ r
  gi|119720653|ref|YP_921148.1| 123 ADEINRAVPRTQSALLQAMQEREVTIGDRSYRLEVRER 160
                                    69***********************9877665555555 PP

>> MCM_lid  MCM AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00022      0.33      49      80 ..     277     308 ..     251     313 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00022
                                    HHHHHHHHHHHHHHHHHHTSSSE-HHHHHHHH CS
                        MCM_lid  49 vRqLesliRLseAlAklrlsevvteedveeai 80 
                                    +R   +l++ s+AlA +r s+vv++ dv++a+
  gi|119720653|ref|YP_921148.1| 277 PRSGIALVKASKALAAMRGSTVVERVDVDRAL 308
                                    666679***********************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.67u 0.34s 00:00:01.01 Elapsed: 00:00:00.54
# Mc/sec: 1965.97
//
Query:       gi|119720654|ref|YP_921149.1|  [L=302]
Description: ABC transporter related [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-22   81.0   0.0    1.9e-22   80.3   0.0    1.4  1  ABC_tran    ABC transporter
    2.1e-11   44.2   0.7    7.5e-06   26.0   0.1    2.1  2  AAA_21      AAA domain, putative AbiEii toxin, Type IV TA sys
    0.00068   19.4   0.0      0.001   18.8   0.0    1.4  1  AAA_30      AAA domain
    0.00082   18.9   0.1       0.89    8.9   0.1    2.1  2  SMC_N       RecF/RecN/SMC N terminal domain
     0.0039   17.0   0.0     0.0066   16.3   0.0    1.3  1  ATP_bind_1  Conserved hypothetical ATP binding protein
     0.0072   16.6   0.0      0.014   15.7   0.0    1.4  1  AAA_22      AAA domain
     0.0096   15.6   0.2      0.015   15.0   0.2    1.2  1  SRP54       SRP54-type protein, GTPase domain
  ------ inclusion threshold ------
      0.011   15.3   0.3      0.043   13.4   0.3    2.0  1  AAA_25      AAA domain
      0.036   13.1   0.3      0.065   12.2   0.3    1.3  1  MeaB        Methylmalonyl Co-A mutase-associated GTPase MeaB
      0.081   12.7   0.1       0.14   11.9   0.1    1.3  1  AAA_29      P-loop containing region of AAA domain
      0.085   13.3   0.1       0.13   12.7   0.1    1.2  1  AAA_23      AAA domain
       0.11   11.5   0.0       0.48    9.4   0.0    1.9  2  T2SSE       Type II/IV secretion system protein
       0.14   12.0   1.3       0.27   11.1   0.9    1.6  2  NTPase_1    NTPase
       0.15   12.4   0.6       0.29   11.5   0.6    1.4  1  AAA_19      AAA domain
       0.16   12.1   0.0       0.36   11.0   0.0    1.6  1  AAA_33      AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.3   0.0   1.6e-25   1.9e-22       1     137 []      17     157 ..      17     157 .. 0.94

  Alignments for each domain:
  == domain 1  score: 80.3 bits;  conditional E-value: 1.6e-25
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren. 79 
                                    l+ +++++ +g + ++vG+nG+GK+t +kl  gllk+  Ge+++ g d  + +  +lr+++gvl+++p   +++tvr+  
  gi|119720654|ref|YP_921149.1|  17 LRGLDMHIPRGVTAGLVGPNGSGKTTTIKLAVGLLKKSGGEVRVLGLDPWY-DGVELRRRVGVLHEKPLYPQDVTVRRLl 95 
                                    567899***************************************988888.8999********************9999 PP

                                    ........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    ........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                               +e+ ++++  g+++  ++ v    ssLS G  qr+ +a al+ +p+llllDEpta
  gi|119720654|ref|YP_921149.1|  96 ehlaglrgLPAQEAVRVARLAGIEGYMERSV----SSLSRGYLQRLGIAIALMGEPELLLLDEPTA 157
                                    9999999877788889999999999999999....*****************************97 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   3.8e-06    0.0045       3      23 ..      31      51 ..      29      74 .. 0.79
   2 !   26.0   0.1   6.2e-09   7.5e-06     231     297 ..     123     187 ..      95     192 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.8e-06
                         AAA_21  3 vliGpNgsGKSnLLdaldlla 23
                                   +l+GpNgsGK++ +++  +l 
  gi|119720654|ref|YP_921149.1| 31 GLVGPNGSGKTTTIKLAVGLL 51
                                   79*************998874 PP

  == domain 2  score: 26.0 bits;  conditional E-value: 6.2e-09
                         AAA_21 231 elparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTH 297
                                    e+++++lS G ++ l+++ al   +    lll+DEp ++L+P++  ++l++l++l++  g+  ++++H
  gi|119720654|ref|YP_921149.1| 123 ERSVSSLSRGYLQRLGIAIALMGEP---ELLLLDEPTANLDPSARFEILGMLENLKKdLGVTMVISSH 187
                                    5677788999888889999999988...9***********************99998899999****9 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   8.6e-07     0.001      21      54 ..      30      63 ..      22     154 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 8.6e-07
                         AAA_30 21 avltGpAGtGKttalkalreaweaaggrviglAp 54
                                   a l+Gp G+GKtt++k ++ +++++gg+v +l  
  gi|119720654|ref|YP_921149.1| 30 AGLVGPNGSGKTTTIKLAVGLLKKSGGEVRVLGL 63
                                   6799*********************999988754 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.1   0.00074      0.89      28      40 ..      31      43 ..      12      54 .. 0.79
   2 !    7.9   0.0    0.0016       1.9     151     195 ..     139     184 ..     111     203 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00074
                                   EEEESTTSSHHHH CS
                                   xxxxxxxxxxxxx RF
                          SMC_N 28 aivGpNGSGKsnl 40
                                    +vGpNGSGK+  
  gi|119720654|ref|YP_921149.1| 31 GLVGPNGSGKTTT 43
                                   59********975 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0016
                                    HHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEE.EEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx RF
                          SMC_N 151 fAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQf.ivi 195
                                    +Ai  +    l llDe  a+LD + + ++  +l++ +k+  + +vi
  gi|119720654|ref|YP_921149.1| 139 IAIALMGEPELLLLDEPTANLDPSARFEILGMLENLKKDLGVtMVI 184
                                    566666677799***********************99985431333 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   5.5e-06    0.0066       2      35 ..      33      66 ..      32      78 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5.5e-06
                     ATP_bind_1  2 vGpaGsGKttfvgalseilelrgrsvavvNLDPA 35
                                   vGp GsGKtt ++  + +l+++g +v+v+ LDP 
  gi|119720654|ref|YP_921149.1| 33 VGPNGSGKTTTIKLAVGLLKKSGGEVRVLGLDPW 66
                                   8********************************5 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.1e-05     0.014      10     113 ..      32     175 ..      29     204 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.1e-05
                         AAA_22  10 vtGesGtGKTtllrrlleqldeeakaee..................erpevv..fvtlpsstsskdllrellralglelk 69 
                                    ++G+ G+GKTt+++  +  l++                        +r++v+  +   p++ + + ll++l+   gl++ 
  gi|119720654|ref|YP_921149.1|  32 LVGPNGSGKTTTIKLAVGLLKKS----GgevrvlgldpwydgvelrRRVGVLheKPLYPQDVTVRRLLEHLAGLRGLPAQ 107
                                    79****************99532....135789***********9999999965555555559**************999 PP

                         AAA_22  70 a.............erlsseell.ealeqalrarav...ielliiDEaqh.lr.s.....eealeeLr 113
                                    +              + s + l   +l++   a a    +ell++DE    l+ s       +le+L+
  gi|119720654|ref|YP_921149.1| 108 EavrvarlagiegyMERSVSSLSrGYLQRLGIAIALmgePELLLLDEPTAnLDpSarfeiLGMLENLK 175
                                    99*9999999988744444444446666666666669999*******877798634555666666662 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.2   1.2e-05     0.015       6      38 ..      32      64 ..      28      69 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.2e-05
                                   EEESTTSSHHHHHHHHHHHHHHT.TS-EEEEEES CS
                          SRP54  6 lvGlqGaGKTttlaKLaallkke.gkkvllvaaD 38
                                   lvG++G+GKTtt+ KLa  l k+ g +v +  +D
  gi|119720654|ref|YP_921149.1| 32 LVGPNGSGKTTTI-KLAVGLLKKsGGEVRVLGLD 64
                                   8***********9.77765555548888887777 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.3   3.6e-05     0.043      28      96 ..      22      82 ..      17     189 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.6e-05
                         AAA_25 28 gllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgea 96
                                    ++p+g +a l+G+ g+GKtt ++ la+ +++ +   g      ++Vl ++   +  elrrR+  ++e+
  gi|119720654|ref|YP_921149.1| 22 MHIPRGVTAGLVGPNGSGKTT-TIKLAVGLLKKS---G----GEVRVLGLDPWYDGVELRRRVGVLHEK 82
                                   589*****************9.789999888433...2....223444444444444444444444433 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.3   5.4e-05     0.065      27      67 ..      25      65 ..      15      69 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.4e-05
                                   S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE-- CS
                           MeaB 27 GraqvvGltGvPGaGkstlvealglelrrrGkrvavlavDP 67
                                    r    Gl G  G+Gk t+++  +  l++ G  v vl +DP
  gi|119720654|ref|YP_921149.1| 25 PRGVTAGLVGPNGSGKTTTIKLAVGLLKKSGGEVRVLGLDP 65
                                   567788***************99999**************9 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00012      0.14      17      39 ..      22      44 ..      11      51 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00012
                         AAA_29 17 ieidlkg.atlltGpsGsGKSTll 39
                                   ++i  +g +  l+Gp+GsGK+T +
  gi|119720654|ref|YP_921149.1| 22 MHIP-RGvTAGLVGPNGSGKTTTI 44
                                   5554.666777**********976 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   0.00011      0.13      19      36 ..      26      44 ..      10      47 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00011
                         AAA_23 19 kglt.lItGpNGaGKTTil 36
                                   +g+t  ++GpNG+GKTT +
  gi|119720654|ref|YP_921149.1| 26 RGVTaGLVGPNGSGKTTTI 44
                                   55553589*********87 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0    0.0004      0.48     135     160 ..      33      60 ..      24     102 .. 0.77
   2 ?   -0.7   0.0       0.5     6e+02      44      72 ..     210     238 ..     196     253 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0004
                          T2SSE 135 sGgTgsGKttllyallkeinks..deri 160
                                     G+ gsGKtt++  ++  ++ks  + r+
  gi|119720654|ref|YP_921149.1|  33 VGPNGSGKTTTIKLAVGLLKKSggEVRV 60 
                                    59*****************999544444 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.5
                          T2SSE  44 kaalerlisriaalakldiseerplqdar 72 
                                    +  l  l++r++a+ +l+i++++p + a+
  gi|119720654|ref|YP_921149.1| 210 QGSLLELARRFMATLELRIETRSPRLAAS 238
                                    556778999************99988774 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.9   0.00022      0.27       4      30 ..      32      58 ..      29      63 .. 0.87
   2 ?   -2.9   0.0       4.8   5.7e+03     136     162 ..     264     293 ..     250     298 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00022
                                   EE--TTSSHHHHHHHHHHHH...GGGE CS
                       NTPase_1  4 iTGppGvGKtTlvkkvlellkssgvkv 30
                                   + Gp G+GKtT +k ++ llk+sg +v
  gi|119720654|ref|YP_921149.1| 32 LVGPNGSGKTTTIKLAVGLLKKSGGEV 58
                                   67********************98665 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.8
                                    -...-SHHHHHHHT-TT-EEEE--TTTTTT CS
                       NTPase_1 136 k...dlalveeirerkdvkvfevteenrda 162
                                    k    +a+ve++r++  ++  +vt ++  +
  gi|119720654|ref|YP_921149.1| 264 KlreAEAVVEDLRRSGLAESWSVTSRSLGE 293
                                    444467788888888777777777766555 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.6   0.00024      0.29      14      40 ..      31      57 ..      23      64 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00024
                         AAA_19 14 lvtaGpGtGKTrvlkhivallvelggv 40
                                    ++++ G+GKT+++k +v ll++ gg+
  gi|119720654|ref|YP_921149.1| 31 GLVGPNGSGKTTTIKLAVGLLKKSGGE 57
                                   578999**************9998864 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0    0.0003      0.36       4      32 ..      32      65 ..      31     109 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0003
                         AAA_33  4 lvGlpGsGKstlae...rllkklg..avllssdt 32
                                   lvG++GsGK+t ++   +llkk g  + +l  d 
  gi|119720654|ref|YP_921149.1| 32 LVGPNGSGKTTTIKlavGLLKKSGgeVRVLGLDP 65
                                   69*********76611156888886555577776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.65u 0.36s 00:00:01.01 Elapsed: 00:00:00.55
# Mc/sec: 1641.52
//
Query:       gi|119720655|ref|YP_921150.1|  [L=250]
Description: hypothetical protein Tpen_1752 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.42   10.1   6.7        1.2    8.7   6.6    2.0  1  ABC2_membrane_5  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane_5  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   6.6   6.6e-05       1.2      16     103 ..      40     128 ..      31     246 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 6.6e-05
                ABC2_membrane_5  16 illivllllaiiiliflndsvllifsilslvisiililttls.yDekskwnkylltLPvtrkeiVksKYlfvlililiai 94 
                                    ++++vl+ ++   l+ +    ++ ++++s +  +++++ ++s   e  ++ +++l+ P++r+e+V+s  l v++  l+++
  gi|119720655|ref|YP_921150.1|  40 QFFLVLAYASSRGLAGGPPFSYFPLMLMSYAYGFLVLMGLSSlAGELKGSAALYLSQPLSRSEYVASWALAVVVSPLASL 119
                                    455544444444444445555566777777777777776666558889*******************7777777777777 PP

                ABC2_membrane_5  95 litllllii 103
                                    + ++l+++ 
  gi|119720655|ref|YP_921150.1| 120 VASALFSAA 128
                                    766666642 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       670  (0.0373696); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.39s 00:00:01.00 Elapsed: 00:00:00.58
# Mc/sec: 1290.29
//
Query:       gi|119720656|ref|YP_921151.1|  [L=301]
Description: hypothetical protein Tpen_1753 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.64u 0.34s 00:00:00.98 Elapsed: 00:00:00.57
# Mc/sec: 1599.36
//
Query:       gi|119720657|ref|YP_921152.1|  [L=327]
Description: von Willebrand factor, type A [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      4e-19   69.2   0.0    7.1e-19   68.4   0.0    1.4  1  VWA_2          von Willebrand factor type A domain
    1.3e-12   48.4   0.0    1.8e-12   47.8   0.0    1.2  1  VWA            von Willebrand factor type A domain
    7.2e-06   25.6   0.0    1.5e-05   24.5   0.0    1.5  1  VWA_CoxE       VWA domain containing CoxE-like protein
     0.0063   16.7   0.0       0.02   15.0   0.0    1.7  1  vWA-TerF-like  vWA found in TerF C terminus
  ------ inclusion threshold ------
      0.029   14.8   0.0       0.96    9.8   0.0    2.6  3  Radical_SAM    Radical SAM superfamily
      0.043   13.8   0.0      0.079   12.9   0.0    1.5  1  VWA_3          von Willebrand factor type A domain
       0.28   11.6   8.2        1.2    9.5   3.9    2.9  2  BatA           Aerotolerance regulator N-terminal


Domain annotation for each model (and alignments):
>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.4   0.0   2.8e-22   7.1e-19       2     106 ..     103     208 ..     102     209 .. 0.97

  Alignments for each domain:
  == domain 1  score: 68.4 bits;  conditional E-value: 2.8e-22
                          VWA_2   2 vfvlDtSgSmrngdygptrleaakdaveallkslp.gdrvglvtfsdgpevlipltkdkakilnalrnleakgggtnlaa 80 
                                    v+v+D+SgSm+++  g  ++e a++a++ l++++p g+ vgl++fsd+  + +p+t d++++l+a+++l++ gggt ++ 
  gi|119720657|ref|YP_921152.1| 103 VLVVDVSGSMEDSIPGGVKIEVARRAATLLVERMPgGVDVGLLAFSDRIVLSLPPTGDRRRVLDAIESLKP-GGGTMYTY 181
                                    89***********99*******************9899********************************9.5******* PP

                          VWA_2  81 aLqlarkalkkrr.kgekrvivlitDg 106
                                     Lq a ++lk  + ++++  +v+++Dg
  gi|119720657|ref|YP_921152.1| 182 PLQAALSWLKPYKlFNASTLVVFVSDG 208
                                    **********999*************9 PP

>> VWA  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.8   0.0   7.2e-16   1.8e-12       3     172 ..     103     269 ..     102     272 .. 0.88

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 7.2e-16
                                    EEEEE-STTS.....CHHHHHHHHHHHHHHHHHHTBTTTTEEEEEEEESSSEEEEEETTSHCHHHHHHHHHHTGSGGGGS CS
                            VWA   3 vfvlDgSgsm.....geenfekvkefikklveklevgpegtrvglvqfssevktefslndysskeellsalnnlkysggg 77 
                                    v+v+D+Sgsm     g+ ++e +++++  lve++     g+ vgl+ fs+ +    + + ++    +l+a+++l   ggg
  gi|119720657|ref|YP_921152.1| 103 VLVVDVSGSMedsipGGVKIEVARRAATLLVERMP---GGVDVGLLAFSDRIVLSLPPTGDR--RRVLDAIESL-KPGGG 176
                                    89********99999999*****************...**************9999999977..9********7.67777 PP

                                    SC-HHHHHHHHHHHHHHHHGTSSTTSEEEEEEEESS--CS.SHTHHHHHHHHGCTEEEEEEEE...SSSHHHHHHHHHSS CS
                            VWA  78 ttntgkalkyaleklfkssagaRenakkviilltdGksnd.gdpkeaaneakeqgikvfavGv...gnadekelLnkias 153
                                    t+     l++al+ l   +     na+ ++++++dG + d   +++ + e ++ gi v++v +   g+  e+e L+ ia+
  gi|119720657|ref|YP_921152.1| 177 TM-YTYPLQAALSWLKPYKLF---NASTLVVFVSDGLPADaATYRTLLSEFRSLGIPVYTVYIgpgGDEGERE-LKLIAG 251
                                    77.777899888866555555...9*************9955*********************9988888888.****** PP

                                    SSCHHCEEEESSHHHHHHH CS
                            VWA 154 epgeghvftvtdfeeleel 172
                                    ++g g  +t+ + eel ++
  gi|119720657|ref|YP_921152.1| 252 STG-GEEYTAGSAEELLKA 269
                                    **9.777887777776655 PP

>> VWA_CoxE  VWA domain containing CoxE-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0     6e-09   1.5e-05      56     165 ..      99     213 ..      87     233 .. 0.71

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 6e-09
                       VWA_CoxE  56 kprelvllvDvSgSmaaysaiflallhA......llqqlp...rtevfaFdtrlvdlTralrerDpaeaLarvsaavedl 126
                                    +p   vl+vDvSgSm++     +++  A      l++++p   ++ ++aF++r+v   +     D+ ++L+ ++    + 
  gi|119720657|ref|YP_921152.1|  99 RP-AAVLVVDVSGSMEDSIPGGVKIEVArraatlLVERMPggvDVGLLAFSDRIVLSLPPTG--DRRRVLDAIE--SLKP 173
                                    45.78***********9443333332221111224566669999*********996544443..6666666665..2339 PP

                       VWA_CoxE 127 gGgTrigaalaeflelvtrpaL.srravvvlvsDglergd 165
                                    gGgT +   l+++l++ +   L +  ++vv vsDgl  ++
  gi|119720657|ref|YP_921152.1| 174 GGGTMYTYPLQAALSWLKPYKLfNASTLVVFVSDGLPADA 213
                                    ****************986665266888999****86654 PP

>> vWA-TerF-like  vWA found in TerF C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   7.9e-06      0.02       5     140 ..     103     236 ..      99     243 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 7.9e-06
                  vWA-TerF-like   5 vlVlDasgSmsklykkgvvqavverllavaa.qlDddgelevwlfaskakr.lpdvtladleeyvkeeeegllelkklgg 82 
                                    vlV+D+sgSm+++   gv  +v+ r++++ + ++     +   +f++++   lp   ++d ++ ++ ++    e  k gg
  gi|119720657|ref|YP_921152.1| 103 VLVVDVSGSMEDSIPGGVKIEVARRAATLLVeRMPGGVDVGLLAFSDRIVLsLP--PTGDRRRVLD-AI----ESLKPGG 175
                                    79***********************99875516666666777777776643133..2345555553.22....3334566 PP

                  vWA-TerF-like  83 vneeapvleevlekvrk.epaelptlvlFitDGgvkkkkeiekalreaske..piFwqFvg 140
                                     ++++  l++ l+ ++  +  ++ tlv+F++DG  ++++  +++l e  ++  p++  ++g
  gi|119720657|ref|YP_921152.1| 176 GTMYTYPLQAALSWLKPyKLFNASTLVVFVSDGLPADAATYRTLLSEFRSLgiPVYTVYIG 236
                                    699999999999999876678899**************99999998866542266666666 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00038      0.96      90     143 ..     114     177 ..      72     189 .. 0.81
   2 ?    0.2   0.0      0.35   8.9e+02     133     156 ..     219     241 ..     210     252 .. 0.73
   3 ?    0.2   0.0      0.34   8.8e+02     125     141 ..     261     277 ..     254     292 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00038
                                    G...........HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSE CS
                                    x...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  90 d...........eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagik 143
                                    d           ++ + +l+e+ +  v +gl a++d+ vl l  +++++ +vl+a+e l+  g+ 
  gi|119720657|ref|YP_921152.1| 114 DsipggvkievaRRAATLLVERMPGGVDVGLLAFSDRIVLSLP-PTGDRRRVLDAIESLKPGGGT 177
                                    45555555567688888899989**************999999.*************99987655 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.35
                                    HHHHHHHTTSETEEEEEEEBTTTS CS
                                    xxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM 133 aleklreagikrvvdrivglpGen 156
                                    +l  +r++gi+ v+++++g+ G  
  gi|119720657|ref|YP_921152.1| 219 LLSEFRSLGIP-VYTVYIGPGGDE 241
                                    5678999****.777777776654 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.34
                                    SHHHHHHHHHHHHHHTT CS
                                    xxxxxxxxxxxxxxxxx RF
                    Radical_SAM 125 htfeevlealeklreag 141
                                    ++ ee+l+a+++l+e+ 
  gi|119720657|ref|YP_921152.1| 261 GSAEELLKAFKTLAEKA 277
                                    67899*******99985 PP

>> VWA_3  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   3.1e-05     0.079       3     151 ..     102     255 ..     100     259 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.1e-05
                          VWA_3   3 vvivvDvsssmsaen......klvkdaLsvalrqLptndkiavllfgtkprplfpgsravsaaelqealqkikelelslg 76 
                                    +v+vvDvs sm++++      + ++ a  ++++ +p ++ + +l+f ++ +       +    +++++l++i+ l++  g
  gi|119720657|ref|YP_921152.1| 102 AVLVVDVSGSMEDSIpggvkiEVARRAATLLVERMPGGVDVGLLAFSDRIV--LSLPPT---GDRRRVLDAIESLKP-GG 175
                                    79***********999999999*************************9955..333333...5699***********.99 PP

                          VWA_3  77 asnlegaLkealr..qp.akpgevrsvilltDgssaqgeervsdlisrarekirfhalglgsslsa..amlqaLAeasgG 151
                                    ++     L++al+  +p +       v+ ++Dg +a  +++   l +     i++ ++ +g+  ++  + l+++A  +gG
  gi|119720657|ref|YP_921152.1| 176 GTMYTYPLQAALSwlKPyKLFNASTLVVFVSDGLPADAATYRTLLSEFRSLGIPVYTVYIGPGGDEgeRELKLIAGSTGG 255
                                    99999999999985444444455566788899999665544433333333689999999999777444999999998888 PP

>> BatA  Aerotolerance regulator N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   3.9   0.00047       1.2       1      77 []       1      75 [.       1      75 [. 0.70
   2 ?    2.5   0.1     0.075   1.9e+02       8      28 ..     302     321 ..     298     326 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00047
                           BatA  1 MlpFlnPllLlallllplpiillyllkrrpqevvfsslrlleevekdeealqrlkknllllLrllalallvlalArP 77
                                   M  F  P+lLla  ll++++++l +   r+  ++ ssl+   ++   +    + ++   l+L++l+++l+ +alA+P
  gi|119720657|ref|YP_921152.1|  1 M-YFEKPELLLAGPLLAVLLYYLHVKGYRRFYAKKSSLKNPLAAYAGTGG-AEPRRLGTLALKVLLAVLVGVALAGP 75
                                   7.699***998888777733333333333333366777766666555555.578888899****************9 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.075
                           BatA   8 llLlallllplpiillyllkr 28 
                                    +++++ +l++  +illy++ r
  gi|119720657|ref|YP_921152.1| 302 WAFAVSALIVT-LILLYARSR 321
                                    44444445555.788887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.67u 0.34s 00:00:01.01 Elapsed: 00:00:00.57
# Mc/sec: 1739.40
//
Query:       gi|119720658|ref|YP_921153.1|  [L=305]
Description: von Willebrand factor, type A [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.4e-13   48.8   0.0    1.3e-12   48.3   0.0    1.1  1  VWA       von Willebrand factor type A domain
    7.8e-11   42.6   0.0    1.4e-10   41.7   0.0    1.4  1  VWA_2     von Willebrand factor type A domain
  ------ inclusion threshold ------
      0.032   13.6   0.0      0.081   12.3   0.0    1.5  1  VWA_CoxE  VWA domain containing CoxE-like protein


Domain annotation for each model (and alignments):
>> VWA  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3   0.0   2.2e-16   1.3e-12       3     168 ..      93     249 ..      93     257 .. 0.89

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 2.2e-16
                                    EEEEE-STTSCHHHHH.....HHHHHHHHHHHHHTBTTTTEEEEEEEESSSEEEEEETTSHCHHHHHHHHHHTGSGGGGS CS
                            VWA   3 vfvlDgSgsmgeenfe.....kvkefikklveklevgpegtrvglvqfssevktefslndysskeellsalnnlkysggg 77 
                                    v+vlD S+sm   ++       +k+f++k +e l+   +++ v lv fss+     +l +    + +l+al+  + ++  
  gi|119720658|ref|YP_921153.1|  93 VVVLDESKSMLSADVYpdrctLAKRFAEKYIEGLQ---PSDLVVLVFFSSSSNATGPLPR----DNALRALDGYTCRYRY 165
                                    79********6666666666699999999999999...**********************....569******9999998 PP

                                    SC-HHHHHHHHHHHHHHHHGTSSTTSEEEEEEEESS--CSS.HTHHHHHHHHGCTEEEEEEEESSSHHHHHHHHHSSSSC CS
                            VWA  78 ttntgkalkyaleklfkssagaRenakkviilltdGksndg.dpkeaaneakeqgikvfavGvgnadekelLnkiasepg 156
                                    t+ +g+al  a++ ++ +s       +  +++++dG  n g dp+++a+++++++++++ v vg +   +l+++ as+ +
  gi|119720658|ref|YP_921153.1| 166 TA-LGDALVSAYS-VLAASGL-----PGAVVVVSDGGWNYGsDPLQVAQSIRASNYSLVLVRVGGDPRGSLMRDVASKAN 238
                                    99.**********.4444444.....89**********9977*************************************9 PP

                                    HHCEEEESSHHH CS
                            VWA 157 eghvftvtdfee 168
                                     g++ +++ f++
  gi|119720658|ref|YP_921153.1| 239 -GKYLELDAFSQ 249
                                    .99999888874 PP

>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.7   0.0   2.4e-14   1.4e-10       2     106 ..      93     194 ..      92     195 .. 0.95

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 2.4e-14
                          VWA_2   2 vfvlDtSgSmrngdygptrleaakdaveallksl.pgdrvglvtfsdgpevlipltkdkakilnalrnleakgggtnlaa 80 
                                    v+vlD S+Sm + d+ p r+  ak+++e++++ l p d v lv fs++++   pl +d    l+al++ +++   t l++
  gi|119720658|ref|YP_921153.1|  93 VVVLDESKSMLSADVYPDRCTLAKRFAEKYIEGLqPSDLVVLVFFSSSSNATGPLPRD--NALRALDGYTCRYRYTALGD 170
                                    89******************************9945*******************995..669***************** PP

                          VWA_2  81 aLqlarkalkkrrkgekrvivlitDg 106
                                    aL  a ++l +   g +  +v+++Dg
  gi|119720658|ref|YP_921153.1| 171 ALVSAYSVLAAS--GLPGAVVVVSDG 194
                                    *********977..79*********8 PP

>> VWA_CoxE  VWA domain containing CoxE-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.4e-05     0.081      58     163 ..      90     198 ..      84     219 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.4e-05
                       VWA_CoxE  58 relvllvDvSgSmaaysaif.......lallhAllqqlp..rtevfaFdtrlvdlTralrerDpaeaLarvsaavedlgG 128
                                    + +v+++D S Sm + + ++        ++++   ++l+  +  v++F ++  + T  l  + + +aL+        ++ 
  gi|119720658|ref|YP_921153.1|  90 TLHVVVLDESKSMLS-ADVYpdrctlaKRFAEKYIEGLQpsDLVVLVFFSSSSNATGPLPRDNALRALDGYT----CRYR 164
                                    568999999999988.666621111112333344444447788999**************777777777776....7889 PP

                       VWA_CoxE 129 gTrigaalaeflelvtrpaLsrravvvlvsD.gler 163
                                     T +g+al ++ ++ + + L    +vv+vsD g++ 
  gi|119720658|ref|YP_921153.1| 165 YTALGDALVSAYSVLAASGL--PGAVVVVSDgGWNY 198
                                    9***************9998..66788899933443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.65u 0.32s 00:00:00.97 Elapsed: 00:00:00.56
# Mc/sec: 1641.20
//
Query:       gi|119720659|ref|YP_921154.1|  [L=288]
Description: hypothetical protein Tpen_1756 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.047   13.4   0.0      0.067   12.9   0.0    1.2  1  NMT1_2    NMT1-like family


Domain annotation for each model (and alignments):
>> NMT1_2  NMT1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   3.8e-06     0.067      53     104 ..     192     243 ..     180     281 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.8e-06
                         NMT1_2  53 lagelDaahv.ltpapllidlGiggakadmkvlaslnlnGqaitlsnklkdkk 104
                                    +++ +Daa+  l+ ++l++d++  ++++++++l++  + G +i +s++l+ + 
  gi|119720659|ref|YP_921154.1| 192 ASEAVDAAQRyLKQLLLAVDITS-KHPEELDALCKARKAGRSIAVSEQLARSL 243
                                    57899*****************9.9**********************987654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.34s 00:00:00.95 Elapsed: 00:00:00.53
# Mc/sec: 1630.97
//
Query:       gi|119720660|ref|YP_921155.1|  [L=305]
Description: hypothetical protein Tpen_1757 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00042   20.2   6.5      0.019   14.8   5.0    2.4  2  MCPsignal        Methyl-accepting chemotaxis protein (MCP) si
     0.0011   19.1  14.1       0.37   10.9   1.8    4.2  4  COG2             COG (conserved oligomeric Golgi) complex com
     0.0011   18.4  22.2      0.033   13.5  14.4    2.2  2  DUF632           Protein of unknown function (DUF632)
     0.0011   16.7   6.6     0.0014   16.3   6.6    1.1  1  SidE             Dot/Icm substrate protein
     0.0011   19.5  40.1      0.013   16.1  20.1    3.2  3  APG6_N           Apg6 coiled-coil region
      0.003   17.9  10.0        1.2    9.6   2.1    3.9  3  Snapin_Pallidin  Snapin/Pallidin
     0.0038   17.0  11.0     0.0071   16.1  10.7    1.6  1  Laminin_I        Laminin Domain I
      0.005   17.5  14.3       0.34   11.6   4.1    2.9  2  YabA             Initiation control protein YabA
     0.0054   16.1  20.5     0.0054   16.1  20.5    2.4  2  GAS              Growth-arrest specific micro-tubule binding
     0.0073   15.6  10.5       0.16   11.3   0.6    2.3  2  DUF4763          Domain of unknown function (DUF4763)
     0.0077   15.1  19.0      0.013   14.5  19.0    1.4  1  Spc7             Spc7 kinetochore protein
     0.0089   14.6   2.0      0.012   14.2   2.0    1.2  1  FUSC             Fusaric acid resistance protein family
  ------ inclusion threshold ------
      0.013   14.8  15.9      0.016   14.4   3.6    2.1  2  TMPIT            TMPIT-like protein
      0.014   15.1   8.3       0.68    9.6   1.9    3.4  3  RPW8             Arabidopsis broad-spectrum mildew resistance
      0.014   15.4  14.1       0.37   10.8   1.1    3.4  3  DUF1664          Protein of unknown function (DUF1664)
      0.015   14.0   9.5      0.019   13.6   9.5    1.2  1  AAA_13           AAA domain
      0.015   15.6  19.7       0.25   11.6  12.6    2.2  2  zf-C4H2          Zinc finger-containing protein
      0.017   14.9   8.8      0.083   12.7   1.2    3.4  2  SKA2             Spindle and kinetochore-associated protein 2
      0.026   14.1   9.6       0.13   11.9   6.2    2.2  2  DUF2968          Protein of unknown function (DUF2968)
      0.027   14.9   0.6       0.61   10.5   0.1    2.7  2  FCD              FCD domain
      0.053   12.7  19.7      0.098   11.9  19.7    1.5  1  HAP1_N           HAP1 N-terminal conserved region
      0.054   13.5  34.1       0.14   12.2   9.4    3.4  3  TMF_DNA_bd       TATA element modulatory factor 1 DNA binding
      0.054   12.8  17.5      0.038   13.3   8.6    2.2  2  DUF3450          Protein of unknown function (DUF3450)
      0.072   13.4   2.9         16    5.8   1.5    3.6  2  DUF948           Bacterial protein of unknown function (DUF94
      0.073   13.4   0.0       0.16   12.4   0.0    1.6  1  E3_binding       e3 binding domain
      0.074   12.9  29.4       0.11   12.3  27.5    1.9  1  ERM              Ezrin/radixin/moesin family
      0.085   12.7  18.3      0.053   13.3   7.4    2.2  2  DUF724           Protein of unknown function (DUF724)
       0.11   12.6   8.9         15    5.7   0.4    4.9  3  bPH_6            Bacterial PH domain
       0.12   11.5   3.3        2.1    7.5   2.4    2.5  2  IF-2B            Initiation factor 2 subunit family
       0.14   12.8  18.6        1.9    9.1   2.1    4.5  4  SlyX             SlyX
       0.14   12.3  19.7        1.9    8.6   8.8    2.7  3  Mod_r            Modifier of rudimentary (Mod(r)) protein
       0.14   11.8  11.6      0.081   12.5   5.9    2.3  2  PTRF_SDPR        PTRF/SDPR family
       0.14   11.9  23.3       0.54   10.0  22.7    2.1  1  KASH_CCD         Coiled-coil region of CCDC155 or KASH
       0.19   12.0  22.1       0.53   10.5  17.0    2.8  3  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
        0.2    9.8  18.7         11    4.0  18.4    2.4  1  EzrA             Septation ring formation regulator, EzrA
       0.23   11.6   5.9        8.5    6.5   0.2    3.0  3  Cauli_DNA-bind   Caulimovirus DNA-binding protein
       0.24   10.0  18.3        1.1    7.7   5.9    2.1  2  FapA             Flagellar Assembly Protein A
       0.24   11.8  22.6        0.4   11.1   8.6    2.9  2  CENP-H           Centromere protein H (CENP-H)
       0.27   12.0   8.2        3.4    8.4   2.1    2.9  3  Occludin_ELL     Occludin homology domain
       0.28   10.6  20.1       0.27   10.7  18.4    1.7  1  Golgin_A5        Golgin subfamily A member 5
       0.28   11.0  18.8        1.3    8.8   3.9    2.9  2  Sec5             Exocyst complex component Sec5
       0.28    9.0   7.3       0.35    8.7   7.3    1.2  1  V_ATPase_I       V-type ATPase 116kDa subunit family
       0.32   10.0  12.6       0.79    8.7   6.5    2.7  3  TelA             Toxic anion resistance protein (TelA)
       0.45   10.6  16.6       0.29   11.2  14.3    2.0  1  BRE1             BRE1 E3 ubiquitin ligase
       0.49   10.1  20.4       0.98    9.1   6.4    2.8  2  DUF4201          Domain of unknown function (DUF4201)
       0.49    9.7  14.9       0.18   11.1  11.6    1.6  1  DUF2353          Uncharacterized coiled-coil protein (DUF2353
       0.51   10.3  10.5        4.3    7.3   1.2    3.0  3  DUF4446          Protein of unknown function (DUF4446)
       0.51   10.7  12.0         19    5.6   5.1    3.9  3  BLOC1_2          Biogenesis of lysosome-related organelles co
       0.52    8.5   6.7       0.44    8.7   1.8    2.0  2  COG6             Conserved oligomeric complex COG6
       0.52   10.2   4.5        3.3    7.6   1.1    2.4  2  Sec34            Sec34-like family
       0.56   10.3  23.0        1.7    8.7  10.4    2.3  2  UPF0242          Uncharacterised protein family (UPF0242) N-t
       0.69    9.9  30.8      0.092   12.8  22.6    2.4  2  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
       0.79    9.0  10.8       0.61    9.3   8.6    1.8  1  S_4TM            SMODS-associating 4TM effector domain
       0.93    9.7   7.6        6.5    7.0   6.7    2.4  2  DUF4771          Domain of unknown function (DUF4771)
       0.97    8.8   4.1        1.8    7.9   0.3    1.9  2  DUF4735          Domain of unknown function (DUF4735)
        1.1    9.5  18.6    1.9e+02    2.3  16.6    3.3  1  DUF5082          Domain of unknown function (DUF5082)
        1.2    9.4   4.6        4.7    7.6   0.7    3.0  2  KxDL             Uncharacterized conserved protein
        1.5    7.6  10.0          2    7.2  10.0    1.2  1  LMBR1            LMBR1-like membrane protein
        1.5    6.7   5.7        1.8    6.5   3.6    1.5  2  Prominin         Prominin
        1.6    8.8  10.8         19    5.3   0.3    4.7  4  DUF4023          Protein of unknown function (DUF4023)
        1.6    8.3  17.4         25    4.4   9.1    3.2  2  DUF4795          Domain of unknown function (DUF4795)
        1.6    8.9   7.9         13    6.0   7.9    2.3  1  Fib_alpha        Fibrinogen alpha/beta chain family
          2    8.5   9.0         23    5.1   2.8    3.4  2  Barstar          Barstar (barnase inhibitor)
        2.4    7.2  15.3        3.7    6.5  15.3    1.3  1  Atg14            Vacuolar sorting 38 and autophagy-related su
        2.8    7.9   6.6        1.6    8.6   3.7    2.2  1  NleF_casp_inhib  NleF caspase inhibitor
        3.1    8.4  12.6          2    9.0   0.9    3.1  3  Phage_H_T_join   Phage head-tail joining protein
        3.3    8.2  17.4         27    5.3   8.3    3.5  2  DUF16            Protein of unknown function DUF16
        3.5    8.2  12.6    1.5e+02    3.0   0.3    5.8  7  MobC             Bacterial mobilisation protein (MobC)
        3.5    7.9  11.3        8.4    6.7   2.9    3.3  3  Ntox28           Bacterial toxin 28
        3.9    7.9  13.4        4.9    7.6   4.0    3.1  2  TSNAXIP1_N       Translin-associated factor X-interacting N-t
        4.4    7.1  29.8       0.56   10.0   3.5    4.1  4  DivIC            Septum formation initiator
        4.5    7.5  12.5         23    5.2   0.3    4.4  4  DUF4081          Domain of unknown function (DUF4081)
        4.7    7.7  30.4        2.3    8.7  24.2    2.6  2  DUF4200          Domain of unknown function (DUF4200)
        5.2    7.2  25.4        4.9    7.2  20.7    2.5  2  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
        5.2    7.3  25.7        3.7    7.8   7.1    2.8  2  TMF_TATA_bd      TATA element modulatory factor 1 TATA bindin
        6.4    7.1  16.4         29    5.0   3.1    3.1  2  Spc24            Spc24 subunit of Ndc80
        6.8    7.1  10.2         50    4.3   4.5    3.1  3  eIF3_N           eIF3 subunit 6 N terminal domain
        7.5    6.2  19.6         11    5.6  18.6    1.7  1  YkyA             Putative cell-wall binding lipoprotein
        7.7    6.9   9.0    1.3e+03   -0.2   9.0    3.1  1  Img2             Mitochondrial large subunit ribosomal protei
        9.7    5.3   9.2        2.6    7.2   1.2    2.0  2  DUF1394          Protein of unknown function (DUF1394)
         10    3.8  15.0         17    3.1  15.0    1.4  1  Nup88            Nuclear pore component


Domain annotation for each model (and alignments):
>> MCPsignal  Methyl-accepting chemotaxis protein (MCP) signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   5.0   8.4e-05     0.019      75     162 ..      44     131 ..      42     138 .. 0.75
   2 !   14.4   1.3   0.00011     0.025      75     167 ..      93     188 ..      89     193 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 8.4e-05
                                    HHHHHHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      MCPsignal  75 dEVrkLAersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeq 154
                                    +EVr+L e+ a + keie++  ei+k  ++ +++ +e ++  ee +++ +e ++  +e + + +e++++ +ei +  eeq
  gi|119720660|ref|YP_921155.1|  44 EEVRDLREEQARTWKEIEKVWGEIEKLREEQAKTWKEIERLREEQAKTWKEIEKLREEQARTWKEIKKVWEEIEKLREEQ 123
                                    8*******************888888887777777777766666666666666666666777777777777777777777 PP

                                    HHHHHHHH CS
                      MCPsignal 155 sasieevn 162
                                    ++  ee+ 
  gi|119720660|ref|YP_921155.1| 124 TKIWEEIE 131
                                    77777765 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 0.00011
                                    HHHHHHHHHHHHHHHHHHHHH.................HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHH CS
                      MCPsignal  75 dEVrkLAersaqaakeiealiieiqkeindsv...esleetrqrveegselveetgealkeiveavaevadlvqeiaaas 151
                                    +E+ kL e+ a + kei+++ +ei+k  ++ +   e +ee r++  +  e+++  +e   +i +++ae+++    i ++ 
  gi|119720660|ref|YP_921155.1|  93 KEIEKLREEQARTWKEIKKVWEEIEKLREEQTkiwEEIEELRKEQTKMWEEIKGLREGQTKIWQEIAELKEGQGKIWVTL 172
                                    6999****************888887666666111556777777777778888889999999999999999999999999 PP

                                    HHHHHHHHHHHHHHHH CS
                      MCPsignal 152 eeqsasieevnqavee 167
                                    + +s+++e  + +vee
  gi|119720660|ref|YP_921155.1| 173 NRLSKTVERLTLTVEE 188
                                    9999999999888876 PP

>> COG2  COG (conserved oligomeric Golgi) complex component, COG2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   1.8    0.0017      0.37      56     131 ..      21      97 ..       1      99 [. 0.70
   2 !    9.1   2.7     0.006       1.3      69     113 ..      79     123 ..      75     125 .. 0.94
   3 !    9.3   2.3     0.005       1.1      69     116 ..     114     161 ..     108     188 .. 0.80
   4 ?    0.1   0.0       3.7   8.1e+02      40      55 ..     258     273 ..     234     276 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0017
                           COG2  56 dFvslSghLvglqeeleevesplaaarkkvesvreklsereeeveskleeakeleekr.....ellklllkldevvekle 130
                                    +F +  + L+g++e le++     +++++v+++re+ +++ +e+e+   e ++l+e++     e+ +l  + +++ +++e
  gi|119720660|ref|YP_921155.1|  21 EFRHAVAGLIGMREILEKL----DRLWEEVRDLREEQARTWKEIEKVWGEIEKLREEQaktwkEIERLREEQAKTWKEIE 96 
                                    5666677888888877765....578888888888888888888888888888888887666666666666666666666 PP

                           COG2 131 a 131
                                    +
  gi|119720660|ref|YP_921155.1|  97 K 97 
                                    5 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.006
                           COG2  69 eeleevesplaaarkkvesvreklsereeeveskleeakeleekr 113
                                    +e+e+++ + a+++k++e++re+ +++ +e+++  ee ++l+e++
  gi|119720660|ref|YP_921155.1|  79 KEIERLREEQAKTWKEIEKLREEQARTWKEIKKVWEEIEKLREEQ 123
                                    6899************************************99987 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.005
                           COG2  69 eeleevesplaaarkkvesvreklsereeeveskleeakeleekrell 116
                                    ee+e+++ + +++++++e++r++  ++ ee+++  e ++++ ++ + l
  gi|119720660|ref|YP_921155.1| 114 EEIEKLREEQTKIWEEIEELRKEQTKMWEEIKGLREGQTKIWQEIAEL 161
                                    799*****************************9999999887776333 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 3.7
                           COG2  40 kllekellelvnedya 55 
                                     ll++++++++  dya
  gi|119720660|ref|YP_921155.1| 258 DLLRSRMIKVIYADYA 273
                                    4677777777777776 PP

>> DUF632  Protein of unknown function (DUF632)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   8.4   0.00029     0.064     125     197 ..      37     111 ..      32     114 .. 0.93
   2 !   13.5  14.4   0.00015     0.033     128     217 ..      89     185 ..      79     195 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00029
                         DUF632 125 skidktraavkklstkikvaiqsvdsiskrIekLRDee..LqpqLveLiqglirmWksmlecHqvQlqiiseaks 197
                                    +k+d+ + +v++l+ +   + + ++++  +IekLR+e+   +  ++ L +  +++Wk + +  + Q ++ +e+k+
  gi|119720660|ref|YP_921155.1|  37 EKLDRLWEEVRDLREEQARTWKEIEKVWGEIEKLREEQakTWKEIERLREEQAKTWKEIEKLREEQARTWKEIKK 111
                                    799*********************************9844699****************************9997 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00015
                         DUF632 128 dktraavkklstkikvaiqsvdsiskrIekLRDee..LqpqLveLiqglirmWksmlecHqvQlqiiseaksldsskis. 204
                                     kt+++++kl+ +   + + ++++ ++IekLR+e+   +  ++eL +  ++mW+ +    + Q++i +e+ +l+  + + 
  gi|119720660|ref|YP_921155.1|  89 AKTWKEIEKLREEQARTWKEIKKVWEEIEKLREEQtkIWEEIEELRKEQTKMWEEIKGLREGQTKIWQEIAELKEGQGKi 168
                                    59*******************************97558********************************9999877433 PP

                         DUF632 205 ....kstseshrqatlq 217
                                        +  s++  + tl 
  gi|119720660|ref|YP_921155.1| 169 wvtlNRLSKTVERLTLT 185
                                    22234444444444444 PP

>> SidE  Dot/Icm substrate protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   6.6   6.4e-06    0.0014    1129    1233 ..      28     140 ..      11     161 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 6.4e-06
                           SidE 1129 dldavkkaisnlnnlqeelkllrnekirmhtgtdkvdfsdieklekklkkleekly..daylvevtkeisalekeksk 1204
                                      l ++++ + +l++l ee++ lr+e++r  ++ +kv + +iekl ++  k  +++       +++ kei++l +e+++
  gi|119720660|ref|YP_921155.1|   28 GLIGMREILEKLDRLWEEVRDLREEQARTWKEIEKV-WGEIEKLREEQAKTWKEIErlREEQAKTWKEIEKLREEQAR 104 
                                     5667889999*************************9.89*****65544443333201334567889*********99 PP

                           SidE 1205 nltdvkkm...isklndrl....aeieqlrqekikk 1233
                                       +++kk+   i kl ++     +eie+lr+e+ k 
  gi|119720660|ref|YP_921155.1|  105 TWKEIKKVweeIEKLREEQtkiwEEIEELRKEQTKM 140 
                                     999998762225555554312225788888888775 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4  14.9   0.00075      0.17      44     104 ..      25      94 ..       2      94 .. 0.80
   2 !   16.1  20.1   5.7e-05     0.013      54     118 ..      79     143 ..      75     147 .. 0.88
   3 ?    8.3  17.3     0.014       3.1      57     113 ..      96     152 ..      95     199 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00075
                         APG6_N  44 k.........qdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwre 104
                                    +           e+l++l ee+++l++e+++  +e++++  e e+l++e a+ ++e e+l ee+++ w+e
  gi|119720660|ref|YP_921155.1|  25 AvagligmreILEKLDRLWEEVRDLREEQARTWKEIEKVWGEIEKLREEQAKTWKEIERLREEQAKTWKE 94 
                                    145555554456788999999**********************************************987 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 5.7e-05
                         APG6_N  54 eeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynelqlelleleee 118
                                    +e+e+l++e+++  +e+++l +e+++  +e+++ +ee e+l ee+++ w+e  el+ e++++ ee
  gi|119720660|ref|YP_921155.1|  79 KEIERLREEQAKTWKEIEKLREEQARTWKEIKKVWEEIEKLREEQTKIWEEIEELRKEQTKMWEE 143
                                    89999999999999999999999999999999999999999999999999999999999888776 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.014
                         APG6_N  57 eklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynelqlell 113
                                    ekl++e+++  +e+k++ +e e+l++e  +++ee e+l +e+++ w+e + l+  ++
  gi|119720660|ref|YP_921155.1|  96 EKLREEQARTWKEIKKVWEEIEKLREEQTKIWEEIEELRKEQTKMWEEIKGLREGQT 152
                                    566666666666666666666666666666666666666666666666554443333 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   1.3    0.0089         2      11      65 ..      35      88 ..      29     104 .. 0.78
   2 !    9.6   2.1    0.0053       1.2      12      86 ..     106     182 ..     102     183 .. 0.71
   3 ?    1.8   0.0       1.5   3.2e+02      20      46 ..     156     182 ..     150     196 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0089
                Snapin_Pallidin 11 lepkldeldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKL 65
                                   +  kld+l e++++lr++Q    +++++   ++++l+e+q  ++ +++++ ++  
  gi|119720660|ref|YP_921155.1| 35 ILEKLDRLWEEVRDLREEQARTWKEIEKVWGEIEKLREEQA-KTWKEIERLREEQ 88
                                   5568999*****************************99998.6666666555554 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0053
                Snapin_Pallidin  12 epkldeldeklkelrqsQeeLleqldrlnekLkel.eeaqe.aevlpdlkeyakKLvnikkrmsslnerlqklkkRa 86 
                                    + +++++ e++++lr++Q++  e++++l+++ +++ ee++   e  +++ + ++ L++ + ++    +rl+k+ +R+
  gi|119720660|ref|YP_921155.1| 106 WKEIKKVWEEIEKLREEQTKIWEEIEELRKEQTKMwEEIKGlREGQTKIWQEIAELKEGQGKIWVTLNRLSKTVERL 182
                                    67899999999999999999999999998876665144444666666666666666666666666666666666665 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 1.5
                Snapin_Pallidin  20 eklkelrqsQeeLleqldrlnekLkel 46 
                                    ++++el++ Q +   +l+rl++ +++l
  gi|119720660|ref|YP_921155.1| 156 QEIAELKEGQGKIWVTLNRLSKTVERL 182
                                    679999999999999999999988776 PP

>> Laminin_I  Laminin Domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1  10.7   3.2e-05    0.0071      19     132 ..      44     142 ..      26     165 .. 0.51

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.2e-05
                      Laminin_I  19 anledltkeLqeklskesakkskieilekelesLaqeteeLqkkatqvlakaqkvnaesertlnnakeLaekikkladni 98 
                                    +++ dl++e  +  +++++   +ie l +e  +  +e+e+L ++  ++ ++ +k+++e  rt +++k+  e+i+kl+++ 
  gi|119720660|ref|YP_921155.1|  44 EEVRDLREEQARTWKEIEKVWGEIEKLREEQAKTWKEIERLREEQAKTWKEIEKLREEQARTWKEIKKVWEEIEKLREEQ 123
                                    33333333333333333333333333333333333455666666666666666666666666666666666666666666 PP

                      Laminin_I  99 keilekvatlneneealpssklseelaeaqrlLe 132
                                    + i e +++l +++                ++ e
  gi|119720660|ref|YP_921155.1| 124 TKIWEEIEELRKEQT---------------KMWE 142
                                    666666666666554...............4444 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   4.1    0.0016      0.34       5      72 ..      41     108 ..      30     114 .. 0.66
   2 !    9.3   7.0    0.0076       1.7       7      60 ..      92     145 ..      87     193 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0016
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXXXXXXX CS
                           YabA   5 elfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkkelsegken 72 
                                     l +++++l e+ +++ +e+e++  e+++l ee a+   e e+lre+++++ k+ ++ ++e+ ++ ++
  gi|119720660|ref|YP_921155.1|  41 RLWEEVRDLREEQARTWKEIEKVWGEIEKLREEQAKTWKEIERLREEQAKTWKEIEKLREEQARTWKE 108
                                    36677777777777778888888888888888888888888888888755555555555544444444 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0076
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXX CS
                           YabA   7 fdkleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkek 60 
                                     +++e+l e+ +++ +e++++ ee+++l ee +++  e e+lr+++++  ++ k
  gi|119720660|ref|YP_921155.1|  92 WKEIEKLREEQARTWKEIKKVWEEIEKLREEQTKIWEEIEELRKEQTKMWEEIK 145
                                    567788888888888888888888888888888888888888887743333322 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1  20.5   2.4e-05    0.0054      23     137 ..      34     145 ..      32     155 .. 0.91
   2 ?    2.9   0.2      0.27        59      31      80 ..     140     189 ..     137     201 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.4e-05
                            GAS  23 nNLelIkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelk 102
                                    + Le+ ++l ee+ +l+++++r+ ke++++  e ++l+e+  k  +e+e+Lr++ ++  k   ++++l+++  ++ ke+k
  gi|119720660|ref|YP_921155.1|  34 EILEKLDRLWEEVRDLREEQARTWKEIEKVWGEIEKLREEQAKTWKEIERLREEQAKTWK---EIEKLREEQARTWKEIK 110
                                    5699999*********************************************98777666...6667777778899**** PP

                            GAS 103 dlkwehevleqrfekvekerdelykkfeaaiqevq 137
                                    ++ +e e l+++ +k+ +e++el+k+++++ +e++
  gi|119720660|ref|YP_921155.1| 111 KVWEEIEKLREEQTKIWEEIEELRKEQTKMWEEIK 145
                                    *****************************999886 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.27
                            GAS  31 lKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlkny 80 
                                    + eei+ l++ +++  +e++e+++   ++  +L+++ + ve+L   +++ 
  gi|119720660|ref|YP_921155.1| 140 MWEEIKGLREGQTKIWQEIAELKEGQGKIWVTLNRLSKTVERLTLTVEEE 189
                                    56899999999999999999999999999999999999999998877765 PP

>> DUF4763  Domain of unknown function (DUF4763)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   7.2    0.0029      0.65      44     156 ..      15     121 ..       2     126 .. 0.72
   2 !   11.3   0.6    0.0007      0.16      98     149 ..     112     163 ..     107     181 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0029
                        DUF4763  44 eeeeeldLdeiydelekiKqrvlelrskLalnvpecPeidecvdedlelelltseqpeileLqrnnhkLrqqlaelqqhl 123
                                    + ee+ ++  + + l  +++ +++l++    +v+     d  ++++   ++++++  ei +L+ +++k   ++++l +  
  gi|119720660|ref|YP_921155.1|  15 TLEEDAEFRHAVAGLIGMREILEKLDRLWE-EVR-----DLREEQARTWKEIEKVWGEIEKLREEQAKTWKEIERLREEQ 88 
                                    666666666666777777776666666554.444.....44444444445555567899999999999999999999999 PP

                        DUF4763 124 kasrkslkelreslcqekkrlrklqkrlnelds 156
                                     +++k++++lre++ +  k ++k  +++++l +
  gi|119720660|ref|YP_921155.1|  89 AKTWKEIEKLREEQARTWKEIKKVWEEIEKLRE 121
                                    999999999999999999999999999998865 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.0007
                        DUF4763  98 eqpeileLqrnnhkLrqqlaelqqhlkasrkslkelreslcqekkrlrklqk 149
                                    +  ei +L+ ++ k+  +++el +  +++++++k lre + +  + +++l++
  gi|119720660|ref|YP_921155.1| 112 VWEEIEKLREEQTKIWEEIEELRKEQTKMWEEIKGLREGQTKIWQEIAELKE 163
                                    5579*********************************999888888877765 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5  19.0   5.7e-05     0.013     143     272 ..      41     162 ..      32     210 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.7e-05
                           Spc7 143 gleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkel 222
                                    +l e++ +l+e++++  k+ e++    ++l+ee+a+  +e+e+l+e++++    + +e+e+lree a+  +ei++  +e+
  gi|119720660|ref|YP_921155.1|  41 RLWEEVRDLREEQARTWKEIEKVWGEIEKLREEQAKTWKEIERLREEQAK----TWKEIEKLREEQARTWKEIKKVWEEI 116
                                    56788999999999999999999999********************7776....789*********************** PP

                           Spc7 223 aelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlk 272
                                    ++l+e+ +++ e+ieel+++ +++ eei+  ++     +    +e+ +lk
  gi|119720660|ref|YP_921155.1| 117 EKLREEQTKIWEEIEELRKEQTKMWEEIKGLRE----GQTKIWQEIAELK 162
                                    ************************999995433....2223334555555 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   2.0   5.4e-05     0.012     220     336 ..      24     137 ..      15     171 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.4e-05
                           FUSC 220 alrrllsrmlallallsslarllarlraeeaaavpelaallaelaaleaaaaaealeaalaalrarlralrraleadadt 299
                                    ++ + l  m ++l  l+ l+++ ++lr+e+a++++e++++  e+++l  ++ ++++ +++++lr++ +++ ++ e+ ++ 
  gi|119720660|ref|YP_921155.1|  24 HAVAGLIGMREILEKLDRLWEEVRDLREEQARTWKEIEKVWGEIEKL--REEQAKTWKEIERLREEQAKTWKEIEKLREE 101
                                    55555666888999999*****************************6..4467777788888888888888888877777 PP

                           FUSC 300 aalllarlaellaelaqllaslraleaaiaaarraer 336
                                    +a+ + + + + +e   l+++  + +++i++  r+e+
  gi|119720660|ref|YP_921155.1| 102 QARTWKEIKKVWEEIEKLREEQTKIWEEIEE-LRKEQ 137
                                    7777777777777777766666666666666.33332 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   7.2    0.0074       1.6       2      77 ..      44     118 ..      31     120 .. 0.65
   2 ?   14.4   3.6   7.4e-05     0.016       2      82 ..     107     186 ..     106     210 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0074
                          TMPIT   2 eeweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelke 77 
                                    ee+++l++e+ +  ++ +++  ++e+l + q k+ kei++ +++  + +++++kl++++ +++ +e++++ ee+++
  gi|119720660|ref|YP_921155.1|  44 EEVRDLREEQARTWKEIEKVWGEIEKLREEQAKTWKEIERLREEQAKTWKEIEKLREEQ-ARTWKEIKKVWEEIEK 118
                                    45666666666666666666677777777777777777777777777777777776663.4556666666666654 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 7.4e-05
                          TMPIT   2 eeweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkv 81 
                                    +e++++ +e+++l+e+++++ +++eel k q+k+ +eik  ++  +++++++ +lk+ ++ +   ++++l++++++ + +
  gi|119720660|ref|YP_921155.1| 107 KEIKKVWEEIEKLREEQTKIWEEIEELRKEQTKMWEEIKGLREGQTKIWQEIAELKEGQG-KIWVTLNRLSKTVERLTLT 185
                                    68899999************************************************9965.4444444444444444433 PP

                          TMPIT  82 l 82 
                                    +
  gi|119720660|ref|YP_921155.1| 186 V 186
                                    3 PP

>> RPW8  Arabidopsis broad-spectrum mildew resistance protein RPW8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.4     0.018       3.9      38      73 ..      54      89 ..      32      99 .. 0.83
   2 ?    9.6   1.9    0.0031      0.68      29      71 ..      94     136 ..      87     151 .. 0.83
   3 ?    0.3   0.0       2.3     5e+02      18      49 ..     156     187 ..     146     202 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.018
                           RPW8 38 estleritPvvkeieklnkeldrpreeieeLkklLe 73
                                   ++t ++i+ v  eiekl++e  +  +eie+L+++  
  gi|119720660|ref|YP_921155.1| 54 ARTWKEIEKVWGEIEKLREEQAKTWKEIERLREEQA 89
                                   67999999*************88999****998755 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0031
                           RPW8  29 dfksilkrLestleritPvvkeieklnkeldrpreeieeLkkl 71 
                                    +++   ++ ++t ++i+ v +eiekl++e  +  eeieeL+k+
  gi|119720660|ref|YP_921155.1|  94 EIEKLREEQARTWKEIKKVWEEIEKLREEQTKIWEEIEELRKE 136
                                    5555566668999*****************99999*****986 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 2.3
                           RPW8  18 kaileakkksldfksilkrLestleritPvvk 49 
                                    + i e k+ + ++  +l+rL +t+er+t  v+
  gi|119720660|ref|YP_921155.1| 156 QEIAELKEGQGKIWVTLNRLSKTVERLTLTVE 187
                                    55666666666677789999999999986665 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   1.1    0.0017      0.37      45     108 ..      34     100 ..      30     106 .. 0.83
   2 ?    8.8   4.6    0.0073       1.6      59     123 ..     100     164 ..      95     190 .. 0.57
   3 ?    1.5   0.2       1.3     3e+02      74     120 ..     212     252 ..     167     256 .. 0.42

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0017
                        DUF1664  45 svskqleqvseslaatkrh...Lssridrvdkkldeqkeiskeikeevtevredlseigedvesvke 108
                                    ++ ++l++++e++++ +++     ++i++v  ++++  e ++++ +e++++re+ +++ +++e+++e
  gi|119720660|ref|YP_921155.1|  34 EILEKLDRLWEEVRDLREEqarTWKEIEKVWGEIEKLREEQAKTWKEIERLREEQAKTWKEIEKLRE 100
                                    56678999998887766651116689*****************************999999998875 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0073
                        DUF1664  59 atkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerieek 123
                                    + + +  ++i++v +++++  e +++i ee++e+r++ +++ e+++ ++e  +++ +++++++e 
  gi|119720660|ref|YP_921155.1| 100 EEQARTWKEIKKVWEEIEKLREEQTKIWEEIEELRKEQTKMWEEIKGLREGQTKIWQEIAELKEG 164
                                    44555555566666666666666666666666666666666666555555555555555544443 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 1.3
                        DUF1664  74 kldeqkeiskeikeevtevredlseigedvesv.keavegleskleri 120
                                     +d+        + +v  v++dl  +ge    + +e+v++le k+e i
  gi|119720660|ref|YP_921155.1| 212 VVDD-------KEINVYGVSDDLCVVGEATVRLgDELVKELERKVEYI 252
                                    3333.......3334444455554444433222145566666666655 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   9.5   8.7e-05     0.019     357     462 ..      39     146 ..      17     195 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.7e-05
                         AAA_13 357 lesvkakiesikklvaeineliakhNekvanleeekeeakkklelhlveele..seldeykkkykklekaieklekelke 434
                                    l+++ +++  + +++a+  + i+k    +++l ee+++  k++e+ + e+++  +e++++ ++ +++ k+i+k+ +e+++
  gi|119720660|ref|YP_921155.1|  39 LDRLWEEVRDLREEQARTWKEIEKVWGEIEKLREEQAKTWKEIERLREEQAKtwKEIEKLREEQARTWKEIKKVWEEIEK 118
                                    45555666777888888888899999999999999999999999877655543378999999999999999999999999 PP

                         AAA_13 435 eeaelkkleeeikeLekqlrdekpaaee 462
                                      +e+ k+ eei+eL+k+ ++  + ++ 
  gi|119720660|ref|YP_921155.1| 119 LREEQTKIWEEIEELRKEQTKMWEEIKG 146
                                    9999999999999999988877666665 PP

>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6  12.6    0.0011      0.25       5      99 ..      32     126 ..      29     130 .. 0.90
   2 ?    8.8   1.0    0.0083       1.8      38     107 ..     128     197 ..     124     212 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0011
                        zf-C4H2   5 irektleleklknklakevealekeekcleeykkelelLeqEkmaHveeLrlIhaDinalEsvikeaeeekekslekakk 84 
                                    +re +++l++l +++++  e+  ++ k +e++  e+e+L +E+ +   e+  +++   +  + i++ +ee+ ++++++kk
  gi|119720660|ref|YP_921155.1|  32 MREILEKLDRLWEEVRDLREEQARTWKEIEKVWGEIEKLREEQAKTWKEIERLREEQAKTWKEIEKLREEQARTWKEIKK 111
                                    5667778888888888888888888999**************************************************** PP

                        zf-C4H2  85 lyeeykklkeevnel 99 
                                    + ee++kl+ee  ++
  gi|119720660|ref|YP_921155.1| 112 VWEEIEKLREEQTKI 126
                                    *********987666 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0083
                        zf-C4H2  38 kelelLeqEkmaHveeLrlIhaDinalEsvikeaeeekekslekakklyeeykklkeevnelrselglek 107
                                    +e+e+L +E+++  ee++ +++   ++ + i e +e + k + + ++l++ +++l  +v+e   e++  +
  gi|119720660|ref|YP_921155.1| 128 EEIEELRKEQTKMWEEIKGLREGQTKIWQEIAELKEGQGKIWVTLNRLSKTVERLTLTVEEEAGEVISYR 197
                                    799****************************************************999998877765555 PP

>> SKA2  Spindle and kinetochore-associated protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.9      0.11        24      24      70 ..      41      90 ..      11      96 .. 0.60
   2 ?   12.7   1.2   0.00037     0.083      28      89 ..      94     158 ..      92     165 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.11
                           SKA2 24 rLekefqqsypdna...eNpvkLlerlkkvkeelqaLkeqceellaekke 70
                                   rL +e+++  +++a   ++  k+  +++k++ee ++  +++e l +e+ +
  gi|119720660|ref|YP_921155.1| 41 RLWEEVRDLREEQArtwKEIEKVWGEIEKLREEQAKTWKEIERLREEQAK 90
                                   44455555555555555555555555556666555555555555555554 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00037
                           SKA2  28 efqqsypdna...eNpvkLlerlkkvkeelqaLkeqceellaekkelidkirttlvanrellqqL 89 
                                    e+++  +++a   ++  k+ e+++k++ee +++ e++eel +e+ ++ ++i+    +++++ q++
  gi|119720660|ref|YP_921155.1|  94 EIEKLREEQArtwKEIKKVWEEIEKLREEQTKIWEEIEELRKEQTKMWEEIKGLREGQTKIWQEI 158
                                    66667777778888999******************************999988777777777765 PP

>> DUF2968  Protein of unknown function (DUF2968)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   6.2   0.00057      0.13     104     179 ..      49     124 ..      42     125 .. 0.93
   2 ?    3.5   0.1      0.23        50     121     178 ..     129     186 ..     124     188 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00057
                        DUF2968 104 leaqkaqlerqiaasearaerLqadlavarqQeqavaerQkqarkeaaaLeaqreaaqaqlralqrqirqLqaqqe 179
                                    l  ++a++ ++i++   ++e+L++++a + +  +++ e+Q+++ ke ++L+++++++ ++++++ ++i++L ++q+
  gi|119720660|ref|YP_921155.1|  49 LREEQARTWKEIEKVWGEIEKLREEQAKTWKEIERLREEQAKTWKEIEKLREEQARTWKEIKKVWEEIEKLREEQT 124
                                    5567899999*************************************************************99875 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.23
                        DUF2968 121 raerLqadlavarqQeqavaerQkqarkeaaaLeaqreaaqaqlralqrqirqLqaqq 178
                                    ++e+L+++++ + +  + + e Q ++ +e a L++ + ++   l++l + +++L  + 
  gi|119720660|ref|YP_921155.1| 129 EIEELRKEQTKMWEEIKGLREGQTKIWQEIAELKEGQGKIWVTLNRLSKTVERLTLTV 186
                                    678889999999999999999999999**********999999999999999997665 PP

>> FCD  FCD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1    0.0028      0.61      48     102 ..      15      69 ..       4      91 .. 0.90
   2 ?    1.7   0.0       1.5   3.2e+02      13      41 ..     229     257 ..     227     270 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0028
                            FCD  48 faeadraFHralaeaagnpvlaelleelrarlrrlrrlalssperleeslaeHra 102
                                      e d++F  a+a++ g + + e l++l++++r lr  + ++ +++e++  e ++
  gi|119720660|ref|YP_921155.1|  15 TLEEDAEFRHAVAGLIGMREILEKLDRLWEEVRDLREEQARTWKEIEKVWGEIEK 69 
                                    5689**********************************99999999988887665 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 1.5
                            FCD  13 aarlaarratdadlaeleellealeeaaa 41 
                                    ++ +a+ r  d+ ++ele+ +e +++a +
  gi|119720660|ref|YP_921155.1| 229 VVGEATVRLGDELVKELERKVEYIAKARP 257
                                    577899999**********9999998865 PP

>> HAP1_N  HAP1 N-terminal conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9  19.7   0.00044     0.098     157     287 ..      31     164 ..       1     183 [. 0.76

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00044
                         HAP1_N 157 eslqklvqldlLqeklreLeeeNekLreeasqLktetdtlEekEqqL...vldcveqlseanqqiaelseelarkleele 233
                                     +++ l +ld L e +r+L ee  +  +e +++  e ++l e+ ++    +  + e+ +++ ++i++l ee ar   e++
  gi|119720660|ref|YP_921155.1|  31 GMREILEKLDRLWEEVRDLREEQARTWKEIEKVWGEIEKLREEQAKTwkeIERLREEQAKTWKEIEKLREEQARTWKEIK 110
                                    3444556788888999999999988888999998888888776665512255566788888999**************** PP

                         HAP1_N 234 rqqeeissLlaqivdlqqklkelgveneelkqhLaaskeaqrqLtaELqdlqek 287
                                    +  eei++L+ + +++ + ++el +e+ ++ ++++  +e q+++ +E+ +l+e 
  gi|119720660|ref|YP_921155.1| 111 KVWEEIEKLREEQTKIWEEIEELRKEQTKMWEEIKGLREGQTKIWQEIAELKEG 164
                                    ***********************************************9999985 PP

>> TMF_DNA_bd  TATA element modulatory factor 1 DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8  10.6    0.0017      0.38      12      72 ..      44     104 ..      34     105 .. 0.92
   2 ?   12.2   9.4   0.00063      0.14      13      68 ..     108     163 ..     107     168 .. 0.95
   3 ?    3.5   0.5      0.32        70      13      52 ..     157     196 ..     156     201 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0017
                     TMF_DNA_bd  12 eqIaqLmeEGekLskkelklnntikkLrkknkelekeikelkkkleklekeleeleerlke 72 
                                    e++  L+eE  +  k+  k    i kLr++ +++ kei++l ++ +k  ke+e+l+e++++
  gi|119720660|ref|YP_921155.1|  44 EEVRDLREEQARTWKEIEKVWGEIEKLREEQAKTWKEIERLREEQAKTWKEIEKLREEQAR 104
                                    788899*************************************************999876 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00063
                     TMF_DNA_bd  13 qIaqLmeEGekLskkelklnntikkLrkknkelekeikelkkkleklekeleelee 68 
                                    +I+++ eE ekL+ ++ k  + i +Lrk+  ++ +eik l +   k  +e++el+e
  gi|119720660|ref|YP_921155.1| 108 EIKKVWEEIEKLREEQTKIWEEIEELRKEQTKMWEEIKGLREGQTKIWQEIAELKE 163
                                    799**************************************************997 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.32
                     TMF_DNA_bd  13 qIaqLmeEGekLskkelklnntikkLrkknkelekeikel 52 
                                    +Ia+L+e   k   + ++l++t+ +L  +++e   e+ ++
  gi|119720660|ref|YP_921155.1| 157 EIAELKEGQGKIWVTLNRLSKTVERLTLTVEEEAGEVISY 196
                                    899**98888****************99999988777655 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   7.4      0.15        34      17      81 ..      45     109 ..      36     111 .. 0.73
   2 ?   13.3   8.6   0.00017     0.038      16     104 ..      93     181 ..      88     190 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.15
                        DUF3450  17 tldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqei 81 
                                    +++++++e++++ ++ +++  +i+kl +e+++  +e+++l+ee++++ ++ e+l++ +a   +ei
  gi|119720660|ref|YP_921155.1|  45 EVRDLREEQARTWKEIEKVWGEIEKLREEQAKTWKEIERLREEQAKTWKEIEKLREEQARTWKEI 109
                                    56777777888888888888888888888888888888888888877777777776666655555 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.00017
                        DUF3450  16 atldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeie 95 
                                    ++++++++e++++ ++ +++ ++i+kl +e++++ +e+++l++e+ ++  + + l++ +++  qeia+l+e + +i  + 
  gi|119720660|ref|YP_921155.1|  93 KEIEKLREEQARTWKEIKKVWEEIEKLREEQTKIWEEIEELRKEQTKMWEEIKGLREGQTKIWQEIAELKEGQGKIWVTL 172
                                    678999*****************************************************************999998887 PP

                        DUF3450  96 relvpllek 104
                                    ++l+   e+
  gi|119720660|ref|YP_921155.1| 173 NRLSKTVER 181
                                    777665555 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   1.5     0.073        16      60      71 ..     106     117 ..      24     183 .. 0.63
   2 ?    1.8   0.1       1.3   2.8e+02      18      37 ..     169     188 ..     165     196 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.073
                         DUF948  60 ledvneklekvd 71 
                                     +++++  e+++
  gi|119720660|ref|YP_921155.1| 106 WKEIKKVWEEIE 117
                                    222222222222 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 1.3
                         DUF948  18 ivvllklkktldeaaatiee 37 
                                     v+l++l+kt+++++ t+ee
  gi|119720660|ref|YP_921155.1| 169 WVTLNRLSKTVERLTLTVEE 188
                                    57889999999999888875 PP

>> E3_binding  e3 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00071      0.16       3      16 ..     273     286 ..     272     296 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00071
                                    E-HHHHHHHHHCT- CS
                     E3_binding   3 AsPaaRklAkelGi 16 
                                    A+P+a +lA+e+Gi
  gi|119720660|ref|YP_921155.1| 273 ATPSALRLAEEMGI 286
                                    9************9 PP

>> ERM  Ezrin/radixin/moesin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3  27.5   0.00051      0.11      29     136 ..      33     140 ..       6     185 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00051
                            ERM  29 reseetaelLaekarraeeeaelLeqkaaeaeeeiqrlkesaekeeeekeklerklreaeleaarleeeserkeeeaerL 108
                                    re  e+ ++L e+ r ++ee+ +  ++ +++  ei++l+e+++k+ +e e+l ++ ++   e+++l+ee+ r  +e ++ 
  gi|119720660|ref|YP_921155.1|  33 REILEKLDRLWEEVRDLREEQARTWKEIEKVWGEIEKLREEQAKTWKEIERLREEQAKTWKEIEKLREEQARTWKEIKKV 112
                                    66678888889999999999999999999999999999999999999999999999999999999999999999999999 PP

                            ERM 109 keeleeareaeeeakekllealstpsks 136
                                     ee+e+ re++++  e++ e+ ++++k 
  gi|119720660|ref|YP_921155.1| 113 WEEIEKLREEQTKIWEEIEELRKEQTKM 140
                                    9999999999988888888887777433 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   6.0      0.23        51      94     171 ..      36      92 ..       6     101 .. 0.48
   2 ?   13.3   7.4   0.00024     0.053      98     183 ..      96     181 ..      90     185 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.23
                         DUF724  94 lnkLlslkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaekle 171
                                    l+kL  l +e + l+ee+ +  k+ie+   e +kl ee +++ k+i +l++++a                     k  
  gi|119720660|ref|YP_921155.1|  36 LEKLDRLWEEVRDLREEQARTWKEIEKVWGEIEKLREEQAKTWKEIERLREEQA---------------------KTW 92 
                                    333333333333333333333333333333333333333333333333333333.....................222 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.00024
                         DUF724  98 lslkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaekleeeledv 177
                                     +l++eq+++ +e+kk+ ++ie+ ++e++k+ eei+el k+  ++ ++ + l+e + + ++eia+lk  + k+ ++l++ 
  gi|119720660|ref|YP_921155.1|  96 EKLREEQARTWKEIKKVWEEIEKLREEQTKIWEEIEELRKEQTKMWEEIKGLREGQTKIWQEIAELKEGQGKIWVTLNRL 175
                                    5799******************************************************************9999999888 PP

                         DUF724 178 eqeFea 183
                                     + +e+
  gi|119720660|ref|YP_921155.1| 176 SKTVER 181
                                    877765 PP

>> bPH_6  Bacterial PH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.4     0.068        15      24      45 ..      43      64 ..      42      73 .. 0.87
   2 ?    3.8   2.0      0.27        59      24      43 ..      78      97 ..      63     139 .. 0.72
   3 ?    2.7   0.1      0.59   1.3e+02      23      39 ..     140     159 ..     123     190 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.068
                          bPH_6 24 Wsaiagvrfpegrrlarldlrd 45
                                   W++++++r  ++r++ +++  +
  gi|119720660|ref|YP_921155.1| 43 WEEVRDLREEQARTWKEIEKVW 64
                                   ***************8887666 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.27
                          bPH_6 24 Wsaiagvrfpegrrlarldl 43
                                   W +i+++r  +++++ +++ 
  gi|119720660|ref|YP_921155.1| 78 WKEIERLREEQAKTWKEIEK 97
                                   66666666666666644443 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.59
                          bPH_6  23 pWsaiagvrfpegrrl...a 39 
                                     W++i+g+r  + + +   a
  gi|119720660|ref|YP_921155.1| 140 MWEEIKGLREGQTKIWqeiA 159
                                    58888888877776665443 PP

>> IF-2B  Initiation factor 2 subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   2.4    0.0096       2.1       8      96 ..      24     122 ..      17     230 .. 0.72
   2 ?    2.4   0.0      0.33        72      22      48 ..     232     258 ..     212     269 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0096
                                    HHHHHHHHHHHHHHHCC..CSTHHHH.......HHHHHHHHHHHHTSSTS-HHHHHHHHHHHH.HHHCCTTTSSHHHHHH CS
                          IF-2B   8 iaiaalevllevikdak..tskvaeL.......keelrkaidlLkkarPtavslgnairrllk.eiselksssdvkeakk 77 
                                     a+a+l +++e++++ +  +++v++L       ++e++k   +++k r  + +    i+rl + + +  k+ +++ e ++
  gi|119720660|ref|YP_921155.1|  24 HAVAGLIGMREILEKLDrlWEEVRDLreeqartWKEIEKVWGEIEKLREEQAKTWKEIERLREeQAKTWKEIEKLREEQA 103
                                    67777888888877776678888888888888888888888888888888888888888888843333444444445555 PP

                                    HHHHHHHHHHHHHHHHHHH CS
                          IF-2B  78 sliekikelikeieeadek 96 
                                    +  ++ik++ +eie+ +e 
  gi|119720660|ref|YP_921155.1| 104 RTWKEIKKVWEEIEKLREE 122
                                    5555555555554443332 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.33
                                    HCCCSTHHHHHHHHHHHHHHHHTSSTS CS
                          IF-2B  22 daktskvaeLkeelrkaidlLkkarPt 48 
                                    +a+   ++eL++el+++++++ karP 
  gi|119720660|ref|YP_921155.1| 232 EATVRLGDELVKELERKVEYIAKARPD 258
                                    566677899****************95 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1       2.1   4.7e+02      32      54 ..      38      53 ..      32      63 .. 0.55
   2 ?    9.1   2.2    0.0089         2      19      55 ..      67     103 ..      65     108 .. 0.80
   3 ?    9.1   2.1    0.0087       1.9      18      54 ..     115     151 ..     108     167 .. 0.86
   4 ?   -0.5   0.0       9.1     2e+03      28      47 ..     167     186 ..     152     200 .. 0.61

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 2.1
                                   HHHHHHHHHHHHHHT-XXXXXXX CS
                           SlyX 32 qidrlqrqlrllaerlkeleess 54
                                   ++drl +++r l+e+       +
  gi|119720660|ref|YP_921155.1| 38 KLDRLWEEVRDLREE-------Q 53
                                   445555555555543.......3 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0089
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXX CS
                           SlyX  19 ieeLndvvaeqqqqidrlqrqlrllaerlkeleessg 55 
                                    ie+L ++ a+ +++i+rl+++ ++  +++++l+e+++
  gi|119720660|ref|YP_921155.1|  67 IEKLREEQAKTWKEIERLREEQAKTWKEIEKLREEQA 103
                                    7888888888888888888888888888888888765 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.0087
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXX CS
                           SlyX  18 tieeLndvvaeqqqqidrlqrqlrllaerlkeleess 54 
                                     ie+L ++ ++ +++i++l+++  ++ e++k l+e +
  gi|119720660|ref|YP_921155.1| 115 EIEKLREEQTKIWEEIEELRKEQTKMWEEIKGLREGQ 151
                                    5899999999999999999999999999999888765 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 9.1
                                    HHHHHHHHHHHHHHHHHHT- CS
                           SlyX  28 eqqqqidrlqrqlrllaerl 47 
                                    + + ++ rl + +++l+  +
  gi|119720660|ref|YP_921155.1| 167 KIWVTLNRLSKTVERLTLTV 186
                                    44555556666666655544 PP

>> Mod_r  Modifier of rudimentary (Mod(r)) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   8.4     0.029       6.4      26      83 ..      44     108 ..       2     113 .. 0.50
   2 ?    6.4  16.5     0.041         9      26      90 ..      65     129 ..      44     145 .. 0.58
   3 ?    8.6   8.8    0.0085       1.9       3      93 ..      90     181 ..      88     187 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.029
                          Mod_r  26 pevkqlkeekeellaenesla.......eknlslepeleelrselqekleelkelekefeekeqe 83 
                                    +ev++l+ee+    +e+e++        e++ +  +e+e lr+e +++ +e+++l++e  + ++e
  gi|119720660|ref|YP_921155.1|  44 EEVRDLREEQARTWKEIEKVWgeieklrEEQAKTWKEIERLREEQAKTWKEIEKLREEQARTWKE 108
                                    33333333333333333333311111114444444455555555555555555555555555554 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.041
                          Mod_r  26 pevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqeldellqk 90 
                                     e+++l+ee+ +  +e+e+l e++ +  +e+e+lr+e + + +e+k++ +e e++ +e+ ++ ++
  gi|119720660|ref|YP_921155.1|  65 GEIEKLREEQAKTWKEIERLREEQAKTWKEIEKLREEQARTWKEIKKVWEEIEKLREEQTKIWEE 129
                                    55666666666666666666666666666666666666666666666666666666666555433 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0085
                          Mod_r   3 lSkeeLqelledeeklealvktl.pevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeeke 81 
                                    ++ +e+++l e++    + +k++ +e+++l+ee++++ +e+e+l +++ +  +e++ lr+  ++  +e++el++   + +
  gi|119720660|ref|YP_921155.1|  90 KTWKEIEKLREEQARTWKEIKKVwEEIEKLREEQTKIWEEIEELRKEQTKMWEEIKGLREGQTKIWQEIAELKEGQGKIW 169
                                    56678889999887777777777799999999999999999999999999999999999998888889888888888888 PP

                          Mod_r  82 qeldellqkfsp 93 
                                      l++l++ +  
  gi|119720660|ref|YP_921155.1| 170 VTLNRLSKTVER 181
                                    888887766555 PP

>> PTRF_SDPR  PTRF/SDPR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   5.9   0.00037     0.081      15      97 ..      36     118 ..      26     126 .. 0.84
   2 ?    2.1   0.4      0.56   1.2e+02      13      74 ..     125     186 ..     123     193 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00037
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      PTRF_SDPR  15 vgivdsvqesqkrlEerqaelenavksiqgdllkLakshssTsntvnklleksrkvsvnvkevrerlekqavqvkklEan 94 
                                     + +d + e+ + l e qa   + ++ + g++ kL  ++++T + +++l e   k+ +++ ++re+  +  +++kk+ ++
  gi|119720660|ref|YP_921155.1|  36 LEKLDRLWEEVRDLREEQARTWKEIEKVWGEIEKLREEQAKTWKEIERLREEQAKTWKEIEKLREEQARTWKEIKKVWEE 115
                                    44455555666678888999999999**************************************************9766 PP

                                    HHH CS
                      PTRF_SDPR  95 eae 97 
                                     ++
  gi|119720660|ref|YP_921155.1| 116 IEK 118
                                    555 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.56
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      PTRF_SDPR  13 kvvgivdsvqesqkrlEerqaelenavksiqgdllkLakshssTsntvnklleksrkvsvnv 74 
                                    k+ + +++++++q+++ e  + l +  + i ++++ L   + +   t+n+l + + + + +v
  gi|119720660|ref|YP_921155.1| 125 KIWEEIEELRKEQTKMWEEIKGLREGQTKIWQEIAELKEGQGKIWVTLNRLSKTVERLTLTV 186
                                    77788999999999999999999999999999999999998888888888877776666555 PP

>> KASH_CCD  Coiled-coil region of CCDC155 or KASH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0  22.7    0.0025      0.54       8     165 ..      44     204 ..      38     218 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0025
                       KASH_CCD   8 stvadLqlnNkkLaeenskLkkavetaeetnakLteeieeLkkklkstQqalqkakl....leeEleelkalvkeleEkr 83 
                                      v dL+    +  +e +k+   +e+  e+ ak   eie L++    t + ++k +       +E+  + + +++l E++
  gi|119720660|ref|YP_921155.1|  44 EEVRDLREEQARTWKEIEKVWGEIEKLREEQAKTWKEIERLREEQAKTWKEIEKLREeqarTWKEIKKVWEEIEKLREEQ 123
                                    56888888888888999999999999999999999999999876655555555544311113456666666777788999 PP

                       KASH_CCD  84 arlkaqnkqlekenqsLiakiesLqeenikllaekdelkkklkeLlkekaeLkkqlheleellaekealleektkqieeL 163
                                     ++  + ++l ke+  + ++i+ L e  +k+ +e+ elk+   ++  + + L k + e  +l++e ea  + + +  ee+
  gi|119720660|ref|YP_921155.1| 124 TKIWEEIEELRKEQTKMWEEIKGLREGQTKIWQEIAELKEGQGKIWVTLNRLSKTV-ERLTLTVEEEAGEVISYRMREEM 202
                                    99999999999999999999999999999999999999999999988888888888.55556666665544455555555 PP

                       KASH_CCD 164 kl 165
                                     +
  gi|119720660|ref|YP_921155.1| 203 GV 204
                                    55 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.4      0.57   1.3e+02      44      99 ..      15      69 ..       2      71 .. 0.66
   2 ?   10.5  17.0    0.0024      0.53      12     102 ..      47     142 ..      38     147 .. 0.75
   3 ?    9.6   6.3    0.0046         1      26     102 ..     111     184 ..     107     195 .. 0.61

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.57
                                   HHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH CS
                   Seryl_tRNA_N 44 eleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaelek 99
                                   +lee  + r +++  Ig+     e+ ++l +ev++l ee +++ +e +++  e+ek
  gi|119720660|ref|YP_921155.1| 15 TLEEDAEFRHAVAGLIGMREIL-EKLDRLWEEVRDLREEQARTWKEIEKVWGEIEK 69
                                   4555556666777777766654.688888888888888888888888887777766 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0024
                                    HHHHHHHCCCT.CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT....S-TCCCCCCCHHHHHHHHHH CS
                   Seryl_tRNA_N  12 eavkeklkkRg.edkadvdelleldekrrelqveleelqaerNelskeIgkakkkk....edaeeliaevkelkeelkal 86 
                                      ++e +++   e ++   e+ +l e++ ++ +e+e l++e+ +  keI+k+ +++    ++++++ +e+++l ee  ++
  gi|119720660|ref|YP_921155.1|  47 RDLREEQARTWkEIEKVWGEIEKLREEQAKTWKEIERLREEQAKTWKEIEKLREEQartwKEIKKVWEEIEKLREEQTKI 126
                                    55556554333467777789999999999999999999999999999999999888888888888888888888888888 PP

                                    HHHHHHHHHHHHHHHC CS
                   Seryl_tRNA_N  87 eaelkeleaeleklll 102
                                     +e +el++e++k+  
  gi|119720660|ref|YP_921155.1| 127 WEEIEELRKEQTKMWE 142
                                    8888888888777655 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.0046
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                   Seryl_tRNA_N  26 advdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaeleklll 102
                                    +  +e+ +l e++ ++  e+eel++e+ ++ +eI+ + +     +++ +e++elke   ++  +l+ l++ +e l+l
  gi|119720660|ref|YP_921155.1| 111 KVWEEIEKLREEQTKIWEEIEELRKEQTKMWEEIKGLREG---QTKIWQEIAELKEGQGKIWVTLNRLSKTVERLTL 184
                                    4456677777777777777777777777777777766643...4555555555555555555555555555555554 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0  18.4     0.051        11     286     420 ..      38     162 ..      32     185 .. 0.44

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.051
                                    HHHHHHHHHHHHHHHHHHHTTTSSSSSHHHHT--HHHHTTGGG-TTTS-GGGSSTTTSTTHHHHHHHHHHHHHHHHHHHH CS
                           EzrA 286 eidsLyddlekEveAkkeveknlkelkeklehlekqnkelkeeldrlkqsYeLseeeleklrelekelkelekdyeelee 365
                                    ++d L +  +   e + +  k+++++  ++e+l+++  ++ +e++rl++      e+ ++ +e+ek  +e  +  +e+++
  gi|119720660|ref|YP_921155.1|  38 KLDRLWEEVRDLREEQARTWKEIEKVWGEIEKLREEQAKTWKEIERLRE------EQAKTWKEIEKLREEQARTWKEIKK 111
                                    4444444444433333344444444444555555555555555554433......3333333333333333333333333 PP

                                    HHS-SS---STTGGGTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           EzrA 366 kleekkvaYSelqeeleeleekleeieekqeeileslkslrkdEkrAreqldeik 420
                                     +ee +    +l+ee+ ++ e++ee+ ++q +++e++k+lr+  ++  ++++e+k
  gi|119720660|ref|YP_921155.1| 112 VWEEIE----KLREEQTKIWEEIEELRKEQTKMWEEIKGLREGQTKIWQEIAELK 162
                                    333322....344444444444444444444444444444444444444444433 PP

>> Cauli_DNA-bind  Caulimovirus DNA-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   1.0     0.099        22       6      53 ..      65     112 ..      60     118 .. 0.61
   2 ?    5.2   0.2     0.095        21       2      38 ..      89     125 ..      88     128 .. 0.87
   3 ?    6.5   0.2     0.038       8.5       3      46 ..     125     168 ..     123     187 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.099
                                    HHHHHHHHHHHHHHHHHHHHHHHHHTS--HHHHHHHHHHHHHHHHHHH CS
                 Cauli_DNA-bind   6 seieevlsdqkkieaeikaileklgstkpekesleevaakiikdltkk 53 
                                     eie++ ++q k+ +ei+ + e  + t +e e+l e  a+  k++ k 
  gi|119720660|ref|YP_921155.1|  65 GEIEKLREEQAKTWKEIERLREEQAKTWKEIEKLREEQARTWKEIKKV 112
                                    566777777777777777776666666666666666666655555544 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.095
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTS--HHHH CS
                 Cauli_DNA-bind   2 aaiaseieevlsdqkkieaeikaileklgstkpekes 38 
                                    a++ +eie++ ++q ++ +eik++ e +   ++e+++
  gi|119720660|ref|YP_921155.1|  89 AKTWKEIEKLREEQARTWKEIKKVWEEIEKLREEQTK 125
                                    57889********************999888777766 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.038
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHTS--HHHHHHHHHHHH CS
                 Cauli_DNA-bind   3 aiaseieevlsdqkkieaeikaileklgstkpekesleevaaki 46 
                                    +i +eiee+ ++q+k+ +eik + e  +   +e  +l e   ki
  gi|119720660|ref|YP_921155.1| 125 KIWEEIEELRKEQTKMWEEIKGLREGQTKIWQEIAELKEGQGKI 168
                                    6889*****************99887777666666666666666 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   6.9     0.014         3     337     410 ..      44     111 ..      27     116 .. 0.71
   2 ?    7.7   5.9    0.0051       1.1     339     411 ..     109     175 ..     107     225 .. 0.54

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.014
                           FapA 337 eklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeeles 410
                                    e++++l+ee  ++ +e+ek+  +i+kl++++a      +  +++++l+e++ k  +e+e+l+ee+++  +e+++
  gi|119720660|ref|YP_921155.1|  44 EEVRDLREEQARTWKEIEKVWGEIEKLREEQA------KTWKEIERLREEQAKTWKEIEKLREEQARTWKEIKK 111
                                    44455666666666666666666888888554......456999999999999999999999999988777776 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0051
                           FapA 339 lkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeelesk 411
                                    +k++ ee+e+l+ee++k+ ++i++l+k++       ++ e++k l+e + k+ +e++el+e + ++   l++ 
  gi|119720660|ref|YP_921155.1| 109 IKKVWEEIEKLREEQTKIWEEIEELRKEQT------KMWEEIKGLREGQTKIWQEIAELKEGQGKIWVTLNRL 175
                                    555666666666666666666666666322......3345555555555555555555555444444333333 PP

>> CENP-H  Centromere protein H (CENP-H)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   8.6    0.0018       0.4       3      76 ..      34     110 ..      32     112 .. 0.81
   2 ?    7.1   9.0     0.032         7      13      77 ..      93     163 ..      91     202 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0018
                         CENP-H   3 plieqrdelssellklsqelrelqeeltevekenlrlkrknrelaaellela.kekesek..eklkeelekleaelk 76 
                                    +++e+ d+l +e+ +l +e + + +e+++v  e+ +l++++++ ++e+++l+ ++++++k  ekl+ee+++  +e+k
  gi|119720660|ref|YP_921155.1|  34 EILEKLDRLWEEVRDLREEQARTWKEIEKVWGEIEKLREEQAKTWKEIERLReEQAKTWKeiEKLREEQARTWKEIK 110
                                    788999******************************************75550555666677777777776666665 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.032
                         CENP-H  13 sellklsqelrelqeeltevekenlrlkrknrelaaellelakekes.ek.....eklkeelekleaelkk 77 
                                    +e++kl +e + + +e+ +v +e+ +l++++ ++++e++el+ke+ + ++      + + ++ +  aelk+
  gi|119720660|ref|YP_921155.1|  93 KEIEKLREEQARTWKEIKKVWEEIEKLREEQTKIWEEIEELRKEQTKmWEeikglREGQTKIWQEIAELKE 163
                                    57889999999999999999999999999999999999666555444044566664444444444444444 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   2.6      0.25        55      23      72 ..      45      85 ..      20     111 .. 0.47
   2 ?    3.8   5.0      0.44        97      19      69 ..      76     119 ..      52     135 .. 0.38
   3 ?    8.4   2.1     0.015       3.4      15      71 ..     107     163 ..      93     184 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.25
                   Occludin_ELL 23 eYkelhaeleevskkfseLerelkelkegsk.eykkieeeilqeykklkk.d 72
                                   e ++l +e + ++k+++++  e+++l+e++  +           +k++++  
  gi|119720660|ref|YP_921155.1| 45 EVRDLREEQARTWKEIEKVWGEIEKLREEQAkT-----------WKEIERlR 85
                                   333444444444444444444444444433322...........22222211 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.44
                   Occludin_ELL  19 keYkeYkelhaeleevskkfseLerelkelkegskeykkieeeilqeykkl 69 
                                    k++ke  +l +e ++++k++++L+       e++ ++ k ++++++e +kl
  gi|119720660|ref|YP_921155.1|  76 KTWKEIERLREEQAKTWKEIEKLR-------EEQARTWKEIKKVWEEIEKL 119
                                    222333333333333333333333.......22221111111112222222 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.015
                   Occludin_ELL  15 aeFnkeYkeYkelhaeleevskkfseLerelkelkegskeykkieeeilqeykklkk 71 
                                    +e +k ++e  +l +e ++++++++eL++e  ++ e+ k  ++ + +i+qe ++lk+
  gi|119720660|ref|YP_921155.1| 107 KEIKKVWEEIEKLREEQTKIWEEIEELRKEQTKMWEEIKGLREGQTKIWQEIAELKE 163
                                    456778888999999999999999999999999999999999999999999999987 PP

>> Golgin_A5  Golgin subfamily A member 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7  18.4    0.0012      0.27      25     150 ..      11     143 ..       3     153 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0012
                      Golgin_A5  25 kliasLkegs....geeglesstalsaeldelkqerdllreelqklnqqieqlrtelqdleaqqq...aeaeslreqlqe 97 
                                    +++ +L e++    ++ gl + ++   +ld l +e   lree +++ ++ie++  e+++l ++q    +e+e lre++++
  gi|119720660|ref|YP_921155.1|  11 RILRTLEEDAefrhAVAGLIGMREILEKLDRLWEEVRDLREEQARTWKEIEKVWGEIEKLREEQAktwKEIERLREEQAK 90 
                                    5666666655211123334457778888999999999999999999999999999998875544312279999*****99 PP

                      Golgin_A5  98 leeqleeerkakeeveaelerlkeelryleeelvrskatlqsrikdrekeiek 150
                                      +++e+ r+++ ++ +e++++ ee++ l+ee+++  +++++  k++ k+ e+
  gi|119720660|ref|YP_921155.1|  91 TWKEIEKLREEQARTWKEIKKVWEEIEKLREEQTKIWEEIEELRKEQTKMWEE 143
                                    999999999999999*******************9999999988888877665 PP

>> Sec5  Exocyst complex component Sec5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   3.9     0.006       1.3     124     173 ..      50      98 ..      33     100 .. 0.82
   2 ?    5.3   9.4     0.069        15     124     173 ..      99     147 ..      93     188 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.006
                           Sec5 124 veedkkqvkvfkkvwsevekiieeyrkklwekLleldesqeeflkliskL 173
                                     ee++++ k ++kvw e+ek+ ee + k+w+++  l+e+q +  k i+kL
  gi|119720660|ref|YP_921155.1|  50 REEQARTWKEIEKVWGEIEKLREE-QAKTWKEIERLREEQAKTWKEIEKL 98 
                                    3777889999**********9777.899*****************99999 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.069
                           Sec5 124 veedkkqvkvfkkvwsevekiieeyrkklwekLleldesqeeflkliskL 173
                                     ee++++ k +kkvw+e+ek+ ee ++k+we++ el+++q+++ + i+ L
  gi|119720660|ref|YP_921155.1|  99 REEQARTWKEIKKVWEEIEKLREE-QTKIWEEIEELRKEQTKMWEEIKGL 147
                                    4667788899*********98777.89**********9999987777665 PP

>> V_ATPase_I  V-type ATPase 116kDa subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   7.3    0.0016      0.35      33     120 ..      58     145 ..      27     202 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0016
                     V_ATPase_I  33 demerklrfleeeieklekavikeeeaeesleapeekeldeleeelekleeelkelnenleklkkelnelvelkavleka 112
                                     e+e+    +e+  e+ + +++ke e  ++++a++ ke+++l ee  ++ +e+k++ e+ ekl++e++++ e+ + l+k 
  gi|119720660|ref|YP_921155.1|  58 KEIEKVWGEIEKLREE-QAKTWKEIERLREEQAKTWKEIEKLREEQARTWKEIKKVWEEIEKLREEQTKIWEEIEELRKE 136
                                    4444444444444444.444555555566666666666666666666666666666666666666666666666666655 PP

                     V_ATPase_I 113 kefleee.e 120
                                    ++ + ee +
  gi|119720660|ref|YP_921155.1| 137 QTKMWEEiK 145
                                    555444322 PP

>> TelA  Toxic anion resistance protein (TelA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   6.5    0.0036      0.79      79     172 ..      41     134 ..      11     140 .. 0.62
   2 ?    6.4   1.1     0.019       4.1     102     145 ..     116     159 ..     103     167 .. 0.71
   3 ?    3.3   0.0      0.16        35     103     145 ..     145     187 ..     143     202 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0036
                           TelA  79 kaknkieklfakYekaeeqidkIvkeLekgqdellkdnaaLdqlyeknleyfkeLekyiaaGekkleeldekllpeleak 158
                                    ++ +++++l ++ +++ ++i+k+  e+ek ++e  k  +++++l+e+  ++ ke+ek      + ++e++ k+ +e+e+ 
  gi|119720660|ref|YP_921155.1|  41 RLWEEVRDLREEQARTWKEIEKVWGEIEKLREEQAKTWKEIERLREEQAKTWKEIEKLREEQARTWKEIK-KVWEEIEKL 119
                                    4555677777777788889999987777777776666666666666555555555555555555555666.455555555 PP

                           TelA 159 aeasgdp.edaqalr 172
                                    +e++++  e++++lr
  gi|119720660|ref|YP_921155.1| 120 REEQTKIwEEIEELR 134
                                    552222124444444 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.019
                           TelA 102 vkeLekgqdellkdnaaLdqlyeknleyfkeLekyiaaGekkle 145
                                    +++L+++q+++ + +++L +++ k++e +k L++  +   ++++
  gi|119720660|ref|YP_921155.1| 116 IEKLREEQTKIWEEIEELRKEQTKMWEEIKGLREGQTKIWQEIA 159
                                    46778888888889999999999999999988875554444444 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.16
                           TelA 103 keLekgqdellkdnaaLdqlyeknleyfkeLekyiaaGekkle 145
                                    k L++gq+++ + +a+L++ + k + ++++L+k +   ++ +e
  gi|119720660|ref|YP_921155.1| 145 KGLREGQTKIWQEIAELKEGQGKIWVTLNRLSKTVERLTLTVE 187
                                    67999***************************99876665555 PP

>> BRE1  BRE1 E3 ubiquitin ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2  14.3    0.0013      0.29       3      91 ..      58     146 ..      56     150 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0013
                           BRE1   3 kELvklekafeelseqlskkvkeltileekklrleaekakadqkyfaamrskdalenelkkLnkllsKsselieqLkele 82 
                                    kE++k+  ++e+l+e+  k  ke+++l e+++++ +e++k ++++  + ++++++  e+ kL++  +K  e ie+L   +
  gi|119720660|ref|YP_921155.1|  58 KEIEKVWGEIEKLREEQAKTWKEIERLREEQAKTWKEIEKLREEQARTWKEIKKVWEEIEKLREEQTKIWEEIEELRKEQ 137
                                    7999999*********************************************************************9999 PP

                           BRE1  83 kefvrklke 91 
                                    +++ +++k 
  gi|119720660|ref|YP_921155.1| 138 TKMWEEIKG 146
                                    988887775 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   3.1     0.012       2.6      78     134 ..      31      87 ..      23      90 .. 0.88
   2 ?    9.1   6.4    0.0044      0.98      63     136 ..      93     166 ..      89     172 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.012
                        DUF4201  78 althlkeklhmleselselkkelkekeerlaklrkelykvklerdklrkqneklkqq 134
                                     + ++ ekl+ l +e+++l++e  +  ++++k++ e++k+++e +k  k+ e+l+++
  gi|119720660|ref|YP_921155.1|  31 GMREILEKLDRLWEEVRDLREEQARTWKEIEKVWGEIEKLREEQAKTWKEIERLREE 87 
                                    56777899999999*********************************9999999986 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0044
                        DUF4201  63 keLkrlkkkttktvhalthlkeklhmleselselkkelkekeerlaklrkelykvklerdklrkqneklkqqgg 136
                                    ke+++l++  ++t ++++ + e    l++e+ +  +e++e+ ++++k+++e+  +++  +k+ ++ ++lk+  g
  gi|119720660|ref|YP_921155.1|  93 KEIEKLREEQARTWKEIKKVWEEIEKLREEQTKIWEEIEELRKEQTKMWEEIKGLREGQTKIWQEIAELKEGQG 166
                                    67888888899999999999999999999999999999999999999999999999999999888888887655 PP

>> DUF2353  Uncharacterized coiled-coil protein (DUF2353)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1  11.6   0.00082      0.18      16     107 ..      65     153 ..      58     193 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00082
                        DUF2353  16 keLekcrqerdqyklmaeqLqerlsalkkqleeekakaadlkeekekekklsqlleesreenkalkleveeLrqklkeaq 95 
                                     e+ek r+e+ +    +e+L+e+  ++ k+ e+  + +a++    ++ kk+ + +e+ ree+ ++ +e+eeLr+  + + 
  gi|119720660|ref|YP_921155.1|  65 GEIEKLREEQAKTWKEIERLREEQAKTWKEIEKLREEQART---WKEIKKVWEEIEKLREEQTKIWEEIEELRKEQTKMW 141
                                    58999999999999999999999888777777766666554...578899999999999999999999999999999999 PP

                        DUF2353  96 gDiklLR..eqlar 107
                                    + ik LR  +  ++
  gi|119720660|ref|YP_921155.1| 142 EEIKGLRegQ--TK 153
                                    9999999542..32 PP

>> DUF4446  Protein of unknown function (DUF4446)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   1.2     0.019       4.3      23      83 ..      38      96 ..      24      99 .. 0.74
   2 ?    6.7   2.6     0.031       6.8      39      82 ..     101     144 ..      90     148 .. 0.81
   3 ?   -0.9   0.0       6.8   1.5e+03      52      79 ..     156     183 ..     142     217 .. 0.48

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.019
                        DUF4446 23 klkklkkkykklmkgkdgksleellkekleeveelkeeseelekeieeleeklkkslqkvg 83
                                   kl +l ++++ l  +++++   + +++   e+e+l+ee++++ keie+l+e+++k+ ++++
  gi|119720660|ref|YP_921155.1| 38 KLDRLWEEVRDL--REEQARTWKEIEKVWGEIEKLREEQAKTWKEIERLREEQAKTWKEIE 96
                                   333344444444..336666778899999***********************999988775 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.031
                        DUF4446  39 dgksleellkekleeveelkeeseelekeieeleeklkkslqkv 82 
                                    +++   + +k+  ee+e+l+ee++++ +eieel+++++k+ +++
  gi|119720660|ref|YP_921155.1| 101 EQARTWKEIKKVWEEIEKLREEQTKIWEEIEELRKEQTKMWEEI 144
                                    55566678999************************999988776 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 6.8
                        DUF4446  52 eeveelkeeseelekeieeleeklkksl 79 
                                    +e+ elke + ++  ++++l++++++  
  gi|119720660|ref|YP_921155.1| 156 QEIAELKEGQGKIWVTLNRLSKTVERLT 183
                                    4455555555554444444444443333 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.2      0.17        37      37      79 ..      30      72 ..       2      77 .. 0.84
   2 ?    5.6   5.1     0.085        19      26      79 ..      68     121 ..      64     188 .. 0.74
   3 ?    0.5   0.1       3.6   7.9e+02      79      95 ..     233     249 ..     232     250 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.17
                        BLOC1_2 37 kklkdvaaslekkleklnekyeelqpylqqidqiekqvteLee 79
                                     +++++++l +  e+++ + ee +   ++i+++  ++++L e
  gi|119720660|ref|YP_921155.1| 30 IGMREILEKLDRLWEEVRDLREEQARTWKEIEKVWGEIEKLRE 72
                                   5799999999999999999999999999999999999999964 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.085
                        BLOC1_2  26 eklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLee 79 
                                    ekl e++++  k++++  ++ +k+ ++++++ ee +   ++i+++ +++++L e
  gi|119720660|ref|YP_921155.1|  68 EKLREEQAKTWKEIERLREEQAKTWKEIEKLREEQARTWKEIKKVWEEIEKLRE 121
                                    566666666666666666666666666666666666666666666666666654 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 3.6
                        BLOC1_2  79 eavseLDeyskeLEakf 95 
                                    ++v   De +keLE k+
  gi|119720660|ref|YP_921155.1| 233 ATVRLGDELVKELERKV 249
                                    5566669*******998 PP

>> COG6  Conserved oligomeric complex COG6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.5      0.15        33      41      87 ..      55     101 ..      14     105 .. 0.59
   2 ?    8.7   1.8     0.002      0.44      27     113 ..     104     190 ..      97     191 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.15
                           COG6  41 pvaeqLkriesdveklnelcdemkkklssakeetsdlleeaeeLkee 87 
                                    +  ++++++  ++ekl e   ++ k+++  +ee+++  +e+e+L+ee
  gi|119720660|ref|YP_921155.1|  55 RTWKEIEKVWGEIEKLREEQAKTWKEIERLREEQAKTWKEIEKLREE 101
                                    33345555555555555555555566666666666666666666555 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.002
                           COG6  27 ellkineefleefqpvaeqLkriesdveklnelcdemkkklssakeetsdlleeaeeLkeekkklelkqkllkaflkkFt 106
                                    +  k+ +++ ee ++++e+  +i +++e+l +   +m ++++  +e ++++ +e++eLke + k+    + l++  ++ t
  gi|119720660|ref|YP_921155.1| 104 RTWKEIKKVWEEIEKLREEQTKIWEEIEELRKEQTKMWEEIKGLREGQTKIWQEIAELKEGQGKIWVTLNRLSKTVERLT 183
                                    55677788999999999999999999*********************************999999999999999999999 PP

                           COG6 107 LseeEea 113
                                    L+ eEea
  gi|119720660|ref|YP_921155.1| 184 LTVEEEA 190
                                    9999975 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.3      0.23        52      14      66 ..      34      86 ..      30     101 .. 0.58
   2 ?    7.6   1.1     0.015       3.3       6      64 ..      96     154 ..      89     163 .. 0.62

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.23
                          Sec34 14 elleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeiee 66
                                   e+le++d++ e++++l+e+  +  ++ +++  + e+l eeq +  +  e ++e
  gi|119720660|ref|YP_921155.1| 34 EILEKLDRLWEEVRDLREEQARTWKEIEKVWGEIEKLREEQAKTWKEIERLRE 86
                                   56666666666666666666666666666666666666666665554444433 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.015
                          Sec34   6 eskeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeei 64 
                                    e+ +ee  +  ++++++ e++e+l+e+ +++ e+ ++l+++  ++ ee k l+e + +i
  gi|119720660|ref|YP_921155.1|  96 EKLREEQARTWKEIKKVWEEIEKLREEQTKIWEEIEELRKEQTKMWEEIKGLREGQTKI 154
                                    44444455555666666666777777777777777777776666666666666665555 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7  10.4    0.0077       1.7      83     165 ..      31     113 ..       3     115 .. 0.79
   2 ?    5.1  11.2     0.099        22      76     137 ..      97     162 ..      93     192 .. 0.57

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0077
                        UPF0242  83 glktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelkleleeqLaekqellqeyqetieeqr 162
                                    g++++ e+l  l ee ++L+ee++   +e+e+   e ++L+e+  ++ +++e+l+ e  ++ +e ++l +e ++t +e +
  gi|119720660|ref|YP_921155.1|  31 GMREILEKLDRLWEEVRDLREEQARTWKEIEKVWGEIEKLREEQAKTWKEIERLREEQAKTWKEIEKLREEQARTWKEIK 110
                                    56777889999999999999999999999999999999999999999999999999999999999999999998888888 PP

                        UPF0242 163 svl 165
                                    +v 
  gi|119720660|ref|YP_921155.1| 111 KVW 113
                                    765 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.099
                        UPF0242  76 klteld....eglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelk 137
                                    kl e++    +++k+  e++e+l+ee+ +  ee+++  +e  ++ ee + L+e   +i ++++elk
  gi|119720660|ref|YP_921155.1|  97 KLREEQartwKEIKKVWEEIEKLREEQTKIWEEIEELRKEQTKMWEEIKGLREGQTKIWQEIAELK 162
                                    333333333334444444555555555555555555555555555555555555555555555554 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8  22.6   0.00042     0.092      13     125 ..      33     145 ..      23     146 .. 0.96
   2 ?    7.3  14.8      0.02       4.4      26     125 ..      95     203 ..      94     210 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00042
                 CENP-F_leu_zip  13 KeserkadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelqkk 92 
                                    +e+ +k d L + v  L  e     ++ ekv  e E+ ++e  +  +eie+l+ee  +   ++++lr+e+    ke++k 
  gi|119720660|ref|YP_921155.1|  33 REILEKLDRLWEEVRDLREEQARTWKEIEKVWGEIEKLREEQAKTWKEIERLREEQAKTWKEIEKLREEQARTWKEIKKV 112
                                    77788999************************************************************************ PP

                 CENP-F_leu_zip  93 qervseLeslnsslenlleekEqekvqmkeesk 125
                                     e+++ L + + ++ + +ee+ +e+ +m ee k
  gi|119720660|ref|YP_921155.1| 113 WEEIEKLREEQTKIWEEIEELRKEQTKMWEEIK 145
                                    ****************************99976 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.02
                 CENP-F_leu_zip  26 venLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLeke...lqkkqerv.seLes 101
                                    +e+L  e     ++  kv  e E+ ++e  ++ eeieel++e +++  +++ lr+ + ++ +e   l++ q ++  +L++
  gi|119720660|ref|YP_921155.1|  95 IEKLREEQARTWKEIKKVWEEIEKLREEQTKIWEEIEELRKEQTKMWEEIKGLREGQTKIWQEiaeLKEGQGKIwVTLNR 174
                                    88899999999999999999999999999999999999999999999999999999999987522267788888448888 PP

                 CENP-F_leu_zip 102 lnsslenlleekEqe.....kvqmkeesk 125
                                    l  ++e+l    E+e       +m+ee+ 
  gi|119720660|ref|YP_921155.1| 175 LSKTVERLTLTVEEEageviSYRMREEMG 203
                                    88888888777777766666667777765 PP

>> S_4TM  SMODS-associating 4TM effector domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   8.6    0.0027      0.61     214     281 ..      71     138 ..      66     145 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0027
                          S_4TM 214 yreqresakelerlkeeiesllndaasgkleeeelkeelrklQdeiyqhRkssplipdwlYkrlrkkd 281
                                      eq ++ ke+erl+ee  ++++++ +  +e++++++e+ k+ +ei + R+++++i++ + ++++++ 
  gi|119720660|ref|YP_921155.1|  71 REEQAKTWKEIERLREEQAKTWKEIEKLREEQARTWKEIKKVWEEIEKLREEQTKIWEEIEELRKEQT 138
                                    57899*****************************************************9999988775 PP

>> DUF4771  Domain of unknown function (DUF4771)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   6.7     0.029       6.5      58     121 ..      66     128 ..      53     156 .. 0.82
   2 ?    2.0   0.2         1   2.2e+02      57      94 ..     128     165 ..     123     201 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.029
                        DUF4771  58 elkellkeskkvfekltelekkelkklpslkllklkkkkitfadkkklkkkakklkkeyrkkln 121
                                    e+++l +e+ k+++++++l+++++k++ ++++l+ ++ + t+++ kk+ ++++kl++e +k   
  gi|119720660|ref|YP_921155.1|  66 EIEKLREEQAKTWKEIERLREEQAKTWKEIEKLREEQ-ARTWKEIKKVWEEIEKLREEQTKIWE 128
                                    789999999*************999999999999877.9999**********999999887544 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 1
                        DUF4771  57 kelkellkeskkvfekltelekkelkklpslkllklkk 94 
                                    +e++el ke++k++e+++ l++ ++k + ++  lk  +
  gi|119720660|ref|YP_921155.1| 128 EEIEELRKEQTKMWEEIKGLREGQTKIWQEIAELKEGQ 165
                                    67888888888888888888877766666665555444 PP

>> DUF4735  Domain of unknown function (DUF4735)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.3    0.0083       1.8       2      62 ..      28      88 ..      27     107 .. 0.83
   2 ?    1.9   1.6      0.55   1.2e+02      18      61 ..      93     136 ..      81     197 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0083
                        DUF4735  2 gvlGlrvlegqlkaileeleassslssqlldrikqlskkaselidkalpylaksdpeyyee 62
                                   g++G+r + ++l+++ ee+++ ++ ++++ ++i++++ ++++l ++ ++++++ ++   e+
  gi|119720660|ref|YP_921155.1| 28 GLIGMREILEKLDRLWEEVRDLREEQARTWKEIEKVWGEIEKLREEQAKTWKEIERLREEQ 88
                                   789******************************************9999888765544443 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.55
                        DUF4735  18 eeleassslssqlldrikqlskkaselidkalpylaksdpeyye 61 
                                    +e+e+ ++ ++++ ++ik++++++++l ++ ++++++ ++   e
  gi|119720660|ref|YP_921155.1|  93 KEIEKLREEQARTWKEIKKVWEEIEKLREEQTKIWEEIEELRKE 136
                                    44566666667777777777777777777766665543333222 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3  16.6      0.84   1.9e+02       4     107 ..      59     168 ..      56     183 .. 0.57

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.84
                        DUF5082   4 kisklqaqiaelrseiaaleekIerLk..eaktklsdekeslkqkk..kklekplnssesWkGkeennydgirs..nles 77 
                                    +i+k+  +i++lr+e a++ + IerL+  +akt  + ek + +q++  k+++k   + e ++ ++++  ++i++  + ++
  gi|119720660|ref|YP_921155.1|  59 EIEKVWGEIEKLREEQAKTWKEIERLReeQAKTWKEIEKLREEQARtwKEIKKVWEEIEKLREEQTKIWEEIEElrKEQT 138
                                    67777777777777777777777777755344322222222222221133334444444677777777777777666666 PP

                        DUF5082  78 syqtyvdkldelidaieeEIerLenqisea 107
                                    ++ + ++ l+e + +i +EI +L++   + 
  gi|119720660|ref|YP_921155.1| 139 KMWEEIKGLREGQTKIWQEIAELKEGQGKI 168
                                    666666777777777777777777665555 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1      0.27        59      12      61 ..      47      96 ..      34      98 .. 0.85
   2 ?    7.6   0.7     0.021       4.7       9      61 ..      93     145 ..      87     154 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.27
                           KxDL 12 deilalQaqtsgrlnkknreLlelnalsqerlaklrarfkqgtkllkevk 61
                                         Qa t ++++k   e+++l+++  +  ++++   ++++k+ ke+ 
  gi|119720660|ref|YP_921155.1| 47 RDLREEQARTWKEIEKVWGEIEKLREEQAKTWKEIERLREEQAKTWKEIE 96
                                   55677899999999999999999999999999999999999999999886 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.021
                           KxDL   9 edldeilalQaqtsgrlnkknreLlelnalsqerlaklrarfkqgtkllkevk 61 
                                    +++++    Qa t ++++k  +e+++l+++  +  +++++  k++tk+  e+k
  gi|119720660|ref|YP_921155.1|  93 KEIEKLREEQARTWKEIKKVWEEIEKLREEQTKIWEEIEELRKEQTKMWEEIK 145
                                    57899999****************************************99998 PP

>> LMBR1  LMBR1-like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2  10.0     0.009         2     220     328 ..      28     140 ..       4     180 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.009
                          LMBR1 220 e........reledllkevkklrksisesdplrkyleeilkkvPeeiaeklksnenkteeslaklekqlikalqkrerte 291
                                             ++l+ l++ev+ lr++  ++    k +e++  ++ + ++e+ +++  k  e+l +++ +++k+++k ++++
  gi|119720660|ref|YP_921155.1|  28 GligmreilEKLDRLWEEVRDLREEQARTW---KEIEKVWGEIEK-LREE-QAKTWKEIERLREEQAKTWKEIEKLREEQ 102
                                    155555555788888888888877665554...444444333332.1111.12334588899999999999999999999 PP

                          LMBR1 292 kqwkrllekal.elediiknksskekefkssessrrge 328
                                    ++  + ++k++ e+e++ ++++++++e++++ +++++ 
  gi|119720660|ref|YP_921155.1| 103 ARTWKEIKKVWeEIEKLREEQTKIWEEIEELRKEQTKM 140
                                    99999999996347788888888888888775544433 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   3.6    0.0079       1.8     625     724 ..      38     138 ..       1     146 [. 0.64
   2 ?    2.0   0.3      0.18        40     649     716 ..     124     194 ..     117     211 .. 0.55

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0079
                       Prominin 625 nletlaekleelanelsngkknlkqslkneaqdlraiqqelvlplessvkklkksvkklde...ensdlqesikkllaav 701
                                     l+ l e++++l +e+ +  ++  ++++ e ++lr+ q+++ +++e++ ++  k+ k++++   e+    ++ikk+ +++
  gi|119720660|ref|YP_921155.1|  38 KLDRLWEEVRDLREEQART-WKEIEKVWGEIEKLREEQAKTWKEIERLREEQAKTWKEIEKlreEQARTWKEIKKVWEEI 116
                                    3667778888888888777.666677888888888888888887777777666666666666557777778888888888 PP

                       Prominin 702 eraenflkkngseiinneskkll 724
                                    e++ ++ ++++ e i++++k+ +
  gi|119720660|ref|YP_921155.1| 117 EKLREE-QTKIWEEIEELRKEQT 138
                                    887776.4444445555555444 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.18
                       Prominin 649 qslkneaqdlraiqqelvlp...lessvkklkksvkkldeensdlqesikkllaaveraenflkkngseii 716
                                    +++++e ++lr+ q+++ ++   l++   k+ +++ +l+e + ++  ++++l ++ver+   +++++ e+i
  gi|119720660|ref|YP_921155.1| 124 TKIWEEIEELRKEQTKMWEEikgLREGQTKIWQEIAELKEGQGKIWVTLNRLSKTVERLTLTVEEEAGEVI 194
                                    44555555555555544443222445555555555555555555555555555555555555555555555 PP

>> DUF4023  Protein of unknown function (DUF4023)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.3     0.087        19       8      18 ..      67      77 ..      67      80 .. 0.87
   2 ?    2.6   0.2      0.63   1.4e+02       8      18 ..      81      91 ..      79      94 .. 0.87
   3 ?    1.8   0.1       1.1   2.5e+02       8      17 ..      95     104 ..      95     110 .. 0.86
   4 ?    2.3   0.1      0.75   1.7e+02       8      17 ..     116     125 ..     114     126 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.087
                        DUF4023  8 VeklhetQaKd 18
                                   +ekl+e+QaK 
  gi|119720660|ref|YP_921155.1| 67 IEKLREEQAKT 77
                                   79********6 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.63
                        DUF4023  8 VeklhetQaKd 18
                                   +e l+e+QaK 
  gi|119720660|ref|YP_921155.1| 81 IERLREEQAKT 91
                                   799*******6 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 1.1
                        DUF4023   8 VeklhetQaK 17 
                                    +ekl+e+Qa 
  gi|119720660|ref|YP_921155.1|  95 IEKLREEQAR 104
                                    79******96 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.75
                        DUF4023   8 VeklhetQaK 17 
                                    +ekl+e+Q K
  gi|119720660|ref|YP_921155.1| 116 IEKLREEQTK 125
                                    89******99 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   9.1      0.12        25      91     153 ..      37     103 ..      13     121 .. 0.49
   2 ?    1.5   9.8      0.84   1.9e+02      16      71 ..      81     145 ..      78     167 .. 0.64

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.12
                        DUF4795  91 keLekmleellekleeqeealkkaldtLqeelkekld.....rlelepLkeqleerlkelqkelqeam 153
                                    ++L++  ee+++  eeq + +k++ +++  e+++  +      +e+e+L+e+  +++ke++k  +e++
  gi|119720660|ref|YP_921155.1|  37 EKLDRLWEEVRDLREEQARTWKEI-EKVWGEIEKLREeqaktWKEIERLREEQAKTWKEIEKLREEQA 103
                                    333333333333333444444333.2222222222222333456666666666666666664444433 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.84
                        DUF4795  16 ieklqeelekleekvkelekrledkekklealkkqieelekvk.........adkeeveeelaek 71 
                                    ie l ee++k  ++ ++l ++++++ k+++ ++++ie+l+++            ke++++++++k
  gi|119720660|ref|YP_921155.1|  81 IERLREEQAKTWKEIEKLREEQARTWKEIKKVWEEIEKLREEQtkiweeieeLRKEQTKMWEEIK 145
                                    56666666666666666666666666666666666666666655555555555555555655554 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   7.9     0.057        13      46     124 ..      73     136 ..      31     188 .. 0.50

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.057
                                    CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Fib_alpha  46 eisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnvlesneqkiqkLeqd 124
                                    e +++ ke+e+l +e  ++++e                ++l+ee++r  ++i++  ++i++L++   +  ++i++L+++
  gi|119720660|ref|YP_921155.1|  73 EQAKTWKEIERLREEQAKTWKEI---------------EKLREEQARTWKEIKKVWEEIEKLREEQTKIWEEIEELRKE 136
                                    12222222222222222222333...............33333444444444444444444444444444444444332 PP

>> Barstar  Barstar (barnase inhibitor)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   2.8       0.1        23      45      76 ..      75     106 ..      32     109 .. 0.51
   2 ?    3.9   0.3      0.24        53      47      77 ..     112     142 ..     109     144 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.1
                        Barstar  45 viviegsaalrkalpeafetllevledaaeew 76 
                                    + ++++ ++lr+++++ +++++++ e+ a+ w
  gi|119720660|ref|YP_921155.1|  75 AKTWKEIERLREEQAKTWKEIEKLREEQARTW 106
                                    33455555555555555555555555555555 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.24
                        Barstar  47 viegsaalrkalpeafetllevledaaeewa 77 
                                    v+e+ ++lr+++ + +e+++e+ ++  + w+
  gi|119720660|ref|YP_921155.1| 112 VWEEIEKLREEQTKIWEEIEELRKEQTKMWE 142
                                    89******************99999888886 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5  15.3     0.017       3.7      26     173 ..       7     149 ..       2     180 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.017
                          Atg14  26 elrerlaklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkkla 105
                                    e++ r+ ++++e ++++  +  ++  +e      +k++++ + +++l+ ++a++ ++++++   +++l++e +++ k+++
  gi|119720660|ref|YP_921155.1|   7 EEKLRILRTLEEDAEFRHAVAGLIGMRE----ILEKLDRLWEEVRDLREEQARTWKEIEKVWGEIEKLREEQAKTWKEIE 82 
                                    4566666667777777777777777777....668888888899999999999999999999999999999999999999 PP

                          Atg14 106 klsdklkkRrsdleslqneleerrkkqiaklqdaikrieqklsslssktlesrsslcselaklyglrr 173
                                    +l+++ +k  +++e+l++e ++r  k+i+k+ ++i + ++ ++++  ++ e r ++ ++  ++ glr+
  gi|119720660|ref|YP_921155.1|  83 RLREEQAKTWKEIEKLREE-QARTWKEIKKVWEEIEKLREEQTKIWEEIEELRKEQTKMWEEIKGLRE 149
                                    9999999888888888877.567778888999999988888888888888888888888888888887 PP

>> NleF_casp_inhib  NleF caspase inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   3.7    0.0074       1.6       3      56 ..      96     149 ..      82     181 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0074
                NleF_casp_inhib   3 nkiteetektlkdIkdklklifereiastTaeekikElsdkltklknsvlsere 56 
                                    +k+ ee+ +t k+Ik+  ++i +   + t   e+i+El+ + tk+ ++++  re
  gi|119720660|ref|YP_921155.1|  96 EKLREEQARTWKEIKKVWEEIEKLREEQTKIWEEIEELRKEQTKMWEEIKGLRE 149
                                    57899*****************99999999******************998776 PP

>> Phage_H_T_join  Phage head-tail joining protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.9    0.0091         2      12      42 ..      45      75 ..      38      83 .. 0.80
   2 ?    4.5   2.8      0.22        48      19      42 ..     101     124 ..      80     141 .. 0.77
   3 ?   -0.8   0.3       9.8   2.2e+03      25      56 ..     135     168 ..     120     193 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0091
                 Phage_H_T_join 12 etqdeeggpvetwvdlatvwAeveslsgrea 42
                                   e++d   ++ +tw+++ +vw+e+e+l+  +a
  gi|119720660|ref|YP_921155.1| 45 EVRDLREEQARTWKEIEKVWGEIEKLREEQA 75
                                   566765666789*************976664 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.22
                 Phage_H_T_join  19 gpvetwvdlatvwAeveslsgrea 42 
                                    ++ +tw+++++vw e+e+l+  ++
  gi|119720660|ref|YP_921155.1| 101 EQARTWKEIKKVWEEIEKLREEQT 124
                                    33478************9976665 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 9.8
                 Phage_H_T_join  25 vdlatvwAeveslsgrea..iaagaeqaettvri 56 
                                    +++ ++w e++ l+  ++  +++ ae  e + +i
  gi|119720660|ref|YP_921155.1| 135 KEQTKMWEEIKGLREGQTkiWQEIAELKEGQGKI 168
                                    4444566666655332222455555555545555 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   5.3      0.64   1.4e+02      46      84 ..      49      87 ..      31     112 .. 0.50
   2 ?    5.3   8.3      0.12        27      41      94 ..     107     160 ..      88     190 .. 0.68

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.64
                                   ..HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......H CS
                          DUF16 46 lgeqinkleqkvekqgekikelkveqkaqgeelnkvdet 84
                                   l e++++  +++ek   +i++l++eq +  +e++++ e 
  gi|119720660|ref|YP_921155.1| 49 LREEQARTWKEIEKVWGEIEKLREEQAKTWKEIERLREE 87
                                   444444444445555555555555555544444422222 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.12
                                    HHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHH CS
                          DUF16  41 akvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetleliletLqk 94 
                                    ++++k  e+i+kl ++ +k  e+i+el++eq +  ee++ + e    i + +++
  gi|119720660|ref|YP_921155.1| 107 KEIKKVWEEIEKLREEQTKIWEEIEELRKEQTKMWEEIKGLREGQTKIWQEIAE 160
                                    356666777777777777777888888888877777777555555555544444 PP

>> MobC  Bacterial mobilisation protein (MobC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       6.2   1.4e+03      28      44 ..      46      62 ..      42      63 .. 0.86
   2 ?    3.0   0.3      0.67   1.5e+02      27      45 .]      80      98 ..      65      98 .. 0.76
   3 ?    2.1   0.2       1.2   2.7e+02      29      45 .]     103     119 ..      93     119 .. 0.68
   4 ?    2.9   0.1      0.71   1.6e+02      27      45 .]     115     133 ..     113     133 .. 0.89
   5 ?    1.9   0.1       1.4   3.1e+02      27      43 ..     129     145 ..     127     147 .. 0.89
   6 ?    2.5   0.1      0.97   2.1e+02      28      45 .]     144     161 ..     142     161 .. 0.87
   7 ?    2.9   0.0      0.72   1.6e+02      27      45 .]     157     175 ..     151     175 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 6.2
                           MobC 28 laelkeelaeinkeLdq 44
                                   + +l ee+a+ +ke+++
  gi|119720660|ref|YP_921155.1| 46 VRDLREEQARTWKEIEK 62
                                   678999********987 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.67
                           MobC 27 vlaelkeelaeinkeLdql 45
                                    +++l ee+a+ +ke+++l
  gi|119720660|ref|YP_921155.1| 80 EIERLREEQAKTWKEIEKL 98
                                   5677888888888888775 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 1.2
                           MobC  29 aelkeelaeinkeLdql 45 
                                    a++ +e++++++e+++l
  gi|119720660|ref|YP_921155.1| 103 ARTWKEIKKVWEEIEKL 119
                                    45557778888887765 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.71
                           MobC  27 vlaelkeelaeinkeLdql 45 
                                     ++ l ee+++i++e+++l
  gi|119720660|ref|YP_921155.1| 115 EIEKLREEQTKIWEEIEEL 133
                                    578899**********997 PP

  == domain 5  score: 1.9 bits;  conditional E-value: 1.4
                           MobC  27 vlaelkeelaeinkeLd 43 
                                     ++el +e++++++e++
  gi|119720660|ref|YP_921155.1| 129 EIEELRKEQTKMWEEIK 145
                                    6899***********97 PP

  == domain 6  score: 2.5 bits;  conditional E-value: 0.97
                           MobC  28 laelkeelaeinkeLdql 45 
                                    +++l e +++i++e+ +l
  gi|119720660|ref|YP_921155.1| 144 IKGLREGQTKIWQEIAEL 161
                                    788999*********987 PP

  == domain 7  score: 2.9 bits;  conditional E-value: 0.72
                           MobC  27 vlaelkeelaeinkeLdql 45 
                                     +aelke + +i+  L++l
  gi|119720660|ref|YP_921155.1| 157 EIAELKEGQGKIWVTLNRL 175
                                    6899*********999987 PP

>> Ntox28  Bacterial toxin 28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   2.9     0.038       8.4      47     101 ..      43      98 ..      37     102 .. 0.76
   2 ?    1.9   0.9       1.1   2.5e+02      47      81 ..     106     140 ..      98     163 .. 0.61
   3 ?    4.1   0.3      0.24        54      55      95 ..     142     182 ..     127     188 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.038
                         Ntox28  47 ydHvkeltdaqkGLenvrralekelenppdsdteR.evLerklkeavleLdrvedf 101
                                    ++ v++l++ q    + ++++++e+e++++ +++  +++er ++e  +  + +e++
  gi|119720660|ref|YP_921155.1|  43 WEEVRDLREEQARTWKEIEKVWGEIEKLREEQAKTwKEIERLREEQAKTWKEIEKL 98 
                                    99**********999***********999888776655555555555555444443 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 1.1
                         Ntox28  47 ydHvkeltdaqkGLenvrralekelenppdsdteR 81 
                                    +  +k + +  + L + + ++++e+e++++ +t+ 
  gi|119720660|ref|YP_921155.1| 106 WKEIKKVWEEIEKLREEQTKIWEEIEELRKEQTKM 140
                                    55555666666666666666666666666655554 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.24
                         Ntox28  55 daqkGLenvrralekelenppdsdteRevLerklkeavleL 95 
                                    +  kGL + + ++++e+ ++++++ +  v +++l+++v++L
  gi|119720660|ref|YP_921155.1| 142 EEIKGLREGQTKIWQEIAELKEGQGKIWVTLNRLSKTVERL 182
                                    55689999999**********99999999899999999887 PP

>> TSNAXIP1_N  Translin-associated factor X-interacting N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.9     0.036       7.9      65     111 .]      39      85 ..      27      85 .. 0.87
   2 ?    7.6   4.0     0.022       4.9      63     111 .]      85     134 ..      81     134 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.036
                     TSNAXIP1_N  65 aqylkaklktlsessdkraleleekreelralekeskalleeidklr 111
                                    +  l ++++ l e+++++  e+e+   e+++l++e+++  +ei++lr
  gi|119720660|ref|YP_921155.1|  39 LDRLWEEVRDLREEQARTWKEIEKVWGEIEKLREEQAKTWKEIERLR 85 
                                    55556788899999999****************************98 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.022
                     TSNAXIP1_N  63 reaqyl.kaklktlsessdkraleleekreelralekeskalleeidklr 111
                                    re q++  ++++ l e+++++  e+++  ee+++l++e+ ++ eei++lr
  gi|119720660|ref|YP_921155.1|  85 REEQAKtWKEIEKLREEQARTWKEIKKVWEEIEKLREEQTKIWEEIEELR 134
                                    3444444567778888888888899999999*****************98 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.2      0.73   1.6e+02      15      49 ..      28      62 ..      24      64 .. 0.73
   2 ?    8.2   8.1    0.0095       2.1      13      62 ..      61     104 ..      59     111 .. 0.86
   3 ?   10.0   3.5    0.0025      0.56      13      54 ..     110     151 ..     108     159 .. 0.87
   4 ?   -0.9   0.1       6.4   1.4e+03      39      50 ..     171     182 ..     151     202 .. 0.53

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.73
                                   XXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC CS
                          DivIC 15 gllaykqlkqeiaalqaelaklkaeneeLeaevkd 49
                                   gl  ++++ +++++l +e+  l++e+++  +e+++
  gi|119720660|ref|YP_921155.1| 28 GLIGMREILEKLDRLWEEVRDLREEQARTWKEIEK 62
                                   55667777778888888888888888887777765 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0095
                                    XXXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXXXXXXX CS
                          DivIC  13 kkgllaykqlkqeiaalqaelaklkaeneeLeaevkdLksdedyieerAR 62 
                                    +k +  + +l++e a+  +e+++l++e+++  +e+++L+ +      +AR
  gi|119720660|ref|YP_921155.1|  61 EKVWGEIEKLREEQAKTWKEIERLREEQAKTWKEIEKLREE------QAR 104
                                    67788999******************************944......444 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.0025
                                    XXXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXX CS
                          DivIC  13 kkgllaykqlkqeiaalqaelaklkaeneeLeaevkdLksde 54 
                                    kk +  + +l++e +++ +e+++l++e+ ++ +e+k L+ ++
  gi|119720660|ref|YP_921155.1| 110 KKVWEEIEKLREEQTKIWEEIEELRKEQTKMWEEIKGLREGQ 151
                                    677889999999999999*************99999998765 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 6.4
                                    HHHHHHHHHCC- CS
                          DivIC  39 eneeLeaevkdL 50 
                                    + ++L + v++L
  gi|119720660|ref|YP_921155.1| 171 TLNRLSKTVERL 182
                                    333333333333 PP

>> DUF4081  Domain of unknown function (DUF4081)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.3       0.1        23      58      77 ..      34      53 ..      23      56 .. 0.90
   2 ?    4.0   0.1      0.26        57      59      77 ..      56      74 ..      54      78 .. 0.92
   3 ?   -0.4   0.1       5.9   1.3e+03      58      77 ..      83     102 ..      76     105 .. 0.75
   4 ?    3.1   1.1      0.49   1.1e+02      60      78 ..     106     124 ..      99     146 .. 0.63

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.1
                        DUF4081 58 aLwerLeeawgparevRaeQ 77
                                   ++ e+L++ w+++r++R+eQ
  gi|119720660|ref|YP_921155.1| 34 EILEKLDRLWEEVRDLREEQ 53
                                   67899**************9 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.26
                        DUF4081 59 LwerLeeawgparevRaeQ 77
                                    w+++e+ wg+  ++R+eQ
  gi|119720660|ref|YP_921155.1| 56 TWKEIEKVWGEIEKLREEQ 74
                                   5*****************9 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 5.9
                        DUF4081  58 aLwerLeeawgparevRaeQ 77 
                                     L e+ +++w++  ++R+eQ
  gi|119720660|ref|YP_921155.1|  83 RLREEQAKTWKEIEKLREEQ 102
                                    45566668999999999998 PP

  == domain 4  score: 3.1 bits;  conditional E-value: 0.49
                        DUF4081  60 werLeeawgparevRaeQp 78 
                                    w+++++ w++  ++R+eQ 
  gi|119720660|ref|YP_921155.1| 106 WKEIKKVWEEIEKLREEQT 124
                                    6666666666666666664 PP

>> DUF4200  Domain of unknown function (DUF4200)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7  24.2      0.01       2.3       8     108 ..      32     135 ..      31     135 .. 0.80
   2 ?    7.5  23.6     0.023         5       7     100 ..      66     162 ..      65     184 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.01
                        DUF4200   8 mfevqealeakkeeiqrleealkqreeelekkeqeleedllkfdkflkendakraralkkaeeerklkkeke...aeikk 84 
                                    m+e+ e+l++  ee + l e++++ ++e+ek   e+e+  ++  k  ke+++ r++  k  +e +kl++e +   +eikk
  gi|119720660|ref|YP_921155.1|  32 MREILEKLDRLWEEVRDLREEQARTWKEIEKVWGEIEKLREEQAKTWKEIERLREEQAKTWKEIEKLREEQArtwKEIKK 111
                                    7889999************************987777777777777777777666666655555555555443339**** PP

                        DUF4200  85 lkaeietlkseiekleekleeykk 108
                                      +eie+l++e++k  e++ee++k
  gi|119720660|ref|YP_921155.1| 112 VWEEIEKLREEQTKIWEEIEELRK 135
                                    ********************9875 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.023
                        DUF4200   7 emfevqealeakkeeiqrleealkqreeelekkeqeleedllkfdkflkendakraralkkaeeerklkkekea...eik 83 
                                    e++++ e++++  +ei+rl e++++ ++e+ek ++e  ++  + +k  +e+++ r++  k  ee ++l+ke ++   eik
  gi|119720660|ref|YP_921155.1|  66 EIEKLREEQAKTWKEIERLREEQAKTWKEIEKLREEQARTWKEIKKVWEEIEKLREEQTKIWEEIEELRKEQTKmweEIK 145
                                    7899999*********************************************9999999988877777776665122566 PP

                        DUF4200  84 klkaeietlkseiekle 100
                                     l++  +++ +ei++l+
  gi|119720660|ref|YP_921155.1| 146 GLREGQTKIWQEIAELK 162
                                    66665666666666655 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2  20.7     0.022       4.9       2     108 ..      38     144 ..      37     149 .. 0.85
   2 ?    1.2   4.2       1.6   3.5e+02      57      91 ..     128     162 ..     122     197 .. 0.52

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.022
                     TPR_MLP1_2   2 elksleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeae 81 
                                    +l++l ee+ +l+ee+++  ++++k+  ++ek +e+ ++  +  er   ++a+++ke+++lree +++ +ei+++ +e e
  gi|119720660|ref|YP_921155.1|  38 KLDRLWEEVRDLREEQARTWKEIEKVWGEIEKLREEQAKTWKEIERLREEQAKTWKEIEKLREEQARTWKEIKKVWEEIE 117
                                    6888999*****************************************************************99999999 PP

                     TPR_MLP1_2  82 sakaeleeseesweeqkeelekelsel 108
                                    ++++e  +  e++ee ++e  k  +e+
  gi|119720660|ref|YP_921155.1| 118 KLREEQTKIWEEIEELRKEQTKMWEEI 144
                                    998876666666666555555544444 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 1.6
                     TPR_MLP1_2  57 kelqalreelnelkaeiaelkaeaesakaeleese 91 
                                    +e+++lr+e  ++ +ei+ l++   +  +e++e +
  gi|119720660|ref|YP_921155.1| 128 EEIEELRKEQTKMWEEIKGLREGQTKIWQEIAELK 162
                                    55555555555555555555554444433333322 PP

>> TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   8.1     0.027         6      14      78 ..      39     103 ..      31     109 .. 0.81
   2 ?    7.8   7.1     0.017       3.7      20      93 ..     108     181 ..     104     189 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.027
                    TMF_TATA_bd  14 verlsseirrlEgElaslkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqe 78 
                                    ++rl  e+r l  E a + +e+e++  e +++ree +k  ke e+l+e++++  +  ++l+e q 
  gi|119720660|ref|YP_921155.1|  39 LDRLWEEVRDLREEQARTWKEIEKVWGEIEKLREEQAKTWKEIERLREEQAKTWKEIEKLREEQA 103
                                    56888999999999999999999999999999999999999999999988776555555555444 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.017
                    TMF_TATA_bd  20 eirrlEgElaslkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqeryetlLellGeksEe 93 
                                    ei++   E+++l+ee +++ +e +e+r+e  k+ +e   l+e ++++ +  +el+e q +   +L  l +  E+
  gi|119720660|ref|YP_921155.1| 108 EIKKVWEEIEKLREEQTKIWEEIEELRKEQTKMWEEIKGLREGQTKIWQEIAELKEGQGKIWVTLNRLSKTVER 181
                                    68888899**************************************9999999999999999999988888776 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   3.1      0.13        29       2      43 ..      49      90 ..      48     102 .. 0.83
   2 ?    4.8   7.5      0.15        34       2      44 ..      98     142 ..      97     227 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.13
                          Spc24  2 ldnekfriakelsdleselesleselaelkeeleeleeesee 43
                                   l +e+ r+ ke++++  e+e+l++e+a+  +e+e l ee+ +
  gi|119720660|ref|YP_921155.1| 49 LREEQARTWKEIEKVWGEIEKLREEQAKTWKEIERLREEQAK 90
                                   567888999***************************999887 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.15
                          Spc24   2 ldnekfriakelsdleselesleselaelkeeleeleeesee..k 44 
                                    l +e+ r+ ke++++ +e+e+l++e+++  ee+eel +e+ +  +
  gi|119720660|ref|YP_921155.1|  98 LREEQARTWKEIKKVWEEIEKLREEQTKIWEEIEELRKEQTKmwE 142
                                    7789999******************************99988541 PP

>> eIF3_N  eIF3 subunit 6 N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   1.6       0.3        67      52      96 ..      41      85 ..       3     102 .. 0.61
   2 ?    4.3   4.5      0.23        50      52      96 ..      90     134 ..      86     165 .. 0.71
   3 ?    1.2   0.1       2.1   4.7e+02      43      94 ..     137     188 ..     132     201 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.3
                         eIF3_N 52 dlykelegeeevpeelekkreevleeleeleeeaekvlelledee 96
                                    l++e+ + +e ++   k+ e+v  e+e+l+ee +k  + +e+  
  gi|119720660|ref|YP_921155.1| 41 RLWEEVRDLREEQARTWKEIEKVWGEIEKLREEQAKTWKEIERLR 85
                                   555566555555555556666666666666666666655554422 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.23
                         eIF3_N  52 dlykelegeeevpeelekkreevleeleeleeeaekvlelledee 96 
                                    +++ke+e+ +e ++   k+ ++v ee+e+l+ee +k+ e +e+  
  gi|119720660|ref|YP_921155.1|  90 KTWKEIEKLREEQARTWKEIKKVWEEIEKLREEQTKIWEEIEELR 134
                                    567777777777777777777888888888888888877775433 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 2.1
                         eIF3_N  43 kTnmvdyaadlykelegeeevpeelekkreevleeleeleeeaekvlelled 94 
                                    +T+m + ++ l++   +  +  +el++ + ++  +l++l++++e+++  +e+
  gi|119720660|ref|YP_921155.1| 137 QTKMWEEIKGLREGQTKIWQEIAELKEGQGKIWVTLNRLSKTVERLTLTVEE 188
                                    6777777777777666655566788888888888888888888887766655 PP

>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6  18.6      0.05        11       8     105 ..      48     143 ..      43     161 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.05
                           YkyA   8 ealeeavelEkefeeqqekLtelekkeqelyeeiielgmdefdkikklsdealenveeReellekekesieeakeefeki 87 
                                    +  ee +   ke+e+   ++++l +++ ++ +ei  l  ++  k  k+++++ e     +++++k  e ie+ +ee +ki
  gi|119720660|ref|YP_921155.1|  48 DLREEQARTWKEIEKVWGEIEKLREEQAKTWKEIERLREEQ-AKTWKEIEKLREEQARTWKEIKKVWEEIEKLREEQTKI 126
                                    55578888889999999999999999999999998888666.66666666666666677777777777799999999999 PP

                           YkyA  88 keeieeiedeelkkeaee 105
                                     eeiee+ +e + k  ee
  gi|119720660|ref|YP_921155.1| 127 WEEIEELRKE-QTKMWEE 143
                                    9999999655.3444443 PP

>> Img2  Mitochondrial large subunit ribosomal protein (Img2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   9.0       5.8   1.3e+03      18      53 ..      48      83 ..      46     223 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 5.8
                           Img2 18 dvkrggtkkltvirkieGDiaalredLrkaleelvk 53
                                   d ++++ +++ +i k+ G+i++lre+ +k+ +e+ +
  gi|119720660|ref|YP_921155.1| 48 DLREEQARTWKEIEKVWGEIEKLREEQAKTWKEIER 83
                                   667788889999999999999999998888887322 PP

>> DUF1394  Protein of unknown function (DUF1394)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   2.5         1   2.3e+02       8      72 ..      53     115 ..      46     122 .. 0.75
   2 ?    7.2   1.2     0.012       2.6      13      73 ..     121     179 ..     114     202 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 1
                        DUF1394   8 naqPteeErevyeeveevlkeaeeileelksYkgaeeeireaisnpsdeeaqekawkavlplvak 72 
                                    +a+  +e ++v+ e+e++ +e+ +  +e+++ ++ + +  + i++ +  e+q ++wk + +  ++
  gi|119720660|ref|YP_921155.1|  53 QARTWKEIEKVWGEIEKLREEQAKTWKEIERLREEQAKTWKEIEKLR--EEQARTWKEIKKVWEE 115
                                    45555566789999999999999999999999999998899998888..7777888877655444 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.012
                        DUF1394  13 eeErevyeeveevlkeaeeileelksYkgaeeeireaisnpsdeeaqekawkavlplvakl 73 
                                    ee ++++ee+ee+ ke++++ ee+k  ++ +++i + i++ +  e q k w ++  l +++
  gi|119720660|ref|YP_921155.1| 121 EEQTKIWEEIEELRKEQTKMWEEIKGLREGQTKIWQEIAELK--EGQGKIWVTLNRLSKTV 179
                                    56789*********************************9998..77888887765554444 PP

>> Nup88  Nuclear pore component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1  15.0     0.075        17     561     699 ..      47     183 ..      30     200 .. 0.50

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.075
                          Nup88 561 kllkkqkeqqleelqsleeerkslseraeklAekyeeikdkQeklvrrvkkvlkrlnsklpvlseaeremkkelekikek 640
                                    + l++++++  +e++++  e ++l+e+  k  ++ e  +++Q k  + ++k+    ++++  + +  +++ +e+ek++e+
  gi|119720660|ref|YP_921155.1|  47 RDLREEQARTWKEIEKVWGEIEKLREEQAKTWKEIERLREEQAKTWKEIEKL----REEQARTWKEIKKVWEEIEKLREE 122
                                    4555555555555555555555555554444444444444444444444332....222222222223345555555555 PP

                          Nup88 641 lkslknalkqvkkkldkqrkqia...kskeeekksslelsekqkktikeiLkeegeeieeli 699
                                      ++ +++++++k + k  ++i+   +++++  ++  el+e q k i  +L+ +++++e+l 
  gi|119720660|ref|YP_921155.1| 123 QTKIWEEIEELRKEQTKMWEEIKglrEGQTKIWQEIAELKEGQGK-IWVTLNRLSKTVERLT 183
                                    555555555555544444444431113344444455555555544.4455566666655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2145  (0.119639); expected 358.6 (0.02)
Passed bias filter:                      791  (0.0441185); expected 358.6 (0.02)
Passed Vit filter:                       213  (0.0118802); expected 17.9 (0.001)
Passed Fwd filter:                       127  (0.0070835); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              81  [number of targets reported over threshold]
# CPU time: 1.58u 0.42s 00:00:02.00 Elapsed: 00:00:00.60
# Mc/sec: 1519.02
//
Query:       gi|119720661|ref|YP_921156.1|  [L=93]
Description: hypothetical protein Tpen_1758 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.52
# Mc/sec: 537.31
//
Query:       gi|119720662|ref|YP_921157.1|  [L=180]
Description: hypothetical protein Tpen_1759 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.021   14.6   0.6       0.03   14.0   0.6    1.2  1  DUF745        Protein of unknown function (DUF745)
       0.29   11.2   2.1       0.68   10.0   0.3    2.1  2  AcylCoA_DH_N  Acyl-CoA dehydrogenase N terminal


Domain annotation for each model (and alignments):
>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.6   3.4e-06      0.03      65     127 ..      93     155 ..      90     162 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.4e-06
                         DUF745  65 eqleqelreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqva 127
                                    ++l   l ++++v++++ k+ +s ++ ++aaa++++q q+ lea k++l+++++ +++a++++
  gi|119720662|ref|YP_921157.1|  93 KHLATALIHTDEVIEKVLKKARSGQQDLEAAARINSQLQSLLEARKSILDSIEDLVARAKALS 155
                                    6778888999*******************************************9999998876 PP

>> AcylCoA_DH_N  Acyl-CoA dehydrogenase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.3   7.6e-05      0.68      15      31 ..      35      51 ..      34      51 .. 0.93
   2 ?    0.6   0.1     0.066   5.9e+02      16      31 ..      66      81 ..      66      81 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 7.6e-05
                   AcylCoA_DH_N 15 EvLdaealaalPgfada 31
                                   ++L a+a++++P+f+d+
  gi|119720662|ref|YP_921157.1| 35 HLLEADAYLGRPAFGDL 51
                                   89*************95 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.066
                   AcylCoA_DH_N 16 vLdaealaalPgfada 31
                                   ++ +eal a++g +d+
  gi|119720662|ref|YP_921157.1| 66 LFEIEALEARGGGGDF 81
                                   799*********9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       813  (0.0453455); expected 358.6 (0.02)
Passed bias filter:                      597  (0.033298); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.35s 00:00:00.96 Elapsed: 00:00:00.54
# Mc/sec: 997.34
//
Query:       gi|119720663|ref|YP_921158.1|  [L=323]
Description: radical SAM domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.3e-14   53.6   0.0      5e-14   53.0   0.0    1.3  1  Radical_SAM  Radical SAM superfamily
  ------ inclusion threshold ------
      0.054   13.6   0.0      0.091   12.9   0.0    1.3  1  DUF1272      Protein of unknown function (DUF1272)


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.0   0.0   5.6e-18     5e-14       3     167 .]      25     195 ..      23     195 .. 0.91

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 5.6e-18
                                    EESEESS--TTTSCCTT.....HHHHHHHHHHHHHHHHHHHHHHHHHTT..SEEEEEE.SSTGGGSTTHHHHHHHHHHTC CS
                                    xxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM   3 vtrgCnlrCsfCarpet.....vrregrgrslsveeileevkelkaekg..vkevilg.ggepllypdfvellerlakla 74 
                                    + + C++ C++C++++t     +rr  ++ ++  e +++++ e++ ++g  v++v+++  gep+l++++ +++  l+ l 
  gi|119720663|ref|YP_921158.1|  25 PAKVCSYSCVYCQVGRTtvltvERRAFYEPEKVYEAVKAKLGEAA-SRGerVDFVTFVpDGEPTLDANLGREISLLKGL- 102
                                    6789******************9*********************5.55556999999999*******************. PP

                                    CCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHH...HHHHHHTCTSHHHHHHHHHHHHHHTTSET..EEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxx RF
                    Radical_SAM  75 vpgiritvetngtlpdeeklerllelgvdrvslgleaadde...kvlklmnrghtfeevlealeklreagikr..vvdri 149
                                      g  ++v tn+ l+ +e +++ l  g d vs+ ++a+ +    +v ++  r  ++e+vle++  ++e  +k   v+ ++
  gi|119720663|ref|YP_921158.1| 103 --GKPVAVLTNASLLWREDVREDLA-GADFVSVKVDAVEEGlwrRVNRPS-RELSLEKVLEGVSVFAEE-FKGtlVSETM 177
                                    ..*************9999999998.78*************888888888.999***************.8888888888 PP

                                    EEBTTTSHHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxx RF
                    Radical_SAM 150 vglpGendeeleellell 167
                                    +++  e  eel+ l+++l
  gi|119720663|ref|YP_921158.1| 178 LVGGVEYGEELQRLADFL 195
                                    88888889*******996 PP

>> DUF1272  Protein of unknown function (DUF1272)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0     1e-05     0.091      14      39 ..      18      43 ..      13      47 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1e-05
                        DUF1272 14 dlppdseearicsyEctFCaeCaeev 39
                                   +l  ++  a++csy c +C+   ++v
  gi|119720663|ref|YP_921158.1| 18 SLGVNNIPAKVCSYSCVYCQVGRTTV 43
                                   67778889***********9776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.53
# Mc/sec: 1837.72
//
Query:       gi|119720664|ref|YP_921159.1|  [L=468]
Description: hypothetical protein Tpen_1761 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   1.2e-118  396.2   0.0   1.4e-118  396.0   0.0    1.0  1  DUF790      Protein of unknown function (DUF790)
     0.0077   16.1   0.0      0.044   13.6   0.0    2.2  2  PASTA       PASTA domain
  ------ inclusion threshold ------
      0.087   12.9   0.4        7.3    6.8   0.0    2.6  2  Sigma70_r3  Sigma-70 region 3


Domain annotation for each model (and alignments):
>> DUF790  Protein of unknown function (DUF790)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  396.0   0.0  2.4e-122  1.4e-118       1     387 []       1     392 [.       1     392 [. 0.97

  Alignments for each domain:
  == domain 1  score: 396.0 bits;  conditional E-value: 2.4e-122
                         DUF790   1 MLpsdllrvrrrggkivpkflk..eenlelaaelielfeehvGekrgeleeelkeleeea....tdyklvrGLakllere 74 
                                    MLps+ll++r r+g+i+p  l+     ++la+e++elfe+ vG+ r+elee l++lee a     d ++vr++ +l  r+
  gi|119720664|ref|YP_921159.1|   1 MLPSNLLVARARRGRIEPLLLEpsGLPVALASEVLELFERGVGKGRRELEEGLADLEELAlelgLDLRVVRAMFTLAARH 80 
                                    **********************76677899****************************5566679*************** PP

                         DUF790  75 aefete.spldpeelReevFeaaaea...vvseeereevleevaeelgvspeeveealyadleenkiLtefeeitpeeLl 150
                                    a+fe + +p+dp ++R evFe+a ++   +v+eeer++vl++vae+lg+s e++e++l + lee  +L+e +++++e+L+
  gi|119720664|ref|YP_921159.1|  81 ARFEPPkAPVDPVKARMEVFEEACREfgvAVTEEERSTVLRRVAERLGCSVEDLESVLGGYLEE--VLAEPPALKAEDLV 158
                                    ****8659****************999*99********************************98..9************* PP

                         DUF790 151 krYNlslvqtlLfkatelrirvsd..aeykelfravkllgLmyeieedaeegleitvdGPaslfkaterYGlalAkllpa 228
                                    ++ Nls+vqtlLfka++l++ +++  a  k+l+ravk+lgL+y +e+   eg+++tvdGPasl+++t+rYG++lAkl+p 
  gi|119720664|ref|YP_921159.1| 159 RMLNLSMVQTLLFKASQLEVVFRSdgATAKKLLRAVKRLGLLYVAEQLG-EGVRLTVDGPASLLRQTRRYGTRLAKLVPL 237
                                    ********************999988778*******************9.68**************************** PP

                         DUF790 229 llkvekWeleAeikdrdkkkrelrfeldsedsglvshyeeeke..fdssveeefaerfeklktdwelerepellkiggsv 306
                                    ++ +e+W+++A++  r+   r+l fel +e+sgl++++eee e  fds+ve+ef++++++l++ w++erepe+l++g++v
  gi|119720664|ref|YP_921159.1| 238 VMLAERWRIRARVPARG---RDLFFELGDEKSGLFPRVEEEPEplFDSEVEREFYRSISSLARGWRVEREPEPLVAGNKV 314
                                    ****************9...********************9999************************************ PP

                         DUF790 307 miPDFaleekdgrrvyleIvGfwtpeylkkKleklrkaerkelivavserlklekagvkakdlrvilfkdklrvkdVlev 386
                                    +iPDF++ ++++r+vy+eI+Gfwt++yl++K++klr+++ ++++vav+e+l++++  vk+  ++v++fk++lr +dV+ v
  gi|119720664|ref|YP_921159.1| 315 LIPDFSV-SNGERKVYIEILGFWTKDYLERKMQKLRELRGVNIVVAVNEELACSS--VKDLPHDVVVFKGRLRGADVYPV 391
                                    *******.**********************************************8..9*******************987 PP

                         DUF790 387 l 387
                                    l
  gi|119720664|ref|YP_921159.1| 392 L 392
                                    6 PP

>> PASTA  PASTA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.76   4.5e+03      12      25 ..     185     201 ..     183     219 .. 0.67
   2 !   13.6   0.0   7.3e-06     0.044       4      24 ..     415     435 ..     414     453 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.76
                                    HHHHHHHHH...TT--C CS
                          PASTA  12 deAkatLka...lGlki 25 
                                    ++Ak++L+a   lGl +
  gi|119720664|ref|YP_921159.1| 185 ATAKKLLRAvkrLGLLY 201
                                    56777777755566644 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 7.3e-06
                                    -TTTTSBHHHHHHHHHHTT-- CS
                          PASTA   4 PdvtGmsvdeAkatLkalGlk 24 
                                    Pd+ G++++eA+++L++lG++
  gi|119720664|ref|YP_921159.1| 415 PDLSGRTLSEAIRELRKLGVP 435
                                    *******************93 PP

>> Sigma70_r3  Sigma-70 region 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0    0.0012       7.3      10      46 ..      46      79 ..      41      87 .. 0.84
   2 ?    3.6   0.1     0.012        73      24      41 ..     121     138 ..     111     156 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0012
                                   HHHHHHHHSSXXXHHHHHHHHTXXHHHHHHHHHHHXX CS
                     Sigma70_r3 10 qreLeqelgrePtpeEiAeeLglseekVrevleaare 46
                                   +reLe+ l   +  eE+A eLgl++  Vr +  +a +
  gi|119720664|ref|YP_921159.1| 46 RRELEEGL---ADLEELALELGLDLRVVRAMFTLAAR 79
                                   57777777...899****************9988866 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.012
                                    HHHHHHHTXXHHHHHHHH CS
                     Sigma70_r3  24 eEiAeeLglseekVrevl 41 
                                      +Ae+Lg s+e++++vl
  gi|119720664|ref|YP_921159.1| 121 RRVAERLGCSVEDLESVL 138
                                    579***********9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (468 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.68u 0.35s 00:00:01.03 Elapsed: 00:00:00.53
# Mc/sec: 2654.26
//
Query:       gi|119720665|ref|YP_921160.1|  [L=451]
Description: type III restriction enzyme, res subunit [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.4e-24   84.3   0.0    4.7e-23   82.0   0.0    2.0  2  ResIII         Type III restriction enzyme, res subunit
    1.6e-21   76.7   0.0    4.7e-21   75.1   0.0    1.7  2  ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
    1.3e-18   66.6   0.1      3e-18   65.4   0.1    1.7  1  XPB_DRD        Xeroderma pigmentosum group B helicase damage 
    4.8e-17   62.3   0.0    3.2e-16   59.7   0.0    2.1  2  Helicase_C     Helicase conserved C-terminal domain
    7.1e-10   38.9   0.0    1.2e-08   35.0   0.0    2.3  1  DEAD           DEAD/DEAH box helicase
    5.5e-06   25.3   0.0    2.9e-05   23.0   0.0    2.1  1  SNF2_N         SNF2 family N-terminal domain
  ------ inclusion threshold ------
      0.023   14.5   0.3      0.072   12.9   0.1    1.9  2  TauD           Taurine catabolism dioxygenase TauD, TfdA fami
      0.079   13.2   0.1        2.3    8.5   0.0    3.0  2  AAA_22         AAA domain


Domain annotation for each model (and alignments):
>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.0   0.0   2.1e-26   4.7e-23       2     171 .]      72     210 ..      71     210 .. 0.95
   2 ?   -0.6   0.0      0.52   1.2e+03      44      81 ..     319     356 ..     315     387 .. 0.76

  Alignments for each domain:
  == domain 1  score: 82.0 bits;  conditional E-value: 2.1e-26
                                    -EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG. CS
                         ResIII   2 lelreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflsea 81 
                                    ++lr+yQeea+e++++       +rg+++++TG+GKT+va+++i+rl+       +l++vp+++l++q++e +++ l  a
  gi|119720665|ref|YP_921160.1|  72 VQLRDYQEEALERWMAG------RRGVVVLPTGAGKTMVALAAIARLAC-----PTLIVVPTLELMDQWEEGVRRHLGVA 140
                                    78************954......69***********************9.....8**********************986 PP

                                    ...GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.TTTHHHHHT---SE CS
                         ResIII  82 ykeigkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakkswreilekfkeav 161
                                         + + g +k+          ++v+t++s++ +         e+l d+f+++++DE+H+l +   +r+++e   +  
  gi|119720665|ref|YP_921160.1| 141 ----PGRYGGGEKEV-------GCVTVATYDSAYVNA--------EFLGDKFELLVFDEVHHLPS-PGYRQVAELSAAPW 200
                                    ....68888888888.......8**************........********************.************** PP

                                    EEEEESS-S- CS
                         ResIII 162 llglTATper 171
                                    ++glTATper
  gi|119720665|ref|YP_921160.1| 201 RMGLTATPER 210
                                    ********86 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.52
                                    HHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG. CS
                         ResIII  44 lierllkkgkeekflflvprkslleqtleefkkflsea 81 
                                    + e+ll  ++ +k+l+++   +++ +  ++f     ++
  gi|119720665|ref|YP_921160.1| 319 VLEELLARHRGDKVLIFAEHGDVVRRISSRFLVPEITY 356
                                    566777778888************99999995444444 PP

>> ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.64   1.4e+03       6      35 ..     238     267 ..     235     286 .. 0.77
   2 !   75.1   0.0   2.1e-24   4.7e-21      38     184 ..     309     446 ..     299     449 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.64
                  ERCC3_RAD25_C   6 ylakvqcaevWcpmtaefykeylkakskkk 35 
                                    +la+   + v+++m++e  +ey + + + +
  gi|119720665|ref|YP_921160.1| 238 WLAEFDVVRVYAEMSPEEREEYERLTRTYR 267
                                    688889999999999999999977665544 PP

  == domain 2  score: 75.1 bits;  conditional E-value: 2.1e-24
                  ERCC3_RAD25_C  38 lyvmnpnkfracefLikyhekrgDkiivfsDnvfaLkeyakklkkpyiyGetseaerlkilqkfkknpkvntiflskvgD 117
                                    ++   ++k++++e L+  h  rgDk+++f+++   ++++++++  p i+ +t+e+er +++++f+k   v++i+ skv +
  gi|119720665|ref|YP_921160.1| 309 IALHASSKMEVLEELLARH--RGDKVLIFAEHGDVVRRISSRFLVPEITYRTPEEERRAVMSAFRKG-LVRAIVTSKVLE 385
                                    5556678899999998876..9******************************************987.89********** PP

                  ERCC3_RAD25_C 118 tsiDlPeanvliqisshfgsrrqeaqrlGriLrakkksneeefnaffYsLvskDtkemaystkrqqf 184
                                    + +D+P+anv + + s ++srr   qrlGr+Lr++++     ++a  Y +v + tke++ s+kr++ 
  gi|119720665|ref|YP_921160.1| 386 EGVDVPDANVAVIL-SGTASRREFVQRLGRVLRPREG-----KRAVVYEVVTSGTKEVEISRKRRKA 446
                                    **********9855.5689***************988.....79********************985 PP

>> XPB_DRD  Xeroderma pigmentosum group B helicase damage recognition domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.4   0.1   1.4e-21     3e-18       1      57 []       4      59 ..       4      59 .. 0.95

  Alignments for each domain:
  == domain 1  score: 65.4 bits;  conditional E-value: 1.4e-21
                                   EEEETTEEEECSSSTT...-CT.EEETTTTEEEEEGGGHHHHHHHHHCTT--EEEES CS
                        XPB_DRD  1 LrYdrGTllidgdprgkaslpfvewDeRvekyRapAlrYrdlveaLraagiefeDrv 57
                                   L + +GT+l+ g+p+  +  p++ +D+Rv++yRa+A++Yr +veaLr+ag+efeD+v
  gi|119720665|ref|YP_921160.1|  4 LEWSAGTILLRGSPPP-SVAPYFRFDPRVKGYRALAIQYRWIVEALREAGVEFEDDV 59
                                   7899***********7.459***********************************98 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.53   1.2e+03      40      60 ..     241     261 ..     229     270 .. 0.81
   2 !   59.7   0.0   1.4e-19   3.2e-16       2     109 ..     316     417 ..     315     419 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.53
                                    TSTEEEESTTSTHHHHHHHHH CS
                     Helicase_C  40 gikvavlhgelpqnereeile 60 
                                    ++ v+++++e++ +eree  +
  gi|119720665|ref|YP_921160.1| 241 EFDVVRVYAEMSPEEREEYER 261
                                    688999**********98655 PP

  == domain 2  score: 59.7 bits;  conditional E-value: 1.4e-19
                                    HHHHHHHHHHHTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSST CS
                     Helicase_C   2 kleallellkleeeggkilifvntidrlekvklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGid 81 
                                    k+e l ell  +++g+k+lif++  d +   + +  ++ + v  ++ ++p +er++++++f+kg ++ +++++v+e+G+d
  gi|119720665|ref|YP_921160.1| 316 KMEVLEELL-ARHRGDKVLIFAEHGDVV---RRI--SSRFLVPEITYRTPEEERRAVMSAFRKGLVRAIVTSKVLEEGVD 389
                                    889999999.9***************99...777..56688999999********************************* PP

                                    STTESEEEESSSSSSHHHHHHHHTTSSS CS
                     Helicase_C  82 ipkvnlVinfdlprnvtsyiqriGRtgR 109
                                    +p++n+ ++++   + ++++qr GR+ R
  gi|119720665|ref|YP_921160.1| 390 VPDANVAVILSGTASRREFVQRLGRVLR 417
                                    **************************99 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.0   5.2e-12   1.2e-08       2     145 ..      76     196 ..      75     212 .. 0.79

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 5.2e-12
                                    HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD   2 diQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlli 81 
                                    d+Q+ea++  + g+  +v  +TG+GKT+++l ++  ++       +  +liv+Pt eL+ q  + +++ +  +       
  gi|119720665|ref|YP_921160.1|  76 DYQEEALERWMAGRRGVVVLPTGAGKTMVALAAIA-RL-------ACPTLIVVPTLELMDQWEEGVRRHLGVA----PGR 143
                                    89***************************988888.33.......4678******************999942....256 PP

                                    ETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  82 iggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinri 145
                                    +gg +++    ++ +++d  + + + l d          ++++lV+DE++ l + g+++  +  
  gi|119720665|ref|YP_921160.1| 144 YGGGEKEVGCVTV-ATYDSAYVNAEFLGD----------KFELLVFDEVHHLPSPGYRQVAELS 196
                                    7887775555555.667777777777766..........7899***********9999987764 PP

>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   1.3e-08   2.9e-05      55     216 ..      88     209 ..      45     245 .. 0.70

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 1.3e-08
                                    T--EEE---TTS--HHHHHHHHH...HHTTTS---.......S-EEEE--H.HHHHHHHHHHHHH-TTS-EEE--SSHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SNF2_N  55 vrGGiLaDemGLGKTvqvlalilaqrakeekdkekkrkdtlagptLivvPa.slldqWeneierhvsssalrvlvyggqk 133
                                     r G+    +G+GKT+ +la i+                +la ptLivvP+ +l+dqWe+ ++rh+         ygg++
  gi|119720665|ref|YP_921160.1|  88 GRRGVVVLPTGAGKTMVALAAIA----------------RLACPTLIVVPTlELMDQWEEGVRRHLGVAP---GRYGGGE 148
                                    55566666689***********9................5789**********************86543...2444443 PP

                                    H-----------------EEEE-HHHHHHHT......TTS-S-S-SEEEES-GGGT--T.TSHHHHHHHH---S-EEEE- CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx RF
                         SNF2_N 134 kmkkkntkvapklladydvvittYdvlsreaelqkkrsvlkqvewkrvvlDEghtlkns.tskaaeavskLstsnrwilt 212
                                        k         +   v + tYd    +        ++   + + +v DE h l +   +++ae  s  ++  r+ lt
  gi|119720665|ref|YP_921160.1| 149 ----K---------EVGCVTVATYDSAYVN-------AEFLGDKFELLVFDEVHHLPSPgYRQVAEL-S--AAPWRMGLT 205
                                    ....1.........2233556666666622.......456666666666666666666633333333.2..366666666 PP

                                    S--S CS
                                    xxxx RF
                         SNF2_N 213 GTPi 216
                                    +TP 
  gi|119720665|ref|YP_921160.1| 206 ATPE 209
                                    6665 PP

>> TauD  Taurine catabolism dioxygenase TauD, TfdA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   3.2e-05     0.072     131     218 ..     243     320 ..     242     359 .. 0.69
   2 ?   -2.4   0.0       1.4   3.2e+03      52      79 ..     405     432 ..     394     447 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.2e-05
                           TauD 131 DgraaynaLpeelpellegltavrvyyhyrggglrteqelpavdkhprtghpvvrthpvltgrkallvnppfatrieglg 210
                                    D +++y ++++e +e++e+lt +++ + +++       ++ ++ ++ ++   +  ++p  + r+all    +a+ri  l+
  gi|119720665|ref|YP_921160.1| 243 DVVRVYAEMSPEEREEYERLTRTYRSFLRKR------GLRIRGPRDFERLAALSVKDP--EAREALLAW-YRARRI-ALH 312
                                    899************************9999......334444444444444444444..444444443.444444.444 PP

                           TauD 211 tpeskell 218
                                         e+l
  gi|119720665|ref|YP_921160.1| 313 ASSKMEVL 320
                                    44444444 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.4
                           TauD  52 qlefarrfGplygtpgrgtntkygevld 79 
                                     +ef +r+G + +++ +++   y+ v +
  gi|119720665|ref|YP_921160.1| 405 RREFVQRLGRVLRPREGKRAVVYEVVTS 432
                                    5667777777777777666666666655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0     0.001       2.3       9     105 ..      92     185 ..      86     203 .. 0.60
   2 ?   -1.8   0.0       1.6   3.5e+03     120     135 ..     392     407 ..     376     424 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.001
                         AAA_22   9 vvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.sskdl.lrellralglelkaerlsseell.ealeqa 85 
                                    vv+ ++G+GKT+++     +l         +p+++ v   +++  +++  +r+l  a g    ++++ ++e+   +++ +
  gi|119720665|ref|YP_921160.1|  92 VVVLPTGAGKTMVALAAIARLA--------CPTLIVVPTLELMdQWEEGvRRHLGVAPG----RYGGGEKEVGcVTVATY 159
                                    66668999***99999999994........88887666666664444332444444433....33333333333333333 PP

                         AAA_22  86 lrarav.......ielliiDEaqhlrs 105
                                     +a+          ell+ DE++hl +
  gi|119720665|ref|YP_921160.1| 160 DSAYVNaeflgdkFELLVFDEVHHL-P 185
                                    3333333455667799999999999.4 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.6
                         AAA_22 120 rkgvqliLvGtpelrk 135
                                    + +v++iL Gt + r+
  gi|119720665|ref|YP_921160.1| 392 DANVAVILSGTASRRE 407
                                    4788888888876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.77u 0.36s 00:00:01.12 Elapsed: 00:00:00.60
# Mc/sec: 2247.79
//
Query:       gi|119720666|ref|YP_921161.1|  [L=116]
Description: hypothetical protein Tpen_1763 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.6e-20   72.0   0.0    5.8e-20   71.7   0.0    1.0  1  DUF134         Protein of unknown function  DUF134
    1.6e-07   30.8   0.2    2.2e-07   30.3   0.2    1.2  1  Sigma70_r4     Sigma-70, region 4
    1.9e-06   27.4   0.1    2.7e-06   27.0   0.1    1.2  1  Sigma70_r4_2   Sigma-70, region 4
    2.7e-05   23.8   0.0    4.2e-05   23.2   0.0    1.3  1  HTH_23         Homeodomain-like domain
     0.0036   17.6   0.8     0.0055   17.0   0.8    1.6  1  HTH_31         Helix-turn-helix domain
  ------ inclusion threshold ------
      0.014   15.6   0.0      0.022   14.9   0.0    1.4  1  HTH_17         Helix-turn-helix domain
      0.015   15.2   0.1       0.02   14.8   0.1    1.1  1  Sigma70_ECF    ECF sigma factor
      0.044   13.5   0.0      0.075   12.8   0.0    1.3  1  HTH_38         Helix-turn-helix domain
      0.049   13.7   0.0      0.068   13.2   0.0    1.2  1  HTH_3          Helix-turn-helix
       0.05   13.4   0.0      0.076   12.9   0.0    1.3  1  HTH_AsnC-type  AsnC-type helix-turn-helix domain
       0.11   12.5   0.0       0.16   11.9   0.0    1.3  1  HTH_11         HTH domain
       0.15   11.8   0.0       0.22   11.3   0.0    1.2  1  HTH_Tnp_4      Helix-turn-helix of DDE superfamily endonuclea


Domain annotation for each model (and alignments):
>> DUF134  Protein of unknown function  DUF134
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.7   0.0   3.9e-23   5.8e-20       3      90 ..      14     103 ..       9     107 .. 0.87

  Alignments for each domain:
  == domain 1  score: 71.7 bits;  conditional E-value: 3.9e-23
                         DUF134   3 rkgrprklrdileePkvrifkPea.vee.tgkvaisldeleairlvdyedlkqeeaaklmGiskatlwrlltearkkiak 80 
                                    r grp k+  +   P v+ f+P    ++  + v+++ +e+ea+rlvd e+l++eea + mG+s++t+wrl++++r+k+ +
  gi|119720666|ref|YP_921161.1|  14 RIGRPPKPVSVGFLPSVQGFNPYPpPPLpIEPVVLEPAEVEALRLVDLEKLSYEEAGARMGVSRTTVWRLVESGREKLVS 93 
                                    45677777777778*******99843331456************************************************ PP

                         DUF134  81 alveGraiil 90 
                                    a++eGr+i++
  gi|119720666|ref|YP_921161.1|  94 AILEGRPIVI 103
                                    ******9998 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.2   1.5e-10   2.2e-07       4      48 ..      47      91 ..      46      92 .. 0.96

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 1.5e-10
                                   HS-HHHHHHHHHHHTTT--HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                     Sigma70_r4  4 sLpererevlelrfgeglTleEIgerlgiSrerVrqiekrAlrkL 48
                                   +L++ e e l+l+ +e+l++eE g+r+g+Sr +V ++   +++kL
  gi|119720666|ref|YP_921161.1| 47 VLEPAEVEALRLVDLEKLSYEEAGARMGVSRTTVWRLVESGREKL 91
                                   599**********************************99999998 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.1   1.8e-09   2.7e-06      11      54 .]      48      91 ..      47      91 .. 0.93

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 1.8e-09
                                   S-HHHHHHHHHHHTS---HHHHHHHHT--HHHHHHHHHHHHHHH CS
                   Sigma70_r4_2 11 LperqreifllryleglsykEIAellgisegtVksrlsRArkkL 54
                                   L + + e++ l +le lsy+E+ +++g+s +tV + +  +r+kL
  gi|119720666|ref|YP_921161.1| 48 LEPAEVEALRLVDLEKLSYEEAGARMGVSRTTVWRLVESGREKL 91
                                   6677779******************************9999998 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   2.8e-08   4.2e-05       9      38 ..      54      84 ..      52      91 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 2.8e-08
                         HTH_23  9 rilllla.eGlsvreIAreLgvsrrTvyrwl 38
                                   ++l+l++ e+ls++e+ +++gvsr Tv+r +
  gi|119720666|ref|YP_921161.1| 54 EALRLVDlEKLSYEEAGARMGVSRTTVWRLV 84
                                   689999955********************87 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.8   3.7e-06    0.0055      14      43 ..      63      93 ..       5     106 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.7e-06
                         HTH_31 14 GLsqeevAerlgvsestlsrl.EqGrrgrps 43
                                    Ls ee+++r gvs++t+ rl E+Gr+ ++s
  gi|119720666|ref|YP_921161.1| 63 KLSYEEAGARMGVSRTTVWRLvESGREKLVS 93
                                   8****************99964779987665 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   1.5e-05     0.022       2      26 ..      64      88 ..      64     105 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.5e-05
                         HTH_17  2 ltveEaAelLgvsrstvyrlirrge 26
                                   l+ eEa +  gvsr+tv rl+ +g+
  gi|119720666|ref|YP_921161.1| 64 LSYEEAGARMGVSRTTVWRLVESGR 88
                                   6779999**************9994 PP

>> Sigma70_ECF  ECF sigma factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   1.4e-05      0.02     137     180 ..      49      92 ..      45      96 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.4e-05
                    Sigma70_ECF 137 dpeqarlvelrkleGlsveEiAeklgvskrtverrlalaRawle 180
                                    +p+  + + l  le ls eE+++++gvs+ tv r  +  R++l 
  gi|119720666|ref|YP_921161.1|  49 EPAEVEALRLVDLEKLSYEEAGARMGVSRTTVWRLVESGREKLV 92 
                                    6667777777788889******************9999999875 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     5e-05     0.075      14      41 ..      57      84 ..      48      86 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5e-05
                         HTH_38 14 erllaeGlslreIArrLgrspsTIsREl 41
                                        e+ls+ e + r+g+s++T+ R +
  gi|119720666|ref|YP_921161.1| 57 RLVDLEKLSYEEAGARMGVSRTTVWRLV 84
                                   3334599*******************87 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.6e-05     0.068       3      26 ..      55      80 ..      53      91 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.6e-05
                                   HHHH..HTTHHHHHHHHHHTSSHHHH CS
                          HTH_3  3 elRk..qlglsqeeLAeklGvsrsti 26
                                   +lR+    +ls ee+ +++Gvsr+t+
  gi|119720666|ref|YP_921161.1| 55 ALRLvdLEKLSYEEAGARMGVSRTTV 80
                                   66777789*****************8 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   5.1e-05     0.076      18      36 ..      64      82 ..      58      85 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.1e-05
                  HTH_AsnC-type 18 isyaeLAervGlSestvlr 36
                                   +sy+e ++r G+S++tv+r
  gi|119720666|ref|YP_921161.1| 64 LSYEEAGARMGVSRTTVWR 82
                                   79****************8 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00011      0.16      17      37 ..      65      85 ..      55     100 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                         HTH_11 17 sgeeLAeeLnvSrrtvrrdIk 37
                                   s ee   +++vSr+tv+r ++
  gi|119720666|ref|YP_921161.1| 65 SYEEAGARMGVSRTTVWRLVE 85
                                   555556799********9765 PP

>> HTH_Tnp_4  Helix-turn-helix of DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00015      0.22      20      41 ..      64      85 ..      62      91 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00015
                      HTH_Tnp_4 20 ltyqdLayrFgvsestvsrifh 41
                                   l+y+  ++r gvs++tv+r + 
  gi|119720666|ref|YP_921161.1| 64 LSYEEAGARMGVSRTTVWRLVE 85
                                   78999**************885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.54u 0.36s 00:00:00.90 Elapsed: 00:00:00.55
# Mc/sec: 634.17
//
Query:       gi|119720667|ref|YP_921162.1|  [L=90]
Description: hypothetical protein Tpen_1764 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00027   21.9   2.8     0.0014   19.7   1.7    2.0  2  DUF5320       Family of unknown function (DUF5320)
      0.005   16.8   0.7     0.0062   16.5   0.7    1.1  1  Prefoldin_2   Prefoldin subunit
     0.0076   17.0   0.1     0.0096   16.6   0.1    1.1  1  Occludin_ELL  Occludin homology domain
     0.0091   15.3   0.2      0.011   15.0   0.2    1.0  1  DUF3450       Protein of unknown function (DUF3450)
  ------ inclusion threshold ------
      0.016   15.6   1.6       0.02   15.2   1.6    1.1  1  CCDC-167      Coiled-coil domain-containing protein 167
      0.016   15.2   0.7      0.021   14.8   0.7    1.2  1  Cut12         Spindle pole body formation-associated protein
      0.029   14.5   0.2      0.035   14.2   0.2    1.0  1  UPF0242       Uncharacterised protein family (UPF0242) N-term
      0.038   14.5   0.7      0.048   14.2   0.7    1.1  1  APG6_N        Apg6 coiled-coil region
      0.076   12.4   0.4      0.091   12.2   0.4    1.0  1  DUF4618       Domain of unknown function (DUF4618)
      0.081   12.7   0.1      0.098   12.5   0.1    1.0  1  DUF724        Protein of unknown function (DUF724)
       0.11   12.8   0.2       0.13   12.5   0.2    1.1  1  DUF1319       Protein of unknown function (DUF1319)
       0.16   12.0   2.8       0.19   11.8   2.8    1.1  1  TPR_MLP1_2    TPR/MLP1/MLP2-like protein
       0.22   11.7   0.0       0.26   11.5   0.0    1.0  1  Fib_alpha     Fibrinogen alpha/beta chain family
       0.38   10.9   2.6        3.1    8.0   2.6    2.0  1  HR1           Hr1 repeat


Domain annotation for each model (and alignments):
>> DUF5320  Family of unknown function (DUF5320)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   1.7   1.1e-06    0.0014      47      98 ..       6      71 ..       1      72 [. 0.64
   2 !    9.1   0.6    0.0022       2.8      75      99 .]      55      79 ..      53      79 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.1e-06
                        DUF5320 47 grgfgrrrraggarla..............aaetaeaskeeekelLeeqaeaLeeeleaikkrlke 98
                                   +r+++ ++ ++g++++               +e++    e+ ++ Lee+ ++Leee++ ++++lke
  gi|119720667|ref|YP_921162.1|  6 RRYWRAGWGGWGYPPYygyppamppwappmSPEQELRYLEDYRRWLEEYRKSLEEEIKGVEEELKE 71
                                   333333333333333334446665555666777777888889999999999999999999999998 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0022
                        DUF5320 75 kelLeeqaeaLeeeleaikkrlkel 99
                                   ++ Lee+++  eeel+++++r++el
  gi|119720667|ref|YP_921162.1| 55 RKSLEEEIKGVEEELKEVDSRIEEL 79
                                   5789999999********9999997 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.7   4.8e-06    0.0062      60      99 ..      44      83 ..      41      85 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.8e-06
                                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    Prefoldin_2 60 keevkeeLeerketlekeiktlekqleklekeleelkeel 99
                                   +e+ +  Lee  ++le+eik +e++l+++  ++eel+ +l
  gi|119720667|ref|YP_921162.1| 44 LEDYRRWLEEYRKSLEEEIKGVEEELKEVDSRIEELRRML 83
                                   6788888999999999***********9999999999876 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   7.5e-06    0.0096       6      50 ..      36      81 ..      32      85 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 7.5e-06
                   Occludin_ELL  6 saeqrerYkaeFnkeYkeYk.elhaeleevskkfseLerelkelke 50
                                   s eq  rY +++++  +eY+ +l++e++ v+++++e++++++el++
  gi|119720667|ref|YP_921162.1| 36 SPEQELRYLEDYRRWLEEYRkSLEEEIKGVEEELKEVDSRIEELRR 81
                                   67999**************72699****************999875 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.2   8.7e-06     0.011      50      94 ..      38      82 ..      35      86 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 8.7e-06
                        DUF3450 50 laeyralkeeleslevyneqlerlvasqeqeiasleeqieeieei 94
                                   ++e+r l++   +le y++ le+ ++ +e+e+++++ +iee++++
  gi|119720667|ref|YP_921162.1| 38 EQELRYLEDYRRWLEEYRKSLEEEIKGVEEELKEVDSRIEELRRM 82
                                   689999999999999999999999999999999999999999876 PP

>> CCDC-167  Coiled-coil domain-containing protein 167
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   1.6   1.6e-05      0.02      34      63 ..      52      81 ..      34      86 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.6e-05
                       CCDC-167 34 eeeResleeEeaslkeqleenekeLksLrk 63
                                   ee R+sleeE + ++e+l+e +++ ++Lr+
  gi|119720667|ref|YP_921162.1| 52 EEYRKSLEEEIKGVEEELKEVDSRIEELRR 81
                                   566*************************97 PP

>> Cut12  Spindle pole body formation-associated protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.7   1.6e-05     0.021      81     128 ..      38      85 ..      35      89 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.6e-05
                          Cut12  81 elEieklikyrslaksyakkKdeealrlkeklkeEeekvaemekkvse 128
                                    e+E++ l  yr+ +++y k  +ee+  ++e+lke  ++++e  + + +
  gi|119720667|ref|YP_921162.1|  38 EQELRYLEDYRRWLEEYRKSLEEEIKGVEEELKEVDSRIEELRRMLGR 85 
                                    789************************************998887665 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.2   2.7e-05     0.035     120     165 ..      39      83 ..      35      86 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.7e-05
                        UPF0242 120 qqLqekleaiaedfeelkleleeqLaekqellqeyqetieeqrsvl 165
                                    q+L+  le+  +  ee+++ lee+++  +e l+e    iee+r +l
  gi|119720667|ref|YP_921162.1|  39 QELR-YLEDYRRWLEEYRKSLEEEIKGVEEELKEVDSRIEELRRML 83 
                                    6666.688889999******************************98 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.7   3.8e-05     0.048      48      89 ..      40      81 ..      33      85 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.8e-05
                         APG6_N 48 eleeleeeleklekeeeelleeLkelekereeleaelaalee 89
                                   el+ le+  + le+ +++l+ee+k +e+e +e+++ +++l++
  gi|119720667|ref|YP_921162.1| 40 ELRYLEDYRRWLEEYRKSLEEEIKGVEEELKEVDSRIEELRR 81
                                   444455555557777777888888888888888888877765 PP

>> DUF4618  Domain of unknown function (DUF4618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.4   7.1e-05     0.091      64     101 ..      43      80 ..      36      84 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.1e-05
                        DUF4618  64 qleqakaeLqeweekeekklekLeqqleqlnakvqklq 101
                                     le+ ++ L+e  + +e++++  e++l+++++++++l+
  gi|119720667|ref|YP_921162.1|  43 YLEDYRRWLEEYRKSLEEEIKGVEEELKEVDSRIEELR 80 
                                    58999999**************************9986 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   7.7e-05     0.098      95     137 ..      39      81 ..      33      85 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.7e-05
                         DUF724  95 nkLlslkdeqtklleerkklekkieeeesekrkleeeidelek 137
                                    ++L  l d +++l+e rk le++i+  e+e +++++ i+el +
  gi|119720667|ref|YP_921162.1|  39 QELRYLEDYRRWLEEYRKSLEEEIKGVEEELKEVDSRIEELRR 81 
                                    678899999********************99999999999876 PP

>> DUF1319  Protein of unknown function (DUF1319)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   9.9e-05      0.13      41      68 ..      51      78 ..      40      86 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.9e-05
                        DUF1319 41 vkekrrslekqlkklkselkklrelyle 68
                                   + e r+sle+++k++++elk++ +   e
  gi|119720667|ref|YP_921162.1| 51 LEEYRKSLEEEIKGVEEELKEVDSRIEE 78
                                   678899*************999887666 PP

>> TPR_MLP1_2  TPR/MLP1/MLP2-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   2.8   0.00015      0.19      81     116 ..      45      80 ..      39      82 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00015
                     TPR_MLP1_2  81 esakaeleeseesweeqkeelekelselekriedln 116
                                    e+ +  lee ++s+ee+ +  e+el+e+ +rie+l 
  gi|119720667|ref|YP_921162.1|  45 EDYRRWLEEYRKSLEEEIKGVEEELKEVDSRIEELR 80 
                                    67788899**************************96 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0    0.0002      0.26      73     111 ..      45      83 ..      35      87 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0002
                                    HHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHH CS
                      Fib_alpha  73 kdndnvikksskeleeeilrlketidaqesnirvLqnvl 111
                                    +d  + +++++k+leeei  ++e++++  s+i++L+ +l
  gi|119720667|ref|YP_921162.1|  45 EDYRRWLEEYRKSLEEEIKGVEEELKEVDSRIEELRRML 83 
                                    556778899*****************999******9986 PP

>> HR1  Hr1 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   2.6    0.0024       3.1      39      58 ..      64      83 ..      38      86 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0024
                            HR1 39 eaeselsesnskielLreqL 58
                                    +e el+e +s+ie+Lr+ L
  gi|119720667|ref|YP_921162.1| 64 GVEEELKEVDSRIEELRRML 83
                                   589**************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1488  (0.082994); expected 358.6 (0.02)
Passed bias filter:                     1267  (0.0706676); expected 358.6 (0.02)
Passed Vit filter:                       308  (0.0171789); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.64u 0.34s 00:00:00.98 Elapsed: 00:00:00.53
# Mc/sec: 510.35
//
Query:       gi|119720668|ref|YP_921163.1|  [L=358]
Description: glyceraldehyde-3-phosphate dehydrogenase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-08   34.8   0.0    1.5e-08   34.4   0.0    1.2  1  Gp_dh_C   Glyceraldehyde 3-phosphate dehydrogenase, C-termina
      9e-05   22.6   0.2     0.0003   20.9   0.2    1.8  1  DapB_N    Dihydrodipicolinate reductase, N-terminus
  ------ inclusion threshold ------
      0.011   16.1   0.0      0.028   14.8   0.0    1.7  1  Gp_dh_N   Glyceraldehyde 3-phosphate dehydrogenase, NAD bindi


Domain annotation for each model (and alignments):
>> Gp_dh_C  Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   0.0   2.6e-12   1.5e-08       3     111 ..     157     255 ..     155     301 .. 0.84

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 2.6e-12
                                    HHHHHHHHHHEEEEEEEEEEEECTTTSBSSSS--.SSTTTTSBTTCSS.EEEE-THHHHHHHHSGGGTTTEEEEEEEESS CS
                        Gp_dh_C   3 plakvlndkfgikkglmttvhaytndQkllDgpskkdlrraraaaeni.iptstgaakavglVlpelkgkldglAvrVPt 81 
                                    +++ +l +  ++ ++++++ ++++++          d + ar +a ++   +++++a +v +Vlp    ++ ++Av+VPt
  gi|119720668|ref|YP_921163.1| 157 RVVSALSSLGELREVFVVIARRAADP---------ADRKGARLNALSLdGGVPSHHASDVRTVLPW--LNVFTVAVKVPT 225
                                    67788888888888999999999988.........899*******7773579*************6..5689******** PP

                                    SSEEEEEEEEEESSTS-HHHHHHHHHHHHH CS
                        Gp_dh_C  82 pnvsvvdlvvelekevtveevnaalkeaae 111
                                    +  +++   v+l  + ++ +v++al+   +
  gi|119720668|ref|YP_921163.1| 226 TLAHLHVARVRLGGRLSRGDVIEALESHRR 255
                                    *************************98876 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.2     5e-08    0.0003       1      95 [.       5     116 ..       5     128 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 5e-08
                                    EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHH..............HHSSSS.--S-BEBSSHHHHH CS
                         DapB_N   1 ikvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdag..............ellglg.klgvavtddleevl 65 
                                    i+v+v+G+ G++Gk+v++av+ ++d+ lv++ + ++s  + ++++                 +l+ + gv v   le++l
  gi|119720668|ref|YP_921163.1|   5 IRVLVNGI-GTIGKRVAHAVSLQPDMVLVGVSSPRPSLGVLSSLSrggvlegvpfyvrgASPSLFeERGVRVGGVLEDLL 83 
                                    79*****9.**********************99999654444444779999999999985555555999*********** PP

                                    HH..-SEEEE-S-HHHHHHHH.HHHHHTT-EEE CS
                         DapB_N  66 ek..advliDFTtpeavlenl.klalekgvklV 95 
                                     +  +dv++D       l n  +l+ ++gv++V
  gi|119720668|ref|YP_921163.1|  84 GSgrVDVVVDAAPGGEGLRNRdELYSRYGVRAV 116
                                    99999****988444444443033334466666 PP

>> Gp_dh_N  Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   4.7e-06     0.028       1      32 [.       5      36 ..       5      49 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.7e-06
                                   CEEEEESTSHHHHHHHHHHHHHTTCEEEEEE- CS
                        Gp_dh_N  1 vkvainGfGRIGrlvlralleekelevvaind 32
                                   ++v +nG G IG+ v+ a+  ++++ +v + +
  gi|119720668|ref|YP_921163.1|  5 IRVLVNGIGTIGKRVAHAVSLQPDMVLVGVSS 36
                                   689**********************9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       254  (0.014167); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.36s 00:00:00.98 Elapsed: 00:00:00.55
# Mc/sec: 1959.92
//
Query:       gi|119720669|ref|YP_921164.1|  [L=331]
Description: putative glutamate synthase subunit beta [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.4e-37  127.9   0.0    5.9e-37  127.5   0.0    1.1  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    4.9e-15   55.8   0.3    3.1e-07   30.9   0.1    2.4  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
      2e-09   37.2   0.0    2.2e-05   23.9   0.0    2.6  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    4.5e-09   36.4   0.0    1.5e-07   31.5   0.0    2.5  2  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    1.2e-06   27.9   0.1      0.011   14.8   0.0    2.9  3  FAD_binding_2  FAD binding domain
    5.7e-05   22.5   0.4    0.00025   20.4   0.1    2.0  2  FAD_binding_3  FAD binding domain
    7.6e-05   21.6   0.1    0.00039   19.2   0.1    1.9  2  HI0933_like    HI0933-like protein
    0.00047   19.8   0.5        1.3    8.5   0.0    3.3  3  DAO            FAD dependent oxidoreductase
    0.00049   19.5   0.0       0.12   11.7   0.0    2.5  3  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
    0.00051   19.4   0.3     0.0033   16.8   0.0    2.0  2  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
     0.0019   17.6   0.0      0.003   17.0   0.0    1.3  1  FAD_oxidored   FAD dependent oxidoreductase
     0.0088   15.9   0.2        1.1    9.2   0.0    2.4  2  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
  ------ inclusion threshold ------
      0.017   15.0   0.0       0.23   11.3   0.0    2.1  2  YjeF_N         YjeF-related protein N-terminus
      0.023   14.0   0.0      0.058   12.6   0.0    1.6  1  Thi4           Thi4 family
      0.041   13.2   0.0        5.4    6.2   0.0    2.2  2  Amino_oxidase  Flavin containing amine oxidoreductase
      0.082   12.0   0.1       0.65    9.0   0.0    2.4  3  GIDA           Glucose inhibited division protein A
      0.086   12.0   0.2        5.1    6.1   0.0    3.1  5  K_oxygenase    L-lysine 6-monooxygenase (NADPH-requiring)
      0.093   12.7   0.9        0.7    9.9   0.1    2.5  2  NAD_binding_9  FAD-NAD(P)-binding


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.5   0.0     6e-40   5.9e-37       1     293 [.      17     314 ..      17     316 .. 0.81

  Alignments for each domain:
  == domain 1  score: 127.5 bits;  conditional E-value: 6e-40
                                    CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHHHHHHCHHHH.CCCCHCCTCEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx RF
                    Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeiasevvkklnqg.ielllgeevvkid 79 
                                    k+v+++G+GpAGlaaa  l+  g+kv ++   + ++  g +l  ++ +++ +++ ++e +k +    + ++++      +
  gi|119720669|ref|YP_921164.1|  17 KKVAIVGSGPAGLAAASVLRCLGHKVDVF---DRLPEPGGMLMFTIPEFRIPKKDVRESIKAIAGIgVSFYTD-----TE 88 
                                    58***************************...66777788888899999999998877644333332444444.....33 PP

                                    ESCEEEEETEEECTCEEEEEESEEEE---E.EE-BCTCTTC.TTBEECCSECHHHHHHCCSS-T..........SEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..........xxxxxx RF
                    Pyr_redox_2  80 pgkkkvklekkkegdeekiaydklvlAtGs.sprdlgipGvaenvgklvrtldsaealklkllp..........krivvv 148
                                     g +++k+e++        +yd++v+ tG  + r lgipG+  n g++  +ld    + + +l            r+ +v
  gi|119720669|ref|YP_921164.1|  89 AG-RDLKVEELL------EDYDAVVISTGTwKGRSLGIPGE--NKGRVYNALDWIYHFMSYKLGyassppppleGRVGIV 159
                                    34.488886666......47*********8356666*****..4444445777777777777778889999********* PP

                                    S-SHHHHHHHHH.HHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE.....EEE.EEET CS
                                    xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxx.xxxx RF
                    Pyr_redox_2 149 GgGyiGvElAaa.laklgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgnge.....kle.vvle 221
                                    G+G+++v++A    +++g++  l+++r+  +     + ++ + ++le+ Gv++  + +++e+ g ++         v+ +
  gi|119720669|ref|YP_921164.1| 160 GAGLTAVDVAELaVHEYGAKPILLYRRPMSV-----APAKHMLKHLEELGVQFIENVVPVEVVGGDSisglkL-ArVKPT 233
                                    **********9956******99****77776.....5699**************************9997751.345555 PP

                                    TSCE............EEESEEEE-S-EEES-HHCS.HCCT-EEEETTEEE--TTSBESSTTEEE-GGGCTECCSS--HH CS
                                    xxxx............xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 222 dgee............idadlvvvavGvrpstelle.eklglelderggivvdeflrtnvpgiyaiGDvaggkggpelaq 288
                                    + ++            i+ d +v avG++p ++  + ++lg+el+++g i+vde+  t+v+g++a+GDva   +gp ++ 
  gi|119720669|ref|YP_921164.1| 234 TSRTaatevipgsefvIELDSLVAAVGLQPTPPP-GlQSLGVELNRDGSIKVDENFMTSVKGLFAAGDVA---HGPSNIG 309
                                    5555666788888888***************987.66*********************************...6666665 PP

                                    HHHHH CS
                                    xxxxx RF
                    Pyr_redox_2 289 aAvqq 293
                                     A+++
  gi|119720669|ref|YP_921164.1| 310 LAMRS 314
                                    55555 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   1.1e-07   0.00011       1      35 [.      18      52 ..      18      59 .. 0.93
   2 !   30.9   0.1   3.1e-10   3.1e-07       1      78 [.     155     227 ..     155     232 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.1e-07
                                   EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                      Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                   kv++vG+G  gl +A++l+ lg+kV v++r +++ 
  gi|119720669|ref|YP_921164.1| 18 KVAIVGSGPAGLAAASVLRCLGHKVDVFDRLPEPG 52
                                   79*****************************9987 PP

  == domain 2  score: 30.9 bits;  conditional E-value: 3.1e-10
                                    EEEEECSSHHHHHHHHHH.HHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEEE CS
                      Pyr_redox   1 kvvvvGgGyiglElAgal.aelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedgvesvkl 78 
                                    +v +vG+G++++++A+ + +e+g+k  ++ r+++       + +k + ++le++g++++ n +++e++g ++ ++++kl
  gi|119720669|ref|YP_921164.1| 155 RVGIVGAGLTAVDVAELAvHEYGAKPILLYRRPMSV-----APAKHMLKHLEELGVQFIENVVPVEVVGGDS-ISGLKL 227
                                    688*************98678***************.....899************************9988.677766 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.1   0.00035      0.34       2      24 ..      21      42 ..      20      53 .. 0.85
   2 !   23.9   0.0   2.2e-08   2.2e-05     157     305 .]     146     299 ..      88     299 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00035
                    Pyr_redox_3  2 IiGaGPaGlaaaielkkagledy 24
                                   I+G GPaGlaaa  l+ +g  ++
  gi|119720669|ref|YP_921164.1| 21 IVGSGPAGLAAASVLRCLGH-KV 42
                                   9************9998887.45 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 2.2e-08
                    Pyr_redox_3 157 kefhkyagqkvvViGgknSavDaA.lelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvke.....ekikvl 230
                                    +++ +  + +v ++G++ +avD+A l + ++ga+  +++r+    +  +++  +l+    + +e++v       ++i  l
  gi|119720669|ref|YP_921164.1| 146 SSPPPPLEGRVGIVGAGLTAVDVAeLAVHEYGAKPILLYRRPMSVAPAKHMLKHLEELGVQFIENVVPVevvggDSISGL 225
                                    34444557899***********996778889**********99999999****************998767776667777 PP

                    Pyr_redox_3 231 fnaevkeikekeeeykvktedgkkvevkddvvlatGykpdlsf.lkkslfeldedgrpvlteeteetnvpglflaG 305
                                    + a+vk  + ++   +v   + + v + d  v+a+G +p+  + l++ ++el++dg ++++e+ +   v+glf aG
  gi|119720669|ref|YP_921164.1| 226 KLARVKPTTSRTAATEVIPGS-EFVIELDSLVAAVGLQPTPPPgLQSLGVELNRDGSIKVDENFMT-SVKGLFAAG 299
                                    777888777777777776655.556667889999******9887999**************99985.5******99 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.0   1.5e-10   1.5e-07       1      34 [.      21      54 ..      21      71 .. 0.94
   2 ?    2.1   0.1      0.23   2.3e+02       1      20 [.     158     178 ..     158     186 .. 0.72

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 1.5e-10
                                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGG CS
                  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGr 34
                                   IvG+G +Gl+aA+ L+  g++v+++++ + +GG 
  gi|119720669|ref|YP_921164.1| 21 IVGSGPAGLAAASVLRCLGHKVDVFDRLPEPGGM 54
                                   9*******************************96 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.23
                                    EE--SHHHHHHHHHHHCC.TE CS
                  NAD_binding_8   1 IvGaGlsGlvaAylLaka.gf 20 
                                    IvGaGl++   A l+  + g+
  gi|119720669|ref|YP_921164.1| 158 IVGAGLTAVDVAELAVHEyGA 178
                                    9******99888876554355 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.1e-05     0.011       2      36 ..      19      53 ..      18      58 .. 0.89
   2 ?    0.0   0.0      0.35   3.5e+02      85     142 ..     189     247 ..     185     262 .. 0.66
   3 !    8.9   0.0   0.00069      0.68     376     404 ..     282     304 ..     270     312 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.1e-05
                                   EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS CS
                  FAD_binding_2  2 viViGsGlAGLaAAleaaeaGlkvavvekeqefgg 36
                                   v ++GsG AGLaAA  ++  G+kv v +  +e gg
  gi|119720669|ref|YP_921164.1| 19 VAIVGSGPAGLAAASVLRCLGHKVDVFDRLPEPGG 53
                                   89**********************99999888666 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.35
                                    HHHTHHHHHHHHHHTT----BCCTSSB-EEE-TT-SST....EEEE-.STT-......HHHH CS
                  FAD_binding_2  85 fveaapeavdeLeelgvpfsrtedgpvdvrelGglsat....artlhdaadarretlvtgha 142
                                     v+ a+++++ Leelgv+f +   ++v v  +Gg s      ar+ +++++   +++++g +
  gi|119720669|ref|YP_921164.1| 189 SVAPAKHMLKHLEELGVQFIE---NVVPVEVVGGDSISglklARVKPTTSRTAATEVIPGSE 247
                                    567789999999999999999...77777777776666444445555444443355555555 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.00069
                                    EEBETTSBESTTEEESSBTEEE-STCEES CS
                  FAD_binding_2 376 vetdengrvldadgqpipGLYAaGevaag 404
                                    +++den+ +       ++GL+AaG va+g
  gi|119720669|ref|YP_921164.1| 282 IKVDENFMT------SVKGLFAAGDVAHG 304
                                    567777777......************65 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.1   2.5e-07   0.00025       3      33 ..      18      48 ..      17      52 .. 0.91
   2 ?   -0.5   0.1      0.57   5.7e+02       3      33 ..     155     186 ..     153     203 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.5e-07
                                   EEEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                  FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlvekr 33
                                   +V+IVG+GpaGl +a++L+  G +v + ++ 
  gi|119720669|ref|YP_921164.1| 18 KVAIVGSGPAGLAAASVLRCLGHKVDVFDRL 48
                                   69********************999999987 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.57
                                    EEEEE--SHHHHHHHHH.HHHTTHHEEEEESS CS
                  FAD_binding_3   3 dVlIVGaGpaGlmlall.LseaGvrvvlvekr 33 
                                     V IVGaG++ +  a l  +e+G + +l+ +r
  gi|119720669|ref|YP_921164.1| 155 RVGIVGAGLTAVDVAELaVHEYGAKPILLYRR 186
                                    589******98877765367888887777666 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   3.9e-07   0.00039       2      36 ..      18      52 ..      17      58 .. 0.91
   2 ?    0.1   0.0      0.26   2.6e+02     364     406 ..     283     318 ..     250     321 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 3.9e-07
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                    HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklg 36
                                   +v+++G G+AGl aA  ++  g++V ++++ +++g
  gi|119720669|ref|YP_921164.1| 18 KVAIVGSGPAGLAAASVLRCLGHKVDVFDRLPEPG 52
                                   79***************************999888 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.26
                                    GB-TTT-BBTTSTTEEE-GGGBSEEE-TTTHHHHHHHHHHHHH CS
                    HI0933_like 364 evssktmeskkvpgLffaGEvlDvegvtGGynlqaAwasgyaA 406
                                    +v+++ m   +v+gLf aG v       G  n+  A  sg +A
  gi|119720669|ref|YP_921164.1| 283 KVDENFM--TSVKGLFAAGDVA-----HGPSNIGLAMRSGRLA 318
                                    5788888..7899******884.....2444555555555555 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0013       1.3       1      33 [.      18      52 ..      18      54 .. 0.86
   2 ?    4.6   0.0      0.02        20     155     205 ..      75     114 ..      65     130 .. 0.68
   3 ?    3.1   0.0      0.06        60     150     184 ..     194     236 ..     186     279 .. 0.60

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0013
                                   EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                            DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiag 33
                                   +v+i+G+G +Gl++A  L   g  V ++++ +++g
  gi|119720669|ref|YP_921164.1| 18 KVAIVGSGPAGLAAASVLRCLGhkVDVFDRLPEPG 52
                                   59****************444778****9988888 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.02
                                    HHHHTT-EEEESECEEE.EEEEETCEEEEEEECTEEEEEEEEEEE--GGGHH CS
                            DAO 155 aaealGveilegtevtg.leeedgkvwgverttpgendaadavVnaaGawsd 205
                                    a++  Gv +++ te+ + l     kv ++      e   +davV+++G w +
  gi|119720669|ref|YP_921164.1|  75 AIAGIGVSFYTDTEAGRdL-----KVEEL-----LE--DYDAVVISTGTWKG 114
                                    4555578888887775423.....35555.....22..37**********55 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.06
                                    HHHHHHHHHTT-EEEES...ECEEEEEEEETCEEEEE.........E CS
                            DAO 150 aalaraaealGveileg...tevtgleeedgkvwgve.........r 184
                                    + +++ +e+lGv+++e+    ev+g +     ++g++         r
  gi|119720669|ref|YP_921164.1| 194 KHMLKHLEELGVQFIENvvpVEVVGGD----SISGLKlarvkpttsR 236
                                    569999**********95443333332....2333333321133221 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   0.00012      0.12      35      70 ..      15      50 ..      10      62 .. 0.92
   2 ?   -3.0   0.0         4     4e+03      83      98 ..      93     108 ..      84     110 .. 0.77
   3 ?    4.9   0.0     0.014        14      38      73 ..     155     191 ..     150     231 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00012
                                   TTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHH CS
                   2-Hacid_dh_C 35 sgktvGiiGlGrIGqavakrlkafgmkviaydrskk 70
                                   +gk+v+i+G G  G a+a +l+ +g kv ++dr ++
  gi|119720669|ref|YP_921164.1| 15 TGKKVAIVGSGPAGLAAASVLRCLGHKVDVFDRLPE 50
                                   69******************************9876 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4
                                    CSHHHHHHH-SEEEE- CS
                   2-Hacid_dh_C  83 vsleellaesDivslh 98 
                                     ++eell++ D v++ 
  gi|119720669|ref|YP_921164.1|  93 LKVEELLEDYDAVVIS 108
                                    5789999999999986 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.014
                                    EEEEES-SHHHHHHHHHHH.HTT-EEEEESSSHHHHH CS
                   2-Hacid_dh_C  38 tvGiiGlGrIGqavakrlk.afgmkviaydrskkkee 73 
                                    +vGi+G+G  +  va+++  + g+k i   r++ + +
  gi|119720669|ref|YP_921164.1| 155 RVGIVGAGLTAVDVAELAVhEYGAKPILLYRRPMSVA 191
                                    79***************98799998776666666444 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   3.3e-06    0.0033      30      60 ..      18      48 ..      12      55 .. 0.92
   2 ?    0.4   0.0      0.34   3.4e+02      29      48 ..     154     173 ..     149     285 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.3e-06
                                   EEEEESTSHHHHHHHHHHHHTT-EEEEEESS CS
                    AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvr 60
                                   kv ++G G aGl+A+++ + lg kV v+D  
  gi|119720669|ref|YP_921164.1| 18 KVAIVGSGPAGLAAASVLRCLGHKVDVFDRL 48
                                   8****************************75 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.34
                                    -EEEEESTSHHHHHHHHHHH CS
                    AlaDh_PNT_C  29 akvlviGgGvaGlqAiatak 48 
                                    ++v ++G+G   +  ++ a+
  gi|119720669|ref|YP_921164.1| 154 GRVGIVGAGLTAVDVAELAV 173
                                    78899999988888887775 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0     3e-06     0.003       2      67 ..      19      87 ..      18     106 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3e-06
                   FAD_oxidored  2 vvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaee...qvvtgiareflerl 67
                                   v +vG+gpaG+aAA      G kv + ++ +  GG+l   +    i +k  +   +++ gi   f+   
  gi|119720669|ref|YP_921164.1| 19 VAIVGSGPAGLAAASVLRCLGHKVDVFDRLPEPGGMLMFTIPEFRIPKKDVResiKAIAGIGVSFYTDT 87
                                   89**********************************987765555544433356667777766666665 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0    0.0011       1.1       1      33 [.      18      50 ..      18     104 .. 0.75
   2 ?    4.9   0.0     0.022        22       2      44 ..     156     199 ..     155     252 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0011
                                   EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HH CS
                        3HCDH_N  1 kvaviGaGtmGagiaavfasagleVvlvdisee 33
                                   kva++G+G  G   a+v+   g++V ++d+ +e
  gi|119720669|ref|YP_921164.1| 18 KVAIVGSGPAGLAAASVLRCLGHKVDVFDRLPE 50
                                   79**************************99766 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.022
                                    EEEE--SCCHHHHHHHHHHT.T-EEEEE-S-HHHHHHHHHHHHH CS
                        3HCDH_N   2 vaviGaGtmGagiaavfasa.gleVvlvdiseealekalekiek 44 
                                    v+++GaG+    +a++++++ g +  l+ +++ +++ a++++++
  gi|119720669|ref|YP_921164.1| 156 VGIVGAGLTAVDVAELAVHEyGAKPILLYRRPMSVAPAKHMLKH 199
                                    9***************9988899988888888887777777765 PP

>> YjeF_N  YjeF-related protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00023      0.23      38     129 ..      24     134 ..      13     144 .. 0.80
   2 ?    1.3   0.0      0.28   2.8e+02      47      88 ..     169     210 ..     157     234 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00023
                         YjeF_N  38 nGgdglaaArhLaqegakVtv............llleeeekldedaeralellkkaggkvveekpeedleekls..apvd 103
                                    +G  glaaA  L+  g+kV+v            +++ e +  ++d+++ +++   +g+++++++++  + +  +  +++d
  gi|119720669|ref|YP_921164.1|  24 SGPAGLAAASVLRCLGHKVDVfdrlpepggmlmFTIPEFRIPKKDVRESIKAIAGIGVSFYTDTEAGRDLKVEEllEDYD 103
                                    7999**************************998888899999*******************9999988776665887777 PP

                         YjeF_N 104 lviDAllGi......glrgelreelaeliewl 129
                                     v+   +G+      g+ ge +++++++++w+
  gi|119720669|ref|YP_921164.1| 104 AVVI-STGTwkgrslGIPGENKGRVYNALDWI 134
                                    7763.244455556666666666666666666 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.28
                         YjeF_N  47 rhLaqegakVtvllleeeekldedaeralellkkaggkvvee 88 
                                    ++La +++ ++ +ll +++   + a+ +l++l+++g++++e+
  gi|119720669|ref|YP_921164.1| 169 AELAVHEYGAKPILLYRRPMSVAPAKHMLKHLEELGVQFIEN 210
                                    57888888999999999999999**************99875 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   5.9e-05     0.058      19      55 ..      18      53 ..      14      58 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.9e-05
                                   EEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--T CS
                           Thi4 19 DvvivGaGssGLtaayylakkpdlkvailersvspGG 55
                                    v+ivG+G++GL+aa +l    + kv +++r   pGG
  gi|119720669|ref|YP_921164.1| 18 KVAIVGSGPAGLAAASVLRCL-GHKVDVFDRLPEPGG 53
                                   699**************9888.999999999888877 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0    0.0054       5.4       2      28 ..      27      53 ..      26      56 .. 0.95
   2 ?    4.9   0.0     0.013        13     418     451 ..     291     322 ..     276     323 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0054
                                   HHHHHHHHHHHTTEEEEEEESSSSSBT CS
                  Amino_oxidase  2 aGLaaArqLlsaGfdVtvlEardrvGG 28
                                   aGLaaA+ L   G++V v+   + +GG
  gi|119720669|ref|YP_921164.1| 27 AGLAAASVLRCLGHKVDVFDRLPEPGG 53
                                   9********************999999 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.013
                                    CSTTEEE.SGGGCTTTTTSHHHHHHHHHHHHHHH CS
                  Amino_oxidase 418 gdprlffAGehtsreypgtvegAilSGlraAari 451
                                     +++lf AG+  +   p+ +  A++SG+ aA+ +
  gi|119720669|ref|YP_921164.1| 291 SVKGLFAAGDVAH--GPSNIGLAMRSGRLAAQKV 322
                                    589********99..9999************987 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   0.00065      0.65       1      28 [.      18      45 ..      18      81 .. 0.88
   2 ?   -1.1   0.0       0.8   7.9e+02     142     154 ..     103     115 ..      87     129 .. 0.73
   3 ?   -1.9   0.0       1.3   1.3e+03     351     364 ..     289     301 ..     281     305 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00065
                                   CEEEE-SSHHHHHHHHHHHHTT--EEEE CS
                           GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi 28
                                   +v ++G G AG++AA  +  lG+kv  +
  gi|119720669|ref|YP_921164.1| 18 KVAIVGSGPAGLAAASVLRCLGHKVDVF 45
                                   699*********************9876 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.8
                                    CEEEE--TT-BT- CS
                           GIDA 142 kavviatGtflkg 154
                                    +avvi+tGt+   
  gi|119720669|ref|YP_921164.1| 103 DAVVISTGTWKGR 115
                                    59*******6544 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.3
                                    BBSSSBTEEE-CGG CS
                           GIDA 351 etkkvkgLflAGqi 364
                                     t +vkgLf+AG++
  gi|119720669|ref|YP_921164.1| 289 MT-SVKGLFAAGDV 301
                                    44.499******97 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.11   1.1e+02     188     203 ..      13      28 ..       5      49 .. 0.66
   2 ?   -3.6   0.0       4.8   4.8e+03     328     339 ..      99     110 ..      92     111 .. 0.81
   3 ?    6.1   0.0    0.0051       5.1     192     232 ..     154     194 ..     131     214 .. 0.88
   4 ?   -2.1   0.0       1.6   1.6e+03     142     169 ..     245     272 ..     225     278 .. 0.74
   5 ?   -2.6   0.0       2.3   2.3e+03      10      22 ..     303     315 ..     301     323 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.11
                    K_oxygenase 188 llakkriaVvGsGqSa 203
                                     +++k++a+vGsG  +
  gi|119720669|ref|YP_921164.1|  13 PETGKKVAIVGSGPAG 28 
                                    5678899999987543 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 4.8
                    K_oxygenase 328 tlevdavvlATG 339
                                     +++davv++TG
  gi|119720669|ref|YP_921164.1|  99 LEDYDAVVISTG 110
                                    57899****999 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0051
                    K_oxygenase 192 kriaVvGsGqSaaeifedllrrqkkvelklvtrsealepld 232
                                     r+ +vG+G +a +++e +++++ ++ + l+ r  ++ p+ 
  gi|119720669|ref|YP_921164.1| 154 GRVGIVGAGLTAVDVAELAVHEYGAKPILLYRRPMSVAPAK 194
                                    6899******************9999999999988888875 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 1.6
                    K_oxygenase 142 geeeelearnlvlgvGtepkiPevlekl 169
                                    g+e  +e  +lv +vG +p+ P+ l++l
  gi|119720669|ref|YP_921164.1| 245 GSEFVIELDSLVAAVGLQPTPPPGLQSL 272
                                    5555566677899999999999888876 PP

  == domain 5  score: -2.6 bits;  conditional E-value: 2.3
                    K_oxygenase  10 iGpsnLsLaille 22 
                                     Gpsn++La+++ 
  gi|119720669|ref|YP_921164.1| 303 HGPSNIGLAMRSG 315
                                    59*******9865 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1    0.0007       0.7       1      41 [.      20      55 ..      20      61 .. 0.83
   2 ?    0.5   0.1      0.55   5.4e+02       2      17 ..     158     173 ..     157     182 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0007
                  NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdp.sepgagrv 41
                                   aivG Gp+Gla++  L         +++++fd+  epg g+ 
  gi|119720669|ref|YP_921164.1| 20 AIVGSGPAGLAAASVLRCL-----GHKVDVFDRlPEPG-GML 55
                                   8**********99888777.....699999**966778.765 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.55
                  NAD_binding_9   2 ivGaGprGlavlerLl 17 
                                    ivGaG +++ v+e  +
  gi|119720669|ref|YP_921164.1| 158 IVGAGLTAVDVAELAV 173
                                    9********9998655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.68u 0.33s 00:00:01.01 Elapsed: 00:00:00.52
# Mc/sec: 1909.94
//
Query:       gi|119720670|ref|YP_921165.1|  [L=491]
Description: polysaccharide biosynthesis protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-05   23.3   9.5    3.2e-05   23.3   9.5    3.1  2  Polysacc_synt_3  Polysaccharide biosynthesis protein


Domain annotation for each model (and alignments):
>> Polysacc_synt_3  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   9.5   1.8e-09   3.2e-05       1     280 [.      25     297 ..      25     301 .. 0.83
   2 ?   -2.5   2.1      0.13   2.4e+03     129     167 ..     369     412 ..     303     441 .. 0.50

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 1.8e-09
                Polysacc_synt_3   1 vLARLLspedFGvvaialvvislanlfvdmGlssaliqkedlteedlstvftfnlvlgllialvlfllapliasfynqpe 80 
                                    +++R Lspe+FG  +++ +++s a++ + +      ++++   e  +s    ++l+++l+ + + ++l p+++  ++ ++
  gi|119720670|ref|YP_921165.1|  25 IVTRSLSPEEFGAWSVISTLLSYATVATVVNYWVTRLRSRGVVEVTVSG-LALSLLFALASSGAYLVLLPYLSGEFGVAR 103
                                    68999****************9999988765555555566666665554.57889999999999**************** PP

                Polysacc_synt_3  81 lvtvlrvlalvlil.sglssvqeallrrelkFkklfkitlvssvvgvivaivlAll.glgvwALvigtllssllslvllw 158
                                     + ++++l + ++  +g+   +   +       + ++ +++  +  +++a++ Al  g ++ + +i  l+ ++l+ ++l 
  gi|119720670|ref|YP_921165.1| 104 SALLVSTLYIPVLYvNGALYSSLYAV----SPARAAVSEFLFETGKTVAAVLFALSgGVSLVSALIAVLAGHILQGAFLA 179
                                    *******9998765144444333333....33455666666666677777777776257888889999999999999999 PP

                Polysacc_synt_3 159 laskwrprlkfslkslkelfsfglklllsnllnylarnldnlliGkvlssaaLGlYsvakrlaslpvaeitsviakVlfP 238
                                    ++++  +  + s   +k+++s +   ++++   +l ++ld  li  v ++ ++++Y+v +++++l+    + v++k l+P
  gi|119720670|ref|YP_921165.1| 180 VSTRRDLVRRPSAALAKRVLSLSTFNFAAQP-STLLSSLDVPLISAVRGNLSVAYYTVVNTFSNLVGY--SGVLSKGLYP 256
                                    9999999999999*************99986.567789**************************9976..8********* PP

                Polysacc_synt_3 239 alSrlqddkkklrelylkvlrlialivlPiavglavvaellv 280
                                    +l ++ dd+++ re ++++lrl+ l+ +P+a+g+a++a  l+
  gi|119720670|ref|YP_921165.1| 257 SLLSV-DDSSAHRERIEESLRLVLLVGIPAAAGVAALAPNLL 297
                                    **887.778999**************************9876 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.13
                Polysacc_synt_3 129 aivlAllglg...vwALv..igtllssllslvllwlaskwrprl 167
                                    ++v+A+ + g   + AL+   ++l+++l+ +++l++ ++   rl
  gi|119720670|ref|YP_921165.1| 369 GVVAAVYLSGdplAVALLgkASWLAAELVVFAILLWWIRGHARL 412
                                    33333333332223344411235555555555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (491 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.71u 0.33s 00:00:01.04 Elapsed: 00:00:00.55
# Mc/sec: 2681.96
//
Query:       gi|119720671|ref|YP_921166.1|  [L=175]
Description: NUDIX hydrolase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-15   56.0   1.1    5.2e-15   55.7   1.1    1.1  1  NUDIX     NUDIX domain


Domain annotation for each model (and alignments):
>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.7   1.1   2.9e-19   5.2e-15       4     115 ..      42     150 ..      39     164 .. 0.74

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 2.9e-19
                                    EEEEEEEEETTSEEEEEEESSSSTTT.E..ESSEEECBTTSHHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEEEEEEE CS
                          NUDIX   4 ravgvvllnekgevLlvrrskkpfpg.W..elPgGkvepgEtpeeAArREleEEtGleaellellgrlhylapydgpygd 80 
                                     +v vv   e g+++ vr+  +p  + W  elP+G+ve gE + eAA REleEEtG++a  l+ +g   +++ ++g+   
  gi|119720671|ref|YP_921166.1|  42 ESVVVVPVLEGGALVFVRQW-RPAINrWivELPAGRVELGEGVLEAAGRELEEETGFKAGALREVG---SFYVSPGY--- 114
                                    57888866666689999999.6666669666**************************997777777...33444333... PP

                                    EEEEEEEEE.EEECSGCSSTSTTTEEEEEEEEHHHH CS
                          NUDIX  81 eheilyvfl.eevegelepndenevsevrwvpleel 115
                                     +e+++v++ e++    ++++++ev +v  +++ee 
  gi|119720671|ref|YP_921166.1| 115 SDELIHVVVaERLVAAKAHPEPGEVLSVVVMRPEEY 150
                                    344555555355555555557*************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       223  (0.0124379); expected 358.6 (0.02)
Passed bias filter:                      203  (0.0113224); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.33s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 1008.05
//
Query:       gi|119720672|ref|YP_921167.1|  [L=66]
Description: hypothetical protein Tpen_1769 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-05   25.3   0.0    2.2e-05   25.1   0.0    1.2  1  VAPB_antitox  Putative antitoxin


Domain annotation for each model (and alignments):
>> VAPB_antitox  Putative antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   1.2e-09   2.2e-05       1      34 [.       3      37 ..       3      57 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.2e-09
                   VAPB_antitox  1 KtIsIsdevYekLkklKr..egeSFsdvIerLlekk 34
                                   K+I++++++Y++L++lK+    +SF++v+ +L+  k
  gi|119720672|ref|YP_921167.1|  3 KSIRLRESTYRALVRLKErmGARSFDEVVAKLAY-K 37
                                   89***************97789**********74.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       200  (0.0111551); expected 358.6 (0.02)
Passed bias filter:                      180  (0.0100396); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.34s 00:00:00.84 Elapsed: 00:00:00.53
# Mc/sec: 374.63
//
Query:       gi|119720673|ref|YP_921168.1|  [L=234]
Description: short-chain dehydrogenase/reductase SDR [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-39  134.6   0.0    3.4e-39  134.3   0.0    1.0  1  adh_short       short chain dehydrogenase
    8.2e-27   94.3   0.0    9.9e-27   94.0   0.0    1.0  1  adh_short_C2    Enoyl-(Acyl carrier protein) reductase
      0.001   19.1   0.0     0.0015   18.4   0.0    1.3  1  KR              KR domain
     0.0028   17.1   0.0      0.012   15.1   0.0    1.9  2  Epimerase       NAD dependent epimerase/dehydratase family
      0.006   16.5   0.0      0.016   15.1   0.0    1.6  2  NAD_binding_10  NAD(P)H-binding
  ------ inclusion threshold ------
      0.092   11.8   0.0       0.16   11.0   0.0    1.4  1  RmlD_sub_bind   RmlD substrate binding domain


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.3   0.0   1.1e-42   3.4e-39       3     188 ..       4     184 ..       2     190 .. 0.97

  Alignments for each domain:
  == domain 1  score: 134.3 bits;  conditional E-value: 1.1e-42
                                    EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEEE CS
                      adh_short   3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldvLv 82 
                                    +++tGassGIGr+++ e  ++G++v+ ++r+e++l+e+a+e  ++   + ++ +D++d +++e++ e + +++ +l +Lv
  gi|119720673|ref|YP_921168.1|   4 AVITGASSGIGRELSAEACRRGYRVLGIGRNEAALRELASEHPDC---FAYLVLDLSDPASAERVAEFVSSEFRSLSLLV 80 
                                    89*****************************************98...******************************** PP

                                    E---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHHHHHH CS
                      adh_short  83 nNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaavagltrs 162
                                    nNAG    + + e++ +e+ ++++vN+ +++llt+++lp+m   +sG++vnv     +v +  ++ Y+A+K a++  +++
  gi|119720673|ref|YP_921168.1|  81 NNAGYGVGRGILEMTPREILDTVNVNFAAPLLLTKLLLPYME--RSGTVVNVVTAGIHVLMTRLPLYGATKIALHYASEA 158
                                    ****************************************98..9********9999*********************** PP

                                    HHHHHGGGTEEEEEEEESSBSSHHHH CS
                      adh_short 163 lakelaptgirvnavaPGlvdTdmak 188
                                    l++el+++g++   v PG+v+T + +
  gi|119720673|ref|YP_921168.1| 159 LRRELSDRGVNLLEVFPGVVETSFHE 184
                                    **********************9876 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.0   0.0   3.3e-30   9.9e-27       1     181 [.       8     185 ..       8     201 .. 0.96

  Alignments for each domain:
  == domain 1  score: 94.0 bits;  conditional E-value: 3.3e-30
                                    TTTTSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSEE..EE--TTSHHHHHHHHHHHHHHHSSEEEEEE--- CS
                   adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneeakkrveelaeelgaev..lecDVtdeeqvealveevvekfgklDilvnnag 78 
                                    Ga sgIGr++  ++ ++G++v+   +ne+a   ++ela+e++  +  l +D +d+++ e+++e v ++f +l  lvnnag
  gi|119720673|ref|YP_921168.1|   8 GASSGIGRELSAEACRRGYRVLGIGRNEAA---LRELASEHPDCFayLVLDLSDPASAERVAEFVSSEFRSLSLLVNNAG 84 
                                    899**************************9...9*******988447********************************* PP

                                    --EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSCCEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHHHHH CS
                   adh_short_C2  79 iapklkgpfletsreefdraldvnlyslfllakaalplmkeggsivnlssvgaervvpnynaygaaKaalealtrylAve 158
                                    +       +le++  e+ ++++vn+ + +ll+k +lp+m+++g +vn+   g ++ ++    yga+K al+  + +l +e
  gi|119720673|ref|YP_921168.1|  85 YGVG--RGILEMTPREILDTVNVNFAAPLLLTKLLLPYMERSGTVVNVVTAGIHVLMTRLPLYGATKIALHYASEALRRE 162
                                    ***9..************************************************************************** PP

                                    HGGGTEEEEEEEE--BHCTGGGG CS
                   adh_short_C2 159 lgpkgiRvNavspgpikTlaasg 181
                                    l ++g+    v pg+++T   ++
  gi|119720673|ref|YP_921168.1| 163 LSDRGVNLLEVFPGVVETSFHER 185
                                    ******************98665 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   5.2e-07    0.0015       2     122 ..       3     116 ..       2     131 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 5.2e-07
                                    EEEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-.EEEE----TT-HHHHHHHHHHHHHHSS CS
                             KR   2 tylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealga.evevvaaDvsdkdavealleeikaeep 80 
                                    + +itG+  g+G+el+   +++g r l  ++R+       +a ++el++       ++ +D+sd+++ e++ e +++e++
  gi|119720673|ref|YP_921168.1|   3 SAVITGASSGIGRELSAEACRRGYRVL-GIGRN-------EAALRELASEHPdCFAYLVLDLSDPASAERVAEFVSSEFR 74 
                                    569********************9866.57999.......467888888755157899********************** PP

                                    ---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHH CS
                             KR  81 pikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhel 122
                                    +++  ++ Ag    + + emt  ++   ++  +++   L +l
  gi|119720673|ref|YP_921168.1|  75 SLSLLVNNAGYGVGRGILEMTPREILDTVNVNFAAPLLLTKL 116
                                    *************99999999999887777766666666655 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   3.9e-06     0.012       2      61 ..       5      67 ..       4     111 .. 0.87
   2 ?   -0.2   0.0      0.18   5.5e+02     142     160 ..     145     163 ..     138     213 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.9e-06
                                   EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC...EEEE--TT-HHHHHHHHH CS
                      Epimerase  2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl...elveldltdrsalerlfk 61
                                   ++tGa+  iG+ l  +  ++gy+v+g+ r++ a ++ + e+        ldl d+++ er+ +
  gi|119720673|ref|YP_921168.1|  5 VITGASSGIGRELSAEACRRGYRVLGIGRNEAALRELASEHPdcfAYLVLDLSDPASAERVAE 67
                                   79****************************877777777776999888999999997777654 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.18
                                    HHHHHHHHHHHHHHHHHHH CS
                      Epimerase 142 YaaaKlageklveayaaqy 160
                                    Y+a+K+a +   ea++++ 
  gi|119720673|ref|YP_921168.1| 145 YGATKIALHYASEALRREL 163
                                    9999999999999998875 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   5.3e-06     0.016       1      57 [.       8      65 ..       8      71 .. 0.83
   2 ?   -3.4   0.0       2.6   7.8e+03      74      89 ..     196     211 ..     185     216 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5.3e-06
                                   TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHH.CTTTC.EEEE--TT-CCHHHHH CS
                 NAD_binding_10  1 GAtGkvGrllvkellargghevtalvRnpeklaele.aeegl.evvegdvtdvedlaea 57
                                   GA+ ++Gr+l +e+ +r g++v  + Rn++ l el+ +++ +   +++d++d+++ +++
  gi|119720673|ref|YP_921168.1|  8 GASSGIGRELSAEACRR-GYRVLGIGRNEAALRELAsEHPDCfAYLVLDLSDPASAERV 65
                                   9****************.5***************9844454425677899988887665 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.6
                                    HHHHHHHHHHHHHHCT CS
                 NAD_binding_10  74 deegaknivdaakeag 89 
                                     +++a+ i+da+++ +
  gi|119720673|ref|YP_921168.1| 196 ARRVAVEILDAVEKRK 211
                                    5566888888888765 PP

>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   5.5e-05      0.16       4      45 ..       5      64 ..       2      87 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 5.5e-05
                                   EEESTTSHHHHHHHHHCTTTSEEEEEE-TT..................T--TTSHHHHHH CS
                  RmlD_sub_bind  4 lvtGanGqlGseLakqlaeeglevlaltre..................eldltdaeavae 45
                                   ++tGa+  +G+eL +++ ++g+ vl+++r+                   ldl+d++++++
  gi|119720673|ref|YP_921168.1|  5 VITGASSGIGRELSAEACRRGYRVLGIGRNeaalrelasehpdcfaylVLDLSDPASAER 64
                                   79***************************9666776666666666666555555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.59u 0.36s 00:00:00.95 Elapsed: 00:00:00.54
# Mc/sec: 1296.53
//
Query:       gi|119720674|ref|YP_921169.1|  [L=1111]
Description: hypothetical protein Tpen_1771 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
        0.6   10.2   5.2        8.7    6.4   0.0    3.9  4  DUF2505     Protein of unknown function (DUF2505)


Domain annotation for each model (and alignments):
>> DUF2505  Protein of unknown function (DUF2505)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0   0.00049       8.7      59     110 ..     458     509 ..     448     529 .. 0.81
   2 ?    0.6   0.3      0.03   5.4e+02      85     129 ..     534     582 ..     521     584 .. 0.77
   3 ?   -4.0   0.1      0.81   1.5e+04      99     127 ..     749     778 ..     740     781 .. 0.64
   4 ?    2.4   0.0    0.0083   1.5e+02      92     130 ..     927     970 ..     908     984 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.00049
                        DUF2505  59 alPeavrkvvsgdlkitrteswgplsdgratgtvsasvkgapvelsGtltLe 110
                                     lP +vr  v+++l ++   +   ls+g  t ++s sv+gap++ +G + + 
  gi|119720674|ref|YP_921169.1| 458 SLPLVVRPPVNSSLAFQSLSQTLSLSPGDNTVRLSFSVTGAPAQGTGYVDVL 509
                                    6899999999999996665555566789******************988654 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.03
                        DUF2505  85 dgratgtvsasvkgapvelsGtltLepege....gtrlevegevkvkiP 129
                                     ++a+g+  ++v+ +p+ l+ t+++ + g+         + g v+v+iP
  gi|119720674|ref|YP_921169.1| 534 YDGARGKTIVDVAVQPAALTVTVEVGGLGGkaavPLSTYIVGVVEVSIP 582
                                    378899999999999**99999999996664445455567888999998 PP

  == domain 3  score: -4.0 bits;  conditional E-value: 0.81
                        DUF2505  99 apvels.GtltLepegegtrlevegevkvk 127
                                    + v++s  +++L p++ + r++ve e+ vk
  gi|119720674|ref|YP_921169.1| 749 VKVHVSaPEVVLIPNAVTVRVTVETEAVVK 778
                                    555555456777776667777777777776 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.0083
                        DUF2505  92 vsasvkgapvelsGtltLep...ege..gtrlevegevkvkiPl 130
                                    v ++ +gap   +Gt+t ++   +g+   +r++v+ge +v +  
  gi|119720674|ref|YP_921169.1| 927 VLGTLDGAPIVGNGTVTGRAyfaNGSavPARVKVDGEYSVTVAE 970
                                    55688999999999999999885444678**********99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.88u 0.34s 00:00:01.22 Elapsed: 00:00:00.54
# Mc/sec: 6165.76
//
Query:       gi|119720675|ref|YP_921170.1|  [L=369]
Description: THUMP domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-72  241.9   0.4      4e-72  241.2   0.4    1.3  1  SPOUT_MTase_2  AF2226-like SPOUT RNA Methylase fused to THUMP
    2.5e-26   92.5   0.3    5.2e-26   91.5   0.3    1.5  1  THUMP          THUMP domain
  ------ inclusion threshold ------
      0.015   15.4   0.0      0.037   14.1   0.0    1.6  1  DUF2148        Uncharacterized protein containing a ferredoxi


Domain annotation for each model (and alignments):
>> SPOUT_MTase_2  AF2226-like SPOUT RNA Methylase fused to THUMP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  241.2   0.4   6.7e-76     4e-72       1     173 []     177     353 ..     177     353 .. 0.98

  Alignments for each domain:
  == domain 1  score: 241.2 bits;  conditional E-value: 6.7e-76
                  SPOUT_MTase_2   1 kvvlvqlpYlgdlkaakelgeriGRavqafevkeliiapkekvdayelaeflrgvreGqesRyeiqkksygrevrkvpvl 80 
                                    k+v++++pYlg+ +a++ +g+riGR+vq fev++l+++p+++vday+l++flrg +eGq+sR+e+qk+sygrev k++v+
  gi|119720675|ref|YP_921170.1| 177 KLVVAHEPYLGPPDASYVMGTRIGREVQVFEVGKLYVTPVGAVDAYSLYSFLRGAFEGQRSRFELQKRSYGREVVKTEVY 256
                                    799***************************************************************************** PP

                  SPOUT_MTase_2  81 vqdlyqlvrkrrkkellivtdPeGeeisevkeelaeal.....rkakevvvlvGsReGiPkGlfrfadfvvDlaPgvtla 155
                                    vqd+yq++r+r + ++li+++PeGe++s+v+ e+a+++     ++++ev+++vG+ReG+P+Glfrfadfv+D+aPgv+++
  gi|119720675|ref|YP_921170.1| 257 VQDMYQFARSRLG-KPLIIFEPEGEPVSRVAGEVADFIirkvfKEKEEVAIMVGAREGVPTGLFRFADFVLDVAPGVVIS 335
                                    *************.9*******************9988888889************************************ PP

                  SPOUT_MTase_2 156 teyaiaaalialvtvlee 173
                                    teya+++ lial+t+l+e
  gi|119720675|ref|YP_921170.1| 336 TEYALSSGLIALATILHE 353
                                    ***************997 PP

>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.5   0.3   8.7e-30   5.2e-26      23     143 ..      40     155 ..      21     156 .. 0.87

  Alignments for each domain:
  == domain 1  score: 91.5 bits;  conditional E-value: 8.7e-30
                                    EEEEECTEEEEEETHHHHHHHHHTSTTECEEEEEEEEEESSHHHHHHHHHHHHHHHHHHCT-EEEEEEEESSSTSSSHHH CS
                          THUMP  23 rivvelkgekpeedeellkealekargiqrvipvcevceadledileaakeivkkkfeeeketFaVrvkrrgkhfeftsr 102
                                    ++v++  ++   ++eel+    e+++ +++v+++ ++c+a++e+i ++a+ i     +ee  +FaVr+ rrg+h  fts 
  gi|119720675|ref|YP_921170.1|  40 GLVLV--RPGNLKAEELARAVKERVPEAEKVFVADAECNASIEEIVRCAVGISAGISREE--SFAVRTVRRGSH-GFTSL 114
                                    33333..3344667777777888899999*****************************99..************.***** PP

                                    HHHHHHHHHHHCCTT-EE-SSS-SEEEEEEEETTEEEEEEE CS
                          THUMP 103 einrevGkaivektglkVdlenPdivvrveiikdkayisid 143
                                    ++n +vG a++e+tg++VdlenPd+v++v+i++dkay+s++
  gi|119720675|ref|YP_921170.1| 115 DVNVAVGSAVKEATGARVDLENPDKVIFVQILQDKAYLSLV 155
                                    **************************************987 PP

>> DUF2148  Uncharacterized protein containing a ferredoxin domain (DUF2148)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   6.2e-06     0.037       7      29 ..     111     133 ..     108     135 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.2e-06
                        DUF2148   7 fkaiDlGiAlgsavkvaadlrvD 29 
                                    f+++D+++A+gsavk a  +rvD
  gi|119720675|ref|YP_921170.1| 111 FTSLDVNVAVGSAVKEATGARVD 133
                                    6789******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.53
# Mc/sec: 2106.64
//
Query:       gi|119720676|ref|YP_921171.1|  [L=157]
Description: hypothetical protein Tpen_1773 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 891.88
//
Query:       gi|119720677|ref|YP_921172.1|  [L=588]
Description: hypothetical protein Tpen_1774 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0016   17.5   1.4     0.0074   15.2   1.6    1.7  1  DUF812        Protein of unknown function (DUF812)
     0.0091   16.2   0.1      0.022   15.0   0.1    1.6  1  DUF3107       Protein of unknown function (DUF3107)
  ------ inclusion threshold ------
      0.025   14.1   0.6      0.087   12.3   0.0    2.0  2  FAP206        Domain of unknown function
      0.025   15.0   4.3       0.86   10.0   2.0    3.0  3  HsbA          Hydrophobic surface binding protein A
      0.072   13.2   1.0        8.5    6.4   0.1    2.3  2  ADIP          Afadin- and alpha -actinin-Binding
       0.21   11.9   4.5        5.5    7.4   0.1    3.5  4  BLOC1_2       Biogenesis of lysosome-related organelles compl
       0.94    9.0   3.7        2.9    7.4   3.7    1.8  1  Exonuc_VII_L  Exonuclease VII, large subunit
          5    6.6   9.8        1.7    8.2   2.7    2.2  2  MscS_porin    Mechanosensitive ion channel porin domain


Domain annotation for each model (and alignments):
>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   1.6   3.3e-06    0.0074     326     468 ..     302     445 ..     260     454 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.3e-06
                         DUF812 326 kkreeeleelqeqieeleskieeleeeikklessikqveeeleeekeeneelekevklk.kktlell.pdaeeniekLqa 403
                                    ++ +  + +  +qi++l+ ++ +l+ e +++ ++ +++  +++e   + +++++ ++ k kk+l+ l  +a  n+++  +
  gi|119720677|ref|YP_921172.1| 302 EQASSYMFTAAQQIKNLSGRAGSLRGEAAAWLQNASELVAKAKEALGSASRNASLTDEKvKKVLAALnSSAYVNVSAVTS 381
                                    4455556677899*****************************9998888888876544324555555388********** PP

                         DUF812 404 lveasaqrlvelakqWekhRvplieeyrelkesksekekeaerkleeikklrekmkevaeelrqk 468
                                    l+e s+++l e++   e++++ +++e++ l+ ++se +++  +  ++++ + + ++e+a +lr+ 
  gi|119720677|ref|YP_921172.1| 382 LIEVSRNQLGEVEGLLERYKS-ILAEIEGLQGQASEAAENLASGAQRLRLMSSMLREAAYNLRSL 445
                                    *******************97.569*********************************9999875 PP

>> DUF3107  Protein of unknown function (DUF3107)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   9.7e-06     0.022      20      64 ..     334     378 ..     327     382 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 9.7e-06
                        DUF3107  20 qsadeveaaveealagdegvltLeDekGrrvlvpaakiaYVeiGs 64 
                                    q+a e++a+ +eal ++++  +L+Dek ++vl   ++ aYV++++
  gi|119720677|ref|YP_921172.1| 334 QNASELVAKAKEALGSASRNASLTDEKVKKVLAALNSSAYVNVSA 378
                                    67899*************************************987 PP

>> FAP206  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.32   7.3e+02      40      55 ..     284     299 ..     241     368 .. 0.58
   2 ?   12.3   0.0   3.9e-05     0.087       5      86 ..     378     464 ..     376     466 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.32
                         FAP206  40 aevaeeqlerlkqali 55 
                                    ++  +e+ ++l+ a  
  gi|119720677|ref|YP_921172.1| 284 SKGFGEEASMLESAAG 299
                                    2222233333333333 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 3.9e-05
                         FAP206   5 aipatreaiekeleeaqelasrytallekl.....veeseaevaeeqlerlkqalinvrqyeaylrilledveksaeeve 79 
                                    a++++ e  +++l e++ l +ry+++l ++     + +++ae+  +  +rl+ +  ++r +   lr+l e ++++a+ ++
  gi|119720677|ref|YP_921172.1| 378 AVTSLIEVSRNQLGEVEGLLERYKSILAEIeglqgQASEAAENLASGAQRLRLMSSMLREAAYNLRSLSEGLARAASLID 457
                                    6778889999*********************99988888888888999*******************************9 PP

                         FAP206  80 ellkrfe 86 
                                    ++l +++
  gi|119720677|ref|YP_921172.1| 458 SSLGKLS 464
                                    9988876 PP

>> HsbA  Hydrophobic surface binding protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.1    0.0078        17       7      59 ..     265     319 ..     261     324 .. 0.91
   2 ?   10.0   2.0   0.00038      0.86      19      85 ..     312     383 ..     308     390 .. 0.82
   3 ?    0.5   0.0      0.34   7.7e+02      64     117 ..     401     452 ..     397     454 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0078
                                    HHHHHHHHHHHHHHHHHH--S..H..HHHHHHHHHHHHHHHHHHHHHHHTS---- CS
                           HsbA   7 dittistavtaldtavnafnG..gasalpilsasnalvsaikkattdaqasaplt 59 
                                    ++t+++++vt+l + + + +   g +a  + sa+ + ++a     t+aq+  +l+
  gi|119720677|ref|YP_921172.1| 265 NLTQLEENVTQLRDLLYNLSKgfGEEASMLESAAGQAEQASSYMFTAAQQIKNLS 319
                                    799****************7767589************************99998 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00038
                                    HHHHHH--S....H...HHHHHHHHHHHHHHHHHHHHHHHTS----HHHHHHHHHHHHHCHHHHHHHHHHHH CS
                           HsbA  19 dtavnafnG....g.asalpilsasnalvsaikkattdaqasapltdeealalaqavqtLepdvkaaldali 85 
                                     +++++ +G      ++a++ l+ +++lv++ k+a   a+  a+ltde  +++++a+++ +    +a+++li
  gi|119720677|ref|YP_921172.1| 312 AQQIKNLSGragsLrGEAAAWLQNASELVAKAKEALGSASRNASLTDEKVKKVLAALNSSAYVNVSAVTSLI 383
                                    456666666666524579****************************************87777777777776 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.34
                                    HHHHHHHHHCHHHHHHHHHHHHHTHHHHHHHT-HHHHHHHHHHHHHHHHHHHHH CS
                           HsbA  64 lalaqavqtLepdvkaaldaliaKkpafdkagltslvlssLqdlkaasdaLsda 117
                                    +++++++++L+ + + a ++l++  + +    ++s+ +    +l+++s+ L+ a
  gi|119720677|ref|YP_921172.1| 401 KSILAEIEGLQGQASEAAENLASGAQRLR--LMSSMLREAAYNLRSLSEGLARA 452
                                    67999999999999999999999999999..78999999999999999999876 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1    0.0096        22      22     107 ..     264     346 ..     248     371 .. 0.84
   2 ?    6.4   0.1    0.0038       8.5      39     111 ..     377     449 ..     356     454 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0096
                           ADIP  22 lfdtatekveeniaaiinviysLlqardrdleqreslnetirkleaeierlqskierlktqleqlerelalvqakerqle 101
                                     + t   ++een+ ++ +++y L +   +++ + es + + ++ ++ +    ++i+ l+ +  +l+ e+a++ ++  +l 
  gi|119720677|ref|YP_921172.1| 264 GNLT---QLEENVTQLRDLLYNLSKGFGEEASMLESAAGQAEQASSYMFTAAQQIKNLSGRAGSLRGEAAAWLQNASELV 340
                                    4444...499************************************************************9999999888 PP

                           ADIP 102 kklktl 107
                                    +k k++
  gi|119720677|ref|YP_921172.1| 341 AKAKEA 346
                                    887765 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0038
                           ADIP  39 nviysLlqardrdleqreslnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqkl 111
                                      + sL+  ++  l + e l e+ +++ aeie lq + +   ++l++ +++l l  + +r++  +l++l++ l
  gi|119720677|ref|YP_921172.1| 377 SAVTSLIEVSRNQLGEVEGLLERYKSILAEIEGLQGQASEAAENLASGAQRLRLMSSMLREAAYNLRSLSEGL 449
                                    35899**********************************************************9999998765 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1    0.0024       5.5      56      84 ..     255     283 ..     248     289 .. 0.89
   2 ?    3.8   0.1     0.031        69      23      74 ..     363     414 ..     349     429 .. 0.67
   3 ?   -1.4   0.0       1.3     3e+03      15      46 ..     421     452 ..     415     466 .. 0.65
   4 ?   -3.0   0.0       4.2   9.4e+03      61      78 ..     566     583 ..     560     586 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0024
                        BLOC1_2  56 kyeelqpylqqidqiekqvteLeeavseL 84 
                                    +y+ l+++l ++ q+e++vt+L ++ + L
  gi|119720677|ref|YP_921172.1| 255 MYKFLESNLGNLTQLEENVTQLRDLLYNL 283
                                    578899*****************999887 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.031
                        BLOC1_2  23 klLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqv 74 
                                    k+L +lN +a  ++ ++++ ++  +++l +++ + e  ++ l +i+ ++ q 
  gi|119720677|ref|YP_921172.1| 363 KVLAALNSSAYVNVSAVTSLIEVSRNQLGEVEGLLERYKSILAEIEGLQGQA 414
                                    4566777777777777777777777777777776666666666666665554 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 1.3
                        BLOC1_2  15 leatvedyklLeklNeaasekykklkdvaasl 46 
                                    l++ ++ ++l+  + ++a+++  +l++ +a +
  gi|119720677|ref|YP_921172.1| 421 LASGAQRLRLMSSMLREAAYNLRSLSEGLARA 452
                                    55666667777777777777766666655544 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 4.2
                        BLOC1_2  61 qpylqqidqiekqvteLe 78 
                                    ++ l++i  ++++++++e
  gi|119720677|ref|YP_921172.1| 566 EEALSRIRSLKERISRIE 583
                                    567788888888888776 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   3.7    0.0013       2.9     150     269 ..     319     476 ..     241     501 .. 0.57

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0013
                   Exonuc_VII_L 150 eelerrlekaikrlleekkqrleklasrlkspeellerkrqrldeleerleralkkq.......lkkkrerleelkerlk 222
                                    +  + +l+ +++  l+++++ + k++++l s+++  +   ++++++ + l+++   +       ++ +r++l e++  l+
  gi|119720677|ref|YP_921172.1| 319 SGRAGSLRGEAAAWLQNASELVAKAKEALGSASRNASLTDEKVKKVLAALNSSAYVNvsavtslIEVSRNQLGEVEGLLE 398
                                    22223444455555666666666777777666666666666666666666664444422333333333333333332221 PP

                   Exonuc_VII_L 223 ....................ekleekkerlkklkerle..................lleekkerleeleeklealsplkv 264
                                                        e+l++ ++rl       +                   l+++ + +++   kl++l+ ++v
  gi|119720677|ref|YP_921172.1| 399 ryksilaeieglqgqaseaaENLASGAQRL-------RlmssmlreaaynlrslseGLARAASLIDSSLGKLSKLGSSSV 471
                                    233344333333221111111111111222.......2222222233333334333466666666677777777777777 PP

                   Exonuc_VII_L 265 LkrGy 269
                                    +  G+
  gi|119720677|ref|YP_921172.1| 472 MPEGF 476
                                    77776 PP

>> MscS_porin  Mechanosensitive ion channel porin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   2.7   0.00074       1.7      80     158 ..     266     345 ..     261     358 .. 0.82
   2 ?    1.9   1.5     0.061   1.4e+02      62     139 ..     358     438 ..     340     455 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00074
                     MscS_porin  80 leeLeqrllqtssqlqelqeqlaqlnsqlvelqtrperaqqqltearqrlqeirnrLnstaaage.alsqaqrtalqael 158
                                    l++Le  ++q  + l +l++   ++ s l ++  + e+a + +++a q+++ ++ r  s++ + +  l++a     +a++
  gi|119720677|ref|YP_921172.1| 266 LTQLEENVTQLRDLLYNLSKGFGEEASMLESAAGQAEQASSYMFTAAQQIKNLSGRAGSLRGEAAaWLQNASELVAKAKE 345
                                    89************************************************999887655533333455555555555555 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.061
                     MscS_porin  62 alqkkkeeaskeilaklsleeLeqrllqtssqlqelqeqlaqlnsqlvel...qtrperaqqqltearqrlqeirnrLns 138
                                     ++ kk  a  ++ a    ++  + ++   +ql e++  l  ++s l+e+   q + ++a + l++  qrl  +++ L +
  gi|119720677|ref|YP_921172.1| 358 DEKVKKVLAALNSSAYVNVSAVTSLIEVSRNQLGEVEGLLERYKSILAEIeglQGQASEAAENLASGAQRLRLMSSMLRE 437
                                    44566666666777777777888888888899999999999888877665111566677777777777777766666654 PP

                     MscS_porin 139 t 139
                                     
  gi|119720677|ref|YP_921172.1| 438 A 438
                                    4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (588 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       771  (0.043003); expected 358.6 (0.02)
Passed bias filter:                      590  (0.0329076); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.82u 0.42s 00:00:01.24 Elapsed: 00:00:00.59
# Mc/sec: 3010.10
//
Query:       gi|119720678|ref|YP_921173.1|  [L=298]
Description: ABC transporter related [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.9e-32  112.0   0.0    4.3e-32  111.5   0.0    1.3  1  ABC_tran     ABC transporter
    1.6e-08   34.8   0.6    0.00074   19.4   0.0    2.3  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    1.8e-06   27.6   0.3     0.0012   18.3   0.0    2.2  2  SMC_N        RecF/RecN/SMC N terminal domain
    0.00032   20.4   0.2    0.00068   19.3   0.2    1.5  1  AAA_29       P-loop containing region of AAA domain
    0.00073   18.3   0.5      0.029   13.0   0.0    2.7  3  AAA_13       AAA domain
     0.0019   17.8   0.0      0.025   14.1   0.0    2.2  2  AAA_25       AAA domain
     0.0036   16.4   0.3       0.12   11.4   0.1    2.1  2  T2SSE        Type II/IV secretion system protein
     0.0057   16.4   0.1        1.8    8.3   0.0    2.5  3  IstB_IS21    IstB-like ATP binding protein
  ------ inclusion threshold ------
      0.011   16.0   0.4       0.22   11.8   0.1    2.6  3  AAA_22       AAA domain
      0.012   15.5   0.0      0.023   14.6   0.0    1.4  1  RsgA_GTPase  RsgA GTPase
      0.013   14.4   0.0      0.019   13.8   0.0    1.2  1  DLIC         Dynein light intermediate chain (DLIC)
      0.014   15.8   0.2      0.027   14.9   0.2    1.7  1  AAA_16       AAA ATPase domain
      0.018   15.5   0.4      0.093   13.2   0.0    2.0  2  AAA_23       AAA domain
      0.023   14.4   0.1       0.09   12.5   0.1    1.9  2  AAA_30       AAA domain
      0.045   14.0   0.1       0.43   10.8   0.1    2.2  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
        0.1   12.1   0.0       0.16   11.5   0.0    1.3  1  cobW         CobW/HypB/UreG, nucleotide-binding domain
        0.2   11.4   0.0       0.54    9.9   0.0    1.7  2  AAA_24       AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.5   0.0   4.1e-35   4.3e-32       1     136 [.      25     174 ..      25     175 .. 0.87

  Alignments for each domain:
  == domain 1  score: 111.5 bits;  conditional E-value: 4.1e-35
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS--S-TTSBH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke....qeleslrkeigvlpqepqlfpeltv 76 
                                    lk v+l++++ge+  i+G++G+GKStLl++  gl++p +G++ + g d+++    + +++  ++ig+++q  +l ++lt+
  gi|119720678|ref|YP_921173.1|  25 LKGVNLSVNQGELAIIMGPSGSGKSTLLSIAGGLERPSKGRVIVGGVDITDldedELTKIRARKIGFVFQSFNLIRNLTA 104
                                    799***************************************999****99998666778889****************9 PP

                                    HHH..........HHHTC....HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    xxx..........xxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  77 ren..........esdee....iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                     en          +s ++    + k+l+ +glk+ ++    + p++LSgGq+qrva+aral+  p+++l+DEpt
  gi|119720678|ref|YP_921173.1| 105 VENvmmpliftgmYSWRQareiALKMLEIVGLKGHEE----KFPRQLSGGQQQRVAIARALAPSPDIILMDEPT 174
                                    999**********555553123455555555555444....456*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.2   4.1e-05     0.044       1      25 [.      37      61 ..      37     103 .. 0.71
   2 !   19.4   0.0     7e-07   0.00074     235     301 ..     145     209 ..     121     211 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.1e-05
                         AAA_21  1 lnvliGpNgsGKSnLLdaldllarl 25
                                   l+++ Gp gsGKS+LL +  +l r 
  gi|119720678|ref|YP_921173.1| 37 LAIIMGPSGSGKSTLLSIAGGLERP 61
                                   57899*************9999554 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 7e-07
                         AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQv.iltTHSpll 301
                                    r+lS G+++  a++ al+  +   +++l DEp  +L+    +r+l l+k l++  +Q  i++TH+p++
  gi|119720678|ref|YP_921173.1| 145 RQLSGGQQQRVAIARALAPSP---DIILMDEPTGSLDVDSASRVLSLVKWLNEAFGQTiIIVTHNPEI 209
                                    677889888866666666655...**************999999988855555445555*******98 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.2    0.0025       2.6      25      41 ..      36      52 ..      24      55 .. 0.84
   2 !   18.3   0.0   1.2e-06    0.0012     136     210 ..     146     218 ..      75     224 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0025
                                   SEEEEEESTTSSHHHHH CS
                                   xxxxxxxxxxxxxxxxx RF
                          SMC_N 25 sftaivGpNGSGKsnll 41
                                   ++ +i+Gp GSGKs ll
  gi|119720678|ref|YP_921173.1| 36 ELAIIMGPSGSGKSTLL 52
                                   5789**********986 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 1.2e-06
                                    CS-HHHHHHHHHHHHHHHHCCS--S.EEEECTTTTTS-HHHHHHHHHHHHHHCTT.SE.EEEE-SSHHHCCC-SCEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx.xxxxxxxxxxxxxxxxxxx RF
                          SMC_N 136 lLSgGektLvalaLlfAiqkvkpap.lyllDeidaaLDeknvkkvaellkekskn.aQ.fivislreemlekadklvg 210
                                    +LSgG+++ va+a  +A     p+p + l+De    LD    ++v +l+k  ++   Q +i+++++ e+ e a +++ 
  gi|119720678|ref|YP_921173.1| 146 QLSGGQQQRVAIARALA-----PSPdIILMDEPTGSLDVDSASRVLSLVKWLNEAfGQtIIIVTHNPEIAELATRTFY 218
                                    8*********9997765.....6665999*********************8887755626678999999999987765 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.2   6.4e-07   0.00068      15      39 ..      28      52 ..      24      55 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 6.4e-07
                         AAA_29 15 htieidlkgatlltGpsGsGKSTll 39
                                     +++++ +  +++GpsGsGKSTll
  gi|119720678|ref|YP_921173.1| 28 VNLSVNQGELAIIMGPSGSGKSTLL 52
                                   55677755599*************8 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.082        87      20      52 ..      39      70 ..      29     162 .. 0.61
   2 !   13.0   0.0   2.7e-05     0.029     527     575 ..     165     211 ..     156     226 .. 0.86
   3 ?    0.5   0.1      0.17   1.8e+02     388     451 ..     233     294 ..     226     298 .] 0.70

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.082
                         AAA_13 20 liYGwNGaGKTtLSrllrslelgetepkfangs 52
                                   +i G  G+GK+tL ++   le+ + + +   g 
  gi|119720678|ref|YP_921173.1| 39 IIMGPSGSGKSTLLSIAGGLERPS-KGRVIVGG 70
                                   79999********98888887644.33444444 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 2.7e-05
                         AAA_13 527 dkivviDDPvSSLDsnslfivfsliksrllkkkkakQ.lfiLTHnleffk 575
                                      i+ +D P  SLD +s   v sl+k      + + Q ++i THn e   
  gi|119720678|ref|YP_921173.1| 165 PDIILMDEPTGSLDVDSASRVLSLVKWLN---EAFGQtIIIVTHNPEIAE 211
                                    579***********************996...7777758999***87665 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.17
                         AAA_13 388 leeekeeakkklelhlveeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLek 451
                                    l+++++e+k++  +   +++  +ld +k k+++le+a+++ +   +  e elk le++i+ Lek
  gi|119720678|ref|YP_921173.1| 233 LADKVKELKSSAGYGSFAKV--QLDLLKIKLEALEAAAKQGKIPPEVLEGELKSLEARISKLEK 294
                                    56666666666666555544..555677778888888888888888888888888888888887 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   2.4e-05     0.025      30      51 ..      32      53 ..       5     114 .. 0.87
   2 ?    1.3   0.0       0.2   2.1e+02     164     188 ..     181     205 ..     170     207 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.4e-05
                         AAA_25 30 lpagelallaGapgtGKttlal 51
                                   +  gela+++G++g+GK+tl++
  gi|119720678|ref|YP_921173.1| 32 VNQGELAIIMGPSGSGKSTLLS 53
                                   4789***************975 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.2
                         AAA_25 164 dvgalvealeriarrtgaavllvhH 188
                                     ++++++ ++++ +++g ++++v H
  gi|119720678|ref|YP_921173.1| 181 SASRVLSLVKWLNEAFGQTIIIVTH 205
                                    46888999999999**********9 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.1   0.00011      0.12     118     149 ..      24      55 ..       3      69 .. 0.77
   2 ?    3.0   0.0     0.042        44      69     116 ..      94     151 ..      80     210 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00011
                          T2SSE 118 iaevlrkavrerglilvsGgTgsGKttllyal 149
                                    + + ++ +v++  l ++ G+ gsGK+tll ++
  gi|119720678|ref|YP_921173.1|  24 VLKGVNLSVNQGELAIIMGPSGSGKSTLLSIA 55 
                                    556677889999999**************876 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.042
                          T2SSE  69 qdarlpekgvrlrvvllPvvagealviRkksakeltlddlgaeealk..........e 116
                                    q+ +l ++ + ++ v++P++ +  ++ R+ ++ +l++ +++  +  +          +
  gi|119720678|ref|YP_921173.1|  94 QSFNLIRNLTAVENVMMPLIFTGMYSWRQAREIALKMLEIVGLKGHEekfprqlsggQ 151
                                    6677888889999***************999999988888776666624444444442 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0017       1.8      44      69 ..      32      58 ..      15      79 .. 0.79
   2 ?    5.5   0.0     0.012        12     106     153 ..     162     211 ..     144     216 .. 0.77
   3 ?   -3.0   0.0       4.8   5.1e+03      83     111 ..     233     261 ..     231     268 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0017
                      IstB_IS21 44 iekkenivllGpsGvGKshl.aialgv 69
                                   +++ e  +++GpsG GKs l +ia g 
  gi|119720678|ref|YP_921173.1| 32 VNQGELAIIMGPSGSGKSTLlSIAGGL 58
                                   56778899*********8651666555 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.012
                      IstB_IS21 106 llkvdllilDd.lgllpldqaeae.llfeviekryerrsiiitsnlpfae 153
                                       +d++++D+  g l++d+a++   l + ++++++++ ii+t n ++ae
  gi|119720678|ref|YP_921173.1| 162 APSPDIILMDEpTGSLDVDSASRVlSLVKWLNEAFGQTIIIVTHNPEIAE 211
                                    345699999996799999999886258999**************998877 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 4.8
                      IstB_IS21  83 vedLveelkrarrdgklaralkrllkvdl 111
                                    ++d v+elk   + g++a+ +  llk++l
  gi|119720678|ref|YP_921173.1| 233 LADKVKELKSSAGYGSFAKVQLDLLKIKL 261
                                    67778999999999999999888888876 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00021      0.22       5      22 ..      35      52 ..      32      56 .. 0.87
   2 ?    0.7   0.0      0.58   6.1e+02     106     134 ..      93     121 ..      77     124 .. 0.74
   3 ?   -0.7   0.0       1.5   1.6e+03      55     104 ..     125     178 ..     119     212 .. 0.50

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00021
                         AAA_22  5 agilvvtGesGtGKTtll 22
                                     + +++G+sG+GK+tll
  gi|119720678|ref|YP_921173.1| 35 GELAIIMGPSGSGKSTLL 52
                                   56789***********97 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.58
                         AAA_22 106 eealeeLrsllnlsrkgvqliLvGtpelr 134
                                     + ++ +r+l  ++   ++li+ G+++ r
  gi|119720678|ref|YP_921173.1|  93 FQSFNLIRNLTAVENVMMPLIFTGMYSWR 121
                                    6788889888888999*********9766 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.5
                         AAA_22  55 dllrellralglelkaerlsseell.ealeqalrarav...ielliiDEaqh.lr 104
                                    +++ ++l+++gl++++ ++  ++l   + ++ + ara    + +++ DE    l+
  gi|119720678|ref|YP_921173.1| 125 EIALKMLEIVGLKGHE-EKFPRQLSgGQQQRVAIARALapsPDIILMDEPTGsLD 178
                                    5566666666666666.33333333233333333333345556777776544444 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   2.2e-05     0.023      98     117 ..      34      53 ..       9      63 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.2e-05
                                    TTSEEEEECSTTSSHHHHHH CS
                    RsgA_GTPase  98 kdktsvlvGqSGvGKStLin 117
                                    ++++++++G+SG GKStL+ 
  gi|119720678|ref|YP_921173.1|  34 QGELAIIMGPSGSGKSTLLS 53 
                                    4599**************85 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.8e-05     0.019      28      78 ..      38      87 ..      28     115 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.8e-05
                           DLIC 28 vlvlGedgsGkttliaklqGveeekkGrGleylyldvkdedrddltrlnvw 78
                                    +++G +gsGk+tl++   G+e + kGr +    +d+ d d d+lt++ ++
  gi|119720678|ref|YP_921173.1| 38 AIIMGPSGSGKSTLLSIAGGLERPSKGRVIV-GGVDITDLDEDELTKIRAR 87
                                   689*************************875.6799999999999998776 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.2   2.5e-05     0.027      20      42 ..      33      53 ..      23     190 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.5e-05
                         AAA_16 20 rsgrpelvllsGesGvGKsslvr 42
                                   +  ++el ++ G+sG+GKs+l+ 
  gi|119720678|ref|YP_921173.1| 33 N--QGELAIIMGPSGSGKSTLLS 53
                                   3..44899*************95 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   8.8e-05     0.093      20      36 ..      36      52 ..      12      54 .. 0.78
   2 ?    0.3   0.1      0.82   8.7e+02     169     197 ..     254     294 ..     190     297 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.8e-05
                         AAA_23 20 gltlItGpNGaGKTTil 36
                                    l +I Gp G+GK+T+l
  gi|119720678|ref|YP_921173.1| 36 ELAIIMGPSGSGKSTLL 52
                                   588*************8 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.82
                         AAA_23 169 kkllekleqekekek............eleeleeeleeilk 197
                                     +ll+ +++++e  +            el+ le ++ +++k
  gi|119720678|ref|YP_921173.1| 254 LDLLKIKLEALEAAAkqgkippevlegELKSLEARISKLEK 294
                                    22222222222222223334445555555555555555554 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   8.5e-05      0.09      17      50 ..      34      67 ..      27      73 .. 0.79
   2 ?   -1.1   0.0       1.2   1.3e+03      88     112 ..     163     189 ..     136     246 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.5e-05
                         AAA_30 17 gdrvavltGpAGtGKttalkalreaweaaggrvi 50
                                   +  +a++ Gp G+GK+t+l+ +  + + ++grvi
  gi|119720678|ref|YP_921173.1| 34 QGELAIIMGPSGSGKSTLLSIAGGLERPSKGRVI 67
                                   4459***************988777777766666 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.2
                         AAA_30  88 pg.tllivDE.agmvdtkqlaallkaa 112
                                    p+ ++++ DE +g +d +++ ++l+ +
  gi|119720678|ref|YP_921173.1| 163 PSpDIILMDEpTGSLDVDSASRVLSLV 189
                                    444566666644555666666665554 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00041      0.43      61      88 ..     162     189 ..     120     190 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00041
                        SbcCD_C  61 epalrlvfLDEAFsklDeesiatllell 88 
                                     p+++++++DE  ++lD +s++++l+l+
  gi|119720678|ref|YP_921173.1| 162 APSPDIILMDEPTGSLDVDSASRVLSLV 189
                                    5789********************9987 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00016      0.16       3      47 ..      38      82 ..      36      96 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00016
                                   EEEEESTTCCHHHHHHHHHCT--SS-EEEEESS-SSCHCCCCCCH CS
                           cobW  3 tvltGflGsGKTtLlnhllenraglklavivNefgevsiDaellr 47
                                    ++ G+ GsGK+tLl+     ++  k  viv+ +  +++D++ l+
  gi|119720678|ref|YP_921173.1| 38 AIIMGPSGSGKSTLLSIAGGLERPSKGRVIVGGVDITDLDEDELT 82
                                   5899***********998888888888999998888888877665 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00051      0.54       6      23 ..      39      58 ..      36     120 .. 0.80
   2 ?   -2.0   0.0       2.4   2.5e+03     109     131 ..     183     206 ..     165     216 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00051
                         AAA_24  6 liyGpsgiGKTtlakel..g 23
                                   +i+Gpsg+GK+tl++ +   
  gi|119720678|ref|YP_921173.1| 39 IIMGPSGSGKSTLLSIAggL 58
                                   69***********9987661 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.4
                         AAA_24 109 eefrrllkklqelrk.nvifiahe 131
                                     ++ +l+k l+e+ + ++i++ h 
  gi|119720678|ref|YP_921173.1| 183 SRVLSLVKWLNEAFGqTIIIVTHN 206
                                    567788888877666689888885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); expected 358.6 (0.02)
Passed Vit filter:                       118  (0.00658152); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.62u 0.37s 00:00:00.99 Elapsed: 00:00:00.53
# Mc/sec: 1695.03
//
Query:       gi|119720679|ref|YP_921174.1|  [L=383]
Description: hypothetical protein Tpen_1776 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      7e-16   58.5   3.1      7e-16   58.5   3.1    3.0  3  FtsX       FtsX-like permease family
    1.8e-15   57.8   5.2    1.8e-15   57.8   5.2    2.0  2  MacB_PCD   MacB-like periplasmic core domain
  ------ inclusion threshold ------
      0.091   12.7   0.0       0.29   11.1   0.0    1.9  1  GreA_GreB  Transcription elongation factor, GreA/GreB, C-term


Domain annotation for each model (and alignments):
>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.2     0.061   3.7e+02      28      49 ..      22      43 ..      13      76 .. 0.61
   2 ?   -0.2   0.1      0.24   1.4e+03      64      84 ..     245     265 ..     206     276 .. 0.70
   3 !   58.5   3.1   1.2e-19     7e-16       1      96 []     282     376 ..     282     376 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.061
                           FtsX 28 itlvalviGlglgllaaqllsd 49
                                    +l  l+i+ g++++++  + +
  gi|119720679|ref|YP_921174.1| 22 AALTILAIASGVATFVSLRILS 43
                                   2333333333344444443333 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.24
                           FtsX  64 idlitvliiivlllllallag 84 
                                    +++++++++++l++ l+ la+
  gi|119720679|ref|YP_921174.1| 245 FKVMSLIEGLLLSTTLVGLAV 265
                                    555555555555555555543 PP

  == domain 3  score: 58.5 bits;  conditional E-value: 1.2e-19
                           FtsX   1 kreigilralGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllssvfsselkisidlitvliiivllllla 80 
                                    +rei+i+ra G ++++++l++++e+l++++ + ++G+++g++ aq+   v++s+ f  ++++ + + t+l++++l+  l 
  gi|119720679|ref|YP_921174.1| 282 QREIAIMRAGGSSRRDIALIFMLESLVYGVSGGILGIVFGIVGAQVGIEVVSSYGF-LNPPLILEPATLLLGFLLAAGLS 360
                                    59****************************************************99.*********************** PP

                           FtsX  81 llagllsiskilkkep 96 
                                    +l++l++++k++ + p
  gi|119720679|ref|YP_921174.1| 361 VLSSLYPVWKATSIRP 376
                                    ***********99876 PP

>> MacB_PCD  MacB-like periplasmic core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.8   5.2     3e-19   1.8e-15       2     191 ..      23     224 ..      22     227 .. 0.72
   2 ?   -0.2   0.4      0.18   1.1e+03      12      45 ..     261     291 ..     253     339 .. 0.57

  Alignments for each domain:
  == domain 1  score: 57.8 bits;  conditional E-value: 3e-19
                       MacB_PCD   2 lltvLGiaiGvaaviaivslgeglqasvlsqisdl..gnlvtvtpgkgsgeslsdpdvealrrevp.veavapvv..tvr 76 
                                    +lt+L+ia Gva ++++ +l  g++ +    +++   g  v+v+ + g   ++s++ +++++ ++p v+ v+p +  t +
  gi|119720679|ref|YP_921174.1|  23 ALTILAIASGVATFVSLRILSLGSRTAAMNIVQQVlpGE-VVVYGQ-GL-YDVSEDVLSDIK-RLPgVKDVTPAIlvTGY 98 
                                    8****************9999999977777666556564.445554.32.233543333444.4899******9874334 PP

                       MacB_PCD  77 gggsgeeevtvvgvdpdyfk..vfglklaeGrffteadlrggpnvvvigeelaerlf.pvGdtirl........kpftVv 145
                                     g+    +v + gv p+  k  v  +  + G++ft   l+ g++ ++ + +la++l  +vGd++++        k+++Vv
  gi|119720679|ref|YP_921174.1|  99 VGR---NAVFLLGVRPEDIKnvVSRF--VDGQPFTG--LT-GAY-AIADVGLARKLGlKVGDKVTVkppygtyfKQYEVV 169
                                    553...34789998875555233444..66988865..44.888.999*******99*****************99**** PP

                       MacB_PCD 146 Gvled.pp....gsgsalgddavylplttl........qrrsitvrlkdgadleaaaae 191
                                    G++e  ++    g  +a    +++lpl+++        ++++ +v+++dg+d+++++  
  gi|119720679|ref|YP_921174.1| 170 GIAEVaMKieeiG--AA--GGYLILPLREAqnllgrpgYVSMAVVKVEDGVDPQEVKTL 224
                                    **73344565343..33..358****7776333565545666*************9875 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.18
                       MacB_PCD  12 vaaviaivslgeglqasvlsqisdlgnlvtvtpg 45 
                                    v+  +a+++ +++++++v++  +    +++++ g
  gi|119720679|ref|YP_921174.1| 261 VGLAVAVFGTTSTITSTVREHQR---EIAIMRAG 291
                                    44555666666666666555333...23344443 PP

>> GreA_GreB  Transcription elongation factor, GreA/GreB, C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   4.9e-05      0.29      51      75 ..     145     171 ..     141     173 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.9e-05
                                    TT--TT-EE---BTTB.---.EEEEEE CS
                      GreA_GreB  51 lgkkvGdevevkapsg.kik.veIlki 75 
                                    lg kvGd+v+vk p g ++k +e++ i
  gi|119720679|ref|YP_921174.1| 145 LGLKVGDKVTVKPPYGtYFKqYEVVGI 171
                                    799*************76666999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 2229.12
//
Query:       gi|119720680|ref|YP_921175.1|  [L=191]
Description: methyltransferase type 11 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-13   51.4   0.0      2e-13   50.8   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
    1.1e-08   35.7   0.0    1.9e-08   34.9   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
    1.1e-05   25.2   0.1    6.7e-05   22.7   0.1    1.9  1  Methyltransf_31  Methyltransferase domain
    1.7e-05   24.5   0.0    2.4e-05   24.0   0.0    1.1  1  MetW             Methionine biosynthesis protein MetW
  ------ inclusion threshold ------
      0.042   14.6   0.0      0.069   13.9   0.0    1.3  1  Methyltransf_12  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.8   0.0   5.7e-17     2e-13       2      90 ..      38     121 ..      37     126 .. 0.88

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 5.7e-17
                                    EET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHHHHH CS
                Methyltransf_11   2 dvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedpekal 81 
                                    dvG+G+G+++  la r++  vgvD+++e++k++    ++++ +  +vva+a  lpf+d+ fD  v + +lhh+ +p +al
  gi|119720680|ref|YP_921175.1|  38 DVGSGRGLFLGSLAGRYGFAVGVDVDAELVKAS----PRSP-HACYVVASACMLPFRDSCFDTAVFHDSLHHFVRPFDAL 112
                                    9*************9999************444....3333.3668********************************** PP

                                    HHHHHHEEE CS
                Methyltransf_11  82 keiaRvLkp 90 
                                    +e+ Rv ++
  gi|119720680|ref|YP_921175.1| 113 EEALRVSRK 121
                                    ******887 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.0   5.3e-12   1.9e-08       2      94 ..      37     120 ..      36     122 .. 0.88

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 5.3e-12
                                    EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHH CS
                Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsded 81 
                                    +d+G G+G ++  la r+  +  +gvD+++e+++a  +      +++ +v+++a  lpf d+ fD  v   +lhh+ ++ 
  gi|119720680|ref|YP_921175.1|  37 IDVGSGRGLFLGSLAGRY--GFAVGVDVDAELVKASPRS-----PHACYVVASACMLPFRDSCFDTAVFHDSLHHFVRP- 108
                                    69***************8..8***********9976555.....5899*********************877***8754. PP

                                    HHHHHHHHHHHEE CS
                Methyltransf_25  82 lekalkeiarvLk 94 
                                      +al+e+ rv +
  gi|119720680|ref|YP_921175.1| 109 -FDALEEALRVSR 120
                                    .379999999976 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.1   1.9e-08   6.7e-05       7     105 ..      36     123 ..      34     150 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.9e-08
                Methyltransf_31   7 vlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnevlna 86 
                                    ++D+G+G G ++  la + g+    vG+D ++e ++ +   + +  +      ++++  l+  + d++fD  + ++ l++
  gi|119720680|ref|YP_921175.1|  36 LIDVGSGRGLFLGSLAGRYGF---AVGVDVDAELVKASPR-SPHACY-----VVASACMLP--FRDSCFDTAVFHDSLHH 104
                                    69**************77665...***********98877.344444.....455566677..88899************ PP

                Methyltransf_31  87 ladpdkileeiervlkpgg 105
                                    +  p ++lee+ rv ++  
  gi|119720680|ref|YP_921175.1| 105 FVRPFDALEEALRVSRKSV 123
                                    **************99654 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   6.8e-09   2.4e-05      10     109 ..      29     126 ..      21     134 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 6.8e-09
                           MetW  10 likpgsrvldlGcGdGellellkeekqvdgrGleldeegvaecvakGlsviqgdldkdlenfedksfdyvvlsqtlqatr 89 
                                     ++    ++d+G+G G +l  l+  +   + G+++d+e v+++  +  +     +   +  f+d+ fd +v+  +l    
  gi|119720680|ref|YP_921175.1|  29 EVPYSPMLIDVGSGRGLFLGSLAG-RYGFAVGVDVDAELVKAS-PRSPHACYVVASACMLPFRDSCFDTAVFHDSLHHFV 106
                                    566667789*************88.555789*****9988765.56666666777888999******************* PP

                           MetW  90 npkevldellrigrraivsf 109
                                    +p   l+e lr++r+ ++ f
  gi|119720680|ref|YP_921175.1| 107 RPFDALEEALRVSRKSVLIF 126
                                    ****************9988 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.9e-05     0.069       2      91 ..      38     117 ..      37     123 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.9e-05
                Methyltransf_12   2 eiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlkd 81 
                                    ++G+G G +l  l+ +      +gvD++++ + +a+ +  + +   ++ + l  +d+        fD+ v ++ lhh+  
  gi|119720680|ref|YP_921175.1|  38 DVGSGRGLFLGSLAGR--YGFAVGVDVDAELV-KASPRSPHACYVVASACMLPFRDS-------CFDTAVFHDSLHHFVR 107
                                    9************999..99999*********.777777777776666666666664.......8*************66 PP

                Methyltransf_12  82 irevldnirk 91 
                                    + ++l+++ +
  gi|119720680|ref|YP_921175.1| 108 PFDALEEALR 117
                                    6666665544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       278  (0.0155056); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.35s 00:00:00.95 Elapsed: 00:00:00.57
# Mc/sec: 1016.06
//
Query:       gi|119720681|ref|YP_921176.1|  [L=516]
Description: glycosyl transferase, group 1 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-15   55.2   0.1    3.3e-13   48.9   0.0    2.8  2  Phosphorylase    Carbohydrate phosphorylase
    2.4e-07   30.4   0.0    4.7e-07   29.5   0.0    1.4  1  Glycos_transf_1  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Phosphorylase  Carbohydrate phosphorylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    2.6   0.1    0.0037        33     326     385 ..     222     273 ..     210     280 .. 0.67
   2 !   48.9   0.0   3.6e-17   3.3e-13     416     608 ..     283     454 ..     274     489 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.0037
                                    HHHHHCCSEEEESSHHHHHHHHHTTTHHHHHHSGGGEEE----B-CHHHCCCTSHHHHHH CS
                  Phosphorylase 326 nlaivgshsvngvaalhsellkkevlkdfyelypekfnnktnGitprrwlllanpelael 385
                                     +  +++++v  v++ h +++++ v+ ++y    +k + +tnG++  rw+   np+l +l
  gi|119720681|ref|YP_921176.1| 222 SIGAATAYEVVMVSSKHFDIMRR-VIPQYY----HKARFVTNGVNIDRWM---NPKLRNL 273
                                    55555666666677777766643.444444....566779*********8...5666555 PP

  == domain 2  score: 48.9 bits;  conditional E-value: 3.6e-17
                                    HHHHHHHHHHHHHHHHHHHHHSS---TTSEEEEEES-SCCCCTHHHHHHHHHHHHHHHHHSTTS----EEEEEE----TT CS
                  Phosphorylase 416 elaeikqenKerlaelikekegvevdpeslfdvqvkRlheYkRqlLnvLhiitlYneikenpekkvvprtvifggkaapg 495
                                    +l+ ++ e + +l++++k++++v+vd+++++    +R+ +YkR  + v     l +e+ ++      ++ +++ggka p 
  gi|119720681|ref|YP_921176.1| 283 TLRGVRLEMRDQLVRFLKSRKQVNVDQDTFIFAWTRRVTKYKRPYFPV----RLIEELGDR------DTLFVLGGKAHPE 352
                                    67889999*********************9999**********99876....444566666......589*********9 PP

                                    -HHHHHHHHHHHHHHHHHCC-TTTCCCEEEEEETT-SHHHHHHHGGG-SEEEE---TTTSSS-SHHHHHHHTT-EEEEES CS
                  Phosphorylase 496 YalAkkiiklinsvaevvnndpevkdklkvvflenynvslaekiipaadlseqistagkeASGTgnmkfmlnGaltigtl 575
                                     +   + ++  +++ +          + +vv++++y+v  a++i+++ad+       g eASGT+ mk  +n    i++ 
  gi|119720681|ref|YP_921176.1| 353 DKEGLQYMRKFKELEK---------TRPNVVYVHDYSVESAKIILSGADVLAFTPFPGWEASGTSFMKAGVNAVPSIASR 423
                                    8666666555555543.........34469************************************************** PP

                                    STCHHHHHHHH-GGGSEEES-BHHHHHHHHHHT CS
                  Phosphorylase 576 DGanvEiaeevgeenifiFGltaeeveelkkkg 608
                                    DGa vE+       n ++FG +  e+ ++ k+ 
  gi|119720681|ref|YP_921176.1| 424 DGAVVELLTD--GVNGWLFGEDIRELIDFGKDP 454
                                    ******9865..457788998888887776654 PP

>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.0   5.3e-11   4.7e-07       4     142 ..     300     442 ..     298     469 .. 0.91

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 5.3e-11
                                    HHHHHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES......STTHHHHHHHHHHHCTTCGGGEE CS
                Glycos_transf_1   4 kkrkklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaG.....ngeeekelkklaeelelsdnvifl 78 
                                    k rk+ + +++  i+    r++k+K++   ++++++l    + ++ +v+ G     ++e +++++k  e  + + nv ++
  gi|119720681|ref|YP_921176.1| 300 KSRKQVNVDQDTFIFAWTRRVTKYKRPYFPVRLIEELG---DRDTLFVLGGkahpeDKEGLQYMRKFKELEKTRPNVVYV 376
                                    678999999999999999*****************995...5688888888**999999999999999999999****** PP

                                    ECCHSSSHHHHHHCESEEEEEESS..BSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-T CS
                Glycos_transf_1  79 gevsredleellknadifvlpsis..EgfGivllEAmaaglpviasnaggpaevvkdgetGllvkp 142
                                       s+e  + +l+ ad+++++     E+ G++ + A    +p ias  g + e+++dg++G+l+ +
  gi|119720681|ref|YP_921176.1| 377 HDYSVESAKIILSGADVLAFTPFPgwEASGTSFMKAGVNAVPSIASRDGAVVELLTDGVNGWLFGE 442
                                    *********************87666*************************************966 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (516 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.74u 0.38s 00:00:01.12 Elapsed: 00:00:00.56
# Mc/sec: 2796.60
//
Query:       gi|119720682|ref|YP_921177.1|  [L=258]
Description: zinc/iron permease [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-19   70.3  22.6    3.1e-17   62.8   8.5    2.1  2  Zip           ZIP Zinc transporter
     0.0069   15.9   0.6        0.2   11.2   0.0    2.7  2  E1-E2_ATPase  E1-E2 ATPase


Domain annotation for each model (and alignments):
>> Zip  ZIP Zinc transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   5.7     2e-06     0.018       9      97 ..      22      97 ..      14     109 .. 0.79
   2 !   62.8   8.5   3.4e-21   3.1e-17     185     332 ..     117     254 ..      98     255 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2e-06
                            Zip  9 iaililsllgllgpllvpkiskllsklllslllafavGvllgtaflhLlPealealeesqleeehthplagllvllGfllll 90
                                   + + +++ lg +++l+ +k  +      ++l+l f++Gv+l  +f +L+ +alea  +          l+   +llG l+++
  gi|119720682|ref|YP_921177.1| 22 LFVAFTTSLGAVPVLFGKKAWR-----HFTLALSFSAGVMLVSSFTSLILPALEATRSF--------ALVSSGILLGVLAIM 90
                                   3344455556666666665554.....599************************99996........578899999999999 PP

                            Zip 91 lvekllt 97
                                    v++l+ 
  gi|119720682|ref|YP_921177.1| 91 AVDRLVP 97
                                   9999986 PP

  == domain 2  score: 62.8 bits;  conditional E-value: 3.4e-21
                            Zip 185 raiilllglilHsfidGLAlG..vssssstgislfiAvllHelpeelglgaiLlkaglsrkkavllnllfaltaplGili 262
                                     ++++ l++i+H++++GLA+G  ++ s+  g+++ +A+ l  +pe++++  ++++   +rk    + +l++l+  l +++
  gi|119720682|ref|YP_921177.1| 117 KSWLIALAVIIHNIPEGLAVGtsIAYSVPLGVATGLAIGLQDIPEGFAVAFPMAQVAGPRKGLA-YGVLSGLSETLMAVL 195
                                    38********************99*******************************888777665.666666666666666 PP

                            Zip 263 GilvrsisessgaeivsgillalsaGtflYvalvellphEllnekgssslkqsllqllglllGfalmlll 332
                                    G         +  +++ +i +++s+G +lYv++ e++p E+ +e+     + +  + +g+llGf+lml+l
  gi|119720682|ref|YP_921177.1| 196 GAY-----FFTVFSALLPIGMSFSGGAMLYVTVKEVVP-EIYREQ-----SGEYAATAGFLLGFLLMLFL 254
                                    666.....5666889999********************.******.....5799**************98 PP

>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0   2.2e-05       0.2     120     174 ..      73     145 ..      63     150 .. 0.71
   2 ?    2.0   0.0     0.014   1.3e+02     153     177 ..     153     177 ..     148     180 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2.2e-05
                                    HHHHHHHHHHHHHHHHS-STTTSSTT..................HHHHHHHHHHHHHS-TTHHHHHHHHHHHH CS
                   E1-E2_ATPase 120 kvlvpvvlliallvflialllgksla..................eallralallvaaiPcaLplavplalalg 174
                                    + +++v+  i+l v++i+ + +  +                   ++ l ala+++  iP++L++ +++a+++ 
  gi|119720682|ref|YP_921177.1|  73 RSFALVSSGILLGVLAIMAVDRLVPHehllkgyegppegrrllkKSWLIALAVIIHNIPEGLAVGTSIAYSVP 145
                                    4455555555555555554433333333477777778888999999999********************9985 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.014
                                    HHHHHHS-TTHHHHHHHHHHHHHHH CS
                   E1-E2_ATPase 153 allvaaiPcaLplavplalalgarr 177
                                    a+ +  iP+++++a+p+a ++g r+
  gi|119720682|ref|YP_921177.1| 153 AIGLQDIPEGFAVAFPMAQVAGPRK 177
                                    5555669************999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.35s 00:00:00.98 Elapsed: 00:00:00.56
# Mc/sec: 1383.13
//
Query:       gi|119720683|ref|YP_921178.1|  [L=170]
Description: hypothetical protein Tpen_1780 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.35s 00:00:00.90 Elapsed: 00:00:00.54
# Mc/sec: 945.92
//
Query:       gi|119720684|ref|YP_921179.1|  [L=408]
Description: hypothetical protein Tpen_1781 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-95  319.6   0.0    2.6e-95  319.3   0.0    1.1  1  Nre_N     Archaeal Nre, N-terminal
    1.4e-35  121.5   0.1    2.4e-35  120.7   0.1    1.4  1  Nre_C     Archaeal Nre, C-terminal


Domain annotation for each model (and alignments):
>> Nre_N  Archaeal Nre, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  319.3   0.0   2.9e-99   2.6e-95       1     270 []      18     283 ..      18     283 .. 0.98

  Alignments for each domain:
  == domain 1  score: 319.3 bits;  conditional E-value: 2.9e-99
                          Nre_N   1 LcglkkcpileklravekakkkisskeleGsspPsvfVGrygYPkVsvgplvppvegdasvldspekwlglslediiklr 80 
                                    Lcg+++cp+l+ + a+e++   + ++e++G spP+vfVGr+gYP+V++ + vp +egd++ ++++e+wl+++l+d+i +r
  gi|119720684|ref|YP_921179.1|  18 LCGKSSCPVLDLWLALERVRVPE-TREIDGYSPPTVFVGRHGYPEVRFSVGVPSIEGDPALFEDQERWLSMPLRDVIGMR 96 
                                    8****************987666.9******************************************************* PP

                          Nre_N  81 lslvrgekkvkvkkakedklleeiqelalsekpvdvevelekkpkaklkfdevlaPvGpsaeleklkvaenpkvprkvek 160
                                    l +vrge +vkv+      l +e++ +als++pvdve+ lek p+a+  +d +++P+Gp++++ k++v +np+vpr++ek
  gi|119720684|ref|YP_921179.1|  97 LGIVRGEVRVKVDGR---GLSDEVRLAALSSRPVDVEILLEKAPRARPLVDLFSPPLGPAGPAAKISVLGNPSVPRSLEK 173
                                    ************976...599*********************************************************** PP

                          Nre_N 161 lveDtdlkAeeavveLyrsgvdvykiqrlLSvGlLGekkkrrlVPTrWsITAvddivgkelkkeikdlpeidevevfsge 240
                                    +++D dl A+ea++ Lyr+gv v++iqr+LSvG+LG   +rr+VPTrW+ITAvd+++++el++e+k+l+  de+ +f+++
  gi|119720684|ref|YP_921179.1| 174 AYYDYDLGAREAIYALYREGVPVHYIQRALSVGALGLGGRRRIVPTRWAITAVDSTLSQELIEEVKRLDYFDEYLFFERK 253
                                    ******************************************************************************** PP

                          Nre_N 241 ylgNrflviLaPgkwsfelvEawapgslwn 270
                                    + +N+f++i+aPg+ws+e++Eaw+p+++wn
  gi|119720684|ref|YP_921179.1| 254 FSDNTFVAIIAPGAWSYEWIEAWFPHTTWN 283
                                    *****************************8 PP

>> Nre_C  Archaeal Nre, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.7   0.1   2.7e-39   2.4e-35       1     110 []     295     404 ..     295     404 .. 0.98

  Alignments for each domain:
  == domain 1  score: 120.7 bits;  conditional E-value: 2.7e-39
                          Nre_C   1 egyegrkeyseiaGaYyaarlavleaLekikrqakvivlreitpeYwaPvGvWqvReavrkalekkpkefesleealeev 80 
                                    eg++gr++y++++G+Yyaarla++e + ++krq ++i+lrei++++++P+GvW+vRe+vr+ +++kp+++eslee+l+ +
  gi|119720684|ref|YP_921179.1| 295 EGFKGRTTYASLGGCYYAARLATAEFMLREKRQGTAILLREIYEGFFLPIGVWFVRENVRELFRSKPERYESLEEVLRRL 374
                                    6899**************************************************************************** PP

                          Nre_C  81 seklklplkkllkkskllkelkkqktLddF 110
                                    +++++lpl ++l++s+ll++l +q++++++
  gi|119720684|ref|YP_921179.1| 375 EKSTRLPLGTWLAASTLLRRLLRQSSIEAY 404
                                    **************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.35s 00:00:00.99 Elapsed: 00:00:00.55
# Mc/sec: 2237.11
//
Query:       gi|119720685|ref|YP_921180.1|  [L=281]
Description: radical SAM domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.5e-15   55.9   0.0    9.2e-15   55.4   0.0    1.2  1  Radical_SAM  Radical SAM superfamily
     0.0038   16.7   0.0     0.0055   16.2   0.0    1.2  1  DUF5131      Protein of unknown function (DUF5131)
  ------ inclusion threshold ------
       0.42   10.3   5.4         25    4.5   7.2    2.1  2  DUF1848      Domain of unknown function (DUF1848)
        7.4    6.4   7.9       0.77    9.6   0.3    2.6  3  Lsm_C        Lsm C-terminal


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.4   0.0   2.1e-18   9.2e-15       2     163 ..      28     196 ..      27     201 .. 0.79

  Alignments for each domain:
  == domain 1  score: 55.4 bits;  conditional E-value: 2.1e-18
                                    EEESEESS--TTTSCCTT.........HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM   2 vvtrgCnlrCsfCarpet.........vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlak 72 
                                    +++ gC+++C +C+ +            +r +++++  ve + +ev+ ++    +++v ++  +  ++p ++++ + ++ 
  gi|119720685|ref|YP_921180.1|  28 NPYVGCSHGCAYCYARAYtrhtevarnWGRVVYVKENAVEVLRREVRVAR----KGVVGVSTLTDPYQPVEEVEELTRRG 103
                                    6889************99*****655555555555555555555555554....55555555555566644444444444 PP

                                    TC...CCTEEEEEEECSSCHGHHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEE CS
                                    xx...xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM  73 la...vpgiritvetngtlpdeeklerllelg.vdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvd 147
                                    l+    +g+r++v t  +l+  + l+ l ++  +  v +++ ++d+e + +l++ + + +  ++ al+k  eag++  v+
  gi|119720685|ref|YP_921180.1| 104 LEvllGEGFRVSVQTKSPLV-VRDLDVLEKYAgLVDVGFTVTTLDPE-TARLVEpGAPPPASRVGALRKVSEAGVETWVF 181
                                    447*****************.**************************.******99999*****************9999 PP

                                    EEEEBTTTSHHHHHHH CS
                                    xxxxxxxxxxxxxxxx RF
                    Radical_SAM 148 rivglpGendeeleel 163
                                    + ++++G+nd+  e+l
  gi|119720685|ref|YP_921180.1| 182 VGPIMRGVNDSA-ENL 196
                                    99********84.554 PP

>> DUF5131  Protein of unknown function (DUF5131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.2e-06    0.0055       8      85 ..      24      91 ..      18     121 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.2e-06
                        DUF5131  8 datwnpvtGCtkvspgCdnCyaerlakrlkaakaekyglkltgkkaervrlseekleeplrwkkprrvfvnslsDlfh 85
                                   d ++np +GC   s gC+ Cya++ ++ ++ a++        g+    ++   e l++ +r  ++  v v++l+D ++
  gi|119720685|ref|YP_921180.1| 24 DYAYNPYVGC---SHGCAYCYARAYTRHTEVARNW-------GRVVYVKENAVEVLRREVRVARKGVVGVSTLTDPYQ 91
                                   6789******...68*******9977665555533.......333444455556666777777777777777777665 PP

>> DUF1848  Domain of unknown function (DUF1848)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   7.2    0.0055        25     253     265 .]      30      42 ..      26      42 .. 0.89
   2 ?    2.0   0.0     0.032   1.4e+02      77     108 ..     142     174 ..     114     231 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0055
                        DUF1848 253 yntClhgCvYCYA 265
                                    y  C+hgC+YCYA
  gi|119720685|ref|YP_921180.1|  30 YVGCSHGCAYCYA 42 
                                    668*********9 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.032
                        DUF1848  77 fqfTltdyeke.lepnvpsleerietfkelsek 108
                                      +Tl + ++  +ep+ p+ ++r+ +++++se 
  gi|119720685|ref|YP_921180.1| 142 TVTTLDPETARlVEPGAPPPASRVGALRKVSEA 174
                                    2345556655579****************9986 PP

>> Lsm_C  Lsm C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.2       2.2   9.8e+03      29      36 ..       4      11 ..       4      13 .. 0.83
   2 ?    9.6   0.3   0.00017      0.77      18      46 ..      57      85 ..      42      89 .. 0.78
   3 ?    1.1   0.1     0.075   3.4e+02      35      42 ..     170     177 ..     164     189 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2.2
                                   EETTTEEE CS
                          Lsm_C 29 vvldrikV 36
                                   vv++ri+V
  gi|119720685|ref|YP_921180.1|  4 VVYRRIRV 11
                                   68999999 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00017
                                   TEEEETTTTEEEETTTEEEETTEEE--SH CS
                          Lsm_C 18 lVkvieeanvvvvldrikVsekGVeGsGp 46
                                    V +++e  v v  ++++V +kGV G+ +
  gi|119720685|ref|YP_921180.1| 57 RVVYVKENAVEVLRREVRVARKGVVGVST 85
                                   5777777666666677*********9865 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.075
                                    EEETTEEE CS
                          Lsm_C  35 kVsekGVe 42 
                                    kVse+GVe
  gi|119720685|ref|YP_921180.1| 170 KVSEAGVE 177
                                    9******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.37s 00:00:00.97 Elapsed: 00:00:00.54
# Mc/sec: 1564.64
//
Query:       gi|119720686|ref|YP_921181.1|  [L=236]
Description: hypothetical protein Tpen_1783 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.045   14.2   0.3      0.063   13.7   0.3    1.2  1  DUF1180   Protein of unknown function (DUF1180)


Domain annotation for each model (and alignments):
>> DUF1180  Protein of unknown function (DUF1180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.3   3.5e-06     0.063       5     106 ..      10     117 ..       6     124 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.5e-06
                        DUF1180   5 LalvlLL..lllLaa.saadasralspaasspeaepPlpp......gataaespgkataieaksaqaaeggngssprags 75 
                                    La+ lL+  +llL a +  d+ + ++p ++ + + +P +p      g+ ++++p +a+  ++++++a++gg ++   ag 
  gi|119720686|ref|YP_921181.1|  10 LAVGLLVaaTLLLVAlAWYDVESRTAPLPRVNPTPQPRQPpagaeqGPETGGEPRNASLPSTSGSTAGQGGTAPV--AGN 87 
                                    666666644444543366777777778777777776766645555555555566666664444444444444444..555 PP

                        DUF1180  76 aadaggslavvpelssntdkpmtlqrallvl 106
                                       +ggs   + ++s++ +      r+++ l
  gi|119720686|ref|YP_921181.1|  88 L-TGGGSPCPSCNVSAPGNWSPGAWRVIYAL 117
                                    4.46777777778888877655556666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.52
# Mc/sec: 1365.04
//
Query:       gi|119720687|ref|YP_921182.1|  [L=140]
Description: zinc finger SWIM domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.053   13.2   0.1      0.086   12.5   0.1    1.3  1  SWIM      SWIM zinc finger
       0.12   12.2   0.0       0.16   11.8   0.0    1.1  1  HrpE      HrpE/YscL/FliH and V-type ATPase subunit E


Domain annotation for each model (and alignments):
>> SWIM  SWIM zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   9.6e-06     0.086       4      38 ..      93     126 ..      90     127 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.6e-06
                           SWIM   4 tlddervrlnkatCsCpefqk....ngipCkHalAvlla 38 
                                    t  ++        CsC +  +     + +C H+ Av+l+
  gi|119720687|ref|YP_921182.1|  93 TFTGD-----RYECSCYRGAYgwarRRSICTHIGAVMLE 126
                                    55555.....678***********************986 PP

>> HrpE  HrpE/YscL/FliH and V-type ATPase subunit E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   1.8e-05      0.16      78     135 ..      17      75 ..      10      83 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.8e-05
                           HrpE  78 rglqqeRealeeqlltaveqLLsdalarlLdetplaeRa.sALlRqLlksqqgearatL 135
                                    ++l++ Re ++++l  + +  L++al+ l + +p  e   +AL+R Ll + + ++ +t 
  gi|119720687|ref|YP_921182.1|  17 QALREAREIIRRTLGGQPGGSLEEALRDLYERVPREEWLrRALARYLLGTVERQGSSTW 75 
                                    789********************************997527*******99998888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.35s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 797.37
//
Query:       gi|119720688|ref|YP_921183.1|  [L=275]
Description: hypothetical protein Tpen_1785 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00016   21.9   0.0    0.00027   21.2   0.0    1.3  1  Acetyltransf_1  Acetyltransferase (GNAT) family
    0.00049   20.3   0.1    0.00098   19.3   0.1    1.5  1  Acetyltransf_6  Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0     3e-08   0.00027      28     104 ..      41     117 ..       6     128 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 3e-08
                                    HHSTTCEEEE.EEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETT CS
                 Acetyltransf_1  28 fsleaegllv.aeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlaveed 104
                                    ++  ++gl++ a   g+l+G+  ++   d  g + y +   V pey  kG+G aL  +  e+a++ g+ ++ + ++++
  gi|119720688|ref|YP_921183.1|  41 AIARNGGLVLgAFARGRLVGYSFGFLARDSQGLYLYSHHTGVIPEYEDKGVGFALKAKQREYALRMGLSRVKW-TFDP 117
                                    344666777767777*******9999999889999999******************************99977.5555 PP

>> Acetyltransf_6  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1   1.1e-07   0.00098      18     133 ..       2     113 ..       1     119 [. 0.89

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.1e-07
                 Acetyltransf_6  18 gevrfrvatdpedleallelfraqwarrpdvfadpltraflrdllaalaargalrlyvlrldgrpvAvalglrsgd.... 93 
                                    +ev++r  + +e++++++e     w++  d+     + ++l ++++       + ++ + + gr+v++ +g+ ++d    
  gi|119720688|ref|YP_921183.1|   2 EEVEVRPLEKAEEFSQAMEVQKTAWGMP-DIE--VIPSRILIAIARNG-----GLVLGAFARGRLVGYSFGFLARDsqgl 73 
                                    689999999*******************.998..78889998886664.....78999*****************97766 PP

                 Acetyltransf_6  94 rlyywlggydpelaklspgllllweliedaaeeGlrrfdl 133
                                     ly + +g+ pe+++ ++g  l ++  e a + Gl+r+ +
  gi|119720688|ref|YP_921183.1|  74 YLYSHHTGVIPEYEDKGVGFALKAKQREYALRMGLSRVKW 113
                                    677899999*************************999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       248  (0.0138323); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 1699.89
//
Query:       gi|119720689|ref|YP_921184.1|  [L=221]
Description: glycerophosphoryl diester phosphodiesterase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-29  101.9   0.0    2.6e-27   96.2   0.0    2.0  1  GDPD      Glycerophosphoryl diester phosphodiesterase family
  ------ inclusion threshold ------
      0.084   13.4   0.1         22    5.7   0.1    2.5  2  GDPD_2    Glycerophosphoryl diester phosphodiesterase family


Domain annotation for each model (and alignments):
>> GDPD  Glycerophosphoryl diester phosphodiesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.2   0.0   2.9e-31   2.6e-27      13     258 ..       1     208 [.       1     209 [. 0.85

  Alignments for each domain:
  == domain 1  score: 96.2 bits;  conditional E-value: 2.9e-31
                                    HHHHHHHHHTT-SEEEEEEEE-TTS-EEE-SSSBSTTTCSCCCH.BGGGS-HHHHHTSTECCTTCCCCSCCCSSGCCB.. CS
                           GDPD  13 lesfakAaelGadyiEfDvqlTkDgvpVvlHDfnldrttdvagrldvkdltleelkrldkiakenkaqlsenrvrlefpf 92 
                                    +++f++A+ +Gad++E+Dv+ T+Dg +V++HD +l+rtt+++g  +v++ t++ +++ld ++++ ++ + + +v      
  gi|119720689|ref|YP_921184.1|   1 MPAFEEAVRAGADFVETDVHRTRDGALVCIHDATLNRTTNGDG--YVSEKTVDYVRSLD-AGSWFSGRYAGVQV------ 71 
                                    689****************************************..**************.88999888888887...... PP

                                    .BHHHHHHHHHHCCSEEEEEEECCCCCCCHHHHHHTCHHHCCCCCSCHHTT..STTCSCEEEESTHHHHHHHHHTCTCTE CS
                           GDPD  93 ptleevlkkpqnvglnieikipmlseakeeeelqivkeilksvdeilkkvlkkadkrkvifssfnpdilkllrekqpklp 172
                                    p +ee+l+ +++  + + +++++            + e++  + +++        + + ++ s  ++ l++++e++p   
  gi|119720689|ref|YP_921184.1|  72 PLFEEFLDYIASTSAGVFVEVKVPGI---------EEEVVGRILQWG-------LEERAVVLSGYWSVLRRVKELDP--G 133
                                    89999998755555555555554433.........333444555555.......56667778999************..7 PP

                                    EEEEEHHHHHHC-E.EECHCCCCCCCTCCCCHHCCCHCCCEB.CHHHHHHHTT-EEEEBSB-THSHHHHHHHHCCC-SEE CS
                           GDPD 173 llflteggteaeadssleraakfakadallgevsavaeglgdpdlVkraksrglvvhvytvnnedeeemkrlleagvdgv 252
                                    ++ l + ++++++      a+k+a+  ++++  ++ +++        +a++rgl v v++vn    e+  r++e+g d v
  gi|119720689|ref|YP_921184.1| 134 IATLADLPSPSPQS--ISSAVKVANIVSIHAALFEEEHA-------LQAHRRGLLVNVWGVNGC--EDALRVVELGADFV 202
                                    78888877777777..44799999999999999999999.......59****************..9999********** PP

                                    EES-HH CS
                           GDPD 253 itDfpd 258
                                     +D+p+
  gi|119720689|ref|YP_921184.1| 203 TVDNPG 208
                                    ****98 PP

>> GDPD_2  Glycerophosphoryl diester phosphodiesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0    0.0038        35      14      28 ..       5      19 ..       3      19 .. 0.87
   2 ?    5.7   0.1    0.0025        22       2      29 ..     180     207 ..     180     208 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0038
                         GDPD_2 14 relvgaGVdgInTDd 28
                                    e+v+aG+d++ TD+
  gi|119720689|ref|YP_921184.1|  5 EEAVRAGADFVETDV 19
                                   589********9996 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0025
                         GDPD_2   2 vrfWttddeavwrelvgaGVdgInTDdl 29 
                                    v  W+++   +    v++G+d+++ D++
  gi|119720689|ref|YP_921184.1| 180 VNVWGVNGCEDALRVVELGADFVTVDNP 207
                                    567888888889999********99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       245  (0.013665); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1360.93
//
Query:       gi|119720690|ref|YP_921185.1|  [L=628]
Description: peptidase S16, lon domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-14   53.1   0.2    5.8e-14   52.1   0.2    1.4  1  Lon_C     Lon protease (S16) C-terminal proteolytic domain
    0.00031   20.6   0.0     0.0007   19.4   0.0    1.6  1  ChlI      Subunit ChlI of Mg-chelatase


Domain annotation for each model (and alignments):
>> Lon_C  Lon protease (S16) C-terminal proteolytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.1   0.2   6.4e-18   5.8e-14      91     170 ..     100     179 ..      43     189 .. 0.84

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 6.4e-18
                                    TTT-EEEEEE-S-B-GGGGGGGHHHHHHHHHHHHTS--B-TTBEE--EE-TT-BEE--S-HHHHHHHHHHTT-SBEEEEG CS
                          Lon_C  91 fekkdihihvPeGavPkdGPsaGvtlatalvslltgkkvrkdvamtGeitLrGrvlpiGGlkekllaakragikkvilPk 170
                                    f++++ +  v   av   GPsaGv++a+a++s+ltgk++++ v +tG i+  G v p+GG+ ek  a  +ag k  ++P 
  gi|119720690|ref|YP_921185.1| 100 FSQYNYYFKVQGDAVIVGGPSAGVAMAVAVYSALTGKPINRTVFVTGMISPDGTVGPVGGVFEKAQAVAQAGAKVFLVPP 179
                                    66677788888899999*********************************************************999995 PP

>> ChlI  Subunit ChlI of Mg-chelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   7.9e-08    0.0007      62     119 ..     122     179 ..      99     181 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 7.9e-08
                           ChlI  62 DLpiAigilaaleqieaeeetlflGeLsldGslrpvkgvlpialaakkegikkvivpk 119
                                      ++A+++++al  ++ ++++++ G +s dG++ pv gv++ a a++++g k ++vp 
  gi|119720690|ref|YP_921185.1| 122 GVAMAVAVYSALTGKPINRTVFVTGMISPDGTVGPVGGVFEKAQAVAQAGAKVFLVPP 179
                                    579*****************************************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (628 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.46
# Mc/sec: 4079.18
//
Query:       gi|119720691|ref|YP_921186.1|  [L=362]
Description: hypothetical protein Tpen_1788 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.8e-05   22.6   7.3        0.1   12.7   0.6    3.1  3  PTS_IIA         PTS system, Lactose/Cellobiose specific IIA s
     0.0039   17.5   5.0       0.13   12.6   0.1    3.7  4  DUF1771         Domain of unknown function (DUF1771)
  ------ inclusion threshold ------
      0.015   15.2  10.3       0.55   10.2   0.3    3.1  2  YfdX            YfdX protein
       0.13   12.6  11.6       0.35   11.2   0.2    3.2  4  DBINO           DNA-binding domain
       0.15   12.8   7.0         15    6.3   0.1    4.3  4  Cytochrom_B562  Cytochrome b562
       0.23   11.6   6.6        3.4    7.8   0.4    4.3  4  DUF4363         Domain of unknown function (DUF4363)
       0.33   11.2   7.5        6.4    7.1   0.4    3.3  3  FliS            Flagellar protein FliS
       0.73    9.2   6.9       0.14   11.6   0.8    2.6  3  DUF4735         Domain of unknown function (DUF4735)
        1.1    9.1   6.2       0.46   10.3   1.3    2.8  3  DASH_Duo1       DASH complex subunit Duo1
        1.3    9.3   6.1       0.95    9.6   0.2    3.1  4  TPR_22          Tetratricopeptide repeat
        2.1    7.7  11.3         11    5.4   9.7    2.5  2  Rogdi_lz        Rogdi leucine zipper containing protein


Domain annotation for each model (and alignments):
>> PTS_IIA  PTS system, Lactose/Cellobiose specific IIA subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.1     7e-05      0.11      12      45 ..      74     107 ..      68     128 .. 0.89
   2 !   12.7   0.6   6.2e-05       0.1      12      49 ..     165     202 ..     163     223 .. 0.88
   3 ?   -1.4   0.1       1.5   2.5e+03      10      46 ..     313     349 ..     305     351 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7e-05
                        PTS_IIA  12 eArslameAlkaakegdfeeaeellkeAeeelke 45 
                                    +Ars + +Al+ +++gd++  +el++eA+ el++
  gi|119720691|ref|YP_921186.1|  74 TARSTLQQALQTLQSGDVNGTKELVREASAELRS 107
                                    69***************************99975 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 6.2e-05
                        PTS_IIA  12 eArslameAlkaakegdfeeaeellkeAeeelkeAhka 49 
                                    eA sl+ +Al+++k++++ +a +l+++A+ ++keA ++
  gi|119720691|ref|YP_921186.1| 165 EASSLLDQALNSLKQNNMAQASQLVEQARLKVKEAERS 202
                                    5889999****************************876 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 1.5
                        PTS_IIA  10 aGeArslameAlkaakegdfeeaeellkeAeeelkeA 46 
                                    aGe  + a +  +aa+++d+++++el ++ ++ l eA
  gi|119720691|ref|YP_921186.1| 313 AGEISKVAAQLRDAASKRDLQKVRELSAQLRDLLVEA 349
                                    5666666667777888888888888877776666666 PP

>> DUF1771  Domain of unknown function (DUF1771)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1     0.024        40      11      43 ..      71     103 ..      63     129 .. 0.77
   2 ?   -0.6   0.2       1.1   1.7e+03      12      55 ..     103     146 ..     100     148 .. 0.71
   3 !   12.6   0.1     8e-05      0.13      10      50 ..     161     201 ..     157     202 .. 0.90
   4 ?   -1.4   0.1         2   3.2e+03      23      43 ..     324     344 ..     312     353 .. 0.66

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.024
                        DUF1771  11 harkrnelfekAaeAyrrGdgaaAkelseqGke 43 
                                    +  + ++ +++A +  ++Gd    kel++++  
  gi|119720691|ref|YP_921186.1|  71 QISTARSTLQQALQTLQSGDVNGTKELVREASA 103
                                    566788999***********9999999888654 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.1
                        DUF1771  12 arkrnelfekAaeAyrrGdgaaAkelseqGkehgekmeeanreA 55 
                                    a++r+ +++  +e ++r + +aA+ l  + + ++++ +++   A
  gi|119720691|ref|YP_921186.1| 103 AELRSVALQLYKEIREREKLRAAHLLEVEIRVLQNQLRALRNVA 146
                                    56677777777778888888888888888887777777766665 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 8e-05
                        DUF1771  10 eharkrnelfekAaeAyrrGdgaaAkelseqGkehgekmee 50 
                                    ++ ++ ++l+++A +  ++++ a+A++l+eq++   +++e+
  gi|119720691|ref|YP_921186.1| 161 RLIDEASSLLDQALNSLKQNNMAQASQLVEQARLKVKEAER 201
                                    6778899**************************99988886 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 2
                        DUF1771  23 aeAyrrGdgaaAkelseqGke 43 
                                    ++A ++ d ++ +els+q ++
  gi|119720691|ref|YP_921186.1| 324 RDAASKRDLQKVRELSAQLRD 344
                                    456666777777777777555 PP

>> YfdX  YfdX protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.3   0.00034      0.55       5      41 ..      79     115 ..      75     147 .. 0.77
   2 ?    7.2   4.7    0.0028       4.6       5      43 ..     170     208 ..     166     346 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00034
                                    HHHHHHHHCTT-HHHHHHHHHHHHHHHTS-HHHHHCC CS
                           YfdX   5 iqkArlaldqgdtkeAkkllekAqgkleaaladdpkl 41 
                                    +q+A++ l+ gd  ++k+l+ +A+++l  +  +  k 
  gi|119720691|ref|YP_921186.1|  79 LQQALQTLQSGDVNGTKELVREASAELRSVALQLYKE 115
                                    79***********************998776555444 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0028
                                    HHHHHHHHCTT-HHHHHHHHHHHHHHHTS-HHHHHCCB- CS
                           YfdX   5 iqkArlaldqgdtkeAkkllekAqgkleaaladdpklvk 43 
                                    +++A++ l+q+++++A +l+e+A+ k ++a+    +l +
  gi|119720691|ref|YP_921186.1| 170 LDQALNSLKQNNMAQASQLVEQARLKVKEAERSIWSLAV 208
                                    689************************999876655544 PP

>> DBINO  DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   0.00022      0.35     100     132 ..      28      60 ..      25      62 .. 0.88
   2 ?   -1.6   0.1         2   3.2e+03      44      47 ..     114     117 ..      72     148 .. 0.55
   3 ?    8.5   0.3    0.0015       2.4      26      83 ..     172     231 ..     156     249 .. 0.68
   4 ?   -2.7   0.1       4.4   7.2e+03      41      50 ..     322     331 ..     295     345 .. 0.49

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00022
                          DBINO 100 eeeereakRqqrkLnFLitQTELYshFiskklk 132
                                    ++   e++R qr + FL++QT    +F++ +++
  gi|119720691|ref|YP_921186.1|  28 QQASTEQERLQRHISFLLNQTARLENFVNSRVS 60 
                                    56789****************999999999876 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2
                          DBINO  44 revr 47 
                                    +e+r
  gi|119720691|ref|YP_921186.1| 114 KEIR 117
                                    1111 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0015
                          DBINO  26 qaekkrlanakkvaklcarevrrkasksska..tkdlqlrakrlvremllfwkknekeer 83 
                                    qa ++ ++n+   a++  +++r k+++++++  +  +qlr+kr+ +++ lf   + k  +
  gi|119720691|ref|YP_921186.1| 172 QALNSLKQNNMAQASQLVEQARLKVKEAERSiwSLAVQLRSKRAEKDLELFANASRKVYE 231
                                    44444444444444444455566666666552256899*************988887655 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 4.4
                          DBINO  41 lcarevrrka 50 
                                    + +  + ++ 
  gi|119720691|ref|YP_921186.1| 322 QLRDAASKRD 331
                                    2222222222 PP

>> Cytochrom_B562  Cytochrome b562
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1     0.069   1.1e+02      52      89 ..      63     100 ..      17     107 .. 0.71
   2 ?    6.3   0.1    0.0091        15      61      89 ..     163     191 ..     131     198 .. 0.87
   3 ?    1.5   0.0      0.29   4.8e+02      67      89 ..     251     273 ..     212     278 .. 0.69
   4 ?    2.2   0.0      0.18   2.9e+02       7      38 ..     317     348 ..     306     354 .. 0.63

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.069
                 Cytochrom_B562  52 eeqkdYqeGldklidqldkaealakagkleeakaalke 89 
                                       +   + +++  ++l++a + +++g+++  k++++e
  gi|119720691|ref|YP_921186.1|  63 TLKELLLQQISTARSTLQQALQTLQSGDVNGTKELVRE 100
                                    445555667778889999***********999999987 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0091
                 Cytochrom_B562  61 ldklidqldkaealakagkleeakaalke 89 
                                    +d+  + ld+a +++k++++++a++++++
  gi|119720691|ref|YP_921186.1| 163 IDEASSLLDQALNSLKQNNMAQASQLVEQ 191
                                    67888889*****************9987 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.29
                 Cytochrom_B562  67 qldkaealakagkleeakaalke 89 
                                     + ++++l+ +gk  +a +++++
  gi|119720691|ref|YP_921186.1| 251 RISEIKKLISEGKHVAALEEIRK 273
                                    46677777888877777655543 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.18
                 Cytochrom_B562   7 kqmkkalkqvakaddaeelkkalkelraaaed 38 
                                    ++++++l+ +a+  d +++++  ++lr +  +
  gi|119720691|ref|YP_921186.1| 317 SKVAAQLRDAASKRDLQKVRELSAQLRDLLVE 348
                                    44555666666666666666666666665555 PP

>> DUF4363  Domain of unknown function (DUF4363)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1       0.1   1.7e+02      10      44 ..      71     105 ..      65     144 .. 0.81
   2 ?    7.8   0.4    0.0021       3.4       6      47 ..     158     199 ..     154     211 .. 0.85
   3 ?    0.6   0.0      0.37     6e+02      66      87 ..     251     272 ..     244     278 .. 0.58
   4 ?   -0.2   0.0      0.65   1.1e+03      12      42 ..     314     344 ..     304     350 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.1
                        DUF4363  10 stdelsekleeleeaienedweeakekleelekeW 44 
                                    ++++  ++l+++ + ++++d + +ke ++e++ e 
  gi|119720691|ref|YP_921186.1|  71 QISTARSTLQQALQTLQSGDVNGTKELVREASAEL 105
                                    56667778888888888888888888888877664 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0021
                        DUF4363   6 ylkkstdelsekleeleeaienedweeakekleelekeWekk 47 
                                     +++ +de s+ l+++ +++++++ ++a + +e+++ + ++ 
  gi|119720691|ref|YP_921186.1| 158 NVTRLIDEASSLLDQALNSLKQNNMAQASQLVEQARLKVKEA 199
                                    578899***************************998776665 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.37
                        DUF4363  66 slaklkayietedkeealaela 87 
                                     ++++k++i+++    al+e++
  gi|119720691|ref|YP_921186.1| 251 RISEIKKLISEGKHVAALEEIR 272
                                    4455555555555555555544 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 0.65
                        DUF4363  12 delsekleeleeaienedweeakekleelek 42 
                                     e+s+   +l++a+++ d ++  e +++l++
  gi|119720691|ref|YP_921186.1| 314 GEISKVAAQLRDAASKRDLQKVRELSAQLRD 344
                                    4566666777777777777777777777766 PP

>> FliS  Flagellar protein FliS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.3    0.0053       8.7       4      53 ..      54     103 ..      51     124 .. 0.88
   2 ?    7.1   0.4    0.0039       6.4      21      67 ..     169     215 ..     156     265 .. 0.62
   3 ?   -0.3   0.1      0.75   1.2e+03      83     107 ..     321     345 ..     290     348 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0053
                                    CSHCCHHH-HHHHHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHH CS
                           FliS   4 YkqnsvetaspeklvlmLydgalkflkrakeaieekdiekkgeaiskaqd 53 
                                    + +++v++a+ ++l+l  +  a + l++a + ++++d+  ++e +  a +
  gi|119720691|ref|YP_921186.1|  54 FVNSRVSNATLKELLLQQISTARSTLQQALQTLQSGDVNGTKELVREASA 103
                                    56899*********************************999998887765 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0039
                                    HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHHHTCCTTTS CS
                           FliS  21 LydgalkflkrakeaieekdiekkgeaiskaqdIiseLrasLdlekg 67 
                                    L+d+al++lk+   a +++ +e+++ +++ a + i  L   L  ++ 
  gi|119720691|ref|YP_921186.1| 169 LLDQALNSLKQNNMAQASQLVEQARLKVKEAERSIWSLAVQLRSKRA 215
                                    67888888888888888777888888888888888888888866443 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.75
                                    HHHHHHHHCT-HHHHHHHHHHHHHH CS
                           FliS  83 rrlleanlkkdaekldeviklleel 107
                                     +l +a  k+d +k++e   +l++l
  gi|119720691|ref|YP_921186.1| 321 AQLRDAASKRDLQKVRELSAQLRDL 345
                                    4566666666666666666666655 PP

>> DUF4735  Domain of unknown function (DUF4735)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.2      0.68   1.1e+03      18      20 ..      70      72 ..      26     121 .. 0.57
   2 ?   11.6   0.8   8.5e-05      0.14       6     100 ..     132     226 ..     128     239 .. 0.70
   3 ?   -0.7   0.0      0.47   7.6e+02      13      48 ..     316     349 ..     308     357 .. 0.65

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.68
                        DUF4735 18 eel 20
                                   +++
  gi|119720691|ref|YP_921186.1| 70 QQI 72
                                   222 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 8.5e-05
                        DUF4735   6 lrvlegqlkaileeleassslssqlldrikqlskkaselidkalpylaksdpeyyeefsklvskp.wklpkrlr...kld 81 
                                    +rvl+ ql+a+ + +  +      + +++++l+++as+l+d+al+ l++++ ++ +   +lv+++  k++++ r   +l 
  gi|119720691|ref|YP_921186.1| 132 IRVLQNQLRALRNVA-SRLGSLGADTSNVTRLIDEASSLLDQALNSLKQNNMAQAS---QLVEQArLKVKEAERsiwSLA 207
                                    79*******999555.88888899999************************99987...555555555555555224444 PP

                        DUF4735  82 eslilsekepvksfseekS 100
                                     +l  ++ e+   +  + S
  gi|119720691|ref|YP_921186.1| 208 VQLRSKRAEKDLELFANAS 226
                                    4444444433333555555 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.47
                        DUF4735  13 lkaileeleassslssqlldrikqlskkaselidka 48 
                                    + +++ +l  ++ +s+++l+++++ls ++++l+ +a
  gi|119720691|ref|YP_921186.1| 316 ISKVAAQL--RDAASKRDLQKVRELSAQLRDLLVEA 349
                                    55555444..66677777777777777777665544 PP

>> DASH_Duo1  DASH complex subunit Duo1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1       0.9   1.5e+03      10      30 ..      70      91 ..      64     104 .. 0.53
   2 ?   10.3   1.3   0.00028      0.46       2      55 ..     128     181 ..     127     191 .. 0.91
   3 ?   -1.7   0.0       1.5   2.5e+03      16      26 ..     316     326 ..     293     346 .. 0.55

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.9
                      DASH_Duo1 10 rkinevienviesLkkak.sni 30
                                   ++i ++ ++++++L++ + +++
  gi|119720691|ref|YP_921186.1| 70 QQISTARSTLQQALQTLQsGDV 91
                                   4444444444445554444444 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00028
                      DASH_Duo1   2 LekEleqLrkinevienviesLkkaksniervketvestntLLdkWirIlsqte 55 
                                    Le E++ L++  +++ nv + L +   ++++v++ ++++++LLd+  + l+q++
  gi|119720691|ref|YP_921186.1| 128 LEVEIRVLQNQLRALRNVASRLGSLGADTSNVTRLIDEASSLLDQALNSLKQNN 181
                                    788999**************************************9888777776 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 1.5
                      DASH_Duo1  16 ienviesLkka 26 
                                    i++v ++L++a
  gi|119720691|ref|YP_921186.1| 316 ISKVAAQLRDA 326
                                    34444444444 PP

>> TPR_22  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       1.8   2.9e+03       5      22 ..      64      81 ..      31      95 .. 0.60
   2 ?   -1.3   0.1       1.5   2.4e+03       5      33 ..      64      92 ..      60     115 .. 0.72
   3 ?    9.6   0.2   0.00058      0.95       8      50 ..     158     200 ..     153     210 .. 0.88
   4 ?    0.8   0.1      0.32   5.3e+02      13      50 ..     294     331 ..     285     340 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.8
                         TPR_22  5 laeklgrhlitpqealkk 22
                                   l+e l +++ t++ +l++
  gi|119720691|ref|YP_921186.1| 64 LKELLLQQISTARSTLQQ 81
                                   334444444444444444 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.5
                         TPR_22  5 laeklgrhlitpqealkkLlkilskkeqe 33
                                   l+e l +++ t++ +l++ l+ l++ + +
  gi|119720691|ref|YP_921186.1| 64 LKELLLQQISTARSTLQQALQTLQSGDVN 92
                                   56777788888888888888877766554 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00058
                         TPR_22   8 klgrhlitpqealkkLlkilskkeqeevsklvsrerlklsand 50 
                                    +++r + +++  l++ l+ l++++  + s+lv + rlk++ ++
  gi|119720691|ref|YP_921186.1| 158 NVTRLIDEASSLLDQALNSLKQNNMAQASQLVEQARLKVKEAE 200
                                    567777788999**************************99765 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 0.32
                         TPR_22  13 litpqealkkLlkilskkeqeevsklvsrerlklsand 50 
                                    l +  e +++++k+ +++   e+sk+ ++ r   s+ d
  gi|119720691|ref|YP_921186.1| 294 LAREGERVASVIKVCNATLAGEISKVAAQLRDAASKRD 331
                                    5556677889999*************999886666655 PP

>> Rogdi_lz  Rogdi leucine zipper containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   9.7    0.0065        11      66     116 ..      50     142 ..      37     218 .. 0.66
   2 ?   -2.1   0.0       1.3   2.1e+03     117     134 ..     310     327 ..     263     347 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0065
                       Rogdi_lz  66 rlrtlpkltlklnptkpivleqLtdlrtlltqaldlLd.........ltlktgdelsks..................... 115
                                    rl+++ +  ++ ++ k++ l+q++++r+ l+qal++L+         l  ++++    +                     
  gi|119720691|ref|YP_921186.1|  50 RLENFVNSRVSNATLKELLLQQISTARSTLQQALQTLQsgdvngtkeLVREASA----Elrsvalqlykeirereklraa 125
                                    45555566666666789*********************8776644442222223....1344455555555666666665 PP

                       Rogdi_lz 116 ................a 116
                                                     
  gi|119720691|ref|YP_921186.1| 126 hlleveirvlqnqlraL 142
                                    55555544444444440 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.3
                       Rogdi_lz 117 qflssqLrllleslseAk 134
                                    ++l+ ++ +++++l++A 
  gi|119720691|ref|YP_921186.1| 310 ATLAGEISKVAAQLRDAA 327
                                    444444444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1623  (0.0905237); expected 358.6 (0.02)
Passed bias filter:                      603  (0.0336327); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.66u 0.37s 00:00:01.03 Elapsed: 00:00:00.55
# Mc/sec: 1964.91
//
Query:       gi|119720692|ref|YP_921187.1|  [L=273]
Description: 4Fe-4S ferredoxin iron-sulfur binding domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.2e-14   51.5   9.6    2.3e-10   40.3   3.5    4.7  5  Fer4_5    4Fe-4S binding domain
    1.2e-13   50.3  20.6      7e-10   38.3   4.2    4.5  4  Fer4      4Fe-4S binding domain
    1.6e-08   35.0  16.9    2.2e-06   28.1   4.4    3.4  3  Fer4_7    4Fe-4S dicluster domain
      2e-08   34.3  10.9      2e-08   34.3  10.9    2.6  3  Fer4_9    4Fe-4S dicluster domain
    5.9e-08   32.5  21.8    2.6e-07   30.4   4.0    3.2  3  Fer4_6    4Fe-4S binding domain
    2.7e-07   30.6   9.4    2.7e-07   30.6   9.4    3.3  4  Fer4_21   4Fe-4S dicluster domain
    7.1e-07   30.1  14.7    0.00015   22.6   4.9    4.0  4  Fer4_16   4Fe-4S double cluster binding domain
    1.4e-06   28.3  13.1    1.4e-06   28.3  13.1    2.9  3  Fer4_10   4Fe-4S dicluster domain
    8.6e-06   25.5   3.0    8.6e-06   25.5   3.0    3.9  4  Fer4_2    4Fe-4S binding domain
    0.00035   20.7   9.1    0.00035   20.7   9.1    2.4  3  Fer4_18   4Fe-4S dicluster domain
     0.0018   18.6   4.1     0.0018   18.6   4.1    4.1  4  Fer4_4    4Fe-4S binding domain
     0.0048   17.8   6.0     0.0048   17.8   6.0    4.7  4  Fer4_3    4Fe-4S binding domain
  ------ inclusion threshold ------
      0.074   13.6   3.7      0.074   13.6   3.7    2.9  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
       0.13   13.0   1.2       0.13   13.0   1.2    2.9  2  Fer4_15   4Fe-4S single cluster domain
       0.54   10.8  21.8         11    6.6  14.4    3.7  4  Fer4_8    4Fe-4S dicluster domain
        5.4    7.9  14.1    1.1e+02    3.7  14.1    2.5  1  Fer4_22   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4_5  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.6       6.2     7e+03      12      15 ..      33      36 ..      25      45 .. 0.49
   2 !   40.3   3.5     2e-13   2.3e-10       3      42 ..      78     116 ..      75     127 .. 0.84
   3 ?    1.2   1.9      0.32   3.5e+02      12      30 ..     139     157 ..     133     165 .. 0.75
   4 !   22.2   0.4   8.9e-08    0.0001      12      46 ..     178     210 ..     170     212 .. 0.74
   5 ?    2.0   0.0      0.18     2e+02      27      35 ..     227     235 ..     224     242 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 6.2
                         Fer4_5 12 ivlv 15
                                   +vl+
  gi|119720692|ref|YP_921187.1| 33 LVLL 36
                                   2222 PP

  == domain 2  score: 40.3 bits;  conditional E-value: 2e-13
                         Fer4_5   3 llllilflaivlvtllfGRafCgWiCPfGalqellakllr 42 
                                    +lll ++++ +l +ll+GR+fCg +CP+G+l +l++k ++
  gi|119720692|ref|YP_921187.1|  78 WLLLTFAAVPLLGSLLLGRFFCGLMCPVGTLLDLFGK-VK 116
                                    6777888899999999********************9.33 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.32
                         Fer4_5  12 ivlvtllfGR.afCgWiCPf 30 
                                    + + ++l G  afC  iCP+
  gi|119720692|ref|YP_921187.1| 139 FAAASTLTGFpAFCT-ICPI 157
                                    45566666666****.***6 PP

  == domain 4  score: 22.2 bits;  conditional E-value: 8.9e-08
                         Fer4_5  12 ivlvtllfGRafCgWiCPfGalqellakllrrklg 46 
                                     v++ +  +Ra+C ++CP+Ga+   ++  +r+ +g
  gi|119720692|ref|YP_921187.1| 178 PVVLEFSEKRAWCRYFCPVGAVLGAVG--FRKVFG 210
                                    4555555689************99998..477666 PP

  == domain 5  score: 2.0 bits;  conditional E-value: 0.18
                         Fer4_5  27 iCPfGalqe 35 
                                    +CP Ga++e
  gi|119720692|ref|YP_921187.1| 227 VCPTGAITE 235
                                    8******98 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1      0.28   3.1e+02      14      22 ..      99     107 ..      98     108 .. 0.81
   2 ?    4.5   0.1     0.031        34      14      23 ..     190     199 ..     189     200 .. 0.87
   3 !   38.3   4.2   6.3e-13     7e-10       1      24 []     211     234 ..     211     234 .. 0.96
   4 !   15.0   1.3   1.4e-05     0.016       3      23 ..     243     263 ..     242     264 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.28
                                    HHHHSTTTE CS
                           Fer4  14 CvevCPvgA 22 
                                    C  +CPvg 
  gi|119720692|ref|YP_921187.1|  99 CGLMCPVGT 107
                                    7789***95 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.031
                                    HHHHSTTTEE CS
                           Fer4  14 CvevCPvgAI 23 
                                    C   CPvgA 
  gi|119720692|ref|YP_921187.1| 190 CRYFCPVGAV 199
                                    8999****95 PP

  == domain 3  score: 38.3 bits;  conditional E-value: 6.3e-13
                                    EEEETTTSSS-THHHHHSTTTEEE CS
                           Fer4   1 vvideekCigCGaCvevCPvgAIt 24 
                                    v+id+ekCi+C+aC+ vCP+gAIt
  gi|119720692|ref|YP_921187.1| 211 VKIDTEKCINCKACMRVCPTGAIT 234
                                    68*********************7 PP

  == domain 4  score: 15.0 bits;  conditional E-value: 1.4e-05
                                    EETTTSSS-THHHHHSTTTEE CS
                           Fer4   3 ideekCigCGaCvevCPvgAI 23 
                                    +    Ci C +C++vC ++A+
  gi|119720692|ref|YP_921187.1| 243 VSRTECIMCLRCYDVCMYDAL 263
                                    56679***********77776 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   2.4      0.53   5.9e+02      29      52 .]     143     198 ..      97     198 .. 0.52
   2 !   28.1   4.4     2e-09   2.2e-06       8      52 .]     190     232 ..     186     232 .. 0.85
   3 !   13.8   0.4   6.1e-05     0.068       2      18 ..     248     264 ..     235     271 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.53
                         Fer4_7  29 ekveidpekClgC...............................ga.CvavCPtga 52 
                                     ++++ p  C+ C                               +a C   CP+ga
  gi|119720692|ref|YP_921187.1| 143 STLTGFPAFCTICpirglctaygslkgvelalaaapvvlefsekRAwCRYFCPVGA 198
                                    44566677777777777777777777777777777777777765346888888886 PP

  == domain 2  score: 28.1 bits;  conditional E-value: 2e-09
                         Fer4_7   8 CvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                    C   Cpv+a+        +++  v+id ekC++C+aC++vCPtga
  gi|119720692|ref|YP_921187.1| 190 CRYFCPVGAVLGAVGF--RKVFGVKIDTEKCINCKACMRVCPTGA 232
                                    8899999999986543..345669*******************98 PP

  == domain 3  score: 13.8 bits;  conditional E-value: 6.1e-05
                         Fer4_7   2 CigCgaCvaaCpvkaie 18 
                                    Ci C +C ++C+++a++
  gi|119720692|ref|YP_921187.1| 248 CIMCLRCYDVCMYDALK 264
                                    88888888888888876 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       6.6   7.4e+03      36      39 ..     152     155 ..     128     163 .. 0.70
   2 ?   -0.4   0.0       1.2   1.3e+03       8      17 ..     190     199 ..     186     211 .. 0.76
   3 !   34.3  10.9   1.8e-11     2e-08       1      50 [.     217     262 ..     217     263 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 6.6
                         Fer4_9  36 CigC 39 
                                    C+ C
  gi|119720692|ref|YP_921187.1| 152 CTIC 155
                                    3333 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.2
                         Fer4_9   8 CveaCpagvv 17 
                                    C + Cp g+v
  gi|119720692|ref|YP_921187.1| 190 CRYFCPVGAV 199
                                    6667776654 PP

  == domain 3  score: 34.3 bits;  conditional E-value: 1.8e-11
                         Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50 
                                    kC++C+aC+++Cp+g+++ed++++    r     +Ci+C +C+++C  +a
  gi|119720692|ref|YP_921187.1| 217 KCINCKACMRVCPTGAITEDSFKTGEVSRT----ECIMCLRCYDVCMYDA 262
                                    7***********************999876....5***********9886 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       5.4     6e+03      19      23 ..     194     198 ..     193     199 .. 0.88
   2 !   30.4   4.0   2.3e-10   2.6e-07       2      24 .]     211     233 ..     211     233 .. 0.96
   3 !   14.1   2.1   3.4e-05     0.038       9      24 .]     248     263 ..     242     263 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 5.4
                         Fer4_6  19 CPega 23 
                                    CP ga
  gi|119720692|ref|YP_921187.1| 194 CPVGA 198
                                    **998 PP

  == domain 2  score: 30.4 bits;  conditional E-value: 2.3e-10
                         Fer4_6   2 veidpdkCigCgdCvrvCPegai 24 
                                    v id +kCi C +C+rvCP+gai
  gi|119720692|ref|YP_921187.1| 211 VKIDTEKCINCKACMRVCPTGAI 233
                                    689*******************8 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 3.4e-05
                         Fer4_6   9 CigCgdCvrvCPegai 24 
                                    Ci C +C++vC ++a+
  gi|119720692|ref|YP_921187.1| 248 CIMCLRCYDVCMYDAL 263
                                    ***********99986 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       1.1   1.2e+03      46      53 ..      98     105 ..      94     110 .. 0.80
   2 ?   -1.9   0.3       3.4   3.8e+03      49      55 ..     153     159 ..     146     163 .. 0.73
   3 ?   -0.1   0.0      0.92     1e+03      46      56 ..     189     198 ..     176     204 .. 0.86
   4 !   30.6   9.4   2.4e-10   2.7e-07       2      52 ..     212     259 ..     208     265 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.1
                        Fer4_21  46 lCssvCPv 53 
                                     C  +CPv
  gi|119720692|ref|YP_921187.1|  98 FCGLMCPV 105
                                    59999**9 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.4
                        Fer4_21  49 svCPved 55 
                                    ++CP+ +
  gi|119720692|ref|YP_921187.1| 153 TICPIRG 159
                                    5788865 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.92
                        Fer4_21  46 lCssvCPvedc 56 
                                     C   CPv ++
  gi|119720692|ref|YP_921187.1| 189 WCRYFCPV-GA 198
                                    59999999.44 PP

  == domain 4  score: 30.6 bits;  conditional E-value: 2.4e-10
                        Fer4_21   2 ridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCP 52 
                                    +id +kCi+C+ C+ +C+   + ai+ d+ ++ +v   eC+ C  C++vC 
  gi|119720692|ref|YP_921187.1| 212 KIDTEKCINCKACMRVCP---TGAITEDSFKTGEVSRTECIMCLRCYDVCM 259
                                    69****************...699**************************5 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1       1.4   1.6e+03       8      19 ..      99     110 ..      98     157 .. 0.44
   2 ?    1.3   0.0      0.62     7e+02       8      18 ..     190     200 ..     186     208 .. 0.82
   3 !   22.6   4.9   1.4e-07   0.00015       1      26 [.     217     242 ..     217     248 .. 0.82
   4 !    9.4   0.7    0.0018         2       2      18 ..     248     264 ..     247     271 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.4
                        Fer4_16   8 CaevCPtnaike 19 
                                    C  +CP++ +  
  gi|119720692|ref|YP_921187.1|  99 CGLMCPVGTLLD 110
                                    555677766553 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.62
                        Fer4_16   8 CaevCPtnaik 18 
                                    C   CP++a+ 
  gi|119720692|ref|YP_921187.1| 190 CRYFCPVGAVL 200
                                    89999999975 PP

  == domain 3  score: 22.6 bits;  conditional E-value: 1.4e-07
                        Fer4_16   1 rCgtCgkCaevCPtnaikekkekeie 26 
                                    +C++C++C+ vCPt+ai+e++ k+ e
  gi|119720692|ref|YP_921187.1| 217 KCINCKACMRVCPTGAITEDSFKTGE 242
                                    5******************9666554 PP

  == domain 4  score: 9.4 bits;  conditional E-value: 0.0018
                        Fer4_16   2 CgtCgkCaevCPtnaik 18 
                                    C+ C +C +vC  +a+k
  gi|119720692|ref|YP_921187.1| 248 CIMCLRCYDVCMYDALK 264
                                    ***********999987 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.6       1.9   2.1e+03      18      24 ..     102     129 ..      99     164 .. 0.41
   2 ?   -0.9   0.1       1.7   1.9e+03      15      21 ..     190     196 ..     188     204 .. 0.81
   3 !   28.3  13.1   1.2e-09   1.4e-06       2      55 ..     211     258 ..     210     259 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.9
                        Fer4_10  18 aCPadl.....................t 24 
                                    +CP+                       +
  gi|119720692|ref|YP_921187.1| 102 MCPVGTlldlfgkvkrvnflgklrlnnK 129
                                    5666444444444444444444333331 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.7
                        Fer4_10  15 CvkaCPa 21 
                                    C+ +CP+
  gi|119720692|ref|YP_921187.1| 190 CRYFCPV 196
                                    8899998 PP

  == domain 3  score: 28.3 bits;  conditional E-value: 1.2e-09
                        Fer4_10   2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaC 55 
                                    v+id+++Ci+C++C+++CP+     ga+ e+s  ++ ++   +C++c  C+++C
  gi|119720692|ref|YP_921187.1| 211 VKIDTEKCINCKACMRVCPT-----GAITEDS-FKTGEVSRTECIMCLRCYDVC 258
                                    689*****************.....3333333.3344556789*********** PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   1.0       6.9   7.7e+03      16      21 ..     152     156 ..     150     163 .. 0.67
   2 ?    0.1   0.7      0.99   1.1e+03      16      21 ..     190     195 ..     190     196 .. 0.90
   3 !   25.5   3.0   7.7e-09   8.6e-06       3      22 .]     211     230 ..     210     230 .. 0.94
   4 !    8.0   2.1    0.0029       3.2      10      20 ..     248     258 ..     242     260 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 6.9
                         Fer4_2  16 CvsaCP 21 
                                    C + CP
  gi|119720692|ref|YP_921187.1| 152 C-TICP 156
                                    5.5565 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.99
                         Fer4_2  16 CvsaCP 21 
                                    C+  CP
  gi|119720692|ref|YP_921187.1| 190 CRYFCP 195
                                    9***** PP

  == domain 3  score: 25.5 bits;  conditional E-value: 7.7e-09
                         Fer4_2   3 vvvdtdrCigCgaCvsaCPa 22 
                                    v++dt++Ci+C+aC  +CP+
  gi|119720692|ref|YP_921187.1| 211 VKIDTEKCINCKACMRVCPT 230
                                    689****************7 PP

  == domain 4  score: 8.0 bits;  conditional E-value: 0.0029
                         Fer4_2  10 CigCgaCvsaC 20 
                                    Ci C  C+++C
  gi|119720692|ref|YP_921187.1| 248 CIMCLRCYDVC 258
                                    *********** PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       6.6   7.4e+03       5      14 ..      98     107 ..      97     112 .. 0.75
   2 ?   -0.3   0.1       1.1   1.2e+03       4      17 ..     188     201 ..     185     216 .. 0.77
   3 !   20.7   9.1   3.1e-07   0.00035      58      96 ..     215     259 ..     202     268 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 6.6
                        Fer4_18   5 vcvyvcPyar 14 
                                    +c ++cP + 
  gi|119720692|ref|YP_921187.1|  98 FCGLMCPVGT 107
                                    6888888765 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.1
                        Fer4_18   4 dvcvyvcPyarvqs 17 
                                      c y cP + v +
  gi|119720692|ref|YP_921187.1| 188 AWCRYFCPVGAVLG 201
                                    6799****987765 PP

  == domain 3  score: 20.7 bits;  conditional E-value: 3.1e-07
                        Fer4_18  58 agdcidcescvkvcPtgidirkGl......qleciscllcidacd 96 
                                    + +ci+c++c++vcPtg    + +      + eci cl+c d c 
  gi|119720692|ref|YP_921187.1| 215 TEKCINCKACMRVCPTGAITEDSFktgevsRTECIMCLRCYDVCM 259
                                    678*************98665554111122579***********5 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.6       8.1   9.1e+03      14      15 ..     155     156 ..     151     165 .. 0.52
   2 ?    4.5   0.1     0.054        61      10      17 .]     190     197 ..     184     198 .. 0.86
   3 !   18.6   4.1   1.6e-06    0.0018       2      17 .]     216     231 ..     215     231 .. 0.93
   4 ?    5.3   2.9     0.029        32       3      14 ..     247     258 ..     245     261 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 8.1
                         Fer4_4  14 CP 15 
                                    CP
  gi|119720692|ref|YP_921187.1| 155 CP 156
                                    43 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.054
                         Fer4_4  10 CvaaCPqg 17 
                                    C+++CP+g
  gi|119720692|ref|YP_921187.1| 190 CRYFCPVG 197
                                    ******86 PP

  == domain 3  score: 18.6 bits;  conditional E-value: 1.6e-06
                         Fer4_4   2 erCigCgsCvaaCPqg 17 
                                    e+Ci+C++C+++CP+g
  gi|119720692|ref|YP_921187.1| 216 EKCINCKACMRVCPTG 231
                                    89************86 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.029
                         Fer4_4   3 rCigCgsCvaaC 14 
                                     Ci C +C+++C
  gi|119720692|ref|YP_921187.1| 247 ECIMCLRCYDVC 258
                                    5*********** PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.1      0.58   6.6e+02       7      14 ..      99     106 ..      96     107 .. 0.88
   2 ?    5.2   0.2     0.042        47       7      15 .]     190     198 ..     185     198 .. 0.92
   3 !   17.8   6.0   4.3e-06    0.0048       1      15 []     218     232 ..     218     232 .. 0.98
   4 !   11.0   2.4   0.00061      0.69       1      15 []     248     262 ..     248     262 .. 0.95

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.58
                         Fer4_3   7 CvevCPvg 14 
                                    C   CPvg
  gi|119720692|ref|YP_921187.1|  99 CGLMCPVG 106
                                    8889**98 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.042
                         Fer4_3   7 CvevCPvgA 15 
                                    C   CPvgA
  gi|119720692|ref|YP_921187.1| 190 CRYFCPVGA 198
                                    999*****9 PP

  == domain 3  score: 17.8 bits;  conditional E-value: 4.3e-06
                         Fer4_3   1 CtgCgaCvevCPvgA 15 
                                    C++C aC++vCP+gA
  gi|119720692|ref|YP_921187.1| 218 CINCKACMRVCPTGA 232
                                    **************9 PP

  == domain 4  score: 11.0 bits;  conditional E-value: 0.00061
                         Fer4_3   1 CtgCgaCvevCPvgA 15 
                                    C++C +C +vC ++A
  gi|119720692|ref|YP_921187.1| 248 CIMCLRCYDVCMYDA 262
                                    ****99*****9988 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   3.7   6.6e-05     0.074       1      17 [.     213     229 ..     213     231 .. 0.95
   2 ?    3.8   2.8     0.076        85       2      16 ..     244     258 ..     243     259 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.6e-05
                        Fer4_13   1 VDrdtCiacgaCvelaP 17 
                                    +D ++Ci+c+aC  ++P
  gi|119720692|ref|YP_921187.1| 213 IDTEKCINCKACMRVCP 229
                                    899************** PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.076
                        Fer4_13   2 DrdtCiacgaCvela 16 
                                     r +Ci c  C++++
  gi|119720692|ref|YP_921187.1| 244 SRTECIMCLRCYDVC 258
                                    5789*********99 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   1.2   0.00011      0.13       1      20 [.     211     230 ..     211     239 .. 0.87
   2 ?    4.4   1.6     0.058        64       3      18 ..     243     258 ..     242     265 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00011
                        Fer4_15   1 VvvDrdaCigcglCvaeape 20 
                                    V++D ++Ci c +C++++p+
  gi|119720692|ref|YP_921187.1| 211 VKIDTEKCINCKACMRVCPT 230
                                    89****************85 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.058
                        Fer4_15   3 vDrdaCigcglCvaea 18 
                                    v r++Ci+c +C++++
  gi|119720692|ref|YP_921187.1| 243 VSRTECIMCLRCYDVC 258
                                    669**********998 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.2      0.86   9.7e+02      10      22 ..      98     110 ..      96     164 .. 0.59
   2 ?   -1.3   0.0       2.7   3.1e+03      57      64 ..     190     197 ..     186     198 .. 0.81
   3 ?    6.6  14.4    0.0094        11       2      61 ..     215     258 ..     214     261 .. 0.69
   4 ?    5.5   2.9     0.021        24       4      15 ..     247     258 ..     244     270 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.86
                         Fer4_8  10 aCqsaCpvlrrtk 22 
                                    +C  +Cpv    +
  gi|119720692|ref|YP_921187.1|  98 FCGLMCPVGTLLD 110
                                    6888888554433 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.7
                         Fer4_8  57 CtevCpvg 64 
                                    C+  Cpvg
  gi|119720692|ref|YP_921187.1| 190 CRYFCPVG 197
                                    99999986 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.0094
                         Fer4_8   2 lekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevC 61 
                                     ekCi+C aC+  Cp+   t +  ++  ge++                +C +c +C +vC
  gi|119720692|ref|YP_921187.1| 215 TEKCINCKACMRVCPTGAITEDSFKT--GEVSR--------------TECIMCLRCYDVC 258
                                    589************98888543222..22222..............3588888888888 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.021
                         Fer4_8   4 kCieCgaCqsaC 15 
                                    +Ci C +C + C
  gi|119720692|ref|YP_921187.1| 247 ECIMCLRCYDVC 258
                                    688888888888 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7  14.1       0.1   1.1e+02       1      43 [.     217     261 ..     217     263 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.1
                        Fer4_22   1 rClsCgaCtlvCptCsCfdvedet..keeskegervrvwdsClle 43 
                                    +C++C aC  vCpt   ++ + +t   ++++    +r++d C+++
  gi|119720692|ref|YP_921187.1| 217 KCINCKACMRVCPTGAITEDSFKTgeVSRTECIMCLRCYDVCMYD 261
                                    7*************9987766665654456788899******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1760.83
//
Query:       gi|119720693|ref|YP_921188.1|  [L=229]
Description: 4Fe-4S ferredoxin iron-sulfur binding domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.2e-21   72.8  37.0    3.2e-08   33.1   3.9    4.4  4  Fer4          4Fe-4S binding domain
    1.1e-20   73.9  42.5    7.6e-12   45.6  10.8    2.8  3  Fer4_7        4Fe-4S dicluster domain
    8.7e-19   66.7  32.4    7.5e-08   32.1   2.8    4.2  4  Fer4_6        4Fe-4S binding domain
    2.2e-15   56.5  51.3    5.2e-09   36.1  10.9    3.1  4  Fer4_9        4Fe-4S dicluster domain
    2.1e-14   52.6  31.1    3.1e-05   23.8   2.5    4.4  4  Fer4_2        4Fe-4S binding domain
    2.9e-14   52.9  28.4    8.6e-10   38.6  11.6    3.2  3  Fer4_10       4Fe-4S dicluster domain
    2.7e-13   50.6  24.4    0.00031   21.6   1.8    4.3  5  Fer4_16       4Fe-4S double cluster binding domain
    1.7e-12   47.2  24.6    5.1e-11   42.5   7.8    2.7  2  Fer4_21       4Fe-4S dicluster domain
    6.6e-12   45.7  18.9    0.00012   22.5  11.6    4.0  4  Fer4_8        4Fe-4S dicluster domain
    1.6e-08   34.4  35.1     0.0037   17.6   4.6    4.4  4  Fer4_4        4Fe-4S binding domain
    1.6e-08   35.0  21.4      0.013   16.0   0.2    4.1  4  Fer4_17       4Fe-4S dicluster domain
    2.5e-08   34.3  41.5      0.011   16.7   7.0    4.5  4  Fer4_3        4Fe-4S binding domain
    7.4e-06   26.6  23.6     0.0067   17.1   0.8    4.3  4  Fer4_15       4Fe-4S single cluster domain
    4.8e-05   24.1  24.4        0.1   13.5   1.5    4.0  4  Fer4_22       4Fe-4S dicluster domain
     0.0041   17.6  31.2      0.025   15.1   2.8    4.2  4  Fer4_13       4Fe-4S single cluster domain of Ferredoxin I
     0.0056   16.9  29.2        0.5   10.6   2.0    3.9  3  Fer4_18       4Fe-4S dicluster domain
     0.0089   16.1  10.1      0.039   14.1   5.9    2.2  2  DUF678        Protein of unknown function (DUF678)
  ------ inclusion threshold ------
       0.11   12.1   0.0       0.96    9.0   0.0    2.0  2  TauE          Sulfite exporter TauE/SafE
       0.25   10.1   0.0       0.34    9.6   0.0    1.1  1  GPDPase_memb  Membrane domain of glycerophosphoryl diester ph
        4.1    7.6   6.9         12    6.1   0.2    2.6  3  ETF_QO        Electron transfer flavoprotein-ubiquinone oxido


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   6.1     1e-05    0.0092       8      23 ..      90     105 ..      89     106 .. 0.91
   2 !   15.1   0.4   1.6e-05     0.015      13      23 ..     133     143 ..     122     144 .. 0.87
   3 !   25.3   4.9     1e-08   9.3e-06       3      18 ..     158     173 ..     156     173 .. 0.94
   4 !   33.1   3.9   3.5e-11   3.2e-08       1      23 [.     189     211 ..     189     212 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1e-05
                                    SSS-THHHHHSTTTEE CS
                           Fer4   8 CigCGaCvevCPvgAI 23 
                                    C +CG+C+evCP   I
  gi|119720693|ref|YP_921188.1|  90 CARCGRCAEVCPQKII 105
                                    99**********9988 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 1.6e-05
                                    HHHHHSTTTEE CS
                           Fer4  13 aCvevCPvgAI 23 
                                    +Cv+vCP+gA+
  gi|119720693|ref|YP_921188.1| 133 KCVDVCPTGAL 143
                                    6*********8 PP

  == domain 3  score: 25.3 bits;  conditional E-value: 1e-08
                                    EETTTSSS-THHHHHS CS
                           Fer4   3 ideekCigCGaCvevC 18 
                                     d++kCigCGaCv+vC
  gi|119720693|ref|YP_921188.1| 158 LDKDKCIGCGACVSVC 173
                                    599************* PP

  == domain 4  score: 33.1 bits;  conditional E-value: 3.5e-11
                                    EEEETTTSSS-THHHHHSTTTEE CS
                           Fer4   1 vvideekCigCGaCvevCPvgAI 23 
                                    v++d  kC gCGaCv+ CPvgA+
  gi|119720693|ref|YP_921188.1| 189 VEVDAAKCLGCGACVKECPVGAL 211
                                    589*******************8 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   7.3   3.9e-08   3.5e-05       2      52 .]      90     142 ..      89     142 .. 0.79
   2 !   30.0   8.4   6.7e-10     6e-07       7      49 ..     133     174 ..     127     177 .. 0.88
   3 !   45.6  10.8   8.5e-15   7.6e-12       1      52 []     162     210 ..     162     210 .. 0.93

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 3.9e-08
                         Fer4_7   2 CigCgaCvaaCpvkaieldee...enekgtekveidpekClgCgaCvavCPtga 52 
                                    C  Cg+C+++Cp+k i   ++    +++g   v +d   C+   +Cv+vCPtga
  gi|119720693|ref|YP_921188.1|  90 CARCGRCAEVCPQKIIVQVPVwesVVAAG-TPVLVDGGVCVLDFKCVDVCPTGA 142
                                    99************999886521033334.446678899*************98 PP

  == domain 2  score: 30.0 bits;  conditional E-value: 6.7e-10
                         Fer4_7   7 aCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCP 49 
                                    +Cv++Cp++a++  ++e ++++ ++ +d +kC+gCgaCv+vC 
  gi|119720693|ref|YP_921188.1| 133 KCVDVCPTGALQRLPKE-KAKMGTALLDKDKCIGCGACVSVCA 174
                                    7***********99985.5567999*****************6 PP

  == domain 3  score: 45.6 bits;  conditional E-value: 8.5e-15
                         Fer4_7   1 rCigCgaCvaaCp..vkaieldeeenekgtekveidpekClgCgaCvavCPtga 52 
                                    +CigCgaCv++C   ++ai+++++    g +kve+d+ kClgCgaCv++CP+ga
  gi|119720693|ref|YP_921188.1| 162 KCIGCGACVSVCAsiAGAIKWRKS----G-RKVEVDAAKCLGCGACVKECPVGA 210
                                    7***********988999999887....4.89********************98 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   4.4   0.00023      0.21       9      23 ..      90     104 ..      89     107 .. 0.88
   2 !   14.2   0.4   3.9e-05     0.035       9      24 .]     128     143 ..     121     143 .. 0.88
   3 !   25.0   3.3   1.5e-08   1.3e-05       5      24 .]     159     180 ..     158     180 .. 0.86
   4 !   32.1   2.8   8.4e-11   7.5e-08       1      24 []     188     211 ..     188     211 .. 0.96

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00023
                         Fer4_6   9 CigCgdCvrvCPega 23 
                                    C  Cg+C+ vCP ++
  gi|119720693|ref|YP_921188.1|  90 CARCGRCAEVCPQKI 104
                                    999*********665 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 3.9e-05
                         Fer4_6   9 CigCgdCvrvCPegai 24 
                                    C+   +Cv+vCP+ga+
  gi|119720693|ref|YP_921188.1| 128 CVLDFKCVDVCPTGAL 143
                                    888889********97 PP

  == domain 3  score: 25.0 bits;  conditional E-value: 1.5e-08
                         Fer4_6   5 dpdkCigCgdCvrvCP..egai 24 
                                    d+dkCigCg+Cv+vC   +gai
  gi|119720693|ref|YP_921188.1| 159 DKDKCIGCGACVSVCAsiAGAI 180
                                    89*************9555665 PP

  == domain 4  score: 32.1 bits;  conditional E-value: 8.4e-11
                         Fer4_6   1 vveidpdkCigCgdCvrvCPegai 24 
                                    +ve+d+ kC+gCg+Cv+ CP ga+
  gi|119720693|ref|YP_921188.1| 188 KVEVDAAKCLGCGACVKECPVGAL 211
                                    79********************97 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   2.6   1.1e-05    0.0097      34      51 .]      88     105 ..      67     105 .. 0.70
   2 !   19.0   7.7   1.3e-06    0.0011       2      50 ..      90     142 ..      89     143 .. 0.90
   3 !   24.0   6.4   3.6e-08   3.2e-05       7      48 ..     133     175 ..     126     180 .. 0.75
   4 !   36.1  10.9   5.8e-12   5.2e-09       1      50 [.     162     210 ..     162     211 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.1e-05
                         Fer4_9  34 eaCigCgaCveaCpkgai 51 
                                      C  Cg+C+e+Cp+++i
  gi|119720693|ref|YP_921188.1|  88 VVCARCGRCAEVCPQKII 105
                                    569999999999999965 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 1.3e-06
                         Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraase....eaCigCgaCveaCpkga 50 
                                    C++Cg+C e+Cp++++v+  + + +    +        C+   +Cv++Cp+ga
  gi|119720693|ref|YP_921188.1|  90 CARCGRCAEVCPQKIIVQVPVWESVVAAGTPVlvdgGVCVLDFKCVDVCPTGA 142
                                    *****************999999999876666999988**99*********97 PP

  == domain 3  score: 24.0 bits;  conditional E-value: 3.6e-08
                         Fer4_9   7 aCveaCpagvvvedaaerk.arlraaseeaCigCgaCveaCpk 48 
                                    +Cv++Cp+g+ ++  +e+  +     ++++CigCgaCv +C +
  gi|119720693|ref|YP_921188.1| 133 KCVDVCPTGALQRLPKEKAkMGTALLDKDKCIGCGACVSVCAS 175
                                    7*********97665555404444444489***********86 PP

  == domain 4  score: 36.1 bits;  conditional E-value: 5.8e-12
                         Fer4_9   1 kCtgCgaCveaC..pagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50 
                                    kC+gCgaCv++C   ag+++ ++++rk++++aa   +C+gCgaCv+ Cp ga
  gi|119720693|ref|YP_921188.1| 162 KCIGCGACVSVCasIAGAIKWRKSGRKVEVDAA---KCLGCGACVKECPVGA 210
                                    7***********777888888888888888775...8************987 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   3.7   3.1e-05     0.028       9      22 .]      89     102 ..      77     102 .. 0.77
   2 !    6.8   0.4    0.0091       8.1      15      22 .]     133     140 ..     121     140 .. 0.90
   3 !   23.8   2.5   3.4e-08   3.1e-05       5      20 ..     158     173 ..     156     175 .. 0.92
   4 !   23.8   3.0   3.5e-08   3.2e-05       2      21 ..     188     207 ..     187     208 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.1e-05
                         Fer4_2   9 rCigCgaCvsaCPa 22 
                                     C +Cg C  +CP+
  gi|119720693|ref|YP_921188.1|  89 VCARCGRCAEVCPQ 102
                                    7************6 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0091
                         Fer4_2  15 aCvsaCPa 22 
                                    +Cv++CP+
  gi|119720693|ref|YP_921188.1| 133 KCVDVCPT 140
                                    7******7 PP

  == domain 3  score: 23.8 bits;  conditional E-value: 3.4e-08
                         Fer4_2   5 vdtdrCigCgaCvsaC 20 
                                     d d+CigCgaCvs+C
  gi|119720693|ref|YP_921188.1| 158 LDKDKCIGCGACVSVC 173
                                    799************* PP

  == domain 4  score: 23.8 bits;  conditional E-value: 3.5e-08
                         Fer4_2   2 pvvvdtdrCigCgaCvsaCP 21 
                                    +v+vd+++C+gCgaCv+ CP
  gi|119720693|ref|YP_921188.1| 188 KVEVDAAKCLGCGACVKECP 207
                                    689***************** PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   9.8   4.9e-05     0.044       8      56 .]      89     139 ..      87     139 .. 0.70
   2 !    9.1   0.2    0.0016       1.4       5      22 ..     124     141 ..     120     156 .. 0.70
   3 !   38.6  11.6   9.6e-13   8.6e-10       3      56 .]     157     207 ..     155     207 .. 0.96

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.9e-05
                        Fer4_10   8 tCirCgkCvkaCPadl..tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                     C rCg+C ++CP+++  +  + +     + +v ++ + C   ++Cv++CP
  gi|119720693|ref|YP_921188.1|  89 VCARCGRCAEVCPQKIivQVPVWESVVAAGTPVLVDGGVCVLDFKCVDVCP 139
                                    6*************886522222333334445555667899999******9 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0016
                        Fer4_10   5 dddtCirCgkCvkaCPad 22 
                                    d   C+   kCv++CP+ 
  gi|119720693|ref|YP_921188.1| 124 DGGVCVLDFKCVDVCPTG 141
                                    666799999*******93 PP

  == domain 3  score: 38.6 bits;  conditional E-value: 9.6e-13
                        Fer4_10   3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                     +d+d+Ci+Cg+Cv++C a  +  ga++ ++ + +v+++  kC gcgaCv++CP
  gi|119720693|ref|YP_921188.1| 157 LLDKDKCIGCGACVSVC-A--SIAGAIKWRKSGRKVEVDAAKCLGCGACVKECP 207
                                    679**************.6..7*******************************9 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   1.8   3.5e-07   0.00031       2      26 ..      90     112 ..      89     118 .. 0.90
   2 !   12.8   0.1   0.00019      0.17       7      23 ..     133     149 ..     127     161 .. 0.76
   3 !    9.2   4.0    0.0025       2.3      52      64 ..     161     173 ..     145     176 .. 0.71
   4 !    9.4   3.9    0.0023       2.1       1      14 [.     162     175 ..     162     193 .. 0.76
   5 !   19.4   0.5   1.7e-06    0.0015       1      24 [.     195     216 ..     195     227 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 3.5e-07
                        Fer4_16   2 CgtCgkCaevCPtnaikekkekeie 26 
                                    C +Cg+CaevCP++ i +   +++e
  gi|119720693|ref|YP_921188.1|  90 CARCGRCAEVCPQKIIVQV--PVWE 112
                                    ****************998..7776 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00019
                        Fer4_16   7 kCaevCPtnaikekkek 23 
                                    kC++vCPt+a++   ++
  gi|119720693|ref|YP_921188.1| 133 KCVDVCPTGALQRLPKE 149
                                    8**********965343 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0025
                        Fer4_16  52 eaitgCdiCqdvC 64 
                                     +++gC++C+ vC
  gi|119720693|ref|YP_921188.1| 161 DKCIGCGACVSVC 173
                                    5667777777777 PP

  == domain 4  score: 9.4 bits;  conditional E-value: 0.0023
                        Fer4_16   1 rCgtCgkCaevCPt 14 
                                    +C++Cg+C++vC +
  gi|119720693|ref|YP_921188.1| 162 KCIGCGACVSVCAS 175
                                    59999999999975 PP

  == domain 5  score: 19.4 bits;  conditional E-value: 1.7e-06
                        Fer4_16   1 rCgtCgkCaevCPtnaikekkeke 24 
                                    +C +Cg+C++ CP++a++ +  ++
  gi|119720693|ref|YP_921188.1| 195 KCLGCGACVKECPVGALSLT--PS 216
                                    5****************988..33 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   9.0    0.0012       1.1       7      56 ..      89     142 ..      81     145 .. 0.76
   2 !   42.5   7.8   5.7e-14   5.1e-11       1      57 [.     156     211 ..     156     213 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0012
                        Fer4_21   7 kCigCgkCliaCedtshqai.....eidaktvlkvvedeCvGCnlCssvCPvedc 56 
                                     C  Cg+C+ +C+++ +  +      ++a t + v    Cv    C++vCP+ ++
  gi|119720693|ref|YP_921188.1|  89 VCARCGRCAEVCPQKIIVQVpvwesVVAAGTPVLVDGGVCVLDFKCVDVCPT-GA 142
                                    599**********86665556665334444555566789************6.65 PP

  == domain 2  score: 42.5 bits;  conditional E-value: 5.7e-14
                        Fer4_21   1 AridedkCigCgkCliaCedtshqaieidak.tvlkvvedeCvGCnlCssvCPvedci 57 
                                    A +d+dkCigCg C+ +C  +   ai+  ++ ++++v + +C GC  C++ CPv +++
  gi|119720693|ref|YP_921188.1| 156 ALLDKDKCIGCGACVSVCA-SIAGAIKWRKSgRKVEVDAAKCLGCGACVKECPV-GAL 211
                                    679****************.68899*976542788999***************9.665 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   2.5e-06    0.0023      45      65 .]      84     104 ..      35     104 .. 0.81
   2 ?    5.5   0.1     0.026        24      51      64 ..     128     141 ..     124     155 .. 0.84
   3 !   22.5  11.6   1.3e-07   0.00012       3      64 ..     161     209 ..     159     210 .. 0.82
   4 !   15.4   2.5   2.1e-05     0.019       2      18 ..     193     209 ..     192     221 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.5e-06
                         Fer4_8  45 eealwsCttcgaCtevCpvgi 65 
                                    +e +  C  cg+C+evCp++i
  gi|119720693|ref|YP_921188.1|  84 AEFVVVCARCGRCAEVCPQKI 104
                                    667888************997 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.026
                         Fer4_8  51 CttcgaCtevCpvg 64 
                                    C+   +C++vCp+g
  gi|119720693|ref|YP_921188.1| 128 CVLDFKCVDVCPTG 141
                                    78888899999876 PP

  == domain 3  score: 22.5 bits;  conditional E-value: 1.3e-07
                         Fer4_8   3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                    +kCi+CgaC s C ++    k++++ r+   +             + +C++cgaC+++Cpvg
  gi|119720693|ref|YP_921188.1| 161 DKCIGCGACVSVCASIAGAIKWRKSGRKVEVD-------------AAKCLGCGACVKECPVG 209
                                    79***********9999998886666655333.............478************97 PP

  == domain 4  score: 15.4 bits;  conditional E-value: 2.1e-05
                         Fer4_8   2 lekCieCgaCqsaCpvl 18 
                                    + kC +CgaC ++Cpv 
  gi|119720693|ref|YP_921188.1| 193 AAKCLGCGACVKECPVG 209
                                    56888888888888875 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   4.3    0.0012       1.1       4      17 .]      90     103 ..      85     103 .. 0.94
   2 ?    6.9   0.6     0.011        10       9      17 .]     133     141 ..     126     141 .. 0.90
   3 !   17.6   4.6   4.2e-06    0.0037       1      14 [.     160     173 ..     160     175 .. 0.94
   4 !   16.3   3.5   1.1e-05      0.01       3      17 .]     195     209 ..     193     209 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0012
                         Fer4_4   4 CigCgsCvaaCPqg 17 
                                    C +Cg+C  +CPq+
  gi|119720693|ref|YP_921188.1|  90 CARCGRCAEVCPQK 103
                                    9***********85 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.011
                         Fer4_4   9 sCvaaCPqg 17 
                                    +Cv++CP+g
  gi|119720693|ref|YP_921188.1| 133 KCVDVCPTG 141
                                    6******86 PP

  == domain 3  score: 17.6 bits;  conditional E-value: 4.2e-06
                         Fer4_4   1 qerCigCgsCvaaC 14 
                                    +++CigCg+Cv++C
  gi|119720693|ref|YP_921188.1| 160 KDKCIGCGACVSVC 173
                                    69************ PP

  == domain 4  score: 16.3 bits;  conditional E-value: 1.1e-05
                         Fer4_4   3 rCigCgsCvaaCPqg 17 
                                    +C+gCg+Cv  CP+g
  gi|119720693|ref|YP_921188.1| 195 KCLGCGACVKECPVG 209
                                    8************86 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.2   1.5e-05     0.013      41      60 ..      85     104 ..      63     105 .. 0.79
   2 ?    4.0   0.1     0.083        75      46      59 ..     128     141 ..     126     143 .. 0.85
   3 !   13.8  11.8   7.3e-05     0.066       1      58 [.     162     208 ..     162     211 .. 0.74
   4 !   13.3   2.2   0.00011     0.094       1      17 [.     195     211 ..     195     226 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.5e-05
                        Fer4_17  41 ekaslCieCgeCerkCPqgl 60 
                                    e +  C+ Cg+C+++CPq++
  gi|119720693|ref|YP_921188.1|  85 EFVVVCARCGRCAEVCPQKI 104
                                    55667************986 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.083
                        Fer4_17  46 CieCgeCerkCPqg 59 
                                    C+   +C+ +CP g
  gi|119720693|ref|YP_921188.1| 128 CVLDFKCVDVCPTG 141
                                    99999999999975 PP

  == domain 3  score: 13.8 bits;  conditional E-value: 7.3e-05
                        Fer4_17   1 rCiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPq 58 
                                    +Ci+Cg+C+ +C s +           a+k+ +  + + e  a +C++Cg C+++CP 
  gi|119720693|ref|YP_921188.1| 162 KCIGCGACVSVCASIAG----------AIKWRK-SGRKVEVDAAKCLGCGACVKECPV 208
                                    6***********98766..........334421.2222345799*************6 PP

  == domain 4  score: 13.3 bits;  conditional E-value: 0.00011
                        Fer4_17   1 rCiqCgyClpeCpsyea 17 
                                    +C +Cg+C++eCp ++ 
  gi|119720693|ref|YP_921188.1| 195 KCLGCGACVKECPVGAL 211
                                    58889999999987765 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   5.0    0.0021       1.9       1      14 [.      90     103 ..      90     104 .. 0.86
   2 !   12.1   1.3   0.00035      0.31       6      15 .]     133     142 ..     126     142 .. 0.81
   3 !   13.6   5.0   0.00011       0.1       1      11 [.     163     173 ..     163     176 .. 0.96
   4 !   16.7   7.0   1.2e-05     0.011       1      15 []     196     210 ..     196     210 .. 0.98

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0021
                         Fer4_3   1 CtgCgaCvevCPvg 14 
                                    C  Cg+C evCP +
  gi|119720693|ref|YP_921188.1|  90 CARCGRCAEVCPQK 103
                                    667*********87 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00035
                         Fer4_3   6 aCvevCPvgA 15 
                                     Cv+vCP+gA
  gi|119720693|ref|YP_921188.1| 133 KCVDVCPTGA 142
                                    7********9 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 0.00011
                         Fer4_3   1 CtgCgaCvevC 11 
                                    C+gCgaCv vC
  gi|119720693|ref|YP_921188.1| 163 CIGCGACVSVC 173
                                    *********** PP

  == domain 4  score: 16.7 bits;  conditional E-value: 1.2e-05
                         Fer4_3   1 CtgCgaCvevCPvgA 15 
                                    C+gCgaCv+ CPvgA
  gi|119720693|ref|YP_921188.1| 196 CLGCGACVKECPVGA 210
                                    **************9 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   2.5      0.43   3.9e+02       8      20 ..      90     102 ..      89     107 .. 0.79
   2 ?    6.3   0.2     0.019        17       1      20 [.     121     140 ..     121     153 .. 0.88
   3 !   17.1   0.8   7.5e-06    0.0067       3      19 ..     158     174 ..     157     184 .. 0.89
   4 !   14.7   1.3   4.3e-05     0.039       1      19 [.     189     207 ..     189     212 .. 0.95

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.43
                        Fer4_15   8 CigcglCvaeape 20 
                                    C  cg+C++++p+
  gi|119720693|ref|YP_921188.1|  90 CARCGRCAEVCPQ 102
                                    8889999999975 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.019
                        Fer4_15   1 VvvDrdaCigcglCvaeape 20 
                                    V vD   C  ++ Cv+++p+
  gi|119720693|ref|YP_921188.1| 121 VLVDGGVCVLDFKCVDVCPT 140
                                    6799999***********85 PP

  == domain 3  score: 17.1 bits;  conditional E-value: 7.5e-06
                        Fer4_15   3 vDrdaCigcglCvaeap 19 
                                    +D+d+Cigcg+Cv ++ 
  gi|119720693|ref|YP_921188.1| 158 LDKDKCIGCGACVSVCA 174
                                    7*************995 PP

  == domain 4  score: 14.7 bits;  conditional E-value: 4.3e-05
                        Fer4_15   1 VvvDrdaCigcglCvaeap 19 
                                    V+vD  +C gcg+Cv+e+p
  gi|119720693|ref|YP_921188.1| 189 VEVDAAKCLGCGACVKECP 207
                                    89****************8 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.9   0.00018      0.16      80      96 .]      88     104 ..      71     104 .. 0.87
   2 ?    0.0   0.2       1.8   1.6e+03       3      16 ..     129     142 ..     127     156 .. 0.70
   3 !   12.1   2.2    0.0003      0.27      69      93 ..     150     174 ..     142     177 .. 0.77
   4 !   13.5   1.5   0.00011       0.1      75      95 ..     189     209 ..     179     210 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00018
                        Fer4_22  80 sgCvGCgRCieacpvki 96 
                                     +C  CgRC e+cp+ki
  gi|119720693|ref|YP_921188.1|  88 VVCARCGRCAEVCPQKI 104
                                    68************987 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1.8
                        Fer4_22   3 lsCgaCtlvCptCs 16 
                                    +   +C  vCpt  
  gi|119720693|ref|YP_921188.1| 129 VLDFKCVDVCPTGA 142
                                    45557888888865 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 0.0003
                        Fer4_22  69 klsefkekfgesgCvGCgRCieacp 93 
                                    k ++ ++  ++ +C+GCg C+++c 
  gi|119720693|ref|YP_921188.1| 150 KAKMGTALLDKDKCIGCGACVSVCA 174
                                    4455555668999*********997 PP

  == domain 4  score: 13.5 bits;  conditional E-value: 0.00011
                        Fer4_22  75 ekfgesgCvGCgRCieacpvk 95 
                                     ++++ +C GCg C++ cpv+
  gi|119720693|ref|YP_921188.1| 189 VEVDAAKCLGCGACVKECPVG 209
                                    4668999***********985 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   3.2     0.036        32       6      18 ..      90     102 ..      88     103 .. 0.93
   2 ?    2.9   0.4      0.18   1.6e+02       1      17 [.     123     139 ..     123     141 .. 0.90
   3 !   15.1   2.8   2.8e-05     0.025       2      17 ..     159     174 ..     158     176 .. 0.90
   4 !   10.7   3.2   0.00069      0.61       1      17 [.     191     207 ..     191     208 .. 0.96

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.036
                        Fer4_13   6 CiacgaCvelaPd 18 
                                    C  cg C+e++P+
  gi|119720693|ref|YP_921188.1|  90 CARCGRCAEVCPQ 102
                                    9***********6 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.18
                        Fer4_13   1 VDrdtCiacgaCvelaP 17 
                                    VD   C+ + +Cv+++P
  gi|119720693|ref|YP_921188.1| 123 VDGGVCVLDFKCVDVCP 139
                                    78889************ PP

  == domain 3  score: 15.1 bits;  conditional E-value: 2.8e-05
                        Fer4_13   2 DrdtCiacgaCvelaP 17 
                                    D+d+Ci+cgaCv+++ 
  gi|119720693|ref|YP_921188.1| 159 DKDKCIGCGACVSVCA 174
                                    99************96 PP

  == domain 4  score: 10.7 bits;  conditional E-value: 0.00069
                        Fer4_13   1 VDrdtCiacgaCvelaP 17 
                                    VD  +C +cgaCv+ +P
  gi|119720693|ref|YP_921188.1| 191 VDAAKCLGCGACVKECP 207
                                    899*************9 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   2.6    0.0052       4.7      58      76 ..      87     105 ..      67     117 .. 0.83
   2 !   10.5   8.6   0.00058      0.52      59     107 ..     126     185 ..     116     186 .. 0.76
   3 !   10.6   2.0   0.00056       0.5      49      74 ..     184     209 ..     179     211 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0052
                        Fer4_18  58 agdcidcescvkvcPtgid 76 
                                    +  c  c+ c +vcP +i 
  gi|119720693|ref|YP_921188.1|  87 VVVCARCGRCAEVCPQKII 105
                                    4569***********9985 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00058
                        Fer4_18  59 gdcidcescvkvcPtgidir.......kGlql....eciscllcidacdkvmeklgkpkg 107
                                    g c+   +cv+vcPtg   r        G  l    +ci c+ c+  c ++ +++++ k+
  gi|119720693|ref|YP_921188.1| 126 GVCVLDFKCVDVCPTGALQRlpkekakMGTALldkdKCIGCGACVSVCASIAGAIKWRKS 185
                                    56888889*******9855433222214655445558****************9999875 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00056
                        Fer4_18  49 ekeerkekgagdcidcescvkvcPtg 74 
                                    ++ ++ e +a++c+ c++cvk cP+g
  gi|119720693|ref|YP_921188.1| 184 KSGRKVEVDAAKCLGCGACVKECPVG 209
                                    45566678899*************97 PP

>> DUF678  Protein of unknown function (DUF678)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1     0.067        60       6      31 ..      68      93 ..      65      97 .. 0.89
   2 !   14.1   5.9   4.4e-05     0.039       4      64 ..     140     202 ..     136     207 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.067
                         DUF678  6 gkkkrrkrkpkttvededdctTCSlC 31
                                   ++k   kr+p  +v++ + ++ C  C
  gi|119720693|ref|YP_921188.1| 68 AAKTVDKRRPPGAVDEAEFVVVCARC 93
                                   6788899**********999999999 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 4.4e-05
                         DUF678   4 tagkkkrrkrkpk..ttvededdctTCSlCqSkLvkvsdvskvslsklkvavgkgntlrCaAC 64 
                                    t++ ++  k k+k  t++ d+d+c+ C +C S  +++ +  k + s  kv v + + l C AC
  gi|119720693|ref|YP_921188.1| 140 TGALQRLPKEKAKmgTALLDKDKCIGCGACVSVCASIAGAIKWRKSGRKVEVDAAKCLGCGAC 202
                                    5677776666665226799****************************999999********** PP

>> TauE  Sulfite exporter TauE/SafE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.34   3.1e+02      30      69 ..      49      89 ..      46      93 .. 0.79
   2 ?    9.0   0.0    0.0011      0.96      36      75 ..     163     203 ..     153     221 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.34
                           TauE 30 llppavavatsllavvatslsgalahrrr.gnvdwrlllll 69
                                   ++ ++vav t ++++v+  ++ ++  rr  g+vd   ++++
  gi|119720693|ref|YP_921188.1| 49 FFVAKVAVLTGIVTSVPLVAAKTVDKRRPpGAVDEAEFVVV 89
                                   35689999999999999999999999998788887777665 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0011
                           TauE  36 avatsllavvatslsgalahrrr.gnvdwrlllllllgsli 75 
                                    +++  ++++v  s++ga+++r++ ++v++ +++ l++g+++
  gi|119720693|ref|YP_921188.1| 163 CIGCGACVSVCASIAGAIKWRKSgRKVEVDAAKCLGCGACV 203
                                    78888999***************669***********9987 PP

>> GPDPase_memb  Membrane domain of glycerophosphoryl diester phosphodiesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00038      0.34     202     249 ..      30      78 ..      25      89 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00038
                   GPDPase_memb 202 eSwqltkknflrlllklllliliivivltvilsllllllqllldkl.pk 249
                                    e +++tkk+ +r+  + ++++++ v+vlt i++ + l+++ ++dk  p+
  gi|119720693|ref|YP_921188.1|  30 EAFNVTKKQSFRVTRRDFVFFVAKVAVLTGIVTSVPLVAAKTVDKRrPP 78 
                                    56789********9999*****************999999999987555 PP

>> ETF_QO  Electron transfer flavoprotein-ubiquinone oxidoreductase, 4Fe-4S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       5.8   5.2e+03      75      88 ..      90     103 ..      80     120 .. 0.57
   2 ?    6.1   0.2     0.013        12      47      82 ..     135     170 ..     127     185 .. 0.80
   3 ?    5.6   0.3     0.019        17      63     101 ..     184     221 ..     172     224 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 5.8
                                    --S--HHHHH-TT- CS
                         ETF_QO  75 CvhCktCdikdpsq 88 
                                    C  C  C    p++
  gi|119720693|ref|YP_921188.1|  90 CARCGRCAEVCPQK 103
                                    44444444333333 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.013
                                    HHH-TTS-EEEEETTTTSSEEEEE-CCC--S--HHH CS
                         ETF_QO  47 qryCPagvyeivedeeakekklqinaqnCvhCktCd 82 
                                      +CP g  + + +e+ak  +  ++   C+ C +C 
  gi|119720693|ref|YP_921188.1| 135 VDVCPTGALQRLPKEKAKMGTALLDKDKCIGCGACV 170
                                    568*********999999999999**********94 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.019
                                    TSSEEEEE-CCC--S--HHHHH-TT--EEE---STT-C- CS
                         ETF_QO  63 akekklqinaqnCvhCktCdikdpsqniewvvPeGggGP 101
                                    +++ k++++a+ C+ C +C    p   ++  +P G+  P
  gi|119720693|ref|YP_921188.1| 184 KSGRKVEVDAAKCLGCGACVKECPVGALS-LTPSGAYRP 221
                                    467899*************7777766665.467776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 1411.04
//
Query:       gi|119720694|ref|YP_921189.1|  [L=183]
Description: methylpurine-DNA glycosylase (MPG) [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-33  115.2   0.0    2.6e-33  114.9   0.0    1.0  1  Pur_DNA_glyco  Methylpurine-DNA glycosylase (MPG)


Domain annotation for each model (and alignments):
>> Pur_DNA_glyco  Methylpurine-DNA glycosylase (MPG)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.9   0.0   1.4e-37   2.6e-33       1     172 [.       4     174 ..       4     176 .. 0.94

  Alignments for each domain:
  == domain 1  score: 114.9 bits;  conditional E-value: 1.4e-37
                  Pur_DNA_glyco   1 effdrdalevAkeLLGkvlvreleegkvagrivEtEAYlgeeDpAshayrgrternavmFgppgtlYvYliygihhclnv 80 
                                    eff+r++++vA+ LLGk+lvr+le g  ag+i+E+E Y g+eDpAs+a rg  + ++vm g+  t+ vY ++  +++lnv
  gi|119720694|ref|YP_921189.1|   4 EFFARQPDAVARMLLGKLLVRRLEGGVRAGIIIEVEPYFGAEDPASRARRG-GDLARVMCGEVCTALVYGVHR-QWLLNV 81 
                                    69**********************99**********************998.57889****************.****** PP

                  Pur_DNA_glyco  81 vteeegeasaVLiRalevveglelmrarrglanGPgkLcqaLgidkelngadlle.seelvle.keeaeeeeivagpRiG 158
                                    v++e g  +a+LiR++ +v+   l    r+ + GPg++++++++dk+l+++ l++ +++l++  + + ++e i ++pR+G
  gi|119720694|ref|YP_921189.1|  82 VAHEPGLCGAILIRGILPVDPGTLKPLGRE-VLGPGRVTRYFSVDKALHRTYLCDeDSPLRILdGLTFDDECISRSPRVG 160
                                    *********************999999999.89********************9988899887667789999******** PP

                  Pur_DNA_glyco 159 iskaaelpwRfyik 172
                                    ++++  +p+ f i+
  gi|119720694|ref|YP_921189.1| 161 VREDLPIPLNFRIR 174
                                    *********99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       169  (0.00942607); expected 358.6 (0.02)
Passed bias filter:                      159  (0.00886831); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 1204.63
//
Query:       gi|119720695|ref|YP_921190.1|  [L=93]
Description: hypothetical protein Tpen_1792 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-10   42.0   0.4    1.2e-10   41.9   0.4    1.1  1  ATP-cone  ATP cone domain
     0.0074   16.0   0.1      0.015   15.0   0.1    1.5  1  KNOX1     KNOX1 domain


Domain annotation for each model (and alignments):
>> ATP-cone  ATP cone domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9   0.4   1.3e-14   1.2e-10       1      70 [.       3      71 ..       3      86 .. 0.90

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 1.3e-14
                                   -EEE-TTS-EEE--HHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHIIT-BHHHHHHHHHHHHHHSS- CS
                       ATP-cone  1 ikViKRdGtvepfdvekIkraiekAcegseeeideiaeeveaevrkrlrdgisteeIqdlvektliehpd 70
                                   i+V+KRdG++e+f  ekI  +  kA  + +e +++ia+ ve ++ kr++++++t+++ + v   l+e+++
  gi|119720695|ref|YP_921190.1|  3 IYVVKRDGRKEEFAYEKIVVSCLKAGAP-LEVARKIAKIVEGDLLKRKVSEVTTKDLMKEVLALLKEENE 71
                                   69***********************999.****************************9999998875554 PP

>> KNOX1  KNOX1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   1.7e-06     0.015      20      39 ..      22      41 ..      17      43 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.7e-06
                          KNOX1 20 ldCqKVGAPpevvarLdeia 39
                                   + C+K GAP ev+ ++ +i+
  gi|119720695|ref|YP_921190.1| 22 VSCLKAGAPLEVARKIAKIV 41
                                   68**************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       804  (0.0448435); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 580.65
//
Query:       gi|119720696|ref|YP_921191.1|  [L=318]
Description: ABC-type tungstate transport system permease component-like [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.7e-25   88.5   0.0    7.1e-25   88.2   0.0    1.1  1  PBP_like_2      PBP superfamily domain
    1.7e-12   47.6   0.0    2.6e-12   47.0   0.0    1.2  1  SBP_bac_11      Bacterial extracellular solute-binding protei
    1.4e-05   24.6   0.1    2.9e-05   23.5   0.0    1.5  2  LysR_substrate  LysR substrate binding domain
    0.00035   20.6   2.6     0.0076   16.2   2.1    2.6  2  SBP_bac_1       Bacterial extracellular solute-binding protei
  ------ inclusion threshold ------
      0.012   14.7   0.0       0.02   14.0   0.0    1.4  1  PBP_like        PBP superfamily domain
      0.033   14.4   1.5       0.69   10.1   0.9    2.4  2  DUF4148         Domain of unknown function (DUF4148)


Domain annotation for each model (and alignments):
>> PBP_like_2  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.2   0.0   2.4e-28   7.1e-25       7     280 ..      40     269 ..      30     271 .. 0.79

  Alignments for each domain:
  == domain 1  score: 88.2 bits;  conditional E-value: 2.4e-28
                     PBP_like_2   7 tsvgeifgaGsttpa.palrklada.fekaapgakvnyastGSgagikalrngdvdfagsdrplteseia.agwaangag 83 
                                      + ++++a++t+++ ++l+++ +  fe ++p + v++ ++G+g++i+  + gd+d+++++ +  e +++ +g++  g  
  gi|119720696|ref|YP_921191.1|  40 GKRVTLRIATTTSMDaTGLLDAVKKrFEAKYPWINVTWVAVGTGQAIEIAKRGDADLVIVHNRDLENQFIaQGYGVHG-- 117
                                    33345888888888535666655555***********************************77777778889999999.. PP

                     PBP_like_2  84 gliqvpvaigaialvvnkdnpln.....lsreaLakIfsgkItnWndvlglpadgpIkvvhrsdgsgttflfstalaeqg 158
                                        + +a+++++l +++++p++      + ea++kI+              ++g   +v+r+d+sg      t+l e  
  gi|119720696|ref|YP_921191.1| 118 ----ITFAYNDFVLLGPPEDPAGvsgagSAVEAFKKIYEAG-----------VAGKAVFVSRGDKSG------THLRELS 176
                                    ....*************99777777777*********9954...........6**************......******* PP

                     PBP_like_2 159 pwtasgigasgsegvasav.snngaigyvsvaywlavkgysladvtngagkfvlptaataasalkvakiasnplawslqp 237
                                    +w+++g++   + g a +  +++g+ +++ va+ l  ++y+l+d     + ++l++    ++++  + +           
  gi|119720696|ref|YP_921191.1| 177 IWKQAGLK---PQGQAWYKeTGQGMSQTLMVADQL--NAYTLSD-----RSTYLAF----KDKIHLVIL----------- 231
                                    *******9...77777776599**********999..68****9.....9999999....776555333........... PP

                     PBP_like_2 238 veeniadgayPlsrftyiivyqpyayhgnnaalakaFldylls 280
                                          +g+  + + + +i ++p++ +++ + +   F+++l+s
  gi|119720696|ref|YP_921191.1| 232 -H----QGDPLYLNLYRAIPVNPEKFPHVHYNESLLFVKFLVS 269
                                    .2....2444445555555555555556666666666666665 PP

>> SBP_bac_11  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.0   0.0   8.6e-16   2.6e-12       4     222 ..      50     274 ..      45     279 .. 0.82

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 8.6e-16
                                    EE-SSTHHHHHHHHHHHHH.HH---EEEEESSHHHHHHHHHHH..-SEEEESSH.HHHHHHHHGGGGGGG-EEEEEEEEE CS
                     SBP_bac_11   4 aaagslaaalrelaaaFea.htgvkvevsaggsgklarqiadgarpDvwipassawlellaaaglvqaesavplassplv 82 
                                    +++ + +  l+++ ++Fea ++ ++v+  a+g g++++  ++g ++D++i  + +  ++ +a+g+++  ++ ++a++  v
  gi|119720696|ref|YP_921191.1|  50 TTSMDATGLLDAVKKRFEAkYPWINVTWVAVGTGQAIEIAKRG-DADLVIVHNRDLENQFIAQGYGV--HGITFAYNDFV 126
                                    456666889********772577***************99999.***********************..*********** PP

                                    EEESTT-TT---SHHHHHHS.......S-...-EEEE--T-TTTTHH.HHHHGGG--HHHHHHHHHTEEEEESSHHHHHH CS
                     SBP_bac_11  83 iavpkgnpkkikgwadLlkp.......gl...klavadPttspsGlaalalleaagaqellkalekkvvklgessrqllt 152
                                    ++ p++ p++++g  +   +       g+    + v+    s++ l+ l+++++ag   l  + + +    g++ +q+l 
  gi|119720696|ref|YP_921191.1| 127 LLGPPEDPAGVSGAGSAVEAfkkiyeaGVagkAVFVSRGDKSGTHLRELSIWKQAG---LKPQGQAWYKETGQGMSQTLM 203
                                    ********99887666666556666667777458888888999*************...999999999988888888887 PP

                                    HHHTTT-SEEEEEHHHHH..HSTTSSEEEE--TTT--...EEEEEEEE-T.....T--HHHHHHHHHTTSHHHHH CS
                     SBP_bac_11 153 aveageadagivyeseakaaengdkleavylpeglnldpldypaavlkka.....akreaAraFlafLrspeaqa 222
                                     +++ +a  +    + ++    +dk+++v l +g  l +l ++ a++ +       + ++   F++fL spe+q 
  gi|119720696|ref|YP_921191.1| 204 VADQLNAYTLSDRSTYLA---FKDKIHLVILHQGDPL-YLNLYRAIPVNPekfphVHYNESLLFVKFLVSPEGQY 274
                                    777766554444444445...6999999999999998.888888888766555445569**************96 PP

>> LysR_substrate  LysR substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.2       2.2   6.6e+03      12      30 ..      14      29 ..       9      35 .. 0.49
   2 !   23.5   0.0   9.8e-09   2.9e-05       4      89 ..      41     134 ..      38     148 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 2.2
                                   EECCCHHHHHHHHHHHHHH CS
                 LysR_substrate 12 apptlaryllppllarfra 30
                                   +   +a+ l+pp+l+   +
  gi|119720696|ref|YP_921191.1| 14 VALIAAAILVPPMLR---Q 29
                                   333344555666664...4 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 9.8e-09
                                    SCEEEEEEEECCCH.HHHHHHHHHHHHHHSTTEEEEEEEESHHHHHHHHHTTSSSEEEEESSS.......CCTTEEEEEE CS
                 LysR_substrate   4 lrgrLrigapptla.ryllppllarfraryPevelelvegdseelldllaegelDlairagpp.......edsglearpL 75 
                                     r +Lri++++++  + ll  + +rf a+yP + +  v+  + + ++  ++g++Dl+i++++        +  g++   +
  gi|119720696|ref|YP_921191.1|  41 KRVTLRIATTTSMDaTGLLDAVKKRFEAKYPWINVTWVAVGTGQAIEIAKRGDADLVIVHNRDlenqfiaQGYGVHGITF 120
                                    5669*********85777777778***************************************88888888888888888 PP

                                    EEEEEEEEEETTSG CS
                 LysR_substrate  76 aeeplvlvaspdhp 89 
                                    a + +vl+ +p+ p
  gi|119720696|ref|YP_921191.1| 121 AYNDFVLLGPPEDP 134
                                    88888888888765 PP

>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   2.1   2.5e-06    0.0076      10     196 ..      58     207 ..      50     233 .. 0.65
   2 ?   -1.0   0.0      0.44   1.3e+03     303     314 ..     262     273 ..     256     274 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.5e-06
                                    HHHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHHHHTTSSSCSEEEECGGHHH.HHHHTTSBECCHHHHHHTTECTTCC CS
                      SBP_bac_1  10 lqalvakafekehpgikVeiesvgsgslaqkltlaiaaGdgpaDviavdndwia.rlakaglllpldpyvkaylapgvkd 88 
                                    l  +v k+fe+++p i+V+++ vg+g+ ++        Gd  aD+++v n+++  +++ +g+     +++ ++ +   ++
  gi|119720696|ref|YP_921191.1|  58 LLDAVKKRFEAKYPWINVTWVAVGTGQAIE----IAKRGD--ADLVIVHNRDLEnQFIAQGYGVHGITFAYNDFVLLGPP 131
                                    44556588**********************....666666..5*****55555558888866666666666665555443 PP

                                    TEEEEHHHHTHHHHCEEEESEEEEEEEEEEEETTTHHCTTGGGSHBHHHHHHHHHHHHHHCTCTHCCHCCEEHHHHHHHH CS
                      SBP_bac_1  89 aadklsssvlpkildskvlyvPlyaargliYNkdlfekagldppwtWdelveaakklkekgkkpiggarggsasgtayyf 168
                                     +d++  s  ++  +                               ++ ++ea++  k+     + g   g+++++++++
  gi|119720696|ref|YP_921191.1| 132 -EDPAGVSGAGSAVE------------------------------AFKKIYEAGVAGKAVFV--SRGDKSGTHLRELSIW 178
                                    .33333322222222..............................33333333333333333..446678999999**** PP

                                    HHHHHHHHTGGGEECCCTHHCSHHHHS.H CS
                      SBP_bac_1 169 alalakslggkvfdkdgggldnpegvt.a 196
                                     +a +k  g+ ++++ g+g++++  v   
  gi|119720696|ref|YP_921191.1| 179 KQAGLKPQGQAWYKETGQGMSQTLMVAdQ 207
                                    ***************99965555555442 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.44
                                    HHHHHHTSHHHH CS
                      SBP_bac_1 303 kFldfllspeaq 314
                                     F++fl spe+q
  gi|119720696|ref|YP_921191.1| 262 LFVKFLVSPEGQ 273
                                    6*********99 PP

>> PBP_like  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   6.8e-06      0.02       3     120 ..      65     185 ..      63     217 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.8e-06
                                    HHHHH-TTCEEEEEES-HHHHHHHHHTTS-SEEEESS---CCCHHCCCCCEEEEEEEEEEEE-CC-HCHCCCCHCCHHH. CS
                       PBP_like   3 elaeknpgvrvavanvGsggGlkalrageadiagshlldketeeynapalrkaldgievvlvnlarreqglvvakgnpk. 81 
                                    ++++k p + v++  vG+g++++  ++g ad+  +h  d e      +++    +g  v  +++a+    l+  +++p  
  gi|119720696|ref|YP_921191.1|  65 RFEAKYPWINVTWVAVGTGQAIEIAKRGDADLVIVHNRDLEN-----QFIA---QGYGVHGITFAYNDFVLLGPPEDPAg 136
                                    799999******************************999765.....4444...34445668888888888888888884 PP

                                    ......S--BGGGC....-S-B-EEEEE-TTSHHHHHHHHHHC-CEECT CS
                       PBP_like  82 ......kitnwkdl....adaplrlvnRetGSGtrdlfdellkkegisk 120
                                          +++ +k++    +  ++++v R+  SGt +   +  k++g+++
  gi|119720696|ref|YP_921191.1| 137 vsgagsAVEAFKKIyeagVAGKAVFVSRGDKSGTHLRELSIWKQAGLKP 185
                                    44444457777777777777999**********9876555555555555 PP

>> DUF4148  Domain of unknown function (DUF4148)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.9   0.00023      0.69       1      22 [.       1      34 [.       1      44 [. 0.72
   2 ?    2.3   0.0     0.067     2e+02      35      50 ..     173     188 ..     171     191 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00023
                        DUF4148  1 Mkstliaaalaaavaaaaala............a 22
                                   Mk+tl+++++++ava++aa+             +
  gi|119720696|ref|YP_921191.1|  1 MKKTLVILLAVVAVALIAAAIlvppmlrqaapgV 34
                                   9999999999998988888656666666555552 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.067
                        DUF4148  35 aELaqaeaaGylpsgd 50 
                                    +EL  +++aG+ p+g+
  gi|119720696|ref|YP_921191.1| 173 RELSIWKQAGLKPQGQ 188
                                    79***********976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      581  (0.0324056); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2125.94
//
Query:       gi|119720697|ref|YP_921192.1|  [L=218]
Description: binding-protein-dependent transport systems inner membrane component [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.3e-11   42.3  13.0      9e-11   41.8  13.0    1.1  1  BPD_transp_1     Binding-protein-dependent transport system i
  ------ inclusion threshold ------
      0.043   14.0   1.4       0.29   11.4   0.2    2.7  2  Phage_holin_Dp1  Putative phage holin Dp-1


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.8  13.0     1e-14     9e-11       1     180 [.      28     214 ..      28     217 .. 0.84

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 1e-14
                   BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf.....vilsilghlilpviillllsaapyvrlirraa 75 
                                    g++lG+l+a  +++k +++l +l+++++++P+++l+++l+l++       + +  ++  +++++ +l ++p+++ ++ +a
  gi|119720697|ref|YP_921192.1|  28 GVFLGSLIA-TSSSKYKNALVTLVNTFMGTPPVLLGLVLYLLLsrsgpLGFLGMLFTPEAMVLAQFLLTLPIITGLTISA 106
                                    899******.999***************************999***6644445556666689999*************** PP

                   BPD_transp_1  76 lrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG.....lgtllleailgydy 150
                                    ++slp++l+e+ +    sr +  +  +l  + + ++  ++ a+++++ +  ++ ++g++       l+t ++  ++    
  gi|119720697|ref|YP_921192.1| 107 VESLPSELREFVKSISPSRLHESV-LLLNESRIGVFGAVLAALARAVSEVGAVIIVGGNIRyytrvLTTAIVYYTNTGE- 184
                                    *********************655.********************************7765544444444444444444. PP

                   BPD_transp_1 151 seis...nggvlalviavlllnlvadilqrlld 180
                                            ++ ++l++++l++n+v+  + + l 
  gi|119720697|ref|YP_921192.1| 185 ---FetsLWLGATLTAIYLAINVVLVYVRTRLG 214
                                    ...155569999999999999999988877765 PP

>> Phage_holin_Dp1  Putative phage holin Dp-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   3.3e-05      0.29      38      63 .]      19      44 ..       5      44 .. 0.84
   2 ?    0.5   0.1     0.083   7.4e+02      43      52 ..      47      56 ..      45      66 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.3e-05
                Phage_holin_Dp1 38 lvVgtitaiatFLGvilgvstsnykk 63
                                   ++V   t+++ FLG+++  s+s+yk+
  gi|119720697|ref|YP_921192.1| 19 TAVSLSTLVGVFLGSLIATSSSKYKN 44
                                   6788889*****************95 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.083
                Phage_holin_Dp1 43 itaiatFLGv 52
                                   +t+++tF+G+
  gi|119720697|ref|YP_921192.1| 47 VTLVNTFMGT 56
                                   7999****95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.36s 00:00:00.96 Elapsed: 00:00:00.56
# Mc/sec: 1165.79
//
Query:       gi|119720698|ref|YP_921193.1|  [L=234]
Description: ABC transporter related [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-27   96.6   0.0    2.1e-27   96.3   0.0    1.1  1  ABC_tran         ABC transporter
    2.5e-18   67.0   0.1    1.8e-10   41.1   0.0    2.1  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    3.5e-10   39.7   0.0    6.2e-05   22.5   0.0    2.1  2  SMC_N            RecF/RecN/SMC N terminal domain
    7.5e-06   26.6   0.0    1.1e-05   26.0   0.0    1.2  1  AAA_23           AAA domain
    2.6e-05   24.5   0.1    0.00019   21.7   0.1    2.0  1  AAA_22           AAA domain
    3.3e-05   24.3   0.0    5.5e-05   23.6   0.0    1.3  1  AAA_16           AAA ATPase domain
    5.6e-05   22.8   0.0    0.00011   21.9   0.0    1.4  1  AAA_29           P-loop containing region of AAA domain
    0.00025   21.4   0.1       0.19   12.0   0.0    2.2  2  AAA_28           AAA domain
    0.00025   20.9   0.0    0.00058   19.7   0.0    1.5  2  AAA_15           AAA ATPase domain
     0.0013   17.5   0.0      0.076   11.7   0.0    2.1  2  AAA_13           AAA domain
     0.0024   17.6   0.0     0.0037   17.0   0.0    1.3  1  AAA_24           AAA domain
     0.0043   17.3   0.1      0.096   12.9   0.1    2.3  1  SbcCD_C          Putative exonuclease SbcCD, C subunit
     0.0054   16.7   0.0      0.011   15.7   0.0    1.4  1  ATPase_2         ATPase domain predominantly from Archaea
     0.0071   16.0   0.0      0.011   15.3   0.0    1.2  1  AAA_27           AAA domain
     0.0084   15.7   0.6      0.037   13.6   0.4    1.8  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
  ------ inclusion threshold ------
      0.011   15.9   0.0      0.034   14.3   0.0    1.9  1  AAA_33           AAA domain
      0.011   15.6   0.1      0.034   14.1   0.0    1.8  2  NACHT            NACHT domain
      0.016   15.0   0.1      0.024   14.4   0.1    1.2  1  WES_acyltransf   Wax ester synthase-like Acyl-CoA acyltransfe
      0.018   13.9   0.8       0.35    9.6   0.2    2.2  2  ABC_ATPase       Predicted ATPase of the ABC class
       0.02   14.6   0.0      0.066   12.9   0.0    1.8  2  AAA_30           AAA domain
      0.024   12.2   0.1      0.032   11.8   0.1    1.1  1  DUF3584          Protein of unknown function (DUF3584)
      0.024   14.0   0.0       0.11   11.9   0.0    1.9  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.029   14.4   0.0       0.13   12.3   0.0    1.9  2  AAA_14           AAA domain
      0.037   14.4   0.0       0.37   11.2   0.0    2.2  1  AAA              ATPase family associated with various cellul
      0.043   13.7   0.1      0.093   12.6   0.0    1.5  1  Rad17            Rad17 P-loop domain
       0.06   12.9   0.1      0.094   12.3   0.1    1.6  1  AAA_25           AAA domain
      0.072   13.0   0.1       0.14   12.0   0.1    1.4  1  RsgA_GTPase      RsgA GTPase
      0.073   12.1   0.1        0.2   10.7   0.0    1.7  2  T2SSE            Type II/IV secretion system protein
       0.14   12.2   0.0       0.19   11.8   0.0    1.2  1  Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation dom
       0.17   11.6   0.1        5.4    6.7   0.0    2.7  3  IstB_IS21        IstB-like ATP binding protein
       0.19   10.5   0.1       0.34    9.7   0.1    1.3  1  Adeno_IVa2       Adenovirus IVa2 protein
       0.23   11.0   0.0       0.85    9.2   0.0    1.9  2  SRP54            SRP54-type protein, GTPase domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.3   0.0   3.7e-30   2.1e-27       2     137 .]      21     167 ..      20     167 .. 0.93

  Alignments for each domain:
  == domain 1  score: 96.3 bits;  conditional E-value: 3.7e-30
                                    EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG...B-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke...qeleslrkeigvlpqepqlfpeltvre 78 
                                    + vsl+++++++++i+G+nG+GK+tLl++l  ll p+ G +++dg +l +   + ++ + ++++++pq+p +     v++
  gi|119720698|ref|YP_921193.1|  21 RGVSLDVERSRITVIMGPNGSGKTTLLRMLGLLLPPDGGLLEMDGVNLLSldeEGRRGFLRRVAFVPQKPVVLTAN-VYR 99 
                                    679*******************************************999988888999999********9998888.889 PP

                                    H.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                    x.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  79 n.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                    n             ++d+e+ ++l++++l++ + + +    +sLSgG++q +alaral+  p++lllDEpt+
  gi|119720698|ref|YP_921193.1| 100 NiaiplrlrgldprTADAEAWRWLKEVNLEKHAWKSA----HSLSGGERQLLALARALALSPDVLLLDEPTS 167
                                    99**********999999999*****99999666666....*****************************96 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   5.1e-08   2.8e-05       1      23 [.      32      54 ..      32      87 .. 0.84
   2 !   41.1   0.0   3.3e-13   1.8e-10     233     298 ..     135     198 ..     108     200 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 5.1e-08
                         AAA_21  1 lnvliGpNgsGKSnLLdaldlla 23
                                   ++v+ GpNgsGK++LL+ l ll 
  gi|119720698|ref|YP_921193.1| 32 ITVIMGPNGSGKTTLLRMLGLLL 54
                                   79*****************9995 PP

  == domain 2  score: 41.1 bits;  conditional E-value: 3.3e-13
                         AAA_21 233 parelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTHS 298
                                    +a++lS G ++llal+ al+  +   ++ll+DEp ++L+Pk  + + +l+ ++ s++g+ +++++H+
  gi|119720698|ref|YP_921193.1| 135 SAHSLSGGERQLLALARALALSP---DVLLLDEPTSHLDPKNAAFIQRLVkEYVSERGIHCVVVSHN 198
                                    3899********99999999988...************************777777**********8 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.7e-05    0.0097      24      42 ..      30      48 ..      20      55 .. 0.83
   2 !   22.5   0.0   1.1e-07   6.2e-05     132     199 ..     128     199 ..      67     217 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.7e-05
                                   SSEEEEEESTTSSHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxx RF
                          SMC_N 24 ksftaivGpNGSGKsnlld 42
                                   +++t+i+GpNGSGK+ ll 
  gi|119720698|ref|YP_921193.1| 30 SRITVIMGPNGSGKTTLLR 48
                                   579************9875 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 1.1e-07
                                    -STT......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSH CS
                                    xxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxx RF
                          SMC_N 132 iske......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQfivislre 199
                                    ++k+      +LSgGe++L+ala  +A+    p  + llDe  ++LD kn + + +l+ke  ++     +v+s++ 
  gi|119720698|ref|YP_921193.1| 128 LEKHawksahSLSGGERQLLALARALALS---PD-VLLLDEPTSHLDPKNAAFIQRLVKEYVSErgIHCVVVSHNV 199
                                    44445555558*************99985...54.569*********************97766346677777764 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0     2e-08   1.1e-05      11      42 ..      21      53 ..      13      55 .. 0.80

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 2e-08
                         AAA_23 11 rdqeidF.skgltlItGpNGaGKTTildAikla 42
                                   r++++d   + +t+I GpNG+GKTT+l+ + l 
  gi|119720698|ref|YP_921193.1| 21 RGVSLDVeRSRITVIMGPNGSGKTTLLRMLGLL 53
                                   66677775569****************988765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.1   3.3e-07   0.00019       4      38 ..      29      88 ..      26     202 .. 0.51

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 3.3e-07
                         AAA_22  4 tagilvvtGesGtGKTtllrrlleqldeeakaee.........................e 38
                                   + +i+v++G+ G+GKTtllr+l   l+ +    e                         +
  gi|119720698|ref|YP_921193.1| 29 RSRITVIMGPNGSGKTTLLRMLGLLLPPDGGLLEmdgvnllsldeegrrgflrrvafvpQ 88
                                   5789******************99997554444466666666666655554444444430 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   9.8e-08   5.5e-05      23     169 ..      29     194 ..      19     195 .. 0.71

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 9.8e-08
                         AAA_16  23 rpelvllsGesGvGKsslvrellralekd........................ggiflrgkcdqlesaipysalaqalar 78 
                                    r++++++ G+ G+GK++l+r+l   l  d                        ++ f+ +k + l+++     + + + +
  gi|119720698|ref|YP_921193.1|  29 RSRITVIMGPNGSGKTTLLRMLGLLLPPDggllemdgvnllsldeegrrgflrRVAFVPQKPVVLTAN-----VYRNI-A 102
                                    4489*******************777777999999999999999998888886688888888888444.....44444.2 PP

                         AAA_16  79 eellrqlldeaesaeleawrekleeala.....avpelagaea....srllellkrllallsrderplvlvlDdlq.wad 148
                                       lr  + ++++a++eawr   e +l+     ++       +    +r l +l+r+lal++      vl+lD+    +d
  gi|119720698|ref|YP_921193.1| 103 -IPLRLRGLDPRTADAEAWRWLKEVNLEkhawkSAH------SlsggERQLLALARALALSPD-----VLLLDEPTsHLD 170
                                    .34555566688999******988888855444333......233447777777777766665.....777776555788 PP

                         AAA_16 149 easlqllaaLlrl..lesk.pllv 169
                                    +  +++++ L+++  +e++ +++v
  gi|119720698|ref|YP_921193.1| 171 PKNAAFIQRLVKEyvSERGiHCVV 194
                                    888888888877754444555555 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0     2e-07   0.00011      14      48 ..      22      55 ..      18      59 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 2e-07
                         AAA_29 14 ghtieidlkgatlltGpsGsGKSTllDAiqalLvp 48
                                   g +++++++ +t+++Gp+GsGK+Tll  +  lL+p
  gi|119720698|ref|YP_921193.1| 22 GVSLDVERSRITVIMGPNGSGKTTLL-RMLGLLLP 55
                                   5678888888***************9.44455554 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   0.00033      0.19       3      19 ..      34      50 ..      32      84 .. 0.92
   2 !    7.5   0.0    0.0078       4.4     129     161 ..     169     200 ..     110     202 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00033
                         AAA_28  3 vitGgestGKTtlleaL 19
                                   vi+G+ ++GKTtll+ L
  gi|119720698|ref|YP_921193.1| 34 VIMGPNGSGKTTLLRML 50
                                   9*************988 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0078
                         AAA_28 129 edleereaiderlrealrelgipviivpsgdve 161
                                     d+++++ i+++++e + e+gi++++v s +v 
  gi|119720698|ref|YP_921193.1| 169 LDPKNAAFIQRLVKEYVSERGIHCVVV-SHNVR 200
                                    48999**********************.77765 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0     1e-06   0.00058      19      47 ..      25      54 ..      20      74 .. 0.86
   2 ?   -2.1   0.0       4.3   2.4e+03     324     353 ..     157     186 ..     148     198 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1e-06
                         AAA_15 19 idlsee.ltvliGkNnsGKSsilealdlFl 47
                                   +d++ + +tv+ G+N+sGK+++l++l l+l
  gi|119720698|ref|YP_921193.1| 25 LDVERSrITVIMGPNGSGKTTLLRMLGLLL 54
                                   5555556*******************9987 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.3
                         AAA_15 324 nvilliEEPEahLHpqaqkvlikllkelan 353
                                    +++ll++EP  hL p++   + +l ke ++
  gi|119720698|ref|YP_921193.1| 157 PDVLLLDEPTSHLDPKNAAFIQRLVKEYVS 186
                                    688999999999999988777777776665 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   0.00014     0.076      16      36 ..      30      50 ..      20      55 .. 0.88
   2 ?    3.8   0.0     0.033        19     497     572 ..     136     200 ..     128     210 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00014
                         AAA_13 16 kriNliYGwNGaGKTtLSrll 36
                                   +ri +i G NG+GKTtL r+l
  gi|119720698|ref|YP_921193.1| 30 SRITVIMGPNGSGKTTLLRML 50
                                   68999************9887 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.033
                         AAA_13 497 aetLSeGEktaIaflYFlkslkeddseigkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnle 572
                                    a++LS GE+ + a+     +l           +  +D P S LD +   ++  l+k+++ + +   +  +  Hn+ 
  gi|119720698|ref|YP_921193.1| 136 AHSLSGGERQLLALA---RALA------LSPDVLLLDEPTSHLDPKNAAFIQRLVKEYV-S-ERGIHCVVVSHNVR 200
                                    667777777777764...2222......367899************************9.4.44455566679885 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   6.6e-06    0.0037       5      45 ..      33      70 ..      29     103 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6.6e-06
                         AAA_24  5 iliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpd 45
                                    +i+Gp+g+GKTtl+++l    l++  ++Gl ++d+ ++ +
  gi|119720698|ref|YP_921193.1| 33 TVIMGPNGSGKTTLLRML---GLLLPPDGGLLEMDGVNLLS 70
                                   69****************...89999999999999988765 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.1   0.00017     0.096      27      84 ..     133     177 ..     110     183 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00017
                        SbcCD_C  27 srssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatl 84 
                                     +s+ +lSGGe+  l++      la ++        ++++++LDE  s lD++++a +
  gi|119720698|ref|YP_921193.1| 133 WKSAHSLSGGER-QLLA------LARALAL------SPDVLLLDEPTSHLDPKNAAFI 177
                                    578899******.4444......4444444......4788999999999999988755 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.9e-05     0.011      16      38 ..      26      48 ..      22      51 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.9e-05
                       ATPase_2 16 erepneiyfiYGpegsGKtaLlk 38
                                   + e+++i +i Gp gsGKt+Ll+
  gi|119720698|ref|YP_921193.1| 26 DVERSRITVIMGPNGSGKTTLLR 48
                                   568899****************8 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0     2e-05     0.011      17      49 ..      21      53 ..       5      54 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2e-05
                         AAA_27 17 rsldfsaeeadlhliyGpNEAGKstalrAisdl 49
                                   r ++++ e++++++i+GpN +GK+t+lr +  l
  gi|119720698|ref|YP_921193.1| 21 RGVSLDVERSRITVIMGPNGSGKTTLLRMLGLL 53
                                   456777789******************987655 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.4   6.5e-05     0.037       2      20 ..      32      50 ..      31      54 .. 0.91
   2 ?   -0.3   0.0       1.2   6.9e+02      82     124 ..     156     199 ..     136     215 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.5e-05
                                   EEEEEESTTCCHHHHHHHH CS
                           cobW  2 vtvltGflGsGKTtLlnhl 20
                                   +tv+ G+ GsGKTtLl+ l
  gi|119720698|ref|YP_921193.1| 32 ITVIMGPNGSGKTTLLRML 50
                                   69**************975 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.2
                                    T-SEEEE.EECTTTTHHHHHTTSHHHHHCCCECEEEEEEETTTH CS
                           cobW  82 rldvili.EttGlaePapvafteeelksdltldavvavvDaknl 124
                                    ++dv+l+ E t  ++P+  af ++ +k+ + + ++ +vv ++n+
  gi|119720698|ref|YP_921193.1| 156 SPDVLLLdEPTSHLDPKNAAFIQRLVKEYVSERGIHCVVVSHNV 199
                                    36777774777899999999999999999999988888877666 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   6.1e-05     0.034       2      33 ..      33      97 ..      32     216 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.1e-05
                         AAA_33  2 vllvGlpGsGKstlaerl..........lkklgavllssdt.......................l 33
                                   +++ G++GsGK+tl++ l          l+  g+ lls d+                       +
  gi|119720698|ref|YP_921193.1| 33 TVIMGPNGSGKTTLLRMLglllppdgglLEMDGVNLLSLDEegrrgflrrvafvpqkpvvltanV 97
                                   5789************9877666666655555577777777666665555555555555555550 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0     6e-05     0.034       1      21 [.      31      51 ..      31      81 .. 0.90
   2 ?   -1.4   0.0       3.5     2e+03      91     130 ..     163     199 ..     146     215 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6e-05
                                   SCEEEEC-TTTCHHHHHHHHH CS
                          NACHT  1 rlvilqGeaGsGKTtLlqkla 21
                                   r+ ++ G++GsGKTtLl+ l 
  gi|119720698|ref|YP_921193.1| 31 RITVIMGPNGSGKTTLLRMLG 51
                                   5789*************9875 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.5
                                    TT-SS-TCH.........HHHHHCTTTTT--EEEEEEECC CS
                          NACHT  91 DelvtdlgqkekqpvrtlLselirkkllpeasllltvrpr 130
                                    De  ++l++k+++ +++l +e +++   ++ ++++ +++ 
  gi|119720698|ref|YP_921193.1| 163 DEPTSHLDPKNAAFIQRLVKEYVSE---RGIHCVVVSHNV 199
                                    6666666665666666666666665...445554444444 PP

>> WES_acyltransf  Wax ester synthase-like Acyl-CoA acyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   4.3e-05     0.024      65     106 ..     114     155 ..      90     159 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.3e-05
                 WES_acyltransf  65 glaapvWvededfDldyHvRrvalpaPGterellelvsrLas 106
                                     ++a +W+  ++++l+ H +++a +  G+er+ll+l+  La 
  gi|119720698|ref|YP_921193.1| 114 TADAEAWRWLKEVNLEKHAWKSAHSLSGGERQLLALARALAL 155
                                    4566677777889***********************999875 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.2   0.00062      0.35     244     264 ..      30      50 ..      15      52 .. 0.79
   2 ?    2.5   0.0     0.089        50     324     378 ..     140     195 ..     129     219 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00062
                                    SSEEEEEE-TTSSHHHHHHHH CS
                     ABC_ATPase 244 kGvtlIvGggfhGKsTLLeAl 264
                                      +t+I+G++  GK+TLL+ l
  gi|119720698|ref|YP_921193.1|  30 SRITVIMGPNGSGKTTLLRML 50 
                                    34****************976 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.089
                                    -HHHHHHHHHHHHHHTT-SEEEEEGGGS-...HHHH---HHHHHHS-GGG--B--HHH CS
                     ABC_ATPase 324 SGStsqAanimealeagakllLiDEDtsA...tNlmirDermqelvskekepitplvd 378
                                    SG   q  ++++al +  ++lL+DE ts     N  +  ++++e+v  ++++i+++v 
  gi|119720698|ref|YP_921193.1| 140 SGGERQLLALARALALSPDVLLLDEPTSHldpKNAAFIQRLVKEYV--SERGIHCVVV 195
                                    7777777788888888888888888888422245555556666666..4444555543 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00012     0.066      17      38 ..      29      50 ..      22      70 .. 0.87
   2 ?   -1.0   0.0       2.2   1.2e+03      36      52 ..     179     195 ..     116     215 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00012
                         AAA_30 17 gdrvavltGpAGtGKttalkal 38
                                   + r++v+ Gp G+GKtt+l+ l
  gi|119720698|ref|YP_921193.1| 29 RSRITVIMGPNGSGKTTLLRML 50
                                   4579***************976 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.2
                         AAA_30  36 kalreaweaaggrvigl 52 
                                    + ++e + ++g + +++
  gi|119720698|ref|YP_921193.1| 179 RLVKEYVSERGIHCVVV 195
                                    22333334444444444 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   5.7e-05     0.032      19      37 ..      32      50 ..      19      53 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.7e-05
                        DUF3584 19 htnieGtNaaGKTtLlrLi 37
                                    t i G N++GKTtLlr++
  gi|119720698|ref|YP_921193.1| 32 ITVIMGPNGSGKTTLLRML 50
                                   5889*************98 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0    0.0002      0.11      26      50 ..      34      58 ..      10      91 .. 0.80
   2 ?   -0.2   0.0      0.95   5.3e+02      81     116 ..     130     166 ..     115     214 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0002
                   Mg_chelatase 26 llvGppGsGKtmlakrlpsllppls 50
                                   +++Gp GsGKt l + l  llpp  
  gi|119720698|ref|YP_921193.1| 34 VIMGPNGSGKTTLLRMLGLLLPPDG 58
                                   689*******************965 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.95
                   Mg_chelatase  81 phhsaskaalvGggskpkpGeislahn.GvLfLDElp 116
                                     h   s+ +l Gg ++    + +la    vL+LDE +
  gi|119720698|ref|YP_921193.1| 130 KHAWKSAHSLSGGERQLLALARALALSpDVLLLDEPT 166
                                    5777788889999888877777777542688888854 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00023      0.13       2      23 ..      30      51 ..      29      83 .. 0.82
   2 ?   -0.3   0.0       1.9     1e+03      64      90 ..     156     184 ..     121     216 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00023
                         AAA_14  2 rkilvitGaRrvGKTtllkqli 23
                                   ++i vi+G+  +GKTtll+ l 
  gi|119720698|ref|YP_921193.1| 30 SRITVIMGPNGSGKTTLLRMLG 51
                                   5899*************98775 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.9
                         AAA_14  64 kktylflDEiqev..pewekalkslvdeg 90 
                                       +l+lDE      p+   ++++lv+e+
  gi|119720698|ref|YP_921193.1| 156 SPDVLLLDEPTSHldPKNAAFIQRLVKEY 184
                                    45678888865443356666666666644 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00065      0.37       3      35 ..      35      69 ..      33     188 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00065
                                   EESSTTSSHHHHHHHHHHHH..THEEEEEETTTCS CS
                            AAA  3 lyGppGtGKTllakavakel..gvefleisgsell 35
                                   ++Gp G GKT+l + +   l  +  +le++g +ll
  gi|119720698|ref|YP_921193.1| 35 IMGPNGSGKTTLLRMLGLLLppDGGLLEMDGVNLL 69
                                   78************998877443556666666666 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00017     0.093      37      66 ..      22      51 ..      14      60 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00017
                          Rad17 37 advLesrkkriLLisGPsGCgkstvvkvLs 66
                                     +L+ ++ ri +i GP G gk+t +++L 
  gi|119720698|ref|YP_921193.1| 22 GVSLDVERSRITVIMGPNGSGKTTLLRMLG 51
                                   567888999*****************9986 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00017     0.094      31      91 ..      28      84 ..      18     198 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00017
                         AAA_25 31 pagelallaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVlyvsaEdsedelrrRlr 91
                                    +  +++++G+ g+GKttl+  l+l +   G  +l+ +    ++ l ++ E+++ ++ rR++
  gi|119720698|ref|YP_921193.1| 28 ERSRITVIMGPNGSGKTTLLRMLGLLLPpDGG-LLE-M--DGVNLLSLDEEGRR-GFLRRVA 84
                                   567889**************999988885333.334.3..78888888877777.8888776 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00025      0.14      98     119 ..      29      50 ..      19      54 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00025
                                    TTSEEEEECSTTSSHHHHHHHH CS
                    RsgA_GTPase  98 kdktsvlvGqSGvGKStLinal 119
                                    +++++v++G+ G GK+tL+ +l
  gi|119720698|ref|YP_921193.1|  29 RSRITVIMGPNGSGKTTLLRML 50 
                                    4599**************9887 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00036       0.2     126     149 ..      27      50 ..      18      60 .. 0.81
   2 ?   -2.1   0.0       2.8   1.6e+03      32      57 ..     196     220 ..     172     230 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00036
                          T2SSE 126 vrerglilvsGgTgsGKttllyal 149
                                    v++  + ++ G+ gsGKttll +l
  gi|119720698|ref|YP_921193.1|  27 VERSRITVIMGPNGSGKTTLLRML 50 
                                    677788899***********9765 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.8
                          T2SSE  32 dgielreveelekaalerlisriaal 57 
                                     + ++re+++l ++ l ++  ri+a 
  gi|119720698|ref|YP_921193.1| 196 SH-NVREAKFLADEILVMVSGRIKAR 220
                                    33.55666666666666666666654 PP

>> Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00034      0.19     144     183 ..     163     200 ..     143     201 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00034
                                    HHSSHHHHTTCSSSEEEEEEEEETTCTTEEEEEEEEETTT CS
                Semialdhyde_dhC 144 drPtpaavaggtnsvsVGRirkdemgdeglklvvvgDNll 183
                                    d+Pt  ++ +  n++++ R+ k  + ++g++ vvv++N++
  gi|119720698|ref|YP_921193.1| 163 DEPTSHLDPK--NAAFIQRLVKEYVSERGIHCVVVSHNVR 200
                                    5688888884..9*************************97 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0097       5.4      44      68 ..      27      51 ..      17      58 .. 0.85
   2 ?   -0.4   0.0       1.5   8.3e+02     111     149 ..      60      97 ..      53     100 .. 0.83
   3 ?    1.1   0.0       0.5   2.8e+02     107     148 ..     155     198 ..     137     210 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0097
                      IstB_IS21 44 iekkenivllGpsGvGKshlaialg 68
                                   +e++   v++Gp G GK+ l   lg
  gi|119720698|ref|YP_921193.1| 27 VERSRITVIMGPNGSGKTTLLRMLG 51
                                   56777889**********9987776 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.5
                      IstB_IS21 111 llilDdlgllpldqaeaellfeviekryerrsiiitsnl 149
                                    ll +D + ll ld++ ++ +++ ++  + ++++++t+n+
  gi|119720698|ref|YP_921193.1|  60 LLEMDGVNLLSLDEEGRRGFLRRVA-FVPQKPVVLTANV 97 
                                    6778999999999999999999886.4677889999886 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.5
                      IstB_IS21 107 lkvdllilDdlgllpldqaeaellfeviekryerrsi...iitsn 148
                                    l +d+l+lD+  + +ld ++a+ + +++++ +  r i   +++ n
  gi|119720698|ref|YP_921193.1| 155 LSPDVLLLDEP-TSHLDPKNAAFIQRLVKEYVSERGIhcvVVSHN 198
                                    46799***996.567999999999999998887765422155555 PP

>> Adeno_IVa2  Adenovirus IVa2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1    0.0006      0.34      88     107 ..      31      50 ..      21      56 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0006
                     Adeno_IVa2  88 viGviyGPtGsGksqllrnl 107
                                     i vi GP GsGk+ llr l
  gi|119720698|ref|YP_921193.1|  31 RITVIMGPNGSGKTTLLRML 50 
                                    489***************87 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0    0.0015      0.85       3      21 ..      32      50 ..      30      58 .. 0.83
   2 ?   -1.7   0.0       3.3   1.9e+03     141     173 ..      62      94 ..      59      98 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0015
                                   EEEEEESTTSSHHHHHHHH CS
                          SRP54  3 villvGlqGaGKTttlaKL 21
                                   +++++G++G+GKTt l  L
  gi|119720698|ref|YP_921193.1| 32 ITVIMGPNGSGKTTLLRML 50
                                   7899**********98766 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.3
                                    SCSEEEEESTTSSSSTTHHHHHHHHHTS-EEEE CS
                          SRP54 141 gitgviltklDgdakgGaalsiaaelklPikfi 173
                                    +++gv l  lD++ + G +  +a   ++P++++
  gi|119720698|ref|YP_921193.1|  62 EMDGVNLLSLDEEGRRGFLRRVAFVPQKPVVLT 94 
                                    7889999999*******9999999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                       116  (0.00646996); expected 17.9 (0.001)
Passed Fwd filter:                        32  (0.00178482); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              32  [number of targets reported over threshold]
# CPU time: 0.69u 0.38s 00:00:01.06 Elapsed: 00:00:00.56
# Mc/sec: 1251.97
//
Query:       gi|119720699|ref|YP_921194.1|  [L=289]
Description: molybdate-binding domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      3e-51  173.3   0.0    4.2e-51  172.8   0.0    1.2  1  PBP_like        PBP superfamily domain
    0.00049   19.9   0.0    0.00076   19.3   0.0    1.3  1  SBP_bac_11      Bacterial extracellular solute-binding protei
  ------ inclusion threshold ------
      0.011   15.7   4.1      0.044   13.7   0.5    3.1  3  HTH_1           Bacterial regulatory helix-turn-helix protein
      0.022   14.3   0.0      0.031   13.9   0.0    1.2  1  Phosphonate-bd  ABC transporter, phosphonate, periplasmic sub


Domain annotation for each model (and alignments):
>> PBP_like  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.8   0.0   9.5e-55   4.2e-51       4     192 ..      75     263 ..      72     264 .. 0.95

  Alignments for each domain:
  == domain 1  score: 172.8 bits;  conditional E-value: 9.5e-55
                                    HHHH-TTCEEEEEES-HHHHHHHHHTTS-SEEEESS---CCCHHCCCCCEEEEEEEEEEEE-CC-HCHCCCCHCCHHHS- CS
                       PBP_like   4 laeknpgvrvavanvGsggGlkalrageadiagshlldketeeynapalrkaldgievvlvnlarreqglvvakgnpkki 83 
                                    l+e  +gv++++  vGs +Gl  l++g +++ag+h+ d+et++yn   +r   +g  ++l++++ re+g++v +gnpk+i
  gi|119720699|ref|YP_921194.1|  75 LEE--RGVFAEYLRVGSIAGLDLLKRGYCHLAGVHVVDPETGRYNEVVVR---EG--LALIRGYWREIGFMVLPGNPKNI 147
                                    555..49****************************************999...56..89********************* PP

                                    -BGGGC-S-B-EEEEE-TTSHHHHHHHHHHC-CEECT........E-SSTTSEEESSHHHHHCCHCCETTCCECCCGG-H CS
                       PBP_like  84 tnwkdladaplrlvnRetGSGtrdlfdellkkegisk........ssikgyaqearshlavaaaVaagradvgvgieava 155
                                     + +dl +++++l+nR++GSG+ +l+++llk+   s          +i+g ++e+ sh+++  aV +g+adv++g++ +a
  gi|119720699|ref|YP_921194.1| 148 YSPADLLRRNVVLANRNRGSGSYVLLEKLLKDLSSSLgvpvqalkRRIRGFETEYISHGEAGLAVLNGKADVAIGPRWTA 227
                                    ******************************997544488889999*********************************** PP

                                    CCCCCCECTTCE-EEEEEEEECTCCCSHHHHHHHHHH CS
                       PBP_like 156 eelkgldfvplaeerydlvvrkealddpevqaflefl 192
                                    ++l gldfvpla+er+d+++r+e l+d+ v+ f+e+l
  gi|119720699|ref|YP_921194.1| 228 RQL-GLDFVPLAKERFDFATRRELLKDENVETFVEVL 263
                                    *98.*******************************98 PP

>> SBP_bac_11  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.7e-07   0.00076      80     186 ..     134     240 ..     129     277 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.7e-07
                                    EEEEEESTT-TT---SHHHHHHSS--EEEE--T-TTTTHH.HHHHGGG--..HHHHHHHHHTEEEEESSH...HHHHHHH CS
                     SBP_bac_11  80 plviavpkgnpkkikgwadLlkpglklavadPttspsGlaalalleaaga..qellkalekkvvklgess...rqlltav 154
                                     + ++v +gnpk+i++ adLl+ ++ la  +   s+s+   ++ll+ +       ++al+++++++++ +   + +  av
  gi|119720699|ref|YP_921194.1| 134 EIGFMVLPGNPKNIYSPADLLRRNVVLANRNR-GSGSYVLLEKLLKDLSSslGVPVQALKRRIRGFETEYishGEAGLAV 212
                                    57899*****************9887777773.4677777789999664334478999999999999888777888888* PP

                                    HTTT-SEEEEEHHHHH..HSTTSSEEEE--TT CS
                     SBP_bac_11 155 eageadagivyeseakaaengdkleavylpeg 186
                                     +g+ad++i+++  a     + +l++v+l ++
  gi|119720699|ref|YP_921194.1| 213 LNGKADVAIGPRWTAR----QLGLDFVPLAKE 240
                                    ************9999....999999998766 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.5   9.7e-06     0.044      35      60 .]       2      32 ..       1      32 [. 0.81
   2 ?   -1.2   0.0      0.44     2e+03      22      39 ..     183     200 ..     175     202 .. 0.74
   3 ?    1.3   0.1     0.074   3.3e+02       4      25 ..     256     277 ..     254     279 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 9.7e-06
                                   HHHHHHHTS-SEEESSSE.....EEE-HHHH CS
                          HTH_1 35 krLEeelgvpLfeRtgrg.....lrLTeaGe 60
                                   ++LE++lgv+L+ Rt +g     + LT+ ++
  gi|119720699|ref|YP_921194.1|  2 SNLERRLGVQLVRRTRGGlgggrVMLTATAQ 32
                                   79************76655567799998775 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.44
                                    HHTS-HHHHHHHHHHHHH CS
                          HTH_1  22 eLglsqpavsrqikrLEe 39 
                                     Lg+   a+ r+i+  E 
  gi|119720699|ref|YP_921194.1| 183 SLGVPVQALKRRIRGFET 200
                                    477777888888887776 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.074
                                    HHHHHHHHHHSSHHHHHHHHTS CS
                          HTH_1   4 lrlfvavaeegsftrAAeeLgl 25 
                                    +++fv+v +++ f++ A  +gl
  gi|119720699|ref|YP_921194.1| 256 VETFVEVLRSKEFAEKAASVGL 277
                                    79**********9987777766 PP

>> Phosphonate-bd  ABC transporter, phosphonate, periplasmic substrate-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   6.8e-06     0.031      95     163 ..     145     230 ..     116     286 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.8e-06
                                    SS--SHHHHGG-EEEE--TT-TTTTHHHHHHTCCCCT--HH..........HHSSEEEE--HHHHHHHHHTTSSSEEE.. CS
                 Phosphonate-bd  95 sdiqsledLkgktiafvspsStsGylvpaalLvkeagldpe..........ddfsevfsgshdaavlavlsgdadaaa.. 162
                                     +i s +dL  ++++++ ++  sG++v +  L+k+    ++          + f++++  sh +a lavl+g+ad+a   
  gi|119720699|ref|YP_921194.1| 145 KNIYSPADLLRRNVVLANRNRGSGSYVLLEKLLKDLSSSLGvpvqalkrriRGFETEYI-SHGEAGLAVLNGKADVAIgp 223
                                    4577899***********************99755433333555577666678999877.7****************944 PP

                                    ......E CS
                 Phosphonate-bd 163 ......v 163
                                          +
  gi|119720699|ref|YP_921194.1| 224 rwtarqL 230
                                    4444440 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 1753.70
//
Query:       gi|119720700|ref|YP_921195.1|  [L=173]
Description: transporter [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.5e-25   89.0  17.5    3.9e-25   88.8  17.5    1.0  1  QueT          QueT transporter
  ------ inclusion threshold ------
      0.037   14.3   1.2      0.086   13.1   1.2    1.7  1  DUF3007       Protein of unknown function (DUF3007)
       0.14   12.4   0.2       0.14   12.4   0.2    2.2  2  MscL          Large-conductance mechanosensitive channel, Msc


Domain annotation for each model (and alignments):
>> QueT  QueT transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.8  17.5   6.5e-29   3.9e-25       3     139 .]       8     165 ..       6     165 .. 0.90

  Alignments for each domain:
  == domain 1  score: 88.8 bits;  conditional E-value: 6.5e-29
                           QueT   3 raaviaAlYvvltlvlapisfgaiqvRiseaLtlLpv.ftpaailGltiGcliaNlls......plgllDvifGslatli 75 
                                     aav  AlY++l++vl+pisf a+qvR+++aL+ L++ ++  a++G+ +Gc++ Nl+       +lgl+D +fGsla++ 
  gi|119720700|ref|YP_921195.1|   8 VAAVLGALYAALVIVLQPISFLAFQVRLADALLPLSMvLGVPAAVGVSVGCFFGNLVAapwgslALGLFDAVFGSLANFA 87 
                                    689**********************************99999*************8655666789*************** PP

                           QueT  76 aalltyllkkkr.....llaalppvlvnalivgav.....l....lelpflltvltvglgelivlyvlGlpllkalek 139
                                    a +l y+++ ++     l  a++ ++v++ ivg++     l    +++p+ +++l v++g +++++++G+pl +++ek
  gi|119720700|ref|YP_921195.1|  88 ASYLAYIVAYNKgrrakLAGAVLEAVVVSGIVGFYlkyllLwamgVDMPLEAVFLGVLAGSVVSIIAIGYPLAILVEK 165
                                    ********8777888755666999999999999886665515668999*************************99986 PP

>> DUF3007  Protein of unknown function (DUF3007)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   1.2   1.4e-05     0.086       6      55 ..      78     127 ..      75     141 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.4e-05
                        DUF3007   6 vlaiglgvlllgglaylvlqalGldslsagiwsqavlvlglvgWvltYll 55 
                                    +++ +l+ ++++ lay+v    G  +  ag + +av+v g+vg  l Yll
  gi|119720700|ref|YP_921195.1|  78 AVFGSLANFAASYLAYIVAYNKGRRAKLAGAVLEAVVVSGIVGFYLKYLL 127
                                    556678999***************************************97 PP

>> MscL  Large-conductance mechanosensitive channel, MscL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.2     0.088   5.3e+02      16      33 ..       5      22 ..       2      32 .. 0.85
   2 ?   12.4   0.2   2.4e-05      0.14      18      90 ..      51     129 ..      48     139 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.088
                           MscL 16 dLAvgviiGaaftkiVts 33
                                    L+v+ ++Ga + ++V  
  gi|119720700|ref|YP_921195.1|  5 SLSVAAVLGALYAALVIV 22
                                   699********9999965 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 2.4e-05
                           MscL  18 AvgviiGaaftkiVtslvkdiimpliglllggv.dfselkikl....kaeaavlkygafiqavinFliiafvi.Flivk 90 
                                    Avgv +G  f+++V +   ++   l+++++g++ +f+  +++     +++  +   ga+++av+   i++f + +l++ 
  gi|119720700|ref|YP_921195.1|  51 AVGVSVGCFFGNLVAAPWGSLALGLFDAVFGSLaNFAASYLAYivayNKGRRAKLAGAVLEAVVVSGIVGFYLkYLLLW 129
                                    9*****************************8854888665555667655566666899999999999999998887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.34s 00:00:00.92 Elapsed: 00:00:00.53
# Mc/sec: 977.81
//
Query:       gi|119720701|ref|YP_921196.1|  [L=219]
Description: hypothetical protein Tpen_1798 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-18   66.2  27.4    3.9e-18   65.9  27.4    1.2  1  DUF4013   Protein of unknown function (DUF4013)


Domain annotation for each model (and alignments):
>> DUF4013  Protein of unknown function (DUF4013)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.9  27.4   2.2e-22   3.9e-18       2     166 ..      30     189 ..      28     206 .. 0.81

  Alignments for each domain:
  == domain 1  score: 65.9 bits;  conditional E-value: 2.2e-22
                        DUF4013   2 lsllliiaivlslvllGYlvrvlrdtirgddelPefd..dwgkllvdGlkafvvslvYllipliialltllvalaslaag 79 
                                    l++l i++i+  +++ GY+v v+r   +  +e+P++d  ++g+++v+Glk+f+ sl+ +l+p++i  l +l+ l++ +a 
  gi|119720701|ref|YP_921196.1|  30 LIVLSIVPIIN-FIVIGYFVYVVR---HDLEEPPKLDtsKLGDYFVEGLKVFLASLI-ILVPVLI--LGVLAGLVAGLAY 102
                                    34444444444.999*********...44455*****999*****************.66*****..4444444444445 PP

                        DUF4013  80 dsaagallvlallglllalllvllllllfglllpvalarfartgslsaafnfkeilklikkki.gkyiialilllvigiv 158
                                    + +a+ + +   + l+l++ +++++l  ++++++  la+++rtg+ls+ + f+e+l+li++   ++y++ +++l+v+g++
  gi|119720701|ref|YP_921196.1| 103 PLGAFPFYFHRAFVLALFIPVLFVALA-IAFIAVPLLAIVMRTGDLSKILAFQEALSLIQSYGlVDYAVLFLVLVVVGFL 181
                                    555555555555566666655555555.9******************************9988***************** PP

                        DUF4013 159 lsllaill 166
                                     +++ +ll
  gi|119720701|ref|YP_921196.1| 182 PYYVHWLL 189
                                    99999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       884  (0.0493056); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.67u 0.34s 00:00:01.01 Elapsed: 00:00:00.53
# Mc/sec: 1238.00
//
Query:       gi|119720702|ref|YP_921197.1|  [L=248]
Description: hypothetical protein Tpen_1799 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.60u 0.34s 00:00:00.94 Elapsed: 00:00:00.53
# Mc/sec: 1397.17
//
Query:       gi|119720703|ref|YP_921198.1|  [L=469]
Description: ATP-dependent protease La [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.1e-141  472.5   0.0   1.3e-141  472.3   0.0    1.0  1  Lon_2     Putative ATP-dependent Lon protease
  ------ inclusion threshold ------
      0.047   13.4   0.0       0.11   12.2   0.0    1.6  1  RuvB_N    Holliday junction DNA helicase RuvB P-loop domain


Domain annotation for each model (and alignments):
>> Lon_2  Putative ATP-dependent Lon protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  472.3   0.0  1.4e-145  1.3e-141       2     454 ..      12     463 ..      11     464 .. 0.97

  Alignments for each domain:
  == domain 1  score: 472.3 bits;  conditional E-value: 1.4e-145
                          Lon_2   2 vFegkvvrKdltkklkeganvPtyvleyLlgkycatddeeeieeglekvkeilaenyvrpdekeliksklreegevklid 81 
                                    +F   +++K +++++    +vP+++ eyL++ +c ++++   +e++++++++++e y++p+++el+ s+l+e+g++kl+d
  gi|119720703|ref|YP_921198.1|  12 IFGMVAINKAVANNVAI-SRVPRFISEYLINFKCGESQD---AECVSRLSRYISELYPDPSDRELFLSRLKERGSLKLLD 87 
                                    799999*********99.89**********999876666...779*********************************** PP

                          Lon_2  82 kvsvkldekkdkyeaelsnlglkeveieeelvkkneklltggvwgiieleyepee..ekkespfviedlkpiqlskvdle 159
                                    +++v++d k+++y  e+++l++ ++ ++e++v++n++l++ g+wg+  l y+pe   +k+++p+v++d++p+q+s vdl+
  gi|119720703|ref|YP_921198.1|  88 EFKVRVDLKRNTYLLEIPSLQIADAFVNEDIVRENARLFS-GLWGVGLLYYKPELsrSKNRTPVVLHDYRPFQASYVDLK 166
                                    **************************************98.9*********8887888899******************* PP

                          Lon_2 160 elkeaRkeftkeeWidlllrsvglepealserqkllllaRLlplveknlnliELgPrgTGKsyvykeispysilvsGGkv 239
                                     ++e+R++ft eeW+dll++s+gl+p+a++  q+llll+RL+p+ e+n+n++ELgPr+TGK+ +y++++ ys++ +GG++
  gi|119720703|ref|YP_921198.1| 167 LFVESRSKFTFEEWVDLLVTSIGLNPKAYTLGQRLLLLSRLIPVAEPNVNILELGPRATGKTSLYRNVAYYSRIYAGGTI 246
                                    ******************************************************************************** PP

                          Lon_2 240 tvakLFvnnstkkvGlvglwdvvafDEvagikfkdk.elvqilKdYmesgsfsrgk.eeisaeaslvlvGNideeveell 317
                                    t+a+LF++ + + +G ++l+dv++fDE+++++++++ elv++lKdYm +g f+rg  +++++++slv++GN+d+e    +
  gi|119720703|ref|YP_921198.1| 247 TPARLFFDARLSVPGDLALHDVIVFDEISRVRLSNPdELVAKLKDYMVDGFFERGAlKRAHSTCSLVFLGNVDVERI--A 324
                                    ************************************9*******************899*************98655..5 PP

                          Lon_2 318 ktsdlfeelpeemrdsAfldRihgyipGweipkl..rkelltkgyglivdylaeilhelrkesytevveelvelgkklsq 395
                                      s+++e lp++mrdsAfldRihg+ipGw++pk+  ++e l++gygl++dylae+lh+lr+   ++vv ++ve+ +k+++
  gi|119720703|ref|YP_921198.1| 325 DPSHILEYLPSFMRDSAFLDRIHGFIPGWRLPKImrSEESLASGYGLASDYLAEVLHRLRDVAAESVVADHVEFVGKYTI 404
                                    56*******************************988899***************************************** PP

                          Lon_2 396 RdekavkktvsgllKllfPdeevtkeeleellelalelrrrvkeqlkkideaefadvnl 454
                                    Rdekavk+++sg +K+lfP+ e++++el+++ +  + lr++v + l+ i+++ef  ++l
  gi|119720703|ref|YP_921198.1| 405 RDEKAVKRLLSGAVKILFPNFEFDNAELARVARGIVGLRNNVSRLLTAISPSEFPPKKL 463
                                    ******************************************************87665 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.2e-05      0.11      36     125 ..     217     306 ..     210     314 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.2e-05
                         RuvB_N  36 vllyGpPGlGkttlakiiakelgvklkitsgPvlekagdlaalltnleekdvlfideihrlsraveevlysamedfrldi 115
                                    +l  Gp   Gkt+l + +a    +    t +P+        ++  +l  +dv+  dei r++ +  + l + + d+++d 
  gi|119720703|ref|YP_921198.1| 217 ILELGPRATGKTSLYRNVAYYSRIYAGGTITPARLFFDARLSVPGDLALHDVIVFDEISRVRLSNPDELVAKLKDYMVDG 296
                                    6778999999999999999998888888888887777777789999******************9999***********9 PP

                         RuvB_N 116 vigkGpsars 125
                                      ++G+  r+
  gi|119720703|ref|YP_921198.1| 297 FFERGALKRA 306
                                    9999987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (469 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.67u 0.37s 00:00:01.04 Elapsed: 00:00:00.54
# Mc/sec: 2595.13
//
Query:       gi|119720704|ref|YP_921199.1|  [L=134]
Description: hypothetical protein Tpen_1801 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.2e-18   64.2   0.9    7.2e-18   64.2   0.9    1.9  2  DUF1641   Protein of unknown function (DUF1641)


Domain annotation for each model (and alignments):
>> DUF1641  Protein of unknown function (DUF1641)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0      0.31   5.5e+03      10      22 ..      30      42 ..      30      42 .. 0.78
   2 !   64.2   0.9     4e-22   7.2e-18       3      39 .]      93     129 ..      91     129 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.31
                        DUF1641 10 GlfgLlraLrDPD 22
                                   Gl++ +  L DP+
  gi|119720704|ref|YP_921199.1| 30 GLLDAVNGLVDPE 42
                                   7788888888887 PP

  == domain 2  score: 64.2 bits;  conditional E-value: 4e-22
                        DUF1641   3 leepkpvGlfgLlraLrDPDVqrGLGfllalLKalGk 39 
                                    ++epkpvGl gLlraL+DP+VqrGLG+++++LKalG+
  gi|119720704|ref|YP_921199.1|  93 QKEPKPVGLAGLLRALSDPEVQRGLGVAIEVLKALGR 129
                                    79**********************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.33s 00:00:00.88 Elapsed: 00:00:00.53
# Mc/sec: 766.79
//
Query:       gi|119720705|ref|YP_921200.1|  [L=392]
Description: FAD-dependent pyridine nucleotide-disulphide oxidoreductase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.2e-19   68.9   0.0    6.3e-18   65.0   0.0    2.0  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    0.00011   22.6   0.5      0.066   13.8   0.0    2.8  3  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
     0.0035   17.3   0.1        0.3   11.1   0.0    2.4  2  NAD_binding_9   FAD-NAD(P)-binding
     0.0054   16.0   0.0      0.009   15.3   0.0    1.3  1  FAD_binding_3   FAD binding domain
     0.0069   16.0   0.4        2.5    7.6   0.5    2.4  2  DAO             FAD dependent oxidoreductase
     0.0098   14.8   0.9       0.19   10.5   0.2    2.1  2  Trp_halogenase  Tryptophan halogenase
  ------ inclusion threshold ------
       0.06   12.0   0.0         13    4.4   0.0    2.7  3  HI0933_like     HI0933-like protein
      0.074   13.3   0.2       0.81   10.0   0.1    2.2  2  TrkA_N          TrkA-N domain
       0.16   11.0   0.2        1.8    7.5   0.1    2.1  2  Lycopene_cycl   Lycopene cyclase protein


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.0   0.0   3.2e-21   6.3e-18       2     291 ..       3     299 ..       2     302 .. 0.74

  Alignments for each domain:
  == domain 1  score: 65.0 bits;  conditional E-value: 3.2e-21
                                    SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHH.HCHHHHHHHHHHHHH..HHHHCHHHHCCCCHCCTCEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcll.skallgvaedaeias..evvkklnqgielllgeevvki 78 
                                    +vv+iGgG +G  +a  l + ++kvt+v ++ +++++++     a+ gv++++  +        l+  +e++++ evv++
  gi|119720705|ref|YP_921200.1|   3 RVVIIGGGGGGAILANLLPE-EFKVTVV-DKSEVHFFQPGNlWIAFKGVRKEKFLRPlrS---LLKPRVEFVHD-EVVSV 76 
                                    7**********999988887.*******.8888888888771444444444443333542...35568******.***** PP

                                    EESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC....TTBEECCSECHHHHHHCCSS-T..SEEEEES-SHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxx RF
                    Pyr_redox_2  79 dpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGv...aenvgklvrtldsaealklkllp..krivvvGgGyi 153
                                    d +++ vk       +++++ yd++v A+G++     +pG     e  g++ +t ++ae+l+  l+   +   v+G    
  gi|119720705|ref|YP_921200.1|  77 DLNERVVKT-----ASGKSLSYDYVVFASGAELDYGSVPGHrelLERFGDFYSTPENAEKLHASLRGlkEGRFVIGIADP 151
                                    ****77777.....56779************999999**9999988889999**********999998866677773222 PP

                                    ......HHHHHHHH.......HHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEE CS
                                    ......xxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 154 ......GvElAaal.......aklgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgngeklevvl 220
                                          G   Aa+l       + l ++v +v a + +     k +++++e +l+ +G+e+++  +v+e+d  ++  + v 
  gi|119720705|ref|YP_921200.1| 152 vykcppGPHKAAFLsweffarRGLSDKVKVVLAVPVPHAYPSKTIADIIEPELNSRGIELHTFFTVNEVDVANK--RIVS 229
                                    011111333333324444443455558999999999987788****************************9999..5445 PP

                                    TTSCE..EEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTS.BES.STTEEE-GGGCTECCSS--HHHHH CS
                                    xxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 221 edgee..idadlvvvavGvrpstelleeklglelderggivvdefl.rtn.vpgiyaiGDvaggkggpelaqaAv 291
                                     +gee  +d+  vv    + ps +   + + ++ d  g+i++d++  r++  ++ yaiGD++ +  + ++ ++A+
  gi|119720705|ref|YP_921200.1| 230 LEGEElsFDVAAVVPPH-RGPSYAV--NPAEVK-DGSGYIKIDKYTsRVEgFDDAYAIGDCT-NAPTSKSGVTAH 299
                                    55555126666666555.6666544..788887.69*********978888***********.445555555555 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.5     0.013        26       1      31 [.       3      32 ..       3      36 .. 0.82
   2 !   13.8   0.0   3.3e-05     0.066      20      73 ..     174     227 ..     165     234 .. 0.83
   3 ?   -2.2   0.0       3.1   6.2e+03      51      66 ..     292     307 ..     283     311 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.013
                                   EEEEECSSHHHHHHHHHHHHTTSEEEEEESS CS
                      Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvvers 31
                                   +vv++GgG  g  lA+ l e   kVtvv+ s
  gi|119720705|ref|YP_921200.1|  3 RVVIIGGGGGGAILANLLPEEF-KVTVVDKS 32
                                   79*************9996644.68888766 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 3.3e-05
                                    HTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSE CS
                      Pyr_redox  20 elgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedgv 73 
                                     l +kV+vv + + +  +  +++++i++ +l  +gie+++  +v+e++  ++ +
  gi|119720705|ref|YP_921200.1| 174 GLSDKVKVVLAVPVPHAYPSKTIADIIEPELNSRGIELHTFFTVNEVDVANKRI 227
                                    355899999999999988899***************************888763 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 3.1
                                    HHTTEEEECSEEEEEE CS
                      Pyr_redox  51 ekngievllntkveei 66 
                                    +k g++ +l+++v++ 
  gi|119720705|ref|YP_921200.1| 292 SKSGVTAHLQAEVVAA 307
                                    6789999999999876 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1     0.023        46       1      36 [.       5      34 ..       5      44 .. 0.73
   2 !   11.1   0.0   0.00015       0.3     115     154 ..      64     101 ..      51     103 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.023
                  NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsep 36
                                   +i+G+G  G+ +++ Ll +     ++++t++d+se 
  gi|119720705|ref|YP_921200.1|  5 VIIGGGGGGAILAN-LLPE-----EFKVTVVDKSEV 34
                                   69****98876655.5544.....489999998764 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00015
                  NAD_binding_9 115 vtvevhraevvdleeradgqavlladgaslaadaVvLAlG 154
                                     +ve++++evv+++ +++   v +a+g+sl +d+Vv A G
  gi|119720705|ref|YP_921200.1|  64 PRVEFVHDEVVSVDLNER--VVKTASGKSLSYDYVVFASG 101
                                    389**********97654..6999**************99 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   4.5e-06     0.009       4      34 ..       4      33 ..       2      39 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.5e-06
                                   EEEE--SHHHHHHHHHHHHTTHHEEEEESSS CS
                  FAD_binding_3  4 VlIVGaGpaGlmlallLseaGvrvvlvekrs 34
                                   V+I+G+G  G++la+lL e   +v++v+k +
  gi|119720705|ref|YP_921200.1|  4 VVIIGGGGGGAILANLLPEE-FKVTVVDKSE 33
                                   9*******************.*******987 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.5    0.0013       2.5       1      29 [.       3      32 ..       3      36 .. 0.86
   2 !    5.7   0.0    0.0046       9.2     148     207 ..      54     108 ..      47     149 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0013
                                   EEEEECTSHHHHHHHHHHHHTT.EEEEESS CS
                            DAO  1 dvviiGGGiiGlstAyeLarrg.Vtllekg 29
                                   +vviiGGG  G+  A  L ++  Vt+++k+
  gi|119720705|ref|YP_921200.1|  3 RVVIIGGGGGGAILANLLPEEFkVTVVDKS 32
                                   59****************66525*****98 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0046
                                    HHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHH.HH CS
                            DAO 148 ltaalaraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsd.ll 207
                                    +++ l++ ++ + ve++   ev++++ ++     v  +t+ g   ++d+vV a Ga  d  +
  gi|119720705|ref|YP_921200.1|  54 FLRPLRSLLKPR-VEFVHD-EVVSVDLNE---RVV--KTAsGKSLSYDYVVFASGAELDyGS 108
                                    555555555545.999999.999996642...233..5555766467*********987633 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.2   9.7e-05      0.19       1      43 [.       3      41 ..       3      46 .. 0.91
   2 ?    2.9   0.0      0.02        40     168     210 ..      65     103 ..      46     106 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 9.7e-05
                                   EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS---SS-E CS
                 Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlveseeigtvgvGe 43
                                   ++vi+GGG  G + A++l + +    +vt+v+++e+   + G 
  gi|119720705|ref|YP_921200.1|  3 RVVIIGGGGGGAILANLLPEEF----KVTVVDKSEVHFFQPGN 41
                                   69***************99999....89*******99888885 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.02
                                    T-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-SEEEE-SGGG CS
                 Trp_halogenase 168 GvtrvegkvvevqldedgrveslrledgreveadlfiDcsGfr 210
                                     v+ v+++vv+v+l+e+     +++++g+++++d ++ +sG +
  gi|119720705|ref|YP_921200.1|  65 RVEFVHDEVVSVDLNER----VVKTASGKSLSYDYVVFASGAE 103
                                    58899999988888774....589999**************75 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.1    0.0074        15       2      32 ..       3      32 ..       2      35 .. 0.87
   2 ?   -1.4   0.0      0.36   7.2e+02     132     165 ..      73     103 ..      63     124 .. 0.70
   3 ?    4.4   0.0    0.0063        13     105     158 ..     190     242 ..     168     253 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0074
                                   SEEEE--SHHHHHHHHHHHHTT--EEEE-SS CS
                    HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVllleka 32
                                   +v++iGgG  G   A  +  ++ +V++++k 
  gi|119720705|ref|YP_921200.1|  3 RVVIIGGGGGGAILANLL-PEEFKVTVVDKS 32
                                   69**********999877.788999999997 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.36
                                    EEEEECETTE.EEEEE.TTEEEEESEEEE----S CS
                    HI0933_like 132 vksvekeedgkfrvktkseeeleadklvlAtGGl 165
                                    v sv+   ++   vkt s+++l+ d++v+A+G +
  gi|119720705|ref|YP_921200.1|  73 VVSVDL--NE-RVVKTASGKSLSYDYVVFASGAE 103
                                    555533..33.45777799***********9864 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.0063
                                    T.-CHHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEE CS
                    HI0933_like 105 sdkaedivdallkelkeagvklrletevksvekeedgkfrvktkseeeleadkl 158
                                    +  +++i d+++ el+++g++l++  +v++v+  ++++++++  +e ++  +++
  gi|119720705|ref|YP_921200.1| 190 AYPSKTIADIIEPELNSRGIELHTFFTVNEVDVANKRIVSLEG-EELSFDVAAV 242
                                    55799**************************999888666665.5555555555 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00041      0.81       1      32 [.       4      34 ..       4      40 .. 0.91
   2 ?    0.8   0.0      0.29   5.8e+02      22      42 ..      71      93 ..      58     105 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00041
                                   EEEES-SHHHHHHHHHHHHTTEEEEEEESSHH CS
                         TrkA_N  1 iiiiGlGrvGrslaeeLseggkdvvvidkdee 32
                                   ++iiG G  G  la+ L e+  +v+v+dk+e 
  gi|119720705|ref|YP_921200.1|  4 VVIIGGGGGGAILANLLPEEF-KVTVVDKSEV 34
                                   79*****************99.5******985 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.29
                                   EEEEEEESSHHHHHHHHHTT..S CS
                         TrkA_N 22 kdvvvidkdeerveelreeg..l 42
                                   ++vv +d +e++v++++ +   +
  gi|119720705|ref|YP_921200.1| 71 DEVVSVDLNERVVKTASGKSlsY 93
                                   569************98777343 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.1    0.0009       1.8       2      47 ..       4      46 ..       3      55 .. 0.90
   2 ?    1.7   0.0     0.052     1e+02      84     145 ..      49     105 ..      44     119 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0009
                  Lycopene_cycl  2 vvviGaGpAglslAarlteakpglkvvlieaspsllfpnnyvWsde 47
                                   vv+iG+G  g  lA+ l     + kv++++ s+   f +   W  +
  gi|119720705|ref|YP_921200.1|  4 VVIIGGGGGGAILANLL---PEEFKVTVVDKSEVHFFQPGNLWIAF 46
                                   8**************99...889**********9999988888765 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.052
                  Lycopene_cycl  84 vsskrlkeellerlvengvklleakvesveeeeageslvvleggrkirarlvvdarglaslk 145
                                    v+++++ + l ++l + +v++++  v sv  +e    +v ++ g+ +    vv a+g a+l+
  gi|119720705|ref|YP_921200.1|  49 VRKEKFLRPL-RSLLKPRVEFVHDEVVSVDLNER---VVKTASGKSLSYDYVVFASG-AELD 105
                                    5666665554.34555778888877777766655...9*******************.5554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.69u 0.35s 00:00:01.04 Elapsed: 00:00:00.54
# Mc/sec: 2193.64
//
Query:       gi|119720706|ref|YP_921201.1|  [L=78]
Description: hypothetical protein Tpen_1803 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-17   62.8   0.0    2.2e-17   62.6   0.0    1.0  1  TusA      Sulfurtransferase TusA
  ------ inclusion threshold ------
       0.14   12.0   0.0       0.15   11.9   0.0    1.0  1  HrpE      HrpE/YscL/FliH and V-type ATPase subunit E


Domain annotation for each model (and alignments):
>> TusA  Sulfurtransferase TusA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.6   0.0   2.5e-21   2.2e-17       1      69 [.       4      73 ..       4      74 .. 0.93

  Alignments for each domain:
  == domain 1  score: 62.6 bits;  conditional E-value: 2.5e-21
                                   EEEEBTT-STTCCHHHHHHHHCCCGCT-EEEEEESSCHHHHHHHHHHHHHTEEEEEEE-GCC-E.EEEEE CS
                           TusA  1 ielDlrGlvCPePllklkkalekleegevlevladdpaatediprfakklghelveveeedgey.rivir 69
                                   i++D+rG++CP+P+  l +a ++++ g+ + vla+dp+++ d++++++++++elve  + dg++ + vi+
  gi|119720706|ref|YP_921201.1|  4 ITVDARGMACPGPISALTRAYRNAQNGDLIIVLATDPGFEPDVKAWVERTKNELVELAKVDGNViKAVIK 73
                                   69*********************************************************88665477775 PP

>> HrpE  HrpE/YscL/FliH and V-type ATPase subunit E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   1.7e-05      0.15     115     161 ..      16      62 ..       9      76 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.7e-05
                           HrpE 115 RasALlRqLlksqqgearatLycHPeaaadvaaWLaehsdleWklks 161
                                     +sAL R   + q+g+    L+  P+   dv+aW++ ++++   l++
  gi|119720706|ref|YP_921201.1|  16 PISALTRAYRNAQNGDLIIVLATDPGFEPDVKAWVERTKNELVELAK 62 
                                    579*********************************99988777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.50
# Mc/sec: 472.31
//
Query:       gi|119720707|ref|YP_921202.1|  [L=135]
Description: hypothetical protein Tpen_1804 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-11   45.0   0.6    1.9e-05   24.6   0.1    2.0  2  DrsE_2    DsrE/DsrF/DrsH-like family
    2.5e-06   27.9   0.0    6.4e-06   26.5   0.0    1.6  1  DrsE      DsrE/DsrF-like family
     0.0046   17.4   0.0     0.0061   17.0   0.0    1.1  1  DUF2482   Hypothetical protein of unknown function (DUF2482)


Domain annotation for each model (and alignments):
>> DrsE_2  DsrE/DsrF/DrsH-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.1   9.5e-08   0.00057       3      40 ..       3      40 ..       1      64 [. 0.89
   2 !   24.6   0.1   3.2e-09   1.9e-05      89     149 ..      69     131 ..      42     135 .] 0.83

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 9.5e-08
                                   -EEEEEE----H.HHHHHHHHHHHHHHTT-EEEEEE-G CS
                         DrsE_2  3 kklaiifskgtldkalaalilAsgAaalglevtiFftF 40
                                   k laii+++gt dk ++  +l ++Aa+lg+ v iF t 
  gi|119720707|ref|YP_921202.1|  3 KGLAIIMFSGTADKFIPLGVLTQTAANLGVPVRIFVTG 40
                                   6689*******************************995 PP

  == domain 2  score: 24.6 bits;  conditional E-value: 3.2e-09
                                    HHHHCT---HHHHHHHHHHT.T-EEEEEHHHHHHHT--GGGB-TT-.EEE-HHHHHHHHHC-S CS
                         DrsE_2  89 vmkekgvasleeLleaakea.gvklvaCqmtmdlmglkkeelidgv.eiagaatylkeaeead 149
                                     +++ +++s  +++ +ake  +vk++ C +  + +glkke+l + v  i+ga+ ++ke +e +
  gi|119720707|ref|YP_921202.1|  69 GLEKMKAPSWYDMVREAKEVgDVKVYVCSLIAEALGLKKEDLDPIVdDIVGATFFMKETAEYE 131
                                    3478899999********9736************************99*******99988765 PP

>> DrsE  DsrE/DsrF-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0   1.1e-09   6.4e-06      23     100 ..      23     119 ..       4     134 .. 0.77

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 1.1e-09
                                    HHHHHHTTT-EEEEEE-GGGGGGGBS..................---TGGGTS---GGGGGGCGGGT.-EEEEEHHHHHH CS
                           DrsE  23 lalaaaalghevsvffygdGvllllk..................gqtanpadeknlaellkalkeyg.vklyvCgqaaka 83 
                                    l + aa+lg  v +f++g ++ +++k                   +  ++ + ++ +++++++ke g vk+yvC   a+a
  gi|119720707|ref|YP_921202.1|  23 LTQTAANLGVPVRIFVTGFATPYFTKnkpqprfpkefedmvpglLKGLEKMKAPSWYDMVREAKEVGdVKVYVCSLIAEA 102
                                    456789999*****************999999999988888888555566667788*********777************ PP

                                    TT--GGGE-.T--EEEE- CS
                           DrsE  84 rgldededl.gvgvevsg 100
                                     gl+ +edl  +   ++g
  gi|119720707|ref|YP_921202.1| 103 LGLK-KEDLdPIVDDIVG 119
                                    ****.5666323333333 PP

>> DUF2482  Hypothetical protein of unknown function (DUF2482)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0     1e-06    0.0061       1      78 [.      57     133 ..      57     134 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1e-06
                        DUF2482   1 kefKdmtqeeikdllaeKskeLyelieeikeetdFdillfsai....gvsdgdaqvsssslvvGkivglanlLkneeefk 76 
                                    kef dm    +k l + K+ + y++++e ke  d ++++ s i    g++++d      + +v +ivg + ++k++ e++
  gi|119720707|ref|YP_921202.1|  57 KEFEDMVPGLLKGLEKMKAPSWYDMVREAKEVGDVKVYVCSLIaealGLKKED-----LDPIVDDIVGATFFMKETAEYE 131
                                    79***************************************997777888888.....5566666666666666677777 PP

                        DUF2482  77 di 78 
                                     i
  gi|119720707|ref|YP_921202.1| 132 VI 133
                                    65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 806.63
//
Query:       gi|119720708|ref|YP_921203.1|  [L=249]
Description: creatininase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.2e-52  177.9   0.0    2.5e-52  177.8   0.0    1.1  1  Creatininase  Creatinine amidohydrolase


Domain annotation for each model (and alignments):
>> Creatininase  Creatinine amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  177.8   0.0   1.4e-56   2.5e-52       2     195 ..       8     192 ..       7     237 .. 0.82

  Alignments for each domain:
  == domain 1  score: 177.8 bits;  conditional E-value: 1.4e-56
                   Creatininase   2 eltwpeveea..lkeddvailPvGstEqHGphlplgtDtliaealaervaeklgakalvlPtlpyGvseehlgfpGTisl 79 
                                    el++ e++e   +++ d  +lPvG +E HG+hlplgtDtli++al e vaek++  a++lP+++yGv++   g+ G++ +
  gi|119720708|ref|YP_921203.1|   8 ELSYVELKEEveKRKIDSFVLPVGTVEPHGTHLPLGTDTLIPSALGEYVAEKVN--AVLLPPVHYGVTTGLHGYFGSVRV 85 
                                    78888886665566669***********************************99..99*********988899******* PP

                   Creatininase  80 spetliavlrdileslarhGfrrivlvngHggnsaalkeaarelraehdaaavrvtaaekelaaalkleeaae.aaeese 158
                                    +petl a++++iles++ hGfr  +++ngHggn++al++aa++++ ++ + av          ++++++  a+ ++ ++e
  gi|119720708|ref|YP_921203.1|  86 QPETLEALVYEILESMSLHGFRYGLILNGHGGNTQALDNAAKKAWLRN-KLAV----------MVVDWWILAReKGVTRE 154
                                    ************************************************.5543..........45667888887888888 PP

                   Creatininase 159 eee.gggHAgelEtSlmlalrpelVrmdraedpeeakl 195
                                        +ggHA  +Et+++la+rpelV+ + +++++   +
  gi|119720708|ref|YP_921203.1| 155 VLGkEGGHAATDETAMVLAIRPELVKRNLYTPSAVYVY 192
                                    88889***********************9988776543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1641.43
//
Query:       gi|119720709|ref|YP_921204.1|  [L=356]
Description: ABC transporter related [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.3e-36  125.3   0.0    8.6e-36  123.5   0.0    1.9  2  ABC_tran      ABC transporter
    4.2e-09   36.5   0.3      4e-08   33.3   0.1    2.6  2  TOBE_2        TOBE domain
    5.1e-08   33.1   0.1    0.00042   20.2   0.1    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    0.00047   20.1   0.0    0.00078   19.4   0.0    1.3  1  Rad17         Rad17 P-loop domain
    0.00071   19.8   0.4      0.004   17.4   0.0    2.3  2  TOBE          TOBE domain
     0.0019   18.5   0.0     0.0037   17.6   0.0    1.4  1  RNA_helicase  RNA helicase
     0.0051   17.3   1.3      0.011   16.3   1.3    1.7  1  AAA_23        AAA domain
  ------ inclusion threshold ------
      0.017   14.6   0.3       0.32   10.4   0.0    2.1  2  SMC_N         RecF/RecN/SMC N terminal domain
      0.018   15.5   0.0        0.2   12.1   0.0    2.1  2  AAA           ATPase family associated with various cellular 
      0.032   14.5   1.9       0.32   11.2   1.9    2.1  1  AAA_22        AAA domain
      0.053   12.9   0.2       0.72    9.2   0.2    2.1  2  TniB          Bacterial TniB protein
      0.053   13.9   0.1      0.089   13.2   0.1    1.6  1  AAA_16        AAA ATPase domain
       0.12   12.6   0.4        0.4   10.9   0.1    2.0  1  AAA_28        AAA domain
       0.13   12.1   0.0       0.22   11.4   0.0    1.4  1  ATPase_2      ATPase domain predominantly from Archaea
       0.14   12.2   0.0       0.27   11.3   0.0    1.6  1  AAA_14        AAA domain
       0.25   10.5   0.0       0.76    8.9   0.0    1.7  1  G-alpha       G-protein alpha subunit


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.5   0.0   7.7e-39   8.6e-36       1     136 [.      19     165 ..      19     166 .. 0.98
   2 ?   -1.3   0.0       2.6   2.9e+03      23      41 ..     322     340 ..     321     349 .. 0.89

  Alignments for each domain:
  == domain 1  score: 123.5 bits;  conditional E-value: 7.7e-39
                                    EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH. CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                       ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren. 79 
                                    ++nv+l+++ ge+  i+G++G+GK+t l+++ag + p+eG++ +d++d++   l+ + +e ++++q+  l+p++tv en 
  gi|119720709|ref|YP_921204.1|  19 VDNVNLEINDGELFTILGPSGCGKTTTLRIIAGFEVPDEGRVYFDDEDVTF--LKPYMRETAMVFQNYALWPHMTVFENv 96 
                                    58*************************************************..*************************** PP

                                    ................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                    ................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  80 ................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                    e ++++++als ++l++l+d+       +LSgGq+qrvalaral+ +pk+lllDEp 
  gi|119720709|ref|YP_921204.1|  97 ayglrirkkqlrltdeEIERRVKEALSLVRLEGLEDRYP----LQLSGGQQQRVALARALVVQPKVLLLDEPL 165
                                    *************99999999************999998....*****************************7 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.6
                                    SHHHHHHHHTTSS--SEEE CS
                                    xxxxxxxxxxxxxxxxxxx RF
                       ABC_tran  23 GKStLlkllagllkpteGe 41 
                                    GK +L++ l + + p+ Ge
  gi|119720709|ref|YP_921204.1| 322 GKASLIAYLPNTYYPQVGE 340
                                    9**************9997 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0         1   1.1e+03      30      51 ..     129     150 ..     106     157 .. 0.80
   2 !   33.3   0.1   3.5e-11     4e-08       1      69 [.     282     347 ..     282     354 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1
                         TOBE_2  30 Gsstryvvelaggqlvvvrqpn 51 
                                    G + ry ++l ggq+++v+ + 
  gi|119720709|ref|YP_921204.1| 129 GLEDRYPLQLSGGQQQRVALAR 150
                                    5566888999999999998765 PP

  == domain 2  score: 33.3 bits;  conditional E-value: 3.5e-11
                         TOBE_2   1 laiRPEklrlaaagg.anglsGtVedveylGsstryvvelaggqlvvvrqpnadrdsalapGdtVelswd 69 
                                    +++RPE  ++ ++ g  n+++GtV+ v +lG+ t+++++++  +l +++ pn+     +++G+++els +
  gi|119720709|ref|YP_921204.1| 282 VVVRPEVFTVGGQRGePNTVKGTVDFVMFLGDRTEVRLKVGKASL-IAYLPNTY---YPQVGEELELSAP 347
                                    78********74444369*************************99.999****9...9*********976 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   0.00025      0.28       2      22 ..      32      52 ..      31      86 .. 0.77
   2 !   20.2   0.1   3.7e-07   0.00042     220     299 ..     121     198 ..      86     203 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00025
                         AAA_21  2 nvliGpNgsGKSnLLdaldll 22
                                     + Gp g+GK++ L+++ ++
  gi|119720709|ref|YP_921204.1| 32 FTILGPSGCGKTTTLRIIAGF 52
                                   5699**************776 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 3.7e-07
                         AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHS 298
                                     + ++  ++  ++ + +lS G+++  al+ al  ++   ++ll+DEp ++L+ kl  +  e +k+ ++  g+  + +TH+
  gi|119720709|ref|YP_921204.1| 121 ALSLVRLEGLEDRYPLQLSGGQQQRVALARALVVQP---KVLLLDEPLSNLDAKLRIEMREEIKRIQKsLGITTVYVTHD 197
                                    555555567778888899******99*******999...9***********************8888889*********9 PP

                         AAA_21 299 p 299
                                     
  gi|119720709|ref|YP_921204.1| 198 Q 198
                                    5 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0     7e-07   0.00078      33      67 ..      17      51 ..       9      97 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 7e-07
                          Rad17 33 ewlkadvLesrkkriLLisGPsGCgkstvvkvLsk 67
                                   ++++   Le +  ++  i GPsGCgk+t++++++ 
  gi|119720709|ref|YP_921204.1| 17 KAVDNVNLEINDGELFTILGPSGCGKTTTLRIIAG 51
                                   566777889998999*****************986 PP

>> TOBE  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.4       2.7     3e+03      13      26 ..     248     261 ..     247     267 .. 0.73
   2 !   17.4   0.0   3.5e-06     0.004       4      57 ..     298     346 ..     296     353 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 2.7
                           TOBE  13 vveplgseveVrvd 26 
                                    vve +++ v+Vrv+
  gi|119720709|ref|YP_921204.1| 248 VVERGEGYVVVRVE 261
                                    67777788888775 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 3.5e-06
                           TOBE   4 rNqlpgtVvvveplgseveVrvdlgggatLtArvtrrsaeeLgLapGeeVfali 57 
                                    +N+++gtV+ v +lg ++eVr+ +g    L+A ++    ++    +Gee+ ++ 
  gi|119720709|ref|YP_921204.1| 298 PNTVKGTVDFVMFLGDRTEVRLKVGKAS-LIAYLPNTYYPQ----VGEELELSA 346
                                    7***************************.******999999....999988875 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   3.3e-06    0.0037       3      58 ..      34      84 ..      32      96 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.3e-06
                   RNA_helicase  3 lyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYtgqevvvidDf 58
                                   + Gpsg+GK+t+ +         ++ + +++vy+   + +f++ Y +++++v++  
  gi|119720709|ref|YP_921204.1| 34 ILGPSGCGKTTTLRI-----IAGFEVPDEGRVYFDDEDVTFLKPYMRETAMVFQNY 84
                                   78***********99.....345679**************************9865 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   1.3   9.6e-06     0.011      10      39 ..      12      49 ..       3     189 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 9.6e-06
                         AAA_23 10 f.......rdqeidFsk.gltlItGpNGaGKTTildAi 39
                                           ++++++ ++  l+ I Gp G+GKTT l+ i
  gi|119720709|ref|YP_921204.1| 12 VygavkavDNVNLEINDgELFTILGPSGCGKTTTLRII 49
                                   4455544477778885537***************9987 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.079        89      26      41 ..      31      46 ..      11      52 .. 0.76
   2 ?   10.4   0.0   0.00029      0.32     135     211 ..     133     208 ..      59     216 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.079
                                   EEEEEESTTSSHHHHH CS
                                   xxxxxxxxxxxxxxxx RF
                          SMC_N 26 ftaivGpNGSGKsnll 41
                                   +  i+Gp G+GK+  l
  gi|119720709|ref|YP_921204.1| 31 LFTILGPSGCGKTTTL 46
                                   55799*******9765 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00029
                                    T...CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEE CS
                                    x...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          SMC_N 135 e...lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadklvgv 211
                                        +LSgG+++ vala  + +   +p+ + llDe  ++LD+k + ++ e +k+ +k+  +  + +++++le ++   ++
  gi|119720709|ref|YP_921204.1| 133 RyplQLSGGQQQRVALARALVV---QPK-VLLLDEPLSNLDAKLRIEMREEIKRIQKSLGITTVYVTHDQLEAMSISDKI 208
                                    15558*******9999987655...455.5689**********************9999999998998888888555444 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00018       0.2       3      20 ..      34      51 ..      32      85 .. 0.89
   2 ?    1.2   0.0      0.41   4.6e+02      43      66 ..     139     163 ..      92     199 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00018
                                   EESSTTSSHHHHHHHHHH CS
                            AAA  3 lyGppGtGKTllakavak 20
                                   + Gp G+GKT++ + +a 
  gi|119720709|ref|YP_921204.1| 34 ILGPSGCGKTTTLRIIAG 51
                                   68*************995 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.41
                                    HHHHHHHHHHHHHTS.TSEEEEEET CS
                            AAA  43 ekkirelfkeakeka.kpsilfiDE 66 
                                    +   ++ ++ a++   +p++l++DE
  gi|119720709|ref|YP_921204.1| 139 SGGQQQRVALARALVvQPKVLLLDE 163
                                    4444444444544445699****99 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.9   0.00029      0.32       7      30 ..      31      54 ..      26     202 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00029
                         AAA_22  7 ilvvtGesGtGKTtllrrlleqld 30
                                   + ++ G+sG+GKTt+lr ++   +
  gi|119720709|ref|YP_921204.1| 31 LFTILGPSGCGKTTTLRIIAGFEV 54
                                   67899***********98876654 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.18     2e+02      39      53 ..      33      47 ..      26      65 .. 0.87
   2 ?    9.2   0.2   0.00065      0.72      95     164 ..     131     198 ..     115     209 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.18
                           TniB 39 llvGdsnnGKtmive 53
                                    ++G+s +GKt+ ++
  gi|119720709|ref|YP_921204.1| 33 TILGPSGCGKTTTLR 47
                                   699********9765 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00065
                           TniB  95 gaplkararvskleqqvlrllrelkvrvLiiDEihnllagsarkqreflnalksLgnelkipivlvGtee 164
                                    + ++  + +  ++++ +l+    ++++vL++DE  + l   a+ + e+ + +k+++  l i+ v+v  ++
  gi|119720709|ref|YP_921204.1| 131 EDRYPLQLSGGQQQRVALARALVVQPKVLLLDEPLSNL--DAKLRIEMREEIKRIQKSLGITTVYVTHDQ 198
                                    5555555555566666666666799********87777..7888999*****************995443 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1     8e-05     0.089      22      46 ..      27      51 ..      16     201 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8e-05
                         AAA_16 22 grpelvllsGesGvGKsslvrellr 46
                                   +++el  + G+sG+GK++ +r ++ 
  gi|119720709|ref|YP_921204.1| 27 NDGELFTILGPSGCGKTTTLRIIAG 51
                                   4558899*************98774 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00036       0.4       3      20 ..      33      50 ..      31      78 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00036
                         AAA_28  3 vitGgestGKTtlleaLa 20
                                    i+G++++GKTt+l+ +a
  gi|119720709|ref|YP_921204.1| 33 TILGPSGCGKTTTLRIIA 50
                                   699***********9988 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0    0.0002      0.22      19      66 ..      28      74 ..      17     129 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0002
                       ATPase_2 19 pneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskld 66
                                     e   i Gp g+GKt+ l+ ii   e  d+ ++y+++    +++ + 
  gi|119720709|ref|YP_921204.1| 28 DGELFTILGPSGCGKTTTLR-IIAGFEVPDEGRVYFDDEDVTFLKPYM 74
                                   55677899*********998.566666778888888887766666555 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00024      0.27       4      45 ..      31      71 ..      28     112 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00024
                         AAA_14  4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderdkk 45
                                   + +i G+  +GKTt l+ ++  + v++e  +y++ +d ++ k
  gi|119720709|ref|YP_921204.1| 31 LFTILGPSGCGKTTTLRIIAGFE-VPDEGRVYFDDEDVTFLK 71
                                   6789***********98777544.599999999888877754 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0   0.00067      0.76      27     161 ..      33     210 ..      25     316 .. 0.49

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00067
                                    EEEESTTSSHHHHHHHHHHHCS--.....--HHHHHCCHH..................HHHHHHHHHHHHHHHHHHHTT. CS
                        G-alpha  27 lllGqseSGKsTilkqlkllykkg.....fseeelatwra..................viqlnivrsiktilealesles 83 
                                     +lG s++GK+T+l+ +  ++ +      f++e++  +++                   +++n+   ++   ++l+ +++
  gi|119720709|ref|YP_921204.1|  33 TILGPSGCGKTTTLRIIAGFEVPDegrvyFDDEDVTFLKPymretamvfqnyalwphmTVFENVAYGLRIRKKQLRLTDE 112
                                    589************99988877777898777755546662223333222233322222222222222222222222333 PP

                                    ......HHHC-SS-SCCCS-HCHHHH.........................HHCCHHC..........-HCHHHHHHHHC CS
                        G-alpha  84 elsesfelqelkerldplkkveasliaklssateee...............qeiefnp..........raevgedikaLw 138
                                    e+++++   +   +l +l  +e++   +ls++++++                     +          r+e++e+ik++ 
  gi|119720709|ref|YP_921204.1| 113 EIERRV---KEALSLVRLEGLEDRYPLQLSGGQQQRvalaralvvqpkvllL-----DeplsnldaklRIEMREEIKRIQ 184
                                    332221...2222222233333333334444444446666444444433331.....03333345555667777777777 PP

                                    CSHHHHHHHCCGCCTT...--TTHHH CS
                        G-alpha 139 ndpgiqelyerrnkik...lednaey 161
                                    ++ gi  +y   ++++   ++d++++
  gi|119720709|ref|YP_921204.1| 185 KSLGITTVYVTHDQLEamsISDKIAV 210
                                    77777777664434432224466655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.71u 0.43s 00:00:01.13 Elapsed: 00:00:00.59
# Mc/sec: 1806.80
//
Query:       gi|119720710|ref|YP_921205.1|  [L=732]
Description: binding-protein-dependent transport systems inner membrane component [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-22   79.6  47.2    9.6e-17   61.3  18.7    5.1  5  BPD_transp_1     Binding-protein-dependent transport system i
  ------ inclusion threshold ------
       0.03   14.3   0.5       0.03   14.3   0.5    5.4  5  Sdh_cyt          Succinate dehydrogenase/Fumarate reductase t
      0.066   13.5   0.0        0.2   12.0   0.0    1.8  1  Sterol_MT_C      Sterol methyltransferase C-terminal


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   4.9       0.2   1.2e+03     126     177 ..      31      79 ..       7      98 .. 0.69
   2 ?   -4.4   8.3       2.3   1.4e+04      17      44 ..     134     175 ..     123     239 .. 0.64
   3 !   33.0  20.5     8e-12   4.8e-08       4     168 ..     239     422 ..     236     471 .. 0.81
   4 ?   -3.5   3.8       1.2   7.3e+03     147     155 ..     497     510 ..     441     534 .. 0.41
   5 !   61.3  18.7   1.6e-20   9.6e-17       3     182 ..     530     726 ..     528     728 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.2
                   BPD_transp_1 126 vlleflgswpGlgtllleailgydyseisnggvlalviavlllnlvadilqr 177
                                    vl+  l++  Gl   ll + lgydy +i    +  ++ ++ +++l+++++++
  gi|119720710|ref|YP_921205.1|  31 VLVDNLFTALGLAVGLLLVALGYDYRWIK---FSSGLSFLSVFSLLYNLFVA 79 
                                    56677777778888889999999999777...55566666666666665554 PP

  == domain 2  score: -4.4 bits;  conditional E-value: 2.3
                   BPD_transp_1  17 dkllrpliivllslPsfvlaillvlvf..............v 44 
                                     + l+p++ +++ + s++l+++lv+ +               
  gi|119720710|ref|YP_921205.1| 134 FYQLDPVMWFFMVFSSVALVVFLVVPIllvllhafqapaglP 175
                                    556777777777777777777766543333334334444440 PP

  == domain 3  score: 33.0 bits;  conditional E-value: 8e-12
                   BPD_transp_1   4 lGilaa...lnrnkkldkllrpliivllslPsfv...laillvlvf.............vilsilghlilpviillllsa 64 
                                    lG+ +a    ++++++++llr+l+ ++l + +fv   +   +  +f             + +s+  ++  +v+++ ++s+
  gi|119720710|ref|YP_921205.1| 239 LGVAVAfviARYSFPGKELLRILSMIPLFVTPFVnsyV---VKILFseygpismitsklFGWSVRVDGLVGVALAQIISF 315
                                    5555555555999************9999999995553...33333455777777787788899999************* PP

                   BPD_transp_1  65 apyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtlllea 144
                                     p+v+l+ ++a+ +++ + +e  + lGa+ + +fr+v++P+alp i++g+i++ +++l +  +++++  w   +++  ++
  gi|119720710|ref|YP_921205.1| 316 YPIVYLNAYSAFLNVDPSTEEQGENLGAKGFLLFRTVTFPLALPGIVAGAIIVYIFSLEDVGAPLIFQEW---NLMSAQI 392
                                    ********************************************************************99...5777888 PP

                   BPD_transp_1 145 ilgydyseis..........nggvlalviavlll 168
                                      g+ ++ ++          +    +l iavl +
  gi|119720710|ref|YP_921205.1| 393 FKGFVTQTGIvspesaalglV----MLFIAVLGF 422
                                    888888877776666432222....222222222 PP

  == domain 4  score: -3.5 bits;  conditional E-value: 1.2
                   BPD_transp_1 147 gydyseis.....n 155
                                      dy e +     +
  gi|119720710|ref|YP_921205.1| 497 TLDYFEKLfldpgI 510
                                    22222222222221 PP

  == domain 5  score: 61.3 bits;  conditional E-value: 1.6e-20
                   BPD_transp_1   3 llGilaa....lnrnkkldkllrpliivllslPsfvlaillvlvf..........vilsilghlilpviillllsaapyv 68 
                                    +l+i+++    + + ++l+++l++l  ++l++P +v+a+  +++f            + ++ +++  +++++ +  +pyv
  gi|119720710|ref|YP_921205.1| 530 VLAIMVGysvsRVKVSWLSNVLDTLATIPLAIPGLVIALGYYYFFttffagtpldPASIGAFQAWVVLVVAYSIRKLPYV 609
                                    56666666666999**************************99999********98555556667888999999999**** PP

                   BPD_transp_1  69 rlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgy 148
                                    ++ + a+++++ ++l+eaa+ lGasr ++++ vvlP +++++++g++l f+++ ++ +   ++g+     ++   +  +y
  gi|119720710|ref|YP_921205.1| 610 VRSVFAGFQQVHEGLEEAALNLGASRSKVIFGVVLPYIISYVFSGAVLGFIYMATEVSTSITIGNF----NPSQAPMTYY 685
                                    ****************************************************************55....5555555555 PP

                   BPD_transp_1 149 dyseis.......nggvlalviavlllnlvadilqrlldpr 182
                                    +++           ++++++v+++l+ ++++ i+++++ +r
  gi|119720710|ref|YP_921205.1| 686 MMNVYKggspvgvQVAAAMGVLLILIQLVAILIVVKIFKQR 726
                                    55555555555533666666666666666677777777766 PP

>> Sdh_cyt  Succinate dehydrogenase/Fumarate reductase transmembrane subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   4.9      0.77   4.6e+03      28      52 ..      11      34 ..       8      95 .. 0.68
   2 ?   14.3   0.5     5e-06      0.03       6      50 ..     125     168 ..     118     186 .. 0.79
   3 ?   -0.4   1.1      0.19   1.1e+03      32      77 ..     411     463 ..     361     469 .. 0.53
   4 ?   -1.3   2.4      0.36   2.1e+03      22      63 ..     555     595 ..     510     604 .. 0.52
   5 ?   -0.2   1.0      0.16   9.5e+02      26      63 ..     559     595 ..     541     645 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.77
                        Sdh_cyt 28 itGvallvglllllvwlllalslss 52
                                   ++G+al+v++++l+ ++l a++l++
  gi|119720710|ref|YP_921205.1| 11 VSGIALAVVYIVLYNFSL-ANVLVD 34
                                   799999995555554433.333443 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 5e-06
                        Sdh_cyt   6 plsphlqlyrlplgawlsilhritGvallv.glllllvwlllalsl 50 
                                    pls++l+   ++l+ +++ ++ ++ val+v +++++l++  l+ ++
  gi|119720710|ref|YP_921205.1| 125 PLSRRLKALFYQLDPVMWFFMVFSSVALVVfLVVPILLV--LLHAF 168
                                    79****************************777776655..33333 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.19
                        Sdh_cyt  32 allvglllllvwlllalslsspesfarv.......vallas.....piklilllllll 77 
                                    +l++ l++ ++ +l+    ++  s+a++       +    +     p  l+ + ll++
  gi|119720710|ref|YP_921205.1| 411 GLVM-LFIAVLGFLAIRNYVGMRSYAMIsrggrlvS----RqrpagPLALAAIYLLVV 463
                                    2222.2222223333444445555555544433221....222223333333334443 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 0.36
                        Sdh_cyt  22 lsilhritGvallv.glllllvwlllalslsspesfarvvall 63 
                                    + i   i G+++++  ++++  +  +a + ++p+s  ++ a++
  gi|119720710|ref|YP_921205.1| 555 ATIPLAIPGLVIALgYYYFFTTF--FAGTPLDPASIGAFQAWV 595
                                    33333444555555333333332..233334555555554444 PP

  == domain 5  score: -0.2 bits;  conditional E-value: 0.16
                        Sdh_cyt  26 hritGvallv.glllllvwlllalslsspesfarvvall 63 
                                      i G+++++  ++++  +  +a + ++p+s  ++ a++
  gi|119720710|ref|YP_921205.1| 559 LAIPGLVIALgYYYFFTTF--FAGTPLDPASIGAFQAWV 595
                                    5677999999666666654..444457888888887666 PP

>> Sterol_MT_C  Sterol methyltransferase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   3.4e-05       0.2      22      55 ..     608     641 ..     591     647 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.4e-05
                    Sterol_MT_C  22 eflglapkGtqkvaefLekAadsLvaGGkegiFT 55 
                                     +++ + +G q+v+e Le+Aa +L a++ + iF 
  gi|119720710|ref|YP_921205.1| 608 YVVRSVFAGFQQVHEGLEEAALNLGASRSKVIFG 641
                                    67889999************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (732 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       995  (0.0554967); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.79u 0.38s 00:00:01.17 Elapsed: 00:00:00.55
# Mc/sec: 4003.10
//
Query:       gi|119720711|ref|YP_921206.1|  [L=514]
Description: extracellular solute-binding protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.7e-20   72.5   0.7    8.4e-20   71.7   0.0    1.6  2  SBP_bac_8       Bacterial extracellular solute-binding protei
    1.7e-16   60.4   0.1      3e-16   59.6   0.1    1.4  1  SBP_bac_6       Bacterial extracellular solute-binding protei
    7.3e-15   55.7   1.0    7.3e-15   55.7   1.0    1.5  2  SBP_bac_1       Bacterial extracellular solute-binding protei
    2.4e-08   34.0   0.1    8.5e-08   32.2   0.0    1.9  2  SBP_bac_11      Bacterial extracellular solute-binding protei
  ------ inclusion threshold ------
        0.1   12.8   0.2       0.26   11.5   0.2    1.7  1  DUF2749         Protein of unknown function (DUF2749)
       0.76    7.8   3.5        1.1    7.2   3.5    1.1  1  Totivirus_coat  Totivirus coat protein


Domain annotation for each model (and alignments):
>> SBP_bac_8  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.7   0.0   2.8e-23   8.4e-20       9     280 ..      96     380 ..      90     382 .. 0.78
   2 ?   -1.9   0.1      0.76   2.3e+03      95     127 ..     429     464 ..     397     499 .. 0.69

  Alignments for each domain:
  == domain 1  score: 71.7 bits;  conditional E-value: 2.8e-23
                                    H-TEE.EEEEE--SSSHHHHHHHHHHTT---SEE.EEE-HHHHHHHHH.TTSB-..-GGGSTTHHH.......-HHHHHT CS
                      SBP_bac_8   9 ktgvk.vnvvtaasndleqklkaalaagtapdidvvwanedalatlae.eglla..dlsdldnldd.......ltdalaa 77 
                                    k+++k + + +++ ++  + +k+a+++g+   idv+w+ +  l +l++ +gl++  dl++ ++ +        l++++a+
  gi|119720711|ref|YP_921206.1|  96 KYNIKnIVFLPINAEQWPDYIKNAAQKGQ--GIDVAWGGGPTLFNLIDdMGLIEpiDLDKHPEFKIvmdevakLPKTIAG 173
                                    44443344444444444444889999988..69999**99998777777*****55555777777755555555554444 PP

                                    T.....--TS.----EEEEEEE-EEEEEHHHHHHS...---BHHHHHHHHHHH....H..HH-SEGG---G..GGGGGTH CS
                      SBP_bac_8  78 v.....gydgklygvPyasetpyvliynkdlleka..edpktwdellaaakkl....k..gkfglpdpasg..wlqaall 142
                                    +     g dgk+ ++   +++  ++ +n dll       p+ w++l    +++    +  + +g++dp+ +  + +++ +
  gi|119720711|ref|YP_921206.1| 174 AetykvGSDGKIHWIGASVSS-FGFTVNRDLLNRYklPMPQRWADLGN--PAYavtlPalQLVGIADPTMStsNTRIFEI 250
                                    47778788********99997.9*********9735889*******98..666222223355577666543224455555 PP

                                    HETTEE---H..HHH.HHHHHHHHHHHHTT-EE-S..--SSTTTTTSBSEEEE-TTHHHHHH-TTTSEEEE--S--EEEE CS
                      SBP_bac_8 143 akdgksldddggkdglkealellkklkdngktydtgadavsefanGevaftingswdiaaaqkagkklgaivpkqgsfag 222
                                    + +        +  g+++ ++ l+ + +n k+++ ++d+ +++  G++a++++ +    +aq++++   +i+p+  s+++
  gi|119720711|ref|YP_921206.1| 251 I-L--------QAYGWDKGWRTLTLIAANSKIFSGSSDVRDAVIRGDIAIGTTIDFYGYTAQQQNPSCLYIIPPGESIVN 321
                                    5.4........22379*****************************************99*******9999998888**** PP

                                    EEEEEEBTTS-HHHHHHHHHHHHHTTSH.HHHHHHH.HH---BS-S-TTTHHHHHH-HHH CS
                      SBP_bac_8 223 gkglavpknaknedlaAldFlkwltspe.nqaalae.ktgyipvnksaalspevkkdpal 280
                                    ++++a++k++ +++ aA++F+ w++++  +q  + + +++ +p+n+ + ++p+ ++ p+l
  gi|119720711|ref|YP_921206.1| 322 ADPIAILKGSRHPE-AAAAFVAWVLNETgGQLVWLDpNINRLPINPRVFDTPQGARRPDL 380
                                    **************.6************88888999***********9999988877765 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.76
                                    -EEEEEHHHHHHS....---BHHHHHHHHHHHHHH- CS
                      SBP_bac_8  95 yvliynkdlleka...edpktwdellaaakklkgkf 127
                                     v +y+++++ +a   + ++ + +++++ + l+g+ 
  gi|119720711|ref|YP_921206.1| 429 IVKAYRDKKITEAqfqQLVTQLTDFVTFTDPLTGQQ 464
                                    455677777777667666666777777777776554 PP

>> SBP_bac_6  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.6   0.1     1e-19     3e-16       5     208 ..     127     352 ..      98     383 .. 0.87

  Alignments for each domain:
  == domain 1  score: 59.6 bits;  conditional E-value: 1e-19
                      SBP_bac_6   5 dlilsfdkdflekfieeglfqpld..........panlpnvnkdfa.eeglkdp.dgkyy..pygvgplvlavnkdrlkg 70 
                                    d+ ++ ++ ++    + gl++p+d          ++ +++++k +a +e++k + dgk+   + +v+ +++ vn+d l+ 
  gi|119720711|ref|YP_921206.1| 127 DVAWGGGPTLFNLIDDMGLIEPIDldkhpefkivMDEVAKLPKTIAgAETYKVGsDGKIHwiGASVSSFGFTVNRDLLNR 206
                                    778888888888888999999999999999999988888888888886677666666554449****************8 PP

                      SBP_bac_6  71 rpv..PksWaDLldPeykg......kvalpgnngsdlfealllalykdfgedgvkkllrnlkanlhpaq.mvkaagsles 141
                                     ++  P++WaDL +P y+        v++ ++  s++++ ++ ++ + +g+d++++ l  ++an +    + +  ++++ 
  gi|119720711|ref|YP_921206.1| 207 YKLpmPQRWADLGNPAYAVtlpalqLVGIADPTMSTSNTRIFEIILQAYGWDKGWRTLTLIAANSKIFSgSSDVRDAVIR 286
                                    777558***********98777666677777777***********************************99999****** PP

                      SBP_bac_6 142 gepavsvvpyffadilpekkkgknlkvvwPedGalvspifmlvkkg.kkkelakafidfllspevqai 208
                                    g+ a+  +++f++ ++++++    l ++ P + ++v+ + +++ kg +++e a+af+ + l +++++ 
  gi|119720711|ref|YP_921206.1| 287 GDIAIGTTIDFYGYTAQQQN-PSCLYIIPPGE-SIVNADPIAILKGsRHPEAAAAFVAWVLNETGGQL 352
                                    **9999999**999999998.44566666666.999999999999999*************9997764 PP

>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.7   1.0   2.4e-18   7.3e-15      21     312 ..      96     348 ..      80     351 .. 0.86
   2 ?   -3.5   0.1       2.5   7.6e+03      67      87 ..     400     420 ..     382     446 .. 0.52

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 2.4e-18
                                    HHTTEEEEEEEECHHHHHHHHHHHHHTTSSSCSEEEE.CGGHHHHHHHTTSBECCHHHHHHTTECTTCCTEEEEHHHHTH CS
                      SBP_bac_1  21 ehpgikVeiesvgsgslaqkltlaiaaGdgpaDviav.dndwiarlakaglllpldpyvkaylapgvkdaadklsssvlp 99 
                                    +++  ++++ ++   ++ + ++ a ++G+  +Dv+++ +++ +    + gl +p+d +  ++ + + ++ a+      ++
  gi|119720711|ref|YP_921206.1|  96 KYNIKNIVFLPINAEQWPDYIKNAAQKGQ-GIDVAWGgGPTLFNLIDDMGLIEPIDLDKHPEFKIVMDEVAKLPKTIAGA 174
                                    36778899889988888887788888888.88*****666666666666************9988876666665555555 PP

                                    HHHCEEE.......ES.EEEEE.EEEEEEETTTHHCTTGGGSHBHHHHHHHHHHHHHHCTCTHCCHCCEEHHHHHHHHHH CS
                      SBP_bac_1 100 kildskv.......ly.vPlya.argliYNkdlfekagldppwtWdelveaakklkekgkkpiggarggsasgtayyfal 170
                                     +    +       +  +     + g+ +N dl+  ++l++p  W +l  +a  ++ +     +g++  + s+ +   ++
  gi|119720711|ref|YP_921206.1| 175 ET----YkvgsdgkIHwIGASVsSFGFTVNRDLLNRYKLPMPQRWADLGNPAYAVTLPALQL-VGIADPTMSTSNTRIFE 249
                                    55....3445569*777999955**********************************99999.99999999999999999 PP

                                    HHHHHHTGGGEECCCTHHCSHHHHSHHHHHHHHHHHHHHHHHHHTTEEECSSHHHHHHHHHTTSCSEEEEEHHHHHHHHC CS
                      SBP_bac_1 171 alakslggkvfdkdgggldnpegvtaatylvklyavanltkelkgkgaenkdgaaalalfeaGeaamaivglwaalaamk 250
                                     +++ +g                  +++ ++ l          + +++  ++++++++++ +G++a++    ++ ++a +
  gi|119720711|ref|YP_921206.1| 250 IILQAYG------------------WDKGWRTLT-------LIAANSKIFSGSSDVRDAVIRGDIAIGTTIDFYGYTAQQ 304
                                    999****..................999999999.......99999********************************** PP

                                    EEEEECHHCHHHHTTSTEEEECEEBETTTTSEEEEEEEEEEBTTCSTHHHHHHHHHHHTSHH CS
                      SBP_bac_1 251 vapkvafaadkekpkeelgvaplPagkggkpgilgayglaipkgsknpeaAkkFldfllspe 312
                                    ++p   ++++  +                     +a+++ai+kgs +peaA +F++++l++ 
  gi|119720711|ref|YP_921206.1| 305 QNPSCLYIIPPGESIV------------------NADPIAILKGSRHPEAAAAFVAWVLNET 348
                                    ********99999976..................************************9975 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.5
                                    HTTSBECCHHHHHHTTECTTC CS
                      SBP_bac_1  67 kaglllpldpyvkaylapgvk 87 
                                    ++++++ + +y+ka l++  +
  gi|119720711|ref|YP_921206.1| 400 SSAWVTAVVDYFKATLVNAHD 420
                                    335666666666666655532 PP

>> SBP_bac_11  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.0   2.9e-11   8.5e-08      93     221 ..     212     350 ..     191     353 .. 0.78
   2 ?   -2.2   0.0      0.94   2.8e+03       5      22 ..     418     436 ..     365     469 .. 0.67

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 2.9e-11
                                    --SHHHHHHS.......S-.-EEEE--T-TTTTHH.H.HHHGGG--HHHHHHHHHTEEEEESSH......HHHHHHHHTT CS
                     SBP_bac_11  93 ikgwadLlkp.......gl.klavadPttspsGlaal.alleaagaqellkalekkvvklgess......rqlltaveag 157
                                    ++ wadL++p        l  +++adPt s+s ++++  +l+a+g   ++k  +  +   + +s      +++ +av +g
  gi|119720711|ref|YP_921206.1| 212 PQRWADLGNPayavtlpALqLVGIADPTMSTSNTRIFeIILQAYG---WDKGWRTLTL-IAANSkifsgsSDVRDAVIRG 287
                                    678*******88876665545*************99945566667...7777776666.4444447777799******** PP

                                    T-SEEEEEHHHH..H..HSTTSSEEEE--TTT--...EEEEEEEE-TT--HHHHHHHHHTTSHHHH CS
                     SBP_bac_11 158 eadagivyesea..kaaengdkleavylpeglnldpldypaavlkkaakreaAraFlafLrspeaq 221
                                    ++++g++       ++++n+  l ++++ e+++    + p+a+lk+++++eaA+aF+a+++ + + 
  gi|119720711|ref|YP_921206.1| 288 DIAIGTTIDFYGytAQQQNPSCLYIIPPGESIVN---ADPIAILKGSRHPEAAAAFVAWVLNETGG 350
                                    *999998765442266788889999999999995...449*******************9988775 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.94
                                    E-SSTHHHHHHHHHHH.HH CS
                     SBP_bac_11   5 aagslaaalrelaaaF.ea 22 
                                    a  +l+++ +++++a+  +
  gi|119720711|ref|YP_921206.1| 418 AHDDLQPVWAQIVKAYrDK 436
                                    3344445555555555222 PP

>> DUF2749  Protein of unknown function (DUF2749)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   8.6e-05      0.26       1      40 [.       1      39 [.       1      42 [. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8.6e-05
                        DUF2749  1 msprilIvlviavaagagtilwlvvqpragtsgsgeaqRe 40
                                   m+ ++l+vl+++v ++ g +l + +q +a+ s+ +++q +
  gi|119720711|ref|YP_921206.1|  1 MNSKVLLVLAVLVLVALGVALVV-LQQKAPPSAPPANQTQ 39
                                   8899********98777777655.9***998888887755 PP

>> Totivirus_coat  Totivirus coat protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   3.5   0.00038       1.1     680     729 ..      16      64 ..      12      86 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00038
                 Totivirus_coat 680 argdpvrltahhaalrapqlpraggasdGgggvppppalgaaagdapspp 729
                                    a g ++ + ++ a++ ap++++ +++s G+++ +p  +++a  +++p+ +
  gi|119720711|ref|YP_921206.1|  16 ALGVALVVLQQKAPPSAPPANQTQQPSPGPVNQTPSTKPPANQTQQPP-A 64 
                                    67899999**********************************999993.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (514 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       989  (0.055162); expected 358.6 (0.02)
Passed bias filter:                      826  (0.0460706); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.82u 0.40s 00:00:01.22 Elapsed: 00:00:00.58
# Mc/sec: 2674.29
//
Query:       gi|119720712|ref|YP_921207.1|  [L=396]
Description: hypothetical protein Tpen_1809 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.9e-05   22.7   0.0    9.9e-05   21.9   0.0    1.3  1  ABC_transp_aux  ABC-type uncharacterized transport system
     0.0013   19.1   3.9      0.053   13.9   2.2    2.3  2  LPP             Lipoprotein leucine-zipper
     0.0039   17.2   0.3     0.0075   16.3   0.3    1.4  1  DUF1664         Protein of unknown function (DUF1664)
     0.0074   16.3   3.0      0.015   15.4   3.0    1.4  1  Baculo_PEP_C    Baculovirus polyhedron envelope protein, PEP,
  ------ inclusion threshold ------
      0.029   14.8   1.0        5.7    7.4   0.1    2.3  2  FlaC_arch       Flagella accessory protein C (FlaC)
      0.034   14.6   0.0       0.11   12.9   0.0    1.9  1  DUF4350         Domain of unknown function (DUF4350)
      0.088   13.2   4.1       0.34   11.3   4.0    1.8  1  HsbA            Hydrophobic surface binding protein A
      0.092   13.0   0.0       0.16   12.3   0.0    1.3  1  KxDL            Uncharacterized conserved protein
       0.14   12.7   0.1       0.29   11.6   0.1    1.5  1  DUF16           Protein of unknown function DUF16
       0.14   12.8   0.1       0.31   11.7   0.0    1.6  2  SlyX            SlyX


Domain annotation for each model (and alignments):
>> ABC_transp_aux  ABC-type uncharacterized transport system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   5.5e-08   9.9e-05     146     259 ..      29     131 ..      20     136 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 5.5e-08
                 ABC_transp_aux 146 kkpkvgfltghgelslsspse.adfleelee.nYnveevdldsedilpedidvlviakptkdlseeelykldqflmnGgk 223
                                    ++ ++++  ghge +     + + ++ ++   + +v + +++  d l +++d+l++ +pt ++s++e+++++++l +G+k
  gi|119720712|ref|YP_921207.1|  29 QPVTIAVDLGHGESNK----YlKYIMGNITYvQWKVINGTIT-PDVL-KGVDILLLGQPTVAFSPDEIQAIKNWLFSGNK 102
                                    678899999***9776....5466888888888899998888.6666.9******************************* PP

                 ABC_transp_aux 224 llvfldpvaeeqdslsepsaaprtsnLedllaeyGv 259
                                    +l +    +           +++ ++L+dlla  G 
  gi|119720712|ref|YP_921207.1| 103 VLYVGGDSDYGP-------GQKTVLQLNDLLAGIGT 131
                                    *99877766322.......33446788888887775 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   2.2     3e-05     0.053       1      34 [.     308     348 ..     308     350 .. 0.84
   2 !    6.1   0.1    0.0081        15       4      24 ..     346     366 ..     343     370 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3e-05
                            LPP   1 kldeLssqVsqLkskvdqlssd.......vnsakaaaqaak 34 
                                    k+  Ls+ Vs+L s v+q+ss+       +++++ ++q++k
  gi|119720712|ref|YP_921207.1| 308 KVVDLSNTVSSLTSTVNQVSSQvssqgglIQKMQGDLQTVK 348
                                    6778******************7777887788888888777 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0081
                            LPP   4 eLssqVsqLkskvdqlssdvn 24 
                                     + s+V++Lk+ vd+l+  vn
  gi|119720712|ref|YP_921207.1| 346 TVKSDVNTLKASVDALTGTVN 366
                                    5679***********998877 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.3   4.2e-06    0.0075      55     113 ..     310     368 ..     300     373 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.2e-06
                        DUF1664  55 eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegl 113
                                     +l++t   L+s +++v +++ +q  ++++++ ++++v++d+++++  v+++  +v+ l
  gi|119720712|ref|YP_921207.1| 310 VDLSNTVSSLTSTVNQVSSQVSSQGGLIQKMQGDLQTVKSDVNTLKASVDALTGTVNLL 368
                                    56788889999999999999999999999999999999999999999999998888765 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   3.0   8.1e-06     0.015      64     111 ..     311     368 ..     296     382 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 8.1e-06
                   Baculo_PEP_C  64 rldtlltnLtdalnalq..........dtlrneLtnlnsiltnLlssvtNinstLnnl 111
                                    +l+++++ Lt+++n+++          ++++ +L++++s++++L +sv  +  t+n l
  gi|119720712|ref|YP_921207.1| 311 DLSNTVSSLTSTVNQVSsqvssqggliQKMQGDLQTVKSDVNTLKASVDALTGTVNLL 368
                                    5666677777777777666777778888888888888888888888888888887643 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.1    0.0099        18       5      30 ..     305     330 ..     302     332 .. 0.89
   2 ?    7.4   0.1    0.0032       5.7       9      38 ..     337     366 ..     335     376 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0099
                      FlaC_arch   5 lEnklsklsteletvkkeneelsksv 30 
                                    +E k+ +ls +++++ ++ +++s++v
  gi|119720712|ref|YP_921207.1| 305 IERKVVDLSNTVSSLTSTVNQVSSQV 330
                                    89999****************99998 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0032
                      FlaC_arch   9 lsklsteletvkkeneelsksveelkenVk 38 
                                    ++k++  l+tvk++ + l+ sv+ l  +V+
  gi|119720712|ref|YP_921207.1| 337 IQKMQGDLQTVKSDVNTLKASVDALTGTVN 366
                                    578888999999999999999999998884 PP

>> DUF4350  Domain of unknown function (DUF4350)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   6.2e-05      0.11      37      68 ..      75     106 ..      59     107 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.2e-05
                        DUF4350  37 tllvvapdlrlteeelaallewvarGntlvla 68 
                                     ll+  p++ ++++e++a+ +w+ +Gn+++++
  gi|119720712|ref|YP_921207.1|  75 ILLLGQPTVAFSPDEIQAIKNWLFSGNKVLYV 106
                                    6788889999*******************998 PP

>> HsbA  Hydrophobic surface binding protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   4.0   0.00019      0.34       3      69 ..     318     382 ..     303     386 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00019
                                    HHHHHHHHHHHHHHHHHHHHHH--SH..HHHHHHHHHHHHHHHHHHHHHHHTS----HHHHHHHHHH CS
                           HsbA   3 tvisdittistavtaldtavnafnGgasalpilsasnalvsaikkattdaqasapltdeealalaqa 69 
                                    +++s ++++s++v++    +++ +G+  +++++s++n+l++++++ t +++  + l   ea+ +++ 
  gi|119720712|ref|YP_921207.1| 318 SLTSTVNQVSSQVSSQGGLIQKMQGD--LQTVKSDVNTLKASVDALTGTVNLLTVLVIVEAILIIAL 382
                                    44445555555555555555555554..888888888888888888888888888888888777765 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   8.9e-05      0.16      23      78 ..     303     358 ..     300     360 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.9e-05
                           KxDL  23 grlnkknreLlelnalsqerlaklrarfkqgtkllkevkkdLesifkkirslkakl 78 
                                    g ++ k   L++    + + ++++++++ ++  l+++++ dL+++++ +++lka +
  gi|119720712|ref|YP_921207.1| 303 GPIERKVVDLSNTVSSLTSTVNQVSSQVSSQGGLIQKMQGDLQTVKSDVNTLKASV 358
                                    668888889999999**************************************975 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00016      0.29      37      90 ..     310     363 ..     285     371 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00016
                                    HHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHH CS
                          DUF16  37 kkieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetlelile 90 
                                     ++ ++v++l   +n++  +v+ qg  i++++ + ++ + ++n+++ +++ +  
  gi|119720712|ref|YP_921207.1| 310 VDLSNTVSSLTSTVNQVSSQVSSQGGLIQKMQGDLQTVKSDVNTLKASVDALTG 363
                                    566788888899999999999999999999998888888888877776666555 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0         9   1.6e+04      17      27 ..     117     127 ..     116     133 .. 0.77
   2 ?   11.7   0.0   0.00018      0.31       2      54 ..     306     358 ..     305     363 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 9
                                    HHHHHHHHHHH CS
                           SlyX  17 dtieeLndvva 27 
                                    +t+ +Lnd +a
  gi|119720712|ref|YP_921207.1| 117 KTVLQLNDLLA 127
                                    68889999887 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00018
                                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXX CS
                           SlyX   2 eerleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkeleess 54 
                                    e ++++L   ++ +  t+++ + +v  q   i+++q  l+ ++  +++l++s 
  gi|119720712|ref|YP_921207.1| 306 ERKVVDLSNTVSSLTSTVNQVSSQVSSQGGLIQKMQGDLQTVKSDVNTLKASV 358
                                    6788999999999*********************************9998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1029  (0.0573931); expected 358.6 (0.02)
Passed bias filter:                      761  (0.0424452); expected 358.6 (0.02)
Passed Vit filter:                       134  (0.00747392); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.76u 0.39s 00:00:01.14 Elapsed: 00:00:00.58
# Mc/sec: 2057.28
//
Query:       gi|119720713|ref|YP_921208.1|  [L=706]
Description: metallophosphoesterase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-16   61.8   1.0    2.7e-16   60.7   1.0    1.6  1  Metallophos    Calcineurin-like phosphoesterase
    1.5e-05   25.2   0.0    4.8e-05   23.6   0.0    1.7  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
  ------ inclusion threshold ------
      0.052   14.1   0.2      0.097   13.2   0.2    1.5  1  CEND1          Cell cycle exit and neuronal differentiation p
        1.7    9.3  11.6       0.85   10.3   9.0    2.0  2  Pex14_N        Peroxisomal membrane anchor protein (Pex14p) c


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.7   1.0   5.9e-20   2.7e-16       1     203 [.     147     353 ..     147     354 .. 0.75

  Alignments for each domain:
  == domain 1  score: 60.7 bits;  conditional E-value: 5.9e-20
                                    EEEEEEESBTBTTCCTHHHHHHHHHHHH.....HHHTTESEEEEESTSSSSSHHHHHHHHH.HHHHHHHTSEEEEEC-TT CS
                    Metallophos   1 lrilvigDlHlalgggqlddllkllddl.....lreekpdlvllaGDlvdrgdlekellel.laalvkypipvylllGNH 74 
                                    lri++++D H  +g gq d +   ++++     ++  +pdlv+ +GD+ d+ + +++ +   +++ + y  p+++++GNH
  gi|119720713|ref|YP_921208.1| 147 LRIVHVSDQH--YGAGQPDVITGDMNRFagylvASLLGPDLVIDTGDIADTASEDQYAQAVsYEQAFLYSFPIFAVPGNH 224
                                    69********..5555555555555555444447779**************97777666666666666678********* PP

                                    SCHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESE.CEEETHHHHHHHHHHHSCHHHHCC...HHH CS
                    Metallophos  75 egfeeellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGg.spellvsldklgslnleleapepg...dew 150
                                    +   +   n+y+          +++++  ++ l++      + ll+ G  spe+              +         +w
  gi|119720713|ref|YP_921208.1| 225 D---HPPDNFYK----------YYGDT-YWYRLIG------DKLLVVGLfSPEQ------------GYP----PmeqLQW 268
                                    *...33333333..........33444.4788888......7777777744444............112....1223888 PP

                                    HHH.HHHHTTCSEEEEEESSESS............................CSSSCSCCHHHHH...HHHHHTTESEEEE CS
                    Metallophos 151 lkd.lekrekadwvivlgHsply............................rgsgylfgdeale...dllkkygvdlvis 198
                                      + le  + ++++ivl H+p+                              +s+++ + ea++   +  ++y+v +v+s
  gi|119720713|ref|YP_921208.1| 269 AGQvLESNKAVPVKIVLVHHPVFyfqgelktryddqnviapydpqknpnspVSSYWSTNMEAVRtflRMVEDYRVNYVFS 348
                                    88899********************9999999999999999999999988777777777777778889999********* PP

                                    ESSSS CS
                    Metallophos 199 GHtHv 203
                                    GH+H+
  gi|119720713|ref|YP_921208.1| 349 GHVHR 353
                                    ****7 PP

>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   1.1e-08   4.8e-05       2     135 ..     148     364 ..     147     395 .. 0.61

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 1.1e-08
                  Metallophos_2   2 klaiiSDlH..........snldaleav......lealkevgvdaiihaGDl.eeeepevleellela.......pvlaV 57 
                                    +++++SD H          +              +  ++  g+d++i +GD+  +++ +  +++ + +       p+ aV
  gi|119720713|ref|YP_921208.1| 148 RIVHVSDQHygagqpdvitG-------DmnrfagYLVASLLGPDLVIDTGDIaDTASEDQYAQAVSYEqaflysfPIFAV 220
                                    78999999966666655441.......0333334333444667********963333333333333224455678***** PP

                  Metallophos_2  58 rGNnD............................eevveedvlreaaelgtdl.....peeaelelagek..........v 94 
                                    +GN+D                                                    p  ++l++ag+           +
  gi|119720713|ref|YP_921208.1| 221 PGNHDhppdnfykyygdtywyrligdkllvvglF-----------------SpeqgyPPMEQLQWAGQVlesnkavpvkI 283
                                    *****99999998888666655555443333330.................22222222222222222222223444559 PP

                  Metallophos_2  95 lliHgdpl.................................gvkdalaellke..aeegsdvvvcGHtHvp.....evek 134
                                     l+H+                                    + + +  +++ +  +++++++v++GH H+      + ++
  gi|119720713|ref|YP_921208.1| 284 VLVHHPVFyfqgelktryddqnviapydpqknpnspvssywSTNMEAVRTFLRmvEDYRVNYVFSGHVHRDlfvkyTSTR 363
                                    999997559999999999999******999*999999987733333334333333447777*********9655443333 PP

                  Metallophos_2 135 e 135
                                    +
  gi|119720713|ref|YP_921208.1| 364 T 364
                                    3 PP

>> CEND1  Cell cycle exit and neuronal differentiation protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   2.2e-05     0.097      84     146 ..     642     704 ..     624     705 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.2e-05
                          CEND1  84 apsspdatpepkgpgdgaeedeaasPgGrGpsifenlkPLlvaGGvavaalalilGvafLark 146
                                     + ++++t +p  p +  +   a+ P  +   + + l PLl++G   v   a il va+L r+
  gi|119720713|ref|YP_921208.1| 642 QQPPANQTQQPSTPPQTQQPPVAEQPPAQEVKPAQPLSPLLLVGASLVVVAAAILVVALLRRR 704
                                    34456777788888888888878888889****************99999999*******997 PP

>> Pex14_N  Peroxisomal membrane anchor protein (Pex14p) conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.7   7.5e+03     129     152 ..     367     389 ..     303     391 .. 0.61
   2 ?   10.3   9.0   0.00019      0.85      73     147 ..     630     698 ..     573     703 .. 0.62

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.7
                        Pex14_N 129 rdllitatalaglgaglyglskry 152
                                     +++it+t + g+g+ +y    +y
  gi|119720713|ref|YP_921208.1| 367 TTYFITIT-TLGMGSAIYDGLDYY 389
                                    34555555.445555555555555 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00019
                        Pex14_N  73 ssatpqpqaasqtsqsspspsppaqqqqqqyrpPivtypefltkppkppppPlrtwrdlli.tatalaglgaglyg 147
                                     s++++pq++ ++       +ppa+q+qq++ pP++++p +  +pp+++  P + ++ ll   a +++ ++a+l+ 
  gi|119720713|ref|YP_921208.1| 630 VSYEAPPQQQVPQ-------QPPANQTQQPSTPPQTQQPPVAEQPPAQEVKPAQPLSPLLLvGASLVVVAAAILVV 698
                                    2233333333222.......22333334444566666666666666666666666665555355555555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (706 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.78u 0.40s 00:00:01.18 Elapsed: 00:00:00.59
# Mc/sec: 3630.84
//
Query:       gi|119720714|ref|YP_921209.1|  [L=202]
Description: hypothetical protein Tpen_1811 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.33s 00:00:00.83 Elapsed: 00:00:00.52
# Mc/sec: 1173.86
//
Query:       gi|119720715|ref|YP_921210.1|  [L=617]
Description: DEAD_2 domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-29  103.8   0.0      2e-29  103.0   0.0    1.4  1  Helicase_C_2  Helicase C-terminal domain
    8.1e-22   77.7   0.0    1.3e-21   77.0   0.0    1.3  1  DEAD_2        DEAD_2
    4.1e-11   42.9   0.0      8e-11   42.0   0.0    1.5  1  HBB           Helical and beta-bridge domain
    7.1e-05   22.6   0.0      0.011   15.5   0.0    2.4  2  DEAD          DEAD/DEAH box helicase
    0.00018   21.6   0.0      0.016   15.2   0.0    2.3  2  ResIII        Type III restriction enzyme, res subunit
  ------ inclusion threshold ------
        0.2   11.0   0.0       0.38   10.0   0.0    1.4  1  DUF3638       Protein of unknown function (DUF3638)


Domain annotation for each model (and alignments):
>> Helicase_C_2  Helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.0   0.0   6.6e-33     2e-29       5     168 ..     427     593 ..     423     596 .. 0.88

  Alignments for each domain:
  == domain 1  score: 103.0 bits;  conditional E-value: 6.6e-33
                   Helicase_C_2   5 levvpggvlvffpSyklleevve.rlkeeleskkieifvee...keesrekvleeyke.kkkkgaillavcrGklsEGid 79 
                                    l  v+ +  vf+ Sy++l+++ e  lkee e+ ++e++ve+   + ++  + le++k+ + + + +lla ++G++ EG d
  gi|119720715|ref|YP_921210.1| 427 LGRVKRNSAVFTASYRVLQRLLEaGLKEEAERLGYEVVVERrdmSGQEAGAALEKFKNlAAEGRGLLLAPMGGRFAEGAD 506
                                    55688999*************994589999999******999888889999******97699999*************** PP

                   Helicase_C_2  80 fsddllraviivglPfpnpkdpeveakreyldekgk.knsgkewylpealravnQaiGRliRhkdDygaivllDeRfake 158
                                    f++++l +v++ g+Pf++p+  +++++ +y++e  + +++  ++y ++alr+  QaiGR++R+ +D ++ivl D+R+++ 
  gi|119720715|ref|YP_921210.1| 507 FPGEELMCVFLAGIPFEKPT-TKTNLYIKYYEELYGpEKGRLYAYVYPALRRASQAIGRALRSPRDQAVIVLGDSRYRN- 584
                                    *******************6.66799999999988834555689*********************************98. PP

                   Helicase_C_2 159 eireklpkwl 168
                                     +   lp+++
  gi|119720715|ref|YP_921210.1| 585 -YMGLLPDYV 593
                                    .555666655 PP

>> DEAD_2  DEAD_2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.0   0.0   4.4e-25   1.3e-21       2     162 ..      63     215 ..      62     219 .. 0.87

  Alignments for each domain:
  == domain 1  score: 77.0 bits;  conditional E-value: 4.4e-25
                                    EESSHHHHHHHHHHHHHHHHHCHHHS---EEEE--CCCC-SCHHCCC.HHCCCCHHHHHHHHHCCHHCCHTTTTTT-SCC CS
                         DEAD_2   2 csRThsqleqvvkelkklesykkkkekvkvviLgSRknlCineevkk.ekkekavneaCkelkkkkaeekeekCsffenl 80 
                                    ++RT s+ ++ v+e++   +  k+ +++ +v+L ++k++C+    +  + + ++v+ +C+     ++++   +C+++++l
  gi|119720715|ref|YP_921210.1|  63 AVRTGSETDRPVEEFRVFRE--KSGARFVAVGLRGKKDMCLLAGERGgQLDYSEVSYICS-----RERR---RCKYYRRL 132
                                    79**************9853..34799*************98544430233555555554.....3333...7******* PP

                                    CCHHHHHHHHHHC---CHHHHHHHHHCT--HHHHHHHHHCCTSEEEEEHHHHTSCCCHHHHH.T..GCGCEEEECTCCCH CS
                         DEAD_2  81 eelkklkkllleevvdiedlvelgeklklCPYylsrelledadiiilpYqyLldekireslk.gislknsivilDEAhNi 159
                                    +e  ++++ll +++++  d+ e  ++ ++CPY+l rell+ ad++ l+Y+y++de    +l+  + +++si+++DEAhN+
  gi|119720715|ref|YP_921210.1| 133 QEGVDYSELLERGALTYRDVFEWARREGVCPYFLQRELLKVADLVALSYNYVVDEDLSWTLRgAFPTSQSILVVDEAHNL 212
                                    999999*******************************************************98899************** PP

                                    HHH CS
                         DEAD_2 160 edv 162
                                    +++
  gi|119720715|ref|YP_921210.1| 213 QEL 215
                                    985 PP

>> HBB  Helical and beta-bridge domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.0   0.0   2.7e-14     8e-11      64     190 .]     280     410 ..     269     410 .. 0.89

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 2.7e-14
                                    HHHHHHHHHHHHCCHHCCCTCC-SHHHHHHHHHHHHHHHTS.TTTEEEEEE.STT.EECCCCS-TCCHHHHHHHC....H CS
                            HBB  64 sllkrlveygkarreekieksesPrsflsrlaefllawlssdeedYvrlvskeegesLeavcldPskalrflker....l 139
                                    +++++   +g+ +re++    + Prs  ++laefl + ++ +  + ++l++++ +  +++   d  +  + l+ +    +
  gi|119720715|ref|YP_921210.1| 280 DIIEKTLRLGELVREKRYRSGARPRSSAHHLAEFLRKAVDLEGVKGIALIAEKVDGRVHLNIWD-MRSGEILSGVwrrfR 358
                                    57889999******************************************99999777777777.666666554422227 PP

                                    CCCCCCTS-SSHHHHHHHHT.....EEE.S..S.GGHCCCCCCCCCSHTCCC CS
                            HBB 140 ssllmsgtltpleeysdiiGle.aklkkfpspfpkEnlivlfatdVsTkyke 190
                                    ++++msgtl+p+e++++ +Gl    + + psp  + n+ v +++d++T+++e
  gi|119720715|ref|YP_921210.1| 359 RVIFMSGTLSPIEAFAETVGLSdYTPVTVPSPYDETNASVYLVKDLTTRGEE 410
                                    89********************9999***********************986 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   3.6e-06     0.011       6      36 ..      21      51 ..      13      85 .. 0.80
   2 !    4.5   0.0    0.0087        26     121     136 ..     201     215 ..     167     237 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.6e-06
                                   HHHHHHHTTCEEEEEESTTSSHHHHHHHHHH CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DEAD  6 eaiplilgggdvlvaaeTGsGKTlaflipvl 36
                                   e i ++l+ g+v+++a+TG GKT + + ++l
  gi|119720715|ref|YP_921210.1| 21 EKIVELLKRGNVVLEAPTGFGKTPVVIYALL 51
                                   3344455899*************99887776 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0087
                                    TEEEEEEETHHHHHHT CS
                                    xxxxxxxxxxxxxxxx RF
                           DEAD 121 qvrflVlDEadrlldq 136
                                    q ++lV+DEa++l++ 
  gi|119720715|ref|YP_921210.1| 201 Q-SILVVDEAHNLQEL 215
                                    3.69********9986 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   5.4e-06     0.016       2      76 ..      10      79 ..       9     101 .. 0.79
   2 ?    3.9   0.0     0.016        47     131     146 ..     199     214 ..     182     237 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.4e-06
                                   -EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGG CS
                         ResIII  2 lelreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkk 76
                                   +++r +Q e+ e+++e lk   + +++++++TG GKT v + +   +++ g+  +++  v + s +++  eef+ 
  gi|119720715|ref|YP_921210.1| 10 YKPRRHQLEVAEKIVELLK---RGNVVLEAPTGFGKTPVVIYALLPFMERGG--RVVWAVRTGSETDRPVEEFRV 79
                                   589**************97...899************999888777777666..666666666555555555555 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.016
                                    TT-SEEEEETGGGTTS CS
                         ResIII 131 drfdviiiDEaHrlga 146
                                    +++ ++++DEaH+l++
  gi|119720715|ref|YP_921210.1| 199 TSQSILVVDEAHNLQE 214
                                    455699*******998 PP

>> DUF3638  Protein of unknown function (DUF3638)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00013      0.38      24      72 ..      13      61 ..      11      70 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00013
                        DUF3638 24 ReeQaevAkemispssgensvlQLnmGeGKssvIvPivaaaladgkkLv 72
                                   R++Q evA+++++  ++ n vl    G GK+ v++  ++ ++  g ++v
  gi|119720715|ref|YP_921210.1| 13 RRHQLEVAEKIVELLKRGNVVLEAPTGFGKTPVVIYALLPFMERGGRVV 61
                                   899*******************************988888777777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (617 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 3804.96
//
Query:       gi|119720716|ref|YP_921211.1|  [L=366]
Description: Sua5/YciO/YrdC/YwlC family protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-59  199.8   0.0    3.5e-59  199.3   0.0    1.2  1  Sua5_yciO_yrdC  Telomere recombination
    3.4e-29  102.1   0.0    5.5e-29  101.4   0.0    1.3  1  SUA5            Putative GTP-binding controlling metal-bindin


Domain annotation for each model (and alignments):
>> Sua5_yciO_yrdC  Telomere recombination
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.3   0.0   3.9e-63   3.5e-59       2     179 .]      36     211 ..      35     211 .. 0.98

  Alignments for each domain:
  == domain 1  score: 199.3 bits;  conditional E-value: 3.9e-63
                                    HHHTTSEEEEE-SSSEEEEEETTSHHHHHHHHHHHTSHCCC--EEEESSCCCCCCCC-TC--HHHHHHHHCT-SSSCEEE CS
                 Sua5_yciO_yrdC   2 alrkGgivaiptetvYgLacdatneeaverlreiKgrpsdkplavlvasledlkklaeseveeealkllerfwPGpitll 81 
                                    +lrkGg+va+ptetvYgL++    ++av r++++K+rp d+pl+++++s++++ +la+ ev+e++ +l+e+fwPGp+t++
  gi|119720716|ref|YP_921211.1|  36 ILRKGGVVAFPTETVYGLGAVYHMRDAVIRVFKVKRRPPDNPLILHISSFSQIYTLAS-EVPEAVHRLAEKFWPGPLTVV 114
                                    79*******************************************************8.********************* PP

                                    EE..E-TS-HHHHTTTTEEEEEE-SSHHHHHHHHHCTS-EEEEES-STTS-S-SSHHHHHHHC-TTSECB-SS---SSS- CS
                 Sua5_yciO_yrdC  82 lkrskeklpkevapglktvGvrlPdtplarlLlealgeplvaTSanlsgepsitdaeeveeelgeivdlildggeiavgv 161
                                    l+++++ +p ev++gl++v+vr+P++++a++L+ea+g p++a+Sanlsg+ps+t+a++v  +lg+++d +ld+ge+  gv
  gi|119720716|ref|YP_921211.1| 115 LPKTSR-VPYEVTGGLEKVAVRMPAHNVALRLIEAVGDPIAAPSANLSGRPSPTTAQHVLADLGDEIDGVLDAGETLYGV 193
                                    **8766.************************************************************************* PP

                                    --EEEETTSSTSSECEXX CS
                 Sua5_yciO_yrdC 162 dstVvdltegkpkilRrG 179
                                    +stV+dlt ++p +lR+G
  gi|119720716|ref|YP_921211.1| 194 ESTVIDLTADPPVLLRPG 211
                                    ****************98 PP

>> SUA5  Putative GTP-binding controlling metal-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.4   0.0   6.1e-33   5.5e-29       3     133 ..     215     360 ..     213     361 .. 0.86

  Alignments for each domain:
  == domain 1  score: 101.4 bits;  conditional E-value: 6.1e-33
                                    HHHHHHHS-.-.-..........-------------S-SSEEEEE--GGGHHHH..........HHHHHTTS-EEEEEEG CS
                           SUA5   3 leeleevld.a.vek......keekpraPGmkyrHYaPkapvvlveaeeeeeaake.....ekleekkksgkkvgvlats 69 
                                    lee+e+vl+   v +      + e+  aPG++yrHY+P+a++vlve ++ ++ +k      + ++e+  +g +vgvl+t+
  gi|119720716|ref|YP_921211.1| 215 LEEVEKVLGkVcVPAfarglgEAERALAPGTRYRHYSPRAQLVLVELKDYSDLSKLvdrvkRLVAENAGRGLRVGVLCTD 294
                                    79999999532322234456778899******************99998777766599999999**************** PP

                                    GGTGG....TSEEEEE..E-TT-HHHHHHHHHHHHHHHHHS--SEEEEE----STTHHHHHHHHHHHT CS
                           SUA5  70 eskea....assvlslslgsrsdleeaarnLFaaLrelDeegvdlilvegvpeeglglAvmnRLrkAA 133
                                    e++e+     + vls  lgsr+d+  +ar+L++ +re+D+ gvd+i++egv+e+glgl +mnR+rkA+
  gi|119720716|ref|YP_921211.1| 295 ETREHysglGAVVLS--LGSRRDPFGIARRLYSSFREMDSLGVDVIVAEGVDERGLGLTIMNRMRKAS 360
                                    ***999765555555..5*************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2622.67
//
Query:       gi|119720717|ref|YP_921212.1|  [L=217]
Description: phosphoribosyltransferase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.1e-23   82.0   0.1    6.1e-23   81.1   0.1    1.4  1  Pribosyltran  Phosphoribosyl transferase domain
  ------ inclusion threshold ------
      0.047   13.1   0.3      0.067   12.6   0.3    1.3  1  UPRTase       Uracil phosphoribosyltransferase


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.1   0.1   6.8e-27   6.1e-23      10     158 ..       7     196 ..       3     197 .. 0.94

  Alignments for each domain:
  == domain 1  score: 81.1 bits;  conditional E-value: 6.8e-27
                                    -EEEEEEETTEEEEEE.--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE................. CS
                   Pribosyltran  10 aildavarlaaeilee.yngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdes......... 79 
                                    + +da ++la+++l e  +g  + v+gi+rgGv++ak ++ +L+v+l++v ++k r++g++e  +g+++e          
  gi|119720717|ref|YP_921212.1|   7 NREDAGKQLAEKLLAEgVGGPDVKVLGIPRGGVVVAKSVSEALGVQLDVVVSRKLRAPGNPELGIGAVAELdavyinrei 86 
                                    456899999*****9977777778******************************************************** PP

                                    ..............................EE----TTSEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-HHH CS
                   Pribosyltran  80 ..............................rlledpagkkVliVDDildtGgTllaalelLkekgpeevriavlvdkpat 129
                                                                    + d++g + ++VDD+++tG T++aa  + +++g+e+v +a++v  ++ 
  gi|119720717|ref|YP_921212.1|  87 vdalgigedyirseveyqrrvvasyvekfrGTALDLRGFTAVVVDDGVATGATVIAASIAARKAGAEKVVVATPVIARDV 166
                                    *****************************98899*****************************************88888 PP

                                    HHHHHHH-TTS......EEEEEEE-SEE-T CS
                   Pribosyltran 130 eeevdknakrvfsls.pdnfvavvgfelds 158
                                       v+ +a++v+ ++ p + +av +f+ d+
  gi|119720717|ref|YP_921212.1| 167 LGVVSRYADKVVAVTvPLILYAVGEFYRDF 196
                                    8888888899999999**999999999887 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.3   7.5e-06     0.067     122     177 ..     125     178 ..      80     190 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.5e-06
                        UPRTase 122 rtvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvlaseegvkrlaeefpkvk 177
                                     t++++D  +aTG++++aa    ++  +g ek++v++ + ++  +  +++   kv 
  gi|119720717|ref|YP_921212.1| 125 FTAVVVDDGVATGATVIAASIAARK--AGAEKVVVATPVIARDVLGVVSRYADKVV 178
                                    4599**************9877777..67799**9999999886655544444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1445.40
//
Query:       gi|119720718|ref|YP_921213.1|  [L=375]
Description: signal-transduction protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-23   82.2   4.1      3e-06   27.6   0.1    4.4  4  CBS       CBS domain
     0.0044   17.2   0.4       0.84    9.9   0.0    3.5  4  IF3_N     Translation initiation factor IF-3, N-terminal doma


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   1.4e-08   0.00012      15      53 ..      21      59 ..      13      62 .. 0.89
   2 !   27.6   0.1   3.4e-10     3e-06       9      52 ..      75     117 ..      68     120 .. 0.90
   3 !   20.4   0.1   5.8e-08   0.00052      12      55 ..     138     180 ..     127     182 .. 0.88
   4 !   10.2   0.1   9.1e-05      0.82      31      55 ..     230     253 ..     223     255 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.4e-08
                                   TSBHHHHHHHHHHHT..SSEEEEEETTTBEEEEEEHHHHHH CS
                            CBS 15 dttleealelmrekg..vsrlPVVdedgklvGivtlrDllr 53
                                   ++t++ a+e+m   +  + ++PVVd++g++ Giv+   llr
  gi|119720718|ref|YP_921213.1| 21 NDTVSVAAERM--WRfeLPAVPVVDGEGRYAGIVSIFSLLR 59
                                   79*********..776699****************999987 PP

  == domain 2  score: 27.6 bits;  conditional E-value: 3.4e-10
                                    CEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHH CS
                            CBS   9 vvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDll 52 
                                     ++v p+ +l e++++++++g  +l VV e g++vGiv+ r ll
  gi|119720718|ref|YP_921213.1|  75 APVVEPSLPLTEVARMLVKTGQPGLAVV-EGGRVVGIVSARRLL 117
                                    4599************************.89**********998 PP

  == domain 3  score: 20.4 bits;  conditional E-value: 5.8e-08
                                    EETTSBHHHHHHHHHHHTSSEE.EEEETTTBEEEEEEHHHHHHHH CS
                            CBS  12 vppdttleealelmrekgvsrl.PVVdedgklvGivtlrDllral 55 
                                    + p+++le+a +l+++ g+ rl PV  edgk vG+v   Dl++++
  gi|119720718|ref|YP_921213.1| 138 LAPSDPLEKARKLIVDLGL-RLvPVA-EDGKAVGVVRVYDLVNFV 180
                                    689***********9*888.774665.9*************9986 PP

  == domain 4  score: 10.2 bits;  conditional E-value: 9.1e-05
                                    SEEEEEETTTBEEEEEEHHHHHHHH CS
                            CBS  31 srlPVVdedgklvGivtlrDllral 55 
                                    +++ VVd++gk+ Gi++   llr l
  gi|119720718|ref|YP_921213.1| 230 GSV-VVDSSGKVYGIISPYLLLRRL 253
                                    567.99***********98888776 PP

>> IF3_N  Translation initiation factor IF-3, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.012   1.1e+02       8      46 ..      37      75 ..      33      92 .. 0.83
   2 !    9.9   0.0   9.4e-05      0.84      25      66 ..     144     186 ..     142     189 .. 0.86
   3 ?   -3.2   0.0       1.2   1.1e+04      12      24 ..     233     245 ..     229     252 .. 0.83
   4 ?   -2.5   0.0      0.72   6.4e+03      33      60 ..     332     359 ..     329     364 .. 0.53

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.012
                                   SEEEEE-SSS-EEEEEEHHHHHHHHHHHTSEEEEEESSS CS
                          IF3_N  8 revrlvdedGeqlGvistreAlrlaeekgldLVevspna 46
                                   + v +vd +G   G++s+   lr+  ++g +L  v ++a
  gi|119720718|ref|YP_921213.1| 37 PAVPVVDGEGRYAGIVSIFSLLRTRYQAGTKLGSVLEKA 75
                                   6789******************99999999987776664 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 9.4e-05
                                    HHHHHHHHHHHTSEEEEEESSSSS.-EEEEE-HHHHHHHHHHH CS
                          IF3_N  25 treAlrlaeekgldLVevspnaep.PVcrimdygkfrYeqkkk 66 
                                    +++A +l+ ++gl+LV v+++ +   V+r+ d   f Y+  ++
  gi|119720718|ref|YP_921213.1| 144 LEKARKLIVDLGLRLVPVAEDGKAvGVVRVYDLVNFVYNTPLR 186
                                    578999*************9986626************87665 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 1.2
                                    EE-SSS-EEEEEE CS
                          IF3_N  12 lvdedGeqlGvis 24 
                                    +vd+ G+  G+is
  gi|119720718|ref|YP_921213.1| 233 VVDSSGKVYGIIS 245
                                    8999999999997 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 0.72
                                    HHHTSEEEEEESSSSS-EEEEE-HHHHH CS
                          IF3_N  33 eekgldLVevspnaepPVcrimdygkfr 60 
                                    +++g d Ve   +a    +++++ +k +
  gi|119720718|ref|YP_921213.1| 332 RSSGWDAVETVYEALDSAYKVFSKSKEK 359
                                    5556666665555555555555555443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 2510.64
//
Query:       gi|119720719|ref|YP_921214.1|  [L=131]
Description: 4Fe-4S ferredoxin iron-sulfur binding domain-containing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-18   65.1  43.7    1.1e-08   34.5   4.0    4.9  5  Fer4      4Fe-4S binding domain
    1.6e-16   59.6  37.3    3.4e-06   26.9   3.6    4.5  4  Fer4_6    4Fe-4S binding domain
    7.4e-15   55.3  30.8    6.9e-06   26.6   0.6    3.8  4  Fer4_7    4Fe-4S dicluster domain
    2.9e-14   52.2  34.9      9e-05   22.3   3.7    4.2  4  Fer4_2    4Fe-4S binding domain
    2.9e-12   46.5  51.6    2.9e-07   30.5  11.7    3.1  4  Fer4_9    4Fe-4S dicluster domain
    1.8e-11   44.0  33.3    1.6e-05   25.0  13.8    3.6  4  Fer4_10   4Fe-4S dicluster domain
    2.8e-09   37.8  27.4     0.0038   18.1   1.5    4.2  4  Fer4_16   4Fe-4S double cluster binding domain
    4.5e-09   36.3  12.2    4.5e-09   36.3  12.2    2.5  2  Fer4_11   4Fe-4S dicluster domain
    4.6e-08   33.0  37.6     0.0011   19.4   2.6    4.6  4  Fer4_4    4Fe-4S binding domain
    2.5e-07   30.7  31.6     0.0002   21.4  12.1    3.2  2  Fer4_21   4Fe-4S dicluster domain
      1e-06   29.1  29.2     0.0092   16.4   1.2    3.9  3  Fer4_8    4Fe-4S dicluster domain
      4e-05   24.2  48.4      0.033   15.1   6.3    4.5  4  Fer4_3    4Fe-4S binding domain
      5e-05   23.8  31.6      0.025   15.1   1.9    4.1  3  Fer4_17   4Fe-4S dicluster domain
    0.00046   20.9  22.3      0.074   13.8   6.6    3.8  3  Fer4_15   4Fe-4S single cluster domain
     0.0084   16.3  24.3        0.5   10.6   1.7    3.4  3  Fer4_18   4Fe-4S dicluster domain
     0.0088   16.9  27.6       0.13   13.1   2.9    4.1  4  Fer4_22   4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.043   14.4   0.3      0.043   14.4   0.3    4.1  4  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   4.4   4.3e-07   0.00045       1      18 [.       5      22 ..       5      24 .. 0.95
   2 ?   -0.1   0.4      0.91   9.6e+02      11      15 ..      53      57 ..      51      58 .. 0.76
   3 !   10.8   1.6   0.00033      0.34      14      23 ..      61      70 ..      61      71 .. 0.94
   4 !   34.5   4.0   1.1e-11   1.1e-08       1      23 [.      78     100 ..      78     101 .. 0.93
   5 !   22.5   4.2   6.4e-08   6.7e-05       8      23 ..     112     127 ..     109     128 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 4.3e-07
                                   EEEETTTSSS-THHHHHS CS
                           Fer4  1 vvideekCigCGaCvevC 18
                                   v++d +kC+gC+ C+ +C
  gi|119720719|ref|YP_921214.1|  5 VIVDVDKCVGCMSCMFAC 22
                                   689*************** PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.91
                                   -THHH CS
                           Fer4 11 CGaCv 15
                                   C aC+
  gi|119720719|ref|YP_921214.1| 53 CRACE 57
                                   99997 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00033
                                   HHHHSTTTEE CS
                           Fer4 14 CvevCPvgAI 23
                                   C+ vCP++A+
  gi|119720719|ref|YP_921214.1| 61 CAAVCPTNAL 70
                                   *********8 PP

  == domain 4  score: 34.5 bits;  conditional E-value: 1.1e-11
                                    EEEETTTSSS-THHHHHSTTTEE CS
                           Fer4   1 vvideekCigCGaCvevCPvgAI 23 
                                    vv +++kC+gCG+C+ +CP gA 
  gi|119720719|ref|YP_921214.1|  78 VVLNPSKCVGCGNCARACPIGAV 100
                                    588******************97 PP

  == domain 5  score: 22.5 bits;  conditional E-value: 6.4e-08
                                    SSS-THHHHHSTTTEE CS
                           Fer4   8 CigCGaCvevCPvgAI 23 
                                    C++CG+Cv+ CP+g++
  gi|119720719|ref|YP_921214.1| 112 CVHCGYCVNYCPYGVL 127
                                    **************87 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   1.0     6e-08   6.3e-05       2      20 ..       5      23 ..       4      32 .. 0.90
   2 !    8.5   5.9     0.002       2.2       9      24 .]      53      70 ..      51      70 .. 0.87
   3 !   26.9   3.6   3.2e-09   3.4e-06       5      23 ..      81      99 ..      78     100 .. 0.91
   4 !   18.6   4.1   1.4e-06    0.0014       9      24 .]     112     127 ..     108     127 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 6e-08
                         Fer4_6  2 veidpdkCigCgdCvrvCP 20
                                   v +d dkC+gC+ C+ +C 
  gi|119720719|ref|YP_921214.1|  5 VIVDVDKCVGCMSCMFACS 23
                                   669***************7 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.002
                         Fer4_6  9 CigCgd..CvrvCPegai 24
                                   C  C++  C++vCP++a+
  gi|119720719|ref|YP_921214.1| 53 CRACENppCAAVCPTNAL 70
                                   88897779********97 PP

  == domain 3  score: 26.9 bits;  conditional E-value: 3.2e-09
                         Fer4_6  5 dpdkCigCgdCvrvCPega 23
                                   +p+kC+gCg+C+r+CP ga
  gi|119720719|ref|YP_921214.1| 81 NPSKCVGCGNCARACPIGA 99
                                   89**************887 PP

  == domain 4  score: 18.6 bits;  conditional E-value: 1.4e-06
                         Fer4_6   9 CigCgdCvrvCPegai 24 
                                    C++Cg Cv+ CP+g++
  gi|119720719|ref|YP_921214.1| 112 CVHCGYCVNYCPYGVL 127
                                    *************986 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   3.9   0.00083      0.88      34      48 ..       8      22 ..       3      26 .. 0.68
   2 !   14.9  14.6   2.8e-05      0.03       1      52 []      11      69 ..      11      69 .. 0.72
   3 !   26.6   0.6   6.5e-09   6.9e-06       1      22 [.      84     105 ..      72     109 .. 0.83
   4 !   22.6   1.8   1.1e-07   0.00012       2      19 ..     112     129 ..     111     131 .] 0.92

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00083
                         Fer4_7 34 dpekClgCgaCvavC 48
                                   d +kC+gC +C+ +C
  gi|119720719|ref|YP_921214.1|  8 DVDKCVGCMSCMFAC 22
                                   566777777777666 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 2.8e-05
                         Fer4_7  1 rCigCgaCvaaCpvkaieldeeenek.....gtekveidpekClgCga..CvavCPtga 52
                                   +C+gC  C+ aC+ +  e   ++++      g  +  ++   C  C++  C+avCPt+a
  gi|119720719|ref|YP_921214.1| 11 KCVGCMSCMFACSRRFGEGGLAKSAIhvssiGGVERGFKVVVCRACENppCAAVCPTNA 69
                                   7***********866666654432222222333444677889***************97 PP

  == domain 3  score: 26.6 bits;  conditional E-value: 6.5e-09
                         Fer4_7   1 rCigCgaCvaaCpvkaieldee 22 
                                    +C+gCg+C++aCp +a+++d+e
  gi|119720719|ref|YP_921214.1|  84 KCVGCGNCARACPIGAVQWDYE 105
                                    6888888888888888888876 PP

  == domain 4  score: 22.6 bits;  conditional E-value: 1.1e-07
                         Fer4_7   2 CigCgaCvaaCpvkaiel 19 
                                    C++Cg+Cv++Cp+++++l
  gi|119720719|ref|YP_921214.1| 112 CVHCGYCVNYCPYGVLSL 129
                                    **************9976 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   2.1   3.1e-07   0.00033       3      20 ..       5      22 ..       2      24 .. 0.90
   2 !    7.7   5.5    0.0038         4       9      22 .]      52      67 ..      47      67 .. 0.92
   3 !   22.3   3.7   8.5e-08     9e-05       3      21 ..      78      96 ..      76      96 .. 0.94
   4 !   19.2   1.1   8.8e-07   0.00092       9      22 .]     111     124 ..      99     124 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3.1e-07
                         Fer4_2  3 vvvdtdrCigCgaCvsaC 20
                                   v vd d+C+gC +C  aC
  gi|119720719|ref|YP_921214.1|  5 VIVDVDKCVGCMSCMFAC 22
                                   789*************** PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0038
                         Fer4_2  9 rCigCg..aCvsaCPa 22
                                    C +C+  +C  +CP+
  gi|119720719|ref|YP_921214.1| 52 VCRACEnpPCAAVCPT 67
                                   5****999*******7 PP

  == domain 3  score: 22.3 bits;  conditional E-value: 8.5e-08
                         Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                                   vv ++ +C+gCg C  aCP
  gi|119720719|ref|YP_921214.1| 78 VVLNPSKCVGCGNCARACP 96
                                   689***************9 PP

  == domain 4  score: 19.2 bits;  conditional E-value: 8.8e-07
                         Fer4_2   9 rCigCgaCvsaCPa 22 
                                    +C++Cg Cv+ CP+
  gi|119720719|ref|YP_921214.1| 111 ICVHCGYCVNYCPY 124
                                    7************5 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   2.8   0.00019       0.2      34      48 ..      10      24 ..       2      27 .. 0.76
   2 !   14.7  12.0   2.4e-05     0.025       1      50 [.      11      69 ..      11      70 .. 0.78
   3 !   25.7  11.8   9.1e-09   9.6e-06       2      50 ..      53      99 ..      51     100 .. 0.91
   4 !   30.5  11.7   2.8e-10   2.9e-07       1      49 [.      84     125 ..      84     127 .. 0.96

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00019
                         Fer4_9 34 eaCigCgaCveaCpk 48
                                   ++C+gC++C+ aC +
  gi|119720719|ref|YP_921214.1| 10 DKCVGCMSCMFACSR 24
                                   478888888888876 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 2.4e-05
                         Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraase.......eaCigCga..CveaCpkga 50
                                   kC+gC +C+ aC     ++  a+  + +   +          C  C+   C+++Cp++a
  gi|119720719|ref|YP_921214.1| 11 KCVGCMSCMFACSRRFGEGGLAKSAIHVSSIGGvergfkvVVCRACENppCAAVCPTNA 69
                                   7***********666666666666666655555666667777***************97 PP

  == domain 3  score: 25.7 bits;  conditional E-value: 9.1e-09
                         Fer4_9  2 CtgCga..CveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50
                                   C  C +  C ++Cp+++ v++++++ + +      +C+gCg C+ aCp ga
  gi|119720719|ref|YP_921214.1| 53 CRACENppCAAVCPTNALVRREGGGVVLNPS----KCVGCGNCARACPIGA 99
                                   999*9888******************99865....6************876 PP

  == domain 4  score: 30.5 bits;  conditional E-value: 2.8e-10
                         Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkg 49 
                                    kC+gCg+C +aCp g+v+ d    k  +       C++Cg Cv+ Cp g
  gi|119720719|ref|YP_921214.1|  84 KCVGCGNCARACPIGAVQWDYESMKPII-------CVHCGYCVNYCPYG 125
                                    7************************998.......************98 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8  13.2   5.1e-06    0.0053       2      56 .]       5      66 ..       4      66 .. 0.88
   2 !   19.6  15.6   6.7e-07   0.00071       8      56 .]      52      96 ..      48      96 .. 0.87
   3 !   25.0  13.8   1.5e-08   1.6e-05       2      56 .]      78     123 ..      77     123 .. 0.84
   4 !   15.0   2.4   1.9e-05      0.02       6      21 ..     109     124 ..     105     129 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.1e-06
                        Fer4_10  2 vvidddtCirCgkCvkaCPadl......tsvgakgeaseeeavrk.kvekCtgcg..aCveaCP 56
                                   v++d d+C++C  C+ aC  +        +++a+   s+++++r+ kv  C +c+   C+++CP
  gi|119720719|ref|YP_921214.1|  5 VIVDVDKCVGCMSCMFAC--SRrfgeggLAKSAIHVSSIGGVERGfKVVVCRACEnpPCAAVCP 66
                                   789***************..5669*9997777888888888888889*******9889*****9 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 6.7e-07
                        Fer4_10  8 tCirCg..kCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                    C  C+   C ++CP+      +   + e++ v  +++kC gcg+C++aCP
  gi|119720719|ref|YP_921214.1| 52 VCRACEnpPCAAVCPT------NALVRREGGGVVLNPSKCVGCGNCARACP 96
                                   6*****889*******......77777777777778**************9 PP

  == domain 3  score: 25.0 bits;  conditional E-value: 1.5e-08
                        Fer4_10   2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                    vv+++++C++Cg+C +aCP           a + + ++ k+  C +cg+Cv  CP
  gi|119720719|ref|YP_921214.1|  78 VVLNPSKCVGCGNCARACPI---------GAVQWDYESMKPIICVHCGYCVNYCP 123
                                    6899****************.........55555555666667***********9 PP

  == domain 4  score: 15.0 bits;  conditional E-value: 1.9e-05
                        Fer4_10   6 ddtCirCgkCvkaCPa 21 
                                    +  C++Cg Cv+ CP+
  gi|119720719|ref|YP_921214.1| 109 PIICVHCGYCVNYCPY 124
                                    568************8 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   2.5     0.014        15       1      13 [.      11      23 ..       9      26 .. 0.81
   2 !   13.6   1.5   9.6e-05       0.1       2      20 ..      53      73 ..      52      81 .. 0.89
   3 !   18.1   1.5   3.6e-06    0.0038       1      20 [.      84     103 ..      84     109 .. 0.85
   4 !   15.7   0.7   2.1e-05     0.022       2      19 ..     112     129 ..     111     131 .] 0.89

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.014
                        Fer4_16  1 rCgtCgkCaevCP 13
                                   +C++C  C+ +C 
  gi|119720719|ref|YP_921214.1| 11 KCVGCMSCMFACS 23
                                   5888888888885 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 9.6e-05
                        Fer4_16  2 CgtCgk..CaevCPtnaikek 20
                                   C  C++  Ca vCPtna+  +
  gi|119720719|ref|YP_921214.1| 53 CRACENppCAAVCPTNALVRR 73
                                   999*9999*********9876 PP

  == domain 3  score: 18.1 bits;  conditional E-value: 3.6e-06
                        Fer4_16   1 rCgtCgkCaevCPtnaikek 20 
                                    +C++Cg+Ca +CP +a++ +
  gi|119720719|ref|YP_921214.1|  84 KCVGCGNCARACPIGAVQWD 103
                                    5**************99866 PP

  == domain 4  score: 15.7 bits;  conditional E-value: 2.1e-05
                        Fer4_16   2 CgtCgkCaevCPtnaike 19 
                                    C+ Cg C++ CP ++++ 
  gi|119720719|ref|YP_921214.1| 112 CVHCGYCVNYCPYGVLSL 129
                                    *************99875 PP

>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.3       1.1   1.1e+03      68      76 ..       9      17 ..       4      29 .. 0.62
   2 !   36.3  12.2   4.2e-12   4.5e-09       8      75 ..      51     116 ..      44     130 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.1
                        Fer4_11 68 vekCdmcld 76
                                   v kC +c++
  gi|119720719|ref|YP_921214.1|  9 VDKCVGCMS 17
                                   445555543 PP

  == domain 2  score: 36.3 bits;  conditional E-value: 4.2e-12
                        Fer4_11   8 eqCrhCleppCvasapseaivkdeetGaVlldektkkeevrevveacPykivrkneetgkvekCdmcl 75 
                                      Cr C++ppC+a++p++a+v++e  G V+l+++++  ++ ++++acP  +v+++ e++k   C  c 
  gi|119720719|ref|YP_921214.1|  51 VVCRACENPPCAAVCPTNALVRRE-GGGVVLNPSKCV-GCGNCARACPIGAVQWDYESMKPIICVHCG 116
                                    58*********************9.888899999997.********************9888777774 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   3.3   0.00018      0.19       2      15 ..      10      23 ..      10      27 .. 0.89
   2 ?    3.7   3.5      0.11   1.1e+02       4      17 .]      53      68 ..      51      68 .. 0.79
   3 !   15.5   4.6   1.7e-05     0.018       2      15 ..      83      96 ..      82     108 .. 0.88
   4 !   19.4   2.6     1e-06    0.0011       4      17 .]     112     125 ..     101     125 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00018
                         Fer4_4  2 erCigCgsCvaaCP 15
                                   ++C+gC+sC+ aC+
  gi|119720719|ref|YP_921214.1| 10 DKCVGCMSCMFACS 23
                                   79*******99997 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.11
                         Fer4_4  4 CigCgs..CvaaCPqg 17
                                   C  C    C a+CP++
  gi|119720719|ref|YP_921214.1| 53 CRACENppCAAVCPTN 68
                                   66777688******85 PP

  == domain 3  score: 15.5 bits;  conditional E-value: 1.7e-05
                         Fer4_4  2 erCigCgsCvaaCP 15
                                   ++C+gCg C +aCP
  gi|119720719|ref|YP_921214.1| 83 SKCVGCGNCARACP 96
                                   79***********9 PP

  == domain 4  score: 19.4 bits;  conditional E-value: 1e-06
                         Fer4_4   4 CigCgsCvaaCPqg 17 
                                    C++Cg Cv++CP+g
  gi|119720719|ref|YP_921214.1| 112 CVHCGYCVNYCPYG 125
                                    ************86 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1  11.5   7.4e-05     0.078       3      55 ..       7      69 ..       5      73 .. 0.69
   2 !   21.4  12.1   1.9e-07    0.0002       3      53 ..      80     124 ..      78     129 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.4e-05
                        Fer4_21  3 idedkCigCgkCliaCedt......shqaieidaktvl..kvvedeCvGCnl..CssvCPved 55
                                   +d dkC+gC +C+ aC+        +  ai++++   +        C +C+   C++vCP++ 
  gi|119720719|ref|YP_921214.1|  7 VDVDKCVGCMSCMFACSRRfgegglAKSAIHVSSIGGVerGFKVVVCRACENppCAAVCPTNA 69
                                   899*************97533333367788766544331122345799999666******854 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 1.9e-07
                        Fer4_21   3 idedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPv 53 
                                    ++++kC+gCg+C+ aC+   + a++ d +++ +++   Cv C  C++ CP 
  gi|119720719|ref|YP_921214.1|  80 LNPSKCVGCGNCARACP---IGAVQWDYESMKPII---CVHCGYCVNYCPY 124
                                    6899*************...899999999998886...************4 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9  11.8    0.0019         2       2      64 ..       9      68 ..       8      69 .. 0.62
   2 !   16.4   1.2   8.7e-06    0.0092       3      18 ..      83      98 ..      81     109 .. 0.78
   3 !   13.0   1.6    0.0001      0.11       5      17 ..     112     124 ..     110     131 .] 0.80

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0019
                         Fer4_8  2 lekCieCgaCqsaCpvlrrtkkhlldargeaae....dvqeeqvleeeealwsCttcga..CtevCpvg 64
                                   ++kC++C+ C+ aC   rr+++    a+          v++         +  C +c++  C+ vCp++
  gi|119720719|ref|YP_921214.1|  9 VDKCVGCMSCMFACS--RRFGEG-GLAKSAIHVssigGVER------GFKVVVCRACENppCAAVCPTN 68
                                   79************4..333322.22222211112222222......235899**************87 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 8.7e-06
                         Fer4_8  3 ekCieCgaCqsaCpvl 18
                                   +kC++Cg C  aCp+ 
  gi|119720719|ref|YP_921214.1| 83 SKCVGCGNCARACPIG 98
                                   5788888888888864 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 0.0001
                         Fer4_8   5 CieCgaCqsaCpv 17 
                                    C++Cg+C + Cp 
  gi|119720719|ref|YP_921214.1| 112 CVHCGYCVNYCPY 124
                                    9999999999994 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   5.2     0.023        25       1      11 [.      12      22 ..      12      25 .. 0.92
   2 !    7.8   5.4     0.007       7.3       1      15 []      53      69 ..      53      69 .. 0.84
   3 !   14.3   7.2   5.8e-05     0.061       1      15 []      85      99 ..      85      99 .. 0.98
   4 !   15.1   6.3   3.1e-05     0.033       1      14 [.     112     125 ..     112     126 .. 0.96

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.023
                         Fer4_3  1 CtgCgaCvevC 11
                                   C+gC+ C+ +C
  gi|119720719|ref|YP_921214.1| 12 CVGCMSCMFAC 22
                                   *********** PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.007
                         Fer4_3  1 CtgCg..aCvevCPvgA 15
                                   C  C+  +C  vCP++A
  gi|119720719|ref|YP_921214.1| 53 CRACEnpPCAAVCPTNA 69
                                   66687778*******98 PP

  == domain 3  score: 14.3 bits;  conditional E-value: 5.8e-05
                         Fer4_3  1 CtgCgaCvevCPvgA 15
                                   C+gCg C ++CP gA
  gi|119720719|ref|YP_921214.1| 85 CVGCGNCARACPIGA 99
                                   *************98 PP

  == domain 4  score: 15.1 bits;  conditional E-value: 3.1e-05
                         Fer4_3   1 CtgCgaCvevCPvg 14 
                                    C++Cg Cv+ CP+g
  gi|119720719|ref|YP_921214.1| 112 CVHCGYCVNYCPYG 125
                                    ************98 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   1.5    0.0035       3.7      44      57 ..      10      23 ..       7      27 .. 0.80
   2 ?    4.9  13.0     0.036        38      43      58 ..      82      97 ..      52     100 .. 0.79
   3 !   15.1   1.9   2.4e-05     0.025      46      60 ..     112     126 ..      97     128 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0035
                        Fer4_17 44 slCieCgeCerkCP 57
                                   ++C++C  C  +C 
  gi|119720719|ref|YP_921214.1| 10 DKCVGCMSCMFACS 23
                                   78999999999996 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.036
                        Fer4_17 43 aslCieCgeCerkCPq 58
                                    s+C++Cg+C+r+CP 
  gi|119720719|ref|YP_921214.1| 82 PSKCVGCGNCARACPI 97
                                   579***********95 PP

  == domain 3  score: 15.1 bits;  conditional E-value: 2.4e-05
                        Fer4_17  46 CieCgeCerkCPqgl 60 
                                    C++Cg C+ +CP+g+
  gi|119720719|ref|YP_921214.1| 112 CVHCGYCVNYCPYGV 126
                                    677777777777664 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   6.6     7e-05     0.074       1      63 [.       5      69 ..       5      71 .. 0.73
   2 !   13.1   0.7   0.00012      0.12       1      19 [.      78      96 ..      78     104 .. 0.92
   3 ?    2.8   1.3       0.2   2.1e+02       8      19 ..     112     123 ..     110     128 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7e-05
                        Fer4_15  1 VvvDrdaCigcglCvaeapevfeldedglasvllddgeiaegevpddeeeaaqeA......araCPvdA 63
                                   V vD d+C gc  C+ +++++f + +  ++ ++++    + g v+   +  + +A      a++CP+ A
  gi|119720719|ref|YP_921214.1|  5 VIVDVDKCVGCMSCMFACSRRFGEGGLAKSAIHVS----SIGGVERGFKVVVCRAcenppcAAVCPTNA 69
                                   78***********************9888888875....356666666666555533333366666666 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00012
                        Fer4_15  1 VvvDrdaCigcglCvaeap 19
                                   Vv++ ++C gcg+C++++p
  gi|119720719|ref|YP_921214.1| 78 VVLNPSKCVGCGNCARACP 96
                                   789999************8 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.2
                        Fer4_15   8 CigcglCvaeap 19 
                                    C  cg Cv  +p
  gi|119720719|ref|YP_921214.1| 112 CVHCGYCVNYCP 123
                                    9*********98 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.5    0.0048       5.1      84     111 ..      11      38 ..       7      41 .. 0.84
   2 !    8.2   8.4    0.0027       2.8      61      95 ..      53      95 ..      44     103 .. 0.77
   3 !   10.6   1.7   0.00047       0.5      61      75 ..     112     126 ..      99     128 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0048
                        Fer4_18  84 eciscllcidacdkvmeklgkpkgliry 111
                                    +c+ c+ c+ ac++  ++ g+ k+ i+ 
  gi|119720719|ref|YP_921214.1|  11 KCVGCMSCMFACSRRFGEGGLAKSAIHV 38 
                                    69**********9999888888887765 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0027
                        Fer4_18 61 cidces..cvkvcPtgidirk...Glql...eciscllcidac 95
                                   c +ce   c +vcPt+  +r    G+ l   +c+ c++c  ac
  gi|119720719|ref|YP_921214.1| 53 CRACENppCAAVCPTNALVRReggGVVLnpsKCVGCGNCARAC 95
                                   88898666*******99998544355544447*********** PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00047
                        Fer4_18  61 cidcescvkvcPtgi 75 
                                    c++c++cv+ cP g+
  gi|119720719|ref|YP_921214.1| 112 CVHCGYCVNYCPYGV 126
                                    ************987 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   1.7    0.0069       7.3      79      94 ..       9      24 ..       4      26 .. 0.76
   2 ?    2.1   1.3      0.35   3.6e+02       2      14 ..      53      67 ..      49      75 .. 0.80
   3 !   13.1   2.9   0.00012      0.13      79      94 ..      82      97 ..      77      99 .. 0.85
   4 !   10.3   0.6   0.00097         1      77      95 ..     107     125 ..     100     126 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0069
                        Fer4_22 79 esgCvGCgRCieacpv 94
                                     +CvGC  C+ ac  
  gi|119720719|ref|YP_921214.1|  9 VDKCVGCMSCMFACSR 24
                                   5678888888888865 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.35
                        Fer4_22  2 ClsCga..CtlvCpt 14
                                   C +C +  C++vCpt
  gi|119720719|ref|YP_921214.1| 53 CRACENppCAAVCPT 67
                                   77787666999**99 PP

  == domain 3  score: 13.1 bits;  conditional E-value: 0.00012
                        Fer4_22 79 esgCvGCgRCieacpv 94
                                    s+CvGCg C +acp 
  gi|119720719|ref|YP_921214.1| 82 PSKCVGCGNCARACPI 97
                                   578***********96 PP

  == domain 4  score: 10.3 bits;  conditional E-value: 0.00097
                        Fer4_22  77 fgesgCvGCgRCieacpvk 95 
                                    ++   Cv Cg C++ cp +
  gi|119720719|ref|YP_921214.1| 107 MKPIICVHCGYCVNYCPYG 125
                                    5667899999999999965 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.3   4.1e-05     0.043       1      23 [.       7      29 ..       7      41 .. 0.85
   2 ?   -1.2   2.7         3   3.1e+03      12      53 ..      61      67 ..      51      72 .. 0.62
   3 ?   10.2   2.6   0.00083      0.88       3      17 ..      82      96 ..      80      97 .. 0.91
   4 ?    6.0   2.5     0.017        18       6      17 ..     112     123 ..     110     124 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.1e-05
                        Fer4_13  1 VDrdtCiacgaCvelaPdvFeed 23
                                   VD d+C++c++C  ++   F e 
  gi|119720719|ref|YP_921214.1|  7 VDVDKCVGCMSCMFACSRRFGEG 29
                                   8999************9999775 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 3
                        Fer4_13 12 CvelaPdvFeeddeggasvvaeqptseeekadaeeAadaCPv 53
                                   C++++P                                   +
  gi|119720719|ref|YP_921214.1| 61 CAAVCP-----------------------------------T 67
                                   666666...................................4 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.00083
                        Fer4_13  3 rdtCiacgaCvelaP 17
                                    ++C++cg+C+ ++P
  gi|119720719|ref|YP_921214.1| 82 PSKCVGCGNCARACP 96
                                   689***********9 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.017
                        Fer4_13   6 CiacgaCvelaP 17 
                                    C+ cg Cv+ +P
  gi|119720719|ref|YP_921214.1| 112 CVHCGYCVNYCP 123
                                    ***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       743  (0.0414412); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 844.69
//
Query:       gi|119720720|ref|YP_921215.1|  [L=595]
Description: aldehyde ferredoxin oxidoreductase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-64  217.4   0.1    2.5e-64  216.8   0.1    1.3  1  AFOR_N    Aldehyde ferredoxin oxidoreductase, N-terminal doma
    1.2e-62  212.2   0.0    1.6e-62  211.7   0.0    1.1  1  AFOR_C    Aldehyde ferredoxin oxidoreductase, domains 2 & 3


Domain annotation for each model (and alignments):
>> AFOR_N  Aldehyde ferredoxin oxidoreductase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  216.8   0.1   2.8e-68   2.5e-64       2     197 ..       8     206 ..       7     207 .. 0.96

  Alignments for each domain:
  == domain 1  score: 216.8 bits;  conditional E-value: 2.8e-68
                                    EEEEEETTTTEEEEEE--HHHHHHH-SCHHHHHHHHHHHS-TTS-TTSTTS-EEEEE-TTTTSSSTTB-EEEEEEE-TTT CS
                         AFOR_N   2 kilrvdLstgkieveelpeelaekylGgrglaakllldevppgvdplspenplvfatGpltgtpapgsgrlvvvaksPlt 81 
                                    k+l++dLs+++++ve+   +l+e+ylGg+g+a+kll +e+p++vdpl+pen++vfa+Gp++   +p+++++v+++ksP+t
  gi|119720720|ref|YP_921215.1|   8 KVLYIDLSSKRYWVEDRL-DLFEEYLGGTGVATKLLEEELPRNVDPLGPENVIVFAVGPFNAL-YPTASKTVAMFKSPHT 85 
                                    89**************99.79*****************************************9.**************** PP

                                    SSEEEEEEETCHHHHHHHCT-SEEEEES--SS-EEEEEETTEEEEEE-TTTTTS-HHHHHHHHHHHHTS.....EEEEE- CS
                         AFOR_N  82 gtlgesnaGgrfgaelkraGydaivieGkaekpvylvieddkveiedaedlwgldtyettealkeelgd.....kvaviG 156
                                    g+lges+aGgr + +++ aGy aivi+G+++ pv+++++ dkv ++da+ +wg++ ++t  ++ +e++      +++ iG
  gi|119720720|ref|YP_921215.1|  86 GNLGESHAGGRSAVAIRLAGYGAIVIKGASDLPVWVSVHGDKVYFRDARAIWGMTSSHTVGRILREVEPgsgvrTIMRIG 165
                                    ************************************************************99888666666887778*** PP

                                    HHHHTT-TTB-E.EETTEEE-SSSHHHHHHHTTEEEEEEE- CS
                         AFOR_N 157 paGenlvrfAsisvddgraagrgGlGavmgsKnlkaivvrg 197
                                     aGe+++++A+++++++r++gr GlGav+gsK+lka+vv+g
  gi|119720720|ref|YP_921215.1| 166 RAGERMISYANVITETYRHFGRLGLGAVFGSKKLKALVVSG 206
                                    ************888************************98 PP

>> AFOR_C  Aldehyde ferredoxin oxidoreductase, domains 2 & 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  211.7   0.0   1.8e-66   1.6e-62       2     355 ..     221     572 ..     220     583 .. 0.91

  Alignments for each domain:
  == domain 1  score: 211.7 bits;  conditional E-value: 1.8e-66
                                    HHHHHHHHHHHSH.HHHHHHHH-GGGHHHHHHHTT---BTTTTBS--TTGGGGSHHHHHHHTEEEE.E-TT-SS--EEEE CS
                         AFOR_C   2 lgkkiqkeiksspqvtaelrkyGTaelvnianetgalptknfqegtfekaekisgealeekylvknegCfsCpiaCgrev 81 
                                    +  ki k i +sp  ++++++ GT+  v ++n+ galp  n q+ + + a+ isge+++ +yl ++ +C+ Cp+aC +  
  gi|119720720|ref|YP_921215.1| 221 VYDKIFKLIVDSP-LMKKYHEIGTPINVRVLNALGALPSLNLQKASIDSADAISGEYIATNYLGRRVSCAHCPVACIHLA 299
                                    6678999999***.666***************************99999*****************99************ PP

                                    E.......ET......EE---HHHHHHHTGGGT---HHHHHHHHHHHHHHTB-HHHHHHHHHHHHHHHHTTSS-HHHHTS CS
                         AFOR_C  82 kveegkk.vk......vegpeyetlaalGsnlgiddleailklnelcdelGlDtisaGntiafamelyekGllkkedtdg 154
                                     v+e+ +  +        g++ye ++alGs+lg  +   +l+l +l+d +GlD +++G ++a+a e+ ++G+++++d+ g
  gi|119720720|ref|YP_921215.1| 300 VVREPYEeEPyfykttFIGYDYEPIYALGSMLGAGEARDVLRLIDLVDSYGLDAMTTGVVLAWATEALSRGIISEKDLAG 379
                                    *9998875449*99997799************************************************************ PP

                                    ----TT-THHHHHHHHHHHTT-T.THHHHTT-HHHHHHCTT-GGG--EETTEE--SS-GGG-HHHHHHHHH-TTSS-SGG CS
                         AFOR_C 155 lelefgdaeallellekiAkreg.igdllAeGvkrlaeklgaeelamhvkGlelpaydprgakgmalaYatsnrGacHlr 233
                                    ++l++gd +a +++++ i ++   + + lA G+ ++a+k+g+e++a +  G e++ y      +   ++a   r  +Hl+
  gi|119720720|ref|YP_921215.1| 380 VKLRWGDYNAYMKAVQYIVEQPTeLYRDLARGALYAARKWGGEDFALSFGGNEMAGYHTGP--AAYANFAFGAR-HSHLD 456
                                    *********************************************************8764..66668888888.77888 PP

                                    G-THHHH.S---TT--.HHHHHHHHHHHHHHHHHHHHT--GGGG-HHH......HHHHHHHHHT----HHHHHHHHHHHH CS
                         AFOR_C 234 ayliale.ekvdplet.egkaelvkwfqdltalvdslglCkftseaeerldlelyakllsavtGidvteeellkaGeRiy 311
                                    +  + l+ e   + ++  + ++ +   + ++ ++ sl++C+f++   + +++e ++++l+   Gi+++ ++l+  G++iy
  gi|119720720|ref|YP_921215.1| 457 SAGYDLDqETIGRTPEpGELVRRLYEEESWRQVLTSLVVCLFAR---KVYKPEVVSEALKP-LGIEMSVDDLYSLGRKIY 532
                                    777777766666666657999999********************...789**********9.9***************** PP

                                    HHHHHHHHHHT--HHHS---HHHHHS---SSTTTT---..-HHH CS
                         AFOR_C 312 nleRlfnlreGltrkddtlperlleeplkegpakgkvledelee 355
                                      +  + lreG++++d + p+r++e p + g    +     +e+
  gi|119720720|ref|YP_921215.1| 533 REKYRLKLREGFRPEDVSFPRRIFETPTPHGLLSPEY----MEK 572
                                    ************************9999888766444....333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (595 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.51
# Mc/sec: 3509.27
//
Query:       gi|119720721|ref|YP_921216.1|  [L=234]
Description: sugar fermentation stimulation protein A [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    9.2e-34  116.3   0.0    1.4e-33  115.7   0.0    1.2  1  SfsA       Sugar fermentation stimulation protein RE domain
    3.5e-17   62.3   0.3    6.7e-17   61.4   0.3    1.5  1  SfsA_N     SfsA N-terminal OB domain
  ------ inclusion threshold ------
      0.052   13.5   0.0        2.4    8.1   0.0    2.3  2  PDDEXK_10  PD-(D/E)XK nuclease superfamily


Domain annotation for each model (and alignments):
>> SfsA  Sugar fermentation stimulation protein RE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.7   0.0   2.3e-37   1.4e-33       5     137 ..      87     218 ..      83     219 .. 0.92

  Alignments for each domain:
  == domain 1  score: 115.7 bits;  conditional E-value: 2.3e-37
                                    HHHHHHHEE..........EEES-EETTEE-SEEEE-S.SSEEEEEEEE--EE..EEEEE-SS--HHHHHHHHHHHHHHH CS
                           SfsA   5 klveealesglielagyeeikrevkygnsriDfllekeeeekcyvEVKsvtleeggialfPdapteRgqkhleeLaelvk 84 
                                    +++e+++e+g+   +g++   r  ++g+sr+D+ll ++ +e+++vEVKs++l+e+ +a++Pd+pt Rg+++++eL++l++
  gi|119720721|ref|YP_921216.1|  87 NALESLFEQGIEPWSGCSVKARAPRLGSSRLDYLLVCN-GEEVFVEVKSAVLREDSYAMYPDCPTLRGRRQISELIRLAE 165
                                    566777777665456788889999*************9.***************99************************ PP

                                    TT-EEEEEEEE-SSS--EEEE-TTT-HHHHHHHHHHHHHT-EEEEEEEEE-TT CS
                           SfsA  85 egyravvlfvvqredarefkpnkeidpefaealreaaeaGVevlaydckvtpe 137
                                     g +a+++fv+  +++++fkp+ e dpe+a +l ea+++GV + a++++++p+
  gi|119720721|ref|YP_921216.1| 166 GGGKAMIIFVAALPGVKAFKPYGEGDPEVAVLLGEAKKKGVVLRAVALHYDPS 218
                                    *************************************************9986 PP

>> SfsA_N  SfsA N-terminal OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.4   0.3   1.1e-20   6.7e-17       1      62 [.      17      79 ..      17      80 .. 0.90

  Alignments for each domain:
  == domain 1  score: 61.4 bits;  conditional E-value: 1.1e-20
                                   EEEEETTEEEEEEE.....EE----S--TTT--TT-EEEEE....ESSS-SEEEEEEEETTEEEE CS
                         SfsA_N  1 lrRpnRFladveldg...tvHvpntGrlkelllpGarvllsksdnpkrKtkytleavekegtwvg 62
                                   +rR nRF++ ve++g   ++H++ntGrl e l+pG+r+++ +   ++ Kt+y+l ave  g+ ++
  gi|119720721|ref|YP_921216.1| 17 IRRENRFVVLVEVEGrayRAHINNTGRLLEFLVPGRRAFCLR--RERSKTAYRLFAVEDAGSAAL 79
                                   89************96666*********************96..5678**********9987666 PP

>> PDDEXK_10  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.019   1.1e+02      11      36 ..      21      46 ..      15      48 .. 0.83
   2 ?    8.1   0.0   0.00041       2.4       7      31 ..     120     144 ..     116     146 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.019
                      PDDEXK_10 11 dgkvilvEiksslkrgDlavikrkke 36
                                   ++ v+lvE++ +  r+ +    r  e
  gi|119720721|ref|YP_921216.1| 21 NRFVVLVEVEGRAYRAHINNTGRLLE 46
                                   7789***********99988777655 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00041
                      PDDEXK_10   7 vvvkdgkvilvEiksslkrgDlavi 31 
                                    ++v +g+ + vE+ks++ r D +++
  gi|119720721|ref|YP_921216.1| 120 LLVCNGEEVFVEVKSAVLREDSYAM 144
                                    6789***************998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       256  (0.0142785); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 1437.83
//
Query:       gi|119720722|ref|YP_921217.1|  [L=320]
Description: methionine synthase, vitamin-B12 independent [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-06   27.9   0.0    2.8e-05   23.6   0.0    2.1  2  Meth_synt_2  Cobalamin-independent synthase, Catalytic domain
  ------ inclusion threshold ------
      0.099   11.3   0.0       0.15   10.7   0.0    1.2  1  RdRP_3       Viral RNA dependent RNA polymerase
       0.13   12.1   0.5         74    3.3   0.0    3.5  3  TrmB         Sugar-specific transcriptional regulator TrmB


Domain annotation for each model (and alignments):
>> Meth_synt_2  Cobalamin-independent synthase, Catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.013        76       2      23 ..       4      25 ..       3      31 .. 0.80
   2 !   23.6   0.0   4.7e-09   2.8e-05     148     303 ..     132     287 ..      66     315 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.013
                                   -BB--SB---SS---------- CS
                    Meth_synt_2  2 pTttiGSfPqtaevrearaevk 23
                                   +Tt +GSfP +  ++++ +++k
  gi|119720722|ref|YP_921217.1|  4 ATTLVGSFPLDYSRENIARALK 25
                                   7999*****9988887766655 PP

  == domain 2  score: 23.6 bits;  conditional E-value: 4.7e-09
                                    HHHHHHHHHHHHHHHHHHTT-SEEEEE-TTSSTT--SSGGGHHHHHHHHHHHHHHHHTTS-TTSEEE.EEES-S--CCCH CS
                    Meth_synt_2 148 aaaqialalrdevkdLeaaGikviQiDepalreGlplkkadwaayldwaveafrldtiaaaddtqvh.tHlCyselndil 226
                                    a+ + ++    ev+   ++   ++ +Dep l+  +  k  +    ++     ++ld++ a+    +  +H+C+  l+ +l
  gi|119720722|ref|YP_921217.1| 132 AVLEYVVETAREVASTLNP--FIVCVDEPVLSVIVGSK--SVMFGYTAEEITRALDSVLARFRSPMRgVHVCSR-LPPLL 206
                                    5555555566666644445..59999999998544433..34444444445678999999998888648***75.66666 PP

                                    .HHHHTT.--SEEEESBSSS-SSGGGGTTT..T---SEEEEBSS-TTSSS--THHHHHHHHHCHHCTS-STSB-BB-SS- CS
                    Meth_synt_2 227 .saiaal.dvDvitieasrsdeellealee..vkygrgvglGvydihsprvpsmeeiaalikkaldvapkerlwvnPdCG 302
                                       + +l ++  ++ e+s+ +e+   + +    ++g+ +g Gv+      v+  e + al+++al+++ +   ++ PdCG
  gi|119720722|ref|YP_921217.1| 207 kTVLLQLsNANFLDHEHSDIPENRAYYQASelRESGKVLGYGVVSSRNTSVERLEDVVALARDALERYGESLAFIKPDCG 286
                                    34455662588899999999854433322235679*********************************99999******9 PP

                                    S CS
                    Meth_synt_2 303 L 303
                                    +
  gi|119720722|ref|YP_921217.1| 287 F 287
                                    5 PP

>> RdRP_3  Viral RNA dependent RNA polymerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   2.6e-05      0.15     171     203 ..     161     193 ..     138     196 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 2.6e-05
                                    HHHHHGGGBGGG--HHHHHHHHHHHHHTSSSEE CS
                         RdRP_3 171 dkavggptvlkgytveqrgeillkkwesfkkPv 203
                                      +vg+++v++gyt+e++ ++l +   +f++P+
  gi|119720722|ref|YP_921217.1| 161 SVIVGSKSVMFGYTAEEITRALDSVLARFRSPM 193
                                    6789****************************8 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1     0.021   1.3e+02      39      55 ..      44      60 ..      40      66 .. 0.87
   2 ?    3.3   0.0     0.012        74      12      33 ..     128     149 ..     125     150 .. 0.88
   3 ?    1.9   0.0     0.036   2.1e+02      29      51 ..     221     243 ..     208     245 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.021
                                   HHHHHHHHHHCTSEEEE CS
                           TrmB 39 vYevLrsLedkGlVere 55
                                   vY  ++ L++kG+V re
  gi|119720722|ref|YP_921217.1| 44 VYMFIEPLVKKGVVVRE 60
                                   8999**********987 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.012
                                    CHCHHHHHHCCCHHCHHCCCTT CS
                           TrmB  12 kvYlaLlklgpatadeiaeelg 33 
                                    + ++a+l++   ta+e+a+ l+
  gi|119720722|ref|YP_921217.1| 128 EGFQAVLEYVVETAREVASTLN 149
                                    56899*************9986 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.036
                                    CCCTTSSCHCHHHHHHHHHHCTS CS
                           TrmB  29 aeelgvprskvYevLrsLedkGl 51 
                                    +e++++p++++Y   ++L + G 
  gi|119720722|ref|YP_921217.1| 221 HEHSDIPENRAYYQASELRESGK 243
                                    6899********98888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2112.32
//
Query:       gi|119720723|ref|YP_921218.1|  [L=246]
Description: molybdopterin-guanine dinucleotide biosynthesis protein B [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-19   69.2   0.0    4.4e-19   68.7   0.0    1.2  1  MobB             Molybdopterin guanine dinucleotide synthesis
      1e-10   41.1   2.3    1.7e-10   40.4   2.3    1.4  1  FeS              Putative Fe-S cluster
     0.0013   18.8   0.0     0.0018   18.3   0.0    1.5  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
  ------ inclusion threshold ------
      0.013   14.5   0.5      0.021   13.8   0.5    1.3  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
      0.015   14.9   0.1      0.021   14.4   0.1    1.3  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
      0.016   15.3   0.0      0.026   14.7   0.0    1.2  1  AAA_33           AAA domain
      0.032   14.6   0.0      0.053   13.9   0.0    1.4  1  AAA              ATPase family associated with various cellul
      0.038   14.5   0.0      0.048   14.2   0.0    1.5  1  AAA_18           AAA domain
      0.041   13.8   0.1      0.083   12.8   0.1    1.5  1  NTPase_1         NTPase
      0.052   13.5   0.0       0.19   11.6   0.1    1.8  2  NACHT            NACHT domain
      0.059   13.8   0.1       0.11   12.9   0.1    1.6  1  AAA_16           AAA ATPase domain
      0.068   13.4   0.0       0.13   12.6   0.0    1.4  1  AAA_22           AAA domain
      0.068   13.7   0.0        0.1   13.1   0.0    1.4  1  ABC_tran         ABC transporter
      0.082   12.9   0.6       0.26   11.3   0.0    2.1  2  HTH_15           Helix-turn-helix domain of alkylmercury lyas
      0.087   13.2   0.8        2.6    8.4   0.2    2.5  3  AAA_19           AAA domain
      0.091   11.8   0.2       0.14   11.3   0.2    1.2  1  LpxK             Tetraacyldisaccharide-1-P 4'-kinase
       0.14   12.0   0.0       0.19   11.6   0.0    1.2  1  AAA_26           AAA domain
       0.14   12.3   0.0       0.24   11.5   0.0    1.3  1  Torsin           Torsin
       0.16   12.0   0.0       0.27   11.3   0.0    1.3  1  Fer2_2           [2Fe-2S] binding domain
       0.18   11.5   0.0       0.28   10.9   0.0    1.2  1  Thymidylate_kin  Thymidylate kinase
        0.2   10.9   0.6       0.66    9.2   0.6    1.7  2  MipZ             ATPase MipZ


Domain annotation for each model (and alignments):
>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.7   0.0   5.2e-22   4.4e-19       2     118 ..       4     116 ..       3     128 .. 0.86

  Alignments for each domain:
  == domain 1  score: 68.7 bits;  conditional E-value: 5.2e-22
                           MobB   2 lgivgksgsGKTtLleklipelkarglrvgtiKhahhgfdvdkpgkDsyrhrkAGAkevlvaskerlalikeleeaelsl 81 
                                    ++++g++gsGKTt  + ++ elk+rglrv+++Khah g++v+  + Ds r+  AGA+ v+ +s++ +  +++   ++ sl
  gi|119720723|ref|YP_921218.1|   4 VAVIGFKGSGKTTVASYIVGELKRRGLRVAAVKHAHGGISVN--DEDSGRLFGAGADRVIAVSDDVVEEYRR---SRASL 78 
                                    6899**********************************9886..56******************98887777...4579* PP

                           MobB  82 eellarlsevDlvlvEGfkke.alpkievlraelgkee 118
                                     e++++l+  D+ + EGfk+e +  ++ v r+  +  e
  gi|119720723|ref|YP_921218.1|  79 WEVISQLRGFDFAVFEGFKSEfPGVRLAVARNVEEARE 116
                                    *******************9845678888887554444 PP

>> FeS  Putative Fe-S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   2.3   1.9e-13   1.7e-10       1      33 []     163     195 ..     163     195 .. 0.98

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 1.9e-13
                            FeS   1 LPgtNCgaCGypgCmafAealvegeaqledCpp 33 
                                    LPg+NCg C y +C a+Aea+++gea   +C++
  gi|119720723|ref|YP_921218.1| 163 LPGLNCGFCRYGSCVALAEAVARGEAGHGECTV 195
                                    9******************************96 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   2.1e-06    0.0018       2      37 ..       5      39 ..       4     158 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.1e-06
                                   EEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEE CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           CbiA  2 aiastkGGvGKTtlaanLaralarrglrVllvDaDp 37
                                   a++++k G+GKTt+a  +   l+rrglrV++v+   
  gi|119720723|ref|YP_921218.1|  5 AVIGFK-GSGKTTVASYIVGELKRRGLRVAAVKHAH 39
                                   677777.69***********************9544 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.5   2.5e-05     0.021      31      63 ..       3      35 ..       1      43 [. 0.92

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.5e-05
                                   EEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEE CS
                           MeaB 31 vvGltGvPGaGkstlvealglelrrrGkrvavl 63
                                    v + G+ G+Gk t+ + ++ el+rrG rva +
  gi|119720723|ref|YP_921218.1|  3 AVAVIGFKGSGKTTVASYIVGELKRRGLRVAAV 35
                                   57899*************************976 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   2.4e-05     0.021       3      40 ..       4      43 ..       2      63 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.4e-05
                                   EEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SSCH CS
                           cobW  3 tvltGflGsGKTtLlnhll..enraglklavivNefgevs 40
                                   + + Gf GsGKTt+ + ++   +r+gl++a +    g +s
  gi|119720723|ref|YP_921218.1|  4 VAVIGFKGSGKTTVASYIVgeLKRRGLRVAAVKHAHGGIS 43
                                   6789****************9999******9976666555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0     3e-05     0.026       2      70 ..       4      75 ..       4      83 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3e-05
                         AAA_33  2 vllvGlpGsGKstlaerllkklg..avllss.dtlrrrlfgtdqqsktdytrvldrlyqilnelarkalsag 70
                                   v ++G +GsGK+t+a  ++ +l+  + +++    ++  + ++d++s +     +dr+++   ++++++++++
  gi|119720723|ref|YP_921218.1|  4 VAVIGFKGSGKTTVASYIVGELKrrGLRVAAvKHAHGGISVNDEDSGRLFGAGADRVIAVSDDVVEEYRRSR 75
                                   5689**************999995544443313355555558888888777777888888777777777766 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   6.2e-05     0.053       2      35 ..       5      38 ..       4      76 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.2e-05
                                   EEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCS CS
                            AAA  2 llyGppGtGKTllakavakelgvefleisgsell 35
                                    ++G +G GKT++a+ ++ el+++ l++ + +  
  gi|119720723|ref|YP_921218.1|  5 AVIGFKGSGKTTVASYIVGELKRRGLRVAAVKHA 38
                                   5799*****************9988887776665 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   5.6e-05     0.048       1      30 [.       4      46 ..       4     161 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.6e-05
                         AAA_18  1 IlltGtpGvGKttlakeLskrlgf.............gvnlrd 30
                                   +++ G  G+GKtt+a ++  +l+              g+ ++d
  gi|119720723|ref|YP_921218.1|  4 VAVIGFKGSGKTTVASYIVGELKRrglrvaavkhahgGISVND 46
                                   6899*************95555333223333333333333333 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   9.7e-05     0.083       2      31 ..       4      33 ..       3      40 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.7e-05
                                   EEEE--TTSSHHHHHHHHHHHH...GGGEE CS
                       NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvkvg 31
                                   v++ G  G+GKtT+ + ++ +lk++g++v+
  gi|119720723|ref|YP_921218.1|  4 VAVIGFKGSGKTTVASYIVGELKRRGLRVA 33
                                   6788999********************997 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00022      0.19       1      30 [.       2      31 ..       2      38 .. 0.88
   2 ?   -1.4   0.0       2.2   1.9e+03       6      30 ..     185     209 ..     182     222 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00022
                                   SCEEEEC-TTTCHHHHHHHHHHHHCTS-SC CS
                          NACHT  1 rlvilqGeaGsGKTtLlqklalawaegklp 30
                                   r v++ G  GsGKTt +  ++ +++++ l 
  gi|119720723|ref|YP_921218.1|  2 RAVAVIGFKGSGKTTVASYIVGELKRRGLR 31
                                   5799********************998865 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.2
                                    EC-TTTCHHHHHHHHHHHHCTS-SC CS
                          NACHT   6 qGeaGsGKTtLlqklalawaegklp 30 
                                    +GeaG G  t l + + ++ +gk+ 
  gi|119720723|ref|YP_921218.1| 185 RGEAGHGECTVLSSKVKLLVDGKPV 209
                                    7999999888887777777666655 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   0.00013      0.11      25      59 ..       2      36 ..       1      87 [. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00013
                         AAA_16 25 elvllsGesGvGKsslvrellralekdggiflrgk 59
                                   ++v ++G +G+GK++++  +  +l+++g  +++ k
  gi|119720723|ref|YP_921218.1|  2 RAVAVIGFKGSGKTTVASYIVGELKRRGLRVAAVK 36
                                   5799****************999999986665444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00015      0.13       8      32 ..       4      28 ..       2      53 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00015
                         AAA_22  8 lvvtGesGtGKTtllrrlleqldee 32
                                   ++v+G +G+GKTt++  ++ +l+++
  gi|119720723|ref|YP_921218.1|  4 VAVIGFKGSGKTTVASYIVGELKRR 28
                                   78*************9999988654 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00012       0.1      13      37 ..       3      27 ..       1      86 [. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00012
                                   EEEEEESTTSSHHHHHHHHTTSS-- CS
                                   xxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ABC_tran 13 kvaivGenGaGKStLlkllagllkp 37
                                    va++G  G+GK+t+++ + g+lk 
  gi|119720723|ref|YP_921218.1|  3 AVAVIGFKGSGKTTVASYIVGELKR 27
                                   689******************9986 PP

>> HTH_15  Helix-turn-helix domain of alkylmercury lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       8.2     7e+03      61      74 .]      43      56 ..      36      56 .. 0.84
   2 ?   11.3   0.0    0.0003      0.26       6      39 ..     179     212 ..     176     220 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 8.2
                         HTH_15 61 stEydedGrvvGfG 74
                                   s+  ++ Gr  G G
  gi|119720723|ref|YP_921218.1| 43 SVNDEDSGRLFGAG 56
                                   56778899999988 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.0003
                         HTH_15   6 lseslakgeeggssaellrpLlrlLakGepVtve 39 
                                    l+e+ a+ge g ++ ++l +  +lL++G+pV ++
  gi|119720723|ref|YP_921218.1| 179 LAEAVARGEAGHGECTVLSSKVKLLVDGKPVELN 212
                                    789999*************************875 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.2     0.003       2.6      12      38 ..       3      29 ..       1      39 [. 0.86
   2 ?   -2.5   0.0       6.7   5.7e+03      42      57 ..     117     132 ..     104     134 .. 0.68
   3 ?    2.4   0.0      0.21   1.8e+02      17      45 ..     186     214 ..     179     221 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.003
                         AAA_19 12 vllvtaGpGtGKTrvlkhivallvelg 38
                                    ++v++  G+GKT+v   iv +l+++g
  gi|119720723|ref|YP_921218.1|  3 AVAVIGFKGSGKTTVASYIVGELKRRG 29
                                   678999**************9999887 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 6.7
                         AAA_19  42 peeillvaftgrAake 57 
                                    + + l va tgr ake
  gi|119720723|ref|YP_921218.1| 117 LLTPLTVAITGRVAKE 132
                                    4566789999998876 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.21
                         AAA_19  17 aGpGtGKTrvlkhivallvelggvkpeei 45 
                                    + +G G  +vl  +v+llv+ + v+++++
  gi|119720723|ref|YP_921218.1| 186 GEAGHGECTVLSSKVKLLVDGKPVELNPF 214
                                    779****************9998887765 PP

>> LpxK  Tetraacyldisaccharide-1-P 4'-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   0.00016      0.14      46      77 ..      10      41 ..       3      50 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00016
                                   S-HSHHHHHHHHHHHTTTS..-EEEEE--TSS CS
                           LpxK 46 GGtGKTPlvialvkllqarglkvgvlSRGYgg 77
                                    G+GKT ++ ++v  l++rgl+v+ +   +gg
  gi|119720723|ref|YP_921218.1| 10 KGSGKTTVASYIVGELKRRGLRVAAVKHAHGG 41
                                   59**********************99877776 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00022      0.19      10      48 ..      10      49 ..       2      76 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00022
                         AAA_26 10 tgvGKTvvslgLvralkrkgvkvgyfKPiqtgiee.deds 48
                                   +g+GKT+v+  +v  lkr+g +v+ +K    gi+  deds
  gi|119720723|ref|YP_921218.1| 10 KGSGKTTVASYIVGELKRRGLRVAAVKHAHGGISVnDEDS 49
                                   58*************************9998887534444 PP

>> Torsin  Torsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00028      0.24      57      91 ..       5      39 ..       2      49 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00028
                                   EEEE-TTSSHHHHHHHHHHHHSTTGGGSTTEEEEE CS
                         Torsin 57 sfhGwtGtGknfvaeiiaenlyrdGlrsdyvkkfv 91
                                   ++ G+ G+Gk  va+ i+ +l r+Glr   vk+  
  gi|119720723|ref|YP_921218.1|  5 AVIGFKGSGKTTVASYIVGELKRRGLRVAAVKHAH 39
                                   56799*************************99865 PP

>> Fer2_2  [2Fe-2S] binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00031      0.27      17      45 ..     158     186 ..     146     215 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00031
                         Fer2_2  17 eafveegasqCGyCtpGfvmsaaalleen 45 
                                    +af    ++ CG+C  G ++++a+ +++ 
  gi|119720723|ref|YP_921218.1| 158 KAFEPLPGLNCGFCRYGSCVALAEAVARG 186
                                    5666677999************9998876 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00032      0.28       3      31 ..       8      37 ..       7      46 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00032
                                   ESTTSSHHHHHHHHHHHHHHTTE..EEEES CS
                Thymidylate_kin  3 GlDGaGKttqaellkerlkeegik.vvltr 31
                                   G  G+GKtt+a +++  lk++g++ + +++
  gi|119720723|ref|YP_921218.1|  8 GFKGSGKTTVASYIVGELKRRGLRvAAVKH 37
                                   778*******************99555555 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.6   0.00077      0.66      11      35 ..      11      35 ..       4      42 .. 0.92
   2 ?   -1.5   0.0       1.4   1.2e+03      78     129 ..      67     121 ..      58     125 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00077
                                   TSSHHHHHHHHHHHHHTTT--EEEE CS
                           MipZ 11 GsGksttavhvavaLlkkGarvaai 35
                                   GsGk+t+a +++  L ++G+rvaa+
  gi|119720723|ref|YP_921218.1| 11 GSGKTTVASYIVGELKRRGLRVAAV 35
                                   9**********************98 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.4
                                    TTS-HHHHHHHHHHHHHHHHHH-SEEEEE-.....-SS--HHHHHHHHT-SEEEEEE CS
                           MipZ  78 veeeeeaevaeleelvadleaeldfividt.....PGsdsalsrlahsladtlvtPl 129
                                    v ee   + a+l e++++l + +df v++      PG   a++r + ++a  l+tPl
  gi|119720723|ref|YP_921218.1|  67 VVEEYRRSRASLWEVISQL-RGFDFAVFEGfksefPGVRLAVARNV-EEARELLTPL 121
                                    5555555556677777665.57888888751111244444444443.4577788887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                       103  (0.00574488); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1651.18
//
Query:       gi|119720724|ref|YP_921219.1|  [L=264]
Description: short chain dehydrogenase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-46  158.2   0.0    3.1e-46  157.8   0.0    1.1  1  adh_short_C2   Enoyl-(Acyl carrier protein) reductase
      2e-32  112.3   0.0    2.3e-32  112.0   0.0    1.1  1  adh_short      short chain dehydrogenase
    4.9e-05   23.3   0.0    9.1e-05   22.4   0.0    1.5  2  KR             KR domain
  ------ inclusion threshold ------
      0.025   15.3   0.2      0.071   13.9   0.1    1.8  2  PSK_trans_fac  Rv0623-like transcription factor
      0.036   14.0   0.0        1.8    8.6   0.0    2.4  2  YAcAr          YspA, cpYpsA-related SLOG family
       0.15   12.0   0.0       0.25   11.2   0.0    1.3  1  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.8   0.0     1e-49   3.1e-46       4     232 ..      19     258 ..      15     260 .. 0.93

  Alignments for each domain:
  == domain 1  score: 157.8 bits;  conditional E-value: 1e-49
                                    TSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSEE..EE--TTSHHHHHHHHHHHHHHHSSEEEEEE----- CS
                   adh_short_C2   4 sgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgaev..lecDVtdeeqvealveevvekfgklDilvnnagia 80 
                                    +gIG+++A+ la+ G +v+l+ ++ e+ +k+  ++ +e + +v  +++D t++e++e++v+ev   +g  D+++ + g  
  gi|119720724|ref|YP_921219.1|  19 RGIGFGVARVLARCGSDVILVSRSAEGlEKARSAILSESPVDVftVQADLTRREDLERMVKEVLG-IGVPDVFFYSTGGP 97 
                                    9**************************999999999999999669*****************986.6************* PP

                                    EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH.HCTSC.CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHHHHH CS
                   adh_short_C2  81 pklkgpfletsreefdraldvnlyslfllakaalp.lmkeg.gsivnlssvgaervvpnynaygaaKaalealtrylAve 158
                                    ++  g+fle+s +++d a    +y ++++++ +lp +++++ g+++ lss++ +  +pn +  ++ + a+ +l+r+lA+e
  gi|119720724|ref|YP_921219.1|  98 RP--GSFLELSMDDWDSAYRLLVYPAVYITRSILPgMVEKRwGRLIYLSSLAIKEPMPNLALSNVMRIAIAGLVRTLARE 175
                                    **..*******************************6555558************************************** PP

                                    HGGGTEEEEEEEE--BHCTGGGGSTT.........HHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEEEEE CS
                   adh_short_C2 159 lgpkgiRvNavspgpikTlaasgikg.........fdelleelearaplgrlgtpeevaeaalfLasdeasyitGqtlvv 229
                                    +g++gi+vN + pg ikT  +++++           de +++l++ +p grlg pee++ +++fLasd asyi+G+ + v
  gi|119720724|ref|YP_921219.1| 176 VGRYGITVNGIMPGTIKTSRVEELAAdiarrqgvsLDEAYRQLARDIPAGRLGYPEEIGYLVAFLASDYASYINGAMIPV 255
                                    ******************9877665544445555567899999************************************* PP

                                    STT CS
                   adh_short_C2 230 DgG 232
                                    DgG
  gi|119720724|ref|YP_921219.1| 256 DGG 258
                                    **9 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.0   0.0   7.8e-36   2.3e-32       4     192 ..      13     201 ..      10     204 .. 0.96

  Alignments for each domain:
  == domain 1  score: 112.0 bits;  conditional E-value: 7.8e-36
                                    EEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT.TSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEEE CS
                      adh_short   4 lvtGassGIGraiakelakeGakvvvvdrseekleevakelkee.gakalaiqvDvtdreevealvekavkklgkldvLv 82 
                                    l t  s+GIG  +a+ la+ G +v++v+rs+e le++ + + +e   +++++q+D+t re++e++v+++   +g  dv+ 
  gi|119720724|ref|YP_921219.1|  13 LTTASSRGIGFGVARVLARCGSDVILVSRSAEGLEKARSAILSEsPVDVFTVQADLTRREDLERMVKEV-LGIGVPDVFF 91 
                                    67999*************************************999999*********************.578999**** PP

                                    E---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHHHHHH CS
                      adh_short  83 nNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaavagltrs 162
                                      +G  ++g+f els ++w++ + + +  ++ +tr++lp m+++++Gr +  sS a k+p++++a       a+agl+r+
  gi|119720724|ref|YP_921219.1|  92 YSTGGPRPGSFLELSMDDWDSAYRLLVYPAVYITRSILPGMVEKRWGRLIYLSSLAIKEPMPNLALSNVMRIAIAGLVRT 171
                                    ******************************************************************************** PP

                                    HHHHHGGGTEEEEEEEESSBSSHHHHHHCT CS
                      adh_short 163 lakelaptgirvnavaPGlvdTdmakelre 192
                                    la+e+ ++gi+vn+++PG ++T  ++el +
  gi|119720724|ref|YP_921219.1| 172 LAREVGRYGITVNGIMPGTIKTSRVEELAA 201
                                    **********************99888766 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0     3e-08   9.1e-05      10     109 ..      19     114 ..      12     148 .. 0.77
   2 ?   -3.8   0.0       3.5   1.1e+04      54      68 ..     195     209 ..     190     213 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 3e-08
                                    SHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS---EE.EE- CS
                             KR  10 GgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeeppikGv.iha 88 
                                     g+G  +ar la+ g + ++l+sRs  a+  +ka+ a l+++ ++v +v+aD++ ++++e++++e+   +  +  v + +
  gi|119720724|ref|YP_921219.1|  19 RGIGFGVARVLARCG-SDVILVSRS--AEGLEKARSAILSESPVDVFTVQADLTRREDLERMVKEVLGIG--VPDVfFYS 93 
                                    589999***998765.6899*****..455666678999*************************997444..44441456 PP

                                    --------TTT--HHHHHHHH CS
                             KR  89 Agvlrdklleemtaedleqvl 109
                                     g  r + + e++++d+++++
  gi|119720724|ref|YP_921219.1|  94 TGGPRPGSFLELSMDDWDSAY 114
                                    666677777777777776665 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 3.5
                                    EEEE----TT-HHHH CS
                             KR  54 evevvaaDvsdkdav 68 
                                    +ve +aaD++ ++ v
  gi|119720724|ref|YP_921219.1| 195 RVEELAADIARRQGV 209
                                    678888888887765 PP

>> PSK_trans_fac  Rv0623-like transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0         6   1.8e+04      13      22 ..     168     177 ..     167     179 .. 0.62
   2 ?   13.9   0.1   2.4e-05     0.071       4      30 ..     190     216 ..     187     220 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 6
                                    XXXXXXXXXX CS
                  PSK_trans_fac  13 lareLarltg 22 
                                    l+r+Lar  g
  gi|119720724|ref|YP_921219.1| 168 LVRTLAREVG 177
                                    5666666554 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 2.4e-05
                                    XXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                  PSK_trans_fac   4 nIkdpeverlareLarltgeskteAvr 30 
                                    +Ik  +ve+la  +ar+ g+s+ eA r
  gi|119720724|ref|YP_921219.1| 190 TIKTSRVEELAADIARRQGVSLDEAYR 216
                                    8*********************99965 PP

>> YAcAr  YspA, cpYpsA-related SLOG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0   0.00061       1.8      23      66 ..      27      70 ..      24      71 .. 0.93
   2 ?    2.9   0.0     0.036   1.1e+02      42      57 ..     196     211 ..     186     217 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00061
                          YAcAr 23 klhaeapidmvlvhGgakGaDrlAarWAaergvelvrfpaDwkr 66
                                   +++a++++d++lv+ +a+G ++  ++   e  v++ +++aD +r
  gi|119720724|ref|YP_921219.1| 27 RVLARCGSDVILVSRSAEGLEKARSAILSESPVDVFTVQADLTR 70
                                   6899*******************999**************9876 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.036
                          YAcAr  42 aDrlAarWAaergvel 57 
                                    ++ lAa+ A+++gv l
  gi|119720724|ref|YP_921219.1| 196 VEELAADIARRQGVSL 211
                                    799***********88 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   8.3e-05      0.25      10      44 ..      21      55 ..      20      82 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 8.3e-05
                                   CHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHH CS
                        3HCDH_N 10 mGagiaavfasagleVvlvdiseealekalekiek 44
                                   +G g+a v+a+ g +V lv +s+e leka+++i +
  gi|119720724|ref|YP_921219.1| 21 IGFGVARVLARCGSDVILVSRSAEGLEKARSAILS 55
                                   799***************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1572.69
//
Query:       gi|119720725|ref|YP_921220.1|  [L=256]
Description: UBA/THIF-type NAD/FAD binding protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-67  227.3   0.0    2.2e-67  227.0   0.0    1.0  1  ThiF             ThiF family
    1.1e-05   25.7   0.9    5.5e-05   23.4   1.0    1.9  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
    5.3e-05   23.3   0.5     0.0014   18.7   0.1    2.1  2  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
     0.0039   16.8   0.1     0.0055   16.4   0.1    1.2  1  ApbA             Ketopantoate reductase PanE/ApbA
     0.0066   15.8   0.2       0.03   13.7   0.1    1.9  2  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
     0.0089   15.6   4.3        1.4    8.4   2.6    2.2  2  DAO              FAD dependent oxidoreductase
  ------ inclusion threshold ------
      0.012   15.6   0.1      0.017   15.0   0.1    1.2  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
      0.016   15.7   0.1      0.026   14.9   0.1    1.3  1  NAD_binding_7    Putative NAD(P)-binding
      0.023   13.9   0.2      0.037   13.2   0.2    1.3  1  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
      0.053   13.1   0.0      0.071   12.7   0.0    1.3  1  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
      0.067   13.3   1.1       0.16   12.1   1.1    1.7  1  Ldh_1_N          lactate/malate dehydrogenase, NAD binding do
       0.12   11.6   0.2       0.18   11.1   0.2    1.2  1  FAD_binding_3    FAD binding domain
        0.2   11.4   1.1        6.2    6.6   0.0    2.4  2  DUF3090          Protein of unknown function (DUF3090)
        1.4    9.5   3.6        2.5    8.7   0.3    2.5  2  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas


Domain annotation for each model (and alignments):
>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  227.0   0.0   1.7e-70   2.2e-67       1     240 [.      12     239 ..      12     246 .. 0.94

  Alignments for each domain:
  == domain 1  score: 227.0 bits;  conditional E-value: 1.7e-70
                                    THHHHHHHHHHHHHHHHTSEEEEE--SHHHHHHHHHHHHHTTTEEEEEESSB--GGGGGTBTTS-GGGTTSBHHHHHHHH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ThiF   1 ysrqlallgedgqekLrdskvllvGaGglGsellknLalsGvgkltlvDnDkielsNlnRqflfreediGkpKaevaaea 80 
                                    y+rq++++g + q+kL++s+vl+vGaGglGs+++ +L+++Gvgkl +vD + +elsNlnRq+l+ ++d Gk+K+e+a+e+
  gi|119720725|ref|YP_921220.1|  12 YDRQIRVWGVEAQKKLKSSTVLVVGAGGLGSPVAFYLVAAGVGKLIIVDAEDVELSNLNRQILHWTSDLGKAKVESAKEK 91 
                                    89****************************************************************************** PP

                                    HHHT-TTSEEEEEES-CCG.CCS-HHHHTT-SEEEEESSSHHHHHHHHHHHHHHT-EEEEEEEETTEEEEEEEEECCS-E CS
                                    xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ThiF  81 lqeinpdveveavteritd.etvleellesvDlVvdalDniearrlvnracvkkgiplieagtlgfegqvvviipgktgc 159
                                    l+++np+vev++++++i + e  + +l+e++D+Vvd+lDn+++r+l+n+acvk g+pl+++++ g++gq++v+ p + +c
  gi|119720725|ref|YP_921220.1|  92 LEKLNPHVEVVTLKQKIRSlED-ALKLVEDADVVVDCLDNWSTRFLLNEACVKLGKPLVHGAVRGLYGQLTVVKPFEGPC 170
                                    *******************887.56************************************************99***** PP

                                    CTSS-TGGS.EECCCCEEHHHHHHCTE-B-HHHHHHHHHHHHHHHHHHHTTBCGGGCCEEEECCTTTTEEEEECCEEEEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           ThiF 160 yeCldpsstedptekkvplctsiagnipaiatttavvaglaalellkllsgkeklenslltqvdllesrfenvelerakk 239
                                    ++C  p   e p+e+ +p+           ++t++v+++l ale++k+l g  + ++ +l ++d+ +++f+ v++er ++
  gi|119720725|ref|YP_921220.1| 171 LRCILP--REPPEERPFPV----------AGPTPGVIGSLEALEVIKILTGYGEPMVGRLLFYDGVRNTFDVVKVERRPD 238
                                    ****99..44444454444..........59******************888888888888**************99997 PP

                                    E CS
                                    x RF
                           ThiF 240 s 240
                                    +
  gi|119720725|ref|YP_921220.1| 239 C 239
                                    6 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   1.0   4.3e-08   5.5e-05       1      98 [.      32     150 ..      32     167 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 4.3e-08
                                    EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH.......................TTTCEEEEE--TT CS
                Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka.......................lgvrfeaialdae 57 
                                    vl++GaG+ G++va +l++ +    +++++d ++ +l +l  ++                        +v++ + +  + 
  gi|119720725|ref|YP_921220.1|  32 VLVVGAGGLGSPVAFYLVAAGVG--KLIIVDAEDVELSNLNRQIlhwtsdlgkakvesakekleklnPHVEVVTLKQKIR 109
                                    89*****************9976..9**************9999*******************99888888888888899 PP

                                    THHHHHHHHHTTSSEEEE-SSGGGHH.HHHHHHHHHT-EEEE CS
                Sacchrp_dh_NADP  58 nyeavLaallkegdlvvnlsppissl.dvlkaCietgvhyvd 98 
                                      e+   +l++++d+vv+++ ++s++  + +aC++ g   v 
  gi|119720725|ref|YP_921220.1| 110 SLED-ALKLVEDADVVVDCLDNWSTRfLLNEACVKLGKPLVH 150
                                    9999.78899999**********77647779***99988776 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   1.1e-06    0.0014       8      45 ..      25      62 ..      21      96 .. 0.83
   2 ?    3.1   0.1     0.073        94      60      83 ..     105     128 ..      86     147 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.1e-06
                                   S..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESS CS
                   Shikimate_DH  8 eslkekkvlliGaGemaelvakhLlakgvkkvvvaNRt 45
                                   ++lk+++vl++GaG +++ va +L+a+gv k++++  +
  gi|119720725|ref|YP_921220.1| 25 KKLKSSTVLVVGAGGLGSPVAFYLVAAGVGKLIIVDAE 62
                                   4689******************************9755 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.073
                                    T-EEEEGCGHHHHHHT-SEEEE-S CS
                   Shikimate_DH  60 eiealkleelkellaeadvvisat 83 
                                    + ++++le+  +l+++advv+ + 
  gi|119720725|ref|YP_921220.1| 105 KQKIRSLEDALKLVEDADVVVDCL 128
                                    346899**************9875 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   4.3e-06    0.0055       1      89 [.      32     119 ..      32     125 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 4.3e-06
                                    EEEES-SHHHHHHHHHHHHHTHC.EEEE-SCH.HHHHHHHHCEEEEETTCEEEEEECEEECCHSCCCCS-ESEEEE-SSG CS
                           ApbA   1 iailGaGaiGsllaakLakagad.vtlilrsr.rlealkknGlrltseggeeilrppealsaeekselepidlvivtvKa 78 
                                    ++++GaG++Gs +a +L +ag    ++++ ++ +l +l+++ l+ ts+ g+ +++  ++  ++    + ++++v +  K 
  gi|119720725|ref|YP_921220.1|  32 VLVVGAGGLGSPVAFYLVAAGVGkLIIVDAEDvELSNLNRQILHWTSDLGKAKVESAKEKLEK---LNPHVEVVTLKQKI 108
                                    68***************9977765999999999999*************88888888777777...67888888887788 PP

                                    GGHHHHHHHHG CS
                           ApbA  79 yqteealeeik 89 
                                     ++e+al+ ++
  gi|119720725|ref|YP_921220.1| 109 RSLEDALKLVE 119
                                    88888887665 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.1   2.3e-05      0.03      29      70 ..      22      64 ..       7     104 .. 0.84
   2 ?   -0.1   0.0       0.4   5.1e+02      81     116 ..     110     144 ..      87     149 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.3e-05
                                   GSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-.EEEEESSSHH CS
                   2-Hacid_dh_C 29 llgkelsgktvGiiGlGrIGqavakrlkafgm.kviaydrskk 70
                                     +k+l+ +tv ++G+G +G+ va +l a g+ k+i++d    
  gi|119720725|ref|YP_921220.1| 22 EAQKKLKSSTVLVVGAGGLGSPVAFYLVAAGVgKLIIVDAEDV 64
                                   56789**************************989999987754 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.4
                                    EECSHHHHHHH-SEEEE-S--STTTTTSBSHHHHHC CS
                   2-Hacid_dh_C  81 elvsleellaesDivslhlpltpetrhlinaeelak 116
                                    +l++  +l++++D+v+ +l  + +tr l+n++  ++
  gi|119720725|ref|YP_921220.1| 110 SLEDALKLVEDADVVVDCL-DNWSTRFLLNEACVKL 144
                                    4456667888999886554.5888888888877665 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   2.6    0.0011       1.4       2      30 ..      32      63 ..      31      75 .. 0.90
   2 !    6.6   0.0    0.0038       4.9     179     233 ..     108     169 ..      87     194 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0011
                                   EEEECTSHHHHHHHHHHHHTT...EEEEESSS CS
                            DAO  2 vviiGGGiiGlstAyeLarrg...Vtllekgd 30
                                   v+++G+G  G+ +A++L ++g    ++++++d
  gi|119720725|ref|YP_921220.1| 32 VLVVGAGGLGSPVAFYLVAAGvgkLIIVDAED 63
                                   99***************999888999999983 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0038
                                    EEEEEEECT.EEEEEEEEEEE--GGGHH.HH.HTT.CTT.....TSEEEEEEEEEEEEEECCTH CS
                            DAO 179 vwgverttp.gendaadavVnaaGawsd.ll.gll.kel.....dlpispvrgqvlvlkplsek 233
                                    +  +e   +   ++ ad vV +   ws+ +l + +  +l     +  ++++ gq  v+kp + +
  gi|119720725|ref|YP_921220.1| 108 IRSLE--DAlKLVEDADVVVDCLDNWSTrFLlNEAcVKLgkplvHGAVRGLYGQLTVVKPFEGP 169
                                    33332..11122222699**********955555555554444556778899999***887654 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1   1.3e-05     0.017       1      84 [.      31     119 ..      31     128 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.3e-05
                                    EEEEE--SCCHHHHHHHHHHTT-.EEEEE-S-HHHHHHHHHHHHH...HH.HCCTTTTSS-HHHHCCCHHCEEEES-HHH CS
                        3HCDH_N   1 kvaviGaGtmGagiaavfasagl.eVvlvdiseealekalekiek...sl.eklvekgklkeeeveaalarisfttdlee 75 
                                    +v v+GaG +G+ +a  +++ag+ +  +vd ++  l + +++i +    l +  ve+ k k e+ + +++ ++ ++++++
  gi|119720725|ref|YP_921220.1|  31 TVLVVGAGGLGSPVAFYLVAAGVgKLIIVDAEDVELSNLNRQILHwtsDLgKAKVESAKEKLEKLNPHVEVVTLKQKIRS 110
                                    588******************98567888888888777777776533333122333333344566666666666666666 PP

                                    HHC-SEEEE CS
                        3HCDH_N  76 avdadlviE 84 
                                    + da   +E
  gi|119720725|ref|YP_921220.1| 111 LEDALKLVE 119
                                    665544444 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.1   2.1e-05     0.026       4      86 ..      26     145 ..      25     151 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.1e-05
                  NAD_binding_7   4 dlkgkkvlvvGgGevAarkvrklleag.akvtvvapevkeele............................elvklaeee 54 
                                    +lk  +vlvvG+G ++   +  l++ag  k+++v+ e     e                            +        
  gi|119720725|ref|YP_921220.1|  26 KLKSSTVLVVGAGGLGSPVAFYLVAAGvGKLIIVDAEDV---ElsnlnrqilhwtsdlgkakvesakekleK-------- 94 
                                    57899**********************768888877743...333477766667776665333333333330........ PP

                  NAD_binding_7  55 lekd......................legadlviaatddrelneriaeaakarr 86 
                                                              +e+ad+v+ + d+ + +  + ea+ + +
  gi|119720725|ref|YP_921220.1|  95 ---LnphvevvtlkqkirsledalklVEDADVVVDCLDNWSTRFLLNEACVKLG 145
                                    ...2444444444444555555677799999***99999887777777775555 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   2.9e-05     0.037     137     214 ..      24     100 ..      13     128 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.9e-05
                                    CCSS-TSEEEEES-SHHHHHHHHHHHHHT-.EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 137 klkllpkrivvvGgGyiGvElAaalaklgk.evtlveardrllraldkelsaaleealekeGvevklgtsvkeidgnge 214
                                    ++kl+   ++vvG+G  G+ +A +l  +g+ +  +v+a d  l++l++++  +    l k +ve   +++ ++++++ e
  gi|119720725|ref|YP_921220.1|  24 QKKLKSSTVLVVGAGGLGSPVAFYLVAAGVgKLIIVDAEDVELSNLNRQILHWT-SDLGKAKVESA-KEKLEKLNPHVE 100
                                    566777999***************999999437777777777777777776663.33444455555.555555555544 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   5.6e-05     0.071       2      47 ..      31      77 ..      30     124 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.6e-05
                                   EEEEE--STTHHHHHHHHHHCT.SEEEEE-S-HHHHHHHCTTS-SS- CS
                 UDPG_MGDP_dh_N  2 kisviGlGYvGlvtaavlaeig.hevigvDideekvdklnsgkipiy 47
                                   ++ v+G+G +G + a  l ++g  ++i+vD ++   ++ln++ ++ +
  gi|119720725|ref|YP_921220.1| 31 TVLVVGAGGLGSPVAFYLVAAGvGKLIIVDAEDVELSNLNRQILHWT 77
                                   688**************99999779***************9988754 PP

>> Ldh_1_N  lactate/malate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.1   0.00012      0.16       3      42 ..      32      69 ..      30     126 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00012
                                   EEEETTTSHHHHHHHHHHHHTTSSSEEEEE-SSHHHHHHH CS
                        Ldh_1_N  3 vavvGaaGgiGqslalllankkladelaLlDiakekleGv 42
                                   v vvGa Gg G+++a+ l++ ++++ l ++D+++ +l+  
  gi|119720725|ref|YP_921220.1| 32 VLVVGA-GGLGSPVAFYLVAAGVGK-LIIVDAEDVELSNL 69
                                   89****.******************.99999987666554 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   0.00014      0.18       3      30 ..      31      58 ..      29      77 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00014
                                   EEEEE--SHHHHHHHHHHHHTTHHEEEE CS
                  FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlv 30
                                   +Vl+VGaG  G   a  L  aGv  +++
  gi|119720725|ref|YP_921220.1| 31 TVLVVGAGGLGSPVAFYLVAAGVGKLII 58
                                   7**********************96655 PP

>> DUF3090  Protein of unknown function (DUF3090)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0049       6.2       6      61 ..      30      85 ..      26     125 .. 0.80
   2 ?    3.2   0.2     0.052        66     146     163 ..     227     245 ..     222     250 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0049
                        DUF3090  6 pdrfvagtvGepGeRtFyLqaregervvsvalekeqvaaLaerieelLdelarreg 61
                                    + +v+g+ G     +FyL a+  ++++ v  e  +++ L ++i +  ++l +++ 
  gi|119720725|ref|YP_921220.1| 30 STVLVVGAGGLGSPVAFYLVAAGVGKLIIVDAEDVELSNLNRQILHWTSDLGKAKV 85
                                   5678888888888889***************************9999888888764 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.052
                        DUF3090 146 arevvaa.GrpsCplCgqP 163
                                    + +vv+   rp Cp+Cg  
  gi|119720725|ref|YP_921220.1| 227 TFDVVKVeRRPDCPVCGVS 245
                                    55677763689*****975 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.3     0.002       2.5       2      46 ..      32      77 ..      31      86 .. 0.82
   2 ?    1.2   0.0      0.45   5.7e+02      17      39 ..      91     113 ..      81     120 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.002
                                   EEEECSSHHHHHHHHHHHHTTS.EEEEEESSSSSSTTSSHHHHHHH CS
                      Pyr_redox  2 vvvvGgGyiglElAgalaelgk.kVtvversdkllrllDeeaskil 46
                                   v+vvG+G +g  +A +l + g  k  +v+++d  l++l++++  ++
  gi|119720725|ref|YP_921220.1| 32 VLVVGAGGLGSPVAFYLVAAGVgKLIIVDAEDVELSNLNRQILHWT 77
                                   89***************99996377888887777788888876665 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.45
                                    HHHHTTSEEEEEESSSSSSTTSS CS
                      Pyr_redox  17 alaelgkkVtvversdkllrllD 39 
                                     l +l+ +V vv  + k+++l+D
  gi|119720725|ref|YP_921220.1|  91 KLEKLNPHVEVVTLKQKIRSLED 113
                                    47889999999999999997666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       939  (0.0523733); expected 358.6 (0.02)
Passed bias filter:                      868  (0.0484132); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.51
# Mc/sec: 1516.40
//
Query:       gi|119720726|ref|YP_921221.1|  [L=396]
Description: major facilitator transporter [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.1e-27   94.5  63.6    1.4e-24   86.7  39.0    2.0  2  MFS_1           Major Facilitator Superfamily
  ------ inclusion threshold ------
       0.21   11.1   1.1       0.51    9.9   1.1    1.6  1  APA3_viroporin  Coronavirus accessory protein 3a
        2.4    7.5   8.0        1.6    8.0   4.0    2.3  2  TssN            Type VI secretion system, TssN


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.7  39.0   2.3e-28   1.4e-24       2     350 ..      13     358 ..      12     359 .. 0.79
   2 !   21.5  16.5   1.6e-08   9.5e-05      33     167 ..     251     387 ..     234     393 .. 0.84

  Alignments for each domain:
  == domain 1  score: 86.7 bits;  conditional E-value: 2.3e-28
                          MFS_1   2 llaaflsalarsilgpalpl..alaedlgispse.igllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglll 78 
                                    ++a+fl++  r+++g++  +   +a+++g+ p++  ++++++y+ ++a+++lp+G l+d +G++r++ +++ll++lg++l
  gi|119720726|ref|YP_921221.1|  13 YVAYFLVYVHRTMTGVVQEElgGIASAHGLPPAAfTSIVAAAYFYTYAAMQLPAGILADALGAKRYVGTSMLLLGLGSAL 92 
                                    678899999999988888655677888888888846668888***********************************555 PP

                          MFS_1  79 llfasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailg.pllggllasslgWravfyi 156
                                    ++  +  + l+lv+r++ G+ga++++ + + +i  ++ k+  +  +gl+ a  +lGa+++ ++l  ++  ++g ravf+ 
  gi|119720726|ref|YP_921221.1|  93 AS--TCDPtLILVGRLVIGVGAASVWVSLQRVIGVYAEKNVGATLTGLALAVGNLGALFAtAPLREAVD-AVGLRAVFLY 169
                                    55..557779*****************************8888888***********999677777666.********** PP

                          MFS_1 157 laivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsg.........ll 227
                                    la++++++ v   ++l  ++p  +r s k+         l++ +k + ++++     ial+l+f+g+++         ++
  gi|119720726|ref|YP_921221.1| 170 LAVAAFILSVA--AFLGINDPGISRGSLKRG----LAETLRQ-LKVVARSRHS----IALALAFAGTYSavlafqslwAS 238
                                    ********887..999999999999999999....8999999.9999999954....22222222333323323223333 PP

                          MFS_1 228 tllplylqevlgls..glllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllll 305
                                    +++  y+      +     ++ lll llal+++++ +l+g++sd +  ++r  + l++++l +l+++ l v+s  +l+l+
  gi|119720726|ref|YP_921221.1| 239 IYVSRYF------PeyR-RETPLLLLLLALAFLVSVPLVGYVSDAVL-KKRKPVLLAGIVLHFLAWVGLLVASRLSLGLA 310
                                    3333343......3332.44555555555555555999*****9844.56888888888999999999999988888888 PP

                          MFS_1 306 ....vlvliGfglgfvfpsllalasdlappeeagtasglfntagslgga 350
                                        +++l+G+ +++    +  l  + ++pe +gt ++++n++g +++a
  gi|119720726|ref|YP_921221.1| 311 eleaIFLLLGVVAAT-HMVIPPLSREAYSPEFSGTTLAFVNMVGFVAIA 358
                                    999777778886664.78888888888899**************99987 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 1.6e-08
                          MFS_1  33 eigllltlyalgaavaslplGrlsdr.fGrrr.vlllglllfalglllllfa.sslwl....llvlrvlqGlgagalfpa 105
                                    e  lll l al+++v+++++G++sd  +  r+ vll+g++l +l+ +++l++ s l l    l +  +l G+  +a   +
  gi|119720726|ref|YP_921221.1| 251 ETPLLLLLLALAFLVSVPLVGYVSDAvLKKRKpVLLAGIVLHFLA-WVGLLVaSRLSLglaeLEAIFLLLGVV-AATHMV 328
                                    66789999*****************96677777************.888853244333334488889999999.799999 PP

                          MFS_1 106 gaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvl 167
                                    +  l ++ +++e  g  ++++++   +++++   +g+++      + + +++a+vsl a++l
  gi|119720726|ref|YP_921221.1| 329 IPPLSREAYSPEFSGTTLAFVNMVGFVAIAVYQSIGAVVG---DPSIPLVVFALVSLAALLL 387
                                    99**************************************...7778888999999998775 PP

>> APA3_viroporin  Coronavirus accessory protein 3a
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   1.1   8.5e-05      0.51      42     116 ..     102     178 ..      90     186 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 8.5e-05
                 APA3_viroporin  42 pfgwlvigvaflavfqsatkiialnkrwql.alykgfqf.icnllllfvtiyshlllvaagmeaqflylyaliyflq 116
                                     +g lvigv   +v+ s  ++i +    ++ a   g+ + + nl  lf t   +  + a g+ a flyl    ++l 
  gi|119720726|ref|YP_921221.1| 102 LVGRLVIGVGAASVWVSLQRVIGVYAEKNVgATLTGLALaVGNLGALFATAPLREAVDAVGLRAVFLYLAVAAFILS 178
                                    5799******************986554442677888763789*************************977666654 PP

>> TssN  Type VI secretion system, TssN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1     0.064   3.9e+02      22      52 ..     155     185 ..     134     191 .. 0.80
   2 ?    8.0   4.0   0.00027       1.6       4     120 ..     255     369 ..     253     394 .. 0.69

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.064
                           TssN  22 akknkllkkkkliiyiLlaglvlalpgllgf 52 
                                    ++   ++  + +++y+ +a+++l++ ++lg+
  gi|119720726|ref|YP_921221.1| 155 REAVDAVGLRAVFLYLAVAAFILSVAAFLGI 185
                                    5556677788999***************996 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00027
                           TssN   4 ylllpllavilllilsliakknkllkkkkliiyiLlaglvlalpgllgflknefvpygyillqilylllGilhlylllkk 83 
                                    +lll++la+++++ l+   ++  l+k+k     +Llag+vl  ++ +g+l  +    g+  l+ ++lllG++ ++ ++  
  gi|119720726|ref|YP_921221.1| 255 LLLLLALAFLVSVPLVGYVSDAVLKKRKP----VLLAGIVLHFLAWVGLLVASRLSLGLAELEAIFLLLGVVAATHMVIP 330
                                    57888888888888888888666555554....6899************999999****************999866543 PP

                           TssN  84 .ffkelkekk.ilfeilltlivillglvlfvlvfnllse 120
                                     + +e  + +  + ++ ++ +v++++++++  +  ++ +
  gi|119720726|ref|YP_921221.1| 331 pLSREAYSPEfSGTTLAFVNMVGFVAIAVYQSIGAVVGD 369
                                    144444444433344444555666666677666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       744  (0.041497); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 2525.07
//
Query:       gi|119720727|ref|YP_921222.1|  [L=469]
Description: dihydrolipoamide dehydrogenase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.8e-48  163.2   0.1    9.9e-47  159.6   0.0    2.0  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    1.8e-24   86.1   0.3    3.1e-24   85.4   0.3    1.4  1  Pyr_redox_dim   Pyridine nucleotide-disulphide oxidoreductase
    3.2e-13   50.0   0.1      1e-12   48.4   0.1    1.9  1  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    5.4e-09   35.7   0.1    2.2e-08   33.7   0.0    2.0  3  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
     0.0027   17.0   1.8      0.022   14.0   0.2    2.1  2  FAD_binding_3   FAD binding domain
     0.0036   17.0   0.2       0.18   11.4   0.0    2.3  2  DAO             FAD dependent oxidoreductase
     0.0088   15.2   1.7       0.91    8.5   0.0    2.6  3  FAD_binding_2   FAD binding domain
  ------ inclusion threshold ------
      0.017   14.2   0.2        2.9    6.9   0.1    2.6  3  GIDA            Glucose inhibited division protein A
      0.023   14.9   0.1      0.068   13.4   0.1    1.8  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
      0.034   14.0   0.0      0.078   12.9   0.0    1.6  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
       0.04   13.5   0.0      0.075   12.6   0.0    1.5  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
      0.077   12.3   0.0        0.2   10.9   0.0    1.7  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.6   0.0   6.6e-50   9.9e-47       1     290 [.       5     321 ..       5     327 .. 0.88
   2 ?    1.6   0.0     0.086   1.3e+02     189     243 ..     329     384 ..     324     391 .. 0.81

  Alignments for each domain:
  == domain 1  score: 159.6 bits;  conditional E-value: 6.6e-50
                                    CSEEEE--SHHHHHHHHHHHH..HTS-EEEEE...TTHCHHHCSHHHHCHHHHHHHHHHHHH.................. CS
                                    xxxxxxxxxxxxxxxxxxxxx..xxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx.................. RF
                    Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaq..agakvtlve...legtclnggcllskallgvaedaeias.................. 57 
                                    +dv+v G G A ++   +l +  + ++ +++e    +g cl++gc++sk ll+va++ + ++                  
  gi|119720727|ref|YP_921222.1|   5 YDVIVFGTGSA-MNIVSELINegKRLRFAVIEnnmVGGICLTRGCIPSKMLLEVARNIRRIKeaekfgiqvslagvdftg 83 
                                    68999999998.55555555548899999999999***********************99999***************** PP

                                    ..........HHHHCHHHHCCCCHCCT.CEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEEC CS
                                    ..........xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2  58 ..........evvkklnqgielllgee.vvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgkl 126
                                                    +++ie  l+++  +++++  ++++   +++  +++i+ d+++l+tGs+p+  + pGv e+v   
  gi|119720727|ref|YP_921222.1|  84 vmervwrriyA----ESKEIEHSLKHHpLIDLYQVDGTFVGDYTVDVGGREIEGDTILLCTGSRPHVVKAPGV-EEV--- 155
                                    ***99955442....55678888887779***9999*************************************.444... PP

                                    CSECHHHHHHCC.SS-TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCE CS
                                    xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 127 vrtldsaealkl.kllpkrivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgts 205
                                     +++++++ +++  +lp+r+vv+GgG++G+El  +la +g++vt++++r+r+l++ ++e+s+ l++ l +   ++++ ++
  gi|119720727|ref|YP_921222.1| 156 -KYYTNDNFFRElRKLPRRTVVIGGGFVGLELGFFLAMMGSQVTVLQRRERILPEEEPEISELLARDLSR-YMDIRTLHE 233
                                    .7788988887526777***************************************************99.5999999** PP

                                    EEEEEETTE....EEE.EEETTSCEEEESEEEE-S-EEES-HHCS.HCCT-EEEETTEEE--TTSBESSTTEEE-GGGCT CS
                                    xxxxxxxxx....xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 206 vkeidgnge....kle.vvledgeeidadlvvvavGvrpstelle.eklglelderggivvdeflrtnvpgiyaiGDvag 279
                                    v+e+++ ge     +e   ++d+ e++ad +++a+G++  +++   ek g+++de+g+i+vde+lrt+ +g++a GD + 
  gi|119720727|ref|YP_921222.1| 234 VVEFRRSGErqivVAEnKATGDNVEFEADAILMAAGRESYSDITRpEKTGVKTDEKGWILVDEYLRTTKDGVWAFGDAT- 312
                                    ********97553333566666666******************99********************************99. PP

                                    ECCSS--HHHH CS
                                    xxxxxxxxxxx RF
                    Pyr_redox_2 280 gkggpelaqaA 290
                                      g+++  ++A
  gi|119720727|ref|YP_921222.1| 313 --GKMMFKHKA 321
                                    ..777777766 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.086
                                    HHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCE.EEESEEEE-S-EEES-HH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx RF
                    Pyr_redox_2 189 leealekeGvevklgtsvkeidgngeklevvledgee.idadlvvvavGvrpstel 243
                                    +++a++ e+v+ + +++++++  ++e ++v l+++e   ++d +v  +G++   ++
  gi|119720727|ref|YP_921222.1| 329 YRNAFRGENVKARYHAVPHAVFTEPEVASVGLKEEEAaKKYDILVGIAGYEETAKG 384
                                    6789999******************955555555555589****999999877655 PP

>> Pyr_redox_dim  Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.4   0.3   2.1e-27   3.1e-24       1     109 [.     345     453 ..     345     454 .. 0.94

  Alignments for each domain:
  == domain 1  score: 85.4 bits;  conditional E-value: 2.1e-27
                                    BEEEEESSSEEEEEES-HHHHHHHHSGEEEEEEEEECGHHHCHTTHTEEEEEEEEETTTTBEEEEEEECTTHHHHHHHHH CS
                  Pyr_redox_dim   1 iptvvftdpevasvGlteeeAkaagieikvgkfpfkangralayaetkgfvKlvadaktgkvlGahivGpgageliqela 80 
                                    +p +vft+pevasvGl eeeA +++ +i vg + ++++++  a+   + fvK++ d++t ++lGahi+Gp+a+ liqe+ 
  gi|119720727|ref|YP_921222.1| 345 VPHAVFTEPEVASVGLKEEEAAKKY-DILVGIAGYEETAKGEAMMLHDYFVKVILDRDTFRILGAHIIGPEASILIQEIV 423
                                    799**********************.******************99********************************98 PP

                                    HHHHTT.SBHHHHHTSBSSSSSTGGGGHCH CS
                  Pyr_redox_dim  81 vaikag.ltvedladtihihPtlsealkea 109
                                     ++ ag  t+e + + +hihP lse+++ a
  gi|119720727|ref|YP_921222.1| 424 NLMYAGdGTAEPIYEGMHIHPALSEVVERA 453
                                    877776268889************998765 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.4   0.1   6.7e-16     1e-12       1      72 [.     173     243 ..     173     252 .. 0.91

  Alignments for each domain:
  == domain 1  score: 48.4 bits;  conditional E-value: 6.7e-16
                                    EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTS CS
                      Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedg 72 
                                    + vv+GgG++glEl+ +la +g++Vtv++r++++l+ +++e+s++l++ l++  +++++ ++v+e++ s++ 
  gi|119720727|ref|YP_921222.1| 173 RTVVIGGGFVGLELGFFLAMMGSQVTVLQRRERILPEEEPEISELLARDLSRY-MDIRTLHEVVEFRRSGER 243
                                    579************************************************99.***********9988874 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.5   2.3e+03     168     192 ..       7      31 ..       3      37 .. 0.79
   2 !   33.7   0.0   1.5e-11   2.2e-08     112     298 ..     120     302 ..      99     309 .. 0.76
   3 ?   -2.4   0.0       1.5   2.2e+03     225     270 ..     336     381 ..     327     387 .. 0.66

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.5
                    Pyr_redox_3 168 vViGgknSavDaAlelvrkgaeVtv 192
                                    v++ g  Sa+ +  el+++g++ + 
  gi|119720727|ref|YP_921222.1|   7 VIVFGTGSAMNIVSELINEGKRLRF 31 
                                    4566678************999775 PP

  == domain 2  score: 33.7 bits;  conditional E-value: 1.5e-11
                    Pyr_redox_3 112 egfevetsketyeAkkviiAtGefdkPnklnipGeeklvkhyskvkefhkya..gqkvvViGgknSavDaAlelvrkgae 189
                                    + ++v+   +++e +++++ tG   +P++ + pG e  vk y +++ f++++   ++ vViGg+  + +  + l+ +g++
  gi|119720727|ref|YP_921222.1| 120 GDYTVDVGGREIEGDTILLCTGS--RPHVVKAPGVE-EVKYYTNDNFFRELRklPRRTVVIGGGFVGLELGFFLAMMGSQ 196
                                    5689999999************9..**********9.78888888888888844589*********************** PP

                    Pyr_redox_3 190 Vtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfnaevkeikekee...eykvktedgkkvevkddvvla.t 265
                                    Vtv+ r++ i  ee   + +++      l ++     +++ + +ev e +++ e    +  ++++g++ve + d +l+  
  gi|119720727|ref|YP_921222.1| 197 VTVLQRRERILPEE---EPEISELLARDLSRY-----MDIRTLHEVVEFRRSGErqiVVAENKATGDNVEFEADAILMaA 268
                                    *******9888875...333455555555554.....4555555555555544400044445778899999999999945 PP

                    Pyr_redox_3 266 Gykpdlsflkk...slfeldedgrpvlteeteetnv 298
                                    G ++ +s +++    ++++de+g+++++e    t  
  gi|119720727|ref|YP_921222.1| 269 GRES-YSDITRpekTGVKTDEKGWILVDEYLRTT-K 302
                                    6555.555544477999********999865544.4 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.5
                    Pyr_redox_3 225 ekikvlfnaevkeikekeeeykvktedgkkvevkddvvlatGykpd 270
                                    e++k+ ++a  +++ ++ e   v  ++++  +++d  v + Gy+ +
  gi|119720727|ref|YP_921222.1| 336 ENVKARYHAVPHAVFTEPEVASVGLKEEEAAKKYDILVGIAGYEET 381
                                    4566666666666666666677777777777777777777777765 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.2   1.5e-05     0.022       4      36 ..     174     206 ..     172     216 .. 0.91
   2 ?    2.5   0.1     0.048        72     111     182 ..     218     287 ..     210     356 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.5e-05
                                    EEEE--SHHHHHHHHHHHHTTHHEEEEESSSSS CS
                  FAD_binding_3   4 VlIVGaGpaGlmlallLseaGvrvvlvekrstt 36 
                                    ++++G+G +Gl l+ +L++ G +v+++ +r++ 
  gi|119720727|ref|YP_921222.1| 174 TVVIGGGFVGLELGFFLAMMGSQVTVLQRRERI 206
                                    589**************************9875 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.048
                                    HHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEEEEEE--GTT-HHHHHHTGGEEEEEEE CS
                  FAD_binding_3 111 LvehaeerglqvrfktevesleqdeegvtaevrdketgeeetvrakYlvGaDGgrStvrktlgiefegeetv 182
                                    L+ +  +r++++r  +ev+ +++ +e    ++ +k+tg + +++a+ +  a G  S +  t + + +g +t+
  gi|119720727|ref|YP_921222.1| 218 LARD-LSRYMDIRTLHEVVEFRRSGERQIVVAENKATGDNVEFEADAILMAAGRESYSDITRPEK-TGVKTD 287
                                    4444.67889*****************99999*****************9999999877766644.444444 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   0.00012      0.18       2      30 ..     174     204 ..     173     209 .. 0.91
   2 ?    3.3   0.0     0.035        52     161     203 ..     226     271 ..     214     306 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00012
                                    EEEECTSHHHHHHHHHHHHTT..EEEEESSS CS
                            DAO   2 vviiGGGiiGlstAyeLarrg..Vtllekgd 30 
                                     v+iGGG +Gl   ++La  g  Vt+l +++
  gi|119720727|ref|YP_921222.1| 174 TVVIGGGFVGLELGFFLAMMGsqVTVLQRRE 204
                                    69***************99899*****9985 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.035
                                    -EEEESECEEEEEEEETCEEEEE..EECT.EEE..EEEEEEEE--GGG CS
                            DAO 161 veilegtevtgleeedgkvwgve..rttp.gen..daadavVnaaGaw 203
                                     +i++ +ev+++++ +++   v   +  + g n  ++ada+ +aaG  
  gi|119720727|ref|YP_921222.1| 226 MDIRTLHEVVEFRRSGERQIVVAenK--AtGDNveFEADAILMAAGRE 271
                                    6888889*****88766644454533..336554348899*****954 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5   0.1    0.0051       7.7       3      31 ..     175     203 ..     173     207 .. 0.91
   2 !    8.5   0.0   0.00061      0.91     142     200 ..     216     269 ..     202     287 .. 0.84
   3 ?   -2.6   0.0       1.5   2.2e+03     374     405 ..     282     315 ..     279     319 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0051
                                    EEE--SHHHHHHHHHHHHTTT-EEEEESS CS
                  FAD_binding_2   3 iViGsGlAGLaAAleaaeaGlkvavveke 31 
                                    +ViG+G+ GL  +  +a  G +v+v+   
  gi|119720727|ref|YP_921222.1| 175 VVIGGGFVGLELGFFLAMMGSQVTVLQRR 203
                                    9************************9875 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00061
                                    HHHHHHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE--- CS
                  FAD_binding_2 142 allarlvesarkagvdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatg 200
                                    +llar + ++    +d+++ +e++e+ +++g+   +v+en+++g +v+++a+a+++a+g
  gi|119720727|ref|YP_921222.1| 216 ELLARDLSRY----MDIRTLHEVVEF-RRSGERQIVVAENKATGDNVEFEADAILMAAG 269
                                    4555555555....9***********.66999999**********************98 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1.5
                                    -EEEBETTSBE..STTEEESSBTEEE-STCEESS CS
                  FAD_binding_2 374 gGvetdengrv..ldadgqpipGLYAaGevaagg 405
                                     Gv+tde+g    ++   ++ +G +A G +++ +
  gi|119720727|ref|YP_921222.1| 282 TGVKTDEKGWIlvDEYLRTTKDGVWAFGDATGKM 315
                                    6899999887754666677999999999998544 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.012        17      64     155 ..      64     143 ..      37     173 .. 0.79
   2 ?    6.9   0.1    0.0019       2.9       3      28 ..     175     200 ..     173     217 .. 0.88
   3 ?   -1.7   0.0       0.8   1.2e+03     133     209 ..     253     327 ..     211     348 .. 0.69

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.012
                                    HHHHHHHEEEEEEESTTS-CCC-EEEEEE-HHHH..HHHHHHHHHTSTTEEEEES-EEEEEECTTEEEEEEETTS-EEEE CS
                           GIDA  64 ikaadkagiqfrilNrskGpavralraqvdrely..skevteklenepnleiieeeveeliveekkvkgvvtedgetika 141
                                    ik a+k giq+ +     G    + +  v r+ y  ske+++ l+++p +++ +   + + +        v   g++i+ 
  gi|119720727|ref|YP_921222.1|  64 IKEAEKFGIQVSLA----GVDFTGVMERVWRRIYaeSKEIEHSLKHHPLIDLYQVDGTFVGD------YTVDVGGREIEG 133
                                    56677778877775....777777777888888844689******************99988......67788999**** PP

                                    CEEEE--TT-BT-E CS
                           GIDA 142 kavviatGtflkgk 155
                                    +++ + tG+    +
  gi|119720727|ref|YP_921222.1| 134 DTILLCTGS----R 143
                                    ********9....3 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0019
                                    EEE-SSHHHHHHHHHHHHTT--EEEE CS
                           GIDA   3 iViGgGhAGceAAlaaarlGakvlLi 28 
                                    +ViGgG  G+e  + +a +G +v+ +
  gi|119720727|ref|YP_921222.1| 175 VVIGGGFVGLELGFFLAMMGSQVTVL 200
                                    8**********************987 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.8
                                    ETTS-EEEECEEEE--TT-BT-EEEETTEEEESSCTTC--B-THHHHHHHTT--EEEEEEEE--EEEGGGS-TTTSE CS
                           GIDA 133 tedgetikakavviatGtflkgkihigekelsaGrlgeltseglseslkelgfellrlktgtppridkesidfskle 209
                                    t d+ +++a+a+ +a+G   ++ + i + e    +++e+    + e l+ +++ + ++ ++t  ++ k+  ++++++
  gi|119720727|ref|YP_921222.1| 253 TGDNVEFEADAILMAAGR--ESYSDITRPEKTGVKTDEKGWILVDEYLRTTKDGVWAFGDATGKMMFKHKANYESVI 327
                                    446677788888888888..666666666666666666666777777777888888888888777766666666655 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   4.5e-05     0.068       1      31 [.     176     206 ..     176     206 .. 0.97

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.5e-05
                                    EE--SHHHHHHHHHHHCCTEEEEEE-SSSSS CS
                  NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrl 31 
                                    ++G+G+ Gl +  +La  g +v++l++r+r+
  gi|119720727|ref|YP_921222.1| 176 VIGGGFVGLELGFFLAMMGSQVTVLQRRERI 206
                                    8***************************986 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   5.2e-05     0.078       3      50 ..     175     222 ..     173     248 .. 0.90
   2 ?   -3.4   0.0       5.2   7.8e+03     130     153 ..     403     426 ..     400     438 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.2e-05
                                    EEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCT CS
                        3HCDH_N   3 aviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklv 50 
                                     viG G +G ++   +a  g +V++++++e++l + + +i++ l++  
  gi|119720727|ref|YP_921222.1| 175 VVIGGGFVGLELGFFLAMMGSQVTVLQRRERILPEEEPEISELLARDL 222
                                    59***********************************99999888765 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 5.2
                                    GGEEEEEE-SSTTT--EEEEEE-T CS
                        3HCDH_N 130 erviglHFfnPpplmkLvEvvrge 153
                                     r++g+H + P   + + E+v+  
  gi|119720727|ref|YP_921222.1| 403 FRILGAHIIGPEASILIQEIVNLM 426
                                    588999999999998888888755 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0     5e-05     0.075       3      56 ..     174     227 ..     172     249 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5e-05
                                    EEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS--TTHHHHHH CS
                 UDPG_MGDP_dh_N   3 isviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipiyepgLeelvk 56 
                                     +viG G+vGl  +  la +g +v+++   e+   + + + +++  ++L++++ 
  gi|119720727|ref|YP_921222.1| 174 TVVIGGGFVGLELGFFLAMMGSQVTVLQRRERILPEEEPEISELLARDLSRYMD 227
                                    689**********************98777666666666666666666666655 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00013       0.2      29      64 ..     172     207 ..     168     236 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00013
                                    -EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHH CS
                    AlaDh_PNT_C  29 akvlviGgGvaGlqAiatakglgakVtvlDvrparl 64 
                                     +++viGgG +Gl+     + +g +Vtvl  r++ l
  gi|119720727|ref|YP_921222.1| 172 RRTVVIGGGFVGLELGFFLAMMGSQVTVLQRRERIL 207
                                    689**************************9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (469 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 2908.71
//
Query:       gi|119720728|ref|YP_921223.1|  [L=307]
Description: signal peptide peptidase SppA, 36K type [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-32  112.6   0.0    2.1e-32  112.2   0.0    1.1  1  Peptidase_S49  Peptidase family S49
    4.6e-05   23.4   0.0     0.0033   17.3   0.0    2.2  2  CLP_protease   Clp protease
  ------ inclusion threshold ------
      0.015   14.4   0.0      0.018   14.0   0.0    1.2  1  SDH_sah        Serine dehydrogenase proteinase
      0.067   12.5   0.1       0.58    9.4   0.0    2.3  3  ECH_1          Enoyl-CoA hydratase/isomerase
       0.21   11.6   1.7       0.59   10.1   1.7    1.7  1  DUF3377        Domain of unknown function (DUF3377)


Domain annotation for each model (and alignments):
>> Peptidase_S49  Peptidase family S49
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.2   0.0     6e-36   2.1e-32       3     153 ..     109     256 ..     107     257 .. 0.95

  Alignments for each domain:
  == domain 1  score: 112.2 bits;  conditional E-value: 6e-36
                                    HHTT--EEEEEEEEEETHHHHHHTTSSEEEE-TT-EEE---EEEEEEE-HHHHHHTT-EEEEEESSTTCCCCCTTSS--H CS
                  Peptidase_S49   3 kkakkPvvasaenvaaSggYylasaadkivanpstivgsiGvitqllnlenlldklgvevqvvkaGeyksavslrrelte 82 
                                    +++kk vv +a+++ aSg+Y++a  +  i+a+p++ vgs+Gvi   ln+ nll k+gv+v ++k+Ge+k+++s++r++te
  gi|119720728|ref|YP_921223.1| 109 LSQKKVVVSYAKGLLASGAYMAALPSRAILASPTSEVGSVGVIVTVLNVGNLLGKIGVTVYTFKSGELKDVGSPYRPMTE 188
                                    678999999*********************************************************************** PP

                                    HHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHCHHCCHEEEHHHHHHTTSSSEETSHHHHHHHHHHHCHC CS
                  Peptidase_S49  83 eereilqrlldetyqqFvqtVaknRnlsveqvdkiAegrvltgqqAlklgLvdelgtvddavaeleelakv 153
                                    e  + l+++++  +  F+  V ++R+   +   ++ +gr +t ++Al++gL+d++ t+++av+  + la++
  gi|119720728|ref|YP_921223.1| 189 EDAKVLEEMVNYYFGLFKGRVLEHRG---NVSSEVFSGRPFTPDKALQAGLIDKVCTYQEAVNYTRALANL 256
                                    *************************8...55567778**************************99998876 PP

>> CLP_protease  Clp protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   9.2e-07    0.0033      41      99 ..      77     129 ..      65     147 .. 0.69
   2 ?    3.9   0.0     0.012        45     158     180 ..     220     242 ..     187     244 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 9.2e-07
                                    HHH-SSS-EEEEEEE--B-HHHHHHHHHHHHHSSS-EEEEEE..EEEETHHHHHHHTS-TT CS
                   CLP_protease  41 eaedpdkdillyinspGGsvtaglaIydtmqyikpdvsticl..GlaaSmgslllaagekg 99 
                                    e+    k +ll+ +spGG vta+ ++y +++ ++ + +++    Gl aS +          
  gi|119720728|ref|YP_921223.1|  77 EEDPMAKAVLLVFDSPGGTVTASDELYQAVKELSQKKVVVSYakGLLASGAY--------M 129
                                    4445578999*********************997666433222266555443........3 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.012
                                    HCSTEEEEHHHHHHHTSSSEE-S CS
                   CLP_protease 158 ldrdtflsaeeAveyGLidevie 180
                                    +   + ++++ A++ GLid+v++
  gi|119720728|ref|YP_921223.1| 220 VFSGRPFTPDKALQAGLIDKVCT 242
                                    5555668999***********87 PP

>> SDH_sah  Serine dehydrogenase proteinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   5.1e-06     0.018      75     229 ..      66     229 ..       8     244 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.1e-06
                        SDH_sah  75 iedseevlrairltpkdkpidliihtpGGlvlaatqiakalkehkaktrvivphya....msGGtlialaadeiildena 150
                                    +e+  ++++     p  k + l+  +pGG v a++++ +a+ke   k  v v  ya     sG  + al +  i+  + +
  gi|119720728|ref|YP_921223.1|  66 VEEYIKLVKQAEEDPMAKAVLLVFDSPGGTVTASDELYQAVKELSQKKVV-VS-YAkgllASGAYMAALPSRAILASPTS 143
                                    56666677777777888999**********************98766544.43.33222258888999999999999999 PP

                        SDH_sah 151 vlGpvdpqlgqypaasil.....kvvekk..eakdiddktliladiakkaikqveefvyellkdkydeekakeiakklte 223
                                     +G v   ++ +    +l      v+  k  e kd+      +++   k +++++++ + l+k ++ e + + ++ ++ +
  gi|119720728|ref|YP_921223.1| 144 EVGSVGVIVTVLNVGNLLgkigvTVYTFKsgELKDVGSPYRPMTEEDAKVLEEMVNYYFGLFKGRVLEHRGN-VSSEVFS 222
                                    999987655544444333111114444331144566666667777777777777777777777777665554.4444444 PP

                        SDH_sah 224 Gr.wthd 229
                                    Gr +t d
  gi|119720728|ref|YP_921223.1| 223 GRpFTPD 229
                                    4325555 PP

>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.18   6.6e+02      26      46 ..      67      87 ..      64     123 .. 0.79
   2 ?   -1.2   0.0      0.29     1e+03      78     104 ..     100     127 ..      90     150 .. 0.63
   3 ?    9.4   0.0   0.00016      0.58     153     187 ..     220     254 ..     213     263 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.18
                                   HHHHHHHHHHHHSTTECEEEE CS
                          ECH_1 26 tEliqalekleddksvravvL 46
                                   +E i+  +++e+d+ ++av L
  gi|119720728|ref|YP_921223.1| 67 EEYIKLVKQAEEDPMAKAVLL 87
                                   677888888999999888877 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.29
                                    HHHHHHHHHS..SSEEEEEE-SEEETHHH CS
                          ECH_1  78 lelwtklytv..pkpviaavnGaaigGGl 104
                                    +el++++ ++  +k+v++  +G  + G +
  gi|119720728|ref|YP_921223.1| 100 DELYQAVKELsqKKVVVSYAKGLLASG-A 127
                                    455555543222678888888865444.3 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.00016
                                    HHHT-EEEHHHHHHCTSSSEEESGGGHHHHHHHHH CS
                          ECH_1 153 lllgkkisaqealkvGlvdkvvpeeqlleealela 187
                                    +  g++++++ al++Gl+dkv+  ++ ++++++la
  gi|119720728|ref|YP_921223.1| 220 VFSGRPFTPDKALQAGLIDKVCTYQEAVNYTRALA 254
                                    56799*******************99999998876 PP

>> DUF3377  Domain of unknown function (DUF3377)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   1.7   0.00016      0.59      34      62 ..      12      40 ..       6      44 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00016
                        DUF3377 34 vPlvLllciLvliyailqfrrkgtprrll 62
                                   +Pl+L++ +++l ++++ +r+  t+ rl+
  gi|119720728|ref|YP_921223.1| 12 LPLLLIVAVVILGAVLVLLRQGATQTRLT 40
                                   6************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       703  (0.0392102); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.32s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1860.15
//
Query:       gi|119720729|ref|YP_921224.1|  [L=480]
Description: cell wall biosynthesis glycosyltransferase-like protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-25   90.7   0.1    1.1e-25   90.7   0.1    2.1  2  Glyco_trans_2_3  Glycosyl transferase family group 2
    7.3e-13   48.9   0.0    1.8e-12   47.6   0.0    1.5  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    4.7e-06   26.2   0.0    7.5e-06   25.5   0.0    1.3  1  Glyco_transf_21  Glycosyl transferase family 21
    1.1e-05   25.4   0.0    1.7e-05   24.7   0.0    1.3  1  Glycos_transf_2  Glycosyl transferase family 2


Domain annotation for each model (and alignments):
>> Glyco_trans_2_3  Glycosyl transferase family group 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -6.7   5.0         4   1.8e+04     163     182 ..       5      24 ..       1      34 [. 0.34
   2 !   90.7   0.1   2.5e-29   1.1e-25       3     192 ..     137     317 ..     135     326 .. 0.92

  Alignments for each domain:
  == domain 1  score: -6.7 bits;  conditional E-value: 4
                Glyco_trans_2_3 163 lwsalplhlallllfsllal 182
                                    l+s ++l+l++++l  ll +
  gi|119720729|ref|YP_921224.1|   5 LASIIVLLLIAVPLLLLLLY 24 
                                    33333333322222222222 PP

  == domain 2  score: 90.7 bits;  conditional E-value: 2.5e-29
                Glyco_trans_2_3   3 lllDaDtvlppdclreiaaelaspevaivqgpvlvmnvanwleelaalffaedhgkdilvrealgrvvpsvGsgaflrrs 82 
                                    ++lDaD v++p + +++++   s + a+v    ++++ ++ l+e  ++f+++    +   r++ g  v+  Gsg++ +r+
  gi|119720729|ref|YP_921224.1| 137 MILDADAVVDPCVAEKLCRNTLS-DGALVVPWEGYYAYRTRLAEAVKFFTDLGTEVLYELRSRAGFYVFPLGSGTVYPRK 215
                                    79***************886665.46999999***9999***************************************** PP

                Glyco_trans_2_3  83 alqevggwdgdessvsEDfdmglrlqrkGyrvrfvpeslvkekspltlraalrQrkRwayGceleklillvrllgylgsl 162
                                    ++ +vggw   ++ v +D  mg++l+  Gyr+r+ ++s  k  +p+tl a+ +Q +Rw yG      +  v ++ +l+ l
  gi|119720729|ref|YP_921224.1| 216 VVLDVGGWG--DGIVQDDIWMGVKLALGGYRTRLLSGSRLKVLVPSTLGAFKKQQRRWSYG------TSDVLRRSFLRVL 287
                                    *********..9*************************************************......8899999999999 PP

                Glyco_trans_2_3 163 lwsalplhlallllfsllalalvlllllll 192
                                     + +lplh++l +l++++  al++ ++l +
  gi|119720729|ref|YP_921224.1| 288 KHGGLPLHVRLEMLAYMSLPALTIPPALAV 317
                                    9999***************98886443333 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.6   0.0   4.1e-16   1.8e-12      48     230 .]      97     274 ..      84     274 .. 0.78

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 4.1e-16
                Glyco_tranf_2_3  48 vaeelaaalpdvrvrvvvnarnlgstgksralnealravksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfll 127
                                     +  l+ + p+v v+  +++r++   g+  al + +   +s ++ ++D+D+vv+P++ ++l++  l++++ +v    +  
  gi|119720729|ref|YP_921224.1|  97 ALSRLVSDAPGVAVWR-RRERRG---GRTGALDDYFASSSSSHLMILDADAVVDPCVAEKLCRNTLSDGALVVPWEGYYA 172
                                    4555555666665552.344545...5555566999999***********************999899777777666666 PP

                Glyco_tranf_2_3 128 nrstlvsalgalefaerhlrflaarralgv.ltlnGsgslirrevlkelegldplflltdDyelglrlrragfrtayvpg 206
                                    +r++l  a+   +++        +r + g+ +++ Gsg++++r+v+ + +g++  +++ dD+ +g+ l   g+rt  + g
  gi|119720729|ref|YP_921224.1| 173 YRTRLAEAVKF-FTDLGTEVLYELRSRAGFyVFPLGSGTVYPRKVVLDVGGWGD-GIVQDDIWMGVKLALGGYRTRLLSG 250
                                    67776664443.32332223334555666668899*******************.************************* PP

                Glyco_tranf_2_3 207 aavrevfpsslkayikqrnRwvyg 230
                                    +    + ps+l a+ kq +Rw+yg
  gi|119720729|ref|YP_921224.1| 251 SRLKVLVPSTLGAFKKQQRRWSYG 274
                                    **********************97 PP

>> Glyco_transf_21  Glycosyl transferase family 21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   1.7e-09   7.5e-06      27     172 ..     129     272 ..     109     273 .. 0.90

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 1.7e-09
                Glyco_transf_21  27 eaakydllvisDsdvrvkpdyLeellaaledpkvglVtslpvgsdakglaaaleaaflntlagvlqa...klsglgfavG 103
                                    ++   ++l+i+D+d++v+p   e+l+++  + + +lV+    +++ ++  a+ ++ f   +  vl+    +++   f +G
  gi|119720729|ref|YP_921224.1| 129 ASSSSSHLMILDADAVVDPCVAEKLCRNTLS-DGALVVPWEGYYAYRTRLAEAVKFFTDLGTEVLYElrsRAGFYVFPLG 207
                                    5577899***********************7.9************************988888888865334445899** PP

                Glyco_transf_21 104 ksmalrreaLeaiGGfealadeLAeDyalgkllraaGlkvvlspapiaqtsvprrsslrallaRqlrWa 172
                                    +  ++ r+++ ++GG       + +D  +g  l+  G++++l +   +++ vp+  +l a+ ++q rW+
  gi|119720729|ref|YP_921224.1| 208 SGTVYPRKVVLDVGGWGD--GIVQDDIWMGVKLALGGYRTRLLSGSRLKVLVPS--TLGAFKKQQRRWS 272
                                    ***************998..7788*********************999999995..9***********7 PP

>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   3.7e-09   1.7e-05       2     113 ..      52     165 ..      51     219 .. 0.74

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 3.7e-09
                                    EEEEESS-TTTHHHHHHHHHHH......GGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-.HHHHHHHHH CS
                Glycos_transf_2   2 vviptyNeektlletlesllaq......dpypdfeiivvDDgStDetveileelakedprvrvirreenv.Gkagalnag 74 
                                    vv+p+y e+  l +++    ++        +   ++ ++ D S  e ve l +l++  p+v v rr e++ G  gal   
  gi|119720729|ref|YP_921224.1|  52 VVMPVYSEPLDLVASVS---KRdfeafsRAPCFARLTILSDDS-AEYVEALSRLVSDAPGVAVWRRRERRgGRTGALDDY 127
                                    67777777444433333...22235566445555555555666.599999999999************************ PP

                                    HHH--SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEE CS
                Glycos_transf_2  75 lraatgdyilflDaDdepdpdwleklvealekdgadvvl 113
                                    ++ +++  +++lDaD ++dp   ekl +    dga +v+
  gi|119720729|ref|YP_921224.1| 128 FASSSSSHLMILDADAVVDPCVAEKLCRNTLSDGA-LVV 165
                                    *********************99999998888777.444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (480 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 3268.79
//
Query:       gi|119720730|ref|YP_921225.1|  [L=219]
Description: hypothetical protein Tpen_1827 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0042   17.0   1.2     0.0042   17.0   1.2    2.8  3  TM_helix         Conserved TM helix
  ------ inclusion threshold ------
      0.026   15.2   4.1      0.026   15.2   4.1    1.8  2  Multi_Drug_Res   Small Multidrug Resistance protein
       0.21   11.4  12.7      0.068   13.0   3.6    3.0  3  LapA_dom         Lipopolysaccharide assembly protein A domain
        1.1    9.2   6.5       0.75    9.7   1.9    2.4  2  Cortexin         Cortexin of kidney
        3.4    5.8  11.9        4.6    5.4  11.5    1.5  1  DUF2070          Predicted membrane protein (DUF2070)


Domain annotation for each model (and alignments):
>> TM_helix  Conserved TM helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   1.2   1.2e-06    0.0042       4      39 ..      11      46 ..       8      57 .. 0.86
   2 ?   -1.5   0.0      0.69   2.5e+03      11      35 ..     106     130 ..     102     134 .. 0.73
   3 ?   -5.2   4.8         5   1.8e+04      17      35 ..     167     186 ..     165     190 .. 0.64

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.2e-06
                                   XSXXHHHHTTHSHHHHHHHHHHHHHHHHHHHHHHHH CS
                       TM_helix  4 nnllnellsflPnLvgAilILlvGwiiAkfvsrlvt 39
                                   ++ + e+++  P++ +A lIL+v +++ k+v + ++
  gi|119720730|ref|YP_921225.1| 11 QQVVIEIAALAPKVGLATLILFVTLLVVKLVNKSIR 46
                                   66778999***********************99876 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.69
                                    HTTHSHHHHHHHHHHHHHHHHHHHH CS
                       TM_helix  11 lsflPnLvgAilILlvGwiiAkfvs 35 
                                    ls++ ++   +++ l  ++++  + 
  gi|119720730|ref|YP_921225.1| 106 LSYISRIGSVAVLSLFSFVVIDALV 130
                                    8888888888888887777777665 PP

  == domain 3  score: -5.2 bits;  conditional E-value: 5
                                    HHHHHHHHH.HHHHHHHHHH CS
                       TM_helix  17 LvgAilILl.vGwiiAkfvs 35 
                                    L +A+ I++ +G++++ f++
  gi|119720730|ref|YP_921225.1| 167 LALALGIAIgIGFLVGAFAA 186
                                    55666555438888877765 PP

>> Multi_Drug_Res  Small Multidrug Resistance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       3.2   1.1e+04      31      31 ..      31      31 ..      13      51 .. 0.55
   2 ?   15.2   4.1   7.3e-06     0.026      14      84 ..     124     196 ..     106     200 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 3.2
                                   - CS
                 Multi_Drug_Res 31 p 31
                                   +
  gi|119720730|ref|YP_921225.1| 31 L 31
                                   1 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 7.3e-06
                                    HHHHHH--------------HHHHHHHHHHHH..HHHHH-------HHHHHHHHHHHHHHHHHHHHH------ CS
                 Multi_Drug_Res  14 vvgailLklsegftkltpsllvivgygisfll..LskalkslpvsvAYavwsGiGtvlivlvgillfgeslsl 84 
                                    vv  +l k++  ++k+  + +++  +++ +l+  L+   +++++++A  +  GiG+++ + +++ +fge l++
  gi|119720730|ref|YP_921225.1| 124 VVIDALVKSMRMERKTERFFVMMSLLVVTLLIvdLASLSNEIKLALALGIAIGIGFLVGAFAAWAFFGEYLDA 196
                                    5666677776666665555555554444444411555567799**************************9875 PP

>> LapA_dom  Lipopolysaccharide assembly protein A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.5       1.4   4.9e+03      17      27 ..      24      34 ..      11      41 .. 0.63
   2 ?    3.9   0.0     0.013        47      16      42 ..      67      93 ..      61     108 .. 0.80
   3 ?   13.0   3.6   1.9e-05     0.068      13      40 ..     162     188 ..     148     201 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.4
                       LapA_dom 17 lpLsllllvaf 27
                                   + L++l+l++ 
  gi|119720730|ref|YP_921225.1| 24 VGLATLILFVT 34
                                   55666666554 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.013
                       LapA_dom 16 elpLsllllvafgiGallgwllslwsy 42
                                    +pLs+ll++++ +G+l    + ++++
  gi|119720730|ref|YP_921225.1| 67 RIPLSTLLVLVADAGILTSSAALVVRV 93
                                   68**********999998877777655 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 1.9e-05
                       LapA_dom  13 aqvelpLsllllvafgiGallgwllslw 40 
                                    +  e+ L+l l +a+giG+l+g ++++ 
  gi|119720730|ref|YP_921225.1| 162 S-NEIKLALALGIAIGIGFLVGAFAAWA 188
                                    2.399*******************9994 PP

>> Cortexin  Cortexin of kidney
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.2     0.088   3.2e+02      24      37 ..      28      41 ..      12      63 .. 0.71
   2 ?    9.7   1.9   0.00021      0.75      15      41 ..     130     156 ..     116     161 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.088
                       Cortexin 24 tvfafvilLlifLg 37
                                   t   fv lL++ L+
  gi|119720730|ref|YP_921225.1| 28 TLILFVTLLVVKLV 41
                                   44456666655555 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00021
                       Cortexin  15 avsldleqktvfafvilLlifLglLiv 41 
                                      s+ +e+kt   fv++ l++++lLiv
  gi|119720730|ref|YP_921225.1| 130 VKSMRMERKTERFFVMMSLLVVTLLIV 156
                                    579***********************9 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4  11.5    0.0013       4.6       2     131 ..      52     198 ..      17     207 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0013
                        DUF2070   2 eklskyifr.lPswkvsllliillalligllaflssk.....................lfgillfglpalvaflltlpvl 59 
                                    ++l  y+ + lP+  + + l+ ll+l++++   +ss                      + +i  + +  l++f++   ++
  gi|119720730|ref|YP_921225.1|  52 ARLDEYLRKsLPEG-TRIPLSTLLVLVADAGILTSSAalvvrvfvpeysqayrealsyISRIGSVAVLSLFSFVVIDALV 130
                                    56667777767776.66667777777777766666667788999999999988888888888888888999999999988 PP

                        DUF2070  60 rilggrltykrslflalltelivviisllaillsallqalvllalvlslalvfalrllvlvavsdesllkav 131
                                    ++    + ++r++   ++++ ++v+++l+  l+s+  +  + lal +++ + f +  +  +a+++e l   v
  gi|119720730|ref|YP_921225.1| 131 KS----MRMERKTERFFVMMSLLVVTLLIVDLASLSNEIKLALALGIAIGIGFLVGAFAAWAFFGEYLDALV 198
                                    88....566777666666666666666666666643344555666666777777777777777776666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       895  (0.0499191); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1423.40
//
Query:       gi|119720731|ref|YP_921226.1|  [L=442]
Description: hypothetical protein Tpen_1828 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.91    8.4  53.8      0.064   12.2  17.0    3.2  3  MFS_1     Major Facilitator Superfamily


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   9.3    0.0098   1.8e+02     214     323 ..      16     121 ..       4     137 .. 0.70
   2 ?    3.5  21.7    0.0016        28      87     266 ..     101     262 ..      87     270 .. 0.71
   3 ?   12.2  17.0   3.6e-06     0.064      63     187 ..     269     391 ..     267     440 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.0098
                          MFS_1 214 ialllfffgfsglltllplylqevlglsglllaglllallalvgailallagrls.drlgrrrrlllallllllaalgla 292
                                     all++f +  +   ++p+  +   g+s l  ++l++  +++ ga+l   +g +       rr+ +l+l+  ++  + ++
  gi|119720731|ref|YP_921226.1|  16 EALLGGFYVAVTRGLFVPM--MAYSGYS-LENMALVFLPTSISGAAL--SWGLYKyPEEATRRFKVLSLATHIAERFVWL 90 
                                    3455555555556666666..7779999.999999999999999877..5555332334558999999999999999999 PP

                          MFS_1 293 llavtssavllllvlvliGfglgfvfpslla 323
                                     l+++ ++++++++l+++G +++ v++++l 
  gi|119720731|ref|YP_921226.1|  91 TLPFFLEKPIVVAFLYMLGNAVSAVVSIFLG 121
                                    99999**************966666555543 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.0016
                          MFS_1  87 lllvlrvlqGlgagalfpagaaliadwfpk.eergraigllsagfslGailgpllggllasslgWravfyilaivsllaf 165
                                    ++++l +l  + ++++    ++li  +f +  e +++  + sa+  ++++lg++   ++++ l  + ++y+  + +++++
  gi|119720731|ref|YP_921226.1| 101 VVAFLYMLGNAVSAVVSIFLGSLIYSYFGDvGEVMKVSVWRSAAGTAASLLGAIYMTAVSAVLPAPQSYYVSYVTAFVVG 180
                                    5778888888889999999999999999999999999999999999999********99999998888888888888888 PP

                          MFS_1 166 v...lfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlglsg 242
                                    +   ++ lll+  +p+   +++ +       +   +   +++ ++ +  l++++ l++  +   l++ pl   +++g + 
  gi|119720731|ref|YP_921226.1| 181 LgssVA-LLLVPAYPKQIVETGGRA------S---E-EVLIRGSQAF--LVLTFMLAG-SNLVGLSWAPL--LKDMGAP- 243
                                    866333.333333333333333333......2...3.3568899977..888888886.666699*****..8******. PP

                          MFS_1 243 lllaglllallalvgailallagr 266
                                     l+++l+l++++ +g ++    g 
  gi|119720731|ref|YP_921226.1| 244 -LYVSLALSITGNIGGVI----GS 262
                                    .77775566655555333....22 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 3.6e-06
                          MFS_1  63 rvlllglllfalg.lllllfasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpll 140
                                    + +++gl++  +  +++++   +l+ +++ l ++++l+  a++ +++ ++a++ +++ r ra ++++ag+ lG +++ l+
  gi|119720731|ref|YP_921226.1| 269 KAYVAGLVANTVLtAVIPF--LPLPgMHVGLSFFTSLTFMAANLLAMQIFAEINSHMGRVRASAYMTAGNYLGLLVASLV 346
                                    5789999999999555555..67999****************************************************** PP

                          MFS_1 141 ggllasslgWrav...fyilaivsllafvlfllllpeepperkrkspkee 187
                                    +  la     r++    +++a++ l+a vl+l+ +pe++  ++rk+ +  
  gi|119720731|ref|YP_921226.1| 347 ALTLA-----RSPflgLLLAAALKLVATVLALVAIPETAIVPERKAYEFS 391
                                    *****.....5551115666666666777777777777666666554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (442 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.25s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2827.29
//
Query:       gi|119720732|ref|YP_921227.1|  [L=299]
Description: nucleotidyl transferase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-32  111.9   0.0    7.1e-32  110.9   0.0    1.4  1  NTP_transferase  Nucleotidyl transferase
    2.7e-08   34.3   0.0    3.6e-08   33.9   0.0    1.4  1  NTP_transf_3     MobA-like NTP transferase domain
  ------ inclusion threshold ------
      0.018   14.9   0.0      0.033   14.1   0.0    1.4  1  LpxI_N           LpxI N-terminal domain


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.9   0.0   1.2e-35   7.1e-32       1     242 [.       6     272 ..       6     277 .. 0.86

  Alignments for each domain:
  == domain 1  score: 110.9 bits;  conditional E-value: 1.2e-35
                                    EEEEE--S--GGGTTCCTTSSGGGSEETTE.....T..ETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGT. CS
                NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgk.....e..rliqatlsrlansgieeiivvltqehsflveeqlkegskfg. 72 
                                    k+v+La G GtRL P +++++k ++pv  +     +  ++iqa++++  ++gi+e  +v+ + ++  +e++++  ++f  
  gi|119720732|ref|YP_921227.1|   6 KGVLLAAGLGTRLVPYSKEMPKEMLPVFFGvnnsvYlkPVIQAVFEQFYEAGIREFCFVVGRGKR-VIEDHFTPDWDFVe 84 
                                    69************************8764333443559****************8888886655.56777777766767 PP

                                    ....................SEEEEEE...ESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEEST.THHHHHHHHHT CS
                NTP_transferase  73 ....................vevlial...epegkgtAdAvalaaelledeksdelvlvLggDhlikd.ayeeavkkaie 128
                                                        ve ++++   +p ++gt +Av+ a+ +++d++    +    ++ + ++   +++++ +  
  gi|119720732|ref|YP_921227.1|  85 ylektgkndyaellrdfyekVEKSYITwvnQPVPRGTGHAVYMAKGFVGDDYF---MAAATDNLFLGEnIPRRLLEYFDR 161
                                    999999999***********6655554333999*******************6...888899999999445666666666 PP

                                    HSSTTSEEEEEEESS-CTTSEEEEEC..TTS..BEEEEECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHH CS
                NTP_transferase 129 kaakgtvtfgivpveeateyGviead..eeg..rverfvEKPkeakaselassGiYvfnsevllflakdleelkrgedei 204
                                     ++    ++++++v+++++yGv+  +  ++   rve +vEKP+e+  s+la++ +Y+f +e++  + ++ ++++rge e+
  gi|119720732|ref|YP_921227.1| 162 LRS---PMLAVKRVRDPRRYGVVIGSrvDTSiyRVEGIVEKPREPL-SYLANTSLYIFPPEIFRAI-EQTTPSPRGELEV 236
                                    666...8999*************8886633367***********99.******************9.88*********** PP

                                    HHHHHHHHHTTEEEEEECSTTEE-EEEXSSHHHHHHHH CS
                NTP_transferase 205 tdilpkaleegkvalaflfkdaeyWsDvGtldsllean 242
                                    td ++ ++++g++ +a+ +++   W D+Gt++ +l+a+
  gi|119720732|ref|YP_921227.1| 237 TDSIQILIRSGYQFYAYEAEA--DWIDIGTWETFLRAA 272
                                    ****************99999..6**********9987 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.0   6.1e-12   3.6e-08       1     128 [.       7     201 ..       7     291 .. 0.80

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 6.1e-12
                                    EEEEEESS-TTT....TT.THHHHCC.CCC.......CHHHHHHHHHCTT.-CEEEEECSH.CHHHH............. CS
                   NTP_transf_3   1 aviLAGGrSsRm....gg.dKallpl.ggk.......pllervldalraagvdevvvvggd.eevla............. 53 
                                    +v+LA+G ++R+    ++ +K +lp+  g        p+++ v++++ +ag++e + v+g+ + v +             
  gi|119720732|ref|YP_921227.1|   7 GVLLAAGLGTRLvpysKEmPKEMLPVfFGVnnsvylkPVIQAVFEQFYEAGIREFCFVVGRgKRVIEdhftpdwdfveyl 86 
                                    79**********6665347*******95555678888***************9888887775555455888899999999 PP

                                    .................HHTTCTS-EEE-TTSS-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTS CS
                   NTP_transf_3  54 .................alarlgvrvvededpgkgplaslaaalraaadadavlvlacDmPlltpelverllaaaaasga 116
                                                      ++++ +++v+++   +g++++++ a   + ++d+++ +a D  +l +++ +rll+ +++ ++
  gi|119720732|ref|YP_921227.1|  87 ektgkndyaellrdfyeKVEKSYITWVNQPV-PRGTGHAVYMAKGFV-GDDYFMAAATDNLFLGENIPRRLLEYFDRLRS 164
                                    9999999998888877777777788888876.69**********999.9**************************99998 PP

                                    SEEEEESSSEE.........................E CS
                   NTP_transf_3 117 dvvvptyeger.........................g 128
                                     ++++++  ++                          
  gi|119720732|ref|YP_921227.1| 165 PMLAVKRVRDPrrygvvigsrvdtsiyrvegivekpR 201
                                    8877776655455566666666666666666666661 PP

>> LpxI_N  LpxI N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   5.5e-06     0.033      54     120 ..      46     113 ..       6     116 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.5e-06
                         LpxI_N  54 lgklikaLkregvtevvmaGkvekpkll.dlrpDlralkllaklkdrgddalLravveelekeGikvl 120
                                    ++ +++ + ++g++e +++ +  k  +  + +pD+ +++ l k  +++  +lLr + e +ek  i+ +
  gi|119720732|ref|YP_921227.1|  46 IQAVFEQFYEAGIREFCFVVGRGKRVIEdHFTPDWDFVEYLEKTGKNDYAELLRDFYEKVEKSYITWV 113
                                    5778999**********9866677777758899************888899**********9887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1854.79
//
Query:       gi|119720733|ref|YP_921228.1|  [L=125]
Description: desulfoferrodoxin, ferrous iron-binding region [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-29  102.5   0.0    1.7e-29  102.2   0.0    1.1  1  Desulfoferrodox  Desulfoferrodoxin
    1.3e-05   25.4   0.0    1.6e-05   25.1   0.0    1.2  1  SoxY             Sulfur oxidation protein SoxY


Domain annotation for each model (and alignments):
>> Desulfoferrodox  Desulfoferrodoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.2   0.0   1.9e-33   1.7e-29       3      95 ..      20     118 ..      18     119 .. 0.96

  Alignments for each domain:
  == domain 1  score: 102.2 bits;  conditional E-value: 1.9e-33
                                    HTTTHTTSEEEEEESEEEETTEEEEEEEESSSS--BSSSS-EEEEEEEEEETTSS.......EEEE-TBS.ESEEEEEEE CS
                Desulfoferrodox   3 dekeekHvPvieadevvkagelfevkvkvgkipHpneeeHyIewielyleeegek.......rvelsaed.epevtftvk 74 
                                     +k e+H+P iea+++vkage+f vk+ vg  pHpn+ +H+I+wie+y+eeeg+        r++l++e  epevt+++ 
  gi|119720733|ref|YP_921228.1|  20 ISKVETHTPRIEAPDSVKAGEPFYVKIYVG--PHPNTLQHSIRWIEVYFEEEGRPfnpvmlsRIHLEPELvEPEVTLKLV 97 
                                    57899*************************..**********************9999**99******9967******** PP

                                    ESSSEEEEEEEEETTTEEEEE CS
                Desulfoferrodox  75 lkkekklvalsyCnlHGlWes 95 
                                    lkk+++++al+yCnlHG+We 
  gi|119720733|ref|YP_921228.1|  98 LKKSGVIYALEYCNLHGVWEG 118
                                    *******************96 PP

>> SoxY  Sulfur oxidation protein SoxY
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   1.8e-09   1.6e-05      17     108 ..      28     125 .]      13     125 .] 0.84

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.8e-09
                           SoxY  17 vkldaPeiAengavVpvtvsvd.lpgteadkvksiallvdkNpapl....aatfelgp.ageaevstrirlaetsnvrav 90 
                                     +++aP+ ++ g+ + v++ v  +p+t +++++ i ++ ++   p     + +++l+p  +e+ev++++ l+++  ++a+
  gi|119720733|ref|YP_921228.1|  28 PRIEAPDSVKAGEPFYVKIYVGpHPNTLQHSIRWIEVYFEEEGRPFnpvmLSRIHLEPeLVEPEVTLKLVLKKSGVIYAL 107
                                    489***********99999985367788888999****99986553222478999**988******************** PP

                           SoxY  91 aetsdgklyvaskeVkvt 108
                                     +++ + +++++k+Vkv+
  gi|119720733|ref|YP_921228.1| 108 EYCNLHGVWEGRKQVKVQ 125
                                    ****************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.32s 00:00:00.80 Elapsed: 00:00:00.51
# Mc/sec: 733.22
//
Query:       gi|119720734|ref|YP_921229.1|  [L=430]
Description: major facilitator transporter [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.4e-34  117.0  27.7    8.9e-34  116.8  27.7    1.1  1  MFS_2            MFS/sugar transport protein
    3.7e-15   55.7  35.9    3.7e-15   55.7  35.9    1.7  2  MFS_1            Major Facilitator Superfamily
  ------ inclusion threshold ------
       0.26    9.5   8.5        1.1    7.5   0.7    2.5  2  OATP             Organic Anion Transporter Polypeptide (OATP)
          6    7.6   6.7        2.5    8.9   0.1    3.4  3  NADH-u_ox-rdase  NADH-ubiquinone oxidoreductase complex I, 21


Domain annotation for each model (and alignments):
>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.8  27.7     2e-37   8.9e-34       1     383 [.       9     388 ..       9     424 .. 0.85

  Alignments for each domain:
  == domain 1  score: 116.8 bits;  conditional E-value: 2e-37
                          MFS_2   1 syglgalaanilsvllatylliFytdvlglsaalvglvllvarlvDaitDpivGtlidktstrwGrrrPwlllsaiilav 80 
                                    +yg+  ++ +i++ l ++   + y +v++l++ l g +  + +++  +   +vG+l+d+  trwGrr+P++  +a++la+
  gi|119720734|ref|YP_921229.1|   9 AYGFARFGSTIFMGLYDFASFYIYWQVFRLDPLLSGYMGAIGKITIMVASLLVGYLSDSIWTRWGRRKPFIATGAPLLAF 88 
                                    59***************7777779******************************************************** PP

                          MFS_2  81 siillftppelsqs....akfiwllvtyillrilytlfeipyvslvpvltkdydeRtsltsvrsflsvlggvlaailafl 156
                                    s +l ftp+ + q+    a+f+w ++t+ +++ +y+ +  p+ +++p++ ++++eR +++   +++++lg ++ ++  fl
  gi|119720734|ref|YP_921229.1|  89 SGFLHFTPIYFLQGatqeALFLWGAATSSMFHFFYAWLLTPFQAWLPEI-SEPSERIDISMLQNVANILGNIVSTVTGFL 167
                                    **********99999**********************************.899****************99999888777 PP

                          MFS_2 157 lvlilgglkserkgylifaliialLmllgviivvlgtkervemrkkekteqkeklslleqlkevfrnraflillllflla 236
                                         +            +l++ l+ + + ++v+l+t   v   +  + +++   + l++l  vfr r +++++++  l 
  gi|119720734|ref|YP_921229.1| 168 AKMLVAR-----------GLLMPLVGAYALVLVALFTPPVVLL-PV-ERRAEPTRPSLKDLLTVFRYREYMKWMAVRGLM 234
                                    7444444...........4444444444444444444443333.22.2244555566788899************98888 PP

                          MFS_2 237 alalgvlnglllYyltyvlg.ngsaasvfllvv.tisallgiplwqplakrlgkkntyllgalltivllvlvlll..... 309
                                    + ++ +l    + y+++v+g + s as++++v+ ++ ++ ++plw +l kr gk ++  l+++l+ + l+++ l      
  gi|119720734|ref|YP_921229.1| 235 SSSVQMLTITIIAYIEKVIGvEHSLASASFGVIlVVFVAGAFPLWGRLGKRAGKGRALTLSMTLLGATLLMTPLPhfvdp 314
                                    88888888888889*****************9977888899*****************9999998887776555456655 PP

                          MFS_2 310 qpsnlllflvllviagfgvgvaallpwsmladvvDygelktGkrregvffavlsfisklatgiglgvsgllLsa 383
                                    +   +ll +vl++++ ++v + +l+p++ lad++   e++tG++r+g+f+++ ++  ++   ++ +v+g+l s+
  gi|119720734|ref|YP_921229.1| 315 GVFRVLLGYVLVALGAVAVSAYVLFPYAVLADLAHWYEVQTGEKRAGLFTGFEGIPINVFESLAYLVTGFLMSL 388
                                    555678889999999999999**********************************************9999876 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.7  35.9   8.3e-19   3.7e-15       4     324 ..      13     343 ..       9     369 .. 0.77
   2 ?   -1.2   0.5      0.17   7.4e+02     130     170 ..     371     416 ..     343     425 .. 0.53

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 8.3e-19
                          MFS_1   4 aaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsd....rfGrrr.vlllglllfalglll 78 
                                    a f s++ ++++ +a   ++ + + ++p   g + ++  ++ +vasl++G+lsd    r+Grr+ ++ +g+ l+a++++l
  gi|119720734|ref|YP_921229.1|  13 ARFGSTIFMGLYDFASFYIYWQVFRLDPLLSGYMGAIGKITIMVASLLVGYLSDsiwtRWGRRKpFIATGAPLLAFSGFL 92 
                                    5566666666666666667788999*****************************999999****9999999999999444 PP

                          MFS_1  79 ll....f...a..sslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllassl 148
                                     +    f   a    l+ + ++   +  +++++l++  +a++ +++ ++er     l ++++ lG i+   + g+la  l
  gi|119720734|ref|YP_921229.1|  93 HFtpiyFlqgAtqEALFlWGAATSSMFHFFYAWLLTPFQAWLPEISEPSERIDISMLQNVANILGNIVS-TVTGFLAKML 171
                                    4436543443244446667788888*****************************************999.999****999 PP

                          MFS_1 149 gWravfyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvl.willialllfffgfsgll 227
                                      r++ + l ++++l++v   +l++ + +  + ++ +e      + +l+++++ ++ + ++ w+++ +l +    +++l+
  gi|119720734|ref|YP_921229.1| 172 VARGLLMPLVGAYALVLV---ALFTPPVVLLPVERRAEP----TRPSLKDLLTVFRYREYMkWMAVRGLMSS--SVQMLT 242
                                    999888888888888766...666666666666666666....66667777888888887755555555555..9***** PP

                          MFS_1 228 tllplylqevlgls.glllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllll. 305
                                    +++  y+ +v g   + l ++ +  +l +++a++++l+grl +r g+ r+l+l++ ll +++l+  l  + +  v+ +l 
  gi|119720734|ref|YP_921229.1| 243 ITIIAYIEKVIGVEhS-LASASFGVILVVFVAGAFPLWGRLGKRAGKGRALTLSMTLLGATLLMTPLPHFVDPGVFRVLl 321
                                    **************55.44444555555555555*************************************555555556 PP

                          MFS_1 306 ..vlvliGf.glgfvfpsllal 324
                                      vlv +G  +++ ++    a+
  gi|119720734|ref|YP_921229.1| 322 gyVLVALGAvAVSAYVLFPYAV 343
                                    4466667774444444333344 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.17
                          MFS_1 130 fslGailgpllggllasslg.....Wravfyilaivsllafvlfll 170
                                    +++   l++l+ g+l+s+       +++  ++ ++v+ l+ +++l+
  gi|119720734|ref|YP_921229.1| 371 INVFESLAYLVTGFLMSLPQvpgseYTYGLILWGPVASLFTLVALA 416
                                    4444445555555555444444444444444444444444443333 PP

>> OATP  Organic Anion Transporter Polypeptide (OATP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.7   0.00025       1.1      31      91 ..      36     101 ..       8     145 .. 0.87
   2 ?    5.6   1.4   0.00087       3.9       7      89 ..     229     312 ..     223     319 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00025
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           OATP  31 FklpsstsgliassneignillilfvsYfggr.....ghrPrwigigallmalgslllalPhfisg 91 
                                    F+l+   sg + ++  i+ ++++l+v+Y+ ++     g+r  +i++ga l+a++ +l   P ++ +
  gi|119720734|ref|YP_921229.1|  36 FRLDPLLSGYMGAIGKITIMVASLLVGYLSDSiwtrwGRRKPFIATGAPLLAFSGFLHFTPIYFLQ 101
                                    888888999999*****************9876666789999*******************98875 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.00087
                                    xxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           OATP   7 sllglvqamvsgyfkstittiEk....rFklpsstsgliassneignillilfvsYfggrghrPrwigigallmalgsll 82 
                                     + gl+   v +++ ++i  iEk    + +l s++ g+i++++  g+  l    + +g+r+ + r + +++ l++   l+
  gi|119720734|ref|YP_921229.1| 229 AVRGLMSSSVQMLTITIIAYIEKvigvEHSLASASFGVILVVFVAGAFPLW---GRLGKRAGKGRALTLSMTLLGATLLM 305
                                    555566666666777777777773333566778888888888888888765...56789999999999999999999999 PP

                                    xxxxxxx RF
                           OATP  83 lalPhfi 89 
                                    + lPhf+
  gi|119720734|ref|YP_921229.1| 306 TPLPHFV 312
                                    9999996 PP

>> NADH-u_ox-rdase  NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.4      0.19   8.4e+02      35      65 ..      28      66 ..      13     173 .. 0.67
   2 ?    8.9   0.1   0.00055       2.5      10      34 ..     209     233 ..     207     306 .. 0.84
   3 ?   -3.2   0.1       3.2   1.4e+04      27      37 ..     330     341 ..     312     352 .. 0.56

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.19
                NADH-u_ox-rdase 35 fplallaleklsPsvagka........mtlagligflgg 65
                                    ++ ++ + +l+P  +g +        m+++ l+g l++
  gi|119720734|ref|YP_921229.1| 28 SFYIYWQVFRLDPLLSGYMgaigkitiMVASLLVGYLSD 66
                                   555566666666666554455555555555555555552 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00055
                NADH-u_ox-rdase  10 dPsfsrvlrnfrpsDYvkaaaitaa 34 
                                     Ps ++ l  fr  +Y+k++a+   
  gi|119720734|ref|YP_921229.1| 209 RPSLKDLLTVFRYREYMKWMAVRGL 233
                                    79*******************9543 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 3.2
                NADH-u_ox-rdase  27 kaaaita.afpl 37 
                                    ++a+ +   fp+
  gi|119720734|ref|YP_921229.1| 330 AVAVSAYvLFPY 341
                                    333333334444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2718.53
//
Query:       gi|119720735|ref|YP_921230.1|  [L=298]
Description: hypothetical protein Tpen_1832 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.9e-37  127.5  35.5    1.2e-19   70.8  14.2    2.0  2  EamA            EamA-like transporter family
    2.3e-06   27.2   9.4     0.0018   17.7   1.3    2.4  2  TPT             Triose-phosphate Transporter family
     0.0015   18.5   4.3     0.0061   16.6   0.8    2.7  2  TMEM234         Putative transmembrane family 234
     0.0044   16.3   0.1     0.0093   15.2   0.1    1.5  1  Nuc_sug_transp  Nucleotide-sugar transporter
  ------ inclusion threshold ------
      0.048   13.9   0.2       0.17   12.1   0.2    1.9  1  DMT_6           Putative member of DMT superfamily (DUF486)


Domain annotation for each model (and alignments):
>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.8  14.2   3.4e-23   1.2e-19       2     136 ..      18     153 ..      17     154 .. 0.96
   2 !   63.0  13.3   8.6e-21   3.1e-17       2     134 ..     165     295 ..     164     298 .] 0.97

  Alignments for each domain:
  == domain 1  score: 70.8 bits;  conditional E-value: 3.4e-23
                           EamA   2 lgillallaalfwaiyfvlskil..lrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlaf 79 
                                    lg+++al+aal+++ ++++ +++   ++v+p+ l+++r ++a +lll++ ++ +  + + ++  +l+++l  l +++l+ 
  gi|119720735|ref|YP_921230.1|  18 LGEVFALVAALSFSGAAIFYRAGvrGSQVNPIVLSGLRGMFALALLLVVGFFYRVDF-SKPPVFYLAVFLSMLGSFILGD 96 
                                    6999******************9666778****************************.999999**************** PP

                           EamA  80 llffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                    + f+y+l++ + +++ ++ ++  vft+++s+++lge ltl++ ++ +li+lGv+l++
  gi|119720735|ref|YP_921230.1|  97 SSFLYGLQRAPLGVVYPVAYTFSVFTALFSHFILGEELTLRDAVSSLLIVLGVALVY 153
                                    *******************************************************96 PP

  == domain 2  score: 63.0 bits;  conditional E-value: 8.6e-21
                           EamA   2 lgillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlafll 81 
                                     g+l  l a+++w+++++l+  +lr  + ++++  r+ +  i+ l+++l + +    +++  + ll+l g+lg+ +++ll
  gi|119720735|ref|YP_921230.1| 165 VGALAGLSASVSWGAGATLMGLALRWGNAVEVNISRLSMLVIATLPLILKNSSEV--FRQVRVHLLALGGILGIGVGPLL 242
                                    58999*********************************************99999..*********************** PP

                           EamA  82 ffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvll 134
                                    f+ +++ ++as+ s+++s +Pv+t++ls ++lgek + k llg++ + +G++l
  gi|119720735|ref|YP_921230.1| 243 FMNSISFIGASRSSIFISSTPVLTVLLSRIFLGEKTGGKLLLGTLAVSAGLAL 295
                                    **************************************************998 PP

>> TPT  Triose-phosphate Transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   1.3     5e-07    0.0018     100     152 ..     117     169 ..      36     176 .. 0.84
   2 !   14.3   1.3   5.3e-06     0.019      81     136 ..     242     297 ..     192     298 .] 0.72

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 5e-07
                            TPT 100 sePiFtvilsrlllgeklsllvylsLlpivgGvalasvtElsFnligfisAli 152
                                    +  +Ft+++s+++lge+l+l   +s l iv Gval      s    ++++Al+
  gi|119720735|ref|YP_921230.1| 117 TFSVFTALFSHFILGEELTLRDAVSSLLIVLGVALVYSENFSLGKQALVGALA 169
                                    5569*******************************999999999999999986 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 5.3e-06
                            TPT  81 lavvslskvaVSfthtvKasePiFtvilsrlllgeklsllvylsLlpivgGvalas 136
                                    l + s+s +  S + +  +s P+ tv+lsr++lgek+  +++l  l + +G+al s
  gi|119720735|ref|YP_921230.1| 242 LFMNSISFIGASRSSIFISSTPVLTVLLSRIFLGEKTGGKLLLGTLAVSAGLALQS 297
                                    4445666666777788889********************************99977 PP

>> TMEM234  Putative transmembrane family 234
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.8   1.7e-06    0.0061      49     115 ..      82     152 ..      57     153 .. 0.75
   2 ?    2.5   0.1     0.041   1.5e+02      78     114 ..     259     295 ..     237     297 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.7e-06
                        TMEM234  49 iplllNqsgSvl.....fflllgkadlslavpiaNslafvfTvltelllgekvlkkktvlgmllvvvgialc 115
                                    +++ l ++gS +     f + l++a+l ++ p+a + ++ + +    +lge+++ +++v   ll+v+g+al+
  gi|119720735|ref|YP_921230.1|  82 LAVFLSMLGSFIlgdssFLYGLQRAPLGVVYPVAYTFSVFTALFSHFILGEELTLRDAV-SSLLIVLGVALV 152
                                    555555555543333339****************9987655555558899988877766.567888899987 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.041
                        TMEM234  78 NslafvfTvlte.lllgekvlkkktvlgmllvvvgial 114
                                     s + v+Tvl +  +lgek+ + k +lg+l v +g+al
  gi|119720735|ref|YP_921230.1| 259 ISSTPVLTVLLSrIFLGEKT-GGKLLLGTLAVSAGLAL 295
                                    35566788888835666665.56789999999999987 PP

>> Nuc_sug_transp  Nucleotide-sugar transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   2.6e-06    0.0093     111     160 ..     111     159 ..     102     188 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.6e-06
                 Nuc_sug_transp 111 tyqvtyqlkilttalfsvllLkrklskkqWlslllLvaGvalvqlkqkes 160
                                    +y v+y + ++ talfs ++L+ +l+ +  +s ll+v+Gvalv  ++ + 
  gi|119720735|ref|YP_921230.1| 111 VYPVAYTFSVF-TALFSHFILGEELTLRDAVSSLLIVLGVALVYSENFSL 159
                                    69999999987.79*****************************8887665 PP

>> DMT_6  Putative member of DMT superfamily (DUF486)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   4.7e-05      0.17      69     105 .]     116     153 ..     101     153 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.7e-05
                          DMT_6  69 itlvvfv.lfsvlllkeklklnhlvaflllvlavyfvf 105
                                     t++vf+ lfs+++l+e+l+l+ +v+ ll+vl+v +v+
  gi|119720735|ref|YP_921230.1| 116 YTFSVFTaLFSHFILGEELTLRDAVSSLLIVLGVALVY 153
                                    6889997369************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1873.73
//
Query:       gi|119720736|ref|YP_921231.1|  [L=323]
Description: asparagine synthetase A [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-30  106.3   0.0    1.9e-30  106.1   0.0    1.0  1  tRNA-synt_2  tRNA synthetases class II (D, K and N)


Domain annotation for each model (and alignments):
>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.1   0.0     1e-34   1.9e-30      20     312 ..      30     315 ..      19     317 .. 0.84

  Alignments for each domain:
  == domain 1  score: 106.1 bits;  conditional E-value: 1e-34
                                    HHHHHHHHHHHHHHHHHHHTT-EE----SEESS--SS.SS--EEEEETTT.TEEE....-E-S-SHHHHHHHHHCTHSEE CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxx RF
                    tRNA-synt_2  20 kvlrlrstvtkavrkyleengfieietPiLsksdtee.garlFkvksrekekeff....aLtqspqlylellivagidrv 94 
                                    ++ r+ +  ++ + +yl e+gf  + + ++sks+ +     +F +++r +  e +      tqs+  ++++l++    ++
  gi|119720736|ref|YP_921231.1|  30 SIARITTYTLSFLSRYLVERGFDWVLPVVFSKSTDPLwPDPDFSIEKRIE-VEIYgetvRSTQSMIVHKQVLVSLLSPKI 108
                                    56666777777788899999998887777777744431356899988887.35555655889*************999** PP

                                    EEEEEEE--S--B...TTB-S-CEEEEEEEEET-SCHHHHHHHHHHHHHHHHHHHHCSCCCCCHTTTTTSEE-SSS-EEE CS
                                    xxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    tRNA-synt_2  95 fqiaraFRaEdsr...tdrhlaEFtqieaemsfieeedimqvleelikslvkevlessakdiefvirrnskdlkkpfkrl 171
                                    f ++++ R E  +   t  h  EFtq+++e+  ++ + i +++e+++ks v+ +++++++++ f  ++   ++ +pfk +
  gi|119720736|ref|YP_921231.1| 109 FVFSPNVRIETRKrasTGIHAYEFTQLDFEVRGASSSYIRSLVEDMLKSYVSSLKREMEHELSFLGSELP-EIMTPFKVV 187
                                    **********754333777999********************************9999888888888876.88889**** PP

                                    EHHHHHHHHHTS-SS--HHHHHHHHHHS--SEEEEEEEBGGGSTTCBBBSTTSTTBBSEEEEEETTE.EEEEEEEB--SH CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
                    tRNA-synt_2 172 tykeaieklneigkdldkaderalvkkeknepvfvtdfPaelkpFyarkeeddkkltesyDllingv.ElvgGslRiedp 250
                                    + ke  e++ ++     +  +r  +k    epv+v++ P+e   F  +++     + ++yDl+++ v E+++G+ R+ ++
  gi|119720736|ref|YP_921231.1| 188 DSKELEEEYGKEW----QTSLRSTLK----EPVWVVNIPREFYDFEDPET----GRWDNYDLYVPRVgEILSGARREYEY 255
                                    *999999943222....345566555....*********88666666555....559*********************** PP

                                    HHHHHHHHHCCHHSSSGGGGHHHHHHHHCT.--SEEEEEEEHHHHHHHHCT-SSGGGCSSS-X CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    tRNA-synt_2 251 eeleeklkskgldeeaeekfswylealeyG.apphgGlglGldRlvmlllgsesIrdviaFPk 312
                                    e+   k+k+ g+    +e++  +l++ + G + p +G g+G++Rl+ +++g ++I  v++FP+
  gi|119720736|ref|YP_921231.1| 256 EKILSKMKRDGVR---PENYRVLLDLAREGrLLPSAGAGIGVERLLLWVTGVRHIGIVQPFPR 315
                                    *************...*********99998468*****************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 2069.14
//
Query:       gi|119720737|ref|YP_921232.1|  [L=139]
Description: hypothetical protein Tpen_1834 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.061   13.0   0.0      0.068   12.9   0.0    1.1  1  MAF_flag10  Protein of unknown function DUF115
        0.1   12.7   0.0       0.18   11.9   0.0    1.4  1  DUF1940     Domain of unknown function (DUF1940)


Domain annotation for each model (and alignments):
>> MAF_flag10  Protein of unknown function DUF115
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   7.6e-06     0.068      16      92 ..      17      97 ..       7     130 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.6e-06
                     MAF_flag10 16 kellnkfkgnkpaiivgaGP..SLeknlellkelrdkaviiaadtal..kaLlkegIkPDivvslDpqea.syevfkeaekk 92
                                    +ll+++ + +++ +vg GP  S ++ l+l++el+ + v+ a+   +  ++Ll+ g++P ++++ D  e  s e + e+e+k
  gi|119720737|ref|YP_921232.1| 17 VRLLEESLK-DQVQVVGVGPlySADEVLKLIRELEADEVVTAIEDPCemNKLLSSGVQPLVMITEDVAECgSREECLEYESK 97
                                   455554544.799*******9999********************9763379*************998554144456666665 PP

>> DUF1940  Domain of unknown function (DUF1940)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0     2e-05      0.18      31      67 ..     102     138 ..      89     139 .] 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2e-05
                                    HHHHT-SSHHHHHHHHHHHHHHHHTTT-------HHH CS
                        DUF1940  31 laiseGikvqatrelldilDtlyqslsDpeskLkDeq 67 
                                    l   +G+kv a +e l ++D + q +  +e++++De+
  gi|119720737|ref|YP_921232.1| 102 LEKEDGVKVVALKEFLRVVDIMFQLVEPSEVHVHDEE 138
                                    55568***************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.49
# Mc/sec: 856.33
//
Query:       gi|119720738|ref|YP_921233.1|  [L=245]
Description: hypothetical protein Tpen_1835 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.2e-31  106.1   0.0    1.6e-30  105.4   0.0    1.4  1  Cyclophil_like   Cyclophilin-like
    0.00029   20.8   0.0    0.00046   20.1   0.0    1.3  1  Cyclophil_like2  Cyclophilin-like family


Domain annotation for each model (and alignments):
>> Cyclophil_like  Cyclophilin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.4   0.0   1.7e-34   1.6e-30       1     119 []       3     113 ..       3     113 .. 0.97

  Alignments for each domain:
  == domain 1  score: 105.4 bits;  conditional E-value: 1.7e-34
                                    EEEEEEET.TEEEEEEEETTHHHHHHHHC-SEEEEEEECTTEEEEE-S-----SSSEESSB-TTEEEEECCCTEEEEESS CS
                 Cyclophil_like   1 kkikidie.sseveveLddtetaraikealPiesrvntWgeEiYfstpvklekeenakevveagdiaywppGkalclffG 79 
                                    ++++i+++ s+e++v+++d ++++a+++alPies++++W+eE+Yfst+++l+  ++++  v++g++aywppGkalclf +
  gi|119720738|ref|YP_921233.1|   3 MYLRIIFGgSREIPVYVSDPSYHDALRKALPIESTAELWKEEVYFSTNLDLRGPTSSR--VPSGTFAYWPPGKALCLFAW 80 
                                    789*****9*******************************************888888..******************** PP

                                    --TT-TTSB--SSSEEEEEEEEC-GGGGGG--TTEEEEEE CS
                 Cyclophil_like  80 ktPisddeirpaspvnviGrivedlellkkvkdgekvrve 119
                                     +       +p+++v  +G++++++++++ ++++++vrve
  gi|119720738|ref|YP_921233.1|  81 VS-------QPYGAVIPLGWLLGPKHYVLLLDKESSVRVE 113
                                    **.......*****************************97 PP

>> Cyclophil_like2  Cyclophilin-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   5.1e-08   0.00046       6     104 ..      13     104 ..       7     113 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 5.1e-08
                Cyclophil_like2   6 qtftatLednaaaralleklPltltmedyngnEkiaylpeklptddapegssikaGdlayyapwgnlvlfykdfeesysy 85 
                                    +++ +   d +  +al + lP++ t e  +  E +++   +l+  +  ++s + +G++ay++p++ l+lf    +   + 
  gi|119720738|ref|YP_921233.1|  13 REIPVYVSDPSYHDALRKALPIESTAELWK-EEVYFS--TNLDLRGP-TSSRVPSGTFAYWPPGKALCLFAWVSQP--YG 86 
                                    667777777778889999999999887666.676655..77888886.9999******************999955..89 PP

                Cyclophil_like2  86 gltrlGrieedaeelaeal 104
                                     +++lG + + ++ ++ +l
  gi|119720738|ref|YP_921233.1|  87 AVIPLGWLLG-PKHYVLLL 104
                                    9*****9845.44443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1557.96
//
Query:       gi|119720739|ref|YP_921234.1|  [L=335]
Description: hypothetical protein Tpen_1836 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2376.95
//
Query:       gi|119720740|ref|YP_921235.1|  [L=356]
Description: mandelate racemase/muconate lactonizing protein [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.6e-49  166.4   0.0    9.6e-49  165.9   0.0    1.2  1  MR_MLE_C     Enolase C-terminal domain-like
    8.1e-12   45.4   0.0    3.1e-11   43.5   0.0    2.0  2  MR_MLE_N     Mandelate racemase / muconate lactonizing enzyme
     0.0065   16.9   0.7      0.029   14.8   0.4    2.1  2  Radical_SAM  Radical SAM superfamily
  ------ inclusion threshold ------
       0.01   15.0   0.1      0.015   14.5   0.1    1.3  1  MAAL_C       Methylaspartate ammonia-lyase C-terminus
      0.014   14.6   0.0       0.13   11.5   0.0    2.0  2  Enolase_C    Enolase, C-terminal TIM barrel domain


Domain annotation for each model (and alignments):
>> MR_MLE_C  Enolase C-terminal domain-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.9   0.0   2.7e-52   9.6e-49       1     216 [.     137     346 ..     137     349 .. 0.91

  Alignments for each domain:
  == domain 1  score: 165.9 bits;  conditional E-value: 2.7e-52
                                    HHHHHHHHHHHHHT-SEEEEETSSSHHHHHHHHHHHHHHHHTTTSTSEEEEE-TTTSBHHHHHHHHHHHGGGTESEEESS CS
                       MR_MLE_C   1 elaeearelvaeqgfravKlkvggddvaedvervravreavgpgddvdlmvDanqawdlatAirvareleeldllwlEEP 80 
                                    e+ae+a + +ae+gfr++Klk+g++ ++edv rv+avr++v  gd ++++vDan++w++++A+rv++++++++++++E+P
  gi|119720740|ref|YP_921235.1| 137 EMAERALR-YAEKGFRIFKLKLGEN-PEEDVLRVKAVRDVV--GD-ATIRVDANEGWTREDAVRVIERIADYGVELVEQP 211
                                    58899966.8888********8886.***************..53.69******************************** PP

                                    SSTTTHHHHHHHHHHHH.SSEEEESTTSSSHHHHHHHHHHTSESEEEEBHHHHTSHHHHHHHHHHHHHTT-EEEEBSCS. CS
                       MR_MLE_C  81 vppeddleglaelrara.sipiaagEslysradfrelleagavdivqpdvsrvgGitearkvaalaeafgvpvapHsgs. 158
                                    +++ dd+egl++lr+ + +ipia++Es++++ d+  +++++a+di++++++++ Git+a++++ + ea+g++ ++++ s 
  gi|119720740|ref|YP_921235.1| 212 LRH-DDIEGLRALRR-EsPIPIAVDESVKTARDALLVAKKEAADIINIKLMKSRGITGAIRIIMVSEAAGLKNMVGCFSe 289
                                    **9.78********5.55***********************************************************976 PP

                                    SHHHHHHHHHHHHTTTTBEEEEEEGGGGHTSGCSBSSSSEEETTEEECTSSSBTSSEB CS
                       MR_MLE_C 159 gglglaaslhlaaaipnllileyfldaelleeelleeplevedGrvtvpdgpGlGvel 216
                                    + lg  a++ la a +n+l+++ + d     + ++++  e+   r +++ +pGlG+ +
  gi|119720740|ref|YP_921235.1| 290 SRLGITATAYLAQAFSNVLFYDLDCDIL-SADPVFTGGSEPIGDRRRASPKPGLGISP 346
                                    9**********************99997.5666666666666666778999****976 PP

>> MR_MLE_N  Mandelate racemase / muconate lactonizing enzyme, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.5   0.0   8.6e-15   3.1e-11       5     117 .]       6     118 ..       2     118 .. 0.68
   2 ?   -1.7   0.0      0.92   3.3e+03      24      42 ..     250     268 ..     223     284 .. 0.67

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 8.6e-15
                                    EEEEEEEEEC.EEEETTEEEEEEEEEEEEEEECTTEEEEEEEE-STTGHHHHHHHHHHHHHHHHTTSBTTH..HHHHHHH CS
                       MR_MLE_N   5 vvveeavklr.PvqlavttvqkqslvlvkietseGvvGigeatsvggraetikaelddhlapllvgkdaan..isdlaql 81 
                                     v e++   r P++++  t ++q+ ++++++ ++ ++G+gea              +d l  l  + da +  + d  ++
  gi|119720740|ref|YP_921235.1|   6 WVCEVPL--RePLRISAATYHTQRSIVLRLR-DGDLEGWGEACQSRR---VLGESFEDALESLRASVDAIKraEYDSLEK 79 
                                    4554443..44********************.999*******98873...223333333333333333322003333344 PP

                                    HHHHCSS...CHHHHHHHHHHHHHHHHHHTTSBHHHHTT CS
                       MR_MLE_N  82 lkravlg...nmsAkaaidmAlwDlkakalnlpladLlG 117
                                    ++r+      + s kaa++mAl+Dl ak+ + pl+ LlG
  gi|119720740|ref|YP_921235.1|  80 IHRFTEElnaTPSIKAAVNMALLDLYAKSEGRPLWRLLG 118
                                    44444334448999************************9 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.92
                                    EEEEEEEEEEEECTTEEEE CS
                       MR_MLE_N  24 qkqslvlvkietseGvvGi 42 
                                    + + ++ +k+  s G++G 
  gi|119720740|ref|YP_921235.1| 250 EAADIINIKLMKSRGITGA 268
                                    4455566666667777775 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       0.4   1.4e+03     109     144 ..      38      71 ..      35      86 .. 0.76
   2 !   14.8   0.4   8.1e-06     0.029      27     140 ..     131     243 ..     105     275 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.4
                                    EBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    Radical_SAM 109 leaaddekvlklmnrghtfeevlealeklreagikr 144
                                    le + + +  +++  g++fe+ le+l++  +a ikr
  gi|119720740|ref|YP_921235.1|  38 LEGWGEACQSRRV-LGESFEDALESLRASVDA-IKR 71 
                                    5666666444555.789999999999998888.776 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 8.1e-06
                                    HHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHG...HHHHHHHHHTT-S CS
                                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxx RF
                    Radical_SAM  27 rslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritvetngtlpd...eeklerllelgvd 103
                                     ++ +ee +e + ++ aekg + + l  g    +p++ +l  ++++  v + +i+v +n+++ +    +++er++++gv 
  gi|119720740|ref|YP_921235.1| 131 GIMRPEEMAERALRY-AEKGFRIFKLKLG---ENPEEDVLRVKAVRDVVGDATIRVDANEGWTRedaVRVIERIADYGVE 206
                                    567788888888888.5766666666655...367777777777777799************99**************** PP

                                    EEEEEEBSSSHHHHHHHHTCTSHH..HHHHHHHHHHHHT CS
                                    xxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxx RF
                    Radical_SAM 104 rvslgleaaddekvlklmnrghtf..eevlealeklrea 140
                                     v+ +l + d e  l+ ++ ++++   +v e+++++r+a
  gi|119720740|ref|YP_921235.1| 207 LVEQPLRHDDIE-GLRALR-RESPipIAVDESVKTARDA 243
                                    ************.899995.4444454455555555554 PP

>> MAAL_C  Methylaspartate ammonia-lyase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   4.2e-06     0.015     122     197 ..     216     286 ..     171     308 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.2e-06
                         MAAL_C 122 qierlaelreklkekgikvelvaDeWcntledirefvdaeaadlvqiktPDlGginntieavlyckekgvgaylGG 197
                                    +ie l +lr     + + + +  De   t  d    + +eaad++ ik     gi+ +i  +++++  g++ ++G 
  gi|119720740|ref|YP_921235.1| 216 DIEGLRALR-----RESPIPIAVDESVKTARDALLVAKKEAADIINIKLMKSRGITGAIRIIMVSEAAGLKNMVGC 286
                                    455555554.....457899999***********************************************999875 PP

>> Enolase_C  Enolase, C-terminal TIM barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0     0.073   2.6e+02      37      97 ..      12      76 ..       7      85 .. 0.63
   2 ?   11.5   0.0   3.5e-05      0.13     145     235 ..     199     286 ..     178     305 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.073
                                   HHHHHHHHHHHHHHHHHHHHH.CC.GGGG...-B-TTS-B----SSHHHHHHHHHHHHHHCT-TC CS
                      Enolase_C 37 fkealrlGaevyhklksvlkk.kygksat...nvGdeGGfaPnlqsnkealdliveaiekaGykg 97
                                   ++e lr+ a +yh+ +s++ + + g   +   +      +  +++++ e+l   v+ai++a y++
  gi|119720740|ref|YP_921235.1| 12 LREPLRISAATYHTQRSIVLRlRDGDLEGwgeACQSRRVLGESFEDALESLRASVDAIKRAEYDS 76
                                   67899999999999998765414444433111222233344555666666777788888888875 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 3.5e-05
                                    HHHHS-EEEEES-S-TT-HHHHHHHHHHHTTTSEEEESTTTTT-HHHHHHHHHCT--SEEEE-HHHH-SHHHHHHHHHHH CS
                      Enolase_C 145 lvkkyPivsiedpldeddweawkklteelgdkvqivGddltvtnpkrlkeaiekkaanalllkvnqiGsltesleavkla 224
                                     + +y +  +e pl +dd e+ + l  e    + i  d+ + t  + l  a +k+aa+ + +k+ +   +t ++  + ++
  gi|119720740|ref|YP_921235.1| 199 RIADYGVELVEQPLRHDDIEGLRALRRESP--IPIAVDESVKTARDALLVA-KKEAADIINIKLMKSRGITGAIRIIMVS 275
                                    4679**********************9998..99999*9999999988766.788999********************** PP

                                    HHTT-EEEEE- CS
                      Enolase_C 225 keagygvvvsh 235
                                    ++ag   +v  
  gi|119720740|ref|YP_921235.1| 276 EAAGLKNMVGC 286
                                    *****999964 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.31s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 2170.07
//
Query:       gi|119720741|ref|YP_921236.1|  [L=166]
Description: hypothetical protein Tpen_1838 [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1062.70
//
Query:       gi|119720742|ref|YP_921237.1|  [L=284]
Description: pyrroline-5-carboxylate reductase [Thermofilum pendens Hrk 5]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-31  107.6   0.3      6e-31  106.8   0.3    1.4  1  P5CR_dimer       Pyrroline-5-carboxylate reductase dimerisati
      1e-18   67.7   0.2    2.6e-18   66.4   0.1    1.8  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    6.2e-05   22.7   1.5    0.00048   19.8   1.2    2.2  2  ApbA             Ketopantoate reductase PanE/ApbA
    0.00011   22.0   0.6    0.00021   21.1   0.6    1.4  1  Rossmann-like    Rossmann-like domain
    0.00019   21.4   3.2      0.004   17.2   0.0    2.5  3  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
    0.00023   20.6   0.3    0.00062   19.2   0.2    1.7  2  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
    0.00053   20.2   0.1    0.00097   19.3   0.1    1.4  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
     0.0016   18.7   0.1     0.0031   17.8   0.1    1.5  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0038   17.7   0.1     0.0064   17.0   0.1    1.4  1  CoA_binding_2    CoA binding domain


Domain annotation for each model (and alignments):
>> P5CR_dimer  Pyrroline-5-carboxylate reductase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.8   0.3     3e-34     6e-31       1     102 [.     159     263 ..     159     264 .. 0.95

  Alignments for each domain:
  == domain 1  score: 106.8 bits;  conditional E-value: 3e-34
                                    CCHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHHHHCHS...HHHHHHHH--TTSHHHHHH CS
                     P5CR_dimer   1 EkqldavtalsGsgpAyvflliealadagvklGlsreeArelaaqtvaGaaklllese...paelrdkvtspgGtTiagl 77 
                                    E++ld++t+l+GsgpA+++ +++ala ++v++G++re +++ +  +++G+a ll+++    pa lrd vt+p+GtTi+gl
  gi|119720742|ref|YP_921237.1| 159 EEYLDVWTGLAGSGPAFIAEVLDALAMGAVAAGMPRELSYKAVLDVLEGTAILLKNGFyqhPAMLRDDVTTPAGTTIRGL 238
                                    899**************************************************97443556******************* PP

                                    HHHHHTTHHHHHHHHHHHHHHHHHH CS
                     P5CR_dimer  78 keleegglraavieaveaaakrske 102
                                    ++le+gg++a++++++eaaa+rs+e
  gi|119720742|ref|YP_921237.1| 239 MVLESGGVKATLMKVIEAAARRSRE 263
                                    ***********************99 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.4   0.1   1.3e-21   2.6e-18       2      97 .]       9      99 ..       8      99 .. 0.91
   2 ?   -3.0   0.0       5.6   1.1e+04      13      23 ..     182     192 ..     178     206 .. 0.61

  Alignments for each domain:
  == domain 1  score: 66.4 bits;  conditional E-value: 1.3e-21
                                   EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHHHHCGH CS
                  F420_oxidored  2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveevlselak 83
                                   ++i+GaG++g a+++++l++      ++ a+ r  e+++ + e+lg+ +t  dn ea+++++ vv+avkp++++++lse+++
  gi|119720742|ref|YP_921237.1|  9 VAILGAGKIGGAFVRQILQKT--GIRVY-ATGRRVETLRGA-ESLGAVATR-DNDEAVRRSELVVIAVKPYHFPQLLSEVKQ 85
                                   8**************987664..49999.99*****99887.677766666.****************************** PP

                                   HHHTTSEEEEESSS CS
                  F420_oxidored 84 dalkgklvisvlag 97
                                   +++kgk+v+s +ag
  gi|119720742|ref|YP_921237.1| 86 ESWKGKIVVSLMAG 99
                                   ************97 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 5.6
                                    HHHHHHHHTTS CS
                  F420_oxidored  13 alasgllaaga 23 
                                    ala g++aag+
  gi|119720742|ref|YP_921237.1| 182 ALAMGAVAAGM 192
                                    56666666663 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   1.2   2.4e-07   0.00048       1     129 [.       9     123 ..       9     134 .. 0.78
   2 ?   -3.7   0.0       4.1   8.2e+03      98     113 ..     209     225 ..     199     244 .. 0.63

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 2.4e-07
                                    EEEES-SHHHHHHHHHHHH.HTHCEEEE-SCH.HHHHHHHHCEEEEETTCEEEEEECEEECCHSCCCCS-ESEEEE-SSG CS
                           ApbA   1 iailGaGaiGsllaakLak.agadvtlilrsr.rlealkknGlrltseggeeilrppealsaeekselepidlvivtvKa 78 
                                    +ailGaG iG+ +  ++ + +g  v+  +r+   l   ++ G   t+++       +e          +  +lv+++vK 
  gi|119720742|ref|YP_921237.1|   9 VAILGAGKIGGAFVRQILQkTGIRVYATGRRVeTLRGAESLGAVATRDN-------DE--------AVRRSELVVIAVKP 73 
                                    6899999999999999877799999999997744444444444444444.......33........345569******** PP

                                    GGHHHHHHHHGGGECTCEEEEEESSSSCHHHHHTTTSTTSEEEEEEEE-EE CS
                           ApbA  79 yqteealeeikplldpntvvlllqNGlgheeelrealpkprvlggvtthga 129
                                    y+  + l+e+k+   +  +v++l  G++ + +lr+al  ++v+ ++  ++a
  gi|119720742|ref|YP_921237.1|  74 YHFPQLLSEVKQESWKGKIVVSLMAGVKLA-TLRAALHGAKVFRAMPNLNA 123
                                    ***************************866.67888878888888766665 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 4.1
                                    EEEESSS.SCHHHHHTT CS
                           ApbA  98 vlllqNG.lgheeelre 113
                                     +ll NG ++h   lr+
  gi|119720742|ref|YP_921237.1| 209 AILLKNGfYQHPAMLRD 225
                                    56788883344444444 PP

>> Rossmann-like  Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.6   1.1e-07   0.00021      12     104 ..       8      97 ..       3     112 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.1e-07
                  Rossmann-like  12 svGiisaGrvGtalg.aaleraghvvvgisaisaasreraerrlPdvpvlevedvaaraellllavPdaelpglvkglaa 90 
                                    sv i++aG++G a+  + l+++g  v +          r  + l  v+  + ++ ++r+el+++av   ++p+l++++ +
  gi|119720742|ref|YP_921237.1|   8 SVAILGAGKIGGAFVrQILQKTGIRVYATGRRV--ETLRGAESLGAVATRDNDEAVRRSELVVIAVKPYHFPQLLSEVKQ 85 
                                    799*******99976267888888887766544..45678899***********************************99 PP

                  Rossmann-like  91 tgavraGtivahts 104
                                    + ++ +G+iv+   
  gi|119720742|ref|YP_921237.1|  86 E-SW-KGKIVVSLM 97 
                                    8.55.689987554 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.2     0.016        32       1      32 [.       8      40 ..       8      49 .. 0.76
   2 !   17.2   0.0     2e-06     0.004      58     112 ..      52     106 ..      47     116 .. 0.92
   3 ?   -3.3   0.0         4   7.9e+03     131     150 ..     171     190 ..     171     195 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.016
                                   -EEEE--SHHHHHHH.HHHHTTT--EEEE-S-H CS
                 NAD_Gly3P_dh_N  1 kiavlGaGswGtalA.kvlaenghevrlwvree 32
                                   ++a+lGaG+ G a+  ++l+++g +v   +r+ 
  gi|119720742|ref|YP_921237.1|  8 SVAILGAGKIGGAFVrQILQKTGIRVYATGRRV 40
                                   59*********9976267788887777666665 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 2e-06
                                    EEES-HHHHHTT--EEEE---HHHHHHHHHHHCCC--TT-EEEE---SEET.TTE CS
                 NAD_Gly3P_dh_N  58 vattdlaealkgadiivlvvPsqalrevlkklkgllkkkailvsliKGieegtlk 112
                                    vat d +ea+++++++v++v   ++ + l ++k+   k +i+vsl+ G++  tl+
  gi|119720742|ref|YP_921237.1|  52 VATRDNDEAVRRSELVVIAVKPYHFPQLLSEVKQESWKGKIVVSLMAGVKLATLR 106
                                    6899*********************************************887665 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 4
                                    ESS--HHHHHTT--EEEEEE CS
                 NAD_Gly3P_dh_N 131 sGpslAeEvakgkptavvia 150
                                    sGp +  Ev +     +v+a
  gi|119720742|ref|YP_921237.1| 171 SGPAFIAEVLDALAMGAVAA 190
                                    79999999998887777665 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.2   3.1e-07   0.00062      38      99 ..       8      71 ..       3      78 .. 0.87
   2 ?   -3.0   0.0         2     4e+03     148     169 ..     199     220 ..     187     223 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 3.1e-07
                                   EEEEES-SHHHHH.HHHHHHHTT-EEEEESSSHHHHHCHHHHTC.EECSHHHHHHH-SEEEE-S CS
                   2-Hacid_dh_C 38 tvGiiGlGrIGqa.vakrlkafgmkviaydrskkkeeeeeelgv.elvsleellaesDivslhl 99
                                    v+i+G+G+IG a v ++l++ g++v+a+ r+ ++ + +e+lg+    + +e++++s+ v++++
  gi|119720742|ref|YP_921237.1|  8 SVAILGAGKIGGAfVRQILQKTGIRVYATGRRVETLRGAESLGAvATRDNDEAVRRSELVVIAV 71
                                   799*******9983456899************9988899999995666*************987 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2
                                    EEEES--SSSSSGTCHHHHHST CS
                   2-Hacid_dh_C 148 gaalDvfeeeplpedspllelp 169
                                     a+lDv+e   +  ++ ++++p
  gi|119720742|ref|YP_921237.1| 199 KAVLDVLEGTAILLKNGFYQHP 220
                                    6899999988777777777776 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1   4.9e-07   0.00097       2      88 ..       9      95 ..       8     109 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 4.9e-07
                                   EEEE--SHHHHHHHHHH.HHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSHCCC--T CS
                  NAD_binding_2  2 igfiGlGvMGsnmalnl.lkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdeviegllealkk 82
                                   ++++G G++G  +++++ +k g++v++  r+ e ++ + + ga+a+ +  e+v++ ++v++ vk   +  +++++++++  k
  gi|119720742|ref|YP_921237.1|  9 VAILGAGKIGGAFVRQIlQKTGIRVYATGRRVETLRGAESLGAVATRDNDEAVRRSELVVIAVKP-YHFPQLLSEVKQESWK 89
                                   899*************94589******************************************85.8899999999999999 PP

                                   T-EEEE CS
                  NAD_binding_2 83 gdilid 88
                                   g+i++ 
  gi|119720742|ref|YP_921237.1| 90 GKIVVS 95
                                   999985 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   1.5e-06    0.0031       1      84 [.       9     104 ..       9     123 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.5e-06
                                    EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH............TTTCEEEEE--TTTHHHHHHHHHT CS
                Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka............lgvrfeaialdaenyeavLaallk 68 
                                    v i+GaG++G a+++ ++++  +  ++   +r  e l+ + +++            +++++  ia+ +   +++L+++ +
  gi|119720742|ref|YP_921237.1|   9 VAILGAGKIGGAFVRQILQKTGI--RVYATGRRVETLRGA-ESLgavatrdndeavRRSELVVIAVKPYHFPQLLSEVKQ 85 
                                    689********************..*******99997665.4556889999*****99***************8888777 PP

                                    TS...SEEEE-SSGGGHHH CS
                Sacchrp_dh_NADP  69 eg...dlvvnlsppissld 84 
                                    e    ++vv+l+  +  ++
  gi|119720742|ref|YP_921237.1|  86 ESwkgKIVVSLMAGVKLAT 104
                                    6699999999998775555 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   3.2e-06    0.0064       3      88 ..       9      99 ..       7     132 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.2e-06
                                   EEEET--S-TTSHHHHHHHHHHH.HT--EEEESSS-SEETTEES----T......T--...EEEE-S-HHHHGGGHHHHHHH CS
                  CoA_binding_2  3 iaVvGasdnpgkfgykvlrylle.hglpvvpVnpkeeeilgekvyaslae.d.pepvd...lvdvftppeatpeivkealal 78
                                   +a++G     gk g   +r++l+  g++v++   + e++ g+++   +a+ d +e+v    lv+++++p + p+++ e++++
  gi|119720742|ref|YP_921237.1|  9 VAILG----AGKIGGAFVRQILQkTGIRVYATGRRVETLRGAESLGAVATrDnDEAVRrseLVVIAVKPYHFPQLLSEVKQE 86
                                   67777....45555555555444399****************9888888655556665777******************999 PP

                                   ...--SEEEE-TT CS
                  CoA_binding_2 79 ...gakavwlqpg 88
                                      g  +v l++g
  gi|119720742|ref|YP_921237.1| 87 swkGKIVVSLMAG 99
                                   4433333344444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1707.45
//
[ok]
